X-Git-Url: https://hackdaworld.org/cgi-bin/gitweb.cgi?a=blobdiff_plain;f=moldyn.c;h=d74b391a72362cd33d5ed6e6e698de9e2bb359de;hb=0656efc2936da55ecf0b818fe33bb2acebc689c6;hp=0fd1aca88d3b7243ee58cbe2d219cf0e4e2190f9;hpb=512390ceb93a2dd630943165b35bba683e0ffcfc;p=physik%2Fposic.git

diff --git a/moldyn.c b/moldyn.c
index 0fd1aca..d74b391 100644
--- a/moldyn.c
+++ b/moldyn.c
@@ -21,6 +21,7 @@
 #include "init/init.h"
 #include "random/random.h"
 #include "visual/visual.h"
+#include "list/list.h"
 
 int moldyn_usage(char **argv) {
 
@@ -33,8 +34,20 @@ int moldyn_usage(char **argv) {
 	printf("-V <steps> <filebase> (rasmol file)\n");
 	printf("--- physics options ---\n");
 	printf("-T <temperature> [K] (%f)\n",MOLDYN_TEMP);
-	printf("-t <timestep tau> [s] (%f)\n",MOLDYN_TAU);
+	printf("-t <timestep tau> [s] (%.15f)\n",MOLDYN_TAU);
+	printf("-C <cutoff radius> [m] (%.15f)\n",MOLDYN_CUTOFF);
 	printf("-R <runs> (%d)\n",MOLDYN_RUNS);
+	printf(" -- integration algo --\n");
+	printf("  -I <number> (%d)\n",MOLDYN_INTEGRATE_DEFAULT);
+	printf("     0: velocity verlet\n");
+	printf(" -- potential --\n");
+	printf("  -P <number> <param1 param2 ...>\n");
+	printf("     0: harmonic oscillator\n");
+	printf("        param1: spring constant\n");
+	printf("        param2: equilibrium distance\n");
+	printf("     1: lennard jones\n");
+	printf("        param1: epsilon\n");
+	printf("        param2: sigma\n");
 	printf("\n");
 
 	return 0;
@@ -43,6 +56,10 @@ 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;
+	t_tersoff_params tp;
+	double s,e;
 
 	memset(moldyn,0,sizeof(t_moldyn));
 
@@ -50,6 +67,8 @@ 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++) {
@@ -63,10 +82,6 @@ int moldyn_parse_argv(t_moldyn *moldyn,int argc,char **argv) {
 					moldyn->mwrite=atoi(argv[++i]);
 					strncpy(moldyn->mfb,argv[++i],64);
 					break;
-				case 'D':
-					moldyn->dwrite=atoi(argv[++i]);
-					strncpy(moldyn->dfb,argv[++i],64);
-					break;
 				case 'S':
 					moldyn->swrite=atoi(argv[++i]);
 					strncpy(moldyn->sfb,argv[++i],64);
@@ -81,9 +96,50 @@ int moldyn_parse_argv(t_moldyn *moldyn,int argc,char **argv) {
 				case 't':
 					moldyn->tau=atof(argv[++i]);
 					break;
+				case 'C':
+					moldyn->cutoff=atof(argv[++i]);
+					break;
 				case 'R':
 					moldyn->time_steps=atoi(argv[++i]);
 					break;
+				case 'I':
+	/* integration algorithm */
+	switch(atoi(argv[++i])) {
+		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);
@@ -98,12 +154,12 @@ int moldyn_parse_argv(t_moldyn *moldyn,int argc,char **argv) {
 	return 0;
 }
 
-int moldyn_log_init(t_moldyn *moldyn,void *v) {
+int moldyn_log_init(t_moldyn *moldyn) {
 
 	moldyn->lvstat=0;
 	t_visual *vis;
 
-	vis=v;
+	vis=&(moldyn->vis);
 
 	if(moldyn->ewrite) {
 		moldyn->efd=open(moldyn->efb,O_WRONLY|O_CREAT|O_TRUNC);
@@ -128,16 +184,6 @@ int moldyn_log_init(t_moldyn *moldyn,void *v) {
 	if(moldyn->swrite)
 		moldyn->lvstat|=MOLDYN_LVSTAT_SAVE;
 
