X-Git-Url: https://www.hackdaworld.org/gitweb/?a=blobdiff_plain;f=moldyn.c;h=dae975cedcd6a0b0b4baf41e26ff572a1046ab87;hb=296a35b943e922173ce648ec76a4472e287af108;hp=817a72788b45f2572258873aaa8ca64cace0397f;hpb=f3e4193447ac49a8953515910d4b4e6ce2c7608b;p=physik%2Fposic.git diff --git a/moldyn.c b/moldyn.c index 817a727..dae975c 100644 --- a/moldyn.c +++ b/moldyn.c @@ -16,6 +16,7 @@ #include #include "moldyn.h" +#include "report/report.h" int moldyn_init(t_moldyn *moldyn,int argc,char **argv) { @@ -72,7 +73,7 @@ int set_temperature(t_moldyn *moldyn,double t_ref) { moldyn->t_ref=t_ref; - printf("[moldyn] temperature: %f\n",moldyn->t_ref); + printf("[moldyn] temperature [K]: %f\n",moldyn->t_ref); return 0; } @@ -81,7 +82,7 @@ int set_pressure(t_moldyn *moldyn,double p_ref) { moldyn->p_ref=p_ref; - printf("[moldyn] pressure: %f\n",moldyn->p_ref); + printf("[moldyn] pressure [atm]: %f\n",moldyn->p_ref/ATM); return 0; } @@ -164,7 +165,6 @@ int set_pbc(t_moldyn *moldyn,u8 x,u8 y,u8 z) { int set_potential1b(t_moldyn *moldyn,pf_func1b func,void *params) { moldyn->func1b=func; - moldyn->pot1b_params=params; return 0; } @@ -172,7 +172,6 @@ int set_potential1b(t_moldyn *moldyn,pf_func1b func,void *params) { int set_potential2b(t_moldyn *moldyn,pf_func2b func,void *params) { moldyn->func2b=func; - moldyn->pot2b_params=params; return 0; } @@ -180,7 +179,6 @@ int set_potential2b(t_moldyn *moldyn,pf_func2b func,void *params) { int set_potential2b_post(t_moldyn *moldyn,pf_func2b_post func,void *params) { moldyn->func2b_post=func; - moldyn->pot2b_params=params; return 0; } @@ -188,7 +186,13 @@ int set_potential2b_post(t_moldyn *moldyn,pf_func2b_post func,void *params) { int set_potential3b(t_moldyn *moldyn,pf_func3b func,void *params) { moldyn->func3b=func; - moldyn->pot3b_params=params; + + return 0; +} + +int set_potential_params(t_moldyn *moldyn,void *params) { + + moldyn->pot_params=params; return 0; } @@ -338,17 +342,25 @@ int create_lattice(t_moldyn *moldyn,u8 type,double lc,int element,double mass, } moldyn->atom=ptr; atom=&(moldyn->atom[count]); - - v3_zero(&origin); + + /* no atoms on the boundaries (only reason: it looks better!) */ + origin.x=0.5*lc; + origin.y=0.5*lc; + origin.z=0.5*lc; switch(type) { case CUBIC: - ret=cubic_init(a,b,c,lc,atom,NULL); + set_nn_dist(moldyn,lc); + ret=cubic_init(a,b,c,lc,atom,&origin); break; case FCC: - ret=fcc_init(a,b,c,lc,atom,NULL); + v3_scale(&origin,&origin,0.5); + set_nn_dist(moldyn,0.5*sqrt(2.0)*lc); + ret=fcc_init(a,b,c,lc,atom,&origin); break; case DIAMOND: + v3_scale(&origin,&origin,0.25); + set_nn_dist(moldyn,0.25*sqrt(3.0)*lc); ret=diamond_init(a,b,c,lc,atom,&origin); break; default: @@ -398,8 +410,8 @@ int cubic_init(int a,int b,int c,double lc,t_atom *atom,t_3dvec *origin) { for(i=0;iatom; - - double_ekin=0; - for(i=0;icount;i++) - double_ekin+=atom[i].mass*v3_absolute_square(&(atom[i].v)); + /* assume up to date kinetic energy, which is 3/2 N k_B T */ - /* kinetic energy = 3/2 N k_B T */ - moldyn->t=double_ekin/(3.0*K_BOLTZMANN*moldyn->count); + moldyn->t=(2.0*moldyn->ekin)/(3.0*K_BOLTZMANN*moldyn->count); return moldyn->t; } @@ -682,16 +675,21 @@ double pressure_calc(t_moldyn *moldyn) { double v; t_virial *virial; + /* + * P = 1/(3V) sum_i ( p_i^2 / 2m + f_i r_i ) + * + * virial = f_i r_i + */ + v=0.0; for(i=0;icount;i++) { virial=&(moldyn->atom[i].virial); v+=(virial->xx+virial->yy+virial->zz); } - v*=ONE_THIRD; -printf("kieck mal: %f %f %f\n",v,moldyn->count*K_BOLTZMANN*moldyn->t,v/moldyn->count); - moldyn->p=moldyn->count*K_BOLTZMANN*moldyn->t+v; - moldyn->p/=moldyn->volume; + /* assume up to date kinetic energy */ + moldyn->p=2.0*moldyn->ekin+v; + moldyn->p/=(3.0*moldyn->volume); return moldyn->p; } @@ -720,7 +718,7 @@ double thermodynamic_pressure_calc(t_moldyn *moldyn) { scale_dim(moldyn,scale,TRUE,0,0); scale_atoms(moldyn,scale,TRUE,0,0); link_cell_shutdown(moldyn); - link_cell_init(moldyn); + link_cell_init(moldyn,QUIET); potential_force_calc(moldyn); tp->x=(moldyn->energy-u)/moldyn->dv; p=tp->x*tp->x; @@ -734,7 +732,7 @@ double thermodynamic_pressure_calc(t_moldyn *moldyn) { scale_dim(moldyn,scale,0,TRUE,0); scale_atoms(moldyn,scale,0,TRUE,0); link_cell_shutdown(moldyn); - link_cell_init(moldyn); + link_cell_init(moldyn,QUIET); potential_force_calc(moldyn); tp->y=(moldyn->energy-u)/moldyn->dv; p+=tp->y*tp->y; @@ -748,7 +746,7 @@ double thermodynamic_pressure_calc(t_moldyn *moldyn) { scale_dim(moldyn,scale,0,0,TRUE); scale_atoms(moldyn,scale,0,0,TRUE); link_cell_shutdown(moldyn); - link_cell_init(moldyn); + link_cell_init(moldyn,QUIET); potential_force_calc(moldyn); tp->z=(moldyn->energy-u)/moldyn->dv; p+=tp->z*tp->z; @@ -765,7 +763,7 @@ printf("debug: %f %f\n",moldyn->atom[0].r.x,moldyn->dim.x); scale_dim(moldyn,scale,1,1,1); scale_atoms(moldyn,scale,1,1,1); link_cell_shutdown(moldyn); - link_cell_init(moldyn); + link_cell_init(moldyn,QUIET); potential_force_calc(moldyn); printf("debug: %f %f\n",moldyn->atom[0].r.x,moldyn->dim.x); @@ -779,7 +777,7 @@ printf("debug: %f %f\n",moldyn->atom[0].r.x,moldyn->dim.x); moldyn->energy=u; link_cell_shutdown(moldyn); - link_cell_init(moldyn); + link_cell_init(moldyn,QUIET); return sqrt(p); } @@ -820,61 +818,48 @@ int scale_atoms(t_moldyn *moldyn,double scale,u8 x,u8 y,u8 z) { int scale_volume(t_moldyn *moldyn) { - t_atom *atom; t_3dvec *dim,*vdim; - double scale,v; - t_virial virial; + double scale; t_linkcell *lc; - int i; - atom=moldyn->atom; - dim=&(moldyn->dim); vdim=&(moldyn->vis.dim); + dim=&(moldyn->dim); lc=&(moldyn->lc); - memset(&virial,0,sizeof(t_virial)); + /* scaling factor */ + if(moldyn->pt_scale&P_SCALE_BERENDSEN) { + scale=1.0-(moldyn->p_ref-moldyn->p)/moldyn->p_tc; + scale=pow(scale,ONE_THIRD); + } + else { + scale=pow(moldyn->p/moldyn->p_ref,ONE_THIRD); + } +moldyn->debug=scale; - for(i=0;icount;i++) { - virial.xx+=atom[i].virial.xx; - virial.yy+=atom[i].virial.yy; - virial.zz+=atom[i].virial.zz; - virial.xy+=atom[i].virial.xy; - virial.xz+=atom[i].virial.xz; - virial.yz+=atom[i].virial.yz; + /* scale the atoms and dimensions */ + scale_atoms(moldyn,scale,TRUE,TRUE,TRUE); + scale_dim(moldyn,scale,TRUE,TRUE,TRUE); + + /* visualize dimensions */ + if(vdim->x!