X-Git-Url: https://www.hackdaworld.org/gitweb/?a=blobdiff_plain;f=moldyn.c;h=82ae543c073457a47372253f6c238f76d1bfe6b5;hb=0d1dfb1e5027d215fced8ca306dd658f692a2a44;hp=80cf5721a195991a0fa0bdf7a7aca18c83ea8337;hpb=f828bb665c033d828c520c68a98abdb6fa63a83a;p=physik%2Fposic.git

diff --git a/moldyn.c b/moldyn.c
index 80cf572..82ae543 100644
--- a/moldyn.c
+++ b/moldyn.c
@@ -20,6 +20,17 @@
 #include "moldyn.h"
 #include "report/report.h"
 
+/* potential includes */
+#include "potentials/harmonic_oscillator.h"
+#include "potentials/lennard_jones.h"
+#include "potentials/albe.h"
+#ifdef TERSOFF_ORIG
+#include "potentials/tersoff_orig.h"
+#else
+#include "potentials/tersoff.h"
+#endif
+
+
 /*
  * global variables, pse and atom colors (only needed here)
  */ 
@@ -68,6 +79,52 @@ static char *pse_col[]={
 	"Ar",
 };
 
+/*
+static double pse_mass[]={
+	0,
+	0,
+	0,
+	0,
+	0,
+	0,
+	M_C,
+	0,
+	0,
+	0,
+	0,
+	0,
+	0,
+	0,
+	M_SI,
+	0,
+	0,
+	0,
+	0,
+};
+
+static double pse_lc[]={
+	0,
+	0,
+	0,
+	0,
+	0,
+	0,
+	LC_C,
+	0,
+	0,
+	0,
+	0,
+	0,
+	0,
+	0,
+	LC_SI,
+	0,
+	0,
+	0,
+	0,
+};
+*/
+
 /*
  * the moldyn functions
  */
@@ -120,24 +177,13 @@ int set_int_alg(t_moldyn *moldyn,u8 algo) {
 int set_cutoff(t_moldyn *moldyn,double cutoff) {
 
 	moldyn->cutoff=cutoff;
+	moldyn->cutoff_square=cutoff*cutoff;
 
 	printf("[moldyn] cutoff [A]: %f\n",moldyn->cutoff);
 
 	return 0;
 }
 
-int set_bondlen(t_moldyn *moldyn,double b0,double b1,double bm) {
-
-	moldyn->bondlen[0]=b0*b0;
-	moldyn->bondlen[1]=b1*b1;
-	if(bm<0)
-		moldyn->bondlen[2]=b0*b1;
-	else
-		moldyn->bondlen[2]=bm*bm;
-
-	return 0;
-}
-
 int set_temperature(t_moldyn *moldyn,double t_ref) {
 
 	moldyn->t_ref=t_ref;
@@ -156,6 +202,38 @@ int set_pressure(t_moldyn *moldyn,double p_ref) {
 	return 0;
 }
 
+int set_p_scale(t_moldyn *moldyn,u8 ptype,double ptc) {
+
+	moldyn->pt_scale&=(~(P_SCALE_MASK));
+	moldyn->pt_scale|=ptype;
+	moldyn->p_tc=ptc;
+
+	printf("[moldyn] p/t scaling:\n");
+
+	printf("  p: %s",ptype?"yes":"no ");
+	if(ptype)
+		printf(" | type: %02x | factor: %f",ptype,ptc);
+	printf("\n");
+
+	return 0;
+}
+
+int set_t_scale(t_moldyn *moldyn,u8 ttype,double ttc) {
+
+	moldyn->pt_scale&=(~(T_SCALE_MASK));
+	moldyn->pt_scale|=ttype;
+	moldyn->t_tc=ttc;
+
+	printf("[moldyn] p/t scaling:\n");
+
+	printf("  t: %s",ttype?"yes":"no ");
+	if(ttype)
+		printf(" | type: %02x | factor: %f",ttype,ttc);
+	printf("\n");
+
+	return 0;
+}
+
 int set_pt_scale(t_moldyn *moldyn,u8 ptype,double ptc,u8 ttype,double ttc) {
 
 	moldyn->pt_scale=(ptype|ttype);
@@ -191,15 +269,12 @@ 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;
 }
@@ -231,58 +306,37 @@ int set_pbc(t_moldyn *moldyn,u8 x,u8 y,u8 z) {
 	return 0;
 }
 
