X-Git-Url: https://hackdaworld.org/gitweb/?a=blobdiff_plain;f=moldyn.c;h=edda007d9290ff6cfe1001d4105c3f8a9ab12863;hb=e1080fc0dd66b0cf5b7715c5e99e7a34ac04a8cf;hp=2631d6a675549e183a41fa91ca863dee215bed0f;hpb=746278fb5c566b621b70c78b38d8b6c0b4e2677f;p=physik%2Fposic.git

diff --git a/moldyn.c b/moldyn.c
index 2631d6a..edda007 100644
--- a/moldyn.c
+++ b/moldyn.c
@@ -13,26 +13,74 @@
 #include <sys/stat.h>
 #include <fcntl.h>
 #include <unistd.h>
+#include <sys/time.h>
+#include <time.h>
 #include <math.h>
 
 #include "moldyn.h"
+#include "report/report.h"
 
-#include "math/math.h"
-#include "init/init.h"
-#include "random/random.h"
-#include "visual/visual.h"
-#include "list/list.h"
+/*
+ * global variables, pse and atom colors (only needed here)
+ */ 
+
+static char *pse_name[]={
+	"*",
+	"H",
+	"He",
+	"Li",
+	"Be",
+	"B",
+	"C",
+	"N",
+	"O",
+	"F",
+	"Ne",
+	"Na",
+	"Mg",
+	"Al",
+	"Si",
+	"P",
+	"S",
+	"Cl",
+	"Ar",
+};
+
+static char *pse_col[]={
+	"*",
+	"White",
+	"He",
+	"Li",
+	"Be",
+	"B",
+	"Gray",
+	"N",
+	"Blue",
+	"F",
+	"Ne",
+	"Na",
+	"Mg",
+	"Al",
+	"Yellow",
+	"P",
+	"S",
+	"Cl",
+	"Ar",
+};
 
+/*
+ * the moldyn functions
+ */
 
 int moldyn_init(t_moldyn *moldyn,int argc,char **argv) {
 
-	//int ret;
-
-	//ret=moldyn_parse_argv(moldyn,argc,argv);
-	//if(ret<0) return ret;
+	printf("[moldyn] init\n");
 
 	memset(moldyn,0,sizeof(t_moldyn));
 
+	moldyn->argc=argc;
+	moldyn->args=argv;
+
 	rand_init(&(moldyn->random),NULL,1);
 	moldyn->random.status|=RAND_STAT_VERBOSE;
 
@@ -42,6 +90,7 @@ int moldyn_init(t_moldyn *moldyn,int argc,char **argv) {
 int moldyn_shutdown(t_moldyn *moldyn) {
 
 	printf("[moldyn] shutdown\n");
+
 	moldyn_log_shutdown(moldyn);
 	link_cell_shutdown(moldyn);
 	rand_close(&(moldyn->random));
@@ -52,12 +101,16 @@ int moldyn_shutdown(t_moldyn *moldyn) {
 
 int set_int_alg(t_moldyn *moldyn,u8 algo) {
 
+	printf("[moldyn] integration algorithm: ");
+
 	switch(algo) {
 		case MOLDYN_INTEGRATE_VERLET:
 			moldyn->integrate=velocity_verlet;
+			printf("velocity verlet\n");
 			break;
 		default:
 			printf("unknown integration algorithm: %02x\n",algo);
+			printf("unknown\n");
 			return -1;
 	}
 
@@ -68,6 +121,20 @@ int set_cutoff(t_moldyn *moldyn,double cutoff) {
 
 	moldyn->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;
 }
 
@@ -75,6 +142,17 @@ int set_temperature(t_moldyn *moldyn,double t_ref) {
 
 	moldyn->t_ref=t_ref;
 
+	printf("[moldyn] temperature [K]: %f\n",moldyn->t_ref);
+
+	return 0;
+}
+
+int set_pressure(t_moldyn *moldyn,double p_ref) {
+
+	moldyn->p_ref=p_ref;
+
+	printf("[moldyn] pressure [bar]: %f\n",moldyn->p_ref/BAR);
+
 	return 0;
 }
 
@@ -84,6 +162,18 @@ int set_pt_scale(t_moldyn *moldyn,u8 ptype,double ptc,u8 ttype,double ttc) {
 	moldyn->t_tc=ttc;
 	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");
+
+	printf("  t: %s",ttype?"yes":"no ");
+	if(ttype)
+		printf(" | type: %02x | factor: %f",ttype,ttc);
+	printf("\n");
+
 	return 0;
 }
 
@@ -93,12 +183,24 @@ int set_dim(t_moldyn *moldyn,double x,double y,double z,u8 visualize) {
 	moldyn->dim.y=y;
 	moldyn->dim.z=z;
 
+	moldyn->volume=x*y*z;
+
 	if(visualize) {
 		moldyn->vis.dim.x=x;
 		moldyn->vis.dim.y=y;
 		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;
 }
 
@@ -111,6 +213,8 @@ int set_nn_dist(t_moldyn *moldyn,double dist) {
 
 int set_pbc(t_moldyn *moldyn,u8 x,u8 y,u8 z) {
 
+	printf("[moldyn] periodic boundary conditions:\n");
+
 	if(x)
 		moldyn->status|=MOLDYN_STAT_PBX;
 
@@ -120,73 +224,223 @@ int set_pbc(t_moldyn *moldyn,u8 x,u8 y,u8 z) {
 	if(z)
 		moldyn->status|=MOLDYN_STAT_PBZ;
 
+	printf("  x: %s\n",x?"yes":"no");
+	printf("  y: %s\n",y?"yes":"no");
+	printf("  z: %s\n",z?"yes":"no");
+
 	return 0;
 }
 
-int set_potential1b(t_moldyn *moldyn,pf_func1b func,void *params) {
+int set_potential1b(t_moldyn *moldyn,pf_func1b func) {
 
 	moldyn->func1b=func;
-	moldyn->pot1b_params=params;
 
 	return 0;
 }
 
-int set_potential2b(t_moldyn *moldyn,pf_func2b func,void *params) {
+int set_potential2b(t_moldyn *moldyn,pf_func2b func) {
 
 	moldyn->func2b=func;
-	moldyn->pot2b_params=params;
 
 	return 0;
 }
 
-int set_potential2b_post(t_moldyn *moldyn,pf_func2b_post func,void *params) {
+int set_potential3b_j1(t_moldyn *moldyn,pf_func2b func) {
 
-	moldyn->func2b=func;
-	moldyn->pot2b_params=params;
+	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;
+
+	return 0;
+}
+
+int set_avg_skip(t_moldyn *moldyn,int skip) {
+
+	printf("[moldyn] skip %d steps before starting average calc\n",skip);
+	moldyn->avg_skip=skip;
+
+	return 0;
+}
+
+int moldyn_set_log_dir(t_moldyn *moldyn,char *dir) {
+
+	strncpy(moldyn->vlsdir,dir,127);
 
 	return 0;
 }
 
-int set_potential3b(t_moldyn *moldyn,pf_func3b func,void *params) {
+int moldyn_set_report(t_moldyn *moldyn,char *author,char *title) {
 
-	moldyn->func3b=func;
-	moldyn->pot3b_params=params;
+	strncpy(moldyn->rauthor,author,63);
+	strncpy(moldyn->rtitle,title,63);
 
 	return 0;
 }
+	
+int moldyn_set_log(t_moldyn *moldyn,u8 type,int timer) {
+
+	char filename[128];
+	int ret;
 
-int moldyn_set_log(t_moldyn *moldyn,u8 type,char *fb,int timer) {
+	printf("[moldyn] set log: ");
 
 	switch(type) {
 		case LOG_TOTAL_ENERGY:
 			moldyn->ewrite=timer;
-			moldyn->efd=open(fb,O_WRONLY|O_CREAT|O_TRUNC);
+			snprintf(filename,127,"%s/energy",moldyn->vlsdir);
+			moldyn->efd=open(filename,
+			                 O_WRONLY|O_CREAT|O_EXCL,
+			                 S_IRUSR|S_IWUSR);
 			if(moldyn->efd<0) {
-				perror("[moldyn] efd open");
+				perror("[moldyn] energy log fd open");
 				return moldyn->efd;
 			}
 			dprintf(moldyn->efd,"# total energy log file\n");
+			printf("total energy (%d)\n",timer);
 			break;
 		case LOG_TOTAL_MOMENTUM:
 			moldyn->mwrite=timer;
-			moldyn->mfd=open(fb,O_WRONLY|O_CREAT|O_TRUNC);
+			snprintf(filename,127,"%s/momentum",moldyn->vlsdir);
+			moldyn->mfd=open(filename,
+			                 O_WRONLY|O_CREAT|O_EXCL,
+			                 S_IRUSR|S_IWUSR);
 			if(moldyn->mfd<0) {
-				perror("[moldyn] mfd open");
+				perror("[moldyn] momentum log fd open");
 				return moldyn->mfd;
 			}
 			dprintf(moldyn->efd,"# total momentum log file\n");
+			printf("total momentum (%d)\n",timer);
+			break;
+		case LOG_PRESSURE:
+			moldyn->pwrite=timer;
+			snprintf(filename,127,"%s/pressure",moldyn->vlsdir);
+			moldyn->pfd=open(filename,
+			                 O_WRONLY|O_CREAT|O_EXCL,
+			                 S_IRUSR|S_IWUSR);
+			if(moldyn->pfd<0) {
+				perror("[moldyn] pressure log file\n");
+				return moldyn->pfd;
+			}
+			dprintf(moldyn->pfd,"# pressure log file\n");
+			printf("pressure (%d)\n",timer);
+			break;
+		case LOG_TEMPERATURE:
+			moldyn->twrite=timer;
+			snprintf(filename,127,"%s/temperature",moldyn->vlsdir);
+			moldyn->tfd=open(filename,
+			                 O_WRONLY|O_CREAT|O_EXCL,
+			                 S_IRUSR|S_IWUSR);
+			if(moldyn->tfd<0) {
+				perror("[moldyn] temperature log file\n");
+				return moldyn->tfd;
+			}
+			dprintf(moldyn->tfd,"# temperature log file\n");
+			printf("temperature (%d)\n",timer);
 			break;
 		case SAVE_STEP:
 			moldyn->swrite=timer;
-			strncpy(moldyn->sfb,fb,63);
+			printf("save file (%d)\n",timer);
 			break;
 		case VISUAL_STEP:
 			moldyn->vwrite=timer;
-			strncpy(moldyn->vfb,fb,63);
-			visual_init(&(moldyn->vis),fb);
+			ret=visual_init(moldyn,moldyn->vlsdir);
+			if(ret<0) {
+				printf("[moldyn] visual init failure\n");
+				return ret;
+			}
+			printf("visual file (%d)\n",timer);
+			break;
+		case CREATE_REPORT:
+			snprintf(filename,127,"%s/report.tex",moldyn->vlsdir);
+			moldyn->rfd=open(filename,
+			                 O_WRONLY|O_CREAT|O_EXCL,
+			                 S_IRUSR|S_IWUSR);
+			if(moldyn->rfd<0) {
+				perror("[moldyn] report fd open");	
+				return moldyn->rfd;
+			}
+			printf("report -> ");
+			if(moldyn->efd) {
+				snprintf(filename,127,"%s/e_plot.scr",
+				         moldyn->vlsdir);
+				moldyn->epfd=open(filename,
+			 	                 O_WRONLY|O_CREAT|O_EXCL,
+			  	                 S_IRUSR|S_IWUSR);
+				if(moldyn->epfd<0) {
+					perror("[moldyn] energy plot fd open");
+					return moldyn->epfd;
+				}
+				dprintf(moldyn->epfd,e_plot_script);
+				close(moldyn->epfd);
+				printf("energy ");
+			}
+			if(moldyn->pfd) {
+				snprintf(filename,127,"%s/pressure_plot.scr",
+				         moldyn->vlsdir);
+				moldyn->ppfd=open(filename,
+			 	                  O_WRONLY|O_CREAT|O_EXCL,
+			  	                  S_IRUSR|S_IWUSR);
+				if(moldyn->ppfd<0) {
+					perror("[moldyn] p plot fd open");
+					return moldyn->ppfd;
+				}
+				dprintf(moldyn->ppfd,pressure_plot_script);
+				close(moldyn->ppfd);
+				printf("pressure ");
+			}
+			if(moldyn->tfd) {
+				snprintf(filename,127,"%s/temperature_plot.scr",
+				         moldyn->vlsdir);
+				moldyn->tpfd=open(filename,
+			 	                  O_WRONLY|O_CREAT|O_EXCL,
+			  	                  S_IRUSR|S_IWUSR);
+				if(moldyn->tpfd<0) {
+					perror("[moldyn] t plot fd open");
+					return moldyn->tpfd;
+				}
+				dprintf(moldyn->tpfd,temperature_plot_script);
+				close(moldyn->tpfd);
+				printf("temperature ");
+			}
+			dprintf(moldyn->rfd,report_start,
+			        moldyn->rauthor,moldyn->rtitle);
+			printf("\n");
 			break;
 		default:
-			printf("unknown log mechanism: %02x\n",type);
+			printf("unknown log type: %02x\n",type);
 			return -1;
 	}
 
