X-Git-Url: https://www.hackdaworld.org/gitweb/?a=blobdiff_plain;f=moldyn.c;h=af0132dff157564f46f593c3280700b045a1810c;hb=a9fbc66448c52bc4138176739b33d17ba86b7eae;hp=82749b2f10abf978c9636e213585e21c8393741a;hpb=85abe46fecc79a3d7885ff6124186b2be2ca96ac;p=physik%2Fposic.git

diff --git a/moldyn.c b/moldyn.c
index 82749b2..af0132d 100644
--- a/moldyn.c
+++ b/moldyn.c
@@ -5,19 +5,198 @@
  *
  */
 
-#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 "moldyn.h"
+
 #include "math/math.h"
 #include "init/init.h"
 #include "random/random.h"
+#include "visual/visual.h"
+#include "list/list.h"
+
+
+int moldyn_init(t_moldyn *moldyn,int argc,char **argv) {
+
+	//int ret;
+
+	//ret=moldyn_parse_argv(moldyn,argc,argv);
+	//if(ret<0) return ret;
+
+	memset(moldyn,0,sizeof(t_moldyn));
+
+	rand_init(&(moldyn->random),NULL,1);
+	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) {
+
+	switch(algo) {
+		case MOLDYN_INTEGRATE_VERLET:
+			moldyn->integrate=velocity_verlet;
+			break;
+		default:
+			printf("unknown integration algorithm: %02x\n",algo);
+			return -1;
+	}
+
+	return 0;
+}
+
+int set_cutoff(t_moldyn *moldyn,double cutoff) {
+
+	moldyn->cutoff=cutoff;
+
+	return 0;
+}
+
+int set_temperature(t_moldyn *moldyn,double t_ref) {
+
+	moldyn->t_ref=t_ref;
+
+	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;
+
+	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;
+
+	if(visualize) {
+		moldyn->vis.dim.x=x;
+		moldyn->vis.dim.y=y;
+		moldyn->vis.dim.z=z;
+	}
+
+	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) {
 
-int create_lattice(unsigned char type,int element,double mass,double lc,
-                   int a,int b,int c,t_atom **atom) {
+	if(x)
+		moldyn->status|=MOLDYN_STAT_PBX;
+
+	if(y)
+		moldyn->status|=MOLDYN_STAT_PBY;
+
+	if(z)
+		moldyn->status|=MOLDYN_STAT_PBZ;
+
+	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_potential3b(t_moldyn *moldyn,pf_func3b func,void *params) {
+
+	moldyn->func3b=func;
+	moldyn->pot3b_params=params;
+
+	return 0;
+}
+
+int moldyn_set_log(t_moldyn *moldyn,u8 type,char *fb,int timer) {
+
+	switch(type) {
+		case LOG_TOTAL_ENERGY:
+			moldyn->ewrite=timer;
+			moldyn->efd=open(fb,O_WRONLY|O_CREAT|O_TRUNC);
+			if(moldyn->efd<0) {
+				perror("[moldyn] efd open");
+				return moldyn->efd;
+			}
+			dprintf(moldyn->efd,"# total energy log file\n");
+			break;
+		case LOG_TOTAL_MOMENTUM:
+			moldyn->mwrite=timer;
+			moldyn->mfd=open(fb,O_WRONLY|O_CREAT|O_TRUNC);
+			if(moldyn->mfd<0) {
+				perror("[moldyn] mfd open");
+				return moldyn->mfd;
+			}
+			dprintf(moldyn->efd,"# total momentum log file\n");
+			break;
+		case SAVE_STEP:
+			moldyn->swrite=timer;
+			strncpy(moldyn->sfb,fb,63);
+			break;
+		case VISUAL_STEP:
+			moldyn->vwrite=timer;
+			strncpy(moldyn->vfb,fb,63);
+			visual_init(&(moldyn->vis),fb);
+			break;
+		default:
+			printf("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(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;
@@ -26,10 +205,11 @@ 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;
 	}
@@ -38,10 +218,10 @@ 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);
@@ -56,23 +236,58 @@ 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_atom *atom,t_random *random,int count,double t) {
+int thermal_init(t_moldyn *moldyn,u8 equi_init) {
 
 	/*
 	 * - gaussian distribution of velocities
@@ -83,11 +298,16 @@ 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);
 