-int set_potential1b(t_moldyn *moldyn,pf_func1b func) {
-
-	moldyn->func1b=func;
-
-	return 0;
-}
-
-int set_potential2b(t_moldyn *moldyn,pf_func2b func) {
+int set_potential(t_moldyn *moldyn,u8 type) {
 
-	moldyn->func2b=func;
-
-	return 0;
-}
-
-int set_potential3b_j1(t_moldyn *moldyn,pf_func2b func) {
-
-	moldyn->func3b_j1=func;
-
-	return 0;
-}
-
-int set_potential3b_j2(t_moldyn *moldyn,pf_func2b func) {
-
-	moldyn->func3b_j2=func;
-
-	return 0;
-}
-
-int set_potential3b_j3(t_moldyn *moldyn,pf_func2b func) {
-
-	moldyn->func3b_j3=func;
-
-	return 0;
-}
-
-int set_potential3b_k1(t_moldyn *moldyn,pf_func3b func) {
-
-	moldyn->func3b_k1=func;
-
-	return 0;
-}
-
-int set_potential3b_k2(t_moldyn *moldyn,pf_func3b func) {
-
-	moldyn->func3b_k2=func;
-
-	return 0;
-}
-
-int set_potential_params(t_moldyn *moldyn,void *params) {
-
-	moldyn->pot_params=params;
+	switch(type) {
+		case MOLDYN_POTENTIAL_TM:
+			moldyn->func1b=tersoff_mult_1bp;
+			moldyn->func3b_j1=tersoff_mult_3bp_j1;
+			moldyn->func3b_k1=tersoff_mult_3bp_k1;
+			moldyn->func3b_j2=tersoff_mult_3bp_j2;
+			moldyn->func3b_k2=tersoff_mult_3bp_k2;
+			// missing: check 2b bond func
+			break;
+		case MOLDYN_POTENTIAL_AM:
+			moldyn->func3b_j1=albe_mult_3bp_j1;
+			moldyn->func3b_k1=albe_mult_3bp_k1;
+			moldyn->func3b_j2=albe_mult_3bp_j2;
+			moldyn->func3b_k2=albe_mult_3bp_k2;
+			moldyn->check_2b_bond=albe_mult_check_2b_bond;
+			break;
+		case MOLDYN_POTENTIAL_HO:
+			moldyn->func2b=harmonic_oscillator;
+			moldyn->check_2b_bond=harmonic_oscillator_check_2b_bond;
+			break;
+		case MOLDYN_POTENTIAL_LJ:
+			moldyn->func2b=lennard_jones;
+			moldyn->check_2b_bond=lennard_jones_check_2b_bond;
+			break;
+		default:
+			printf("[moldyn] set potential: unknown type %02x\n",
+			       type);
+			return -1;
+	}
 
 	return 0;
 }
@@ -370,12 +424,25 @@ 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");
@@ -507,6 +574,7 @@ int create_lattice(t_moldyn *moldyn,u8 type,double lc,int element,double mass,
 	t_3dvec orig;
 	void *ptr;
 	t_atom *atom;
+	char name[16];
 
 	new=a*b*c;
 	count=moldyn->count;
@@ -541,18 +609,21 @@ int create_lattice(t_moldyn *moldyn,u8 type,double lc,int element,double mass,
 		case CUBIC:
 			set_nn_dist(moldyn,lc);
 			ret=cubic_init(a,b,c,lc,atom,&orig);
+			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);
+			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);
+			strcpy(name,"diamond");
 			break;
 		default:
 			printf("unknown lattice type (%02x)\n",type);
@@ -569,7 +640,7 @@ int create_lattice(t_moldyn *moldyn,u8 type,double lc,int element,double mass,
 	}
 