@@ -195,41 +449,110 @@ int moldyn_set_log(t_moldyn *moldyn,u8 type,char *fb,int timer) {
 
 int moldyn_log_shutdown(t_moldyn *moldyn) {
 
+	char sc[256];
+
 	printf("[moldyn] log shutdown\n");
-	if(moldyn->efd) close(moldyn->efd);
+	if(moldyn->efd) {
+		close(moldyn->efd);
+		if(moldyn->rfd) {
+			dprintf(moldyn->rfd,report_energy);
+			snprintf(sc,255,"cd %s && gnuplot e_plot.scr",
+			         moldyn->vlsdir);
+			system(sc);
+		}
+	}
 	if(moldyn->mfd) close(moldyn->mfd);
-	if(&(moldyn->vis)) visual_tini(&(moldyn->vis));
+	if(moldyn->pfd) {
+		close(moldyn->pfd);
+		if(moldyn->rfd)
+			dprintf(moldyn->rfd,report_pressure);
+			snprintf(sc,255,"cd %s && gnuplot pressure_plot.scr",
+			         moldyn->vlsdir);
+			system(sc);
+	}
+	if(moldyn->tfd) {
+		close(moldyn->tfd);
+		if(moldyn->rfd)
+			dprintf(moldyn->rfd,report_temperature);
+			snprintf(sc,255,"cd %s && gnuplot temperature_plot.scr",
+			         moldyn->vlsdir);
+			system(sc);
+	}
+	if(moldyn->rfd) {
+		dprintf(moldyn->rfd,report_end);
+		close(moldyn->rfd);
+		snprintf(sc,255,"cd %s && pdflatex report >/dev/null 2>&1",
+		         moldyn->vlsdir);
+		system(sc);
+		snprintf(sc,255,"cd %s && pdflatex report >/dev/null 2>&1",
+		         moldyn->vlsdir);
+		system(sc);
+		snprintf(sc,255,"cd %s && dvipdf report >/dev/null 2>&1",
+		         moldyn->vlsdir);
+		system(sc);
+	}
 
 	return 0;
 }
 
+/*
+ * creating lattice functions
+ */
+
 int create_lattice(t_moldyn *moldyn,u8 type,double lc,int element,double mass,
-                   u8 attr,u8 bnum,int a,int b,int c) {
+                   u8 attr,u8 brand,int a,int b,int c,t_3dvec *origin) {
 
-	int count;
+	int new,count;
 	int ret;
-	t_3dvec origin;
-
-	count=a*b*c;
+	t_3dvec orig;
+	void *ptr;
+	t_atom *atom;
 
-	if(type==FCC) count*=4;
+	new=a*b*c;
+	count=moldyn->count;
 
-	if(type==DIAMOND) count*=8;
+	/* how many atoms do we expect */
+	if(type==CUBIC) new*=1;
+	if(type==FCC) new*=4;
+	if(type==DIAMOND) new*=8;
 
-	moldyn->atom=malloc(count*sizeof(t_atom));
-	if(moldyn->atom==NULL) {
-		perror("malloc (atoms)");
+	/* allocate space for atoms */
+	ptr=realloc(moldyn->atom,(count+new)*sizeof(t_atom));
+	if(!ptr) {
+		perror("[moldyn] realloc (create lattice)");
 		return -1;
 	}
+	moldyn->atom=ptr;
+	atom=&(moldyn->atom[count]);
 
-	v3_zero(&origin);
+	/* no atoms on the boundaries (only reason: it looks better!) */
+	if(!origin) {
+		orig.x=0.5*lc;
+		orig.y=0.5*lc;
+		orig.z=0.5*lc;
+	}
+	else {
+		orig.x=origin->x;
+		orig.y=origin->y;
+		orig.z=origin->z;
+	}
 
 	switch(type) {
+		case CUBIC:
+			set_nn_dist(moldyn,lc);
+			ret=cubic_init(a,b,c,lc,atom,&orig);
+			break;
 		case FCC:
-			ret=fcc_init(a,b,c,lc,moldyn->atom,&origin);
+			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);
 			break;
 		case DIAMOND:
-			ret=diamond_init(a,b,c,lc,moldyn->atom,&origin);
+			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);
 			break;
 		default:
 			printf("unknown lattice type (%02x)\n",type);
@@ -237,30 +560,34 @@ int create_lattice(t_moldyn *moldyn,u8 type,double lc,int element,double mass,
 	}
 
 	/* debug */
-	if(ret!=count) {
-		printf("ok, there is something wrong ...\n");
-		printf("calculated -> %d atoms\n",count);
-		printf("created -> %d atoms\n",ret);
+	if(ret!=new) {
+		printf("[moldyn] creating lattice failed\n");
+		printf("  amount of atoms\n");
+		printf("  - expected: %d\n",new);
+		printf("  - created: %d\n",ret);
 		return -1;
 	}
 
-	moldyn->count=count;
-	printf("[moldyn] created lattice with %d atoms\n",count);
-
-	while(count) {
-		count-=1;
-		moldyn->atom[count].element=element;
-		moldyn->atom[count].mass=mass;
-		moldyn->atom[count].attr=attr;
-		moldyn->atom[count].bnum=bnum;
-		check_per_bound(moldyn,&(moldyn->atom[count].r));
+	moldyn->count+=new;
+	printf("[moldyn] created lattice with %d atoms\n",new);
+
+	for(ret=0;ret<new;ret++) {
+		atom[ret].element=element;
+		atom[ret].mass=mass;
+		atom[ret].attr=attr;
+		atom[ret].brand=brand;
+		atom[ret].tag=count+ret;
+		check_per_bound(moldyn,&(atom[ret].r));
+		atom[ret].r_0=atom[ret].r;
 	}
 
+	/* update total system mass */
+	total_mass_calc(moldyn);
 
 	return ret;
 }
 
-int add_atom(t_moldyn *moldyn,int element,double mass,u8 bnum,u8 attr,
+int add_atom(t_moldyn *moldyn,int element,double mass,u8 brand,u8 attr,
              t_3dvec *r,t_3dvec *v) {
 
 	t_atom *atom;
@@ -268,9 +595,9 @@ int add_atom(t_moldyn *moldyn,int element,double mass,u8 bnum,u8 attr,
 	int count;
 	
 	atom=moldyn->atom;
-	count=++(moldyn->count);
+	count=(moldyn->count)++;
 
-	ptr=realloc(atom,count*sizeof(t_atom));
+	ptr=realloc(atom,(count+1)*sizeof(t_atom));
 	if(!ptr) {
 		perror("[moldyn] realloc (add atom)");
 		return -1;
@@ -278,16 +605,163 @@ int add_atom(t_moldyn *moldyn,int element,double mass,u8 bnum,u8 attr,
 	moldyn->atom=ptr;
 
 	atom=moldyn->atom;
-	atom[count-1].r=*r;
-	atom[count-1].v=*v;
-	atom[count-1].element=element;
-	atom[count-1].mass=mass;
-	atom[count-1].bnum=bnum;
-	atom[count-1].attr=attr;
+	atom[count].r=*r;
+	atom[count].v=*v;
+	atom[count].element=element;
+	atom[count].mass=mass;
+	atom[count].brand=brand;
+	atom[count].tag=count;
+	atom[count].attr=attr;
+	check_per_bound(moldyn,&(atom[count].r));
+	atom[count].r_0=atom[count].r;
+
+	/* update total system mass */
+	total_mass_calc(moldyn);
+
+	return 0;
+}
+
+int del_atom(t_moldyn *moldyn,int tag) {
+
+	t_atom *new,*old;
+	int cnt;
+
+	old=moldyn->atom;
+
+	new=(t_atom *)malloc((moldyn->count-1)*sizeof(t_atom));
+	if(!new) {
+		perror("[moldyn]malloc (del atom)");
+		return -1;
+	}
+
+	for(cnt=0;cnt<tag;cnt++)
+		new[cnt]=old[cnt];
+	
+	for(cnt=tag+1;cnt<moldyn->count;cnt++) {
+		new[cnt-1]=old[cnt];
+		new[cnt-1].tag=cnt-1;
+	}
+
+	moldyn->count-=1;
+	moldyn->atom=new;
+
+	free(old);
 
