* Update patch documentation
Clarified the definition and purpose of patches.
* Fix typo in RemoveExternalBond tag description
* Update wording in patches
* A few edits to the description of patches
---------
Co-authored-by: Peter Eastman <peter.eastman@gmail.com>
* 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
* 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
* 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
---------
Co-authored-by: peastman <peastman@stanford.edu>
* Initial implementation of C++ API
* Add kernel interface and information for API generation
* API updates for updating electrode parameters
* Add serialization proxy for ConstantPotentialForce
* Update file headers
* Add CG error tolerance and fix units on getCharges() return value
* Initial implementation of matrix solver
* Fixes and conjugate gradient solver
* Try to fix Linux and Windows builds
* Make sure charge constraint target is on total charge
* Restore handling of exceptions like NonbondedForce since they won't involve electrode atoms
* Ameliorate numerical instability in constrained conjugate gradient
* Fix uninitialized pointers, memory leak, and style
* Set CG tolerance units in Python API
* Test ConstantPotentialForce serialization
* Read/write ExceptionsUsePeriodicBoundaryConditions as bool
* Improve constrained conjugate gradient robustness to roundoff error accumulation
* Recompute matrix if electrode atoms move due to setPositions()
* Tolerance is now in gradient (potential) units again
* Add neutralizing background correction
* Add Python API tests
* Fixes for CG and nonbonded exceptions
* Add initial tests checking against existing NonbondedForce behavior
* Expand test suite and fix some implementation issues
* Add additional tests using larger reference system
* Add Gaussian test
* Finish test against reference computation
* CPU platform implementation
* Fixes for compilation on some platforms
* Fixes for constant potential with AVX/AVX2
* Test linking CPU PME library to constant potential test directly
* Older SWIG versions don't support Python set to C++ set conversion
* Add user guide entry
* Increase speed of reference test
* Conditional building constant potential CPU test is unreliable
* Debugging
* Miscellaneous fixes and improvements for CI
* Cache charges so solver will not run if system and coordinates have not changed
* Preconditioner flag, stability, and automatic detection improvements
* Add GPU platform-specific constant potential kernel classes
* PME and device-host I/O changes to support constant potential
* Initial common constant potential implementation
* Constant potential fixes:
* Fix preconditioner PME position/charge save/restore logic
* Fix reduction synchronization in constant potential solver kernels
* Add double-float accumulation for conjugate gradient solver when
double unsupported by hardware
* Improve conditioning of a test system, and make sure particles are in or
out of cutoff for consistency and ease of comparing between platforms
* Reorder guess charges for CG when atom reordering changes positions
* Remove PME queue for now
* Trying to debug optimized direct space derivative kernel
* Remove extraneous debugging lines
* Style updates; just make CPU preconditioner double precision
* Debugging updated optimized direct derivatives kernel for all but OpenCL CPU
* OpenCL CPU implementation of direct space derivatives, and cleanup
* Try to make test even shorter to not time out on CI
* Temporary - Debugging
* Debugging
* Debugging
* Debugging
* Debugging
* Remove debugging code and fix reduction synchronization
* Fix other reductions
* Debugging - are tests hanging or just slow on CI?
