X-Git-Url: https://hackdaworld.org/gitweb/?a=blobdiff_plain;f=moldyn.c;h=fe54330f002f414d345295ff73dd4d1e6b6b557d;hb=1097ea2efb575855edd332c28a9cd8f807cd0716;hp=dc2dd8e5a5e89226a9e68bd22ccf22bd2ff25635;hpb=593bb07bf38d6d32e9eca61d9637d9e5b7f428d0;p=physik%2Fposic.git

diff --git a/moldyn.c b/moldyn.c
index dc2dd8e..fe54330 100644
--- a/moldyn.c
+++ b/moldyn.c
@@ -56,9 +56,6 @@ int moldyn_usage(char **argv) {
 int moldyn_parse_argv(t_moldyn *moldyn,int argc,char **argv) {
 
 	int i;
-	t_ho_params hop;
-	t_lj_params ljp;
-	double s,e;
 
 	memset(moldyn,0,sizeof(t_moldyn));
 
@@ -67,7 +64,6 @@ int moldyn_parse_argv(t_moldyn *moldyn,int argc,char **argv) {
 	moldyn->tau=MOLDYN_TAU;
 	moldyn->time_steps=MOLDYN_RUNS;
 	moldyn->integrate=velocity_verlet;
-	moldyn->potential_force_function=lennard_jones;
 
 	/* parse argv */
 	for(i=1;i<argc;i++) {
@@ -81,10 +77,6 @@ int moldyn_parse_argv(t_moldyn *moldyn,int argc,char **argv) {
 					moldyn->mwrite=atoi(argv[++i]);
 					strncpy(moldyn->mfb,argv[++i],64);
 					break;
-				case 'D':
-					moldyn->dwrite=atoi(argv[++i]);
-					strncpy(moldyn->dfb,argv[++i],64);
-					break;
 				case 'S':
 					moldyn->swrite=atoi(argv[++i]);
 					strncpy(moldyn->sfb,argv[++i],64);
@@ -187,16 +179,6 @@ int moldyn_log_init(t_moldyn *moldyn) {
 	if(moldyn->swrite)
 		moldyn->lvstat|=MOLDYN_LVSTAT_SAVE;
 
-	if(moldyn->dwrite) {
-		moldyn->dfd=open(moldyn->dfb,O_WRONLY|O_CREAT|O_TRUNC);
-                if(moldyn->dfd<0) {
-			perror("[moldyn] dfd open");
-			return moldyn->dfd;
-		}
-		write(moldyn->dfd,moldyn,sizeof(t_moldyn));
-		moldyn->lvstat|=MOLDYN_LVSTAT_DUMP;
-	}
-
 	if((moldyn->vwrite)&&(vis)) {
 		moldyn->visual=vis;
 		visual_init(vis,moldyn->vfb);
@@ -245,20 +227,22 @@ int moldyn_shutdown(t_moldyn *moldyn) {
 	return 0;
 }
 
-int create_lattice(unsigned char type,int element,double mass,double lc,
-                   int a,int b,int c,t_atom **atom) {
+int create_lattice(t_moldyn *moldyn,u8 type,double lc,int element,double mass,
+                   u8 attr,u8 bnum,int a,int b,int c) {
 
 	int count;
 	int ret;
 	t_3dvec origin;
+	t_atom *atom;
 
 	count=a*b*c;
+	atom=moldyn->atom;
 
 	if(type==FCC) count*=4;
 	if(type==DIAMOND) count*=8;
 
-	*atom=malloc(count*sizeof(t_atom));
-	if(*atom==NULL) {
+	atom=malloc(count*sizeof(t_atom));
+	if(atom==NULL) {
 		perror("malloc (atoms)");
 		return -1;
 	}
@@ -267,10 +251,10 @@ int create_lattice(unsigned char type,int element,double mass,double lc,
 
 	switch(type) {
 		case FCC:
-			ret=fcc_init(a,b,c,lc,*atom,&origin);
+			ret=fcc_init(a,b,c,lc,atom,&origin);
 			break;
 		case DIAMOND:
-			ret=diamond_init(a,b,c,lc,*atom,&origin);
+			ret=diamond_init(a,b,c,lc,atom,&origin);
 			break;
 		default:
 			printf("unknown lattice type (%02x)\n",type);
@@ -286,17 +270,45 @@ int create_lattice(unsigned char type,int element,double mass,double lc,
 	}
 
 	while(count) {
-		(*atom)[count-1].element=element;
-		(*atom)[count-1].mass=mass;
+		atom[count-1].element=element;
+		atom[count-1].mass=mass;
+		atom[count-1].attr=attr;
+		atom[count-1].bnum=bnum;
 		count-=1;
 	}
 
 	return ret;
 }
 
-int destroy_lattice(t_atom *atom) {
+int add_atom(t_moldyn *moldyn,int element,double mass,u8 bnum,u8 attr,
+             t_3dvec r,t_3dvec v) {
 