 	return 0;
 }
 
+/* cubic init */
+int cubic_init(int a,int b,int c,double lc,t_atom *atom,t_3dvec *origin) {
+
+	int count;
+	t_3dvec r;
+	int i,j,k;
+	t_3dvec o;
+
+	count=0;
+	if(origin)
+		v3_copy(&o,origin);
+	else
+		v3_zero(&o);
+
+	r.x=o.x;
+	for(i=0;i<a;i++) {
+		r.y=o.y;
+		for(j=0;j<b;j++) {
+			r.z=o.z;
+			for(k=0;k<c;k++) {
+				v3_copy(&(atom[count].r),&r);
+				count+=1;
+				r.z+=lc;
+			}
+			r.y+=lc;
+		}
+		r.x+=lc;
+	}
+
+	for(i=0;i<count;i++) {
+		atom[i].r.x-=(a*lc)/2.0;
+		atom[i].r.y-=(b*lc)/2.0;
+		atom[i].r.z-=(c*lc)/2.0;
+	}
+
+	return count;
+}
+
+/* fcc lattice init */
+int fcc_init(int a,int b,int c,double lc,t_atom *atom,t_3dvec *origin) {
+
+	int count;
+	int i,j,k,l;
+	t_3dvec o,r,n;
+	t_3dvec basis[3];
+
+	count=0;
+	if(origin)
+		v3_copy(&o,origin);
+	else
+		v3_zero(&o);
+
+	/* construct the basis */
+	memset(basis,0,3*sizeof(t_3dvec));
+	basis[0].x=0.5*lc;
+	basis[0].y=0.5*lc;
+	basis[1].x=0.5*lc;
+	basis[1].z=0.5*lc;
+	basis[2].y=0.5*lc;
+	basis[2].z=0.5*lc;
+
+	/* fill up the room */
+	r.x=o.x;
+	for(i=0;i<a;i++) {
+		r.y=o.y;
+		for(j=0;j<b;j++) {
+			r.z=o.z;
+			for(k=0;k<c;k++) {
+				/* first atom */
+				v3_copy(&(atom[count].r),&r);
+				count+=1;
+				r.z+=lc;
+				/* the three face centered atoms */
+				for(l=0;l<3;l++) {
+					v3_add(&n,&r,&basis[l]);
+					v3_copy(&(atom[count].r),&n);
+					count+=1;
+				}
+			}
+			r.y+=lc;
+		}
+		r.x+=lc;
+	}
+				
+	/* coordinate transformation */
+	for(i=0;i<count;i++) {
+		atom[i].r.x-=(a*lc)/2.0;
+		atom[i].r.y-=(b*lc)/2.0;
+		atom[i].r.z-=(c*lc)/2.0;
+	}
+
+	return count;
+}
+
+int diamond_init(int a,int b,int c,double lc,t_atom *atom,t_3dvec *origin) {
+
+	int count;
+	t_3dvec o;
+
+	count=fcc_init(a,b,c,lc,atom,origin);
+
+	o.x=0.25*lc;
+	o.y=0.25*lc;
+	o.z=0.25*lc;
+
+	if(origin) v3_add(&o,&o,origin);
+
+	count+=fcc_init(a,b,c,lc,&atom[count],&o);
+
+	return count;
+}
+
 int destroy_atoms(t_moldyn *moldyn) {
 
 	if(moldyn->atom) free(moldyn->atom);
@@ -312,6 +786,8 @@ int thermal_init(t_moldyn *moldyn,u8 equi_init) {
 	atom=moldyn->atom;
 	random=&(moldyn->random);
 
+	printf("[moldyn] thermal init (equi init: %s)\n",equi_init?"yes":"no");
+
 	/* gaussian distribution of velocities */
 	v3_zero(&p_total);
 	for(i=0;i<moldyn->count;i++) {
@@ -343,6 +819,32 @@ int thermal_init(t_moldyn *moldyn,u8 equi_init) {
 	return 0;
 }
 
+double total_mass_calc(t_moldyn *moldyn) {
+
+	int i;
+
+	moldyn->mass=0.0;
+
+	for(i=0;i<moldyn->count;i++)
+		moldyn->mass+=moldyn->atom[i].mass;
+
+	return moldyn->mass;
+}
+
+double temperature_calc(t_moldyn *moldyn) {
+
+	/* assume up to date kinetic energy, which is 3/2 N k_B T */
+
+	moldyn->t=(2.0*moldyn->ekin)/(3.0*K_BOLTZMANN*moldyn->count);
+
+	return moldyn->t;
+}
+
+double get_temperature(t_moldyn *moldyn) {
+
+	return moldyn->t;
+}
+
 int scale_velocity(t_moldyn *moldyn,u8 equi_init) {
 
 	int i;
@@ -361,18 +863,21 @@ int scale_velocity(t_moldyn *moldyn,u8 equi_init) {
 	count=0;
 	for(i=0;i<moldyn->count;i++) {
 		if((equi_init&TRUE)||(atom[i].attr&ATOM_ATTR_HB)) {
-			e+=0.5*atom[i].mass*v3_absolute_square(&(atom[i].v));
+			e+=atom[i].mass*v3_absolute_square(&(atom[i].v));
 			count+=1;
 		}
 	}
-	if(count!=0) moldyn->t=(2.0*e)/(3.0*count*K_BOLTZMANN);
+	e*=0.5;
+	if(count!=0) moldyn->t=e/(1.5*count*K_BOLTZMANN);
 	else return 0;	/* no atoms involved in scaling! */
 	
 	/* (temporary) hack for e,t = 0 */
 	if(e==0.0) {
 	moldyn->t=0.0;
-		if(moldyn->t_ref!=0.0)
+		if(moldyn->t_ref!=0.0) {
 			thermal_init(moldyn,equi_init);
+			return 0;
+		}
 		else
 			return 0; /* no scaling needed */
 	}
@@ -384,147 +889,492 @@ int scale_velocity(t_moldyn *moldyn,u8 equi_init) {
 		scale*=2.0;
 	else
 		if(moldyn->pt_scale&T_SCALE_BERENDSEN)
-			scale=1.0+moldyn->tau*(scale-1.0)/moldyn->t_tc;
+			scale=1.0+(scale-1.0)/moldyn->t_tc;
 	scale=sqrt(scale);
 
 	/* velocity scaling */
-	for(i=0;i<moldyn->count;i++)
+	for(i=0;i<moldyn->count;i++) {
 		if((equi_init&TRUE)||(atom[i].attr&ATOM_ATTR_HB))
 			v3_scale(&(atom[i].v),&(atom[i].v),scale);
+	}
 
 	return 0;
 }
 
-double get_e_kin(t_moldyn *moldyn) {
+double ideal_gas_law_pressure(t_moldyn *moldyn) {
+
+	double p;
+
+	p=moldyn->count*moldyn->t*K_BOLTZMANN/moldyn->volume;
+
+	return p;
+}
+
+double virial_sum(t_moldyn *moldyn) {
 
 	int i;
-	t_atom *atom;
+	double v;
+	t_virial *virial;
 
-	atom=moldyn->atom;
-	moldyn->ekin=0.0;
+	/* virial (sum over atom virials) */
+	v=0.0;
+	for(i=0;i<moldyn->count;i++) {
+		virial=&(moldyn->atom[i].virial);
+		v+=(virial->xx+virial->yy+virial->zz);
+	}
+	moldyn->virial=v;
 
-	for(i=0;i<moldyn->count;i++)
-		moldyn->ekin+=0.5*atom[i].mass*v3_absolute_square(&(atom[i].v));
+	/* global virial (absolute coordinates) */
+	virial=&(moldyn->gvir);
+	moldyn->gv=virial->xx+virial->yy+virial->zz;
 
-	return moldyn->ekin;
+	return moldyn->virial;
 }
 
-double get_e_pot(t_moldyn *moldyn) {
+double pressure_calc(t_moldyn *moldyn) {
 
-	return moldyn->energy;
-}
+	/*
+	 * PV = NkT + <W>
+	 * with W = 1/3 sum_i f_i r_i (- skipped!)
+	 * virial = sum_i f_i r_i
+	 * 
+	 * => P = (2 Ekin + virial) / (3V)
+	 */
 
-double update_e_kin(t_moldyn *moldyn) {
+	/* assume up to date virial & up to date kinetic energy */
 
-	return(get_e_kin(moldyn));
-}
+	/* pressure (atom virials) */
+	moldyn->p=2.0*moldyn->ekin+moldyn->virial;
+	moldyn->p/=(3.0*moldyn->volume);
 
-double get_total_energy(t_moldyn *moldyn) {
+	/* pressure (absolute coordinates) */
+	moldyn->gp=2.0*moldyn->ekin+moldyn->gv;
+	moldyn->gp/=(3.0*moldyn->volume);
 
-	return(moldyn->ekin+moldyn->energy);
+	return moldyn->p;
 }
 
-t_3dvec get_total_p(t_moldyn *moldyn) {
+int average_and_fluctuation_calc(t_moldyn *moldyn) {
 
-	t_3dvec p,p_total;
-	int i;
-	t_atom *atom;
+	int denom;
 
-	atom=moldyn->atom;
+	if(moldyn->total_steps<moldyn->avg_skip)
+		return 0;
 
-	v3_zero(&p_total);
-	for(i=0;i<moldyn->count;i++) {
-		v3_scale(&p,&(atom[i].v),atom[i].mass);
-		v3_add(&p_total,&p_total,&p);
-	}
+	denom=moldyn->total_steps+1-moldyn->avg_skip;
 
-	return p_total;
-}
+	/* assume up to date energies, temperature, pressure etc */
 
-double estimate_time_step(t_moldyn *moldyn,double nn_dist) {
+	/* kinetic energy */
+	moldyn->k_sum+=moldyn->ekin;
+	moldyn->k2_sum+=(moldyn->ekin*moldyn->ekin);
+	moldyn->k_avg=moldyn->k_sum/denom;
+	moldyn->k2_avg=moldyn->k2_sum/denom;
+	moldyn->dk2_avg=moldyn->k2_avg-(moldyn->k_avg*moldyn->k_avg);
 
-	double tau;
+	/* potential energy */
+	moldyn->v_sum+=moldyn->energy;
+	moldyn->v2_sum+=(moldyn->energy*moldyn->energy);
+	moldyn->v_avg=moldyn->v_sum/denom;
+	moldyn->v2_avg=moldyn->v2_sum/denom;
+	moldyn->dv2_avg=moldyn->v2_avg-(moldyn->v_avg*moldyn->v_avg);
 
-	/* nn_dist is the nearest neighbour distance */
+	/* temperature */
+	moldyn->t_sum+=moldyn->t;
+	moldyn->t_avg=moldyn->t_sum/denom;
 
-	if(moldyn->t==5.0) {
-		printf("[moldyn] i do not estimate timesteps below %f K!\n",
-		       MOLDYN_CRITICAL_EST_TEMP);
-		return 23.42;
-	}
+	/* virial */
+	moldyn->virial_sum+=moldyn->virial;
+	moldyn->virial_avg=moldyn->virial_sum/denom;
+	moldyn->gv_sum+=moldyn->gv;
+	moldyn->gv_avg=moldyn->gv_sum/denom;
 
