X-Git-Url: https://www.hackdaworld.org/gitweb/?a=blobdiff_plain;f=moldyn.c;h=7a77898b958b9a06f326a6f31423a46cfcce02f9;hb=60f40345bc4fcd8448d724dc67bbb512ec081bd4;hp=9d9901c55d90c3effd806ded40ce2d93dc1b2430;hpb=d9e7f195bbb219ad4c2de0e5f54d023ef9e669fb;p=physik%2Fposic.git

diff --git a/moldyn.c b/moldyn.c
index 9d9901c..7a77898 100644
--- a/moldyn.c
+++ b/moldyn.c
@@ -17,13 +17,6 @@
 
 #include "moldyn.h"
 
-#include "math/math.h"
-#include "init/init.h"
-#include "random/random.h"
-#include "visual/visual.h"
-#include "list/list.h"
-
-
 int moldyn_init(t_moldyn *moldyn,int argc,char **argv) {
 
 	//int ret;
@@ -78,6 +71,13 @@ int set_temperature(t_moldyn *moldyn,double t_ref) {
 	return 0;
 }
 
+int set_pressure(t_moldyn *moldyn,double p_ref) {
+
+	moldyn->p_ref=p_ref;
+
+	return 0;
+}
+
 int set_pt_scale(t_moldyn *moldyn,u8 ptype,double ptc,u8 ttype,double ttc) {
 
 	moldyn->pt_scale=(ptype|ttype);
@@ -93,12 +93,21 @@ int set_dim(t_moldyn *moldyn,double x,double y,double z,u8 visualize) {
 	moldyn->dim.y=y;
 	moldyn->dim.z=z;
 
+	moldyn->volume=x*y*z;
+
 	if(visualize) {
 		moldyn->vis.dim.x=x;
 		moldyn->vis.dim.y=y;
 		moldyn->vis.dim.z=z;
 	}
 
+	printf("[moldyn] dimensions in A and A^2 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");
+
 	return 0;
 }
 
@@ -155,38 +164,56 @@ int set_potential3b(t_moldyn *moldyn,pf_func3b func,void *params) {
 	return 0;
 }
 
-int moldyn_set_log(t_moldyn *moldyn,u8 type,char *fb,int timer) {
+int moldyn_set_log_dir(t_moldyn *moldyn,char *dir) {
+
+	strncpy(moldyn->vlsdir,dir,127);
+
+	return 0;
+}
+	
+int moldyn_set_log(t_moldyn *moldyn,u8 type,int timer) {
+
+	char filename[128];
+	int ret;
 
 	switch(type) {
 		case LOG_TOTAL_ENERGY:
 			moldyn->ewrite=timer;
-			moldyn->efd=open(fb,O_WRONLY|O_CREAT|O_TRUNC);
+			snprintf(filename,127,"%s/energy",moldyn->vlsdir);
+			moldyn->efd=open(filename,
+			                 O_WRONLY|O_CREAT|O_EXCL,
+			                 S_IRUSR|S_IWUSR);
 			if(moldyn->efd<0) {
-				perror("[moldyn] efd open");
+				perror("[moldyn] energy log fd open");
 				return moldyn->efd;
 			}
 			dprintf(moldyn->efd,"# total energy log file\n");
 			break;
 		case LOG_TOTAL_MOMENTUM:
 			moldyn->mwrite=timer;
-			moldyn->mfd=open(fb,O_WRONLY|O_CREAT|O_TRUNC);
+			snprintf(filename,127,"%s/momentum",moldyn->vlsdir);
+			moldyn->mfd=open(filename,
+			                 O_WRONLY|O_CREAT|O_EXCL,
+			                 S_IRUSR|S_IWUSR);
 			if(moldyn->mfd<0) {
-				perror("[moldyn] mfd open");
+				perror("[moldyn] momentum log fd open");
 				return moldyn->mfd;
 			}
 			dprintf(moldyn->efd,"# total momentum log file\n");
 			break;
 		case SAVE_STEP:
 			moldyn->swrite=timer;
-			strncpy(moldyn->sfb,fb,63);
 			break;
 		case VISUAL_STEP:
 			moldyn->vwrite=timer;
-			strncpy(moldyn->vfb,fb,63);
-			visual_init(&(moldyn->vis),fb);
+			ret=visual_init(&(moldyn->vis),moldyn->vlsdir);
+			if(ret<0) {
+				printf("[moldyn] visual init failure\n");
+				return ret;
+			}
 			break;
 		default:
-			printf("unknown log mechanism: %02x\n",type);
+			printf("[moldyn] unknown log mechanism: %02x\n",type);
 			return -1;
 	}
 
