From ea1cce4c80ddb68c0b46a6873ef3b64cc4a958a1 Mon Sep 17 00:00:00 2001
From: mihaf <miha.fosnaric@gmail.com>
Date: Mon, 24 Mar 2014 16:37:44 +0000
Subject: [PATCH] Added dmin_interspecies.
---
src/poly.c | 126 ++++++++++++++++++++++++++++++++----------
1 files changed, 96 insertions(+), 30 deletions(-)
diff --git a/src/poly.c b/src/poly.c
index 20529e2..5cfc6e0 100644
--- a/src/poly.c
+++ b/src/poly.c
@@ -4,14 +4,37 @@
#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;
+
+ for(i=0;i<vesicle->poly_list->n;i++){
+ vesicle->poly_list->poly[i]->k = vesicle->spring_constant;
+ }
+
+ return TS_SUCCESS;
+}
ts_poly *init_poly(ts_uint n, ts_vertex *grafted_vtx){
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++){
@@ -19,51 +42,94 @@
vtx_add_neighbour(poly->vlist->vtx[i+1], poly->vlist->vtx[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;
+ ts_uint i=0,j=0; //idx;
ts_uint gvtxi;
ts_double xnorm,ynorm,znorm,normlength;
+ ts_double dphi,dh;
+ ts_uint ji;
- 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;
- }
- normlength=sqrt(xnorm*xnorm+ynorm*ynorm+znorm*znorm);
- xnorm=xnorm/normlength;
- ynorm=ynorm/normlength;
- znorm=znorm/normlength;
-
- 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);
+ 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);
+ }
}
}
+ else
+ {
+ /* Make filaments inside the vesicle. Helix with radius... Dist. between poly vertices put to 1*/
+ dphi = 2.0*asin(1.0/2.0/vesicle->R_nucleus)*1.001;
+ dh = dphi/2.0/M_PI*1.001;
+ for(i=0;i<poly_list->n;i++){
+ for (j=0;j<poly_list->poly[i]->vlist->n;j++){
+ ji = j + i*poly_list->poly[i]->vlist->n;
+ poly_list->poly[i]->vlist->vtx[j]->x = vesicle->R_nucleus*cos(ji*dphi);
+ poly_list->poly[i]->vlist->vtx[j]->y = vesicle->R_nucleus*sin(ji*dphi);
+ poly_list->poly[i]->vlist->vtx[j]->z = 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;
+ for(i=0;i<n_poly;i++){
+ for(j=0;j<n_mono;j++,idx++){
+
+ poly_list->poly[i]->vlist->vtx[j]->idx=idx;
+
+ }
+ }
+*/
return poly_list;
}
--
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