#include "potentials/tersoff.h"
#endif
-/* pse */
-#define PSE_MASS
-#include "pse.h"
-#undef PSE_MASS
-
#define ME "[mdrun]"
/*
case STAGE_DISPLACE_ATOM:
psize=sizeof(t_displace_atom_params);
break;
+ case STAGE_DEL_ATOMS:
+ psize=sizeof(t_del_atoms_params);
+ break;
+ case STAGE_MODIFY_ATOMS:
+ psize=sizeof(t_modify_atoms_params);
+ break;
case STAGE_INSERT_ATOMS:
psize=sizeof(t_insert_atoms_params);
break;
int i,o;
t_displace_atom_params dap;
+ t_modify_atoms_params map;
t_insert_atoms_params iap;
t_insert_mixed_atoms_params imp;
t_continue_params cp;
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);
// reset
memset(&iap,0,sizeof(t_insert_atoms_params));
+ memset(&map,0,sizeof(t_modify_atoms_params));
memset(&imp,0,sizeof(t_insert_mixed_atoms_params));
memset(&cp,0,sizeof(t_continue_params));
memset(&ap,0,sizeof(t_anneal_params));
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;
}
+ // offset
+ if(word[i][0]=='o') {
+ fp.o_params.o.x=atof(word[++i])*fp.lc;
+ fp.o_params.o.y=atof(word[++i])*fp.lc;
+ fp.o_params.o.z=atof(word[++i])*fp.lc;
+ fp.o_params.use=1;
+ continue;
+ }
i+=1;
}
add_stage(mdrun,STAGE_FILL,&fp);
}
i=2;
if(cap.type&CHAATTR_REGION) {
- cap.x0=atof(word[1]);
- cap.y0=atof(word[2]);
- cap.z0=atof(word[3]);
- cap.x1=atof(word[4]);
- cap.y1=atof(word[5]);
- cap.z1=atof(word[6]);
+ cap.x0=atof(word[2]);
+ cap.y0=atof(word[3]);
+ cap.z0=atof(word[4]);
+ cap.x1=atof(word[5]);
+ cap.y1=atof(word[6]);
+ cap.z1=atof(word[7]);
i+=6;
}
if(cap.type&CHAATTR_ELEMENT) {
csp.type=0;
for(i=1;i<wcnt;i++) {
if(!strncmp(word[i],"pctrl",5)) {
- csp.ptau=0.01/(atof(word[++i])*GPA);
+ csp.ptau=atof(word[++i]);
+ if(csp.ptau>0)
+ csp.ptau=0.01/(csp.ptau*GPA);
csp.type|=CHSATTR_PCTRL;
}
if(!strncmp(word[i],"tctrl",5)) {
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],"mod_atoms",8)) {
+ i=2;
+ while(i<wcnt) {
+ if(!strncmp(word[i],"t",1)) {
+ map.tag=atoi(word[++i]);
+ i+=1;
+ }
+ if(!strncmp(word[i],"ekin",5)) {
+ map.ekin.x=atof(word[++i])*EV;
+ map.ekin.y=atof(word[++i])*EV;
+ map.ekin.z=atof(word[++i])*EV;
+ i+=1;
+ }
+ }
+ add_stage(mdrun,STAGE_MODIFY_ATOMS,&map);
+ }
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 modify_atoms(t_moldyn *moldyn,t_mdrun *mdrun) {
+
+ t_modify_atoms_params *map;
+ t_stage *stage;
+ t_atom *atom;
+ t_3dvec v;
+ int i;
+
+ atom=moldyn->atom;
+ stage=mdrun->stage.current->data;
+ map=stage->params;
+ v.x=0.0; v.y=0.0; v.z=0.0;
+
+ for(i=0;i<moldyn->count;i++) {
+ if(atom[i].tag==map->tag) {
+ v.x=sqrt(2.0*fabs(map->ekin.x)/atom[i].mass);
+ if(map->ekin.x<0.0)
+ v.x=-v.x;
