X-Git-Url: https://hackdaworld.org/gitweb/?a=blobdiff_plain;f=moldyn.c;h=433be6824c9663f9bfa745ca0b82d08b566abd2b;hb=refs%2Fheads%2Forigin;hp=dae975cedcd6a0b0b4baf41e26ff572a1046ab87;hpb=296a35b943e922173ce648ec76a4472e287af108;p=physik%2Fposic.git

diff --git a/moldyn.c b/moldyn.c
index dae975c..433be68 100644
--- a/moldyn.c
+++ b/moldyn.c
@@ -82,7 +82,7 @@ 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;
 }
@@ -162,30 +162,51 @@ int set_pbc(t_moldyn *moldyn,u8 x,u8 y,u8 z) {
 	return 0;
 }
 
-int set_potential1b(t_moldyn *moldyn,pf_func1b func,void *params) {
+int set_potential1b(t_moldyn *moldyn,pf_func1b func) {
 
 	moldyn->func1b=func;
 
 	return 0;
 }
 
-int set_potential2b(t_moldyn *moldyn,pf_func2b func,void *params) {
+int set_potential2b(t_moldyn *moldyn,pf_func2b func) {
 
 	moldyn->func2b=func;
 
 	return 0;
 }
 
-int set_potential2b_post(t_moldyn *moldyn,pf_func2b_post func,void *params) {
+int set_potential3b_j1(t_moldyn *moldyn,pf_func2b func) {
 
-	moldyn->func2b_post=func;
+	moldyn->func3b_j1=func;
 
 	return 0;
 }
 
-int set_potential3b(t_moldyn *moldyn,pf_func3b func,void *params) {
+int set_potential3b_j2(t_moldyn *moldyn,pf_func2b func) {
 
-	moldyn->func3b=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;
 }
@@ -197,6 +218,14 @@ 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);
@@ -246,6 +275,32 @@ int moldyn_set_log(t_moldyn *moldyn,u8 type,int timer) {
 			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);
@@ -268,18 +323,52 @@ int moldyn_set_log(t_moldyn *moldyn,u8 type,int timer) {
 				perror("[moldyn] report fd open");	
 				return moldyn->rfd;
 			}
-			snprintf(filename,127,"%s/plot.scr",moldyn->vlsdir);
-			moldyn->pfd=open(filename,
-			                 O_WRONLY|O_CREAT|O_EXCL,
-			                 S_IRUSR|S_IWUSR);
-			if(moldyn->pfd<0) {
-				perror("[moldyn] plot fd open");
-				return moldyn->pfd;
+			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);
-			dprintf(moldyn->pfd,plot_script);
-			close(moldyn->pfd);
+			printf("\n");
 			break;
 		default:
 			printf("unknown log type: %02x\n",type);
@@ -294,18 +383,43 @@ int moldyn_log_shutdown(t_moldyn *moldyn) {
 	char sc[256];
 
 	printf("[moldyn] log shutdown\n");
-	if(moldyn->efd) close(moldyn->efd);
+	if(moldyn->efd) {
+		close(moldyn->efd);
+		if(moldyn->rfd) {
+			dprintf(moldyn->rfd,report_energy);
+			snprintf(sc,255,"cd %s && gnuplot e_plot.scr",
+			         moldyn->vlsdir);
+			system(sc);
+		}
+	}
 	if(moldyn->mfd) close(moldyn->mfd);
+	if(moldyn->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 && gnuplot plot.scr",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 && pdflatex report",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));
@@ -318,11 +432,11 @@ 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;
 
@@ -344,24 +458,33 @@ 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);
@@ -389,6 +512,9 @@ int create_lattice(t_moldyn *moldyn,u8 type,double lc,int element,double mass,
 		check_per_bound(moldyn,&(atom[ret].r));
 	}
 
+	/* update total system mass */
+	total_mass_calc(moldyn);
+
 	return ret;
 }
 
@@ -530,6 +656,9 @@ int add_atom(t_moldyn *moldyn,int element,double mass,u8 brand,u8 attr,
 	atom[count].tag=count;
 	atom[count].attr=attr;
 
+	/* update total system mass */
+	total_mass_calc(moldyn);
+
 	return 0;
 }
 
@@ -590,6 +719,18 @@ 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 */
@@ -669,39 +810,142 @@ 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;
 
-	/*
-	 * P = 1/(3V) sum_i ( p_i^2 / 2m + f_i r_i )
-	 *
-	 * virial = f_i r_i
-	 */
-
+	/* 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 */
 
-	/* 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;
+	double u_up,u_down,dv;
+	double scale,p;
 	t_atom *store;
 
-	tp=&(moldyn->tp);
+	/*
+	 * 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");
@@ -709,77 +953,44 @@ double thermodynamic_pressure_calc(t_moldyn *moldyn) {
 	}
 
