GitLab

License header changes; force duplication factor to 4; fixed potential problem w/ Shake -- if no constraints, pgm crashes

Fixed setting of runtime in BrookPlatform() constructor (constructor w/o args):
if 'brt_runtime' env variable not set, then
internal 'runtime' variable was NULL -- this led to a fault when _setBrookRuntime() was called

Commented out static platform variable, which may have caused initialization problems
Some of the Brook tests now succeed on my computer for the first time.

                                     overrides of bonded gathers for testing
BrookGbsa:                           OBC parameters fixed; added energy calculation
BrookCommon:                         added utility methods for allocating arrays