Added nucleus. Better initial configuration of filaments.

mihaf

2014-03-25 fe24d29b3c8684f08dccd01f5785aa48b7137322

 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 */
@@ -319,6 +361,61 @@
                vesicle->poly_list->poly[i]->blist->bond[j]->vtx1=vesicle->poly_list->poly[i]->vlist->vtx[idx];
                retval=fread(&idx,sizeof(ts_uint),1,fh);
                vesicle->poly_list->poly[i]->blist->bond[j]->vtx2=vesicle->poly_list->poly[i]->vlist->vtx[idx];
        }
    }

    /*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];
        }
    }

@@ -821,6 +918,39 @@



ts_bool write_pov_file(ts_vesicle *vesicle, char *filename){
   FILE *fh;
   ts_uint i;
	
   fh=fopen(filename, "w");
   if(fh==NULL){
      err("Cannot open file %s for writing");
      return TS_FAIL;
   }

   for(i=0;i<vesicle->tlist->n;i++){
	
   fprintf(fh,"\ttriangle {");
   fprintf(fh,"\t<%e,%e,%e> <%e,%e,%e> <%e,%e,%e> }\n", 
   vesicle->tlist->tria[i]->vertex[0]->x,
   vesicle->tlist->tria[i]->vertex[0]->y,
   vesicle->tlist->tria[i]->vertex[0]->z,

   vesicle->tlist->tria[i]->vertex[1]->x,
   vesicle->tlist->tria[i]->vertex[1]->y,
   vesicle->tlist->tria[i]->vertex[1]->z,

   vesicle->tlist->tria[i]->vertex[2]->x,
   vesicle->tlist->tria[i]->vertex[2]->y,
   vesicle->tlist->tria[i]->vertex[2]->z
   );
   }
		
   fclose(fh);
   return TS_SUCCESS;
}


ts_tape *parsetape(char *filename){
  //  long int nshell=17,ncxmax=60, ncymax=60, nczmax=60, npoly=10, nmono=20, pswitch=0;  // THIS IS DUE TO CONFUSE BUG!
    ts_tape *tape=(ts_tape *)calloc(1,sizeof(ts_tape));
@@ -840,6 +970,7 @@
   CFG_SIMPLE_INT("nfono",&tape->nfono),
   CFG_SIMPLE_INT("R_nucleus",&tape->R_nucleus),
   CFG_SIMPLE_FLOAT("dmax", &tape->dmax),
   CFG_SIMPLE_FLOAT("dmin_interspecies", &tape->dmin_interspecies),
        CFG_SIMPLE_FLOAT("xk0",&tape->xk0),
   CFG_SIMPLE_INT("pswitch",&tape->pswitch),
   CFG_SIMPLE_FLOAT("pressure",&tape->pressure),