 	moldyn->count+=new;
-	printf("[moldyn] created lattice with %d atoms\n",new);
+	printf("[moldyn] created %s lattice with %d atoms\n",name,new);
 
 	for(ret=0;ret<new;ret++) {
 		atom[ret].element=element;
@@ -916,16 +987,26 @@ 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);
@@ -982,6 +1063,7 @@ int average_reset(t_moldyn *moldyn) {
 	/* pressure */
 	moldyn->p_sum=0.0;
 	moldyn->gp_sum=0.0;
+	moldyn->tp_sum=0.0;
 
 	return 0;
 }
@@ -1026,6 +1108,8 @@ 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;
 }
@@ -1067,8 +1151,9 @@ double thermodynamic_pressure_calc(t_moldyn *moldyn) {
 
 	t_3dvec dim;
 	//t_3dvec *tp;
-	double u_up,u_down,dv;
-	double scale,p;
+	double h,dv;
+	double y0,y1;
+	double su,sd;
 	t_atom *store;
 
 	/*
@@ -1078,54 +1163,56 @@ 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) {
@@ -1186,13 +1273,12 @@ 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);
@@ -1538,7 +1624,7 @@ 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;
@@ -1560,12 +1646,12 @@ int moldyn_integrate(t_moldyn *moldyn) {
 	m=moldyn->mwrite;
 	s=moldyn->swrite;
 	v=moldyn->vwrite;
+	a=moldyn->awrite;
 	p=moldyn->pwrite;
 	t=moldyn->twrite;
 
 	/* sqaure of some variables */
 	moldyn->tau_square=moldyn->tau*moldyn->tau;
-	moldyn->cutoff_square=moldyn->cutoff*moldyn->cutoff;
 
 	/* get current time */
 	gettimeofday(&t1,NULL);
@@ -1621,6 +1707,13 @@ int moldyn_integrate(t_moldyn *moldyn) {
 		temperature_calc(moldyn);
 		virial_sum(moldyn);
 		pressure_calc(moldyn);
+		/*
+		thermodynamic_pressure_calc(moldyn);
+		printf("\n\nDEBUG: numeric pressure calc: %f\n\n",
+		       moldyn->tp/BAR);
+		*/
+
+		/* calculate fluctuations + averages */
 		average_and_fluctuation_calc(moldyn);
 
 		/* p/t scaling */
@@ -1650,9 +1743,10 @@ 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) {
@@ -1662,6 +1756,12 @@ 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",
@@ -1677,8 +1777,8 @@ 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);
 			}
 		}
@@ -1688,10 +1788,10 @@ int moldyn_integrate(t_moldyn *moldyn) {
 			/* get current time */
 			gettimeofday(&t2,NULL);
 
-printf("\rsched:%d, steps:%d/%d, T:%3.1f/%3.1f P:%4.1f/%4.1f V:%6.1f (%d)",
+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_avg/BAR,moldyn->gp_avg/BAR,
+       moldyn->p/BAR,moldyn->p_avg/BAR,
        moldyn->volume,
        (int)(t2.tv_sec-t1.tv_sec));
 
@@ -2287,6 +2387,13 @@ int moldyn_read_save_file(t_moldyn *moldyn,char *file) {
 	return 0;
 }
 
+int moldyn_free_save_file(t_moldyn *moldyn) {
+
+	free(moldyn->atom);
+
+	return 0;
+}
+
 int moldyn_load(t_moldyn *moldyn) {
 
 	// later ...
@@ -2294,6 +2401,75 @@ int moldyn_load(t_moldyn *moldyn) {
 	return 0;
 }
 
