G4DNAMesh Class Reference

#include <G4DNAMesh.hh>

Inheritance diagram for G4DNAMesh:

Public Types
using	Box = G4DNABoundingBox
using	MolType = const G4MolecularConfiguration*
using	Data = std::map<MolType, size_t>
using	Voxel = std::tuple<Index, Box, Data>
using	IndexMap = std::unordered_map<Index, G4int, G4VDNAMesh::hashFunc>
using	VoxelVector = std::vector<Voxel>

Public Member Functions
	G4DNAMesh (const G4DNABoundingBox &, G4int)
	~G4DNAMesh () override
Index	GetIndex (const G4ThreeVector &position) const
Voxel &	GetVoxel (const Index &index)
size_t	size ()
Index	ConvertIndex (const Index &index, const G4int &) const
std::vector< Index >	FindNeighboringVoxels (const Index &index) const
void	Reset ()
Data &	GetVoxelMapList (const Index &index)
auto	end ()
auto	begin ()
VoxelVector::const_iterator	const_end () const
VoxelVector::const_iterator	const_begin () const
void	PrintMesh ()
void	PrintVoxel (const Index &index)
const G4DNABoundingBox &	GetBoundingBox () const
G4DNABoundingBox	GetBoundingBox (const Index &index)
G4int	GetNumberOfType (MolType type) const
void	InitializeVoxel (const Index &key, Data &&mapList)
G4double	GetResolution () const
Public Member Functions inherited from G4VDNAMesh
	G4VDNAMesh ()=default
virtual	~G4VDNAMesh ()=default

Detailed Description

Definition at line 41 of file G4DNAMesh.hh.

Member Typedef Documentation

Box

using G4DNAMesh::Box = G4DNABoundingBox

Definition at line 44 of file G4DNAMesh.hh.

Data

using G4DNAMesh::Data = std::map<MolType, size_t>

Definition at line 46 of file G4DNAMesh.hh.

IndexMap

using G4DNAMesh::IndexMap = std::unordered_map<Index, G4int, G4VDNAMesh::hashFunc>

Definition at line 48 of file G4DNAMesh.hh.

MolType

using G4DNAMesh::MolType = const G4MolecularConfiguration*

Definition at line 45 of file G4DNAMesh.hh.

Voxel

using G4DNAMesh::Voxel = std::tuple<Index, Box, Data>

Definition at line 47 of file G4DNAMesh.hh.

VoxelVector

using G4DNAMesh::VoxelVector = std::vector<Voxel>

Definition at line 49 of file G4DNAMesh.hh.

Constructor & Destructor Documentation

G4DNAMesh()

G4DNAMesh::G4DNAMesh	(	const G4DNABoundingBox &	boundingBox,
		G4int	pixel )

Definition at line 53 of file G4DNAMesh.cc.

  : fpBoundingMesh(&boundingBox)
  , fResolution((2 * boundingBox.halfSideLengthInY() / pixel))
{}

~G4DNAMesh()

G4DNAMesh::~G4DNAMesh ( )

override

Definition at line 58 of file G4DNAMesh.cc.

{ Reset(); }

Member Function Documentation

begin()

auto G4DNAMesh::begin ( )

inline

Definition at line 60 of file G4DNAMesh.hh.

{ return fVoxelVector.begin(); }

Referenced by G4DNAGillespieDirectMethod::CreateEvents().

const_begin()

VoxelVector::const_iterator G4DNAMesh::const_begin ( ) const

inline

Definition at line 62 of file G4DNAMesh.hh.

  {
    return fVoxelVector.begin();
  }

const_end()

VoxelVector::const_iterator G4DNAMesh::const_end ( ) const

inline

Definition at line 61 of file G4DNAMesh.hh.

{ return fVoxelVector.end(); }

ConvertIndex()

G4VDNAMesh::Index G4DNAMesh::ConvertIndex	(	const Index &	index,
		const G4int &	pixels ) const

Definition at line 213 of file G4DNAMesh.cc.

