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SCM-NV / PLAMS

Python Library for Automating Molecular Simulations
https://www.scm.com/doc/plams
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Manual sync from SCM-svn to GitHub #128

Closed dormrod closed 4 months ago

dormrod commented 4 months ago

Description This is a manual sync of commits from subversion, from the time of the last successful automated sync on 05/01/24 to the time of the 2024 AMS release on 24/04/24.

Notes for Reviewer The copied files have been checked by comparing the commits to the subversion equivalent, by using:

git diff --shortstat <last-synced-commit> <common-ancestor-trunk-fix2024>
230 files changed, 13434 insertions(+), 17600 deletions(-)

Please could the reviewer pull this branch and sanity check the file structure, and also double check that the first and last commits align with what they would expect from subversion.

N.B. the unit tests are not in a passing state at this point in the history, a fix commit will be added later

List of contained Commits Matti Hellström: get_history_length method in plams AMSResults SO-- Erik van Lenthe: typos SO-- Rosa Bulo: Rosa Bulo (REB) SCMSUITE-- SO107 Small change in RKFHistoryFile so that it does not necessarily fail for some CopyRestartTrajectory outputs Matti Hellström: use outcar from ams in plams example SO-- Erik van Lenthe: add link to ionic conductivity tutorial SO-- Robert Rüger: type hint for plams.units.conversion_ratio SO-- Erik van Lenthe: reduce changes SO-- Erik van Lenthe: fix previous fix SO-- Erik van Lenthe: fix plams example Task COSMO-RS Compound SO-- Matti Hellström: emphasize nonconverged plot in basicmdpostanalysis SO-- Erik van Lenthe: add methane.xyz and include init SO-- Erik van Lenthe: include init and include xyz files SO-- Robert Rüger: add some type-hints to PLAMS.Molecule methods SO-- Erik van Lenthe: added a result of the plams calcualtion SO-- Robert Rüger: fix doc building failure after moving CT2 manual SO-- Pier Philipsen: Comment added that calc takes a while:SO-- Pier Philipsen: added free-style key block to cookbook:SO-- Nestor Aguirre: PLAMS example upRobert Rüger: Tutorial testing SCMSUITE-9316: text fixes in MolecularDynamicsAndMonteCarlo -> MDintroPython SO-- Matti Hellström: qe plams example use same capitalization as json file, remove scm_disable_mpi (handled by AMSJob) SO-- Rosa Bulo: Rosa Bulo (REB) SCMSUITE-9234 SO102 - Changed the PLAMS example for IR spectrum to using the BinLog dipolemoment Paul Spiering: Check for pisa object in getrunscript. SCMSUITE-- SO-- Matti Hellström: automatically set SCM_DISABLE_MPI=1 in QE plams jobs SO-- Paul Spiering: Remove old reaxff plams examples and their link SCMSUITE-- SO-- Paul Spiering: Remove system block if empty when reading from input. SCMSUITE-- SO-- Paul Spiering: fix bug for get_input and from_input related to multiple molecules together with properties in the system block that are not part of a plams molecule. SCMSUITE-- SO-- Matti Hellström: remove global_minimum plams recipe from docs, there is no working example. Should perhaps also be removed from the code. SCMSUITE-- SO-- Robert Rüger: bugfix for SCMSUITE-9385 SO-- Robert Rüger: add type hints to convert_run_to_plams.py SO-- Paul Spiering: Add shebang to plams scripts for convenience. SCMSUITE-9003 SO-- Robert Rüger: Tutorial testing SCMSUITE-9316: PLAMS examples -> Conformers Generation SO-- Wei-Lin Chen: SCMSUITE-- SO-- add tutorials link in ADFCOSMORSConformers.rst Robert Rüger: Tutorial testing SCMSUITE-9316: PLAMS examples -> Reuse force field atom types and charges SO-- Wei-Lin Chen: SCMSUITE-- SO-- Bug fix during merge for adfcosmorsconformers.py and adfcosmorscompound.py Wei-Lin Chen: SCMSUITE-- SO-- Bug fix of get_multispecies_dist for calculating LOGP in crs.py Wei-Lin Chen: SCMSUITE-- SO-- Improve for Adding Compound Data in the recipes of adfcosmorsconformers.py and adfcosmorscompound.py Robert Rüger: Tutorial testing SCMSUITE-9316: PLAMS examples -> PackMol SO-- Paul Spiering: Typo in crs doc. SCMSUITE-9003 SO-- Matti Hellström: fix mentioned version number plams qe example SO-- Robert Rüger: format all our Python sourcecode with black SCMSUITE-9345 SO-- Robert Rüger: Tutorial testing SCMSUITE-9316: PLAMS examples -> Quantum ESPRESSO as an AMS engine: Antiferromagnetic FeO SO-- Paul Spiering: Add some missing imports in doc examples. SCMSUITE-9003 SO-- Matti Hellström: simplify conformers multiple molecules exampl,e