Changed BondAngle to be the product of the energy of potentials applied to the central bond and two angles formed by four particles

Fixed groupSitee indexing, added anotehr device sync, included some (commented) printf lines for debugging

This reverts commit c6c19c64, reversing
changes made to c195bf09.

Changed BondAngle to be the product of the energy of potentials applied to the central bond and two angles formed by four particles

hchou10 authored 7 years ago and cmaffeo2 committed 6 years ago

Conflicts:
	src/RandomCUDA.cu

hchou10 authored 7 years ago and cmaffeo2 committed 6 years ago

Conflicts:
	src/Configuration.cpp
	src/GrandBrownTown.cu

HYC: Updated bound checking for angle lookups; Capped maximum force for dihedral angle (perhaps this should be reverted)

Fixed bugs in initialization of Exclusions and in the calculation of forces due to angle potentials . Added coordinate file for RBs. Added normalization of orientation in RB integrator.

Implemented "particleLists" for rigid body--particle interactions; made RigidBodyType class manage its own device data for particle interactions

Added logic to angle code to avoid singularity; improved tabulated bonded kernel arguments; commented out (non-working) get_energy code