X-Git-Url: https://www.hackdaworld.org/gitweb/?a=blobdiff_plain;f=moldyn.c;h=8451c4436f43db2213bec83677c359fb4062f133;hb=787848dc9bf3daa2ccb76296de904688cc504a45;hp=b73cd3432b65971aabc055e7f126fc5efdb3deb4;hpb=cb2811d92cb79b1f24d11d4f4897426ce5f7dc3a;p=physik%2Fposic.git

diff --git a/moldyn.c b/moldyn.c
index b73cd34..8451c44 100644
--- a/moldyn.c
+++ b/moldyn.c
@@ -23,6 +23,10 @@
 #include <omp.h>
 #endif
 
+#if defined PTHREADS || defined VISUAL_THREAD
+#include <pthread.h>
+#endif
+
 #include "moldyn.h"
 #include "report/report.h"
 
@@ -43,6 +47,12 @@
 #undef PSE_NAME
 #undef PSE_COL
 
+#ifdef PTHREADS
+/* global mutexes */
+pthread_mutex_t *amutex;
+pthread_mutex_t emutex;
+#endif
+
 /*
  * the moldyn functions
  */
@@ -62,13 +72,28 @@ int moldyn_init(t_moldyn *moldyn,int argc,char **argv) {
 	rand_init(&(moldyn->random),NULL,1);
 	moldyn->random.status|=RAND_STAT_VERBOSE;
 
+#ifdef PTHREADS
+	pthread_mutex_init(&emutex,NULL);
+#endif
+
 	return 0;
 }
 
 int moldyn_shutdown(t_moldyn *moldyn) {
 
+#ifdef PTHREADS
+	int i;
+#endif
+
 	printf("[moldyn] shutdown\n");
 
+#ifdef PTHREADS
+	for(i=0;i<moldyn->count;i++)
+		pthread_mutex_destroy(&(amutex[i]));
+	free(amutex);
+	pthread_mutex_destroy(&emutex);
+#endif
+
 	moldyn_log_shutdown(moldyn);
 	link_cell_shutdown(moldyn);
 	rand_close(&(moldyn->random));
@@ -488,7 +513,8 @@ int moldyn_log_shutdown(t_moldyn *moldyn) {
  */
 
 int create_lattice(t_moldyn *moldyn,u8 type,double lc,int element,double mass,
-                   u8 attr,u8 brand,int a,int b,int c,t_3dvec *origin) {
+                   u8 attr,u8 brand,int a,int b,int c,t_3dvec *origin,
+                   u8 p_type,t_part_vals *p_vals) {
 
 	int new,count;
 	int ret;
@@ -496,6 +522,9 @@ int create_lattice(t_moldyn *moldyn,u8 type,double lc,int element,double mass,
 	void *ptr;
 	t_atom *atom;
 	char name[16];
+#ifdef PTHREADS
+	pthread_mutex_t *mutex;
+#endif
 
 	new=a*b*c;
 	count=moldyn->count;
@@ -518,6 +547,16 @@ int create_lattice(t_moldyn *moldyn,u8 type,double lc,int element,double mass,
 	moldyn->atom=ptr;
 	atom=&(moldyn->atom[count]);
 
+#ifdef PTHREADS
+	ptr=realloc(amutex,(count+new)*sizeof(pthread_mutex_t));
+	if(!ptr) {
+		perror("[moldyn] mutex realloc (add atom)");
+		return -1;
+	}
+	amutex=ptr;
+	mutex=&(amutex[count]);
+#endif
+
 	/* no atoms on the boundaries (only reason: it looks better!) */
 	if(!origin) {
 		orig.x=0.5*lc;
@@ -533,21 +572,21 @@ int create_lattice(t_moldyn *moldyn,u8 type,double lc,int element,double mass,
 	switch(type) {
 		case CUBIC:
 			set_nn_dist(moldyn,lc);
-			ret=cubic_init(a,b,c,lc,atom,&orig);
+			ret=cubic_init(a,b,c,lc,atom,&orig,p_type,p_vals);
 			strcpy(name,"cubic");
 			break;
 		case FCC:
 			if(!origin)
 				v3_scale(&orig,&orig,0.5);
 			set_nn_dist(moldyn,0.5*sqrt(2.0)*lc);
-			ret=fcc_init(a,b,c,lc,atom,&orig);
+			ret=fcc_init(a,b,c,lc,atom,&orig,p_type,p_vals);
 			strcpy(name,"fcc");
 			break;
 		case DIAMOND:
 			if(!origin)
 				v3_scale(&orig,&orig,0.25);
 			set_nn_dist(moldyn,0.25*sqrt(3.0)*lc);
-			ret=diamond_init(a,b,c,lc,atom,&orig);
+			ret=diamond_init(a,b,c,lc,atom,&orig,p_type,p_vals);
 			strcpy(name,"diamond");
 			break;
 		default:
@@ -575,6 +614,9 @@ int create_lattice(t_moldyn *moldyn,u8 type,double lc,int element,double mass,
 		atom[ret].tag=count+ret;
 		check_per_bound(moldyn,&(atom[ret].r));
 		atom[ret].r_0=atom[ret].r;
+#ifdef PTHREADS
+		pthread_mutex_init(&(mutex[ret]),NULL);
+#endif
 	}
 