-	if(moldyn->dwrite) {
-		moldyn->dfd=open(moldyn->dfb,O_WRONLY|O_CREAT|O_TRUNC);
-                if(moldyn->dfd<0) {
-			perror("[moldyn] dfd open");
-			return moldyn->dfd;
-		}
-		write(moldyn->dfd,moldyn,sizeof(t_moldyn));
-		moldyn->lvstat|=MOLDYN_LVSTAT_DUMP;
-	}
-
 	if((moldyn->vwrite)&&(vis)) {
 		moldyn->visual=vis;
 		visual_init(vis,moldyn->vfb);
@@ -149,7 +195,7 @@ int moldyn_log_init(t_moldyn *moldyn,void *v) {
 	return 0;
 }
 
-int moldyn_shutdown(t_moldyn *moldyn) {
+int moldyn_log_shutdown(t_moldyn *moldyn) {
 
 	if(moldyn->efd) close(moldyn->efd);
 	if(moldyn->mfd) close(moldyn->efd);
@@ -159,6 +205,33 @@ int moldyn_shutdown(t_moldyn *moldyn) {
 	return 0;
 }
 
+int moldyn_init(t_moldyn *moldyn,int argc,char **argv) {
+
+	int ret;
+
+	ret=moldyn_parse_argv(moldyn,argc,argv);
+	if(ret<0) return ret;
+
+	ret=moldyn_log_init(moldyn);
+	if(ret<0) return ret;
+
+	rand_init(&(moldyn->random),NULL,1);
+	moldyn->random.status|=RAND_STAT_VERBOSE;
+
+	moldyn->status=0;
+
+	return 0;
+}
+
+int moldyn_shutdown(t_moldyn *moldyn) {
+
+	moldyn_log_shutdown(moldyn);
+	rand_close(&(moldyn->random));
+	free(moldyn->atom);
+
+	return 0;
+}
+
 int create_lattice(unsigned char type,int element,double mass,double lc,
                    int a,int b,int c,t_atom **atom) {
 
@@ -215,7 +288,7 @@ 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) {
 
 	/*
 	 * - gaussian distribution of velocities
@@ -227,12 +300,14 @@ int thermal_init(t_moldyn *moldyn,t_random *random,int count) {
 	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++) {
+	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);
@@ -249,19 +324,19 @@ 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;
@@ -273,10 +348,10 @@ 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;
@@ -298,7 +373,7 @@ 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) {
@@ -338,6 +413,144 @@ double estimate_time_step(t_moldyn *moldyn,double nn_dist,double t) {
 	return tau;	
 }
 
+/*
+ * numerical tricks
+ */
+
+/* linked list / cell method */
+
+int link_cell_init(t_moldyn *moldyn) {
+
+	t_linkcell *lc;
+	int i;
+
+	lc=&(moldyn->lc);
+
+	/* list log fd */
+	lc->listfd=open("/dev/null",O_WRONLY);
+
+	/* 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("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]));
+
+ 	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<moedyn->count;count++) {
+		i=(atom[count].r.x+(moldyn->dim.x/2))/lc->x;
+		j=(atom[count].r.y+(moldyn->dim.y/2))/lc->y;
+		k=(atom[count].r.z+(moldyn->dim.z/2))/lc->z;
+		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;
+	unsigned char 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=count2;
+	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]));
+
+	if(lc->listfd) close(lc->listfd);
+
+	return 0;
+}
 
 /*
  *
@@ -356,6 +569,10 @@ int moldyn_integrate(t_moldyn *moldyn) {
 	int fd;
 	char fb[128];
 
+	/* initialize linked cell method */
+	link_cell_init(moldyn);
+
+	/* logging & visualization */
 	e=moldyn->ewrite;
 	m=moldyn->mwrite;
 	s=moldyn->swrite;
@@ -367,14 +584,19 @@ int moldyn_integrate(t_moldyn *moldyn) {
 		return -1;
 	}
 
+	/* sqaure of some variables */
+	moldyn->tau_square=moldyn->tau*moldyn->tau;
+	moldyn->cutoff_square=moldyn->cutoff*moldyn->cutoff;
+
 	/* calculate initial forces */
-	moldyn->force(moldyn);
+	moldyn->potential_force_function(moldyn);
 
 	for(i=0;i<moldyn->time_steps;i++) {
+
 		/* integration step */
 		moldyn->integrate(moldyn);
 