+/*
+ * function to find/callback all combinations of 2 body bonds
+ */
+
+int process_2b_bonds(t_moldyn *moldyn,void *data,
+                     int (*process)(t_moldyn *moldyn,t_atom *itom,t_atom *jtom,
+		                    void *data,u8 bc)) {
+
+	t_linkcell *lc;
+#ifdef STATIC_LISTS
+	int *neighbour[27];
+	int p;
+#else
+	t_list neighbour[27];
+#endif
+	u8 bc;
+	t_atom *itom,*jtom;
+	int i,j;
+	t_list *this;
+
+	lc=&(moldyn->lc);
+	itom=moldyn->atom;
+	
+	for(i=0;i<moldyn->count;i++) {
+		/* neighbour indexing */
+		link_cell_neighbour_index(moldyn,
+		                          (itom[i].r.x+moldyn->dim.x/2)/lc->x,
+		                          (itom[i].r.y+moldyn->dim.y/2)/lc->x,
+		                          (itom[i].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]!=0) {
+
+				jtom=&(moldyn->atom[neighbour[j][p]]);
+				p++;
+#else
+			this=&(neighbour[j]);
+			list_reset_f(this);
+
+			if(this->start==NULL)
+				continue;
+
+			do {
+
+				jtom=this->current->data;
+#endif
+
+				/* process bond */
+				process(moldyn,&(itom[i]),jtom,data,bc);
+
+#ifdef STATIC_LISTS
+			}
+#else
+			} while(list_next_f(this)!=L_NO_NEXT_ELEMENT);
+#endif
+		}
+	}
+
+	return 0;
+
+}
+
 /*
  * post processing functions
  */
@@ -2309,7 +2485,8 @@ int get_line(int fd,char *line,int max) {
 		ret=read(fd,line+count,1);
 		if(ret<=0) return ret;
 		if(line[count]=='\n') {
-			line[count]='\0';
+			memset(line+count,0,max-count-1);
+			//line[count]='\0';
 			return count+1;
 		}
 		count+=1;
@@ -2322,33 +2499,121 @@ int pair_correlation_init(t_moldyn *moldyn,double dr) {
 	return 0;
 }
 
-int calculate_pair_correlation(t_moldyn *moldyn,double dr,void *ptr) {
+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 bonding_analyze(t_moldyn *moldyn,double *cnt) {
+
+	return 0;
+}
+
+int calculate_pair_correlation_process(t_moldyn *moldyn,t_atom *itom,
+                                       t_atom *jtom,void *data,u8 bc) {
 
-	int slots;
-	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;
-	//double norm;
-	int o,s;
-	unsigned char ibrand;
+	int s;
+	t_pcc *pcc;
 
-	lc=&(moldyn->lc);
+	/* only count pairs once,
+	 * skip same atoms */
+	if(itom->tag>=jtom->tag)
+		return 0;
+
+	/*
+	 * pair correlation calc
+	 */
+
+	/* get pcc data */
+	pcc=data;
+
+	/* distance */
+	v3_sub(&dist,&(jtom->r),&(itom->r));
+	if(bc) check_per_bound(moldyn,&dist);
+	d=v3_absolute_square(&dist);
+
+	/* ignore if greater cutoff */
+	if(d>moldyn->cutoff_square)
+		return 0;
+
+	/* fill the slots */
+	d=sqrt(d);
+	s=(int)(d/pcc->dr);
+
+	/* should never happen but it does 8) -
+	 * related to -ffloat-store problem! */
+	if(s>=pcc->o1) {
+		printf("[moldyn] WARNING: pcc (%d/%d)",
+		       s,pcc->o1);
+		printf("\n");
+		s=pcc->o1-1;
+	}
+
+	if(itom->brand!=jtom->brand) {
+		/* mixed */
+		pcc->stat[s]+=1;
+	}
+	else {
+		/* type a - type a bonds */
+		if(itom->brand==0)
+			pcc->stat[s+pcc->o1]+=1;
+		else
+		/* type b - type b bonds */
+			pcc->stat[s+pcc->o2]+=1;
+	}
+
+	return 0;
+}
+
+int calculate_pair_correlation(t_moldyn *moldyn,double dr,void *ptr) {
+
+	t_pcc pcc;
+	double norm;
+	int i;
 
