X-Git-Url: https://hackdaworld.org/gitweb/?a=blobdiff_plain;f=moldyn.c;h=433be6824c9663f9bfa745ca0b82d08b566abd2b;hb=refs%2Fheads%2Forigin;hp=e02557c38f78d57e3336fff421697de55c571de1;hpb=dc70c570abec4596355df26ff19756658e33e762;p=physik%2Fposic.git

diff --git a/moldyn.c b/moldyn.c
index e02557c..433be68 100644
--- a/moldyn.c
+++ b/moldyn.c
@@ -16,396 +16,1108 @@
 #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"
-
-int moldyn_usage(char **argv) {
-
-	printf("\n%s usage:\n\n",argv[0]);
-	printf("--- general options ---\n");
-	printf("-E <steps> <file> (log total energy)\n");
-	printf("-M <steps> <file> (log total momentum)\n");
-	printf("-D <steps> <file> (dump total information)\n");
-	printf("-S <steps> <filebase> (single save file)\n");
-	printf("-V <steps> <filebase> (rasmol file)\n");
-	printf("--- physics options ---\n");
-	printf("-T <temperature> [K] (%f)\n",MOLDYN_TEMP);
-	printf("-t <timestep tau> [s] (%.15f)\n",MOLDYN_TAU);
-	printf("-C <cutoff radius> [m] (%.15f)\n",MOLDYN_CUTOFF);
-	printf("-R <runs> (%d)\n",MOLDYN_RUNS);
-	printf(" -- integration algo --\n");
-	printf("  -I <number> (%d)\n",MOLDYN_INTEGRATE_DEFAULT);
-	printf("     0: velocity verlet\n");
-	printf(" -- potential --\n");
-	printf("  -P <number> <param1 param2 ...>\n");
-	printf("     0: harmonic oscillator\n");
-	printf("        param1: spring constant\n");
-	printf("        param2: equilibrium distance\n");
-	printf("     1: lennard jones\n");
-	printf("        param1: epsilon\n");
-	printf("        param2: sigma\n");
-	printf("\n");
+int moldyn_init(t_moldyn *moldyn,int argc,char **argv) {
+
+	printf("[moldyn] init\n");
+
+	memset(moldyn,0,sizeof(t_moldyn));
+
+	rand_init(&(moldyn->random),NULL,1);
+	moldyn->random.status|=RAND_STAT_VERBOSE;
 
 	return 0;
 }
 
-int moldyn_parse_argv(t_moldyn *moldyn,int argc,char **argv) {
+int moldyn_shutdown(t_moldyn *moldyn) {
 
-	int i;
-	t_ho_params hop;
-	t_lj_params ljp;
-	double s,e;
+	printf("[moldyn] shutdown\n");
 
-	memset(moldyn,0,sizeof(t_moldyn));
+	moldyn_log_shutdown(moldyn);
+	link_cell_shutdown(moldyn);
+	rand_close(&(moldyn->random));
+	free(moldyn->atom);
+
+	return 0;
+}
+
+int set_int_alg(t_moldyn *moldyn,u8 algo) {
 
-	/* default values */
-	moldyn->t=MOLDYN_TEMP;
-	moldyn->tau=MOLDYN_TAU;
-	moldyn->time_steps=MOLDYN_RUNS;
-	moldyn->integrate=velocity_verlet;
-	moldyn->potential_force_function=lennard_jones;
-
-	/* parse argv */
-	for(i=1;i<argc;i++) {
-		if(argv[i][0]=='-') {
-			switch(argv[i][1]){
-				case 'E':
-					moldyn->ewrite=atoi(argv[++i]);
-					strncpy(moldyn->efb,argv[++i],64);
-					break;
-				case 'M':
-					moldyn->mwrite=atoi(argv[++i]);
-					strncpy(moldyn->mfb,argv[++i],64);
-					break;
-				case 'D':
-					moldyn->dwrite=atoi(argv[++i]);
-					strncpy(moldyn->dfb,argv[++i],64);
-					break;
-				case 'S':
-					moldyn->swrite=atoi(argv[++i]);
-					strncpy(moldyn->sfb,argv[++i],64);
-					break;
-				case 'V':
-					moldyn->vwrite=atoi(argv[++i]);
-					strncpy(moldyn->vfb,argv[++i],64);
-					break;
-				case 'T':
-					moldyn->t=atof(argv[++i]);
-					break;
-				case 't':
-					moldyn->tau=atof(argv[++i]);
-					break;
-				case 'C':
-					moldyn->cutoff=atof(argv[++i]);
-					break;
-				case 'R':
-					moldyn->time_steps=atoi(argv[++i]);
-					break;
-				case 'I':
-	/* integration algorithm */
-	switch(atoi(argv[++i])) {
+	printf("[moldyn] integration algorithm: ");
+
+	switch(algo) {
 		case MOLDYN_INTEGRATE_VERLET:
 			moldyn->integrate=velocity_verlet;
+			printf("velocity verlet\n");
 			break;
 		default:
-			printf("unknown integration algo %s\n",argv[i]);
-			moldyn_usage(argv);
+			printf("unknown integration algorithm: %02x\n",algo);
+			printf("unknown\n");
 			return -1;
 	}
 
