X-Git-Url: https://hackdaworld.org/gitweb/?a=blobdiff_plain;f=moldyn.c;h=817a72788b45f2572258873aaa8ca64cace0397f;hb=f3e4193447ac49a8953515910d4b4e6ce2c7608b;hp=c21f59f516df771c5153db16232bd844db6064a8;hpb=115ab83cedba54af2d165b8900781b98c5326b55;p=physik%2Fposic.git

diff --git a/moldyn.c b/moldyn.c
index c21f59f..817a727 100644
--- a/moldyn.c
+++ b/moldyn.c
@@ -19,6 +19,8 @@
 
 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);
@@ -30,6 +32,7 @@ int moldyn_init(t_moldyn *moldyn,int argc,char **argv) {
 int moldyn_shutdown(t_moldyn *moldyn) {
 
 	printf("[moldyn] shutdown\n");
+
 	moldyn_log_shutdown(moldyn);
 	link_cell_shutdown(moldyn);
 	rand_close(&(moldyn->random));
@@ -40,12 +43,16 @@ int moldyn_shutdown(t_moldyn *moldyn) {
 
 int set_int_alg(t_moldyn *moldyn,u8 algo) {
 
+	printf("[moldyn] integration algorithm: ");
+
 	switch(algo) {
 		case MOLDYN_INTEGRATE_VERLET:
 			moldyn->integrate=velocity_verlet;
+			printf("velocity verlet\n");
 			break;
 		default:
 			printf("unknown integration algorithm: %02x\n",algo);
+			printf("unknown\n");
 			return -1;
 	}
 
@@ -56,6 +63,8 @@ int set_cutoff(t_moldyn *moldyn,double cutoff) {
 
 	moldyn->cutoff=cutoff;
 
+	printf("[moldyn] cutoff [A]: %f\n",moldyn->cutoff);
+
 	return 0;
 }
 
@@ -63,6 +72,8 @@ int set_temperature(t_moldyn *moldyn,double t_ref) {
 
 	moldyn->t_ref=t_ref;
 
+	printf("[moldyn] temperature: %f\n",moldyn->t_ref);
+
 	return 0;
 }
 
@@ -70,6 +81,8 @@ int set_pressure(t_moldyn *moldyn,double p_ref) {
 
 	moldyn->p_ref=p_ref;
 
+	printf("[moldyn] pressure: %f\n",moldyn->p_ref);
+
 	return 0;
 }
 
@@ -79,6 +92,18 @@ int set_pt_scale(t_moldyn *moldyn,u8 ptype,double ptc,u8 ttype,double ttc) {
 	moldyn->t_tc=ttc;
 	moldyn->p_tc=ptc;
 
+	printf("[moldyn] p/t scaling:\n");
+
+	printf("  p: %s",ptype?"yes":"no ");
+	if(ptype)
+		printf(" | type: %02x | factor: %f",ptype,ptc);
+	printf("\n");
+
+	printf("  t: %s",ttype?"yes":"no ");
+	if(ttype)
+		printf(" | type: %02x | factor: %f",ttype,ttc);
+	printf("\n");
+
 	return 0;
 }
 
@@ -96,12 +121,15 @@ int set_dim(t_moldyn *moldyn,double x,double y,double z,u8 visualize) {
 		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?"on":"off");
+	printf("  visualize simulation box: %s\n",visualize?"yes":"no");
+	printf("  delta volume (pressure calc): %f\n",moldyn->dv);
 
 	return 0;
 }
@@ -115,6 +143,8 @@ int set_nn_dist(t_moldyn *moldyn,double dist) {
 
 int set_pbc(t_moldyn *moldyn,u8 x,u8 y,u8 z) {
 
+	printf("[moldyn] periodic boundary conditions:\n");
+
 	if(x)
 		moldyn->status|=MOLDYN_STAT_PBX;
 
@@ -124,6 +154,10 @@ int set_pbc(t_moldyn *moldyn,u8 x,u8 y,u8 z) {
 	if(z)
 		moldyn->status|=MOLDYN_STAT_PBZ;
 
+	printf("  x: %s\n",x?"yes":"no");
+	printf("  y: %s\n",y?"yes":"no");
+	printf("  z: %s\n",z?"yes":"no");
+
 	return 0;
 }
 
