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Allow parameter reading from files and update data

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Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
This commit is contained in:
Rafael Ravedutti
2022-03-05 03:21:52 +01:00
parent aae29a5b5a
commit ba6785a865
22 changed files with 3246 additions and 676 deletions
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10
gromacs/atom.c
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@@ -31,16 +31,6 @@
#include <allocate.h>
#include <util.h>
#define DELTA 20000
#ifndef MAXLINE
#define MAXLINE 4096
#endif
#ifndef MAX
#define MAX(a,b) ((a) > (b) ? (a) : (b))
#endif
void initAtom(Atom *atom) {
atom->x = NULL; atom->y = NULL; atom->z = NULL;
atom->vx = NULL; atom->vy = NULL; atom->vz = NULL;

2
gromacs/includes/atom.h
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@@ -25,6 +25,8 @@
#ifndef __ATOM_H_
#define __ATOM_H_
#define DELTA 20000
#define CLUSTER_DIM_M 4
#define CLUSTER_DIM_N VECTOR_WIDTH

7
gromacs/includes/parameter.h
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@@ -31,10 +31,12 @@
typedef struct {
int force_field;
char* param_file;
char* input_file;
char* vtk_file;
char *xtc_file;
MD_FLOAT epsilon;
MD_FLOAT sigma;
MD_FLOAT sigma6;
MD_FLOAT temp;
MD_FLOAT rho;
@@ -58,4 +60,9 @@ typedef struct {
double proc_freq;
char* eam_file;
} Parameter;
void initParameter(Parameter*);
void readParameter(Parameter*, const char*);
void printParameter(Parameter*);
#endif

8
gromacs/includes/util.h
View File

@@ -38,6 +38,14 @@
#define DEBUG_MESSAGE
#endif
#ifndef MAXLINE
#define MAXLINE 4096
#endif
#ifndef MAX
#define MAX(a,b) ((a) > (b) ? (a) : (b))
#endif
#define FF_LJ 0
#define FF_EAM 1

51
gromacs/main.c
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@@ -20,16 +20,11 @@
* with MD-Bench. If not, see <https://www.gnu.org/licenses/>.
* =======================================================================================
*/
#include <stdlib.h>
#include <stdio.h>
#include <string.h>
#include <unistd.h>
#include <limits.h>
#include <math.h>
#include <float.h>
//--
#include <likwid-marker.h>
//--
#include <timing.h>
#include <allocate.h>
#include <neighbor.h>
@@ -56,34 +51,6 @@ extern double computeForceEam(Eam*, Parameter*, Atom*, Neighbor*, Stats*);
# define computeForceLJ computeForceLJ_4xn
#endif
void init(Parameter *param) {
param->input_file = NULL;
param->vtk_file = NULL;
param->xtc_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->reneigh_every = 20;
param->prune_every = 1000;
param->x_out_every = 20;
param->v_out_every = 5;
param->proc_freq = 2.4;
}
double setup(Parameter *param, Eam *eam, Atom *atom, Neighbor *neighbor, Stats *stats) {
if(param->force_field == FF_EAM) { initEam(eam, param); }
double S, E;
@@ -194,10 +161,13 @@ 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");
@@ -261,6 +231,7 @@ 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");
@@ -278,6 +249,9 @@ 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);
@@ -349,7 +323,6 @@ int main(int argc, char** argv) {
}
printf(HLINE);
printf("Force field: %s\n", ff2str(param.force_field));
printf("Data layout for positions: %s\n", POS_DATA_LAYOUT);
#if PRECISION == 1
printf("Using single precision floating point.\n");

