X-Git-Url: https://www.hackdaworld.org/gitweb/?a=blobdiff_plain;f=moldyn.c;h=997c32ccb24d44607d746d1e6aed87027e9de6cd;hb=b5b47daaa3718c4dec2056fe5147668023575b8e;hp=9a62b9f7c93d5142f5b15d57d099f4ba160604ce;hpb=ea612b88a0588b8f46fafaebf3b37fb46c83c0cf;p=physik%2Fposic.git

diff --git a/moldyn.c b/moldyn.c
index 9a62b9f..997c32c 100644
--- a/moldyn.c
+++ b/moldyn.c
@@ -13,17 +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"
 
+/*
+ * 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) {
 
 	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;
 
@@ -69,6 +126,18 @@ int set_cutoff(t_moldyn *moldyn,double cutoff) {
 	return 0;
 }
 
+int set_bondlen(t_moldyn *moldyn,double b0,double b1,double bm) {
+
+	moldyn->bondlen[0]=b0*b0;
+	moldyn->bondlen[1]=b1*b1;
+	if(bm<0)
+		moldyn->bondlen[2]=b0*b1;
+	else
+		moldyn->bondlen[2]=bm*bm;
+
+	return 0;
+}
+
 int set_temperature(t_moldyn *moldyn,double t_ref) {
 
 	moldyn->t_ref=t_ref;
@@ -82,7 +151,7 @@ int set_pressure(t_moldyn *moldyn,double p_ref) {
 
 	moldyn->p_ref=p_ref;
 
-	printf("[moldyn] pressure [atm]: %f\n",moldyn->p_ref/ATM);
+	printf("[moldyn] pressure [bar]: %f\n",moldyn->p_ref/BAR);
 
 	return 0;
 }
@@ -176,16 +245,37 @@ int set_potential2b(t_moldyn *moldyn,pf_func2b func) {
 	return 0;
 }
 
-int set_potential2b_post(t_moldyn *moldyn,pf_func2b_post func) {
+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->func2b_post=func;
+	moldyn->func3b_j2=func;
 
 	return 0;
 }
 
-int set_potential3b(t_moldyn *moldyn,pf_func3b func) {
+int set_potential3b_j3(t_moldyn *moldyn,pf_func2b func) {
 
-	moldyn->func3b=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;
 }
@@ -197,6 +287,14 @@ int set_potential_params(t_moldyn *moldyn,void *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);
@@ -278,7 +376,7 @@ int moldyn_set_log(t_moldyn *moldyn,u8 type,int timer) {
 			break;
 		case VISUAL_STEP:
 			moldyn->vwrite=timer;
-			ret=visual_init(&(moldyn->vis),moldyn->vlsdir);
+			ret=visual_init(moldyn,moldyn->vlsdir);
 			if(ret<0) {
 				printf("[moldyn] visual init failure\n");
 				return ret;
@@ -294,6 +392,7 @@ int moldyn_set_log(t_moldyn *moldyn,u8 type,int timer) {
 				perror("[moldyn] report fd open");	
 				return moldyn->rfd;
 			}
+			printf("report -> ");
 			if(moldyn->efd) {
 				snprintf(filename,127,"%s/e_plot.scr",
 				         moldyn->vlsdir);
@@ -306,6 +405,7 @@ int moldyn_set_log(t_moldyn *moldyn,u8 type,int timer) {
 				}
 				dprintf(moldyn->epfd,e_plot_script);
 				close(moldyn->epfd);
+				printf("energy ");
 			}
 			if(moldyn->pfd) {
 				snprintf(filename,127,"%s/pressure_plot.scr",
@@ -319,6 +419,7 @@ int moldyn_set_log(t_moldyn *moldyn,u8 type,int timer) {
 				}
 				dprintf(moldyn->ppfd,pressure_plot_script);
 				close(moldyn->ppfd);
+				printf("pressure ");
 			}
 			if(moldyn->tfd) {
 				snprintf(filename,127,"%s/temperature_plot.scr",
@@ -332,9 +433,11 @@ int moldyn_set_log(t_moldyn *moldyn,u8 type,int timer) {
 				}
 				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 type: %02x\n",type);
@@ -378,14 +481,16 @@ int moldyn_log_shutdown(t_moldyn *moldyn) {
 	if(moldyn->rfd) {
 		dprintf(moldyn->rfd,report_end);
 		close(moldyn->rfd);
-		snprintf(sc,255,"cd %s && pdflatex report",moldyn->vlsdir);
+		snprintf(sc,255,"cd %s && pdflatex report >/dev/null 2>&1",
+		         moldyn->vlsdir);
 		system(sc);
-		snprintf(sc,255,"cd %s && pdflatex report",moldyn->vlsdir);
+		snprintf(sc,255,"cd %s && pdflatex report >/dev/null 2>&1",
+		         moldyn->vlsdir);
 		system(sc);
-		snprintf(sc,255,"cd %s && dvipdf report",moldyn->vlsdir);
+		snprintf(sc,255,"cd %s && dvipdf report >/dev/null 2>&1",
+		         moldyn->vlsdir);
 		system(sc);
 	}
-	if(&(moldyn->vis)) visual_tini(&(moldyn->vis));
 