 	/* update total system mass */
@@ -600,6 +642,25 @@ int add_atom(t_moldyn *moldyn,int element,double mass,u8 brand,u8 attr,
 	}
 	moldyn->atom=ptr;
 
+#ifdef LOWMEM_LISTS
+	ptr=realloc(moldyn->lc.subcell->list,(count+1)*sizeof(int));
+	if(!ptr) {
+		perror("[moldyn] list realloc (add atom)");
+		return -1;
+	}
+	moldyn->lc.subcell->list=ptr;
+#endif
+
+#ifdef PTHREADS
+	ptr=realloc(amutex,(count+1)*sizeof(pthread_mutex_t));
+	if(!ptr) {
+		perror("[moldyn] mutex realloc (add atom)");
+		return -1;
+	}
+	amutex=ptr;
+	pthread_mutex_init(&(amutex[count]),NULL);
+#endif
+
 	atom=moldyn->atom;
 
 	/* initialize new atom */
@@ -650,12 +711,14 @@ int del_atom(t_moldyn *moldyn,int tag) {
 }
 
 /* cubic init */
-int cubic_init(int a,int b,int c,double lc,t_atom *atom,t_3dvec *origin) {
+int cubic_init(int a,int b,int c,double lc,t_atom *atom,t_3dvec *origin,
+               u8 p_type,t_part_vals *p_vals) {
 
 	int count;
 	t_3dvec r;
 	int i,j,k;
 	t_3dvec o;
+	t_3dvec dist;
 
 	count=0;
 	if(origin)
@@ -663,14 +726,39 @@ int cubic_init(int a,int b,int c,double lc,t_atom *atom,t_3dvec *origin) {
 	else
 		v3_zero(&o);
 
+	/* shift partition values */
+	if(p_type) {
+		p_vals->p.x+=(a*lc)/2.0;
+		p_vals->p.y+=(b*lc)/2.0;
+		p_vals->p.z+=(c*lc)/2.0;
+	}
+
 	r.x=o.x;
 	for(i=0;i<a;i++) {
 		r.y=o.y;
 		for(j=0;j<b;j++) {
 			r.z=o.z;
 			for(k=0;k<c;k++) {
+				switch(p_type) {
+					case PART_INSIDE_R:
+						v3_sub(&dist,&r,&(p_vals->p));
+			if(v3_absolute_square(&dist)<(p_vals->r*p_vals->r)) {
 				v3_copy(&(atom[count].r),&r);
 				count+=1;
+			}
+						break;
+					case PART_OUTSIDE_R:
+						v3_sub(&dist,&r,&(p_vals->p));
+			if(v3_absolute_square(&dist)>=(p_vals->r*p_vals->r)) {
+				v3_copy(&(atom[count].r),&r);
+				count+=1;
+			}
+						break;
+					default:	
+						v3_copy(&(atom[count].r),&r);
+						count+=1;
+						break;
+				}
 				r.z+=lc;
 			}
 			r.y+=lc;
@@ -688,12 +776,14 @@ int cubic_init(int a,int b,int c,double lc,t_atom *atom,t_3dvec *origin) {
 }
 