{
  G4int xmax = std::floor(
    (fpBoundingMesh->Getxhi() - fpBoundingMesh->Getxlo()) / fResolution);
  G4int ymax = std::floor(
    (fpBoundingMesh->Getyhi() - fpBoundingMesh->Getylo()) / fResolution);
  G4int zmax = std::floor(
    (fpBoundingMesh->Getzhi() - fpBoundingMesh->Getzlo()) / fResolution);
  auto dx = (G4int) (index.x * pixels / xmax);
  auto dy = (G4int) (index.y * pixels / ymax);
  auto dz = (G4int) (index.z * pixels / zmax);
  if(dx < 0 || dy < 0 || dz < 0)
  {
    G4ExceptionDescription exceptionDescription;
    exceptionDescription << "the old index: " << index
                         << "  to new index : " << Index(dx, dx, dx);
    G4Exception("G4DNAMesh::CheckIndex", "G4DNAMesh013", FatalErrorInArgument,
                exceptionDescription);
  }
  return Index{ dx, dy, dz };
}

end()

auto G4DNAMesh::end ( )

inline

Definition at line 59 of file G4DNAMesh.hh.

{ return fVoxelVector.end(); }

Referenced by G4DNAGillespieDirectMethod::CreateEvents().

FindNeighboringVoxels()

std::vector< G4DNAMesh::Index > G4DNAMesh::FindNeighboringVoxels

(

const Index &

index

)

const

Definition at line 144 of file G4DNAMesh.cc.

{
  std::vector<Index> neighbors;
  neighbors.reserve(6);
  auto xMax = (G4int) (std::floor(
    (fpBoundingMesh->Getxhi() - fpBoundingMesh->Getxlo()) / fResolution));
  auto yMax = (G4int) (std::floor(
    (fpBoundingMesh->Getyhi() - fpBoundingMesh->Getylo()) / fResolution));
  auto zMax = (G4int) (std::floor(
    (fpBoundingMesh->Getzhi() - fpBoundingMesh->Getzlo()) / fResolution));
 
  if(index.x - 1 >= 0)
  {
    neighbors.emplace_back(index.x - 1, index.y, index.z);
  }
  if(index.y - 1 >= 0)
  {
    neighbors.emplace_back(index.x, index.y - 1, index.z);
  }
  if(index.z - 1 >= 0)
  {
    neighbors.emplace_back(index.x, index.y, index.z - 1);
  }
  if(index.x + 1 < xMax)
  {
    neighbors.emplace_back(index.x + 1, index.y, index.z);
  }
  if(index.y + 1 < yMax)
  {
    neighbors.emplace_back(index.x, index.y + 1, index.z);
  }
  if(index.z + 1 < zMax)
  {
    neighbors.emplace_back(index.x, index.y, index.z + 1);
  }
 
  return neighbors;
}

GetBoundingBox() [1/2]

const G4DNABoundingBox & G4DNAMesh::GetBoundingBox

(

)

const

Definition at line 138 of file G4DNAMesh.cc.

{
  return *fpBoundingMesh;
}

Referenced by GetVoxel().

GetBoundingBox() [2/2]

G4DNABoundingBox G4DNAMesh::GetBoundingBox

(

const Index &

index

)

Definition at line 121 of file G4DNAMesh.cc.

{
  auto xlo = fpBoundingMesh->Getxlo() + index.x * fResolution;
  auto ylo = fpBoundingMesh->Getylo() + index.y * fResolution;
  auto zlo = fpBoundingMesh->Getzlo() + index.z * fResolution;
  auto xhi = fpBoundingMesh->Getxlo() + (index.x + 1) * fResolution;
  auto yhi = fpBoundingMesh->Getylo() + (index.y + 1) * fResolution;
  auto zhi = fpBoundingMesh->Getzlo() + (index.z + 1) * fResolution;
  return G4DNABoundingBox({ xhi, xlo, yhi, ylo, zhi, zlo });
}

GetIndex()

G4DNAMesh::Index G4DNAMesh::GetIndex

(

const G4ThreeVector &

position

)

const

Definition at line 185 of file G4DNAMesh.cc.

