Merged branches polyel with constant volume

Samo Penic

2014-03-08 1153c110781fc3add2c22ab2d996e05b0e0b10de

 src/io.c

@@ -22,7 +22,7 @@
    FILE *fh=fopen("dump.bin","wb");

    /* dump vesicle */
    fwrite(vesicle, sizeof(vesicle),1,fh);
    fwrite(vesicle, sizeof(ts_vesicle),1,fh);
    /* dump vertex list */
    fwrite(vesicle->vlist, sizeof(ts_vertex_list),1,fh);
    /* dump bond list */
@@ -127,6 +127,8 @@
        poly_list->poly->bond
*/

   fwrite(vesicle->clist, sizeof(ts_cell_list),1,  fh);

    fclose(fh);
    return TS_SUCCESS;
}
@@ -142,7 +144,9 @@
/* 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);
    retval=fread(vesicle, sizeof(ts_vesicle),1,fh);
//   fprintf(stderr,"was here! %e\n",vesicle->dmax);

    /* restore vertex list */
    vesicle->vlist=(ts_vertex_list *)malloc(sizeof(ts_vertex_list));
    retval=fread(vesicle->vlist, sizeof(ts_vertex_list),1,fh);
@@ -170,11 +174,13 @@
    for(i=0;i<vesicle->tlist->n;i++){
        vesicle->tlist->tria[i]=(ts_triangle *)malloc(sizeof(ts_triangle));
}

  /*restore vertices*/
/* prerequisity. Vertices must be malloced before vertexes are recreated */
    vesicle->vlist->vtx=(ts_vertex **)calloc(vesicle->vlist->n,sizeof(ts_vertex *));
    for(i=0;i<vesicle->vlist->n;i++){
 for(i=0;i<vesicle->vlist->n;i++){
        vesicle->vlist->vtx[i]=(ts_vertex *)malloc(sizeof(ts_vertex));
 }
  /*restore vertices*/
    for(i=0;i<vesicle->vlist->n;i++){
        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 *));
@@ -298,8 +304,14 @@
        }
    }

  

// recreating space for cells // 
   vesicle->clist=(ts_cell_list *)malloc(sizeof(ts_cell_list));
   retval=fread(vesicle->clist, sizeof(ts_cell_list), 1,fh); 
   vesicle->clist->cell=(ts_cell **)malloc(sizeof(ts_cell *)*vesicle->clist->ncmax[0]*vesicle->clist->ncmax[1]*vesicle->clist->ncmax[2]);
   for(i=0;i<vesicle->clist->ncmax[0]*vesicle->clist->ncmax[1]*vesicle->clist->ncmax[2];i++){
           vesicle->clist->cell[i]=(ts_cell *)calloc(1,sizeof(ts_cell));
           vesicle->clist->cell[i]->idx=i+1; // We enumerate cells! Probably never required!
       }

    if(retval); 
    fclose(fh);
@@ -405,11 +417,11 @@
        fprintf(fh," %.17E\t%.17E\t%.17E\t%.17E\t%.17E\t%u\n",
        vlist->vtx[i]->xk,vlist->vtx[i]->c,vlist->vtx[i]->energy,
        vlist->vtx[i]->energy_h, vlist->vtx[i]->curvature, 0);
        for(j=0;j<vlist->vtx[i]->neigh_no;j++){
        for(j=0;j<vlist->vtx[i]->bond_no;j++){
            fprintf(fh," %.17E", vlist->vtx[i]->bond[j]->bond_length_dual);
        }
            fprintf(fh,"\n");
        for(j=0;j<vlist->vtx[i]->neigh_no;j++){
        for(j=0;j<vlist->vtx[i]->bond_no;j++){
            fprintf(fh," %.17E", vlist->vtx[i]->bond[j]->bond_length);
        }
            fprintf(fh,"\n");
@@ -636,12 +648,12 @@


ts_vesicle *parsetape(ts_uint *mcsweeps, ts_uint *inititer, ts_uint *iterations){
    long int nshell=17,ncxmax=60, ncymax=60, nczmax=60, npoly=10, nmono=20;  // THIS IS DUE TO CONFUSE BUG!
    long int nshell=17,ncxmax=60, ncymax=60, nczmax=60, npoly=10, nmono=20, pswitch=0;  // THIS IS DUE TO CONFUSE BUG!
    char *buf=malloc(255*sizeof(char));
    long int brezveze0=1;
    long int brezveze1=1;
    long int brezveze2=1;
    ts_double xk0=25.0, dmax=1.67,stepsize=0.15,kspring=800.0;
    ts_double xk0=25.0, dmax=1.67,stepsize=0.15,kspring=800.0,pressure=0.0;
   long int iter=1000, init=1000, mcsw=1000;


@@ -651,7 +663,9 @@
        CFG_SIMPLE_INT("nmono", &nmono),
        CFG_SIMPLE_FLOAT("dmax", &dmax),
        CFG_SIMPLE_FLOAT("xk0",&xk0),
        CFG_SIMPLE_FLOAT("k_spring",&kspring),
   CFG_SIMPLE_INT("pswitch",&pswitch),
   CFG_SIMPLE_FLOAT("pressure",&pressure),
   CFG_SIMPLE_FLOAT("k_spring",&kspring),
        CFG_SIMPLE_FLOAT("stepsize",&stepsize),
        CFG_SIMPLE_INT("nxmax", &ncxmax),
        CFG_SIMPLE_INT("nymax", &ncymax),
@@ -689,12 +703,16 @@
    vesicle->nshell=nshell;
    vesicle->dmax=dmax*dmax;
    vesicle->bending_rigidity=xk0;
    vtx_set_global_values(vesicle); //copies xk0 to every vertex


    vesicle->stepsize=stepsize;
    vesicle->clist->ncmax[0]=ncxmax;
    vesicle->clist->ncmax[1]=ncymax;
    vesicle->clist->ncmax[2]=nczmax;
    vesicle->clist->max_occupancy=8;

   vesicle->pressure=pressure/vesicle->bending_rigidity;   //all energy contributions need to be divided by bending_rigidity!
    vesicle->pswitch=pswitch;
    cfg_free(cfg);
   free(buf);
  //  fprintf(stderr,"NSHELL=%u\n",vesicle->nshell);