#include <G4DNAMesh.hh>

Public Types
using	Index = G4Voxel::Index

using	Key = unsigned int

using	VoxelMap = std::map< Key, G4Voxel * >

Public Member Functions
VoxelMap::iterator	begin ()

VoxelMap::const_iterator	begin () const

VoxelMap::iterator	end ()

VoxelMap::const_iterator	end () const

std::vector< Index >	FindNeighboringVoxels (const Index &index) const

std::vector< Index >	FindVoxelNeighbors (const Index &index) const

	G4DNAMesh (const G4DNABoundingBox &, G4int)

const G4DNABoundingBox &	GetBoundingBox () const

G4DNABoundingBox	GetBoundingBox (const Index &index)

Index	GetIndex (const G4ThreeVector &position) const

Index	GetIndex (const Index &index, int) const

Index	GetIndex (Key key) const

Key	GetKey (const G4ThreeVector &pos) const

Key	GetKey (const Index &index) const

G4int	GetNumberOfType (G4Voxel::MolType type) const

G4double	GetResolution () const

G4Voxel *	GetVoxel (const Index &index)

G4Voxel *	GetVoxel (Key key)

G4Voxel::MapList &	GetVoxelMapList (const Index &index)

G4Voxel::MapList &	GetVoxelMapList (Key key)

void	PrintMesh ()

void	PrintVoxel (const Index &index)

void	Reset ()

void	SetVoxelMapList (const Key &key, G4Voxel::MapList &&mapList)

size_t	size ()

	~G4DNAMesh ()

Private Attributes
VoxelMap	fMesh

const G4DNABoundingBox *	fpBoundingMesh

G4double	fResolution

Detailed Description

Definition at line 112 of file G4DNAMesh.hh.

Member Typedef Documentation

◆ Index

using G4DNAMesh::Index = G4Voxel::Index

Definition at line 115 of file G4DNAMesh.hh.

◆ Key

using G4DNAMesh::Key = unsigned int

Definition at line 116 of file G4DNAMesh.hh.

◆ VoxelMap

using G4DNAMesh::VoxelMap = std::map<Key, G4Voxel*>

Definition at line 117 of file G4DNAMesh.hh.

Constructor & Destructor Documentation

◆ G4DNAMesh()

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

Definition at line 30 of file G4DNAMesh.cc.

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

◆ ~G4DNAMesh()

G4DNAMesh::~G4DNAMesh ( )

Definition at line 35 of file G4DNAMesh.cc.

35{ Reset(); }

G4DNAMesh::Reset

void Reset()

Definition: G4DNAMesh.cc:198

References Reset().

Member Function Documentation

◆ begin() [1/2]

VoxelMap::iterator G4DNAMesh::begin ( )

inline

Definition at line 138 of file G4DNAMesh.hh.

138{ return fMesh.begin(); }

G4DNAMesh::fMesh

VoxelMap fMesh

Definition: G4DNAMesh.hh:152

References fMesh.

Referenced by G4DNAGillespieDirectMethod::Initialize().

◆ begin() [2/2]

VoxelMap::const_iterator G4DNAMesh::begin ( ) const

inline

Definition at line 140 of file G4DNAMesh.hh.

140{ return fMesh.begin(); }

References fMesh.

◆ end() [1/2]

VoxelMap::iterator G4DNAMesh::end ( )

inline

Definition at line 137 of file G4DNAMesh.hh.

137{ return fMesh.end(); }

References fMesh.

Referenced by G4DNAGillespieDirectMethod::Initialize().

◆ end() [2/2]

VoxelMap::const_iterator G4DNAMesh::end ( ) const

inline

Definition at line 139 of file G4DNAMesh.hh.

139{ return fMesh.end(); }

References fMesh.

◆ FindNeighboringVoxels()

std::vector< G4Voxel::Index > G4DNAMesh::FindNeighboringVoxels ( const Index & index ) const

Definition at line 276 of file G4DNAMesh.cc.