 	/* 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=1.0+moldyn->dv/(moldyn->dim.y*moldyn->dim.z);
-	scale_dim(moldyn,scale,TRUE,0,0);
-	scale_atoms(moldyn,scale,TRUE,0,0);
-	link_cell_shutdown(moldyn);
-	link_cell_init(moldyn,QUIET);
-	potential_force_calc(moldyn);
-	tp->x=(moldyn->energy-u)/moldyn->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=1.0+moldyn->dv/(moldyn->dim.x*moldyn->dim.z);
-	scale_dim(moldyn,scale,0,TRUE,0);
-	scale_atoms(moldyn,scale,0,TRUE,0);
+	/* 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)/moldyn->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=1.0+moldyn->dv/(moldyn->dim.x*moldyn->dim.y);
-	scale_dim(moldyn,scale,0,0,TRUE);
-	scale_atoms(moldyn,scale,0,0,TRUE);
+	/* 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)/moldyn->dv;
-	p+=tp->z*tp->z;
-
-	/* restore atomic configuration + dim */
-	memcpy(moldyn->atom,store,moldyn->count*sizeof(t_atom));
-	moldyn->dim=dim;
-
-	printf("dU/dV komp addiert = %f %f %f\n",tp->x,tp->y,tp->z);
-
-	scale=1.0+pow(moldyn->dv/moldyn->volume,ONE_THIRD);
-
-printf("debug: %f %f\n",moldyn->atom[0].r.x,moldyn->dim.x);
-	scale_dim(moldyn,scale,1,1,1);
-	scale_atoms(moldyn,scale,1,1,1);
-	link_cell_shutdown(moldyn);
-	link_cell_init(moldyn,QUIET);
-	potential_force_calc(moldyn);
-printf("debug: %f %f\n",moldyn->atom[0].r.x,moldyn->dim.x);
-
-	printf("dU/dV einfach = %f\n",((moldyn->energy-u)/moldyn->dv)/ATM);
+	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) {
@@ -788,12 +999,18 @@ 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;
@@ -801,11 +1018,17 @@ 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;
@@ -837,8 +1060,8 @@ 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) {
@@ -866,7 +1089,7 @@ moldyn->debug=scale;
 
 }
 
-double get_e_kin(t_moldyn *moldyn) {
+double e_kin_calc(t_moldyn *moldyn) {
 
 	int i;
 	t_atom *atom;
@@ -880,11 +1103,6 @@ double get_e_kin(t_moldyn *moldyn) {
 	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);
@@ -945,7 +1163,12 @@ 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]));
@@ -980,7 +1203,7 @@ 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]));
 	}
 
@@ -1109,14 +1332,15 @@ int moldyn_set_schedule_hook(t_moldyn *moldyn,set_hook hook,void *hook_params) {
 int moldyn_integrate(t_moldyn *moldyn) {
 
 	int i;
-	unsigned int e,m,s,v;
-	t_3dvec p;
+	unsigned int e,m,s,v,p,t;
+	t_3dvec momentum;
 	t_moldyn_schedule *sched;
 	t_atom *atom;
 	int fd;
 	char dir[128];
 	double ds;
 	double energy_scale;
+	//double tp;
 
 	sched=&(moldyn->schedule);
 	atom=moldyn->atom;
@@ -1129,6 +1353,8 @@ int moldyn_integrate(t_moldyn *moldyn) {
 	m=moldyn->mwrite;
 	s=moldyn->swrite;
 	v=moldyn->vwrite;
+	p=moldyn->pwrite;
+	t=moldyn->twrite;
 
 	/* sqaure of some variables */
 	moldyn->tau_square=moldyn->tau*moldyn->tau;
@@ -1139,6 +1365,9 @@ int moldyn_integrate(t_moldyn *moldyn) {
 
 	/* 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)
@@ -1153,6 +1382,7 @@ int moldyn_integrate(t_moldyn *moldyn) {
 
 	/* zero absolute time */
 	moldyn->time=0.0;
+	moldyn->total_steps=0;
 
 	/* debugging, ignore */
 	moldyn->debug=0;
@@ -1161,7 +1391,8 @@ 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];
@@ -1176,10 +1407,11 @@ 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);
-		//thermodynamic_pressure_calc(moldyn);
+		average_and_fluctuation_calc(moldyn);
 
 		/* p/t scaling */
 		if(moldyn->pt_scale&(T_SCALE_BERENDSEN|T_SCALE_DIRECT))
@@ -1198,9 +1430,26 @@ int moldyn_integrate(t_moldyn *moldyn) {
 		}
 		if(m) {
 			if(!(i%m)) {
-				p=get_total_p(moldyn);
+				momentum=get_total_p(moldyn);
 				dprintf(moldyn->mfd,
-				        "%f %f\n",moldyn->time,v3_norm(&p));
+				        "%f %f %f %f %f\n",moldyn->time,
+				        momentum.x,momentum.y,momentum.z,
+				        v3_norm(&momentum));
+			}
+		}
+		if(p) {
+			if(!(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) {
@@ -1221,24 +1470,35 @@ int moldyn_integrate(t_moldyn *moldyn) {
 			if(!(i%v)) {
 				visual_atoms(&(moldyn->vis),moldyn->time,
 				             moldyn->atom,moldyn->count);
-				printf("\rsched: %d, steps: %d, T: %f, P: %f V: %f",
-				       sched->count,i,
-				       moldyn->t,moldyn->p/ATM,moldyn->volume);
-				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)
+		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;
 
 	}
 
@@ -1316,6 +1576,9 @@ 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++) {
 
@@ -1336,12 +1599,15 @@ 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;
@@ -1356,6 +1622,45 @@ 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]);
@@ -1372,25 +1677,70 @@ 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++) {
 
-				/* copy the neighbour lists */
-				memcpy(neighbour_i2,neighbour_i,
-				       27*sizeof(t_list));
+					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);
+
+				}
+
+				}
+
+				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]);
@@ -1414,37 +1764,53 @@ 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);
 #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;
 }
 
@@ -1466,7 +1832,7 @@ 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) {
@@ -1548,3 +1914,26 @@ int moldyn_bc_check(t_moldyn *moldyn) {
 
 	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;
+	}
+}
+