From ad57c13b2f02e0008b63164f515856e105132da3 Mon Sep 17 00:00:00 2001
From: "Kurt A. O'Hearn" <ohearnk@msu.edu>
Date: Sat, 22 Dec 2018 16:56:19 -0500
Subject: [PATCH] PuReMD-old: minor log file formatting tweaks. Default to full
shell for now.
---
PuReMD/src/forces.c | 308 +++++++++++++++++++++++-----------------
PuReMD/src/io_tools.c | 88 +++++++-----
PuReMD/src/reax_types.h | 2 +-
3 files changed, 228 insertions(+), 170 deletions(-)
diff --git a/PuReMD/src/forces.c b/PuReMD/src/forces.c
index ff3ae3a1..0f836ff4 100644
--- a/PuReMD/src/forces.c
+++ b/PuReMD/src/forces.c
@@ -62,27 +62,33 @@ static int compare_bonds( const void *p1, const void *p2 )
}
-void Dummy_Interaction( reax_system *system, control_params *control,
- simulation_data *data, storage *workspace,
- reax_list **lists, output_controls *out_control )
+static void Dummy_Interaction( reax_system *system, control_params *control,
+ simulation_data *data, storage *workspace,
+ reax_list **lists, output_controls *out_control )
{
+ ;
}
void Init_Force_Functions( control_params *control )
{
- Interaction_Functions[0] = BO;
- Interaction_Functions[1] = Bonds; //Dummy_Interaction;
- Interaction_Functions[2] = Atom_Energy; //Dummy_Interaction;
- Interaction_Functions[3] = Valence_Angles; //Dummy_Interaction;
- Interaction_Functions[4] = Torsion_Angles; //Dummy_Interaction;
+ Interaction_Functions[0] = &BO;
+ Interaction_Functions[1] = &Bonds; //Dummy_Interaction;
+ Interaction_Functions[2] = &Atom_Energy; //Dummy_Interaction;
+ Interaction_Functions[3] = &Valence_Angles; //Dummy_Interaction;
+ Interaction_Functions[4] = &Torsion_Angles; //Dummy_Interaction;
if ( control->hbond_cut > 0 )
- Interaction_Functions[5] = Hydrogen_Bonds;
- else Interaction_Functions[5] = Dummy_Interaction;
- Interaction_Functions[6] = Dummy_Interaction; //empty
- Interaction_Functions[7] = Dummy_Interaction; //empty
- Interaction_Functions[8] = Dummy_Interaction; //empty
- Interaction_Functions[9] = Dummy_Interaction; //empty
+ {
+ Interaction_Functions[5] = &Hydrogen_Bonds;
+ }
+ else
+ {
+ Interaction_Functions[5] = &Dummy_Interaction;
+ }
+ Interaction_Functions[6] = &Dummy_Interaction; //empty
+ Interaction_Functions[7] = &Dummy_Interaction; //empty
+ Interaction_Functions[8] = &Dummy_Interaction; //empty
+ Interaction_Functions[9] = &Dummy_Interaction; //empty
}
@@ -140,7 +146,6 @@ void Compute_NonBonded_Forces( reax_system *system, control_params *control,
}
-
/* this version of Compute_Total_Force computes forces from
coefficients accumulated by all interaction functions.
Saves enormous time & space! */
@@ -190,7 +195,8 @@ void Compute_Total_Force( reax_system *system, control_params *control,
#endif
}
-void Validate_Lists( reax_system *system, storage *workspace, reax_list **lists,
+
+static void Validate_Lists( reax_system *system, storage *workspace, reax_list **lists,
int step, int n, int N, int numH, MPI_Comm comm )
{
int i, comp, Hindex;
@@ -285,7 +291,7 @@ void Validate_Lists( reax_system *system, storage *workspace, reax_list **lists,
}
-real Compute_H( real r, real gamma, real *ctap )
+static real Compute_H( real r, real gamma, real *ctap )
{
real taper, dr3gamij_1, dr3gamij_3;
@@ -303,7 +309,7 @@ real Compute_H( real r, real gamma, real *ctap )
}
-real Compute_tabH( real r_ij, int ti, int tj )
+static real Compute_tabH( real r_ij, int ti, int tj )
{
int r, tmin, tmax;
real val, dif, base;
@@ -326,9 +332,9 @@ real Compute_tabH( real r_ij, int ti, int tj )
}
-void Init_Distance( reax_system *system, control_params *control,
- simulation_data *data, storage *workspace, reax_list **lists,
- output_controls *out_control, MPI_Comm comm, mpi_datatypes *mpi_data )
+static void Init_Distance( reax_system *system, control_params *control,
+ simulation_data *data, storage *workspace, reax_list **lists,
+ output_controls *out_control, MPI_Comm comm, mpi_datatypes *mpi_data )
{
int i, j, pj;
int start_i, end_i;
