X-Git-Url: https://www.hackdaworld.org/gitweb/?a=blobdiff_plain;f=moldyn.c;h=f6c3c81d4bbf95b5787474dbd03e18bea90e183e;hb=cb177e7c208a85b45d77b09fcada23b62d0248b5;hp=08901c783452a006b638787351b735e20e2a56c3;hpb=3961d57b84198e336085fd79263fec40837066a0;p=physik%2Fposic.git

diff --git a/moldyn.c b/moldyn.c
index 08901c7..f6c3c81 100644
--- a/moldyn.c
+++ b/moldyn.c
@@ -5,44 +5,360 @@
  *
  */
 
-#include "moldyn.h"
-
+#define _GNU_SOURCE
 #include <stdio.h>
 #include <stdlib.h>
+#include <string.h>
+#include <sys/types.h>
+#include <sys/stat.h>
+#include <fcntl.h>
+#include <unistd.h>
 #include <math.h>
 
-#include "math/math.h"
-#include "init/init.h"
-#include "random/random.h"
-#include "visual/visual.h"
+#include "moldyn.h"
+#include "report/report.h"
 
+int moldyn_init(t_moldyn *moldyn,int argc,char **argv) {
 
-int create_lattice(unsigned char type,int element,double mass,double lc,
-                   int a,int b,int c,t_atom **atom) {
+	printf("[moldyn] init\n");
 
-	int count;
+	memset(moldyn,0,sizeof(t_moldyn));
+
+	rand_init(&(moldyn->random),NULL,1);
+	moldyn->random.status|=RAND_STAT_VERBOSE;
+
+	return 0;
+}
+
+int moldyn_shutdown(t_moldyn *moldyn) {
+
+	printf("[moldyn] shutdown\n");
+
+	moldyn_log_shutdown(moldyn);
+	link_cell_shutdown(moldyn);
+	rand_close(&(moldyn->random));
+	free(moldyn->atom);
+
+	return 0;
+}
+
+int set_int_alg(t_moldyn *moldyn,u8 algo) {
+
+	printf("[moldyn] integration algorithm: ");
+
+	switch(algo) {
+		case MOLDYN_INTEGRATE_VERLET:
+			moldyn->integrate=velocity_verlet;
+			printf("velocity verlet\n");
+			break;
+		default:
+			printf("unknown integration algorithm: %02x\n",algo);
+			printf("unknown\n");
+			return -1;
+	}
+
+	return 0;
+}
+
+int set_cutoff(t_moldyn *moldyn,double cutoff) {
+
+	moldyn->cutoff=cutoff;
+
+	printf("[moldyn] cutoff [A]: %f\n",moldyn->cutoff);
+
+	return 0;
+}
+
+int set_temperature(t_moldyn *moldyn,double t_ref) {
+
+	moldyn->t_ref=t_ref;
+
+	printf("[moldyn] temperature [K]: %f\n",moldyn->t_ref);
+
+	return 0;
+}
+
+int set_pressure(t_moldyn *moldyn,double p_ref) {
+
+	moldyn->p_ref=p_ref;
+
+	printf("[moldyn] pressure [atm]: %f\n",moldyn->p_ref/ATM);
+
+	return 0;
+}
+
+int set_pt_scale(t_moldyn *moldyn,u8 ptype,double ptc,u8 ttype,double ttc) {
+
+	moldyn->pt_scale=(ptype|ttype);
+	moldyn->t_tc=ttc;
+	moldyn->p_tc=ptc;
+
+	printf("[moldyn] p/t scaling:\n");
+
+	printf("  p: %s",ptype?"yes":"no ");
+	if(ptype)
+		printf(" | type: %02x | factor: %f",ptype,ptc);
+	printf("\n");
+
+	printf("  t: %s",ttype?"yes":"no ");
+	if(ttype)
+		printf(" | type: %02x | factor: %f",ttype,ttc);
+	printf("\n");
+
+	return 0;
+}
+
+int set_dim(t_moldyn *moldyn,double x,double y,double z,u8 visualize) {
+
+	moldyn->dim.x=x;
+	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;
+	}
+
+	moldyn->dv=0.000001*moldyn->volume;
+
+	printf("[moldyn] dimensions in A and A^3 respectively:\n");
+	printf("  x: %f\n",moldyn->dim.x);
+	printf("  y: %f\n",moldyn->dim.y);
+	printf("  z: %f\n",moldyn->dim.z);
+	printf("  volume: %f\n",moldyn->volume);
+	printf("  visualize simulation box: %s\n",visualize?"yes":"no");
+	printf("  delta volume (pressure calc): %f\n",moldyn->dv);
+
+	return 0;
+}
+
+int set_nn_dist(t_moldyn *moldyn,double dist) {
+
+	moldyn->nnd=dist;
+
+	return 0;
+}
+
+int set_pbc(t_moldyn *moldyn,u8 x,u8 y,u8 z) {
+
+	printf("[moldyn] periodic boundary conditions:\n");
+
+	if(x)
+		moldyn->status|=MOLDYN_STAT_PBX;
+
+	if(y)
+		moldyn->status|=MOLDYN_STAT_PBY;
+
+	if(z)
+		moldyn->status|=MOLDYN_STAT_PBZ;
+
+	printf("  x: %s\n",x?"yes":"no");
+	printf("  y: %s\n",y?"yes":"no");
+	printf("  z: %s\n",z?"yes":"no");
+
+	return 0;
+}
+
+int set_potential1b(t_moldyn *moldyn,pf_func1b func,void *params) {
+
+	moldyn->func1b=func;
+	moldyn->pot1b_params=params;
+
+	return 0;
+}
+
+int set_potential2b(t_moldyn *moldyn,pf_func2b func,void *params) {
+
+	moldyn->func2b=func;
+	moldyn->pot2b_params=params;
+
+	return 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 set_potential3b(t_moldyn *moldyn,pf_func3b func,void *params) {
+
+	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_report(t_moldyn *moldyn,char *author,char *title) {
+
+	strncpy(moldyn->rauthor,author,63);
+	strncpy(moldyn->rtitle,title,63);
+
+	return 0;
+}
+	
+int moldyn_set_log(t_moldyn *moldyn,u8 type,int timer) {
+
+	char filename[128];
+	int ret;
+
+	printf("[moldyn] set log: ");
+
+	switch(type) {
+		case LOG_TOTAL_ENERGY:
+			moldyn->ewrite=timer;
+			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");
+			printf("total energy (%d)\n",timer);
+			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");
+			printf("total momentum (%d)\n",timer);
+			break;
+		case SAVE_STEP:
+			moldyn->swrite=timer;
+			printf("save file (%d)\n",timer);
+			break;
+		case VISUAL_STEP:
+			moldyn->vwrite=timer;
+			ret=visual_init(&(moldyn->vis),moldyn->vlsdir);
+			if(ret<0) {
+				printf("[moldyn] visual init failure\n");
+				return ret;
+			}
+			printf("visual file (%d)\n",timer);
+			break;
+		case CREATE_REPORT:
+			snprintf(filename,127,"%s/report.tex",moldyn->vlsdir);
+			moldyn->rfd=open(filename,
+			                 O_WRONLY|O_CREAT|O_EXCL,
+			                 S_IRUSR|S_IWUSR);
+			if(moldyn->rfd<0) {
+				perror("[moldyn] report fd open");	
+				return moldyn->rfd;
+			}
+			snprintf(filename,127,"%s/plot.scr",moldyn->vlsdir);
+			moldyn->pfd=open(filename,
+			                 O_WRONLY|O_CREAT|O_EXCL,
+			                 S_IRUSR|S_IWUSR);
+			if(moldyn->pfd<0) {
+				perror("[moldyn] plot fd open");
+				return moldyn->pfd;
+			}
+			dprintf(moldyn->rfd,report_start,
+			        moldyn->rauthor,moldyn->rtitle);
+			dprintf(moldyn->pfd,plot_script);
+			close(moldyn->pfd);
+			break;
+		default:
+			printf("unknown log type: %02x\n",type);
+			return -1;
+	}
+
+	return 0;
+}
+
+int moldyn_log_shutdown(t_moldyn *moldyn) {
+
+	char sc[256];
+
+	printf("[moldyn] log shutdown\n");
+	if(moldyn->efd) close(moldyn->efd);
+	if(moldyn->mfd) close(moldyn->mfd);
+	if(moldyn->rfd) {
+		dprintf(moldyn->rfd,report_end);
+		close(moldyn->rfd);
+		snprintf(sc,255,"cd %s && gnuplot plot.scr",moldyn->vlsdir);
+		system(sc);
+		snprintf(sc,255,"cd %s && pdflatex report",moldyn->vlsdir);
+		system(sc);
+		snprintf(sc,255,"cd %s && pdflatex report",moldyn->vlsdir);
+		system(sc);
+		snprintf(sc,255,"cd %s && dvipdf report",moldyn->vlsdir);
+		system(sc);
+	}
+	if(&(moldyn->vis)) visual_tini(&(moldyn->vis));
+
+	return 0;
+}
+
+/*
+ * creating lattice functions
+ */
+
+int create_lattice(t_moldyn *moldyn,u8 type,double lc,int element,double mass,
+                   u8 attr,u8 brand,int a,int b,int c) {
+
+	int new,count;
 	int ret;
 	t_3dvec origin;
+	void *ptr;
+	t_atom *atom;
 
