GitLab

Fix case when OBC2 GB model is used and the salt concentration is non-zero. When
the salt concentration is non-zero, the customgbforces implementation has to be
used (since the native kernel does not support salt concentrations).  However,
since the native kernel runs ~2x faster on CUDA (and most likely far more
efficiently on CPU and Reference, most likely), it is worth continuing to use
the native kernel when possible.

implicitSolventKappa is provided it will be used. Otherwise,
implicitSolventSaltConc will be used to compute kappa from the solvent
dielectric constant and simulation temperature.

In order to provide a target temperature, an optional 'temperature' parameter
had to be added to the function call. The docstring makes it clear that
temperature is only used for the salt concentration -> debye length conversion.

Fixed a crash caused by a change to initialization order

Prevent trying to use the CPU OpenCL device on OS X

Fixed a compilation error

Parallelized the initialization of positions and forces in the CPU platform

Parallelized the computation of torsions with CPU platform

Fixed errors in wrapper generation when using Visual Studio 2010

Lots of documentation updates for 6.0

Updated version number to 6.0

Fixed an error in CMake script when compiling with clang

Ensure that PYTHON_EXECUTABLE is visible to all CMake scripts

Fixed a test case that occasionally failed

Test cases detect if CPU is not supported and exit rather than crashing

Fixed a compilation error when building wrappers

implicitSolventKappa the same (black-magic) way that Amber does. I have never
been able to reproduce the prefactor used to convert to kappa in Amber... sigh.

Added methods for changing default parameters on barostats and thermostats

Workaround for bug in Visual Studio

Detect Visual Studio in a way that works correctly with NMake files

Detect Visual Studio in a way that works correctly with NMake files