return 0;
}
+int set_avg_skip(t_moldyn *moldyn,int skip) {
+
+ printf("[moldyn] skip %d steps before starting average calc\n",skip);
+ moldyn->avg_skip=skip;
+
+ return 0;
+}
+
int moldyn_set_log_dir(t_moldyn *moldyn,char *dir) {
strncpy(moldyn->vlsdir,dir,127);
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->t=(2.0*moldyn->ekin)/(3.0*K_BOLTZMANN*moldyn->count);
- moldyn->t_sum+=moldyn->t;
- moldyn->mean_t=moldyn->t_sum/moldyn->total_steps;
return moldyn->t;
}
return p;
}
-double pressure_calc(t_moldyn *moldyn) {
+double virial_sum(t_moldyn *moldyn) {
int i;
double v;
t_virial *virial;
+ /* virial (sum over atom virials) */
+ v=0.0;
+ for(i=0;i<moldyn->count;i++) {
+ virial=&(moldyn->atom[i].virial);
+ v+=(virial->xx+virial->yy+virial->zz);
+ }
+ moldyn->virial=v;
+
+ /* global virial (absolute coordinates) */
+ virial=&(moldyn->gvir);
+ moldyn->gv=virial->xx+virial->yy+virial->zz;
+
+ return moldyn->virial;
+}
+
+double pressure_calc(t_moldyn *moldyn) {
+
/*
* PV = NkT + <W>
- * W = 1/3 sum_i f_i r_i
+ * with W = 1/3 sum_i f_i r_i (- skipped!)
* virial = sum_i f_i r_i
*
* => P = (2 Ekin + virial) / (3V)
*/
- v=0.0;
- for(i=0;i<moldyn->count;i++) {
- virial=&(moldyn->atom[i].virial);
- v+=(virial->xx+virial->yy+virial->zz);
- }
-
- /* virial sum and mean virial */
- moldyn->virial_sum+=v;
- moldyn->mean_v=moldyn->virial_sum/moldyn->total_steps;
+ /* assume up to date virial & up to date kinetic energy */
- /* assume up to date kinetic energy */
- moldyn->p=2.0*moldyn->ekin+moldyn->mean_v;
+ /* pressure (atom virials) */
+ moldyn->p=2.0*moldyn->ekin+moldyn->virial;
moldyn->p/=(3.0*moldyn->volume);
- moldyn->p_sum+=moldyn->p;
- moldyn->mean_p=moldyn->p_sum/moldyn->total_steps;
- /* pressure from 'absolute coordinates' virial */
- virial=&(moldyn->virial);
- v=virial->xx+virial->yy+virial->zz;
- moldyn->gp=2.0*moldyn->ekin+v;
+ /* pressure (absolute coordinates) */
+ moldyn->gp=2.0*moldyn->ekin+moldyn->gv;
moldyn->gp/=(3.0*moldyn->volume);
- moldyn->gp_sum+=moldyn->gp;
- moldyn->mean_gp=moldyn->gp_sum/moldyn->total_steps;
return moldyn->p;
-}
+}
+
+int average_and_fluctuation_calc(t_moldyn *moldyn) {
+
+ if(moldyn->total_steps<moldyn->avg_skip)
+ return 0;
+
+ int denom=moldyn->total_steps+1-moldyn->avg_skip;
+
+ /* assume up to date energies, temperature, pressure etc */
+
+ /* kinetic energy */
+ moldyn->k_sum+=moldyn->ekin;
+ moldyn->k2_sum+=(moldyn->ekin*moldyn->ekin);
+ moldyn->k_avg=moldyn->k_sum/denom;
+ moldyn->k2_avg=moldyn->k2_sum/denom;
+ moldyn->dk2_avg=moldyn->k2_avg-(moldyn->k_avg*moldyn->k_avg);
+
+ /* potential energy */
+ moldyn->v_sum+=moldyn->energy;
+ moldyn->v2_sum+=(moldyn->energy*moldyn->energy);
+ moldyn->v_avg=moldyn->v_sum/denom;
+ moldyn->v2_avg=moldyn->v2_sum/denom;
+ moldyn->dv2_avg=moldyn->v2_avg-(moldyn->v_avg*moldyn->v_avg);
+
+ /* temperature */
+ moldyn->t_sum+=moldyn->t;
+ moldyn->t_avg=moldyn->t_sum/denom;
+
+ /* virial */
+ moldyn->virial_sum+=moldyn->virial;
+ moldyn->virial_avg=moldyn->virial_sum/denom;
+ moldyn->gv_sum+=moldyn->gv;
+ moldyn->gv_avg=moldyn->gv_sum/denom;
+
+ /* pressure */
+ moldyn->p_sum+=moldyn->p;
+ moldyn->p_avg=moldyn->p_sum/denom;
+ moldyn->gp_sum+=moldyn->gp;
+ moldyn->gp_avg=moldyn->gp_sum/denom;
+
+ return 0;
+}
+
+int get_heat_capacity(t_moldyn *moldyn) {
+
+ double temp2,ighc;
+
+ /* averages needed for heat capacity calc */
+ if(moldyn->total_steps<moldyn->avg_skip)
+ return 0;
+
+ /* (temperature average)^2 */
+ temp2=moldyn->t_avg*moldyn->t_avg;
+ printf("[moldyn] specific heat capacity for T=%f K [J/(kg K)]\n",
