+ ptr=realloc(schedule->tau,count*sizeof(double));
+ if(!ptr) {
+ perror("[moldyn] realloc (tau)");
+ return -1;
+ }
+ moldyn->schedule.tau=ptr;
+ moldyn->schedule.tau[count-1]=tau;
+
+ return 0;
+}
+
+int moldyn_set_schedule_hook(t_moldyn *moldyn,void *hook,void *hook_params) {
+
+ moldyn->schedule.hook=hook;
+ moldyn->schedule.hook_params=hook_params;
+
+ return 0;
+}
+
+/*
+ *
+ * 'integration of newtons equation' - algorithms
+ *
+ */
+
+/* start the integration */
+
+int moldyn_integrate(t_moldyn *moldyn) {
+
+ int i,sched;
+ unsigned int e,m,s,v;
+ t_3dvec p;
+ t_moldyn_schedule *schedule;
+ t_atom *atom;
+ int fd;
+ char fb[128];
+ double ds;
+
+ schedule=&(moldyn->schedule);
+ atom=moldyn->atom;
+
+ /* initialize linked cell method */
+ link_cell_init(moldyn);
+
+ /* logging & visualization */
+ e=moldyn->ewrite;
+ m=moldyn->mwrite;
+ s=moldyn->swrite;
+ v=moldyn->vwrite;
+
+ /* 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);
+
+ /* 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)
+ printf("[moldyn] warning: cutoff > 0.5 x dim.y\n");
+ if(moldyn->cutoff>0.5*moldyn->dim.z)
+ printf("[moldyn] warning: cutoff > 0.5 x dim.z\n");
+ ds=0.5*atom[0].f.x*moldyn->tau_square/atom[0].mass;
+ if(ds>0.05*moldyn->nnd)
+ printf("[moldyn] warning: forces too high / tau too small!\n");
+
+ /* zero absolute time */
+ moldyn->time=0.0;
+
+ /* debugging, ignre */
+ moldyn->debug=0;
+
+ /* executing the schedule */
+ for(sched=0;sched<moldyn->schedule.content_count;sched++) {
+
+ /* setting amount of runs and finite time step size */
+ moldyn->tau=schedule->tau[sched];
+ moldyn->tau_square=moldyn->tau*moldyn->tau;
+ moldyn->time_steps=schedule->runs[sched];
+
+ /* integration according to schedule */
+
+ for(i=0;i<moldyn->time_steps;i++) {
+
+ /* integration step */
+printf("MOVE\n");
+ moldyn->integrate(moldyn);
+
+ /* p/t scaling */
+ if(moldyn->pt_scale&(T_SCALE_BERENDSEN|T_SCALE_DIRECT))
+ scale_velocity(moldyn,FALSE);
+
+ /* increase absolute time */
+ moldyn->time+=moldyn->tau;
+
+ /* check for log & visualization */
+ if(e) {
+ if(!(i%e))
+ dprintf(moldyn->efd,
+ "%.15f %.45f %.45f %.45f\n",
+ moldyn->time,update_e_kin(moldyn),
+ moldyn->energy,
+ get_total_energy(moldyn));
+ }
+ if(m) {
+ if(!(i%m)) {
+ p=get_total_p(moldyn);
+ dprintf(moldyn->mfd,
+ "%.15f %.45f\n",moldyn->time,
+ v3_norm(&p));
+ }
+ }
+ if(s) {
+ if(!(i%s)) {
+ snprintf(fb,128,"%s-%f-%.15f.save",moldyn->sfb,
+ moldyn->t,i*moldyn->tau);
+ fd=open(fb,O_WRONLY|O_TRUNC|O_CREAT);
+ if(fd<0) perror("[moldyn] save fd open");
+ else {
+ write(fd,moldyn,sizeof(t_moldyn));
+ write(fd,moldyn->atom,
+ moldyn->count*sizeof(t_atom));
+ }
+ close(fd);
+ }
+ }
+ if(v) {
+ if(!(i%v)) {
+ visual_atoms(&(moldyn->vis),moldyn->time,
+ moldyn->atom,moldyn->count);
+ printf("\rsched: %d, steps: %d, theta: %d",
+ sched,i,moldyn->debug);
+ fflush(stdout);
+ }
+ }
+
+ }
+
+ /* check for hooks */
+ if(schedule->hook)
+ schedule->hook(moldyn,schedule->hook_params);
+
+ /* get a new info line */
+ printf("\n");
+
+ }
+
+ return 0;
+}
+
+/* velocity verlet */
+
+int velocity_verlet(t_moldyn *moldyn) {
+
+ int i,count;
+ double tau,tau_square;
+ t_3dvec delta;
