From 8a66144c9118f8df80eba28c5b363fac574194da Mon Sep 17 00:00:00 2001
From: Samo Penic <samo.penic@gmail.com>
Date: Sat, 08 Mar 2014 18:25:18 +0000
Subject: [PATCH] Parsing command line arguments is still kind-of messy, but it workds for force-from-tape and reset-iteration-count
---
src/poly.c | 96 +++++++++++++++++++++++++++++++++++++++++++++---
1 files changed, 90 insertions(+), 6 deletions(-)
diff --git a/src/poly.c b/src/poly.c
index f362dd0..2057db1 100644
--- a/src/poly.c
+++ b/src/poly.c
@@ -1,3 +1,21 @@
+#include"general.h"
+#include"poly.h"
+#include<stdlib.h>
+#include"vertex.h"
+#include"bond.h"
+#include<math.h>
+#include"energy.h"
+
+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);
@@ -6,31 +24,97 @@
grafted_vtx->grafted_poly = poly;
ts_uint i;
- for(i=0,i<n-1,i++){
+ for(i=0;i<n-1;i++){
vtx_add_cneighbour(poly->blist, poly->vlist->vtx[i], poly->vlist->vtx[i+1]);
+ 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_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 gvtxi;
+ ts_double xnorm,ynorm,znorm,normlength;
if (n_poly > vlist->n){fatal("Number of polymers larger then numbero f vertices on a vesicle.",310);}
- ts_uint i=0;
- ts_uint gvtxi;
while(i<n_poly){
- gvtxi = rand() % vlist->n
+ gvtxi = rand() % vlist->n;
if (vlist->vtx[gvtxi]->grafted_poly == NULL){
- poly_list->poly = init_poly(n_mono, vlist->vtx[gvtxi]);
+ poly_list->poly[i] = init_poly(n_mono, vlist->vtx[gvtxi]);
i++;
}
}
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++){
+
+ 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);
+ }
+ }
+
+ //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;
}
+
+ts_bool poly_free(ts_poly *poly){
+
+ if (poly->grafted_vtx!=NULL){
+ poly->grafted_vtx->grafted_poly=NULL;
+ }
+ vtx_list_free(poly->vlist);
+ bond_list_free(poly->blist);
+ free(poly);
+
+ return TS_SUCCESS;
+}
+
+ts_bool poly_list_free(ts_poly_list *poly_list){
+ ts_uint i;
+
+ for(i=0;i<poly_list->n;i++){
+ poly_free(poly_list->poly[i]);
+ }
+ free(poly_list->poly);
+ free(poly_list);
+
+ return TS_SUCCESS;
+}
--
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