Many changes to the code to allow internal pegs

Samo Penic

2016-07-13 90882f51387b945bc0f660d8b12200b2f48e80fa

Many changes to the code to allow internal pegs

 src/frame.c

@@ -72,20 +72,23 @@
    }

//Add all polymers to cells
if(vesicle->poly_list!=NULL){
    for(i=0;i<vesicle->poly_list->n;i++){
    for(j=0;j<vesicle->poly_list->poly[i]->vlist->n;j++){
        cellidx=vertex_self_avoidance(vesicle, vesicle->poly_list->poly[i]->vlist->vtx[j]);
        cell_add_vertex(vesicle->clist->cell[cellidx],vesicle->poly_list->poly[i]->vlist->vtx[j]);
    }
    }
}
//Add all filaments to cells
if(vesicle->filament_list!=NULL){
     for(i=0;i<vesicle->filament_list->n;i++){
    for(j=0;j<vesicle->filament_list->poly[i]->vlist->n;j++){
        cellidx=vertex_self_avoidance(vesicle, vesicle->filament_list->poly[i]->vlist->vtx[j]);
        cell_add_vertex(vesicle->clist->cell[cellidx],vesicle->filament_list->poly[i]->vlist->vtx[j]);
    }
    }
   
}   

    return TS_SUCCESS;
}

 src/initial_distribution.c

@@ -100,7 +100,7 @@
    vesicle->clist->ncmax[0]=tape->ncxmax;
    vesicle->clist->ncmax[1]=tape->ncymax;
    vesicle->clist->ncmax[2]=tape->nczmax;
    vesicle->clist->max_occupancy=8; /* hard coded max occupancy? */
    vesicle->clist->max_occupancy=16; /* hard coded max occupancy? */

    vesicle->pressure= tape->pressure;
    vesicle->pswitch=tape->pswitch;

 src/io.c

@@ -423,7 +423,7 @@
    vesicle->tape=parsetape(command_line_args.tape_fullfilename);
// recreating space for cells // 
    vesicle->clist=init_cell_list(vesicle->tape->ncxmax, vesicle->tape->ncymax, vesicle->tape->nczmax, vesicle->tape->stepsize);
    vesicle->clist->max_occupancy=8;
    vesicle->clist->max_occupancy=16;
//    vesicle->tape=(ts_tape *)malloc(sizeof(ts_tape));
//    retval=fread(vesicle->tape, sizeof(ts_tape),1,fh);
    retval=fread(iteration,sizeof(ts_uint),1,fh);

 src/main.c

@@ -126,7 +126,8 @@
        }
    }
            //printf("nucleus coords: %.17e %.17e %.17e\n",vesicle->nucleus_center[0], vesicle->nucleus_center[1], vesicle->nucleus_center[2]);

//    write_vertex_xml_file(vesicle,0);
//    exit(1);
    run_simulation(vesicle, tape->mcsweeps, tape->inititer, tape->iterations, start_iteration);
    write_master_xml_file(command_line_args.output_fullfilename);
    write_dout_fcompat_file(vesicle,"dout");

 src/poly.c

@@ -7,6 +7,7 @@
#include<math.h>
#include"energy.h"
#include"cell.h"
#include"frame.h"
ts_bool poly_assign_filament_xi(ts_vesicle *vesicle, ts_tape *tape){
    ts_uint i;

@@ -47,7 +48,7 @@
    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);
    }

    vertex_list_assign_id(poly->vlist,TS_ID_FILAMENT);
    return poly;
}

@@ -59,7 +60,7 @@
    ts_uint gvtxi;
    ts_double xnorm,ynorm,znorm,normlength;
    ts_double dphi,dh;

    cell_occupation(vesicle); //needed for evading the membrane
    // Grafting polymers:
    if (vlist!=NULL){
        if (n_poly > vlist->n){fatal("Number of polymers larger than numbero f vertices on a vesicle.",310);}
@@ -85,7 +86,7 @@
    /* 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_double posX,posY,posZ,prevPosX,prevPosY,prevPosZ, phi,costheta,sintheta;
        ts_bool retval;
        ts_int l;
        for (i=0;i<poly_list->n;i++){
@@ -111,10 +112,16 @@
            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++){
                //if(j==0){
                    posX=prevPosX+xnorm*(vesicle->clist->dmin_interspecies);
                    posY=prevPosY+ynorm*(vesicle->clist->dmin_interspecies);
                    posZ=prevPosZ+znorm*(vesicle->clist->dmin_interspecies);
                //}else{
                //    posX=prevPosX+xnorm;
                //    posY=prevPosY+ynorm;
                //    posZ=prevPosZ+znorm;
                //}
                //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){
@@ -122,31 +129,37 @@
                    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]);
                    //}
                    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]);
                        //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.
                    //    printf("%d %d Cannot put the vertex here. Finding another position\n",i,j);
                        //randomly change the direction.
                        do{
                        costheta=2.0*drand48()-1.0;
                        sintheta=sqrt(1-pow(costheta,2));
                        phi=drand48()*2.0*M_PI;
                        if(j==0){
                        //for special cases, when we are on the edge of bipytamid  the distance od dmin_interspecies is not enough
                        posX=prevPosX+vesicle->dmax*sintheta*cos(phi);
                        posY=prevPosY+vesicle->dmax*sintheta*sin(phi);
                        posZ=prevPosZ+vesicle->dmax*costheta;


                        } else {
                        posX=prevPosX+vesicle->clist->dmin_interspecies*sintheta*cos(phi);
                        posY=prevPosY+vesicle->clist->dmin_interspecies*sintheta*sin(phi);
                        posZ=prevPosZ+vesicle->clist->dmin_interspecies*costheta;
                        }
                    //    if(j>0) break;
                    //    if((xnorm*sintheta*cos(phi)+ynorm*sintheta*sin(phi)+znorm*costheta)<0.0 && j==0) break;
                        }
                    //    while(j==0);
                        //we must move first vertex into the vesicle if the normal is in or out of the vesicle if the normal is out
                        while((xnorm*(poly_list->poly[i]->grafted_vtx->x-posX)+ynorm*(poly_list->poly[i]->grafted_vtx->y-posY)+znorm*(poly_list->poly[i]->grafted_vtx->z-posZ))>0.0 && j==0);
                    }
                    k++;
                    if(k>1000){
@@ -160,37 +173,29 @@
                                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;
			





                                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;
                                prevPosX=poly_list->poly[i]->grafted_vtx->x;
                                prevPosY=poly_list->poly[i]->grafted_vtx->y;
                                prevPosZ=poly_list->poly[i]->grafted_vtx->z;
                                //prepare starting position for building the polymeres
                                posX=prevPosX+xnorm*(vesicle->clist->dmin_interspecies);
                                posY=prevPosY+ynorm*(vesicle->clist->dmin_interspecies);
                                posZ=prevPosZ+znorm*(vesicle->clist->dmin_interspecies);
                                break;
                            }
                        }
@@ -244,7 +249,7 @@
        }
    }
*/

	
    return poly_list;
}


 src/tape

@@ -25,7 +25,7 @@

####### Polymer (brush) definitions ###########
# npoly is a number of polymers attached to npoly distinct vertices on vesicle
npoly=400
npoly=30
# nmono is a number of monomers in each polymer
nmono=10
# Spring constant between monomers of the polymer