X-Git-Url: https://www.hackdaworld.org/gitweb/?a=blobdiff_plain;f=moldyn.c;h=9d9901c55d90c3effd806ded40ce2d93dc1b2430;hb=d9e7f195bbb219ad4c2de0e5f54d023ef9e669fb;hp=f504e6854302093297620c50eb9ed67e3f770cfa;hpb=000e702c884e337f27ae66b6506ff9f9b613f8a8;p=physik%2Fposic.git diff --git a/moldyn.c b/moldyn.c index f504e68..9d9901c 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; @@ -377,12 +385,17 @@ int scale_velocity(t_moldyn *moldyn,u8 equi_init) { else if(moldyn->pt_scale&T_SCALE_BERENDSEN) scale=1.0+moldyn->tau*(scale-1.0)/moldyn->t_tc; +printf("scale=%f\n",scale); scale=sqrt(scale); +printf("debug: %f %f %f %f \n",scale,moldyn->t_ref,moldyn->t,moldyn->tau); /* velocity scaling */ - for(i=0;icount;i++) + for(i=0;icount;i++) { +printf("vorher: %f\n",atom[i].v.x); if((equi_init&TRUE)||(atom[i].attr&ATOM_ATTR_HB)) v3_scale(&(atom[i].v),&(atom[i].v),scale); +printf("nachher: %f\n",atom[i].v.x); + } return 0; } @@ -439,12 +452,6 @@ double estimate_time_step(t_moldyn *moldyn,double nn_dist) { /* nn_dist is the nearest neighbour distance */ - if(moldyn->t==5.0) { - printf("[moldyn] i do not estimate timesteps below %f K!\n", - MOLDYN_CRITICAL_EST_TEMP); - return 23.42; - } - tau=(0.05*nn_dist*moldyn->atom[0].mass)/sqrt(3.0*K_BOLTZMANN*moldyn->t); return tau; @@ -568,9 +575,8 @@ 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 +662,11 @@ 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 +679,11 @@ int moldyn_integrate(t_moldyn *moldyn) { /* zero absolute time */ moldyn->time=0.0; + + /* debugging, ignore */ + moldyn->debug=0; + + /* executing the schedule */ for(sched=0;schedschedule.content_count;sched++) { /* setting amount of runs and finite time step size */ @@ -728,7 +740,8 @@ 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, debug: %d", + sched,i,moldyn->debug); fflush(stdout); } } @@ -739,6 +752,9 @@ 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 +792,6 @@ 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; @@ -815,7 +831,11 @@ 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); @@ -950,10 +920,19 @@ 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) { + moldyn->func2b_post(moldyn, + &(itom[i]), + jtom,bc_ij); + } + } } } +printf("end pot force calc\n"); return 0; } @@ -1006,14 +985,15 @@ int harmonic_oscillator(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc) { sc=params->spring_constant; equi_dist=params->equilibrium_distance; - v3_sub(&distance,&(ai->r),&(aj->r)); + v3_sub(&distance,&(aj->r),&(ai->r)); if(bc) check_per_bound(moldyn,&distance); d=v3_norm(&distance); if(d<=moldyn->cutoff) { /* energy is 1/2 (d-d0)^2, but we will add this twice ... */ moldyn->energy+=(0.25*sc*(d-equi_dist)*(d-equi_dist)); - v3_scale(&force,&distance,-sc*(1.0-(equi_dist/d))); + /* f = -grad E; grad r_ij = -1 1/r_ij distance */ + v3_scale(&force,&distance,sc*(1.0-(equi_dist/d))); v3_add(&(ai->f),&(ai->f),&force); } @@ -1034,7 +1014,7 @@ int