X-Git-Url: https://hackdaworld.org/gitweb/?a=blobdiff_plain;f=moldyn.c;h=80cf5721a195991a0fa0bdf7a7aca18c83ea8337;hb=f828bb665c033d828c520c68a98abdb6fa63a83a;hp=2e0e46810f4ba065ee8d384d0fd556749d53db93;hpb=dff2917d22ed07707d222bc10fab7370356699dc;p=physik%2Fposic.git

diff --git a/moldyn.c b/moldyn.c
index 2e0e468..80cf572 100644
--- a/moldyn.c
+++ b/moldyn.c
@@ -595,7 +595,7 @@ int add_atom(t_moldyn *moldyn,int element,double mass,u8 brand,u8 attr,
 	int count;
 	
 	atom=moldyn->atom;
-	count=(moldyn->count)++;
+	count=(moldyn->count)++;	// asshole style!
 
 	ptr=realloc(atom,(count+1)*sizeof(t_atom));
 	if(!ptr) {
@@ -605,6 +605,9 @@ int add_atom(t_moldyn *moldyn,int element,double mass,u8 brand,u8 attr,
 	moldyn->atom=ptr;
 
 	atom=moldyn->atom;
+
+	/* initialize new atom */
+	memset(&(atom[count]),0,sizeof(t_atom));
 	atom[count].r=*r;
 	atom[count].v=*v;
 	atom[count].element=element;
@@ -954,12 +957,43 @@ double pressure_calc(t_moldyn *moldyn) {
 	return moldyn->p;
 }
 
+int average_reset(t_moldyn *moldyn) {
+
+	printf("[moldyn] average reset\n");
+
+	/* update skip value */
+	moldyn->avg_skip=moldyn->total_steps;
+
+	/* kinetic energy */
+	moldyn->k_sum=0.0;
+	moldyn->k2_sum=0.0;
+	
+	/* potential energy */
+	moldyn->v_sum=0.0;
+	moldyn->v2_sum=0.0;
+
+	/* temperature */
+	moldyn->t_sum=0.0;
+
+	/* virial */
+	moldyn->virial_sum=0.0;
+	moldyn->gv_sum=0.0;
+
+	/* pressure */
+	moldyn->p_sum=0.0;
+	moldyn->gp_sum=0.0;
+
+	return 0;
+}
+
 int average_and_fluctuation_calc(t_moldyn *moldyn) {
 
+	int denom;
+
 	if(moldyn->total_steps<moldyn->avg_skip)
 		return 0;
 
-	int denom=moldyn->total_steps+1-moldyn->avg_skip;
+	denom=moldyn->total_steps+1-moldyn->avg_skip;
 
 	/* assume up to date energies, temperature, pressure etc */
 
@@ -1031,7 +1065,8 @@ printf("  --> <dV2> sim: %f experimental: %f\n",moldyn->dv2_avg,1.5*moldyn->coun
 
 double thermodynamic_pressure_calc(t_moldyn *moldyn) {
 
-	t_3dvec dim,*tp;
+	t_3dvec dim;
+	//t_3dvec *tp;
 	double u_up,u_down,dv;
 	double scale,p;
 	t_atom *store;
@@ -1258,25 +1293,57 @@ int link_cell_init(t_moldyn *moldyn,u8 vol) {
 	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;
+
+#ifdef STATIC_LISTS
+	lc->subcell=malloc(lc->cells*sizeof(int*));
+#else
 	lc->subcell=malloc(lc->cells*sizeof(t_list));
+#endif
+
+	if(lc->subcell==NULL) {
+		perror("[moldyn] cell init (malloc)");
+		return -1;
+	}
 
 	if(lc->cells<27)
 		printf("[moldyn] FATAL: less then 27 subcells!\n");
 
 	if(vol) {
-		printf("[moldyn] initializing linked cells (%d)\n",lc->cells);
+#ifdef STATIC_LISTS
+		printf("[moldyn] initializing 'static' linked cells (%d)\n",
+		       lc->cells);
+#else
+		printf("[moldyn] initializing 'dynamic' linked cells (%d)\n",
+		       lc->cells);
+#endif
 		printf("  x: %d x %f A\n",lc->nx,lc->x);
 		printf("  y: %d x %f A\n",lc->ny,lc->y);
 		printf("  z: %d x %f A\n",lc->nz,lc->z);
 	}
 
