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  • SParTA/PuReMD
  • kaymakme/PuReMD
  • vermaasj/PuReMD
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.gitignore
View file @ de96b3a2
......@@ -3,6 +3,7 @@
*.prs
*.pot
*.trj
*.res*
# TeX
*.aux
......
Makefile.am
View file @ de96b3a2
ACLOCAL_AMFLAGS = -I m4
AM_CFLAGS = -O2 -funroll-loops -Wall
SUBDIRS =
DIST_SUBDIRS =
EXTRA_DIST = data environ tools
......@@ -70,16 +72,16 @@ sPuReMD_lib_libspuremd_la_SOURCES = sPuReMD/src/allocate.c \
sPuReMD/src/valence_angles.h \
sPuReMD/src/vector.c \
sPuReMD/src/vector.h
sPuReMD_lib_libspuremd_la_CFLAGS = @DFT_CFLAGS@ @OMP_CFLAGS@
sPuReMD_lib_libspuremd_la_CPPFLAGS = -I sPuReMD/src
sPuReMD_lib_libspuremd_la_CFLAGS = @DFT_CFLAGS@ @CFLAGS_EXTRA@ @OMP_CFLAGS@
sPuReMD_lib_libspuremd_la_CPPFLAGS = -I sPuReMD/src @CPPFLAGS_EXTRA@
sPuReMD_lib_libspuremd_la_LDFLAGS = -version-info 1:0:0
sPuReMD_lib_libspuremd_la_LIBADD = @OMP_LIBS@ @L_LIBS@
sPuReMD_lib_libspuremd_la_LIBADD = @OMP_LIBS@ @Z_LIBS@ @L_LIBS@ @T_LIBS@ @G_LIBS@
bin_PROGRAMS = sPuReMD/bin/spuremd
sPuReMD_bin_spuremd_SOURCES = sPuReMD/src/driver.c
sPuReMD_bin_spuremd_CFLAGS = @DFT_CFLAGS@ @OMP_CFLAGS@
sPuReMD_bin_spuremd_CPPFLAGS = -I sPuReMD/src
sPuReMD_bin_spuremd_LDADD = sPuReMD/lib/libspuremd.la @OMP_LIBS@ @L_LIBS@
sPuReMD_bin_spuremd_CFLAGS = @DFT_CFLAGS@ @CFLAGS_EXTRA@ @OMP_CFLAGS@
sPuReMD_bin_spuremd_CPPFLAGS = -I sPuReMD/src @CPPFLAGS_EXTRA@
sPuReMD_bin_spuremd_LDADD = sPuReMD/lib/libspuremd.la @OMP_LIBS@ @Z_LIBS@ @L_LIBS@ @T_LIBS@ @G_LIBS@
check_PROGRAMS =
TESTS =
......@@ -180,8 +182,8 @@ PuReMD_bin_puremd_SOURCES = PuReMD/src/allocate.c \
PuReMD/src/vector.c \
PuReMD/src/vector.h
PuReMD_bin_puremd_CFLAGS = @DFT_CFLAGS@ @M_CFLAGS@
PuReMD_bin_puremd_CPPFLAGS = -I PuReMD/src
PuReMD_bin_puremd_CFLAGS = @DFT_CFLAGS@ @CFLAGS_EXTRA@ @M_CFLAGS@
PuReMD_bin_puremd_CPPFLAGS = -I PuReMD/src @CPPFLAGS_EXTRA@
PuReMD_bin_puremd_LDADD = @M_LIBS@ @L_LIBS@
endif
......@@ -190,15 +192,8 @@ if BUILD_GPU
if USE_CUDA
SUFFIXES = .cu
include cuda.am
endif
if USE_CUDA
# flags for CUDA compilation via NVCC (see cuda.am)
# Note: cc 13 for Tesla, cc 20 for Fermi, cc 30 for Kepler K10, cc 35 for Kepler K20/K40, etc.
#NVCCFLAGS += -gencode arch=compute_35,code=sm_35
NVCCFLAGS += $(NVCC_OPT_CODE)
NVCCFLAGS += --compiler-options "$(DEFS) $(NVCC_OPT_CODE_DEFS) @DFT_CFLAGS@"
#NVCCFLAGS += --ptxas-options -v
AM_NVCCFLAGS = --compiler-options="$(DEFS) $(AM_CFLAGS) @CFLAGS_EXTRA@ $(CFLAGS)" @NFLAGS@ @NFLAGS_EXTRA@
endif
bin_PROGRAMS = PuReMD-GPU/bin/spuremd
......@@ -315,8 +310,8 @@ PuReMD_GPU_bin_spuremd_SOURCES += PuReMD-GPU/src/cuda_allocate.cu \
nodist_EXTRA_PuReMD_GPU_bin_spuremd_SOURCES = PuReMD-GPU/src/dummy.c
endif
PuReMD_GPU_bin_spuremd_CFLAGS = @DFT_CFLAGS@
PuReMD_GPU_bin_spuremd_CPPFLAGS = -I PuReMD-GPU/src
PuReMD_GPU_bin_spuremd_CFLAGS = @DFT_CFLAGS@ @CFLAGS_EXTRA@
PuReMD_GPU_bin_spuremd_CPPFLAGS = -I PuReMD-GPU/src @CPPFLAGS_EXTRA@
if USE_CUDA
PuReMD_GPU_bin_spuremd_CFLAGS += @CUDA_CFLAGS@
......@@ -331,17 +326,18 @@ EXTRA_DIST += PG-PuReMD/src/cub
if USE_CUDA
SUFFIXES = .cu
include cuda.am
AM_NVCCFLAGS = --compiler-options="$(DEFS) $(AM_CFLAGS) -std=c++14 @CFLAGS_EXTRA@ $(CFLAGS) @OMP_CFLAGS@ @M_CFLAGS@" -std=c++14 @NFLAGS@ @NFLAGS_EXTRA@
