X-Git-Url: https://hackdaworld.org/gitweb/?a=blobdiff_plain;f=moldyn.c;h=7ea5d5080ab1ab185fa46b2137894239e9233902;hb=1d83ceb2ce2ff5150fd079f1066b7f583e38c8f4;hp=57f76c433ae7d431fc860dc51ddc21b6982a6d29;hpb=06912ca45b46de412570a4bd5b5484aa9e8d6e6b;p=physik%2Fposic.git

diff --git a/moldyn.c b/moldyn.c
index 57f76c4..7ea5d50 100644
--- a/moldyn.c
+++ b/moldyn.c
@@ -23,217 +23,206 @@
 #include "visual/visual.h"
 #include "list/list.h"
 
-int moldyn_usage(char **argv) {
-
-	printf("\n%s usage:\n\n",argv[0]);
-	printf("--- general options ---\n");
-	printf("-E <steps> <file> (log total energy)\n");
-	printf("-M <steps> <file> (log total momentum)\n");
-	printf("-D <steps> <file> (dump total information)\n");
-	printf("-S <steps> <filebase> (single save file)\n");
-	printf("-V <steps> <filebase> (rasmol file)\n");
-	printf("--- physics options ---\n");
-	printf("-T <temperature> [K] (%f)\n",MOLDYN_TEMP);
-	printf("-t <timestep tau> [s] (%.15f)\n",MOLDYN_TAU);
-	printf("-C <cutoff radius> [m] (%.15f)\n",MOLDYN_CUTOFF);
-	printf("-R <runs> (%d)\n",MOLDYN_RUNS);
-	printf(" -- integration algo --\n");
-	printf("  -I <number> (%d)\n",MOLDYN_INTEGRATE_DEFAULT);
-	printf("     0: velocity verlet\n");
-	printf(" -- potential --\n");
-	printf("  -P <number> <param1 param2 ...>\n");
-	printf("     0: harmonic oscillator\n");
-	printf("        param1: spring constant\n");
-	printf("        param2: equilibrium distance\n");
-	printf("     1: lennard jones\n");
-	printf("        param1: epsilon\n");
-	printf("        param2: sigma\n");
-	printf("\n");
+
+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);
+	moldyn->random.status|=RAND_STAT_VERBOSE;
 
 	return 0;
 }
 
-int moldyn_parse_argv(t_moldyn *moldyn,int argc,char **argv) {
+int moldyn_shutdown(t_moldyn *moldyn) {
 
-	int i;
-	t_ho_params hop;
-	t_lj_params ljp;
-	t_tersoff_params tp;
-	double s,e;
+	printf("[moldyn] shutdown\n");
+	moldyn_log_shutdown(moldyn);
+	link_cell_shutdown(moldyn);
+	rand_close(&(moldyn->random));
+	free(moldyn->atom);
 
-	memset(moldyn,0,sizeof(t_moldyn));
+	return 0;
+}
+
+int set_int_alg(t_moldyn *moldyn,u8 algo) {
 
-	/* default values */
-	moldyn->t=MOLDYN_TEMP;
-	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++) {
-		if(argv[i][0]=='-') {
-			switch(argv[i][1]){
-				case 'E':
-					moldyn->ewrite=atoi(argv[++i]);
-					strncpy(moldyn->efb,argv[++i],64);
-					break;
-				case 'M':
-					moldyn->mwrite=atoi(argv[++i]);
-					strncpy(moldyn->mfb,argv[++i],64);
-					break;
-				case 'S':
-					moldyn->swrite=atoi(argv[++i]);
-					strncpy(moldyn->sfb,argv[++i],64);
-					break;
-				case 'V':
-					moldyn->vwrite=atoi(argv[++i]);
-					strncpy(moldyn->vfb,argv[++i],64);
-					break;
-				case 'T':
-					moldyn->t=atof(argv[++i]);
-					break;
-				case 't':
-					moldyn->tau=atof(argv[++i]);
-					break;
-				case 'C':
-					moldyn->cutoff=atof(argv[++i]);
-					break;
-				case 'R':
-					moldyn->time_steps=atoi(argv[++i]);
-					break;
-				case 'I':
-	/* integration algorithm */
-	switch(atoi(argv[++i])) {
+	switch(algo) {
 		case MOLDYN_INTEGRATE_VERLET:
 			moldyn->integrate=velocity_verlet;
 			break;
 		default:
-			printf("unknown integration algo %s\n",argv[i]);
-			moldyn_usage(argv);
+			printf("unknown integration algorithm: %02x\n",algo);
 			return -1;
 	}
 
-				case 'P':
-	/* potential + params */
-	switch(atoi(argv[++i])) {
-		case MOLDYN_POTENTIAL_HO:
-			hop.spring_constant=atof(argv[++i]);
-			hop.equilibrium_distance=atof(argv[++i]);
-			moldyn->pot_params=malloc(sizeof(t_ho_params));
-			memcpy(moldyn->pot_params,&hop,sizeof(t_ho_params));
-			moldyn->potential_force_function=harmonic_oscillator;
-			break;
-		case MOLDYN_POTENTIAL_LJ:
-			e=atof(argv[++i]);
-			s=atof(argv[++i]);
-			ljp.epsilon4=4*e;
-			ljp.sigma6=s*s*s*s*s*s;
-			ljp.sigma12=ljp.sigma6*ljp.sigma6;
-			moldyn->pot_params=malloc(sizeof(t_lj_params));
-			memcpy(moldyn->pot_params,&ljp,sizeof(t_lj_params));
-			moldyn->potential_force_function=lennard_jones;
-			break;
-		default:
-			printf("unknown potential %s\n",argv[i]);
-			moldyn_usage(argv);
-			return -1;
-	}
+	return 0;
+}
 
-				default:
-					printf("unknown option %s\n",argv[i]);
-					moldyn_usage(argv);
-					return -1;
-			}
-		} else {
-			moldyn_usage(argv);
-			return -1;
-		}
-	}
+int set_cutoff(t_moldyn *moldyn,double cutoff) {
+
+	moldyn->cutoff=cutoff;
 
 	return 0;
 }
 
-int moldyn_log_init(t_moldyn *moldyn) {
+int set_temperature(t_moldyn *moldyn,double t_ref) {
 
-	moldyn->lvstat=0;
-	t_visual *vis;
+	moldyn->t_ref=t_ref;
 
-	vis=&(moldyn->vis);
+	return 0;
+}
 
-	if(moldyn->ewrite) {
-		moldyn->efd=open(moldyn->efb,O_WRONLY|O_CREAT|O_TRUNC);
-		if(moldyn->efd<0) {
-			perror("[moldyn] efd open");
-			return moldyn->efd;
-		}
-		dprintf(moldyn->efd,"# moldyn total energy logfile\n");
-		moldyn->lvstat|=MOLDYN_LVSTAT_TOTAL_E;
-	}
+int set_pt_scale(t_moldyn *moldyn,u8 ptype,double ptc,u8 ttype,double ttc) {
 
-	if(moldyn->mwrite) {
-		moldyn->mfd=open(moldyn->mfb,O_WRONLY|O_CREAT|O_TRUNC);
-		if(moldyn->mfd<0) {
-			perror("[moldyn] mfd open");
-			return moldyn->mfd;
-		}
-		dprintf(moldyn->mfd,"# moldyn total momentum logfile\n");
-		moldyn->lvstat|=MOLDYN_LVSTAT_TOTAL_M;
-	}
+	moldyn->pt_scale=(ptype|ttype);
+	moldyn->t_tc=ttc;
+	moldyn->p_tc=ptc;
+
+	return 0;
+}
+
+int set_dim(t_moldyn *moldyn,double x,double y,double z,u8 visualize) {
 
-	if(moldyn->swrite)
-		moldyn->lvstat|=MOLDYN_LVSTAT_SAVE;
+	moldyn->dim.x=x;
+	moldyn->dim.y=y;
+	moldyn->dim.z=z;
 