+#ifdef STATIC_LISTS
+	/* list init */
+	for(i=0;i<lc->cells;i++) {
+		lc->subcell[i]=malloc((MAX_ATOMS_PER_LIST+1)*sizeof(int));
+		if(lc->subcell[i]==NULL) {
+			perror("[moldyn] list init (malloc)");
+			return -1;
+		}
+		/*
+		if(i==0)
+			printf(" ---> %d malloc %p (%p)\n",
+			       i,lc->subcell[0],lc->subcell);
+		*/
+	}
+#else
 	for(i=0;i<lc->cells;i++)
 		list_init_f(&(lc->subcell[i]));
+#endif
+
+	/* update the list */
+	link_cell_update(moldyn);
 
- 	link_cell_update(moldyn);
-	
 	return 0;
 }
 
@@ -1286,7 +1353,9 @@ int link_cell_update(t_moldyn *moldyn) {
 	int nx,ny;
 	t_atom *atom;
 	t_linkcell *lc;
-	double x,y,z;
+#ifdef STATIC_LISTS
+	int p;
+#endif
 
 	atom=moldyn->atom;
 	lc=&(moldyn->lc);
@@ -1294,25 +1363,50 @@ int link_cell_update(t_moldyn *moldyn) {
 	nx=lc->nx;
 	ny=lc->ny;
 
-	x=moldyn->dim.x/2;
-	y=moldyn->dim.y/2;
-	z=moldyn->dim.z/2;
-
 	for(i=0;i<lc->cells;i++)
+#ifdef STATIC_LISTS
+		memset(lc->subcell[i],0,(MAX_ATOMS_PER_LIST+1)*sizeof(int));
+#else
 		list_destroy_f(&(lc->subcell[i]));
-	
+#endif
+
 	for(count=0;count<moldyn->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);
+	
+#ifdef STATIC_LISTS
+		p=0;
+		while(lc->subcell[i+j*nx+k*nx*ny][p]!=0)
+			p++;
+
+		if(p>=MAX_ATOMS_PER_LIST) {
+			printf("[moldyn] FATAL: amount of atoms too high!\n");
+			return -1;
+		}
+
+		lc->subcell[i+j*nx+k*nx*ny][p]=count;
+#else
 		list_add_immediate_f(&(lc->subcell[i+j*nx+k*nx*ny]),
 		                     &(atom[count]));
+		/*
+		if(j==0&&k==0)
+			printf(" ---> %d %d malloc %p (%p)\n",
+			       i,count,lc->subcell[i].current,lc->subcell);
+		*/
+#endif
 	}
 
 	return 0;
 }
 
-int link_cell_neighbour_index(t_moldyn *moldyn,int i,int j,int k,t_list *cell) {
+int link_cell_neighbour_index(t_moldyn *moldyn,int i,int j,int k,
+#ifdef STATIC_LISTS
+                              int **cell
+#else
+                              t_list *cell
+#endif
+			     ) {
 
 	t_linkcell *lc;
 	int a;
@@ -1330,6 +1424,10 @@ int link_cell_neighbour_index(t_moldyn *moldyn,int i,int j,int k,t_list *cell) {
 	count2=27;
 	a=nx*ny;
 
+	if(i>=nx||j>=ny||k>=nz)
+		printf("[moldyn] WARNING: lcni %d/%d %d/%d %d/%d\n",
+		       i,nx,j,ny,k,nz);
+
 	cell[0]=lc->subcell[i+j*nx+k*a];
 	for(ci=-1;ci<=1;ci++) {
 		bx=0;
@@ -1375,8 +1473,14 @@ int link_cell_shutdown(t_moldyn *moldyn) {
 
 	lc=&(moldyn->lc);
 
-	for(i=0;i<lc->nx*lc->ny*lc->nz;i++)
-		list_destroy_f(&(moldyn->lc.subcell[i]));
+	for(i=0;i<lc->cells;i++) {
+#ifdef STATIC_LISTS
+		free(lc->subcell[i]);
+#else
+		//printf(" ---> %d free %p\n",i,lc->subcell[i].start);
+		list_destroy_f(&(lc->subcell[i]));
+#endif
+	}
 
 	free(lc->subcell);
 
