diff --git a/PuReMD/src/basic_comm.c b/PuReMD/src/basic_comm.c
index 92c834efd5a51a7fa708b546570b7992b837cf85..a6606458caeb3db30d939ecc9b10fef52a85bff7 100644
--- a/PuReMD/src/basic_comm.c
+++ b/PuReMD/src/basic_comm.c
@@ -170,19 +170,19 @@ void Dist_NT( reax_system* system, mpi_datatypes *mpi_data,
}
}
- for( d = 0; d < 6; ++d )
+ /*for( d = 0; d < 6; ++d )
{
nbr = &(system->my_nbrs[d]);
if ( nbr->atoms_cnt )
{
MPI_Wait( &(req[d]), &(stat[d]) );
}
- }
+ }*/
- /*for( d = 0; d < count; ++d )
+ for( d = 0; d < count; ++d )
{
MPI_Waitany( REAX_MAX_NT_NBRS, req, &index, stat);
- }*/
+ }
#if defined(DEBUG)
fprintf( stderr, "p%d dist: done\n", system->my_rank );
@@ -326,8 +326,7 @@ void Coll_NT( reax_system* system, mpi_datatypes *mpi_data,
if ( out_bufs[d].cnt )
{
count++;
- MPI_Irecv(in[d], out_bufs[d].cnt, type, nbr->receive_rank, d, comm, &(req[d]));
- //fprintf( stdout, "p%d coll: d = %d, receive_rank = %d, cnt = %d\n", system->my_rank, d, nbr->receive_rank, out_bufs[d].cnt );
+ MPI_Irecv(in[d], out_bufs[d].cnt, type, nbr->rank, d, comm, &(req[d]));
}
}
@@ -338,31 +337,24 @@ void Coll_NT( reax_system* system, mpi_datatypes *mpi_data,
if ( nbr->atoms_cnt )
{
MPI_Send( buf + nbr->atoms_str * scale, nbr->atoms_cnt, type,
- nbr->rank, d, comm );
- //fprintf( stdout, "p%d coll: d = %d, send_rank = %d, cnt = %d\n", system->my_rank, d, nbr->rank, nbr->atoms_cnt );
+ nbr->receive_rank, d, comm );
}
}
- for( d = 0; d < 6; ++d )
+ /*for( d = 0; d < 6; ++d )
{
- //fprintf( stderr, "p%d coll: d = %d\n", system->my_rank, d );
- //fflush( stdout );
if ( out_bufs[d].cnt )
{
MPI_Wait( &(req[d]), &(stat[d]));
- //fprintf( stderr, "p%d coll: %d status complete\n", system->my_rank, d );
- //fflush( stdout );
unpack( in[d], buf, out_bufs + d );
}
- }
- //fprintf( stderr, "p%d coll: entered\n", system->my_rank );
- fflush( stdout );
+ }*/
- /*for( d = 0; d < count; ++d )
+ for( d = 0; d < count; ++d )
{
MPI_Waitany( REAX_MAX_NT_NBRS, req, &index, stat);
unpack( in[index], buf, out_bufs + index );
- }*/
+ }
#if defined(DEBUG)
fprintf( stderr, "p%d coll: done\n", system->my_rank );
diff --git a/PuReMD/src/forces.c b/PuReMD/src/forces.c
index 93cbe8cfe3c25dcd62c6ce1f122205007d0a9565..bd9fa99da8d4ceb1db3efb0eba17f6140f1690c1 100644
--- a/PuReMD/src/forces.c
+++ b/PuReMD/src/forces.c
@@ -412,15 +412,13 @@ void Init_Forces( reax_system *system, control_params *control,
}
#endif
- //TODO: remove those variables
- int local_to_local = 0;
- //FILE *fp;
+ /*int local_to_local = 0;
+ FILE *fp;*/
#if defined(NEUTRAL_TERRITORY)
- //TODO: remove those variables
- int local_to_nt = 0;
+ /*int local_to_nt = 0;
int nt_to_local = 0;
int nt_to_nt = 0;
- //fp = fopen( "NT_Pairs.txt", "w" );
+ fp = fopen( "NT_Pairs.txt", "w" );*/
int mark[6];
mark[0] = mark[1] = 1;
mark[2] = mark[3] = mark[4] = mark[5] = 2;
@@ -474,9 +472,8 @@ void Init_Forces( reax_system *system, control_params *control,
H->entries[Htop].j = i;
H->entries[Htop].val = sbp_i->eta;
++Htop;
- //TODO:
- //fprintf( fp, "%d %d\n", atom_i->orig_id, atom_i->orig_id );
- ++local_to_local;
+ /*fprintf( fp, "%d %d\n", atom_i->orig_id, atom_i->orig_id );
+ ++local_to_local;*/
if ( control->hbond_cut > 0 )
{
@@ -547,16 +544,15 @@ void Init_Forces( reax_system *system, control_params *control,
#if defined(NEUTRAL_TERRITORY)
if( atom_j->nt_dir > 0 || j < system->n )
{
- //TODO
//fprintf( fp, "%d %d\n", atom_i->orig_id, atom_j->orig_id );
if( j < system->n )
{
- ++local_to_local;
+ //++local_to_local;
H->entries[Htop].j = j;
}
else
{
- ++local_to_nt;
+ //++local_to_nt;
H->entries[Htop].j = atom_j->pos;
}