-	count=a*b*c;
+	new=a*b*c;
+	count=moldyn->count;
 
-	if(type==FCC) count*=4;
-	if(type==DIAMOND) count*=8;
+	/* how many atoms do we expect */
+	if(type==CUBIC) new*=1;
+	if(type==FCC) new*=4;
+	if(type==DIAMOND) new*=8;
 
-	*atom=malloc(count*sizeof(t_atom));
-	if(*atom==NULL) {
-		perror("malloc (atoms)");
+	/* allocate space for atoms */
+	ptr=realloc(moldyn->atom,(count+new)*sizeof(t_atom));
+	if(!ptr) {
+		perror("[moldyn] realloc (create lattice)");
 		return -1;
 	}
+	moldyn->atom=ptr;
+	atom=&(moldyn->atom[count]);
 
-	v3_zero(&origin);
+	/* no atoms on the boundaries (only reason: it looks better!) */
+	origin.x=0.5*lc;
+	origin.y=0.5*lc;
+	origin.z=0.5*lc;
 
 	switch(type) {
+		case CUBIC:
+			set_nn_dist(moldyn,lc);
+			ret=cubic_init(a,b,c,lc,atom,&origin);
+			break;
 		case FCC:
-			ret=fcc_init(a,b,c,lc,*atom,&origin);
+			v3_scale(&origin,&origin,0.5);
+			set_nn_dist(moldyn,0.5*sqrt(2.0)*lc);
+			ret=fcc_init(a,b,c,lc,atom,&origin);
 			break;
 		case DIAMOND:
-			ret=diamond_init(a,b,c,lc,*atom,&origin);
+			v3_scale(&origin,&origin,0.25);
+			set_nn_dist(moldyn,0.25*sqrt(3.0)*lc);
+			ret=diamond_init(a,b,c,lc,atom,&origin);
 			break;
 		default:
 			printf("unknown lattice type (%02x)\n",type);
@@ -50,30 +366,178 @@ int create_lattice(unsigned char type,int element,double mass,double lc,
 	}
 
 	/* debug */
-	if(ret!=count) {
-		printf("ok, there is something wrong ...\n");
-		printf("calculated -> %d atoms\n",count);
-		printf("created -> %d atoms\n",ret);
+	if(ret!=new) {
+		printf("[moldyn] creating lattice failed\n");
+		printf("  amount of atoms\n");
+		printf("  - expected: %d\n",new);
+		printf("  - created: %d\n",ret);
 		return -1;
 	}
 
-	while(count) {
-		(*atom)[count-1].element=element;
-		(*atom)[count-1].mass=mass;
-		count-=1;
+	moldyn->count+=new;
+	printf("[moldyn] created lattice with %d atoms\n",new);
+
+	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 destroy_lattice(t_atom *atom) {
+/* cubic init */
+int cubic_init(int a,int b,int c,double lc,t_atom *atom,t_3dvec *origin) {
+
+	int count;
+	t_3dvec r;
+	int i,j,k;
+	t_3dvec o;
+
+	count=0;
+	if(origin)
+		v3_copy(&o,origin);
+	else
+		v3_zero(&o);
+
+	r.x=o.x;
+	for(i=0;i<a;i++) {
+		r.y=o.y;
+		for(j=0;j<b;j++) {
+			r.z=o.z;
+			for(k=0;k<c;k++) {
+				v3_copy(&(atom[count].r),&r);
+				count+=1;
+				r.z+=lc;
+			}
+			r.y+=lc;
+		}
+		r.x+=lc;
+	}
+
+	for(i=0;i<count;i++) {
+		atom[i].r.x-=(a*lc)/2.0;
+		atom[i].r.y-=(b*lc)/2.0;
+		atom[i].r.z-=(c*lc)/2.0;
+	}
+
+	return count;
+}
+
+/* fcc lattice init */
+int fcc_init(int a,int b,int c,double lc,t_atom *atom,t_3dvec *origin) {
+
+	int count;
+	int i,j,k,l;
+	t_3dvec o,r,n;
+	t_3dvec basis[3];
+
+	count=0;
+	if(origin)
+		v3_copy(&o,origin);
+	else
+		v3_zero(&o);
+
+	/* construct the basis */
+	memset(basis,0,3*sizeof(t_3dvec));
+	basis[0].x=0.5*lc;
+	basis[0].y=0.5*lc;
+	basis[1].x=0.5*lc;
+	basis[1].z=0.5*lc;
+	basis[2].y=0.5*lc;
+	basis[2].z=0.5*lc;
+
+	/* fill up the room */
+	r.x=o.x;
+	for(i=0;i<a;i++) {
+		r.y=o.y;
+		for(j=0;j<b;j++) {
+			r.z=o.z;
+			for(k=0;k<c;k++) {
+				/* first atom */
+				v3_copy(&(atom[count].r),&r);
+				count+=1;
+				r.z+=lc;
+				/* the three face centered atoms */
+				for(l=0;l<3;l++) {
+					v3_add(&n,&r,&basis[l]);
+					v3_copy(&(atom[count].r),&n);
+					count+=1;
+				}
+			}
+			r.y+=lc;
+		}
+		r.x+=lc;
+	}
+				
+	/* coordinate transformation */
+	for(i=0;i<count;i++) {
+		atom[i].r.x-=(a*lc)/2.0;
+		atom[i].r.y-=(b*lc)/2.0;
+		atom[i].r.z-=(c*lc)/2.0;
+	}
+
+	return count;
+}
+
+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;
+	void *ptr;
+	int count;
+	
+	atom=moldyn->atom;
+	count=(moldyn->count)++;
+
+	ptr=realloc(atom,(count+1)*sizeof(t_atom));
+	if(!ptr) {
+		perror("[moldyn] realloc (add atom)");
+		return -1;
+	}
+	moldyn->atom=ptr;
+
+	atom=moldyn->atom;
+	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;
+}
+
+int destroy_atoms(t_moldyn *moldyn) {
 
