From 8b8301c0fe0fd6828b9103f66e9fd77b0bb11632 Mon Sep 17 00:00:00 2001
From: Abdullah Alperen <alperena@msu.edu>
Date: Fri, 4 Jan 2019 20:45:28 -0500
Subject: [PATCH] PuReMD: fix the calculation of bond_mark and move it to
Init_Distance func
---
PuReMD/src/forces.c | 242 +++++++++++++++++++++++++++++---------------
1 file changed, 160 insertions(+), 82 deletions(-)
diff --git a/PuReMD/src/forces.c b/PuReMD/src/forces.c
index 4ebaf651..5b3af47b 100644
--- a/PuReMD/src/forces.c
+++ b/PuReMD/src/forces.c
@@ -342,6 +342,14 @@ static void Init_Distance( reax_system *system, control_params *control,
reax_list *far_nbrs;
reax_atom *atom_i, *atom_j;
+ int type_i, type_j;
+ int k, push;
+ int btop_i, num_bonds;
+ int *q;
+ reax_list *bonds;
+ single_body_parameters *sbp_i, *sbp_j;
+ two_body_parameters *twbp;
+
far_nbrs = lists[FAR_NBRS];
renbr = (data->step - data->prev_steps) % control->reneighbor == 0;
@@ -367,6 +375,153 @@ static void Init_Distance( reax_system *system, control_params *control,
}
}
}
+
+
+ //Computing bond_mark
+ push = 0;
+ num_bonds = 0;
+ btop_i = 0;
+ bonds = lists[BONDS];
+ q = smalloc( sizeof( int ) * (system->N - system->n),
+ "Init_Distance::q", MPI_COMM_WORLD );
+
+ 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
+ //workspace->done_after[i] = Start_Index( i, far_nbrs );
+ }
+
+ //bonds that are directly connected to local atoms
+ for ( i = 0; i < system->n; ++i )
+ {
+ atom_i = &system->my_atoms[i];
+ type_i = atom_i->type;
+ btop_i = End_Index( i, bonds );
+ sbp_i = &system->reax_param.sbp[type_i];
+ start_i = Start_Index( i, far_nbrs );
+ end_i = End_Index( i, far_nbrs );
+
+ for ( pj = start_i; pj < end_i; ++pj )
+ {
+ j = far_nbrs->far_nbr_list.nbr[pj];
+ atom_j = &system->my_atoms[j];
+ if ( far_nbrs->far_nbr_list.d[pj] <= control->nonb_cut )
+ {
+ type_j = atom_j->type;
+ sbp_j = &system->reax_param.sbp[type_j];
+ twbp = &system->reax_param.tbp[type_i][type_j];
+
+ if ( BOp( workspace, bonds, control->bo_cut,
+ i, btop_i, far_nbrs->far_nbr_list.nbr[pj],
+ &far_nbrs->far_nbr_list.rel_box[pj], far_nbrs->far_nbr_list.d[pj],
+ &far_nbrs->far_nbr_list.dvec[pj], far_nbrs->format,
+ sbp_i, sbp_j, twbp ) )
+ {
+ num_bonds += 2;
+ ++btop_i;
+
+ if ( workspace->bond_mark[j] == 1000 )
+ {
+ workspace->bond_mark[j] = 1;
+ q[ push++ ] = j;
+ }
+ }
+ }
+ }
+
+ Set_End_Index( i, btop_i, bonds );
+ }
+
+ //bonds that are indirectly connected to local atoms
+ for ( k = 0; k < push; ++k )
+ {
+ i = q[k];
+ if( workspace->bond_mark[i] == 0 || workspace->bond_mark[i] == 1000 || i < system->n)
+ {
+ fprintf( stdout, "we got a problem, mark[%d] = %d\n\n", i , workspace->bond_mark[i] );
+ fflush( stdout );
+ }
+ atom_i = &system->my_atoms[i];
+ type_i = atom_i->type;
+ btop_i = End_Index( i, bonds );
+ sbp_i = &system->reax_param.sbp[type_i];
+ start_i = Start_Index( i, far_nbrs );
+ end_i = End_Index( i, far_nbrs );
+
+ for ( pj = start_i; pj < end_i; ++pj )
+ {
+ j = far_nbrs->far_nbr_list.nbr[pj];
+ atom_j = &system->my_atoms[j];
+ if ( far_nbrs->far_nbr_list.d[pj] <= control->bond_cut )
