#include <sys/stat.h>
#include <fcntl.h>
#include <unistd.h>
+#include <sys/time.h>
+#include <time.h>
#include <math.h>
#include "moldyn.h"
return 0;
}
+int del_atom(t_moldyn *moldyn,int tag) {
+
+ t_atom *new,*old;
+ int cnt;
+
+ old=moldyn->atom;
+
+ new=(t_atom *)malloc((moldyn->count-1)*sizeof(t_atom));
+ if(!new) {
+ perror("[moldyn]malloc (del atom)");
+ return -1;
+ }
+
+ for(cnt=0;cnt<tag;cnt++)
+ new[cnt]=old[cnt];
+
+ for(cnt=tag+1;cnt<moldyn->count;cnt++) {
+ new[cnt-1]=old[cnt];
+ new[cnt-1].tag=cnt-1;
+ }
+
+ moldyn->count-=1;
+ moldyn->atom=new;
+
+ free(old);
+
+ return 0;
+}
+
/* cubic init */
int cubic_init(int a,int b,int c,double lc,t_atom *atom,t_3dvec *origin) {
char dir[128];
double ds;
double energy_scale;
+ struct timeval t1,t2;
//double tp;
sched=&(moldyn->schedule);
moldyn->tau_square=moldyn->tau*moldyn->tau;
moldyn->cutoff_square=moldyn->cutoff*moldyn->cutoff;
- /* energy scaling factor */
- energy_scale=moldyn->count*EV;
+ /* get current time */
+ gettimeofday(&t1,NULL);
/* calculate initial forces */
potential_force_calc(moldyn);
moldyn->tau_square=moldyn->tau*moldyn->tau;
moldyn->time_steps=sched->runs[sched->count];
+ /* energy scaling factor (might change!) */
+ energy_scale=moldyn->count*EV;
+
/* integration according to schedule */
for(i=0;i<moldyn->time_steps;i++) {
/* check for log & visualization */
if(e) {
- if(!(i%e))
+ if(!(moldyn->total_steps%e))
dprintf(moldyn->efd,
"%f %f %f %f\n",
moldyn->time,moldyn->ekin/energy_scale,
get_total_energy(moldyn)/energy_scale);
}
if(m) {
- if(!(i%m)) {
+ if(!(moldyn->total_steps%m)) {
momentum=get_total_p(moldyn);
dprintf(moldyn->mfd,
"%f %f %f %f %f\n",moldyn->time,
}
}
if(p) {
- if(!(i%p)) {
+ if(!(moldyn->total_steps%p)) {
dprintf(moldyn->pfd,
"%f %f %f %f %f\n",moldyn->time,
moldyn->p/BAR,moldyn->p_avg/BAR,
}
}
if(t) {
- if(!(i%t)) {
+ if(!(moldyn->total_steps%t)) {
dprintf(moldyn->tfd,
"%f %f %f\n",
moldyn->time,moldyn->t,moldyn->t_avg);
}
}
if(s) {
- if(!(i%s)) {
+ if(!(moldyn->total_steps%s)) {
snprintf(dir,128,"%s/s-%07.f.save",
moldyn->vlsdir,moldyn->time);
fd=open(dir,O_WRONLY|O_TRUNC|O_CREAT,
}
}
if(v) {
- if(!(i%v)) {
+ if(!(moldyn->total_steps%v)) {
visual_atoms(&(moldyn->vis),moldyn->time,
moldyn->atom,moldyn->count);
}
}
/* display progress */
- if(!(i%10)) {
- printf("\rsched:%d, steps:%d, T:%3.1f/%3.1f P:%4.1f/%4.1f V:%6.1f",
+ if(!(moldyn->total_steps%10)) {
+ /* get current time */
+ gettimeofday(&t2,NULL);
+
+ printf("\rsched:%d, steps:%d, T:%3.1f/%3.1f P:%4.1f/%4.1f V:%6.1f (%d)",
sched->count,i,
moldyn->t,moldyn->t_avg,
moldyn->p_avg/BAR,moldyn->gp_avg/BAR,
- moldyn->volume);
+ moldyn->volume,
+ (int)(t2.tv_sec-t1.tv_sec));
fflush(stdout);
+
+ /* copy over time */
+ t1=t2;
}
/* increase absolute time */