X-Git-Url: https://www.hackdaworld.org/gitweb/?a=blobdiff_plain;f=moldyn.c;h=f6c3c81d4bbf95b5787474dbd03e18bea90e183e;hb=cb177e7c208a85b45d77b09fcada23b62d0248b5;hp=817a72788b45f2572258873aaa8ca64cace0397f;hpb=f3e4193447ac49a8953515910d4b4e6ce2c7608b;p=physik%2Fposic.git

diff --git a/moldyn.c b/moldyn.c
index 817a727..f6c3c81 100644
--- a/moldyn.c
+++ b/moldyn.c
@@ -16,6 +16,7 @@
 #include <math.h>
 
 #include "moldyn.h"
+#include "report/report.h"
 
 int moldyn_init(t_moldyn *moldyn,int argc,char **argv) {
 
@@ -72,7 +73,7 @@ int set_temperature(t_moldyn *moldyn,double t_ref) {
 
 	moldyn->t_ref=t_ref;
 
-	printf("[moldyn] temperature: %f\n",moldyn->t_ref);
+	printf("[moldyn] temperature [K]: %f\n",moldyn->t_ref);
 
 	return 0;
 }
@@ -81,7 +82,7 @@ int set_pressure(t_moldyn *moldyn,double p_ref) {
 
 	moldyn->p_ref=p_ref;
 
-	printf("[moldyn] pressure: %f\n",moldyn->p_ref);
+	printf("[moldyn] pressure [atm]: %f\n",moldyn->p_ref/ATM);
 
 	return 0;
 }
@@ -338,17 +339,25 @@ int create_lattice(t_moldyn *moldyn,u8 type,double lc,int element,double mass,
 	}
 	moldyn->atom=ptr;
 	atom=&(moldyn->atom[count]);
-		
-	v3_zero(&origin);
+
+	/* 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;
 
 	switch(type) {
 		case CUBIC:
-			ret=cubic_init(a,b,c,lc,atom,NULL);
+			set_nn_dist(moldyn,lc);
+			ret=cubic_init(a,b,c,lc,atom,&origin);
 			break;
 		case FCC:
-			ret=fcc_init(a,b,c,lc,atom,NULL);
+			v3_scale(&origin,&origin,0.5);
+			set_nn_dist(moldyn,0.5*sqrt(2.0)*lc);
+			ret=fcc_init(a,b,c,lc,atom,&origin);
 			break;
 		case DIAMOND:
+			v3_scale(&origin,&origin,0.25);
+			set_nn_dist(moldyn,0.25*sqrt(3.0)*lc);
 			ret=diamond_init(a,b,c,lc,atom,&origin);
 			break;
 		default:
@@ -398,8 +407,8 @@ int cubic_init(int a,int b,int c,double lc,t_atom *atom,t_3dvec *origin) {
 	for(i=0;i<a;i++) {
 		r.y=o.y;
 		for(j=0;j<b;j++) {
+			r.z=o.z;
 			for(k=0;k<c;k++) {
-				r.z=o.z;
 				v3_copy(&(atom[count].r),&r);
 				count+=1;
 				r.z+=lc;
@@ -422,65 +431,55 @@ int cubic_init(int a,int b,int c,double lc,t_atom *atom,t_3dvec *origin) {
 int fcc_init(int a,int b,int c,double lc,t_atom *atom,t_3dvec *origin) {
 
 	int count;
-	int i,j;
+	int i,j,k,l;
 	t_3dvec o,r,n;
 	t_3dvec basis[3];
-	double help[3];
-	double x,y,z;
 
-	x=a*lc;
-	y=b*lc;
-	z=c*lc;
-
-	if(origin) v3_copy(&o,origin);
-	else v3_zero(&o);
+	count=0;
+	if(origin)
+		v3_copy(&o,origin);
+	else
+		v3_zero(&o);
 
 	/* construct the basis */
-	for(i=0;i<3;i++) {
-		for(j=0;j<3;j++) {
-			if(i!=j) help[j]=0.5*lc;
-			else help[j]=.0;
-		}
-		v3_set(&basis[i],help);
-	}
+	memset(basis,0,3*sizeof(t_3dvec));
+	basis[0].x=0.5*lc;
+	basis[0].y=0.5*lc;
+	basis[1].x=0.5*lc;
+	basis[1].z=0.5*lc;
+	basis[2].y=0.5*lc;
+	basis[2].z=0.5*lc;
 