@@ -165,12 +199,22 @@ int moldyn_set_log_dir(t_moldyn *moldyn,char *dir) {
 
 	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;
@@ -183,6 +227,7 @@ int moldyn_set_log(t_moldyn *moldyn,u8 type,int timer) {
 				return moldyn->efd;
 			}
 			dprintf(moldyn->efd,"# total energy log file\n");
+			printf("total energy (%d)\n",timer);
 			break;
 		case LOG_TOTAL_MOMENTUM:
 			moldyn->mwrite=timer;
@@ -195,9 +240,11 @@ int moldyn_set_log(t_moldyn *moldyn,u8 type,int timer) {
 				return moldyn->mfd;
 			}
 			dprintf(moldyn->efd,"# total momentum log file\n");
+			printf("total momentum (%d)\n",timer);
 			break;
 		case SAVE_STEP:
 			moldyn->swrite=timer;
+			printf("save file (%d)\n",timer);
 			break;
 		case VISUAL_STEP:
 			moldyn->vwrite=timer;
@@ -206,9 +253,32 @@ int moldyn_set_log(t_moldyn *moldyn,u8 type,int timer) {
 				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;
+			}
+			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;
+			}
+			dprintf(moldyn->rfd,report_start,
+			        moldyn->rauthor,moldyn->rtitle);
+			dprintf(moldyn->pfd,plot_script);
+			close(moldyn->pfd);
 			break;
 		default:
-			printf("[moldyn] unknown log mechanism: %02x\n",type);
+			printf("unknown log type: %02x\n",type);
 			return -1;
 	}
 
@@ -217,9 +287,23 @@ int moldyn_set_log(t_moldyn *moldyn,u8 type,int timer) {
 
 int moldyn_log_shutdown(t_moldyn *moldyn) {
 
+	char sc[256];
+
 	printf("[moldyn] log shutdown\n");
 	if(moldyn->efd) close(moldyn->efd);
 	if(moldyn->mfd) close(moldyn->mfd);
+	if(moldyn->rfd) {
+		dprintf(moldyn->rfd,report_end);
+		close(moldyn->rfd);
+		snprintf(sc,255,"cd %s && gnuplot plot.scr",moldyn->vlsdir);
+		system(sc);
+		snprintf(sc,255,"cd %s && pdflatex report",moldyn->vlsdir);
+		system(sc);
+		snprintf(sc,255,"cd %s && pdflatex report",moldyn->vlsdir);
+		system(sc);
+		snprintf(sc,255,"cd %s && dvipdf report",moldyn->vlsdir);
+		system(sc);
+	}
 	if(&(moldyn->vis)) visual_tini(&(moldyn->vis));
 
 	return 0;
@@ -242,6 +326,7 @@ int create_lattice(t_moldyn *moldyn,u8 type,double lc,int element,double mass,
 	count=moldyn->count;
 
 	/* how many atoms do we expect */
+	if(type==CUBIC) new*=1;
 	if(type==FCC) new*=4;
 	if(type==DIAMOND) new*=8;
 
@@ -257,8 +342,11 @@ int create_lattice(t_moldyn *moldyn,u8 type,double lc,int element,double mass,
 	v3_zero(&origin);
 
 	switch(type) {
+		case CUBIC:
+			ret=cubic_init(a,b,c,lc,atom,NULL);
+			break;
 		case FCC:
-			ret=fcc_init(a,b,c,lc,atom,&origin);
+			ret=fcc_init(a,b,c,lc,atom,NULL);
 			break;
 		case DIAMOND:
 			ret=diamond_init(a,b,c,lc,atom,&origin);
@@ -292,6 +380,44 @@ int create_lattice(t_moldyn *moldyn,u8 type,double lc,int element,double mass,
 	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++) {
+			for(k=0;k<c;k++) {
+				r.z=o.z;
+				v3_copy(&(atom[count].r),&r);
+				count+=1;
+				r.z+=lc;
+			}
+			r.y+=lc;
+		}
+		r.x+=lc;
+	}
+
+	for(i=0;i<count;i++) {
+		atom[i].r.x-=(a*lc)/2.0;
+		atom[i].r.y-=(b*lc)/2.0;
+		atom[i].r.z-=(c*lc)/2.0;
+	}
+
+	return count;
+}
+
 /* fcc lattice init */
 int fcc_init(int a,int b,int c,double lc,t_atom *atom,t_3dvec *origin) {
 
