From: hackbard <hackbard>
Date: Fri, 28 Apr 2006 15:02:29 +0000 (+0000)
Subject: implemented link cell method, segfaulting by now!
X-Git-Url: https://hackdaworld.org/gitweb/?a=commitdiff_plain;h=e6f456c0fa807b86e1b25996e70efcdcfe390ea5;p=physik%2Fposic.git

implemented link cell method, segfaulting by now!
---

diff --git a/moldyn.c b/moldyn.c
index 1772067..4b58089 100644
--- a/moldyn.c
+++ b/moldyn.c
@@ -36,6 +36,17 @@ int moldyn_usage(char **argv) {
 	printf("-T <temperature> [K] (%f)\n",MOLDYN_TEMP);
 	printf("-t <timestep tau> [s] (%.15f)\n",MOLDYN_TAU);
 	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");
 
 	return 0;
@@ -44,6 +55,9 @@ int moldyn_usage(char **argv) {
 int moldyn_parse_argv(t_moldyn *moldyn,int argc,char **argv) {
 
 	int i;
+	t_ho_params hop;
+	t_lj_params ljp;
+	double s,e;
 
 	memset(moldyn,0,sizeof(t_moldyn));
 
@@ -51,6 +65,8 @@ int moldyn_parse_argv(t_moldyn *moldyn,int argc,char **argv) {
 	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++) {
@@ -85,6 +101,44 @@ int moldyn_parse_argv(t_moldyn *moldyn,int argc,char **argv) {
 				case 'R':
 					moldyn->time_steps=atoi(argv[++i]);
 					break;
+				case 'I':
+	/* integration algorithm */
+	switch(atoi(argv[++i])) {
+		case MOLDYN_INTEGRATE_VERLET:
+			moldyn->integrate=velocity_verlet;
+			break;
+		default:
+			printf("unknown integration algo %s\n",argv[i]);
+			moldyn_usage(argv);
+			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;
+	}
+
 				default:
 					printf("unknown option %s\n",argv[i]);
 					moldyn_usage(argv);
@@ -216,7 +270,7 @@ int destroy_lattice(t_atom *atom) {
 	return 0;
 }
 
-int thermal_init(t_moldyn *moldyn,t_random *random,int count) {
+int thermal_init(t_moldyn *moldyn,t_random *random) {
 
 	/*
 	 * - gaussian distribution of velocities
@@ -233,7 +287,7 @@ int thermal_init(t_moldyn *moldyn,t_random *random,int count) {
 
 	/* gaussian distribution of velocities */
 	v3_zero(&p_total);
-	for(i=0;i<count;i++) {
+	for(i=0;i<moldyn->count;i++) {
 		sigma=sqrt(2.0*K_BOLTZMANN*moldyn->t/atom[i].mass);
 		/* x direction */
 		v=sigma*rand_get_gauss(random);
@@ -250,19 +304,19 @@ int thermal_init(t_moldyn *moldyn,t_random *random,int count) {
 	}
 
 	/* 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(moldyn,count);
+	scale_velocity(moldyn);
 
 	return 0;
 }
 
-int scale_velocity(t_moldyn *moldyn,int count) {
+int scale_velocity(t_moldyn *moldyn) {
 
 	int i;
 	double e,c;
@@ -274,10 +328,10 @@ int scale_velocity(t_moldyn *moldyn,int count) {
 	 * - velocity scaling (E = 3/2 N k T), E: kinetic energy
 	 */
 	e=0.0;
-	for(i=0;i<count;i++)
+	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*count*K_BOLTZMANN*moldyn->t));
-	for(i=0;i<count;i++)
+	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));
 
 	return 0;
@@ -299,7 +353,7 @@ double get_e_kin(t_atom *atom,int count) {
 
 double get_e_pot(t_moldyn *moldyn) {
 
-	return(moldyn->potential(moldyn));
+	return moldyn->energy;
 }
 
 double get_total_energy(t_moldyn *moldyn) {
@@ -343,31 +397,7 @@ double estimate_time_step(t_moldyn *moldyn,double nn_dist,double t) {
  * numerical tricks
  */
 
