GitLab

* Make reference/CPU minimizer into a kernel

* Add per-platform support for GPU minimization

* Initial implementation of GPU minimization

* Fixes

* Increase robustness when initial gradient is huge

* Handle overflow leading to non-finite values gracefully

* Handle large forces in single precision more robustly

* Optimize kernels

* Fix kernel launch size

* Update banner years

* Don't create MinimizeKernel until first minimization requested

* Make some compile-time constants into kernel arguments

* Consolidate scale calculation kernel

* Condense alpha/beta reduction kernels using atomics

* Condense line search dot kernels with reductions

* Remove a download, and download grad norm separately

* Asynchronously check lbfgs convergence condition

* Restructure line search to avoid download waiting

* Start line search preemptively in case CPU evaluation is not needed

* In rare cases, constraint error might not decrease after one optimization round

* Better handling of unsupported 64-bit atomics, use FLT_MAX

* Pick gradient mode based on GPU vs. CPU evaluation

* Rework getDiff/getScale reduction, remove reduceBuffer

* Older CUDA might not like float hex literals

* Fix error in a comment

* Residue templates can specify constraints

* Patched template generation preserves constraints

* API for querying devices

* CUDA and HIP implementations of getDevices()

* Fix test failures

* Fix test failures

* CUDA returns correct devices even if no context has been created

* Return a single device for Reference and CPU

* Fix CI failure

* Templates can match whole molecules

* addExtraParticles() supports molecule templates

* Documentation on molecule templates

* Bug fix

* Remove std::enable_if, warpRotateLeft is always used with TILE_SIZE

* Do not use built-in warpSize in constexpr contexts

Starting from ROCm 7 warpSize is no longer constexpr.
findInteractingBlocks.hip uses it for sizes of __shared__ arrays.

* Check if hipHostMallocNumaUser is allowed before using it

adaptFrictionPart1 is executed first, it reads randomForce and
segmentVelocity buffers before other kernels write them so they can
contain garbage after allocation (cuMemAlloc/hipMalloc/clCreateBuffer
do not clear allocated memory).

* Prevent running out of disk space in OpenCL CI build

* Removed incorrect lines

* Delete more

* Fixed incorrect paths

* Removed some paths

* 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

* Minor optimization to PME

* Minor simplification

Added pythonforce.i to SWIG input files for Python.

* Initial implementation of PythonForce

* Continuing implementation of PythonForce

* Tests for PythonForce

* Fix memory leaks

* Documentation for PythonForce

* Fixed incorrect return type

* Fix compilation error on Python older than 3.12

* Handle all dtypes

* Optimizations to PythonForce

* Optimized getPositions()

* Test all platforms

* Fix test failures

* Ensure that neighbor list is valid before solving for charges

* Add test with neighbor list that needs to be resized

* Try another approach to skip interactions for neighbor list generation only

* Increase CG error tolerance for test

* 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

* Replace SimTK-containing file headers

* Update file headers for new Tinker reader files added

* Add basic version of TinkerFiles

* Refactor TinkerFiles

* Update docstring, type hints, and fix bug when setting box vectors

* Small fixes

* Add unit tests for the TinkerFiles class

* Fixes and updates to TinkerFiles

* Add simuteTinker example

* Update Modeller to work with AMOEBA force fields

* Small fixes

* Relax type hinting

* Fix indices in modeller

* Fix modeller indices

* Fix type hints and usage of Quantity

* Remove numpy protector

* Add reader of .seq files

* Add topology parsing of some protein residues, waters, ions, and generic molecules.

* Miscellaneous improvements

* Update amino acids and nucleotides list

* Various fixes to XML writing, and separate XML writing into a new class

* Comments/warnings

* Add nucleic topological definitions

* Improved handling of peptide residues

* Fix for CYX (disulfide bonds)

* Refactor the topology creation methods

* General improvements, and add support for nucleic-like residues

* No need to handle MP, DP, TP

* Minor improvements

* General refactoring, add automatic determination of topology

* Add TinkerAtomType dataclass, and remove references to biotypes as they are not needed

* Re-add missing parsing of forces and scalars

* Updates to createSystem()

* Add AMOEBA forces

* Add angle-related forces to createSystem

* Add placeholders for missing forces

* Beginning of support for AmoebaMultipoleForce

* Finished support for AmoebaMultipoleForce

* Support for AmoebaVdwForce

* TinkerFiles supports vdw

* Misc updates, and add AmoebaTorsionTorsion, AmoebaWcaDispersion, and AmoebaGeneralizedKirkwood

* Remove XML writer

* Fixes

* Fix wrong indentation in _findBitorsions

* Remove pdb debugging

* Documentation and fixes

* Remove files

* Revert checks in AmoebaVdwForceBuilder and ## @private  markers

* Remove duplicated static methods _getChiralAtomIndex

* Fix GK force

* Fix WcaDispersion force

* Fix WcaDisp

* Fixes and updates

* Cleanup and removing duplicated code

* Bug fixes

* A few more unit conversions

* Minor cleanup

* Misc fixes and updates

* Fix Add AmoebaStretchBendForce

* Simplify force builders

* Update ForceField

* Fix AmoebaPiTorsionForce

* Only add AmoebaWcaDispersionForce if using implicitSolvent

* Simplify amoebaforces

* Stretch torsion and angle torsion

* Misc. fixes

* Improve tests

* Fix cap group identification

* Add/improve tests

* Remove whitespaces from residue names

* Improve tests

* Consistent use of atomClasses list

* Fix match condition in AmoebaOutOfPlaneBendForceBuilder

* Fix AmoebaStretchBendForce

* Final fix for AmoebaStretchBendForce

* Fix AmoebaAngleForce

* Small fixes and improvements

* Update assertion tolerances

* Simplify torsion-torsion force creation

* Small fixes in the tests

* Review comments, type hints, docs for tinkerfiles.py

* Only use standard PDB for AA

* Type hint and docs for amoebaforces

* Reduce tolerances for failing tests

* Fixed error with ZOnly axis type when x particle is not specified

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Co-authored-by: peastman <peastman@stanford.edu>