-	if(atom) free(atom);
+	if(moldyn->atom) free(moldyn->atom);
 
 	return 0;
 }
 
-int thermal_init(t_atom *atom,t_random *random,int count,double t) {
+int thermal_init(t_moldyn *moldyn,u8 equi_init) {
 
 	/*
 	 * - gaussian distribution of velocities
@@ -84,11 +548,18 @@ int thermal_init(t_atom *atom,t_random *random,int count,double t) {
 	int i;
 	double v,sigma;
 	t_3dvec p_total,delta;
+	t_atom *atom;
+	t_random *random;
+
+	atom=moldyn->atom;
+	random=&(moldyn->random);
+
+	printf("[moldyn] thermal init (equi init: %s)\n",equi_init?"yes":"no");
 
 	/* gaussian distribution of velocities */
 	v3_zero(&p_total);
-	for(i=0;i<count;i++) {
-		sigma=sqrt(2.0*K_BOLTZMANN*t/atom[i].mass);
+	for(i=0;i<moldyn->count;i++) {
+		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;
@@ -104,104 +575,668 @@ int thermal_init(t_atom *atom,t_random *random,int count,double t) {
 	}
 
 	/* zero total momentum */
-	v3_scale(&p_total,&p_total,1.0/count);
-	for(i=0;i<count;i++) {
+	v3_scale(&p_total,&p_total,1.0/moldyn->count);
+	for(i=0;i<moldyn->count;i++) {
 		v3_scale(&delta,&p_total,1.0/atom[i].mass);
 		v3_sub(&(atom[i].v),&(atom[i].v),&delta);
 	}
 
 	/* velocity scaling */
-	scale_velocity(atom,count,t);
+	scale_velocity(moldyn,equi_init);
 
 	return 0;
 }
 
-int scale_velocity(t_atom *atom,int count,double t) {
+double temperature_calc(t_moldyn *moldyn) {
+
+	/* assume up to date kinetic energy, which is 3/2 N k_B T */
+
+	moldyn->t=(2.0*moldyn->ekin)/(3.0*K_BOLTZMANN*moldyn->count);
+
+	return moldyn->t;
+}
+
+double get_temperature(t_moldyn *moldyn) {
+
+	return moldyn->t;
+}
+
+int scale_velocity(t_moldyn *moldyn,u8 equi_init) {
 
 	int i;
-	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<count;i++)
-		e+=0.5*atom[i].mass*v3_absolute_square(&(atom[i].v));
-	c=sqrt((2.0*e)/(3.0*count*K_BOLTZMANN*t));
-	for(i=0;i<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+=atom[i].mass*v3_absolute_square(&(atom[i].v));
+			count+=1;
+		}
+	}
+	e*=0.5;
+	if(count!=0) moldyn->t=e/(1.5*count*K_BOLTZMANN);
+	else return 0;	/* no atoms involved in scaling! */
+	
+	/* (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 ideal_gas_law_pressure(t_moldyn *moldyn) {
+
+	double p;
+
+	p=moldyn->count*moldyn->t*K_BOLTZMANN/moldyn->volume;
+
+	return p;
+}
+
+double pressure_calc(t_moldyn *moldyn) {
 
 	int i;
-	double e;
+	double v;
+	t_virial *virial;
 
-	e=0.0;
+	/*
+	 * P = 1/(3V) sum_i ( p_i^2 / 2m + f_i r_i )
+	 *
+	 * virial = f_i r_i
+	 */
 
-	for(i=0;i<count;i++) {
-		e+=0.5*atom[i].mass*v3_absolute_square(&(atom[i].v));
+	v=0.0;
+	for(i=0;i<moldyn->count;i++) {
+		virial=&(moldyn->atom[i].virial);
+		v+=(virial->xx+virial->yy+virial->zz);
+	}
+
+	/* assume up to date kinetic energy */
+	moldyn->p=2.0*moldyn->ekin+v;
+	moldyn->p/=(3.0*moldyn->volume);
+
+	return moldyn->p;
+}	
+
+double thermodynamic_pressure_calc(t_moldyn *moldyn) {
+
+	t_3dvec dim,*tp;
+	double u,p;
+	double scale;
+	t_atom *store;
+
+	tp=&(moldyn->tp);
+	store=malloc(moldyn->count*sizeof(t_atom));
+	if(store==NULL) {
+		printf("[moldyn] allocating store mem failed\n");
+		return -1;
 	}
 
-	return e;
+	/* save unscaled potential energy + atom/dim configuration */
+	u=moldyn->energy;
+	memcpy(store,moldyn->atom,moldyn->count*sizeof(t_atom));
+	dim=moldyn->dim;
+
+	/* derivative with respect to x direction */
+	scale=1.0+moldyn->dv/(moldyn->dim.y*moldyn->dim.z);
+	scale_dim(moldyn,scale,TRUE,0,0);
+	scale_atoms(moldyn,scale,TRUE,0,0);
+	link_cell_shutdown(moldyn);
+	link_cell_init(moldyn,QUIET);
+	potential_force_calc(moldyn);
+	tp->x=(moldyn->energy-u)/moldyn->dv;
+	p=tp->x*tp->x;
+
+	/* restore atomic configuration + dim */
+	memcpy(moldyn->atom,store,moldyn->count*sizeof(t_atom));
+	moldyn->dim=dim;
+
+	/* derivative with respect to y direction */
+	scale=1.0+moldyn->dv/(moldyn->dim.x*moldyn->dim.z);
+	scale_dim(moldyn,scale,0,TRUE,0);
+	scale_atoms(moldyn,scale,0,TRUE,0);
+	link_cell_shutdown(moldyn);
+	link_cell_init(moldyn,QUIET);
+	potential_force_calc(moldyn);
+	tp->y=(moldyn->energy-u)/moldyn->dv;
+	p+=tp->y*tp->y;
+
+	/* restore atomic configuration + dim */
+	memcpy(moldyn->atom,store,moldyn->count*sizeof(t_atom));
+	moldyn->dim=dim;
+
+	/* derivative with respect to z direction */
+	scale=1.0+moldyn->dv/(moldyn->dim.x*moldyn->dim.y);
+	scale_dim(moldyn,scale,0,0,TRUE);
+	scale_atoms(moldyn,scale,0,0,TRUE);
+	link_cell_shutdown(moldyn);
+	link_cell_init(moldyn,QUIET);
+	potential_force_calc(moldyn);
+	tp->z=(moldyn->energy-u)/moldyn->dv;
+	p+=tp->z*tp->z;
+
+	/* restore atomic configuration + dim */
+	memcpy(moldyn->atom,store,moldyn->count*sizeof(t_atom));
+	moldyn->dim=dim;
+
+	printf("dU/dV komp addiert = %f %f %f\n",tp->x,tp->y,tp->z);
+
+	scale=1.0+pow(moldyn->dv/moldyn->volume,ONE_THIRD);
+
+printf("debug: %f %f\n",moldyn->atom[0].r.x,moldyn->dim.x);
+	scale_dim(moldyn,scale,1,1,1);
+	scale_atoms(moldyn,scale,1,1,1);
+	link_cell_shutdown(moldyn);
+	link_cell_init(moldyn,QUIET);
+	potential_force_calc(moldyn);
+printf("debug: %f %f\n",moldyn->atom[0].r.x,moldyn->dim.x);
+
+	printf("dU/dV einfach = %f\n",((moldyn->energy-u)/moldyn->dv)/ATM);
+
+	/* restore atomic configuration + dim */
+	memcpy(moldyn->atom,store,moldyn->count*sizeof(t_atom));
+	moldyn->dim=dim;
+
+	/* restore energy */
+	moldyn->energy=u;
+
+	link_cell_shutdown(moldyn);
+	link_cell_init(moldyn,QUIET);
+
+	return sqrt(p);
 }
 
