X-Git-Url: https://www.hackdaworld.org/gitweb/?a=blobdiff_plain;f=moldyn.c;h=faa6b7c3ea6354a7f1ab08a51cca462d567fd405;hb=2d562a1946322ae5b70bdce180321f32adbeab62;hp=7a77898b958b9a06f326a6f31423a46cfcce02f9;hpb=60f40345bc4fcd8448d724dc67bbb512ec081bd4;p=physik%2Fposic.git

diff --git a/moldyn.c b/moldyn.c
index 7a77898..faa6b7c 100644
--- a/moldyn.c
+++ b/moldyn.c
@@ -19,11 +19,6 @@
 
 int moldyn_init(t_moldyn *moldyn,int argc,char **argv) {
 
-	//int ret;
-
-	//ret=moldyn_parse_argv(moldyn,argc,argv);
-	//if(ret<0) return ret;
-
 	memset(moldyn,0,sizeof(t_moldyn));
 
 	rand_init(&(moldyn->random),NULL,1);
@@ -101,7 +96,7 @@ int set_dim(t_moldyn *moldyn,double x,double y,double z,u8 visualize) {
 		moldyn->vis.dim.z=z;
 	}
 
-	printf("[moldyn] dimensions in A and A^2 respectively:\n");
+	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);
@@ -230,34 +225,43 @@ int moldyn_log_shutdown(t_moldyn *moldyn) {
 	return 0;
 }
 
+/*
+ * creating lattice functions
+ */
+
 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==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);
 
 	switch(type) {
 		case FCC:
-			ret=fcc_init(a,b,c,lc,moldyn->atom,&origin);
+			ret=fcc_init(a,b,c,lc,atom,&origin);
 			break;
 		case DIAMOND:
-			ret=diamond_init(a,b,c,lc,moldyn->atom,&origin);
+			ret=diamond_init(a,b,c,lc,atom,&origin);
 			break;
 		default:
 			printf("unknown lattice type (%02x)\n",type);
@@ -265,30 +269,114 @@ 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;
 }
 
-int add_atom(t_moldyn *moldyn,int element,double mass,u8 bnum,u8 attr,
+/* 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;
+	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);
+
+	/* 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);
+	}
+
+	v3_zero(&r);
+	count=0;
+	
+	/* fill up the room */
+	r.x=o.x;
+	while(r.x<x) {
+		r.y=o.y;
+		while(r.y<y) {
+			r.z=o.z;
+			while(r.z<z) {
+				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;	
+			}
+			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);
+		
+	return count;
+}
+
+int diamond_init(int a,int b,int c,double lc,t_atom *atom,t_3dvec *origin) {
+
+	int count;
+	t_3dvec o;
+
+	count=fcc_init(a,b,c,lc,atom,origin);
+
+	o.x=0.25*lc;
+	o.y=0.25*lc;
+	o.z=0.25*lc;
+
+	if(origin) v3_add(&o,&o,origin);
+
+	count+=fcc_init(a,b,c,lc,&atom[count],&o);
+
+	return count;
+}
+
+int add_atom(t_moldyn *moldyn,int element,double mass,u8 brand,u8 attr,
              t_3dvec *r,t_3dvec *v) {
 
 	t_atom *atom;
@@ -296,9 +384,9 @@ 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;
@@ -306,12 +394,13 @@ 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;
 }
@@ -430,7 +519,8 @@ int scale_volume(t_moldyn *moldyn) {
 
 	t_atom *atom;
 	t_3dvec *dim,*vdim;
-	double virial,scale;
+	double scale,v;
+	t_virial virial;
 	t_linkcell *lc;
 	int i;
 
@@ -439,14 +529,25 @@ int scale_volume(t_moldyn *moldyn) {
 	vdim=&(moldyn->vis.dim);
 	lc=&(moldyn->lc);
 
-	for(i=0;i<moldyn->count;i++)
-		virial+=v3_norm(&(atom[i].virial));
+	memset(&virial,0,sizeof(t_virial));
+
+	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;
+	}
 