+ t_atom *atom;
+
+ atom=moldyn->atom;
+ count=moldyn->count;
+ tau=moldyn->tau;
+ tau_square=moldyn->tau_square;
+
+ for(i=0;i<count;i++) {
+ /* new positions */
+ v3_scale(&delta,&(atom[i].v),tau);
+ v3_add(&(atom[i].r),&(atom[i].r),&delta);
+ v3_scale(&delta,&(atom[i].f),0.5*tau_square/atom[i].mass);
+ v3_add(&(atom[i].r),&(atom[i].r),&delta);
+ check_per_bound(moldyn,&(atom[i].r));
+
+ /* velocities */
+ v3_scale(&delta,&(atom[i].f),0.5*tau/atom[i].mass);
+ v3_add(&(atom[i].v),&(atom[i].v),&delta);
+ }
+
+ /* neighbour list update */
+ link_cell_update(moldyn);
+
+ /* forces depending on chosen potential */
+ potential_force_calc(moldyn);
+
+ for(i=0;i<count;i++) {
+ /* again velocities */
+ v3_scale(&delta,&(atom[i].f),0.5*tau/atom[i].mass);
+ v3_add(&(atom[i].v),&(atom[i].v),&delta);
+ }
+
+ return 0;
+}
+
+
+/*
+ *
+ * potentials & corresponding forces
+ *
+ */
+
+/* generic potential and force calculation */
+
+int potential_force_calc(t_moldyn *moldyn) {
+
+ int i,j,k,count;
+ t_atom *itom,*jtom,*ktom;
+ t_linkcell *lc;
+ t_list neighbour_i[27];
+ t_list neighbour_i2[27];
+ //t_list neighbour_j[27];
+ t_list *this,*that;
+ u8 bc_ij,bc_ik;
+ int dnlc;
+
+ count=moldyn->count;
+ itom=moldyn->atom;
+ lc=&(moldyn->lc);
+
+ /* reset energy */
+ moldyn->energy=0.0;
+
+ /* get energy and force of every atom */
+ for(i=0;i<count;i++) {
+
+ /* reset force */
+ v3_zero(&(itom[i].f));
+
+ /* single particle potential/force */
+ if(itom[i].attr&ATOM_ATTR_1BP)
+ moldyn->func1b(moldyn,&(itom[i]));
+
+ /* 2 body pair potential/force */
+ if(itom[i].attr&(ATOM_ATTR_2BP|ATOM_ATTR_3BP)) {
+
+ link_cell_neighbour_index(moldyn,
+ (itom[i].r.x+moldyn->dim.x/2)/lc->x,
+ (itom[i].r.y+moldyn->dim.y/2)/lc->y,
+ (itom[i].r.z+moldyn->dim.z/2)/lc->z,
+ neighbour_i);
+
+ dnlc=lc->dnlc;
+
+ for(j=0;j<27;j++) {
+
+ this=&(neighbour_i[j]);
+ list_reset(this);
+
+ if(this->start==NULL)
+ continue;
+
+ bc_ij=(j<dnlc)?0:1;
+
+ do {
+ jtom=this->current->data;
+
+ if(jtom==&(itom[i]))
+ continue;
+
+ if((jtom->attr&ATOM_ATTR_2BP)&
+ (itom[i].attr&ATOM_ATTR_2BP))
+ moldyn->func2b(moldyn,
+ &(itom[i]),
+ jtom,
+ bc_ij);
+
+ /* 3 body potential/force */
+
+ if(!(itom[i].attr&ATOM_ATTR_3BP)||
+ !(jtom->attr&ATOM_ATTR_3BP))
+ continue;
+
+ /* copy the neighbour lists */
+ memcpy(neighbour_i2,neighbour_i,
+ 27*sizeof(t_list));
+
+ /* get neighbours of i */
+ for(k=0;k<27;k++) {
+
+ that=&(neighbour_i2[k]);
+ list_reset(that);
+
+ if(that->start==NULL)
+ continue;
+
+ bc_ik=(k<dnlc)?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_ik|bc_ij);
+
+ } while(list_next(that)!=\
+ L_NO_NEXT_ELEMENT);
+
+ }
+
+ } 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("debug atom %d: %.15f %.15f %.15f\n",i,itom[i].r.x,itom[i].v.x,itom[i].f.x);
+ }
+
+ return 0;
+}
+
+/*
+ * periodic boundayr checking
+ */
+
+int check_per_bound(t_moldyn *moldyn,t_3dvec *a) {
+
+ double x,y,z;
+ t_3dvec *dim;
+
+ dim=&(moldyn->dim);
+
+ x=0.5*dim->x;
+ y=0.5*dim->y;
+ z=0.5*dim->z;
+
+ if(moldyn->status&MOLDYN_STAT_PBX) {
+ if(a->x>=x) a->x-=dim->x;
+ else if(-a->x>x) a->x+=dim->x;
+ }
+ if(moldyn->status&MOLDYN_STAT_PBY) {
+ if(a->y>=y) a->y-=dim->y;