{
  std::vector<Index> neighbors;
  // auto key = GetKey(index);
  auto xMax = (int) (std::floor(
    (fpBoundingMesh->Getxhi() - fpBoundingMesh->Getxlo()) / fResolution));
  auto yMax = (int) (std::floor(
    (fpBoundingMesh->Getyhi() - fpBoundingMesh->Getylo()) / fResolution));
  auto zMax = (int) (std::floor(
    (fpBoundingMesh->Getzhi() - fpBoundingMesh->Getzlo()) / fResolution));
 
  if(index.x - 1 >= 0)
  {
    neighbors.emplace_back(Index(index.x - 1, index.y, index.z));
  }
  if(index.y - 1 >= 0)
  {
    neighbors.emplace_back(Index(index.x, index.y - 1, index.z));
  }
  if(index.z - 1 >= 0)
  {
    neighbors.emplace_back(Index(index.x, index.y, index.z - 1));
  }
  if(index.x + 1 < xMax)
  {
    neighbors.emplace_back(Index(index.x + 1, index.y, index.z));
  }
  if(index.y + 1 < yMax)
  {
    neighbors.emplace_back(Index(index.x, index.y + 1, index.z));
  }
  if(index.z + 1 < zMax)
  {
    neighbors.emplace_back(Index(index.x, index.y, index.z + 1));
  }
 
#ifdef DEBUG
  G4cout << "Neighbors of : " << index << G4endl;
  for(const auto& it : neighbors)
  {
    G4cout << it << G4endl;
  }
#endif
 
  if(neighbors.size() > 6)
  {
    G4ExceptionDescription exceptionDescription;
    exceptionDescription << "neighbors.size() > 6";
    G4Exception("G4DNAMesh::FindVoxelNeighbors", "G4DNAMesh002",
                FatalErrorInArgument, exceptionDescription);
  }
  return neighbors;
}

References FatalErrorInArgument, fpBoundingMesh, fResolution, G4cout, G4endl, G4Exception(), G4DNABoundingBox::Getxhi(), G4DNABoundingBox::Getxlo(), G4DNABoundingBox::Getyhi(), G4DNABoundingBox::Getylo(), G4DNABoundingBox::Getzhi(), G4DNABoundingBox::Getzlo(), G4Voxel::Index::x, G4Voxel::Index::y, and G4Voxel::Index::z.

Referenced by G4DNAGillespieDirectMethod::DiffusiveJumping().

◆ FindVoxelNeighbors()

std::vector< G4Voxel::Index > G4DNAMesh::FindVoxelNeighbors ( const Index & index ) const

Definition at line 232 of file G4DNAMesh.cc.

{
  std::vector<Index> neighbors;
 
  auto xMax = (int) (std::floor(
    (fpBoundingMesh->Getxhi() - fpBoundingMesh->Getxlo()) / fResolution));
  auto yMax = (int) (std::floor(
    (fpBoundingMesh->Getyhi() - fpBoundingMesh->Getylo()) / fResolution));
  auto zMax = (int) (std::floor(
    (fpBoundingMesh->Getzhi() - fpBoundingMesh->Getzlo()) / fResolution));
 
  auto xmin = (index.x - 1) < 0 ? 0 : (index.x - 1);
  auto ymin = (index.y - 1) < 0 ? 0 : (index.y - 1);
  auto zmin = (index.z - 1) < 0 ? 0 : (index.z - 1);
 
  auto xmax = (index.x + 1) > xMax ? xMax : (index.x + 1);
  auto ymax = (index.y + 1) > yMax ? yMax : (index.y + 1);
  auto zmax = (index.z + 1) > zMax ? zMax : (index.z + 1);
  for(int ix = xmin; ix <= xmax; ix++)
  {
    for(int iy = ymin; iy <= ymax; iy++)
    {
      for(int iz = zmin; iz <= zmax; iz++)
      {
        auto key = iz * yMax * xMax + iy * xMax + ix;
        if(GetIndex(key) != index)
        {  // deleting the middle element
          neighbors.push_back(GetIndex(key));
        }
      }
    }
  }
  if(neighbors.empty())
  {
    G4ExceptionDescription exceptionDescription;
    exceptionDescription << "neighbors.empty()";
    G4Exception("G4DNAMesh::FindVoxelNeighbors", "G4DNAMesh001",
                FatalErrorInArgument, exceptionDescription);
  }
 
