Polymers thermicaly move now! HArmonic potential added.

Miha

2014-02-06 fedf2b217113800a15f367e111e2dbcad4a3c92c

 src/io.c

@@ -1,29 +1,35 @@
#include<general.h>
#include "general.h"
#include<stdio.h>
#include "io.h"
#include "confuse.h"
#include <confuse.h>
#include "vertex.h"
#include "bond.h"
#include<string.h>
#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;
   printf("Number of vertices: %u\n",vlist->n);
   for(i=0;i<vlist->n;i++){
      printf("%u: %f %f %f\n", vlist->vertex[i].idx,vlist->vertex[i].x, vlist->vertex[i].y, vlist->vertex[i].z);
      printf("%u: %f %f %f\n",
vlist->vtx[i]->idx,vlist->vtx[i]->x, vlist->vtx[i]->y, vlist->vtx[i]->z);
   }
   return TS_SUCCESS;
}

ts_bool print_vertex_neighbours(ts_vertex_list *vlist){
   ts_uint i,j;
   ts_vertex *vtx=vlist->vertex;
   ts_vertex **vtx=vlist->vtx;
   printf("Vertex id(neigh no): (neighvertex coord) (neighvertex coord) ...\n");
   for(i=0;i<vlist->n;i++){
      printf("%u(%u): ",vtx[i].idx,vtx[i].neigh_no);
      for(j=0;j<vtx[i].neigh_no;j++){
         printf("(%f,%f,%f)",vtx[i].neigh[j]->x, vtx[i].neigh[j]->y,vtx[i].neigh[j]->z);
      printf("%u(%u): ",vtx[i]->idx,vtx[i]->neigh_no);
      for(j=0;j<vtx[i]->neigh_no;j++){
         printf("(%f,%f,%f)",vtx[i]->neigh[j]->x,
vtx[i]->neigh[j]->y,vtx[i]->neigh[j]->z);
      }
      printf("\n");
   }
@@ -32,7 +38,7 @@
}

ts_bool write_vertex_fcompat_file(ts_vertex_list *vlist,ts_char *filename){
   ts_vertex *vtx=vlist->vertex;
   ts_vertex **vtx=vlist->vtx;
   ts_uint i;
   FILE *fh;
   
@@ -42,7 +48,7 @@
      return TS_FAIL;
   }
   for(i=0;i<vlist->n;i++)
      fprintf(fh," %E\t%E\t%E\n",vtx[i].x,vtx[i].y, vtx[i].z);
      fprintf(fh," %E\t%E\t%E\n",vtx[i]->x,vtx[i]->y, vtx[i]->z);

   fclose(fh);
return TS_SUCCESS;
@@ -52,10 +58,12 @@
ts_bool fprint_vertex_list(FILE *fh,ts_vertex_list *vlist){
    ts_uint i,j;
   for(i=0;i<vlist->n;i++){
      fprintf(fh," %.17E\t%.17E\t%.17E\t%u\n",vlist->vertex[i].x,
         vlist->vertex[i].y, vlist->vertex[i].z, vlist->vertex[i].neigh_no);
      for(j=0;j<vlist->vertex[i].neigh_no;j++){
         fprintf(fh,"\t%u",(ts_uint)(vlist->vertex[i].neigh[j]-vlist->vertex+1));
      fprintf(fh," %.17E\t%.17E\t%.17E\t%u\n",vlist->vtx[i]->x,
         vlist->vtx[i]->y, vlist->vtx[i]->z,
            vlist->vtx[i]->neigh_no);
      for(j=0;j<vlist->vtx[i]->neigh_no;j++){
         fprintf(fh,"\t%u",(ts_uint)(vlist->vtx[i]->neigh[j]->idx));
        //-vlist->vtx+1));
      }
      fprintf(fh,"\n");
   }
@@ -64,10 +72,10 @@

