diff --git a/PG-PuReMD/src/cuda/cuda_init_md.cu b/PG-PuReMD/src/cuda/cuda_init_md.cu
index 81b9b3e13f82f5eb0755fc4c3980738e99be324b..5e91eaee32fc15ce63731fb7131a0c800c1ea4fe 100644
--- a/PG-PuReMD/src/cuda/cuda_init_md.cu
+++ b/PG-PuReMD/src/cuda/cuda_init_md.cu
@@ -301,14 +301,7 @@ void Cuda_Initialize( reax_system *system, control_params *control,
Cuda_Init_ScratchArea( );
/* MPI_DATATYPES */
- if ( Init_MPI_Datatypes( system, workspace, mpi_data, msg ) == FAILURE )
- {
- fprintf( stderr, "p%d: init_mpi_datatypes: could not create datatypes\n",
- system->my_rank );
- fprintf( stderr, "p%d: mpi_data couldn't be initialized! terminating.\n",
- system->my_rank );
- MPI_Abort( MPI_COMM_WORLD, CANNOT_INITIALIZE );
- }
+ Init_MPI_Datatypes( system, workspace, mpi_data, msg );
/* SYSTEM */
if ( Cuda_Init_System( system, control, data, workspace, mpi_data, msg ) == FAILURE )
diff --git a/PuReMD/src/allocate.c b/PuReMD/src/allocate.c
index 7d7af3e972125b4bf93be4de28365ce04dc969eb..0753ea1090ec9b2f4c60007047c86f7c4a91728e 100644
--- a/PuReMD/src/allocate.c
+++ b/PuReMD/src/allocate.c
@@ -814,7 +814,7 @@ void ReAllocate( reax_system *system, control_params *control,
/* far neighbors */
if ( renbr )
{
- far_nbrs = *lists + FAR_NBRS;
+ far_nbrs = lists[FAR_NBRS];
if ( Nflag || realloc->num_far >= far_nbrs->num_intrs * DANGER_ZONE )
{
@@ -878,7 +878,7 @@ void ReAllocate( reax_system *system, control_params *control,
if ( Hflag || realloc->hbonds )
{
- ret = Reallocate_HBonds_List( system, (*lists) + HBONDS, comm );
+ ret = Reallocate_HBonds_List( system, lists[HBONDS], comm );
realloc->hbonds = 0;
#if defined(DEBUG_FOCUS)
fprintf(stderr, "p%d: reallocating hbonds: total_hbonds=%d space=%dMB\n",
@@ -891,7 +891,7 @@ void ReAllocate( reax_system *system, control_params *control,
num_bonds = est_3body = -1;
if ( Nflag || realloc->bonds )
{
- Reallocate_Bonds_List( system, (*lists) + BONDS, &num_bonds,
+ Reallocate_Bonds_List( system, lists[BONDS], &num_bonds,
&est_3body, comm );
realloc->bonds = 0;
realloc->num_3body = MAX( realloc->num_3body, est_3body );
@@ -911,15 +911,15 @@ void ReAllocate( reax_system *system, control_params *control,
(int)(realloc->num_3body * sizeof(three_body_interaction_data) /
(1024 * 1024)) );
#endif
- Delete_List( (*lists) + THREE_BODIES, comm );
+ Delete_List( lists[THREE_BODIES], comm );
if ( num_bonds == -1 )
- num_bonds = ((*lists) + BONDS)->num_intrs;
+ num_bonds = lists[BONDS]->num_intrs;
realloc->num_3body = (int)(MAX(realloc->num_3body * SAFE_ZONE, MIN_3BODIES));
if ( !Make_List( num_bonds, realloc->num_3body, TYP_THREE_BODY,
- (*lists) + THREE_BODIES, comm ) )
+ lists[THREE_BODIES], comm ) )
{
fprintf( stderr, "Problem in initializing angles list. Terminating!\n" );
MPI_Abort( comm, CANNOT_INITIALIZE );
diff --git a/PuReMD/src/analyze.c b/PuReMD/src/analyze.c
index 228e7a6f25cc44f3fab360e653c09e1c1166d56b..5307d97feb32a6574b64de424008bba4822d2a6c 100644
--- a/PuReMD/src/analyze.c
+++ b/PuReMD/src/analyze.c
@@ -89,8 +89,8 @@ void Analyze_Fragments( reax_system *system, control_params *control,
char fragments[MAX_FRAGMENT_TYPES][MAX_ATOM_TYPES];
int fragment_count[MAX_FRAGMENT_TYPES];
molecule m;
- reax_list *new_bonds = (*lists) + BONDS;
- //list *old_bonds = (*lists) + OLD_BONDS;
+ reax_list *new_bonds = lists[BONDS];
+ //list *old_bonds = lists[OLD_BONDS];
/* fragment analysis */
fprintf( fout, "step%d fragments\n", data->step );
diff --git a/PuReMD/src/bond_orders.c b/PuReMD/src/bond_orders.c
index 71dd1f44ecf387efcba9313275187055c655c8b5..ca54db6f77f6701bdc05b851920c9f9cde5f4471 100644
--- a/PuReMD/src/bond_orders.c
+++ b/PuReMD/src/bond_orders.c
@@ -35,8 +35,8 @@
void Get_dBO( reax_system *system, reax_list **lists,
int i, int pj, real C, rvec *v )
{
- reax_list *bonds = (*lists) + BONDS;
- reax_list *dBOs = (*lists) + DBOS;
+ reax_list *bonds = lists[BONDS];
+ reax_list *dBOs = lists[DBOS];
int start_pj, end_pj, k;
pj = bonds->bond_list[pj].dbond_index;
@@ -52,8 +52,8 @@ void Get_dBO( reax_system *system, reax_list **lists,
void Get_dBOpinpi2( reax_system *system, reax_list **lists,
int i, int pj, real Cpi, real Cpi2, rvec *vpi, rvec *vpi2 )
{
- reax_list *bonds = (*lists) + BONDS;
- reax_list *dBOs = (*lists) + DBOS;
+ reax_list *bonds = lists[BONDS];
+ reax_list *dBOs = lists[DBOS];
dbond_data *dbo_k;
int start_pj, end_pj, k;
@@ -73,8 +73,8 @@ void Get_dBOpinpi2( reax_system *system, reax_list **lists,
void Add_dBO( reax_system *system, reax_list **lists,
int i, int pj, real C, rvec *v )
{
- reax_list *bonds = (*lists) + BONDS;
- reax_list *dBOs = (*lists) + DBOS;
+ reax_list *bonds = lists[BONDS];
+ reax_list *dBOs = lists[DBOS];
int start_pj, end_pj, k;
pj = bonds->bond_list[pj].dbond_index;
@@ -92,8 +92,8 @@ void Add_dBO( reax_system *system, reax_list **lists,
void Add_dBOpinpi2( reax_system *system, reax_list **lists,
int i, int pj, real Cpi, real Cpi2, rvec *vpi, rvec *vpi2 )
{
- reax_list *bonds = (*lists) + BONDS;
- reax_list *dBOs = (*lists) + DBOS;
+ reax_list *bonds = lists[BONDS];
