*
*/
-#include "moldyn.h"
-
+#define _GNU_SOURCE
#include <stdio.h>
#include <stdlib.h>
+#include <string.h>
+#include <sys/types.h>
+#include <sys/stat.h>
+#include <fcntl.h>
+#include <unistd.h>
#include <math.h>
+#include "moldyn.h"
+
#include "math/math.h"
#include "init/init.h"
#include "random/random.h"
#include "visual/visual.h"
+int moldyn_usage(char **argv) {
+
+ printf("\n%s usage:\n\n",argv[0]);
+ printf("--- general options ---\n");
+ printf("-E <steps> <file> (log total energy)\n");
+ printf("-M <steps> <file> (log total momentum)\n");
+ printf("-D <steps> <file> (dump total information)\n");
+ printf("-S <steps> <filebase> (single save file)\n");
+ printf("-V <steps> <filebase> (rasmol file)\n");
+ printf("--- physics options ---\n");
+ printf("-T <temperature> [K] (%f)\n",MOLDYN_TEMP);
+ printf("-t <timestep tau> [s] (%f)\n",MOLDYN_TAU);
+ printf("-R <runs> (%d)\n",MOLDYN_RUNS);
+ printf("\n");
+
+ return 0;
+}
+
+int moldyn_parse_argv(t_moldyn *moldyn,int argc,char **argv) {
+
+ int i;
+
+ memset(moldyn,0,sizeof(t_moldyn));
+
+ /* default values */
+ moldyn->t=MOLDYN_TEMP;
+ moldyn->tau=MOLDYN_TAU;
+ moldyn->time_steps=MOLDYN_RUNS;
+
+ /* parse argv */
+ for(i=1;i<argc;i++) {
+ if(argv[i][0]=='-') {
+ switch(argv[i][1]){
+ case 'E':
+ moldyn->ewrite=atoi(argv[++i]);
+ strncpy(moldyn->efb,argv[++i],64);
+ break;
+ case 'M':
+ moldyn->mwrite=atoi(argv[++i]);
+ strncpy(moldyn->mfb,argv[++i],64);
+ break;
+ case 'D':
+ moldyn->dwrite=atoi(argv[++i]);
+ strncpy(moldyn->dfb,argv[++i],64);
+ break;
+ case 'S':
+ moldyn->swrite=atoi(argv[++i]);
+ strncpy(moldyn->sfb,argv[++i],64);
+ break;
+ case 'V':
+ moldyn->vwrite=atoi(argv[++i]);
+ strncpy(moldyn->vfb,argv[++i],64);
+ break;
+ case 'T':
+ moldyn->t=atof(argv[++i]);
+ break;
+ case 't':
+ moldyn->tau=atof(argv[++i]);
+ break;
+ case 'R':
+ moldyn->time_steps=atoi(argv[++i]);
+ break;
+ default:
+ printf("unknown option %s\n",argv[i]);
+ moldyn_usage(argv);
+ return -1;
+ }
+ } else {
+ moldyn_usage(argv);
+ return -1;
+ }
+ }
+
+ return 0;
+}
+
+int moldyn_log_init(t_moldyn *moldyn,void *v) {
+
+ moldyn->lvstat=0;
+ t_visual *vis;
+
+ vis=v;
+
+ if(moldyn->ewrite) {
+ moldyn->efd=open(moldyn->efb,O_WRONLY|O_CREAT|O_TRUNC);
+ if(moldyn->efd<0) {
+ perror("[moldyn] efd open");
+ return moldyn->efd;
+ }
+ dprintf(moldyn->efd,"# moldyn total energy logfile\n");
+ moldyn->lvstat|=MOLDYN_LVSTAT_TOTAL_E;
+ }
+
+ if(moldyn->mwrite) {
+ moldyn->mfd=open(moldyn->mfb,O_WRONLY|O_CREAT|O_TRUNC);
+ if(moldyn->mfd<0) {
+ perror("[moldyn] mfd open");
+ return moldyn->mfd;
+ }
+ dprintf(moldyn->mfd,"# moldyn total momentum logfile\n");
+ moldyn->lvstat|=MOLDYN_LVSTAT_TOTAL_M;
+ }
+
+ if(moldyn->swrite)
+ moldyn->lvstat|=MOLDYN_LVSTAT_SAVE;
+
+ if(moldyn->dwrite) {
+ moldyn->dfd=open(moldyn->dfb,O_WRONLY|O_CREAT|O_TRUNC);
+ if(moldyn->dfd<0) {
+ perror("[moldyn] dfd open");
+ return moldyn->dfd;
+ }
+ write(moldyn->dfd,moldyn,sizeof(t_moldyn));
+ moldyn->lvstat|=MOLDYN_LVSTAT_DUMP;
+ }
+
+ if((moldyn->vwrite)&&(vis)) {
+ moldyn->visual=vis;