@@ -350,9 +356,9 @@ void Init_Distance( reax_system *system, control_params *control,
/* update i-j distance for non-reneighboring steps */
for ( pj = start_i; pj < end_i; ++pj )
{
- nbr_pj = &( far_nbrs->far_nbr_list[pj] );
+ nbr_pj = &far_nbrs->far_nbr_list[pj];
j = nbr_pj->nbr;
- atom_j = &(system->my_atoms[j]);
+ atom_j = &system->my_atoms[j];
if ( !renbr )
{
@@ -360,7 +366,7 @@ void Init_Distance( reax_system *system, control_params *control,
nbr_pj->dvec[1] = atom_j->x[1] - atom_i->x[1];
nbr_pj->dvec[2] = atom_j->x[2] - atom_i->x[2];
nbr_pj->d = rvec_Norm_Sqr( nbr_pj->dvec );
- nbr_pj->d = sqrt(nbr_pj->d);
+ nbr_pj->d = sqrt( nbr_pj->d );
}
}
@@ -369,9 +375,9 @@ void Init_Distance( reax_system *system, control_params *control,
#if defined(NEUTRAL_TERRITORY)
-void Init_CM_Half_NT( reax_system *system, control_params *control,
- simulation_data *data, storage *workspace, reax_list **lists,
- output_controls *out_control, MPI_Comm comm, mpi_datatypes *mpi_data )
+static void Init_CM_Half_NT( reax_system *system, control_params *control,
+ simulation_data *data, storage *workspace, reax_list **lists,
+ output_controls *out_control, MPI_Comm comm, mpi_datatypes *mpi_data )
{
int i, j, pj;
int start_i, end_i;
@@ -443,9 +449,9 @@ void Init_CM_Half_NT( reax_system *system, control_params *control,
for ( i = 0; i < system->N; ++i )
{
atom_i = &system->my_atoms[i];
- type_i = atom_i->type;
- start_i = Start_Index(i, far_nbrs);
- end_i = End_Index(i, far_nbrs);
+ type_i = atom_i->type;
+ start_i = Start_Index( i, far_nbrs );
+ end_i = End_Index( i, far_nbrs );
sbp_i = &system->reax_param.sbp[type_i];
@@ -476,9 +482,10 @@ void Init_CM_Half_NT( reax_system *system, control_params *control,
for ( pj = start_i; pj < end_i; ++pj )
{
- nbr_pj = &( far_nbrs->far_nbr_list[pj] );
+ nbr_pj = &far_nbrs->far_nbr_list[pj];
j = nbr_pj->nbr;
- atom_j = &(system->my_atoms[j]);
+ atom_j = &system->my_atoms[j];
+
if ( nbr_pj->d <= cutoff )
{
flag = 1;
@@ -492,14 +499,14 @@ void Init_CM_Half_NT( reax_system *system, control_params *control,
{
type_j = atom_j->type;
r_ij = nbr_pj->d;
- twbp = &(system->reax_param.tbp[type_i][type_j]);
+ twbp = &system->reax_param.tbp[type_i][type_j];
if ( local == 1 )
{
/* H matrix entry */
- if ( atom_j->nt_dir > 0 || (j < system->n && i < j))
+ if ( atom_j->nt_dir > 0 || (j < system->n && i < j) )
{
- if( j < system->n )
+ if ( j < system->n )
{
H->entries[Htop].j = j;
}
@@ -510,11 +517,11 @@ void Init_CM_Half_NT( reax_system *system, control_params *control,
if ( control->tabulate == 0 )
{
- H->entries[Htop].val = Compute_H(r_ij, twbp->gamma, workspace->Tap);
+ H->entries[Htop].val = Compute_H( r_ij, twbp->gamma, workspace->Tap );
}
else
{
- H->entries[Htop].val = Compute_tabH(r_ij, type_i, type_j);
+ H->entries[Htop].val = Compute_tabH( r_ij, type_i, type_j );
}
++Htop;
@@ -524,15 +531,17 @@ void Init_CM_Half_NT( reax_system *system, control_params *control,
else if ( local == 2 )
{
/* H matrix entry */
- if ( atom_j->nt_dir != -1 && mark[atom_i->nt_dir] != mark[atom_j->nt_dir] && atom_i->pos < atom_j->pos )
+ if ( atom_j->nt_dir != -1
+ && mark[atom_i->nt_dir] != mark[atom_j->nt_dir]
+ && atom_i->pos < atom_j->pos )
{
- if( !nt_flag )
+ if ( !nt_flag )
{
nt_flag = 1;
H->start[atom_i->pos] = Htop;
}
- if( j < system->n )
+ if ( j < system->n )
{
H->entries[Htop].j = j;
}
@@ -543,11 +552,11 @@ void Init_CM_Half_NT( reax_system *system, control_params *control,
if ( control->tabulate == 0 )
{
- H->entries[Htop].val = Compute_H(r_ij, twbp->gamma, workspace->Tap);
+ H->entries[Htop].val = Compute_H( r_ij, twbp->gamma, workspace->Tap );
}
else
{
- H->entries[Htop].val = Compute_tabH(r_ij, type_i, type_j);
+ H->entries[Htop].val = Compute_tabH( r_ij, type_i, type_j );
}
++Htop;
@@ -563,7 +572,7 @@ void Init_CM_Half_NT( reax_system *system, control_params *control,
}
else if ( local == 2 )
{
- if( nt_flag )
+ if ( nt_flag )
{
H->end[atom_i->pos] = Htop;
}
@@ -592,9 +601,9 @@ void Init_CM_Half_NT( reax_system *system, control_params *control,