-printf("%f\n",virial);
+	/* 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*virial;
+	moldyn->p=moldyn->count*K_BOLTZMANN*moldyn->t+ONE_THIRD*v;
 	moldyn->p/=moldyn->volume;
-printf("%f\n",moldyn->p/(ATM));
+printf("%f | %f\n",moldyn->p/(ATM),moldyn->p_ref/ATM);
 
 	/* scale factor */
 	if(moldyn->pt_scale&P_SCALE_BERENDSEN)
@@ -571,24 +672,28 @@ int link_cell_init(t_moldyn *moldyn) {
 int link_cell_update(t_moldyn *moldyn) {
 
 	int count,i,j,k;
-	int nx,ny,nz;
+	int nx,ny;
 	t_atom *atom;
 	t_linkcell *lc;
+	double x,y,z;
 
 	atom=moldyn->atom;
 	lc=&(moldyn->lc);
 
 	nx=lc->nx;
 	ny=lc->ny;
-	nz=lc->nz;
+
+	x=moldyn->dim.x/2;
+	y=moldyn->dim.y/2;
+	z=moldyn->dim.z/2;
 
 	for(i=0;i<lc->cells;i++)
-		list_destroy_f(&(moldyn->lc.subcell[i]));
+		list_destroy_f(&(lc->subcell[i]));
 	
 	for(count=0;count<moldyn->count;count++) {
-		i=(atom[count].r.x+(moldyn->dim.x/2))/lc->x;
-		j=(atom[count].r.y+(moldyn->dim.y/2))/lc->y;
-		k=(atom[count].r.z+(moldyn->dim.z/2))/lc->z;
+		i=((atom[count].r.x+(moldyn->dim.x/2))/lc->x);
+		j=((atom[count].r.y+(moldyn->dim.y/2))/lc->y);
+		k=((atom[count].r.z+(moldyn->dim.z/2))/lc->z);
 		list_add_immediate_f(&(moldyn->lc.subcell[i+j*nx+k*nx*ny]),
 		                     &(atom[count]));
 	}
@@ -674,23 +779,23 @@ 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;
 
 	return 0;
 }
@@ -713,16 +818,16 @@ 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;
 
-	schedule=&(moldyn->schedule);
+	sched=&(moldyn->schedule);
 	atom=moldyn->atom;
 
 	/* initialize linked cell method */
@@ -759,12 +864,12 @@ int moldyn_integrate(t_moldyn *moldyn) {
 	moldyn->debug=0;
 
 	/* 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 */
 
@@ -777,11 +882,7 @@ int moldyn_integrate(t_moldyn *moldyn) {
 		if(moldyn->pt_scale&(T_SCALE_BERENDSEN|T_SCALE_DIRECT))
 			scale_velocity(moldyn,FALSE);
 		if(moldyn->pt_scale&(P_SCALE_BERENDSEN|P_SCALE_DIRECT))
-{
-printf("going to do p scale ...\n");
 			scale_volume(moldyn);
-printf("done\n");
-}
 
 		/* check for log & visualization */
 		if(e) {
@@ -818,7 +919,7 @@ printf("done\n");
 				visual_atoms(&(moldyn->vis),moldyn->time,
 				             moldyn->atom,moldyn->count);
 				printf("\rsched: %d, steps: %d, debug: %d",
-				       sched,i,moldyn->debug);
+				       sched->count,i,moldyn->debug);
 				fflush(stdout);
 			}
 		}
@@ -829,8 +930,8 @@ printf("done\n");
 	}
 
 		/* 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");
@@ -860,16 +961,13 @@ int velocity_verlet(t_moldyn *moldyn) {
 		v3_add(&(atom[i].r),&(atom[i].r),&delta);
 		v3_scale(&delta,&(atom[i].f),0.5*tau_square/atom[i].mass);
 		v3_add(&(atom[i].r),&(atom[i].r),&delta);
-//if(i==5) printf("v: %f %f %f\n",atom[i].r.x,(atom[i].r.x+moldyn->dim.x/2)/moldyn->lc.x,2*atom[i].r.x/moldyn->dim.x);
 		check_per_bound(moldyn,&(atom[i].r));
-//if(i==5) printf("n: %f %f %f\n",atom[i].r.x,(atom[i].r.x+moldyn->dim.x/2)/moldyn->lc.x,2*atom[i].r.x/moldyn->dim.x);
 
