diff --git a/PuReMD/src/forces.c b/PuReMD/src/forces.c
index e8693c09bee8db7d82f3b05b6a0bd1ed610a0745..2eb3a19e1ec2bd9fbe08c25ff54e662933b0bdb8 100644
--- a/PuReMD/src/forces.c
+++ b/PuReMD/src/forces.c
@@ -353,9 +353,6 @@ void Init_Forces( reax_system *system, control_params *control,
int total_sum[6];
int nt_flag;
#endif
- real t_start, t_cm_init, total_cm_init;
-
- t_cm_init = 0;
far_nbrs = lists[FAR_NBRS];
bonds = lists[BONDS];
@@ -379,7 +376,6 @@ void Init_Forces( reax_system *system, control_params *control,
renbr = (data->step - data->prev_steps) % control->reneighbor == 0;
#if defined(NEUTRAL_TERRITORY)
- t_start = MPI_Wtime();
nt_flag = 1;
if( renbr )
{
@@ -421,7 +417,6 @@ void Init_Forces( reax_system *system, control_params *control,
mark[0] = mark[1] = 1;
mark[2] = mark[3] = mark[4] = mark[5] = 2;
- t_cm_init += MPI_Wtime() - t_start;
#endif
for ( i = 0; i < system->N; ++i )
@@ -466,12 +461,10 @@ void Init_Forces( reax_system *system, control_params *control,
ihb_top = -1;
if ( local == 1 )
{
- t_start = MPI_Wtime();
H->start[i] = Htop;
H->entries[Htop].j = i;
H->entries[Htop].val = sbp_i->eta;
++Htop;
- t_cm_init += MPI_Wtime() - t_start;
if ( control->hbond_cut > 0 )
{
@@ -534,7 +527,6 @@ void Init_Forces( reax_system *system, control_params *control,
if ( local == 1 )
{
- t_start = MPI_Wtime();
/* H matrix entry */
#if defined(NEUTRAL_TERRITORY)
if ( atom_j->nt_dir > 0 || (j < system->n
@@ -580,7 +572,6 @@ void Init_Forces( reax_system *system, control_params *control,
++Htop;
}
#endif
- t_cm_init += MPI_Wtime() - t_start;
/* hydrogen bond lists */
if ( control->hbond_cut > 0 && (ihb == 1 || ihb == 2) &&
@@ -612,7 +603,6 @@ void Init_Forces( reax_system *system, control_params *control,
#if defined(NEUTRAL_TERRITORY)
else if ( local == 2 )
{
- t_start = MPI_Wtime();
/* H matrix entry */
if( ( atom_j->nt_dir != -1 && mark[atom_i->nt_dir] != mark[atom_j->nt_dir]
&& ( H->format == SYM_FULL_MATRIX
@@ -645,7 +635,6 @@ void Init_Forces( reax_system *system, control_params *control,
++Htop;
}
- t_cm_init += MPI_Wtime() - t_start;
}
#endif
@@ -670,7 +659,6 @@ void Init_Forces( reax_system *system, control_params *control,
}
Set_End_Index( i, btop_i, bonds );
- t_start = MPI_Wtime();
if ( local == 1 )
{
H->end[i] = Htop;
@@ -691,7 +679,6 @@ void Init_Forces( reax_system *system, control_params *control,
}
}
#endif
- t_cm_init += MPI_Wtime() - t_start;
}
if ( far_nbrs->format == FULL_LIST )
@@ -725,12 +712,6 @@ void Init_Forces( reax_system *system, control_params *control,
}
}
- MPI_Reduce(&t_cm_init, &total_cm_init, 1, MPI_DOUBLE, MPI_SUM, MASTER_NODE, mpi_data->world);
- if( system->my_rank == MASTER_NODE )
- {
- data->timing.init_qeq += total_cm_init / control->nprocs;
- }
-
#if defined(DEBUG)
Print_Sparse_Matrix2( system, H, NULL );
#endif
@@ -1211,7 +1192,7 @@ void Compute_Forces( reax_system *system, control_params *control,
MPI_Comm comm;
int qeq_flag;
#if defined(LOG_PERFORMANCE)
- real t_start = 0, t_elapsed;
+ real t_start, t_end;
//MPI_Barrier( mpi_data->world );
if ( system->my_rank == MASTER_NODE )
@@ -1237,14 +1218,12 @@ void Compute_Forces( reax_system *system, control_params *control,