=0) { + vdim->x=dim->x; + vdim->y=dim->y; + vdim->z=dim->z; } - /* just a guess so far ... */ - v=virial.xx+virial.yy+virial.zz; - -printf("%f\n",v); - /* get pressure from virial */ - moldyn->p=moldyn->count*K_BOLTZMANN*moldyn->t+ONE_THIRD*v; - moldyn->p/=moldyn->volume; -printf("%f | %f\n",moldyn->p/(ATM),moldyn->p_ref/ATM); - - /* scale factor */ - if(moldyn->pt_scale&P_SCALE_BERENDSEN) - scale=3*sqrt(1-(moldyn->p_ref-moldyn->p)/moldyn->p_tc); - else - /* should actually never be used */ - scale=pow(moldyn->p/moldyn->p_ref,1.0/3.0); - -printf("scale = %f\n",scale); - /* actual scaling */ - dim->x*=scale; - dim->y*=scale; - dim->z*=scale; - if(vdim->x) vdim->x=dim->x; - if(vdim->y) vdim->y=dim->y; - if(vdim->z) vdim->z=dim->z; - moldyn->volume*=(scale*scale*scale); - - /* check whether we need a new linkcell init */ - if((dim->x/moldyn->cutoff!=lc->nx)|| - (dim->y/moldyn->cutoff!=lc->ny)|| - (dim->z/moldyn->cutoff!=lc->nx)) { + /* recalculate scaled volume */ + moldyn->volume=dim->x*dim->y*dim->z; + + /* adjust/reinit linkcell */ + if(((int)(dim->x/moldyn->cutoff)!=lc->nx)|| + ((int)(dim->y/moldyn->cutoff)!=lc->ny)|| + ((int)(dim->z/moldyn->cutoff)!=lc->nx)) { link_cell_shutdown(moldyn); - link_cell_init(moldyn); + link_cell_init(moldyn,QUIET); + } else { + lc->x*=scale; + lc->y*=scale; + lc->z*=scale; } return 0; @@ -939,7 +924,7 @@ double estimate_time_step(t_moldyn *moldyn,double nn_dist) { /* linked list / cell method */ -int link_cell_init(t_moldyn *moldyn) { +int link_cell_init(t_moldyn *moldyn,u8 vol) { t_linkcell *lc; int i; @@ -960,7 +945,7 @@ int link_cell_init(t_moldyn *moldyn) { if(lc->cells<27) printf("[moldyn] FATAL: less then 27 subcells!\n"); - printf("[moldyn] initializing linked cells (%d)\n",lc->cells); + if(vol) printf("[moldyn] initializing linked cells (%d)\n",lc->cells); for(i=0;icells;i++) list_init_f(&(lc->subcell[i])); @@ -1137,7 +1122,7 @@ int moldyn_integrate(t_moldyn *moldyn) { atom=moldyn->atom; /* initialize linked cell method */ - link_cell_init(moldyn); + link_cell_init(moldyn,VERBOSE); /* logging & visualization */ e=moldyn->ewrite; @@ -1190,20 +1175,21 @@ int moldyn_integrate(t_moldyn *moldyn) { /* integration step */ moldyn->integrate(moldyn); + /* calculate kinetic energy, temperature and pressure */ + update_e_kin(moldyn); + temperature_calc(moldyn); + pressure_calc(moldyn); + //thermodynamic_pressure_calc(moldyn); + /* p/t scaling */ if(moldyn->pt_scale&(T_SCALE_BERENDSEN|T_SCALE_DIRECT)) scale_velocity(moldyn,FALSE); if(moldyn->pt_scale&(P_SCALE_BERENDSEN|P_SCALE_DIRECT)) scale_volume(moldyn); - temperature_calc(moldyn); - pressure_calc(moldyn); - //thermodynamic_pressure_calc(moldyn); - /* check for log & visualization */ if(e) { if(!(i%e)) - update_e_kin(moldyn); dprintf(moldyn->efd, "%f %f %f %f\n", moldyn->time,moldyn->ekin/energy_scale, @@ -1235,8 +1221,9 @@ int moldyn_integrate(t_moldyn *moldyn) { if(!