@@ -571,10 +567,9 @@ void Init_Forces( reax_system *system, control_params *control,
++Htop;
}
#else
- //TODO
- //fprintf( fp, "%d %d\n", atom_i->orig_id, atom_j->orig_id );
+ /*fprintf( fp, "%d %d\n", atom_i->orig_id, atom_j->orig_id );
if( j < system->n )
- ++local_to_local;
+ ++local_to_local;*/
H->entries[Htop].j = j;
if ( control->tabulate == 0 )
{
@@ -619,7 +614,6 @@ void Init_Forces( reax_system *system, control_params *control,
else if ( local == 2 )
{
/* H matrix entry */
- //TODO
if( ( atom_j->nt_dir != -1 && mark[atom_i->nt_dir] != mark[atom_j->nt_dir] ) || ( j < system->n && atom_i->nt_dir != 0 ))
{
//fprintf( fp, "%d %d\n", atom_i->orig_id, atom_j->orig_id );
@@ -630,12 +624,12 @@ void Init_Forces( reax_system *system, control_params *control,
}
if( j < system->n )
{
- ++nt_to_local;
+ //++nt_to_local;
H->entries[Htop].j = j;
}
else
{
- ++nt_to_nt;
+ //++nt_to_nt;
H->entries[Htop].j = atom_j->pos;
}
@@ -726,7 +720,7 @@ void Init_Forces( reax_system *system, control_params *control,
}
}
- int Htot, localtot;
+/* int Htot, localtot;
MPI_Allreduce(&Htop, &Htot, 1, MPI_INT, MPI_SUM, MPI_COMM_WORLD);
MPI_Allreduce(&local_to_local, &localtot, 1, MPI_INT, MPI_SUM, MPI_COMM_WORLD);
@@ -748,7 +742,7 @@ void Init_Forces( reax_system *system, control_params *control,
fprintf( stdout, "total number of nt to nt entries across all matrices: %d\n", tot4 );
#endif
fflush( stdout );
- }
+ }*/
workspace->realloc.Htop = Htop;
workspace->realloc.num_bonds = num_bonds;
diff --git a/PuReMD/src/init_md.c b/PuReMD/src/init_md.c
index 9ea85cca95800896486f0655b3e895997c6ce783..4e3000b58763a22ae047c22d5806a6f1c903be1a 100644
--- a/PuReMD/src/init_md.c
+++ b/PuReMD/src/init_md.c
@@ -589,7 +589,7 @@ int Init_Lists( reax_system *system, control_params *control,
comm = mpi_data->world;
- if ( control->cm_solver_pre_comp_type == SAI_PC || 1 )
+ if ( control->cm_solver_pre_comp_type == SAI_PC )
{
far_nbr_list_format = FULL_LIST;
cm_format = SYM_FULL_MATRIX;
diff --git a/PuReMD/src/linear_solvers.c b/PuReMD/src/linear_solvers.c
index 1d1ccc9a9960f932b6132721af7ad6f795088874..f9c9345f9548a5eb031c32b9fd82bc24ea10afd3 100644
--- a/PuReMD/src/linear_solvers.c
+++ b/PuReMD/src/linear_solvers.c
@@ -1192,9 +1192,6 @@ int CG( reax_system *system, control_params *control, simulation_data *data,
storage *workspace, sparse_matrix *H, real *b,
real tol, real *x, mpi_datatypes* mpi_data, FILE *fout, int nprocs )
{
- fprintf(stdout, "%d %d\n", H->n, H->NT);
- fflush(stdout);
-
int i, j, scale;
real tmp, alpha, beta, b_norm;
real sig_old, sig_new;
@@ -1283,8 +1280,6 @@ int CG( reax_system *system, control_params *control, simulation_data *data,
for ( i = 0; i < control->cm_solver_max_iters && sqrt(sig_new) / b_norm > tol; ++i )
{
- //fprintf( stdout, "p%d, i = %d, res = %.6f\n", system->my_rank, i, sqrt(sig_new) / b_norm );
- //fflush( stdout );
t_start = Get_Time( );
#if defined(NEUTRAL_TERRITORY)
Dist_NT( system, mpi_data, workspace->d, MPI_DOUBLE, scale, real_packer );
diff --git a/PuReMD/src/reax_types.h b/PuReMD/src/reax_types.h
index 8a08c5ad572b1b818ce77b8e943fdfe5597cabd7..e91117f5e0c2603f2469d274c49e62a399f69f63 100644
--- a/PuReMD/src/reax_types.h
+++ b/PuReMD/src/reax_types.h
@@ -552,6 +552,7 @@ typedef struct
int wsize, my_rank, num_nbrs;
ivec my_coords;
neighbor_proc my_nbrs[REAX_MAX_NBRS];
+ neighbor_proc my_nt_nbrs[REAX_MAX_NT_NBRS];
int *global_offset;
simulation_box big_box, my_box, my_ext_box;
grid my_grid;
@@ -561,7 +562,6 @@ typedef struct
#if defined(NEUTRAL_TERRITORY)
int num_nt_nbrs;
- neighbor_proc my_nt_nbrs[REAX_MAX_NT_NBRS];
#endif
} reax_system;