X-Git-Url: https://www.hackdaworld.org/gitweb/?a=blobdiff_plain;f=moldyn.c;h=f6c3c81d4bbf95b5787474dbd03e18bea90e183e;hb=cb177e7c208a85b45d77b09fcada23b62d0248b5;hp=c25fed3ae9d4c21587336bc2cf321d0bd96b5bbb;hpb=785f05e0c0ddb57428dc71b0a3f7798673799871;p=physik%2Fposic.git

diff --git a/moldyn.c b/moldyn.c
index c25fed3..f6c3c81 100644
--- a/moldyn.c
+++ b/moldyn.c
@@ -16,9 +16,12 @@
 #include <math.h>
 
 #include "moldyn.h"
+#include "report/report.h"
 
 int moldyn_init(t_moldyn *moldyn,int argc,char **argv) {
 
+	printf("[moldyn] init\n");
+
 	memset(moldyn,0,sizeof(t_moldyn));
 
 	rand_init(&(moldyn->random),NULL,1);
@@ -30,6 +33,7 @@ int moldyn_init(t_moldyn *moldyn,int argc,char **argv) {
 int moldyn_shutdown(t_moldyn *moldyn) {
 
 	printf("[moldyn] shutdown\n");
+
 	moldyn_log_shutdown(moldyn);
 	link_cell_shutdown(moldyn);
 	rand_close(&(moldyn->random));
@@ -40,12 +44,16 @@ int moldyn_shutdown(t_moldyn *moldyn) {
 
 int set_int_alg(t_moldyn *moldyn,u8 algo) {
 
+	printf("[moldyn] integration algorithm: ");
+
 	switch(algo) {
 		case MOLDYN_INTEGRATE_VERLET:
 			moldyn->integrate=velocity_verlet;
+			printf("velocity verlet\n");
 			break;
 		default:
 			printf("unknown integration algorithm: %02x\n",algo);
+			printf("unknown\n");
 			return -1;
 	}
 
@@ -56,6 +64,8 @@ int set_cutoff(t_moldyn *moldyn,double cutoff) {
 
 	moldyn->cutoff=cutoff;
 
+	printf("[moldyn] cutoff [A]: %f\n",moldyn->cutoff);
+
 	return 0;
 }
 
@@ -63,6 +73,8 @@ int set_temperature(t_moldyn *moldyn,double t_ref) {
 
 	moldyn->t_ref=t_ref;
 
+	printf("[moldyn] temperature [K]: %f\n",moldyn->t_ref);
+
 	return 0;
 }
 
@@ -70,6 +82,8 @@ int set_pressure(t_moldyn *moldyn,double p_ref) {
 
 	moldyn->p_ref=p_ref;
 
+	printf("[moldyn] pressure [atm]: %f\n",moldyn->p_ref/ATM);
+
 	return 0;
 }
 
@@ -79,6 +93,18 @@ int set_pt_scale(t_moldyn *moldyn,u8 ptype,double ptc,u8 ttype,double ttc) {
 	moldyn->t_tc=ttc;
 	moldyn->p_tc=ptc;
 
+	printf("[moldyn] p/t scaling:\n");
+
+	printf("  p: %s",ptype?"yes":"no ");
+	if(ptype)
+		printf(" | type: %02x | factor: %f",ptype,ptc);
+	printf("\n");
+
+	printf("  t: %s",ttype?"yes":"no ");
+	if(ttype)
+		printf(" | type: %02x | factor: %f",ttype,ttc);
+	printf("\n");
+
 	return 0;
 }
 
@@ -96,12 +122,15 @@ int set_dim(t_moldyn *moldyn,double x,double y,double z,u8 visualize) {
 		moldyn->vis.dim.z=z;
 	}
 
+	moldyn->dv=0.000001*moldyn->volume;
+
 	printf("[moldyn] dimensions in A and A^3 respectively:\n");
 	printf("  x: %f\n",moldyn->dim.x);
 	printf("  y: %f\n",moldyn->dim.y);
 	printf("  z: %f\n",moldyn->dim.z);
 	printf("  volume: %f\n",moldyn->volume);
-	printf("  visualize simulation box: %s\n",visualize?"on":"off");
+	printf("  visualize simulation box: %s\n",visualize?"yes":"no");
+	printf("  delta volume (pressure calc): %f\n",moldyn->dv);
 
 	return 0;
 }
@@ -115,6 +144,8 @@ int set_nn_dist(t_moldyn *moldyn,double dist) {
 
 int set_pbc(t_moldyn *moldyn,u8 x,u8 y,u8 z) {
 
+	printf("[moldyn] periodic boundary conditions:\n");
+
 	if(x)
 		moldyn->status|=MOLDYN_STAT_PBX;
 
@@ -124,6 +155,10 @@ int set_pbc(t_moldyn *moldyn,u8 x,u8 y,u8 z) {
 	if(z)
 		moldyn->status|=MOLDYN_STAT_PBZ;
 
+	printf("  x: %s\n",x?"yes":"no");
+	printf("  y: %s\n",y?"yes":"no");
+	printf("  z: %s\n",z?"yes":"no");
+
 	return 0;
 }
 
@@ -165,12 +200,22 @@ int moldyn_set_log_dir(t_moldyn *moldyn,char *dir) {
 
 	return 0;
 }
+
+int moldyn_set_report(t_moldyn *moldyn,char *author,char *title) {
+
+	strncpy(moldyn->rauthor,author,63);
+	strncpy(moldyn->rtitle,title,63);
+
+	return 0;
+}
 	
 int moldyn_set_log(t_moldyn *moldyn,u8 type,int timer) {
 
 	char filename[128];
 	int ret;
 