-double get_e_pot(t_moldyn *moldyn) {
+double get_pressure(t_moldyn *moldyn) {
+
+	return moldyn->p;
 
-	return(moldyn->potential(moldyn));
 }
 
-double get_total_energy(t_moldyn *moldyn) {
+int scale_dim(t_moldyn *moldyn,double scale,u8 x,u8 y,u8 z) {
+
+	t_3dvec *dim;
 
-	double e;
+	dim=&(moldyn->dim);
 
-	e=get_e_kin(moldyn->atom,moldyn->count);
-	e+=get_e_pot(moldyn);
+	if(x) dim->x*=scale;
+	if(y) dim->y*=scale;
+	if(z) dim->z*=scale;
 
-	return e;
+	return 0;
 }
 
-t_3dvec get_total_p(t_atom *atom, int count) {
+int scale_atoms(t_moldyn *moldyn,double scale,u8 x,u8 y,u8 z) {
 
-	t_3dvec p,p_total;
 	int i;
+	t_3dvec *r;
 
-	v3_zero(&p_total);
-	for(i=0;i<count;i++) {
-		v3_scale(&p,&(atom[i].v),atom[i].mass);
-		v3_add(&p_total,&p_total,&p);
+	for(i=0;i<moldyn->count;i++) {
+		r=&(moldyn->atom[i].r);
+		if(x) r->x*=scale;
+		if(y) r->y*=scale;
+		if(z) r->z*=scale;
 	}
 
-	return p_total;
+	return 0;
 }
 
+int scale_volume(t_moldyn *moldyn) {
 
-/*
- *
- * 'integration of newtons equation' - algorithms
- *
- */
-
-/* start the integration */
+	t_3dvec *dim,*vdim;
+	double scale;
+	t_linkcell *lc;
 
-int moldyn_integrate(t_moldyn *moldyn) {
+	vdim=&(moldyn->vis.dim);
+	dim=&(moldyn->dim);
+	lc=&(moldyn->lc);
 
-	int i;
+	/* scaling factor */
+	if(moldyn->pt_scale&P_SCALE_BERENDSEN) {
+		scale=1.0-(moldyn->p_ref-moldyn->p)/moldyn->p_tc;
+		scale=pow(scale,ONE_THIRD);
+	}
+	else {
+		scale=pow(moldyn->p/moldyn->p_ref,ONE_THIRD);
+	}
+moldyn->debug=scale;
 
-	/* calculate initial forces */
-	moldyn->force(moldyn);
+	/* scale the atoms and dimensions */
+	scale_atoms(moldyn,scale,TRUE,TRUE,TRUE);
+	scale_dim(moldyn,scale,TRUE,TRUE,TRUE);
 