@@ -429,6 +555,8 @@ int thermal_init(t_moldyn *moldyn,u8 equi_init) {
 	atom=moldyn->atom;
 	random=&(moldyn->random);
 
+	printf("[moldyn] thermal init (equi init: %s)\n",equi_init?"yes":"no");
+
 	/* gaussian distribution of velocities */
 	v3_zero(&p_total);
 	for(i=0;i<moldyn->count;i++) {
@@ -460,6 +588,29 @@ int thermal_init(t_moldyn *moldyn,u8 equi_init) {
 	return 0;
 }
 
+double temperature_calc(t_moldyn *moldyn) {
+
+	double double_ekin;
+	int i;
+	t_atom *atom;
+
+	atom=moldyn->atom;
+
+	double_ekin=0;
+	for(i=0;i<moldyn->count;i++)
+		double_ekin+=atom[i].mass*v3_absolute_square(&(atom[i].v));
+
+	/* kinetic energy = 3/2 N k_B T */
+	moldyn->t=double_ekin/(3.0*K_BOLTZMANN*moldyn->count);
+
+	return moldyn->t;
+}
+
+double get_temperature(t_moldyn *moldyn) {
+
+	return moldyn->t;
+}
+
 int scale_velocity(t_moldyn *moldyn,u8 equi_init) {
 
 	int i;
@@ -478,10 +629,11 @@ int scale_velocity(t_moldyn *moldyn,u8 equi_init) {
 	count=0;
 	for(i=0;i<moldyn->count;i++) {
 		if((equi_init&TRUE)||(atom[i].attr&ATOM_ATTR_HB)) {
-			e+=0.5*atom[i].mass*v3_absolute_square(&(atom[i].v));
+			e+=atom[i].mass*v3_absolute_square(&(atom[i].v));
 			count+=1;
 		}
 	}
+	e*=0.5;
 	if(count!=0) moldyn->t=e/(1.5*count*K_BOLTZMANN);
 	else return 0;	/* no atoms involved in scaling! */
 	
@@ -515,6 +667,157 @@ int scale_velocity(t_moldyn *moldyn,u8 equi_init) {
 	return 0;
 }
 
+double ideal_gas_law_pressure(t_moldyn *moldyn) {
+
+	double p;
+
+	p=moldyn->count*moldyn->t*K_BOLTZMANN/moldyn->volume;
+
+	return p;
+}
+
+double pressure_calc(t_moldyn *moldyn) {
+
+	int i;
+	double v;
+	t_virial *virial;
+
+	v=0.0;
+	for(i=0;i<moldyn->count;i++) {
+		virial=&(moldyn->atom[i].virial);
+		v+=(virial->xx+virial->yy+virial->zz);
+	}
+	v*=ONE_THIRD;
+printf("kieck mal: %f %f %f\n",v,moldyn->count*K_BOLTZMANN*moldyn->t,v/moldyn->count);
+
+	moldyn->p=moldyn->count*K_BOLTZMANN*moldyn->t+v;
+	moldyn->p/=moldyn->volume;
+
+	return moldyn->p;
+}	
+
+double thermodynamic_pressure_calc(t_moldyn *moldyn) {
+
+	t_3dvec dim,*tp;
+	double u,p;
+	double scale;
+	t_atom *store;
+
+	tp=&(moldyn->tp);
+	store=malloc(moldyn->count*sizeof(t_atom));
+	if(store==NULL) {
+		printf("[moldyn] allocating store mem failed\n");
+		return -1;
+	}
+
+	/* 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);
+	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);
+	link_cell_shutdown(moldyn);
+	link_cell_init(moldyn);
+	potential_force_calc(moldyn);
+	tp->y=(moldyn->energy-u)/moldyn->dv;
+	p+=tp->y*tp->y;
+
+	/* 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);
+	link_cell_shutdown(moldyn);
+	link_cell_init(moldyn);
+	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);
+	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);
+
+	/* restore atomic configuration + dim */
+	memcpy(moldyn->atom,store,moldyn->count*sizeof(t_atom));
+	moldyn->dim=dim;
+
+	/* restore energy */
+	moldyn->energy=u;
+
+	link_cell_shutdown(moldyn);
+	link_cell_init(moldyn);
+
+	return sqrt(p);
+}
+
+double get_pressure(t_moldyn *moldyn) {
+
+	return moldyn->p;
+
+}
+
+int scale_dim(t_moldyn *moldyn,double scale,u8 x,u8 y,u8 z) {
+
+	t_3dvec *dim;
+
+	dim=&(moldyn->dim);
+
+	if(x) dim->x*=scale;
+	if(y) dim->y*=scale;
+	if(z) dim->z*=scale;
+
+	return 0;
+}
+
+int scale_atoms(t_moldyn *moldyn,double scale,u8 x,u8 y,u8 z) {
+
+	int i;
+	t_3dvec *r;
+
+	for(i=0;i<moldyn->count;i++) {
+		r=&(moldyn->atom[i].r);
+		if(x) r->x*=scale;
+		if(y) r->y*=scale;
+		if(z) r->z*=scale;
+	}
+
+	return 0;
+}
+
 int scale_volume(t_moldyn *moldyn) {
 