-				case 'P':
-	/* potential + params */
-	switch(atoi(argv[++i])) {
-		case MOLDYN_POTENTIAL_HO:
-			hop.spring_constant=atof(argv[++i]);
-			hop.equilibrium_distance=atof(argv[++i]);
-			moldyn->pot_params=malloc(sizeof(t_ho_params));
-			memcpy(moldyn->pot_params,&hop,sizeof(t_ho_params));
-			moldyn->potential_force_function=harmonic_oscillator;
+	return 0;
+}
+
+int set_cutoff(t_moldyn *moldyn,double cutoff) {
+
+	moldyn->cutoff=cutoff;
+
+	printf("[moldyn] cutoff [A]: %f\n",moldyn->cutoff);
+
+	return 0;
+}
+
+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;
+}
+
+int set_pt_scale(t_moldyn *moldyn,u8 ptype,double ptc,u8 ttype,double ttc) {
+
+	moldyn->pt_scale=(ptype|ttype);
+	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;
+}
+
+int set_dim(t_moldyn *moldyn,double x,double y,double z,u8 visualize) {
+
+	moldyn->dim.x=x;
+	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;
+}
+
+int set_nn_dist(t_moldyn *moldyn,double dist) {
+
+	moldyn->nnd=dist;
+
+	return 0;
+}
+
+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;
+
+	if(y)
+		moldyn->status|=MOLDYN_STAT_PBY;
+
+	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) {
+
+	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) {
+
+	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 moldyn_set_report(t_moldyn *moldyn,char *author,char *title) {
+
+	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;
+
+	printf("[moldyn] set log: ");
+
+	switch(type) {
+		case LOG_TOTAL_ENERGY:
+			moldyn->ewrite=timer;
+			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] energy log fd open");
+				return moldyn->efd;
+			}
+			dprintf(moldyn->efd,"# total energy log file\n");
+			printf("total energy (%d)\n",timer);
 			break;
-		case MOLDYN_POTENTIAL_LJ:
-			e=atof(argv[++i]);
-			s=atof(argv[++i]);
-			ljp.epsilon4=4*e;
-			ljp.sigma6=s*s*s*s*s*s;
-			ljp.sigma12=ljp.sigma6*ljp.sigma6;
-			moldyn->pot_params=malloc(sizeof(t_lj_params));
-			memcpy(moldyn->pot_params,&ljp,sizeof(t_lj_params));
-			moldyn->potential_force_function=lennard_jones;
+		case LOG_TOTAL_MOMENTUM:
+			moldyn->mwrite=timer;
+			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] 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;
+			printf("save file (%d)\n",timer);
+			break;
+		case VISUAL_STEP:
+			moldyn->vwrite=timer;
+			ret=visual_init(&(moldyn->vis),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 potential %s\n",argv[i]);
-			moldyn_usage(argv);
+			printf("unknown log type: %02x\n",type);
 			return -1;
 	}
 
-				default:
-					printf("unknown option %s\n",argv[i]);
-					moldyn_usage(argv);
-					return -1;
-			}
-		} else {
-			moldyn_usage(argv);
-			return -1;
+	return 0;
+}
+
+int moldyn_log_shutdown(t_moldyn *moldyn) {
+
+	char sc[256];
+
+	printf("[moldyn] log shutdown\n");
+	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->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);
+	}
+	if(&(moldyn->vis)) visual_tini(&(moldyn->vis));
 
 	return 0;
 }
 
-int moldyn_log_init(t_moldyn *moldyn) {
+/*
+ * creating lattice functions
+ */
+
+int create_lattice(t_moldyn *moldyn,u8 type,double lc,int element,double mass,
+                   u8 attr,u8 brand,int a,int b,int c,t_3dvec *origin) {
 
-	moldyn->lvstat=0;
-	t_visual *vis;
+	int new,count;
+	int ret;
+	t_3dvec orig;
+	void *ptr;
+	t_atom *atom;
 
-	vis=&(moldyn->vis);
+	new=a*b*c;
+	count=moldyn->count;
 
-	if(moldyn->ewrite) {
-		moldyn->efd=open(moldyn->efb,O_WRONLY|O_CREAT|O_TRUNC);
-		if(moldyn->efd<0) {
-			perror("[moldyn] efd open");
-			return moldyn->efd;
-		}
-		dprintf(moldyn->efd,"# moldyn total energy logfile\n");
-		moldyn->lvstat|=MOLDYN_LVSTAT_TOTAL_E;
+	/* how many atoms do we expect */
+	if(type==CUBIC) new*=1;
+	if(type==FCC) new*=4;
+	if(type==DIAMOND) new*=8;
+
+	/* 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]);
+
+	/* 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;
 	}
 
-	if(moldyn->mwrite) {
-		moldyn->mfd=open(moldyn->mfb,O_WRONLY|O_CREAT|O_TRUNC);
-		if(moldyn->mfd<0) {
-			perror("[moldyn] mfd open");
-			return moldyn->mfd;
+	switch(type) {
+		case CUBIC:
+			set_nn_dist(moldyn,lc);
+			ret=cubic_init(a,b,c,lc,atom,&orig);
+			break;
+		case FCC:
+			if(!origin)
+				v3_scale(&orig,&orig,0.5);
+			set_nn_dist(moldyn,0.5*sqrt(2.0)*lc);
+			ret=fcc_init(a,b,c,lc,atom,&orig);
+			break;
+		case DIAMOND:
+			if(!origin)
+				v3_scale(&orig,&orig,0.25);
+			set_nn_dist(moldyn,0.25*sqrt(3.0)*lc);
+			ret=diamond_init(a,b,c,lc,atom,&orig);
+			break;
+		default:
+			printf("unknown lattice type (%02x)\n",type);
+			return -1;
+	}
+
+	/* debug */
+	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+=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));
+	}
+
+	/* update total system mass */
+	total_mass_calc(moldyn);
+
+	return ret;
+}
+
+/* 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;
 		}
-		dprintf(moldyn->mfd,"# moldyn total momentum logfile\n");
-		moldyn->lvstat|=MOLDYN_LVSTAT_TOTAL_M;
+		r.x+=lc;
 	}
 
-	if(moldyn->swrite)
-		moldyn->lvstat|=MOLDYN_LVSTAT_SAVE;
+	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) {
 
-	if(moldyn->dwrite) {
-		moldyn->dfd=open(moldyn->dfb,O_WRONLY|O_CREAT|O_TRUNC);
-                if(moldyn->dfd<0) {
-			perror("[moldyn] dfd open");
-			return moldyn->dfd;
+	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;
 		}
-		write(moldyn->dfd,moldyn,sizeof(t_moldyn));
-		moldyn->lvstat|=MOLDYN_LVSTAT_DUMP;
+		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;
 	}
 
-	if((moldyn->vwrite)&&(vis)) {
-		moldyn->visual=vis;
-		visual_init(vis,moldyn->vfb);
-		moldyn->lvstat|=MOLDYN_LVSTAT_VISUAL;
+	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 add_atom(t_moldyn *moldyn,int element,double mass,u8 brand,u8 attr,
+             t_3dvec *r,t_3dvec *v) {
+
+	t_atom *atom;
+	void *ptr;
+	int count;
+	
+	atom=moldyn->atom;
+	count=(moldyn->count)++;
+
+	ptr=realloc(atom,(count+1)*sizeof(t_atom));
+	if(!ptr) {
+		perror("[moldyn] realloc (add atom)");
+		return -1;
 	}
+	moldyn->atom=ptr;
 
