X-Git-Url: https://hackdaworld.org/gitweb/?a=blobdiff_plain;f=moldyn.c;h=91fead7739a0aeb4d45165ccfd48ea1427e56bc1;hb=a32468230b319b32819f1b20fd28aa9659574d45;hp=6d5f9e4ce39d5cf8124c615e99a330297803a71e;hpb=099c05fce45cacbbd7bbf6a7c5f1067e150d30ac;p=physik%2Fposic.git

diff --git a/moldyn.c b/moldyn.c
index 6d5f9e4..91fead7 100644
--- a/moldyn.c
+++ b/moldyn.c
@@ -191,15 +191,12 @@ int set_dim(t_moldyn *moldyn,double x,double y,double z,u8 visualize) {
 		moldyn->vis.dim.z=z;
 	}
 
-	moldyn->dv=0.000001*moldyn->volume;
-
 	printf("[moldyn] dimensions in A and A^3 respectively:\n");
 	printf("  x: %f\n",moldyn->dim.x);
 	printf("  y: %f\n",moldyn->dim.y);
 	printf("  z: %f\n",moldyn->dim.z);
 	printf("  volume: %f\n",moldyn->volume);
 	printf("  visualize simulation box: %s\n",visualize?"yes":"no");
-	printf("  delta volume (pressure calc): %f\n",moldyn->dv);
 
 	return 0;
 }
@@ -370,12 +367,25 @@ int moldyn_set_log(t_moldyn *moldyn,u8 type,int timer) {
 			dprintf(moldyn->tfd,"# temperature log file\n");
 			printf("temperature (%d)\n",timer);
 			break;
+		case LOG_VOLUME:
+			moldyn->vwrite=timer;
+			snprintf(filename,127,"%s/volume",moldyn->vlsdir);
+			moldyn->vfd=open(filename,
+			                 O_WRONLY|O_CREAT|O_EXCL,
+			                 S_IRUSR|S_IWUSR);
+			if(moldyn->vfd<0) {
+				perror("[moldyn] volume log file\n");
+				return moldyn->vfd;
+			}
+			dprintf(moldyn->vfd,"# volume log file\n");
+			printf("volume (%d)\n",timer);
+			break;
 		case SAVE_STEP:
 			moldyn->swrite=timer;
 			printf("save file (%d)\n",timer);
 			break;
 		case VISUAL_STEP:
-			moldyn->vwrite=timer;
+			moldyn->awrite=timer;
 			ret=visual_init(moldyn,moldyn->vlsdir);
 			if(ret<0) {
 				printf("[moldyn] visual init failure\n");
@@ -595,7 +605,7 @@ 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 +615,9 @@ 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;
@@ -913,16 +926,26 @@ double ideal_gas_law_pressure(t_moldyn *moldyn) {
 double virial_sum(t_moldyn *moldyn) {
 
 	int i;
-	double v;
 	t_virial *virial;
 
 	/* virial (sum over atom virials) */
-	v=0.0;
+	moldyn->virial=0.0;
+	moldyn->vir.xx=0.0;
+	moldyn->vir.yy=0.0;
+	moldyn->vir.zz=0.0;
+	moldyn->vir.xy=0.0;
+	moldyn->vir.xz=0.0;
+	moldyn->vir.yz=0.0;
 	for(i=0;i<moldyn->count;i++) {
 		virial=&(moldyn->atom[i].virial);
-		v+=(virial->xx+virial->yy+virial->zz);
+		moldyn->virial+=(virial->xx+virial->yy+virial->zz);
+		moldyn->vir.xx+=virial->xx;
+		moldyn->vir.yy+=virial->yy;
+		moldyn->vir.zz+=virial->zz;
+		moldyn->vir.xy+=virial->xy;
+		moldyn->vir.xz+=virial->xz;
+		moldyn->vir.yz+=virial->yz;
 	}
-	moldyn->virial=v;
 
 	/* global virial (absolute coordinates) */
 	virial=&(moldyn->gvir);
@@ -954,12 +977,44 @@ 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;
+	moldyn->tp_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 */
 
