Added function to calculate absolute value of ulm2

Samo Penic

2018-06-26 0661f62a1a4b5bc87310421d198e7df8538c7363

 src/vertexmove.c

@@ -21,7 +21,8 @@
    ts_double dist;
    ts_bool retval; 
    ts_uint cellidx; 
    ts_double delta_energy, delta_energy_cv,oenergy,dvol=0.0, darea=0.0;
    ts_double delta_energy, delta_energy_cv,oenergy,dvol=0.0, darea=0.0, dstretchenergy=0.0;
    ts_double temp_area=0.0; //for stretching
    ts_double costheta,sintheta,phi,r;
   //This will hold all the information of vtx and its neighbours
   ts_vertex backupvtx[20], *constvol_vtx_moved=NULL, *constvol_vtx_backup=NULL;
@@ -72,21 +73,23 @@

// TODO: Maybe faster if checks only nucleus-neighboring cells
// Nucleus penetration check:
#define SQ(x) x*x
//#define SQ(x) x*x
if(vesicle->R_nucleus>0.0){
   if (SQ(vtx->x-vesicle->nucleus_center[0])+ SQ(vtx->y-vesicle->nucleus_center[1]) + SQ(vtx->z-vesicle->nucleus_center[2]) < vesicle->R_nucleus){
   if ((vtx->x-vesicle->nucleus_center[0])*(vtx->x-vesicle->nucleus_center[0])+ (vtx->y-vesicle->nucleus_center[1])*(vtx->y-vesicle->nucleus_center[1]) + (vtx->z-vesicle->nucleus_center[2])*(vtx->z-vesicle->nucleus_center[2]) < vesicle->R_nucleus){
      vtx=memcpy((void *)vtx,(void *)&backupvtx[0],sizeof(ts_vertex));
      return TS_FAIL;
   }
} else if(vesicle->R_nucleusX>0.0){
//   fprintf(stderr,"DEBUG, (Rx, Ry,Rz)^2=(%f,%f,%f)\n",vesicle->R_nucleusX, vesicle->R_nucleusY, vesicle->R_nucleusZ);
   if (SQ(vtx->x-vesicle->nucleus_center[0])/vesicle->R_nucleusX + SQ(vtx->y-vesicle->nucleus_center[1])/vesicle->R_nucleusY + SQ(vtx->z-vesicle->nucleus_center[2])/vesicle->R_nucleusZ < 1.0){
//   if (SQ(vtx->x-vesicle->nucleus_center[0])/vesicle->R_nucleusX + SQ(vtx->y-vesicle->nucleus_center[1])/vesicle->R_nucleusY + SQ(vtx->z-vesicle->nucleus_center[2])/vesicle->R_nucleusZ < 1.0){
   if ((vtx->x-vesicle->nucleus_center[0])*(vtx->x-vesicle->nucleus_center[0])/vesicle->R_nucleusX + (vtx->y-vesicle->nucleus_center[1])*(vtx->y-vesicle->nucleus_center[1])/vesicle->R_nucleusY + (vtx->z-vesicle->nucleus_center[2])*(vtx->z-vesicle->nucleus_center[2])/vesicle->R_nucleusZ < 1.0){
//   if (SQ(vtx->x)/vesicle->R_nucleusX + SQ(vtx->y)/vesicle->R_nucleusY + SQ(vtx->z)/vesicle->R_nucleusZ < 1.0){
      vtx=memcpy((void *)vtx,(void *)&backupvtx[0],sizeof(ts_vertex));
      return TS_FAIL;
   }

}
#undef SQ
//#undef SQ
//self avoidance check with distant vertices
   cellidx=vertex_self_avoidance(vesicle, vtx);
   //check occupation number
@@ -111,7 +114,16 @@
      for(i=0;i<vtx->tristar_no;i++) darea-=vtx->tristar[i]->area;
    
    }

   //stretching energy 1 of 3
   if(vesicle->tape->stretchswitch==1){
      temp_area=vesicle->area;
      dstretchenergy-=stretchenergy2(vesicle->area,vesicle->tlist->a0*vesicle->tlist->n);
      for(i=0;i<vtx->tristar_no;i++){
         temp_area-=vtx->tristar[i]->area;
      }
      //0.5*vesicle->tape->xkA0*pow((vesicle->area-vesicle->tlist->a0*vesicle->tlist->n),2)/(vesicle->tlist->a0*vesicle->tlist->n);
      //for(i=0;i<vtx->tristar_no;i++) dstretchenergy-=vtx->tristar[i]->energy;
   }
    delta_energy=0;
    
//    vesicle_volume(vesicle);
@@ -187,6 +199,21 @@
    delta_energy+=delta_energy_cv;
//    fprintf(stderr,"Denergy after=%e\n",delta_energy);
    }
/* Vertices with spontaneous curvature may have spontaneous force perpendicular to the surface of the vesicle. additional delta energy is calculated in this function */
   delta_energy+=direct_force_energy(vesicle,vtx,backupvtx);

   //stretching energy 2 of 3
   if(vesicle->tape->stretchswitch==1){
      for(i=0;i<vtx->tristar_no;i++){
         temp_area+=vtx->tristar[i]->area; 
         }
      dstretchenergy+=stretchenergy2(temp_area,vesicle->tlist->a0*vesicle->tlist->n);
      dstretchenergy=0.5*vesicle->tape->xkA0*dstretchenergy;
		
   }

   delta_energy+=dstretchenergy;	
		
/* No poly-bond energy for now!
   if(vtx->grafted_poly!=NULL){
      delta_energy+=
@@ -196,6 +223,7 @@
*/
//   fprintf(stderr, "DE=%f\n",delta_energy);
    //MONTE CARLOOOOOOOO
//   if(vtx->c!=0.0) printf("DE=%f\n",delta_energy);
    if(delta_energy>=0){
#ifdef TS_DOUBLE_DOUBLE
        if(exp(-delta_energy)< drand48())
@@ -216,7 +244,13 @@
   
    //update the normals of triangles that share bead i.
   for(i=0;i<vtx->tristar_no;i++) triangle_normal_vector(vtx->tristar[i]);

/*   //stretching energy 3 of 3
   if(vesicle->tape->stretchswitch==1){
      for(i=0;i<vtx->tristar_no;i++){ 
         stretchenergy(vesicle,vtx->tristar[i]);
         }
   }
*/
//    fprintf(stderr, "before vtx(x,y,z)=%e,%e,%e\n",constvol_vtx_moved->x, constvol_vtx_moved->y, constvol_vtx_moved->z);
    if(vesicle->tape->constvolswitch == 1){
        constvolumerestore(constvol_vtx_moved,constvol_vtx_backup);
@@ -247,6 +281,10 @@
    if(vesicle->tape->constareaswitch==2){
        vesicle->area+=darea;
    }
   //stretching energy 3 of 3
   if(vesicle->tape->stretchswitch==1){
      vesicle->area=temp_area;
   }
//   if(oldcellidx);
    //END MONTE CARLOOOOOOO
//    vesicle_volume(vesicle);