}
-void Init_CM_Full_NT( reax_system *system, control_params *control,
- simulation_data *data, storage *workspace, reax_list **lists,
- output_controls *out_control, MPI_Comm comm, mpi_datatypes *mpi_data )
+static void Init_CM_Full_NT( reax_system *system, control_params *control,
+ simulation_data *data, storage *workspace, reax_list **lists,
+ output_controls *out_control, MPI_Comm comm, mpi_datatypes *mpi_data )
{
int i, j, pj;
int start_i, end_i;
@@ -622,7 +631,7 @@ void Init_CM_Full_NT( reax_system *system, control_params *control,
renbr = (data->step - data->prev_steps) % control->reneighbor == 0;
nt_flag = 1;
- if( renbr )
+ if ( renbr )
{
for ( i = 0; i < 6; ++i )
{
@@ -635,7 +644,7 @@ void Init_CM_Full_NT( reax_system *system, control_params *control,
{
atom_i = &system->my_atoms[i];
- if( atom_i->nt_dir != -1 )
+ if ( atom_i->nt_dir != -1 )
{
total_cnt[ atom_i->nt_dir ]++;
}
@@ -651,7 +660,7 @@ void Init_CM_Full_NT( reax_system *system, control_params *control,
{
atom_i = &system->my_atoms[i];
- if( atom_i->nt_dir != -1 )
+ if ( atom_i->nt_dir != -1 )
{
atom_i->pos = total_sum[ atom_i->nt_dir ] + bin[ atom_i->nt_dir ];
bin[ atom_i->nt_dir ]++;
@@ -666,9 +675,9 @@ void Init_CM_Full_NT( reax_system *system, control_params *control,
for ( i = 0; i < system->N; ++i )
{
atom_i = &system->my_atoms[i];
- type_i = atom_i->type;
- start_i = Start_Index(i, far_nbrs);
- end_i = End_Index(i, far_nbrs);
+ type_i = atom_i->type;
+ start_i = Start_Index( i, far_nbrs );
+ end_i = End_Index( i, far_nbrs );
sbp_i = &system->reax_param.sbp[type_i];
@@ -699,9 +708,10 @@ void Init_CM_Full_NT( reax_system *system, control_params *control,
for ( pj = start_i; pj < end_i; ++pj )
{
- nbr_pj = &( far_nbrs->far_nbr_list[pj] );
+ nbr_pj = &far_nbrs->far_nbr_list[pj];
j = nbr_pj->nbr;
- atom_j = &(system->my_atoms[j]);
+ atom_j = &system->my_atoms[j];
+
if ( nbr_pj->d <= cutoff )
{
flag = 1;
@@ -715,14 +725,14 @@ void Init_CM_Full_NT( reax_system *system, control_params *control,
{
type_j = atom_j->type;
r_ij = nbr_pj->d;
- twbp = &(system->reax_param.tbp[type_i][type_j]);
+ twbp = &system->reax_param.tbp[type_i][type_j];
if ( local == 1 )
{
/* H matrix entry */
if ( atom_j->nt_dir > 0 || (j < system->n) )
{
- if( j < system->n )
+ if ( j < system->n )
{
H->entries[Htop].j = j;
}
@@ -747,16 +757,17 @@ void Init_CM_Full_NT( reax_system *system, control_params *control,
else if ( local == 2 )
{
/* H matrix entry */
- if( ( atom_j->nt_dir != -1 && mark[atom_i->nt_dir] != mark[atom_j->nt_dir] ) ||
- ( j < system->n && atom_i->nt_dir != 0 ) )
+ if ( ( atom_j->nt_dir != -1
+ && mark[atom_i->nt_dir] != mark[atom_j->nt_dir] )
+ || ( j < system->n && atom_i->nt_dir != 0 ) )
{
- if( !nt_flag )
+ if ( !nt_flag )
{
nt_flag = 1;
H->start[atom_i->pos] = Htop;
}
- if( j < system->n )
+ if ( j < system->n )
{
H->entries[Htop].j = j;
}
@@ -767,11 +778,11 @@ void Init_CM_Full_NT( reax_system *system, control_params *control,
if ( control->tabulate == 0 )
{
- H->entries[Htop].val = Compute_H(r_ij, twbp->gamma, workspace->Tap);
+ H->entries[Htop].val = Compute_H( r_ij, twbp->gamma, workspace->Tap );
}
else
{
- H->entries[Htop].val = Compute_tabH(r_ij, type_i, type_j);
+ H->entries[Htop].val = Compute_tabH( r_ij, type_i, type_j );
}
++Htop;
@@ -787,7 +798,7 @@ void Init_CM_Full_NT( reax_system *system, control_params *control,
}
else if ( local == 2 )
{
- if( nt_flag )
+ if ( nt_flag )
{
H->end[atom_i->pos] = Htop;
}
@@ -817,9 +828,9 @@ void Init_CM_Full_NT( reax_system *system, control_params *control,
#else
-void Init_CM_Half_FS( reax_system *system, control_params *control,
- simulation_data *data, storage *workspace, reax_list **lists,
- output_controls *out_control, MPI_Comm comm, mpi_datatypes *mpi_data )
+static void Init_CM_Half_FS( reax_system *system, control_params *control,
+ simulation_data *data, storage *workspace, reax_list **lists,
+ output_controls *out_control, MPI_Comm comm, mpi_datatypes *mpi_data )