lennard_jones(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc) { sig6=params->sigma6; sig12=params->sigma12; - v3_sub(&distance,&(ai->r),&(aj->r)); + v3_sub(&distance,&(aj->r),&(ai->r)); if(bc) check_per_bound(moldyn,&distance); d=v3_absolute_square(&distance); /* 1/r^2 */ if(d<=moldyn->cutoff_square) { @@ -1050,7 +1030,7 @@ int lennard_jones(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc) { h1*=12*sig12; d=+h1-h2; d*=eps; - v3_scale(&force,&distance,d); + v3_scale(&force,&distance,-1.0*d); /* f = - grad E */ v3_add(&(ai->f),&(ai->f),&force); } @@ -1072,6 +1052,21 @@ int tersoff_mult_complete_params(t_tersoff_mult_params *p) { p->lambda_m=0.5*(p->lambda[0]+p->lambda[1]); p->mu_m=0.5*(p->mu[0]+p->mu[1]); + printf("[moldyn] tersoff mult parameter info:\n"); + printf(" S (A) | %f | %f | %f\n",p->S[0],p->S[1],p->Smixed); + printf(" R (A) | %f | %f | %f\n",p->R[0],p->R[1],p->Rmixed); + printf(" A (eV) | %f | %f | %f\n",p->A[0]/EV,p->A[1]/EV,p->Amixed/EV); + printf(" B (eV) | %f | %f | %f\n",p->B[0]/EV,p->B[1]/EV,p->Bmixed/EV); + printf(" lambda | %f | %f | %f\n",p->lambda[0],p->lambda[1], + p->lambda_m); + printf(" mu | %f | %f | %f\n",p->mu[0],p->mu[1],p->mu_m); + printf(" beta | %.10f | %.10f\n",p->beta[0],p->beta[1]); + printf(" n | %f | %f\n",p->n[0],p->n[1]); + printf(" c | %f | %f\n",p->c[0],p->c[1]); + printf(" d | %f | %f\n",p->d[0],p->d[1]); + printf(" h | %f | %f\n",p->h[0],p->h[1]); + printf(" chi | %f \n",p->chi); + return 0; } @@ -1091,16 +1086,16 @@ int tersoff_mult_1bp(t_moldyn *moldyn,t_atom *ai) { * their right values */ - exchange->beta=&(params->beta[num]); - exchange->n=&(params->n[num]); - exchange->c=&(params->c[num]); - exchange->d=&(params->d[num]); - exchange->h=&(params->h[num]); + 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->betan=pow(*(exchange->beta),*(exchange->n)); - exchange->c2=params->c[num]*params->c[num]; - exchange->d2=params->d[num]*params->d[num]; - exchange->c2d2=exchange->c2/exchange->d2; + 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->ci2di2=exchange->ci2/exchange->di2; return 0; } @@ -1118,40 +1113,49 @@ int tersoff_mult_2bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc) { int num; double s_r; double arg; - double scale; params=moldyn->pot2b_params; - num=ai->bnum; + num=aj->bnum; exchange=&(params->exchange); + /* clear 3bp and 2bp post run */ exchange->run3bp=0; + exchange->run2bp_post=0; + + /* reset S > r > R mark */ + exchange->d_ij_between_rs=0; /* - * we need: f_c, df_c, f_r, df_r + * calc of 2bp contribution of V_ij and dV_ij/ji + * + * for Vij and dV_ij we need: + * - f_c_ij, df_c_ij + * - f_r_ij, df_r_ij + * + * for dV_ji we need: + * - f_c_ji = f_c_ij, df_c_ji = df_c_ij + * - f_r_ji = f_r_ij; df_r_ji = df_r_ij * - * therefore we need: R, S, A, lambda */ - v3_sub(&dist_ij,&(ai->r),&(aj->r)); - + /* dist_ij, d_ij */ + v3_sub(&dist_ij,&(aj->r),&(ai->r)); if(bc) check_per_bound(moldyn,&dist_ij); - d_ij=v3_norm(&dist_ij); /* save for use in 3bp */ exchange->d_ij=d_ij; exchange->dist_ij=dist_ij; - exchange->d_ij2=d_ij*d_ij; /* constants */ - if(num==aj->bnum) { + 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]; - params->exchange.chi=1.0; + exchange->chi=1.0; } else { S=params->Smixed; @@ -1163,42 +1167,178 @@ int tersoff_mult_2bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc) { params->exchange.chi=params->chi; } + /* if d_ij > S => no force & potential energy contribution */ if(d_ij>S) 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->betajnj=exchange->betaini; + exchange->cj2=exchange->ci2; + exchange->dj2=exchange->di2; + exchange->cj2dj2=exchange->ci2di2; + } + 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->cj2dj2=exchange->cj2/exchange->dj2; + } + + /* f_r_ij = f_r_ji, df_r_ij = df_r_ji */ f_r=A*exp(-lambda*d_ij); - df_r=-lambda*f_r/d_ij; + df_r=lambda*f_r/d_ij; - /* f_a, df_a calc + save for 3bp use */ + /* f_a, df_a calc (again, same for ij and ji) | save for later use! */ exchange->f_a=-B*exp(-mu*d_ij); exchange->df_a=-mu*exchange->f_a/d_ij; + /* f_c, df_c calc (again, same for ij and ji) */ if(d_ij r > R */ + exchange->d_ij_between_rs=1; } - /* add forces */ + /* add forces of 2bp (ij, ji) contribution + * dVij = dVji and we sum up both: no 1/2) */ v3_add(&(ai->f),&(ai->f),&force); - /* energy is 0.5 f_r f_c ... */ + + /* energy 2bp contribution (ij, ji) is 0.5 f_r f_c ... */ moldyn->energy+=(0.5*f_r*f_c); /* save for use in 3bp */ 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->zeta_ij=0.0; + exchange->zeta_ji=0.0; + v3_zero(&(exchange->dzeta_ij)); + v3_zero(&(exchange->dzeta_ji)); + + return 0; +} + +/* tersoff 2 body post part */ + +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 + * + * that is: + * - zeta_ij, dzeta_ij + * - zeta_ji, dzeta_ji + * + * to compute the 3bp contribution to: + * - Vij, dVij + * - dVji + * + */ + + t_tersoff_mult_params *params; + t_tersoff_exchange *exchange; + + t_3dvec force,temp; + t_3dvec *dist_ij; + double b,db,tmp; + double f_c,df_c,f_a,df_a; + double chi,ni,betaini,nj,betajnj; + double zeta; + + params=moldyn->pot2b_params; + exchange=&(params->exchange); + + /* we do not run if f_c_ij was detected to be 0! */ + if(!(exchange->run2bp_post)) + return 0; + + f_c=exchange->f_c; + df_c=exchange->df_c; + f_a=exchange->f_a; + df_a=exchange->df_a; + betaini=exchange->betaini; + betajnj=exchange->betajnj; + ni=*(exchange->n_i); + nj=*(exchange->n_j); + chi=exchange->chi; + dist_ij=&(exchange->dist_ij); + + /* Vij and dVij */ + zeta=exchange->zeta_ij; + if(zeta==0.0) { + moldyn->debug++; /* just for debugging ... */ + db=0.0; + b=chi; + v3_scale(&force,dist_ij,df_a*b*f_c); + } + else { + tmp=betaini*pow(zeta,ni-1.0); /* beta^n * zeta^n-1 */ + b=(1+zeta*tmp); /* 1 + beta^n zeta^n */ + db=chi*pow(b,-1.0/(2*ni)-1); /* x(...)