From: hackbard Date: Fri, 15 Dec 2006 00:41:11 +0000 (+0000) Subject: actually just bullshit ... (added unique tag -> maybe symmetry) X-Git-Url: https://www.hackdaworld.org/gitweb/?p=physik%2Fposic.git;a=commitdiff_plain;h=9c2172b5fce9688fa6be8d8a30745f9ef0b31419 actually just bullshit ... (added unique tag -> maybe symmetry) --- diff --git a/moldyn.c b/moldyn.c index 551e07a..f8bfd3f 100644 --- a/moldyn.c +++ b/moldyn.c @@ -230,33 +230,38 @@ int moldyn_log_shutdown(t_moldyn *moldyn) { */ int create_lattice(t_moldyn *moldyn,u8 type,double lc,int element,double mass, - u8 attr,u8 bnum,int a,int b,int c) { + u8 attr,u8 brand,int a,int b,int c) { - int count; + int new,count; int ret; t_3dvec origin; + void *ptr; + t_atom *atom; - count=a*b*c; + new=a*b*c; + count=moldyn->count; /* how many atoms do we expect */ - if(type==FCC) count*=4; - if(type==DIAMOND) count*=8; + if(type==FCC) new*=4; + if(type==DIAMOND) new*=8; /* allocate space for atoms */ - moldyn->atom=malloc(count*sizeof(t_atom)); - if(moldyn->atom==NULL) { - perror("malloc (atoms)"); + ptr=realloc(moldyn->atom,(count+new)*sizeof(t_atom)); + if(!ptr) { + perror("[moldyn] realloc (create lattice)"); return -1; } - + moldyn->atom=ptr; + atom=&(moldyn->atom[count]); + v3_zero(&origin); switch(type) { case FCC: - ret=fcc_init(a,b,c,lc,moldyn->atom,&origin); + ret=fcc_init(a,b,c,lc,atom,&origin); break; case DIAMOND: - ret=diamond_init(a,b,c,lc,moldyn->atom,&origin); + ret=diamond_init(a,b,c,lc,atom,&origin); break; default: printf("unknown lattice type (%02x)\n",type); @@ -264,24 +269,24 @@ int create_lattice(t_moldyn *moldyn,u8 type,double lc,int element,double mass, } /* debug */ - if(ret!=count) { + if(ret!=new) { printf("[moldyn] creating lattice failed\n"); printf(" amount of atoms\n"); - printf(" - expected: %d\n",count); + printf(" - expected: %d\n",new); printf(" - created: %d\n",ret); return -1; } - moldyn->count=count; - printf("[moldyn] created lattice with %d atoms\n",count); + moldyn->count+=new; + printf("[moldyn] created lattice with %d atoms\n",new); - while(count) { - count-=1; - moldyn->atom[count].element=element; - moldyn->atom[count].mass=mass; - moldyn->atom[count].attr=attr; - moldyn->atom[count].bnum=bnum; - check_per_bound(moldyn,&(moldyn->atom[count].r)); + for(ret=0;retatom; - count=++(moldyn->count); + count=(moldyn->count)++; - ptr=realloc(atom,count*sizeof(t_atom)); + ptr=realloc(atom,(count+1)*sizeof(t_atom)); if(!ptr) { perror("[moldyn] realloc (add atom)"); return -1; @@ -389,12 +394,13 @@ int add_atom(t_moldyn *moldyn,int element,double mass,u8 bnum,u8 attr, moldyn->atom=ptr; atom=moldyn->atom; - atom[count-1].r=*r; - atom[count-1].v=*v; - atom[count-1].element=element; - atom[count-1].mass=mass; - atom[count-1].bnum=bnum; - atom[count-1].attr=attr; + atom[count].r=*r; + atom[count].v=*v; + atom[count].element=element; + atom[count].mass=mass; + atom[count].brand=brand; + atom[count].tag=count; + atom[count].attr=attr; return 0; } @@ -1243,11 +1249,11 @@ int tersoff_mult_complete_params(t_tersoff_mult_params *p) { /* tersoff 1 body part */ int tersoff_mult_1bp(t_moldyn *moldyn,t_atom *ai) { - int num; + int brand; t_tersoff_mult_params *params; t_tersoff_exchange *exchange; - num=ai->bnum; + brand=ai->brand; params=moldyn->pot1b_params; exchange=&(params->exchange); @@ -1256,15 +1262,15 @@ int tersoff_mult_1bp(t_moldyn *moldyn,t_atom *ai) { * their right values */ - exchange->beta_i=&(params->beta[num]); - exchange->n_i=&(params->n[num]); - exchange->c_i=&(params->c[num]); - exchange->d_i=&(params->d[num]); - exchange->h_i=&(params->h[num]); + exchange->beta_i=&(params->beta[brand]); + exchange->n_i=&(params->n[brand]); + exchange->c_i=&(params->c[brand]); + exchange->d_i=&(params->d[brand]); + exchange->h_i=&(params->h[brand]); exchange->betaini=pow(*(exchange->beta_i),*(exchange->n_i)); - exchange->ci2=params->c[num]*params->c[num]; - exchange->di2=params->d[num]*params->d[num]; + exchange->ci2=params->c[brand]*params->c[brand]; + exchange->di2=params->d[brand]*params->d[brand]; exchange->ci2di2=exchange->ci2/exchange->di2; return 0; @@ -1280,12 +1286,12 @@ int tersoff_mult_2bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc) { double A,B,R,S,lambda,mu; double f_r,df_r; double f_c,df_c; - int num; + int brand; double s_r; double arg; params=moldyn->pot2b_params; - num=aj->bnum; + brand=aj->brand; exchange=&(params->exchange); /* clear 3bp and 2bp post run */ @@ -1318,13 +1324,13 @@ int tersoff_mult_2bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc) { exchange->dist_ij=dist_ij; /* constants */ - if(num==ai->bnum) { - S=params->S[num]; - R=params->R[num]; - A=params->A[num]; - B=params->B[num]; - lambda=params->lambda[num]; - mu=params->mu[num]; + if(brand==ai->brand) { + S=params->S[brand]; + R=params->R[brand]; + A=params->A[brand]; + B=params->B[brand]; + lambda=params->lambda[brand]; + mu=params->mu[brand]; exchange->chi=1.0; } else { @@ -1342,12 +1348,12 @@ int tersoff_mult_2bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc) { return 0; /* more constants */ - exchange->beta_j=&(params->beta[num]); - exchange->n_j=&(params->n[num]); - exchange->c_j=&(params->c[num]); - exchange->d_j=&(params->d[num]); - exchange->h_j=&(params->h[num]); - if(num==ai->bnum) { + exchange->beta_j=&(params->beta[brand]); + exchange->n_j=&(params->n[brand]); + exchange->c_j=&(params->c[brand]); + exchange->d_j=&(params->d[brand]); + exchange->h_j=&(params->h[brand]); + if(brand==ai->brand) { exchange->betajnj=exchange->betaini; exchange->cj2=exchange->ci2; exchange->dj2=exchange->di2; @@ -1355,8 +1361,8 @@ int tersoff_mult_2bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc) { } else { exchange->betajnj=pow(*(exchange->beta_j),*(exchange->n_j)); - exchange->cj2=params->c[num]*params->c[num]; - exchange->dj2=params->d[num]*params->d[num]; + exchange->cj2=params->c[brand]*params->c[brand]; + exchange->dj2=params->d[brand]*params->d[brand]; exchange->cj2dj2=exchange->cj2/exchange->dj2; } @@ -1536,7 +1542,7 @@ int tersoff_mult_3bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,t_atom *ak,u8 bc) { double h_cos,d2_h_cos2; double frac,g,zeta,chi; double