-		/* check for log & visualiziation */
+		/* check for log & visualization */
 		if(e) {
 			if(!(i%e))
 				dprintf(moldyn->efd,
@@ -400,18 +622,16 @@ int moldyn_integrate(t_moldyn *moldyn) {
 					write(fd,moldyn->atom,
 					      moldyn->count*sizeof(t_atom));
 				}
+				close(fd);
 			}	
 		}
-		if(d) {
-			if(!(i%d))
-				write(moldyn->dfd,moldyn->atom,
-				      moldyn->count*sizeof(t_atom));
-
-		}
 		if(v) {
-			if(!(i%v))
+			if(!(i%v)) {
 				visual_atoms(moldyn->visual,i*moldyn->tau,
 				             moldyn->atom,moldyn->count);
+				printf("\rsteps: %d",i);
+				fflush(stdout);
+			}
 		}
 	}
 
@@ -430,8 +650,7 @@ int velocity_verlet(t_moldyn *moldyn) {
 	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 */
@@ -446,8 +665,16 @@ int velocity_verlet(t_moldyn *moldyn) {
 		v3_add(&(atom[i].v),&(atom[i].v),&delta);
 	}
 
+	/* neighbour list update */
+printf("list update ...\n");
+	link_cell_update(moldyn);
+printf("done\n");
+
 	/* forces depending on chosen potential */
-	moldyn->force(moldyn);
+printf("calc potential/force ...\n");
+	potential_force_calc(moldyn);
+	//moldyn->potential_force_function(moldyn);
+printf("done\n");
 
 	for(i=0;i<count;i++) {
 		/* again velocities */
@@ -465,148 +692,721 @@ int velocity_verlet(t_moldyn *moldyn) {
  * 
  */
 
-/* harmonic oscillator potential and force */
+/* generic potential and force calculation */
 
-double potential_harmonic_oscillator(t_moldyn *moldyn) {
+int potential_force_calc(t_moldyn *moldyn) {
 
-	t_ho_params *params;
+	int i,count;
 	t_atom *atom;
-	int i,j;
-	int count;
-	t_3dvec distance;
-	double d,u;
-	double sc,equi_dist;
+	t_linkcell *lc;
+	t_list neighbour[27];
+	t_list *this;
+	double u;
+	unsigned char bc,bc3;
+	int countn,dnlc;
 
-	params=moldyn->pot_params;
-	atom=moldyn->atom;
-	sc=params->spring_constant;
-	equi_dist=params->equilibrium_distance;
 	count=moldyn->count;
+	atom=moldyn->atom;
+	lc=&(moldyn->lc);
+
+	/* reset energy */
+	moldyn->energy=0.0;
 
-	u=0.0;
 	for(i=0;i<count;i++) {
-		for(j=0;j<i;j++) {
-			v3_sub(&distance,&(atom[i].r),&(atom[j].r));
-			d=v3_norm(&distance);
-			u+=(0.5*sc*(d-equi_dist)*(d-equi_dist));
+	
+		/* reset force */
+		v3_zero(&(atom[i].f));
+
+		/* single particle potential/force */
+		if(atom[i].attr&ATOM_ATTR_1BP)
+			moldyn->pf_func1b(moldyn,&(atom[i]));
+
+		/* 2 body pair potential/force */
+		if(atom[i].attr&(ATOM_ATTR_2BP|ATOM_ATTR_3BP)) {
+		
+			link_cell_neighbour_index(moldyn,
+				(atom[i].r.x+moldyn->dim.x/2)/lc->x,
+				(atom[i].r.y+moldyn->dim.y/2)/lc->y,
+				(atom[i].r.z+moldyn->dim.z/2)/lc->z,
+				neighbour);
+
+			countn=lc->countn;
+			dnlc=lc->dnlc;
+
+			for(j=0;j<countn;j++) {
+
+				this=&(neighbour[j]);
+				list_reset(this);
+
+				if(this->start==NULL)
+					continue;
+
+				bc=(j<dnlc)?0:1;
+
+				do {
+					btom=this->current->data;
+
+					if(btom==&(atom[i]))
+						continue;
+
+					if((btom->attr&ATOM_ATTR_2BP)&
+					   (atom[i].attr&ATOM_ATTR_2BP))
+						moldyn->pf_func2b(moldyn,
+						                  &(atom[i]),
+						                  btom,
+						                  bc);
+
+					/* 3 body potential/force */
+
+					if(!(atom[i].attr&ATOM_ATTR_3BP)||
+					   !(btom->attr&ATOM_ATTR_3BP))
+						continue;
+
+					link_cell_neighbour_index(moldyn,
+					   (btom->r.x+moldyn->dim.x/2)/lc->x,
+					   (btom->r.y+moldyn->dim.y/2)/lc->y,
+					   (btom->r.z+moldyn->dim.z/2)/lc->z,
+					   neighbourk);
+
+					for(k=0;k<lc->countn;k++) {
+
+						thisk=&(neighbourk[k]);
+						list_reset(thisk);
+					
+						if(thisk->start==NULL)
+							continue;
+
+						bck=(k<lc->dnlc)?0:1;
+
+						do {
+
+			ktom=thisk->current->data;
+
+			if(!(ktom->attr&ATOM_ATTR_3BP))
+				continue;
+
+			if(ktom==btom)
+				continue;
+
+			if(ktom==&(atom[i]))
+				continue;
+
+			moldyn->pf_func3b(moldyn,&(atom[i]),btom,ktom,bck);
+
+						} while(list_next(thisk)!=\
+						        L_NO_NEXT_ELEMENT);
+					
+				} while(list_next(this)!=L_NO_NEXT_ELEMENT);
+			}
 		}
 	}
 