endif
if USE_CUDA
# flags for CUDA compilation via NVCC (see cuda.am)
# Note: cc 13 for Tesla, cc 20 for Fermi, cc 30 for Kepler K10, cc 35 for Kepler K20/K40, etc.
#NVCCFLAGS += -gencode arch=compute_35,code=sm_35
NVCCFLAGS += $(NVCC_OPT_CODE)
NVCCFLAGS += --compiler-options "$(DEFS) $(NVCC_OPT_CODE_DEFS) @DFT_CFLAGS@ @M_CFLAGS@"
#NVCCFLAGS += --ptxas-options -v
if USE_HIP
SUFFIXES = .cu
include hip.am
AM_HIPCCFLAGS = $(DEFS) $(AM_CFLAGS) -std=c++14 @CFLAGS_EXTRA@ $(CFLAGS) @OMP_CFLAGS@ @M_CFLAGS@
endif
bin_PROGRAMS = PG-PuReMD/bin/pg-puremd
PG_PuReMD_bin_pg_puremd_SOURCES = PG-PuReMD/src/allocate.c \
PG-PuReMD/src/allocate.h \
......@@ -392,6 +388,7 @@ PG_PuReMD_bin_pg_puremd_SOURCES = PG-PuReMD/src/allocate.c \
PG-PuReMD/src/nonbonded.c \
PG-PuReMD/src/nonbonded.h \
PG-PuReMD/src/puremd.c \
PG-PuReMD/src/puremd.h \
PG-PuReMD/src/random.c \
PG-PuReMD/src/random.h \
PG-PuReMD/src/reax_types.h \
......@@ -413,6 +410,8 @@ PG_PuReMD_bin_pg_puremd_SOURCES = PG-PuReMD/src/allocate.c \
if USE_CUDA
PG_PuReMD_bin_pg_puremd_SOURCES += PG-PuReMD/src/cuda/cuda_allocate.cu \
PG-PuReMD/src/cuda/cuda_allocate.h \
PG-PuReMD/src/cuda/cuda_basic_comm.cu \
PG-PuReMD/src/cuda/cuda_basic_comm.h \
PG-PuReMD/src/cuda/cuda_bond_orders.cu \
PG-PuReMD/src/cuda/cuda_bond_orders.h \
PG-PuReMD/src/cuda/cuda_bonds.cu \
......@@ -423,6 +422,8 @@ PG_PuReMD_bin_pg_puremd_SOURCES += PG-PuReMD/src/cuda/cuda_allocate.cu \
PG-PuReMD/src/cuda/cuda_charges.h \
PG-PuReMD/src/cuda/cuda_copy.cu \
PG-PuReMD/src/cuda/cuda_copy.h \
PG-PuReMD/src/cuda/cuda_dense_lin_alg.cu \
PG-PuReMD/src/cuda/cuda_dense_lin_alg.h \
PG-PuReMD/src/cuda/cuda_environment.cu \
PG-PuReMD/src/cuda/cuda_environment.h \
PG-PuReMD/src/cuda/cuda_forces.cu \
......@@ -434,8 +435,6 @@ PG_PuReMD_bin_pg_puremd_SOURCES += PG-PuReMD/src/cuda/cuda_allocate.cu \
PG-PuReMD/src/cuda/cuda_init_md.h \
PG-PuReMD/src/cuda/cuda_integrate.cu \
PG-PuReMD/src/cuda/cuda_integrate.h \
PG-PuReMD/src/cuda/cuda_lin_alg.cu \
PG-PuReMD/src/cuda/cuda_lin_alg.h \
PG-PuReMD/src/cuda/cuda_list.cu \
PG-PuReMD/src/cuda/cuda_list.h \
PG-PuReMD/src/cuda/cuda_lookup.cu \
......@@ -454,7 +453,8 @@ PG_PuReMD_bin_pg_puremd_SOURCES += PG-PuReMD/src/cuda/cuda_allocate.cu \
PG-PuReMD/src/cuda/cuda_reduction.h \
PG-PuReMD/src/cuda/cuda_reset_tools.cu \
PG-PuReMD/src/cuda/cuda_reset_tools.h \
PG-PuReMD/src/cuda/cuda_shuffle.h \
PG-PuReMD/src/cuda/cuda_spar_lin_alg.cu \
PG-PuReMD/src/cuda/cuda_spar_lin_alg.h \
PG-PuReMD/src/cuda/cuda_system_props.cu \
PG-PuReMD/src/cuda/cuda_system_props.h \
PG-PuReMD/src/cuda/cuda_torsion_angles.cu \
......@@ -464,21 +464,81 @@ PG_PuReMD_bin_pg_puremd_SOURCES += PG-PuReMD/src/cuda/cuda_allocate.cu \
PG-PuReMD/src/cuda/cuda_valence_angles.cu \
PG-PuReMD/src/cuda/cuda_valence_angles.h \
PG-PuReMD/src/cuda/cuda_vector.h
if CUDA_DEBUG
PG_PuReMD_bin_pg_puremd_SOURCES += PG-PuReMD/src/cuda/cuda_validation.cu \
PG-PuReMD/src/cuda/cuda_validation.h
# dummy source to trigger C linking
nodist_EXTRA_PG_PuReMD_bin_pg_puremd_SOURCES = src/dummy.c
endif
if USE_HIP
PG_PuReMD_bin_pg_puremd_SOURCES += PG-PuReMD/src/hip/hip_allocate.cu \
PG-PuReMD/src/hip/hip_allocate.h \
PG-PuReMD/src/hip/hip_basic_comm.cu \
PG-PuReMD/src/hip/hip_basic_comm.h \
PG-PuReMD/src/hip/hip_bond_orders.cu \
PG-PuReMD/src/hip/hip_bond_orders.h \
PG-PuReMD/src/hip/hip_bonds.cu \
PG-PuReMD/src/hip/hip_bonds.h \
PG-PuReMD/src/hip/hip_box.cu \
PG-PuReMD/src/hip/hip_box.h \
PG-PuReMD/src/hip/hip_charges.cu \
PG-PuReMD/src/hip/hip_charges.h \
PG-PuReMD/src/hip/hip_copy.cu \
PG-PuReMD/src/hip/hip_copy.h \
PG-PuReMD/src/hip/hip_dense_lin_alg.cu \
PG-PuReMD/src/hip/hip_dense_lin_alg.h \
PG-PuReMD/src/hip/hip_environment.cu \
PG-PuReMD/src/hip/hip_environment.h \
PG-PuReMD/src/hip/hip_forces.cu \
PG-PuReMD/src/hip/hip_forces.h \
