Update dev/gp3_ipea to latest state
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* Interface for the qm program turbomole Signed-off-by: Jonathan Schöps <[email protected]> * support for turbomole Signed-off-by: Jonathan Schöps <[email protected]> * corrected some typos Signed-off-by: Jonathan Schöps <[email protected]> * changed the PARNODES command Signed-off-by: Jonathan Schöps <[email protected]> * coord handling Signed-off-by: Jonathan Schöps <[email protected]> * requestet changes are build in Signed-off-by: Jonathan Schöps <[email protected]> * Implementation of the requested changes and the test of the read_mol_from_coord function Signed-off-by: Jonathan Schöps <[email protected]> * Implementation of two pathes for turbomole Signed-off-by: Jonathan Schöps <[email protected]> * Ignore HOMO-LUMO gap not implemented as refine engine for Orca and Trubomole Signed-off-by: Jonathan Schöps <[email protected]> * improve TURBOMOLE configuration Signed-off-by: Marcel Müller <[email protected]> * correct linting errors Signed-off-by: Marcel Mueller <[email protected]> * exclude more recent interfaces from coverage check Signed-off-by: Marcel Müller <[email protected]> * added a test for the 'write_coord_to_file' function Signed-off-by: Jonathan Schöps <[email protected]> * sync the lokal branch with the remote branch Signed-off-by: Jonathan Schöps <[email protected]> --------- Signed-off-by: Jonathan Schöps <[email protected]> Signed-off-by: Marcel Müller <[email protected]> Signed-off-by: Marcel Mueller <[email protected]> Co-authored-by: Marcel Müller <[email protected]>
* initial work * new parallelization preliminary done * small fix in tests * commented unnecessary code * updated construction sites * hopefully fixed parallelization * small test fix * initial work * new parallelization preliminary done * small fix in tests * commented unnecessary code * updated construction sites * hopefully fixed parallelization * small test fix * only print when verbosity > 0, otherwise nothing is printed (bad) * pre-commit fixes * added ncores to config + implemented setting ncores for external programs * fixed tests * added check for number of cores available vs needed * pre-commit * test fix * fixed tm implementation * updated main.py * tqdm progress bar * updated dependencies * mypy types import * moved warnings in correct bracket * updated default config toml * added final output of molecules and timing * fixed time * better time info * print formatting * shift block setup to parallel.py Signed-off-by: Marcel Müller <[email protected]> * avoid UnboundLocalError Signed-off-by: Marcel Müller <[email protected]> * some code formatting and printout adjustments Signed-off-by: Marcel Müller <[email protected]> * shifted CHANGELOG entry to correct position Signed-off-by: Marcel Müller <[email protected]> * update CODEOWNERS file Signed-off-by: Marcel Müller <[email protected]> --------- Signed-off-by: Marcel Müller <[email protected]> Co-authored-by: Marcel Müller <[email protected]>
* update environment.yaml and format files Signed-off-by: Marcel Müller <[email protected]> * add Python>=3.12 to dependencies Signed-off-by: Marcel Müller <[email protected]> --------- Signed-off-by: Marcel Müller <[email protected]>
* New file which contains all constants used in the program Signed-off-by: Jonathan Schöps <[email protected]> * updated the wrong placed import statement Signed-off-by: Jonathan Schöps <[email protected]> * Added a new ordner named data containing constants.py and parameters.py Signed-off-by: Jonathan Schöps <[email protected]> * moved the covalent radii to the parameters file and give both in angstroem. Signed-off-by: Jonathan Schöps <[email protected]> * move get_cov_radii, indent else after return, make tests faster Signed-off-by: Marcel Müller <[email protected]> * update CHANGELOG.md accordingly§ Signed-off-by: Marcel Müller <[email protected]> --------- Signed-off-by: Jonathan Schöps <[email protected]> Signed-off-by: Marcel Müller <[email protected]> Co-authored-by: Marcel Müller <[email protected]>
* Interface for the qm program turbomole Signed-off-by: Jonathan Schöps <[email protected]> * support for turbomole Signed-off-by: Jonathan Schöps <[email protected]> * corrected some typos Signed-off-by: Jonathan Schöps <[email protected]> * structure_mod baseline Signed-off-by: Jonathan Schöps <[email protected]> * baseline for the symmetrie class Signed-off-by: Jonathan Schöps <[email protected]> * update to the structure_modification routine and implemented unit tests. Signed-off-by: Jonathan Schöps <[email protected]> * removal of left over dead code snippets Signed-off-by: Jonathan Schöps <[email protected]> * changed a typo in the change log Signed-off-by: Jonathan Schöps <[email protected]> * Re structerization of Structure_modification Signed-off-by: Jonathan Schöps <[email protected]> * bug fixes to get the structure mod classes working Signed-off-by: Jonathan Schöps <[email protected]> * changed a word in mindlessgen.toml Signed-off-by: Jonathan Schöps <[email protected]> * reorganize translation and initialization Signed-off-by: Marcel Müller <[email protected]> * refactored object-orientation of structure modification classes; fixed and extended tests Signed-off-by: Marcel Müller <[email protected]> * abstract structure merge; minor revisions for config Signed-off-by: Marcel Müller <[email protected]> * Fix to print the correct output of tm and remove of a redundant singlepoint calculation Signed-off-by: Jonathan Schöps <[email protected]> * distance check for clashes and iterative distance increase if too low Signed-off-by: Marcel Müller <[email protected]> * rename some file and Class names to typical conventions Signed-off-by: Marcel Müller <[email protected]> * further variable renaming; config clean-up Signed-off-by: Marcel Müller <[email protected]> * add CLI access for arguments and minor adaptions Signed-off-by: Marcel Müller <[email protected]> * update default TOML file Signed-off-by: Marcel Müller <[email protected]> * some renamings, better docstrings, remove useless variable copies Signed-off-by: Marcel Müller <[email protected]> --------- Signed-off-by: Jonathan Schöps <[email protected]> Signed-off-by: Marcel Müller <[email protected]> Co-authored-by: Marcel Müller <[email protected]>
Conflicts:
CHANGELOG.md
environment.yml
mindlessgen.toml
src/mindlessgen/generator/main.py
src/mindlessgen/molecules/molecule.py
src/mindlessgen/prog/__init__.py
src/mindlessgen/prog/config.py
src/mindlessgen/qm/tm.py
Conflicts manually resolved.
Signed-off-by: Marcel Müller <[email protected]>
* add check for non-convergence Signed-off-by: Marcel Mueller <[email protected]> * remove print statement Signed-off-by: Marcel Mueller <[email protected]> --------- Signed-off-by: Marcel Mueller <[email protected]>
marcelmbn
requested review from
jonathan-schoeps and
lmseidler
as code owners
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