-	v3_zero(&r);
-	count=0;
-	
 	/* fill up the room */
 	r.x=o.x;
-	while(r.x<x) {
+	for(i=0;i<a;i++) {
 		r.y=o.y;
-		while(r.y<y) {
+		for(j=0;j<b;j++) {
 			r.z=o.z;
-			while(r.z<z) {
+			for(k=0;k<c;k++) {
+				/* first atom */
 				v3_copy(&(atom[count].r),&r);
-				atom[count].element=1;
 				count+=1;
-				for(i=0;i<3;i++) {
-					v3_add(&n,&r,&basis[i]);
-					if((n.x<x+o.x)&&
-					   (n.y<y+o.y)&&
-					   (n.z<z+o.z)) {
-						v3_copy(&(atom[count].r),&n);
-						count+=1;
-					}
+				r.z+=lc;
+				/* the three face centered atoms */
+				for(l=0;l<3;l++) {
+					v3_add(&n,&r,&basis[l]);
+					v3_copy(&(atom[count].r),&n);
+					count+=1;
 				}
-				r.z+=lc;	
 			}
 			r.y+=lc;
 		}
 		r.x+=lc;
 	}
-
+				
 	/* coordinate transformation */
-	help[0]=x/2.0;
-	help[1]=y/2.0;
-	help[2]=z/2.0;
-	v3_set(&n,help);
-	for(i=0;i<count;i++)
-		v3_sub(&(atom[i].r),&(atom[i].r),&n);
-		
+	for(i=0;i<count;i++) {
+		atom[i].r.x-=(a*lc)/2.0;
+		atom[i].r.y-=(b*lc)/2.0;
+		atom[i].r.z-=(c*lc)/2.0;
+	}
+
 	return count;
 }
 
@@ -590,18 +589,9 @@ int thermal_init(t_moldyn *moldyn,u8 equi_init) {
 
 double temperature_calc(t_moldyn *moldyn) {
 
-	double double_ekin;
-	int i;
-	t_atom *atom;
-
-	atom=moldyn->atom;
-
-	double_ekin=0;
-	for(i=0;i<moldyn->count;i++)
-		double_ekin+=atom[i].mass*v3_absolute_square(&(atom[i].v));
+	/* assume up to date kinetic energy, which is 3/2 N k_B T */
 
-	/* kinetic energy = 3/2 N k_B T */
-	moldyn->t=double_ekin/(3.0*K_BOLTZMANN*moldyn->count);
+	moldyn->t=(2.0*moldyn->ekin)/(3.0*K_BOLTZMANN*moldyn->count);
 
 	return moldyn->t;
 }
@@ -682,16 +672,21 @@ double pressure_calc(t_moldyn *moldyn) {
 	double v;
 	t_virial *virial;
 
+	/*
+	 * P = 1/(3V) sum_i ( p_i^2 / 2m + f_i r_i )
+	 *
+	 * virial = f_i r_i
+	 */
+
 	v=0.0;
 	for(i=0;i<moldyn->count;i++) {
 		virial=&(moldyn->atom[i].virial);
 		v+=(virial->xx+virial->yy+virial->zz);
 	}
-	v*=ONE_THIRD;
-printf("kieck mal: %f %f %f\n",v,moldyn->count*K_BOLTZMANN*moldyn->t,v/moldyn->count);
 
-	moldyn->p=moldyn->count*K_BOLTZMANN*moldyn->t+v;
-	moldyn->p/=moldyn->volume;
+	/* assume up to date kinetic energy */
+	moldyn->p=2.0*moldyn->ekin+v;
+	moldyn->p/=(3.0*moldyn->volume);
 
