X-Git-Url: https://hackdaworld.org/gitweb/?a=blobdiff_plain;f=moldyn.c;h=36086581e666b082c6a3d554706609800beafbb2;hb=ade81aa2afb15f22e98ed9595ff303d4fedfe122;hp=52a716e2bdfb6552a1ee13bb22f0e5eb60e29380;hpb=dfbe75140f5a113f898809c529a882034507f6d1;p=physik%2Fposic.git diff --git a/moldyn.c b/moldyn.c index 52a716e..3608658 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_post=func; + moldyn->pot2b_params=params; + + return 0; +} + int set_potential3b(t_moldyn *moldyn,pf_func3b func,void *params) { moldyn->func3b=func; @@ -568,9 +576,8 @@ int link_cell_neighbour_index(t_moldyn *moldyn,int i,int j,int k,t_list *cell) { } lc->dnlc=count1; - lc->countn=27; - return count2; + return count1; } int link_cell_shutdown(t_moldyn *moldyn) { @@ -656,10 +663,11 @@ int moldyn_integrate(t_moldyn *moldyn) { /* sqaure of some variables */ moldyn->tau_square=moldyn->tau*moldyn->tau; moldyn->cutoff_square=moldyn->cutoff*moldyn->cutoff; + /* calculate initial forces */ potential_force_calc(moldyn); - /* do some checks before we actually start calculating bullshit */ + /* some stupid checks before we actually start calculating bullshit */ if(moldyn->cutoff>0.5*moldyn->dim.x) printf("[moldyn] warning: cutoff > 0.5 x dim.x\n"); if(moldyn->cutoff>0.5*moldyn->dim.y) @@ -672,6 +680,11 @@ int moldyn_integrate(t_moldyn *moldyn) { /* zero absolute time */ moldyn->time=0.0; + + /* debugging, ignre */ + moldyn->debug=0; + + /* executing the schedule */ for(sched=0;schedschedule.content_count;sched++) { /* setting amount of runs and finite time step size */ @@ -728,7 +741,8 @@ int moldyn_integrate(t_moldyn *moldyn) { if(!(i%v)) { visual_atoms(&(moldyn->vis),moldyn->time, moldyn->atom,moldyn->count); - printf("\rsched: %d, steps: %d",sched,i); + printf("\rsched: %d, steps: %d, theta: %d", + sched,i,moldyn->debug); fflush(stdout); } } @@ -739,6 +753,9 @@ int moldyn_integrate(t_moldyn *moldyn) { if(schedule->hook) schedule->hook(moldyn,schedule->hook_params); + /* get a new info line */ + printf("\n"); + } return 0; @@ -776,7 +793,6 @@ int velocity_verlet(t_moldyn *moldyn) { /* forces depending on chosen potential */ potential_force_calc(moldyn); - //moldyn->potential_force_function(moldyn); for(i=0;icount; itom=moldyn->atom; @@ -815,6 +831,7 @@ int potential_force_calc(t_moldyn *moldyn) { /* reset energy */ moldyn->energy=0.0; + /* get energy and force of every atom */ for(i=0;idim.z/2)/lc->z, neighbour_i); - countn=lc->countn; dnlc=lc->dnlc; - for(j=0;jattr&ATOM_ATTR_3BP)) continue; - /* - * according to mr. nordlund, we dont need to take the - * sum over all atoms now, as 'this is centered' around - * atom i ... - * i am not quite sure though! there is a not vanishing - * part even if f_c_ik is zero ... - * this analytical potentials suck! - * switching from mc to md to dft soon! - */ - - // link_cell_neighbour_index(moldyn, - // (jtom->r.x+moldyn->dim.x/2)/lc->x, - // (jtom->r.y+moldyn->dim.y/2)/lc->y, - // (jtom->r.z+moldyn->dim.z/2)/lc->z, - // neighbour_j); - -// /* neighbours of j */ -// for(k=0;kcountn;k++) { -// -// that=&(neighbour_j[k]); -// list_reset(that); -// -// if(that->start==NULL) -// continue; -// -// bc_ijk=(kdnlc)?0:1; -// -// do { -// -// ktom=that->current->data; -// -// if(!(ktom->attr&ATOM_ATTR_3BP)) -// continue; -// -// if(ktom==jtom) -// continue; -// -// if(ktom==&(itom[i])) -// continue; -// -// moldyn->func3b(moldyn,&(itom[i]),jtom,ktom,bc_ijk); -// -/* } while(list_next(that)!=\ */ -// L_NO_NEXT_ELEMENT); -// -// } - /* copy the neighbour lists */ memcpy(neighbour_i2,neighbour_i, 27*sizeof(t_list)); /* get neighbours of i */ - for(k=0;kstart==NULL) continue; - bc_ijk=(kfunc3b(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); + moldyn->func3b(moldyn,&(itom[i]),jtom,ktom,bc_ik|bc_ij); } while(list_next(that)!=\ L_NO_NEXT_ELEMENT); @@ -952,10 +919,13 @@ printf("Debug: atom %d after 3bp: %08x %08x %08x | %.15f %.15f %.15f\n",i,&itom[ } while(list_next(this)!