From 0e7db3ba19db4dcd775197cb02a715e0d9200d03 Mon Sep 17 00:00:00 2001
From: "Kurt A. O'Hearn" <ohearnk@msu.edu>
Date: Tue, 18 Dec 2018 20:21:33 -0500
Subject: [PATCH] sPuReMD: screen out non-periodic self-interactions when
constructing far nbr list.
---
sPuReMD/src/box.c | 24 ++++++++++++------------
1 file changed, 12 insertions(+), 12 deletions(-)
diff --git a/sPuReMD/src/box.c b/sPuReMD/src/box.c
index aa0ed4eb..c6ff1257 100644
--- a/sPuReMD/src/box.c
+++ b/sPuReMD/src/box.c
@@ -366,7 +366,7 @@ int Find_Non_Periodic_Far_Neighbors( rvec x1, rvec x2, int atom, int nbr_atom,
rvec_ScaledSum( dvec, 1.0, x2, -1.0, x1 );
norm_sqr = rvec_Norm_Sqr( dvec );
- if ( norm_sqr <= SQR( vlist_cut ) )
+ if ( norm_sqr <= SQR( vlist_cut ) && norm_sqr >= 0.01 )
{
data->nbr = nbr_atom;
ivec_MakeZero( data->rel_box );
@@ -396,7 +396,7 @@ int Count_Non_Periodic_Far_Neighbors( rvec x1, rvec x2, int atom, int nbr_atom,
rvec_ScaledSum( d, 1.0, x2, -1.0, x1 );
norm_sqr = rvec_Norm_Sqr( d );
- if ( norm_sqr <= SQR( vlist_cut ) )
+ if ( norm_sqr <= SQR( vlist_cut ) && norm_sqr >= 0.01 )
{
count = 1;
}
@@ -454,7 +454,7 @@ int Find_Periodic_Far_Neighbors_Big_Box( rvec x1, rvec x2, int atom, int nbr_ato
}
}
- if ( norm_sqr <= SQR( vlist_cut ) )
+ if ( norm_sqr <= SQR( vlist_cut ) && norm_sqr >= 0.01 )
{
data->nbr = nbr_atom;
ivec_Copy( data->rel_box, rel_box );
@@ -506,7 +506,7 @@ int Count_Periodic_Far_Neighbors_Big_Box( rvec x1, rvec x2, int atom, int nbr_at
}
}
- if ( norm_sqr <= SQR( vlist_cut ) )
+ if ( norm_sqr <= SQR( vlist_cut ) && norm_sqr >= 0.01 )
{
count = 1;
}
@@ -532,10 +532,10 @@ int Find_Periodic_Far_Neighbors_Small_Box( rvec x1, rvec x2, int atom, int nbr_a
{
int i, j, k, count;
int imax, jmax, kmax;
- real sqr_norm, d_i, d_j, d_k, sqr_cutoff2;
+ real sqr_norm, d_i, d_j, d_k, sqr_vlist_cut;
count = 0;
- sqr_cutoff2 = SQR( vlist_cut );
+ sqr_vlist_cut = SQR( vlist_cut );
/* determine the max stretch of imaginary boxs in each direction
* to handle periodic boundary conditions correctly */
@@ -564,7 +564,7 @@ int Find_Periodic_Far_Neighbors_Small_Box( rvec x1, rvec x2, int atom, int nbr_a
sqr_norm = SQR(d_i) + SQR(d_j) + SQR(d_k);
- if ( sqr_norm <= sqr_cutoff2 )
+ if ( sqr_norm <= sqr_vlist_cut )
{
data[count].nbr = nbr_atom;
@@ -638,7 +638,7 @@ int Find_Periodic_Far_Neighbors_Small_Box( rvec x1, rvec x2, int atom, int nbr_a
sqr_norm = SQR(d_i) + SQR(d_j) + SQR(d_k);
- if ( sqr_norm <= sqr_cutoff2 && sqr_norm >= 0.01 )
+ if ( sqr_norm <= sqr_vlist_cut && sqr_norm >= 0.01 )
{
data[count].nbr = nbr_atom;
@@ -707,10 +707,10 @@ int Count_Periodic_Far_Neighbors_Small_Box( rvec x1, rvec x2, int atom, int nbr_
{
int i, j, k, count;
int imax, jmax, kmax;
- real sqr_norm, d_i, d_j, d_k, sqr_cutoff2;
+ real sqr_norm, d_i, d_j, d_k, sqr_vlist_cut;
count = 0;
- sqr_cutoff2 = SQR( vlist_cut );
+ sqr_vlist_cut = SQR( vlist_cut );
/* determine the max stretch of imaginary boxs in each direction
* to handle periodic boundary conditions correctly */
@@ -738,7 +738,7 @@ int Count_Periodic_Far_Neighbors_Small_Box( rvec x1, rvec x2, int atom, int nbr_
sqr_norm = SQR(d_i) + SQR(d_j) + SQR(d_k);
- if ( sqr_norm <= sqr_cutoff2 )
+ if ( sqr_norm <= sqr_vlist_cut )
{
++count;
}
@@ -763,7 +763,7 @@ int Count_Periodic_Far_Neighbors_Small_Box( rvec x1, rvec x2, int atom, int nbr_
sqr_norm = SQR(d_i) + SQR(d_j) + SQR(d_k);
- if ( sqr_norm <= sqr_cutoff2 && sqr_norm >= 0.01 )
+ if ( sqr_norm <= sqr_vlist_cut && sqr_norm >= 0.01 )
{
++count;
}
--
GitLab