X-Git-Url: https://www.hackdaworld.org/gitweb/?a=blobdiff_plain;f=moldyn.c;h=def5079dbbd949fa55e4f65b9aa4a77e165077db;hb=4c2140b0f76fb191bdd9b9c2a329877eb0aae531;hp=edda007d9290ff6cfe1001d4105c3f8a9ab12863;hpb=e1080fc0dd66b0cf5b7715c5e99e7a34ac04a8cf;p=physik%2Fposic.git

diff --git a/moldyn.c b/moldyn.c
index edda007..def5079 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)
  */ 
@@ -191,15 +202,12 @@ 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 +239,29 @@ 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) {
-
-	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) {
+int set_potential(t_moldyn *moldyn,u8 type) {
 
-	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;
+		default:
+			printf("[moldyn] set potential: unknown type %02x\n",
+			       type);
+			return -1;
+	}
 
 	return 0;
 }
@@ -370,12 +349,25 @@ 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 +587,7 @@ 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 +597,9 @@ 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 +908,26 @@ 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);
@@ -954,6 +959,36 @@ 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;
@@ -994,6 +1029,8 @@ 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;
 }
@@ -1035,8 +1072,9 @@ 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;
 
 	/*
@@ -1046,54 +1084,56 @@ 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) {
@@ -1154,13 +1194,12 @@ 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);
@@ -1342,7 +1381,7 @@ int link_cell_update(t_moldyn *moldyn) {
 		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)
@@ -1392,6 +1431,10 @@ int link_cell_neighbour_index(t_moldyn *moldyn,int i,int j,int k,
 	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;
@@ -1502,7 +1545,7 @@ 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;
@@ -1524,6 +1567,7 @@ int moldyn_integrate(t_moldyn *moldyn) {
 	m=moldyn->mwrite;
 	s=moldyn->swrite;
 	v=moldyn->vwrite;
+	a=moldyn->awrite;
 	p=moldyn->pwrite;
 	t=moldyn->twrite;
 
@@ -1542,14 +1586,14 @@ 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;
@@ -1585,6 +1629,9 @@ 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 */
@@ -1614,9 +1661,10 @@ 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) {
@@ -1626,6 +1674,12 @@ 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",
@@ -1641,8 +1695,8 @@ 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);
 			}
 		}
@@ -1652,10 +1706,10 @@ 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));
 
@@ -1702,6 +1756,9 @@ 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);
@@ -1715,6 +1772,9 @@ 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);
 
@@ -1722,6 +1782,9 @@ 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);
@@ -2049,20 +2112,27 @@ 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;
@@ -2177,6 +2247,8 @@ 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) {
@@ -2184,6 +2256,9 @@ 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);
 
 	while(size) {
@@ -2197,6 +2272,19 @@ int moldyn_read_save_file(t_moldyn *moldyn,char *file) {
 
 	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)");
@@ -2217,46 +2305,28 @@ int moldyn_read_save_file(t_moldyn *moldyn,char *file) {
 	return 0;
 }
 
-int moldyn_load(t_moldyn *moldyn) {
+int moldyn_free_save_file(t_moldyn *moldyn) {
 
-	// later ...
+	free(moldyn->atom);
 
 	return 0;
 }
 
-/*
- * post processing functions
- */
-
-int get_line(int fd,char *line,int max) {
-
-	int count,ret;
-
-	count=0;
-
-	while(1) {
-		if(count==max) return count;
-		ret=read(fd,line+count,1);
-		if(ret<=0) return ret;
-		if(line[count]=='\n') {
-			line[count]='\0';
-			return count+1;
-		}
-		count+=1;
-	}
-}
+int moldyn_load(t_moldyn *moldyn) {
 
-int pair_correlation_init(t_moldyn *moldyn,double dr) {
+	// later ...
 
-	
 	return 0;
 }
 
-int calculate_pair_correlation(t_moldyn *moldyn,double dr,void *ptr) {
+/*
+ * 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)) {
 
-	int slots;
-	double *stat;
-	int i,j;
 	t_linkcell *lc;
 #ifdef STATIC_LISTS
 	int *neighbour[27];
@@ -2264,39 +2334,13 @@ int calculate_pair_correlation(t_moldyn *moldyn,double dr,void *ptr) {
 #else
 	t_list neighbour[27];
 #endif
+	u8 bc;
 	t_atom *itom,*jtom;
+	int i,j;
 	t_list *this;
-	unsigned char bc;
-	t_3dvec dist;
-	double d;
-	//double norm;
-	int o,s;
-	unsigned char ibrand;
 
 	lc=&(moldyn->lc);
 
