Filament inside the vesicle added and debugged. Testing time...

mihaf

2014-03-21 bcf4557ddd61890f130247430267feac5b05c5b7

 src/initial_distribution.c

@@ -9,26 +9,91 @@
#include "triangle.h"
#include "initial_distribution.h"
#include "energy.h"
#include "poly.h"
#include "io.h"

ts_vesicle *initial_distribution_dipyramid(ts_uint nshell, ts_uint ncmax1, ts_uint ncmax2, ts_uint ncmax3, ts_double stepsize){
    ts_fprintf(stderr,"Starting initial_distribution on vesicle with %u shells!...\n",nshell);
   ts_fprintf(stdout,"Starting initial_distribution on vesicle with %u shells!...\n",nshell);
   ts_bool retval;
    ts_uint no_vertices=5*nshell*nshell+2;
	
    ts_vesicle *vesicle=init_vesicle(no_vertices,ncmax1,ncmax2,ncmax3,stepsize);
    vesicle->nshell=nshell;
    retval = vtx_set_global_values(vesicle);
    retval = pentagonal_dipyramid_vertex_distribution(vesicle->vlist);
    retval = init_vertex_neighbours(vesicle->vlist);
    retval = init_sort_neighbours(vesicle->vlist);
    retval = init_vesicle_bonds(vesicle);
    retval = init_triangles(vesicle);
    retval = init_triangle_neighbours(vesicle);
    retval = init_common_vertex_triangle_neighbours(vesicle);
    retval = mean_curvature_and_energy(vesicle);
 ts_fprintf(stderr,"initial_distribution finished!\n");
   ts_uint no_vertices=5*nshell*nshell+2;	
   ts_vesicle *vesicle=init_vesicle(no_vertices,ncmax1,ncmax2,ncmax3,stepsize);
   vesicle->nshell=nshell;
   //retval = vtx_set_global_values(vesicle);
   retval = pentagonal_dipyramid_vertex_distribution(vesicle->vlist);
   retval = init_vertex_neighbours(vesicle->vlist);
   vesicle->vlist = init_sort_neighbours(vesicle->blist,vesicle->vlist);
   // retval = init_vesicle_bonds(vesicle); // bonds are created in sort_neigh
   retval = init_triangles(vesicle);
   retval = init_triangle_neighbours(vesicle);
   retval = init_common_vertex_triangle_neighbours(vesicle);
   retval = init_normal_vectors(vesicle->tlist);
   retval = mean_curvature_and_energy(vesicle);
   ts_fprintf(stdout,"initial_distribution finished!\n");
   if(retval);
   return vesicle;
} 



ts_vesicle *create_vesicle_from_tape(ts_tape *tape){
   ts_vesicle *vesicle;
   ts_vertex *vtx;

   vesicle=initial_distribution_dipyramid(tape->nshell,tape->ncxmax,tape->ncymax,tape->nczmax,tape->stepsize);
   // Nucleus:
   vesicle->R_nucleus=tape->R_nucleus;

   //Initialize grafted polymers (brush):
   vesicle->poly_list=init_poly_list(tape->npoly,tape->nmono, vesicle->vlist, vesicle);
   vesicle->spring_constant=tape->kspring;
   poly_assign_spring_const(vesicle);

   //Initialize filaments (polymers inside the vesicle):
   vesicle->filament_list=init_poly_list(tape->nfil,tape->nfono, NULL, vesicle);
   poly_assign_filament_xi(vesicle,tape);

   ts_uint i,j;
   for(i=0;i<vesicle->filament_list->n;i++){
      for(j=0;j<vesicle->filament_list->poly[i]->blist->n;j++){
         bond_vector(vesicle->filament_list->poly[i]->blist->bond[j]);
         vesicle->filament_list->poly[i]->blist->bond[j]->bond_length = sqrt(vtx_distance_sq(vesicle->filament_list->poly[i]->blist->bond[j]->vtx1,vesicle->filament_list->poly[i]->blist->bond[j]->vtx2));
      }
   }

