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USER-DPD: remove use of ssaAIR[], move coord2ssaAIR() to nbin_ssa.cpp

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Saves an int per atom and ghost, also simplifies and reduces code size.
This commit is contained in:
Tim Mattox
2017-01-27 16:47:19 -05:00
parent f73c9a43ab
commit 641bb4bb16
4 changed files with 38 additions and 132 deletions
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116
src/USER-DPD/fix_shardlow.cpp
View File

@ -109,26 +109,12 @@ FixShardlow::FixShardlow(LAMMPS *lmp, int narg, char **arg) :
if(pairDPD == NULL && pairDPDE == NULL)
error->all(FLERR,"Must use pair_style dpd/fdt or dpd/fdt/energy with fix shardlow");
// Setup the ssaAIR array
atom->ssaAIR = NULL;
grow_arrays(atom->nmax);
memset(atom->ssaAIR, 0, sizeof(int)*atom->nlocal);
// Setup callbacks for maintaining atom->ssaAIR[]
atom->add_callback(0); // grow (aka exchange)
atom->add_callback(1); // restart
atom->add_callback(2); // border
}
/* ---------------------------------------------------------------------- */
FixShardlow::~FixShardlow()
{
atom->delete_callback(id, 0);
atom->delete_callback(id, 1);
atom->delete_callback(id, 2);
memory->destroy(atom->ssaAIR);
}
/* ---------------------------------------------------------------------- */
@ -137,7 +123,6 @@ int FixShardlow::setmask()
{
int mask = 0;
mask |= INITIAL_INTEGRATE;
mask |= PRE_EXCHANGE | MIN_PRE_EXCHANGE;
return mask;
}
@ -161,27 +146,6 @@ void FixShardlow::init_list(int id, NeighList *ptr)
/* ---------------------------------------------------------------------- */
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::setup(int vflag)
{
bool fixShardlow = false;
@ -659,91 +623,11 @@ void FixShardlow::unpack_reverse_comm(int n, int *list, double *buf)
}
}
/* ----------------------------------------------------------------------
convert atom coords into the ssa active interaction region number
------------------------------------------------------------------------- */
int FixShardlow::coord2ssaAIR(double *x)
{
int ix, iy, iz;
ix = iy = iz = 0;
if (x[2] < domain->sublo[2]) iz = -1;
if (x[2] >= domain->subhi[2]) iz = 1;
if (x[1] < domain->sublo[1]) iy = -1;
if (x[1] >= domain->subhi[1]) iy = 1;
if (x[0] < domain->sublo[0]) ix = -1;
if (x[0] >= domain->subhi[0]) ix = 1;
if(iz < 0){
return -1;
} else if(iz == 0){
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
} else { // iz > 0
if((ix==0) && (iy==0)) return 5; // Back atoms
if((ix==0) && (iy!=0)) return 6; // Top-back and bottom-back atoms
if((ix!=0) && (iy==0)) return 7; // Left-back and right-back atoms
if((ix!=0) && (iy!=0)) return 8; // Back corner atoms
}
return -2;
}
/* ---------------------------------------------------------------------- */
void FixShardlow::grow_arrays(int nmax)
{
memory->grow(atom->ssaAIR,nmax,"fix_shardlow:ssaAIR");
}
void FixShardlow::copy_arrays(int i, int j, int delflag)
{
atom->ssaAIR[j] = atom->ssaAIR[i];
}
void FixShardlow::set_arrays(int 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)
{
int i,last = first + n;
for (i = first; i < last; i++) {
atom->ssaAIR[i] = coord2ssaAIR(atom->x[i]);
}
return 0;
}
int FixShardlow::unpack_exchange(int i, double *buf)
{
atom->ssaAIR[i] = 0; /* coord2ssaAIR(x[i]) */
return 0;
}
void FixShardlow::unpack_restart(int i, int nth)
{
atom->ssaAIR[i] = 0; /* coord2ssaAIR(x[i]) */
}
double FixShardlow::memory_usage()
{
double bytes = 0.0;
bytes += memory->usage(atom->ssaAIR,atom->nmax);
bytes += sizeof(double)*3*atom->nghost; // v_t0[]
return bytes;
}