-	if((moldyn->vwrite)&&(vis)) {
-		moldyn->visual=vis;
-		visual_init(vis,moldyn->vfb);
-		moldyn->lvstat|=MOLDYN_LVSTAT_VISUAL;
+	if(visualize) {
+		moldyn->vis.dim.x=x;
+		moldyn->vis.dim.y=y;
+		moldyn->vis.dim.z=z;
 	}
 
-	moldyn->lvstat|=MOLDYN_LVSTAT_INITIALIZED;
+	return 0;
+}
+
+int set_nn_dist(t_moldyn *moldyn,double dist) {
+
+	moldyn->nnd=dist;
 
 	return 0;
 }
 
-int moldyn_log_shutdown(t_moldyn *moldyn) {
+int set_pbc(t_moldyn *moldyn,u8 x,u8 y,u8 z) {
 
-	if(moldyn->efd) close(moldyn->efd);
-	if(moldyn->mfd) close(moldyn->efd);
-	if(moldyn->dfd) close(moldyn->efd);
-	if(moldyn->visual) visual_tini(moldyn->visual);
+	if(x)
+		moldyn->status|=MOLDYN_STAT_PBX;
+
+	if(y)
+		moldyn->status|=MOLDYN_STAT_PBY;
+
+	if(z)
+		moldyn->status|=MOLDYN_STAT_PBZ;
 
 	return 0;
 }
 
-int moldyn_init(t_moldyn *moldyn,int argc,char **argv) {
+int set_potential1b(t_moldyn *moldyn,pf_func1b func,void *params) {
 
-	int ret;
+	moldyn->func1b=func;
+	moldyn->pot1b_params=params;
 
-	ret=moldyn_parse_argv(moldyn,argc,argv);
-	if(ret<0) return ret;
+	return 0;
+}
 
-	ret=moldyn_log_init(moldyn);
-	if(ret<0) return ret;
+int set_potential2b(t_moldyn *moldyn,pf_func2b func,void *params) {
 
-	rand_init(&(moldyn->random),NULL,1);
-	moldyn->random.status|=RAND_STAT_VERBOSE;
+	moldyn->func2b=func;
+	moldyn->pot2b_params=params;
+
+	return 0;
+}
 
-	moldyn->status=0;
+int set_potential2b_post(t_moldyn *moldyn,pf_func2b_post func,void *params) {
+
+	moldyn->func2b_post=func;
+	moldyn->pot2b_params=params;
 
 	return 0;
 }
 
-int moldyn_shutdown(t_moldyn *moldyn) {
+int set_potential3b(t_moldyn *moldyn,pf_func3b func,void *params) {
 
-	moldyn_log_shutdown(moldyn);
-	rand_close(&(moldyn->random));
-	free(moldyn->atom);
+	moldyn->func3b=func;
+	moldyn->pot3b_params=params;
+
+	return 0;
+}
+
+int moldyn_set_log_dir(t_moldyn *moldyn,char *dir) {
+
+	strncpy(moldyn->vlsdir,dir,127);
+
+	return 0;
+}
+	
+int moldyn_set_log(t_moldyn *moldyn,u8 type,int timer) {
+
+	char filename[128];
+	int ret;
+
+	switch(type) {
+		case LOG_TOTAL_ENERGY:
+			moldyn->ewrite=timer;
+			snprintf(filename,127,"%s/energy",moldyn->vlsdir);
+			moldyn->efd=open(filename,
+			                 O_WRONLY|O_CREAT|O_EXCL,
+			                 S_IRUSR|S_IWUSR);
+			if(moldyn->efd<0) {
+				perror("[moldyn] energy log fd open");
+				return moldyn->efd;
+			}
+			dprintf(moldyn->efd,"# total energy log file\n");
+			break;
+		case LOG_TOTAL_MOMENTUM:
+			moldyn->mwrite=timer;
+			snprintf(filename,127,"%s/momentum",moldyn->vlsdir);
+			moldyn->mfd=open(filename,
+			                 O_WRONLY|O_CREAT|O_EXCL,
+			                 S_IRUSR|S_IWUSR);
+			if(moldyn->mfd<0) {
+				perror("[moldyn] momentum log fd open");
+				return moldyn->mfd;
+			}
+			dprintf(moldyn->efd,"# total momentum log file\n");
+			break;
+		case SAVE_STEP:
+			moldyn->swrite=timer;
+			break;
+		case VISUAL_STEP:
+			moldyn->vwrite=timer;
+			ret=visual_init(&(moldyn->vis),moldyn->vlsdir);
+			if(ret<0) {
+				printf("[moldyn] visual init failure\n");
+				return ret;
+			}
+			break;
+		default:
+			printf("[moldyn] unknown log mechanism: %02x\n",type);
+			return -1;
+	}
+
+	return 0;
+}
+
+int moldyn_log_shutdown(t_moldyn *moldyn) {
+
+	printf("[moldyn] log shutdown\n");
+	if(moldyn->efd) close(moldyn->efd);
+	if(moldyn->mfd) close(moldyn->mfd);
+	if(&(moldyn->vis)) visual_tini(&(moldyn->vis));
 
 	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;
@@ -242,10 +231,11 @@ int create_lattice(unsigned char type,int element,double mass,double lc,
 	count=a*b*c;
 
 	if(type==FCC) count*=4;
+
 	if(type==DIAMOND) count*=8;
 
-	*atom=malloc(count*sizeof(t_atom));
-	if(*atom==NULL) {
+	moldyn->atom=malloc(count*sizeof(t_atom));
+	if(moldyn->atom==NULL) {
 		perror("malloc (atoms)");
 		return -1;
 	}
@@ -254,10 +244,10 @@ 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,moldyn->atom,&origin);
 			break;
 		case DIAMOND:
-			ret=diamond_init(a,b,c,lc,*atom,&origin);
+			ret=diamond_init(a,b,c,lc,moldyn->atom,&origin);
 			break;
 		default:
 			printf("unknown lattice type (%02x)\n",type);
@@ -272,23 +262,58 @@ int create_lattice(unsigned char type,int element,double mass,double lc,
 		return -1;
 	}
 
+	moldyn->count=count;
+	printf("[moldyn] created lattice with %d atoms\n",count);
+
 	while(count) {
-		(*atom)[count-1].element=element;
-		(*atom)[count-1].mass=mass;
 		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));
 	}
 
+
 	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) {
+
+	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;
+	}
+	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;
+
+	return 0;
+}
+
+int destroy_atoms(t_moldyn *moldyn) {
 
-	if(atom) free(atom);
+	if(moldyn->atom) free(moldyn->atom);
 
 	return 0;
 }
 
-int thermal_init(t_moldyn *moldyn) {
+int thermal_init(t_moldyn *moldyn,u8 equi_init) {
 
 	/*
 	 * - gaussian distribution of velocities
@@ -308,7 +333,7 @@ int thermal_init(t_moldyn *moldyn) {
 	/* gaussian distribution of velocities */
 	v3_zero(&p_total);
 	for(i=0;i<moldyn->count;i++) {
-		sigma=sqrt(2.0*K_BOLTZMANN*moldyn->t/atom[i].mass);
+		sigma=sqrt(2.0*K_BOLTZMANN*moldyn->t_ref/atom[i].mass);
 		/* x direction */
 		v=sigma*rand_get_gauss(random);
 		atom[i].v.x=v;
@@ -331,44 +356,78 @@ int thermal_init(t_moldyn *moldyn) {
 	}
 
 	/* velocity scaling */
-	scale_velocity(moldyn);
+	scale_velocity(moldyn,equi_init);
 
 	return 0;
 }
 
-int scale_velocity(t_moldyn *moldyn) {
+int scale_velocity(t_moldyn *moldyn,u8 equi_init) {
 
 	int i;
-	double e,c;
+	double e,scale;
 	t_atom *atom;
+	int count;
 
 	atom=moldyn->atom;
 
