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Co-authored-by: Zane Beckwith <zane.beckwith@sandboxquantum.com>

* addSolvent now only replaces newly added water molecules with ions

previously pre-existing (i.e. potentially crystallographic waters) were candidates for replacement with an ion.

concentration calculations (i.e. total water molecules) still include these pre-existing water molecules

* only include added water in concentration calc

* 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

* enable atom subset in PDBReporter

* adds optional atomSubset argument to PDBReporter
* adds functions in PDBReporter which create a new topology
  and positions with chosen subset of atoms
* PDBReporter write PDB files with the subset topology and positions.

* refactor PDBReporter

* make _createTopologySubset a method that is called only the first time it is needed
* more efficient creation of subset positions
* check that atomSubset is ordered

* refactoring PDBReporter and add PDBx

* move checks on atomSubset to _createSubsetTopology
* copy periodic box vectors from topology to subsetTopology
* add atomSubset to PDBx reporter

* add bond subset to createSubsetTopology

* formatting changes to pdbreporter

* loop over atoms cleaned up
* put file opening inside parameter loop in
  TestPdbReporter::testinvalidSubsets to try and fix failing tests on windows

* add thorough tests to TestPdbReporter

* spelling changes
* Add tests for atom positions, elements, names etc
* attempt at fixing PyPy and Windows failing test cases

* fix spellings

* close output file before raising exceptions

* closes output files before raising exception in pdbreporter
createSubsetTopology
* changes assertVecAlmostEqual from a method to function to avoid
  repeating

This PR should fix the docstring rendering of `Quantity`, which currently looks the following way: http://docs.openmm.org/latest/api-python/generated/openmm.unit.quantity.Quantity.html#openmm.unit.quantity.Quantity

* Fix misleading documentation of `Topology.bonds`

`Topology.bonds()` states that iterates over a tuple of `Atom` objects. While this is technically correct, as the `Bond` class is a named tuple, this also hides the fact, that `Bond` objects also provide the `order` and `type` attributes. Therefore, I propose to change the sentence, so that it uses the capitalized *Bonds* indicating that they are actually objects.

* Update docstring

* 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

Fix #3790: Collision rate for MTS BAOAB Langevin integrator now correctly accounts for number of substeps (#3791)

* Fix #3790: Collision rate for MTS BAOAB Langevin integrator now correctly accounts for number of substeps. Fix suggested by Charlie Matthews (@c-matthews)

* Fix computation of total number of substeps

* Add test for MTS friction

* Fix typo

* Fix yet another typo

* Fix typo and check against analytical result

* Fix typo

* Fix typos

* Fix more typos

* Integrate MTSLangevinIntegrator for longer to allow thermalization

* Revert number of integrator steps

* Update TestIntegrators.py

Fixed a failing test case
Co-authored-by: Peter Eastman <peter.eastman@gmail.com>

* add swm4-ndp water to addSolvent

* add equilibrated box

* typo of water radius

* fixed addSolvent description

* add swm4 to tests

* update modeller.addSolvent docstring

* update docstring for modeller.addSolvent

* Support kernel files with extensions of any length (like .hip)

* Do not allow to replace symbols in single-line comments

* Add OPENMM_BUILD_COMMON CMake option

It allows to build and install common platform files even if
CUDA or OpenCL platforms are not built.
This is required for HIP platform (openmm-hip) if ROCm OpenCL
packages are not installed.

* Add an option for Python wrapper to install into user packages

OPENMM_PYTHON_USER_INSTALL is OFF be default.

* Support FFT backends in Amoeba plugin

The HIP platform supports FFT backends, this commit moves
findLegalFFTDimension to ComputeContext, so platforms can have their own
implementations.

* Compatibility for common platform w/ new HIP platform

* Do not use volatile with private and local AtomData parameters on HIP

The generated code is not optimal, for example, the compiler generates
flat_load instructions instead of ds_read.

* Tune launch bounds for PME grid-related kernels and add WA for RDNA

Force the compiler to use all registers for gridSpreadCharge and
gridInterpolateForce by limiting max waves per EU to 1 on CDNA GPUs,
RDNA GPUs work better without it.

* Optimize atom data structs in GBSA and Amoeba on HIP

Manually rearrange fields, add paddings and force alignments to
have faster accesses to shared memory: ds_read and ds_write may
work slower if addresses are not aligned by 16 bytes.
Co-authored-by: Anton Gorenko <anton@streamhpc.com>
Co-authored-by: Nick Curtis <nicholas.curtis@amd.com>

* 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>

* ZeroDivisionError Fix to Metadynamics Bias

* Corrected Error Message

* Avoid adding duplicate exclusions to CustomNonbondedForce

* Fixed error in adding explicit constraints

* Added temperature adjustment to MC barostat for simulated tempering

fixes #3612

* Added test for simulated tempering with MC barostat.

* Fixed typo in TestSimulatedTempering.py

* Updated NPT test for SimulatedTempering

* Updated variable naming

* Reverted back to harmonic oscillator test

* Added FAQ links to error messages

* Added missing Windows export