+ reax_list *dBOs = lists[DBOS];
dbond_data *dbo_k;
int start_pj, end_pj, k;
@@ -113,8 +113,8 @@ void Add_dBOpinpi2( reax_system *system, reax_list **lists,
void Add_dBO_to_Forces( reax_system *system, reax_list **lists,
int i, int pj, real C )
{
- reax_list *bonds = (*lists) + BONDS;
- reax_list *dBOs = (*lists) + DBOS;
+ reax_list *bonds = lists[BONDS];
+ reax_list *dBOs = lists[DBOS];
int start_pj, end_pj, k;
pj = bonds->bond_list[pj].dbond_index;
@@ -130,8 +130,8 @@ void Add_dBO_to_Forces( reax_system *system, reax_list **lists,
void Add_dBOpinpi2_to_Forces( reax_system *system, reax_list **lists,
int i, int pj, real Cpi, real Cpi2 )
{
- reax_list *bonds = (*lists) + BONDS;
- reax_list *dBOs = (*lists) + DBOS;
+ reax_list *bonds = lists[BONDS];
+ reax_list *dBOs = lists[DBOS];
dbond_data *dbo_k;
int start_pj, end_pj, k;
@@ -150,7 +150,7 @@ void Add_dBOpinpi2_to_Forces( reax_system *system, reax_list **lists,
void Add_dDelta( reax_system *system, reax_list **lists, int i, real C, rvec *v )
{
- reax_list *dDeltas = &((*lists)[DDELTAS]);
+ reax_list *dDeltas = lists[DDELTAS];
int start = Start_Index(i, dDeltas);
int end = End_Index(i, dDeltas);
int k;
@@ -164,7 +164,7 @@ void Add_dDelta( reax_system *system, reax_list **lists, int i, real C, rvec *v
void Add_dDelta_to_Forces( reax_system *system, reax_list **lists,
int i, real C )
{
- reax_list *dDeltas = &((*lists)[DDELTAS]);
+ reax_list *dDeltas = lists[DDELTAS];
int start = Start_Index(i, dDeltas);
int end = End_Index(i, dDeltas);
int k;
@@ -194,8 +194,8 @@ void Calculate_dBO( int i, int pj,
// memset(due_j_pi, 0, sizeof(rvec)*1000 );
// memset(due_i_pi, 0, sizeof(rvec)*1000 );
- bonds = *lists + BONDS;
- dBOs = *lists + DBOS;
+ bonds = lists[BONDS];
+ dBOs = lists[DBOS];
start_i = Start_Index(i, bonds);
end_i = End_Index(i, bonds);
@@ -395,7 +395,7 @@ void Calculate_dBO( int i, int pj,
void Add_dBond_to_Forces_NPT( int i, int pj, simulation_data *data,
storage *workspace, reax_list **lists )
{
- reax_list *bonds = (*lists) + BONDS;
+ reax_list *bonds = lists[BONDS];
bond_data *nbr_j, *nbr_k;
bond_order_data *bo_ij, *bo_ji;
dbond_coefficients coef;
@@ -551,7 +551,7 @@ void Add_dBond_to_Forces_NPT( int i, int pj, simulation_data *data,
void Add_dBond_to_Forces( int i, int pj,
storage *workspace, reax_list **lists )
{
- reax_list *bonds = (*lists) + BONDS;
+ reax_list *bonds = lists[BONDS];
bond_data *nbr_j, *nbr_k;
bond_order_data *bo_ij, *bo_ji;
dbond_coefficients coef;
@@ -822,7 +822,7 @@ void BO( reax_system *system, control_params *control, simulation_data *data,
single_body_parameters *sbp_i, *sbp_j;
two_body_parameters *twbp;
bond_order_data *bo_ij, *bo_ji;
- reax_list *bonds = (*lists) + BONDS;
+ reax_list *bonds = lists[BONDS];
#ifdef TEST_FORCES
int k, pk, start_j, end_j;
int top_dbo, top_dDelta;
@@ -831,8 +831,8 @@ void BO( reax_system *system, control_params *control, simulation_data *data,
reax_list *dDeltas, *dBOs;
top_dbo = 0;
top_dDelta = 0;
- dDeltas = (*lists) + DDELTAS;
- dBOs = (*lists) + DBOS;
+ dDeltas = lists[DDELTAS];
+ dBOs = lists[DBOS];
//for( i = 0; i < system->N; ++i )
// qsort( &(bonds->bond_list[Start_Index(i, bonds)]),
diff --git a/PuReMD/src/bonds.c b/PuReMD/src/bonds.c
index 5b0b31f6df68b824837b252fc37534504d482e21..dec58cdb6daa0be7f01d33523db428ad7e39cd50 100644
--- a/PuReMD/src/bonds.c
+++ b/PuReMD/src/bonds.c
@@ -51,7 +51,7 @@ void Bonds( reax_system *system, control_params *control,
bond_order_data *bo_ij;
reax_list *bonds;
- bonds = (*lists) + BONDS;
+ bonds = lists[BONDS];
gp3 = system->reax_param.gp.l[3];
gp4 = system->reax_param.gp.l[4];
gp7 = system->reax_param.gp.l[7];
diff --git a/PuReMD/src/comm_tools.c b/PuReMD/src/comm_tools.c
index 93ac4dee2b14297b7246f15149454d1a0c770411..8419e3efe44377e7d1680fe09b2bc06ef5756ca6 100644
--- a/PuReMD/src/comm_tools.c
+++ b/PuReMD/src/comm_tools.c
@@ -245,7 +245,7 @@ void Pack_Boundary_Atom( boundary_atom *matm, reax_atom *ratm, int i )
{
matm->orig_id = ratm->orig_id;
matm->imprt_id = i;
- matm->type = ratm->type;
+ matm->type = ratm->type;
matm->num_bonds = ratm->num_bonds;
matm->num_hbonds = ratm->num_hbonds;
rvec_Copy( matm->x, ratm->x );
@@ -278,12 +278,15 @@ void Sort_Boundary_Atoms( reax_system *system, int start, int end,
fprintf( stderr, "p%d sort_exchange: start=%d end=%d dim=%d starting...\n",
system->my_rank, start, end, dim );
#endif
+
atoms = system->my_atoms;
my_box = &( system->my_box );
/* place each atom into the appropriate outgoing list */
for ( i = start; i < end; ++i )
+ {
for ( d = dim; d < 3; ++d )
+ {
for ( p = 2 * d; p < 2 * d + 2; ++p )
{
nbr_pr = &( system->my_nbrs[p] );
@@ -296,12 +299,16 @@ void Sort_Boundary_Atoms( reax_system *system, int start, int end,
Pack_Boundary_Atom( out_buf + out_cnt, atoms + i, i );
}
}
+ }
+ }
#if defined(DEBUG_FOCUS)
for ( i = 2 * dim; i < 2 * dim + 2; ++i )
+ {
fprintf( stderr, "p%d to p%d(nbr%d) # of exchanges to send = %d\n",
system->my_rank, system->my_nbrs[i].rank, i,
out_bufs[i].cnt );
+ }
