X-Git-Url: https://hackdaworld.org/gitweb/?a=blobdiff_plain;f=moldyn.c;h=57f76c433ae7d431fc860dc51ddc21b6982a6d29;hb=06912ca45b46de412570a4bd5b5484aa9e8d6e6b;hp=ecba8baffc40a07c641eee9bfed8838c7c8116cc;hpb=eceebe3ee412aa8cea3e6a7f0038883707f78460;p=physik%2Fposic.git

diff --git a/moldyn.c b/moldyn.c
index ecba8ba..57f76c4 100644
--- a/moldyn.c
+++ b/moldyn.c
@@ -5,16 +5,232 @@
  *
  */
 
-#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_usage(char **argv) {
+
+	printf("\n%s usage:\n\n",argv[0]);
+	printf("--- general options ---\n");
+	printf("-E <steps> <file> (log total energy)\n");
+	printf("-M <steps> <file> (log total momentum)\n");
+	printf("-D <steps> <file> (dump total information)\n");
+	printf("-S <steps> <filebase> (single save file)\n");
+	printf("-V <steps> <filebase> (rasmol file)\n");
+	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);
+	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;
+}
+
+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));
+
+	/* default values */
+	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++) {
+		if(argv[i][0]=='-') {
+			switch(argv[i][1]){
+				case 'E':
+					moldyn->ewrite=atoi(argv[++i]);
+					strncpy(moldyn->efb,argv[++i],64);
+					break;
+				case 'M':
+					moldyn->mwrite=atoi(argv[++i]);
+					strncpy(moldyn->mfb,argv[++i],64);
+					break;
+				case 'S':
+					moldyn->swrite=atoi(argv[++i]);
+					strncpy(moldyn->sfb,argv[++i],64);
+					break;
+				case 'V':
+					moldyn->vwrite=atoi(argv[++i]);
+					strncpy(moldyn->vfb,argv[++i],64);
+					break;
+				case 'T':
+					moldyn->t=atof(argv[++i]);
+					break;
+				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);
+					return -1;
+			}
+		} else {
+			moldyn_usage(argv);
+			return -1;
+		}
+	}
+
+	return 0;
+}
+
+int moldyn_log_init(t_moldyn *moldyn) {
+
+	moldyn->lvstat=0;
+	t_visual *vis;
+
+	vis=&(moldyn->vis);
+
+	if(moldyn->ewrite) {
+		moldyn->efd=open(moldyn->efb,O_WRONLY|O_CREAT|O_TRUNC);
+		if(moldyn->efd<0) {
+			perror("[moldyn] efd open");
+			return moldyn->efd;
+		}
+		dprintf(moldyn->efd,"# moldyn total energy logfile\n");
+		moldyn->lvstat|=MOLDYN_LVSTAT_TOTAL_E;
+	}
+
+	if(moldyn->mwrite) {
+		moldyn->mfd=open(moldyn->mfb,O_WRONLY|O_CREAT|O_TRUNC);
+		if(moldyn->mfd<0) {
+			perror("[moldyn] mfd open");
+			return moldyn->mfd;
+		}
+		dprintf(moldyn->mfd,"# moldyn total momentum logfile\n");
+		moldyn->lvstat|=MOLDYN_LVSTAT_TOTAL_M;
+	}
+
+	if(moldyn->swrite)
+		moldyn->lvstat|=MOLDYN_LVSTAT_SAVE;
+
+	if((moldyn->vwrite)&&(vis)) {
+		moldyn->visual=vis;
+		visual_init(vis,moldyn->vfb);
+		moldyn->lvstat|=MOLDYN_LVSTAT_VISUAL;
+	}
 
+	moldyn->lvstat|=MOLDYN_LVSTAT_INITIALIZED;
+
+	return 0;
+}
+
+int moldyn_log_shutdown(t_moldyn *moldyn) {
+
+	if(moldyn->efd) close(moldyn->efd);
+	if(moldyn->mfd) close(moldyn->efd);
+	if(moldyn->dfd) close(moldyn->efd);
+	if(moldyn->visual) visual_tini(moldyn->visual);
+
+	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) {
@@ -72,7 +288,7 @@ int destroy_lattice(t_atom *atom) {
 	return 0;
 }
 
-int thermal_init(t_atom *atom,t_random *random,int count,double t) {
+int thermal_init(t_moldyn *moldyn) {
 
 	/*
 	 * - gaussian distribution of velocities
@@ -83,11 +299,16 @@ 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/atom[i].mass);
 		/* x direction */
 		v=sigma*rand_get_gauss(random);
 		atom[i].v.x=v;
@@ -103,31 +324,34 @@ 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);
 
 	return 0;
 }
 
-int scale_velocity(t_atom *atom,int count,double t) {
+int scale_velocity(t_moldyn *moldyn) {
 
 	int i;
 	double e,c;
+	t_atom *atom;
+
+	atom=moldyn->atom;
 
 	/*
 	 * - 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*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;
@@ -147,6 +371,21 @@ double get_e_kin(t_atom *atom,int count) {
 	return e;
 }
 
+double get_e_pot(t_moldyn *moldyn) {
+
+	return moldyn->energy;
+}
+
+double get_total_energy(t_moldyn *moldyn) {
+
+	double e;
+
+	e=get_e_kin(moldyn->atom,moldyn->count);
+	e+=get_e_pot(moldyn);
+
+	return e;
+}
+
 t_3dvec get_total_p(t_atom *atom, int count) {
 
 	t_3dvec p,p_total;
@@ -161,37 +400,991 @@ t_3dvec get_total_p(t_atom *atom, int count) {
 	return p_total;
 }
 
-double potential_lennard_jones_2(t_moldyn *moldyn,void *ptr) {
+double estimate_time_step(t_moldyn *moldyn,double nn_dist,double t) {
 
