GitLab

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.

    - Adjust CharmmPsfFile parser to accept multiple blank lines before the
      NATOM record (I saw 1 PSF file like this... not sure how common it really
      is)
    - Removed the shebang line from element.py and removed execute permissions--
      it should never be executed directly (evidenced by the fact that the
      original shebang line was wrong and would never work, anyway).
    - Fix a test to determine if a Bond is part of an Angle in the PSF data
      structures.

Added a test case to make sure future changes to ForceField do not change forces

[WIP] experiments to figure out how to get nose running in parallel

GromacsTopFile parses define value with one extra leading character

Speed up a slow test case by using a smaller topology file

Commented out testEinsteinCrystal(), since it failed much too often

Fixed some test failures

Fixed a rare memory corruption error when roundoff causes tile indices to be wrong

Fix error in setting up AMOEBA systems when useDispersionCorrection is specified (retry)

Removed 'void' declarations from getCutoff/getCutoffDistance methods so that swigInputBuilder.py would correctly wrap return values.

Fix Clang warning about unhandled enum values.

In travis, use multiple cores.

Travis VM's have up through 2 cores. Passing a -j2 flag should make/ctest the builds/tests faster.

Clang had been generating the following warning:

```
ParsedExpression.cpp:123:13:
warning:
      30 enumeration values not handled in switch: 'CONSTANT', 'VARIABLE',
      'CUSTOM'...
            [-Wswitch]
                switch (node.getOperation().getId()) {
                                ^
                                1 warning generated.
```

To get rid of this warning, I added a default case, which does nothing.

XmlSerializer generates XML directly rather than going through TinyXml

Fix residue assignment in PSF parser

(which means that consecutive residues may have the same residue number _and_
name, but are different residues).

GromacsTopFile adds exclusions based on [ exclusions ] directives