+	printf("[moldyn] set log: ");
+
 	switch(type) {
 		case LOG_TOTAL_ENERGY:
 			moldyn->ewrite=timer;
@@ -183,6 +228,7 @@ int moldyn_set_log(t_moldyn *moldyn,u8 type,int timer) {
 				return moldyn->efd;
 			}
 			dprintf(moldyn->efd,"# total energy log file\n");
+			printf("total energy (%d)\n",timer);
 			break;
 		case LOG_TOTAL_MOMENTUM:
 			moldyn->mwrite=timer;
@@ -195,9 +241,11 @@ int moldyn_set_log(t_moldyn *moldyn,u8 type,int timer) {
 				return moldyn->mfd;
 			}
 			dprintf(moldyn->efd,"# total momentum log file\n");
+			printf("total momentum (%d)\n",timer);
 			break;
 		case SAVE_STEP:
 			moldyn->swrite=timer;
+			printf("save file (%d)\n",timer);
 			break;
 		case VISUAL_STEP:
 			moldyn->vwrite=timer;
@@ -206,9 +254,32 @@ int moldyn_set_log(t_moldyn *moldyn,u8 type,int timer) {
 				printf("[moldyn] visual init failure\n");
 				return ret;
 			}
+			printf("visual file (%d)\n",timer);
+			break;
+		case CREATE_REPORT:
+			snprintf(filename,127,"%s/report.tex",moldyn->vlsdir);
+			moldyn->rfd=open(filename,
+			                 O_WRONLY|O_CREAT|O_EXCL,
+			                 S_IRUSR|S_IWUSR);
+			if(moldyn->rfd<0) {
+				perror("[moldyn] report fd open");	
+				return moldyn->rfd;
+			}
+			snprintf(filename,127,"%s/plot.scr",moldyn->vlsdir);
+			moldyn->pfd=open(filename,
+			                 O_WRONLY|O_CREAT|O_EXCL,
+			                 S_IRUSR|S_IWUSR);
+			if(moldyn->pfd<0) {
+				perror("[moldyn] plot fd open");
+				return moldyn->pfd;
+			}
+			dprintf(moldyn->rfd,report_start,
+			        moldyn->rauthor,moldyn->rtitle);
+			dprintf(moldyn->pfd,plot_script);
+			close(moldyn->pfd);
 			break;
 		default:
-			printf("[moldyn] unknown log mechanism: %02x\n",type);
+			printf("unknown log type: %02x\n",type);
 			return -1;
 	}
 
@@ -217,9 +288,23 @@ int moldyn_set_log(t_moldyn *moldyn,u8 type,int timer) {
 
 int moldyn_log_shutdown(t_moldyn *moldyn) {
 
+	char sc[256];
+
 	printf("[moldyn] log shutdown\n");
 	if(moldyn->efd) close(moldyn->efd);
 	if(moldyn->mfd) close(moldyn->mfd);
+	if(moldyn->rfd) {
+		dprintf(moldyn->rfd,report_end);
+		close(moldyn->rfd);
+		snprintf(sc,255,"cd %s && gnuplot plot.scr",moldyn->vlsdir);
+		system(sc);
+		snprintf(sc,255,"cd %s && pdflatex report",moldyn->vlsdir);
+		system(sc);
+		snprintf(sc,255,"cd %s && pdflatex report",moldyn->vlsdir);
+		system(sc);
+		snprintf(sc,255,"cd %s && dvipdf report",moldyn->vlsdir);
+		system(sc);
+	}
 	if(&(moldyn->vis)) visual_tini(&(moldyn->vis));
 
 	return 0;
@@ -230,33 +315,50 @@ int moldyn_log_shutdown(t_moldyn *moldyn) {
  */
 
 int create_lattice(t_moldyn *moldyn,u8 type,double lc,int element,double mass,
-                   u8 attr,u8 bnum,int a,int b,int c) {
+                   u8 attr,u8 brand,int a,int b,int c) {
 
-	int count;
+	int new,count;
 	int ret;
 	t_3dvec origin;
+	void *ptr;
+	t_atom *atom;
 
-	count=a*b*c;
+	new=a*b*c;
+	count=moldyn->count;
 
 	/* how many atoms do we expect */
-	if(type==FCC) count*=4;
-	if(type==DIAMOND) count*=8;
+	if(type==CUBIC) new*=1;
+	if(type==FCC) new*=4;
+	if(type==DIAMOND) new*=8;
 
 	/* allocate space for atoms */
-	moldyn->atom=malloc(count*sizeof(t_atom));
-	if(moldyn->atom==NULL) {
-		perror("malloc (atoms)");
+	ptr=realloc(moldyn->atom,(count+new)*sizeof(t_atom));
+	if(!ptr) {
+		perror("[moldyn] realloc (create lattice)");
 		return -1;
 	}
+	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:
+			set_nn_dist(moldyn,lc);
+			ret=cubic_init(a,b,c,lc,atom,&origin);
+			break;
 		case FCC:
-			ret=fcc_init(a,b,c,lc,moldyn->atom,&origin);
+			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:
-			ret=diamond_init(a,b,c,lc,moldyn->atom,&origin);
+			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:
 			printf("unknown lattice type (%02x)\n",type);
@@ -264,92 +366,120 @@ int create_lattice(t_moldyn *moldyn,u8 type,double lc,int element,double mass,
 	}
 
 	/* debug */
-	if(ret!=count) {
+	if(ret!=new) {
 		printf("[moldyn] creating lattice failed\n");
 		printf("  amount of atoms\n");
-		printf("  - expected: %d\n",count);
+		printf("  - expected: %d\n",new);
 		printf("  - created: %d\n",ret);
 		return -1;
 	}
 
-	moldyn->count=count;
-	printf("[moldyn] created lattice with %d atoms\n",count);
+	moldyn->count+=new;
+	printf("[moldyn] created lattice with %d atoms\n",new);
 
-	while(count) {
-		count-=1;
-		moldyn->atom[count].element=element;
-		moldyn->atom[count].mass=mass;
-		moldyn->atom[count].attr=attr;
-		moldyn->atom[count].bnum=bnum;
-		check_per_bound(moldyn,&(moldyn->atom[count].r));
+	for(ret=0;ret<new;ret++) {
+		atom[ret].element=element;
+		atom[ret].mass=mass;
+		atom[ret].attr=attr;
+		atom[ret].brand=brand;
+		atom[ret].tag=count+ret;
+		check_per_bound(moldyn,&(atom[ret].r));
 	}
 
 	return ret;
 }
 
+/* cubic init */
+int cubic_init(int a,int b,int c,double lc,t_atom *atom,t_3dvec *origin) {
+
+	int count;
+	t_3dvec r;
+	int i,j,k;
+	t_3dvec o;
+
+	count=0;
+	if(origin)
+		v3_copy(&o,origin);
+	else
+		v3_zero(&o);
+
+	r.x=o.x;
+	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++) {
+				v3_copy(&(atom[count].r),&r);
+				count+=1;
+				r.z+=lc;
+			}
+			r.y+=lc;
+		}
+		r.x+=lc;
+	}
+
+	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;
+}
+
 /* fcc lattice init */
 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;
 }
 
@@ -371,7 +501,7 @@ int diamond_init(int a,int b,int c,double lc,t_atom *atom,t_3dvec *origin) {
 	return count;
 }
 
-int add_atom(t_moldyn *moldyn,int element,double mass,u8 bnum,u8 attr,
+int add_atom(t_moldyn *moldyn,int element,double mass,u8 brand,u8 attr,
              t_3dvec *r,t_3dvec *v) {
 
 	t_atom *atom;
@@ -379,9 +509,9 @@ int add_atom(t_moldyn *moldyn,int element,double mass,u8 bnum,u8 attr,
 	int count;
 	
 	atom=moldyn->atom;
-	count=++(moldyn->count);
+	count=(moldyn->count)++;
 