 /* fcc lattice init */
-int fcc_init(int a,int b,int c,double lc,t_atom *atom,t_3dvec *origin) {
+int fcc_init(int a,int b,int c,double lc,t_atom *atom,t_3dvec *origin,
+             u8 p_type,t_part_vals *p_vals) {
 
 	int count;
 	int i,j,k,l;
 	t_3dvec o,r,n;
 	t_3dvec basis[3];
+	t_3dvec dist;
 
 	count=0;
 	if(origin)
@@ -710,6 +800,13 @@ int fcc_init(int a,int b,int c,double lc,t_atom *atom,t_3dvec *origin) {
 	basis[2].y=0.5*lc;
 	basis[2].z=0.5*lc;
 
+	/* shift partition values */
+	if(p_type) {
+		p_vals->p.x+=(a*lc)/2.0;
+		p_vals->p.y+=(b*lc)/2.0;
+		p_vals->p.z+=(c*lc)/2.0;
+	}
+
 	/* fill up the room */
 	r.x=o.x;
 	for(i=0;i<a;i++) {
@@ -718,15 +815,51 @@ int fcc_init(int a,int b,int c,double lc,t_atom *atom,t_3dvec *origin) {
 			r.z=o.z;
 			for(k=0;k<c;k++) {
 				/* first atom */
+				switch(p_type) {
+					case PART_INSIDE_R:
+						v3_sub(&dist,&r,&(p_vals->p));
+			if(v3_absolute_square(&dist)<(p_vals->r*p_vals->r)) {
 				v3_copy(&(atom[count].r),&r);
 				count+=1;
-				r.z+=lc;
+			}
+						break;
+					case PART_OUTSIDE_R:
+						v3_sub(&dist,&r,&(p_vals->p));
+			if(v3_absolute_square(&dist)>=(p_vals->r*p_vals->r)) {
+				v3_copy(&(atom[count].r),&r);
+				count+=1;
+			}
+						break;
+					default:
+						v3_copy(&(atom[count].r),&r);
+						count+=1;
+						break;
+				}
 				/* the three face centered atoms */
 				for(l=0;l<3;l++) {
 					v3_add(&n,&r,&basis[l]);
+					switch(p_type) {
+						case PART_INSIDE_R:
+			v3_sub(&dist,&n,&(p_vals->p));
+			if(v3_absolute_square(&dist)<(p_vals->r*p_vals->r)) {
+				v3_copy(&(atom[count].r),&r);
+				count+=1;
+			}
+							break;
+						case PART_OUTSIDE_R:
+			v3_sub(&dist,&n,&(p_vals->p));
+			if(v3_absolute_square(&dist)>=(p_vals->r*p_vals->r)) {
+				v3_copy(&(atom[count].r),&r);
+				count+=1;
+			}
+							break;
+						default:
 					v3_copy(&(atom[count].r),&n);
 					count+=1;
+							break;
+					}
 				}
+				r.z+=lc;
 			}
 			r.y+=lc;
 		}
@@ -743,12 +876,13 @@ int fcc_init(int a,int b,int c,double lc,t_atom *atom,t_3dvec *origin) {
 	return count;
 }
 
-int diamond_init(int a,int b,int c,double lc,t_atom *atom,t_3dvec *origin) {
+int diamond_init(int a,int b,int c,double lc,t_atom *atom,t_3dvec *origin,
+                 u8 p_type,t_part_vals *p_vals) {
 
 	int count;
 	t_3dvec o;
 
-	count=fcc_init(a,b,c,lc,atom,origin);
+	count=fcc_init(a,b,c,lc,atom,origin,p_type,p_vals);
 
 	o.x=0.25*lc;
 	o.y=0.25*lc;
@@ -756,7 +890,7 @@ int diamond_init(int a,int b,int c,double lc,t_atom *atom,t_3dvec *origin) {
 
 	if(origin) v3_add(&o,&o,origin);
 
-	count+=fcc_init(a,b,c,lc,&atom[count],&o);
+	count+=fcc_init(a,b,c,lc,&atom[count],&o,p_type,p_vals);
 
 	return count;
 }
@@ -1293,7 +1427,9 @@ double estimate_time_step(t_moldyn *moldyn,double nn_dist) {
 int link_cell_init(t_moldyn *moldyn,u8 vol) {
 
 	t_linkcell *lc;
+#ifndef LOWMEM_LISTS
 	int i;
+#endif
 
 	lc=&(moldyn->lc);
 