(i%v)) { visual_atoms(&(moldyn->vis),moldyn->time, moldyn->atom,moldyn->count); - printf("\rsched: %d, steps: %d, debug: %f | %f", - sched->count,i,moldyn->p/ATM,moldyn->debug/ATM); + printf("\rsched: %d, steps: %d, T: %f, P: %f V: %f", + sched->count,i, + moldyn->t,moldyn->p/ATM,moldyn->volume); fflush(stdout); } } @@ -1465,7 +1452,8 @@ printf("\n\n"); * virial calculation */ -inline int virial_calc(t_atom *a,t_3dvec *f,t_3dvec *d) { +//inline int virial_calc(t_atom *a,t_3dvec *f,t_3dvec *d) { +int virial_calc(t_atom *a,t_3dvec *f,t_3dvec *d) { a->virial.xx+=f->x*d->x; a->virial.yy+=f->y*d->y; @@ -1481,7 +1469,8 @@ inline int virial_calc(t_atom *a,t_3dvec *f,t_3dvec *d) { * periodic boundayr checking */ -inline int check_per_bound(t_moldyn *moldyn,t_3dvec *a) { +//inline int check_per_bound(t_moldyn *moldyn,t_3dvec *a) { +int check_per_bound(t_moldyn *moldyn,t_3dvec *a) { double x,y,z; t_3dvec *dim; @@ -1508,778 +1497,6 @@ inline int check_per_bound(t_moldyn *moldyn,t_3dvec *a) { return 0; } - -/* - * example potentials - */ - -/* harmonic oscillator potential and force */ - -int harmonic_oscillator(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc) { - - t_ho_params *params; - t_3dvec force,distance; - double d,f; - double sc,equi_dist; - - params=moldyn->pot2b_params; - sc=params->spring_constant; - equi_dist=params->equilibrium_distance; - - if(air),&(ai->r)); - - if(bc) check_per_bound(moldyn,&distance); - d=v3_norm(&distance); - if(d<=moldyn->cutoff) { - moldyn->energy+=(0.5*sc*(d-equi_dist)*(d-equi_dist)); - /* f = -grad E; grad r_ij = -1 1/r_ij distance */ - f=sc*(1.0-equi_dist/d); - v3_scale(&force,&distance,f); - v3_add(&(ai->f),&(ai->f),&force); - virial_calc(ai,&force,&distance); - virial_calc(aj,&force,&distance); /* f and d signe switched */ - v3_scale(&force,&distance,-f); - v3_add(&(aj->f),&(aj->f),&force); - } - - return 0; -} - -/* lennard jones potential & force for one sort of atoms */ - -int lennard_jones(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc) { - - t_lj_params *params; - t_3dvec force,distance; - double d,h1,h2; - double eps,sig6,sig12; - - params=moldyn->pot2b_params; - eps=params->epsilon4; - sig6=params->sigma6; - sig12=params->sigma12; - - if(air),&(ai->r)); - if(bc) check_per_bound(moldyn,&distance); - d=v3_absolute_square(&distance); /* 1/r^2 */ - if(d<=moldyn->cutoff_square) { - d=1.0/d; /* 1/r^2 */ - h2=d*d; /* 1/r^4 */ - h2*=d; /* 1/r^6 */ - h1=h2*h2; /* 1/r^12 */ - moldyn->energy+=(eps*(sig12*h1-sig6*h2)-params->uc); - h2*=d; /* 1/r^8 */ - h1*=d; /* 1/r^14 */ - h2*=6*sig6; - h1*=12*sig12; - d=+h1-h2; - d*=eps; - v3_scale(&force,&distance,d); - v3_add(&(aj->f),&(aj->f),&force); - v3_scale(&force,&distance,-1.0*d); /* f = - grad E */ - v3_add(&(ai->f),&(ai->f),&force); - virial_calc(ai,&force,&distance); - virial_calc(aj,&force,&distance); /* f and d signe switched */ - } - - return 0; -} - -/* - * tersoff potential & force for 2 sorts of atoms - */ - -/* create mixed terms