GitLab

* 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 1d44dc3f60153defb6252ab56a3b85350fa24826.

* Edit documentation

* Added documentation on HIP

* Instructions for building HIP on Windows

* VkFFT-based 3D FFT;
* Caching of compiled VkFFT kernels;
* Extend FFT tests with more sizes.

* Debug CI failures

* Debugging

* Debugging

* Debugging

* Debugging

* Debugging

* Debugging

* Debugging

* Debugging

* Removed build that was failing

* Fixed URL that had changed

* Update references to "openmmforcefields" project

* Org name, too

* Can use getPlatform() instead of getPlatformByName()

* More concise arguments for getState()

* Replaces sub tags for python API docs

* Changes string to pathlib

* Adds support for sup html tags

* Corrects function description

* Implemented MinimizationReporter

* PythonAPI for MinimizationReporter

* Improved test case

* SWIG fix

* Reporter returns a bool instead of throwing an exception

* Implemented CustomCPPForceImpl

* Documentation for CustomCPPForceImpl

* Attempt at fixing Windows compilation error

* Improved documentation

* Draft integration of the Alchemical Transfer Method (ATM) plugin

* Attempt to store and retrieve forces--does not compile

* Implement addForce()/getForce() methods

* Throw exception when specifying properties without a Platform (#4130)

* Fixed DOF calculation for NoseHooverIntegrator (#4128)

* Fix variance in documentation of VerletIntegrator (#4138)

* Python API for ATMForce

* Fixed compilation error

* Minor cleanup of formatting and documentation

* Files for ATMForce test cases

* More cleanup

* Removed variable groups

* Test ATMForce with two particles

* More tests for ATMForce plus fixes

* Added missing header

* Rework interface to pass displacements as vector of parameters

* Revert "Rework interface to pass displacements as vector of parameters"

This reverts commit 5e092031f31ded1137b677588f007add1c2d6f82.

* Test with nonbonded force

* Allow energy expression to be customized

* Optional displacements at the initial state

* Fixed compilation error build C wrapper

* Address edge case of default energy expression

* Consistent naming of the variables of the displacement states

* Test of soft core function of the default energy expression

* Mark addForce() as taking ownership

* initial python test for ATMForce

* Test custom expressions

* Expanded C++ API documentation for ATMForce

* Energy parameter derivatives

* Serialization for ATMForce

* Documentation, cleanup, and fixes

* Fixed typos

* getPerturbationEnergy() computes energy

* Another test case

* Minor edits

---------
Co-authored-by: Peter Eastman <peastman@stanford.edu>
Co-authored-by: Michael Plainer <plainer@ymail.com>

* Always use nvrtc for compilation

* Install nvrtc on CI

* Workaround for compiler error

* Set empty values for deprecated properties

* Preliminary work on XTC reporter
1. Move and adapt xtc writer/reader from moleculekit (explicit permission
granted by the authors to do so)
2. Create XTCTrajectoryFile
3. Create XTCReporter

* Add licence and attribution to c++ xtc library
Apply clang-format to it
Remove some unused functions and document the rest

* Add attribution and licence to cython wrappers for the xtc library
Remove some unused functions

* Change XTCTrajectoryFile to XTCFile
Simplify the interface and document the class

* Add test for the xtc file parser

* Update XTC reporter with new parser name

* Fix incorrect function name in XTCReporter

* XTCFile:
	* Add function to get number of frames
	* Add function to read a group of frames from a file
	* Add tests for the above

* Ensure data is passed as float32 in XTC file

* Add XTCReporter and tests

* Add more tests to XTCReporter

* Remove unnecessary pdb reporter in XTC tests

* Copy test xtc file in python/tests/systems to build directory for testing

* Remove XTC file reading from the interface
Make XTCFile mimic DCDFile more closely

* Use xtc_read to test the correctness of the XTC reporter

* Add a test for reporting triclinic boxes

* Make XTC library compatible with triclinic boxes.
Adapt XTCFile to triclinic boxes

* Change XTCFile to take a file as argument instead of a filename

* Match DCDFile handling of the box

* Fix comment

* Revert "Change XTCFile to take a file as argument instead of a filename"

This reverts commit 9815d4790b3886cc8a741586792268e80a227ba0.

