GitLab

Replaced TinyXML with irrXML

Python layer supports triclinic boxes

Generalize Amoeba Stretch-Bend term

argument.

Update the Python application layer to use both force constants when building
the AmoebaStretchBendForce.

one in the Reference platform (pulled over via meld to limit possible mistakes).

stretch-bend test correctly.

The potential energy calculation done in the ReferenceStretchBendTest file was
updated to mirror that of the Reference kernel, but first I made sure that the
test passed *before* updating to the new energy expression, just to make sure
that the energies and forces didn't *change* with the new expression.

of just 1.  Backwards compatibility is provided by making the 2nd force constant
default to -1, which is reinterpreted as "copy the first force constant".

Updates both the reference and CUDA kernels.

Add error checking for the input GB radii in the GBn methods.

Fixes vs2013 warnings 4251, 4267 in lepton.

The pragma to ignore 4251 already existed in windowsIncludes.h, and it works
when compiling lepton itself. However, when clients use lepton, they get this
warning. I think this is why @sherm1 put the define as shown here:
https://github.com/simbody/simbody/blob/master/SimTKcommon/include/SimTKcommon/internal/common.h#L168
 (whether or not the shared library is being built or used).

C++ libraries support triclinic boxes

between 1 and 2 Angstroms, or they fall outside the bounds of the neck lookup
tables.

At least on my Mac, this results in a C++ exception that does not get translated
into a Python exception (i.e., it is not catchable and crashes the application)

Check for nan positions was being done incorrectly

Fixed Fortran compilation errors caused by function names being too long

Fixgb

cutoff GB.