-/* verlet list */
-
-int verlet_list_init(t_moldyn *moldyn) {
-
-	int i,fd;
-
-	fd=open("/dev/null",O_WRONLY);
-
-	for(i=0;i<moldyn->count;i++)
-		list_init(&(moldyn->atom[i].verlet),fd);
-
-	moldyn->r_verlet=1.1*moldyn->cutoff;
-	/* +moldyn->tau*\
-		sqrt(3.0*K_BOLTZMANN*moldyn->t/moldyn->atom[0].mass); */
-
-	printf("debug: r verlet = %.15f\n",moldyn->r_verlet);
-	printf("       r cutoff = %.15f\n",moldyn->cutoff);
-	printf("       dim      = %.15f\n",moldyn->dim.x);
-
-	/* make sure to update the list in the beginning */
-	moldyn->dr_max1=moldyn->r_verlet;
-	moldyn->dr_max2=moldyn->r_verlet;
-
-	return 0;
-}
+/* linked list / cell method */
 
 int link_cell_init(t_moldyn *moldyn) {
 
@@ -390,64 +420,27 @@ int link_cell_init(t_moldyn *moldyn) {
 	return 0;
 }
 
-int verlet_list_update(t_moldyn *moldyn) {
-
-	int i,j;
-	t_3dvec d;
-	t_atom *atom;
-
-	atom=moldyn->atom;
-
-	puts("debug: list update start");
-
-	for(i=0;i<moldyn->count;i++) {
-		list_destroy(&(atom[i].verlet));
-		for(j=0;j<moldyn->count;j++) {
-			if(i!=j) {
-				v3_sub(&d,&(atom[i].r),&(atom[j].r));
-				v3_per_bound(&d,&(moldyn->dim));
-				if(v3_norm(&d)<=moldyn->r_verlet)
-					list_add_immediate_ptr(&(atom[i].verlet),&(atom[j]));
-			}
-		}
-	}
-
-	moldyn->dr_max1=0.0;
-	moldyn->dr_max2=0.0;
-
-	puts("debug: list update end");
-
-	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;
-	nx=moldyn->lc.nx; ny=moldyn->lc.ny; nz=moldyn->lc.nz;
+	lc=&(moldyn->lc);
+
+	nx=lc->nx;
+	ny=lc->ny;
+	nz=lc->nz;
 
 	for(i=0;i<nx*ny*nz;i++)
 		list_destroy(&(moldyn->lc.subcell[i]));
 	
 	for(count=0;count<moldyn->count;count++) {
-		for(i=0;i<nx;i++) {
-			if((atom[count].r.x>=i*moldyn->dim.x) && \
-			   (atom[count].r.x<(i+1)*moldyn->dim.x))
-				break;
-		}
-		for(j=0;j<ny;j++) {
-			if((atom[count].r.y>=j*moldyn->dim.y) && \
-			   (atom[count].r.y<(j+1)*moldyn->dim.y))
-				break;
-		}
-		for(k=0;k<nz;k++) {
-			if((atom[count].r.z>=k*moldyn->dim.z) && \
-			   (atom[count].r.z<(k+1)*moldyn->dim.z))
-				break;
-		}
+		i=atom[count].r.x/lc->x;
+		j=atom[count].r.y/lc->y;
+		k=atom[count].r.z/lc->z;
 		list_add_immediate_ptr(&(moldyn->lc.subcell[i+j*nx+k*nx*ny]),
 		                       &(atom[count]));
 	}
@@ -455,14 +448,58 @@ int link_cell_update(t_moldyn *moldyn) {
 	return 0;
 }
 