{
int i, j, pj;
int start_i, end_i;
@@ -843,9 +854,9 @@ void Init_CM_Half_FS( reax_system *system, control_params *control,
for ( i = 0; i < system->N; ++i )
{
atom_i = &system->my_atoms[i];
- type_i = atom_i->type;
- start_i = Start_Index(i, far_nbrs);
- end_i = End_Index(i, far_nbrs);
+ type_i = atom_i->type;
+ start_i = Start_Index( i, far_nbrs );
+ end_i = End_Index( i, far_nbrs );
sbp_i = &system->reax_param.sbp[type_i];
@@ -870,11 +881,11 @@ void Init_CM_Half_FS( reax_system *system, control_params *control,
for ( pj = start_i; pj < end_i; ++pj )
{
- nbr_pj = &( far_nbrs->far_nbr_list[pj] );
+ nbr_pj = &far_nbrs->far_nbr_list[pj];
j = nbr_pj->nbr;
- atom_j = &(system->my_atoms[j]);
+ atom_j = &system->my_atoms[j];
- if (nbr_pj->d <= cutoff)
+ if ( nbr_pj->d <= cutoff )
{
flag = 1;
}
@@ -887,7 +898,7 @@ void Init_CM_Half_FS( reax_system *system, control_params *control,
{
type_j = atom_j->type;
r_ij = nbr_pj->d;
- twbp = &(system->reax_param.tbp[type_i][type_j]);
+ twbp = &system->reax_param.tbp[type_i][type_j];
if ( local )
{
@@ -898,11 +909,11 @@ void Init_CM_Half_FS( reax_system *system, control_params *control,
if ( control->tabulate == 0 )
{
- H->entries[Htop].val = Compute_H(r_ij, twbp->gamma, workspace->Tap);
+ H->entries[Htop].val = Compute_H( r_ij, twbp->gamma, workspace->Tap );
}
else
{
- H->entries[Htop].val = Compute_tabH(r_ij, type_i, type_j);
+ H->entries[Htop].val = Compute_tabH( r_ij, type_i, type_j );
}
++Htop;
@@ -933,9 +944,9 @@ void Init_CM_Half_FS( reax_system *system, control_params *control,
}
-void Init_CM_Full_FS( reax_system *system, control_params *control,
- simulation_data *data, storage *workspace, reax_list **lists,
- output_controls *out_control, MPI_Comm comm, mpi_datatypes *mpi_data )
+static void Init_CM_Full_FS( reax_system *system, control_params *control,
+ simulation_data *data, storage *workspace, reax_list **lists,
+ output_controls *out_control, MPI_Comm comm, mpi_datatypes *mpi_data )
{
int i, j, pj;
int start_i, end_i;
@@ -959,9 +970,9 @@ void Init_CM_Full_FS( reax_system *system, control_params *control,
for ( i = 0; i < system->N; ++i )
{
atom_i = &system->my_atoms[i];
- type_i = atom_i->type;
- start_i = Start_Index(i, far_nbrs);
- end_i = End_Index(i, far_nbrs);
+ type_i = atom_i->type;
+ start_i = Start_Index( i, far_nbrs );
+ end_i = End_Index( i, far_nbrs );
sbp_i = &system->reax_param.sbp[type_i];
@@ -986,11 +997,11 @@ void Init_CM_Full_FS( reax_system *system, control_params *control,
for ( pj = start_i; pj < end_i; ++pj )
{
- nbr_pj = &( far_nbrs->far_nbr_list[pj] );
+ nbr_pj = &far_nbrs->far_nbr_list[pj];
j = nbr_pj->nbr;
- atom_j = &(system->my_atoms[j]);
+ atom_j = &system->my_atoms[j];
- if (nbr_pj->d <= cutoff)
+ if ( nbr_pj->d <= cutoff )
{
flag = 1;
}
@@ -1003,7 +1014,7 @@ void Init_CM_Full_FS( reax_system *system, control_params *control,
{
type_j = atom_j->type;
r_ij = nbr_pj->d;
- twbp = &(system->reax_param.tbp[type_i][type_j]);
+ twbp = &system->reax_param.tbp[type_i][type_j];
if ( local )
{
@@ -1047,9 +1058,9 @@ void Init_CM_Full_FS( reax_system *system, control_params *control,
#endif
-void Init_Bond_Half( reax_system *system, control_params *control,
- simulation_data *data, storage *workspace, reax_list **lists,
- output_controls *out_control, MPI_Comm comm, mpi_datatypes *mpi_data )
+static void Init_Bond_Half( reax_system *system, control_params *control,
+ simulation_data *data, storage *workspace, reax_list **lists,
+ output_controls *out_control, MPI_Comm comm, mpi_datatypes *mpi_data )
{
int i, j, pj;
int start_i, end_i;
@@ -1069,9 +1080,10 @@ void Init_Bond_Half( reax_system *system, control_params *control,
bonds = lists[BONDS];
hbonds = lists[HBONDS];
-
for ( i = 0; i < system->n; ++i )
+ {
workspace->bond_mark[i] = 0;
+ }
for ( i = system->n; i < system->N; ++i )
{
workspace->bond_mark[i] = 1000; // put ghost atoms to an infinite distance