   for(i=0;i<vesicle->filament_list->n;i++){
      for(j=0;j<vesicle->filament_list->poly[i]->vlist->n;j++){
         vtx = vesicle->filament_list->poly[i]->vlist->vtx[j];
         if(vtx->bond_no == 2){
         vtx->energy = -(vtx->bond[0]->x*vtx->bond[1]->x + vtx->bond[0]->y*vtx->bond[1]->y + vtx->bond[0]->z*vtx->bond[1]->z)/vtx->bond[0]->bond_length/vtx->bond[1]->bond_length;
         }
      }
   }


//   vesicle->spring_constant=tape->kspring;
//   poly_assign_spring_const(vesicle);

	
   vesicle->nshell=tape->nshell;
   vesicle->dmax=tape->dmax*tape->dmax; /* dmax^2 in the vesicle dmax variable */
   vesicle->bending_rigidity=tape->xk0;
   vtx_set_global_values(vesicle); /* make xk0 default value for every vertex */ 
   ts_fprintf(stdout, "Tape setting: xk0=%e\n",tape->xk0);
   vesicle->stepsize=tape->stepsize;
   vesicle->clist->ncmax[0]=tape->ncxmax;
   vesicle->clist->ncmax[1]=tape->ncymax;
   vesicle->clist->ncmax[2]=tape->nczmax;
   vesicle->clist->max_occupancy=8; /* hard coded max occupancy? */

   vesicle->pressure= tape->pressure;
   vesicle->pswitch=tape->pswitch;

    return vesicle;

}





ts_bool pentagonal_dipyramid_vertex_distribution(ts_vertex_list *vlist){
@@ -62,40 +127,40 @@
   ts_double dx,dy; // end loop prereq

   /* topmost vertex */
   vtx[1]->data->x=0.0;
   vtx[1]->data->y=0.0;
   vtx[1]->data->z=z0*(ts_double)nshell;
   vtx[1]->x=0.0;
   vtx[1]->y=0.0;
   vtx[1]->z=z0*(ts_double)nshell;
   
   /* starting from to in circular order on pentagrams */   
   for(i=1;i<=nshell;i++){
      n0=2+5*i*(i-1)/2; //-1 would be for the reason that C index starts from 0 
      vtx[n0]->data->x=0.0;
      vtx[n0]->data->y=(ts_double)i*xl0;
      vtx[n0+i]->data->x=vtx[n0]->data->y*s1;
      vtx[n0+i]->data->y=vtx[n0]->data->y*c1;
      vtx[n0+2*i]->data->x=vtx[n0]->data->y*s2;
      vtx[n0+2*i]->data->y=vtx[n0]->data->y*c2;
      vtx[n0+3*i]->data->x=-vtx[n0+2*i]->data->x;
      vtx[n0+3*i]->data->y=vtx[n0+2*i]->data->y;
      vtx[n0+4*i]->data->x=-vtx[n0+i]->data->x;
      vtx[n0+4*i]->data->y=vtx[n0+i]->data->y;
      vtx[n0]->x=0.0;
      vtx[n0]->y=(ts_double)i*xl0;
      vtx[n0+i]->x=vtx[n0]->y*s1;
      vtx[n0+i]->y=vtx[n0]->y*c1;
      vtx[n0+2*i]->x=vtx[n0]->y*s2;
      vtx[n0+2*i]->y=vtx[n0]->y*c2;
      vtx[n0+3*i]->x=-vtx[n0+2*i]->x;
      vtx[n0+3*i]->y=vtx[n0+2*i]->y;
      vtx[n0+4*i]->x=-vtx[n0+i]->x;
      vtx[n0+4*i]->y=vtx[n0+i]->y;
   }

