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present, defaulting to 1.2 (SCEE) and 2.0 (SCNB) if they're not present. If
values for scee and scnb are provided to readAmberSystem they will override any
values in the topology file, but a warning will be printed (since ignoring the
scaling parameters in the topology file really changes the force field).

Prevent segfaults when a simulation blows up

Created optimized CPU platform

correct minor bug in GBn screening parameter determination.

instead of gb is intentional.

was:

if symbl[0] == ('c' or 'C'):
   ...do stuff...

This logic will match only 'c' as ('c' or 'C') evaluates to 'c' while
('c' and 'C') evaluates to 'C':

>>> 'c' or 'C'
'c'
>>> 'C' == ('c' or 'C')
False

The correct logic is either

if symbl[0].upper() == 'C':
   ...do stuff...

or

if symbl[0] in ('C', 'c'):
   ...do stuff...

(Alternatives can be [ if symbl[0] in 'cC' ] or [ if symbl[0].lower() == 'c'])

Separated hardware query functions into a separate file.  CPU platform checks for the correct hardware.

Python records where OpenMM is installed, so it doesn't need to be specified with environment variables at runtime

Lots of code cleanup related to constraints in the reference platform

Added option to omit PILE thermostat from RPMD

Created reference implementation of SETTLE

Python records where OpenMM is installed, so it doesn't need to be specified with environment variables at runtime

dmstests

Fix to PR #152

Added unittest and 1 system tests. Includes 1 bugfix to resolving a circular import and 1 bugfix where dms wasn't creating the topology correctly when the water was specified in different chains

Ignore constraints that connect two massless particles (feature request 1915)