GitLab

A large number of unit cleanups and fix numpy wart

numpy.

Fixed a bug in runForClockTime()

This should be *lower* than that of Unit (and ScaledUnit/BaseUnit), since we
still want Units to take priority over Quantities (but Quantity to take
precedence over regular ndarrays) for reasons like this:

>>> a = np.array([1]) * u.angstroms
>>> b = a * u.angstroms # should be np.array([1])*u.angstroms**2
>>> np.arange(10) * a # utilize broadcasting
[1 2 3 4 5 6 7 8 9 10] A**2

The main thing that's done here is that numpy arrays can be given units via the
* operator, rather than relying on the Quantity constructor

e.g.,

>>> import numpy as np
>>> np.zeros(10) * u.angstroms
Quantity(value=array([ 0.,  0.,  0.,  0.,  0.,  0.,  0.,  0.,  0.,  0.]), unit=angstrom)

yay!

Add travis build matrix for static and dynamic builds

Updates to documentation for 6.3

[WIP] Removed code that disabled OpenCL on OS X packaging.

Add check for null context inside integrator.step()

Fixed a compiler warning

Fixed a compilation error on some compilers

Update packaging devtools scripts for CUDA 7.0 on linux

Make sure RBTorsion parameters are returned with the correct units.

Minor enhancements to Topology

- Add an informative __repr__ to Topology
- Add __len__ to Chain and Residue to quickly tell how many residues or atoms
  are in them, respectively

Look in cuda dir for opencl headers

Useful when cuda is not installed in the default location.

Fixed race condition doing PME in a separate stream

GBn now uses Discrete2DFunctions

Move to using a continuous 2D function.

Ported OpenCL FFT to CUDA

Add elapsed time column in statedatareporter