+ moldyn->t_avg);
+
+ /* 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_avg/(K_BOLTZMANN*temp2)+ighc;
+ moldyn->c_v_nvt/=moldyn->mass;
+
+ /* specific heat for nve ensemble */
+ moldyn->c_v_nve=ighc/(1.0-(moldyn->dv2_avg/(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);
+printf(" --> <dV2> sim: %f experimental: %f\n",moldyn->dv2_avg,1.5*moldyn->count*K_B2*moldyn->t_avg*moldyn->t_avg*(1.0-1.5*moldyn->count*K_BOLTZMANN/(700*moldyn->mass*JOULE/KILOGRAM)));
+
+ return 0;
+}
double thermodynamic_pressure_calc(t_moldyn *moldyn) {
printf("[moldyn] integration start, go get a coffee ...\n");
/* executing the schedule */
- for(sched->count=0;sched->count<sched->total_sched;sched->count++) {
+ sched->count=0;
+ while(sched->count<sched->total_sched) {
/* setting amount of runs and finite time step size */
moldyn->tau=sched->tau[sched->count];
/* calculate kinetic energy, temperature and pressure */
e_kin_calc(moldyn);
temperature_calc(moldyn);
+ virial_sum(moldyn);
pressure_calc(moldyn);
- //tp=thermodynamic_pressure_calc(moldyn);
-//printf("thermodynamic p: %f\n",thermodynamic_pressure_calc(moldyn)/BAR);
+ average_and_fluctuation_calc(moldyn);
/* p/t scaling */
if(moldyn->pt_scale&(T_SCALE_BERENDSEN|T_SCALE_DIRECT))
if(!(i%p)) {
dprintf(moldyn->pfd,
"%f %f %f %f %f\n",moldyn->time,
- moldyn->p/BAR,moldyn->mean_p/BAR,
- moldyn->gp/BAR,moldyn->mean_gp/BAR);
+ moldyn->p/BAR,moldyn->p_avg/BAR,
+ moldyn->gp/BAR,moldyn->gp_avg/BAR);
}
}
if(t) {
if(!(i%t)) {
dprintf(moldyn->tfd,
"%f %f %f\n",
- moldyn->time,moldyn->t,moldyn->mean_t);
+ moldyn->time,moldyn->t,moldyn->t_avg);
}
}
if(s) {
/* display progress */
if(!(i%10)) {
- printf("\rsched: %d, steps: %d, T: %f, P: %f %f V: %f",
- sched->count,i,
- moldyn->mean_t,
- moldyn->mean_p/BAR,
- moldyn->mean_gp/BAR,
- moldyn->volume);
- fflush(stdout);
+ printf("\rsched:%d, steps:%d, T:%3.1f/%3.1f P:%4.1f/%4.1f V:%6.1f",
+ sched->count,i,
+ moldyn->t,moldyn->t_avg,
+ moldyn->p_avg/BAR,moldyn->p/BAR,
+ moldyn->volume);
+ fflush(stdout);
}
/* increase absolute time */
}
/* check for hooks */
- if(sched->hook)
+ if(sched->hook) {
+ printf("\n ## schedule hook %d/%d start ##\n",
+ sched->count+1,sched->total_sched-1);
sched->hook(moldyn,sched->hook_params);
+ printf(" ## schedule hook end ##\n");
+ }
- /* get a new info line */
- printf("\n");
+ /* increase the schedule counter */
+ sched->count+=1;
}
moldyn->energy=0.0;
/* reset global virial */
- memset(&(moldyn->virial),0,sizeof(t_virial));
+ memset(&(moldyn->gvir),0,sizeof(t_virial));
/* reset force, site energy and virial of every atom */
for(i=0;i<count;i++) {
/* calculate global virial */
for(i=0;i<count;i++) {
- moldyn->virial.xx+=moldyn->atom[i].r.x*moldyn->atom[i].f.x;
- moldyn->virial.yy+=moldyn->atom[i].r.y*moldyn->atom[i].f.y;
- moldyn->virial.zz+=moldyn->atom[i].r.z*moldyn->atom[i].f.z;
- moldyn->virial.xy+=moldyn->atom[i].r.y*moldyn->atom[i].f.x;
- moldyn->virial.xz+=moldyn->atom[i].r.z*moldyn->atom[i].f.x;
- moldyn->virial.yz+=moldyn->atom[i].r.z*moldyn->atom[i].f.y;
+ moldyn->gvir.xx+=moldyn->atom[i].r.x*moldyn->atom[i].f.x;
+ moldyn->gvir.yy+=moldyn->atom[i].r.y*moldyn->atom[i].f.y;
+ moldyn->gvir.zz+=moldyn->atom[i].r.z*moldyn->atom[i].f.z;
+ moldyn->gvir.xy+=moldyn->atom[i].r.y*moldyn->atom[i].f.x;
+ moldyn->gvir.xz+=moldyn->atom[i].r.z*moldyn->atom[i].f.x;
+ moldyn->gvir.yz+=moldyn->atom[i].r.z*moldyn->atom[i].f.y;
}
return 0;
}
/*
- * 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;
-}
projects / physik / posic.git / blobdiff