  return neighbors;
}

References FatalErrorInArgument, fpBoundingMesh, fResolution, G4Exception(), GetIndex(), G4DNABoundingBox::Getxhi(), G4DNABoundingBox::Getxlo(), G4DNABoundingBox::Getyhi(), G4DNABoundingBox::Getylo(), G4DNABoundingBox::Getzhi(), G4DNABoundingBox::Getzlo(), G4Voxel::Index::x, G4Voxel::Index::y, and G4Voxel::Index::z.

◆ GetBoundingBox() [1/2]

const G4DNABoundingBox & G4DNAMesh::GetBoundingBox ( ) const

Definition at line 211 of file G4DNAMesh.cc.

{
  return *fpBoundingMesh;
}

References fpBoundingMesh.

Referenced by G4DNAGillespieDirectMethod::FindScavenging(), G4DNAGillespieDirectMethod::PropensityFunction(), SetVoxelMapList(), and G4DNAGillespieDirectMethod::VolumeOfNode().

◆ GetBoundingBox() [2/2]

G4DNABoundingBox G4DNAMesh::GetBoundingBox ( const Index & index )

Definition at line 152 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 });
}

References fpBoundingMesh, fResolution, G4DNABoundingBox::Getxlo(), G4DNABoundingBox::Getylo(), G4DNABoundingBox::Getzlo(), G4Voxel::Index::x, G4Voxel::Index::y, and G4Voxel::Index::z.

◆ GetIndex() [1/3]

G4Voxel::Index G4DNAMesh::GetIndex ( const G4ThreeVector & position ) const

Definition at line 129 of file G4DNAMesh.cc.

{
  int dx = std::floor((position.x() - fpBoundingMesh->Getxlo()) / fResolution);
  int dy = std::floor((position.y() - fpBoundingMesh->Getylo()) / fResolution);
  int dz = std::floor((position.z() - fpBoundingMesh->Getzlo()) / fResolution);
  assert(dx >= 0 && dy >= 0 && dz >= 0);
  return G4Voxel::Index{ dx, dy, dz };
}

References fpBoundingMesh, fResolution, G4DNABoundingBox::Getxlo(), G4DNABoundingBox::Getylo(), and G4DNABoundingBox::Getzlo().

◆ GetIndex() [2/3]

G4Voxel::Index G4DNAMesh::GetIndex	(	const Index &	index,
		int	pixels
	)		const

Definition at line 137 of file G4DNAMesh.cc.

{
  int xmax =
    std::floor((fpBoundingMesh->Getxhi() - fpBoundingMesh->Getxlo()) / fResolution);
  int ymax =
    std::floor((fpBoundingMesh->Getyhi() - fpBoundingMesh->Getylo()) / fResolution);
  int zmax =
    std::floor((fpBoundingMesh->Getzhi() - fpBoundingMesh->Getzlo()) / fResolution);
  int dx = (int) (index.x * pixels / xmax);
  int dy = (int) (index.y * pixels / ymax);
  int dz = (int) (index.z * pixels / zmax);
  assert(dx >= 0 && dy >= 0 && dz >= 0);
  return Index{ dx, dy, dz };
}

References fpBoundingMesh, fResolution, G4DNABoundingBox::Getxhi(), G4DNABoundingBox::Getxlo(), G4DNABoundingBox::Getyhi(), G4DNABoundingBox::Getylo(), G4DNABoundingBox::Getzhi(), G4DNABoundingBox::Getzlo(), G4Voxel::Index::x, G4Voxel::Index::y, and G4Voxel::Index::z.

