X-Git-Url: https://www.hackdaworld.org/gitweb/?a=blobdiff_plain;f=moldyn.c;h=db9185911137ca3862f77fb5135fa83c9ec029d4;hb=150c5f804a5088a01ef2bb1e934b5e65d10ac23e;hp=73becdeed1a9b27220a714d55eed845d2ec71db2;hpb=72df64eacc634e315f2205fc7bd2406223f92bf3;p=physik%2Fposic.git

diff --git a/moldyn.c b/moldyn.c
index 73becde..db91859 100644
--- a/moldyn.c
+++ b/moldyn.c
@@ -17,20 +17,8 @@
 
 #include "moldyn.h"
 
-#include "math/math.h"
-#include "init/init.h"
-#include "random/random.h"
-#include "visual/visual.h"
-#include "list/list.h"
-
-
 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);
@@ -78,6 +66,13 @@ int set_temperature(t_moldyn *moldyn,double t_ref) {
 	return 0;
 }
 
+int set_pressure(t_moldyn *moldyn,double p_ref) {
+
+	moldyn->p_ref=p_ref;
+
+	return 0;
+}
+
 int set_pt_scale(t_moldyn *moldyn,u8 ptype,double ptc,u8 ttype,double ttc) {
 
 	moldyn->pt_scale=(ptype|ttype);
@@ -93,16 +88,19 @@ int set_dim(t_moldyn *moldyn,double x,double y,double z,u8 visualize) {
 	moldyn->dim.y=y;
 	moldyn->dim.z=z;
 
+	moldyn->volume=x*y*z;
+
 	if(visualize) {
 		moldyn->vis.dim.x=x;
 		moldyn->vis.dim.y=y;
 		moldyn->vis.dim.z=z;
 	}
 
-	printf("[moldyn] dimensions in A:\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);
+	printf("  volume: %f\n",moldyn->volume);
 	printf("  visualize simulation box: %s\n",visualize?"on":"off");
 
 	return 0;
@@ -227,34 +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);
@@ -262,30 +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;
@@ -293,9 +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;
@@ -303,12 +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;
 }
@@ -390,7 +482,7 @@ int scale_velocity(t_moldyn *moldyn,u8 equi_init) {
 			count+=1;
 		}
 	}
-	if(count!=0) moldyn->t=(2.0*e)/(3.0*count*K_BOLTZMANN);
+	if(count!=0) moldyn->t=e/(1.5*count*K_BOLTZMANN);
 	else return 0;	/* no atoms involved in scaling! */
 	
 	/* (temporary) hack for e,t = 0 */
@@ -423,6 +515,69 @@ int scale_velocity(t_moldyn *moldyn,u8 equi_init) {
 	return 0;
 }
 
+int scale_volume(t_moldyn *moldyn) {
+
+	t_atom *atom;
+	t_3dvec *dim,*vdim;
+	double scale,v;
+	t_virial virial;
+	t_linkcell *lc;
+	int i;
+
+	atom=moldyn->atom;
+	dim=&(moldyn->dim);
+	vdim=&(moldyn->vis.dim);
+	lc=&(moldyn->lc);
+
+	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;
+	}
+
+	/* just a guess so far ... */
+	v=sqrt(virial.xx*virial.xx+virial.yy*virial.yy+virial.zz+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\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)) {
+		link_cell_shutdown(moldyn);
+		link_cell_init(moldyn);
+	}
+
+	return 0;
+
+}
+
 double get_e_kin(t_moldyn *moldyn) {
 
 	int i;
@@ -490,9 +645,6 @@ int link_cell_init(t_moldyn *moldyn) {
 
 	t_linkcell *lc;
 	int i;
-	int fd;
-
-	fd=open("/dev/null",O_WRONLY);
 
 	lc=&(moldyn->lc);
 
@@ -510,8 +662,7 @@ int link_cell_init(t_moldyn *moldyn) {
 	printf("[moldyn] initializing linked cells (%d)\n",lc->cells);
 
 	for(i=0;i<lc->cells;i++)
-		//list_init(&(lc->subcell[i]),1);
-		list_init(&(lc->subcell[i]),fd);
+		list_init_f(&(lc->subcell[i]));
 
  	link_cell_update(moldyn);
 	
@@ -521,26 +672,30 @@ 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(&(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;
-		list_add_immediate_ptr(&(moldyn->lc.subcell[i+j*nx+k*nx*ny]),
-		                       &(atom[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);
+		list_add_immediate_f(&(moldyn->lc.subcell[i+j*nx+k*nx*ny]),
+		                     &(atom[count]));
 	}
 
 	return 0;
@@ -610,7 +765,9 @@ int link_cell_shutdown(t_moldyn *moldyn) {
 	lc=&(moldyn->lc);
 
 	for(i=0;i<lc->nx*lc->ny*lc->nz;i++)
-		list_shutdown(&(moldyn->lc.subcell[i]));
+		list_destroy_f(&(moldyn->lc.subcell[i]));
+
+	free(lc->subcell);
 
 	return 0;
 }
@@ -622,23 +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;
 }
@@ -661,16 +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 */
@@ -707,12 +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 */
 