 	/* 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;
@@ -103,72 +323,109 @@ 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) {
+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+=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);
+		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+moldyn->tau*(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) {
 
-	return(moldyn->potential(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);
 	}
@@ -176,6 +433,360 @@ t_3dvec get_total_p(t_atom *atom, int count) {
 	return p_total;
 }
 
+double estimate_time_step(t_moldyn *moldyn,double nn_dist) {
+
+	double tau;
+
+	/* nn_dist is the nearest neighbour distance */
+
+	if(moldyn->t==5.0) {
+		printf("[moldyn] i do not estimate timesteps below %f K!\n",
+		       MOLDYN_CRITICAL_EST_TEMP);
+		return 23.42;
+	}
+
+	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) {
+
+	t_linkcell *lc;
+	int i;
+	int fd;
+
+	fd=open("/dev/null",O_WRONLY);
+
+	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));
+
+	printf("[moldyn] initializing linked cells (%d)\n",lc->cells);
+
+	for(i=0;i<lc->cells;i++)
+		//list_init(&(lc->subcell[i]),1);
+		list_init(&(lc->subcell[i]),fd);
+
+ 	link_cell_update(moldyn);
+	
+	return 0;
+}
+
+int link_cell_update(t_moldyn *moldyn) {
+
+	int count,i,j,k;
+	int nx,ny,nz;
+	t_atom *atom;
+	t_linkcell *lc;
+
+	atom=moldyn->atom;
+	lc=&(moldyn->lc);
+
+	nx=lc->nx;
+	ny=lc->ny;
+	nz=lc->nz;
+
+	for(i=0;i<lc->cells;i++)
+		list_destroy(&(moldyn->lc.subcell[i]));
+	
+	for(count=0;count<moldyn->count;count++) {
+		i=(atom[count].r.x+(moldyn->dim.x/2))/lc->x;
+		j=(atom[count].r.y+(moldyn->dim.y/2))/lc->y;
+		k=(atom[count].r.z+(moldyn->dim.z/2))/lc->z;
+		list_add_immediate_ptr(&(moldyn->lc.subcell[i+j*nx+k*nx*ny]),
+		                       &(atom[count]));
+	}
+
+	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;
+	lc->countn=27;
+
+	return count2;
+}
+
+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_shutdown(&(moldyn->lc.subcell[i]));
+
+	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
+ *
+ */
+
+/* start the integration */
+
+int moldyn_integrate(t_moldyn *moldyn) {
+
+	int i,sched;
+	unsigned int e,m,s,v;
+	t_3dvec p;
+	t_moldyn_schedule *schedule;
+	t_atom *atom;
+	int fd;
+	char fb[128];
+	double ds;
+
+	schedule=&(moldyn->schedule);
+	atom=moldyn->atom;
+
+	/* initialize linked cell method */
+	link_cell_init(moldyn);
+
+	/* 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;
+	/* calculate initial forces */
+	potential_force_calc(moldyn);
+
+	/* do some 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;
+	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);
+
+		/* increase absolute time */
+		moldyn->time+=moldyn->tau;
+
+		/* check for log & visualization */
+		if(e) {
+			if(!(i%e))
+				dprintf(moldyn->efd,
+				        "%.15f %.45f %.45f %.45f\n",
+				        moldyn->time,update_e_kin(moldyn),
+				        moldyn->energy,
+				        get_total_energy(moldyn));
+		}
+		if(m) {
+			if(!(i%m)) {
+				p=get_total_p(moldyn);
+				dprintf(moldyn->mfd,
+				        "%.15f %.45f\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);
+				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",sched,i);
+				fflush(stdout);
+			}
+		}
+
+	}
+
+		/* check for hooks */
+		if(schedule->hook)
+			schedule->hook(moldyn,schedule->hook_params);
+
+	}
+
+	return 0;
+}
+
+/* velocity verlet */
+
+int velocity_verlet(t_moldyn *moldyn) {
+
+	int i,count;
+	double tau,tau_square;
+	t_3dvec delta;
+	t_atom *atom;
+
+	atom=moldyn->atom;
+	count=moldyn->count;
+	tau=moldyn->tau;
+	tau_square=moldyn->tau_square;
+
+	for(i=0;i<count;i++) {
+		/* new positions */
+		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_add(&(atom[i].r),&(atom[i].r),&delta);
+		check_per_bound(moldyn,&(atom[i].r));
+
+		/* velocities */
+		v3_scale(&delta,&(atom[i].f),0.5*tau/atom[i].mass);
+		v3_add(&(atom[i].v),&(atom[i].v),&delta);
+	}
+
+	/* neighbour list update */
+	link_cell_update(moldyn);
+
+	/* forces depending on chosen potential */
+	potential_force_calc(moldyn);
+	//moldyn->potential_force_function(moldyn);
+
+	for(i=0;i<count;i++) {
+		/* again velocities */
+		v3_scale(&delta,&(atom[i].f),0.5*tau/atom[i].mass);
+		v3_add(&(atom[i].v),&(atom[i].v),&delta);
+	}
+
+	return 0;
+}
+
 
