From 472fe29a89973e3d84739c198ca83bd59509c856 Mon Sep 17 00:00:00 2001
From: sjplimp <sjplimp@f3b2605a-c512-4ea7-a41b-209d697bcdaa>
Date: Fri, 15 Jul 2016 23:12:28 +0000
Subject: [PATCH] git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15328
f3b2605a-c512-4ea7-a41b-209d697bcdaa
---
src/USER-DPD/fix_shardlow.cpp | 70 ++++++++++++++++++++++++++---------
src/USER-DPD/fix_shardlow.h | 8 +++-
2 files changed, 59 insertions(+), 19 deletions(-)
diff --git a/src/USER-DPD/fix_shardlow.cpp b/src/USER-DPD/fix_shardlow.cpp
index 444379a1ee..fd9f4d7d74 100644
--- a/src/USER-DPD/fix_shardlow.cpp
+++ b/src/USER-DPD/fix_shardlow.cpp
@@ -108,9 +108,7 @@ FixShardlow::FixShardlow(LAMMPS *lmp, int narg, char **arg) :
// Setup the ssaAIR array
atom->ssaAIR = NULL;
grow_arrays(atom->nmax);
- for (int i = 0; i < atom->nlocal; i++) {
- atom->ssaAIR[i] = 1; /* coord2ssaAIR(x[i]) */
- }
+ memset(atom->ssaAIR, 0, sizeof(int)*atom->nlocal);
// Setup callbacks for maintaining atom->ssaAIR[]
atom->add_callback(0); // grow (aka exchange)
@@ -137,11 +135,40 @@ int FixShardlow::setmask()
{
int mask = 0;
mask |= INITIAL_INTEGRATE;
+ mask |= PRE_EXCHANGE | MIN_PRE_EXCHANGE;
return mask;
}
/* ---------------------------------------------------------------------- */
+void FixShardlow::pre_exchange()
+{
+ memset(atom->ssaAIR, 0, sizeof(int)*atom->nlocal);
+}
+
+/* ---------------------------------------------------------------------- */
+
+void FixShardlow::setup_pre_exchange()
+{
+ memset(atom->ssaAIR, 0, sizeof(int)*atom->nlocal);
+}
+
+/* ---------------------------------------------------------------------- */
+
+void FixShardlow::min_pre_exchange()
+{
+ memset(atom->ssaAIR, 0, sizeof(int)*atom->nlocal);
+}
+
+/* ---------------------------------------------------------------------- */
+
+void FixShardlow::min_setup_pre_exchange()
+{
+ memset(atom->ssaAIR, 0, sizeof(int)*atom->nlocal);
+}
+
+/* ---------------------------------------------------------------------- */
+
void FixShardlow::reset_dt()
{
dtsqrt = sqrt(update->dt);
@@ -173,11 +200,10 @@ void FixShardlow::setup(int vflag)
NOTE: only implemented for orthogonal boxes, not triclinic
------------------------------------------------------------------------- */
-void FixShardlow::do_ssaAIR_for(
- int airnum,
+void FixShardlow::ssa_update(
int i,
- int jnum,
int *jlist,
+ int jlen,
class RanMars *pRNG
)
{
@@ -241,10 +267,9 @@ void FixShardlow::do_ssaAIR_for(
massinv_i = 1.0 / mass_i;
// Loop over Directional Neighbors only
- for (jj = 0; jj < jnum; jj++) {
+ for (jj = 0; jj < jlen; jj++) {
j = jlist[jj];
j &= NEIGHMASK;
- if (ssaAIR[j] != airnum) continue;
jtype = type[j];
delx = xtmp - x[j][0];
@@ -444,7 +469,9 @@ void FixShardlow::initial_integrate(int vflag)
// Loop over neighbors of my atoms
for (ii = 0; ii < inum; ii++) {
i = ilist[ii];
- do_ssaAIR_for(airnum, i, list->numneigh[i], list->firstneigh[i], pRNG);
+ int start = (airnum < 2) ? 0 : list->ndxAIR_ssa[i][airnum - 2];
+ int len = list->ndxAIR_ssa[i][airnum - 1] - start;