   /* vertexes on the faces of the dipyramid */
   for(i=1;i<=nshell;i++){
      n0=2+5*i*(i-1)/2; // -1 would be because of C!
      for(j=1;j<=i-1;j++){
         dx=(vtx[n0]->data->x-vtx[n0+4*i]->data->x)/(ts_double)i;
         dy=(vtx[n0]->data->y-vtx[n0+4*i]->data->y)/(ts_double)i;
         vtx[n0+4*i+j]->data->x=(ts_double)j*dx+vtx[n0+4*i]->data->x;
         vtx[n0+4*i+j]->data->y=(ts_double)j*dy+vtx[n0+4*i]->data->y;
         dx=(vtx[n0]->x-vtx[n0+4*i]->x)/(ts_double)i;
         dy=(vtx[n0]->y-vtx[n0+4*i]->y)/(ts_double)i;
         vtx[n0+4*i+j]->x=(ts_double)j*dx+vtx[n0+4*i]->x;
         vtx[n0+4*i+j]->y=(ts_double)j*dy+vtx[n0+4*i]->y;
      }
      for(k=0;k<=3;k++){ // I would be worried about zero starting of for
         dx=(vtx[n0+(k+1)*i]->data->x - vtx[n0+k*i]->data->x)/(ts_double) i;
         dy=(vtx[n0+(k+1)*i]->data->y - vtx[n0+k*i]->data->y)/(ts_double) i;
         dx=(vtx[n0+(k+1)*i]->x - vtx[n0+k*i]->x)/(ts_double) i;
         dy=(vtx[n0+(k+1)*i]->y - vtx[n0+k*i]->y)/(ts_double) i;
         for(j=1; j<=i-1;j++){
            vtx[n0+k*i+j]->data->x= (ts_double)j*dx+vtx[n0+k*i]->data->x;
            vtx[n0+k*i+j]->data->y= (ts_double)j*dy+vtx[n0+k*i]->data->y;
            vtx[n0+k*i+j]->x= (ts_double)j*dx+vtx[n0+k*i]->x;
            vtx[n0+k*i+j]->y= (ts_double)j*dy+vtx[n0+k*i]->y;
         } 
      } 
   }
@@ -103,15 +168,15 @@
   for(i=1;i<=nshell;i++){
      n0= 2+ 5*i*(i-1)/2;
      for(j=0;j<=5*i-1;j++){
      vtx[n0+j]->data->z= z0*(ts_double)(nshell-i);   // I would be worried about zero starting of for
      vtx[n0+j]->z= z0*(ts_double)(nshell-i);   // I would be worried about zero starting of for
      }
   }

/* for botom part of dipyramide we calculate the positions of vertices */
   for(i=2+5*nshell*(nshell+1)/2;i<=vlist->n;i++){
      vtx[i]->data->x=vtx[vlist->n - i +1]->data->x;
      vtx[i]->data->y=vtx[vlist->n - i +1]->data->y;
      vtx[i]->data->z=-vtx[vlist->n - i +1]->data->z;
      vtx[i]->x=vtx[vlist->n - i +1]->x;
      vtx[i]->y=vtx[vlist->n - i +1]->y;
      vtx[i]->z=-vtx[vlist->n - i +1]->z;
   }

   for(i=1;i<=vlist->n;i++){
@@ -150,29 +215,30 @@
   return TS_SUCCESS;
}

// TODO: with new datastructure can be rewritten.
ts_bool init_sort_neighbours(ts_vertex_list *vlist){
// TODO: with new datastructure can be rewritten. Partially it is done, but it is complicated.
ts_vertex_list *init_sort_neighbours(ts_bond_list *blist,ts_vertex_list *vlist){
   ts_vertex **vtx=vlist->vtx -1; // take a look at dipyramid function for comment.
   ts_uint i,l,j,jj,jjj,k=0;   
    ts_double eps=0.001; // Take a look if EPS from math.h can be used