-	tau=(0.05*nn_dist*moldyn->atom[0].mass)/sqrt(3.0*K_BOLTZMANN*moldyn->t);
+	/* pressure */
+	moldyn->p_sum+=moldyn->p;
+	moldyn->p_avg=moldyn->p_sum/denom;
+	moldyn->gp_sum+=moldyn->gp;
+	moldyn->gp_avg=moldyn->gp_sum/denom;
 
-	return tau;	
+	return 0;
 }
 
-/*
- * numerical tricks
- */
-
-/* linked list / cell method */
-
-int link_cell_init(t_moldyn *moldyn) {
+int get_heat_capacity(t_moldyn *moldyn) {
 
-	t_linkcell *lc;
-	int i;
-	int fd;
+	double temp2,ighc;
 
-	fd=open("/dev/null",O_WRONLY);
+	/* averages needed for heat capacity calc */
+	if(moldyn->total_steps<moldyn->avg_skip)
+		return 0;
 
-	lc=&(moldyn->lc);
+	/* (temperature average)^2 */
+	temp2=moldyn->t_avg*moldyn->t_avg;
+	printf("[moldyn] specific heat capacity for T=%f K [J/(kg K)]\n",
+	       moldyn->t_avg);
 
-	/* 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;
+	/* ideal gas contribution */
+	ighc=3.0*moldyn->count*K_BOLTZMANN/2.0;
+	printf("  ideal gas contribution: %f\n",
+	       ighc/moldyn->mass*KILOGRAM/JOULE);
 
-	lc->cells=lc->nx*lc->ny*lc->nz;
-	lc->subcell=malloc(lc->cells*sizeof(t_list));
+	/* specific heat for nvt ensemble */
+	moldyn->c_v_nvt=moldyn->dv2_avg/(K_BOLTZMANN*temp2)+ighc;
+	moldyn->c_v_nvt/=moldyn->mass;
 
-	printf("[moldyn] initializing linked cells (%d)\n",lc->cells);
+	/* specific heat for nve ensemble */
+	moldyn->c_v_nve=ighc/(1.0-(moldyn->dv2_avg/(ighc*K_BOLTZMANN*temp2)));
+	moldyn->c_v_nve/=moldyn->mass;
 
-	for(i=0;i<lc->cells;i++)
-		//list_init(&(lc->subcell[i]),1);
-		list_init(&(lc->subcell[i]),fd);
+	printf("  NVE: %f\n",moldyn->c_v_nve*KILOGRAM/JOULE);
+	printf("  NVT: %f\n",moldyn->c_v_nvt*KILOGRAM/JOULE);
+printf("  --> <dV2> sim: %f experimental: %f\n",moldyn->dv2_avg,1.5*moldyn->count*K_B2*moldyn->t_avg*moldyn->t_avg*(1.0-1.5*moldyn->count*K_BOLTZMANN/(700*moldyn->mass*JOULE/KILOGRAM)));
 
- 	link_cell_update(moldyn);
-	
 	return 0;
 }
 
-int link_cell_update(t_moldyn *moldyn) {
+double thermodynamic_pressure_calc(t_moldyn *moldyn) {
 
-	int count,i,j,k;
-	int nx,ny,nz;
-	t_atom *atom;
-	t_linkcell *lc;
+	t_3dvec dim;
+	//t_3dvec *tp;
+	double u_up,u_down,dv;
+	double scale,p;
+	t_atom *store;
 
-	atom=moldyn->atom;
-	lc=&(moldyn->lc);
+	/*
+	 * dU = - p dV
+	 *
+	 * => p = - dU/dV
+	 *
+	 */
 
-	nx=lc->nx;
-	ny=lc->ny;
-	nz=lc->nz;
+	scale=0.00001;
+	dv=8*scale*scale*scale*moldyn->volume;
 
-	for(i=0;i<lc->cells;i++)
-		list_destroy(&(moldyn->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_ptr(&(moldyn->lc.subcell[i+j*nx+k*nx*ny]),
-		                       &(atom[count]));
+	store=malloc(moldyn->count*sizeof(t_atom));
+	if(store==NULL) {
+		printf("[moldyn] allocating store mem failed\n");
+		return -1;
 	}
 
-	return 0;
-}
+	/* save unscaled potential energy + atom/dim configuration */
+	memcpy(store,moldyn->atom,moldyn->count*sizeof(t_atom));
+	dim=moldyn->dim;
 
-int link_cell_neighbour_index(t_moldyn *moldyn,int i,int j,int k,t_list *cell) {
+	/* scale up dimension and atom positions */
+	scale_dim(moldyn,SCALE_UP,scale,TRUE,TRUE,TRUE);
+	scale_atoms(moldyn,SCALE_UP,scale,TRUE,TRUE,TRUE);
+	link_cell_shutdown(moldyn);
+	link_cell_init(moldyn,QUIET);
+	potential_force_calc(moldyn);
+	u_up=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);
+	link_cell_shutdown(moldyn);
+	link_cell_init(moldyn,QUIET);
+	potential_force_calc(moldyn);
+	u_down=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);
+
+	/* restore atomic configuration + dim */
+	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);
+
+	return p;
+}
+
+double get_pressure(t_moldyn *moldyn) {
+
+	return moldyn->p;
+
+}
+
+int scale_dim(t_moldyn *moldyn,u8 dir,double scale,u8 x,u8 y,u8 z) {
+
+	t_3dvec *dim;
+
+	dim=&(moldyn->dim);
+
+	if(dir==SCALE_UP)
+		scale=1.0+scale;
+
+	if(dir==SCALE_DOWN)
+		scale=1.0-scale;
+
+	if(x) dim->x*=scale;
+	if(y) dim->y*=scale;
+	if(z) dim->z*=scale;
+
+	return 0;
+}
+
+int scale_atoms(t_moldyn *moldyn,u8 dir,double scale,u8 x,u8 y,u8 z) {
+
+	int i;
+	t_3dvec *r;
+
+	if(dir==SCALE_UP)
+		scale=1.0+scale;
+
+	if(dir==SCALE_DOWN)
+		scale=1.0-scale;
+
+	for(i=0;i<moldyn->count;i++) {
+		r=&(moldyn->atom[i].r);
+		if(x) r->x*=scale;
+		if(y) r->y*=scale;
+		if(z) r->z*=scale;
+	}
+
+	return 0;
+}
+
+int scale_volume(t_moldyn *moldyn) {
+
+	t_3dvec *dim,*vdim;
+	double scale;
+	t_linkcell *lc;
+
+	vdim=&(moldyn->vis.dim);
+	dim=&(moldyn->dim);
+	lc=&(moldyn->lc);
+
+	/* scaling factor */
+	if(moldyn->pt_scale&P_SCALE_BERENDSEN) {
+		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);
+	scale_dim(moldyn,SCALE_DIRECT,scale,TRUE,TRUE,TRUE);
+
+	/* visualize dimensions */
+	if(vdim->x!=0) {
+		vdim->x=dim->x;
+		vdim->y=dim->y;
+		vdim->z=dim->z;
+	}
+
+	/* recalculate scaled volume */
+	moldyn->volume=dim->x*dim->y*dim->z;
+
+	/* adjust/reinit linkcell */
+	if(((int)(dim->x/moldyn->cutoff)!=lc->nx)||
+	   ((int)(dim->y/moldyn->cutoff)!=lc->ny)||
+	   ((int)(dim->z/moldyn->cutoff)!=lc->nx)) {
+		link_cell_shutdown(moldyn);
+		link_cell_init(moldyn,QUIET);
+	} else {
+		lc->x*=scale;
+		lc->y*=scale;
+		lc->z*=scale;
+	}
+
+	return 0;
+
+}
+
+double e_kin_calc(t_moldyn *moldyn) {
+
+	int i;
+	t_atom *atom;
+
+	atom=moldyn->atom;
+	moldyn->ekin=0.0;
+
+	for(i=0;i<moldyn->count;i++) {
+		atom[i].ekin=0.5*atom[i].mass*v3_absolute_square(&(atom[i].v));
+		moldyn->ekin+=atom[i].ekin;
+	}
+
+	return moldyn->ekin;
+}
+
+double get_total_energy(t_moldyn *moldyn) {
+
+	return(moldyn->ekin+moldyn->energy);
+}
+
+t_3dvec get_total_p(t_moldyn *moldyn) {
+
+	t_3dvec p,p_total;
+	int i;
+	t_atom *atom;
+
+	atom=moldyn->atom;
+
+	v3_zero(&p_total);
+	for(i=0;i<moldyn->count;i++) {
+		v3_scale(&p,&(atom[i].v),atom[i].mass);
+		v3_add(&p_total,&p_total,&p);
+	}
+
+	return p_total;
+}
+
+double estimate_time_step(t_moldyn *moldyn,double nn_dist) {
+
+	double tau;
+
+	/* nn_dist is the nearest neighbour distance */
+
+	tau=(0.05*nn_dist*moldyn->atom[0].mass)/sqrt(3.0*K_BOLTZMANN*moldyn->t);
+
+	return tau;	
+}
+
+/*
+ * numerical tricks
+ */
+
+/* linked list / cell method */
+
+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;
+
+#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));
+		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);
+
+	return 0;
+}
+
+int link_cell_update(t_moldyn *moldyn) {
+
+	int count,i,j,k;
+	int nx,ny;
+	t_atom *atom;
+	t_linkcell *lc;
+#ifdef STATIC_LISTS
+	int p;
+#endif
+
+	atom=moldyn->atom;
+	lc=&(moldyn->lc);
+
+	nx=lc->nx;
+	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++;
+
+		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,
+#ifdef STATIC_LISTS
+                              int **cell
+#else
+                              t_list *cell
+#endif
+			     ) {
 
 	t_linkcell *lc;
 	int a;
@@ -576,9 +1426,8 @@ int link_cell_neighbour_index(t_moldyn *moldyn,int i,int j,int k,t_list *cell) {
 	}
 
 	lc->dnlc=count1;
-	lc->countn=27;
 
-	return count2;
+	return count1;
 }
 
 int link_cell_shutdown(t_moldyn *moldyn) {
@@ -588,8 +1437,16 @@ int link_cell_shutdown(t_moldyn *moldyn) {
 
 	lc=&(moldyn->lc);
 
-	for(i=0;i<lc->nx*lc->ny*lc->nz;i++)
-		list_shutdown(&(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);
 
 	return 0;
 }
@@ -601,28 +1458,32 @@ int moldyn_add_schedule(t_moldyn *moldyn,int runs,double tau) {
 	t_moldyn_schedule *schedule;
 
 	schedule=&(moldyn->schedule);
-	count=++(schedule->content_count);
+	count=++(schedule->total_sched);
 