@@ -212,10 +239,11 @@ int create_lattice(t_moldyn *moldyn,u8 type,double lc,int element,double mass,
 
 	count=a*b*c;
 
+	/* how many atoms do we expect */
 	if(type==FCC) count*=4;
-
 	if(type==DIAMOND) count*=8;
 
+	/* allocate space for atoms */
 	moldyn->atom=malloc(count*sizeof(t_atom));
 	if(moldyn->atom==NULL) {
 		perror("malloc (atoms)");
@@ -238,9 +266,10 @@ int create_lattice(t_moldyn *moldyn,u8 type,double lc,int element,double mass,
 
 	/* debug */
 	if(ret!=count) {
-		printf("ok, there is something wrong ...\n");
-		printf("calculated -> %d atoms\n",count);
-		printf("created -> %d atoms\n",ret);
+		printf("[moldyn] creating lattice failed\n");
+		printf("  amount of atoms\n");
+		printf("  - expected: %d\n",count);
+		printf("  - created: %d\n",ret);
 		return -1;
 	}
 
@@ -256,7 +285,6 @@ int create_lattice(t_moldyn *moldyn,u8 type,double lc,int element,double mass,
 		check_per_bound(moldyn,&(moldyn->atom[count].r));
 	}
 
-
 	return ret;
 }
 
@@ -365,14 +393,16 @@ int scale_velocity(t_moldyn *moldyn,u8 equi_init) {
 			count+=1;
 		}
 	}
-	if(count!=0) moldyn->t=(2.0*e)/(3.0*count*K_BOLTZMANN);
+	if(count!=0) moldyn->t=e/(1.5*count*K_BOLTZMANN);
 	else return 0;	/* no atoms involved in scaling! */
 	
 	/* (temporary) hack for e,t = 0 */
 	if(e==0.0) {
 	moldyn->t=0.0;
-		if(moldyn->t_ref!=0.0)
+		if(moldyn->t_ref!=0.0) {
 			thermal_init(moldyn,equi_init);
+			return 0;
+		}
 		else
 			return 0; /* no scaling needed */
 	}
@@ -384,22 +414,69 @@ int scale_velocity(t_moldyn *moldyn,u8 equi_init) {
 		scale*=2.0;
 	else
 		if(moldyn->pt_scale&T_SCALE_BERENDSEN)
-			scale=1.0+moldyn->tau*(scale-1.0)/moldyn->t_tc;
-printf("scale=%f\n",scale);
+			scale=1.0+(scale-1.0)/moldyn->t_tc;
 	scale=sqrt(scale);
-printf("debug: %f %f %f %f \n",scale,moldyn->t_ref,moldyn->t,moldyn->tau);
 
 	/* velocity scaling */
 	for(i=0;i<moldyn->count;i++) {
-printf("vorher: %f\n",atom[i].v.x);
 		if((equi_init&TRUE)||(atom[i].attr&ATOM_ATTR_HB))
 			v3_scale(&(atom[i].v),&(atom[i].v),scale);
-printf("nachher: %f\n",atom[i].v.x);
 	}
 