 	t_atom *atom;
@@ -592,11 +895,6 @@ double get_e_kin(t_moldyn *moldyn) {
 	return moldyn->ekin;
 }
 
-double get_e_pot(t_moldyn *moldyn) {
-
-	return moldyn->energy;
-}
-
 double update_e_kin(t_moldyn *moldyn) {
 
 	return(get_e_kin(moldyn));
@@ -659,6 +957,9 @@ int link_cell_init(t_moldyn *moldyn) {
 	lc->cells=lc->nx*lc->ny*lc->nz;
 	lc->subcell=malloc(lc->cells*sizeof(t_list));
 
+	if(lc->cells<27)
+		printf("[moldyn] FATAL: less then 27 subcells!\n");
+
 	printf("[moldyn] initializing linked cells (%d)\n",lc->cells);
 
 	for(i=0;i<lc->cells;i++)
@@ -797,10 +1098,14 @@ int moldyn_add_schedule(t_moldyn *moldyn,int runs,double tau) {
 	schedule->tau=ptr;
 	schedule->tau[count-1]=tau;
 
+	printf("[moldyn] schedule added:\n");
+	printf("  number: %d | runs: %d | tau: %f\n",count-1,runs,tau);
+	                               
+
 	return 0;
 }
 
-int moldyn_set_schedule_hook(t_moldyn *moldyn,void *hook,void *hook_params) {
+int moldyn_set_schedule_hook(t_moldyn *moldyn,set_hook hook,void *hook_params) {
 
 	moldyn->schedule.hook=hook;
 	moldyn->schedule.hook_params=hook_params;
@@ -826,6 +1131,7 @@ int moldyn_integrate(t_moldyn *moldyn) {
 	int fd;
 	char dir[128];
 	double ds;
+	double energy_scale;
 
 	sched=&(moldyn->schedule);
 	atom=moldyn->atom;
@@ -843,6 +1149,9 @@ 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;
+
 	/* calculate initial forces */
 	potential_force_calc(moldyn);
 
@@ -863,6 +1172,9 @@ int moldyn_integrate(t_moldyn *moldyn) {
 	/* debugging, ignore */
 	moldyn->debug=0;
 
+	/* tell the world */
+	printf("[moldyn] integration start, go get a coffee ...\n");
+
 	/* executing the schedule */
 	for(sched->count=0;sched->count<sched->total_sched;sched->count++) {
 
@@ -884,14 +1196,19 @@ int moldyn_integrate(t_moldyn *moldyn) {
 		if(moldyn->pt_scale&(P_SCALE_BERENDSEN|P_SCALE_DIRECT))
 			scale_volume(moldyn);
 
