First step in dump and restore. Grafted vtx still missing in the process

Samo Penic

2014-03-05 e9eab4fb2f72383a1a2adbe5f09f7bbd1fd45768

First step in dump and restore. Grafted vtx still missing in the process

 src/io.c

@@ -11,6 +11,328 @@
#include "initial_distribution.h"
#include "poly.h"



/** DUMP STATE TO DISK DRIVE **/

ts_bool dump_state(ts_vesicle *vesicle){

    /* save current state with wrong pointers. Will fix that later */
    ts_uint i,j,k;
    ts_ulong off;
    FILE *fh=fopen("dump.bin","wb");

    /* dump vesicle */
    fwrite(vesicle, sizeof(vesicle),1,fh);
    /* dump vertex list */
    fwrite(vesicle->vlist, sizeof(ts_vertex_list),1,fh);
    /* dump bond list */
    fwrite(vesicle->blist, sizeof(ts_bond_list),1,fh);
    /* dump triangle list */
    fwrite(vesicle->tlist, sizeof(ts_triangle_list),1,fh);
    /* dump cell list */
    fwrite(vesicle->clist, sizeof(ts_cell_list),1,fh);
    /* dump poly list */
    fwrite(vesicle->poly_list, sizeof(ts_poly_list),1,fh);
    /* level 1 complete */

    /*dump vertices*/
    for(i=0;i<vesicle->vlist->n;i++){
        fwrite(vesicle->vlist->vtx[i],sizeof(ts_vertex),1,fh);
        /* dump pointer offsets for:
                    neigh
                    bond
                    tria
                    cell is ignored
        */
        for(j=0;j<vesicle->vlist->vtx[i]->neigh_no;j++){
            off=(ts_ulong)(vesicle->vlist->vtx[i]->neigh[j]-vesicle->vlist->vtx[0]);
            fwrite(&off,sizeof(ts_ulong),1,fh); 
        }
        for(j=0;j<vesicle->vlist->vtx[i]->bond_no;j++){
            off=(ts_ulong)(vesicle->vlist->vtx[i]->bond[j]-vesicle->blist->bond[0]);
            fwrite(&off,sizeof(ts_ulong),1,fh); 
        }
        for(j=0;j<vesicle->vlist->vtx[i]->tristar_no;j++){
            off=(ts_ulong)(vesicle->vlist->vtx[i]->tristar[j]-vesicle->tlist->tria[0]);
            fwrite(&off,sizeof(ts_ulong),1,fh); 
        }
//        off=(ts_ulong)(vesicle->vlist->vtx[i]->cell-vesicle->clist->cell[0]);
//        fwrite(&off,sizeof(ts_ulong),1,fh); 

    }

    /*dump bonds*/
    for(i=0;i<vesicle->blist->n;i++){
        fwrite(vesicle->blist->bond[i],sizeof(ts_bond),1,fh);
        /* dump pointer offsets for vtx1 and vtx2 */
        off=(ts_ulong)(vesicle->blist->bond[i]->vtx1-vesicle->vlist->vtx[0]);
        fwrite(&off,sizeof(ts_ulong),1,fh); 
        off=(ts_ulong)(vesicle->blist->bond[i]->vtx2-vesicle->vlist->vtx[0]);
        fwrite(&off,sizeof(ts_ulong),1,fh); 
    }

    /*dump triangles*/
    for(i=0;i<vesicle->tlist->n;i++){
        fwrite(vesicle->tlist->tria[i],sizeof(ts_triangle),1,fh);
        /* dump pointer offsets for vertex */
        off=(ts_ulong)(vesicle->tlist->tria[i]->vertex[0]-vesicle->vlist->vtx[0]);
        fwrite(&off,sizeof(ts_ulong),1,fh); 
        off=(ts_ulong)(vesicle->tlist->tria[i]->vertex[1]-vesicle->vlist->vtx[0]);
        fwrite(&off,sizeof(ts_ulong),1,fh); 
        off=(ts_ulong)(vesicle->tlist->tria[i]->vertex[2]-vesicle->vlist->vtx[0]);
        fwrite(&off,sizeof(ts_ulong),1,fh); 
        /* dump pointer offsets for neigh */
        for(j=0;j<vesicle->tlist->tria[i]->neigh_no;j++){
            off=(ts_ulong)(vesicle->tlist->tria[i]->neigh[j]-vesicle->tlist->tria[0]);
            fwrite(&off,sizeof(ts_ulong),1,fh); 
        }
    }
   
