+ v3_sub(&distance,&(ai->r),&(aj->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,d);
+ v3_add(&(ai->f),&(aj->f),&force);
+ }
+
+ return 0;
+}
+
+/*
+ * tersoff potential & force for 2 sorts of atoms
+ */
+
+/* tersoff 2 body part */
+
+int tersoff_2bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc) {
+
+ t_tersoff_params *params;
+ t_3dvec dist_ij;
+ double d_ij;
+
+ params=moldyn->pot_params;
+
+ /*
+ * we need: f_c, df_c, f_r, df_r
+ *
+ * therefore we need: R, S
+ */
+
+ v3_sub(&dist_ij,&(ai->r),&(aj->r));
+
+ if(bc) check_per_bound(moldyn,&dist_ij);
+
+ if(ai->bnum==aj->bnum) {
+ S=params->S[ai->bnum];
+ R=params->R[ai->bnum];
+ }
+ else {
+ S=params->Smixed;
+ R=params->Rmixed;
+ }
+
+ d_ij=v3_norm(&dist_ij);
+
+ if(d_ij<=S) {
+ f_r=A*exp(-lamda*d_ij);
+ df_r=-lambda*f_r/d_ij;
+ if(d_ij<R) {
+ /* f_c = 1, df_c = 0 */
+ v3_scale(&force,&dist_ij,df_r);
+ }
+ else {
+ s_r=S-R;
+ arg=PI*(d_ij-R)/s_r;
+ f_c=0.5+0.5*cos(arg);
+ df_c=-0.5*sin(arg)*(PI/(s_r*d_ij));
+ scale=df_c*f_r+df_r*f_c;
+ v3_scale(&force,&dist_ij,scale);
+ v3_add(&(ai->f),&(ai->f),&force);
+ }
+ moldyn->energy+=(f_r*f_c);
+ }
+
+ return 0;
+}
+
+/* tersoff 3 body part */
+
+int tersoff(t_moldyn *moldyn,t_atom *ai,t_atom *aj,t_atom *ak,u8 bc,u8 bck) {
+
+ t_tersoff_params *params;
+ t_3dvec dist_ij;
+ double d_ij;
+
+ params=moldyn->pot_params;
+
+ /* 2 body part of the tersoff potential */
+
+ v3_sub(&dist_ij,&(ai->r),&(aj->r));
+ if(bc) check_per_bound(moldyn,&dist_ij);
+ d_ij=v3_norm(&dist_ij);
+ if(d_ij<=S) {
+
+ /* determine the tersoff parameters */
+ if(atom[i].element!=btom->element) {
+ S=sqrt(TERSOFF_S[e1]*TERSOFF_S[e2]);
+ R=R_m;
+ A=;
+ lambda=;
+ B=;
+ mu=;
+ chi=;
+ beta=;
+ betaN=;
+
+ if(d_ij<=R) {
+ df_r=-lambda*A*exp(-lambda*d_ij)/d_ij;
+ v3_scale(&force,&dist_ij,df_r);
+ v3_add(&(atom[i].f),&(atom[i].f),
+ &force);
+ }
+ else {
+ s_r=S-R;
+ arg1=PI*(d_ij-R)/s_r;
+ f_c=0.5+0.5*cos(arg1);
+ df_c=-0.5*sin(arg1)*(PI/(s_r*d_ij));
+ f_r=A*exp(-lambda*d_ij);
+ df_r=-lambda*f_r/d_ij;
+ scale=df_c*f_r+df_r*f_c;
+ v3_scale(&force,&dist_ij,scale);
+ v3_add(&(atom[i].f),&(atom[i].f),
+ &force);
+ }
+ }
+ else
+ continue;
+
+
+ /* end 2 body stuff */
+
+ /* determine cell neighbours of btom */
+ ki=(btom->r.x+(moldyn->dim.x/2))/lc->x;
+ kj=(btom->r.y+(moldyn->dim.y/2))/lc->y;
+ kk=(btom->r.z+(moldyn->dim.z/2))/lc->z;
+ ck=link_cell_neighbour_index(moldyn,ki,kj,kk,
+ neighbourk);
+
+ /* go for zeta - 3 body stuff! */
+ zeta=0.0;
+ d_ij2=d_ij*d_ij;
+
+ /* cell of btom */
+ thisk=&(neighbourk[0]);
+ list_reset(thisk);
+ do {
+ ktom=thisk->current->data;
+ if(ktom==btom)
+ continue;
+ if(ktom==&(atom[i]))
+ continue;
+
+ /* 3 body stuff (1) */
+