fprintf( stderr, "p%d sort_exchange: start=%d end=%d dim=%d done!\n",
system->my_rank, start, end, dim );
#endif
@@ -356,6 +363,7 @@ void Estimate_Boundary_Atoms( reax_system *system, int start, int end,
/* sort the atoms to their outgoing buffers */
for ( i = 0; i < end; ++i )
+ {
for ( p = 2 * d; p < 2 * d + 2; ++p )
{
nbr_pr = &( system->my_nbrs[p] );
@@ -368,6 +376,7 @@ void Estimate_Boundary_Atoms( reax_system *system, int start, int end,
Pack_Boundary_Atom( out_buf + out_cnt, atoms + i, i );
}
}
+ }
#if defined(DEBUG_FOCUS)
fprintf( stderr, "p%d estimate_exchange: end=%d dim=%d done!\n",
@@ -525,7 +534,11 @@ int SendRecv( reax_system* system, mpi_datatypes *mpi_data, MPI_Datatype type,
#if defined(DEBUG_FOCUS)
fprintf( stderr, "p%d sendrecv: entered\n", system->my_rank );
#endif
- if ( clr ) Reset_Out_Buffers( mpi_data->out_buffers, system->num_nbrs );
+
+ if ( clr )
+ {
+ Reset_Out_Buffers( mpi_data->out_buffers, system->num_nbrs );
+ }
comm = mpi_data->comm_mesh3D;
in1 = mpi_data->in1_buffer;
in2 = mpi_data->in2_buffer;
@@ -545,8 +558,10 @@ int SendRecv( reax_system* system, mpi_datatypes *mpi_data, MPI_Datatype type,
/* for estimates in1_buffer & in2_buffer will be NULL */
if ( est_flag )
+ {
Estimate_Init_Storage( system->my_rank, nbr1, nbr2, d,
- &max, nrecv, &in1, &in2, comm );
+ &max, nrecv, &in1, &in2, comm );
+ }
/* initiate recvs */
MPI_Irecv( in1, nrecv[2 * d], type, nbr1->rank, 2 * d + 1, comm, &req1 );
@@ -554,9 +569,9 @@ int SendRecv( reax_system* system, mpi_datatypes *mpi_data, MPI_Datatype type,
/* send both messages in dimension d */
MPI_Send( out_bufs[2 * d].out_atoms, out_bufs[2 * d].cnt, type,
- nbr1->rank, 2 * d, comm );
+ nbr1->rank, 2 * d, comm );
MPI_Send( out_bufs[2 * d + 1].out_atoms, out_bufs[2 * d + 1].cnt, type,
- nbr2->rank, 2 * d + 1, comm );
+ nbr2->rank, 2 * d + 1, comm );
/* recv and unpack atoms from nbr1 in dimension d */
MPI_Wait( &req1, &stat1 );
@@ -593,42 +608,62 @@ void Comm_Atoms( reax_system *system, control_params *control,
real t_start = 0, t_elapsed = 0;
if ( system->my_rank == MASTER_NODE )
+ {
t_start = Get_Time( );
+ }
#endif
if ( renbr )
{
- for ( i = 0; i < MAX_NBRS; ++i ) nrecv[i] = system->est_trans;
+ for ( i = 0; i < MAX_NBRS; ++i )
+ {
+ nrecv[i] = system->est_trans;
+ }
system->n = SendRecv( system, mpi_data, mpi_data->mpi_atom_type, nrecv,
- Sort_Transfer_Atoms, Unpack_Transfer_Message, 1 );
+ Sort_Transfer_Atoms, Unpack_Transfer_Message, 1 );
Bin_My_Atoms( system, &(workspace->realloc) );
Reorder_My_Atoms( system, workspace );
+
#if defined(DEBUG_FOCUS)
fprintf( stderr, "p%d updated local atoms, n=%d\n",
system->my_rank, system->n );
MPI_Barrier( mpi_data->world );
#endif
- for ( i = 0; i < MAX_NBRS; ++i ) nrecv[i] = system->my_nbrs[i].est_recv;
- system->N = SendRecv(system, mpi_data, mpi_data->boundary_atom_type, nrecv,
- Sort_Boundary_Atoms, Unpack_Exchange_Message, 1);
+ for ( i = 0; i < MAX_NBRS; ++i )
+ {
+ nrecv[i] = system->my_nbrs[i].est_recv;
+ }
+ system->N = SendRecv( system, mpi_data, mpi_data->boundary_atom_type, nrecv,
+ Sort_Boundary_Atoms, Unpack_Exchange_Message, 1 );
+
#if defined(DEBUG_FOCUS)
fprintf( stderr, "p%d: exchanged boundary atoms, N=%d\n",
- system->my_rank, system->N );
+ system->my_rank, system->N );
+
for ( i = 0; i < MAX_NBRS; ++i )
+ {
fprintf( stderr, "p%d: nbr%d(p%d) str=%d cnt=%d end=%d\n",
system->my_rank, i, system->my_nbrs[i].rank,
system->my_nbrs[i].atoms_str, system->my_nbrs[i].atoms_cnt,
system->my_nbrs[i].atoms_str + system->my_nbrs[i].atoms_cnt );
+ }
+
MPI_Barrier( mpi_data->world );
#endif
+
Bin_Boundary_Atoms( system );
}
else
{
- for ( i = 0; i < MAX_NBRS; ++i ) nrecv[i] = system->my_nbrs[i].atoms_cnt;
+ for ( i = 0; i < MAX_NBRS; ++i )
+ {
+ nrecv[i] = system->my_nbrs[i].atoms_cnt;
+ }
+
SendRecv( system, mpi_data, mpi_data->mpi_rvec, nrecv,
- Sort_Position_Updates, Unpack_Position_Updates, 0 );
+ Sort_Position_Updates, Unpack_Position_Updates, 0 );
+
#if defined(DEBUG_FOCUS)
fprintf( stderr, "p%d: updated positions\n", system->my_rank );
MPI_Barrier( mpi_data->world );
@@ -642,6 +677,7 @@ void Comm_Atoms( reax_system *system, control_params *control,
data->timing.comm += t_elapsed;
}
#endif
+
#if defined(DEBUG_FOCUS)
fprintf(stderr, "p%d @ renbr=%d: comm_atoms done\n", system->my_rank, renbr);
fprintf( stderr, "p%d: system->n = %d, system->N = %d\n",
diff --git a/PuReMD/src/control.c b/PuReMD/src/control.c
index 07b46d3a4d096f10d390ad203d13b14d151e36f9..cd95c2465dc9a17edcf951295babb9527506b0c4 100644
--- a/PuReMD/src/control.c
+++ b/PuReMD/src/control.c
@@ -114,9 +114,8 @@ char Read_Control_File( char *control_file, control_params* control,
tmp[i] = (char*) malloc(sizeof(char) * MAX_LINE);
/* read control parameters file */
- while (!feof(fp))
+ while ( fgets( s, MAX_LINE, fp ) )
{
- fgets( s, MAX_LINE, fp );
c = Tokenize( s, &tmp );
//fprintf( stderr, "%s\n", s );
diff --git a/PuReMD/src/forces.c b/PuReMD/src/forces.c
index 888c6acae9db372721326582558605acc73c464e..d438a0eba65d50ae11a8f6bd03fa5fe79492474b 100644