 	return 0;
 }
 
+int scale_volume(t_moldyn *moldyn) {
+
+	t_atom *atom;
+	t_3dvec *dim,*vdim;
+	double virial,scale;
+	t_linkcell *lc;
+	int i;
+
+	atom=moldyn->atom;
+	dim=&(moldyn->dim);
+	vdim=&(moldyn->vis.dim);
+	lc=&(moldyn->lc);
+
+	for(i=0;i<moldyn->count;i++)
+		virial+=v3_norm(&(atom[i].virial));
+
+printf("%f\n",virial);
+	/* get pressure from virial */
+	moldyn->p=moldyn->count*K_BOLTZMANN*moldyn->t-ONE_THIRD*virial;
+	moldyn->p/=moldyn->volume;
+printf("%f\n",moldyn->p/(ATM));
+
+	/* scale factor */
+	if(moldyn->pt_scale&P_SCALE_BERENDSEN)
+		scale=3*sqrt(1-(moldyn->p_ref-moldyn->p)/moldyn->p_tc);
+	else 
+		/* should actually never be used */
+		scale=pow(moldyn->p/moldyn->p_ref,1.0/3.0);
+
+printf("scale = %f\n",scale);
+	/* actual scaling */
+	dim->x*=scale;
+	dim->y*=scale;
+	dim->z*=scale;
+	if(vdim->x) vdim->x=dim->x;
+	if(vdim->y) vdim->y=dim->y;
+	if(vdim->z) vdim->z=dim->z;
+	moldyn->volume*=(scale*scale*scale);
+
+	/* check whether we need a new linkcell init */
+	if((dim->x/moldyn->cutoff!=lc->nx)||
+	   (dim->y/moldyn->cutoff!=lc->ny)||
+	   (dim->z/moldyn->cutoff!=lc->nx)) {
+		link_cell_shutdown(moldyn);
+		link_cell_init(moldyn);
+	}
+
+	return 0;
+
+}
+
 double get_e_kin(t_moldyn *moldyn) {
 
 	int i;
@@ -467,9 +544,6 @@ int link_cell_init(t_moldyn *moldyn) {
 
 	t_linkcell *lc;
 	int i;
-	int fd;
-
-	fd=open("/dev/null",O_WRONLY);
 
 	lc=&(moldyn->lc);
 
@@ -487,8 +561,7 @@ int link_cell_init(t_moldyn *moldyn) {
 	printf("[moldyn] initializing linked cells (%d)\n",lc->cells);
 
 	for(i=0;i<lc->cells;i++)
-		//list_init(&(lc->subcell[i]),1);
-		list_init(&(lc->subcell[i]),fd);
+		list_init_f(&(lc->subcell[i]));
 
  	link_cell_update(moldyn);
 	
@@ -510,14 +583,14 @@ int link_cell_update(t_moldyn *moldyn) {
 	nz=lc->nz;
 
 	for(i=0;i<lc->cells;i++)
-		list_destroy(&(moldyn->lc.subcell[i]));
+		list_destroy_f(&(moldyn->lc.subcell[i]));
 	
 	for(count=0;count<moldyn->count;count++) {
 		i=(atom[count].r.x+(moldyn->dim.x/2))/lc->x;
 		j=(atom[count].r.y+(moldyn->dim.y/2))/lc->y;
 		k=(atom[count].r.z+(moldyn->dim.z/2))/lc->z;
-		list_add_immediate_ptr(&(moldyn->lc.subcell[i+j*nx+k*nx*ny]),
-		                       &(atom[count]));
+		list_add_immediate_f(&(moldyn->lc.subcell[i+j*nx+k*nx*ny]),
+		                     &(atom[count]));
 	}
 
 	return 0;
@@ -587,7 +660,9 @@ int link_cell_shutdown(t_moldyn *moldyn) {
 	lc=&(moldyn->lc);
 
 	for(i=0;i<lc->nx*lc->ny*lc->nz;i++)
-		list_shutdown(&(moldyn->lc.subcell[i]));
+		list_destroy_f(&(moldyn->lc.subcell[i]));
+
+	free(lc->subcell);
 
 	return 0;
 }
@@ -644,7 +719,7 @@ int moldyn_integrate(t_moldyn *moldyn) {
 	t_moldyn_schedule *schedule;
 	t_atom *atom;
 	int fd;
-	char fb[128];
+	char dir[128];
 	double ds;
 
 	schedule=&(moldyn->schedule);
@@ -701,15 +776,18 @@ int moldyn_integrate(t_moldyn *moldyn) {
 		/* p/t scaling */
 		if(moldyn->pt_scale&(T_SCALE_BERENDSEN|T_SCALE_DIRECT))
 			scale_velocity(moldyn,FALSE);
-
-		/* increase absolute time */
-		moldyn->time+=moldyn->tau;
+		if(moldyn->pt_scale&(P_SCALE_BERENDSEN|P_SCALE_DIRECT))
+{
+printf("going to do p scale ...\n");
+			scale_volume(moldyn);
+printf("done\n");
+}
 