@@ -1085,9 +1097,9 @@ void Init_Bond_Half( reax_system *system, control_params *control,
for ( i = 0; i < system->N; ++i )
{
atom_i = &system->my_atoms[i];
- type_i = atom_i->type;
- start_i = Start_Index(i, far_nbrs);
- end_i = End_Index(i, far_nbrs);
+ type_i = atom_i->type;
+ start_i = Start_Index( i, far_nbrs );
+ end_i = End_Index( i, far_nbrs );
/* start at end because other atoms
* can add to this atom's list (half-list) */
@@ -1128,11 +1140,11 @@ void Init_Bond_Half( reax_system *system, control_params *control,
/* update i-j distance - check if j is within cutoff */
for ( pj = start_i; pj < end_i; ++pj )
{
- nbr_pj = &( far_nbrs->far_nbr_list[pj] );
+ nbr_pj = &far_nbrs->far_nbr_list[pj];
j = nbr_pj->nbr;
- atom_j = &(system->my_atoms[j]);
+ atom_j = &system->my_atoms[j];
- if (nbr_pj->d <= cutoff)
+ if ( nbr_pj->d <= cutoff )
{
flag = 1;
}
@@ -1144,17 +1156,19 @@ void Init_Bond_Half( reax_system *system, control_params *control,
if ( flag )
{
type_j = atom_j->type;
- sbp_j = &(system->reax_param.sbp[type_j]);
- twbp = &(system->reax_param.tbp[type_i][type_j]);
+ sbp_j = &system->reax_param.sbp[type_j];
+ twbp = &system->reax_param.tbp[type_i][type_j];
if ( local == 1 )
{
/* hydrogen bond lists */
- if ( control->hbond_cut > 0 && (ihb == 1 || ihb == 2) &&
- nbr_pj->d <= control->hbond_cut )
+ if ( control->hbond_cut > 0
+ && (ihb == 1 || ihb == 2)
+ && nbr_pj->d <= control->hbond_cut )
{
// fprintf( stderr, "%d %d\n", atom1, atom2 );
jhb = sbp_j->p_hbond;
+
if ( ihb == 1 && jhb == 2 )
{
hbonds->hbond_list[ihb_top].nbr = j;
@@ -1178,8 +1192,8 @@ void Init_Bond_Half( reax_system *system, control_params *control,
/* uncorrected bond orders */
if ( //(workspace->bond_mark[i] < 3 || workspace->bond_mark[j] < 3) &&
- nbr_pj->d <= control->bond_cut &&
- BOp( workspace, bonds, control->bo_cut,
+ nbr_pj->d <= control->bond_cut
+ && BOp( workspace, bonds, control->bo_cut,
i, btop_i, nbr_pj, far_nbrs->format,
sbp_i, sbp_j, twbp ) )
{
@@ -1187,7 +1201,9 @@ void Init_Bond_Half( reax_system *system, control_params *control,
++btop_i;
if ( workspace->bond_mark[j] > workspace->bond_mark[i] + 1 )
+ {
workspace->bond_mark[j] = workspace->bond_mark[i] + 1;
+ }
else if ( workspace->bond_mark[i] > workspace->bond_mark[j] + 1 )
{
workspace->bond_mark[i] = workspace->bond_mark[j] + 1;
@@ -1197,10 +1213,13 @@ void Init_Bond_Half( reax_system *system, control_params *control,
}
Set_End_Index( i, btop_i, bonds );
+
if ( local == 1 )
{
if ( ihb == 1 )
+ {
Set_End_Index( atom_i->Hindex, ihb_top, hbonds );
+ }
}
}
@@ -1219,14 +1238,14 @@ void Init_Bond_Half( reax_system *system, control_params *control,
#endif
Validate_Lists( system, workspace, lists, data->step,
- system->n, system->N, system->numH, comm );
+ system->n, system->N, system->numH, comm );
}
-void Init_Bond_Full( reax_system *system, control_params *control,
- simulation_data *data, storage *workspace, reax_list **lists,
- output_controls *out_control, MPI_Comm comm, mpi_datatypes *mpi_data )
+static void Init_Bond_Full( reax_system *system, control_params *control,
+ simulation_data *data, storage *workspace, reax_list **lists,
+ output_controls *out_control, MPI_Comm comm, mpi_datatypes *mpi_data )
{
int i, j, pj;
int start_i, end_i;
@@ -1249,7 +1268,9 @@ void Init_Bond_Full( reax_system *system, control_params *control,
for ( i = 0; i < system->n; ++i )
+ {
workspace->bond_mark[i] = 0;
+ }
for ( i = system->n; i < system->N; ++i )
{
workspace->bond_mark[i] = 1000; // put ghost atoms to an infinite distance
@@ -1263,9 +1284,9 @@ void Init_Bond_Full( reax_system *system, control_params *control,
for ( i = 0; i < system->N; ++i )
{
atom_i = &system->my_atoms[i];
- type_i = atom_i->type;
- start_i = Start_Index(i, far_nbrs);
- end_i = End_Index(i, far_nbrs);
+ type_i = atom_i->type;
+ start_i = Start_Index( i, far_nbrs );
+ end_i = End_Index( i, far_nbrs );
btop_i = Start_Index( i, bonds );
sbp_i = &system->reax_param.sbp[type_i];
@@ -1288,6 +1309,7 @@ void Init_Bond_Full( reax_system *system, control_params *control,
