#include "potentials/tersoff.h"
#endif
+/* pse */
+#define PSE_MASS
+#include "pse.h"
+#undef PSE_MASS
+
#define ME "[mdrun]"
/*
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;
+ case STAGE_FILL:
+ psize=sizeof(t_fill_params);
+ break;
+ case STAGE_THERMAL_INIT:
+ psize=0;
+ break;
default:
printf("%s unknown stage type: %02x\n",ME,type);
return -1;
char error[128];
char line[128];
char *wptr;
- char word[16][64];
+ char word[32][64];
int wcnt;
int i,o;
t_anneal_params ap;
t_chaattr_params cap;
t_chsattr_params csp;
+ t_set_temp_params stp;
+ t_set_timestep_params stsp;
+ t_fill_params fp;
/* open config file */
fd=open(mdrun->cfile,O_RDONLY);
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));
+ memset(&fp,0,sizeof(t_fill_params));
// get command + args
wcnt=0;
mdrun->lattice=DIAMOND;
if(!strncmp(word[1],"none",4))
mdrun->lattice=NONE;
+ if(wcnt==3)
+ mdrun->lc=atof(word[2]);
}
else if(!strncmp(word[0],"element1",8)) {
mdrun->element1=atoi(word[1]);
- mdrun->m1=pse_mass[mdrun->element1];
}
else if(!strncmp(word[0],"element2",8)) {
mdrun->element2=atoi(word[1]);
- mdrun->m2=pse_mass[mdrun->element2];
}
else if(!strncmp(word[0],"fill",6)) {
- // only lc mode by now
- mdrun->lx=atoi(word[2]);
- mdrun->ly=atoi(word[3]);
- mdrun->lz=atoi(word[4]);
- mdrun->lc=atof(word[5]);
+ // default values
+ fp.fill_element=mdrun->element1;
+ fp.fill_brand=0;
+ fp.lattice=mdrun->lattice;
+ fp.p_params.type=0;
+ fp.d_params.type=0;
+ fp.d_params.stype=0;
+ // parse fill command
+ i=1;
+ while(i<wcnt) {
+ if(!strncmp(word[i],"lc",2)) {
+ fp.lx=atoi(word[++i]);
+ fp.ly=atoi(word[++i]);
+ fp.lz=atoi(word[++i]);
+ fp.lc=atof(word[++i]);
+ mdrun->lc=fp.lc;
+ }
+ if(!strncmp(word[i],"eb",2)) {
+ fp.fill_element=atoi(word[++i]);
+ fp.fill_brand=atoi(word[++i]);
+ }
+ if(word[i][0]=='p') {
+ i+=1;
+ switch(word[i][0]) {
+ case 'i':
+ if(word[i][1]=='r')
+ fp.p_params.type=PART_INSIDE_R;
+ else
+ fp.p_params.type=PART_INSIDE_D;
+ break;
+ case 'o':
+ if(word[i][1]=='r')
+ fp.p_params.type=PART_OUTSIDE_R;
+ else
+ fp.p_params.type=PART_OUTSIDE_D;
+ break;
+ default:
+ break;
+ }
+ if((fp.p_params.type==PART_INSIDE_R)||
+ (fp.p_params.type==PART_OUTSIDE_R)) {
+ fp.p_params.r=atof(word[++i]);
+ fp.p_params.p.x=atof(word[++i]);
+ fp.p_params.p.y=atof(word[++i]);
+ fp.p_params.p.z=atof(word[++i]);
+ }
+ if((fp.p_params.type==PART_INSIDE_D)||
+ (fp.p_params.type==PART_OUTSIDE_D)) {
+ fp.p_params.p.x=atof(word[++i]);
+ fp.p_params.p.y=atof(word[++i]);
+ fp.p_params.p.z=atof(word[++i]);
+ fp.p_params.d.x=atof(word[++i]);
+ fp.p_params.d.y=atof(word[++i]);
+ fp.p_params.d.z=atof(word[++i]);
+ }
+ }
+ if(word[i][0]=='d') {
+ switch(word[++i][0]) {
+ case '0':
+
+ fp.d_params.type=DEFECT_TYPE_0D;
+ if(!strncmp(word[i+1],"dbx",3)) {
+ fp.d_params.stype=DEFECT_STYPE_DB_X;
+ }
+ if(!strncmp(word[i+1],"dby",3)) {
+ fp.d_params.stype=DEFECT_STYPE_DB_Y;
+ }
+ if(!strncmp(word[i+1],"dbz",3)) {
+ fp.d_params.stype=DEFECT_STYPE_DB_Z;
+ }
+ if(!strncmp(word[i+1],"dbr",3)) {
+ fp.d_params.stype=DEFECT_STYPE_DB_R;
+ }
+ i+=1;
+ fp.d_params.od=atof(word[++i]);
+ fp.d_params.dd=atof(word[++i]);
+ fp.d_params.element=atoi(word[++i]);
+ fp.d_params.brand=atoi(word[++i]);
+ // parsed in future
+ fp.d_params.attr=ATOM_ATTR_HB|ATOM_ATTR_VA;
+ fp.d_params.attr|=ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP;
+ break;
+
+ case '1':
+ fp.d_params.type=DEFECT_TYPE_1D;
+ break;
+ case '2':
+ fp.d_params.type=DEFECT_TYPE_2D;
+ break;
+ case '3':
+ fp.d_params.type=DEFECT_TYPE_3D;
+ break;
+ default:
+ break;
+ }
+
+ }
+ i+=1;
+ }
+ add_stage(mdrun,STAGE_FILL,&fp);
+ }
+ else if(!strncmp(word[0],"thermal_init",12)) {
+ add_stage(mdrun,STAGE_THERMAL_INIT,NULL);