-	ptr=realloc(moldyn->schedule.runs,count*sizeof(int));
+	ptr=realloc(schedule->runs,count*sizeof(int));
 	if(!ptr) {
 		perror("[moldyn] realloc (runs)");
 		return -1;
 	}
-	moldyn->schedule.runs=ptr;
-	moldyn->schedule.runs[count-1]=runs;
+	schedule->runs=ptr;
+	schedule->runs[count-1]=runs;
 
 	ptr=realloc(schedule->tau,count*sizeof(double));
 	if(!ptr) {
 		perror("[moldyn] realloc (tau)");
 		return -1;
 	}
-	moldyn->schedule.tau=ptr;
-	moldyn->schedule.tau[count-1]=tau;
+	schedule->tau=ptr;
+	schedule->tau[count-1]=tau;
+
+	printf("[moldyn] schedule added:\n");
+	printf("  number: %d | runs: %d | tau: %f\n",count-1,runs,tau);
+	                               
 
 	return 0;
 }
 
-int moldyn_set_schedule_hook(t_moldyn *moldyn,void *hook,void *hook_params) {
+int moldyn_set_schedule_hook(t_moldyn *moldyn,set_hook hook,void *hook_params) {
 
 	moldyn->schedule.hook=hook;
 	moldyn->schedule.hook_params=hook_params;
@@ -640,34 +1501,46 @@ int moldyn_set_schedule_hook(t_moldyn *moldyn,void *hook,void *hook_params) {
 
 int moldyn_integrate(t_moldyn *moldyn) {
 
-	int i,sched;
-	unsigned int e,m,s,v;
-	t_3dvec p;
-	t_moldyn_schedule *schedule;
+	int i;
+	unsigned int e,m,s,v,p,t;
+	t_3dvec momentum;
+	t_moldyn_schedule *sched;
 	t_atom *atom;
 	int fd;
-	char fb[128];
+	char dir[128];
 	double ds;
+	double energy_scale;
+	struct timeval t1,t2;
+	//double tp;
 
-	schedule=&(moldyn->schedule);
+	sched=&(moldyn->schedule);
 	atom=moldyn->atom;
 
 	/* initialize linked cell method */
-	link_cell_init(moldyn);
+	link_cell_init(moldyn,VERBOSE);
 
 	/* logging & visualization */
 	e=moldyn->ewrite;
 	m=moldyn->mwrite;
 	s=moldyn->swrite;
 	v=moldyn->vwrite;
+	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);
+
 	/* calculate initial forces */
 	potential_force_calc(moldyn);
+#ifdef DEBUG
+//return 0;
+#endif
 
-	/* do some checks before we actually start calculating bullshit */
+	/* 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");
 	if(moldyn->cutoff>0.5*moldyn->dim.y)
@@ -680,12 +1553,25 @@ int moldyn_integrate(t_moldyn *moldyn) {
 
 	/* zero absolute time */
 	moldyn->time=0.0;
-	for(sched=0;sched<moldyn->schedule.content_count;sched++) {
+	moldyn->total_steps=0;
+
+	/* debugging, ignore */
+	moldyn->debug=0;
+
+	/* tell the world */
+	printf("[moldyn] integration start, go get a coffee ...\n");
+
+	/* executing the schedule */
+	sched->count=0;
+	while(sched->count<sched->total_sched) {
 
 		/* setting amount of runs and finite time step size */
-		moldyn->tau=schedule->tau[sched];
+		moldyn->tau=sched->tau[sched->count];
 		moldyn->tau_square=moldyn->tau*moldyn->tau;
-		moldyn->time_steps=schedule->runs[sched];
+		moldyn->time_steps=sched->runs[sched->count];
+
+		/* energy scaling factor (might change!) */
+		energy_scale=moldyn->count*EV;
 
 	/* integration according to schedule */
 
@@ -694,35 +1580,58 @@ int moldyn_integrate(t_moldyn *moldyn) {
 		/* integration step */
 		moldyn->integrate(moldyn);
 
+		/* calculate kinetic energy, temperature and pressure */
+		e_kin_calc(moldyn);
+		temperature_calc(moldyn);
+		virial_sum(moldyn);
+		pressure_calc(moldyn);
+		average_and_fluctuation_calc(moldyn);
+
 		/* p/t scaling */
 		if(moldyn->pt_scale&(T_SCALE_BERENDSEN|T_SCALE_DIRECT))
 			scale_velocity(moldyn,FALSE);
-
-		/* increase absolute time */
-		moldyn->time+=moldyn->tau;
+		if(moldyn->pt_scale&(P_SCALE_BERENDSEN|P_SCALE_DIRECT))
+			scale_volume(moldyn);
 
 		/* check for log & visualization */
 		if(e) {
-			if(!(i%e))
+			if(!(moldyn->total_steps%e))
 				dprintf(moldyn->efd,
-				        "%.15f %.45f %.45f %.45f\n",
-				        moldyn->time,update_e_kin(moldyn),
-				        moldyn->energy,
-				        get_total_energy(moldyn));
+				        "%f %f %f %f\n",
+				        moldyn->time,moldyn->ekin/energy_scale,
+				        moldyn->energy/energy_scale,
+				        get_total_energy(moldyn)/energy_scale);
 		}
 		if(m) {
-			if(!(i%m)) {
-				p=get_total_p(moldyn);
+			if(!(moldyn->total_steps%m)) {
+				momentum=get_total_p(moldyn);
 				dprintf(moldyn->mfd,
-				        "%.15f %.45f\n",moldyn->time,
-				        v3_norm(&p));
+				        "%f %f %f %f %f\n",moldyn->time,
+				        momentum.x,momentum.y,momentum.z,
+				        v3_norm(&momentum));
+			}
+		}
+		if(p) {
+			if(!(moldyn->total_steps%p)) {
+				dprintf(moldyn->pfd,
+				        "%f %f %f %f %f\n",moldyn->time,
+				         moldyn->p/BAR,moldyn->p_avg/BAR,
+				         moldyn->gp/BAR,moldyn->gp_avg/BAR);
+			}
+		}
+		if(t) {
+			if(!(moldyn->total_steps%t)) {
+				dprintf(moldyn->tfd,
+				        "%f %f %f\n",
+				        moldyn->time,moldyn->t,moldyn->t_avg);
 			}
 		}
 		if(s) {
-			if(!(i%s)) {
-				snprintf(fb,128,"%s-%f-%.15f.save",moldyn->sfb,
-				         moldyn->t,i*moldyn->tau);
-				fd=open(fb,O_WRONLY|O_TRUNC|O_CREAT);
+			if(!(moldyn->total_steps%s)) {
+				snprintf(dir,128,"%s/s-%07.f.save",
+				         moldyn->vlsdir,moldyn->time);
+				fd=open(dir,O_WRONLY|O_TRUNC|O_CREAT,
+				        S_IRUSR|S_IWUSR);
 				if(fd<0) perror("[moldyn] save fd open");
 				else {
 					write(fd,moldyn,sizeof(t_moldyn));
@@ -733,19 +1642,45 @@ int moldyn_integrate(t_moldyn *moldyn) {
 			}	
 		}
 		if(v) {
-			if(!(i%v)) {
-				visual_atoms(&(moldyn->vis),moldyn->time,
-				             moldyn->atom,moldyn->count);
-				printf("\rsched: %d, steps: %d",sched,i);
-				fflush(stdout);
+			if(!(moldyn->total_steps%v)) {
+				visual_atoms(moldyn);
 			}
 		}
 
+		/* display progress */
+		//if(!(moldyn->total_steps%10)) {
+			/* 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)",
+       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;
+		//}
+
+		/* increase absolute time */
+		moldyn->time+=moldyn->tau;
+		moldyn->total_steps+=1;
+
 	}
 
 		/* check for hooks */
-		if(schedule->hook)
-			schedule->hook(moldyn,schedule->hook_params);
+		if(sched->hook) {
+			printf("\n ## schedule hook %d start ##\n",
+			       sched->count);
+			sched->hook(moldyn,sched->hook_params);
+			printf(" ## schedule hook end ##\n");
+		}
+
+		/* increase the schedule counter */
+		sched->count+=1;
 
 	}
 
@@ -757,7 +1692,7 @@ int moldyn_integrate(t_moldyn *moldyn) {
 int velocity_verlet(t_moldyn *moldyn) {
 
 	int i,count;
-	double tau,tau_square;
+	double tau,tau_square,h;
 	t_3dvec delta;
 	t_atom *atom;
 
@@ -768,14 +1703,15 @@ int velocity_verlet(t_moldyn *moldyn) {
 
 	for(i=0;i<count;i++) {
 		/* new positions */
+		h=0.5/atom[i].mass;
 		v3_scale(&delta,&(atom[i].v),tau);
 		v3_add(&(atom[i].r),&(atom[i].r),&delta);
-		v3_scale(&delta,&(atom[i].f),0.5*tau_square/atom[i].mass);
+		v3_scale(&delta,&(atom[i].f),h*tau_square);
 		v3_add(&(atom[i].r),&(atom[i].r),&delta);
 		check_per_bound(moldyn,&(atom[i].r));
 
-		/* velocities */
-		v3_scale(&delta,&(atom[i].f),0.5*tau/atom[i].mass);
+		/* velocities [actually v(t+tau/2)] */
+		v3_scale(&delta,&(atom[i].f),h*tau);
 		v3_add(&(atom[i].v),&(atom[i].v),&delta);
 	}
 
@@ -784,10 +1720,9 @@ int velocity_verlet(t_moldyn *moldyn) {
 
 	/* forces depending on chosen potential */
 	potential_force_calc(moldyn);
-	//moldyn->potential_force_function(moldyn);
 
 	for(i=0;i<count;i++) {
-		/* again velocities */
+		/* 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);
 	}
@@ -798,7 +1733,7 @@ int velocity_verlet(t_moldyn *moldyn) {
 
 /*
  *
- * potentials & corresponding forces
+ * potentials & corresponding forces & virial routine
  * 
  */
 
@@ -808,52 +1743,107 @@ int potential_force_calc(t_moldyn *moldyn) {
 
 	int i,j,k,count;
 	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 neighbour_j[27];
 	t_list *this,*that;
-	u8 bc_ij,bc_ijk;
-	int countn,dnlc;
+#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;
 
+	/* reset global virial */
+	memset(&(moldyn->gvir),0,sizeof(t_virial));
+
+	/* reset force, site energy and virial of every atom */
 	for(i=0;i<count;i++) {
 
 		/* reset force */
 		v3_zero(&(itom[i].f));
 
+		/* reset virial */
+		virial=(&(itom[i].virial));
+		virial->xx=0.0;
+		virial->yy=0.0;
+		virial->zz=0.0;
+		virial->xy=0.0;
+		virial->xz=0.0;
+		virial->yz=0.0;
+	
+		/* reset site energy */
+		itom[i].e=0.0;
+
+	}
+
+	/* get energy, force and virial of every atom */
+
+	/* first (and only) loop over atoms i */
+	for(i=0;i<count;i++) {
+
 		/* single particle potential/force */
 		if(itom[i].attr&ATOM_ATTR_1BP)
-			moldyn->func1b(moldyn,&(itom[i]));
+			if(moldyn->func1b)
+				moldyn->func1b(moldyn,&(itom[i]));
+
+		if(!(itom[i].attr&(ATOM_ATTR_2BP|ATOM_ATTR_3BP)))
+			continue;
 
