X-Git-Url: https://www.hackdaworld.org/gitweb/?p=physik%2Fposic.git;a=blobdiff_plain;f=sic.c;h=375c6d54b38756aef74f12431075dd8fd6b446fc;hp=05de728c9e9cdd4be50bf73a1e1a51fd6956d195;hb=HEAD;hpb=b5b47daaa3718c4dec2056fe5147668023575b8e diff --git a/sic.c b/sic.c index 05de728..375c6d5 100644 --- a/sic.c +++ b/sic.c @@ -13,182 +13,242 @@ #include "potentials/harmonic_oscillator.h" #include "potentials/lennard_jones.h" #include "potentials/albe.h" - #ifdef TERSOFF_ORIG #include "potentials/tersoff_orig.h" #else #include "potentials/tersoff.h" #endif -//#define INJECT 800 -#define INJECT 1 -#define NR_ATOMS 1 -#define R_C 1.5 -#define T_C 5.0 -//#define INJ_LENX (1*ALBE_LC_SIC) -//#define INJ_LENY (1*ALBE_LC_SIC) -//#define INJ_LENZ (1*ALBE_LC_SIC) -#define INJ_LENX (1*ALBE_LC_SI) -#define INJ_LENY (1*ALBE_LC_SI) -#define INJ_LENZ (1*ALBE_LC_SI) -#define INJ_TYPE_SILICON -//#define INJ_TYPE_CARBON -#define INJ_OFFSET (ALBE_LC_SI/8.0) -#define RELAX_S 20 - -#define LCNTX 9 -#define LCNTY 9 -#define LCNTZ 9 -#define PRERUN 40 -#define POSTRUN 3000 - -#define R_TITLE "Silicon self-interstitial" -#define LOG_E 10 -#define LOG_T 10 -#define LOG_P 10 -#define LOG_S 100 -#define LOG_V 20 - typedef struct s_hp { - int a_count; /* atom count */ - u8 quit; /* quit mark */ - int argc; /* arg count */ - char **argv; /* args */ + int prerun_count; /* prerun count */ + int insert_count; /* insert count */ + int postrun_count; /* post run count */ + unsigned char state; /* current state */ + int argc; /* arg count */ + char **argv; /* args */ } t_hp; -int hook_del_atom(void *moldyn,void *hook_params) { - - t_moldyn *md; - t_hp *hp; +#define STATE_PRERUN 0x00 +#define STATE_INSERT 0x01 +#define STATE_POSTRUN 0x02 - md=moldyn; - hp=hook_params; - - set_pt_scale(md,0,0,T_SCALE_BERENDSEN,100.0); - del_atom(md,2); - - return 0; -} +/* include the config file */ +#include "config.h" -int hook_add_atom(void *moldyn,void *hook_params) { +int insert_atoms(t_moldyn *moldyn) { - t_moldyn *md; - t_3dvec r,v,dist; - double d; - unsigned char run; int i,j; - t_atom *atom; - t_hp *hp; - - md=moldyn; - hp=hook_params; - - /* quit */ - if(hp->quit) - return 0; + u8 run; + t_3dvec r,v,dist; + double d,dmin; - /* switch on t scaling */ - if(md->schedule.count==0) - set_pt_scale(md,0,0,T_SCALE_BERENDSEN,100.0); + t_atom *atom; - /* last schedule add if there is enough carbon inside */ - if(hp->a_count==(INJECT*NR_ATOMS)) { - hp->quit=1; - moldyn_add_schedule(md,POSTRUN,1.0); - return 0; - } + atom=moldyn->atom; - /* more relaxing time for too high temperatures */ - if(md->t-md->t_ref>T_C) { - moldyn_add_schedule(md,RELAX_S,1.0); - return 0; - } + v.x=0; v.y=0; v.z=0; - /* inject carbon atoms */ - printf("injecting another %d atoms ... (-> %d / %d)\n", - NR_ATOMS,hp->a_count+NR_ATOMS,INJECT*NR_ATOMS); - for(j=0;jatom[4372].r.x=(-0.5+0.125+0.125)*ALBE_LC_SI; - md->atom[4372].r.y=(-0.5+0.125+0.125)*ALBE_LC_SI; - */ + moldyn->atom[4372].r.x=(-0.5+0.125+0.125)*ALBE_LC_SI; + moldyn->atom[4372].r.y=(-0.5+0.125+0.125)*ALBE_LC_SI; +#endif +#ifdef INS_001DB + // 001 dumbbell + r.x=(-0.5+0.25)*ALBE_LC_SI; + r.y=(-0.5+0.25)*ALBE_LC_SI; + r.z=(-0.1)*ALBE_LC_SI; + moldyn->atom[4372].r.z=(-0.4)*ALBE_LC_SI; +#endif +#ifdef INS_USER + // 001 dumbbell + r.x=INS_UX*ALBE_LC_SI; + r.y=INS_UY*ALBE_LC_SI; + r.z=INS_UZ*ALBE_LC_SI; +#endif +#ifdef INS_RAND // random - /* - r.x=(rand_get_double(&(md->random))-0.5)*INJ_LENX; - r.y=(rand_get_double(&(md->random))-0.5)*INJ_LENY; - r.z=(rand_get_double(&(md->random))-0.5)*INJ_LENZ; - */ +#ifdef INS_DYNAMIC_LEN + r.x=(rand_get_double(&(moldyn->random))-0.5)*\ + moldyn->dim.x; + r.y=(rand_get_double(&(moldyn->random))-0.5)*\ + moldyn->dim.y; + r.z=(rand_get_double(&(moldyn->random))-0.5)*\ + moldyn->dim.z; +#else + r.x=(rand_get_double(&(moldyn->random))-0.5)*INS_LENX; + r.y=(rand_get_double(&(moldyn->random))-0.5)*INS_LENY; + r.z=(rand_get_double(&(moldyn->random))-0.5)*INS_LENZ; +#endif +#endif // offset - r.x+=INJ_OFFSET; - r.y+=INJ_OFFSET; - r.z+=INJ_OFFSET; + r.x+=INS_OFFSET; + r.y+=INS_OFFSET; + r.z+=INS_OFFSET; /* assume valid coordinates */ run=0; - for(i=0;icount;i++) { - atom=&(md->atom[i]); + dmin=10000000000.0; // for sure too high! + for(i=0;icount;i++) { + atom=&(moldyn->atom[i]); v3_sub(&dist,&(atom->r),&r); + check_per_bound(moldyn,&dist); d=v3_absolute_square(&dist); /* reject coordinates */ - if(dcount-1,r.x,r.y,r.z,dmin); + } + + return 0; +} + +int sic_hook(void *moldyn,void *hook_params) { + + t_hp *hp; + t_moldyn *md; + int steps; + double tau; + double dt; + double dp; + + hp=hook_params; + md=moldyn; + + tau=1.0; + steps=0; + + /* switch on t scaling */ + if(md->schedule.count==0) + set_pt_scale(md,P_SCALE_BERENDSEN,P_SCALE_TAU, + T_SCALE_BERENDSEN,T_SCALE_TAU); + + /* my lousy state machine ! */ + + /* switch to insert state immediately */ + if(hp->state==STATE_PRERUN) + hp->state=STATE_INSERT; + + switch(hp->state) { + case STATE_INSERT: + goto insert; + break; + case STATE_POSTRUN: + goto postrun; + break; + default: + printf("[sic hook] unknown state\n"); + return -1; + } + + /* act according to state */ + +insert: + + /* assigne values */ + steps=INS_RELAX; + tau=INS_TAU; + + /* check temperature */ + dt=md->t_avg-md->t_ref; + dp=md->p_avg-md->p_ref; + if(dt<0) + dt=-dt; + if(dp<0) + dp=-dp; + if((dt>INS_DELTA_TC)|(dp>INS_DELTA_PC)) + goto addsched; + + /* immediately go on if no job is to be done */ + if(hp->insert_count==INS_RUNS) { + printf(" --- leaving insert state ---\n"); + hp->state=STATE_POSTRUN; + goto postrun; } - hp->a_count+=NR_ATOMS; - /* add schedule for simulating injected atoms ;) */ - moldyn_add_schedule(md,RELAX_S,1.0); + /* else -> insert atoms */ + hp->insert_count+=1; + printf(" ### insert atoms (%d/%d) ###\n", + hp->insert_count*INS_ATOMS,INS_RUNS*INS_ATOMS); + insert_atoms(md); + goto addsched; + +postrun: + + /* assigne values */ + steps=POST_RELAX; + tau=POST_TAU; + + /* check temperature */ + dt=md->t_avg-md->t_ref; + dp=md->p_avg-md->p_ref; + if(dt<0) + dt=-dt; + if(dp<0) + dp=-dp; + if((dt>POST_DELTA_TC)|(dp>POST_DELTA_PC)) + goto addsched; + + /* immediately return if no job is to be done */ + if(hp->postrun_count==POST_RUNS) { + printf(" --- leaving post run state ---\n"); + return 0; + } + + /* postrun action */ + hp->postrun_count+=1; + printf(" ### postrun (%d/%d) ###\n", + hp->postrun_count,POST_RUNS); + set_temperature(md,md->t_ref-POST_DT); + +addsched: + + /* reset the average counters */ + average_reset(md); + + /* add schedule */ + moldyn_add_schedule(md,steps,tau); return 0; } int main(int argc,char **argv) { - /* check argv */ - //if(argc!=3) { - // printf("[sic] usage: %s \n",argv[0]); - // return -1; - //} - /* main moldyn structure */ t_moldyn md; /* hook parameter structure */ t_hp hookparam; - /* potential parameters */ - t_tersoff_mult_params tp; - t_albe_mult_params ap; - /* testing location & velocity vector */ t_3dvec r,v; memset(&r,0,sizeof(t_3dvec)); @@ -202,32 +262,19 @@ int main(int argc,char **argv) { /* choose potential */ #ifdef ALBE - set_potential3b_j1(&md,albe_mult_3bp_j1); - set_potential3b_k1(&md,albe_mult_3bp_k1); - set_potential3b_j2(&md,albe_mult_3bp_j2); - set_potential3b_k2(&md,albe_mult_3bp_k2); + if(set_potential(&md,MOLDYN_POTENTIAL_AM)<0) + return -1; #else - set_potential1b(&md,tersoff_mult_1bp); - set_potential3b_j1(&md,tersoff_mult_3bp_j1); - set_potential3b_k1(&md,tersoff_mult_3bp_k1); - set_potential3b_j2(&md,tersoff_mult_3bp_j2); - set_potential3b_k2(&md,tersoff_mult_3bp_k2); -#endif - -#ifdef ALBE - set_potential_params(&md,&ap); -#else - set_potential_params(&md,&tp); + if(set_potential(&md,MOLDYN_POTENTIAL_TM)<0) + return -1; #endif /* cutoff radius & bondlen */ #ifdef ALBE set_cutoff(&md,ALBE_S_SI); - set_bondlen(&md,ALBE_S_SI,ALBE_S_C,ALBE_S_SIC); //set_cutoff(&md,ALBE_S_C); #else set_cutoff(&md,TM_S_SI); - set_bondlen(&md,TM_S_SI,TM_S_C,-1.0); //set_cutoff(&md,TM_S_C); #endif @@ -235,128 +282,93 @@ int main(int argc,char **argv) { * potential parameters */ +#ifndef ALBE /* * tersoff mult potential parameters for SiC */ - tp.S[0]=TM_S_SI; - tp.R[0]=TM_R_SI; - tp.A[0]=TM_A_SI; - tp.B[0]=TM_B_SI; - tp.lambda[0]=TM_LAMBDA_SI; - tp.mu[0]=TM_MU_SI; - tp.beta[0]=TM_BETA_SI; - tp.n[0]=TM_N_SI; - tp.c[0]=TM_C_SI; - tp.d[0]=TM_D_SI; - tp.h[0]=TM_H_SI; - - tp.S[1]=TM_S_C; - tp.R[1]=TM_R_C; - tp.A[1]=TM_A_C; - tp.B[1]=TM_B_C; - tp.lambda[1]=TM_LAMBDA_C; - tp.mu[1]=TM_MU_C; - tp.beta[1]=TM_BETA_C; - tp.n[1]=TM_N_C; - tp.c[1]=TM_C_C; - tp.d[1]=TM_D_C; - tp.h[1]=TM_H_C; - - tp.chi=TM_CHI_SIC; - - tersoff_mult_complete_params(&tp); - + tersoff_mult_set_params(&md,SI,C); +#else /* * albe mult potential parameters for SiC */ - ap.S[0]=ALBE_S_SI; - ap.R[0]=ALBE_R_SI; - ap.A[0]=ALBE_A_SI; - ap.B[0]=ALBE_B_SI; - ap.r0[0]=ALBE_R0_SI; - ap.lambda[0]=ALBE_LAMBDA_SI; - ap.mu[0]=ALBE_MU_SI; - ap.gamma[0]=ALBE_GAMMA_SI; - ap.c[0]=ALBE_C_SI; - ap.d[0]=ALBE_D_SI; - ap.h[0]=ALBE_H_SI; - - ap.S[1]=ALBE_S_C; - ap.R[1]=ALBE_R_C; - ap.A[1]=ALBE_A_C; - ap.B[1]=ALBE_B_C; - ap.r0[1]=ALBE_R0_C; - ap.lambda[1]=ALBE_LAMBDA_C; - ap.mu[1]=ALBE_MU_C; - ap.gamma[1]=ALBE_GAMMA_C; - ap.c[1]=ALBE_C_C; - ap.d[1]=ALBE_D_C; - ap.h[1]=ALBE_H_C; - - ap.Smixed=ALBE_S_SIC; - ap.Rmixed=ALBE_R_SIC; - ap.Amixed=ALBE_A_SIC; - ap.Bmixed=ALBE_B_SIC; - ap.r0_mixed=ALBE_R0_SIC; - ap.lambda_m=ALBE_LAMBDA_SIC; - ap.mu_m=ALBE_MU_SIC; - ap.gamma_m=ALBE_GAMMA_SIC; - ap.c_mixed=ALBE_C_SIC; - ap.d_mixed=ALBE_D_SIC; - ap.h_mixed=ALBE_H_SIC; - - albe_mult_complete_params(&ap); + albe_mult_set_params(&md,SI,C); +#endif /* set (initial) dimensions of simulation volume */ #ifdef ALBE + #ifdef INIT_SI set_dim(&md,LCNTX*ALBE_LC_SI,LCNTY*ALBE_LC_SI,LCNTZ*ALBE_LC_SI,TRUE); - //set_dim(&md,LCNTX*ALBE_LC_C,LCNTY*ALBE_LC_C,LCNTZ*ALBE_LC_C,TRUE); - //set_dim(&md,LCNTX*ALBE_LC_SIC,LCNTY*ALBE_LC_SIC,LCNTZ*ALBE_LC_SIC,TRUE); + #endif + #ifdef INIT_C + set_dim(&md,LCNTX*ALBE_LC_C,LCNTY*ALBE_LC_C,LCNTZ*ALBE_LC_C,TRUE); + #endif + #ifdef INIT_3CSIC + set_dim(&md,LCNTX*ALBE_LC_SIC,LCNTY*ALBE_LC_SIC,LCNTZ*ALBE_LC_SIC,TRUE); + #endif #else + #ifdef INIT_SI set_dim(&md,LCNTX*LC_SI,LCNTY*LC_SI,LCNTZ*LC_SI,TRUE); - //set_dim(&md,LCNTX*LC_C,LCNTY*LC_C,LCNTZ*LC_C,TRUE); - //set_dim(&md,LCNTX*TM_LC_SIC,LCNTY*TM_LC_SIC,LCNTZ*TM_LC_SIC,TRUE); + #endif + #ifdef INIT_C + set_dim(&md,LCNTX*LC_C,LCNTY*LC_C,LCNTZ*LC_C,TRUE); + #endif + #ifdef INIT_3CSIC + set_dim(&md,LCNTX*TM_LC_SIC,LCNTY*TM_LC_SIC,LCNTZ*TM_LC_SIC,TRUE); + #endif #endif /* set periodic boundary conditions in all directions */ set_pbc(&md,TRUE,TRUE,TRUE); /* create the lattice / place atoms */ - // + + // diamond #ifdef ALBE - create_lattice(&md,DIAMOND,ALBE_LC_SI,SI,M_SI, - //create_lattice(&md,DIAMOND,ALBE_LC_C,C,M_C, + #ifdef INIT_SI + create_lattice(&md,DIAMOND,ALBE_LC_SI,SI, + ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB, + 0,LCNTX,LCNTY,LCNTZ,NULL,0,NULL); + #endif + #ifdef INIT_C + create_lattice(&md,DIAMOND,ALBE_LC_C,C, + ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB, + 1,LCNTX,LCNTY,LCNTZ,NULL,0,NULL); + #endif #else - create_lattice(&md,DIAMOND,LC_SI,SI,M_SI, -#endif + #ifdef INIT_SI + create_lattice(&md,DIAMOND,LC_SI,SI, ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB, - // ATOM_ATTR_2BP|ATOM_ATTR_HB, - 0,LCNTX,LCNTY,LCNTZ,NULL); - // 1,LCNTX,LCNTY,LCNTZ,NULL); - // + 0,LCNTX,LCNTY,LCNTZ,NULL,0,NULL); + #endif + #ifdef INIT_C + create_lattice(&md,DIAMOND,LC_C,SI, + ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB, + 1,LCNTX,LCNTY,LCNTZ,NULL,0,NULL); + #endif +#endif - /* create zinkblende structure */ - /* -#ifdef ALBE + // zinkblende +#ifdef INIT_3CSIC + #ifdef ALBE r.x=0.5*0.25*ALBE_LC_SIC; r.y=r.x; r.z=r.x; - create_lattice(&md,FCC,ALBE_LC_SIC,SI,M_SI, + create_lattice(&md,FCC,ALBE_LC_SIC,SI, ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB, - 0,LCNTX,LCNTY,LCNTZ,&r); + 0,LCNTX,LCNTY,LCNTZ,&r,0,NULL); r.x+=0.25*ALBE_LC_SIC; r.y=r.x; r.z=r.x; - create_lattice(&md,FCC,ALBE_LC_SIC,C,M_C, - ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB, - 1,LCNTX,LCNTY,LCNTZ,&r); -#else + create_lattice(&md,FCC,ALBE_LC_SIC,C, + ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB|ATOM_ATTR_VB, + 1,LCNTX,LCNTY,LCNTZ,&r,0,NULL); + #else r.x=0.5*0.25*TM_LC_SIC; r.y=r.x; r.z=r.x; - create_lattice(&md,FCC,TM_LC_SIC,SI,M_SI, + create_lattice(&md,FCC,TM_LC_SIC,SI, ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB, - 0,LCNTX,LCNTY,LCNTZ,&r); + 0,LCNTX,LCNTY,LCNTZ,&r,0,NULL); r.x+=0.25*TM_LC_SIC; r.y=r.x; r.z=r.x; - create_lattice(&md,FCC,TM_LC_SIC,C,M_C, + create_lattice(&md,FCC,TM_LC_SIC,C, ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB, - 1,LCNTX,LCNTY,LCNTZ,&r); + 1,LCNTX,LCNTY,LCNTZ,&r,0,NULL); + #endif #endif - */ /* check for right atom placing */ moldyn_bc_check(&md); @@ -395,14 +407,14 @@ int main(int argc,char **argv) { /* set temperature & pressure */ set_temperature(&md,atof(argv[2])+273.0); - set_pressure(&md,BAR); + set_pressure(&md,0.0); /* set amount of steps to skip before average calc */ - set_avg_skip(&md,(8.0/10.0*PRERUN)); + set_avg_skip(&md,AVG_SKIP); /* set p/t scaling */ //set_pt_scale(&md,0,0,T_SCALE_BERENDSEN,100.0); - //set_pt_scale(&md,P_SCALE_BERENDSEN,0.001, + //set_pt_scale(&md,P_SCALE_BERENDSEN,0.01/(100*GPA), // T_SCALE_BERENDSEN,100.0); //set_pt_scale(&md,0,0,T_SCALE_DIRECT,1.0); //set_pt_scale(&md,P_SCALE_BERENDSEN,0.001,0,0); @@ -411,13 +423,13 @@ int main(int argc,char **argv) { thermal_init(&md,TRUE); /* create the simulation schedule */ - moldyn_add_schedule(&md,PRERUN,1.0); + moldyn_add_schedule(&md,PRERUN,PRE_TAU); /* schedule hook function */ memset(&hookparam,0,sizeof(t_hp)); hookparam.argc=argc; hookparam.argv=argv; - moldyn_set_schedule_hook(&md,&hook_add_atom,&hookparam); + moldyn_set_schedule_hook(&md,&sic_hook,&hookparam); //moldyn_set_schedule_hook(&md,&hook_del_atom,&hookparam); //moldyn_add_schedule(&md,POSTRUN,1.0); @@ -427,10 +439,14 @@ int main(int argc,char **argv) { moldyn_set_log(&md,LOG_TOTAL_ENERGY,LOG_E); moldyn_set_log(&md,LOG_TEMPERATURE,LOG_T); moldyn_set_log(&md,LOG_PRESSURE,LOG_P); - moldyn_set_log(&md,VISUAL_STEP,LOG_V); + moldyn_set_log(&md,LOG_VOLUME,LOG_V); + moldyn_set_log(&md,VISUAL_STEP,LOG_A); moldyn_set_log(&md,SAVE_STEP,LOG_S); moldyn_set_log(&md,CREATE_REPORT,0); + /* next neighbour distance for critical checking */ + set_nn_dist(&md,0.25*ALBE_LC_SI*sqrt(3.0)); + /* * let's do the actual md algorithm now *