 	/*
 	 * - velocity scaling (E = 3/2 N k T), E: kinetic energy
 	 */
+
+	/* get kinetic energy / temperature & count involved atoms */
 	e=0.0;
-	for(i=0;i<moldyn->count;i++)
-		e+=0.5*atom[i].mass*v3_absolute_square(&(atom[i].v));
-	c=sqrt((2.0*e)/(3.0*moldyn->count*K_BOLTZMANN*moldyn->t));
-	for(i=0;i<moldyn->count;i++)
-		v3_scale(&(atom[i].v),&(atom[i].v),(1.0/c));
+	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));
+			count+=1;
+		}
+	}
+	if(count!=0) moldyn->t=(2.0*e)/(3.0*count*K_BOLTZMANN);
+	else return 0;	/* no atoms involved in scaling! */
+	
+	/* (temporary) hack for e,t = 0 */
+	if(e==0.0) {
+	moldyn->t=0.0;
+		if(moldyn->t_ref!=0.0) {
+			thermal_init(moldyn,equi_init);
+			return 0;
+		}
+		else
+			return 0; /* no scaling needed */
+	}
+
+
+	/* get scaling factor */
+	scale=moldyn->t_ref/moldyn->t;
+	if(equi_init&TRUE)
+		scale*=2.0;
+	else
+		if(moldyn->pt_scale&T_SCALE_BERENDSEN)
+			scale=1.0+(scale-1.0)/moldyn->t_tc;
+	scale=sqrt(scale);
+
+	/* velocity scaling */
+	for(i=0;i<moldyn->count;i++) {
+		if((equi_init&TRUE)||(atom[i].attr&ATOM_ATTR_HB))
+			v3_scale(&(atom[i].v),&(atom[i].v),scale);
+	}
 
 	return 0;
 }
 
-double get_e_kin(t_atom *atom,int count) {
+double get_e_kin(t_moldyn *moldyn) {
 
 	int i;
-	double e;
+	t_atom *atom;
 
-	e=0.0;
+	atom=moldyn->atom;
+	moldyn->ekin=0.0;
 
-	for(i=0;i<count;i++) {
-		e+=0.5*atom[i].mass*v3_absolute_square(&(atom[i].v));
-	}
+	for(i=0;i<moldyn->count;i++)
+		moldyn->ekin+=0.5*atom[i].mass*v3_absolute_square(&(atom[i].v));
 
-	return e;
+	return moldyn->ekin;
 }
 
 double get_e_pot(t_moldyn *moldyn) {
@@ -376,23 +435,26 @@ double get_e_pot(t_moldyn *moldyn) {
 	return moldyn->energy;
 }
 
-double get_total_energy(t_moldyn *moldyn) {
+double update_e_kin(t_moldyn *moldyn) {
 
-	double e;
+	return(get_e_kin(moldyn));
+}
 
-	e=get_e_kin(moldyn->atom,moldyn->count);
-	e+=get_e_pot(moldyn);
+double get_total_energy(t_moldyn *moldyn) {
 
-	return e;
+	return(moldyn->ekin+moldyn->energy);
 }
 
-t_3dvec get_total_p(t_atom *atom, int count) {
+t_3dvec get_total_p(t_moldyn *moldyn) {
 
 	t_3dvec p,p_total;
 	int i;
+	t_atom *atom;
+
+	atom=moldyn->atom;
 
 	v3_zero(&p_total);
-	for(i=0;i<count;i++) {
+	for(i=0;i<moldyn->count;i++) {
 		v3_scale(&p,&(atom[i].v),atom[i].mass);
 		v3_add(&p_total,&p_total,&p);
 	}
@@ -400,15 +462,13 @@ t_3dvec get_total_p(t_atom *atom, int count) {
 	return p_total;
 }
 
-double estimate_time_step(t_moldyn *moldyn,double nn_dist,double t) {
+double estimate_time_step(t_moldyn *moldyn,double nn_dist) {
 
 	double tau;
 
-	tau=0.05*nn_dist/(sqrt(3.0*K_BOLTZMANN*t/moldyn->atom[0].mass));
-	tau*=1.0E-9;
-	if(tau<moldyn->tau)
-		printf("[moldyn] warning: time step  (%f > %.15f)\n",
-		       moldyn->tau,tau);
+	/* nn_dist is the nearest neighbour distance */
+
+	tau=(0.05*nn_dist*moldyn->atom[0].mass)/sqrt(3.0*K_BOLTZMANN*moldyn->t);
 
 	return tau;	
 }
@@ -423,11 +483,11 @@ int link_cell_init(t_moldyn *moldyn) {
 
 	t_linkcell *lc;
 	int i;
+	int fd;
 
-	lc=&(moldyn->lc);
+	fd=open("/dev/null",O_WRONLY);
 
-	/* list log fd */
-	lc->listfd=open("/dev/null",O_WRONLY);
+	lc=&(moldyn->lc);
 
 	/* partitioning the md cell */
 	lc->nx=moldyn->dim.x/moldyn->cutoff;
@@ -440,11 +500,11 @@ int link_cell_init(t_moldyn *moldyn) {
 	lc->cells=lc->nx*lc->ny*lc->nz;
 	lc->subcell=malloc(lc->cells*sizeof(t_list));
 
-	printf("initializing linked cells (%d)\n",lc->cells);
+	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]));
+		list_init(&(lc->subcell[i]),fd);
 
  	link_cell_update(moldyn);
 	
@@ -468,7 +528,7 @@ int link_cell_update(t_moldyn *moldyn) {
 	for(i=0;i<lc->cells;i++)
 		list_destroy(&(moldyn->lc.subcell[i]));
 	
-	for(count=0;count<moedyn->count;count++) {
+	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;
@@ -487,7 +547,7 @@ 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;
@@ -497,7 +557,6 @@ int link_cell_neighbour_index(t_moldyn *moldyn,int i,int j,int k,t_list *cell) {
 	count2=27;
 	a=nx*ny;
 
-
 	cell[0]=lc->subcell[i+j*nx+k*a];
 	for(ci=-1;ci<=1;ci++) {
 		bx=0;
@@ -531,10 +590,9 @@ int link_cell_neighbour_index(t_moldyn *moldyn,int i,int j,int k,t_list *cell) {
 		}
 	}
 
-	lc->dnlc=count2;
-	lc->countn=27;
+	lc->dnlc=count1;
 
-	return count2;
+	return count1;
 }
 
 int link_cell_shutdown(t_moldyn *moldyn) {
@@ -547,11 +605,45 @@ int link_cell_shutdown(t_moldyn *moldyn) {
 	for(i=0;i<lc->nx*lc->ny*lc->nz;i++)
 		list_shutdown(&(moldyn->lc.subcell[i]));
 
-	if(lc->listfd) close(lc->listfd);
+	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=ptr;
+	moldyn->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;
 
 	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
@@ -562,12 +654,17 @@ int link_cell_shutdown(t_moldyn *moldyn) {
 
 int moldyn_integrate(t_moldyn *moldyn) {
 
-	int i;
-	unsigned int e,m,s,d,v;
+	int i,sched;
+	unsigned int e,m,s,v;
 	t_3dvec p;
-
+	t_moldyn_schedule *schedule;
+	t_atom *atom;
 	int fd;
-	char fb[128];
+	char dir[128];
+	double ds;
+
+	schedule=&(moldyn->schedule);
+	atom=moldyn->atom;
 
 	/* initialize linked cell method */
 	link_cell_init(moldyn);
@@ -576,46 +673,72 @@ int moldyn_integrate(t_moldyn *moldyn) {
 	e=moldyn->ewrite;
 	m=moldyn->mwrite;
 	s=moldyn->swrite;
-	d=moldyn->dwrite;
 	v=moldyn->vwrite;
 