@@ -1474,14 +1578,14 @@ int moldyn_integrate(t_moldyn *moldyn) {
 
 	/* some stupid checks before we actually start calculating bullshit */
 	if(moldyn->cutoff>0.5*moldyn->dim.x)
-		printf("[moldyn] warning: cutoff > 0.5 x dim.x\n");
+		printf("[moldyn] WARNING: cutoff > 0.5 x dim.x\n");
 	if(moldyn->cutoff>0.5*moldyn->dim.y)
-		printf("[moldyn] warning: cutoff > 0.5 x dim.y\n");
+		printf("[moldyn] WARNING: cutoff > 0.5 x dim.y\n");
 	if(moldyn->cutoff>0.5*moldyn->dim.z)
-		printf("[moldyn] warning: cutoff > 0.5 x dim.z\n");
+		printf("[moldyn] WARNING: cutoff > 0.5 x dim.z\n");
 	ds=0.5*atom[0].f.x*moldyn->tau_square/atom[0].mass;
 	if(ds>0.05*moldyn->nnd)
-		printf("[moldyn] warning: forces too high / tau too small!\n");
+		printf("[moldyn] WARNING: forces too high / tau too small!\n");
 
 	/* zero absolute time */
 	moldyn->time=0.0;
@@ -1584,13 +1688,14 @@ int moldyn_integrate(t_moldyn *moldyn) {
 			/* get current time */
 			gettimeofday(&t2,NULL);
 
-	printf("\rsched:%d, steps:%d, T:%3.1f/%3.1f P:%4.1f/%4.1f V:%6.1f (%d)",
-	       sched->count,i,
-	       moldyn->t,moldyn->t_avg,
-	       moldyn->p_avg/BAR,moldyn->gp_avg/BAR,
-	       moldyn->volume,
-	       (int)(t2.tv_sec-t1.tv_sec));
-	fflush(stdout);
+printf("\rsched:%d, steps:%d/%d, T:%3.1f/%3.1f P:%4.1f/%4.1f V:%6.1f (%d)",
+       sched->count,i,moldyn->total_steps,
+       moldyn->t,moldyn->t_avg,
+       moldyn->p_avg/BAR,moldyn->gp_avg/BAR,
+       moldyn->volume,
+       (int)(t2.tv_sec-t1.tv_sec));
+
+			fflush(stdout);
 
 			/* copy over time */
 			t1=t2;
@@ -1604,8 +1709,8 @@ int moldyn_integrate(t_moldyn *moldyn) {
 
 		/* check for hooks */
 		if(sched->hook) {
-			printf("\n ## schedule hook %d/%d start ##\n",
-			       sched->count+1,sched->total_sched-1);
+			printf("\n ## schedule hook %d start ##\n",
+			       sched->count);
 			sched->hook(moldyn,sched->hook_params);
 			printf(" ## schedule hook end ##\n");
 		}
@@ -1633,6 +1738,9 @@ int velocity_verlet(t_moldyn *moldyn) {
 	tau_square=moldyn->tau_square;
 
 	for(i=0;i<count;i++) {
+		/* check whether fixed atom */
+		if(atom[i].attr&ATOM_ATTR_FP)
+			continue;
 		/* new positions */
 		h=0.5/atom[i].mass;
 		v3_scale(&delta,&(atom[i].v),tau);
@@ -1646,6 +1754,9 @@ int velocity_verlet(t_moldyn *moldyn) {
 		v3_add(&(atom[i].v),&(atom[i].v),&delta);
 	}
 
+	/* criticial check */
+	moldyn_bc_check(moldyn);
+
 	/* neighbour list update */
 	link_cell_update(moldyn);
 