/*lets initialize memory for temporary vertex_list. Should we write a function instead */
    ts_vertex_list *tvlist=init_vertex_list(vlist->n);
    ts_vertex_list *tvlist=vertex_list_copy(vlist);
    ts_vertex **tvtx=tvlist->vtx -1;  /* again to compensate for 0-indexing */

   ts_double dist2; // Square of distance of neighbours
    ts_double direct; // Something, dont know what, but could be normal of some kind
   for(i=1;i<=vlist->n;i++){
      k++; // WHY i IS NOT GOOD??
          vtx_add_neighbour(tvtx[k], tvtx[vtx[i]->data->neigh[0]->idx+1]); //always add 1st
          vtx_add_cneighbour(blist,tvtx[k], tvtx[vtx[i]->neigh[0]->idx+1]); //always add 1st
          jjj=1;
          jj=1;
          for(l=2;l<=vtx[i]->data->neigh_no;l++){
              for(j=2;j<=vtx[i]->data->neigh_no;j++){
                  dist2=vtx_distance_sq(vtx[i]->data->neigh[j-1],vtx[i]->data->neigh[jj-1]);
                  direct=vtx_direct(vtx[i],vtx[i]->data->neigh[j-1],vtx[i]->data->neigh[jj-1]);
          for(l=2;l<=vtx[i]->neigh_no;l++){
              for(j=2;j<=vtx[i]->neigh_no;j++){
                  dist2=vtx_distance_sq(vtx[i]->neigh[j-1],vtx[i]->neigh[jj-1]);
                  direct=vtx_direct(vtx[i],vtx[i]->neigh[j-1],vtx[i]->neigh[jj-1]);
// TODO: check if fabs can be used with all floating point types!!
                  if( (fabs(dist2-A0*A0)<=eps) && (direct>0.0) && (j!=jjj) ){
                    vtx_add_neighbour(tvtx[k],tvtx[vtx[i]->data->neigh[j-1]->idx+1]);
                    vtx_add_cneighbour(blist,tvtx[k],tvtx[vtx[i]->neigh[j-1]->idx+1]);
                    jjj=jj;
                    jj=j;
                    break;
@@ -180,24 +246,19 @@
             }
          }   
   }

    for(i=1;i<=vlist->n;i++){
        for(j=1;j<=vtx[i]->data->neigh_no;j++){
            if(vtx[i]->data->neigh_no!=tvtx[i]->data->neigh_no){ //doesn't work with nshell=1!
//                fprintf(stderr,"data1=%u data2=%u\n",vtx[i]->data->neigh_no,tvtx[i]->data->neigh_no);
                fatal("Number of neighbours not the same in init_sort_neighbours.",4);
            }
            //we must correct the pointers in original to point to their
            //neighbours according to indexes. Must be sure not to do it any
            //other way! Also, we need to repair the collection of bonds...
            vtx[i]->data->neigh[j-1]=vtx[tvtx[i]->data->neigh[j-1]->idx+1];
        }
/* We use the temporary vertex for our main vertices and we abandon main
 * vertices, because their neighbours are not correctly ordered */
   // tvtx=vlist->vtx;
   // vlist->vtx=tvtx;
   // tvlist->vtx=vtx;
    vtx_list_free(vlist);
/* Let's make a check if the number of bonds is correct */
    if((blist->n)!=3*(tvlist->n-2)){
        ts_fprintf(stderr,"Number of bonds is %u should be %u!\n", blist->n, 3*(tvlist->n-2));
        fatal("Number of bonds is not 3*(no_vertex-2).",4);
    }

   // Must free memory for temporary vertex array to avoid memory leak! HERE! NOW!
//    free_vertex(tvlist.vertex,tvlist.n);
    vtx_list_free(tvlist);
   return TS_SUCCESS;
   return tvlist;
}