from parameters and set them */ -int tersoff_mult_complete_params(t_tersoff_mult_params *p) { - - printf("[moldyn] tersoff parameter completion\n"); - p->S2[0]=p->S[0]*p->S[0]; - p->S2[1]=p->S[1]*p->S[1]; - p->Smixed=sqrt(p->S[0]*p->S[1]); - p->S2mixed=p->Smixed*p->Smixed; - p->Rmixed=sqrt(p->R[0]*p->R[1]); - p->Amixed=sqrt(p->A[0]*p->A[1]); - p->Bmixed=sqrt(p->B[0]*p->B[1]); - 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; -} - -/* tersoff 1 body part */ -int tersoff_mult_1bp(t_moldyn *moldyn,t_atom *ai) { - - int brand; - t_tersoff_mult_params *params; - t_tersoff_exchange *exchange; - - brand=ai->brand; - params=moldyn->pot1b_params; - exchange=&(params->exchange); - - /* - * simple: point constant parameters only depending on atom i to - * their right values - */ - - 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[brand]*params->c[brand]; - exchange->di2=params->d[brand]*params->d[brand]; - exchange->ci2di2=exchange->ci2/exchange->di2; - - return 0; -} - -/* tersoff 2 body part */ -int tersoff_mult_2bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc) { - - t_tersoff_mult_params *params; - t_tersoff_exchange *exchange; - t_3dvec dist_ij,force; - double d_ij,d_ij2; - double A,B,R,S,S2,lambda,mu; - double f_r,df_r; - double f_c,df_c; - int brand; - double s_r; - double arg; - - params=moldyn->pot2b_params; - brand=aj->brand; - 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; - - /* - * 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 - * - */ - - /* constants */ - if(brand==ai->brand) { - S=params->S[brand]; - S2=params->S2[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 { - S=params->Smixed; - S2=params->S2mixed; - R=params->Rmixed; - A=params->Amixed; - B=params->Bmixed; - lambda=params->lambda_m; - mu=params->mu_m; - params->exchange.chi=params->chi; - } - - /* dist_ij, d_ij */ - v3_sub(&dist_ij,&(aj->r),&(ai->r)); - if(bc) check_per_bound(moldyn,&dist_ij); - d_ij2=v3_absolute_square(&dist_ij); - - /* if d_ij2 > S2 => no force & potential energy contribution */ - if(d_ij2>S2) - return 0; - - /* now we will need the distance */ - //d_ij=v3_norm(&dist_ij); - d_ij=sqrt(d_ij2); - - /* save for use in 3bp */ - exchange->d_ij=d_ij; - exchange->d_ij2=d_ij2; - exchange->dist_ij=dist_ij; - - /* more constants */ - 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; - exchange->cj2dj2=exchange->ci2di2; - } - else { - exchange->betajnj=pow(*(exchange->beta_j),*(exchange->n_j)); - exchange->cj2=params->c[brand]*params->c[brand]; - exchange->dj2=params->d[brand]*params->d[brand]; - 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; - - /* 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 of 2bp (ij, ji) contribution - * dVij = dVji and we sum up both: no 1/2) */ - v3_add(&(ai->f),&(ai->f),&force); - - /* virial */ - ai->virial.xx-=force.x*dist_ij.x; - ai->virial.yy-=force.y*dist_ij.y; - ai->virial.zz-=force.z*dist_ij.z; - ai->virial.xy-=force.x*dist_ij.y; - ai->virial.xz-=force.x*dist_ij.z; - ai->virial.yz-=force.y*dist_ij.z; - -#ifdef