-int verlet_list_shutdown(t_moldyn *moldyn) {
+int link_cell_neighbour_index(t_moldyn *moldyn,int i,int j,int k,t_list *cell) {
 
-	int i;
+	t_linkcell *lc;
+	int a;
+	int count1,count2;
+	int ci,cj,ck;
+	int nx,ny,nz;
+	int x,y,z;
+	unsigned char bx,by,bz;
 
-	for(i=0;i<moldyn->count;i++)
-		list_shutdown(&(moldyn->atom[i].verlet));
+	lc=&(moldyn->lc);
+	nx=lc->nx;
+	ny=lc->ny;
+	nx=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(!(x|y|z)) continue;
+				if(bx|by|bz) {
+					cell[--count2]=lc->subcell[x+y*nx+z*a];
+				}
+				else {
+					cell[count1++]=lc->subcell[x+y*nx+z*a];
+				}
+			}
+		}
+	}
 
-	return 0;
+	return count2;
 }
 
 int link_cell_shutdown(t_moldyn *moldyn) {
@@ -491,7 +528,6 @@ int moldyn_integrate(t_moldyn *moldyn) {
 	int i;
 	unsigned int e,m,s,d,v;
 	t_3dvec p;
-	double rlc;
 
 	int fd;
 	char fb[128];
@@ -503,20 +539,20 @@ int moldyn_integrate(t_moldyn *moldyn) {
 	d=moldyn->dwrite;
 	v=moldyn->vwrite;
 
-	/* verlet list */	
-	rlc=moldyn->r_verlet-moldyn->cutoff;
-
 	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;
+
 	/* create the neighbour list */
-	//verlet_list_update(moldyn);
 	link_cell_update(moldyn);
 
 	/* calculate initial forces */
-	moldyn->force(moldyn);
+	moldyn->potential_force_function(moldyn);
 
 	for(i=0;i<moldyn->time_steps;i++) {
 		/* show runs */
@@ -524,15 +560,11 @@ int moldyn_integrate(t_moldyn *moldyn) {
 
 		/* neighbour list update */
 		link_cell_update(moldyn);
-		//if(moldyn->dr_max1+moldyn->dr_max2>rlc) {
-		//	printf("\n");
-		//	verlet_list_update(moldyn);
-		//}
 
 		/* integration step */
 		moldyn->integrate(moldyn);
 
-		/* check for log & visualiziation */
+		/* check for log & visualization */
 		if(e) {
 			if(!(i%e))
 				dprintf(moldyn->efd,
@@ -581,41 +613,30 @@ int moldyn_integrate(t_moldyn *moldyn) {
 int velocity_verlet(t_moldyn *moldyn) {
 
 	int i,count;
-	double tau,tau_square,dr;
+	double tau,tau_square;
 	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 */
 		v3_scale(&delta,&(atom[i].v),tau);
 		v3_add(&(atom[i].r),&(atom[i].r),&delta);
-		v3_add(&(atom[i].dr),&(atom[i].dr),&delta);
 		v3_scale(&delta,&(atom[i].f),0.5*tau_square/atom[i].mass);
 		v3_add(&(atom[i].r),&(atom[i].r),&delta);
-		v3_add(&(atom[i].dr),&(atom[i].dr),&delta);
 		v3_per_bound(&(atom[i].r),&(moldyn->dim));
 
-		/* set maximum dr (possible list update) [obsolete] */
-		//dr=v3_norm(&(atom[i].dr));
-		//if(dr>moldyn->dr_max1) {
-		//	moldyn->dr_max2=moldyn->dr_max1;
-		//	moldyn->dr_max1=dr;
-		//}
-		//else if(dr>moldyn->dr_max2) moldyn->dr_max2=dr;
-
 		/* velocities */
 		v3_scale(&delta,&(atom[i].f),0.5*tau/atom[i].mass);
 		v3_add(&(atom[i].v),&(atom[i].v),&delta);
 	}
 