    /*dump cells and its contents is not dumped but recalculated on restore*/

/*    for(i=0;i<vesicle->clist->cellno;i++){
        fwrite(vesicle->clist->cell[i],sizeof(ts_cell),1,fh);
        for(j=0;j<vesicle->clist->cell[i]->nvertex;j++){
            off=(ts_ulong)(vesicle->clist->cell[i]->vertex[j]-vesicle->vlist->vtx[0]);
            fwrite(&off,sizeof(ts_ulong),1,fh);
        }
    }
*/


    /*dump polymeres */
    for(i=0;i<vesicle->poly_list->n;i++){
        fwrite(vesicle->poly_list->poly[i],sizeof(ts_poly),1,fh);
    } 
     
    /* dump poly vertex(monomer) list*/
    for(i=0;i<vesicle->poly_list->n;i++){
        for(j=0;j<vesicle->poly_list->poly[i]->vlist->n;j++){
            fwrite(vesicle->poly_list->poly[i]->vlist->vtx[j],sizeof(ts_vertex),1,fh);
            /* dump offset for neigh and bond */
            for(k=0;k<vesicle->poly_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(&off,sizeof(ts_ulong),1,fh); 
            }
            for(k=0;k<vesicle->poly_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(&off,sizeof(ts_ulong),1,fh); 
            }
        }
    }
    /* dump poly bonds between monomers list*/
    for(i=0;i<vesicle->poly_list->n;i++){
        for(j=0;j<vesicle->poly_list->poly[i]->blist->n;j++){
            fwrite(vesicle->poly_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(&off,sizeof(ts_ulong),1,fh); 
            off=(ts_ulong)(vesicle->poly_list->poly[i]->blist->bond[j]->vtx2-vesicle->poly_list->poly[i]->vlist->vtx[0]);
            fwrite(&off,sizeof(ts_ulong),1,fh); 
        }
    }

/* pointer offsets for fixing the restored pointers */
/* need pointers for 
    vlist->vtx
    blist->bond
    tlist->tria
    clist->cell
    poly_list->poly
    and for each poly:
        poly_list->poly->vtx
        poly_list->poly->bond
*/

    fwrite(vesicle->vlist->vtx, sizeof(ts_vertex *),1,fh);
    fwrite(vesicle->blist->bond, sizeof(ts_bond *),1,fh);
    fwrite(vesicle->tlist->tria, sizeof(ts_triangle *),1,fh);
    fwrite(vesicle->clist->cell, sizeof(ts_cell *),1,fh);
    fwrite(vesicle->poly_list->poly, sizeof(ts_poly *),1,fh);
    for(i=0;i<vesicle->poly_list->n;i++){
        fwrite(vesicle->poly_list->poly[i]->vlist->vtx, sizeof(ts_vertex *),1,fh);
        fwrite(vesicle->poly_list->poly[i]->blist->bond, sizeof(ts_bond *),1,fh);
    }
    fclose(fh);
    return TS_SUCCESS;
}


/** RESTORE DUMP FROM DISK **/
ts_vesicle *restore_state(){
    ts_uint i,j,k;
    FILE *fh=fopen("dump.bin","rb");
    ts_uint retval;
    ts_ulong off;

/* we restore all the data from the dump */
    /* restore vesicle */
    ts_vesicle *vesicle=(ts_vesicle *)calloc(1,sizeof(ts_vesicle));
    retval=fread(vesicle, sizeof(vesicle),1,fh);
    /* restore vertex list */
    vesicle->vlist=(ts_vertex_list *)malloc(sizeof(ts_vertex_list));
    retval=fread(vesicle->vlist, sizeof(ts_vertex_list),1,fh);
    /* restore bond list */
    vesicle->blist=(ts_bond_list *)malloc(sizeof(ts_bond_list));
    retval=fread(vesicle->blist, sizeof(ts_bond_list),1,fh);
    /* restore triangle list */
    vesicle->tlist=(ts_triangle_list *)malloc(sizeof(ts_triangle_list));
    retval=fread(vesicle->tlist, sizeof(ts_triangle_list),1,fh);
    /* restore cell list */
    vesicle->clist=(ts_cell_list *)malloc(sizeof(ts_cell_list));
    retval=fread(vesicle->clist, sizeof(ts_cell_list),1,fh);
    /* 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);
    /* level 1 complete */