PG-PuReMD/src/hip/hip_helpers.h \
PG-PuReMD/src/hip/hip_hydrogen_bonds.cu \
PG-PuReMD/src/hip/hip_hydrogen_bonds.h \
PG-PuReMD/src/hip/hip_init_md.cu \
PG-PuReMD/src/hip/hip_init_md.h \
PG-PuReMD/src/hip/hip_integrate.cu \
PG-PuReMD/src/hip/hip_integrate.h \
PG-PuReMD/src/hip/hip_list.cu \
PG-PuReMD/src/hip/hip_list.h \
PG-PuReMD/src/hip/hip_lookup.cu \
PG-PuReMD/src/hip/hip_lookup.h \
PG-PuReMD/src/hip/hip_multi_body.cu \
PG-PuReMD/src/hip/hip_multi_body.h \
PG-PuReMD/src/hip/hip_neighbors.cu \
PG-PuReMD/src/hip/hip_neighbors.h \
PG-PuReMD/src/hip/hip_nonbonded.cu \
PG-PuReMD/src/hip/hip_nonbonded.h \
PG-PuReMD/src/hip/hip_post_evolve.cu \
PG-PuReMD/src/hip/hip_post_evolve.h \
PG-PuReMD/src/hip/hip_random.cu \
PG-PuReMD/src/hip/hip_random.h \
PG-PuReMD/src/hip/hip_reduction.cu \
PG-PuReMD/src/hip/hip_reduction.h \
PG-PuReMD/src/hip/hip_reset_tools.cu \
PG-PuReMD/src/hip/hip_reset_tools.h \
PG-PuReMD/src/hip/hip_spar_lin_alg.cu \
PG-PuReMD/src/hip/hip_spar_lin_alg.h \
PG-PuReMD/src/hip/hip_system_props.cu \
PG-PuReMD/src/hip/hip_system_props.h \
PG-PuReMD/src/hip/hip_torsion_angles.cu \
PG-PuReMD/src/hip/hip_torsion_angles.h \
PG-PuReMD/src/hip/hip_utils.cu \
PG-PuReMD/src/hip/hip_utils.h \
PG-PuReMD/src/hip/hip_valence_angles.cu \
PG-PuReMD/src/hip/hip_valence_angles.h \
PG-PuReMD/src/hip/hip_vector.h
# dummy source to trigger C linking
nodist_EXTRA_PG_PuReMD_bin_pg_puremd_SOURCES = src/dummy.c
endif
PG_PuReMD_bin_pg_puremd_CFLAGS = @DFT_CFLAGS@ @M_CFLAGS@
PG_PuReMD_bin_pg_puremd_CPPFLAGS = -I PG-PuReMD/src
PG_PuReMD_bin_pg_puremd_LDADD = @M_LIBS@ @L_LIBS@ -lstdc++
PG_PuReMD_bin_pg_puremd_CFLAGS = -std=c11 @CFLAGS_EXTRA@ @OMP_CFLAGS@ @M_CFLAGS@
PG_PuReMD_bin_pg_puremd_CPPFLAGS = -I PG-PuReMD/src @CPPFLAGS_EXTRA@
PG_PuReMD_bin_pg_puremd_LDADD = @OMP_LIBS@ @M_LIBS@ @L_LIBS@ -lstdc++
if USE_CUDA
PG_PuReMD_bin_pg_puremd_CFLAGS += @CUDA_CFLAGS@
PG_PuReMD_bin_pg_puremd_LDADD += @CUDA_LIBS@
endif
if USE_HIP
PG_PuReMD_bin_pg_puremd_CFLAGS += @HIP_CFLAGS@
PG_PuReMD_bin_pg_puremd_LDADD += @HIP_LIBS@
endif
endif
if BUILD_DOC
......
PG-PuReMD/src/allocate.c
View file @ de96b3a2
This diff is collapsed.
PG-PuReMD/src/allocate.h
View file @ de96b3a2
......@@ -33,18 +33,21 @@ void Init_Matrix_Row_Indices( sparse_matrix * const, int * const );
void PreAllocate_Space( reax_system * const, control_params * const, storage * const );
void ReAllocate_System( reax_system * const, int, int );
void Reallocate_System_Part1( reax_system * const, int );
void Allocate_Workspace( reax_system * const, control_params * const, storage * const,
int, int );
void Reallocate_System_Part2( reax_system * const, int, int );
void Allocate_Workspace_Part1( reax_system * const,
control_params * const, storage * const, int );
void Allocate_Workspace_Part2( reax_system * const,
control_params * const, storage * const, int );
void Allocate_Grid( reax_system * const, MPI_Comm );
void Deallocate_Grid( grid * const );
void Allocate_MPI_Buffers( mpi_datatypes * const, int, neighbor_proc * const );
void Allocate_Matrix( sparse_matrix * const, int, int, int );
void Allocate_Matrix( sparse_matrix * const, int, int, int, int );
void Deallocate_Matrix( sparse_matrix * const );
......@@ -54,7 +57,11 @@ int Allocate_Bond_List( int, int * const, reax_list * const );
void Deallocate_MPI_Buffers( mpi_datatypes * const );
void ReAllocate( reax_system * const, control_params * const,
void Reallocate_Part1( reax_system * const, control_params * const,
simulation_data * const, storage * const,
reax_list** const, mpi_datatypes * const );
void Reallocate_Part2( reax_system * const, control_params * const,
simulation_data * const, storage * const,
reax_list** const, mpi_datatypes * const );
......
PG-PuReMD/src/analyze.c
View file @ de96b3a2
......@@ -19,7 +19,10 @@
<http://www.gnu.org/licenses/>.
