GitLab

* Replace distutils with setuptools

* Replace more uses of distutils

* 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

* remove std::binary_function from ConstraintOrderer functor

* whoops whitespace

Test no longer runs and prints out a warning when running benchmark.py with --verbose. Fixes #3391

* Amoeba minor cleanup

- Fix variable name in string
- Remove odd space between variable and period that is inconsistently styled

* Replaces random tabs with spaces in ATM Force

* Support GROMOS bond and angle types

* Support NBFIX with geometric combining rule

* Continuing GROMOS support

* Bug fixes

* Fixes to test case

* Update wrappers/python/openmm/app/gromacstopfile.py
Co-authored-by: Jason Swails <jason@entos.ai>

* Improve logic for handling dihedraltypes

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Co-authored-by: Jason Swails <jason@entos.ai>

Fix bad link that directs to unsafe HTTP and then HTTP-HTTPS redirect

* 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

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

* 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