  /*restore vertices*/
    vesicle->vlist->vtx=(ts_vertex **)calloc(vesicle->vlist->n,sizeof(ts_vertex *));
    for(i=0;i<vesicle->vlist->n;i++){
        vesicle->vlist->vtx[i]=(ts_vertex *)malloc(sizeof(ts_vertex));
        retval=fread(vesicle->vlist->vtx[i],sizeof(ts_vertex),1,fh);
        /*restore neigh, bond, tristar. Ignoring cell */
        vesicle->vlist->vtx[i]->neigh=(ts_vertex **)calloc(vesicle->vlist->vtx[i]->neigh_no, sizeof(ts_vertex *));
        for(j=0;j<vesicle->vlist->vtx[i]->neigh_no;j++){
            retval=fread(&off,sizeof(ts_ulong),1,fh);
            vesicle->vlist->vtx[i]->neigh[j]=vesicle->vlist->vtx[0]+off;
        }
        vesicle->vlist->vtx[i]->bond=(ts_bond **)calloc(vesicle->vlist->vtx[i]->bond_no, sizeof(ts_bond *));
        for(j=0;j<vesicle->vlist->vtx[i]->bond_no;j++){
            retval=fread(&off,sizeof(ts_ulong),1,fh);
            vesicle->vlist->vtx[i]->bond[j]=vesicle->blist->bond[0]+off;    
        }

        vesicle->vlist->vtx[i]->tristar=(ts_triangle **)calloc(vesicle->vlist->vtx[i]->tristar_no, sizeof(ts_triangle *));
        for(j=0;j<vesicle->vlist->vtx[i]->tristar_no;j++){
            retval=fread(&off,sizeof(ts_ulong),1,fh);
            vesicle->vlist->vtx[i]->tristar[j]=vesicle->tlist->tria[0]+off;
        }

    }

    /*restore bonds*/
    vesicle->blist->bond=(ts_bond **)calloc(vesicle->blist->n,sizeof(ts_bond *));
    for(i=0;i<vesicle->blist->n;i++){
        vesicle->blist->bond[i]=(ts_bond *)malloc(sizeof(ts_bond));
        retval=fread(vesicle->blist->bond[i],sizeof(ts_bond),1,fh);
        /* restore vtx1 and vtx2 */
        retval=fread(&off,sizeof(ts_ulong),1,fh);
        vesicle->blist->bond[i]->vtx1=vesicle->vlist->vtx[0]+off;
        retval=fread(&off,sizeof(ts_ulong),1,fh);
        vesicle->blist->bond[i]->vtx2=vesicle->vlist->vtx[0]+off;
    }

    /*restore triangles*/
    vesicle->tlist->tria=(ts_triangle **)calloc(vesicle->tlist->n,sizeof(ts_triangle *));
    for(i=0;i<vesicle->tlist->n;i++){
        vesicle->tlist->tria[i]=(ts_triangle *)malloc(sizeof(ts_triangle));
        retval=fread(vesicle->tlist->tria[i],sizeof(ts_triangle),1,fh);
        /* restore pointers for vertices */
        retval=fread(&off,sizeof(ts_ulong),1,fh);
        vesicle->tlist->tria[i]->vertex[0]=vesicle->vlist->vtx[0]+off;
        retval=fread(&off,sizeof(ts_ulong),1,fh);
        vesicle->tlist->tria[i]->vertex[1]=vesicle->vlist->vtx[0]+off;
        retval=fread(&off,sizeof(ts_ulong),1,fh);
        vesicle->tlist->tria[i]->vertex[2]=vesicle->vlist->vtx[0]+off;
        /* restore pointers for neigh */
        for(j=0;j<vesicle->tlist->tria[i]->neigh_no;j++){
            retval=fread(&off,sizeof(ts_ulong),1,fh);
            vesicle->tlist->tria[i]->neigh[j]=vesicle->tlist->tria[0]+off;
        }

    }
   
    /*restore cells */
/*TODO: do we need to recalculate cells here? */
/*    vesicle->clist->cell=(ts_cell **)malloc(vesicle->clist->cellno*sizeof(ts_cell *));
    for(i=0;i<vesicle->clist->cellno;i++){
        vesicle->clist->cell[i]=(ts_cell *)malloc(sizeof(ts_cell));
        retval=fread(vesicle->clist->cell[i],sizeof(ts_cell),1,fh);
    }
*/
    /*restore polymeres */
    vesicle->poly_list->poly = (ts_poly **)calloc(vesicle->poly_list->n,sizeof(ts_poly *));
    for(i=0;i<vesicle->poly_list->n;i++){
        vesicle->poly_list->poly[i]=(ts_poly *)calloc(1,sizeof(ts_poly));
        retval=fread(vesicle->poly_list->poly[i],sizeof(ts_poly),1,fh);
    } 
     