 	/* forces depending on chosen potential */
-	moldyn->force(moldyn);
+	moldyn->potential_force_function(moldyn);
 
 	for(i=0;i<count;i++) {
 		/* again velocities */
@@ -635,84 +656,112 @@ int velocity_verlet(t_moldyn *moldyn) {
 
 /* harmonic oscillator potential and force */
 
-double potential_harmonic_oscillator(t_moldyn *moldyn) {
+int harmonic_oscillator(t_moldyn *moldyn) {
 
 	t_ho_params *params;
-	t_atom *atom;
-	int i,j;
+	t_atom *atom,*btom;
+	t_linkcell *lc;
+	t_list *this,neighbour[27];
+	int i,j,c;
 	int count;
-	t_3dvec distance;
+	t_3dvec force,distance;
 	double d,u;
 	double sc,equi_dist;
+	int ni,nj,nk;
 
 	params=moldyn->pot_params;
 	atom=moldyn->atom;
+	lc=&(moldyn->lc);
 	sc=params->spring_constant;
 	equi_dist=params->equilibrium_distance;
 	count=moldyn->count;
 
 	u=0.0;
 	for(i=0;i<count;i++) {
-		for(j=0;j<i;j++) {
-			v3_sub(&distance,&(atom[i].r),&(atom[j].r));
+		/* determine cell + neighbours */
+		ni=atom[i].r.x/lc->x;
+		nj=atom[i].r.y/lc->y;
+		nk=atom[i].r.z/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_norm(&distance);
 			u+=(0.5*sc*(d-equi_dist)*(d-equi_dist));
-		}
-	}
-
-	return u;
-}
-
-int force_harmonic_oscillator(t_moldyn *moldyn) {
-
-	t_ho_params *params;
-	int i,j,count;
-	t_atom *atom;
-	t_3dvec distance;
-	t_3dvec force;
-	double d;
-	double sc,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);
+
+		/* neighbours not doing boundary condition overflow */
+		for(j=1;j<c;j++) {
+			this=&(neighbour[j]);
+			list_reset(this); /* there might not be a single atom */
+			if(this->start!=NULL) {
+
+			do {
+				btom=this->current->data;
+				v3_sub(&distance,&(atom[i].r),&(btom->r));
+				d=v3_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);
 
-	atom=moldyn->atom;	
-	count=moldyn->count;
-	params=moldyn->pot_params;
-	sc=params->spring_constant;
-	equi_dist=params->equilibrium_distance;
+			}
+		}
 
-	for(i=0;i<count;i++) v3_zero(&(atom[i].f));
+		/* 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_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);
 
-	for(i=0;i<count;i++) {
-		for(j=0;j<i;j++) {
-			v3_sub(&distance,&(atom[i].r),&(atom[j].r));
-			v3_per_bound(&distance,&(moldyn->dim));
-			d=v3_norm(&distance);
-			if(d<=moldyn->cutoff) {
-				v3_scale(&force,&distance,
-				         -sc*(1.0-(equi_dist/d)));
-				v3_add(&(atom[i].f),&(atom[i].f),&force);
-				v3_sub(&(atom[j].f),&(atom[j].f),&force);
 			}
 		}
 	}
 
+	moldyn->energy=u;
+
 	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_lj_params *params;
 	t_atom *atom,*btom;
 	t_linkcell *lc;
-	int i;
+	t_list *this,neighbour[27];
+	int i,j,c;
 	int count;
-	t_3dvec distance;
-	double d,help;
-	double u;
+	t_3dvec force,distance;
+	double d,h1,h2,u;
 	double eps,sig6,sig12;
-	int i,j,k;
 	int ni,nj,nk;
 
 	params=moldyn->pot_params;
@@ -725,80 +774,101 @@ double potential_lennard_jones(t_moldyn *moldyn) {
 
