Filament inside the vesicle added and debugged. Testing time...

mihaf

2014-03-21 bcf4557ddd61890f130247430267feac5b05c5b7

Filament inside the vesicle added and debugged. Testing time...

 src/bond.c

 src/initial_distribution.c

@@ -37,22 +37,39 @@

ts_vesicle *create_vesicle_from_tape(ts_tape *tape){
    ts_vesicle *vesicle;
    ts_vertex *vtx;

    vesicle=initial_distribution_dipyramid(tape->nshell,tape->ncxmax,tape->ncymax,tape->nczmax,tape->stepsize);
    // Nucleus:
    vesicle->R_nucleus=tape->R_nucleus;

    //Initialize grafted polymers (brush):
    vesicle->poly_list=init_poly_list(tape->npoly,tape->nmono, vesicle->vlist, vesicle);
    vesicle->spring_constant=tape->kspring;
    poly_assign_spring_const(vesicle);

    //Initialize filaments (polymers inside the vesicle):
    vesicle->filament_list=init_poly_list(tape->nfil,tape->nfono, NULL, vesicle);
    poly_assign_filament_xi(vesicle,tape);

ts_uint i,j;
    for(i=0;i<vesicle->filament_list->n;i++){
            for(j=0;j<vesicle->filament_list->poly[i]->vlist->n;j++){
        for(j=0;j<vesicle->filament_list->poly[i]->blist->n;j++){
            bond_vector(vesicle->filament_list->poly[i]->blist->bond[j]);
            vesicle->filament_list->poly[i]->blist->bond[j]->bond_length = sqrt(vtx_distance_sq(vesicle->filament_list->poly[i]->blist->bond[j]->vtx1,vesicle->filament_list->poly[i]->blist->bond[j]->vtx2));
        }
    }

    fprintf(stderr,"%e %e %e\n", vesicle->filament_list->poly[i]->vlist->vtx[j]->x,vesicle->filament_list->poly[i]->vlist->vtx[j]->y, vesicle->filament_list->poly[i]->vlist->vtx[j]->z );
    for(i=0;i<vesicle->filament_list->n;i++){
        for(j=0;j<vesicle->filament_list->poly[i]->vlist->n;j++){
            vtx = vesicle->filament_list->poly[i]->vlist->vtx[j];
            if(vtx->bond_no == 2){
            vtx->energy = -(vtx->bond[0]->x*vtx->bond[1]->x + vtx->bond[0]->y*vtx->bond[1]->y + vtx->bond[0]->z*vtx->bond[1]->z)/vtx->bond[0]->bond_length/vtx->bond[1]->bond_length;
    }
    }
    }


//    vesicle->spring_constant=tape->kspring;
//    poly_assign_spring_const(vesicle);


 src/io.c

@@ -36,6 +36,8 @@
    fwrite(vesicle->clist, sizeof(ts_cell_list),1,fh);
    /* dump poly list */
    fwrite(vesicle->poly_list, sizeof(ts_poly_list),1,fh);
    /* dump filament list */
    fwrite(vesicle->filament_list, sizeof(ts_poly_list),1,fh);
    /* level 1 complete */

    /*dump vertices*/
@@ -118,6 +120,43 @@
        }
    }


  /*dump filamentes grandes svinjas */
    for(i=0;i<vesicle->filament_list->n;i++){
        fwrite(vesicle->filament_list->poly[i],sizeof(ts_poly),1,fh);
        fwrite(vesicle->filament_list->poly[i]->vlist,sizeof(ts_vertex_list),1,fh);
        fwrite(vesicle->filament_list->poly[i]->blist,sizeof(ts_bond_list),1,fh);
    } 
     