@@ -1308,6 +1444,8 @@ int link_cell_init(t_moldyn *moldyn,u8 vol) {
 
 #ifdef STATIC_LISTS
 	lc->subcell=malloc(lc->cells*sizeof(int*));
+#elif LOWMEM_LISTS
+	lc->subcell=malloc(sizeof(t_lowmem_list));
 #else
 	lc->subcell=malloc(lc->cells*sizeof(t_list));
 #endif
@@ -1325,6 +1463,9 @@ int link_cell_init(t_moldyn *moldyn,u8 vol) {
 #ifdef STATIC_LISTS
 		printf("[moldyn] initializing 'static' linked cells (%d)\n",
 		       lc->cells);
+#elif LOWMEM_LISTS
+		printf("[moldyn] initializing 'lowmem' linked cells (%d)\n",
+		       lc->cells);
 #else
 		printf("[moldyn] initializing 'dynamic' linked cells (%d)\n",
 		       lc->cells);
@@ -1348,6 +1489,17 @@ int link_cell_init(t_moldyn *moldyn,u8 vol) {
 			       i,lc->subcell[0],lc->subcell);
 		*/
 	}
+#elif LOWMEM_LISTS
+	lc->subcell->head=malloc(lc->cells*sizeof(int));
+	if(lc->subcell->head==NULL) {
+		perror("[moldyn] head init (malloc)");
+		return -1;
+	}
+	lc->subcell->list=malloc(moldyn->count*sizeof(int));
+	if(lc->subcell->list==NULL) {
+		perror("[moldyn] list init (malloc)");
+		return -1;
+	}
 #else
 	for(i=0;i<lc->cells;i++)
 		list_init_f(&(lc->subcell[i]));
@@ -1362,22 +1514,26 @@ int link_cell_init(t_moldyn *moldyn,u8 vol) {
 int link_cell_update(t_moldyn *moldyn) {
 
 	int count,i,j,k;
-	int nx,ny;
+	int nx,nxy;
 	t_atom *atom;
 	t_linkcell *lc;
 #ifdef STATIC_LISTS
 	int p;
+#elif LOWMEM_LISTS
+	int p;
 #endif
 
 	atom=moldyn->atom;
 	lc=&(moldyn->lc);
 
 	nx=lc->nx;
-	ny=lc->ny;
+	nxy=nx*lc->ny;
 
 	for(i=0;i<lc->cells;i++)
 #ifdef STATIC_LISTS
-		memset(lc->subcell[i],0,(MAX_ATOMS_PER_LIST+1)*sizeof(int));
+		memset(lc->subcell[i],-1,(MAX_ATOMS_PER_LIST+1)*sizeof(int));
+#elif LOWMEM_LISTS
+		lc->subcell->head[i]=-1;
 #else
 		list_destroy_f(&(lc->subcell[i]));
 #endif
@@ -1389,7 +1545,7 @@ int link_cell_update(t_moldyn *moldyn) {
 	
 #ifdef STATIC_LISTS
 		p=0;
-		while(lc->subcell[i+j*nx+k*nx*ny][p]!=0)
+		while(lc->subcell[i+j*nx+k*nxy][p]!=-1)
 			p++;
 
 		if(p>=MAX_ATOMS_PER_LIST) {
@@ -1397,9 +1553,13 @@ int link_cell_update(t_moldyn *moldyn) {
 			return -1;
 		}
 
-		lc->subcell[i+j*nx+k*nx*ny][p]=count;
+		lc->subcell[i+j*nx+k*nxy][p]=count;
+#elif LOWMEM_LISTS
+		p=i+j*nx+k*nxy;
+		lc->subcell->list[count]=lc->subcell->head[p];
+		lc->subcell->head[p]=count;
 #else
-		list_add_immediate_f(&(lc->subcell[i+j*nx+k*nx*ny]),
+		list_add_immediate_f(&(lc->subcell[i+j*nx+k*nxy]),
 		                     &(atom[count]));
 		/*
 		if(j==0&&k==0)
@@ -1415,6 +1575,8 @@ int link_cell_update(t_moldyn *moldyn) {
 int link_cell_neighbour_index(t_moldyn *moldyn,int i,int j,int k,
 #ifdef STATIC_LISTS
                               int **cell
+#elif LOWMEM_LISTS
+                              int *cell
 #else
                               t_list *cell
 #endif
@@ -1440,7 +1602,11 @@ int link_cell_neighbour_index(t_moldyn *moldyn,int i,int j,int k,
 		printf("[moldyn] WARNING: lcni %d/%d %d/%d %d/%d\n",
 		       i,nx,j,ny,k,nz);
 