+ v3_sub(&dist_ik,ktom,&(atom[i]));
+ d_ik=v3_norm(&dist_ik);
+ if(d_ik<=Sik) {
+
+ Rik=;
+ Sik=;
+ Aik=;
+ lambda_ik=;
+ Bik=;
+ mu_ik=;
+ omega_ik=;
+ c_i=;
+ d_i=;
+ h_i=;
+
+
+ if(d_ik<=Rik) {
+ f_cik=1.0;
+ df_cik=0.0;
+ }
+ else {
+ sik_rik=Sik-Rik;
+ arg1ik=PI*(d_ik-Rik)/sik_rik;
+ f_cik=0.5+0.5*cos(arg1ik);
+ df_cik=-0.5*sin(arg1ik)* \
+ (PI/(sik_rik*d_ik));
+ f_rik=Aik*exp(-lambda_ik*d_ik);
+ f_aik=-Bik*exp(-mu_ik*d_ik);
+ }
+
+ v3_sub(&distance_jk,ktom,btom);
+ cos_theta=(d_ij2+d_ik*d_ik-d_jk*d_jk)/\
+ (2*d_ij*d_ik);
+ sin_theta=sqrt(1.0/\
+ (cos_theta*cos_theta));
+ theta=arccos(cos_theta);
+
+
+ }
+ else
+ continue;
+
+ /* end 3 body stuff (1) */
+
+
+ } while(list_next(thisk)!=L_NO_NEXT_ELEMENT);
+
+ /* direct neighbours of btom cell */
+ for(k=1;k<ck;k++) {
+ thisk=&(neighbourk[k]);
+ list_reset(thisk);
+ if(thisk->start!=NULL) {
+
+ do {
+ ktom=thisk->current->data;
+ if(ktom==&(atom[i]))
+ continue;
+
+ /* 3 body stuff (2) */
+
+ } while(list_next(thisk)!=L_NO_NEXT_ELEMENT);
+
+ }
+ }
+
+ /* indirect neighbours of btom cell */
+ for(k=ck;k<27;k++) {
+ thisk=&(neighbourk[k]);
+ list_reset(thisk);
+ if(thisk->start!=NULL) {
+
+ do {
+ ktom=thisk->current->data;
+ if(ktom==&(atom[i]))
+ continue;
+
+ /* 3 body stuff */
+
+ } while(list_next(thisk)!=L_NO_NEXT_ELEMENT);
+
+ }
+ }
+
+
+ } while(list_next(this)!=L_NO_NEXT_ELEMENT);
+
+ /*
+ * direct neighbour cells of atom i
+ */
+ for(j=1;j<c;j++) {
+ this=&(neighbour[j]);
+ list_reset(this);
+ if(this->start!=NULL) {
+
+ do {
+ btom=this->current->data;
+
+ /* 2 body stuff */
+
+
+ /* determine cell neighbours of btom */
+ ki=(btom->r.x+(moldyn->dim.x/2))/lc->x;
+ kj=(btom->r.y+(moldyn->dim.y/2))/lc->y;
+ kk=(btom->r.z+(moldyn->dim.z/2))/lc->z;
+ ck=link_cell_neighbour_index(moldyn,ki,kj,kk,
+ neighbourk);
+
+ /* cell of btom */
+ thisk=&(neighbourk[0]);
+ list_reset(thisk);
+ do {
+ ktom=thisk->current->data;
+ if(ktom==btom)
+ continue;
+ if(ktom==&(atom[i]))
+ continue;
+
+ /* 3 body stuff (1) */
+
+ } while(list_next(thisk)!=L_NO_NEXT_ELEMENT);
+
+ /* direct neighbours of btom cell */
+ for(k=1;k<ck;k++) {
+ thisk=&(neighbourk[k]);
+ list_reset(thisk);
+ if(thisk->start!=NULL) {
+
+ do {
+ ktom=thisk->current->data;
+ if(ktom==&(atom[i]))
+ continue;
+
+ /* 3 body stuff (2) */
+
+ } while(list_next(thisk)!=L_NO_NEXT_ELEMENT);
+
+ }
+ }
+
+ /* indirect neighbours of btom cell */
+ for(k=ck;k<27;k++) {
+ thisk=&(neighbourk[k]);
+ list_reset(thisk);
+ if(thisk->start!=NULL) {
+
+ do {
+ ktom=thisk->current->data;
+ if(ktom==&(atom[i]))
+ continue;
+
+ /* 3 body stuff (3) */
+
+ } while(list_next(thisk)!=L_NO_NEXT_ELEMENT);
+
+ }
+ }
+
+
+ } while(list_next(this)!=L_NO_NEXT_ELEMENT);