-	if(atom) free(atom);
+	t_atom *atom;
+	void *ptr;
+	int count;
+	
+	atom=moldyn->atom;
+	count=++(moldyn->count);
+
+	ptr=realloc(atom,count*sizeof(t_atom));
+	if(!ptr) {
+		perror("[moldyn] realloc (add atom)");
+		return -1;
+	}
+	
+	atom=ptr;
+	atom->r=r;
+	atom->v=v;
+	atom->element=element;
+	atom->bnum=bnum;
+	atom->attr=attr;
+
+	return 0;
+}
+
+int destroy_atoms(t_moldyn *moldyn) {
+
+	if(moldyn->atom) free(moldyn->atom);
 
 	return 0;
 }
@@ -481,7 +493,7 @@ int link_cell_update(t_moldyn *moldyn) {
 	for(i=0;i<lc->cells;i++)
 		list_destroy(&(moldyn->lc.subcell[i]));
 	
-	for(count=0;count<moldyn->count;count++) {
+	for(count=0;count<moedyn->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;
@@ -500,7 +512,7 @@ int link_cell_neighbour_index(t_moldyn *moldyn,int i,int j,int k,t_list *cell) {
 	int ci,cj,ck;
 	int nx,ny,nz;
 	int x,y,z;
-	unsigned char bx,by,bz;
+	u8 bx,by,bz;
 
 	lc=&(moldyn->lc);
 	nx=lc->nx;
@@ -544,6 +556,9 @@ int link_cell_neighbour_index(t_moldyn *moldyn,int i,int j,int k,t_list *cell) {
 		}
 	}
 
+	lc->dnlc=count2;
+	lc->countn=27;
+
 	return count2;
 }
 
@@ -562,6 +577,40 @@ int link_cell_shutdown(t_moldyn *moldyn) {
 	return 0;
 }
 
+int moldyn_add_schedule(t_moldyn *moldyn,int runs,double tau ) {
+
+	int count;
+	void *ptr;
+	t_moldyn_schedule *schedule;
+
+	schedule=moldyn->schedule;
+	count=++(schedule->content_count);
+
+	ptr=realloc(moldyn->schedule.runs,count*sizeof(int));
+	if(!ptr) {
+		perror("[moldyn] realloc (runs)");
+		return -1;
+	}
+	moldyn->schedule.runs[count-1]=runs;
+
+	ptr=realloc(schedule->tau,count*sizeof(double));
+	if(!ptr) {
+		perror("[moldyn] realloc (tau)");
+		return -1;
+	}
+	moldyn->schedule.tau[count-1]=tau;
+
+	return 0;
+}
+
+int moldyn_set_schedule_hook(t_moldyn *moldyn,void *hook,void *hook_params) {
+
+	moldyn->schedule.hook=hook;
+	moldyn->schedule.hook_params=hook_params;
+	
+	return 0;
+}
+
 /*
  *
  * 'integration of newtons equation' - algorithms
@@ -572,7 +621,7 @@ int link_cell_shutdown(t_moldyn *moldyn) {
 
 int moldyn_integrate(t_moldyn *moldyn) {
 
-	int i;
+	int i,sched;
 	unsigned int e,m,s,d,v;
 	t_3dvec p;
 
@@ -601,6 +650,15 @@ int moldyn_integrate(t_moldyn *moldyn) {
 	/* calculate initial forces */
 	moldyn->potential_force_function(moldyn);
 
+	for(sched=0;sched<moldyn->schedule.content_count;sched++) {
+
+		/* setting amont of runs and finite time step size */
+		moldyn->tau=schedule->tau[sched];
+		moldyn->tau_square=moldyn->tau*moldyn->tau;
+		moldyn->timesteps=schedule->runs[sched];
+
+	/* integration according to schedule */
+
 	for(i=0;i<moldyn->time_steps;i++) {
 
 		/* integration step */
@@ -632,14 +690,9 @@ int moldyn_integrate(t_moldyn *moldyn) {
 					write(fd,moldyn->atom,
 					      moldyn->count*sizeof(t_atom));
 				}
+				close(fd);
 			}	
 		}
-		if(d) {
-			if(!(i%d))
-				write(moldyn->dfd,moldyn->atom,
-				      moldyn->count*sizeof(t_atom));
-
-		}
 		if(v) {
 			if(!(i%v)) {
 				visual_atoms(moldyn->visual,i*moldyn->tau,
@@ -650,6 +703,10 @@ int moldyn_integrate(t_moldyn *moldyn) {
 		}
 	}
 
+		/* check for hooks */
+		if(schedule->hook)
+			schedule->hook(moldyn,schedule->hook_params);
+
 	return 0;
 }
 
@@ -687,7 +744,8 @@ printf("done\n");
 
 	/* forces depending on chosen potential */
 printf("calc potential/force ...\n");
-	moldyn->potential_force_function(moldyn);
+	potential_force_calc(moldyn);
+	//moldyn->potential_force_function(moldyn);
 printf("done\n");
 
 	for(i=0;i<count;i++) {
@@ -706,543 +764,491 @@ printf("done\n");
  * 
  */
 
-/* harmonic oscillator potential and force */
+/* generic potential and force calculation */
 
-int harmonic_oscillator(t_moldyn *moldyn) {
+int potential_force_calc(t_moldyn *moldyn) {
 