-	t_lj_params *params;
+	double tau;
+
+	tau=0.05*nn_dist/(sqrt(3.0*K_BOLTZMANN*t/moldyn->atom[0].mass));
+	tau*=1.0E-9;
+	if(tau<moldyn->tau)
+		printf("[moldyn] warning: time step  (%f > %.15f)\n",
+		       moldyn->tau,tau);
+
+	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;
-	int i,j;
-	int count;
-	t_3dvec distance;
-	double d,help;
+	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;
+}
+
+/*
+ *
+ * 'integration of newtons equation' - algorithms
+ *
+ */
+
+/* start the integration */
+
+int moldyn_integrate(t_moldyn *moldyn) {
+
+	int i;
+	unsigned int e,m,s,d,v;
+	t_3dvec p;
+
+	int fd;
+	char fb[128];
+
+	/* initialize linked cell method */
+	link_cell_init(moldyn);
+
+	/* logging & visualization */
+	e=moldyn->ewrite;
+	m=moldyn->mwrite;
+	s=moldyn->swrite;
+	d=moldyn->dwrite;
+	v=moldyn->vwrite;
+
+	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;
+
+	/* calculate initial forces */
+	moldyn->potential_force_function(moldyn);
+
+	for(i=0;i<moldyn->time_steps;i++) {
+
+		/* integration step */
+		moldyn->integrate(moldyn);
+
+		/* check for log & visualization */
+		if(e) {
+			if(!(i%e))
+				dprintf(moldyn->efd,
+				        "%.15f %.45f\n",i*moldyn->tau,
+				        get_total_energy(moldyn));
+		}
+		if(m) {
+			if(!(i%m)) {
+				p=get_total_p(moldyn->atom,moldyn->count);
+				dprintf(moldyn->mfd,
+				        "%.15f %.45f\n",i*moldyn->tau,
+				        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->visual,i*moldyn->tau,
+				             moldyn->atom,moldyn->count);
+				printf("\rsteps: %d",i);
+				fflush(stdout);
+			}
+		}
+	}
+
+	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);
+		v3_per_bound(&(atom[i].r),&(moldyn->dim));
+
+		/* 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 */
+printf("list update ...\n");
+	link_cell_update(moldyn);
+printf("done\n");
+
+	/* forces depending on chosen potential */
+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 */
+		v3_scale(&delta,&(atom[i].f),0.5*tau/atom[i].mass);
+		v3_add(&(atom[i].v),&(atom[i].v),&delta);
+	}
+
+	return 0;
+}
+
+
+/*
+ *
+ * potentials & corresponding forces
+ * 
+ */
+
+/* generic potential and force calculation */
+
+#define		CREATE_CELL_LIST(nb_list) \
+	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,\
+	                          nb_list);
+
+
+int potential_force_calc(t_moldyn *moldyn) {
+
+	int i,count;
+	t_atom *atom;
+	t_linkcell *lc;
+	t_list neighbour[27];
+	t_list *this;
 	double u;
+
+	count=moldyn->count;
+	atom=moldyn->atom;
+	lc=&(moldyn->lc);
+
+	/* reset energy */
+	u=0.0;
+
+	for(i=0;i<count;i++) {
+	
+		/* reset force */
+		v3_zero(&(atom[i].f));
+
+		/* single particle potential/force */
+		if(moldyn->status&MOLDYN_STAT_1BP)
+			moldyn->pf_func1b(moldyn,&(atom[i]));
+
+		/* 2 body pair potential/force */
+		if(moldyn->status&MOLDYN_STAT_2BP) {
+		
+			CREATE_CELL_LIST(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]))
+					moldyn->pf_func2b(moldyn,
+					                  &(atom[i]),btom);
+			} while(list_next(this)!=L_NO_NEXT_ELEMENT);
+
+			/*
+			 * direct neighbour cells
+			 * => no boundary condition check necessary
+			 */
+			for(j=0;j<lc->dnlc;j++) {
+				this=&(neighbour[j]);
+				list_reset(this);
+				if(this->start!=NULL) {
+					do {
+						btom=this->current->data;
+						moldyn->pf_func2b(moldyn,
+						                  &(atom[i]),
+						                  btom);
+					} while(list_next(this)!=\
+					        L_NO_NEXT_ELEMENT);
+			}
+
+			/*
+			 * neighbour cells due to periodic bc
+			 * => check boundary conditions
+			 */
+			for(j=lc->dnlc;j<lc->countn;j++) {
+				this=&(neighbour[j]);
+				list_reset(this);
+				if(this->start!=NULL) {
+					do {
+						btom=this->current->data;
+						moldyn->pf_func2b(moldyn,
+						                  &(atom[i]),
+						                  btom);
+
+			}
+
+		}
+
+	return 0;
+}
+
+
+/* harmonic oscillator potential and force */
+
+int harmonic_oscillator(t_moldyn *moldyn) {
+
+	t_ho_params *params;
+	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;
+
+	params=moldyn->pot_params;
+	atom=moldyn->atom;
+	lc=&(moldyn->lc);
+	sc=params->spring_constant;
+	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+(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)));
+				v3_add(&(atom[i].f),&(atom[i].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 */
+ 
+int lennard_jones(t_moldyn *moldyn) {
+
+	t_lj_params *params;
+	t_atom *atom,*btom;
+	t_linkcell *lc;
+	t_list *this,neighbour[27];
+	int i,j,c;
+	int count;
+	t_3dvec force,distance;
+	double d,h1,h2,u;
 	double eps,sig6,sig12;
+	int ni,nj,nk;
 
-	params=ptr;
+	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=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;
 }
 
+/* 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 */
+
+			/* 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;
+}