| | |
| | | #include"vertex.h" |
| | | #include"bond.h" |
| | | #include<math.h> |
| | | #include"energy.h" |
| | | |
| | | ts_bool poly_assign_filament_xi(ts_vesicle *vesicle, ts_tape *tape){ |
| | | ts_uint i; |
| | | |
| | | for(i=0;i<vesicle->filament_list->n;i++){ |
| | | vesicle->filament_list->poly[i]->k = tape->xi; |
| | | } |
| | | |
| | | return TS_SUCCESS; |
| | | } |
| | | |
| | | |
| | | ts_bool poly_assign_spring_const(ts_vesicle *vesicle){ |
| | | ts_uint i; |
| | |
| | | ts_poly *poly=(ts_poly *)calloc(1,sizeof(ts_poly)); |
| | | poly->vlist = init_vertex_list(n); |
| | | poly->blist = init_bond_list(); |
| | | poly->grafted_vtx = grafted_vtx; |
| | | grafted_vtx->grafted_poly = poly; |
| | | if (grafted_vtx!=NULL){ |
| | | poly->grafted_vtx = grafted_vtx; |
| | | grafted_vtx->grafted_poly = poly; |
| | | } |
| | | |
| | | ts_uint i; |
| | | for(i=0;i<n-1;i++){ |
| | |
| | | |
| | | for(i=0;i<poly->blist->n;i++){ |
| | | poly->blist->bond[i]->bond_length=sqrt(vtx_distance_sq(poly->blist->bond[i]->vtx1,poly->blist->bond[i]->vtx2)); |
| | | bond_energy(poly->blist->bond[i],poly); |
| | | } |
| | | |
| | | return poly; |
| | | } |
| | | |
| | | |
| | | ts_poly_list *init_poly_list(ts_uint n_poly, ts_uint n_mono, ts_vertex_list *vlist){ |
| | | ts_poly_list *init_poly_list(ts_uint n_poly, ts_uint n_mono, ts_vertex_list *vlist, ts_vesicle *vesicle){ |
| | | ts_poly_list *poly_list=(ts_poly_list *)calloc(1,sizeof(ts_poly_list)); |
| | | poly_list->poly = (ts_poly **)calloc(n_poly,sizeof(ts_poly *)); |
| | | ts_uint i=0,j=0, idx; |
| | | ts_uint i=0,j=0; //idx; |
| | | ts_uint gvtxi; |
| | | ts_double xnorm,ynorm,znorm,normlength; |
| | | ts_double dphi,dh; |
| | | |
| | | if (n_poly > vlist->n){fatal("Number of polymers larger then numbero f vertices on a vesicle.",310);} |
| | | // Grafting polymers: |
| | | if (vlist!=NULL){ |
| | | if (n_poly > vlist->n){fatal("Number of polymers larger then numbero f vertices on a vesicle.",310);} |
| | | |
| | | while(i<n_poly){ |
| | | gvtxi = rand() % vlist->n; |
| | | if (vlist->vtx[gvtxi]->grafted_poly == NULL){ |
| | | poly_list->poly[i] = init_poly(n_mono, vlist->vtx[gvtxi]); |
| | | i++; |
| | | while(i<n_poly){ |
| | | gvtxi = rand() % vlist->n; |
| | | if (vlist->vtx[gvtxi]->grafted_poly == NULL){ |
| | | poly_list->poly[i] = init_poly(n_mono, vlist->vtx[gvtxi]); |
| | | i++; |
| | | } |
| | | } |
| | | } |
| | | |
| | | else |
| | | { |
| | | for(i=0;i<n_poly;i++){ |
| | | poly_list->poly[i] = init_poly(n_mono, NULL); |
| | | } |
| | | } |
| | | |
| | | poly_list->n = n_poly; |
| | | |
| | | /* Make straight poylmers normal to membrane. Dist. between poly vertices put to 1*/ |
| | | for (i=0;i<poly_list->n;i++){ |
| | | if (vlist!=NULL){ |
| | | /* Make straight grafted poylmers normal to membrane (polymer brush). Dist. between poly vertices put to 1*/ |
| | | for (i=0;i<poly_list->n;i++){ |
| | | |
| | | xnorm=0.0; |
| | | ynorm=0.0; |
| | | znorm=0.0; |
| | | for (j=0;j<poly_list->poly[i]->grafted_vtx->tristar_no;j++){ |
| | | xnorm-=poly_list->poly[i]->grafted_vtx->tristar[j]->xnorm; |