@@ -992,6 +1047,8 @@ int average_and_fluctuation_calc(t_moldyn *moldyn) {
 	moldyn->p_avg=moldyn->p_sum/denom;
 	moldyn->gp_sum+=moldyn->gp;
 	moldyn->gp_avg=moldyn->gp_sum/denom;
+	moldyn->tp_sum+=moldyn->tp;
+	moldyn->tp_avg=moldyn->tp_sum/denom;
 
 	return 0;
 }
@@ -1031,9 +1088,11 @@ 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;
-	double u_up,u_down,dv;
-	double scale,p;
+	t_3dvec dim;
+	//t_3dvec *tp;
+	double h,dv;
+	double y0,y1;
+	double su,sd;
 	t_atom *store;
 
 	/*
@@ -1043,54 +1102,56 @@ double thermodynamic_pressure_calc(t_moldyn *moldyn) {
 	 *
 	 */
 
-	scale=0.00001;
-	dv=8*scale*scale*scale*moldyn->volume;
-
+	/* store atomic configuration + dimension */
 	store=malloc(moldyn->count*sizeof(t_atom));
 	if(store==NULL) {
 		printf("[moldyn] allocating store mem failed\n");
 		return -1;
 	}
-
-	/* save unscaled potential energy + atom/dim configuration */
 	memcpy(store,moldyn->atom,moldyn->count*sizeof(t_atom));
 	dim=moldyn->dim;
 
+	/* x1, y1 */
+	sd=0.00001;
+	h=(1.0-sd)*(1.0-sd)*(1.0-sd);
+	su=pow(2.0-h,ONE_THIRD)-1.0;
+	dv=(1.0-h)*moldyn->volume;
+
 	/* scale up dimension and atom positions */
-	scale_dim(moldyn,SCALE_UP,scale,TRUE,TRUE,TRUE);
-	scale_atoms(moldyn,SCALE_UP,scale,TRUE,TRUE,TRUE);
+	scale_dim(moldyn,SCALE_UP,su,TRUE,TRUE,TRUE);
+	scale_atoms(moldyn,SCALE_UP,su,TRUE,TRUE,TRUE);
 	link_cell_shutdown(moldyn);
 	link_cell_init(moldyn,QUIET);
 	potential_force_calc(moldyn);
-	u_up=moldyn->energy;
+	y1=moldyn->energy;
 
 	/* restore atomic configuration + dim */
 	memcpy(moldyn->atom,store,moldyn->count*sizeof(t_atom));
 	moldyn->dim=dim;
 
 	/* scale down dimension and atom positions */
-	scale_dim(moldyn,SCALE_DOWN,scale,TRUE,TRUE,TRUE);
-	scale_atoms(moldyn,SCALE_DOWN,scale,TRUE,TRUE,TRUE);
+	scale_dim(moldyn,SCALE_DOWN,sd,TRUE,TRUE,TRUE);
+	scale_atoms(moldyn,SCALE_DOWN,sd,TRUE,TRUE,TRUE);
 	link_cell_shutdown(moldyn);
 	link_cell_init(moldyn,QUIET);
 	potential_force_calc(moldyn);
-	u_down=moldyn->energy;
+	y0=moldyn->energy;
 	
 	/* calculate pressure */
-	p=-(u_up-u_down)/dv;
-printf("-------> %.10f %.10f %f\n",u_up/EV/moldyn->count,u_down/EV/moldyn->count,p/BAR);
+	moldyn->tp=-(y1-y0)/(2.0*dv);
 
-	/* restore atomic configuration + dim */
+	/* restore atomic configuration */
 	memcpy(moldyn->atom,store,moldyn->count*sizeof(t_atom));
 	moldyn->dim=dim;
-
-	/* restore energy */
-	potential_force_calc(moldyn);
-
 	link_cell_shutdown(moldyn);
 	link_cell_init(moldyn,QUIET);
+	//potential_force_calc(moldyn);
 