 /*
  *
@@ -183,69 +794,575 @@ t_3dvec get_total_p(t_atom *atom, int count) {
  * 
  */
 
+/* generic potential and force calculation */
+
+int potential_force_calc(t_moldyn *moldyn) {
+
+	int i,j,k,count;
+	t_atom *itom,*jtom,*ktom;
+	t_linkcell *lc;
+	t_list neighbour_i[27];
+	t_list neighbour_i2[27];
+	//t_list neighbour_j[27];
+	t_list *this,*that;
+	u8 bc_ij,bc_ijk;
+	int countn,dnlc;
+
+	count=moldyn->count;
+	itom=moldyn->atom;
+	lc=&(moldyn->lc);
+
+	/* reset energy */
+	moldyn->energy=0.0;
+
+	for(i=0;i<count;i++) {
+
+		/* reset force */
+		v3_zero(&(itom[i].f));
+
+		/* single particle potential/force */
+		if(itom[i].attr&ATOM_ATTR_1BP)
+			moldyn->func1b(moldyn,&(itom[i]));
+
+		/* 2 body pair potential/force */
+		if(itom[i].attr&(ATOM_ATTR_2BP|ATOM_ATTR_3BP)) {
+	
+			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);
+
+			countn=lc->countn;
+			dnlc=lc->dnlc;
+
+			for(j=0;j<countn;j++) {
+
+				this=&(neighbour_i[j]);
+				list_reset(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;
+
+			/*
+			 * according to mr. nordlund, we dont need to take the 
+			 * sum over all atoms now, as 'this is centered' around
+			 * atom i ...
+			 * i am not quite sure though! there is a not vanishing
+			 * part even if f_c_ik is zero ...
+			 * this analytical potentials suck!
+			 * switching from mc to md to dft soon!
+			 */
+
+			//		link_cell_neighbour_index(moldyn,
+			//		   (jtom->r.x+moldyn->dim.x/2)/lc->x,
+			//		   (jtom->r.y+moldyn->dim.y/2)/lc->y,
+			//		   (jtom->r.z+moldyn->dim.z/2)/lc->z,
+			//		   neighbour_j);
+
+//					/* neighbours of j */
+//					for(k=0;k<lc->countn;k++) {
+//
+//						that=&(neighbour_j[k]);
+//						list_reset(that);
+//					
+//						if(that->start==NULL)
+//							continue;
+//
+//						bc_ijk=(k<lc->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_ijk);
+//
+/*						} while(list_next(that)!=\ */
+//						        L_NO_NEXT_ELEMENT);
+//
+//					}
+			
+					/* copy the neighbour lists */
+					memcpy(neighbour_i2,neighbour_i,
+					       27*sizeof(t_list));
+
+					/* get neighbours of i */
+					for(k=0;k<countn;k++) {
+
+						that=&(neighbour_i2[k]);
+						list_reset(that);
+					
+						if(that->start==NULL)
+							continue;
+
+						bc_ijk=(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;
+
+printf("Debug: atom %d before 3bp: %08x %08x %08x | %.15f %.15f %.15f\n",i,&itom[i],jtom,ktom,itom[i].r.x,itom[i].f.x,itom[i].v.x);
+			moldyn->func3b(moldyn,&(itom[i]),jtom,ktom,bc_ijk);
+printf("Debug: atom %d after 3bp: %08x %08x %08x | %.15f %.15f %.15f\n",i,&itom[i],jtom,ktom,itom[i].r.x,itom[i].f.x,itom[i].v.x);
+
+						} while(list_next(that)!=\
+						        L_NO_NEXT_ELEMENT);
+
+					}
+					
+				} while(list_next(this)!=L_NO_NEXT_ELEMENT);
+			}
+		}
+	}
+
+	return 0;
+}
+
+/*
+ * periodic boundayr checking
+ */
+
+int check_per_bound(t_moldyn *moldyn,t_3dvec *a) {
+	
+	double x,y,z;
+	t_3dvec *dim;
+
+	dim=&(moldyn->dim);
+
+	x=0.5*dim->x;
+	y=0.5*dim->y;
+	z=0.5*dim->z;
+
+	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;
+	double sc,equi_dist;
+
+	params=moldyn->pot2b_params;
+	sc=params->spring_constant;
+	equi_dist=params->equilibrium_distance;
+
+	v3_sub(&distance,&(ai->r),&(aj->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));
+		v3_scale(&force,&distance,-sc*(1.0-(equi_dist/d)));
+		v3_add(&(ai->f),&(ai->f),&force);
+	}
+
+	return 0;
+}
+
 /* lennard jones potential & force for one sort of atoms */
  
