From 3cd5f4a96d445b55da8a7e6da8509bbd7d5d41b8 Mon Sep 17 00:00:00 2001
From: Samo Penic <samo.penic@fe.uni-lj.si>
Date: Thu, 15 Sep 2016 06:29:31 +0000
Subject: [PATCH] Fixes #19.
---
src/poly.c | 83 +++++++++++++++++++++++++++++++++++------
1 files changed, 71 insertions(+), 12 deletions(-)
diff --git a/src/poly.c b/src/poly.c
index c1dc0f6..7c7450b 100644
--- a/src/poly.c
+++ b/src/poly.c
@@ -1,3 +1,4 @@
+/* vim: set ts=4 sts=4 sw=4 noet : */
#include"general.h"
#include"poly.h"
#include<stdlib.h>
@@ -58,11 +59,10 @@
ts_uint gvtxi;
ts_double xnorm,ynorm,znorm,normlength;
ts_double dphi,dh;
- ts_uint ji;
// Grafting polymers:
if (vlist!=NULL){
- if (n_poly > vlist->n){fatal("Number of polymers larger then numbero f vertices on a vesicle.",310);}
+ 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;
@@ -83,6 +83,7 @@
if (vlist!=NULL){
/* Make straight grafted poylmers normal to membrane (polymer brush). Dist. between poly vertices put to 1*/
+ ts_int intpoly=vesicle->tape->internal_poly;
for (i=0;i<poly_list->n;i++){
xnorm=0.0;
@@ -94,6 +95,9 @@
znorm-=poly_list->poly[i]->grafted_vtx->tristar[j]->znorm;
}
normlength=sqrt(xnorm*xnorm+ynorm*ynorm+znorm*znorm);
+ if(intpoly && i%2){
+ normlength=-normlength;
+ }
xnorm=xnorm/normlength;
ynorm=ynorm/normlength;
znorm=znorm/normlength;
@@ -108,14 +112,29 @@
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)*1.01;
- dh = dphi/2.0/M_PI*1.01;
+ 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++){
- 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);
+ 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);
}
}
}
@@ -137,9 +156,9 @@
ts_bool poly_free(ts_poly *poly){
- if (poly->grafted_vtx!=NULL){
- poly->grafted_vtx->grafted_poly=NULL;
- }
+// if (poly->grafted_vtx!=NULL){
+// poly->grafted_vtx->grafted_poly=NULL;
+// }
vtx_list_free(poly->vlist);
bond_list_free(poly->blist);
free(poly);
@@ -149,8 +168,9 @@
ts_bool poly_list_free(ts_poly_list *poly_list){
ts_uint i;
-
+ //fprintf(stderr,"no. of polys=%d\n", poly_list->n);
for(i=0;i<poly_list->n;i++){
+ // fprintf(stderr,"%d poly address in mem=%ld\n",i+1,(long)&(poly_list->poly[i]));
poly_free(poly_list->poly[i]);
}
free(poly_list->poly);
@@ -158,3 +178,42 @@
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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