GitLab

Swigged python docstrings now include documented return values and type
information or their arguments. They are generated in numpydoc format.
Furthermore, all of the Python app layer docstrings have been changed
to numpydoc format. The filterPythonFiles.py script which helps to
generate the Doxygen Python API docs has been updated to reflect these
changes.

Enable testing of OpenCL platform on Travis-CI

Fixed some test failures on OpenCL with CPU device

Check for index validity when setting interaction groups

[WIP] Per-atom parameters can be taken from residue templates

Reinstate fast copy methods

Fix segfault in swig wrappers

Modify Context.getState to accept a set of indices or bitmask

Ensure context can be created when selecting CUDA device

Fixed test failures on OpenCL CPU device

Minor optimizations to CPU neighbor list

New advanced options OPENMM_BUILD_CPU_TESTS, OPENMM_BUILD_SERIALIZATION_TESTS,
OPENMM_BUILD_REFERENCE_TESTS were added to the cmake configuration and disabled
in the OpenCL test matrix element to increase speed. Redundant or unnecessary
apt packages removed from the travis installation.

Added getNumAtoms, getNumResidues, getNumChains to simtk.openmm.app.Topology

Fix force deepcopy bug

Control what device is used for OpenCL tests

This patch creates a new build in the Travis-CI matrix that compiles and
runs the OpenCL tests using the CPU OpenCL device (AMD drivers). Because
not all of the tests can complete in the allotted 50 minutes, the ctest
invocation is changed to run them in a random order.

This also adds a new executable, TestOpenCLDeviceQuery, that prints
out information about all of the OpenCL devices on the system.

No GMX include directory in example

Fix thread synchronization in customCentroidBond.cl