 	return 0;
 }
@@ -395,11 +500,11 @@ int moldyn_log_shutdown(t_moldyn *moldyn) {
  */
 
 int create_lattice(t_moldyn *moldyn,u8 type,double lc,int element,double mass,
-                   u8 attr,u8 brand,int a,int b,int c) {
+                   u8 attr,u8 brand,int a,int b,int c,t_3dvec *origin) {
 
 	int new,count;
 	int ret;
-	t_3dvec origin;
+	t_3dvec orig;
 	void *ptr;
 	t_atom *atom;
 
@@ -421,24 +526,33 @@ int create_lattice(t_moldyn *moldyn,u8 type,double lc,int element,double mass,
 	atom=&(moldyn->atom[count]);
 
 	/* no atoms on the boundaries (only reason: it looks better!) */
-	origin.x=0.5*lc;
-	origin.y=0.5*lc;
-	origin.z=0.5*lc;
+	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,&origin);
+			ret=cubic_init(a,b,c,lc,atom,&orig);
 			break;
 		case FCC:
-			v3_scale(&origin,&origin,0.5);
+			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,&origin);
+			ret=fcc_init(a,b,c,lc,atom,&orig);
 			break;
 		case DIAMOND:
-			v3_scale(&origin,&origin,0.25);
+			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,&origin);
+			ret=diamond_init(a,b,c,lc,atom,&orig);
 			break;
 		default:
 			printf("unknown lattice type (%02x)\n",type);
@@ -464,11 +578,78 @@ int create_lattice(t_moldyn *moldyn,u8 type,double lc,int element,double mass,
 		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 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;
+
+	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;
+	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) {
 
@@ -581,35 +762,6 @@ int diamond_init(int a,int b,int c,double lc,t_atom *atom,t_3dvec *origin) {
 	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;
-
-	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;
-
-	return 0;
-}
-
 int destroy_atoms(t_moldyn *moldyn) {
 
 	if(moldyn->atom) free(moldyn->atom);
@@ -667,6 +819,18 @@ 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 */
@@ -746,38 +910,130 @@ double ideal_gas_law_pressure(t_moldyn *moldyn) {
 	return p;
 }
 
-double pressure_calc(t_moldyn *moldyn) {
+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>
-	 * W = 1/3 sum_i f_i r_i
+	 * with W = 1/3 sum_i f_i r_i (- skipped!)
 	 * virial = sum_i f_i r_i
 	 * 
 	 * => P = (2 Ekin + virial) / (3V)
 	 */
 
-	v=0.0;
-	for(i=0;i<moldyn->count;i++) {
-		virial=&(moldyn->atom[i].virial);
-		v+=(virial->xx+virial->yy+virial->zz);
-	}
+	/* assume up to date virial & up to date kinetic energy */
 