-	if(!(moldyn->lvstat&MOLDYN_LVSTAT_INITIALIZED)) {
-		printf("[moldyn] warning, lv system not initialized\n");
-		return -1;
-	}
-
 	/* sqaure of some variables */
 	moldyn->tau_square=moldyn->tau*moldyn->tau;
 	moldyn->cutoff_square=moldyn->cutoff*moldyn->cutoff;
 
 	/* calculate initial forces */
-	moldyn->potential_force_function(moldyn);
+	potential_force_calc(moldyn);
+
+	/* some stupid checks before we actually start calculating bullshit */
+	if(moldyn->cutoff>0.5*moldyn->dim.x)
+		printf("[moldyn] warning: cutoff > 0.5 x dim.x\n");
+	if(moldyn->cutoff>0.5*moldyn->dim.y)
+		printf("[moldyn] warning: cutoff > 0.5 x dim.y\n");
+	if(moldyn->cutoff>0.5*moldyn->dim.z)
+		printf("[moldyn] warning: cutoff > 0.5 x dim.z\n");
+	ds=0.5*atom[0].f.x*moldyn->tau_square/atom[0].mass;
+	if(ds>0.05*moldyn->nnd)
+		printf("[moldyn] warning: forces too high / tau too small!\n");
+
+	/* zero absolute time */
+	moldyn->time=0.0;
+
+	/* debugging, ignore */
+	moldyn->debug=0;
+
+	/* executing the schedule */
+	for(sched=0;sched<moldyn->schedule.content_count;sched++) {
+
+		/* setting amount of runs and finite time step size */
+		moldyn->tau=schedule->tau[sched];
+		moldyn->tau_square=moldyn->tau*moldyn->tau;
+		moldyn->time_steps=schedule->runs[sched];
+
+	/* integration according to schedule */
 
 	for(i=0;i<moldyn->time_steps;i++) {
 
 		/* integration step */
 		moldyn->integrate(moldyn);
 
+		/* p/t scaling */
+		if(moldyn->pt_scale&(T_SCALE_BERENDSEN|T_SCALE_DIRECT))
+			scale_velocity(moldyn,FALSE);
+
 		/* check for log & visualization */
 		if(e) {
 			if(!(i%e))
 				dprintf(moldyn->efd,
-				        "%.15f %.45f\n",i*moldyn->tau,
+				        "%f %f %f %f\n",
+				        moldyn->time,update_e_kin(moldyn),
+				        moldyn->energy,
 				        get_total_energy(moldyn));
 		}
 		if(m) {
 			if(!(i%m)) {
-				p=get_total_p(moldyn->atom,moldyn->count);
+				p=get_total_p(moldyn);
 				dprintf(moldyn->mfd,
-				        "%.15f %.45f\n",i*moldyn->tau,
-				        v3_norm(&p));
+				        "%f %f\n",moldyn->time,v3_norm(&p));
 			}
 		}
 		if(s) {
 			if(!(i%s)) {
-				snprintf(fb,128,"%s-%f-%.15f.save",moldyn->sfb,
-				         moldyn->t,i*moldyn->tau);
-				fd=open(fb,O_WRONLY|O_TRUNC|O_CREAT);
+				snprintf(dir,128,"%s/s-%07.f.save",
+				         moldyn->vlsdir,moldyn->time);
+				fd=open(dir,O_WRONLY|O_TRUNC|O_CREAT);
 				if(fd<0) perror("[moldyn] save fd open");
 				else {
 					write(fd,moldyn,sizeof(t_moldyn));
@@ -627,12 +750,26 @@ int moldyn_integrate(t_moldyn *moldyn) {
 		}
 		if(v) {
 			if(!(i%v)) {
-				visual_atoms(moldyn->visual,i*moldyn->tau,
+				visual_atoms(&(moldyn->vis),moldyn->time,
 				             moldyn->atom,moldyn->count);
-				printf("\rsteps: %d",i);
+				printf("\rsched: %d, steps: %d, debug: %d",
+				       sched,i,moldyn->debug);
 				fflush(stdout);
 			}
 		}
+
+		/* increase absolute time */
+		moldyn->time+=moldyn->tau;
+
+	}
+
+		/* check for hooks */
+		if(schedule->hook)
+			schedule->hook(moldyn,schedule->hook_params);
+
+		/* get a new info line */
+		printf("\n");
+
 	}
 
 	return 0;
@@ -658,7 +795,7 @@ 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);
-		v3_per_bound(&(atom[i].r),&(moldyn->dim));
+		check_per_bound(moldyn,&(atom[i].r));
 
 		/* velocities */
 		v3_scale(&delta,&(atom[i].f),0.5*tau/atom[i].mass);
@@ -666,15 +803,10 @@ int velocity_verlet(t_moldyn *moldyn) {
 	}
 
 	/* neighbour list update */
-printf("list update ...\n");
 	link_cell_update(moldyn);
-printf("done\n");
 
 	/* forces depending on chosen potential */
-printf("calc potential/force ...\n");
 	potential_force_calc(moldyn);
-	//moldyn->potential_force_function(moldyn);
-printf("done\n");
 
 	for(i=0;i<count;i++) {
 		/* again velocities */
@@ -694,697 +826,823 @@ printf("done\n");
 
 /* generic potential and force calculation */
 
-#define		CREATE_CELL_LIST(nb_list) \
-	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,\
-	                          nb_list);
-
-
 int potential_force_calc(t_moldyn *moldyn) {
 
-	int i,count;
-	t_atom *atom;
+	int i,j,k,count;
+	t_atom *itom,*jtom,*ktom;
 	t_linkcell *lc;
-	t_list neighbour[27];
-	t_list *this;
-	double u;
+	t_list neighbour_i[27];
+	t_list neighbour_i2[27];
+	//t_list neighbour_j[27];
+	t_list *this,*that;
+	u8 bc_ij,bc_ik;
+	int dnlc;
 
 	count=moldyn->count;
-	atom=moldyn->atom;
+	itom=moldyn->atom;
 	lc=&(moldyn->lc);
 
 	/* reset energy */
-	u=0.0;
+	moldyn->energy=0.0;
 
+	/* get energy and force of every atom */
 	for(i=0;i<count;i++) {
-	
+
 		/* reset force */
-		v3_zero(&(atom[i].f));
+		v3_zero(&(itom[i].f));
 
 		/* single particle potential/force */
-		if(moldyn->status&MOLDYN_STAT_1BP)
-			moldyn->pf_func1b(moldyn,&(atom[i]));
-
-		/* 2 body pair potential/force */
-		if(moldyn->status&MOLDYN_STAT_2BP) {
-		
-			CREATE_CELL_LIST(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]))
-					moldyn->pf_func2b(moldyn,
-					                  &(atom[i]),btom);
-			} while(list_next(this)!=L_NO_NEXT_ELEMENT);
+		if(itom[i].attr&ATOM_ATTR_1BP)
+			moldyn->func1b(moldyn,&(itom[i]));
 
-			/*
-			 * direct neighbour cells
-			 * => no boundary condition check necessary
-			 */
-			for(j=0;j<lc->dnlc;j++) {
-				this=&(neighbour[j]);
-				list_reset(this);
-				if(this->start!=NULL) {
-					do {
-						btom=this->current->data;
-						moldyn->pf_func2b(moldyn,
-						                  &(atom[i]),
-						                  btom);
-					} while(list_next(this)!=\
-					        L_NO_NEXT_ELEMENT);
-			}
+		if(!(itom[i].attr&(ATOM_ATTR_2BP|ATOM_ATTR_3BP)))
+			continue;
 