-	for(i=0;i<moldyn->time_steps;i++) {
-		/* integration step */
-		moldyn->integrate(moldyn);
+	/* visualize dimensions */
+	if(vdim->x!=0) {
+		vdim->x=dim->x;
+		vdim->y=dim->y;
+		vdim->z=dim->z;
+	}
+
+	/* recalculate scaled volume */
+	moldyn->volume=dim->x*dim->y*dim->z;
+
+	/* adjust/reinit linkcell */
+	if(((int)(dim->x/moldyn->cutoff)!=lc->nx)||
+	   ((int)(dim->y/moldyn->cutoff)!=lc->ny)||
+	   ((int)(dim->z/moldyn->cutoff)!=lc->nx)) {
+		link_cell_shutdown(moldyn);
+		link_cell_init(moldyn,QUIET);
+	} else {
+		lc->x*=scale;
+		lc->y*=scale;
+		lc->z*=scale;
+	}
+
+	return 0;
+
+}
+
+double get_e_kin(t_moldyn *moldyn) {
+
+	int i;
+	t_atom *atom;
+
+	atom=moldyn->atom;
+	moldyn->ekin=0.0;
+
+	for(i=0;i<moldyn->count;i++)
+		moldyn->ekin+=0.5*atom[i].mass*v3_absolute_square(&(atom[i].v));
+
+	return moldyn->ekin;
+}
+
+double update_e_kin(t_moldyn *moldyn) {
+
+	return(get_e_kin(moldyn));
+}
+
+double get_total_energy(t_moldyn *moldyn) {
+
+	return(moldyn->ekin+moldyn->energy);
+}
+
+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<moldyn->count;i++) {
+		v3_scale(&p,&(atom[i].v),atom[i].mass);
+		v3_add(&p_total,&p_total,&p);
+	}
+
+	return p_total;
+}
+
+double estimate_time_step(t_moldyn *moldyn,double nn_dist) {
+
+	double 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;	
+}
+
+/*
+ * numerical tricks
+ */
+
+/* linked list / cell method */
+
+int link_cell_init(t_moldyn *moldyn,u8 vol) {
+
+	t_linkcell *lc;
+	int i;
+
+	lc=&(moldyn->lc);
+
+	/* partitioning the md cell */
+	lc->nx=moldyn->dim.x/moldyn->cutoff;
+	lc->x=moldyn->dim.x/lc->nx;
+	lc->ny=moldyn->dim.y/moldyn->cutoff;
+	lc->y=moldyn->dim.y/lc->ny;
+	lc->nz=moldyn->dim.z/moldyn->cutoff;
+	lc->z=moldyn->dim.z/lc->nz;
+
+	lc->cells=lc->nx*lc->ny*lc->nz;
+	lc->subcell=malloc(lc->cells*sizeof(t_list));
+
+	if(lc->cells<27)
+		printf("[moldyn] FATAL: less then 27 subcells!\n");
+
+	if(vol) printf("[moldyn] initializing linked cells (%d)\n",lc->cells);
+
+	for(i=0;i<lc->cells;i++)
+		list_init_f(&(lc->subcell[i]));
+
+ 	link_cell_update(moldyn);
+	
+	return 0;
+}
+
+int link_cell_update(t_moldyn *moldyn) {
+
+	int count,i,j,k;
+	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;
+
+	x=moldyn->dim.x/2;
+	y=moldyn->dim.y/2;
+	z=moldyn->dim.z/2;
+
+	for(i=0;i<lc->cells;i++)
+		list_destroy_f(&(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_f(&(moldyn->lc.subcell[i+j*nx+k*nx*ny]),
+		                     &(atom[count]));
+	}
+
+	return 0;
+}
+
+int link_cell_neighbour_index(t_moldyn *moldyn,int i,int j,int k,t_list *cell) {
+
+	t_linkcell *lc;
+	int a;
+	int count1,count2;
+	int ci,cj,ck;
+	int nx,ny,nz;
+	int x,y,z;
+	u8 bx,by,bz;
+
+	lc=&(moldyn->lc);
+	nx=lc->nx;
+	ny=lc->ny;
+	nz=lc->nz;
+	count1=1;
+	count2=27;
+	a=nx*ny;
+
+	cell[0]=lc->subcell[i+j*nx+k*a];
+	for(ci=-1;ci<=1;ci++) {
+		bx=0;
+		x=i+ci;
+		if((x<0)||(x>=nx)) {
+			x=(x+nx)%nx;
+			bx=1;
+		}
+		for(cj=-1;cj<=1;cj++) {
+			by=0;
+			y=j+cj;
+			if((y<0)||(y>=ny)) {
+				y=(y+ny)%ny;
+				by=1;
+			}
+			for(ck=-1;ck<=1;ck++) {
+				bz=0;
+				z=k+ck;
+				if((z<0)||(z>=nz)) {
+					z=(z+nz)%nz;
+					bz=1;
+				}
+				if(!(ci|cj|ck)) continue;
+				if(bx|by|bz) {
+					cell[--count2]=lc->subcell[x+y*nx+z*a];
+				}
+				else {
+					cell[count1++]=lc->subcell[x+y*nx+z*a];
+				}
+			}
+		}
+	}
+
+	lc->dnlc=count1;
+
+	return count1;
+}
+
+int link_cell_shutdown(t_moldyn *moldyn) {
+
+	int i;
+	t_linkcell *lc;
+
+	lc=&(moldyn->lc);
+
+	for(i=0;i<lc->nx*lc->ny*lc->nz;i++)
+		list_destroy_f(&(moldyn->lc.subcell[i]));
+
+	free(lc->subcell);
+
+	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->total_sched);
+
+	ptr=realloc(schedule->runs,count*sizeof(int));
+	if(!ptr) {
+		perror("[moldyn] realloc (runs)");
+		return -1;
+	}
+	schedule->runs=ptr;
+	schedule->runs[count-1]=runs;
+
+	ptr=realloc(schedule->tau,count*sizeof(double));
+	if(!ptr) {
+		perror("[moldyn] realloc (tau)");
+		return -1;
+	}
+	schedule->tau=ptr;
+	schedule->tau[count-1]=tau;
+
+	printf("[moldyn] schedule added:\n");
+	printf("  number: %d | runs: %d | tau: %f\n",count-1,runs,tau);
+	                               
+
+	return 0;
+}
+
+int moldyn_set_schedule_hook(t_moldyn *moldyn,set_hook hook,void *hook_params) {
+
+	moldyn->schedule.hook=hook;
+	moldyn->schedule.hook_params=hook_params;
+	
+	return 0;
+}
+
+/*
+ *
+ * 'integration of newtons equation' - algorithms
+ *
+ */
+
+/* start the integration */
+
+int moldyn_integrate(t_moldyn *moldyn) {
+
+	int i;
+	unsigned int e,m,s,v;
+	t_3dvec p;
+	t_moldyn_schedule *sched;
+	t_atom *atom;
+	int fd;
+	char dir[128];
+	double ds;
+	double energy_scale;
+
+	sched=&(moldyn->schedule);
+	atom=moldyn->atom;
+
+	/* initialize linked cell method */
+	link_cell_init(moldyn,VERBOSE);
+
+	/* logging & visualization */
+	e=moldyn->ewrite;
+	m=moldyn->mwrite;
+	s=moldyn->swrite;
+	v=moldyn->vwrite;
+
+	/* sqaure of some variables */
+	moldyn->tau_square=moldyn->tau*moldyn->tau;
+	moldyn->cutoff_square=moldyn->cutoff*moldyn->cutoff;
+
+	/* energy scaling factor */
+	energy_scale=moldyn->count*EV;
+
+	/* calculate initial forces */
+	potential_force_calc(moldyn);
+
+	/* 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;
+
+	/* tell the world */
+	printf("[moldyn] integration start, go get a coffee ...\n");
+
+	/* executing the schedule */
+	for(sched->count=0;sched->count<sched->total_sched;sched->count++) {
+
+		/* setting amount of runs and finite time step size */
+		moldyn->tau=sched->tau[sched->count];
+		moldyn->tau_square=moldyn->tau*moldyn->tau;
+		moldyn->time_steps=sched->runs[sched->count];
+
+	/* integration according to schedule */
+
+	for(i=0;i<moldyn->time_steps;i++) {
+
+		/* integration step */
+		moldyn->integrate(moldyn);
+
+		/* calculate kinetic energy, temperature and pressure */
+		update_e_kin(moldyn);
+		temperature_calc(moldyn);
+		pressure_calc(moldyn);
+		//thermodynamic_pressure_calc(moldyn);
+
+		/* p/t scaling */
+		if(moldyn->pt_scale&(T_SCALE_BERENDSEN|T_SCALE_DIRECT))
+			scale_velocity(moldyn,FALSE);
+		if(moldyn->pt_scale&(P_SCALE_BERENDSEN|P_SCALE_DIRECT))
+			scale_volume(moldyn);
+
+		/* check for log & visualization */
+		if(e) {
+			if(!(i%e))
+				dprintf(moldyn->efd,
+				        "%f %f %f %f\n",
+				        moldyn->time,moldyn->ekin/energy_scale,
+				        moldyn->energy/energy_scale,
+				        get_total_energy(moldyn)/energy_scale);
+		}
+		if(m) {
+			if(!(i%m)) {
+				p=get_total_p(moldyn);
+				dprintf(moldyn->mfd,
+				        "%f %f\n",moldyn->time,v3_norm(&p));
+			}
+		}
+		if(s) {
+			if(!(i%s)) {
+				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));
+					write(fd,moldyn->atom,
+					      moldyn->count*sizeof(t_atom));
+				}
+				close(fd);
+			}	
+		}
+		if(v) {
+			if(!(i%v)) {
+				visual_atoms(&(moldyn->vis),moldyn->time,
+				             moldyn->atom,moldyn->count);
+				printf("\rsched: %d, steps: %d, T: %f, P: %f V: %f",
+				       sched->count,i,
+				       moldyn->t,moldyn->p/ATM,moldyn->volume);
+				fflush(stdout);
+			}
+		}
+
+		/* increase absolute time */
+		moldyn->time+=moldyn->tau;
+
+	}
+
+		/* check for hooks */
+		if(sched->hook)
+			sched->hook(moldyn,sched->hook_params);
+
+		/* get a new info line */
+		printf("\n");
 
-		/* check for visualiziation */
-		// to be continued ...
-		if(!(i%100)) 
-			visual_atoms(moldyn->visual,i*moldyn->tau,
-			             moldyn->atom,moldyn->count);
 	}
 
 	return 0;
@@ -212,34 +1247,37 @@ int moldyn_integrate(t_moldyn *moldyn) {
 int velocity_verlet(t_moldyn *moldyn) {
 
 	int i,count;
-	double tau,tau_square;
+	double tau,tau_square,h;
 	t_3dvec delta;
 	t_atom *atom;
 
 	atom=moldyn->atom;
 	count=moldyn->count;
 	tau=moldyn->tau;
-
-	tau_square=tau*tau;
+	tau_square=moldyn->tau_square;
 
 	for(i=0;i<count;i++) {
 		/* new positions */
+		h=0.5/atom[i].mass;
 		v3_scale(&delta,&(atom[i].v),tau);
 		v3_add(&(atom[i].r),&(atom[i].r),&delta);
-		v3_scale(&delta,&(atom[i].f),0.5*tau_square/atom[i].mass);
+		v3_scale(&delta,&(atom[i].f),h*tau_square);
 		v3_add(&(atom[i].r),&(atom[i].r),&delta);
-		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);
-		v3_add(&(atom[i].r),&(atom[i].r),&delta);
+		/* velocities [actually v(t+tau/2)] */
+		v3_scale(&delta,&(atom[i].f),h*tau);
+		v3_add(&(atom[i].v),&(atom[i].v),&delta);
 	}
 
+	/* neighbour list update */
+	link_cell_update(moldyn);
+
 	/* forces depending on chosen potential */
-	moldyn->force(moldyn);
+	potential_force_calc(moldyn);
 
 	for(i=0;i<count;i++) {
-		/* again velocities */
+		/* again velocities [actually v(t+tau)] */
 		v3_scale(&delta,&(atom[i].f),0.5*tau/atom[i].mass);
 		v3_add(&(atom[i].v),&(atom[i].v),&delta);
 	}
@@ -250,86 +1288,1031 @@ int velocity_verlet(t_moldyn *moldyn) {
 
