restoring vertices with spontaneous curvatures seems to work, however, the ...

Samo Penic

2016-07-03 def8b5262e183297ccee42ebbf9ebdb89c10f44c

 src/initial_distribution.c

@@ -1,3 +1,4 @@
/* vim: set ts=4 sts=4 sw=4 noet : */
#include<stdlib.h>
#include<math.h>
#include<stdio.h>
@@ -11,6 +12,8 @@
#include "energy.h"
#include "poly.h"
#include "io.h"
#include "sh.h"
#include "shcomplex.h"

ts_vesicle *initial_distribution_dipyramid(ts_uint nshell, ts_uint ncmax1, ts_uint ncmax2, ts_uint ncmax3, ts_double stepsize){
   ts_fprintf(stdout,"Starting initial_distribution on vesicle with %u shells!...\n",nshell);
@@ -37,22 +40,54 @@

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

   vesicle=initial_distribution_dipyramid(tape->nshell,tape->ncxmax,tape->ncymax,tape->nczmax,tape->stepsize);
       vesicle->tape=tape;
   set_vesicle_values_from_tape(vesicle);
      initial_population_with_c0(vesicle,tape);
   return vesicle;
}

ts_bool set_vesicle_values_from_tape(ts_vesicle *vesicle){
   // Nucleus:
   vesicle->R_nucleus=tape->R_nucleus;
   ts_vertex *vtx;
   ts_tape *tape=vesicle->tape;
   vesicle->R_nucleus=tape->R_nucleus*tape->R_nucleus;
   vesicle->R_nucleusX=tape->R_nucleusX*tape->R_nucleusX;
   vesicle->R_nucleusY=tape->R_nucleusY*tape->R_nucleusY;
   vesicle->R_nucleusZ=tape->R_nucleusZ*tape->R_nucleusZ;
   vesicle->clist->dmin_interspecies = tape->dmin_interspecies*tape->dmin_interspecies;

   //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);
ts_uint i,j;
   for(i=0;i<vesicle->filament_list->n;i++){
         for(j=0;j<vesicle->filament_list->poly[i]->vlist->n;j++){
   poly_assign_filament_xi(vesicle,tape);

   fprintf(stderr,"%e %e %e\n", vesicle->filament_list->poly[i]->vlist->vtx[j]->x,vesicle->filament_list->poly[i]->vlist->vtx[j]->y, vesicle->filament_list->poly[i]->vlist->vtx[j]->z );
   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;
         }
      }
   }

   for(i=0;i<vesicle->filament_list->n;i++){
      vertex_list_assign_id(vesicle->filament_list->poly[i]->vlist,TS_ID_FILAMENT);
   }

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

@@ -61,7 +96,7 @@
   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);
//   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;
@@ -70,13 +105,44 @@

   vesicle->pressure= tape->pressure;
   vesicle->pswitch=tape->pswitch;
    if(tape->shc>0){
       vesicle->sphHarmonics=complex_sph_init(vesicle->vlist,tape->shc);
    }
    else {
        vesicle->sphHarmonics=NULL;
    }

    return vesicle;
    
    return TS_SUCCESS;

}



ts_bool initial_population_with_c0(ts_vesicle *vesicle, ts_tape *tape){
   int rndvtx,i,j;
   if(tape->number_of_vertices_with_c0>0){
      ts_fprintf(stderr,"Setting values for spontaneous curvature as defined in tape\n");
      j=0;
      for(i=0;i<tape->number_of_vertices_with_c0;i++){
         rndvtx=rand() % vesicle->vlist->n;
         if(fabs(vesicle->vlist->vtx[rndvtx]->c-tape->c0)<1e-15){
            j++;
            i--;
            if(j>10*vesicle->vlist->n){
               fatal("cannot populate vesicle with vertices with spontaneous curvature. Too many spontaneous curvature vertices?",100);
            }
            continue;
         }
         vesicle->vlist->vtx[rndvtx]->c=tape->c0;
      }
      mean_curvature_and_energy(vesicle);
      if(fabs(tape->w)>1e-16){ //if nonzero energy
         ts_fprintf(stderr,"Setting attraction between vertices with spontaneous curvature\n");
         sweep_attraction_bond_energy(vesicle);
      }
   }
   return TS_SUCCESS;
}


ts_bool pentagonal_dipyramid_vertex_distribution(ts_vertex_list *vlist){
@@ -87,15 +153,15 @@
   const ts_double c2= cos(4.0*M_PI/5.0);

   /* Calculates projection lenght of an edge bond to pentagram plane */
   const ts_double xl0=A0/(2.0*sin(M_PI/5.0));
   const ts_double xl0=DEF_A0/(2.0*sin(M_PI/5.0));
#ifdef TS_DOUBLE_DOUBLE
   const ts_double z0=sqrt(pow(A0,2)-pow(xl0,2));
   const ts_double z0=sqrt(pow(DEF_A0,2)-pow(xl0,2));
#endif
#ifdef TS_DOUBLE_FLOAT
   const ts_double z0=sqrtf(powf(A0,2)-powf(xl0,2));
   const ts_double z0=sqrtf(powf(DEF_A0,2)-powf(xl0,2));
#endif
#ifdef TS_DOUBLE_LONGDOUBLE
   const ts_double z0=sqrtl(powl(A0,2)-powl(xl0,2));
   const ts_double z0=sqrtl(powl(DEF_A0,2)-powl(xl0,2));
#endif
//   const z0=sqrt(A0*A0 -xl0*xl0); /* I could use pow function but if pow is used make a check on the float type. If float then powf, if long double use powl */

@@ -187,7 +253,7 @@
   for(i=1;i<=vlist->n;i++){
      for(j=1;j<=vlist->n;j++){
         dist2=vtx_distance_sq(vtx[i],vtx[j]);
         if( (dist2>eps) && (dist2<(A0*A0+eps))){ 
         if( (dist2>eps) && (dist2<(DEF_A0*DEF_A0+eps))){ 
   //if it is close enough, but not too much close (solves problem of comparing when i==j)
            vtx_add_neighbour(vtx[i],vtx[j]);
         }
@@ -220,7 +286,7 @@
                  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) ){
                  if( (fabs(dist2-DEF_A0*DEF_A0)<=eps) && (direct>0.0) && (j!=jjj) ){
                    vtx_add_cneighbour(blist,tvtx[k],tvtx[vtx[i]->neigh[j-1]->idx+1]);
                    jjj=jj;
                    jj=j;
@@ -286,7 +352,7 @@
            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){
            if(fabs(dist-DEF_A0*DEF_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]);
            }   
         }