| 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 | |
| 48bb92 | 9 | ts_bool poly_assign_spring_const(ts_vesicle *vesicle){ |
| M | 10 | ts_uint i; |
| 11 | ||
| 12 | for(i=0;i<vesicle->poly_list->n;i++){ | |
| 13 | vesicle->poly_list->poly[i]->k = vesicle->spring_constant; | |
| 14 | } | |
| 15 | ||
| 16 | return TS_SUCCESS; | |
| 17 | } | |
| 8db569 | 18 | |
| 1d5dff | 19 | ts_poly *init_poly(ts_uint n, ts_vertex *grafted_vtx){ |
| M | 20 | ts_poly *poly=(ts_poly *)calloc(1,sizeof(ts_poly)); |
| 21 | poly->vlist = init_vertex_list(n); | |
| 22 | poly->blist = init_bond_list(); | |
| 624f81 | 23 | if (grafted_vtx!=NULL){ |
| M | 24 | poly->grafted_vtx = grafted_vtx; |
| 25 | grafted_vtx->grafted_poly = poly; | |
| 26 | } | |
| 1d5dff | 27 | |
| M | 28 | ts_uint i; |
| 8db569 | 29 | for(i=0;i<n-1;i++){ |
| 1d5dff | 30 | vtx_add_cneighbour(poly->blist, poly->vlist->vtx[i], poly->vlist->vtx[i+1]); |
| 8db569 | 31 | vtx_add_neighbour(poly->vlist->vtx[i+1], poly->vlist->vtx[i]); |
| 1d5dff | 32 | } |
| M | 33 | |
| 48bb92 | 34 | for(i=0;i<poly->blist->n;i++){ |
| M | 35 | poly->blist->bond[i]->bond_length=sqrt(vtx_distance_sq(poly->blist->bond[i]->vtx1,poly->blist->bond[i]->vtx2)); |
| fedf2b | 36 | bond_energy(poly->blist->bond[i],poly); |
| 48bb92 | 37 | } |
| M | 38 | |
| 1d5dff | 39 | return poly; |
| M | 40 | } |
| 41 | ||
| 42 | ||
| 624f81 | 43 | ts_poly_list *init_poly_list(ts_uint n_poly, ts_uint n_mono, ts_vertex_list *vlist, ts_vesicle *vesicle){ |
| 1d5dff | 44 | ts_poly_list *poly_list=(ts_poly_list *)calloc(1,sizeof(ts_poly_list)); |
| 8db569 | 45 | poly_list->poly = (ts_poly **)calloc(n_poly,sizeof(ts_poly *)); |
| 3c1ac1 | 46 | ts_uint i=0,j=0; //idx; |
| 8db569 | 47 | ts_uint gvtxi; |
| M | 48 | ts_double xnorm,ynorm,znorm,normlength; |
| 624f81 | 49 | ts_double dphi,dh; |
| M | 50 | ts_uint ji; |
| 1d5dff | 51 | |
| 624f81 | 52 | // Grafting polymers: |
| M | 53 | if (vlist!=NULL){ |
| 54 | if (n_poly > vlist->n){fatal("Number of polymers larger then numbero f vertices on a vesicle.",310);} | |
| 1d5dff | 55 | |
| 624f81 | 56 | while(i<n_poly){ |
| M | 57 | gvtxi = rand() % vlist->n; |
| 58 | if (vlist->vtx[gvtxi]->grafted_poly == NULL){ | |
| 59 | poly_list->poly[i] = init_poly(n_mono, vlist->vtx[gvtxi]); | |
| 60 | i++; | |
| 61 | } | |
| 1d5dff | 62 | } |
| M | 63 | } |
| 624f81 | 64 | else |
| M | 65 | { |
| 66 | for(i=0;i<n_poly;i++){ | |
| 67 | poly_list->poly[i] = init_poly(n_mono, NULL); | |
| 68 | } | |
| 69 | } | |
| 70 | ||
| 1d5dff | 71 | poly_list->n = n_poly; |
| M | 72 | |
| 624f81 | 73 | if (vlist!=NULL){ |
| M | 74 | /* Make straight grafted poylmers normal to membrane (polymer brush). Dist. between poly vertices put to 1*/ |
| 75 | for (i=0;i<poly_list->n;i++){ | |
| 76 | ||
| 77 | xnorm=0.0; | |
| 78 | ynorm=0.0; | |
