From d6406285e9e97a3ca152b5bbde45b6f5edcbe72d Mon Sep 17 00:00:00 2001
From: Abdullah Alperen <alperena@msu.edu>
Date: Thu, 10 Jan 2019 10:50:02 -0500
Subject: [PATCH] PuReMD: fix bond_list
---
PuReMD/src/forces.c | 44 +++++++++++++++++++++++++-------------------
1 file changed, 25 insertions(+), 19 deletions(-)
diff --git a/PuReMD/src/forces.c b/PuReMD/src/forces.c
index 4588515d..e57adbb2 100644
--- a/PuReMD/src/forces.c
+++ b/PuReMD/src/forces.c
@@ -1146,23 +1146,23 @@ static void Init_Bond_Full( reax_system *system, control_params *control,
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 )
-// if ( i <= j && far_nbrs->far_nbr_list.d[pj] <= control->nonb_cut )
+// if ( far_nbrs->far_nbr_list.d[pj] <= control->nonb_cut )
+ if ( i <= j && 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_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,
+// 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],
+ &far_nbrs->far_nbr_list.dvec[pj], far_nbrs->format,
+ sbp_i, sbp_j, twbp ) )
{
num_bonds += 2;
++btop_i;
@@ -1171,7 +1171,7 @@ static void Init_Bond_Full( reax_system *system, control_params *control,
* to search for it's bonded neighbors later */
if ( workspace->bond_mark[j] == 1000 )
{
- workspace->bond_mark[j] = 1;
+ workspace->bond_mark[j] = 101;
q[ push++ ] = j;
}
}
@@ -1185,6 +1185,7 @@ static void Init_Bond_Full( reax_system *system, control_params *control,
for ( k = 0; k < push; ++k )
{
i = q[k];
+ workspace->bond_mark[i] -= 100;
atom_i = &system->my_atoms[i];
type_i = atom_i->type;
btop_i = End_Index( i, bonds );
@@ -1201,35 +1202,40 @@ 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 ( i <= j && far_nbrs->far_nbr_list.d[pj] <= control->bond_cut )
+// 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 )
{
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,
+// 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],
+ &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;
+ workspace->bond_mark[j] = workspace->bond_mark[i] + 100;
- if ( workspace->bond_mark[j] < 4 )
+ if ( workspace->bond_mark[i] < 3 )
{
q[ push++ ] = j;
}
--
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