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_per_bound(moldyn,&(atom[ret].r));
}
+ /* update total system mass */
+ total_mass_calc(moldyn);
+
return ret;
}
atom[count].tag=count;
atom[count].attr=attr;
+ /* update total system mass */
+ total_mass_calc(moldyn);
+
return 0;
}
return 0;
}
+double total_mass_calc(t_moldyn *moldyn) {
+
+ int i;
+
+ moldyn->mass=0.0;
+
+ for(i=0;i<moldyn->count;i++)
+ moldyn->mass+=moldyn->atom[i].mass;
+
+ return moldyn->mass;
+}
+
double temperature_calc(t_moldyn *moldyn) {
/* assume up to date kinetic energy, which is 3/2 N k_B T */
moldyn->mean_gp=moldyn->gp_sum/moldyn->total_steps;
return moldyn->p;
-}
+}
+
+int energy_fluctuation_calc(t_moldyn *moldyn) {
+
+ /* assume up to date energies */
+
+ /* kinetic energy */
+ moldyn->k_sum+=moldyn->ekin;
+ moldyn->k2_sum+=(moldyn->ekin*moldyn->ekin);
+ moldyn->k_mean=moldyn->k_sum/moldyn->total_steps;
+ moldyn->k2_mean=moldyn->k2_sum/moldyn->total_steps;
+ moldyn->dk2_mean=moldyn->k2_mean-(moldyn->k_mean*moldyn->k_mean);
+
+ /* potential energy */
+ moldyn->v_sum+=moldyn->energy;
+ moldyn->v2_sum+=(moldyn->energy*moldyn->energy);
+ moldyn->v_mean=moldyn->v_sum/moldyn->total_steps;
+ moldyn->v2_mean=moldyn->v2_sum/moldyn->total_steps;
+ moldyn->dv2_mean=moldyn->v2_mean-(moldyn->v_mean*moldyn->v_mean);
+
+ return 0;
+}
+
+int get_heat_capacity(t_moldyn *moldyn) {
+
+ double temp2,ighc;
+
+ /* (temperature average)^2 */
+ temp2=moldyn->mean_t*moldyn->mean_t;
+ printf("[moldyn] specific heat capacity for T=%f K [J/(kg K)]\n",
+ moldyn->mean_t);
+
+ /* ideal gas contribution */
+ ighc=3.0*moldyn->count*K_BOLTZMANN/2.0;
+ printf(" ideal gas contribution: %f\n",
+ ighc/moldyn->mass*KILOGRAM/JOULE);
+
+ /* specific heat for nvt ensemble */
+ moldyn->c_v_nvt=moldyn->dv2_mean/(K_BOLTZMANN*temp2)+ighc;
+ moldyn->c_v_nvt/=moldyn->mass;
+
+ /* specific heat for nve ensemble */
+ moldyn->c_v_nve=ighc/(1.0-(moldyn->dv2_mean/(ighc*K_BOLTZMANN*temp2)));
+ moldyn->c_v_nve/=moldyn->mass;
+
+ printf(" NVE: %f\n",moldyn->c_v_nve*KILOGRAM/JOULE);
+ printf(" NVT: %f\n",moldyn->c_v_nvt*KILOGRAM/JOULE);
+
+ return 0;
+}
double thermodynamic_pressure_calc(t_moldyn *moldyn) {
e_kin_calc(moldyn);
temperature_calc(moldyn);
pressure_calc(moldyn);
+ energy_fluctuation_calc(moldyn);
//tp=thermodynamic_pressure_calc(moldyn);
//printf("thermodynamic p: %f\n",thermodynamic_pressure_calc(moldyn)/BAR);
moldyn->mean_gp/BAR,
moldyn->volume);
fflush(stdout);
+printf("\n");
+get_heat_capacity(moldyn);
}
/* increase absolute time */
}
/* 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
+ * post processing 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 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];
-
- fd=open(file,O_RDONLY);
- if(fd<0) {
- perror("[moldyn] post proc open");
- return fd;
- }
-
- /* first calc the averages */
- 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;
- if(buf[0]=='#') continue;
- sscanf(buf,"%lf %lf %lf %lf",&time,&kin,&pot,&tot);
- 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;
- }
- }
-
- p2_m=p_sum/count;
- k2_m=k_sum/count;
- t2_m=t_sum/count;
-
- 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);
-
- close(fd);
-
- return 0;
-}