-	return p;
+	/* free store buffer */
+	if(store)
+		free(store);
+
+	return moldyn->tp;
 }
 
 double get_pressure(t_moldyn *moldyn) {
@@ -1151,13 +1212,12 @@ int scale_volume(t_moldyn *moldyn) {
 
 	/* scaling factor */
 	if(moldyn->pt_scale&P_SCALE_BERENDSEN) {
-		scale=1.0-(moldyn->p_ref-moldyn->p)/moldyn->p_tc;
+		scale=1.0-(moldyn->p_ref-moldyn->p)*moldyn->p_tc;
 		scale=pow(scale,ONE_THIRD);
 	}
 	else {
 		scale=pow(moldyn->p/moldyn->p_ref,ONE_THIRD);
 	}
-moldyn->debug=scale;
 
 	/* scale the atoms and dimensions */
 	scale_atoms(moldyn,SCALE_DIRECT,scale,TRUE,TRUE,TRUE);
@@ -1244,13 +1304,10 @@ double estimate_time_step(t_moldyn *moldyn,double nn_dist) {
 
 /* linked list / cell method */
 
-#ifdef STATIC_LISTS
-
 int link_cell_init(t_moldyn *moldyn,u8 vol) {
 
 	t_linkcell *lc;
 	int i;
-	int *foo;
 
 	lc=&(moldyn->lc);
 
@@ -1261,21 +1318,36 @@ 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) {
+#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));
@@ -1283,8 +1355,16 @@ int link_cell_init(t_moldyn *moldyn,u8 vol) {
 			perror("[moldyn] list init (malloc)");
 			return -1;
 		}
-//if(i==0) printf(" --- add one here! %d %p %p ----\n",i,lc->subcell,lc->subcell[0]);
+		/*
+		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);
@@ -1298,7 +1378,9 @@ int link_cell_update(t_moldyn *moldyn) {
 	int nx,ny;
 	t_atom *atom;
 	t_linkcell *lc;
+#ifdef STATIC_LISTS
 	int p;
+#endif
 
 	atom=moldyn->atom;
 	lc=&(moldyn->lc);
@@ -1307,13 +1389,18 @@ int link_cell_update(t_moldyn *moldyn) {
 	ny=lc->ny;
 
 	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++;
@@ -1324,12 +1411,27 @@ int link_cell_update(t_moldyn *moldyn) {
 		}
 
 		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,int **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;
@@ -1347,6 +1449,10 @@ int link_cell_neighbour_index(t_moldyn *moldyn,int i,int j,int k,int **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;
@@ -1389,170 +1495,23 @@ int link_cell_shutdown(t_moldyn *moldyn) {
 
 	int i;
 	t_linkcell *lc;
-	int *foo;
 
 	lc=&(moldyn->lc);
 
-	for(i=0;i<lc->cells;i++)
-{
-//printf(" --- free %p , %d\n",lc->subcell[i],i);
+	for(i=0;i<lc->cells;i++) {
+#ifdef STATIC_LISTS
 		free(lc->subcell[i]);
-}
-
-	free(lc->subcell);
-
-	return 0;
-}
-
 #else
-
-int link_cell_init(t_moldyn *moldyn,u8 vol) {
-
-	t_linkcell *lc;
-	int i;
-
-	lc=&(moldyn->lc);
-
-	/* 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));
-
-	if(lc->cells<27)
-		printf("[moldyn] FATAL: less then 27 subcells!\n");
-
-	if(vol) {
-		printf("[moldyn] initializing 'dynamic' linked cells (%d)\n",
-		       lc->cells);
-		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);
-	}
-
-	for(i=0;i<lc->cells;i++)
-		list_init_f(&(lc->subcell[i]));
-
- 	link_cell_update(moldyn);
-	
-	return 0;
-}
-
-int link_cell_update(t_moldyn *moldyn) {
-
-	int count,i,j,k;
-	int nx,ny;
-	t_atom *atom;
-	t_linkcell *lc;
-	double x,y,z;
-
-	atom=moldyn->atom;
-	lc=&(moldyn->lc);
-
-	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++)
+		//printf(" ---> %d free %p\n",i,lc->subcell[i].start);
 		list_destroy_f(&(lc->subcell[i]));
-	
-	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);
-		list_add_immediate_f(&(lc->subcell[i+j*nx+k*nx*ny]),
-		                     &(atom[count]));
-//if(i==0&&j==0&&k==0) printf(" --- add one here! %d %p ----\n",count,lc->subcell[0].current);
-	}
-
-	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;
-	u8 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];
-				}
-			}
-		}
+#endif
 	}
 