 		/* 2 body pair potential/force */
-		if(itom[i].attr&(ATOM_ATTR_2BP|ATOM_ATTR_3BP)) {
 	
-			link_cell_neighbour_index(moldyn,
-				(itom[i].r.x+moldyn->dim.x/2)/lc->x,
-				(itom[i].r.y+moldyn->dim.y/2)/lc->y,
-				(itom[i].r.z+moldyn->dim.z/2)/lc->z,
-				neighbour_i);
+		link_cell_neighbour_index(moldyn,
+		                          (itom[i].r.x+moldyn->dim.x/2)/lc->x,
+		                          (itom[i].r.y+moldyn->dim.y/2)/lc->y,
+		                          (itom[i].r.z+moldyn->dim.z/2)/lc->z,
+		                          neighbour_i);
+
+		dnlc=lc->dnlc;
+
+		/* first loop over atoms j */
+		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) {
 
-			countn=lc->countn;
-			dnlc=lc->dnlc;
+					jtom=&(atom[neighbour_i[j][p]]);
+					p++;
 
-			for(j=0;j<countn;j++) {
+					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(this);
+				list_reset_f(this);
 
 				if(this->start==NULL)
 					continue;
 
-				bc_ij=(j<dnlc)?0:1;
-
 				do {
 					jtom=this->current->data;
 
@@ -861,113 +1851,245 @@ int potential_force_calc(t_moldyn *moldyn) {
 						continue;
 
 					if((jtom->attr&ATOM_ATTR_2BP)&
-					   (itom[i].attr&ATOM_ATTR_2BP))
+					   (itom[i].attr&ATOM_ATTR_2BP)) {
 						moldyn->func2b(moldyn,
 						               &(itom[i]),
 						               jtom,
-						               bc_ij);
+					        	       bc_ij);
+					}
+				} while(list_next_f(this)!=L_NO_NEXT_ELEMENT);
+#endif
 
-					/* 3 body potential/force */
+			}
+		}
 
-					if(!(itom[i].attr&ATOM_ATTR_3BP)||
-					   !(jtom->attr&ATOM_ATTR_3BP))
-						continue;
+		/* 3 body potential/force */
+
+		if(!(itom[i].attr&ATOM_ATTR_3BP))
+			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;
+
+			do {
+
+				jtom=this->current->data;
+#endif
+
+				if(jtom==&(itom[i]))
+					continue;
+
+				if(!(jtom->attr&ATOM_ATTR_3BP))
+					continue;
+
+				/* reset 3bp run */
+				moldyn->run3bp=1;
 
-			/* neighbourhood of atom j is not needed! */
-
-			//		link_cell_neighbour_index(moldyn,
-			//		   (jtom->r.x+moldyn->dim.x/2)/lc->x,
-			//		   (jtom->r.y+moldyn->dim.y/2)/lc->y,
-			//		   (jtom->r.z+moldyn->dim.z/2)/lc->z,
-			//		   neighbour_j);
-
-//					/* neighbours of j */
-//					for(k=0;k<lc->countn;k++) {
-//
-//						that=&(neighbour_j[k]);
-//						list_reset(that);
-//					
-//						if(that->start==NULL)
-//							continue;
-//
-//						bc_ijk=(k<lc->dnlc)?0:1;
-//
-//						do {
-//
-//			ktom=that->current->data;
-//
-//			if(!(ktom->attr&ATOM_ATTR_3BP))
-//				continue;
-//
-//			if(ktom==jtom)
-//				continue;
-//
-//			if(ktom==&(itom[i]))
-//				continue;
-//
-//			moldyn->func3b(moldyn,&(itom[i]),jtom,ktom,bc_ijk);
-//
-/*						} while(list_next(that)!=\ */
-//						        L_NO_NEXT_ELEMENT);
-//
-//					}
+				if(moldyn->func3b_j1)
+					moldyn->func3b_j1(moldyn,
+					                  &(itom[i]),
+					                  jtom,
+					                  bc_ij);
+
+				/* in first j loop, 3bp run can be skipped */
+				if(!(moldyn->run3bp))
+					continue;
 			
-					/* copy the neighbour lists */
-					memcpy(neighbour_i2,neighbour_i,
-					       27*sizeof(t_list));
+				/* first loop over atoms k */
+				if(moldyn->func3b_k1) {
+
+				for(k=0;k<27;k++) {
 
-					/* get neighbours of i */
-					for(k=0;k<countn;k++) {
+					bc_ik=(k<dnlc)?0:1;
+#ifdef STATIC_LISTS
+					q=0;
 
-						that=&(neighbour_i2[k]);
-						list_reset(that);
+					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)
+					if(that->start==NULL)
+						continue;
+
+					do {
+						ktom=that->current->data;
+#endif
+
+						if(!(ktom->attr&ATOM_ATTR_3BP))
 							continue;
 
-						bc_ijk=(k<dnlc)?0:1;
+						if(ktom==jtom)
+							continue;
 
-						do {
+						if(ktom==&(itom[i]))
+							continue;
 
-			ktom=that->current->data;
+						moldyn->func3b_k1(moldyn,
+						                  &(itom[i]),
+						                  jtom,
+						                  ktom,
+						                  bc_ik|bc_ij);
+#ifdef STATIC_LISTS
+					}
+#else
+					} while(list_next_f(that)!=\
+					        L_NO_NEXT_ELEMENT);
+#endif
 
-			if(!(ktom->attr&ATOM_ATTR_3BP))
-				continue;
+				}
 
-			if(ktom==jtom)
-				continue;
+				}
 
-			if(ktom==&(itom[i]))
-				continue;
+				if(moldyn->func3b_j2)
+					moldyn->func3b_j2(moldyn,
+					                  &(itom[i]),
+					                  jtom,
+					                  bc_ij);
 
-//printf("Debug: atom %d before 3bp: %08x %08x %08x | %.15f %.15f %.15f\n",i,&itom[i],jtom,ktom,itom[i].r.x,itom[i].f.x,itom[i].v.x);
-			moldyn->func3b(moldyn,&(itom[i]),jtom,ktom,bc_ijk);
-//printf("Debug: atom %d after 3bp: %08x %08x %08x | %.15f %.15f %.15f\n",i,&itom[i],jtom,ktom,itom[i].r.x,itom[i].f.x,itom[i].v.x);
+				/* second loop over atoms k */
+				if(moldyn->func3b_k2) {
 
-						} while(list_next(that)!=\
-						        L_NO_NEXT_ELEMENT);
+				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);
 					
-				} while(list_next(this)!=L_NO_NEXT_ELEMENT);
-		
-				/* 2bp post function */
-				if(moldyn->func2b_post)
-					moldyn->func2b_post(moldyn,
-					                    &(itom[i]),
-					                    jtom,bc_ij);
+					if(that->start==NULL)
+						continue;
+
+					do {
+						ktom=that->current->data;
+#endif
 
+						if(!(ktom->attr&ATOM_ATTR_3BP))
+							continue;
+
+						if(ktom==jtom)
+							continue;
+
+						if(ktom==&(itom[i]))
+							continue;
+
+						moldyn->func3b_k2(moldyn,
+						                  &(itom[i]),
+						                  jtom,
+						                  ktom,
+						                  bc_ik|bc_ij);
+
+#ifdef STATIC_LISTS
+					}
+#else
+					} while(list_next_f(that)!=\
+					        L_NO_NEXT_ELEMENT);
+#endif
+
+				}
+				
+				}
+
+				/* 2bp post function */
+				if(moldyn->func3b_j3) {
+					moldyn->func3b_j3(moldyn,
+					                  &(itom[i]),
+					                  jtom,bc_ij);
+				}
+#ifdef STATIC_LISTS
 			}
+#else
+			} while(list_next_f(this)!=L_NO_NEXT_ELEMENT);
+#endif
+		
 		}
+		
+#ifdef DEBUG
+	//printf("\n\n");
+#endif
+#ifdef VDEBUG
+	printf("\n\n");
+#endif
+
+	}
+
+#ifdef DEBUG
+	//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);
+	}
+#endif
+
+	/* calculate global virial */
+	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;
 	}
 
 	return 0;
 }
 
 /*
- * periodic boundayr checking
+ * virial calculation
  */
 
+//inline int virial_calc(t_atom *a,t_3dvec *f,t_3dvec *d) {
+int virial_calc(t_atom *a,t_3dvec *f,t_3dvec *d) {
+
+	a->virial.xx+=f->x*d->x;
+	a->virial.yy+=f->y*d->y;
+	a->virial.zz+=f->z*d->z;
+	a->virial.xy+=f->x*d->y;
+	a->virial.xz+=f->x*d->z;
+	a->virial.yz+=f->y*d->z;
+
+	return 0;
+}
+
+/*
+ * periodic boundary checking
+ */
+
+//inline int check_per_bound(t_moldyn *moldyn,t_3dvec *a) {
 int check_per_bound(t_moldyn *moldyn,t_3dvec *a) {
 	
 	double x,y,z;
@@ -975,9 +2097,9 @@ int check_per_bound(t_moldyn *moldyn,t_3dvec *a) {
 
 	dim=&(moldyn->dim);
 
-	x=0.5*dim->x;
-	y=0.5*dim->y;
-	z=0.5*dim->z;
+	x=dim->x/2;
+	y=dim->y/2;
+	z=dim->z/2;
 
 	if(moldyn->status&MOLDYN_STAT_PBX) {
 		if(a->x>=x) a->x-=dim->x;
@@ -995,459 +2117,464 @@ int check_per_bound(t_moldyn *moldyn,t_3dvec *a) {
 	return 0;
 }
         
-
 /*
- * example potentials
+ * debugging / critical check functions
  */
 
-/* harmonic oscillator potential and force */
+int moldyn_bc_check(t_moldyn *moldyn) {
 
-int harmonic_oscillator(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc) {
-
-	t_ho_params *params;
-	t_3dvec force,distance;
-	double d;
-	double sc,equi_dist;
+	t_atom *atom;
+	t_3dvec *dim;
+	int i;
+	double x;
+	u8 byte;
+	int j,k;
 
-	params=moldyn->pot2b_params;
-	sc=params->spring_constant;
-	equi_dist=params->equilibrium_distance;
+	atom=moldyn->atom;
+	dim=&(moldyn->dim);
+	x=dim->x/2;
 