-	/* assume up to date kinetic energy */
-	moldyn->p=2.0*moldyn->ekin+v;
+	/* 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,p;
-	double scale,dv;
+	double u_up,u_down,dv;
+	double scale,p;
 	t_atom *store;
 
 	/*
@@ -785,13 +1041,11 @@ double thermodynamic_pressure_calc(t_moldyn *moldyn) {
 	 *
 	 * => p = - dU/dV
 	 *
-	 * dV: dx,y,z = 0.001 x,y,z
 	 */
 
-	scale=1.00001;
-printf("\n\nP-DEBUG:\n");
+	scale=0.00001;
+	dv=8*scale*scale*scale*moldyn->volume;
 
-	tp=&(moldyn->tp);
 	store=malloc(moldyn->count*sizeof(t_atom));
 	if(store==NULL) {
 		printf("[moldyn] allocating store mem failed\n");
@@ -799,60 +1053,44 @@ printf("\n\nP-DEBUG:\n");
 	}
 
 	/* save unscaled potential energy + atom/dim configuration */
-	u=moldyn->energy;
 	memcpy(store,moldyn->atom,moldyn->count*sizeof(t_atom));
 	dim=moldyn->dim;
 
-	/* derivative with respect to x direction */
-	scale_dim(moldyn,scale,TRUE,0,0);
-	scale_atoms(moldyn,scale,TRUE,0,0);
-	dv=0.00001*moldyn->dim.x*moldyn->dim.y*moldyn->dim.z;
-	link_cell_shutdown(moldyn);
-	link_cell_init(moldyn,QUIET);
-	potential_force_calc(moldyn);
-	tp->x=(moldyn->energy-u)/dv;
-	p=tp->x*tp->x;
-printf("e: %f eV de: %f eV dV: %f A^3\n",moldyn->energy/moldyn->count/EV,(moldyn->energy-u)/moldyn->count/EV,dv);
-
-	/* restore atomic configuration + dim */
-	memcpy(moldyn->atom,store,moldyn->count*sizeof(t_atom));
-	moldyn->dim=dim;
-
-	/* derivative with respect to y direction */
-	scale_dim(moldyn,scale,0,TRUE,0);
-	scale_atoms(moldyn,scale,0,TRUE,0);
-	dv=0.00001*moldyn->dim.y*moldyn->dim.x*moldyn->dim.z;
+	/* 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);
-	tp->y=(moldyn->energy-u)/dv;
-	p+=tp->y*tp->y;
+	u_up=moldyn->energy;
 
 	/* restore atomic configuration + dim */
 	memcpy(moldyn->atom,store,moldyn->count*sizeof(t_atom));
 	moldyn->dim=dim;
 
-	/* derivative with respect to z direction */
-	scale_dim(moldyn,scale,0,0,TRUE);
-	scale_atoms(moldyn,scale,0,0,TRUE);
-	dv=0.00001*moldyn->dim.z*moldyn->dim.x*moldyn->dim.y;
+	/* 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);
-	tp->z=(moldyn->energy-u)/dv;
-	p+=tp->z*tp->z;
+	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 */
-	moldyn->energy=u;
+	potential_force_calc(moldyn);
 
 	link_cell_shutdown(moldyn);
 	link_cell_init(moldyn,QUIET);
 
-	return sqrt(p);
+	return p;
 }
 
 double get_pressure(t_moldyn *moldyn) {
@@ -861,12 +1099,18 @@ double get_pressure(t_moldyn *moldyn) {
 
 }
 
-int scale_dim(t_moldyn *moldyn,double scale,u8 x,u8 y,u8 z) {
+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;
@@ -874,11 +1118,17 @@ int scale_dim(t_moldyn *moldyn,double scale,u8 x,u8 y,u8 z) {
 	return 0;
 }
 
-int scale_atoms(t_moldyn *moldyn,double scale,u8 x,u8 y,u8 z) {
+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;
@@ -910,8 +1160,8 @@ int scale_volume(t_moldyn *moldyn) {
 moldyn->debug=scale;
 