    /* dump filamentes vertex(monomer) list*/
    for(i=0;i<vesicle->filament_list->n;i++){
        for(j=0;j<vesicle->filament_list->poly[i]->vlist->n;j++){
            fwrite(vesicle->filament_list->poly[i]->vlist->vtx[j],sizeof(ts_vertex),1,fh);
            /* dump offset for neigh and bond */
            for(k=0;k<vesicle->filament_list->poly[i]->vlist->vtx[j]->neigh_no;k++){
               // off=(ts_ulong)(vesicle->poly_list->poly[i]->vlist->vtx[j]->neigh[k]-vesicle->poly_list->poly[i]->vlist->vtx[0]);
                fwrite(&vesicle->filament_list->poly[i]->vlist->vtx[j]->neigh[k]->idx,sizeof(ts_uint),1,fh); 
            }
            for(k=0;k<vesicle->filament_list->poly[i]->vlist->vtx[j]->bond_no;k++){
                //off=(ts_ulong)(vesicle->poly_list->poly[i]->vlist->vtx[j]->bond[k]-vesicle->poly_list->poly[i]->blist->bond[0]);
                fwrite(&vesicle->filament_list->poly[i]->vlist->vtx[j]->bond[k]->idx,sizeof(ts_uint),1,fh); 
            }
        }
    }
    /* dump poly bonds between monomers list*/
    for(i=0;i<vesicle->filament_list->n;i++){
        for(j=0;j<vesicle->filament_list->poly[i]->blist->n;j++){
            fwrite(vesicle->filament_list->poly[i]->blist->bond[j],sizeof(ts_bond),1,fh);
            /* dump vtx1 and vtx2 offsets */
            //off=(ts_ulong)(vesicle->poly_list->poly[i]->blist->bond[j]->vtx1-vesicle->poly_list->poly[i]->vlist->vtx[0]);
            fwrite(&vesicle->filament_list->poly[i]->blist->bond[j]->vtx1->idx,sizeof(ts_uint),1,fh); 
//            off=(ts_ulong)(vesicle->poly_list->poly[i]->blist->bond[j]->vtx2-vesicle->poly_list->poly[i]->vlist->vtx[0]);
            fwrite(&vesicle->filament_list->poly[i]->blist->bond[j]->vtx2->idx,sizeof(ts_uint),1,fh); 
        }
    }



/* pointer offsets for fixing the restored pointers */
/* need pointers for 
    vlist->vtx
@@ -180,6 +219,9 @@
    /* restore poly list */
    vesicle->poly_list=(ts_poly_list *)calloc(1,sizeof(ts_poly_list));
    retval=fread(vesicle->poly_list, sizeof(ts_poly_list),1,fh);
    /* restore filament list */
    vesicle->filament_list=(ts_poly_list *)calloc(1,sizeof(ts_poly_list));
    retval=fread(vesicle->filament_list, sizeof(ts_poly_list),1,fh);
    /* level 1 complete */

/* prerequisity. Bonds must be malloced before vertexes are recreated */
@@ -322,6 +364,61 @@
        }
    }

    /*restore filaments */
    vesicle->filament_list->poly = (ts_poly **)calloc(vesicle->filament_list->n,sizeof(ts_poly *));
    for(i=0;i<vesicle->filament_list->n;i++){
        vesicle->filament_list->poly[i]=(ts_poly *)calloc(1,sizeof(ts_poly));
        retval=fread(vesicle->filament_list->poly[i],sizeof(ts_poly),1,fh);
        vesicle->filament_list->poly[i]->vlist=(ts_vertex_list *)calloc(1,sizeof(ts_vertex_list));
        retval=fread(vesicle->filament_list->poly[i]->vlist,sizeof(ts_vertex_list),1,fh);
        vesicle->filament_list->poly[i]->blist=(ts_bond_list *)calloc(1,sizeof(ts_bond_list));
        retval=fread(vesicle->filament_list->poly[i]->blist,sizeof(ts_bond_list),1,fh);
    /* initialize adress space for pointers that will hold specific vertices (monomers) and bonds */
        vesicle->filament_list->poly[i]->vlist->vtx=(ts_vertex **)calloc(vesicle->filament_list->poly[i]->vlist->n,sizeof(ts_vertex *));
        vesicle->filament_list->poly[i]->blist->bond=(ts_bond **)calloc(vesicle->filament_list->poly[i]->blist->n,sizeof(ts_bond *));
     for(j=0;j<vesicle->filament_list->poly[i]->vlist->n;j++){
            vesicle->filament_list->poly[i]->vlist->vtx[j]=(ts_vertex *)malloc(sizeof(ts_vertex));
    }
    for(j=0;j<vesicle->filament_list->poly[i]->blist->n;j++){
            vesicle->filament_list->poly[i]->blist->bond[j]=(ts_bond *)malloc(sizeof(ts_bond));
    }

    } 

     
    /* restore poly vertex(monomer) list*/
    for(i=0;i<vesicle->filament_list->n;i++){
        for(j=0;j<vesicle->filament_list->poly[i]->vlist->n;j++){
            retval=fread(vesicle->filament_list->poly[i]->vlist->vtx[j],sizeof(ts_vertex),1,fh);
           	 