-	moldyn->lvstat|=MOLDYN_LVSTAT_INITIALIZED;
+	atom=moldyn->atom;
+	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;
+
+	/* update total system mass */
+	total_mass_calc(moldyn);
 
 	return 0;
 }
 
-int moldyn_log_shutdown(t_moldyn *moldyn) {
+int destroy_atoms(t_moldyn *moldyn) {
 
-	if(moldyn->efd) close(moldyn->efd);
-	if(moldyn->mfd) close(moldyn->efd);
-	if(moldyn->dfd) close(moldyn->efd);
-	if(moldyn->visual) visual_tini(moldyn->visual);
+	if(moldyn->atom) free(moldyn->atom);
 
 	return 0;
 }
 
-int moldyn_init(t_moldyn *moldyn,int argc,char **argv) {
+int thermal_init(t_moldyn *moldyn,u8 equi_init) {
 
-	int ret;
+	/*
+	 * - gaussian distribution of velocities
+	 * - zero total momentum
+	 * - velocity scaling (E = 3/2 N k T), E: kinetic energy
+	 */
 
-	ret=moldyn_parse_argv(moldyn,argc,argv);
-	if(ret<0) return ret;
+	int i;
+	double v,sigma;
+	t_3dvec p_total,delta;
+	t_atom *atom;
+	t_random *random;
 
-	ret=moldyn_log_init(moldyn);
-	if(ret<0) return ret;
+	atom=moldyn->atom;
+	random=&(moldyn->random);
 
-	rand_init(&(moldyn->random),NULL,1);
-	moldyn->random.status|=RAND_STAT_VERBOSE;
+	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++) {
+		sigma=sqrt(2.0*K_BOLTZMANN*moldyn->t_ref/atom[i].mass);
+		/* x direction */
+		v=sigma*rand_get_gauss(random);
+		atom[i].v.x=v;
+		p_total.x+=atom[i].mass*v;
+		/* y direction */
+		v=sigma*rand_get_gauss(random);
+		atom[i].v.y=v;
+		p_total.y+=atom[i].mass*v;
+		/* z direction */
+		v=sigma*rand_get_gauss(random);
+		atom[i].v.z=v;
+		p_total.z+=atom[i].mass*v;
+	}
 
-	moldyn->status=0;
+	/* zero total momentum */
+	v3_scale(&p_total,&p_total,1.0/moldyn->count);
+	for(i=0;i<moldyn->count;i++) {
+		v3_scale(&delta,&p_total,1.0/atom[i].mass);
+		v3_sub(&(atom[i].v),&(atom[i].v),&delta);
+	}
+
+	/* velocity scaling */
+	scale_velocity(moldyn,equi_init);
 
 	return 0;
 }
 
-int moldyn_shutdown(t_moldyn *moldyn) {
+double total_mass_calc(t_moldyn *moldyn) {
 
-	moldyn_log_shutdown(moldyn);
-	rand_close(&(moldyn->random));
-	free(moldyn->atom);
+	int i;
 
-	return 0;
+	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;
 }
 
-int create_lattice(unsigned char type,int element,double mass,double lc,
-                   int a,int b,int c,t_atom **atom) {
+double get_temperature(t_moldyn *moldyn) {
 
+	return moldyn->t;
+}
+
+int scale_velocity(t_moldyn *moldyn,u8 equi_init) {
+
+	int i;
+	double e,scale;
+	t_atom *atom;
 	int count;
-	int ret;
-	t_3dvec origin;
 
-	count=a*b*c;
+	atom=moldyn->atom;
 
-	if(type==FCC) count*=4;
-	if(type==DIAMOND) count*=8;
+	/*
+	 * - velocity scaling (E = 3/2 N k T), E: kinetic energy
+	 */
 
-	*atom=malloc(count*sizeof(t_atom));
-	if(*atom==NULL) {
-		perror("malloc (atoms)");
-		return -1;
+	/* get kinetic energy / temperature & count involved atoms */
+	e=0.0;
+	count=0;
+	for(i=0;i<moldyn->count;i++) {
+		if((equi_init&TRUE)||(atom[i].attr&ATOM_ATTR_HB)) {
+			e+=atom[i].mass*v3_absolute_square(&(atom[i].v));
+			count+=1;
+		}
+	}
+	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) {
+			thermal_init(moldyn,equi_init);
+			return 0;
+		}
+		else
+			return 0; /* no scaling needed */
 	}
 
-	v3_zero(&origin);
 
-	switch(type) {
-		case FCC:
-			ret=fcc_init(a,b,c,lc,*atom,&origin);
-			break;
-		case DIAMOND:
-			ret=diamond_init(a,b,c,lc,*atom,&origin);
-			break;
-		default:
-			printf("unknown lattice type (%02x)\n",type);
-			return -1;
+	/* get scaling factor */
+	scale=moldyn->t_ref/moldyn->t;
+	if(equi_init&TRUE)
+		scale*=2.0;
+	else
+		if(moldyn->pt_scale&T_SCALE_BERENDSEN)
+			scale=1.0+(scale-1.0)/moldyn->t_tc;
+	scale=sqrt(scale);
+
+	/* velocity scaling */
+	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);
 	}
 