-	t_ho_params *params;
-	t_atom *atom,*btom;
+	int i,count;
+	t_atom *atom;
 	t_linkcell *lc;
-	t_list *this,neighbour[27];
-	int i,j,c;
-	int count;
-	t_3dvec force,distance;
-	double d,u;
-	double sc,equi_dist;
-	int ni,nj,nk;
+	t_list neighbour[27];
+	t_list *this;
+	double u;
+	u8 bc,bc3;
+	int countn,dnlc;
 
-	params=moldyn->pot_params;
+	count=moldyn->count;
 	atom=moldyn->atom;
 	lc=&(moldyn->lc);
-	sc=params->spring_constant;
-	equi_dist=params->equilibrium_distance;
-	count=moldyn->count;
 
-	/* reset energy counter */
-	u=0.0;
+	/* reset energy */
+	moldyn->energy=0.0;
 
 	for(i=0;i<count;i++) {
+	
 		/* reset force */
 		v3_zero(&(atom[i].f));
 
-		/* determine cell + neighbours */
-		ni=(atom[i].r.x+(moldyn->dim.x/2))/lc->x;
-		nj=(atom[i].r.y+(moldyn->dim.y/2))/lc->y;
-		nk=(atom[i].r.z+(moldyn->dim.z/2))/lc->z;
-		c=link_cell_neighbour_index(moldyn,ni,nj,nk,neighbour);
-
-		/*
-		 * processing cell of atom i
-		 * => no need to check for empty list (1 element at minimum)
-		 */
-		this=&(neighbour[0]);
-		list_reset(this);
-		do {
-			btom=this->current->data;
-			if(btom==&(atom[i]))
-				continue;
-			v3_sub(&distance,&(atom[i].r),&(btom->r));
-			d=v3_norm(&distance);
-			if(d<=moldyn->cutoff) {
-				u+=(0.5*sc*(d-equi_dist)*(d-equi_dist));
-				v3_scale(&force,&distance,
-				         -sc*(1.0-(equi_dist/d)));
-				v3_add(&(atom[i].f),&(atom[i].f),&force);
-			}
-		} while(list_next(this)!=L_NO_NEXT_ELEMENT);
-
-		/*
-		 * direct neighbour cells
-		 * => no boundary condition check necessary
-		 */
-		for(j=1;j<c;j++) {
-			this=&(neighbour[j]);
-			list_reset(this); /* there might not be a single atom */
-			if(this->start!=NULL) {
-
-			do {
-				btom=this->current->data;
-				v3_sub(&distance,&(atom[i].r),&(btom->r));
-				d=v3_norm(&distance);
-				if(d<=moldyn->cutoff) {
-					u+=(0.5*sc*(d-equi_dist)*(d-equi_dist));
-					v3_scale(&force,&distance,
-					         -sc*(1.0-(equi_dist/d)));
-					v3_add(&(atom[i].f),&(atom[i].f),
-					       &force);
-				}
-			} while(list_next(this)!=L_NO_NEXT_ELEMENT);
+		/* single particle potential/force */
+		if(atom[i].attr&ATOM_ATTR_1BP)
+			moldyn->pf_func1b(moldyn,&(atom[i]));
 
-			}
-		}
+		/* 2 body pair potential/force */
+		if(atom[i].attr&(ATOM_ATTR_2BP|ATOM_ATTR_3BP)) {
+		
+			link_cell_neighbour_index(moldyn,
+				(atom[i].r.x+moldyn->dim.x/2)/lc->x,
+				(atom[i].r.y+moldyn->dim.y/2)/lc->y,
+				(atom[i].r.z+moldyn->dim.z/2)/lc->z,
+				neighbour);
 
-		/*
-		 * indirect neighbour cells
-		 * => check boundary conditions
-		 */
-		for(j=c;j<27;j++) {
-			this=&(neighbour[j]);
-			list_reset(this); /* check boundary conditions */
-			if(this->start!=NULL) {
-
-			do {
-				btom=this->current->data;
-				v3_sub(&distance,&(atom[i].r),&(btom->r));
-				v3_per_bound(&distance,&(moldyn->dim));
-				d=v3_norm(&distance);
-				if(d<=moldyn->cutoff) {
-					u+=(0.5*sc*(d-equi_dist)*(d-equi_dist));
-					v3_scale(&force,&distance,
-					         -sc*(1.0-(equi_dist/d)));
-					v3_add(&(atom[i].f),&(atom[i].f),
-					       &force);
-				}
-			} while(list_next(this)!=L_NO_NEXT_ELEMENT);
+			countn=lc->countn;
+			dnlc=lc->dnlc;
 
-			}
-		}
-	}
+			for(j=0;j<countn;j++) {
 
-	moldyn->energy=0.5*u;
+				this=&(neighbour[j]);
+				list_reset(this);
 
-	return 0;
-}
+				if(this->start==NULL)
+					continue;
 
-/* lennard jones potential & force for one sort of atoms */
- 
-int lennard_jones(t_moldyn *moldyn) {
+				bc=(j<dnlc)?0:1;
 
-	t_lj_params *params;
-	t_atom *atom,*btom;
-	t_linkcell *lc;
-	t_list *this,neighbour[27];
-	int i,j,c;
-	int count;
-	t_3dvec force,distance;
-	double d,h1,h2,u;
-	double eps,sig6,sig12;
-	int ni,nj,nk;
+				do {
+					btom=this->current->data;
 