-	return u;
+	return 0;
 }
 
-int force_harmonic_oscillator(t_moldyn *moldyn) {
+/*
+ * example potentials
+ */
+
+/* harmonic oscillator potential and force */
+
+int harmonic_oscillator(t_moldyn *moldyn,t_atom *ai,t_atom *aj,unsigned char bc)) {
 
 	t_ho_params *params;
-	int i,j,count;
-	t_atom *atom;
-	t_3dvec distance;
-	t_3dvec force;
-	double d;
+	t_atom *atom,*btom;
+	t_linkcell *lc;
+	t_list *this,neighbour[27];
+	int i,j,c;
+	int count;
+	t_3dvec force,distance;
+	double d,u;
 	double sc,equi_dist;
+	int ni,nj,nk;
 
-	atom=moldyn->atom;	
-	count=moldyn->count;
 	params=moldyn->pot_params;
+	atom=moldyn->atom;
+	lc=&(moldyn->lc);
 	sc=params->spring_constant;
 	equi_dist=params->equilibrium_distance;
+	count=moldyn->count;
 
-	for(i=0;i<count;i++) v3_zero(&(atom[i].f));
+	/* reset energy counter */
+	u=0.0;
 
 	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));
+		/* reset force */
+		v3_zero(&(atom[i].f));
+
+		/* determine cell + neighbours */
+		ni=(atom[i].r.x+(moldyn->dim.x/2))/lc->x;
+		nj=(atom[i].r.y+(moldyn->dim.y/2))/lc->y;
+		nk=(atom[i].r.z+(moldyn->dim.z/2))/lc->z;
+		c=link_cell_neighbour_index(moldyn,ni,nj,nk,neighbour);
+
+		/*
+		 * processing cell of atom i
+		 * => no need to check for empty list (1 element at minimum)
+		 */
+		this=&(neighbour[0]);
+		list_reset(this);
+		do {
+			btom=this->current->data;
+			if(btom==&(atom[i]))
+				continue;
+			v3_sub(&distance,&(atom[i].r),&(btom->r));
 			d=v3_norm(&distance);
 			if(d<=moldyn->cutoff) {
+				u+=(0.5*sc*(d-equi_dist)*(d-equi_dist));
 				v3_scale(&force,&distance,
-				         (-sc*(1.0-(equi_dist/d))));
+				         -sc*(1.0-(equi_dist/d)));
 				v3_add(&(atom[i].f),&(atom[i].f),&force);
-				v3_sub(&(atom[j].f),&(atom[j].f),&force);
+			}
+		} while(list_next(this)!=L_NO_NEXT_ELEMENT);
+
+		/*
+		 * direct neighbour cells
+		 * => no boundary condition check necessary
+		 */
+		for(j=1;j<c;j++) {
+			this=&(neighbour[j]);
+			list_reset(this); /* there might not be a single atom */
+			if(this->start!=NULL) {
+
+			do {
+				btom=this->current->data;
+				v3_sub(&distance,&(atom[i].r),&(btom->r));
+				d=v3_norm(&distance);
+				if(d<=moldyn->cutoff) {
+					u+=(0.5*sc*(d-equi_dist)*(d-equi_dist));
+					v3_scale(&force,&distance,
+					         -sc*(1.0-(equi_dist/d)));
+					v3_add(&(atom[i].f),&(atom[i].f),
+					       &force);
+				}
+			} while(list_next(this)!=L_NO_NEXT_ELEMENT);
+
+			}
+		}
+
+		/*
+		 * indirect neighbour cells
+		 * => check boundary conditions
+		 */
+		for(j=c;j<27;j++) {
+			this=&(neighbour[j]);
+			list_reset(this); /* check boundary conditions */
+			if(this->start!=NULL) {
+
+			do {
+				btom=this->current->data;
+				v3_sub(&distance,&(atom[i].r),&(btom->r));
+				v3_per_bound(&distance,&(moldyn->dim));
+				d=v3_norm(&distance);
+				if(d<=moldyn->cutoff) {
+					u+=(0.5*sc*(d-equi_dist)*(d-equi_dist));
+					v3_scale(&force,&distance,
+					         -sc*(1.0-(equi_dist/d)));
+					v3_add(&(atom[i].f),&(atom[i].f),
+					       &force);
+				}
+			} while(list_next(this)!=L_NO_NEXT_ELEMENT);
+
 			}
 		}
 	}
 