-double potential_lennard_jones(t_moldyn *moldyn) {
+int lennard_jones(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc) {
 
 	t_lj_params *params;
-	t_atom *atom;
-	int i,j;
-	int count;
-	t_3dvec distance;
-	double d,help;
-	double u;
+	t_3dvec force,distance;
+	double d,h1,h2;
 	double eps,sig6,sig12;
 
-	params=moldyn->pot_params;
-	atom=moldyn->atom;
-	count=moldyn->count;
-	eps=params->epsilon;
+	params=moldyn->pot2b_params;
+	eps=params->epsilon4;
 	sig6=params->sigma6;
 	sig12=params->sigma12;
 
-	u=0.0;
-	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);
-		}
+	v3_sub(&distance,&(ai->r),&(aj->r));
+	if(bc) check_per_bound(moldyn,&distance);
+	d=v3_absolute_square(&distance);	/* 1/r^2 */
+	if(d<=moldyn->cutoff_square) {
+		d=1.0/d;			/* 1/r^2 */
+		h2=d*d; 			/* 1/r^4 */
+		h2*=d;	 			/* 1/r^6 */
+		h1=h2*h2; 			/* 1/r^12 */
+		/* energy is eps*..., but we will add this twice ... */
+		moldyn->energy+=0.5*eps*(sig12*h1-sig6*h2);
+		h2*=d;				/* 1/r^8 */
+		h1*=d;				/* 1/r^14 */
+		h2*=6*sig6;
+		h1*=12*sig12;
+		d=+h1-h2;
+		d*=eps;
+		v3_scale(&force,&distance,d);
+		v3_add(&(ai->f),&(ai->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->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]);
+
+	return 0;
+}
+
+/* tersoff 1 body part */
+int tersoff_mult_1bp(t_moldyn *moldyn,t_atom *ai) {
+
+	int num;
+	t_tersoff_mult_params *params;
+	t_tersoff_exchange *exchange;
 	
-	return u;
+	num=ai->bnum;
+	params=moldyn->pot1b_params;
+	exchange=&(params->exchange);
+
+	/*
+	 * simple: point constant parameters only depending on atom i to
+	 *         their right values
+	 */
+
+	exchange->beta=&(params->beta[num]);
+	exchange->n=&(params->n[num]);
+	exchange->c=&(params->c[num]);
+	exchange->d=&(params->d[num]);
+	exchange->h=&(params->h[num]);
+
+	exchange->betan=pow(*(exchange->beta),*(exchange->n));
+	exchange->c2=params->c[num]*params->c[num];
+	exchange->d2=params->d[num]*params->d[num];
+	exchange->c2d2=exchange->c2/exchange->d2;
+
+	return 0;
 }
+	
+/* tersoff 2 body part */
+int tersoff_mult_2bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc) {
 
-int force_lennard_jones(t_moldyn *moldyn) {
+	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;
+	double scale;
 