+#ifndef LOWMEM_LISTS
 	cell[0]=lc->subcell[i+j*nx+k*a];
+#else
+	cell[0]=lc->subcell->head[i+j*nx+k*a];
+#endif
 	for(ci=-1;ci<=1;ci++) {
 		bx=0;
 		x=i+ci;
@@ -1464,10 +1630,19 @@ int link_cell_neighbour_index(t_moldyn *moldyn,int i,int j,int k,
 				}
 				if(!(ci|cj|ck)) continue;
 				if(bx|by|bz) {
+#ifndef LOWMEM_LISTS
 					cell[--count2]=lc->subcell[x+y*nx+z*a];
+#else
+				cell[--count2]=lc->subcell->head[x+y*nx+z*a];
+#endif
+					
 				}
 				else {
+#ifndef LOWMEM_LISTS
 					cell[count1++]=lc->subcell[x+y*nx+z*a];
+#else
+				cell[count1++]=lc->subcell->head[x+y*nx+z*a];
+#endif
 				}
 			}
 		}
@@ -1480,11 +1655,19 @@ int link_cell_neighbour_index(t_moldyn *moldyn,int i,int j,int k,
 
 int link_cell_shutdown(t_moldyn *moldyn) {
 
+#ifndef LOWMEM_LISTS
 	int i;
+#endif
 	t_linkcell *lc;
 
 	lc=&(moldyn->lc);
 
+#if LOWMEM_LISTS
+	free(lc->subcell->head);
+	free(lc->subcell->list);
+
+#else
+
 	for(i=0;i<lc->cells;i++) {
 #ifdef STATIC_LISTS
 		free(lc->subcell[i]);
@@ -1493,6 +1676,7 @@ int link_cell_shutdown(t_moldyn *moldyn) {
 		list_destroy_f(&(lc->subcell[i]));
 #endif
 	}
+#endif
 
 	free(lc->subcell);
 
@@ -1561,6 +1745,17 @@ int moldyn_integrate(t_moldyn *moldyn) {
 	struct timeval t1,t2;
 	//double tp;
 
+#ifdef VISUAL_THREAD
+	u8 first,change;
+	pthread_t io_thread;
+	int ret;
+	t_moldyn md_copy;
+	t_atom *atom_copy;
+
+	first=1;
+	change=0;
+#endif
+
 	sched=&(moldyn->schedule);
 	atom=moldyn->atom;
 
@@ -1609,6 +1804,21 @@ int moldyn_integrate(t_moldyn *moldyn) {
 	/* debugging, ignore */
 	moldyn->debug=0;
 
+	/* zero & init moldyn copy */
+#ifdef VISUAL_THREAD
+	memset(&md_copy,0,sizeof(t_moldyn));
+	atom_copy=malloc(moldyn->count*sizeof(t_atom));
+	if(atom_copy==NULL) {
+		perror("[moldyn] malloc atom copy (init)");
+		return -1;
+	}
+#endif
+
+#ifdef PTHREADS
+	printf("##################\n");
+	printf("# USING PTHREADS #\n");
+	printf("##################\n");
+#endif
 	/* tell the world */
 	printf("[moldyn] integration start, go get a coffee ...\n");
 
