| commit | author | age | ||
| 8db569 | 1 | #include"general.h" |
| M | 2 | #include"poly.h" |
| 3 | #include<stdlib.h> | |
| 4 | #include"vertex.h" | |
| 5 | #include"bond.h" | |
| 6 | #include<math.h> | |
| fedf2b | 7 | #include"energy.h" |
| 8db569 | 8 | |
| bcf455 | 9 | ts_bool poly_assign_filament_xi(ts_vesicle *vesicle, ts_tape *tape){ |
| M | 10 | ts_uint i; |
| 11 | ||
| 12 | for(i=0;i<vesicle->filament_list->n;i++){ | |
| 13 | vesicle->filament_list->poly[i]->k = tape->xi; | |
| 14 | } | |
| 15 | ||
| 16 | return TS_SUCCESS; | |
| 17 | } | |
| 18 | ||
| 19 | ||
| 48bb92 | 20 | ts_bool poly_assign_spring_const(ts_vesicle *vesicle){ |
| M | 21 | ts_uint i; |
| 22 | ||
| 23 | for(i=0;i<vesicle->poly_list->n;i++){ | |
| 24 | vesicle->poly_list->poly[i]->k = vesicle->spring_constant; | |
| 25 | } | |
| 26 | ||
| 27 | return TS_SUCCESS; | |
| 28 | } | |
| 8db569 | 29 | |
| 1d5dff | 30 | ts_poly *init_poly(ts_uint n, ts_vertex *grafted_vtx){ |
| M | 31 | ts_poly *poly=(ts_poly *)calloc(1,sizeof(ts_poly)); |
| 32 | poly->vlist = init_vertex_list(n); | |
| 33 | poly->blist = init_bond_list(); | |
| 624f81 | 34 | if (grafted_vtx!=NULL){ |
| M | 35 | poly->grafted_vtx = grafted_vtx; |
| 36 | grafted_vtx->grafted_poly = poly; | |
| 37 | } | |
| 1d5dff | 38 | |
| M | 39 | ts_uint i; |
| 8db569 | 40 | for(i=0;i<n-1;i++){ |
| 1d5dff | 41 | vtx_add_cneighbour(poly->blist, poly->vlist->vtx[i], poly->vlist->vtx[i+1]); |
| 8db569 | 42 | vtx_add_neighbour(poly->vlist->vtx[i+1], poly->vlist->vtx[i]); |
| 1d5dff | 43 | } |
| M | 44 | |
| 48bb92 | 45 | for(i=0;i<poly->blist->n;i++){ |
| M | 46 | poly->blist->bond[i]->bond_length=sqrt(vtx_distance_sq(poly->blist->bond[i]->vtx1,poly->blist->bond[i]->vtx2)); |
| fedf2b | 47 | bond_energy(poly->blist->bond[i],poly); |
| 48bb92 | 48 | } |
| M | 49 | |
| 1d5dff | 50 | return poly; |
| M | 51 | } |
| 52 | ||
| 53 | ||
| 624f81 | 54 | ts_poly_list *init_poly_list(ts_uint n_poly, ts_uint n_mono, ts_vertex_list *vlist, ts_vesicle *vesicle){ |
| 1d5dff | 55 | ts_poly_list *poly_list=(ts_poly_list *)calloc(1,sizeof(ts_poly_list)); |
| 8db569 | 56 | poly_list->poly = (ts_poly **)calloc(n_poly,sizeof(ts_poly *)); |
| 3c1ac1 | 57 | ts_uint i=0,j=0; //idx; |
| 8db569 | 58 | ts_uint gvtxi; |
| M | 59 | ts_double xnorm,ynorm,znorm,normlength; |
| 624f81 | 60 | ts_double dphi,dh; |
| 1d5dff | 61 | |
| 624f81 | 62 | // Grafting polymers: |
| M | 63 | if (vlist!=NULL){ |
| 64 | if (n_poly > vlist->n){fatal("Number of polymers larger then numbero f vertices on a vesicle.",310);} | |
| 1d5dff | 65 | |
| 624f81 | 66 | while(i<n_poly){ |
| M | 67 | gvtxi = rand() % vlist->n; |
| 68 | if (vlist->vtx[gvtxi]->grafted_poly == NULL){ | |
| 69 | poly_list->poly[i] = init_poly(n_mono, vlist->vtx[gvtxi]); | |
| 70 | i++; | |
| 71 | } | |
| 1d5dff | 72 | } |
| M | 73 | } |
| 624f81 | 74 | else |
| M | 75 | { |
| 76 | for(i=0;i<n_poly;i++){ | |
| 77 | poly_list->poly[i] = init_poly(n_mono, NULL); | |
| 78 | } | |
| 79 | } | |
| 80 | ||
| 1d5dff | 81 | poly_list->n = n_poly; |
| M | 82 | |
| 624f81 | 83 | if (vlist!=NULL){ |
| M | 84 | /* Make straight grafted poylmers normal to membrane (polymer brush). Dist. between poly vertices put to 1*/ |
| 85 | for (i=0;i<poly_list->n;i++){ | |
| 86 | ||
| 87 | xnorm=0.0; | |
| 88 | ynorm=0.0; | |
| 89 | znorm=0.0; | |
| 90 | for (j=0;j<poly_list->poly[i]->grafted_vtx->tristar_no;j++){ | |