^(-1/2n - 1) */ + b=db*b; /* b_ij */ + db*=-0.5*tmp; /* db_ij */ + v3_scale(&force,&(exchange->dzeta_ij),f_a*db); + v3_scale(&temp,dist_ij,df_a*b); + v3_add(&force,&force,&temp); + v3_scale(&force,&force,f_c); + } + v3_scale(&temp,dist_ij,df_c*b*f_a); + v3_add(&force,&force,&temp); + v3_scale(&force,&force,-0.5); + + /* add force */ + v3_add(&(ai->f),&(ai->f),&force); + + /* add energy of 3bp sum */ + moldyn->energy+=(0.5*f_c*b*f_a); + + /* dVji */ + zeta=exchange->zeta_ji; + if(zeta==0.0) { + moldyn->debug++; + b=chi; + v3_scale(&force,dist_ij,df_a*b*f_c); + } + else { + tmp=betajnj*pow(zeta,nj-1.0); /* beta^n * zeta^n-1 */ + b=(1+zeta*tmp); /* 1 + beta^n zeta^n */ + db=chi*pow(b,-1.0/(2*nj)-1); /* x(...)^(-1/2n - 1) */ + b=db*b; /* b_ij */ + db*=-0.5*tmp; /* db_ij */ + v3_scale(&force,&(exchange->dzeta_ji),f_a*db); + v3_scale(&temp,dist_ij,df_a*b); + v3_add(&force,&force,&temp); + v3_scale(&force,&force,f_c); + } + v3_scale(&temp,dist_ij,df_c*b*f_a); + v3_add(&force,&force,&temp); + v3_scale(&force,&force,-0.5); + + /* add force */ + v3_sub(&(ai->f),&(ai->f),&force); return 0; } @@ -1210,59 +1350,74 @@ int tersoff_mult_3bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,t_atom *ak,u8 bc) { t_tersoff_mult_params *params; t_tersoff_exchange *exchange; t_3dvec dist_ij,dist_ik,dist_jk; - t_3dvec temp,force; + t_3dvec temp1,temp2; + t_3dvec *dzeta; 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 B,mu; + double d_ij,d_ik,d_jk; + double rr,dd; + double f_c,df_c; double f_c_ik,df_c_ik,arg; - double scale; - double chi; - double n,c,d,h,beta,betan; + double f_c_jk; + 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 cos_theta,d_costheta1,d_costheta2; + double h_cos,d2_h_cos2; + double frac,g,zeta,chi; + double tmp; int num; params=moldyn->pot3b_params; - num=ai->bnum; exchange=&(params->exchange); if(!(exchange->run3bp)) return 0; /* - * we need: f_c, d_fc, b_ij, db_ij, f_a, df_a + * calc of 3bp contribution of V_ij and dV_ij/ji/jk & + * 2bp contribution of dV_jk + * + * for Vij and dV_ij we still need: + * - b_ij, db_ij (zeta_ij) + * - f_c_ik, df_c_ik, constants_i, cos_theta_ijk, d_costheta_ijk + * + * for dV_ji we still need: + * - b_ji, db_ji (zeta_ji) + * - f_c_jk, d_c_jk, constants_j, cos_theta_jik, d_costheta_jik + * + * for dV_jk we need: + * - f_c_jk + * - f_a_jk + * - db_jk (zeta_jk) + * - f_c_ji, df_c_ji, constants_j, cos_theta_jki, d_costheta_jki * - * we got f_c, df_c, f_a, df_a from 2bp calculation */ + /* + * get exchange data + */ + + /* dist_ij, d_ij - this is < S_ij ! */ + dist_ij=exchange->dist_ij; d_ij=exchange->d_ij; - d_ij2=exchange->d_ij2; - f_a=params->exchange.f_a; - df_a=params->exchange.df_a; - - /* d_ij is <= S, as we didn't return so far! */ + /* f_c_ij, df_c_ij (same for ji) */ + f_c=exchange->f_c; + df_c=exchange->df_c; /* - * calc of b_ij (scalar) and db_ij (vector) - * - * - for b_ij: chi, beta, f_c_ik, w(=1), c, d, h, n, cos_theta - * - * - for db_ij: d_theta, sin_theta, cos_theta, f_c_ik, df_c_ik, - * w_ik, - * + * calculate unknown values now ... */ - v3_sub(&dist_ik,&(ai->r),&(ak->r)); + /* V_ij and dV_ij stuff (in b_ij there is f_c_ik) */ + + /* dist_ik, d_ik */ + v3_sub(&dist_ik,&(ak->r),&(ai->r)); if(bc) check_per_bound(moldyn,&dist_ik); d_ik=v3_norm(&dist_ik); - /* constants for f_c_ik calc */ + /* ik constants */ + num=ai->bnum; if(num==ak->bnum) { R=params->R[num]; S=params->S[num]; @@ -1272,106 +1427,206 @@ int tersoff_mult_3bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,t_atom *ak,u8 bc) { S=params->Smixed; } - /* calc of f_c_ik */ - if(d_ik>S) { - f_c_ik=0.0; - df_c_ik=0.0; - } - else if(d_ikn_i); + c=*(exchange->c_i); + d=*(exchange->d_i); + h=*(exchange->h_i); + c2=exchange->ci2; + d2=exchange->di2; + c2d2=exchange->ci2di2; + + /* cosine of theta_ijk by scalaproduct */ + rr=v3_scalar_product(&dist_ij,&dist_ik); + dd=d_ij*d_ik; + cos_theta=rr/dd; + + /* d_costheta */ + tmp=1.0/dd; + d_costheta1=cos_theta/(d_ij*d_ij)-tmp; + d_costheta2=cos_theta/(d_ik*d_ik)-tmp; + + /* some usefull values */ + h_cos=(h-cos_theta); + d2_h_cos2=d2+(h_cos*h_cos); + frac=c2/(d2_h_cos2); + + /* g(cos_theta) */ + g=1.0+c2d2-frac; + + /* d_costheta_ij and dg(cos_theta) - needed in any case! */ + v3_scale(&temp1,&dist_ij,d_costheta1); + v3_scale(&temp2,&dist_ik,d_costheta2); + v3_add(&temp1,&temp1,&temp2); + v3_scale(&temp1,&temp1,-2.0*frac*h_cos/d2_h_cos2); /* dg */ + + /* f_c_ik & df_c_ik + {d,}zeta contribution */ + dzeta=&(exchange->dzeta_ij); + if(d_ik f_c_ik=1.0; + // => df_c_ik=0.0; of course we do not set this! + + /* zeta_ij */ + exchange->zeta_ij+=g; + + /* dzeta_ij */ + v3_add(dzeta,dzeta,&temp1); + } + else { + /* {d,}f_c_ik */ + s_r=S-R; + arg=M_PI*(d_ik-R)/s_r; + f_c_ik=0.5+0.5*cos(arg); + df_c_ik=-0.5*sin(arg)*(M_PI/(s_r*d_ik)); + + /* zeta_ij */ + exchange->zeta_ij+=f_c_ik*g; + + /* dzeta_ij */ + v3_scale(&temp1,&temp1,f_c_ik); + v3_scale(&temp2,&dist_ik,g*df_c_ik); + v3_add(&temp1,&temp1,&temp2); + v3_add(dzeta,dzeta,&temp1); + } } - - v3_sub(&dist_jk,&(aj->r),&(ak->r)); + + /* dV_ji stuff (in b_ji there is f_c_jk) + dV_jk stuff! */ + + /* dist_jk, d_jk */ + v3_sub(&dist_jk,&(ak->r),&(aj->r)); if(bc) check_per_bound(moldyn,&dist_jk); d_jk=v3_norm(&dist_jk); - beta=*(exchange->beta); - betan=exchange->betan; - n=*(exchange->n); - c=*(exchange->c); - d=*(exchange->d); - h=*(exchange->h); - chi=exchange->chi; - c2=exchange->c2; - d2=exchange->d2; - c2d2=exchange->c2d2; - - 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); - 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); - d_theta1=2*denom-numer*2*d_ik/d_ij; - d_theta2=2*denom-numer*2*d_ij/d_ik; - d_theta1*=d_theta; - d_theta2*=d_theta; - - h_cos=(h-cos_theta); - h_cos2=h_cos*h_cos; - d2_h_cos2=d2-h_cos2; - - /* 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: "); + /* 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]; + chi=1.0; } 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: "); + R=params->Rmixed; + S=params->Smixed; + B=params->Bmixed; + mu=params->mu_m; + chi=params->chi; } - bracket3_pow_1=pow(bracket3,(-1.0/(2.0*n))-1.0); -printf("THETA: %.15f %.15f\n",cos_theta,theta*180/(2*M_PI)); - bracket3_pow=bracket3_pow_1*bracket3; - /* now