 		/* check for log & visualization */
 		if(e) {
 			if(!(i%e))
 				dprintf(moldyn->efd,
-				        "%.15f %.45f %.45f %.45f\n",
+				        "%f %f %f %f\n",
 				        moldyn->time,update_e_kin(moldyn),
 				        moldyn->energy,
 				        get_total_energy(moldyn));
@@ -718,15 +796,14 @@ int moldyn_integrate(t_moldyn *moldyn) {
 			if(!(i%m)) {
 				p=get_total_p(moldyn);
 				dprintf(moldyn->mfd,
-				        "%.15f %.45f\n",moldyn->time,
-				        v3_norm(&p));
+				        "%f %f\n",moldyn->time,v3_norm(&p));
 			}
 		}
 		if(s) {
 			if(!(i%s)) {
-				snprintf(fb,128,"%s-%f-%.15f.save",moldyn->sfb,
-				         moldyn->t,i*moldyn->tau);
-				fd=open(fb,O_WRONLY|O_TRUNC|O_CREAT);
+				snprintf(dir,128,"%s/s-%07.f.save",
+				         moldyn->vlsdir,moldyn->time);
+				fd=open(dir,O_WRONLY|O_TRUNC|O_CREAT);
 				if(fd<0) perror("[moldyn] save fd open");
 				else {
 					write(fd,moldyn,sizeof(t_moldyn));
@@ -746,6 +823,9 @@ int moldyn_integrate(t_moldyn *moldyn) {
 			}
 		}
 
+		/* increase absolute time */
+		moldyn->time+=moldyn->tau;
+
 	}
 
 		/* check for hooks */
@@ -780,13 +860,16 @@ int velocity_verlet(t_moldyn *moldyn) {
 		v3_add(&(atom[i].r),&(atom[i].r),&delta);
 		v3_scale(&delta,&(atom[i].f),0.5*tau_square/atom[i].mass);
 		v3_add(&(atom[i].r),&(atom[i].r),&delta);
+//if(i==5) printf("v: %f %f %f\n",atom[i].r.x,(atom[i].r.x+moldyn->dim.x/2)/moldyn->lc.x,2*atom[i].r.x/moldyn->dim.x);
 		check_per_bound(moldyn,&(atom[i].r));
+//if(i==5) printf("n: %f %f %f\n",atom[i].r.x,(atom[i].r.x+moldyn->dim.x/2)/moldyn->lc.x,2*atom[i].r.x/moldyn->dim.x);
 
 		/* velocities */
 		v3_scale(&delta,&(atom[i].f),0.5*tau/atom[i].mass);
 		v3_add(&(atom[i].v),&(atom[i].v),&delta);
 	}
 
+//moldyn_bc_check(moldyn);
 	/* neighbour list update */
 	link_cell_update(moldyn);
 
@@ -812,14 +895,12 @@ int velocity_verlet(t_moldyn *moldyn) {
 /* generic potential and force calculation */
 
 int potential_force_calc(t_moldyn *moldyn) {
-printf("start pot force calc\n");
 
 	int i,j,k,count;
 	t_atom *itom,*jtom,*ktom;
 	t_linkcell *lc;
 	t_list neighbour_i[27];
 	t_list neighbour_i2[27];
-	//t_list neighbour_j[27];
 	t_list *this,*that;
 	u8 bc_ij,bc_ik;
 	int dnlc;
@@ -830,109 +911,115 @@ printf("start pot force calc\n");
 