----------------------------------------------------------------------*/
#include "reax_types.h"
#if (defined(HAVE_CONFIG_H) && !defined(__CONFIG_H_))
#define __CONFIG_H_
#include "../../common/include/config.h"
#endif
#include "analyze.h"
......@@ -27,20 +30,25 @@
#include "list.h"
#include "vector.h"
#define MAX_FRAGMENT_TYPES 100
#define MAX_FRAGMENT_TYPES (100)
void Print_Molecule( reax_system *system, molecule *m, int mode, char *s )
void Print_Molecule( reax_system *system, molecule *m, int mode,
char * const s, size_t size )
{
int j, atom;
s[0] = 0;
if ( mode == 1 )
{
/* print molecule summary */
for ( j = 0; j < MAX_ATOM_TYPES; ++j )
{
if ( m->mtypes[j] )
sprintf( s, "%s%s%d", s, system->reax_param.sbp[j].name, m->mtypes[j] );
{
snprintf( s, size - 1, "%s%d",
system->reax_param.sbp[j].name, m->mtypes[j] );
s[size - 1] = '\0';
}
}
}
else if ( mode == 2 )
{
......@@ -48,10 +56,11 @@ void Print_Molecule( reax_system *system, molecule *m, int mode, char *s )
for ( j = 0; j < m->atom_count; ++j )
{
atom = m->atom_list[j];
sprintf( s, "%s%s(%d)",
s,
system->reax_param.sbp[system->my_atoms[atom].type].name,
atom );
snprintf( s, size - 1, "%s(%d)",
system->reax_param.sbp[system->my_atoms[atom].type].name,
atom );
s[size - 1] = '\0';
}
}
}
......@@ -91,15 +100,14 @@ void Analyze_Fragments( reax_system *system, control_params *control,
simulation_data *data, storage *workspace,
reax_list **lists, FILE *fout, int ignore )
{
int atom, i, flag;
int *mark = workspace->mark;
int num_fragments, num_fragment_types;
char fragment[MAX_ATOM_TYPES];
char fragments[MAX_FRAGMENT_TYPES][MAX_ATOM_TYPES];
int fragment_count[MAX_FRAGMENT_TYPES];
int atom, i, flag, *mark;
int num_fragments, num_fragment_types, fragment_count[MAX_FRAGMENT_TYPES];
char fragment[MAX_ATOM_TYPES], fragments[MAX_FRAGMENT_TYPES][MAX_ATOM_TYPES];
molecule m;
reax_list *new_bonds = lists[BONDS];
//list *old_bonds = lists[OLD_BONDS];
reax_list *new_bonds;
mark = workspace->mark;
new_bonds = lists[BONDS];
/* fragment analysis */
fprintf( fout, "step%d fragments\n", data->step );
......@@ -108,47 +116,51 @@ void Analyze_Fragments( reax_system *system, control_params *control,
memset( mark, 0, system->N * sizeof(int) );
for ( atom = 0; atom < system->N; ++atom )
{
if ( !mark[atom] )
{
/* discover a new fragment */
memset( m.mtypes, 0, MAX_ATOM_TYPES * sizeof(int) );
Visit_Bonds( atom, mark, m.mtypes, system, control, new_bonds, ignore );
++num_fragments;
Print_Molecule( system, &m, 1, fragment );
Print_Molecule( system, &m, 1, fragment, sizeof(fragment) );
/* check if a similar fragment already exists */
flag = 0;
for ( i = 0; i < num_fragment_types; ++i )
if ( !strcmp( fragments[i], fragment ) )
{
if ( strncmp( fragments[i], fragment, MAX_ATOM_TYPES ) == 0 )
{
fragment_count[i]++;
flag = 1;
break;
}
}
if ( flag == 0 )
{
/* it is a new one, add to the fragments list */
strcpy( fragments[num_fragment_types], fragment );
strncpy( fragments[num_fragment_types], fragment, sizeof(fragments[num_fragment_types]) - 1 );
fragments[num_fragment_types][sizeof(fragments[num_fragment_types]) - 1] = '\0';
fragment_count[num_fragment_types] = 1;
++num_fragment_types;
}
}
}
/* output the results of fragment analysis */
for ( i = 0; i < num_fragment_types; ++i )
{
/* strlen safe here as fragments[i] is NULL-terminated above */
if ( strlen(fragments[i]) )
{
fprintf( fout, "%d of %s\n", fragment_count[i], fragments[i] );
}
}
fprintf( fout, "\n" );
#if defined(DEBUG)
fflush( fout );
/* compare new bonds to old bonds */
//for( atom = 0; atom < system->N; ++atom ) {
// fprintf( fout, "atom: %d\n", atom ); fflush( fout );
// Compare_Bonding( atom, system, control, workspace,
// old_bonds, new_bonds, fout );
//}
//Copy_Bond_List( system, control, lists );
#endif
}
......@@ -175,8 +187,4 @@ void Analysis( reax_system *system, control_params *control,
Analyze_Fragments( system, control, data, workspace, lists,
out_control->ign, 1 );
}
#if defined(DEBUG)
fprintf( stderr, "analysis... done\n" );
#endif
}
PG-PuReMD/src/basic_comm.c
View file @ de96b3a2
This diff is collapsed.
PG-PuReMD/src/basic_comm.h
View file @ de96b3a2
......@@ -38,18 +38,14 @@ enum pointer_type
extern "C" {
#endif
void Dist( const reax_system * const, mpi_datatypes * const,
void*, int, MPI_Datatype );
void Dist( reax_system const * const, mpi_datatypes * const,
void const * const, int, MPI_Datatype );
void Coll( const reax_system * const, mpi_datatypes * const,
void*, int, MPI_Datatype );
real Parallel_Norm( const real * const, const int, MPI_Comm );
void Coll( reax_system const * const, mpi_datatypes * const,
void * const , int, MPI_Datatype );
real Parallel_Dot( const real * const, const real * const, const int, MPI_Comm );
real Parallel_Vector_Acc( const real * const, const int, MPI_Comm );
#if defined(TEST_FORCES)
void Coll_ids_at_Master( reax_system*, storage*, mpi_datatypes* );
......
PG-PuReMD/src/bond_orders.c
View file @ de96b3a2
This diff is collapsed.
