dnadamage2/include/PhysGeoImport.hh

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0025 //
0026 /// \file PhysGeoImport.hh
0027 /// \brief Definition of the PhysGeoImport class
0028 ///
0029 /// Definition of the plasmid load methods for the geometry
0030
0031
0032 // Authors: S. Meylan and C. Villagrasa (IRSN, France)
0033 // Update: H. Tran (IRSN, France) :20/12/2018
0034 //         J. Naoki D. Kondo (UCSF, US): 10/10/2021
0035 //
0036
0037 #ifndef DNADAMAGE2_GeoImport_h
0038 #define DNADAMAGE2_GeoImport_h 1
0039
0040 #include "G4Box.hh"
0041 #include "G4Electron_aq.hh"
0042 #include "G4H2O.hh"
0043 #include "G4LogicalVolume.hh"
0044 #include "G4NistManager.hh"
0045 #include "G4Orb.hh"
0046 #include "G4PVPlacement.hh"
0047 #include "G4String.hh"
0048 #include "G4SubtractionSolid.hh"
0049 #include "G4SystemOfUnits.hh"
0050 #include "G4ThreeVector.hh"
0051 #include "G4VSolid.hh"
0052 #include "G4VisAttributes.hh"
0053
0054 #include <algorithm>
0055 #include <fstream>
0056 #include <map>
0057 #include <memory>
0058
0059 class G4VPhysicalVolume;
0060
0061 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
0062
0063 struct Molecule
0064 {
0065     Molecule(G4String name, G4int copyNumber, G4ThreeVector position, G4double radius,
0066              G4double waterRadius, std::string material, G4int strand)
0067     {
0068       fName = name;
0069       fMaterial = material;
0070       fCopyNumber = copyNumber;
0071       fPosition = position;
0072       fRadius = radius;
0073       fRadiusWater = waterRadius;
0074       fStrand = strand;
0075     }
0076
0077     G4String fName = "none";
0078     G4String fMaterial = "none";
0079
0080     G4int fCopyNumber = -1;
0081     G4int fStrand = -1;
0082
0083     G4ThreeVector fPosition = G4ThreeVector();
0084
0085     G4double fRadius = 1;
0086     G4double fRadiusWater = 1;
0087 };
0088
0089 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
0090
0091 class PhysGeoImport
0092 {
0093   public:
0094     PhysGeoImport();
0095     ~PhysGeoImport() = default;
0096
0097     G4LogicalVolume* CreateLogicVolumeXYZ(G4String fileName);
0098
0099     std::vector<G4String> GetMoleculesNames() { return fSampleDNANames; }
0100     std::vector<G4ThreeVector> GetMoleculesPositions() { return fSampleDNAPositions; }
0101     std::vector<std::vector<G4int>> GetMoleculesDetails() { return fSampleDNADetails; }
0102
0103   private:
0104     std::string fGeoName = "VoxelStraight";
0105
0106     std::map<G4String, G4double> fRadiusMap;
0107     std::map<G4String, G4double> fWaterRadiusMap;
0108
0109     std::vector<Molecule> fMolecules;
0110
0111     // Materials
0112     G4Material* fpWater = nullptr;
0113     G4Material* fEnvelopeWater = nullptr;
0114
0115     void ReadFile(G4String fileName);
0116
0117     G4double fOffsetX = 0;
0118     G4double fOffsetY = 0;
0119     G4double fOffsetZ = 0;
0120     G4double fXMin = 1000;
0121     G4double fXMax = -1000;
0122     G4double fYMin = 1000;
0123     G4double fYMax = -1000;
0124     G4double fZMin = 1000;
0125     G4double fZMax = -1000;
0126     std::ofstream fOutDNA;
0127
0128     std::vector<G4ThreeVector> fVertexes;
0129
0130     std::vector<G4String> fSampleDNANames;
0131     std::vector<G4ThreeVector> fSampleDNAPositions;
0132     std::vector<std::vector<G4int>> fSampleDNADetails;
0133 };
0134
0135 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
0136
0137 #endif