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Fix integration with mass and add VTK output

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Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
This commit is contained in:
Rafael Ravedutti
2021-10-29 16:52:19 +02:00
parent d9c9cba12d
commit 0f1e824507
6 changed files with 93 additions and 3 deletions
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18
src/main.c
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@@ -40,6 +40,7 @@
#include <pbc.h>
#include <timers.h>
#include <eam.h>
#include <vtk.h>
#define HLINE "----------------------------------------------------------------------------\n"
@@ -50,6 +51,7 @@ extern double computeForceEam(Eam* eam, Atom *atom, Neighbor *neighbor, Stats *s
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;
@@ -77,6 +79,7 @@ double setup(
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));
param->xprd = param->nx * param->lattice;
@@ -84,7 +87,6 @@ double setup(
param->zprd = param->nz * param->lattice;
S = getTimeStamp();
if(param->force_field == FF_EAM) { initEam(eam, param); }
initAtom(atom);
initNeighbor(neighbor, param);
initPbc();
@@ -232,6 +234,11 @@ int main(int argc, char** argv)
param.proc_freq = atof(argv[++i]);
continue;
}
if((strcmp(argv[i], "--vtk") == 0))
{
param.vtk_file = strdup(argv[++i]);
continue;
}
if((strcmp(argv[i], "-h") == 0) || (strcmp(argv[i], "--help") == 0))
{
printf("MD Bench: A minimalistic re-implementation of miniMD\n");
@@ -241,6 +248,7 @@ int main(int argc, char** argv)
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("--freq <real>: processor frequency (GHz)\n");
printf("--vtk <string>: VTK file for visualization\n");
printf(HLINE);
exit(EXIT_SUCCESS);
}
@@ -262,6 +270,10 @@ int main(int argc, char** argv)
timer[NEIGH] = 0.0;
timer[TOTAL] = getTimeStamp();
if(param.vtk_file != NULL) {
write_atoms_to_vtk_file(param.vtk_file, &atom, 0);
}
for(int n = 0; n < param.ntimes; n++) {
initialIntegrate(&param, &atom);
@@ -285,6 +297,10 @@ int main(int argc, char** argv)
if(!((n + 1) % param.nstat) && (n+1) < param.ntimes) {
computeThermo(n + 1, &param, &atom);
}
if(param.vtk_file != NULL) {
write_atoms_to_vtk_file(param.vtk_file, &atom, n + 1);
}
}
timer[TOTAL] = getTimeStamp() - timer[TOTAL];