+ {
+ type_j = atom_j->type;
+ sbp_j = &system->reax_param.sbp[type_j];
+ twbp = &system->reax_param.tbp[type_i][type_j];
+
+ if ( BOp( workspace, bonds, control->bo_cut,
+ i, btop_i, far_nbrs->far_nbr_list.nbr[pj],
+ &far_nbrs->far_nbr_list.rel_box[pj], far_nbrs->far_nbr_list.d[pj],
+ &far_nbrs->far_nbr_list.dvec[pj], far_nbrs->format,
+ sbp_i, sbp_j, twbp ) )
+ {
+ num_bonds += 2;
+ ++btop_i;
+
+ if ( workspace->bond_mark[j] == 1000 )
+ {
+ workspace->bond_mark[j] = workspace->bond_mark[i] + 1;
+ q[ push++ ] = j;
+ }
+ }
+ }
+ }
+
+ Set_End_Index( i, btop_i, bonds );
+ }
+
+ //bonds that are between ghost atoms
+ for ( i = system->n; i < system->N; ++i )
+ {
+ if ( workspace->bond_mark[i] == 1000 )
+ {
+ atom_i = &system->my_atoms[i];
+ type_i = atom_i->type;
+ btop_i = End_Index( i, bonds );
+ sbp_i = &system->reax_param.sbp[type_i];
+ start_i = Start_Index( i, far_nbrs );
+ end_i = End_Index( i, far_nbrs );
+
+ for ( pj = start_i; pj < end_i; ++pj )
+ {
+ j = far_nbrs->far_nbr_list.nbr[pj];
+ atom_j = &system->my_atoms[j];
+ if ( far_nbrs->far_nbr_list.d[pj] <= control->bond_cut )
+ {
+ type_j = atom_j->type;
+ sbp_j = &system->reax_param.sbp[type_j];
+ twbp = &system->reax_param.tbp[type_i][type_j];
+
+ if ( BOp( workspace, bonds, control->bo_cut,
+ i, btop_i, far_nbrs->far_nbr_list.nbr[pj],
+ &far_nbrs->far_nbr_list.rel_box[pj], far_nbrs->far_nbr_list.d[pj],
+ &far_nbrs->far_nbr_list.dvec[pj], far_nbrs->format,
+ sbp_i, sbp_j, twbp ) )
+ {
+ num_bonds += 2;
+ ++btop_i;
+ }
+ }
+ }
+
+ Set_End_Index( i, btop_i, bonds );
+ }
+ }
+ workspace->realloc.num_bonds = num_bonds;
+
}
@@ -969,33 +1124,19 @@ static void Init_Bond_Half( reax_system *system, control_params *control,
int i, j, pj;
int start_i, end_i;
int type_i, type_j;
- int btop_i, num_bonds, num_hbonds;
+ int num_hbonds;
int ihb, jhb, ihb_top;
int local;
real cutoff;
reax_list *far_nbrs, *bonds, *hbonds;
single_body_parameters *sbp_i, *sbp_j;
- two_body_parameters *twbp;
reax_atom *atom_i, *atom_j;
int jhb_top;
far_nbrs = lists[FAR_NBRS];
- 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
- //workspace->done_after[i] = Start_Index( i, far_nbrs );
- }
-
- num_bonds = 0;
num_hbonds = 0;
- btop_i = 0;
for ( i = 0; i < system->N; ++i )
{
@@ -1006,7 +1147,6 @@ static void Init_Bond_Half( reax_system *system, control_params *control,
/* start at end because other atoms
* can add to this atom's list (half-list) */
- btop_i = End_Index( i, bonds );
sbp_i = &system->reax_param.sbp[type_i];
if ( i < system->n )
@@ -1051,7 +1191,6 @@ static void Init_Bond_Half( reax_system *system, control_params *control,
{
type_j = atom_j->type;
sbp_j = &system->reax_param.sbp[type_j];
- twbp = &system->reax_param.tbp[type_i][type_j];
if ( local == 1 )
{
@@ -1084,43 +1223,20 @@ static void Init_Bond_Half( reax_system *system, control_params *control,
}
}
- /* uncorrected bond orders */
- if ( //(workspace->bond_mark[i] < 3 || workspace->bond_mark[j] < 3) &&
- BOp( workspace, bonds, control->bo_cut,
- i, btop_i, far_nbrs->far_nbr_list.nbr[pj],