if ( control->hbond_cut > 0 )
{
ihb = sbp_i->p_hbond;
+
if ( ihb == 1 )
{
ihb_top = Start_Index( atom_i->Hindex, hbonds );
@@ -1302,11 +1324,11 @@ void Init_Bond_Full( reax_system *system, control_params *control,
/* update i-j distance - check if j is within cutoff */
for ( pj = start_i; pj < end_i; ++pj )
{
- nbr_pj = &( far_nbrs->far_nbr_list[pj] );
+ nbr_pj = &far_nbrs->far_nbr_list[pj];
j = nbr_pj->nbr;
- atom_j = &(system->my_atoms[j]);
+ atom_j = &system->my_atoms[j];
- if (nbr_pj->d <= cutoff)
+ if ( nbr_pj->d <= cutoff )
{
flag = 1;
}
@@ -1318,17 +1340,19 @@ void Init_Bond_Full( reax_system *system, control_params *control,
if ( flag )
{
type_j = atom_j->type;
- sbp_j = &(system->reax_param.sbp[type_j]);
- twbp = &(system->reax_param.tbp[type_i][type_j]);
+ sbp_j = &system->reax_param.sbp[type_j];
+ twbp = &system->reax_param.tbp[type_i][type_j];
if ( local == 1 )
{
/* hydrogen bond lists */
- if ( control->hbond_cut > 0 && (ihb == 1 || ihb == 2) &&
- nbr_pj->d <= control->hbond_cut )
+ if ( control->hbond_cut > 0
+ && (ihb == 1 || ihb == 2)
+ && nbr_pj->d <= control->hbond_cut )
{
// fprintf( stderr, "%d %d\n", atom1, atom2 );
jhb = sbp_j->p_hbond;
+
if ( ihb == 1 && jhb == 2 )
{
hbonds->hbond_list[ihb_top].nbr = j;
@@ -1342,8 +1366,8 @@ void Init_Bond_Full( reax_system *system, control_params *control,
/* uncorrected bond orders */
if ( //(workspace->bond_mark[i] < 3 || workspace->bond_mark[j] < 3) &&
- nbr_pj->d <= control->bond_cut &&
- BOp( workspace, bonds, control->bo_cut,
+ nbr_pj->d <= control->bond_cut
+ && BOp( workspace, bonds, control->bo_cut,
i, btop_i, nbr_pj, far_nbrs->format,
sbp_i, sbp_j, twbp ) )
{
@@ -1351,7 +1375,9 @@ void Init_Bond_Full( reax_system *system, control_params *control,
++btop_i;
if ( workspace->bond_mark[j] > workspace->bond_mark[i] + 1 )
+ {
workspace->bond_mark[j] = workspace->bond_mark[i] + 1;
+ }
else if ( workspace->bond_mark[i] > workspace->bond_mark[j] + 1 )
{
workspace->bond_mark[i] = workspace->bond_mark[j] + 1;
@@ -1361,16 +1387,21 @@ void Init_Bond_Full( reax_system *system, control_params *control,
}
Set_End_Index( i, btop_i, bonds );
+
if ( local == 1 )
{
if ( ihb == 1 )
+ {
Set_End_Index( atom_i->Hindex, ihb_top, hbonds );
+ }
}
}
for( i = 0; i < system->N; ++i )
+ {
qsort( &bonds->bond_list[Start_Index(i, bonds)],
Num_Entries(i, bonds), sizeof(bond_data), compare_bonds );
+ }
/* set sym_index for bonds list (far_nbrs full list) */
for ( i = 0; i < system->N; ++i )
@@ -1410,7 +1441,7 @@ void Init_Bond_Full( reax_system *system, control_params *control,
#endif
Validate_Lists( system, workspace, lists, data->step,
- system->n, system->N, system->numH, comm );
+ system->n, system->N, system->numH, comm );
}
@@ -1422,11 +1453,11 @@ void Init_Forces( reax_system *system, control_params *control,
double t_start, t_dist, t_cm, t_bond;
double timings[3], t_total[3];
- t_start = MPI_Wtime();
+ t_start = MPI_Wtime( );
Init_Distance( system, control, data, workspace, lists, out_control, comm, mpi_data );
- t_dist = MPI_Wtime();
+ t_dist = MPI_Wtime( );
#if defined(NEUTRAL_TERRITORY)
if ( workspace->H->format == SYM_HALF_MATRIX )
@@ -1465,7 +1496,7 @@ void Init_Forces( reax_system *system, control_params *control,
timings[1] = t_cm - t_dist;
timings[2] = t_bond - t_cm;
- MPI_Reduce(timings, t_total, 3, MPI_DOUBLE, MPI_SUM, MASTER_NODE, mpi_data->world);
+ MPI_Reduce( timings, t_total, 3, MPI_DOUBLE, MPI_SUM, MASTER_NODE, mpi_data->world );
if ( system->my_rank == MASTER_NODE )
{
@@ -1898,9 +1929,8 @@ void Init_Forces( reax_system *system, control_params *control,
void Init_Forces_noQEq( reax_system *system, control_params *control,
- simulation_data *data, storage *workspace,
- reax_list **lists, output_controls *out_control,
- MPI_Comm comm )
+ simulation_data *data, storage *workspace,
+ reax_list **lists, output_controls *out_control, MPI_Comm comm )
{
int i, j, pj;
int start_i, end_i;