tmp; - int num; + int brand; params=moldyn->pot3b_params; exchange=&(params->exchange); @@ -1588,10 +1594,10 @@ int tersoff_mult_3bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,t_atom *ak,u8 bc) { d_ik=v3_norm(&dist_ik); /* ik constants */ - num=ai->bnum; - if(num==ak->bnum) { - R=params->R[num]; - S=params->S[num]; + brand=ai->brand; + if(brand==ak->brand) { + R=params->R[brand]; + S=params->S[brand]; } else { R=params->Rmixed; @@ -1674,12 +1680,12 @@ int tersoff_mult_3bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,t_atom *ak,u8 bc) { d_jk=v3_norm(&dist_jk); /* jk constants */ - num=aj->bnum; - if(num==ak->bnum) { - R=params->R[num]; - S=params->S[num]; - B=params->B[num]; - mu=params->mu[num]; + brand=aj->brand; + if(brand==ak->brand) { + R=params->R[brand]; + S=params->S[brand]; + B=params->B[brand]; + mu=params->mu[brand]; chi=1.0; } else { @@ -1787,13 +1793,13 @@ int moldyn_bc_check(t_moldyn *moldyn) { t_atom *atom; t_3dvec *dim; int i; -double x; -u8 byte; -int j,k; + double x; + u8 byte; + int j,k; atom=moldyn->atom; dim=&(moldyn->dim); -x=dim->x/2; + x=dim->x/2; for(i=0;icount;i++) { if(atom[i].r.x>=dim->x/2||-atom[i].r.x>dim->x/2) { diff --git a/moldyn.h b/moldyn.h index b4f71d6..9493f5f 100644 --- a/moldyn.h +++ b/moldyn.h @@ -27,11 +27,12 @@ typedef struct s_atom { t_3dvec r; /* position */ t_3dvec v; /* velocity */ t_3dvec f; /* force */ - t_3dvec virial; /* virial */ + t_3dvec virial; /* virial (v_xx, v_yy, v_zz) */ double e; /* site energy */ int element; /* number of element in pse */ double mass; /* atom mass */ - u8 bnum; /* brand number */ + u8 brand; /* brand id */ + int tag; /* atom unique id (number of atom) */ u8 attr; /* attributes */ } t_atom; @@ -377,10 +378,10 @@ int moldyn_set_log(t_moldyn *moldyn,u8 type,int timer); int moldyn_log_shutdown(t_moldyn *moldyn); int create_lattice(t_moldyn *moldyn,u8 type,double lc,int element,double mass, - u8 attr,u8 bnum,int a,int b,int c); + u8 attr,u8 brand,int a,int b,int c); int fcc_init(int a,int b,int c,double lc,t_atom *atom,t_3dvec *origin); int diamond_init(int a,int b,int c,double lc,t_atom *atom,t_3dvec *origin); -int add_atom(t_moldyn *moldyn,int element,double mass,u8 bnum,u8 attr, +int add_atom(t_moldyn *moldyn,int element,double mass,u8 brand,u8 attr, t_3dvec *r,t_3dvec *v); int destroy_atoms(t_moldyn *moldyn); diff --git a/sic.c b/sic.c index a105987..f4cdd7d 100644 --- a/sic.c +++ b/sic.c @@ -137,8 +137,8 @@ int main(int argc,char **argv) { /* set temperature */ printf("[sic] setting temperature\n"); - set_temperature(&md,273.0+1410.0); - //set_temperature(&md,273.0+450.0); + //set_temperature(&md,273.0+1410.0); + set_temperature(&md,273.0+450.0); //set_temperature(&md,273.0); //set_temperature(&md,1.0); //set_temperature(&md,0.0); @@ -151,6 +151,7 @@ int main(int argc,char **argv) { printf("[sic] set p/t scaling\n"); //set_pt_scale(&md,P_SCALE_BERENDSEN,100.0, // T_SCALE_BERENDSEN,100.0); + set_pt_scale(&md,0,0,T_SCALE_BERENDSEN,100.0); /* initial thermal fluctuations of particles (in equilibrium) */ printf("[sic] thermal init\n");