From 7010269f3bc74c764f5b4e9c72dd069ce34fb244 Mon Sep 17 00:00:00 2001
From: Samo Penic <samo@altea>
Date: Wed, 18 May 2016 17:56:30 +0000
Subject: [PATCH] Fix in memory leak. There were also leaks in the old code probably.
---
src/poly.c | 206 ++++++++++++++++++++++++++++++++++++++++++++++++---
1 files changed, 192 insertions(+), 14 deletions(-)
diff --git a/src/poly.c b/src/poly.c
index f362dd0..3c93d0c 100644
--- a/src/poly.c
+++ b/src/poly.c
@@ -1,36 +1,214 @@
+/* vim: set ts=4 sts=4 sw=4 noet : */
+#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_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++){
+ 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_vesicle *vesicle){
ts_poly_list *poly_list=(ts_poly_list *)calloc(1,sizeof(ts_poly_list));
-
- if (n_poly > vlist->n){fatal("Number of polymers larger then numbero f vertices on a vesicle.",310);}
-
- ts_uint i=0;
+ poly_list->poly = (ts_poly **)calloc(n_poly,sizeof(ts_poly *));
+ ts_uint i=0,j=0; //idx;
ts_uint gvtxi;
- while(i<n_poly){
- gvtxi = rand() % vlist->n
- if (vlist->vtx[gvtxi]->grafted_poly == NULL){
- poly_list->poly = init_poly(n_mono, vlist->vtx[gvtxi]);
- i++;
+ ts_double xnorm,ynorm,znorm,normlength;
+ ts_double dphi,dh;
+
+ // Grafting polymers:
+ if (vlist!=NULL){
+ if (n_poly > vlist->n){fatal("Number of polymers larger than 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++;
+ }
}
}
-
+ else
+ {
+ for(i=0;i<n_poly;i++){
+ poly_list->poly[i] = init_poly(n_mono, NULL);
+ }
+ }
+
poly_list->n = n_poly;
+ 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;
+
+ 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*/
+ ts_double a,R,H,tantheta,h,r,phi,A0=1.2;
+
+ a = A0*(ts_double)vesicle->nshell;
+ R = A0*((ts_double)vesicle->nshell)/(2.0*sin(M_PI/5.0));
+ H = sqrt(a*a - R*R);
+ tantheta = sqrt(R*R - a*a/4.0)/H;
+
+ h = -H + sqrt(vesicle->clist->dmin_interspecies)*1.5;
+ r = (H-fabs(h))*tantheta - sqrt(vesicle->clist->dmin_interspecies)*1.5;
+ dphi = 2.0*asin(1.0/2.0/r)*1.001;
+ dh = dphi/2.0/M_PI*1.001;
+ phi=0.0;
+ for(i=0;i<poly_list->n;i++){
+ for (j=0;j<poly_list->poly[i]->vlist->n;j++){
+ h = h + dh;
+ r = (H-fabs(h))*tantheta - sqrt(vesicle->clist->dmin_interspecies)*1.5;
+ dphi = 2.0*asin(1.0/2.0/r)*1.001;
+ dh = dphi/2.0/M_PI*1.001;
+ phi+=dphi;
+ //ji = j + i*poly_list->poly[i]->vlist->n;
+ poly_list->poly[i]->vlist->vtx[j]->x = r*cos(phi);
+ poly_list->poly[i]->vlist->vtx[j]->y = r*sin(phi);
+ poly_list->poly[i]->vlist->vtx[j]->z = h;// 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;
}
+
+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;
+}
+
+
+ts_poly *remove_poly_with_index(ts_poly_list *poly_list, ts_uint idx){
+ ts_uint i;
+ ts_poly *removed_poly=poly_list->poly[idx];
+
+ poly_list->n--; //decrease the total number of polymeres
+ for(i=idx;i<poly_list->n;i++){ //move the rest of the polymeres up.
+ poly_list->poly[i]=poly_list->poly[i+1];
+// poly_list->poly[idx]->idx=idx;
+ }
+
+ return removed_poly;
+}
+
+
+ts_bool remove_random_polymeres(ts_poly_list *poly_list, ts_uint number){
+
+ ts_uint i, idx;
+ ts_poly *poly;
+
+ ts_poly **new_poly_array;
+ if(number>poly_list->n) fatal("The number of polymeres to be removed from the list is greater than the number of total polymeres in the list",999);
+ for(i=number;i>0;i--){
+ idx=rand() % poly_list->n;
+ poly=remove_poly_with_index(poly_list, idx);
+ poly_free(poly);
+ }
+ printf("Addr before %ld\n", (long)poly_list->poly);
+ new_poly_array=(ts_poly **)calloc(poly_list->n,sizeof(ts_poly *));
+ for(i=0;i<poly_list->n;i++){
+ new_poly_array[i]=poly_list->poly[i];
+ }
+ free(poly_list->poly);
+ poly_list->poly=new_poly_array;
+ printf("Addr after %ld\n", (long)poly_list->poly);
+ return TS_SUCCESS;
+}
+
--
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