-	ptr=realloc(atom,count*sizeof(t_atom));
+	ptr=realloc(atom,(count+1)*sizeof(t_atom));
 	if(!ptr) {
 		perror("[moldyn] realloc (add atom)");
 		return -1;
@@ -389,12 +519,13 @@ int add_atom(t_moldyn *moldyn,int element,double mass,u8 bnum,u8 attr,
 	moldyn->atom=ptr;
 
 	atom=moldyn->atom;
-	atom[count-1].r=*r;
-	atom[count-1].v=*v;
-	atom[count-1].element=element;
-	atom[count-1].mass=mass;
-	atom[count-1].bnum=bnum;
-	atom[count-1].attr=attr;
+	atom[count].r=*r;
+	atom[count].v=*v;
+	atom[count].element=element;
+	atom[count].mass=mass;
+	atom[count].brand=brand;
+	atom[count].tag=count;
+	atom[count].attr=attr;
 
 	return 0;
 }
@@ -423,6 +554,8 @@ int thermal_init(t_moldyn *moldyn,u8 equi_init) {
 	atom=moldyn->atom;
 	random=&(moldyn->random);
 
+	printf("[moldyn] thermal init (equi init: %s)\n",equi_init?"yes":"no");
+
 	/* gaussian distribution of velocities */
 	v3_zero(&p_total);
 	for(i=0;i<moldyn->count;i++) {
@@ -454,6 +587,20 @@ int thermal_init(t_moldyn *moldyn,u8 equi_init) {
 	return 0;
 }
 
+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);
+
+	return moldyn->t;
+}
+
+double get_temperature(t_moldyn *moldyn) {
+
+	return moldyn->t;
+}
+
 int scale_velocity(t_moldyn *moldyn,u8 equi_init) {
 
 	int i;
@@ -472,10 +619,11 @@ int scale_velocity(t_moldyn *moldyn,u8 equi_init) {
 	count=0;
 	for(i=0;i<moldyn->count;i++) {
 		if((equi_init&TRUE)||(atom[i].attr&ATOM_ATTR_HB)) {
-			e+=0.5*atom[i].mass*v3_absolute_square(&(atom[i].v));
+			e+=atom[i].mass*v3_absolute_square(&(atom[i].v));
 			count+=1;
 		}
 	}
+	e*=0.5;
 	if(count!=0) moldyn->t=e/(1.5*count*K_BOLTZMANN);
 	else return 0;	/* no atoms involved in scaling! */
 	
@@ -509,51 +657,206 @@ int scale_velocity(t_moldyn *moldyn,u8 equi_init) {
 	return 0;
 }
 
+double ideal_gas_law_pressure(t_moldyn *moldyn) {
+
+	double p;
+
+	p=moldyn->count*moldyn->t*K_BOLTZMANN/moldyn->volume;
+
+	return p;
+}
+
+double pressure_calc(t_moldyn *moldyn) {
+
+	int i;
+	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);
+	}
+
+	/* assume up to date kinetic energy */
+	moldyn->p=2.0*moldyn->ekin+v;
+	moldyn->p/=(3.0*moldyn->volume);
+
+	return moldyn->p;
+}	
+
+double thermodynamic_pressure_calc(t_moldyn *moldyn) {
+
+	t_3dvec dim,*tp;
+	double u,p;
+	double scale;
+	t_atom *store;
+
+	tp=&(moldyn->tp);
+	store=malloc(moldyn->count*sizeof(t_atom));
+	if(store==NULL) {
+		printf("[moldyn] allocating store mem failed\n");
+		return -1;
+	}
+
+	/* 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=1.0+moldyn->dv/(moldyn->dim.y*moldyn->dim.z);
+	scale_dim(moldyn,scale,TRUE,0,0);
+	scale_atoms(moldyn,scale,TRUE,0,0);
+	link_cell_shutdown(moldyn);
+	link_cell_init(moldyn,QUIET);
+	potential_force_calc(moldyn);
+	tp->x=(moldyn->energy-u)/moldyn->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=1.0+moldyn->dv/(moldyn->dim.x*moldyn->dim.z);
+	scale_dim(moldyn,scale,0,TRUE,0);
+	scale_atoms(moldyn,scale,0,TRUE,0);
+	link_cell_shutdown(moldyn);
+	link_cell_init(moldyn,QUIET);
+	potential_force_calc(moldyn);
+	tp->y=(moldyn->energy-u)/moldyn->dv;
+	p+=tp->y*tp->y;
+
+	/* restore atomic configuration + dim */
+	memcpy(moldyn->atom,store,moldyn->count*sizeof(t_atom));
+	moldyn->dim=dim;
+
+	/* derivative with respect to z direction */
+	scale=1.0+moldyn->dv/(moldyn->dim.x*moldyn->dim.y);
+	scale_dim(moldyn,scale,0,0,TRUE);
+	scale_atoms(moldyn,scale,0,0,TRUE);
+	link_cell_shutdown(moldyn);
+	link_cell_init(moldyn,QUIET);
+	potential_force_calc(moldyn);
+	tp->z=(moldyn->energy-u)/moldyn->dv;
+	p+=tp->z*tp->z;
+
+	/* restore atomic configuration + dim */
+	memcpy(moldyn->atom,store,moldyn->count*sizeof(t_atom));
+	moldyn->dim=dim;
+
+	printf("dU/dV komp addiert = %f %f %f\n",tp->x,tp->y,tp->z);
+
+	scale=1.0+pow(moldyn->dv/moldyn->volume,ONE_THIRD);
+
+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,QUIET);
+	potential_force_calc(moldyn);
+printf("debug: %f %f\n",moldyn->atom[0].r.x,moldyn->dim.x);
+
+	printf("dU/dV einfach = %f\n",((moldyn->energy-u)/moldyn->dv)/ATM);
+
+	/* restore atomic configuration + dim */
+	memcpy(moldyn->atom,store,moldyn->count*sizeof(t_atom));
+	moldyn->dim=dim;
+
+	/* restore energy */
+	moldyn->energy=u;
+
+	link_cell_shutdown(moldyn);
+	link_cell_init(moldyn,QUIET);
+
+	return sqrt(p);
+}
+
+double get_pressure(t_moldyn *moldyn) {
+
+	return moldyn->p;
+
+}
+
+int scale_dim(t_moldyn *moldyn,double scale,u8 x,u8 y,u8 z) {
+
+	t_3dvec *dim;
+
+	dim=&(moldyn->dim);
+
+	if(x) dim->x*=scale;
+	if(y) dim->y*=scale;
+	if(z) dim->z*=scale;
+
+	return 0;
+}
+
+int scale_atoms(t_moldyn *moldyn,double scale,u8 x,u8 y,u8 z) {
+
+	int i;
+	t_3dvec *r;
+
+	for(i=0;i<moldyn->count;i++) {
+		r=&(moldyn->atom[i].r);
+		if(x) r->x*=scale;
+		if(y) r->y*=scale;
+		if(z) r->z*=scale;
+	}
+
+	return 0;
+}
+
 int scale_volume(t_moldyn *moldyn) {
 