 	/* reset energy */
 	moldyn->energy=0.0;
-
+	
 	/* get energy and force of every atom */
 	for(i=0;i<count;i++) {
-printf("atom %d: %f\n",i,itom[i].r.x);
-printf("atom %d: %f\n",i,itom[i].v.x);
-printf("atom %d: %f\n",i,itom[i].f.x);
 
 		/* reset force */
 		v3_zero(&(itom[i].f));
 
+		/* reset viral of atom i */
+		v3_zero(&(itom[i].virial));
+
 		/* single particle potential/force */
 		if(itom[i].attr&ATOM_ATTR_1BP)
 			moldyn->func1b(moldyn,&(itom[i]));
 
+		if(!(itom[i].attr&(ATOM_ATTR_2BP|ATOM_ATTR_3BP)))
+			continue;
+
 		/* 2 body pair potential/force */
-		if(itom[i].attr&(ATOM_ATTR_2BP|ATOM_ATTR_3BP)) {
 	
-			link_cell_neighbour_index(moldyn,
-				(itom[i].r.x+moldyn->dim.x/2)/lc->x,
-				(itom[i].r.y+moldyn->dim.y/2)/lc->y,
-				(itom[i].r.z+moldyn->dim.z/2)/lc->z,
-				neighbour_i);
+		link_cell_neighbour_index(moldyn,
+		                          (itom[i].r.x+moldyn->dim.x/2)/lc->x,
+		                          (itom[i].r.y+moldyn->dim.y/2)/lc->y,
+		                          (itom[i].r.z+moldyn->dim.z/2)/lc->z,
+		                          neighbour_i);
 
-			dnlc=lc->dnlc;
+		dnlc=lc->dnlc;
 
-			for(j=0;j<27;j++) {
+		for(j=0;j<27;j++) {
 
-				this=&(neighbour_i[j]);
-				list_reset(this);
+			this=&(neighbour_i[j]);
+			list_reset_f(this);
 
-				if(this->start==NULL)
-					continue;
+			if(this->start==NULL)
+				continue;
 
-				bc_ij=(j<dnlc)?0:1;
+			bc_ij=(j<dnlc)?0:1;
 
-				do {
-					jtom=this->current->data;
+			do {
+				jtom=this->current->data;
 
-					if(jtom==&(itom[i]))
-						continue;
+				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_2BP)&
+				   (itom[i].attr&ATOM_ATTR_2BP)) {
+					moldyn->func2b(moldyn,
+					               &(itom[i]),
+					               jtom,
+					               bc_ij);
+				}
 
-					/* 3 body potential/force */
+				/* 3 body potential/force */
 
-					if(!(itom[i].attr&ATOM_ATTR_3BP)||
-					   !(jtom->attr&ATOM_ATTR_3BP))
-						continue;
+				if(!(itom[i].attr&ATOM_ATTR_3BP)||
+				   !(jtom->attr&ATOM_ATTR_3BP))
+					continue;
 
-					/* copy the neighbour lists */
-					memcpy(neighbour_i2,neighbour_i,
-					       27*sizeof(t_list));
+				/* copy the neighbour lists */
+				memcpy(neighbour_i2,neighbour_i,
+				       27*sizeof(t_list));
 
-					/* get neighbours of i */
-					for(k=0;k<27;k++) {
+				/* get neighbours of i */
+				for(k=0;k<27;k++) {
 
-						that=&(neighbour_i2[k]);
-						list_reset(that);
+					that=&(neighbour_i2[k]);
+					list_reset_f(that);
 					
-						if(that->start==NULL)
-							continue;
+					if(that->start==NULL)
+						continue;
 
-						bc_ik=(k<dnlc)?0:1;
+					bc_ik=(k<dnlc)?0:1;
 
-						do {
+					do {
 
-			ktom=that->current->data;
+						ktom=that->current->data;
 
-			if(!(ktom->attr&ATOM_ATTR_3BP))
-				continue;
+						if(!(ktom->attr&ATOM_ATTR_3BP))
+							continue;
 
-			if(ktom==jtom)
-				continue;
+						if(ktom==jtom)
+							continue;
 
