case STAGE_DISPLACE_ATOM:
psize=sizeof(t_displace_atom_params);
break;
+ case STAGE_DEL_ATOMS:
+ psize=sizeof(t_del_atoms_params);
+ break;
case STAGE_INSERT_ATOMS:
psize=sizeof(t_insert_atoms_params);
break;
t_set_temp_params stp;
t_set_timestep_params stsp;
t_fill_params fp;
+ t_del_atoms_params delp;
/* open config file */
fd=open(mdrun->cfile,O_RDONLY);
memset(&stp,0,sizeof(t_set_temp_params));
memset(&stsp,0,sizeof(t_set_timestep_params));
memset(&fp,0,sizeof(t_fill_params));
+ memset(&delp,0,sizeof(t_del_atoms_params));
// get command + args
wcnt=0;
fp.lz=atoi(word[++i]);
fp.lc=atof(word[++i]);
mdrun->lc=fp.lc;
+ continue;
}
if(!strncmp(word[i],"eb",2)) {
fp.fill_element=atoi(word[++i]);
fp.fill_brand=atoi(word[++i]);
+ continue;
}
if(word[i][0]=='p') {
i+=1;
fp.p_params.d.y=atof(word[++i]);
fp.p_params.d.z=atof(word[++i]);
}
+ continue;
}
if(word[i][0]=='d') {
switch(word[++i][0]) {
default:
break;
}
+ continue;
}
i+=1;
dap.dz=atof(word[5]);
add_stage(mdrun,STAGE_DISPLACE_ATOM,&dap);
}
+ else if(!strncmp(word[1],"del_atoms",9)) {
+ delp.o.x=atof(word[2]);
+ delp.o.y=atof(word[3]);
+ delp.o.z=atof(word[4]);
+ delp.r=atof(word[5]);
+ add_stage(mdrun,STAGE_DEL_ATOMS,&delp);
+ }
else if(!strncmp(word[1],"ins_atoms",9)) {
iap.ins_steps=atoi(word[2]);
iap.ins_atoms=atoi(word[3]);
return 0;
}
+int del_atoms(t_moldyn *moldyn,t_mdrun *mdrun) {
+
+ t_stage *stage;
+ t_del_atoms_params *delp;
+ int i;
+ t_3dvec dist;
+
+ stage=mdrun->stage.current->data;
+ delp=stage->params;
+
+ for(i=0;i<moldyn->count;i++) {
+ v3_sub(&dist,&(delp->o),&(moldyn->atom[i].r));
+//printf("%d ----> %f %f %f = %f | %f\n",i,dist.x,dist.y,dist.z,v3_absolute_square(&dist),delp->r*delp->r);
+ if(v3_absolute_square(&dist)<=(delp->r*delp->r)) {
+ del_atom(moldyn,moldyn->atom[i].tag);
+ printf("%s atom deleted: %d %d %d\n",ME,
+ moldyn->atom[i].tag,moldyn->atom[i].element,
+ moldyn->atom[i].brand);
+ }
+ }
+
+ return 0;
+
+}
+
int insert_atoms(t_moldyn *moldyn,t_mdrun *mdrun) {
t_insert_atoms_params *iap;
displace_atom(moldyn,mdrun);
change_stage=TRUE;
break;
+ case STAGE_DEL_ATOMS:
+ stage_print(" -> del atoms\n\n");
+ del_atoms(moldyn,mdrun);
+ change_stage=TRUE;
+ break;
case STAGE_INSERT_ATOMS:
stage_print(" -> insert atoms\n\n");
iap=stage->params;
create_lattice(moldyn,
fp->lattice,fp->lc,
- mdrun->element1,
- DEFAULT_ATOM_ATTR,0,
+ fp->fill_element,
+ DEFAULT_ATOM_ATTR,
+ fp->fill_brand,
fp->lx,fp->ly,fp->lz,
NULL,
&(fp->p_params),