-	t_lj_params *params;
-	int i,j,count;
-	t_atom *atom;
-	t_3dvec distance;
-	t_3dvec force;
-	double d,h1,h2;
+	params=moldyn->pot2b_params;
+	num=ai->bnum;
+	exchange=&(params->exchange);
 
-	atom=moldyn->atom;	
-	count=moldyn->count;
-	params=moldyn->pot_params;
+	exchange->run3bp=0;
+	
+	/*
+	 * we need: f_c, df_c, f_r, df_r
+	 *
+	 * therefore we need: R, S, A, lambda
+	 */
 
-	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 */
-			}
-		}
+	v3_sub(&dist_ij,&(ai->r),&(aj->r));
+
+	if(bc) check_per_bound(moldyn,&dist_ij);
+
+	d_ij=v3_norm(&dist_ij);
+
+	/* save for use in 3bp */
+	exchange->dist_ij=dist_ij; /* <- needed ? */
+	exchange->d_ij=d_ij;
+
+	/* constants */
+	if(num==aj->bnum) {
+		S=params->S[num];
+		R=params->R[num];
+		A=params->A[num];
+		lambda=params->lambda[num];
+		/* more constants depending of atoms i and j, needed in 3bp */
+		params->exchange.B=&(params->B[num]);
+		params->exchange.mu=&(params->mu[num]);
+		mu=params->mu[num];
+		params->exchange.chi=1.0;
+	}
+	else {
+		S=params->Smixed;
+		R=params->Rmixed;
+		A=params->Amixed;
+		lambda=params->lambda_m;
+		/* more constants depending of atoms i and j, needed in 3bp */
+		params->exchange.B=&(params->Bmixed);
+		params->exchange.mu=&(params->mu_m);
+		mu=params->mu_m;
+		params->exchange.chi=params->chi;
 	}
 