-	lc->dnlc=count1;
-
-	return count1;
-}
-
-int link_cell_shutdown(t_moldyn *moldyn) {
-
-	int i;
-	t_linkcell *lc;
-
-	lc=&(moldyn->lc);
-
-printf("FOO:\n");
-	for(i=0;i<lc->nx*lc->ny*lc->nz;i++) {
-printf(" %d\n",i);
-		list_destroy_f(&(moldyn->lc.subcell[i]));
-printf(" %d!\n",i);
-}
-
 	free(lc->subcell);
 
 	return 0;
 }
 
-#endif
-
 int moldyn_add_schedule(t_moldyn *moldyn,int runs,double tau) {
 
 	int count;
@@ -1604,7 +1563,7 @@ int moldyn_set_schedule_hook(t_moldyn *moldyn,set_hook hook,void *hook_params) {
 int moldyn_integrate(t_moldyn *moldyn) {
 
 	int i;
-	unsigned int e,m,s,v,p,t;
+	unsigned int e,m,s,v,p,t,a;
 	t_3dvec momentum;
 	t_moldyn_schedule *sched;
 	t_atom *atom;
@@ -1626,6 +1585,7 @@ int moldyn_integrate(t_moldyn *moldyn) {
 	m=moldyn->mwrite;
 	s=moldyn->swrite;
 	v=moldyn->vwrite;
+	a=moldyn->awrite;
 	p=moldyn->pwrite;
 	t=moldyn->twrite;
 
@@ -1644,14 +1604,14 @@ 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;
@@ -1687,6 +1647,9 @@ int moldyn_integrate(t_moldyn *moldyn) {
 		temperature_calc(moldyn);
 		virial_sum(moldyn);
 		pressure_calc(moldyn);
+		//thermodynamic_pressure_calc(moldyn);
+
+		/* calculate fluctuations + averages */
 		average_and_fluctuation_calc(moldyn);
 
 		/* p/t scaling */
@@ -1716,9 +1679,10 @@ int moldyn_integrate(t_moldyn *moldyn) {
 		if(p) {
 			if(!(moldyn->total_steps%p)) {
 				dprintf(moldyn->pfd,
-				        "%f %f %f %f %f\n",moldyn->time,
+				        "%f %f %f %f %f %f %f\n",moldyn->time,
 				         moldyn->p/BAR,moldyn->p_avg/BAR,
-				         moldyn->gp/BAR,moldyn->gp_avg/BAR);
+				         moldyn->gp/BAR,moldyn->gp_avg/BAR,
+					 moldyn->tp/BAR,moldyn->tp_avg/BAR);
 			}
 		}
 		if(t) {
@@ -1728,6 +1692,12 @@ int moldyn_integrate(t_moldyn *moldyn) {
 				        moldyn->time,moldyn->t,moldyn->t_avg);
 			}
 		}
+		if(v) {
+			if(!(moldyn->total_steps%v)) {
+				dprintf(moldyn->vfd,
+				        "%f %f\n",moldyn->time,moldyn->volume);
+			}
+		}
 		if(s) {
 			if(!(moldyn->total_steps%s)) {
 				snprintf(dir,128,"%s/s-%07.f.save",
@@ -1743,8 +1713,8 @@ int moldyn_integrate(t_moldyn *moldyn) {
 				close(fd);
 			}	
 		}
-		if(v) {
-			if(!(moldyn->total_steps%v)) {
+		if(a) {
+			if(!(moldyn->total_steps%a)) {
 				visual_atoms(moldyn);
 			}
 		}
@@ -1754,13 +1724,14 @@ 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:%4.1f/%4.1f P:%4.1f/%4.1f V:%6.1f (%d)",
+       sched->count,i,moldyn->total_steps,
+       moldyn->t,moldyn->t_avg,
+       moldyn->p/BAR,moldyn->p_avg/BAR,
+       moldyn->volume,
+       (int)(t2.tv_sec-t1.tv_sec));
+
+			fflush(stdout);
 