-	slots=moldyn->cutoff/dr;
-	o=2*slots;
+	pcc.dr=dr;
+	pcc.o1=moldyn->cutoff/dr;
+	pcc.o2=2*pcc.o1;
 
-	if(slots*dr<=moldyn->cutoff)
+	if(pcc.o1*dr<=moldyn->cutoff)
 		printf("[moldyn] WARNING: pcc (low #slots)\n");
 
 	printf("[moldyn] pair correlation calc info:\n");
@@ -2358,133 +2623,145 @@ int calculate_pair_correlation(t_moldyn *moldyn,double dr,void *ptr) {
 	printf("  temperature: cur=%f avg=%f\n",moldyn->t,moldyn->t_avg);
 
 	if(ptr!=NULL) {
-		stat=(double *)ptr;
+		pcc.stat=(double *)ptr;
 	}
 	else {
-		stat=(double *)malloc(3*slots*sizeof(double));
-		if(stat==NULL) {
+		pcc.stat=(double *)malloc(3*pcc.o1*sizeof(double));
+		if(pcc.stat==NULL) {
 			perror("[moldyn] pair correlation malloc");
 			return -1;
 		}
 	}
 
-	memset(stat,0,3*slots*sizeof(double));
+	memset(pcc.stat,0,3*pcc.o1*sizeof(double));
 
-	link_cell_init(moldyn,VERBOSE);
+	/* process */
+	process_2b_bonds(moldyn,&pcc,calculate_pair_correlation_process);
 
-	itom=moldyn->atom;
-	
-	for(i=0;i<moldyn->count;i++) {
-		/* neighbour indexing */
-		link_cell_neighbour_index(moldyn,
-		                          (itom[i].r.x+moldyn->dim.x/2)/lc->x,
-		                          (itom[i].r.y+moldyn->dim.y/2)/lc->x,
-		                          (itom[i].r.z+moldyn->dim.z/2)/lc->x,
-		                          neighbour);
+	/* normalization */
+	for(i=1;i<pcc.o1;i++) {
+		 // normalization: 4 pi r^2 dr
+		 // here: not double counting pairs -> 2 pi r r dr
+		 // ... and actually it's a constant times r^2
+		norm=i*i*dr*dr;
+		pcc.stat[i]/=norm;
+		pcc.stat[pcc.o1+i]/=norm;
+		pcc.stat[pcc.o2+i]/=norm;
+	}
+	/* */
 
-		/* brand of atom i */
-		ibrand=itom[i].brand;
-	
-		for(j=0;j<27;j++) {
+	if(ptr==NULL) {
+		/* todo: store/print pair correlation function */
+		free(pcc.stat);
+	}
 
-			bc=(j<lc->dnlc)?0:1;
+	return 0;
+}
 
-#ifdef STATIC_LISTS
-			p=0;
+int bond_analyze_process(t_moldyn *moldyn,t_atom *itom,t_atom *jtom,
+                         void *data,u8 bc) {
 
-			while(neighbour[j][p]!=0) {
+	t_ba *ba;
+	t_3dvec dist;
+	double d;
 
-				jtom=&(moldyn->atom[neighbour[j][p]]);
-				p++;
-#else
-			this=&(neighbour[j]);
-			list_reset_f(this);
+	if(itom->tag>=jtom->tag)
+		return 0;
 
-			if(this->start==NULL)
-				continue;
+	/* distance */
+	v3_sub(&dist,&(jtom->r),&(itom->r));
+	if(bc) check_per_bound(moldyn,&dist);
+	d=v3_absolute_square(&dist);
 
-			do {
+	/* ignore if greater or equal cutoff */
+	if(d>moldyn->cutoff_square)
+		return 0;
 
-				jtom=this->current->data;
-#endif
-				/* only count pairs once,
-				 * skip same atoms */
-				if(itom[i].tag>=jtom->tag)
-					continue;
+	/* check for potential bond */
+	if(moldyn->check_2b_bond(moldyn,itom,jtom,bc)==FALSE)
+		return 0;
 