+	moldyn->energy=0.5*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;
-	int i,j;
+	t_atom *atom,*btom;
+	t_linkcell *lc;
+	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 ni,nj,nk;
 
 	params=moldyn->pot_params;
 	atom=moldyn->atom;
+	lc=&(moldyn->lc);
 	count=moldyn->count;
-	eps=params->epsilon;
+	eps=params->epsilon4;
 	sig6=params->sigma6;
 	sig12=params->sigma12;
 
+	/* reset energy counter */
 	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);
+		/* reset force */
+		v3_zero(&(atom[i].f));
+
+		/* determine cell + neighbours */
+		ni=(atom[i].r.x+(moldyn->dim.x/2))/lc->x;
+		nj=(atom[i].r.y+(moldyn->dim.y/2))/lc->y;
+		nk=(atom[i].r.z+(moldyn->dim.z/2))/lc->z;
+		c=link_cell_neighbour_index(moldyn,ni,nj,nk,neighbour);
+
+		/* processing cell of atom i */
+		this=&(neighbour[0]);
+		list_reset(this); /* list has 1 element at minimum */
+		do {
+			btom=this->current->data;
+			if(btom==&(atom[i]))
+				continue;
+			v3_sub(&distance,&(atom[i].r),&(btom->r));
+			d=v3_absolute_square(&distance);	/* 1/r^2 */
+			if(d<=moldyn->cutoff_square) {
+				d=1.0/d;	/* 1/r^2 */
+				h2=d*d; 	/* 1/r^4 */
+				h2*=d;	 	/* 1/r^6 */
+				h1=h2*h2; 	/* 1/r^12 */
+				u+=eps*(sig12*h1-sig6*h2);
+				h2*=d;		/* 1/r^8 */
+				h1*=d;		/* 1/r^14 */
+				h2*=6*sig6;
+				h1*=12*sig12;
+				d=+h1-h2;
+				d*=eps;
+				v3_scale(&force,&distance,d);
+				v3_add(&(atom[i].f),&(atom[i].f),&force);
+			}
+		} while(list_next(this)!=L_NO_NEXT_ELEMENT);
+
+		/* neighbours not doing boundary condition overflow */
+		for(j=1;j<c;j++) {
+			this=&(neighbour[j]);
+			list_reset(this); /* there might not be a single atom */
+			if(this->start!=NULL) {
+
+			do {
+				btom=this->current->data;
+				v3_sub(&distance,&(atom[i].r),&(btom->r));
+				d=v3_absolute_square(&distance); /* r^2 */
+				if(d<=moldyn->cutoff_square) {
+					d=1.0/d;	/* 1/r^2 */
+					h2=d*d; 	/* 1/r^4 */
+					h2*=d;	 	/* 1/r^6 */
+					h1=h2*h2; 	/* 1/r^12 */
+					u+=eps*(sig12*h1-sig6*h2);
+					h2*=d;		/* 1/r^8 */
+					h1*=d;		/* 1/r^14 */
+					h2*=6*sig6;
+					h1*=12*sig12;
+					d=+h1-h2;
+					d*=eps;
+					v3_scale(&force,&distance,d);
+					v3_add(&(atom[i].f),&(atom[i].f),
+					       &force);
+				}
+			} while(list_next(this)!=L_NO_NEXT_ELEMENT);
+				
+			}
+		}
+
+		/* neighbours due to boundary conditions */
+		for(j=c;j<27;j++) {
+			this=&(neighbour[j]);
+			list_reset(this); /* check boundary conditions */
+			if(this->start!=NULL) {
+
+			do {
+				btom=this->current->data;
+				v3_sub(&distance,&(atom[i].r),&(btom->r));
+				v3_per_bound(&distance,&(moldyn->dim));
+				d=v3_absolute_square(&distance); /* r^2 */
+				if(d<=moldyn->cutoff_square) {
+					d=1.0/d;	/* 1/r^2 */
+					h2=d*d; 	/* 1/r^4 */
+					h2*=d; 		/* 1/r^6 */
+					h1=h2*h2; 	/* 1/r^12 */
+					u+=eps*(sig12*h1-sig6*h2);
+					h2*=d;		/* 1/r^8 */
+					h1*=d;		/* 1/r^14 */
+					h2*=6*sig6;
+					h1*=12*sig12;
+					d=+h1-h2;
+					d*=eps;
+					v3_scale(&force,&distance,d);
+					v3_add(&(atom[i].f),&(atom[i].f),
+					       &force);
+				}
+			} while(list_next(this)!=L_NO_NEXT_ELEMENT);
+
+			}
 		}
 	}
+
+	moldyn->energy=0.5*u;
 	
