Merge branch 'pegs'

Samo Penic

2016-09-15 bbe7df469c40beb309542c01f25c262340978629

Merge branch '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

@@ -127,7 +127,8 @@
        }
    }
            //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

@@ -6,7 +6,8 @@
#include"bond.h"
#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;

@@ -47,45 +48,20 @@
    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;
}


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 gvtxi;
    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){
ts_bool poly_initial_distribution(ts_poly_list *poly_list, ts_int i, ts_vesicle *vesicle){
    /* Make straight grafted poylmers normal to membrane (polymer brush). Dist. between poly vertices put to 1*/
        ts_double xnorm,ynorm,znorm,normlength;
        ts_int intpoly=vesicle->tape->internal_poly;
        for (i=0;i<poly_list->n;i++){
	
        ts_int cellidx;
        ts_double posX,posY,posZ,prevPosX,prevPosY,prevPosZ, phi,costheta,sintheta;
        ts_bool retval;
        ts_int j,k,l,m;
            xnorm=0.0;
            ynorm=0.0;
            znorm=0.0;
@@ -101,13 +77,123 @@
            xnorm=xnorm/normlength;
            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);
                //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
                k=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]);
                    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 vertex here. Finding another position\n",i,j);
                        //randomly change the direction.
                        m=0;
                        //we must move first vertex into the vesicle if the normal is in or out of the vesicle if the normal is out
                        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 bipyramid  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;
                            }
                            m++;
                            if(m>1000) {
                                k=9999; //break also ot of the outer loop
                                printf("was here\n");
                                break;
            }
        }
                        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){
                        //undo changes to the cell
                        for(l=0;l<j;l++){
                            cellidx=vertex_self_avoidance(vesicle, poly_list->poly[i]->vlist->vtx[l]);
                            cell_remove_vertex(vesicle->clist->cell[cellidx],poly_list->poly[i]->vlist->vtx[l]);
                        }
                        return TS_FAIL;
                    }
                }
                prevPosX=posX;
                prevPosY=posY;
                prevPosZ=posZ;
            }
    printf("did it\n");
    return TS_SUCCESS;

}


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 gvtxi;
    ts_bool retval;
    ts_double dphi,dh;
    cell_occupation(vesicle); //needed for evading the membrane
    // Grafting polymers:
    int tries=0;
    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]);
                retval=poly_initial_distribution(poly_list, i, vesicle);
                if(retval==TS_FAIL){
                    ts_fprintf(stdout,"Found new potential grafting vertex %d for poly %d\n",gvtxi,i);
                    poly_free(poly_list->poly[i]);
                    tries++;
                }
                else {
                    tries=0;
                    i++;
                }
                if(tries>5000){
                    fatal("Cannot find space for inner polymeres",1001);
                }
            }
        }
    }
    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){
    }
    else
    {

 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