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Integrating physics-ml potentials (#27)
* Remove unused implementation parameter in YAML files and potential factory class * Refactor potential initialization code * Refactor test functions to use PotentialFactory * Refactor test functions to use parameterized inputs * allow multiple potentials * Fix potential typo and update physicsml-model configuration * tests are passing locally * add pretrained mace * adopt names * refactor * Refactor potential initialization code and update YAML files * update yaml * update name * update path * update dicsstring * add docs * add type hint * Update README.md * Update README.md * Update README.md * Update setup.py * Update setup.py * Update setup.py * Update setup.py * Update setup.py * Removed eval and added device in yaml and setup. * bugfix * Update README.md * expression to float * expression to float * cast precision to str * expression to float * fix passing of platform proerties * better visualization * Fixed multiplication error * Fixed output file name bug Added conditions for the name of the nnp to avoid the openmmml pointer name being used in the file name. * Added experimental water rdf to output Useful for comparing against the NNP calculated water rdfs * Fixed DOF test PDB writer fixed, positions set correctly and system generated from opt not name. * First round of fixing tests * Removed stability tests output data and more test fixing * Removed generic .dcd and .pdb from gitignore We need to upload some pdb and dcd files for testing purposes and cannot ignore them globally. * Second round of fixing tests * Third round of fixing tests. * Added maximum bond length user option for DOF scan * Removed exs physicsml and fixed typo --------- Co-authored-by: exs-adambaskerville <[email protected]>
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