◆ GetIndex() [3/3]

G4Voxel::Index G4DNAMesh::GetIndex ( Key key ) const

Definition at line 164 of file G4DNAMesh.cc.

{
  G4int xmax =
    std::floor((fpBoundingMesh->Getxhi() - fpBoundingMesh->Getxlo()) / fResolution);
  G4int ymax =
    std::floor((fpBoundingMesh->Getyhi() - fpBoundingMesh->Getylo()) / fResolution);
  G4int id = key;
  G4int x_ = id % xmax;
  id /= xmax;
  G4int y_ = id % ymax;
  id /= ymax;
  G4int z_ = id;
 
  if(xmax != ymax)
  {
    G4cout << xmax << " " << ymax << " " << key << G4endl;
    G4ExceptionDescription exceptionDescription;
    exceptionDescription << "xmax != ymax";
    G4Exception("G4DNAMesh::GetIndex", "G4DNAMesh006", FatalErrorInArgument,
                exceptionDescription);
  }
 
  if(x_ < 0 || y_ < 0 || z_ < 0)
  {
    G4cout << xmax << " " << ymax << " " << key << G4endl;
    G4cout << x_ << " " << y_ << " " << z_ << G4endl;
    G4ExceptionDescription exceptionDescription;
    exceptionDescription << "x_ < 0 || y_ < 0 || z_ < 0";
    G4Exception("G4DNAMesh::GetIndex", "G4DNAMesh005", FatalErrorInArgument,
                exceptionDescription);
  }
  return Index{ x_, y_, z_ };
}

References FatalErrorInArgument, fpBoundingMesh, fResolution, G4cout, G4endl, G4Exception(), G4DNABoundingBox::Getxhi(), G4DNABoundingBox::Getxlo(), G4DNABoundingBox::Getyhi(), and G4DNABoundingBox::Getylo().

Referenced by G4DNAGillespieDirectMethod::CreateEvent(), FindVoxelNeighbors(), G4DNAGillespieDirectMethod::Initialize(), and SetVoxelMapList().

◆ GetKey() [1/2]

G4DNAMesh::Key G4DNAMesh::GetKey ( const G4ThreeVector & pos ) const

Definition at line 332 of file G4DNAMesh.cc.

{
  if(!fpBoundingMesh->contains(position))
  {
    G4ExceptionDescription exceptionDescription;
    exceptionDescription << "the position: " << position
                         << " is not in the box";
    G4Exception("G4DNAMesh::GetKey", "G4DNAMesh010", FatalErrorInArgument,
                exceptionDescription);
  }
 
  auto dx = std::floor((position.x() - fpBoundingMesh->Getxlo()) / fResolution);
  auto dy = std::floor((position.y() - fpBoundingMesh->Getylo()) / fResolution);
  auto dz = std::floor((position.z() - fpBoundingMesh->Getzlo()) / fResolution);
  auto xmax =
    std::floor((fpBoundingMesh->Getxhi() - fpBoundingMesh->Getxlo()) / fResolution);
  auto ymax =
    std::floor((fpBoundingMesh->Getyhi() - fpBoundingMesh->Getylo()) / fResolution);
  return dz * ymax * xmax + dy * xmax + dx;
}

References G4DNABoundingBox::contains(), FatalErrorInArgument, fpBoundingMesh, fResolution, G4Exception(), G4DNABoundingBox::Getxhi(), G4DNABoundingBox::Getxlo(), G4DNABoundingBox::Getyhi(), G4DNABoundingBox::Getylo(), and G4DNABoundingBox::Getzlo().

Referenced by GetVoxel(), GetVoxelMapList(), and PrintVoxel().

◆ GetKey() [2/2]

G4DNAMesh::Key G4DNAMesh::GetKey ( const Index & index ) const

Definition at line 58 of file G4DNAMesh.cc.

