GitLab

* save atomIndex order in MCBarostat kernel

* Update device indices

* Only setAtomIndex if there was a reorder

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

* Attempt at fixing errors with barostat

* Missing ContextSelector

* 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

* Skip neighbor list for very small systems

* Fixed typos

* Don't skip box size check when not using neighbor list

* Made test larger to ensure it uses neighbor list

* Faster implementation of CustomHbondForce

* Minor optimization

* Optimized writing forces, which are often zero

* Fix test failure on CPU OpenCL

* Bug fix

* Store bounding box sizes in half precision

* Work correctly in double precision mode

* 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

It may contain a garbage value, and if it is large then
updateNeighborListSize does not force reorder atoms after 25 steps
in extremal cases.

* 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

* Use 768 instead of 384 threads in generic kernels

* Use 1536 instead of 1024 threads in force kernels.

Fix specifying a device will fail to run when multiple OpenCL platforms are available. Specifying `--verbose` prints the following exception:
```
Specified DeviceIndex but not OpenCLPlatformIndex. When multiple platforms are available, a platform index is needed to specify a device.
```

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