@@ -1653,6 +1764,9 @@ int velocity_verlet(t_moldyn *moldyn) {
 	potential_force_calc(moldyn);
 
 	for(i=0;i<count;i++) {
+		/* check whether fixed atom */
+		if(atom[i].attr&ATOM_ATTR_FP)
+			continue;
 		/* again velocities [actually v(t+tau)] */
 		v3_scale(&delta,&(atom[i].f),0.5*tau/atom[i].mass);
 		v3_add(&(atom[i].v),&(atom[i].v),&delta);
@@ -1676,15 +1790,24 @@ int potential_force_calc(t_moldyn *moldyn) {
 	t_atom *itom,*jtom,*ktom;
 	t_virial *virial;
 	t_linkcell *lc;
+#ifdef STATIC_LISTS
+	int *neighbour_i[27];
+	int p,q;
+	t_atom *atom;
+#else
 	t_list neighbour_i[27];
 	t_list neighbour_i2[27];
 	t_list *this,*that;
+#endif
 	u8 bc_ij,bc_ik;
 	int dnlc;
 
 	count=moldyn->count;
 	itom=moldyn->atom;
 	lc=&(moldyn->lc);
+#ifdef STATIC_LISTS
+	atom=moldyn->atom;
+#endif
 
 	/* reset energy */
 	moldyn->energy=0.0;
@@ -1739,14 +1862,33 @@ int potential_force_calc(t_moldyn *moldyn) {
 		if(moldyn->func2b) {
 			for(j=0;j<27;j++) {
 
+				bc_ij=(j<dnlc)?0:1;
+#ifdef STATIC_LISTS
+				p=0;
+
+				while(neighbour_i[j][p]!=0) {
+
+					jtom=&(atom[neighbour_i[j][p]]);
+					p++;
+
+					if(jtom==&(itom[i]))
+						continue;
+
+					if((jtom->attr&ATOM_ATTR_2BP)&
+					   (itom[i].attr&ATOM_ATTR_2BP)) {
+						moldyn->func2b(moldyn,
+						               &(itom[i]),
+						               jtom,
+					        	       bc_ij);
+					}
+				}
+#else
 				this=&(neighbour_i[j]);
 				list_reset_f(this);
 
 				if(this->start==NULL)
 					continue;
 
-				bc_ij=(j<dnlc)?0:1;
-
 				do {
 					jtom=this->current->data;
 
@@ -1761,6 +1903,7 @@ int potential_force_calc(t_moldyn *moldyn) {
 					        	       bc_ij);
 					}
 				} while(list_next_f(this)!=L_NO_NEXT_ELEMENT);
+#endif
 
 			}
 		}
@@ -1771,21 +1914,34 @@ int potential_force_calc(t_moldyn *moldyn) {
 			continue;
 
 		/* copy the neighbour lists */
+#ifdef STATIC_LISTS
+		/* no copy needed for static lists */
+#else
 		memcpy(neighbour_i2,neighbour_i,27*sizeof(t_list));
+#endif
 
 		/* second loop over atoms j */
 		for(j=0;j<27;j++) {
 
+			bc_ij=(j<dnlc)?0:1;
+#ifdef STATIC_LISTS
+			p=0;
+
+			while(neighbour_i[j][p]!=0) {
+
+				jtom=&(atom[neighbour_i[j][p]]);
+				p++;
+#else
 			this=&(neighbour_i[j]);
 			list_reset_f(this);
 
 			if(this->start==NULL)
 				continue;
 
-			bc_ij=(j<dnlc)?0:1;
-
 			do {
+
 				jtom=this->current->data;
+#endif
 
 				if(jtom==&(itom[i]))
 					continue;
@@ -1811,17 +1967,24 @@ int potential_force_calc(t_moldyn *moldyn) {
 
 				for(k=0;k<27;k++) {
 
+					bc_ik=(k<dnlc)?0:1;
+#ifdef STATIC_LISTS
+					q=0;
+
+					while(neighbour_i[j][q]!=0) {
+
+						ktom=&(atom[neighbour_i[k][q]]);
+						q++;
+#else
 					that=&(neighbour_i2[k]);
 					list_reset_f(that);
 					
 					if(that->start==NULL)
 						continue;
 
-					bc_ik=(k<dnlc)?0:1;
-
 					do {
-
 						ktom=that->current->data;
+#endif
 
 						if(!(ktom->attr&ATOM_ATTR_3BP))
 							continue;
@@ -1837,9 +2000,12 @@ int potential_force_calc(t_moldyn *moldyn) {
 						                  jtom,
 						                  ktom,
 						                  bc_ik|bc_ij);
-
+#ifdef STATIC_LISTS
+					}
+#else
 					} while(list_next_f(that)!=\
 					        L_NO_NEXT_ELEMENT);
+#endif
 