-			if(ktom==&(itom[i]))
-				continue;
+						if(ktom==&(itom[i]))
+							continue;
 
-			moldyn->func3b(moldyn,&(itom[i]),jtom,ktom,bc_ik|bc_ij);
+						moldyn->func3b(moldyn,
+						               &(itom[i]),
+						               jtom,
+						               ktom,
+						               bc_ik|bc_ij);
 
-						} while(list_next(that)!=\
-						        L_NO_NEXT_ELEMENT);
+					} while(list_next_f(that)!=\
+					        L_NO_NEXT_ELEMENT);
+
+				}
 
-					}
-					
-				} while(list_next(this)!=L_NO_NEXT_ELEMENT);
-		
 				/* 2bp post function */
 				if(moldyn->func2b_post) {
 					moldyn->func2b_post(moldyn,
 					                    &(itom[i]),
 					                    jtom,bc_ij);
 				}
-
-			}
+					
+			} while(list_next_f(this)!=L_NO_NEXT_ELEMENT);
+		
 		}
+
 	}
 
-printf("end pot force calc\n");
 	return 0;
 }
 
@@ -947,9 +1034,9 @@ int check_per_bound(t_moldyn *moldyn,t_3dvec *a) {
 
 	dim=&(moldyn->dim);
 
-	x=0.5*dim->x;
-	y=0.5*dim->y;
-	z=0.5*dim->z;
+	x=dim->x/2;
+	y=dim->y/2;
+	z=dim->z/2;
 
 	if(moldyn->status&MOLDYN_STAT_PBX) {
 		if(a->x>=x) a->x-=dim->x;
@@ -1196,7 +1283,7 @@ int tersoff_mult_2bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc) {
 
 	/* f_a, df_a calc (again, same for ij and ji) | save for later use! */
 	exchange->f_a=-B*exp(-mu*d_ij);
-	exchange->df_a=-mu*exchange->f_a/d_ij;
+	exchange->df_a=mu*exchange->f_a/d_ij;
 
 	/* f_c, df_c calc (again, same for ij and ji) */
 	if(d_ij<R) {
@@ -1210,7 +1297,8 @@ int tersoff_mult_2bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc) {
 		s_r=S-R;
 		arg=M_PI*(d_ij-R)/s_r;
 		f_c=0.5+0.5*cos(arg);
-		df_c=-0.5*sin(arg)*(M_PI/(s_r*d_ij));
+		//df_c=-0.5*sin(arg)*(M_PI/(s_r*d_ij));	/* MARK! */
+		df_c=0.5*sin(arg)*(M_PI/(s_r*d_ij));
 		/* two body contribution (ij, ji) */
 		v3_scale(&force,&dist_ij,-df_c*f_r-df_r*f_c);
 		/* tell 3bp that S > r > R */
@@ -1338,7 +1426,7 @@ int tersoff_mult_post_2bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc) {
 	v3_scale(&force,&force,-0.5);
 
 	/* add force */
-	v3_sub(&(ai->f),&(ai->f),&force);
+	v3_add(&(ai->f),&(ai->f),&force);
 
 	return 0;
 }
@@ -1481,7 +1569,8 @@ int tersoff_mult_3bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,t_atom *ak,u8 bc) {
 			s_r=S-R;
 			arg=M_PI*(d_ik-R)/s_r;
 			f_c_ik=0.5+0.5*cos(arg);
-			df_c_ik=-0.5*sin(arg)*(M_PI/(s_r*d_ik));
+			//df_c_ik=-0.5*sin(arg)*(M_PI/(s_r*d_ik)); /* MARK */
+			df_c_ik=0.5*sin(arg)*(M_PI/(s_r*d_ik));
 
 			/* zeta_ij */
 			exchange->zeta_ij+=f_c_ik*g;
@@ -1531,13 +1620,13 @@ int tersoff_mult_3bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,t_atom *ak,u8 bc) {
 		c2d2=exchange->cj2dj2;
 