 		/* velocities */
 		v3_scale(&delta,&(atom[i].f),0.5*tau/atom[i].mass);
 		v3_add(&(atom[i].v),&(atom[i].v),&delta);
 	}
 
-//moldyn_bc_check(moldyn);
 	/* neighbour list update */
 	link_cell_update(moldyn);
 
@@ -898,6 +996,7 @@ 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];
@@ -919,7 +1018,16 @@ int potential_force_calc(t_moldyn *moldyn) {
 		v3_zero(&(itom[i].f));
 
 		/* reset viral of atom i */
-		v3_zero(&(itom[i].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;
 
 		/* single particle potential/force */
 		if(itom[i].attr&ATOM_ATTR_1BP)
@@ -1019,6 +1127,9 @@ int potential_force_calc(t_moldyn *moldyn) {
 		}
 
 	}
+#ifdef DEBUG
+printf("\n\n");
+#endif
 
 	return 0;
 }
@@ -1027,7 +1138,7 @@ int potential_force_calc(t_moldyn *moldyn) {
  * periodic boundayr checking
  */
 
-int check_per_bound(t_moldyn *moldyn,t_3dvec *a) {
+inline int check_per_bound(t_moldyn *moldyn,t_3dvec *a) {
 	
 	double x,y,z;
 	t_3dvec *dim;
@@ -1132,7 +1243,10 @@ 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]);
@@ -1160,11 +1274,11 @@ 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);
 
@@ -1173,15 +1287,15 @@ 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;
@@ -1193,16 +1307,16 @@ 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 */
@@ -1225,27 +1339,20 @@ 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;
@@ -1254,17 +1361,30 @@ 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->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;
@@ -1272,8 +1392,8 @@ 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;
 	}
 
@@ -1297,7 +1417,6 @@ 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);
@@ -1309,6 +1428,23 @@ 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
+
 	/* energy 2bp contribution (ij, ji) is 0.5 f_r f_c ... */
 	moldyn->energy+=(0.5*f_r*f_c);
 
@@ -1400,6 +1536,23 @@ 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
+
 	/* add energy of 3bp sum */
 	moldyn->energy+=(0.5*f_c*b*f_a);
 
@@ -1428,6 +1581,23 @@ 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??) */
+	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
+
 	return 0;
 }
 
@@ -1453,7 +1623,7 @@ 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);
@@ -1505,10 +1675,10 @@ int tersoff_mult_3bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,t_atom *ak,u8 bc) {
 	d_ik=v3_norm(&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];
 	}
 	else {
 		R=params->Rmixed;
@@ -1569,7 +1739,6 @@ 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 */
@@ -1591,12 +1760,12 @@ int tersoff_mult_3bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,t_atom *ak,u8 bc) {
 	d_jk=v3_norm(&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];
+		B=params->B[brand];
+		mu=params->mu[brand];
 		chi=1.0;
 	}
 	else {
@@ -1689,6 +1858,23 @@ 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
+
 	}
 
 	return 0;
@@ -1704,13 +1890,13 @@ 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) {
@@ -1746,91 +1932,3 @@ x=dim->x/2;
 
 	return 0;
 }
-
-/*
- * lattice creation functions
- */
-
-/* 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;
-	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);
-
-	/* 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);
-	}
-
-	v3_zero(&r);
-	count=0;
-	
-	/* fill up the room */
-	r.x=o.x;
-	while(r.x<x) {
-		r.y=o.y;
-		while(r.y<y) {
-			r.z=o.z;
-			while(r.z<z) {
-				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;	
-			}
-			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);
-		
-	return count;
-}
-
-int diamond_init(int a,int b,int c,double lc,t_atom *atom,t_3dvec *origin) {
-
-	int count;
-	t_3dvec o;
-
-	count=fcc_init(a,b,c,lc,atom,origin);
-
-	o.x=0.25*lc;
-	o.y=0.25*lc;
-	o.z=0.25*lc;
-
-	if(origin) v3_add(&o,&o,origin);
-
-	count+=fcc_init(a,b,c,lc,&atom[count],&o);
-
-	return count;
-}