moebiusband/MD-Bench
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

Add cutoff radius and skin as parameters of simulation

Browse Source 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
This commit is contained in:
Rafael Ravedutti 2022-02-28 22:34:42 +01:00
parent 1389f89fb7
commit 022aa75c75
4 changed files with 48 additions and 42 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

1
gromacs/includes/parameter.h
View File

@ -46,6 +46,7 @@ typedef struct {
MD_FLOAT dt; MD_FLOAT dt;
MD_FLOAT dtforce; MD_FLOAT dtforce;
MD_FLOAT cutforce; MD_FLOAT cutforce;
MD_FLOAT skin;
MD_FLOAT cutneigh; MD_FLOAT cutneigh;
int nx, ny, nz; int nx, ny, nz;
MD_FLOAT lattice; MD_FLOAT lattice;

44
gromacs/main.c
View File

@ -69,7 +69,8 @@ void init(Parameter *param) {
param->ny = 32; param->ny = 32;
param->nz = 32; param->nz = 32;
param->cutforce = 2.5; param->cutforce = 2.5;
param->cutneigh = param->cutforce + 0.30; param->skin = 0.3;
param->cutneigh = param->cutforce + param->skin;
param->temp = 1.44; param->temp = 1.44;
param->nstat = 100; param->nstat = 100;
param->mass = 1.0; param->mass = 1.0;
@ -193,56 +194,54 @@ int main(int argc, char** argv) {
for(int i = 0; i < argc; i++) for(int i = 0; i < argc; i++)
{ {
if((strcmp(argv[i], "-f") == 0)) if((strcmp(argv[i], "-f") == 0)) {
{
if((param.force_field = str2ff(argv[++i])) < 0) { if((param.force_field = str2ff(argv[++i])) < 0) {
fprintf(stderr, "Invalid force field!\n"); fprintf(stderr, "Invalid force field!\n");
exit(-1); exit(-1);
} }
continue; continue;
} }
if((strcmp(argv[i], "-i") == 0)) if((strcmp(argv[i], "-i") == 0)) {
{
param.input_file = strdup(argv[++i]); param.input_file = strdup(argv[++i]);
continue; continue;
} }
if((strcmp(argv[i], "-e") == 0)) if((strcmp(argv[i], "-e") == 0)) {
{
param.eam_file = strdup(argv[++i]); param.eam_file = strdup(argv[++i]);
continue; continue;
} }
if((strcmp(argv[i], "-n") == 0) || (strcmp(argv[i], "--nsteps") == 0)) if((strcmp(argv[i], "-n") == 0) || (strcmp(argv[i], "--nsteps") == 0)) {
{
param.ntimes = atoi(argv[++i]); param.ntimes = atoi(argv[++i]);
continue; continue;
} }
if((strcmp(argv[i], "-nx") == 0)) if((strcmp(argv[i], "-nx") == 0)) {
{
param.nx = atoi(argv[++i]); param.nx = atoi(argv[++i]);
continue; continue;
} }
if((strcmp(argv[i], "-ny") == 0)) if((strcmp(argv[i], "-ny") == 0)) {
{
param.ny = atoi(argv[++i]); param.ny = atoi(argv[++i]);