+ if (len > 0) ssa_update(i, &(list->firstneigh[i][start]), len, pRNG);
}
// Communicate the ghost deltas to the atom owners
@@ -554,11 +581,11 @@ int FixShardlow::coord2ssaAIR(double *x)
if (x[0] >= domain->subhi[0]) ix = 1;
if(iz < 0){
- return 0;
+ return -1;
} else if(iz == 0){
- if( iy<0 ) return 0; // bottom left/middle/right
- if( (iy==0) && (ix<0) ) return 0; // left atoms
- if( (iy==0) && (ix==0) ) return 1; // Locally owned atoms
+ if( iy<0 ) return -1; // bottom left/middle/right
+ if( (iy==0) && (ix<0) ) return -1; // left atoms
+ if( (iy==0) && (ix==0) ) return 0; // Locally owned atoms
if( (iy==0) && (ix>0) ) return 3; // Right atoms
if( (iy>0) && (ix==0) ) return 2; // Top-middle atoms
if( (iy>0) && (ix!=0) ) return 4; // Top-right and top-left atoms
@@ -569,7 +596,7 @@ int FixShardlow::coord2ssaAIR(double *x)
if((ix!=0) && (iy!=0)) return 8; // Back corner atoms
}
- return 0;
+ return -2;
}
/* ---------------------------------------------------------------------- */
@@ -586,7 +613,16 @@ void FixShardlow::copy_arrays(int i, int j, int delflag)
void FixShardlow::set_arrays(int i)
{
- atom->ssaAIR[i] = 1; /* coord2ssaAIR(x[i]) */
+ atom->ssaAIR[i] = 0; /* coord2ssaAIR(x[i]) */
+}
+
+int FixShardlow::pack_border(int n, int *list, double *buf)
+{
+ for (int i = 0; i < n; i++) {
+ int j = list[i];
+ if (atom->ssaAIR[j] == 0) atom->ssaAIR[j] = 1; // not purely local anymore
+ }
+ return 0;
}
int FixShardlow::unpack_border(int n, int first, double *buf)
@@ -600,13 +636,13 @@ int FixShardlow::unpack_border(int n, int first, double *buf)
int FixShardlow::unpack_exchange(int i, double *buf)
{
- atom->ssaAIR[i] = 1; /* coord2ssaAIR(x[i]) */
+ atom->ssaAIR[i] = 0; /* coord2ssaAIR(x[i]) */
return 0;
}
void FixShardlow::unpack_restart(int i, int nth)
{
- atom->ssaAIR[i] = 1; /* coord2ssaAIR(x[i]) */
+ atom->ssaAIR[i] = 0; /* coord2ssaAIR(x[i]) */
}
double FixShardlow::memory_usage()
diff --git a/src/USER-DPD/fix_shardlow.h b/src/USER-DPD/fix_shardlow.h
index a64774c57b..5d6b1f7c7e 100644
--- a/src/USER-DPD/fix_shardlow.h
+++ b/src/USER-DPD/fix_shardlow.h
@@ -31,6 +31,10 @@ class FixShardlow : public Fix {
int setmask();
virtual void setup(int);
virtual void initial_integrate(int);
+ void setup_pre_exchange();
+ void pre_exchange();
+ void min_setup_pre_exchange();
+ void min_pre_exchange();
void grow_arrays(int);
void copy_arrays(int, int, int);
@@ -38,7 +42,7 @@ class FixShardlow : public Fix {
void reset_dt();
-// int pack_border(int, int *, double *);
+ int pack_border(int, int *, double *);
int unpack_border(int, int, double *);
int unpack_exchange(int, double *);
void unpack_restart(int, int);
@@ -59,7 +63,7 @@ class FixShardlow : public Fix {
double dtsqrt; // = sqrt(update->dt);
int coord2ssaAIR(double *); // map atom coord to an AIR number
- void do_ssaAIR_for(int, int, int, int *, class RanMars *);
+ void ssa_update(int, int *, int, class RanMars *);
};
--
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