PG-PuReMD: merge memory management and step retry logic from MPI+GPU code into...
PG-PuReMD: merge memory management and step retry logic from MPI+GPU code into MPI-only code. Fix and backport numerous bugs (void pointer arithmetic and dereferences, etc.). Update code to match new data structures. Begin merging changes from OpenMP code (sPuReMD) for preconditioning work.
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- PG-PuReMD/src/allocate.c 374 additions, 396 deletionsPG-PuReMD/src/allocate.c
- PG-PuReMD/src/allocate.h 5 additions, 3 deletionsPG-PuReMD/src/allocate.h
- PG-PuReMD/src/analyze.c 8 additions, 2 deletionsPG-PuReMD/src/analyze.c
- PG-PuReMD/src/basic_comm.c 50 additions, 22 deletionsPG-PuReMD/src/basic_comm.c
- PG-PuReMD/src/basic_comm.h 12 additions, 3 deletionsPG-PuReMD/src/basic_comm.h
- PG-PuReMD/src/bond_orders.c 751 additions, 949 deletionsPG-PuReMD/src/bond_orders.c
- PG-PuReMD/src/bond_orders.h 9 additions, 14 deletionsPG-PuReMD/src/bond_orders.h
- PG-PuReMD/src/bonds.c 18 additions, 17 deletionsPG-PuReMD/src/bonds.c
- PG-PuReMD/src/charges.c 2 additions, 3 deletionsPG-PuReMD/src/charges.c
- PG-PuReMD/src/comm_tools.c 29 additions, 30 deletionsPG-PuReMD/src/comm_tools.c
- PG-PuReMD/src/comm_tools.h 1 addition, 1 deletionPG-PuReMD/src/comm_tools.h
- PG-PuReMD/src/control.c 368 additions, 368 deletionsPG-PuReMD/src/control.c
- PG-PuReMD/src/control.h 1 addition, 1 deletionPG-PuReMD/src/control.h
- PG-PuReMD/src/cuda/cuda_allocate.cu 9 additions, 9 deletionsPG-PuReMD/src/cuda/cuda_allocate.cu
- PG-PuReMD/src/cuda/cuda_allocate.h 1 addition, 1 deletionPG-PuReMD/src/cuda/cuda_allocate.h
- PG-PuReMD/src/cuda/cuda_bond_orders.h 25 additions, 22 deletionsPG-PuReMD/src/cuda/cuda_bond_orders.h
- PG-PuReMD/src/cuda/cuda_copy.cu 5 additions, 5 deletionsPG-PuReMD/src/cuda/cuda_copy.cu
- PG-PuReMD/src/cuda/cuda_forces.cu 281 additions, 65 deletionsPG-PuReMD/src/cuda/cuda_forces.cu
- PG-PuReMD/src/cuda/cuda_init_md.cu 11 additions, 48 deletionsPG-PuReMD/src/cuda/cuda_init_md.cu
- PG-PuReMD/src/cuda/cuda_integrate.cu 4 additions, 4 deletionsPG-PuReMD/src/cuda/cuda_integrate.cu
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