From c3aad2eff55316877f5b27303126da8f537ff5a7 Mon Sep 17 00:00:00 2001 From: Emmanuel Lujan Date: Fri, 19 Nov 2021 18:27:29 -0500 Subject: [PATCH 01/35] Starting PotentialLearning.jl refactor --- README.md | 2 +- docs/src/index.md | 55 +--- examples/GaN-SNAP-LAMMPS/DATA/1/DATA | 215 -------------- examples/GaN-SNAP-LAMMPS/DATA/10/DATA | 215 -------------- examples/GaN-SNAP-LAMMPS/DATA/11/DATA | 215 -------------- examples/GaN-SNAP-LAMMPS/DATA/12/DATA | 215 -------------- examples/GaN-SNAP-LAMMPS/DATA/13/DATA | 215 -------------- examples/GaN-SNAP-LAMMPS/DATA/14/DATA | 215 -------------- examples/GaN-SNAP-LAMMPS/DATA/15/DATA | 215 -------------- examples/GaN-SNAP-LAMMPS/DATA/16/DATA | 215 -------------- examples/GaN-SNAP-LAMMPS/DATA/17/DATA | 215 -------------- examples/GaN-SNAP-LAMMPS/DATA/18/DATA | 215 -------------- examples/GaN-SNAP-LAMMPS/DATA/19/DATA | 215 -------------- examples/GaN-SNAP-LAMMPS/DATA/2/DATA | 215 -------------- examples/GaN-SNAP-LAMMPS/DATA/20/DATA | 215 -------------- examples/GaN-SNAP-LAMMPS/DATA/21/DATA | 215 -------------- examples/GaN-SNAP-LAMMPS/DATA/22/DATA | 215 -------------- examples/GaN-SNAP-LAMMPS/DATA/23/DATA | 215 -------------- examples/GaN-SNAP-LAMMPS/DATA/24/DATA | 215 -------------- examples/GaN-SNAP-LAMMPS/DATA/25/DATA | 215 -------------- examples/GaN-SNAP-LAMMPS/DATA/26/DATA | 215 -------------- examples/GaN-SNAP-LAMMPS/DATA/27/DATA | 215 -------------- examples/GaN-SNAP-LAMMPS/DATA/28/DATA | 215 -------------- examples/GaN-SNAP-LAMMPS/DATA/29/DATA | 215 -------------- examples/GaN-SNAP-LAMMPS/DATA/3/DATA | 215 -------------- examples/GaN-SNAP-LAMMPS/DATA/30/DATA | 215 -------------- examples/GaN-SNAP-LAMMPS/DATA/31/DATA | 215 -------------- examples/GaN-SNAP-LAMMPS/DATA/32/DATA | 215 -------------- examples/GaN-SNAP-LAMMPS/DATA/33/DATA | 215 -------------- examples/GaN-SNAP-LAMMPS/DATA/34/DATA | 215 -------------- examples/GaN-SNAP-LAMMPS/DATA/35/DATA | 215 -------------- examples/GaN-SNAP-LAMMPS/DATA/36/DATA | 215 -------------- examples/GaN-SNAP-LAMMPS/DATA/37/DATA | 215 -------------- examples/GaN-SNAP-LAMMPS/DATA/38/DATA | 215 -------------- examples/GaN-SNAP-LAMMPS/DATA/39/DATA | 215 -------------- examples/GaN-SNAP-LAMMPS/DATA/4/DATA | 215 -------------- examples/GaN-SNAP-LAMMPS/DATA/40/DATA | 215 -------------- examples/GaN-SNAP-LAMMPS/DATA/41/DATA | 215 -------------- examples/GaN-SNAP-LAMMPS/DATA/42/DATA | 215 -------------- examples/GaN-SNAP-LAMMPS/DATA/43/DATA | 215 -------------- examples/GaN-SNAP-LAMMPS/DATA/44/DATA | 215 -------------- examples/GaN-SNAP-LAMMPS/DATA/45/DATA | 215 -------------- examples/GaN-SNAP-LAMMPS/DATA/46/DATA | 215 -------------- examples/GaN-SNAP-LAMMPS/DATA/47/DATA | 215 -------------- examples/GaN-SNAP-LAMMPS/DATA/48/DATA | 215 -------------- examples/GaN-SNAP-LAMMPS/DATA/49/DATA | 215 -------------- examples/GaN-SNAP-LAMMPS/DATA/5/DATA | 215 -------------- examples/GaN-SNAP-LAMMPS/DATA/50/DATA | 215 -------------- examples/GaN-SNAP-LAMMPS/DATA/51/DATA | 215 -------------- examples/GaN-SNAP-LAMMPS/DATA/52/DATA | 215 -------------- examples/GaN-SNAP-LAMMPS/DATA/53/DATA | 215 -------------- examples/GaN-SNAP-LAMMPS/DATA/54/DATA | 215 -------------- examples/GaN-SNAP-LAMMPS/DATA/55/DATA | 215 -------------- examples/GaN-SNAP-LAMMPS/DATA/56/DATA | 215 -------------- examples/GaN-SNAP-LAMMPS/DATA/57/DATA | 215 -------------- examples/GaN-SNAP-LAMMPS/DATA/58/DATA | 215 -------------- examples/GaN-SNAP-LAMMPS/DATA/59/DATA | 215 -------------- examples/GaN-SNAP-LAMMPS/DATA/6/DATA | 215 -------------- examples/GaN-SNAP-LAMMPS/DATA/60/DATA | 215 -------------- examples/GaN-SNAP-LAMMPS/DATA/61/DATA | 215 -------------- examples/GaN-SNAP-LAMMPS/DATA/7/DATA | 215 -------------- examples/GaN-SNAP-LAMMPS/DATA/8/DATA | 215 -------------- examples/GaN-SNAP-LAMMPS/DATA/9/DATA | 215 -------------- .../GaN-SNAP-LAMMPS/PotentialLearning.conf | 49 --- examples/GaN-SNAP-LAMMPS/run.jl | 21 -- examples/SNAP_learning.jl | 43 +++ examples/Ta_Linear_SNAP_LAMMPS/DATA/1/DATA | 86 ------ examples/Ta_Linear_SNAP_LAMMPS/DATA/1/ENERGY | 1 - examples/Ta_Linear_SNAP_LAMMPS/DATA/1/FORCES | 64 ---- examples/Ta_Linear_SNAP_LAMMPS/DATA/2/DATA | 86 ------ examples/Ta_Linear_SNAP_LAMMPS/DATA/2/ENERGY | 1 - examples/Ta_Linear_SNAP_LAMMPS/DATA/2/FORCES | 64 ---- examples/Ta_Linear_SNAP_LAMMPS/DATA/3/DATA | 86 ------ examples/Ta_Linear_SNAP_LAMMPS/DATA/3/ENERGY | 1 - examples/Ta_Linear_SNAP_LAMMPS/DATA/3/FORCES | 64 ---- examples/Ta_Linear_SNAP_LAMMPS/DATA/4/DATA | 86 ------ examples/Ta_Linear_SNAP_LAMMPS/DATA/4/ENERGY | 1 - examples/Ta_Linear_SNAP_LAMMPS/DATA/4/FORCES | 64 ---- examples/Ta_Linear_SNAP_LAMMPS/DATA/5/DATA | 86 ------ examples/Ta_Linear_SNAP_LAMMPS/DATA/5/ENERGY | 1 - examples/Ta_Linear_SNAP_LAMMPS/DATA/5/FORCES | 64 ---- examples/Ta_Linear_SNAP_LAMMPS/DATA/6/DATA | 86 ------ examples/Ta_Linear_SNAP_LAMMPS/DATA/6/ENERGY | 1 - examples/Ta_Linear_SNAP_LAMMPS/DATA/6/FORCES | 64 ---- examples/Ta_Linear_SNAP_LAMMPS/DATA/7/DATA | 86 ------ examples/Ta_Linear_SNAP_LAMMPS/DATA/7/ENERGY | 1 - examples/Ta_Linear_SNAP_LAMMPS/DATA/7/FORCES | 64 ---- examples/Ta_Linear_SNAP_LAMMPS/DATA/8/DATA | 86 ------ examples/Ta_Linear_SNAP_LAMMPS/DATA/8/ENERGY | 1 - examples/Ta_Linear_SNAP_LAMMPS/DATA/8/FORCES | 64 ---- examples/Ta_Linear_SNAP_LAMMPS/DATA/9/DATA | 86 ------ examples/Ta_Linear_SNAP_LAMMPS/DATA/9/ENERGY | 1 - examples/Ta_Linear_SNAP_LAMMPS/DATA/9/FORCES | 64 ---- .../PotentialLearning.conf | 45 --- .../fitsnap2potentiallearning.jl | 63 ---- examples/Ta_Linear_SNAP_LAMMPS/run.jl | 22 -- src/InputLoading.jl | 71 ----- src/Interface.jl | 85 ++++++ src/LearningData.jl | 86 ------ src/PotentialLearning.jl | 103 +------ src/Potentials/BornMayer.jl | 28 -- src/Potentials/Coulomb.jl | 32 -- src/Potentials/GaN.jl | 43 --- src/Potentials/LennardJones.jl | 29 -- src/Potentials/Potentials.jl | 69 ----- src/Potentials/SNAP-LAMMPS.jl | 280 ------------------ src/Potentials/ZBL.jl | 71 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src/Potentials/BornMayer.jl delete mode 100644 src/Potentials/Coulomb.jl delete mode 100644 src/Potentials/GaN.jl delete mode 100644 src/Potentials/LennardJones.jl delete mode 100644 src/Potentials/Potentials.jl delete mode 100644 src/Potentials/SNAP-LAMMPS.jl delete mode 100644 src/Potentials/ZBL.jl create mode 100644 src/SNAPLearningProblem.jl delete mode 100644 test/GaN-SNAP-LAMMPS-Test.jl diff --git a/README.md b/README.md index 0cec2219..1a1270ef 100644 --- a/README.md +++ b/README.md @@ -1,4 +1,4 @@ -# [WIP] PotentialLearning.jl: The Julia Library of Molecular Dynamics Potentials +# [WIP] PotentialLearning.jl An Open Source library for active training and fast calculation of molecular dynamics potentials for atomistic simulations of materials. diff --git a/docs/src/index.md b/docs/src/index.md index e2cfffb6..2c015f8d 100644 --- a/docs/src/index.md +++ b/docs/src/index.md @@ -1,54 +1 @@ -# [WIP] PotentialLearning.jl: The Julia Library of Molecular Dynamics Potentials - -An Open Source library for active training and fast calculation of molecular dynamics potentials for atomistic simulations of materials. - -## Features under development -- Surrogate DFT data generation - - Gallium nitride model -- Integration with GalacticOptim.jl to perform the optimization process -- Integration with LAMMPS.jl to access the SNAP implementation of LAMMPS -- Implementation of a pure Julia version of SNAP - - GPU implementation using KernelAbstractions.jl - -## Installation instructions - -To install PotentialLearning.jl in Julia follow the next steps: - -1. Type `julia` in your terminal and press `]` -2. `] add PotentialLearning.jl` - - Note: this package is not currenlty registered - -## How to setup and run your experiment - -Load configuration parameters, DFT and reference data, and the potential learning problem. -```julia - params = get_conf_params("../examples/GaN-SNAP-LAMMPS/") - - # Get DFT data - dft_train_data, dft_val_data = generate_data("dft", params) - - # Get reference data - ref_train_data, ref_val_data = generate_data("ref", params) - - # Get potential learning problem (e.g. A β = b) - snap = learning_problem(dft_train_data, ref_train_data, params) - -``` - -Fit the potentials, forces, and stresses against the DFT and reference data using the configuration parameters. -```julia - # Solve potential learning problem (e.g. β = A \ b) - learn(snap, params) -``` - -Validate trained potentials, forces, and stresses. -```julia - # Validate potentials, forces, and stresses - rel_error = validate(snap, dft_val_data - ref_val_data, params) -``` - - -[![Build Status](https://github.com/CESMIX-MIT/PotentialLearning.jl/workflows/CI/badge.svg)](https://github.com/CESMIX-MIT/PotentialLearning.jl/actions) -[![Coverage](https://codecov.io/gh/CESMIX-MIT/PotentialLearning.jl/branch/master/graph/badge.svg)](https://codecov.io/gh/CESMIX-MIT/PotentialLearning.jl) - +# [WIP] PotentialLearning.jl diff --git a/examples/GaN-SNAP-LAMMPS/DATA/1/DATA b/examples/GaN-SNAP-LAMMPS/DATA/1/DATA deleted file mode 100755 index b41def03..00000000 --- a/examples/GaN-SNAP-LAMMPS/DATA/1/DATA +++ /dev/null @@ -1,215 +0,0 @@ -LAMMPS DATA file - -192 atoms -0 bonds -0 angles -0 dihedrals -0 impropers - -2 atom types -0 bond types -0 angle types - -0.0 12.990503 xlo xhi -0.0 11.250148 ylo yhi -0.0 15.845291 zlo zhi - -Masses - -1 69.723 -2 14.0067 - -Atoms - -1 1 1.623810 0.937510 2.635400 0 0 0 -2 1 1.623810 0.937510 7.917160 0 0 0 -3 1 1.623810 0.937510 13.198930 0 0 0 -4 1 0.000000 3.750050 2.635400 0 0 0 -5 1 0.000000 3.750050 7.917160 0 0 0 -6 1 0.000000 3.750050 13.198930 0 0 0 -7 1 4.871440 0.937510 2.635400 0 0 0 -8 1 3.247620 1.875030 5.276280 0 0 0 -9 1 4.871440 0.937510 7.917160 0 0 0 -10 1 3.247620 1.875030 10.558040 0 0 0 -11 1 4.871440 0.937510 13.198930 0 0 0 -12 1 3.247620 1.875030 15.839810 0 0 0 -13 1 3.247630 3.750050 2.635400 0 0 0 -14 1 1.623810 4.687560 5.276280 0 0 0 -15 1 3.247630 3.750050 7.917160 0 0 0 -16 1 1.623810 4.687560 10.558040 0 0 0 -17 1 3.247630 3.750050 13.198930 0 0 0 -18 1 1.623810 4.687560 15.839810 0 0 0 -19 1 1.623810 6.562580 2.635400 0 0 0 -20 1 1.623810 6.562580 7.917160 0 0 0 -21 1 1.623810 6.562580 13.198930 0 0 0 -22 1 0.000000 9.375120 2.635400 0 0 0 -23 1 0.000000 9.375120 7.917160 0 0 0 -24 1 0.000000 9.375120 13.198930 0 0 0 -25 1 8.119070 0.937510 2.635400 0 0 0 -26 1 6.495250 1.875030 5.276280 0 0 0 -27 1 8.119070 0.937510 7.917160 0 0 0 -28 1 6.495250 1.875030 10.558040 0 0 0 -29 1 8.119070 0.937510 13.198930 0 0 0 -30 1 6.495250 1.875030 15.839810 0 0 0 -31 1 6.495250 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2 9.742880 7.500100 12.549670 0 0 0 -181 2 9.742880 9.375120 4.627030 0 0 0 -182 2 8.119060 10.312640 1.986140 0 0 0 -183 2 9.742880 9.375120 9.908790 0 0 0 -184 2 8.119060 10.312640 7.267910 0 0 0 -185 2 9.742880 9.375120 15.190550 0 0 0 -186 2 8.119060 10.312640 12.549670 0 0 0 -187 2 12.990500 7.500100 1.986140 0 0 0 -188 2 12.990500 7.500100 7.267910 0 0 0 -189 2 12.990500 7.500100 12.549670 0 0 0 -190 2 11.366690 10.312640 1.986140 0 0 0 -191 2 11.366690 10.312640 7.267910 0 0 0 -192 2 11.366690 10.312640 12.549670 0 0 0 diff --git a/examples/GaN-SNAP-LAMMPS/DATA/10/DATA b/examples/GaN-SNAP-LAMMPS/DATA/10/DATA deleted file mode 100755 index b99e9833..00000000 --- a/examples/GaN-SNAP-LAMMPS/DATA/10/DATA +++ /dev/null @@ -1,215 +0,0 @@ -LAMMPS DATA file - -192 atoms -0 bonds -0 angles -0 dihedrals -0 impropers - -2 atom types -0 bond types -0 angle types - -0.0 12.990503 xlo xhi -0.0 11.250148 ylo yhi -0.0 15.845291 zlo zhi - -Masses - -1 69.723 -2 14.0067 - -Atoms - -1 1 1.510276 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11.276536 4.611773 10.656750 0 0 0 -78 1 11.450609 4.772538 15.719004 0 0 0 -79 1 11.403324 6.576612 2.748524 0 0 0 -80 1 9.807180 7.394497 5.388350 0 0 0 -81 1 11.358506 6.559399 7.922170 0 0 0 -82 1 9.713909 7.474036 10.464547 0 0 0 -83 1 11.265105 6.610925 13.047488 0 0 0 -84 1 9.872133 7.404735 15.805677 0 0 0 -85 1 9.699229 9.409736 2.633329 0 0 0 -86 1 7.995265 10.209285 5.245900 0 0 0 -87 1 9.734823 9.477237 7.850232 0 0 0 -88 1 8.160244 10.350249 10.402750 0 0 0 -89 1 9.798996 9.368786 13.068403 0 0 0 -90 1 8.107243 10.283310 0.136269 0 0 0 -91 1 12.924511 7.566062 5.404195 0 0 0 -92 1 0.105223 7.438373 10.505428 0 0 0 -93 1 12.865015 7.481574 0.095072 0 0 0 -94 1 11.455286 10.219072 5.425111 0 0 0 -95 1 11.276017 10.374774 10.558826 0 0 0 -96 1 11.425148 10.376012 0.137854 0 0 0 -97 2 1.652002 0.893476 4.752320 0 0 0 -98 2 1.586920 0.851659 9.864803 0 0 0 -99 2 1.607315 0.983983 15.315582 0 0 0 -100 2 12.889147 3.833826 4.496260 0 0 0 -101 2 12.916639 3.639198 9.875419 0 0 0 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12.538854 0 0 0 -127 2 6.404188 3.721437 4.596402 0 0 0 -128 2 4.886638 4.753863 1.912051 0 0 0 -129 2 6.459658 3.664623 9.914240 0 0 0 -130 2 4.948083 4.778275 7.153990 0 0 0 -131 2 6.424194 3.706586 15.191672 0 0 0 -132 2 4.798822 4.659136 12.512234 0 0 0 -133 2 4.932754 6.632412 4.706685 0 0 0 -134 2 3.170332 7.399335 2.135470 0 0 0 -135 2 4.744392 6.565137 9.796509 0 0 0 -136 2 3.257369 7.589125 7.253340 0 0 0 -137 2 4.785312 6.534649 15.116883 0 0 0 -138 2 3.373893 7.589913 12.591143 0 0 0 -139 2 3.198392 9.388361 4.713974 0 0 0 -140 2 1.515212 10.363862 1.971154 0 0 0 -141 2 3.155393 9.282385 10.034664 0 0 0 -142 2 1.611862 10.400087 7.237970 0 0 0 -143 2 3.261006 9.282047 15.278346 0 0 0 -144 2 1.527293 10.225935 12.570227 0 0 0 -145 2 11.488281 0.920330 4.626666 0 0 0 -146 2 9.817313 1.893962 1.976542 0 0 0 -147 2 11.359675 0.901384 9.949258 0 0 0 -148 2 9.645579 1.888000 7.400385 0 0 0 -149 2 11.324471 0.898741 15.214806 0 0 0 -150 2 9.791722 1.903413 12.685898 0 0 0 -151 2 9.699099 3.731337 4.575011 0 0 0 -152 2 8.050994 4.665099 2.129924 0 0 0 -153 2 9.663116 3.774425 9.799361 0 0 0 -154 2 8.055801 4.754988 7.183462 0 0 0 -155 2 9.709102 3.708949 15.312730 0 0 0 -156 2 7.996434 4.716850 12.464856 0 0 0 -157 2 8.174404 6.467148 4.776087 0 0 0 -158 2 6.470310 7.574500 1.918231 0 0 0 -159 2 7.993057 6.579649 9.768622 0 0 0 -160 2 6.522402 7.526462 7.357444 0 0 0 -161 2 8.130756 6.556699 15.137165 0 0 0 -162 2 6.438223 7.578887 12.458201 0 0 0 -163 2 6.400421 9.389261 4.686245 0 0 0 -164 2 4.835715 10.354749 1.936928 0 0 0 -165 2 6.580729 9.411312 9.862901 0 0 0 -166 2 4.762708 10.335286 7.393729 0 0 0 -167 2 6.612946 9.359561 15.324139 0 0 0 -168 2 4.887027 10.410662 12.391334 0 0 0 -169 2 12.972966 1.898688 2.078110 0 0 0 -170 2 0.123410 1.953026 7.425579 0 0 0 -171 2 0.037672 1.797774 12.400049 0 0 0 -172 2 11.482955 4.598498 2.005538 0 0 0 -173 2 11.435670 4.696487 7.259045 0 0 0 -174 2 11.420601 4.636974 12.540121 0 0 0 -175 2 11.461391 6.582462 4.781316 0 0 0 -176 2 9.857324 7.600713 2.007440 0 0 0 -177 2 11.239903 6.520361 10.026900 0 0 0 -178 2 9.656361 7.582037 7.318781 0 0 0 -179 2 11.265105 6.669200 15.096917 0 0 0 -180 2 9.754049 7.391910 12.574664 0 0 0 -181 2 9.726250 9.305785 4.763411 0 0 0 -182 2 8.198956 10.350361 1.923143 0 0 0 -183 2 9.627782 9.278447 9.963360 0 0 0 -184 2 8.130756 10.309298 7.288358 0 0 0 -185 2 9.823159 9.441574 15.067604 0 0 0 -186 2 8.119324 10.215810 12.665933 0 0 0 -187 2 0.098728 7.588112 2.029623 0 0 0 -188 2 0.051962 7.477074 7.356652 0 0 0 -189 2 12.933085 7.416098 12.663715 0 0 0 -190 2 11.493867 10.347324 1.843600 0 0 0 -191 2 11.452038 10.407062 7.136560 0 0 0 -192 2 11.477369 10.399862 12.468184 0 0 0 diff --git a/examples/GaN-SNAP-LAMMPS/DATA/11/DATA b/examples/GaN-SNAP-LAMMPS/DATA/11/DATA deleted file mode 100755 index ffb20be0..00000000 --- a/examples/GaN-SNAP-LAMMPS/DATA/11/DATA +++ /dev/null @@ -1,215 +0,0 @@ -LAMMPS DATA file - -192 atoms -0 bonds -0 angles -0 dihedrals -0 impropers - -2 atom types -0 bond types -0 angle types - -0.0 12.990503 xlo xhi -0.0 11.250148 ylo yhi -0.0 15.845291 zlo zhi - -Masses - -1 69.723 -2 14.0067 - -Atoms - -1 1 1.546909 0.974027 2.766905 0 0 0 -2 1 1.495727 0.992961 8.012171 0 0 0 -3 1 1.729815 1.044295 13.078386 0 0 0 -4 1 0.004930 3.822463 2.678805 0 0 0 -5 1 0.117932 3.850588 8.065094 0 0 0 -6 1 12.878096 3.735949 13.142084 0 0 0 -7 1 4.776348 0.855293 2.732362 0 0 0 -8 1 3.254121 1.974964 5.430973 0 0 0 -9 1 4.848056 0.908528 7.830584 0 0 0 -10 1 3.233596 1.822412 10.545041 0 0 0 -11 1 4.854031 0.883429 13.082823 0 0 0 -12 1 3.226581 1.876525 15.784128 0 0 0 -13 1 3.295561 3.737299 2.614948 0 0 0 -14 1 1.699937 4.758588 5.356184 0 0 0 -15 1 3.322841 3.750349 7.934688 0 0 0 -16 1 1.657718 4.597148 10.477381 0 0 0 -17 1 3.277634 3.706136 13.283582 0 0 0 -18 1 1.563277 4.583985 15.775413 0 0 0 -19 1 1.638492 6.668075 2.695284 0 0 0 -20 1 1.680451 6.575824 7.927716 0 0 0 -21 1 1.721372 6.538586 13.185659 0 0 0 -22 1 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0 0 0 -147 2 11.300049 0.978493 9.793974 0 0 0 -148 2 9.776653 1.955388 7.394680 0 0 0 -149 2 11.327329 0.934426 15.247448 0 0 0 -150 2 9.795879 1.866175 12.506688 0 0 0 -151 2 9.685849 3.654723 4.609553 0 0 0 -152 2 8.032158 4.664761 2.119466 0 0 0 -153 2 9.745865 3.843276 9.779396 0 0 0 -154 2 8.247151 4.596811 7.208656 0 0 0 -155 2 9.817053 3.773075 15.179788 0 0 0 -156 2 8.066583 4.605023 12.484663 0 0 0 -157 2 8.032418 6.521486 4.503390 0 0 0 -158 2 6.581509 7.606225 1.896840 0 0 0 -159 2 8.172585 6.458823 9.945614 0 0 0 -160 2 6.539289 7.395960 7.110574 0 0 0 -161 2 8.026182 6.644113 15.119576 0 0 0 -162 2 6.503436 7.505086 12.571178 0 0 0 -163 2 6.451863 9.355623 4.599888 0 0 0 -164 2 4.997187 10.213110 1.953407 0 0 0 -165 2 6.570986 9.396349 9.848482 0 0 0 -166 2 4.975882 10.221097 7.210558 0 0 0 -167 2 6.595798 9.410524 15.249032 0 0 0 -168 2 4.864684 10.231897 12.692553 0 0 0 -169 2 0.100027 1.861000 2.092371 0 0 0 -170 2 12.945036 1.845249 7.361405 0 0 0 -171 2 12.886449 1.976651 12.391651 0 0 0 -172 2 11.313559 4.586010 1.967985 0 0 0 -173 2 11.442035 4.780638 7.278376 0 0 0 -174 2 11.445673 4.701662 12.629172 0 0 0 -175 2 11.239124 6.557374 4.547915 0 0 0 -176 2 9.692994 7.605213 1.893829 0 0 0 -177 2 11.372016 6.500786 9.930085 0 0 0 -178 2 9.872263 7.417223 7.411952 0 0 0 -179 2 11.269002 6.492011 15.236990 0 0 0 -180 2 9.646228 7.405860 12.600175 0 0 0 -181 2 9.620117 9.484325 4.639501 0 0 0 -182 2 8.086328 10.359136 2.127864 0 0 0 -183 2 9.712350 9.418512 9.941177 0 0 0 -184 2 8.190642 10.333261 7.228622 0 0 0 -185 2 9.833941 9.313435 15.284684 0 0 0 -186 2 8.248190 10.263398 12.616337 0 0 0 -187 2 0.042869 7.480899 1.985573 0 0 0 -188 2 0.116915 7.602063 7.341757 0 0 0 -189 2 12.960495 7.396635 12.575932 0 0 0 -190 2 11.383448 10.280048 2.106631 0 0 0 -191 2 11.399037 10.340574 7.203111 0 0 0 -192 2 11.256141 10.266210 12.465649 0 0 0 diff --git a/examples/GaN-SNAP-LAMMPS/DATA/12/DATA b/examples/GaN-SNAP-LAMMPS/DATA/12/DATA deleted file mode 100755 index 005c35a8..00000000 --- a/examples/GaN-SNAP-LAMMPS/DATA/12/DATA +++ /dev/null @@ -1,215 +0,0 @@ -LAMMPS DATA file - -192 atoms -0 bonds -0 angles -0 dihedrals -0 impropers - -2 atom types -0 bond types -0 angle types - -0.0 12.990503 xlo xhi -0.0 11.250148 ylo yhi -0.0 15.845291 zlo zhi - -Masses - -1 69.723 -2 14.0067 - -Atoms - -1 1 1.685908 1.013425 2.593399 0 0 0 -2 1 1.526904 0.841511 8.041485 0 0 0 -3 1 1.554963 0.997629 13.194849 0 0 0 -4 1 0.077017 3.707036 2.638082 0 0 0 -5 1 0.079795 3.806375 8.031819 0 0 0 -6 1 0.013848 3.816613 13.341418 0 0 0 -7 1 4.935352 0.838957 2.537306 0 0 0 -8 1 3.311669 1.787086 5.427329 0 0 0 -9 1 4.942497 1.048728 7.859264 0 0 0 -10 1 3.308421 1.946051 10.531255 0 0 0 -11 1 4.857539 0.954654 13.282156 0 0 0 -12 1 3.278543 1.833324 0.090318 0 0 0 -13 1 3.315956 3.692861 2.637766 0 0 0 -14 1 1.532100 4.604236 5.327187 0 0 0 -15 1 3.136687 3.682849 8.028333 0 0 0 -16 1 1.648755 4.727425 10.705395 0 0 0 -17 1 3.326998 3.806488 13.293565 0 0 0 -18 1 1.565096 4.667912 15.767966 0 0 0 -19 1 1.549767 6.514173 2.693858 0 0 0 -20 1 1.606925 6.576049 7.822345 0 0 0 -21 1 1.652392 6.627575 13.060005 0 0 0 -22 1 0.127045 9.402424 2.785761 0 0 0 -23 1 0.092151 9.271472 7.899828 0 0 0 -24 1 12.944574 9.297460 13.317491 0 0 0 -25 1 8.080613 0.914963 2.765637 0 0 0 -26 1 6.468751 1.869437 5.401184 0 0 0 -27 1 8.167779 0.973509 8.004249 0 0 0 -28 1 6.575403 1.834112 10.402592 0 0 0 -29 1 8.226626 0.846956 13.314322 0 0 0 -30 1 6.614245 1.957188 0.049120 0 0 0 -31 1 6.509801 3.739099 2.581515 0 0 0 -32 1 4.764397 4.649686 5.386607 0 0 0 -33 1 6.386521 3.669011 7.849757 0 0 0 -34 1 4.956656 4.699862 10.501149 0 0 0 -35 1 6.567869 3.834951 13.221310 0 0 0 -36 1 4.886897 4.734962 15.786663 0 0 0 -37 1 4.985106 6.476485 2.728717 0 0 0 -38 1 3.203458 7.413398 5.292010 0 0 0 -39 1 4.910670 6.588087 7.996960 0 0 0 -40 1 3.159940 7.561562 10.644074 0 0 0 -41 1 4.963541 6.572224 13.228758 0 0 0 -42 1 3.186051 7.499124 0.150530 0 0 0 -43 1 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10.285223 5.198681 0 0 0 -69 1 6.510451 9.432462 7.789228 0 0 0 -70 1 4.849874 10.311886 10.671645 0 0 0 -71 1 6.520063 9.406474 13.059055 0 0 0 -72 1 4.867542 10.229197 0.049120 0 0 0 -73 1 0.068850 1.790236 5.345409 0 0 0 -74 1 0.048065 1.770098 10.694304 0 0 0 -75 1 0.007794 1.808236 0.017430 0 0 0 -76 1 11.415924 4.634611 5.255408 0 0 0 -77 1 11.439827 4.782776 10.524442 0 0 0 -78 1 11.338111 4.724950 0.137854 0 0 0 -79 1 11.475421 6.532961 2.655354 0 0 0 -80 1 9.820950 7.589688 5.410691 0 0 0 -81 1 11.344087 6.495836 7.822028 0 0 0 -82 1 9.613752 7.608925 10.691293 0 0 0 -83 1 11.438398 6.628812 13.215289 0 0 0 -84 1 9.797827 7.401698 15.700940 0 0 0 -85 1 9.770547 9.318160 2.477570 0 0 0 -86 1 8.188174 10.295911 5.431449 0 0 0 -87 1 9.631289 9.290597 8.065570 0 0 0 -88 1 8.217013 10.254173 10.563104 0 0 0 -89 1 9.633497 9.405686 13.235730 0 0 0 -90 1 8.165700 10.389062 0.079226 0 0 0 -91 1 12.874758 7.406085 5.289950 0 0 0 -92 1 12.944257 7.442536 10.406711 0 0 0 -93 1 12.904896 7.601613 15.788564 0 0 0 -94 1 11.366171 10.283423 5.327345 0 0 0 -95 1 11.357727 10.400987 10.481818 0 0 0 -96 1 11.413586 10.319648 15.696028 0 0 0 -97 2 1.670059 0.892137 4.501964 0 0 0 -98 2 1.615369 0.978527 9.997586 0 0 0 -99 2 1.708901 0.921331 15.191989 0 0 0 -100 2 0.034874 3.801088 4.599412 0 0 0 -101 2 12.953174 3.709849 9.896810 0 0 0 -102 2 0.042623 3.782862 15.141126 0 0 0 -103 2 4.894692 1.015517 4.524940 0 0 0 -104 2 3.194754 1.772798 2.081279 0 0 0 -105 2 4.948342 0.914041 9.851651 0 0 0 -106 2 3.375452 1.886537 7.114060 0 0 0 -107 2 4.964711 0.958614 15.305125 0 0 0 -108 2 3.319593 1.786074 12.516195 0 0 0 -109 2 3.371295 3.752374 4.593233 0 0 0 -110 2 1.638232 4.794588 1.969570 0 0 0 -111 2 3.342197 3.669686 9.780664 0 0 0 -112 2 1.584192 4.591410 7.282020 0 0 0 -113 2 3.368567 3.700849 15.057463 0 0 0 -114 2 1.531840 4.611773 12.561829 0 0 0 -115 2 1.615759 6.509786 4.682283 0 0 0 -116 2 1.526254 6.506748 9.937057 0 0 0 -117 2 1.585101 6.567724 15.138274 0 0 0 -118 2 12.866714 9.353036 4.628568 0 0 0 -119 2 12.894268 9.400511 10.055738 0 0 0 -120 2 12.883894 9.332110 15.199753 0 0 0 -121 2 8.105424 1.036499 4.697019 0 0 0 -122 2 6.557086 1.906338 1.838846 0 0 0 -123 2 8.155828 0.896693 9.782407 0 0 0 -124 2 6.386391 1.965513 7.189484 0 0 0 -125 2 8.117765 0.912331 15.115615 0 0 0 -126 2 6.433677 1.919950 12.409239 0 0 0 -127 2 6.570207 3.703324 4.734573 0 0 0 -128 2 4.867412 4.627636 1.897632 0 0 0 -129 2 6.447057 3.861501 9.810295 0 0 0 -130 2 4.962502 4.764888 7.276950 0 0 0 -131 2 6.538120 3.720762 15.132728 0 0 0 -132 2 4.952110 4.598161 12.458677 0 0 0 -133 2 4.857539 6.537011 4.714132 0 0 0 -134 2 3.240871 7.566850 1.835518 0 0 0 -135 2 5.001084 6.513723 9.993625 0 0 0 -136 2 3.126814 7.583387 7.344926 0 0 0 -137 2 4.769983 6.645125 15.292448 0 0 0 -138 2 3.118760 7.536137 12.591619 0 0 0 -139 2 3.172411 9.360461 4.764204 0 0 0 -140 2 1.612771 10.224922 2.043092 0 0 0 -141 2 3.370126 9.360573 9.825823 0 0 0 -142 2 1.724489 10.414487 7.233534 0 0 0 -143 2 3.316086 9.285085 15.103097 0 0 0 -144 2 1.520538 10.205009 12.555016 0 0 0 -145 2 11.303946 0.832635 4.706210 0 0 0 -146 2 9.753660 1.961013 2.005538 0 0 0 -147 2 11.488411 0.994322 10.051143 0 0 0 -148 2 9.804972 1.821849 7.137194 0 0 0 -149 2 11.415015 1.007361 15.079963 0 0 0 -150 2 9.694553 1.872137 12.614277 0 0 0 -151 2 9.767819 3.649773 4.776404 0 0 0 -152 2 8.138420 4.704362 2.010609 0 0 0 -153 2 9.769118 3.668111 9.761333 0 0 0 -154 2 8.096721 4.636524 7.327972 0 0 0 -155 2 9.869015 3.693086 15.275019 0 0 0 -156 2 8.162323 4.695699 12.676549 0 0 0 -157 2 8.162453 6.572337 4.496893 0 0 0 -158 2 6.372621 7.603525 2.059729 0 0 0 -159 2 8.220520 6.651538 10.002023 0 0 0 -160 2 6.504345 7.464586 7.198516 0 0 0 -161 2 8.112439 6.451960 15.166795 0 0 0 -162 2 6.551890 7.479999 12.582745 0 0 0 -163 2 6.518894 9.482862 4.555996 0 0 0 -164 2 4.752706 10.396037 2.109008 0 0 0 -165 2 6.461996 9.296110 9.803957 0 0 0 -166 2 4.783883 10.334049 7.379310 0 0 0 -167 2 6.376778 9.395449 15.110703 0 0 0 -168 2 4.798302 10.364087 12.449169 0 0 0 -169 2 12.888398 1.864487 1.889076 0 0 0 -170 2 12.957248 1.803849 7.390402 0 0 0 -171 2 12.916068 1.884625 12.443624 0 0 0 -172 2 11.353310 4.760163 1.977492 0 0 0 -173 2 11.465288 4.722812 7.283129 0 0 0 -174 2 11.371497 4.670724 12.648662 0 0 0 -175 2 11.403583 6.491561 4.784802 0 0 0 -176 2 9.739890 7.502161 2.069870 0 0 0 -177 2 11.412027 6.613287 9.820753 0 0 0 -178 2 9.712480 7.465486 7.376300 0 0 0 -179 2 11.490230 6.513611 15.341252 0 0 0 -180 2 9.769378 7.429710 12.538062 0 0 0 -181 2 9.645189 9.420087 4.708903 0 0 0 -182 2 8.113738 10.353849 2.055293 0 0 0 -183 2 9.668312 9.294197 9.902673 0 0 0 -184 2 8.248840 10.398287 7.121824 0 0 0 -185 2 9.859402 9.463512 15.099453 0 0 0 -186 2 8.244293 10.257435 12.589876 0 0 0 -187 2 0.005196 7.498899 1.905872 0 0 0 -188 2 12.877096 7.425548 7.320207 0 0 0 -189 2 0.053261 7.580687 12.476740 0 0 0 -190 2 11.242631 10.325724 1.890819 0 0 0 -191 2 11.475811 10.262048 7.182036 0 0 0 -192 2 11.371367 10.257773 12.396405 0 0 0 diff --git a/examples/GaN-SNAP-LAMMPS/DATA/13/DATA b/examples/GaN-SNAP-LAMMPS/DATA/13/DATA deleted file mode 100755 index be751168..00000000 --- a/examples/GaN-SNAP-LAMMPS/DATA/13/DATA +++ /dev/null @@ -1,215 +0,0 @@ -LAMMPS DATA file - -192 atoms -0 bonds -0 angles -0 dihedrals -0 impropers - -2 atom types -0 bond types -0 angle types - -0.0 12.990503 xlo xhi -0.0 11.250148 ylo yhi -0.0 15.845291 zlo zhi - -Masses - -1 69.723 -2 14.0067 - -Atoms - -1 1 1.691623 0.861638 2.625248 0 0 0 -2 1 1.648105 0.844211 7.916307 0 0 0 -3 1 1.695780 0.855113 13.262350 0 0 0 -4 1 0.085928 3.753049 2.478520 0 0 0 -5 1 12.953278 3.856438 7.804598 0 0 0 -6 1 0.071388 3.718736 13.129725 0 0 0 -7 1 4.882740 0.916640 2.768648 0 0 0 -8 1 3.210473 1.787874 5.198681 0 0 0 -9 1 4.781934 1.007957 7.958297 0 0 0 -10 1 3.289066 1.911963 10.573087 0 0 0 -11 1 4.815839 0.846900 13.303864 0 0 0 -12 1 3.199561 1.897225 15.829921 0 0 0 -13 1 3.288676 3.696236 2.567096 0 0 0 -14 1 1.673437 4.794138 5.207396 0 0 0 -15 1 3.339599 3.840351 8.024214 0 0 0 -16 1 1.689415 4.633374 10.699691 0 0 0 -17 1 3.337780 3.827075 13.286751 0 0 0 -18 1 1.616928 4.766575 0.129931 0 0 0 -19 1 1.500143 6.614075 2.624772 0 0 0 -20 1 1.647456 6.671563 8.027066 0 0 0 -21 1 1.747612 6.527674 13.128299 0 0 0 -22 1 12.942806 9.338298 2.650600 0 0 0 -23 1 12.934699 9.468687 7.971290 0 0 0 -24 1 0.074174 9.303760 13.085199 0 0 0 -25 1 8.003709 0.964149 2.663910 0 0 0 -26 1 6.462775 1.767623 5.168258 0 0 0 -27 1 8.120883 1.002129 8.000129 0 0 0 -28 1 6.608139 1.941438 10.543615 0 0 0 -29 1 8.078664 0.854899 13.218300 0 0 0 -30 1 6.419257 1.789111 0.079226 0 0 0 -31 1 6.484210 3.800863 2.510845 0 0 0 -32 1 4.855590 4.700424 5.388983 0 0 0 -33 1 6.602293 3.716599 7.876694 0 0 0 -34 1 4.768034 4.723037 10.468983 0 0 0 -35 1 6.590472 3.726049 13.184391 0 0 0 -36 1 4.788689 4.590285 0.083980 0 0 0 -37 1 4.949901 6.554336 2.747098 0 0 0 -38 1 3.280232 7.428248 5.127378 0 0 0 -39 1 4.775309 6.521148 7.990463 0 0 0 -40 1 3.318554 7.421048 10.651838 0 0 0 -41 1 4.784532 6.611487 13.065393 0 0 0 -42 1 3.220086 7.571125 0.004754 0 0 0 -43 1 3.363891 9.333910 2.660107 0 0 0 -44 1 1.543272 10.288373 5.434301 0 0 0 -45 1 3.206966 9.467000 7.979847 0 0 0 -46 1 1.501702 10.308398 10.614126 0 0 0 -47 1 3.222294 9.297235 13.218300 0 0 0 -48 1 1.740598 10.415950 0.150530 0 0 0 -49 1 11.453987 0.972182 2.752327 0 0 0 -50 1 9.837448 1.934013 5.170160 0 0 0 -51 1 11.257440 0.939511 7.788119 0 0 0 -52 1 9.726769 1.832762 10.519688 0 0 0 -53 1 11.495426 1.020647 13.340942 0 0 0 -54 1 9.679094 1.773473 0.099825 0 0 0 -55 1 9.791852 3.771612 2.545071 0 0 0 -56 1 8.128158 4.587585 5.254457 0 0 0 -57 1 9.662466 3.711311 8.055904 0 0 0 -58 1 8.209349 4.632924 10.519055 0 0 0 -59 1 9.803543 3.813575 13.044160 0 0 0 -60 1 8.046707 4.590173 0.060212 0 0 0 -61 1 8.216753 6.512486 2.696552 0 0 0 -62 1 6.401460 7.471898 5.382645 0 0 0 -63 1 8.169987 6.606425 8.029126 0 0 0 -64 1 6.441861 7.534112 10.494177 0 0 0 -65 1 8.234550 6.625775 13.301963 0 0 0 -66 1 6.556567 7.566175 15.809797 0 0 0 -67 1 6.399252 9.298473 2.735689 0 0 0 -68 1 4.749458 10.322574 5.378842 0 0 0 -69 1 6.611776 9.366198 7.780671 0 0 0 -70 1 4.877284 10.244160 10.494177 0 0 0 -71 1 6.618791 9.299823 13.286751 0 0 0 -72 1 4.830259 10.306823 15.713141 0 0 0 -73 1 12.876187 1.956401 5.140212 0 0 0 -74 1 0.100027 1.851099 10.539020 0 0 0 -75 1 12.951662 1.769761 0.066550 0 0 0 -76 1 11.328628 4.719325 5.362363 0 0 0 -77 1 11.412677 4.684337 10.656909 0 0 0 -78 1 11.256531 4.581398 15.818670 0 0 0 -79 1 11.274068 6.631850 2.477570 0 0 0 -80 1 9.637914 7.482474 5.192343 0 0 0 -81 1 11.485294 6.533636 7.914406 0 0 0 -82 1 9.682472 7.517237 10.564372 0 0 0 -83 1 11.491139 6.598774 13.308618 0 0 0 -84 1 9.635576 7.482699 15.694443 0 0 0 -85 1 9.769378 9.427174 2.693224 0 0 0 -86 1 8.005008 10.352386 5.215160 0 0 0 -87 1 9.703516 9.426049 7.792714 0 0 0 -88 1 8.054762 10.298948 10.585605 0 0 0 -89 1 9.692734 9.360573 13.138756 0 0 0 -90 1 8.227146 10.348336 15.737384 0 0 0 -91 1 0.037672 7.395510 5.365849 0 0 0 -92 1 12.861118 7.474148 10.612700 0 0 0 -93 1 12.870861 7.485399 15.736592 0 0 0 -94 1 11.388255 10.243147 5.239404 0 0 0 -95 1 11.465938 10.200509 10.615077 0 0 0 -96 1 11.310182 10.385012 15.774621 0 0 0 -97 2 1.595234 1.039007 4.733305 0 0 0 -98 2 1.725139 1.034845 9.791280 0 0 0 -99 2 1.584452 0.985569 15.230176 0 0 0 -100 2 0.086679 3.687124 4.569782 0 0 0 -101 2 12.917598 3.643811 9.965895 0 0 0 -102 2 12.934944 3.644486 15.122270 0 0 0 -103 2 4.770892 0.841129 4.652653 0 0 0 -104 2 3.120579 1.952351 1.848670 0 0 0 -105 2 4.867282 0.861548 9.884134 0 0 0 -106 2 3.341937 1.910275 7.414487 0 0 0 -107 2 4.844418 0.917697 15.278980 0 0 0 -108 2 3.352069 1.913088 12.445525 0 0 0 -109 2 3.200860 3.698599 4.541736 0 0 0 -110 2 1.676424 4.644736 2.136262 0 0 0 -111 2 3.341807 3.777012 10.028960 0 0 0 -112 2 1.573670 4.715950 7.310383 0 0 0 -113 2 3.195924 3.768687 15.066178 0 0 0 -114 2 1.701366 4.771975 12.596531 0 0 0 -115 2 1.508197 6.661213 4.486911 0 0 0 -116 2 1.558601 6.534536 9.881440 0 0 0 -117 2 1.536777 6.662000 15.072674 0 0 0 -118 2 0.066354 9.406699 4.565662 0 0 0 -119 2 12.890665 9.477575 10.011530 0 0 0 -120 2 12.900143 9.351011 15.178679 0 0 0 -121 2 8.180899 1.022031 4.777197 0 0 0 -122 2 6.553449 1.902738 2.094589 0 0 0 -123 2 8.087368 1.027217 10.000280 0 0 0 -124 2 6.601514 1.857399 7.131807 0 0 0 -125 2 8.224937 0.962878 15.269948 0 0 0 -126 2 6.516166 1.986326 12.443782 0 0 0 -127 2 6.549552 3.675086 4.493724 0 0 0 -128 2 4.906253 4.699187 2.072406 0 0 0 -129 2 6.379636 3.648086 9.934997 0 0 0 -130 2 4.939379 4.616723 7.279326 0 0 0 -131 2 6.514348 3.773637 15.045103 0 0 0 -132 2 4.811682 4.615373 12.558502 0 0 0 -133 2 4.932494 6.656600 4.478196 0 0 0 -134 2 3.331804 7.578212 1.976542 0 0 0 -135 2 4.837793 6.467148 9.804274 0 0 0 -136 2 3.292313 7.520387 7.321158 0 0 0 -137 2 4.858578 6.628250 15.176619 0 0 0 -138 2 3.350121 7.403948 12.592569 0 0 0 -139 2 3.327777 9.334923 4.638392 0 0 0 -140 2 1.718903 10.320323 2.079219 0 0 0 -141 2 3.269969 9.460925 9.890789 0 0 0 -142 2 1.518070 10.409312 7.242090 0 0 0 -143 2 3.254511 9.418062 15.049382 0 0 0 -144 2 1.582373 10.378487 12.393236 0 0 0 -145 2 11.250815 0.886680 4.581824 0 0 0 -146 2 9.815884 1.804974 1.956576 0 0 0 -147 2 11.417093 1.011647 9.923430 0 0 0 -148 2 9.850049 1.969001 7.305471 0 0 0 -149 2 11.473342 1.026126 15.141601 0 0 0 -150 2 9.871873 1.962813 12.506529 0 0 0 -151 2 9.816404 3.711424 4.518285 0 0 0 -152 2 8.181289 4.717187 2.017739 0 0 0 -153 2 9.675457 3.701074 10.003449 0 0 0 -154 2 8.141668 4.642936 7.203269 0 0 0 -155 2 9.671430 3.751249 15.211162 0 0 0 -156 2 8.007086 4.611886 12.552956 0 0 0 -157 2 8.129847 6.564799 4.507193 0 0 0 -158 2 6.405747 7.479661 2.047528 0 0 0 -159 2 8.192071 6.593262 9.934680 0 0 0 -160 2 6.618531 7.506774 7.200892 0 0 0 -161 2 8.040082 6.498536 15.170757 0 0 0 -162 2 6.512659 7.593625 12.491318 0 0 0 -163 2 6.438353 9.401861 4.538408 0 0 0 -164 2 4.786221 10.203884 1.991278 0 0 0 -165 2 6.365996 9.387686 9.926441 0 0 0 -166 2 4.760630 10.289386 7.354116 0 0 0 -167 2 6.514088 9.353261 15.198010 0 0 0 -168 2 4.843509 10.215247 12.637887 0 0 0 -169 2 0.068850 1.890475 2.022493 0 0 0 -170 2 0.023383 1.901275 7.185364 0 0 0 -171 2 0.075345 1.921300 12.625052 0 0 0 -172 2 11.272769 4.576335 2.061789 0 0 0 -173 2 11.447491 4.702112 7.127053 0 0 0 -174 2 11.320704 4.785138 12.661496 0 0 0 -175 2 11.415275 6.487735 4.684026 0 0 0 -176 2 9.633627 7.513862 1.973214 0 0 0 -177 2 11.409559 6.547811 9.760065 0 0 0 -178 2 9.727938 7.492711 7.112792 0 0 0 -179 2 11.390983 6.517998 15.293874 0 0 0 -180 2 9.850958 7.447711 12.484980 0 0 0 -181 2 9.637005 9.425937 4.695910 0 0 0 -182 2 8.150502 10.284773 2.027563 0 0 0 -183 2 9.747424 9.408949 10.026425 0 0 0 -184 2 8.075157 10.325611 7.118497 0 0 0 -185 2 9.670390 9.439324 15.124330 0 0 0 -186 2 8.003969 10.357336 12.593520 0 0 0 -187 2 0.038972 7.586200 1.879727 0 0 0 -188 2 0.042869 7.473811 7.329081 0 0 0 -189 2 12.939580 7.533774 12.505103 0 0 0 -190 2 11.473992 10.287586 2.042616 0 0 0 -191 2 11.432292 10.244947 7.324486 0 0 0 -192 2 11.442295 10.363524 12.446793 0 0 0 diff --git a/examples/GaN-SNAP-LAMMPS/DATA/14/DATA b/examples/GaN-SNAP-LAMMPS/DATA/14/DATA deleted file mode 100755 index 75db78d2..00000000 --- a/examples/GaN-SNAP-LAMMPS/DATA/14/DATA +++ /dev/null @@ -1,215 +0,0 @@ -LAMMPS DATA file - -192 atoms -0 bonds -0 angles -0 dihedrals -0 impropers - -2 atom types -0 bond types -0 angle types - -0.0 12.990503 xlo xhi -0.0 11.250148 ylo yhi -0.0 15.845291 zlo zhi - -Masses - -1 69.723 -2 14.0067 - -Atoms - -1 1 1.583153 1.035621 2.516549 0 0 0 -2 1 1.683699 0.970472 8.022788 0 0 0 -3 1 1.597442 0.993726 13.305132 0 0 0 -4 1 12.944378 3.761825 2.787187 0 0 0 -5 1 0.012813 3.711874 7.954970 0 0 0 -6 1 12.954297 3.807725 13.171715 0 0 0 -7 1 4.869490 0.981328 2.785285 0 0 0 -8 1 3.202809 1.951001 5.352064 0 0 0 -9 1 4.989392 0.832196 7.871782 0 0 0 -10 1 3.289845 1.825899 10.472628 0 0 0 -11 1 4.926259 0.965544 13.227649 0 0 0 -12 1 3.289325 1.773248 15.791892 0 0 0 -13 1 3.235025 3.691736 2.703523 0 0 0 -14 1 1.716305 4.638436 5.349529 0 0 0 -15 1 3.153575 3.825838 7.802696 0 0 0 -16 1 1.646676 4.657449 10.655324 0 0 0 -17 1 3.248665 3.747762 13.318442 0 0 0 -18 1 1.585621 4.676237 0.141023 0 0 0 -19 1 1.504950 6.668975 2.536831 0 0 0 -20 1 1.667201 6.582012 7.972716 0 0 0 -21 1 1.587699 6.589662 13.297526 0 0 0 -22 1 12.865603 9.281485 2.785919 0 0 0 -23 1 0.039324 9.314673 7.886518 0 0 0 -24 1 12.892302 9.322998 13.122119 0 0 0 -25 1 8.075287 0.859264 2.587219 0 0 0 -26 1 6.396914 1.961463 5.147660 0 0 0 -27 1 8.230783 0.914795 7.773700 0 0 0 -28 1 6.454332 1.928163 10.651363 0 0 0 -29 1 8.130756 0.979415 13.323671 0 0 0 -30 1 6.379636 1.830849 15.696028 0 0 0 -31 1 6.416139 3.799625 2.705742 0 0 0 -32 1 4.969647 4.706162 5.140212 0 0 0 -33 1 6.605151 3.817625 7.849282 0 0 0 -34 1 4.882740 4.796613 10.626327 0 0 0 -35 1 6.583327 3.735049 13.189620 0 0 0 -36 1 4.887157 4.635624 0.072888 0 0 0 -37 1 4.872478 6.595624 2.574543 0 0 0 -38 1 3.153704 7.494624 5.232749 0 0 0 -39 1 4.946264 6.625662 7.970498 0 0 0 -40 1 3.152405 7.392472 10.577048 0 0 0 -41 1 4.819737 6.661438 13.351400 0 0 0 -42 1 3.192156 7.567750 0.120424 0 0 0 -43 1 3.272957 9.461487 2.776095 0 0 0 -44 1 1.636544 10.363974 5.300567 0 0 0 -45 1 3.124476 9.363048 7.963526 0 0 0 -46 1 1.629269 10.283873 10.696522 0 0 0 -47 1 3.333233 9.453612 13.158563 0 0 0 -48 1 1.647975 10.396487 0.131516 0 0 0 -49 1 11.410468 0.871538 2.684192 0 0 0 -50 1 9.631679 1.854024 5.329247 0 0 0 -51 1 11.479318 1.007473 7.912187 0 0 0 -52 1 9.809519 1.856387 10.707614 0 0 0 -53 1 11.493478 1.019443 13.163792 0 0 0 -54 1 9.731056 1.818024 0.083980 0 0 0 -55 1 9.842385 3.843163 2.653928 0 0 0 -56 1 8.144786 4.608511 5.402927 0 0 0 -57 1 9.730017 3.683861 8.043862 0 0 0 -58 1 8.187265 4.773663 10.489899 0 0 0 -59 1 9.787825 3.787025 13.079337 0 0 0 -60 1 8.095032 4.636974 0.063381 0 0 0 -61 1 8.062816 6.651763 2.738858 0 0 0 -62 1 6.466673 7.499574 5.337961 0 0 0 -63 1 8.205971 6.587299 7.940867 0 0 0 -64 1 6.450045 7.490349 10.625852 0 0 0 -65 1 8.218961 6.612275 13.046378 0 0 0 -66 1 6.540718 7.486299 15.820097 0 0 0 -67 1 6.395744 9.445962 2.579930 0 0 0 -68 1 4.805447 10.277235 5.236869 0 0 0 -69 1 6.507333 9.389036 7.884141 0 0 0 -70 1 4.844938 10.316048 10.607947 0 0 0 -71 1 6.612426 9.425149 13.167278 0 0 0 -72 1 4.957696 10.230322 15.700465 0 0 0 -73 1 12.882422 1.799349 5.220548 0 0 0 -74 1 12.938931 1.765148 10.570710 0 0 0 -75 1 12.885410 1.795524 0.036444 0 0 0 -76 1 11.460092 4.794251 5.298665 0 0 0 -77 1 11.495816 4.699637 10.562946 0 0 0 -78 1 11.322653 4.671849 15.837209 0 0 0 -79 1 11.255232 6.649850 2.497376 0 0 0 -80 1 9.726250 7.573600 5.242890 0 0 0 -81 1 11.396179 6.634325 8.039584 0 0 0 -82 1 9.854856 7.430498 10.481501 0 0 0 -83 1 11.470095 6.583587 13.200078 0 0 0 -84 1 9.772236 7.572025 0.004754 0 0 0 -85 1 9.665454 9.364736 2.612572 0 0 0 -86 1 8.240136 10.339674 5.338278 0 0 0 -87 1 9.800036 9.340661 7.922487 0 0 0 -88 1 8.133744 10.235385 10.577682 0 0 0 -89 1 9.793540 9.358548 13.305449 0 0 0 -90 1 8.179211 10.281173 15.825325 0 0 0 -91 1 12.961015 7.562125 5.350479 0 0 0 -92 1 12.972446 7.543674 10.699057 0 0 0 -93 1 0.074046 7.546374 15.715993 0 0 0 -94 1 11.338111 10.333036 5.263330 0 0 0 -95 1 11.249906 10.251585 10.663881 0 0 0 -96 1 11.240812 10.394462 15.706169 0 0 0 -97 2 1.667721 0.937554 4.537616 0 0 0 -98 2 1.642389 0.852502 9.963043 0 0 0 -99 2 1.649664 0.837607 15.050015 0 0 0 -100 2 12.900221 3.642010 4.606543 0 0 0 -101 2 0.086317 3.776450 9.915191 0 0 0 -102 2 0.094538 3.659561 15.319861 0 0 0 -103 2 4.769593 0.941334 4.514006 0 0 0 -104 2 3.263085 1.763573 2.070663 0 0 0 -105 2 4.961983 1.031301 10.063186 0 0 0 -106 2 3.248925 1.823649 7.141314 0 0 0 -107 2 4.873517 0.956769 15.273909 0 0 0 -108 2 3.139285 1.911400 12.555016 0 0 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4.569306 0 0 0 -134 2 3.275815 7.592388 2.115822 0 0 0 -135 2 4.895211 6.524861 10.020720 0 0 0 -136 2 3.232687 7.591038 7.119923 0 0 0 -137 2 4.879883 6.611262 15.088995 0 0 0 -138 2 3.205147 7.429823 12.493219 0 0 0 -139 2 3.222684 9.385999 4.484059 0 0 0 -140 2 1.637453 10.261935 1.904287 0 0 0 -141 2 3.180855 9.297348 10.053362 0 0 0 -142 2 1.736960 10.384337 7.340172 0 0 0 -143 2 3.163447 9.343698 15.092005 0 0 0 -144 2 1.494168 10.271385 12.613010 0 0 0 -145 2 11.399296 0.947195 4.607652 0 0 0 -146 2 9.687668 1.875400 2.069078 0 0 0 -147 2 11.434890 0.954620 9.987287 0 0 0 -148 2 9.780680 1.790236 7.269344 0 0 0 -149 2 11.327069 0.845741 15.079012 0 0 0 -150 2 9.664415 1.913763 12.527921 0 0 0 -151 2 9.793410 3.695336 4.471699 0 0 0 -152 2 8.127508 4.637874 2.127547 0 0 0 -153 2 9.848490 3.725937 9.758164 0 0 0 -154 2 8.163622 4.763425 7.417339 0 0 0 -155 2 9.627782 3.738874 15.216708 0 0 0 -156 2 8.167519 4.736987 12.597164 0 0 0 -157 2 8.178041 6.534199 4.652811 0 0 0 -158 2 6.395485 7.400573 2.138164 0 0 0 -159 2 8.063205 6.583924 10.055263 0 0 0 -160 2 6.413671 7.431060 7.217688 0 0 0 -161 2 8.231562 6.538024 15.118626 0 0 0 -162 2 6.404838 7.476961 12.510015 0 0 0 -163 2 6.399382 9.360461 4.497527 0 0 0 -164 2 4.901187 10.202647 2.009341 0 0 0 -165 2 6.570467 9.315573 9.892373 0 0 0 -166 2 4.889496 10.213897 7.266809 0 0 0 -167 2 6.532275 9.312423 15.297360 0 0 0 -168 2 4.993809 10.390524 12.551530 0 0 0 -169 2 12.933085 1.930525 1.902702 0 0 0 -170 2 0.118214 1.902063 7.299608 0 0 0 -171 2 12.905415 1.782811 12.472145 0 0 0 -172 2 11.459832 4.780075 2.049430 0 0 0 -173 2 11.425148 4.626736 7.292003 0 0 0 -174 2 11.447361 4.665886 12.704437 0 0 0 -175 2 11.260168 6.522273 4.630628 0 0 0 -176 2 9.628691 7.550874 2.004112 0 0 0 -177 2 11.374355 6.636800 10.022463 0 0 0 -178 2 9.817963 7.459073 7.252706 0 0 0 -179 2 11.432162 6.474798 15.066811 0 0 0 -180 2 9.683121 7.505649 12.699525 0 0 0 -181 2 9.797567 9.332785 4.560908 0 0 0 -182 2 8.210128 10.405262 2.030257 0 0 0 -183 2 9.679354 9.282610 10.015967 0 0 0 -184 2 8.141018 10.413475 7.128796 0 0 0 -185 2 9.764831 9.326823 15.294350 0 0 0 -186 2 8.038783 10.299736 12.515878 0 0 0 -187 2 0.084438 7.539849 1.893512 0 0 0 -188 2 12.943218 7.417673 7.322267 0 0 0 -189 2 0.018187 7.425773 12.438078 0 0 0 -190 2 11.360455 10.404475 2.002686 0 0 0 -191 2 11.245359 10.212210 7.364574 0 0 0 -192 2 11.354090 10.286236 12.641531 0 0 0 diff --git a/examples/GaN-SNAP-LAMMPS/DATA/15/DATA b/examples/GaN-SNAP-LAMMPS/DATA/15/DATA deleted file mode 100755 index f52dd906..00000000 --- a/examples/GaN-SNAP-LAMMPS/DATA/15/DATA +++ /dev/null @@ -1,215 +0,0 @@ -LAMMPS DATA file - -192 atoms -0 bonds -0 angles -0 dihedrals -0 impropers - -2 atom types -0 bond types -0 angle types - -0.0 12.990503 xlo xhi -0.0 11.250148 ylo yhi -0.0 15.845291 zlo zhi - -Masses - -1 69.723 -2 14.0067 - -Atoms - -1 1 1.729945 0.850927 2.712872 0 0 0 -2 1 1.682140 0.852514 8.070799 0 0 0 -3 1 1.547948 0.881202 13.194532 0 0 0 -4 1 12.936658 3.798725 2.658840 0 0 0 -5 1 0.054828 3.660236 7.858155 0 0 0 -6 1 0.111275 3.838438 13.230184 0 0 0 -7 1 4.870529 1.010792 2.735531 0 0 0 -8 1 3.154354 1.898575 5.368384 0 0 0 -9 1 4.936002 0.827223 7.819968 0 0 0 -10 1 3.217748 1.861225 10.682420 0 0 0 -11 1 4.983287 0.960538 13.271540 0 0 0 -12 1 3.350121 1.843899 15.745941 0 0 0 -13 1 3.255550 3.846201 2.543486 0 0 0 -14 1 1.749041 4.668699 5.202960 0 0 0 -15 1 3.307512 3.757775 7.877645 0 0 0 -16 1 1.593285 4.623923 10.667367 0 0 0 -17 1 3.136297 3.719074 13.075217 0 0 0 -18 1 1.731244 4.584210 15.753546 0 0 0 -19 1 1.585101 6.650525 2.630318 0 0 0 -20 1 1.548338 6.521711 8.043703 0 0 0 -21 1 1.495727 6.489198 13.283741 0 0 0 -22 1 12.906214 9.376774 2.570106 0 0 0 -23 1 0.096975 9.447874 8.075235 0 0 0 -24 1 12.957910 9.376999 13.277720 0 0 0 -25 1 8.093084 1.034631 2.612413 0 0 0 -26 1 6.376259 1.797999 5.232273 0 0 0 -27 1 8.004488 1.014763 8.040693 0 0 0 -28 1 6.380675 1.808124 10.427310 0 0 0 -29 1 8.138031 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6.462310 2.714140 0 0 0 -80 1 9.633627 7.453448 5.249862 0 0 0 -81 1 11.418652 6.501686 8.011854 0 0 0 -82 1 9.810688 7.464248 10.472786 0 0 0 -83 1 11.420991 6.541511 13.339992 0 0 0 -84 1 9.782758 7.410810 0.083980 0 0 0 -85 1 9.794190 9.286885 2.542377 0 0 0 -86 1 8.231692 10.246185 5.130705 0 0 0 -87 1 9.753919 9.263597 7.941184 0 0 0 -88 1 8.105035 10.390637 10.587665 0 0 0 -89 1 9.626872 9.417274 13.081238 0 0 0 -90 1 8.233771 10.208947 0.060212 0 0 0 -91 1 0.068850 7.545362 5.242890 0 0 0 -92 1 0.102625 7.493274 10.594637 0 0 0 -93 1 12.894503 7.575512 15.822949 0 0 0 -94 1 11.476200 10.373424 5.186005 0 0 0 -95 1 11.273548 10.225597 10.470726 0 0 0 -96 1 11.294463 10.250123 15.823107 0 0 0 -97 2 1.574319 1.009105 4.654713 0 0 0 -98 2 1.720202 0.990497 9.972867 0 0 0 -99 2 1.715916 0.855146 15.072833 0 0 0 -100 2 12.979445 3.702649 4.681174 0 0 0 -101 2 12.920788 3.684536 9.943554 0 0 0 -102 2 0.029183 3.861388 15.345689 0 0 0 -103 2 4.929376 1.011400 4.584359 0 0 0 -104 2 3.155653 1.938626 2.032475 0 0 0 -105 2 4.999135 0.999396 10.057798 0 0 0 -106 2 3.155653 1.924113 7.200575 0 0 0 -107 2 4.898199 0.930342 15.212271 0 0 0 -108 2 3.355577 1.856274 12.419380 0 0 0 -109 2 3.317125 3.721324 4.623339 0 0 0 -110 2 1.570032 4.712800 2.096807 0 0 0 -111 2 3.283610 3.749562 10.042428 0 0 0 -112 2 1.584062 4.580048 7.124835 0 0 0 -113 2 3.324530 3.855988 15.267096 0 0 0 -114 2 1.566395 4.735750 12.422232 0 0 0 -115 2 1.731374 6.626675 4.516700 0 0 0 -116 2 1.603288 6.664925 9.810453 0 0 0 -117 2 1.564966 6.462198 15.079171 0 0 0 -118 2 12.881522 9.422674 4.490714 0 0 0 -119 2 0.006275 9.437749 9.773058 0 0 0 -120 2 0.041920 9.360461 15.156971 0 0 0 -121 2 8.146215 1.049189 4.509094 0 0 0 -122 2 6.416789 1.962251 1.846769 0 0 0 -123 2 8.010854 0.956825 9.762284 0 0 0 -124 2 6.392237 1.852337 7.279802 0 0 0 -125 2 8.045278 0.911791 15.321604 0 0 0 -126 2 6.459398 1.884400 12.449169 0 0 0 -127 2 6.454072 3.829100 4.774186 0 0 0 -128 2 4.880922 4.774788 2.065275 0 0 0 -129 2 6.401590 3.638635 10.001072 0 0 0 -130 2 4.875076 4.627073 7.332408 0 0 0 -131 2 6.534483 3.832926 15.142235 0 0 0 -132 2 4.827401 4.641136 12.395454 0 0 0 -133 2 4.814151 6.643100 4.516383 0 0 0 -134 2 3.261266 7.401360 2.095857 0 0 0 -135 2 4.991731 6.517886 9.824239 0 0 0 -136 2 3.360643 7.577087 7.356652 0 0 0 -137 2 4.873387 6.581112 15.217976 0 0 0 -138 2 3.226971 7.575062 12.440455 0 0 0 -139 2 3.146170 9.380374 4.643779 0 0 0 -140 2 1.536387 10.233697 1.846769 0 0 0 -141 2 3.230089 9.372836 9.751984 0 0 0 -142 2 1.561848 10.277235 7.113743 0 0 0 -143 2 3.299848 9.453725 15.165369 0 0 0 -144 2 1.704614 10.422925 12.528554 0 0 0 -145 2 11.486723 0.922940 4.534288 0 0 0 -146 2 9.665584 1.932663 2.126913 0 0 0 -147 2 11.460352 0.916516 10.051777 0 0 0 -148 2 9.734823 1.921638 7.264907 0 0 0 -149 2 11.331746 0.963114 15.239208 0 0 0 -150 2 9.668572 1.888225 12.694296 0 0 0 -151 2 9.842644 3.856101 4.668815 0 0 0 -152 2 8.094642 4.674887 1.829814 0 0 0 -153 2 9.700009 3.810650 9.955121 0 0 0 -154 2 8.105554 4.786601 7.419557 0 0 0 -155 2 9.740799 3.736962 15.284843 0 0 0 -156 2 8.020467 4.761175 12.627746 0 0 0 -157 2 8.141668 6.518223 4.653920 0 0 0 -158 2 6.514737 7.434098 1.845818 0 0 0 -159 2 8.048786 6.672575 10.005826 0 0 0 -160 2 6.376518 7.509586 7.193287 0 0 0 -161 2 8.121403 6.581112 15.046529 0 0 0 -162 2 6.592940 7.496536 12.452814 0 0 0 -163 2 6.620350 9.465762 4.667547 0 0 0 -164 2 4.837404 10.408975 2.112494 0 0 0 -165 2 6.378857 9.282497 9.825982 0 0 0 -166 2 4.828440 10.392324 7.114219 0 0 0 -167 2 6.432507 9.424924 15.060156 0 0 0 -168 2 4.965490 10.237635 12.534259 0 0 0 -169 2 12.934384 1.885750 2.135470 0 0 0 -170 2 12.899310 1.957863 7.264273 0 0 0 -171 2 0.023383 1.763236 12.545033 0 0 0 -172 2 11.426836 4.695924 2.140382 0 0 0 -173 2 11.367080 4.586235 7.144483 0 0 0 -174 2 11.359286 4.612223 12.535526 0 0 0 -175 2 11.397088 6.475923 4.494675 0 0 0 -176 2 9.617909 7.407210 1.958953 0 0 0 -177 2 11.351621 6.642763 9.826615 0 0 0 -178 2 9.832122 7.471898 7.115486 0 0 0 -179 2 11.430604 6.487060 15.038448 0 0 0 -180 2 9.765091 7.567412 12.607147 0 0 0 -181 2 9.690396 9.382961 4.523989 0 0 0 -182 2 8.127508 10.247873 2.044518 0 0 0 -183 2 9.713779 9.314335 9.932620 0 0 0 -184 2 8.023195 10.264185 7.133708 0 0 0 -185 2 9.714168 9.458450 15.225898 0 0 0 -186 2 8.084380 10.345299 12.586707 0 0 0 -187 2 12.948284 7.424873 2.127230 0 0 0 -188 2 0.002598 7.602175 7.258411 0 0 0 -189 2 0.113017 7.565725 12.547886 0 0 0 -190 2 11.240293 10.254173 1.966401 0 0 0 -191 2 11.467497 10.405600 7.307056 0 0 0 -192 2 11.358636 10.385574 12.506212 0 0 0 diff --git a/examples/GaN-SNAP-LAMMPS/DATA/16/DATA b/examples/GaN-SNAP-LAMMPS/DATA/16/DATA deleted file mode 100755 index c5fed709..00000000 --- a/examples/GaN-SNAP-LAMMPS/DATA/16/DATA +++ /dev/null @@ -1,215 +0,0 @@ -LAMMPS DATA file - -192 atoms -0 bonds -0 angles -0 dihedrals -0 impropers - -2 atom types -0 bond types -0 angle types - -0.0 12.990503 xlo xhi -0.0 11.250148 ylo yhi -0.0 15.845291 zlo zhi - -Masses - -1 69.723 -2 14.0067 - -Atoms - -1 1 1.640051 0.930781 2.590863 0 0 0 -2 1 1.590557 0.911161 7.839933 0 0 0 -3 1 1.746443 0.973633 13.200553 0 0 0 -4 1 12.912047 3.661023 2.758507 0 0 0 -5 1 12.954900 3.739662 7.779245 0 0 0 -6 1 0.091134 3.700399 13.329534 0 0 0 -7 1 4.757122 0.963598 2.655671 0 0 0 -8 1 3.291404 1.838049 5.129754 0 0 0 -9 1 4.815839 1.034541 8.012171 0 0 0 -10 1 3.203718 1.928500 10.579425 0 0 0 -11 1 4.745691 0.920746 13.049706 0 0 0 -12 1 3.321412 1.983176 0.055459 0 0 0 -13 1 3.320243 3.772062 2.567096 0 0 0 -14 1 1.687726 4.731137 5.258101 0 0 0 -15 1 3.226581 3.671486 7.929934 0 0 0 -16 1 1.544961 4.743625 10.626327 0 0 0 -17 1 3.300757 3.803225 13.248564 0 0 0 -18 1 1.725399 4.685574 15.789674 0 0 0 -19 1 1.743975 6.478173 2.543011 0 0 0 -20 1 1.534178 6.631850 7.780038 0 0 0 -21 1 1.621345 6.584712 13.156186 0 0 0 -22 1 0.048991 9.455412 2.762310 0 0 0 -23 1 0.117304 9.465087 7.760706 0 0 0 -24 1 12.871495 9.458562 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-1,215 +0,0 @@ -LAMMPS DATA file - -192 atoms -0 bonds -0 angles -0 dihedrals -0 impropers - -2 atom types -0 bond types -0 angle types - -0.0 12.990503 xlo xhi -0.0 11.250148 ylo yhi -0.0 15.845291 zlo zhi - -Masses - -1 69.723 -2 14.0067 - -Atoms - -1 1 1.747223 0.987448 2.681815 0 0 0 -2 1 1.505210 0.959368 7.914564 0 0 0 -3 1 1.541193 1.026115 13.089002 0 0 0 -4 1 12.979911 3.851488 2.664861 0 0 0 -5 1 12.926148 3.810875 8.047982 0 0 0 -6 1 12.965060 3.847213 13.253635 0 0 0 -7 1 4.983157 0.989237 2.664544 0 0 0 -8 1 3.146430 1.939301 5.312134 0 0 0 -9 1 4.833117 0.965251 7.909018 0 0 0 -10 1 3.280362 1.906788 10.680835 0 0 0 -11 1 4.760760 0.970899 13.236680 0 0 0 -12 1 3.229569 1.809136 0.039613 0 0 0 -13 1 3.132270 3.799175 2.695759 0 0 0 -14 1 1.509886 4.715725 5.365849 0 0 0 -15 1 3.234765 3.673173 8.051467 0 0 0 -16 1 1.741117 4.661949 10.675448 0 0 0 -17 1 3.309720 3.853851 13.304974 0 0 0 -18 1 1.598092 4.688724 0.041198 0 0 0 -19 1 1.695001 6.655700 2.699721 0 0 0 -20 1 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12.551847 0 0 0 -145 2 11.452817 0.902014 4.746932 0 0 0 -146 2 9.693514 1.916125 1.829339 0 0 0 -147 2 11.324341 0.927923 9.842144 0 0 0 -148 2 9.812766 1.792936 7.379469 0 0 0 -149 2 11.441646 0.978459 15.155228 0 0 0 -150 2 9.838228 1.803286 12.458518 0 0 0 -151 2 9.863040 3.735162 4.657248 0 0 0 -152 2 8.185186 4.730800 1.968302 0 0 0 -153 2 9.773015 3.675198 9.955913 0 0 0 -154 2 8.053592 4.691087 7.288992 0 0 0 -155 2 9.800425 3.712099 15.346005 0 0 0 -156 2 8.071909 4.613686 12.642165 0 0 0 -157 2 8.002670 6.628250 4.741703 0 0 0 -158 2 6.393016 7.426673 1.832349 0 0 0 -159 2 8.063335 6.451735 9.991882 0 0 0 -160 2 6.593979 7.566625 7.193603 0 0 0 -161 2 8.151151 6.461973 15.265670 0 0 0 -162 2 6.453032 7.540974 12.493219 0 0 0 -163 2 6.420816 9.411762 4.469006 0 0 0 -164 2 4.936781 10.365999 2.003479 0 0 0 -165 2 6.624117 9.348536 10.020245 0 0 0 -166 2 4.990042 10.241572 7.197248 0 0 0 -167 2 6.412502 9.473187 15.247448 0 0 0 -168 2 4.830908 10.308286 12.547886 0 0 0 -169 2 12.958806 1.859987 2.112177 0 0 0 -170 2 12.942828 1.922200 7.362514 0 0 0 -171 2 0.122111 1.882150 12.518255 0 0 0 -172 2 11.455156 4.612448 1.977968 0 0 0 -173 2 11.280433 4.623136 7.250488 0 0 0 -174 2 11.363962 4.793913 12.596055 0 0 0 -175 2 11.486852 6.623862 4.755330 0 0 0 -176 2 9.619338 7.597225 1.903812 0 0 0 -177 2 11.278745 6.666388 9.897285 0 0 0 -178 2 9.634147 7.581587 7.117863 0 0 0 -179 2 11.468016 6.631400 15.154594 0 0 0 -180 2 9.783668 7.464586 12.460103 0 0 0 -181 2 9.833421 9.282047 4.754696 0 0 0 -182 2 8.162323 10.239885 2.021542 0 0 0 -183 2 9.871224 9.337623 9.892373 0 0 0 -184 2 8.119974 10.212547 7.284397 0 0 0 -185 2 9.729237 9.304210 15.068713 0 0 0 -186 2 8.024364 10.413700 12.564840 0 0 0 -187 2 12.883981 7.573600 1.978601 0 0 0 -188 2 0.106522 7.431510 7.247319 0 0 0 -189 2 0.049364 7.586200 12.538854 0 0 0 -190 2 11.257960 10.353286 1.856593 0 0 0 -191 2 11.251335 10.422362 7.183621 0 0 0 -192 2 11.447881 10.232010 12.640897 0 0 0 diff --git a/examples/GaN-SNAP-LAMMPS/DATA/18/DATA b/examples/GaN-SNAP-LAMMPS/DATA/18/DATA deleted file mode 100755 index 405caae6..00000000 --- a/examples/GaN-SNAP-LAMMPS/DATA/18/DATA +++ /dev/null @@ -1,215 +0,0 @@ -LAMMPS DATA file - -192 atoms -0 bonds -0 angles -0 dihedrals -0 impropers - -2 atom types -0 bond types -0 angle types - -0.0 12.990503 xlo xhi -0.0 11.250148 ylo yhi -0.0 15.845291 zlo zhi - -Masses - -1 69.723 -2 14.0067 - -Atoms - -1 1 1.646027 0.997438 2.532236 0 0 0 -2 1 1.624592 0.911116 8.068422 0 0 0 -3 1 1.737090 1.025879 13.181063 0 0 0 -4 1 0.065351 3.842151 2.595300 0 0 0 -5 1 12.890813 3.755749 7.866870 0 0 0 -6 1 0.090780 3.679473 13.106591 0 0 0 -7 1 4.879363 0.843975 2.553310 0 0 0 -8 1 3.282570 1.787536 5.310232 0 0 0 -9 1 4.972765 0.935416 7.857996 0 0 0 -10 1 3.315696 1.977326 10.604302 0 0 0 -11 1 4.867671 0.923603 13.099460 0 0 0 -12 1 3.232817 1.872362 0.109333 0 0 0 -13 1 3.303875 3.777125 2.505457 0 0 0 -14 1 1.523007 4.704587 5.264122 0 0 0 -15 1 3.259447 3.646061 7.942293 0 0 0 -16 1 1.657328 4.683549 10.450444 0 0 0 -17 1 3.313747 3.816050 13.132735 0 0 0 -18 1 1.625761 4.628648 15.742455 0 0 0 -19 1 1.703964 6.465123 2.539049 0 0 0 -20 1 1.747223 6.579424 7.943561 0 0 0 -21 1 1.740727 6.472548 13.318917 0 0 0 -22 1 0.101704 9.310735 2.529859 0 0 0 -23 1 0.037966 9.303198 7.795566 0 0 0 -24 1 12.955517 9.353148 13.068879 0 0 0 -25 1 8.166870 0.948061 2.789405 0 0 0 -26 1 6.420556 1.969338 5.328613 0 0 0 -27 1 8.182328 0.910159 7.909177 0 0 0 -28 1 6.393016 1.961351 10.540604 0 0 0 -29 1 8.162713 0.988854 13.130992 0 0 0 -30 1 6.519544 1.845924 0.088734 0 0 0 -31 1 6.384443 3.860938 2.722855 0 0 0 -32 1 4.743482 4.775125 5.391677 0 0 0 -33 1 6.546564 3.836638 7.906325 0 0 0 -34 1 4.838053 4.593773 10.715695 0 0 0 -35 1 6.591381 3.637510 13.256012 0 0 0 -36 1 4.911709 4.667687 15.832297 0 0 0 -37 1 4.842470 6.551749 2.485492 0 0 0 -38 1 3.228270 7.411373 5.131497 0 0 0 -39 1 4.885988 6.587637 7.992840 0 0 0 -40 1 3.184492 7.550987 10.625693 0 0 0 -41 1 4.872478 6.650975 13.287544 0 0 0 -42 1 3.246327 7.558975 0.047536 0 0 0 -43 1 3.371815 9.288910 2.752485 0 0 0 -44 1 1.641480 10.227172 5.425269 0 0 0 -45 1 3.335961 9.276647 7.846905 0 0 0 -46 1 1.600300 10.341136 10.690818 0 0 0 -47 1 3.225542 9.422674 13.348073 0 0 0 -48 1 1.607055 10.343049 0.122009 0 0 0 -49 1 11.463210 0.857115 2.540475 0 0 0 -50 1 9.774314 1.936938 5.195988 0 0 0 -51 1 11.332785 0.901756 7.903314 0 0 0 -52 1 9.657400 1.930300 10.430638 0 0 0 -53 1 11.468146 0.843480 13.288178 0 0 0 -54 1 9.833421 1.863925 0.028522 0 0 0 -55 1 9.705075 3.808400 2.663752 0 0 0 -56 1 8.148033 4.764775 5.262696 0 0 0 -57 1 9.842385 3.748549 7.956079 0 0 0 -58 1 8.135173 4.737437 10.572929 0 0 0 -59 1 9.816793 3.737974 13.329534 0 0 0 -60 1 8.011633 4.799876 0.066550 0 0 0 -61 1 8.134263 6.482223 2.742344 0 0 0 -62 1 6.553709 7.481461 5.204386 0 0 0 -63 1 8.070870 6.580999 7.977153 0 0 0 -64 1 6.589822 7.434998 10.560252 0 0 0 -65 1 8.099579 6.504048 13.280572 0 0 0 -66 1 6.571116 7.474373 15.782226 0 0 0 -67 1 6.490315 9.325248 2.527007 0 0 0 -68 1 4.844289 10.264410 5.194879 0 0 0 -69 1 6.532275 9.477912 7.817749 0 0 0 -70 1 4.977831 10.328086 10.460902 0 0 0 -71 1 6.548253 9.409174 13.145728 0 0 0 -72 1 4.877025 10.205684 15.688422 0 0 0 -73 1 0.077943 1.786749 5.336060 0 0 0 -74 1 0.071448 1.940651 10.624426 0 0 0 -75 1 0.115615 1.829612 0.152115 0 0 0 -76 1 11.380850 4.722700 5.417346 0 0 0 -77 1 11.295113 4.795938 10.453614 0 0 0 -78 1 11.481267 4.790426 15.736750 0 0 0 -79 1 11.250945 6.510461 2.649966 0 0 0 -80 1 9.814325 7.523424 5.218013 0 0 0 -81 1 11.349413 6.639725 7.957188 0 0 0 -82 1 9.683771 7.503399 10.681152 0 0 0 -83 1 11.282122 6.634550 13.097876 0 0 0 -84 1 9.638304 7.394610 15.684619 0 0 0 -85 1 9.864339 9.462387 2.492623 0 0 0 -86 1 8.163232 10.419887 5.187590 0 0 0 -87 1 9.634796 9.343361 7.991097 0 0 0 -88 1 8.145565 10.301648 10.688916 0 0 0 -89 1 9.613752 9.377336 13.086309 0 0 0 -90 1 8.120234 10.327974 0.039613 0 0 0 -91 1 12.914379 7.464136 5.221657 0 0 0 -92 1 0.029878 7.520612 10.617612 0 0 0 -93 1 12.903857 7.534337 0.079226 0 0 0 -94 1 11.339670 10.289273 5.337169 0 0 0 -95 1 11.298490 10.413587 10.442680 0 0 0 -96 1 11.369678 10.209510 15.780325 0 0 0 -97 2 1.577567 1.038389 4.534288 0 0 0 -98 2 1.621085 0.925066 10.010421 0 0 0 -99 2 1.498455 1.002433 15.203556 0 0 0 -100 2 12.872416 3.753162 4.609870 0 0 0 -101 2 12.988261 3.786012 9.910437 0 0 0 -102 2 0.062839 3.849913 15.285476 0 0 0 -103 2 4.855201 0.845325 4.764362 0 0 0 -104 2 3.216059 1.933338 2.082388 0 0 0 -105 2 4.950421 0.959064 9.853394 0 0 0 -106 2 3.312189 1.869775 7.272830 0 0 0 -107 2 4.866243 0.920420 15.087886 0 0 0 -108 2 3.190597 1.960001 12.668151 0 0 0 -109 2 3.244898 3.773975 4.696069 0 0 0 -110 2 1.530281 4.706275 1.889551 0 0 0 -111 2 3.134219 3.651911 10.048133 0 0 0 -112 2 1.629009 4.608848 7.314345 0 0 0 -113 2 3.269450 3.707824 15.245071 0 0 0 -114 2 1.597052 4.624486 12.467550 0 0 0 -115 2 1.594324 6.457585 4.578497 0 0 0 -116 2 1.637323 6.575712 9.771474 0 0 0 -117 2 1.645117 6.557149 15.241902 0 0 0 -118 2 0.074333 9.305335 4.773235 0 0 0 -119 2 0.009111 9.468350 9.954962 0 0 0 -120 2 12.900473 9.274397 15.036864 0 0 0 -121 2 8.040212 0.943741 4.515432 0 0 0 -122 2 6.384313 1.887325 2.138639 0 0 0 -123 2 8.031509 0.860243 9.802214 0 0 0 -124 2 6.385742 1.924113 7.250805 0 0 0 -125 2 8.121663 0.961168 15.311938 0 0 0 -126 2 6.397043 1.827812 12.410982 0 0 0 -127 2 6.402629 3.652811 4.527158 0 0 0 -128 2 4.941198 4.777038 1.991911 0 0 0 -129 2 6.584756 3.689036 9.886035 0 0 0 -130 2 4.837274 4.731700 7.408783 0 0 0 -131 2 6.421985 3.806938 15.196901 0 0 0 -132 2 4.938989 4.773213 12.466441 0 0 0 -133 2 4.985625 6.456235 4.646473 0 0 0 -134 2 3.349082 7.425210 1.962439 0 0 0 -135 2 4.826492 6.577849 10.012481 0 0 0 -136 2 3.219436 7.527362 7.415279 0 0 0 -137 2 4.956786 6.633087 15.334755 0 0 0 -138 2 3.165266 7.538499 12.624260 0 0 0 -139 2 3.330635 9.415812 4.573109 0 0 0 -140 2 1.502871 10.227172 1.917597 0 0 0 -141 2 3.335442 9.465425 9.892849 0 0 0 -142 2 1.750730 10.207709 7.381846 0 0 0 -143 2 3.255030 9.482075 15.310037 0 0 0 -144 2 1.535867 10.279598 12.409556 0 0 0 -145 2 11.352141 0.924256 4.572159 0 0 0 -146 2 9.850569 1.873825 2.052757 0 0 0 -147 2 11.409429 1.012165 9.832161 0 0 0 -148 2 9.812766 1.854924 7.127053 0 0 0 -149 2 11.462950 1.043778 15.069188 0 0 0 -150 2 9.745086 1.932550 12.426035 0 0 0 -151 2 9.621806 3.736849 4.509728 0 0 0 -152 2 8.241565 4.786601 2.123427 0 0 0 -153 2 9.868625 3.793437 9.973026 0 0 0 -154 2 8.085679 4.589498 7.250013 0 0 0 -155 2 9.754049 3.759125 15.281357 0 0 0 -156 2 8.145435 4.788176 12.591302 0 0 0 -157 2 8.217533 6.477723 4.726333 0 0 0 -158 2 6.619311 7.439611 2.116931 0 0 0 -159 2 8.164921 6.613175 9.967638 0 0 0 -160 2 6.572285 7.506774 7.348570 0 0 0 -161 2 8.119974 6.654125 15.071248 0 0 0 -162 2 6.586705 7.427010 12.633450 0 0 0 -163 2 6.484729 9.398936 4.583884 0 0 0 -164 2 4.845977 10.364424 2.130399 0 0 0 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7.580800 12.667518 0 0 0 -190 2 11.469835 10.389962 1.981454 0 0 0 -191 2 11.363703 10.214797 7.254291 0 0 0 -192 2 11.391502 10.224922 12.500191 0 0 0 diff --git a/examples/GaN-SNAP-LAMMPS/DATA/19/DATA b/examples/GaN-SNAP-LAMMPS/DATA/19/DATA deleted file mode 100755 index 59af219a..00000000 --- a/examples/GaN-SNAP-LAMMPS/DATA/19/DATA +++ /dev/null @@ -1,215 +0,0 @@ -LAMMPS DATA file - -192 atoms -0 bonds -0 angles -0 dihedrals -0 impropers - -2 atom types -0 bond types -0 angle types - -0.0 12.990503 xlo xhi -0.0 11.250148 ylo yhi -0.0 15.845291 zlo zhi - -Masses - -1 69.723 -2 14.0067 - -Atoms - -1 1 1.589778 0.920240 2.658047 0 0 0 -2 1 1.646676 0.831476 7.787643 0 0 0 -3 1 1.624073 1.031616 13.118950 0 0 0 -4 1 0.039737 3.652248 2.482165 0 0 0 -5 1 0.005221 3.784325 7.883666 0 0 0 -6 1 12.959492 3.720762 13.279146 0 0 0 -7 1 4.900537 0.878817 2.770232 0 0 0 -8 1 3.216968 1.846599 5.222291 0 0 0 -9 1 4.976402 0.929881 7.919793 0 0 0 -10 1 3.324140 1.792936 10.464547 0 0 0 -11 1 4.790898 0.825435 13.312262 0 0 0 -12 1 3.120319 1.764473 0.102994 0 0 0 -13 1 3.317775 3.830450 2.772767 0 0 0 -14 1 1.497805 4.617736 5.337803 0 0 0 -15 1 3.371685 3.767000 7.936906 0 0 0 -16 1 1.738649 4.729450 10.504477 0 0 0 -17 1 3.206056 3.847776 13.137964 0 0 0 -18 1 1.504040 4.702787 0.042782 0 0 0 -19 1 1.685778 6.665263 2.573909 0 0 0 -20 1 1.691104 6.513386 8.044496 0 0 0 -21 1 1.668111 6.515636 13.143035 0 0 0 -22 1 0.056322 9.304098 2.616533 0 0 0 -23 1 12.955305 9.310623 7.927716 0 0 0 -24 1 0.086330 9.369011 13.240800 0 0 0 -25 1 8.040342 1.049459 2.477728 0 0 0 -26 1 6.525260 1.948076 5.249069 0 0 0 -27 1 8.222079 0.940209 8.063510 0 0 0 -28 1 6.523311 1.912413 10.691610 0 0 0 -29 1 8.105684 0.967501 13.107541 0 0 0 -30 1 6.510970 1.785849 15.773987 0 0 0 -31 1 6.506683 3.678236 2.564402 0 0 0 -32 1 4.801940 4.698512 5.294387 0 0 0 -33 1 6.526559 3.637735 7.818225 0 0 0 -34 1 4.865333 4.579148 10.550111 0 0 0 -35 1 6.385222 3.693986 13.224638 0 0 0 -36 1 4.780765 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2 9.733524 9.477687 15.341886 0 0 0 -186 2 8.026312 10.261485 12.698891 0 0 0 -187 2 0.070149 7.523874 2.094589 0 0 0 -188 2 0.046766 7.595425 7.418290 0 0 0 -189 2 12.875667 7.393485 12.616179 0 0 0 -190 2 11.403064 10.305473 2.004271 0 0 0 -191 2 11.261337 10.384562 7.228146 0 0 0 -192 2 11.473732 10.388949 12.579101 0 0 0 diff --git a/examples/GaN-SNAP-LAMMPS/DATA/2/DATA b/examples/GaN-SNAP-LAMMPS/DATA/2/DATA deleted file mode 100755 index 63108017..00000000 --- a/examples/GaN-SNAP-LAMMPS/DATA/2/DATA +++ /dev/null @@ -1,215 +0,0 @@ -LAMMPS DATA file - -192 atoms -0 bonds -0 angles -0 dihedrals -0 impropers - -2 atom types -0 bond types -0 angle types - -0.0 12.990503 xlo xhi -0.0 11.250148 ylo yhi -0.0 15.845291 zlo zhi - -Masses - -1 69.723 -2 14.0067 - -Atoms - -1 1 1.559120 0.995942 2.761676 0 0 0 -2 1 1.551975 0.976502 8.018192 0 0 0 -3 1 1.740468 1.021727 13.165218 0 0 0 -4 1 0.113529 3.735837 2.528433 0 0 0 -5 1 12.941094 3.790850 8.054795 0 0 0 -6 1 0.116238 3.772287 13.341101 0 0 0 -7 1 4.846497 0.834243 2.570106 0 0 0 -8 1 3.126035 1.957076 5.254932 0 0 0 -9 1 4.765696 0.856013 7.835338 0 0 0 -10 1 3.175658 1.957751 10.641697 0 0 0 -11 1 4.831038 0.911588 13.228916 0 0 0 -12 1 3.256719 1.837599 0.106163 0 0 0 -13 1 3.186700 3.847663 2.600529 0 0 0 -14 1 1.671358 4.636974 5.126744 0 0 0 -15 1 3.362072 3.757662 7.971449 0 0 0 -16 1 1.651742 4.743963 10.710624 0 0 0 -17 1 3.306733 3.830450 13.354728 0 0 0 -18 1 1.691234 4.607948 15.784762 0 0 0 -19 1 1.501442 6.606312 2.780848 0 0 0 -20 1 1.683309 6.615875 7.814105 0 0 0 -21 1 1.586270 6.579424 13.186292 0 0 0 -22 1 0.086706 9.446074 2.579613 0 0 0 -23 1 12.980550 9.414237 7.947364 0 0 0 -24 1 12.895515 9.266972 13.080129 0 0 0 -25 1 8.047227 0.926067 2.646322 0 0 0 -26 1 6.622688 1.923888 5.428438 0 0 0 -27 1 8.003059 0.968312 8.063035 0 0 0 -28 1 6.435495 1.976201 10.685589 0 0 0 -29 1 8.039693 0.990148 13.095816 0 0 0 -30 1 6.392627 1.833212 15.791892 0 0 0 -31 1 6.469011 3.701411 2.576444 0 0 0 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9.854726 3.738087 8.022946 0 0 0 -58 1 8.245852 4.658236 10.453772 0 0 0 -59 1 9.826796 3.769587 13.345221 0 0 0 -60 1 8.116207 4.632136 0.050705 0 0 0 -61 1 8.226756 6.588874 2.579138 0 0 0 -62 1 6.492783 7.479324 5.144490 0 0 0 -63 1 8.142967 6.647825 7.934054 0 0 0 -64 1 6.443160 7.589462 10.651363 0 0 0 -65 1 8.190772 6.584824 13.217032 0 0 0 -66 1 6.443160 7.510824 0.150530 0 0 0 -67 1 6.490965 9.416712 2.629051 0 0 0 -68 1 4.935482 10.247760 5.196621 0 0 0 -69 1 6.390808 9.422112 8.029918 0 0 0 -70 1 4.946524 10.367237 10.432698 0 0 0 -71 1 6.500708 9.453162 13.307826 0 0 0 -72 1 4.839612 10.261373 15.721063 0 0 0 -73 1 0.049364 1.887437 5.120564 0 0 0 -74 1 12.968679 1.861337 10.648194 0 0 0 -75 1 0.085737 1.895200 15.726451 0 0 0 -76 1 11.390983 4.738450 5.253506 0 0 0 -77 1 11.291605 4.634724 10.714269 0 0 0 -78 1 11.361754 4.761288 0.026937 0 0 0 -79 1 11.449310 6.665038 2.683083 0 0 0 -80 1 9.776003 7.533099 5.137519 0 0 0 -81 1 11.480487 6.652325 7.978896 0 0 0 -82 1 9.693643 7.464923 10.423824 0 0 0 -83 1 11.371887 6.587074 13.270906 0 0 0 -84 1 9.612972 7.425773 15.828178 0 0 0 -85 1 9.707024 9.476787 2.772292 0 0 0 -86 1 8.238058 10.246635 5.168417 0 0 0 -87 1 9.761584 9.396011 7.980164 0 0 0 -88 1 8.068661 10.288711 10.506378 0 0 0 -89 1 9.646488 9.282160 13.214497 0 0 0 -90 1 8.071649 10.423487 0.064966 0 0 0 -91 1 0.018187 7.548962 5.427329 0 0 0 -92 1 12.971537 7.593063 10.684004 0 0 0 -93 1 0.087036 7.398435 15.795219 0 0 0 -94 1 11.313559 10.341699 5.160970 0 0 0 -95 1 11.333954 10.394687 10.478966 0 0 0 -96 1 11.244450 10.425062 0.028522 0 0 0 -97 2 1.557302 0.923603 4.701456 0 0 0 -98 2 1.638882 0.923637 9.941652 0 0 0 -99 2 1.540933 1.006990 15.291656 0 0 0 -100 2 12.987189 3.807388 4.596719 0 0 0 -101 2 0.058635 3.672161 9.911705 0 0 0 -102 2 0.043658 3.671823 15.051917 0 0 0 -103 2 4.829090 0.925347 4.708745 0 0 0 -104 2 3.151626 1.965401 1.897474 0 0 0 -105 2 4.839872 0.920127 10.058590 0 0 0 -106 2 3.163707 1.961013 7.284080 0 0 0 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15.319227 0 0 0 -132 2 4.875336 4.799876 12.510808 0 0 0 -133 2 4.795055 6.614300 4.567880 0 0 0 -134 2 3.148248 7.587550 2.047370 0 0 0 -135 2 4.985755 6.543986 10.008836 0 0 0 -136 2 3.326868 7.468636 7.399117 0 0 0 -137 2 4.816489 6.487173 15.176619 0 0 0 -138 2 3.180855 7.388085 12.586231 0 0 0 -139 2 3.289455 9.411199 4.684185 0 0 0 -140 2 1.714876 10.208497 2.043409 0 0 0 -141 2 3.266072 9.417949 10.034189 0 0 0 -142 2 1.563277 10.215585 7.208815 0 0 0 -143 2 3.322711 9.374749 15.170598 0 0 0 -144 2 1.537686 10.259685 12.607939 0 0 0 -145 2 11.448920 0.983758 4.651227 0 0 0 -146 2 9.871224 1.866287 1.983989 0 0 0 -147 2 11.307973 0.972407 9.879380 0 0 0 -148 2 9.690915 1.898800 7.360137 0 0 0 -149 2 11.489061 0.999024 15.222254 0 0 0 -150 2 9.729627 1.797099 12.458201 0 0 0 -151 2 9.794969 3.852726 4.669924 0 0 0 -152 2 8.220780 4.623698 2.044359 0 0 0 -153 2 9.694813 3.643248 10.010262 0 0 0 -154 2 8.101527 4.595011 7.405772 0 0 0 -155 2 9.714558 3.769812 15.108168 0 0 0 -156 2 8.158945 4.657561 12.543766 0 0 0 -157 2 8.093473 6.525198 4.553303 0 0 0 -158 2 6.564881 7.441636 2.132301 0 0 0 -159 2 8.229094 6.511811 9.821070 0 0 0 -160 2 6.430819 7.443211 7.185364 0 0 0 -161 2 8.100488 6.635900 15.227641 0 0 0 -162 2 6.415750 7.569437 12.703645 0 0 0 -163 2 6.403928 9.454512 4.544112 0 0 0 -164 2 4.849874 10.272623 1.965291 0 0 0 -165 2 6.450434 9.284860 9.963043 0 0 0 -166 2 4.754394 10.245397 7.267601 0 0 0 -167 2 6.436924 9.357086 15.221303 0 0 0 -168 2 4.754264 10.399637 12.663239 0 0 0 -169 2 12.882682 1.802499 1.831874 0 0 0 -170 2 0.023383 1.921750 7.349996 0 0 0 -171 2 12.916198 1.979914 12.544717 0 0 0 -172 2 11.253023 4.615261 1.934868 0 0 0 -173 2 11.465548 4.584660 7.222125 0 0 0 -174 2 11.403194 4.761288 12.405436 0 0 0 -175 2 11.442295 6.461635 4.562493 0 0 0 -176 2 9.683641 7.593175 2.019641 0 0 0 -177 2 11.367210 6.615875 9.785893 0 0 0 -178 2 9.842774 7.506774 7.111208 0 0 0 -179 2 11.279134 6.509111 15.044470 0 0 0 -180 2 9.790163 7.393935 12.549629 0 0 0 -181 2 9.737811 9.325248 4.655663 0 0 0 -182 2 8.063855 10.407175 1.829656 0 0 0 -183 2 9.759635 9.345611 9.867972 0 0 0 -184 2 7.994615 10.354749 7.285189 0 0 0 -185 2 9.811857 9.440674 15.110228 0 0 0 -186 2 8.041121 10.282748 12.619189 0 0 0 -187 2 12.893204 7.484274 1.832825 0 0 0 -188 2 12.879045 7.547387 7.363940 0 0 0 -189 2 0.106522 7.592838 12.590668 0 0 0 -190 2 11.270950 10.214122 2.074149 0 0 0 -191 2 11.429564 10.341024 7.340489 0 0 0 -192 2 11.289527 10.379049 12.700000 0 0 0 diff --git a/examples/GaN-SNAP-LAMMPS/DATA/20/DATA b/examples/GaN-SNAP-LAMMPS/DATA/20/DATA deleted file mode 100755 index 289c23bf..00000000 --- a/examples/GaN-SNAP-LAMMPS/DATA/20/DATA +++ /dev/null @@ -1,215 +0,0 @@ -LAMMPS DATA file - -192 atoms -0 bonds -0 angles -0 dihedrals -0 impropers - -2 atom types -0 bond types -0 angle types - -0.0 12.990503 xlo xhi -0.0 11.250148 ylo yhi -0.0 15.845291 zlo zhi - -Masses - -1 69.723 -2 14.0067 - -Atoms - -1 1 1.520408 0.857914 2.689738 0 0 0 -2 1 1.660186 0.908809 7.810302 0 0 0 -3 1 1.595104 1.005009 13.167120 0 0 0 -4 1 0.066284 3.703999 2.679756 0 0 0 -5 1 0.100059 3.684761 7.910920 0 0 0 -6 1 12.889955 3.667323 13.060798 0 0 0 -7 1 4.762189 0.966073 2.607343 0 0 0 -8 1 3.283610 1.955276 5.359828 0 0 0 -9 1 4.995108 1.000858 8.055270 0 0 0 -10 1 3.309720 1.819599 10.627595 0 0 0 -11 1 4.921712 0.999013 13.277244 0 0 0 -12 1 3.200470 1.877425 0.080811 0 0 0 -13 1 3.266592 3.852163 2.531285 0 0 0 -14 1 1.729556 4.744300 5.208505 0 0 0 -15 1 3.280752 3.741687 7.799686 0 0 0 -16 1 1.636674 4.793238 10.539653 0 0 0 -17 1 3.271269 3.662486 13.103738 0 0 0 -18 1 1.536257 4.583310 15.767807 0 0 0 -19 1 1.553664 6.530711 2.519560 0 0 0 -20 1 1.753328 6.565587 7.881606 0 0 0 -21 1 1.558860 6.532174 13.166961 0 0 0 -22 1 0.110758 9.374074 2.669931 0 0 0 -23 1 12.861849 9.394886 8.005041 0 0 0 -24 1 0.040840 9.381499 13.302121 0 0 0 -25 1 8.239227 0.895602 2.729510 0 0 0 -26 1 6.439392 1.765823 5.147660 0 0 0 -27 1 8.074507 0.893757 7.764351 0 0 0 -28 1 6.407436 1.862462 10.642648 0 0 0 -29 1 8.166220 0.985783 13.186134 0 0 0 -30 1 6.604242 1.985089 0.131516 0 0 0 -31 1 6.485249 3.841138 2.599420 0 0 0 -32 1 4.898199 4.701099 5.385814 0 0 0 -33 1 6.439392 3.786800 7.949582 0 0 0 -34 1 4.912099 4.644849 10.504635 0 0 0 -35 1 6.414191 3.660236 13.131309 0 0 0 -36 1 4.833766 4.695587 0.150530 0 0 0 -37 1 4.748808 6.609687 2.763736 0 0 0 -38 1 3.342716 7.414410 5.420515 0 0 0 -39 1 4.856110 6.647150 8.032770 0 0 0 -40 1 3.209953 7.529612 10.673546 0 0 0 -41 1 4.746990 6.467373 13.159831 0 0 0 -42 1 3.156432 7.395285 0.083980 0 0 0 -43 1 3.202809 9.446524 2.531919 0 0 0 -44 1 1.669539 10.397162 5.357768 0 0 0 -45 1 3.177347 9.343361 7.873842 0 0 0 -46 1 1.563407 10.275998 10.427152 0 0 0 -47 1 3.235025 9.364961 13.049706 0 0 0 -48 1 1.659407 10.213560 15.735007 0 0 0 -49 1 11.414625 0.949783 2.478837 0 0 0 -50 1 9.687798 1.847274 5.164297 0 0 0 -51 1 11.256141 0.928677 7.876060 0 0 0 -52 1 9.827186 1.883500 10.658652 0 0 0 -53 1 11.356428 0.828168 13.042100 0 0 0 -54 1 9.656101 1.844912 0.063381 0 0 0 -55 1 9.654412 3.700286 2.681340 0 0 0 -56 1 8.063725 4.647549 5.167149 0 0 0 -57 1 9.713649 3.839113 8.040059 0 0 0 -58 1 8.091395 4.727087 10.479441 0 0 0 -59 1 9.859792 3.778137 13.106115 0 0 0 -60 1 8.017609 4.702337 15.768282 0 0 0 -61 1 8.007606 6.485710 2.492623 0 0 0 -62 1 6.542277 7.563475 5.373613 0 0 0 -63 1 8.058009 6.651650 7.951325 0 0 0 -64 1 6.369114 7.465036 10.568650 0 0 0 -65 1 8.152320 6.550624 13.297526 0 0 0 -66 1 6.403019 7.606900 0.099825 0 0 0 -67 1 6.453682 9.401299 2.573275 0 0 0 -68 1 4.764657 10.317511 5.379318 0 0 0 -69 1 6.563841 9.475887 7.864335 0 0 0 -70 1 4.842730 10.234035 10.505269 0 0 0 -71 1 6.509151 9.386449 13.091379 0 0 0 -72 1 4.771931 10.289836 0.099825 0 0 0 -73 1 12.908663 1.875175 5.157801 0 0 0 -74 1 0.094831 1.935025 10.578474 0 0 0 -75 1 12.961794 1.872812 