DEBUG -if(ai==&(moldyn->atom[0])) { - printf("dVij, dVji (2bp) contrib:\n"); - printf("%f | %f\n",force.x,ai->f.x); - printf("%f | %f\n",force.y,ai->f.y); - printf("%f | %f\n",force.z,ai->f.z); -} -#endif -#ifdef VDEBUG -if(ai==&(moldyn->atom[0])) { - printf("dVij, dVji (2bp) contrib:\n"); - printf("%f | %f\n",force.x*dist_ij.x,ai->virial.xx); - printf("%f | %f\n",force.y*dist_ij.y,ai->virial.yy); - printf("%f | %f\n",force.z*dist_ij.z,ai->virial.zz); -} -#endif - - /* 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 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 ... */ - 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); - - /* virial */ - ai->virial.xx-=force.x*dist_ij->x; - ai->virial.yy-=force.y*dist_ij->y; - ai->virial.zz-=force.z*dist_ij->z; - ai->virial.xy-=force.x*dist_ij->y; - ai->virial.xz-=force.x*dist_ij->z; - ai->virial.yz-=force.y*dist_ij->z; - -#ifdef DEBUG -if(ai==&(moldyn->atom[0])) { - printf("dVij (3bp) contrib:\n"); - printf("%f | %f\n",force.x,ai->f.x); - printf("%f | %f\n",force.y,ai->f.y); - printf("%f | %f\n",force.z,ai->f.z); -} -#endif -#ifdef VDEBUG -if(ai==&(moldyn->atom[0])) { - printf("dVij (3bp) contrib:\n"); - printf("%f | %f\n",force.x*dist_ij->x,ai->virial.xx); - printf("%f | %f\n",force.y*dist_ij->y,ai->virial.yy); - printf("%f | %f\n",force.z*dist_ij->z,ai->virial.zz); -} -#endif - - /* 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_add(&(ai->f),&(ai->f),&force); - - /* virial - plus sign, as dist_ij = - dist_ji - (really??) */ -// TEST ... with a minus instead - ai->virial.xx-=force.x*dist_ij->x; - ai->virial.yy-=force.y*dist_ij->y; - ai->virial.zz-=force.z*dist_ij->z; - ai->virial.xy-=force.x*dist_ij->y; - ai->virial.xz-=force.x*dist_ij->z; - ai->virial.yz-=force.y*dist_ij->z; - -#ifdef DEBUG -if(ai==&(moldyn->atom[0])) { - printf("dVji (3bp) contrib:\n"); - printf("%f | %f\n",force.x,ai->f.x); - printf("%f | %f\n",force.y,ai->f.y); - printf("%f | %f\n",force.z,ai->f.z); -} -#endif -#ifdef VDEBUG -if(ai==&(moldyn->atom[0])) { - printf("dVji (3bp) contrib:\n"); - printf("%f | %f\n",force.x*dist_ij->x,ai->virial.xx); - printf("%f | %f\n",force.y*dist_ij->y,ai->virial.yy); - printf("%f | %f\n",force.z*dist_ij->z,ai->virial.zz); -} -#endif - - return 0; -} - -/* tersoff 3 body part */ - -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 temp1,temp2; - t_3dvec *dzeta; - double R,S,S2,s_r; - double B,mu; - double d_ij,d_ik,d_jk,d_ij2,d_ik2,d_jk2; - double rr,dd; - double f_c,df_c; - double f_c_ik,df_c_ik,arg; - double f_c_jk; - double n,c,d,h; - double c2,d2,c2d2; - double cos_theta,d_costheta1,d_costheta2; - double h_cos,d2_h_cos2; - double frac,g,zeta,chi; - double tmp; - int brand; - - params=moldyn->pot3b_params; - exchange=&(params->exchange); - - if(!