go on with calc of b_ij and derivation of b_ij */ - b_ij=chi*bracket3_pow; + /* zeta_ji/dzeta_ji contribution only for d_jk < S_jk */ + if(d_jkn_j); + c=*(exchange->c_j); + d=*(exchange->d_j); + h=*(exchange->h_j); + c2=exchange->cj2; + d2=exchange->dj2; + c2d2=exchange->cj2dj2; + + /* cosine of theta_jik by scalaproduct */ + rr=v3_scalar_product(&dist_ij,&dist_jk); /* times -1 */ + dd=d_ij*d_jk; + cos_theta=rr/dd; + + /* d_costheta */ + d_costheta1=1.0/(d_jk*d_ij); + d_costheta2=cos_theta/(d_ij*d_ij); /* in fact -cos(), but ^ */ + + /* some usefull values */ + h_cos=(h-cos_theta); + d2_h_cos2=d2+(h_cos*h_cos); + frac=c2/(d2_h_cos2); + + /* g(cos_theta) */ + g=1.0+c2d2-frac; + + /* d_costheta_ij and dg(cos_theta) - needed in any case! */ + v3_scale(&temp1,&dist_jk,d_costheta1); + v3_scale(&temp2,&dist_ij,-d_costheta2); /* ji -> ij => -1 */ + v3_add(&temp1,&temp1,&temp2); + v3_scale(&temp1,&temp1,-2.0*frac*h_cos/d2_h_cos2); /* dg */ + + /* f_c_jk + {d,}zeta contribution (df_c_jk = 0) */ + dzeta=&(exchange->dzeta_ji); + if(d_jkzeta_ji+=g; + + /* dzeta_ji */ + v3_add(dzeta,dzeta,&temp1); + } + else { + /* f_c_jk */ + s_r=S-R; + arg=M_PI*(d_jk-R)/s_r; + f_c_jk=0.5+0.5*cos(arg); + + /* zeta_ji */ + exchange->zeta_ji+=f_c_jk*g; + + /* dzeta_ij */ + v3_scale(&temp1,&temp1,f_c_jk); + v3_add(dzeta,dzeta,&temp1); + } - /* derivation of theta */ - v3_scale(&force,&dist_ij,d_theta1); - v3_scale(&temp,&dist_ik,d_theta2); - v3_add(&force,&force,&temp); + /* dV_jk stuff | add force contribution on atom i immediately */ + if(exchange->d_ij_between_rs) { + zeta=f_c*g; + v3_scale(&temp1,&temp1,f_c); + v3_scale(&temp2,&dist_ij,df_c); + v3_add(&temp1,&temp1,&temp2); + } + else { + zeta=g; + // dzeta_jk is simply dg, which is temp1 + } + /* betajnj * zeta_jk ^ nj-1 */ + tmp=exchange->betajnj*pow(zeta,(n-1.0)); + tmp=-chi/2.0*pow(1+tmp*zeta,-1.0/(2.0*n)-1)*tmp; + v3_scale(&temp1,&temp1,tmp*B*exp(-mu*d_jk)*f_c_jk*0.5); + v3_add(&(ai->f),&(ai->f),&temp1); /* -1 skipped in f_a calc ^ */ + /* scaled with 0.5 ^ */ + } + + return 0; +} - /* 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); +/* + * debugging / critical check functions + */ - /* 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); +int moldyn_bc_check(t_moldyn *moldyn) { - /* 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); - 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); + t_atom *atom; + t_3dvec *dim; + int i; + + atom=moldyn->atom; + dim=&(moldyn->dim); + + for(i=0;icount;i++) { + if(atom[i].r.x>=dim->x/2||-atom[i].r.x>dim->x/2) + printf("FATAL: atom %d: x: %.20f (%.20f)\n", + i,atom[i].r.x*1e10,dim->x/2*1e10); + if(atom[i].r.y>=dim->y/2||-atom[i].r.y>dim->y/2) + printf("FATAL: atom %d: y: %.20f (%.20f)\n", + i,atom[i].r.y*1e10,dim->y/2*1e10); + if(atom[i].r.z>=dim->z/2||-atom[i].r.z>dim->z/2) + printf("FATAL: atom %d: z: %.20f (%.20f)\n", + i,atom[i].r.z*1e10,dim->z/2*1e10); + } - /* 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); - return 0; }