-	/* debug */
-	if(ret!=count) {
-		printf("ok, there is something wrong ...\n");
-		printf("calculated -> %d atoms\n",count);
-		printf("created -> %d atoms\n",ret);
+	return 0;
+}
+
+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;
+	double v;
+	t_virial *virial;
+
+	/* 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;
+
+	/* global virial (absolute coordinates) */
+	virial=&(moldyn->gvir);
+	moldyn->gv=virial->xx+virial->yy+virial->zz;
+
+	return moldyn->virial;
+}
+
+double pressure_calc(t_moldyn *moldyn) {
+
+	/*
+	 * 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)
+	 */
+
+	/* assume up to date virial & up to date kinetic energy */
+
+	/* pressure (atom virials) */
+	moldyn->p=2.0*moldyn->ekin+moldyn->virial;
+	moldyn->p/=(3.0*moldyn->volume);
+
+	/* pressure (absolute coordinates) */
+	moldyn->gp=2.0*moldyn->ekin+moldyn->gv;
+	moldyn->gp/=(3.0*moldyn->volume);
+
+	return moldyn->p;
+}
+
+int average_and_fluctuation_calc(t_moldyn *moldyn) {
+
+	if(moldyn->total_steps<moldyn->avg_skip)
+		return 0;
+
+	int denom=moldyn->total_steps+1-moldyn->avg_skip;
+
+	/* assume up to date energies, temperature, pressure etc */
+
+	/* 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);
+
+	/* 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);
+
+	/* temperature */
+	moldyn->t_sum+=moldyn->t;
+	moldyn->t_avg=moldyn->t_sum/denom;
+
+	/* 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;
+
+	/* 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 0;
+}
+
+int get_heat_capacity(t_moldyn *moldyn) {
+
+	double temp2,ighc;
+
+	/* averages needed for heat capacity calc */
+	if(moldyn->total_steps<moldyn->avg_skip)
+		return 0;
+
+	/* (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);
+
+	/* ideal gas contribution */
+	ighc=3.0*moldyn->count*K_BOLTZMANN/2.0;
+	printf("  ideal gas contribution: %f\n",
+	       ighc/moldyn->mass*KILOGRAM/JOULE);
+
+	/* specific heat for nvt ensemble */
+	moldyn->c_v_nvt=moldyn->dv2_avg/(K_BOLTZMANN*temp2)+ighc;
+	moldyn->c_v_nvt/=moldyn->mass;
+
+	/* 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;
+
+	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)));
+
+	return 0;
+}
+
+double thermodynamic_pressure_calc(t_moldyn *moldyn) {
+
+	t_3dvec dim,*tp;
+	double u_up,u_down,dv;
+	double scale,p;
+	t_atom *store;
+
+	/*
+	 * dU = - p dV
+	 *
+	 * => p = - dU/dV
+	 *
+	 */
+
+	scale=0.00001;
+	dv=8*scale*scale*scale*moldyn->volume;
+
+	store=malloc(moldyn->count*sizeof(t_atom));
+	if(store==NULL) {
+		printf("[moldyn] allocating store mem failed\n");
 		return -1;
 	}
 
-	while(count) {
-		(*atom)[count-1].element=element;
-		(*atom)[count-1].mass=mass;
-		count-=1;
-	}
+	/* save unscaled potential energy + atom/dim configuration */
+	memcpy(store,moldyn->atom,moldyn->count*sizeof(t_atom));
+	dim=moldyn->dim;
+
+	/* 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;
 
-	return ret;
+	/* restore energy */
+	potential_force_calc(moldyn);
+
+	link_cell_shutdown(moldyn);
+	link_cell_init(moldyn,QUIET);
+
+	return p;
 }
 
-int destroy_lattice(t_atom *atom) {
+double get_pressure(t_moldyn *moldyn) {
 
-	if(atom) free(atom);
+	return moldyn->p;
 
-	return 0;
 }
 
-int thermal_init(t_moldyn *moldyn) {
-
-	/*
-	 * - gaussian distribution of velocities
-	 * - zero total momentum
-	 * - velocity scaling (E = 3/2 N k T), E: kinetic energy
-	 */
+int scale_dim(t_moldyn *moldyn,u8 dir,double scale,u8 x,u8 y,u8 z) {
 
-	int i;
-	double v,sigma;
-	t_3dvec p_total,delta;
-	t_atom *atom;
-	t_random *random;
+	t_3dvec *dim;
 
-	atom=moldyn->atom;
-	random=&(moldyn->random);
+	dim=&(moldyn->dim);
 
-	/* gaussian distribution of velocities */
-	v3_zero(&p_total);
-	for(i=0;i<moldyn->count;i++) {
-		sigma=sqrt(2.0*K_BOLTZMANN*moldyn->t/atom[i].mass);
-		/* x direction */
-		v=sigma*rand_get_gauss(random);
-		atom[i].v.x=v;
-		p_total.x+=atom[i].mass*v;
-		/* y direction */
-		v=sigma*rand_get_gauss(random);
-		atom[i].v.y=v;
-		p_total.y+=atom[i].mass*v;
-		/* z direction */
-		v=sigma*rand_get_gauss(random);
-		atom[i].v.z=v;
-		p_total.z+=atom[i].mass*v;
-	}
+	if(dir==SCALE_UP)
+		scale=1.0+scale;
 
-	/* zero total momentum */
-	v3_scale(&p_total,&p_total,1.0/moldyn->count);
-	for(i=0;i<moldyn->count;i++) {
-		v3_scale(&delta,&p_total,1.0/atom[i].mass);
-		v3_sub(&(atom[i].v),&(atom[i].v),&delta);
-	}
+	if(dir==SCALE_DOWN)
+		scale=1.0-scale;
 
-	/* velocity scaling */
-	scale_velocity(moldyn);
+	if(x) dim->x*=scale;
+	if(y) dim->y*=scale;
+	if(z) dim->z*=scale;
 
 	return 0;
 }
 
-int scale_velocity(t_moldyn *moldyn) {
+int scale_atoms(t_moldyn *moldyn,u8 dir,double scale,u8 x,u8 y,u8 z) {
 
 	int i;
-	double e,c;
-	t_atom *atom;
+	t_3dvec *r;
 
-	atom=moldyn->atom;
+	if(dir==SCALE_UP)
+		scale=1.0+scale;
 
-	/*
-	 * - velocity scaling (E = 3/2 N k T), E: kinetic energy
-	 */
-	e=0.0;
-	for(i=0;i<moldyn->count;i++)
-		e+=0.5*atom[i].mass*v3_absolute_square(&(atom[i].v));
-	c=sqrt((2.0*e)/(3.0*moldyn->count*K_BOLTZMANN*moldyn->t));
-	for(i=0;i<moldyn->count;i++)
-		v3_scale(&(atom[i].v),&(atom[i].v),(1.0/c));
+	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;
 }
 
-double get_e_kin(t_atom *atom,int count) {
+int scale_volume(t_moldyn *moldyn) {
 
-	int i;
-	double e;
+	t_3dvec *dim,*vdim;
+	double scale;
+	t_linkcell *lc;
 
-	e=0.0;
+	vdim=&(moldyn->vis.dim);
+	dim=&(moldyn->dim);
+	lc=&(moldyn->lc);
 
