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Added step limit for LocalEnergyMinimizer in Modeller.addHydrogens() to fix hangs on bad structures

Added step limit for LocalEnergyMinimizer in Modeller.addHydrogens() to prevent hangs with bad structures.

Add CheckpointReporter

Fixed some bugs in addExtraParticles() that affect the CHARMM polarizable force field

Fixed a potential divide by zero

loadCheckpoint/createCheckpoint should use bytes

Fixed compilation errors on Windows, plus an error in a test case

Created an optimized CPU implementation of CustomNonbondedForce

Created RPMDIntegrator::getTotalEnergy()

Fixed compilation errors on Windows

Fix Travis-CI

AMOEBA No Quadrupole Optimization

Added option to explicitly set PME parameters