 	u=0.0;
 	for(i=0;i<count;i++) {
-		/* verlet list [obsolete] */
-		//list_reset(&(atom[i].verlet));
-		//if(atom[i].verlet.current==NULL) continue;
-
-		/* determine cell */
+		/* determine cell + neighbours */
 		ni=atom[i].r.x/lc->x;
 		nj=atom[i].r.y/lc->y;
 		nk=atom[i].r.z/lc->z;
-
-		while(1) {
-			btom=atom[i].verlet.current->data;
+		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));
-			v3_per_bound(&distance,&(moldyn->dim));
-			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);
-			if(list_next(&(atom[i].verlet))==L_NO_NEXT_ELEMENT)
-				break;
+			d=1.0/v3_absolute_square(&distance); /* 1/r^2 */
+			h1=d*d; 	/* 1/r^4 */
+			h2*=d;	 	/* 1/r^6 */
+			h1=h2*h2; 	/* 1/r^12 */
+			u+=eps*(sig12*h1-sig6*h2);
+			h2*=d;		/* 1/r^8 */
+			h1*=d;		/* 1/r^14 */
+			h2*=6*sig6;
+			h1*=12*sig12;
+			d=-h1+h2;
+			d*=eps;
+			v3_scale(&force,&distance,d);
+			v3_add(&(atom[i].f),&(atom[i].f),&force);
+		} while(list_next(this)!=L_NO_NEXT_ELEMENT);
+
+		/* neighbours not doing boundary condition overflow */
+		for(j=1;j<c;j++) {
+			this=&(neighbour[j]);
+			list_reset(this); /* there might not be a single atom */
+			if(this->start!=NULL) {
+
+			do {
+				btom=this->current->data;
+				v3_sub(&distance,&(atom[i].r),&(btom->r));
+				d=v3_absolute_square(&distance); /* r^2 */
+				if(d<=moldyn->cutoff_square) {
+					d=1.0/d;	/* 1/r^2 */
+					h1=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);
+				
+			}
 		}
-	}
-	
-	return u;
-}
-
-int force_lennard_jones(t_moldyn *moldyn) {
-
-	t_lj_params *params;
-	int i,count;
-	t_atom *atom,*btom;
-	t_3dvec distance;
-	t_3dvec force;
-	double d,h1,h2;
-	double eps,sig6,sig12;
 
-	atom=moldyn->atom;	
-	count=moldyn->count;
-	params=moldyn->pot_params;
-	eps=params->epsilon4;
-	sig6=6*params->sigma6;
-	sig12=12*params->sigma12;
-
-	for(i=0;i<count;i++) v3_zero(&(atom[i].f));
+		/* 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 */
+					h1=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);
 
-	for(i=0;i<count;i++) {
-		list_reset(&(atom[i].verlet));
-		if(atom[i].verlet.current==NULL) continue;
-		while(1) {
-			btom=atom[i].verlet.current->data;
-			v3_sub(&distance,&(atom[i].r),&(btom->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;
-				/* actually there would be a '-',	*
-				 * but f=-d/dr potential		*/
-				d=h1+h2;
-				d*=eps;
-				v3_scale(&force,&distance,d);
-				v3_add(&(atom[i].f),&(atom[i].f),&force);
-				//v3_sub(&(atom[j].f),&(atom[j].f),&force);
 			}
-			if(list_next(&(atom[i].verlet))==L_NO_NEXT_ELEMENT)
-				break;
 		}
 	}
 