-	for(i=0;i<count;i++) {
-		e+=0.5*atom[i].mass*v3_absolute_square(&(atom[i].v));
+	/* 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;
 
-	return e;
-}
+	/* 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;
+	}
 
-double get_e_pot(t_moldyn *moldyn) {
+	return 0;
 
-	return moldyn->energy;
 }
 
-double get_total_energy(t_moldyn *moldyn) {
+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++)
+		moldyn->ekin+=0.5*atom[i].mass*v3_absolute_square(&(atom[i].v));
 
-	double e;
+	return moldyn->ekin;
+}
 
-	e=get_e_kin(moldyn->atom,moldyn->count);
-	e+=get_e_pot(moldyn);
+double get_total_energy(t_moldyn *moldyn) {
 
-	return e;
+	return(moldyn->ekin+moldyn->energy);
 }
 
-t_3dvec get_total_p(t_atom *atom, int count) {
+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<count;i++) {
+	for(i=0;i<moldyn->count;i++) {
 		v3_scale(&p,&(atom[i].v),atom[i].mass);
 		v3_add(&p_total,&p_total,&p);
 	}
@@ -413,15 +1125,13 @@ t_3dvec get_total_p(t_atom *atom, int count) {
 	return p_total;
 }
 
-double estimate_time_step(t_moldyn *moldyn,double nn_dist,double t) {
+double estimate_time_step(t_moldyn *moldyn,double nn_dist) {
 
 	double tau;
 
-	tau=0.05*nn_dist/(sqrt(3.0*K_BOLTZMANN*t/moldyn->atom[0].mass));
-	tau*=1.0E-9;
-	if(tau<moldyn->tau)
-		printf("[moldyn] warning: time step  (%f > %.15f)\n",
-		       moldyn->tau,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;	
 }
@@ -432,16 +1142,13 @@ double estimate_time_step(t_moldyn *moldyn,double nn_dist,double t) {
 
 /* linked list / cell method */
 
-int link_cell_init(t_moldyn *moldyn) {
+int link_cell_init(t_moldyn *moldyn,u8 vol) {
 
 	t_linkcell *lc;
 	int i;
 
 	lc=&(moldyn->lc);
 
-	/* list log fd */
-	lc->listfd=open("/dev/null",O_WRONLY);
-
 	/* partitioning the md cell */
 	lc->nx=moldyn->dim.x/moldyn->cutoff;
 	lc->x=moldyn->dim.x/lc->nx;
@@ -453,11 +1160,18 @@ int link_cell_init(t_moldyn *moldyn) {
 	lc->cells=lc->nx*lc->ny*lc->nz;
 	lc->subcell=malloc(lc->cells*sizeof(t_list));
 
-	printf("initializing linked cells (%d)\n",lc->cells);
+	if(lc->cells<27)
+		printf("[moldyn] FATAL: less then 27 subcells!\n");
+
+	if(vol) {
+		printf("[moldyn] initializing linked cells (%d)\n",lc->cells);
+		printf("  x: %d x %f A\n",lc->nx,lc->x);
+		printf("  y: %d x %f A\n",lc->ny,lc->y);
+		printf("  z: %d x %f A\n",lc->nz,lc->z);
+	}
 
 	for(i=0;i<lc->cells;i++)
-		//list_init(&(lc->subcell[i]),1);
-		list_init(&(lc->subcell[i]),lc->listfd);
+		list_init_f(&(lc->subcell[i]));
 
  	link_cell_update(moldyn);
 	
@@ -467,26 +1181,30 @@ int link_cell_init(t_moldyn *moldyn) {
 int link_cell_update(t_moldyn *moldyn) {
 
 	int count,i,j,k;
-	int nx,ny,nz;
+	int nx,ny;
 	t_atom *atom;
 	t_linkcell *lc;
+	double x,y,z;
 
 	atom=moldyn->atom;
 	lc=&(moldyn->lc);
 
 	nx=lc->nx;
 	ny=lc->ny;
-	nz=lc->nz;
+
+	x=moldyn->dim.x/2;
+	y=moldyn->dim.y/2;
+	z=moldyn->dim.z/2;
 
 	for(i=0;i<lc->cells;i++)
-		list_destroy(&(moldyn->lc.subcell[i]));
+		list_destroy_f(&(lc->subcell[i]));
 	
 	for(count=0;count<moldyn->count;count++) {
-		i=(atom[count].r.x+(moldyn->dim.x/2))/lc->x;
-		j=(atom[count].r.y+(moldyn->dim.y/2))/lc->y;
-		k=(atom[count].r.z+(moldyn->dim.z/2))/lc->z;
-		list_add_immediate_ptr(&(moldyn->lc.subcell[i+j*nx+k*nx*ny]),
-		                       &(atom[count]));
+		i=((atom[count].r.x+(moldyn->dim.x/2))/lc->x);
+		j=((atom[count].r.y+(moldyn->dim.y/2))/lc->y);
+		k=((atom[count].r.z+(moldyn->dim.z/2))/lc->z);
+		list_add_immediate_f(&(lc->subcell[i+j*nx+k*nx*ny]),
+		                     &(atom[count]));
 	}
 
 	return 0;
@@ -500,7 +1218,7 @@ int link_cell_neighbour_index(t_moldyn *moldyn,int i,int j,int k,t_list *cell) {
 	int ci,cj,ck;
 	int nx,ny,nz;
 	int x,y,z;
-	unsigned char bx,by,bz;
+	u8 bx,by,bz;
 
 	lc=&(moldyn->lc);
 	nx=lc->nx;
@@ -510,7 +1228,6 @@ int link_cell_neighbour_index(t_moldyn *moldyn,int i,int j,int k,t_list *cell) {
 	count2=27;
 	a=nx*ny;
 
-
 	cell[0]=lc->subcell[i+j*nx+k*a];
 	for(ci=-1;ci<=1;ci++) {
 		bx=0;
@@ -544,7 +1261,9 @@ int link_cell_neighbour_index(t_moldyn *moldyn,int i,int j,int k,t_list *cell) {
 		}
 	}
 
-	return count2;
+	lc->dnlc=count1;
+
+	return count1;
 }
 
 int link_cell_shutdown(t_moldyn *moldyn) {
@@ -555,10 +1274,50 @@ 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]));
+		list_destroy_f(&(moldyn->lc.subcell[i]));
+
+	free(lc->subcell);
+
+	return 0;
+}
+
+int moldyn_add_schedule(t_moldyn *moldyn,int runs,double tau) {
+
+	int count;
+	void *ptr;
+	t_moldyn_schedule *schedule;
+
+	schedule=&(moldyn->schedule);
+	count=++(schedule->total_sched);
 