-	v3_sub(&distance,&(ai->r),&(aj->r));
-	
-	if(bc) check_per_bound(moldyn,&distance);
-	d=v3_norm(&distance);
-	if(d<=moldyn->cutoff) {
-		/* energy is 1/2 (d-d0)^2, but we will add this twice ... */
-		moldyn->energy+=(0.25*sc*(d-equi_dist)*(d-equi_dist));
-		v3_scale(&force,&distance,-sc*(1.0-(equi_dist/d)));
-		v3_add(&(ai->f),&(ai->f),&force);
+	for(i=0;i<moldyn->count;i++) {
+		if(atom[i].r.x>=dim->x/2||-atom[i].r.x>dim->x/2) {
+			printf("FATAL: atom %d: x: %.20f (%.20f)\n",
+			       i,atom[i].r.x,dim->x/2);
+			printf("diagnostic:\n");
+			printf("-----------\natom.r.x:\n");
+			for(j=0;j<8;j++) {
+				memcpy(&byte,(u8 *)(&(atom[i].r.x))+j,1);
+				for(k=0;k<8;k++)
+					printf("%d%c",
+					((byte)&(1<<k))?1:0,
+					(k==7)?'\n':'|');
+			}
+			printf("---------------\nx=dim.x/2:\n");
+			for(j=0;j<8;j++) {
+				memcpy(&byte,(u8 *)(&x)+j,1);
+				for(k=0;k<8;k++)
+					printf("%d%c",
+					((byte)&(1<<k))?1:0,
+					(k==7)?'\n':'|');
+			}
+			if(atom[i].r.x==x) printf("the same!\n");
+			else printf("different!\n");
+		}
+		if(atom[i].r.y>=dim->y/2||-atom[i].r.y>dim->y/2)
+			printf("FATAL: atom %d: y: %.20f (%.20f)\n",
+			       i,atom[i].r.y,dim->y/2);
+		if(atom[i].r.z>=dim->z/2||-atom[i].r.z>dim->z/2)
+			printf("FATAL: atom %d: z: %.20f (%.20f)\n",
+			       i,atom[i].r.z,dim->z/2);
 	}
 
 	return 0;
 }
 
-/* lennard jones potential & force for one sort of atoms */
- 
-int lennard_jones(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc) {
-
-	t_lj_params *params;
-	t_3dvec force,distance;
-	double d,h1,h2;
-	double eps,sig6,sig12;
-
-	params=moldyn->pot2b_params;
-	eps=params->epsilon4;
-	sig6=params->sigma6;
-	sig12=params->sigma12;
-
-	v3_sub(&distance,&(ai->r),&(aj->r));
-	if(bc) check_per_bound(moldyn,&distance);
-	d=v3_absolute_square(&distance);	/* 1/r^2 */
-	if(d<=moldyn->cutoff_square) {
-		d=1.0/d;			/* 1/r^2 */
-		h2=d*d; 			/* 1/r^4 */
-		h2*=d;	 			/* 1/r^6 */
-		h1=h2*h2; 			/* 1/r^12 */
-		/* energy is eps*..., but we will add this twice ... */
-		moldyn->energy+=0.5*eps*(sig12*h1-sig6*h2);
-		h2*=d;				/* 1/r^8 */
-		h1*=d;				/* 1/r^14 */
-		h2*=6*sig6;
-		h1*=12*sig12;
-		d=+h1-h2;
-		d*=eps;
-		v3_scale(&force,&distance,d);
-		v3_add(&(ai->f),&(ai->f),&force);
+/*
+ * restore function
+ */
+
+int moldyn_read_save_file(t_moldyn *moldyn,char *file) {
+
+	int fd;
+	int cnt,size;
+
+	fd=open(file,O_RDONLY);
+	if(fd<0) {
+		perror("[moldyn] load save file open");
+		return fd;
+	}
+
+	size=sizeof(t_moldyn);
+
+	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);
+
+	moldyn->atom=(t_atom *)malloc(size);
+	if(moldyn->atom==NULL) {
+		perror("[moldyn] load save file malloc (atoms)");
+		return -1;
+	}
+
+	while(size) {
+		cnt=read(fd,moldyn->atom,size);
+		if(cnt<0) {
+			perror("[moldyn] load save file read (atoms)");
+			return cnt;
+		}
+		size-=cnt;
 	}
 
+	// hooks etc ...
+
 	return 0;
 }
 
-/*
- * tersoff potential & force for 2 sorts of atoms
- */
+int moldyn_load(t_moldyn *moldyn) {
 
-/* create mixed terms from parameters and set them */
-int tersoff_mult_complete_params(t_tersoff_mult_params *p) {
-
-	printf("[moldyn] tersoff parameter completion\n");
-	p->Smixed=sqrt(p->S[0]*p->S[1]);
-	p->Rmixed=sqrt(p->R[0]*p->R[1]);
-	p->Amixed=sqrt(p->A[0]*p->A[1]);
-	p->Bmixed=sqrt(p->B[0]*p->B[1]);
-	p->lambda_m=0.5*(p->lambda[0]+p->lambda[1]);
-	p->mu_m=0.5*(p->mu[0]+p->mu[1]);
-
-	printf("[moldyn] tersoff mult parameter info:\n");
-	printf("  S (m)  | %.12f | %.12f | %.12f\n",p->S[0],p->S[1],p->Smixed);
-	printf("  R (m)  | %.12f | %.12f | %.12f\n",p->R[0],p->R[1],p->Rmixed);
-	printf("  A (eV) | %f | %f | %f\n",p->A[0]/EV,p->A[1]/EV,p->Amixed/EV);
-	printf("  B (eV) | %f | %f | %f\n",p->B[0]/EV,p->B[1]/EV,p->Bmixed/EV);
-	printf("  lambda | %f | %f | %f\n",p->lambda[0],p->lambda[1],
-	                                  p->lambda_m);
-	printf("  mu     | %f | %f | %f\n",p->mu[0],p->mu[1],p->mu_m);
-	printf("  beta   | %.10f | %.10f\n",p->beta[0],p->beta[1]);
-	printf("  n      | %f | %f\n",p->n[0],p->n[1]);
-	printf("  c      | %f | %f\n",p->c[0],p->c[1]);
-	printf("  d      | %f | %f\n",p->d[0],p->d[1]);
-	printf("  h      | %f | %f\n",p->h[0],p->h[1]);
-	printf("  chi    | %f \n",p->chi);
+	// later ...
 
 	return 0;
 }
 
-/* tersoff 1 body part */
-int tersoff_mult_1bp(t_moldyn *moldyn,t_atom *ai) {
-
-	int num;
-	t_tersoff_mult_params *params;
-	t_tersoff_exchange *exchange;
-	
-	num=ai->bnum;
-	params=moldyn->pot1b_params;
-	exchange=&(params->exchange);
+/*
+ * post processing functions
+ */
 
-	/*
-	 * simple: point constant parameters only depending on atom i to
-	 *         their right values
-	 */
+int get_line(int fd,char *line,int max) {
 
-	exchange->beta=&(params->beta[num]);
-	exchange->n=&(params->n[num]);
-	exchange->c=&(params->c[num]);
-	exchange->d=&(params->d[num]);
-	exchange->h=&(params->h[num]);
+	int count,ret;
 
-	exchange->betan=pow(*(exchange->beta),*(exchange->n));
-	exchange->n_betan=*(exchange->n)*exchange->betan;
-	exchange->c2=params->c[num]*params->c[num];
-	exchange->d2=params->d[num]*params->d[num];
-	exchange->c2d2=exchange->c2/exchange->d2;
+	count=0;
 
-	return 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;
+	}
 }
-	
-/* tersoff 2 body part */
-int tersoff_mult_2bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc) {
-
-	t_tersoff_mult_params *params;
-	t_tersoff_exchange *exchange;
-	t_3dvec dist_ij,force;
-	double d_ij;
-	double A,B,R,S,lambda,mu;
-	double f_r,df_r;
-	double f_c,df_c;
-	int num;
-	double s_r;
-	double arg;
-	double scale;
 
-	params=moldyn->pot2b_params;
-	num=ai->bnum;
-	exchange=&(params->exchange);
+int pair_correlation_init(t_moldyn *moldyn,double dr) {
 
-	exchange->run3bp=0;
-	exchange->run2bp_post=0;
 	
-	/*
-	 * we need: f_c, df_c, f_r, df_r
-	 *
-	 * therefore we need: R, S, A, lambda
-	 */
+	return 0;
+}
 
-	v3_sub(&dist_ij,&(ai->r),&(aj->r));
+int calculate_pair_correlation(t_moldyn *moldyn,double dr,void *ptr) {
 
-	if(bc) check_per_bound(moldyn,&dist_ij);
+	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;
 
-	d_ij=v3_norm(&dist_ij);
+	lc=&(moldyn->lc);
 
-	/* save for use in 3bp */
-	exchange->d_ij=d_ij;
-	exchange->dist_ij=dist_ij;
-	exchange->d_ij2=d_ij*d_ij;
+	slots=moldyn->cutoff/dr;
+	o=2*slots;
 
-	/* constants */
-	if(num==aj->bnum) {
-		S=params->S[num];
-		R=params->R[num];
-		A=params->A[num];
-		B=params->B[num];
-		lambda=params->lambda[num];
-		mu=params->mu[num];
-		params->exchange.chi=1.0;
+	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 {
-		S=params->Smixed;
-		R=params->Rmixed;
-		A=params->Amixed;
-		B=params->Bmixed;
-		lambda=params->lambda_m;
-		mu=params->mu_m;
-		params->exchange.chi=params->chi;
+		stat=(double *)malloc(3*slots*sizeof(double));
+		if(stat==NULL) {
+			perror("[moldyn] pair correlation malloc");
+			return -1;
+		}
 	}
 
-	if(d_ij>S)
-		return 0;
-
-	f_r=A*exp(-lambda*d_ij);
-	df_r=-lambda*f_r/d_ij;
+	memset(stat,0,3*slots*sizeof(double));
 
-	/* f_a, df_a calc + save for later use */
-	exchange->f_a=-B*exp(-mu*d_ij);
-	exchange->df_a=-mu*exchange->f_a/d_ij;
+	link_cell_init(moldyn,VERBOSE);
 
-	if(d_ij<R) {
-		/* f_c = 1, df_c = 0 */
-		f_c=1.0;
-		df_c=0.0;
-		v3_scale(&force,&dist_ij,df_r);
-	}
-	else {
-		s_r=S-R;
-		arg=M_PI*(d_ij-R)/s_r;
-		f_c=0.5+0.5*cos(arg);
-		df_c=-0.5*sin(arg)*(M_PI/(s_r*d_ij));
-		scale=df_c*f_r+df_r*f_c;
-		v3_scale(&force,&dist_ij,scale);
-	}
+	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);
+
+		/* brand of atom i */
+		ibrand=itom[i].brand;
+	
+		for(j=0;j<27;j++) {
 
-	/* add forces */
-	v3_add(&(ai->f),&(ai->f),&force);
-	/* energy is 0.5 f_r f_c ... */
-	moldyn->energy+=(0.5*f_r*f_c);
+			bc=(j<lc->dnlc)?0:1;
 
-	/* save for use in 3bp */
-	exchange->f_c=f_c;
-	exchange->df_c=df_c;
+#ifdef STATIC_LISTS
+			p=0;
 
