Added comments for spontaneous curvature in energy.c and tape

Samo Penic

2017-09-19 e6efc61995516174081e923004477e3ff0853515

 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>
@@ -43,6 +44,7 @@
   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;
}

@@ -51,7 +53,9 @@
   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):
@@ -92,12 +96,12 @@
   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;
   vesicle->clist->ncmax[2]=tape->nczmax;
   vesicle->clist->max_occupancy=8; /* hard coded max occupancy? */
   vesicle->clist->max_occupancy=16; /* hard coded max occupancy? */

   vesicle->pressure= tape->pressure;
   vesicle->pswitch=tape->pswitch;
@@ -107,12 +111,38 @@
    else {
        vesicle->sphHarmonics=NULL;
    }

    
    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){
@@ -123,15 +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 */

@@ -223,7 +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]);
         }
@@ -256,7 +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;
@@ -322,7 +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]);
            }   
         }