ts_bool fprint_tristar(FILE *fh, ts_vesicle *vesicle){
    ts_uint i,j;
   for(i=0;i<vesicle->vlist.n;i++){
      fprintf(fh,"\t%u",vesicle->vlist.vertex[i].tristar_no);
      for(j=0;j<vesicle->vlist.vertex[i].tristar_no;j++){
         fprintf(fh,"\t%u",(ts_uint)(vesicle->vlist.vertex[i].tristar[j]-vesicle->tlist.triangle+1));
   for(i=0;i<vesicle->vlist->n;i++){
      fprintf(fh,"\t%u",vesicle->vlist->vtx[i]->tristar_no);
      for(j=0;j<vesicle->vlist->vtx[i]->tristar_no;j++){
         fprintf(fh,"\t%u",(ts_uint)(vesicle->vlist->vtx[i]->tristar[j]->idx));//-vesicle->tlist->tria+1));
      }
      fprintf(fh,"\n");
   }
@@ -75,20 +83,20 @@
}

ts_bool fprint_triangle_list(FILE *fh, ts_vesicle *vesicle){
        ts_triangle_list *tlist=&vesicle->tlist;
        ts_triangle_list *tlist=vesicle->tlist;
      ts_uint i,j;
   for(i=0;i<tlist->n;i++){
        fprintf(fh,"\t%u",tlist->triangle[i].neigh_no);
       for(j=0;j<tlist->triangle[i].neigh_no;j++){
          fprintf(fh,"\t%u",(ts_uint)(tlist->triangle[i].neigh[j]-tlist->triangle+1)); 
        fprintf(fh,"\t%u",tlist->tria[i]->neigh_no);
       for(j=0;j<tlist->tria[i]->neigh_no;j++){
          fprintf(fh,"\t%u",(ts_uint)(tlist->tria[i]->neigh[j]->idx));//-tlist->tria+1)); 
        }
        fprintf(fh,"\n");
            for(j=0;j<3;j++){
          fprintf(fh,"\t%u",(ts_uint)(tlist->triangle[i].vertex[j]-vesicle->vlist.vertex+1)); 
          fprintf(fh,"\t%u",(ts_uint)(tlist->tria[i]->vertex[j]->idx));//-vesicle->vlist->vtx+1)); 
            }
        fprintf(fh,"\n");
      fprintf(fh,"%.17E\t%.17E\t%.17E\n",tlist->triangle[i].xnorm,
tlist->triangle[i].ynorm,tlist->triangle[i].znorm);
      fprintf(fh,"%.17E\t%.17E\t%.17E\n",tlist->tria[i]->xnorm,
tlist->tria[i]->ynorm,tlist->tria[i]->znorm);
        fprintf(fh,"0.00000000000000000\n0.00000000000000000\n");
    }
    return TS_SUCCESS;
@@ -98,14 +106,14 @@
    ts_uint i,j;
    for(i=0;i<vlist->n;i++){
        fprintf(fh," %.17E\t%.17E\t%.17E\t%.17E\t%.17E\t%u\n",
        vlist->vertex[i].xk,vlist->vertex[i].c,vlist->vertex[i].energy,
        vlist->vertex[i].energy_h, vlist->vertex[i].curvature, 0);
        for(j=0;j<vlist->vertex[i].neigh_no;j++){
            fprintf(fh," %.17E", vlist->vertex[i].bond_length_dual[j]);
        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++){
            fprintf(fh," %.17E", vlist->vtx[i]->bond[j]->bond_length_dual);
        }
            fprintf(fh,"\n");
        for(j=0;j<vlist->vertex[i].neigh_no;j++){
            fprintf(fh," %.17E", vlist->vertex[i].bond_length[j]);
        for(j=0;j<vlist->vtx[i]->neigh_no;j++){
            fprintf(fh," %.17E", vlist->vtx[i]->bond[j]->bond_length);
        }
            fprintf(fh,"\n");
    }
@@ -114,8 +122,11 @@

