Structures for grafted polymers (Samo&Miha)

mihaf

2013-11-29 1d5dff5a3576a028f691608ef9369844efdfe82b

 src/initial_distribution.c

@@ -14,8 +14,14 @@
    ts_fprintf(stderr,"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);

//TODO: debugging only. Please remove ASAP!
   vesicle->bending_rigidity=25.0;

    vesicle->nshell=nshell;
    retval = vtx_set_global_values(vesicle);
    retval = pentagonal_dipyramid_vertex_distribution(vesicle->vlist);
@@ -64,40 +70,40 @@
   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;
         } 
      } 
   }
@@ -105,15 +111,15 @@
   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++){
@@ -166,15 +172,16 @@
    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_cneighbour(blist,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_cneighbour(blist,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;
@@ -206,8 +213,8 @@
   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;
            }
@@ -232,14 +239,15 @@
   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]);
            }   
         }   
      }
@@ -254,7 +262,7 @@
            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)){
@@ -334,11 +342,11 @@
    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]->vertex[0];
                k4=tria[k]->vertex[1];