X-Git-Url: https://hackdaworld.org/gitweb/?a=blobdiff_plain;f=moldyn.c;h=ad0f9a383ea7ae3e01a5a7c3ebc67de518756dc6;hb=e763f6e3072fbbbc5ecf7345b989d7d29929a38f;hp=4b580890f3eaab417494fa497130f53570130ce4;hpb=e6f456c0fa807b86e1b25996e70efcdcfe390ea5;p=physik%2Fposic.git

diff --git a/moldyn.c b/moldyn.c
index 4b58089..ad0f9a3 100644
--- a/moldyn.c
+++ b/moldyn.c
@@ -35,6 +35,7 @@ int moldyn_usage(char **argv) {
 	printf("--- physics options ---\n");
 	printf("-T <temperature> [K] (%f)\n",MOLDYN_TEMP);
 	printf("-t <timestep tau> [s] (%.15f)\n",MOLDYN_TAU);
+	printf("-C <cutoff radius> [m] (%.15f)\n",MOLDYN_CUTOFF);
 	printf("-R <runs> (%d)\n",MOLDYN_RUNS);
 	printf(" -- integration algo --\n");
 	printf("  -I <number> (%d)\n",MOLDYN_INTEGRATE_DEFAULT);
@@ -98,6 +99,9 @@ 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;
@@ -153,12 +157,12 @@ 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);
@@ -204,7 +208,7 @@ 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);
@@ -214,6 +218,33 @@ 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) {
 
@@ -270,7 +301,7 @@ int destroy_lattice(t_atom *atom) {
 	return 0;
 }
 
-int thermal_init(t_moldyn *moldyn,t_random *random) {
+int thermal_init(t_moldyn *moldyn) {
 
 	/*
 	 * - gaussian distribution of velocities
@@ -282,8 +313,10 @@ int thermal_init(t_moldyn *moldyn,t_random *random) {
 	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);
@@ -402,9 +435,13 @@ double estimate_time_step(t_moldyn *moldyn,double nn_dist,double t) {
 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;
@@ -413,7 +450,14 @@ int link_cell_init(t_moldyn *moldyn) {
 	lc->nz=moldyn->dim.z/moldyn->cutoff;
 	lc->z=moldyn->dim.z/lc->nz;
 
-	lc->subcell=malloc(lc->nx*lc->ny*lc->nz*sizeof(t_list));
+	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);
 	
@@ -434,13 +478,13 @@ int link_cell_update(t_moldyn *moldyn) {
 	ny=lc->ny;
 	nz=lc->nz;
 
-	for(i=0;i<nx*ny*nz;i++)
+	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/lc->x;
-		j=atom[count].r.y/lc->y;
-		k=atom[count].r.z/lc->z;
+		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]));
 	}
@@ -461,11 +505,12 @@ int link_cell_neighbour_index(t_moldyn *moldyn,int i,int j,int k,t_list *cell) {
 	lc=&(moldyn->lc);
 	nx=lc->nx;
 	ny=lc->ny;
-	nx=lc->nz;
+	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;
@@ -488,7 +533,7 @@ int link_cell_neighbour_index(t_moldyn *moldyn,int i,int j,int k,t_list *cell) {
 					z=(z+nz)%nz;
 					bz=1;
 				}
-				if(!(x|y|z)) continue;
+				if(!(ci|cj|ck)) continue;
 				if(bx|by|bz) {
 					cell[--count2]=lc->subcell[x+y*nx+z*a];
 				}
@@ -512,6 +557,8 @@ int link_cell_shutdown(t_moldyn *moldyn) {
 	for(i=0;i<lc->nx*lc->ny*lc->nz;i++)
 		list_shutdown(&(moldyn->lc.subcell[i]));
 
+	if(lc->listfd) close(lc->listfd);
+
 	return 0;
 }
 
@@ -532,6 +579,9 @@ 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;
@@ -548,18 +598,10 @@ int moldyn_integrate(t_moldyn *moldyn) {
 	moldyn->tau_square=moldyn->tau*moldyn->tau;
 	moldyn->cutoff_square=moldyn->cutoff*moldyn->cutoff;
 
-	/* create the neighbour list */
-	link_cell_update(moldyn);
-
 	/* calculate initial forces */
 	moldyn->potential_force_function(moldyn);
 
 	for(i=0;i<moldyn->time_steps;i++) {
-		/* show runs */
-		printf(".");
-
-		/* neighbour list update */
-		link_cell_update(moldyn);
 
 		/* integration step */
 		moldyn->integrate(moldyn);
@@ -599,9 +641,12 @@ int moldyn_integrate(t_moldyn *moldyn) {
 
