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;
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]);
iap.z0=atof(word[10]);
break;
case 'r':
- if(word[8][0]=='t') {
+ switch(word[8][0]) {
+
+ case 't':
iap.type=INS_TOTAL;
iap.cr=atof(word[9]);
- }
- else {
- iap.type=INS_REGION;
- iap.x0=atof(word[8]);
- iap.y0=atof(word[9]);
- iap.z0=atof(word[10]);
- iap.x1=atof(word[11]);
- iap.y1=atof(word[12]);
- iap.z1=atof(word[13]);
- iap.cr=atof(word[14]);
+ break;
+ case 'r':
+ iap.type=INS_RECT;
+ iap.x0=atof(word[9]);
+ iap.y0=atof(word[10]);
+ iap.z0=atof(word[11]);
+ iap.x1=atof(word[12]);
+ iap.y1=atof(word[13]);
+ iap.z1=atof(word[14]);
+ iap.cr=atof(word[15]);
+ break;
+ case 's':
+ iap.type=INS_SPHERE;
+ iap.x0=atof(word[9]);
+ iap.y0=atof(word[10]);
+ iap.z0=atof(word[11]);
+ iap.x1=atof(word[12]);
+ iap.cr=atof(word[13]);
+ break;
+ default:
+ break;
}
default:
break;
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;
z0=-z/2.0;
cr_check=TRUE;
break;
- case INS_REGION:
+ case INS_RECT:
x=iap->x1-iap->x0;
x0=iap->x0;
y=iap->y1-iap->y0;
z0=iap->z0;
cr_check=TRUE;
break;
+ case INS_SPHERE:
+ x=2.0*iap->x1;
+ x0=iap->x0-iap->x1;
+ y=x;
+ y0=iap->y0-iap->x1;
+ z=x;
+ z0=iap->z0-iap->x1;
+ cr_check=TRUE;
+ break;
case INS_POS:
x0=iap->x0;
y0=iap->y0;
dmin=d;
}
}
+ if(iap->type==INS_SPHERE) {
+ if((r.x-iap->x0)*(r.x-iap->x0)+
+ (r.y-iap->y0)*(r.y-iap->y0)+
+ (r.z-iap->z0)*(r.z-iap->z0)>
+ (iap->x1*iap->x1)) {
+ run=1;
+ }
+ }
}
add_atom(moldyn,iap->element,
iap->brand,iap->attr,&r,&v);
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;