#include "potentials/tersoff.h"
#endif
+/* pse */
+#define PSE_MASS
+#include "pse.h"
+#undef PSE_MASS
+
#define ME "[mdrun]"
/*
case STAGE_INSERT_ATOMS:
psize=sizeof(t_insert_atoms_params);
break;
+ case STAGE_INSERT_MIXED_ATOMS:
+ psize=sizeof(t_insert_mixed_atoms_params);
+ break;
case STAGE_CONTINUE:
psize=sizeof(t_continue_params);
break;
case STAGE_CHSATTR:
psize=sizeof(t_chsattr_params);
break;
+ case STAGE_SET_TEMP:
+ psize=sizeof(t_set_temp_params);
+ break;
+ case STAGE_SET_TIMESTEP:
+ psize=sizeof(t_set_timestep_params);
+ break;
default:
printf("%s unknown stage type: %02x\n",ME,type);
return -1;
t_displace_atom_params dap;
t_insert_atoms_params iap;
+ t_insert_mixed_atoms_params imp;
t_continue_params cp;
t_anneal_params ap;
t_chaattr_params cap;
t_chsattr_params csp;
+ t_set_temp_params stp;
+ t_set_timestep_params stsp;
/* open config file */
fd=open(mdrun->cfile,O_RDONLY);
// reset
memset(&iap,0,sizeof(t_insert_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(&cap,0,sizeof(t_chaattr_params));
memset(&csp,0,sizeof(t_chsattr_params));
+ memset(&stp,0,sizeof(t_set_temp_params));
+ memset(&stsp,0,sizeof(t_set_timestep_params));
// get command + args
wcnt=0;
mdrun->lattice=FCC;
if(!strncmp(word[1],"diamond",7))
mdrun->lattice=DIAMOND;
+ if(!strncmp(word[1],"none",4))
+ mdrun->lattice=NONE;
}
else if(!strncmp(word[0],"element1",8)) {
mdrun->element1=atoi(word[1]);
}
add_stage(mdrun,STAGE_INSERT_ATOMS,&iap);
}
+
+
+ // HERE WE GO ...
+
+ else if(!strncmp(word[1],"ins_m_atoms",11)) {
+ imp.element1=atoi(word[2]);
+ imp.element2=atoi(word[3]);
+ imp.amount1=atoi(word[4]);
+ imp.amount2=atoi(word[5]);
+ imp.brand1=atoi(word[6]);
+ imp.brand2=atoi(word[7]);
+ imp.crmin=atof(word[8]);
+ imp.crmax=atof(word[9]);
+ /* do this later ...
+ for(i=0;i<strlen(word[8]);i++) {
+ switch(word[8][i]) {
+ case 'b':
+ imp.attr|=ATOM_ATTR_VB;
+ break;
+ case 'h':
+ imp.attr|=ATOM_ATTR_HB;
+ break;
+ case 'v':
+ imp.attr|=ATOM_ATTR_VA;
+ break;
+ case 'f':
+ imp.attr|=ATOM_ATTR_FP;
+ break;
+ case '1':
+ imp.attr|=ATOM_ATTR_1BP;
+ break;
+ case '2':
+ imp.attr|=ATOM_ATTR_2BP;
+ break;
+ case '3':
+ imp.attr|=ATOM_ATTR_3BP;
+ break;
+ default:
+ break;
+ }
+ }
+ */
+ imp.attr1=ATOM_ATTR_HB|ATOM_ATTR_VA|ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_FP;
+ imp.attr2=ATOM_ATTR_HB|ATOM_ATTR_VA|ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_FP;
+ add_stage(mdrun,STAGE_INSERT_MIXED_ATOMS,&imp);
+ }
+
+
+
+
+
else if(!strncmp(word[1],"continue",8)) {
cp.runs=atoi(word[2]);
add_stage(mdrun,STAGE_CONTINUE,&cp);
ap.count=0;
ap.runs=atoi(word[2]);
ap.dt=atof(word[3]);
+ ap.interval=atoi(word[4]);
add_stage(mdrun,STAGE_ANNEAL,&ap);
}
+ else if(!strncmp(word[1],"set_temp",8)) {
+ if(word[2][0]=='c') {
+ stp.type=SET_TEMP_CURRENT;
+ stp.val=0.0;
+ }
+ else {
+ stp.type=SET_TEMP_VALUE;
+ stp.val=atof(word[2]);
+ }
+ add_stage(mdrun,STAGE_SET_TEMP,&stp);
+ }
+ else if(!strncmp(word[1],"set_timestep",12)) {
+ stsp.tau=atof(word[2]);
+ add_stage(mdrun,STAGE_SET_TIMESTEP,&stsp);
+ }
else {
printf("%s unknown stage type: %s\n",
ME,word[1]);
return 0;
}
+int insert_mixed_atoms(t_moldyn *moldyn,t_mdrun *mdrun) {
+
+ t_stage *stage;
+ t_insert_mixed_atoms_params *imp;
+ t_atom *atom;
+ double x,x0,y,y0,z,z0;
+ double dmin,d,cmin,cmax;
+ u8 retry;
+ t_3dvec r,v,dist;
+ int i;
+
+
+ stage=mdrun->stage.current->data;
+ imp=stage->params;
+
+ x=moldyn->dim.x;
+ x0=-x/2.0;
+ y=moldyn->dim.y;
+ y0=-y/2.0;
+ z=moldyn->dim.z;
+ z0=-z/2.0;
+
+ v.x=0.0;
+ v.y=0.0;
+ v.z=0.0;
+
+ cmin=imp->crmin*imp->crmin;
+ cmax=imp->crmax*imp->crmax;
+
+ while(imp->amount1|imp->amount2) {
+ if(imp->amount1) {
+ retry=1;
+ while(retry) {
+ retry=0;
+ r.x=rand_get_double(&(moldyn->random))*x;
+ r.y=rand_get_double(&(moldyn->random))*y;
+ r.z=rand_get_double(&(moldyn->random))*z;
+ r.x+=x0;
+ r.y+=y0;
+ r.z+=z0;
+ dmin=1000.0; // for sure too high!