(exchange->run3bp)) - return 0; - - /* - * 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 - * - */ - - /* - * 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_c_ij, df_c_ij (same for ji) */ - f_c=exchange->f_c; - df_c=exchange->df_c; - - /* - * calculate unknown values now ... - */ - - /* 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_ik2=v3_absolute_square(&dist_ik); - - /* ik constants */ - brand=ai->brand; - if(brand==ak->brand) { - R=params->R[brand]; - S=params->S[brand]; - S2=params->S2[brand]; - } - else { - R=params->Rmixed; - S=params->Smixed; - S2=params->S2mixed; - } - - /* zeta_ij/dzeta_ij contribution only for d_ik < S */ - if(d_ik2n_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_ij2-tmp; - d_costheta2=cos_theta/d_ik2-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); - } - } - - /* 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_jk2=v3_absolute_square(&dist_jk); - - /* jk constants */ - brand=aj->brand; - if(brand==ak->brand) { - R=params->R[brand]; - S=params->S[brand]; - S2=params->S2[brand]; - B=params->B[brand]; - mu=params->mu[brand]; - chi=1.0; - } - else { - R=params->Rmixed; - S=params->Smixed; - S2=params->S2mixed; - B=params->Bmixed; - mu=params->mu_m; - chi=params->chi; - } - - /* zeta_ji/dzeta_ji contribution only for d_jk < S_jk */ - if(d_jk2n_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); /* -1, as ij -> ji */ - dd=d_ij*d_jk; - cos_theta=rr/dd; - - /* d_costheta */ - d_costheta1=1.0/dd; - d_costheta2=cos_theta/d_ij2; - - /* 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_jik 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_sub(&temp1,&temp1,&temp2); /* there is a minus! */ - v3_scale(&temp1,&temp1,-2.0*frac*h_cos/d2_h_cos2); /* dg */ - - /* store dg in temp2 and use it for dVjk later */ - v3_copy(&temp2,&temp1); - - /* 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_ji */ - v3_scale(&temp1,&temp1,f_c_jk); - v3_add(dzeta,dzeta,&temp1); - } - - /* dV_jk stuff | add force contribution on atom i immediately */ - if(exchange->d_ij_between_rs) { - zeta=f_c*g; - v3_scale(&temp1,&temp2,f_c); - v3_scale(&temp2,&dist_ij,df_c*g); - v3_add(&temp2,&temp2,&temp1); /* -> dzeta_jk in temp2 */ - } - else { - zeta=g; - // dzeta_jk is simply dg, which is stored in temp2 - } - /* 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(&temp2,&temp2,tmp*B*exp(-mu*d_jk)*f_c_jk*0.5); - v3_add(&(ai->f),&(ai->f),&temp2); /* -1 skipped in f_a calc ^ */ - /* scaled with 0.5 ^ */ - - /* virial */ - ai->virial.xx-=temp2.x*dist_jk.x; - ai->virial.yy-=temp2.y*dist_jk.y; - ai->virial.zz-=temp2.z*dist_jk.z; - ai->virial.xy-=temp2.x*dist_jk.y; - ai->virial.xz-=temp2.x*dist_jk.z; - ai->virial.yz-=temp2.y*dist_jk.z; - -#ifdef DEBUG -if(ai==&(moldyn->atom[0])) { - printf("dVjk (3bp) contrib:\n"); - printf("%f | %f\n",temp2.x,ai->f.x); - printf("%f | %f\n",temp2.y,ai->f.y); - printf("%f | %f\n",temp2.z,ai->f.z); -} -#endif -#ifdef VDEBUG -if(ai==&(moldyn->atom[0])) { - printf("dVjk (3bp) contrib:\n"); - printf("%f | %f\n",temp2.x*dist_jk.x,ai->virial.xx); - printf("%f | %f\n",temp2.y*dist_jk.y,ai->virial.yy); - printf("%f | %f\n",temp2.z*dist_jk.z,ai->virial.zz); -} -#endif - - } - - return 0; -} - - /* * debugging / critical check functions */