Confinement planes, not debugged

Samo Penic

2018-09-23 267cf14b1ced6fce480e4292131a987a1802e28a

 src/vertexmove.c

@@ -1,3 +1,4 @@
/* vim: set ts=4 sts=4 sw=4 noet : */
#include<stdlib.h>
#include<math.h>
#include "general.h"
@@ -71,11 +72,23 @@

// TODO: Maybe faster if checks only nucleus-neighboring cells
// Nucleus penetration check:
   if (vtx->x*vtx->x + vtx->y*vtx->y + vtx->z*vtx->z < vesicle->R_nucleus){
//#define SQ(x) x*x
if(vesicle->R_nucleus>0.0){
   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 ((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
//self avoidance check with distant vertices
   cellidx=vertex_self_avoidance(vesicle, vtx);
   //check occupation number
@@ -86,7 +99,13 @@
        return TS_FAIL;
    } 
   
 
// plane confinement test
   if(vesicle->tape->plane_confinement_switch){
      if(vtx->z >= vesicle->confinement_plane.z_max || vtx->z <= vesicle->confinement_plane.z_min){
            vtx=memcpy((void *)vtx,(void *)&backupvtx[0],sizeof(ts_vertex));
            return TS_FAIL;
      }
   }
//if all the tests are successful, then energy for vtx and neighbours is calculated
   for(i=0;i<vtx->neigh_no;i++){
   memcpy((void *)&backupvtx[i+1],(void *)vtx->neigh[i],sizeof(ts_vertex));
@@ -176,6 +195,8 @@
    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);
/* No poly-bond energy for now!
   if(vtx->grafted_poly!=NULL){
      delta_energy+=
@@ -185,6 +206,17 @@
*/
//   fprintf(stderr, "DE=%f\n",delta_energy);
    //MONTE CARLOOOOOOOO
//   if(vtx->c!=0.0) printf("DE=%f\n",delta_energy);
// plane confinement
   if(vesicle->tape->plane_confinement_switch){
      //if planes are not close enough, then repusion force is on
      if(vesicle->confinement_plane.z_max-vesicle->confinement_plane.z_min > vesicle->tape->plane_d){	
         delta_energy+=vesicle->tape->plane_F * 1.0/( (backupvtx->z-vesicle->confinement_plane.z_min) + (backupvtx->z-vesicle->confinement_plane.z_max) );
         delta_energy+=-(vesicle->tape->plane_F * 1.0/( (vtx->z-vesicle->confinement_plane.z_min) + (vtx->z-vesicle->confinement_plane.z_max) ) );

      }
   }
// end plane confinement
    if(delta_energy>=0){
#ifdef TS_DOUBLE_DOUBLE
        if(exp(-delta_energy)< drand48())