 				}
 
@@ -1856,17 +2022,24 @@ int potential_force_calc(t_moldyn *moldyn) {
 
 				for(k=0;k<27;k++) {
 
+					bc_ik=(k<dnlc)?0:1;
+#ifdef STATIC_LISTS
+					q=0;
+
+					while(neighbour_i[j][q]!=0) {
+
+						ktom=&(atom[neighbour_i[k][q]]);
+						q++;
+#else
 					that=&(neighbour_i2[k]);
 					list_reset_f(that);
 					
 					if(that->start==NULL)
 						continue;
 
-					bc_ik=(k<dnlc)?0:1;
-
 					do {
-
 						ktom=that->current->data;
+#endif
 
 						if(!(ktom->attr&ATOM_ATTR_3BP))
 							continue;
@@ -1883,8 +2056,12 @@ int potential_force_calc(t_moldyn *moldyn) {
 						                  ktom,
 						                  bc_ik|bc_ij);
 
+#ifdef STATIC_LISTS
+					}
+#else
 					} while(list_next_f(that)!=\
 					        L_NO_NEXT_ELEMENT);
+#endif
 
 				}
 				
@@ -1896,8 +2073,11 @@ int potential_force_calc(t_moldyn *moldyn) {
 					                  &(itom[i]),
 					                  jtom,bc_ij);
 				}
-					
+#ifdef STATIC_LISTS
+			}
+#else
 			} while(list_next_f(this)!=L_NO_NEXT_ELEMENT);
+#endif
 		
 		}
 		
@@ -1914,20 +2094,27 @@ int potential_force_calc(t_moldyn *moldyn) {
 	//printf("\nATOM 0: %f %f %f\n\n",itom->f.x,itom->f.y,itom->f.z);
 	if(moldyn->time>DSTART&&moldyn->time<DEND) {
 		printf("force:\n");
-		printf("  x: %0.40f\n",moldyn->atom[5832].f.x);
-		printf("  y: %0.40f\n",moldyn->atom[5832].f.y);
-		printf("  z: %0.40f\n",moldyn->atom[5832].f.z);
+		printf("  x: %0.40f\n",moldyn->atom[DATOM].f.x);
+		printf("  y: %0.40f\n",moldyn->atom[DATOM].f.y);
+		printf("  z: %0.40f\n",moldyn->atom[DATOM].f.z);
 	}
 #endif
 
-	/* calculate global virial */
+	/* some postprocessing */
 	for(i=0;i<count;i++) {
-		moldyn->gvir.xx+=moldyn->atom[i].r.x*moldyn->atom[i].f.x;
-		moldyn->gvir.yy+=moldyn->atom[i].r.y*moldyn->atom[i].f.y;
-		moldyn->gvir.zz+=moldyn->atom[i].r.z*moldyn->atom[i].f.z;
-		moldyn->gvir.xy+=moldyn->atom[i].r.y*moldyn->atom[i].f.x;
-		moldyn->gvir.xz+=moldyn->atom[i].r.z*moldyn->atom[i].f.x;
-		moldyn->gvir.yz+=moldyn->atom[i].r.z*moldyn->atom[i].f.y;
+		/* calculate global virial */
+		moldyn->gvir.xx+=itom[i].r.x*itom[i].f.x;
+		moldyn->gvir.yy+=itom[i].r.y*itom[i].f.y;
+		moldyn->gvir.zz+=itom[i].r.z*itom[i].f.z;
+		moldyn->gvir.xy+=itom[i].r.y*itom[i].f.x;
+		moldyn->gvir.xz+=itom[i].r.z*itom[i].f.x;
+		moldyn->gvir.yz+=itom[i].r.z*itom[i].f.y;
+
+		/* check forces regarding the given timestep */
+		if(v3_norm(&(itom[i].f))>\
+		   0.1*moldyn->nnd*itom[i].mass/moldyn->tau_square)
+			printf("[moldyn] WARNING: pfc (high force: atom %d)\n",
+			       i);
 	}
 
 	return 0;
@@ -2042,6 +2229,8 @@ int moldyn_read_save_file(t_moldyn *moldyn,char *file) {
 
 	int fd;
 	int cnt,size;
+	int fsize;
+	int corr;
 
 	fd=open(file,O_RDONLY);
 	if(fd<0) {
@@ -2049,28 +2238,51 @@ int moldyn_read_save_file(t_moldyn *moldyn,char *file) {
 		return fd;
 	}
 