-	t_atom *atom;
 	t_3dvec *dim,*vdim;
-	double virial,scale;
+	double scale;
 	t_linkcell *lc;
-	int i;
 
-	atom=moldyn->atom;
-	dim=&(moldyn->dim);
 	vdim=&(moldyn->vis.dim);
+	dim=&(moldyn->dim);
 	lc=&(moldyn->lc);
 
-	for(i=0;i<moldyn->count;i++)
-		virial+=v3_norm(&(atom[i].virial));
-
-printf("%f\n",virial);
-	/* get pressure from virial */
-	moldyn->p=moldyn->count*K_BOLTZMANN*moldyn->t-ONE_THIRD*virial;
-	moldyn->p/=moldyn->volume;
-printf("%f\n",moldyn->p/(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)) {
+	/* 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;
+
+	/* 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;
+	}
+
+	/* 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;
@@ -574,11 +877,6 @@ double get_e_kin(t_moldyn *moldyn) {
 	return moldyn->ekin;
 }
 
-double get_e_pot(t_moldyn *moldyn) {
-
-	return moldyn->energy;
-}
-
 double update_e_kin(t_moldyn *moldyn) {
 
 	return(get_e_kin(moldyn));
@@ -623,7 +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;
@@ -641,7 +939,10 @@ int link_cell_init(t_moldyn *moldyn) {
 	lc->cells=lc->nx*lc->ny*lc->nz;
 	lc->subcell=malloc(lc->cells*sizeof(t_list));
 
-	printf("[moldyn] initializing linked cells (%d)\n",lc->cells);
+	if(lc->cells<27)
+		printf("[moldyn] FATAL: less then 27 subcells!\n");
+
+	if(vol) printf("[moldyn] initializing linked cells (%d)\n",lc->cells);
 
 	for(i=0;i<lc->cells;i++)
 		list_init_f(&(lc->subcell[i]));
@@ -761,28 +1062,32 @@ int moldyn_add_schedule(t_moldyn *moldyn,int runs,double tau) {
 	t_moldyn_schedule *schedule;
 
 	schedule=&(moldyn->schedule);
-	count=++(schedule->content_count);
+	count=++(schedule->total_sched);
 
-	ptr=realloc(moldyn->schedule.runs,count*sizeof(int));
+	ptr=realloc(schedule->runs,count*sizeof(int));
 	if(!ptr) {
 		perror("[moldyn] realloc (runs)");
 		return -1;
 	}
-	moldyn->schedule.runs=ptr;
-	moldyn->schedule.runs[count-1]=runs;
+	schedule->runs=ptr;
+	schedule->runs[count-1]=runs;
 
 	ptr=realloc(schedule->tau,count*sizeof(double));
 	if(!ptr) {
 		perror("[moldyn] realloc (tau)");
 		return -1;
 	}
-	moldyn->schedule.tau=ptr;
-	moldyn->schedule.tau[count-1]=tau;
+	schedule->tau=ptr;
+	schedule->tau[count-1]=tau;
+
+	printf("[moldyn] schedule added:\n");
+	printf("  number: %d | runs: %d | tau: %f\n",count-1,runs,tau);
+	                               
 
 	return 0;
 }
 
-int moldyn_set_schedule_hook(t_moldyn *moldyn,void *hook,void *hook_params) {
+int moldyn_set_schedule_hook(t_moldyn *moldyn,set_hook hook,void *hook_params) {
 
 	moldyn->schedule.hook=hook;
 	moldyn->schedule.hook_params=hook_params;
@@ -800,20 +1105,21 @@ int moldyn_set_schedule_hook(t_moldyn *moldyn,void *hook,void *hook_params) {
 
 int moldyn_integrate(t_moldyn *moldyn) {
 
-	int i,sched;
+	int i;
 	unsigned int e,m,s,v;
 	t_3dvec p;
-	t_moldyn_schedule *schedule;
+	t_moldyn_schedule *sched;
 	t_atom *atom;
 	int fd;
 	char dir[128];
 	double ds;
+	double energy_scale;
 
-	schedule=&(moldyn->schedule);
+	sched=&(moldyn->schedule);
 	atom=moldyn->atom;
 
 	/* initialize linked cell method */
-	link_cell_init(moldyn);
+	link_cell_init(moldyn,VERBOSE);
 
 	/* logging & visualization */
 	e=moldyn->ewrite;
@@ -825,6 +1131,9 @@ int moldyn_integrate(t_moldyn *moldyn) {
 	moldyn->tau_square=moldyn->tau*moldyn->tau;
 	moldyn->cutoff_square=moldyn->cutoff*moldyn->cutoff;
 
+	/* energy scaling factor */
+	energy_scale=moldyn->count*EV;
+
 	/* calculate initial forces */
 	potential_force_calc(moldyn);
 
@@ -845,13 +1154,16 @@ int moldyn_integrate(t_moldyn *moldyn) {
 	/* debugging, ignore */
 	moldyn->debug=0;
 
+	/* tell the world */
+	printf("[moldyn] integration start, go get a coffee ...\n");
+
 	/* executing the schedule */
-	for(sched=0;sched<moldyn->schedule.content_count;sched++) {
+	for(sched->count=0;sched->count<sched->total_sched;sched->count++) {
 
 		/* setting amount of runs and finite time step size */
-		moldyn->tau=schedule->tau[sched];
+		moldyn->tau=sched->tau[sched->count];
 		moldyn->tau_square=moldyn->tau*moldyn->tau;
-		moldyn->time_steps=schedule->runs[sched];
+		moldyn->time_steps=sched->runs[sched->count];
 
 	/* integration according to schedule */
 
@@ -860,6 +1172,12 @@ 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);
@@ -871,9 +1189,9 @@ int moldyn_integrate(t_moldyn *moldyn) {
 			if(!(i%e))
 				dprintf(moldyn->efd,
 				        "%f %f %f %f\n",
-				        moldyn->time,update_e_kin(moldyn),
-				        moldyn->energy,
-				        get_total_energy(moldyn));
+				        moldyn->time,moldyn->ekin/energy_scale,
+				        moldyn->energy/energy_scale,
+				        get_total_energy(moldyn)/energy_scale);
 		}
 		if(m) {
 			if(!(i%m)) {
@@ -900,8 +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: %d",
-				       sched,i,moldyn->debug);
+				printf("\rsched: %d, steps: %d, T: %f, P: %f V: %f",
+				       sched->count,i,
+				       moldyn->t,moldyn->p/ATM,moldyn->volume);
 				fflush(stdout);
 			}
 		}
@@ -912,8 +1231,8 @@ int moldyn_integrate(t_moldyn *moldyn) {
 	}
 
