Rings dev

README.md

@@ -181,6 +181,12 @@ can be run with the `yodaStruct_test` binary, which will drop into the
 ```{bash}
 # Just run this
 ./testBuild.sh
+# At this point the binary and library are copied into the root
+# One might, in a foolhardy attempt, use gdb at this point
+# Here be dragons :)
+# USE NIX
+# Anyway
+gdb --args ./yodaStruct -c lua_inputs/config.yml
 # quit gdb with quit
 # Go run the test binary
 cd shellBuild
@@ -261,6 +267,35 @@ Note that we expect compliance with the `clang-format` as mentioned above, and t
 
 This will ensure that new commits are in accordance to the `clang-format` file.
 
+## Development Builds
+
+The general idea is to drop into an interactive shell with the dependencies and then use `cmake` as usual.
+
+```bash
+nix-shell --pure --run bash --show-trace --verbose
+cd build
+cmake .. -DCMAKE_BUILD_TYPE=Debug -DNO_WARN=TRUE \
+ -DFIND_EIGEN=TRUE \
+ -DCMAKE_EXPORT_COMPILE_COMMANDS=1 \
+ -G "Ninja"
+ninja
+# Test
+cd ../
+yodaStruct -c lua_inputs/config.yml
+# Debug
+gdb --args yodaStruct -c lua_inputs/config.yml
+```
+To load debugging symbols from the shared library, when you are inside `gdb` (from the top-level directory, for instance), use the following command:
+
+```bash
+add-symbol-file build/libyodaLib.so
+```
+Then you can set breakpoints in the C++ code; for instance: 
+
+```bash
+b seams_input.cpp:408
+```
+
 # Acknowledgements
 
 The following tools are used in this project:
@@ -290,3 +325,4 @@ The libraries used are:
 - [Boost Math](https://www.boost.org/doc/libs/?view=category_math) for spherical harmonics
 - [Blaze](https://bitbucket.org/blaze-lib/blaze/) for very fast modern linear algebra
 - [nanoflann](https://github.com/jlblancoc/nanoflann) to calculate nearest neighbors
+- [icecream-cpp](https://github.com/renatoGarcia/icecream-cpp) for pretty-printing and debugging

example_lua/bulkPrimitiveRings/config.yml

@@ -0,0 +1,10 @@
+trajectory: "input/traj/clathrate-thf.lammpstrj"
+variables: "lua_inputs/iceType/vars.lua"
+bulk:
+  use: true
+  topologicalNetworkCriterion: false
+  bondOrderParameters: false
+topoOneDim:
+  use: false
+topoTwoDim:
+  use: false

example_lua/bulkPrimitiveRings/iceType/functions.lua

@@ -0,0 +1,10 @@
+print("\n Welcome to the manual lua function evaluation environment.\n");
+
+for frame=targetFrame,finalFrame,frameGap do
+   resCloud=readFrameOnlyOne(trajectory,frame,resCloud,oxygenAtomType,isSlice,sliceLowerLimits,sliceUpperLimits) --- Get the frame
+   nList=neighborList(cutoffRadius, resCloud, oxygenAtomType); --- Calculate the neighborlist by ID
+   hbnList=getHbondNetwork(trajectory,resCloud,nList,frame,hydrogenAtomType) --- Get the hydrogen-bonded network for the current frame
+   hbnList=bondNetworkByIndex(resCloud,hbnList) --- Hydrogen-bonded network using indices not IDs
+   rings=getPrimitiveRings(hbnList,maxDepth); --- Gets every ring (non-primitives included)
+   bulkRingNumberAnalysis(outDir, rings, hbnList, resCloud, maxDepth, targetFrame); --- Writes out primitive rings for a bulk system 
+end

example_lua/bulkPrimitiveRings/iceType/vars.lua

@@ -0,0 +1,16 @@
+print("\n Welcome to the Ice Type Determination Module\n");
+cutoffRadius = 3.5; --- This is for H2O
+oxygenAtomType = 1; --- This is assigned by LAMMPS
+hydrogenAtomType = 2; --- Hydrogen atom type assigned
+targetFrame=1; --- The first frame
+finalFrame=1; --- This is inclusive
+frameGap=1; --- The gap between frames
+maxDepth = 6; --- The maximum depth upto which rings will be searched.