//MPI_Barrier( mpi_data->world );
if ( system->my_rank == MASTER_NODE )
{
- //Update_Timing_Info( &t_start, &(data->timing.init_forces) );
- real t_end = MPI_Wtime();
+ t_end = MPI_Wtime();
data->timing.init_forces += t_end - t_start;
t_start = t_end;
}
#endif
-
/********* bonded interactions ************/
Compute_Bonded_Forces( system, control, data, workspace,
lists, out_control, mpi_data->world );
@@ -1253,7 +1232,9 @@ void Compute_Forces( reax_system *system, control_params *control,
//MPI_Barrier( mpi_data->world );
if ( system->my_rank == MASTER_NODE )
{
- t_start = MPI_Wtime();
+ t_end = MPI_Wtime();
+ data->timing.bonded += t_end - t_start;
+ t_start = t_end;
}
#endif
#if defined(DEBUG_FOCUS)
@@ -1262,7 +1243,6 @@ void Compute_Forces( reax_system *system, control_params *control,
MPI_Barrier( mpi_data->world );
#endif
-
/**************** qeq ************************/
#if defined(PURE_REAX)
if ( qeq_flag )
@@ -1272,8 +1252,9 @@ void Compute_Forces( reax_system *system, control_params *control,
//MPI_Barrier( mpi_data->world );
if ( system->my_rank == MASTER_NODE )
{
- t_elapsed = MPI_Wtime() - t_start;
- data->timing.cm += t_elapsed;
+ t_end = MPI_Wtime();
+ data->timing.cm += t_end - t_start;
+ t_start = t_end;
}
#endif
#if defined(DEBUG_FOCUS)
@@ -1282,7 +1263,6 @@ void Compute_Forces( reax_system *system, control_params *control,
#endif
#endif //PURE_REAX
-
/********* nonbonded interactions ************/
Compute_NonBonded_Forces( system, control, data, workspace,
lists, out_control, mpi_data->world );
@@ -1291,9 +1271,8 @@ void Compute_Forces( reax_system *system, control_params *control,
//MPI_Barrier( mpi_data->world );
if ( system->my_rank == MASTER_NODE )
{
- //Update_Timing_Info( &t_start, &(data->timing.nonb) );
- real t_end = MPI_Wtime();
- data->timing.nonb += t_end - t_start;
+ t_end = MPI_Wtime();
+ data->timing.nonb += t_end - t_start + data->timing.cm;;
t_start = t_end;
}
#endif
@@ -1303,7 +1282,6 @@ void Compute_Forces( reax_system *system, control_params *control,
MPI_Barrier( mpi_data->world );
#endif
-
/*********** total force ***************/
Compute_Total_Force( system, control, data, workspace, lists, mpi_data );
@@ -1311,10 +1289,8 @@ void Compute_Forces( reax_system *system, control_params *control,
//MPI_Barrier( mpi_data->world );
if ( system->my_rank == MASTER_NODE )
{
- //Update_Timing_Info( &t_start, &(data->timing.bonded) );
- real t_end = MPI_Wtime();
+ t_end = MPI_Wtime();
data->timing.bonded += t_end - t_start;
- t_start = t_end;
}
#endif
#if defined(DEBUG_FOCUS)
diff --git a/PuReMD/src/integrate.c b/PuReMD/src/integrate.c
index c3b2719ce8c2a306bdbf25d2a974d51e2e7c73a3..6b9d6b5ae11cda6c847f604d3a1f202927afbd6c 100644
--- a/PuReMD/src/integrate.c
+++ b/PuReMD/src/integrate.c
@@ -56,16 +56,16 @@ void Velocity_Verlet_NVE( reax_system* system, control_params* control,
/* HACK: currently required that preconditioner (re)computation step
* and reneighbor step (i.e., (re)construct far nbr list)
* are the same value, so use reneighbor for now */
- if ( renbr )
- {
- lists[FAR_NBRS]->format = FULL_LIST;
