From fc6f3ef0a9822f3d5f06d38e556dbb5f2e985f4a Mon Sep 17 00:00:00 2001
From: Samo Penic <samo.penic@gmail.com>
Date: Wed, 13 Jul 2016 17:33:28 +0000
Subject: [PATCH] First attempt in solving an issue of dense packed internal pegs. They are recreated as many times as needed.
---
src/poly.c | 105 ++++++++++++++++++++++++++++++++++++++++++++++++++--
src/tape | 6 +-
2 files changed, 103 insertions(+), 8 deletions(-)
diff --git a/src/poly.c b/src/poly.c
index 252b1c6..cfaa354 100644
--- a/src/poly.c
+++ b/src/poly.c
@@ -6,7 +6,7 @@
#include"bond.h"
#include<math.h>
#include"energy.h"
-
+#include"cell.h"
ts_bool poly_assign_filament_xi(ts_vesicle *vesicle, ts_tape *tape){
ts_uint i;
@@ -55,7 +55,7 @@
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; //idx;
+ ts_uint i=0,j=0,k; //idx;
ts_uint gvtxi;
ts_double xnorm,ynorm,znorm,normlength;
ts_double dphi,dh;
@@ -84,6 +84,10 @@
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;
+ ts_int cellidx;
+ ts_double posX,posY,posZ,prevPosX,prevPosY,prevPosZ, phi,theta;
+ ts_bool retval;
+ ts_int l;
for (i=0;i<poly_list->n;i++){
xnorm=0.0;
@@ -102,10 +106,101 @@
ynorm=ynorm/normlength;
znorm=znorm/normlength;
+ //prepare starting position for building the polymeres
+ prevPosX=poly_list->poly[i]->grafted_vtx->x;
+ prevPosY=poly_list->poly[i]->grafted_vtx->y;
+ prevPosZ=poly_list->poly[i]->grafted_vtx->z;
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);
+ //trying to go towards normal
+ posX=prevPosX+(ts_double)xnorm;
+ posY=prevPosY+(ts_double)ynorm;
+ posZ=prevPosZ+(ts_double)znorm;
+ k=0;
+ l=0;
+ while(1){
+ poly_list->poly[i]->vlist->vtx[j]->x = posX;
+ poly_list->poly[i]->vlist->vtx[j]->y = posY;
+ poly_list->poly[i]->vlist->vtx[j]->z = posZ;
+ cellidx=vertex_self_avoidance(vesicle, poly_list->poly[i]->vlist->vtx[j]);
+ //distance from neighbors
+ //retval=TS_SUCCESS;
+ /*for(k=0;k<poly_list->poly[i]->vlist->vtx[j]->neigh_no;k++){
+ dist=vtx_distance_sq(poly_list->poly[i]->vlist->vtx[j],poly_list->poly[i]->vlist->vtx[j]->neigh[k]);
+ if(dist<1.0 || dist>vesicle->dmax){
+ retval=TS_FAIL;
+ printf("dist_fail! %e\n", dist);
+ }
+ }*/
+ //if(retval!=TS_FAIL){
+ //check occupation number
+ retval=cell_occupation_number_and_internal_proximity(vesicle->clist,cellidx,poly_list->poly[i]->vlist->vtx[j]);
+ //}
+ if(retval==TS_SUCCESS){
+ retval=cell_add_vertex(vesicle->clist->cell[cellidx],poly_list->poly[i]->vlist->vtx[j]);
+ break;
+ }
+ else{
+ // printf("%d %d Cannot put the vesicle here. Finding another position\n",i,j);
+ theta=drand48()*M_PI-M_PI/2;
+ phi=drand48()*2*M_PI;
+ posX=prevPosX+sin(phi)*cos(theta);
+ posY=prevPosY+sin(phi)*sin(theta);
+ posZ=prevPosZ+cos(theta);
+ //randomly change the normal.
+ }
+ k++;
+ if(k>1000){
+ //lets choose another grafting vertex;
+ while(1){
+ gvtxi = rand() % vesicle->vlist->n;
+ if (vesicle->vlist->vtx[gvtxi]->grafted_poly == NULL){
+ ts_fprintf(stdout,"Found new potential grafting vertex %d for poly %d\n",gvtxi,i);
+ poly_list->poly[i]->grafted_vtx->grafted_poly=NULL;
+ poly_list->poly[i]->grafted_vtx = vesicle->vlist->vtx[gvtxi];
+ vesicle->vlist->vtx[gvtxi]->grafted_poly = poly_list->poly[i];
+ l++;
+ k=0;
+
+
+
+
+ xnorm=0.0;
+ ynorm=0.0;
+ znorm=0.0;
+ int o;
+ for (o=0;o<poly_list->poly[i]->grafted_vtx->tristar_no;o++){
+ xnorm-=poly_list->poly[i]->grafted_vtx->tristar[o]->xnorm;
+ ynorm-=poly_list->poly[i]->grafted_vtx->tristar[o]->ynorm;
+ znorm-=poly_list->poly[i]->grafted_vtx->tristar[o]->znorm;
+ }
+ normlength=sqrt(xnorm*xnorm+ynorm*ynorm+znorm*znorm);
+ if(intpoly && i%2){
+ normlength=-normlength;
+ }
+ xnorm=xnorm/normlength;
+ ynorm=ynorm/normlength;
+ znorm=znorm/normlength;
+
+ //prepare starting position for building the polymeres
+ posX=poly_list->poly[i]->grafted_vtx->x+xnorm;
+ posY=poly_list->poly[i]->grafted_vtx->y+ynorm;
+ posZ=poly_list->poly[i]->grafted_vtx->z+znorm;
+
+
+
+
+
+
+ break;
+ }
+ }
+ if(l>1000)
+ fatal("Cannot make internal polymeres. No space inside the vesicle?",1001);
+ }
+ }
+ prevPosX=posX;
+ prevPosY=posY;
+ prevPosZ=posZ;
}
}
}
diff --git a/src/tape b/src/tape
index a7baa73..93e42d7 100644
--- a/src/tape
+++ b/src/tape
@@ -25,9 +25,9 @@
####### Polymer (brush) definitions ###########
# npoly is a number of polymers attached to npoly distinct vertices on vesicle
-npoly=800
+npoly=400
# nmono is a number of monomers in each polymer
-nmono=6
+nmono=10
# Spring constant between monomers of the polymer
k_spring=800
#set to 1 if half of the polymeres are inside the vesicle
@@ -59,7 +59,7 @@
mcsweeps=200
#how many initial mcsweeps*inititer MC sweeps before recording to disk?
#2
-inititer=10
+inititer=1
#how many records do you want on the disk iteration are there in a run?
#10000
iterations=100
--
Gitblit v1.9.3