+	fsize=lseek(fd,0,SEEK_END);
+	lseek(fd,0,SEEK_SET);
+
 	size=sizeof(t_moldyn);
-	cnt=read(fd,moldyn,size);
-	if(cnt!=size) {
-		perror("[moldyn] load save file read (moldyn)");
-		return cnt;
+
+	while(size) {
+		cnt=read(fd,moldyn,size);
+		if(cnt<0) {
+			perror("[moldyn] load save file read (moldyn)");
+			return cnt;
+		}
+		size-=cnt;
 	}
 
 	size=moldyn->count*sizeof(t_atom);
 
+	/* correcting possible atom data offset */
+	corr=0;
+	if(fsize!=sizeof(t_moldyn)+size) {
+		corr=fsize-sizeof(t_moldyn)-size;
+		printf("[moldyn] WARNING: lsf (illegal file size)\n");
+		printf("  moifying offset:\n");
+		printf("  - current pos: %d\n",sizeof(t_moldyn));
+		printf("  - atom size: %d\n",size);
+		printf("  - file size: %d\n",fsize);
+		printf("  => correction: %d\n",corr);
+		lseek(fd,corr,SEEK_CUR);
+	}
+
 	moldyn->atom=(t_atom *)malloc(size);
 	if(moldyn->atom==NULL) {
 		perror("[moldyn] load save file malloc (atoms)");
 		return -1;
 	}
 
-	cnt=read(fd,moldyn->atom,size);
-	if(cnt!=size) {
-		perror("[moldyn] load save file read (atoms)");
-		return cnt;
+	while(size) {
+		cnt=read(fd,moldyn->atom,size);
+		if(cnt<0) {
+			perror("[moldyn] load save file read (atoms)");
+			return cnt;
+		}
+		size-=cnt;
 	}
 
-	// hooks
+	// hooks etc ...
 
 	return 0;
 }
@@ -2116,20 +2328,35 @@ int calculate_pair_correlation(t_moldyn *moldyn,double dr,void *ptr) {
 	double *stat;
 	int i,j;
 	t_linkcell *lc;
+#ifdef STATIC_LISTS
+	int *neighbour[27];
+	int p;
+#else
 	t_list neighbour[27];
+#endif
 	t_atom *itom,*jtom;
 	t_list *this;
 	unsigned char bc;
 	t_3dvec dist;
-	double d,norm;
+	double d;
+	//double norm;
 	int o,s;
 	unsigned char ibrand;
 
 	lc=&(moldyn->lc);
 
-	slots=(int)(moldyn->cutoff/dr);
+	slots=moldyn->cutoff/dr;
 	o=2*slots;
 
+	if(slots*dr<=moldyn->cutoff)
+		printf("[moldyn] WARNING: pcc (low #slots)\n");
+
+	printf("[moldyn] pair correlation calc info:\n");
+	printf("  time: %f\n",moldyn->time);
+	printf("  count: %d\n",moldyn->count);
+	printf("  cutoff: %f\n",moldyn->cutoff);
+	printf("  temperature: cur=%f avg=%f\n",moldyn->t,moldyn->t_avg);
+
 	if(ptr!=NULL) {
 		stat=(double *)ptr;
 	}
@@ -2159,26 +2386,30 @@ int calculate_pair_correlation(t_moldyn *moldyn,double dr,void *ptr) {
 		ibrand=itom[i].brand;
 	
 		for(j=0;j<27;j++) {
-			/* prepare the neighbour cell list */
+
+			bc=(j<lc->dnlc)?0:1;
+
+#ifdef STATIC_LISTS
+			p=0;
+
+			while(neighbour[j][p]!=0) {
+
+				jtom=&(moldyn->atom[neighbour[j][p]]);
+				p++;
+#else
 			this=&(neighbour[j]);
 			list_reset_f(this);
 
-			/* check for atoms */
 			if(this->start==NULL)
 				continue;
 