-	if(lc->listfd) close(lc->listfd);
+	ptr=realloc(schedule->runs,count*sizeof(int));
+	if(!ptr) {
+		perror("[moldyn] realloc (runs)");
+		return -1;
+	}
+	schedule->runs=ptr;
+	schedule->runs[count-1]=runs;
+
+	ptr=realloc(schedule->tau,count*sizeof(double));
+	if(!ptr) {
+		perror("[moldyn] realloc (tau)");
+		return -1;
+	}
+	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,set_hook hook,void *hook_params) {
 
+	moldyn->schedule.hook=hook;
+	moldyn->schedule.hook_params=hook_params;
+	
 	return 0;
 }
 
@@ -573,81 +1332,174 @@ int link_cell_shutdown(t_moldyn *moldyn) {
 int moldyn_integrate(t_moldyn *moldyn) {
 
 	int i;
-	unsigned int e,m,s,d,v;
-	t_3dvec p;
-
+	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;
+	//double tp;
+
+	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;
-	d=moldyn->dwrite;
 	v=moldyn->vwrite;
-
-	if(!(moldyn->lvstat&MOLDYN_LVSTAT_INITIALIZED)) {
-		printf("[moldyn] warning, lv system not initialized\n");
-		return -1;
-	}
+	p=moldyn->pwrite;
+	t=moldyn->twrite;
 
 	/* sqaure of some variables */
 	moldyn->tau_square=moldyn->tau*moldyn->tau;
 	moldyn->cutoff_square=moldyn->cutoff*moldyn->cutoff;
 
+	/* energy scaling factor */
+	energy_scale=moldyn->count*EV;
+
 	/* calculate initial forces */
-	moldyn->potential_force_function(moldyn);
+	potential_force_calc(moldyn);
+#ifdef DEBUG
+return 0;
+#endif
+
+	/* 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)
+		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");
+	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");
+
+	/* zero absolute time */
+	moldyn->time=0.0;
+	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=sched->tau[sched->count];
+		moldyn->tau_square=moldyn->tau*moldyn->tau;
+		moldyn->time_steps=sched->runs[sched->count];
+
+	/* integration according to schedule */
 
 	for(i=0;i<moldyn->time_steps;i++) {
 
 		/* 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);
+		if(moldyn->pt_scale&(P_SCALE_BERENDSEN|P_SCALE_DIRECT))
+			scale_volume(moldyn);
+
 		/* check for log & visualization */
 		if(e) {
 			if(!(i%e))
 				dprintf(moldyn->efd,
-				        "%.15f %.45f\n",i*moldyn->tau,
-				        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->atom,moldyn->count);
+				momentum=get_total_p(moldyn);
 				dprintf(moldyn->mfd,
-				        "%.15f %.45f\n",i*moldyn->tau,
-				        v3_norm(&p));
+				        "%f %f %f %f %f\n",moldyn->time,
+				        momentum.x,momentum.y,momentum.z,
+				        v3_norm(&momentum));
+			}
+		}
+		if(p) {
+			if(!(i%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(!(i%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);
+				snprintf(dir,128,"%s/s-%07.f.save",
+				         moldyn->vlsdir,moldyn->time);
+				fd=open(dir,O_WRONLY|O_TRUNC|O_CREAT);
 				if(fd<0) perror("[moldyn] save fd open");
 				else {
 					write(fd,moldyn,sizeof(t_moldyn));
 					write(fd,moldyn->atom,
 					      moldyn->count*sizeof(t_atom));
 				}
+				close(fd);
 			}	
 		}
-		if(d) {
-			if(!(i%d))
-				write(moldyn->dfd,moldyn->atom,
-				      moldyn->count*sizeof(t_atom));
-
-		}
 		if(v) {
 			if(!(i%v)) {
-				visual_atoms(moldyn->visual,i*moldyn->tau,
+				visual_atoms(&(moldyn->vis),moldyn->time,
 				             moldyn->atom,moldyn->count);
-				printf("\rsteps: %d",i);
-				fflush(stdout);
 			}
 		}
+
+		/* display progress */
+		if(!(i%10)) {
+	printf("\rsched:%d, steps:%d, T:%3.1f/%3.1f P:%4.1f/%4.1f V:%6.1f",
+	       sched->count,i,
+	       moldyn->t,moldyn->t_avg,
+	       moldyn->p_avg/BAR,moldyn->p/BAR,
+	       moldyn->volume);
+	fflush(stdout);
+		}
+
+		/* increase absolute time */
+		moldyn->time+=moldyn->tau;
+		moldyn->total_steps+=1;
+
+	}
+
+		/* check for hooks */
+		if(sched->hook) {
+			printf("\n ## schedule hook %d/%d start ##\n",
+			       sched->count+1,sched->total_sched-1);
+			sched->hook(moldyn,sched->hook_params);
+			printf(" ## schedule hook end ##\n");
+		}
+
+		/* increase the schedule counter */
+		sched->count+=1;
+
 	}
 
 	return 0;
@@ -658,7 +1510,7 @@ 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;
 
@@ -669,14 +1521,15 @@ 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);
-		v3_per_bound(&(atom[i].r),&(moldyn->dim));
+		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);
 	}
 
@@ -684,10 +1537,10 @@ int velocity_verlet(t_moldyn *moldyn) {
 	link_cell_update(moldyn);
 
 	/* forces depending on chosen potential */
-	moldyn->potential_force_function(moldyn);
+	potential_force_calc(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);
 	}
@@ -698,250 +1551,389 @@ int velocity_verlet(t_moldyn *moldyn) {
 
 /*
  *
- * potentials & corresponding forces
+ * potentials & corresponding forces & virial routine
  * 
  */
 
-/* harmonic oscillator potential and force */
+/* generic potential and force calculation */
 
-int harmonic_oscillator(t_moldyn *moldyn) {
+int potential_force_calc(t_moldyn *moldyn) {
 
