X-Git-Url: https://hackdaworld.org/gitweb/?a=blobdiff_plain;f=moldyn.c;h=997c32ccb24d44607d746d1e6aed87027e9de6cd;hb=b5b47daaa3718c4dec2056fe5147668023575b8e;hp=705a28ca43be21b0839c4937e8fe22294c62c309;hpb=57847266c05bc38218bf162efdb08e8dd40894d7;p=physik%2Fposic.git

diff --git a/moldyn.c b/moldyn.c
index 705a28c..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;
@@ -218,6 +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);
@@ -299,7 +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;
@@ -404,14 +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;
 }
@@ -421,11 +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;
 
@@ -447,24 +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);
@@ -490,11 +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) {
 
@@ -607,35 +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);
@@ -693,13 +819,23 @@ 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);
-	moldyn->t_sum+=moldyn->t;
-	moldyn->mean_t=moldyn->t_sum/moldyn->total_steps;
 
 	return moldyn->t;
 }
@@ -774,48 +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);
-	moldyn->p_sum+=moldyn->p;
-	moldyn->mean_p=moldyn->p_sum/moldyn->total_steps;
 
-	/* pressure from 'absolute coordinates' virial */
-	virial=&(moldyn->virial);
-	v=virial->xx+virial->yy+virial->zz;
-	moldyn->gp=2.0*moldyn->ekin+v;
+	/* pressure (absolute coordinates) */
+	moldyn->gp=2.0*moldyn->ekin+moldyn->gv;
 	moldyn->gp/=(3.0*moldyn->volume);
-	moldyn->gp_sum+=moldyn->gp;
-	moldyn->mean_gp=moldyn->gp_sum/moldyn->total_steps;
 
 	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;
 
 	/*
@@ -823,13 +1041,11 @@ double thermodynamic_pressure_calc(t_moldyn *moldyn) {
 	 *
 	 * => p = - dU/dV
 	 *
-	 * dV: dx,y,z = 0.001 x,y,z
 	 */
 
-	scale=1.00000000000001;
-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");
@@ -837,59 +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=0.00000000000001*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;
-
-	/* 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=0.00000000000001*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=0.00000000000001*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) {
@@ -898,12 +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;
@@ -911,11 +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;
@@ -947,8 +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) {
@@ -984,8 +1197,10 @@ double e_kin_calc(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;
 }
@@ -1227,6 +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);
@@ -1247,11 +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)
@@ -1275,13 +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++) {
@@ -1292,9 +1515,9 @@ int moldyn_integrate(t_moldyn *moldyn) {
 		/* calculate kinetic energy, temperature and pressure */
 		e_kin_calc(moldyn);
 		temperature_calc(moldyn);
+		virial_sum(moldyn);
 		pressure_calc(moldyn);
-		//tp=thermodynamic_pressure_calc(moldyn);
-//printf("thermodynamic p: %f %f %f - %f\n",moldyn->tp.x/BAR,moldyn->tp.y/BAR,moldyn->tp.z/BAR,tp/BAR);
+		average_and_fluctuation_calc(moldyn);
 
 		/* p/t scaling */
 		if(moldyn->pt_scale&(T_SCALE_BERENDSEN|T_SCALE_DIRECT))
@@ -1304,7 +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,
@@ -1312,7 +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,
@@ -1321,25 +1544,26 @@ int moldyn_integrate(t_moldyn *moldyn) {
 			}
 		}
 		if(p) {
-			if(!(i%p)) {
+			if(!(moldyn->total_steps%p)) {
 				dprintf(moldyn->pfd,
 				        "%f %f %f %f %f\n",moldyn->time,
-				         moldyn->p/BAR,moldyn->mean_p/BAR,
-				         moldyn->gp/BAR,moldyn->mean_gp/BAR);
+				         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 %f\n",
-				        moldyn->time,moldyn->t,moldyn->mean_t);
+				        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));
@@ -1350,21 +1574,26 @@ 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 %f V: %f",
-			       sched->count,i,
-			       moldyn->mean_t,
-			       moldyn->mean_p/BAR,
-			       moldyn->mean_gp/BAR,
-			       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 */
@@ -1374,11 +1603,15 @@ int moldyn_integrate(t_moldyn *moldyn) {
 	}
 
 		/* 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;
 
 	}
 
@@ -1457,7 +1690,7 @@ int potential_force_calc(t_moldyn *moldyn) {
 	moldyn->energy=0.0;
 
 	/* reset global virial */
-	memset(&(moldyn->virial),0,sizeof(t_virial));
+	memset(&(moldyn->gvir),0,sizeof(t_virial));
 
 	/* reset force, site energy and virial of every atom */
 	for(i=0;i<count;i++) {
@@ -1486,7 +1719,8 @@ int potential_force_calc(t_moldyn *moldyn) {
 
 		/* 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;
@@ -1677,17 +1911,23 @@ int potential_force_calc(t_moldyn *moldyn) {
 	}
 
 #ifdef DEBUG
-	printf("\nATOM 0: %f %f %f\n\n",itom->f.x,itom->f.y,itom->f.z);
+	//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->virial.xx+=moldyn->atom[i].r.x*moldyn->atom[i].f.x;
-		moldyn->virial.yy+=moldyn->atom[i].r.y*moldyn->atom[i].f.y;
-		moldyn->virial.zz+=moldyn->atom[i].r.z*moldyn->atom[i].f.z;
-		moldyn->virial.xy+=moldyn->atom[i].r.y*moldyn->atom[i].f.x;
-		moldyn->virial.xz+=moldyn->atom[i].r.z*moldyn->atom[i].f.x;
-		moldyn->virial.yz+=moldyn->atom[i].r.z*moldyn->atom[i].f.y;
+		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;
@@ -1793,3 +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;
+}
+