 	/* scale the atoms and dimensions */
-	scale_atoms(moldyn,scale,TRUE,TRUE,TRUE);
-	scale_dim(moldyn,scale,TRUE,TRUE,TRUE);
+	scale_atoms(moldyn,SCALE_DIRECT,scale,TRUE,TRUE,TRUE);
+	scale_dim(moldyn,SCALE_DIRECT,scale,TRUE,TRUE,TRUE);
 
 	/* visualize dimensions */
 	if(vdim->x!=0) {
@@ -939,7 +1189,7 @@ moldyn->debug=scale;
 
 }
 
-double get_e_kin(t_moldyn *moldyn) {
+double e_kin_calc(t_moldyn *moldyn) {
 
 	int i;
 	t_atom *atom;
@@ -947,17 +1197,14 @@ double get_e_kin(t_moldyn *moldyn) {
 	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));
+	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 update_e_kin(t_moldyn *moldyn) {
-
-	return(get_e_kin(moldyn));
-}
-
 double get_total_energy(t_moldyn *moldyn) {
 
 	return(moldyn->ekin+moldyn->energy);
@@ -1018,7 +1265,12 @@ int link_cell_init(t_moldyn *moldyn,u8 vol) {
 	if(lc->cells<27)
 		printf("[moldyn] FATAL: less then 27 subcells!\n");
 
-	if(vol) printf("[moldyn] initializing linked cells (%d)\n",lc->cells);
+	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_f(&(lc->subcell[i]));
@@ -1053,7 +1305,7 @@ int link_cell_update(t_moldyn *moldyn) {
 		i=((atom[count].r.x+(moldyn->dim.x/2))/lc->x);
 		j=((atom[count].r.y+(moldyn->dim.y/2))/lc->y);
 		k=((atom[count].r.z+(moldyn->dim.z/2))/lc->z);
-		list_add_immediate_f(&(moldyn->lc.subcell[i+j*nx+k*nx*ny]),
+		list_add_immediate_f(&(lc->subcell[i+j*nx+k*nx*ny]),
 		                     &(atom[count]));
 	}
 
@@ -1190,6 +1442,7 @@ int moldyn_integrate(t_moldyn *moldyn) {
 	char dir[128];
 	double ds;
 	double energy_scale;
+	struct timeval t1,t2;
 	//double tp;
 
 	sched=&(moldyn->schedule);
@@ -1210,11 +1463,14 @@ int moldyn_integrate(t_moldyn *moldyn) {
 	moldyn->tau_square=moldyn->tau*moldyn->tau;
 	moldyn->cutoff_square=moldyn->cutoff*moldyn->cutoff;
 
-	/* energy scaling factor */
-	energy_scale=moldyn->count*EV;
+	/* get current time */
+	gettimeofday(&t1,NULL);
 
 	/* calculate initial forces */
 	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)
@@ -1229,6 +1485,7 @@ int moldyn_integrate(t_moldyn *moldyn) {
 
 	/* zero absolute time */
 	moldyn->time=0.0;
+	moldyn->total_steps=0;
 
 	/* debugging, ignore */
 	moldyn->debug=0;
@@ -1237,13 +1494,17 @@ int moldyn_integrate(t_moldyn *moldyn) {
 	printf("[moldyn] integration start, go get a coffee ...\n");
 
 	/* executing the schedule */
-	for(sched->count=0;sched->count<sched->total_sched;sched->count++) {
+	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];
 
+		/* energy scaling factor (might change!) */
+		energy_scale=moldyn->count*EV;
+
 	/* integration according to schedule */
 
 	for(i=0;i<moldyn->time_steps;i++) {
@@ -1252,10 +1513,11 @@ int moldyn_integrate(t_moldyn *moldyn) {
 		moldyn->integrate(moldyn);
 
 		/* calculate kinetic energy, temperature and pressure */
-		update_e_kin(moldyn);
+		e_kin_calc(moldyn);
 		temperature_calc(moldyn);
+		virial_sum(moldyn);
 		pressure_calc(moldyn);
-		//tp=thermodynamic_pressure_calc(moldyn);
+		average_and_fluctuation_calc(moldyn);
 