156
gromacs/parameter.c Normal file
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@@ -0,0 +1,156 @@
/*
* =======================================================================================
*
* 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 <stdio.h>
#include <stdlib.h>
#include <string.h>
//---
#include <parameter.h>
#include <util.h>
void initParameter(Parameter *param) {
param->input_file = NULL;
param->vtk_file = NULL;
param->xtc_file = NULL;
param->eam_file = NULL;
param->force_field = FF_LJ;
param->epsilon = 1.0;
param->sigma = 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->reneigh_every = 20;
param->prune_every = 1000;
param->x_out_every = 20;
param->v_out_every = 5;
param->proc_freq = 2.4;
}
void readParameter(Parameter *param, const char *filename) {
FILE *fp = fopen(filename, "r");
char line[MAXLINE];
int i;
if(!fp) {
fprintf(stderr, "Could not open parameter file: %s\n", filename);
exit(-1);
}
while(!feof(fp)) {
line[0] = '\0';
fgets(line, MAXLINE, fp);
for(i = 0; line[i] != '\0' && line[i] != '#'; i++);
line[i] = '\0';
char *tok = strtok(line, " ");
char *val = strtok(NULL, " ");
#define PARSE_PARAM(p,f) if(strncmp(tok, #p, sizeof(#p) / sizeof(#p[0]) - 1) == 0) { param->p = f(val); }
#define PARSE_STRING(p) PARSE_PARAM(p, strdup)
#define PARSE_INT(p) PARSE_PARAM(p, atoi)
#define PARSE_REAL(p) PARSE_PARAM(p, atof)
if(tok != NULL && val != NULL) {
PARSE_PARAM(force_field, str2ff);
PARSE_STRING(input_file);
PARSE_STRING(eam_file);
PARSE_STRING(vtk_file);
PARSE_STRING(xtc_file);
PARSE_REAL(epsilon);
PARSE_REAL(sigma);
PARSE_REAL(rho);
PARSE_REAL(dt);
PARSE_REAL(cutforce);
PARSE_REAL(skin);
PARSE_REAL(temp);
PARSE_REAL(mass);
PARSE_REAL(proc_freq);
PARSE_INT(ntypes);
PARSE_INT(ntimes);
PARSE_INT(nx);
PARSE_INT(ny);
PARSE_INT(nz);
PARSE_INT(nstat);
PARSE_INT(reneigh_every);
PARSE_INT(prune_every);
PARSE_INT(x_out_every);
PARSE_INT(v_out_every);
}
}
// Update sigma6 parameter
MD_FLOAT s2 = param->sigma * param->sigma;
param->sigma6 = s2 * s2 * s2;
fclose(fp);
}
void printParameter(Parameter *param) {
printf("Parameters:\n");
if(param->input_file != NULL) {
printf("Input file: %s\n", param->input_file);
}
if(param->vtk_file != NULL) {
printf("VTK file: %s\n", param->vtk_file);
}
if(param->xtc_file != NULL) {
printf("XTC file: %s\n", param->xtc_file);
}
if(param->eam_file != NULL) {
printf("EAM file: %s\n", param->eam_file);
}
printf("\tForce field: %s\n", ff2str(param->force_field));
printf("\tUnit cells (nx, ny, nz): %d, %d, %d\n", param->nx, param->ny, param->nz);
printf("\tDomain box sizes (x, y, z): %e, %e, %e\n", param->xprd, param->yprd, param->zprd);
printf("\tLattice size: %e\n", param->lattice);
printf("\tEpsilon: %e\n", param->epsilon);
printf("\tSigma: %e\n", param->sigma);
printf("\tTemperature: %e\n", param->temp);
printf("\tRHO: %e\n", param->rho);
printf("\tMass: %e\n", param->mass);
printf("\tNumber of types: %d\n", param->ntypes);
printf("\tNumber of timesteps: %d\n", param->ntimes);
printf("\tReport stats every (timesteps): %d\n", param->nstat);
printf("\tReneighbor every (timesteps): %d\n", param->reneigh_every);
printf("\tPrune every (timesteps): %d\n", param->prune_every);
printf("\tOutput positions every (timesteps): %d\n", param->x_out_every);
printf("\tOutput velocities every (timesteps): %d\n", param->v_out_every);
printf("\tDelta time (dt): %e\n", param->dt);
printf("\tCutoff radius: %e\n", param->cutforce);
printf("\tSkin: %e\n", param->skin);
printf("\tProcessor frequency (GHz): %.4f\n\n", param->proc_freq);
}

2
gromacs/thermo.c
View File

@@ -65,8 +65,6 @@ void setupThermo(Parameter *param, int natoms)
e_scale = 524287.985533;//16.0;
param->dtforce /= mvv2e;
}
printf("step\ttemp\t\tpressure\n");
}
void computeThermo(int iflag, Parameter *param, Atom *atom)