GitLab

* 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 custom...

* Detect NaN to avoid infinite loop in JAMA::Eigenvalue

* Update to more modern version of pymbar

* No reason to modify spacing

* Use large blocks to optimize building the neighbor list

* Large blocks optimization for OpenCL

* Fix test failures

* Select whether to use large blocks based on system size

* Always use nvrtc for compilation

* Install nvrtc on CI

* Workaround for compiler error

* Set empty values for deprecated properties

* 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