continue; continue;
} }
if((strcmp(argv[i], "-nz") == 0)) if((strcmp(argv[i], "-nz") == 0)) {
{
param.nz = atoi(argv[++i]); param.nz = atoi(argv[++i]);
continue; continue;
} }
if((strcmp(argv[i], "--freq") == 0)) if((strcmp(argv[i], "-r") == 0) || (strcmp(argv[i], "--radius") == 0)) {
{ param.cutforce = atof(argv[++i]);
continue;
}
if((strcmp(argv[i], "-s") == 0) || (strcmp(argv[i], "--skin") == 0)) {
param.skin = atof(argv[++i]);
continue;
}
if((strcmp(argv[i], "--freq") == 0)) {
param.proc_freq = atof(argv[++i]); param.proc_freq = atof(argv[++i]);
continue; continue;
} }
if((strcmp(argv[i], "--vtk") == 0)) if((strcmp(argv[i], "--vtk") == 0)) {
{
param.vtk_file = strdup(argv[++i]); param.vtk_file = strdup(argv[++i]);
continue; continue;
} }
if((strcmp(argv[i], "-h") == 0) || (strcmp(argv[i], "--help") == 0)) if((strcmp(argv[i], "-h") == 0) || (strcmp(argv[i], "--help") == 0)) {
{
printf("MD Bench: A minimalistic re-implementation of miniMD\n"); printf("MD Bench: A minimalistic re-implementation of miniMD\n");
printf(HLINE); printf(HLINE);
printf("-f <string>: force field (lj or eam), default lj\n"); printf("-f <string>: force field (lj or eam), default lj\n");
@ -250,6 +249,8 @@ int main(int argc, char** argv) {
printf("-e <string>: input file for EAM\n"); printf("-e <string>: input file for EAM\n");
printf("-n / --nsteps <int>: set number of timesteps for simulation\n"); printf("-n / --nsteps <int>: set number of timesteps for simulation\n");
printf("-nx/-ny/-nz <int>: set linear dimension of systembox in x/y/z direction\n"); printf("-nx/-ny/-nz <int>: set linear dimension of systembox in x/y/z direction\n");
printf("-r / --radius <real>: set cutoff radius\n");
printf("-s / --skin <real>: set skin (verlet buffer)\n");
printf("--freq <real>: processor frequency (GHz)\n"); printf("--freq <real>: processor frequency (GHz)\n");
printf("--vtk <string>: VTK file for visualization\n"); printf("--vtk <string>: VTK file for visualization\n");
printf(HLINE); printf(HLINE);
@ -257,6 +258,7 @@ int main(int argc, char** argv) {
} }
} }
param.cutneigh = param.cutforce + param.skin;
setup(&param, &eam, &atom, &neighbor, &stats); setup(&param, &eam, &atom, &neighbor, &stats);
computeThermo(0, &param, &atom); computeThermo(0, &param, &atom);
#if defined(MEM_TRACER) || defined(INDEX_TRACER) #if defined(MEM_TRACER) || defined(INDEX_TRACER)