--- a/PuReMD/src/forces.c
+++ b/PuReMD/src/forces.c
@@ -142,7 +142,7 @@ void Compute_Total_Force( reax_system *system, control_params *control,
reax_list **lists, mpi_datatypes *mpi_data )
{
int i, pj;
- reax_list *bonds = (*lists) + BONDS;
+ reax_list *bonds = lists[BONDS];
for ( i = 0; i < system->N; ++i )
for ( pj = Start_Index(i, bonds); pj < End_Index(i, bonds); ++pj )
@@ -194,7 +194,7 @@ void Validate_Lists( reax_system *system, storage *workspace, reax_list **lists,
/* bond list */
if ( N > 0 )
{
- bonds = *lists + BONDS;
+ bonds = lists[BONDS];
for ( i = 0; i < N; ++i )
{
@@ -221,7 +221,7 @@ void Validate_Lists( reax_system *system, storage *workspace, reax_list **lists,
/* hbonds list */
if ( numH > 0 )
{
- hbonds = *lists + HBONDS;
+ hbonds = lists[HBONDS];
for ( i = 0; i < n; ++i )
{
@@ -337,9 +337,9 @@ void Init_Forces( reax_system *system, control_params *control,
far_neighbor_data *nbr_pj;
reax_atom *atom_i, *atom_j;
- far_nbrs = *lists + FAR_NBRS;
- bonds = *lists + BONDS;
- hbonds = *lists + HBONDS;
+ far_nbrs = lists[FAR_NBRS];
+ bonds = lists[BONDS];
+ hbonds = lists[HBONDS];
for ( i = 0; i < system->n; ++i )
workspace->bond_mark[i] = 0;
@@ -605,9 +605,9 @@ void Init_Forces_noQEq( reax_system *system, control_params *control,
far_neighbor_data *nbr_pj;
reax_atom *atom_i, *atom_j;
- far_nbrs = *lists + FAR_NBRS;
- bonds = *lists + BONDS;
- hbonds = *lists + HBONDS;
+ far_nbrs = lists[FAR_NBRS];
+ bonds = lists[BONDS];
+ hbonds = lists[HBONDS];
for ( i = 0; i < system->n; ++i )
workspace->bond_mark[i] = 0;
@@ -791,7 +791,7 @@ void Estimate_Storages( reax_system *system, control_params *control,
far_neighbor_data *nbr_pj;
reax_atom *atom_i, *atom_j;
- far_nbrs = *lists + FAR_NBRS;
+ far_nbrs = lists[FAR_NBRS];
*Htop = 0;
memset( hb_top, 0, sizeof(int) * system->local_cap );
memset( bond_top, 0, sizeof(int) * system->total_cap );
diff --git a/PuReMD/src/geo_tools.c b/PuReMD/src/geo_tools.c
index dd5115c07649d3c7571ae36fc79cd221eb9ad0f1..c1e3549fedf2039f96af84aa263cd114c7dee3cb 100644
--- a/PuReMD/src/geo_tools.c
+++ b/PuReMD/src/geo_tools.c
@@ -212,10 +212,8 @@ void Count_PDB_Atoms( FILE *geo, reax_system *system )
system->bigN = system->n = system->N = 0;
/* increment number of atoms for each line denoting an atom desc */
- while ( !feof( geo ) )
+ while ( fgets( line, MAX_LINE, geo ) )
{
- fgets( line, MAX_LINE, geo );
-
if ( strncmp( line, "ATOM", 4 ) == 0 ||
strncmp( line, "HETATM", 6 ) == 0 )
{
diff --git a/PuReMD/src/hydrogen_bonds.c b/PuReMD/src/hydrogen_bonds.c
index 6aea423234e68ba53729b8841d6cae15155bbb9e..cba267fffa71ef7a11ac23def3c72cae92838653 100644
--- a/PuReMD/src/hydrogen_bonds.c
+++ b/PuReMD/src/hydrogen_bonds.c
@@ -59,9 +59,9 @@ void Hydrogen_Bonds( reax_system *system, control_params *control,
bond_data *bond_list;
hbond_data *hbond_list;
- bonds = (*lists) + BONDS;
+ bonds = lists[BONDS];
bond_list = bonds->bond_list;
- hbonds = (*lists) + HBONDS;
+ hbonds = lists[HBONDS];
hbond_list = hbonds->hbond_list;
/* loops below discover the Hydrogen bonds between i-j-k triplets.
diff --git a/PuReMD/src/init_md.c b/PuReMD/src/init_md.c
index b35a46887e638424b5d570841cd12e63c00462f9..caad5420453b4e9329cc0b4ee9382462c0d9e862 100644
--- a/PuReMD/src/init_md.c
+++ b/PuReMD/src/init_md.c
@@ -553,8 +553,8 @@ int Init_Lists( reax_system *system, control_params *control,
system->my_rank, system->local_cap, system->total_cap );
#endif
- if (!Make_List( system->total_cap, num_nbrs, TYP_FAR_NEIGHBOR,
- *lists + FAR_NBRS, comm ))
+ if ( !Make_List( system->total_cap, num_nbrs, TYP_FAR_NEIGHBOR,
+ lists[FAR_NBRS], comm ) )
{
fprintf(stderr, "Problem in initializing far nbrs list. Terminating!\n");
MPI_Abort( comm, INSUFFICIENT_MEMORY );
@@ -605,7 +605,7 @@ int Init_Lists( reax_system *system, control_params *control,
total_hbonds = MAX( total_hbonds * SAFER_ZONE, MIN_CAP * MIN_HBONDS );
if ( !Make_List( system->Hcap, total_hbonds, TYP_HBOND,
- *lists + HBONDS, comm ) )
+ lists[HBONDS], comm ) )
{
fprintf( stderr, "not enough space for hbonds list. terminating!\n" );
MPI_Abort( comm, INSUFFICIENT_MEMORY );
@@ -618,7 +618,7 @@ int Init_Lists( reax_system *system, control_params *control,
}
/* bonds list */
- //Allocate_Bond_List( system->N, bond_top, (*lists)+BONDS );
+ //Allocate_Bond_List( system->N, bond_top, lists[BONDS] );
//num_bonds = bond_top[system->N-1];
total_bonds = 0;
for ( i = 0; i < system->N; ++i )
@@ -629,7 +629,7 @@ int Init_Lists( reax_system *system, control_params *control,
bond_cap = MAX( total_bonds * SAFE_ZONE, MIN_CAP * MIN_BONDS );
if ( !Make_List( system->total_cap, bond_cap, TYP_BOND,
- *lists + BONDS, comm ) )
+ lists[BONDS], comm ) )
{
fprintf( stderr, "not enough space for bonds list. terminating!\n" );
MPI_Abort( comm, INSUFFICIENT_MEMORY );
@@ -643,7 +643,7 @@ int Init_Lists( reax_system *system, control_params *control,
/* 3bodies list */
cap_3body = MAX( num_3body * SAFE_ZONE, MIN_3BODIES );
if ( !Make_List( bond_cap, cap_3body, TYP_THREE_BODY,
