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;
}
}
}
- lc->dnlc=count2;
+ lc->dnlc=count1;
lc->countn=27;
return count2;
/* 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);
moldyn->energy=0.0;
for(i=0;i<count;i++) {
-
+
/* reset force */
v3_zero(&(atom[i].f));
!(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++) {
* 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) {