-	params=moldyn->pot_params;
-	atom=moldyn->atom;
-	lc=&(moldyn->lc);
-	count=moldyn->count;
-	eps=params->epsilon4;
-	sig6=params->sigma6;
-	sig12=params->sigma12;
+					if(btom==&(atom[i]))
+						continue;
 
-	/* reset energy counter */
-	u=0.0;
+					if((btom->attr&ATOM_ATTR_2BP)&
+					   (atom[i].attr&ATOM_ATTR_2BP))
+						moldyn->pf_func2b(moldyn,
+						                  &(atom[i]),
+						                  btom,
+						                  bc);
 
-	for(i=0;i<count;i++) {
-		/* reset force */
-		v3_zero(&(atom[i].f));
+					/* 3 body potential/force */
 
-		/* determine cell + neighbours */
-		ni=(atom[i].r.x+(moldyn->dim.x/2))/lc->x;
-		nj=(atom[i].r.y+(moldyn->dim.y/2))/lc->y;
-		nk=(atom[i].r.z+(moldyn->dim.z/2))/lc->z;
-		c=link_cell_neighbour_index(moldyn,ni,nj,nk,neighbour);
-
-		/* processing cell of atom i */
-		this=&(neighbour[0]);
-		list_reset(this); /* list has 1 element at minimum */
-		do {
-			btom=this->current->data;
-			if(btom==&(atom[i]))
-				continue;
-			v3_sub(&distance,&(atom[i].r),&(btom->r));
-			d=v3_absolute_square(&distance);	/* 1/r^2 */
-			if(d<=moldyn->cutoff_square) {
-				d=1.0/d;	/* 1/r^2 */
-				h2=d*d; 	/* 1/r^4 */
-				h2*=d;	 	/* 1/r^6 */
-				h1=h2*h2; 	/* 1/r^12 */
-				u+=eps*(sig12*h1-sig6*h2);
-				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,d);
-				v3_add(&(atom[i].f),&(atom[i].f),&force);
-			}
-		} while(list_next(this)!=L_NO_NEXT_ELEMENT);
-
-		/* neighbours not doing boundary condition overflow */
-		for(j=1;j<c;j++) {
-			this=&(neighbour[j]);
-			list_reset(this); /* there might not be a single atom */
-			if(this->start!=NULL) {
-
-			do {
-				btom=this->current->data;
-				v3_sub(&distance,&(atom[i].r),&(btom->r));
-				d=v3_absolute_square(&distance); /* r^2 */
-				if(d<=moldyn->cutoff_square) {
-					d=1.0/d;	/* 1/r^2 */
-					h2=d*d; 	/* 1/r^4 */
-					h2*=d;	 	/* 1/r^6 */
-					h1=h2*h2; 	/* 1/r^12 */
-					u+=eps*(sig12*h1-sig6*h2);
-					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,d);
-					v3_add(&(atom[i].f),&(atom[i].f),
-					       &force);
-				}
-			} while(list_next(this)!=L_NO_NEXT_ELEMENT);
-				
-			}
-		}
+					if(!(atom[i].attr&ATOM_ATTR_3BP)||
+					   !(btom->attr&ATOM_ATTR_3BP))
+						continue;
 
-		/* neighbours due to boundary conditions */
-		for(j=c;j<27;j++) {
-			this=&(neighbour[j]);
-			list_reset(this); /* check boundary conditions */
-			if(this->start!=NULL) {
-
-			do {
-				btom=this->current->data;
-				v3_sub(&distance,&(atom[i].r),&(btom->r));
-				v3_per_bound(&distance,&(moldyn->dim));
-				d=v3_absolute_square(&distance); /* r^2 */
-				if(d<=moldyn->cutoff_square) {
-					d=1.0/d;	/* 1/r^2 */
-					h2=d*d; 	/* 1/r^4 */
-					h2*=d; 		/* 1/r^6 */
-					h1=h2*h2; 	/* 1/r^12 */
-					u+=eps*(sig12*h1-sig6*h2);
-					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,d);
-					v3_add(&(atom[i].f),&(atom[i].f),
-					       &force);
-				}
-			} while(list_next(this)!=L_NO_NEXT_ELEMENT);
+					link_cell_neighbour_index(moldyn,
+					   (btom->r.x+moldyn->dim.x/2)/lc->x,
+					   (btom->r.y+moldyn->dim.y/2)/lc->y,
+					   (btom->r.z+moldyn->dim.z/2)/lc->z,
+					   neighbourk);
 
-			}
-		}
-	}
+					for(k=0;k<lc->countn;k++) {
 
-	moldyn->energy=0.5*u;
-	
-	return 0;
-}
+						thisk=&(neighbourk[k]);
+						list_reset(thisk);
+					
+						if(thisk->start==NULL)
+							continue;
 
-/* tersoff potential & force for 2 sorts of atoms */
+						bck=(k<lc->dnlc)?0:1;
 
-int tersoff(t_moldyn *moldyn) {
+						do {
 
-	t_tersoff_params *params;
-	t_atom *atom,*btom,*ktom;
-	t_linkcell *lc;
-	t_list *this,*thisk,neighbour[27],neighbourk[27];
-	int i,j,k,c,ck;
-	int count;
-	double u;
-	int ni,nj,nk;
-	int ki,kj,kk;
-	
+			ktom=thisk->current->data;
 