-				/*
-				 * pair correlation calc
-				 */
+	d=sqrt(d);
 
-				/* distance */
-				v3_sub(&dist,&(jtom->r),&(itom[i].r));
-				if(bc) check_per_bound(moldyn,&dist);
-				d=v3_absolute_square(&dist);
+	/* now count this bonding ... */
+	ba=data;
 
-				/* ignore if greater or equal cutoff */
-				if(d>=moldyn->cutoff_square)
-					continue;
+	/* increase total bond counter
+	 * ... double counting!
+	 */
+	ba->tcnt+=2;
 
-				/* 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(itom->brand==0)
+		ba->acnt[jtom->tag]+=1;
+	else
+		ba->bcnt[jtom->tag]+=1;
+	
+	if(jtom->brand==0)
+		ba->acnt[itom->tag]+=1;
+	else
+		ba->bcnt[itom->tag]+=1;
 
-				if(ibrand!=jtom->brand) {
-					/* mixed */
-					stat[s]+=1;
-				}
-				else {
-					/* type a - type a bonds */
-					if(ibrand==0)
-						stat[s+slots]+=1;
-					else
-					/* type b - type b bonds */
-						stat[s+o]+=1;
-				}
-#ifdef STATIC_LISTS
-			}
-#else
-			} while(list_next_f(this)!=L_NO_NEXT_ELEMENT);
-#endif
-		}
-	}
+	return 0;
+}
 
-	/* normalization 
-	for(i=1;i<slots;i++) {
-		 // 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;
+int bond_analyze(t_moldyn *moldyn,double *quality) {
+
+	// by now: # bonds of type 'a-4b' and 'b-4a' / # bonds total
+
+	int qcnt;
+	int ccnt,cset;
+	t_ba ba;
+	int i;
+	t_atom *atom;
+
+	ba.acnt=malloc(moldyn->count*sizeof(int));
+	if(ba.acnt==NULL) {
+		perror("[moldyn] bond analyze malloc (a)");
+		return -1;
 	}
-	*/
+	memset(ba.acnt,0,moldyn->count*sizeof(int));
 
-	if(ptr==NULL) {
-		/* todo: store/print pair correlation function */
-		free(stat);
+	ba.bcnt=malloc(moldyn->count*sizeof(int));
+	if(ba.bcnt==NULL) {
+		perror("[moldyn] bond analyze malloc (b)");
+		return -1;
 	}
+	memset(ba.bcnt,0,moldyn->count*sizeof(int));
 
-	free(moldyn->atom);
+	ba.tcnt=0;
+	qcnt=0;
+	ccnt=0;
+	cset=0;
 
-	link_cell_shutdown(moldyn);
+	atom=moldyn->atom;
 
-	return 0;
-}
+	process_2b_bonds(moldyn,&ba,bond_analyze_process);
 
-int analyze_bonds(t_moldyn *moldyn) {
+	for(i=0;i<moldyn->count;i++) {
+		if(atom[i].brand==0) {
+			if((ba.acnt[i]==0)&(ba.bcnt[i]==4))
+				qcnt+=4;
+		}
+		else {
+			if((ba.acnt[i]==4)&(ba.bcnt[i]==0)) {
+				qcnt+=4;
+				ccnt+=1;
+			}
+			cset+=1;
+		}
+	}
 
-	
-	
+	printf("[moldyn] bond analyze: c_cnt=%d | set=%d\n",ccnt,cset);
+	printf("[moldyn] bond analyze: q_cnt=%d | tot=%d\n",qcnt,ba.tcnt);
+
+	if(quality) {
+		quality[0]=1.0*ccnt/cset;
+		quality[1]=1.0*qcnt/ba.tcnt;
+	}
+	else {
+		printf("[moldyn] bond analyze: c_bnd_q=%f\n",1.0*qcnt/ba.tcnt);
+		printf("[moldyn] bond analyze:   tot_q=%f\n",1.0*qcnt/ba.tcnt);
+	}
 
 	return 0;
 }
@@ -2500,39 +2777,48 @@ int visual_init(t_moldyn *moldyn,char *filebase) {
 	return 0;
 }
 