@@ -209,8 +270,8 @@
   ts_uint i,j,k;
   for(i=1;i<=vlist->n;i++){
      for(j=i+1;j<=vlist->n;j++){
         for(k=0;k<vtx[i]->data->neigh_no;k++){ // has changed 0 to < instead of 1 and <=
            if(vtx[i]->data->neigh[k]==vtx[j]){  //if addresses matches it is the same
         for(k=0;k<vtx[i]->neigh_no;k++){ // has changed 0 to < instead of 1 and <=
            if(vtx[i]->neigh[k]==vtx[j]){  //if addresses matches it is the same
               bond_add(blist,vtx[i],vtx[j]);
               break;
            }
@@ -235,14 +296,15 @@
   ts_double eps=0.001; // can we use EPS from math.h?
   k=0;
   for(i=1;i<=vesicle->vlist->n;i++){
      for(j=1;j<=vtx[i]->data->neigh_no;j++){
         for(jj=1;jj<=vtx[i]->data->neigh_no;jj++){
      for(j=1;j<=vtx[i]->neigh_no;j++){
         for(jj=1;jj<=vtx[i]->neigh_no;jj++){
      //      ts_fprintf(stderr,"%u: (%u,%u) neigh_no=%u ",i,j,jj,vtx[i].neigh_no);
        //      ts_fprintf(stderr,"%e, %e",vtx[i].neigh[j-1]->x,vtx[i].neigh[jj-1]->x);
            dist=vtx_distance_sq(vtx[i]->data->neigh[j-1],vtx[i]->data->neigh[jj-1]);
            direct=vtx_direct(vtx[i],vtx[i]->data->neigh[j-1],vtx[i]->data->neigh[jj-1]);				
            if(fabs(dist-A0*A0)<=eps && direct < 0.0 && vtx[i]->data->neigh[j-1]->idx+1 > i && vtx[i]->data->neigh[jj-1]->idx+1 >i){
               triangle_add(tlist,vtx[i],vtx[i]->data->neigh[j-1],vtx[i]->data->neigh[jj-1]);
            dist=vtx_distance_sq(vtx[i]->neigh[j-1],vtx[i]->neigh[jj-1]);
            direct=vtx_direct(vtx[i],vtx[i]->neigh[j-1],vtx[i]->neigh[jj-1]);				
// TODO: same as above				
            if(fabs(dist-A0*A0)<=eps && direct < 0.0 && vtx[i]->neigh[j-1]->idx+1 > i && vtx[i]->neigh[jj-1]->idx+1 >i){
               triangle_add(tlist,vtx[i],vtx[i]->neigh[j-1],vtx[i]->neigh[jj-1]);
            }   
         }   
      }
@@ -253,11 +315,11 @@
   for(i=0;i<tlist->n;i++){
        k=0;
      for(j=0;j<3;j++){
         if(tlist->tria[i]->data->vertex[j]!=NULL)
         if(tlist->tria[i]->vertex[j]!=NULL)
            k++;
      }
            if(k!=3){
                fatal("Some triangles has less than 3 vertices..",4);
                fatal("Some triangles have less than 3 vertices..",4);
            }   
   } 
    if(tlist->n!=2*(vesicle->vlist->n -2)){
@@ -277,14 +339,14 @@
    ts_triangle **tria=tlist->tria -1;
    nobo=0;
    for(i=1;i<=tlist->n;i++){
        i1=tria[i]->data->vertex[0]; 
        i2=tria[i]->data->vertex[1]; 
        i3=tria[i]->data->vertex[2]; 
        i1=tria[i]->vertex[0]; 
        i2=tria[i]->vertex[1]; 
        i3=tria[i]->vertex[2]; 
        for(j=1;j<=tlist->n;j++){
            if(j==i) continue;
            j1=tria[j]->data->vertex[0]; 
            j2=tria[j]->data->vertex[1]; 
            j3=tria[j]->data->vertex[2]; 
            j1=tria[j]->vertex[0]; 
            j2=tria[j]->vertex[1]; 
            j3=tria[j]->vertex[2]; 
            if((i1==j1 && i3==j2) || (i1==j2 && i3==j3) || (i1==j3 && i3==j1)){
                    triangle_add_neighbour(tria[i],tria[j]);
                    nobo++;
@@ -292,14 +354,14 @@
        }
    }
    for(i=1;i<=tlist->n;i++){
        i1=tria[i]->data->vertex[0]; 
        i2=tria[i]->data->vertex[1]; 
        i3=tria[i]->data->vertex[2]; 
        i1=tria[i]->vertex[0]; 
        i2=tria[i]->vertex[1]; 
        i3=tria[i]->vertex[2]; 
        for(j=1;j<=tlist->n;j++){
            if(j==i) continue;
            j1=tria[j]->data->vertex[0]; 
            j2=tria[j]->data->vertex[1]; 
            j3=tria[j]->data->vertex[2]; 
            j1=tria[j]->vertex[0]; 
            j2=tria[j]->vertex[1]; 
            j3=tria[j]->vertex[2]; 
            if((i1==j1 && i2==j3) || (i1==j3 && i2==j2) || (i1==j2 && i2==j1)){
                triangle_add_neighbour(tria[i],tria[j]);
                nobo++;
@@ -307,14 +369,14 @@
        }
    }
    for(i=1;i<=tlist->n;i++){
        i1=tria[i]->data->vertex[0]; 
        i2=tria[i]->data->vertex[1]; 
        i3=tria[i]->data->vertex[2]; 
        i1=tria[i]->vertex[0]; 
        i2=tria[i]->vertex[1]; 
        i3=tria[i]->vertex[2]; 
        for(j=1;j<=tlist->n;j++){
            if(j==i) continue;
            j1=tria[j]->data->vertex[0]; 
            j2=tria[j]->data->vertex[1]; 
            j3=tria[j]->data->vertex[2]; 
            j1=tria[j]->vertex[0]; 
            j2=tria[j]->vertex[1]; 
            j3=tria[j]->vertex[2]; 
            if((i2==j1 && i3==j3) || (i2==j3 && i3==j2) || (i2==j2 && i3==j1)){
                triangle_add_neighbour(tria[i],tria[j]);
                nobo++;
@@ -337,20 +399,23 @@
    ts_triangle **tria=tlist->tria -1;