- &far_nbrs->far_nbr_list.rel_box[pj], far_nbrs->far_nbr_list.d[pj],
- &far_nbrs->far_nbr_list.dvec[pj], far_nbrs->format,
- sbp_i, sbp_j, twbp ) )
- {
- num_bonds += 2;
- ++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;
- }
- }
}
}
- Set_End_Index( i, btop_i, bonds );
-
if ( local == 1 && ihb == 1 )
{
Set_End_Index( atom_i->Hindex, ihb_top, hbonds );
}
}
- workspace->realloc.num_bonds = num_bonds;
workspace->realloc.num_hbonds = num_hbonds;
#if defined(DEBUG_FOCUS)
fprintf( stderr, "p%d @ step%d: Htop = %d num_bonds = %d num_hbonds = %d\n",
- system->my_rank, data->step, workspace->realloc.Htop, num_bonds, num_hbonds );
+ system->my_rank, data->step, workspace->realloc.Htop, workspace->realloc.num_bonds, num_hbonds );
MPI_Barrier( comm );
#endif
@@ -1142,34 +1258,21 @@ static void Init_Bond_Full( reax_system *system, control_params *control,
int i, j, pj;
int start_i, end_i;
int type_i, type_j;
- int btop_i, num_bonds, num_hbonds;
+ int num_hbonds;
int ihb, jhb, ihb_top;
int local;
real cutoff;
reax_list *far_nbrs, *bonds, *hbonds;
single_body_parameters *sbp_i, *sbp_j;
- two_body_parameters *twbp;
reax_atom *atom_i, *atom_j;
int start_j, end_j;
- int btop_j;
+ int btop_i, btop_j;
far_nbrs = lists[FAR_NBRS];
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
- //workspace->done_after[i] = Start_Index( i, far_nbrs );
- }
-
- num_bonds = 0;
num_hbonds = 0;
- btop_i = 0;
for ( i = 0; i < system->N; ++i )
{
@@ -1178,7 +1281,6 @@ static void Init_Bond_Full( reax_system *system, control_params *control,
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];
if ( i < system->n )
@@ -1221,7 +1323,6 @@ static void Init_Bond_Full( reax_system *system, control_params *control,
{
type_j = atom_j->type;
sbp_j = &system->reax_param.sbp[type_j];
- twbp = &system->reax_param.tbp[type_i][type_j];
if ( local == 1 )
{
@@ -1244,31 +1345,9 @@ static void Init_Bond_Full( reax_system *system, control_params *control,
}
}
- /* uncorrected bond orders */
- if ( //(workspace->bond_mark[i] < 3 || workspace->bond_mark[j] < 3) &&
- BOp( workspace, bonds, control->bo_cut,
- i, btop_i, far_nbrs->far_nbr_list.nbr[pj],
- &far_nbrs->far_nbr_list.rel_box[pj], far_nbrs->far_nbr_list.d[pj],
- &far_nbrs->far_nbr_list.dvec[pj], far_nbrs->format,
- sbp_i, sbp_j, twbp ) )
- {
- num_bonds += 2;
- ++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;
- }
- }
}
}
- Set_End_Index( i, btop_i, bonds );
-
if ( local == 1 && ihb == 1 )
{
Set_End_Index( atom_i->Hindex, ihb_top, hbonds );
@@ -1304,12 +1383,11 @@ static void Init_Bond_Full( reax_system *system, control_params *control,
}
}
- workspace->realloc.num_bonds = num_bonds;
workspace->realloc.num_hbonds = num_hbonds;
#if defined(DEBUG_FOCUS)
fprintf( stderr, "p%d @ step%d: Htop = %d num_bonds = %d num_hbonds = %d\n",
- system->my_rank, data->step, workspace->realloc.Htop, num_bonds, num_hbonds );
+ system->my_rank, data->step, workspace->realloc.Htop, workspace->realloc.num_bonds, num_hbonds );
MPI_Barrier( comm );
#endif
--
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