-	slots=moldyn->cutoff/dr;
-	o=2*slots;
-
-	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;
-	}
-	else {
-		stat=(double *)malloc(3*slots*sizeof(double));
-		if(stat==NULL) {
-			perror("[moldyn] pair correlation malloc");
-			return -1;
-		}
-	}
-
-	memset(stat,0,3*slots*sizeof(double));
-
 	link_cell_init(moldyn,VERBOSE);
 
 	itom=moldyn->atom;
@@ -2309,9 +2353,6 @@ int calculate_pair_correlation(t_moldyn *moldyn,double dr,void *ptr) {
 		                          (itom[i].r.z+moldyn->dim.z/2)/lc->x,
 		                          neighbour);
 
-		/* brand of atom i */
-		ibrand=itom[i].brand;
-	
 		for(j=0;j<27;j++) {
 
 			bc=(j<lc->dnlc)?0:1;
@@ -2334,44 +2375,10 @@ int calculate_pair_correlation(t_moldyn *moldyn,double dr,void *ptr) {
 
 				jtom=this->current->data;
 #endif
-				/* only count pairs once,
-				 * skip same atoms */
-				if(itom[i].tag>=jtom->tag)
-					continue;
-
-				/*
-				 * pair correlation calc
-				 */
-
-				/* distance */
-				v3_sub(&dist,&(jtom->r),&(itom[i].r));
-				if(bc) check_per_bound(moldyn,&dist);
-				d=v3_absolute_square(&dist);
-
-				/* 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) s=slots-1;
+				/* process bond */
+				process(moldyn,&(itom[i]),jtom,data,bc);
 
-				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
@@ -2380,33 +2387,301 @@ int calculate_pair_correlation(t_moldyn *moldyn,double dr,void *ptr) {
 		}
 	}
 
-	/* normalization 
-	for(i=1;i<slots;i++) {
-		 // normalization: 4 pi r r dr
+	return 0;
+
+}
+
+/*
+ * post processing functions
+ */
+
+int get_line(int fd,char *line,int max) {
+
+	int count,ret;
+
+	count=0;
+
+	while(1) {
+		if(count==max) return count;
+		ret=read(fd,line+count,1);
+		if(ret<=0) return ret;
+		if(line[count]=='\n') {
+			line[count]='\0';
+			return count+1;
+		}
+		count+=1;
+	}
+}
+
+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 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) {
+
+	t_3dvec dist;
+	double d;
+	int s;
+	t_pcc *pcc;
+
+	/* 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;
+
+	pcc.dr=dr;
+	pcc.o1=moldyn->cutoff/dr;
+	pcc.o2=2*pcc.o1;
+
+	if(pcc.o1*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) {
+		pcc.stat=(double *)ptr;
+	}
+	else {
+		pcc.stat=(double *)malloc(3*pcc.o1*sizeof(double));
+		if(pcc.stat==NULL) {
+			perror("[moldyn] pair correlation malloc");
+			return -1;
+		}
+	}
+
+	memset(pcc.stat,0,3*pcc.o1*sizeof(double));
+
+	/* process */
+	process_2b_bonds(moldyn,&pcc,calculate_pair_correlation_process);
+
+	/* normalization */
+	for(i=1;i<pcc.o1;i++) {
+		 // 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;
-		stat[i]/=norm;
-		stat[slots+i]/=norm;
-		stat[o+i]/=norm;
+		 // ... 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;
 	}
-	*/
+	/* */
 
 	if(ptr==NULL) {
 		/* todo: store/print pair correlation function */
-		free(stat);
+		free(pcc.stat);
 	}
 
-	free(moldyn->atom);
+	return 0;
+}
 
-	link_cell_shutdown(moldyn);
+int bond_analyze_process(t_moldyn *moldyn,t_atom *itom,t_atom *jtom,
+                         void *data,u8 bc) {
+
+	t_ba *ba;
+	t_3dvec dist;
+	double d;
+
+	if(itom->tag>=jtom->tag)
+		return 0;
+
+	/* distance */
+	v3_sub(&dist,&(jtom->r),&(itom->r));
+	if(bc) check_per_bound(moldyn,&dist);
+	d=v3_absolute_square(&dist);
+
+	/* ignore if greater or equal cutoff */
+	if(d>moldyn->cutoff_square)
+		return 0;
+
+	/* check for potential bond */
+	if(moldyn->check_2b_bond(moldyn,itom,jtom,bc)==FALSE)
+		return 0;
+
+	d=sqrt(d);
+
+	/* now count this bonding ... */
+	ba=data;
+
+	/* increase total bond counter
+	 * ... double counting!
+	 */
+	ba->tcnt+=2;
+
+	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;
 
 	return 0;
 }
 
-int analyze_bonds(t_moldyn *moldyn) {
+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));
+
+	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));
+
+	ba.tcnt=0;
+	qcnt=0;
+	ccnt=0;
+	cset=0;
+
+	atom=moldyn->atom;
+
+	process_2b_bonds(moldyn,&ba,bond_analyze_process);
+
+	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;
 }