RagnarB83

Add testsuite

1

Integrate current testsuite into repository and figure out automatic testing

- Remove old uncommented code - Remove unused variables - Remove duplicate versions of code (e.g. xyz-file read in module_coords) - Fix Python faux pas - Adhere to PEP8 style-guide...

Safires implementation

1

Should work together with ASE (to be tested more) but enforcing Rattle constraints in ASE-MD is too slow to be useful for fast MM MD or xTB/MM MD. Open_MM MD...

Interface DL-FIND code with Gaussian Process Regression (https://pubs.acs.org/doi/pdf/10.1021/acs.jctc.1c00517) GPR code: https://www.chemshell.org/dl-find/gpr_snapshot Regular code: https://www.chemshell.org/dl-find

Interface to DFTB+ Contains range-separated hybrid tight-binding Hamiltonians: https://github.com/dftbplus/dftbplus/blob/21.1/CHANGELOG.rst

Need to write docstrings for pretty much everything

Introduced a bug at some point in openmm-basic-test.py and MD-cluster-openMMMD.py that converts from ASH forcefield file to OpenMM xml file: `openmmobject = OpenMMTheory(cluster_fragment=Cluster, ASH_FF_file=ff_file, platform='CPU')` Error message: ``` Traceback (most...

Clean up error handling: exceptions, assertions etc.

- OpenMM_MD: energy_file option - OpenMMTheory: ML-potentials - QM/MM MD: minor cleanup - NEB: minor change - MLatom interface: cleanup - MRCC interface: direct writing of integral-file and simple inputfile...