-			/*
-			 * neighbour cells due to periodic bc
-			 * => check boundary conditions
-			 */
-			for(j=lc->dnlc;j<lc->countn;j++) {
-				this=&(neighbour[j]);
-				list_reset(this);
-				if(this->start!=NULL) {
-					do {
-						btom=this->current->data;
-						moldyn->pf_func2b(moldyn,
-						                  &(atom[i]),
-						                  btom);
-
-			}
-
-		}
-
-	return 0;
-}
+		/* 2 body pair potential/force */
+	
+		link_cell_neighbour_index(moldyn,
+		                          (itom[i].r.x+moldyn->dim.x/2)/lc->x,
+		                          (itom[i].r.y+moldyn->dim.y/2)/lc->y,
+		                          (itom[i].r.z+moldyn->dim.z/2)/lc->z,
+		                          neighbour_i);
 
+		dnlc=lc->dnlc;
 
-/* harmonic oscillator potential and force */
+		for(j=0;j<27;j++) {
 
-int harmonic_oscillator(t_moldyn *moldyn) {
+			this=&(neighbour_i[j]);
+			list_reset(this);
 
-	t_ho_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,u;
-	double sc,equi_dist;
-	int ni,nj,nk;
+			if(this->start==NULL)
+				continue;
 
-	params=moldyn->pot_params;
-	atom=moldyn->atom;
-	lc=&(moldyn->lc);
-	sc=params->spring_constant;
-	equi_dist=params->equilibrium_distance;
-	count=moldyn->count;
+			bc_ij=(j<dnlc)?0:1;
 
-	/* reset energy counter */
-	u=0.0;
+			do {
+				jtom=this->current->data;
 
-	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);
+				if(jtom==&(itom[i]))
+					continue;
 
-		/*
-		 * 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) {
+				if((jtom->attr&ATOM_ATTR_2BP)&
+				   (itom[i].attr&ATOM_ATTR_2BP))
+					moldyn->func2b(moldyn,
+					               &(itom[i]),
+					               jtom,
+					               bc_ij);
 
-			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);
+				/* 3 body potential/force */
 
-			}
-		}
+				if(!(itom[i].attr&ATOM_ATTR_3BP)||
+				   !(jtom->attr&ATOM_ATTR_3BP))
+					continue;
 
-		/*
-		 * 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) {
+				/* copy the neighbour lists */
+				memcpy(neighbour_i2,neighbour_i,
+				       27*sizeof(t_list));
 
-			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);
+				/* get neighbours of i */
+				for(k=0;k<27;k++) {
 
-			}
-		}
-	}
+					that=&(neighbour_i2[k]);
+					list_reset(that);
+					
+					if(that->start==NULL)
+						continue;
 
-	moldyn->energy=0.5*u;
+					bc_ik=(k<dnlc)?0:1;
 
-	return 0;
-}
+					do {
 
-/* lennard jones potential & force for one sort of atoms */
- 
-int lennard_jones(t_moldyn *moldyn) {
+						ktom=that->current->data;
 
-	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;
+						if(!(ktom->attr&ATOM_ATTR_3BP))
+							continue;
 
-	params=moldyn->pot_params;
-	atom=moldyn->atom;
-	lc=&(moldyn->lc);
-	count=moldyn->count;
-	eps=params->epsilon4;
-	sig6=params->sigma6;
-	sig12=params->sigma12;
+						if(ktom==jtom)
+							continue;
 
-	/* reset energy counter */
-	u=0.0;
+						if(ktom==&(itom[i]))
+							continue;
 
-	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 */
-		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);
+						moldyn->func3b(moldyn,
+						               &(itom[i]),
+						               jtom,
+						               ktom,
+						               bc_ik|bc_ij);
 
-		/* 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) {
+					} while(list_next(that)!=\
+					        L_NO_NEXT_ELEMENT);
 
-			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);
-				
-			}
-		}
-
-		/* 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);
+				/* 2bp post function */
+				if(moldyn->func2b_post) {
+					moldyn->func2b_post(moldyn,
+					                    &(itom[i]),
+					                    jtom,bc_ij);
 				}
+					
 			} while(list_next(this)!=L_NO_NEXT_ELEMENT);
-
-			}
+		
 		}
+
 	}
 
-	moldyn->energy=0.5*u;
-	
 	return 0;
 }
 
-/* tersoff potential & force for 2 sorts of atoms */
-
-int tersoff(t_moldyn *moldyn) {
+/*
+ * periodic boundayr checking
+ */
 
-	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;
+int check_per_bound(t_moldyn *moldyn,t_3dvec *a) {
 	
+	double x,y,z;
+	t_3dvec *dim;
 
-	params=moldyn->pot_params;
-	atom=moldyn->atom;
-	lc=&(moldyn->lc);
-	count=moldyn->count;
-	
-	/* reset energy counter */
-	u=0.0;
+	dim=&(moldyn->dim);
 
-	for(i=0;i<count;i++) {
-		/* reset force */
-		v3_zero(&(atom[i].f));
-
-		/* 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]))
-				continue;
+	x=0.5*dim->x;
+	y=0.5*dim->y;
+	z=0.5*dim->z;
 
-			/* 2 body stuff */
-
-			/* we need: f_c, df_c, f_r, df_r */
-
-			v3_sub(&dist_ij,btom,&(atom[i]));
-			d_ij=v3_norm(&dist_ij);
-			if(d_ij<=S) {
-
-				/* determine the tersoff parameters */
-				if(atom[i].element!=btom->element) {
-				S=sqrt(TERSOFF_S[e1]*TERSOFF_S[e2]);
-				R=R_m;
-				A=;
-				lambda=;
-				B=;
-				mu=;
-				chi=;
-				beta=;
-				betaN=;
-
-				if(d_ij<=R) {
-					df_r=-lambda*A*exp(-lambda*d_ij)/d_ij;
-					v3_scale(&force,&dist_ij,df_r);
-					v3_add(&(atom[i].f),&(atom[i].f),
-						&force);
-				}
-				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));
-					f_r=A*exp(-lambda*d_ij);
-					df_r=-lambda*f_r/d_ij;
-					scale=df_c*f_r+df_r*f_c;
-					v3_scale(&force,&dist_ij,scale);
-					v3_add(&(atom[i].f),&(atom[i].f),
-					       &force);
-				}
-			}
-			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);
-
-			/* go for zeta - 3 body stuff! */
-			zeta=0.0;
-			d_ij2=d_ij*d_ij;
-
-			/* 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) */
-				
-				v3_sub(&dist_ik,ktom,&(atom[i]));
-				d_ik=v3_norm(&dist_ik);
-				if(d_ik<=Sik) {
-
-				Rik=;
-				Sik=;
-				Aik=;
-				lambda_ik=;
-				Bik=;
-				mu_ik=;
-				omega_ik=;
-				c_i=;
-				d_i=;
-				h_i=;
-			
-
-					if(d_ik<=Rik) {
-						f_cik=1.0;
-						df_cik=0.0;
-					}
-					else {
-						sik_rik=Sik-Rik;
-						arg1ik=PI*(d_ik-Rik)/sik_rik;
-						f_cik=0.5+0.5*cos(arg1ik);
-						df_cik=-0.5*sin(arg1ik)* \
-						       (PI/(sik_rik*d_ik));
-						f_rik=Aik*exp(-lambda_ik*d_ik);
-						f_aik=-Bik*exp(-mu_ik*d_ik);
-					}
-			
-					v3_sub(&distance_jk,ktom,btom);
-					cos_theta=(d_ij2+d_ik*d_ik-d_jk*d_jk)/\
-					          (2*d_ij*d_ik);
-					sin_theta=sqrt(1.0/\
-					          (cos_theta*cos_theta));
-					theta=arccos(cos_theta);
+	if(moldyn->status&MOLDYN_STAT_PBX) {
+		if(a->x>=x) a->x-=dim->x;
+		else if(-a->x>x) a->x+=dim->x;
+	}
+	if(moldyn->status&MOLDYN_STAT_PBY) {
+		if(a->y>=y) a->y-=dim->y;
+		else if(-a->y>y) a->y+=dim->y;
+	}
+	if(moldyn->status&MOLDYN_STAT_PBZ) {
+		if(a->z>=z) a->z-=dim->z;
+		else if(-a->z>z) a->z+=dim->z;
+	}
 
