From 15dd7ee084a5db24a3e1a15428cd47e8d61fda5b Mon Sep 17 00:00:00 2001 From: hackbard Date: Mon, 4 Dec 2006 22:05:23 +0000 Subject: [PATCH] no segfaulst anymore BUT take care, definetly calculating bullshit --- moldyn.c | 113 ++++++++++++++++++++++++++----------------------------- moldyn.h | 6 ++- sic.c | 3 +- 3 files changed, 60 insertions(+), 62 deletions(-) diff --git a/moldyn.c b/moldyn.c index 52a716e..716a087 100644 --- a/moldyn.c +++ b/moldyn.c @@ -139,6 +139,14 @@ int set_potential2b(t_moldyn *moldyn,pf_func2b func,void *params) { return 0; } +int set_potential2b_post(t_moldyn *moldyn,pf_func2b_post func,void *params) { + + moldyn->func2b=func; + moldyn->pot2b_params=params; + + return 0; +} + int set_potential3b(t_moldyn *moldyn,pf_func3b func,void *params) { moldyn->func3b=func; @@ -940,9 +948,9 @@ int potential_force_calc(t_moldyn *moldyn) { if(ktom==&(itom[i])) continue; -printf("Debug: atom %d before 3bp: %08x %08x %08x | %.15f %.15f %.15f\n",i,&itom[i],jtom,ktom,itom[i].r.x,itom[i].f.x,itom[i].v.x); +//printf("Debug: atom %d before 3bp: %08x %08x %08x | %.15f %.15f %.15f\n",i,&itom[i],jtom,ktom,itom[i].r.x,itom[i].f.x,itom[i].v.x); moldyn->func3b(moldyn,&(itom[i]),jtom,ktom,bc_ijk); -printf("Debug: atom %d after 3bp: %08x %08x %08x | %.15f %.15f %.15f\n",i,&itom[i],jtom,ktom,itom[i].r.x,itom[i].f.x,itom[i].v.x); +//printf("Debug: atom %d after 3bp: %08x %08x %08x | %.15f %.15f %.15f\n",i,&itom[i],jtom,ktom,itom[i].r.x,itom[i].f.x,itom[i].v.x); } while(list_next(that)!=\ L_NO_NEXT_ELEMENT); @@ -953,7 +961,7 @@ printf("Debug: atom %d after 3bp: %08x %08x %08x | %.15f %.15f %.15f\n",i,&itom[ /* 2bp post function */ if(moldyn->func2b_post) - mlodyn->func2b_post(moldyn, + moldyn->func2b_post(moldyn, &(itom[i]), jtom,bc_ij); @@ -1120,6 +1128,7 @@ int tersoff_mult_1bp(t_moldyn *moldyn,t_atom *ai) { exchange->h=&(params->h[num]); exchange->betan=pow(*(exchange->beta),*(exchange->n)); + exchange->n_betan=*(exchange->n)*exchange->betan; exchange->c2=params->c[num]*params->c[num]; exchange->d2=params->d[num]*params->d[num]; exchange->c2d2=exchange->c2/exchange->d2; @@ -1223,37 +1232,44 @@ int tersoff_mult_2bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc) { exchange->run3bp=1; /* reset 3bp sums */ - exchange->3bp_sum1=0.0; - exchange->3bp_sum2=0.0; + exchange->sum1_3bp=0.0; + exchange->sum2_3bp=0.0; + v3_zero(&(exchange->db_ij)); return 0; } /* tersoff 2 body post part */ -int tersoff_mult_3bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,t_atom *ak,u8 bc) { +int tersoff_mult_post_2bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc) { /* here we have to allow for the 3bp sums */ t_tersoff_mult_params *params; t_tersoff_exchange *exchange; - t_3dvec force,temp,*db_ij; + t_3dvec force,temp,*db_ij,*dist_ij; double db_ij_scale1,db_ij_scale2; double b_ij; double f_c,df_c,f_a,df_a; + double chi,betan; + double help; + double