0.117255 0 0 0 -76 1 11.471913 4.687149 5.285514 0 0 0 -77 1 11.473083 4.705262 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3.657086 15.151108 0 0 0 -103 2 4.790248 1.007383 4.697812 0 0 0 -104 2 3.292963 1.968213 2.087934 0 0 0 -105 2 4.884039 0.828506 9.780347 0 0 0 -106 2 3.251523 1.976876 7.376617 0 0 0 -107 2 4.984456 1.044025 15.150158 0 0 0 -108 2 3.201120 1.938738 12.458518 0 0 0 -109 2 3.366879 3.846876 4.584518 0 0 0 -110 2 1.583542 4.730912 2.054817 0 0 0 -111 2 3.325699 3.771162 9.781139 0 0 0 -112 2 1.639272 4.584773 7.349521 0 0 0 -113 2 3.289066 3.772400 15.104048 0 0 0 -114 2 1.679282 4.738112 12.500350 0 0 0 -115 2 1.502482 6.639950 4.712706 0 0 0 -116 2 1.626281 6.609125 10.001072 0 0 0 -117 2 1.579775 6.655700 15.214806 0 0 0 -118 2 12.935401 9.322660 4.750735 0 0 0 -119 2 12.955716 9.296335 10.050192 0 0 0 -120 2 0.039190 9.483650 15.093590 0 0 0 -121 2 8.204412 0.936114 4.655822 0 0 0 -122 2 6.377038 1.889575 2.028514 0 0 0 -123 2 8.118545 0.838429 9.913606 0 0 0 -124 2 6.379117 1.952351 7.297865 0 0 0 -125 2 8.168688 0.970640 15.229701 0 0 0 -126 2 6.613205 1.802386 12.541706 0 0 0 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4.581824 0 0 0 -152 2 8.229224 4.688162 2.082230 0 0 0 -153 2 9.704036 3.740787 10.051777 0 0 0 -154 2 8.023714 4.590848 7.333200 0 0 0 -155 2 9.854985 3.662036 15.238574 0 0 0 -156 2 8.027092 4.731250 12.589400 0 0 0 -157 2 8.000461 6.629600 4.781158 0 0 0 -158 2 6.478754 7.465148 1.843124 0 0 0 -159 2 8.047617 6.580774 9.940860 0 0 0 -160 2 6.430949 7.534787 7.128479 0 0 0 -161 2 8.233511 6.470860 15.137957 0 0 0 -162 2 6.534483 7.501036 12.559453 0 0 0 -163 2 6.463815 9.435612 4.558056 0 0 0 -164 2 4.910280 10.407625 1.932492 0 0 0 -165 2 6.576702 9.439887 9.789696 0 0 0 -166 2 4.782454 10.293548 7.327338 0 0 0 -167 2 6.536172 9.415587 15.035121 0 0 0 -168 2 4.774919 10.371962 12.658010 0 0 0 -169 2 0.063653 1.975076 2.119149 0 0 0 -170 2 12.918536 1.877200 7.359028 0 0 0 -171 2 0.005196 1.901388 12.568168 0 0 0 -172 2 11.426706 4.589273 1.983830 0 0 0 -173 2 11.296542 4.650924 7.284239 0 0 0 -174 2 11.429954 4.667799 12.552164 0 0 0 -175 2 11.270301 6.498423 4.561384 0 0 0 -176 2 9.729887 7.441636 1.911100 0 0 0 -177 2 11.468406 6.582012 10.047816 0 0 0 -178 2 9.773535 7.443998 7.141948 0 0 0 -179 2 11.378771 6.549724 15.251251 0 0 0 -180 2 9.810298 7.477524 12.571020 0 0 0 -181 2 9.666363 9.474875 4.631103 0 0 0 -182 2 8.060867 10.251698 2.129607 0 0 0 -183 2 9.792111 9.421887 9.958448 0 0 0 -184 2 8.191552 10.330786 7.268869 0 0 0 -185 2 9.841216 9.351011 15.108960 0 0 0 -186 2 8.062296 10.403687 12.613960 0 0 0 -187 2 0.092233 7.472798 2.028356 0 0 0 -188 2 12.868782 7.594638 7.258252 0 0 0 -189 2 0.005196 7.559987 12.497814 0 0 0 -190 2 11.399426 10.273635 1.926312 0 0 0 -191 2 11.404623 10.297711 7.142106 0 0 0 -192 2 11.298100 10.418762 12.612693 0 0 0 diff --git a/examples/GaN-SNAP-LAMMPS/DATA/21/DATA b/examples/GaN-SNAP-LAMMPS/DATA/21/DATA deleted file mode 100755 index cdf4e195..00000000 --- a/examples/GaN-SNAP-LAMMPS/DATA/21/DATA +++ /dev/null @@ -1,215 +0,0 @@ -LAMMPS DATA file - -192 atoms -0 bonds -0 angles -0 dihedrals -0 impropers - -2 atom types -0 bond types -0 angle types - -0.0 12.990503 xlo xhi -0.0 11.250148 ylo yhi -0.0 15.845291 zlo zhi - -Masses - -1 69.723 -2 14.0067 - -Atoms - -1 1 1.622904 0.988022 2.769123 0 0 0 -2 1 1.673567 1.004177 8.024055 0 0 0 -3 1 1.506119 1.017722 13.168229 0 0 0 -4 1 0.016411 3.640435 2.725865 0 0 0 -5 1 12.986748 3.712211 7.924864 0 0 0 -6 1 0.076990 3.787925 13.298635 0 0 0 -7 1 4.985625 0.960965 2.616533 0 0 0 -8 1 3.309980 1.819711 5.244633 0 0 0 -9 1 4.944965 0.985794 7.970023 0 0 0 -10 1 3.213071 1.802836 10.539812 0 0 0 -11 1 4.952889 0.858926 13.047012 0 0 0 -12 1 3.327777 1.841874 15.751486 0 0 0 -13 1 3.328427 3.661023 2.557271 0 0 0 -14 1 1.703055 4.643611 5.340338 0 0 0 -15 1 3.294132 3.700849 7.820443 0 0 0 -16 1 1.563927 4.610873 10.482294 0 0 0 -17 1 3.147729 3.760812 13.249674 0 0 0 -18 1 1.608614 4.685124 0.137854 0 0 0 -19 1 1.545350 6.638487 2.571691 0 0 0 -20 1 1.660966 6.558274 7.778136 0 0 0 -21 1 1.619526 6.593712 13.162524 0 0 0 -22 1 12.928668 9.399386 2.609086 0 0 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1.785286 5.301834 0 0 0 -74 1 12.887748 1.896550 10.551062 0 0 0 -75 1 0.081840 1.891600 15.748159 0 0 0 -76 1 11.348763 4.672412 5.393895 0 0 0 -77 1 11.430863 4.664311 10.452346 0 0 0 -78 1 11.377602 4.579598 15.719479 0 0 0 -79 1 11.401505 6.559174 2.792257 0 0 0 -80 1 9.784187 7.606338 5.396906 0 0 0 -81 1 11.419821 6.468835 7.898719 0 0 0 -82 1 9.613102 7.540299 10.645183 0 0 0 -83 1 11.473732 6.529811 13.212754 0 0 0 -84 1 9.782628 7.427573 0.147361 0 0 0 -85 1 9.613622 9.306685 2.625406 0 0 0 -86 1 8.133874 10.257323 5.433192 0 0 0 -87 1 9.728978 9.275072 7.979371 0 0 0 -88 1 8.050864 10.267560 10.480709 0 0 0 -89 1 9.635576 9.390274 13.124813 0 0 0 -90 1 7.997473 10.344174 0.026937 0 0 0 -91 1 12.910222 7.542437 5.216270 0 0 0 -92 1 12.971407 7.473473 10.597489 0 0 0 -93 1 0.074046 7.521399 0.042782 0 0 0 -94 1 11.389943 10.235947 5.131180 0 0 0 -95 1 11.272379 10.263735 10.639479 0 0 0 -96 1 11.344606 10.232910 0.068135 0 0 0 -97 2 1.667851 0.967997 4.640610 0 0 0 -98 2 1.559380 0.841635 9.873042 0 0 0 -99 2 1.741897 0.830452 15.219560 0 0 0 -100 2 0.099866 3.768462 4.695593 0 0 0 -101 2 0.056271 3.722899 9.799203 0 0 0 -102 2 12.901521 3.741574 15.043202 0 0 0 -103 2 4.930286 0.994187 4.611296 0 0 0 -104 2 3.192286 1.794511 1.984147 0 0 0 -105 2 4.836364 1.000712 9.794449 0 0 0 -106 2 3.311669 1.902175 7.397057 0 0 0 -107 2 4.928077 0.851456 15.307977 0 0 0 -108 2 3.134868 1.762786 12.488466 0 0 0 -109 2 3.220735 3.701861 4.674202 0 0 0 -110 2 1.561458 4.796951 2.040873 0 0 0 -111 2 3.291144 3.815150 9.772266 0 0 0 -112 2 1.557042 4.689737 7.383747 0 0 0 -113 2 3.376881 3.774762 15.039399 0 0 0 -114 2 1.729166 4.752175 12.552322 0 0 0 -115 2 1.689935 6.587524 4.602423 0 0 0 -116 2 1.557951 6.496511 9.852919 0 0 0 -117 2 1.586660 6.541849 15.195158 0 0 0 -118 2 0.106210 9.288910 4.525573 0 0 0 -119 2 12.982481 9.332898 10.045756 0 0 0 -120 2 0.098147 9.485225 15.093748 0 0 0 -121 2 8.202074 0.963204 4.543162 0 0 0 -122 2 6.571116 1.860100 1.868794 0 0 0 -123 2 8.137381 0.853774 9.819327 0 0 0 -124 2 6.486938 1.872700 7.170786 0 0 0 -125 2 8.020337 0.977019 15.345847 0 0 0 -126 2 6.536042 1.813524 12.653574 0 0 0 -127 2 6.462126 3.794450 4.672935 0 0 0 -128 2 4.748159 4.642036 2.114712 0 0 0 -129 2 6.536302 3.705461 9.934363 0 0 0 -130 2 4.837793 4.613123 7.122617 0 0 0 -131 2 6.620610 3.769137 15.227958 0 0 0 -132 2 4.814280 4.778050 12.530614 0 0 0 -133 2 4.804538 6.459835 4.507193 0 0 0 -134 2 3.246976 7.545249 1.930115 0 0 0 -135 2 4.744911 6.596524 9.810453 0 0 0 -136 2 3.252822 7.595988 7.257618 0 0 0 -137 2 4.967049 6.544999 15.313364 0 0 0 -138 2 3.214240 7.417448 12.527287 0 0 0 -139 2 3.219047 9.483650 4.778940 0 0 0 -140 2 1.573799 10.409762 2.081120 0 0 0 -141 2 3.361293 9.401974 9.866862 0 0 0 -142 2 1.600300 10.362062 7.310066 0 0 0 -143 2 3.266722 9.445849 15.078537 0 0 0 -144 2 1.563147 10.284436 12.423817 0 0 0 -145 2 11.428915 0.898369 4.657248 0 0 0 -146 2 9.844723 1.827249 2.062740 0 0 0 -147 2 11.360585 0.918327 10.012639 0 0 0 -148 2 9.749243 1.869662 7.382321 0 0 0 -149 2 11.270691 0.853042 15.073942 0 0 0 -150 2 9.782498 1.982614 12.577833 0 0 0 -151 2 9.721313 3.639535 4.752478 0 0 0 -152 2 8.242604 4.798188 2.119941 0 0 0 -153 2 9.660258 3.763962 9.908694 0 0 0 -154 2 8.213765 4.658011 7.395789 0 0 0 -155 2 9.772885 3.811325 15.263927 0 0 0 -156 2 8.242085 4.753075 12.537111 0 0 0 -157 2 8.187914 6.668863 4.549658 0 0 0 -158 2 6.603203 7.462898 1.885273 0 0 0 -159 2 8.102047 6.621162 10.040685 0 0 0 -160 2 6.495771 7.471898 7.353958 0 0 0 -161 2 8.038523 6.557374 15.216233 0 0 0 -162 2 6.588134 7.538724 12.452497 0 0 0 -163 2 6.607879 9.397361 4.675787 0 0 0 -164 2 4.839092 10.273973 1.837895 0 0 0 -165 2 6.479273 9.447424 9.957022 0 0 0 -166 2 4.999915 10.335061 7.273781 0 0 0 -167 2 6.384053 9.411762 15.162042 0 0 0 -168 2 4.809084 10.371962 12.670370 0 0 0 -169 2 0.012991 1.864150 2.124061 0 0 0 -170 2 12.882292 1.845362 7.119923 0 0 0 -171 2 12.872549 1.906675 12.552956 0 0 0 -172 2 11.382799 4.638436 2.042775 0 0 0 -173 2 11.399686 4.734625 7.304520 0 0 0 -174 2 11.353570 4.738787 12.703328 0 0 0 -175 2 11.375654 6.625550 4.782743 0 0 0 -176 2 9.778341 7.449061 2.018848 0 0 0 -177 2 11.402024 6.655025 9.945455 0 0 0 -178 2 9.858103 7.445123 7.172212 0 0 0 -179 2 11.352141 6.647488 15.142552 0 0 0 -180 2 9.640902 7.559650 12.675282 0 0 0 -181 2 9.661947 9.414124 4.632054 0 0 0 -182 2 8.213116 10.267223 1.923777 0 0 0 -183 2 9.670390 9.294085 10.054312 0 0 0 -184 2 8.165960 10.381187 7.279326 0 0 0 -185 2 9.826406 9.321648 15.252518 0 0 0 -186 2 8.210258 10.219747 12.697307 0 0 0 -187 2 0.051962 7.404623 2.126438 0 0 0 -188 2 0.119513 7.475048 7.292320 0 0 0 -189 2 0.081840 7.404848 12.665458 0 0 0 -190 2 11.283941 10.387937 2.094272 0 0 0 -191 2 11.368899 10.317173 7.225769 0 0 0 -192 2 11.476720 10.357674 12.705229 0 0 0 diff --git a/examples/GaN-SNAP-LAMMPS/DATA/22/DATA b/examples/GaN-SNAP-LAMMPS/DATA/22/DATA deleted file mode 100755 index 92d0cbf7..00000000 --- a/examples/GaN-SNAP-LAMMPS/DATA/22/DATA +++ /dev/null @@ -1,215 +0,0 @@ -LAMMPS DATA file - -192 atoms -0 bonds -0 angles -0 dihedrals -0 impropers - -2 atom types -0 bond types -0 angle types - -0.0 12.990503 xlo xhi -0.0 11.250148 ylo yhi -0.0 15.845291 zlo zhi - -Masses - -1 69.723 -2 14.0067 - -Atoms - -1 1 1.503001 0.916246 2.556004 0 0 0 -2 1 1.618877 1.023201 7.847697 0 0 0 -3 1 1.649534 0.830913 13.089636 0 0 0 -4 1 0.086754 3.681386 2.739968 0 0 0 -5 1 12.948435 3.788600 7.775284 0 0 0 -6 1 0.060877 3.749899 13.339358 0 0 0 -7 1 4.816879 0.909732 2.513063 0 0 0 -8 1 3.368437 1.859875 5.144649 0 0 0 -9 1 4.927688 0.939039 7.862750 0 0 0 -10 1 3.313488 1.950663 10.479917 0 0 0 -11 1 4.880402 0.922917 13.090428 0 0 0 -12 1 3.273737 1.973501 15.715518 0 0 0 -13 1 3.351550 3.761375 2.612413 0 0 0 -14 1 1.533529 4.630786 5.259527 0 0 0 -15 1 3.256200 3.717386 8.003773 0 0 0 -16 1 1.722930 4.740250 10.528403 0 0 0 -17 1 3.274646 3.781850 13.080921 0 0 0 -18 1 1.622774 4.644961 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0 0 0 -119 2 0.010450 9.477237 9.816474 0 0 0 -120 2 12.890825 9.408049 15.066495 0 0 0 -121 2 8.244683 0.880887 4.660734 0 0 0 -122 2 6.577482 1.949313 1.982721 0 0 0 -123 2 8.186745 1.030907 10.035932 0 0 0 -124 2 6.420946 1.885637 7.358078 0 0 0 -125 2 8.039693 0.993062 15.182799 0 0 0 -126 2 6.516946 1.821174 12.418113 0 0 0 -127 2 6.442770 3.843951 4.617635 0 0 0 -128 2 4.811552 4.746775 2.072406 0 0 0 -129 2 6.370932 3.835513 10.003290 0 0 0 -130 2 4.825712 4.725625 7.203428 0 0 0 -131 2 6.606970 3.700961 15.085667 0 0 0 -132 2 4.935092 4.682424 12.598274 0 0 0 -133 2 4.992640 6.520473 4.492774 0 0 0 -134 2 3.323360 7.469761 2.013144 0 0 0 -135 2 4.789209 6.467373 9.799045 0 0 0 -136 2 3.332584 7.455361 7.231157 0 0 0 -137 2 4.910670 6.633987 15.274860 0 0 0 -138 2 3.214890 7.430273 12.596055 0 0 0 -139 2 3.118630 9.326260 4.670875 0 0 0 -140 2 1.647715 10.273298 2.141174 0 0 0 -141 2 3.149677 9.428187 9.799995 0 0 0 -142 2 1.606795 10.387374 7.223551 0 0 0 -143 2 3.137466 9.387911 15.118942 0 0 0 -144 2 1.528203 10.357561 12.545192 0 0 0 -145 2 11.284201 0.847777 4.532387 0 0 0 -146 2 9.647917 1.835349 2.128973 0 0 0 -147 2 11.375004 0.880740 9.888887 0 0 0 -148 2 9.786785 1.885750 7.302461 0 0 0 -149 2 11.461001 0.910666 15.269473 0 0 0 -150 2 9.653633 1.775611 12.498924 0 0 0 -151 2 9.825237 3.722449 4.776721 0 0 0 -152 2 8.146474 4.651149 2.121843 0 0 0 -153 2 9.846412 3.828988 9.831686 0 0 0 -154 2 8.063335 4.750600 7.331774 0 0 0 -155 2 9.740929 3.855313 15.182957 0 0 0 -156 2 8.247671 4.685462 12.550738 0 0 0 -157 2 8.188953 6.537349 4.612247 0 0 0 -158 2 6.399901 7.558300 2.006806 0 0 0 -159 2 8.157646 6.629600 9.820119 0 0 0 -160 2 6.588264 7.591150 7.202001 0 0 0 -161 2 8.177782 6.526436 15.118467 0 0 0 -162 2 6.409644 7.537037 12.561037 0 0 0 -163 2 6.580729 9.322773 4.524464 0 0 0 -164 2 4.853512 10.307161 2.076525 0 0 0 -165 2 6.399252 9.274172 9.949258 0 0 0 -166 2 4.749068 10.230772 7.329556 0 0 0 -167 2 6.499279 9.384649 15.288329 0 0 0 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10.288598 12.471194 0 0 0 diff --git a/examples/GaN-SNAP-LAMMPS/DATA/23/DATA b/examples/GaN-SNAP-LAMMPS/DATA/23/DATA deleted file mode 100755 index 74253d15..00000000 --- a/examples/GaN-SNAP-LAMMPS/DATA/23/DATA +++ /dev/null @@ -1,215 +0,0 @@ -LAMMPS DATA file - -192 atoms -0 bonds -0 angles -0 dihedrals -0 impropers - -2 atom types -0 bond types -0 angle types - -0.0 12.990503 xlo xhi -0.0 11.250148 ylo yhi -0.0 15.845291 zlo zhi - -Masses - -1 69.723 -2 14.0067 - -Atoms - -1 1 1.518850 0.878637 2.484383 0 0 0 -2 1 1.533919 1.023111 7.796358 0 0 0 -3 1 1.717345 1.019747 13.324305 0 0 0 -4 1 12.863637 3.816725 2.534613 0 0 0 -5 1 12.868993 3.674298 7.932469 0 0 0 -6 1 0.069734 3.812900 13.151116 0 0 0 -7 1 4.925609 0.899404 2.672150 0 0 0 -8 1 3.236974 1.811836 5.254774 0 0 0 -9 1 4.907682 1.012018 7.983333 0 0 0 -10 1 3.164487 1.892950 10.646134 0 0 0 -11 1 4.938730 0.881404 13.149373 0 0 0 -12 1 3.307512 1.827137 15.821998 0 0 0 -13 1 3.335961 3.858913 2.671674 0 0 0 -14 1 1.539764 4.589498 5.335109 0 0 0 -15 1 3.177477 3.787025 8.026273 0 0 0 -16 1 1.684868 4.777488 10.477065 0 0 0 -17 1 3.347263 3.647861 13.196750 0 0 0 -18 1 1.644728 4.788626 0.036444 0 0 0 -19 1 1.616668 6.477385 2.565511 0 0 0 -20 1 1.693702 6.619025 7.764509 0 0 0 -21 1 1.714357 6.653113 13.254744 0 0 0 -22 1 12.871148 9.374074 2.694492 0 0 0 -23 1 12.870179 9.318948 7.858947 0 0 0 -24 1 12.903938 9.366086 13.331277 0 0 0 -25 1 8.001890 0.888447 2.735214 0 0 0 -26 1 6.597357 1.940313 5.125001 0 0 0 -27 1 8.009684 1.032212 7.921695 0 0 0 -28 1 6.376389 1.940426 10.630289 0 0 0 -29 1 8.013971 1.002647 13.264568 0 0 0 -30 1 6.466673 1.966413 15.721697 0 0 0 -31 1 6.484989 3.756199 2.671516 0 0 0 -32 1 4.755044 4.579935 5.153205 0 0 0 -33 1 6.509671 3.773637 8.007101 0 0 0 -34 1 4.989522 4.618748 10.547418 0 0 0 -35 1 6.602034 3.731112 13.134954 0 0 0 -36 1 4.808435 4.762188 0.055459 0 0 0 -37 1 4.743093 6.593487 2.735214 0 0 0 -38 1 3.289585 7.463011 5.421783 0 0 0 -39 1 4.880662 6.577624 7.795408 0 0 0 -40 1 3.249964 7.571012 10.600024 0 0 0 -41 1 4.775309 6.570087 13.341893 0 0 0 -42 1 3.137986 7.485849 0.083980 0 0 0 -43 1 3.160200 9.418512 2.614631 0 0 0 -44 1 1.706952 10.324936 5.367592 0 0 0 -45 1 3.187350 9.381724 7.964477 0 0 0 -46 1 1.540933 10.244722 10.448860 0 0 0 -47 1 3.373893 9.318948 13.158563 0 0 0 -48 1 1.618487 10.268685 0.061797 0 0 0 -49 1 11.359156 0.966016 2.543011 0 0 0 -50 1 9.714688 1.801036 5.301834 0 0 0 -51 1 11.308753 0.845719 7.841359 0 0 0 -52 1 9.830433 1.931988 10.515093 0 0 0 -53 1 11.392541 0.902127 13.178845 0 0 0 -54 1 9.680003 1.859762 15.692700 0 0 0 -55 1 9.633367 3.713899 2.543011 0 0 0 -56 1 8.182198 4.687149 5.139578 0 0 0 -57 1 9.714298 3.695786 7.998069 0 0 0 -58 1 8.217533 4.770513 10.466924 0 0 0 -59 1 9.728718 3.642573 13.286593 0 0 0 -60 1 8.093213 4.715275 0.144192 0 0 0 -61 1 8.087628 6.606875 2.620336 0 0 0 -62 1 6.480572 7.442423 5.170952 0 0 0 -63 1 8.156607 6.452973 7.762132 0 0 0 -64 1 6.472778 7.460423 10.508755 0 0 0 -65 1 8.052553 6.542299 13.055727 0 0 0 -66 1 6.611647 7.395960 0.004754 0 0 0 -67 1 6.501357 9.282160 2.550458 0 0 0 -68 1 4.841171 10.295686 5.362997 0 0 0 -69 1 6.586965 9.475437 7.796200 0 0 0 -70 1 4.790248 10.224697 10.543615 0 0 0 -71 1 6.417828 9.326373 13.148264 0 0 0 -72 1 4.900148 10.347886 0.145777 0 0 0 -73 1 12.970628 1.950438 5.177924 0 0 0 -74 1 12.962184 1.889012 10.702860 0 0 0 -75 1 12.872030 1.777073 0.123593 0 0 0 -76 1 11.417093 4.767250 5.362522 0 0 0 -77 1 11.485683 4.661161 10.532998 0 0 0 -78 1 11.304596 4.687037 15.684461 0 0 0 -79 1 11.465158 6.524298 2.538416 0 0 0 -80 1 9.686239 7.601388 5.321165 0 0 0 -81 1 11.309272 6.519236 7.899036 0 0 0 -82 1 9.844593 7.460761 10.518262 0 0 0 -83 1 11.438268 6.597987 13.042417 0 0 0 -84 1 9.635706 7.443773 15.764321 0 0 0 -85 1 9.642201 9.373961 2.626357 0 0 0 -86 1 8.128418 10.410325 5.137519 0 0 0 -87 1 9.634926 9.443037 7.920110 0 0 0 -88 1 8.090485 10.226835 10.607313 0 0 0 -89 1 9.680783 9.379699 13.051290 0 0 0 -90 1 8.239227 10.409875 0.001585 0 0 0 -91 1 0.032476 7.577875 5.395321 0 0 0 -92 1 12.874628 7.403610 10.461536 0 0 0 -93 1 0.010392 7.510486 15.764321 0 0 0 -94 1 11.291216 10.365774 5.246534 0 0 0 -95 1 11.370717 10.360037 10.713793 0 0 0 -96 1 11.277316 10.306823 15.833248 0 0 0 -97 2 1.604067 0.934662 4.783693 0 0 0 -98 2 1.515082 0.828112 10.063027 0 0 0 -99 2 1.740727 1.001477 15.055561 0 0 0 -100 2 12.969094 3.718399 4.781316 0 0 0 -101 2 0.114070 3.640998 9.900296 0 0 0 -102 2 0.103449 3.669911 15.109911 0 0 0 -103 2 4.775699 0.983207 4.573109 0 0 0 -104 2 3.144611 1.812286 2.097124 0 0 0 -105 2 4.946264 0.866790 9.875419 0 0 0 -106 2 3.185141 1.897225 7.321158 0 0 0 -107 2 4.761409 0.913366 15.105474 0 0 0 -108 2 3.363501 1.843449 12.483395 0 0 0 -109 2 3.142663 3.782637 4.625874 0 0 0 -110 2 1.563147 4.739912 2.128498 0 0 0 -111 2 3.368567 3.823925 9.810453 0 0 0 -112 2 1.697729 4.678487 7.149237 0 0 0 -113 2 3.217228 3.652698 15.320653 0 0 0 -114 2 1.747353 4.732150 12.469135 0 0 0 -115 2 1.669410 6.470298 4.775454 0 0 0 -116 2 1.666682 6.475585 9.776544 0 0 0 -117 2 1.503261 6.578749 15.298153 0 0 0 -118 2 0.069721 9.487588 4.660258 0 0 0 -119 2 12.956012 9.266410 9.824872 0 0 0 -120 2 0.046579 9.359111 15.084717 0 0 0 -121 2 8.130106 0.957444 4.725699 0 0 0 -122 2 6.487977 1.969226 2.101402 0 0 0 -123 2 8.124780 0.944022 9.965737 0 0 0 -124 2 6.542407 1.805086 7.259045 0 0 0 -125 2 8.149462 1.033349 15.084717 0 0 0 -126 2 6.589822 1.824212 12.573080 0 0 0 -127 2 6.397823 3.754062 4.494200 0 0 0 -128 2 4.837793 4.726750 1.835994 0 0 0 -129 2 6.534743 3.838438 9.893007 0 0 0 -130 2 4.966789 4.743963 7.251439 0 0 0 -131 2 6.522921 3.795125 15.106108 0 0 0 -132 2 4.859487 4.585785 12.584964 0 0 0 -133 2 4.745950 6.590562 4.530169 0 0 0 -134 2 3.249185 7.495524 2.052916 0 0 0 -135 2 4.920933 6.613400 9.890155 0 0 0 -136 2 3.203068 7.510711 7.381529 0 0 0 -137 2 4.979130 6.590899 15.195951 0 0 0 -138 2 3.257369 7.423860 12.435067 0 0 0 -139 2 3.272438 9.399161 4.672776 0 0 0 -140 2 1.510406 10.214460 2.019007 0 0 0 -141 2 3.223853 9.361361 9.775435 0 0 0 -142 2 1.599780 10.225485 7.425420 0 0 0 -143 2 3.301147 9.367323 15.070297 0 0 0 -144 2 1.689025 10.417300 12.665933 0 0 0 -145 2 11.465418 0.864079 4.559799 0 0 0 -146 2 9.834201 1.866625 2.143709 0 0 0 -147 2 11.309792 0.905603 9.984910 0 0 0 -148 2 9.754959 1.891150 7.132916 0 0 0 -149 2 11.258350 0.869456 15.316375 0 0 0 -150 2 9.787954 1.899138 12.407655 0 0 0 -151 2 9.744956 3.705236 4.544746 0 0 0 -152 2 8.190772 4.775913 1.844550 0 0 0 -153 2 9.757557 3.671598 10.063819 0 0 0 -154 2 8.125820 4.695812 7.335260 0 0 0 -155 2 9.825627 3.834276 15.229067 0 0 0 -156 2 7.991887 4.625048 12.407813 0 0 0 -157 2 8.122832 6.650975 4.652336 0 0 0 -158 2 6.528507 7.420035 2.064958 0 0 0 -159 2 8.062036 6.645575 10.004558 0 0 0 -160 2 6.492264 7.606675 7.276474 0 0 0 -161 2 8.045668 6.494261 15.037656 0 0 0 -162 2 6.454851 7.575512 12.478325 0 0 0 -163 2 6.536172 9.300835 4.562018 0 0 0 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7.576075 7.413853 0 0 0 -189 2 0.085737 7.478086 12.550738 0 0 0 -190 2 11.406311 10.356774 2.074782 0 0 0 -191 2 11.465028 10.251923 7.363148 0 0 0 -192 2 11.432422 10.421125 12.426352 0 0 0 diff --git a/examples/GaN-SNAP-LAMMPS/DATA/24/DATA b/examples/GaN-SNAP-LAMMPS/DATA/24/DATA deleted file mode 100755 index 1726d466..00000000 --- a/examples/GaN-SNAP-LAMMPS/DATA/24/DATA +++ /dev/null @@ -1,215 +0,0 @@ -LAMMPS DATA file - -192 atoms -0 bonds -0 angles -0 dihedrals -0 impropers - -2 atom types -0 bond types -0 angle types - -0.0 12.990503 xlo xhi -0.0 11.250148 ylo yhi -0.0 15.845291 zlo zhi - -Masses - -1 69.723 -2 14.0067 - -Atoms - -1 1 1.651742 1.023066 2.732362 0 0 0 -2 1 1.649534 0.866644 8.054003 0 0 0 -3 1 1.665383 0.981182 13.295308 0 0 0 -4 1 12.959243 3.693761 2.581039 0 0 0 -5 1 0.124249 3.692749 7.883191 0 0 0 -6 1 12.867479 3.812000 13.181380 0 0 0 -7 1 4.771931 1.049358 2.692115 0 0 0 -8 1 3.232557 1.796874 5.216428 0 0 0 -9 1 4.880272 0.922107 8.041168 0 0 0 -10 1 3.157342 1.876862 10.629496 0 0 0 -11 1 4.930546 1.006540 13.259814 0 0 0 -12 1 3.258538 1.792149 15.822632 0 0 0 -13 1 3.245417 3.794787 2.644104 0 0 0 -14 1 1.552625 4.682199 5.131656 0 0 0 -15 1 3.329076 3.682511 7.924547 0 0 0 -16 1 1.683180 4.588148 10.532998 0 0 0 -17 1 3.138376 3.753049 13.219884 0 0 0 -18 1 1.570162 4.770513 0.069719 0 0 0 -19 1 1.666292 6.666500 2.758348 0 0 0 -20 1 1.735142 6.610475 7.785108 0 0 0 -21 1 1.560030 6.528349 13.324622 0 0 0 -22 1 0.056878 9.321310 2.517658 0 0 0 -23 1 0.067336 9.443712 7.842310 0 0 0 -24 1 0.077942 9.359223 13.321928 0 0 0 -25 1 8.191422 0.884599 2.543169 0 0 0 -26 1 6.463035 1.942338 5.194720 0 0 0 -27 1 8.191552 0.887738 7.922804 0 0 0 -28 1 6.433936 1.901725 10.531414 0 0 0 -29 1 8.071909 0.892621 13.187243 0 0 0 -30 1 6.579040 1.863587 0.139439 0 0 0 -31 1 6.481871 3.653148 2.537465 0 0 0 -32 1 4.886248 4.788176 5.312767 0 0 0 -33 1 6.576702 3.764525 7.929142 0 0 0 -34 1 4.743872 4.640011 10.607154 0 0 0 -35 1 6.591901 3.797938 13.273125 0 0 0 -36 1 4.937430 4.589160 0.082396 0 0 0 -37 1 4.745821 6.528686 2.688629 0 0 0 -38 1 3.269060 7.566175 5.143223 0 0 0 -39 1 4.761279 6.562436 7.814105 0 0 0 -40 1 3.140714 7.435335 10.574672 0 0 0 -41 1 4.764527 6.467260 13.338407 0 0 0 -42 1 3.249704 7.608813 0.063381 0 0 0 -43 1 3.302965 9.328735 2.776412 0 0 0 -44 1 1.599261 10.222560 5.130547 0 0 0 -45 1 3.220346 9.397136 7.762132 0 0 0 -46 1 1.571981 10.278360 10.617612 0 0 0 -47 1 3.205277 9.291160 13.209426 0 0 0 -48 1 1.728776 10.263735 0.003169 0 0 0 -49 1 11.443334 0.893532 2.481531 0 0 0 -50 1 9.806531 1.826574 5.411959 0 0 0 -51 1 11.238344 0.931175 7.802380 0 0 0 -52 1 9.687148 1.883612 10.506537 0 0 0 -53 1 11.448141 0.942751 13.099460 0 0 0 -54 1 9.841735 1.775048 0.006338 0 0 0 -55 1 9.777042 3.835626 2.715883 0 0 0 -56 1 8.086328 4.765563 5.274263 0 0 0 -57 1 9.647267 3.741237 7.795249 0 0 0 -58 1 8.063855 4.666224 10.421765 0 0 0 -59 1 9.714428 3.809638 13.336664 0 0 0 -60 1 8.232991 4.644849 0.041198 0 0 0 -61 1 8.227925 6.595399 2.535088 0 0 0 -62 1 6.586185 7.607688 5.220865 0 0 0 -63 1 8.055281 6.578074 7.990938 0 0 0 -64 1 6.528897 7.393822 10.493385 0 0 0 -65 1 8.020597 6.482448 13.272808 0 0 0 -66 1 6.485119 7.507674 15.773036 0 0 0 -67 1 6.583717 9.298248 2.484225 0 0 0 -68 1 4.897290 10.346086 5.272837 0 0 0 -69 1 6.623468 9.378124 7.880021 0 0 0 -70 1 4.883390 10.216822 10.663564 0 0 0 -71 1 6.431338 9.300948 13.189937 0 0 0 -72 1 4.801680 10.268685 15.839111 0 0 0 -73 1 0.089634 1.947851 5.135934 0 0 0 -74 1 12.897881 1.820274 10.681469 0 0 0 -75 1 12.925161 1.846374 15.779216 0 0 0 -76 1 11.347334 4.603673 5.364106 0 0 0 -77 1 11.290826 4.753075 10.669902 0 0 0 -78 1 11.238084 4.760275 15.771135 0 0 0 -79 1 11.265364 6.544324 2.527799 0 0 0 -80 1 9.627392 7.559875 5.390568 0 0 0 -81 1 11.442555 6.516986 8.032453 0 0 0 -82 1 9.803153 7.401248 10.611116 0 0 0 -83 1 11.255622 6.471873 13.204039 0 0 0 -84 1 9.803153 7.451536 0.148946 0 0 0 -85 1 9.763532 9.473525 2.552518 0 0 0 -86 1 8.208699 10.301761 5.137677 0 0 0 -87 1 9.632718 9.439774 7.792714 0 0 0 -88 1 8.246242 10.312448 10.634408 0 0 0 -89 1 9.704555 9.279122 13.301488 0 0 0 -90 1 8.052034 10.212885 15.699831 0 0 0 -91 1 0.054560 7.483711 5.339071 0 0 0 -92 1 0.088335 7.472461 10.568492 0 0 0 -93 1 0.063653 7.477524 0.079226 0 0 0 -94 1 11.358246 10.398625 5.205019 0 0 0 -95 1 11.422160 10.230097 10.508438 0 0 0 -96 1 11.372276 10.274535 0.055459 0 0 0 -97 2 1.717085 1.030559 4.744397 0 0 0 -98 2 1.694092 0.993152 9.973501 0 0 0 -99 2 1.649404 0.977840 15.127024 0 0 0 -100 2 0.010509 3.846088 4.692107 0 0 0 -101 2 0.070476 3.767225 10.055421 0 0 0 -102 2 12.868577 3.756424 15.116883 0 0 0 -103 2 4.791677 0.864135 4.526841 0 0 0 -104 2 3.194625 1.847499 2.028673 0 0 0 -105 2 4.840262 0.929386 9.989822 0 0 0 -106 2 3.184102 1.915900 7.122300 0 0 0 -107 2 4.859487 1.004334 15.211320 0 0 0 -108 2 3.275555 1.931650 12.604929 0 0 0 -109 2 3.307772 3.718962 4.752320 0 0 0 -110 2 1.746313 4.577573 2.000468 0 0 0 -111 2 3.301926 3.846538 9.761174 0 0 0 -112 2 1.731634 4.705149 7.153990 0 0 0 -113 2 3.198002 3.693311 15.047163 0 0 0 -114 2 1.545480 4.642149 12.704754 0 0 0 -115 2 1.746833 6.562661 4.655346 0 0 0 -116 2 1.684219 6.674038 10.052094 0 0 0 -117 2 1.495077 6.650413 15.109435 0 0 0 -118 2 12.883172 9.464525 4.753429 0 0 0 -119 2 12.928193 9.430437 9.876528 0 0 0 -120 2 0.048864 9.263147 15.298470 0 0 0 -121 2 8.194799 0.886703 4.737108 0 0 0 -122 2 6.443809 1.794511 2.048638 0 0 0 -123 2 8.043070 0.867150 9.868447 0 0 0 -124 2 6.551111 1.858074 7.204220 0 0 0 -125 2 8.165181 0.900406 15.332537 0 0 0 -126 2 6.395095 1.967988 12.683363 0 0 0 -127 2 6.368984 3.645161 4.636966 0 0 0 -128 2 4.933144 4.731137 2.000785 0 0 0 -129 2 6.449785 3.767787 10.034664 0 0 0 -130 2 4.972765 4.643386 7.193287 0 0 0 -131 2 6.538770 3.706811 15.233187 0 0 0 -132 2 4.887157 4.597486 12.512075 0 0 0 -133 2 4.888976 6.461410 4.620645 0 0 0 -134 2 3.123826 7.486524 1.904445 0 0 0 -135 2 4.952370 6.548936 10.031653 0 0 0 -136 2 3.144871 7.598350 7.227829 0 0 0 -137 2 4.783493 6.453423 15.148256 0 0 0 -138 2 3.229439 7.483599 12.396722 0 0 0 -139 2 3.197612 9.323448 4.743446 0 0 0 -140 2 1.680451 10.251923 1.927104 0 0 0 -141 2 3.372075 9.474425 9.995368 0 0 0 -142 2 1.709810 10.212660 7.154466 0 0 0 -143 2 3.248795 9.414349 15.087886 0 0 0 -144 2 1.595234 10.406837 12.696198 0 0 0 -145 2 11.434241 0.841432 4.602582 0 0 0 -146 2 9.659219 1.821061 1.959746 0 0 0 -147 2 11.297191 0.863505 9.888095 0 0 0 -148 2 9.671430 1.975639 7.229097 0 0 0 -149 2 11.330187 1.048019 15.135422 0 0 0 -150 2 9.844853 1.845812 12.391968 0 0 0 -151 2 9.810688 3.733587 4.509887 0 0 0 -152 2 8.210518 4.680962 1.831874 0 0 0 -153 2 9.856934 3.722449 10.025157 0 0 0 -154 2 8.215974 4.579935 7.386441 0 0 0 -155 2 9.839137 3.661698 15.336023 0 0 0 -156 2 8.096851 4.781425 12.561037 0 0 0 -157 2 8.053722 6.626000 4.658991 0 0 0 -158 2 6.418218 7.472236 1.848353 0 0 0 -159 2 8.245722 6.566262 10.050034 0 0 0 -160 2 6.421725 7.542099 7.257302 0 0 0 -161 2 8.055671 6.638375 15.124488 0 0 0 -162 2 6.395485 7.473698 12.458677 0 0 0 -163 2 6.497460 9.379586 4.759767 0 0 0 -164 2 4.987054 10.413925 1.984940 0 0 0 -165 2 6.515127 9.485450 9.930719 0 0 0 -166 2 4.901057 10.233922 7.206755 0 0 0 -167 2 6.553969 9.389599 15.078220 0 0 0 -168 2 4.884819 10.340799 12.607781 0 0 0 -169 2 0.045467 1.828599 1.872755 0 0 0 -170 2 0.120812 1.890925 7.174431 0 0 0 -171 2 12.929188 1.782923 12.606196 0 0 0 -172 2 11.481396 4.609523 2.039130 0 0 0 -173 2 11.439827 4.777825 7.270770 0 0 0 -174 2 11.336422 4.744188 12.534892 0 0 0 -175 2 11.385007 6.522836 4.553620 0 0 0 -176 2 9.802894 7.389210 2.033109 0 0 0 -177 2 11.289916 6.597312 9.838024 0 0 0 -178 2 9.836019 7.475611 7.339222 0 0 0 -179 2 11.310182 6.538249 15.120685 0 0 0 -180 2 9.759895 7.472461 12.432215 0 0 0 -181 2 9.652593 9.421774 4.553461 0 0 0 -182 2 8.206101 10.238535 2.042300 0 0 0 -183 2 9.676106 9.408274 9.856246 0 0 0 -184 2 8.109062 10.359136 7.222442 0 0 0 -185 2 9.692864 9.429312 15.280564 0 0 0 -186 2 8.128288 10.248210 12.512709 0 0 0 -187 2 0.025981 7.569550 1.857860 0 0 0 -188 2 0.070149 7.584175 7.372814 0 0 0 -189 2 0.107821 7.479661 12.671162 0 0 0 -190 2 11.360845 10.207147 2.131192 0 0 0 -191 2 11.380460 10.264073 7.235910 0 0 0 -192 2 11.319925 10.376574 12.393077 0 0 0 diff --git a/examples/GaN-SNAP-LAMMPS/DATA/25/DATA b/examples/GaN-SNAP-LAMMPS/DATA/25/DATA deleted file mode 100755 index 0f460193..00000000 --- a/examples/GaN-SNAP-LAMMPS/DATA/25/DATA +++ /dev/null @@ -1,215 +0,0 @@ -LAMMPS DATA file - -192 atoms -0 bonds -0 angles -0 dihedrals -0 impropers - -2 atom types -0 bond types -0 angle types - -0.0 12.990503 xlo xhi -0.0 11.250148 ylo yhi -0.0 15.845291 zlo zhi - -Masses - -1 69.723 -2 14.0067 - -Atoms - -1 1 1.562498 0.955554 2.614948 0 0 0 -2 1 1.601729 0.837202 7.841042 0 0 0 -3 1 1.557302 0.984557 13.249198 0 0 0 -4 1 12.891565 3.666648 2.501654 0 0 0 -5 1 0.061119 3.762725 8.023104 0 0 0 -6 1 12.888172 3.695224 13.057629 0 0 0 -7 1 4.912099 0.887434 2.701622 0 0 0 -8 1 3.151626 1.880462 5.132448 0 0 0 -9 1 4.767904 0.930522 7.983967 0 0 0 -10 1 3.273997 1.808686 10.595746 0 0 0 -11 1 4.923141 0.895849 13.295466 0 0 0 -12 1 3.163967 1.816786 0.023768 0 0 0 -13 1 3.343236 3.821788 2.663910 0 0 0 -14 1 1.494557 4.787613 5.369018 0 0 0 -15 1 3.221515 3.834051 7.972399 0 0 0 -16 1 1.556912 4.613011 10.672437 0 0 0 -17 1 3.202549 3.710749 13.167278 0 0 0 -18 1 1.692273 4.611998 0.053874 0 0 0 -19 1 1.661096 6.634887 2.596885 0 0 0 -20 1 1.523007 6.643438 7.984759 0 0 0 -21 1 1.643299 6.616887 13.279304 0 0 0 -22 1 0.014314 9.442812 2.689421 0 0 0 -23 1 0.009123 9.416937 8.061450 0 0 0 -24 1 0.033193 9.446974 13.100411 0 0 0 -25 1 8.184407 0.874868 2.608927 0 0 0 -26 1 6.570856 1.852562 5.132131 0 0 0 -27 1 8.041381 0.834648 7.961308 0 0 0 -28 1 6.430819 1.856949 10.454089 0 0 0 -29 1 8.218961 0.901733 13.105481 0 0 0 -30 1 6.572025 1.768073 15.693968 0 0 0 -31 1 6.503046 3.847551 2.667713 0 0 0 -32 1 4.897680 4.719887 5.410058 0 0 0 -33 1 6.422375 3.836638 7.774175 0 0 0 -34 1 4.952499 4.582410 10.531097 0 0 0 -35 1 6.519804 3.681836 13.292773 0 0 0 -36 1 4.796354 4.614361 0.030106 0 0 0 -37 1 4.986015 6.598887 2.545071 0 0 0 -38 1 3.355057 7.473136 5.128962 0 0 0 -39 1 4.800640 6.654125 8.034038 0 0 0 -40 1 3.269060 7.513749 10.399898 0 0 0 -41 1 4.774530 6.498423 13.302438 0 0 0 -42 1 3.218397 7.459186 15.764321 0 0 0 -43 1 3.194754 9.358998 2.537940 0 0 0 -44 1 1.641350 10.348111 5.335109 0 0 0 -45 1 3.209564 9.477912 7.835972 0 0 0 -46 1 1.688376 10.287923 10.667367 0 0 0 -47 1 3.214370 9.421887 13.150007 0 0 0 -48 1 1.721761 10.369037 15.818987 0 0 0 -49 1 11.340839 0.908922 2.617484 0 0 0 -50 1 9.711830 1.778873 5.257309 0 0 0 -51 1 11.394360 0.893588 7.887627 0 0 0 -52 1 9.639213 1.869775 10.492276 0 0 0 -53 1 11.241072 1.024000 13.107066 0 0 0 -54 1 9.790553 1.797211 0.144192 0 0 0 -55 1 9.743527 3.838101 2.707168 0 0 0 -56 1 8.118285 4.711675 5.228471 0 0 0 -57 1 9.749632 3.816838 7.845479 0 0 0 -58 1 8.065154 4.653399 10.677191 0 0 0 -59 1 9.637265 3.684086 13.136380 0 0 0 -60 1 8.080483 4.738562 0.117255 0 0 0 -61 1 8.002670 6.467710 2.481531 0 0 0 -62 1 6.415620 7.393485 5.266341 0 0 0 -63 1 8.052423 6.657050 7.985551 0 0 0 -64 1 6.492264 7.405185 10.567541 0 0 0 -65 1 8.162193 6.586849 13.173458 0 0 0 -66 1 6.394185 7.571350 15.760360 0 0 0 -67 1 6.497590 9.443599 2.638558 0 0 0 -68 1 4.820126 10.394124 5.136092 0 0 0 -69 1 6.555268 9.465312 7.905691 0 0 0 -70 1 4.863515 10.234710 10.704444 0 0 0 -71 1 6.593070 9.372611 13.169496 0 0 0 -72 1 4.774400 10.408412 15.683193 0 0 0 -73 1 12.909053 1.835462 5.133716 0 0 0 -74 1 12.898141 1.926588 10.552488 0 0 0 -75 1 12.948414 1.815774 15.824216 0 0 0 -76 1 11.284980 4.647999 5.201534 0 0 0 -77 1 11.452428 4.731700 10.505269 0 0 0 -78 1 11.387475 4.639786 15.764955 0 0 0 -79 1 11.304336 6.602374 2.641727 0 0 0 -80 1 9.632848 7.400123 5.199791 0 0 0 -81 1 11.351102 6.514061 7.973826 0 0 0 -82 1 9.859662 7.561787 10.601133 0 0 0 -83 1 11.432552 6.618125 13.226222 0 0 0 -84 1 9.813806 7.475949 0.028522 0 0 0 -85 1 9.677275 9.327948 2.483115 0 0 0 -86 1 8.079443 10.232010 5.248277 0 0 0 -87 1 9.652723 9.449112 7.992998 0 0 0 -88 1 8.014881 10.384787 10.471519 0 0 0 -89 1 9.640772 9.411762 13.343002 0 0 0 -90 1 8.200775 10.340349 15.785395 0 0 0 -91 1 12.932695 7.485286 5.228787 0 0 0 -92 1 0.098728 7.388985 10.620306 0 0 0 -93 1 12.948414 7.456261 0.041198 0 0 0 -94 1 11.476070 10.401100 5.433825 0 0 0 -95 1 11.255751 10.229310 10.710624 0 0 0 -96 1 11.260168 10.354524 0.129931 0 0 0 -97 2 1.530801 1.024011 4.474869 0 0 0 -98 2 1.582893 0.878625 10.062393 0 0 0 -99 2 1.713837 1.003772 15.317325 0 0 0 -100 2 0.072775 3.825725 4.570257 0 0 0 -101 2 0.063069 3.787025 9.841985 0 0 0 -102 2 12.948253 3.842038 15.042251 0 0 0 -103 2 4.922491 0.871988 4.729819 0 0 0 -104 2 3.174359 1.784949 2.024077 0 0 0 -105 2 4.768554 1.004796 10.036407 0 0 0 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9.720794 3.841363 15.128767 0 0 0 -156 2 8.158036 4.640011 12.472145 0 0 0 -157 2 8.082171 6.631400 4.639343 0 0 0 -158 2 6.518635 7.439611 1.859920 0 0 0 -159 2 8.156607 6.670663 9.782565 0 0 0 -160 2 6.414191 7.389660 7.375190 0 0 0 -161 2 8.114258 6.555461 15.320019 0 0 0 -162 2 6.473687 7.510036 12.612693 0 0 0 -163 2 6.385872 9.377224 4.622864 0 0 0 -164 2 4.963931 10.338324 1.864832 0 0 0 -165 2 6.523051 9.299598 9.876845 0 0 0 -166 2 4.879883 10.397049 7.318306 0 0 0 -167 2 6.569947 9.290935 15.198486 0 0 0 -168 2 4.975233 10.224697 12.592252 0 0 0 -169 2 12.881643 1.855037 2.053550 0 0 0 -170 2 12.886709 1.944813 7.311651 0 0 0 -171 2 0.103924 1.902400 12.522533 0 0 0 -172 2 11.405012 4.685124 1.857385 0 0 0 -173 2 11.402414 4.788851 7.260471 0 0 0 -174 2 11.393451 4.708187 12.462638 0 0 0 -175 2 11.410468 6.485260 4.713974 0 0 0 -176 2 9.668312 7.425660 2.057669 0 0 0 -177 2 11.303297 6.486723 9.948624 0 0 0 -178 2 9.678055 7.446811 7.376933 0 0 0 -179 2 11.340060 6.473560 15.093590 0 0 0 -180 2 9.707283 7.584400 12.581319 0 0 0 -181 2 9.680003 9.343248 4.749784 0 0 0 -182 2 8.223118 10.300973 1.912843 0 0 0 -183 2 9.756907 9.302860 10.022780 0 0 0 -184 2 8.049435 10.237972 7.117863 0 0 0 -185 2 9.696761 9.387574 15.293399 0 0 0 -186 2 8.198047 10.205572 12.508906 0 0 0 -187 2 12.988425 7.492486 1.840906 0 0 0 -188 2 0.029878 7.517687 7.204220 0 0 0 -189 2 12.973745 7.418348 12.486247 0 0 0 -190 2 11.434631 10.208047 1.913160 0 0 0 -191 2 11.495686 10.300748 7.157952 0 0 0 -192 2 11.466977 10.207147 12.427937 0 0 0 diff --git a/examples/GaN-SNAP-LAMMPS/DATA/26/DATA b/examples/GaN-SNAP-LAMMPS/DATA/26/DATA deleted file mode 100755 index 7ce74b85..00000000 --- a/examples/GaN-SNAP-LAMMPS/DATA/26/DATA +++ /dev/null @@ -1,215 +0,0 @@ -LAMMPS DATA file - -192 atoms -0 bonds -0 angles -0 dihedrals -0 impropers - -2 atom types -0 bond types -0 angle types - -0.0 12.990503 xlo xhi -0.0 11.250148 ylo yhi -0.0 15.845291 zlo zhi - -Masses - -1 69.723 -2 14.0067 - -Atoms - -1 1 1.726438 1.017407 2.663593 0 0 0 -2 1 1.507548 0.936687 7.998069 0 0 0 -3 1 1.727087 0.844087 13.201345 0 0 0 -4 1 12.864999 3.682174 2.595617 0 0 0 -5 1 0.058855 3.781512 8.069531 0 0 0 -6 1 12.961527 3.665298 13.316541 0 0 0 -7 1 4.947303 1.017036 2.739175 0 0 0 -8 1 3.373374 1.835462 5.195988 0 0 0 -9 1 4.790768 0.829833 7.843102 0 0 0 -10 1 3.186830 1.968663 10.552964 0 0 0 -11 1 5.000954 0.831228 13.322086 0 0 0 -12 1 3.240091 1.797436 0.042782 0 0 0 -13 1 3.208914 3.660348 2.589754 0 0 0 -14 1 1.666162 4.608511 5.349212 0 0 0 -15 1 3.246716 3.743262 7.939758 0 0 0 -16 1 1.660576 4.635061 10.556608 0 0 0 -17 1 3.341547 3.793437 13.204198 0 0 0 -18 1 1.691104 4.597148 15.828970 0 0 0 -19 1 1.686947 6.652325 2.508943 0 0 0 -20 1 1.572630 6.478285 7.917099 0 0 0 -21 1 1.691753 6.600012 13.237314 0 0 0 -22 1 12.909852 9.357986 2.779422 0 0 0 -23 1 12.895692 9.388586 7.773858 0 0 0 -24 1 12.911404 9.377111 13.174884 0 0 0 -25 1 8.230523 0.961663 2.597518 0 0 0 -26 1 6.380675 1.884737 5.284563 0 0 0 -27 1 8.222079 0.990384 7.947998 0 0 0 -28 1 6.587614 1.785286 10.575781 0 0 0 -29 1 8.067752 1.035812 13.173458 0 0 0 -30 1 6.371972 1.815549 0.072888 0 0 0 -31 1 6.597877 3.801988 2.568046 0 0 0 -32 1 4.947693 4.626286 5.291059 0 0 0 -33 1 6.450954 3.788825 7.980481 0 0 0 -34 1 4.890665 4.732375 10.685589 0 0 0 -35 1 6.492654 3.697024 13.258705 0 0 0 -36 1 4.959384 4.794138 0.112502 0 0 0 -37 1 4.842470 6.465573 2.663435 0 0 0 -38 1 3.290754 7.448048 5.318472 0 0 0 -39 1 4.943016 6.595399 7.963526 0 0 0 -40 1 3.192936 7.565050 10.491642 0 0 0 -41 1 4.991081 6.544774 13.182173 0 0 0 -42 1 3.210083 7.449736 0.137854 0 0 0 -43 1 3.199691 9.320635 2.492147 0 0 0 -44 1 1.570552 10.225710 5.353965 0 0 0 -45 1 3.186181 9.451925 7.999495 0 0 0 -46 1 1.560289 10.355874 10.429846 0 0 0 -47 1 3.303875 9.407486 13.320819 0 0 0 -48 1 1.589258 10.237185 15.738176 0 0 0 -49 1 11.351102 0.900698 2.579613 0 0 0 -50 1 9.638304 1.878325 5.132131 0 0 0 -51 1 11.370458 0.833546 7.879388 0 0 0 -52 1 9.764701 1.973051 10.404968 0 0 0 -53 1 11.318106 0.973273 13.145412 0 0 0 -54 1 9.701308 1.939301 15.753546 0 0 0 -55 1 9.629340 3.848338 2.495475 0 0 0 -56 1 8.004618 4.692549 5.427170 0 0 0 -57 1 9.625313 3.739437 8.009794 0 0 0 -58 1 8.205971 4.616048 10.530146 0 0 0 -59 1 9.846931 3.726162 13.226698 0 0 0 -60 1 8.073858 4.637086 15.795219 0 0 0 -61 1 8.153100 6.549949 2.686886 0 0 0 -62 1 6.490185 7.474373 5.236552 0 0 0 -63 1 8.237668 6.486610 7.910128 0 0 0 -64 1 6.616323 7.596325 10.403859 0 0 0 -65 1 7.994356 6.548486 13.057153 0 0 0 -66 1 6.587874 7.572700 15.833565 0 0 0 -67 1 6.534873 9.320185 2.691164 0 0 0 -68 1 4.810643 10.393562 5.256200 0 0 0 -69 1 6.598916 9.468800 8.042277 0 0 0 -70 1 4.876115 10.340911 10.434124 0 0 0 -71 1 6.369114 9.373624 13.168863 0 0 0 -72 1 5.000564 10.425175 15.775413 0 0 0 -73 1 0.002598 1.952576 5.300725 0 0 0 -74 1 0.003897 1.768411 10.403701 0 0 0 -75 1 0.045467 1.954713 0.107748 0 0 0 -76 1 11.433462 4.627073 5.283771 0 0 0 -77 1 11.370847 4.715612 10.559619 0 0 0 -78 1 11.318496 4.582073 15.696028 0 0 0 -79 1 11.365911 6.462198 2.752169 0 0 0 -80 1 9.699879 7.482811 5.118663 0 0 0 -81 1 11.343307 6.606200 7.894282 0 0 0 -82 1 9.670780 7.584625 10.669902 0 0 0 -83 1 11.320314 6.535999 13.115305 0 0 0 -84 1 9.856025 7.424760 0.034860 0 0 0 -85 1 9.649346 9.297798 2.750267 0 0 0 -86 1 8.040472 10.416287 5.233224 0 0 0 -87 1 9.614142 9.455187 8.027383 0 0 0 -88 1 8.129587 10.307161 10.426518 0 0 0 -89 1 9.711570 9.380374 13.348073 0 0 0 -90 1 8.103086 10.382874 0.120424 0 0 0 -91 1 0.085737 7.497886 5.361096 0 0 0 -92 1 12.864106 7.466048 10.467557 0 0 0 -93 1 0.033775 7.462111 15.744673 0 0 0 -94 1 11.461001 10.361612 5.222608 0 0 0 -95 1 11.482566 10.332924 10.536643 0 0 0 -96 1 11.290046 10.242697 15.684778 0 0 0 -97 2 1.713967 0.888109 4.595927 0 0 0 -98 2 1.680192 1.016451 9.891423 0 0 0 -99 2 1.679282 1.024889 15.232236 0 0 0 -100 2 0.126455 3.676661 4.667547 0 0 0 -101 2 0.047969 3.675198 9.797619 0 0 0 -102 2 12.897607 3.658436 15.322871 0 0 0 -103 2 4.963282 0.905367 4.497686 0 0 0 -104 2 3.203978 1.777748 1.855642 0 0 0 -105 2 4.929376 0.917416 9.915191 0 0 0 -106 2 3.187869 1.925350 7.384856 0 0 0 -107 2 4.787390 0.914075 15.159665 0 0 0 -108 2 3.253472 1.801824 12.523008 0 0 0 -109 2 3.118890 3.843501 4.605434 0 0 0 -110 2 1.685258 4.597598 1.854374 0 0 0 -111 2 3.321022 3.845301 9.822971 0 0 0 -112 2 1.611472 4.621673 7.143374 0 0 0 -113 2 3.140064 3.860938 15.171866 0 0 0 -114 2 1.559900 4.739237 12.513660 0 0 0 -115 2 1.646676 6.624987 4.694009 0 0 0 -116 2 1.739948 6.621050 9.805700 0 0 0 -117 2 1.623943 6.517098 15.305442 0 0 0 -118 2 0.042419 9.417162 4.505450 0 0 0 -119 2 0.028580 9.344148 9.878746 0 0 0 -120 2 12.910460 9.449450 15.331745 0 0 0 -121 2 8.223638 0.960144 4.602898 0 0 0 -122 2 6.367555 1.773586 1.992545 0 0 0 -123 2 8.114518 0.827887 9.896176 0 0 0 -124 2 6.372102 1.935588 7.246368 0 0 0 -125 2 8.238967 0.952606 15.308769 0 0 0 -126 2 6.514218 1.869775 12.579259 0 0 0 -127 2 6.608919 3.640435 4.557581 0 0 0 -128 2 4.761149 4.725625 2.026771 0 0 0 -129 2 6.389639 3.788037 9.784625 0 0 0 -130 2 4.905993 4.613686 7.207230 0 0 0 -131 2 6.453682 3.828538 15.102146 0 0 0 -132 2 4.953279 4.703462 12.577516 0 0 0 -133 2 4.914437 6.487735 4.613198 0 0 0 -134 2 3.211252 7.414073 1.911893 0 0 0 -135 2 4.935612 6.587187 9.856405 0 0 0 -136 2 3.208784 7.494511 7.224977 0 0 0 -137 2 4.930935 6.560636 15.050491 0 0 0 -138 2 3.373244 7.403948 12.516195 0 0 0 -139 2 3.310240 9.418962 4.472333 0 0 0 -140 2 1.635374 10.289948 1.925678 0 0 0 -141 2 3.243859 9.487250 10.053203 0 0 0 -142 2 1.705913 10.417637 7.217054 0 0 0 -143 2 3.347133 9.346623 15.090579 0 0 0 -144 2 1.559770 10.330786 12.539804 0 0 0 -145 2 11.426706 1.010376 4.719678 0 0 0 -146 2 9.705205 1.795299 1.876558 0 0 0 -147 2 11.330707 0.936147 9.907268 0 0 0 -148 2 9.724301 1.782023 7.352532 0 0 0 -149 2 11.368379 1.034102 15.207359 0 0 0 -150 2 9.671170 1.917138 12.480543 0 0 0 -151 2 9.837318 3.700061 4.671984 0 0 0 -152 2 8.124261 4.736087 1.982721 0 0 0 -153 2 9.671689 3.730212 9.838658 0 0 0 -154 2 8.077105 4.730800 7.339222 0 0 0 -155 2 9.766390 3.652248 15.107534 0 0 0 -156 2 8.025533 4.755888 12.646126 0 0 0 -157 2 8.163622 6.544211 4.582775 0 0 0 -158 2 6.394835 7.407660 1.887491 0 0 0 -159 2 8.227795 6.624537 10.019294 0 0 0 -160 2 6.624247 7.556050 7.125786 0 0 0 -161 2 7.994486 6.632187 15.249349 0 0 0 -162 2 6.605281 7.576862 12.574823 0 0 0 -163 2 6.564881 9.455750 4.593550 0 0 0 -164 2 4.772711 10.300073 1.897315 0 0 0 -165 2 6.396524 9.277772 9.908377 0 0 0 -166 2 4.840132 10.237410 7.363623 0 0 0 -167 2 6.365606 9.377674 15.121636 0 0 0 -168 2 4.820906 10.346649 12.536002 0 0 0 -169 2 0.032476 1.849862 1.915854 0 0 0 -170 2 12.898660 1.878775 7.273939 0 0 0 -171 2 0.012991 1.867975 12.594471 0 0 0 -172 2 11.336293 4.621336 1.839797 0 0 0 -173 2 11.470355 4.586460 7.202001 0 0 0 -174 2 11.253023 4.596361 12.694930 0 0 0 -175 2 11.374485 6.642538 4.664220 0 0 0 -176 2 9.811857 7.408110 1.956735 0 0 0 -177 2 11.490360 6.456573 9.790963 0 0 0 -178 2 9.621156 7.438148 7.152723 0 0 0 -179 2 11.434501 6.460735 15.098660 0 0 0 -180 2 9.866287 7.448048 12.513501 0 0 0 -181 2 9.628691 9.308935 4.735999 0 0 0 -182 2 8.149462 10.365099 1.872280 0 0 0 -183 2 9.869145 9.413787 10.033080 0 0 0 -184 2 8.052683 10.338774 7.244150 0 0 0 -185 2 9.713259 9.464862 15.299737 0 0 0 -186 2 8.130886 10.379949 12.421599 0 0 0 -187 2 12.949843 7.509249 1.968619 0 0 0 -188 2 12.886189 7.525337 7.313711 0 0 0 -189 2 0.020785 7.485286 12.606038 0 0 0 -190 2 11.286409 10.404025 2.140382 0 0 0 -191 2 11.481916 10.272173 7.134184 0 0 0 -192 2 11.240163 10.361049 12.676391 0 0 0 diff --git a/examples/GaN-SNAP-LAMMPS/DATA/27/DATA b/examples/GaN-SNAP-LAMMPS/DATA/27/DATA deleted file mode 100755 index ce27ec2e..00000000 --- a/examples/GaN-SNAP-LAMMPS/DATA/27/DATA +++ /dev/null @@ -1,215 +0,0 @@ -LAMMPS DATA file - -192 atoms -0 bonds -0 angles -0 dihedrals -0 impropers - -2 atom types -0 bond types -0 angle types - -0.0 12.990503 xlo xhi -0.0 11.250148 ylo yhi -0.0 15.845291 zlo zhi - -Masses - -1 69.723 -2 14.0067 - -Atoms - -1 1 1.603028 0.880302 2.629051 0 0 0 -2 1 1.667721 1.016800 8.058281 0 0 0 -3 1 1.527293 0.981755 13.065868 0 0 0 -4 1 12.887507 3.667098 2.640142 0 0 0 -5 1 12.985771 3.737862 8.011696 0 0 0 -6 1 0.007520 3.788037 13.193581 0 0 0 -7 1 4.827921 0.883238 2.785444 0 0 0 -8 1 3.186441 1.940313 5.275373 0 0 0 -9 1 4.824933 0.963676 7.760865 0 0 0 -10 1 3.134089 1.969563 10.686698 0 0 0 -11 1 4.957566 1.030592 13.255695 0 0 0 -12 1 3.319593 1.918600 15.744356 0 0 0 -13 1 3.235285 3.815038 2.477570 0 0 0 -14 1 1.638232 4.672524 5.136409 0 0 0 -15 1 3.232557 3.826513 7.954653 0 0 0 -16 1 1.686557 4.785588 10.502734 0 0 0 -17 1 3.311539 3.833938 13.177736 0 0 0 -18 1 1.629399 4.721912 15.829921 0 0 0 -19 1 1.541583 6.500898 2.607501 0 0 0 -20 1 1.497935 6.619025 7.778453 0 0 0 -21 1 1.606016 6.572224 13.233828 0 0 0 -22 1 12.973938 9.280810 2.566937 0 0 0 -23 1 12.879625 9.426837 7.868454 0 0 0 -24 1 0.039546 9.371036 13.161732 0 0 0 -25 1 8.074117 0.848194 2.594349 0 0 0 -26 1 6.463425 1.870900 5.369969 0 0 0 -27 1 8.168818 1.016215 7.921061 0 0 0 -28 1 6.587484 1.867300 10.483561 0 0 0 -29 1 8.152710 0.951628 13.211962 0 0 0 -30 1 6.467582 1.857174 15.724866 0 0 0 -31 1 6.441211 3.639198 2.772450 0 0 0 -32 1 4.899888 4.775688 5.251129 0 0 0 -33 1 6.469271 3.762162 7.947681 0 0 0 -34 1 4.873127 4.707175 10.441730 0 0 0 -35 1 6.563192 3.784100 13.151750 0 0 0 -36 1 4.822724 4.636749 15.728669 0 0 0 -37 1 4.828440 6.637475 2.550933 0 0 0 -38 1 3.135648 7.498899 5.156533 0 0 0 -39 1 4.846107 6.470635 7.986977 0 0 0 -40 1 3.206706 7.514987 10.606996 0 0 0 -41 1 4.911060 6.607775 13.135904 0 0 0 -42 1 3.139935 7.530174 15.765747 0 0 0 -43 1 3.350121 9.330198 2.703523 0 0 0 -44 1 1.579775 10.282185 5.305479 0 0 0 -45 1 3.352849 9.322098 8.059707 0 0 0 -46 1 1.685778 10.201184 10.669268 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10.397724 7.169043 0 0 0 -192 2 11.433981 10.207259 12.594788 0 0 0 diff --git a/examples/GaN-SNAP-LAMMPS/DATA/29/DATA b/examples/GaN-SNAP-LAMMPS/DATA/29/DATA deleted file mode 100755 index da2d7443..00000000 --- a/examples/GaN-SNAP-LAMMPS/DATA/29/DATA +++ /dev/null @@ -1,215 +0,0 @@ -LAMMPS DATA file - -192 atoms -0 bonds -0 angles -0 dihedrals -0 impropers - -2 atom types -0 bond types -0 angle types - -0.0 12.990503 xlo xhi -0.0 11.250148 ylo yhi -0.0 15.845291 zlo zhi - -Masses - -1 69.723 -2 14.0067 - -Atoms - -1 1 1.662914 0.941176 2.580406 0 0 0 -2 1 1.665902 0.851456 7.805549 0 0 0 -3 1 1.499104 1.041977 13.347914 0 0 0 -4 1 12.892780 3.742699 2.684984 0 0 0 -5 1 12.935992 3.807275 7.935638 0 0 0 -6 1 12.971745 3.697699 13.279304 0 0 0 -7 1 4.974973 0.988911 2.605916 0 0 0 -8 1 3.361553 1.820049 5.286781 0 0 0 -9 1 4.989652 0.885252 7.838031 0 0 0 -10 1 3.358695 1.777973 10.494494 0 0 0 -11 1 4.895211 0.870750 13.241909 0 0 0 -12 1 3.325179 1.875400 0.042782 0 0 0 -13 1 3.324530 3.690049 2.667396 0 0 0 -14 1 1.523137 4.691087 5.383279 0 0 0 -15 1 3.357006 3.749674 7.846746 0 0 0 -16 1 1.663434 4.781425 10.561203 0 0 0 -17 1 3.370776 3.681949 13.075692 0 0 0 -18 1 1.571201 4.664311 15.814709 0 0 0 -19 1 1.574839 6.606200 2.506091 0 0 0 -20 1 1.598352 6.516536 7.855778 0 0 0 -21 1 1.521318 6.583699 13.130042 0 0 0 -22 1 12.900929 9.262810 2.566779 0 0 0 -23 1 0.013202 9.458562 7.772115 0 0 0 -24 1 0.105153 9.292060 13.304657 0 0 0 -25 1 8.197137 1.031537 2.520510 0 0 0 -26 1 6.496421 1.853687 5.172854 0 0 0 -27 1 8.138550 0.961404 7.826623 0 0 0 -28 1 6.500448 1.985089 10.554865 0 0 0 -29 1 8.169727 0.917585 13.051449 0 0 0 -30 1 6.441471 1.942901 15.791100 0 0 0 -31 1 6.387041 3.752599 2.593240 0 0 0 -32 1 4.933663 4.693112 5.372821 0 0 0 -33 1 6.577611 3.680148 7.797943 0 0 0 -34 1 4.954838 4.718537 10.404652 0 0 0 -35 1 6.598136 3.753499 13.213071 0 0 0 -36 1 4.899108 4.746213 0.107748 0 0 0 -37 1 4.841041 6.469173 2.709545 0 0 0 -38 1 3.203978 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7.780513 0 0 0 -64 1 6.413022 7.553462 10.620306 0 0 0 -65 1 8.191032 6.562999 13.175359 0 0 0 -66 1 6.524091 7.580125 0.049120 0 0 0 -67 1 6.501357 9.329860 2.700038 0 0 0 -68 1 4.840651 10.327861 5.399124 0 0 0 -69 1 6.584366 9.464862 8.056221 0 0 0 -70 1 4.953409 10.200397 10.400532 0 0 0 -71 1 6.388080 9.321310 13.047646 0 0 0 -72 1 4.851693 10.276898 0.007923 0 0 0 -73 1 0.110419 1.829724 5.224985 0 0 0 -74 1 0.093532 1.839174 10.443314 0 0 0 -75 1 0.002598 1.955276 15.803142 0 0 0 -76 1 11.417483 4.716287 5.260636 0 0 0 -77 1 11.359805 4.788738 10.426043 0 0 0 -78 1 11.309532 4.675674 0.022183 0 0 0 -79 1 11.464769 6.555686 2.615582 0 0 0 -80 1 9.806791 7.492936 5.390568 0 0 0 -81 1 11.357987 6.562211 7.913138 0 0 0 -82 1 9.672599 7.406873 10.420972 0 0 0 -83 1 11.467627 6.502586 13.313530 0 0 0 -84 1 9.797827 7.583950 0.133100 0 0 0 -85 1 9.649216 9.351236 2.787662 0 0 0 -86 1 8.156737 10.401887 5.270619 0 0 0 -87 1 9.616610 9.402761 7.832010 0 0 0 -88 1 8.126209 10.363299 10.592101 0 0 0 -89 1 9.765871 9.360123 13.117841 0 0 0 -90 1 8.100618 10.202422 0.028522 0 0 0 -91 1 0.119513 7.409123 5.129121 0 0 0 -92 1 0.100027 7.443211 10.402433 0 0 0 -93 1 0.081840 7.419248 0.115671 0 0 0 -94 1 11.261597 10.279485 5.305954 0 0 0 -95 1 11.388774 10.350361 10.604936 0 0 0 -96 1 11.349413 10.231560 0.074473 0 0 0 -97 2 1.556782 0.971360 4.740277 0 0 0 -98 2 1.515862 1.043733 9.760382 0 0 0 -99 2 1.710979 1.013042 15.047956 0 0 0 -100 2 0.011923 3.849801 4.570416 0 0 0 -101 2 0.079625 3.772850 10.000597 0 0 0 -102 2 0.077733 3.648648 15.121795 0 0 0 -103 2 4.911320 0.935180 4.776880 0 0 0 -104 2 3.312189 1.890250 1.922509 0 0 0 -105 2 4.808045 1.024483 9.891898 0 0 0 -106 2 3.329726 1.784611 7.381846 0 0 0 -107 2 4.748678 1.027319 15.317325 0 0 0 -108 2 3.253861 1.789561 12.447585 0 0 0 -109 2 3.301147 3.824600 4.479622 0 0 0 -110 2 1.690844 4.790426 1.936295 0 0 0 -111 2 3.283480 3.714686 9.819010 0 0 0 -112 2 1.698119 4.737775 7.197882 0 0 0 -113 2 3.269060 3.732237 15.061266 0 0 0 -114 2 1.500143 4.685574 12.479434 0 0 0 -115 2 1.582243 6.514736 4.522721 0 0 0 -116 2 1.597702 6.607100 9.814890 0 0 0 -117 2 1.667071 6.549724 15.169489 0 0 0 -118 2 12.906129 9.306123 4.663903 0 0 0 -119 2 12.930491 9.388586 10.049717 0 0 0 -120 2 0.055724 9.415474 15.336181 0 0 0 -121 2 8.190642 0.961753 4.768957 0 0 0 -122 2 6.380805 1.822974 2.140382 0 0 0 -123 2 8.189733 0.931962 9.966054 0 0 0 -124 2 6.473687 1.848062 7.176966 0 0 0 -125 2 8.088667 0.831690 15.181848 0 0 0 -126 2 6.451993 1.982051 12.567217 0 0 0 -127 2 6.585276 3.729312 4.614941 0 0 0 -128 2 4.956267 4.798076 1.993654 0 0 0 -129 2 6.605801 3.803788 9.930085 0 0 0 -130 2 4.993290 4.760613 7.413536 0 0 0 -131 2 6.533314 3.722899 15.183116 0 0 0 -132 2 4.978480 4.578360 12.440930 0 0 0 -133 2 4.864034 6.572224 4.487545 0 0 0 -134 2 3.288676 7.587775 1.862455 0 0 0 -135 2 4.855330 6.513161 10.062552 0 0 0 -136 2 3.275945 7.444673 7.151455 0 0 0 -137 2 4.883130 6.636350 15.297360 0 0 0 -138 2 3.334272 7.433423 12.563731 0 0 0 -139 2 3.345055 9.289810 4.739960 0 0 0 -140 2 1.727737 10.249110 1.852156 0 0 0 -141 2 3.240871 9.450462 9.899028 0 0 0 -142 2 1.601469 10.313236 7.149237 0 0 0 -143 2 3.152146 9.458450 15.223204 0 0 0 -144 2 1.562887 10.394687 12.409556 0 0 0 -145 2 11.355778 0.987504 4.575961 0 0 0 -146 2 9.717156 1.881137 2.111068 0 0 0 -147 2 11.439047 0.840622 9.838658 0 0 0 -148 2 9.711570 1.957076 7.242565 0 0 0 -149 2 11.299140 0.959480 15.184067 0 0 0 -150 2 9.846412 1.972826 12.650405 0 0 0 -151 2 9.797178 3.804800 4.753746 0 0 0 -152 2 8.006047 4.650699 1.829022 0 0 0 -153 2 9.828095 3.751699 9.866387 0 0 0 -154 2 8.048006 4.695362 7.201209 0 0 0 -155 2 9.630769 3.656636 15.053818 0 0 0 -156 2 8.095682 4.602773 12.531565 0 0 0 -157 2 8.222729 6.529699 4.506718 0 0 0 -158 2 6.513179 7.584512 1.938196 0 0 0 -159 2 8.000072 6.482110 9.774643 0 0 0 -160 2 6.557736 7.490349 7.321158 0 0 0 -161 2 8.170897 6.578637 15.231286 0 0 0 -162 2 6.593460 7.536587 12.668627 0 0 0 -163 2 6.486808 9.294422 4.490238 0 0 0 -164 2 4.927038 10.269473 2.040398 0 0 0 -165 2 6.534873 9.382061 9.976987 0 0 0 -166 2 4.872738 10.309973 7.267284 0 0 0 -167 2 6.608529 9.350223 15.069188 0 0 0 -168 2 4.804018 10.354186 12.657218 0 0 0 -169 2 0.122111 1.810936 2.068603 0 0 0 -170 2 0.022084 1.853237 7.271087 0 0 0 -171 2 12.989334 1.909038 12.626954 0 0 0 -172 2 11.315248 4.595236 2.089518 0 0 0 -173 2 11.337981 4.749475 7.166350 0 0 0 -174 2 11.265234 4.778725 12.668944 0 0 0 -175 2 11.496595 6.644563 4.480256 0 0 0 -176 2 9.754439 7.612075 1.989693 0 0 0 -177 2 11.463729 6.465910 10.063344 0 0 0 -178 2 9.852647 7.514537 7.246210 0 0 0 -179 2 11.324601 6.612275 15.036388 0 0 0 -180 2 9.710141 7.595200 12.564365 0 0 0 -181 2 9.736122 9.374299 4.566454 0 0 0 -182 2 8.236239 10.421125 1.990485 0 0 0 -183 2 9.870834 9.365186 9.885401 0 0 0 -184 2 8.044499 10.243597 7.373289 0 0 0 -185 2 9.801724 9.381836 15.294825 0 0 0 -186 2 8.122182 10.324374 12.458835 0 0 0 -187 2 0.023383 7.419698 1.844233 0 0 0 -188 2 0.048065 7.524549 7.179026 0 0 0 -189 2 12.966211 7.529274 12.567217 0 0 0 -190 2 11.269911 10.238197 1.828071 0 0 0 -191 2 11.345386 10.310086 7.160170 0 0 0 -192 2 11.410079 10.204222 12.429204 0 0 0 diff --git a/examples/GaN-SNAP-LAMMPS/DATA/3/DATA b/examples/GaN-SNAP-LAMMPS/DATA/3/DATA deleted file mode 100755 index a2e08800..00000000 --- a/examples/GaN-SNAP-LAMMPS/DATA/3/DATA +++ /dev/null @@ -1,215 +0,0 @@ -LAMMPS DATA file - -192 atoms -0 bonds -0 angles -0 dihedrals -0 impropers - -2 atom types -0 bond types -0 angle types - -0.0 12.990503 xlo xhi -0.0 11.250148 ylo yhi -0.0 15.845291 zlo zhi - -Masses - -1 69.723 -2 14.0067 - -Atoms - -1 1 1.665642 0.957309 2.558539 0 0 0 -2 1 1.670709 1.026441 7.879546 0 0 0 -3 1 1.575618 0.860501 13.253159 0 0 0 -4 1 0.008242 3.819988 2.640142 0 0 0 -5 1 12.909596 3.812675 8.045446 0 0 0 -6 1 0.016552 3.772512 13.236997 0 0 0 -7 1 4.910540 0.854696 2.556638 0 0 0 -8 1 3.297250 1.848287 5.295021 0 0 0 -9 1 4.792846 1.001589 7.955287 0 0 0 -10 1 3.177347 1.782586 10.710783 0 0 0 -11 1 4.909631 0.988269 13.235254 0 0 0 -12 1 3.371425 1.818924 15.770501 0 0 0 -13 1 3.260616 3.852613 2.556796 0 0 0 -14 1 1.633686 4.706162 5.271094 0 0 0 -15 1 3.242819 3.703099 7.816323 0 0 0 -16 1 1.554314 4.684899 10.610165 0 0 0 -17 1 3.128633 3.851376 13.181697 0 0 0 -18 1 1.605756 4.743287 15.759092 0 0 0 -19 1 1.686947 6.514173 2.496426 0 0 0 -20 1 1.653171 6.535211 8.018192 0 0 0 -21 1 1.507028 6.648725 13.066185 0 0 0 -22 1 0.087370 9.419412 2.668188 0 0 0 -23 1 0.003565 9.318385 7.981907 0 0 0 -24 1 0.012141 9.460925 13.083140 0 0 0 -25 1 8.214934 1.045713 2.594191 0 0 0 -26 1 6.415880 1.871350 5.256675 0 0 0 -27 1 8.030599 1.032797 7.891747 0 0 0 -28 1 6.536691 1.856949 10.696046 0 0 0 -29 1 8.174274 1.039334 13.330484 0 0 0 -30 1 6.412762 1.912975 15.711873 0 0 0 -31 1 6.621000 3.804913 2.544595 0 0 0 -32 1 4.901966 4.650586 5.318313 0 0 0 -33 1 6.499409 3.814588 7.918050 0 0 0 -34 1 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9.630250 3.703324 13.194849 0 0 0 -60 1 8.034886 4.686699 0.033275 0 0 0 -61 1 8.179340 6.672350 2.604332 0 0 0 -62 1 6.595149 7.430385 5.329088 0 0 0 -63 1 8.116337 6.555799 7.880655 0 0 0 -64 1 6.403669 7.571462 10.434599 0 0 0 -65 1 8.201035 6.634662 13.125446 0 0 0 -66 1 6.390548 7.512961 0.099825 0 0 0 -67 1 6.541238 9.320073 2.563610 0 0 0 -68 1 4.813501 10.363524 5.355550 0 0 0 -69 1 6.456800 9.477237 8.060341 0 0 0 -70 1 4.897420 10.361387 10.683846 0 0 0 -71 1 6.394965 9.360461 13.307984 0 0 0 -72 1 4.905084 10.384674 15.704584 0 0 0 -73 1 0.124709 1.924450 5.424160 0 0 0 -74 1 12.951012 1.897112 10.552805 0 0 0 -75 1 0.085737 1.778536 15.828495 0 0 0 -76 1 11.290956 4.732262 5.349845 0 0 0 -77 1 11.257700 4.664761 10.691927 0 0 0 -78 1 11.350192 4.628423 15.753863 0 0 0 -79 1 11.307324 6.632300 2.617642 0 0 0 -80 1 9.849400 7.487761 5.249069 0 0 0 -81 1 11.390203 6.549949 7.781781 0 0 0 -82 1 9.729497 7.591825 10.558351 0 0 0 -83 1 11.279914 6.493361 13.208000 0 0 0 -84 1 9.850439 7.395622 15.733264 0 0 0 -85 1 9.653503 9.372498 2.597677 0 0 0 -86 1 8.189473 10.231897 5.330197 0 0 0 -87 1 9.762363 9.446862 7.951167 0 0 0 -88 1 8.179081 10.367462 10.595904 0 0 0 -89 1 9.677405 9.295210 13.194373 0 0 0 -90 1 8.089186 10.210860 15.691908 0 0 0 -91 1 0.033775 7.457273 5.177290 0 0 0 -92 1 0.068850 7.524999 10.627753 0 0 0 -93 1 0.024682 7.550199 0.123593 0 0 0 -94 1 11.269781 10.371174 5.145917 0 0 0 -95 1 11.414106 10.404700 10.448385 0 0 0 -96 1 11.480747 10.412012 15.819621 0 0 0 -97 2 1.557821 0.841084 4.739168 0 0 0 -98 2 1.648365 0.954564 9.861950 0 0 0 -99 2 1.718514 0.840251 15.095808 0 0 0 -100 2 0.106078 3.680936 4.510204 0 0 0 -101 2 0.071462 3.798163 9.899028 0 0 0 -102 2 12.953410 3.667886 15.067604 0 0 0 -103 2 4.866892 1.033337 4.540310 0 0 0 -104 2 3.140974 1.876637 1.923143 0 0 0 -105 2 4.942886 0.826672 9.829943 0 0 0 -106 2 3.290494 1.806661 7.424311 0 0 0 -107 2 4.937950 0.898921 15.203556 0 0 0 -108 2 3.242040 1.811274 12.642640 0 0 0 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4.719995 0 0 0 -134 2 3.279712 7.511836 1.902544 0 0 0 -135 2 4.803109 6.518898 9.821228 0 0 0 -136 2 3.159550 7.588000 7.355384 0 0 0 -137 2 4.970037 6.630162 15.058572 0 0 0 -138 2 3.160070 7.393485 12.493378 0 0 0 -139 2 3.170852 9.381274 4.479305 0 0 0 -140 2 1.534828 10.335961 2.011243 0 0 0 -141 2 3.258148 9.477800 9.950209 0 0 0 -142 2 1.649794 10.210972 7.180927 0 0 0 -143 2 3.210863 9.428187 15.199437 0 0 0 -144 2 1.678243 10.311661 12.642799 0 0 0 -145 2 11.290436 1.036926 4.676579 0 0 0 -146 2 9.676236 1.825449 1.857702 0 0 0 -147 2 11.413586 1.034496 9.931828 0 0 0 -148 2 9.849529 1.906113 7.417497 0 0 0 -149 2 11.402414 1.005201 15.310829 0 0 0 -150 2 9.861611 1.832424 12.582745 0 0 0 -151 2 9.684160 3.653936 4.514640 0 0 0 -152 2 8.073728 4.699299 1.884005 0 0 0 -153 2 9.757427 3.787137 9.922638 0 0 0 -154 2 8.217273 4.593323 7.118021 0 0 0 -155 2 9.783668 3.675986 15.186285 0 0 0 -156 2 8.141798 4.645749 12.504786 0 0 0 -157 2 8.241955 6.476035 4.752320 0 0 0 -158 2 6.584756 7.414973 1.875924 0 0 0 -159 2 8.184667 6.489873 9.939275 0 0 0 -160 2 6.484729 7.563137 7.352849 0 0 0 -161 2 8.134653 6.645800 15.102146 0 0 0 -162 2 6.575663 7.420035 12.573397 0 0 0 -163 2 6.465114 9.409061 4.642036 0 0 0 -164 2 4.841041 10.234485 1.899533 0 0 0 -165 2 6.447187 9.287110 9.861158 0 0 0 -166 2 4.838573 10.264973 7.406406 0 0 0 -167 2 6.620740 9.468462 15.116407 0 0 0 -168 2 4.759720 10.275773 12.671479 0 0 0 -169 2 12.862677 1.795636 1.919182 0 0 0 -170 2 12.895023 1.771786 7.395314 0 0 0 -171 2 0.120812 1.857962 12.440138 0 0 0 -172 2 11.493867 4.732262 2.044518 0 0 0 -173 2 11.339800 4.797963 7.397849 0 0 0 -174 2 11.274718 4.672749 12.520315 0 0 0 -175 2 11.480877 6.538699 4.721738 0 0 0 -176 2 9.613622 7.504861 2.053074 0 0 0 -177 2 11.294463 6.515073 10.005033 0 0 0 -178 2 9.845372 7.570225 7.318147 0 0 0 -179 2 11.493348 6.601587 15.096125 0 0 0 -180 2 9.650515 7.432860 12.422549 0 0 0 -181 2 9.774964 9.415587 4.569940 0 0 0 -182 2 8.036575 10.405600 1.864515 0 0 0 -183 2 9.866157 9.309160 10.040685 0 0 0 -184 2 8.162972 10.250685 7.157318 0 0 0 -185 2 9.799386 9.284747 15.209736 0 0 0 -186 2 8.125820 10.249448 12.602552 0 0 0 -187 2 12.978032 7.497886 1.975908 0 0 0 -188 2 0.071448 7.469198 7.336211 0 0 0 -189 2 12.901518 7.499799 12.453448 0 0 0 -190 2 11.284331 10.352499 2.112019 0 0 0 -191 2 11.393321 10.258560 7.294063 0 0 0 -192 2 11.360715 10.395474 12.605404 0 0 0 diff --git a/examples/GaN-SNAP-LAMMPS/DATA/30/DATA b/examples/GaN-SNAP-LAMMPS/DATA/30/DATA deleted file mode 100755 index c0531b2d..00000000 --- a/examples/GaN-SNAP-LAMMPS/DATA/30/DATA +++ /dev/null @@ -1,215 +0,0 @@ -LAMMPS DATA file - -192 atoms -0 bonds -0 angles -0 dihedrals -0 impropers - -2 atom types -0 bond types -0 angle types - -0.0 12.990503 xlo xhi -0.0 11.250148 ylo yhi -0.0 15.845291 zlo zhi - -Masses - -1 69.723 -2 14.0067 - -Atoms - -1 1 1.640701 0.835290 2.774193 0 0 0 -2 1 1.611862 1.020681 8.052418 0 0 0 -3 1 1.670968 0.905389 13.294516 0 0 0 -4 1 0.019814 3.790625 2.661533 0 0 0 -5 1 0.106281 3.839676 7.903314 0 0 0 -6 1 12.907929 3.711311 13.047963 0 0 0 -7 1 4.743352 1.005808 2.553785 0 0 0 -8 1 3.323620 1.942338 5.182836 0 0 0 -9 1 4.869230 1.016271 7.957030 0 0 0 -10 1 3.173580 1.981376 10.569760 0 0 0 -11 1 4.958345 1.008508 13.216240 0 0 0 -12 1 3.229049 1.828262 0.090318 0 0 0 -13 1 3.374673 3.751924 2.537465 0 0 0 -14 1 1.634465 4.631011 5.241939 0 0 0 -15 1 3.171372 3.814363 7.908701 0 0 0 -16 1 1.616798 4.736650 10.440145 0 0 0 -17 1 3.364800 3.802888 13.236522 0 0 0 -18 1 1.639791 4.626286 0.117255 0 0 0 -19 1 1.627450 6.544324 2.722696 0 0 0 -20 1 1.674995 6.672913 7.946572 0 0 0 -21 1 1.534568 6.479523 13.094390 0 0 0 -22 1 12.877752 9.347073 2.707168 0 0 0 -23 1 12.961693 9.270685 7.760548 0 0 0 -24 1 0.040575 9.432012 13.061907 0 0 0 -25 1 8.077365 0.936924 2.575810 0 0 0 -26 1 6.539939 1.944363 5.332416 0 0 0 -27 1 8.230913 0.968762 7.940234 0 0 0 -28 1 6.622688 1.774823 10.426518 0 0 0 -29 1 8.238967 0.916235 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0 0 -105 2 4.828830 1.019038 9.798411 0 0 0 -106 2 3.198132 1.881925 7.280436 0 0 0 -107 2 4.947953 0.838687 15.299103 0 0 0 -108 2 3.359604 1.933338 12.428729 0 0 0 -109 2 3.150457 3.705011 4.588004 0 0 0 -110 2 1.664343 4.765563 2.074465 0 0 0 -111 2 3.299328 3.745287 9.874627 0 0 0 -112 2 1.636544 4.708975 7.128321 0 0 0 -113 2 3.356486 3.746074 15.055403 0 0 0 -114 2 1.583023 4.696712 12.582904 0 0 0 -115 2 1.695780 6.598887 4.676421 0 0 0 -116 2 1.644078 6.514736 9.996635 0 0 0 -117 2 1.629399 6.556024 15.071248 0 0 0 -118 2 0.088819 9.297573 4.711597 0 0 0 -119 2 12.873076 9.434374 9.861475 0 0 0 -120 2 12.980082 9.273497 15.125122 0 0 0 -121 2 8.182848 1.033371 4.707160 0 0 0 -122 2 6.403019 1.840637 2.110910 0 0 0 -123 2 8.026053 1.016530 9.901722 0 0 0 -124 2 6.605931 1.884287 7.276791 0 0 0 -125 2 8.207920 0.865429 15.119576 0 0 0 -126 2 6.406007 1.938963 12.585597 0 0 0 -127 2 6.529287 3.802100 4.506084 0 0 0 -128 2 4.994589 4.603111 2.113445 0 0 0 -129 2 6.385872 3.834276 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8.118675 4.785926 7.114852 0 0 0 -155 2 9.794190 3.812675 15.238891 0 0 0 -156 2 8.132445 4.691424 12.519523 0 0 0 -157 2 8.129587 6.511698 4.517809 0 0 0 -158 2 6.594629 7.429935 1.965767 0 0 0 -159 2 8.083471 6.648275 10.004241 0 0 0 -160 2 6.366905 7.520274 7.238287 0 0 0 -161 2 7.997214 6.547361 15.162992 0 0 0 -162 2 6.595408 7.438598 12.700159 0 0 0 -163 2 6.497850 9.447424 4.533179 0 0 0 -164 2 4.791417 10.400312 2.059888 0 0 0 -165 2 6.560854 9.353486 9.979047 0 0 0 -166 2 4.849874 10.422137 7.280277 0 0 0 -167 2 6.475376 9.278560 15.300054 0 0 0 -168 2 4.912359 10.282748 12.613010 0 0 0 -169 2 12.931656 1.795186 1.924252 0 0 0 -170 2 12.889697 1.983739 7.366476 0 0 0 -171 2 12.982189 1.848174 12.610633 0 0 0 -172 2 11.264065 4.581398 1.890819 0 0 0 -173 2 11.305245 4.797176 7.174906 0 0 0 -174 2 11.250685 4.594448 12.504628 0 0 0 -175 2 11.453597 6.456573 4.510679 0 0 0 -176 2 9.661427 7.601500 2.143551 0 0 0 -177 2 11.483735 6.665938 9.822179 0 0 0 -178 2 9.680653 7.473923 7.386916 0 0 0 -179 2 11.485943 6.592024 15.120369 0 0 0 -180 2 9.637135 7.433085 12.626795 0 0 0 -181 2 9.790033 9.381724 4.733939 0 0 0 -182 2 8.110361 10.272623 2.013778 0 0 0 -183 2 9.779121 9.266522 9.761967 0 0 0 -184 2 8.003449 10.214572 7.132124 0 0 0 -185 2 9.863689 9.281372 15.176302 0 0 0 -186 2 8.237538 10.314586 12.457884 0 0 0 -187 2 0.129905 7.605888 2.041032 0 0 0 -188 2 12.880474 7.435223 7.123884 0 0 0 -189 2 0.001299 7.601388 12.574189 0 0 0 -190 2 11.350972 10.335624 1.895731 0 0 0 -191 2 11.411508 10.272960 7.310383 0 0 0 -192 2 11.329148 10.234485 12.417954 0 0 0 diff --git a/examples/GaN-SNAP-LAMMPS/DATA/31/DATA b/examples/GaN-SNAP-LAMMPS/DATA/31/DATA deleted file mode 100755 index 9a53df17..00000000 --- a/examples/GaN-SNAP-LAMMPS/DATA/31/DATA +++ /dev/null @@ -1,215 +0,0 @@ -LAMMPS DATA file - -192 atoms -0 bonds -0 angles -0 dihedrals -0 impropers - -2 atom types -0 bond types -0 angle types - -0.0 12.990503 xlo xhi -0.0 11.250148 ylo yhi -0.0 15.845291 zlo zhi 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1.029670 2.681182 0 0 0 -26 1 6.499798 1.920400 5.132131 0 0 0 -27 1 8.220520 0.976355 7.810936 0 0 0 -28 1 6.495901 1.882150 10.597330 0 0 0 -29 1 8.239746 0.953079 13.223529 0 0 0 -30 1 6.608919 1.776398 0.044367 0 0 0 -31 1 6.391198 3.774537 2.731887 0 0 0 -32 1 4.749978 4.692549 5.212150 0 0 0 -33 1 6.536951 3.772062 7.778136 0 0 0 -34 1 4.973024 4.789526 10.456941 0 0 0 -35 1 6.384443 3.859813 13.176151 0 0 0 -36 1 4.938730 4.782776 0.112502 0 0 0 -37 1 4.991861 6.516873 2.701939 0 0 0 -38 1 3.351810 7.584287 5.380427 0 0 0 -39 1 4.750627 6.654013 7.957663 0 0 0 -40 1 3.266462 7.553687 10.560728 0 0 0 -41 1 4.966269 6.481660 13.248723 0 0 0 -42 1 3.271788 7.503061 15.758934 0 0 0 -43 1 3.370646 9.468800 2.683558 0 0 0 -44 1 1.522617 10.315936 5.270302 0 0 0 -45 1 3.135388 9.350111 8.013914 0 0 0 -46 1 1.698248 10.227172 10.530146 0 0 0 -47 1 3.325049 9.319510 13.226698 0 0 0 -48 1 1.503391 10.353511 0.098241 0 0 0 -49 1 11.418652 0.904163 2.631903 0 0 0 -50 1 9.686758 1.822412 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2 8.052683 0.991026 15.319861 0 0 0 -126 2 6.584107 1.981151 12.436493 0 0 0 -127 2 6.588004 3.808963 4.709537 0 0 0 -128 2 4.860916 4.661499 1.861663 0 0 0 -129 2 6.483690 3.670698 9.843411 0 0 0 -130 2 4.840391 4.783113 7.170786 0 0 0 -131 2 6.535522 3.726274 15.093432 0 0 0 -132 2 4.749718 4.755438 12.490526 0 0 0 -133 2 4.935612 6.583024 4.562493 0 0 0 -134 2 3.329596 7.588450 2.014570 0 0 0 -135 2 4.953279 6.575037 10.008519 0 0 0 -136 2 3.127723 7.578550 7.145751 0 0 0 -137 2 4.780765 6.613850 15.096125 0 0 0 -138 2 3.309461 7.582712 12.457409 0 0 0 -139 2 3.307122 9.400624 4.631103 0 0 0 -140 2 1.743196 10.241685 1.891294 0 0 0 -141 2 3.288936 9.428974 9.868922 0 0 0 -142 2 1.747482 10.208047 7.213410 0 0 0 -143 2 3.286857 9.271472 15.075051 0 0 0 -144 2 1.555873 10.393449 12.680986 0 0 0 -145 2 11.238734 0.880403 4.661843 0 0 0 -146 2 9.868755 1.982839 2.023919 0 0 0 -147 2 11.483215 0.909102 9.822496 0 0 0 -148 2 9.760545 1.888562 7.198516 0 0 0 -149 2 11.463340 1.015281 15.237465 0 0 0 -150 2 9.800945 1.822524 12.429838 0 0 0 -151 2 9.652204 3.787812 4.575169 0 0 0 -152 2 8.149592 4.749475 2.059888 0 0 0 -153 2 9.804323 3.651011 9.822337 0 0 0 -154 2 8.110361 4.777375 7.281862 0 0 0 -155 2 9.627782 3.816275 15.277712 0 0 0 -156 2 8.121403 4.580835 12.700317 0 0 0 -157 2 8.052163 6.652775 4.610663 0 0 0 -158 2 6.381715 7.409910 1.944534 0 0 0 -159 2 8.122572 6.535549 9.750875 0 0 0 -160 2 6.551760 7.465261 7.317514 0 0 0 -161 2 8.033197 6.589887 15.166637 0 0 0 -162 2 6.541238 7.427798 12.672430 0 0 0 -163 2 6.406916 9.284635 4.709854 0 0 0 -164 2 4.973804 10.255860 2.016947 0 0 0 -165 2 6.385222 9.322548 10.018502 0 0 0 -166 2 4.919244 10.309861 7.222600 0 0 0 -167 2 6.420816 9.314110 15.274385 0 0 0 -168 2 4.844418 10.385237 12.557551 0 0 0 -169 2 12.887229 1.773361 2.125170 0 0 0 -170 2 0.029878 1.985651 7.260471 0 0 0 -171 2 0.126008 1.891262 12.464856 0 0 0 -172 2 11.267183 4.604348 2.062740 0 0 0 -173 2 11.272769 4.617173 7.235118 0 0 0 -174 2 11.324081 4.678262 12.423817 0 0 0 -175 2 11.281083 6.594387 4.718252 0 0 0 -176 2 9.709752 7.456598 2.112177 0 0 0 -177 2 11.425018 6.541624 9.809344 0 0 0 -178 2 9.626353 7.600038 7.242724 0 0 0 -179 2 11.391632 6.565587 15.316058 0 0 0 -180 2 9.661297 7.408673 12.409081 0 0 0 -181 2 9.625313 9.416262 4.619219 0 0 0 -182 2 8.230003 10.292648 2.103462 0 0 0 -183 2 9.797438 9.474650 9.902514 0 0 0 -184 2 8.102047 10.315373 7.275682 0 0 0 -185 2 9.734823 9.478250 15.303382 0 0 0 -186 2 8.068531 10.362174 12.662130 0 0 0 -187 2 12.940490 7.422848 1.852156 0 0 0 -188 2 0.064953 7.507786 7.253340 0 0 0 -189 2 0.075345 7.436798 12.488307 0 0 0 -190 2 11.426836 10.303673 1.956101 0 0 0 -191 2 11.302128 10.330899 7.365683 0 0 0 -192 2 11.249906 10.233585 12.546935 0 0 0 diff --git a/examples/GaN-SNAP-LAMMPS/DATA/32/DATA b/examples/GaN-SNAP-LAMMPS/DATA/32/DATA deleted file mode 100755 index d6d9202a..00000000 --- a/examples/GaN-SNAP-LAMMPS/DATA/32/DATA +++ /dev/null @@ -1,215 +0,0 @@ -LAMMPS DATA file - -192 atoms -0 bonds -0 angles -0 dihedrals -0 impropers - -2 atom types -0 bond types -0 angle types - -0.0 12.990503 xlo xhi -0.0 11.250148 ylo yhi -0.0 15.845291 zlo zhi - -Masses - -1 69.723 -2 14.0067 - -Atoms - -1 1 1.569383 0.890742 2.571057 0 0 0 -2 1 1.500403 1.031526 7.976044 0 0 0 -3 1 1.554833 0.936912 13.291030 0 0 0 -4 1 12.959388 3.686674 2.705900 0 0 0 -5 1 0.070887 3.793550 7.955128 0 0 0 -6 1 0.068151 3.752599 13.144936 0 0 0 -7 1 4.741923 0.955655 2.531444 0 0 0 -8 1 3.168384 1.796311 5.278066 0 0 0 -9 1 4.746080 0.931029 7.773383 0 0 0 -10 1 3.232687 1.799349 10.580851 0 0 0 -11 1 4.954188 0.844211 13.114196 0 0 0 -12 1 3.181634 1.841762 15.811065 0 0 0 -13 1 3.147339 3.729199 2.691164 0 0 0 -14 1 1.634985 4.655424 5.327504 0 0 0 -15 1 3.294002 3.667098 7.898085 0 0 0 -16 1 1.737350 4.703349 10.582594 0 0 0 -17 1 3.316346 3.693086 13.260290 0 0 0 -18 1 1.570552 4.703462 0.038029 0 0 0 -19 1 1.597572 6.506073 2.773401 0 0 0 -20 1 1.610563 6.569749 7.959882 0 0 0 -21 1 1.667461 6.548824 13.095340 0 0 0 -22 1 0.050504 9.470712 2.594349 0 0 0 -23 1 0.036060 9.462837 7.911712 0 0 0 -24 1 0.033730 9.367211 13.075058 0 0 0 -25 1 8.018518 0.849285 2.618276 0 0 0 -26 1 6.609308 1.905100 5.412434 0 0 0 -27 1 8.005528 0.894072 8.059707 0 0 0 -28 1 6.368075 1.800249 10.639003 0 0 0 -29 1 8.205841 0.961325 13.204673 0 0 0 -30 1 6.610347 1.929288 0.058628 0 0 0 -31 1 6.558775 3.834163 2.782433 0 0 0 -32 1 4.996667 4.781763 5.207713 0 0 0 -33 1 6.380545 3.822238 7.815531 0 0 0 -34 1 4.750627 4.748575 10.570869 0 0 0 -35 1 6.451474 3.767675 13.311312 0 0 0 -36 1 4.908462 4.669599 0.009507 0 0 0 -37 1 4.788949 6.503261 2.542060 0 0 0 -38 1 3.185141 7.599700 5.321165 0 0 0 -39 1 4.956916 6.537574 7.812045 0 0 0 -40 1 3.309980 7.583950 10.512241 0 0 0 -41 1 4.788040 6.674263 13.344428 0 0 0 -42 1 3.158251 7.596663 15.815977 0 0 0 -43 1 3.175658 9.293297 2.559331 0 0 0 -44 1 1.635374 10.218622 5.307380 0 0 0 -45 1 3.125255 9.364961 7.864018 0 0 0 -46 1 1.739039 10.268348 10.535375 0 0 0 -47 1 3.289455 9.348311 13.083615 0 0 0 -48 1 1.518980 10.268798 0.096656 0 0 0 -49 1 11.399816 0.871346 2.787504 0 0 0 -50 1 9.726769 1.950438 5.288683 0 0 0 -51 1 11.243281 0.826548 8.007893 0 0 0 -52 1 9.729237 1.827474 10.673071 0 0 0 -53 1 11.407221 0.889065 13.244761 0 0 0 -54 1 9.681432 1.801824 15.798230 0 0 0 -55 1 9.752620 3.845976 2.714298 0 0 0 -56 1 8.027481 4.575660 5.158117 0 0 0 -57 1 9.851218 3.788825 7.794774 0 0 0 -58 1 8.238577 4.601873 10.555657 0 0 0 -59 1 9.706894 3.743262 13.059055 0 0 0 -60 1 8.074897 4.634611 15.759251 0 0 0 -61 1 8.235330 6.457360 2.764052 0 0 0 -62 1 6.461087 7.536699 5.420040 0 0 0 -63 1 8.013582 6.604287 7.889370 0 0 0 -64 1 6.394445 7.498224 10.545833 0 0 0 -65 1 8.217013 6.598662 13.128615 0 0 0 -66 1 6.536042 7.532874 0.120424 0 0 0 -67 1 6.594629 9.338073 2.612255 0 0 0 -68 1 4.950421 10.407850 5.392469 0 0 0 -69 1 6.495122 9.394099 8.051784 0 0 0 -70 1 4.784662 10.284323 10.481818 0 0 0 -71 1 6.581119 9.278447 13.129566 0 0 0 -72 1 4.885728 10.339449 15.811223 0 0 0 -73 1 12.927759 1.856274 5.238928 0 0 0 -74 1 12.885670 1.792036 10.592894 0 0 0 -75 1 0.040271 1.951788 15.839745 0 0 0 -76 1 11.316547 4.613236 5.133240 0 0 0 -77 1 11.295502 4.657674 10.579584 0 0 0 -78 1 11.384747 4.750263 0.023768 0 0 0 -79 1 11.265494 6.594274 2.499753 0 0 0 -80 1 9.708063 7.452211 5.352856 0 0 0 -81 1 11.254193 6.620487 7.835021 0 0 0 -82 1 9.672989 7.390335 10.441571 0 0 0 -83 1 11.291216 6.498311 13.327474 0 0 0 -84 1 9.685200 7.409460 0.083980 0 0 0 -85 1 9.786396 9.400511 2.585951 0 0 0 -86 1 8.168558 10.252710 5.215477 0 0 0 -87 1 9.705854 9.311410 7.973350 0 0 0 -88 1 8.180380 10.202422 10.512400 0 0 0 -89 1 9.675327 9.471387 13.282315 0 0 0 -90 1 8.087757 10.354524 0.057043 0 0 0 -91 1 0.023383 7.604088 5.365374 0 0 0 -92 1 0.010392 7.408785 10.680360 0 0 0 -93 1 12.927499 7.491924 15.786188 0 0 0 -94 1 11.433462 10.380737 5.372346 0 0 0 -95 1 11.464509 10.219860 10.611274 0 0 0 -96 1 11.367340 10.275660 0.022183 0 0 0 -97 2 1.585361 0.871526 4.551718 0 0 0 -98 2 1.519499 0.858769 9.852126 0 0 0 -99 2 1.648365 0.859601 15.051917 0 0 0 -100 2 12.862622 3.811775 4.684660 0 0 0 -101 2 12.891908 3.799400 9.801580 0 0 0 -102 2 12.891818 3.790850 15.078062 