-	t_ho_params *params;
-	t_atom *atom,*btom;
+	int i,j,k,count;
+	t_atom *itom,*jtom,*ktom;
+	t_virial *virial;
 	t_linkcell *lc;
-	t_list *this,neighbour[27];
-	int i,j,c;
-	int count;
-	t_3dvec force,distance;
-	double d,u;
-	double sc,equi_dist;
-	int ni,nj,nk;
+	t_list neighbour_i[27];
+	t_list neighbour_i2[27];
+	t_list *this,*that;
+	u8 bc_ij,bc_ik;
+	int dnlc;
 
-	params=moldyn->pot_params;
-	atom=moldyn->atom;
-	lc=&(moldyn->lc);
-	sc=params->spring_constant;
-	equi_dist=params->equilibrium_distance;
 	count=moldyn->count;
+	itom=moldyn->atom;
+	lc=&(moldyn->lc);
+
+	/* reset energy */
+	moldyn->energy=0.0;
 
-	/* reset energy counter */
-	u=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(&(atom[i].f));
-
-		/* determine cell + neighbours */
-		ni=(atom[i].r.x+(moldyn->dim.x/2))/lc->x;
-		nj=(atom[i].r.y+(moldyn->dim.y/2))/lc->y;
-		nk=(atom[i].r.z+(moldyn->dim.z/2))/lc->z;
-		c=link_cell_neighbour_index(moldyn,ni,nj,nk,neighbour);
-
-		/*
-		 * processing cell of atom i
-		 * => no need to check for empty list (1 element at minimum)
-		 */
-		this=&(neighbour[0]);
-		list_reset(this);
-		do {
-			btom=this->current->data;
-			if(btom==&(atom[i]))
-				continue;
-			v3_sub(&distance,&(atom[i].r),&(btom->r));
-			d=v3_norm(&distance);
-			if(d<=moldyn->cutoff) {
-				u+=(0.5*sc*(d-equi_dist)*(d-equi_dist));
-				v3_scale(&force,&distance,
-				         -sc*(1.0-(equi_dist/d)));
-				v3_add(&(atom[i].f),&(atom[i].f),&force);
-			}
-		} while(list_next(this)!=L_NO_NEXT_ELEMENT);
+		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;
 
-		/*
-		 * direct neighbour cells
-		 * => no boundary condition check necessary
-		 */
-		for(j=1;j<c;j++) {
-			this=&(neighbour[j]);
-			list_reset(this); /* there might not be a single atom */
-			if(this->start!=NULL) {
+	}
 
-			do {
-				btom=this->current->data;
-				v3_sub(&distance,&(atom[i].r),&(btom->r));
-				d=v3_norm(&distance);
-				if(d<=moldyn->cutoff) {
-					u+=(0.5*sc*(d-equi_dist)*(d-equi_dist));
-					v3_scale(&force,&distance,
-					         -sc*(1.0-(equi_dist/d)));
-					v3_add(&(atom[i].f),&(atom[i].f),
-					       &force);
-				}
-			} while(list_next(this)!=L_NO_NEXT_ELEMENT);
+	/* 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)
+			if(moldyn->func1b)
+				moldyn->func1b(moldyn,&(itom[i]));
+
+		if(!(itom[i].attr&(ATOM_ATTR_2BP|ATOM_ATTR_3BP)))
+			continue;
+
+		/* 2 body pair potential/force */
+	
+		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++) {
+
+				this=&(neighbour_i[j]);
+				list_reset_f(this);
+
+				if(this->start==NULL)
+					continue;
+
+				bc_ij=(j<dnlc)?0:1;
+
+				do {
+					jtom=this->current->data;
+
+					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);
+					}
+				} while(list_next_f(this)!=L_NO_NEXT_ELEMENT);
 
 			}
 		}
 
-		/*
-		 * indirect neighbour cells
-		 * => check boundary conditions
-		 */
-		for(j=c;j<27;j++) {
-			this=&(neighbour[j]);
-			list_reset(this); /* check boundary conditions */
-			if(this->start!=NULL) {
+		/* 3 body potential/force */
+
+		if(!(itom[i].attr&ATOM_ATTR_3BP))
+			continue;
+
+		/* copy the neighbour lists */
+		memcpy(neighbour_i2,neighbour_i,27*sizeof(t_list));
+
+		/* second loop over atoms j */
+		for(j=0;j<27;j++) {
+
+			this=&(neighbour_i[j]);
+			list_reset_f(this);
+
+			if(this->start==NULL)
+				continue;
+
+			bc_ij=(j<dnlc)?0:1;
 
 			do {
-				btom=this->current->data;
-				v3_sub(&distance,&(atom[i].r),&(btom->r));
-				v3_per_bound(&distance,&(moldyn->dim));
-				d=v3_norm(&distance);
-				if(d<=moldyn->cutoff) {
-					u+=(0.5*sc*(d-equi_dist)*(d-equi_dist));
-					v3_scale(&force,&distance,
-					         -sc*(1.0-(equi_dist/d)));
-					v3_add(&(atom[i].f),&(atom[i].f),
-					       &force);
+				jtom=this->current->data;
+
+				if(jtom==&(itom[i]))
+					continue;
+
+				if(!(jtom->attr&ATOM_ATTR_3BP))
+					continue;
+
+				/* reset 3bp run */
+				moldyn->run3bp=1;
+
+				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;
+			
+				/* first loop over atoms k */
+				if(moldyn->func3b_k1) {
+
+				for(k=0;k<27;k++) {
+
+					that=&(neighbour_i2[k]);
+					list_reset_f(that);
+					
+					if(that->start==NULL)
+						continue;
+
+					bc_ik=(k<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_k1(moldyn,
+						                  &(itom[i]),
+						                  jtom,
+						                  ktom,
+						                  bc_ik|bc_ij);
+
+					} while(list_next_f(that)!=\
+					        L_NO_NEXT_ELEMENT);
+
 				}
-			} while(list_next(this)!=L_NO_NEXT_ELEMENT);
 
