It seems that bondlip is debugged. Still, recommend testing

Samo Penic

2014-03-08 7efbb1dbd7c2c1368c429858a32fbeb9467420a8

 src/io.c

@@ -8,7 +8,8 @@
#include<stdlib.h>
#include <sys/types.h>
#include <dirent.h>

#include "initial_distribution.h"
#include "poly.h"

ts_bool print_vertex_list(ts_vertex_list *vlist){
   ts_uint i;
@@ -206,7 +207,7 @@
   ts_vertex_list *vlist=vesicle->vlist;
   ts_bond_list *blist=vesicle->blist;
   ts_vertex **vtx=vlist->vtx;
    ts_uint i;
    ts_uint i,j;
       char filename[255];
   FILE *fh;

@@ -217,29 +218,69 @@
      return TS_FAIL;
   }
   /* Here comes header of the file */

   //find number of extra vtxs and bonds of polymeres
   ts_uint monono=0, polyno=0;
   ts_bool poly=0;
   if(vesicle->poly_list!=NULL){
      if(vesicle->poly_list->poly[0]!=NULL){
      polyno=vesicle->poly_list->n;
      monono=vesicle->poly_list->poly[0]->vlist->n;
      poly=1;
      }
   }
   fprintf(fh, "<?xml version=\"1.0\"?>\n<VTKFile type=\"UnstructuredGrid\" version=\"0.1\" byte_order=\"LittleEndian\" compressor=\"vtkZLibDataCompressor\">\n <UnstructuredGrid>\n");
    fprintf(fh, "<Piece NumberOfPoints=\"%u\" NumberOfCells=\"%u\">\n",vlist->n, blist->n);
    fprintf(fh, "<Piece NumberOfPoints=\"%u\" NumberOfCells=\"%u\">\n",vlist->n+monono*polyno, blist->n+monono*polyno);
    fprintf(fh,"<PointData Scalars=\"scalars\">\n<DataArray type=\"Int64\" Name=\"scalars\" format=\"ascii\">");
      for(i=0;i<vlist->n;i++){
      fprintf(fh,"%u ",vtx[i]->idx);
    }
   //polymeres
   if(poly){
      for(i=0;i<vesicle->poly_list->n;i++){
         for(j=0;j<vesicle->poly_list->poly[i]->vlist->n;j++){
            fprintf(fh,"%u ", vesicle->poly_list->poly[i]->vlist->vtx[j]->idx);
         }
      }
   }

    fprintf(fh,"</DataArray>\n</PointData>\n<CellData>\n</CellData>\n<Points>\n<DataArray type=\"Float64\" Name=\"Koordinate tock\" NumberOfComponents=\"3\" format=\"ascii\">\n");
   for(i=0;i<vlist->n;i++){
      fprintf(fh,"%e %e %e\n",vtx[i]->x,vtx[i]->y, vtx[i]->z);
   }
   //polymeres
   if(poly){
      for(i=0;i<vesicle->poly_list->n;i++){
         for(j=0;j<vesicle->poly_list->poly[i]->vlist->n;j++){
            fprintf(fh,"%e %e %e\n", vesicle->poly_list->poly[i]->vlist->vtx[j]->x,vesicle->poly_list->poly[i]->vlist->vtx[j]->y, vesicle->poly_list->poly[i]->vlist->vtx[j]->z );
         }
      }
   }

    fprintf(fh,"</DataArray>\n</Points>\n<Cells>\n<DataArray type=\"Int64\" Name=\"connectivity\" format=\"ascii\">");
   for(i=0;i<blist->n;i++){
         fprintf(fh,"%u %u\n",blist->bond[i]->vtx1->idx,blist->bond[i]->vtx2->idx);
   }
   //polymeres
   if(poly){
      for(i=0;i<vesicle->poly_list->n;i++){
         for(j=0;j<vesicle->poly_list->poly[i]->blist->n;j++){
            fprintf(fh,"%u %u\n", vesicle->poly_list->poly[i]->blist->bond[j]->vtx1->idx,vesicle->poly_list->poly[i]->blist->bond[j]->vtx2->idx);
         }
   //grafted bonds
      fprintf(fh,"%u %u\n", vesicle->poly_list->poly[i]->grafted_vtx->idx, vesicle->poly_list->poly[i]->vlist->vtx[0]->idx);
      }

   }
	

    fprintf(fh,"</DataArray>\n<DataArray type=\"Int64\" Name=\"offsets\" format=\"ascii\">");
    for (i=2;i<blist->n*2+1;i+=2){
    for (i=2;i<(blist->n+monono*polyno)*2+1;i+=2){
    fprintf(fh,"%u ",i);
    }
    fprintf(fh,"\n");
    fprintf(fh,"</DataArray>\n<DataArray type=\"UInt8\" Name=\"types\" format=\"ascii\">\n");
     for (i=0;i<blist->n;i++){
     for (i=0;i<blist->n+monono*polyno;i++){
        fprintf(fh,"3 ");
    }

@@ -294,20 +335,37 @@



ts_bool parsetape(ts_vesicle *vesicle,ts_uint *iterations){
    long int nshell=17,ncxmax=60, ncymax=60, nczmax=60;  // THIS IS DUE TO CONFUSE BUG!
    ts_double xk0=25.0, dmax=1.67,stepsize=0.15;
    *iterations=1000;
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, 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,pressure=0.0;
   long int iter=1000, init=1000, mcsw=1000;


    cfg_opt_t opts[] = {
        CFG_SIMPLE_INT("nshell", &nshell),
        CFG_SIMPLE_INT("npoly", &npoly),
        CFG_SIMPLE_INT("nmono", &nmono),
        CFG_SIMPLE_FLOAT("dmax", &dmax),
        CFG_SIMPLE_FLOAT("xk0",&xk0),
   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),
        CFG_SIMPLE_INT("nzmax", &nczmax),
        CFG_SIMPLE_INT("iterations",iterations),
        CFG_SIMPLE_INT("iterations",&iter),
   CFG_SIMPLE_INT("mcsweeps",&mcsw),
   CFG_SIMPLE_INT("inititer", &init),
        CFG_SIMPLE_BOOL("quiet",&quiet),
        CFG_SIMPLE_STR("multiprocessing",buf),
        CFG_SIMPLE_INT("smp_cores",&brezveze0),
        CFG_SIMPLE_INT("cluster_nodes",&brezveze1),
        CFG_SIMPLE_INT("distributed_processes",&brezveze2),
        CFG_END()
    };
    cfg_t *cfg;    
@@ -320,17 +378,36 @@
    else if(retval==CFG_PARSE_ERROR){
   fatal("Invalid tape!",100);
   }
   ts_vesicle *vesicle;
       *iterations=iter;
   *inititer=init;
   *mcsweeps=mcsw;
   vesicle=initial_distribution_dipyramid(nshell,ncxmax,ncymax,nczmax,stepsize);
   vesicle->poly_list=init_poly_list(npoly,nmono, vesicle->vlist);
   vesicle->spring_constant=kspring;
   poly_assign_spring_const(vesicle);
	

    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);
//    fprintf(stderr,"NSHELL=%u\n",vesicle->nshell);
    return TS_SUCCESS;
   free(buf);
  //  fprintf(stderr,"NSHELL=%u\n",vesicle->nshell);

			

    return vesicle;

}