 	return moldyn->p;
 }	
@@ -720,7 +715,7 @@ double thermodynamic_pressure_calc(t_moldyn *moldyn) {
 	scale_dim(moldyn,scale,TRUE,0,0);
 	scale_atoms(moldyn,scale,TRUE,0,0);
 	link_cell_shutdown(moldyn);
-	link_cell_init(moldyn);
+	link_cell_init(moldyn,QUIET);
 	potential_force_calc(moldyn);
 	tp->x=(moldyn->energy-u)/moldyn->dv;
 	p=tp->x*tp->x;
@@ -734,7 +729,7 @@ double thermodynamic_pressure_calc(t_moldyn *moldyn) {
 	scale_dim(moldyn,scale,0,TRUE,0);
 	scale_atoms(moldyn,scale,0,TRUE,0);
 	link_cell_shutdown(moldyn);
-	link_cell_init(moldyn);
+	link_cell_init(moldyn,QUIET);
 	potential_force_calc(moldyn);
 	tp->y=(moldyn->energy-u)/moldyn->dv;
 	p+=tp->y*tp->y;
@@ -748,7 +743,7 @@ double thermodynamic_pressure_calc(t_moldyn *moldyn) {
 	scale_dim(moldyn,scale,0,0,TRUE);
 	scale_atoms(moldyn,scale,0,0,TRUE);
 	link_cell_shutdown(moldyn);
-	link_cell_init(moldyn);
+	link_cell_init(moldyn,QUIET);
 	potential_force_calc(moldyn);
 	tp->z=(moldyn->energy-u)/moldyn->dv;
 	p+=tp->z*tp->z;
@@ -765,7 +760,7 @@ printf("debug: %f %f\n",moldyn->atom[0].r.x,moldyn->dim.x);
 	scale_dim(moldyn,scale,1,1,1);
 	scale_atoms(moldyn,scale,1,1,1);
 	link_cell_shutdown(moldyn);
-	link_cell_init(moldyn);
+	link_cell_init(moldyn,QUIET);
 	potential_force_calc(moldyn);
 printf("debug: %f %f\n",moldyn->atom[0].r.x,moldyn->dim.x);
 
@@ -779,7 +774,7 @@ printf("debug: %f %f\n",moldyn->atom[0].r.x,moldyn->dim.x);
 	moldyn->energy=u;
 
 	link_cell_shutdown(moldyn);
-	link_cell_init(moldyn);
+	link_cell_init(moldyn,QUIET);
 
 	return sqrt(p);
 }
@@ -820,61 +815,48 @@ int scale_atoms(t_moldyn *moldyn,double scale,u8 x,u8 y,u8 z) {
 
 int scale_volume(t_moldyn *moldyn) {
 
-	t_atom *atom;
 	t_3dvec *dim,*vdim;
-	double scale,v;
-	t_virial virial;
+	double scale;
 	t_linkcell *lc;
-	int i;
 
-	atom=moldyn->atom;
-	dim=&(moldyn->dim);
 	vdim=&(moldyn->vis.dim);
+	dim=&(moldyn->dim);
 	lc=&(moldyn->lc);
 
-	memset(&virial,0,sizeof(t_virial));
+	/* scaling factor */
+	if(moldyn->pt_scale&P_SCALE_BERENDSEN) {
+		scale=1.0-(moldyn->p_ref-moldyn->p)/moldyn->p_tc;
+		scale=pow(scale,ONE_THIRD);
+	}
+	else {
+		scale=pow(moldyn->p/moldyn->p_ref,ONE_THIRD);
+	}
+moldyn->debug=scale;
 
-	for(i=0;i<moldyn->count;i++) {
-		virial.xx+=atom[i].virial.xx;
-		virial.yy+=atom[i].virial.yy;
-		virial.zz+=atom[i].virial.zz;
-		virial.xy+=atom[i].virial.xy;
-		virial.xz+=atom[i].virial.xz;
-		virial.yz+=atom[i].virial.yz;
+	/* scale the atoms and dimensions */
+	scale_atoms(moldyn,scale,TRUE,TRUE,TRUE);
+	scale_dim(moldyn,scale,TRUE,TRUE,TRUE);
+
+	/* visualize dimensions */
+	if(vdim->x!=0) {
+		vdim->x=dim->x;
+		vdim->y=dim->y;
+		vdim->z=dim->z;
 	}
 
-	/* just a guess so far ... */
-	v=virial.xx+virial.yy+virial.zz;
-
-printf("%f\n",v);
-	/* get pressure from virial */
-	moldyn->p=moldyn->count*K_BOLTZMANN*moldyn->t+ONE_THIRD*v;
-	moldyn->p/=moldyn->volume;
-printf("%f | %f\n",moldyn->p/(ATM),moldyn->p_ref/ATM);
-
-	/* scale factor */
-	if(moldyn->pt_scale&P_SCALE_BERENDSEN)
-		scale=3*sqrt(1-(moldyn->p_ref-moldyn->p)/moldyn->p_tc);
-	else 
-		/* should actually never be used */
-		scale=pow(moldyn->p/moldyn->p_ref,1.0/3.0);
-
-printf("scale = %f\n",scale);
-	/* actual scaling */
-	dim->x*=scale;
-	dim->y*=scale;
-	dim->z*=scale;
-	if(vdim->x) vdim->x=dim->x;
-	if(vdim->y) vdim->y=dim->y;
-	if(vdim->z) vdim->z=dim->z;
-	moldyn->volume*=(scale*scale*scale);
-
-	/* check whether we need a new linkcell init */
-	if((dim->x/moldyn->cutoff!=lc->nx)||
-	   (dim->y/moldyn->cutoff!=lc->ny)||
-	   (dim->z/moldyn->cutoff!=lc->nx)) {
+	/* recalculate scaled volume */
+	moldyn->volume=dim->x*dim->y*dim->z;
+
+	/* adjust/reinit linkcell */
+	if(((int)(dim->x/moldyn->cutoff)!=lc->nx)||
+	   ((int)(dim->y/moldyn->cutoff)!=lc->ny)||
+	   ((int)(dim->z/moldyn->cutoff)!=lc->nx)) {
 		link_cell_shutdown(moldyn);
-		link_cell_init(moldyn);
+		link_cell_init(moldyn,QUIET);
+	} else {
+		lc->x*=scale;
+		lc->y*=scale;
+		lc->z*=scale;
 	}
 
