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

hchou10 authored 7 years ago and cmaffeo2 committed 6 years ago

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

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: Added Langevin particle dynamics, including momenta and kinetic energy routines; changed whitespace in some areas

Fixed bug where replicas were not receiving random forces; removed unneeded restart file writes and memcpy

  (1) PairlistDistance is properly passed on to ComputeForce objects;
  (2) Power of 2 threads are now used in particle-grid force reduction;
  (3) Fixed accidental transpose of threads and blocks in grids' particleList kernel call

Fixed bug where pairlistDistance in Confugration.cpp was not being used; problem still remains where CellDecompoisiont ignores pairlistDistance; added IMD forces

Fixed issue in BaseGrid::interpolateForceDLinearlyPeriodic; made BD particle PMF use periodic boundary

Fixed issues with coordinate wrapping during integration; improved implementation of select matrix operations

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