1
lammps/includes/parameter.h
View File

@ -44,6 +44,7 @@ typedef struct {
int every; int every;
MD_FLOAT dt; MD_FLOAT dt;
MD_FLOAT dtforce; MD_FLOAT dtforce;
MD_FLOAT skin;
MD_FLOAT cutforce; MD_FLOAT cutforce;
MD_FLOAT cutneigh; MD_FLOAT cutneigh;
int nx, ny, nz; int nx, ny, nz;

44
lammps/main.c
View File

@ -63,7 +63,8 @@ void init(Parameter *param)
param->ny = 32; param->ny = 32;
param->nz = 32; param->nz = 32;
param->cutforce = 2.5; param->cutforce = 2.5;
param->cutneigh = param->cutforce + 0.30; param->skin = 0.3;
param->cutneigh = param->cutforce + param->skin;
param->temp = 1.44; param->temp = 1.44;
param->nstat = 100; param->nstat = 100;
param->mass = 1.0; param->mass = 1.0;
@ -186,56 +187,54 @@ int main(int argc, char** argv)
for(int i = 0; i < argc; i++) for(int i = 0; i < argc; i++)
{ {
if((strcmp(argv[i], "-f") == 0)) if((strcmp(argv[i], "-f") == 0)) {
{
if((param.force_field = str2ff(argv[++i])) < 0) { if((param.force_field = str2ff(argv[++i])) < 0) {
fprintf(stderr, "Invalid force field!\n"); fprintf(stderr, "Invalid force field!\n");
exit(-1); exit(-1);
} }
continue; continue;
} }
if((strcmp(argv[i], "-i") == 0)) if((strcmp(argv[i], "-i") == 0)) {
{
param.input_file = strdup(argv[++i]); param.input_file = strdup(argv[++i]);
continue; continue;
} }
if((strcmp(argv[i], "-e") == 0)) if((strcmp(argv[i], "-e") == 0)) {
{
param.eam_file = strdup(argv[++i]); param.eam_file = strdup(argv[++i]);
continue; continue;
} }
if((strcmp(argv[i], "-n") == 0) || (strcmp(argv[i], "--nsteps") == 0)) if((strcmp(argv[i], "-n") == 0) || (strcmp(argv[i], "--nsteps") == 0)) {
{
param.ntimes = atoi(argv[++i]); param.ntimes = atoi(argv[++i]);
continue; continue;
} }
if((strcmp(argv[i], "-nx") == 0)) if((strcmp(argv[i], "-nx") == 0)) {
{
param.nx = atoi(argv[++i]); param.nx = atoi(argv[++i]);
continue; continue;
} }
if((strcmp(argv[i], "-ny") == 0)) if((strcmp(argv[i], "-ny") == 0)) {
{
param.ny = atoi(argv[++i]); param.ny = atoi(argv[++i]);
continue; continue;
} }
if((strcmp(argv[i], "-nz") == 0)) if((strcmp(argv[i], "-nz") == 0)) {
{
param.nz = atoi(argv[++i]); param.nz = atoi(argv[++i]);
continue; continue;
} }
if((strcmp(argv[i], "--freq") == 0)) if((strcmp(argv[i], "-r") == 0) || (strcmp(argv[i], "--radius") == 0)) {
{ param.cutforce = atof(argv[++i]);
continue;
}
if((strcmp(argv[i], "-s") == 0) || (strcmp(argv[i], "--skin") == 0)) {
param.skin = atof(argv[++i]);
continue;
}
if((strcmp(argv[i], "--freq") == 0)) {
param.proc_freq = atof(argv[++i]); param.proc_freq = atof(argv[++i]);
continue; continue;
} }
if((strcmp(argv[i], "--vtk") == 0)) if((strcmp(argv[i], "--vtk") == 0)) {
{
param.vtk_file = strdup(argv[++i]); param.vtk_file = strdup(argv[++i]);
continue; continue;
} }
if((strcmp(argv[i], "-h") == 0) || (strcmp(argv[i], "--help") == 0)) if((strcmp(argv[i], "-h") == 0) || (strcmp(argv[i], "--help") == 0)) {
{
printf("MD Bench: A minimalistic re-implementation of miniMD\n"); printf("MD Bench: A minimalistic re-implementation of miniMD\n");
printf(HLINE); printf(HLINE);
printf("-f <string>: force field (lj or eam), default lj\n"); printf("-f <string>: force field (lj or eam), default lj\n");
@ -243,6 +242,8 @@ int main(int argc, char** argv)
printf("-e <string>: input file for EAM\n"); printf("-e <string>: input file for EAM\n");
printf("-n / --nsteps <int>: set number of timesteps for simulation\n"); printf("-n / --nsteps <int>: set number of timesteps for simulation\n");
printf("-nx/-ny/-nz <int>: set linear dimension of systembox in x/y/z direction\n"); printf("-nx/-ny/-nz <int>: set linear dimension of systembox in x/y/z direction\n");
printf("-r / --radius <real>: set cutoff radius\n");
printf("-s / --skin <real>: set skin (verlet buffer)\n");
printf("--freq <real>: processor frequency (GHz)\n"); printf("--freq <real>: processor frequency (GHz)\n");
printf("--vtk <string>: VTK file for visualization\n"); printf("--vtk <string>: VTK file for visualization\n");
printf(HLINE); printf(HLINE);
@ -250,6 +251,7 @@ int main(int argc, char** argv)
} }
} }
param.cutneigh = param.cutforce + param.skin;
setup(&param, &eam, &atom, &neighbor, &stats); setup(&param, &eam, &atom, &neighbor, &stats);
computeThermo(0, &param, &atom); computeThermo(0, &param, &atom);
#if defined(MEM_TRACER) || defined(INDEX_TRACER) #if defined(MEM_TRACER) || defined(INDEX_TRACER)