 		/* check for hooks */
-		if(schedule->hook)
-			schedule->hook(moldyn,schedule->hook_params);
+		if(sched->hook)
+			sched->hook(moldyn,sched->hook_params);
 
 		/* get a new info line */
 		printf("\n");
@@ -928,7 +1247,7 @@ int moldyn_integrate(t_moldyn *moldyn) {
 int velocity_verlet(t_moldyn *moldyn) {
 
 	int i,count;
-	double tau,tau_square;
+	double tau,tau_square,h;
 	t_3dvec delta;
 	t_atom *atom;
 
@@ -939,14 +1258,15 @@ int velocity_verlet(t_moldyn *moldyn) {
 
 	for(i=0;i<count;i++) {
 		/* new positions */
+		h=0.5/atom[i].mass;
 		v3_scale(&delta,&(atom[i].v),tau);
 		v3_add(&(atom[i].r),&(atom[i].r),&delta);
-		v3_scale(&delta,&(atom[i].f),0.5*tau_square/atom[i].mass);
+		v3_scale(&delta,&(atom[i].f),h*tau_square);
 		v3_add(&(atom[i].r),&(atom[i].r),&delta);
 		check_per_bound(moldyn,&(atom[i].r));
 
-		/* velocities */
-		v3_scale(&delta,&(atom[i].f),0.5*tau/atom[i].mass);
+		/* velocities [actually v(t+tau/2)] */
+		v3_scale(&delta,&(atom[i].f),h*tau);
 		v3_add(&(atom[i].v),&(atom[i].v),&delta);
 	}
 
@@ -957,7 +1277,7 @@ int velocity_verlet(t_moldyn *moldyn) {
 	potential_force_calc(moldyn);
 
 	for(i=0;i<count;i++) {
-		/* again velocities */
+		/* again velocities [actually v(t+tau)] */
 		v3_scale(&delta,&(atom[i].f),0.5*tau/atom[i].mass);
 		v3_add(&(atom[i].v),&(atom[i].v),&delta);
 	}
@@ -968,7 +1288,7 @@ int velocity_verlet(t_moldyn *moldyn) {
 
 /*
  *
- * potentials & corresponding forces
+ * potentials & corresponding forces & virial routine
  * 
  */
 
@@ -978,6 +1298,7 @@ int potential_force_calc(t_moldyn *moldyn) {
 
 	int i,j,k,count;
 	t_atom *itom,*jtom,*ktom;
+	t_virial *virial;
 	t_linkcell *lc;
 	t_list neighbour_i[27];
 	t_list neighbour_i2[27];
@@ -991,15 +1312,29 @@ int potential_force_calc(t_moldyn *moldyn) {
 
 	/* reset energy */
 	moldyn->energy=0.0;
-	
-	/* get energy and force of every atom */
+
+	/* reset force, site energy and virial of every atom */
 	for(i=0;i<count;i++) {
 
 		/* reset force */
 		v3_zero(&(itom[i].f));
 
-		/* reset viral of atom i */
-		v3_zero(&(itom[i].virial));
+		/* reset virial */
+		virial=(&(itom[i].virial));
+		virial->xx=0.0;
+		virial->yy=0.0;
+		virial->zz=0.0;
+		virial->xy=0.0;
+		virial->xz=0.0;
+		virial->yz=0.0;
+	
+		/* reset site energy */
+		itom[i].e=0.0;
+
+	}
+
+	/* get energy,force and virial of every atom */
+	for(i=0;i<count;i++) {
 
 		/* single particle potential/force */
 		if(itom[i].attr&ATOM_ATTR_1BP)
@@ -1100,6 +1435,29 @@ int potential_force_calc(t_moldyn *moldyn) {
 
 	}
 
+#ifdef DEBUG
+printf("\n\n");
+#endif
+#ifdef VDEBUG
+printf("\n\n");
+#endif
+
+	return 0;
+}
+
+/*
+ * virial calculation
+ */
+
+inline int virial_calc(t_atom *a,t_3dvec *f,t_3dvec *d) {
+
+	a->virial.xx+=f->x*d->x;
+	a->virial.yy+=f->y*d->y;
+	a->virial.zz+=f->z*d->z;
+	a->virial.xy+=f->x*d->y;
+	a->virial.xz+=f->x*d->z;
+	a->virial.yz+=f->y*d->z;
+
 	return 0;
 }
 
@@ -1145,23 +1503,29 @@ int harmonic_oscillator(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc) {
 
 	t_ho_params *params;
 	t_3dvec force,distance;
-	double d;
+	double d,f;
 	double sc,equi_dist;
 
 	params=moldyn->pot2b_params;
 	sc=params->spring_constant;
 	equi_dist=params->equilibrium_distance;
 
+	if(ai<aj) return 0;
+
 	v3_sub(&distance,&(aj->r),&(ai->r));
 	
 	if(bc) check_per_bound(moldyn,&distance);
 	d=v3_norm(&distance);
 	if(d<=moldyn->cutoff) {
-		/* energy is 1/2 (d-d0)^2, but we will add this twice ... */
-		moldyn->energy+=(0.25*sc*(d-equi_dist)*(d-equi_dist));
+		moldyn->energy+=(0.5*sc*(d-equi_dist)*(d-equi_dist));
 		/* f = -grad E; grad r_ij = -1 1/r_ij distance */
-		v3_scale(&force,&distance,sc*(1.0-(equi_dist/d)));
+		f=sc*(1.0-equi_dist/d);
+		v3_scale(&force,&distance,f);
 		v3_add(&(ai->f),&(ai->f),&force);
+		virial_calc(ai,&force,&distance);
+		virial_calc(aj,&force,&distance); /* f and d signe switched */
+		v3_scale(&force,&distance,-f);
+		v3_add(&(aj->f),&(aj->f),&force);
 	}
 
 	return 0;
@@ -1181,6 +1545,8 @@ int lennard_jones(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc) {
 	sig6=params->sigma6;
 	sig12=params->sigma12;
 