-	return u;
+	return 0;
 }
 
-int force_lennard_jones(t_moldyn *moldyn) {
+/* tersoff potential & force for 2 sorts of atoms */
 
-	t_lj_params *params;
-	int i,j,count;
-	t_atom *atom;
-	t_3dvec distance;
-	t_3dvec force;
-	double d,h1,h2;
-	double eps,sig6,sig12;
+int tersoff(t_moldyn *moldyn) {
 
-	atom=moldyn->atom;	
-	count=moldyn->count;
-	params=moldyn->pot_params;
-	eps=params->epsilon;
-	sig6=params->sigma6;
-	sig12=params->sigma12;
+	t_tersoff_params *params;
+	t_atom *atom,*btom,*ktom;
+	t_linkcell *lc;
+	t_list *this,*thisk,neighbour[27],neighbourk[27];
+	int i,j,k,c,ck;
+	int count;
+	double u;
+	int ni,nj,nk;
+	int ki,kj,kk;
+	
 
-	for(i=0;i<count;i++) v3_zero(&(atom[i].f));
+	params=moldyn->pot_params;
+	atom=moldyn->atom;
+	lc=&(moldyn->lc);
+	count=moldyn->count;
+	
+	/* reset energy counter */
+	u=0.0;
 
 	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);
+		/* reset force */
+		v3_zero(&(atom[i].f));
+
+		/* determin cell neighbours */
+		ni=(atom[i].r.x+(moldyn->dim.x/2))/lc->x;
+		nj=(atom[i].r.y+(moldyn->dim.y/2))/lc->y;
+		nk=(atom[i].r.z+(moldyn->dim.z/2))/lc->z;
+		c=link_cell_neighbour_index(moldyn,ni,nj,nk,neighbour);
+
+		/*
+		 * processing cell of atom i
+		 * => no need to check for empty list (1 element at minimum)
+		 */
+		this=&(neighbour[0]);
+		list_reset(this);
+		do {
+			btom=this->current->data;
+			if(btom==&(atom[i]))
+				continue;
+
+			/* 2 body stuff */
+
+			/* we need: f_c, df_c, f_r, df_r */
+
+			v3_sub(&dist_ij,btom,&(atom[i]));
+			d_ij=v3_norm(&dist_ij);
+			if(d_ij<=S) {
+
+				/* determine the tersoff parameters */
+				if(atom[i].element!=btom->element) {
+				S=sqrt(TERSOFF_S[e1]*TERSOFF_S[e2]);
+				R=R_m;
+				A=;
+				lambda=;
+				B=;
+				mu=;
+				chi=;
+				beta=;
+				betaN=;
+
+				if(d_ij<=R) {
+					df_r=-lambda*A*exp(-lambda*d_ij)/d_ij;
+					v3_scale(&force,&dist_ij,df_r);
+					v3_add(&(atom[i].f),&(atom[i].f),
+						&force);
+				}
+				else {
+					s_r=S-R;
+					arg1=PI*(d_ij-R)/s_r;
+					f_c=0.5+0.5*cos(arg1);
+					df_c=-0.5*sin(arg1)*(PI/(s_r*d_ij));
+					f_r=A*exp(-lambda*d_ij);
+					df_r=-lambda*f_r/d_ij;
+					scale=df_c*f_r+df_r*f_c;
+					v3_scale(&force,&dist_ij,scale);
+					v3_add(&(atom[i].f),&(atom[i].f),
+					       &force);
+				}
+			}
+			else 
+				continue;		
+
+			
+			/* end 2 body stuff */ 
+
+			/* determine cell neighbours of btom */
+			ki=(btom->r.x+(moldyn->dim.x/2))/lc->x;
+			kj=(btom->r.y+(moldyn->dim.y/2))/lc->y;
+			kk=(btom->r.z+(moldyn->dim.z/2))/lc->z;
+			ck=link_cell_neighbour_index(moldyn,ki,kj,kk,
