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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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2
src/eam_utils.c
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@@ -44,11 +44,13 @@ void initEam(Eam* eam, Parameter* param) {
void coeff(Eam* eam, Parameter* param) {
read_file(&eam->file, param->input_file);
param->mass = eam->file.mass;
param->cutforce = eam->file.cut;
param->cutneigh = param->cutforce + 1.0;
param->temp = 600.0;
param->dt = 0.001;
param->rho = 0.07041125;
param->dtforce = 0.5 * param->dt / param->mass;
}
void init_style(Eam* eam, Parameter* param) {

1
src/includes/parameter.h
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@@ -35,6 +35,7 @@
typedef struct {
int force_field;
char* input_file;
char* vtk_file;
MD_FLOAT epsilon;
MD_FLOAT sigma6;
MD_FLOAT temp;

28
src/includes/vtk.h Normal file
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@@ -0,0 +1,28 @@
/*
* =======================================================================================
*
* Author: Jan Eitzinger (je), jan.eitzinger@fau.de
* Copyright (c) 2020 RRZE, University Erlangen-Nuremberg
*
* This file is part of MD-Bench.
*
* MD-Bench is free software: you can redistribute it and/or modify it
* under the terms of the GNU Lesser General Public License as published
* by the Free Software Foundation, either version 3 of the License, or
* (at your option) any later version.
*
* MD-Bench is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A
* PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License along
* with MD-Bench. If not, see <https://www.gnu.org/licenses/>.
* =======================================================================================
*/
#include <atom.h>
#ifndef __VTK_H_
#define __VTK_H_
extern int write_atoms_to_vtk_file(const char* filename, Atom* atom, int timestep);
#endif

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];

3
src/thermo.c
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@@ -31,7 +31,7 @@ static MD_FLOAT *tmparr;
static MD_FLOAT *engarr;
static MD_FLOAT *prsarr;
static MD_FLOAT mvv2e;
static int dof_boltz;
static MD_FLOAT dof_boltz;
static MD_FLOAT t_scale;
static MD_FLOAT p_scale;
static MD_FLOAT e_scale;
@@ -81,7 +81,6 @@ void computeThermo(int iflag, Parameter *param, Atom *atom)
t = t * t_scale;
p = (t * dof_boltz) * p_scale;
int istep = iflag;
if(iflag == -1){

44
src/vtk.c Normal file
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@@ -0,0 +1,44 @@
#include <stdio.h>
#include <stdlib.h>
#include <atom.h>
int write_atoms_to_vtk_file(const char* filename, Atom* atom, int timestep) {
char timestep_filename[128];
snprintf(timestep_filename, sizeof timestep_filename, "%s_%d.vtk", filename, timestep);
FILE* fp = fopen(timestep_filename, "wb");
if(fp == NULL) {
fprintf(stderr, "Could not open VTK file for writing!\n");
return -1;
}
fprintf(fp, "# vtk DataFile Version 2.0\n");
fprintf(fp, "Particle data\n");
fprintf(fp, "ASCII\n");
fprintf(fp, "DATASET UNSTRUCTURED_GRID\n");
fprintf(fp, "POINTS %d double\n", atom->Nlocal);
for(int i = 0; i < atom->Nlocal; ++i) {
fprintf(fp, "%.4f %.4f %.4f\n", atom_x(i), atom_y(i), atom_z(i));
}
fprintf(fp, "\n\n");
fprintf(fp, "CELLS %d %d\n", atom->Nlocal, atom->Nlocal * 2);
for(int i = 0; i < atom->Nlocal; ++i) {
fprintf(fp, "1 %d\n", i);
}
fprintf(fp, "\n\n");
fprintf(fp, "CELL_TYPES %d\n", atom->Nlocal);
for(int i = 0; i < atom->Nlocal; ++i) {
fprintf(fp, "1\n");
}
fprintf(fp, "\n\n");
fprintf(fp, "POINT_DATA %d\n", atom->Nlocal);
fprintf(fp, "SCALARS mass double\n");
fprintf(fp, "LOOKUP_TABLE default\n");
for(int i = 0; i < atom->Nlocal; i++) {
fprintf(fp, "1.0\n");
}
fprintf(fp, "\n\n");
fclose(fp);
return 0;
}