-	params=moldyn->pot_params;
-	atom=moldyn->atom;
-	lc=&(moldyn->lc);
-	count=moldyn->count;
-	
-	/* reset energy counter */
-	u=0.0;
+			if(!(ktom->attr&ATOM_ATTR_3BP))
+				continue;
 
-	for(i=0;i<count;i++) {
-		/* reset force */
-		v3_zero(&(atom[i].f));
+			if(ktom==btom)
+				continue;
 
-		/* determin cell neighbours */
-		ni=(atom[i].r.x+(moldyn->dim.x/2))/lc->x;
-		nj=(atom[i].r.y+(moldyn->dim.y/2))/lc->y;
-		nk=(atom[i].r.z+(moldyn->dim.z/2))/lc->z;
-		c=link_cell_neighbour_index(moldyn,ni,nj,nk,neighbour);
-
-		/*
-		 * processing cell of atom i
-		 * => no need to check for empty list (1 element at minimum)
-		 */
-		this=&(neighbour[0]);
-		list_reset(this);
-		do {
-			btom=this->current->data;
-			if(btom==&(atom[i]))
+			if(ktom==&(atom[i]))
 				continue;
 
-			/* 2 body stuff */
+			moldyn->pf_func3b(moldyn,&(atom[i]),btom,ktom,bck);
 
-			v3_sub(&dist_ij,btom,&(atom[i]));
-			d_ij=v3_norm(&dist_ij);
-			if(d_ij<=S) {
-				if(d_ij<=R) {
-					f_c=1.0;
-					df_c=0.0;
-				}
-				else {
-					s_r=S-R;
-					arg1=PI*(d_ij-R)/s_r;
-					f_c=0.5+0.5*cos(arg1);
-					df_c=-0.5*sin(arg1)*(PI/(s_r*d_ij));
-				}
+						} while(list_next(thisk)!=\
+						        L_NO_NEXT_ELEMENT);
+					
+				} while(list_next(this)!=L_NO_NEXT_ELEMENT);
 			}
-			else 
-				continue;		
-
-			
-			/* end 2 body stuff */ 
-
-			/* determine cell neighbours of btom */
-			ki=(btom->r.x+(moldyn->dim.x/2))/lc->x;
-			kj=(btom->r.y+(moldyn->dim.y/2))/lc->y;
-			kk=(btom->r.z+(moldyn->dim.z/2))/lc->z;
-			ck=link_cell_neighbour_index(moldyn,ki,kj,kk,
-			                             neighbourk);
-
-			/* cell of btom */
-			thisk=&(neighbourk[0]);
-			list_reset(thisk);
-			do {
-				ktom=thisk->current->data;
-				if(ktom==btom)
-					continue;
-				if(ktom==&(atom[i]))
-					continue;
-				
-				/* 3 body stuff (1) */
-				
-				theta_ijk=;
-				sin_theta=;
-				cos_theta=;
-				hi_cos=;
-				hi_cos_square=;
-
+		}
+	}
 
-				/* end 3 body stuff (1) */
+	return 0;
+}
 
+/*
+ * periodic boundayr checking
+ */
 
-			} while(list_next(thisk)!=L_NO_NEXT_ELEMENT);
+int check_per_bound(t_moldyn *moldyn,t_3dvec *a) {
+	
+	double x,y,z;
+
+	x=0.5*dim->x;
+	y=0.5*dim->y;
+	z=0.5*dim->z;
+
+	if(moldyn->MOLDYN_ATTR_PBX)
+		if(a->x>=x) a->x-=dim->x;
+		else if(-a->x>x) a->x+=dim->x;
+	if(moldyn->MOLDYN_ATTR_PBY)
+		if(a->y>=y) a->y-=dim->y;
+		else if(-a->y>y) a->y+=dim->y;
+	if(moldyn->MOLDYN_ATTR_PBZ)
+		if(a->z>=z) a->z-=dim->z;
+		else if(-a->z>z) a->z+=dim->z;
 
-			/* direct neighbours of btom cell */
-			for(k=1;k<ck;k++) {
-				thisk=&(neighbourk[k]);
-				list_reset(thisk);
-				if(thisk->start!=NULL) {
+	return 0;
+}
+        
 
-				do {
-					ktom=thisk->current->data;
-					if(ktom==&(atom[i]))
-						continue;
+/*
+ * example potentials
+ */
 
-				/* 3 body stuff (2) */
+/* harmonic oscillator potential and force */
 
-				} while(list_next(thisk)!=L_NO_NEXT_ELEMENT);
+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 sc,equi_dist;
 
-			/* indirect neighbours of btom cell */
-			for(k=ck;k<27;k++) {
-				thisk=&(neighbourk[k]);
-				list_reset(thisk);
-				if(thisk->start!=NULL) {
+	params=moldyn->pot2b_params;
+	sc=params->spring_constant;
+	equi_dist=params->equilibrium_distance;
 
-				do {
-					ktom=thisk->current->data;
-					if(ktom==&(atom[i]))
-						continue;
+	v3_sub(&distance,&(ai->r),&(aj->r);
+	
+	v3_per_bound(&distance,&(moldyn->dim));
+	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));
+		v3_scale(&force,&distance,-sc*(1.0-(equi_dist/d)));
+		v3_add(&(ai->f),&(ai->f),&force);
+	}
 
