GitLab

CustomIntegrator variables are saved to checkpoints

Fix for CharmmPsfFile parser constrains with CHARMM TIP3 water topology

Make CharmmPsfFile ignore H-H water bond that is required for rigid water with original CHARMM implementation of constrains.

Fixed an edge condition that could cause errors in CMAPTorsionForce

Lepton: define M_PI if needed with MingW (in addition to MSVC)

See https://github.com/lammps/lammps/pull/1992

Improved counting of degrees of freedom

Fixed errors in sorting on some AMD GPUs

Update JAMA to version 1.0.3

ARM64 support

Adapted from https://math.nist.gov/javanumerics/jama/

Added drudeMass argument for setting mass of Drude particles

Changes to support CHARMM polarizable force field

Fix bug in __ne__ implementation from #2616

Apparently it is the slightly more correct way of doing thigns, as explained in
https://stackoverflow.com/a/30676267/538973

* Use list-comprehension in Python code

A minor change, but slighly easier to understand the initialization of
`parent_exclude_list` in my opinion.

* Implement __ne__ in Python classes that has __eq__

In Python 3, `__ne__` is automatically implemented as `not __eq__`.

However, in Python 2 it seems to be implemented as `not is` (so based on object
identity).

Based on setup.py [0] which says that "OpenMM requires Python 2.7 or better", it
should be useful to have better support for Python 2 :)

This was already done in 4 of the 12 classes that implements `__eq__`

```
>>> class WildCard(object):
...     def __eq__(self, other): return True

>>> w = WildCard()

>>> w == 42
True

>>> w != 42
True

>>> w != w
False
```

[0]: https://github.com/openmm/openmm/blob/5cef29ce8d4e17b6d0f9fd8a3c6cc1669ca0ba2b/wrappers/python/setup.py#L237

* Use umambiguous floor division for index calculations in Python

This makes the code work as intended if run...

Add __ARM64__ to differentiate between 32 and 64 bit ARM

Update Azure VM to newer version

* Remove unused variable from CpuCustomGBForce::calculateIxn

* Remove unused variable from CpuCalcCustomManyParticleForceKernel::initialize

* Remove unused variable from CudaCalcCustomCVForceKernel::initialize

* Remove unused variable from ReferenceCalcCustomManyParticleForceKernel::initialize

* Remove unused variables from ReferenceObc::computeBornEnergyForces

* Remove unused variable from AmoebaTorsionTorsionForceProxy::serialize

Accept more variants of labels in CHARMM files

bug fix for handling constraints and rigidWater in CharmmPsfFile