if(moldyn->rfd) {
dprintf(moldyn->rfd,report_end);
close(moldyn->rfd);
- snprintf(sc,255,"cd %s && pdflatex report",moldyn->vlsdir);
+ snprintf(sc,255,"cd %s && pdflatex report >/dev/null 2>&1",
+ moldyn->vlsdir);
system(sc);
- snprintf(sc,255,"cd %s && pdflatex report",moldyn->vlsdir);
+ snprintf(sc,255,"cd %s && pdflatex report >/dev/null 2>&1",
+ moldyn->vlsdir);
system(sc);
- snprintf(sc,255,"cd %s && dvipdf report",moldyn->vlsdir);
+ snprintf(sc,255,"cd %s && dvipdf report >/dev/null 2>&1",
+ moldyn->vlsdir);
system(sc);
}
if(&(moldyn->vis)) visual_tini(&(moldyn->vis));
}
/* check for hooks */
- if(sched->hook)
- sched->hook(moldyn,sched->hook_params);
+ if(sched->count+1<sched->total_sched)
+ if(sched->hook)
+ sched->hook(moldyn,sched->hook_params);
/* get a new info line */
printf("\n");
/*
* postprocessing functions
*/
-#define LINE_MAX 128
-int read_line(int fd,char *line) {
+
+int get_line(int fd,char *line,int max) {
int count,ret;
count=0;
while(1) {
- if(count==LINE_MAX) return count;
+ if(count==max) return count;
ret=read(fd,line+count,1);
- if(ret<0) return ret;
+ if(ret<=0) return ret;
if(line[count]=='\n') {
line[count]='\0';
return count+1;
}
}
-int calc_fluctuations(double start,double end,char *file) {
+int calc_fluctuations(double start,double end,t_moldyn *moldyn) {
int fd;
int count,ret;
double time,pot,kin,tot;
- double p_m,k_m,t_m;
- double p2_m,k2_m,t2_m;
double p_sum,k_sum,t_sum;
- char buf[LINE_MAX];
+ double p2_sum,k2_sum,t2_sum;
+ char buf[64];
+ char file[128+7];
+
+ printf("[moldyn] calculating energy fluctuations [eV]:\n");
+ snprintf(file,128+7,"%s/energy",moldyn->vlsdir);
fd=open(file,O_RDONLY);
if(fd<0) {
- perror("[moldyn] post proc open");
+ perror("[moldyn] post proc energy open");
return fd;
}
- /* first calc the averages */
+ /* calc the averages of A and A^2 */
p_sum=0.0;
k_sum=0.0;
t_sum=0.0;
count=0;
while(1) {
- ret=read_line(fd,buf);
- if(ret<0) break;
-printf("%d\n",ret);
- if(buf[0]=='#') continue;
- sscanf(buf,"%lf %lf %lf %lf",&time,&kin,&pot,&tot);
-printf("%f %f %f %f\n",time,pot,kin,tot);
- //if(time>end) break;
- if((time>=start)&(time<=end)) {
- p_sum+=pot;
- k_sum+=kin;
- t_sum+=tot;
- count+=1;
- }
- }
-
- p_m=p_sum/count;
- k_m=k_sum/count;
- t_m=t_sum/count;
-
- /* mean square fluctuations */
- if(lseek(fd,SEEK_SET,0)<0) {
- perror("[moldyn] lseek");
- return -1;
- }
- count=0;
- p_sum=0.0;
- k_sum=0.0;
- t_sum=0.0;
- while(1) {
- ret=read_line(fd,buf);
- if(ret<0) break;
+ ret=get_line(fd,buf,63);
+ if(ret<=0) break;
if(buf[0]=='#') continue;
sscanf(buf,"%lf %lf %lf %lf",&time,&kin,&pot,&tot);
+ if(time<start) continue;
if(time>end) break;
- if((time>=start)&(time<=end)) {
- p_sum+=((pot-p_m)*(pot-p_m));
- k_sum+=((kin-k_m)*(kin-k_m));
- t_sum+=((tot-t_m)*(tot-t_m));
- count+=1;
- }
+ p_sum+=pot;
+ k_sum+=kin;
+ t_sum+=tot;
+ p2_sum+=(pot*pot);
+ k2_sum+=(kin*kin);
+ t2_sum+=(tot*tot);
+ count+=1;
}
- p2_m=p_sum/count;
- k2_m=k_sum/count;
- t2_m=t_sum/count;
+ /* averages */
+ moldyn->k_m=k_sum/count;
+ moldyn->p_m=p_sum/count;
+ moldyn->t_m=t_sum/count;
+
+ /* rms */
+ moldyn->dk2_m=k2_sum/count-moldyn->k_m*moldyn->k_m;
+ moldyn->dp2_m=p2_sum/count-moldyn->p_m*moldyn->p_m;
+ moldyn->dt2_m=t2_sum/count-moldyn->t_m*moldyn->t_m;
- printf("[moldyn] fluctuations (%f - %f):\n",start,end);
- printf(" - averages : %f %f %f\n",k_m,p_m,t_m);
- printf(" - mean square: %f %f %f\n",k2_m,p2_m,t2_m);
+ printf(" averages : %f %f %f\n",moldyn->k_m,
+ moldyn->p_m,
+ moldyn->t_m);
+ printf(" mean square: %f %f %f\n",moldyn->dk2_m,
+ moldyn->dp2_m,
+ moldyn->dt2_m);
close(fd);
return 0;
}
+
+int get_heat_capacity(t_moldyn *moldyn) {
+
+ double temp2,mass,ighc;
+ int i;
+
+ /* (temperature average)^2 */
+ temp2=2.0*moldyn->k_m*EV/(3.0*K_BOLTZMANN);
+ printf("[moldyn] specific heat capacity for T=%f K [J/(kg K)]\n",temp2);
+ temp2*=temp2;
+
+ /* total mass */
+ mass=0.0;
+ for(i=0;i<moldyn->count;i++)
+ mass+=moldyn->atom[i].mass;
+
+ /* ideal gas contribution */
+ ighc=3.0*moldyn->count*K_BOLTZMANN/2.0;
+ printf(" ideal gas contribution: %f\n",ighc/mass*KILOGRAM/JOULE);
+
+ moldyn->c_v_nvt=moldyn->dp2_m*moldyn->count*moldyn->count*EV/(K_BOLTZMANN*temp2)+ighc;
+ moldyn->c_v_nvt/=mass;
+ moldyn->c_v_nve=ighc/(1.0-(moldyn->dp2_m*moldyn->count*moldyn->count*EV/(ighc*K_BOLTZMANN*temp2)));
+ moldyn->c_v_nve/=mass;
+
+ printf(" NVE: %f\n",moldyn->c_v_nve*KILOGRAM/JOULE);
+ printf(" NVT: %f\n",moldyn->c_v_nvt*KILOGRAM/JOULE);
+
+ return 0;
+}