    /* restore poly vertex(monomer) list*/
    for(i=0;i<vesicle->poly_list->n;i++){
        vesicle->poly_list->poly[i]->vlist->vtx=(ts_vertex **)calloc(vesicle->poly_list->poly[i]->vlist->n,sizeof(ts_vertex *));
        for(j=0;j<vesicle->poly_list->poly[i]->vlist->n;j++){
            vesicle->poly_list->poly[i]->vlist->vtx[j]=(ts_vertex *)malloc(sizeof(ts_vertex));
            retval=fread(vesicle->poly_list->poly[i]->vlist->vtx[j],sizeof(ts_vertex),1,fh);
            
            /* restore neigh and bonds */
            vesicle->poly_list->poly[i]->vlist->vtx[j]->neigh=(ts_vertex **)calloc(vesicle->poly_list->poly[i]->vlist->vtx[j]->neigh_no, sizeof(ts_vertex *));
            for(k=0;k<vesicle->poly_list->poly[i]->vlist->vtx[j]->neigh_no;k++){
                retval=fread(&off,sizeof(ts_ulong),1,fh);
                vesicle->poly_list->poly[i]->vlist->vtx[j]->neigh[k]=vesicle->poly_list->poly[i]->vlist->vtx[0]+off;
            }
            vesicle->poly_list->poly[i]->vlist->vtx[j]->bond=(ts_bond **)calloc(vesicle->poly_list->poly[i]->vlist->vtx[j]->bond_no, sizeof(ts_bond *));
            for(k=0;k<vesicle->poly_list->poly[i]->vlist->vtx[j]->bond_no;k++){
                retval=fread(&off,sizeof(ts_ulong),1,fh);
                vesicle->poly_list->poly[i]->vlist->vtx[j]->bond[k]=vesicle->poly_list->poly[i]->blist->bond[0]+off;
            }

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


    /* recalculate pointers using saved information on pointer addresses */
    /* following pointers need to be recalculated:
        all vtx->neigh
        all vtx->tristar
        all vtx->bond
        vtx->cell
        vtx->grafted_poly
        bond->vtx1
        bond->vtx2
        tria->vertex[*]
        tria->neigh
        cell->vertex
        poly->grafted_vtx
        poly->vlist->vtx->neigh
        poly->vlist->vtx->bond
        poly->vlist->vtx->cell
    */

    /* read pointers from disk */
/*    fwrite(vesicle->vlist->vtx, sizeof(ts_vertex *),1,fh);
    fwrite(vesicle->blist->bond, sizeof(ts_bond *),1,fh);
    fwrite(vesicle->tlist->tria, sizeof(ts_triangle *),1,fh);
    fwrite(vesicle->clist->cell, sizeof(ts_cell *),1,fh);
    fwrite(vesicle->poly_list->poly, sizeof(ts_poly *),1,fh);
    for(i=0;i<vesicle->poly_list->n;i++){
        fwrite(vesicle->poly_list->poly[i]->vlist->vtx, sizeof(ts_vertex *),1,fh);
        fwrite(vesicle->poly_list->poly[i]->blist->bond, sizeof(ts_bond *),1,fh);
    }
*/


    if(retval); 
    fclose(fh);
    return vesicle;
}



ts_bool print_vertex_list(ts_vertex_list *vlist){
    ts_uint i;
    printf("Number of vertices: %u\n",vlist->n);

 src/io.h

@@ -50,4 +50,6 @@
ts_bool write_master_xml_file(ts_char *filename);
ts_vesicle *parsetape(ts_uint *mcsweeps, ts_uint *inititer, ts_uint *iterations);

ts_bool dump_state(ts_vesicle *vesicle);
ts_vesicle *restore_state();
#endif

 src/main.c

@@ -71,6 +71,17 @@

//poly_list_free(vesicle->poly_list);
/*End testing*/
printf("Vertex %d ima x komponento %e\n",123,vesicle->vlist->vtx[123]->x);
dump_state(vesicle);
vesicle->vlist->vtx[123]->x=123.0;
printf("Vertex %d ima x komponento %e\n",123,vesicle->vlist->vtx[123]->x);
write_vertex_xml_file(vesicle,0);
vesicle=restore_state();
printf("Stevilo vertexov je %d\n",vesicle->vlist->n);
printf("Vertex %d ima x komponento %e\n",123,vesicle->vlist->vtx[123]->x);
write_vertex_xml_file(vesicle,1);
write_master_xml_file("test.pvd");
return 0;

run_simulation(vesicle, mcsweeps, inititer, iterations);