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Added 3-body neighbor list building for faster short range 3 body forces.

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This commit is contained in:
Anders Hafreager
2016-08-16 23:28:32 -04:00
committed by Axel Kohlmeyer
parent 944ebdcf44
commit 82d9f5f5e6
3 changed files with 61 additions and 22 deletions
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47
src/MANYBODY/pair_vashishta.cpp
View File

@ -54,6 +54,10 @@ PairVashishta::PairVashishta(LAMMPS *lmp) : Pair(lmp)
elem2param = NULL;
map = NULL;
neigh3BodyMax = 0;
neigh3BodyCount = NULL;
neigh3Body = NULL;
useTable = true;
tableSize = 65536;
forceTable = NULL;
@ -78,8 +82,7 @@ PairVashishta::~PairVashishta()
delete [] map;
}
}
#include <iostream>
using namespace std;
void PairVashishta::modify_params(int narg, char **arg)
{
if(narg < 2 || narg > 3) // We accept table yes/no [tableSize]
@ -102,6 +105,16 @@ void PairVashishta::modify_params(int narg, char **arg)
}
}
void PairVashishta::validateNeigh3Body() {
if (atom->nlocal > neigh3BodyMax) {
neigh3BodyMax = atom->nmax;
memory->destroy(neigh3BodyCount);
memory->destroy(neigh3Body);
memory->create(neigh3BodyCount,neigh3BodyMax, "pair:vashishta:neigh3BodyCount");
memory->create(neigh3Body,neigh3BodyMax, 1000, "pair:vashishta:neigh3Body"); // TODO: pick this number more wisely?
}
}
void PairVashishta::createTable()
{
int ntypes = atom->ntypes+1;
@ -140,6 +153,7 @@ void PairVashishta::createTable()
void PairVashishta::compute(int eflag, int vflag)
{
validateNeigh3Body();
int i,j,k,ii,jj,kk,inum,jnum,jnumm1;
int itype,jtype,ktype,ijparam,ikparam,ijkparam;
tagint itag,jtag;
@ -174,6 +188,8 @@ void PairVashishta::compute(int eflag, int vflag)
ytmp = x[i][1];
ztmp = x[i][2];
neigh3BodyCount[i] = 0; // Reset the 3-body neighbor list
// two-body interactions, skip half of them
jlist = firstneigh[i];
@ -184,6 +200,21 @@ void PairVashishta::compute(int eflag, int vflag)
j &= NEIGHMASK;
jtag = tag[j];
jtype = map[type[j]];
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];
delz = ztmp - x[j][2];
rsq = delx*delx + dely*dely + delz*delz;
ijparam = elem2param[itype][jtype][jtype];
if (rsq <= params[ijparam].cutsq2) {
neigh3Body[i][neigh3BodyCount[i]] = j;
neigh3BodyCount[i]++;
}
if (rsq > params[ijparam].cutsq) continue;
if (itag > jtag) {
if ((itag+jtag) % 2 == 0) continue;
} else if (itag < jtag) {
@ -194,16 +225,6 @@ void PairVashishta::compute(int eflag, int vflag)
if (x[j][2] == ztmp && x[j][1] == ytmp && x[j][0] < xtmp) continue;
}
jtype = map[type[j]];
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];
delz = ztmp - x[j][2];
rsq = delx*delx + dely*dely + delz*delz;
ijparam = elem2param[itype][jtype][jtype];
if (rsq > params[ijparam].cutsq) continue;
twobody(&params[ijparam],rsq,fpair,eflag,evdwl, useTable);
f[i][0] += delx*fpair;
@ -217,6 +238,8 @@ void PairVashishta::compute(int eflag, int vflag)
evdwl,0.0,fpair,delx,dely,delz);
}
jlist = neigh3Body[i];
jnum = neigh3BodyCount[i];
jnumm1 = jnum - 1;
for (jj = 0; jj < jnumm1; jj++) {

5
src/MANYBODY/pair_vashishta.h
View File

@ -53,6 +53,10 @@ class PairVashishta : public Pair {
double ***forceTable; // Table containing the forces
double ***potentialTable; // Table containing the potential energies
int neigh3BodyMax; // Max size of short neighborlist
int *neigh3BodyCount; // Number of neighbors in short range 3 particle forces neighbor list
int **neigh3Body; // Neighborlist for short range 3 particle forces
double cutmax; // max cutoff for all elements
int nelements; // # of unique elements
char **elements; // names of unique elements
@ -66,6 +70,7 @@ class PairVashishta : public Pair {
void read_file(char *);
void setup_params();
void createTable();
void validateNeigh3Body();
void twobody(Param *, double, double &, int, double &, bool);
void threebody(Param *, Param *, Param *, double, double, double *, double *,
double *, double *, int, double &);

31
src/USER-OMP/pair_vashishta_omp.cpp
View File

@ -36,6 +36,8 @@ PairVashishtaOMP::PairVashishtaOMP(LAMMPS *lmp) :
void PairVashishtaOMP::compute(int eflag, int vflag)
{
validateNeigh3Body();
if (eflag || vflag) {
ev_setup(eflag,vflag);
} else evflag = vflag_fdotr = 0;
@ -105,6 +107,8 @@ void PairVashishtaOMP::eval(int iifrom, int iito, ThrData * const thr)
ztmp = x[i].z;
fxtmp = fytmp = fztmp = 0.0;
neigh3BodyCount[i] = 0;
// two-body interactions, skip half of them
jlist = firstneigh[i];
@ -114,6 +118,21 @@ void PairVashishtaOMP::eval(int iifrom, int iito, ThrData * const thr)
j = jlist[jj];
j &= NEIGHMASK;
jtag = tag[j];
jtype = map[type[j]];
delx = xtmp - x[j].x;
dely = ytmp - x[j].y;
delz = ztmp - x[j].z;
rsq = delx*delx + dely*dely + delz*delz;
ijparam = elem2param[itype][jtype][jtype];
if (rsq <= params[ijparam].cutsq2) {
neigh3Body[i][neigh3BodyCount[i]] = j;
neigh3BodyCount[i]++;
}
if (rsq >= params[ijparam].cutsq) continue;
if (itag > jtag) {
if ((itag+jtag) % 2 == 0) continue;
@ -125,16 +144,6 @@ void PairVashishtaOMP::eval(int iifrom, int iito, ThrData * const thr)
if (x[j].z == ztmp && x[j].y == ytmp && x[j].x < xtmp) continue;
}
jtype = map[type[j]];
delx = xtmp - x[j].x;
dely = ytmp - x[j].y;
delz = ztmp - x[j].z;
rsq = delx*delx + dely*dely + delz*delz;
ijparam = elem2param[itype][jtype][jtype];
if (rsq >= params[ijparam].cutsq) continue;
twobody(&params[ijparam],rsq,fpair,EFLAG,evdwl, useTable);
fxtmp += delx*fpair;
@ -148,6 +157,8 @@ void PairVashishtaOMP::eval(int iifrom, int iito, ThrData * const thr)
evdwl,0.0,fpair,delx,dely,delz,thr);
}
jlist = neigh3Body[i];
jnum = neigh3BodyCount[i];
jnumm1 = jnum - 1;
for (jj = 0; jj < jnumm1; jj++) {