PG-PuReMD/src/bond_orders.h
View file @ de96b3a2
......@@ -48,14 +48,16 @@ typedef struct
extern "C" {
#endif
void Add_dBond_to_Forces( int, int, storage * const, reax_list ** const );
void Add_dBond_to_Forces( int, int, reax_system*, simulation_data*,
storage*, reax_list** );
void Add_dBond_to_Forces_NPT( int, int, simulation_data * const, storage * const,
reax_list ** const );
void Add_dBond_to_Forces_NPT( int, int, reax_system*, simulation_data*,
storage*, reax_list** );
int BOp( storage * const, reax_list * const, real, int, int, const far_neighbor_data * const,
const single_body_parameters * const, const single_body_parameters * const,
const two_body_parameters * const );
int BOp( storage * const, reax_list * const, real, int, int, int,
ivec * const, real, rvec * const, int,
single_body_parameters const * const, single_body_parameters const * const,
two_body_parameters const * const );
void BO( reax_system * const, control_params * const, simulation_data * const,
storage * const, reax_list ** const, output_controls * const );
......
PG-PuReMD/src/bonds.c
View file @ de96b3a2
......@@ -19,16 +19,21 @@
<http://www.gnu.org/licenses/>.
----------------------------------------------------------------------*/
#include "reax_types.h"
#if (defined(HAVE_CONFIG_H) && !defined(__CONFIG_H_))
#define __CONFIG_H_
#include "../../common/include/config.h"
#endif
#if defined(PURE_REAX)
#include "bonds.h"
#include "bond_orders.h"
#include "list.h"
#include "tool_box.h"
#include "vector.h"
#elif defined(LAMMPS_REAX)
#include "reax_bonds.h"
#include "reax_bond_orders.h"
#include "reax_list.h"
#include "reax_tool_box.h"
......@@ -46,22 +51,24 @@ void Bonds( reax_system * const system, control_params * const control,
int start_i, end_i;
int type_i, type_j;
real ebond, pow_BOs_be2, exp_be12, CEbo;
const real gp3 = system->reax_param.gp.l[3];
const real gp4 = system->reax_param.gp.l[4];
const real gp7 = system->reax_param.gp.l[7];
const real gp10 = system->reax_param.gp.l[10];
const real gp37 = (int) system->reax_param.gp.l[37];
real gp3, gp4, gp7, gp10;
real exphu, exphua1, exphub1, exphuov, hulpov, estriph;
real decobdbo, decobdboua, decobdboub;
single_body_parameters *sbp_i, *sbp_j;
two_body_parameters *twbp;
bond_order_data *bo_ij;
reax_list * const bond_list = lists[BONDS];
reax_list *bond_list;
bond_list = lists[BONDS];
gp3 = system->reax_param.gp.l[3];
gp4 = system->reax_param.gp.l[4];
gp7 = system->reax_param.gp.l[7];
gp10 = system->reax_param.gp.l[10];
for ( i = 0; i < system->n; ++i )
{
start_i = Start_Index( i, bond_list );
end_i = End_Index( i, bond_list );
start_i = Start_Index(i, bond_list);
end_i = End_Index(i, bond_list);
for ( pj = start_i; pj < end_i; ++pj )
{
......@@ -77,74 +84,78 @@ void Bonds( reax_system * const system, control_params * const control,
index_tbp(type_i, type_j, system->reax_param.num_atom_types) ];
bo_ij = &bond_list->bond_list[pj].bo_data;
/* calculate the constants */
pow_BOs_be2 = POW( bo_ij->BO_s, twbp->p_be2 );
exp_be12 = EXP( twbp->p_be1 * ( 1.0 - pow_BOs_be2 ) );
CEbo = -twbp->De_s * exp_be12 *
( 1.0 - twbp->p_be1 * twbp->p_be2 * pow_BOs_be2 );
CEbo = -twbp->De_s * exp_be12
* (1.0 - twbp->p_be1 * twbp->p_be2 * pow_BOs_be2);
/* calculate the Bond Energy */
/* calculate bond energy */
ebond = -twbp->De_s * bo_ij->BO_s * exp_be12
- twbp->De_p * bo_ij->BO_pi
- twbp->De_pp * bo_ij->BO_pi2;
data->my_en.e_bond += ebond;
data->my_en->e_bond += ebond;
/* calculate derivatives of Bond Orders */
/* calculate derivatives of bond orders */
bo_ij->Cdbo += CEbo;
bo_ij->Cdbopi -= (CEbo + twbp->De_p);
bo_ij->Cdbopi2 -= (CEbo + twbp->De_pp);
bo_ij->Cdbopi -= CEbo + twbp->De_p;
bo_ij->Cdbopi2 -= CEbo + twbp->De_pp;
#ifdef TEST_ENERGY
#if defined(TEST_ENERGY)
//fprintf( out_control->ebond, "%6d%6d%24.15e%24.15e%24.15e\n",
fprintf( out_control->ebond, "%6d%6d%12.4f%12.4f%12.4f\n",
system->my_atoms[i].orig_id,
system->my_atoms[j].orig_id,
bo_ij->BO, ebond, data->my_en.e_bond );
bo_ij->BO, ebond, data->my_en->e_bond );
#endif
#ifdef TEST_FORCES
#if defined(TEST_FORCES)
Add_dBO( system, lists, i, pj, CEbo, workspace->f_be );
Add_dBOpinpi2( system, lists, i, pj,
-(CEbo + twbp->De_p), -(CEbo + twbp->De_pp),
workspace->f_be, workspace->f_be );
-(CEbo + twbp->De_p),
-(CEbo + twbp->De_pp),
workspace->f_be, workspace->f_be );
#endif
/* Stabilisation terminal triple bond */
/* Stabilisation terminal triple bond in C-O */
if ( bo_ij->BO >= 1.00 )
{
/* changed to avoid equality checks of doubles, but really need better approach... */
if ( gp37 == 2
|| (sbp_i->mass - 12.0000 < 1e-6 && sbp_j->mass - 15.9990 < 1e-6)
|| (sbp_j->mass - 12.0000 < 1e-6 && sbp_i->mass - 15.9990 < 1e-6) )