}
else if(!strncmp(word[0],"aattr",5)) {
// for aatrib line we need a special stage
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;
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]);
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,pse_mass[iap->element],
+ add_atom(moldyn,iap->element,
iap->brand,iap->attr,&r,&v);
printf("%s atom inserted (%d/%d): %f %f %f\n",
ME,(iap->cnt_steps+1)*iap->ins_atoms,
if(dmin>cmax)
retry=1;
}
- add_atom(moldyn,imp->element1,pse_mass[imp->element1],
+ add_atom(moldyn,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);
if(dmin>cmax)
retry=1;
}
- add_atom(moldyn,imp->element2,pse_mass[imp->element2],
+ add_atom(moldyn,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);
t_stage *stage;
t_list *sl;
int steps;
- double tau;
u8 change_stage;
+ t_3dvec o;
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;
+ t_fill_params *fp;
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)&\
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;
+ case STAGE_FILL:
+ stage_print(" -> fill lattice\n\n");
+ fp=stage->params;
+ switch(fp->lattice) {
+ case ZINCBLENDE:
+
+ o.x=0.5*0.25*fp->lc;
+ o.y=o.x;
+ o.z=o.x;
+ create_lattice(moldyn,
+ FCC,fp->lc,
+ mdrun->element1,
+ DEFAULT_ATOM_ATTR,0,
+ fp->lx,fp->ly,fp->lz,
+ &o,
+ &(fp->p_params),
+ &(fp->d_params));
+ o.x+=0.25*fp->lc;
+ o.y=o.x;
+ o.z=o.x;
+ create_lattice(moldyn,
+ FCC,fp->lc,
+ mdrun->element2,
+ DEFAULT_ATOM_ATTR,1,
+ fp->lx,fp->ly,fp->lz,
+ &o,
+ &(fp->p_params),
+ &(fp->d_params));
+ break;
+
+ default:
+
+ create_lattice(moldyn,
+ fp->lattice,fp->lc,
+ mdrun->element1,
+ DEFAULT_ATOM_ATTR,0,
+ fp->lx,fp->ly,fp->lz,
+ NULL,
+ &(fp->p_params),
+ &(fp->d_params));
+ break;
+ }
+ moldyn_bc_check(moldyn);
+ change_stage=TRUE;
+ break;
+ case STAGE_THERMAL_INIT:
+ stage_print(" -> thermal init\n\n");
+ thermal_init(moldyn,TRUE);
+ 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;
}
t_mdrun mdrun;
t_moldyn moldyn;
- t_3dvec o;
+ //t_3dvec o;
/* clear structs */
memset(&mdrun,0,sizeof(t_mdrun));
/* initial lattice and dimensions */
set_dim(&moldyn,mdrun.dim.x,mdrun.dim.y,mdrun.dim.z,mdrun.vis);
set_pbc(&moldyn,mdrun.pbcx,mdrun.pbcy,mdrun.pbcz);
+ /* replaced by fill stage !!
switch(mdrun.lattice) {
case FCC:
- create_lattice(&moldyn,FCC,mdrun.lc,mdrun.element1,
- mdrun.m1,DEFAULT_ATOM_ATTR,0,mdrun.lx,
- mdrun.ly,mdrun.lz,NULL);
+ create_lattice(&moldyn,FCC,mdrun.lc,mdrun.fill_element,
+ mdrun.m1,DEFAULT_ATOM_ATTR,
+ mdrun.fill_brand,mdrun.lx,
+ mdrun.ly,mdrun.lz,NULL,0,NULL);
break;
case DIAMOND:
- create_lattice(&moldyn,DIAMOND,mdrun.lc,mdrun.element1,
- mdrun.m1,DEFAULT_ATOM_ATTR,0,mdrun.lx,
- mdrun.ly,mdrun.lz,NULL);
+ create_lattice(&moldyn,DIAMOND,mdrun.lc,
+ mdrun.fill_element,
+ mdrun.m1,DEFAULT_ATOM_ATTR,
+ mdrun.fill_brand,mdrun.lx,
+ mdrun.ly,mdrun.lz,NULL,0,NULL);
break;
case ZINCBLENDE:
o.x=0.5*0.25*mdrun.lc; o.y=o.x; o.z=o.x;
create_lattice(&moldyn,FCC,mdrun.lc,mdrun.element1,
mdrun.m1,DEFAULT_ATOM_ATTR,0,mdrun.lx,
- mdrun.ly,mdrun.lz,&o);
+ mdrun.ly,mdrun.lz,&o,0,NULL);
o.x+=0.25*mdrun.lc; o.y=o.x; o.z=o.x;
create_lattice(&moldyn,FCC,mdrun.lc,mdrun.element2,
mdrun.m2,DEFAULT_ATOM_ATTR,1,mdrun.lx,
- mdrun.ly,mdrun.lz,&o);
+ mdrun.ly,mdrun.lz,&o,0,NULL);
break;
case NONE:
+ set_nn_dist(&moldyn,mdrun.nnd);
break;
default:
printf("%s unknown lattice type: %02x\n",
return -1;
}
moldyn_bc_check(&moldyn);
+ replaced by fill stage !! */
/* temperature and pressure */
set_temperature(&moldyn,mdrun.temperature);
set_pressure(&moldyn,mdrun.pressure);
+ /* replaced thermal_init stage
thermal_init(&moldyn,TRUE);
+ */
addsched:
/* first schedule */
projects / physik / posic.git / blobdiff