* Basic LCPO support
* Add basic test for LCPO from a prmtop file
* API for LCPOForce
* Started LCPO reference implementation
* Finished reference forces & test cases
* Use other test for finite difference since grid might have discontinuous forces
* Reference platform formatting
* Initial implementation of CPU platform
* Bugfixes
* More vectorization and improve neighbor list query speed
* Parallelize part of neighbor search
* Check box size for LCPO with periodic boundary conditions
* Fixes for updating parameters in context
* GBSAOBCForce doesn't use first & last indices for updates, so no need for this optimization here
* Changes to neighbor checking and optimization
* Fixes and minor changes
* Add global surface tension parameter
* Only process half of the pairs in the neighbor list
* Remove unnecessary checks
* Initial version of common platform implementation
* Asynchronously download neighbor list size
* Debugging
* Do pair precomputation in copyPairsToNeighborList
* Recompute interactions instead of scanning neighbor list in inner loop
* Condense position array before computations
* Also make neighbor count download asynchronous on device
* Fixes for kernel launching
* Topology-based LCPO parameter assignment
* Fixes, and use test system for LCPO with nucleic acids
* Always raise instead of warn when LCPO parameters can't be assigned
* Use Amber convention for phosphates
* Correct AmoebaAngleTorsion in test_Amoeba18Nucleic of TestForceField
* Update processTinkerForceField to handle latest .prm Tinker files
* Update amoeba2018 XML files
* Update amoeba2013 XML files
* Update amoeba2009 XML files
* Adapt addTorTor to new format in the .prm files
* Fix TorsionTorsion
* Also update the total energy in test_Amoeba18Nucleic
* Update amoebabio18.prm
* Fix nucleic acid test energies
* Correct AmoebaAngleTorsionForce params
* Add new addTorTor to TinkerFiles
* Revert unit fix
* Change to .pdb file which Tinker likes
* Update test_Amoeba18BPTI
* Remove trailing zeros from XML files
* Leave trailing zeros only on 2018 ff
* New element names in 2018
* More digits for surfaceAreaFactor
* More digits for surfaceAreaFactor
* More digits
* Remove debugging print
* Add support to 2009 and 2013 AMOEBA ffs to processTinkerForceField.py
* Add FF specific residues XML files
* Delete old residuesFinal.xml
* Update AMOEBA XML ffs
* Update FFs
* Fix some formatting issues
* Fix "." in scientific notation
* Remove old assertions
* Fresh branch refactoring the new AMOEBA code
* Finish cleaning up AmoebaAngleForce and AmoebaInPlaneAngleForce
* Cleanup AmoebaTorsionTorsionForce
* Cleanup AmoebaOutOfPlaneBend
* Cleanup AmoebaMultipoleForce
* Remove unnecessary gkForce
* Simplify usage of atomClasses in ForceField
* Formatting
* Fix type of class on WCA
* Simplify angle forces
* Add parsing of units to PiTorsion and StretchBond, and misc. formatting adjustments
* Update code per review feedback
* Clearly defined API for TorsionTorsion, and correct matching for UB,
* Unindent break statements
* Raise ValueError if classes and types are mixed in a Urey-Bradley term definition
* Properly handle duplicate atom type definitions without elements
* Correct the description of a test in a docstring
* Correctly handle existing type without element and duplicate type with element
* Try to update actions/cache to v4
* Include more cases in TestForceField.test_NBFix
* Reduce LennardJonesGenerator NBFIX memory consumption
* Restored test case to use multiple elements to avoid ambiguity
* Add benchmarks from Amber20 benchmark suite to standard benchmark script
* Add ensemble option; don't change hydrogen mass in amber input files
* Download and extract .tar.gz using pure python code, no wget/tar dependencies
* Rename amber tests
* add opc and opc3 models
* update to match https://bioinformatics.cs.vt.edu/~izadi/OPC_Gromacs/opc.top
* opc box, converted from ambertools-22.0-py38h6177452_1/dat/leap/lib/opcbox.off
* change values to make serialized system match one created from prmtop as close as possible
* unit test for opc water
* opc - final values, match frcmod.opc; derivation in comments
* opc3 water - final values, shows derivation
* opc3box made from ambertools 22 dat/leap/lib/opc3box.off
* add opc3 water test
* add opc and opc3 to docs
* move tests to TestForceField.py
* move opc tests out of amoeba tests, oops
* move opcbox and opc3box pdb files
Co-authored-by: Alex Izvorski <alex@genesistherapeutics.ai>
* Reference implementation of computed values for CustomNonbondedForce
* CPU implementation of computed values for CustomNonbondedForce
* Common implementation of computed values for CustomNonbondedForce
* Serialization of computed values
* ForceField supports computed values
* Adding support for new AMOEBA features
* Support modern method of specifying in-plane angles
* Implemented stretch-torsions
* Implemented angle-torsions
* More AMOEBA fixes
* Bug fix
* Converted AMOEBA 2018 force field
* Added documentation for AMOEBA 2018
* Added a missing file for tests
* Created OBC2 that works with current force fields
* Created HCT, OBC1, GBn, and GBn2 that works with current force fields
* Added documentation for GB models
* Updates to documentation and tests based on comments
* Added formula for screening parameter
* Top level Python module is now "openmm"
* Updated module names in examples
* Updated module names in documentation
* Updated module in CI scripts
* Added deprecation warning