- *lists + THREE_BODIES, comm ) )
+ lists[THREE_BODIES], comm ) )
{
fprintf( stderr, "Problem in initializing angles list. Terminating!\n" );
MPI_Abort( comm, INSUFFICIENT_MEMORY );
@@ -656,7 +656,7 @@ int Init_Lists( reax_system *system, control_params *control,
#if defined(TEST_FORCES)
if ( !Make_List( system->total_cap, bond_cap * 8, TYP_DDELTA,
- *lists + DDELTAS, comm ) )
+ lists[DDELTAS], comm ) )
{
fprintf( stderr, "Problem in initializing dDelta list. Terminating!\n" );
MPI_Abort( comm, INSUFFICIENT_MEMORY );
@@ -665,7 +665,7 @@ int Init_Lists( reax_system *system, control_params *control,
system->my_rank, bond_cap * 30,
bond_cap * 8 * sizeof(dDelta_data) / (1024 * 1024) );
- if ( !Make_List( bond_cap, bond_cap * 50, TYP_DBO, *lists + DBOS, comm ) )
+ if ( !Make_List( bond_cap, bond_cap * 50, TYP_DBO, lists[DBOS], comm ) )
{
fprintf( stderr, "Problem in initializing dBO list. Terminating!\n" );
MPI_Abort( comm, INSUFFICIENT_MEMORY );
@@ -709,7 +709,7 @@ int Init_Lists( reax_system *system, control_params *control,
total_hbonds = (int)(MAX( total_hbonds * SAFER_ZONE, MIN_CAP * MIN_HBONDS ));
if ( !Make_List( system->Hcap, total_hbonds, TYP_HBOND,
- *lists + HBONDS, comm ) )
+ lists[HBONDS], comm ) )
{
fprintf( stderr, "not enough space for hbonds list. terminating!\n" );
MPI_Abort( comm, INSUFFICIENT_MEMORY );
@@ -722,7 +722,7 @@ int Init_Lists( reax_system *system, control_params *control,
}
/* bonds list */
- //Allocate_Bond_List( system->N, bond_top, (*lists)+BONDS );
+ //Allocate_Bond_List( system->N, bond_top, lists[BONDS] );
//num_bonds = bond_top[system->N-1];
total_bonds = 0;
for ( i = 0; i < system->N; ++i )
@@ -733,7 +733,7 @@ int Init_Lists( reax_system *system, control_params *control,
bond_cap = (int)(MAX( total_bonds * SAFE_ZONE, MIN_CAP * MIN_BONDS ));
if ( !Make_List( system->total_cap, bond_cap, TYP_BOND,
- *lists + BONDS, comm ) )
+ lists[BONDS], comm ) )
{
fprintf( stderr, "not enough space for bonds list. terminating!\n" );
MPI_Abort( comm, INSUFFICIENT_MEMORY );
@@ -747,7 +747,7 @@ int Init_Lists( reax_system *system, control_params *control,
/* 3bodies list */
cap_3body = (int)(MAX( num_3body * SAFE_ZONE, MIN_3BODIES ));
if ( !Make_List( bond_cap, cap_3body, TYP_THREE_BODY,
- *lists + THREE_BODIES, comm ) )
+ lists[THREE_BODIES], comm ) )
{
fprintf( stderr, "Problem in initializing angles list. Terminating!\n" );
MPI_Abort( comm, INSUFFICIENT_MEMORY );
@@ -760,7 +760,7 @@ int Init_Lists( reax_system *system, control_params *control,
#if defined(TEST_FORCES)
if ( !Make_List( system->total_cap, bond_cap * 8, TYP_DDELTA,
- *lists + DDELTAS, comm ) )
+ lists[DDELTAS], comm ) )
{
fprintf( stderr, "Problem in initializing dDelta list. Terminating!\n" );
MPI_Abort( comm, INSUFFICIENT_MEMORY );
@@ -769,7 +769,7 @@ int Init_Lists( reax_system *system, control_params *control,
system->my_rank, bond_cap * 30,
bond_cap * 8 * sizeof(dDelta_data) / (1024 * 1024) );
- if ( !Make_List( bond_cap, bond_cap * 50, TYP_DBO, (*lists) + DBOS, comm ) )
+ if ( !Make_List( bond_cap, bond_cap * 50, TYP_DBO, lists[DBOS], comm ) )
{
fprintf( stderr, "Problem in initializing dBO list. Terminating!\n" );
MPI_Abort( comm, INSUFFICIENT_MEMORY );
diff --git a/PuReMD/src/io_tools.c b/PuReMD/src/io_tools.c
index 5a5e6f2a08026ba5c9b6f785aa7f607360300c07..6c0cc5c8e755ff0b23fdf8234e7530a3abceed5d 100644
--- a/PuReMD/src/io_tools.c
+++ b/PuReMD/src/io_tools.c
@@ -844,7 +844,7 @@ void Print_Far_Neighbors( reax_system *system, reax_list **lists,
sprintf( fname, "%s.far_nbrs.%d", control->sim_name, system->my_rank );
fout = fopen( fname, "w" );
- far_nbrs = (*lists) + FAR_NBRS;
+ far_nbrs = lists[FAR_NBRS];
natoms = system->N;
for ( i = 0; i < natoms; ++i )
@@ -1258,8 +1258,8 @@ void Print_Bond_Orders( reax_system *system, control_params *control,
int i, pj, pk;
bond_order_data *bo_ij;
dbond_data *dbo_k;
- reax_list *bonds = (*lists) + BONDS;
- reax_list *dBOs = (*lists) + DBOS;
+ reax_list *bonds = lists[BONDS];
+ reax_list *dBOs = lists[DBOS];
/* bond orders */
fprintf( out_control->fbo, "step: %d\n", data->step );
@@ -1421,7 +1421,7 @@ void Print_Far_Neighbors_List( reax_system *system, reax_list **lists,
int temp[500];
reax_list *far_nbrs;
- far_nbrs = (*lists) + FAR_NBRS;
+ far_nbrs = lists[FAR_NBRS];
fprintf( out_control->flist, "step: %d\n", data->step );
fprintf( out_control->flist, "%6s\t%-38s\n", "atom", "Far_nbrs_list");
@@ -1452,7 +1452,7 @@ void Print_Bond_List( reax_system *system, control_params *control,
output_controls *out_control)
{
int i, j, id_i, id_j, nbr, pj;
- reax_list *bonds = (*lists) + BONDS;
+ reax_list *bonds = lists[BONDS];
int temp[500];
int num = 0;
diff --git a/PuReMD/src/list.c b/PuReMD/src/list.c
index 19f233db605687076fea2e03786fc0b597b6a373..4ccb03ed94174c6a5bb184ae48687a6e40c73515 100644
--- a/PuReMD/src/list.c
+++ b/PuReMD/src/list.c
@@ -41,11 +41,12 @@ int Make_List(int n, int num_intrs, int type, reax_list *l, MPI_Comm comm)
l->end_index = (int*) smalloc( n * sizeof(int), "list:end_index", comm );
