return 0;
}
+int set_mean_skip(t_moldyn *moldyn,int skip) {
+
+ printf("[moldyn] skip %d steps before starting average calc\n",skip);
+ moldyn->mean_skip=skip;
+
+ return 0;
+}
+
int moldyn_set_log_dir(t_moldyn *moldyn,char *dir) {
strncpy(moldyn->vlsdir,dir,127);
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);
+
+ if(moldyn->total_steps<moldyn->mean_skip)
+ return 0;
+
moldyn->t_sum+=moldyn->t;
- moldyn->mean_t=moldyn->t_sum/moldyn->total_steps;
+ moldyn->mean_t=moldyn->t_sum/(moldyn->total_steps+1-moldyn->mean_skip);
return moldyn->t;
}
/* virial sum and mean virial */
moldyn->virial_sum+=v;
- moldyn->mean_v=moldyn->virial_sum/moldyn->total_steps;
+ if(moldyn->total_steps>=moldyn->mean_skip)
+ moldyn->mean_v=moldyn->virial_sum/
+ (moldyn->total_steps+1-moldyn->mean_skip);
/* assume up to date kinetic energy */
moldyn->p=2.0*moldyn->ekin+moldyn->mean_v;
moldyn->p/=(3.0*moldyn->volume);
- moldyn->p_sum+=moldyn->p;
- moldyn->mean_p=moldyn->p_sum/moldyn->total_steps;
+ if(moldyn->total_steps>=moldyn->mean_skip) {
+ moldyn->p_sum+=moldyn->p;
+ moldyn->mean_p=moldyn->p_sum/
+ (moldyn->total_steps+1-moldyn->mean_skip);
+ }
/* pressure from 'absolute coordinates' virial */
virial=&(moldyn->virial);
v=virial->xx+virial->yy+virial->zz;
moldyn->gp=2.0*moldyn->ekin+v;
moldyn->gp/=(3.0*moldyn->volume);
- moldyn->gp_sum+=moldyn->gp;
- moldyn->mean_gp=moldyn->gp_sum/moldyn->total_steps;
+ if(moldyn->total_steps>=moldyn->mean_skip) {
+ moldyn->gp_sum+=moldyn->gp;
+ moldyn->mean_gp=moldyn->gp_sum/
+ (moldyn->total_steps+1-moldyn->mean_skip);
+ }
return moldyn->p;
-}
+}
+
+int energy_fluctuation_calc(t_moldyn *moldyn) {
+
+ if(moldyn->total_steps<moldyn->mean_skip)
+ return 0;
+
+ /* 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+1-moldyn->mean_skip);
+ moldyn->k2_mean=moldyn->k2_sum/
+ (moldyn->total_steps+1-moldyn->mean_skip);
+ 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+1-moldyn->mean_skip);
+ moldyn->v2_mean=moldyn->v2_sum/
+ (moldyn->total_steps+1-moldyn->mean_skip);
+ moldyn->dv2_mean=moldyn->v2_mean-(moldyn->v_mean*moldyn->v_mean);
+
+ return 0;
+}
+
+int get_heat_capacity(t_moldyn *moldyn) {
+
+ double temp2,ighc;
+
+ /* averages needed for heat capacity calc */
+ if(moldyn->total_steps<moldyn->mean_skip)
+ return 0;
+
+ /* (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);
+printf(" --> <dV2> sim: %f experimental: %f\n",moldyn->dv2_mean,1.5*moldyn->count*K_B2*moldyn->mean_t*moldyn->mean_t*(1.0-1.5*moldyn->count*K_BOLTZMANN/(700*moldyn->mass*JOULE/KILOGRAM)));
+
+ 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 */
}
/*
- * postprocessing functions
+ * post processing functions
*/
int get_line(int fd,char *line,int max) {
}
}
-int calc_fluctuations(double start,double end,t_moldyn *moldyn) {
-
- int fd;
- int count,ret;
- double time,pot,kin,tot;
- double p_sum,k_sum,t_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 energy open");
- return fd;
- }
-
- /* first calc the averages */
- p_sum=0.0;
- k_sum=0.0;
- t_sum=0.0;
- count=0;
- while(1) {
- 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;
- p_sum+=pot;
- k_sum+=kin;
- t_sum+=tot;
- count+=1;
- }
-
- moldyn->p_m=p_sum/count;
- moldyn->k_m=k_sum/count;
- moldyn->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=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;
- k_sum+=((kin-moldyn->k_m)*(kin-moldyn->k_m));
- p_sum+=((pot-moldyn->p_m)*(pot-moldyn->p_m));
- t_sum+=((tot-moldyn->t_m)*(tot-moldyn->t_m));
- count+=1;
- }
-
- moldyn->dp2_m=p_sum/count;
- moldyn->dk2_m=k_sum/count;
- moldyn->dt2_m=t_sum/count;
-
- 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;
-}
projects / physik / posic.git / blobdiff