First attempt in solving an issue of dense packed internal pegs. They are r...

Samo Penic

2016-07-13 fc6f3ef0a9822f3d5f06d38e556dbb5f2e985f4a

First attempt in solving an issue of dense packed internal pegs. They are recreated as many times as needed.

 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;
            }
        }
    }

 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