add crosslinks SCMSUITE-- SO-- Matti Hellström: add plot_conformers to scm.conformers for reuse in SAL example SCMSUITE-- SO-- Rosa Bulo: Rosa Bulo (REB) SCMSUITE-- SO102 Added example of conformer generation with multiple molecules. Matti Hellström: fix plams what's new method names SCMSUITE-- SO-- Paul Spiering: Use python code blocks in plams getting started. SCMSUITE-9003 SO-- Paul Spiering: Added import to recipes that's no longer accesible from plams init. SCMSUITE-9003 SO-- Matti Hellström: use packmol instead of old packmol_liquid in plams basic md analysis example SCMSUITE-- SO-- Pier Philipsen: an example of load_all in the cookbook:SO-- Erik van Lenthe: also literal include NO2 xyz files SO-- Erik van Lenthe: add init and add download of xyz file to rst SO-- Robert Rüger: PLAMS: read at most nLatticeVectors cell shifts from file in AMSResults.get_history_molecule() SCMSUITE-9282 SCMSUITE-9285 SO-- Robert Rüger: bugfix for yesterday's fix in AMSResults.get_history_molecule() SCMSUITE-9282 SCMSUITE-9285 SO-- Matti Hellström: link sal docs from plams docs SCMSUITE-- SO-- Wei-Lin Chen: SCMSUITE-- SO-- fix the link for ADFCOSMORSConformers Robert Rüger: fix AMSResults.get_history_molecule() for cellShifts in 1D and 2D systems SCMSUITE-9285 SO-- Matti Hellström: add m3gnet-up-2022 into plams quick jobs SCMSUITE-- SO-- Nestor Aguirre: 1) Improved K_Points specification and defaults. 2) Small bug fixes -- SO103 Matti Hellström: move plot_msd from sal notebook into plams SCMSUITE-- SO-- Wei-Lin Chen: SCMSUITE-- SO-- change the link to COSMO-RS documentation in plams examples.rst Wei-Lin Chen: SCMSUITE-- SO-- change link for COSMO-RS documentation for COSMO-RS and property prediction Wei-Lin Chen: SCMSCUITE-- SO-- change link for Conformers for COSMORS Matti Hellström: replace ir spectrum from md example SCMSUITE-- SO-- Paul Spiering: Allow importing of redox recipes from scm.plams. SCMSUITE-9003 SO-- Wei-Lin Chen: SCMSUITE-- SO-- Improving the output for struct name Giulio Benedini: Postprocess results documentation added SO209 Giulio Benedini: postprocess_results file added, broadening function has been includedSO209 Rosa Bulo: Rosa Bulo (REB) SCMSUITE-- SO107 Added a tiny bit to the docstring for wrapping Wei-Lin Chen: SCMSUITE-- SO-- fixed bug for atomic ion setting in solvation. It should be 'method=atom corr' instead of 'method=Conj corr' Matti Hellström: move get_exit_condition_message from AMSJob to AMSResults SCMSUITE-- SO-- Giulio Benedini: bug fix SO209 Paul Spiering: Improve name of method for getting the exit condition message. SCMSUITE-- SO-- Matti Hellström: hybrid committee engine settings in plams set Hybrid.Committee.Enabled SCMSUITE-- SO-- Paul Spiering: Doc engine uncertainty and exit conditions. ECs now also write to rkf instead of WARNING. SCMSUITE-- SO-- Paul Spiering: PLAMS access to uncertainties. SCMSUITE-9227 SO103 Robert Rüger: PLAMS: handle supercell keyword in AMSJob.settings_to_mol method SO-- Giulio Benedini: SO209 added methods get_zero_point_energy get_ir_intensities, get_ir_spectrum and get_dipole_history, get_dipole_derivatives_acf, get_ir_spectrum_md Paul Spiering: Molecule.separate now uses non-recursive algorithm to avoid errors for large molecules. SCMSUITE-- SO-- Nestor Aguirre: Example QE_AMS_HubbardU.py upGiulio Benedini: documentation for what's new in plams SO209 Matti Hellström: upMatti Hellström: remove PISA recommendations in PLAMS docs SCMSUITE-- SO-- Rosa Bulo: Rosa Bulo (REB) SCMSUITE-- SO102 Added regions to the trajectory analysis tools Rosa Bulo: Rosa Bulo (REB) SCMSUITE-- SO102 Added ionic conductivity to the MSD part of the trajectory analysis tools Laurens Groot: Use SCM_PKG_ADFCRSDIR envvar instead of running and parsing amspackages cmd to get the crs database path. The parsing of stdout had several bugs on Windows. SO--- SCMSUITE-9207 Wei-Lin Chen: SCMSUITE-- SO-- 'minor bug fix for adfcosmorscompound.py' Giulio Benedini: added to molecule get_gyration_radius and related methods, also with related testing, added some typehint, corrected some spelling errors SO209 Wei-Lin Chen: SCMSUITE-- SO101 'resolve the conflict using adfcosmorscompound in https://www.scm.com/doc/plams/examples/ams_crs.html' Giulio Benedini: The get_errormsg function has undergone modification. Formerly, it employed self.ok(), which returned TRUE even if the state was copied, thereby preventing the retrieval of the error message. SO209 Giulio Benedini: added Ang to distance units EU209