+	if(d_ij>S)
+		return 0;
+
+	f_r=A*exp(-lambda*d_ij);
+	df_r=-lambda*f_r/d_ij;
+
+	/* f_a, df_a calc + save for 3bp use */
+	exchange->f_a=-B*exp(-mu*d_ij);
+	exchange->df_a=-mu*exchange->f_a/d_ij;
+
+	if(d_ij<R) {
+		/* f_c = 1, df_c = 0 */
+		f_c=1.0;
+		df_c=0.0;
+		v3_scale(&force,&dist_ij,df_r);
+	}
+	else {
+		s_r=S-R;
+		arg=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));
+		scale=df_c*f_r+df_r*f_c;
+		v3_scale(&force,&dist_ij,scale);
+	}
+
+	/* add forces */
+	v3_add(&(ai->f),&(ai->f),&force);
+	/* energy 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 */
+	exchange->run3bp=1;
+
+	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 temp,force;
+	double R,S,s_r;
+	double d_ij,d_ij2,d_ik,d_jk;
+	double f_c,df_c,b_ij,f_a,df_a;
+	double f_c_ik,df_c_ik,arg;
+	double scale;
+	double chi;
+	double n,c,d,h,beta,betan;
+	double c2,d2,c2d2;
+	double numer,denom;
+	double theta,cos_theta,sin_theta;
+	double d_theta,d_theta1,d_theta2;
+	double h_cos,h_cos2,d2_h_cos2;
+	double frac1,bracket1,bracket2,bracket2_n_1,bracket2_n;
+	double bracket3,bracket3_pow_1,bracket3_pow;
+	int num;
+
+	params=moldyn->pot3b_params;
+	num=ai->bnum;
+	exchange=&(params->exchange);
+
+	if(!(exchange->run3bp))
+		return 0;
+
+	/*
+	 * we need: f_c, d_fc, b_ij, db_ij, f_a, df_a
+	 *
+	 * we got f_c, df_c, f_a, df_a from 2bp calculation
+	 */
+
+	d_ij=exchange->d_ij;
+	d_ij2=exchange->d_ij2;
+
+	f_a=params->exchange.f_a;
+	df_a=params->exchange.df_a;
+	
+	/* d_ij is <= S, as we didn't return so far! */
+
+	/*
+	 * calc of b_ij (scalar) and db_ij (vector)
+	 *
+	 * - for b_ij: chi, beta, f_c_ik, w(=1), c, d, h, n, cos_theta
+	 *
+	 * - for db_ij: d_theta, sin_theta, cos_theta, f_c_ik, df_c_ik,
+	 *              w_ik,
+	 *
+	 */
+
+	
+	v3_sub(&dist_ik,&(ai->r),&(ak->r));
+	if(bc) check_per_bound(moldyn,&dist_ik);
+	d_ik=v3_norm(&dist_ik);
+
+	/* constants for f_c_ik calc */
+	if(num==ak->bnum) {
+		R=params->R[num];
+		S=params->S[num];
+	}
+	else {
+		R=params->Rmixed;
+		S=params->Smixed;
+	}
+
+	/* calc of f_c_ik */
+	if(d_ik>S)
+		return 0;
+
+	if(d_ik<R) {
+		/* f_c_ik = 1, df_c_ik = 0 */
+		f_c_ik=1.0;
+		df_c_ik=0.0;
+	}
+	else {
+		s_r=S-R;
+		arg=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));
+	}
+	
+	v3_sub(&dist_jk,&(aj->r),&(ak->r));
+	if(bc) check_per_bound(moldyn,&dist_jk);
+	d_jk=v3_norm(&dist_jk);
+
+	beta=*(exchange->beta);
+	betan=exchange->betan;
+	n=*(exchange->n);
+	c=*(exchange->c);
+	d=*(exchange->d);
+	h=*(exchange->h);
+	c2=exchange->c2;
+	d2=exchange->d2;
+	c2d2=exchange->c2d2;
+
+	numer=d_ij2+d_ik*d_ik-d_jk*d_jk;
+	denom=2*d_ij*d_ik;
+	cos_theta=numer/denom;
+	sin_theta=sqrt(1.0-(cos_theta*cos_theta));
+	theta=acos(cos_theta);
+	d_theta=(-1.0/sqrt(1.0-cos_theta*cos_theta))/(denom*denom);
+	d_theta1=2*denom-numer*2*d_ik/d_ij;
+	d_theta2=2*denom-numer*2*d_ij/d_ik;
+	d_theta1*=d_theta;
+	d_theta2*=d_theta;
+
+	h_cos=(h-cos_theta);
+	h_cos2=h_cos*h_cos;
+	d2_h_cos2=d2-h_cos2;
+
+	/* some usefull expressions */
+	frac1=c2/(d2-h_cos2);
+	bracket1=1+c2d2-frac1;
+	bracket2=f_c_ik*bracket1;
+	bracket2_n_1=pow(bracket2,n-1.0);
+	bracket2_n=bracket2_n_1*bracket2;
+	bracket3=1+betan*bracket2_n;
+	bracket3_pow_1=pow(bracket3,(-1.0/(2.0*n))-1.0);
+	bracket3_pow=bracket3_pow_1*bracket3;
+
+	/* now go on with calc of b_ij and derivation of b_ij */
+	b_ij=chi*bracket3_pow;
+
+	/* derivation of theta */
+	v3_scale(&force,&dist_ij,d_theta1);
+	v3_scale(&temp,&dist_ik,d_theta2);
+	v3_add(&force,&force,&temp);
+
+	/* part 1 of derivation of b_ij */
+	v3_scale(&force,&force,sin_theta*2*h_cos*f_c_ik*frac1);
+
+	/* part 2 of derivation of b_ij */
+	v3_scale(&temp,&dist_ik,df_c_ik*bracket1);
+
+	/* sum up and scale ... */
+	v3_add(&temp,&temp,&force);
+	scale=bracket2_n_1*n*betan*(1+betan*bracket3_pow_1)*chi*(1.0/(2.0*n));
+	v3_scale(&temp,&temp,scale);
+
+	/* now construct an energy and a force out of that */
+	v3_scale(&temp,&temp,f_a);
+	v3_scale(&force,&dist_ij,df_a*b_ij);
+	v3_add(&temp,&temp,&force);
+	v3_scale(&temp,&temp,f_c);
+	v3_scale(&force,&dist_ij,df_c*b_ij*f_a);
+	v3_add(&force,&force,&temp);
+
+	/* add forces */
+	v3_add(&(ai->f),&(ai->f),&force);
+	/* energy is 0.5 f_r f_c, but we will sum it up twice ... */
+	moldyn->energy+=(0.25*f_a*b_ij*f_c);
+				
 	return 0;
 }