X-Git-Url: https://hackdaworld.org/gitweb/?a=blobdiff_plain;f=moldyn.c;h=c130ef442b838175272e62f375daa4fbaa8e199b;hb=58fd691b276fbe87593036714f26dbfe7486cbeb;hp=4d736179550d68c7402e89b4412dec3dfc9d40bb;hpb=0b96eb313c9bfec6272b1f8de0d99c4ce26d1686;p=physik%2Fposic.git

diff --git a/moldyn.c b/moldyn.c
index 4d73617..c130ef4 100644
--- a/moldyn.c
+++ b/moldyn.c
@@ -404,11 +404,14 @@ int moldyn_log_shutdown(t_moldyn *moldyn) {
 	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));
@@ -421,11 +424,11 @@ int moldyn_log_shutdown(t_moldyn *moldyn) {
  */
 
 int create_lattice(t_moldyn *moldyn,u8 type,double lc,int element,double mass,
-                   u8 attr,u8 brand,int a,int b,int c) {
+                   u8 attr,u8 brand,int a,int b,int c,t_3dvec *origin) {
 
 	int new,count;
 	int ret;
-	t_3dvec origin;
+	t_3dvec orig;
 	void *ptr;
 	t_atom *atom;
 
@@ -447,24 +450,33 @@ int create_lattice(t_moldyn *moldyn,u8 type,double lc,int element,double mass,
 	atom=&(moldyn->atom[count]);
 
 	/* no atoms on the boundaries (only reason: it looks better!) */
-	origin.x=0.5*lc;
-	origin.y=0.5*lc;
-	origin.z=0.5*lc;
+	if(!origin) {
+		orig.x=0.5*lc;
+		orig.y=0.5*lc;
+		orig.z=0.5*lc;
+	}
+	else {
+		orig.x=origin->x;
+		orig.y=origin->y;
+		orig.z=origin->z;
+	}
 
 	switch(type) {
 		case CUBIC:
 			set_nn_dist(moldyn,lc);
-			ret=cubic_init(a,b,c,lc,atom,&origin);
+			ret=cubic_init(a,b,c,lc,atom,&orig);
 			break;
 		case FCC:
-			v3_scale(&origin,&origin,0.5);
+			if(!origin)
+				v3_scale(&orig,&orig,0.5);
 			set_nn_dist(moldyn,0.5*sqrt(2.0)*lc);
-			ret=fcc_init(a,b,c,lc,atom,&origin);
+			ret=fcc_init(a,b,c,lc,atom,&orig);
 			break;
 		case DIAMOND:
-			v3_scale(&origin,&origin,0.25);
+			if(!origin)
+				v3_scale(&orig,&orig,0.25);
 			set_nn_dist(moldyn,0.25*sqrt(3.0)*lc);
-			ret=diamond_init(a,b,c,lc,atom,&origin);
+			ret=diamond_init(a,b,c,lc,atom,&orig);
 			break;
 		default:
 			printf("unknown lattice type (%02x)\n",type);
@@ -794,8 +806,12 @@ 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+v;
+	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;
@@ -814,8 +830,8 @@ double pressure_calc(t_moldyn *moldyn) {
 double thermodynamic_pressure_calc(t_moldyn *moldyn) {
 
 	t_3dvec dim,*tp;
-	double u,p;
-	double scale,dv;
+	double u_up,u_down,dv;
+	double scale,p;
 	t_atom *store;
 
 	/*
@@ -823,13 +839,11 @@ double thermodynamic_pressure_calc(t_moldyn *moldyn) {
 	 *
 	 * => p = - dU/dV
 	 *
-	 * dV: dx,y,z = 0.001 x,y,z
 	 */
 
-	scale=1.00000000000001;
-printf("\n\nP-DEBUG:\n");
+	scale=0.00001;
+	dv=8*scale*scale*scale*moldyn->volume;
 
-	tp=&(moldyn->tp);
 	store=malloc(moldyn->count*sizeof(t_atom));
 	if(store==NULL) {
 		printf("[moldyn] allocating store mem failed\n");
@@ -837,59 +851,44 @@ printf("\n\nP-DEBUG:\n");
 	}
 