-			/* boundary check */	
-			bc=(j<lc->dnlc)?0:1;
-
 			do {
-				jtom=this->current->data;
-
 
-				if(jtom==&(itom[i]))
-					continue;
-
-				/* only count pairs once */
-				if(itom[i].tag>jtom->tag)
+				jtom=this->current->data;
+#endif
+				/* only count pairs once,
+				 * skip same atoms */
+				if(itom[i].tag>=jtom->tag)
 					continue;
 
 				/*
@@ -2190,14 +2421,23 @@ int calculate_pair_correlation(t_moldyn *moldyn,double dr,void *ptr) {
 				if(bc) check_per_bound(moldyn,&dist);
 				d=v3_absolute_square(&dist);
 
-				/* ignore if greater cutoff */
-				if(d>moldyn->cutoff_square)
+				/* ignore if greater or equal cutoff */
+				if(d>=moldyn->cutoff_square)
 					continue;
 
 				/* fill the slots */
 				d=sqrt(d);
 				s=(int)(d/dr);
 
+				/* should never happen but it does 8) -
+				 * related to -ffloat-store problem! */
+				if(s>=slots) {
+					printf("[moldyn] WARNING: pcc (%d/%d)",
+					       s,slots);
+					printf("\n");
+					s=slots-1;
+				}
+
 				if(ibrand!=jtom->brand) {
 					/* mixed */
 					stat[s]+=1;
@@ -2210,22 +2450,24 @@ int calculate_pair_correlation(t_moldyn *moldyn,double dr,void *ptr) {
 					/* type b - type b bonds */
 						stat[s+o]+=1;
 				}
-
+#ifdef STATIC_LISTS
+			}
+#else
 			} while(list_next_f(this)!=L_NO_NEXT_ELEMENT);
+#endif
 		}
 	}
 
-	/* normalization */
+	/* normalization 
 	for(i=1;i<slots;i++) {
-		/*
-		 * normalization: 4 pi r r dr
-		 * here: not double counting pairs -> 2 pi r r dr
-		 */
+		 // normalization: 4 pi r r dr
+		 // here: not double counting pairs -> 2 pi r r dr
 		norm=2*M_PI*moldyn->count*(i*dr*i*dr)*dr;
 		stat[i]/=norm;
 		stat[slots+i]/=norm;
 		stat[o+i]/=norm;
 	}
+	*/
 
 	if(ptr==NULL) {
 		/* todo: store/print pair correlation function */
@@ -2268,7 +2510,12 @@ int visual_atoms(t_moldyn *moldyn) {
 	t_atom *atom;
 	t_atom *btom;
 	t_linkcell *lc;
+#ifdef STATIC_LISTS
+	int *neighbour[27];
+	int p;
+#else
 	t_list neighbour[27];
+#endif
 	u8 bc;
 	t_3dvec dist;
 	double d2;
@@ -2322,12 +2569,19 @@ int visual_atoms(t_moldyn *moldyn) {
 		                          (atom[i].r.z+moldyn->dim.z/2)/lc->z,
 		                          neighbour);
 		for(j=0;j<27;j++) {
+			bc=j<lc->dnlc?0:1;
+#ifdef STATIC_LISTS
+			p=0;
+			while(neighbour[j][p]!=0) {
+				btom=&(atom[neighbour[j][p]]);
+				p++;
+#else
 			list_reset_f(&neighbour[j]);
 			if(neighbour[j].start==NULL)
 				continue;
-			bc=j<lc->dnlc?0:1;
 			do {
 				btom=neighbour[j].current->data;
+#endif
 				if(btom==&atom[i])	// skip identical atoms
 					continue;
 				//if(btom<&atom[i])	// skip half of them
@@ -2347,7 +2601,11 @@ int visual_atoms(t_moldyn *moldyn) {
 				dprintf(fd,"# [B] %f %f %f %f %f %f\n",
 				        atom[i].r.x,atom[i].r.y,atom[i].r.z,
 		       		        btom->r.x,btom->r.y,btom->r.z);
+#ifdef STATIC_LISTS
+			}
+#else
 			} while(list_next_f(&neighbour[j])!=L_NO_NEXT_ELEMENT);
+#endif
 		}
 	}