+	moldyn->energy=u;
+	
 	return 0;
 }
 
diff --git a/moldyn.h b/moldyn.h
index 53a22fd..e9f1495 100644
--- a/moldyn.h
+++ b/moldyn.h
@@ -18,10 +18,8 @@ typedef struct s_atom {
 	t_3dvec r;	/* positions */
 	t_3dvec v;	/* velocities */
 	t_3dvec f;	/* forces */
-	t_3dvec dr;	/* delta r for verlet list updates */
 	int element;	/* number of element in pse */
 	double mass;	/* atom mass */
-	t_list verlet;	/* verlet neighbour list */
 } t_atom;
 
 typedef struct s_linkcell {
@@ -38,15 +36,11 @@ typedef struct s_moldyn {
 	t_atom *atom;
 	t_3dvec dim;
 	/* potential, force & parameters */
-	double (*potential)(struct s_moldyn *moldyn);
-	int (*force)(struct s_moldyn *moldyn);
+	int (*potential_force_function)(struct s_moldyn *moldyn);
 	void *pot_params;
-	/* cut off radius, verlet list & co */
+	/* cut off radius */
 	double cutoff;
 	double cutoff_square;
-	double r_verlet;
-	double dr_max1;
-	double dr_max2;
 	/* linked list / cell method */
 	t_linkcell lc;
 	/* temperature */
@@ -55,6 +49,9 @@ typedef struct s_moldyn {
 	int (*integrate)(struct s_moldyn *moldyn);
 	int time_steps;
 	double tau;
+	double tau_square;
+	/* energy */
+	double energy;
 	/* logging & visualization */
 	unsigned char lvstat;
 	unsigned int ewrite;
@@ -107,6 +104,13 @@ typedef struct s_lj_params {
 #define MOLDYN_TAU			1.0e-15
 #define MOLDYN_RUNS			1000000
 
+#define MOLDYN_INTEGRATE_VERLET		0x00
+#define MOLDYN_INTEGRATE_DEFAULT MOLDYN_INTEGRATE_VERLET
+
+#define MOLDYN_POTENTIAL_HO		0x00
+#define MOLDYN_POTENTIAL_LJ		0x01
+#define MOLDYN_POTENTIAL_DEFAULT MOLDYN_POTENTIAL_LJ
+
 /* phsical values */
 
 #define K_BOLTZMANN		1.3807e-27			/* Nm/K */
@@ -134,8 +138,8 @@ int moldyn_shutdown(t_moldyn *moldyn);
 int create_lattice(unsigned char type,int element,double mass,double lc,
                    int a,int b,int c,t_atom **atom);
 int destroy_lattice(t_atom *atom);
-int thermal_init(t_moldyn *moldyn,t_random *random,int count);
-int scale_velocity(t_moldyn *moldyn,int count);
+int thermal_init(t_moldyn *moldyn,t_random *random);
+int scale_velocity(t_moldyn *moldyn);
 double get_e_kin(t_atom *atom,int count);
 double get_e_pot(t_moldyn *moldyn);
 double get_total_energy(t_moldyn *moldyn);
@@ -143,19 +147,15 @@ t_3dvec get_total_p(t_atom *atom,int count);
 
 double estimate_time_step(t_moldyn *moldyn,double nn_dist,double t);
 
-int verlet_list_init(t_moldyn *moldyn);
 int link_cell_init(t_moldyn *moldyn);
-int verlet_list_update(t_moldyn *moldyn);
 int link_cell_update(t_moldyn *moldyn);
-int verlet_list_shutdown(t_moldyn *moldyn);
+int link_cell_neighbour_index(t_moldyn *moldyn,int i,int j,int k,t_list *cell);
 int link_cell_shutdown(t_moldyn *moldyn);
 
 int moldyn_integrate(t_moldyn *moldyn);
 int velocity_verlet(t_moldyn *moldyn);
 
-double potential_harmonic_oscillator(t_moldyn *moldyn);
-int force_harmonic_oscillator(t_moldyn *moldyn);
-double potential_lennard_jones(t_moldyn *moldyn);
-int force_lennard_jones(t_moldyn *moldyn);
+int harmonic_oscillator(t_moldyn *moldyn);
+int lennard_jones(t_moldyn *moldyn);
 