| 79 | znorm=0.0; | |
| 80 | for (j=0;j<poly_list->poly[i]->grafted_vtx->tristar_no;j++){ | |
| 81 | xnorm-=poly_list->poly[i]->grafted_vtx->tristar[j]->xnorm; | |
| 82 | ynorm-=poly_list->poly[i]->grafted_vtx->tristar[j]->ynorm; | |
| 83 | znorm-=poly_list->poly[i]->grafted_vtx->tristar[j]->znorm; | |
| 84 | } | |
| 85 | normlength=sqrt(xnorm*xnorm+ynorm*ynorm+znorm*znorm); | |
| 86 | xnorm=xnorm/normlength; | |
| 87 | ynorm=ynorm/normlength; | |
| 88 | znorm=znorm/normlength; | |
| 8db569 | 89 | |
| 624f81 | 90 | for (j=0;j<poly_list->poly[i]->vlist->n;j++){ |
| M | 91 | poly_list->poly[i]->vlist->vtx[j]->x = poly_list->poly[i]->grafted_vtx->x + xnorm*(ts_double)(j+1); |
| 92 | poly_list->poly[i]->vlist->vtx[j]->y = poly_list->poly[i]->grafted_vtx->y + ynorm*(ts_double)(j+1); | |
| 93 | poly_list->poly[i]->vlist->vtx[j]->z = poly_list->poly[i]->grafted_vtx->z + znorm*(ts_double)(j+1); | |
| 94 | } | |
| 8db569 | 95 | } |
| 624f81 | 96 | } |
| M | 97 | else |
| 98 | { | |
| 99 | /* Make filaments inside the vesicle. Helix with radius... Dist. between poly vertices put to 1*/ | |
| 58230a | 100 | dphi = 2.0*asin(1.0/2.0/vesicle->R_nucleus)*1.001; |
| M | 101 | dh = dphi/2.0/M_PI*1.001; |
| 624f81 | 102 | for(i=0;i<poly_list->n;i++){ |
| M | 103 | for (j=0;j<poly_list->poly[i]->vlist->n;j++){ |
| 104 | ji = j + i*poly_list->poly[i]->vlist->n; | |
| 105 | poly_list->poly[i]->vlist->vtx[j]->x = vesicle->R_nucleus*cos(ji*dphi); | |
| 106 | poly_list->poly[i]->vlist->vtx[j]->y = vesicle->R_nucleus*sin(ji*dphi); | |
| 58230a | 107 | poly_list->poly[i]->vlist->vtx[j]->z = ji*dh - (dh*poly_list->n*poly_list->poly[i]->vlist->n/2.0); |
| 624f81 | 108 | } |
| 8db569 | 109 | } |
| M | 110 | } |
| 111 | ||
| 40aa5b | 112 | //index correction for polymeres. Important, since each vtx has to have unique id |
| 3c1ac1 | 113 | /* idx=vlist->n; |
| 40aa5b | 114 | for(i=0;i<n_poly;i++){ |
| SP | 115 | for(j=0;j<n_mono;j++,idx++){ |
| 116 | ||
| 117 | poly_list->poly[i]->vlist->vtx[j]->idx=idx; | |
| 118 | ||
| 119 | } | |
| 120 | } | |
| 3c1ac1 | 121 | */ |
| 40aa5b | 122 | |
| 1d5dff | 123 | return poly_list; |
| M | 124 | } |
| 125 | ||
| 8db569 | 126 | |
| M | 127 | ts_bool poly_free(ts_poly *poly){ |
| 128 | ||
| 129 | if (poly->grafted_vtx!=NULL){ | |
| 130 | poly->grafted_vtx->grafted_poly=NULL; | |
| 131 | } | |
| 132 | vtx_list_free(poly->vlist); | |
| 133 | bond_list_free(poly->blist); | |
| 134 | free(poly); | |
| 135 | ||
| 136 | return TS_SUCCESS; | |
| 137 | } | |
| 138 | ||
| 139 | ts_bool poly_list_free(ts_poly_list *poly_list){ | |
| 140 | ts_uint i; | |
| 141 | ||
| 142 | for(i=0;i<poly_list->n;i++){ | |
| 143 | poly_free(poly_list->poly[i]); | |
| 144 | } | |
| 145 | free(poly_list->poly); | |
| 146 | free(poly_list); | |
| 147 | ||
| 148 | return TS_SUCCESS; | |
| 149 | } | |