+	if(ai<aj) return 0;
+
 	v3_sub(&distance,&(aj->r),&(ai->r));
 	if(bc) check_per_bound(moldyn,&distance);
 	d=v3_absolute_square(&distance);	/* 1/r^2 */
@@ -1189,16 +1555,20 @@ int lennard_jones(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc) {
 		h2=d*d; 			/* 1/r^4 */
 		h2*=d;	 			/* 1/r^6 */
 		h1=h2*h2; 			/* 1/r^12 */
-		/* energy is eps*..., but we will add this twice ... */
-		moldyn->energy+=0.5*eps*(sig12*h1-sig6*h2);
+		moldyn->energy+=(eps*(sig12*h1-sig6*h2)-params->uc);
 		h2*=d;				/* 1/r^8 */
 		h1*=d;				/* 1/r^14 */
 		h2*=6*sig6;
 		h1*=12*sig12;
 		d=+h1-h2;
 		d*=eps;
-		v3_scale(&force,&distance,-1.0*d); /* f = - grad E */
+		v3_scale(&force,&distance,d);
+		v3_add(&(aj->f),&(aj->f),&force);
+		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 */
 	}
 
 	return 0;
@@ -1212,7 +1582,10 @@ int lennard_jones(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc) {
 int tersoff_mult_complete_params(t_tersoff_mult_params *p) {
 
 	printf("[moldyn] tersoff parameter completion\n");
+	p->S2[0]=p->S[0]*p->S[0];
+	p->S2[1]=p->S[1]*p->S[1];
 	p->Smixed=sqrt(p->S[0]*p->S[1]);
+	p->S2mixed=p->Smixed*p->Smixed;
 	p->Rmixed=sqrt(p->R[0]*p->R[1]);
 	p->Amixed=sqrt(p->A[0]*p->A[1]);
 	p->Bmixed=sqrt(p->B[0]*p->B[1]);
@@ -1240,11 +1613,11 @@ int tersoff_mult_complete_params(t_tersoff_mult_params *p) {
 /* tersoff 1 body part */
 int tersoff_mult_1bp(t_moldyn *moldyn,t_atom *ai) {
 
-	int num;
+	int brand;
 	t_tersoff_mult_params *params;
 	t_tersoff_exchange *exchange;
 	
-	num=ai->bnum;
+	brand=ai->brand;
 	params=moldyn->pot1b_params;
 	exchange=&(params->exchange);
 
@@ -1253,15 +1626,15 @@ int tersoff_mult_1bp(t_moldyn *moldyn,t_atom *ai) {
 	 *         their right values
 	 */
 
-	exchange->beta_i=&(params->beta[num]);
-	exchange->n_i=&(params->n[num]);
-	exchange->c_i=&(params->c[num]);
-	exchange->d_i=&(params->d[num]);
-	exchange->h_i=&(params->h[num]);
+	exchange->beta_i=&(params->beta[brand]);
+	exchange->n_i=&(params->n[brand]);
+	exchange->c_i=&(params->c[brand]);
+	exchange->d_i=&(params->d[brand]);
+	exchange->h_i=&(params->h[brand]);
 
 	exchange->betaini=pow(*(exchange->beta_i),*(exchange->n_i));
-	exchange->ci2=params->c[num]*params->c[num];
-	exchange->di2=params->d[num]*params->d[num];
+	exchange->ci2=params->c[brand]*params->c[brand];
+	exchange->di2=params->d[brand]*params->d[brand];
 	exchange->ci2di2=exchange->ci2/exchange->di2;
 
 	return 0;
@@ -1273,16 +1646,16 @@ int tersoff_mult_2bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc) {
 	t_tersoff_mult_params *params;
 	t_tersoff_exchange *exchange;
 	t_3dvec dist_ij,force;
-	double d_ij;
-	double A,B,R,S,lambda,mu;
+	double d_ij,d_ij2;
+	double A,B,R,S,S2,lambda,mu;
 	double f_r,df_r;
 	double f_c,df_c;
-	int num;
+	int brand;
 	double s_r;
 	double arg;
 
 	params=moldyn->pot2b_params;
-	num=aj->bnum;
+	brand=aj->brand;
 	exchange=&(params->exchange);
 
 	/* clear 3bp and 2bp post run */
@@ -1305,27 +1678,20 @@ int tersoff_mult_2bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc) {
 	 *
 	 */
 
-	/* dist_ij, d_ij */
-	v3_sub(&dist_ij,&(aj->r),&(ai->r));
-	if(bc) check_per_bound(moldyn,&dist_ij);
-	d_ij=v3_norm(&dist_ij);
-
-	/* save for use in 3bp */
-	exchange->d_ij=d_ij;
-	exchange->dist_ij=dist_ij;
-
 	/* constants */
-	if(num==ai->bnum) {
-		S=params->S[num];
-		R=params->R[num];
-		A=params->A[num];
-		B=params->B[num];
-		lambda=params->lambda[num];
-		mu=params->mu[num];
+	if(brand==ai->brand) {
+		S=params->S[brand];
+		S2=params->S2[brand];
+		R=params->R[brand];
+		A=params->A[brand];
+		B=params->B[brand];
+		lambda=params->lambda[brand];
+		mu=params->mu[brand];
 		exchange->chi=1.0;
 	}
 	else {
 		S=params->Smixed;
+		S2=params->S2mixed;
 		R=params->Rmixed;
 		A=params->Amixed;
 		B=params->Bmixed;
@@ -1334,17 +1700,31 @@ int tersoff_mult_2bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc) {
 		params->exchange.chi=params->chi;
 	}
 
-	/* if d_ij > S => no force & potential energy contribution */
-	if(d_ij>S)
+	/* dist_ij, d_ij */
+	v3_sub(&dist_ij,&(aj->r),&(ai->r));
+	if(bc) check_per_bound(moldyn,&dist_ij);
+	d_ij2=v3_absolute_square(&dist_ij);
+
+	/* if d_ij2 > S2 => no force & potential energy contribution */
+	if(d_ij2>S2)
 		return 0;
 
+	/* now we will need the distance */
+	//d_ij=v3_norm(&dist_ij);
+	d_ij=sqrt(d_ij2);
+
+	/* save for use in 3bp */
+	exchange->d_ij=d_ij;
+	exchange->d_ij2=d_ij2;
+	exchange->dist_ij=dist_ij;
+
 	/* more constants */
-	exchange->beta_j=&(params->beta[num]);
-	exchange->n_j=&(params->n[num]);
-	exchange->c_j=&(params->c[num]);
-	exchange->d_j=&(params->d[num]);
-	exchange->h_j=&(params->h[num]);
-	if(num==ai->bnum) {
+	exchange->beta_j=&(params->beta[brand]);
+	exchange->n_j=&(params->n[brand]);
+	exchange->c_j=&(params->c[brand]);
+	exchange->d_j=&(params->d[brand]);
+	exchange->h_j=&(params->h[brand]);
+	if(brand==ai->brand) {
 		exchange->betajnj=exchange->betaini;
 		exchange->cj2=exchange->ci2;
 		exchange->dj2=exchange->di2;
@@ -1352,8 +1732,8 @@ int tersoff_mult_2bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc) {
 	}
 	else {
 		exchange->betajnj=pow(*(exchange->beta_j),*(exchange->n_j));
-		exchange->cj2=params->c[num]*params->c[num];
-		exchange->dj2=params->d[num]*params->d[num];
+		exchange->cj2=params->c[brand]*params->c[brand];
+		exchange->dj2=params->d[brand]*params->d[brand];
 		exchange->cj2dj2=exchange->cj2/exchange->dj2;
 	}
 