l->type = type;
+
#if defined(DEBUG_FOCUS)
fprintf( stderr, "list: n=%d num_intrs=%d type=%d\n", l->n, l->num_intrs, l->type );
#endif
- switch (l->type)
+ switch ( l->type )
{
case TYP_VOID:
l->v = (void*) smalloc(l->num_intrs * sizeof(void*), "list:v", comm);
@@ -129,31 +130,3 @@ void Delete_List( reax_list *l, MPI_Comm comm )
MPI_Abort( comm, INVALID_INPUT );
}
}
-
-
-#if defined(PURE_REAX)
-inline int Num_Entries( int i, reax_list *l )
-{
- return l->end_index[i] - l->index[i];
-}
-
-inline int Start_Index( int i, reax_list *l )
-{
- return l->index[i];
-}
-
-inline int End_Index( int i, reax_list *l )
-{
- return l->end_index[i];
-}
-
-inline void Set_Start_Index( int i, int val, reax_list *l )
-{
- l->index[i] = val;
-}
-
-inline void Set_End_Index( int i, int val, reax_list *l )
-{
- l->end_index[i] = val;
-}
-#endif
diff --git a/PuReMD/src/list.h b/PuReMD/src/list.h
index 5cc3a62630fdb29f3ac07ffb8b30469de49f34ea..da400b76e1303bf5e587e949f664bc93225de3dc 100644
--- a/PuReMD/src/list.h
+++ b/PuReMD/src/list.h
@@ -24,40 +24,40 @@
#include "reax_types.h"
-int Make_List( int, int, int, reax_list*, MPI_Comm );
+
+int Make_List( int, int, int, reax_list*, MPI_Comm );
+
void Delete_List( reax_list*, MPI_Comm );
-inline int Num_Entries(int, reax_list*);
-inline int Start_Index( int, reax_list* );
-inline int End_Index( int, reax_list* );
-inline void Set_Start_Index(int, int, reax_list*);
-inline void Set_End_Index(int, int, reax_list*);
-#if defined(LAMMPS_REAX)
-inline int Num_Entries( int i, reax_list *l )
+static inline int Num_Entries( int i, reax_list *l )
{
return l->end_index[i] - l->index[i];
}
-inline int Start_Index( int i, reax_list *l )
+
+static inline int Start_Index( int i, reax_list *l )
{
return l->index[i];
}
-inline int End_Index( int i, reax_list *l )
+
+static inline int End_Index( int i, reax_list *l )
{
return l->end_index[i];
}
-inline void Set_Start_Index( int i, int val, reax_list *l )
+
+static inline void Set_Start_Index( int i, int val, reax_list *l )
{
l->index[i] = val;
}
-inline void Set_End_Index( int i, int val, reax_list *l )
+
+static inline void Set_End_Index( int i, int val, reax_list *l )
{
l->end_index[i] = val;
}
-#endif // LAMMPS_REAX
+
#endif
diff --git a/PuReMD/src/multi_body.c b/PuReMD/src/multi_body.c
index 1c80cd86f0b24b9af718d6c8c877a347cca6e98c..7ef1f12d1103c5d3ef73fe15487329627b26caee 100644
--- a/PuReMD/src/multi_body.c
+++ b/PuReMD/src/multi_body.c
@@ -53,7 +53,7 @@ void Atom_Energy( reax_system *system, control_params *control,
two_body_parameters *twbp;
bond_data *pbond;
bond_order_data *bo_ij;
- reax_list *bonds = (*lists) + BONDS;
+ reax_list *bonds = lists[BONDS];
/* Initialize parameters */
p_lp1 = system->reax_param.gp.l[15];
diff --git a/PuReMD/src/neighbors.c b/PuReMD/src/neighbors.c
index 8f96541e2dd347a4565622f542a7b784352769a8..5be0016eda64a6e4ec56f02d77695cd212fcdd55 100644
--- a/PuReMD/src/neighbors.c
+++ b/PuReMD/src/neighbors.c
@@ -86,7 +86,7 @@ void Generate_Neighbor_Lists( reax_system *system, simulation_data *data,
// fprintf( stderr, "\n\tentered nbrs - " );
g = &( system->my_grid );
- far_nbrs = (*lists) + FAR_NBRS;
+ far_nbrs = lists[FAR_NBRS];
num_far = 0;
/* first pick up a cell in the grid */
diff --git a/PuReMD/src/nonbonded.c b/PuReMD/src/nonbonded.c
index 1bdd2ab6e6a5bd2b932a126aedb3b2ca3abc9814..ab25b807d5e0a0263a4d8f89ecc475c8615b8bdd 100644
--- a/PuReMD/src/nonbonded.c
+++ b/PuReMD/src/nonbonded.c
@@ -52,7 +52,7 @@ void vdW_Coulomb_Energy( reax_system *system, control_params *control,
// rtensor temp_rtensor, total_rtensor;
natoms = system->n;
- far_nbrs = (*lists) + FAR_NBRS;
+ far_nbrs = lists[FAR_NBRS];
p_vdW1 = system->reax_param.gp.l[28];
p_vdW1i = 1.0 / p_vdW1;
e_core = 0;
@@ -230,7 +230,7 @@ void Tabulated_vdW_Coulomb_Energy( reax_system *system, control_params *control,
LR_lookup_table *t;
natoms = system->n;
- far_nbrs = (*lists) + FAR_NBRS;
+ far_nbrs = lists[FAR_NBRS];
steps = data->step - data->prev_steps;
update_freq = out_control->energy_update_freq;
update_energies = update_freq > 0 && steps % update_freq == 0;
diff --git a/PuReMD/src/parallelreax.c b/PuReMD/src/parallelreax.c
index 6d0955c70c4dfd5813a2a29ae3be191996270dea..4b401ad603db53f5b982a2c7fc24861a9b9a6495 100644
--- a/PuReMD/src/parallelreax.c
+++ b/PuReMD/src/parallelreax.c
@@ -125,46 +125,60 @@ int main( int argc, char* argv[] )
int i;
real t_start = 0, t_elapsed;
+ MPI_Init( &argc, &argv );
+
if ( argc != 4 )
{
- usage(argv);
- exit( INVALID_INPUT );
+ usage( argv );
+ MPI_Abort( MPI_COMM_WORLD, INVALID_INPUT );
}
/* allocated main datastructures */
system = (reax_system *)
- smalloc( sizeof(reax_system), "system", MPI_COMM_WORLD );
+ smalloc( sizeof(reax_system), "system", MPI_COMM_WORLD );
control = (control_params *)
- smalloc( sizeof(control_params), "control", MPI_COMM_WORLD );
+ smalloc( sizeof(control_params), "control", MPI_COMM_WORLD );
data = (simulation_data *)
- smalloc( sizeof(simulation_data), "data", MPI_COMM_WORLD );