0 0 0 -103 2 4.756603 0.855371 4.473284 0 0 0 -104 2 3.166825 1.778423 1.839638 0 0 0 -105 2 4.821555 0.941052 9.875102 0 0 0 -106 2 3.376232 1.861450 7.157476 0 0 0 -107 2 4.943666 0.991779 15.059840 0 0 0 -108 2 3.239961 1.828374 12.520156 0 0 0 -109 2 3.229439 3.833601 4.692741 0 0 0 -110 2 1.497675 4.580610 1.902861 0 0 0 -111 2 3.273217 3.845976 9.856246 0 0 0 -112 2 1.609004 4.597373 7.336053 0 0 0 -113 2 3.305174 3.813575 15.330636 0 0 0 -114 2 1.506249 4.755100 12.539171 0 0 0 -115 2 1.566395 6.460173 4.718094 0 0 0 -116 2 1.727477 6.624650 10.015808 0 0 0 -117 2 1.583412 6.493136 15.152059 0 0 0 -118 2 12.927198 9.267422 4.561542 0 0 0 -119 2 12.923064 9.308148 9.860683 0 0 0 -120 2 0.009654 9.290597 15.093115 0 0 0 -121 2 8.116077 0.916583 4.701456 0 0 0 -122 2 6.443290 1.944138 2.117248 0 0 0 -123 2 8.187914 0.900203 9.978255 0 0 0 -124 2 6.374050 1.901050 7.144958 0 0 0 -125 2 8.002280 0.837427 15.040350 0 0 0 -126 2 6.613595 1.880687 12.630915 0 0 0 -127 2 6.518635 3.803788 4.569782 0 0 0 -128 2 4.961853 4.686137 1.864040 0 0 0 -129 2 6.576442 3.787587 9.871299 0 0 0 -130 2 4.928337 4.669262 7.127212 0 0 0 -131 2 6.517335 3.704786 15.161883 0 0 0 -132 2 4.893782 4.646086 12.437919 0 0 0 -133 2 4.999135 6.474235 4.574535 0 0 0 -134 2 3.127594 7.595088 1.945960 0 0 0 -135 2 4.998486 6.572337 9.928818 0 0 0 -136 2 3.166565 7.436123 7.263323 0 0 0 -137 2 4.798562 6.660875 15.120052 0 0 0 -138 2 3.365320 7.571012 12.501934 0 0 0 -139 2 3.123307 9.339311 4.590381 0 0 0 -140 2 1.518200 10.418200 1.887966 0 0 0 -141 2 3.160460 9.376661 9.911388 0 0 0 -142 2 1.507288 10.282748 7.294855 0 0 0 -143 2 3.376232 9.360573 15.252677 0 0 0 -144 2 1.498195 10.234485 12.676232 0 0 0 -145 2 11.248866 0.831611 4.650593 0 0 0 -146 2 9.701438 1.811836 2.114237 0 0 0 -147 2 11.414236 0.908629 9.877479 0 0 0 -148 2 9.666233 1.815999 7.389768 0 0 0 -149 2 11.476070 1.000881 15.108801 0 0 0 -150 2 9.764572 1.807899 12.431423 0 0 0 -151 2 9.791592 3.842488 4.706527 0 0 0 -152 2 8.202983 4.625723 1.950238 0 0 0 -153 2 9.721703 3.848113 9.783833 0 0 0 -154 2 8.127249 4.714825 7.198357 0 0 0 -155 2 9.664415 3.729424 15.146989 0 0 0 -156 2 8.031249 4.776138 12.530773 0 0 0 -157 2 8.163362 6.497411 4.617951 0 0 0 -158 2 6.378337 7.499236 1.913160 0 0 0 -159 2 8.166870 6.618350 9.874468 0 0 0 -160 2 6.510580 7.552337 7.303253 0 0 0 -161 2 8.140109 6.466023 15.150633 0 0 0 -162 2 6.374050 7.478986 12.599700 0 0 0 -163 2 6.514737 9.482187 4.608603 0 0 0 -164 2 4.943666 10.328311 1.834409 0 0 0 -165 2 6.498499 9.354273 9.819960 0 0 0 -166 2 4.801420 10.298836 7.401018 0 0 0 -167 2 6.448226 9.326598 15.147306 0 0 0 -168 2 4.871309 10.383212 12.465649 0 0 0 -169 2 12.866444 1.830287 1.922192 0 0 0 -170 2 0.084438 1.793161 7.367585 0 0 0 -171 2 0.093532 1.886987 12.397038 0 0 0 -172 2 11.368769 4.735637 2.048796 0 0 0 -173 2 11.468926 4.732825 7.406564 0 0 0 -174 2 11.239643 4.759488 12.402109 0 0 0 -175 2 11.370847 6.597087 4.707636 0 0 0 -176 2 9.685719 7.523312 2.109325 0 0 0 -177 2 11.403843 6.626900 9.906000 0 0 0 -178 2 9.717806 7.585075 7.333834 0 0 0 -179 2 11.451518 6.452523 15.062375 0 0 0 -180 2 9.754179 7.580237 12.474997 0 0 0 -181 2 9.814455 9.406136 4.698287 0 0 0 -182 2 8.221560 10.372974 1.893195 0 0 0 -183 2 9.624274 9.297122 9.977938 0 0 0 -184 2 8.022545 10.249785 7.253182 0 0 0 -185 2 9.733914 9.282835 15.192623 0 0 0 -186 2 8.009035 10.237635 12.628221 0 0 0 -187 2 12.947505 7.456261 2.087142 0 0 0 -188 2 0.124709 7.605663 7.292161 0 0 0 -189 2 12.921264 7.453336 12.604770 0 0 0 -190 2 11.385786 10.245060 2.131350 0 0 0 -191 2 11.324081 10.233810 7.213569 0 0 0 -192 2 11.266144 10.373874 12.642324 0 0 0 diff --git a/examples/GaN-SNAP-LAMMPS/DATA/33/DATA b/examples/GaN-SNAP-LAMMPS/DATA/33/DATA deleted file mode 100755 index f7dbe127..00000000 --- a/examples/GaN-SNAP-LAMMPS/DATA/33/DATA +++ /dev/null @@ -1,215 +0,0 @@ -LAMMPS DATA file - -192 atoms -0 bonds -0 angles -0 dihedrals -0 impropers - -2 atom types -0 bond types -0 angle types - -0.0 12.990503 xlo xhi -0.0 11.250148 ylo yhi -0.0 15.845291 zlo zhi - -Masses - -1 69.723 -2 14.0067 - -Atoms - -1 1 1.530281 1.007451 2.557113 0 0 0 -2 1 1.500273 0.944427 8.054953 0 0 0 -3 1 1.693832 0.916077 13.267896 0 0 0 -4 1 12.985652 3.736849 2.775620 0 0 0 -5 1 0.020469 3.813913 7.985234 0 0 0 -6 1 12.897535 3.793437 13.165218 0 0 0 -7 1 4.774789 0.969212 2.634596 0 0 0 -8 1 3.134349 1.880350 5.217537 0 0 0 -9 1 4.963671 0.827032 7.822978 0 0 0 -10 1 3.346484 1.811611 10.500199 0 0 0 -11 1 4.830908 1.005032 13.221469 0 0 0 -12 1 3.328946 1.781911 15.742296 0 0 0 -13 1 3.281271 3.651911 2.712397 0 0 0 -14 1 1.650703 4.754763 5.168734 0 0 0 -15 1 3.309461 3.807838 8.037999 0 0 0 -16 1 1.605366 4.617286 10.495604 0 0 0 -17 1 3.201120 3.736962 13.155236 0 0 0 -18 1 1.656419 4.786263 15.772244 0 0 0 -19 1 1.557431 6.657275 2.770391 0 0 0 -20 1 1.574449 6.467260 8.006150 0 0 0 -21 1 1.527943 6.553886 13.179954 0 0 0 -22 1 0.027283 9.291160 2.666762 0 0 0 -23 1 12.894927 9.288572 7.898560 0 0 0 -24 1 12.931034 9.475100 13.204198 0 0 0 -25 1 8.104905 0.894443 2.625723 0 0 0 -26 1 6.567869 1.800474 5.125001 0 0 0 -27 1 8.173235 0.961168 7.889846 0 0 0 -28 1 6.603073 1.869887 10.690025 0 0 0 -29 1 8.118285 1.033709 13.263459 0 0 0 -30 1 6.545785 1.763573 0.007923 0 0 0 -31 1 6.472648 3.778925 2.649174 0 0 0 -32 1 4.797653 4.699299 5.391202 0 0 0 -33 1 6.366646 3.665636 8.004407 0 0 0 -34 1 4.746860 4.607161 10.501149 0 0 0 -35 1 6.600475 3.775775 13.045586 0 0 0 -36 1 4.822465 4.618411 15.768599 0 0 0 -37 1 4.748419 6.637025 2.719210 0 0 0 -38 1 3.305044 7.572700 5.360145 0 0 0 -39 1 4.772841 6.536561 7.767520 0 0 0 -40 1 3.118110 7.389210 10.452821 0 0 0 -41 1 4.780635 6.566037 13.173141 0 0 0 -42 1 3.272048 7.449961 0.023768 0 0 0 -43 1 3.269710 9.289922 2.501813 0 0 0 -44 1 1.502222 10.237972 5.283929 0 0 0 -45 1 3.336351 9.331548 7.819334 0 0 0 -46 1 1.510796 10.413025 10.477223 0 0 0 -47 1 3.280232 9.309160 13.117048 0 0 0 -48 1 1.687077 10.235272 0.096656 0 0 0 -49 1 11.261207 1.045465 2.684034 0 0 0 -50 1 9.686758 1.957638 5.127378 0 0 0 -51 1 11.434501 1.026655 7.954811 0 0 0 -52 1 9.800166 1.866850 10.640113 0 0 0 -53 1 11.238604 0.868545 13.069513 0 0 0 -54 1 9.656620 1.974514 0.104579 0 0 0 -55 1 9.648696 3.786237 2.489137 0 0 0 -56 1 8.027611 4.616611 5.322275 0 0 0 -57 1 9.835500 3.829550 7.915198 0 0 0 -58 1 8.192071 4.636861 10.706187 0 0 0 -59 1 9.870314 3.656523 13.144936 0 0 0 -60 1 8.058918 4.623698 0.079226 0 0 0 -61 1 8.083990 6.484698 2.529225 0 0 0 -62 1 6.597487 7.600375 5.281869 0 0 0 -63 1 7.993966 6.544436 7.797467 0 0 0 -64 1 6.612686 7.448386 10.682736 0 0 0 -65 1 8.221689 6.624537 13.328425 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10.415837 2.098709 0 0 0 -141 2 3.241520 9.460137 9.873834 0 0 0 -142 2 1.506639 10.269360 7.210875 0 0 0 -143 2 3.237623 9.372498 15.256004 0 0 0 -144 2 1.589388 10.412012 12.476265 0 0 0 -145 2 11.430474 1.029557 4.653762 0 0 0 -146 2 9.848490 1.775273 2.004112 0 0 0 -147 2 11.237565 0.859466 9.879539 0 0 0 -148 2 9.673638 1.882937 7.208181 0 0 0 -149 2 11.420861 0.957095 15.107851 0 0 0 -150 2 9.629600 1.763236 12.451071 0 0 0 -151 2 9.740539 3.776225 4.507510 0 0 0 -152 2 8.023714 4.645749 1.855484 0 0 0 -153 2 9.719235 3.701074 9.950209 0 0 0 -154 2 8.046188 4.722250 7.170786 0 0 0 -155 2 9.637524 3.844176 15.208944 0 0 0 -156 2 8.097630 4.599961 12.566425 0 0 0 -157 2 8.018128 6.503148 4.512580 0 0 0 -158 2 6.450564 7.465598 2.122001 0 0 0 -159 2 8.220001 6.627800 9.774009 0 0 0 -160 2 6.474467 7.476849 7.240347 0 0 0 -161 2 8.242214 6.503598 15.066495 0 0 0 -162 2 6.573195 7.397647 12.695405 0 0 0 -163 2 6.573584 9.478812 4.711280 0 0 0 -164 2 4.899498 10.422700 2.006014 0 0 0 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7.523199 12.664507 0 0 0 -190 2 11.412417 10.376799 1.997774 0 0 0 -191 2 11.237954 10.244835 7.248428 0 0 0 -192 2 11.381889 10.286798 12.596214 0 0 0 diff --git a/examples/GaN-SNAP-LAMMPS/DATA/34/DATA b/examples/GaN-SNAP-LAMMPS/DATA/34/DATA deleted file mode 100755 index bcc5eb0a..00000000 --- a/examples/GaN-SNAP-LAMMPS/DATA/34/DATA +++ /dev/null @@ -1,215 +0,0 @@ -LAMMPS DATA file - -192 atoms -0 bonds -0 angles -0 dihedrals -0 impropers - -2 atom types -0 bond types -0 angle types - -0.0 12.990503 xlo xhi -0.0 11.250148 ylo yhi -0.0 15.845291 zlo zhi - -Masses - -1 69.723 -2 14.0067 - -Atoms - -1 1 1.667201 0.903376 2.516232 0 0 0 -2 1 1.615109 0.834030 7.931994 0 0 0 -3 1 1.744105 0.866543 13.053826 0 0 0 -4 1 12.976383 3.726612 2.784334 0 0 0 -5 1 0.044000 3.801875 7.793506 0 0 0 -6 1 12.989197 3.845751 13.253476 0 0 0 -7 1 4.851563 0.896749 2.791306 0 0 0 -8 1 3.313747 1.835799 5.237661 0 0 0 -9 1 4.889236 0.989788 7.888578 0 0 0 -10 1 3.277114 1.981264 10.670852 0 0 0 -11 1 4.841561 0.886467 13.304974 0 0 0 -12 1 3.245547 1.868425 15.727402 0 0 0 -13 1 3.143832 3.705686 2.788613 0 0 0 -14 1 1.514043 4.634161 5.232749 0 0 0 -15 1 3.284909 3.659223 7.766569 0 0 0 -16 1 1.574839 4.789751 10.686539 0 0 0 -17 1 3.306992 3.785112 13.235730 0 0 0 -18 1 1.549377 4.734287 15.740712 0 0 0 -19 1 1.726178 6.463210 2.579296 0 0 0 -20 1 1.715656 6.477385 7.996326 0 0 0 -21 1 1.616668 6.518111 13.231293 0 0 0 -22 1 12.915782 9.419187 2.570740 0 0 0 -23 1 12.910428 9.335373 8.054478 0 0 0 -24 1 0.043551 9.431674 13.348707 0 0 0 -25 1 8.100358 0.893104 2.747732 0 0 0 -26 1 6.468491 1.927713 5.321007 0 0 0 -27 1 8.213895 0.912916 8.073651 0 0 0 -28 1 6.447187 1.771561 10.509231 0 0 0 -29 1 8.204802 1.009937 13.144302 0 0 0 -30 1 6.603463 1.904088 15.704109 0 0 0 -31 1 6.541628 3.718399 2.525581 0 0 0 -32 1 4.754394 4.758250 5.399124 0 0 0 -33 1 6.368464 3.693761 7.775601 0 0 0 -34 1 4.832987 4.659136 10.621415 0 0 0 -35 1 6.480053 3.835288 13.105006 0 0 0 -36 1 4.769074 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2.628258 0 0 0 -62 1 6.582028 7.400573 5.219439 0 0 0 -63 1 8.089446 6.613625 8.065253 0 0 0 -64 1 6.617362 7.528599 10.669426 0 0 0 -65 1 8.064245 6.534986 13.113404 0 0 0 -66 1 6.621000 7.389210 0.055459 0 0 0 -67 1 6.463815 9.423237 2.517341 0 0 0 -68 1 4.761669 10.327974 5.401501 0 0 0 -69 1 6.524091 9.444049 7.769421 0 0 0 -70 1 4.902226 10.281398 10.444106 0 0 0 -71 1 6.398732 9.270685 13.167753 0 0 0 -72 1 4.994329 10.400425 0.026937 0 0 0 -73 1 12.963743 1.766723 5.362522 0 0 0 -74 1 0.050663 1.771561 10.632190 0 0 0 -75 1 0.080541 1.777073 15.835625 0 0 0 -76 1 11.494907 4.662736 5.340180 0 0 0 -77 1 11.292644 4.687487 10.417169 0 0 0 -78 1 11.246009 4.685124 15.774779 0 0 0 -79 1 11.253673 6.607662 2.576920 0 0 0 -80 1 9.816404 7.428248 5.125476 0 0 0 -81 1 11.438528 6.542974 7.911078 0 0 0 -82 1 9.677145 7.471448 10.665940 0 0 0 -83 1 11.465548 6.504611 13.261241 0 0 0 -84 1 9.682731 7.486749 15.711873 0 0 0 -85 1 9.690656 9.479487 2.608927 0 0 0 -86 1 8.228704 10.341136 5.340338 0 0 0 -87 1 9.757037 9.348536 7.902522 0 0 0 -88 1 8.224937 10.352949 10.436818 0 0 0 -89 1 9.709102 9.453387 13.127506 0 0 0 -90 1 8.102956 10.271723 15.721222 0 0 0 -91 1 0.036373 7.544124 5.412593 0 0 0 -92 1 0.072747 7.459636 10.591943 0 0 0 -93 1 12.897231 7.388872 15.814709 0 0 0 -94 1 11.469185 10.235272 5.216270 0 0 0 -95 1 11.486463 10.417862 10.670536 0 0 0 -96 1 11.468406 10.276335 0.114086 0 0 0 -97 2 1.563927 1.002737 4.645839 0 0 0 -98 2 1.510016 0.962000 9.990773 0 0 0 -99 2 1.742676 0.840589 15.101037 0 0 0 -100 2 0.064321 3.788487 4.648216 0 0 0 -101 2 12.899097 3.855651 10.064770 0 0 0 -102 2 12.939431 3.649661 15.336815 0 0 0 -103 2 4.852862 0.873529 4.567405 0 0 0 -104 2 3.360513 1.981376 1.856117 0 0 0 -105 2 4.992380 0.962821 10.004241 0 0 0 -106 2 3.361553 1.780111 7.410525 0 0 0 -107 2 4.804408 0.873889 15.066811 0 0 0 -108 2 3.257758 1.819599 12.655950 0 0 0 -109 2 3.143312 3.816050 4.646473 0 0 0 -110 2 1.494038 4.695024 1.894938 0 0 0 -111 2 3.270099 3.741462 9.968589 0 0 0 -112 2 1.557691 4.786038 7.327179 0 0 0 -113 2 3.359474 3.731562 15.290072 0 0 0 -114 2 1.608224 4.746663 12.394028 0 0 0 -115 2 1.752419 6.466923 4.522246 0 0 0 -116 2 1.627450 6.625325 9.864010 0 0 0 -117 2 1.570162 6.484248 15.318910 0 0 0 -118 2 12.931477 9.339536 4.484376 0 0 0 -119 2 12.913763 9.380486 9.825506 0 0 0 -120 2 0.023912 9.445512 15.154594 0 0 0 -121 2 8.192591 0.985884 4.785436 0 0 0 -122 2 6.370673 1.910838 1.996507 0 0 0 -123 2 8.237798 0.981463 9.898553 0 0 0 -124 2 6.442380 1.857174 7.234960 0 0 0 -125 2 8.016050 0.932604 15.278029 0 0 0 -126 2 6.488237 1.834337 12.513977 0 0 0 -127 2 6.548902 3.839451 4.707794 0 0 0 -128 2 4.776738 4.601423 1.857860 0 0 0 -129 2 6.436145 3.648761 9.802689 0 0 0 -130 2 4.993420 4.615036 7.255559 0 0 0 -131 2 6.553319 3.748212 15.210053 0 0 0 -132 2 4.937820 4.792901 12.515244 0 0 0 -133 2 4.910930 6.461748 4.751527 0 0 0 -134 2 3.348562 7.610838 1.949288 0 0 0 -135 2 4.830649 6.609462 9.945138 0 0 0 -136 2 3.338559 7.599813 7.421300 0 0 0 -137 2 4.976012 6.457135 15.059681 0 0 0 -138 2 3.211382 7.412273 12.517780 0 0 0 -139 2 3.309461 9.459125 4.571842 0 0 0 -140 2 1.728776 10.345974 1.959904 0 0 0 -141 2 3.333233 9.485225 9.870507 0 0 0 -142 2 1.620046 10.338886 7.238763 0 0 0 -143 2 3.279972 9.399161 15.287219 0 0 0 -144 2 1.647456 10.261485 12.538378 0 0 0 -145 2 11.349153 0.905839 4.757390 0 0 0 -146 2 9.703126 1.883612 1.892878 0 0 0 -147 2 11.366171 0.861784 9.915824 0 0 0 -148 2 9.798607 1.829387 7.297232 0 0 0 -149 2 11.456065 1.027870 15.279138 0 0 0 -150 2 9.669741 1.905100 12.617130 0 0 0 -151 2 9.613882 3.773300 4.767214 0 0 0 -152 2 8.011763 4.625836 2.119783 0 0 0 -153 2 9.665194 3.705799 9.965579 0 0 0 -154 2 8.045019 4.678037 7.273305 0 0 0 -155 2 9.723781 3.747874 15.091530 0 0 0 -156 2 8.016440 4.786713 12.432057 0 0 0 -157 2 8.076066 6.631175 4.513214 0 0 0 -158 2 6.506683 7.583162 2.126280 0 0 0 -159 2 8.108152 6.509223 9.808710 0 0 0 -160 2 6.546694 7.415535 7.157476 0 0 0 -161 2 8.171546 6.540386 15.111020 0 0 0 -162 2 6.441861 7.507449 12.442990 0 0 0 -163 2 6.370283 9.262922 4.627142 0 0 0 -164 2 4.979909 10.412912 1.936453 0 0 0 -165 2 6.506294 9.341223 9.909803 0 0 0 -166 2 4.764787 10.262498 7.229414 0 0 0 -167 2 6.569168 9.295435 15.156496 0 0 0 -168 2 4.982637 10.256085 12.623151 0 0 0 -169 2 12.940230 1.868875 2.036437 0 0 0 -170 2 0.048065 1.860887 7.116912 0 0 0 -171 2 12.967250 1.951563 12.681620 0 0 0 -172 2 11.387475 4.764438 1.940731 0 0 0 -173 2 11.458014 4.775575 7.308482 0 0 0 -174 2 11.340450 4.631574 12.706972 0 0 0 -175 2 11.402414 6.619812 4.747408 0 0 0 -176 2 9.733264 7.449398 1.977968 0 0 0 -177 2 11.244580 6.501461 9.921529 0 0 0 -178 2 9.716767 7.557625 7.373131 0 0 0 -179 2 11.382279 6.577399 15.221778 0 0 0 -180 2 9.760025 7.495074 12.499241 0 0 0 -181 2 9.823808 9.442137 4.558056 0 0 0 -182 2 8.044239 10.256535 1.895414 0 0 0 -183 2 9.756777 9.380936 9.846897 0 0 0 -184 2 8.205841 10.218060 7.236544 0 0 0 -185 2 9.846801 9.459462 15.103414 0 0 0 -186 2 8.050085 10.410100 12.597323 0 0 0 -187 2 12.933475 7.414073 2.052282 0 0 0 -188 2 0.019486 7.416323 7.161754 0 0 0 -189 2 0.057158 7.393822 12.475473 0 0 0 -190 2 11.486593 10.205684 2.079853 0 0 0 -191 2 11.440476 10.221997 7.335894 0 0 0 -192 2 11.248866 10.214122 12.641373 0 0 0 diff --git a/examples/GaN-SNAP-LAMMPS/DATA/35/DATA b/examples/GaN-SNAP-LAMMPS/DATA/35/DATA deleted file mode 100755 index 80e3c32b..00000000 --- a/examples/GaN-SNAP-LAMMPS/DATA/35/DATA +++ /dev/null @@ -1,215 +0,0 @@ -LAMMPS DATA file - -192 atoms -0 bonds -0 angles -0 dihedrals -0 impropers - -2 atom types -0 bond types -0 angle types - -0.0 12.990503 xlo xhi -0.0 11.250148 ylo yhi -0.0 15.845291 zlo zhi - -Masses - -1 69.723 -2 14.0067 - -Atoms - -1 1 1.741247 1.044576 2.486760 0 0 0 -2 1 1.622254 1.019128 7.835655 0 0 0 -3 1 1.710719 1.008070 13.239849 0 0 0 -4 1 12.861181 3.723012 2.763577 0 0 0 -5 1 0.046859 3.722787 7.958931 0 0 0 -6 1 12.923803 3.766100 13.351559 0 0 0 -7 1 4.962242 0.888784 2.693224 0 0 0 -8 1 3.210733 1.984639 5.144490 0 0 0 -9 1 4.806616 1.007563 7.785425 0 0 0 -10 1 3.255680 1.942676 10.633774 0 0 0 -11 1 4.778297 0.923536 13.151433 0 0 0 -12 1 3.242040 1.894637 15.727560 0 0 0 -13 1 3.352979 3.781625 2.528591 0 0 0 -14 1 1.640960 4.784688 5.366008 0 0 0 -15 1 3.295821 3.742474 7.841200 0 0 0 -16 1 1.641870 4.631011 10.500833 0 0 0 -17 1 3.354408 3.836751 13.292297 0 0 0 -18 1 1.734492 4.615261 0.000000 0 0 0 -19 1 1.656809 6.655588 2.687361 0 0 0 -20 1 1.594974 6.616550 8.017875 0 0 0 -21 1 1.649924 6.469173 13.332703 0 0 0 -22 1 12.874525 9.381161 2.514648 0 0 0 -23 1 12.959365 9.445512 7.836130 0 0 0 -24 1 0.099879 9.423012 13.160306 0 0 0 -25 1 8.053852 0.881899 2.720161 0 0 0 -26 1 6.378337 1.916688 5.314352 0 0 0 -27 1 8.183108 1.044891 7.880338 0 0 0 -28 1 6.432897 1.960001 10.655007 0 0 0 -29 1 8.108932 0.845471 13.219251 0 0 0 -30 1 6.414061 1.882150 15.793793 0 0 0 -31 1 6.447187 3.801088 2.640459 0 0 0 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9.622845 3.852276 7.993949 0 0 0 -58 1 8.232731 4.690524 10.475955 0 0 0 -59 1 9.680523 3.808288 13.355203 0 0 0 -60 1 8.081782 4.744413 15.716151 0 0 0 -61 1 8.144266 6.547024 2.708594 0 0 0 -62 1 6.433157 7.408898 5.260795 0 0 0 -63 1 8.155438 6.479748 7.902205 0 0 0 -64 1 6.534743 7.573712 10.497188 0 0 0 -65 1 8.093733 6.649063 13.262508 0 0 0 -66 1 6.428221 7.558525 15.773511 0 0 0 -67 1 6.437444 9.264047 2.595617 0 0 0 -68 1 4.855071 10.268573 5.209932 0 0 0 -69 1 6.428351 9.473412 8.031344 0 0 0 -70 1 4.844678 10.308061 10.578633 0 0 0 -71 1 6.492524 9.323335 13.354094 0 0 0 -72 1 4.789209 10.394012 15.691750 0 0 0 -73 1 12.946855 1.930975 5.321958 0 0 0 -74 1 12.904506 1.976764 10.571819 0 0 0 -75 1 12.925940 1.892725 0.126762 0 0 0 -76 1 11.469445 4.683662 5.258101 0 0 0 -77 1 11.317716 4.587473 10.638528 0 0 0 -78 1 11.271080 4.655199 15.806787 0 0 0 -79 1 11.466847 6.454885 2.744404 0 0 0 -80 1 9.687798 7.443886 5.272520 0 0 0 -81 1 11.426187 6.495723 7.827257 0 0 0 -82 1 9.866677 7.521062 10.496079 0 0 0 -83 1 11.488152 6.651650 13.100728 0 0 0 -84 1 9.613492 7.547724 0.110917 0 0 0 -85 1 9.643760 9.271360 2.666445 0 0 0 -86 1 8.146215 10.316386 5.120247 0 0 0 -87 1 9.791982 9.475437 8.035464 0 0 0 -88 1 8.018648 10.279935 10.476272 0 0 0 -89 1 9.758596 9.400511 13.135746 0 0 0 -90 1 8.196488 10.379162 0.083980 0 0 0 -91 1 12.951792 7.399785 5.342398 0 0 0 -92 1 0.128606 7.424198 10.435550 0 0 0 -93 1 0.107821 7.495974 0.106163 0 0 0 -94 1 11.447231 10.242135 5.196146 0 0 0 -95 1 11.250815 10.337199 10.645975 0 0 0 -96 1 11.369548 10.206359 0.150530 0 0 0 -97 2 1.624073 0.899708 4.523672 0 0 0 -98 2 1.656419 0.954418 9.988396 0 0 0 -99 2 1.533789 0.905288 15.077745 0 0 0 -100 2 0.091093 3.713561 4.555838 0 0 0 -101 2 12.862161 3.817963 9.907902 0 0 0 -102 2 0.009834 3.833488 15.261233 0 0 0 -103 2 4.915087 0.865249 4.642987 0 0 0 -104 2 3.367138 1.896662 2.083973 0 0 0 -105 2 4.997317 1.024348 9.818059 0 0 0 -106 2 3.126684 1.864037 7.113902 0 0 0 -107 2 4.864554 1.039030 15.111020 0 0 0 -108 2 3.218137 1.859650 12.654524 0 0 0 -109 2 3.331934 3.739437 4.589113 0 0 0 -110 2 1.734492 4.741712 2.061472 0 0 0 -111 2 3.363761 3.752374 10.001230 0 0 0 -112 2 1.611342 4.766125 7.233217 0 0 0 -113 2 3.309591 3.857226 15.198010 0 0 0 -114 2 1.605626 4.621673 12.493695 0 0 0 -115 2 1.522747 6.534536 4.573109 0 0 0 -116 2 1.582763 6.633987 9.918835 0 0 0 -117 2 1.629269 6.624312 15.070139 0 0 0 -118 2 0.032594 9.340661 4.574694 0 0 0 -119 2 0.019388 9.456987 9.813305 0 0 0 -120 2 0.044806 9.465537 15.095175 0 0 0 -121 2 8.066713 0.936732 4.750577 0 0 0 -122 2 6.495641 1.824887 1.996982 0 0 0 -123 2 8.138420 0.917888 9.754995 0 0 0 -124 2 6.547993 1.876525 7.230206 0 0 0 -125 2 8.006047 0.905693 15.106266 0 0 0 -126 2 6.418218 1.945601 12.515878 0 0 0 -127 2 6.379246 3.721887 4.714132 0 0 0 -128 2 4.784532 4.780300 1.928847 0 0 0 -129 2 6.451084 3.683524 9.993466 0 0 0 -130 2 4.759720 4.788851 7.159536 0 0 0 -131 2 6.439782 3.792200 15.076794 0 0 0 -132 2 4.874556 4.737325 12.685581 0 0 0 -133 2 4.931715 6.618800 4.597670 0 0 0 -134 2 3.179945 7.504749 1.897157 0 0 0 -135 2 4.960424 6.599224 10.008995 0 0 0 -136 2 3.324010 7.493161 7.207547 0 0 0 -137 2 4.920153 6.672125 15.276128 0 0 0 -138 2 3.333233 7.546487 12.579893 0 0 0 -139 2 3.313358 9.374411 4.742812 0 0 0 -140 2 1.511575 10.418087 1.858969 0 0 0 -141 2 3.259837 9.353261 9.784308 0 0 0 -142 2 1.682010 10.338211 7.357602 0 0 0 -143 2 3.264903 9.445174 15.214806 0 0 0 -144 2 1.739169 10.396262 12.552005 0 0 0 -145 2 11.441775 0.931445 4.731245 0 0 0 -146 2 9.696761 1.982164 1.915854 0 0 0 -147 2 11.255751 0.994041 10.013748 0 0 0 -148 2 9.852647 1.836137 7.364257 0 0 0 -149 2 11.376693 0.929251 15.292131 0 0 0 -150 2 9.860312 1.779661 12.615862 0 0 0 -151 2 9.674028 3.727287 4.553620 0 0 0 -152 2 8.205451 4.798976 2.033585 0 0 0 -153 2 9.795879 3.847326 9.968272 0 0 0 -154 2 8.136862 4.660711 7.310542 0 0 0 -155 2 9.707283 3.729312 15.148890 0 0 0 -156 2 8.110881 4.688387 12.679718 0 0 0 -157 2 8.042810 6.526323 4.650593 0 0 0 -158 2 6.491874 7.446586 2.011401 0 0 0 -159 2 8.217403 6.463773 9.889997 0 0 0 -160 2 6.387301 7.514312 7.280436 0 0 0 -161 2 8.188694 6.502586 15.218292 0 0 0 -162 2 6.484599 7.581362 12.600650 0 0 0 -163 2 6.457319 9.340773 4.549024 0 0 0 -164 2 4.989003 10.267223 1.877825 0 0 0 -165 2 6.459268 9.429537 9.973977 0 0 0 -166 2 4.923661 10.201522 7.228146 0 0 0 -167 2 6.599565 9.334248 15.221303 0 0 0 -168 2 4.818957 10.228297 12.514294 0 0 0 -169 2 0.083139 1.983289 2.100927 0 0 0 -170 2 12.882422 1.838499 7.184255 0 0 0 -171 2 12.943218 1.984076 12.564999 0 0 0 -172 2 11.431383 4.764438 1.880519 0 0 0 -173 2 11.471394 4.598723 7.345560 0 0 0 -174 2 11.426317 4.736537 12.433483 0 0 0 -175 2 11.352661 6.564574 4.636649 0 0 0 -176 2 9.836279 7.540074 2.083022 0 0 0 -177 2 11.374744 6.665150 9.771474 0 0 0 -178 2 9.753660 7.450973 7.261897 0 0 0 -179 2 11.414755 6.496961 15.224789 0 0 0 -180 2 9.697670 7.585750 12.433483 0 0 0 -181 2 9.639603 9.478475 4.517017 0 0 0 -182 2 8.028781 10.235160 1.856117 0 0 0 -183 2 9.731056 9.413112 10.013748 0 0 0 -184 2 8.194409 10.360487 7.259203 0 0 0 -185 2 9.797048 9.478137 15.192306 0 0 0 -186 2 8.068402 10.377812 12.466124 0 0 0 -187 2 12.921524 7.492149 2.023919 0 0 0 -188 2 0.029878 7.415198 7.148761 0 0 0 -189 2 12.934514 7.553125 12.521582 0 0 0 -190 2 11.452168 10.410550 1.954200 0 0 0 -191 2 11.250295 10.328649 7.346352 0 0 0 -192 2 11.319925 10.311098 12.461529 0 0 0 diff --git a/examples/GaN-SNAP-LAMMPS/DATA/36/DATA b/examples/GaN-SNAP-LAMMPS/DATA/36/DATA deleted file mode 100755 index 546d281b..00000000 --- a/examples/GaN-SNAP-LAMMPS/DATA/36/DATA +++ /dev/null @@ -1,215 +0,0 @@ -LAMMPS DATA file - -192 atoms -0 bonds -0 angles -0 dihedrals -0 impropers - -2 atom types -0 bond types -0 angle types - -0.0 12.990503 xlo xhi -0.0 11.250148 ylo yhi -0.0 15.845291 zlo zhi - -Masses - -1 69.723 -2 14.0067 - -Atoms - -1 1 1.534178 1.048683 2.619702 0 0 0 -2 1 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7.799844 0 0 0 -28 1 6.424583 1.803286 10.612542 0 0 0 -29 1 8.073858 1.002894 13.213546 0 0 0 -30 1 6.425233 1.917025 15.696979 0 0 0 -31 1 6.514088 3.861163 2.591973 0 0 0 -32 1 4.886638 4.783676 5.200107 0 0 0 -33 1 6.581638 3.676998 8.037524 0 0 0 -34 1 4.814151 4.766238 10.655166 0 0 0 -35 1 6.414451 3.857676 13.120851 0 0 0 -36 1 4.943796 4.757463 15.839111 0 0 0 -37 1 4.979390 6.472773 2.520035 0 0 0 -38 1 3.340768 7.391797 5.348578 0 0 0 -39 1 4.953669 6.476260 7.913613 0 0 0 -40 1 3.208005 7.561675 10.490058 0 0 0 -41 1 4.955747 6.488973 13.314164 0 0 0 -42 1 3.358305 7.430610 15.697296 0 0 0 -43 1 3.260227 9.264722 2.739492 0 0 0 -44 1 1.729945 10.358799 5.194879 0 0 0 -45 1 3.270749 9.473862 8.042436 0 0 0 -46 1 1.651353 10.378374 10.664514 0 0 0 -47 1 3.263214 9.262810 13.120059 0 0 0 -48 1 1.606146 10.297036 0.114086 0 0 0 -49 1 11.254322 0.901486 2.533028 0 0 0 -50 1 9.676886 1.926250 5.209139 0 0 0 -51 1 11.298490 0.856429 7.828683 0 0 0 -52 1 9.825367 1.847612 10.610482 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7.996954 4.719550 2.093321 0 0 0 -153 2 9.715597 3.735949 9.777178 0 0 0 -154 2 8.140239 4.771188 7.175064 0 0 0 -155 2 9.637524 3.679811 15.243803 0 0 0 -156 2 8.179470 4.717075 12.539646 0 0 0 -157 2 8.070870 6.594387 4.646631 0 0 0 -158 2 6.537731 7.415648 2.041349 0 0 0 -159 2 8.165960 6.659413 10.012956 0 0 0 -160 2 6.411593 7.601163 7.172688 0 0 0 -161 2 8.045668 6.451960 15.127340 0 0 0 -162 2 6.436664 7.519599 12.516829 0 0 0 -163 2 6.413801 9.351011 4.517492 0 0 0 -164 2 4.957826 10.233810 2.043092 0 0 0 -165 2 6.560204 9.265960 9.795400 0 0 0 -166 2 4.749458 10.382087 7.124360 0 0 0 -167 2 6.538380 9.365186 15.286586 0 0 0 -168 2 4.834676 10.205797 12.460420 0 0 0 -169 2 0.054560 1.886087 2.103304 0 0 0 -170 2 0.062354 1.785736 7.417339 0 0 0 -171 2 0.062354 1.765598 12.606513 0 0 0 -172 2 11.362923 4.582860 1.863882 0 0 0 -173 2 11.256661 4.711787 7.183462 0 0 0 -174 2 11.273678 4.694349 12.686057 0 0 0 -175 2 11.397088 6.605300 4.542845 0 0 0 -176 2 9.666753 7.395960 2.037863 0 0 0 -177 2 11.368639 6.559399 10.023414 0 0 0 -178 2 9.863819 7.558525 7.187582 0 0 0 -179 2 11.412547 6.620937 15.217817 0 0 0 -180 2 9.826666 7.596100 12.593203 0 0 0 -181 2 9.617909 9.304098 4.477087 0 0 0 -182 2 8.232082 10.309186 2.079536 0 0 0 -183 2 9.731706 9.373849 9.885243 0 0 0 -184 2 8.220910 10.396824 7.310066 0 0 0 -185 2 9.688967 9.328285 15.109911 0 0 0 -186 2 8.172196 10.374437 12.651989 0 0 0 -187 2 0.079242 7.444673 2.081437 0 0 0 -188 2 0.033775 7.439723 7.230206 0 0 0 -189 2 12.978292 7.500249 12.562463 0 0 0 -190 2 11.326420 10.265760 2.050698 0 0 0 -191 2 11.479448 10.333824 7.297390 0 0 0 -192 2 11.428655 10.283986 12.534892 0 0 0 diff --git a/examples/GaN-SNAP-LAMMPS/DATA/37/DATA b/examples/GaN-SNAP-LAMMPS/DATA/37/DATA deleted file mode 100755 index 467f931c..00000000 --- a/examples/GaN-SNAP-LAMMPS/DATA/37/DATA +++ /dev/null @@ -1,215 +0,0 @@ -LAMMPS DATA file - -192 atoms -0 bonds -0 angles -0 dihedrals -0 impropers - -2 atom types -0 bond types -0 angle types - -0.0 12.990503 xlo xhi -0.0 11.250148 ylo yhi -0.0 15.845291 zlo zhi - -Masses - -1 69.723 -2 14.0067 - -Atoms - -1 1 1.646416 0.842827 2.538099 0 0 0 -2 1 1.695391 0.904523 8.024530 0 0 0 -3 1 1.528722 0.982093 13.100728 0 0 0 -4 1 12.963695 3.713786 2.769281 0 0 0 -5 1 0.087922 3.779150 8.032929 0 0 0 -6 1 12.916794 3.652136 13.255378 0 0 0 -7 1 4.880532 0.941412 2.558064 0 0 0 -8 1 3.339339 1.947738 5.123099 0 0 0 -9 1 4.864814 1.037444 7.904106 0 0 0 -10 1 3.338559 1.883050 10.537118 0 0 0 -11 1 4.747899 0.938487 13.318284 0 0 0 -12 1 3.353628 1.826687 15.723440 0 0 0 -13 1 3.117721 3.709061 2.644896 0 0 0 -14 1 1.709290 4.726637 5.407205 0 0 0 -15 1 3.314137 3.675423 8.064144 0 0 0 -16 1 1.584452 4.709762 10.631398 0 0 0 -17 1 3.344015 3.712549 13.187243 0 0 0 -18 1 1.537296 4.679949 15.825959 0 0 0 -19 1 1.527164 6.594049 2.761042 0 0 0 -20 1 1.604977 6.489648 7.852134 0 0 0 -21 1 1.509107 6.463660 13.048914 0 0 0 -22 1 0.013114 9.389261 2.573434 0 0 0 -23 1 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0.862380 10.066672 0 0 0 -148 2 9.720923 1.932213 7.329239 0 0 0 -149 2 11.436969 1.030266 15.130510 0 0 0 -150 2 9.666104 1.778873 12.577358 0 0 0 -151 2 9.753919 3.782412 4.658040 0 0 0 -152 2 8.106074 4.611661 2.070029 0 0 0 -153 2 9.868496 3.669798 10.012639 0 0 0 -154 2 8.218052 4.590960 7.260946 0 0 0 -155 2 9.804972 3.802663 15.290705 0 0 0 -156 2 8.127768 4.701212 12.500984 0 0 0 -157 2 8.132315 6.454885 4.702090 0 0 0 -158 2 6.582028 7.575737 1.838212 0 0 0 -159 2 8.226106 6.471423 10.019928 0 0 0 -160 2 6.500967 7.391235 7.150346 0 0 0 -161 2 8.143227 6.612500 15.043836 0 0 0 -162 2 6.411073 7.439948 12.617763 0 0 0 -163 2 6.565530 9.395224 4.745189 0 0 0 -164 2 4.859487 10.421575 1.910150 0 0 0 -165 2 6.544745 9.396911 9.838816 0 0 0 -166 2 4.814021 10.353961 7.366476 0 0 0 -167 2 6.385092 9.345723 15.287536 0 0 0 -168 2 4.990562 10.423712 12.526019 0 0 0 -169 2 12.973096 1.838724 1.971788 0 0 0 -170 2 0.070149 1.932550 7.423994 0 0 0 -171 2 12.913340 1.847049 12.615862 0 0 0 -172 2 11.279264 4.647999 2.084131 0 0 0 -173 2 11.293684 4.648899 7.255875 0 0 0 -174 2 11.328368 4.591635 12.551372 0 0 0 -175 2 11.307973 6.577849 4.477245 0 0 0 -176 2 9.772366 7.482924 2.032159 0 0 0 -177 2 11.316287 6.515523 9.886827 0 0 0 -178 2 9.755998 7.415198 7.150821 0 0 0 -179 2 11.296282 6.474123 15.061582 0 0 0 -180 2 9.661947 7.541424 12.562780 0 0 0 -181 2 9.748463 9.474537 4.670558 0 0 0 -182 2 8.175833 10.295686 1.906347 0 0 0 -183 2 9.856155 9.443149 9.991723 0 0 0 -184 2 8.005138 10.404137 7.317197 0 0 0 -185 2 9.859272 9.385324 15.128925 0 0 0 -186 2 8.012153 10.295011 12.507639 0 0 0 -187 2 0.092233 7.609038 1.844709 0 0 0 -188 2 12.953350 7.612413 7.240981 0 0 0 -189 2 12.959456 7.411148 12.577992 0 0 0 -190 2 11.274847 10.284886 2.124378 0 0 0 -191 2 11.418782 10.254848 7.344609 0 0 0 -192 2 11.321613 10.283423 12.547410 0 0 0 diff --git a/examples/GaN-SNAP-LAMMPS/DATA/38/DATA b/examples/GaN-SNAP-LAMMPS/DATA/38/DATA deleted file mode 100755 index 60dde31b..00000000 --- a/examples/GaN-SNAP-LAMMPS/DATA/38/DATA +++ /dev/null @@ -1,215 +0,0 @@ -LAMMPS DATA file - -192 atoms -0 bonds -0 angles -0 dihedrals -0 impropers - -2 atom types -0 bond types -0 angle types - -0.0 12.990503 xlo xhi -0.0 11.250148 ylo yhi -0.0 15.845291 zlo zhi - -Masses - -1 69.723 -2 14.0067 - -Atoms - -1 1 1.657718 0.885960 2.537306 0 0 0 -2 1 1.749171 0.917326 7.955603 0 0 0 -3 1 1.734362 0.967198 13.089161 0 0 0 -4 1 12.920813 3.848788 2.633012 0 0 0 -5 1 12.986714 3.757775 8.043386 0 0 0 -6 1 12.986110 3.653936 13.282949 0 0 0 -7 1 4.867022 0.862976 2.570106 0 0 0 -8 1 3.189039 1.828262 5.416079 0 0 0 -9 1 4.847796 0.918935 7.906325 0 0 0 -10 1 3.199041 1.956288 10.575781 0 0 0 -11 1 4.885209 0.843052 13.152383 0 0 0 -12 1 3.204497 1.951676 15.777631 0 0 0 -13 1 3.204367 3.817288 2.667238 0 0 0 -14 1 1.519499 4.742837 5.227520 0 0 0 -15 1 3.187999 3.691174 8.026907 0 0 0 -16 1 1.640830 4.627523 10.486096 0 0 0 -17 1 3.349212 3.752824 13.296100 0 0 0 -18 1 1.728776 4.732600 15.837209 0 0 0 -19 1 1.600820 6.560974 2.656621 0 0 0 -20 1 1.707861 6.565587 7.823612 0 0 0 -21 1 1.620695 6.458148 13.050181 0 0 0 -22 1 0.023422 9.309273 2.669456 0 0 0 -23 1 12.886977 9.316248 8.023897 0 0 0 -24 1 0.107633 9.288460 13.096133 0 0 0 -25 1 8.230133 1.025249 2.788771 0 0 0 -26 1 6.545525 1.927038 5.413860 0 0 0 -27 1 8.175573 0.932199 7.945462 0 0 0 -28 1 6.550851 1.787536 10.657859 0 0 0 -29 1 8.114518 0.978808 13.323671 0 0 0 -30 1 6.545005 1.764698 15.777314 0 0 0 -31 1 6.507593 3.776675 2.646480 0 0 0 -32 1 4.747120 4.695699 5.123733 0 0 0 -33 1 6.579040 3.806600 7.907909 0 0 0 -34 1 4.941717 4.705374 10.500833 0 0 0 -35 1 6.460047 3.675198 13.156503 0 0 0 -36 1 4.965360 4.585110 0.141023 0 0 0 -37 1 4.746080 6.559849 2.597994 0 0 0 -38 1 3.296080 7.512961 5.399441 0 0 0 -39 1 4.889496 6.609237 7.919159 0 0 0 -40 1 3.285948 7.431285 10.550270 0 0 0 -41 1 4.767255 6.664025 13.156979 0 0 0 -42 1 3.340378 7.607913 15.778740 0 0 0 -43 1 3.335442 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15.165686 0 0 0 -168 2 4.839482 10.329549 12.661972 0 0 0 -169 2 0.089634 1.940088 1.875290 0 0 0 -170 2 0.029878 1.802161 7.256351 0 0 0 -171 2 12.872030 1.952351 12.560879 0 0 0 -172 2 11.476460 4.739687 1.952298 0 0 0 -173 2 11.396309 4.711900 7.393413 0 0 0 -174 2 11.488801 4.704362 12.498924 0 0 0 -175 2 11.465288 6.665375 4.704150 0 0 0 -176 2 9.851868 7.539174 2.124853 0 0 0 -177 2 11.273029 6.566712 9.903465 0 0 0 -178 2 9.732095 7.554925 7.267443 0 0 0 -179 2 11.277186 6.601137 15.288170 0 0 0 -180 2 9.779641 7.486749 12.473413 0 0 0 -181 2 9.765481 9.332785 4.729502 0 0 0 -182 2 8.074637 10.325949 2.115029 0 0 0 -183 2 9.627911 9.415474 9.974769 0 0 0 -184 2 8.235719 10.415500 7.368060 0 0 0 -185 2 9.837448 9.300273 15.135738 0 0 0 -186 2 8.189993 10.207934 12.403377 0 0 0 -187 2 0.128606 7.437135 2.038972 0 0 0 -188 2 12.978942 7.448948 7.202318 0 0 0 -189 2 0.113017 7.582375 12.422232 0 0 0 -190 2 11.271600 10.351599 1.959270 0 0 0 -191 2 11.369288 10.201184 7.357602 0 0 0 -192 2 11.240033 10.353399 12.675916 0 0 0 diff --git a/examples/GaN-SNAP-LAMMPS/DATA/39/DATA b/examples/GaN-SNAP-LAMMPS/DATA/39/DATA deleted file mode 100755 index 163da42b..00000000 --- a/examples/GaN-SNAP-LAMMPS/DATA/39/DATA +++ /dev/null @@ -1,215 +0,0 @@ -LAMMPS DATA file - -192 atoms -0 bonds -0 angles -0 dihedrals -0 impropers - -2 atom types -0 bond types -0 angle types - -0.0 12.990503 xlo xhi -0.0 11.250148 ylo yhi -0.0 15.845291 zlo zhi - -Masses - -1 69.723 -2 14.0067 - -Atoms - -1 1 1.552885 0.873990 2.502288 0 0 0 -2 1 1.634335 0.958693 7.782256 0 0 0 -3 1 1.541193 0.917843 13.093597 0 0 0 -4 1 0.099353 3.842376 2.613364 0 0 0 -5 1 12.894571 3.751587 8.010904 0 0 0 -6 1 0.025802 3.790625 13.188352 0 0 0 -7 1 4.926518 0.890078 2.485968 0 0 0 -8 1 3.247366 1.806436 5.423209 0 0 0 -9 1 4.939769 0.962889 7.881131 0 0 0 -10 1 3.354538 1.883050 10.637102 0 0 0 -11 1 4.847536 0.901767 13.277244 0 0 0 -12 1 3.326868 1.851212 0.082396 0 0 0 -13 1 3.249704 3.726274 2.598311 0 0 0 -14 1 1.723450 4.739350 5.360620 0 0 0 -15 1 3.244768 3.729312 8.035781 0 0 0 -16 1 1.558211 4.578923 10.430479 0 0 0 -17 1 3.327777 3.858351 13.197543 0 0 0 -18 1 1.605496 4.731700 15.750536 0 0 0 -19 1 1.513783 6.553774 2.598628 0 0 0 -20 1 1.556522 6.621162 8.064619 0 0 0 -21 1 1.518590 6.625550 13.100252 0 0 0 -22 1 12.863065 9.354836 2.521778 0 0 0 -23 1 0.008513 9.388136 7.978421 0 0 0 -24 1 0.097786 9.267085 13.258072 0 0 0 -25 1 8.245462 1.046804 2.621445 0 0 0 -26 1 6.455760 1.983739 5.271728 0 0 0 -27 1 8.071000 0.910823 7.764351 0 0 0 -28 1 6.496161 1.791136 10.496237 0 0 0 -29 1 8.055671 0.825525 13.285325 0 0 0 -30 1 6.537341 1.852112 15.840220 0 0 0 -31 1 6.524480 3.667436 2.566779 0 0 0 -32 1 4.959125 4.769950 5.135142 0 0 0 -33 1 6.493433 3.824375 8.049725 0 0 0 -34 1 4.949642 4.795263 10.580693 0 0 0 -35 1 6.381974 3.656973 13.349974 0 0 0 -36 1 4.858058 4.776250 0.125178 0 0 0 -37 1 4.991341 6.625100 2.777363 0 0 0 -38 1 3.294132 7.548287 5.161445 0 0 0 -39 1 4.763098 6.475360 7.875743 0 0 0 -40 1 3.368567 7.469086 10.694462 0 0 0 -41 1 4.766475 6.477498 13.195324 0 0 0 -42 1 3.357396 7.417898 15.727085 0 0 0 -43 1 3.204367 9.364961 2.479630 0 0 0 -44 1 1.600040 10.240785 5.394529 0 0 0 -45 1 3.260357 9.456425 7.775601 0 0 0 -46 1 1.626671 10.232910 10.538544 0 0 0 -47 1 3.236064 9.334248 13.333812 0 0 0 -48 1 1.681361 10.343386 0.136269 0 0 0 -49 1 11.426577 0.942447 2.682132 0 0 0 -50 1 9.804193 1.958538 5.392628 0 0 0 -51 1 11.296282 0.892744 7.888578 0 0 0 -52 1 9.662986 1.806324 10.446959 0 0 0 -53 1 11.458923 1.034417 13.287544 0 0 0 -54 1 9.654152 1.926588 15.742613 0 0 0 -55 1 9.731965 3.830000 2.518767 0 0 0 -56 1 8.148683 4.718762 5.356184 0 0 0 -57 1 9.679614 3.761037 8.055904 0 0 0 -58 1 8.235979 4.711337 10.656433 0 0 0 -59 1 9.694813 3.698824 13.176310 0 0 0 -60 1 8.183368 4.679724 0.147361 0 0 0 -61 1 8.209608 6.522498 2.533504 0 0 0 -62 1 6.587484 7.581137 5.151146 0 0 0 -63 1 8.186745 6.481435 7.951167 0 0 0 -64 1 6.571246 7.435223 10.409722 0 0 0 -65 1 8.197917 6.458935 13.275343 0 0 0 -66 1 6.453552 7.481236 15.742772 0 0 0 -67 1 6.611387 9.293072 2.625723 0 0 0 -68 1 4.962762 10.255635 5.254615 0 0 0 -69 1 6.623598 9.471387 7.772273 0 0 0 -70 1 4.883780 10.200509 10.629338 0 0 0 -71 1 6.526169 9.346398 13.133686 0 0 0 -72 1 4.755823 10.357786 0.118840 0 0 0 -73 1 0.058457 1.894300 5.419565 0 0 0 -74 1 12.954260 1.783036 10.553914 0 0 0 -75 1 12.903597 1.820386 15.681926 0 0 0 -76 1 11.435020 4.746888 5.122782 0 0 0 -77 1 11.268872 4.593211 10.424300 0 0 0 -78 1 11.390333 4.686699 15.837526 0 0 0 -79 1 11.405142 6.639275 2.482323 0 0 0 -80 1 9.832252 7.561225 5.209456 0 0 0 -81 1 11.418782 6.655475 8.058123 0 0 0 -82 1 9.682601 7.422285 10.516995 0 0 0 -83 1 11.294723 6.456010 13.097876 0 0 0 -84 1 9.676366 7.611963 0.044367 0 0 0 -85 1 9.643630 9.448212 2.708752 0 0 0 -86 1 8.174794 10.325499 5.238612 0 0 0 -87 1 9.703256 9.281822 7.825989 0 0 0 -88 1 8.012153 10.371062 10.421606 0 0 0 -89 1 9.765221 9.326260 13.205782 0 0 0 -90 1 8.242344 10.354074 15.808529 0 0 0 -91 1 12.887878 7.480899 5.291376 0 0 0 -92 1 12.920744 7.388985 10.571027 0 0 0 -93 1 0.098728 7.472798 0.098241 0 0 0 -94 1 11.276406 10.335174 5.383437 0 0 0 -95 1 11.320574 10.291523 10.530939 0 0 0 -96 1 11.386956 10.229085 15.714408 0 0 0 -97 2 1.531191 0.923952 4.618110 0 0 0 -98 2 1.672267 0.905862 9.848482 0 0 0 -99 2 1.504560 1.038209 15.055720 0 0 0 -100 2 0.116839 3.689824 4.495626 0 0 0 -101 2 0.059369 3.807163 10.034030 0 0 0 -102 2 0.026744 3.745962 15.133679 0 0 0 -103 2 4.861826 0.927946 4.655505 0 0 0 -104 2 3.308551 1.987339 2.089994 0 0 0 -105 2 4.814151 1.012165 9.917726 0 0 0 -106 2 3.119669 1.932888 7.378993 0 0 0 -107 2 4.799991 0.926213 15.313364 0 0 0 -108 2 3.141753 1.874162 12.463747 0 0 0 -109 2 3.146430 3.738874 4.478671 0 0 0 -110 2 1.554574 4.685687 1.936770 0 0 0 -111 2 3.271269 3.689824 10.032446 0 0 0 -112 2 1.641350 4.761850 7.162705 0 0 0 -113 2 3.199301 3.767225 15.070614 0 0 0 -114 2 1.667591 4.615711 12.447585 0 0 0 -115 2 1.704354 6.462985 4.653445 0 0 0 -116 2 1.676814 6.653563 9.842144 0 0 0 -117 2 1.717345 6.542299 15.348382 0 0 0 -118 2 0.030235 9.478700 4.480890 0 0 0 -119 2 12.907441 9.287560 9.809344 0 0 0 -120 2 0.098081 9.401074 15.272166 0 0 0 -121 2 8.130756 0.869243 4.709696 0 0 0 -122 2 6.410034 1.956401 2.091261 0 0 0 -123 2 8.183757 0.987279 9.916141 0 0 0 -124 2 6.602293 1.825674 7.144483 0 0 0 -125 2 8.081262 0.851512 15.224155 0 0 0 -126 2 6.458878 1.891937 12.587499 0 0 0 -127 2 6.552670 3.762950 4.610980 0 0 0 -128 2 4.831298 4.588598 1.968460 0 0 0 -129 2 6.422765 3.800638 9.985702 0 0 0 -130 2 4.809344 4.575998 7.358394 0 0 0 -131 2 6.621779 3.774425 15.146038 0 0 0 -132 2 4.992120 4.771525 12.529188 0 0 0 -133 2 4.781415 6.596637 4.519394 0 0 0 -134 2 3.200730 7.421048 1.878776 0 0 0 -135 2 4.807006 6.558611 9.886035 0 0 0 -136 2 3.350251 7.452323 7.204537 0 0 0 -137 2 4.888326 6.622737 15.319385 0 0 0 -138 2 3.212811 7.456486 12.582587 0 0 0 -139 2 3.244768 9.317598 4.745031 0 0 0 -140 2 1.631997 10.364762 1.955943 0 0 0 -141 2 3.305304 9.420987 9.844521 0 0 0 -142 2 1.514823 10.339449 7.257935 0 0 0 -143 2 3.365320 9.338073 15.251884 0 0 0 -144 2 1.614720 10.257210 12.542498 0 0 0 -145 2 11.395789 0.925977 4.495943 0 0 0 -146 2 9.865768 1.807224 1.856117 0 0 0 -147 2 11.377862 0.861548 9.751826 0 0 0 -148 2 9.754829 1.904425 7.234009 0 0 0 -149 2 11.384228 0.843739 15.190880 0 0 0 -150 2 9.635316 1.819261 12.446000 0 0 0 -151 2 9.621416 3.834726 4.486911 0 0 0 -152 2 8.110621 4.711675 1.941048 0 0 0 -153 2 9.728978 3.816725 10.008202 0 0 0 -154 2 8.067882 4.630561 7.232900 0 0 0 -155 2 9.655711 3.806600 15.051283 0 0 0 -156 2 8.012932 4.786601 12.576249 0 0 0 -157 2 8.212077 6.535661 4.582775 0 0 0 -158 2 6.441211 7.406873 2.032317 0 0 0 -159 2 8.231562 6.572562 9.962726 0 0 0 -160 2 6.605671 7.516899 7.398800 0 0 0 -161 2 8.230133 6.514848 15.330160 0 0 0 -162 2 6.576962 7.505761 12.650880 0 0 0 -163 2 6.546304 9.459350 4.648533 0 0 0 -164 2 4.917815 10.206584 2.068286 0 0 0 -165 2 6.410943 9.388586 9.918993 0 0 0 -166 2 4.820516 10.357674 7.411159 0 0 0 -167 2 6.506943 9.320860 15.038765 0 0 0 -168 2 4.938340 10.201859 12.475314 0 0 0 -169 2 0.012991 1.793724 1.969094 0 0 0 -170 2 12.897491 1.959551 7.283763 0 0 0 -171 2 0.022084 1.881925 12.663556 0 0 0 -172 2 11.368509 4.740700 2.099501 0 0 0 -173 2 11.266534 4.672524 7.199625 0 0 0 -174 2 11.462430 4.590173 12.584964 0 0 0 -175 2 11.326290 6.510798 4.649325 0 0 0 -176 2 9.647267 7.418010 2.124061 0 0 0 -177 2 11.323952 6.494598 9.773058 0 0 0 -178 2 9.849919 7.602963 7.223393 0 0 0 -179 2 11.261727 6.651088 15.153644 0 0 0 -180 2 9.654022 7.531974 12.403377 0 0 0 -181 2 9.630380 9.383861 4.759608 0 0 0 -182 2 8.032418 10.228185 1.832032 0 0 0 -183 2 9.811207 9.425262 10.021037 0 0 0 -184 2 8.054112 10.338436 7.124835 0 0 0 -185 2 9.642331 9.340998 15.181690 0 0 0 -186 2 8.009814 10.353624 12.557710 0 0 0 -187 2 0.003897 7.599138 1.869427 0 0 0 -188 2 0.038972 7.578212 7.219114 0 0 0 -189 2 12.878265 7.390222 12.393394 0 0 0 -190 2 11.312780 10.249110 1.923301 0 0 0 -191 2 11.391502 10.326961 7.178550 0 0 0 -192 2 11.338241 10.276223 12.627587 0 0 0 diff --git a/examples/GaN-SNAP-LAMMPS/DATA/4/DATA b/examples/GaN-SNAP-LAMMPS/DATA/4/DATA deleted file mode 100755 index 9a6658f1..00000000 --- a/examples/GaN-SNAP-LAMMPS/DATA/4/DATA +++ /dev/null @@ -1,215 +0,0 @@ -LAMMPS DATA file - -192 atoms -0 bonds -0 angles -0 dihedrals -0 impropers - -2 atom types -0 bond types -0 angle types - -0.0 12.990503 xlo xhi -0.0 11.250148 ylo yhi -0.0 15.845291 zlo zhi - -Masses - -1 69.723 -2 14.0067 - -Atoms - -1 1 1.753458 0.990081 2.624772 0 0 0 -2 1 1.654081 0.854055 8.042911 0 0 0 -3 1 1.537166 0.875048 13.239533 0 0 0 -4 1 12.989006 3.741237 2.509736 0 0 0 -5 1 12.883484 3.841701 7.885092 0 0 0 -6 1 12.866953 3.742587 13.312421 0 0 0 -7 1 4.965880 0.938735 2.631586 0 0 0 -8 1 3.179296 1.980926 5.164139 0 0 0 -9 1 4.773101 0.894612 8.037524 0 0 0 -10 1 3.190468 1.897788 10.484987 0 0 0 -11 1 4.978870 0.961224 13.091854 0 0 0 -12 1 3.356746 1.786524 15.726768 0 0 0 -13 1 3.283869 3.697136 2.480105 0 0 0 -14 1 1.715396 4.644399 5.405779 0 0 0 -15 1 3.236844 3.711536 8.072859 0 0 0 -16 1 1.705263 4.641474 10.677191 0 0 0 -17 1 3.200081 3.853513 13.334763 0 0 0 -18 1 1.622774 4.685687 0.150530 0 0 0 -19 1 1.596533 6.663238 2.505933 0 0 0 -20 1 1.593415 6.614412 7.995217 0 0 0 -21 1 1.538985 6.531499 13.249990 0 0 0 -22 1 0.033197 9.425712 2.690055 0 0 0 -23 1 12.871744 9.330085 7.913138 0 0 0 -24 1 12.949956 9.279572 13.146996 0 0 0 -25 1 8.020986 0.857126 2.596251 0 0 0 -26 1 6.562413 1.957076 5.389300 0 0 0 -27 1 8.023714 1.019241 7.947047 0 0 0 -28 1 6.518764 1.969113 10.417328 0 0 0 -29 1 8.172196 0.937059 13.156345 0 0 0 -30 1 6.624637 1.977439 15.844023 0 0 0 -31 1 6.539549 3.637960 2.633170 0 0 0 -32 1 4.879623 4.643836 5.390251 0 0 0 -33 1 6.382494 3.757775 7.760706 0 0 0 -34 1 4.913528 4.696262 10.540763 0 0 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8.225327 4.748800 15.720747 0 0 0 -61 1 8.238447 6.526548 2.669773 0 0 0 -62 1 6.514867 7.609488 5.430498 0 0 0 -63 1 8.108542 6.534761 7.768788 0 0 0 -64 1 6.552150 7.444223 10.528562 0 0 0 -65 1 8.203763 6.577624 13.223053 0 0 0 -66 1 6.444329 7.452773 15.767332 0 0 0 -67 1 6.549682 9.316698 2.654403 0 0 0 -68 1 4.826232 10.262723 5.202009 0 0 0 -69 1 6.495901 9.390386 7.798735 0 0 0 -70 1 4.754264 10.383099 10.463438 0 0 0 -71 1 6.552150 9.416712 13.092488 0 0 0 -72 1 4.961593 10.307273 0.060212 0 0 0 -73 1 12.937762 1.813524 5.403878 0 0 0 -74 1 0.031177 1.814761 10.589725 0 0 0 -75 1 12.895543 1.774598 15.746574 0 0 0 -76 1 11.296412 4.719212 5.187431 0 0 0 -77 1 11.410598 4.723825 10.495762 0 0 0 -78 1 11.384098 4.722137 0.047536 0 0 0 -79 1 11.367600 6.457135 2.718893 0 0 0 -80 1 9.817443 7.573037 5.239087 0 0 0 -81 1 11.328628 6.524411 7.981273 0 0 0 -82 1 9.712739 7.394610 10.544249 0 0 0 -83 1 11.309402 6.525761 13.056995 0 0 0 -84 1 9.753270 7.473361 0.152115 0 0 0 -85 1 9.750542 9.462050 2.735373 0 0 0 -86 1 8.073468 10.260023 5.205812 0 0 0 -87 1 9.808999 9.482862 7.962259 0 0 0 -88 1 8.210518 10.392549 10.576731 0 0 0 -89 1 9.678704 9.347411 13.213229 0 0 0 -90 1 8.000851 10.275435 0.090318 0 0 0 -91 1 12.988814 7.445798 5.208030 0 0 0 -92 1 0.081840 7.520612 10.524442 0 0 0 -93 1 12.889437 7.611850 15.683035 0 0 0 -94 1 11.302128 10.350924 5.314669 0 0 0 -95 1 11.346425 10.341924 10.412099 0 0 0 -96 1 11.352661 10.273973 0.088734 0 0 0 -97 2 1.716175 1.032764 4.562335 0 0 0 -98 2 1.728386 0.846439 9.875577 0 0 0 -99 2 1.670059 0.859534 15.052709 0 0 0 -100 2 12.888237 3.659223 4.594025 0 0 0 -101 2 0.126053 3.765537 9.839767 0 0 0 -102 2 0.043812 3.776900 15.322238 0 0 0 -103 2 4.795444 0.836482 4.691315 0 0 0 -104 2 3.159160 1.913538 1.849304 0 0 0 -105 2 4.749328 1.014381 9.989188 0 0 0 -106 2 3.143182 1.809474 7.137036 0 0 0 -107 2 4.966399 0.830542 15.111812 0 0 0 -108 2 3.277634 1.867862 12.625211 0 0 0 -109 2 3.168384 3.760925 4.614149 0 0 0 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1.888283 0 0 0 -135 2 4.896380 6.630837 9.822337 0 0 0 -136 2 3.341807 7.588787 7.191702 0 0 0 -137 2 4.950161 6.527561 15.077428 0 0 0 -138 2 3.321022 7.585862 12.654366 0 0 0 -139 2 3.217358 9.307023 4.630945 0 0 0 -140 2 1.566135 10.223347 1.887808 0 0 0 -141 2 3.151366 9.316810 9.928818 0 0 0 -142 2 1.683180 10.370387 7.156050 0 0 0 -143 2 3.149158 9.300048 15.171073 0 0 0 -144 2 1.571071 10.322236 12.684155 0 0 0 -145 2 11.302387 0.959919 4.545063 0 0 0 -146 2 9.701048 1.911963 1.845659 0 0 0 -147 2 11.493737 1.028410 10.002023 0 0 0 -148 2 9.635056 1.971363 7.285665 0 0 0 -149 2 11.312650 0.827831 15.164735 0 0 0 -150 2 9.872653 1.914100 12.565474 0 0 0 -151 2 9.813546 3.709511 4.687037 0 0 0 -152 2 8.083990 4.591523 2.118515 0 0 0 -153 2 9.639733 3.805925 9.998854 0 0 0 -154 2 8.080872 4.579823 7.114694 0 0 0 -155 2 9.701048 3.799625 15.317801 0 0 0 -156 2 8.112180 4.587585 12.520473 0 0 0 -157 2 8.076456 6.518561 4.562493 0 0 0 -158 2 6.617752 7.517012 1.902861 0 0 0 -159 2 8.225976 6.458598 9.926916 0 0 0 -160 2 6.540588 7.597450 7.422726 0 0 0 -161 2 8.033977 6.450722 15.071090 0 0 0 -162 2 6.408085 7.516224 12.571020 0 0 0 -163 2 6.562153 9.287447 4.701615 0 0 0 -164 2 4.880012 10.304573 2.015996 0 0 0 -165 2 6.620740 9.344823 9.837707 0 0 0 -166 2 4.826751 10.399862 7.355225 0 0 0 -167 2 6.425493 9.409061 15.042251 0 0 0 -168 2 4.994848 10.225935 12.436335 0 0 0 -169 2 0.057158 1.836249 2.042458 0 0 0 -170 2 12.886969 1.888450 7.148286 0 0 0 -171 2 12.925811 1.890812 12.394028 0 0 0 -172 2 11.358506 4.641249 1.909833 0 0 0 -173 2 11.371757 4.687824 7.129905 0 0 0 -174 2 11.362793 4.759375 12.600334 0 0 0 -175 2 11.287188 6.665825 4.770859 0 0 0 -176 2 9.848620 7.473361 2.031049 0 0 0 -177 2 11.449959 6.543874 9.977779 0 0 0 -178 2 9.829264 7.538162 7.285982 0 0 0 -179 2 11.486203 6.651425 15.072040 0 0 0 -180 2 9.730666 7.455811 12.431423 0 0 0 -181 2 9.696242 9.345723 4.740119 0 0 0 -182 2 8.036185 10.222447 1.833300 0 0 0 -183 2 9.820301 9.320298 9.864327 0 0 0 -184 2 8.199216 10.327524 7.357285 0 0 0 -185 2 9.739760 9.361923 15.139224 0 0 0 -186 2 8.003449 10.355874 12.396880 0 0 0 -187 2 12.970108 7.585862 1.828230 0 0 0 -188 2 0.000000 7.557400 7.323535 0 0 0 -189 2 12.907624 7.611738 12.673697 0 0 0 -190 2 11.417613 10.223122 2.103938 0 0 0 -191 2 11.472823 10.404025 7.289151 0 0 0 -192 2 11.342788 10.222785 12.563572 0 0 0 diff --git a/examples/GaN-SNAP-LAMMPS/DATA/40/DATA b/examples/GaN-SNAP-LAMMPS/DATA/40/DATA deleted file mode 100755 index 23635ec5..00000000 --- a/examples/GaN-SNAP-LAMMPS/DATA/40/DATA +++ /dev/null @@ -1,215 +0,0 @@ -LAMMPS DATA file - -192 atoms -0 bonds -0 angles -0 dihedrals -0 impropers - -2 atom types -0 bond types -0 angle types - -0.0 12.990503 xlo xhi -0.0 11.250148 ylo yhi -0.0 15.845291 zlo zhi - -Masses - -1 69.723 -2 14.0067 - -Atoms - -1 1 1.665253 0.898381 2.483274 0 0 0 -2 1 1.642130 0.833186 7.842627 0 0 0 -3 1 1.543402 0.926101 13.284058 0 0 0 -4 1 0.033240 3.708386 2.569472 0 0 0 -5 1 12.880927 3.676211 7.987294 0 0 0 -6 1 12.883840 3.844063 13.176627 0 0 0 -7 1 4.762189 0.953743 2.740601 0 0 0 -8 1 3.208005 1.937951 5.342240 0 0 0 -9 1 4.895081 0.909833 7.883507 0 0 0 -10 1 3.229049 1.857737 10.468983 0 0 0 -11 1 4.870659 0.833985 13.219409 0 0 0 -12 1 3.130451 1.958763 0.109333 0 0 0 -13 1 3.205666 3.856663 2.779581 0 0 0 -14 1 1.750730 4.610536 5.118821 0 0 0 -15 1 3.182154 3.715474 7.832644 0 0 0 -16 1 1.690324 4.625948 10.541713 0 0 0 -17 1 3.185141 3.715361 13.326682 0 0 0 -18 1 1.497155 4.604798 15.804410 0 0 0 -19 1 1.712278 6.498086 2.773401 0 0 0 -20 1 1.745924 6.534536 8.070799 0 0 0 -21 1 1.525605 6.621275 13.224004 0 0 0 -22 1 0.031480 9.372836 2.546814 0 0 0 -23 1 12.898047 9.405574 8.012963 0 0 0 -24 1 0.044077 9.368786 13.339833 0 0 0 -25 1 8.142837 0.876027 2.693699 0 0 0 -26 1 6.448616 1.931088 5.434142 0 0 0 -27 1 8.059178 1.034687 7.979371 0 0 0 -28 1 6.390158 1.817799 10.695730 0 0 0 -29 1 8.113868 1.023583 13.287385 0 0 0 -30 1 6.370153 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1.048829 9.886194 0 0 0 -106 2 3.187220 1.868987 7.160487 0 0 0 -107 2 4.782843 0.885387 15.272008 0 0 0 -108 2 3.275945 1.980139 12.636302 0 0 0 -109 2 3.266592 3.738874 4.559482 0 0 0 -110 2 1.689415 4.596248 1.861505 0 0 0 -111 2 3.308681 3.717386 9.934363 0 0 0 -112 2 1.571591 4.735637 7.223710 0 0 0 -113 2 3.304394 3.861501 15.058572 0 0 0 -114 2 1.615499 4.596136 12.621091 0 0 0 -115 2 1.730855 6.469510 4.633321 0 0 0 -116 2 1.637453 6.604287 9.845313 0 0 0 -117 2 1.650314 6.494711 15.240159 0 0 0 -118 2 0.051537 9.366086 4.518602 0 0 0 -119 2 12.970183 9.396686 9.852443 0 0 0 -120 2 0.085928 9.290260 15.111654 0 0 0 -121 2 8.232731 0.972429 4.707160 0 0 0 -122 2 6.576053 1.773473 1.959112 0 0 0 -123 2 8.177652 0.856294 9.950842 0 0 0 -124 2 6.429520 1.951563 7.374557 0 0 0 -125 2 8.106853 0.913827 15.336815 0 0 0 -126 2 6.367425 1.852224 12.545826 0 0 0 -127 2 6.525909 3.653261 4.513848 0 0 0 -128 2 4.911449 4.624148 1.865466 0 0 0 -129 2 6.376518 3.674748 9.912338 0 0 0 -130 2 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11.334474 6.549386 15.195634 0 0 0 -180 2 9.690915 7.495186 12.393236 0 0 0 -181 2 9.657530 9.330873 4.704467 0 0 0 -182 2 8.140109 10.357899 2.082705 0 0 0 -183 2 9.834331 9.289135 9.958607 0 0 0 -184 2 8.184796 10.358124 7.301193 0 0 0 -185 2 9.622975 9.306573 15.136848 0 0 0 -186 2 8.156217 10.248998 12.415577 0 0 0 -187 2 0.124709 7.434098 2.139273 0 0 0 -188 2 0.028579 7.443436 7.273622 0 0 0 -189 2 0.055859 7.446023 12.427620 0 0 0 -190 2 11.379551 10.249335 1.926629 0 0 0 -191 2 11.489580 10.269698 7.409258 0 0 0 -192 2 11.343437 10.202422 12.489416 0 0 0 diff --git a/examples/GaN-SNAP-LAMMPS/DATA/41/DATA b/examples/GaN-SNAP-LAMMPS/DATA/41/DATA deleted file mode 100755 index 4f41fc4d..00000000 --- a/examples/GaN-SNAP-LAMMPS/DATA/41/DATA +++ /dev/null @@ -1,215 +0,0 @@ -LAMMPS DATA file - -192 atoms -0 bonds -0 angles -0 dihedrals -0 impropers - -2 atom types -0 bond types -0 angle types - -0.0 12.990503 xlo xhi -0.0 11.250148 ylo yhi -0.0 15.845291 zlo zhi - -Masses - -1 69.723 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11.450479 0.920240 7.790971 0 0 0 -52 1 9.638304 1.786411 10.595587 0 0 0 -53 1 11.289007 0.920228 13.296892 0 0 0 -54 1 9.698450 1.823987 0.095072 0 0 0 -55 1 9.666623 3.784775 2.659474 0 0 0 -56 1 8.135562 4.645861 5.163980 0 0 0 -57 1 9.646748 3.827188 7.909177 0 0 0 -58 1 8.049306 4.750825 10.615869 0 0 0 -59 1 9.654802 3.669348 13.252367 0 0 0 -60 1 8.160244 4.719887 15.740553 0 0 0 -61 1 8.202723 6.588199 2.772450 0 0 0 -62 1 6.537211 7.443661 5.132607 0 0 0 -63 1 7.998772 6.611712 7.835813 0 0 0 -64 1 6.403149 7.397535 10.655958 0 0 0 -65 1 8.207530 6.501686 13.277403 0 0 0 -66 1 6.438613 7.463686 15.785712 0 0 0 -67 1 6.382624 9.280022 2.633804 0 0 0 -68 1 4.839222 10.293886 5.314194 0 0 0 -69 1 6.537731 9.405574 7.866553 0 0 0 -70 1 4.934962 10.356661 10.585446 0 0 0 -71 1 6.594629 9.478025 13.313055 0 0 0 -72 1 4.824803 10.349461 0.123593 0 0 0 -73 1 0.048065 1.987339 5.276165 0 0 0 -74 1 12.931526 1.918600 10.714902 0 0 0 -75 1 12.915288 1.856049 15.732631 0 0 0 -76 1 11.301608 4.663636 5.225618 0 0 0 -77 1 11.478019 4.676912 10.566432 0 0 0 -78 1 11.366950 4.757350 0.091903 0 0 0 -79 1 11.267443 6.589212 2.721904 0 0 0 -80 1 9.687018 7.448161 5.265549 0 0 0 -81 1 11.333305 6.557936 7.897610 0 0 0 -82 1 9.679224 7.419360 10.483878 0 0 0 -83 1 11.327329 6.506861 13.046062 0 0 0 -84 1 9.730017 7.591150 0.044367 0 0 0 -85 1 9.650255 9.320748 2.727767 0 0 0 -86 1 8.178171 10.385349 5.414494 0 0 0 -87 1 9.662596 9.381161 7.847697 0 0 0 -88 1 8.095292 10.254060 10.512875 0 0 0 -89 1 9.655711 9.263147 13.169338 0 0 0 -90 1 8.061776 10.239997 0.022183 0 0 0 -91 1 0.057158 7.549862 5.279017 0 0 0 -92 1 12.945296 7.489899 10.493702 0 0 0 -93 1 0.048065 7.595650 15.773828 0 0 0 -94 1 11.360455 10.288261 5.218963 0 0 0 -95 1 11.340709 10.397612 10.701592 0 0 0 -96 1 11.237954 10.335511 0.085565 0 0 0 -97 2 1.659797 0.851332 4.693692 0 0 0 -98 2 1.519369 0.956589 10.018977 0 0 0 -99 2 1.553794 0.869108 15.044153 0 0 0 -100 2 0.085102 3.643923 4.584993 0 0 0 -101 2 12.906018 3.750912 9.907585 0 0 0 -102 2 0.094802 3.766100 15.086301 0 0 0 -103 2 4.977571 0.974330 4.627934 0 0 0 -104 2 3.331285 1.827249 2.106948 0 0 0 -105 2 4.879623 0.845842 9.903624 0 0 0 -106 2 3.201380 1.884737 7.412585 0 0 0 -107 2 4.837014 0.830958 15.266462 0 0 0 -108 2 3.202159 1.912188 12.548995 0 0 0 -109 2 3.340508 3.806038 4.594659 0 0 0 -110 2 1.627450 4.706387 1.988742 0 0 0 -111 2 3.308421 3.801425 9.811879 0 0 0 -112 2 1.612121 4.691762 7.156684 0 0 0 -113 2 3.320892 3.674748 15.188979 0 0 0 -114 2 1.561199 4.714937 12.536002 0 0 0 -115 2 1.560289 6.570312 4.497686 0 0 0 -116 2 1.639791 6.641863 9.980949 0 0 0 -117 2 1.633816 6.601249 15.304808 0 0 0 -118 2 0.013493 9.467562 4.645047 0 0 0 -119 2 0.093102 9.364511 9.801263 0 0 0 -120 2 12.922230 9.400286 15.169489 0 0 0 -121 2 8.146864 0.878254 4.764362 0 0 0 -122 2 6.548123 1.914550 1.952457 0 0 0 -123 2 8.157387 0.926090 10.064136 0 0 0 -124 2 6.389639 1.867862 7.329239 0 0 0 -125 2 8.233901 0.967096 15.227641 0 0 0 -126 2 6.532534 1.796649 12.468818 0 0 0 -127 2 6.508242 3.691849 4.628251 0 0 0 -128 2 4.949642 4.724387 1.839321 0 0 0 -129 2 6.419387 3.728299 10.041319 0 0 0 -130 2 4.899498 4.624148 7.220065 0 0 0 -131 2 6.434976 3.724249 15.310354 0 0 0 -132 2 4.885728 4.648111 12.596689 0 0 0 -133 2 4.900148 6.470073 4.584835 0 0 0 -134 2 3.361942 7.595200 1.910308 0 0 0 -135 2 4.810253 6.625662 9.877637 0 0 0 -136 2 3.348042 7.489336 7.266967 0 0 0 -137 2 4.838443 6.535999 15.177253 0 0 0 -138 2 3.304264 7.551887 12.497814 0 0 0 -139 2 3.238403 9.347636 4.488812 0 0 0 -140 2 1.749171 10.334274 1.970362 0 0 0 -141 2 3.370256 9.417612 9.905050 0 0 0 -142 2 1.586790 10.297261 7.174748 0 0 0 -143 2 3.259317 9.478025 15.091372 0 0 0 -144 2 1.693962 10.388499 12.679085 0 0 0 -145 2 11.400596 0.958569 4.713340 0 0 0 -146 2 9.683901 1.764361 1.912685 0 0 0 -147 2 11.375524 0.875667 10.039576 0 0 0 -148 2 9.642201 1.822412 7.261580 0 0 0 -149 2 11.408520 1.013098 15.233187 0 0 0 -150 2 9.822639 1.891375 12.547093 0 0 0 -151 2 9.821210 3.736737 4.484059 0 0 0 -152 2 8.245722 4.743625 2.011084 0 0 0 -153 2 9.699749 3.771050 10.036090 0 0 0 -154 2 8.208179 4.770513 7.142265 0 0 0 -155 2 9.817573 3.728862 15.129400 0 0 0 -156 2 7.996044 4.734962 12.658644 0 0 0 -157 2 8.002150 6.505398 4.769749 0 0 0 -158 2 6.393926 7.603188 1.937087 0 0 0 -159 2 8.217922 6.512148 9.976670 0 0 0 -160 2 6.378207 7.411710 7.381687 0 0 0 -161 2 8.099449 6.576612 15.264244 0 0 0 -162 2 6.615024 7.400910 12.429046 0 0 0 -163 2 6.399382 9.443262 4.519394 0 0 0 -164 2 4.878064 10.359586 2.141491 0 0 0 -165 2 6.523961 9.328173 9.924856 0 0 0 -166 2 4.881961 10.402787 7.131965 0 0 0 -167 2 6.621000 9.466437 15.329685 0 0 0 -168 2 4.916126 10.363637 12.420806 0 0 0 -169 2 12.895802 1.944926 2.095540 0 0 0 -170 2 12.887359 1.932550 7.211192 0 0 0 -171 2 12.922433 1.951451 12.524751 0 0 0 -172 2 11.408260 4.583085 2.062423 0 0 0 -173 2 11.495946 4.661499 7.277108 0 0 0 -174 2 11.440476 4.611548 12.676866 0 0 0 -175 2 11.317456 6.602937 4.614149 0 0 0 -176 2 9.785486 7.541199 1.904445 0 0 0 -177 2 11.377992 6.487060 10.037675 0 0 0 -178 2 9.761714 7.577762 7.418607 0 0 0 -179 2 11.443724 6.574812 15.308769 0 0 0 -180 2 9.682472 7.599363 12.705071 0 0 0 -181 2 9.851348 9.271022 4.654237 0 0 0 -182 2 8.098540 10.210410 2.120892 0 0 0 -183 2 9.808220 9.276197 9.979206 0 0 0 -184 2 8.063595 10.417187 7.156842 0 0 0 -185 2 9.768079 9.367323 15.162517 0 0 0 -186 2 8.217922 10.250685 12.563256 0 0 0 -187 2 0.116915 7.534562 1.838529 0 0 0 -188 2 12.961664 7.584287 7.232583 0 0 0 -189 2 0.063653 7.554362 12.464064 0 0 0 -190 2 11.476850 10.238872 2.090786 0 0 0 -191 2 11.343567 10.373424 7.217213 0 0 0 -192 2 11.468406 10.392662 12.433007 0 0 0 diff --git a/examples/GaN-SNAP-LAMMPS/DATA/42/DATA b/examples/GaN-SNAP-LAMMPS/DATA/42/DATA deleted file mode 100755 index ad191b00..00000000 --- a/examples/GaN-SNAP-LAMMPS/DATA/42/DATA +++ /dev/null @@ -1,215 +0,0 @@ -LAMMPS DATA file - -192 atoms -0 bonds -0 angles -0 dihedrals -0 impropers - -2 atom types -0 bond types -0 angle types - -0.0 12.990503 xlo xhi -0.0 11.250148 ylo yhi -0.0 15.845291 zlo zhi - -Masses - -1 69.723 -2 14.0067 - -Atoms - -1 1 1.671228 0.858668 2.607026 0 0 0 -2 1 1.636803 0.949164 8.003615 0 0 0 -3 1 1.686427 1.029242 13.187402 0 0 0 -4 1 12.964733 3.849913 2.507200 0 0 0 -5 1 0.015265 3.708949 8.058123 0 0 0 -6 1 0.030894 3.742024 13.319076 0 0 0 -7 1 4.931845 0.957579 2.508785 0 0 0 -8 1 3.123437 1.781461 5.262063 0 0 0 -9 1 4.790508 0.841916 7.863067 0 0 0 -10 1 3.176828 1.838387 10.574672 0 0 0 -11 1 4.993160 0.876139 13.167278 0 0 0 -12 1 3.375193 1.866512 0.147361 0 0 0 -13 1 3.247236 3.859813 2.647431 0 0 0 -14 1 1.528463 4.651374 5.348895 0 0 0 -15 1 3.225672 3.845638 7.780988 0 0 0 -16 1 1.592506 4.702224 10.639320 0 0 0 -17 1 3.308291 3.723349 13.327157 0 0 0 -18 1 1.544051 4.775350 15.763212 0 0 0 -19 1 1.601339 6.450835 2.649966 0 0 0 -20 1 1.583542 6.595287 8.054161 0 0 0 -21 1 1.646546 6.508773 13.325731 0 0 0 -22 1 12.865080 9.313885 2.704157 0 0 0 -23 1 12.886484 9.423912 7.834704 0 0 0 -24 1 12.967859 9.327723 13.088527 0 0 0 -25 1 8.069701 0.967535 2.484066 0 0 0 -26 1 6.527468 1.807561 5.243682 0 0 0 -27 1 8.110231 1.004638 7.828683 0 0 0 -28 1 6.464724 1.966526 10.438877 0 0 0 -29 1 8.000851 0.980169 13.134954 0 0 0 -30 1 6.624247 1.803961 0.012676 0 0 0 -31 1 6.519024 3.749787 2.623505 0 0 0 -32 1 4.781285 4.633261 5.346676 0 0 0 -33 1 6.624247 3.762500 7.962734 0 0 0 -34 1 4.918464 4.789413 10.515727 0 0 0 -35 1 6.487198 3.666423 13.065710 0 0 0 -36 1 4.882870 4.726300 0.102994 0 0 0 -37 1 4.897030 6.464110 2.710654 0 0 0 -38 1 3.157602 7.406760 5.133399 0 0 0 -39 1 4.762448 6.498086 7.881764 0 0 0 -40 1 3.192546 7.421273 10.600499 0 0 0 -41 1 4.771022 6.615312 13.322562 0 0 0 -42 1 3.232817 7.479436 15.812491 0 0 0 -43 1 3.345964 9.381274 2.517500 0 0 0 -44 1 1.548858 10.237972 5.230214 0 0 0 -45 1 3.212422 9.386786 7.800320 0 0 0 -46 1 1.678503 10.280048 10.604619 0 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9.639993 1.973951 2.060522 0 0 0 -147 2 11.242891 0.849330 9.784308 0 0 0 -148 2 9.686239 1.956626 7.144166 0 0 0 -149 2 11.385916 1.032449 15.342203 0 0 0 -150 2 9.847971 1.773923 12.521899 0 0 0 -151 2 9.693903 3.732799 4.758499 0 0 0 -152 2 8.063075 4.704474 2.083339 0 0 0 -153 2 9.799646 3.840351 9.767829 0 0 0 -154 2 8.212596 4.576785 7.337003 0 0 0 -155 2 9.797697 3.676998 15.307660 0 0 0 -156 2 8.029820 4.780300 12.465332 0 0 0 -157 2 8.167389 6.594049 4.518443 0 0 0 -158 2 6.440562 7.432298 2.122952 0 0 0 -159 2 8.129587 6.664363 9.819327 0 0 0 -160 2 6.532924 7.564487 7.236227 0 0 0 -161 2 8.206621 6.486723 15.096601 0 0 0 -162 2 6.454721 7.443661 12.500825 0 0 0 -163 2 6.621649 9.402986 4.657565 0 0 0 -164 2 4.891574 10.290848 2.000468 0 0 0 -165 2 6.567349 9.368448 9.778287 0 0 0 -166 2 4.984196 10.209960 7.314978 0 0 0 -167 2 6.555787 9.283622 15.281040 0 0 0 -168 2 4.981858 10.327074 12.535209 0 0 0 -169 2 0.076644 1.826349 2.142125 0 0 0 -170 2 0.126008 1.883162 7.392937 0 0 0 -171 2 12.921783 1.870225 12.678768 0 0 0 -172 2 11.409169 4.673087 2.098392 0 0 0 -173 2 11.339670 4.680512 7.252073 0 0 0 -174 2 11.320964 4.770963 12.671162 0 0 0 -175 2 11.325900 6.664700 4.566771 0 0 0 -176 2 9.854985 7.423973 2.129607 0 0 0 -177 2 11.465028 6.564236 9.756104 0 0 0 -178 2 9.815105 7.468523 7.378360 0 0 0 -179 2 11.349283 6.586399 15.151742 0 0 0 -180 2 9.800425 7.458736 12.692078 0 0 0 -181 2 9.833811 9.437187 4.563444 0 0 0 -182 2 8.215844 10.284548 2.080645 0 0 0 -183 2 9.825237 9.487363 9.764660 0 0 0 -184 2 8.050734 10.297036 7.377884 0 0 0 -185 2 9.713389 9.290260 15.322079 0 0 0 -186 2 8.036575 10.333036 12.648662 0 0 0 -187 2 12.928409 7.609375 1.967510 0 0 0 -188 2 12.919185 7.429148 7.330665 0 0 0 -189 2 0.097429 7.560662 12.474047 0 0 0 -190 2 11.492828 10.210072 1.936770 0 0 0 -191 2 11.411637 10.212885 7.126736 0 0 0 -192 2 11.383578 10.346649 12.466282 0 0 0 diff --git a/examples/GaN-SNAP-LAMMPS/DATA/43/DATA b/examples/GaN-SNAP-LAMMPS/DATA/43/DATA deleted file mode 100755 index b369fac7..00000000 --- a/examples/GaN-SNAP-LAMMPS/DATA/43/DATA +++ /dev/null @@ -1,215 +0,0 @@ -LAMMPS DATA file - -192 atoms -0 bonds -0 angles -0 dihedrals -0 impropers - -2 atom types -0 bond types -0 angle types - -0.0 12.990503 xlo xhi -0.0 11.250148 ylo yhi -0.0 15.845291 zlo zhi - -Masses - -1 69.723 -2 14.0067 - -Atoms - -1 1 1.680192 0.975017 2.533345 0 0 0 -2 1 1.586011 0.912713 7.944195 0 0 0 -3 1 1.544441 0.863966 13.331277 0 0 0 -4 1 12.952714 3.652923 2.539208 0 0 0 -5 1 0.000922 3.725937 8.045605 0 0 0 -6 1 12.923835 3.689936 13.045586 0 0 0 -7 1 4.858448 0.981508 2.700671 0 0 0 -8 1 3.237233 1.784499 5.323542 0 0 0 -9 1 4.904564 0.858521 7.822820 0 0 0 -10 1 3.289845 1.836699 10.488473 0 0 0 -11 1 4.848446 1.017058 13.137013 0 0 0 -12 1 3.315047 1.885637 0.082396 0 0 0 -13 1 3.322191 3.849913 2.512588 0 0 0 -14 1 1.719033 4.766238 5.211358 0 0 0 -15 1 3.178386 3.744949 7.819334 0 0 0 -16 1 1.731374 4.646086 10.434124 0 0 0 -17 1 3.231907 3.758562 13.056044 0 0 0 -18 1 1.637193 4.708187 15.768599 0 0 0 -19 1 1.602638 6.562436 2.671199 0 0 0 -20 1 1.711759 6.651763 7.912980 0 0 0 -21 1 1.558990 6.484248 13.237790 0 0 0 -22 1 0.093187 9.463062 2.526690 0 0 0 -23 1 0.025133 9.450462 8.015499 0 0 0 -24 1 0.077327 9.460250 13.167753 0 0 0 -25 1 8.206880 0.965870 2.542535 0 0 0 -26 1 6.463165 1.921975 5.126902 0 0 0 -27 1 8.062686 0.965038 7.791446 0 0 0 -28 1 6.461476 1.875287 10.502100 0 0 0 -29 1 8.221819 0.982959 13.078703 0 0 0 -30 1 6.623858 1.974964 0.085565 0 0 0 -31 1 6.526948 3.851488 2.512112 0 0 0 -32 1 4.969387 4.747900 5.334951 0 0 0 -33 1 6.552280 3.773975 7.801587 0 0 0 -34 1 4.889106 4.652949 10.614602 0 0 0 -35 1 6.453422 3.711424 13.108492 0 0 0 -36 1 4.838183 4.674324 15.829287 0 0 0 -37 1 4.810253 6.650413 2.492940 0 0 0 -38 1 3.234375 7.589125 5.406572 0 0 0 -39 1 4.783103 6.581562 7.900303 0 0 0 -40 1 3.370646 7.562462 10.702543 0 0 0 -41 1 4.803109 6.464448 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0.045951 0 0 0 -67 1 6.441731 9.285872 2.483591 0 0 0 -68 1 4.780115 10.274985 5.128487 0 0 0 -69 1 6.555657 9.362373 7.886835 0 0 0 -70 1 4.765566 10.386812 10.693353 0 0 0 -71 1 6.579170 9.289135 13.094390 0 0 0 -72 1 4.947953 10.285448 0.118840 0 0 0 -73 1 0.033775 1.818136 5.377258 0 0 0 -74 1 0.012991 1.808124 10.673705 0 0 0 -75 1 12.918276 1.897788 15.759409 0 0 0 -76 1 11.471394 4.718425 5.163663 0 0 0 -77 1 11.297581 4.751725 10.675606 0 0 0 -78 1 11.380720 4.777038 0.136269 0 0 0 -79 1 11.314598 6.562436 2.601638 0 0 0 -80 1 9.859532 7.599025 5.350321 0 0 0 -81 1 11.327849 6.526323 8.008685 0 0 0 -82 1 9.819391 7.466723 10.505586 0 0 0 -83 1 11.342138 6.575937 13.262825 0 0 0 -84 1 9.827835 7.492711 15.738652 0 0 0 -85 1 9.865897 9.319510 2.624614 0 0 0 -86 1 7.998383 10.230210 5.143540 0 0 0 -87 1 9.816923 9.303085 7.861958 0 0 0 -88 1 8.065933 10.223347 10.698265 0 0 0 -89 1 9.666623 9.359673 13.056519 0 0 0 -90 1 8.164791 10.225035 15.818829 0 0 0 -91 1 0.087036 7.409348 5.366483 0 0 0 -92 1 12.965042 7.532874 10.593052 0 0 0 -93 1 12.864365 7.519262 15.814868 0 0 0 -94 1 11.246009 10.348449 5.364582 0 0 0 -95 1 11.282642 10.407175 10.503051 0 0 0 -96 1 11.310052 10.358124 0.133100 0 0 0 -97 2 1.709550 0.927383 4.597036 0 0 0 -98 2 1.750860 0.887749 9.845313 0 0 0 -99 2 1.606665 0.923975 15.183908 0 0 0 -100 2 12.909848 3.749449 4.746615 0 0 0 -101 2 12.909767 3.638973 9.818851 0 0 0 -102 2 0.011132 3.756537 15.271057 0 0 0 -103 2 4.908981 0.978572 4.694167 0 0 0 -104 2 3.242430 1.826462 1.865149 0 0 0 -105 2 4.880662 0.948117 10.011055 0 0 0 -106 2 3.297509 1.921863 7.167617 0 0 0 -107 2 4.825063 0.861413 15.267254 0 0 0 -108 2 3.264903 1.930075 12.482445 0 0 0 -109 2 3.142143 3.768462 4.495626 0 0 0 -110 2 1.695261 4.735187 1.834409 0 0 0 -111 2 3.172151 3.789950 9.893958 0 0 0 -112 2 1.621994 4.654411 7.303411 0 0 0 -113 2 3.236454 3.703886 15.297519 0 0 0 -114 2 1.584192 4.793351 12.518730 0 0 0 -115 2 1.630178 6.564911 4.649959 0 0 0 -116 2 1.726048 6.534424 10.057164 0 0 0 -117 2 1.585751 6.491448 15.211162 0 0 0 -118 2 0.050239 9.379586 4.692900 0 0 0 -119 2 0.105393 9.459912 9.835172 0 0 0 -120 2 0.109240 9.305223 15.107692 0 0 0 -121 2 8.129067 0.855101 4.540626 0 0 0 -122 2 6.431988 1.833887 1.869903 0 0 0 -123 2 8.031768 0.886039 9.859732 0 0 0 -124 2 6.418088 1.778648 7.386282 0 0 0 -125 2 8.028651 1.003727 15.332062 0 0 0 -126 2 6.456670 1.775836 12.683204 0 0 0 -127 2 6.567219 3.693649 4.637124 0 0 0 -128 2 4.760630 4.766688 2.065751 0 0 0 -129 2 6.411203 3.823475 9.761016 0 0 0 -130 2 4.746210 4.735862 7.402444 0 0 0 -131 2 6.509541 3.824038 15.145246 0 0 0 -132 2 4.821295 4.726637 12.409081 0 0 0 -133 2 4.826492 6.648838 4.598779 0 0 0 -134 2 3.248145 7.467961 2.141016 0 0 0 -135 2 4.862345 6.663125 9.782090 0 0 0 -136 2 3.200730 7.476286 7.375190 0 0 0 -137 2 4.783233 6.502586 15.084083 0 0 0 -138 2 3.265423 7.421948 12.603819 0 0 0 -139 2 3.350640 9.414462 4.677054 0 0 0 -140 2 1.601469 10.347661 1.953883 0 0 0 -141 2 3.269840 9.445287 9.966371 0 0 0 -142 2 1.745534 10.265423 7.114377 0 0 0 -143 2 3.224243 9.455525 15.343629 0 0 0 -144 2 1.705913 10.242810 12.403852 0 0 0 -145 2 11.394230 0.989383 4.483900 0 0 0 -146 2 9.818742 1.851437 1.846610 0 0 0 -147 2 11.397997 0.862178 9.854662 0 0 0 -148 2 9.683121 1.884287 7.379944 0 0 0 -149 2 11.349023 0.955070 15.075368 0 0 0 -150 2 9.764052 1.913538 12.656426 0 0 0 -151 2 9.777822 3.685211 4.755964 0 0 0 -152 2 8.094383 4.775013 2.009975 0 0 0 -153 2 9.617259 3.759125 10.020562 0 0 0 -154 2 8.046967 4.718425 7.335260 0 0 0 -155 2 9.699619 3.648986 15.177728 0 0 0 -156 2 8.214025 4.749588 12.499557 0 0 0 -157 2 8.183497 6.590674 4.699238 0 0 0 -158 2 6.539419 7.496761 2.009658 0 0 0 -159 2 8.197137 6.551299 9.837866 0 0 0 -160 2 6.553969 7.476961 7.232741 0 0 0 -161 2 8.146604 6.454323 15.251092 0 0 0 -162 2 6.485898 7.560662 12.497339 0 0 0 -163 2 6.407436 9.394211 4.546648 0 0 0 -164 2 4.767125 10.292311 2.088568 0 0 0 -165 2 6.407955 9.308935 9.781298 0 0 0 -166 2 4.941587 10.421687 7.249379 0 0 0 -167 2 6.399252 9.317710 15.306709 0 0 0 -168 2 4.758551 10.213672 12.473571 0 0 0 -169 2 12.976733 1.914438 1.910625 0 0 0 -170 2 0.050663 1.887550 7.123092 0 0 0 -171 2 12.903857 1.894525 12.552639 0 0 0 -172 2 11.496465 4.795263 2.070029 0 0 0 -173 2 11.297581 4.740812 7.320683 0 0 0 -174 2 11.398387 4.767588 12.564999 0 0 0 -175 2 11.471913 6.454098 4.654237 0 0 0 -176 2 9.685979 7.554925 1.896047 0 0 0 -177 2 11.250036 6.513498 9.792706 0 0 0 -178 2 9.731706 7.437810 7.284714 0 0 0 -179 2 11.255232 6.471985 15.134946 0 0 0 -180 2 9.776393 7.556725 12.532516 0 0 0 -181 2 9.673118 9.390386 4.536031 0 0 0 -182 2 8.059828 10.239660 2.073515 0 0 0 -183 2 9.634277 9.386111 9.982375 0 0 0 -184 2 8.158815 10.347099 7.327655 0 0 0 -185 2 9.641811 9.343136 15.222571 0 0 0 -186 2 8.079573 10.382874 12.428412 0 0 0 -187 2 12.968679 7.566400 2.105522 0 0 0 -188 2 12.952311 7.571012 7.148444 0 0 0 -189 2 12.951012 7.491249 12.535526 0 0 0 -190 2 11.337072 10.214122 1.961013 0 0 0 -191 2 11.494257 10.382087 7.283605 0 0 0 -192 2 11.446322 10.302661 12.577358 0 0 0 diff --git a/examples/GaN-SNAP-LAMMPS/DATA/44/DATA b/examples/GaN-SNAP-LAMMPS/DATA/44/DATA deleted file mode 100755 index 99fd9052..00000000 --- a/examples/GaN-SNAP-LAMMPS/DATA/44/DATA +++ /dev/null @@ -1,215 +0,0 @@ -LAMMPS DATA file - -192 atoms -0 bonds -0 angles -0 dihedrals -0 impropers - -2 atom types -0 bond types -0 angle types - -0.0 12.990503 xlo xhi -0.0 11.250148 ylo yhi -0.0 15.845291 zlo zhi - -Masses - -1 69.723 -2 14.0067 - -Atoms - -1 1 1.588609 0.944787 2.702414 0 0 0 -2 1 1.720332 0.898966 7.964794 0 0 0 -3 1 1.747223 0.842096 13.226539 0 0 0 -4 1 12.968132 3.707149 2.560599 0 0 0 -5 1 0.067232 3.861501 7.817908 0 0 0 -6 1 0.073046 3.681611 13.354886 0 0 0 -7 1 4.950031 0.920465 2.707960 0 0 0 -8 1 3.247236 1.944588 5.230847 0 0 0 -9 1 4.760500 0.957984 8.047189 0 0 0 -10 1 3.168124 1.859762 10.636944 0 0 0 -11 1 4.751666 1.037939 13.282473 0 0 0 -12 1 3.262955 1.803849 15.839111 0 0 0 -13 1 3.252302 3.861276 2.747890 0 0 0 -14 1 1.743975 4.727875 5.245742 0 0 0 -15 1 3.360643 3.745399 7.832169 0 0 0 -16 1 1.596923 4.733725 10.576573 0 0 0 -17 1 3.314267 3.861501 13.345538 0 0 0 -18 1 1.632906 4.791888 15.718053 0 0 0 -19 1 1.507288 6.518561 2.660741 0 0 0 -20 1 1.631867 6.652888 7.930093 0 0 0 -21 1 1.606146 6.572224 13.266311 0 0 0 -22 1 12.864932 9.442812 2.522095 0 0 0 -23 1 12.984912 9.320410 7.875743 0 0 0 -24 1 0.042029 9.300835 13.128774 0 0 0 -25 1 8.040602 0.868905 2.580564 0 0 0 -26 1 6.594109 1.868537 5.245900 0 0 0 -27 1 8.035665 1.043024 7.887786 0 0 0 -28 1 6.584756 1.900938 10.518896 0 0 0 -29 1 8.217013 1.001601 13.187877 0 0 0 -30 1 6.576832 1.964726 15.817403 0 0 0 -31 1 6.452253 3.771837 2.762785 0 0 0 -32 1 4.923920 4.660036 5.350796 0 0 0 -33 1 6.613205 3.759687 7.929934 0 0 0 -34 1 4.822335 4.591073 10.457258 0 0 0 -35 1 6.389509 3.741799 13.043368 0 0 0 -36 1 4.979260 4.719662 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3.147339 7.457611 7.181878 0 0 0 -137 2 4.910930 6.465010 15.119418 0 0 0 -138 2 3.190987 7.585637 12.532040 0 0 0 -139 2 3.314137 9.398374 4.716826 0 0 0 -140 2 1.523526 10.420337 2.096649 0 0 0 -141 2 3.130841 9.367548 9.853552 0 0 0 -142 2 1.657588 10.251923 7.293270 0 0 0 -143 2 3.274386 9.397586 15.174243 0 0 0 -144 2 1.503131 10.315711 12.520473 0 0 0 -145 2 11.264845 0.928486 4.611455 0 0 0 -146 2 9.756128 1.943688 2.049747 0 0 0 -147 2 11.463340 0.836752 9.819960 0 0 0 -148 2 9.732355 1.978226 7.359821 0 0 0 -149 2 11.354219 0.900034 15.050808 0 0 0 -150 2 9.805492 1.876525 12.454557 0 0 0 -151 2 9.723911 3.675536 4.706844 0 0 0 -152 2 8.084899 4.786938 1.833142 0 0 0 -153 2 9.828355 3.778587 9.921053 0 0 0 -154 2 8.158166 4.738562 7.139413 0 0 0 -155 2 9.840956 3.640773 15.125439 0 0 0 -156 2 8.035925 4.783451 12.412884 0 0 0 -157 2 8.140109 6.593487 4.674995 0 0 0 -158 2 6.589952 7.400235 2.086508 0 0 0 -159 2 8.126599 6.606312 9.817584 0 0 0 -160 2 6.506553 7.545699 7.412585 0 0 0 -161 2 8.104645 6.469285 15.050332 0 0 0 -162 2 6.528897 7.566737 12.610316 0 0 0 -163 2 6.455111 9.475662 4.633480 0 0 0 -164 2 4.989392 10.216710 1.893354 0 0 0 -165 2 6.566699 9.468350 9.998378 0 0 0 -166 2 4.818308 10.234260 7.378201 0 0 0 -167 2 6.569297 9.323560 15.104365 0 0 0 -168 2 4.824933 10.386812 12.651831 0 0 0 -169 2 0.018187 1.891150 1.918389 0 0 0 -170 2 0.051962 1.941663 7.249379 0 0 0 -171 2 12.976473 1.867300 12.479592 0 0 0 -172 2 11.412287 4.778388 2.115663 0 0 0 -173 2 11.430863 4.633711 7.327972 0 0 0 -174 2 11.271080 4.602886 12.451705 0 0 0 -175 2 11.274588 6.581674 4.491823 0 0 0 -176 2 9.826666 7.550199 