dormrod
commented
2 months ago I think the following files do not exist in amshome anymore, but still exist on the branch here on Github:
deleted: doc/source/examples/PackMolExample/PackMol_files/PackMol_12_0.png deleted: doc/source/examples/PackMolExample/PackMol_files/PackMol_16_1.png deleted: doc/source/examples/PackMolExample/PackMol_files/PackMol_19_1.png deleted: doc/source/examples/PackMolExample/PackMol_files/PackMol_24_1.png deleted: doc/source/examples/PackMolExample/PackMol_files/PackMol_30_0.png deleted: doc/source/examples/PackMolExample/PackMol_files/PackMol_31_1.png deleted: doc/source/examples/PackMolExample/PackMol_files/PackMol_32_1.png deleted: doc/source/examples/PackMolExample/PackMol_files/PackMol_34_0.png deleted: doc/source/examples/PackMolExample/PackMol_files/PackMol_35_1.png
Thanks, good spot, I saw the +/- diff was correct but totally missed this. Removed these in follow-up commit.
chen: SO-- Formating crs.py with Black Rosa Bulo: Rosa Bulo (REB) SCMSUITE-- SO107: Added bonds to the PDBHandling David Ormrod Morley: Fix PLAMS unit tests running on slurm SCMSUITE-8687 SO107 Robert Rüger: fix block quote in CRS page in PLAMS manual SO-- chen: SO-- Fix the sytax error of the doc in get_structure_energy function. chen: SO-- Update crs for OUTPUT_ENERGY_COMPONENTS option to report the energy components in multispecies. Added the get_structure_energy function in crs.py in PLAMS. chen: SO-- Bug fix for coskfpath in adfcosmorscompound Rosa Bulo: SCMSUITE-- SO102 ACErxn bug in fragment charges David Ormrod Morley: Update PLAMS docs on settings object SCMSUITE-8687 SO107 David Ormrod Morley: Add config patch for PLAMS unit tests SCMSUITE-8687 SO107 David Ormrod Morley: Swap PLAMS global config object to be ConfigSettings SCMSUITE-8687 SO107 David Ormrod Morley: Add PLAMS config settings class and unit tests SCMSUITE-8687 SO107 David Ormrod Morley: Add unit tests for PLAMS init and finish functions SCMSUITE-8687 SO107 David Ormrod Morley: Update legacy input parser to have same casing as libbase input parser SO-- SCMSUITE-9732 David Ormrod Morley: Update plams package version to 2024.203 SO-- SCMSUITE-9732 David Ormrod Morley: Update plams package version to 2024.103 SO-- SCMSUITE-9732 David Ormrod Morley: Make plams package version independent of scm.version SO-- SCMSUITE-9732 David Ormrod Morley: Add fallback input parser when scm.libbase unavailable SO-- SCMSUITE-9732 David Ormrod Morley: Skip pisa unit tests if package unavailable SO-- SCMSUITE-9732 David Ormrod Morley: Single-source plams package version SO-- SCMSUITE-9732 David Ormrod Morley: Merge pull request 'Add unit tests for PLAMS Settings and minor fixes SO-- SCMSUITE-8687' (!3) from SCMSUITE-9732.plams_settings_unit_tests into trunk David Ormrod Morley: Include PLAMS test pdb files in setup.py SCMSUITE-- SO107 David Ormrod Morley: Normalise line endings in settings test assertion SO-- SCMSUITE-8687 David Ormrod Morley: Move import in settings tests SO-- SCMSUITE-8687 David Ormrod Morley: Swap regex for isidentifier in PLAMS settings dir method SO-- SCMSUITE-8687 David Ormrod Morley: Make dynamically added attributes in PLAMS settings objects visible to interactive editor SO-- SCMSUITE-8687 David Ormrod Morley: Add unit tests for PLAMS settings class SO-- SCMSUITE-8687 David Ormrod Morley: Move test pdb files into PLAMS unit test directory SCMSUITE-- SO107 Matti Hellström: add shakemd plams quickjob SO-- Matti Hellström: explicitly cast molecule charge to int in plams packmol in case it was read as a string SO-- Rosa Bulo: Rosa Bulo (REB) SCMSUITE-- SO107 Rosa Bulo: Rosa Bulo (REB) SCMSUITE-5711 SO107 Rosa Bulo: Rosa Bulo (REB) SCMSUITE-5711 SO107 Rosa Bulo: Rosa Bulo (REB) SCMSUITE-- SO107 Rosa Bulo: Rosa Bulo (REB) SCMSUITE-- SO107 Matti Hellström: guess density in plams packmol SO103 Matti Hellström: fix amsredoxscreeningjob, allow mol_info again in adfcosmorscompoundjob. add type hints. SCMSUITE-9508 SO103 Wei-Lin Chen: fix adfcosmorscompoundjob: (1) input of mol_info such as CAS (2) singlepoint=True will calculate the Gas Phase Bond Energy SCMSUITE-9508 SO101 Rosa Bulo: Rosa Bulo (REB) SCMSUITE-- SO1027 Matti Hellström: reuse the preamble_lines from subengines in hybrid_committee_engine_settings plams SO-- Matti Hellström: Reintroduce atomic_ion in adfcosmorscompoundjob SO-- SCMSUITE-9508 Matti Hellström: adfcosmorscompoundjob work for molecule=None, fix issue in amsredoxscreeningjob SCMSUITE-9508 SO103 Rosa Bulo: Rosa Bulo (REB) SCMSUITE-- SO102 Matti Hellström: allow ASE calculators form other Python envs, SCM_ASE_PYTHON_EXECUTABLE. SO103. SCMSUITE-9498 Matti Hellström: plams packmol interface allow small noise in lattice for packmol_on_slab SO-- Rosa Bulo: Rosa Bulo (REB) SCMSUITE-- SO102 Rosa Bulo: Rosa Bulo (REB) SCMSUITE-- SO102 Robert Rüger: libbase: Fortran input reader now emits preferred capitalization (from the definition file) of entries in the JSON input representation SCMSUITE-8593 SO-- Rosa Bulo: Rosa Bulo (REB) SCMSUITE-- SO107 Rosa Bulo: Rosa Bulo (REB) SCMSUITE-- SO107 Rosa Bulo: Rosa Bulo (REB) SCMSUITE-- SO107 Rosa Bulo: Rosa Bulo (REB) SCMSUITE-- SO107