+ v.y=sqrt(2.0*fabs(map->ekin.y)/atom[i].mass);
+ if(map->ekin.y<0.0)
+ v.y=-v.y;
+ v.z=sqrt(2.0*fabs(map->ekin.z)/atom[i].mass);
+ if(map->ekin.z<0.0)
+ v.z=-v.z;
+ v3_copy(&(atom[i].v),&v);
+ printf("%s atom modified: v = (%f %f %f)\n",
+ ME,v.x,v.y,v.z);
+ }
+ }
+
+ return 0;
+}
+
int insert_atoms(t_moldyn *moldyn,t_mdrun *mdrun) {
t_insert_atoms_params *iap;
printf("%s atom inserted (%d/%d): %f %f %f\n",
ME,(iap->cnt_steps+1)*iap->ins_atoms,
iap->ins_steps*iap->ins_atoms,r.x,r.y,r.z);
- printf(" -> d2 = %f/%f\n",dmin,iap->cr*iap->cr);
+ printf(" attributes: ");
+ if(iap->attr&ATOM_ATTR_VB)
+ printf("b ");
+ if(iap->attr&ATOM_ATTR_HB)
+ printf("h ");
+ if(iap->attr&ATOM_ATTR_VA)
+ printf("v ");
+ if(iap->attr&ATOM_ATTR_FP)
+ printf("f ");
+ if(iap->attr&ATOM_ATTR_1BP)
+ printf("1 ");
+ if(iap->attr&ATOM_ATTR_2BP)
+ printf("2 ");
+ if(iap->attr&ATOM_ATTR_3BP)
+ printf("3 ");
+ printf("\n");
+ printf(" d2 = %f/%f\n",dmin,iap->cr*iap->cr);
cnt+=1;
}
continue;
}
if(cap->type&CHAATTR_REGION) {
- if(cap->x0<atom->r.x)
+ if(cap->x0>atom->r.x)
continue;
- if(cap->y0<atom->r.y)
+ if(cap->y0>atom->r.y)
continue;
- if(cap->z0<atom->r.z)
+ if(cap->z0>atom->r.z)
continue;
- if(cap->x1>atom->r.x)
+ if(cap->x1<atom->r.x)
continue;
- if(cap->y1>atom->r.y)
+ if(cap->y1<atom->r.y)
continue;
- if(cap->z1>atom->r.z)
+ if(cap->z1<atom->r.z)
continue;
}
+ if(!(cap->type&CHAATTR_TOTALV))
+ printf(" changing attributes of atom %d (0x%x)\n",
+ i,cap->attr);
atom->attr=cap->attr;
}
+ printf("\n\n");
+
return 0;
}
if(csp->ptau>0)
set_p_scale(moldyn,P_SCALE_BERENDSEN,csp->ptau);
else
- set_p_scale(moldyn,P_SCALE_BERENDSEN,csp->ptau);
+ set_p_scale(moldyn,P_SCALE_NONE,1.0);
}
if(csp->type&CHSATTR_TCTRL) {
if(csp->ttau>0)
set_t_scale(moldyn,T_SCALE_BERENDSEN,csp->ttau);
else
- set_t_scale(moldyn,T_SCALE_BERENDSEN,csp->ttau);
+ set_t_scale(moldyn,T_SCALE_NONE,1.0);
}
if(csp->type&CHSATTR_PRELAX) {
if(csp->dp<0)
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_MODIFY_ATOMS:
+ stage_print(" -> modify atoms\n\n");
+ modify_atoms(moldyn,mdrun);
+ change_stage=TRUE;
+ break;
case STAGE_INSERT_ATOMS:
stage_print(" -> insert atoms\n\n");
iap=stage->params;
fp->lx,fp->ly,fp->lz,
&o,
&(fp->p_params),
- &(fp->d_params));
+ &(fp->d_params),
+ &(fp->o_params));
o.x+=0.25*fp->lc;
o.y=o.x;
o.z=o.x;
fp->lx,fp->ly,fp->lz,
&o,
&(fp->p_params),
- &(fp->d_params));
+ &(fp->d_params),
+ &(fp->o_params));
break;
default:
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),
- &(fp->d_params));
+ &(fp->d_params),
+ &(fp->o_params));
break;
}
moldyn_bc_check(moldyn);