+ smalloc( sizeof(simulation_data), "data", MPI_COMM_WORLD );
workspace = (storage *)
- smalloc( sizeof(storage), "workspace", MPI_COMM_WORLD );
+ smalloc( sizeof(storage), "workspace", MPI_COMM_WORLD );
lists = (reax_list **)
- smalloc( LIST_N * sizeof(reax_list*), "lists", MPI_COMM_WORLD );
+ smalloc( LIST_N * sizeof(reax_list*), "lists", MPI_COMM_WORLD );
for ( i = 0; i < LIST_N; ++i )
{
lists[i] = (reax_list *)
- smalloc( sizeof(reax_list), "lists[i]", MPI_COMM_WORLD );
+ smalloc( sizeof(reax_list), "lists[i]", MPI_COMM_WORLD );
lists[i]->allocated = 0;
+ lists[i]->n = 0;
+ lists[i]->num_intrs = 0;
+ lists[i]->index = NULL;
+ lists[i]->end_index = NULL;
+ lists[i]->type = 0;
+ lists[i]->v = NULL;
+ lists[i]->three_body_list = NULL;
+ lists[i]->bond_list = NULL;
+ lists[i]->dbo_list = NULL;
+ lists[i]->dDelta_list = NULL;
+ lists[i]->far_nbr_list = NULL;
+ lists[i]->hbond_list = NULL;
}
out_control = (output_controls *)
- smalloc( sizeof(output_controls), "out_control", MPI_COMM_WORLD );
+ smalloc( sizeof(output_controls), "out_control", MPI_COMM_WORLD );
mpi_data = (mpi_datatypes *)
- smalloc( sizeof(mpi_datatypes), "mpi_data", MPI_COMM_WORLD );
+ smalloc( sizeof(mpi_datatypes), "mpi_data", MPI_COMM_WORLD );
/* setup the parallel environment */
- MPI_Init( &argc, &argv );
MPI_Comm_size( MPI_COMM_WORLD, &(control->nprocs) );
MPI_Comm_rank( MPI_COMM_WORLD, &(system->my_rank) );
system->wsize = control->nprocs;
system->global_offset = (int*)
- scalloc( system->wsize + 1, sizeof(int), "global_offset", MPI_COMM_WORLD );
+ scalloc( system->wsize + 1, sizeof(int), "global_offset", MPI_COMM_WORLD );
/* read system description files */
Read_System( argv[1], argv[2], argv[3], system, control,
- data, workspace, out_control, mpi_data );
+ data, workspace, out_control, mpi_data );
+
#if defined(DEBUG)
fprintf( stderr, "p%d: read simulation info\n", system->my_rank );
MPI_Barrier( MPI_COMM_WORLD );
@@ -176,6 +190,7 @@ int main( int argc, char* argv[] )
/* initialize datastructures */
Initialize( system, control, data, workspace, lists, out_control, mpi_data );
+
#if defined(DEBUG)
fprintf( stderr, "p%d: initializated data structures\n", system->my_rank );
MPI_Barrier( mpi_data->world );
@@ -186,9 +201,10 @@ int main( int argc, char* argv[] )
Reset( system, control, data, workspace, lists, MPI_COMM_WORLD );
Generate_Neighbor_Lists( system, data, workspace, lists );
Compute_Forces( system, control, data, workspace,
- lists, out_control, mpi_data );
+ lists, out_control, mpi_data );
Compute_Kinetic_Energy( system, data, mpi_data->comm_mesh3D );
Output_Results( system, control, data, lists, out_control, mpi_data );
+
#if defined(DEBUG)
fprintf( stderr, "p%d: computed forces at t0\n", system->my_rank );
MPI_Barrier( mpi_data->world );
@@ -214,6 +230,7 @@ int main( int argc, char* argv[] )
else if ( out_control->restart_format == WRITE_BINARY )
Write_Binary_Restart( system, control, data, out_control, mpi_data );
}
+
#if defined(DEBUG)
fprintf( stderr, "p%d: step%d completed\n", system->my_rank, data->step );
MPI_Barrier( mpi_data->world );
diff --git a/PuReMD/src/reax_types.h b/PuReMD/src/reax_types.h
index 073918c4a8309130207e3fdce05a7d7a0be0f0ca..3ebcd73cb15c89910d87df80714eb73dcec5604b 100644
--- a/PuReMD/src/reax_types.h
+++ b/PuReMD/src/reax_types.h
@@ -22,15 +22,15 @@
#ifndef __REAX_TYPES_H_
#define __REAX_TYPES_H_
-#include "ctype.h"
-#include "math.h"
-#include "mpi.h"
-#include "stdio.h"
-#include "stdlib.h"
-#include "string.h"
-#include "sys/time.h"
-#include "time.h"
-#include "zlib.h"
+#include <ctype.h>
+#include <math.h>
+#include <mpi.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
+#include <sys/time.h>
+#include <time.h>
+#include <zlib.h>
/************* SOME DEFS - crucial for reax_types.h *********/
@@ -678,8 +678,11 @@ typedef struct
{
int thb;
int pthb; // pointer to the third body on the central atom's nbrlist
- real theta, cos_theta;
- rvec dcos_di, dcos_dj, dcos_dk;
+ real theta;
+ real cos_theta;
+ rvec dcos_di;
+ rvec dcos_dj;
+ rvec dcos_dk;
} three_body_interaction_data;
@@ -715,12 +718,28 @@ typedef struct
typedef struct
{
- real BO, BO_s, BO_pi, BO_pi2;
- real Cdbo, Cdbopi, Cdbopi2;
- real C1dbo, C2dbo, C3dbo;
- real C1dbopi, C2dbopi, C3dbopi, C4dbopi;
- real C1dbopi2, C2dbopi2, C3dbopi2, C4dbopi2;
- rvec dBOp, dln_BOp_s, dln_BOp_pi, dln_BOp_pi2;
+ real BO;
+ real BO_s;
+ real BO_pi;
+ real BO_pi2;
+ real Cdbo;
+ real Cdbopi;
+ real Cdbopi2;
+ real C1dbo;
+ real C2dbo;
+ real C3dbo;
+ real C1dbopi;
+ real C2dbopi;
+ real C3dbopi;
+ real C4dbopi;
+ real C1dbopi2;
+ real C2dbopi2;
+ real C3dbopi2;
+ real C4dbopi2;
+ rvec dBOp;
+ rvec dln_BOp_s;
+ rvec dln_BOp_pi;
+ rvec dln_BOp_pi2;
} bond_order_data;
typedef struct
@@ -729,7 +748,7 @@ typedef struct
int sym_index;
int dbond_index;
ivec rel_box;
- // rvec ext_factor;
+// rvec ext_factor;
real d;
rvec dvec;
bond_order_data bo_data;
@@ -867,15 +886,15 @@ typedef struct
int *end_index;
int type;
- list_type select;
+// list_type select;