-					
-				}
-				else
-					continue;
+	return 0;
+}
+        
 
-				/* end 3 body stuff (1) */
+/*
+ * example potentials
+ */
 
+/* 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) {
 
-			/* direct neighbours of btom cell */
-			for(k=1;k<ck;k++) {
-				thisk=&(neighbourk[k]);
-				list_reset(thisk);
-				if(thisk->start!=NULL) {
+	t_ho_params *params;
+	t_3dvec force,distance;
+	double d;
+	double sc,equi_dist;
 
-				do {
-					ktom=thisk->current->data;
-					if(ktom==&(atom[i]))
-						continue;
+	params=moldyn->pot2b_params;
+	sc=params->spring_constant;
+	equi_dist=params->equilibrium_distance;
+
+	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));
+		/* f = -grad E; grad r_ij = -1 1/r_ij distance */
+		v3_scale(&force,&distance,sc*(1.0-(equi_dist/d)));
+		v3_add(&(ai->f),&(ai->f),&force);
+	}
 
-				/* 3 body stuff (2) */
+	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;
+	double eps,sig6,sig12;
 
-			/* 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;
+	eps=params->epsilon4;
+	sig6=params->sigma6;
+	sig12=params->sigma12;
 
-				do {
-					ktom=thisk->current->data;
-					if(ktom==&(atom[i]))
-						continue;
+	v3_sub(&distance,&(aj->r),&(ai->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,-1.0*d); /* f = - grad E */
+		v3_add(&(ai->f),&(ai->f),&force);
+	}
 
-				/* 3 body stuff */
+	return 0;
+}
 
-				} while(list_next(thisk)!=L_NO_NEXT_ELEMENT);
+/*
+ * tersoff potential & force for 2 sorts of atoms
+ */
 
-				}
-			}
+/* create mixed terms from parameters and set them */
+int tersoff_mult_complete_params(t_tersoff_mult_params *p) {
+
+	printf("[moldyn] tersoff parameter completion\n");
+	p->Smixed=sqrt(p->S[0]*p->S[1]);
+	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]);
+	p->lambda_m=0.5*(p->lambda[0]+p->lambda[1]);
+	p->mu_m=0.5*(p->mu[0]+p->mu[1]);
+
+	printf("[moldyn] tersoff mult parameter info:\n");
+	printf("  S (A)  | %f | %f | %f\n",p->S[0],p->S[1],p->Smixed);
+	printf("  R (A)  | %f | %f | %f\n",p->R[0],p->R[1],p->Rmixed);
+	printf("  A (eV) | %f | %f | %f\n",p->A[0]/EV,p->A[1]/EV,p->Amixed/EV);
+	printf("  B (eV) | %f | %f | %f\n",p->B[0]/EV,p->B[1]/EV,p->Bmixed/EV);
+	printf("  lambda | %f | %f | %f\n",p->lambda[0],p->lambda[1],
+	                                  p->lambda_m);
+	printf("  mu     | %f | %f | %f\n",p->mu[0],p->mu[1],p->mu_m);
+	printf("  beta   | %.10f | %.10f\n",p->beta[0],p->beta[1]);
+	printf("  n      | %f | %f\n",p->n[0],p->n[1]);
+	printf("  c      | %f | %f\n",p->c[0],p->c[1]);
+	printf("  d      | %f | %f\n",p->d[0],p->d[1]);
+	printf("  h      | %f | %f\n",p->h[0],p->h[1]);
+	printf("  chi    | %f \n",p->chi);
 
+	return 0;
+}
 
-		} while(list_next(this)!=L_NO_NEXT_ELEMENT);
+/* tersoff 1 body part */
+int tersoff_mult_1bp(t_moldyn *moldyn,t_atom *ai) {
 
-		/*
-		 * direct neighbour cells of atom i
-		 */
-		for(j=1;j<c;j++) {
-			this=&(neighbour[j]);
-			list_reset(this);
-			if(this->start!=NULL) {
+	int num;
+	t_tersoff_mult_params *params;
+	t_tersoff_exchange *exchange;
+	
+	num=ai->bnum;
+	params=moldyn->pot1b_params;
+	exchange=&(params->exchange);
 
-			do {
-				btom=this->current->data;
+	/*
+	 * simple: point constant parameters only depending on atom i to
+	 *         their right values
+	 */
 
-				/* 2 body stuff */
+	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->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->ci2di2=exchange->ci2/exchange->di2;
 
-			/* 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);
+	return 0;
+}
+	
+/* tersoff 2 body part */
+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 f_r,df_r;
+	double f_c,df_c;
+	int num;
+	double s_r;
+	double arg;
+
+	params=moldyn->pot2b_params;
+	num=aj->bnum;
+	exchange=&(params->exchange);
+
+	/* clear 3bp and 2bp post run */
+	exchange->run3bp=0;
+	exchange->run2bp_post=0;
+
+	/* reset S > r > R mark */
+	exchange->d_ij_between_rs=0;
+	
+	/*
+	 * calc of 2bp contribution of V_ij and dV_ij/ji
+	 *
+	 * for Vij and dV_ij we need:
+	 * - f_c_ij, df_c_ij
+	 * - f_r_ij, df_r_ij
+	 *
+	 * for dV_ji we need:
+	 * - f_c_ji = f_c_ij, df_c_ji = df_c_ij
+	 * - f_r_ji = f_r_ij; df_r_ji = df_r_ij
+	 *
+	 */
 
-			/* 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) */
+	/* 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];
+		exchange->chi=1.0;
+	}
+	else {
+		S=params->Smixed;
+		R=params->Rmixed;
+		A=params->Amixed;
+		B=params->Bmixed;
+		lambda=params->lambda_m;
+		mu=params->mu_m;
+		params->exchange.chi=params->chi;
+	}
 
-			} while(list_next(thisk)!=L_NO_NEXT_ELEMENT);
+	/* if d_ij > S => no force & potential energy contribution */
+	if(d_ij>S)
+		return 0;
+
+	/* 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->betajnj=exchange->betaini;
+		exchange->cj2=exchange->ci2;
+		exchange->dj2=exchange->di2;
+		exchange->cj2dj2=exchange->ci2di2;
+	}
+	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->cj2dj2=exchange->cj2/exchange->dj2;
+	}
 
-			/* direct neighbours of btom cell */
-			for(k=1;k<ck;k++) {
-				thisk=&(neighbourk[k]);
-				list_reset(thisk);
-				if(thisk->start!=NULL) {
+	/* f_r_ij = f_r_ji, df_r_ij = df_r_ji */
+	f_r=A*exp(-lambda*d_ij);
+	df_r=lambda*f_r/d_ij;
+
+	/* f_a, df_a calc (again, same for ij and ji) | save for later use! */
+	exchange->f_a=-B*exp(-mu*d_ij);
+	exchange->df_a=-mu*exchange->f_a/d_ij;
+
+	/* f_c, df_c calc (again, same for ij and ji) */
+	if(d_ij<R) {
+		/* f_c = 1, df_c = 0 */
+		f_c=1.0;
+		df_c=0.0;
+		/* two body contribution (ij, ji) */
+		v3_scale(&force,&dist_ij,-df_r);
+	}
+	else {
+		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));
+		/* two body contribution (ij, ji) */
+		v3_scale(&force,&dist_ij,-df_c*f_r-df_r*f_c);
+		/* tell 3bp that S > r > R */
+		exchange->d_ij_between_rs=1;
+	}
 
-				do {
-					ktom=thisk->current->data;
-					if(ktom==&(atom[i]))
-						continue;
+	/* add forces of 2bp (ij, ji) contribution
+	 * dVij = dVji and we sum up both: no 1/2) */
+	v3_add(&(ai->f),&(ai->f),&force);
 