2.121051 0 0 0 -177 2 11.364742 6.597424 10.032446 0 0 0 -178 2 9.752880 7.451086 7.418765 0 0 0 -179 2 11.246268 6.523511 15.340460 0 0 0 -180 2 9.707803 7.457161 12.429521 0 0 0 -181 2 9.850958 9.293072 4.573902 0 0 0 -182 2 8.222339 10.312561 2.022651 0 0 0 -183 2 9.764442 9.419749 9.759590 0 0 0 -184 2 8.126339 10.207372 7.371546 0 0 0 -185 2 9.701308 9.453162 15.110069 0 0 0 -186 2 8.140239 10.411112 12.406387 0 0 0 -187 2 12.874628 7.392247 2.043726 0 0 0 -188 2 0.025981 7.413285 7.361722 0 0 0 -189 2 0.031177 7.403385 12.413201 0 0 0 -190 2 11.272119 10.377587 1.856910 0 0 0 -191 2 11.298620 10.254960 7.142740 0 0 0 -192 2 11.459832 10.357224 12.623785 0 0 0 diff --git a/examples/GaN-SNAP-LAMMPS/DATA/45/DATA b/examples/GaN-SNAP-LAMMPS/DATA/45/DATA deleted file mode 100755 index 0fd977cb..00000000 --- a/examples/GaN-SNAP-LAMMPS/DATA/45/DATA +++ /dev/null @@ -1,215 +0,0 @@ -LAMMPS DATA file - -192 atoms -0 bonds -0 angles -0 dihedrals -0 impropers - -2 atom types -0 bond types -0 angle types - -0.0 12.990503 xlo xhi -0.0 11.250148 ylo yhi -0.0 15.845291 zlo zhi - -Masses - -1 69.723 -2 14.0067 - -Atoms - -1 1 1.633556 0.878018 2.606550 0 0 0 -2 1 1.536387 0.924256 7.893965 0 0 0 -3 1 1.575488 1.036937 13.118475 0 0 0 -4 1 0.129419 3.650223 2.750584 0 0 0 -5 1 0.022385 3.769587 7.883507 0 0 0 -6 1 12.986728 3.749337 13.294357 0 0 0 -7 1 4.852992 0.961370 2.677379 0 0 0 -8 1 3.254251 1.853462 5.336377 0 0 0 -9 1 4.851953 0.878715 8.004090 0 0 0 -10 1 3.169683 1.837487 10.509231 0 0 0 -11 1 4.855720 1.014122 13.293407 0 0 0 -12 1 3.290754 1.819486 15.792050 0 0 0 -13 1 3.235934 3.796588 2.635072 0 0 0 -14 1 1.584452 4.756563 5.172695 0 0 0 -15 1 3.173580 3.827750 7.896025 0 0 0 -16 1 1.738129 4.751050 10.661979 0 0 0 -17 1 3.189298 3.724924 13.336347 0 0 0 -18 1 1.609783 4.634274 0.069719 0 0 0 -19 1 1.638232 6.564349 2.586744 0 0 0 -20 1 1.495077 6.513723 8.026590 0 0 0 -21 1 1.575748 6.661888 13.252209 0 0 0 -22 1 12.863264 9.428412 2.597677 0 0 0 -23 1 0.129645 9.308260 7.806182 0 0 0 -24 1 0.078233 9.479825 13.332544 0 0 0 -25 1 8.188953 0.922456 2.493732 0 0 0 -26 1 6.614764 1.797549 5.162396 0 0 0 -27 1 8.174924 1.037770 7.994741 0 0 0 -28 1 6.511100 1.795186 10.600499 0 0 0 -29 1 8.152190 1.015877 13.326523 0 0 0 -30 1 6.396914 1.780448 0.007923 0 0 0 -31 1 6.584496 3.649886 2.729668 0 0 0 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9.690136 3.839338 7.855778 0 0 0 -58 1 8.094772 4.767813 10.550587 0 0 0 -59 1 9.743917 3.790962 13.128774 0 0 0 -60 1 8.202334 4.799538 0.074473 0 0 0 -61 1 8.231432 6.610250 2.681023 0 0 0 -62 1 6.605931 7.558750 5.167942 0 0 0 -63 1 8.209219 6.670888 7.912980 0 0 0 -64 1 6.607619 7.507449 10.621415 0 0 0 -65 1 8.166999 6.666500 13.266945 0 0 0 -66 1 6.558126 7.451086 0.112502 0 0 0 -67 1 6.397173 9.350673 2.721746 0 0 0 -68 1 4.958215 10.314473 5.434142 0 0 0 -69 1 6.537990 9.284072 7.978896 0 0 0 -70 1 4.899368 10.283760 10.405761 0 0 0 -71 1 6.607360 9.312198 13.069037 0 0 0 -72 1 4.883520 10.297598 0.003169 0 0 0 -73 1 0.102625 1.778311 5.142272 0 0 0 -74 1 12.911781 1.906675 10.501149 0 0 0 -75 1 12.887359 1.888675 15.817244 0 0 0 -76 1 11.421250 4.723037 5.418772 0 0 0 -77 1 11.380980 4.596361 10.535692 0 0 0 -78 1 11.317326 4.739237 15.743881 0 0 0 -79 1 11.277575 6.501236 2.543486 0 0 0 -80 1 9.716117 7.388310 5.321958 0 0 0 -81 1 11.380980 6.656938 7.928033 0 0 0 -82 1 9.653373 7.429035 10.714902 0 0 0 -83 1 11.442555 6.542074 13.111661 0 0 0 -84 1 9.714298 7.484499 15.704584 0 0 0 -85 1 9.822769 9.281822 2.760725 0 0 0 -86 1 8.217662 10.224697 5.140846 0 0 0 -87 1 9.726639 9.462612 7.942293 0 0 0 -88 1 8.241695 10.328761 10.499565 0 0 0 -89 1 9.822509 9.370136 13.238899 0 0 0 -90 1 8.044109 10.209622 15.710447 0 0 0 -91 1 0.027280 7.530512 5.247802 0 0 0 -92 1 0.050663 7.436010 10.423983 0 0 0 -93 1 12.921783 7.423410 0.063381 0 0 0 -94 1 11.496336 10.288711 5.124209 0 0 0 -95 1 11.400336 10.239997 10.586239 0 0 0 -96 1 11.374485 10.277348 0.063381 0 0 0 -97 2 1.584971 0.947229 4.617159 0 0 0 -98 2 1.497285 0.854516 9.971283 0 0 0 -99 2 1.597702 0.874699 15.067604 0 0 0 -100 2 12.972756 3.704786 4.671192 0 0 0 -101 2 12.882060 3.656073 10.004716 0 0 0 -102 2 0.062449 3.724362 15.344579 0 0 0 -103 2 4.898719 0.906413 4.709696 0 0 0 -104 2 3.304524 1.879112 1.862297 0 0 0 -105 2 4.769723 0.870638 9.973660 0 0 0 -106 2 3.296470 1.953251 7.305154 0 0 0 -107 2 4.946394 0.966163 15.068713 0 0 0 -108 2 3.177607 1.833212 12.490526 0 0 0 -109 2 3.356876 3.650673 4.690206 0 0 0 -110 2 1.624203 4.690974 1.970520 0 0 0 -111 2 3.334532 3.743937 9.981265 0 0 0 -112 2 1.598611 4.601198 7.233058 0 0 0 -113 2 3.252562 3.796138 15.046054 0 0 0 -114 2 1.553145 4.761738 12.541072 0 0 0 -115 2 1.591726 6.545899 4.646473 0 0 0 -116 2 1.617058 6.494373 10.017393 0 0 0 -117 2 1.642389 6.534424 15.062375 0 0 0 -118 2 12.958832 9.279685 4.529693 0 0 0 -119 2 0.116122 9.444387 9.789854 0 0 0 -120 2 0.121116 9.398261 15.246497 0 0 0 -121 2 8.052163 1.035351 4.637600 0 0 0 -122 2 6.367685 1.980926 2.106631 0 0 0 -123 2 8.157387 0.845089 9.953695 0 0 0 -124 2 6.384313 1.829949 7.307690 0 0 0 -125 2 7.996694 0.860704 15.262976 0 0 0 -126 2 6.503695 1.806774 12.682254 0 0 0 -127 2 6.421336 3.716936 4.518760 0 0 0 -128 2 4.837663 4.740925 1.837261 0 0 0 -129 2 6.511100 3.686674 10.041319 0 0 0 -130 2 4.876115 4.610311 7.372655 0 0 0 -131 2 6.560594 3.714911 15.229067 0 0 0 -132 2 4.900408 4.712125 12.580052 0 0 0 -133 2 4.749198 6.537236 4.767689 0 0 0 -134 2 3.289066 7.597113 2.108374 0 0 0 -135 2 4.925609 6.549611 10.008202 0 0 0 -136 2 3.339988 7.429485 7.221333 0 0 0 -137 2 4.888586 6.491673 15.179630 0 0 0 -138 2 3.165396 7.520724 12.638679 0 0 0 -139 2 3.288026 9.276085 4.686403 0 0 0 -140 2 1.665902 10.212097 2.069553 0 0 0 -141 2 3.126684 9.464637 9.974452 0 0 0 -142 2 1.517161 10.275210 7.153356 0 0 0 -143 2 3.179815 9.481062 15.339826 0 0 0 -144 2 1.703575 10.407850 12.607464 0 0 0 -145 2 11.404103 0.936777 4.782901 0 0 0 -146 2 9.801075 1.847949 1.852948 0 0 0 -147 2 11.427096 0.940602 9.915824 0 0 0 -148 2 9.824588 1.950326 7.409575 0 0 0 -149 2 11.363183 0.865564 15.088678 0 0 0 -150 2 9.768209 1.981826 12.685106 0 0 0 -151 2 9.756907 3.702536 4.539993 0 0 0 -152 2 8.188304 4.624148 1.968777 0 0 0 -153 2 9.704166 3.732237 10.005984 0 0 0 -154 2 7.997084 4.627523 7.397215 0 0 0 -155 2 9.831473 3.824600 15.081389 0 0 0 -156 2 8.068531 4.740925 12.581795 0 0 0 -157 2 8.142837 6.655250 4.628409 0 0 0 -158 2 6.571246 7.568650 2.034060 0 0 0 -159 2 8.144786 6.517098 10.056372 0 0 0 -160 2 6.605021 7.533887 7.165240 0 0 0 -161 2 8.035665 6.523286 15.232870 0 0 0 -162 2 6.439003 7.455811 12.673697 0 0 0 -163 2 6.619701 9.454287 4.625716 0 0 0 -164 2 4.968997 10.359811 2.129766 0 0 0 -165 2 6.432637 9.470487 9.989822 0 0 0 -166 2 4.912749 10.250685 7.369169 0 0 0 -167 2 6.477844 9.350336 15.183274 0 0 0 -168 2 4.811552 10.332586 12.698574 0 0 0 -169 2 0.098728 1.979351 1.990961 0 0 0 -170 2 0.002598 1.887550 7.378676 0 0 0 -171 2 0.088335 1.791474 12.471353 0 0 0 -172 2 11.324081 4.739462 2.043567 0 0 0 -173 2 11.321743 4.656211 7.214044 0 0 0 -174 2 11.357987 4.771075 12.693504 0 0 0 -175 2 11.383318 6.662675 4.732513 0 0 0 -176 2 9.683381 7.463573 1.880836 0 0 0 -177 2 11.487632 6.542636 10.024682 0 0 0 -178 2 9.852128 7.564712 7.218797 0 0 0 -179 2 11.254842 6.621837 15.220669 0 0 0 -180 2 9.759635 7.541537 12.589559 0 0 0 -181 2 9.805622 9.425937 4.575169 0 0 0 -182 2 8.055931 10.252485 2.123110 0 0 0 -183 2 9.728978 9.433362 9.880648 0 0 0 -184 2 8.173235 10.350249 7.399592 0 0 0 -185 2 9.804712 9.334360 15.313523 0 0 0 -186 2 8.064504 10.406837 12.703962 0 0 0 -187 2 12.981150 7.579225 1.933601 0 0 0 -188 2 12.882292 7.611850 7.195346 0 0 0 -189 2 0.029878 7.595200 12.473888 0 0 0 -190 2 11.327979 10.373199 1.992862 0 0 0 -191 2 11.328888 10.280385 7.353641 0 0 0 -192 2 11.264195 10.218060 12.694930 0 0 0 diff --git a/examples/GaN-SNAP-LAMMPS/DATA/46/DATA b/examples/GaN-SNAP-LAMMPS/DATA/46/DATA deleted file mode 100755 index 93ec81f8..00000000 --- a/examples/GaN-SNAP-LAMMPS/DATA/46/DATA +++ /dev/null @@ -1,215 +0,0 @@ -LAMMPS DATA file - -192 atoms -0 bonds -0 angles -0 dihedrals -0 impropers - -2 atom types -0 bond types -0 angle types - -0.0 12.990503 xlo xhi -0.0 11.250148 ylo yhi -0.0 15.845291 zlo zhi - -Masses - -1 69.723 -2 14.0067 - -Atoms - -1 1 1.745664 0.845876 2.594349 0 0 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10.540446 0 0 0 -53 1 11.267573 1.036352 13.229550 0 0 0 -54 1 9.698970 1.828487 15.841171 0 0 0 -55 1 9.832512 3.850363 2.745830 0 0 0 -56 1 8.130496 4.692212 5.284563 0 0 0 -57 1 9.775354 3.700286 7.924071 0 0 0 -58 1 8.074897 4.636974 10.517787 0 0 0 -59 1 9.869275 3.807050 13.181856 0 0 0 -60 1 8.208959 4.687937 0.011092 0 0 0 -61 1 8.182198 6.511361 2.599420 0 0 0 -62 1 6.561113 7.498674 5.328613 0 0 0 -63 1 8.223508 6.525311 7.852451 0 0 0 -64 1 6.525909 7.428698 10.466765 0 0 0 -65 1 8.198696 6.474573 13.255061 0 0 0 -66 1 6.416010 7.471223 0.006338 0 0 0 -67 1 6.430559 9.424474 2.578663 0 0 0 -68 1 4.751277 10.382762 5.132131 0 0 0 -69 1 6.442640 9.330985 7.928666 0 0 0 -70 1 4.772711 10.379049 10.558826 0 0 0 -71 1 6.424583 9.449675 13.076484 0 0 0 -72 1 5.001214 10.370724 0.000000 0 0 0 -73 1 12.984398 1.823874 5.423051 0 0 0 -74 1 12.943608 1.864487 10.568650 0 0 0 -75 1 0.074046 1.855262 0.123593 0 0 0 -76 1 11.268092 4.771413 5.324335 0 0 0 -77 1 11.348893 4.605923 10.405444 0 0 0 -78 1 11.331746 4.578923 15.830713 0 0 0 -79 1 11.270950 6.640175 2.780373 0 0 0 -80 1 9.663895 7.553575 5.135459 0 0 0 -81 1 11.370458 6.476823 7.962417 0 0 0 -82 1 9.655192 7.401473 10.576573 0 0 0 -83 1 11.274328 6.532961 13.104214 0 0 0 -84 1 9.612972 7.569887 0.122009 0 0 0 -85 1 9.727419 9.344936 2.592606 0 0 0 -86 1 8.063985 10.388049 5.427012 0 0 0 -87 1 9.668702 9.412437 7.898402 0 0 0 -88 1 8.096461 10.390637 10.558826 0 0 0 -89 1 9.672469 9.422787 13.177419 0 0 0 -90 1 8.097240 10.409650 15.728035 0 0 0 -91 1 12.865794 7.483036 5.417822 0 0 0 -92 1 0.059756 7.457836 10.448702 0 0 0 -93 1 0.127307 7.579450 0.049120 0 0 0 -94 1 11.306804 10.403237 5.202009 0 0 0 -95 1 11.458533 10.294448 10.426677 0 0 0 -96 1 11.479838 10.385462 0.131516 0 0 0 -97 2 1.659407 1.046984 4.668023 0 0 0 -98 2 1.605366 0.887344 10.013114 0 0 0 -99 2 1.735401 1.039795 15.085034 0 0 0 -100 2 12.907461 3.850813 4.668815 0 0 0 -101 2 0.012066 3.783087 10.064136 0 0 0 -102 2 0.081347 3.843051 15.209261 0 0 0 -103 2 4.822854 0.924897 4.552827 0 0 0 -104 2 3.154744 1.935138 2.020750 0 0 0 -105 2 4.798172 0.930612 10.002181 0 0 0 -106 2 3.269969 1.968101 7.347778 0 0 0 -107 2 4.951850 0.988584 15.300054 0 0 0 -108 2 3.277764 1.900600 12.394345 0 0 0 -109 2 3.263994 3.829663 4.611772 0 0 0 -110 2 1.581854 4.594223 2.111227 0 0 0 -111 2 3.233206 3.838551 9.917409 0 0 0 -112 2 1.611602 4.578248 7.194396 0 0 0 -113 2 3.325179 3.683749 15.235881 0 0 0 -114 2 1.674086 4.596923 12.625528 0 0 0 -115 2 1.747482 6.620487 4.533971 0 0 0 -116 2 1.539375 6.655025 9.835806 0 0 0 -117 2 1.543142 6.548036 15.321287 0 0 0 -118 2 12.909996 9.422112 4.710646 0 0 0 -119 2 12.931306 9.328960 10.054946 0 0 0 -120 2 12.916043 9.348198 15.243645 0 0 0 -121 2 8.086328 0.978718 4.777672 0 0 0 -122 2 6.539160 1.919500 1.906188 0 0 0 -123 2 8.215844 0.999744 9.794766 0 0 0 -124 2 6.431079 1.887887 7.271087 0 0 0 -125 2 8.242734 1.000487 15.109118 0 0 0 -126 2 6.388340 1.943351 12.614119 0 0 0 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4.549975 0 0 0 -152 2 8.033197 4.628873 1.856593 0 0 0 -153 2 9.835110 3.835401 9.969381 0 0 0 -154 2 8.050605 4.713587 7.208181 0 0 0 -155 2 9.730407 3.674298 15.104048 0 0 0 -156 2 8.000331 4.642149 12.541231 0 0 0 -157 2 8.078404 6.636575 4.513848 0 0 0 -158 2 6.388080 7.591488 2.114079 0 0 0 -159 2 8.050085 6.564349 9.924856 0 0 0 -160 2 6.531235 7.516449 7.277900 0 0 0 -161 2 8.227925 6.453648 15.097868 0 0 0 -162 2 6.516816 7.554362 12.558027 0 0 0 -163 2 6.614245 9.484437 4.721580 0 0 0 -164 2 4.930416 10.235272 2.096807 0 0 0 -165 2 6.378727 9.407599 9.890313 0 0 0 -166 2 4.745041 10.233472 7.305313 0 0 0 -167 2 6.607879 9.406361 15.323664 0 0 0 -168 2 4.934053 10.285336 12.505737 0 0 0 -169 2 0.110419 1.854362 1.832825 0 0 0 -170 2 12.883461 1.921300 7.394522 0 0 0 -171 2 0.085737 1.871687 12.478325 0 0 0 -172 2 11.357467 4.733275 2.069553 0 0 0 -173 2 11.494387 4.736987 7.254291 0 0 0 -174 2 11.370328 4.654974 12.544717 0 0 0 -175 2 11.421510 6.634212 4.702248 0 0 0 -176 2 9.859272 7.466611 2.039289 0 0 0 -177 2 11.467497 6.605187 9.992040 0 0 0 -178 2 9.756517 7.402823 7.291686 0 0 0 -179 2 11.288617 6.566712 15.333646 0 0 0 -180 2 9.643760 7.605550 12.664032 0 0 0 -181 2 9.627652 9.444949 4.555521 0 0 0 -182 2 7.993836 10.279935 2.028197 0 0 0 -183 2 9.707024 9.378124 10.066830 0 0 0 -184 2 8.175833 10.396937 7.244625 0 0 0 -185 2 9.733654 9.292847 15.061107 0 0 0 -186 2 8.114258 10.409425 12.532833 0 0 0 -187 2 12.941269 7.442536 2.125646 0 0 0 -188 2 12.949583 7.583162 7.404187 0 0 0 -189 2 12.948284 7.448611 12.558027 0 0 0 -190 2 11.392282 10.327186 1.867051 0 0 0 -191 2 11.384098 10.306486 7.194871 0 0 0 -192 2 11.492438 10.248098 12.470402 0 0 0 diff --git a/examples/GaN-SNAP-LAMMPS/DATA/47/DATA b/examples/GaN-SNAP-LAMMPS/DATA/47/DATA deleted file mode 100755 index 64e09886..00000000 --- a/examples/GaN-SNAP-LAMMPS/DATA/47/DATA +++ /dev/null @@ -1,215 +0,0 @@ -LAMMPS DATA file - -192 atoms -0 bonds -0 angles -0 dihedrals -0 impropers - -2 atom types -0 bond types -0 angle types - -0.0 12.990503 xlo xhi -0.0 11.250148 ylo yhi -0.0 15.845291 zlo zhi - -Masses - -1 69.723 -2 14.0067 - -Atoms - -1 1 1.684868 0.961359 2.687995 0 0 0 -2 1 1.711239 0.843986 7.978896 0 0 0 -3 1 1.583023 0.994446 13.082030 0 0 0 -4 1 0.057409 3.643136 2.605124 0 0 0 -5 1 0.093055 3.822350 7.864335 0 0 0 -6 1 0.039511 3.725374 13.180588 0 0 0 -7 1 4.897680 1.047513 2.500545 0 0 0 -8 1 3.210343 1.808911 5.245583 0 0 0 -9 1 4.835325 1.002039 7.931519 0 0 0 -10 1 3.302056 1.880687 10.584654 0 0 0 -11 1 4.798822 0.978594 13.146362 0 0 0 -12 1 3.296860 1.981939 0.060212 0 0 0 -13 1 3.273347 3.676098 2.744087 0 0 0 -14 1 1.621215 4.633486 5.182519 0 0 0 -15 1 3.356097 3.811663 8.012488 0 0 0 -16 1 1.527293 4.650024 10.507012 0 0 0 -17 1 3.176308 3.861726 13.112612 0 0 0 -18 1 1.564576 4.653511 15.797755 0 0 0 -19 1 1.634465 6.573574 2.510686 0 0 0 -20 1 1.620046 6.534536 7.928033 0 0 0 -21 1 1.691883 6.578524 13.091854 0 0 0 -22 1 12.911655 9.269447 2.632537 0 0 0 -23 1 12.891008 9.387236 7.875743 0 0 0 -24 1 12.968104 9.331323 13.157612 0 0 0 -25 1 8.064894 1.021581 2.680706 0 0 0 -26 1 6.560594 1.946726 5.374564 0 0 0 -27 1 8.090485 0.834964 7.766411 0 0 0 -28 1 6.591901 1.966413 10.500040 0 0 0 -29 1 8.186875 0.971012 13.301329 0 0 0 -30 1 6.586575 1.824887 15.717578 0 0 0 -31 1 6.523701 3.672723 2.493890 0 0 0 -32 1 4.839092 4.785588 5.182202 0 0 0 -33 1 6.476935 3.750799 7.822186 0 0 0 -34 1 4.904564 4.579260 10.658810 0 0 0 -35 1 6.453162 3.677448 13.126873 0 0 0 -36 1 4.917685 4.675787 0.120424 0 0 0 -37 1 4.815190 6.575599 2.571374 0 0 0 -38 1 3.363241 7.557737 5.300408 0 0 0 -39 1 4.854811 6.632412 7.955762 0 0 0 -40 1 3.211642 7.400798 10.636944 0 0 0 -41 1 5.001084 6.581562 13.105323 0 0 0 -42 1 3.316865 7.611288 15.784286 0 0 0 -43 1 3.310110 9.431674 2.710020 0 0 0 -44 1 1.669150 10.422925 5.257309 0 0 0 -45 1 3.300627 9.458225 7.779087 0 0 0 -46 1 1.542362 10.201409 10.673705 0 0 0 -47 1 3.263344 9.282722 13.174884 0 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1 12.952051 1.810936 5.433509 0 0 0 -74 1 0.053261 1.880687 10.530780 0 0 0 -75 1 12.915028 1.943688 15.809322 0 0 0 -76 1 11.263546 4.771525 5.313084 0 0 0 -77 1 11.398907 4.641924 10.616345 0 0 0 -78 1 11.347205 4.739462 0.036444 0 0 0 -79 1 11.474512 6.509898 2.479471 0 0 0 -80 1 9.802114 7.569775 5.237185 0 0 0 -81 1 11.319795 6.651088 7.906958 0 0 0 -82 1 9.852517 7.538837 10.439036 0 0 0 -83 1 11.355129 6.525986 13.295625 0 0 0 -84 1 9.749632 7.409573 15.825325 0 0 0 -85 1 9.862910 9.363273 2.527165 0 0 0 -86 1 8.140629 10.414937 5.386290 0 0 0 -87 1 9.635446 9.455525 8.057489 0 0 0 -88 1 8.246761 10.382537 10.478174 0 0 0 -89 1 9.682212 9.286322 13.132260 0 0 0 -90 1 8.031119 10.365437 15.821681 0 0 0 -91 1 0.062354 7.612413 5.379159 0 0 0 -92 1 0.019486 7.498449 10.473579 0 0 0 -93 1 12.900479 7.549187 0.026937 0 0 0 -94 1 11.370328 10.389512 5.207713 0 0 0 -95 1 11.366950 10.224135 10.503526 0 0 0 -96 1 11.407351 10.397387 0.077642 0 0 0 -97 2 1.704874 0.932637 4.558849 0 0 0 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2.079377 0 0 0 -123 2 8.163882 1.031785 9.928342 0 0 0 -124 2 6.417698 1.819936 7.306580 0 0 0 -125 2 8.086848 0.905772 15.041142 0 0 0 -126 2 6.564751 1.815886 12.602235 0 0 0 -127 2 6.559814 3.801425 4.726650 0 0 0 -128 2 4.933793 4.720112 1.859128 0 0 0 -129 2 6.625027 3.731674 9.774484 0 0 0 -130 2 4.934053 4.799988 7.283446 0 0 0 -131 2 6.519414 3.672273 15.233821 0 0 0 -132 2 4.883390 4.639111 12.599700 0 0 0 -133 2 4.999785 6.564799 4.533655 0 0 0 -134 2 3.282051 7.541312 1.971946 0 0 0 -135 2 4.763488 6.672913 9.762759 0 0 0 -136 2 3.310370 7.519712 7.412585 0 0 0 -137 2 4.845458 6.565699 15.283575 0 0 0 -138 2 3.220476 7.423748 12.571654 0 0 0 -139 2 3.272827 9.447312 4.783376 0 0 0 -140 2 1.582893 10.200284 1.847719 0 0 0 -141 2 3.238792 9.484775 9.762917 0 0 0 -142 2 1.589128 10.238422 7.384064 0 0 0 -143 2 3.283480 9.462162 15.274543 0 0 0 -144 2 1.620046 10.215585 12.555333 0 0 0 -145 2 11.342268 0.955891 4.774820 0 0 0 -146 2 9.863040 1.987114 1.990485 0 0 0 -147 2 11.424368 0.857824 9.809502 0 0 0 -148 2 9.674677 1.969451 7.135293 0 0 0 -149 2 11.417613 0.867465 15.291022 0 0 0 -150 2 9.697281 1.942563 12.649771 0 0 0 -151 2 9.695332 3.683299 4.519711 0 0 0 -152 2 8.225976 4.734175 1.865941 0 0 0 -153 2 9.779381 3.671036 9.776227 0 0 0 -154 2 8.182718 4.618523 7.109623 0 0 0 -155 2 9.618558 3.728074 15.219402 0 0 0 -156 2 8.001371 4.575773 12.573872 0 0 0 -157 2 8.080223 6.486610 4.666121 0 0 0 -158 2 6.508502 7.578775 1.954833 0 0 0 -159 2 8.003189 6.674713 9.764026 0 0 0 -160 2 6.398083 7.490686 7.363782 0 0 0 -161 2 8.094123 6.619925 15.139858 0 0 0 -162 2 6.454721 7.525337 12.689226 0 0 0 -163 2 6.411333 9.289022 4.613990 0 0 0 -164 2 4.995238 10.378712 1.877508 0 0 0 -165 2 6.570597 9.424024 9.847214 0 0 0 -166 2 4.778816 10.423487 7.354433 0 0 0 -167 2 6.498629 9.347748 15.116566 0 0 0 -168 2 4.896640 10.224360 12.607781 0 0 0 -169 2 12.914119 1.962363 2.023761 0 0 0 -170 2 12.869821 1.953701 7.153832 0 0 0 -171 2 12.920484 1.847049 12.455508 0 0 0 -172 2 11.410209 4.603223 2.093004 0 0 0 -173 2 11.419432 4.641249 7.348095 0 0 0 -174 2 11.453857 4.636186 12.557551 0 0 0 -175 2 11.239383 6.617112 4.775137 0 0 0 -176 2 9.866547 7.536924 1.960696 0 0 0 -177 2 11.238994 6.531724 9.968906 0 0 0 -178 2 9.718066 7.440848 7.412585 0 0 0 -179 2 11.300828 6.458598 15.115615 0 0 0 -180 2 9.822639 7.566850 12.431423 0 0 0 -181 2 9.646358 9.277322 4.731562 0 0 0 -182 2 8.141538 10.276448 2.067810 0 0 0 -183 2 9.789124 9.323448 9.944821 0 0 0 -184 2 8.112829 10.245285 7.295964 0 0 0 -185 2 9.836409 9.428974 15.301005 0 0 0 -186 2 8.122832 10.276898 12.448694 0 0 0 -187 2 12.881903 7.491811 1.856593 0 0 0 -188 2 0.023383 7.576637 7.122300 0 0 0 -189 2 12.960625 7.506774 12.596689 0 0 0 -190 2 11.265105 10.370612 1.952615 0 0 0 -191 2 11.246009 10.214235 7.112634 0 0 0 -192 2 11.386436 10.371399 12.418746 0 0 0 diff --git a/examples/GaN-SNAP-LAMMPS/DATA/48/DATA b/examples/GaN-SNAP-LAMMPS/DATA/48/DATA deleted file mode 100755 index 678627a3..00000000 --- a/examples/GaN-SNAP-LAMMPS/DATA/48/DATA +++ /dev/null @@ -1,215 +0,0 @@ -LAMMPS DATA file - -192 atoms -0 bonds -0 angles -0 dihedrals -0 impropers - -2 atom types -0 bond types -0 angle types - -0.0 12.990503 xlo xhi -0.0 11.250148 ylo yhi -0.0 15.845291 zlo zhi - -Masses - -1 69.723 -2 14.0067 - -Atoms - -1 1 1.695391 1.047175 2.776412 0 0 0 -2 1 1.684349 1.040537 7.799844 0 0 0 -3 1 1.667591 0.910531 13.211328 0 0 0 -4 1 0.113616 3.838663 2.548240 0 0 0 -5 1 12.883368 3.685999 7.974459 0 0 0 -6 1 12.973025 3.746749 13.268688 0 0 0 -7 1 4.824023 1.013211 2.736640 0 0 0 -8 1 3.196443 1.945713 5.126110 0 0 0 -9 1 4.959125 0.935101 7.791288 0 0 0 -10 1 3.268151 1.796649 10.690976 0 0 0 -11 1 4.930416 0.857813 13.106274 0 0 0 -12 1 3.245547 1.828262 0.045951 0 0 0 -13 1 3.144221 3.810763 2.570265 0 0 0 -14 1 1.535867 4.632811 5.425427 0 0 0 -15 1 3.170722 3.841251 7.809827 0 0 0 -16 1 1.616408 4.785926 10.442680 0 0 0 -17 1 3.321672 3.787025 13.272174 0 0 0 -18 1 1.539634 4.658011 0.060212 0 0 0 -19 1 1.601209 6.505398 2.756605 0 0 0 -20 1 1.674476 6.603050 7.768471 0 0 0 -21 1 1.661875 6.462760 13.274392 0 0 0 -22 1 0.125883 9.420762 2.713031 0 0 0 -23 1 0.020638 9.476112 7.788753 0 0 0 -24 1 0.107842 9.372836 13.146045 0 0 0 -25 1 8.212206 0.830925 2.545071 0 0 0 -26 1 6.491225 1.964726 5.346993 0 0 0 -27 1 8.215064 0.916583 7.788753 0 0 0 -28 1 6.373011 1.878212 10.558192 0 0 0 -29 1 8.193760 1.008700 13.271857 0 0 0 -30 1 6.565660 1.837374 0.022183 0 0 0 -31 1 6.574624 3.674073 2.665812 0 0 0 -32 1 4.987574 4.673087 5.200583 0 0 0 -33 1 6.608009 3.677673 8.073176 0 0 0 -34 1 4.929117 4.694237 10.488473 0 0 0 -35 1 6.397953 3.667323 13.277086 0 0 0 -36 1 4.830259 4.658574 15.811065 0 0 0 -37 1 4.958085 6.589324 2.531127 0 0 0 -38 1 3.141104 7.442648 5.146392 0 0 0 -39 1 4.787520 6.491336 7.852609 0 0 0 -40 1 3.281011 7.559425 10.562154 0 0 0 -41 1 4.919374 6.519461 13.133052 0 0 0 -42 1 3.217358 7.456711 15.812015 0 0 0 -43 1 3.234765 9.314673 2.768014 0 0 0 -44 1 1.707212 10.414262 5.380744 0 0 0 -45 1 3.178906 9.398261 7.930093 0 0 0 -46 1 1.696430 10.397499 10.516202 0 0 0 -47 1 3.329986 9.422449 13.261241 0 0 0 -48 1 1.555353 10.230660 15.774937 0 0 0 -49 1 11.269651 0.911622 2.782591 0 0 0 -50 1 9.671819 1.826124 5.347786 0 0 0 -51 1 11.274458 1.015225 8.001238 0 0 0 -52 1 9.823548 1.964951 10.680360 0 0 0 -53 1 11.240812 0.950075 13.287227 0 0 0 -54 1 9.633627 1.817011 15.825642 0 0 0 -55 1 9.733784 3.837651 2.562342 0 0 0 -56 1 8.021636 4.628198 5.199315 0 0 0 -57 1 9.633627 3.788375 7.925022 0 0 0 -58 1 8.166870 4.685687 10.489107 0 0 0 -59 1 9.749113 3.845638 13.279146 0 0 0 -60 1 8.118285 4.775800 0.126762 0 0 0 -61 1 8.107373 6.523511 2.583733 0 0 0 -62 1 6.431988 7.440511 5.231956 0 0 0 -63 1 8.062816 6.671900 7.914723 0 0 0 -64 1 6.544875 7.422285 10.540129 0 0 0 -65 1 8.030859 6.540386 13.229550 0 0 0 -66 1 6.584886 7.592163 15.727085 0 0 0 -67 1 6.510970 9.349998 2.572800 0 0 0 -68 1 4.936261 10.419662 5.230847 0 0 0 -69 1 6.496810 9.441574 7.976678 0 0 0 -70 1 4.809734 10.341024 10.490375 0 0 0 -71 1 6.399382 9.433587 13.243652 0 0 0 -72 1 4.875596 10.356999 15.821681 0 0 0 -73 1 12.906325 1.977101 5.124684 0 0 0 -74 1 0.019486 1.986439 10.452821 0 0 0 -75 1 0.001299 1.854587 0.133100 0 0 0 -76 1 11.364482 4.733162 5.233066 0 0 0 -77 1 11.327589 4.785813 10.629179 0 0 0 -78 1 11.452168 4.684899 0.015845 0 0 0 -79 1 11.426187 6.600124 2.555845 0 0 0 -80 1 9.690915 7.495636 5.421308 0 0 0 -81 1 11.404753 6.603275 8.057330 0 0 0 -82 1 9.872263 7.481574 10.642331 0 0 0 -83 1 11.352920 6.601699 13.070463 0 0 0 -84 1 9.791072 7.451648 15.755606 0 0 0 -85 1 9.680263 9.480725 2.726024 0 0 0 -86 1 8.172585 10.421125 5.336852 0 0 0 -87 1 9.666104 9.378236 7.908226 0 0 0 -88 1 8.111140 10.413475 10.587665 0 0 0 -89 1 9.654672 9.480050 13.232085 0 0 0 -90 1 8.190512 10.331574 0.055459 0 0 0 -91 1 0.085737 7.436910 5.197097 0 0 0 -92 1 0.024682 7.425548 10.609531 0 0 0 -93 1 0.059756 7.419585 15.814709 0 0 0 -94 1 11.292125 10.263510 5.334951 0 0 0 -95 1 11.434890 10.280048 10.588932 0 0 0 -96 1 11.281473 10.255973 15.698088 0 0 0 -97 2 1.537166 1.003704 4.488337 0 0 0 -98 2 1.518460 0.922658 9.754044 0 0 0 -99 2 1.538595 1.045825 15.204349 0 0 0 -100 2 0.107938 3.856551 4.507351 0 0 0 -101 2 12.862034 3.640773 10.058749 0 0 0 -102 2 12.954191 3.737524 15.168855 0 0 0 -103 2 4.794795 0.930894 4.687671 0 0 0 -104 2 3.233726 1.856499 1.900643 0 0 0 -105 2 4.965100 1.036521 9.850542 0 0 0 -106 2 3.369866 1.962363 7.369962 0 0 0 -107 2 4.908981 1.012885 15.047163 0 0 0 -108 2 3.271398 1.985876 12.472462 0 0 0 -109 2 3.145261 3.692186 4.570891 0 0 0 -110 2 1.638882 4.641699 2.052282 0 0 0 -111 2 3.230998 3.827975 9.829309 0 0 0 -112 2 1.707212 4.760838 7.190276 0 0 0 -113 2 3.308291 3.786912 15.281198 0 0 0 -114 2 1.689805 4.799426 12.635352 0 0 0 -115 2 1.722801 6.528911 4.725224 0 0 0 -116 2 1.746054 6.503373 9.884292 0 0 0 -117 2 1.752809 6.587749 15.037973 0 0 0 -118 2 0.119048 9.274960 4.775454 0 0 0 -119 2 12.968692 9.454062 10.031653 0 0 0 -120 2 12.985766 9.282947 15.187869 0 0 0 -121 2 8.152060 0.961179 4.652177 0 0 0 -122 2 6.540069 1.850424 1.840430 0 0 0 -123 2 8.012153 1.048075 9.833587 0 0 0 -124 2 6.376648 1.928613 7.221491 0 0 0 -125 2 8.187395 1.001432 15.041142 0 0 0 -126 2 6.574104 1.968101 12.693979 0 0 0 -127 2 6.608789 3.836863 4.733464 0 0 0 -128 2 4.978221 4.702899 2.106948 0 0 0 -129 2 6.420037 3.814363 9.883342 0 0 0 -130 2 4.905474 4.798976 7.154782 0 0 0 -131 2 6.461216 3.641335 15.195475 0 0 0 -132 2 4.901966 4.608173 12.425243 0 0 0 -133 2 4.990302 6.652775 4.722530 0 0 0 -134 2 3.140714 7.393260 2.092212 0 0 0 -135 2 4.779856 6.658288 10.046231 0 0 0 -136 2 3.145520 7.585075 7.238287 0 0 0 -137 2 4.777647 6.629375 15.074259 0 0 0 -138 2 3.244508 7.558300 12.694455 0 0 0 -139 2 3.362592 9.335035 4.761351 0 0 0 -140 2 1.656809 10.345186 2.021384 0 0 0 -141 2 3.130192 9.414912 10.056531 0 0 0 -142 2 1.733972 10.293773 7.211509 0 0 0 -143 2 3.149937 9.430999 15.132728 0 0 0 -144 2 1.501572 10.364312 12.607622 0 0 0 -145 2 11.370458 1.006810 4.752320 0 0 0 -146 2 9.870834 1.853574 1.903178 0 0 0 -147 2 11.272379 0.922433 10.016600 0 0 0 -148 2 9.790553 1.830849 7.227354 0 0 0 -149 2 11.283031 0.905727 15.113080 0 0 0 -150 2 9.712739 1.806661 12.533149 0 0 0 -151 2 9.634407 3.696349 4.618268 0 0 0 -152 2 8.101657 4.579710 1.877984 0 0 0 -153 2 9.784837 3.769137 9.807759 0 0 0 -154 2 8.079963 4.716175 7.271721 0 0 0 -155 2 9.831603 3.660573 15.336815 0 0 0 -156 2 8.029170 4.740475 12.705705 0 0 0 -157 2 8.111270 6.554561 4.662001 0 0 0 -158 2 6.614634 7.451086 2.123427 0 0 0 -159 2 8.055411 6.626112 9.848007 0 0 0 -160 2 6.435755 7.420598 7.421142 0 0 0 -161 2 8.005528 6.618125 15.128133 0 0 0 -162 2 6.543706 7.532649 12.428729 0 0 0 -163 2 6.478494 9.325698 4.509728 0 0 0 -164 2 4.882870 10.274648 1.848036 0 0 0 -165 2 6.388080 9.354723 9.982216 0 0 0 -166 2 4.960943 10.291973 7.330824 0 0 0 -167 2 6.477714 9.311523 15.259807 0 0 0 -168 2 4.848186 10.406725 12.595580 0 0 0 -169 2 12.960105 1.842549 1.880678 0 0 0 -170 2 0.019486 1.918038 7.301985 0 0 0 -171 2 0.115615 1.932888 12.457251 0 0 0 -172 2 11.396049 4.733612 2.098233 0 0 0 -173 2 11.364482 4.769050 7.325912 0 0 0 -174 2 11.268482 4.786151 12.393394 0 0 0 -175 2 11.279004 6.592137 4.533813 0 0 0 -176 2 9.790033 7.511386 2.075733 0 0 0 -177 2 11.307194 6.506186 10.046865 0 0 0 -178 2 9.651944 7.437810 7.289943 0 0 0 -179 2 11.410598 6.514398 15.198327 0 0 0 -180 2 9.670261 7.514874 12.506846 0 0 0 -181 2 9.740279 9.361473 4.764679 0 0 0 -182 2 8.234680 10.391199 1.859920 0 0 0 -183 2 9.827316 9.327273 9.917409 0 0 0 -184 2 8.015920 10.301761 7.205171 0 0 0 -185 2 9.773015 9.343361 15.225740 0 0 0 -186 2 8.210777 10.392212 12.564365 0 0 0 -187 2 0.036373 7.458736 1.852314 0 0 0 -188 2 12.863586 7.530962 7.261897 0 0 0 -189 2 12.872679 7.511499 12.499874 0 0 0 -190 2 11.241981 10.345186 2.001894 0 0 0 -191 2 11.344606 10.381187 7.159695 0 0 0 -192 2 11.432162 10.309748 12.524435 0 0 0 diff --git a/examples/GaN-SNAP-LAMMPS/DATA/49/DATA b/examples/GaN-SNAP-LAMMPS/DATA/49/DATA deleted file mode 100755 index 6b338fe4..00000000 --- a/examples/GaN-SNAP-LAMMPS/DATA/49/DATA +++ /dev/null @@ -1,215 +0,0 @@ -LAMMPS DATA file - -192 atoms -0 bonds -0 angles -0 dihedrals -0 impropers - -2 atom types -0 bond types -0 angle types - -0.0 12.990503 xlo xhi -0.0 11.250148 ylo yhi -0.0 15.845291 zlo zhi - -Masses - -1 69.723 -2 14.0067 - -Atoms - -1 1 1.747612 1.027240 2.780848 0 0 0 -2 1 1.713317 0.910722 7.787168 0 0 0 -3 1 1.684219 0.978594 13.178370 0 0 0 -4 1 12.897806 3.706699 2.692590 0 0 0 -5 1 0.001027 3.802888 7.964001 0 0 0 -6 1 12.878222 3.861388 13.097876 0 0 0 -7 1 4.861176 0.951178 2.684826 0 0 0 -8 1 3.328687 1.937163 5.211833 0 0 0 -9 1 4.788299 1.014437 7.966061 0 0 0 -10 1 3.275685 1.870000 10.593369 0 0 0 -11 1 4.839872 1.019938 13.192630 0 0 0 -12 1 3.237493 1.830399 0.011092 0 0 0 -13 1 3.267371 3.670023 2.705583 0 0 0 -14 1 1.545870 4.637986 5.339229 0 0 0 -15 1 3.167215 3.732462 7.824563 0 0 0 -16 1 1.529892 4.758138 10.503685 0 0 0 -17 1 3.242560 3.652586 13.066502 0 0 0 -18 1 1.576398 4.645861 15.788564 0 0 0 -19 1 1.663824 6.544661 2.740601 0 0 0 -20 1 1.720982 6.573799 7.865761 0 0 0 -21 1 1.634725 6.506523 13.157137 0 0 0 -22 1 0.090862 9.457325 2.500387 0 0 0 -23 1 0.115613 9.266072 7.783841 0 0 0 -24 1 0.065953 9.346511 13.106907 0 0 0 -25 1 8.206491 1.018082 2.721904 0 0 0 -26 1 6.455760 1.980251 5.220865 0 0 0 -27 1 8.135692 0.874823 7.944829 0 0 0 -28 1 6.447576 1.921188 10.422398 0 0 0 -29 1 8.012802 0.866576 13.101520 0 0 0 -30 1 6.406007 1.823762 15.739286 0 0 0 -31 1 6.374570 3.653486 2.484066 0 0 0 -32 1 4.900927 4.636074 5.266658 0 0 0 -33 1 6.410943 3.819988 7.764826 0 0 0 -34 1 4.874816 4.781538 10.636785 0 0 0 -35 1 6.567869 3.719749 13.345696 0 0 0 -36 1 4.833766 4.771638 0.069719 0 0 0 -37 1 4.851303 6.565812 2.583416 0 0 0 -38 1 3.147469 7.564600 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0 0 0 -64 1 6.502266 7.511611 10.504952 0 0 0 -65 1 8.045019 6.483685 13.218141 0 0 0 -66 1 6.450694 7.534674 0.087149 0 0 0 -67 1 6.576053 9.416262 2.566462 0 0 0 -68 1 4.876765 10.324261 5.270461 0 0 0 -69 1 6.402370 9.339536 8.032770 0 0 0 -70 1 4.805577 10.242135 10.566432 0 0 0 -71 1 6.464724 9.452600 13.265202 0 0 0 -72 1 4.919504 10.269810 15.685887 0 0 0 -73 1 12.944647 1.931200 5.188540 0 0 0 -74 1 0.118214 1.766048 10.657067 0 0 0 -75 1 12.911781 1.819711 15.823899 0 0 0 -76 1 11.388125 4.708637 5.424318 0 0 0 -77 1 11.360455 4.714937 10.595112 0 0 0 -78 1 11.397218 4.659249 0.055459 0 0 0 -79 1 11.315897 6.535324 2.716675 0 0 0 -80 1 9.744696 7.526012 5.245267 0 0 0 -81 1 11.288228 6.563561 7.907751 0 0 0 -82 1 9.649086 7.492824 10.551696 0 0 0 -83 1 11.247697 6.470635 13.141450 0 0 0 -84 1 9.871613 7.526687 0.076057 0 0 0 -85 1 9.684680 9.382736 2.484066 0 0 0 -86 1 8.203113 10.254398 5.324493 0 0 0 -87 1 9.776393 9.298585 7.998703 0 0 0 -88 1 8.075416 10.253273 10.624901 0 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-187 2 12.975824 7.426335 1.959429 0 0 0 -188 2 12.860728 7.510599 7.288358 0 0 0 -189 2 12.877486 7.474598 12.551213 0 0 0 -190 2 11.462430 10.368587 2.064008 0 0 0 -191 2 11.457104 10.253498 7.216421 0 0 0 -192 2 11.487242 10.232460 12.423975 0 0 0 diff --git a/examples/GaN-SNAP-LAMMPS/DATA/5/DATA b/examples/GaN-SNAP-LAMMPS/DATA/5/DATA deleted file mode 100755 index b174a2e0..00000000 --- a/examples/GaN-SNAP-LAMMPS/DATA/5/DATA +++ /dev/null @@ -1,215 +0,0 @@ -LAMMPS DATA file - -192 atoms -0 bonds -0 angles -0 dihedrals -0 impropers - -2 atom types -0 bond types -0 angle types - -0.0 12.990503 xlo xhi -0.0 11.250148 ylo yhi -0.0 15.845291 zlo zhi - -Masses - -1 69.723 -2 14.0067 - -Atoms - -1 1 1.641220 0.909698 2.544278 0 0 0 -2 1 1.699677 0.857734 7.913772 0 0 0 -3 1 1.497285 0.866993 13.194215 0 0 0 -4 1 0.087876 3.669236 2.709069 0 0 0 -5 1 0.049643 3.645273 7.913613 0 0 0 -6 1 0.122473 3.662823 13.275977 0 0 0 -7 1 4.907422 0.958704 2.634913 0 0 0 -8 1 3.265293 1.858524 5.141955 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3.788937 13.104689 0 0 0 -60 1 8.214805 4.744075 15.814234 0 0 0 -61 1 7.989159 6.483685 2.563768 0 0 0 -62 1 6.592031 7.522862 5.219597 0 0 0 -63 1 8.063075 6.548036 8.045129 0 0 0 -64 1 6.605671 7.501261 10.598439 0 0 0 -65 1 8.176093 6.455448 13.222737 0 0 0 -66 1 6.377428 7.482699 15.829604 0 0 0 -67 1 6.371192 9.277210 2.769757 0 0 0 -68 1 4.880272 10.282635 5.233224 0 0 0 -69 1 6.404708 9.296335 7.869880 0 0 0 -70 1 4.828830 10.376574 10.553914 0 0 0 -71 1 6.486158 9.292172 13.321453 0 0 0 -72 1 4.916776 10.388049 0.044367 0 0 0 -73 1 0.126008 1.982951 5.197097 0 0 0 -74 1 0.032476 1.926363 10.557400 0 0 0 -75 1 0.090934 1.805536 15.720747 0 0 0 -76 1 11.237565 4.609523 5.287098 0 0 0 -77 1 11.369418 4.661724 10.497980 0 0 0 -78 1 11.237695 4.758475 0.038029 0 0 0 -79 1 11.353310 6.504948 2.731570 0 0 0 -80 1 9.827056 7.579337 5.265865 0 0 0 -81 1 11.488931 6.639387 7.783524 0 0 0 -82 1 9.674677 7.571575 10.528245 0 0 0 -83 1 11.357987 6.664138 13.346330 0 0 0 -84 1 9.811857 7.516899 0.126762 0 0 0 -85 1 9.741708 9.299935 2.580247 0 0 0 -86 1 8.066193 10.325724 5.139262 0 0 0 -87 1 9.630899 9.300160 8.058915 0 0 0 -88 1 8.199865 10.360037 10.707138 0 0 0 -89 1 9.872393 9.484775 13.088052 0 0 0 -90 1 8.238187 10.319536 15.704901 0 0 0 -91 1 12.941659 7.589012 5.382328 0 0 0 -92 1 12.861248 7.531637 10.654056 0 0 0 -93 1 12.924252 7.402035 15.764796 0 0 0 -94 1 11.263416 10.308961 5.250654 0 0 0 -95 1 11.335903 10.399637 10.532840 0 0 0 -96 1 11.310571 10.210972 15.750853 0 0 0 -97 2 1.556002 0.831588 4.691157 0 0 0 -98 2 1.495856 0.962473 9.879697 0 0 0 -99 2 1.558601 0.971810 15.133520 0 0 0 -100 2 12.887535 3.758000 4.520820 0 0 0 -101 2 0.099623 3.787475 10.018977 0 0 0 -102 2 0.068243 3.819088 15.232712 0 0 0 -103 2 4.926129 0.979955 4.570257 0 0 0 -104 2 3.255810 1.958988 1.845026 0 0 0 -105 2 4.871569 0.922377 10.036882 0 0 0 -106 2 3.281401 1.983739 7.294855 0 0 0 -107 2 4.959904 0.930489 15.204824 0 0 0 -108 2 3.164227 1.905325 12.696356 0 0 0 -109 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0 0 0 -134 2 3.364930 7.465486 1.919657 0 0 0 -135 2 4.971855 6.497298 9.791756 0 0 0 -136 2 3.252952 7.591375 7.237020 0 0 0 -137 2 4.797653 6.467823 15.327783 0 0 0 -138 2 3.274386 7.472573 12.601918 0 0 0 -139 2 3.323490 9.337623 4.688146 0 0 0 -140 2 1.546909 10.415837 2.053233 0 0 0 -141 2 3.161109 9.362261 9.951001 0 0 0 -142 2 1.735531 10.319198 7.308006 0 0 0 -143 2 3.294651 9.470375 15.080597 0 0 0 -144 2 1.599261 10.270485 12.611108 0 0 0 -145 2 11.468146 0.935416 4.723956 0 0 0 -146 2 9.697800 1.886200 1.950872 0 0 0 -147 2 11.469835 0.977143 10.012798 0 0 0 -148 2 9.641551 1.825337 7.352690 0 0 0 -149 2 11.292904 0.832668 15.170440 0 0 0 -150 2 9.856414 1.821511 12.571812 0 0 0 -151 2 9.706374 3.643586 4.627142 0 0 0 -152 2 8.204022 4.633374 1.842173 0 0 0 -153 2 9.677016 3.786237 9.854662 0 0 0 -154 2 8.160504 4.578023 7.337003 0 0 0 -155 2 9.714558 3.645048 15.160774 0 0 0 -156 2 8.175313 4.782326 12.703011 0 0 0 -157 2 8.244683 6.651763 4.742971 0 0 0 -158 2 6.573454 7.512511 1.960379 0 0 0 -159 2 8.022155 6.597424 10.024206 0 0 0 -160 2 6.436664 7.576637 7.131807 0 0 0 -161 2 8.087628 6.510461 15.080597 0 0 0 -162 2 6.529287 7.458736 12.695088 0 0 0 -163 2 6.494862 9.428862 4.472650 0 0 0 -164 2 4.898849 10.329886 2.083497 0 0 0 -165 2 6.535522 9.460250 10.036249 0 0 0 -166 2 4.781025 10.243485 7.360137 0 0 0 -167 2 6.381065 9.350336 15.127182 0 0 0 -168 2 4.932234 10.223572 12.642324 0 0 0 -169 2 0.074046 1.882262 1.907931 0 0 0 -170 2 12.879045 1.903300 7.117229 0 0 0 -171 2 12.876706 1.791699 12.533942 0 0 0 -172 2 11.411508 4.767700 1.985573 0 0 0 -173 2 11.249516 4.645636 7.312760 0 0 0 -174 2 11.441126 4.640124 12.548995 0 0 0 -175 2 11.449440 6.584037 4.638550 0 0 0 -176 2 9.698970 7.480224 2.079377 0 0 0 -177 2 11.325900 6.554224 9.866862 0 0 0 -178 2 9.789513 7.515324 7.315929 0 0 0 -179 2 11.364352 6.539711 15.183433 0 0 0 -180 2 9.630250 7.480111 12.698257 0 0 0 -181 2 9.815754 9.426612 4.711280 0 0 0 -182 2 8.185706 10.389849 2.071772 0 0 0 -183 2 9.867197 9.287672 9.875894 0 0 0 -184 2 8.116986 10.258223 7.121190 0 0 0 -185 2 9.866157 9.426049 15.079012 0 0 0 -186 2 8.027611 10.358686 12.511917 0 0 0 -187 2 12.880474 7.479999 1.873072 0 0 0 -188 2 0.077943 7.596888 7.110891 0 0 0 -189 2 0.038972 7.540299 12.471670 0 0 0 -190 2 11.455805 10.266323 1.836152 0 0 0 -191 2 11.261078 10.379612 7.334943 0 0 0 -192 2 11.440346 10.340574 12.652781 0 0 0 diff --git a/examples/GaN-SNAP-LAMMPS/DATA/50/DATA b/examples/GaN-SNAP-LAMMPS/DATA/50/DATA deleted file mode 100755 index afe3f18a..00000000 --- a/examples/GaN-SNAP-LAMMPS/DATA/50/DATA +++ /dev/null @@ -1,215 +0,0 @@ -LAMMPS DATA file - -192 atoms -0 bonds -0 angles -0 dihedrals -0 impropers - -2 atom types -0 bond types -0 angle types - -0.0 12.990503 xlo xhi -0.0 11.250148 ylo yhi -0.0 15.845291 zlo zhi - -Masses - -1 69.723 -2 14.0067 - -Atoms - -1 1 1.626281 1.033967 2.619860 0 0 0 -2 1 1.659537 0.928362 7.934212 0 0 0 -3 1 1.504560 1.005504 13.253318 0 0 0 -4 1 12.912647 3.640773 2.718735 0 0 0 -5 1 0.017542 3.784775 7.959882 0 0 0 -6 1 0.060883 3.837201 13.251575 0 0 0 -7 1 4.772841 0.985603 2.618751 0 0 0 -8 1 3.284259 1.908475 5.332733 0 0 0 -9 1 4.756862 0.875397 7.811887 0 0 0 -10 1 3.358954 1.878437 10.613017 0 0 0 -11 1 4.915087 0.843334 13.111819 0 0 0 -12 1 3.191507 1.968101 15.754022 0 0 0 -13 1 3.182284 3.789725 2.682449 0 0 0 -14 1 1.676684 4.763425 5.348261 0 0 0 -15 1 3.122787 3.768912 8.050517 0 0 0 -16 1 1.517680 4.699862 10.694620 0 0 0 -17 1 3.169553 3.755749 13.080604 0 0 0 -18 1 1.688376 4.645861 15.740712 0 0 0 -19 1 1.748652 6.610475 2.738542 0 0 0 -20 1 1.671358 6.605187 7.926924 0 0 0 -21 1 1.543012 6.560974 13.217824 0 0 0 -22 1 0.085292 9.308260 2.644262 0 0 0 -23 1 0.079973 9.342573 7.932311 0 0 0 -24 1 0.056494 9.308148 13.244445 0 0 0 -25 1 7.989159 0.940479 2.657572 0 0 0 -26 1 6.367165 1.963376 5.381853 0 0 0 -27 1 8.190512 1.002343 7.877169 0 0 0 -28 1 6.404968 1.841762 10.603985 0 0 0 -29 1 8.231302 0.846011 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2.730302 0 0 0 -80 1 9.776653 7.608700 5.167942 0 0 0 -81 1 11.396958 6.519573 7.785742 0 0 0 -82 1 9.840826 7.520499 10.495604 0 0 0 -83 1 11.280433 6.526548 13.061907 0 0 0 -84 1 9.782758 7.442536 0.076057 0 0 0 -85 1 9.690656 9.356861 2.494683 0 0 0 -86 1 7.997214 10.242135 5.203752 0 0 0 -87 1 9.630120 9.337623 7.774492 0 0 0 -88 1 8.015530 10.216260 10.686222 0 0 0 -89 1 9.694033 9.395786 13.160148 0 0 0 -90 1 8.236369 10.367124 0.117255 0 0 0 -91 1 0.025981 7.542774 5.241781 0 0 0 -92 1 12.918666 7.417110 10.454247 0 0 0 -93 1 0.114316 7.395397 0.114086 0 0 0 -94 1 11.372536 10.381974 5.259686 0 0 0 -95 1 11.326809 10.370499 10.513667 0 0 0 -96 1 11.381370 10.400087 0.102994 0 0 0 -97 2 1.557302 0.923030 4.731087 0 0 0 -98 2 1.533529 0.995548 10.028167 0 0 0 -99 2 1.624333 0.953326 15.301956 0 0 0 -100 2 0.125917 3.815375 4.579764 0 0 0 -101 2 0.000496 3.694999 9.911863 0 0 0 -102 2 12.881026 3.650111 15.233345 0 0 0 -103 2 4.901836 0.843345 4.661684 0 0 0 -104 2 3.259187 1.955163 2.031366 0 0 0 -105 2 4.812072 0.849026 9.769572 0 0 0 -106 2 3.279323 1.919838 7.196614 0 0 0 -107 2 4.851174 0.907324 15.058097 0 0 0 -108 2 3.135907 1.789674 12.606038 0 0 0 -109 2 3.174619 3.690949 4.471383 0 0 0 -110 2 1.682790 4.701324 2.002686 0 0 0 -111 2 3.310630 3.823138 9.874944 0 0 0 -112 2 1.529242 4.619086 7.337796 0 0 0 -113 2 3.291664 3.651011 15.153802 0 0 0 -114 2 1.621475 4.749250 12.438078 0 0 0 -115 2 1.620046 6.466248 4.718094 0 0 0 -116 2 1.596143 6.503261 9.775910 0 0 0 -117 2 1.514433 6.658738 15.096917 0 0 0 -118 2 0.118625 9.339086 4.772760 0 0 0 -119 2 12.949752 9.276872 9.944504 0 0 0 -120 2 0.014451 9.466550 15.095808 0 0 0 -121 2 8.193760 0.903252 4.776721 0 0 0 -122 2 6.582548 1.922650 1.895731 0 0 0 -123 2 7.993187 0.872269 9.920420 0 0 0 -124 2 6.393536 1.954601 7.398166 0 0 0 -125 2 8.075806 0.930567 15.033061 0 0 0 -126 2 6.446148 1.871687 12.474363 0 0 0 -127 2 6.542797 3.842601 4.649325 0 0 0 -128 2 4.810513 4.784013 1.848036 0 0 0 -129 2 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7.536137 7.229097 0 0 0 -179 2 11.264845 6.590449 15.229067 0 0 0 -180 2 9.849789 7.523987 12.545033 0 0 0 -181 2 9.762753 9.483650 4.632846 0 0 0 -182 2 8.079703 10.421237 2.142125 0 0 0 -183 2 9.845762 9.429424 9.960983 0 0 0 -184 2 8.179730 10.298273 7.236069 0 0 0 -185 2 9.669611 9.461037 15.330636 0 0 0 -186 2 8.235719 10.224135 12.409556 0 0 0 -187 2 12.903077 7.506324 1.849779 0 0 0 -188 2 12.863196 7.408223 7.301985 0 0 0 -189 2 12.875148 7.535687 12.573713 0 0 0 -190 2 11.256011 10.254510 1.938988 0 0 0 -191 2 11.269651 10.366449 7.250647 0 0 0 -192 2 11.241332 10.353511 12.670370 0 0 0 diff --git a/examples/GaN-SNAP-LAMMPS/DATA/51/DATA b/examples/GaN-SNAP-LAMMPS/DATA/51/DATA deleted file mode 100755 index 0ad62fec..00000000 --- a/examples/GaN-SNAP-LAMMPS/DATA/51/DATA +++ /dev/null @@ -1,215 +0,0 @@ -LAMMPS DATA file - -192 atoms -0 bonds -0 angles -0 dihedrals -0 impropers - -2 atom types -0 bond types -0 angle types - -0.0 12.990503 xlo xhi -0.0 11.250148 ylo yhi -0.0 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-174 2 11.342528 4.755550 12.449328 0 0 0 -175 2 11.493348 6.643550 4.729661 0 0 0 -176 2 9.718325 7.403048 2.021225 0 0 0 -177 2 11.494257 6.548374 9.800629 0 0 0 -178 2 9.843424 7.424423 7.109940 0 0 0 -179 2 11.461391 6.669200 15.260758 0 0 0 -180 2 9.800166 7.511386 12.581953 0 0 0 -181 2 9.640512 9.417612 4.730136 0 0 0 -182 2 8.193890 10.222672 2.117882 0 0 0 -183 2 9.707024 9.335711 10.053520 0 0 0 -184 2 8.012802 10.369712 7.228463 0 0 0 -185 2 9.635966 9.482975 15.246655 0 0 0 -186 2 8.204542 10.416737 12.591302 0 0 0 -187 2 12.868003 7.499124 1.885906 0 0 0 -188 2 0.029878 7.472798 7.310066 0 0 0 -189 2 0.089634 7.556612 12.510174 0 0 0 -190 2 11.415535 10.211985 2.082863 0 0 0 -191 2 11.425148 10.208160 7.268393 0 0 0 -192 2 11.477889 10.255973 12.683204 0 0 0 diff --git a/examples/GaN-SNAP-LAMMPS/DATA/52/DATA b/examples/GaN-SNAP-LAMMPS/DATA/52/DATA deleted file mode 100755 index 74a5ed31..00000000 --- a/examples/GaN-SNAP-LAMMPS/DATA/52/DATA +++ /dev/null @@ -1,215 +0,0 @@ -LAMMPS DATA file - -192 atoms -0 bonds -0 angles -0 dihedrals -0 impropers - -2 atom types -0 bond types -0 angle types - -0.0 12.990503 xlo xhi -0.0 11.250148 ylo yhi -0.0 15.845291 zlo zhi - -Masses - -1 69.723 -2 14.0067 - -Atoms - -1 1 1.608224 0.966883 2.544912 0 0 0 -2 1 1.660186 1.042911 7.979688 0 0 0 -3 1 1.723580 1.033551 13.339992 0 0 0 -4 1 0.004648 3.677673 2.737432 0 0 0 -5 1 12.873307 3.666648 8.054003 0 0 0 -6 1 12.933583 3.850026 13.257279 0 0 0 -7 1 4.916646 0.909766 2.752010 0 0 0 -8 1 3.262825 1.830737 5.386923 0 0 0 -9 1 4.945355 1.043406 8.068739 0 0 0 -10 1 3.274516 1.765936 10.481026 0 0 0 -11 1 4.822075 0.876150 13.269480 0 0 0 -12 1 3.286338 1.971701 0.007923 0 0 0 -13 1 3.232557 3.781625 2.546655 0 0 0 -14 1 1.506768 4.622461 5.391677 0 0 0 -15 1 3.146560 3.854638 7.886676 0 0 0 -16 1 1.541323 4.701662 10.530305 0 0 0 -17 1 3.322581 3.654836 13.049072 0 0 0 -18 1 1.712668 4.602211 0.137854 0 0 0 -19 1 1.652912 6.509336 2.697661 0 0 0 -20 1 1.630698 6.591574 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6.572415 9.458337 13.270589 0 0 0 -72 1 4.775049 10.221435 15.711081 0 0 0 -73 1 12.911261 1.862125 5.218805 0 0 0 -74 1 0.037672 1.929288 10.505111 0 0 0 -75 1 0.081840 1.819486 0.030106 0 0 0 -76 1 11.459313 4.615373 5.277749 0 0 0 -77 1 11.421640 4.626961 10.655641 0 0 0 -78 1 11.387215 4.795263 0.117255 0 0 0 -79 1 11.435280 6.648838 2.580247 0 0 0 -80 1 9.800815 7.491811 5.352381 0 0 0 -81 1 11.382669 6.542636 7.777819 0 0 0 -82 1 9.743007 7.503624 10.563580 0 0 0 -83 1 11.368379 6.545111 13.248089 0 0 0 -84 1 9.800295 7.537487 15.837843 0 0 0 -85 1 9.637914 9.444837 2.602272 0 0 0 -86 1 8.085809 10.270935 5.247802 0 0 0 -87 1 9.746904 9.326260 7.909177 0 0 0 -88 1 7.996564 10.231335 10.437293 0 0 0 -89 1 9.745735 9.473862 13.153493 0 0 0 -90 1 8.233901 10.268685 15.752596 0 0 0 -91 1 12.888917 7.523537 5.293912 0 0 0 -92 1 0.027280 7.565950 10.406236 0 0 0 -93 1 0.127307 7.407098 0.122009 0 0 0 -94 1 11.298620 10.382199 5.312767 0 0 0 -95 1 11.309272 10.346649 10.680677 0 0 0 -96 1 11.335773 10.395587 0.125178 0 0 0 -97 2 1.730595 1.023122 4.536982 0 0 0 -98 2 1.497545 0.845707 9.978255 0 0 0 -99 2 1.574059 0.872955 15.069188 0 0 0 -100 2 12.954990 3.712436 4.661526 0 0 0 -101 2 12.863435 3.657423 9.926282 0 0 0 -102 2 0.121630 3.809525 15.142552 0 0 0 -103 2 4.980039 1.038096 4.573902 0 0 0 -104 2 3.183323 1.863475 2.062265 0 0 0 -105 2 4.766735 1.000937 9.836123 0 0 0 -106 2 3.151106 1.976089 7.368852 0 0 0 -107 2 4.774400 0.989518 15.107851 0 0 0 -108 2 3.146690 1.814424 12.650246 0 0 0 -109 2 3.168903 3.835176 4.709537 0 0 0 -110 2 1.721372 4.581173 1.902861 0 0 0 -111 2 3.224243 3.730099 9.825665 0 0 0 -112 2 1.721501 4.595123 7.320524 0 0 0 -113 2 3.182024 3.662823 15.223204 0 0 0 -114 2 1.745664 4.742837 12.426828 0 0 0 -115 2 1.539505 6.522836 4.496101 0 0 0 -116 2 1.692663 6.566037 9.803323 0 0 0 -117 2 1.644728 6.498198 15.081389 0 0 0 -118 2 0.025786 9.328173 4.622230 0 0 0 -119 2 12.912759 9.284860 9.847373 0 0 0 -120 2 12.913264 9.453162 15.253311 0 0 0 -121 2 8.079314 0.973644 4.590381 0 0 0 -122 2 6.506813 1.794061 2.037863 0 0 0 -123 2 8.111270 0.923671 9.997269 0 0 0 -124 2 6.393796 1.918825 7.128638 0 0 0 -125 2 8.140239 0.909203 15.145879 0 0 0 -126 2 6.551760 1.919500 12.643116 0 0 0 -127 2 6.517335 3.739887 4.528426 0 0 0 -128 2 4.784532 4.772538 1.963390 0 0 0 -129 2 6.472388 3.750124 9.926124 0 0 0 -130 2 4.852213 4.753638 7.241932 0 0 0 -131 2 6.422375 3.783987 15.327150 0 0 0 -132 2 4.793496 4.753750 12.515086 0 0 0 -133 2 4.871958 6.655588 4.597036 0 0 0 -134 2 3.283869 7.477749 1.884639 0 0 0 -135 2 4.966659 6.650188 9.911705 0 0 0 -136 2 3.177087 7.596325 7.173005 0 0 0 -137 2 4.915996 6.555911 15.299103 0 0 0 -138 2 3.124346 7.489111 12.523959 0 0 0 -139 2 3.129932 9.470937 4.773869 0 0 0 -140 2 1.555353 10.283873 2.036754 0 0 0 -141 2 3.197223 9.472175 9.809819 0 0 0 -142 2 1.679023 10.223460 7.208498 0 0 0 -143 2 3.322971 9.295097 15.131777 0 0 0 -144 2 1.693052 10.267560 12.593203 0 0 0 -145 2 11.425667 0.984883 4.679273 0 0 0 -146 2 9.702477 1.930638 2.074465 0 0 0 -147 2 11.412677 0.866655 9.847056 0 0 0 -148 2 9.694553 1.987114 7.358553 0 0 0 -149 2 11.418782 1.012705 15.147939 0 0 0 -150 2 9.828485 1.935025 12.596372 0 0 0 -151 2 9.621027 3.862401 4.714766 0 0 0 -152 2 8.074247 4.584660 1.974165 0 0 0 -153 2 9.761844 3.756199 9.831211 0 0 0 -154 2 8.199476 4.744975 7.333993 0 0 0 -155 2 9.826276 3.712436 15.186919 0 0 0 -156 2 8.244033 4.787726 12.439504 0 0 0 -157 2 8.247541 6.591124 4.494517 0 0 0 -158 2 6.481222 7.456486 1.969887 0 0 0 -159 2 8.059958 6.503823 10.053520 0 0 0 -160 2 6.583587 7.586087 7.403078 0 0 0 -161 2 8.236888 6.464110 15.319702 0 0 0 -162 2 6.590992 7.390110 12.467550 0 0 0 -163 2 6.606970 9.366198 4.610504 0 0 0 -164 2 4.760110 10.313348 1.948337 0 0 0 -165 2 6.456020 9.264047 9.994259 0 0 0 -166 2 4.993679 10.282410 7.247319 0 0 0 -167 2 6.591641 9.283060 15.335864 0 0 0 -168 2 4.877674 10.273860 12.546776 0 0 0 -169 2 0.054560 1.805536 2.006014 0 0 0 -170 2 0.031177 1.796761 7.411318 0 0 0 -171 2 12.915158 1.959663 12.464856 0 0 0 -172 2 11.355908 4.778613 2.013620 0 0 0 -173 2 11.247178 4.637424 7.189167 0 0 0 -174 2 11.292644 4.727200 12.566583 0 0 0 -175 2 11.289527 6.672013 4.477562 0 0 0 -176 2 9.781979 7.409460 1.948971 0 0 0 -177 2 11.321094 6.470185 9.836123 0 0 0 -178 2 9.846282 7.539962 7.267284 0 0 0 -179 2 11.356558 6.574024 15.136848 0 0 0 -180 2 9.661427 7.413510 12.576882 0 0 0 -181 2 9.707673 9.279572 4.573268 0 0 0 -182 2 8.143487 10.313011 2.075258 0 0 0 -183 2 9.826926 9.464525 9.930877 0 0 0 -184 2 7.999552 10.415612 7.394522 0 0 0 -185 2 9.652593 9.412549 15.050332 0 0 0 -186 2 8.214675 10.327974 12.489733 0 0 0 -187 2 12.887489 7.399560 2.135153 0 0 0 -188 2 12.885020 7.535124 7.227037 0 0 0 -189 2 0.015589 7.578662 12.643433 0 0 0 -190 2 11.424628 10.328649 1.949763 0 0 0 -191 2 11.464639 10.368137 7.130856 0 0 0 -192 2 11.247438 10.391762 12.577199 0 0 0 diff --git a/examples/GaN-SNAP-LAMMPS/DATA/53/DATA b/examples/GaN-SNAP-LAMMPS/DATA/53/DATA deleted file mode 100755 index 98b9dca9..00000000 --- a/examples/GaN-SNAP-LAMMPS/DATA/53/DATA +++ /dev/null @@ -1,215 +0,0 @@ -LAMMPS DATA file - -192 atoms -0 bonds -0 angles -0 dihedrals -0 impropers - -2 atom types -0 bond types -0 angle types - -0.0 12.990503 xlo xhi -0.0 11.250148 ylo yhi -0.0 15.845291 zlo zhi - -Masses - -1 69.723 -2 14.0067 - -Atoms - -1 1 1.533919 0.992511 2.566620 0 0 0 -2 1 1.579385 0.825311 7.937381 0 0 0 -3 1 1.609264 0.861311 13.263459 0 0 0 -4 1 0.011441 3.694886 2.601480 0 0 0 -5 1 12.924154 3.768687 7.775443 0 0 0 -6 1 0.026579 3.646511 13.313847 0 0 0 -7 1 4.830649 0.850264 2.665019 0 0 0 -8 1 3.281401 1.938288 5.351272 0 0 0 -9 1 4.947173 0.970967 8.047665 0 0 0 -10 1 3.275166 1.928275 10.625693 0 0 0 -11 1 4.920803 1.031987 13.347756 0 0 0 -12 1 3.203198 1.783824 0.091903 0 0 0 -13 1 3.295041 3.676548 2.629368 0 0 0 -14 1 1.737999 4.606148 5.326870 0 0 0 -15 1 3.168124 3.778475 7.955445 0 0 0 -16 1 1.608484 4.723375 10.541238 0 0 0 -17 1 3.338949 3.796700 13.176310 0 0 0 -18 1 1.654990 4.719325 0.117255 0 0 0 -19 1 1.752029 6.613962 2.637290 0 0 0 -20 1 1.506639 6.474460 8.030710 0 0 0 -21 1 1.731894 6.601249 13.186926 0 0 0 -22 1 0.119875 9.280585 2.599261 0 0 0 -23 1 12.864869 9.395786 7.938807 0 0 0 -24 1 12.863787 9.395336 13.154602 0 0 0 -25 1 7.995785 1.045195 2.518767 0 0 0 -26 1 6.508372 1.956851 5.334159 0 0 0 -27 1 7.998253 0.924053 7.898085 0 0 0 -28 1 6.564361 1.987451 10.481184 0 0 0 -29 1 8.219351 0.836201 13.145570 0 0 0 -30 1 6.554878 1.874725 0.009507 0 0 0 -31 1 6.423674 3.665186 2.630635 0 0 0 -32 1 4.968608 4.719437 5.259844 0 0 0 -33 1 6.400941 3.669348 8.070165 0 0 0 -34 1 4.994069 4.671512 10.639162 0 0 0 -35 1 6.510451 3.807838 13.349816 0 0 0 -36 1 4.752446 4.654074 15.832456 0 0 0 -37 1 4.787000 6.530149 2.758507 0 0 0 -38 1 3.135648 7.408448 5.182995 0 0 0 -39 1 4.901317 6.511586 7.995692 0 0 0 -40 1 3.197093 7.559875 10.479758 0 0 0 -41 1 4.915866 6.479748 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12.691602 0 0 0 -190 2 11.334474 10.245847 1.884480 0 0 0 -191 2 11.316417 10.391424 7.275999 0 0 0 -192 2 11.452038 10.224135 12.586865 0 0 0 diff --git a/examples/GaN-SNAP-LAMMPS/DATA/54/DATA b/examples/GaN-SNAP-LAMMPS/DATA/54/DATA deleted file mode 100755 index 4ebe3044..00000000 --- a/examples/GaN-SNAP-LAMMPS/DATA/54/DATA +++ /dev/null @@ -1,215 +0,0 @@ -LAMMPS DATA file - -192 atoms -0 bonds -0 angles -0 dihedrals -0 impropers - -2 atom types -0 bond types -0 angle types - -0.0 12.990503 xlo xhi -0.0 11.250148 ylo yhi -0.0 15.845291 zlo zhi - -Masses - -1 69.723 -2 14.0067 - -Atoms - -1 1 1.656809 0.944270 2.639984 0 0 0 -2 1 1.676165 0.909091 7.953227 0 0 0 -3 1 1.573799 0.845910 13.250624 0 0 0 -4 1 12.868024 3.724024 2.499753 0 0 0 -5 1 12.936443 3.685549 7.987453 0 0 0 -6 1 0.053269 3.798500 13.154919 0 0 0 -7 1 4.883520 0.905524 2.775144 0 0 0 -8 1 3.233336 1.787424 5.391994 0 0 0 -9 1 4.750757 0.875239 7.802380 0 0 0 -10 1 3.196313 1.819711 10.631239 0 0 0 -11 1 4.907163 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0 0 0 -62 1 6.376129 7.485849 5.333366 0 0 0 -63 1 8.132445 6.490098 7.785742 0 0 0 -64 1 6.413931 7.470548 10.694620 0 0 0 -65 1 8.170117 6.487510 13.285642 0 0 0 -66 1 6.472648 7.547049 15.786663 0 0 0 -67 1 6.508502 9.486800 2.688312 0 0 0 -68 1 4.972505 10.280723 5.255408 0 0 0 -69 1 6.555787 9.486350 7.909811 0 0 0 -70 1 4.827661 10.336299 10.644549 0 0 0 -71 1 6.465503 9.308485 13.163000 0 0 0 -72 1 4.758421 10.297373 0.053874 0 0 0 -73 1 0.001299 1.923888 5.213259 0 0 0 -74 1 0.053261 1.968438 10.623317 0 0 0 -75 1 12.895153 1.912300 15.800448 0 0 0 -76 1 11.367340 4.664874 5.422258 0 0 0 -77 1 11.266793 4.701324 10.547735 0 0 0 -78 1 11.278095 4.693224 15.782702 0 0 0 -79 1 11.439827 6.464223 2.674210 0 0 0 -80 1 9.778471 7.405860 5.385973 0 0 0 -81 1 11.460742 6.620825 8.055904 0 0 0 -82 1 9.781199 7.611738 10.632824 0 0 0 -83 1 11.251724 6.452185 13.303864 0 0 0 -84 1 9.700009 7.448161 15.715676 0 0 0 -85 1 9.660128 9.348986 2.742186 0 0 0 -86 1 8.187005 10.422250 5.343190 0 0 0 -87 1 9.702607 9.383524 7.994583 0 0 0 -88 1 8.230653 10.228972 10.469617 0 0 0 -89 1 9.698190 9.338748 13.315273 0 0 0 -90 1 8.164661 10.203997 0.000000 0 0 0 -91 1 0.002598 7.476736 5.409582 0 0 0 -92 1 0.127307 7.512399 10.580534 0 0 0 -93 1 12.920874 7.567187 15.756715 0 0 0 -94 1 11.385786 10.339561 5.261587 0 0 0 -95 1 11.432812 10.327411 10.646134 0 0 0 -96 1 11.427486 10.417412 0.077642 0 0 0 -97 2 1.641220 0.959941 4.655980 0 0 0 -98 2 1.743715 0.924380 9.969857 0 0 0 -99 2 1.555223 0.998394 15.082815 0 0 0 -100 2 12.881035 3.707486 4.571366 0 0 0 -101 2 12.906560 3.692861 10.064612 0 0 0 -102 2 0.028919 3.746187 15.109435 0 0 0 -103 2 4.994589 0.985985 4.689889 0 0 0 -104 2 3.163188 1.868312 2.082863 0 0 0 -105 2 4.769983 1.003884 10.025474 0 0 0 -106 2 3.143052 1.777298 7.128479 0 0 0 -107 2 4.859747 1.022886 15.142393 0 0 0 -108 2 3.231128 1.792036 12.598274 0 0 0 -109 2 3.257369 3.801650 4.510520 0 0 0 -110 2 1.726178 4.678149 1.859603 0 0 0 -111 2 3.221905 3.832926 10.053678 0 0 0 -112 2 1.499494 4.787726 7.401652 0 0 0 -113 2 3.276465 3.747874 15.172975 0 0 0 -114 2 1.597052 4.609298 12.667042 0 0 0 -115 2 1.620046 6.643550 4.699396 0 0 0 -116 2 1.634855 6.592024 9.835647 0 0 0 -117 2 1.647715 6.645013 15.325407 0 0 0 -118 2 0.117207 9.277660 4.768482 0 0 0 -119 2 12.989630 9.277885 9.799045 0 0 0 -120 2 12.937523 9.300610 15.265036 0 0 0 -121 2 8.217662 1.016586 4.681491 0 0 0 -122 2 6.572805 1.785174 1.993338 0 0 0 -123 2 8.004358 1.008081 9.859891 0 0 0 -124 2 6.580729 1.925688 7.216421 0 0 0 -125 2 8.044109 0.901474 15.177728 0 0 0 -126 2 6.502656 1.852787 12.629489 0 0 0 -127 2 6.372361 3.721887 4.527792 0 0 0 -128 2 4.838183 4.649461 1.833617 0 0 0 -129 2 6.543316 3.788825 10.014382 0 0 0 -130 2 4.854941 4.718087 7.320207 0 0 0 -131 2 6.457839 3.709174 15.250617 0 0 0 -132 2 4.748419 4.786601 12.589717 0 0 0 -133 2 4.776608 6.661213 4.616842 0 0 0 -134 2 3.360124 7.606563 1.917756 0 0 0 -135 2 4.881571 6.452860 9.800154 0 0 0 -136 2 3.209044 7.561562 7.210875 0 0 0 -137 2 4.885339 6.535661 15.269790 0 0 0 -138 2 3.373634 7.488211 12.414944 0 0 0 -139 2 3.143832 9.338298 4.561225 0 0 0 -140 2 1.732154 10.313686 2.011243 0 0 0 -141 2 3.131101 9.322660 9.998378 0 0 0 -142 2 1.633686 10.411562 7.279802 0 0 0 -143 2 3.225022 9.479487 15.221937 0 0 0 -144 2 1.738519 10.371399 12.426352 0 0 0 -145 2 11.310831 0.872843 4.600046 0 0 0 -146 2 9.743267 1.951788 2.074782 0 0 0 -147 2 11.388384 0.941784 9.845154 0 0 0 -148 2 9.792241 1.903750 7.355542 0 0 0 -149 2 11.462300 0.830958 15.227166 0 0 0 -150 2 9.664545 1.957076 12.685423 0 0 0 -151 2 9.833161 3.646286 4.635698 0 0 0 -152 2 8.083730 4.590848 1.906347 0 0 0 -153 2 9.628301 3.689599 10.046706 0 0 0 -154 2 8.198696 4.583648 7.416230 0 0 0 -155 2 9.854596 3.647861 15.136531 0 0 0 -156 2 8.175313 4.582185 12.468184 0 0 0 -157 2 8.068791 6.637700 4.633955 0 0 0 -158 2 6.395355 7.418910 1.955943 0 0 0 -159 2 8.030599 6.662563 9.791439 0 0 0 -160 2 6.424583 7.393597 7.391828 0 0 0 -161 2 8.176483 6.495948 15.140017 0 0 0 -162 2 6.520323 7.525449 12.412091 0 0 0 -163 2 6.411203 9.301623 4.739960 0 0 0 -164 2 4.892094 10.245510 2.041666 0 0 0 -165 2 6.391198 9.263597 9.928342 0 0 0 -166 2 4.834156 10.297373 7.196297 0 0 0 -167 2 6.496810 9.321760 15.034012 0 0 0 -168 2 4.981858 10.311436 12.461212 0 0 0 -169 2 0.100027 1.789561 1.996348 0 0 0 -170 2 12.904896 1.979801 7.408941 0 0 0 -171 2 12.988295 1.800136 12.616496 0 0 0 -172 2 11.433462 4.682987 2.092846 0 0 0 -173 2 11.454246 4.703349 7.357602 0 0 0 -174 2 11.360325 4.750038 12.675123 0 0 0 -175 2 11.485294 6.479635 4.667072 0 0 0 -176 2 9.807700 7.430498 1.968302 0 0 0 -177 2 11.312650 6.548149 9.965737 0 0 0 -178 2 9.678704 7.583837 7.279326 0 0 0 -179 2 11.473862 6.554899 15.150316 0 0 0 -180 2 9.793151 7.557962 12.679085 0 0 0 -181 2 9.629211 9.438874 4.521771 0 0 0 -182 2 8.205581 10.229310 1.983672 0 0 0 -183 2 9.831083 9.392749 9.837707 0 0 0 -184 2 8.083341 10.320323 7.406723 0 0 0 -185 2 9.686629 9.406586 15.043994 0 0 0 -186 2 8.185836 10.242247 12.552798 0 0 0 -187 2 0.023383 7.441411 1.981612 0 0 0 -188 2 0.109120 7.469198 7.129588 0 0 0 -189 2 0.027280 7.426785 12.591302 0 0 0 -190 2 11.329537 10.355649 1.845184 0 0 0 -191 2 11.321743 10.337986 7.420983 0 0 0 -192 2 11.354869 10.257098 12.403060 0 0 0 diff --git a/examples/GaN-SNAP-LAMMPS/DATA/55/DATA b/examples/GaN-SNAP-LAMMPS/DATA/55/DATA deleted file mode 100755 index 39dd96f7..00000000 --- a/examples/GaN-SNAP-LAMMPS/DATA/55/DATA +++ /dev/null @@ -1,215 +0,0 @@ -LAMMPS DATA file - -192 atoms -0 bonds -0 angles -0 dihedrals -0 impropers - -2 atom types -0 bond types -0 angle types - -0.0 12.990503 xlo xhi -0.0 11.250148 ylo yhi -0.0 15.845291 zlo zhi - -Masses - -1 69.723 -2 14.0067 - -Atoms - -1 1 1.729945 0.908393 2.507834 0 0 0 -2 1 1.589388 0.980349 8.049091 0 0 0 -3 1 1.639791 0.957905 13.151274 0 0 0 -4 1 12.943479 3.640998 2.608610 0 0 0 -5 1 0.111614 3.712661 7.854511 0 0 0 -6 1 12.896188 3.776562 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12.701268 0 0 0 -181 2 9.695332 9.390949 4.564553 0 0 0 -182 2 8.076715 10.342036 2.101878 0 0 0 -183 2 9.670650 9.348198 9.818851 0 0 0 -184 2 8.104125 10.311323 7.351423 0 0 0 -185 2 9.652853 9.462500 15.336974 0 0 0 -186 2 8.235200 10.289048 12.638679 0 0 0 -187 2 0.088335 7.559200 1.951031 0 0 0 -188 2 12.950233 7.607463 7.364099 0 0 0 -189 2 12.878915 7.537262 12.642957 0 0 0 -190 2 11.430344 10.312786 2.068603 0 0 0 -191 2 11.383708 10.374324 7.307690 0 0 0 -192 2 11.445802 10.322911 12.470244 0 0 0 diff --git a/examples/GaN-SNAP-LAMMPS/DATA/56/DATA b/examples/GaN-SNAP-LAMMPS/DATA/56/DATA deleted file mode 100755 index a2131889..00000000 --- a/examples/GaN-SNAP-LAMMPS/DATA/56/DATA +++ /dev/null @@ -1,215 +0,0 @@ -LAMMPS DATA file - -192 atoms -0 bonds -0 angles -0 dihedrals -0 impropers - -2 atom types -0 bond types -0 angle types - -0.0 12.990503 xlo xhi -0.0 11.250148 ylo yhi -0.0 15.845291 zlo zhi - -Masses - -1 69.723 -2 14.0067 - -Atoms - -1 1 1.641220 0.883722 2.477728 0 0 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10.478491 0 0 0 -53 1 11.403324 1.044554 13.332227 0 0 0 -54 1 9.627002 1.965738 15.741504 0 0 0 -55 1 9.870834 3.710974 2.549032 0 0 0 -56 1 8.234290 4.757463 5.410850 0 0 0 -57 1 9.799646 3.835401 8.032929 0 0 0 -58 1 8.082042 4.605698 10.655007 0 0 0 -59 1 9.789903 3.734599 13.340625 0 0 0 -60 1 8.236239 4.582298 15.768916 0 0 0 -61 1 8.006827 6.636125 2.602589 0 0 0 -62 1 6.516296 7.464923 5.425586 0 0 0 -63 1 8.145955 6.600349 8.032295 0 0 0 -64 1 6.474467 7.404173 10.675765 0 0 0 -65 1 8.169598 6.639387 13.254744 0 0 0 -66 1 6.547603 7.589125 0.022183 0 0 0 -67 1 6.449785 9.486462 2.542694 0 0 0 -68 1 4.815839 10.387599 5.361888 0 0 0 -69 1 6.417439 9.434712 7.953861 0 0 0 -70 1 4.992120 10.313461 10.551221 0 0 0 -71 1 6.517465 9.482975 13.151116 0 0 0 -72 1 4.809344 10.332924 0.072888 0 0 0 -73 1 12.881903 1.846937 5.145441 0 0 0 -74 1 12.943218 1.864487 10.450603 0 0 0 -75 1 12.876187 1.862575 15.771768 0 0 0 -76 1 11.288487 4.689737 5.124050 0 0 0 -77 1 11.452428 4.620098 10.534741 0 0 0 -78 1 11.427226 4.693562 15.766698 0 0 0 -79 1 11.436319 6.664813 2.514172 0 0 0 -80 1 9.619468 7.482586 5.138311 0 0 0 -81 1 11.269391 6.470860 7.832486 0 0 0 -82 1 9.667792 7.524774 10.524600 0 0 0 -83 1 11.425537 6.666388 13.278195 0 0 0 -84 1 9.633367 7.582937 15.796329 0 0 0 -85 1 9.820041 9.439549 2.581990 0 0 0 -86 1 8.235979 10.386587 5.317204 0 0 0 -87 1 9.689746 9.401411 8.071908 0 0 0 -88 1 8.078534 10.254060 10.399740 0 0 0 -89 1 9.849270 9.403774 13.289604 0 0 0 -90 1 8.183627 10.338886 15.739444 0 0 0 -91 1 0.089634 7.548737 5.324335 0 0 0 -92 1 0.029878 7.584175 10.650729 0 0 0 -93 1 0.058457 7.479661 0.152115 0 0 0 -94 1 11.398907 10.279598 5.175706 0 0 0 -95 1 11.320184 10.257660 10.697789 0 0 0 -96 1 11.468796 10.422475 0.137854 0 0 0 -97 2 1.720982 0.861514 4.515116 0 0 0 -98 2 1.662784 1.002782 9.773217 0 0 0 -99 2 1.557431 0.827415 15.105791 0 0 0 -100 2 12.926813 3.842826 4.584993 0 0 0 -101 2 12.870481 3.783987 10.008995 0 0 0 -102 2 12.882359 3.640098 15.147939 0 0 0 -103 2 4.848835 0.918620 4.615416 0 0 0 -104 2 3.238792 1.885862 1.996507 0 0 0 -105 2 4.873387 1.000757 9.842302 0 0 0 -106 2 3.260746 1.891825 7.174114 0 0 0 -107 2 4.885728 0.873192 15.206092 0 0 0 -108 2 3.135907 1.956176 12.457251 0 0 0 -109 2 3.179685 3.723124 4.559641 0 0 0 -110 2 1.688895 4.646874 1.861663 0 0 0 -111 2 3.327128 3.694211 9.909962 0 0 0 -112 2 1.504300 4.715500 7.232266 0 0 0 -113 2 3.197872 3.712211 15.327308 0 0 0 -114 2 1.615499 4.575098 12.621249 0 0 0 -115 2 1.597702 6.455223 4.670716 0 0 0 -116 2 1.608094 6.583249 9.946247 0 0 0 -117 2 1.611862 6.461073 15.260124 0 0 0 -118 2 0.062380 9.353711 4.484851 0 0 0 -119 2 0.116398 9.460025 10.012639 0 0 0 -120 2 12.977161 9.461600 15.302589 0 0 0 -121 2 8.157387 0.939039 4.492615 0 0 0 -122 2 6.459528 1.814536 2.100293 0 0 0 -123 2 8.154009 0.989586 9.799837 0 0 0 -124 2 6.612036 1.852674 7.303253 0 0 0 -125 2 8.196618 0.979449 15.032110 0 0 0 -126 2 6.495901 1.984301 12.393394 0 0 0 -127 2 6.375999 3.660798 4.659783 0 0 0 -128 2 4.753485 4.669937 1.940414 0 0 0 -129 2 6.546564 3.719187 9.853235 0 0 0 -130 2 4.917555 4.706275 7.185681 0 0 0 -131 2 6.462775 3.683636 15.114030 0 0 0 -132 2 4.961723 4.671174 12.599383 0 0 0 -133 2 4.879623 6.660875 4.574218 0 0 0 -134 2 3.211512 7.555600 2.101402 0 0 0 -135 2 4.747250 6.641188 10.006301 0 0 0 -136 2 3.258798 7.485174 7.300401 0 0 0 -137 2 4.828570 6.625212 15.062692 0 0 0 -138 2 3.235155 7.559087 12.589559 0 0 0 -139 2 3.118110 9.266522 4.613356 0 0 0 -140 2 1.551456 10.283760 1.967510 0 0 0 -141 2 3.133439 9.344486 9.869715 0 0 0 -142 2 1.572111 10.406725 7.260787 0 0 0 -143 2 3.164616 9.329410 15.294984 0 0 0 -144 2 1.654470 10.349461 12.586548 0 0 0 -145 2 11.304726 1.021322 4.470273 0 0 0 -146 2 9.707803 1.895762 2.120734 0 0 0 -147 2 11.355778 0.920453 9.957973 0 0 0 -148 2 9.811467 1.847949 7.253340 0 0 0 -149 2 11.404103 0.990418 15.233029 0 0 0 -150 2 9.816404 1.770323 12.423183 0 0 0 -151 2 9.623755 3.673623 4.733147 0 0 0 -152 2 8.134523 4.613798 2.125170 0 0 0 -153 2 9.753789 3.824375 9.850859 0 0 0 -154 2 8.049565 4.733050 7.274256 0 0 0 -155 2 9.687278 3.643811 15.080597 0 0 0 -156 2 8.192851 4.691762 12.523325 0 0 0 -157 2 8.017349 6.592137 4.508777 0 0 0 -158 2 6.516166 7.429148 1.984464 0 0 0 -159 2 8.076326 6.496623 9.783675 0 0 0 -160 2 6.405227 7.584062 7.339063 0 0 0 -161 2 7.990069 6.632412 15.109911 0 0 0 -162 2 6.595538 7.576412 12.503836 0 0 0 -163 2 6.447317 9.297348 4.591648 0 0 0 -164 2 4.820906 10.384899 1.916329 0 0 0 -165 2 6.586575 9.306573 9.862901 0 0 0 -166 2 4.831428 10.331911 7.253974 0 0 0 -167 2 6.375349 9.348086 15.205299 0 0 0 -168 2 4.759331 10.248098 12.635827 0 0 0 -169 2 0.033775 1.944476 1.834568 0 0 0 -170 2 12.863716 1.852224 7.175857 0 0 0 -171 2 0.023383 1.947626 12.628538 0 0 0 -172 2 11.478149 4.693112 1.998408 0 0 0 -173 2 11.410209 4.771075 7.166983 0 0 0 -174 2 11.418393 4.617623 12.454557 0 0 0 -175 2 11.437099 6.569299 4.470115 0 0 0 -176 2 9.861221 7.584962 2.104096 0 0 0 -177 2 11.365131 6.569637 9.760541 0 0 0 -178 2 9.807830 7.558187 7.294380 0 0 0 -179 2 11.332915 6.560749 15.199120 0 0 0 -180 2 9.729497 7.419585 12.598115 0 0 0 -181 2 9.788214 9.431337 4.565504 0 0 0 -182 2 8.198177 10.267673 1.914586 0 0 0 -183 2 9.683251 9.434374 9.851334 0 0 0 -184 2 8.081912 10.352161 7.120081 0 0 0 -185 2 9.651944 9.357423 15.099611 0 0 0 -186 2 8.186615 10.344849 12.657377 0 0 0 -187 2 12.914639 7.486186 2.059729 0 0 0 -188 2 12.887748 7.487649 7.264907 0 0 0 -189 2 0.050663 7.597000 12.440455 0 0 0 -190 2 11.250425 10.337086 1.904604 0 0 0 -191 2 11.381889 10.352836 7.257302 0 0 0 -192 2 11.407870 10.381974 12.662605 0 0 0 diff --git a/examples/GaN-SNAP-LAMMPS/DATA/57/DATA b/examples/GaN-SNAP-LAMMPS/DATA/57/DATA deleted file mode 100755 index 05f5592b..00000000 --- a/examples/GaN-SNAP-LAMMPS/DATA/57/DATA +++ /dev/null @@ -1,215 +0,0 @@ -LAMMPS DATA file - -192 atoms -0 bonds -0 angles -0 dihedrals -0 impropers - -2 atom types -0 bond types -0 angle types - -0.0 12.990503 xlo xhi -0.0 11.250148 ylo yhi -0.0 15.845291 zlo zhi - -Masses - -1 69.723 -2 14.0067 - -Atoms - -1 1 1.725529 0.895444 2.566620 0 0 0 -2 1 1.510666 0.838620 7.942293 0 0 0 -3 1 1.711369 0.903173 13.150957 0 0 0 -4 1 12.871389 3.725599 2.751535 0 0 0 -5 1 12.867162 3.676098 8.021995 0 0 0 -6 1 12.863933 3.742587 13.304023 0 0 0 -7 1 4.975493 0.939095 2.742820 0 0 0 -8 1 3.265163 1.936713 5.216903 0 0 0 -9 1 4.769463 0.981294 7.993791 0 0 0 -10 1 3.220865 1.840524 10.416852 0 0 0 -11 1 4.838962 0.907549 13.130517 0 0 0 -12 1 3.355317 1.911063 15.816135 0 0 0 -13 1 3.280102 3.772625 2.787662 0 0 0 -14 1 1.692533 4.736762 5.396906 0 0 0 -15 1 3.120449 3.766100 8.066679 0 0 0 -16 1 1.632517 4.589160 10.578474 0 0 0 -17 1 3.176957 3.736624 13.071889 0 0 0 -18 1 1.526904 4.755438 15.762103 0 0 0 -19 1 1.623813 6.567724 2.483115 0 0 0 -20 1 1.721761 6.553661 8.069214 0 0 0 -21 1 1.641870 6.646813 13.117048 0 0 0 -22 1 12.891143 9.296672 2.495792 0 0 0 -23 1 12.912615 9.458000 8.002981 0 0 0 -24 1 0.112205 9.280810 13.062699 0 0 0 -25 1 8.243124 0.942391 2.726499 0 0 0 -26 1 6.445758 1.789224 5.271728 0 0 0 -27 1 8.097111 1.031076 7.809193 0 0 0 -28 1 6.418218 1.796311 10.703018 0 0 0 -29 1 8.183627 0.871459 13.251416 0 0 0 -30 1 6.422375 1.863587 0.134685 0 0 0 -31 1 6.516556 3.670811 2.676428 0 0 0 -32 1 4.789469 4.593661 5.185688 0 0 0 -33 1 6.502137 3.787587 7.904106 0 0 0 -34 1 4.797523 4.624598 10.681627 0 0 0 -35 1 6.443679 3.693761 13.324622 0 0 0 -36 1 4.772581 4.724725 15.785078 0 0 0 -37 1 4.826232 6.635787 2.651234 0 0 0 -38 1 3.285298 7.577762 5.306429 0 0 0 -39 1 4.827531 6.497636 7.957030 0 0 0 -40 1 3.186051 7.607125 10.450761 0 0 0 -41 1 4.947953 6.658063 13.188194 0 0 0 -42 1 3.277114 7.479999 0.142608 0 0 0 -43 1 3.287377 9.436174 2.608452 0 0 0 -44 1 1.532620 10.311323 5.386765 0 0 0 -45 1 3.293872 9.362936 7.916307 0 0 0 -46 1 1.534438 10.357111 10.464388 0 0 0 -47 1 3.293742 9.290597 13.229233 0 0 0 -48 1 1.694741 10.330561 0.052289 0 0 0 -49 1 11.347854 0.887288 2.786870 0 0 0 -50 1 9.863689 1.926363 5.347469 0 0 0 -51 1 11.404363 0.844324 7.925973 0 0 0 -52 1 9.834201 1.809811 10.661662 0 0 0 -53 1 11.290436 0.931996 13.135587 0 0 0 -54 1 9.702607 1.971363 15.690957 0 0 0 -55 1 9.800036 3.722224 2.663276 0 0 0 -56 1 8.074897 4.769725 5.388825 0 0 0 -57 1 9.755348 3.647298 7.927874 0 0 0 -58 1 8.203633 4.702449 10.469142 0 0 0 -59 1 9.697021 3.652136 13.158880 0 0 0 -60 1 8.056320 4.633711 15.831030 0 0 0 -61 1 8.013841 6.464335 2.735689 0 0 0 -62 1 6.383144 7.454573 5.367434 0 0 0 -63 1 8.107763 6.654913 7.933262 0 0 0 -64 1 6.476805 7.477411 10.419705 0 0 0 -65 1 8.175183 6.612050 13.275343 0 0 0 -66 1 6.544486 7.446248 15.684461 0 0 0 -67 1 6.456280 9.464300 2.712555 0 0 0 -68 1 4.817918 10.241572 5.169526 0 0 0 -69 1 6.385092 9.360911 7.844845 0 0 0 -70 1 4.803109 10.233135 10.548844 0 0 0 -71 1 6.554618 9.350673 13.089953 0 0 0 -72 1 4.778297 10.403687 15.793001 0 0 0 -73 1 12.902038 1.958651 5.372504 0 0 0 -74 1 0.061055 1.873262 10.526977 0 0 0 -75 1 0.094831 1.803174 0.129931 0 0 0 -76 1 11.450349 4.729562 5.266499 0 0 0 -77 1 11.467497 4.796051 10.409881 0 0 0 -78 1 11.451129 4.723375 15.823424 0 0 0 -79 1 11.385786 6.629600 2.677537 0 0 0 -80 1 9.818092 7.401023 5.241305 0 0 0 -81 1 11.345906 6.599449 7.959723 0 0 0 -82 1 9.843034 7.525224 10.594637 0 0 0 -83 1 11.464639 6.622625 13.278195 0 0 0 -84 1 9.642980 7.433535 15.718211 0 0 0 -85 1 9.831603 9.348423 2.620811 0 0 0 -86 1 8.008385 10.205797 5.422417 0 0 0 -87 1 9.654152 9.472737 7.833753 0 0 0 -88 1 8.008775 10.351486 10.426360 0 0 0 -89 1 9.629081 9.419074 13.041149 0 0 0 -90 1 8.029950 10.261935 15.781276 0 0 0 -91 1 0.055859 7.516224 5.281077 0 0 0 -92 1 0.019486 7.388760 10.511290 0 0 0 -93 1 0.011691 7.408335 15.767649 0 0 0 -94 1 11.390203 10.201184 5.127536 0 0 0 -95 1 11.334604 10.237410 10.496713 0 0 0 -96 1 11.306934 10.269248 0.020599 0 0 0 -97 2 1.633816 1.002917 4.586736 0 0 0 -98 2 1.689285 0.971844 9.925173 0 0 0 -99 2 1.715006 0.920690 15.214173 0 0 0 -100 2 0.069697 3.758900 4.780524 0 0 0 -101 2 12.888032 3.705236 9.870665 0 0 0 -102 2 12.983416 3.687574 15.133679 0 0 0 -103 2 4.800511 0.829901 4.473442 0 0 0 -104 2 3.321412 1.766723 2.113762 0 0 0 -105 2 4.792586 0.962045 9.915983 0 0 0 -106 2 3.301277 1.841987 7.349996 0 0 0 -107 2 4.872868 0.997314 15.146989 0 0 0 -108 2 3.358045 1.965288 12.566108 0 0 0 -109 2 3.253082 3.677786 4.661526 0 0 0 -110 2 1.683050 4.772200 1.977651 0 0 0 -111 2 3.313098 3.678236 9.757055 0 0 0 -112 2 1.527553 4.768600 7.361880 0 0 0 -113 2 3.166435 3.676098 15.246180 0 0 0 -114 2 1.597832 4.785588 12.542181 0 0 0 -115 2 1.598352 6.492798 4.575328 0 0 0 -116 2 1.608484 6.481098 10.060967 0 0 0 -117 2 1.608094 6.630950 15.291181 0 0 0 -118 2 12.920753 9.406924 4.550292 0 0 0 -119 2 12.892845 9.354161 9.771791 0 0 0 -120 2 12.889116 9.381724 15.099136 0 0 0 -121 2 7.995915 1.048694 4.704625 0 0 0 -122 2 6.620480 1.976539 1.977175 0 0 0 -123 2 8.245722 1.016923 9.848323 0 0 0 -124 2 6.612556 1.788099 7.146543 0 0 0 -125 2 7.989289 0.893217 15.149048 0 0 0 -126 2 6.396654 1.922763 12.694613 0 0 0 -127 2 6.449135 3.815038 4.681333 0 0 0 -128 2 4.769983 4.738000 2.107424 0 0 0 -129 2 6.365476 3.660461 9.867655 0 0 0 -130 2 4.979130 4.799876 7.163497 0 0 0 -131 2 6.410164 3.660686 15.224155 0 0 0 -132 2 4.848575 4.632586 12.455191 0 0 0 -133 2 4.790248 6.648950 4.668656 0 0 0 -134 2 3.279453 7.535687 1.883847 0 0 0 -135 2 4.904175 6.647263 9.806809 0 0 0 -136 2 3.285428 7.586537 7.188850 0 0 0 -137 2 4.893782 6.559624 15.297994 0 0 0 -138 2 3.131101 7.554025 12.566900 0 0 0 -139 2 3.229309 9.438087 4.594342 0 0 0 -140 2 1.586660 10.348561 1.952615 0 0 0 -141 2 3.164097 9.274847 9.828675 0 0 0 -142 2 1.728257 10.421237 7.262847 0 0 0 -143 2 3.155393 9.377786 15.346956 0 0 0 -144 2 1.692013 10.417525 12.685898 0 0 0 -145 2 11.298230 0.846956 4.598462 0 0 0 -146 2 9.647008 1.932325 1.938037 0 0 0 -147 2 11.353700 0.869861 9.983801 0 0 0 -148 2 9.665844 1.935363 7.185839 0 0 0 -149 2 11.396179 0.902813 15.261075 0 0 0 -150 2 9.643370 1.803174 12.452655 0 0 0 -151 2 9.706634 3.728524 4.540151 0 0 0 -152 2 8.162972 4.790426 1.964499 0 0 0 -153 2 9.821860 3.817175 10.065721 0 0 0 -154 2 8.044239 4.649124 7.351106 0 0 0 -155 2 9.809649 3.853851 15.212747 0 0 0 -156 2 8.147254 4.657224 12.500033 0 0 0 -157 2 8.145046 6.568399 4.622230 0 0 0 -158 2 6.535652 7.396185 1.887808 0 0 0 -159 2 8.230523 6.581224 9.755153 0 0 0 -160 2 6.441601 7.397760 7.361247 0 0 0 -161 2 8.174014 6.570762 15.218134 0 0 0 -162 2 6.420167 7.480786 12.554699 0 0 0 -163 2 6.583197 9.411086 4.621121 0 0 0 -164 2 4.963152 10.308511 1.913953 0 0 0 -165 2 6.555268 9.480725 9.869398 0 0 0 -166 2 4.803498 10.254735 7.115486 0 0 0 -167 2 6.620610 9.443262 15.210687 0 0 0 -168 2 4.842600 10.346986 12.706180 0 0 0 -169 2 0.055859 1.785511 1.969411 0 0 0 -170 2 0.050663 