ts_bool fprint_bonds(FILE *fh,ts_vesicle *vesicle){
    ts_uint i;
    for(i=0;i<vesicle->blist.n;i++){
        fprintf(fh,"\t%u\t%u\n",(ts_uint)(vesicle->blist.bond[i].vtx1-vesicle->vlist.vertex+1),(ts_uint)(vesicle->blist.bond[i].vtx2-vesicle->vlist.vertex+1));
    for(i=0;i<vesicle->blist->n;i++){
        fprintf(fh,"\t%u\t%u\n",(ts_uint)(vesicle->blist->bond[i]->vtx1->idx),
//-vesicle->vlist->vtx+1),
        (ts_uint)(vesicle->blist->bond[i]->vtx2->idx));
    //-vesicle->vlist.vtx+1));
    }
    return TS_SUCCESS;
}
@@ -123,17 +134,16 @@

ts_bool write_dout_fcompat_file(ts_vesicle *vesicle, ts_char *filename){
   FILE *fh;
   ts_uint i,j;
   fh=fopen(filename, "w");
    if(fh==NULL){
        err("Cannot open file %s for writing");
        return TS_FAIL;
    }
    fprintf(fh,"%.17E\n%.17E\n",vesicle->stepsize,vesicle->dmax);
    fprint_vertex_list(fh,&vesicle->vlist);
    fprint_vertex_list(fh,vesicle->vlist);
    fprint_tristar(fh,vesicle);
    fprint_triangle_list(fh,vesicle);
    fprint_vertex_data(fh,&vesicle->vlist);
    fprint_vertex_data(fh,vesicle->vlist);
    fprint_bonds(fh,vesicle);
   fclose(fh);   
   return TS_SUCCESS;
@@ -147,7 +157,7 @@
                err("Cannot open file for reading... Nonexistant file?");
                return TS_FAIL;
        }
   ts_uint retval;
   ts_uint retval=1;
   while(retval!=EOF){
      retval=fscanf(fh,"%s",line);
      
@@ -181,22 +191,23 @@
                    j=rindex(ent->d_name,'_');
                    if(j==NULL) continue;
                    number=strndup(j+1,j-i); 
                fprintf(fh,"<DataSet timestep=\"%u\" group=\"\" part=\"0\" file=\"%s\"/>\n",atol(number),ent->d_name);
                fprintf(fh,"<DataSet timestep=\"%u\" group=\"\" part=\"0\" file=\"%s\"/>\n",atoi(number),ent->d_name);
                tstep++;
                    free(number);
            }  
      }
   }
    free(dir);
   fprintf(fh,"</Collection>\n</VTKFile>\n");
   fclose(fh);
   return TS_SUCCESS;
}

ts_bool write_vertex_xml_file(ts_vesicle *vesicle, ts_uint timestepno){
   ts_vertex_list *vlist=&vesicle->vlist;
   ts_bond_list *blist=&vesicle->blist;
   ts_vertex *vtx=vlist->vertex;
   ts_uint i,j;
   ts_vertex_list *vlist=vesicle->vlist;
   ts_bond_list *blist=vesicle->blist;
   ts_vertex **vtx=vlist->vtx;
    ts_uint i,j;
       char filename[255];
   FILE *fh;

@@ -207,29 +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 ",vlist->vertex[i].idx);
      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);
      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);
         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 ");
    }

@@ -240,10 +291,10 @@
}

ts_bool write_vertex_vtk_file(ts_vesicle *vesicle,ts_char *filename, ts_char *text){
   ts_vertex_list *vlist=&vesicle->vlist;
   ts_bond_list *blist=&vesicle->blist;
   ts_vertex *vtx=vlist->vertex;
   ts_uint i,j;
   ts_vertex_list *vlist=vesicle->vlist;
   ts_bond_list *blist=vesicle->blist;
   ts_vertex **vtx=vlist->vtx;
   ts_uint i;
   FILE *fh;
   
   fh=fopen(filename, "w");
@@ -260,12 +311,12 @@
   fprintf(fh,"DATASET UNSTRUCTURED_GRID\n");
   fprintf(fh,"POINTS %u double\n", vlist->n);
   for(i=0;i<vlist->n;i++){
      fprintf(fh,"%e %e %e\n",vtx[i].x,vtx[i].y, vtx[i].z);
      fprintf(fh,"%e %e %e\n",vtx[i]->x,vtx[i]->y, vtx[i]->z);
   }
   