 	/* save unscaled potential energy + atom/dim configuration */
-	u=moldyn->energy;
 	memcpy(store,moldyn->atom,moldyn->count*sizeof(t_atom));
 	dim=moldyn->dim;
 
-	/* derivative with respect to x direction */
-	scale_dim(moldyn,scale,TRUE,0,0);
-	scale_atoms(moldyn,scale,TRUE,0,0);
-	dv=0.00000000000001*moldyn->dim.x*moldyn->dim.y*moldyn->dim.z;
-	link_cell_shutdown(moldyn);
-	link_cell_init(moldyn,QUIET);
-	potential_force_calc(moldyn);
-	tp->x=(moldyn->energy-u)/dv;
-	p=tp->x*tp->x;
-
-	/* restore atomic configuration + dim */
-	memcpy(moldyn->atom,store,moldyn->count*sizeof(t_atom));
-	moldyn->dim=dim;
-
-	/* derivative with respect to y direction */
-	scale_dim(moldyn,scale,0,TRUE,0);
-	scale_atoms(moldyn,scale,0,TRUE,0);
-	dv=0.00000000000001*moldyn->dim.y*moldyn->dim.x*moldyn->dim.z;
+	/* scale up dimension and atom positions */
+	scale_dim(moldyn,SCALE_UP,scale,TRUE,TRUE,TRUE);
+	scale_atoms(moldyn,SCALE_UP,scale,TRUE,TRUE,TRUE);
 	link_cell_shutdown(moldyn);
 	link_cell_init(moldyn,QUIET);
 	potential_force_calc(moldyn);
-	tp->y=(moldyn->energy-u)/dv;
-	p+=tp->y*tp->y;
+	u_up=moldyn->energy;
 
 	/* restore atomic configuration + dim */
 	memcpy(moldyn->atom,store,moldyn->count*sizeof(t_atom));
 	moldyn->dim=dim;
 
-	/* derivative with respect to z direction */
-	scale_dim(moldyn,scale,0,0,TRUE);
-	scale_atoms(moldyn,scale,0,0,TRUE);
-	dv=0.00000000000001*moldyn->dim.z*moldyn->dim.x*moldyn->dim.y;
+	/* scale down dimension and atom positions */
+	scale_dim(moldyn,SCALE_DOWN,scale,TRUE,TRUE,TRUE);
+	scale_atoms(moldyn,SCALE_DOWN,scale,TRUE,TRUE,TRUE);
 	link_cell_shutdown(moldyn);
 	link_cell_init(moldyn,QUIET);
 	potential_force_calc(moldyn);
-	tp->z=(moldyn->energy-u)/dv;
-	p+=tp->z*tp->z;
+	u_down=moldyn->energy;
+	
+	/* calculate pressure */
+	p=-(u_up-u_down)/dv;
+printf("-------> %.10f %.10f %f\n",u_up/EV/moldyn->count,u_down/EV/moldyn->count,p/BAR);
 
 	/* restore atomic configuration + dim */
 	memcpy(moldyn->atom,store,moldyn->count*sizeof(t_atom));
 	moldyn->dim=dim;
 
 	/* restore energy */
-	moldyn->energy=u;
+	potential_force_calc(moldyn);
 
 	link_cell_shutdown(moldyn);
 	link_cell_init(moldyn,QUIET);
 
-	return sqrt(p);
+	return p;
 }
 
 double get_pressure(t_moldyn *moldyn) {
@@ -898,12 +897,18 @@ double get_pressure(t_moldyn *moldyn) {
 
 }
 
-int scale_dim(t_moldyn *moldyn,double scale,u8 x,u8 y,u8 z) {
+int scale_dim(t_moldyn *moldyn,u8 dir,double scale,u8 x,u8 y,u8 z) {
 
 	t_3dvec *dim;
 
 	dim=&(moldyn->dim);
 