{
  auto xmax = (unsigned int) (std::floor(
    (fpBoundingMesh->Getxhi() - fpBoundingMesh->Getxlo()) / fResolution));
  auto ymax = (unsigned int) (std::floor(
    (fpBoundingMesh->Getyhi() - fpBoundingMesh->Getylo()) / fResolution));
  return index.z * ymax * xmax + index.y * xmax + index.x;
}

References fpBoundingMesh, fResolution, G4DNABoundingBox::Getxhi(), G4DNABoundingBox::Getxlo(), G4DNABoundingBox::Getyhi(), G4DNABoundingBox::Getylo(), G4Voxel::Index::x, G4Voxel::Index::y, and G4Voxel::Index::z.

◆ GetNumberOfType()

G4int G4DNAMesh::GetNumberOfType ( G4Voxel::MolType type ) const

Definition at line 78 of file G4DNAMesh.cc.

{
  G4int output = 0;
  auto iter    = fMesh.begin();
  for(; iter != fMesh.end(); iter++)
  {
    auto node = dynamic_cast<G4Voxel*>(iter->second);
    if(node == nullptr)
    {
      continue;
    }
    auto it = node->GetMapList().find(type);
    if(it != node->GetMapList().end())
    {
      output += it->second;
    }
  }
  return output;
}

References fMesh, and G4Voxel::GetMapList().

Referenced by G4DNAUpdateSystemModel::UpdateSystem().

◆ GetResolution()

G4double G4DNAMesh::GetResolution ( ) const

Definition at line 330 of file G4DNAMesh.cc.

330{ return fResolution; }

References fResolution.

◆ GetVoxel() [1/2]

G4Voxel * G4DNAMesh::GetVoxel ( const Index & index )

Definition at line 226 of file G4DNAMesh.cc.

{
  return GetVoxel(GetKey(index));
}

References GetKey(), and GetVoxel().

◆ GetVoxel() [2/2]

G4Voxel * G4DNAMesh::GetVoxel ( Key key )

Definition at line 216 of file G4DNAMesh.cc.

{
  auto it = fMesh.find(key);
  if(it != fMesh.end())
  {
    return it->second;
  }
  return nullptr;
}

References fMesh.

Referenced by GetVoxel().

◆ GetVoxelMapList() [1/2]

G4Voxel::MapList & G4DNAMesh::GetVoxelMapList ( const Index & index )

Definition at line 52 of file G4DNAMesh.cc.

{
  auto key = GetKey(index);
  return GetVoxelMapList(key);
}

References GetKey(), and GetVoxelMapList().

◆ GetVoxelMapList() [2/2]

G4Voxel::MapList & G4DNAMesh::GetVoxelMapList ( Key key )

Definition at line 37 of file G4DNAMesh.cc.

{
  auto iter = fMesh.find(key);
  if(iter == fMesh.end())
  {
    G4Voxel::MapList maplist;
    SetVoxelMapList(key, std::move(maplist));
    return GetVoxelMapList(key);
  }
  else
  {
    return iter->second->GetMapList();
  }
}

References fMesh, GetVoxelMapList(), and SetVoxelMapList().

Referenced by G4DNAGillespieDirectMethod::ComputeNumberInNode(), G4DNAUpdateSystemModel::CreateMolecule(), GetVoxelMapList(), G4DNAUpdateSystemModel::JumpIn(), G4DNAUpdateSystemModel::JumpTo(), G4DNAUpdateSystemModel::KillMolecule(), PrintVoxel(), and G4DNAGillespieDirectMethod::PropensityFunction().

◆ PrintMesh()

void G4DNAMesh::PrintMesh ( )

Definition at line 67 of file G4DNAMesh.cc.

{
  G4cout << "*********PrintMesh::Size : " << fMesh.size() << G4endl;
  auto iter = fMesh.begin();
  for(; iter != fMesh.end(); iter++)
  {
    auto index = iter->second->GetIndex();
    PrintVoxel(index);
  }
  G4cout << G4endl;
}

References fMesh, G4cout, G4endl, and PrintVoxel().