@@ -2343,33 +2373,45 @@ void Compute_Forces( reax_system *system, control_params *control,
MPI_Comm comm;
int qeq_flag;
#if defined(LOG_PERFORMANCE)
- real t_start, t_end;
+ real t_start = 0.0, t_end;
//MPI_Barrier( mpi_data->world );
if ( system->my_rank == MASTER_NODE )
+ {
t_start = MPI_Wtime();
+ }
#endif
-
comm = mpi_data->world;
+
/********* init forces ************/
#if defined(PURE_REAX)
if ( control->charge_freq && (data->step - data->prev_steps) % control->charge_freq == 0 )
+ {
qeq_flag = 1;
- else qeq_flag = 0;
+ }
+ else
+ {
+ qeq_flag = 0;
+ }
#elif defined(LAMMPS_REAX)
qeq_flag = 0;
#endif
+
if ( qeq_flag )
+ {
Init_Forces( system, control, data, workspace, lists, out_control, comm, mpi_data );
+ }
else
+ {
Init_Forces_noQEq( system, control, data, workspace,
- lists, out_control, comm );
+ lists, out_control, comm );
+ }
#if defined(LOG_PERFORMANCE)
//MPI_Barrier( mpi_data->world );
if ( system->my_rank == MASTER_NODE )
{
- t_end = MPI_Wtime();
+ t_end = MPI_Wtime( );
data->timing.init_forces += t_end - t_start;
t_start = t_end;
}
@@ -2383,7 +2425,7 @@ void Compute_Forces( reax_system *system, control_params *control,
//MPI_Barrier( mpi_data->world );
if ( system->my_rank == MASTER_NODE )
{
- t_end = MPI_Wtime();
+ t_end = MPI_Wtime( );
data->timing.bonded += t_end - t_start;
t_start = t_end;
}
@@ -2403,7 +2445,7 @@ void Compute_Forces( reax_system *system, control_params *control,
//MPI_Barrier( mpi_data->world );
if ( system->my_rank == MASTER_NODE )
{
- t_end = MPI_Wtime();
+ t_end = MPI_Wtime( );
data->timing.cm += t_end - t_start;
t_start = t_end;
}
@@ -2422,7 +2464,7 @@ void Compute_Forces( reax_system *system, control_params *control,
//MPI_Barrier( mpi_data->world );
if ( system->my_rank == MASTER_NODE )
{
- t_end = MPI_Wtime();
+ t_end = MPI_Wtime( );
data->timing.nonb += t_end - t_start + data->timing.cm;;
t_start = t_end;
}
@@ -2440,7 +2482,7 @@ void Compute_Forces( reax_system *system, control_params *control,
//MPI_Barrier( mpi_data->world );
if ( system->my_rank == MASTER_NODE )
{
- t_end = MPI_Wtime();
+ t_end = MPI_Wtime( );
data->timing.bonded += t_end - t_start;
}
#endif
diff --git a/PuReMD/src/io_tools.c b/PuReMD/src/io_tools.c
index 07c92cae..308086ea 100644
--- a/PuReMD/src/io_tools.c
+++ b/PuReMD/src/io_tools.c
@@ -99,10 +99,10 @@ int Init_Output_Files( reax_system *system, control_params *control,
sprintf( temp, "%s.log", control->sim_name );
out_control->log = sfopen( temp, "w", "Init_Output_Files" );
fprintf( out_control->log, "%-6s %10s %10s %10s %10s %10s %10s %10s %10s %10s %10s %10s %10s %10s %10s %10s %10s %10s %10s %10s %10s\n",
- "step", "total", "comm", "neighbors", "init", "bonded", "nonbonded",
- "Init Dist", "Init CM", "Init Bond",
- "CM", "CM Sort", "S iters", "Pre Comp", "Pre App", "S comm", "S allr",
- "S spmv", "S vec ops", "S orthog", "S tsolve" );
+ "step", "total", "comm", "neighbors", "init",
+ "init_dist", "init_cm", "init_bond", "bonded", "nonbonded",
+ "cm", "cm_sort", "s_iters", "pre_comp", "pre_app", "s_comm", "s_allr",
+ "s_spmv", "s_vec_ops", "s_orthog", "s_tsolve" );
fflush( out_control->log );
#endif
}
@@ -222,7 +222,7 @@ int Init_Output_Files( reax_system *system, control_params *control,
{
/* open bond forces file */
sprintf( temp, "%s.fbond", control->sim_name );
- Output_Files" )) == NULL )
+ out_control->fbond = sfopen( temp, "w", "Init_Output_Files" );
/* open lone-pair forces file */
sprintf( temp, "%s.flp", control->sim_name );
@@ -763,10 +763,12 @@ void Print_Symmetric_Sparse(reax_system *system, sparse_matrix *A, char *fname)
void Print_Linear_System( reax_system *system, control_params *control,
storage *workspace, int step )
{
- int i, j;
- char fname[100];
- reax_atom *ai, *aj;
- sparse_matrix *H;
+ int i;
+// int j;
+ char fname[100];
+ reax_atom *ai;
+// reax_atom *aj;
+// sparse_matrix *H;
FILE *out;
// print rhs and init guesses for QEq
@@ -787,26 +789,35 @@ void Print_Linear_System( reax_system *system, control_params *control,