+ visual_init(vis,moldyn->vfb);
+ moldyn->lvstat|=MOLDYN_LVSTAT_VISUAL;
+ }
+
+ moldyn->lvstat|=MOLDYN_LVSTAT_INITIALIZED;
+
+ return 0;
+}
+
+int moldyn_shutdown(t_moldyn *moldyn) {
+
+ if(moldyn->efd) close(moldyn->efd);
+ if(moldyn->mfd) close(moldyn->efd);
+ if(moldyn->dfd) close(moldyn->efd);
+ if(moldyn->visual) visual_tini(moldyn->visual);
+
+ return 0;
+}
int create_lattice(unsigned char type,int element,double mass,double lc,
int a,int b,int c,t_atom **atom) {
return 0;
}
-int thermal_init(t_atom *atom,t_random *random,int count,double t) {
+int thermal_init(t_moldyn *moldyn,t_random *random,int count) {
/*
* - gaussian distribution of velocities
int i;
double v,sigma;
t_3dvec p_total,delta;
+ t_atom *atom;
+
+ atom=moldyn->atom;
/* gaussian distribution of velocities */
v3_zero(&p_total);
for(i=0;i<count;i++) {
- sigma=sqrt(2.0*K_BOLTZMANN*t/atom[i].mass);
+ sigma=sqrt(2.0*K_BOLTZMANN*moldyn->t/atom[i].mass);
/* x direction */
v=sigma*rand_get_gauss(random);
atom[i].v.x=v;
}
/* velocity scaling */
- scale_velocity(atom,count,t);
+ scale_velocity(moldyn,count);
return 0;
}
-int scale_velocity(t_atom *atom,int count,double t) {
+int scale_velocity(t_moldyn *moldyn,int count) {
int i;
double e,c;
+ t_atom *atom;
+
+ atom=moldyn->atom;
/*
* - velocity scaling (E = 3/2 N k T), E: kinetic energy
e=0.0;
for(i=0;i<count;i++)
e+=0.5*atom[i].mass*v3_absolute_square(&(atom[i].v));
- c=sqrt((2.0*e)/(3.0*count*K_BOLTZMANN*t));
+ c=sqrt((2.0*e)/(3.0*count*K_BOLTZMANN*moldyn->t));
for(i=0;i<count;i++)
v3_scale(&(atom[i].v),&(atom[i].v),(1.0/c));
int moldyn_integrate(t_moldyn *moldyn) {
int i;
- int write;
+ unsigned int e,m,s,d,v;
+ t_3dvec p;
- write=moldyn->write;
+ int fd;
+ char fb[128];
+
+ e=moldyn->ewrite;
+ m=moldyn->mwrite;
+ s=moldyn->swrite;
+ d=moldyn->dwrite;
+ v=moldyn->vwrite;
+
+ if(!(moldyn->lvstat&MOLDYN_LVSTAT_INITIALIZED)) {
+ printf("[moldyn] warning, lv system not initialized\n");
+ return -1;
+ }
/* calculate initial forces */
moldyn->force(moldyn);
/* integration step */
moldyn->integrate(moldyn);
- /* check for visualiziation */
- if(!(i%write)) {
- visual_atoms(moldyn->visual,i*moldyn->tau,
- moldyn->atom,moldyn->count);
+ /* check for log & visualiziation */
+ if(e) {
+ if(!(i%e))
+ dprintf(moldyn->efd,
+ "%.15f %.45f\n",i*moldyn->tau,
+ get_total_energy(moldyn));
+ }
+ if(m) {
+ if(!(i%m)) {
+ p=get_total_p(moldyn->atom,moldyn->count);
+ dprintf(moldyn->mfd,
+ "%.15f %.45f\n",i*moldyn->tau,
+ v3_norm(&p));
+ }
+ }
+ if(s) {
+ if(!(i%s)) {
+ snprintf(fb,128,"%s-%f-%.15f.save",moldyn->sfb,
+ moldyn->t,i*moldyn->tau);
+ fd=open(fb,O_WRONLY|O_TRUNC|O_CREAT);
+ if(fd<0) perror("[moldyn] save fd open");
+ else {
+ write(fd,moldyn,sizeof(t_moldyn));
+ write(fd,moldyn->atom,
+ moldyn->count*sizeof(t_atom));
+ }
+ }
+ }
+ if(d) {
+ if(!(i%d))
+ write(moldyn->dfd,moldyn->atom,
+ moldyn->count*sizeof(t_atom));
+
+ }
+ if(v) {
+ if(!(i%v))
+ visual_atoms(moldyn->visual,i*moldyn->tau,
+ moldyn->atom,moldyn->count);
}
}
projects / physik / posic.git / blobdiff