 		/* cosine of theta_jik by scalaproduct */
-		rr=v3_scalar_product(&dist_ij,&dist_jk); /* times -1 */
+		rr=-v3_scalar_product(&dist_ij,&dist_jk); /* -1, as ij -> ji */
 		dd=d_ij*d_jk;
 		cos_theta=rr/dd;
 
 		/* d_costheta */
-		d_costheta1=1.0/(d_jk*d_ij);
-		d_costheta2=cos_theta/(d_ij*d_ij); /* in fact -cos(), but ^ */
+		d_costheta1=1.0/dd;
+		d_costheta2=cos_theta/(d_ij*d_ij);
 
 		/* some usefull values */
 		h_cos=(h-cos_theta);
@@ -1553,6 +1642,9 @@ int tersoff_mult_3bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,t_atom *ak,u8 bc) {
 		v3_add(&temp1,&temp1,&temp2);
 		v3_scale(&temp1,&temp1,-2.0*frac*h_cos/d2_h_cos2); /* dg */
 
+		/* store dg in temp2 and use it for dVjk later */
+		v3_copy(&temp2,&temp1);
+
 		/* f_c_jk + {d,}zeta contribution (df_c_jk = 0) */
 		dzeta=&(exchange->dzeta_ji);
 		if(d_jk<R) {
@@ -1574,7 +1666,7 @@ int tersoff_mult_3bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,t_atom *ak,u8 bc) {
 			/* zeta_ji */
 			exchange->zeta_ji+=f_c_jk*g;
 
-			/* dzeta_ij */
+			/* dzeta_ji */
 			v3_scale(&temp1,&temp1,f_c_jk);
 			v3_add(dzeta,dzeta,&temp1);
 		}
@@ -1582,20 +1674,21 @@ int tersoff_mult_3bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,t_atom *ak,u8 bc) {
 		/* dV_jk stuff | add force contribution on atom i immediately */
 		if(exchange->d_ij_between_rs) {
 			zeta=f_c*g;
-			v3_scale(&temp1,&temp1,f_c);
-			v3_scale(&temp2,&dist_ij,df_c);
-			v3_add(&temp1,&temp1,&temp2);
+			v3_scale(&temp1,&temp2,f_c);
+			v3_scale(&temp2,&dist_ij,df_c*g);
+			v3_add(&temp2,&temp2,&temp1); /* -> dzeta_jk in temp2 */
 		}
 		else {
 			zeta=g;
-			// dzeta_jk is simply dg, which is temp1
+			// dzeta_jk is simply dg, which is stored in temp2
 		}
 		/* betajnj * zeta_jk ^ nj-1 */
 		tmp=exchange->betajnj*pow(zeta,(n-1.0));
-		tmp=-chi/2.0*pow(1+tmp*zeta,-1.0/(2.0*n)-1)*tmp;
-		v3_scale(&temp1,&temp1,tmp*B*exp(-mu*d_jk)*f_c_jk*0.5);
-		v3_add(&(ai->f),&(ai->f),&temp1); /* -1 skipped in f_a calc ^ */
+		tmp=-chi/2.0*pow((1+tmp*zeta),(-1.0/(2.0*n)-1))*tmp;
+		v3_scale(&temp2,&temp2,tmp*B*exp(-mu*d_jk)*f_c_jk*0.5);
+		v3_add(&(ai->f),&(ai->f),&temp2); /* -1 skipped in f_a calc ^ */
 		                                  /* scaled with 0.5 ^ */
+
 	}
 
 	return 0;
@@ -1611,22 +1704,133 @@ int moldyn_bc_check(t_moldyn *moldyn) {
 	t_atom *atom;
 	t_3dvec *dim;
 	int i;
+double x;
+u8 byte;
+int j,k;
 
 	atom=moldyn->atom;
 	dim=&(moldyn->dim);
+x=dim->x/2;
 