@@ -1693,7 +1903,7 @@ int moldyn_integrate(t_moldyn *moldyn) {
 		}
 		if(s) {
 			if(!(moldyn->total_steps%s)) {
-				snprintf(dir,128,"%s/s-%07.f.save",
+				snprintf(dir,128,"%s/s-%08.f.save",
 				         moldyn->vlsdir,moldyn->time);
 				fd=open(dir,O_WRONLY|O_TRUNC|O_CREAT,
 				        S_IRUSR|S_IWUSR);
@@ -1708,16 +1918,45 @@ int moldyn_integrate(t_moldyn *moldyn) {
 		}
 		if(a) {
 			if(!(moldyn->total_steps%a)) {
+#ifdef VISUAL_THREAD
+	/* check whether thread has not terminated yet */
+	if(!first) {
+		ret=pthread_join(io_thread,NULL);
+	}
+	first=0;
+	/* prepare and start thread */
+	if(moldyn->count!=md_copy.count) {
+		free(atom_copy);
+		change=1;
+	}
+	memcpy(&md_copy,moldyn,sizeof(t_moldyn));
+	if(change) {
+		atom_copy=malloc(moldyn->count*sizeof(t_atom));
+		if(atom_copy==NULL) {
+			perror("[moldyn] malloc atom copy (change)");
+			return -1;
+		}
+	}
+	md_copy.atom=atom_copy;
+	memcpy(atom_copy,moldyn->atom,moldyn->count*sizeof(t_atom));
+	change=0;
+	ret=pthread_create(&io_thread,NULL,visual_atoms,&md_copy);
+	if(ret) {
+		perror("[moldyn] create visual atoms thread\n");
+		return -1;
+	}
+#else
 				visual_atoms(moldyn);
+#endif
 			}
 		}
 
 		/* display progress */
-		//if(!(moldyn->total_steps%10)) {
+		if(!(i%10)) {
 			/* get current time */
 			gettimeofday(&t2,NULL);
 
-printf("\rsched:%d, steps:%d/%d, T:%4.1f/%4.1f P:%4.1f/%4.1f V:%6.1f (%d)",
+printf("sched:%d, steps:%d/%d, T:%4.1f/%4.1f P:%4.1f/%4.1f V:%6.1f (%d)\n",
        sched->count,i,moldyn->total_steps,
        moldyn->t,moldyn->t_avg,
        moldyn->p/BAR,moldyn->p_avg/BAR,
@@ -1729,7 +1968,7 @@ printf("\rsched:%d, steps:%d/%d, T:%4.1f/%4.1f P:%4.1f/%4.1f V:%6.1f (%d)",
 
 			/* copy over time */
 			t1=t2;
-		//}
+		}
 
 		/* increase absolute time */
 		moldyn->time+=moldyn->tau;
@@ -1828,6 +2067,9 @@ int potential_force_calc(t_moldyn *moldyn) {
 	int *neighbour_i[27];
 	int p,q;
 	t_atom *atom;
+#elif LOWMEM_LISTS
+	int neighbour_i[27];
+	int p,q;
 #else
 	t_list neighbour_i[27];
 	t_list neighbour_i2[27];
@@ -1851,6 +2093,7 @@ int potential_force_calc(t_moldyn *moldyn) {
 
 	/* reset force, site energy and virial of every atom */
 #ifdef PARALLEL
+	i=omp_get_thread_num();
 	#pragma omp parallel for private(virial)
 #endif
 	for(i=0;i<count;i++) {
@@ -1903,10 +2146,17 @@ int potential_force_calc(t_moldyn *moldyn) {
 #ifdef STATIC_LISTS
 				p=0;
 
-				while(neighbour_i[j][p]!=0) {
+				while(neighbour_i[j][p]!=-1) {
 
 					jtom=&(atom[neighbour_i[j][p]]);
 					p++;
+#elif LOWMEM_LISTS
+				p=neighbour_i[j];
+
+				while(p!=-1) {
+
+					jtom=&(itom[p]);
+					p=lc->subcell->list[p];
 #else
 				this=&(neighbour_i[j]);
 				list_reset_f(this);
@@ -1930,6 +2180,8 @@ int potential_force_calc(t_moldyn *moldyn) {
 					}
 #ifdef STATIC_LISTS
 				}
+#elif LOWMEM_LISTS
+				}
 #else
 				} while(list_next_f(this)!=L_NO_NEXT_ELEMENT);
 #endif
@@ -1945,6 +2197,8 @@ int potential_force_calc(t_moldyn *moldyn) {
 		/* copy the neighbour lists */
 #ifdef STATIC_LISTS
 		/* no copy needed for static lists */
+#elif LOWMEM_LISTS
+		/* no copy needed for lowmem lists */
 #else
 		memcpy(neighbour_i2,neighbour_i,27*sizeof(t_list));
 #endif
@@ -1956,10 +2210,17 @@ int potential_force_calc(t_moldyn *moldyn) {
 #ifdef STATIC_LISTS
 			p=0;
 