- workspace->H->format = SYM_FULL_MATRIX;
- }
- else
- {
- lists[FAR_NBRS]->format = HALF_LIST;
- workspace->H->format = SYM_HALF_MATRIX;
- }
+// if ( renbr )
+// {
+// lists[FAR_NBRS]->format = FULL_LIST;
+// workspace->H->format = SYM_FULL_MATRIX;
+// }
+// else
+// {
+// lists[FAR_NBRS]->format = HALF_LIST;
+// workspace->H->format = SYM_HALF_MATRIX;
+// }
}
for ( i = 0; i < system->n; i++ )
@@ -135,16 +135,16 @@ void Velocity_Verlet_Nose_Hoover_NVT_Klein( reax_system* system,
/* HACK: currently required that preconditioner (re)computation step
* and reneighbor step (i.e., (re)construct far nbr list)
* are the same value, so use reneighbor for now */
- if ( renbr )
- {
- lists[FAR_NBRS]->format = FULL_LIST;
- workspace->H->format = SYM_FULL_MATRIX;
- }
- else
- {
- lists[FAR_NBRS]->format = HALF_LIST;
- workspace->H->format = SYM_HALF_MATRIX;
- }
+// if ( renbr )
+// {
+// lists[FAR_NBRS]->format = FULL_LIST;
+// workspace->H->format = SYM_FULL_MATRIX;
+// }
+// else
+// {
+// lists[FAR_NBRS]->format = HALF_LIST;
+// workspace->H->format = SYM_HALF_MATRIX;
+// }
}
for ( i = 0; i < system->n; i++ )
@@ -246,16 +246,16 @@ void Velocity_Verlet_Berendsen_NVT( reax_system* system,
/* HACK: currently required that preconditioner (re)computation step
* and reneighbor step (i.e., (re)construct far nbr list)
* are the same value, so use reneighbor for now */
- if ( renbr )
- {
- lists[FAR_NBRS]->format = FULL_LIST;
- workspace->H->format = SYM_FULL_MATRIX;
- }
- else
- {
- lists[FAR_NBRS]->format = HALF_LIST;
- workspace->H->format = SYM_HALF_MATRIX;
- }
+// if ( renbr )
+// {
+// lists[FAR_NBRS]->format = FULL_LIST;
+// workspace->H->format = SYM_FULL_MATRIX;
+// }
+// else
+// {
+// lists[FAR_NBRS]->format = HALF_LIST;
+// workspace->H->format = SYM_HALF_MATRIX;
+// }
}
/* velocity verlet, 1st part */
@@ -353,16 +353,16 @@ void Velocity_Verlet_Berendsen_NPT( reax_system* system,
/* HACK: currently required that preconditioner (re)computation step
* and reneighbor step (i.e., (re)construct far nbr list)
* are the same value, so use reneighbor for now */
- if ( renbr )
- {
- lists[FAR_NBRS]->format = FULL_LIST;
- workspace->H->format = SYM_FULL_MATRIX;
- }
- else
- {
- lists[FAR_NBRS]->format = HALF_LIST;
- workspace->H->format = SYM_HALF_MATRIX;
- }
+// if ( renbr )
+// {
+// lists[FAR_NBRS]->format = FULL_LIST;
+// workspace->H->format = SYM_FULL_MATRIX;
+// }
+// else
+// {
+// lists[FAR_NBRS]->format = HALF_LIST;
+// workspace->H->format = SYM_HALF_MATRIX;
+// }
}
/* velocity verlet, 1st part */
diff --git a/PuReMD/src/linear_solvers.c b/PuReMD/src/linear_solvers.c
index 4a7b258e0102c6c0e50246684234d79f8b09d427..395c6934d98b9bb9c8bf46498b8401b57a739a19 100644
--- a/PuReMD/src/linear_solvers.c
+++ b/PuReMD/src/linear_solvers.c
@@ -188,7 +188,7 @@ real setup_sparse_approx_inverse( reax_system *system, simulation_data *data, st
{
n_local += A->end[i] - A->start[i];
}
- s_local = (int) (12.0 * log2(n_local * nprocs));
+ s_local = (int) (12.0 * (log2(n_local) + log2(nprocs)));
t_start = MPI_Wtime();
MPI_Allreduce( &n_local, &n, 1, MPI_INT, MPI_SUM, comm );