if ( (strncmp( sbp_i->name, "C", sizeof(sbp_i->name) ) == 0
&& strncmp( sbp_j->name, "O", sizeof(sbp_j->name) ) == 0)
|| (strncmp( sbp_i->name, "O", sizeof(sbp_i->name) ) == 0
&& strncmp( sbp_j->name, "C", sizeof(sbp_j->name) ) == 0) )
{
exphu = EXP( -gp7 * SQR(bo_ij->BO - 2.50) );
exphua1 = EXP( -gp3 * (workspace->total_bond_order[i] - bo_ij->BO) );
exphub1 = EXP( -gp3 * (workspace->total_bond_order[j] - bo_ij->BO) );
exphuov = EXP( gp4 * (workspace->Delta[i] + workspace->Delta[j]) );
//ba = SQR( bo_ij->BO - 2.5 );
exphu = EXP( -gp7 * SQR(bo_ij->BO - 2.5) );
//oboa = abo(j1) - boa;
//obob = abo(j2) - boa;
exphua1 = EXP(-gp3 * (workspace->total_bond_order[i] - bo_ij->BO));
exphub1 = EXP(-gp3 * (workspace->total_bond_order[j] - bo_ij->BO));
//ovoab = abo(j1) - aval(it1) + abo(j2) - aval(it2);
exphuov = EXP(gp4 * (workspace->Delta[i] + workspace->Delta[j]));
hulpov = 1.0 / (1.0 + 25.0 * exphuov);
estriph = gp10 * exphu * hulpov * (exphua1 + exphub1);
data->my_en.e_bond += estriph;
data->my_en->e_bond += estriph;
decobdbo = gp10 * exphu * hulpov * (exphua1 + exphub1)
* ( gp3 - 2.0 * gp7 * (bo_ij->BO - 2.50) );
decobdboua = -gp10 * exphu * hulpov * (gp3 * exphua1
+ 25.0 * gp4 * exphuov * hulpov * (exphua1 + exphub1));
decobdboub = -gp10 * exphu * hulpov * (gp3 * exphub1
+ 25.0 * gp4 * exphuov * hulpov * (exphua1 + exphub1));
* ( gp3 - 2.0 * gp7 * (bo_ij->BO - 2.5) );
decobdboua = -gp10 * exphu * hulpov
* (gp3 * exphua1 + 25.0 * gp4 * exphuov * hulpov * (exphua1 + exphub1));
decobdboub = -gp10 * exphu * hulpov
* (gp3 * exphub1 + 25.0 * gp4 * exphuov * hulpov * (exphua1 + exphub1));
bo_ij->Cdbo += decobdbo;
workspace->CdDelta[i] += decobdboua;
workspace->CdDelta[j] += decobdboub;
#ifdef TEST_ENERGY
#if defined(TEST_ENERGY)
//fprintf( out_control->ebond,
// "%6d%6d%24.15e%24.15e%24.15e%24.15e\n",
// system->my_atoms[i].orig_id, system->my_atoms[j].orig_id,
// estriph, decobdbo, decobdboua, decobdboub );
#endif
#ifdef TEST_FORCES
#if defined(TEST_FORCES)
Add_dBO( system, lists, i, pj, decobdbo, workspace->f_be );
Add_dDelta( system, lists, i, decobdboua, workspace->f_be );
Add_dDelta( system, lists, j, decobdboub, workspace->f_be );
......
PG-PuReMD/src/box.c
View file @ de96b3a2
......@@ -19,14 +19,26 @@
<http://www.gnu.org/licenses/>.
----------------------------------------------------------------------*/
#include "reax_types.h"
#include "box.h"
#if (defined(HAVE_CONFIG_H) && !defined(__CONFIG_H_))
#define __CONFIG_H_
#include "../../common/include/config.h"
#endif
#include "comm_tools.h"
#include "io_tools.h"
#include "system_props.h"
#include "vector.h"
#if defined(PURE_REAX)
#include "box.h"
#include "comm_tools.h"
#include "io_tools.h"
#include "system_props.h"
#include "vector.h"
#elif defined(LAMMPS_REAX)
#include "reax_box.h"
#include "reax_comm_tools.h"
#include "reax_io_tools.h"
#include "reax_system_props.h"
#include "reax_vector.h"
#endif
void Make_Consistent( simulation_box * const box )
......@@ -144,10 +156,10 @@ void Setup_Big_Box( real a, real b, real c, real alpha, real beta, real gamma,
{
double c_alpha, c_beta, c_gamma, s_gamma, zi;
if ( IS_NAN_REAL(a) || IS_NAN_REAL(b) || IS_NAN_REAL(c)
|| IS_NAN_REAL(alpha) || IS_NAN_REAL(beta) || IS_NAN_REAL(gamma) )
if ( !isfinite(a) || !isfinite(b) || !isfinite(c)
|| !isfinite(alpha) || !isfinite(beta) || !isfinite(gamma) )
{
fprintf( stderr, "[ERROR] Invalid simulation box boundaries for big box (NaN). Terminating...\n" );
fprintf( stderr, "[ERROR] Invalid simulation box boundaries for big box (NaN or infinite). Terminating...\n" );
exit( INVALID_INPUT );
}
......@@ -169,8 +181,8 @@ void Setup_Big_Box( real a, real b, real c, real alpha, real beta, real gamma,
box->box[2][1] = c * zi;
box->box[2][2] = c * SQRT(1.0 - SQR(c_beta) - SQR(zi));
#if defined(DEBUG)
fprintf( stderr, "box is %8.2f x %8.2f x %8.2f\n",
#if defined(DEBUG_FOCUS)
fprintf( stderr, "[INFO] box = (%8.4f, %8.4f, %8.4f)\n",
box->box[0][0], box->box[1][1], box->box[2][2] );
#endif
......@@ -184,7 +196,7 @@ void Init_Box( rtensor box_tensor, simulation_box * const box )
rtensor_Copy( box->box, box_tensor );
Make_Consistent( box );
#if defined(DEBUG)
#if defined(DEBUG_FOCUS)
fprintf( stderr, "box is %8.2f x %8.2f x %8.2f\n",
box->box[0][0], box->box[1][1], box->box[2][2] );
#endif
......@@ -232,14 +244,14 @@ void Setup_My_Ext_Box( reax_system * const system, control_params * const contro
for ( d = 0; d < 3; ++d )
{
/* estimate the number of native cells */
native_gcells[d] = (int)(my_box->box_norms[d] / (control->vlist_cut / 2));
native_gcells[d] = (int) (my_box->box_norms[d] / (control->vlist_cut / 2.0));
