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Parity with main #313

Merged
merged 48 commits into from
Sep 17, 2024
Merged

Parity with main #313

merged 48 commits into from
Sep 17, 2024

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YHordijk
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SiebeLeDe and others added 30 commits June 27, 2024 20:51
@SiebeLeDe
Python API for IRC concatenation
d30f0e3
@SiebeLeDe
docstring fix
fdbeeeb
@SiebeLeDe
no changes
1bdd330
@YHordijk
Now exposing the DensfJob at the tcutility.job level
8494ebf
@YHordijk
Added orbital spin to cube file path
4dd6d17
@SiebeLeDe
Merge pull request #274 from TheoChem-VU/256-irc-api
fe378b2 
Python API for IRC concatenation
@YHordijk
Added checking for the new orbital objects when generating orbital cu…
ecb286b 
…be files
@YHordijk
Added some data for the dummy atom. It can now be drawn as small purp…
241c81b 
…le atoms
@YHordijk
Atom data indexing works properly again
f37315c
@SiebeLeDe
Merge pull request #292 from TheoChem-VU/291-add-dummy-atom-data-to-t…
5989c93 
…cutilitydataatoms

Added dummy atom data to `tcutility.data.atoms`
@YHordijk
Orbitals were not using the symlabel index, but the global index of t…
6c73066 
…he orbital
@YHordijk
[#293] switched composition ordering for transformation matrices
02b19f5
@YHordijk
[#294] added the get_rotmat and get_translation methods for transform…
714f47d 
… objects
@YHordijk
[#294] added a function to convert rotation matrices into angles
b3fdbc3
@YHordijk
[#295] Added the new MolTransform class, currently supports centering…
c0d76f2 
…, align_to_vector and align_to_plane
@YHordijk
[#293] the KabschTransform matrix was not being built correctly
5bf507f
@YHordijk
Merge pull request #296 from TheoChem-VU/geometry-improvements
5940b8e 
Made improvements to the `tcutility.geometry.Transform` classes
@YHordijk
Merge pull request #300 from TheoChem-VU/main
2d38bfe 
Parity with main
@YHordijk
Merge pull request #297 from TheoChem-VU/densfjob-improvements
3398526 
Improvements related to `DensfJob`
@YHordijk @github-actions
Documentation build
79a54c9
@YHordijk
Added the character width text files
5b9e57b 
We were not exporting the character width files
@YHordijk
Merge pull request #303 from TheoChem-VU/manifest_patch
a3f85d3 
Added `_char_widths.txt` to MANIFEST
@YHordijk @github-actions
Documentation build
f600819
@YHordijk
Added listfunc to the required libraries
fad4e84
@YHordijk
Merge pull request #305 from TheoChem-VU/add_requirements
53df4dc 
Added `listfunc` to the required libraries
@YHordijk @github-actions
Documentation build
8d90da5
@YHordijk
Fixed a runtimewarning that occurs when a function was not called
dfcffde
@YHordijk
Merge pull request #307 from TheoChem-VU/306-numpy-runtimewarning-rel…
b1f7edb 
…ated-to-timings-module

Fixed a `timer` runtimewarning that occurs when a function was not called
@YHordijk @github-actions
Documentation build
ae785bc
@YHordijk
Added pathfunc to the imports in init
73608e6
SiebeLeDe and others added 17 commits September 2, 2024 09:36
@SiebeLeDe
Merge pull request #309 from TheoChem-VU/308-cant-import-pathfunc-fro…
b3dab04 
…m-tcutility

`pathfunc` is now importable from `tcutility` directly
@SiebeLeDe @github-actions
Documentation build
b9d1b7f
@YHordijk @github-actions
Documentation build
2e838c9
@YHordijk
Added the decompose_elstat option for ADFFragmentJob calculations
652d1b7
@YHordijk
Added the number_of_electrons function to calculate the total number …
54312b1 
…of electrons for a molecule
@YHordijk
Renamed energy.elstat to energy.elstat.total
2e35573
@YHordijk
Now reading the electrostatic interaction terms if they are available…
e83f3ec 
… in the output
@YHordijk
Now obtaining the output files from calculation directories
82b86c4
@YHordijk
Fixed frag_indices, it was not correctly ordered w.r.t. read molecules
df6083f
@YHordijk
Added an example that uses the electrostatic decomposition analysis
5a84b6f
@YHordijk
Renamed atom variables to at to not shadow the atom module from tcuti…
a32a136 
…lity.data
@YHordijk
Fix ruff complaint
d82f687
@YHordijk
Fixed a test case due to changing order of fragment indices
160908d
@SiebeLeDe
Merge pull request #310 from TheoChem-VU/279-add-option-to-perform-el…
10f6562 
…ectrostatic-decomposition-calculation-for-adffragmentjob-calculations

Added option to perform electrostatic potential energy decomposition for `ADFFragmentJob`
@SiebeLeDe
laptop sync
25a7ac7
@SiebeLeDe @github-actions
Documentation build
e520e9d
@YHordijk
Removed the _build folder temporarily
479e84b
@YHordijk YHordijk closed this Sep 17, 2024
@YHordijk YHordijk reopened this Sep 17, 2024
@YHordijk YHordijk merged commit 82a0447 into 287-add-option-to-not-use-slurm-for-jobs Sep 17, 2024
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2 participants
@YHordijk @SiebeLeDe