-			while(neighbour_i[j][p]!=0) {
+			while(neighbour_i[j][p]!=-1) {
 
 				jtom=&(atom[neighbour_i[j][p]]);
 				p++;
+#elif LOWMEM_LISTS
+				p=neighbour_i[j];
+
+				while(p!=-1) {
+
+					jtom=&(itom[p]);
+					p=lc->subcell->list[p];
 #else
 			this=&(neighbour_i[j]);
 			list_reset_f(this);
@@ -2000,10 +2261,17 @@ int potential_force_calc(t_moldyn *moldyn) {
 #ifdef STATIC_LISTS
 					q=0;
 
-					while(neighbour_i[j][q]!=0) {
+					while(neighbour_i[k][q]!=-1) {
 
 						ktom=&(atom[neighbour_i[k][q]]);
 						q++;
+#elif LOWMEM_LISTS
+					q=neighbour_i[k];
+
+					while(q!=-1) {
+
+						ktom=&(itom[q]);
+						q=lc->subcell->list[q];
 #else
 					that=&(neighbour_i2[k]);
 					list_reset_f(that);
@@ -2029,8 +2297,11 @@ int potential_force_calc(t_moldyn *moldyn) {
 						                  jtom,
 						                  ktom,
 						                  bc_ik|bc_ij);
+
 #ifdef STATIC_LISTS
 					}
+#elif LOWMEM_LISTS
+					}
 #else
 					} while(list_next_f(that)!=\
 					        L_NO_NEXT_ELEMENT);
@@ -2055,10 +2326,17 @@ int potential_force_calc(t_moldyn *moldyn) {
 #ifdef STATIC_LISTS
 					q=0;
 
-					while(neighbour_i[j][q]!=0) {
+					while(neighbour_i[k][q]!=-1) {
 
 						ktom=&(atom[neighbour_i[k][q]]);
 						q++;
+#elif LOWMEM_LISTS
+					q=neighbour_i[k];
+
+					while(q!=-1) {
+
+						ktom=&(itom[q]);
+						q=lc->subcell->list[q];
 #else
 					that=&(neighbour_i2[k]);
 					list_reset_f(that);
@@ -2087,6 +2365,8 @@ int potential_force_calc(t_moldyn *moldyn) {
 
 #ifdef STATIC_LISTS
 					}
+#elif LOWMEM_LISTS
+					}
 #else
 					} while(list_next_f(that)!=\
 					        L_NO_NEXT_ELEMENT);
@@ -2104,6 +2384,8 @@ int potential_force_calc(t_moldyn *moldyn) {
 				}
 #ifdef STATIC_LISTS
 			}
+#elif LOWMEM_LISTS
+			}
 #else
 			} while(list_next_f(this)!=L_NO_NEXT_ELEMENT);
 #endif
@@ -2345,6 +2627,9 @@ int process_2b_bonds(t_moldyn *moldyn,void *data,
 #ifdef STATIC_LISTS
 	int *neighbour[27];
 	int p;
+#elif LOWMEM_LISTS
+	int neighbour[27];
+	int p;
 #else
 	t_list neighbour[27];
 	t_list *this;
@@ -2371,10 +2656,17 @@ int process_2b_bonds(t_moldyn *moldyn,void *data,
 #ifdef STATIC_LISTS
 			p=0;
 
-			while(neighbour[j][p]!=0) {
+			while(neighbour[j][p]!=-1) {
 
 				jtom=&(moldyn->atom[neighbour[j][p]]);
 				p++;
+#elif LOWMEM_LISTS
+			p=neighbour[j];
+
+			while(p!=-1) {
+
+				jtom=&(itom[p]);
+				p=lc->subcell->list[p];
 #else
 			this=&(neighbour[j]);
 			list_reset_f(this);
@@ -2392,6 +2684,8 @@ int process_2b_bonds(t_moldyn *moldyn,void *data,
 
 #ifdef STATIC_LISTS
 			}
+#elif LOWMEM_LISTS
+			}
 #else
 			} while(list_next_f(this)!=L_NO_NEXT_ELEMENT);
 #endif
@@ -2402,6 +2696,84 @@ int process_2b_bonds(t_moldyn *moldyn,void *data,
 
