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Start to introduce halfneigh version

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This commit is contained in:
Jan Eitzinger 2022-03-10 16:30:37 +01:00
parent ca7775a62a
commit 6203cb12b6
4 changed files with 96 additions and 5 deletions
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82
lammps/force_lj.c
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@ -28,7 +28,8 @@
#include <atom.h>
#include <stats.h>
double computeForceLJ(Parameter *param, Atom *atom, Neighbor *neighbor, Stats *stats) {
double computeForceLJFullNeigh(Parameter *param, Atom *atom, Neighbor *neighbor, Stats *stats)
{
int Nlocal = atom->Nlocal;
int* neighs;
MD_FLOAT* fx = atom->fx;
@ -64,7 +65,6 @@ double computeForceLJ(Parameter *param, Atom *atom, Neighbor *neighbor, Stats *s
const int type_i = atom->type[i];
#endif
for(int k = 0; k < numneighs; k++) {
int j = neighs[k];
MD_FLOAT delx = xtmp - atom_x(j);
@ -102,3 +102,81 @@ double computeForceLJ(Parameter *param, Atom *atom, Neighbor *neighbor, Stats *s
double E = getTimeStamp();
return E-S;
}
double computeForceLJHalfNeigh(Parameter *param, Atom *atom, Neighbor *neighbor, Stats *stats)
{
int Nlocal = atom->Nlocal;
int* neighs;
MD_FLOAT* fx = atom->fx;
MD_FLOAT* fy = atom->fy;
MD_FLOAT* fz = atom->fz;
#ifndef EXPLICIT_TYPES
MD_FLOAT cutforcesq = param->cutforce * param->cutforce;
MD_FLOAT sigma6 = param->sigma6;
MD_FLOAT epsilon = param->epsilon;
#endif
for(int i = 0; i < Nlocal; i++) {
fx[i] = 0.0;
fy[i] = 0.0;
fz[i] = 0.0;
}
double S = getTimeStamp();
LIKWID_MARKER_START("forceLJ-halfneigh");
for(int i = 0; i < Nlocal; i++) {
neighs = &neighbor->neighbors[i * neighbor->maxneighs];
int numneighs = neighbor.numneigh[i];
MD_FLOAT xtmp = atom_x(i);
MD_FLOAT ytmp = atom_y(i);
MD_FLOAT ztmp = atom_z(i);
MD_FLOAT fix = 0;
MD_FLOAT fiy = 0;
MD_FLOAT fiz = 0;
#ifdef EXPLICIT_TYPES
const int type_i = atom->type[i];
#endif
for(int k = 0; k < numneighs; k++) {
int j = neighs[k];
MD_FLOAT delx = xtmp - atom_x(j);
MD_FLOAT dely = ytmp - atom_y(j);
MD_FLOAT delz = ztmp - atom_z(j);
MD_FLOAT rsq = delx * delx + dely * dely + delz * delz;
#ifdef EXPLICIT_TYPES
const int type_j = atom->type[j];
const int type_ij = type_i * atom->ntypes + type_j;
const MD_FLOAT cutforcesq = atom->cutforcesq[type_ij];
const MD_FLOAT sigma6 = atom->sigma6[type_ij];
const MD_FLOAT epsilon = atom->epsilon[type_ij];
#endif
if(rsq < cutforcesq) {
MD_FLOAT sr2 = 1.0 / rsq;
MD_FLOAT sr6 = sr2 * sr2 * sr2 * sigma6;
MD_FLOAT force = 48.0 * sr6 * (sr6 - 0.5) * sr2 * epsilon;
fix += delx * force;
fiy += dely * force;
fiz += delz * force;
fx[j] -= delx * force;
fy[j] -= dely * force;
fz[j] -= delz * force;
}
}
fx[i] += fix;
fy[i] += fiy;
fz[i] += fiz;
addStat(stats->total_force_neighs, numneighs);
addStat(stats->total_force_iters, (numneighs + VECTOR_WIDTH - 1) / VECTOR_WIDTH);
}
LIKWID_MARKER_STOP("forceLJ-halfneigh");
double E = getTimeStamp();
return E-S;
}

1
lammps/includes/parameter.h
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@ -42,6 +42,7 @@ typedef struct {
int ntimes;
int nstat;
int every;
int halfneigh;
MD_FLOAT dt;
MD_FLOAT dtforce;
MD_FLOAT cutforce;

16
lammps/main.c
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@ -45,7 +45,8 @@
#define HLINE "----------------------------------------------------------------------------\n"
extern double computeForceLJ(Parameter*, Atom*, Neighbor*, Stats*);
extern double computeForceLJFullNeigh(Parameter*, Atom*, Neighbor*, Stats*);
extern double computeForceLJHalfNeigh(Parameter*, Atom*, Neighbor*, Stats*);
extern double computeForceEam(Eam*, Parameter*, Atom*, Neighbor*, Stats*);
void init(Parameter *param)
@ -70,6 +71,7 @@ void init(Parameter *param)
param->dtforce = 0.5 * param->dt;
param->every = 20;
param->proc_freq = 2.4;
param->halfneigh = 0;
}
double setup(
@ -258,7 +260,11 @@ int main(int argc, char** argv)
if(param.force_field == FF_EAM) {
timer[FORCE] = computeForceEam(&eam, &param, &atom, &neighbor, &stats);
} else {
timer[FORCE] = computeForceLJ(&param, &atom, &neighbor, &stats);
if( param.halfneigh ) {
timer[FORCE] = computeForceLJHalfNeigh(&param, &atom, &neighbor, &stats);
} else {
timer[FORCE] = computeForceLJFullNeigh(&param, &atom, &neighbor, &stats);
}
}
timer[NEIGH] = 0.0;
@ -284,7 +290,11 @@ int main(int argc, char** argv)
if(param.force_field == FF_EAM) {
timer[FORCE] += computeForceEam(&eam, &param, &atom, &neighbor, &stats);
} else {
timer[FORCE] += computeForceLJ(&param, &atom, &neighbor, &stats);
if( param.halfneigh ) {
timer[FORCE] = computeForceLJHalfNeigh(&param, &atom, &neighbor, &stats);
} else {
timer[FORCE] = computeForceLJFullNeigh(&param, &atom, &neighbor, &stats);
}
}
finalIntegrate(&param, &atom);

2
lammps/neighbor.c
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@ -46,6 +46,7 @@ static int nmax;
static int nstencil; // # of bins in stencil
static int* stencil; // stencil list of bin offsets
static MD_FLOAT binsizex, binsizey, binsizez;
static int halfneigh; //use half neighbour list
static int coord2bin(MD_FLOAT, MD_FLOAT , MD_FLOAT);
static MD_FLOAT bindist(int, int, int);
@ -69,6 +70,7 @@ void initNeighbor(Neighbor *neighbor, Parameter *param)
neighbor->maxneighs = 100;
neighbor->numneigh = NULL;
neighbor->neighbors = NULL;
neighbor->halfneigh = param->halfneigh;
}
void setupNeighbor(Parameter* param)