Trisurf Monte Carlo simulator
Samo Penic
2014-06-15 7d62fc765adc11bbcb7db0716ac5dc19145dca80
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 }