+--- Slice Information
+isSlice = true; --- This is true if the analysis is to be done only for a volume slice
+sliceLowerLimits = {0,0,0}; --- Lower limit of the slice (for box dim, keep the values the same as 0)
+sliceUpperLimits = {34.728,0,0}; --- Upper limit of the slice   
+
+--- Paths for the output directories and lua scipt
+outDir="runOne/"; --- The subdirectory used; 
+functionScript="lua_inputs/iceType/functions.lua" --- This is relative to the binary location

example_lua/iceNanotube/shapeMatching/iceType/vars.lua

@@ -2,8 +2,8 @@ print("\n Welcome to the Ice Type Determination Module\n");
 cutoffRadius = 3.5; --- This is for H2O
 oxygenAtomType = 2; --- This is assigned by LAMMPS
 hydrogenAtomType = 1; --- Hydrogen atom type assigned
-targetFrame=100; --- The first frame
-finalFrame=100; --- This is inclusive
+targetFrame=1; --- The first frame
+finalFrame=1; --- This is inclusive
 frameGap=1; --- The gap between frames
 maxDepth = 6; --- The maximum depth upto which rings will be searched.
 --- Slice Information

example_lua/iceNanotube/strictCriterion/config.yml

@@ -1,5 +1,5 @@
-trajectory: "../input/traj/dump-240-square.lammpstrj"
-variables: "../lua_inputs/iceType/vars.lua"
+trajectory: "input/traj/exampleTraj.lammpstrj"
+variables: "lua_inputs/iceType/vars.lua"
 bulk:
   use: false
   topologicalNetworkCriterion: false

example_lua/iceNanotube/strictCriterion/iceType/vars.lua

@@ -2,8 +2,8 @@ print("\n Welcome to the Ice Type Determination Module\n");
 cutoffRadius = 3.5; --- This is for H2O
 oxygenAtomType = 2; --- This is assigned by LAMMPS
 hydrogenAtomType = 1; --- Hydrogen atom type assigned
-targetFrame=100; --- The first frame
-finalFrame=100; --- This is inclusive
+targetFrame=1; --- The first frame
+finalFrame=1; --- This is inclusive
 frameGap=1; --- The gap between frames
 maxDepth = 6; --- The maximum depth upto which rings will be searched.
 --- Slice Information
@@ -12,5 +12,5 @@ sliceLowerLimits = {0,0,0}; --- Lower limit of the slice (for box dim, keep the
 sliceUpperLimits = {0,0,0}; --- Upper limit of the slice 
 
 --- Paths for the output directories and lua scipt
-outDir="../runOne/"; --- The subdirectory used; 
-functionScript="../lua_inputs/iceType/functions.lua" --- This is relative to the binary location 
+outDir="runOne/"; --- The subdirectory used; 
+functionScript="lua_inputs/iceType/functions.lua" --- This is relative to the binary location 

example_lua/selection/clathrate-system/config.yml

@@ -0,0 +1,10 @@
+trajectory: "input/traj/clathrate-thf.lammpstrj"
+variables: "lua_inputs/iceType/vars.lua"
+bulk:
+  use: true
+  topologicalNetworkCriterion: false
+  bondOrderParameters: false
+topoOneDim:
+  use: false
+topoTwoDim:
+  use: false

example_lua/selection/clathrate-system/iceType/functions.lua

@@ -0,0 +1,18 @@
+print("\n Welcome to the manual lua function evaluation environment.\n");
+
+for frame=targetFrame,finalFrame,frameGap do
+    -- Read in all atom types without applying the slice 
+    resCloud=readFrameOnlyOneAllAtoms(trajectory, frame,resCloud,false, {0,0,0}, {0,0,0});
+    -- Get just the O atoms from the PointCloud with all the atoms  (including those not in the slice)
+    oCloud=getPointCloudAtomsOfOneAtomType(resCloud,oCloud,oxygenAtomType,false, {0,0,0}, {0,0,0});
+    -- Get the H atoms (including those not in the slice) for the entire system  
+    hCloud=getPointCloudAtomsOfOneAtomType(resCloud,hCloud,hydrogenAtomType,false,{0,0,0}, {0,0,0});
+    nList=neighborList(cutoffRadius, oCloud, oxygenAtomType); --- Calculate the neighborlist by ID
+    hbnList=getHbondNetworkFromClouds(oCloud,hCloud,nList); --- Get the hydrogen-bonded network for the current frame
+    hbnList=bondNetworkByIndex(oCloud,hbnList); --- Hydrogen-bonded network using indices not IDs
+    rings=getPrimitiveRings(hbnList,maxDepth); --- Gets every ring (non-primitives included)
+    -- bulkRingNumberAnalysis(outDir, rings, hbnList, oCloud, maxDepth, targetFrame); --- Writes out primitive rings for a bulk system
+    -- All atoms within the slice will have an inSlice bool attribute of true. If a single atom of a molecule is in the
+    -- slice, then all atoms in the molecule will also be inside the slice. We will also select edge atoms in rings
+    selectAtomsInSliceWithRingEdgeAtoms(outDir,rings,oCloud,resCloud,sliceLowerLimits,sliceUpperLimits,false);
+end

example_lua/selection/clathrate-system/iceType/vars.lua

@@ -0,0 +1,16 @@
+print("\n Welcome to the Ice Type Determination Module\n");
+cutoffRadius = 3.5; --- This is for H2O
+oxygenAtomType = 1; --- This is assigned by LAMMPS
+hydrogenAtomType = 2; --- Hydrogen atom type assigned
+targetFrame=1; --- The first frame
+finalFrame=1; --- This is inclusive
+frameGap=1; --- The gap between frames
+maxDepth = 6; --- The maximum depth upto which rings will be searched.