+int visual_bonds_process(t_moldyn *moldyn,t_atom *itom,t_atom *jtom,
+                         void *data,u8 bc) {
+
+	t_vb *vb;
+
+	vb=data;
+
+	if(itom->tag>=jtom->tag)
+		return 0;
+	
+	if(moldyn->check_2b_bond(moldyn,itom,jtom,bc)==FALSE)
+		return 0;
+
+	if((itom->attr&ATOM_ATTR_VB)|(jtom->attr&ATOM_ATTR_VB))
+		dprintf(vb->fd,"# [B] %f %f %f %f %f %f\n",
+		        itom->r.x,itom->r.y,itom->r.z,
+		        jtom->r.x,jtom->r.y,jtom->r.z);
+
+	return 0;
+}
+
 int visual_atoms(t_moldyn *moldyn) {
 
-	int i,j,fd;
+	int i;
  	char file[128+64];
 	t_3dvec dim;
 	double help;
 	t_visual *v;
 	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;
-	u8 brand;
+	t_vb vb;
 
 	v=&(moldyn->vis);
 	dim.x=v->dim.x;
 	dim.y=v->dim.y;
 	dim.z=v->dim.z;
 	atom=moldyn->atom;
-	lc=&(moldyn->lc);
 
 	help=(dim.x+dim.y);
 
 	sprintf(file,"%s/atomic_conf_%07.f.xyz",v->fb,moldyn->time);
-	fd=open(file,O_WRONLY|O_CREAT|O_TRUNC,S_IRUSR|S_IWUSR);
-	if(fd<0) {
+	vb.fd=open(file,O_WRONLY|O_CREAT|O_TRUNC,S_IRUSR|S_IWUSR);
+	if(vb.fd<0) {
 		perror("open visual save file fd");
 		return -1;
 	}
@@ -2540,118 +2826,65 @@ int visual_atoms(t_moldyn *moldyn) {
 	/* write the actual data file */
 
 	// povray header
-	dprintf(fd,"# [P] %d %07.f <%f,%f,%f>\n",
+	dprintf(vb.fd,"# [P] %d %07.f <%f,%f,%f>\n",
 	        moldyn->count,moldyn->time,help/40.0,help/40.0,-0.8*help);
 
 	// atomic configuration
-	for(i=0;i<moldyn->count;i++) {
+	for(i=0;i<moldyn->count;i++)
 		// atom type, positions, color and kinetic energy
-		dprintf(fd,"%s %f %f %f %s %f\n",pse_name[atom[i].element],
-		                                 atom[i].r.x,
-		                                 atom[i].r.y,
-		                                 atom[i].r.z,
-		                                 pse_col[atom[i].element],
-		                                 atom[i].ekin);
-
-		/*
-		 * bond detection should usually be done by potential
-		 * functions. brrrrr! EVIL!
-		 * 
-		 * todo: potentials need to export a 'find_bonds' function!
-		 */
-
-		// bonds between atoms
-		if(!(atom[i].attr&ATOM_ATTR_VB))
-			continue;
-		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,
-		                          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;
-			do {
-				btom=neighbour[j].current->data;
-#endif
-				if(btom==&atom[i])	// skip identical atoms
-					continue;
-				//if(btom<&atom[i])	// skip half of them
-				//	continue;
-				v3_sub(&dist,&(atom[i].r),&(btom->r));
-				if(bc) check_per_bound(moldyn,&dist);
-				d2=v3_absolute_square(&dist);
-				brand=atom[i].brand;
-				if(brand==btom->brand) {
-					if(d2>moldyn->bondlen[brand])
-						continue;
-				}
-				else {
-					if(d2>moldyn->bondlen[2])
-						continue;
-				}
-				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
-		}
-	}
-
+		dprintf(vb.fd,"%s %f %f %f %s %f\n",pse_name[atom[i].element],
+		                                    atom[i].r.x,
+		                                    atom[i].r.y,
+		                                    atom[i].r.z,
+		                                    pse_col[atom[i].element],
+		                                    atom[i].ekin);
+	
+	// bonds between atoms
+	process_2b_bonds(moldyn,&vb,visual_bonds_process);
+	
 	// boundaries
 	if(dim.x) {
-		dprintf(fd,"# [D] %f %f %f %f %f %f\n",
+		dprintf(vb.fd,"# [D] %f %f %f %f %f %f\n",
 		        -dim.x/2,-dim.y/2,-dim.z/2,
 		        dim.x/2,-dim.y/2,-dim.z/2);
-		dprintf(fd,"# [D] %f %f %f %f %f %f\n",
+		dprintf(vb.fd,"# [D] %f %f %f %f %f %f\n",
 		        -dim.x/2,-dim.y/2,-dim.z/2,
 		        -dim.x/2,dim.y/2,-dim.z/2);
-		dprintf(fd,"# [D] %f %f %f %f %f %f\n",
+		dprintf(vb.fd,"# [D] %f %f %f %f %f %f\n",
 		        dim.x/2,dim.y/2,-dim.z/2,
 		        dim.x/2,-dim.y/2,-dim.z/2);
-		dprintf(fd,"# [D] %f %f %f %f %f %f\n",
+		dprintf(vb.fd,"# [D] %f %f %f %f %f %f\n",
 		        -dim.x/2,dim.y/2,-dim.z/2,
 		        dim.x/2,dim.y/2,-dim.z/2);
 