n; params=moldyn->pot2b_params; - exchange=&(moldyn->exchange); + exchange=&(params->exchange); db_ij=&(exchange->db_ij); f_c=exchange->f_c; df_c=exchange->df_c; f_a=exchange->f_a; df_a=exchange->df_a; + betan=exchange->betan; + n=*(exchange->n); + dist_ij=&(exchange->dist_ij); - db_ij_scale1=(1+betan*3bp_sum1); - db_ij_scale2=(n*betan*3bp_sum2); + db_ij_scale1=(1+betan*exchange->sum1_3bp); + db_ij_scale2=(exchange->n_betan*exchange->sum2_3bp); help=pow(db_ij_scale1,-1.0/(2*n)-1); b_ij=chi*db_ij_scale1*help; db_ij_scale1=-chi/(2*n)*help; @@ -1266,7 +1282,7 @@ int tersoff_mult_3bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,t_atom *ak,u8 bc) { v3_add(&force,&temp,db_ij); v3_scale(&force,&force,f_c); - v3_scale(&temp,&dist_ij,f_a*b_ij*df_c); + v3_scale(&temp,dist_ij,f_a*b_ij*df_c); /* add energy of 3bp sum */ moldyn->energy+=(0.5*f_c*b_ij*f_a); @@ -1286,18 +1302,16 @@ int tersoff_mult_3bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,t_atom *ak,u8 bc) { t_3dvec temp,force; double R,S,s_r; double d_ij,d_ij2,d_ik,d_jk; - double f_c,df_c,b_ij,f_a,df_a; + double f_c,df_c,f_a,df_a; double f_c_ik,df_c_ik,arg; - double scale; - double chi; - double n,c,d,h,beta,betan; + double n,c,d,h; double c2,d2,c2d2; double numer,denom; double theta,cos_theta,sin_theta; double d_theta,d_theta1,d_theta2; - double h_cos,h_cos2,d2_h_cos2; - double frac1,bracket1,bracket2,bracket2_n_1,bracket2_n; - double bracket3,bracket3_pow_1,bracket3_pow; + double h_cos,d2_h_cos2; + double frac,bracket,bracket_n_1,bracket_n; + double g; int num; params=moldyn->pot3b_params; @@ -1369,13 +1383,11 @@ int tersoff_mult_3bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,t_atom *ak,u8 bc) { if(bc) check_per_bound(moldyn,&dist_jk); d_jk=v3_norm(&dist_jk); - beta=*(exchange->beta); - betan=exchange->betan; + /* get exchange data */ n=*(exchange->n); c=*(exchange->c); d=*(exchange->d); h=*(exchange->h); - chi=exchange->chi; c2=exchange->c2; d2=exchange->d2; c2d2=exchange->c2d2; @@ -1383,6 +1395,7 @@ int tersoff_mult_3bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,t_atom *ak,u8 bc) { numer=d_ij2+d_ik*d_ik-d_jk*d_jk; denom=2*d_ij*d_ik; cos_theta=numer/denom; + /* prefere law of cosines, dot product -> nan (often) */ //cos_theta=v3_scalar_product(&dist_ij,&dist_ik)/(d_ij*d_ik); sin_theta=sqrt(1.0-(cos_theta*cos_theta)); theta=acos(cos_theta); @@ -1393,61 +1406,43 @@ int tersoff_mult_3bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,t_atom *ak,u8 bc) { d_theta2*=d_theta; h_cos=(h-cos_theta); - h_cos2=h_cos*h_cos; - d2_h_cos2=d2+h_cos2; + d2_h_cos2=d2+(h_cos*h_cos); + + frac=c2/(d2_h_cos2); + g=1.0+c2d2-frac; - /* some usefull expressions */ - frac1=c2/(d2_h_cos2); - bracket1=1+c2d2-frac1; if(f_c_ik==0.0) { - bracket2=0.0; - bracket2_n_1=0.0; - bracket2_n=0.0; - bracket3=1.0; + bracket=0.0; + bracket_n_1=0.0; + bracket_n=0.0; printf("Foo -> 0: "); } else { - bracket2=f_c_ik*bracket1; - bracket2_n_1=pow(bracket2,n-1.0); - bracket2_n=bracket2_n_1*bracket2; - bracket3=1.0+betan*bracket2_n; + bracket=f_c_ik*g; + bracket_n_1=pow(bracket,n-1.0); + bracket_n=bracket_n_1*bracket; printf("Foo -> 1: "); } - bracket3_pow_1=pow(bracket3,(-1.0/(2.0*n))-1.0); - bracket3_pow=bracket3_pow_1*bracket3; -printf("%.15f %.15f %.15f\n",bracket2_n_1,bracket2_n); +//printf("%.15f %.15f %.15f\n",bracket_n_1,bracket_n,bracket); - /* now go on with calc of b_ij and derivation of b_ij */ - b_ij=chi*bracket3_pow; + /* calc of db_ij and the 2 sums */ + exchange->sum1_3bp+=bracket_n; + exchange->sum2_3bp+=bracket_n_1; /* derivation of theta */ v3_scale(&force,&dist_ij,d_theta1); v3_scale(&temp,&dist_ik,d_theta2); v3_add(&force,&force,&temp); - /* part 1 of derivation of b_ij */ - v3_scale(&force,&force,sin_theta*2*h_cos*f_c_ik*frac1); - - /* part 2 of derivation of b_ij */ - v3_scale(&temp,&dist_ik,df_c_ik*bracket1); + /* part 1 of db_ij */ + v3_scale(&force,&force,sin_theta*2*h_cos*f_c_ik*frac/d2_h_cos2); - /* sum up and scale ... */ - v3_add(&temp,&temp,&force); - scale=bracket2_n_1*n*betan*(1+betan*bracket3_pow_1)*chi*(1.0/(2.0*n)); - v3_scale(&temp,&temp,scale); + /* part 2 of db_ij */ + v3_scale(&temp,&dist_ik,df_c_ik*g); - /* now construct an energy and a force out of that */ - v3_scale(&temp,&temp,f_a); - v3_scale(&force,&dist_ij,df_a*b_ij); + /* sum up and add to db_ij */ v3_add(&temp,&temp,&force); - v3_scale(&temp,&temp,f_c); - v3_scale(&force,&dist_ij,df_c*b_ij*f_a); - v3_add(&force,&force,&temp); - - /* add forces */ - v3_add(&(ai->f),&(ai->f),&force); - /* energy is 0.5 f_r f_c */ - moldyn->energy+=(0.5*f_a*b_ij*f_c); + v3_add(&(exchange->db_ij),&(exchange->db_ij),&temp); return 0; } diff --git a/moldyn.h b/moldyn.h index 41b711a..09471a1 100644 --- a/moldyn.h +++ b/moldyn.h @@ -194,12 +194,13 @@ typedef struct s_tersoff_exchange { double d2; double c2d2; double betan; + double n_betan; u8 run3bp; t_3dvec db_ij; - double 3bp_sum1; - double 3bp_sum2; + double sum1_3bp; + double sum2_3bp; } t_tersoff_exchange; /* tersoff multi (2!) potential parameters */ @@ -372,6 +373,7 @@ int lennard_jones(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc); int tersoff_mult_complete_params(t_tersoff_mult_params *p); int tersoff_mult_1bp(t_moldyn *moldyn,t_atom *ai); int tersoff_mult_2bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc); +int tersoff_mult_post_2bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc); int tersoff_mult_3bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,t_atom *ak,u8 bc); #endif diff --git a/sic.c b/sic.c index 3408895..5f50bd8 100644 --- a/sic.c +++ b/sic.c @@ -41,6 +41,7 @@ int main(int argc,char **argv) { printf("[sic] selecting potential\n"); set_potential1b(&md,tersoff_mult_1bp,&tp); set_potential2b(&md,tersoff_mult_2bp,&tp); + set_potential2b_post(&md,tersoff_mult_post_2bp,&tp); set_potential3b(&md,tersoff_mult_3bp,&tp); //set_potential2b(&md,lennard_jones,&lj); @@ -125,7 +126,7 @@ int main(int argc,char **argv) { /* create the simulation schedule */ printf("[sic] adding schedule\n"); - moldyn_add_schedule(&md,10,1.0e-15); + moldyn_add_schedule(&md,100,1.0e-15); /* activate logging */ printf("[sic] activate logging\n"); -- 2.20.1