GitLab

Modeller preserves chain, residue, and atom ids when reasonable

Workaround for Nvidia bug on Maxwell in CUDA 6

Topology records PDB ids for chains, residues, and atoms

Custom expressions support floor() and ceil()

Lepton exceptions have more informative messages

Support CUDA runtime compilation

Updated to latest asmjit, which supports 32 bit mode

Fix for unit cell vector calculation

truncated octahedron inpcrd and prmtop file.

to support triclinic cells.

Also extend unitcell.computePeriodicBoxVectors to take Quantity inputs rather
than *just* scalars assumed to be nanometers.

Replaced TinyXML with irrXML

Python layer supports triclinic boxes

now that triclinics are supported this is important).

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.