+		temperature_calc(moldyn);
+		pressure_calc(moldyn);
+		//thermodynamic_pressure_calc(moldyn);
+
 		/* check for log & visualization */
 		if(e) {
 			if(!(i%e))
+				update_e_kin(moldyn);
 				dprintf(moldyn->efd,
 				        "%f %f %f %f\n",
-				        moldyn->time,update_e_kin(moldyn),
-				        moldyn->energy,
-				        get_total_energy(moldyn));
+				        moldyn->time,moldyn->ekin/energy_scale,
+				        moldyn->energy/energy_scale,
+				        get_total_energy(moldyn)/energy_scale);
 		}
 		if(m) {
 			if(!(i%m)) {
@@ -918,8 +1235,8 @@ int moldyn_integrate(t_moldyn *moldyn) {
 			if(!(i%v)) {
 				visual_atoms(&(moldyn->vis),moldyn->time,
 				             moldyn->atom,moldyn->count);
-				printf("\rsched: %d, steps: %d, debug: %d",
-				       sched->count,i,moldyn->debug);
+				printf("\rsched: %d, steps: %d, debug: %f | %f",
+				       sched->count,i,moldyn->p/ATM,moldyn->debug/ATM);
 				fflush(stdout);
 			}
 		}
@@ -946,7 +1263,7 @@ 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;
 
@@ -957,14 +1274,15 @@ int velocity_verlet(t_moldyn *moldyn) {
 
 	for(i=0;i<count;i++) {
 		/* new positions */
+		h=0.5/atom[i].mass;
 		v3_scale(&delta,&(atom[i].v),tau);
 		v3_add(&(atom[i].r),&(atom[i].r),&delta);
-		v3_scale(&delta,&(atom[i].f),0.5*tau_square/atom[i].mass);
+		v3_scale(&delta,&(atom[i].f),h*tau_square);
 		v3_add(&(atom[i].r),&(atom[i].r),&delta);
 		check_per_bound(moldyn,&(atom[i].r));
 
-		/* velocities */
-		v3_scale(&delta,&(atom[i].f),0.5*tau/atom[i].mass);
+		/* velocities [actually v(t+tau/2)] */
+		v3_scale(&delta,&(atom[i].f),h*tau);
 		v3_add(&(atom[i].v),&(atom[i].v),&delta);
 	}
 
@@ -975,7 +1293,7 @@ int velocity_verlet(t_moldyn *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);
 	}
@@ -986,7 +1304,7 @@ int velocity_verlet(t_moldyn *moldyn) {
 
 /*
  *
- * potentials & corresponding forces
+ * potentials & corresponding forces & virial routine
  * 
  */
 
@@ -1010,25 +1328,30 @@ int potential_force_calc(t_moldyn *moldyn) {
 
 	/* reset energy */
 	moldyn->energy=0.0;
-	
-	/* get energy and force of every atom */
+
+	/* reset force, site energy and virial of every atom */
 	for(i=0;i<count;i++) {
 
 		/* reset force */
 		v3_zero(&(itom[i].f));
 
-		/* reset viral of atom i */
-		virial=&(itom[i].virial);
+		/* reset virial */
+		virial=(&(itom[i].virial));
 		virial->xx=0.0;
 		virial->yy=0.0;
 		virial->zz=0.0;
 		virial->xy=0.0;
 		virial->xz=0.0;
 		virial->yz=0.0;
-
+	
 		/* reset site energy */
 		itom[i].e=0.0;
 
+	}
+
+	/* get energy,force and virial of every atom */
+	for(i=0;i<count;i++) {
+
 		/* single particle potential/force */
 		if(itom[i].attr&ATOM_ATTR_1BP)
 			moldyn->func1b(moldyn,&(itom[i]));
@@ -1127,6 +1450,7 @@ int potential_force_calc(t_moldyn *moldyn) {
 		}
 
 	}
+
 #ifdef DEBUG
 printf("\n\n");
 #endif
@@ -1137,6 +1461,22 @@ printf("\n\n");
 	return 0;
 }
 
+/*
+ * virial calculation
+ */
+
+inline int virial_calc(t_atom *a,t_3dvec *f,t_3dvec *d) {
+
+	a->virial.xx+=f->x*d->x;
+	a->virial.yy+=f->y*d->y;
+	a->virial.zz+=f->z*d->z;
+	a->virial.xy+=f->x*d->y;
+	a->virial.xz+=f->x*d->z;
+	a->virial.yz+=f->y*d->z;
+
+	return 0;
+}
+
 /*
  * periodic boundayr checking
  */
@@ -1179,23 +1519,29 @@ int harmonic_oscillator(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc) {
 
 	t_ho_params *params;
 	t_3dvec force,distance;
-	double d;
+	double d,f;
 	double sc,equi_dist;
 
 	params=moldyn->pot2b_params;
 	sc=params->spring_constant;
 	equi_dist=params->equilibrium_distance;
 