 	return 0;
@@ -939,7 +921,7 @@ double estimate_time_step(t_moldyn *moldyn,double nn_dist) {
 
 /* linked list / cell method */
 
-int link_cell_init(t_moldyn *moldyn) {
+int link_cell_init(t_moldyn *moldyn,u8 vol) {
 
 	t_linkcell *lc;
 	int i;
@@ -960,7 +942,7 @@ int link_cell_init(t_moldyn *moldyn) {
 	if(lc->cells<27)
 		printf("[moldyn] FATAL: less then 27 subcells!\n");
 
-	printf("[moldyn] initializing linked cells (%d)\n",lc->cells);
+	if(vol) printf("[moldyn] initializing linked cells (%d)\n",lc->cells);
 
 	for(i=0;i<lc->cells;i++)
 		list_init_f(&(lc->subcell[i]));
@@ -1137,7 +1119,7 @@ int moldyn_integrate(t_moldyn *moldyn) {
 	atom=moldyn->atom;
 
 	/* initialize linked cell method */
-	link_cell_init(moldyn);
+	link_cell_init(moldyn,VERBOSE);
 
 	/* logging & visualization */
 	e=moldyn->ewrite;
@@ -1190,20 +1172,21 @@ int moldyn_integrate(t_moldyn *moldyn) {
 		/* integration step */
 		moldyn->integrate(moldyn);
 
+		/* calculate kinetic energy, temperature and pressure */
+		update_e_kin(moldyn);
+		temperature_calc(moldyn);
+		pressure_calc(moldyn);
+		//thermodynamic_pressure_calc(moldyn);
+
 		/* p/t scaling */
 		if(moldyn->pt_scale&(T_SCALE_BERENDSEN|T_SCALE_DIRECT))
 			scale_velocity(moldyn,FALSE);
 		if(moldyn->pt_scale&(P_SCALE_BERENDSEN|P_SCALE_DIRECT))
 			scale_volume(moldyn);
 
-		temperature_calc(moldyn);
-		pressure_calc(moldyn);
-		//thermodynamic_pressure_calc(moldyn);
-
 		/* check for log & visualization */
 		if(e) {
 			if(!(i%e))
-				update_e_kin(moldyn);
 				dprintf(moldyn->efd,
 				        "%f %f %f %f\n",
 				        moldyn->time,moldyn->ekin/energy_scale,
@@ -1235,8 +1218,9 @@ int moldyn_integrate(t_moldyn *moldyn) {
 			if(!(i%v)) {
 				visual_atoms(&(moldyn->vis),moldyn->time,
 				             moldyn->atom,moldyn->count);
-				printf("\rsched: %d, steps: %d, debug: %f | %f",
-				       sched->count,i,moldyn->p/ATM,moldyn->debug/ATM);
+				printf("\rsched: %d, steps: %d, T: %f, P: %f V: %f",
+				       sched->count,i,
+				       moldyn->t,moldyn->p/ATM,moldyn->volume);
 				fflush(stdout);
 			}
 		}
@@ -1580,9 +1564,10 @@ int lennard_jones(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc) {
 		d*=eps;
 		v3_scale(&force,&distance,d);
 		v3_add(&(aj->f),&(aj->f),&force);
-		v3_scale(&force,&distance,-1.0*d); /* f = - grad E */
+		v3_scale(&force,&force,-1.0); /* f = - grad E */
 		v3_add(&(ai->f),&(ai->f),&force);
 		virial_calc(ai,&force,&distance);
+if(force.x*distance.x<=0) printf("virial xx: %.15f -> %f %f %f\n",force.x*distance.x,distance.x,distance.y,distance.z);
 		virial_calc(aj,&force,&distance); /* f and d signe switched */
 	}