+ else if(-a->y>y) a->y+=dim->y;
+ }
+ if(moldyn->status&MOLDYN_STAT_PBZ) {
+ if(a->z>=z) a->z-=dim->z;
+ else if(-a->z>z) a->z+=dim->z;
+ }
+
+ 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;
+ double sc,equi_dist;
+
+ params=moldyn->pot2b_params;
+ sc=params->spring_constant;
+ equi_dist=params->equilibrium_distance;
+
+ 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));
+ /* 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);
+ }
+
+ 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;
+
+ 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) {
+ d=1.0/d; /* 1/r^2 */
+ h2=d*d; /* 1/r^4 */
+ h2*=d; /* 1/r^6 */
+ h1=h2*h2; /* 1/r^12 */
+ /* energy is eps*..., but we will add this twice ... */
+ moldyn->energy+=0.5*eps*(sig12*h1-sig6*h2);
+ 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,-1.0*d); /* f = - grad E */
+ v3_add(&(ai->f),&(ai->f),&force);
+ }
+
+ 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->Smixed=sqrt(p->S[0]*p->S[1]);
+ 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 (m) | %.12f | %.12f | %.12f\n",p->S[0],p->S[1],p->Smixed);
+ printf(" R (m) | %.12f | %.12f | %.12f\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 num;
+ t_tersoff_mult_params *params;
+ t_tersoff_exchange *exchange;
+
+ num=ai->bnum;
+ params=moldyn->pot1b_params;
+ exchange=&(params->exchange);
+
+ /*
+ * simple: point constant parameters only depending on atom i to
+ * 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->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;
+
+ 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;
+ double A,B,R,S,lambda,mu;
+ double f_r,df_r;
+ double f_c,df_c;
+ int num;
+ double s_r;
+ double arg;
+ double scale;
+
+ params=moldyn->pot2b_params;
+ num=ai->bnum;
+ exchange=&(params->exchange);
+
+ exchange->run3bp=0;
+ exchange->run2bp_post=0;
+
+ /*
+ * we need: f_c, df_c, f_r, df_r
+ *
+ * therefore we need: R, S, A, lambda
+ */
+
+ 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;
+
+ /* constants */
+ if(num==aj->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;
+ }
+ else {
+ S=params->Smixed;
+ R=params->Rmixed;
+ A=params->Amixed;
+ B=params->Bmixed;
+ lambda=params->lambda_m;
+ 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 later use */
+ exchange->f_a=-B*exp(-mu*d_ij);
+ exchange->df_a=-mu*exchange->f_a/d_ij;
+
+ if(d_ij<R) {
+ /* f_c = 1, df_c = 0 */
+ f_c=1.0;
+ df_c=0.0;
+ v3_scale(&force,&dist_ij,df_r);
+ }
+ else {
+ s_r=S-R;
+ arg=M_PI*(d_ij-R)/s_r;
+ f_c=0.5+0.5*cos(arg);
+ df_c=-0.5*sin(arg)*(M_PI/(s_r*d_ij));
+ scale=df_c*f_r+df_r*f_c;
+ v3_scale(&force,&dist_ij,scale);
+ }
+
+ /* add forces */
+ v3_add(&(ai->f),&(ai->f),&force);
+ /* energy 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=0.0;
+ v3_zero(&(exchange->db_ij));
+
+ 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 */
+
+ t_tersoff_mult_params *params;
+ t_tersoff_exchange *exchange;
+
+ 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,n,n_betan;
+ 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;
+
+ 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;
+ n_betan=exchange->n_betan;
+ n=*(exchange->n);
+ chi=exchange->chi;