+--- Slice Information
+isSlice = true; --- This is true if the analysis is to be done only for a volume slice
+sliceLowerLimits = {0,0,0}; --- Lower limit of the slice (for box dim, keep the values the same as 0)
+sliceUpperLimits = {34.728,0,0}; --- Upper limit of the slice   
+
+--- Paths for the output directories and lua scipt
+outDir="runOne/"; --- The subdirectory used; 
+functionScript="lua_inputs/iceType/functions.lua" --- This is relative to the binary location

example_lua/selection/tiny-selection/config.yml

@@ -0,0 +1,10 @@
+trajectory: "input/traj/tiny-selectionTest.lammpstrj"
+variables: "lua_inputs/iceType/vars.lua"
+bulk:
+  use: true
+  topologicalNetworkCriterion: false
+  bondOrderParameters: false
+topoOneDim:
+  use: false
+topoTwoDim:
+  use: false

example_lua/selection/tiny-selection/iceType/functions.lua

@@ -0,0 +1,18 @@
+print("\n Welcome to the manual lua function evaluation environment.\n");
+
+for frame=targetFrame,finalFrame,frameGap do
+    -- Read in all atom types without applying the slice 
+    resCloud=readFrameOnlyOneAllAtoms(trajectory, frame,resCloud,false, {0,0,0}, {0,0,0});
+    -- Get just the O atoms from the PointCloud with all the atoms  (including those not in the slice)
+    oCloud=getPointCloudAtomsOfOneAtomType(resCloud,oCloud,oxygenAtomType,false, {0,0,0}, {0,0,0});
+    -- Get the H atoms (including those not in the slice) for the entire system  
+    hCloud=getPointCloudAtomsOfOneAtomType(resCloud,hCloud,hydrogenAtomType,false,{0,0,0}, {0,0,0});
+    nList=neighborList(cutoffRadius, oCloud, oxygenAtomType); --- Calculate the neighborlist by ID
+    hbnList=getHbondNetworkFromClouds(oCloud,hCloud,nList); --- Get the hydrogen-bonded network for the current frame
+    hbnList=bondNetworkByIndex(oCloud,hbnList); --- Hydrogen-bonded network using indices not IDs
+    rings=getPrimitiveRings(hbnList,maxDepth); --- Gets every ring (non-primitives included)
+    -- bulkRingNumberAnalysis(outDir, rings, hbnList, oCloud, maxDepth, targetFrame); --- Writes out primitive rings for a bulk system
+    -- All atoms within the slice will have an inSlice bool attribute of true. If a single atom of a molecule is in the
+    -- slice, then all atoms in the molecule will also be inside the slice. We will also select edge atoms in rings
+    selectAtomsInSliceWithRingEdgeAtoms(outDir,rings,oCloud,resCloud,sliceLowerLimits,sliceUpperLimits,false);
+end

example_lua/selection/tiny-selection/iceType/vars.lua

@@ -0,0 +1,16 @@
+print("\n Welcome to the Ice Type Determination Module\n");
+cutoffRadius = 3.5; --- This is for H2O
+oxygenAtomType = 1; --- This is assigned by LAMMPS
+hydrogenAtomType = 2; --- Hydrogen atom type assigned
+targetFrame=1; --- The first frame
+finalFrame=1; --- This is inclusive
+frameGap=1; --- The gap between frames
+maxDepth = 6; --- The maximum depth upto which rings will be searched.
+--- Slice Information
+isSlice = true; --- This is true if the analysis is to be done only for a volume slice
+sliceLowerLimits = {0,0,0}; --- Lower limit of the slice (for box dim, keep the values the same as 0)
+sliceUpperLimits = {31.728,0,0}; --- Upper limit of the slice   
+
+--- Paths for the output directories and lua scipt
+outDir="runOne/"; --- The subdirectory used; 
+functionScript="lua_inputs/iceType/functions.lua" --- This is relative to the binary location