 /*
  *
- * potentials & corresponding forces
+ * potentials & corresponding forces & virial routine
  * 
  */
 
-/* lennard jones potential & force for one sort of atoms */
- 
-double potential_lennard_jones(t_moldyn *moldyn) {
+/* generic potential and force calculation */
 
-	t_lj_params *params;
-	t_atom *atom;
-	int i,j;
-	int count;
-	t_3dvec distance;
-	double d,help;
-	double u;
-	double eps,sig6,sig12;
+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];
+	t_list *this,*that;
+	u8 bc_ij,bc_ik;
+	int dnlc;
 
-	params=moldyn->pot_params;
-	atom=moldyn->atom;
 	count=moldyn->count;
-	eps=params->epsilon;
-	sig6=params->sigma6;
-	sig12=params->sigma12;
+	itom=moldyn->atom;
+	lc=&(moldyn->lc);
 
-	u=0.0;
+	/* reset energy */
+	moldyn->energy=0.0;
+
+	/* reset force, site energy and virial of every atom */
 	for(i=0;i<count;i++) {
-		for(j=0;j<i;j++) {
-			v3_sub(&distance,&(atom[j].r),&(atom[i].r));
-			d=1.0/v3_absolute_square(&distance); 	/* 1/r^2 */
-			help=d*d; 				/* 1/r^4 */
-			help*=d; 				/* 1/r^6 */
-			d=help*help; 				/* 1/r^12 */
-			u+=eps*(sig12*d-sig6*help);
+
+		/* reset force */
+		v3_zero(&(itom[i].f));
+
+		/* reset virial */
+		virial=(&(itom[i].virial));
+		virial->xx=0.0;
+		virial->yy=0.0;
+		virial->zz=0.0;
+		virial->xy=0.0;
+		virial->xz=0.0;
+		virial->yz=0.0;
+	
+		/* reset site energy */
+		itom[i].e=0.0;
+
+	}
+
+	/* get energy,force and virial of every atom */
+	for(i=0;i<count;i++) {
+
+		/* single particle potential/force */
+		if(itom[i].attr&ATOM_ATTR_1BP)
+			moldyn->func1b(moldyn,&(itom[i]));
+
+		if(!(itom[i].attr&(ATOM_ATTR_2BP|ATOM_ATTR_3BP)))
+			continue;
+
+		/* 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;
+
+		for(j=0;j<27;j++) {
+
+			this=&(neighbour_i[j]);
+			list_reset_f(this);
+
+			if(this->start==NULL)
+				continue;
+
+			bc_ij=(j<dnlc)?0:1;
+
+			do {
+				jtom=this->current->data;
+
+				if(jtom==&(itom[i]))
+					continue;
+
+				if((jtom->attr&ATOM_ATTR_2BP)&
+				   (itom[i].attr&ATOM_ATTR_2BP)) {
+					moldyn->func2b(moldyn,
+					               &(itom[i]),
+					               jtom,
+					               bc_ij);
+				}
+
+				/* 3 body potential/force */
+
+				if(!(itom[i].attr&ATOM_ATTR_3BP)||
+				   !(jtom->attr&ATOM_ATTR_3BP))
+					continue;
+
+				/* copy the neighbour lists */
+				memcpy(neighbour_i2,neighbour_i,
+				       27*sizeof(t_list));
+
+				/* get neighbours of i */
+				for(k=0;k<27;k++) {
+
+					that=&(neighbour_i2[k]);
+					list_reset_f(that);
+					
+					if(that->start==NULL)
+						continue;
+
+					bc_ik=(k<dnlc)?0:1;
+
+					do {
+
+						ktom=that->current->data;
+
+						if(!(ktom->attr&ATOM_ATTR_3BP))
+							continue;
+
+						if(ktom==jtom)
+							continue;
+
+						if(ktom==&(itom[i]))
+							continue;
+
+						moldyn->func3b(moldyn,
+						               &(itom[i]),
+						               jtom,
+						               ktom,
+						               bc_ik|bc_ij);
+
+					} while(list_next_f(that)!=\
+					        L_NO_NEXT_ELEMENT);
+
+				}
+
+				/* 2bp post function */
+				if(moldyn->func2b_post) {
+					moldyn->func2b_post(moldyn,
+					                    &(itom[i]),
+					                    jtom,bc_ij);
+				}
+					
+			} while(list_next_f(this)!=L_NO_NEXT_ELEMENT);
+		
 		}
+
+	}
+
+#ifdef DEBUG
+printf("\n\n");
+#endif
+#ifdef VDEBUG
+printf("\n\n");
+#endif
+
+	return 0;
+}
+
+/*
+ * virial calculation
+ */
+
+inline int virial_calc(t_atom *a,t_3dvec *f,t_3dvec *d) {
+
+	a->virial.xx+=f->x*d->x;
+	a->virial.yy+=f->y*d->y;
+	a->virial.zz+=f->z*d->z;
+	a->virial.xy+=f->x*d->y;
+	a->virial.xz+=f->x*d->z;
+	a->virial.yz+=f->y*d->z;
+
+	return 0;
+}
+
+/*
+ * periodic boundayr checking
+ */
+
+inline int check_per_bound(t_moldyn *moldyn,t_3dvec *a) {
+	
+	double x,y,z;
+	t_3dvec *dim;
+
+	dim=&(moldyn->dim);
+
+	x=dim->x/2;
+	y=dim->y/2;
+	z=dim->z/2;
+
+	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;
+	}
+
+	return 0;
+}
+        
+
+/*
+ * example potentials
+ */
+
+/* harmonic oscillator potential and force */
+
+int harmonic_oscillator(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc) {
+
+	t_ho_params *params;
+	t_3dvec force,distance;
+	double d,f;
+	double sc,equi_dist;
+
+	params=moldyn->pot2b_params;
+	sc=params->spring_constant;
+	equi_dist=params->equilibrium_distance;
+
+	if(ai<aj) return 0;
+
+	v3_sub(&distance,&(aj->r),&(ai->r));
 	
-	return u;
+	if(bc) check_per_bound(moldyn,&distance);
+	d=v3_norm(&distance);
+	if(d<=moldyn->cutoff) {
+		moldyn->energy+=(0.5*sc*(d-equi_dist)*(d-equi_dist));
+		/* f = -grad E; grad r_ij = -1 1/r_ij distance */
+		f=sc*(1.0-equi_dist/d);
+		v3_scale(&force,&distance,f);
+		v3_add(&(ai->f),&(ai->f),&force);
+		virial_calc(ai,&force,&distance);
+		virial_calc(aj,&force,&distance); /* f and d signe switched */
+		v3_scale(&force,&distance,-f);
+		v3_add(&(aj->f),&(aj->f),&force);
+	}
+
+	return 0;
 }
 
-int force_lennard_jones(t_moldyn *moldyn) {
+/* 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;
-	int i,j,count;
-	t_atom *atom;
-	t_3dvec distance;
-	t_3dvec force;
+	t_3dvec force,distance;
 	double d,h1,h2;
 	double eps,sig6,sig12;
 
-	atom=moldyn->atom;	
-	count=moldyn->count;
-	params=moldyn->pot_params;
-	eps=params->epsilon;
+	params=moldyn->pot2b_params;
+	eps=params->epsilon4;
 	sig6=params->sigma6;
 	sig12=params->sigma12;
 