 }
 
+/*
+ * function to find neighboured atoms
+ */
+
+int process_neighbours(t_moldyn *moldyn,void *data,t_atom *atom,
+                       int (*process)(t_moldyn *moldyn,t_atom *atom,t_atom *natom,
+		                      void *data,u8 bc)) {
+
+	t_linkcell *lc;
+#ifdef STATIC_LISTS
+	int *neighbour[27];
+	int p;
+#elif LOWMEM_LISTS
+	int neighbour[27];
+	int p;
+#else
+	t_list neighbour[27];
+	t_list *this;
+#endif
+	u8 bc;
+	t_atom *natom;
+	int j;
+
+	lc=&(moldyn->lc);
+	
+	/* neighbour indexing */
+	link_cell_neighbour_index(moldyn,
+	                          (atom->r.x+moldyn->dim.x/2)/lc->x,
+	                          (atom->r.y+moldyn->dim.y/2)/lc->x,
+	                          (atom->r.z+moldyn->dim.z/2)/lc->x,
+	                          neighbour);
+
+	for(j=0;j<27;j++) {
+
+		bc=(j<lc->dnlc)?0:1;
+
+#ifdef STATIC_LISTS
+		p=0;
+
+		while(neighbour[j][p]!=-1) {
+
+			natom=&(moldyn->atom[neighbour[j][p]]);
+			p++;
+#elif LOWMEM_LISTS
+		p=neighbour[j];
+
+		while(p!=-1) {
+
+			natom=&(moldyn->atom[p]);
+			p=lc->subcell->list[p];
+#else
+		this=&(neighbour[j]);
+		list_reset_f(this);
+
+		if(this->start==NULL)
+			continue;
+
+		do {
+
+			natom=this->current->data;
+#endif
+
+			/* process bond */
+			process(moldyn,atom,natom,data,bc);
+
+#ifdef STATIC_LISTS
+		}
+#elif LOWMEM_LISTS
+		}
+#else
+		} while(list_next_f(this)!=L_NO_NEXT_ELEMENT);
+#endif
+	}
+
+	return 0;
+
+}
+
 /*
  * post processing functions
  */
@@ -2728,7 +3100,11 @@ int visual_bonds_process(t_moldyn *moldyn,t_atom *itom,t_atom *jtom,
 	return 0;
 }
 
+#ifdef VISUAL_THREAD
+void *visual_atoms(void *ptr) {
+#else
 int visual_atoms(t_moldyn *moldyn) {
+#endif
 
 	int i;
  	char file[128+64];
@@ -2737,6 +3113,11 @@ int visual_atoms(t_moldyn *moldyn) {
 	t_visual *v;
 	t_atom *atom;
 	t_vb vb;
+#ifdef VISUAL_THREAD
+	t_moldyn *moldyn;
+
+	moldyn=ptr;
+#endif
 
 	v=&(moldyn->vis);
 	dim.x=v->dim.x;
@@ -2746,17 +3127,19 @@ int visual_atoms(t_moldyn *moldyn) {
 
 	help=(dim.x+dim.y);
 
-	sprintf(file,"%s/atomic_conf_%07.f.xyz",v->fb,moldyn->time);
+	sprintf(file,"%s/atomic_conf_%08.f.xyz",v->fb,moldyn->time);
 	vb.fd=open(file,O_WRONLY|O_CREAT|O_TRUNC,S_IRUSR|S_IWUSR);
 	if(vb.fd<0) {
 		perror("open visual save file fd");
+#ifndef VISUAL_THREAD
 		return -1;
+#endif
 	}
 
 	/* write the actual data file */
 
 	// povray header
-	dprintf(vb.fd,"# [P] %d %07.f <%f,%f,%f>\n",
+	dprintf(vb.fd,"# [P] %d %08.f <%f,%f,%f>\n",
 	        moldyn->count,moldyn->time,help/40.0,help/40.0,-0.8*help);
 
 	// atomic configuration
@@ -2770,7 +3153,9 @@ int visual_atoms(t_moldyn *moldyn) {
 		                                    atom[i].ekin);
 	
 	// bonds between atoms
+#ifndef VISUAL_THREAD
 	process_2b_bonds(moldyn,&vb,visual_bonds_process);
+#endif
 	
 	// boundaries
 	if(dim.x) {
@@ -2816,8 +3201,15 @@ int visual_atoms(t_moldyn *moldyn) {
 
 	close(vb.fd);
 
+#ifdef VISUAL_THREAD
+	pthread_exit(NULL);
+
+}
+#else
+
 	return 0;
 }
+#endif
 
 /*
  * fpu cntrol functions