* Fix dangling file name issue

* Remove index file functionality from XTC parser.
Remove unused define switch PLATFORM_Linux

* Fix formatting

* Remove inconsistent variable naming in xtcfile.py

* Change file argument name to match other reporters

* Do not turn off error checking in cython wrappers

* Fix leftover fileName in reporter

* Rewrite wrapper to xtclib in C++

* Small changes to wrapper code

* Small changes to wrapper code

* Small changes to wrapper code

* XTCFile: Get number of atoms directly from topology

* DCDFile: Get number of atoms directly from topology

* Change constexpr to const

* Check precision in XTC file matches the written one

* Add a write function to XTCFrame.
Make write check for errors C++ side.

* Rewrite large trajectory files without loading the whole file to memory

* Remove unused code in XTC test

* Avoid spurious copy of the positions array when calling xtc_write_frame

* Pass box as reference

* Remove unnecessary imports and definitions

* Fix formatting

* Use std::string instead of char*

* Use .c_str()  instead of .data()

* Fix crash in Mac by correctly checking precision

* Use TemporaryDirectory for tests instead of NamedTemporaryFile (Fixes windows ci)

* Remove unnecessary file creation

* Propagate exceptions via cython

* Switch to TemporaryDirectory in xtcfile.py

* Remove unnecessary include

* Update some comments and document functions

* Add XTC reporter to the docs

* Update 05_cpu_platform.rst

* Update 04_platform_specifics.rst

* copy opc ions and opc*standard.xml from https://github.com/openmm/openmmforcefields/commit/b12c2e871b60275a10b3f8f56dfc2f6d5447591f

* auto-merged files

* move charges to residue definition

* remove unmerged files

* add docs

* rename U to U4+

* rename Ag+, Tl+, Gd3+ and I- residue names

* fix O-H bond length typo

* add opc3 constraints test

* Use PocketFFT instead of FFTW

* Minor cleanup

* Use PocketFFT instead of fftpack for reference platform

* Remove FFTW as a dependency

* Converted a test case to use PocketFFT

* Fixed an incorrect comment

* 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>

* Added documentation to clarify behavior of nonbonded exceptions

* Added documentation to clarify behavior of nonbonded exceptions

* 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

Without this restriction, the compilation fails if the project folder has parent folders called "tests", "internal" or other words in these generic patterns.

* Minor clarification to manual

* Another minor clarification

* Added GLYCAM

* Improved tests and documentation

* Fixed incorrect external bonds

* 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 MonteCarloFlexibleBarostat

* Improved test cases

* Documentation for MonteCarloFlexibleBarostat

* Added a missing include

* Serialization for MonteCarloFlexibleBarostat

* Added MonteCarloFlexibleBarostat to C++ API docs index

* Added citation for MonteCarloFlexibleBarostat

* 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

* Proof of concept matching current behaviour with Breathe

* Reorganise C++ API docs to work without autosummary

* Revert to Sphinx-native search

* Move remaining pip deps to conda

* Remove unnecessary lunrsearch templates

* Remove lunrsearch from cmake

* Tidy up layout of API docs

* Get code blocks to work with Breathe

Breathe doesn't seem to support the Doxygen <preformatted> tag.
It does support the <code> tag, but better yet it supports using
<verbatim> tags to embed rst into docstrings. This commit changes
all <pre> tags to use RST verbatim, and updates the Python
documentation machinery to support it too.

* Clarified some language

* Have doxygen exclude undocumented classes and have sphinx fail on warnings for C++ API docs

* List custom forces and integrators last

* Add breathe to documentation CI

* Typo

* Fix link to custom forces in extras.rst

* Have Breathe process only public classes

* Strip OpenMM:: prefix from rst files to avoid colons in links

* Remove existing private classes from EXCLUDE_SYMBOLS

* Add comment to C++ cmake describing why we promote warnings to errors

* Revise documentation build instructions for new dependencies