 	for(i=0;i<moldyn->count;i++) {
-		if(atom[i].r.x>=dim->x/2||-atom[i].r.x>dim->x/2)
+		if(atom[i].r.x>=dim->x/2||-atom[i].r.x>dim->x/2) {
 			printf("FATAL: atom %d: x: %.20f (%.20f)\n",
-			       i,atom[i].r.x*1e10,dim->x/2*1e10);
+			       i,atom[i].r.x,dim->x/2);
+			printf("diagnostic:\n");
+			printf("-----------\natom.r.x:\n");
+			for(j=0;j<8;j++) {
+				memcpy(&byte,(u8 *)(&(atom[i].r.x))+j,1);
+				for(k=0;k<8;k++)
+					printf("%d%c",
+					((byte)&(1<<k))?1:0,
+					(k==7)?'\n':'|');
+			}
+			printf("---------------\nx=dim.x/2:\n");
+			for(j=0;j<8;j++) {
+				memcpy(&byte,(u8 *)(&x)+j,1);
+				for(k=0;k<8;k++)
+					printf("%d%c",
+					((byte)&(1<<k))?1:0,
+					(k==7)?'\n':'|');
+			}
+			if(atom[i].r.x==x) printf("the same!\n");
+			else printf("different!\n");
+		}
 		if(atom[i].r.y>=dim->y/2||-atom[i].r.y>dim->y/2)
 			printf("FATAL: atom %d: y: %.20f (%.20f)\n",
-			       i,atom[i].r.y*1e10,dim->y/2*1e10);
+			       i,atom[i].r.y,dim->y/2);
 		if(atom[i].r.z>=dim->z/2||-atom[i].r.z>dim->z/2)
 			printf("FATAL: atom %d: z: %.20f (%.20f)\n",
-			       i,atom[i].r.z*1e10,dim->z/2*1e10);
+			       i,atom[i].r.z,dim->z/2);
 	}
 
 	return 0;
 }
 
+/*
+ * lattice creation functions
+ */
+
+/* fcc lattice init */
+int fcc_init(int a,int b,int c,double lc,t_atom *atom,t_3dvec *origin) {
+
+	int count;
+	int i,j;
+	t_3dvec o,r,n;
+	t_3dvec basis[3];
+	double help[3];
+	double x,y,z;
+
+	x=a*lc;
+	y=b*lc;
+	z=c*lc;
+
+	if(origin) v3_copy(&o,origin);
+	else v3_zero(&o);
+
+	/* construct the basis */
+	for(i=0;i<3;i++) {
+		for(j=0;j<3;j++) {
+			if(i!=j) help[j]=0.5*lc;
+			else help[j]=.0;
+		}
+		v3_set(&basis[i],help);
+	}
+
+	v3_zero(&r);
+	count=0;
+	
+	/* fill up the room */
+	r.x=o.x;
+	while(r.x<x) {
+		r.y=o.y;
+		while(r.y<y) {
+			r.z=o.z;
+			while(r.z<z) {
+				v3_copy(&(atom[count].r),&r);
+				atom[count].element=1;
+				count+=1;
+				for(i=0;i<3;i++) {
+					v3_add(&n,&r,&basis[i]);
+					if((n.x<x+o.x)&&
+					   (n.y<y+o.y)&&
+					   (n.z<z+o.z)) {
+						v3_copy(&(atom[count].r),&n);
+						count+=1;
+					}
+				}
+				r.z+=lc;	
+			}
+			r.y+=lc;
+		}
+		r.x+=lc;
+	}
+
+	/* coordinate transformation */
+	help[0]=x/2.0;
+	help[1]=y/2.0;
+	help[2]=z/2.0;
+	v3_set(&n,help);
+	for(i=0;i<count;i++)
+		v3_sub(&(atom[i].r),&(atom[i].r),&n);
+		
+	return count;
+}
+
+int diamond_init(int a,int b,int c,double lc,t_atom *atom,t_3dvec *origin) {
+
+	int count;
+	t_3dvec o;
+
+	count=fcc_init(a,b,c,lc,atom,origin);
+
+	o.x=0.25*lc;
+	o.y=0.25*lc;
+	o.z=0.25*lc;
+
+	if(origin) v3_add(&o,&o,origin);
+
+	count+=fcc_init(a,b,c,lc,&atom[count],&o);
+
+	return count;
+}