dnadamage2/include/PhysGeoImport.hh

0001 //
0002 // ********************************************************************
0003 // * License and Disclaimer                                           *
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0015 // * use.  Please see the license in the file  LICENSE  and URL above *
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0017 // *                                                                  *
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0019 // * technical work of the GEANT4 collaboration.                      *
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0023 // * acceptance of all terms of the Geant4 Software license.          *
0024 // ********************************************************************
0025 //
0026 // Authors: S. Meylan and C. Villagrasa (IRSN, France)
0027 // Update: H. Tran (IRSN, France) :20/12/2018
0028 //         J. Naoki D. Kondo (UCSF, US): 10/10/2021
0029 //
0030 /// \file PhysGeoImport.hh
0031 /// \brief Definition of the plasmid load methods for the geometry
0032
0033 #ifndef DNADAMAGE2_GeoImport_h
0034 #define DNADAMAGE2_GeoImport_h 1
0035
0036 #include "G4Box.hh"
0037 #include "G4Electron_aq.hh"
0038 #include "G4H2O.hh"
0039 #include "G4LogicalVolume.hh"
0040 #include "G4NistManager.hh"
0041 #include "G4Orb.hh"
0042 #include "G4PVPlacement.hh"
0043 #include "G4String.hh"
0044 #include "G4SubtractionSolid.hh"
0045 #include "G4SystemOfUnits.hh"
0046 #include "G4ThreeVector.hh"
0047 #include "G4VSolid.hh"
0048 #include "G4VisAttributes.hh"
0049
0050 #include <algorithm>
0051 #include <fstream>
0052 #include <map>
0053 #include <memory>
0054
0055 class G4VPhysicalVolume;
0056
0057 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
0058
0059 struct Molecule
0060 {
0061     Molecule(G4String name, G4int copyNumber, G4ThreeVector position, G4double radius,
0062              G4double waterRadius, std::string material, G4int strand)
0063     {
0064       fName = name;
0065       fMaterial = material;
0066       fCopyNumber = copyNumber;
0067       fPosition = position;
0068       fRadius = radius;
0069       fRadiusWater = waterRadius;
0070       fStrand = strand;
0071     }
0072
0073     G4String fName = "none";
0074     G4String fMaterial = "none";
0075
0076     G4int fCopyNumber = -1;
0077     G4int fStrand = -1;
0078
0079     G4ThreeVector fPosition = G4ThreeVector();
0080
0081     G4double fRadius = 1;
0082     G4double fRadiusWater = 1;
0083 };
0084
0085 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
0086
0087 class PhysGeoImport
0088 {
0089   public:
0090     PhysGeoImport();
0091     ~PhysGeoImport() = default;
0092
0093     G4LogicalVolume* CreateLogicVolumeXYZ(G4String fileName);
0094
0095     std::vector<G4String> GetMoleculesNames() { return fSampleDNANames; }
0096     std::vector<G4ThreeVector> GetMoleculesPositions() { return fSampleDNAPositions; }
0097     std::vector<std::vector<G4int>> GetMoleculesDetails() { return fSampleDNADetails; }
0098
0099   private:
0100     std::string fGeoName = "VoxelStraight";
0101
0102     std::map<G4String, G4double> fRadiusMap;
0103     std::map<G4String, G4double> fWaterRadiusMap;
0104
0105     std::vector<Molecule> fMolecules;
0106
0107     // Materials
0108     G4Material* fpWater = nullptr;
0109     G4Material* fEnvelopeWater = nullptr;
0110
0111     void ReadFile(G4String fileName);
0112
0113     G4double fOffsetX = 0;
0114     G4double fOffsetY = 0;
0115     G4double fOffsetZ = 0;
0116     G4double fXMin = 1000;
0117     G4double fXMax = -1000;
0118     G4double fYMin = 1000;
0119     G4double fYMax = -1000;
0120     G4double fZMin = 1000;
0121     G4double fZMax = -1000;
0122     std::ofstream fOutDNA;
0123
0124     std::vector<G4ThreeVector> fVertexes;
0125
0126     std::vector<G4String> fSampleDNANames;
0127     std::vector<G4ThreeVector> fSampleDNAPositions;
0128     std::vector<std::vector<G4int>> fSampleDNADetails;
0129 };
0130
0131 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
0132
0133 #endif