 #endif
diff --git a/posic.c b/posic.c
index 7cde6e2..236e208 100644
--- a/posic.c
+++ b/posic.c
@@ -25,7 +25,6 @@ int main(int argc,char **argv) {
 	double e;
 	double help;
 	t_3dvec p;
-	int count;
 
 	t_lj_params lj;
 	t_ho_params ho;
@@ -53,12 +52,12 @@ int main(int argc,char **argv) {
 	vis.dim.y=b*LC_SI;
 	vis.dim.z=c*LC_SI;
 
-	/* init lattice */
+	/* init lattice
 	printf("placing silicon atoms ... ");
-	count=create_lattice(DIAMOND,SI,M_SI,LC_SI,a,b,c,&si);
-	printf("(%d) ok!\n",count);
-	/* testing purpose
-	count=2;
+	md.count=create_lattice(DIAMOND,SI,M_SI,LC_SI,a,b,c,&si);
+	printf("(%d) ok!\n",md.count);
+	testing purpose */
+	md.count=2;
 	si=malloc(2*sizeof(t_atom));
 	si[0].r.x=0.13*sqrt(3.0)*LC_SI/2.0;
 	si[0].r.y=0;
@@ -70,22 +69,15 @@ int main(int argc,char **argv) {
 	si[1].r.z=0;
 	si[1].element=SI;
 	si[1].mass=M_SI;
-	*/
+	/* */
 
 	/* moldyn init (now si is a valid address) */
-	md.count=count;
 	md.atom=si;
-	md.potential=potential_lennard_jones;
-	md.force=force_lennard_jones;
-	//md.potential=potential_harmonic_oscillator;
-	//md.force=force_harmonic_oscillator;
+	md.potential_force_function=lennard_jones;
+	//md.potential_force_function=harmonic_oscillator;
 	md.cutoff=R_CUTOFF*LC_SI;
-	md.cutoff_square=md.cutoff*md.cutoff;
 	md.pot_params=&lj;
 	//md.pot_params=&ho;
-	md.integrate=velocity_verlet;
-	//md.time_steps=RUNS;
-	//md.tau=TAU;
 	md.status=0;
 	md.visual=&vis;
 	/* dimensions of the simulation cell */
@@ -93,23 +85,19 @@ int main(int argc,char **argv) {
 	md.dim.y=b*LC_SI;
 	md.dim.z=c*LC_SI;
 
-	/* verlet list init */
-	// later integrated in moldyn_init function!
-	verlet_list_init(&md);
-
 	printf("setting thermal fluctuations (T=%f K)\n",md.t);
-	thermal_init(&md,&random,count);
-	//for(a=0;a<count;a++) v3_zero(&(si[0].v));
+	// thermal_init(&md,&random);
+	for(a=0;a<md.count;a++) v3_zero(&(si[0].v));
 
 	/* check kinetic energy */
 
-	e=get_e_kin(si,count);
+	e=get_e_kin(si,md.count);
 	printf("kinetic energy: %.40f [J]\n",e);
 	printf("3/2 N k T = %.40f [J] (T=%f [K])\n",
-	       1.5*count*K_BOLTZMANN*md.t,md.t);
+	       1.5*md.count*K_BOLTZMANN*md.t,md.t);
 
 	/* check total momentum */
-	p=get_total_p(si,count);
+	p=get_total_p(si,md.count);
 	printf("total momentum: %.30f [Ns]\n",v3_norm(&p));
 
 	/* potential paramters */
@@ -125,7 +113,6 @@ int main(int argc,char **argv) {
 	printf("estimated accurate time step: %.30f [s]\n",
 	       estimate_time_step(&md,3.0,md.t));
 
-
 	/*
 	 * let's do the actual md algorithm now
 	 *
@@ -139,7 +126,7 @@ int main(int argc,char **argv) {
 
 	/* close */
 
-	verlet_list_shutdown(&md);
+	link_cell_shutdown(&md);
 
 	rand_close(&random);