From 4e99b3489ebfbe9d3432912a28641e77ef3545f6 Mon Sep 17 00:00:00 2001
From: "Kurt A. O'Hearn" <ohearnku@msu.edu>
Date: Thu, 10 Jan 2019 16:06:50 -0500
Subject: [PATCH] PuReMD-old: optimizations in Init_Bond_Full for fusing hbond
and bond list computation and removing unnecessary sorting and sym_index
updating.
---
PuReMD/src/forces.c | 150 +++++++-------------------------------------
1 file changed, 22 insertions(+), 128 deletions(-)
diff --git a/PuReMD/src/forces.c b/PuReMD/src/forces.c
index a513c2a4..833fb261 100644
--- a/PuReMD/src/forces.c
+++ b/PuReMD/src/forces.c
@@ -1075,50 +1075,11 @@ static void Init_Bond_Full( reax_system *system, control_params *control,
bonds = lists[BONDS];
hbonds = lists[HBONDS];
num_hbonds = 0;
-
- /* hbonds */
- if ( control->hbond_cut > 0.0 )
- {
- for ( i = 0; i < system->n; ++i )
- {
- atom_i = &system->my_atoms[i];
- type_i = atom_i->type;
- sbp_i = &system->reax_param.sbp[type_i];
- ihb = sbp_i->p_hbond;
-
- if ( ihb == 1 )
- {
- start_i = Start_Index( i, far_nbrs );
- end_i = End_Index( i, far_nbrs );
- ihb_top = Start_Index( atom_i->Hindex, hbonds );
-
- /* check if j is within cutoff */
- 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->hbond_cut
- && system->reax_param.sbp[atom_j->type].p_hbond == 2 )
- {
- hbonds->hbond_list[ihb_top].nbr = j;
- hbonds->hbond_list[ihb_top].scl = 1;
- hbonds->hbond_list[ihb_top].ptr = pj;
- ++ihb_top;
- ++num_hbonds;
- }
- }
-
- Set_End_Index( atom_i->Hindex, ihb_top, hbonds );
- }
- }
- }
-
- /* compute 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 );
@@ -1141,24 +1102,34 @@ static void Init_Bond_Full( reax_system *system, control_params *control,
sbp_i = &system->reax_param.sbp[type_i];
start_i = Start_Index( i, far_nbrs );
end_i = End_Index( i, far_nbrs );
+ ihb = sbp_i->p_hbond;
+ ihb_top = Start_Index( atom_i->Hindex, hbonds );
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 )
+ if ( control->hbond_cut > 0.0 && ihb == 1 )
+ {
+ /* check if j is within cutoff */
+ if ( far_nbrs->far_nbr_list.d[pj] <= control->hbond_cut
+ && system->reax_param.sbp[atom_j->type].p_hbond == 2 )
+ {
+ hbonds->hbond_list[ihb_top].nbr = j;
+ hbonds->hbond_list[ihb_top].scl = 1;
+ hbonds->hbond_list[ihb_top].ptr = pj;
+ ++ihb_top;
+ ++num_hbonds;
+ }
+ }
+
if ( i <= j && 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_redundant( 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 ) )
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],
@@ -1179,6 +1150,11 @@ static void Init_Bond_Full( reax_system *system, control_params *control,
}
}
+ if ( control->hbond_cut > 0.0 && ihb == 1 )
+ {
+ Set_End_Index( atom_i->Hindex, ihb_top, hbonds );
+ }
+
Set_End_Index( i, btop_i, bonds );
}
@@ -1203,15 +1179,9 @@ static void Init_Bond_Full( reax_system *system, control_params *control,
{
continue;
}
-/* if ( i>j && workspace->bond_mark[i] > workspace->bond_mark[j]
- && workspace->bond_mark[j] == 1000 )
- {
- continue;
- }*/
atom_j = &system->my_atoms[j];
-// if ( far_nbrs->far_nbr_list.d[pj] <= control->bond_cut )
if ( workspace->bond_mark[j] > 100
&& far_nbrs->far_nbr_list.d[pj] <= control->bond_cut )
{
@@ -1219,11 +1189,6 @@ static void Init_Bond_Full( reax_system *system, control_params *control,
sbp_j = &system->reax_param.sbp[type_j];
twbp = &system->reax_param.tbp[type_i][type_j];
-// if ( BOp_redundant( 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 ) )
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],
@@ -1249,80 +1214,9 @@ static void Init_Bond_Full( reax_system *system, control_params *control,
Set_End_Index( i, btop_i, bonds );
}
- //we do not need to include bonded interactions
- //between ghost atoms that do not share any
- //neighborhood relationship with any local atoms
- //those atoms have their bond_mark value still
- //equal to 1000
-// 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;
sfree( q, "Init_Bond_Full::q" );
- 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 )
- {
- start_i = Start_Index( i, bonds );
- end_i = End_Index( i, bonds );
-
- for ( btop_i = start_i; btop_i < end_i; ++btop_i )
- {
- j = bonds->bond_list[btop_i].nbr;
- start_j = Start_Index( j, bonds );
- end_j = End_Index( j, bonds );
-
- for ( btop_j = start_j; btop_j < end_j; ++btop_j )
- {
- if ( bonds->bond_list[btop_j].nbr == i )
- {
- bonds->bond_list[btop_i].sym_index = btop_j;
- break;
- }
- }
- }
- }
-
workspace->realloc.num_hbonds = num_hbonds;
#if defined(DEBUG_FOCUS)
--
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