 		/* p/t scaling */
 		if(moldyn->pt_scale&(T_SCALE_BERENDSEN|T_SCALE_DIRECT))
@@ -1265,7 +1527,7 @@ int moldyn_integrate(t_moldyn *moldyn) {
 
 		/* check for log & visualization */
 		if(e) {
-			if(!(i%e))
+			if(!(moldyn->total_steps%e))
 				dprintf(moldyn->efd,
 				        "%f %f %f %f\n",
 				        moldyn->time,moldyn->ekin/energy_scale,
@@ -1273,7 +1535,7 @@ int moldyn_integrate(t_moldyn *moldyn) {
 				        get_total_energy(moldyn)/energy_scale);
 		}
 		if(m) {
-			if(!(i%m)) {
+			if(!(moldyn->total_steps%m)) {
 				momentum=get_total_p(moldyn);
 				dprintf(moldyn->mfd,
 				        "%f %f %f %f %f\n",moldyn->time,
@@ -1282,22 +1544,26 @@ int moldyn_integrate(t_moldyn *moldyn) {
 			}
 		}
 		if(p) {
-			if(!(i%p)) {
+			if(!(moldyn->total_steps%p)) {
 				dprintf(moldyn->pfd,
-				        "%f %f\n",moldyn->time,moldyn->p/ATM);
+				        "%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)) {
+			if(!(moldyn->total_steps%t)) {
 				dprintf(moldyn->tfd,
-				        "%f %f\n",moldyn->time,moldyn->t);
+				        "%f %f %f\n",
+				        moldyn->time,moldyn->t,moldyn->t_avg);
 			}
 		}
 		if(s) {
-			if(!(i%s)) {
+			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);
+				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));
@@ -1308,31 +1574,44 @@ int moldyn_integrate(t_moldyn *moldyn) {
 			}	
 		}
 		if(v) {
-			if(!(i%v)) {
-				visual_atoms(&(moldyn->vis),moldyn->time,
-				             moldyn->atom,moldyn->count);
+			if(!(moldyn->total_steps%v)) {
+				visual_atoms(moldyn);
 			}
 		}
 
 		/* display progress */
-		if(!(i%10)) {
-			printf("\rsched: %d, steps: %d, T: %f, P: %f V: %f",
-			       sched->count,i,
-			       moldyn->t,moldyn->p/ATM,moldyn->volume);
-			fflush(stdout);
+		if(!(moldyn->total_steps%10)) {
+			/* get current time */
+			gettimeofday(&t2,NULL);
+
+	printf("\rsched:%d, steps:%d, T:%3.1f/%3.1f P:%4.1f/%4.1f V:%6.1f (%d)",
+	       sched->count,i,
+	       moldyn->t,moldyn->t_avg,
+	       moldyn->p_avg/BAR,moldyn->gp_avg/BAR,
+	       moldyn->volume,
+	       (int)(t2.tv_sec-t1.tv_sec));
+	fflush(stdout);
+
+			/* copy over time */
+			t1=t2;
 		}
 
 		/* increase absolute time */
 		moldyn->time+=moldyn->tau;
+		moldyn->total_steps+=1;
 
 	}
 
 		/* check for hooks */
-		if(sched->hook)
+		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");
+		}
 
-		/* get a new info line */
-		printf("\n");
+		/* increase the schedule counter */
+		sched->count+=1;
 
 	}
 
@@ -1410,6 +1689,9 @@ int potential_force_calc(t_moldyn *moldyn) {
 	/* 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++) {
 
@@ -1430,12 +1712,15 @@ int potential_force_calc(t_moldyn *moldyn) {
 
 	}
 
-	/* get energy,force and virial of every atom */
+	/* 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;
@@ -1450,6 +1735,45 @@ int potential_force_calc(t_moldyn *moldyn) {
 