=L_NO_NEXT_ELEMENT); /* 2bp post function */ - if(moldyn->func2b_post) - mlodyn->func2b_post(moldyn, + if(moldyn->func2b_post) { +printf("pre(%d): %.15f %.15f %.15f\n",i,itom[i].f.x,itom[i].r.x,itom[i].v.x); + moldyn->func2b_post(moldyn, &(itom[i]), jtom,bc_ij); +printf("post(%d): %.15f %.15f %.15f\n",i,itom[i].f.x,itom[i].r.x,itom[i].v.x); + } } } @@ -1120,6 +1090,7 @@ 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; @@ -1147,6 +1118,7 @@ int tersoff_mult_2bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc) { exchange=&(params->exchange); exchange->run3bp=0; + exchange->run2bp_post=0; /* * we need: f_c, df_c, f_r, df_r @@ -1184,14 +1156,13 @@ int tersoff_mult_2bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc) { mu=params->mu_m; params->exchange.chi=params->chi; } - if(d_ij>S) return 0; f_r=A*exp(-lambda*d_ij); df_r=-lambda*f_r/d_ij; - /* f_a, df_a calc + save for 3bp use */ + /* f_a, df_a calc + save for later use */ exchange->f_a=-B*exp(-mu*d_ij); exchange->df_a=-mu*exchange->f_a/d_ij; @@ -1219,58 +1190,77 @@ int tersoff_mult_2bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc) { exchange->f_c=f_c; exchange->df_c=df_c; - /* enable the run of 3bp function */ + /* enable the run of 3bp function and 2bp post processing */ exchange->run3bp=1; + exchange->run2bp_post=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); + + /* we do not run if f_c_ij was detected to be 0! */ + if(!(exchange->run2bp_post)) + return 0; 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); + chi=exchange->chi; + 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; +printf("debug: %.20f %.20f %.20f\n",db_ij->x,exchange->sum1_3bp,exchange->sum2_3bp); + /* db_ij part */ v3_scale(db_ij,db_ij,(db_ij_scale1*db_ij_scale2)); v3_scale(db_ij,db_ij,f_a); + /* df_a part */ v3_scale(&temp,dist_ij,b_ij*df_a); + /* db_ij + df_a part */ v3_add(&force,&temp,db_ij); v3_scale(&force,&force,f_c); - v3_scale(&temp,&dist_ij,f_a*b_ij*df_c); + /* df_c part */ + 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); - /* add force of 3bp calculation */ + + /* add force of 3bp calculation (all three parts) */ v3_add(&(ai->f),&temp,&force); return 0; @@ -1286,18 +1276,16 @@ 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; @@ -1369,21 +1357,35 @@ 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; + /* cosine of theta by scalaproduct, * + * derivation of theta by law of cosines! */ numer=d_ij2+d_ik*d_ik-d_jk*d_jk; denom=2*d_ij*d_ik; cos_theta=numer/denom; - //cos_theta=v3_scalar_product(&dist_ij,&dist_ik)/(d_ij*d_ik); + cos_theta=v3_scalar_product(&dist_ij,&dist_ik)/(d_ij*d_ik); +printf("cos theta: %.25f\n",cos_theta); + + /* hack - cos theta machine accuracy problems! */ + if(cos_theta>1.0||cos_theta<-1.0) { + moldyn->debug++; + if(fabs(cos_theta)>1.0+ACCEPTABLE_ERROR) + printf("[moldyn] WARNING: cos theta failure!\n"); + if(cos_theta<0) + cos_theta=-1.0; + else + cos_theta=1.0; + printf("THETA CORRECTION\n"); + } + sin_theta=sqrt(1.0-(cos_theta*cos_theta)); theta=acos(cos_theta); d_theta=(-1.0/sqrt(1.0-cos_theta*cos_theta))/(denom*denom); @@ -1391,63 +1393,44 @@ int tersoff_mult_3bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,t_atom *ak,u8 bc) { d_theta2=2*denom-numer*2*d_ij/d_ik; d_theta1*=d_theta; d_theta2*=d_theta; +printf("FOO %.15f %.15f\n",sin_theta,cos_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; - printf("Foo -> 0: "); + bracket=0.0; + bracket_n_1=0.0; + bracket_n=0.0; } 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; - printf("Foo -> 1: "); + bracket=f_c_ik*g; + bracket_n_1=pow(bracket,n-1.0); + bracket_n=bracket_n_1*bracket; } - 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); - /* 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); +printf("DA:%.20f %.20f %.20f\n",d_theta1,force.x,temp.x); + /* part 1 of db_ij */ + v3_scale(&force,&force,sin_theta*2*h_cos*f_c_ik*frac/d2_h_cos2); - /* part 2 of derivation of b_ij */ - v3_scale(&temp,&dist_ik,df_c_ik*bracket1); - - /* 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; }