GitLab

Convert AmberInpcrdFile data structures from lists to Vec3

- Convert coordinates, velocities, and box vectors into Vec3 objects to avoid a
  subtle bug in the units module with respect to silently modifying mutable
  collections in-place when converting to a new set of units.

Fixed bug when running on a CPU device

Revert to older Travis-CI testing framework to separate testing from conda dev builds

Implemented CHARMM polarizable force field

Depressing compromise to make the ordering of atoms in improper torsions as consistent as possible with both AMBER and CHARMM

Update default long-range option and expand test

added.

correction by default. Then add a test for using the long-range correction and
_not_ using the long-range correction.  Comment out the test using the
long-range correction since it currently segfaults.  When the fix for the
segfault is added, this test can be reinstated (but the energy has to be
updated)

This change in default makes it consistent with the default behavior for the
classical NonbondedForce, and I would have set that as the default to begin with
if I had known it was supposed to work.

Updated long range correction code to work with new style tabulated functions

Fix error reporting in a corner case.  Looks like a case of incomplete copy-and-paste...

Add support for Amber prmtop files with NBFIX

copy-and-paste...

TestAmberPrmtopFile.py tests take 17 seconds combined on my laptop).

force field utilizes nbfix functionality. Without this commit, using a ff14IPQ
topology file (or one modified by ParmEd to contain off-diagonal LJ elements),
would happily run, but ignore off-diagonal elements.

The new Chen and Garcia RNA force field (see doi:10.1073/pnas.1309392110) also
utilizes off-diagonal terms in its parametrization scheme.

One shortcoming is that the approach taken here -- using a pair parameter lookup
table -- cannot be currently used with a long-range correction because it is not
a `Continuous1DFunction' by virtue of using two `Discrete2DFunction'
TabulatedFunction classes.

Energies here match the values obtained with Amber to 0.01 -- 0.1 kcal/mol
(within 0.1% of the total).

itself. This way each parm is only read once for every test (rather than being
read for every test, even when they're not used, as part of the setUp routine).
For large systems, this makes the tests run a lot faster (for small systems it's
not a large speedup).

All tests continue to pass. This change also tests that the various calls to
createSystem and such do not actually change the object in a detrimental way.

Remove wierd unicode thing

Docstring for ForceField constructor

Fix lepton size_t VS2013 warnings by casting to int.

Lots of changes to support Android

Automated conda packaging of openmm-dev [ready to merge]

Began creating API for programmatically building and editing ForceFields

Small fixes:

the switchDistance argument to CharmmPsfFile.createSystem().

Also add a check to protect against negative switching distances.