            /* restore neigh and bonds */
            vesicle->filament_list->poly[i]->vlist->vtx[j]->neigh=(ts_vertex **)calloc(vesicle->filament_list->poly[i]->vlist->vtx[j]->neigh_no, sizeof(ts_vertex *));
            for(k=0;k<vesicle->filament_list->poly[i]->vlist->vtx[j]->neigh_no;k++){
                retval=fread(&idx,sizeof(ts_uint),1,fh);
                vesicle->filament_list->poly[i]->vlist->vtx[j]->neigh[k]=vesicle->filament_list->poly[i]->vlist->vtx[idx];
            }
            vesicle->filament_list->poly[i]->vlist->vtx[j]->bond=(ts_bond **)calloc(vesicle->filament_list->poly[i]->vlist->vtx[j]->bond_no, sizeof(ts_bond *));
            for(k=0;k<vesicle->filament_list->poly[i]->vlist->vtx[j]->bond_no;k++){
                retval=fread(&idx,sizeof(ts_uint),1,fh);
                vesicle->filament_list->poly[i]->vlist->vtx[j]->bond[k]=vesicle->filament_list->poly[i]->blist->bond[idx];
            }

        }
    }

    /* restore poly bonds between monomers list*/
    for(i=0;i<vesicle->filament_list->n;i++){
        for(j=0;j<vesicle->filament_list->poly[i]->blist->n;j++){
       //     vesicle->poly_list->poly[i]->blist->bond[j]=(ts_bond *)malloc(sizeof(ts_bond));
            retval=fread(vesicle->filament_list->poly[i]->blist->bond[j],sizeof(ts_bond),1,fh);
            /* restore vtx1 and vtx2 */
                retval=fread(&idx,sizeof(ts_uint),1,fh);
                vesicle->filament_list->poly[i]->blist->bond[j]->vtx1=vesicle->filament_list->poly[i]->vlist->vtx[idx];
                retval=fread(&idx,sizeof(ts_uint),1,fh);
                vesicle->filament_list->poly[i]->blist->bond[j]->vtx2=vesicle->filament_list->poly[i]->vlist->vtx[idx];
        }
    }

// recreating space for cells // 
    vesicle->clist=(ts_cell_list *)malloc(sizeof(ts_cell_list));
    retval=fread(vesicle->clist, sizeof(ts_cell_list), 1,fh); 

 src/main.c

@@ -47,6 +47,7 @@
        vtx_set_global_values(vesicle);
        vesicle->pressure=tape->pressure;
        vesicle->dmax=tape->dmax*tape->dmax;
        poly_assign_filament_xi(vesicle,tape);

        if(command_line_args.reset_iteration_count) start_iteration=tape->inititer+1;
        else start_iteration++;

 src/poly.c

@@ -6,6 +6,17 @@
#include<math.h>
#include"energy.h"

ts_bool poly_assign_filament_xi(ts_vesicle *vesicle, ts_tape *tape){
    ts_uint i;

    for(i=0;i<vesicle->filament_list->n;i++){
     vesicle->filament_list->poly[i]->k = tape->xi;
        }
	
    return TS_SUCCESS;
}


ts_bool poly_assign_spring_const(ts_vesicle *vesicle){
    ts_uint i;

@@ -97,8 +108,8 @@
    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)*1.001;
        dh = dphi/2.0/M_PI*1.001;
        dphi = 2.0*asin(1.0/2.0/vesicle->R_nucleus)*1.01;
        dh = dphi/2.0/M_PI*1.01;
        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;

 src/poly.h

@@ -1,5 +1,6 @@
#ifndef _POLY_H
#define _POLY_H
#include"io.h"

#include"general.h"

@@ -13,4 +14,6 @@

ts_bool poly_assign_spring_const(ts_vesicle *vesicle);

ts_bool poly_assign_filament_xi(ts_vesicle *vesicle, ts_tape *tape);

#endif

 src/tape

@@ -26,9 +26,9 @@
# nfil is a number of filaments inside the vesicle
nfil=1
# nfono is a number of monomers in each filament
nfono=300
nfono=30
# Persistence lenght of the filaments (in units l_min)
xi=10
xi=0

####### Nucleus (inside the vesicle) ###########
# Radius of an impenetrable hard sphere inside the vesicle
@@ -46,7 +46,7 @@
#how many initial mcsweeps*inititer MC sweeps before recording to disk?
inititer=0
#how many records do you want on the disk iteration are there in a run?
iterations=300
iterations=30


#shut up if we are using cluster!!!