| 91 | xnorm-=poly_list->poly[i]->grafted_vtx->tristar[j]->xnorm; | |
| 92 | ynorm-=poly_list->poly[i]->grafted_vtx->tristar[j]->ynorm; | |
| 93 | znorm-=poly_list->poly[i]->grafted_vtx->tristar[j]->znorm; | |
| 94 | } | |
| 95 | normlength=sqrt(xnorm*xnorm+ynorm*ynorm+znorm*znorm); | |
| 96 | xnorm=xnorm/normlength; | |
| 97 | ynorm=ynorm/normlength; | |
| 98 | znorm=znorm/normlength; | |
| 8db569 | 99 | |
| 624f81 | 100 | for (j=0;j<poly_list->poly[i]->vlist->n;j++){ |
| M | 101 | poly_list->poly[i]->vlist->vtx[j]->x = poly_list->poly[i]->grafted_vtx->x + xnorm*(ts_double)(j+1); |
| 102 | poly_list->poly[i]->vlist->vtx[j]->y = poly_list->poly[i]->grafted_vtx->y + ynorm*(ts_double)(j+1); | |
| 103 | poly_list->poly[i]->vlist->vtx[j]->z = poly_list->poly[i]->grafted_vtx->z + znorm*(ts_double)(j+1); | |
| 104 | } | |
| 8db569 | 105 | } |
| 624f81 | 106 | } |
| M | 107 | else |
| 108 | { | |
| 109 | /* Make filaments inside the vesicle. Helix with radius... Dist. between poly vertices put to 1*/ | |
| fe24d2 | 110 | ts_double a,R,H,tantheta,h,r,phi,A0=1.2; |
| M | 111 | |
| 112 | a = A0*(ts_double)vesicle->nshell; | |
| 113 | R = A0*((ts_double)vesicle->nshell)/(2.0*sin(M_PI/5.0)); | |
| 114 | H = sqrt(a*a - R*R); | |
| 115 | tantheta = sqrt(R*R - a*a/4.0)/H; | |
| 116 | ||
| 117 | h = -H + sqrt(vesicle->clist->dmin_interspecies)*1.5; | |
| 118 | r = (H-fabs(h))*tantheta - sqrt(vesicle->clist->dmin_interspecies)*1.5; | |
| 119 | dphi = 2.0*asin(1.0/2.0/r)*1.001; | |
| 402e8f | 120 | dh = dphi/2.0/M_PI*1.001; |
| fe24d2 | 121 | phi=0.0; |
| 624f81 | 122 | for(i=0;i<poly_list->n;i++){ |
| M | 123 | for (j=0;j<poly_list->poly[i]->vlist->n;j++){ |
| fe24d2 | 124 | h = h + dh; |
| M | 125 | r = (H-fabs(h))*tantheta - sqrt(vesicle->clist->dmin_interspecies)*1.5; |
| 126 | dphi = 2.0*asin(1.0/2.0/r)*1.001; | |
| 127 | dh = dphi/2.0/M_PI*1.001; | |
| 128 | phi+=dphi; | |
| 129 | //ji = j + i*poly_list->poly[i]->vlist->n; | |
| 130 | poly_list->poly[i]->vlist->vtx[j]->x = r*cos(phi); | |
| 131 | poly_list->poly[i]->vlist->vtx[j]->y = r*sin(phi); | |
| 132 | poly_list->poly[i]->vlist->vtx[j]->z = h;// ji*dh - (dh*poly_list->n*poly_list->poly[i]->vlist->n/2.0); | |
| 624f81 | 133 | } |
| 8db569 | 134 | } |
| M | 135 | } |
| 136 | ||
| 40aa5b | 137 | //index correction for polymeres. Important, since each vtx has to have unique id |
| 3c1ac1 | 138 | /* idx=vlist->n; |
| 40aa5b | 139 | for(i=0;i<n_poly;i++){ |
| SP | 140 | for(j=0;j<n_mono;j++,idx++){ |
| 141 | ||
| 142 | poly_list->poly[i]->vlist->vtx[j]->idx=idx; | |
| 143 | ||
| 144 | } | |
| 145 | } | |
| 3c1ac1 | 146 | */ |
| 40aa5b | 147 | |
| 1d5dff | 148 | return poly_list; |
| M | 149 | } |
| 150 | ||
| 8db569 | 151 | |
| M | 152 | ts_bool poly_free(ts_poly *poly){ |
| 153 | ||
| 154 | if (poly->grafted_vtx!=NULL){ | |
| 155 | poly->grafted_vtx->grafted_poly=NULL; | |
| 156 | } | |
| 157 | vtx_list_free(poly->vlist); | |
| 158 | bond_list_free(poly->blist); | |
| 159 | free(poly); | |
| 160 | ||
| 161 | return TS_SUCCESS; | |
| 162 | } | |
| 163 | ||
| 164 | ts_bool poly_list_free(ts_poly_list *poly_list){ | |
| 165 | ts_uint i; | |
| 166 | ||
| 167 | for(i=0;i<poly_list->n;i++){ | |
| 168 | poly_free(poly_list->poly[i]); | |
| 169 | } | |
| 170 | free(poly_list->poly); | |
| 171 | free(poly_list); | |
| 172 | ||
| 173 | return TS_SUCCESS; | |
| 174 | } | |