* Debugging
* Debugging
* Fix macro for case when double precision is available on hardware
* Remove changes for debugging again
* Try to improve matrix solver cache locality by uploading transpose
* Fixes for atom ordering and periodic images
* Can't rely on reorder listener for cell offset updates
* Test reducing number of contexts and timing for CI
* Debugging
* Remove timing code and revert debugging changes
* Matrix solver and plasma term optimizations
* Reduce CG solver kernel calls and downloads
* Don't read back convergence flag from global memory
* Update PME due to refactoring in master branch
* Faster matrix solver (1st step)
* Faster matrix solver for CUDA
* Faster matrix solver compatibility with non-CUDA platforms
* Matrix solver fixes
* Use warp shuffle reductions when possible
* Attempt to work around intermittent compiler crash in Intel CPU OpenCL
* Optimize CG solver kernel 1
* Rework CG solver so some kernels can use more than 1 block
* Don't run out of shared memory
* Asynchronously download convergence flag while clearing buffers
---------
Co-authored-by: Evan Pretti <pretti@sh03-17n15.int>
* Replace C++ code examples in Python API docs
* Use newer Python for building docs
* Remove sphinx version pin
* Add Python versions of code examples
* Minor edit
* Add Python version of one more code example
* Variable displacements based on particle positions
* set variable displacements when adding particles
* update documentation
* address compilation error in OpenMMFortranWrapper
* update python API tests
* fix stray 'and'
* addParticle() without arguments add a particle that is not displaced
* pack displacement particles into int4
* put back default displacement removed in error
* ATMForce interface with coordinate transformation objects
* revise variable displacement API
* documentation, formatting, serialization
* Fixed C and Fortran wrappers
* Fixed Python wrappers
* Fixed factory
* Sort files to ensure classes are listed in the correct order
* Converted APIUnits test to new ATMForce API
* write class name
* skip the documentation for forward declarations
* undo 9e91d0b since it does not fix the doc build
* remove temporary doc files for nested classes
* Clean away tabs
---------
Co-authored-by: Peter Eastman <peastman@stanford.edu>
* Began implementing QTBIntegrator
* Adaptation and deconvolution
* Continuing reference implementation
* Continuing to implement QTBIntegrator
* Use common thread pool
* More tests, documentation, and threading
* Fix segfault
* Serialize adapted friction when creating a State
* Beginning of GPU implementation
* Added missing files
* Bug fixes
* Fixed inverse FFT
* Continuing GPU implementation
* Checkpointing
* Bug fixes
* Test cases run faster
* Changes needed for latest main branch
* Minor optimizations
* Documentation
* Fixed atom reordering
* Added parahydrogen test case
* Workaround for bug in Microsoft's compiler
* Added a Python test
* Normalize kernel in deconvolution
* Minor documentation improvements
* Reference implementation of SymmetrySite
* Common implementation of SymmetrySite
* Removed duplicated code
* Serialization for SymmetrySite
* Fixed compilation error building C wrapper
* Added SymmetrySite to user guide
* Bug fix
* Added P21 test case
* Added computeCurrentPressure() to MonteCarloBarostat
* Use instantaneous temperature to compute pressure
* Added computeCurrentPressure() to MonteCarloAnisotropicBarostat
* Added computeCurrentPressure() to MonteCarloMembraneBarostat
* Fixed compilation error
* Fixed error in typemap
* Added documentation on computing pressure
* Fixed CUDA compilation errors
* Made test case more robust
* Made a test case more robust
* Added computeCurrentPressure() to MonteCarloFlexibleBarostat
* Fixed compilation error
* More documentation on computing pressure
* Created DPDIntegrator class
* Reference implementation of DPDIntegrator
* Build neighbor list for DPDIntegrator
* Minor fixes
* Documentation for DPDIntegrator
* Python API for DPDIntegrator
* Preliminary OpenCL implementation of DPDIntegrator
* Enable USE_PERIODIC
* Use updated positions in DPD thermostat
* Working on neighbor list for OpenCL DPDIntegrator
* ReorderListener for particle types
* Serialization for DPDIntegrator
* CUDA implementation of DPDIntegrator
* HIP implementation of DPDIntegrator
* Fixed compile error in Python wrapper
* Fixed compile error in wrappers
* Fixed uninitialized memory in reference neighbor list
* Added DPDIntegrator to C++ API docs
* Fixed incorrect launch size
* Fixed nan in DPD random number generator
* Minor optimizations
* Improved load balancing
* Fixed an indexing error
* Neighbor list uses the maximum cutoff of any force
* Fixed HIP compilation error
* Fixed access to invalid memory
* Added test case for diffusion coefficient
* Try to debug segfaults on CI
* Debugging
* Debugging
* Debugging
* Debugging
* Debugging
* Debugging
* Possible fix
* Debugging
* Debugging
* Debugging
* Use correct block size on CPU OpenCL
* Workaround for bug in Intel's OpenCL for CPUs
* Removed an unnecessary define
* Removed debugging code
* Include Dart
* More Intel workarounds
* Workaround for error in NVIDIA OpenCL
* added type checking for Simulation.step()
* changed how to check if step is an integer number
* allow for dicts to be returned from Reporter.describeNextReport
remove deprecated getState parameters ( #4437 )
* convert old format into new format
* update docstring
* nested set comprehension to set.union
* Allow 'periodic':None
update describeNextReport in all occurrences in the code
* debug
* update documentation
* add a reporter for energyParameterDerivative
* Revert "add a reporter for energyParameterDerivative"
This reverts commit 1d44dc3f60.
* Edit documentation
