X-Git-Url: https://hackdaworld.org/gitweb/?a=blobdiff_plain;f=mdrun.c;h=17ce2776544d765276f48a68eae4ffc11328f2f9;hb=302ab3d5071520fcfd17be54c13dc44bb1f39ab7;hp=31943efc65bd39680dc8dec02fec465ce39c7e90;hpb=67df6b3a722a44e36fd56f3f040c3c9726b3fc3f;p=physik%2Fposic.git diff --git a/mdrun.c b/mdrun.c index 31943ef..17ce277 100644 --- a/mdrun.c +++ b/mdrun.c @@ -17,6 +17,11 @@ #include "potentials/tersoff.h" #endif +/* pse */ +#define PSE_MASS +#include "pse.h" +#undef PSE_MASS + #define ME "[mdrun]" /* @@ -111,6 +116,12 @@ int add_stage(t_mdrun *mdrun,u8 type,void *params) { 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; @@ -155,6 +166,8 @@ int mdrun_parse_config(t_mdrun *mdrun) { 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); @@ -184,6 +197,8 @@ int mdrun_parse_config(t_mdrun *mdrun) { 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; @@ -269,6 +284,14 @@ int mdrun_parse_config(t_mdrun *mdrun) { mdrun->ly=atoi(word[3]); mdrun->lz=atoi(word[4]); mdrun->lc=atof(word[5]); + if(wcnt==8) { + mdrun->fill_element=atoi(word[6]); + mdrun->fill_brand=atoi(word[7]); + } + else { + mdrun->fill_element=mdrun->element1; + mdrun->fill_brand=0; + } } else if(!strncmp(word[0],"aattr",5)) { // for aatrib line we need a special stage @@ -459,7 +482,8 @@ int mdrun_parse_config(t_mdrun *mdrun) { imp.amount2=atoi(word[5]); imp.brand1=atoi(word[6]); imp.brand2=atoi(word[7]); - imp.cr=atof(word[8]); + imp.crmin=atof(word[8]); + imp.crmax=atof(word[9]); /* do this later ... for(i=0;icr*imp->cr; + cmin=imp->crmin*imp->crmin; + cmax=imp->crmax*imp->crmax; while(imp->amount1|imp->amount2) { if(imp->amount1) { @@ -745,20 +786,22 @@ int insert_mixed_atoms(t_moldyn *moldyn,t_mdrun *mdrun) { v3_sub(&dist,&(atom->r),&r); check_per_bound(moldyn,&dist); d=v3_absolute_square(&dist); - if(dcmax) + 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\n",dmin,c); + printf(" -> d2 = %f/%f/%f\n",dmin,cmin,cmax); imp->amount1-=1; } if(imp->amount2) { @@ -777,20 +820,22 @@ int insert_mixed_atoms(t_moldyn *moldyn,t_mdrun *mdrun) { v3_sub(&dist,&(atom->r),&r); check_per_bound(moldyn,&dist); d=v3_absolute_square(&dist); - if(dcmax) + 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\n",dmin,c); + printf(" -> d2 = %f/%f/%f\n",dmin,cmin,cmax); imp->amount2-=1; } } @@ -891,13 +936,14 @@ int mdrun_hook(void *ptr1,void *ptr2) { 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; @@ -913,9 +959,8 @@ int mdrun_hook(void *ptr1,void *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)&\ @@ -950,6 +995,7 @@ int mdrun_hook(void *ptr1,void *ptr2) { stage_print(" -> insert mixed atoms\n\n"); imp=stage->params; insert_mixed_atoms(moldyn,mdrun); + change_stage=TRUE; break; @@ -974,17 +1020,35 @@ int mdrun_hook(void *ptr1,void *ptr2) { 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; @@ -1001,7 +1065,6 @@ int mdrun_hook(void *ptr1,void *ptr2) { return 0; } steps=0; - tau=mdrun->timestep; } } @@ -1014,7 +1077,7 @@ int mdrun_hook(void *ptr1,void *ptr2) { } /* continue simulation */ - moldyn_add_schedule(moldyn,steps,tau); + moldyn_add_schedule(moldyn,steps,mdrun->timestep); return 0; } @@ -1100,13 +1163,16 @@ int main(int argc,char **argv) { set_pbc(&moldyn,mdrun.pbcx,mdrun.pbcy,mdrun.pbcz); switch(mdrun.lattice) { case FCC: - create_lattice(&moldyn,FCC,mdrun.lc,mdrun.element1, - mdrun.m1,DEFAULT_ATOM_ATTR,0,mdrun.lx, + create_lattice(&moldyn,FCC,mdrun.lc,mdrun.fill_element, + mdrun.m1,DEFAULT_ATOM_ATTR, + mdrun.fill_brand,mdrun.lx, mdrun.ly,mdrun.lz,NULL); break; case DIAMOND: - create_lattice(&moldyn,DIAMOND,mdrun.lc,mdrun.element1, - mdrun.m1,DEFAULT_ATOM_ATTR,0,mdrun.lx, + create_lattice(&moldyn,DIAMOND,mdrun.lc, + mdrun.fill_element, + mdrun.m1,DEFAULT_ATOM_ATTR, + mdrun.fill_brand,mdrun.lx, mdrun.ly,mdrun.lz,NULL); break; case ZINCBLENDE: @@ -1120,6 +1186,7 @@ int main(int argc,char **argv) { mdrun.ly,mdrun.lz,&o); break; case NONE: + set_nn_dist(&moldyn,mdrun.nnd); break; default: printf("%s unknown lattice type: %02x\n",