MD-Bench/gromacs/thermo.c
Rafael Ravedutti ba6785a865 Allow parameter reading from files and update data
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
2022-03-05 03:21:52 +01:00

137 lines
3.8 KiB
C

/*
* =======================================================================================
*
* 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 <stdlib.h>
#include <stdio.h>
#include <math.h>
#include <thermo.h>
#include <util.h>
static int *steparr;
static MD_FLOAT *tmparr;
static MD_FLOAT *engarr;
static MD_FLOAT *prsarr;
static MD_FLOAT mvv2e;
static MD_FLOAT dof_boltz;
static MD_FLOAT t_scale;
static MD_FLOAT p_scale;
static MD_FLOAT e_scale;
static MD_FLOAT t_act;
static MD_FLOAT p_act;
static MD_FLOAT e_act;
static int mstat;
/* exported subroutines */
void setupThermo(Parameter *param, int natoms)
{
int maxstat = param->ntimes / param->nstat + 2;
steparr = (int*) malloc(maxstat * sizeof(int));
tmparr = (MD_FLOAT*) malloc(maxstat * sizeof(MD_FLOAT));
engarr = (MD_FLOAT*) malloc(maxstat * sizeof(MD_FLOAT));
prsarr = (MD_FLOAT*) malloc(maxstat * sizeof(MD_FLOAT));
if(param->force_field == FF_LJ) {
mvv2e = 1.0;
dof_boltz = (natoms * 3 - 3);
t_scale = mvv2e / dof_boltz;
p_scale = 1.0 / 3 / param->xprd / param->yprd / param->zprd;
e_scale = 0.5;
} else {
mvv2e = 1.036427e-04;
dof_boltz = (natoms * 3 - 3) * 8.617343e-05;
t_scale = mvv2e / dof_boltz;
p_scale = 1.602176e+06 / 3 / param->xprd / param->yprd / param->zprd;
e_scale = 524287.985533;//16.0;
param->dtforce /= mvv2e;
}
}
void computeThermo(int iflag, Parameter *param, Atom *atom)
{
MD_FLOAT t = 0.0, p;
MD_FLOAT* vx = atom->vx;
MD_FLOAT* vy = atom->vy;
MD_FLOAT* vz = atom->vz;
for(int i = 0; i < atom->Nlocal; i++) {
t += (vx[i] * vx[i] + vy[i] * vy[i] + vz[i] * vz[i]) * param->mass;
}
t = t * t_scale;
p = (t * dof_boltz) * p_scale;
int istep = iflag;
if(iflag == -1){
istep = param->ntimes;
}
if(iflag == 0){
mstat = 0;
}
steparr[mstat] = istep;
tmparr[mstat] = t;
prsarr[mstat] = p;
mstat++;
fprintf(stdout, "%i\t%e\t%e\n", istep, t, p);
}
void adjustThermo(Parameter *param, Atom *atom)
{
/* zero center-of-mass motion */
MD_FLOAT vxtot = 0.0; MD_FLOAT vytot = 0.0; MD_FLOAT vztot = 0.0;
MD_FLOAT* vx = atom->vx; MD_FLOAT* vy = atom->vy; MD_FLOAT* vz = atom->vz;
for(int i = 0; i < atom->Nlocal; i++) {
vxtot += vx[i];
vytot += vy[i];
vztot += vz[i];
}
vxtot = vxtot / atom->Natoms;
vytot = vytot / atom->Natoms;
vztot = vztot / atom->Natoms;
for(int i = 0; i < atom->Nlocal; i++) {
vx[i] -= vxtot;
vy[i] -= vytot;
vz[i] -= vztot;
}
t_act = 0;
MD_FLOAT t = 0.0;
for(int i = 0; i < atom->Nlocal; i++) {
t += (vx[i] * vx[i] + vy[i] * vy[i] + vz[i] * vz[i]) * param->mass;
}
t *= t_scale;
MD_FLOAT factor = sqrt(param->temp / t);
for(int i = 0; i < atom->Nlocal; i++) {
vx[i] *= factor;
vy[i] *= factor;
vz[i] *= factor;
}
}