@@ -1377,7 +1757,6 @@ int tersoff_mult_2bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc) {
 		s_r=S-R;
 		arg=M_PI*(d_ij-R)/s_r;
 		f_c=0.5+0.5*cos(arg);
-		//df_c=-0.5*sin(arg)*(M_PI/(s_r*d_ij));	/* MARK! */
 		df_c=0.5*sin(arg)*(M_PI/(s_r*d_ij));
 		/* two body contribution (ij, ji) */
 		v3_scale(&force,&dist_ij,-df_c*f_r-df_r*f_c);
@@ -1389,6 +1768,31 @@ int tersoff_mult_2bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc) {
 	 * dVij = dVji and we sum up both: no 1/2) */
 	v3_add(&(ai->f),&(ai->f),&force);
 
+	/* virial */
+	ai->virial.xx-=force.x*dist_ij.x;
+	ai->virial.yy-=force.y*dist_ij.y;
+	ai->virial.zz-=force.z*dist_ij.z;
+	ai->virial.xy-=force.x*dist_ij.y;
+	ai->virial.xz-=force.x*dist_ij.z;
+	ai->virial.yz-=force.y*dist_ij.z;
+
+#ifdef DEBUG
+if(ai==&(moldyn->atom[0])) {
+	printf("dVij, dVji (2bp) contrib:\n");
+	printf("%f | %f\n",force.x,ai->f.x);
+	printf("%f | %f\n",force.y,ai->f.y);
+	printf("%f | %f\n",force.z,ai->f.z);
+}
+#endif
+#ifdef VDEBUG
+if(ai==&(moldyn->atom[0])) {
+	printf("dVij, dVji (2bp) contrib:\n");
+	printf("%f | %f\n",force.x*dist_ij.x,ai->virial.xx);
+	printf("%f | %f\n",force.y*dist_ij.y,ai->virial.yy);
+	printf("%f | %f\n",force.z*dist_ij.z,ai->virial.zz);
+}
+#endif
+
 	/* energy 2bp contribution (ij, ji) is 0.5 f_r f_c ... */
 	moldyn->energy+=(0.5*f_r*f_c);
 
@@ -1458,7 +1862,6 @@ int tersoff_mult_post_2bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc) {
 	zeta=exchange->zeta_ij;
 	if(zeta==0.0) {
 		moldyn->debug++;		/* just for debugging ... */
-		db=0.0;
 		b=chi;
 		v3_scale(&force,dist_ij,df_a*b*f_c);
 	}
@@ -1480,6 +1883,31 @@ int tersoff_mult_post_2bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc) {
 	/* add force */
 	v3_add(&(ai->f),&(ai->f),&force);
 
+	/* virial */
+	ai->virial.xx-=force.x*dist_ij->x;
+	ai->virial.yy-=force.y*dist_ij->y;
+	ai->virial.zz-=force.z*dist_ij->z;
+	ai->virial.xy-=force.x*dist_ij->y;
+	ai->virial.xz-=force.x*dist_ij->z;
+	ai->virial.yz-=force.y*dist_ij->z;
+
+#ifdef DEBUG
+if(ai==&(moldyn->atom[0])) {
+	printf("dVij (3bp) contrib:\n");
+	printf("%f | %f\n",force.x,ai->f.x);
+	printf("%f | %f\n",force.y,ai->f.y);
+	printf("%f | %f\n",force.z,ai->f.z);
+}
+#endif
+#ifdef VDEBUG
+if(ai==&(moldyn->atom[0])) {
+	printf("dVij (3bp) contrib:\n");
+	printf("%f | %f\n",force.x*dist_ij->x,ai->virial.xx);
+	printf("%f | %f\n",force.y*dist_ij->y,ai->virial.yy);
+	printf("%f | %f\n",force.z*dist_ij->z,ai->virial.zz);
+}
+#endif
+
 	/* add energy of 3bp sum */
 	moldyn->energy+=(0.5*f_c*b*f_a);
 
@@ -1508,6 +1936,32 @@ int tersoff_mult_post_2bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc) {
 	/* add force */
 	v3_add(&(ai->f),&(ai->f),&force);
 
+	/* virial - plus sign, as dist_ij = - dist_ji - (really??) */
+// TEST ... with a minus instead
+	ai->virial.xx-=force.x*dist_ij->x;
+	ai->virial.yy-=force.y*dist_ij->y;
+	ai->virial.zz-=force.z*dist_ij->z;
+	ai->virial.xy-=force.x*dist_ij->y;
+	ai->virial.xz-=force.x*dist_ij->z;
+	ai->virial.yz-=force.y*dist_ij->z;
+
+#ifdef DEBUG
+if(ai==&(moldyn->atom[0])) {
+	printf("dVji (3bp) contrib:\n");
+	printf("%f | %f\n",force.x,ai->f.x);
+	printf("%f | %f\n",force.y,ai->f.y);
+	printf("%f | %f\n",force.z,ai->f.z);
+}
+#endif
+#ifdef VDEBUG
+if(ai==&(moldyn->atom[0])) {
+	printf("dVji (3bp) contrib:\n");
+	printf("%f | %f\n",force.x*dist_ij->x,ai->virial.xx);
+	printf("%f | %f\n",force.y*dist_ij->y,ai->virial.yy);
+	printf("%f | %f\n",force.z*dist_ij->z,ai->virial.zz);
+}
+#endif
+
 	return 0;
 }
 
@@ -1520,9 +1974,9 @@ int tersoff_mult_3bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,t_atom *ak,u8 bc) {
 	t_3dvec dist_ij,dist_ik,dist_jk;
 	t_3dvec temp1,temp2;
 	t_3dvec *dzeta;
-	double R,S,s_r;
+	double R,S,S2,s_r;
 	double B,mu;
-	double d_ij,d_ik,d_jk;
+	double d_ij,d_ik,d_jk,d_ij2,d_ik2,d_jk2;
 	double rr,dd;
 	double f_c,df_c;
 	double f_c_ik,df_c_ik,arg;
@@ -1533,7 +1987,7 @@ int tersoff_mult_3bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,t_atom *ak,u8 bc) {
 	double h_cos,d2_h_cos2;
 	double frac,g,zeta,chi;
 	double tmp;
-	int num;
+	int brand;
 
 	params=moldyn->pot3b_params;
 	exchange=&(params->exchange);
@@ -1568,6 +2022,7 @@ int tersoff_mult_3bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,t_atom *ak,u8 bc) {
 	/* dist_ij, d_ij - this is < S_ij ! */
 	dist_ij=exchange->dist_ij;
 	d_ij=exchange->d_ij;
+	d_ij2=exchange->d_ij2;
 
 	/* f_c_ij, df_c_ij (same for ji) */
 	f_c=exchange->f_c;
@@ -1582,21 +2037,26 @@ int tersoff_mult_3bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,t_atom *ak,u8 bc) {
 	/* dist_ik, d_ik */
 	v3_sub(&dist_ik,&(ak->r),&(ai->r));
 	if(bc) check_per_bound(moldyn,&dist_ik);
-	d_ik=v3_norm(&dist_ik);
+	d_ik2=v3_absolute_square(&dist_ik);
 