13
src/USER-DPD/fix_shardlow.h
View File

@ -35,18 +35,6 @@ class FixShardlow : public Fix {
virtual void init_list(int, class NeighList *);
virtual void setup(int);
virtual void initial_integrate(int);
void setup_pre_exchange();
void pre_exchange();
void min_pre_exchange();
void grow_arrays(int);
void copy_arrays(int, int, int);
void set_arrays(int);
int pack_border(int, int *, double *);
int unpack_border(int, int, double *);
int unpack_exchange(int, double *);
void unpack_restart(int, int);
double memory_usage();
@ -63,7 +51,6 @@ class FixShardlow : public Fix {
private:
double dtsqrt; // = sqrt(update->dt);
int coord2ssaAIR(double *); // map atom coord to an AIR number
void ssa_update_dpd(int, int *, int); // Constant Temperature
void ssa_update_dpde(int, int *, int); // Constant Energy

40
src/USER-DPD/nbin_ssa.cpp
View File

@ -20,6 +20,7 @@
#include "atom.h"
#include "update.h"
#include "group.h"
#include "domain.h"
#include "memory.h"
#include "error.h"
@ -58,7 +59,6 @@ void NBinSSA::bin_atoms()
if (includegroup) nlocal = atom->nfirst;
double **x = atom->x;
int *mask = atom->mask;
int *ssaAIR = atom->ssaAIR;
int xbin,ybin,zbin;
last_bin = update->ntimestep;
@ -82,7 +82,7 @@ void NBinSSA::bin_atoms()
int bitmask = group->bitmask[includegroup];
int nowned = atom->nlocal; // NOTE: nlocal was set to atom->nfirst above
for (i = nall-1; i >= nowned; i--) {
ibin = ssaAIR[i];
ibin = coord2ssaAIR(x[i]);
if (ibin < 2) continue; // skip ghost atoms not in AIR
if (mask[i] & bitmask) {
bins[i] = gairhead_ssa[ibin];
@ -91,7 +91,7 @@ void NBinSSA::bin_atoms()
}
} else {
for (i = nall-1; i >= nlocal; i--) {
ibin = ssaAIR[i];
ibin = coord2ssaAIR(x[i]);
if (ibin < 2) continue; // skip ghost atoms not in AIR
bins[i] = gairhead_ssa[ibin];
gairhead_ssa[ibin] = i;
@ -148,3 +148,37 @@ bigint NBinSSA::memory_usage()
}
return bytes;
}
/* ----------------------------------------------------------------------
convert atom coords into the ssa active interaction region number
------------------------------------------------------------------------- */
int NBinSSA::coord2ssaAIR(const double *x)
{
int ix, iy, iz;
ix = iy = iz = 0;
if (x[2] < domain->sublo[2]) iz = -1;
if (x[2] >= domain->subhi[2]) iz = 1;
if (x[1] < domain->sublo[1]) iy = -1;
if (x[1] >= domain->subhi[1]) iy = 1;
if (x[0] < domain->sublo[0]) ix = -1;
if (x[0] >= domain->subhi[0]) ix = 1;
if(iz < 0){
return -1;
} else if(iz == 0){
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
} else { // iz > 0
if((ix==0) && (iy==0)) return 5; // Back atoms
if((ix==0) && (iy!=0)) return 6; // Top-back and bottom-back atoms
if((ix!=0) && (iy==0)) return 7; // Left-back and right-back atoms
if((ix!=0) && (iy!=0)) return 8; // Back corner atoms
}
return -2;
}

1
src/USER-DPD/nbin_ssa.h
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@ -155,6 +155,7 @@ class NBinSSA : public NBinStandard {
}
private:
int coord2ssaAIR(const double *); // map atom coord to an AIR number
double bboxlo_[3],bboxhi_[3];
};