   fprintf(fh,"CELLS %u %u\n",blist->n,3*blist->n);
   for(i=0;i<blist->n;i++){
         fprintf(fh,"2 %u %u\n",blist->bond[i].vtx1->idx,blist->bond[i].vtx2->idx);
         fprintf(fh,"2 %u %u\n",blist->bond[i]->vtx1->idx,blist->bond[i]->vtx2->idx);
   }
   fprintf(fh,"CELL_TYPES %u\n",blist->n);
   for(i=0;i<blist->n;i++)
@@ -276,7 +327,7 @@
   fprintf(fh,"LOOKUP_TABLE default\n");

   for(i=0;i<vlist->n;i++)
      fprintf(fh,"%u\n",vtx[i].idx);
      fprintf(fh,"%u\n",vtx[i]->idx);

   fclose(fh);
   return TS_SUCCESS;
@@ -284,42 +335,119 @@



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;  // 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;
   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_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;    
    ts_uint retval;
    cfg = cfg_init(opts, 0);
    retval=cfg_parse(cfg, "tape_new");
    retval=cfg_parse(cfg, "tape");
    if(retval==CFG_FILE_ERROR){
   fatal("No tape_new file.",100);
   fatal("No tape file.",100);
   }
    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;
    vesicle->stepsize=stepsize;
    vesicle->clist.ncmax[0]=ncxmax;
    vesicle->clist.ncmax[1]=ncymax;
    vesicle->clist.ncmax[2]=nczmax;
    vesicle->clist.max_occupancy=8;
    cfg_free(cfg);
//    fprintf(stderr,"NSHELL=%u\n",vesicle->nshell);
    return TS_SUCCESS;
    vesicle->clist->ncmax[0]=ncxmax;
    vesicle->clist->ncmax[1]=ncymax;
    vesicle->clist->ncmax[2]=nczmax;
    vesicle->clist->max_occupancy=8;

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

			

    return vesicle;

}


ts_bool read_geometry_file(char *fname, ts_vesicle *vesicle){
   FILE *fh;
    ts_uint i, nvtx,nedges,ntria;
    ts_uint vtxi1,vtxi2;
    float x,y,z;
    ts_vertex_list *vlist;
   fh=fopen(fname, "r");
        if(fh==NULL){
                err("Cannot open file for reading... Nonexistant file?");
                return TS_FAIL;
        }
   ts_uint retval;
   retval=fscanf(fh,"%u %u %u",&nvtx, &nedges, &ntria);
    vesicle->vlist=init_vertex_list(nvtx);
    vlist=vesicle->vlist;
    for(i=0;i<nvtx;i++){
   //     fscanf(fh,"%F %F %F",&vlist->vtx[i]->x,&vlist->vtx[i]->y,&vlist->vtx[i]->z);
       retval=fscanf(fh,"%F %F %F",&x,&y,&z);
        vlist->vtx[i]->x=x;
        vlist->vtx[i]->y=y;
        vlist->vtx[i]->z=z;
    }
    for(i=0;i<nedges;i++){
        retval=fscanf(fh,"%u %u",&vtxi1,&vtxi2);
        bond_add(vesicle->blist,vesicle->vlist->vtx[vtxi1-1],vesicle->vlist->vtx[vtxi2-1]);
    }
    //TODO: neighbours from bonds,
    //TODO: triangles from neigbours

//    Don't need to read triangles. Already have enough data
    /*
    for(i=0;i<ntria;i++){
        retval=fscanf(fh,"%u %u %u", &bi1, &bi2, &bi3);
        vtxi1=vesicle->blist->vertex1->idx;
        vtxi2=vesicle->blist->vertex1->idx;
        
    }
    */
   if(retval);
   fclose(fh);	



    return TS_SUCCESS;
}