X-Git-Url: https://www.hackdaworld.org/gitweb/?a=blobdiff_plain;f=moldyn.c;h=e0881de5db49b1669c5a0b02641e66760dc957a0;hb=e2c5d8b0eb4ce6faeb48830634eef522dbdb52b0;hp=c130ef442b838175272e62f375daa4fbaa8e199b;hpb=58fd691b276fbe87593036714f26dbfe7486cbeb;p=physik%2Fposic.git

diff --git a/moldyn.c b/moldyn.c
index c130ef4..e0881de 100644
--- a/moldyn.c
+++ b/moldyn.c
@@ -218,6 +218,14 @@ int set_potential_params(t_moldyn *moldyn,void *params) {
 	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);
@@ -504,6 +512,9 @@ int create_lattice(t_moldyn *moldyn,u8 type,double lc,int element,double mass,
 		check_per_bound(moldyn,&(atom[ret].r));
 	}
 
+	/* update total system mass */
+	total_mass_calc(moldyn);
+
 	return ret;
 }
 
@@ -645,6 +656,9 @@ int add_atom(t_moldyn *moldyn,int element,double mass,u8 brand,u8 attr,
 	atom[count].tag=count;
 	atom[count].attr=attr;
 
+	/* update total system mass */
+	total_mass_calc(moldyn);
+
 	return 0;
 }
 
@@ -705,13 +719,23 @@ int thermal_init(t_moldyn *moldyn,u8 equi_init) {
 	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;
 }
@@ -794,7 +818,7 @@ 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)
@@ -806,26 +830,98 @@ double pressure_calc(t_moldyn *moldyn) {
 		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 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;
+	/* virial sum and average virial */
+	if(moldyn->total_steps>=moldyn->avg_skip) {
+		moldyn->virial_sum+=v;
+		moldyn->virial_avg=moldyn->virial_sum/
+		                   (moldyn->total_steps+1-moldyn->avg_skip);
+		moldyn->p=2.0*moldyn->k_avg+moldyn->virial_avg;
+		moldyn->p/=(3.0*moldyn->volume);
+		moldyn->p_sum+=moldyn->p;
+		moldyn->p_avg=moldyn->p_sum/
+		              (moldyn->total_steps+1-moldyn->avg_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->avg_skip) {
+		moldyn->gp_sum+=moldyn->gp;
+		moldyn->gp_avg=moldyn->gp_sum/
+		               (moldyn->total_steps+1-moldyn->avg_skip);
+	}
 
 	return moldyn->p;
-}	
+}
+
+int average_and_fluctuation_calc(t_moldyn *moldyn) {
+
+	if(moldyn->total_steps<moldyn->avg_skip)
+		return 0;
+
+	/* 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/(moldyn->total_steps+1-moldyn->avg_skip);
+	moldyn->k2_avg=moldyn->k2_sum/(moldyn->total_steps+1-moldyn->avg_skip);
+	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/(moldyn->total_steps+1-moldyn->avg_skip);
+	moldyn->v2_avg=moldyn->v2_sum/(moldyn->total_steps+1-moldyn->avg_skip);
+	moldyn->dv2_avg=moldyn->v2_avg-(moldyn->v_avg*moldyn->v_avg);
+
+	/* temperature */
+	moldyn->t_sum+=moldyn->t;
+	moldyn->t_avg=moldyn->t_sum/(moldyn->total_steps+1-moldyn->avg_skip);
+
+	/* virial */
+	
+
+	/* pressure */
+
+
+	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) {
 
@@ -1307,8 +1403,7 @@ return 0;
 		e_kin_calc(moldyn);
 		temperature_calc(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))
@@ -1338,15 +1433,15 @@ return 0;
 			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) {
@@ -1374,9 +1469,10 @@ return 0;
 		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->t_avg,
+			       //moldyn->p_avg/BAR,
+			       moldyn->p/BAR,
+			       moldyn->gp_avg/BAR,
 			       moldyn->volume);
 			fflush(stdout);
 		}
@@ -1389,11 +1485,12 @@ return 0;
 
 		/* check for hooks */
 		if(sched->count+1<sched->total_sched)
-			if(sched->hook)
+			if(sched->hook) {
+				printf("\n ## schedule hook %d/%d start ##\n",
+				       sched->count+1,sched->total_sched);
 				sched->hook(moldyn,sched->hook_params);
-
-		/* get a new info line */
-		printf("\n");
+				printf(" ## schedule hook end ##\n");
+			}
 
 	}
 
@@ -1811,7 +1908,7 @@ int moldyn_bc_check(t_moldyn *moldyn) {
 }
 
 /*
- * postprocessing functions
+ * post processing functions
  */
 
 int get_line(int fd,char *line,int max) {
@@ -1832,110 +1929,3 @@ 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;
-}