    for(i=1;i<=vesicle->vlist->n;i++){
        for(j=1;j<=vtx[i]->data->neigh_no;j++){
            k1=vtx[i]->data->neigh[j-1];
        for(j=1;j<=vtx[i]->neigh_no;j++){
            k1=vtx[i]->neigh[j-1];
            jp=j+1;
            if(j == vtx[i]->data->neigh_no) jp=1;
            k2=vtx[i]->data->neigh[jp-1];
            if(j == vtx[i]->neigh_no) jp=1;
            k2=vtx[i]->neigh[jp-1];
            for(k=1;k<=tlist->n;k++){      // VERY NON-OPTIMAL!!! too many loops (vlist.n * vtx.neigh * tlist.n )!
                k3=tria[k]->data->vertex[0];
                k4=tria[k]->data->vertex[1];
                k5=tria[k]->data->vertex[2];
                k3=tria[k]->vertex[0];
                k4=tria[k]->vertex[1];
                k5=tria[k]->vertex[2];
//                ts_fprintf(stderr,"%u %u: k=(%u %u %u)\n",k1,k2,k3,k4,k5);
                if((vtx[i]==k3 && k1==k4 && k2==k5) ||
                (vtx[i]==k4 && k1==k5 && k2==k3) ||
                (vtx[i]==k5 && k1==k3 && k2==k4)){
          //          ts_fprintf(stderr, "Added to tristar! ");

//TODO: probably something wrong with neighbour distribution.
//                if(vtx[i]==k3 || vtx[i]==k4 || vtx[i]==k5){
    //                    if(i==6) ts_fprintf(stdout, "Vtx[%u] > Added to tristar!\n",i);
                    vertex_add_tristar(vtx[i],tria[k]);
                }
            }