+	if(ai<aj) return 0;
+
 	v3_sub(&distance,&(aj->r),&(ai->r));
 	
 	if(bc) check_per_bound(moldyn,&distance);
 	d=v3_norm(&distance);
 	if(d<=moldyn->cutoff) {
-		/* energy is 1/2 (d-d0)^2, but we will add this twice ... */
-		moldyn->energy+=(0.25*sc*(d-equi_dist)*(d-equi_dist));
+		moldyn->energy+=(0.5*sc*(d-equi_dist)*(d-equi_dist));
 		/* f = -grad E; grad r_ij = -1 1/r_ij distance */
-		v3_scale(&force,&distance,sc*(1.0-(equi_dist/d)));
+		f=sc*(1.0-equi_dist/d);
+		v3_scale(&force,&distance,f);
 		v3_add(&(ai->f),&(ai->f),&force);
+		virial_calc(ai,&force,&distance);
+		virial_calc(aj,&force,&distance); /* f and d signe switched */
+		v3_scale(&force,&distance,-f);
+		v3_add(&(aj->f),&(aj->f),&force);
 	}
 
 	return 0;
@@ -1215,6 +1561,8 @@ int lennard_jones(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc) {
 	sig6=params->sigma6;
 	sig12=params->sigma12;
 
+	if(ai<aj) return 0;
+
 	v3_sub(&distance,&(aj->r),&(ai->r));
 	if(bc) check_per_bound(moldyn,&distance);
 	d=v3_absolute_square(&distance);	/* 1/r^2 */
@@ -1223,16 +1571,19 @@ int lennard_jones(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc) {
 		h2=d*d; 			/* 1/r^4 */
 		h2*=d;	 			/* 1/r^6 */
 		h1=h2*h2; 			/* 1/r^12 */
-		/* energy is eps*..., but we will add this twice ... */
-		moldyn->energy+=0.5*eps*(sig12*h1-sig6*h2);
+		moldyn->energy+=(eps*(sig12*h1-sig6*h2)-params->uc);
 		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(&(aj->f),&(aj->f),&force);
 		v3_scale(&force,&distance,-1.0*d); /* f = - grad E */
 		v3_add(&(ai->f),&(ai->f),&force);
+		virial_calc(ai,&force,&distance);
+		virial_calc(aj,&force,&distance); /* f and d signe switched */
 	}
 
 	return 0;
@@ -1526,7 +1877,6 @@ int tersoff_mult_post_2bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc) {
 	zeta=exchange->zeta_ij;
 	if(zeta==0.0) {
 		moldyn->debug++;		/* just for debugging ... */
-		db=0.0;
 		b=chi;
 		v3_scale(&force,dist_ij,df_a*b*f_c);
 	}
@@ -1602,12 +1952,13 @@ if(ai==&(moldyn->atom[0])) {
 	v3_add(&(ai->f),&(ai->f),&force);
 
 	/* virial - plus sign, as dist_ij = - dist_ji - (really??) */
-	ai->virial.xx+=force.x*dist_ij->x;
-	ai->virial.yy+=force.y*dist_ij->y;
-	ai->virial.zz+=force.z*dist_ij->z;
-	ai->virial.xy+=force.x*dist_ij->y;
-	ai->virial.xz+=force.x*dist_ij->z;
-	ai->virial.yz+=force.y*dist_ij->z;
+// TEST ... with a minus instead
+	ai->virial.xx-=force.x*dist_ij->x;
+	ai->virial.yy-=force.y*dist_ij->y;
+	ai->virial.zz-=force.z*dist_ij->z;
+	ai->virial.xy-=force.x*dist_ij->y;
+	ai->virial.xz-=force.x*dist_ij->z;
+	ai->virial.yz-=force.y*dist_ij->z;
 
 #ifdef DEBUG
 if(ai==&(moldyn->atom[0])) {