if ( native_gcells[d] == 0 )
{
native_gcells[d] = 1;
}
gcell_len[d] = my_box->box_norms[d] / native_gcells[d];
ghost_gcells[d] = (int) CEIL(bc->ghost_cutoff / gcell_len[d]);
ghost_gcells[d] = (int) CEIL( bc->ghost_cutoff / gcell_len[d] );
/* extend my box with the ghost regions */
my_ext_box->min[d] = my_box->min[d] - ghost_gcells[d] * gcell_len[d];
......@@ -260,7 +272,7 @@ void Setup_Boundary_Cutoffs( reax_system * const system, control_params * const
bc->ghost_nonb = control->nonb_cut;
bc->ghost_hbond = control->hbond_cut;
bc->ghost_bond = 2 * control->bond_cut;
bc->ghost_bond = 2.0 * control->bond_cut;
bc->ghost_cutoff = MAX( control->vlist_cut, bc->ghost_bond );
#if defined(DEBUG_FOCUS)
......@@ -275,17 +287,21 @@ void Setup_Boundary_Cutoffs( reax_system * const system, control_params * const
void Setup_Environment( reax_system * const system, control_params * const control,
mpi_datatypes * const mpi_data )
{
int ret;
ivec periodic = {1, 1, 1};
#if defined(DEBUG_FOCUS)
char temp[100] = "";
char temp[100];
#endif
/* initialize communicator - 3D mesh with wrap-arounds = 3D torus */
MPI_Cart_create( MPI_COMM_WORLD, 3, control->procs_by_dim, periodic, 1,
ret = MPI_Cart_create( MPI_COMM_WORLD, 3, control->procs_by_dim, periodic, 1,
&mpi_data->comm_mesh3D );
MPI_Comm_rank( mpi_data->comm_mesh3D, &system->my_rank );
MPI_Cart_coords( mpi_data->comm_mesh3D, system->my_rank, 3,
Check_MPI_Error( ret, __FILE__, __LINE__ );
ret = MPI_Comm_rank( mpi_data->comm_mesh3D, &system->my_rank );
Check_MPI_Error( ret, __FILE__, __LINE__ );
ret = MPI_Cart_coords( mpi_data->comm_mesh3D, system->my_rank, 3,
system->my_coords );
Check_MPI_Error( ret, __FILE__, __LINE__ );
Setup_Boundary_Cutoffs( system, control );
Setup_My_Box( system, control );
......@@ -296,13 +312,18 @@ void Setup_Environment( reax_system * const system, control_params * const contr
fprintf( stderr, "p%d coord: %d %d %d\n",
system->my_rank, system->my_coords[0],
system->my_coords[1], system->my_coords[2] );
sprintf( temp, "p%d big_box", system->my_rank );
sprintf( temp, sizeof(temp) - 1, "p%d big_box", system->my_rank );
temp[sizeof(temp) - 1] = '\0';
Print_Box( &system->big_box, temp, stderr );
sprintf( temp, "p%d my_box", system->my_rank );
sprintf( temp, sizeof(temp) - 1, "p%d my_box", system->my_rank );
temp[sizeof(temp) - 1] = '\0';
Print_Box( &system->my_box, temp, stderr );
sprintf( temp, "p%d ext_box", system->my_rank );
sprintf( temp, sizeof(temp) - 1, "p%d ext_box", system->my_rank );
temp[sizeof(temp) - 1] = '\0';
Print_Box( &system->my_ext_box, temp, stderr );
MPI_Barrier( MPI_COMM_WORLD );
fprintf( stderr, "p%d: parallel environment initialized\n",
system->my_rank );
......@@ -324,7 +345,7 @@ void Scale_Box( reax_system * const system, control_params * const control,
if ( control->ensemble == iNPT )
{
mu[0] = POW( 1.0 + (dt / control->Tau_P[0]) * (data->iso_bar.P - control->P[0]),
1. / 3 );
1.0 / 3.0 );
if ( mu[0] < MIN_dV )
{
......@@ -342,8 +363,8 @@ void Scale_Box( reax_system * const system, control_params * const control,
{
for ( d = 0; d < 3; ++d )
{
mu[d] = POW(1.0 + (dt / control->Tau_P[d]) * (data->tot_press[d] - control->P[d]),
1. / 3 );
mu[d] = POW( 1.0 + (dt / control->Tau_P[d]) * (data->tot_press[d] - control->P[d]),
1.0 / 3.0 );
if ( mu[d] < MIN_dV )
{
......@@ -357,45 +378,45 @@ void Scale_Box( reax_system * const system, control_params * const control,
}
/* temperature scaler */
lambda = 1.0 + (dt / control->Tau_T) * (control->T / data->therm.T - 1.0);
lambda = 1.0 + ((dt * 1.0e-12) / control->Tau_T)
* (control->T / data->therm.T - 1.0);
if ( lambda < MIN_dT )
{
lambda = MIN_dT;
}
else if (lambda > MAX_dT )
lambda = SQRT( lambda );
if ( lambda > MAX_dT )
{
lambda = MAX_dT;
}
lambda = SQRT( lambda );
/* Scale velocities and positions at t+dt */
for ( i = 0; i < system->n; ++i )
{
atom = &system->my_atoms[i];
rvec_Scale( atom->v, lambda, atom->v );
atom->x[0] = mu[0] * atom->x[0];
atom->x[1] = mu[1] * atom->x[1];
atom->x[2] = mu[2] * atom->x[2];
}
Compute_Kinetic_Energy( system, data, mpi_data->comm_mesh3D );
#if defined(DEBUG)
fprintf( stderr, "damping - " );
#endif
/* update kinetic energy and temperature based on new positions and velocities */
Compute_Kinetic_Energy( system, data, mpi_data->comm_mesh3D );
/* update box & grid */
system->big_box.box[0][0] *= mu[0];
system->big_box.box[1][1] *= mu[1];
system->big_box.box[2][2] *= mu[2];
Make_Consistent( &(system->big_box) );
Make_Consistent( &system->big_box );
Setup_My_Box( system, control );
Setup_My_Ext_Box( system, control );
Update_Comm( system );
#if defined(DEBUG)
fprintf( stderr, "box & grid updated - " );
#endif
}
......
