X-Git-Url: https://hackdaworld.org/gitweb/?a=blobdiff_plain;f=moldyn.c;h=ed831aed93ec4861c71a383033af863ef1378074;hb=dece53fc37f9ebb52b33c9743333c213be2d6f26;hp=d52fcd3868c2481e70cbc804b5a9cdf92542708d;hpb=180ff86ae35ca0ea6ee857e92e56120e65315d17;p=physik%2Fposic.git

diff --git a/moldyn.c b/moldyn.c
index d52fcd3..ed831ae 100644
--- a/moldyn.c
+++ b/moldyn.c
@@ -231,13 +231,15 @@ int create_lattice(t_moldyn *moldyn,u8 type,double lc,int element,double mass,
 	printf("[moldyn] created lattice with %d atoms\n",count);
 
 	while(count) {
-		moldyn->atom[count-1].element=element;
-		moldyn->atom[count-1].mass=mass;
-		moldyn->atom[count-1].attr=attr;
-		moldyn->atom[count-1].bnum=bnum;
 		count-=1;
+		moldyn->atom[count].element=element;
+		moldyn->atom[count].mass=mass;
+		moldyn->atom[count].attr=attr;
+		moldyn->atom[count].bnum=bnum;
+		check_per_bound(moldyn,&(moldyn->atom[count].r));
 	}
 
+
 	return ret;
 }
 
@@ -529,7 +531,7 @@ int link_cell_neighbour_index(t_moldyn *moldyn,int i,int j,int k,t_list *cell) {
 		}
 	}
 
-	lc->dnlc=count2;
+	lc->dnlc=count1;
 	lc->countn=27;
 
 	return count2;
@@ -618,7 +620,6 @@ int moldyn_integrate(t_moldyn *moldyn) {
 	/* sqaure of some variables */
 	moldyn->tau_square=moldyn->tau*moldyn->tau;
 	moldyn->cutoff_square=moldyn->cutoff*moldyn->cutoff;
-
 	/* calculate initial forces */
 	potential_force_calc(moldyn);
 
@@ -774,7 +775,7 @@ int potential_force_calc(t_moldyn *moldyn) {
 	moldyn->energy=0.0;
 
 	for(i=0;i<count;i++) {
-	
+
 		/* reset force */
 		v3_zero(&(atom[i].f));
 
@@ -823,11 +824,13 @@ int potential_force_calc(t_moldyn *moldyn) {
 					   !(btom->attr&ATOM_ATTR_3BP))
 						continue;
 
+printf("DEBUG: problem exists here ...\n");
 					link_cell_neighbour_index(moldyn,
 					   (btom->r.x+moldyn->dim.x/2)/lc->x,
 					   (btom->r.y+moldyn->dim.y/2)/lc->y,
 					   (btom->r.z+moldyn->dim.z/2)/lc->z,
 					   neighbourk);
+printf("DEBUG: as you won't see that!\n");
 
 					for(k=0;k<lc->countn;k++) {
 
@@ -971,6 +974,20 @@ int lennard_jones(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc) {
  * tersoff potential & force for 2 sorts of atoms
  */
 
+/* create mixed terms from parameters and set them */
+int tersoff_mult_complete_params(t_tersoff_mult_params *p) {
+
+	printf("[moldyn] tersoff parameter completion\n");
+	p->Smixed=sqrt(p->S[0]*p->S[1]);
+	p->Rmixed=sqrt(p->R[0]*p->R[1]);
+	p->Amixed=sqrt(p->A[0]*p->A[1]);
+	p->Bmixed=sqrt(p->B[0]*p->B[1]);
+	p->lambda_m=0.5*(p->lambda[0]+p->lambda[1]);
+	p->mu_m=0.5*(p->mu[0]+p->mu[1]);
+
+	return 0;
+}
+
 /* tersoff 1 body part */
 int tersoff_mult_1bp(t_moldyn *moldyn,t_atom *ai) {