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Add parameter reading for LAMMPS variant

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Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
This commit is contained in:
Rafael Ravedutti
2022-03-17 02:44:34 +01:00
parent d4b34e1fa4
commit 887f41871c
11 changed files with 293 additions and 80 deletions
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75
lammps/main.c
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@@ -49,39 +49,7 @@ 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)
{
param->input_file = NULL;
param->vtk_file = NULL;
param->force_field = FF_LJ;
param->epsilon = 1.0;
param->sigma6 = 1.0;
param->rho = 0.8442;
param->ntypes = 4;
param->ntimes = 200;
param->dt = 0.005;
param->nx = 32;
param->ny = 32;
param->nz = 32;
param->cutforce = 2.5;
param->skin = 0.3;
param->cutneigh = param->cutforce + param->skin;
param->temp = 1.44;
param->nstat = 100;
param->mass = 1.0;
param->dtforce = 0.5 * param->dt;
param->every = 20;
param->proc_freq = 2.4;
param->halfneigh = 1;
}
double setup(
Parameter *param,
Eam *eam,
Atom *atom,
Neighbor *neighbor,
Stats *stats)
{
double setup(Parameter *param, Eam *eam, Atom *atom, Neighbor *neighbor, Stats *stats) {
if(param->force_field == FF_EAM) { initEam(eam, param); }
double S, E;
param->lattice = pow((4.0 / param->rho), (1.0 / 3.0));
@@ -99,6 +67,7 @@ double setup(
} else {
readAtom(atom, param);
}
setupNeighbor(param);
setupThermo(param, atom->Natoms);
if(param->input_file == NULL) { adjustThermo(param, atom); }
@@ -106,17 +75,11 @@ double setup(
updatePbc(atom, param);
buildNeighbor(atom, neighbor);
E = getTimeStamp();
return E-S;
}
double reneighbour(
Parameter *param,
Atom *atom,
Neighbor *neighbor)
{
double reneighbour(Parameter *param, Atom *atom, Neighbor *neighbor) {
double S, E;
S = getTimeStamp();
LIKWID_MARKER_START("reneighbour");
updateAtomsPbc(atom, param);
@@ -126,12 +89,10 @@ double reneighbour(
buildNeighbor(atom, neighbor);
LIKWID_MARKER_STOP("reneighbour");
E = getTimeStamp();
return E-S;
}
void initialIntegrate(Parameter *param, Atom *atom)
{
void initialIntegrate(Parameter *param, Atom *atom) {
MD_FLOAT* fx = atom->fx; MD_FLOAT* fy = atom->fy; MD_FLOAT* fz = atom->fz;
MD_FLOAT* vx = atom->vx; MD_FLOAT* vy = atom->vy; MD_FLOAT* vz = atom->vz;
@@ -145,8 +106,7 @@ void initialIntegrate(Parameter *param, Atom *atom)
}
}
void finalIntegrate(Parameter *param, Atom *atom)
{
void finalIntegrate(Parameter *param, Atom *atom) {
MD_FLOAT* fx = atom->fx; MD_FLOAT* fy = atom->fy; MD_FLOAT* fz = atom->fz;
MD_FLOAT* vx = atom->vx; MD_FLOAT* vy = atom->vy; MD_FLOAT* vz = atom->vz;
@@ -157,8 +117,7 @@ void finalIntegrate(Parameter *param, Atom *atom)
}
}
void printAtomState(Atom *atom)
{
void printAtomState(Atom *atom) {
printf("Atom counts: Natoms=%d Nlocal=%d Nghost=%d Nmax=%d\n",
atom->Natoms, atom->Nlocal, atom->Nghost, atom->Nmax);
@@ -169,8 +128,7 @@ void printAtomState(Atom *atom)
/* } */
}
int main(int argc, char** argv)
{
int main(int argc, char** argv) {
double timer[NUMTIMER];
Eam eam;
Atom atom;
@@ -185,10 +143,13 @@ int main(int argc, char** argv)
//LIKWID_MARKER_REGISTER("reneighbour");
//LIKWID_MARKER_REGISTER("pbc");
}
init(&param);
for(int i = 0; i < argc; i++)
{
initParameter(&param);
for(int i = 0; i < argc; i++) {
if((strcmp(argv[i], "-p") == 0)) {
readParameter(&param, argv[++i]);
continue;
}
if((strcmp(argv[i], "-f") == 0)) {
if((param.force_field = str2ff(argv[++i])) < 0) {
fprintf(stderr, "Invalid force field!\n");
@@ -239,6 +200,7 @@ int main(int argc, char** argv)
if((strcmp(argv[i], "-h") == 0) || (strcmp(argv[i], "--help") == 0)) {
printf("MD Bench: A minimalistic re-implementation of miniMD\n");
printf(HLINE);
printf("-p <string>: file to read parameters from (can be specified more than once)\n");
printf("-f <string>: force field (lj or eam), default lj\n");
printf("-i <string>: input file with atom positions (dump)\n");
printf("-e <string>: input file for EAM\n");
@@ -255,6 +217,9 @@ int main(int argc, char** argv)
param.cutneigh = param.cutforce + param.skin;
setup(&param, &eam, &atom, &neighbor, &stats);
printParameter(&param);
printf("step\ttemp\t\tpressure\n");
computeThermo(0, &param, &atom);
#if defined(MEM_TRACER) || defined(INDEX_TRACER)
traceAddresses(&param, &atom, &neighbor, n + 1);
@@ -262,7 +227,7 @@ int main(int argc, char** argv)
if(param.force_field == FF_EAM) {
timer[FORCE] = computeForceEam(&eam, &param, &atom, &neighbor, &stats);
} else {
if( param.halfneigh ) {
if(param.half_neigh) {
timer[FORCE] = computeForceLJHalfNeigh(&param, &atom, &neighbor, &stats);
} else {
timer[FORCE] = computeForceLJFullNeigh(&param, &atom, &neighbor, &stats);
@@ -279,7 +244,7 @@ int main(int argc, char** argv)
for(int n = 0; n < param.ntimes; n++) {
initialIntegrate(&param, &atom);
if((n + 1) % param.every) {
if((n + 1) % param.reneigh_every) {
updatePbc(&atom, &param);
} else {
timer[NEIGH] += reneighbour(&param, &atom, &neighbor);
@@ -292,7 +257,7 @@ int main(int argc, char** argv)
if(param.force_field == FF_EAM) {
timer[FORCE] += computeForceEam(&eam, &param, &atom, &neighbor, &stats);
} else {
if( param.halfneigh ) {
if(param.half_neigh) {
timer[FORCE] = computeForceLJHalfNeigh(&param, &atom, &neighbor, &stats);
} else {
timer[FORCE] = computeForceLJFullNeigh(&param, &atom, &neighbor, &stats);