| | | ynorm-=poly_list->poly[i]->grafted_vtx->tristar[j]->ynorm; |
| | | znorm-=poly_list->poly[i]->grafted_vtx->tristar[j]->znorm; |
| | | } |
| | | normlength=sqrt(xnorm*xnorm+ynorm*ynorm+znorm*znorm); |
| | | xnorm=xnorm/normlength; |
| | | ynorm=ynorm/normlength; |
| | | znorm=znorm/normlength; |
| | | |
| | | xnorm=0.0; |
| | | ynorm=0.0; |
| | | znorm=0.0; |
| | | for (j=0;j<poly_list->poly[i]->grafted_vtx->tristar_no;j++){ |
| | | xnorm-=poly_list->poly[i]->grafted_vtx->tristar[j]->xnorm; |
| | | ynorm-=poly_list->poly[i]->grafted_vtx->tristar[j]->ynorm; |
| | | znorm-=poly_list->poly[i]->grafted_vtx->tristar[j]->znorm; |
| | | for (j=0;j<poly_list->poly[i]->vlist->n;j++){ |
| | | poly_list->poly[i]->vlist->vtx[j]->x = poly_list->poly[i]->grafted_vtx->x + xnorm*(ts_double)(j+1); |
| | | poly_list->poly[i]->vlist->vtx[j]->y = poly_list->poly[i]->grafted_vtx->y + ynorm*(ts_double)(j+1); |
| | | poly_list->poly[i]->vlist->vtx[j]->z = poly_list->poly[i]->grafted_vtx->z + znorm*(ts_double)(j+1); |
| | | } |
| | | } |
| | | normlength=sqrt(xnorm*xnorm+ynorm*ynorm+znorm*znorm); |
| | | xnorm=xnorm/normlength; |
| | | ynorm=ynorm/normlength; |
| | | znorm=znorm/normlength; |
| | | } |
| | | else |
| | | { |
| | | /* Make filaments inside the vesicle. Helix with radius... Dist. between poly vertices put to 1*/ |
| | | ts_double a,R,H,tantheta,h,r,phi,A0=1.2; |
| | | |
| | | for (j=0;j<poly_list->poly[i]->vlist->n;j++){ |
| | | poly_list->poly[i]->vlist->vtx[j]->x = poly_list->poly[i]->grafted_vtx->x + xnorm*(ts_double)(j+1); |
| | | poly_list->poly[i]->vlist->vtx[j]->y = poly_list->poly[i]->grafted_vtx->y + ynorm*(ts_double)(j+1); |
| | | poly_list->poly[i]->vlist->vtx[j]->z = poly_list->poly[i]->grafted_vtx->z + znorm*(ts_double)(j+1); |
| | | a = A0*(ts_double)vesicle->nshell; |
| | | R = A0*((ts_double)vesicle->nshell)/(2.0*sin(M_PI/5.0)); |
| | | H = sqrt(a*a - R*R); |
| | | tantheta = sqrt(R*R - a*a/4.0)/H; |
| | | |
| | | h = -H + sqrt(vesicle->clist->dmin_interspecies)*1.5; |
| | | r = (H-fabs(h))*tantheta - sqrt(vesicle->clist->dmin_interspecies)*1.5; |
| | | dphi = 2.0*asin(1.0/2.0/r)*1.001; |
| | | dh = dphi/2.0/M_PI*1.001; |
| | | phi=0.0; |
| | | for(i=0;i<poly_list->n;i++){ |
| | | for (j=0;j<poly_list->poly[i]->vlist->n;j++){ |
| | | h = h + dh; |
| | | r = (H-fabs(h))*tantheta - sqrt(vesicle->clist->dmin_interspecies)*1.5; |
| | | dphi = 2.0*asin(1.0/2.0/r)*1.001; |
| | | dh = dphi/2.0/M_PI*1.001; |
| | | phi+=dphi; |
| | | //ji = j + i*poly_list->poly[i]->vlist->n; |
| | | poly_list->poly[i]->vlist->vtx[j]->x = r*cos(phi); |
| | | poly_list->poly[i]->vlist->vtx[j]->y = r*sin(phi); |
| | | poly_list->poly[i]->vlist->vtx[j]->z = h;// ji*dh - (dh*poly_list->n*poly_list->poly[i]->vlist->n/2.0); |
| | | } |
| | | } |
| | | } |
| | | |
| | | //index correction for polymeres. Important, since each vtx has to have unique id |
| | | idx=vlist->n; |
| | | /* idx=vlist->n; |
| | | for(i=0;i<n_poly;i++){ |
| | | for(j=0;j<n_mono;j++,idx++){ |
| | | |
| | |
| | | |
| | | } |
| | | } |
| | | |
| | | */ |
| | | |
| | | return poly_list; |
| | | } |