 		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);
+
+			}
+		}
+
+		/* 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]);
@@ -1466,25 +1790,70 @@ int potential_force_calc(t_moldyn *moldyn) {
 				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);
-				}
+				if(!(jtom->attr&ATOM_ATTR_3BP))
+					continue;
 
-				/* 3 body potential/force */
+				/* reset 3bp run */
+				moldyn->run3bp=1;
 
-				if(!(itom[i].attr&ATOM_ATTR_3BP)||
-				   !(jtom->attr&ATOM_ATTR_3BP))
+				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;
 
-				/* copy the neighbour lists */
-				memcpy(neighbour_i2,neighbour_i,
-				       27*sizeof(t_list));
+						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);
+
+				}
+
+				}
+
+				if(moldyn->func3b_j2)
+					moldyn->func3b_j2(moldyn,
+					                  &(itom[i]),
+					                  jtom,
+					                  bc_ij);
+
+				/* second loop over atoms k */
+				if(moldyn->func3b_k2) {
 
-				/* get neighbours of i */
 				for(k=0;k<27;k++) {
 
 					that=&(neighbour_i2[k]);
@@ -1508,37 +1877,59 @@ int potential_force_calc(t_moldyn *moldyn) {
 						if(ktom==&(itom[i]))
 							continue;
 
-						moldyn->func3b(moldyn,
-						               &(itom[i]),
-						               jtom,
-						               ktom,
-						               bc_ik|bc_ij);
+						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->func2b_post) {
-					moldyn->func2b_post(moldyn,
-					                    &(itom[i]),
-					                    jtom,bc_ij);
+				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
 
 	}
 
 #ifdef DEBUG
-printf("\n\n");
-#endif
-#ifdef VDEBUG
-printf("\n\n");
+	//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;
 }
 
@@ -1560,7 +1951,7 @@ int virial_calc(t_atom *a,t_3dvec *f,t_3dvec *d) {
 }
 
 /*
- * periodic boundayr checking
+ * periodic boundary checking
  */
 
 //inline int check_per_bound(t_moldyn *moldyn,t_3dvec *a) {
@@ -1642,3 +2033,196 @@ int moldyn_bc_check(t_moldyn *moldyn) {
 
 	return 0;
 }
+
+/*
+ * restore function
+ */
+
+int moldyn_load(t_moldyn *moldyn) {
+
+	// later ...
+
+	return 0;
+}
+
+/*
+ * post processing functions
+ */
+
+int get_line(int fd,char *line,int max) {
+
+	int count,ret;
+
+	count=0;
+
+	while(1) {
+		if(count==max) return count;
+		ret=read(fd,line+count,1);
+		if(ret<=0) return ret;
+		if(line[count]=='\n') {
+			line[count]='\0';
+			return count+1;
+		}
+		count+=1;
+	}
+}
+
+int analyze_bonds(t_moldyn *moldyn) {
+
+	
+	
+
+	return 0;
+}
+
+/*
+ * visualization code
+ */
+
+int visual_init(t_moldyn *moldyn,char *filebase) {
+
+	strncpy(moldyn->vis.fb,filebase,128);
+
+	return 0;
+}
+
+int visual_atoms(t_moldyn *moldyn) {
+
+	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;
+	t_list neighbour[27];
+	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);
+
+	help=(dim.x+dim.y);
+
+	sprintf(file,"%s/atomic_conf_%07.f.xyz",v->fb,moldyn->time);
+	fd=open(file,O_WRONLY|O_CREAT|O_TRUNC,S_IRUSR|S_IWUSR);
+	if(fd<0) {
+		perror("open visual save file fd");
+		return -1;
+	}
+
+	/* write the actual data file */
+
+	// 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);
+
+	// 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++) {
+			list_reset_f(&neighbour[j]);
+			if(neighbour[j].start==NULL)
+				continue;
+			bc=j<lc->dnlc?0:1;
+			do {
+				btom=neighbour[j].current->data;
+				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);
+			} while(list_next_f(&neighbour[j])!=L_NO_NEXT_ELEMENT);
+		}
+	}
+
+	// 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);
+	}
+
+	close(fd);
+
+	return 0;
+}
+