 		}
 		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);
+			}
 		}
 	}
 
@@ -635,8 +680,15 @@ 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 */
+printf("calc potential/force ...\n");
 	moldyn->potential_force_function(moldyn);
+printf("done\n");
 
 	for(i=0;i<count;i++) {
 		/* again velocities */
@@ -676,29 +728,43 @@ int harmonic_oscillator(t_moldyn *moldyn) {
 	equi_dist=params->equilibrium_distance;
 	count=moldyn->count;
 
+	/* reset energy counter */
 	u=0.0;
+
 	for(i=0;i<count;i++) {
+		/* reset force */
+		v3_zero(&(atom[i].f));
+
 		/* determine cell + neighbours */
-		ni=atom[i].r.x/lc->x;
-		nj=atom[i].r.y/lc->y;
-		nk=atom[i].r.z/lc->z;
+		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 */
+		/*
+		 * processing cell of atom i
+		 * => no need to check for empty list (1 element at minimum)
+		 */
 		this=&(neighbour[0]);
-		list_reset(this); /* list has 1 element at minimum */
+		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);
-			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);
+			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);
 
-		/* neighbours not doing boundary condition overflow */
+		/*
+		 * 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 */
@@ -720,7 +786,10 @@ int harmonic_oscillator(t_moldyn *moldyn) {
 			}
 		}
 
-		/* neighbours due to boundary conditions */
+		/*
+		 * indirect neighbour cells
+		 * => check boundary conditions
+		 */
 		for(j=c;j<27;j++) {
 			this=&(neighbour[j]);
 			list_reset(this); /* check boundary conditions */
@@ -744,7 +813,7 @@ int harmonic_oscillator(t_moldyn *moldyn) {
 		}
 	}
 
-	moldyn->energy=u;
+	moldyn->energy=0.5*u;
 
 	return 0;
 }
@@ -772,12 +841,17 @@ int lennard_jones(t_moldyn *moldyn) {
 	sig6=params->sigma6;
 	sig12=params->sigma12;
 
+	/* reset energy counter */
 	u=0.0;
+
 	for(i=0;i<count;i++) {
+		/* reset force */
+		v3_zero(&(atom[i].f));
+
 		/* determine cell + neighbours */
-		ni=atom[i].r.x/lc->x;
-		nj=atom[i].r.y/lc->y;
-		nk=atom[i].r.z/lc->z;
+		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 */
@@ -788,19 +862,22 @@ int lennard_jones(t_moldyn *moldyn) {
 			if(btom==&(atom[i]))
 				continue;
 			v3_sub(&distance,&(atom[i].r),&(btom->r));
-			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);
+			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 */
@@ -815,7 +892,7 @@ int lennard_jones(t_moldyn *moldyn) {
 				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*d; 	/* 1/r^4 */
 					h2*=d;	 	/* 1/r^6 */
 					h1=h2*h2; 	/* 1/r^12 */
 					u+=eps*(sig12*h1-sig6*h2);
@@ -823,7 +900,7 @@ int lennard_jones(t_moldyn *moldyn) {
 					h1*=d;		/* 1/r^14 */
 					h2*=6*sig6;
 					h1*=12*sig12;
-					d=-h1+h2;
+					d=+h1-h2;
 					d*=eps;
 					v3_scale(&force,&distance,d);
 					v3_add(&(atom[i].f),&(atom[i].f),
@@ -847,7 +924,7 @@ int lennard_jones(t_moldyn *moldyn) {
 				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*d; 	/* 1/r^4 */
 					h2*=d; 		/* 1/r^6 */
 					h1=h2*h2; 	/* 1/r^12 */
 					u+=eps*(sig12*h1-sig6*h2);
@@ -855,7 +932,7 @@ int lennard_jones(t_moldyn *moldyn) {
 					h1*=d;		/* 1/r^14 */
 					h2*=6*sig6;
 					h1*=12*sig12;
-					d=-h1+h2;
+					d=+h1-h2;
 					d*=eps;
 					v3_scale(&force,&distance,d);
 					v3_add(&(atom[i].f),&(atom[i].f),
@@ -867,8 +944,355 @@ int lennard_jones(t_moldyn *moldyn) {
 		}
 	}
 
-	moldyn->energy=u;
+	moldyn->energy=0.5*u;
 	
 	return 0;
 }
 
+/* tersoff potential & force for 2 sorts of atoms */
+
+int tersoff(t_moldyn *moldyn) {
+
+	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;
+	
+
+	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++) {
+		/* 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 */
+
+			v3_sub(&dist_ij,btom,&(atom[i]));
+			d_ij=v3_norm(&dist_ij);
+			if(d_ij<=S) {
+
+				S=;
+				R=;
+				A=;
+				lambda=;
+				B=;
+				mu=;
+				chi=;
+				beta=;
+				betaN=;
+
+				if(d_ij<=R) {
+					f_c=1.0;
+					df_c=0.0;
+				}
+				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);
+					f_a=-B*exp(-mu*d_ij);
+				}
+			}
+			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);
+					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;
+}
+