-				/* 3 body stuff */
+	return 0;
+}
 
-				} while(list_next(thisk)!=L_NO_NEXT_ELEMENT);
+/* lennard jones potential & force for one sort of atoms */
+ 
+int lennard_jones(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc) {
 
-				}
-			}
+	t_lj_params *params;
+	t_3dvec force,distance;
+	double d,h1,h2,u;
+	double eps,sig6,sig12;
 
+	params=moldyn->pot_params;
+	eps=params->epsilon4;
+	sig6=params->sigma6;
+	sig12=params->sigma12;
 
-		} while(list_next(this)!=L_NO_NEXT_ELEMENT);
+	v3_sub(&distance,&(ai->r),&(aj->r));
+	if(bc) check_per_bound(moldyn,&distance);
+	d=v3_absolute_square(&distance);	/* 1/r^2 */
+	if(d<=moldyn->cutoff_square) {
+		d=1.0/d;			/* 1/r^2 */
+		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);
+		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,d);
+		v3_add(&(ai->f),&(aj->f),&force);
+	}
 
-		/*
-		 * direct neighbour cells of atom i
-		 */
-		for(j=1;j<c;j++) {
-			this=&(neighbour[j]);
-			list_reset(this);
-			if(this->start!=NULL) {
+	return 0;
+}
 
-			do {
-				btom=this->current->data;
+/*
+ * tersoff potential & force for 2 sorts of atoms
+ */
 
-				/* 2 body stuff */
+/* tersoff 1 body part */
+int tersoff_mult_1bp(t_moldyn *moldyn,t_atom *ai) {
 
+	int num;
+	t_tersoff_mult_params *params;
+	t_tersoff_exchange *exchange;
+	
+	num=ai->bnum;
+	params=moldyn->pot1b_params;
+	exchange=&(params->exchange);
 
-			/* determine cell neighbours of btom */
-			ki=(btom->r.x+(moldyn->dim.x/2))/lc->x;
-			kj=(btom->r.y+(moldyn->dim.y/2))/lc->y;
-			kk=(btom->r.z+(moldyn->dim.z/2))/lc->z;
-			ck=link_cell_neighbour_index(moldyn,ki,kj,kk,
-			                             neighbourk);
+	/*
+	 * simple: point constant parameters only depending on atom i to
+	 *         their right values
+	 */
 
-			/* cell of btom */
-			thisk=&(neighbourk[0]);
-			list_reset(thisk);
-			do {
-				ktom=thisk->current->data;
-				if(ktom==btom)
-					continue;
-				if(ktom==&(atom[i]))
-					continue;
-				
-				/* 3 body stuff (1) */
+	exchange->beta=&(params->beta[num]);
+	exchange->n=&(params->n[num]);
+	exchange->c=&(params->c[num]);
+	exchange->d=&(params->d[num]);
+	exchange->h=&(params->h[num]);
 
-			} while(list_next(thisk)!=L_NO_NEXT_ELEMENT);
+	exchange->betan=pow(*(exchange->beta),*(exchange->n));
+	exchange->c2=params->c[num]*params->c[num];
+	exchange->d2=params->d[num]*params->d[num];
+	exchange->c2d2=exchange->c2/exchange->d2;
 
-			/* direct neighbours of btom cell */
-			for(k=1;k<ck;k++) {
-				thisk=&(neighbourk[k]);
-				list_reset(thisk);
-				if(thisk->start!=NULL) {
+	return 0;
+}
+	
+/* tersoff 2 body part */
+int tersoff_mult_2bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc) {
 
-				do {
-					ktom=thisk->current->data;
-					if(ktom==&(atom[i]))
-						continue;
+	t_tersoff_mult_params *params;
+	t_tersoff_exchange *exchange;
+	t_3dvec dist_ij;
+	double d_ij;
+	double A,B,R,S,lambda;
+	int num;
 
-				/* 3 body stuff (2) */
+	params=moldyn->pot_params;
+	num=ai->bnum;
+	exchange=&(params->exchange);
 
-				} while(list_next(thisk)!=L_NO_NEXT_ELEMENT);
+	exchange->run3bp=0;
+	
+	/*
+	 * we need: f_c, df_c, f_r, df_r
+	 *
+	 * therefore we need: R, S, A, lambda
+	 */
 
-				}
-			}
+	v3_sub(&dist_ij,&(ai->r),&(aj->r));
 
-			/* indirect neighbours of btom cell */
-			for(k=ck;k<27;k++) {
-				thisk=&(neighbourk[k]);
-				list_reset(thisk);
-				if(thisk->start!=NULL) {
+	if(bc) check_per_bound(moldyn,&dist_ij);
 
-				do {
-					ktom=thisk->current->data;
-					if(ktom==&(atom[i]))
-						continue;
+	/* save for use in 3bp */ /* REALLY ?!?!?! */
+	exchange->dist_ij=dist_ij;
 