Print_Symmetric_Sparse( system, workspace->H, fname );
// print the incomplete H matrix
- /*sprintf( fname, "%s.p%dHinc%d", control->sim_name, system->my_rank, step );
- out = sfopen( fname, "w", "Print_Linear_System" );
- H = workspace->H;
- for( i = 0; i < H->n; ++i ) {
- ai = &(system->my_atoms[i]);
- for( j = H->start[i]; j < H->end[i]; ++j )
- if( H->entries[j].j < system->n ) {
- aj = &(system->my_atoms[H->entries[j].j]);
- fprintf( out, "%d %d %.15e\n",
- ai->orig_id, aj->orig_id, H->entries[j].val );
- if( ai->orig_id != aj->orig_id )
- fprintf( out, "%d %d %.15e\n",
- aj->orig_id, ai->orig_id, H->entries[j].val );
- }
- }
- sfclose( out, "Print_Linear_System" );*/
+// sprintf( fname, "%s.p%dHinc%d", control->sim_name, system->my_rank, step );
+// out = sfopen( fname, "w", "Print_Linear_System" );
+// H = workspace->H;
+//
+// for( i = 0; i < H->n; ++i )
+// {
+// ai = &(system->my_atoms[i]);
+//
+// for( j = H->start[i]; j < H->end[i]; ++j )
+// {
+// if( H->entries[j].j < system->n ) {
+// aj = &(system->my_atoms[H->entries[j].j]);
+//
+// fprintf( out, "%d %d %.15e\n",
+// ai->orig_id, aj->orig_id, H->entries[j].val );
+//
+// if( ai->orig_id != aj->orig_id )
+// {
+// fprintf( out, "%d %d %.15e\n",
+// aj->orig_id, ai->orig_id, H->entries[j].val );
+// }
+// }
+// }
+// }
+// sfclose( out, "Print_Linear_System" );
// print the L from incomplete cholesky decomposition
- /*sprintf( fname, "%s.p%dL%d", control->sim_name, system->my_rank, step );
- Print_Sparse_Matrix2( system, workspace->L, fname );*/
+// sprintf( fname, "%s.p%dL%d", control->sim_name, system->my_rank, step );
+// Print_Sparse_Matrix2( system, workspace->L, fname );
}
@@ -1096,8 +1107,13 @@ void Output_Results( reax_system *system, control_params *control,
#if defined(LOG_PERFORMANCE)
t_elapsed = MPI_Wtime() - data->timing.total;
if ( data->step - data->prev_steps > 0 )
+ {
denom = 1.0 / out_control->energy_update_freq;
- else denom = 1;
+ }
+ else
+ {
+ denom = 1.0;
+ }
fprintf( out_control->log, "%6d %10.2f %10.2f %10.2f %10.2f %10.2f %10.2f %10.4f %10.4f %10.4f %10.4f %10.4f %10.2f %10.4f %10.4f %10.4f %10.4f %10.4f %10.4f %10.4f %10.4f\n",
data->step,
@@ -1105,14 +1121,14 @@ void Output_Results( reax_system *system, control_params *control,
data->timing.comm * denom,
data->timing.nbrs * denom,
data->timing.init_forces * denom,
- data->timing.bonded * denom,
- data->timing.nonb * denom,
data->timing.init_dist * denom,
data->timing.init_cm * denom,
data->timing.init_bond * denom,
+ data->timing.bonded * denom,
+ data->timing.nonb * denom,
data->timing.cm * denom,
data->timing.cm_sort * denom,
- (double)( data->timing.cm_solver_iters * denom),
+ (double)(data->timing.cm_solver_iters * denom),
data->timing.cm_solver_pre_comp * denom,
data->timing.cm_solver_pre_app * denom,
data->timing.cm_solver_comm * denom,
@@ -1123,15 +1139,15 @@ void Output_Results( reax_system *system, control_params *control,
data->timing.cm_solver_tri_solve * denom );
//Reset_Timing( &(data->timing) );
- data->timing.total = MPI_Wtime();
+ data->timing.total = MPI_Wtime( );
data->timing.comm = ZERO;
- data->timing.nbrs = 0;
- data->timing.init_forces = 0;
- data->timing.bonded = 0;
- data->timing.nonb = 0;
+ data->timing.nbrs = ZERO;
+ data->timing.init_forces = ZERO;
data->timing.init_dist = ZERO;
data->timing.init_cm = ZERO;
data->timing.init_bond = ZERO;
+ data->timing.bonded = ZERO;
+ data->timing.nonb = ZERO;
data->timing.cm = ZERO;
data->timing.cm_sort = ZERO;
data->timing.cm_solver_pre_comp = ZERO;
diff --git a/PuReMD/src/reax_types.h b/PuReMD/src/reax_types.h
index 72d6dc20..b99f95d3 100644
--- a/PuReMD/src/reax_types.h
+++ b/PuReMD/src/reax_types.h
@@ -40,7 +40,7 @@
/************* SOME DEFS - crucial for reax_types.h *********/
#define PURE_REAX
-#define NEUTRAL_TERRITORY
+//#define NEUTRAL_TERRITORY
//#define LAMMPS_REAX
//#define DEBUG
//#define DEBUG_FOCUS
--
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