{
  if(!fpBoundingMesh->contains(position))
  {
    G4ExceptionDescription exceptionDescription;
    exceptionDescription << "the position: " << position
                         << " is not in the box : " << *fpBoundingMesh;
    G4Exception("G4DNAMesh::GetKey", "G4DNAMesh010", FatalErrorInArgument,
                exceptionDescription);
  }
 
  G4int dx =
    std::floor((position.x() - fpBoundingMesh->Getxlo()) / fResolution);
  G4int dy =
    std::floor((position.y() - fpBoundingMesh->Getylo()) / fResolution);
  G4int dz =
    std::floor((position.z() - fpBoundingMesh->Getzlo()) / fResolution);
  if(dx < 0 || dy < 0 || dz < 0)
  {
    G4ExceptionDescription exceptionDescription;
    exceptionDescription << "the old index: " << position
                         << "  to new index : " << Index(dx, dx, dx);
    G4Exception("G4DNAMesh::CheckIndex", "G4DNAMesh015", FatalErrorInArgument,
                exceptionDescription);
  }
  return Index{ dx, dy, dz };
}

GetNumberOfType()

G4int G4DNAMesh::GetNumberOfType

(

G4DNAMesh::MolType

type

)

const

Definition at line 84 of file G4DNAMesh.cc.

{
  G4int output = 0;
 
  for(const auto& iter : fVoxelVector)
  {
    auto data = std::get<2>(iter);
    auto it   = data.find(type);
    if(it != data.end())
    {
      output += it->second;
    }
  }
  return output;
}

GetResolution()

G4double G4DNAMesh::GetResolution

(

)

const

Definition at line 183 of file G4DNAMesh.cc.

{ return fResolution; }

GetVoxel()

G4DNAMesh::Voxel & G4DNAMesh::GetVoxel

(

const Index &

index

)

Definition at line 36 of file G4DNAMesh.cc.

{
  auto iter = fIndexMap.find(key);
  if(iter == fIndexMap.end())
  {
    auto box = GetBoundingBox(key);
    Data mapList;
    G4DNAMesh::Voxel& voxel =
      fVoxelVector.emplace_back(std::make_tuple(key, box, std::move(mapList)));
    fIndexMap[key] = G4int(fVoxelVector.size() - 1);
    return voxel;
  }
  
  auto index = fIndexMap[key];
  return fVoxelVector[index];
}

Referenced by G4DNAGillespieDirectMethod::CreateEvent(), GetVoxelMapList(), and InitializeVoxel().

GetVoxelMapList()

G4DNAMesh::Data & G4DNAMesh::GetVoxelMapList

(

const Index &

index

)

Definition at line 60 of file G4DNAMesh.cc.

{
  auto& pVoxel = GetVoxel(key);
  return std::get<2>(pVoxel);
}

Referenced by PrintVoxel().

InitializeVoxel()

void G4DNAMesh::InitializeVoxel	(	const Index &	key,
		Data &&	mapList )

Definition at line 115 of file G4DNAMesh.cc.

{
  auto& pVoxel        = GetVoxel(index);
  std::get<2>(pVoxel) = std::move(mapList);
}

PrintMesh()

void G4DNAMesh::PrintMesh

(

)

Definition at line 66 of file G4DNAMesh.cc.

{
  G4cout << "*********PrintMesh::Size : " << fVoxelVector.size() << G4endl;
  for(const auto& iter : fVoxelVector)
  {
    auto data = std::get<2>(iter);
    G4cout << "Index : " << std::get<0>(iter)
           << " number of type : " << std::get<2>(iter).size() << G4endl;
    for(const auto& it : data)
    {
      G4cout << "_____________" << it.first->GetName() << " : " << it.second
             << G4endl;
    }
    G4cout << G4endl;
  }
  G4cout << G4endl;
}

PrintVoxel()

void G4DNAMesh::PrintVoxel

(

const Index &

index

)

Definition at line 100 of file G4DNAMesh.cc.

{
  G4cout << "*********PrintVoxel::";
  G4cout << " index : " << index
         << " number of type : " << this->GetVoxelMapList(index).size()
         << G4endl;
 
  for(const auto& it : this->GetVoxelMapList(index))
  {
    G4cout << "_____________" << it.first->GetName() << " : " << it.second
           << G4endl;
  }
  G4cout << G4endl;
}

Referenced by G4DNAGillespieDirectMethod::CreateEvents().

Reset()

void G4DNAMesh::Reset

(

)

Definition at line 132 of file G4DNAMesh.cc.

{
  fIndexMap.clear();
  fVoxelVector.clear();
}

Referenced by ~G4DNAMesh().

size()

size_t G4DNAMesh::size ( )

inline

Definition at line 54 of file G4DNAMesh.hh.

{ return fVoxelVector.size(); };

---

The documentation for this class was generated from the following files:

• G4DNAMesh.hh
• G4DNAMesh.cc