+	if(dir==SCALE_UP)
+		scale=1.0+scale;
+
+	if(dir==SCALE_DOWN)
+		scale=1.0-scale;
+
 	if(x) dim->x*=scale;
 	if(y) dim->y*=scale;
 	if(z) dim->z*=scale;
@@ -911,11 +916,17 @@ int scale_dim(t_moldyn *moldyn,double scale,u8 x,u8 y,u8 z) {
 	return 0;
 }
 
-int scale_atoms(t_moldyn *moldyn,double scale,u8 x,u8 y,u8 z) {
+int scale_atoms(t_moldyn *moldyn,u8 dir,double scale,u8 x,u8 y,u8 z) {
 
 	int i;
 	t_3dvec *r;
 
+	if(dir==SCALE_UP)
+		scale=1.0+scale;
+
+	if(dir==SCALE_DOWN)
+		scale=1.0-scale;
+
 	for(i=0;i<moldyn->count;i++) {
 		r=&(moldyn->atom[i].r);
 		if(x) r->x*=scale;
@@ -947,8 +958,8 @@ int scale_volume(t_moldyn *moldyn) {
 moldyn->debug=scale;
 
 	/* scale the atoms and dimensions */
-	scale_atoms(moldyn,scale,TRUE,TRUE,TRUE);
-	scale_dim(moldyn,scale,TRUE,TRUE,TRUE);
+	scale_atoms(moldyn,SCALE_DIRECT,scale,TRUE,TRUE,TRUE);
+	scale_dim(moldyn,SCALE_DIRECT,scale,TRUE,TRUE,TRUE);
 
 	/* visualize dimensions */
 	if(vdim->x!=0) {
@@ -1252,6 +1263,9 @@ int moldyn_integrate(t_moldyn *moldyn) {
 
 	/* calculate initial forces */
 	potential_force_calc(moldyn);
+#ifdef DEBUG
+return 0;
+#endif
 
 	/* some stupid checks before we actually start calculating bullshit */
 	if(moldyn->cutoff>0.5*moldyn->dim.x)
@@ -1294,7 +1308,7 @@ int moldyn_integrate(t_moldyn *moldyn) {
 		temperature_calc(moldyn);
 		pressure_calc(moldyn);
 		//tp=thermodynamic_pressure_calc(moldyn);
-//printf("thermodynamic p: %f %f %f - %f\n",moldyn->tp.x/BAR,moldyn->tp.y/BAR,moldyn->tp.z/BAR,tp/BAR);
+//printf("thermodynamic p: %f\n",thermodynamic_pressure_calc(moldyn)/BAR);
 
 		/* p/t scaling */
 		if(moldyn->pt_scale&(T_SCALE_BERENDSEN|T_SCALE_DIRECT))
@@ -1374,8 +1388,9 @@ int moldyn_integrate(t_moldyn *moldyn) {
 	}
 
 		/* 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");
@@ -1486,7 +1501,8 @@ int potential_force_calc(t_moldyn *moldyn) {
 
 		/* single particle potential/force */
 		if(itom[i].attr&ATOM_ATTR_1BP)
-			moldyn->func1b(moldyn,&(itom[i]));
+			if(moldyn->func1b)
+				moldyn->func1b(moldyn,&(itom[i]));
 
 		if(!(itom[i].attr&(ATOM_ATTR_2BP|ATOM_ATTR_3BP)))
 			continue;
@@ -1711,7 +1727,7 @@ int virial_calc(t_atom *a,t_3dvec *f,t_3dvec *d) {
 }
 
 /*
- * periodic boundayr checking
+ * periodic boundary checking
  */
 
 //inline int check_per_bound(t_moldyn *moldyn,t_3dvec *a) {
@@ -1793,3 +1809,133 @@ int moldyn_bc_check(t_moldyn *moldyn) {
 
 	return 0;
 }
+
+/*
+ * postprocessing functions
+ */
+
+int get_line(int fd,char *line,int max) {
+
+	int count,ret;
+
+	count=0;
+
+	while(1) {
+		if(count==max) return count;
+		ret=read(fd,line+count,1);
+		if(ret<=0) return ret;
+		if(line[count]=='\n') {
+			line[count]='\0';
+			return count+1;
+		}
+		count+=1;
+	}
+}
+
+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;
+}