+			                             neighbourk);
+
+			/* go for zeta - 3 body stuff! */
+			zeta=0.0;
+			d_ij2=d_ij*d_ij;
+
+			/* cell of btom */
+			thisk=&(neighbourk[0]);
+			list_reset(thisk);
+			do {
+				ktom=thisk->current->data;
+				if(ktom==btom)
+					continue;
+				if(ktom==&(atom[i]))
+					continue;
+				
+				/* 3 body stuff (1) */
+				
+				v3_sub(&dist_ik,ktom,&(atom[i]));
+				d_ik=v3_norm(&dist_ik);
+				if(d_ik<=Sik) {
+
+				Rik=;
+				Sik=;
+				Aik=;
+				lambda_ik=;
+				Bik=;
+				mu_ik=;
+				omega_ik=;
+				c_i=;
+				d_i=;
+				h_i=;
+			
+
+					if(d_ik<=Rik) {
+						f_cik=1.0;
+						df_cik=0.0;
+					}
+					else {
+						sik_rik=Sik-Rik;
+						arg1ik=PI*(d_ik-Rik)/sik_rik;
+						f_cik=0.5+0.5*cos(arg1ik);
+						df_cik=-0.5*sin(arg1ik)* \
+						       (PI/(sik_rik*d_ik));
+						f_rik=Aik*exp(-lambda_ik*d_ik);
+						f_aik=-Bik*exp(-mu_ik*d_ik);
+					}
+			
+					v3_sub(&distance_jk,ktom,btom);
+					cos_theta=(d_ij2+d_ik*d_ik-d_jk*d_jk)/\
+					          (2*d_ij*d_ik);
+					sin_theta=sqrt(1.0/\
+					          (cos_theta*cos_theta));
+					theta=arccos(cos_theta);
+
+					
+				}
+				else
+					continue;
+
+				/* end 3 body stuff (1) */
+
+
+			} while(list_next(thisk)!=L_NO_NEXT_ELEMENT);
+
+			/* direct neighbours of btom cell */
+			for(k=1;k<ck;k++) {
+				thisk=&(neighbourk[k]);
+				list_reset(thisk);
+				if(thisk->start!=NULL) {
+
+				do {
+					ktom=thisk->current->data;
+					if(ktom==&(atom[i]))
+						continue;
+
+				/* 3 body stuff (2) */
+
+				} while(list_next(thisk)!=L_NO_NEXT_ELEMENT);
+
+				}
+			}
+
+			/* indirect neighbours of btom cell */
+			for(k=ck;k<27;k++) {
+				thisk=&(neighbourk[k]);
+				list_reset(thisk);
+				if(thisk->start!=NULL) {
+
+				do {
+					ktom=thisk->current->data;
+					if(ktom==&(atom[i]))
+						continue;
+
+				/* 3 body stuff */
+
+				} while(list_next(thisk)!=L_NO_NEXT_ELEMENT);
+
+				}
+			}
+
+
+		} while(list_next(this)!=L_NO_NEXT_ELEMENT);
+
+		/*
+		 * direct neighbour cells of atom i
+		 */
+		for(j=1;j<c;j++) {
+			this=&(neighbour[j]);
+			list_reset(this);
+			if(this->start!=NULL) {
+
+			do {
+				btom=this->current->data;
+
+				/* 2 body stuff */
+
+
+			/* determine cell neighbours of btom */
+			ki=(btom->r.x+(moldyn->dim.x/2))/lc->x;
+			kj=(btom->r.y+(moldyn->dim.y/2))/lc->y;
+			kk=(btom->r.z+(moldyn->dim.z/2))/lc->z;
+			ck=link_cell_neighbour_index(moldyn,ki,kj,kk,
+			                             neighbourk);
+
+			/* cell of btom */
+			thisk=&(neighbourk[0]);