-	for(i=0;i<count;i++) v3_zero(&(atom[i].f));
+	if(ai<aj) return 0;
+
+	v3_sub(&distance,&(aj->r),&(ai->r));
+	if(bc) check_per_bound(moldyn,&distance);
+	d=v3_absolute_square(&distance);	/* 1/r^2 */
+	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 */
+		moldyn->energy+=(eps*(sig12*h1-sig6*h2)-params->uc);
+		h2*=d;				/* 1/r^8 */
+		h1*=d;				/* 1/r^14 */
+		h2*=6*sig6;
+		h1*=12*sig12;
+		d=+h1-h2;
+		d*=eps;
+		v3_scale(&force,&distance,d);
+		v3_add(&(aj->f),&(aj->f),&force);
+		v3_scale(&force,&force,-1.0); /* f = - grad E */
+		v3_add(&(ai->f),&(ai->f),&force);
+		virial_calc(ai,&force,&distance);
+if(force.x*distance.x<=0) printf("virial xx: %.15f -> %f %f %f\n",force.x*distance.x,distance.x,distance.y,distance.z);
+		virial_calc(aj,&force,&distance); /* f and d signe switched */
+	}
 
-	for(i=0;i<count;i++) {
-		for(j=0;j<i;j++) {
-			v3_sub(&distance,&(atom[j].r),&(atom[i].r));
-			v3_per_bound(&distance,&(moldyn->dim));
-			d=v3_absolute_square(&distance);
-			if(d<=moldyn->cutoff_square) {
-				h1=1.0/d;			/* 1/r^2 */
-				d=h1*h1;			/* 1/r^4 */
-				h2=d*d;				/* 1/r^8 */
-				h1*=d;				/* 1/r^6 */
-				h1*=h2;				/* 1/r^14 */
-				h1*=sig12;
-				h2*=sig6;
-				d=-12.0*h1+6.0*h2;
-				d*=eps;
-				v3_scale(&force,&distance,d);
-				v3_add(&(atom[j].f),&(atom[j].f),&force);
-				v3_sub(&(atom[i].f),&(atom[i].f),&force);
-			}
+	return 0;
+}
+
+/*
+ * 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->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]);
+	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;
+}
+
+/* tersoff 1 body part */
+int tersoff_mult_1bp(t_moldyn *moldyn,t_atom *ai) {
+
+	int brand;
+	t_tersoff_mult_params *params;
+	t_tersoff_exchange *exchange;
+	
+	brand=ai->brand;
+	params=moldyn->pot1b_params;
+	exchange=&(params->exchange);
+
+	/*
+	 * simple: point constant parameters only depending on atom i to
+	 *         their right values
+	 */
+
+	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[brand]*params->c[brand];
+	exchange->di2=params->d[brand]*params->d[brand];
+	exchange->ci2di2=exchange->ci2/exchange->di2;
+
+	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,d_ij2;
+	double A,B,R,S,S2,lambda,mu;
+	double f_r,df_r;
+	double f_c,df_c;
+	int brand;
+	double s_r;
+	double arg;
+
+	params=moldyn->pot2b_params;
+	brand=aj->brand;
+	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
+	 *
+	 */
+
+	/* constants */
+	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;
+		lambda=params->lambda_m;
+		mu=params->mu_m;
+		params->exchange.chi=params->chi;
+	}
+
+	/* dist_ij, d_ij */
+	v3_sub(&dist_ij,&(aj->r),&(ai->r));
+	if(bc) check_per_bound(moldyn,&dist_ij);
+	d_ij2=v3_absolute_square(&dist_ij);
+
+	/* if d_ij2 > S2 => no force & potential energy contribution */
+	if(d_ij2>S2)
+		return 0;
+
+	/* now we will need the distance */
+	//d_ij=v3_norm(&dist_ij);
+	d_ij=sqrt(d_ij2);
+
+	/* save for use in 3bp */
+	exchange->d_ij=d_ij;
+	exchange->d_ij2=d_ij2;
+	exchange->dist_ij=dist_ij;
+
+	/* more constants */
+	exchange->beta_j=&(params->beta[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;
+		exchange->cj2dj2=exchange->ci2di2;
+	}
+	else {
+		exchange->betajnj=pow(*(exchange->beta_j),*(exchange->n_j));
+		exchange->cj2=params->c[brand]*params->c[brand];
+		exchange->dj2=params->d[brand]*params->d[brand];
+		exchange->cj2dj2=exchange->cj2/exchange->dj2;
+	}
+
+	/* 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;
+	}
+
+	/* add forces of 2bp (ij, ji) contribution
+	 * dVij = dVji and we sum up both: no 1/2) */
+	v3_add(&(ai->f),&(ai->f),&force);
+
+	/* virial */
+	ai->virial.xx-=force.x*dist_ij.x;
+	ai->virial.yy-=force.y*dist_ij.y;
+	ai->virial.zz-=force.z*dist_ij.z;
+	ai->virial.xy-=force.x*dist_ij.y;
+	ai->virial.xz-=force.x*dist_ij.z;
+	ai->virial.yz-=force.y*dist_ij.z;
+
+#ifdef DEBUG
+if(ai==&(moldyn->atom[0])) {
+	printf("dVij, dVji (2bp) contrib:\n");
+	printf("%f | %f\n",force.x,ai->f.x);
+	printf("%f | %f\n",force.y,ai->f.y);
+	printf("%f | %f\n",force.z,ai->f.z);
+}
+#endif
+#ifdef VDEBUG
+if(ai==&(moldyn->atom[0])) {
+	printf("dVij, dVji (2bp) contrib:\n");
+	printf("%f | %f\n",force.x*dist_ij.x,ai->virial.xx);
+	printf("%f | %f\n",force.y*dist_ij.y,ai->virial.yy);
+	printf("%f | %f\n",force.z*dist_ij.z,ai->virial.zz);
+}
+#endif
+
+	/* energy 2bp contribution (ij, ji) is 0.5 f_r f_c ... */
+	moldyn->energy+=(0.5*f_r*f_c);
+
+	/* 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;
+
+	/* reset 3bp sums */
+	exchange->zeta_ij=0.0;
+	exchange->zeta_ji=0.0;
+	v3_zero(&(exchange->dzeta_ij));
+	v3_zero(&(exchange->dzeta_ji));
+
+	return 0;
+}
+
+/* tersoff 2 body post part */
+
+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 ... */
+		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);
+
+	/* virial */
+	ai->virial.xx-=force.x*dist_ij->x;
+	ai->virial.yy-=force.y*dist_ij->y;
+	ai->virial.zz-=force.z*dist_ij->z;
+	ai->virial.xy-=force.x*dist_ij->y;
+	ai->virial.xz-=force.x*dist_ij->z;
+	ai->virial.yz-=force.y*dist_ij->z;
+
+#ifdef DEBUG
+if(ai==&(moldyn->atom[0])) {
+	printf("dVij (3bp) contrib:\n");
+	printf("%f | %f\n",force.x,ai->f.x);
+	printf("%f | %f\n",force.y,ai->f.y);
+	printf("%f | %f\n",force.z,ai->f.z);
+}
+#endif
+#ifdef VDEBUG
+if(ai==&(moldyn->atom[0])) {
+	printf("dVij (3bp) contrib:\n");
+	printf("%f | %f\n",force.x*dist_ij->x,ai->virial.xx);
+	printf("%f | %f\n",force.y*dist_ij->y,ai->virial.yy);
+	printf("%f | %f\n",force.z*dist_ij->z,ai->virial.zz);
+}
+#endif
+
+	/* add energy of 3bp sum */
+	moldyn->energy+=(0.5*f_c*b*f_a);
+
+	/* 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);
+
+	/* add force */
+	v3_add(&(ai->f),&(ai->f),&force);
+
+	/* virial - plus sign, as dist_ij = - dist_ji - (really??) */
+// TEST ... with a minus instead
+	ai->virial.xx-=force.x*dist_ij->x;
+	ai->virial.yy-=force.y*dist_ij->y;
+	ai->virial.zz-=force.z*dist_ij->z;
+	ai->virial.xy-=force.x*dist_ij->y;
+	ai->virial.xz-=force.x*dist_ij->z;
+	ai->virial.yz-=force.y*dist_ij->z;
+
+#ifdef DEBUG
+if(ai==&(moldyn->atom[0])) {
+	printf("dVji (3bp) contrib:\n");
+	printf("%f | %f\n",force.x,ai->f.x);
+	printf("%f | %f\n",force.y,ai->f.y);
+	printf("%f | %f\n",force.z,ai->f.z);
+}
+#endif
+#ifdef VDEBUG
+if(ai==&(moldyn->atom[0])) {
+	printf("dVji (3bp) contrib:\n");
+	printf("%f | %f\n",force.x*dist_ij->x,ai->virial.xx);
+	printf("%f | %f\n",force.y*dist_ij->y,ai->virial.yy);
+	printf("%f | %f\n",force.z*dist_ij->z,ai->virial.zz);
+}
+#endif
+
+	return 0;
+}
+
+/* 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,S2,s_r;
+	double B,mu;
+	double d_ij,d_ik,d_jk,d_ij2,d_ik2,d_jk2;
+	double rr,dd;
+	double f_c,df_c;
+	double f_c_ik,df_c_ik,arg;
+	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 brand;
+
+	params=moldyn->pot3b_params;
+	exchange=&(params->exchange);
+
+	if(!(exchange->run3bp))
+		return 0;
+
+	/*
+	 * 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
+	 *
+	 */
+
+	/*
+	 * get exchange data 
+	 */
+
+	/* dist_ij, d_ij - this is < S_ij ! */
+	dist_ij=exchange->dist_ij;
+	d_ij=exchange->d_ij;
+	d_ij2=exchange->d_ij2;
+
+	/* f_c_ij, df_c_ij (same for ji) */
+	f_c=exchange->f_c;
+	df_c=exchange->df_c;
+
+	/*
+	 * calculate unknown values now ...
+	 */
+
+	/* V_ij and dV_ij stuff (in b_ij there is f_c_ik) */
+
+	/* dist_ik, d_ik */
+	v3_sub(&dist_ik,&(ak->r),&(ai->r));
+	if(bc) check_per_bound(moldyn,&dist_ik);
+	d_ik2=v3_absolute_square(&dist_ik);
+
+	/* ik constants */
+	brand=ai->brand;
+	if(brand==ak->brand) {
+		R=params->R[brand];
+		S=params->S[brand];
+		S2=params->S2[brand];
+	}
+	else {
+		R=params->Rmixed;
+		S=params->Smixed;
+		S2=params->S2mixed;
+	}
+
+	/* zeta_ij/dzeta_ij contribution only for d_ik < S */
+	if(d_ik2<S2) {
+
+		/* now we need d_ik */
+		d_ik=sqrt(d_ik2);
+
+		/* 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_ij2-tmp;
+		d_costheta2=cos_theta/d_ik2-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);
 		}
 	}
 