-				/* 3 body stuff (2) */
+	/* energy 2bp contribution (ij, ji) is 0.5 f_r f_c ... */
+	moldyn->energy+=(0.5*f_r*f_c);
 
-				} while(list_next(thisk)!=L_NO_NEXT_ELEMENT);
+	/* save for use in 3bp */
+	exchange->f_c=f_c;
+	exchange->df_c=df_c;
 
-				}
-			}
+	/* enable the run of 3bp function and 2bp post processing */
+	exchange->run3bp=1;
+	exchange->run2bp_post=1;
 
-			/* indirect neighbours of btom cell */
-			for(k=ck;k<27;k++) {
-				thisk=&(neighbourk[k]);
-				list_reset(thisk);
-				if(thisk->start!=NULL) {
+	/* reset 3bp sums */
+	exchange->zeta_ij=0.0;
+	exchange->zeta_ji=0.0;
+	v3_zero(&(exchange->dzeta_ij));
+	v3_zero(&(exchange->dzeta_ji));
 
-				do {
-					ktom=thisk->current->data;
-					if(ktom==&(atom[i]))
-						continue;
+	return 0;
+}
 
-				/* 3 body stuff (3) */
+/* tersoff 2 body post part */
 
-				} while(list_next(thisk)!=L_NO_NEXT_ELEMENT);
+int tersoff_mult_post_2bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc) {
 
-				}
-			}
+	/*
+	 * here we have to allow for the 3bp sums
+	 *
+	 * that is:
+	 * - zeta_ij, dzeta_ij
+	 * - zeta_ji, dzeta_ji
+	 *
+	 * to compute the 3bp contribution to:
+	 * - Vij, dVij
+	 * - dVji
+	 *
+	 */
 
+	t_tersoff_mult_params *params;
+	t_tersoff_exchange *exchange;
+
+	t_3dvec force,temp;
+	t_3dvec *dist_ij;
+	double b,db,tmp;
+	double f_c,df_c,f_a,df_a;
+	double chi,ni,betaini,nj,betajnj;
+	double zeta;
+
+	params=moldyn->pot2b_params;
+	exchange=&(params->exchange);
+
+	/* we do not run if f_c_ij was detected to be 0! */
+	if(!(exchange->run2bp_post))
+		return 0;
+
+	f_c=exchange->f_c;
+	df_c=exchange->df_c;
+	f_a=exchange->f_a;
+	df_a=exchange->df_a;
+	betaini=exchange->betaini;
+	betajnj=exchange->betajnj;
+	ni=*(exchange->n_i);
+	nj=*(exchange->n_j);
+	chi=exchange->chi;
+	dist_ij=&(exchange->dist_ij);
+	
+	/* Vij and dVij */
+	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);
+	}
+	else {
+		tmp=betaini*pow(zeta,ni-1.0);		/* beta^n * zeta^n-1 */
+		b=(1+zeta*tmp);				/* 1 + beta^n zeta^n */
+		db=chi*pow(b,-1.0/(2*ni)-1);		/* x(...)^(-1/2n - 1) */
+		b=db*b;					/* b_ij */
+		db*=-0.5*tmp;				/* db_ij */
+		v3_scale(&force,&(exchange->dzeta_ij),f_a*db);
+		v3_scale(&temp,dist_ij,df_a*b);
+		v3_add(&force,&force,&temp);
+		v3_scale(&force,&force,f_c);
+	}
+	v3_scale(&temp,dist_ij,df_c*b*f_a);
+	v3_add(&force,&force,&temp);
+	v3_scale(&force,&force,-0.5);
+
+	/* add force */
+	v3_add(&(ai->f),&(ai->f),&force);
+
+	/* add energy of 3bp sum */
+	moldyn->energy+=(0.5*f_c*b*f_a);
+
+	/* dVji */
+	zeta=exchange->zeta_ji;
+	if(zeta==0.0) {
+		moldyn->debug++;
+		b=chi;
+		v3_scale(&force,dist_ij,df_a*b*f_c);
+	}
+	else {
+		tmp=betajnj*pow(zeta,nj-1.0);		/* beta^n * zeta^n-1 */
+		b=(1+zeta*tmp);				/* 1 + beta^n zeta^n */
+		db=chi*pow(b,-1.0/(2*nj)-1);		/* x(...)^(-1/2n - 1) */
+		b=db*b;					/* b_ij */
+		db*=-0.5*tmp;				/* db_ij */
+		v3_scale(&force,&(exchange->dzeta_ji),f_a*db);
+		v3_scale(&temp,dist_ij,df_a*b);
+		v3_add(&force,&force,&temp);
+		v3_scale(&force,&force,f_c);
+	}
+	v3_scale(&temp,dist_ij,df_c*b*f_a);
+	v3_add(&force,&force,&temp);
+	v3_scale(&force,&force,-0.5);
 
-			} while(list_next(this)!=L_NO_NEXT_ELEMENT);
+	/* add force */
+	v3_sub(&(ai->f),&(ai->f),&force);
 
-			}
-		}
+	return 0;
+}
 
-		/*
-		 * indirect neighbour cells of atom i
-		 */
-		for(j=c;j<27;j++) {
-			this=&(neighbour[j]);
-			list_reset(this);
-			if(this->start!=NULL) {
+/* tersoff 3 body part */
+
+int tersoff_mult_3bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,t_atom *ak,u8 bc) {
+
+	t_tersoff_mult_params *params;
+	t_tersoff_exchange *exchange;
+	t_3dvec dist_ij,dist_ik,dist_jk;
+	t_3dvec temp1,temp2;
+	t_3dvec *dzeta;
+	double R,S,s_r;
+	double B,mu;
+	double d_ij,d_ik,d_jk;
+	double rr,dd;
+	double f_c,df_c;
+	double f_c_ik,df_c_ik,arg;
+	double f_c_jk;
+	double n,c,d,h;
+	double c2,d2,c2d2;
+	double cos_theta,d_costheta1,d_costheta2;
+	double h_cos,d2_h_cos2;
+	double frac,g,zeta,chi;
+	double tmp;
+	int num;
+
+	params=moldyn->pot3b_params;
+	exchange=&(params->exchange);
+
+	if(!(exchange->run3bp))
+		return 0;
 
-			do {
-				btom=this->current->data;
+	/*
+	 * calc of 3bp contribution of V_ij and dV_ij/ji/jk &
+	 * 2bp contribution of dV_jk
+	 *
+	 * for Vij and dV_ij we still need:
+	 * - b_ij, db_ij (zeta_ij)
+	 *   - f_c_ik, df_c_ik, constants_i, cos_theta_ijk, d_costheta_ijk
+	 *
+	 * for dV_ji we still need:
+	 * - b_ji, db_ji (zeta_ji)
+	 *   - f_c_jk, d_c_jk, constants_j, cos_theta_jik, d_costheta_jik
+	 *
+	 * for dV_jk we need:
+	 * - f_c_jk
+	 * - f_a_jk
+	 * - db_jk (zeta_jk)
+	 *   - f_c_ji, df_c_ji, constants_j, cos_theta_jki, d_costheta_jki
+	 *
+	 */
 
-				/* 2 body stuff */
+	/*
+	 * get exchange data 
+	 */
 
+	/* dist_ij, d_ij - this is < S_ij ! */
+	dist_ij=exchange->dist_ij;
+	d_ij=exchange->d_ij;
 
-			/* 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);
+	/* f_c_ij, df_c_ij (same for ji) */
+	f_c=exchange->f_c;
+	df_c=exchange->df_c;
 
-			/* 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) */
+	/*
+	 * calculate unknown values now ...
+	 */
 
-			} while(list_next(thisk)!=L_NO_NEXT_ELEMENT);
+	/* V_ij and dV_ij stuff (in b_ij there is f_c_ik) */
 