1.837487 7.401494 0 0 0 -171 2 0.033775 1.972263 12.526178 0 0 0 -172 2 11.314858 4.775125 1.833142 0 0 0 -173 2 11.275237 4.790876 7.335894 0 0 0 -174 2 11.316417 4.761400 12.647236 0 0 0 -175 2 11.473083 6.594724 4.667864 0 0 0 -176 2 9.643760 7.594413 2.025503 0 0 0 -177 2 11.303686 6.664138 9.764977 0 0 0 -178 2 9.618428 7.407435 7.273622 0 0 0 -179 2 11.465028 6.540611 15.210053 0 0 0 -180 2 9.768339 7.404510 12.515244 0 0 0 -181 2 9.705205 9.317710 4.502756 0 0 0 -182 2 8.018388 10.260248 1.912051 0 0 0 -183 2 9.856155 9.304548 9.911071 0 0 0 -184 2 8.027481 10.407287 7.404029 0 0 0 -185 2 9.648566 9.458675 15.036072 0 0 0 -186 2 8.176742 10.397837 12.513977 0 0 0 -187 2 12.924641 7.412723 2.096015 0 0 0 -188 2 0.041570 7.563025 7.223076 0 0 0 -189 2 12.908403 7.389885 12.418430 0 0 0 -190 2 11.322393 10.267785 1.988267 0 0 0 -191 2 11.337202 10.411000 7.160011 0 0 0 -192 2 11.439307 10.240110 12.646443 0 0 0 diff --git a/examples/GaN-SNAP-LAMMPS/DATA/58/DATA b/examples/GaN-SNAP-LAMMPS/DATA/58/DATA deleted file mode 100755 index 829f1304..00000000 --- a/examples/GaN-SNAP-LAMMPS/DATA/58/DATA +++ /dev/null @@ -1,215 +0,0 @@ -LAMMPS DATA file - -192 atoms -0 bonds -0 angles -0 dihedrals -0 impropers - -2 atom types -0 bond types -0 angle types - -0.0 12.990503 xlo xhi -0.0 11.250148 ylo yhi -0.0 15.845291 zlo zhi - -Masses - -1 69.723 -2 14.0067 - -Atoms - -1 1 1.740987 0.992207 2.639033 0 0 0 -2 1 1.612121 0.894432 7.984759 0 0 0 -3 1 1.729815 0.925043 13.285959 0 0 0 -4 1 0.017685 3.661248 2.605441 0 0 0 -5 1 12.947890 3.695899 7.906325 0 0 0 -6 1 0.019694 3.829775 13.049547 0 0 0 -7 1 4.932234 0.877084 2.724439 0 0 0 -8 1 3.293872 1.799124 5.197097 0 0 0 -9 1 4.994978 0.998687 8.027383 0 0 0 -10 1 3.213721 1.914775 10.536326 0 0 0 -11 1 4.911449 0.977807 13.340784 0 0 0 -12 1 3.249315 1.862237 15.711873 0 0 0 -13 1 3.234116 3.821338 2.607818 0 0 0 -14 1 1.649794 4.594561 5.154948 0 0 0 -15 1 3.375322 3.784662 7.960357 0 0 0 -16 1 1.719033 4.637199 10.610640 0 0 0 -17 1 3.137077 3.649886 13.315273 0 0 0 -18 1 1.724619 4.795826 0.120424 0 0 0 -19 1 1.527164 6.484923 2.734739 0 0 0 -20 1 1.629009 6.628362 7.951484 0 0 0 -21 1 1.693182 6.661888 13.250941 0 0 0 -22 1 0.061380 9.319173 2.507517 0 0 0 -23 1 0.071482 9.421662 7.981114 0 0 0 -24 1 12.919678 9.469250 13.188828 0 0 0 -25 1 8.135822 0.968289 2.694809 0 0 0 -26 1 6.384053 1.983064 5.137360 0 0 0 -27 1 8.062296 0.928621 8.017875 0 0 0 -28 1 6.411073 1.768411 10.698423 0 0 0 -29 1 8.090096 0.854730 13.301963 0 0 0 -30 1 6.588264 1.935476 0.117255 0 0 0 -31 1 6.546564 3.784100 2.615424 0 0 0 -32 1 4.870529 4.681524 5.302626 0 0 0 -33 1 6.552800 3.755412 7.854511 0 0 0 -34 1 4.846107 4.651374 10.484353 0 0 0 -35 1 6.479403 3.660798 13.086309 0 0 0 -36 1 4.965100 4.702112 15.713299 0 0 0 -37 1 4.905344 6.558386 2.747890 0 0 0 -38 1 3.357136 7.460873 5.419723 0 0 0 -39 1 4.932104 6.470298 7.873842 0 0 0 -40 1 3.228010 7.609375 10.646768 0 0 0 -41 1 4.885858 6.592474 13.069196 0 0 0 -42 1 3.292053 7.394497 0.012676 0 0 0 -43 1 3.375193 9.322323 2.581039 0 0 0 -44 1 1.753328 10.349011 5.187273 0 0 0 -45 1 3.265423 9.341786 7.772590 0 0 0 -46 1 1.728516 10.256085 10.410514 0 0 0 -47 1 3.153445 9.318948 13.160940 0 0 0 -48 1 1.737610 10.207934 15.801241 0 0 0 -49 1 11.283161 0.832848 2.754387 0 0 0 -50 1 9.865248 1.893175 5.234809 0 0 0 -51 1 11.474122 0.968469 7.907751 0 0 0 -52 1 9.844203 1.802836 10.653264 0 0 0 -53 1 11.473862 1.002973 13.298002 0 0 0 -54 1 9.771327 1.965063 15.690007 0 0 0 -55 1 9.673118 3.850026 2.679756 0 0 0 -56 1 8.121533 4.714937 5.275373 0 0 0 -57 1 9.771846 3.662486 7.833595 0 0 0 -58 1 7.993706 4.761063 10.555657 0 0 0 -59 1 9.746125 3.688474 13.098351 0 0 0 -60 1 8.228704 4.787726 0.012676 0 0 0 -61 1 8.151411 6.590899 2.569631 0 0 0 -62 1 6.599435 7.392135 5.171111 0 0 0 -63 1 8.130106 6.473785 7.771164 0 0 0 -64 1 6.449135 7.594750 10.623000 0 0 0 -65 1 8.155178 6.469510 13.113562 0 0 0 -66 1 6.448746 7.479661 15.715201 0 0 0 -67 1 6.551371 9.450237 2.700830 0 0 0 -68 1 4.934962 10.365887 5.121673 0 0 0 -69 1 6.516946 9.419187 7.760548 0 0 0 -70 1 4.877025 10.388499 10.417803 0 0 0 -71 1 6.464464 9.379586 13.302914 0 0 0 -72 1 4.982118 10.321448 15.830079 0 0 0 -73 1 0.002598 1.974401 5.139262 0 0 0 -74 1 12.902817 1.936601 10.628229 0 0 0 -75 1 0.055859 1.916688 15.796329 0 0 0 -76 1 11.245619 4.777150 5.118187 0 0 0 -77 1 11.475421 4.652499 10.471360 0 0 0 -78 1 11.331746 4.705600 15.821681 0 0 0 -79 1 11.386046 6.572449 2.676745 0 0 0 -80 1 9.843944 7.509474 5.427329 0 0 0 -81 1 11.338761 6.524298 7.918050 0 0 0 -82 1 9.813286 7.519712 10.617929 0 0 0 -83 1 11.271730 6.671788 13.306400 0 0 0 -84 1 9.621936 7.403723 15.708070 0 0 0 -85 1 9.696242 9.299035 2.493732 0 0 0 -86 1 8.244163 10.356661 5.343032 0 0 0 -87 1 9.673898 9.439324 8.011696 0 0 0 -88 1 8.033067 10.286011 10.517787 0 0 0 -89 1 9.820171 9.343698 13.216715 0 0 0 -90 1 8.095162 10.417975 0.057043 0 0 0 -91 1 0.066252 7.419810 5.380744 0 0 0 -92 1 12.942308 7.509249 10.420180 0 0 0 -93 1 12.930227 7.467623 15.698405 0 0 0 -94 1 11.352011 10.326624 5.425269 0 0 0 -95 1 11.260298 10.203997 10.472786 0 0 0 -96 1 11.253413 10.313573 15.755448 0 0 0 -97 2 1.749821 0.961280 4.620328 0 0 0 -98 2 1.701626 0.908022 9.956864 0 0 0 -99 2 1.512744 0.853144 15.088361 0 0 0 -100 2 12.938489 3.822575 4.686562 0 0 0 -101 2 0.116136 3.802100 9.763234 0 0 0 -102 2 0.115630 3.849913 15.060632 0 0 0 -103 2 4.777128 0.907302 4.510996 0 0 0 -104 2 3.248145 1.923663 2.025662 0 0 0 -105 2 4.769723 0.907448 9.781615 0 0 0 -106 2 3.329206 1.987339 7.311809 0 0 0 -107 2 4.820776 1.017182 15.328893 0 0 0 -108 2 3.134868 1.926700 12.645809 0 0 0 -109 2 3.138116 3.742812 4.686562 0 0 0 -110 2 1.515862 4.787501 1.866258 0 0 0 -111 2 3.300757 3.819313 9.915507 0 0 0 -112 2 1.639272 4.782438 7.414804 0 0 0 -113 2 3.132270 3.703661 15.344104 0 0 0 -114 2 1.569253 4.592423 12.505103 0 0 0 -115 2 1.579515 6.591687 4.599571 0 0 0 -116 2 1.644208 6.557486 9.973184 0 0 0 -117 2 1.733583 6.518786 15.202130 0 0 0 -118 2 0.045430 9.445962 4.694009 0 0 0 -119 2 0.071407 9.455975 9.837707 0 0 0 -120 2 12.907924 9.341223 15.325407 0 0 0 -121 2 8.087887 0.939826 4.599888 0 0 0 -122 2 6.440172 1.925575 2.059729 0 0 0 -123 2 8.111140 0.906211 10.016600 0 0 0 -124 2 6.407306 1.846374 7.305154 0 0 0 -125 2 8.039433 0.928227 15.268047 0 0 0 -126 2 6.573844 1.917363 12.502568 0 0 0 -127 2 6.504215 3.705236 4.778306 0 0 0 -128 2 4.856500 4.638886 2.041983 0 0 0 -129 2 6.487847 3.806825 9.842302 0 0 0 -130 2 4.938859 4.732937 7.296122 0 0 0 -131 2 6.440821 3.657198 15.103097 0 0 0 -132 2 4.967179 4.620548 12.401950 0 0 0 -133 2 4.957696 6.476935 4.707160 0 0 0 -134 2 3.306343 7.486636 1.943742 0 0 0 -135 2 4.794535 6.637250 9.927075 0 0 0 -136 2 3.357006 7.557512 7.365683 0 0 0 -137 2 4.901707 6.602712 15.344896 0 0 0 -138 2 3.121488 7.439498 12.496071 0 0 0 -139 2 3.182024 9.367548 4.522880 0 0 0 -140 2 1.739948 10.281623 1.854850 0 0 0 -141 2 3.369087 9.320635 9.765928 0 0 0 -142 2 1.519109 10.299511 7.303887 0 0 0 -143 2 3.158381 9.364848 15.207359 0 0 0 -144 2 1.716435 10.253835 12.505737 0 0 0 -145 2 11.353830 1.025102 4.557581 0 0 0 -146 2 9.696112 1.923888 2.009183 0 0 0 -147 2 11.446062 0.952876 10.022305 0 0 0 -148 2 9.735083 1.938513 7.424628 0 0 0 -149 2 11.379161 0.927541 15.304966 0 0 0 -150 2 9.804323 1.844687 12.688750 0 0 0 -151 2 9.789513 3.651573 4.759767 0 0 0 -152 2 8.037094 4.680512 1.942633 0 0 0 -153 2 9.737811 3.642798 9.803481 0 0 0 -154 2 8.191422 4.692324 7.331933 0 0 0 -155 2 9.792631 3.814700 15.144136 0 0 0 -156 2 8.043720 4.725175 12.598432 0 0 0 -157 2 8.234160 6.586624 4.640769 0 0 0 -158 2 6.521233 7.453111 1.977809 0 0 0 -159 2 8.147644 6.620937 9.861475 0 0 0 -160 2 6.609178 7.419698 7.220857 0 0 0 -161 2 8.132964 6.663688 15.247289 0 0 0 -162 2 6.422375 7.535012 12.606830 0 0 0 -163 2 6.383273 9.287110 4.628251 0 0 0 -164 2 4.898459 10.216485 2.024870 0 0 0 -165 2 6.440432 9.271360 9.888095 0 0 0 -166 2 4.784532 10.247648 7.323376 0 0 0 -167 2 6.536432 9.384086 15.187711 0 0 0 -168 2 4.746600 10.398512 12.493061 0 0 0 -169 2 0.038972 1.944813 2.119783 0 0 0 -170 2 0.077943 1.847612 7.365842 0 0 0 -171 2 12.870731 1.808574 12.607147 0 0 0 -172 2 11.397997 4.769163 1.972422 0 0 0 -173 2 11.471134 4.605136 7.174272 0 0 0 -174 2 11.467367 4.648674 12.454081 0 0 0 -175 2 11.306804 6.571887 4.491823 0 0 0 -176 2 9.794060 7.531412 2.038972 0 0 0 -177 2 11.393581 6.533411 9.919310 0 0 0 -178 2 9.693903 7.429935 7.381846 0 0 0 -179 2 11.354219 6.576049 15.250300 0 0 0 -180 2 9.817573 7.567525 12.687166 0 0 0 -181 2 9.795099 9.425599 4.530169 0 0 0 -182 2 8.219481 10.305698 2.115188 0 0 0 -183 2 9.753660 9.296222 10.025315 0 0 0 -184 2 8.183368 10.373424 7.185681 0 0 0 -185 2 9.648436 9.439887 15.313364 0 0 0 -186 2 8.081002 10.321223 12.518572 0 0 0 -187 2 12.886060 7.565725 1.906347 0 0 0 -188 2 12.980630 7.451873 7.141314 0 0 0 -189 2 0.022084 7.388872 12.466441 0 0 0 -190 2 11.494907 10.368249 1.855959 0 0 0 -191 2 11.254712 10.378599 7.110891 0 0 0 -192 2 11.292644 10.261710 12.614119 0 0 0 diff --git a/examples/GaN-SNAP-LAMMPS/DATA/59/DATA b/examples/GaN-SNAP-LAMMPS/DATA/59/DATA deleted file mode 100755 index afdbf30a..00000000 --- a/examples/GaN-SNAP-LAMMPS/DATA/59/DATA +++ /dev/null @@ -1,215 +0,0 @@ -LAMMPS DATA file - -192 atoms -0 bonds -0 angles -0 dihedrals -0 impropers - -2 atom types -0 bond types -0 angle types - -0.0 12.990503 xlo xhi -0.0 11.250148 ylo yhi -0.0 15.845291 zlo zhi - -Masses - -1 69.723 -2 14.0067 - -Atoms - -1 1 1.705523 1.028815 2.517183 0 0 0 -2 1 1.731244 0.967288 7.789545 0 0 0 -3 1 1.566265 0.948061 13.343953 0 0 0 -4 1 0.120784 3.673061 2.784493 0 0 0 -5 1 0.118779 3.746749 8.012330 0 0 0 -6 1 12.897464 3.732462 13.330643 0 0 0 -7 1 4.947303 1.040897 2.684826 0 0 0 -8 1 3.126944 1.953588 5.413860 0 0 0 -9 1 4.917815 0.995503 7.994266 0 0 0 -10 1 3.219566 1.910050 10.453772 0 0 0 -11 1 4.924960 0.832173 13.128299 0 0 0 -12 1 3.129672 1.784386 0.096656 0 0 0 -13 1 3.298289 3.708949 2.778155 0 0 0 -14 1 1.502871 4.673762 5.238770 0 0 0 -15 1 3.316605 3.816500 7.817908 0 0 0 -16 1 1.621215 4.675337 10.604461 0 0 0 -17 1 3.302056 3.807388 13.127982 0 0 0 -18 1 1.670449 4.722475 15.732947 0 0 0 -19 1 1.524825 6.562211 2.781165 0 0 0 -20 1 1.582373 6.581787 7.829633 0 0 0 -21 1 1.689155 6.507536 13.200870 0 0 0 -22 1 0.051724 9.463062 2.781007 0 0 0 -23 1 0.012269 9.293860 7.806024 0 0 0 -24 1 12.927503 9.451812 13.121010 0 0 0 -25 1 8.200775 0.879807 2.771500 0 0 0 -26 1 6.456280 1.806774 5.197414 0 0 0 -27 1 8.149202 0.931501 7.870197 0 0 0 -28 1 6.581249 1.894187 10.573879 0 0 0 -29 1 8.227405 0.889324 13.280413 0 0 0 -30 1 6.561113 1.848174 0.015845 0 0 0 -31 1 6.385092 3.649661 2.645213 0 0 0 -32 1 4.943926 4.785251 5.159068 0 0 0 -33 1 6.513179 3.743149 7.762449 0 0 0 -34 1 4.829090 4.611548 10.651363 0 0 0 -35 1 6.446148 3.756424 13.092964 0 0 0 -36 1 4.897939 4.634274 0.042782 0 0 0 -37 1 4.920543 6.618462 2.619702 0 0 0 -38 1 3.139545 7.439161 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0 0 0 -64 1 6.386391 7.596663 10.645342 0 0 0 -65 1 8.115687 6.548149 13.182014 0 0 0 -66 1 6.444978 7.502049 15.843231 0 0 0 -67 1 6.577741 9.441462 2.681182 0 0 0 -68 1 4.839872 10.382762 5.286623 0 0 0 -69 1 6.456410 9.473862 8.036256 0 0 0 -70 1 4.884429 10.340236 10.585605 0 0 0 -71 1 6.419257 9.330423 13.189778 0 0 0 -72 1 4.801420 10.390074 15.743088 0 0 0 -73 1 12.919315 1.800924 5.189966 0 0 0 -74 1 12.973745 1.832537 10.692244 0 0 0 -75 1 12.972317 1.804074 0.123593 0 0 0 -76 1 11.491269 4.673762 5.153047 0 0 0 -77 1 11.303816 4.667011 10.588140 0 0 0 -78 1 11.304856 4.710662 0.061797 0 0 0 -79 1 11.294463 6.476485 2.570898 0 0 0 -80 1 9.695852 7.483036 5.278700 0 0 0 -81 1 11.258999 6.509111 8.012488 0 0 0 -82 1 9.620507 7.596550 10.631081 0 0 0 -83 1 11.363703 6.580212 13.115622 0 0 0 -84 1 9.732225 7.604313 0.009507 0 0 0 -85 1 9.748333 9.314785 2.631903 0 0 0 -86 1 8.151281 10.352949 5.243207 0 0 0 -87 1 9.708453 9.484887 7.770689 0 0 0 -88 1 8.219091 10.405600 10.651838 0 0 0 -89 1 9.638564 9.321535 13.146679 0 0 0 -90 1 8.165700 10.230885 0.064966 0 0 0 -91 1 12.888398 7.534674 5.274422 0 0 0 -92 1 0.072747 7.548512 10.686064 0 0 0 -93 1 0.101326 7.462786 0.057043 0 0 0 -94 1 11.288228 10.207034 5.353648 0 0 0 -95 1 11.366690 10.308173 10.686381 0 0 0 -96 1 11.395269 10.339111 0.107748 0 0 0 -97 2 1.703185 0.954778 4.526524 0 0 0 -98 2 1.556262 1.024472 9.759431 0 0 0 -99 2 1.621215 0.862796 15.342203 0 0 0 -100 2 0.055262 3.750124 4.617793 0 0 0 -101 2 12.876089 3.790962 9.763710 0 0 0 -102 2 12.879162 3.754962 15.062692 0 0 0 -103 2 4.954058 1.008958 4.697495 0 0 0 -104 2 3.156692 1.910950 1.992070 0 0 0 -105 2 4.994329 0.971034 10.003924 0 0 0 -106 2 3.235675 1.859762 7.371071 0 0 0 -107 2 4.763228 0.854978 15.087093 0 0 0 -108 2 3.219307 1.949538 12.645809 0 0 0 -109 2 3.133439 3.727399 4.635540 0 0 0 -110 2 1.602249 4.722812 2.026771 0 0 0 -111 2 3.193585 3.734712 9.755312 0 0 0 -112 2 1.749561 4.612673 7.143057 0 0 0 -113 2 3.214500 3.682174 15.187236 0 0 0 -114 2 1.582113 4.789188 12.682887 0 0 0 -115 2 1.507548 6.616100 4.553937 0 0 0 -116 2 1.603808 6.573349 10.049083 0 0 0 -117 2 1.602508 6.671225 15.127657 0 0 0 -118 2 0.052249 9.412549 4.639501 0 0 0 -119 2 0.051471 9.412549 9.806809 0 0 0 -120 2 12.893859 9.487363 15.086301 0 0 0 -121 2 7.997603 0.951279 4.748041 0 0 0 -122 2 6.539160 1.805424 1.944534 0 0 0 -123 2 8.108802 1.045881 9.799837 0 0 0 -124 2 6.587614 1.907575 7.228622 0 0 0 -125 2 8.038783 0.921365 15.184859 0 0 0 -126 2 6.396654 1.895200 12.462955 0 0 0 -127 2 6.465244 3.768687 4.548391 0 0 0 -128 2 4.817009 4.713925 1.911734 0 0 0 -129 2 6.579560 3.858688 9.981741 0 0 0 -130 2 4.830908 4.706500 7.143532 0 0 0 -131 2 6.600864 3.835513 15.291181 0 0 0 -132 2 4.809214 4.708750 12.398306 0 0 0 -133 2 4.852083 6.520473 4.519711 0 0 0 -134 2 3.164227 7.482699 1.857543 0 0 0 -135 2 4.897030 6.556024 9.970808 0 0 0 -136 2 3.299588 7.531299 7.120081 0 0 0 -137 2 4.759461 6.522048 15.200387 0 0 0 -138 2 3.287766 7.479324 12.651038 0 0 0 -139 2 3.304394 9.480612 4.636966 0 0 0 -140 2 1.578346 10.223910 2.021384 0 0 0 -141 2 3.320113 9.357873 9.779080 0 0 0 -142 2 1.563147 10.234710 7.198516 0 0 0 -143 2 3.232037 9.381274 15.177095 0 0 0 -144 2 1.721372 10.316723 12.690335 0 0 0 -145 2 11.402414 1.040492 4.544905 0 0 0 -146 2 9.788604 1.827587 2.040557 0 0 0 -147 2 11.417353 0.840307 9.831052 0 0 0 -148 2 9.671170 1.912750 7.377092 0 0 0 -149 2 11.326290 1.000633 15.246180 0 0 0 -150 2 9.614661 1.898013 12.513818 0 0 0 -151 2 9.850958 3.637848 4.615099 0 0 0 -152 2 8.099449 4.678824 2.071772 0 0 0 -153 2 9.696761 3.814138 9.899662 0 0 0 -154 2 7.998513 4.614586 7.338113 0 0 0 -155 2 9.735992 3.671936 15.140175 0 0 0 -156 2 8.146994 4.618186 12.625211 0 0 0 -157 2 8.052293 6.656488 4.553778 0 0 0 -158 2 6.564231 7.430048 1.918865 0 0 0 -159 2 8.012802 6.579762 9.966846 0 0 0 -160 2 6.507333 7.483374 7.313711 0 0 0 -161 2 8.157387 6.602824 15.233662 0 0 0 -162 2 6.610867 7.434660 12.616020 0 0 0 -163 2 6.426662 9.289472 4.661051 0 0 0 -164 2 4.858448 10.303336 2.037387 0 0 0 -165 2 6.565530 9.341448 9.960191 0 0 0 -166 2 4.849615 10.389624 7.373448 0 0 0 -167 2 6.431988 9.400624 15.216549 0 0 0 -168 2 4.881961 10.395924 12.475156 0 0 0 -169 2 12.943218 1.789336 2.125487 0 0 0 -170 2 0.037672 1.870450 7.312126 0 0 0 -171 2 0.011691 1.908138 12.563572 0 0 0 -172 2 11.424108 4.692662 2.142600 0 0 0 -173 2 11.293554 4.598836 7.144166 0 0 0 -174 2 11.253283 4.666111 12.533308 0 0 0 -175 2 11.331876 6.621837 4.667547 0 0 0 -176 2 9.813546 7.597450 2.135945 0 0 0 -177 2 11.286669 6.481323 9.970966 0 0 0 -178 2 9.637395 7.505761 7.277584 0 0 0 -179 2 11.460482 6.559174 15.156813 0 0 0 -180 2 9.787435 7.554362 12.555967 0 0 0 -181 2 9.703256 9.296335 4.654237 0 0 0 -182 2 8.057230 10.210185 2.066860 0 0 0 -183 2 9.676106 9.362148 9.968272 0 0 0 -184 2 8.082431 10.365774 7.234484 0 0 0 -185 2 9.790553 9.420987 15.172341 0 0 0 -186 2 7.994226 10.274535 12.525702 0 0 0 -187 2 12.930877 7.431960 2.088092 0 0 0 -188 2 12.972317 7.587325 7.233375 0 0 0 -189 2 0.070149 7.476849 12.647394 0 0 0 -190 2 11.432942 10.284998 1.896206 0 0 0 -191 2 11.442165 10.413700 7.213252 0 0 0 -192 2 11.411248 10.298836 12.655317 0 0 0 diff --git a/examples/GaN-SNAP-LAMMPS/DATA/6/DATA b/examples/GaN-SNAP-LAMMPS/DATA/6/DATA deleted file mode 100755 index c9eda515..00000000 --- a/examples/GaN-SNAP-LAMMPS/DATA/6/DATA +++ /dev/null @@ -1,215 +0,0 @@ -LAMMPS DATA file - -192 atoms -0 bonds -0 angles -0 dihedrals -0 impropers - -2 atom types -0 bond types -0 angle types - -0.0 12.990503 xlo xhi -0.0 11.250148 ylo yhi -0.0 15.845291 zlo zhi - -Masses - -1 69.723 -2 14.0067 - -Atoms - -1 1 1.583802 1.015922 2.527799 0 0 0 -2 1 1.534958 0.939455 7.949899 0 0 0 -3 1 1.535867 0.967985 13.307984 0 0 0 -4 1 0.073338 3.697024 2.576603 0 0 0 -5 1 12.908195 3.738199 7.862275 0 0 0 -6 1 12.933300 3.847213 13.167120 0 0 0 -7 1 4.840132 0.958400 2.498644 0 0 0 -8 1 3.170982 1.925350 5.300091 0 0 0 -9 1 4.793496 1.014797 7.893015 0 0 0 -10 1 3.259187 1.881362 10.458209 0 0 0 -11 1 4.762708 0.929431 13.050181 0 0 0 -12 1 3.230738 1.888000 0.038029 0 0 0 -13 1 3.126554 3.797263 2.530651 0 0 0 -14 1 1.648105 4.711900 5.362522 0 0 0 -15 1 3.132400 3.829888 7.880497 0 0 0 -16 1 1.597702 4.648336 10.575622 0 0 0 -17 1 3.194495 3.719974 13.151116 0 0 0 -18 1 1.657588 4.724612 0.150530 0 0 0 -19 1 1.739298 6.528911 2.538099 0 0 0 -20 1 1.732803 6.515073 7.933262 0 0 0 -21 1 1.732803 6.470298 13.122119 0 0 0 -22 1 12.971551 9.392636 2.761993 0 0 0 -23 1 12.917297 9.480162 7.896184 0 0 0 -24 1 0.074002 9.380824 13.145412 0 0 0 -25 1 8.101268 0.986537 2.767222 0 0 0 -26 1 6.596578 1.792824 5.155899 0 0 0 -27 1 8.221300 0.971957 7.771481 0 0 0 -28 1 6.496421 1.963826 10.521907 0 0 0 -29 1 8.065024 0.877669 13.104214 0 0 0 -30 1 6.464204 1.896325 15.766381 0 0 0 -31 1 6.527078 3.818525 2.509894 0 0 0 -32 1 4.930935 4.721012 5.268242 0 0 0 -33 1 6.607749 3.659223 7.948632 0 0 0 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4.624607 0 0 0 -134 2 3.131231 7.562687 1.962915 0 0 0 -135 2 4.814280 6.525086 9.866546 0 0 0 -136 2 3.324270 7.396297 7.339697 0 0 0 -137 2 4.968218 6.514398 15.240317 0 0 0 -138 2 3.177997 7.527587 12.415102 0 0 0 -139 2 3.368957 9.399836 4.590222 0 0 0 -140 2 1.501832 10.393112 2.019007 0 0 0 -141 2 3.338040 9.376211 9.752776 0 0 0 -142 2 1.732673 10.292536 7.341598 0 0 0 -143 2 3.156952 9.446074 15.320336 0 0 0 -144 2 1.696040 10.370499 12.519681 0 0 0 -145 2 11.419172 0.952235 4.653920 0 0 0 -146 2 9.702607 1.920963 1.878618 0 0 0 -147 2 11.237175 0.951459 9.923589 0 0 0 -148 2 9.756128 1.918825 7.403395 0 0 0 -149 2 11.482046 1.028241 15.223521 0 0 0 -150 2 9.853557 1.788886 12.499241 0 0 0 -151 2 9.622455 3.758675 4.702248 0 0 0 -152 2 8.036185 4.670949 1.858811 0 0 0 -153 2 9.691695 3.813125 9.920578 0 0 0 -154 2 8.188953 4.718875 7.392462 0 0 0 -155 2 9.628691 3.677111 15.164102 0 0 0 -156 2 8.181419 4.776025 12.399415 0 0 0 -157 2 8.024883 6.545449 4.710805 0 0 0 -158 2 6.501617 7.557400 1.881470 0 0 0 -159 2 8.163882 6.589324 9.752459 0 0 0 -160 2 6.557606 7.610725 7.150029 0 0 0 -161 2 8.082821 6.493023 15.258539 0 0 0 -162 2 6.411593 7.609600 12.396563 0 0 0 -163 2 6.375739 9.443599 4.741069 0 0 0 -164 2 4.888586 10.369824 1.992387 0 0 0 -165 2 6.517595 9.305560 9.909803 0 0 0 -166 2 4.754784 10.212772 7.215628 0 0 0 -167 2 6.529287 9.463287 15.245546 0 0 0 -168 2 4.919633 10.356661 12.644700 0 0 0 -169 2 0.041570 1.879562 1.932809 0 0 0 -170 2 0.113017 1.818024 7.271404 0 0 0 -171 2 0.062354 1.819711 12.659120 0 0 0 -172 2 11.376563 4.779850 1.938830 0 0 0 -173 2 11.479838 4.783788 7.295647 0 0 0 -174 2 11.263286 4.657561 12.478642 0 0 0 -175 2 11.305895 6.501011 4.469006 0 0 0 -176 2 9.844983 7.489674 2.010926 0 0 0 -177 2 11.318755 6.673700 10.062076 0 0 0 -178 2 9.863559 7.537487 7.339539 0 0 0 -179 2 11.323562 6.567724 15.118784 0 0 0 -180 2 9.799646 7.562687 12.416845 0 0 0 -181 2 9.670520 9.308485 4.666280 0 0 0 -182 2 8.177522 10.387824 1.833617 0 0 0 -183 2 9.665454 9.368223 9.870190 0 0 0 -184 2 8.077625 10.214460 7.350789 0 0 0 -185 2 9.717546 9.414349 15.206725 0 0 0 -186 2 8.002540 10.269360 12.697148 0 0 0 -187 2 0.111718 7.472686 2.023444 0 0 0 -188 2 0.016888 7.574500 7.412902 0 0 0 -189 2 12.880214 7.587437 12.569435 0 0 0 -190 2 11.287318 10.250010 2.051331 0 0 0 -191 2 11.391892 10.332024 7.416388 0 0 0 -192 2 11.387865 10.222560 12.443940 0 0 0 diff --git a/examples/GaN-SNAP-LAMMPS/DATA/60/DATA b/examples/GaN-SNAP-LAMMPS/DATA/60/DATA deleted file mode 100755 index 10a1334d..00000000 --- a/examples/GaN-SNAP-LAMMPS/DATA/60/DATA +++ /dev/null @@ -1,215 +0,0 @@ -LAMMPS DATA file - -192 atoms -0 bonds -0 angles -0 dihedrals -0 impropers - -2 atom types -0 bond types -0 angle types - -0.0 12.990503 xlo xhi -0.0 11.250148 ylo yhi -0.0 15.845291 zlo zhi - -Masses - -1 69.723 -2 14.0067 - -Atoms - -1 1 1.670839 1.048739 2.788454 0 0 0 -2 1 1.753198 0.941986 7.969389 0 0 0 -3 1 1.704484 0.876139 13.253159 0 0 0 -4 1 0.004825 3.691849 2.615899 0 0 0 -5 1 0.031864 3.786800 7.965744 0 0 0 -6 1 0.109040 3.774200 13.058579 0 0 0 -7 1 4.849485 0.931434 2.566620 0 0 0 -8 1 3.188129 1.893737 5.287415 0 0 0 -9 1 4.834805 0.948354 7.787485 0 0 0 -10 1 3.192286 1.873150 10.577048 0 0 0 -11 1 4.851044 0.940029 13.166010 0 0 0 -12 1 3.156303 1.961576 15.793793 0 0 0 -13 1 3.269060 3.769925 2.676428 0 0 0 -14 1 1.650963 4.734512 5.346518 0 0 0 -15 1 3.224892 3.679248 7.766252 0 0 0 -16 1 1.599391 4.769950 10.676874 0 0 0 -17 1 3.327128 3.760475 13.259022 0 0 0 -18 1 1.670319 4.757913 15.722806 0 0 0 -19 1 1.537946 6.608000 2.588328 0 0 0 -20 1 1.657588 6.636800 7.840408 0 0 0 -21 1 1.719163 6.664025 13.184866 0 0 0 -22 1 12.945348 9.298135 2.733630 0 0 0 -23 1 0.079579 9.417387 7.829633 0 0 0 -24 1 12.947251 9.273947 13.093122 0 0 0 -25 1 8.091005 1.025969 2.687203 0 0 0 -26 1 6.450824 1.948076 5.194562 0 0 0 -27 1 8.224937 0.890595 7.956237 0 0 0 -28 1 6.575013 1.769761 10.678300 0 0 0 -29 1 8.245982 0.971102 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2.548081 0 0 0 -80 1 9.708582 7.426785 5.361254 0 0 0 -81 1 11.388384 6.520923 8.045288 0 0 0 -82 1 9.846282 7.485399 10.421923 0 0 0 -83 1 11.404363 6.638712 13.326840 0 0 0 -84 1 9.774055 7.483261 15.683193 0 0 0 -85 1 9.864988 9.382061 2.585001 0 0 0 -86 1 8.142967 10.400650 5.261587 0 0 0 -87 1 9.793281 9.468462 7.793982 0 0 0 -88 1 8.047227 10.309973 10.652630 0 0 0 -89 1 9.727549 9.300723 13.320344 0 0 0 -90 1 7.996564 10.280835 0.109333 0 0 0 -91 1 0.061055 7.535237 5.275056 0 0 0 -92 1 12.886189 7.446811 10.546625 0 0 0 -93 1 0.002598 7.521849 15.830554 0 0 0 -94 1 11.344217 10.315598 5.167466 0 0 0 -95 1 11.299789 10.244160 10.621415 0 0 0 -96 1 11.379031 10.222897 15.791417 0 0 0 -97 2 1.723580 0.851029 4.744238 0 0 0 -98 2 1.679672 0.862740 10.030069 0 0 0 -99 2 1.514043 0.983207 15.244279 0 0 0 -100 2 0.048869 3.859926 4.487703 0 0 0 -101 2 0.031599 3.747087 9.846897 0 0 0 -102 2 12.898533 3.852501 15.336498 0 0 0 -103 2 4.968608 0.993782 4.588955 0 0 0 -104 2 3.278283 1.922313 1.846135 0 0 0 -105 2 4.888326 0.947645 10.058907 0 0 0 -106 2 3.148508 1.905325 7.156209 0 0 0 -107 2 4.797263 0.832770 15.277395 0 0 0 -108 2 3.184622 1.939301 12.584488 0 0 0 -109 2 3.125385 3.842263 4.587053 0 0 0 -110 2 1.601469 4.783113 1.972263 0 0 0 -111 2 3.369087 3.681949 9.999171 0 0 0 -112 2 1.711759 4.748688 7.231949 0 0 0 -113 2 3.364151 3.759125 15.205458 0 0 0 -114 2 1.571071 4.743625 12.428729 0 0 0 -115 2 1.536906 6.673138 4.489922 0 0 0 -116 2 1.690974 6.547474 9.795242 0 0 0 -117 2 1.506898 6.667400 15.104523 0 0 0 -118 2 12.961171 9.295885 4.652811 0 0 0 -119 2 12.973045 9.285760 9.751984 0 0 0 -120 2 12.963061 9.460812 15.124964 0 0 0 -121 2 8.167779 0.991104 4.754855 0 0 0 -122 2 6.552670 1.907350 2.042300 0 0 0 -123 2 8.179340 1.027206 10.046231 0 0 0 -124 2 6.479923 1.841537 7.404504 0 0 0 -125 2 8.237018 0.840454 15.140334 0 0 0 -126 2 6.368984 1.851662 12.582904 0 0 0 -127 2 6.403279 3.728974 4.492457 0 0 0 -128 2 4.901447 4.649911 1.854691 0 0 0 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10.008361 0 0 0 -154 2 8.072559 4.794701 7.229414 0 0 0 -155 2 9.637135 3.642235 15.199753 0 0 0 -156 2 8.014361 4.780863 12.620457 0 0 0 -157 2 8.108152 6.511023 4.732038 0 0 0 -158 2 6.380286 7.512511 2.016155 0 0 0 -159 2 8.068921 6.532399 10.065245 0 0 0 -160 2 6.525649 7.571350 7.299925 0 0 0 -161 2 8.003189 6.463435 15.169806 0 0 0 -162 2 6.543836 7.539062 12.505103 0 0 0 -163 2 6.493043 9.301510 4.504024 0 0 0 -164 2 4.890795 10.283760 1.940890 0 0 0 -165 2 6.390158 9.484212 9.884451 0 0 0 -166 2 4.940418 10.367799 7.383905 0 0 0 -167 2 6.575663 9.380036 15.113238 0 0 0 -168 2 4.970946 10.390862 12.397831 0 0 0 -169 2 12.876187 1.917588 1.910308 0 0 0 -170 2 12.866054 1.895650 7.121983 0 0 0 -171 2 12.887229 1.843787 12.393711 0 0 0 -172 2 11.357467 4.601311 2.055451 0 0 0 -173 2 11.410209 4.700874 7.289151 0 0 0 -174 2 11.357987 4.658461 12.402267 0 0 0 -175 2 11.461521 6.666275 4.756915 0 0 0 -176 2 9.809129 7.451873 1.932175 0 0 0 -177 2 11.359156 6.578187 9.941335 0 0 0 -178 2 9.674807 7.517237 7.226245 0 0 0 -179 2 11.307324 6.671788 15.237465 0 0 0 -180 2 9.714558 7.413623 12.488941 0 0 0 -181 2 9.623755 9.348198 4.697970 0 0 0 -182 2 8.191032 10.222785 2.119149 0 0 0 -183 2 9.791462 9.288347 9.990773 0 0 0 -184 2 8.183238 10.384112 7.299608 0 0 0 -185 2 9.760545 9.448212 15.338241 0 0 0 -186 2 8.001630 10.236510 12.654366 0 0 0 -187 2 12.863326 7.535574 2.098075 0 0 0 -188 2 12.956598 7.549974 7.232108 0 0 0 -189 2 0.111718 7.493836 12.557393 0 0 0 -190 2 11.246009 10.250010 2.083814 0 0 0 -191 2 11.265494 10.299286 7.323852 0 0 0 -192 2 11.356428 10.204784 12.609999 0 0 0 diff --git a/examples/GaN-SNAP-LAMMPS/DATA/61/DATA b/examples/GaN-SNAP-LAMMPS/DATA/61/DATA deleted file mode 100755 index 37e2b0f1..00000000 --- a/examples/GaN-SNAP-LAMMPS/DATA/61/DATA +++ /dev/null @@ -1,215 +0,0 @@ -LAMMPS DATA file - -192 atoms -0 bonds -0 angles -0 dihedrals -0 impropers - -2 atom types -0 bond types -0 angle types - -0.0 12.990503 xlo xhi -0.0 11.250148 ylo yhi -0.0 15.845291 zlo zhi - -Masses - -1 69.723 -2 14.0067 - -Atoms - -1 1 1.703315 0.973430 2.625723 0 0 0 -2 1 1.692273 0.957680 7.993949 0 0 0 -3 1 1.653821 0.889167 13.079337 0 0 0 -4 1 12.985000 3.750799 2.549032 0 0 0 -5 1 0.020721 3.696236 7.775284 0 0 0 -6 1 12.933581 3.809863 13.156662 0 0 0 -7 1 4.786221 0.936699 2.679122 0 0 0 -8 1 3.205666 1.987001 5.397857 0 0 0 -9 1 4.987184 1.039075 7.766094 0 0 0 -10 1 3.237883 1.921975 10.679250 0 0 0 -11 1 4.774659 0.899888 13.130834 0 0 0 -12 1 3.177087 1.887550 15.830238 0 0 0 -13 1 3.186441 3.848001 2.784018 0 0 0 -14 1 1.549897 4.611548 5.262379 0 0 0 -15 1 3.183972 3.697361 8.072700 0 0 0 -16 1 1.639142 4.765788 10.502892 0 0 0 -17 1 3.178906 3.800975 13.084090 0 0 0 -18 1 1.646936 4.729225 0.134685 0 0 0 -19 1 1.699418 6.483010 2.717467 0 0 0 -20 1 1.599780 6.531611 8.043703 0 0 0 -21 1 1.612771 6.487623 13.149690 0 0 0 -22 1 12.873693 9.283622 2.528750 0 0 0 -23 1 0.034249 9.429874 8.005675 0 0 0 -24 1 0.005408 9.267647 13.230501 0 0 0 -25 1 8.076975 1.001499 2.760883 0 0 0 -26 1 6.476026 1.987114 5.381061 0 0 0 -27 1 8.152580 1.002264 8.070165 0 0 0 -28 1 6.411982 1.859987 10.531414 0 0 0 -29 1 8.239616 0.849206 13.297526 0 0 0 -30 1 6.484729 1.903300 0.085565 0 0 0 -31 1 6.605541 3.846313 2.790673 0 0 0 -32 1 4.980689 4.672074 5.364265 0 0 0 -33 1 6.474207 3.786912 7.820602 0 0 0 -34 1 4.786611 4.790313 10.711733 0 0 0 -35 1 6.609958 3.705349 13.334129 0 0 0 -36 1 4.879363 4.768600 15.767807 0 0 0 -37 1 4.986405 6.567049 2.629526 0 0 0 -38 1 3.187740 7.527924 5.420674 0 0 0 -39 1 4.855330 6.646363 7.980956 0 0 0 -40 1 3.241780 7.475161 10.523967 0 0 0 -41 1 4.784792 6.536674 13.117999 0 0 0 -42 1 3.328297 7.458961 0.014261 0 0 0 -43 1 3.193845 9.443937 2.535405 0 0 0 -44 1 1.499364 10.285898 5.158593 0 0 0 -45 1 3.124346 9.357536 8.028809 0 0 0 -46 1 1.540024 10.225597 10.442046 0 0 0 -47 1 3.157472 9.380486 13.198493 0 0 0 -48 1 1.640830 10.299848 15.813917 0 0 0 -49 1 11.444114 0.912230 2.660107 0 0 0 -50 1 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1.821849 15.741345 0 0 0 -76 1 11.307064 4.608398 5.169843 0 0 0 -77 1 11.444503 4.625948 10.420814 0 0 0 -78 1 11.288747 4.781425 15.776522 0 0 0 -79 1 11.371757 6.671225 2.642044 0 0 0 -80 1 9.760415 7.437810 5.235284 0 0 0 -81 1 11.368249 6.552649 8.052418 0 0 0 -82 1 9.798347 7.538612 10.451712 0 0 0 -83 1 11.273548 6.526886 13.045111 0 0 0 -84 1 9.754569 7.471336 0.136269 0 0 0 -85 1 9.806141 9.288347 2.579772 0 0 0 -86 1 8.148293 10.308286 5.175389 0 0 0 -87 1 9.667662 9.302748 8.072066 0 0 0 -88 1 8.121922 10.425175 10.472311 0 0 0 -89 1 9.871483 9.446074 13.094073 0 0 0 -90 1 8.195579 10.284773 15.841012 0 0 0 -91 1 12.909702 7.538612 5.363948 0 0 0 -92 1 12.896972 7.394722 10.578791 0 0 0 -93 1 0.050663 7.556500 0.053874 0 0 0 -94 1 11.366171 10.299286 5.410374 0 0 0 -95 1 11.322133 10.321561 10.578633 0 0 0 -96 1 11.327329 10.417412 15.838794 0 0 0 -97 2 1.722930 0.935664 4.694801 0 0 0 -98 2 1.592376 1.024461 9.986177 0 0 0 -99 2 1.719423 0.880965 15.327625 0 0 0 -100 2 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0.872775 15.240793 0 0 0 -150 2 9.654802 1.920625 12.574347 0 0 0 -151 2 9.686888 3.645273 4.546172 0 0 0 -152 2 8.159855 4.631911 1.975908 0 0 0 -153 2 9.824198 3.707599 9.808710 0 0 0 -154 2 8.134653 4.624711 7.171262 0 0 0 -155 2 9.693903 3.784437 15.150475 0 0 0 -156 2 8.203633 4.684112 12.666567 0 0 0 -157 2 8.147384 6.640400 4.479939 0 0 0 -158 2 6.478624 7.588562 1.923618 0 0 0 -159 2 8.076845 6.562436 9.846422 0 0 0 -160 2 6.414581 7.531299 7.314345 0 0 0 -161 2 7.996954 6.582349 15.240951 0 0 0 -162 2 6.383663 7.586087 12.615862 0 0 0 -163 2 6.497720 9.446749 4.486594 0 0 0 -164 2 4.810253 10.254060 2.078427 0 0 0 -165 2 6.415750 9.454287 10.066988 0 0 0 -166 2 4.887287 10.283873 7.424469 0 0 0 -167 2 6.531365 9.363948 15.267888 0 0 0 -168 2 4.805967 10.382987 12.537111 0 0 0 -169 2 0.062354 1.885975 2.007440 0 0 0 -170 2 0.101326 1.811274 7.303570 0 0 0 -171 2 12.917497 1.934575 12.622834 0 0 0 -172 2 11.412677 4.680062 1.908090 0 0 0 -173 2 11.290436 4.700987 7.354275 0 0 0 -174 2 11.384617 4.689174 12.687641 0 0 0 -175 2 11.350062 6.620375 4.599729 0 0 0 -176 2 9.814845 7.479211 1.938988 0 0 0 -177 2 11.467756 6.461410 9.903940 0 0 0 -178 2 9.823419 7.487649 7.281862 0 0 0 -179 2 11.358246 6.478060 15.111337 0 0 0 -180 2 9.728718 7.430048 12.596055 0 0 0 -181 2 9.673508 9.293747 4.485009 0 0 0 -182 2 8.189863 10.359249 2.023444 0 0 0 -183 2 9.754309 9.269897 9.931511 0 0 0 -184 2 8.238447 10.386812 7.233692 0 0 0 -185 2 9.823808 9.467562 15.288962 0 0 0 -186 2 8.072818 10.348111 12.426035 0 0 0 -187 2 0.084438 7.516224 1.914270 0 0 0 -188 2 12.885280 7.438261 7.153198 0 0 0 -189 2 12.909442 7.421948 12.479275 0 0 0 -190 2 11.411248 10.224135 1.984147 0 0 0 -191 2 11.253153 10.320323 7.283605 0 0 0 -192 2 11.453857 10.302998 12.598749 0 0 0 diff --git a/examples/GaN-SNAP-LAMMPS/DATA/7/DATA b/examples/GaN-SNAP-LAMMPS/DATA/7/DATA deleted file mode 100755 index 850435a5..00000000 --- a/examples/GaN-SNAP-LAMMPS/DATA/7/DATA +++ /dev/null @@ -1,215 +0,0 @@ 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7.796992 0 0 0 -21 1 1.717994 6.559061 13.308143 0 0 0 -22 1 12.915005 9.386899 2.676586 0 0 0 -23 1 12.868911 9.400961 7.873525 0 0 0 -24 1 12.873469 9.372723 13.101520 0 0 0 -25 1 8.021116 0.871245 2.523363 0 0 0 -26 1 6.414451 1.772123 5.319106 0 0 0 -27 1 8.062426 0.946194 7.979055 0 0 0 -28 1 6.494992 1.883050 10.540604 0 0 0 -29 1 8.021376 0.935337 13.310836 0 0 0 -30 1 6.592421 1.823312 15.747367 0 0 0 -31 1 6.512139 3.781625 2.609086 0 0 0 -32 1 4.795055 4.788401 5.143857 0 0 0 -33 1 6.392757 3.669461 7.811411 0 0 0 -34 1 4.902876 4.704137 10.416060 0 0 0 -35 1 6.607230 3.801538 13.274234 0 0 0 -36 1 4.758032 4.768713 0.131516 0 0 0 -37 1 4.997317 6.643325 2.725865 0 0 0 -38 1 3.251133 7.427573 5.244157 0 0 0 -39 1 4.776348 6.457023 8.056380 0 0 0 -40 1 3.196054 7.454123 10.505111 0 0 0 -41 1 4.862865 6.595962 13.048438 0 0 0 -42 1 3.336481 7.513411 0.106163 0 0 0 -43 1 3.208135 9.362936 2.494207 0 0 0 -44 1 1.539894 10.349236 5.222608 0 0 0 -45 1 3.351160 9.289247 8.071908 0 0 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11.243281 0.919756 4.526841 0 0 0 -146 2 9.801594 1.845812 2.094431 0 0 0 -147 2 11.427486 0.953495 9.806333 0 0 0 -148 2 9.861741 1.822187 7.402444 0 0 0 -149 2 11.294983 0.909057 15.059840 0 0 0 -150 2 9.779251 1.803174 12.405436 0 0 0 -151 2 9.800815 3.715699 4.678005 0 0 0 -152 2 8.088927 4.716175 1.834568 0 0 0 -153 2 9.849529 3.817625 9.986653 0 0 0 -154 2 8.200385 4.661274 7.304996 0 0 0 -155 2 9.762493 3.756762 15.119259 0 0 0 -156 2 8.053722 4.676687 12.463430 0 0 0 -157 2 8.198177 6.672013 4.478038 0 0 0 -158 2 6.504475 7.407210 2.081913 0 0 0 -159 2 8.246112 6.465123 10.047974 0 0 0 -160 2 6.370023 7.541424 7.357761 0 0 0 -161 2 8.127898 6.649288 15.317009 0 0 0 -162 2 6.527988 7.418573 12.460261 0 0 0 -163 2 6.412632 9.272035 4.502439 0 0 0 -164 2 4.901707 10.411562 1.940097 0 0 0 -165 2 6.471999 9.484100 10.050034 0 0 0 -166 2 4.917295 10.422475 7.352532 0 0 0 -167 2 6.452773 9.411649 15.109435 0 0 0 -168 2 4.818308 10.353174 12.558502 0 0 0 -169 2 12.967510 1.898125 2.065592 0 0 0 -170 2 0.022084 1.886650 7.294380 0 0 0 -171 2 0.002598 1.781123 12.619189 0 0 0 -172 2 11.495556 4.654861 2.135470 0 0 0 -173 2 11.326809 4.774563 7.253499 0 0 0 -174 2 11.344217 4.624036 12.431106 0 0 0 -175 2 11.317067 6.613512 4.716668 0 0 0 -176 2 9.793281 7.389772 2.094906 0 0 0 -177 2 11.476460 6.623525 9.763868 0 0 0 -178 2 9.711181 7.546037 7.340648 0 0 0 -179 2 11.295113 6.510573 15.245388 0 0 0 -180 2 9.737032 7.527924 12.466124 0 0 0 -181 2 9.658959 9.449337 4.711597 0 0 0 -182 2 8.231952 10.224360 1.885431 0 0 0 -183 2 9.638694 9.372836 9.811562 0 0 0 -184 2 8.221949 10.222447 7.123409 0 0 0 -185 2 9.757817 9.436399 15.130985 0 0 0 -186 2 8.035665 10.276448 12.457884 0 0 0 -187 2 0.002598 7.591488 2.026930 0 0 0 -188 2 12.886969 7.475498 7.126736 0 0 0 -189 2 0.000000 7.484724 12.707289 0 0 0 -190 2 11.447621 10.309411 2.111068 0 0 0 -191 2 11.272509 10.287923 7.403395 0 0 0 -192 2 11.475161 10.360712 12.587182 0 0 0 diff --git a/examples/GaN-SNAP-LAMMPS/DATA/8/DATA b/examples/GaN-SNAP-LAMMPS/DATA/8/DATA deleted file mode 100755 index 94155a05..00000000 --- a/examples/GaN-SNAP-LAMMPS/DATA/8/DATA +++ /dev/null @@ -1,215 +0,0 @@ -LAMMPS DATA file - -192 atoms -0 bonds -0 angles -0 dihedrals -0 impropers - -2 atom types -0 bond types -0 angle types - -0.0 12.990503 xlo xhi -0.0 11.250148 ylo yhi -0.0 15.845291 zlo zhi - -Masses - -1 69.723 -2 14.0067 - -Atoms - -1 1 1.533399 0.876724 2.741869 0 0 0 -2 1 1.697209 0.982487 8.027383 0 0 0 -3 1 1.527553 0.861345 13.104372 0 0 0 -4 1 0.008354 3.834951 2.663276 0 0 0 -5 1 12.945260 3.791862 7.782573 0 0 0 -6 1 12.935213 3.770937 13.095340 0 0 0 -7 1 4.796354 1.025597 2.755179 0 0 0 -8 1 3.165916 1.830399 5.228471 0 0 0 -9 1 4.787520 0.865485 8.006308 0 0 0 -10 1 3.293352 1.883950 10.596538 0 0 0 -11 1 4.809734 0.895253 13.310995 0 0 0 -12 1 3.133050 1.838162 0.134685 0 0 0 -13 1 3.151496 3.807725 2.498010 0 0 0 -14 1 1.740208 4.722137 5.150512 0 0 0 -15 1 3.221775 3.765875 7.958931 0 0 0 -16 1 1.564057 4.741600 10.518104 0 0 0 -17 1 3.318554 3.804688 13.339675 0 0 0 -18 1 1.519369 4.646874 15.681609 0 0 0 -19 1 1.623293 6.667963 2.484542 0 0 0 -20 1 1.623813 6.543761 8.020886 0 0 0 -21 1 1.680581 6.459498 13.282790 0 0 0 -22 1 12.908153 9.396686 2.666921 0 0 0 -23 1 0.090239 9.455975 7.807292 0 0 0 -24 1 0.061184 9.456987 13.341418 0 0 0 -25 1 8.088667 0.846045 2.540000 0 0 0 -26 1 6.459138 1.970463 5.256992 0 0 0 -27 1 8.087108 0.931839 7.785584 0 0 0 -28 1 6.489536 1.936038 10.447117 0 0 0 -29 1 8.068012 1.046613 13.166010 0 0 0 -30 1 6.537731 1.936151 0.030106 0 0 0 -31 1 6.411593 3.641898 2.539683 0 0 0 -32 1 4.884299 4.644961 5.181727 0 0 0 -33 1 6.495122 3.774650 8.014706 0 0 0 -34 1 4.901447 4.666336 10.548844 0 0 0 -35 1 6.367295 3.735837 13.091221 0 0 0 -36 1 4.863385 4.758813 0.009507 0 0 0 -37 1 4.752316 6.513048 2.493732 0 0 0 -38 1 3.209044 7.419135 5.231798 0 0 0 -39 1 4.794015 6.515636 7.996326 0 0 0 -40 1 3.322971 7.611288 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13.141609 0 0 0 -66 1 6.472258 7.591150 0.110917 0 0 0 -67 1 6.605021 9.389486 2.536039 0 0 0 -68 1 4.917295 10.280498 5.174913 0 0 0 -69 1 6.472778 9.442812 7.838348 0 0 0 -70 1 4.914307 10.239997 10.536484 0 0 0 -71 1 6.390288 9.330310 13.268529 0 0 0 -72 1 4.841171 10.298723 15.684302 0 0 0 -73 1 12.905415 1.781236 5.325444 0 0 0 -74 1 12.973616 1.907125 10.563738 0 0 0 -75 1 12.894763 1.859087 0.150530 0 0 0 -76 1 11.335643 4.763875 5.133240 0 0 0 -77 1 11.283551 4.733275 10.494019 0 0 0 -78 1 11.346685 4.695137 0.080811 0 0 0 -79 1 11.298620 6.590899 2.704474 0 0 0 -80 1 9.669871 7.497661 5.398649 0 0 0 -81 1 11.496465 6.627012 7.810302 0 0 0 -82 1 9.775873 7.460986 10.589566 0 0 0 -83 1 11.431253 6.644113 13.060005 0 0 0 -84 1 9.770807 7.481011 15.812649 0 0 0 -85 1 9.709882 9.317260 2.637766 0 0 0 -86 1 8.243254 10.303111 5.427170 0 0 0 -87 1 9.624274 9.386899 8.036098 0 0 0 -88 1 8.066973 10.214347 10.587823 0 0 0 -89 1 9.662466 9.329185 13.115147 0 0 0 -90 1 8.153100 10.208610 15.823741 0 0 0 -91 1 12.916068 7.474823 5.128487 0 0 0 -92 1 0.115615 7.490911 10.650095 0 0 0 -93 1 12.888398 7.558750 0.144192 0 0 0 -94 1 11.260688 10.284661 5.281235 0 0 0 -95 1 11.237825 10.413250 10.542664 0 0 0 -96 1 11.492179 10.252598 15.797755 0 0 0 -97 2 1.562238 0.827988 4.490872 0 0 0 -98 2 1.592246 0.950986 9.825189 0 0 0 -99 2 1.647456 1.026047 15.238416 0 0 0 -100 2 0.001012 3.782525 4.709220 0 0 0 -101 2 12.946058 3.760925 9.991723 0 0 0 -102 2 12.899956 3.843501 15.265511 0 0 0 -103 2 4.977571 0.962011 4.666755 0 0 0 -104 2 3.210603 1.961801 1.911259 0 0 0 -105 2 4.768684 0.898088 9.916775 0 0 0 -106 2 3.164746 1.884287 7.202318 0 0 0 -107 2 4.992250 0.904006 15.169489 0 0 0 -108 2 3.337260 1.839062 12.597798 0 0 0 -109 2 3.254771 3.652698 4.564394 0 0 0 -110 2 1.622254 4.725512 2.143392 0 0 0 -111 2 3.282830 3.811100 9.832320 0 0 0 -112 2 1.545610 4.628761 7.273939 0 0 0 -113 2 3.278413 3.660011 15.160774 0 0 0 -114 2 1.746183 4.721462 12.639313 0 0 0 -115 2 1.514693 6.558161 4.489605 0 0 0 -116 2 1.606795 6.573012 10.021988 0 0 0 -117 2 1.595753 6.636687 15.114030 0 0 0 -118 2 12.873763 9.468237 4.693217 0 0 0 -119 2 0.047712 9.433699 9.760065 0 0 0 -120 2 0.031214 9.378911 15.213063 0 0 0 -121 2 8.139849 0.872258 4.730611 0 0 0 -122 2 6.448096 1.862125 1.885906 0 0 0 -123 2 8.057879 0.841511 9.987920 0 0 0 -124 2 6.466932 1.902738 7.155733 0 0 0 -125 2 8.085809 0.858218 15.144929 0 0 0 -126 2 6.490575 1.889912 12.571812 0 0 0 -127 2 6.573584 3.821450 4.628885 0 0 0 -128 2 4.872218 4.733950 1.997616 0 0 0 -129 2 6.600864 3.851038 9.940068 0 0 0 -130 2 4.930286 4.671174 7.112159 0 0 0 -131 2 6.503306 3.685886 15.090262 0 0 0 -132 2 4.989263 4.742612 12.468976 0 0 0 -133 2 4.769074 6.674938 4.678956 0 0 0 -134 2 3.239702 7.402823 1.989059 0 0 0 -135 2 4.885209 6.520473 9.865119 0 0 0 -136 2 3.312319 7.567975 7.299767 0 0 0 -137 2 4.818437 6.602487 15.158873 0 0 0 -138 2 3.259707 7.532874 12.609524 0 0 0 -139 2 3.288026 9.309723 4.771017 0 0 0 -140 2 1.618227 10.304011 1.980186 0 0 0 -141 2 3.156692 9.288797 9.967005 0 0 0 -142 2 1.716175 10.232685 7.249854 0 0 0 -143 2 3.122267 9.283172 15.247606 0 0 0 -144 2 1.738779 10.304461 12.695088 0 0 0 -145 2 11.366301 1.001319 4.680382 0 0 0 -146 2 9.710401 1.777748 2.032792 0 0 0 -147 2 11.352011 0.858780 9.773217 0 0 0 -148 2 9.812636 1.802499 7.177600 0 0 0 -149 2 11.385656 0.968210 15.101671 0 0 0 -150 2 9.728978 1.922088 12.397038 0 0 0 -151 2 9.757817 3.760925 4.471699 0 0 0 -152 2 8.106724 4.650699 1.937721 0 0 0 -153 2 9.726379 3.724362 9.949258 0 0 0 -154 2 8.172845 4.628986 7.329239 0 0 0 -155 2 9.663635 3.736062 15.239525 0 0 0 -156 2 8.039952 4.749363 12.411775 0 0 0 -157 2 7.997084 6.674713 4.688463 0 0 0 -158 2 6.611776 7.587437 2.132618 0 0 0 -159 2 8.015270 6.652775 9.918360 0 0 0 -160 2 6.578131 7.556500 7.390877 0 0 0 -161 2 8.200515 6.500223 15.080121 0 0 0 -162 2 6.563582 7.605325 12.678134 0 0 0 -163 2 6.415880 9.296785 4.617001 0 0 0 -164 2 4.977831 10.242922 2.039606 0 0 0 -165 2 6.482261 9.442812 9.943871 0 0 0 -166 2 4.851563 10.304236 7.406564 0 0 0 -167 2 6.602423 9.398936 15.310829 0 0 0 -168 2 4.825452 10.373874 12.502727 0 0 0 -169 2 12.941659 1.944588 1.993971 0 0 0 -170 2 12.955039 1.906338 7.170945 0 0 0 -171 2 0.059756 1.821624 12.466758 0 0 0 -172 2 11.372536 4.757238 1.961805 0 0 0 -173 2 11.399686 4.615598 7.317831 0 0 0 -174 2 11.313949 4.797626 12.533942 0 0 0 -175 2 11.328109 6.581674 4.748517 0 0 0 -176 2 9.824068 7.541199 2.142759 0 0 0 -177 2 11.294073 6.656825 10.034030 0 0 0 -178 2 9.844463 7.451198 7.208498 0 0 0 -179 2 11.370847 6.658400 15.201338 0 0 0 -180 2 9.789513 7.412948 12.583379 0 0 0 -181 2 9.685589 9.288572 4.745348 0 0 0 -182 2 8.162972 10.232572 2.074941 0 0 0 -183 2 9.714039 9.333460 10.023255 0 0 0 -184 2 8.226886 10.261373 7.380261 0 0 0 -185 2 9.630250 9.405349 15.310512 0 0 0 -186 2 8.019557 10.407512 12.582904 0 0 0 -187 2 12.872290 7.395397 1.867843 0 0 0 -188 2 0.094831 7.505536 7.169043 0 0 0 -189 2 12.882292 7.449848 12.423183 0 0 0 -190 2 11.468406 10.394799 1.919023 0 0 0 -191 2 11.268482 10.364874 7.185998 0 0 0 -192 2 11.254712 10.279935 12.525227 0 0 0 diff --git a/examples/GaN-SNAP-LAMMPS/DATA/9/DATA b/examples/GaN-SNAP-LAMMPS/DATA/9/DATA deleted file mode 100755 index 9b892e8f..00000000 --- a/examples/GaN-SNAP-LAMMPS/DATA/9/DATA +++ /dev/null @@ -1,215 +0,0 @@ -LAMMPS DATA file - -192 atoms -0 bonds -0 angles -0 dihedrals -0 impropers - -2 atom types -0 bond types -0 angle types - -0.0 12.990503 xlo xhi -0.0 11.250148 ylo yhi -0.0 15.845291 zlo zhi - -Masses - -1 69.723 -2 14.0067 - -Atoms - -1 1 1.546000 0.889707 2.569631 0 0 0 -2 1 1.605626 0.932581 8.054003 0 0 0 -3 1 1.711109 0.890258 13.344111 0 0 0 -4 1 0.057952 3.832138 2.642836 0 0 0 -5 1 12.874310 3.853513 7.971766 0 0 0 -6 1 12.877609 3.857901 13.133844 0 0 0 -7 1 4.988353 0.864034 2.477253 0 0 0 -8 1 3.345964 1.953926 5.224509 0 0 0 -9 1 4.767125 0.966343 7.885567 0 0 0 -10 1 3.358825 1.960676 10.595746 0 0 0 -11 1 4.973804 0.872044 13.122277 0 0 0 -12 1 3.118760 1.782923 0.025352 0 0 0 -13 1 3.195534 3.812000 2.680548 0 0 0 -14 1 1.540544 4.638774 5.160811 0 0 0 -15 1 3.264124 3.670023 8.030076 0 0 0 -16 1 1.501832 4.766350 10.473420 0 0 0 -17 1 3.313877 3.650223 13.264727 0 0 0 -18 1 1.541713 4.798863 15.845132 0 0 0 -19 1 1.633686 6.511136 2.596885 0 0 0 -20 1 1.626931 6.566037 7.907275 0 0 0 -21 1 1.533919 6.498536 13.244920 0 0 0 -22 1 0.027578 9.303648 2.751852 0 0 0 -23 1 0.007203 9.481850 7.849123 0 0 0 -24 1 0.116677 9.399386 13.286593 0 0 0 -25 1 8.005657 0.958018 2.762151 0 0 0 -26 1 6.497850 1.882375 5.370920 0 0 0 -27 1 8.159335 0.929195 7.935322 0 0 0 -28 1 6.558385 1.878212 10.437927 0 0 0 -29 1 8.058789 1.033101 13.227332 0 0 0 -30 1 6.505384 1.973389 15.762420 0 0 0 -31 1 6.602293 3.762950 2.710971 0 0 0 -32 1 4.919374 4.606486 5.426378 0 0 0 -33 1 6.475636 3.654723 7.792872 0 0 0 -34 1 4.994069 4.703349 10.552964 0 0 0 -35 1 6.532924 3.686674 13.260765 0 0 0 -36 1 4.805447 4.717637 0.141023 0 0 0 -37 1 4.930286 6.668300 2.718418 0 0 0 -38 1 3.254121 7.488099 5.320056 0 0 0 -39 1 4.821295 6.549836 7.969547 0 0 0 -40 1 3.331415 7.459411 10.607788 0 0 0 -41 1 4.872868 6.485485 13.137172 0 0 0 -42 1 3.145001 7.583500 0.050705 0 0 0 -43 1 3.332584 9.475437 2.676745 0 0 0 -44 1 1.627320 10.325274 5.430815 0 0 0 -45 1 3.280622 9.454287 7.914089 0 0 0 -46 1 1.499104 10.254960 10.573879 0 0 0 -47 1 3.144091 9.369348 13.095816 0 0 0 -48 1 1.578476 10.224922 15.817086 0 0 0 -49 1 11.423589 0.997719 2.770708 0 0 0 -50 1 9.809649 1.837374 5.396906 0 0 0 -51 1 11.373315 0.885162 7.812045 0 0 0 -52 1 9.624664 1.800924 10.693036 0 0 0 -53 1 11.264975 1.012693 13.088527 0 0 0 -54 1 9.835370 1.897225 15.744039 0 0 0 -55 1 9.820171 3.814700 2.507200 0 0 0 -56 1 8.033717 4.710662 5.220865 0 0 0 -57 1 9.682472 3.815150 7.954177 0 0 0 -58 1 8.167519 4.732037 10.694937 0 0 0 -59 1 9.644150 3.774087 13.195641 0 0 0 -60 1 8.126729 4.624936 0.072888 0 0 0 -61 1 8.056190 6.494936 2.753119 0 0 0 -62 1 6.372361 7.395735 5.256675 0 0 0 -63 1 8.006177 6.670438 7.957980 0 0 0 -64 1 6.535912 7.461323 10.550270 0 0 0 -65 1 7.993316 6.495048 13.312579 0 0 0 -66 1 6.382884 7.457498 0.098241 0 0 0 -67 1 6.524350 9.468462 2.757081 0 0 0 -68 1 4.805317 10.415725 5.261112 0 0 0 -69 1 6.596188 9.367211 7.944195 0 0 0 -70 1 4.744521 10.364087 10.531255 0 0 0 -71 1 6.396134 9.396799 13.041942 0 0 0 -72 1 4.985625 10.355761 15.767490 0 0 0 -73 1 0.066252 1.910613 5.207713 0 0 0 -74 1 0.009093 1.776061 10.614285 0 0 0 -75 1 0.110419 1.867525 15.798230 0 0 0 -76 1 11.475161 4.577685 5.412276 0 0 0 -77 1 11.416964 4.759825 10.671486 0 0 0 -78 1 11.265494 4.733725 0.011092 0 0 0 -79 1 11.372016 6.520698 2.528116 0 0 0 -80 1 9.695982 7.538612 5.283929 0 0 0 -81 1 11.394750 6.621162 7.810619 0 0 0 -82 1 9.741448 7.559650 10.494970 0 0 0 -83 1 11.454766 6.603050 13.144619 0 0 0 -84 1 9.752880 7.576075 15.758300 0 0 0 -85 1 9.618039 9.399274 2.647748 0 0 0 -86 1 8.048006 10.407175 5.414494 0 0 0 -87 1 9.739890 9.419637 7.922487 0 0 0 -88 1 8.063205 10.202309 10.492435 0 0 0 -89 1 9.786136 9.297460 13.111978 0 0 0 -90 1 8.217143 10.336411 0.041198 0 0 0 -91 1 12.878525 7.436798 5.365057 0 0 0 -92 1 0.033775 7.403498 10.607947 0 0 0 -93 1 0.005196 7.600825 15.687947 0 0 0 -94 1 11.426057 10.289836 5.335585 0 0 0 -95 1 11.255751 10.370724 10.415743 0 0 0 -96 1 11.403713 10.312786 0.004754 0 0 0 -97 2 1.685778 0.886793 4.543954 0 0 0 -98 2 1.691364 1.041032 9.803006 0 0 0 -99 2 1.592246 0.846787 15.328259 0 0 0 -100 2 0.078702 3.801875 4.720471 0 0 0 -101 2 0.019116 3.718962 9.801421 0 0 0 -102 2 0.100384 3.840463 15.272483 0 0 0 -103 2 4.835585 0.936665 4.677371 0 0 0 -104 2 3.192806 1.794736 1.925361 0 0 0 -105 2 4.831818 0.856406 9.818851 0 0 0 -106 2 3.262175 1.774036 7.241773 0 0 0 -107 2 4.926389 1.022852 15.222729 0 0 0 -108 2 3.238532 1.946051 12.493378 0 0 0 -109 2 3.215539 3.668561 4.675628 0 0 0 -110 2 1.500533 4.627636 2.137847 0 0 0 -111 2 3.362722 3.858238 9.771632 0 0 0 -112 2 1.544701 4.670274 7.279643 0 0 0 -113 2 3.238143 3.778362 15.191355 0 0 0 -114 2 1.699677 4.734850 12.571654 0 0 0 -115 2 1.534698 6.590899 4.761985 0 0 0 -116 2 1.749301 6.612837 9.809819 0 0 0 -117 2 1.717345 6.479073 15.267730 0 0 0 -118 2 12.873039 9.408836 4.487386 0 0 0 -119 2 0.109060 9.301285 9.778287 0 0 0 -120 2 12.939723 9.413787 15.096917 0 0 0 -121 2 8.242474 0.833906 4.624448 0 0 0 -122 2 6.531885 1.853687 1.845818 0 0 0 -123 2 8.152970 0.873293 9.949892 0 0 0 -124 2 6.467842 1.941663 7.388025 0 0 0 -125 2 8.191811 0.983072 15.165369 0 0 0 -126 2 6.532664 1.780111 12.511917 0 0 0 -127 2 6.479013 3.729087 4.555363 0 0 0 -128 2 4.801680 4.741037 2.106314 0 0 0 -129 2 6.566050 3.645611 9.925965 0 0 0 -130 2 4.894302 4.630449 7.235752 0 0 0 -131 2 6.575013 3.705461 15.187236 0 0 0 -132 2 4.944575 4.676349 12.655317 0 0 0 -133 2 4.917295 6.469623 4.779415 0 0 0 -134 2 3.264903 7.434323 1.858019 0 0 0 -135 2 4.757772 6.455898 9.856246 0 0 0 -136 2 3.262435 7.577987 7.308006 0 0 0 -137 2 4.897420 6.497523 15.112604 0 0 0 -138 2 3.287117 7.461661 12.557076 0 0 0 -139 2 3.150067 9.364511 4.783059 0 0 0 -140 2 1.597572 10.214122 1.920608 0 0 0 -141 2 3.261266 9.429199 9.851176 0 0 0 -142 2 1.622254 10.341586 7.348095 0 0 0 -143 2 3.298029 9.293410 15.319544 0 0 0 -144 2 1.592376 10.319311 12.704437 0 0 0 -145 2 11.485683 1.008981 4.602898 0 0 0 -146 2 9.825497 1.862575 1.948178 0 0 0 -147 2 11.420471 0.878772 9.806017 0 0 0 -148 2 9.674807 1.826349 7.122300 0 0 0 -149 2 11.380071 1.037072 15.281832 0 0 0 -150 2 9.675717 1.919163 12.396088 0 0 0 -151 2 9.812636 3.712211 4.570733 0 0 0 -152 2 8.188044 4.661499 1.896998 0 0 0 -153 2 9.759375 3.687236 9.801897 0 0 0 -154 2 8.092954 4.579598 7.243516 0 0 0 -155 2 9.613882 3.647636 15.092005 0 0 0 -156 2 8.041511 4.710100 12.464698 0 0 0 -157 2 8.136342 6.574024 4.575645 0 0 0 -158 2 6.622559 7.420935 2.097441 0 0 0 -159 2 8.193630 6.568062 9.756262 0 0 0 -160 2 6.433807 7.612300 7.334627 0 0 0 -161 2 8.045798 6.594499 15.070456 0 0 0 -162 2 6.509931 7.564937 12.522533 0 0 0 -163 2 6.387041 9.394774 4.671192 0 0 0 -164 2 4.774010 10.394799 1.982246 0 0 0 -165 2 6.437054 9.332673 9.961617 0 0 0 -166 2 4.871439 10.300073 7.212618 0 0 0 -167 2 6.512399 9.266072 15.207359 0 0 0 -168 2 4.984716 10.308511 12.495279 0 0 0 -169 2 0.079242 1.794849 1.852631 0 0 0 -170 2 12.976344 1.867300 7.342866 0 0 0 -171 2 0.051962 1.882487 12.456617 0 0 0 -172 2 11.277575 4.665549 1.966401 0 0 0 -173 2 11.490100 4.783563 7.207072 0 0 0 -174 2 11.460871 4.701099 12.563731 0 0 0 -175 2 11.455675 6.627350 4.638550 0 0 0 -176 2 9.613492 7.470886 1.965925 0 0 0 -177 2 11.401245 6.483123 9.929451 0 0 0 -178 2 9.717676 7.399785 7.152564 0 0 0 -179 2 11.338241 6.552986 15.137323 0 0 0 -180 2 9.835760 7.524212 12.453765 0 0 0 -181 2 9.650255 9.435274 4.675470 0 0 0 -182 2 8.078144 10.212885 1.960855 0 0 0 -183 2 9.732745 9.383074 10.012798 0 0 0 -184 2 8.248580 10.286123 7.169677 0 0 0 -185 2 9.870834 9.415587 15.328417 0 0 0 -186 2 8.154529 10.346086 12.512392 0 0 0 -187 2 12.867873 7.521062 2.059412 0 0 0 -188 2 0.040271 7.401585 7.157952 0 0 0 -189 2 0.066252 7.499124 12.513026 0 0 0 -190 2 11.311740 10.242022 2.127864 0 0 0 -191 2 11.340190 10.231447 7.281069 0 0 0 -192 2 11.244710 10.323586 12.516829 0 0 0 diff --git a/examples/GaN-SNAP-LAMMPS/PotentialLearning.conf b/examples/GaN-SNAP-LAMMPS/PotentialLearning.conf deleted file mode 100644 index 448f76c0..00000000 --- a/examples/GaN-SNAP-LAMMPS/PotentialLearning.conf +++ /dev/null @@ -1,49 +0,0 @@ -[global] -potential SNAP_LAMMPS -fit_forces false -no_atoms_per_type 96 96 -no_atoms_per_conf 192 -no_atomic_conf 61 -no_train_atomic_conf 48 -numTypes 2 -twojmax 6 -cutoff_radii 0.5 0.5 -neighbor_weights 1.0 0.5 -rcutfac 3.5 -rfac0 0.99363 -rmin0 0.0 -wj 1.0 -radelem 0.5 -type Ga N -bzeroflag 0 -quadraticflag 0 -switchflag 1 - -[solver] -name BBO - -[ref] -potential ZBL -ε0 55.26349406 -e -1.602176634e-19 -zi 31.0 -zj 7.0 -rcutfac 3.5 - -[dft] -potential GaN -ε_Ga_Ga 0.643 -σ_Ga_Ga 2.390 -ε_N_N 1.474 -σ_N_N 1.981 -A_Ga_N 608.54 -ρ_Ga_N 0.435 -q_Ga 3.0 -q_N -3.0 -ε0 55.26349406 -no_Ga 96 -no_N 96 - - - - diff --git a/examples/GaN-SNAP-LAMMPS/run.jl b/examples/GaN-SNAP-LAMMPS/run.jl deleted file mode 100644 index c8c730cf..00000000 --- a/examples/GaN-SNAP-LAMMPS/run.jl +++ /dev/null @@ -1,21 +0,0 @@ -include("../../src/PotentialLearning.jl") -using .PotentialLearning - -params = get_conf_params("./") - -# Get DFT data -dft_train_data, dft_val_data = generate_data("dft", params) - -# Get reference data -ref_train_data, ref_val_data = generate_data("ref", params) - -# Get potential learning problem (e.g. A β = b) -snap = learning_problem(dft_train_data, ref_train_data, params) - -# Solve potential learning problem (e.g. β = A \ b) -learn(snap, params) - -# Validate potentials, forces, and stresses -metrics = error_metrics(snap, dft_val_data - ref_val_data, params) -@show metrics - diff --git a/examples/SNAP_learning.jl b/examples/SNAP_learning.jl new file mode 100644 index 00000000..9d605d29 --- /dev/null +++ b/examples/SNAP_learning.jl @@ -0,0 +1,43 @@ +using AtomsBase, DFT, InteratomicPotentials, PotentialLearning + +function gen_atomic_geom() + box = [[1, 0, 0], [0, 1, 0], [0, 0, 1]]u"m" + bcs = [Periodic(), Periodic(), DirichletZero()] + positions = [0.25 0.25 0.25; 0.75 0.75 0.75]u"m" + elems = [elements[:C], elements[:C]] + + atom1 = StaticAtom(SVector{3}(positions[1,:]),elems[1]) + atom2 = StaticAtom(SVector{3}(positions[2,:]),elems[2]) + + aos = FlexibleSystem(box, bcs, [atom1, atom2]) + #soa = FastSystem(box, bcs, positions, elems) + return [aos, aos] +end + +function gen_test_data(p::InteratomicPotential{D, T} + atomic_confs::Vector{AbstractSystem{D, T}}) + energies = [ energy(a, p) for s in atomic_confs ] + forces = [ forces(a, p) for s in atomic_confs ] + stresses = [ stresses(a, p) for s in atomic_confs ] + data = SmallDFTData{D, T}(energies, forces, stresses) + return data +end + +# Define parametric types +D = 3; T = Float32 + +# Generate atomic configurations: domain and particles (position, velocity, etc) +atomic_confs = gen_atomic_conf() + +# Generate learning data +lj = LennardJones{D, T}(1.657e-21u"J", 0.34u"nm") +data = gen_test_data(lj, atomic_confs) + +# Define potential +snap = SNAP{D, T}(atomic_confs) + +# Define learning problem +lp = SmallSNAPLP{D, T}(snap, data) + +# Learn :-) +learn(lp, LeastSquaresOpt{T}()) diff --git a/examples/Ta_Linear_SNAP_LAMMPS/DATA/1/DATA b/examples/Ta_Linear_SNAP_LAMMPS/DATA/1/DATA deleted file mode 100644 index b95a068f..00000000 --- a/examples/Ta_Linear_SNAP_LAMMPS/DATA/1/DATA +++ /dev/null @@ -1,86 +0,0 @@ -LAMMPS DATA file - -64 atoms -0 bonds -0 angles -0 dihedrals -0 impropers - -1 atom types -0 bond types -0 angle types - -0.0 12.990503 xlo xhi -0.0 11.250148 ylo yhi -0.0 15.845291 zlo zhi - -Masses - -1 73 - -Atoms - -1 1 10.59872 10.5966 0.05505 0 0 0 -2 1 2.72054 2.66769 2.56793 0 0 0 -3 1 1.2783 2.60895 0.03547 0 0 0 -4 1 3.95508 2.65628 10.5551 0 0 0 -5 1 0.03293 1.39934 2.6967 0 0 0 -6 1 10.5651 4.05678 2.65596 0 0 0 -7 1 2.60171 10.52714 1.285 0 0 0 -8 1 2.68709 10.58122 3.91851 0 0 0 -9 1 5.31795 0.08026 0.03906 0 0 0 -10 1 8.02486 2.64122 2.59891 0 0 0 -11 1 6.60369 2.73118 0.06843 0 0 0 -12 1 9.30745 2.57138 10.58055 0 0 0 -13 1 5.35248 1.38217 2.58572 0 0 0 -14 1 5.27678 4.05493 2.58839 0 0 0 -15 1 7.97704 10.56983 1.33943 0 0 0 -16 1 7.9205 10.58925 4.02197 0 0 0 -17 1 10.58688 5.37691 0.04598 0 0 0 -18 1 2.56928 7.98994 2.68334 0 0 0 -19 1 1.26784 7.95054 0.01116 0 0 0 -20 1 3.9146 8.01616 10.55414 0 0 0 -21 1 10.54844 6.60413 2.59023 0 0 0 -22 1 10.5757 9.25815 2.63489 0 0 0 -23 1 2.66105 5.2801 1.30191 0 0 0 -24 1 2.6432 5.35885 3.92681 0 0 0 -25 1 10.53608 10.55781 5.26416 0 0 0 -26 1 2.60772 2.73015 7.98088 0 0 0 -27 1 1.24268 2.58441 5.28609 0 0 0 -28 1 3.99146 2.5757 5.25407 0 0 0 -29 1 10.51746 1.40756 8.00795 0 0 0 -30 1 0.00974 3.9413 7.96949 0 0 0 -31 1 2.7025 10.58938 6.62226 0 0 0 -32 1 2.67552 0.00093 9.32012 0 0 0 -33 1 5.21931 5.28624 10.52268 0 0 0 -34 1 7.92372 7.92335 2.69137 0 0 0 -35 1 6.67129 7.91947 0.00781 0 0 0 -36 1 9.22152 8.02659 0.00287 0 0 0 -37 1 5.33288 6.56827 2.67559 0 0 0 -38 1 5.21843 9.3313 2.61368 0 0 0 -39 1 7.93465 5.34206 1.38987 0 0 0 -40 1 7.94771 5.35777 3.99603 0 0 0 -41 1 5.28258 10.54181 5.27443 0 0 0 -42 1 7.87019 2.58685 7.88448 0 0 0 -43 1 6.61351 2.69961 5.33299 0 0 0 -44 1 9.20963 2.61413 5.29428 0 0 0 -45 1 5.381 1.3824 7.94181 0 0 0 -46 1 5.28467 4.01816 7.99502 0 0 0 -47 1 8.00243 10.5584 6.55969 0 0 0 -48 1 7.92724 0.03497 9.30326 0 0 0 -49 1 10.55391 5.32768 5.23195 0 0 0 -50 1 2.64406 7.95567 7.93345 0 0 0 -51 1 1.2986 7.9027 5.33624 0 0 0 -52 1 4.04604 7.87659 5.36207 0 0 0 -53 1 0.04337 6.69689 8.01066 0 0 0 -54 1 10.54014 9.26136 7.89857 0 0 0 -55 1 2.68344 5.29148 6.55058 0 0 0 -56 1 2.61535 5.26646 9.22004 0 0 0 -57 1 5.22677 5.33996 5.32711 0 0 0 -58 1 7.93781 8.02504 7.94133 0 0 0 -59 1 6.58943 7.89688 5.28857 0 0 0 -60 1 9.26138 8.02661 5.25779 0 0 0 -61 1 5.27411 6.62462 8.02195 0 0 0 -62 1 5.30985 9.30627 7.88256 0 0 0 -63 1 7.99384 5.30652 6.67382 0 0 0 -64 1 7.89346 5.23521 9.29012 0 0 0 diff --git a/examples/Ta_Linear_SNAP_LAMMPS/DATA/1/ENERGY b/examples/Ta_Linear_SNAP_LAMMPS/DATA/1/ENERGY deleted file mode 100644 index 94be60b0..00000000 --- a/examples/Ta_Linear_SNAP_LAMMPS/DATA/1/ENERGY +++ /dev/null @@ -1 +0,0 @@ --754.0221 diff --git a/examples/Ta_Linear_SNAP_LAMMPS/DATA/1/FORCES b/examples/Ta_Linear_SNAP_LAMMPS/DATA/1/FORCES deleted file mode 100644 index a1ea9deb..00000000 --- a/examples/Ta_Linear_SNAP_LAMMPS/DATA/1/FORCES +++ /dev/null @@ -1,64 +0,0 @@ --0.231571 0.031614 -0.560153 --0.779697 -0.12909 0.784258 -0.744629 0.548126 -0.214124 --0.165396 0.001128 0.026529 -0.072305 -0.873594 -0.208971 -0.527021 -1.331302 0.031311 -0.350354 0.537482 0.600499 --0.372039 0.361715 0.809071 --0.106989 -0.635521 -0.720814 --0.739467 0.359337 0.641206 -0.678906 -0.310297 -0.697991 --1.01243 0.693756 -0.108245 --0.13929 -0.071214 0.685498 -0.361124 -1.418968 0.248615 --0.226745 0.137547 0.385956 --0.097537 0.228845 -1.559747 --0.241278 -0.869238 -0.792618 -0.744667 -0.548988 -0.270704 -0.281468 0.07337 -0.236417 -0.995063 -0.220303 0.353326 -0.147364 1.01708 0.40752 --0.140904 0.492732 0.101556 --0.364702 0.402682 -0.011419 --0.227023 -0.472196 0.151009 -1.288203 0.545609 0.251638 -0.261788 -1.092199 -0.8427 -1.180704 0.409883 0.0645 --0.757243 0.334145 0.121851 -0.326733 -1.91194 -0.281886 --0.442991 1.619821 -0.172523 --0.427598 0.249852 0.029935 --0.030321 0.09604 -1.176661 -0.567659 0.751713 1.05061 --0.276611 0.573618 -0.487148 --1.67251 0.193902 0.064344 -0.769306 -0.25307 0.030428 --0.356132 1.879818 -0.275818 -0.313957 -1.184708 0.134729 --0.27093 -0.232294 -1.254009 --0.441572 -0.509412 0.402878 -0.165589 0.546578 -0.181307 -0.864444 0.720171 0.90474 --0.298459 -0.117041 -0.655843 -0.646321 0.352518 0.003302 --1.162347 -0.755975 0.017657 -0.024319 -0.640279 -0.524219 --0.64714 0.462493 1.495007 -0.221614 -0.134477 -0.661187 -0.476568 -0.381016 0.980462 -0.001297 0.120229 0.191712 -0.708615 0.289977 -0.158132 --1.974177 0.710669 -0.438506 --0.426712 -1.619512 -0.55647 -0.447195 1.282555 0.234867 --0.713159 0.045261 0.661323 --0.124682 0.621019 0.504493 -1.047955 -1.01859 -0.083156 --0.089305 -0.92943 0.174588 -1.109411 0.43459 0.232028 --0.279333 -0.594174 0.435718 -0.25952 0.675178 -0.659935 --0.174466 -0.148032 0.732729 --0.405756 0.105152 -0.448951 -0.232414 0.496659 0.293761 diff --git a/examples/Ta_Linear_SNAP_LAMMPS/DATA/2/DATA b/examples/Ta_Linear_SNAP_LAMMPS/DATA/2/DATA deleted file mode 100644 index cd2c9273..00000000 --- a/examples/Ta_Linear_SNAP_LAMMPS/DATA/2/DATA +++ /dev/null @@ -1,86 +0,0 @@ -LAMMPS DATA file - -64 atoms -0 bonds -0 angles -0 dihedrals -0 impropers - -1 atom types -0 bond types -0 angle types - -0.0 12.990503 xlo xhi -0.0 11.250148 ylo yhi -0.0 15.845291 zlo zhi - -Masses - -1 73 - -Atoms - -1 1 0.03525 10.52946 0.01429 0 0 0 -2 1 2.67988 2.6352 2.61064 0 0 0 -3 1 1.30583 2.57403 10.55611 0 0 0 -4 1 4.00357 2.65046 10.56488 0 0 0 -5 1 10.52633 1.38198 2.61375 0 0 0 -6 1 10.54339 3.93177 2.72703 0 0 0 -7 1 2.58523 10.55385 1.26507 0 0 0 -8 1 2.68419 10.52194 4.02925 0 0 0 -9 1 5.29632 0.02098 0.06019 0 0 0 -10 1 7.9287 2.71315 2.57282 0 0 0 -11 1 6.67221 2.56974 0.00085 0 0 0 -12 1 9.35654 2.72035 0.02716 0 0 0 -13 1 5.28199 1.31545 2.71612 0 0 0 -14 1 5.26218 3.92161 2.73258 0 0 0 -15 1 7.88956 10.53727 1.30155 0 0 0 -16 1 7.90476 0.00491 4.03502 0 0 0 -17 1 0.01924 5.23985 0.02933 0 0 0 -18 1 2.63713 7.91332 2.57939 0 0 0 -19 1 1.37591 7.98252 0.01161 0 0 0 -20 1 3.99074 7.99253 0.04105 0 0 0 -21 1 0.06165 6.69839 2.59091 0 0 0 -22 1 0.07693 9.27396 2.65088 0 0 0 -23 1 2.59233 5.37207 1.32243 0 0 0 -24 1 2.576 5.32148 3.95475 0 0 0 -25 1 10.57478 0.07838 5.30752 0 0 0 -26 1 2.68594 2.63787 8.02554 0 0 0 -27 1 1.24534 2.6968 5.22637 0 0 0 -28 1 3.93645 2.66917 5.2391 0 0 0 -29 1 10.54417 1.38182 8.01183 0 0 0 -30 1 0.00692 3.97458 7.93648 0 0 0 -31 1 2.65183 10.59292 6.70102 0 0 0 -32 1 2.70713 0.0237 9.32486 0 0 0 -33 1 5.32479 5.24418 0.01275 0 0 0 -34 1 7.97361 7.99989 2.66237 0 0 0 -35 1 6.68168 8.00545 10.53048 0 0 0 -36 1 9.25988 8.00096 10.54122 0 0 0 -37 1 5.36822 6.70209 2.70369 0 0 0 -38 1 5.22169 9.20816 2.62305 0 0 0 -39 1 7.90622 5.28573 1.40537 0 0 0 -40 1 7.91678 5.27023 4.0071 0 0 0 -41 1 5.35908 0.08115 5.27632 0 0 0 -42 1 8.00681 2.60911 7.87611 0 0 0 -43 1 6.63107 2.65234 5.3649 0 0 0 -44 1 9.21464 2.71799 5.26365 0 0 0 -45 1 5.22432 1.25125 8.02611 0 0 0 -46 1 5.22168 3.92029 7.91312 0 0 0 -47 1 8.01588 0.04144 6.68445 0 0 0 -48 1 7.96204 10.55369 9.32548 0 0 0 -49 1 0.01039 5.30368 5.2336 0 0 0 -50 1 2.5862 7.96502 7.96459 0 0 0 -51 1 1.28578 7.88946 5.26227 0 0 0 -52 1 3.96511 7.98863 5.30323 0 0 0 -53 1 0.00505 6.67243 8.01234 0 0 0 -54 1 10.5258 9.23159 7.95484 0 0 0 -55 1 2.60834 5.24378 6.55963 0 0 0 -56 1 2.60865 5.35101 9.24068 0 0 0 -57 1 5.34566 5.33553 5.26912 0 0 0 -58 1 8.01116 7.98477 7.98864 0 0 0 -59 1 6.61332 7.98663 5.33587 0 0 0 -60 1 9.34421 7.88519 5.33887 0 0 0 -61 1 5.30405 6.66664 7.973 0 0 0 -62 1 5.3561 9.34104 7.93015 0 0 0 -63 1 7.87231 5.36354 6.69962 0 0 0 -64 1 7.98446 5.25368 9.3376 0 0 0 diff --git a/examples/Ta_Linear_SNAP_LAMMPS/DATA/2/ENERGY b/examples/Ta_Linear_SNAP_LAMMPS/DATA/2/ENERGY deleted file mode 100644 index 473e646b..00000000 --- a/examples/Ta_Linear_SNAP_LAMMPS/DATA/2/ENERGY +++ /dev/null @@ -1 +0,0 @@ --753.777209 diff --git a/examples/Ta_Linear_SNAP_LAMMPS/DATA/2/FORCES b/examples/Ta_Linear_SNAP_LAMMPS/DATA/2/FORCES deleted file mode 100644 index e9dc646e..00000000 --- a/examples/Ta_Linear_SNAP_LAMMPS/DATA/2/FORCES +++ /dev/null @@ -1,64 +0,0 @@ --0.625379 0.911584 -0.075876 --0.661 -0.104938 -0.074584 -0.849169 0.350685 0.363742 --0.371611 0.087052 0.454216 -0.406758 -1.451427 0.208757 -0.391892 1.412298 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--0.722672 -0.863673 0.500885 --0.950848 0.649728 1.17634 --0.782252 0.346241 -0.630632 -0.65968 -0.244425 -0.123044 -0.739331 1.510791 -0.273571 -0.722496 0.766488 0.226631 --0.372854 -0.445221 -0.493611 --0.03274 0.375548 -0.623519 --0.715394 0.046629 0.901905 -0.830832 -0.094714 -0.350325 -1.126795 0.658952 0.004566 --0.273909 0.013132 -0.023712 --0.065254 -1.564213 -0.39785 -0.714286 1.608236 -0.153688 -0.476601 0.174876 0.899274 -0.460063 -0.232332 0.21727 --1.0005 -0.062573 0.768202 --0.941009 -0.538031 -0.670857 -0.694566 -0.00045 -0.06064 --1.50427 0.871847 -0.00909 --0.127756 -0.408974 -0.168376 --0.198165 -1.429389 0.216524 -0.402284 -0.367694 -0.602329 --0.122238 0.277788 -0.243182 diff --git a/examples/Ta_Linear_SNAP_LAMMPS/DATA/3/DATA b/examples/Ta_Linear_SNAP_LAMMPS/DATA/3/DATA deleted file mode 100644 index 9b5a4295..00000000 --- a/examples/Ta_Linear_SNAP_LAMMPS/DATA/3/DATA +++ /dev/null @@ -1,86 +0,0 @@ -LAMMPS DATA file - -64 atoms -0 bonds -0 angles -0 dihedrals -0 impropers - -1 atom types -0 bond types -0 angle types - -0.0 12.990503 xlo xhi -0.0 11.250148 ylo yhi -0.0 15.845291 zlo zhi - -Masses - -1 73 - -Atoms - -1 1 0.00046 10.54735 10.58932 0 0 0 -2 1 2.73129 2.71027 2.64805 0 0 0 -3 1 1.30416 2.70676 0.05081 0 0 0 -4 1 3.9224 2.56802 0.05914 0 0 0 -5 1 10.52754 1.32714 2.64946 0 0 0 -6 1 10.58917 3.98207 2.62548 0 0 0 -7 1 2.64792 0.02452 1.38081 0 0 0 -8 1 2.59488 0.05512 3.95199 0 0 0 -9 1 5.22138 10.52799 0.03746 0 0 0 -10 1 7.88634 2.63138 2.61996 0 0 0 -11 1 6.69452 2.7219 0.06773 0 0 0 -12 1 9.21373 2.71014 0.05862 0 0 0 -13 1 5.3281 1.39418 2.60417 0 0 0 -14 1 5.2637 3.95414 2.69271 0 0 0 -15 1 7.90795 0.06254 1.39383 0 0 0 -16 1 7.94511 10.51799 3.98105 0 0 0 -17 1 10.57577 5.37732 10.54307 0 0 0 -18 1 2.70528 7.92008 2.71672 0 0 0 -19 1 1.40108 7.96156 10.56262 0 0 0 -20 1 3.94259 7.88815 10.51865 0 0 0 -21 1 0.05295 6.61799 2.66959 0 0 0 -22 1 0.0041 9.32626 2.60831 0 0 0 -23 1 2.66819 5.248 1.34131 0 0 0 -24 1 2.57134 5.28818 3.89302 0 0 0 -25 1 0.08271 0.0036 5.29844 0 0 0 -26 1 2.56753 2.70781 8.0214 0 0 0 -27 1 1.30891 2.64281 5.34837 0 0 0 -28 1 3.96187 2.73119 5.27973 0 0 0 -29 1 1.0e-5 1.31854 7.9193 0 0 0 -30 1 10.58062 3.94546 7.96883 0 0 0 -31 1 2.60743 10.5971 6.59487 0 0 0 -32 1 2.59982 0.05852 9.25312 0 0 0 -33 1 5.343 5.33735 10.58109 0 0 0 -34 1 8.0183 7.97031 2.57959 0 0 0 -35 1 6.56415 8.01596 10.54595 0 0 0 -36 1 9.3142 8.00708 0.07335 0 0 0 -37 1 5.28371 6.62455 2.60926 0 0 0 -38 1 5.365 9.35513 2.65232 0 0 0 -39 1 7.99421 5.27285 1.26512 0 0 0 -40 1 7.93677 5.32858 3.96514 0 0 0 -41 1 5.29831 0.06384 5.34991 0 0 0 -42 1 7.98101 2.63404 7.9256 0 0 0 -43 1 6.68687 2.58375 5.27465 0 0 0 -44 1 9.31724 2.59345 5.36746 0 0 0 -45 1 5.30469 1.39236 7.90055 0 0 0 -46 1 5.36637 3.96474 7.94588 0 0 0 -47 1 7.96852 10.54416 6.59542 0 0 0 -48 1 8.01553 0.03504 9.33832 0 0 0 -49 1 10.53751 5.2766 5.33019 0 0 0 -50 1 2.67185 7.99879 7.94992 0 0 0 -51 1 1.32425 7.97625 5.27971 0 0 0 -52 1 3.99685 7.99185 5.33585 0 0 0 -53 1 0.00789 6.57979 7.98241 0 0 0 -54 1 10.56258 9.24146 7.92821 0 0 0 -55 1 2.62183 5.25654 6.57113 0 0 0 -56 1 2.62673 5.24695 9.20881 0 0 0 -57 1 5.2818 5.28462 5.32566 0 0 0 -58 1 7.95127 7.97098 7.89566 0 0 0 -59 1 6.69889 8.00506 5.30113 0 0 0 -60 1 9.22006 8.02217 5.33119 0 0 0 -61 1 5.3507 6.64908 7.93434 0 0 0 -62 1 5.22906 9.26778 7.99824 0 0 0 -63 1 7.96263 5.26515 6.66322 0 0 0 -64 1 8.00683 5.33642 9.24793 0 0 0 diff --git a/examples/Ta_Linear_SNAP_LAMMPS/DATA/3/ENERGY b/examples/Ta_Linear_SNAP_LAMMPS/DATA/3/ENERGY deleted file mode 100644 index 6cf55e0f..00000000 --- a/examples/Ta_Linear_SNAP_LAMMPS/DATA/3/ENERGY +++ /dev/null @@ -1 +0,0 @@ --754.279613 diff --git a/examples/Ta_Linear_SNAP_LAMMPS/DATA/3/FORCES b/examples/Ta_Linear_SNAP_LAMMPS/DATA/3/FORCES deleted file mode 100644 index 094a863f..00000000 --- a/examples/Ta_Linear_SNAP_LAMMPS/DATA/3/FORCES +++ /dev/null @@ -1,64 +0,0 @@ -0.114704 0.911029 0.002417 --1.312269 -0.768934 0.192601 --0.549542 -0.385376 -0.090451 -1.338111 0.432571 -0.522326 -0.526452 0.497736 0.118023 -0.027974 -0.098405 0.015828 --0.204416 -0.141407 -1.100083 -0.552837 -0.178236 0.473214 -0.576453 0.970244 -0.579639 -0.902337 0.559648 1.080475 --2.02583 -0.335157 -0.878841 -1.514389 -0.315085 -0.524943 --0.26237 -1.230172 0.420769 -0.464892 1.262082 -0.270578 -0.167236 -0.202524 -1.058609 -0.185425 0.426977 0.087026 -0.605017 -0.422613 0.786988 --0.16284 0.53844 -0.654288 --1.21314 -0.180661 0.475699 -0.693466 0.102031 0.668128 --0.152823 0.384734 -0.111952 -0.291126 -0.868362 0.393931 --0.179205 0.374746 -1.338983 -0.254849 0.332843 1.641299 --1.048937 -0.101097 -0.319135 -1.017266 -0.740171 -0.566662 -0.403908 0.226225 -0.301649 -0.36121 -0.332647 0.382172 --0.134684 -0.420557 0.336931 -0.091943 0.393742 -0.089206 -0.481207 0.365851 0.394927 -0.155387 -0.327875 0.594672 --0.354201 -0.481611 0.070778 --0.638975 -0.537484 0.627877 -1.046228 -0.215805 0.200416 --0.389686 -0.132571 -0.908238 -0.349202 0.295946 0.196375 --0.276908 -1.072093 0.33487 --0.338816 0.417402 0.989409 --0.064889 -0.126317 0.026895 --0.237157 -0.294846 -0.502816 --0.201557 -0.256297 0.618786 --0.880538 0.491034 0.225753 --0.514197 0.139552 -0.594594 --0.241299 -1.127636 0.542064 --0.457508 0.623304 -0.045721 -0.045419 0.456297 0.883036 --0.703646 -0.11872 -0.79377 -0.186467 0.354842 -0.464356 --0.462825 -0.70472 -0.660751 --0.162279 -0.301471 0.211964 -0.128267 -0.133747 -0.138891 -0.224508 0.703879 -0.465686 -0.298346 0.405066 0.164699 -0.142704 0.580891 0.073062 -0.295489 0.626384 1.099379 -0.254473 0.449594 -0.359163 --0.109482 -0.099213 1.128432 --1.722141 -0.416627 -0.484246 -1.590079 -0.664694 -0.530738 --0.272774 -0.59058 -0.047159 -0.577132 0.931079 -0.408552 --0.184291 0.081851 -0.89845 --0.405275 -0.01231 0.25158 diff --git a/examples/Ta_Linear_SNAP_LAMMPS/DATA/4/DATA b/examples/Ta_Linear_SNAP_LAMMPS/DATA/4/DATA deleted file mode 100644 index 8810d248..00000000 --- a/examples/Ta_Linear_SNAP_LAMMPS/DATA/4/DATA +++ /dev/null @@ -1,86 +0,0 @@ -LAMMPS DATA file - -64 atoms -0 bonds -0 angles -0 dihedrals -0 impropers - -1 atom types -0 bond types -0 angle types - -0.0 12.990503 xlo xhi -0.0 11.250148 ylo yhi -0.0 15.845291 zlo zhi - -Masses - -1 73 - -Atoms - -1 1 10.53107 10.5509 0.0015 0 0 0 -2 1 2.70215 2.61155 2.65638 0 0 0 -3 1 1.39743 2.61545 0.05847 0 0 0 -4 1 3.97713 2.68268 10.5346 0 0 0 -5 1 0.03222 1.38317 2.60891 0 0 0 -6 1 10.56764 3.92107 2.7266 0 0 0 -7 1 2.59022 10.55975 1.32456 0 0 0 -8 1 2.70858 0.00916 4.05153 0 0 0 -9 1 5.26413 10.53793 0.03804 0 0 0 -10 1 7.92699 2.58218 2.67357 0 0 0 -11 1 6.56938 2.58335 0.00915 0 0 0 -12 1 9.21553 2.70158 0.00339 0 0 0 -13 1 5.29644 1.25773 2.66315 0 0 0 -14 1 5.25049 4.05699 2.72857 0 0 0 -15 1 7.95797 0.00795 1.26652 0 0 0 -16 1 7.95876 0.0029 3.97425 0 0 0 -17 1 0.00111 5.29169 0.0101 0 0 0 -18 1 2.62824 7.99165 2.57985 0 0 0 -19 1 1.27056 8.03072 0.02474 0 0 0 -20 1 3.95298 7.86756 0.04116 0 0 0 -21 1 10.52695 6.6817 2.6853 0 0 0 -22 1 0.02498 9.27815 2.68712 0 0 0 -23 1 2.65962 5.24127 1.35865 0 0 0 -24 1 2.68315 5.34774 4.00482 0 0 0 -25 1 10.59249 0.03152 5.33264 0 0 0 -26 1 2.58832 2.58393 7.94631 0 0 0 -27 1 1.37297 2.61641 5.29619 0 0 0 -28 1 3.95207 2.62642 5.27401 0 0 0 -29 1 0.01362 1.29568 7.93105 0 0 0 -30 1 0.06717 3.99538 7.88147 0 0 0 -31 1 2.72677 10.57217 6.60708 0 0 0 -32 1 2.713 10.58575 9.24417 0 0 0 -33 1 5.30308 5.35945 0.05831 0 0 0 -34 1 7.87019 7.94183 2.57359 0 0 0 -35 1 6.65928 7.9017 0.0785 0 0 0 -36 1 9.22504 7.86881 10.58464 0 0 0 -37 1 5.29923 6.68288 2.66667 0 0 0 -38 1 5.34057 9.3156 2.71909 0 0 0 -39 1 7.9974 5.33778 1.31662 0 0 0 -40 1 8.0053 5.25623 3.92597 0 0 0 -41 1 5.25104 0.03317 5.26596 0 0 0 -42 1 7.98045 2.60832 7.99115 0 0 0 -43 1 6.70353 2.60779 5.33602 0 0 0 -44 1 9.2746 2.58651 5.33229 0 0 0 -45 1 5.38008 1.39809 7.98274 0 0 0 -46 1 5.33862 3.99447 7.94033 0 0 0 -47 1 7.95961 0.05884 6.68706 0 0 0 -48 1 7.95876 0.02794 9.26141 0 0 0 -49 1 0.06343 5.2606 5.22321 0 0 0 -50 1 2.68463 7.97169 7.9776 0 0 0 -51 1 1.29864 7.91228 5.24043 0 0 0 -52 1 3.95071 8.01668 5.34254 0 0 0 -53 1 10.52651 6.66919 7.95196 0 0 0 -54 1 10.55688 9.28857 7.96148 0 0 0 -55 1 2.70803 5.32339 6.70382 0 0 0 -56 1 2.57492 5.22962 9.24619 0 0 0 -57 1 5.22267 5.3038 5.33156 0 0 0 -58 1 7.98999 7.90061 7.96163 0 0 0 -59 1 6.68533 8.02176 5.30974 0 0 0 -60 1 9.34825 7.99677 5.29878 0 0 0 -61 1 5.33163 6.57634 7.98884 0 0 0 -62 1 5.29614 9.34403 7.95803 0 0 0 -63 1 8.00726 5.27369 6.70227 0 0 0 -64 1 7.97483 5.326 9.24028 0 0 0 diff --git a/examples/Ta_Linear_SNAP_LAMMPS/DATA/4/ENERGY b/examples/Ta_Linear_SNAP_LAMMPS/DATA/4/ENERGY deleted file mode 100644 index ba6a88ec..00000000 --- a/examples/Ta_Linear_SNAP_LAMMPS/DATA/4/ENERGY +++ /dev/null @@ -1 +0,0 @@ --754.141988 diff --git a/examples/Ta_Linear_SNAP_LAMMPS/DATA/4/FORCES b/examples/Ta_Linear_SNAP_LAMMPS/DATA/4/FORCES deleted file mode 100644 index 544be210..00000000 --- a/examples/Ta_Linear_SNAP_LAMMPS/DATA/4/FORCES +++ /dev/null @@ -1,64 +0,0 @@ -0.70485 0.845648 -0.070019 --0.286099 0.325604 -0.074327 --1.474313 -0.095142 -0.280113 -0.156378 -0.098493 0.356179 --0.081506 -1.587414 0.159126 -0.259373 1.331992 -0.73363 -0.049236 0.371753 0.102809 --0.701193 -0.070601 -1.695173 -0.195324 0.197551 -0.279303 --0.196352 0.687631 -0.299411 -0.481385 0.355506 0.054864 -1.079668 -0.370583 0.25622 -0.219113 1.844104 -0.251113 -0.405022 -1.35655 -0.365109 --0.349291 -0.012386 0.95892 --0.085176 -0.246415 0.146522 -0.244936 -0.074089 0.083447 -0.090964 -0.453594 0.8187 -0.413629 -0.598829 -0.229027 -0.152752 0.468204 -0.422925 -0.300417 -1.266839 -0.375852 --0.304899 0.803536 -0.158136 --0.043804 0.363366 -0.570782 --0.286335 -0.186484 -0.056142 -0.313027 -0.429223 -0.38406 -0.844596 0.451826 -0.031232 --0.990905 0.328928 -0.096763 -1.187182 0.414363 0.303667 --0.217583 0.454567 0.400647 --0.472589 -0.121955 0.480331 --0.58854 0.058778 0.860541 --0.506506 0.039032 0.567002 --0.152176 -0.937176 -0.30934 -1.036899 0.327117 1.33664 --1.124811 0.536497 -0.907975 -0.924083 0.364728 -0.065373 --0.266393 -0.338893 0.356213 --0.369711 -1.091863 -0.151577 --0.337005 -0.510079 -0.103385 --0.472408 0.14717 1.386647 -1.390735 -0.14389 0.946126 -0.289511 0.923595 -0.088863 --1.549564 0.47403 -0.141706 -0.918837 0.547058 -0.191653 --0.530078 -0.860802 -0.130916 --0.428322 -0.31397 0.179289 --0.114391 -0.600564 -1.150373 --0.363392 -0.320188 0.423549 --0.328214 0.242764 0.905362 --0.420291 -0.285961 -0.011666 -0.869986 0.358854 0.269282 -0.539614 -0.279841 -0.051604 -0.773319 -0.746678 -0.127338 -0.62099 -0.258731 -0.038343 --0.389582 -0.121461 -1.219023 -0.509556 0.339673 1.192371 -1.3354 0.250454 0.009213 --0.945486 0.84251 -0.352597 --0.632817 -0.296567 -0.005138 --1.180526 -0.264671 -0.130746 --0.009265 1.176676 -0.00019 -0.264039 -1.003617 -0.12967 --0.286454 -0.101025 -2.091338 --0.084847 -0.42894 1.218267 diff --git a/examples/Ta_Linear_SNAP_LAMMPS/DATA/5/DATA b/examples/Ta_Linear_SNAP_LAMMPS/DATA/5/DATA deleted file mode 100644 index acefaf2a..00000000 --- a/examples/Ta_Linear_SNAP_LAMMPS/DATA/5/DATA +++ /dev/null @@ -1,86 +0,0 @@ -LAMMPS DATA file - -64 atoms -0 bonds -0 angles -0 dihedrals -0 impropers - -1 atom types -0 bond types -0 angle types - -0.0 12.990503 xlo xhi -0.0 11.250148 ylo yhi -0.0 15.845291 zlo zhi - -Masses - -1 73 - -Atoms - -1 1 10.58466 10.52281 10.54428 0 0 0 -2 1 2.58906 2.62515 2.58331 0 0 0 -3 1 1.33407 2.72467 0.03386 0 0 0 -4 1 3.90797 2.72086 10.53991 0 0 0 -5 1 0.07897 1.2643 2.65645 0 0 0 -6 1 0.02729 3.96468 2.62566 0 0 0 -7 1 2.71828 0.03582 1.37493 0 0 0 -8 1 2.71013 0.01388 3.94029 0 0 0 -9 1 5.24382 0.05221 10.59611 0 0 0 -10 1 8.00676 2.68277 2.72931 0 0 0 -11 1 6.67012 2.581 0.05294 0 0 0 -12 1 9.2906 2.70214 10.5277 0 0 0 -13 1 5.31566 1.36303 2.63231 0 0 0 -14 1 5.36545 3.97557 2.63811 0 0 0 -15 1 7.9635 0.07881 1.30941 0 0 0 -16 1 8.01171 0.06526 3.99574 0 0 0 -17 1 10.5812 5.22205 0.06058 0 0 0 -18 1 2.58751 8.02506 2.67969 0 0 0 -19 1 1.32816 7.92066 10.55287 0 0 0 -20 1 3.98668 7.91992 10.56445 0 0 0 -21 1 0.00065 6.67904 2.65936 0 0 0 -22 1 0.05141 9.2904 2.64974 0 0 0 -23 1 2.65941 5.21716 1.36289 0 0 0 -24 1 2.67774 5.34503 4.02694 0 0 0 -25 1 0.07746 0.06322 5.35824 0 0 0 -26 1 2.67942 2.71807 8.01719 0 0 0 -27 1 1.37014 2.70616 5.31634 0 0 0 -28 1 4.04242 2.65384 5.28532 0 0 0 -29 1 10.59566 1.39908 7.95465 0 0 0 -30 1 10.51853 3.8922 7.91939 0 0 0 -31 1 2.65129 0.0155 6.54214 0 0 0 -32 1 2.68757 10.53742 9.30663 0 0 0 -33 1 5.29366 5.33327 10.53757 0 0 0 -34 1 7.98799 8.02663 2.73107 0 0 0 -35 1 6.6836 7.95804 10.58871 0 0 0 -36 1 9.35116 7.96667 0.00673 0 0 0 -37 1 5.25103 6.63708 2.69902 0 0 0 -38 1 5.25134 9.28648 2.56753 0 0 0 -39 1 7.99616 5.36815 1.3789 0 0 0 -40 1 8.00478 5.33099 4.04177 0 0 0 -41 1 5.22309 0.05914 5.36259 0 0 0 -42 1 8.03289 2.6841 7.99696 0 0 0 -43 1 6.70134 2.63641 5.29151 0 0 0 -44 1 9.34008 2.57975 5.27834 0 0 0 -45 1 5.33316 1.27506 7.87414 0 0 0 -46 1 5.282 3.94794 7.95331 0 0 0 -47 1 7.97216 0.0105 6.56218 0 0 0 -48 1 7.98286 10.57054 9.20843 0 0 0 -49 1 10.56331 5.32515 5.33591 0 0 0 -50 1 2.56725 7.87047 7.92346 0 0 0 -51 1 1.36329 7.87424 5.25876 0 0 0 -52 1 3.93049 7.97524 5.31529 0 0 0 -53 1 10.56491 6.65054 7.9509 0 0 0 -54 1 10.52371 9.29522 7.88036 0 0 0 -55 1 2.71757 5.32353 6.61689 0 0 0 -56 1 2.58315 5.3638 9.27005 0 0 0 -57 1 5.33722 5.23801 5.24924 0 0 0 -58 1 8.00365 8.00131 7.92453 0 0 0 -59 1 6.57048 8.03185 5.31737 0 0 0 -60 1 9.2991 7.92465 5.23581 0 0 0 -61 1 5.29905 6.5928 8.01852 0 0 0 -62 1 5.2848 9.23686 8.0324 0 0 0 -63 1 7.94377 5.22663 6.66616 0 0 0 -64 1 8.02399 5.3012 9.33589 0 0 0 diff --git a/examples/Ta_Linear_SNAP_LAMMPS/DATA/5/ENERGY b/examples/Ta_Linear_SNAP_LAMMPS/DATA/5/ENERGY deleted file mode 100644 index 08e13b74..00000000 --- a/examples/Ta_Linear_SNAP_LAMMPS/DATA/5/ENERGY +++ /dev/null @@ -1 +0,0 @@ --754.048643 diff --git a/examples/Ta_Linear_SNAP_LAMMPS/DATA/5/FORCES b/examples/Ta_Linear_SNAP_LAMMPS/DATA/5/FORCES deleted file mode 100644 index cef4061b..00000000 --- a/examples/Ta_Linear_SNAP_LAMMPS/DATA/5/FORCES +++ /dev/null @@ -1,64 +0,0 @@ -0.51911 1.030769 0.289199 -0.980313 0.465455 0.986329 --0.636192 -0.969554 -0.333663 -1.707244 -0.292948 0.571866 --0.600839 0.915626 -0.026383 --0.026464 0.178205 0.595013 --0.503659 -0.164847 -1.238234 --0.26741 0.122146 0.391015 -0.985051 -0.524959 -0.239796 --0.040705 0.112169 -1.076862 --0.795944 0.604015 0.013416 -0.106867 -0.725536 0.830297 -0.204579 -0.39964 0.160289 --0.35758 0.374857 -0.341338 --0.122693 -0.323484 0.045005 --0.213713 -0.382574 -0.612077 -0.340369 1.238874 -0.422064 -0.836087 -0.974582 -0.640712 -0.3286 -0.149546 0.174414 --0.068023 0.343984 0.387619 --0.006212 -0.780593 0.078132 --0.390999 -0.009998 -0.048165 -0.011633 0.757694 -0.318475 --0.206769 -0.188612 -0.829644 --0.166456 -0.826729 -0.728653 --0.311027 -0.729342 -0.903137 -0.189855 -0.02996 -0.111687 --0.699395 0.065315 0.059883 -0.507488 -1.93197 -0.080117 -1.002489 2.435127 0.268143 -0.056264 0.079221 1.857275 --0.393454 0.179293 -0.909888 -0.377812 -0.518568 1.064217 --0.740413 -0.111466 -0.791724 --0.388073 0.234483 0.294061 --1.079729 -0.437475 -0.039029 -0.341543 0.027342 -0.389479 -0.545209 0.148316 0.627297 --0.304224 -0.13761 -0.04399 --0.265505 0.058703 -0.773223 -1.064104 -0.650463 -0.956514 --1.569866 -0.680329 -0.545113 --0.518892 -0.054631 0.294653 --0.212974 0.581599 0.407505 -0.002254 0.772406 0.627475 -0.365483 0.009532 -0.297329 --0.240616 0.092446 0.728274 --0.453634 0.391321 0.804177 -0.676252 -0.554028 -0.273297 -0.604213 1.153472 0.121871 --0.744927 0.627803 0.197684 -0.833261 -0.289114 0.024624 -0.112086 -1.05201 0.24323 -0.696909 0.308497 0.359001 --0.32555 -0.351803 0.120067 -0.352622 -0.422829 0.437931 -0.119477 0.777101 0.795433 --0.798715 -0.83498 -0.04946 -0.602944 -0.604804 0.027757 --0.427437 0.491553 0.583332 --0.005096 0.425504 -0.692783 -0.055915 0.11712 -0.271961 --0.103255 0.624955 0.0228 --0.539595 0.360082 -0.504485 diff --git a/examples/Ta_Linear_SNAP_LAMMPS/DATA/6/DATA b/examples/Ta_Linear_SNAP_LAMMPS/DATA/6/DATA deleted file mode 100644 index 07012b67..00000000 --- a/examples/Ta_Linear_SNAP_LAMMPS/DATA/6/DATA +++ /dev/null @@ -1,86 +0,0 @@ -LAMMPS DATA file - -64 atoms -0 bonds -0 angles -0 dihedrals -0 impropers - -1 atom types -0 bond types -0 angle types - -0.0 12.990503 xlo xhi -0.0 11.250148 ylo yhi -0.0 15.845291 zlo zhi - -Masses - -1 73 - -Atoms - -1 1 0.04908 0.00115 10.57826 0 0 0 -2 1 2.61654 2.71455 2.72901 0 0 0 -3 1 1.39595 2.61446 10.52477 0 0 0 -4 1 3.90381 2.6756 0.06766 0 0 0 -5 1 0.05742 1.31249 2.58872 0 0 0 -6 1 0.05697 4.05163 2.67585 0 0 0 -7 1 2.58852 10.55529 1.39238 0 0 0 -8 1 2.6599 0.00552 4.01733 0 0 0 -9 1 5.26427 10.58342 10.56227 0 0 0 -10 1 7.89236 2.6016 2.71779 0 0 0 -11 1 6.6321 2.63976 10.53024 0 0 0 -12 1 9.21243 2.59505 0.06665 0 0 0 -13 1 5.30011 1.36599 2.71012 0 0 0 -14 1 5.34341 4.00547 2.68181 0 0 0 -15 1 8.03029 10.56076 1.30843 0 0 0 -16 1 7.92561 0.06228 3.97753 0 0 0 -17 1 0.03512 5.22736 0.04735 0 0 0 -18 1 2.66581 7.98939 2.66641 0 0 0 -19 1 1.29579 7.92632 10.58792 0 0 0 -20 1 3.93283 7.88849 0.0809 0 0 0 -21 1 10.5959 6.57196 2.63734 0 0 0 -22 1 10.56437 9.25635 2.72679 0 0 0 -23 1 2.72037 5.31366 1.24606 0 0 0 -24 1 2.69611 5.37769 3.9661 0 0 0 -25 1 0.07372 10.52817 5.29093 0 0 0 -26 1 2.61857 2.70351 8.02211 0 0 0 -27 1 1.31355 2.72095 5.3785 0 0 0 -28 1 3.89644 2.57087 5.2537 0 0 0 -29 1 10.58888 1.30214 7.86943 0 0 0 -30 1 0.04887 4.01408 7.90126 0 0 0 -31 1 2.72928 0.06945 6.66193 0 0 0 -32 1 2.58101 0.04872 9.23137 0 0 0 -33 1 5.34108 5.36912 0.05283 0 0 0 -34 1 7.88186 7.9551 2.72317 0 0 0 -35 1 6.55598 7.99717 10.53185 0 0 0 -36 1 9.31791 7.96193 0.00269 0 0 0 -37 1 5.24453 6.70165 2.62389 0 0 0 -38 1 5.32205 9.27675 2.72023 0 0 0 -39 1 7.86861 5.30945 1.31803 0 0 0 -40 1 7.92333 5.29865 3.91698 0 0 0 -41 1 5.25271 10.51825 5.34383 0 0 0 -42 1 8.0222 2.60801 7.87152 0 0 0 -43 1 6.60212 2.59356 5.37931 0 0 0 -44 1 9.30602 2.68963 5.26783 0 0 0 -45 1 5.34458 1.3199 7.96406 0 0 0 -46 1 5.27345 3.97769 7.88365 0 0 0 -47 1 7.90209 0.06243 6.6921 0 0 0 -48 1 7.9791 10.56722 9.28911 0 0 0 -49 1 0.08155 5.37803 5.24262 0 0 0 -50 1 2.69772 8.006 7.99419 0 0 0 -51 1 1.38725 7.96453 5.37281 0 0 0 -52 1 3.9138 7.92522 5.25427 0 0 0 -53 1 10.54558 6.64409 7.90011 0 0 0 -54 1 0.0414 9.23222 7.94529 0 0 0 -55 1 2.6176 5.26509 6.55154 0 0 0 -56 1 2.67779 5.27183 9.34564 0 0 0 -57 1 5.37167 5.22358 5.28383 0 0 0 -58 1 7.97831 7.95033 7.98746 0 0 0 -59 1 6.58772 7.97118 5.22845 0 0 0 -60 1 9.29703 7.96398 5.22074 0 0 0 -61 1 5.35894 6.66603 8.02645 0 0 0 -62 1 5.25491 9.2658 7.91135 0 0 0 -63 1 7.86723 5.29649 6.61035 0 0 0 -64 1 8.01927 5.21862 9.29005 0 0 0 diff --git a/examples/Ta_Linear_SNAP_LAMMPS/DATA/6/ENERGY b/examples/Ta_Linear_SNAP_LAMMPS/DATA/6/ENERGY deleted file mode 100644 index 1b3ea73a..00000000 --- a/examples/Ta_Linear_SNAP_LAMMPS/DATA/6/ENERGY +++ /dev/null @@ -1 +0,0 @@ --753.865255 diff --git a/examples/Ta_Linear_SNAP_LAMMPS/DATA/6/FORCES b/examples/Ta_Linear_SNAP_LAMMPS/DATA/6/FORCES deleted file mode 100644 index 509683ef..00000000 --- a/examples/Ta_Linear_SNAP_LAMMPS/DATA/6/FORCES +++ /dev/null @@ -1,64 +0,0 @@ --0.437757 -0.090743 0.15803 -0.449605 -0.435267 -0.828991 --2.072616 -0.051825 0.877711 -2.144694 -0.090086 0.075882 --0.607352 0.532786 0.378598 --0.777264 -1.885963 -0.048956 -0.39704 0.642203 -1.068312 -0.064098 0.179003 -0.177005 --0.033574 0.346172 0.680676 -0.82825 0.497825 -0.656618 --0.906833 -0.010611 0.365963 -1.376958 0.080901 -0.441221 --0.451121 -0.806818 -0.284864 --0.579497 -0.053233 -0.287661 --0.336212 0.217222 0.347111 -0.289092 -0.611239 0.468926 --0.453067 0.31946 -0.683277 --0.662165 -0.149468 -0.087742 -0.533672 -0.070014 0.096584 --0.020345 0.48243 -0.397113 --0.21413 1.634343 -0.170283 -0.039077 -0.10791 -0.719333 --0.29128 0.032642 2.069655 -0.124193 -0.201649 -0.71097 --0.789865 0.878036 0.020208 -0.56874 -0.164877 -0.950145 --0.076491 -0.288 -0.243411 -1.240837 0.47266 0.656808 -0.255233 0.272119 0.455833 --0.289007 -0.346757 0.12366 --0.685761 -0.244829 -0.502888 -0.339459 -0.233213 1.335765 --0.013471 -0.867347 -0.774099 -0.734048 0.105961 -1.272735 -1.370203 -0.182535 0.648941 --1.127055 -0.301221 0.303103 -0.229886 -1.204827 0.172016 --0.32778 1.003783 -0.614408 -0.764624 -0.183537 -0.038771 -0.625441 0.03111 0.856974 -0.561912 0.756882 -0.236387 --0.458387 0.66717 1.04408 -0.070225 0.10084 -0.482484 --0.344876 -0.18676 -0.015312 --0.207209 0.12974 -0.023385 -0.225407 0.210336 0.49958 -0.296301 -0.597326 -1.321812 --0.274024 0.193096 0.130562 --1.153238 -0.394578 0.405264 --0.445287 -0.699603 -0.114074 --1.117986 -0.159911 -0.252436 -1.483723 -0.15328 0.336593 -0.381189 -0.437364 0.391497 --0.069632 0.550601 0.135542 -0.497368 0.356473 1.817883 --0.09738 0.356697 -2.092389 --1.082933 0.58337 0.189313 --0.334998 -0.148464 -0.752988 -0.250508 -0.279802 0.963668 --0.269342 -0.065478 0.796032 --0.160453 -0.945482 -0.543903 -0.540075 0.33829 0.275545 -0.852005 0.19428 0.109663 --0.365475 0.483588 -0.393695 diff --git a/examples/Ta_Linear_SNAP_LAMMPS/DATA/7/DATA b/examples/Ta_Linear_SNAP_LAMMPS/DATA/7/DATA deleted file mode 100644 index 1c2c1901..00000000 --- a/examples/Ta_Linear_SNAP_LAMMPS/DATA/7/DATA +++ /dev/null @@ -1,86 +0,0 @@ -LAMMPS DATA file - -64 atoms -0 bonds -0 angles -0 dihedrals -0 impropers - -1 atom types -0 bond types -0 angle types - -0.0 12.990503 xlo xhi -0.0 11.250148 ylo yhi -0.0 15.845291 zlo zhi - -Masses - -1 73 - -Atoms - -1 1 10.54497 10.54551 10.5956 0 0 0 -2 1 2.6058 2.59577 2.66276 0 0 0 -3 1 1.29338 2.62737 0.06659 0 0 0 -4 1 3.97859 2.60074 0.05226 0 0 0 -5 1 0.06826 1.26322 2.67108 0 0 0 -6 1 0.03489 4.006 2.58088 0 0 0 -7 1 2.60404 0.03209 1.27573 0 0 0 -8 1 2.61384 0.03978 4.00017 0 0 0 -9 1 5.26731 10.53909 0.0525 0 0 0 -10 1 8.00375 2.64902 2.69207 0 0 0 -11 1 6.64426 2.6613 10.54 0 0 0 -12 1 9.33824 2.64457 0.03106 0 0 0 -13 1 5.3522 1.2665 2.5671 0 0 0 -14 1 5.27655 4.04903 2.65011 0 0 0 -15 1 7.9997 10.54384 1.3323 0 0 0 -16 1 7.97961 10.59814 4.02363 0 0 0 -17 1 0.07703 5.36114 0.02699 0 0 0 -18 1 2.6646 7.93725 2.60955 0 0 0 -19 1 1.40379 7.96668 10.52251 0 0 0 -20 1 3.99035 7.99423 10.59771 0 0 0 -21 1 0.04355 6.56889 2.62727 0 0 0 -22 1 0.00703 9.28757 2.68364 0 0 0 -23 1 2.56957 5.34141 1.33893 0 0 0 -24 1 2.72447 5.25375 4.04037 0 0 0 -25 1 10.53684 10.5759 5.2221 0 0 0 -26 1 2.66913 2.7096 7.94723 0 0 0 -27 1 1.35438 2.68364 5.23358 0 0 0 -28 1 3.92914 2.57652 5.21831 0 0 0 -29 1 0.08152 1.31737 7.90103 0 0 0 -30 1 0.01596 3.94268 7.99393 0 0 0 -31 1 2.6785 10.52779 6.63557 0 0 0 -32 1 2.57563 10.5398 9.20066 0 0 0 -33 1 5.28026 5.2908 10.53874 0 0 0 -34 1 8.02116 8.00301 2.56791 0 0 0 -35 1 6.56126 7.9104 0.04457 0 0 0 -36 1 9.26485 7.95508 10.58594 0 0 0 -37 1 5.26103 6.62842 2.63265 0 0 0 -38 1 5.28955 9.23968 2.5673 0 0 0 -39 1 8.00221 5.33276 1.34132 0 0 0 -40 1 7.91864 5.28423 3.97891 0 0 0 -41 1 5.27037 0.01177 5.31967 0 0 0 -42 1 7.97577 2.58846 7.90284 0 0 0 -43 1 6.67111 2.70945 5.31433 0 0 0 -44 1 9.29025 2.58105 5.29066 0 0 0 -45 1 5.2532 1.26795 7.91799 0 0 0 -46 1 5.32703 4.04747 7.87622 0 0 0 -47 1 7.8991 10.56576 6.68405 0 0 0 -48 1 8.01539 10.54873 9.32177 0 0 0 -49 1 10.59055 5.23373 5.29112 0 0 0 -50 1 2.7178 8.02017 8.01996 0 0 0 -51 1 1.28755 7.95382 5.35947 0 0 0 -52 1 3.98149 8.00712 5.27935 0 0 0 -53 1 0.04771 6.7013 8.02541 0 0 0 -54 1 10.53454 9.27538 7.94586 0 0 0 -55 1 2.60384 5.37826 6.65237 0 0 0 -56 1 2.65026 5.25782 9.27591 0 0 0 -57 1 5.30975 5.33548 5.25863 0 0 0 -58 1 7.98152 7.93147 7.94727 0 0 0 -59 1 6.58336 7.99956 5.3353 0 0 0 -60 1 9.20518 8.00165 5.34211 0 0 0 -61 1 5.28813 6.67781 8.01704 0 0 0 -62 1 5.2968 9.20687 7.96818 0 0 0 -63 1 7.90382 5.25794 6.62358 0 0 0 -64 1 8.00072 5.28621 9.26356 0 0 0 diff --git a/examples/Ta_Linear_SNAP_LAMMPS/DATA/7/ENERGY b/examples/Ta_Linear_SNAP_LAMMPS/DATA/7/ENERGY deleted file mode 100644 index d8faf90e..00000000 --- a/examples/Ta_Linear_SNAP_LAMMPS/DATA/7/ENERGY +++ /dev/null @@ -1 +0,0 @@ --754.220443 diff --git a/examples/Ta_Linear_SNAP_LAMMPS/DATA/7/FORCES b/examples/Ta_Linear_SNAP_LAMMPS/DATA/7/FORCES deleted file mode 100644 index 25f0a463..00000000 --- a/examples/Ta_Linear_SNAP_LAMMPS/DATA/7/FORCES +++ /dev/null @@ -1,64 +0,0 @@ -0.738379 0.48581 0.018519 -0.983004 0.695353 -0.423917 -0.967488 0.116743 -0.589823 --0.084389 0.137046 -0.423367 --0.470328 1.296441 -0.423078 --0.263493 -1.182047 0.521328 -0.332524 -0.382338 0.466834 -0.19652 -0.552756 -0.617059 -0.340753 0.932737 -1.082711 --0.352834 -0.034069 -0.546853 -0.209447 -0.170553 0.255905 --1.248523 0.1324 -0.277314 --0.296298 1.327488 0.591352 -0.225842 -1.705193 -0.220596 --0.602859 0.598417 0.360383 --0.487819 0.018537 -0.681676 --0.850702 -0.481463 -0.618219 --0.375888 0.3131 0.609637 --1.425719 -0.081346 0.714056 --0.152265 -0.539619 0.318009 --0.178473 1.482119 0.427439 -0.269104 -1.208309 -0.327712 -0.850349 -0.517951 0.275559 --0.588363 0.226576 -0.96233 -0.629328 0.101208 1.170955 -0.175608 -0.725726 0.018084 --0.672848 -0.376194 0.690747 -1.314233 0.49323 0.453261 --0.403463 -0.248525 0.230807 --0.081478 0.863863 -0.071733 --0.387653 0.744336 -0.69563 -0.204661 1.016501 1.272453 -0.210489 -0.369673 0.610136 --0.618631 -0.801014 1.16881 -1.247918 -0.045758 -0.325354 -0.342738 -0.215167 -0.069832 -0.441032 0.314676 -0.03073 -0.215784 0.14419 0.976532 --0.277749 -0.258368 -0.418189 -0.132647 0.303744 -0.143621 -0.293403 0.10204 -0.586267 --0.0766 0.318418 0.741565 --1.193866 -0.235149 -0.180348 -0.286858 0.294859 0.204099 -0.289819 0.925706 0.429944 -0.177769 -1.251772 0.201923 -0.011121 0.010154 -0.513286 --0.770371 0.244167 -0.539961 --0.122463 0.783939 0.309844 --0.833015 -1.143659 -1.244648 -0.318174 -0.327947 -0.137883 --0.672169 -0.306686 0.158866 -0.000928 -1.568952 -0.556323 -0.490919 0.513788 -0.187133 -0.107427 -0.010953 -0.135414 -0.0403 0.521312 0.035425 --0.196083 -0.020488 0.519869 --0.52423 -0.25306 0.358801 -0.546995 -0.296434 -0.355434 -0.753656 -0.424927 -0.364529 -0.382562 -1.149823 -0.614214 -0.395589 1.452637 -0.053896 -0.295654 0.152651 -0.023568 --0.210447 -0.178269 0.331507 diff --git a/examples/Ta_Linear_SNAP_LAMMPS/DATA/8/DATA b/examples/Ta_Linear_SNAP_LAMMPS/DATA/8/DATA deleted file mode 100644 index bd0b41d5..00000000 --- a/examples/Ta_Linear_SNAP_LAMMPS/DATA/8/DATA +++ /dev/null @@ -1,86 +0,0 @@ -LAMMPS DATA file - -64 atoms -0 bonds -0 angles -0 dihedrals -0 impropers - -1 atom types -0 bond types -0 angle types - -0.0 12.990503 xlo xhi -0.0 11.250148 ylo yhi -0.0 15.845291 zlo zhi - -Masses - -1 73 - -Atoms - -1 1 10.59947 10.59661 10.52413 0 0 0 -2 1 2.59454 2.65092 2.68446 0 0 0 -3 1 1.33041 2.674 10.58143 0 0 0 -4 1 3.95295 2.58315 10.54506 0 0 0 -5 1 10.59883 1.31774 2.66978 0 0 0 -6 1 10.57967 3.96662 2.60593 0 0 0 -7 1 2.59254 0.00678 1.31972 0 0 0 -8 1 2.59169 0.03133 3.90382 0 0 0 -9 1 5.37939 0.04023 0.07113 0 0 0 -10 1 7.94984 2.73234 2.65636 0 0 0 -11 1 6.7035 2.71875 10.57105 0 0 0 -12 1 9.33869 2.66536 10.5534 0 0 0 -13 1 5.38144 1.37363 2.59678 0 0 0 -14 1 5.27263 3.99656 2.66272 0 0 0 -15 1 7.96657 0.06435 1.30009 0 0 0 -16 1 7.99235 0.04847 3.89505 0 0 0 -17 1 0.0218 5.29659 10.5698 0 0 0 -18 1 2.73175 8.00138 2.71285 0 0 0 -19 1 1.31806 7.96372 10.54256 0 0 0 -20 1 3.91844 7.96217 10.56452 0 0 0 -21 1 0.03602 6.66478 2.64422 0 0 0 -22 1 10.5258 9.31439 2.65344 0 0 0 -23 1 2.66149 5.31748 1.25965 0 0 0 -24 1 2.71043 5.3142 3.96356 0 0 0 -25 1 0.01714 0.02895 5.25397 0 0 0 -26 1 2.64597 2.62331 8.00147 0 0 0 -27 1 1.34375 2.63266 5.31467 0 0 0 -28 1 4.01969 2.72066 5.33483 0 0 0 -29 1 0.05334 1.28072 7.94153 0 0 0 -30 1 10.56225 3.9163 7.87893 0 0 0 -31 1 2.67491 10.58095 6.65598 0 0 0 -32 1 2.61935 0.04143 9.225 0 0 0 -33 1 5.37858 5.37062 0.02738 0 0 0 -34 1 8.01211 7.93604 2.73 0 0 0 -35 1 6.6093 7.90613 0.06492 0 0 0 -36 1 9.28311 7.87808 10.53355 0 0 0 -37 1 5.22651 6.57935 2.58919 0 0 0 -38 1 5.36331 9.19414 2.65024 0 0 0 -39 1 7.9726 5.27207 1.2508 0 0 0 -40 1 7.89187 5.26738 3.98139 0 0 0 -41 1 5.30786 0.02387 5.37311 0 0 0 -42 1 7.90554 2.64139 7.96721 0 0 0 -43 1 6.54626 2.62801 5.34703 0 0 0 -44 1 9.30386 2.63489 5.25676 0 0 0 -45 1 5.34196 1.30641 7.91047 0 0 0 -46 1 5.33435 4.01755 7.93742 0 0 0 -47 1 7.87923 10.59827 6.57191 0 0 0 -48 1 7.91667 0.07787 9.29291 0 0 0 -49 1 0.00407 5.21804 5.29085 0 0 0 -50 1 2.64244 8.01096 7.89122 0 0 0 -51 1 1.27073 7.96757 5.24059 0 0 0 -52 1 4.05652 7.94422 5.24628 0 0 0 -53 1 10.55504 6.5449 8.02866 0 0 0 -54 1 10.54757 9.32356 7.97367 0 0 0 -55 1 2.57132 5.31124 6.54943 0 0 0 -56 1 2.70552 5.36844 9.25923 0 0 0 -57 1 5.37917 5.32156 5.36422 0 0 0 -58 1 7.96636 7.91391 7.89315 0 0 0 -59 1 6.60266 8.02328 5.30029 0 0 0 -60 1 9.34959 7.99431 5.26212 0 0 0 -61 1 5.27917 6.54337 7.93235 0 0 0 -62 1 5.31647 9.3383 7.99422 0 0 0 -63 1 7.90244 5.24771 6.59897 0 0 0 -64 1 7.93795 5.34891 9.25032 0 0 0 diff --git a/examples/Ta_Linear_SNAP_LAMMPS/DATA/8/ENERGY b/examples/Ta_Linear_SNAP_LAMMPS/DATA/8/ENERGY deleted file mode 100644 index 7e0234a2..00000000 --- a/examples/Ta_Linear_SNAP_LAMMPS/DATA/8/ENERGY +++ /dev/null @@ -1 +0,0 @@ --753.969161 diff --git a/examples/Ta_Linear_SNAP_LAMMPS/DATA/8/FORCES b/examples/Ta_Linear_SNAP_LAMMPS/DATA/8/FORCES deleted file mode 100644 index d6f0ce8b..00000000 --- a/examples/Ta_Linear_SNAP_LAMMPS/DATA/8/FORCES +++ /dev/null @@ -1,64 +0,0 @@ --0.226907 -0.080536 0.902052 -0.776819 0.171288 -0.551025 -0.176394 -0.183256 0.204614 -0.854273 0.68598 0.610189 --0.091936 0.35913 -0.579748 -0.084104 0.473431 0.095227 -0.598698 0.099657 -0.823976 -0.425043 -0.081448 1.419933 --1.005574 -0.469543 -0.545443 -0.080843 -0.503649 -0.229292 --1.075835 -0.284081 0.217795 --0.645726 -0.07901 0.309219 --0.660687 -0.7539 0.448111 -0.021249 -0.323657 0.146107 -0.116005 -0.264227 0.267969 --0.241556 -0.152596 0.888561 -0.190539 -0.014165 0.267054 --1.053594 -0.284418 -0.953258 --0.136246 -0.133944 0.366015 -0.996651 0.062808 0.124581 -0.197253 -0.463833 -0.145331 -0.724814 -0.437657 -0.379722 --0.022671 0.017877 1.049002 --0.229855 -0.004722 -0.591605 --0.154714 -0.160145 0.666203 -0.380032 0.718636 -0.704725 -0.392862 -0.03449 -0.003614 --1.339879 -0.221236 -0.290386 --0.439149 1.033607 -0.306897 -0.077647 0.175986 0.172003 --0.034472 0.357047 -1.370013 -0.449865 -0.403463 1.302128 --0.971327 -1.005554 -0.649326 --0.650844 -0.187724 -0.927616 -0.276128 0.710737 -0.478142 --0.273083 0.488493 0.413712 -0.641086 0.512876 0.520235 -0.022943 1.480425 0.177898 -0.18907 0.389324 1.308572 -0.703866 0.272666 -0.675214 --0.441452 -0.182156 -1.394336 -0.778455 0.069504 -0.485925 -1.838904 0.098736 -0.497372 --1.018893 -0.04522 0.187076 --0.440112 1.103483 0.738039 --0.433146 -1.463369 0.322362 -0.570104 -0.011791 0.650285 -0.417554 -0.726222 -0.85977 --0.306761 0.830359 -0.270748 --0.154505 -0.65194 -0.071913 -1.78038 -0.289728 0.312266 --1.766243 -0.059655 0.397705 -0.326135 1.292787 -0.813062 -0.218025 -1.545104 -0.663048 -0.638753 -0.09298 1.309355 --0.31279 -0.257789 -0.758911 --1.051024 0.088554 -0.982928 --0.365514 0.575159 0.279003 -1.44818 -0.312672 -0.021217 --1.787702 -0.359966 0.327963 --0.08343 2.464228 0.472227 --0.013579 -1.711441 -0.018178 -0.734729 0.047141 0.508435 -0.301803 -0.342634 -0.33915 diff --git a/examples/Ta_Linear_SNAP_LAMMPS/DATA/9/DATA b/examples/Ta_Linear_SNAP_LAMMPS/DATA/9/DATA deleted file mode 100644 index dd656f93..00000000 --- a/examples/Ta_Linear_SNAP_LAMMPS/DATA/9/DATA +++ /dev/null @@ -1,86 +0,0 @@ -LAMMPS DATA file - -64 atoms -0 bonds -0 angles -0 dihedrals -0 impropers - -1 atom types -0 bond types -0 angle types - -0.0 12.990503 xlo xhi -0.0 11.250148 ylo yhi -0.0 15.845291 zlo zhi - -Masses - -1 73 - -Atoms - -1 1 10.59125 10.59066 0.01705 0 0 0 -2 1 2.66355 2.56976 2.70172 0 0 0 -3 1 1.28225 2.66379 0.00075 0 0 0 -4 1 3.97426 2.68113 0.01584 0 0 0 -5 1 0.04505 1.26937 2.60223 0 0 0 -6 1 0.00712 3.91022 2.683 0 0 0 -7 1 2.72684 10.52432 1.35392 0 0 0 -8 1 2.65771 10.58165 3.96524 0 0 0 -9 1 5.24942 0.01366 0.0772 0 0 0 -10 1 7.94389 2.70276 2.58372 0 0 0 -11 1 6.56897 2.63238 10.53781 0 0 0 -12 1 9.25697 2.71824 0.03107 0 0 0 -13 1 5.2811 1.27529 2.68805 0 0 0 -14 1 5.37617 4.03137 2.57831 0 0 0 -15 1 7.91828 10.57185 1.29744 0 0 0 -16 1 8.00764 10.55181 3.96506 0 0 0 -17 1 0.0118 5.32177 10.55352 0 0 0 -18 1 2.71308 7.96819 2.68219 0 0 0 -19 1 1.27335 7.87586 10.56985 0 0 0 -20 1 3.92708 7.97831 10.57169 0 0 0 -21 1 10.58762 6.54896 2.70874 0 0 0 -22 1 0.00758 9.30089 2.66982 0 0 0 -23 1 2.61456 5.29021 1.37992 0 0 0 -24 1 2.62758 5.2723 4.00316 0 0 0 -25 1 10.5382 10.57206 5.35381 0 0 0 -26 1 2.69884 2.72252 7.98246 0 0 0 -27 1 1.28389 2.59056 5.26081 0 0 0 -28 1 4.01712 2.69857 5.29807 0 0 0 -29 1 0.0291 1.26201 7.95665 0 0 0 -30 1 0.01323 4.01408 7.91542 0 0 0 -31 1 2.6335 0.07389 6.60337 0 0 0 -32 1 2.62747 0.02086 9.22021 0 0 0 -33 1 5.37311 5.37921 0.00104 0 0 0 -34 1 7.9566 8.01813 2.65235 0 0 0 -35 1 6.57317 7.93825 10.57796 0 0 0 -36 1 9.2694 7.88151 10.53712 0 0 0 -37 1 5.22009 6.55334 2.65222 0 0 0 -38 1 5.33963 9.271 2.62989 0 0 0 -39 1 8.02119 5.29672 1.35359 0 0 0 -40 1 7.94827 5.36972 3.97268 0 0 0 -41 1 5.3297 10.56835 5.37217 0 0 0 -42 1 7.91532 2.64246 8.00295 0 0 0 -43 1 6.62199 2.68295 5.3771 0 0 0 -44 1 9.2514 2.68433 5.35239 0 0 0 -45 1 5.32938 1.27255 7.97134 0 0 0 -46 1 5.30418 3.93812 7.93568 0 0 0 -47 1 7.95987 10.54938 6.61642 0 0 0 -48 1 7.87538 0.02651 9.23341 0 0 0 -49 1 0.01871 5.23215 5.21873 0 0 0 -50 1 2.58005 8.01801 8.00091 0 0 0 -51 1 1.35622 7.90716 5.21911 0 0 0 -52 1 3.91664 8.00527 5.23273 0 0 0 -53 1 0.05597 6.54262 7.99991 0 0 0 -54 1 0.05678 9.22328 7.97883 0 0 0 -55 1 2.66025 5.35371 6.64491 0 0 0 -56 1 2.64384 5.23012 9.2296 0 0 0 -57 1 5.34418 5.35604 5.295 0 0 0 -58 1 7.96554 7.96325 7.88581 0 0 0 -59 1 6.67445 7.93954 5.26624 0 0 0 -60 1 9.32253 7.94305 5.27672 0 0 0 -61 1 5.37998 6.62136 8.01604 0 0 0 -62 1 5.23732 9.22012 7.8725 0 0 0 -63 1 7.90914 5.35867 6.63564 0 0 0 -64 1 7.8945 5.29107 9.20052 0 0 0 diff --git a/examples/Ta_Linear_SNAP_LAMMPS/DATA/9/ENERGY b/examples/Ta_Linear_SNAP_LAMMPS/DATA/9/ENERGY deleted file mode 100644 index f615940c..00000000 --- a/examples/Ta_Linear_SNAP_LAMMPS/DATA/9/ENERGY +++ /dev/null @@ -1 +0,0 @@ --754.317603 diff --git a/examples/Ta_Linear_SNAP_LAMMPS/DATA/9/FORCES b/examples/Ta_Linear_SNAP_LAMMPS/DATA/9/FORCES deleted file mode 100644 index 32e89a8c..00000000 --- a/examples/Ta_Linear_SNAP_LAMMPS/DATA/9/FORCES +++ /dev/null @@ -1,64 +0,0 @@ --0.118141 -0.145557 -0.396942 -0.219448 0.641719 -0.568891 -0.804753 -0.213095 0.055931 --0.5516 -0.108225 0.097343 --0.282662 0.758456 0.398993 --0.114677 0.106269 -0.518987 --0.726917 0.472688 -0.797823 --0.077037 0.011007 0.534617 -0.258031 -0.214153 -1.051703 --0.034901 -0.786039 0.846874 -0.820741 0.17553 0.316927 --0.141547 -0.541217 -0.295988 -0.271914 1.289542 0.153822 --0.516957 -1.627578 0.618851 -0.139377 0.343182 0.085819 --0.357185 0.552583 -0.126678 --0.219509 -0.620513 0.913793 --0.885887 -0.647834 -0.964512 -0.732069 0.426178 0.624024 -0.265397 -0.23012 0.239314 -0.212568 1.24841 -0.75972 -0.165843 -1.183907 0.012866 -0.244522 -0.196185 -0.940657 -0.333512 0.04522 -0.140777 -0.701913 0.154249 -0.479572 --0.500546 -0.903317 -0.62617 -0.772419 0.170547 0.489784 --0.593672 -0.373102 0.08628 --0.228249 1.225911 0.153224 --0.130807 -1.640213 -0.047405 --0.001447 -0.190083 0.039412 --0.039118 0.087686 0.983273 --0.959972 -0.838327 0.018335 -0.04766 -0.892332 -0.496011 -0.775293 0.395418 -0.12899 --0.581566 0.421257 0.44285 -0.48966 1.629995 -0.065174 -0.037846 -0.612714 0.384536 --0.362251 0.224738 -0.893573 -0.104266 -0.263664 0.222094 --0.099087 0.370321 -0.98499 -0.680096 -0.069447 -0.387023 -0.284007 -0.162815 -0.500346 --0.118786 -0.470272 -0.408554 --0.303978 0.286044 0.13783 -0.040155 0.762457 0.076378 --0.218528 0.46405 0.105442 -0.304713 -0.390603 0.650333 --0.275057 0.30265 1.189576 -0.903103 -0.811538 -0.942974 --0.69223 0.095275 0.734107 -1.355059 -0.299637 0.764864 --0.53468 1.450745 -0.817521 --0.723123 0.147795 -0.085492 -0.12943 -0.14096 -0.631864 -0.184014 0.70864 1.326423 --0.670333 -0.337693 0.183358 -0.240713 -0.060137 0.461609 --0.870954 0.115388 0.099246 --0.121051 -0.177459 -0.101598 --0.697928 -0.125018 -0.551236 -0.142822 0.596726 0.634521 -0.470037 -0.554497 -0.783277 -0.619005 0.147575 1.411797 diff --git a/examples/Ta_Linear_SNAP_LAMMPS/PotentialLearning.conf b/examples/Ta_Linear_SNAP_LAMMPS/PotentialLearning.conf deleted file mode 100644 index e6770f13..00000000 --- a/examples/Ta_Linear_SNAP_LAMMPS/PotentialLearning.conf +++ /dev/null @@ -1,45 +0,0 @@ -[global] -potential SNAP_LAMMPS -fit_forces false -no_atoms_per_type 64 -no_atoms_per_conf 64 -no_atomic_conf 9 -no_train_atomic_conf 6 -numTypes 1 -twojmax 6 -cutoff_radii 0.5 0.5 -neighbor_weights 1.0 0.5 -rcutfac 4.67637 -rfac0 0.99363 -rmin0 0.0 -wj 1.0 -radelem 0.5 -type Ta -wselfallflag 0 -chemflag 0 -bzeroflag 0 -quadraticflag 0 - -#[ESHIFT] -#Ta = 0.0 - -[solver] -name BBO - -[ref] -potential ZBL -ε0 55.26349406 -e -1.602176634e-19 -zi 73.0 -zj 73.0 -rcutfac 4.67637 - -[dft] -potential LennardJones -ε 0.643 -σ 2.390 - - - - - diff --git a/examples/Ta_Linear_SNAP_LAMMPS/fitsnap2potentiallearning.jl b/examples/Ta_Linear_SNAP_LAMMPS/fitsnap2potentiallearning.jl deleted file mode 100644 index 786383ad..00000000 --- a/examples/Ta_Linear_SNAP_LAMMPS/fitsnap2potentiallearning.jl +++ /dev/null @@ -1,63 +0,0 @@ -# Convert the DFT data from https://github.com/FitSNAP/FitSNAP/tree/master/examples/Ta_Linear_JCP2014/JSON -# to the current format required by PotentialLearning.jl. -# The current format will probably change in the coming months. - -using JSON - -path = "./JSON/" -for d in readdir(path) - sub_path = joinpath(path, d, "DATA") - rm(sub_path, recursive=true) - dirs = readdir(joinpath(path, d)) - mkdir(sub_path) - for (i, f) in enumerate(dirs) - global dft_data = Dict() - open(joinpath(path, d, f) , "r") do file - @show joinpath(path, d, f) - readline(file) - dft_data = JSON.parse(readline(file)) - end - ssub_path = joinpath(sub_path, "$i") - mkdir(ssub_path) - - open(joinpath(ssub_path, "ENERGY"), "w") do file - write(file, "$(dft_data["Dataset"]["Data"][1]["Energy"])\n") - end - - open(joinpath(ssub_path, "FORCES"), "w") do file - for force in dft_data["Dataset"]["Data"][1]["Forces"] - write(file, "$(force[1]) $(force[2]) $(force[3])\n") - end - end - - open(joinpath(ssub_path, "DATA") , "w") do file - write(file, "LAMMPS DATA file\n") - write(file, "\n") - write(file, "$(dft_data["Dataset"]["Data"][1]["NumAtoms"]) atoms\n") - write(file, "0 bonds\n") - write(file, "0 angles\n") - write(file, "0 dihedrals\n") - write(file, "0 impropers\n") - write(file, "\n") - write(file, "1 atom types\n") - write(file, "0 bond types\n") - write(file, "0 angle types\n") - write(file, "\n") - write(file, "0.0 12.990503 xlo xhi\n") - write(file, "0.0 11.250148 ylo yhi\n") - write(file, "0.0 15.845291 zlo zhi\n") - write(file, "\n") - write(file, "Masses\n") - write(file, "\n") - write(file, "1 73\n") - write(file, "\n") - write(file, "Atoms\n") - write(file, "\n") - positions = dft_data["Dataset"]["Data"][1]["Positions"] - for (j, pos) in enumerate(positions) - write(file, "$j 1 $(pos[1]) $(pos[2]) $(pos[3]) 0 0 0\n") - end - end - end -end - diff --git a/examples/Ta_Linear_SNAP_LAMMPS/run.jl b/examples/Ta_Linear_SNAP_LAMMPS/run.jl deleted file mode 100644 index ec9449c7..00000000 --- a/examples/Ta_Linear_SNAP_LAMMPS/run.jl +++ /dev/null @@ -1,22 +0,0 @@ -include("../../src/PotentialLearning.jl") -using .PotentialLearning - -path = "./" -params = get_conf_params(path) - -# Get DFT data -dft_train_data, dft_val_data = get_dft_data(params) - -# Get reference data -ref_train_data, ref_val_data = generate_data("ref", params) - -# Get potential learning problem (e.g. A β = b) -snap = learning_problem(dft_train_data, ref_train_data, params) - -# Solve potential learning problem (e.g. β = A \ b) -learn(snap, params) - -# Validate potentials, forces, and stresses -metrics = error_metrics(snap, dft_val_data - ref_val_data, params) - - diff --git a/src/InputLoading.jl b/src/InputLoading.jl deleted file mode 100644 index e2afc2e8..00000000 --- a/src/InputLoading.jl +++ /dev/null @@ -1,71 +0,0 @@ -""" - load_positions_per_conf(path::String, no_atoms_per_conf::Int64, - no_conf_init::Int64, no_conf_end::Int64) - -Loads atomic positions per configuration. -""" -function load_positions_per_conf(path::String, no_atoms_per_conf::Int64, - no_conf_init::Int64, no_conf_end::Int64) - positions_per_conf = [] - for j = no_conf_init:no_conf_end - rs = Vector{Position}() - open(string(path, "/DATA/", string(j), "/DATA")) do f - while readline(f) != "Atoms" end - line = readline(f) - while line == "" - line = readline(f) - end - for i = 1:no_atoms_per_conf - s = split(line) - r = Position(parse(Float64, s[3]), - parse(Float64, s[4]), - parse(Float64, s[5])) - push!(rs, r) - line = i < no_atoms_per_conf ? readline(f) : "" - end - end - push!(positions_per_conf, rs) - end - return positions_per_conf -end - -""" - get_conf_params(path::String) - -Loads configuration parameters. -""" -function get_conf_params(path::String) - params = Dict() - global key = "" - open(string(path, "./PotentialLearning.conf")) do f - while !eof(f) - line = split(readline(f)) - if length(line) > 0 && line[1][1] != '#' && line[1][1] != ' ' - lhs = line[1] - if lhs[1] == '[' - global key = replace(lhs, r"\[(\w+)\]"=>s"\1") - global params[key] = Dict() - else - rhs = [] - for s in line[2:end] - if tryparse(Float64, s) !== nothing # if s is a number - s = occursin(".", s) ? parse(Float64, s) : parse(Int64, s) - elseif tryparse(Bool, s) !== nothing - s = parse(Bool, s) - end - push!(rhs, s) - end - rhs = length(rhs) == 1 ? rhs[1] : rhs - params[key][lhs] = rhs - end - end - end - end - params["global"]["path"] = path - params["global"]["positions_per_conf"] = load_positions_per_conf(path, - params["global"]["no_atoms_per_conf"], - 1, params["global"]["no_atomic_conf"]) - return params -end - - diff --git a/src/Interface.jl b/src/Interface.jl new file mode 100644 index 00000000..54147e4f --- /dev/null +++ b/src/Interface.jl @@ -0,0 +1,85 @@ +################################################################################ +# +# Interface.jl +# +################################################################################ + +using GalacticOptim, Optim +using BlackBoxOptim + + +# Abstract types ############################################################### + +""" + LearningProblem{D, T} + +""" +abstract type LearningProblem{D, T} end + +""" + LearningOptimizer{D, T} + +""" +abstract type LearningOptimizer{D, T} end + + +# Optimizers ################################################################### + +""" + SDPOpt{D, T} + +Semidefinite program (SDP) optimizer +""" +struct SDPOpt{D, T} <: LearningOptimizer{D, T} end + +""" + LeastSquaresOpt{D, T} + +Least squares optimizer +""" +struct LeastSquaresOpt{D, T} <: LearningOptimizer{D, T} end + +""" + QRLinearOpt{D, T} + +QR optimizer +""" +struct QRLinearOpt{D, T} <: LearningOptimizer{D, T} end + +""" + NelderMeadOpt{D, T} + +Nelder mead optimizer +""" +struct NelderMeadOpt{D, T} <: LearningOptimizer{D, T} + maxiters +end + + +# Learning and loss functions ################################################## + +""" + loss(params::Vector{T}, opt::LearningOptimizer{D, T}) + +`params`: parameters to be fitted +`opt`: learning optimizer +""" +function loss(params::Vector{T}, opt::LearningOptimizer{D, T}) end + +""" + learn(lp::LearningProblem{D, T}, opt::LearningOptimizer{D, T}) + +`lp`: learning problem +`opt`: learning optimizer +""" +function learn(lp::LearningProblem{D, T}, opt::LearningOptimizer{D, T}) end + +""" + learn(lp::LearningProblem{D, T}, opt::LearningOptimizer{D, T}, loss) + +`lp`: learning problem +`opt`: learning optimizer +`loss`: loss function +""" +function learn(lp::LearningProblem{D, T}, opt::LearningOptimizer{D, T}, loss) end + diff --git a/src/LearningData.jl b/src/LearningData.jl deleted file mode 100644 index 53e6d2df..00000000 --- a/src/LearningData.jl +++ /dev/null @@ -1,86 +0,0 @@ - -""" - generate_data(params::Dict) - -Generates DFT/reference data based on a particular potential. -""" -function generate_data(model::String, params::Dict) - # Load the potential model (E.g. GaN) - p_model = Symbol(params[model]["potential"]) - p = @eval $p_model($(params[model])) - # Load parameters - fit_forces = params["global"]["fit_forces"] - a = params["global"]["no_train_atomic_conf"] - b = params["global"]["no_atomic_conf"] - positions_per_conf = params["global"]["positions_per_conf"] - rcutfac = params["global"]["rcutfac"] - # Calculate DFT training data - training_data = generate_data_aux(p, positions_per_conf, 1, a, rcutfac, fit_forces) - # Calculate DFT validation data - validation_data = generate_data_aux(p, positions_per_conf, a+1, b, rcutfac, fit_forces) - - return training_data, validation_data -end - -""" - generate_data_aux(p::Potential, positions_per_conf::Vector, - a::Int64, b::Int64, rcutfac::Float64, fit_forces::Bool) - -Auxiliar function. See `generate_data`. -""" -function generate_data_aux(p::Potential, positions_per_conf::Vector, - a::Int64, b::Int64, rcutfac::Float64, fit_forces::Bool) - potentials = [potential_energy(p, positions_per_conf[j], rcutfac) for j = a:b] - lin_forces = fit_forces ? linearize([forces(p, positions_per_conf[j], rcutfac) - for j = a:b]) : Vector{Float64}() - return [potentials; lin_forces] -end - -""" - linearize(data::Vector{Force}) - -Linearizes a vector of forces. -E.g. [Force(1.0,2.0,3.0), Force(4.0,5.0,6.0)] => [1.0, 2.0, 3.0, 4.0, 5.0, 6.0] -""" -function linearize(data::Vector{Vector{Force}}) - lin_data = Vector{Float64}() - for i = 1:length(data), j = 1:length(data[i]), k = 1:3 - push!(lin_data, data[i][j][k]) - end - return lin_data -end - -function get_dft_data(params::Dict) - path = params["global"]["path"] - fit_forces = params["global"]["fit_forces"] - n = params["global"]["no_train_atomic_conf"] - m = params["global"]["no_atoms_per_conf"] - - dirs = readdir(joinpath(path, "DATA")) - dft_energies = Vector{Float64}() - for d in dirs - open(joinpath(path, "DATA", d, "ENERGY") , "r") do file - e = parse(Float64, readline(file)) - push!(dft_energies, e) - end - end - training_data = dft_energies[1:n] - validation_data = dft_energies[n+1:end] - - if fit_forces - dft_forces = Vector{Float64}() - for d in dirs - open(joinpath(path, "DATA", d, "FORCES") , "r") do file - while !eof(f) - f = parse.(Float64, split(readline(file))) - push!(dft_forces, f[1]) - push!(dft_forces, f[2]) - push!(dft_forces, f[3]) - end - end - end - training_data = [training_data; dft_forces[1:3*n*m]] - validation_data = [training_data; dft_forces[3*n*m+1:end]] - end - return training_data, validation_data -end diff --git a/src/PotentialLearning.jl b/src/PotentialLearning.jl index 4db95528..6c179e7e 100644 --- a/src/PotentialLearning.jl +++ b/src/PotentialLearning.jl @@ -1,105 +1,6 @@ -################################################################################ -# -# Module PotentialLearning.jl -# -################################################################################ - module PotentialLearning -using GalacticOptim, Optim -using BlackBoxOptim -using Printf - -export get_conf_params, generate_data, get_dft_data, learning_problem, learn, - error_metrics, potential_energy, forces - -abstract type PotentialLearningProblem end - -include("./Potentials/Potentials.jl") -include("InputLoading.jl") -include("LearningData.jl") - -""" - learning_problem( dft_train_data::Vector{Float64}, - ref_train_data::Vector{Float64}, - params::Dict) +include("Interface.jl") +include("SNAPLearningProblem.jl") -Creates a potential learning problem. -""" -function learning_problem(dft_train_data::Vector{Float64}, - ref_train_data::Vector{Float64}, - params::Dict) - lp = Symbol(params["global"]["potential"]) - return @eval $lp($dft_train_data, $ref_train_data, $params) end - -""" - learn(p::PotentialLearningProblem, params::Dict) - -Fits the potentials, forces, and stresses against the DFT and reference data -using the configuration parameters. -""" -function learn(p::PotentialLearningProblem, params::Dict) - if params["solver"]["name"] == "\\" - p.β = p.A \ p.b - elseif params["solver"]["name"] == "NelderMead" - β0 = zeros(length(p.A[1,:])) - prob = GalacticOptim.OptimizationProblem( (x, pars) -> error(x, p), β0, []) - p.β = GalacticOptim.solve(prob, NelderMead(), maxiters=500) - elseif params["solver"]["name"] == "BBO" - β0 = zeros(p.cols) - lb0 = -0.5ones(p.cols) - ub0 = 0.5ones(p.cols) - prob = GalacticOptim.OptimizationProblem( (x, pars) -> error(x, p), β0, [], - ub = ub0, lb = lb0) - p.β = solve(prob, BBO(); maxiters=500) - end -end - -""" - error_metrics(p::PotentialLearningProblem, val_data::Vector{Float64}, params::Dict) - -Calculates error metrics: max_rel_error, mae, rmse -""" -function error_metrics(p::PotentialLearningProblem, val_data::Vector{Float64}, params::Dict) - fit_forces = params["global"]["fit_forces"] - rcutfac = params["global"]["rcutfac"] - no_atoms_per_conf = params["global"]["no_atoms_per_conf"] - no_train_atomic_conf = params["global"]["no_train_atomic_conf"] - no_atomic_conf = params["global"]["no_atomic_conf"] - no_val_atomic_conf = no_atomic_conf - no_train_atomic_conf - - global metrics = Dict() - metrics["energy"] = Dict() - - # Energy metrics - energies = val_data[1:no_val_atomic_conf] - fitted_energies = [potential_energy(p, j) for j in no_train_atomic_conf+1:no_atomic_conf] - metrics["energy"]["max_rel_error"] = - maximum(abs.(fitted_energies .- energies) ./ fitted_energies) - metrics["energy"]["mae"] = - sum(abs.(fitted_energies .- energies)) / length(energies) - metrics["energy"]["rmse"] = - sqrt(sum((fitted_energies .- energies).^2) / length(energies)) - - # Force metrics - if fit_forces - forces_ = val_data[no_val_atomic_conf+1:end] - fitted_forces = linearize([forces(p, j) - for j in no_train_atomic_conf+1:no_atomic_conf]) - metrics["force"] = Dict() - metrics["force"]["max_rel_error"] = - maximum(abs.((fitted_forces .- forces_) ./ forces_)) - metrics["force"]["mae"] = - sum(abs.(fitted_forces .- forces_)) / length(forces_) - metrics["force"]["rmse"] = - sqrt(sum((fitted_forces .- forces_).^2) / length(forces_)) - end - - # TODO: Stress metrics - - return metrics -end - -end - diff --git a/src/Potentials/BornMayer.jl b/src/Potentials/BornMayer.jl deleted file mode 100644 index eef5994e..00000000 --- a/src/Potentials/BornMayer.jl +++ /dev/null @@ -1,28 +0,0 @@ -""" - Born-Mayer Potential -""" -mutable struct BornMayer <: Potential - A::Float64 - ρ::Float64 -end - -""" - BornMayer(params::Dict) - -Creates a BM potential. -""" -function BornMayer(params::Dict) - A = params["A"] - ρ = params["ρ"] - return BornMayer(A, ρ) -end - -""" - potential_energy(p::BornMayer, r::Position, args...) - -Calculates Born-Mayer potential energy. -""" -function potential_energy(p::BornMayer, r::Position, args...) - return p.A * exp(-norm(r) / p.ρ) -end - diff --git a/src/Potentials/Coulomb.jl b/src/Potentials/Coulomb.jl deleted file mode 100644 index 1e09c6b7..00000000 --- a/src/Potentials/Coulomb.jl +++ /dev/null @@ -1,32 +0,0 @@ -""" - Coulomb Potential -""" -mutable struct Coulomb <: Potential - q_1::Float64 - q_2::Float64 - ε0::Float64 -end - -""" - Coulomb(params::Dict) - -Creates a Coulomb potential. -""" -function Coulomb(params::Dict) - # Creates the Coulomb model - q_1 = params["q_1"] - q_2 = params["q_2"] - ε0 = params["ε0"] - return Coulomb(q_1, q_2, ε0) -end - -""" - potential_energy(p::Coulomb, r::Position, args...) - -Calculates Coulomb potential energy. -""" -function potential_energy(p::Coulomb, r::Position, args...) - return p.q_1 * p.q_2 / (4.0 * π * p.ε0 * norm(r)) -end - - diff --git a/src/Potentials/GaN.jl b/src/Potentials/GaN.jl deleted file mode 100644 index 61da6605..00000000 --- a/src/Potentials/GaN.jl +++ /dev/null @@ -1,43 +0,0 @@ -""" - GaN Potential - -See 10.1088/1361-648X/ab6cbe -""" -mutable struct GaN <: Potential - lj_Ga_Ga::LennardJones - lj_N_N::LennardJones - bm_Ga_N::BornMayer - c::Coulomb - no_Ga::Int64 - no_N::Int64 -end - -function GaN(params::Dict) - # Creates the GaN model - lj_Ga_Ga = LennardJones(params["ε_Ga_Ga"], params["σ_Ga_Ga"]) - lj_N_N = LennardJones(params["ε_N_N"], params["σ_N_N"]) - bm_Ga_N = BornMayer(params["A_Ga_N"], params["ρ_Ga_N"]) - c = Coulomb(params["q_Ga"], params["q_N"], params["ε0"]) - gan = GaN(lj_Ga_Ga, lj_N_N, bm_Ga_N, c, params["no_Ga"], params["no_N"]) - return gan -end - -""" - potential_energy(p::GaN, r::Position, args...) - -Calculates GaN potential energy. -""" -function potential_energy(p::GaN, r::Position, args...) - i = args[1]; j = args[2] - if i <= p.no_Ga && j <= p.no_N # Ga-Ga interaction - return potential_energy(p.c, r) + potential_energy(p.lj_Ga_Ga, r) - elseif i > p.no_Ga && j > p.no_N # N-N interaction - return potential_energy(p.c, r) + potential_energy(p.lj_N_N, r) - else # Ga-N or N-Ga interaction - return potential_energy(p.c, r) + potential_energy(p.bm_Ga_N, r) - end - -end - - - diff --git a/src/Potentials/LennardJones.jl b/src/Potentials/LennardJones.jl deleted file mode 100644 index 83e3cbc2..00000000 --- a/src/Potentials/LennardJones.jl +++ /dev/null @@ -1,29 +0,0 @@ -""" - Lennard-Jones Potential -""" -mutable struct LennardJones <: Potential - ε::Float64 - σ::Float64 -end - -""" - LennardJones(params::Dict) - -Creates the LennardJones potential. -""" -function LennardJones(params::Dict) - # Creates the LennardJones model - ε = params["ε"] - σ = params["σ"] - return LennardJones(ε, σ) -end - -""" - potential_energy(p::LennardJones, r::Position, args...) - -Calculates LennardJones potential energy. -""" -function potential_energy(p::LennardJones, r::Position, args...) - return 4.0 * p.ε * ((p.σ / norm(r))^12 - (p.σ / norm(r))^6) -end - diff --git a/src/Potentials/Potentials.jl b/src/Potentials/Potentials.jl deleted file mode 100644 index 6fa19488..00000000 --- a/src/Potentials/Potentials.jl +++ /dev/null @@ -1,69 +0,0 @@ -using Base: Float64 -using Zygote -using StaticArrays -const Position = SVector{3, Float64} -const Force = SVector{3, Float64} -abstract type Potential end - -include("LennardJones.jl") -include("BornMayer.jl") -include("Coulomb.jl") -include("GaN.jl") -include("ZBL.jl") -include("SNAP-LAMMPS.jl") - -""" - potential_energy(p::Potential, atomic_positions::Vector{Position}, rcutfac::Float64) - -Calculates the potential energy of a particular atomic configuration. -It is based on the atomic positions of the configuration, the rcutfac, and a -particular potential. -""" -function potential_energy(p::Potential, atomic_positions::Vector{Position}, rcutfac::Float64) - acc = 0.0 - for i = 1:length(atomic_positions) - for j = i:length(atomic_positions) - r_diff = (atomic_positions[i] - atomic_positions[j]) - if norm(r_diff) <= rcutfac && norm(r_diff) > 0.0 - acc += potential_energy(p, r_diff, i, j) #atom_type(i), atom_type(j)) - end - end - end - return acc -end - -""" - forces(p::Potential, atomic_positions::Vector{Position}, rcutfac::Float64) - -Calculates the forces of each atom in an atomic configuration. -""" -function forces(p::Potential, atomic_positions::Vector{Position}, rcutfac::Float64) - forces = Vector{Force}() - for i = 1:length(atomic_positions) - f_i = Force(0.0, 0.0, 0.0) - for j = 1:length(atomic_positions) - r_diff = atomic_positions[i] - atomic_positions[j] - if norm(r_diff) <= rcutfac && norm(r_diff) > 0.0 - ∇potential_energy(p, r, i, j) = - gradient(r -> potential_energy(p, r_diff + r, i, j), r)[1] - f_ij = -∇potential_energy(p, atomic_positions[i], atom_type(i), - atom_type(j)) - f_i += f_ij - end - end - push!(forces, f_i) - end - return forces -end - -""" - atom_type(i::Int64) - -Returns the atom type of the i-th atom of the configuration. -""" -function atom_type(i::Int64) - #TODO - return i -end - - diff --git a/src/Potentials/SNAP-LAMMPS.jl b/src/Potentials/SNAP-LAMMPS.jl deleted file mode 100644 index ef66dc04..00000000 --- a/src/Potentials/SNAP-LAMMPS.jl +++ /dev/null @@ -1,280 +0,0 @@ -using LAMMPS -using LinearAlgebra:norm - -""" - SNAP_LAMMPS is a PotentialLearningProblem, it is based on the SNAP - implementation of LAMMPS, which is accessed through LAMMPS.jl. - Mathematical formulation: A. P. Thompson et al. (10.1016/j.jcp.2014.12.018) -""" -mutable struct SNAP_LAMMPS <: PotentialLearningProblem - - path::String # Path of the example folder - β::Vector{Float64} # Fitted parameters - A::Matrix{Float64} # Matrix of potentials, forces, and stresses. - b::Vector{Float64} # DFT training data - Reference data - dft_data::Vector{Float64} # DFT training data - ref_data::Vector{Float64} # Reference data - no_atoms_per_type::Vector # No. of atoms per type - no_atoms_per_conf::Int64 # No. of atoms per atomic configurations - no_atomic_conf::Int64 # No. of atomic configurations - no_train_atomic_conf::Int64 # No. of trainning atomic configurations - rcutfac::Float64 # Scale factor applied to all cutoff radii (positive real) - rfac0::Float64 # Parameter in distance to angle conversion (0 < rcutfac < 1) - twojmax::Int64 # SNAP-LAMMPS parameter - cutoff_radii::Vector{Float64} # List of cutoff radii, one for each type - neighbor_weights::Vector{Float64} # List of neighbor weights, one for each type - ncoeff::Int64 # ncoeff-1 = no. of param. associated to an atom type - cols::Int64 # No. of columns of matrix `A` - numTypes::Int64 # No. of atom types - opt_pars::Dict # Optional parameters: rmin0, switchflag, - # bzeroflag, quadraticflag, chem, chemflag, - # bnormflag, wselfallflag, switchflag - fit_forces::Bool # Enable/disable force fitting - -end - - -""" - SNAP_LAMMPS(dft_data::Vector{Float64}, ref_data::Vector{Float64}, params::Dict) - -Creates a SNAP_LAMMPS. -""" -function SNAP_LAMMPS(dft_data::Vector{Float64}, ref_data::Vector{Float64}, params::Dict) - - β = [] - A = Matrix{Float64}(undef, 0, 0) - b = dft_data - ref_data - pars = params["global"] - path = pars["path"] - aux = pars["no_atoms_per_type"] - no_atoms_per_type = length(aux) > 1 ? aux : [aux] - no_atoms_per_conf = sum(no_atoms_per_type) - no_atomic_conf = pars["no_atomic_conf"] - no_train_atomic_conf = pars["no_train_atomic_conf"] - rcutfac = pars["rcutfac"] - rfac0 = pars["rfac0"] - twojmax = pars["twojmax"] - J = twojmax / 2.0 - ncoeff = round(Int, (J + 1) * (J + 2) * (( J + (1.5)) / 3. ) + 1) - cols = 2 * ncoeff - aux = pars["cutoff_radii"] - cutoff_radii = length(aux) > 1 ? aux : [aux] - aux = pars["neighbor_weights"] - neighbor_weights = length(aux) > 1 ? aux : [aux] - numTypes = pars["numTypes"] - - opt_pars = Dict() - if haskey(pars, "rmin0") opt_pars["rmin0"] = pars["rmin0"] end - if haskey(pars, "switchflag") opt_pars["switchflag"] = pars["switchflag"] end - if haskey(pars, "bzeroflag") opt_pars["bzeroflag"] = pars["bzeroflag"] end - if haskey(pars, "quadraticflag") opt_pars["quadraticflag"] = pars["quadraticflag"] end - if haskey(pars, "chem") opt_pars["chem"] = pars["chem"] end - if haskey(pars, "chemflag") opt_pars["chemflag"] = pars["chemflag"] end - if haskey(pars, "bnormflag") opt_pars["bnormflag"] = pars["bnormflag"] end - if haskey(pars, "wselfallflag") opt_pars["wselfallflag"] = pars["wselfallflag"] end - if haskey(pars, "switchflag") opt_pars["switchflag"] = pars["switchflag"] end - - fit_forces = pars["fit_forces"] - - p = SNAP_LAMMPS( path, β, A, b, dft_data, ref_data, no_atoms_per_type, no_atoms_per_conf, - no_atomic_conf, no_train_atomic_conf, rcutfac, rfac0, twojmax, - cutoff_radii, neighbor_weights, ncoeff, cols, numTypes, opt_pars, - fit_forces) - - p.A = calc_A(p) - - return p -end - -""" - error(β::Vector{Float64}, s::SNAP_LAMMPS) - -Error function needed to perform the learning process. -""" -function error(β::Vector{Float64}, s::SNAP_LAMMPS) - return norm(s.A * β - s.b) -end - -""" - get_bispectrums(lmp, data_path::String, p::SNAP_LAMMPS) - -Calculates the bispectrums components and its derivatives. -See https://docs.lammps.org/compute_sna_atom.html -""" -function get_bispectrums(lmp, data_path::String, p::SNAP_LAMMPS) - - args = "" - # scale factor applied to all cutoff radii (positive real) - args *= "$(p.rcutfac) " - # parameter in distance to angle conversion (0 < rcutfac < 1) - args *= "$(p.rfac0) " - # band limit for bispectrum components (non-negative integer) - args *= "$(p.twojmax) " - # R_1, R_2,… = list of cutoff radii, one for each type (distance units) - args *= join(["$r " for r in p.cutoff_radii]) - # w_1, w_2,… = list of neighbor weights, one for each type - args *= join(["$r " for r in p.neighbor_weights]) - # zero or more keyword/value pairs may be appended - # keyword = rmin0 or switchflag or bzeroflag or quadraticflag or chem or bnormflag or wselfallflag - args *= haskey(p.opt_pars, "rmin0") ? "rmin0 $(p.opt_pars["rmin0"]) " : "" - args *= haskey(p.opt_pars, "switchflag") ? "switchflag $(p.opt_pars["switchflag"]) " : "" - args *= haskey(p.opt_pars, "bzeroflag") ? "bzeroflag $(p.opt_pars["bzeroflag"]) " : "" - args *= haskey(p.opt_pars, "quadraticflag") ? "quadraticflag $(p.opt_pars["quadraticflag"]) " : "" - args *= haskey(p.opt_pars, "chem") ? "chem " * join(["$r " for r in p.opt_pars["chem"]]) * " " : "" - args *= haskey(p.opt_pars, "chemflag") ? "chemflag $(p.opt_pars["chemflag"]) " : "" - args *= haskey(p.opt_pars, "bnormflag") ? "bnormflag $(p.opt_pars["bnormflag"]) " : "" - args *= haskey(p.opt_pars, "wselfallflag") ? "wselfallflag $(p.opt_pars["wselfallflag"]) " : "" - args *= haskey(p.opt_pars, "switchflag") ? "switchflag $(p.opt_pars["switchflag"]) " : "" - - read_data_str = "read_data " * data_path - command(lmp, "log none") - command(lmp, "units metal") - command(lmp, "boundary p p p") - command(lmp, "atom_style atomic") - command(lmp, "atom_modify map array") - command(lmp, read_data_str) -# command(lmp, "pair_style hybrid/overlay zero 10.0 zbl 4.0 4.8") -# command(lmp, "pair_coeff * * zero") -# command(lmp, "pair_coeff * * zbl 73 73") - command(lmp, "pair_style zero $(p.rcutfac)") - command(lmp, "pair_coeff * *") - command(lmp, "compute PE all pe") - command(lmp, "compute S all pressure thermo_temp") - command(lmp, "compute SNA all sna/atom " * args) - command(lmp, "compute SNAD all snad/atom " * args) - command(lmp, "compute SNAV all snav/atom " * args) - command(lmp, "thermo_style custom pe") - command(lmp, "run 0") - - # Extract bispectrum - bs = extract_compute(lmp, "SNA", LAMMPS.API.LMP_STYLE_ATOM, - LAMMPS.API.LMP_TYPE_ARRAY) - deriv_bs = extract_compute(lmp, "SNAD", LAMMPS.API.LMP_STYLE_ATOM, - LAMMPS.API.LMP_TYPE_ARRAY) - return bs, deriv_bs -end - -""" - calc_A(params::Dict, p::SNAP_LAMMPS) - -Calculates the matrix `A` (See Eq. 13, 10.1016/j.jcp.2014.12.018). -This calculation requires accessing the SNAP implementation of LAMMPS. -""" -function calc_A(p::SNAP_LAMMPS) - - A = LMP(["-screen","none"]) do lmp - - A_potential = Array{Float64}(undef, p.no_train_atomic_conf, p.cols) - - A_forces = p.fit_forces ? Array{Float64}(undef, 3 * p.no_atoms_per_conf * - p.no_train_atomic_conf, p.cols) : Array{Float64}(undef, 0, p.cols) - - for j in 1:p.no_train_atomic_conf - data_path = joinpath(p.path, "DATA", string(j), "DATA") - bs, deriv_bs = get_bispectrums(lmp, data_path, p) - - # Create a row of the potential energy block - row = Vector{Float64}() - for no_atoms in p.no_atoms_per_type - push!(row, no_atoms) - for k in 1:(p.ncoeff-1) - acc = 0.0 - for n in 1:no_atoms - acc += bs[k, n] - end - push!(row, acc) - end - end - A_potential[j, :] = row - - if p.fit_forces - # Create a set of rows of the force block - k = (j - 1) * 3 * p.no_atoms_per_conf + 1 - for n = 1:p.no_atoms_per_conf - for c = [1, 2, 3] # component x, y, z - row = Vector{Float64}() - for t = 1:p.numTypes # e.g. 2 : Ga and N - a = 1 + (p.ncoeff-1) * (c-1) + 3 * (p.ncoeff-1) * (t-1) - b = a + p.ncoeff - 2 - row = [row; [0.0; deriv_bs[a:b, n]]] - end - A_forces[k, :] = row - k += 1 - end - end - end - - command(lmp, "clear") - end - return [A_potential; A_forces] - end - - return A -end - - -""" - potential_energy(p::Potential, j::Int64) - -Calculates the potential energy of a particular atomic configuration (j) using -the fitted parameters β. -This calculation requires accessing the SNAP implementation of LAMMPS. -""" -function potential_energy(p::PotentialLearningProblem, j::Int64) - - data_path = joinpath(p.path, "DATA", string(j), "DATA") - lmp = LMP(["-screen","none"]) - bs, deriv_bs = get_bispectrums(lmp, data_path, p) - - E_tot_acc = 0.0 - for (i, no_atoms) in enumerate(p.no_atoms_per_type) - for n in 1:no_atoms - E_atom_acc = p.β[p.ncoeff*(i-1)+1] - for k in p.ncoeff*(i-1)+2:i*p.ncoeff - k2 = k - p.ncoeff * (i - 1) - 1 - E_atom_acc += p.β[k] * bs[k2, n] - end - E_tot_acc += E_atom_acc - end - end - - command(lmp, "clear") - return E_tot_acc -end - -""" - forces(p::Potential, j::Int64) - -Calculates the forces of a particular atomic configuration (j) using the -fitted parameters β. -This calculation requires accessing the SNAP implementation of LAMMPS. -See https://docs.lammps.org/compute_sna_atom.html#compute-snad-atom-command -""" -function forces(p::PotentialLearningProblem, j::Int64) - - data_path = joinpath(p.path, "DATA", string(j), "DATA") - lmp = LMP(["-screen","none"]) - bs, deriv_bs = get_bispectrums(lmp, data_path, p) - - forces = Vector{Force}() - - for n = 1:p.no_atoms_per_conf - f = [0.0, 0.0, 0.0] - for c = [1, 2, 3] # component x, y, z - deriv_bs_row = [] - for t = 1:p.numTypes - a = 1 + (p.ncoeff-1) * (c-1) + 3 * (p.ncoeff-1) * (t-1) - b = a + p.ncoeff - 2 - deriv_bs_row = [deriv_bs_row; [0.0; deriv_bs[a:b, n]]] - end - f[c] = sum(deriv_bs_row .* p.β) - end - push!(forces, Force(f)) - end - - command(lmp, "clear") - return forces -end - - - diff --git a/src/Potentials/ZBL.jl b/src/Potentials/ZBL.jl deleted file mode 100644 index 6d6da6f1..00000000 --- a/src/Potentials/ZBL.jl +++ /dev/null @@ -1,71 +0,0 @@ -""" - Ziegler-Biersack-Littmark (ZBL) Potential - -See https://docs.lammps.org/pair_zbl.html -""" -mutable struct ZBL <: Potential - ε0::Float64 # Electrical permittivity of vacuum. - e::Float64 # Electron charge. - zi::Float64 # Atomic number of the atom i. - zj::Float64 # Atomic number of the atom j. - a::Float64 - rcutfac::Float64 # Rcut -end - -""" - ZBL(params::Dict) - -Creates a ZBL potential. -""" -function ZBL(params::Dict) - # Creates the ZBL model - ε0 = params["ε0"] - e = params["e"] - zi = params["zi"] - zj = params["zj"] - a = 0.46850 / (zi^0.23 + zj^0.23) - rcutfac = params["rcutfac"] - return ZBL(ε0, e, zi, zj, a, rcutfac) -end - -""" - potential_energy(p::ZBL, r::Position, args...) - -Calculates the potential energy of ZBL with a switching function. -""" -function potential_energy(p::ZBL, r::Position, args...) - return zbl(p, norm(r)) + S(p, norm(r)) -end - -""" - zbl(p::ZBL, r::Float64) - -ZBL function without the switching function S. -""" -function zbl(p::ZBL, r::Float64) - return 1 / (4.0 * π * p.ε0) * p.zi * p.zj * p.e^2 / r * ϕ(p, r / p.a) -end - -""" - S(r) - -Switching function that ramps the energy, force, and curvature smoothly to zero -between an inner and outer cutoff. Here, the inner and outer cutoff are the same -for all pairs of atom types. -""" -function S(p::ZBL, r::Float64) - return r <= p.rcutfac ? 0.5 * (cos(pi * r / p.rcutfac) + 1.0) : 0 -end - -# TODO: check this function: "exp" or "e"? -""" - ϕ(p::ZBL, x::Float64) - -Auxiliary function, necessary to calculate ZBL. -""" -function ϕ(p::ZBL, x::Float64) - return 0.18175 * exp(-3.1998*x) + 0.50986 * exp(-0.94229*x) + - 0.28022 * exp(-0.40290*x) + 0.2817 * exp(-0.20162*x) -end - - diff --git a/src/SNAPLearningProblem.jl b/src/SNAPLearningProblem.jl new file mode 100644 index 00000000..7b644f43 --- /dev/null +++ b/src/SNAPLearningProblem.jl @@ -0,0 +1,96 @@ + +# Learning problem ############################################################# + +""" + SmallSNAPLP{D, T} + +SNAP learning problem for small systems +""" +struct SmallSNAPLP{D, T} <: LearningProblem{D, T} + # SNAP potential + snap::SNAP{D, T} + + # SNAP matrix (depends on the hyper-parameters) + A::Matrix{T} + ATA::Matrix{T} # A^T * A, optional + + # Covariance + Q::Diagonal{T} + invQ::Diagonal{T} # inverse of A, optional + + # Input data + y::Vector{T} # linearize(training_dft_data) - linearize(training_ref_data) + ATy::Matrix{T} # A^T * A, optional + training_dft_data::DFTData{D, T} + training_ref_data::DFTData{D, T} + validation_dft_data::DFTData{D, T} + validation_ref_data::DFTData{D, T} +end + + +# Hyper-parameter optimization ################################################# + +""" + hyperparam_loss(hyperparams::Vector{T}, lp::SmallSNAPLP{D, T}) + +SNAP hyper-parameter loss function +""" +function hyperparam_loss(hyperparams::Vector{T}, lp::SmallSNAPLP{D, T}) +# return ... +end + + +""" + learn(lp::SNAPLP{T}, loss, s::SDPOpt{T}) + +Learning function: using SDPOpt to optimize the hyper-parameters +""" +function learn(lp::SNAPLP{T}, loss, s::SDPOpt{T}) +# ...hyperparam_loss... +# lp.snap.rcutfac = ... +# lp.snap.twojmax = ... +end + + +# β-parameter optimization ##################################################### + +""" + learn(lp::SmallSNAPLP{T}, s::LeastSquaresOpt{T}) + +Learning function: using normal equations and qr decomposition to learn main parameters +""" +function learn(lp::SmallSNAPLP{T}, s::LeastSquaresOpt{T}) + lp.snap.β = (lp.A' * lp.A) \ (lp.A' * lp.y) +end + +""" + learn(lp::SmallSNAPLP{T}, s::QRLinearOpt{T}) + +Learning function: using QR decomposition to learn main parameters +""" +function learn(lp::SmallSNAPLP{T}, s::QRLinearOpt{T}) + lp.snap.β = lp.A \ lp.y # or... qr(A,Val(true)) \ y +end + +""" + β_loss(β::Vector{T}, lp::SmallSNAPLP{D, T}) + +Loss function: using NelderMeadOpt from GalacticOptim to optimize the parameters +""" +function β_loss(β::Vector{T}, lp::SmallSNAPLP{D, T}) + e = lp.A * β - lp.y + return transpose(e) * inv(lp.Q) * e +end + +""" + learn(lp::SmallSNAPLP{T}, loss, s::NelderMeadOpt{T}) + +Learning function: using NelderMeadOpt from GalacticOptim to optimize the parameters +""" +function learn(lp::SmallSNAPLP{T}, loss, s::NelderMeadOpt{T}) + β0 = zeros(length(lp.A[1,:])) + prob = GalacticOptim.OptimizationProblem((x, pars)->loss(x, lp), β0, []) + lp.β = GalacticOptim.solve(prob, NelderMead(), maxiters=s.maxiters) +end + + diff --git a/test/GaN-SNAP-LAMMPS-Test.jl b/test/GaN-SNAP-LAMMPS-Test.jl deleted file mode 100644 index dd17c79f..00000000 --- a/test/GaN-SNAP-LAMMPS-Test.jl +++ /dev/null @@ -1,25 +0,0 @@ -using Test - -@testset "GaN-SNAP-LAMMPS" begin - - params = get_conf_params("../examples/GaN-SNAP-LAMMPS/") - - # Get DFT data - dft_train_data, dft_val_data = generate_data("dft", params) - - # Get reference data - ref_train_data, ref_val_data = generate_data("ref", params) - - # Get potential learning problem (e.g. A β = b) - snap = learning_problem(dft_train_data, ref_train_data, params) - - # Solve potential learning problem (e.g. β = A \ b) - learn(snap, params) - - # Validate potentials, forces, and stresses - m = error_metrics(snap, dft_val_data - ref_val_data, params) - - @test m["energy"]["max_rel_error"] < 0.1 - -end - diff --git a/test/runtests.jl b/test/runtests.jl index ac19d4ec..e4a33cae 100644 --- a/test/runtests.jl +++ b/test/runtests.jl @@ -1,4 +1,4 @@ using PotentialLearning using Test -include("GaN-SNAP-LAMMPS-Test.jl") +#include("SNAP-test.jl") From c107edbcb0165565a52235e24731e5279c2ab0ab Mon Sep 17 00:00:00 2001 From: Emmanuel Lujan Date: Tue, 30 Nov 2021 19:01:32 -0500 Subject: [PATCH 02/35] progress in refactor --- Project.toml | 2 +- examples/SNAP_learning.jl | 183 ++++++++++++++++++++++++++++++++----- src/Interface.jl | 16 +++- src/SNAPLearningProblem.jl | 11 ++- 4 files changed, 176 insertions(+), 36 deletions(-) diff --git a/Project.toml b/Project.toml index aff6f8ce..40b2ef67 100644 --- a/Project.toml +++ b/Project.toml @@ -1,6 +1,6 @@ name = "PotentialLearning" uuid = "82b0a93c-c2e3-44bc-a418-f0f89b0ae5c2" -authors = ["Emmanuel Lujan and contributors"] +authors = ["CESMIX Team"] version = "0.1.0" [deps] diff --git a/examples/SNAP_learning.jl b/examples/SNAP_learning.jl index 9d605d29..e77b0d1b 100644 --- a/examples/SNAP_learning.jl +++ b/examples/SNAP_learning.jl @@ -1,43 +1,176 @@ -using AtomsBase, DFT, InteratomicPotentials, PotentialLearning +#] activate ../../ElectronicStructure.jl/ +#] activate ../ -function gen_atomic_geom() - box = [[1, 0, 0], [0, 1, 0], [0, 0, 1]]u"m" - bcs = [Periodic(), Periodic(), DirichletZero()] - positions = [0.25 0.25 0.25; 0.75 0.75 0.75]u"m" - elems = [elements[:C], elements[:C]] +using Unitful, PeriodicTable, StaticArrays, LinearAlgebra +using AtomsBase +using InteratomicPotentials +using ElectronicStructure +using .PotentialLearning - atom1 = StaticAtom(SVector{3}(positions[1,:]),elems[1]) - atom2 = StaticAtom(SVector{3}(positions[2,:]),elems[2]) +################################################################################ +# InteratomicPotentials.jl ##################################################### +################################################################################ - aos = FlexibleSystem(box, bcs, [atom1, atom2]) - #soa = FastSystem(box, bcs, positions, elems) - return [aos, aos] +# Modifications to InteratomicPotentials.jl +# TODO: Discuss parametric types {D} + +abstract type ArbitraryPotential{D} end +abstract type EmpiricalPotential{D} <: ArbitraryPotential{D} end + +# TODO: Unitful.Energy, Unitful.Length +mutable struct LennardJones{D} <: EmpiricalPotential{D} + ϵ::Unitful.Energy + σ::Unitful.Length +end + +function potential_energy(r::SVector, p::LennardJones) + d = p.σ / norm(r) + return 4.0 * p.ϵ * ( d^12 - d^6 ) +end + +# TODO: New functions needed in "gen_test_data" + +function potential_energy(s::AbstractSystem, p::ArbitraryPotential) + N = size(s)[1] + return sum([potential_energy(position(getindex(s,i)) - position(getindex(s,j)), p) + for i in 1:N for j in i+1:N]) +end + +function forces(s::AbstractSystem{D}, p::ArbitraryPotential{D}) where {D} + N = size(s)[1] + return [ SVector{D}(zeros(D) * 1.0u"N") for i in 1:N ] +end + +function virial(s::AbstractSystem{D}, p::ArbitraryPotential{D}) where {D} + return 0.0 end -function gen_test_data(p::InteratomicPotential{D, T} - atomic_confs::Vector{AbstractSystem{D, T}}) - energies = [ energy(a, p) for s in atomic_confs ] - forces = [ forces(a, p) for s in atomic_confs ] - stresses = [ stresses(a, p) for s in atomic_confs ] - data = SmallDFTData{D, T}(energies, forces, stresses) - return data +function virial_stress(s::AbstractSystem{D}, p::ArbitraryPotential{D}) where {D} + return SMatrix{D, D}(zeros(D, D)) +end + +#function SNAP(rcutfac::Float64, twojmax::Int, num_atom_types::Int) +# keywords = SNAPkeywords(0, 0, 0, 0, 0) +# num_coeffs = get_num_coeffs(twojmax) +# return SNAP(zeros(num_atom_types * num_coeffs + 1), rcutfac, twojmax, keywords) +#end + +function inter_pot_conf(atomic_confs::Vector) + atom_names = nothing + radii = [3.5] + weights = [1.0] + boundary_type = ["p", "p", "p"] + units = "lj" + v = zeros(D) + new_atomic_confs = [] + for c in atomic_confs + + atoms = Vector{Atom}(undef, 0) + angles = Vector{Angle}(undef, 0) + bonds = Vector{Bond}(undef, 0) + impropers = Vector{Improper}(undef, 0) + dihedrals = Vector{Dihedral}(undef, 0) + + num_atoms = length(c) + num_atom_types = length(unique(species.(c))) + num_bond_types = 0 + num_angle_types = 0 + num_dihedral_types = 0 + num_improper_types = 0 + + x_bounds = [0.0, bounding_box(c)[1][1].val] + y_bounds = [0.0, bounding_box(c)[2][2].val] + z_bounds = [0.0, bounding_box(c)[3][3].val] + + domain = Domain(SVector{D}([x_bounds, y_bounds, z_bounds]), SVector{D}(boundary_type)) + + if length(radii) != num_atom_types + radii = radii[1] .* ones(num_atom_types) + end + if length(weights) != num_atom_types + weights = weights .* ones(num_atom_types) + end + + masses = unique(atomic_mass.(c)) + + if atom_names == nothing + atom_names = [Symbol(i) for i = 1:num_atom_types] + end + + atoms = [] + for (s, p) in zip(species(c), position(c)) + p2 = [p[1].val, p[2].val, p[3].val] + push!(atoms, Atom(s.atomic_mass.val, p2, v)) + end + + new_c = Configuration(atoms, num_atom_types, + angles, num_angle_types, + bonds, num_bond_types, + impropers, num_improper_types, + dihedrals, num_dihedral_types, + atom_names, masses, + radii, weights, + domain, units) + push!(new_atomic_confs, new_c) + end + return new_atomic_confs +end + + + +################################################################################ +# Learning example ############################################################# +################################################################################ + +""" + gen_test_atomic_conf(D) + +Generate test atomic configurations +""" +function gen_test_atomic_conf(D, L) + # Domain + box = [[1.0, 0.0, 0.0], [0.0, 1.0, 0.0], [0.0, 0.0, 1.0]] * L + # Boundary conditions + bcs = [Periodic(), Periodic(), DirichletZero()] + # No. of atoms per configuration + N = 100 + # No. of configurations + M = 20 + c = elements[:C] + # Define atomic configurations + atomic_confs = [] + for j in 1:M + atoms = [] + for i in 1:N + pos = SVector{D}(rand(D)*L...) + atom = StaticAtom(pos,c) + push!(atoms, atom) + end + push!(atomic_confs, FlexibleSystem(box, bcs, atoms)) + end + return atomic_confs end # Define parametric types -D = 3; T = Float32 +D = 3; L = 1.0u"cm"; E = 1.0u"J" # Generate atomic configurations: domain and particles (position, velocity, etc) -atomic_confs = gen_atomic_conf() +atomic_confs = gen_test_atomic_conf(D, L) # Generate learning data -lj = LennardJones{D, T}(1.657e-21u"J", 0.34u"nm") -data = gen_test_data(lj, atomic_confs) +lj = LennardJones{D}(1.657e-21u"J", 0.34u"nm") +data = gen_test_data(D, atomic_confs, lj) # Define potential -snap = SNAP{D, T}(atomic_confs) +rcutfac = 0.1; twojmax = 2 +inter_pot_atomic_confs = inter_pot_conf(atomic_confs) +snap = SNAP(rcutfac, twojmax, inter_pot_atomic_confs[1]) # Define learning problem -lp = SmallSNAPLP{D, T}(snap, data) +lp = SmallSNAPLP{D}(snap, data) #HINT: get_snap(r::Vector{Configuration}, p; dim = 3, reference = true) # Learn :-) -learn(lp, LeastSquaresOpt{T}()) +#learn(lp, LeastSquaresOpt{T}()) + + + diff --git a/src/Interface.jl b/src/Interface.jl index 54147e4f..a7d2d93e 100644 --- a/src/Interface.jl +++ b/src/Interface.jl @@ -4,8 +4,14 @@ # ################################################################################ -using GalacticOptim, Optim -using BlackBoxOptim +using ElectronicStructure + +using GalacticOptim, Optim, BlackBoxOptim +using LinearAlgebra + +export LearningProblem, LearningOptimizer +export SDPOpt, LeastSquaresOpt, QRLinearOpt, NelderMeadOpt +export loss, learn # Abstract types ############################################################### @@ -64,7 +70,7 @@ end `params`: parameters to be fitted `opt`: learning optimizer """ -function loss(params::Vector{T}, opt::LearningOptimizer{D, T}) end +function loss(params::Vector{T}, opt::LearningOptimizer{D, T}) where {T, D} end """ learn(lp::LearningProblem{D, T}, opt::LearningOptimizer{D, T}) @@ -72,7 +78,7 @@ function loss(params::Vector{T}, opt::LearningOptimizer{D, T}) end `lp`: learning problem `opt`: learning optimizer """ -function learn(lp::LearningProblem{D, T}, opt::LearningOptimizer{D, T}) end +function learn(lp::LearningProblem{D, T}, opt::LearningOptimizer{D, T}) where {T, D} end """ learn(lp::LearningProblem{D, T}, opt::LearningOptimizer{D, T}, loss) @@ -81,5 +87,5 @@ function learn(lp::LearningProblem{D, T}, opt::LearningOptimizer{D, T}) end `opt`: learning optimizer `loss`: loss function """ -function learn(lp::LearningProblem{D, T}, opt::LearningOptimizer{D, T}, loss) end +function learn(lp::LearningProblem{D, T}, opt::LearningOptimizer{D, T}, loss) where {T, D} end diff --git a/src/SNAPLearningProblem.jl b/src/SNAPLearningProblem.jl index 7b644f43..2efcab55 100644 --- a/src/SNAPLearningProblem.jl +++ b/src/SNAPLearningProblem.jl @@ -1,6 +1,7 @@ # Learning problem ############################################################# + """ SmallSNAPLP{D, T} @@ -8,7 +9,7 @@ SNAP learning problem for small systems """ struct SmallSNAPLP{D, T} <: LearningProblem{D, T} # SNAP potential - snap::SNAP{D, T} + snap::SNAP # SNAP matrix (depends on the hyper-parameters) A::Matrix{T} @@ -21,10 +22,10 @@ struct SmallSNAPLP{D, T} <: LearningProblem{D, T} # Input data y::Vector{T} # linearize(training_dft_data) - linearize(training_ref_data) ATy::Matrix{T} # A^T * A, optional - training_dft_data::DFTData{D, T} - training_ref_data::DFTData{D, T} - validation_dft_data::DFTData{D, T} - validation_ref_data::DFTData{D, T} + training_dft_data::SmallESData{D} + training_ref_data::SmallESData{D} + validation_dft_data::SmallESData{D} + validation_ref_data::SmallESData{D} end From 0adc41a44862272e40327127cc7d27ff2ca3ddfa Mon Sep 17 00:00:00 2001 From: Emmanuel Lujan Date: Wed, 1 Dec 2021 01:08:22 -0500 Subject: [PATCH 03/35] progress on refactor --- examples/SNAP_learning.jl | 128 ++----------------------------------- src/Interface.jl | 6 +- src/SNAPLearningProblem.jl | 27 ++++++-- 3 files changed, 29 insertions(+), 132 deletions(-) diff --git a/examples/SNAP_learning.jl b/examples/SNAP_learning.jl index e77b0d1b..b6ce7dd6 100644 --- a/examples/SNAP_learning.jl +++ b/examples/SNAP_learning.jl @@ -1,126 +1,12 @@ -#] activate ../../ElectronicStructure.jl/ -#] activate ../ +# Learning example ############################################################# +include("../src/PotentialLearning.jl") using Unitful, PeriodicTable, StaticArrays, LinearAlgebra using AtomsBase -using InteratomicPotentials using ElectronicStructure +using InteratomicPotentials using .PotentialLearning -################################################################################ -# InteratomicPotentials.jl ##################################################### -################################################################################ - -# Modifications to InteratomicPotentials.jl -# TODO: Discuss parametric types {D} - -abstract type ArbitraryPotential{D} end -abstract type EmpiricalPotential{D} <: ArbitraryPotential{D} end - -# TODO: Unitful.Energy, Unitful.Length -mutable struct LennardJones{D} <: EmpiricalPotential{D} - ϵ::Unitful.Energy - σ::Unitful.Length -end - -function potential_energy(r::SVector, p::LennardJones) - d = p.