+ dist_ij=&(exchange->dist_ij);
+ zeta=exchange->zeta;
+
+ db_ij_scale2=pow(zeta,n-1.0);
+printf("DEBUG: %.15f %.15f\n",zeta,db_ij_scale2);
+ db_ij_scale1=db_ij_scale2*zeta;
+ db_ij_scale2*=n_betan;
+ db_ij_scale1=pow((1.0+n_betan*db_ij_scale1),-1.0/(2*n)-1);
+ b_ij=chi*db_ij_scale1*(1.0+n_betan*db_ij_scale1);
+ db_ij_scale1*=(-1.0*chi/(2*n));
+
+ /* 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);
+
+ /* 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 (all three parts) */
+ v3_add(&(ai->f),&temp,&force);
+
+ 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;
+ t_3dvec temp,force;
+ double R,S,s_r;
+ double d_ij,d_ik;
+ double rijrik,dijdik;
+ double f_c,df_c,f_a,df_a;
+ double f_c_ik,df_c_ik,arg;
+ double n,c,d,h;
+ double c2,d2,c2d2;
+ double cos_theta,d_costheta1,d_costheta2;
+ double h_cos,d2_h_cos2;
+ double frac;
+ double g;
+ 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
+ *
+ * we got f_c, df_c, f_a, df_a from 2bp calculation
+ */
+
+ d_ij=exchange->d_ij;
+ dist_ij=exchange->dist_ij;
+
+ f_a=params->exchange.f_a;
+ df_a=params->exchange.df_a;
+
+ f_c=exchange->f_c;
+ df_c=exchange->df_c;
+
+ /* d_ij is <= S, as we didn't return so far! */
+
+ /*
+ * 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_costheta, cos_theta, f_c_ik, df_c_ik, w_ik
+ *
+ */
+
+ v3_sub(&dist_ik,&(ak->r),&(ai->r));
+ if(bc) check_per_bound(moldyn,&dist_ik);
+ d_ik=v3_norm(&dist_ik);
+
+ /* constants */
+ if(num==ak->bnum) {
+ R=params->R[num];
+ S=params->S[num];
+ }
+ else {
+ R=params->Rmixed;
+ S=params->Smixed;
+ }
+
+ /* there is no contribution if f_c_ik = 0 */
+ if(d_ik>S)
+ return 0;
+
+ /* get exchange data */
+ n=*(exchange->n);
+ c=*(exchange->c);
+ d=*(exchange->d);
+ h=*(exchange->h);
+ c2=exchange->c2;
+ d2=exchange->d2;
+ c2d2=exchange->c2d2;
+
+ /* cosine of theta by scalaproduct */
+ rijrik=v3_scalar_product(&dist_ij,&dist_ik);
+ dijdik=d_ij*d_ik;
+ cos_theta=rijrik/dijdik;
+
+ /* hack - cos theta machine accuracy problems! */
+ if(cos_theta>1.0||cos_theta<-1.0) {
+ printf("THETA CORRECTION\n");
+ 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;
+ }
+ }
+
+ d_costheta1=dijdik-rijrik*d_ik/d_ij;
+ d_costheta2=dijdik-rijrik*d_ij/d_ik;
+
+ h_cos=(h-cos_theta);
+ d2_h_cos2=d2+(h_cos*h_cos);
+
+ frac=c2/(d2_h_cos2);
+ g=1.0+c2d2-frac;
+
+ /* d_costheta contrib to db_ij (needed in all remaining cases) */
+ v3_scale(&temp,&dist_ij,d_costheta1);
+ v3_scale(&force,&dist_ik,d_costheta2);
+ v3_add(&force,&force,&temp);
+ v3_scale(&force,&force,-2.0*frac*h_cos/d2_h_cos2); /* f_c_ik missing */
+
+ if(d_ik<R) {
+ /* f_c_ik = 1, df_c_ik = 0 */
+ /* => only d_costheta contrib to db_ij */
+ // => do nothing ...
+
+ /* zeta, f_c_ik = 1 */
+ exchange->zeta+=g;
+ }
+ else {
+ 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));
+
+ /* scale d_costheta contrib with f_c_ik */
+ v3_scale(&force,&force,f_c_ik);
+
+ /* df_c_ik contrib to db_ij */
+ v3_scale(&temp,&dist_ik,df_c_ik*g);
+
+ /* sum up both parts */
+ v3_add(&force,&force,&temp);
+
+ /* zeta */
+ exchange->zeta+=f_c_ik*g;
+ }
+printf("%.30f\n",exchange->zeta);
+
+ /* add to db_ij */
+ v3_add(&(exchange->db_ij),&(exchange->db_ij),&force);
+