-			/* direct neighbours of btom cell */
-			for(k=1;k<ck;k++) {
-				thisk=&(neighbourk[k]);
-				list_reset(thisk);
-				if(thisk->start!=NULL) {
+	/* 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);
 
-				do {
-					ktom=thisk->current->data;
-					if(ktom==&(atom[i]))
-						continue;
+	/* ik constants */
+	num=ai->bnum;
+	if(num==ak->bnum) {
+		R=params->R[num];
+		S=params->S[num];
+	}
+	else {
+		R=params->Rmixed;
+		S=params->Smixed;
+	}
 
-				/* 3 body stuff (2) */
+	/* zeta_ij/dzeta_ij contribution only for d_ik < S */
+	if(d_ik<S) {
+
+		/* get constants_i from exchange data */
+		n=*(exchange->n_i);
+		c=*(exchange->c_i);
+		d=*(exchange->d_i);
+		h=*(exchange->h_i);
+		c2=exchange->ci2;
+		d2=exchange->di2;
+		c2d2=exchange->ci2di2;
+
+		/* cosine of theta_ijk by scalaproduct */
+		rr=v3_scalar_product(&dist_ij,&dist_ik);
+		dd=d_ij*d_ik;
+		cos_theta=rr/dd;
+
+		/* d_costheta */
+		tmp=1.0/dd;
+		d_costheta1=cos_theta/(d_ij*d_ij)-tmp;
+		d_costheta2=cos_theta/(d_ik*d_ik)-tmp;
+
+		/* some usefull values */
+		h_cos=(h-cos_theta);
+		d2_h_cos2=d2+(h_cos*h_cos);
+		frac=c2/(d2_h_cos2);
+
+		/* g(cos_theta) */
+		g=1.0+c2d2-frac;
+
+		/* d_costheta_ij and dg(cos_theta) - needed in any case! */
+		v3_scale(&temp1,&dist_ij,d_costheta1);
+		v3_scale(&temp2,&dist_ik,d_costheta2);
+		v3_add(&temp1,&temp1,&temp2);
+		v3_scale(&temp1,&temp1,-2.0*frac*h_cos/d2_h_cos2); /* dg */
+
+		/* f_c_ik & df_c_ik + {d,}zeta contribution */
+		dzeta=&(exchange->dzeta_ij);
+		if(d_ik<R) {
+			/* {d,}f_c_ik */
+			// => f_c_ik=1.0;
+			// => df_c_ik=0.0; of course we do not set this!
+
+			/* zeta_ij */
+			exchange->zeta_ij+=g;
+
+			/* dzeta_ij */
+			v3_add(dzeta,dzeta,&temp1);
+		}
+		else {
+			/* {d,}f_c_ik */
+			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));
+
+			/* zeta_ij */
+			exchange->zeta_ij+=f_c_ik*g;
+
+			/* dzeta_ij */
+			v3_scale(&temp1,&temp1,f_c_ik);
+			v3_scale(&temp2,&dist_ik,g*df_c_ik);
+			v3_add(&temp1,&temp1,&temp2);
+			v3_add(dzeta,dzeta,&temp1);
+		}
+	}
 
-				} while(list_next(thisk)!=L_NO_NEXT_ELEMENT);
+	/* dV_ji stuff (in b_ji there is f_c_jk) + dV_jk stuff! */
+
+	/* 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);
+
+	/* 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];
+		chi=1.0;
+	}
+	else {
+		R=params->Rmixed;
+		S=params->Smixed;
+		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) {
+
+		/* constants_j from exchange data */
+		n=*(exchange->n_j);
+		c=*(exchange->c_j);
+		d=*(exchange->d_j);
+		h=*(exchange->h_j);
+		c2=exchange->cj2;
+		d2=exchange->dj2;
+		c2d2=exchange->cj2dj2;
+
+		/* cosine of theta_jik by scalaproduct */
+		rr=v3_scalar_product(&dist_ij,&dist_jk); /* times -1 */
+		dd=d_ij*d_jk;
+		cos_theta=rr/dd;
+
+		/* d_costheta */
+		d_costheta1=1.0/(d_jk*d_ij);
+		d_costheta2=cos_theta/(d_ij*d_ij); /* in fact -cos(), but ^ */
+
+		/* some usefull values */
+		h_cos=(h-cos_theta);
+		d2_h_cos2=d2+(h_cos*h_cos);
+		frac=c2/(d2_h_cos2);
+
+		/* g(cos_theta) */
+		g=1.0+c2d2-frac;
+
+		/* d_costheta_ij 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_scale(&temp1,&temp1,-2.0*frac*h_cos/d2_h_cos2); /* dg */
+
+		/* f_c_jk + {d,}zeta contribution (df_c_jk = 0) */
+		dzeta=&(exchange->dzeta_ji);
+		if(d_jk<R) {
+			/* f_c_jk */
+			f_c_jk=1.0;
+
+			/* zeta_ji */
+			exchange->zeta_ji+=g;
+
+			/* dzeta_ji */
+			v3_add(dzeta,dzeta,&temp1);
+		}
+		else {
+			/* f_c_jk */
+			s_r=S-R;
+			arg=M_PI*(d_jk-R)/s_r;
+			f_c_jk=0.5+0.5*cos(arg);
+
+			/* zeta_ji */
+			exchange->zeta_ji+=f_c_jk*g;
+
+			/* dzeta_ij */
+			v3_scale(&temp1,&temp1,f_c_jk);
+			v3_add(dzeta,dzeta,&temp1);
+		}
 
-			/* indirect neighbours of btom cell */
-			for(k=ck;k<27;k++) {
-				thisk=&(neighbourk[k]);
-				list_reset(thisk);
-				if(thisk->start!=NULL) {
+		/* dV_jk stuff | add force contribution on atom i immediately */
+		if(exchange->d_ij_between_rs) {
+			zeta=f_c*g;
+			v3_scale(&temp1,&temp1,f_c);
+			v3_scale(&temp2,&dist_ij,df_c);
+			v3_add(&temp1,&temp1,&temp2);
+		}
+		else {
+			zeta=g;
+			// dzeta_jk is simply dg, which is temp1
+		}
+		/* betajnj * zeta_jk ^ nj-1 */
+		tmp=exchange->betajnj*pow(zeta,(n-1.0));
+		tmp=-chi/2.0*pow(1+tmp*zeta,-1.0/(2.0*n)-1)*tmp;
+		v3_scale(&temp1,&temp1,tmp*B*exp(-mu*d_jk)*f_c_jk*0.5);
+		v3_add(&(ai->f),&(ai->f),&temp1); /* -1 skipped in f_a calc ^ */
+		                                  /* scaled with 0.5 ^ */
+	}
 
-				do {
-					ktom=thisk->current->data;
-					if(ktom==&(atom[i]))
-						continue;
+	return 0;
+}
 
-				/* 3 body stuff (3) */
 
-				} while(list_next(thisk)!=L_NO_NEXT_ELEMENT);
+/*
+ * debugging / critical check functions
+ */
 
-				}
-			}
+int moldyn_bc_check(t_moldyn *moldyn) {
 
+	t_atom *atom;
+	t_3dvec *dim;
+	int i;
 
-			} while(list_next(this)!=L_NO_NEXT_ELEMENT);
+	atom=moldyn->atom;
+	dim=&(moldyn->dim);
 
-			}
-		}
-		
+	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*1e10,dim->x/2*1e10);
+		if(atom[i].r.y>=dim->y/2||-atom[i].r.y>dim->y/2)
+			printf("FATAL: atom %d: y: %.20f (%.20f)\n",
+			       i,atom[i].r.y*1e10,dim->y/2*1e10);
+		if(atom[i].r.z>=dim->z/2||-atom[i].r.z>dim->z/2)
+			printf("FATAL: atom %d: z: %.20f (%.20f)\n",
+			       i,atom[i].r.z*1e10,dim->z/2*1e10);
 	}
 
-	moldyn->energy=0.5*u;
-
 	return 0;
 }