+			list_reset(thisk);
+			do {
+				ktom=thisk->current->data;
+				if(ktom==btom)
+					continue;
+				if(ktom==&(atom[i]))
+					continue;
+				
+				/* 3 body stuff (1) */
+
+			} while(list_next(thisk)!=L_NO_NEXT_ELEMENT);
+
+			/* direct neighbours of btom cell */
+			for(k=1;k<ck;k++) {
+				thisk=&(neighbourk[k]);
+				list_reset(thisk);
+				if(thisk->start!=NULL) {
+
+				do {
+					ktom=thisk->current->data;
+					if(ktom==&(atom[i]))
+						continue;
+
+				/* 3 body stuff (2) */
+
+				} while(list_next(thisk)!=L_NO_NEXT_ELEMENT);
+
+				}
+			}
+
+			/* indirect neighbours of btom cell */
+			for(k=ck;k<27;k++) {
+				thisk=&(neighbourk[k]);
+				list_reset(thisk);
+				if(thisk->start!=NULL) {
+
+				do {
+					ktom=thisk->current->data;
+					if(ktom==&(atom[i]))
+						continue;
+
+				/* 3 body stuff (3) */
+
+				} while(list_next(thisk)!=L_NO_NEXT_ELEMENT);
+
+				}
+			}
+
+
+			} while(list_next(this)!=L_NO_NEXT_ELEMENT);
+
 			}
 		}
+
+		/*
+		 * indirect neighbour cells of atom i
+		 */
+		for(j=c;j<27;j++) {
+			this=&(neighbour[j]);
+			list_reset(this);
+			if(this->start!=NULL) {
+
+			do {
+				btom=this->current->data;
+
+				/* 2 body stuff */
+
+
+			/* determine cell neighbours of btom */
+			ki=(btom->r.x+(moldyn->dim.x/2))/lc->x;
+			kj=(btom->r.y+(moldyn->dim.y/2))/lc->y;
+			kk=(btom->r.z+(moldyn->dim.z/2))/lc->z;
+			ck=link_cell_neighbour_index(moldyn,ki,kj,kk,
+			                             neighbourk);
+
+			/* cell of btom */
+			thisk=&(neighbourk[0]);
+			list_reset(thisk);
+			do {
+				ktom=thisk->current->data;
+				if(ktom==btom)
+					continue;
+				if(ktom==&(atom[i]))
+					continue;
+				
+				/* 3 body stuff (1) */
+
+			} while(list_next(thisk)!=L_NO_NEXT_ELEMENT);
+
+			/* direct neighbours of btom cell */
+			for(k=1;k<ck;k++) {
+				thisk=&(neighbourk[k]);
+				list_reset(thisk);
+				if(thisk->start!=NULL) {
+
+				do {
+					ktom=thisk->current->data;
+					if(ktom==&(atom[i]))
+						continue;
+
+				/* 3 body stuff (2) */
+
+				} while(list_next(thisk)!=L_NO_NEXT_ELEMENT);
+
+				}
+			}
+
+			/* indirect neighbours of btom cell */
+			for(k=ck;k<27;k++) {
+				thisk=&(neighbourk[k]);
+				list_reset(thisk);
+				if(thisk->start!=NULL) {
+
+				do {
+					ktom=thisk->current->data;
+					if(ktom==&(atom[i]))
+						continue;
+
+				/* 3 body stuff (3) */
+
+				} while(list_next(thisk)!=L_NO_NEXT_ELEMENT);
+
+				}
+			}
+
+
+			} while(list_next(this)!=L_NO_NEXT_ELEMENT);
+
+			}
+		}
+		
 	}
 
+	moldyn->energy=0.5*u;
+
 	return 0;
 }