-				/* 3 body stuff (3) */
+	/* constants */
+	if(num==aj->bnum) {
+		S=params->S[num];
+		R=params->R[num];
+		A=params->A[num];
+		lambda=params->lambda[num];
+		/* more constants depending of atoms i and j, needed in 3bp */
+		params->exchange.B=&(params->B[num]);
+		params->exchange.mu=params->mu[num];
+		params->exchange.chi=1.0;
+	}
+	else {
+		S=params->Smixed;
+		R=params->Rmixed;
+		A=params->Amixed;
+		lambda=params->lambda_m;
+		/* more constants depending of atoms i and j, needed in 3bp */
+		params->exchange.B=&(params->Bmixed);
+		params->exchange.mu=&(params->mu_m);
+		params->exchange.chi=params->chi;
+	}
 
-				} while(list_next(thisk)!=L_NO_NEXT_ELEMENT);
+	d_ij=v3_norm(&dist_ij);
 
-				}
-			}
+	/* save for use in 3bp */
+	exchange->d_ij=d_ij;
 
+	if(d_ij>S)
+		return 0;
 
-			} while(list_next(this)!=L_NO_NEXT_ELEMENT);
+	f_r=A*exp(-lamda*d_ij);
+	df_r=-lambda*f_r/d_ij;
 
-			}
-		}
+	/* f_a, df_a calc + save for 3bp use */
+	exchange->f_a=-B*exp(-mu*d_ij);
+	exchange->df_a=-mu*exchange->f_a/d_ij;
 
-		/*
-		 * indirect neighbour cells of atom i
-		 */
-		for(j=c;j<27;j++) {
-			this=&(neighbour[j]);
-			list_reset(this);
-			if(this->start!=NULL) {
-
-			do {
-				btom=this->current->data;
-
-				/* 2 body stuff */
-
-
-			/* determine cell neighbours of btom */
-			ki=(btom->r.x+(moldyn->dim.x/2))/lc->x;
-			kj=(btom->r.y+(moldyn->dim.y/2))/lc->y;
-			kk=(btom->r.z+(moldyn->dim.z/2))/lc->z;
-			ck=link_cell_neighbour_index(moldyn,ki,kj,kk,
-			                             neighbourk);
-
-			/* cell of btom */
-			thisk=&(neighbourk[0]);
-			list_reset(thisk);
-			do {
-				ktom=thisk->current->data;
-				if(ktom==btom)
-					continue;
-				if(ktom==&(atom[i]))
-					continue;
-				
-				/* 3 body stuff (1) */
+	if(d_ij<R) {
+		/* f_c = 1, df_c = 0 */
+		f_c=1.0;
+		df_c=0.0;
+		v3_scale(&force,&dist_ij,df_r);
+	}
+	else {
+		s_r=S-R;
+		arg=PI*(d_ij-R)/s_r;
+		f_c=0.5+0.5*cos(arg);
+		df_c=-0.5*sin(arg)*(PI/(s_r*d_ij));
+		scale=df_c*f_r+df_r*f_c;
+		v3_scale(&force,&dist_ij,scale);
+	}
 
-			} while(list_next(thisk)!=L_NO_NEXT_ELEMENT);
+	/* add forces */
+	v3_add(&(ai->f),&(ai->f),&force);
+	/* energy is 0.5 f_r f_c, but we will sum it up twice ... */
+	moldyn->energy+=(0.25*f_r*f_c);
 
-			/* direct neighbours of btom cell */
-			for(k=1;k<ck;k++) {
-				thisk=&(neighbourk[k]);
-				list_reset(thisk);
-				if(thisk->start!=NULL) {
+	/* save for use in 3bp */
+	exchange->f_c=f_c;
+	exchange->df_c=df_c;
 
-				do {
-					ktom=thisk->current->data;
-					if(ktom==&(atom[i]))
-						continue;
+	/* enable the run of 3bp function */
+	exchange->run3bp=1;
 
-				/* 3 body stuff (2) */
+	return 0;
+}
 
-				} while(list_next(thisk)!=L_NO_NEXT_ELEMENT);
+/* tersoff 3 body part */
 
-				}
-			}
+int tersoff_mult_3bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,t_atom *ak,u8 bc) {
 
-			/* indirect neighbours of btom cell */
-			for(k=ck;k<27;k++) {
-				thisk=&(neighbourk[k]);
-				list_reset(thisk);
-				if(thisk->start!=NULL) {
+	t_tersoff_mult_params *params;
+	t_tersoff_exchange *exchange;
+	t_3dvec dist_ij,dist_ik,dist_jk;
+	t_3dvec temp,force;
+	double R,S,s_r;
+	double d_ij,d_ik,d_jk;
+	double f_c,df_c,b_ij,f_a,df_a;
+	double n,c,d,h,neta,betan,betan_1;
+	double theta,cos_theta,sin_theta;
+	int num;
 
-				do {
-					ktom=thisk->current->data;
-					if(ktom==&(atom[i]))
-						continue;
+	params=moldyn->pot_params;
+	num=ai->bnum;
+	exchange=params->exchange;
 
-				/* 3 body stuff (3) */
+	if(!(exchange->run3bp))
+		return 0;
 
-				} while(list_next(thisk)!=L_NO_NEXT_ELEMENT);
+	/*
+	 * we need: f_c, d_fc, b_ij, db_ij, f_a, df_a
+	 *
+	 * we got f_c, df_c, f_a, df_a from 2bp calculation
+	 */
 