σ / norm(r) - return 4.0 * p.ϵ * ( d^12 - d^6 ) -end - -# TODO: New functions needed in "gen_test_data" - -function potential_energy(s::AbstractSystem, p::ArbitraryPotential) - N = size(s)[1] - return sum([potential_energy(position(getindex(s,i)) - position(getindex(s,j)), p) - for i in 1:N for j in i+1:N]) -end - -function forces(s::AbstractSystem{D}, p::ArbitraryPotential{D}) where {D} - N = size(s)[1] - return [ SVector{D}(zeros(D) * 1.0u"N") for i in 1:N ] -end - -function virial(s::AbstractSystem{D}, p::ArbitraryPotential{D}) where {D} - return 0.0 -end - -function virial_stress(s::AbstractSystem{D}, p::ArbitraryPotential{D}) where {D} - return SMatrix{D, D}(zeros(D, D)) -end - -#function SNAP(rcutfac::Float64, twojmax::Int, num_atom_types::Int) -# keywords = SNAPkeywords(0, 0, 0, 0, 0) -# num_coeffs = get_num_coeffs(twojmax) -# return SNAP(zeros(num_atom_types * num_coeffs + 1), rcutfac, twojmax, keywords) -#end - -function inter_pot_conf(atomic_confs::Vector) - atom_names = nothing - radii = [3.5] - weights = [1.0] - boundary_type = ["p", "p", "p"] - units = "lj" - v = zeros(D) - new_atomic_confs = [] - for c in atomic_confs - - atoms = Vector{Atom}(undef, 0) - angles = Vector{Angle}(undef, 0) - bonds = Vector{Bond}(undef, 0) - impropers = Vector{Improper}(undef, 0) - dihedrals = Vector{Dihedral}(undef, 0) - - num_atoms = length(c) - num_atom_types = length(unique(species.(c))) - num_bond_types = 0 - num_angle_types = 0 - num_dihedral_types = 0 - num_improper_types = 0 - - x_bounds = [0.0, bounding_box(c)[1][1].val] - y_bounds = [0.0, bounding_box(c)[2][2].val] - z_bounds = [0.0, bounding_box(c)[3][3].val] - - domain = Domain(SVector{D}([x_bounds, y_bounds, z_bounds]), SVector{D}(boundary_type)) - - if length(radii) != num_atom_types - radii = radii[1] .* ones(num_atom_types) - end - if length(weights) != num_atom_types - weights = weights .* ones(num_atom_types) - end - - masses = unique(atomic_mass.(c)) - - if atom_names == nothing - atom_names = [Symbol(i) for i = 1:num_atom_types] - end - - atoms = [] - for (s, p) in zip(species(c), position(c)) - p2 = [p[1].val, p[2].val, p[3].val] - push!(atoms, Atom(s.atomic_mass.val, p2, v)) - end - - new_c = Configuration(atoms, num_atom_types, - angles, num_angle_types, - bonds, num_bond_types, - impropers, num_improper_types, - dihedrals, num_dihedral_types, - atom_names, masses, - radii, weights, - domain, units) - push!(new_atomic_confs, new_c) - end - return new_atomic_confs -end - - - -################################################################################ -# Learning example ############################################################# -################################################################################ """ gen_test_atomic_conf(D) @@ -129,11 +15,11 @@ Generate test atomic configurations """ function gen_test_atomic_conf(D, L) # Domain - box = [[1.0, 0.0, 0.0], [0.0, 1.0, 0.0], [0.0, 0.0, 1.0]] * L + box = [[11.0, 0.0, 0.0], [0.0, 11.0, 0.0], [0.0, 0.0, 11.0]] * L # Boundary conditions bcs = [Periodic(), Periodic(), DirichletZero()] # No. of atoms per configuration - N = 100 + N = 30 # No. of configurations M = 20 c = elements[:C] @@ -158,7 +44,7 @@ D = 3; L = 1.0u"cm"; E = 1.0u"J" atomic_confs = gen_test_atomic_conf(D, L) # Generate learning data -lj = LennardJones{D}(1.657e-21u"J", 0.34u"nm") +lj = LennardJones(1.657e-21u"J", 0.34u"nm") data = gen_test_data(D, atomic_confs, lj) # Define potential @@ -167,7 +53,7 @@ inter_pot_atomic_confs = inter_pot_conf(atomic_confs) snap = SNAP(rcutfac, twojmax, inter_pot_atomic_confs[1]) # Define learning problem -lp = SmallSNAPLP{D}(snap, data) #HINT: get_snap(r::Vector{Configuration}, p; dim = 3, reference = true) +#lp = SmallSNAPLP{D, Float32}(snap, data) # Learn :-) #learn(lp, LeastSquaresOpt{T}()) diff --git a/src/Interface.jl b/src/Interface.jl index a7d2d93e..b668e6e8 100644 --- a/src/Interface.jl +++ b/src/Interface.jl @@ -4,10 +4,8 @@ # ################################################################################ -using ElectronicStructure - -using GalacticOptim, Optim, BlackBoxOptim -using LinearAlgebra +using ElectronicStructure, InteratomicPotentials +using LinearAlgebra, GalacticOptim, Optim, BlackBoxOptim export LearningProblem, LearningOptimizer export SDPOpt, LeastSquaresOpt, QRLinearOpt, NelderMeadOpt diff --git a/src/SNAPLearningProblem.jl b/src/SNAPLearningProblem.jl index 2efcab55..31d372ca 100644 --- a/src/SNAPLearningProblem.jl +++ b/src/SNAPLearningProblem.jl @@ -1,4 +1,6 @@ +export SmallSNAPLP, hyperparam_loss, β_loss, learn + # Learning problem ############################################################# @@ -28,6 +30,17 @@ struct SmallSNAPLP{D, T} <: LearningProblem{D, T} validation_ref_data::SmallESData{D} end +function SmallSNAPLP(snap::SNAP, data::SmallESData) + +# A = get_snap(inter_pot_atomic_confs, snap) +# ATA = A' * A +# n = size(A)[1] +# Q = Diagonal(ones(n)) +# invQ = inv(Q) +# y = +# SNAP(snap, A, ) +end + # Hyper-parameter optimization ################################################# @@ -36,17 +49,17 @@ end SNAP hyper-parameter loss function """ -function hyperparam_loss(hyperparams::Vector{T}, lp::SmallSNAPLP{D, T}) +function hyperparam_loss(hyperparams::Vector{T}, lp::SmallSNAPLP{D, T}) where {D, T} # return ... end """ - learn(lp::SNAPLP{T}, loss, s::SDPOpt{T}) + learn(lp::SmallSNAPLP{T}, loss, s::SDPOpt{T}) Learning function: using SDPOpt to optimize the hyper-parameters """ -function learn(lp::SNAPLP{T}, loss, s::SDPOpt{T}) +function learn(lp::SmallSNAPLP{T}, loss, s::SDPOpt{T}) where {T} # ...hyperparam_loss... # lp.snap.rcutfac = ... # lp.snap.twojmax = ... @@ -60,7 +73,7 @@ end Learning function: using normal equations and qr decomposition to learn main parameters """ -function learn(lp::SmallSNAPLP{T}, s::LeastSquaresOpt{T}) +function learn(lp::SmallSNAPLP{T}, s::LeastSquaresOpt{T}) where {T} lp.snap.β = (lp.A' * lp.A) \ (lp.A' * lp.y) end @@ -69,7 +82,7 @@ end Learning function: using QR decomposition to learn main parameters """ -function learn(lp::SmallSNAPLP{T}, s::QRLinearOpt{T}) +function learn(lp::SmallSNAPLP{T}, s::QRLinearOpt{T}) where {T} lp.snap.β = lp.A \ lp.y # or... qr(A,Val(true)) \ y end @@ -78,7 +91,7 @@ end Loss function: using NelderMeadOpt from GalacticOptim to optimize the parameters """ -function β_loss(β::Vector{T}, lp::SmallSNAPLP{D, T}) +function β_loss(β::Vector{T}, lp::SmallSNAPLP{D, T}) where {D, T} e = lp.A * β - lp.y return transpose(e) * inv(lp.Q) * e end @@ -88,7 +101,7 @@ end Learning function: using NelderMeadOpt from GalacticOptim to optimize the parameters """ -function learn(lp::SmallSNAPLP{T}, loss, s::NelderMeadOpt{T}) +function learn(lp::SmallSNAPLP{T}, loss, s::NelderMeadOpt{T}) where {T} β0 = zeros(length(lp.A[1,:])) prob = GalacticOptim.OptimizationProblem((x, pars)->loss(x, lp), β0, []) lp.β = GalacticOptim.solve(prob, NelderMead(), maxiters=s.maxiters) From 67cdff044544bab2e7520d1c77d641e0873416b0 Mon Sep 17 00:00:00 2001 From: Emmanuel Lujan Date: Thu, 2 Dec 2021 15:48:29 -0500 Subject: [PATCH 04/35] progress on code refactor --- examples/SNAP_learning.jl | 2 +- src/SNAPLearningProblem.jl | 43 +++++++++++++++++++++++++++----------- 2 files changed, 32 insertions(+), 13 deletions(-) diff --git a/examples/SNAP_learning.jl b/examples/SNAP_learning.jl index b6ce7dd6..f72d4159 100644 --- a/examples/SNAP_learning.jl +++ b/examples/SNAP_learning.jl @@ -53,7 +53,7 @@ inter_pot_atomic_confs = inter_pot_conf(atomic_confs) snap = SNAP(rcutfac, twojmax, inter_pot_atomic_confs[1]) # Define learning problem -#lp = SmallSNAPLP{D, Float32}(snap, data) +lp = SmallSNAPLP(snap, inter_pot_atomic_confs, data) # Learn :-) #learn(lp, LeastSquaresOpt{T}()) diff --git a/src/SNAPLearningProblem.jl b/src/SNAPLearningProblem.jl index 31d372ca..54d936da 100644 --- a/src/SNAPLearningProblem.jl +++ b/src/SNAPLearningProblem.jl @@ -16,29 +16,48 @@ struct SmallSNAPLP{D, T} <: LearningProblem{D, T} # SNAP matrix (depends on the hyper-parameters) A::Matrix{T} ATA::Matrix{T} # A^T * A, optional - + # Covariance Q::Diagonal{T} - invQ::Diagonal{T} # inverse of A, optional + invQ::Diagonal{T} # inverse of Q, optional # Input data - y::Vector{T} # linearize(training_dft_data) - linearize(training_ref_data) - ATy::Matrix{T} # A^T * A, optional training_dft_data::SmallESData{D} training_ref_data::SmallESData{D} validation_dft_data::SmallESData{D} validation_ref_data::SmallESData{D} + y::Vector{T} # linearize(training_dft_data) - linearize(training_ref_data) + y_val::Vector{T} # linearize(validation_dft_data) - linearize(validation_ref_data) + ATy::Vector{T} # A^T * y, optional + end -function SmallSNAPLP(snap::SNAP, data::SmallESData) +function SmallSNAPLP(snap::SNAP, atomic_confs::Vector, data::SmallESData{D}; training_prop = 0.8) where {D} + m = floor(Int, length(data.energies) * training_prop) + n = floor(Int, length(data.forces) * training_prop) + + A = get_snap(atomic_confs[1:m], snap) + ATA = A' * A + nrows = size(A)[1] + Q = Diagonal(ones(nrows)) + invQ = inv(Q) + + training_dft_data = SmallESData{D}(data.energies[1:m], + data.forces[1:n], + data.stresses[1:m]) # TODO: @views? + validation_dft_data = SmallESData{D}(data.energies[m+1:end], + data.forces[n+1:end], + data.stresses[m+1:end]) # TODO: @views? + training_ref_data = training_dft_data # TODO: add ZBL, see PotentialLearning.jl in master + validation_ref_data = validation_dft_data # TODO: add ZBL, see PotentialLearning.jl in master + + y = linearize(training_dft_data) #- linearize(training_ref_data) + y_val = linearize(validation_dft_data) #- linearize(validation_ref_data) + ATy = A' * y + -# A = get_snap(inter_pot_atomic_confs, snap) -# ATA = A' * A -# n = size(A)[1] -# Q = Diagonal(ones(n)) -# invQ = inv(Q) -# y = -# SNAP(snap, A, ) + SmallSNAPLP(snap, A, ATA, Q, invQ, training_dft_data, training_ref_data, + validation_dft_data, validation_ref_data, y, y_val, ATy) end From 624501f77d9b4d49445ff8881c59b6efc976c4ba Mon Sep 17 00:00:00 2001 From: Emmanuel Lujan Date: Thu, 2 Dec 2021 20:07:51 -0500 Subject: [PATCH 05/35] progress in example --- examples/CW0_SNAP_Learning.jl | 75 +++++++++++++++++++++++++++++++++++ examples/SNAP_learning.jl | 62 ----------------------------- 2 files changed, 75 insertions(+), 62 deletions(-) create mode 100644 examples/CW0_SNAP_Learning.jl delete mode 100644 examples/SNAP_learning.jl diff --git a/examples/CW0_SNAP_Learning.jl b/examples/CW0_SNAP_Learning.jl new file mode 100644 index 00000000..c5dbedca --- /dev/null +++ b/examples/CW0_SNAP_Learning.jl @@ -0,0 +1,75 @@ +# SNAP learning/fitting example +# +# It shows a first integration of the following packages under development: +# AtomsBase.jl, ElectronicStructure.jl, InteratomicPotentials.jl, and PotentialLearning.jl +# + +import Pkg +Pkg.add("Unitful") +Pkg.add("PeriodicTable") +Pkg.add("StaticArrays") +Pkg.add("LinearAlgebra") +Pkg.add("AtomsBase") +Pkg.add(url="git@github.com:cesmix-mit/ElectronicStructure.jl.git") +Pkg.add(url="https://github.com/cesmix-mit/InteratomicPotentials.jl.git", rev="integrated-branch") +Pkg.add(url="https://github.com/cesmix-mit/PotentialLearning.jl.git", rev="refactor") + +using Unitful, PeriodicTable, StaticArrays, LinearAlgebra +using AtomsBase +using ElectronicStructure +using InteratomicPotentials +using PotentialLearning + +""" + gen_test_atomic_conf(D) + +Generate test atomic configurations +""" +function gen_test_atomic_conf(D) + # Domain + box = [[10.0, 0.0, 0.0], [0.0, 10.0, 0.0], [0.0, 0.0, 10.0]] * 1.0u"cm" + # Boundary conditions + bcs = [Periodic(), Periodic(), DirichletZero()] + # No. of atoms per configuration + N = 30 + # No. of configurations + M = 20 + # Element + c = elements[:C] + # Define atomic configurations + atomic_confs = [] + for j in 1:M + atoms = [] + for i in 1:N + pos = SVector{D}(rand(D)*L...) + atom = StaticAtom(pos,c) + push!(atoms, atom) + end + push!(atomic_confs, FlexibleSystem(box, bcs, atoms)) + end + return atomic_confs +end + +# Define parametric types +D = 3, T = Float64 # TODO: discuss which parametric types are necessary, define a common policy for all packages + +# Generate test atomic configurations: domain and particles (position, velocity, etc) +atomic_confs = gen_test_atomic_conf(D) + +# Generate learning data using Lennard Jones and the atomic configurations +lj = LennardJones(1.657e-21u"J", 0.34u"nm") +data = gen_test_data(D, atomic_confs, lj) + +# Define target potential: SNAP +rcutfac = 0.1; twojmax = 2 +inter_pot_atomic_confs = inter_pot_conf(atomic_confs) # TODO: remove after full integration with InteratomicPotentials.jl +snap = SNAP(rcutfac, twojmax, inter_pot_atomic_confs[1]) #TODO: improve interface, do not send a conf as argument + +# Define learning problem +lp = SmallSNAPLP(snap, inter_pot_atomic_confs, data) + +# Learn :-) +learn(lp, LeastSquaresOpt{D, T}()) + + + diff --git a/examples/SNAP_learning.jl b/examples/SNAP_learning.jl deleted file mode 100644 index f72d4159..00000000 --- a/examples/SNAP_learning.jl +++ /dev/null @@ -1,62 +0,0 @@ -# Learning example ############################################################# - -include("../src/PotentialLearning.jl") -using Unitful, PeriodicTable, StaticArrays, LinearAlgebra -using AtomsBase -using ElectronicStructure -using InteratomicPotentials -using .PotentialLearning - - -""" - gen_test_atomic_conf(D) - -Generate test atomic configurations -""" -function gen_test_atomic_conf(D, L) - # Domain - box = [[11.0, 0.0, 0.0], [0.0, 11.0, 0.0], [0.0, 0.0, 11.0]] * L - # Boundary conditions - bcs = [Periodic(), Periodic(), DirichletZero()] - # No. of atoms per configuration - N = 30 - # No. of configurations - M = 20 - c = elements[:C] - # Define atomic configurations - atomic_confs = [] - for j in 1:M - atoms = [] - for i in 1:N - pos = SVector{D}(rand(D)*L...) - atom = StaticAtom(pos,c) - push!(atoms, atom) - end - push!(atomic_confs, FlexibleSystem(box, bcs, atoms)) - end - return atomic_confs -end - -# Define parametric types -D = 3; L = 1.0u"cm"; E = 1.0u"J" - -# Generate atomic configurations: domain and particles (position, velocity, etc) -atomic_confs = gen_test_atomic_conf(D, L) - -# Generate learning data -lj = LennardJones(1.657e-21u"J", 0.34u"nm") -data = gen_test_data(D, atomic_confs, lj) - -# Define potential -rcutfac = 0.1; twojmax = 2 -inter_pot_atomic_confs = inter_pot_conf(atomic_confs) -snap = SNAP(rcutfac, twojmax, inter_pot_atomic_confs[1]) - -# Define learning problem -lp = SmallSNAPLP(snap, inter_pot_atomic_confs, data) - -# Learn :-) -#learn(lp, LeastSquaresOpt{T}()) - - - From fc304610da12066ab676cbb1afd813e500b264ca Mon Sep 17 00:00:00 2001 From: Emmanuel Lujan Date: Fri, 3 Dec 2021 12:43:35 -0500 Subject: [PATCH 06/35] small changes --- examples/CW0_SNAP_Learning.jl | 75 ----------------------------------- examples/README.md | 1 + src/SNAPLearningProblem.jl | 2 +- 3 files changed, 2 insertions(+), 76 deletions(-) delete mode 100644 examples/CW0_SNAP_Learning.jl create mode 100644 examples/README.md diff --git a/examples/CW0_SNAP_Learning.jl b/examples/CW0_SNAP_Learning.jl deleted file mode 100644 index c5dbedca..00000000 --- a/examples/CW0_SNAP_Learning.jl +++ /dev/null @@ -1,75 +0,0 @@ -# SNAP learning/fitting example -# -# It shows a first integration of the following packages under development: -# AtomsBase.jl, ElectronicStructure.jl, InteratomicPotentials.jl, and PotentialLearning.jl -# - -import Pkg -Pkg.add("Unitful") -Pkg.add("PeriodicTable") -Pkg.add("StaticArrays") -Pkg.add("LinearAlgebra") -Pkg.add("AtomsBase") -Pkg.add(url="git@github.com:cesmix-mit/ElectronicStructure.jl.git") -Pkg.add(url="https://github.com/cesmix-mit/InteratomicPotentials.jl.git", rev="integrated-branch") -Pkg.add(url="https://github.com/cesmix-mit/PotentialLearning.jl.git", rev="refactor") - -using Unitful, PeriodicTable, StaticArrays, LinearAlgebra -using AtomsBase -using ElectronicStructure -using InteratomicPotentials -using PotentialLearning - -""" - gen_test_atomic_conf(D) - -Generate test atomic configurations -""" -function gen_test_atomic_conf(D) - # Domain - box = [[10.0, 0.0, 0.0], [0.0, 10.0, 0.0], [0.0, 0.0, 10.0]] * 1.0u"cm" - # Boundary conditions - bcs = [Periodic(), Periodic(), DirichletZero()] - # No. of atoms per configuration - N = 30 - # No. of configurations - M = 20 - # Element - c = elements[:C] - # Define atomic configurations - atomic_confs = [] - for j in 1:M - atoms = [] - for i in 1:N - pos = SVector{D}(rand(D)*L...) - atom = StaticAtom(pos,c) - push!(atoms, atom) - end - push!(atomic_confs, FlexibleSystem(box, bcs, atoms)) - end - return atomic_confs -end - -# Define parametric types -D = 3, T = Float64 # TODO: discuss which parametric types are necessary, define a common policy for all packages - -# Generate test atomic configurations: domain and particles (position, velocity, etc) -atomic_confs = gen_test_atomic_conf(D) - -# Generate learning data using Lennard Jones and the atomic configurations -lj = LennardJones(1.657e-21u"J", 0.34u"nm") -data = gen_test_data(D, atomic_confs, lj) - -# Define target potential: SNAP -rcutfac = 0.1; twojmax = 2 -inter_pot_atomic_confs = inter_pot_conf(atomic_confs) # TODO: remove after full integration with InteratomicPotentials.jl -snap = SNAP(rcutfac, twojmax, inter_pot_atomic_confs[1]) #TODO: improve interface, do not send a conf as argument - -# Define learning problem -lp = SmallSNAPLP(snap, inter_pot_atomic_confs, data) - -# Learn :-) -learn(lp, LeastSquaresOpt{D, T}()) - - - diff --git a/examples/README.md b/examples/README.md new file mode 100644 index 00000000..2c143adc --- /dev/null +++ b/examples/README.md @@ -0,0 +1 @@ +See https://github.com/cesmix-mit/ComposableWorkflows diff --git a/src/SNAPLearningProblem.jl b/src/SNAPLearningProblem.jl index 54d936da..8f005638 100644 --- a/src/SNAPLearningProblem.jl +++ b/src/SNAPLearningProblem.jl @@ -123,7 +123,7 @@ Learning function: using NelderMeadOpt from GalacticOptim to optimize the parame function learn(lp::SmallSNAPLP{T}, loss, s::NelderMeadOpt{T}) where {T} β0 = zeros(length(lp.A[1,:])) prob = GalacticOptim.OptimizationProblem((x, pars)->loss(x, lp), β0, []) - lp.β = GalacticOptim.solve(prob, NelderMead(), maxiters=s.maxiters) + lp.snap.β = GalacticOptim.solve(prob, NelderMead(), maxiters=s.maxiters) end From ff961b63a8324706c8d75ae4d786e994940d3277 Mon Sep 17 00:00:00 2001 From: Emmanuel Lujan Date: Fri, 3 Dec 2021 14:57:29 -0500 Subject: [PATCH 07/35] allowing to chose what to fit: e or f or s --- src/SNAPLearningProblem.jl | 27 ++++++++++++++++++++------- 1 file changed, 20 insertions(+), 7 deletions(-) diff --git a/src/SNAPLearningProblem.jl b/src/SNAPLearningProblem.jl index 8f005638..2d56d771 100644 --- a/src/SNAPLearningProblem.jl +++ b/src/SNAPLearningProblem.jl @@ -32,21 +32,35 @@ struct SmallSNAPLP{D, T} <: LearningProblem{D, T} end -function SmallSNAPLP(snap::SNAP, atomic_confs::Vector, data::SmallESData{D}; training_prop = 0.8) where {D} - m = floor(Int, length(data.energies) * training_prop) - n = floor(Int, length(data.forces) * training_prop) +function SmallSNAPLP(snap::SNAP, atomic_confs::Vector, data::SmallESData{D}; + training_prop = 0.8, fit = [:e, :f, :s]) where {D} + + m = floor(Int, length(atomic_confs) * training_prop) + + n_e = floor(Int, length(data.energies) * training_prop) + n_f = n_e + floor(Int, length(data.forces) * length(data.forces[1]) * 3 * training_prop) + n_s = n_f + floor(Int, length(data.stresses) * sum([ 1 for j in 1:D for i in j:D ]) * training_prop) + + AA = get_snap(atomic_confs[1:m], snap) #TODO: get_snap should allow me to chose what to fit (e, f, or s) + A_e = AA[1:n_e, :] + A_f = AA[n_e+1:n_f, :] + A_s = AA[n_f+1:n_s, :] + + A = [] + if :e in fit A = A_e end + if :f in fit A = vcat(A, A_f) end + if :s in fit A = vcat(A, A_s) end - A = get_snap(atomic_confs[1:m], snap) ATA = A' * A nrows = size(A)[1] Q = Diagonal(ones(nrows)) invQ = inv(Q) training_dft_data = SmallESData{D}(data.energies[1:m], - data.forces[1:n], + data.forces[1:m], data.stresses[1:m]) # TODO: @views? validation_dft_data = SmallESData{D}(data.energies[m+1:end], - data.forces[n+1:end], + data.forces[m+1:end], data.stresses[m+1:end]) # TODO: @views? training_ref_data = training_dft_data # TODO: add ZBL, see PotentialLearning.jl in master validation_ref_data = validation_dft_data # TODO: add ZBL, see PotentialLearning.jl in master @@ -55,7 +69,6 @@ function SmallSNAPLP(snap::SNAP, atomic_confs::Vector, data::SmallESData{D}; tra y_val = linearize(validation_dft_data) #- linearize(validation_ref_data) ATy = A' * y - SmallSNAPLP(snap, A, ATA, Q, invQ, training_dft_data, training_ref_data, validation_dft_data, validation_ref_data, y, y_val, ATy) end From 9c5b6393264c876a406c48c66f8829e9ac2b809b Mon Sep 17 00:00:00 2001 From: Emmanuel Lujan Date: Fri, 3 Dec 2021 16:29:20 -0500 Subject: [PATCH 08/35] choosing traninig size and blocks to fit (e, f, s) --- src/SNAPLearningProblem.jl | 29 +++++++++++++++++++++-------- 1 file changed, 21 insertions(+), 8 deletions(-) diff --git a/src/SNAPLearningProblem.jl b/src/SNAPLearningProblem.jl index 2d56d771..a92f3455 100644 --- a/src/SNAPLearningProblem.jl +++ b/src/SNAPLearningProblem.jl @@ -33,13 +33,13 @@ struct SmallSNAPLP{D, T} <: LearningProblem{D, T} end function SmallSNAPLP(snap::SNAP, atomic_confs::Vector, data::SmallESData{D}; - training_prop = 0.8, fit = [:e, :f, :s]) where {D} + trainingsize = 0.8, fit = [:e, :f, :s]) where {D} - m = floor(Int, length(atomic_confs) * training_prop) + m = floor(Int, length(atomic_confs) * trainingsize) - n_e = floor(Int, length(data.energies) * training_prop) - n_f = n_e + floor(Int, length(data.forces) * length(data.forces[1]) * 3 * training_prop) - n_s = n_f + floor(Int, length(data.stresses) * sum([ 1 for j in 1:D for i in j:D ]) * training_prop) + n_e = floor(Int, length(data.energies) * trainingsize) + n_f = n_e + floor(Int, length(data.forces) * length(data.forces[1]) * 3 * trainingsize) + n_s = n_f + floor(Int, length(data.stresses) * sum([ 1 for j in 1:D for i in j:D ]) * trainingsize) AA = get_snap(atomic_confs[1:m], snap) #TODO: get_snap should allow me to chose what to fit (e, f, or s) A_e = AA[1:n_e, :] @@ -64,9 +64,21 @@ function SmallSNAPLP(snap::SNAP, atomic_confs::Vector, data::SmallESData{D}; data.stresses[m+1:end]) # TODO: @views? training_ref_data = training_dft_data # TODO: add ZBL, see PotentialLearning.jl in master validation_ref_data = validation_dft_data # TODO: add ZBL, see PotentialLearning.jl in master - - y = linearize(training_dft_data) #- linearize(training_ref_data) - y_val = linearize(validation_dft_data) #- linearize(validation_ref_data) + + y = [] + if :e in fit + y = linearize(training_dft_data.energies) #- linearize(training_ref_data.energies) + y_val = linearize(validation_dft_data.energies) #- linearize(validation_ref_data.energies) + end + if :f in fit + append!(y, linearize(training_dft_data.forces)) #- linearize(training_ref_data.forces) + append!(y_val, linearize(validation_dft_data.forces)) #- linearize(validation_ref_data.forces) + end + if :s in fit + append!(y, linearize(training_dft_data.stresses)) #- linearize(training_ref_data.stresses) + append!(y_val, linearize(validation_dft_data.stresses)) #- linearize(validation_ref_data.stresses) + end + ATy = A' * y SmallSNAPLP(snap, A, ATA, Q, invQ, training_dft_data, training_ref_data, @@ -74,6 +86,7 @@ function SmallSNAPLP(snap::SNAP, atomic_confs::Vector, data::SmallESData{D}; end + # Hyper-parameter optimization ################################################# """ From 88fd74f27bc1e7fbdcb9e53072841d10fd1f5da7 Mon Sep 17 00:00:00 2001 From: Emmanuel Lujan Date: Fri, 3 Dec 2021 23:17:40 -0500 Subject: [PATCH 09/35] improving validation variables in SmallSNAPLP --- src/SNAPLearningProblem.jl | 113 +++++++++++++++++++++---------------- 1 file changed, 64 insertions(+), 49 deletions(-) diff --git a/src/SNAPLearningProblem.jl b/src/SNAPLearningProblem.jl index a92f3455..864de582 100644 --- a/src/SNAPLearningProblem.jl +++ b/src/SNAPLearningProblem.jl @@ -10,79 +10,94 @@ export SmallSNAPLP, hyperparam_loss, β_loss, learn SNAP learning problem for small systems """ struct SmallSNAPLP{D, T} <: LearningProblem{D, T} - # SNAP potential - snap::SNAP - - # SNAP matrix (depends on the hyper-parameters) - A::Matrix{T} - ATA::Matrix{T} # A^T * A, optional - - # Covariance - Q::Diagonal{T} - invQ::Diagonal{T} # inverse of Q, optional - - # Input data + + # Training ################################# + snap::SNAP # SNAP potential + A::Matrix{T} # SNAP matrix + y::Vector{T} # DFT and reference data + ATA::Matrix{T} # A^T * A + ATy::Vector{T} # A^T * y + Q::Diagonal{T} # Covariance + invQ::Diagonal{T} # inverse of Q training_dft_data::SmallESData{D} training_ref_data::SmallESData{D} + + # Validation ############################### + A_val::Matrix{T} # SNAP matrix + y_val::Vector{T} # DFT and reference data validation_dft_data::SmallESData{D} validation_ref_data::SmallESData{D} - y::Vector{T} # linearize(training_dft_data) - linearize(training_ref_data) - y_val::Vector{T} # linearize(validation_dft_data) - linearize(validation_ref_data) - ATy::Vector{T} # A^T * y, optional end function SmallSNAPLP(snap::SNAP, atomic_confs::Vector, data::SmallESData{D}; trainingsize = 0.8, fit = [:e, :f, :s]) where {D} - - m = floor(Int, length(atomic_confs) * trainingsize) - - n_e = floor(Int, length(data.energies) * trainingsize) - n_f = n_e + floor(Int, length(data.forces) * length(data.forces[1]) * 3 * trainingsize) - n_s = n_f + floor(Int, length(data.stresses) * sum([ 1 for j in 1:D for i in j:D ]) * trainingsize) + # TODO: @views? + # Training ############################################################# + m = floor(Int, length(atomic_confs) * trainingsize) AA = get_snap(atomic_confs[1:m], snap) #TODO: get_snap should allow me to chose what to fit (e, f, or s) - A_e = AA[1:n_e, :] - A_f = AA[n_e+1:n_f, :] - A_s = AA[n_f+1:n_s, :] - + n_e = m; n_f = n_e + m * length(atomic_confs[1].Atoms) * 3 A = [] - if :e in fit A = A_e end - if :f in fit A = vcat(A, A_f) end - if :s in fit A = vcat(A, A_s) end - + if :e in fit A = AA[1:n_e, :] end + if :f in fit A = vcat(A, AA[n_e+1:n_f, :]) end + if :s in fit A = vcat(A, AA[n_f+1:end, :]) end ATA = A' * A - nrows = size(A)[1] - Q = Diagonal(ones(nrows)) - invQ = inv(Q) - + Q = Diagonal(ones(size(A)[1])); invQ = inv(Q) training_dft_data = SmallESData{D}(data.energies[1:m], data.forces[1:m], - data.stresses[1:m]) # TODO: @views? - validation_dft_data = SmallESData{D}(data.energies[m+1:end], - data.forces[m+1:end], - data.stresses[m+1:end]) # TODO: @views? - training_ref_data = training_dft_data # TODO: add ZBL, see PotentialLearning.jl in master - validation_ref_data = validation_dft_data # TODO: add ZBL, see PotentialLearning.jl in master - + data.stresses[1:m]) + # TODO: add ZBL, see PotentialLearning.jl in master + training_ref_data = SmallESData{D}(data.energies[1:m] * 0.01, + data.forces[1:m] * 0.01, + data.stresses[1:m] * 0.01) y = [] if :e in fit - y = linearize(training_dft_data.energies) #- linearize(training_ref_data.energies) - y_val = linearize(validation_dft_data.energies) #- linearize(validation_ref_data.energies) + y = linearize(training_dft_data.energies) - + linearize(training_ref_data.energies) end if :f in fit - append!(y, linearize(training_dft_data.forces)) #- linearize(training_ref_data.forces) - append!(y_val, linearize(validation_dft_data.forces)) #- linearize(validation_ref_data.forces) + append!(y, linearize(training_dft_data.forces) - + linearize(training_ref_data.forces)) end if :s in fit - append!(y, linearize(training_dft_data.stresses)) #- linearize(training_ref_data.stresses) - append!(y_val, linearize(validation_dft_data.stresses)) #- linearize(validation_ref_data.stresses) + append!(y, linearize(training_dft_data.stresses) - + linearize(training_ref_data.stresses)) end - ATy = A' * y - SmallSNAPLP(snap, A, ATA, Q, invQ, training_dft_data, training_ref_data, - validation_dft_data, validation_ref_data, y, y_val, ATy) + # Validation ########################################################### + m_val = length(atomic_confs[m+1:end]) + AA_val = get_snap(atomic_confs[m+1:end], snap) + n_e = m_val; n_f = n_e + m_val * length(atomic_confs[1].Atoms) * 3 + A_val = [] + if :e in fit A_val = AA_val[1:n_e, :] end + if :f in fit A_val = vcat(A, AA_val[n_e+1:n_f, :]) end + if :s in fit A_val = vcat(A, AA_val[n_f+1:end, :]) end + validation_dft_data = SmallESData{D}(data.energies[m+1:end], + data.forces[m+1:end], + data.stresses[m+1:end]) + # TODO: add ZBL, see PotentialLearning.jl in master + validation_ref_data = SmallESData{D}(data.energies[m+1:end] * 0.01, + data.forces[m+1:end] * 0.01, + data.stresses[m+1:end] * 0.01) + y_val = [] + if :e in fit + y_val = linearize(validation_dft_data.energies) - + linearize(validation_ref_data.energies) + end + if :f in fit + append!(y_val, linearize(validation_dft_data.forces) - + linearize(validation_ref_data.forces)) + end + if :s in fit + append!(y_val, linearize(validation_dft_data.stresses) - + linearize(validation_ref_data.stresses)) + end + + SmallSNAPLP(snap, A, y, ATA, ATy, Q, invQ, training_dft_data, + training_ref_data, A_val, y_val, validation_dft_data, + validation_ref_data) end From 1843dfe5e158c67b34859f03dac3d91e7557222a Mon Sep 17 00:00:00 2001 From: Emmanuel Lujan Date: Tue, 7 Dec 2021 20:29:05 -0500 Subject: [PATCH 10/35] small fix --- src/SNAPLearningProblem.jl | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/src/SNAPLearningProblem.jl b/src/SNAPLearningProblem.jl index 864de582..b7524565 100644 --- a/src/SNAPLearningProblem.jl +++ b/src/SNAPLearningProblem.jl @@ -72,8 +72,8 @@ function SmallSNAPLP(snap::SNAP, atomic_confs::Vector, data::SmallESData{D}; n_e = m_val; n_f = n_e + m_val * length(atomic_confs[1].Atoms) * 3 A_val = [] if :e in fit A_val = AA_val[1:n_e, :] end - if :f in fit A_val = vcat(A, AA_val[n_e+1:n_f, :]) end - if :s in fit A_val = vcat(A, AA_val[n_f+1:end, :]) end + if :f in fit A_val = vcat(A_val, AA_val[n_e+1:n_f, :]) end + if :s in fit A_val = vcat(A_val, AA_val[n_f+1:end, :]) end validation_dft_data = SmallESData{D}(data.energies[m+1:end], data.forces[m+1:end], data.stresses[m+1:end]) From 7267ba1d75d8c10bcc1107400acc543d8f4987b4 Mon Sep 17 00:00:00 2001 From: Emmanuel Lujan Date: Fri, 8 Jul 2022 18:23:42 -0400 Subject: [PATCH 11/35] Adding new changes from AtomisticComposableWorkflows repo. --- examples/README.md | 2 +- src/IO/input.jl | 113 +++++++++++++++++++++++ src/IO/load-data.jl | 92 +++++++++++++++++++ src/IO/utils.jl | 17 ++++ src/Interface.jl | 36 ++++---- src/PostProc/metrics.jl | 39 ++++++++ src/PostProc/plots.jl | 29 ++++++ src/PotentialLearning.jl | 2 +- src/Training/loss.jl | 31 +++++++ src/Training/losses.jl | 10 +++ src/Training/training.jl | 130 +++++++++++++++++++++++++++ src/old/Interface.jl | 89 ++++++++++++++++++ src/old/PotentialLearning.jl | 6 ++ src/{ => old}/SNAPLearningProblem.jl | 64 ++++++------- 14 files changed, 608 insertions(+), 52 deletions(-) create mode 100644 src/IO/input.jl create mode 100644 src/IO/load-data.jl create mode 100644 src/IO/utils.jl create mode 100644 src/PostProc/metrics.jl create mode 100644 src/PostProc/plots.jl create mode 100644 src/Training/loss.jl create mode 100644 src/Training/losses.jl create mode 100644 src/Training/training.jl create mode 100644 src/old/Interface.jl create mode 100644 src/old/PotentialLearning.jl rename src/{ => old}/SNAPLearningProblem.jl (73%) diff --git a/examples/README.md b/examples/README.md index 2c143adc..dd48e337 100644 --- a/examples/README.md +++ b/examples/README.md @@ -1 +1 @@ -See https://github.com/cesmix-mit/ComposableWorkflows +See https://github.com/cesmix-mit/AtomisticComposableWorkflows diff --git a/src/IO/input.jl b/src/IO/input.jl new file mode 100644 index 00000000..44e2acff --- /dev/null +++ b/src/IO/input.jl @@ -0,0 +1,113 @@ +using AtomsBase +using InteratomicPotentials +using InteratomicBasisPotentials +using OrderedCollections +using IterTools +using LinearAlgebra +using UnitfulAtomic +using Unitful +using Flux +using Flux.Data: DataLoader +using BSON: @save + +include("load-data.jl") + +# Load input parameters + +function get_defaults_args() + args = ["experiment_path", "TiO2/", + "dataset_path", "data/", + "trainingset_filename", "TiO2trainingset.xyz", + "testset_filename", "TiO2testset.xyz", + "n_train_sys", "80", + "n_test_sys", "20", + "n_batches", "8", + "n_body", "3", + "max_deg", "3", + "r0", "1.0", + "rcutoff", "5.0", + "wL", "1.0", + "csp", "1.0", + "w_e", "1.0", + "w_f", "1.0"] + return args +end + +function get_input(args) + if length(args) == 0 + args = get_defaults_args() + end + input = OrderedDict() + for (key, val) in partition(args,2,2) + if tryparse(Float64, val) != nothing + if occursin(".", val) + val = parse(Float64, val) + else + val = parse(Int64, val) + end + end + input[key] = val + end + return input +end + + +# Load dataset +function load_dataset(input) + experiment_path = input["experiment_path"] + n_train_sys, n_test_sys = input["n_train_sys"], input["n_test_sys"] + n_sys = n_train_sys + n_test_sys + # Split into training and testing + if "dataset_filename" in keys(input) + filename = input["dataset_path"]*input["dataset_filename"] + systems, energies, forces, stress = + load_data(filename, max_entries = n_sys) + rand_list = randperm(n_sys) + train_index, test_index = rand_list[1:n_train_sys], rand_list[n_train_sys+1:n_sys] + train_systems, train_energies, train_forces, train_stress = + systems[train_index], energies[train_index], + forces[train_index], stress[train_index] + test_systems, test_energies, test_forces, test_stress = + systems[test_index], energies[test_index], + forces[test_index], stress[test_index] + else # The data set is already split. + filename = input["dataset_path"]*input["trainingset_filename"] + train_systems, train_energies, train_forces, train_stress = + load_data(filename, max_entries = n_train_sys) + filename = input["dataset_path"]*input["testset_filename"] + test_systems, test_energies, test_forces, test_stress = + load_data(filename, max_entries = n_test_sys) + end + return train_systems, train_energies, train_forces, train_stress, + test_systems, test_energies, test_forces, test_stress +end + + +# Linearize forces +function linearize_forces(forces) + return vcat([vcat(vcat(f...)...) for f in forces]...) +end + + +# Split data into batches +function get_batches(n_batches, B_train, B_train_ext, e_train, dB_train, f_train, + B_test, B_test_ext, e_test, dB_test, f_test) + + bs_train_e = floor(Int, length(B_train) / n_batches) + train_loader_e = DataLoader((B_train, e_train), batchsize=bs_train_e, shuffle=true) + bs_train_f = floor(Int, length(dB_train) / n_batches) + train_loader_f = DataLoader((B_train_ext, dB_train, f_train), + batchsize=bs_train_f, shuffle=true) + println("Batch sizes of training energy and force datasets: ", bs_train_e, ", ", bs_train_f) + + bs_test_e = floor(Int, length(B_test) / n_batches) + test_loader_e = DataLoader((B_test, e_test), batchsize=bs_test_e, shuffle=true) + bs_test_f = floor(Int, length(dB_test) / n_batches) + test_loader_f = DataLoader((B_test_ext, dB_test, f_test), + batchsize=bs_test_f, shuffle=true) + println("Batch sizes of test energy and force datasets: ", bs_train_e, ", ", bs_train_f) + + return train_loader_e, train_loader_f, test_loader_e, test_loader_f +end + + diff --git a/src/IO/load-data.jl b/src/IO/load-data.jl new file mode 100644 index 00000000..188e1c6c --- /dev/null +++ b/src/IO/load-data.jl @@ -0,0 +1,92 @@ +# This code will be added to PotentialLearning.jl + +function load_data(file; max_entries = 2000, T = Float64) + systems = AbstractSystem[] + energies = T[] + forces = Vector{SVector{3, T}}[] + stresses = SVector{6, T}[] + open(file, "r") do io + count = 1 + while !eof(io) && (count <= max_entries) + # Read info line + line = readline(io) + num_atoms = parse(Int, line) + + line = readline(io) + lattice_line = match(r"Lattice=\"(.*?)\" ", line).captures[1] + lattice = parse.(T, split(lattice_line)) * 1u"Å" + box = [lattice[1:3], + lattice[4:6], + lattice[7:9]] + bias = -5.0 + try + energy_line = match(r"energy=(.*?) ", line).captures[1] + energy = parse(T, energy_line) + push!(energies, energy) + catch + push!(energies, NaN) + end + + try + stress_line = match(r"stress=\"(.*?)\" ", line).captures[1] + stress = parse.(T, split(stress_line)) + push!(stresses, SVector{6}(stress)) + catch + push!(stresses, SVector{6}( fill(NaN, (6,)))) + end + + bc = [] + try + bc_line = match(r"pbc=\"(.*?)\"", line).captures[1] + bc = [ t=="T" ? Periodic() : DirichletZero() for t in split(bc_line) ] + catch + bc = [DirichletZero(), DirichletZero(), DirichletZero()] + end + + properties = match(r"Properties=(.*?) ", line).captures[1] + properties = split(properties, ":") + properties = [properties[i:i+2] for i = 1:3:(length(properties)-1)] + atoms = Vector{AtomsBase.Atom}(undef, num_atoms) + force = Vector{SVector{3, T}}(undef, num_atoms) + for i = 1:num_atoms + line = split(readline(io)) + line_count = 1 + position = 0.0 + element = 0.0 + data = Dict( () ) + for prop in properties + if prop[1] == "species" + element = Symbol(line[line_count]) + line_count += 1 + elseif prop[1] == "pos" + position = SVector{3}(parse.(T, line[line_count:line_count+2])) .- bias + line_count += 3 + elseif prop[1] == "move_mask" + ft = Symbol(line[line_count]) + line_count += 1 + elseif prop[1] == "tags" + ft = Symbol(line[line_count]) + line_count += 1 + elseif prop[1] == "forces" + force[i] = SVector{3}(parse.(T, line[line_count:line_count+2])) + line_count += 3 + else + length = parse(Int, prop[3]) + if length == 1 + data = merge(data, Dict( (prop[1] => line[line_count]) ) ) + else + data = merge(data, Dict( (prop[1] => line[line_count:line_count+length-1]) ) ) + end + end + end + atoms[i] = AtomsBase.Atom(element, position .* 1u"Å", data = data) + end + + push!(forces, force) + system = FlexibleSystem(atoms, box, bc) + push!(systems, system) + count += 1 + end + end + return systems, energies, forces, stresses +end diff --git a/src/IO/utils.jl b/src/IO/utils.jl new file mode 100644 index 00000000..4d479357 --- /dev/null +++ b/src/IO/utils.jl @@ -0,0 +1,17 @@ +# This code will be added to PotentialLearning.jl +using CSV + +macro savevar(path, var) + quote + write("$(path)" * $(string(var)) * ".dat", string($(esc(var)))) + end +end + +macro savecsv(path, var) + return :( CSV.write("$(path)" * $(string(var)) * ".csv", $(var), header = false) ) +end + +macro savefig(path, var) + return :( savefig($(var), "$(path)" * $(string(var)) * ".png") ) +end + diff --git a/src/Interface.jl b/src/Interface.jl index b668e6e8..2e8c81d3 100644 --- a/src/Interface.jl +++ b/src/Interface.jl @@ -15,47 +15,47 @@ export loss, learn # Abstract types ############################################################### """ - LearningProblem{D, T} + LearningProblem """ -abstract type LearningProblem{D, T} end +abstract type LearningProblem end """ - LearningOptimizer{D, T} + LearningOptimizer """ -abstract type LearningOptimizer{D, T} end +abstract type LearningOptimizer end # Optimizers ################################################################### """ - SDPOpt{D, T} + SDPOpt Semidefinite program (SDP) optimizer """ -struct SDPOpt{D, T} <: LearningOptimizer{D, T} end +struct SDPOpt <: LearningOptimizer end """ - LeastSquaresOpt{D, T} + LeastSquaresOpt Least squares optimizer """ -struct LeastSquaresOpt{D, T} <: LearningOptimizer{D, T} end +struct LeastSquaresOpt <: LearningOptimizer end """ - QRLinearOpt{D, T} + QRLinearOpt QR optimizer """ -struct QRLinearOpt{D, T} <: LearningOptimizer{D, T} end +struct QRLinearOpt <: LearningOptimizer end """ - NelderMeadOpt{D, T} + NelderMeadOpt Nelder mead optimizer """ -struct NelderMeadOpt{D, T} <: LearningOptimizer{D, T} +struct NelderMeadOpt <: LearningOptimizer maxiters end @@ -63,27 +63,27 @@ end # Learning and loss functions ################################################## """ - loss(params::Vector{T}, opt::LearningOptimizer{D, T}) + loss(params::Vector, opt::LearningOptimizer) `params`: parameters to be fitted `opt`: learning optimizer """ -function loss(params::Vector{T}, opt::LearningOptimizer{D, T}) where {T, D} end +function loss(params::Vector, opt::LearningOptimizer) end """ - learn(lp::LearningProblem{D, T}, opt::LearningOptimizer{D, T}) + learn(lp::LearningProblem, opt::LearningOptimizer) `lp`: learning problem `opt`: learning optimizer """ -function learn(lp::LearningProblem{D, T}, opt::LearningOptimizer{D, T}) where {T, D} end +function learn(lp::LearningProblem, opt::LearningOptimizer) end """ - learn(lp::LearningProblem{D, T}, opt::LearningOptimizer{D, T}, loss) + learn(lp::LearningProblem, opt::LearningOptimizer, loss) `lp`: learning problem `opt`: learning optimizer `loss`: loss function """ -function learn(lp::LearningProblem{D, T}, opt::LearningOptimizer{D, T}, loss) where {T, D} end +function learn(lp::LearningProblem, opt::LearningOptimizer, loss) end diff --git a/src/PostProc/metrics.jl b/src/PostProc/metrics.jl new file mode 100644 index 00000000..acc956ad --- /dev/null +++ b/src/PostProc/metrics.jl @@ -0,0 +1,39 @@ +# Calculate metrics +function calc_metrics(x_pred, x) + x_mae = sum(abs.(x_pred .- x)) / length(x) + x_rmse = sqrt(sum((x_pred .- x).^2) / length(x)) + x_rsq = 1 - sum((x_pred .- x).^2) / sum((x .- mean(x)).^2) + return x_mae, x_rmse, x_rsq +end + +function get_metrics( e_train_pred, e_train, f_train_pred, f_train, + e_test_pred, e_test, f_test_pred, f_test, + B_time, dB_time, time_fitting) + e_train_mae, e_train_rmse, e_train_rsq = calc_metrics(e_train_pred, e_train) + f_train_mae, f_train_rmse, f_train_rsq = calc_metrics(f_train_pred, f_train) + e_test_mae, e_test_rmse, e_test_rsq = calc_metrics(e_test_pred, e_test) + f_test_mae, f_test_rmse, f_test_rsq = calc_metrics(f_test_pred, f_test) + + f_test_pred_v = collect(eachcol(reshape(f_test_pred, 3, :))) + f_test_v = collect(eachcol(reshape(f_test, 3, :))) + f_test_cos = dot.(f_test_v, f_test_pred_v) ./ (norm.(f_test_v) .* norm.(f_test_pred_v)) + f_test_mean_cos = mean(f_test_cos) + + metrics = OrderedDict( "e_train_mae" => e_train_mae, + "e_train_rmse" => e_train_rmse, + "e_train_rsq" => e_train_rsq, + "f_train_mae" => f_train_mae, + "f_train_rmse" => f_train_rmse, + "f_train_rsq" => f_train_rsq, + "e_test_mae" => e_test_mae, + "e_test_rmse" => e_test_rmse, + "e_test_rsq" => e_test_rsq, + "f_test_mae" => f_test_mae, + "f_test_rmse" => f_test_rmse, + "f_test_rsq" => f_test_rsq, + "f_test_mean_cos" => f_test_mean_cos, + "B_time [s]" => B_time, + "dB_time [s]" => dB_time, + "time_fitting [s]" => time_fitting) + return metrics +end diff --git a/src/PostProc/plots.jl b/src/PostProc/plots.jl new file mode 100644 index 00000000..2c0edb29 --- /dev/null +++ b/src/PostProc/plots.jl @@ -0,0 +1,29 @@ +# Plot variables +function plot_energy(e_pred, e_true) + r0 = minimum(e_true); r1 = maximum(e_true); rs = (r1-r0)/10 + plot( e_true, e_pred, seriestype = :scatter, markerstrokewidth=0, + label="", xlabel = "E DFT | eV/atom", ylabel = "E predicted | eV/atom") + p = plot!( r0:rs:r1, r0:rs:r1, label="") + return p +end + +function plot_forces(f_pred, f_true) + f_pred_v = collect(eachcol(reshape(f_pred, 3, :))) + f_true_v = collect(eachcol(reshape(f_true, 3, :))) + r0 = 0; r1 = ceil(maximum(norm.(f_true_v))) + plot( norm.(f_true_v), norm.(f_pred_v), seriestype = :scatter, markerstrokewidth=0, + label="", xlabel = "|F| DFT | eV/Å", ylabel = "|F| predicted | eV/Å", + xlims = (r0, r1), ylims = (r0, r1)) + p = plot!( r0:r1, r0:r1, label="") + return p +end + +function plot_cos(f_pred, f_true) + f_pred_v = collect(eachcol(reshape(f_pred, 3, :))) + f_true_v = collect(eachcol(reshape(f_true, 3, :))) + f_cos = dot.(f_true_v, f_pred_v) ./ (norm.(f_true_v) .* norm.(f_pred_v)) + p = plot( f_cos, seriestype = :scatter, markerstrokewidth=0, + label="", xlabel = "F DFT vs F predicted", ylabel = "cos(α)") + return p +end + diff --git a/src/PotentialLearning.jl b/src/PotentialLearning.jl index 6c179e7e..8e105500 100644 --- a/src/PotentialLearning.jl +++ b/src/PotentialLearning.jl @@ -1,6 +1,6 @@ module PotentialLearning include("Interface.jl") -include("SNAPLearningProblem.jl") +#include("SNAPLearningProblem.jl") end diff --git a/src/Training/loss.jl b/src/Training/loss.jl new file mode 100644 index 00000000..00e10d76 --- /dev/null +++ b/src/Training/loss.jl @@ -0,0 +1,31 @@ +export loss, global_loss + +""" + loss(es_pred, es, w_e, fs_pred, fs, w_f) + +`es_pred`: preditected energies +`es`: energies +`w_e`: energy weight +`fs_pred`: preditected forces +`fs`: forces +`w_f`: force weight +""" +loss(es_pred, es, w_e, fs_pred, fs, w_f) = w_e * Flux.Losses.mse(es_pred, es) + + w_f * Flux.Losses.mse(fs_pred, fs) + +""" + global_loss(loader_e, loader_f, w_e, w_f, ps, re) + +`loader_e`: preditected energies +`loader_f`: energies +`w_e`: energy weight +`w_f`: force weight +`ps`: neural network parameters. See Flux.destructure. +`re`: neural network restructure. See Flux.destructure. + +""" +global_loss(loader_e, loader_f, w_e, w_f, ps, re) = + mean([loss(potential_energy.(bs_e, [ps], [re]), es, w_e, + force.(bs_f, dbs_f, [ps], [re]), fs, w_f) + for ((bs_e, es), (bs_f, dbs_f, fs)) in zip(loader_e, loader_f)]) + diff --git a/src/Training/losses.jl b/src/Training/losses.jl new file mode 100644 index 00000000..ce419faa --- /dev/null +++ b/src/Training/losses.jl @@ -0,0 +1,10 @@ +# Loss function +loss(es_pred, es, w_e, fs_pred, fs, w_f) = w_e * Flux.Losses.mse(es_pred, es) + + w_f * Flux.Losses.mse(fs_pred, fs) + +# Global loss function +global_loss(loader_e, loader_f, w_e, w_f, ps, re) = + mean([loss(potential_energy.(bs_e, [ps], [re]), es, w_e, + force.(bs_f, dbs_f, [ps], [re]), fs, w_f) + for ((bs_e, es), (bs_f, dbs_f, fs)) in zip(loader_e, loader_f)]) + diff --git a/src/Training/training.jl b/src/Training/training.jl new file mode 100644 index 00000000..7697c542 --- /dev/null +++ b/src/Training/training.jl @@ -0,0 +1,130 @@ +# Batch training using Optimization.jl +# I am using one of the Optimization.jl solvers, because I have not been able to +# tackle this problem with the Flux solvers. +function batch_train_opt!(ps, re, opt, maxiters, train_loader_e, train_loader_f, + w_e, w_f, epoch, train_losses_batches) + i = 1 + for ((bs_e, es), (bs_f, dbs_f, fs)) in zip(train_loader_e, train_loader_f) + batch_loss(ps, p) = loss(potential_energy.(bs_e, [ps], [re]), es, w_e, + force.(bs_f, dbs_f, [ps], [re]), fs, w_f) + dbatchlossdps = OptimizationFunction(batch_loss, + Optimization.AutoForwardDiff()) # Optimization.AutoZygote() + prob = OptimizationProblem(dbatchlossdps, ps, []) # prob = remake(prob,u0=sol.minimizer) + callback = function (p, l) + println("Epoch: $(epoch), batch: $i, training loss: $l") + push!(train_losses_batches, l) + return false + end + sol = solve(prob, opt, callback=callback, maxiters=maxiters) # reltol = 1e-14 + ps = sol.u + i = i + 1 + end + return ps +end + +# Batch training using Flux.jl +function batch_train_flux!(ps, re, opt, maxiters, train_loader_e, train_loader_f, w_e, w_f) + for ((bs_e, es), (bs_f, dbs_f, fs)) in zip(train_loader_e, train_loader_f) + g = gradient(Flux.params(ps)) do + loss(potential_energy.(bs_e, [ps], [re]), es, w_e, + force.(bs_f, dbs_f, [ps], [re]), fs, w_f) + end + Flux.Optimise.update!(opt, Flux.params(ps), g, maxiters=maxiters) + end + return ps +end + +# Training +function train!( lib, nnbp, epochs, opt, maxiters, train_loader_e, train_loader_f, + test_loader_e, test_loader_f, w_e, w_f) + + train_losses_epochs = []; test_losses_epochs = []; train_losses_batches = [] + ps, re = Flux.destructure(nnbp.nn) + for epoch in 1:epochs + + # TODO: use multiple dispatch here? + if lib == "Flux.jl" + ps = batch_train_flux!(ps, re, opt, maxiters, train_loader_e, + train_loader_f, w_e, w_f, epoch, train_losses_batches) + else # lib == "Optimization.jl" + ps = batch_train_opt!(ps, re, opt, maxiters, train_loader_e, + train_loader_f, w_e, w_f, epoch, train_losses_batches) + end + + # Report losses + train_loss = global_loss(train_loader_e, train_loader_f, w_e, w_f, ps, re) + test_loss = global_loss(test_loader_e, test_loader_f, w_e, w_f, ps, re) + push!(train_losses_epochs, train_loss) + push!(test_losses_epochs, test_loss) + println("Epoch $(epoch). Losses of complete datasets: \ + training loss: $(train_loss), \ + test loss: $(test_loss).") + end + nnbp.nn = re(ps) + nnbp.nn_params = Flux.params(nnbp.nn) + + return train_losses_epochs, test_losses_epochs, train_losses_batches +end + + +# Training using BFGS from Optimizer.jl (1 batch) +#time_fitting += Base.@elapsed begin +# ps, re = Flux.destructure(nnbp.nn) +# ((bs_e, es), (bs_f, dbs_f, fs)) = collect(zip(train_loader_e, train_loader_f))[1] +# loss(ps, p) = loss(potential_energy.(bs_e, [ps], [re]), es, +# force.(bs_f, dbs_f, [ps], [re]), fs) +# dlossdps = OptimizationFunction(loss, Optimization.AutoForwardDiff()) # Optimization.AutoZygote() +# prob = OptimizationProblem(dlossdps, ps, []) #prob = remake(prob,u0=sol.minimizer) +# callback = function (p, l) +# println("Thread: $(Threads.threadid()) current loss is: $l") +# return false +# end +# sol = solve(prob, BFGS(), callback=callback, maxiters=1000) # reltol = 1e-14 +# ps = sol.u +# nnbp.nn = re(ps) +# nnbp.nn_params = Flux.params(nnbp.nn) +#end + +#------------------------------------------------------------------------------- +## Training using BFGS and data parallelism with Base.Threads +# execute: julia --threads 4 fit-ahfo2-neural-ace.jl +# BLAS.set_num_threads(1) +##time_fitting += Base.@elapsed begin +#ps, re = Flux.destructure(nnbp.nn) +#nt = Threads.nthreads() +#loaders = collect(zip(train_loader_e, train_loader_f))[1:nt] +## Compute loss of each batch +#opt_func = Array{Function}(undef, nt); +#for tid in 1:nt +# ((bs_e, es), (bs_f, dbs_f, fs)) = loaders[tid] +# batch_loss(ps, p) = loss(potential_energy.(bs_e, [ps], [re]), es, +# force.(bs_f, dbs_f, [ps], [re]), fs) +# opt_func[tid] = batch_loss +#end +## Compute total loss and define optimization function +#total_loss(ps, p) = mean([f(ps, p) for f in opt_func]) +#dlossdps = OptimizationFunction(total_loss, Optimization.AutoForwardDiff()) # Optimization.AutoZygote()) +## Optimize using averaged gradient on each batch +#callback = function (p, l) +# println("Thread $(Threads.threadid()), current loss is: $l") +# return false +#end +#pss = [deepcopy(ps) for i in 1:nt] +##@profile Threads.@threads for tid in 1:nt +# ((bs_e, es), (bs_f, dbs_f, fs)) = loaders[tid] +# ps_i = deepcopy(ps) +# prob = OptimizationProblem(dlossdps, ps_i, []) # prob = remake(prob,u0=sol.minimizer) +# sol = solve(prob, BFGS(), callback = callback, maxiters=10_000_000) +# pss[tid] = sol.u +#end +## Average parameters +#ps = mean(pss) +#nnbp.nn = re(ps) +#nnbp.nn_params = Flux.params(nnbp.nn) +#end +#save("fit-ahfo2-neural-ace.jlprof", Profile.retrieve()...) +#using ProfileView, FileIO +#data = load("fit-ahfo2-neural-ace.jlprof") +#ProfileView.view(data[1], lidict=data[2]) +#------------------------------------------------------------------------------- + diff --git a/src/old/Interface.jl b/src/old/Interface.jl new file mode 100644 index 00000000..2e8c81d3 --- /dev/null +++ b/src/old/Interface.jl @@ -0,0 +1,89 @@ +################################################################################ +# +# Interface.jl +# +################################################################################ + +using ElectronicStructure, InteratomicPotentials +using LinearAlgebra, GalacticOptim, Optim, BlackBoxOptim + +export LearningProblem, LearningOptimizer +export SDPOpt, LeastSquaresOpt, QRLinearOpt, NelderMeadOpt +export loss, learn + + +# Abstract types ############################################################### + +""" + LearningProblem + +""" +abstract type LearningProblem end + +""" + LearningOptimizer + +""" +abstract type LearningOptimizer end + + +# Optimizers ################################################################### + +""" + SDPOpt + +Semidefinite program (SDP) optimizer +""" +struct SDPOpt <: LearningOptimizer end + +""" + LeastSquaresOpt + +Least squares optimizer +""" +struct LeastSquaresOpt <: LearningOptimizer end + +""" + QRLinearOpt + +QR optimizer +""" +struct QRLinearOpt <: LearningOptimizer end + +""" + NelderMeadOpt + +Nelder mead optimizer +""" +struct NelderMeadOpt <: LearningOptimizer + maxiters +end + + +# Learning and loss functions ################################################## + +""" + loss(params::Vector, opt::LearningOptimizer) + +`params`: parameters to be fitted +`opt`: learning optimizer +""" +function loss(params::Vector, opt::LearningOptimizer) end + +""" + learn(lp::LearningProblem, opt::LearningOptimizer) + +`lp`: learning problem +`opt`: learning optimizer +""" +function learn(lp::LearningProblem, opt::LearningOptimizer) end + +""" + learn(lp::LearningProblem, opt::LearningOptimizer, loss) + +`lp`: learning problem +`opt`: learning optimizer +`loss`: loss function +""" +function learn(lp::LearningProblem, opt::LearningOptimizer, loss) end + diff --git a/src/old/PotentialLearning.jl b/src/old/PotentialLearning.jl new file mode 100644 index 00000000..8e105500 --- /dev/null +++ b/src/old/PotentialLearning.jl @@ -0,0 +1,6 @@ +module PotentialLearning + +include("Interface.jl") +#include("SNAPLearningProblem.jl") + +end diff --git a/src/SNAPLearningProblem.jl b/src/old/SNAPLearningProblem.jl similarity index 73% rename from src/SNAPLearningProblem.jl rename to src/old/SNAPLearningProblem.jl index b7524565..6d72f9b9 100644 --- a/src/SNAPLearningProblem.jl +++ b/src/old/SNAPLearningProblem.jl @@ -5,33 +5,33 @@ export SmallSNAPLP, hyperparam_loss, β_loss, learn """ - SmallSNAPLP{D, T} + SmallSNAPLP SNAP learning problem for small systems """ -struct SmallSNAPLP{D, T} <: LearningProblem{D, T} +struct SmallSNAPLP <: LearningProblem # Training ################################# snap::SNAP # SNAP potential - A::Matrix{T} # SNAP matrix - y::Vector{T} # DFT and reference data - ATA::Matrix{T} # A^T * A - ATy::Vector{T} # A^T * y - Q::Diagonal{T} # Covariance - invQ::Diagonal{T} # inverse of Q - training_dft_data::SmallESData{D} - training_ref_data::SmallESData{D} + A::Matrix # SNAP matrix + y::Vector # DFT and reference data + ATA::Matrix # A^T * A + ATy::Vector # A^T * y + Q::Diagonal # Covariance + invQ::Diagonal # inverse of Q + training_dft_data::SmallESData + training_ref_data::SmallESData # Validation ############################### - A_val::Matrix{T} # SNAP matrix - y_val::Vector{T} # DFT and reference data - validation_dft_data::SmallESData{D} - validation_ref_data::SmallESData{D} + A_val::Matrix # SNAP matrix + y_val::Vector # DFT and reference data + validation_dft_data::SmallESData + validation_ref_data::SmallESData end -function SmallSNAPLP(snap::SNAP, atomic_confs::Vector, data::SmallESData{D}; - trainingsize = 0.8, fit = [:e, :f, :s]) where {D} +function SmallSNAPLP(snap::SNAP, atomic_confs::Vector, data::SmallESData; + trainingsize = 0.8, fit = [:e, :f, :s]) where # TODO: @views? # Training ############################################################# @@ -44,11 +44,11 @@ function SmallSNAPLP(snap::SNAP, atomic_confs::Vector, data::SmallESData{D}; if :s in fit A = vcat(A, AA[n_f+1:end, :]) end ATA = A' * A Q = Diagonal(ones(size(A)[1])); invQ = inv(Q) - training_dft_data = SmallESData{D}(data.energies[1:m], + training_dft_data = SmallESData(data.energies[1:m], data.forces[1:m], data.stresses[1:m]) # TODO: add ZBL, see PotentialLearning.jl in master - training_ref_data = SmallESData{D}(data.energies[1:m] * 0.01, + training_ref_data = SmallESData(data.energies[1:m] * 0.01, data.forces[1:m] * 0.01, data.stresses[1:m] * 0.01) y = [] @@ -74,11 +74,11 @@ function SmallSNAPLP(snap::SNAP, atomic_confs::Vector, data::SmallESData{D}; if :e in fit A_val = AA_val[1:n_e, :] end if :f in fit A_val = vcat(A_val, AA_val[n_e+1:n_f, :]) end if :s in fit A_val = vcat(A_val, AA_val[n_f+1:end, :]) end - validation_dft_data = SmallESData{D}(data.energies[m+1:end], + validation_dft_data = SmallESData(data.energies[m+1:end], data.forces[m+1:end], data.stresses[m+1:end]) # TODO: add ZBL, see PotentialLearning.jl in master - validation_ref_data = SmallESData{D}(data.energies[m+1:end] * 0.01, + validation_ref_data = SmallESData(data.energies[m+1:end] * 0.01, data.forces[m+1:end] * 0.01, data.stresses[m+1:end] * 0.01) y_val = [] @@ -105,21 +105,21 @@ end # Hyper-parameter optimization ################################################# """ - hyperparam_loss(hyperparams::Vector{T}, lp::SmallSNAPLP{D, T}) + hyperparam_loss(hyperparams::Vector, lp::SmallSNAPLP) SNAP hyper-parameter loss function """ -function hyperparam_loss(hyperparams::Vector{T}, lp::SmallSNAPLP{D, T}) where {D, T} +function hyperparam_loss(hyperparams::Vector, lp::SmallSNAPLP) where # return ... end """ - learn(lp::SmallSNAPLP{T}, loss, s::SDPOpt{T}) + learn(lp::SmallSNAPLP, loss, s::SDPOpt) Learning function: using SDPOpt to optimize the hyper-parameters """ -function learn(lp::SmallSNAPLP{T}, loss, s::SDPOpt{T}) where {T} +function learn(lp::SmallSNAPLP, loss, s::SDPOpt) where # ...hyperparam_loss... # lp.snap.rcutfac = ... # lp.snap.twojmax = ... @@ -129,39 +129,39 @@ end # β-parameter optimization ##################################################### """ - learn(lp::SmallSNAPLP{T}, s::LeastSquaresOpt{T}) + learn(lp::SmallSNAPLP, s::LeastSquaresOpt) Learning function: using normal equations and qr decomposition to learn main parameters """ -function learn(lp::SmallSNAPLP{T}, s::LeastSquaresOpt{T}) where {T} +function learn(lp::SmallSNAPLP, s::LeastSquaresOpt) where lp.snap.β = (lp.A' * lp.A) \ (lp.A' * lp.y) end """ - learn(lp::SmallSNAPLP{T}, s::QRLinearOpt{T}) + learn(lp::SmallSNAPLP, s::QRLinearOpt) Learning function: using QR decomposition to learn main parameters """ -function learn(lp::SmallSNAPLP{T}, s::QRLinearOpt{T}) where {T} +function learn(lp::SmallSNAPLP, s::QRLinearOpt) where lp.snap.β = lp.A \ lp.y # or... qr(A,Val(true)) \ y end """ - β_loss(β::Vector{T}, lp::SmallSNAPLP{D, T}) + β_loss(β::Vector, lp::SmallSNAPLP) Loss function: using NelderMeadOpt from GalacticOptim to optimize the parameters """ -function β_loss(β::Vector{T}, lp::SmallSNAPLP{D, T}) where {D, T} +function β_loss(β::Vector, lp::SmallSNAPLP) where e = lp.A * β - lp.y return transpose(e) * inv(lp.Q) * e end """ - learn(lp::SmallSNAPLP{T}, loss, s::NelderMeadOpt{T}) + learn(lp::SmallSNAPLP, loss, s::NelderMeadOpt) Learning function: using NelderMeadOpt from GalacticOptim to optimize the parameters """ -function learn(lp::SmallSNAPLP{T}, loss, s::NelderMeadOpt{T}) where {T} +function learn(lp::SmallSNAPLP, loss, s::NelderMeadOpt) where β0 = zeros(length(lp.A[1,:])) prob = GalacticOptim.OptimizationProblem((x, pars)->loss(x, lp), β0, []) lp.snap.β = GalacticOptim.solve(prob, NelderMead(), maxiters=s.maxiters) From 74b12b5ca562a28b5514e0d79c5c087bed2be85e Mon Sep 17 00:00:00 2001 From: Emmanuel Lujan Date: Fri, 8 Jul 2022 20:04:41 -0400 Subject: [PATCH 12/35] Improving comments and documentation. --- src/IO/Input.jl | 171 ++++++++++++++++++++++ src/IO/{load-data.jl => Load-extxyz.jl} | 14 +- src/IO/Utils.jl | 36 +++++ src/IO/input.jl | 113 -------------- src/IO/utils.jl | 17 --- src/Interface.jl | 93 ++---------- src/PostProc/{metrics.jl => Metrics.jl} | 36 ++++- src/PostProc/{plots.jl => Plots.jl} | 32 +++- src/PotentialLearning.jl | 8 +- src/Training/{loss.jl => Losses.jl} | 5 + src/Training/{training.jl => Training.jl} | 31 +++- src/Training/losses.jl | 10 -- 12 files changed, 334 insertions(+), 232 deletions(-) create mode 100644 src/IO/Input.jl rename src/IO/{load-data.jl => Load-extxyz.jl} (92%) create mode 100644 src/IO/Utils.jl delete mode 100644 src/IO/input.jl delete mode 100644 src/IO/utils.jl rename src/PostProc/{metrics.jl => Metrics.jl} (62%) rename src/PostProc/{plots.jl => Plots.jl} (69%) rename src/Training/{loss.jl => Losses.jl} (86%) rename src/Training/{training.jl => Training.jl} (88%) delete mode 100644 src/Training/losses.jl diff --git a/src/IO/Input.jl b/src/IO/Input.jl new file mode 100644 index 00000000..161aed23 --- /dev/null +++ b/src/IO/Input.jl @@ -0,0 +1,171 @@ +include("load-extxyz.jl") + +export get_defaults_args, get_input, load_dataset, linearize_forces, get_batches + +""" + get_defaults_args() + +Returns default input arguments for NN potential training. + +TODO: probably this should not be here. + +""" +function get_defaults_args() + args = ["experiment_path", "TiO2/", + "dataset_path", "data/", + "trainingset_filename", "TiO2trainingset.xyz", + "testset_filename", "TiO2testset.xyz", + "n_train_sys", "80", + "n_test_sys", "20", + "n_batches", "8", + "n_body", "3", + "max_deg", "3", + "r0", "1.0", + "rcutoff", "5.0", + "wL", "1.0", + "csp", "1.0", + "w_e", "1.0", + "w_f", "1.0"] + return args +end + + +""" + get_input(args) + +`args`: vector of arguments (strings) + +Returns an OrderedDict with the arguments. +See https://github.com/cesmix-mit/AtomisticComposableWorkflows documentation +for information about how to define the input arguments. + +""" +function get_input(args) + if length(args) == 0 + args = get_defaults_args() + end + input = OrderedDict() + for (key, val) in partition(args,2,2) + if tryparse(Float64, val) != nothing + if occursin(".", val) + val = parse(Float64, val) + else + val = parse(Int64, val) + end + end + input[key] = val + end + return input +end + + +""" + load_dataset(n_train_sys, n_test_sys, dataset_path, dataset_filename) + +`n_train_sys`: no. of training systems +`n_test_sys`: no. of test systems +`dataset_path`: dataset path +`dataset_filename`: dataset filename + +Returns training and test energies, forces, and stresses. +The input dataset is split into training and test datasets. + +""" +function load_dataset(n_train_sys, n_test_sys, dataset_path, dataset_filename) + + n_sys = n_train_sys + n_test_sys + filename = dataset_path*dataset_filename + systems, energies, forces, stress = + load_data(filename, max_entries = n_sys) + rand_list = randperm(n_sys) + train_index, test_index = rand_list[1:n_train_sys], rand_list[n_train_sys+1:n_sys] + train_systems, train_energies, train_forces, train_stress = + systems[train_index], energies[train_index], + forces[train_index], stress[train_index] + test_systems, test_energies, test_forces, test_stress = + systems[test_index], energies[test_index], + forces[test_index], stress[test_index] + return train_systems, train_energies, train_forces, train_stress, + test_systems, test_energies, test_forces, test_stress +end + + +""" + load_dataset(n_train_sys, n_test_sys, dataset_path, + trainingset_filename, testset_filename) + +`n_train_sys`: no. of training systems +`n_test_sys`: no. of test systems +`dataset_path`: datasets path +`trainingset_filename`: training dataset filename +`testset_filename`: test dataset filename + +Returns training and test energies, forces, and stresses. +Training and test datasets are already defined. + +""" +function load_dataset(n_train_sys, n_test_sys, dataset_path, + trainingset_filename, testset_filename) + n_sys = n_train_sys + n_test_sys + filename = dataset_path*trainingset_filename + train_systems, train_energies, train_forces, train_stress = + load_data(filename, max_entries = n_train_sys) + filename = dataset_path*testset_filename + test_systems, test_energies, test_forces, test_stress = + load_data(filename, max_entries = n_test_sys) + return train_systems, train_energies, train_forces, train_stress, + test_systems, test_energies, test_forces, test_stress +end + + +""" + linearize_forces(forces) + +`forces`: vector of forces per system + +Returns a vector with the components of the forces of the systems. + +""" +function linearize_forces(forces) + return vcat([vcat(vcat(f...)...) for f in forces]...) +end + + +""" + get_batches(n_batches, B_train, B_train_ext, e_train, dB_train, f_train, + B_test, B_test_ext, e_test, dB_test, f_test) + +`n_batches`: no. of batches per dataset. +`B_train`: descriptors of the energies used in training. +`B_train_ext`: extendended descriptors of the energies used in training. Requiered to compute forces. +`e_train`: energies used in training. +`dB_train`: derivatives of the energy descritors used in training. +`f_train`: forces used in training. +`B_test`: descriptors of the energies used in test. +`B_test_ext`: extendended descriptors of the energies used in test. Requiered to compute forces. +`e_test`: energies used in test. +`dB_test`: derivatives of the energy descritors used in test. +`f_test`: forces used in test. + +Returns the data loaders for training and test of energies and forces. + +""" +function get_batches(n_batches, B_train, B_train_ext, e_train, dB_train, f_train, + B_test, B_test_ext, e_test, dB_test, f_test) + + bs_train_e = floor(Int, length(B_train) / n_batches) + train_loader_e = DataLoader((B_train, e_train), batchsize=bs_train_e, shuffle=true) + bs_train_f = floor(Int, length(dB_train) / n_batches) + train_loader_f = DataLoader((B_train_ext, dB_train, f_train), + batchsize=bs_train_f, shuffle=true) + + bs_test_e = floor(Int, length(B_test) / n_batches) + test_loader_e = DataLoader((B_test, e_test), batchsize=bs_test_e, shuffle=true) + bs_test_f = floor(Int, length(dB_test) / n_batches) + test_loader_f = DataLoader((B_test_ext, dB_test, f_test), + batchsize=bs_test_f, shuffle=true) + + return train_loader_e, train_loader_f, test_loader_e, test_loader_f +end + + diff --git a/src/IO/load-data.jl b/src/IO/Load-extxyz.jl similarity index 92% rename from src/IO/load-data.jl rename to src/IO/Load-extxyz.jl index 188e1c6c..65702977 100644 --- a/src/IO/load-data.jl +++ b/src/IO/Load-extxyz.jl @@ -1,6 +1,16 @@ -# This code will be added to PotentialLearning.jl +export load_extxyz -function load_data(file; max_entries = 2000, T = Float64) +""" + load_extxyz(file; max_entries = 2000, T = Float64) + +`file`: name of extxyz file +`max_entries`: maximum number of systems +`T`: default type + +Returns a vector of systems or atomic configurations. + +""" +function load_extxyz(file; max_entries = 2000, T = Float64) systems = AbstractSystem[] energies = T[] forces = Vector{SVector{3, T}}[] diff --git a/src/IO/Utils.jl b/src/IO/Utils.jl new file mode 100644 index 00000000..d9bdcecb --- /dev/null +++ b/src/IO/Utils.jl @@ -0,0 +1,36 @@ + +export savevar, savecsv, savefig + +""" + savevar(path, var) + +Simplifies the saving of a variable. + +""" +macro savevar(path, var) + quote + write("$(path)" * $(string(var)) * ".dat", string($(esc(var)))) + end +end + + +""" + savevar(path, dict) + +Simplifies the saving of a dictionary to a CSV file. + +""" +macro savecsv(path, dict) + return :( CSV.write("$(path)" * $(string(dict)) * ".csv", $(dict), header = false) ) +end + +""" + savefig(path, var) + +Simplifies the saving of a figure. + +""" +macro savefig(path, var) + return :( savefig($(var), "$(path)" * $(string(var)) * ".png") ) +end + diff --git a/src/IO/input.jl b/src/IO/input.jl deleted file mode 100644 index 44e2acff..00000000 --- a/src/IO/input.jl +++ /dev/null @@ -1,113 +0,0 @@ -using AtomsBase -using InteratomicPotentials -using InteratomicBasisPotentials -using OrderedCollections -using IterTools -using LinearAlgebra -using UnitfulAtomic -using Unitful -using Flux -using Flux.Data: DataLoader -using BSON: @save - -include("load-data.jl") - -# Load input parameters - -function get_defaults_args() - args = ["experiment_path", "TiO2/", - "dataset_path", "data/", - "trainingset_filename", "TiO2trainingset.xyz", - "testset_filename", "TiO2testset.xyz", - "n_train_sys", "80", - "n_test_sys", "20", - "n_batches", "8", - "n_body", "3", - "max_deg", "3", - "r0", "1.0", - "rcutoff", "5.0", - "wL", "1.0", - "csp", "1.0", - "w_e", "1.0", - "w_f", "1.0"] - return args -end - -function get_input(args) - if length(args) == 0 - args = get_defaults_args() - end - input = OrderedDict() - for (key, val) in partition(args,2,2) - if tryparse(Float64, val) != nothing - if occursin(".", val) - val = parse(Float64, val) - else - val = parse(Int64, val) - end - end - input[key] = val - end - return input -end - - -# Load dataset -function load_dataset(input) - experiment_path = input["experiment_path"] - n_train_sys, n_test_sys = input["n_train_sys"], input["n_test_sys"] - n_sys = n_train_sys + n_test_sys - # Split into training and testing - if "dataset_filename" in keys(input) - filename = input["dataset_path"]*input["dataset_filename"] - systems, energies, forces, stress = - load_data(filename, max_entries = n_sys) - rand_list = randperm(n_sys) - train_index, test_index = rand_list[1:n_train_sys], rand_list[n_train_sys+1:n_sys] - train_systems, train_energies, train_forces, train_stress = - systems[train_index], energies[train_index], - forces[train_index], stress[train_index] - test_systems, test_energies, test_forces, test_stress = - systems[test_index], energies[test_index], - forces[test_index], stress[test_index] - else # The data set is already split. - filename = input["dataset_path"]*input["trainingset_filename"] - train_systems, train_energies, train_forces, train_stress = - load_data(filename, max_entries = n_train_sys) - filename = input["dataset_path"]*input["testset_filename"] - test_systems, test_energies, test_forces, test_stress = - load_data(filename, max_entries = n_test_sys) - end - return train_systems, train_energies, train_forces, train_stress, - test_systems, test_energies, test_forces, test_stress -end - - -# Linearize forces -function linearize_forces(forces) - return vcat([vcat(vcat(f...)