PG-PuReMD/src/charges.c
View file @ de96b3a2
This diff is collapsed.
PG-PuReMD/src/charges.h
View file @ de96b3a2
......@@ -29,9 +29,12 @@
extern "C" {
#endif
void Compute_Charges( reax_system * const, control_params * const,
simulation_data * const, storage * const,
const output_controls * const, mpi_datatypes * const );
int is_refactoring_step( control_params const * const, simulation_data * const );
void Compute_Charges( reax_system const * const, control_params const * const,
simulation_data * const,
storage * const, const output_controls * const,
mpi_datatypes * const );
#ifdef __cplusplus
}
......
PG-PuReMD/src/comm_tools.c
View file @ de96b3a2
This diff is collapsed.
PG-PuReMD/src/comm_tools.h
View file @ de96b3a2
......@@ -29,19 +29,30 @@
extern "C" {
#endif
void Check_MPI_Error( int, const char * const );
#if defined(NEUTRAL_TERRITORY)
void Setup_NT_Comm( reax_system * const, control_params * const,
mpi_datatypes * const );
void Estimate_NT_Atoms( reax_system * const, mpi_datatypes * const );
#endif
void Check_MPI_Error( int, const char * const, int );
void Setup_Comm( reax_system * const, control_params * const, mpi_datatypes * const );
void Update_Comm( reax_system * const );
void Estimate_Boundary_Atoms( reax_system * const, int, int, int, mpi_out_data * const );
void Count_Boundary_Atoms( reax_system const * const,
int, int, int, mpi_out_data * const, int * const );
void Sort_Boundary_Atoms( reax_system * const, int, int,
int, mpi_out_data * const, mpi_datatypes * const );
void Unpack_Estimate_Message( reax_system * const, int, void * const, int,
neighbor_proc * const, int );
void Unpack_Exchange_Message( reax_system * const, int, void * const,
int, neighbor_proc * const, int );
int SendRecv( reax_system * const, mpi_datatypes * const, MPI_Datatype, int * const,
message_sorter, unpacker, int );
int SendRecv( reax_system * const, mpi_datatypes * const, MPI_Datatype,
message_counter, message_sorter, unpacker, int );
void Comm_Atoms( reax_system * const, control_params * const, simulation_data * const, storage * const,
mpi_datatypes * const, int );
......
PG-PuReMD/src/control.c
View file @ de96b3a2
This diff is collapsed.
cub @ c3cceac1
Compare d622848f...c3cceac1
Subproject commit d622848f9fb62f13e5e064e1deb43b6bcbb12bad
Subproject commit c3cceac115c072fb63df1836ff46d8c60d9eb304
PG-PuReMD/src/cuda/cuda_allocate.cu
View file @ de96b3a2
This diff is collapsed.
PG-PuReMD/src/cuda/cuda_allocate.h
View file @ de96b3a2
......@@ -3,39 +3,52 @@
#include "../reax_types.h"
#ifdef __cplusplus
extern "C" {
#endif
void * sCudaHostAllocWrapper( size_t, const char * const, int );
void dev_alloc_system( reax_system * );
void * sCudaHostReallocWrapper( void *, size_t, size_t, const char * const, int );
void dev_alloc_grid( reax_system * );
void * sCudaHostCallocWrapper( size_t, size_t, const char * const, int );
void dev_alloc_simulation_data( simulation_data * );
void sCudaFreeHostWrapper( void *, const char * const, int );
void dev_alloc_workspace( reax_system *, control_params *, storage *, int, int );
#ifdef __cplusplus
}
#endif
void dev_alloc_matrix( sparse_matrix *, int, int );
void Cuda_Allocate_System( reax_system *, control_params * );
void dev_alloc_control( control_params * );
void Cuda_Allocate_Grid( reax_system *, control_params * );
void dev_dealloc_grid_cell_atoms( reax_system * );
void Cuda_Allocate_Simulation_Data( simulation_data *, cudaStream_t );
void dev_alloc_grid_cell_atoms( reax_system *, int );
void Cuda_Allocate_Control( control_params * );
void dev_realloc_system( reax_system *, int , int , char * );
void Cuda_Allocate_Workspace_Part1( reax_system *, control_params *, storage *, int );
void dev_dealloc_workspace( control_params *, storage * );
void Cuda_Allocate_Workspace_Part2( reax_system *, control_params *, storage *, int );
void dev_dealloc_matrix( sparse_matrix * );
void Cuda_Allocate_Matrix( sparse_matrix * const, int, int, int, int, cudaStream_t );
void Cuda_ReAllocate( reax_system*, control_params*, simulation_data*, storage*,
reax_list**, mpi_datatypes* );
void Cuda_Deallocate_Grid_Cell_Atoms( reax_system * );
void Cuda_Allocate_Grid_Cell_Atoms( reax_system *, int );
void Cuda_Deallocate_Workspace_Part1( control_params *, storage * );
void Cuda_Deallocate_Workspace_Part2( control_params *, storage * );
void Cuda_Deallocate_Matrix( sparse_matrix * );
void Cuda_Reallocate_Part1( reax_system *, control_params *, simulation_data *, storage *,
reax_list **, mpi_datatypes * );
void Cuda_Reallocate_Part2( reax_system *, control_params *, simulation_data *, storage *,
reax_list **, mpi_datatypes * );
#ifdef __cplusplus
}
#endif
#endif
PG-PuReMD/src/cuda/cuda_basic_comm.cu 0 → 100644
View file @ de96b3a2
This diff is collapsed.