Code

Parity with main#313

Code

Merged

YHordijk merged 48 commits into287-add-option-to-not-use-slurm-for-jobsTheoChem-VU/TCutility:287-add-option-to-not-use-slurm-for-jobsfrom mainTheoChem-VU/TCutility:mainCopy head branch name to clipboardSep 17, 2024

+646-298

Commits

Commits on Jun 27, 2024

• Python API for IRC concatenation

  SiebeLeDe

  committed
  d30f0e3

Commits on Jul 19, 2024

• docstring fix

  SiebeLeDe

  committed
  fdbeeeb

• no changes

  SiebeLeDe

  committed
  1bdd330

Commits on Jul 24, 2024

• Now exposing the DensfJob at the tcutility.job level

  YHordijk

  committed
  8494ebf

• Added orbital spin to cube file path

  YHordijk

  committed
  4dd6d17

Commits on Jul 27, 2024

• Merge pull request #274 from TheoChem-VU/256-irc-api

  Show description for fe378b2
  SiebeLeDe

  authored
  fe378b2

Commits on Jul 29, 2024

• Added checking for the new orbital objects when generating orbital cube files

  YHordijk

  committed
  ecb286b

• Added some data for the dummy atom. It can now be drawn as small purple atoms

  YHordijk

  committed
  241c81b

• Atom data indexing works properly again

  YHordijk

  committed
  f37315c

Commits on Aug 18, 2024

• Merge pull request #292 from TheoChem-VU/291-add-dummy-atom-data-to-tcutilitydataatoms

  Show description for 5989c93
  SiebeLeDe

  authored
  5989c93

• Orbitals were not using the symlabel index, but the global index of the orbital

  YHordijk

  committed
  6c73066

Commits on Aug 20, 2024

• [#293] switched composition ordering for transformation matrices

  YHordijk

  committed
  02b19f5

• [#294] added the get_rotmat and get_translation methods for transform objects

  YHordijk

  committed
  714f47d

• [#294] added a function to convert rotation matrices into angles

  YHordijk

  committed
  b3fdbc3

• [#295] Added the new MolTransform class, currently supports centering, align_to_vector and align_to_plane

  YHordijk

  committed
  c0d76f2

• [#293] the KabschTransform matrix was not being built correctly

  YHordijk

  committed
  5bf507f

• Merge pull request #296 from TheoChem-VU/geometry-improvements

  Show description for 5940b8e
  YHordijk

  authored
  5940b8e

Commits on Aug 22, 2024

• Merge pull request #300 from TheoChem-VU/main

  Show description for 2d38bfe
  YHordijk

  authored
  2d38bfe

Commits on Aug 23, 2024

• Merge pull request #297 from TheoChem-VU/densfjob-improvements

  Show description for 3398526
  YHordijk

  authored
  3398526

• Documentation build

  

  YHordijk

  authored and

  github-actions[bot]

  committed
  79a54c9

Commits on Aug 29, 2024

• Added the character width text files

  Show description for 5b9e57b
  YHordijk

  authored
  5b9e57b

• Merge pull request #303 from TheoChem-VU/manifest_patch

  Show description for a3f85d3
  YHordijk

  authored
  a3f85d3

• Documentation build

  

  YHordijk

  authored and

  github-actions[bot]

  committed
  f600819

• Added listfunc to the required libraries

  YHordijk

  authored
  fad4e84

• Merge pull request #305 from TheoChem-VU/add_requirements

  Show description for 53df4dc
  YHordijk

  authored
  53df4dc

• Documentation build

  

  YHordijk

  authored and

  github-actions[bot]

  committed
  8d90da5

• Fixed a runtimewarning that occurs when a function was not called

  YHordijk

  committed
  dfcffde

Commits on Aug 30, 2024

• Merge pull request #307 from TheoChem-VU/306-numpy-runtimewarning-related-to-timings-module

  Show description for b1f7edb
  YHordijk

  authored
  b1f7edb

• Documentation build

  

  YHordijk

  authored and

  github-actions[bot]

  committed
  ae785bc

Commits on Sep 1, 2024

• Added pathfunc to the imports in init

  YHordijk

  committed
  73608e6

Commits on Sep 2, 2024

• Merge pull request #309 from TheoChem-VU/308-cant-import-pathfunc-from-tcutility

  Show description for b3dab04
  SiebeLeDe

  authored
  b3dab04

• Documentation build

  

  SiebeLeDe

  authored and

  github-actions[bot]

  committed
  b9d1b7f

• Documentation build

  

  YHordijk

  authored and

  github-actions[bot]

  committed
  2e838c9

Commits on Sep 5, 2024

• Added the decompose_elstat option for ADFFragmentJob calculations

  YHordijk

  committed
  652d1b7

• Added the number_of_electrons function to calculate the total number of electrons for a molecule

  YHordijk

  committed
  54312b1

• Renamed energy.elstat to energy.elstat.total

  YHordijk

  committed
  2e35573

• Now reading the electrostatic interaction terms if they are available in the output

  YHordijk

  committed
  e83f3ec

• Now obtaining the output files from calculation directories

  YHordijk

  committed
  82b86c4

• Fixed frag_indices, it was not correctly ordered w.r.t. read molecules

  YHordijk

  committed
  df6083f

• Added an example that uses the electrostatic decomposition analysis

  YHordijk

  committed
  5a84b6f

• Renamed atom variables to at to not shadow the atom module from tcutility.data

  YHordijk

  committed
  a32a136

• Fix ruff complaint

  YHordijk

  committed
  d82f687

• Fixed a test case due to changing order of fragment indices

  YHordijk

  committed
  160908d

Commits on Sep 13, 2024

• Merge pull request #310 from TheoChem-VU/279-add-option-to-perform-electrostatic-decomposition-calculation-for-adffragmentjob-calculations

  Show description for 10f6562
  SiebeLeDe

  authored
  10f6562

Commits on Sep 16, 2024

• laptop sync

  SiebeLeDe

  committed
  25a7ac7

• Documentation build

  

  SiebeLeDe

  authored and

  github-actions[bot]

  committed
  e520e9d

Commits on Sep 17, 2024

• Removed the _build folder temporarily

  YHordijk

  committed
  479e84b

• Merge branch '287-add-option-to-not-use-slurm-for-jobs' into main

  YHordijk

  authored
  b1fd7d4