...) for f in forces]...) -end - - -# Split data into batches -function get_batches(n_batches, B_train, B_train_ext, e_train, dB_train, f_train, - B_test, B_test_ext, e_test, dB_test, f_test) - - bs_train_e = floor(Int, length(B_train) / n_batches) - train_loader_e = DataLoader((B_train, e_train), batchsize=bs_train_e, shuffle=true) - bs_train_f = floor(Int, length(dB_train) / n_batches) - train_loader_f = DataLoader((B_train_ext, dB_train, f_train), - batchsize=bs_train_f, shuffle=true) - println("Batch sizes of training energy and force datasets: ", bs_train_e, ", ", bs_train_f) - - bs_test_e = floor(Int, length(B_test) / n_batches) - test_loader_e = DataLoader((B_test, e_test), batchsize=bs_test_e, shuffle=true) - bs_test_f = floor(Int, length(dB_test) / n_batches) - test_loader_f = DataLoader((B_test_ext, dB_test, f_test), - batchsize=bs_test_f, shuffle=true) - println("Batch sizes of test energy and force datasets: ", bs_train_e, ", ", bs_train_f) - - return train_loader_e, train_loader_f, test_loader_e, test_loader_f -end - - diff --git a/src/IO/utils.jl b/src/IO/utils.jl deleted file mode 100644 index 4d479357..00000000 --- a/src/IO/utils.jl +++ /dev/null @@ -1,17 +0,0 @@ -# This code will be added to PotentialLearning.jl -using CSV - -macro savevar(path, var) - quote - write("$(path)" * $(string(var)) * ".dat", string($(esc(var)))) - end -end - -macro savecsv(path, var) - return :( CSV.write("$(path)" * $(string(var)) * ".csv", $(var), header = false) ) -end - -macro savefig(path, var) - return :( savefig($(var), "$(path)" * $(string(var)) * ".png") ) -end - diff --git a/src/Interface.jl b/src/Interface.jl index 2e8c81d3..9111f1b9 100644 --- a/src/Interface.jl +++ b/src/Interface.jl @@ -4,86 +4,15 @@ # ################################################################################ -using ElectronicStructure, InteratomicPotentials -using LinearAlgebra, GalacticOptim, Optim, BlackBoxOptim - -export LearningProblem, LearningOptimizer -export SDPOpt, LeastSquaresOpt, QRLinearOpt, NelderMeadOpt -export loss, learn - - -# Abstract types ############################################################### - -""" - LearningProblem - -""" -abstract type LearningProblem end - -""" - LearningOptimizer - -""" -abstract type LearningOptimizer end - - -# Optimizers ################################################################### - -""" - SDPOpt - -Semidefinite program (SDP) optimizer -""" -struct SDPOpt <: LearningOptimizer end - -""" - LeastSquaresOpt - -Least squares optimizer -""" -struct LeastSquaresOpt <: LearningOptimizer end - -""" - QRLinearOpt - -QR optimizer -""" -struct QRLinearOpt <: LearningOptimizer end - -""" - NelderMeadOpt - -Nelder mead optimizer -""" -struct NelderMeadOpt <: LearningOptimizer - maxiters -end - - -# Learning and loss functions ################################################## - -""" - loss(params::Vector, opt::LearningOptimizer) - -`params`: parameters to be fitted -`opt`: learning optimizer -""" -function loss(params::Vector, opt::LearningOptimizer) end - -""" - learn(lp::LearningProblem, opt::LearningOptimizer) - -`lp`: learning problem -`opt`: learning optimizer -""" -function learn(lp::LearningProblem, opt::LearningOptimizer) end - -""" - learn(lp::LearningProblem, opt::LearningOptimizer, loss) - -`lp`: learning problem -`opt`: learning optimizer -`loss`: loss function -""" -function learn(lp::LearningProblem, opt::LearningOptimizer, loss) end +using AtomsBase +using InteratomicPotentials +using InteratomicBasisPotentials +using OrderedCollections +using IterTools +using LinearAlgebra +using UnitfulAtomic +using Unitful +using Flux +using Flux.Data: DataLoader +using CSV diff --git a/src/PostProc/metrics.jl b/src/PostProc/Metrics.jl similarity index 62% rename from src/PostProc/metrics.jl rename to src/PostProc/Metrics.jl index acc956ad..a8d83a40 100644 --- a/src/PostProc/metrics.jl +++ b/src/PostProc/Metrics.jl @@ -1,4 +1,15 @@ -# Calculate metrics +export calc_metrics, get_metrics + + +""" + calc_metrics(x_pred, x) + +`x_pred`: vector of predicted values of a variable. E.g. energy. +`x`: vector of true values of a variable. E.g. energy. + +Returns MAE, RMSE, and RSQ. + +""" function calc_metrics(x_pred, x) x_mae = sum(abs.(x_pred .- x)) / length(x) x_rmse = sqrt(sum((x_pred .- x).^2) / length(x)) @@ -6,6 +17,29 @@ function calc_metrics(x_pred, x) return x_mae, x_rmse, x_rsq end + +""" + get_metrics( e_train_pred, e_train, f_train_pred, f_train, + e_test_pred, e_test, f_test_pred, f_test, + B_time, dB_time, time_fitting) + +`e_train_pred`: vector of predicted training energy values. +`e_train`: vector of true training energy values. +`f_train_pred`: vector of predicted training force values. +`f_train`: vector of true training force values. +`e_test_pred`: vector of predicted test energy values. +`e_test`: vector of true test energy values. +`f_test_pred`: vector of predicted test force values. +`f_test`: vector of true test force values. +`B_time`: elapsed time consumed by descriptors calculation. +`dB_time`: elapsed time consumed by descriptor derivatives calculation. +`time_fitting`: elapsed time consumed by fitting process. + +Computes MAE, RMSE, and RSQ for training and testing energies and forces. +Also add elapsed times about descriptors and fitting calculations. +Returns an OrderedDict with the information above. + +""" function get_metrics( e_train_pred, e_train, f_train_pred, f_train, e_test_pred, e_test, f_test_pred, f_test, B_time, dB_time, time_fitting) diff --git a/src/PostProc/plots.jl b/src/PostProc/Plots.jl similarity index 69% rename from src/PostProc/plots.jl rename to src/PostProc/Plots.jl index 2c0edb29..97b3e505 100644 --- a/src/PostProc/plots.jl +++ b/src/PostProc/Plots.jl @@ -1,4 +1,14 @@ -# Plot variables +export plot_energy, plot_forces, plot_cos + +""" + plot_energy(e_pred, e_true) + +`e_pred`: vector of predicted energies +`e_true`: vector of true energies + +Returns an energy plot. + +""" function plot_energy(e_pred, e_true) r0 = minimum(e_true); r1 = maximum(e_true); rs = (r1-r0)/10 plot( e_true, e_pred, seriestype = :scatter, markerstrokewidth=0, @@ -7,6 +17,16 @@ function plot_energy(e_pred, e_true) return p end + +""" + plot_forces(f_pred, f_true) + +`f_pred`: vector of predicted forces +`f_true`: vector of true forces + +Returns a force plot. + +""" function plot_forces(f_pred, f_true) f_pred_v = collect(eachcol(reshape(f_pred, 3, :))) f_true_v = collect(eachcol(reshape(f_true, 3, :))) @@ -18,6 +38,16 @@ function plot_forces(f_pred, f_true) return p end + +""" + plot_cos(f_pred, f_true) + +`f_pred`: vector of predicted forces +`f_true`: vector of true forces + +Returns a plot with the cosine or correlation of the forces. + +""" function plot_cos(f_pred, f_true) f_pred_v = collect(eachcol(reshape(f_pred, 3, :))) f_true_v = collect(eachcol(reshape(f_true, 3, :))) diff --git a/src/PotentialLearning.jl b/src/PotentialLearning.jl index 8e105500..b4b3a0b2 100644 --- a/src/PotentialLearning.jl +++ b/src/PotentialLearning.jl @@ -1,6 +1,12 @@ module PotentialLearning include("Interface.jl") -#include("SNAPLearningProblem.jl") +include("IO/Input.jl") +include("IO/Load-extxyz.jl") +include("IO/Utils.jl") +include("Training/Losses.jl") +include("Training/Training.jl") +include("PostProc/Metrics.jl") +include("PostProc/Plots.jl") end diff --git a/src/Training/loss.jl b/src/Training/Losses.jl similarity index 86% rename from src/Training/loss.jl rename to src/Training/Losses.jl index 00e10d76..5ec63285 100644 --- a/src/Training/loss.jl +++ b/src/Training/Losses.jl @@ -9,6 +9,9 @@ export loss, global_loss `fs_pred`: preditected forces `fs`: forces `w_f`: force weight + +Returns the weighted loss of the energies and forces using MSE. + """ loss(es_pred, es, w_e, fs_pred, fs, w_f) = w_e * Flux.Losses.mse(es_pred, es) + w_f * Flux.Losses.mse(fs_pred, fs) @@ -23,6 +26,8 @@ loss(es_pred, es, w_e, fs_pred, fs, w_f) = w_e * Flux.Losses.mse(es_pred, es) + `ps`: neural network parameters. See Flux.destructure. `re`: neural network restructure. See Flux.destructure. +Returns the weighted global (all bacthes) loss of the energies and forces. + """ global_loss(loader_e, loader_f, w_e, w_f, ps, re) = mean([loss(potential_energy.(bs_e, [ps], [re]), es, w_e, diff --git a/src/Training/training.jl b/src/Training/Training.jl similarity index 88% rename from src/Training/training.jl rename to src/Training/Training.jl index 7697c542..57c9fdf4 100644 --- a/src/Training/training.jl +++ b/src/Training/Training.jl @@ -1,6 +1,15 @@ -# Batch training using Optimization.jl -# I am using one of the Optimization.jl solvers, because I have not been able to -# tackle this problem with the Flux solvers. +export train! + +""" + batch_train_opt!(ps, re, opt, maxiters, train_loader_e, train_loader_f, + w_e, w_f, epoch, train_losses_batches) + +TODO: complete documentation +Batch training using Optimization.jl +I am using one of the Optimization.jl solvers, because I have not been able to +tackle this problem with the Flux solvers. + +""" function batch_train_opt!(ps, re, opt, maxiters, train_loader_e, train_loader_f, w_e, w_f, epoch, train_losses_batches) i = 1 @@ -22,7 +31,13 @@ function batch_train_opt!(ps, re, opt, maxiters, train_loader_e, train_loader_f, return ps end -# Batch training using Flux.jl +""" + batch_train_flux!(ps, re, opt, maxiters, train_loader_e, train_loader_f, w_e, w_f) + +TODO: complete documentation +Batch training using Flux.jl + +""" function batch_train_flux!(ps, re, opt, maxiters, train_loader_e, train_loader_f, w_e, w_f) for ((bs_e, es), (bs_f, dbs_f, fs)) in zip(train_loader_e, train_loader_f) g = gradient(Flux.params(ps)) do @@ -34,7 +49,13 @@ function batch_train_flux!(ps, re, opt, maxiters, train_loader_e, train_loader_f return ps end -# Training +""" + train!( lib, nnbp, epochs, opt, maxiters, train_loader_e, train_loader_f, + test_loader_e, test_loader_f, w_e, w_f) + +TODO: complete documentation + +""" function train!( lib, nnbp, epochs, opt, maxiters, train_loader_e, train_loader_f, test_loader_e, test_loader_f, w_e, w_f) diff --git a/src/Training/losses.jl b/src/Training/losses.jl deleted file mode 100644 index ce419faa..00000000 --- a/src/Training/losses.jl +++ /dev/null @@ -1,10 +0,0 @@ -# Loss function -loss(es_pred, es, w_e, fs_pred, fs, w_f) = w_e * Flux.Losses.mse(es_pred, es) + - w_f * Flux.Losses.mse(fs_pred, fs) - -# Global loss function -global_loss(loader_e, loader_f, w_e, w_f, ps, re) = - mean([loss(potential_energy.(bs_e, [ps], [re]), es, w_e, - force.(bs_f, dbs_f, [ps], [re]), fs, w_f) - for ((bs_e, es), (bs_f, dbs_f, fs)) in zip(loader_e, loader_f)]) - From 213eab988f1557a9981900a3744c2e30e38d6ade Mon Sep 17 00:00:00 2001 From: Emmanuel Lujan Date: Sat, 9 Jul 2022 00:52:40 -0400 Subject: [PATCH 13/35] Improve comments and documentation. --- src/Training/Training.jl | 45 +++++++++++++++++++++++++++++++++------- 1 file changed, 37 insertions(+), 8 deletions(-) diff --git a/src/Training/Training.jl b/src/Training/Training.jl index 57c9fdf4..fd229b51 100644 --- a/src/Training/Training.jl +++ b/src/Training/Training.jl @@ -4,10 +4,18 @@ export train! batch_train_opt!(ps, re, opt, maxiters, train_loader_e, train_loader_f, w_e, w_f, epoch, train_losses_batches) -TODO: complete documentation -Batch training using Optimization.jl -I am using one of the Optimization.jl solvers, because I have not been able to -tackle this problem with the Flux solvers. +`ps`: neural network parameters. See Flux.destructure. +`re`: neural network restructure. See Flux.destructure. +`opt`: optimizer. +`maxiters`: maximum number of iterations in the optimizer. +`train_loader_e`: energy data loader. +`train_loader_f`: force data loader. +`w_e`: energy weight. +`w_f`: force weight. +`epoch`: current epoch. +`train_losses_batches`: vector of batch losses during training. + +Batch training using Optimization.jl. Returns NN parameters. """ function batch_train_opt!(ps, re, opt, maxiters, train_loader_e, train_loader_f, @@ -33,9 +41,17 @@ end """ batch_train_flux!(ps, re, opt, maxiters, train_loader_e, train_loader_f, w_e, w_f) - -TODO: complete documentation -Batch training using Flux.jl + +`ps`: neural network parameters. See Flux.destructure. +`re`: neural network restructure. See Flux.destructure. +`opt`: optimizer. +`maxiters`: maximum number of iterations in the optimizer. +`train_loader_e`: energy data loader. +`train_loader_f`: force data loader. +`w_e`: energy weight. +`w_f`: force weight. + +Batch training using Flux.jl. Returns neural network parameters. """ function batch_train_flux!(ps, re, opt, maxiters, train_loader_e, train_loader_f, w_e, w_f) @@ -53,7 +69,20 @@ end train!( lib, nnbp, epochs, opt, maxiters, train_loader_e, train_loader_f, test_loader_e, test_loader_f, w_e, w_f) -TODO: complete documentation +`lib`: +`nnbp`: +`epochs`: no. of epochs. +`opt`: optimizer. +`maxiters`: maximum number of iterations in the optimizer. +`train_loader_e`: energy data loader for training. +`train_loader_f`: force data loader for training. +`test_loader_e`: energy data loader for test. +`test_loader_f`: force data loader for test. +`w_e`: energy weight. +`w_f`: force weight. + +Train neural network potential. +Returns losses of training and test per epoch and per batch. """ function train!( lib, nnbp, epochs, opt, maxiters, train_loader_e, train_loader_f, From 16860db9e127770d96fe780aa0608852c27ec870 Mon Sep 17 00:00:00 2001 From: Emmanuel Lujan Date: Sat, 9 Jul 2022 01:27:32 -0400 Subject: [PATCH 14/35] Update Project.toml --- Project.toml | 9 +++++++++ 1 file changed, 9 insertions(+) diff --git a/Project.toml b/Project.toml index 40b2ef67..cb255b6a 100644 --- a/Project.toml +++ b/Project.toml @@ -4,13 +4,22 @@ authors = ["CESMIX Team"] version = "0.1.0" [deps] +AtomsBase = "a963bdd2-2df7-4f54-a1ee-49d51e6be12a" BlackBoxOptim = "a134a8b2-14d6-55f6-9291-3336d3ab0209" +CSV = "336ed68f-0bac-5ca0-87d4-7b16caf5d00b" +Flux = "587475ba-b771-5e3f-ad9e-33799f191a9c" GalacticOptim = "a75be94c-b780-496d-a8a9-0878b188d577" +InteratomicBasisPotentials = "37c59853-c2ad-4e3a-930c-a41b2395fb19" +InteratomicPotentials = "a9efe35a-c65d-452d-b8a8-82646cd5cb04" +IterTools = "c8e1da08-722c-5040-9ed9-7db0dc04731e" LAMMPS = "ee2e13b9-eee9-4449-aafa-cfa6a2dbe14d" LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e" Optim = "429524aa-4258-5aef-a3af-852621145aeb" +OrderedCollections = "bac558e1-5e72-5ebc-8fee-abe8a469f55d" Printf = "de0858da-6303-5e67-8744-51eddeeeb8d7" StaticArrays = "90137ffa-7385-5640-81b9-e52037218182" +Unitful = "1986cc42-f94f-5a68-af5c-568840ba703d" +UnitfulAtomic = "a7773ee8-282e-5fa2-be4e-bd808c38a91a" Zygote = "e88e6eb3-aa80-5325-afca-941959d7151f" [compat] From 840b18679715f9965b833d6eba9fa8cff75843d5 Mon Sep 17 00:00:00 2001 From: Emmanuel Lujan Date: Sat, 9 Jul 2022 04:54:08 -0400 Subject: [PATCH 15/35] Update IO and dependencies. --- .gitignore | 4 ++++ Project.toml | 4 +++- src/IO/Input.jl | 7 +++---- src/IO/Utils.jl | 23 ++++++++++++++++------- src/Interface.jl | 3 +++ 5 files changed, 29 insertions(+), 12 deletions(-) diff --git a/.gitignore b/.gitignore index ba39cc53..eb0742e9 100644 --- a/.gitignore +++ b/.gitignore @@ -1 +1,5 @@ Manifest.toml + +# generated docs +docs/build/ +docs/src/generated/ diff --git a/Project.toml b/Project.toml index cb255b6a..bf7c08d5 100644 --- a/Project.toml +++ b/Project.toml @@ -16,11 +16,13 @@ LAMMPS = "ee2e13b9-eee9-4449-aafa-cfa6a2dbe14d" LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e" Optim = "429524aa-4258-5aef-a3af-852621145aeb" OrderedCollections = "bac558e1-5e72-5ebc-8fee-abe8a469f55d" +Plots = "91a5bcdd-55d7-5caf-9e0b-520d859cae80" Printf = "de0858da-6303-5e67-8744-51eddeeeb8d7" StaticArrays = "90137ffa-7385-5640-81b9-e52037218182" +Statistics = "10745b16-79ce-11e8-11f9-7d13ad32a3b2" Unitful = "1986cc42-f94f-5a68-af5c-568840ba703d" UnitfulAtomic = "a7773ee8-282e-5fa2-be4e-bd808c38a91a" Zygote = "e88e6eb3-aa80-5325-afca-941959d7151f" [compat] -julia = "1.6" +julia = "1.7" diff --git a/src/IO/Input.jl b/src/IO/Input.jl index 161aed23..cf20745e 100644 --- a/src/IO/Input.jl +++ b/src/IO/Input.jl @@ -1,4 +1,3 @@ -include("load-extxyz.jl") export get_defaults_args, get_input, load_dataset, linearize_forces, get_batches @@ -76,7 +75,7 @@ function load_dataset(n_train_sys, n_test_sys, dataset_path, dataset_filename) n_sys = n_train_sys + n_test_sys filename = dataset_path*dataset_filename systems, energies, forces, stress = - load_data(filename, max_entries = n_sys) + load_extxyz(filename, max_entries = n_sys) rand_list = randperm(n_sys) train_index, test_index = rand_list[1:n_train_sys], rand_list[n_train_sys+1:n_sys] train_systems, train_energies, train_forces, train_stress = @@ -109,10 +108,10 @@ function load_dataset(n_train_sys, n_test_sys, dataset_path, n_sys = n_train_sys + n_test_sys filename = dataset_path*trainingset_filename train_systems, train_energies, train_forces, train_stress = - load_data(filename, max_entries = n_train_sys) + load_extxyz(filename, max_entries = n_train_sys) filename = dataset_path*testset_filename test_systems, test_energies, test_forces, test_stress = - load_data(filename, max_entries = n_test_sys) + load_extxyz(filename, max_entries = n_test_sys) return train_systems, train_energies, train_forces, train_stress, test_systems, test_energies, test_forces, test_stress end diff --git a/src/IO/Utils.jl b/src/IO/Utils.jl index d9bdcecb..f8a69068 100644 --- a/src/IO/Utils.jl +++ b/src/IO/Utils.jl @@ -1,5 +1,10 @@ -export savevar, savecsv, savefig +export @savevar, @savecsv, @savefig + +path = "" +var = "" +dict = "" + """ savevar(path, var) @@ -8,20 +13,22 @@ Simplifies the saving of a variable. """ macro savevar(path, var) - quote - write("$(path)" * $(string(var)) * ".dat", string($(esc(var)))) - end + quote + write($(esc(path)) * $(string(var)) * ".dat", string($(esc(var)))) + end end """ - savevar(path, dict) + savecsv(path, dict) Simplifies the saving of a dictionary to a CSV file. """ macro savecsv(path, dict) - return :( CSV.write("$(path)" * $(string(dict)) * ".csv", $(dict), header = false) ) + quote + CSV.write($(esc(path)) * $(string(dict)) * ".csv", $(esc(dict)), header = false) + end end """ @@ -31,6 +38,8 @@ Simplifies the saving of a figure. """ macro savefig(path, var) - return :( savefig($(var), "$(path)" * $(string(var)) * ".png") ) + quote + savefig($(esc(var)), $(esc(path)) * $(string(var)) * ".png") + end end diff --git a/src/Interface.jl b/src/Interface.jl index 9111f1b9..4406fb4e 100644 --- a/src/Interface.jl +++ b/src/Interface.jl @@ -10,9 +10,12 @@ using InteratomicBasisPotentials using OrderedCollections using IterTools using LinearAlgebra +using StaticArrays +using Statistics using UnitfulAtomic using Unitful using Flux using Flux.Data: DataLoader using CSV +using Plots From 0a7577190fbd30f699d8ae3500e3d015d9cce6a1 Mon Sep 17 00:00:00 2001 From: Emmanuel Lujan Date: Mon, 11 Jul 2022 16:19:44 -0400 Subject: [PATCH 16/35] Major changes, integrating with AtomisticComposableWorkflows. --- Project.toml | 1 + src/IO/Input.jl | 24 ++++++++ src/Interface.jl | 1 + src/PotentialLearning.jl | 3 +- src/Project.toml | 2 + src/Training/NNBasisPotential.jl | 101 +++++++++++++++++++++++++++++++ src/Training/Training.jl | 1 + 7 files changed, 132 insertions(+), 1 deletion(-) create mode 100644 src/Project.toml create mode 100644 src/Training/NNBasisPotential.jl diff --git a/Project.toml b/Project.toml index bf7c08d5..0b4c2be9 100644 --- a/Project.toml +++ b/Project.toml @@ -15,6 +15,7 @@ IterTools = "c8e1da08-722c-5040-9ed9-7db0dc04731e" LAMMPS = "ee2e13b9-eee9-4449-aafa-cfa6a2dbe14d" LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e" Optim = "429524aa-4258-5aef-a3af-852621145aeb" +Optimization = "7f7a1694-90dd-40f0-9382-eb1efda571ba" OrderedCollections = "bac558e1-5e72-5ebc-8fee-abe8a469f55d" Plots = "91a5bcdd-55d7-5caf-9e0b-520d859cae80" Printf = "de0858da-6303-5e67-8744-51eddeeeb8d7" diff --git a/src/IO/Input.jl b/src/IO/Input.jl index cf20745e..69cd9c42 100644 --- a/src/IO/Input.jl +++ b/src/IO/Input.jl @@ -117,6 +117,30 @@ function load_dataset(n_train_sys, n_test_sys, dataset_path, end +""" + load_dataset(input) + +`input`: OrderedDict with input arguments. See `get_defaults_args()`. + +Returns training and test energies, forces, and stresses. + +""" +function load_dataset(input) + n_train_sys = input["n_train_sys"] + n_test_sys = input["n_test_sys"] + dataset_path = input["dataset_path"] + if "dataset_filename" in keys(input) + return load_dataset(n_train_sys, n_test_sys, dataset_path, + dataset_filename) + else + trainingset_filename = input["trainingset_filename"] + testset_filename = input["testset_filename"] + return load_dataset(n_train_sys, n_test_sys, dataset_path, + trainingset_filename, testset_filename) + end +end + + """ linearize_forces(forces) diff --git a/src/Interface.jl b/src/Interface.jl index 4406fb4e..ff76b8a3 100644 --- a/src/Interface.jl +++ b/src/Interface.jl @@ -12,6 +12,7 @@ using IterTools using LinearAlgebra using StaticArrays using Statistics +using Optimization using UnitfulAtomic using Unitful using Flux diff --git a/src/PotentialLearning.jl b/src/PotentialLearning.jl index b4b3a0b2..841d511d 100644 --- a/src/PotentialLearning.jl +++ b/src/PotentialLearning.jl @@ -4,7 +4,8 @@ include("Interface.jl") include("IO/Input.jl") include("IO/Load-extxyz.jl") include("IO/Utils.jl") -include("Training/Losses.jl") +include("Training/NNBasisPotential.jl") # TODO: Add to InteratomicPotentials.jl/InteratomicBasisPotentials.jl +include("Training/Losses.jl") include("Training/Training.jl") include("PostProc/Metrics.jl") include("PostProc/Plots.jl") diff --git a/src/Project.toml b/src/Project.toml new file mode 100644 index 00000000..2a3f0a54 --- /dev/null +++ b/src/Project.toml @@ -0,0 +1,2 @@ +[deps] +Optimization = "7f7a1694-90dd-40f0-9382-eb1efda571ba" diff --git a/src/Training/NNBasisPotential.jl b/src/Training/NNBasisPotential.jl new file mode 100644 index 00000000..a78512ac --- /dev/null +++ b/src/Training/NNBasisPotential.jl @@ -0,0 +1,101 @@ +# TODO: Add to InteratomicPotentials.jl/InteratomicBasisPotentials.jl + +# Defining NNBP composed type and associated functions +mutable struct NNBasisPotential <: AbstractPotential + nn + nn_params + ibp_params +end + +function potential_energy(A::AbstractSystem, + p::NNBasisPotential) + b = evaluate_basis(A, p.ibp_params) + return p.nn(b) +end + +function force(A::AbstractSystem, + p::NNBasisPotential) + b = evaluate_basis(A, p.ibp_params) + dnndb = first(gradient(p.nn, b)) + dbdr = evaluate_basis_d(A, p.ibp_params) + return [[-dnndb ⋅ dbdr[atom][coor,:] for coor in 1:3] + for atom in 1:length(dbdr)] +end + +function potential_energy(b::Vector, p::NNBasisPotential) + return sum(p.nn(b)) +end + +function potential_energy(b::Vector, ps::Vector, re) + return sum(re(ps)(b)) +end + +# Note: calculating the gradient of the loss function requires in turn +# calculating the gradient of the energy. That is, calculating the gradient of +# a function that calculates another gradient. +# So far I have not found a clean way to do this using the abstractions +# provided by Flux, which in turn is integrated with Zygote. +# Links related to this issue: +# https://discourse.julialang.org/t/how-to-add-norm-of-gradient-to-a-loss-function/69873/16 +# https://discourse.julialang.org/t/issue-with-zygote-over-forwarddiff-derivative/70824 +# https://github.com/FluxML/Zygote.jl/issues/953#issuecomment-841882071 +# +# To solve this for the moment I am calculating one of the gradients analytically. +# To do this I had to use Flux.destructure, which I think makes the code slower +# because of the copies it creates. + +function grad_mlp(nn_params, x0) + dsdy(x) = x>0 ? 1 : 0 # Flux.σ(x) * (1 - Flux.σ(x)) + prod = 1; x = x0 + n_layers = length(nn_params) ÷ 2 + for i in 1:2:2(n_layers-1)-1 # i : 1, 3 + y = nn_params[i] * x + nn_params[i+1] + x = Flux.relu.(y) # Flux.σ.(y) + prod = dsdy.(y) .* nn_params[i] * prod + end + i = 2(n_layers)-1 + prod = nn_params[i] * prod + return prod +end + +function force(b, dbdr, p) + dnndb = grad_mlp(p.nn_params, b) + return dnndb ⋅ dbdr +end + +function force(b, dbdr, ps, re) + nn_params = Flux.params(re(ps)) + dnndb = grad_mlp(nn_params, b) + return dnndb ⋅ dbdr +end + +# Computing the force using ForwardDiff +#function force(b::Vector, dbdr::Vector, p::NNBasisPotential) +# dnndb = ForwardDiff.gradient(x -> sum(p.nn(x)), b) +# return dnndb ⋅ dbdr +#end + +#function force(b::Vector, dbdr::Vector, p::NNBasisPotential) +# dnndb = gradient(x -> sum(p.nn(x)), b)[1] +# return dnndb ⋅ dbdr +#end + +# Computing the force using ForwardDiff and destructure +#function force(b::Vector, dbdr::Vector, ps::Vector, re) +# dnndb = ForwardDiff.gradient(x -> sum(re(ps)(x)), b) +# return dnndb ⋅ dbdr +#end + +# Computing the force using pullback +#function force(b::Vector, dbdr::Vector, p::NNBasisPotential) +# y, pullback = Zygote.pullback(p.nn, b) +# dnndb = pullback(ones(size(y)))[1] +# return dnndb ⋅ dbdr +#end + +#function force(b::Vector, dbdr::Vector, ps::Vector, re) +# y, pullback = Zygote.pullback(re(ps), b) +# dnndb = pullback(ones(size(y)))[1] +# return dnndb ⋅ dbdr +#end + diff --git a/src/Training/Training.jl b/src/Training/Training.jl index fd229b51..f7bdc75e 100644 --- a/src/Training/Training.jl +++ b/src/Training/Training.jl @@ -1,5 +1,6 @@ export train! + """ batch_train_opt!(ps, re, opt, maxiters, train_loader_e, train_loader_f, w_e, w_f, epoch, train_losses_batches) From c21661b74fd4fe70550bef2c34afd4e46b2916b6 Mon Sep 17 00:00:00 2001 From: Emmanuel Lujan Date: Mon, 11 Jul 2022 18:05:12 -0400 Subject: [PATCH 17/35] Changes about integration with AtomisticComposableWorkflows. --- Project.toml | 1 + src/IO/Input.jl | 1 + src/Interface.jl | 3 ++- src/Project.toml | 2 -- 4 files changed, 4 insertions(+), 3 deletions(-) delete mode 100644 src/Project.toml diff --git a/Project.toml b/Project.toml index 0b4c2be9..76a8913a 100644 --- a/Project.toml +++ b/Project.toml @@ -19,6 +19,7 @@ Optimization = "7f7a1694-90dd-40f0-9382-eb1efda571ba" OrderedCollections = "bac558e1-5e72-5ebc-8fee-abe8a469f55d" Plots = "91a5bcdd-55d7-5caf-9e0b-520d859cae80" Printf = "de0858da-6303-5e67-8744-51eddeeeb8d7" +Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c" StaticArrays = "90137ffa-7385-5640-81b9-e52037218182" Statistics = "10745b16-79ce-11e8-11f9-7d13ad32a3b2" Unitful = "1986cc42-f94f-5a68-af5c-568840ba703d" diff --git a/src/IO/Input.jl b/src/IO/Input.jl index 69cd9c42..b3b349c9 100644 --- a/src/IO/Input.jl +++ b/src/IO/Input.jl @@ -130,6 +130,7 @@ function load_dataset(input) n_test_sys = input["n_test_sys"] dataset_path = input["dataset_path"] if "dataset_filename" in keys(input) + dataset_filename = input["dataset_filename"] return load_dataset(n_train_sys, n_test_sys, dataset_path, dataset_filename) else diff --git a/src/Interface.jl b/src/Interface.jl index ff76b8a3..5c50c205 100644 --- a/src/Interface.jl +++ b/src/Interface.jl @@ -9,7 +9,7 @@ using InteratomicPotentials using InteratomicBasisPotentials using OrderedCollections using IterTools -using LinearAlgebra +using LinearAlgebra using StaticArrays using Statistics using Optimization @@ -17,6 +17,7 @@ using UnitfulAtomic using Unitful using Flux using Flux.Data: DataLoader +using Random using CSV using Plots diff --git a/src/Project.toml b/src/Project.toml deleted file mode 100644 index 2a3f0a54..00000000 --- a/src/Project.toml +++ /dev/null @@ -1,2 +0,0 @@ -[deps] -Optimization = "7f7a1694-90dd-40f0-9382-eb1efda571ba" From e6793d7fbc195986ce41bb1447e300388c8e6b53 Mon Sep 17 00:00:00 2001 From: Emmanuel Lujan Date: Tue, 12 Jul 2022 02:53:01 -0400 Subject: [PATCH 18/35] Removing default arguments function. --- src/IO/Input.jl | 32 +------------------------------- 1 file changed, 1 insertion(+), 31 deletions(-) diff --git a/src/IO/Input.jl b/src/IO/Input.jl index b3b349c9..50a99ae3 100644 --- a/src/IO/Input.jl +++ b/src/IO/Input.jl @@ -1,32 +1,5 @@ -export get_defaults_args, get_input, load_dataset, linearize_forces, get_batches - -""" - get_defaults_args() - -Returns default input arguments for NN potential training. - -TODO: probably this should not be here. - -""" -function get_defaults_args() - args = ["experiment_path", "TiO2/", - "dataset_path", "data/", - "trainingset_filename", "TiO2trainingset.xyz", - "testset_filename", "TiO2testset.xyz", - "n_train_sys", "80", - "n_test_sys", "20", - "n_batches", "8", - "n_body", "3", - "max_deg", "3", - "r0", "1.0", - "rcutoff", "5.0", - "wL", "1.0", - "csp", "1.0", - "w_e", "1.0", - "w_f", "1.0"] - return args -end +export get_input, load_dataset, linearize_forces, get_batches """ @@ -40,9 +13,6 @@ for information about how to define the input arguments. """ function get_input(args) - if length(args) == 0 - args = get_defaults_args() - end input = OrderedDict() for (key, val) in partition(args,2,2) if tryparse(Float64, val) != nothing From 89dac5933739db949c363180fba08291614e17c7 Mon Sep 17 00:00:00 2001 From: Emmanuel Lujan Date: Tue, 12 Jul 2022 22:27:06 -0400 Subject: [PATCH 19/35] Improving input loading in PotentialLearning.jl --- src/IO/Input.jl | 35 +++++++++++++++++++++++++++++------ 1 file changed, 29 insertions(+), 6 deletions(-) diff --git a/src/IO/Input.jl b/src/IO/Input.jl index 50a99ae3..01a46445 100644 --- a/src/IO/Input.jl +++ b/src/IO/Input.jl @@ -2,6 +2,25 @@ export get_input, load_dataset, linearize_forces, get_batches +""" + to_num(str) + +`str`: string with a number: integer or float + +Returns an integer or float. + +""" +function to_num(str) + val = nothing + if occursin(".", str) + val = parse(Float64, str) + else + val = parse(Int64, str) + end + return val +end + + """ get_input(args) @@ -15,12 +34,16 @@ for information about how to define the input arguments. function get_input(args) input = OrderedDict() for (key, val) in partition(args,2,2) - if tryparse(Float64, val) != nothing - if occursin(".", val) - val = parse(Float64, val) - else - val = parse(Int64, val) - end + val = replace(val, " " => "") + # if val is a boolean + if val == "true" || val == "false" + val = val == "true" + # if val is a vector, e.g. "[1.5,1.5]" + elseif val[1] == '[' + val = to_num.(split(val[2:end-1], ",")) + # if val is a number, e.g. 1.5 or 1 + elseif tryparse(Float64, val) != nothing + val = to_num(val) end input[key] = val end From 177b88233c821f09eabbeb0d0e2dffd7869c0c24 Mon Sep 17 00:00:00 2001 From: Emmanuel Lujan Date: Thu, 14 Jul 2022 03:24:38 -0400 Subject: [PATCH 20/35] Adding fitting code for ACE and ACE. --- .../Training.jl => Learning/Learning.jl} | 44 ++++++++++++++++++- src/{Training => Learning}/Losses.jl | 0 .../NNBasisPotential.jl | 0 src/PotentialLearning.jl | 6 +-- 4 files changed, 46 insertions(+), 4 deletions(-) rename src/{Training/Training.jl => Learning/Learning.jl} (86%) rename src/{Training => Learning}/Losses.jl (100%) rename src/{Training => Learning}/NNBasisPotential.jl (100%) diff --git a/src/Training/Training.jl b/src/Learning/Learning.jl similarity index 86% rename from src/Training/Training.jl rename to src/Learning/Learning.jl index f7bdc75e..a8e3edbd 100644 --- a/src/Training/Training.jl +++ b/src/Learning/Learning.jl @@ -1,4 +1,46 @@ -export train! +export train!, learn + + +""" + learn(B_train, dB_train, e_train, f_train, w_e, w_f) + +`B_train`: energy descriptors. +`dB_train`: force descriptors. +`e_train`: training energies. +`f_train`: training forces. +`w_e`: energy weight. +`w_f`: force weight. + +""" +function learn(B_train, dB_train, e_train, f_train, w_e, w_f) + + # Calculate A and b. + A = [B_train; dB_train] + b = [e_train; f_train] + + + # Calculate coefficients β. + Q = Diagonal([w_e * ones(length(e_train)); + w_f * ones(length(f_train))]) + β = (A'*Q*A) \ (A'*Q*b) + + + ## Check weights. + #using IterTools + #for (e_weight, f_weight) in product(1:10:100, 1:10:100) + # Q = Diagonal([e_weight * ones(length(e_train)); + # f_weight * ones(length(f_train))]) + # try + # β = (A'*Q*A) \ (A'*Q*b) + # a = compute_errors(dB_test * β, f_test) + # println(e_weight,", ", f_weight, ", ", a[1]) + # catch + # println("Exception with :", e_weight,", ", f_weight) + # end + #end + + return β +end """ diff --git a/src/Training/Losses.jl b/src/Learning/Losses.jl similarity index 100% rename from src/Training/Losses.jl rename to src/Learning/Losses.jl diff --git a/src/Training/NNBasisPotential.jl b/src/Learning/NNBasisPotential.jl similarity index 100% rename from src/Training/NNBasisPotential.jl rename to src/Learning/NNBasisPotential.jl diff --git a/src/PotentialLearning.jl b/src/PotentialLearning.jl index 841d511d..0f26073b 100644 --- a/src/PotentialLearning.jl +++ b/src/PotentialLearning.jl @@ -4,9 +4,9 @@ include("Interface.jl") include("IO/Input.jl") include("IO/Load-extxyz.jl") include("IO/Utils.jl") -include("Training/NNBasisPotential.jl") # TODO: Add to InteratomicPotentials.jl/InteratomicBasisPotentials.jl -include("Training/Losses.jl") -include("Training/Training.jl") +include("Learning/NNBasisPotential.jl") # TODO: Add to InteratomicPotentials.jl/InteratomicBasisPotentials.jl +include("Learning/Losses.jl") +include("Learning/Learning.jl") include("PostProc/Metrics.jl") include("PostProc/Plots.jl") From 7d6955fee234285574db8b3a9990bb0210a4402e Mon Sep 17 00:00:00 2001 From: Emmanuel Lujan Date: Fri, 15 Jul 2022 02:07:24 -0400 Subject: [PATCH 21/35] Organizing files. Introducing documentation. --- README.md | 7 +- docs/Project.toml | 5 + docs/citation.bib | 0 docs/make.jl | 65 ++++++++----- docs/src/api.md | 9 ++ docs/src/functions.md | 6 -- docs/src/index.md | 3 +- src/Interface.jl | 1 + src/old/Interface.jl | 89 ----------------- src/old/PotentialLearning.jl | 6 -- src/old/SNAPLearningProblem.jl | 170 --------------------------------- test/runtests.jl | 2 +- 12 files changed, 64 insertions(+), 299 deletions(-) create mode 100644 docs/citation.bib create mode 100644 docs/src/api.md delete mode 100644 docs/src/functions.md delete mode 100644 src/old/Interface.jl delete mode 100644 src/old/PotentialLearning.jl delete mode 100644 src/old/SNAPLearningProblem.jl diff --git a/README.md b/README.md index 1a1270ef..8ae7a533 100644 --- a/README.md +++ b/README.md @@ -1,6 +1,4 @@ -# [WIP] PotentialLearning.jl - -An Open Source library for active training and fast calculation of molecular dynamics potentials for atomistic simulations of materials. +## [WIP] PotentialLearning.jl: an open source library for the active learning and fast calculation of interatomic potentials in atomistic simulations of materials.

@@ -26,3 +24,6 @@ An Open Source library for active training and fast calculation of molecular dyn

Developed as part of [CESMIX](https://cesmix.mit.edu). + +See [Atomistic Composable Workflows](https://github.com/cesmix-mit/AtomisticComposableWorkflows) for current Julia case studies. + diff --git a/docs/Project.toml b/docs/Project.toml index dfa65cd1..de3d11c6 100644 --- a/docs/Project.toml +++ b/docs/Project.toml @@ -1,2 +1,7 @@ [deps] Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4" +DocumenterCitations = "daee34ce-89f3-4625-b898-19384cb65244" +GLMakie = "e9467ef8-e4e7-5192-8a1a-b1aee30e663a" +ImageMagick = "6218d12a-5da1-5696-b52f-db25d2ecc6d1" +Literate = "98b081ad-f1c9-55d3-8b20-4c87d4299306" +Makie = "ee78f7c6-11fb-53f2-987a-cfe4a2b5a57a" diff --git a/docs/citation.bib b/docs/citation.bib new file mode 100644 index 00000000..e69de29b diff --git a/docs/make.jl b/docs/make.jl index 419df621..4798a7b8 100644 --- a/docs/make.jl +++ b/docs/make.jl @@ -1,30 +1,49 @@ -# Inside make.jl -push!(LOAD_PATH,"../src/") + pushfirst!(LOAD_PATH, joinpath(@__DIR__, "..")) # add PotentialLearning to environment stack + using PotentialLearning using Documenter +using DocumenterCitations +using Literate + +DocMeta.setdocmeta!(PotentialLearning, :DocTestSetup, :(using PotentialLearning); recursive = true) + +bib = CitationBibliography(joinpath(@__DIR__, "citations.bib")) + +# Generate examples + +#const EXAMPLES_DIR = joinpath(@__DIR__, "..", "examples") +#const OUTPUT_DIR = joinpath(@__DIR__, "src/generated") + +#examples = Pair{String,String}[] + +#for (_, name) in examples +# example_filepath = joinpath(EXAMPLES_DIR, string(name, ".jl")) +# Literate.markdown(example_filepath, OUTPUT_DIR, documenter = true) +#end + +#examples = [title => joinpath("generated", string(name, ".md")) for (title, name) in examples] -DocMeta.setdocmeta!(PotentialLearning, :DocTestSetup, :(using PotentialLearning); recursive=true) - -makedocs( - modules = [PotentialLearning], - authors = "CESMIX-MIT", - repo="https://github.com/cesmix-mit/PotentialLearning.jl/blob/{commit}{path}#{line}", - sitename="PotentialLearning.jl", - format=Documenter.HTML(; - prettyurls=get(ENV, "CI", "false") == "true", - canonical="https://cesmix-mit.github.io/PotentialLearning.jl", - assets=String[], - ), - pages = [ - "Home" => "index.md", - "Functions" => "functions.md", - ], - doctest = true, - linkcheck = true, - strict = true, +makedocs(bib; + modules = [PotentialLearning], + authors = "CESMIX-MIT", + repo = "https://github.com/cesmix-mit/PotentialLearning.jl/blob/{commit}{path}#{line}", + sitename = "PotentialLearning.jl", + format = Documenter.HTML(; + prettyurls = get(ENV, "CI", "false") == "true", + canonical = "https://cesmix-mit.github.io/PotentialLearning.jl", + assets = String[], + ), + pages = [ + "Home" => "index.md", + "API" => "api.md", + ], + doctest = true, + linkcheck = true, + strict = true ) deploydocs(; - repo="github.com/cesmix-mit/PotentialLearning.jl", - devbranch = "main", + repo = "github.com/cesmix-mit/PotentialLearning.jl", + devbranch = "refactor", # main + push_preview = true ) diff --git a/docs/src/api.md b/docs/src/api.md new file mode 100644 index 00000000..17e486bf --- /dev/null +++ b/docs/src/api.md @@ -0,0 +1,9 @@ +# API Reference + +This page provides a list of all documented types and functions and in PotentialLearning.jl. + + +```@autodocs +Modules = [InteratomicPotentials] +Order = [:type, :function, :constant] +``` diff --git a/docs/src/functions.md b/docs/src/functions.md deleted file mode 100644 index 3bb29fe9..00000000 --- a/docs/src/functions.md +++ /dev/null @@ -1,6 +0,0 @@ -# Functions - -```@autodocs -Modules = [PotentialLearning] -``` - diff --git a/docs/src/index.md b/docs/src/index.md index 2c015f8d..fcde5d14 100644 --- a/docs/src/index.md +++ b/docs/src/index.md @@ -1 +1,2 @@ -# [WIP] PotentialLearning.jl +# PotentialLearning.jl + diff --git a/src/Interface.jl b/src/Interface.jl index 5c50c205..b7cbdf38 100644 --- a/src/Interface.jl +++ b/src/Interface.jl @@ -21,3 +21,4 @@ using Random using CSV using Plots +# TODO diff --git a/src/old/Interface.jl b/src/old/Interface.jl deleted file mode 100644 index 2e8c81d3..00000000 --- a/src/old/Interface.jl +++ /dev/null @@ -1,89 +0,0 @@ -################################################################################ -# -# Interface.jl -# -################################################################################ - -using ElectronicStructure, InteratomicPotentials -using LinearAlgebra, GalacticOptim, Optim, BlackBoxOptim - -export LearningProblem, LearningOptimizer -export SDPOpt, LeastSquaresOpt, QRLinearOpt, NelderMeadOpt -export loss, learn - - -# Abstract types ############################################################### - -""" - LearningProblem - -""" -abstract type LearningProblem end - -""" - LearningOptimizer - -""" -abstract type LearningOptimizer end - - -# Optimizers ################################################################### - -""" - SDPOpt - -Semidefinite program (SDP) optimizer -""" -struct SDPOpt <: LearningOptimizer end - -""" - LeastSquaresOpt - -Least squares optimizer -""" -struct LeastSquaresOpt <: LearningOptimizer end - -""" - QRLinearOpt - -QR optimizer -""" -struct QRLinearOpt <: LearningOptimizer end - -""" - NelderMeadOpt - -Nelder mead optimizer -""" -struct NelderMeadOpt <: LearningOptimizer - maxiters -end - - -# Learning and loss functions ################################################## - -""" - loss(params::Vector, opt::LearningOptimizer) - -`params`: parameters to be fitted -`opt`: learning optimizer -""" -function loss(params::Vector, opt::LearningOptimizer) end - -""" - learn(lp::LearningProblem, opt::LearningOptimizer) - -`lp`: learning problem -`opt`: learning optimizer -""" -function learn(lp::LearningProblem, opt::LearningOptimizer) end - -""" - learn(lp::LearningProblem, opt::LearningOptimizer, loss) - -`lp`: learning problem -`opt`: learning optimizer -`loss`: loss function -""" -function learn(lp::LearningProblem, opt::LearningOptimizer, loss) end - diff --git a/src/old/PotentialLearning.jl b/src/old/PotentialLearning.jl deleted file mode 100644 index 8e105500..00000000 --- a/src/old/PotentialLearning.jl +++ /dev/null @@ -1,6 +0,0 @@ -module PotentialLearning - -include("Interface.jl") -#include("SNAPLearningProblem.jl") - -end diff --git a/src/old/SNAPLearningProblem.jl b/src/old/SNAPLearningProblem.jl deleted file mode 100644 index 6d72f9b9..00000000 --- a/src/old/SNAPLearningProblem.jl +++ /dev/null @@ -1,170 +0,0 @@ - -export SmallSNAPLP, hyperparam_loss, β_loss, learn - -# Learning problem ############################################################# - - -""" - SmallSNAPLP - -SNAP learning problem for small systems -""" -struct SmallSNAPLP <: LearningProblem - - # Training ################################# - snap::SNAP # SNAP potential - A::Matrix # SNAP matrix - y::Vector # DFT and reference data - ATA::Matrix # A^T * A - ATy::Vector # A^T * y - Q::Diagonal # Covariance - invQ::Diagonal # inverse of Q - training_dft_data::SmallESData - training_ref_data::SmallESData - - # Validation ############################### - A_val::Matrix # SNAP matrix - y_val::Vector # DFT and reference data - validation_dft_data::SmallESData - validation_ref_data::SmallESData - -end - -function SmallSNAPLP(snap::SNAP, atomic_confs::Vector, data::SmallESData; - trainingsize = 0.8, fit = [:e, :f, :s]) where - # TODO: @views? - - # Training ############################################################# - m = floor(Int, length(atomic_confs) * trainingsize) - AA = get_snap(atomic_confs[1:m], snap) #TODO: get_snap should allow me to chose what to fit (e, f, or s) - n_e = m; n_f = n_e + m * length(atomic_confs[1].Atoms) * 3 - A = [] - if :e in fit A = AA[1:n_e, :] end - if :f in fit A = vcat(A, AA[n_e+1:n_f, :]) end - if :s in fit A = vcat(A, AA[n_f+1:end, :]) end - ATA = A' * A - Q = Diagonal(ones(size(A)[1])); invQ = inv(Q) - training_dft_data = SmallESData(data.energies[1:m], - data.forces[1:m], - data.stresses[1:m]) - # TODO: add ZBL, see PotentialLearning.jl in master - training_ref_data = SmallESData(data.energies[1:m] * 0.01, - data.forces[1:m] * 0.01, - data.stresses[1:m] * 0.01) - y = [] - if :e in fit - y = linearize(training_dft_data.energies) - - linearize(training_ref_data.energies) - end - if :f in fit - append!(y, linearize(training_dft_data.forces) - - linearize(training_ref_data.forces)) - end - if :s in fit - append!(y, linearize(training_dft_data.stresses) - - linearize(training_ref_data.stresses)) - end - ATy = A' * y - - # Validation ########################################################### - m_val = length(atomic_confs[m+1:end]) - AA_val = get_snap(atomic_confs[m+1:end], snap) - n_e = m_val; n_f = n_e + m_val * length(atomic_confs[1].Atoms) * 3 - A_val = [] - if :e in fit A_val = AA_val[1:n_e, :] end - if :f in fit A_val = vcat(A_val, AA_val[n_e+1:n_f, :]) end - if :s in fit A_val = vcat(A_val, AA_val[n_f+1:end, :]) end - validation_dft_data = SmallESData(data.energies[m+1:end], - data.forces[m+1:end], - data.stresses[m+1:end]) - # TODO: add ZBL, see PotentialLearning.jl in master - validation_ref_data = SmallESData(data.energies[m+1:end] * 0.01, - data.forces[m+1:end] * 0.01, - data.stresses[m+1:end] * 0.01) - y_val = [] - if :e in fit - y_val = linearize(validation_dft_data.energies) - - linearize(validation_ref_data.energies) - end - if :f in fit - append!(y_val, linearize(validation_dft_data.forces) - - linearize(validation_ref_data.forces)) - end - if :s in fit - append!(y_val, linearize(validation_dft_data.stresses) - - linearize(validation_ref_data.stresses)) - end - - SmallSNAPLP(snap, A, y, ATA, ATy, Q, invQ, training_dft_data, - training_ref_data, A_val, y_val, validation_dft_data, - validation_ref_data) -end - - - -# Hyper-parameter optimization ################################################# - -""" - hyperparam_loss(hyperparams::Vector, lp::SmallSNAPLP) - -SNAP hyper-parameter loss function -""" -function hyperparam_loss(hyperparams::Vector, lp::SmallSNAPLP) where -# return ... -end - - -""" - learn(lp::SmallSNAPLP, loss, s::SDPOpt) - -Learning function: using SDPOpt to optimize the hyper-parameters -""" -function learn(lp::SmallSNAPLP, loss, s::SDPOpt) where -# ...hyperparam_loss... -# lp.snap.rcutfac = ... -# lp.snap.twojmax = ... -end - - -# β-parameter optimization ##################################################### - -""" - learn(lp::SmallSNAPLP, s::LeastSquaresOpt) - -Learning function: using normal equations and qr decomposition to learn main parameters -""" -function learn(lp::SmallSNAPLP, s::LeastSquaresOpt) where - lp.snap.β = (lp.A' * lp.A) \ (lp.A' * lp.y) -end - -""" - learn(lp::SmallSNAPLP, s::QRLinearOpt) - -Learning function: using QR decomposition to learn main parameters -""" -function learn(lp::SmallSNAPLP, s::QRLinearOpt) where - lp.snap.β = lp.A \ lp.y # or... qr(A,Val(true)) \ y -end - -""" - β_loss(β::Vector, lp::SmallSNAPLP) - -Loss function: using NelderMeadOpt from GalacticOptim to optimize the parameters -""" -function β_loss(β::Vector, lp::SmallSNAPLP) where - e = lp.A * β - lp.y - return transpose(e) * inv(lp.Q) * e -end - -""" - learn(lp::SmallSNAPLP, loss, s::NelderMeadOpt) - -Learning function: using NelderMeadOpt from GalacticOptim to optimize the parameters -""" -function learn(lp::SmallSNAPLP, loss, s::NelderMeadOpt) where - β0 = zeros(length(lp.A[1,:])) - prob = GalacticOptim.OptimizationProblem((x, pars)->loss(x, lp), β0, []) - lp.snap.β = GalacticOptim.solve(prob, NelderMead(), maxiters=s.maxiters) -end - - diff --git a/test/runtests.jl b/test/runtests.jl index e4a33cae..a0084df7 100644 --- a/test/runtests.jl +++ b/test/runtests.jl @@ -1,4 +1,4 @@ using PotentialLearning using Test -#include("SNAP-test.jl") + From ce99559de3077bae5ca78b3ba1749692744b8613 Mon Sep 17 00:00:00 2001 From: Emmanuel Lujan Date: Fri, 15 Jul 2022 02:38:08 -0400 Subject: [PATCH 22/35] Improving github workflows. --- .github/workflows/CI.yml | 37 +++++++---------------- .github/workflows/Documentation.yml | 45 ++++++++++++++++++++++++++++ .github/workflows/PreviewCleanup.yml | 26 ++++++++++++++++ docs/make.jl | 2 +- 4 files changed, 83 insertions(+), 27 deletions(-) create mode 100644 .github/workflows/Documentation.yml create mode 100644 .github/workflows/PreviewCleanup.yml diff --git a/.github/workflows/CI.yml b/.github/workflows/CI.yml index 0b75d381..d1f3893f 100644 --- a/.github/workflows/CI.yml +++ b/.github/workflows/CI.yml @@ -4,7 +4,7 @@ on: push: branches: - main - tags: '*' + tags: "*" jobs: test: name: Julia ${{ matrix.version }} - ${{ matrix.os }} - ${{ matrix.arch }} - ${{ github.event_name }} @@ -13,8 +13,8 @@ jobs: fail-fast: false matrix: version: - - '1.6' - - 'nightly' + - "1.7" + - "nightly" os: - ubuntu-latest - macOS-latest @@ -37,32 +37,17 @@ jobs: ${{ runner.os }}-test-${{ env.cache-name }}- ${{ runner.os }}-test- ${{ runner.os }}- +# - name: add CESMIX registry +# run: | +# julia -e ' +# using Pkg +# Pkg.Registry.add("General") +# Pkg.Registry.add(RegistrySpec(url = "https://github.com/cesmix-mit/CESMIX.git")) +# ' +# shell: bash - uses: julia-actions/julia-buildpkg@v1 - uses: julia-actions/julia-runtest@v1 - uses: julia-actions/julia-processcoverage@v1 - uses: codecov/codecov-action@v1 with: file: lcov.info - docs: - name: Documentation - runs-on: ubuntu-latest - steps: - - uses: actions/checkout@v2 - - uses: julia-actions/setup-julia@v1 - with: - version: '1' - - run: | - julia --project=docs -e ' - using Pkg - Pkg.develop(PackageSpec(path=pwd())) - Pkg.instantiate()' - - run: | - julia --project=docs -e ' - using Documenter: DocMeta, doctest - using PotentialLearning - DocMeta.setdocmeta!(PotentialLearning, :DocTestSetup, :(using PotentialLearning); recursive=true) - doctest(PotentialLearning)' - - run: julia --project=docs docs/make.jl - env: - GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} - DOCUMENTER_KEY: ${{ secrets.DOCUMENTER_KEY }} diff --git a/.github/workflows/Documentation.yml b/.github/workflows/Documentation.yml new file mode 100644 index 00000000..62b50db6 --- /dev/null +++ b/.github/workflows/Documentation.yml @@ -0,0 +1,45 @@ +name: Documentation +on: + pull_request: + push: + branches: + - main + tags: "*" +jobs: + docs: + name: Documentation + runs-on: ubuntu-latest + steps: + - uses: actions/checkout@v2 + - run: sudo apt-get update && sudo apt-get install -y xorg-dev mesa-utils xvfb libgl1 freeglut3-dev libxrandr-dev libxinerama-dev libxcursor-dev libxi-dev libxext-dev + - uses: julia-actions/setup-julia@v1 + with: + version: "1.6" +# - name: add CESMIX registry +# run: | +# julia -e ' +# using Pkg +# Pkg.Registry.add("General") +# Pkg.Registry.add(RegistrySpec(url = "https://github.com/cesmix-mit/CESMIX.git")) +# ' +# shell: bash + - name: instantiate docs + run: | + julia --project=docs -e ' + using Pkg + Pkg.develop(PackageSpec(path=pwd())) + Pkg.instantiate() + ' + - name: run doctests + run: | + julia --project=docs -e ' + using Documenter: DocMeta, doctest + using PotentialLearning + DocMeta.setdocmeta!(PotentialLearning, :DocTestSetup, :(using PotentialLearning); recursive=true) + doctest(PotentialLearning) + ' + - name: generate docs + run: DISPLAY=:0 xvfb-run -s '-screen 0 1024x768x24' julia --project=docs docs/make.jl + env: + GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} + DOCUMENTER_KEY: ${{ secrets.DOCUMENTER_KEY }} diff --git a/.github/workflows/PreviewCleanup.yml b/.github/workflows/PreviewCleanup.yml new file mode 100644 index 00000000..bc29462c --- /dev/null +++ b/.github/workflows/PreviewCleanup.yml @@ -0,0 +1,26 @@ +name: Doc Preview Cleanup + +on: + pull_request: + types: [closed] + +jobs: + doc-preview-cleanup: + runs-on: ubuntu-latest + steps: + - name: Checkout gh-pages branch + uses: actions/checkout@v2 + with: + ref: gh-pages + - name: Delete preview and history + push changes + run: | + if [ -d "previews/PR$PRNUM" ]; then + git config user.name "Documenter.jl" + git config user.email "documenter@juliadocs.github.io" + git rm -rf "previews/PR$PRNUM" + git commit -m "delete preview" + git branch gh-pages-new $(echo "delete history" | git commit-tree HEAD^{tree}) + git push --force origin gh-pages-new:gh-pages + fi + env: + PRNUM: ${{ github.event.number }} diff --git a/docs/make.jl b/docs/make.jl index 4798a7b8..6318aac7 100644 --- a/docs/make.jl +++ b/docs/make.jl @@ -44,6 +44,6 @@ makedocs(bib; deploydocs(; repo = "github.com/cesmix-mit/PotentialLearning.jl", - devbranch = "refactor", # main + devbranch = "main", push_preview = true ) From a2f94f6a2998bcc3bd7a878342855b797dd0f69a Mon Sep 17 00:00:00 2001 From: Emmanuel Lujan Date: Fri, 15 Jul 2022 03:07:18 -0400 Subject: [PATCH 23/35] github workflows: add CESMIX registry --- .github/workflows/CI.yml | 16 ++++++++-------- .github/workflows/Documentation.yml | 18 +++++++++--------- 2 files changed, 17 insertions(+), 17 deletions(-) diff --git a/.github/workflows/CI.yml b/.github/workflows/CI.yml index d1f3893f..6d431a09 100644 --- a/.github/workflows/CI.yml +++ b/.github/workflows/CI.yml @@ -37,14 +37,14 @@ jobs: ${{ runner.os }}-test-${{ env.cache-name }}- ${{ runner.os }}-test- ${{ runner.os }}- -# - name: add CESMIX registry -# run: | -# julia -e ' -# using Pkg -# Pkg.Registry.add("General") -# Pkg.Registry.add(RegistrySpec(url = "https://github.com/cesmix-mit/CESMIX.git")) -# ' -# shell: bash + - name: add CESMIX registry + run: | + julia -e ' + using Pkg + Pkg.Registry.add("General") + Pkg.Registry.add(RegistrySpec(url = "https://github.com/cesmix-mit/CESMIX.git")) + ' + shell: bash - uses: julia-actions/julia-buildpkg@v1 - uses: julia-actions/julia-runtest@v1 - uses: julia-actions/julia-processcoverage@v1 diff --git a/.github/workflows/Documentation.yml b/.github/workflows/Documentation.yml index 62b50db6..f2b8e40b 100644 --- a/.github/workflows/Documentation.yml +++ b/.github/workflows/Documentation.yml @@ -14,15 +14,15 @@ jobs: - run: sudo apt-get update && sudo apt-get install -y xorg-dev mesa-utils xvfb libgl1 freeglut3-dev libxrandr-dev libxinerama-dev libxcursor-dev libxi-dev libxext-dev - uses: julia-actions/setup-julia@v1 with: - version: "1.6" -# - name: add CESMIX registry -# run: | -# julia -e ' -# using Pkg -# Pkg.Registry.add("General") -# Pkg.Registry.add(RegistrySpec(url = "https://github.com/cesmix-mit/CESMIX.git")) -# ' -# shell: bash + version: "1.7" + - name: add CESMIX registry + run: | + julia -e ' + using Pkg + Pkg.Registry.add("General") + Pkg.Registry.add(RegistrySpec(url = "https://github.com/cesmix-mit/CESMIX.git")) + ' + shell: bash - name: instantiate docs run: | julia --project=docs -e ' From 0c05ca11f3bb07588a3533c88dba0eaaf939b356 Mon Sep 17 00:00:00 2001 From: Emmanuel Lujan Date: Fri, 15 Jul 2022 03:14:14 -0400 Subject: [PATCH 24/35] github workflows: add JuliaMol registry --- .github/workflows/CI.yml | 1 + .github/workflows/Documentation.yml | 1 + 2 files changed, 2 insertions(+) diff --git a/.github/workflows/CI.yml b/.github/workflows/CI.yml index 6d431a09..9c4f4e2b 100644 --- a/.github/workflows/CI.yml +++ b/.github/workflows/CI.yml @@ -43,6 +43,7 @@ jobs: using Pkg Pkg.Registry.add("General") Pkg.Registry.add(RegistrySpec(url = "https://github.com/cesmix-mit/CESMIX.git")) + Pkg.Registry.add(RegistrySpec(url = "https://github.com/JuliaMolSim/MolSim.git")) ' shell: bash - uses: julia-actions/julia-buildpkg@v1 diff --git a/.github/workflows/Documentation.yml b/.github/workflows/Documentation.yml index f2b8e40b..ed0f4d8a 100644 --- a/.github/workflows/Documentation.yml +++ b/.github/workflows/Documentation.yml @@ -21,6 +21,7 @@ jobs: using Pkg Pkg.Registry.add("General") Pkg.Registry.add(RegistrySpec(url = "https://github.com/cesmix-mit/CESMIX.git")) + Pkg.Registry.add(RegistrySpec(url = "https://github.com/JuliaMolSim/MolSim.git")) ' shell: bash - name: instantiate docs From 6a4ded4143925d26893c5d0c5e42601f9c4c5c6f Mon Sep 17 00:00:00 2001 From: Emmanuel Lujan Date: Fri, 15 Jul 2022 03:32:29 -0400 Subject: [PATCH 25/35] Add Project.toml in test folder --- test/Project.toml | 2 ++ 1 file changed, 2 insertions(+) create mode 100644 test/Project.toml diff --git a/test/Project.toml b/test/Project.toml new file mode 100644 index 00000000..0c363327 --- /dev/null +++ b/test/Project.toml @@ -0,0 +1,2 @@ +[deps] +Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40" From 060c6caeed25618859af6f8dcadfe61cfd6cbeee Mon Sep 17 00:00:00 2001 From: Emmanuel Lujan Date: Fri, 15 Jul 2022 03:43:08 -0400 Subject: [PATCH 26/35] doc api fix --- docs/src/api.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/src/api.md b/docs/src/api.md index 17e486bf..7bec598d 100644 --- a/docs/src/api.md +++ b/docs/src/api.md @@ -4,6 +4,6 @@ This page provides a list of all documented types and functions and in Potential ```@autodocs -Modules = [InteratomicPotentials] +Modules = [PotentialLearning] Order = [:type, :function, :constant] ``` From eda491530f5e9b4e9fd01bfd9679aff50cae7b00 Mon Sep 17 00:00:00 2001 From: Emmanuel Lujan Date: Fri, 15 Jul 2022 14:37:47 -0400 Subject: [PATCH 27/35] Small change in tests. --- test/runtests.jl | 7 ++++++- 1 file changed, 6 insertions(+), 1 deletion(-) diff --git a/test/runtests.jl b/test/runtests.jl index a0084df7..2bd4bf85 100644 --- a/test/runtests.jl +++ b/test/runtests.jl @@ -1,4 +1,9 @@ -using PotentialLearning +# TODO: Create tests. + +include("../src/PotentialLearning.jl") +using .PotentialLearning using Test +@test 1 == 1 + From fef153c668e598c7a6378c27d32f096dbe41dd3c Mon Sep 17 00:00:00 2001 From: Emmanuel Lujan Date: Fri, 15 Jul 2022 14:51:41 -0400 Subject: [PATCH 28/35] Changing dependencies in tests. --- test/Project.toml | 21 +++++++++++++++++++++ 1 file changed, 21 insertions(+) diff --git a/test/Project.toml b/test/Project.toml index 0c363327..77d13886 100644 --- a/test/Project.toml +++ b/test/Project.toml @@ -1,2 +1,23 @@ [deps] +AtomsBase = "a963bdd2-2df7-4f54-a1ee-49d51e6be12a" +BlackBoxOptim = "a134a8b2-14d6-55f6-9291-3336d3ab0209" +CSV = "336ed68f-0bac-5ca0-87d4-7b16caf5d00b" +Flux = "587475ba-b771-5e3f-ad9e-33799f191a9c" +GalacticOptim = "a75be94c-b780-496d-a8a9-0878b188d577" +InteratomicBasisPotentials = "37c59853-c2ad-4e3a-930c-a41b2395fb19" +InteratomicPotentials = "a9efe35a-c65d-452d-b8a8-82646cd5cb04" +IterTools = "c8e1da08-722c-5040-9ed9-7db0dc04731e" +LAMMPS = "ee2e13b9-eee9-4449-aafa-cfa6a2dbe14d" +LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e" +Optim = "429524aa-4258-5aef-a3af-852621145aeb" +Optimization = "7f7a1694-90dd-40f0-9382-eb1efda571ba" +OrderedCollections = "bac558e1-5e72-5ebc-8fee-abe8a469f55d" +Plots = "91a5bcdd-55d7-5caf-9e0b-520d859cae80" +Printf = "de0858da-6303-5e67-8744-51eddeeeb8d7" +Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c" +StaticArrays = "90137ffa-7385-5640-81b9-e52037218182" +Statistics = "10745b16-79ce-11e8-11f9-7d13ad32a3b2" Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40" +Unitful = "1986cc42-f94f-5a68-af5c-568840ba703d" +UnitfulAtomic = "a7773ee8-282e-5fa2-be4e-bd808c38a91a" +Zygote = "e88e6eb3-aa80-5325-afca-941959d7151f" From 7377c68a34f26852605b519391b7674a9e5a625f Mon Sep 17 00:00:00 2001 From: Emmanuel Lujan Date: Fri, 15 Jul 2022 15:50:52 -0400 Subject: [PATCH 29/35] Improving docstrings. --- src/IO/Load-extxyz.jl | 1 + src/IO/Utils.jl | 4 -- src/Learning/Losses.jl | 2 + src/Learning/NNBasisPotential.jl | 110 +++++++++++++++++++++++++------ 4 files changed, 94 insertions(+), 23 deletions(-) diff --git a/src/IO/Load-extxyz.jl b/src/IO/Load-extxyz.jl index 65702977..e240bbaf 100644 --- a/src/IO/Load-extxyz.jl +++ b/src/IO/Load-extxyz.jl @@ -1,5 +1,6 @@ export load_extxyz + """ load_extxyz(file; max_entries = 2000, T = Float64) diff --git a/src/IO/Utils.jl b/src/IO/Utils.jl index f8a69068..b9f92bdf 100644 --- a/src/IO/Utils.jl +++ b/src/IO/Utils.jl @@ -1,10 +1,6 @@ export @savevar, @savecsv, @savefig -path = "" -var = "" -dict = "" - """ savevar(path, var) diff --git a/src/Learning/Losses.jl b/src/Learning/Losses.jl index 5ec63285..47c7144b 100644 --- a/src/Learning/Losses.jl +++ b/src/Learning/Losses.jl @@ -1,5 +1,6 @@ export loss, global_loss + """ loss(es_pred, es, w_e, fs_pred, fs, w_f) @@ -16,6 +17,7 @@ Returns the weighted loss of the energies and forces using MSE. loss(es_pred, es, w_e, fs_pred, fs, w_f) = w_e * Flux.Losses.mse(es_pred, es) + w_f * Flux.Losses.mse(fs_pred, fs) + """ global_loss(loader_e, loader_f, w_e, w_f, ps, re) diff --git a/src/Learning/NNBasisPotential.jl b/src/Learning/NNBasisPotential.jl index a78512ac..998653e8 100644 --- a/src/Learning/NNBasisPotential.jl +++ b/src/Learning/NNBasisPotential.jl @@ -1,20 +1,41 @@ # TODO: Add to InteratomicPotentials.jl/InteratomicBasisPotentials.jl -# Defining NNBP composed type and associated functions + +""" + NNBasisPotential + +Definition of the neural network basis potential composed type. +""" mutable struct NNBasisPotential <: AbstractPotential nn nn_params ibp_params end -function potential_energy(A::AbstractSystem, - p::NNBasisPotential) + +""" + potential_energy(A::AbstractSystem, p::NNBasisPotential) + +`A`: atomic system or atomic configuration. +`p`: neural network basis potential. + +Returns the potential energy of a system using a neural network basis potential. +""" +function potential_energy(A::AbstractSystem, p::NNBasisPotential) b = evaluate_basis(A, p.ibp_params) return p.nn(b) end -function force(A::AbstractSystem, - p::NNBasisPotential) + +""" + force(A::AbstractSystem, p::NNBasisPotential) + +`A`: atomic system or atomic configuration. +`p`: neural network basis potential. + +Returns the force of a system using a neural network basis potential. +""" +function force(A::AbstractSystem, p::NNBasisPotential) b = evaluate_basis(A, p.ibp_params) dnndb = first(gradient(p.nn, b)) dbdr = evaluate_basis_d(A, p.ibp_params) @@ -22,28 +43,58 @@ function force(A::AbstractSystem, for atom in 1:length(dbdr)] end + +""" + potential_energy(b::Vector, p::NNBasisPotential) + +`b`: vector of energy descriptors. +`p`: neural network basis potential. + +Returns the potential energy of a system using a neural network basis potential. +""" function potential_energy(b::Vector, p::NNBasisPotential) return sum(p.nn(b)) end + +""" + potential_energy(b::Vector, ps::Vector, re) + +`b`: energy descriptors of a system. +`ps`: neural network parameters. See Flux.destructure. +`re`: neural network restructure. See Flux.destructure. + +Returns the potential energy of a system using a neural network basis potential. +""" function potential_energy(b::Vector, ps::Vector, re) return sum(re(ps)(b)) end -# Note: calculating the gradient of the loss function requires in turn -# calculating the gradient of the energy. That is, calculating the gradient of -# a function that calculates another gradient. -# So far I have not found a clean way to do this using the abstractions -# provided by Flux, which in turn is integrated with Zygote. -# Links related to this issue: -# https://discourse.julialang.org/t/how-to-add-norm-of-gradient-to-a-loss-function/69873/16 -# https://discourse.julialang.org/t/issue-with-zygote-over-forwarddiff-derivative/70824 -# https://github.com/FluxML/Zygote.jl/issues/953#issuecomment-841882071 + +# TODO: create issue. +#Note: calculating the gradient of the loss function requires in turn +#calculating the gradient of the energy. That is, calculating the gradient of +#a function that calculates another gradient. +#So far I have not found a clean way to do this using the abstractions +#provided by Flux, which in turn is integrated with Zygote. +#Links related to this issue: +#https://discourse.julialang.org/t/how-to-add-norm-of-gradient-to-a-loss-function/69873/16 +#https://discourse.julialang.org/t/issue-with-zygote-over-forwarddiff-derivative/70824 +#https://github.com/FluxML/Zygote.jl/issues/953#issuecomment-841882071 # -# To solve this for the moment I am calculating one of the gradients analytically. -# To do this I had to use Flux.destructure, which I think makes the code slower -# because of the copies it creates. +#To solve this for the moment I am calculating one of the gradients analytically. +#To do this I had to use Flux.destructure, which I think makes the code slower +#because of the copies it creates. + +""" + grad_mlp(nn_params, x0) + +`nn_params`: neural network parameters. +`x0`: first layer input (energy descriptors). + +Returns the analytical derivative of a feedforward neural network. +""" function grad_mlp(nn_params, x0) dsdy(x) = x>0 ? 1 : 0 # Flux.σ(x) * (1 - Flux.σ(x)) prod = 1; x = x0 @@ -58,12 +109,33 @@ function grad_mlp(nn_params, x0) return prod end -function force(b, dbdr, p) + +""" + force(b::Vector, dbdr::Vector, p::NNBasisPotential) + +`b`: energy descriptors of a system. +`dbdr`: force descriptors of a system. +`p`: neural network basis potential. + +Returns the force of a system using a neural network basis potential. +""" +function force(b::Vector, dbdr::Vector, p::NNBasisPotential) dnndb = grad_mlp(p.nn_params, b) return dnndb ⋅ dbdr end -function force(b, dbdr, ps, re) + +""" + force(b::Vector, dbdr::Vector, ps::Vector, re) + +`b`: energy descriptors of a system. +`dbdr`: force descriptors of a system. +`ps`: neural network parameters. See Flux.destructure. +`re`: neural network restructure. See Flux.destructure. + +Returns the force of a system using a neural network basis potential. +""" +function force(b::Vector, dbdr::Vector, ps::Vector, re) nn_params = Flux.params(re(ps)) dnndb = grad_mlp(nn_params, b) return dnndb ⋅ dbdr From 7f74295748dd496a6eea1dcab3067ee5fb958f92 Mon Sep 17 00:00:00 2001 From: Emmanuel Lujan Date: Fri, 15 Jul 2022 16:13:50 -0400 Subject: [PATCH 30/35] Small changes in doc workflow and tests. --- .github/workflows/Documentation.yml | 1 + test/runtests.jl | 4 ++-- 2 files changed, 3 insertions(+), 2 deletions(-) diff --git a/.github/workflows/Documentation.yml b/.github/workflows/Documentation.yml index ed0f4d8a..5cf307df 100644 --- a/.github/workflows/Documentation.yml +++ b/.github/workflows/Documentation.yml @@ -34,6 +34,7 @@ jobs: - name: run doctests run: | julia --project=docs -e ' + using Pkg; Pkg.activate("./") using Documenter: DocMeta, doctest using PotentialLearning DocMeta.setdocmeta!(PotentialLearning, :DocTestSetup, :(using PotentialLearning); recursive=true) diff --git a/test/runtests.jl b/test/runtests.jl index 2bd4bf85..95a487e5 100644 --- a/test/runtests.jl +++ b/test/runtests.jl @@ -1,7 +1,7 @@ # TODO: Create tests. -include("../src/PotentialLearning.jl") -using .PotentialLearning +using Pkg; Pkg.activate("./") +using PotentialLearning using Test @test 1 == 1 From 49271307c15d13672b961dfea4375ee31e212f69 Mon Sep 17 00:00:00 2001 From: Emmanuel Lujan Date: Fri, 15 Jul 2022 16:22:15 -0400 Subject: [PATCH 31/35] Adding test dependency. --- test/Project.toml | 1 + 1 file changed, 1 insertion(+) diff --git a/test/Project.toml b/test/Project.toml index 77d13886..0076ec7b 100644 --- a/test/Project.toml +++ b/test/Project.toml @@ -12,6 +12,7 @@ LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e" Optim = "429524aa-4258-5aef-a3af-852621145aeb" Optimization = "7f7a1694-90dd-40f0-9382-eb1efda571ba" OrderedCollections = "bac558e1-5e72-5ebc-8fee-abe8a469f55d" +Pkg = "44cfe95a-1eb2-52ea-b672-e2afdf69b78f" Plots = "91a5bcdd-55d7-5caf-9e0b-520d859cae80" Printf = "de0858da-6303-5e67-8744-51eddeeeb8d7" Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c" From 396e22b316bdc67748008047499b6a01d7da5457 Mon Sep 17 00:00:00 2001 From: Emmanuel Lujan Date: Fri, 15 Jul 2022 17:14:28 -0400 Subject: [PATCH 32/35] Small changes in github workflows and tests. --- .github/workflows/Documentation.yml | 4 +++- test/Project.toml | 1 - test/runtests.jl | 4 ++-- 3 files changed, 5 insertions(+), 4 deletions(-) diff --git a/.github/workflows/Documentation.yml b/.github/workflows/Documentation.yml index 5cf307df..60079df2 100644 --- a/.github/workflows/Documentation.yml +++ b/.github/workflows/Documentation.yml @@ -34,7 +34,9 @@ jobs: - name: run doctests run: | julia --project=docs -e ' - using Pkg; Pkg.activate("./") + using Pkg + Pkg.activate("Documenter") + Pkg.activate("./") using Documenter: DocMeta, doctest using PotentialLearning DocMeta.setdocmeta!(PotentialLearning, :DocTestSetup, :(using PotentialLearning); recursive=true) diff --git a/test/Project.toml b/test/Project.toml index 0076ec7b..77d13886 100644 --- a/test/Project.toml +++ b/test/Project.toml @@ -12,7 +12,6 @@ LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e" Optim = "429524aa-4258-5aef-a3af-852621145aeb" Optimization = "7f7a1694-90dd-40f0-9382-eb1efda571ba" OrderedCollections = "bac558e1-5e72-5ebc-8fee-abe8a469f55d" -Pkg = "44cfe95a-1eb2-52ea-b672-e2afdf69b78f" Plots = "91a5bcdd-55d7-5caf-9e0b-520d859cae80" Printf = "de0858da-6303-5e67-8744-51eddeeeb8d7" Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c" diff --git a/test/runtests.jl b/test/runtests.jl index 95a487e5..2bd4bf85 100644 --- a/test/runtests.jl +++ b/test/runtests.jl @@ -1,7 +1,7 @@ # TODO: Create tests. -using Pkg; Pkg.activate("./") -using PotentialLearning +include("../src/PotentialLearning.jl") +using .PotentialLearning using Test @test 1 == 1 From ebcf2c48277a77bb0c006eb350fc463fcb72733d Mon Sep 17 00:00:00 2001 From: Emmanuel Lujan Date: Fri, 15 Jul 2022 17:28:41 -0400 Subject: [PATCH 33/35] Small change in Documentation.yml --- .github/workflows/Documentation.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/Documentation.yml b/.github/workflows/Documentation.yml index 60079df2..1db4d4bc 100644 --- a/.github/workflows/Documentation.yml +++ b/.github/workflows/Documentation.yml @@ -35,7 +35,7 @@ jobs: run: | julia --project=docs -e ' using Pkg - Pkg.activate("Documenter") + Pkg.add("Documenter") Pkg.activate("./") using Documenter: DocMeta, doctest using PotentialLearning From 748582b9ef3643bfa0150d9f51eab00acb59b61e Mon Sep 17 00:00:00 2001 From: Emmanuel Lujan Date: Fri, 15 Jul 2022 17:44:27 -0400 Subject: [PATCH 34/35] Small change in Documentation.yml --- .github/workflows/Documentation.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/Documentation.yml b/.github/workflows/Documentation.yml index 1db4d4bc..385af183 100644 --- a/.github/workflows/Documentation.yml +++ b/.github/workflows/Documentation.yml @@ -35,8 +35,8 @@ jobs: run: | julia --project=docs -e ' using Pkg - Pkg.add("Documenter") Pkg.activate("./") + Pkg.add("Documenter") using Documenter: DocMeta, doctest using PotentialLearning DocMeta.setdocmeta!(PotentialLearning, :DocTestSetup, :(using PotentialLearning); recursive=true) From aa64617330543fa3bd902ae6c1f285dadcb1d9ab Mon Sep 17 00:00:00 2001 From: Emmanuel Lujan Date: Fri, 15 Jul 2022 18:16:40 -0400 Subject: [PATCH 35/35] Small changes related to documenter. --- .github/workflows/CI.yml | 1 - docs/make.jl | 2 +- src/IO/Utils.jl | 23 ++++++++++++++++------- 3 files changed, 17 insertions(+), 9 deletions(-) diff --git a/.github/workflows/CI.yml b/.github/workflows/CI.yml index 9c4f4e2b..a2561b23 100644 --- a/.github/workflows/CI.yml +++ b/.github/workflows/CI.yml @@ -14,7 +14,6 @@ jobs: matrix: version: - "1.7" - - "nightly" os: - ubuntu-latest - macOS-latest diff --git a/docs/make.jl b/docs/make.jl index 6318aac7..49bc779e 100644 --- a/docs/make.jl +++ b/docs/make.jl @@ -39,7 +39,7 @@ makedocs(bib; ], doctest = true, linkcheck = true, - strict = true + strict = false ) deploydocs(; diff --git a/src/IO/Utils.jl b/src/IO/Utils.jl index b9f92bdf..9a7ab709 100644 --- a/src/IO/Utils.jl +++ b/src/IO/Utils.jl @@ -1,10 +1,12 @@ - export @savevar, @savecsv, @savefig """ savevar(path, var) - + +`path`: path where the variable will be saved. +`var`: variable to be saved. + Simplifies the saving of a variable. """ @@ -17,7 +19,10 @@ end """ savecsv(path, dict) - + +`path`: path where the dictionary will be saved. +`dict`: dictionary to be saved. + Simplifies the saving of a dictionary to a CSV file. """ @@ -27,15 +32,19 @@ macro savecsv(path, dict) end end + """ - savefig(path, var) - + savefig(path, fig) + +`path`: path where the figure will be saved. +`fig`: figure to be saved. + Simplifies the saving of a figure. """ -macro savefig(path, var) +macro savefig(path, fig) quote - savefig($(esc(var)), $(esc(path)) * $(string(var)) * ".png") + savefig($(esc(fig)), $(esc(path)) * $(string(fig)) * ".png") end end