 	/* ik constants */
-	num=ai->bnum;
-	if(num==ak->bnum) {
-		R=params->R[num];
-		S=params->S[num];
+	brand=ai->brand;
+	if(brand==ak->brand) {
+		R=params->R[brand];
+		S=params->S[brand];
+		S2=params->S2[brand];
 	}
 	else {
 		R=params->Rmixed;
 		S=params->Smixed;
+		S2=params->S2mixed;
 	}
 
 	/* zeta_ij/dzeta_ij contribution only for d_ik < S */
-	if(d_ik<S) {
+	if(d_ik2<S2) {
+
+		/* now we need d_ik */
+		d_ik=sqrt(d_ik2);
 
 		/* get constants_i from exchange data */
 		n=*(exchange->n_i);
@@ -1614,8 +2074,8 @@ int tersoff_mult_3bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,t_atom *ak,u8 bc) {
 
 		/* d_costheta */
 		tmp=1.0/dd;
-		d_costheta1=cos_theta/(d_ij*d_ij)-tmp;
-		d_costheta2=cos_theta/(d_ik*d_ik)-tmp;
+		d_costheta1=cos_theta/d_ij2-tmp;
+		d_costheta2=cos_theta/d_ik2-tmp;
 
 		/* some usefull values */
 		h_cos=(h-cos_theta);
@@ -1649,7 +2109,6 @@ int tersoff_mult_3bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,t_atom *ak,u8 bc) {
 			s_r=S-R;
 			arg=M_PI*(d_ik-R)/s_r;
 			f_c_ik=0.5+0.5*cos(arg);
-			//df_c_ik=-0.5*sin(arg)*(M_PI/(s_r*d_ik)); /* MARK */
 			df_c_ik=0.5*sin(arg)*(M_PI/(s_r*d_ik));
 
 			/* zeta_ij */
@@ -1668,27 +2127,32 @@ int tersoff_mult_3bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,t_atom *ak,u8 bc) {
 	/* dist_jk, d_jk */
 	v3_sub(&dist_jk,&(ak->r),&(aj->r));
 	if(bc) check_per_bound(moldyn,&dist_jk);
-	d_jk=v3_norm(&dist_jk);
+	d_jk2=v3_absolute_square(&dist_jk);
 
 	/* jk constants */
-	num=aj->bnum;
-	if(num==ak->bnum) {
-		R=params->R[num];
-		S=params->S[num];
-		B=params->B[num];
-		mu=params->mu[num];
+	brand=aj->brand;
+	if(brand==ak->brand) {
+		R=params->R[brand];
+		S=params->S[brand];
+		S2=params->S2[brand];
+		B=params->B[brand];
+		mu=params->mu[brand];
 		chi=1.0;
 	}
 	else {
 		R=params->Rmixed;
 		S=params->Smixed;
+		S2=params->S2mixed;
 		B=params->Bmixed;
 		mu=params->mu_m;
 		chi=params->chi;
 	}
 
 	/* zeta_ji/dzeta_ji contribution only for d_jk < S_jk */
-	if(d_jk<S) {
+	if(d_jk2<S2) {
+
+		/* now we need d_ik */
+		d_jk=sqrt(d_jk2);
 
 		/* constants_j from exchange data */
 		n=*(exchange->n_j);
@@ -1706,7 +2170,7 @@ int tersoff_mult_3bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,t_atom *ak,u8 bc) {
 
 		/* d_costheta */
 		d_costheta1=1.0/dd;
-		d_costheta2=cos_theta/(d_ij*d_ij);
+		d_costheta2=cos_theta/d_ij2;
 
 		/* some usefull values */
 		h_cos=(h-cos_theta);
@@ -1716,10 +2180,11 @@ int tersoff_mult_3bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,t_atom *ak,u8 bc) {
 		/* g(cos_theta) */
 		g=1.0+c2d2-frac;
 
-		/* d_costheta_ij and dg(cos_theta) - needed in any case! */
+		/* d_costheta_jik and dg(cos_theta) - needed in any case! */
 		v3_scale(&temp1,&dist_jk,d_costheta1);
 		v3_scale(&temp2,&dist_ij,-d_costheta2); /* ji -> ij => -1 */
-		v3_add(&temp1,&temp1,&temp2);
+		//v3_add(&temp1,&temp1,&temp2);
+		v3_sub(&temp1,&temp1,&temp2); /* there is a minus! */
 		v3_scale(&temp1,&temp1,-2.0*frac*h_cos/d2_h_cos2); /* dg */
 
 		/* store dg in temp2 and use it for dVjk later */
@@ -1769,6 +2234,31 @@ int tersoff_mult_3bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,t_atom *ak,u8 bc) {
 		v3_add(&(ai->f),&(ai->f),&temp2); /* -1 skipped in f_a calc ^ */
 		                                  /* scaled with 0.5 ^ */
 
+		/* virial */
+		ai->virial.xx-=temp2.x*dist_jk.x;
+		ai->virial.yy-=temp2.y*dist_jk.y;
+		ai->virial.zz-=temp2.z*dist_jk.z;
+		ai->virial.xy-=temp2.x*dist_jk.y;
+		ai->virial.xz-=temp2.x*dist_jk.z;
+		ai->virial.yz-=temp2.y*dist_jk.z;
+
+#ifdef DEBUG
+if(ai==&(moldyn->atom[0])) {
+	printf("dVjk (3bp) contrib:\n");
+	printf("%f | %f\n",temp2.x,ai->f.x);
+	printf("%f | %f\n",temp2.y,ai->f.y);
+	printf("%f | %f\n",temp2.z,ai->f.z);
+}
+#endif
+#ifdef VDEBUG
+if(ai==&(moldyn->atom[0])) {
+	printf("dVjk (3bp) contrib:\n");
+	printf("%f | %f\n",temp2.x*dist_jk.x,ai->virial.xx);
+	printf("%f | %f\n",temp2.y*dist_jk.y,ai->virial.yy);
+	printf("%f | %f\n",temp2.z*dist_jk.z,ai->virial.zz);
+}
+#endif
+
 	}
 
 	return 0;
@@ -1784,13 +2274,13 @@ int moldyn_bc_check(t_moldyn *moldyn) {
 	t_atom *atom;
 	t_3dvec *dim;
 	int i;
-double x;
-u8 byte;
-int j,k;
+	double x;
+	u8 byte;
+	int j,k;
 
 	atom=moldyn->atom;
 	dim=&(moldyn->dim);
-x=dim->x/2;
+	x=dim->x/2;
 
 	for(i=0;i<moldyn->count;i++) {
 		if(atom[i].r.x>=dim->x/2||-atom[i].r.x>dim->x/2) {