+ for(i=0;i<moldyn->count;i++) {
+ atom=&(moldyn->atom[i]);
+ v3_sub(&dist,&(atom->r),&r);
+ check_per_bound(moldyn,&dist);
+ d=v3_absolute_square(&dist);
+ if(d<cmin) {
+ retry=1;
+ break;
+ }
+ if(d<dmin)
+ dmin=d;
+ }
+ if(dmin!=1000.0)
+ if(dmin>cmax)
+ retry=1;
+ }
+ add_atom(moldyn,imp->element1,pse_mass[imp->element1],
+ imp->brand1,imp->attr1,&r,&v);
+ printf("%s (mixed) atom inserted (%d): %f %f %f\n",
+ ME,imp->amount1,r.x,r.y,r.z);
+ printf(" -> d2 = %f/%f/%f\n",dmin,cmin,cmax);
+ imp->amount1-=1;
+ }
+ if(imp->amount2) {
+ retry=1;
+ while(retry) {
+ retry=0;
+ r.x=rand_get_double(&(moldyn->random))*x;
+ r.y=rand_get_double(&(moldyn->random))*y;
+ r.z=rand_get_double(&(moldyn->random))*z;
+ r.x+=x0;
+ r.y+=y0;
+ r.z+=z0;
+ dmin=1000.0; // for sure too high!
+ for(i=0;i<moldyn->count;i++) {
+ atom=&(moldyn->atom[i]);
+ v3_sub(&dist,&(atom->r),&r);
+ check_per_bound(moldyn,&dist);
+ d=v3_absolute_square(&dist);
+ if(d<cmin) {
+ retry=1;
+ break;
+ }
+ if(d<dmin)
+ dmin=d;
+ }
+ if(dmin!=1000.0)
+ if(dmin>cmax)
+ retry=1;
+ }
+ add_atom(moldyn,imp->element2,pse_mass[imp->element2],
+ imp->brand2,imp->attr2,&r,&v);
+ printf("%s (mixed) atom inserted (%d): %f %f %f\n",
+ ME,imp->amount2,r.x,r.y,r.z);
+ printf(" -> d2 = %f/%f/%f\n",dmin,cmin,cmax);
+ imp->amount2-=1;
+ }
+ }
+
+ return 0;
+}
+
int chaatr(t_moldyn *moldyn,t_mdrun *mdrun) {
t_stage *stage;
t_stage *stage;
t_list *sl;
int steps;
- double tau;
u8 change_stage;
t_insert_atoms_params *iap;
+ t_insert_mixed_atoms_params *imp;
t_continue_params *cp;
t_anneal_params *ap;
+ t_set_temp_params *stp;
+ t_set_timestep_params *stsp;
moldyn=ptr1;
mdrun=ptr2;
/* get stage description */
stage=sl->current->data;
- /* default steps and tau values */
+ /* steps in next schedule */
steps=mdrun->relax_steps;
- tau=mdrun->timestep;
/* check whether relaxation steps are necessary */
if((check_pressure(moldyn,mdrun)==TRUE)&\
insert_atoms(moldyn,mdrun);
iap->cnt_steps+=1;
break;
+
+
+
+ case STAGE_INSERT_MIXED_ATOMS:
+ stage_print(" -> insert mixed atoms\n\n");
+ imp=stage->params;
+ insert_mixed_atoms(moldyn,mdrun);
+ change_stage=TRUE;
+ break;
+
+
+
case STAGE_CONTINUE:
stage_print(" -> continue\n\n");
if(stage->executed==TRUE) {
set_temperature(moldyn,
moldyn->t_ref+ap->dt);
ap->count+=1;
+ steps=ap->interval;
break;
case STAGE_CHAATTR:
- stage_print(" -> chaattr\n\n");
+ stage_print(" -> change atom attributes\n\n");
chaatr(moldyn,mdrun);
change_stage=TRUE;
break;
case STAGE_CHSATTR:
- stage_print(" -> chsattr\n\n");
+ stage_print(" -> change sys attributes\n\n");
chsattr(moldyn,mdrun);
change_stage=TRUE;
break;
+ case STAGE_SET_TEMP:
+ stage_print(" -> set temperature\n\n");
+ stp=stage->params;
+ if(stp->type&SET_TEMP_CURRENT) {
+ set_temperature(moldyn,moldyn->t_avg);
+ }
+ else {
+ set_temperature(moldyn,stp->val);
+ }
+ change_stage=TRUE;
+ break;
+ case STAGE_SET_TIMESTEP:
+ stage_print(" -> set timestep\n\n");
+ stsp=stage->params;
+ mdrun->timestep=stsp->tau;
+ change_stage=TRUE;
+ break;
default:
printf("%s unknwon stage type\n",ME);
break;
return 0;
}
steps=0;
- tau=mdrun->timestep;
}
}
}
/* continue simulation */
- moldyn_add_schedule(moldyn,steps,tau);
+ moldyn_add_schedule(moldyn,steps,mdrun->timestep);
return 0;
}
mdrun.m2,DEFAULT_ATOM_ATTR,1,mdrun.lx,
mdrun.ly,mdrun.lz,&o);
break;
+ case NONE:
+ set_nn_dist(&moldyn,mdrun.nnd);
+ break;
default:
printf("%s unknown lattice type: %02x\n",
ME,mdrun.lattice);
projects / physik / posic.git / blobdiff