void *v;
three_body_interaction_data *three_body_list;
- bond_data *bond_list;
- dbond_data *dbo_list;
- dDelta_data *dDelta_list;
- far_neighbor_data *far_nbr_list;
- hbond_data *hbond_list;
+ bond_data *bond_list;
+ dbond_data *dbo_list;
+ dDelta_data *dDelta_list;
+ far_neighbor_data *far_nbr_list;
+ hbond_data *hbond_list;
} reax_list;
diff --git a/PuReMD/src/reset_tools.c b/PuReMD/src/reset_tools.c
index af869e980d8e5b1705bde5e19d156bbeef364b3f..eb7c64652a34f4825121305d256843bb749ace26 100644
--- a/PuReMD/src/reset_tools.c
+++ b/PuReMD/src/reset_tools.c
@@ -74,7 +74,11 @@ void Reset_Energies( energy_data *en )
void Reset_Temperatures( simulation_data *data )
{
- data->therm.T = 0;
+ data->therm.T = 0.0;
+ data->therm.xi = 0.0;
+ data->therm.v_xi = 0.0;
+ data->therm.v_xi_old = 0.0;
+ data->therm.G_xi = 0.0;
}
@@ -181,7 +185,7 @@ void Reset_Neighbor_Lists( reax_system *system, control_params *control,
/* bonds list */
if ( system->N > 0 )
{
- bonds = (*lists) + BONDS;
+ bonds = lists[BONDS];
total_bonds = 0;
/* reset start-end indexes */
@@ -212,7 +216,7 @@ void Reset_Neighbor_Lists( reax_system *system, control_params *control,
/* hbonds list */
if ( control->hbond_cut > 0 && system->numH > 0 )
{
- hbonds = (*lists) + HBONDS;
+ hbonds = lists[HBONDS];
total_hbonds = 0;
/* reset start-end indexes */
diff --git a/PuReMD/src/system_props.c b/PuReMD/src/system_props.c
index 50e328a45f00c986a75cbbc87587363892c7e9cd..05b74323b902a625f15a1a8681c92ee7e3446f47 100644
--- a/PuReMD/src/system_props.c
+++ b/PuReMD/src/system_props.c
@@ -56,7 +56,7 @@ void Temperature_Control( control_params *control, simulation_data *data )
void Compute_Kinetic_Energy( reax_system* system, simulation_data* data,
- MPI_Comm comm )
+ MPI_Comm comm )
{
int i;
rvec p;
@@ -64,7 +64,7 @@ void Compute_Kinetic_Energy( reax_system* system, simulation_data* data,
data->my_en.e_kin = 0.0;
data->sys_en.e_kin = 0.0;
- data->therm.T = 0;
+ data->therm.T = 0.0;
for ( i = 0; i < system->n; i++ )
{
@@ -75,13 +75,15 @@ void Compute_Kinetic_Energy( reax_system* system, simulation_data* data,
}
MPI_Allreduce( &data->my_en.e_kin, &data->sys_en.e_kin,
- 1, MPI_DOUBLE, MPI_SUM, comm );
+ 1, MPI_DOUBLE, MPI_SUM, comm );
- data->therm.T = (2. * data->sys_en.e_kin) / (data->N_f * K_B);
+ data->therm.T = (2.0 * data->sys_en.e_kin) / (data->N_f * K_B);
// avoid T being an absolute zero, might cause F.P.E!
- if ( fabs(data->therm.T) < ALMOST_ZERO )
+ if ( fabs( data->therm.T ) < ALMOST_ZERO )
+ {
data->therm.T = ALMOST_ZERO;
+ }
}
diff --git a/PuReMD/src/torsion_angles.c b/PuReMD/src/torsion_angles.c
index d0947d3efa669056ab06060418a0aa088399fa24..f915fdb8325de91f5c5ea72f47e36ae0ab306992 100644
--- a/PuReMD/src/torsion_angles.c
+++ b/PuReMD/src/torsion_angles.c
@@ -191,8 +191,8 @@ void Torsion_Angles( reax_system *system, control_params *control,
real p_tor3 = system->reax_param.gp.l[24];
real p_tor4 = system->reax_param.gp.l[25];
real p_cot2 = system->reax_param.gp.l[27];
- reax_list *bonds = (*lists) + BONDS;
- reax_list *thb_intrs = (*lists) + THREE_BODIES;
+ reax_list *bonds = lists[BONDS];
+ reax_list *thb_intrs = lists[THREE_BODIES];
// char fname[100];
// FILE *ftor;
diff --git a/PuReMD/src/traj.c b/PuReMD/src/traj.c
index e455d74b3accf3d925a7df81a2c387e0983d288f..40df8bbd1860eff00141ed97013e596430daf69c 100644
--- a/PuReMD/src/traj.c
+++ b/PuReMD/src/traj.c
@@ -1097,10 +1097,10 @@ int Append_Frame( reax_system *system, control_params *control,
Write_Atoms( system, control, out_control, mpi_data );
if ( out_control->write_bonds )
- Write_Bonds( system, control, (*lists + BONDS), out_control, mpi_data );
+ Write_Bonds( system, control, lists[BONDS], out_control, mpi_data );
if ( out_control->write_angles )
- Write_Angles( system, control, (*lists + BONDS), (*lists + THREE_BODIES),
+ Write_Angles( system, control, lists[BONDS], lists[THREE_BODIES],
out_control, mpi_data );
#if defined(DEBUG_FOCUS)
fprintf( stderr, "p%d: appended frame %d\n", system->my_rank, data->step );
diff --git a/PuReMD/src/valence_angles.c b/PuReMD/src/valence_angles.c
index db823abd7a65444d1c2951d93701437b54aa39e7..3e90162b4bb95ef31568626ba44707e3eece5c56 100644
--- a/PuReMD/src/valence_angles.c
+++ b/PuReMD/src/valence_angles.c
@@ -107,8 +107,8 @@ void Valence_Angles( reax_system *system, control_params *control,
three_body_interaction_data *p_ijk, *p_kji;
bond_data *pbond_ij, *pbond_jk, *pbond_jt;
bond_order_data *bo_ij, *bo_jk, *bo_jt;
- reax_list *bonds = (*lists) + BONDS;
- reax_list *thb_intrs = (*lists) + THREE_BODIES;
+ reax_list *bonds = lists[BONDS];
+ reax_list *thb_intrs = lists[THREE_BODIES];
/* global parameters used in these calculations */
diff --git a/sPuReMD/src/testmd.c b/sPuReMD/src/testmd.c
index 620b8a010feaac83a66de5985076826cee7b5b6a..9ef277465c6ff5ca5235087a91cc75a29bfcd9e4 100644
--- a/sPuReMD/src/testmd.c
+++ b/sPuReMD/src/testmd.c
@@ -223,5 +223,5 @@ int main( int argc, char* argv[] )
sfree( lists, "main::lists" );
- return SUCCESS;
+ return 0;
}