@@ -724,6 +881,8 @@ int moldyn_integrate(t_moldyn *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);
 
 		/* check for log & visualization */
 		if(e) {
@@ -760,7 +919,7 @@ int moldyn_integrate(t_moldyn *moldyn) {
 				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);
 			}
 		}
@@ -771,8 +930,8 @@ 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");
@@ -802,16 +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);
 
@@ -840,6 +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];
@@ -853,13 +1010,25 @@ int potential_force_calc(t_moldyn *moldyn) {
 
 	/* reset energy */
 	moldyn->energy=0.0;
-
+	
 	/* get energy and force of every atom */
 	for(i=0;i<count;i++) {
 
 		/* reset force */
 		v3_zero(&(itom[i].f));
 
+		/* reset viral of atom i */
+		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)
 			moldyn->func1b(moldyn,&(itom[i]));
@@ -880,7 +1049,7 @@ int potential_force_calc(t_moldyn *moldyn) {
 		for(j=0;j<27;j++) {
 
 			this=&(neighbour_i[j]);
-			list_reset(this);
+			list_reset_f(this);
 
 			if(this->start==NULL)
 				continue;
@@ -915,7 +1084,7 @@ int potential_force_calc(t_moldyn *moldyn) {
 				for(k=0;k<27;k++) {
 
 					that=&(neighbour_i2[k]);
-					list_reset(that);
+					list_reset_f(that);
 					
 					if(that->start==NULL)
 						continue;
@@ -941,7 +1110,7 @@ int potential_force_calc(t_moldyn *moldyn) {
 						               ktom,
 						               bc_ik|bc_ij);
 
-					} while(list_next(that)!=\
+					} while(list_next_f(that)!=\
 					        L_NO_NEXT_ELEMENT);
 
 				}
@@ -953,11 +1122,14 @@ int potential_force_calc(t_moldyn *moldyn) {
 					                    jtom,bc_ij);
 				}
 					
-			} while(list_next(this)!=L_NO_NEXT_ELEMENT);
+			} while(list_next_f(this)!=L_NO_NEXT_ELEMENT);
 		
 		}
 
 	}
+#ifdef DEBUG
+printf("\n\n");
+#endif
 
 	return 0;
 }
@@ -966,7 +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;
@@ -1071,7 +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]);
@@ -1099,11 +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);
 
@@ -1112,15 +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;
@@ -1132,16 +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 */
@@ -1164,27 +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;
@@ -1193,17 +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;
@@ -1211,8 +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;
 	}
 
@@ -1236,7 +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);
@@ -1247,6 +1427,14 @@ int tersoff_mult_2bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc) {
 	/* add forces of 2bp (ij, ji) contribution
 	 * dVij = dVji and we sum up both: no 1/2) */
 	v3_add(&(ai->f),&(ai->f),&force);
+#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);
@@ -1338,6 +1526,14 @@ 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);
+#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);
@@ -1366,6 +1562,14 @@ 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);
+#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;
 }
@@ -1392,7 +1596,7 @@ 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);
@@ -1444,10 +1648,10 @@ 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;
@@ -1508,7 +1712,6 @@ 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 */
@@ -1530,12 +1733,12 @@ 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 {
@@ -1627,6 +1830,15 @@ int tersoff_mult_3bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,t_atom *ak,u8 bc) {
 		v3_scale(&temp2,&temp2,tmp*B*exp(-mu*d_jk)*f_c_jk*0.5);
 		v3_add(&(ai->f),&(ai->f),&temp2); /* -1 skipped in f_a calc ^ */
 		                                  /* scaled with 0.5 ^ */
+#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;
@@ -1642,19 +1854,20 @@ 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) {
 			printf("FATAL: atom %d: x: %.20f (%.20f)\n",
 			       i,atom[i].r.x,dim->x/2);
 			printf("diagnostic:\n");
+			printf("-----------\natom.r.x:\n");
 			for(j=0;j<8;j++) {
 				memcpy(&byte,(u8 *)(&(atom[i].r.x))+j,1);
 				for(k=0;k<8;k++)
@@ -1662,7 +1875,7 @@ x=dim->x/2;
 					((byte)&(1<<k))?1:0,
 					(k==7)?'\n':'|');
 			}
-			printf("---------------\n");
+			printf("---------------\nx=dim.x/2:\n");
 			for(j=0;j<8;j++) {
 				memcpy(&byte,(u8 *)(&x)+j,1);
 				for(k=0;k<8;k++)
@@ -1670,8 +1883,8 @@ x=dim->x/2;
 					((byte)&(1<<k))?1:0,
 					(k==7)?'\n':'|');
 			}
-			if(atom[i].r.x==x) printf("hier gleich!\n");
-			else printf("hier NICHT gleich!\n");
+			if(atom[i].r.x==x) printf("the same!\n");
+			else printf("different!\n");
 		}
 		if(atom[i].r.y>=dim->y/2||-atom[i].r.y>dim->y/2)
 			printf("FATAL: atom %d: y: %.20f (%.20f)\n",
@@ -1683,4 +1896,3 @@ x=dim->x/2;
 
 	return 0;
 }
-