-			}
+				}
+
+				if(moldyn->func3b_j2)
+					moldyn->func3b_j2(moldyn,
+					                  &(itom[i]),
+					                  jtom,
+					                  bc_ij);
+
+				/* second loop over atoms k */
+				if(moldyn->func3b_k2) {
+
+				for(k=0;k<27;k++) {
+
+					that=&(neighbour_i2[k]);
+					list_reset_f(that);
+					
+					if(that->start==NULL)
+						continue;
+
+					bc_ik=(k<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_k2(moldyn,
+						                  &(itom[i]),
+						                  jtom,
+						                  ktom,
+						                  bc_ik|bc_ij);
+
+					} while(list_next_f(that)!=\
+					        L_NO_NEXT_ELEMENT);
+
+				}
+				
+				}
+
+				/* 2bp post function */
+				if(moldyn->func3b_j3) {
+					moldyn->func3b_j3(moldyn,
+					                  &(itom[i]),
+					                  jtom,bc_ij);
+				}
+					
+			} while(list_next_f(this)!=L_NO_NEXT_ELEMENT);
+		
 		}
+		
+#ifdef DEBUG
+	//printf("\n\n");
+#endif
+#ifdef VDEBUG
+	printf("\n\n");
+#endif
+
 	}
 
-	moldyn->energy=0.5*u;
+#ifdef DEBUG
+	printf("\nATOM 0: %f %f %f\n\n",itom->f.x,itom->f.y,itom->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;
 }
 
-/* lennard jones potential & force for one sort of atoms */
- 
-int lennard_jones(t_moldyn *moldyn) {
+/*
+ * virial calculation
+ */
 
-	t_lj_params *params;
-	t_atom *atom,*btom;
-	t_linkcell *lc;
-	t_list *this,neighbour[27];
-	int i,j,c;
-	int count;
-	t_3dvec force,distance;
-	double d,h1,h2,u;
-	double eps,sig6,sig12;
-	int ni,nj,nk;
+//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) {
 
-	params=moldyn->pot_params;
-	atom=moldyn->atom;
-	lc=&(moldyn->lc);
-	count=moldyn->count;
-	eps=params->epsilon4;
-	sig6=params->sigma6;
-	sig12=params->sigma12;
+	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;
 
-	/* reset energy counter */
-	u=0.0;
+	return 0;
+}
 
-	for(i=0;i<count;i++) {
-		/* reset force */
-		v3_zero(&(atom[i].f));
-
-		/* determine cell + neighbours */
-		ni=(atom[i].r.x+(moldyn->dim.x/2))/lc->x;
-		nj=(atom[i].r.y+(moldyn->dim.y/2))/lc->y;
-		nk=(atom[i].r.z+(moldyn->dim.z/2))/lc->z;
-		c=link_cell_neighbour_index(moldyn,ni,nj,nk,neighbour);
-
-		/* processing cell of atom i */
-		this=&(neighbour[0]);
-		list_reset(this); /* list has 1 element at minimum */
-		do {
-			btom=this->current->data;
-			if(btom==&(atom[i]))
-				continue;
-			v3_sub(&distance,&(atom[i].r),&(btom->r));
-			d=v3_absolute_square(&distance);	/* 1/r^2 */
-			if(d<=moldyn->cutoff_square) {
-				d=1.0/d;	/* 1/r^2 */
-				h1=d*d; 	/* 1/r^4 */
-				h2*=d;	 	/* 1/r^6 */
-				h1=h2*h2; 	/* 1/r^12 */
-				u+=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(&(atom[i].f),&(atom[i].f),&force);
-			}
-		} while(list_next(this)!=L_NO_NEXT_ELEMENT);
+/*
+ * periodic boundary checking
+ */
 
-		/* neighbours not doing boundary condition overflow */
-		for(j=1;j<c;j++) {
-			this=&(neighbour[j]);
-			list_reset(this); /* there might not be a single atom */
-			if(this->start!=NULL) {
+//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;
+	t_3dvec *dim;
 
-			do {
-				btom=this->current->data;
-				v3_sub(&distance,&(atom[i].r),&(btom->r));
-				d=v3_absolute_square(&distance); /* r^2 */
-				if(d<=moldyn->cutoff_square) {
-					d=1.0/d;	/* 1/r^2 */
-					h1=d*d; 	/* 1/r^4 */
-					h2*=d;	 	/* 1/r^6 */
-					h1=h2*h2; 	/* 1/r^12 */
-					u+=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(&(atom[i].f),&(atom[i].f),
-					       &force);
-				}
-			} while(list_next(this)!=L_NO_NEXT_ELEMENT);
-				
-			}
-		}
+	dim=&(moldyn->dim);
 
-		/* neighbours due to boundary conditions */
-		for(j=c;j<27;j++) {
-			this=&(neighbour[j]);
-			list_reset(this); /* check boundary conditions */
-			if(this->start!=NULL) {
+	x=dim->x/2;
+	y=dim->y/2;
+	z=dim->z/2;
 
-			do {
-				btom=this->current->data;
-				v3_sub(&distance,&(atom[i].r),&(btom->r));
-				v3_per_bound(&distance,&(moldyn->dim));
-				d=v3_absolute_square(&distance); /* r^2 */
-				if(d<=moldyn->cutoff_square) {
-					d=1.0/d;	/* 1/r^2 */
-					h1=d*d; 	/* 1/r^4 */
-					h2*=d; 		/* 1/r^6 */
-					h1=h2*h2; 	/* 1/r^12 */
-					u+=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(&(atom[i].f),&(atom[i].f),
-					       &force);
-				}
-			} while(list_next(this)!=L_NO_NEXT_ELEMENT);
+	if(moldyn->status&MOLDYN_STAT_PBX) {
+		if(a->x>=x) a->x-=dim->x;
+		else if(-a->x>x) a->x+=dim->x;
+	}
+	if(moldyn->status&MOLDYN_STAT_PBY) {
+		if(a->y>=y) a->y-=dim->y;
+		else if(-a->y>y) a->y+=dim->y;
+	}
+	if(moldyn->status&MOLDYN_STAT_PBZ) {
+		if(a->z>=z) a->z-=dim->z;
+		else if(-a->z>z) a->z+=dim->z;
+	}
+
+	return 0;
+}
+        
+/*
+ * debugging / critical check functions
+ */
+
+int moldyn_bc_check(t_moldyn *moldyn) {
+
+	t_atom *atom;
+	t_3dvec *dim;
+	int i;
+	double x;
+	u8 byte;
+	int j,k;
+
+	atom=moldyn->atom;
+	dim=&(moldyn->dim);
+	x=dim->x/2;
 
+	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);
 	}
 
-	moldyn->energy=0.5*u;
-	
 	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;
+	}
+}
+