-	/* enable the run of 3bp function and 2bp post processing */
-	exchange->run3bp=1;
-	exchange->run2bp_post=1;
+			while(neighbour[j][p]!=0) {
 
-	/* reset 3bp sums */
-	exchange->sum1_3bp=0.0;
-	exchange->sum2_3bp=0.0;
-	v3_zero(&(exchange->db_ij));
+				jtom=&(moldyn->atom[neighbour[j][p]]);
+				p++;
+#else
+			this=&(neighbour[j]);
+			list_reset_f(this);
 
-	return 0;
-}
+			if(this->start==NULL)
+				continue;
 
-/* tersoff 2 body post part */
+			do {
 
-int tersoff_mult_post_2bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc) {
+				jtom=this->current->data;
+#endif
+				/* only count pairs once,
+				 * skip same atoms */
+				if(itom[i].tag>=jtom->tag)
+					continue;
 
-	/* here we have to allow for the 3bp sums */
+				/*
+				 * pair correlation calc
+				 */
 
-	t_tersoff_mult_params *params;
-	t_tersoff_exchange *exchange;
+				/* distance */
+				v3_sub(&dist,&(jtom->r),&(itom[i].r));
+				if(bc) check_per_bound(moldyn,&dist);
+				d=v3_absolute_square(&dist);
 
-	t_3dvec force,temp,*db_ij,*dist_ij;
-	double db_ij_scale1,db_ij_scale2;
-	double b_ij;
-	double f_c,df_c,f_a,df_a;
-	double chi,betan;
-	double help;
-	double n;
+				/* ignore if greater or equal cutoff */
+				if(d>=moldyn->cutoff_square)
+					continue;
 
-	params=moldyn->pot2b_params;
-	exchange=&(params->exchange);
+				/* fill the slots */
+				d=sqrt(d);
+				s=(int)(d/dr);
 
-	/* we do not run if f_c_ij was dtected to be 0! */
-	if(!(exchange->run2bp_post))
-		return 0;
+				/* should never happen but it does 8) -
+				 * related to -ffloat-store problem! */
+				if(s>=slots) s=slots-1;
 
-	db_ij=&(exchange->db_ij);
-	f_c=exchange->f_c;
-	df_c=exchange->df_c;
-	f_a=exchange->f_a;
-	df_a=exchange->df_a;
-	betan=exchange->betan;
-	n=*(exchange->n);
-	chi=exchange->chi;
-	dist_ij=&(exchange->dist_ij);
+				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
+		}
+	}
 
-	db_ij_scale1=(1+betan*exchange->sum1_3bp);
-	db_ij_scale2=(exchange->n_betan*exchange->sum2_3bp);
-	help=pow(db_ij_scale1,-1.0/(2*n)-1);
-	b_ij=chi*db_ij_scale1*help;
-	db_ij_scale1=-chi/(2*n)*help;
+	/* 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;
+	}
+	*/
 
-	/* db_ij part */
-	v3_scale(db_ij,db_ij,(db_ij_scale1*db_ij_scale2));
-	v3_scale(db_ij,db_ij,f_a);
+	if(ptr==NULL) {
+		/* todo: store/print pair correlation function */
+		free(stat);
+	}
 
-	/* df_a part */
-	v3_scale(&temp,dist_ij,b_ij*df_a);
+	free(moldyn->atom);
 
-	/* db_ij + df_a part */
-	v3_add(&force,&temp,db_ij);
-	v3_scale(&force,&force,f_c);
+	link_cell_shutdown(moldyn);
 
-	/* df_c part */
-	v3_scale(&temp,dist_ij,f_a*b_ij*df_c);
+	return 0;
+}
 
-	/* add energy of 3bp sum */
-	moldyn->energy+=(0.5*f_c*b_ij*f_a);
+int analyze_bonds(t_moldyn *moldyn) {
 
-	/* add force of 3bp calculation (all three parts) */
-	v3_add(&(ai->f),&temp,&force);
+	
+	
 
 	return 0;
 }
 
-/* tersoff 3 body part */
-
-int tersoff_mult_3bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,t_atom *ak,u8 bc) {
-
-	t_tersoff_mult_params *params;
-	t_tersoff_exchange *exchange;
-	t_3dvec dist_ij,dist_ik,dist_jk;
-	t_3dvec temp,force;
-	double R,S,s_r;
-	double d_ij,d_ij2,d_ik,d_jk;
-	double f_c,df_c,f_a,df_a;
-	double f_c_ik,df_c_ik,arg;
-	double n,c,d,h;
-	double c2,d2,c2d2;
-	double numer,denom;
-	double theta,cos_theta,sin_theta;
-	double d_theta,d_theta1,d_theta2;
-	double h_cos,d2_h_cos2;
-	double frac,bracket,bracket_n_1,bracket_n;
-	double g;
-	int num;
-
-	params=moldyn->pot3b_params;
-	num=ai->bnum;
-	exchange=&(params->exchange);
-
-	if(!(exchange->run3bp))
-		return 0;
+/*
+ * visualization code
+ */
 
-	/*
-	 * we need: f_c, d_fc, b_ij, db_ij, f_a, df_a
-	 *
-	 * we got f_c, df_c, f_a, df_a from 2bp calculation
-	 */
+int visual_init(t_moldyn *moldyn,char *filebase) {
 
-	d_ij=exchange->d_ij;
-	d_ij2=exchange->d_ij2;
-	dist_ij=exchange->dist_ij;
+	strncpy(moldyn->vis.fb,filebase,128);
 
-	f_a=params->exchange.f_a;
-	df_a=params->exchange.df_a;
+	return 0;
+}
 
-	f_c=exchange->f_c;
-	df_c=exchange->df_c;
-	
-	/* d_ij is <= S, as we didn't return so far! */
+int visual_atoms(t_moldyn *moldyn) {
 
-	/*
-	 * calc of b_ij (scalar) and db_ij (vector)
-	 *
-	 * - for b_ij: chi, beta, f_c_ik, w(=1), c, d, h, n, cos_theta
-	 *
-	 * - for db_ij: d_theta, sin_theta, cos_theta, f_c_ik, df_c_ik,
-	 *              w_ik,
-	 *
-	 */
+	int i,j,fd;
+ 	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;
+
+	v=&(moldyn->vis);
+	dim.x=v->dim.x;
+	dim.y=v->dim.y;
+	dim.z=v->dim.z;
+	atom=moldyn->atom;
+	lc=&(moldyn->lc);
 
-	v3_sub(&dist_ik,&(ai->r),&(ak->r));
-	if(bc) check_per_bound(moldyn,&dist_ik);
-	d_ik=v3_norm(&dist_ik);
+	help=(dim.x+dim.y);
 
-	/* constants for f_c_ik calc */
-	if(num==ak->bnum) {
-		R=params->R[num];
-		S=params->S[num];
-	}
-	else {
-		R=params->Rmixed;
-		S=params->Smixed;
+	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) {
+		perror("open visual save file fd");
+		return -1;
 	}
 
-	/* calc of f_c_ik */
-	if(d_ik>S) {
-		f_c_ik=0.0;
-		df_c_ik=0.0;
-	}
-	else if(d_ik<R) {
-		f_c_ik=1.0;
-		df_c_ik=0.0;
-	}
-	else {
-		s_r=S-R;
-		arg=M_PI*(d_ik-R)/s_r;
-		f_c_ik=0.5+0.5*cos(arg);
-		df_c_ik=-0.5*sin(arg)*(M_PI/(s_r*d_ik));
-	}
-	
-	v3_sub(&dist_jk,&(aj->r),&(ak->r));
-	if(bc) check_per_bound(moldyn,&dist_jk);
-	d_jk=v3_norm(&dist_jk);
-
-	/* get exchange data */
-	n=*(exchange->n);
-	c=*(exchange->c);
-	d=*(exchange->d);
-	h=*(exchange->h);
-	c2=exchange->c2;
-	d2=exchange->d2;
-	c2d2=exchange->c2d2;
-
-	numer=d_ij2+d_ik*d_ik-d_jk*d_jk;
-	denom=2*d_ij*d_ik;
-	cos_theta=numer/denom;
-	/* prefere law of cosines, dot product -> nan (often) */
-	//cos_theta=v3_scalar_product(&dist_ij,&dist_ik)/(d_ij*d_ik);
-	sin_theta=sqrt(1.0-(cos_theta*cos_theta));
-	theta=acos(cos_theta);
-	d_theta=(-1.0/sqrt(1.0-cos_theta*cos_theta))/(denom*denom);
-	d_theta1=2*denom-numer*2*d_ik/d_ij;
-	d_theta2=2*denom-numer*2*d_ij/d_ik;
-	d_theta1*=d_theta;
-	d_theta2*=d_theta;
-
-	h_cos=(h-cos_theta);
-	d2_h_cos2=d2+(h_cos*h_cos);
-
-	frac=c2/(d2_h_cos2);
-	g=1.0+c2d2-frac;
-
-	if(f_c_ik==0.0) {
-		bracket=0.0;
-		bracket_n_1=0.0;
-		bracket_n=0.0;
-		//printf("Foo -> 0: ");
-	}
-	else {
-		bracket=f_c_ik*g;
-		bracket_n_1=pow(bracket,n-1.0);
-		bracket_n=bracket_n_1*bracket;
-		//printf("Foo -> 1: ");
-	}
-//printf("%.15f %.15f %.15f\n",bracket_n_1,bracket_n,bracket);
+	/* write the actual data file */
 
-	/* calc of db_ij and the 2 sums */
-	exchange->sum1_3bp+=bracket_n;
-	exchange->sum2_3bp+=bracket_n_1;
+	// povray header
+	dprintf(fd,"# [P] %d %07.f <%f,%f,%f>\n",
+	        moldyn->count,moldyn->time,help/40.0,help/40.0,-0.8*help);
 
-	/* derivation of theta */
-	v3_scale(&force,&dist_ij,d_theta1);
-	v3_scale(&temp,&dist_ik,d_theta2);
-	v3_add(&force,&force,&temp);
+	// atomic configuration
+	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
+		}
+	}
 
-	/* part 1 of db_ij */
-	v3_scale(&force,&force,sin_theta*2*h_cos*f_c_ik*frac/d2_h_cos2);
+	// boundaries
+	if(dim.x) {
+		dprintf(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",
+		        -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",
+		        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",
+		        -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",
+		        -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",
+		        -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",
+		        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",
+		        -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",
+		        -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",
+		        -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",
+		        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",
+		        dim.x/2,dim.y/2,dim.z/2,
+		        dim.x/2,dim.y/2,-dim.z/2);
+	}
 
-	/* part 2 of db_ij */
-	v3_scale(&temp,&dist_ik,df_c_ik*g);
+	close(fd);
 
-	/* sum up and add to db_ij */
-	v3_add(&temp,&temp,&force);
-	v3_add(&(exchange->db_ij),&(exchange->db_ij),&temp);
-				
 	return 0;
 }