-				}
-			}
+	d_ij=exchange->d_ij;
+	d_ij2=exchange->d_ij2;
 
+	f_a=params->exchange.f_a;
+	df_a=params->exchange.df_a;
+	
+	/* d_ij is <= S, as we didn't return so far! */
 
-			} while(list_next(this)!=L_NO_NEXT_ELEMENT);
+	/*
+	 * calc of b_ij (scalar) and db_ij (vector)
+	 *
+	 * - for b_ij: chi, beta, f_c_ik, w(=1), c, d, h, n, cos_theta
+	 *
+	 * - for db_ij: d_theta, sin_theta, cos_theta, f_c_ik, df_c_ik,
+	 *              w_ik,
+	 *
+	 */
 
-			}
-		}
-		
+	
+	v3_sub(&dist_ik,&(aj->i),&(ak->r));
+	if(bc) check_per_bound(moldyn,&dist_ik);
+	d_ik=v3_norm(&dist_ik);
+
+	/* constants for f_c_ik calc */
+	if(num==ak->bnum) {
+		R=params->R[num];
+		S=params->S[num];
+	}
+	else {
+		R=params->Rmixed;
+		S=params->Smixed;
 	}
 
-	moldyn->energy=0.5*u;
+	/* calc of f_c_ik */
+	if(d_ik>S)
+		return 0;
 
+	if(d_ik<R) {
+		/* f_c_ik = 1, df_c_ik = 0 */
+		f_c_ik=1.0;
+		df_c_ik=0.0;
+	}
+	else {
+		s_r=S-R;
+		arg=PI*(d_ik-R)/s_r;
+		f_c_ik=0.5+0.5*cos(arg);
+		df_c_ik=-0.5*sin(arg)*(PI/(s_r*d_ik));
+	}
+	
+	v3_sub(&dist_jk,&(aj->r),&(ak->r));
+	if(bc) check_per_bound(moldyn,&dist_jk);
+	d_jk=v3_norm(&dist_jk);
+
+	beta=*(exchange->beta);
+	betan=exchange->betan;
+	n=*(exchange->n);
+	c=*(exchange->c);
+	d=*(exchange->d);
+	h=*(exchange->h);
+	c2=exchange->c2;
+	d2=exchange->d2;
+	c2d2=exchange->c2d2;
+
+	numer=d_ij2+d_ik*d_ik-d_jk*d_jk;
+	denom=2*d_ij*d_ik;
+	cos_theta=numer/denom;
+	sin_theta=sqrt(1.0-(cos_theta*cos_theta));
+	theta=arccos(cos_theta);
+	d_theta=(-1.0/sqrt(1.0-cos_theta*cos_theta))/(denom*denom);
+	d_theta1=2*denom-numer*2*d_ik/d_ij;
+	d_theta2=2*denom-numer*2*d_ij/d_ik;
+	d_theta1*=d_theta;
+	d_theta2*=d_theta;
+
+	h_cos=(h-cos_theta);
+	h_cos2=h_cos*h_cos;
+	d2_h_cos2=d2-h_cos2;
+
+	/* some usefull expressions */
+	frac1=c2/(d2-h_cos2);
+	bracket1=1+c2d2-frac1;
+	bracket2=f_c_ik*bracket1;
+	bracket2_n_1=pow(bracket2,n-1.0);
+	bracket2_n=bracket2_n_1*bracket2;
+	bracket3=1+betan*bracket2_n;
+	bracket3_pow_1=pow(bracket3,(-1.0/(2.0*n))-1.0);
+	bracket3_pow=bracket3_pow_1*bracket3;
+
+	/* now go on with calc of b_ij and derivation of b_ij */
+	b_ij=chi*bracket3_pow;
+
+	/* derivation of theta */
+	v3_scale(&force,&dist_ij,d1_theta);
+	v3_scale(&temp,&dist_ik,d_theta2);
+	v3_add(&force,&force,&temp);
+
+	/* part 1 of derivation of b_ij */
+	v3_scale(&force,sin_theta*2*h_cos*f_c_ik*frac1);
+
+	/* part 2 of derivation of b_ij */
+	v3_scale(&temp,&dist_ik,df_c_ik*bracket1);
+
+	/* sum up and scale ... */
+	v3_add(&temp,&temp,&force);
+	scale=bracket2_n_1*n*betan*(1+betan*bracket3_pow_1)*chi*(1.0/(2.0*n));
+	v3_scale(&temp,&temp,scale);
+
+	/* now construct an energy and a force out of that */
+	v3_scale(&temp,&temp,f_a);
+	v3_scale(&force,&dist_ij,df_a*b_ij);
+	v3_add(&temp,&temp,&force);
+	v3_scale(&temp,&temp,f_c);
+	v3_scale(&force,&dist_ij,df_c*b_ij*f_a);
+	v3_add(&force,&force,&temp);
+
+	/* add forces */
+	v3_add(&(ai->f),&(ai->f),&force);
+	/* energy is 0.5 f_r f_c, but we will sum it up twice ... */
+	moldyn->energy+=(0.25*f_a*b_ij*f_c);
+				
 	return 0;
 }