-		dprintf(fd,"# [D] %f %f %f %f %f %f\n",
+		dprintf(vb.fd,"# [D] %f %f %f %f %f %f\n",
 		        -dim.x/2,-dim.y/2,dim.z/2,
 		        dim.x/2,-dim.y/2,dim.z/2);
-		dprintf(fd,"# [D] %f %f %f %f %f %f\n",
+		dprintf(vb.fd,"# [D] %f %f %f %f %f %f\n",
 		        -dim.x/2,-dim.y/2,dim.z/2,
 		        -dim.x/2,dim.y/2,dim.z/2);
-		dprintf(fd,"# [D] %f %f %f %f %f %f\n",
+		dprintf(vb.fd,"# [D] %f %f %f %f %f %f\n",
 		        dim.x/2,dim.y/2,dim.z/2,
 		        dim.x/2,-dim.y/2,dim.z/2);
-		dprintf(fd,"# [D] %f %f %f %f %f %f\n",
+		dprintf(vb.fd,"# [D] %f %f %f %f %f %f\n",
 		        -dim.x/2,dim.y/2,dim.z/2,
 		        dim.x/2,dim.y/2,dim.z/2);
 
-		dprintf(fd,"# [D] %f %f %f %f %f %f\n",
+		dprintf(vb.fd,"# [D] %f %f %f %f %f %f\n",
 		        -dim.x/2,-dim.y/2,dim.z/2,
 		        -dim.x/2,-dim.y/2,-dim.z/2);
-		dprintf(fd,"# [D] %f %f %f %f %f %f\n",
+		dprintf(vb.fd,"# [D] %f %f %f %f %f %f\n",
 		        -dim.x/2,dim.y/2,dim.z/2,
 		        -dim.x/2,dim.y/2,-dim.z/2);
-		dprintf(fd,"# [D] %f %f %f %f %f %f\n",
+		dprintf(vb.fd,"# [D] %f %f %f %f %f %f\n",
 		        dim.x/2,-dim.y/2,dim.z/2,
 		        dim.x/2,-dim.y/2,-dim.z/2);
-		dprintf(fd,"# [D] %f %f %f %f %f %f\n",
+		dprintf(vb.fd,"# [D] %f %f %f %f %f %f\n",
 		        dim.x/2,dim.y/2,dim.z/2,
 		        dim.x/2,dim.y/2,-dim.z/2);
 	}
 
-	close(fd);
+	close(vb.fd);
 
 	return 0;
 }