+	/* 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_jk2=v3_absolute_square(&dist_jk);
+
+	/* jk constants */
+	brand=aj->brand;
+	if(brand==ak->brand) {
+		R=params->R[brand];
+		S=params->S[brand];
+		S2=params->S2[brand];
+		B=params->B[brand];
+		mu=params->mu[brand];
+		chi=1.0;
+	}
+	else {
+		R=params->Rmixed;
+		S=params->Smixed;
+		S2=params->S2mixed;
+		B=params->Bmixed;
+		mu=params->mu_m;
+		chi=params->chi;
+	}
+
+	/* zeta_ji/dzeta_ji contribution only for d_jk < S_jk */
+	if(d_jk2<S2) {
+
+		/* now we need d_ik */
+		d_jk=sqrt(d_jk2);
+
+		/* 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); /* -1, as ij -> ji */
+		dd=d_ij*d_jk;
+		cos_theta=rr/dd;
+
+		/* d_costheta */
+		d_costheta1=1.0/dd;
+		d_costheta2=cos_theta/d_ij2;
+
+		/* 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_jik and dg(cos_theta) - needed in any case! */
+		v3_scale(&temp1,&dist_jk,d_costheta1);
+		v3_scale(&temp2,&dist_ij,-d_costheta2); /* ji -> ij => -1 */
+		//v3_add(&temp1,&temp1,&temp2);
+		v3_sub(&temp1,&temp1,&temp2); /* there is a minus! */
+		v3_scale(&temp1,&temp1,-2.0*frac*h_cos/d2_h_cos2); /* dg */
+
+		/* store dg in temp2 and use it for dVjk later */
+		v3_copy(&temp2,&temp1);
+
+		/* 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_ji */
+			v3_scale(&temp1,&temp1,f_c_jk);
+			v3_add(dzeta,dzeta,&temp1);
+		}
+
+		/* dV_jk stuff | add force contribution on atom i immediately */
+		if(exchange->d_ij_between_rs) {
+			zeta=f_c*g;
+			v3_scale(&temp1,&temp2,f_c);
+			v3_scale(&temp2,&dist_ij,df_c*g);
+			v3_add(&temp2,&temp2,&temp1); /* -> dzeta_jk in temp2 */
+		}
+		else {
+			zeta=g;
+			// dzeta_jk is simply dg, which is stored in temp2
+		}
+		/* 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(&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 ^ */
+
+		/* virial */
+		ai->virial.xx-=temp2.x*dist_jk.x;
+		ai->virial.yy-=temp2.y*dist_jk.y;
+		ai->virial.zz-=temp2.z*dist_jk.z;
+		ai->virial.xy-=temp2.x*dist_jk.y;
+		ai->virial.xz-=temp2.x*dist_jk.z;
+		ai->virial.yz-=temp2.y*dist_jk.z;
+
+#ifdef DEBUG
+if(ai==&(moldyn->atom[0])) {
+	printf("dVjk (3bp) contrib:\n");
+	printf("%f | %f\n",temp2.x,ai->f.x);
+	printf("%f | %f\n",temp2.y,ai->f.y);
+	printf("%f | %f\n",temp2.z,ai->f.z);
+}
+#endif
+#ifdef VDEBUG
+if(ai==&(moldyn->atom[0])) {
+	printf("dVjk (3bp) contrib:\n");
+	printf("%f | %f\n",temp2.x*dist_jk.x,ai->virial.xx);
+	printf("%f | %f\n",temp2.y*dist_jk.y,ai->virial.yy);
+	printf("%f | %f\n",temp2.z*dist_jk.z,ai->virial.zz);
+}
+#endif
+
+	}
+
 	return 0;
 }
 
+
+/*
+ * debugging / critical check functions
+ */
+
+int moldyn_bc_check(t_moldyn *moldyn) {
+
+	t_atom *atom;
+	t_3dvec *dim;
+	int i;
+	double x;
+	u8 byte;
+	int j,k;
+
+	atom=moldyn->atom;
+	dim=&(moldyn->dim);
+	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++)
+					printf("%d%c",
+					((byte)&(1<<k))?1:0,
+					(k==7)?'\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++)
+					printf("%d%c",
+					((byte)&(1<<k))?1:0,
+					(k==7)?'\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",
+			       i,atom[i].r.y,dim->y/2);
+		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,dim->z/2);
+	}
+
+	return 0;
+}