◆ PrintVoxel()

void G4DNAMesh::PrintVoxel ( const Index & index )

Definition at line 98 of file G4DNAMesh.cc.

{
  G4cout << "*********PrintVoxel::";
  G4cout << "key: " << GetKey(index) << " 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;
}

References G4cout, G4endl, GetKey(), and GetVoxelMapList().

Referenced by G4DNAGillespieDirectMethod::Initialize(), and PrintMesh().

◆ Reset()

void G4DNAMesh::Reset ( )

Definition at line 198 of file G4DNAMesh.cc.

{
  if(fMesh.empty())
  {
    return;
  }
  for(auto iter : fMesh)  // should use smart ptr
  {
    delete iter.second;
  }
  fMesh.clear();
}

References fMesh.

Referenced by ~G4DNAMesh().

◆ SetVoxelMapList()

void G4DNAMesh::SetVoxelMapList	(	const Key &	key,
		G4Voxel::MapList &&	mapList
	)

Definition at line 113 of file G4DNAMesh.cc.

{
  auto index  = GetIndex(key);
  auto pVoxel = fMesh[key];
  if(nullptr == pVoxel)
  {
    pVoxel     = new G4Voxel(std::move(mapList), index, GetBoundingBox(index));
    fMesh[key] = pVoxel;
  }
  else
  {
    assert(pVoxel->GetMapList().empty());  // check if map list is empty
    pVoxel->SetMapList(std::move(mapList));
  }
}

References fMesh, GetBoundingBox(), and GetIndex().

Referenced by GetVoxelMapList().

◆ size()

size_t G4DNAMesh::size ( )

inline

Definition at line 127 of file G4DNAMesh.hh.

127{ return fMesh.size(); }

References fMesh.

Field Documentation

◆ fMesh

VoxelMap G4DNAMesh::fMesh

private

Definition at line 152 of file G4DNAMesh.hh.

Referenced by begin(), end(), GetNumberOfType(), GetVoxel(), GetVoxelMapList(), PrintMesh(), Reset(), SetVoxelMapList(), and size().

◆ fpBoundingMesh

const G4DNABoundingBox* G4DNAMesh::fpBoundingMesh

private

Definition at line 153 of file G4DNAMesh.hh.

Referenced by FindNeighboringVoxels(), FindVoxelNeighbors(), GetBoundingBox(), GetIndex(), and GetKey().

◆ fResolution

G4double G4DNAMesh::fResolution

private

Definition at line 154 of file G4DNAMesh.hh.

Referenced by FindNeighboringVoxels(), FindVoxelNeighbors(), GetBoundingBox(), GetIndex(), GetKey(), and GetResolution().

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

source/processes/electromagnetic/dna/utils/include/G4DNAMesh.hh
source/processes/electromagnetic/dna/utils/src/G4DNAMesh.cc

Public Types

Public Member Functions

Private Attributes

Detailed Description

Member Typedef Documentation

◆ Index

◆ Key

◆ VoxelMap

Constructor & Destructor Documentation

◆ G4DNAMesh()

◆ ~G4DNAMesh()

Member Function Documentation

◆ begin() [1/2]

◆ begin() [2/2]

◆ end() [1/2]

◆ end() [2/2]

◆ FindNeighboringVoxels()

◆ FindVoxelNeighbors()

◆ GetBoundingBox() [1/2]

◆ GetBoundingBox() [2/2]

◆ GetIndex() [1/3]

◆ GetIndex() [2/3]

◆ GetIndex() [3/3]

◆ GetKey() [1/2]

◆ GetKey() [2/2]

◆ GetNumberOfType()

◆ GetResolution()

◆ GetVoxel() [1/2]

◆ GetVoxel() [2/2]

◆ GetVoxelMapList() [1/2]

◆ GetVoxelMapList() [2/2]

◆ PrintMesh()

◆ PrintVoxel()

◆ Reset()

◆ SetVoxelMapList()

◆ size()

Field Documentation

◆ fMesh

◆ fpBoundingMesh

◆ fResolution