 			/* copy over time */
 			t1=t2;
@@ -1774,8 +1745,8 @@ 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");
 		}
@@ -1803,6 +1774,9 @@ 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);
@@ -1816,6 +1790,9 @@ 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);
 
@@ -1823,6 +1800,9 @@ 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);
@@ -2150,20 +2130,27 @@ 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;
@@ -2278,6 +2265,8 @@ 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) {
@@ -2285,28 +2274,51 @@ 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;
 }
@@ -2346,6 +2358,47 @@ int pair_correlation_init(t_moldyn *moldyn,double dr) {
 	return 0;
 }
 
+int calculate_diffusion_coefficient(t_moldyn *moldyn,double *dc) {
+
+	int i;
+	t_atom *atom;
+	t_3dvec dist;
+	double d2;
+	int a_cnt;
+	int b_cnt;
+
+	atom=moldyn->atom;
+	dc[0]=0;
+	dc[1]=0;
+	dc[2]=0;
+	a_cnt=0;
+	b_cnt=0;
+
+	for(i=0;i<moldyn->count;i++) {
+
+		v3_sub(&dist,&(atom[i].r),&(atom[i].r_0));
+		check_per_bound(moldyn,&dist);
+		d2=v3_absolute_square(&dist);
+
+		if(atom[i].brand) {
+			b_cnt+=1;
+			dc[1]+=d2;
+		}
+		else {
+			a_cnt+=1;
+			dc[0]+=d2;
+		}
+
+		dc[2]+=d2;
+	}
+
+	dc[0]*=(1.0/(6.0*moldyn->time*a_cnt));
+	dc[1]*=(1.0/(6.0*moldyn->time*b_cnt));
+	dc[2]*=(1.0/(6.0*moldyn->time*moldyn->count));
+		
+	return 0;
+}
+
 int calculate_pair_correlation(t_moldyn *moldyn,double dr,void *ptr) {
 
 	int slots;
@@ -2362,15 +2415,19 @@ int calculate_pair_correlation(t_moldyn *moldyn,double dr,void *ptr) {
 	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=2.0*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);
@@ -2427,12 +2484,9 @@ int calculate_pair_correlation(t_moldyn *moldyn,double dr,void *ptr) {
 
 				jtom=this->current->data;
 #endif
-
-				if(jtom==&(itom[i]))
-					continue;
-
-				/* only count pairs once */
-				if(itom[i].tag>jtom->tag)
+				/* only count pairs once,
+				 * skip same atoms */
+				if(itom[i].tag>=jtom->tag)
 					continue;
 
 				/*
@@ -2444,14 +2498,23 @@ 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>=4.0*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;
@@ -2464,7 +2527,6 @@ int calculate_pair_correlation(t_moldyn *moldyn,double dr,void *ptr) {
 					/* type b - type b bonds */
 						stat[s+o]+=1;
 				}
-
 #ifdef STATIC_LISTS
 			}
 #else
@@ -2473,16 +2535,17 @@ int calculate_pair_correlation(t_moldyn *moldyn,double dr,void *ptr) {
 		}
 	}
 
-	/* normalization 
+	/* normalization */
 	for(i=1;i<slots;i++) {
-		 // normalization: 4 pi r r dr
+		 // normalization: 4 pi r^2 dr
 		 // here: not double counting pairs -> 2 pi r r dr
-		norm=2*M_PI*moldyn->count*(i*dr*i*dr)*dr;
+		 // ... and actually it's a constant times r^2
+		norm=i*i*dr*dr;
 		stat[i]/=norm;
 		stat[slots+i]/=norm;
 		stat[o+i]/=norm;
 	}
-	*/
+	/* */
 
 	if(ptr==NULL) {
 		/* todo: store/print pair correlation function */