Gabriele Cosmo
305 lines
14 KiB
C++
305 lines
14 KiB
C++
//
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// ********************************************************************
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// * License and Disclaimer *
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// * *
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// * The Geant4 software is copyright of the Copyright Holders of *
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// * the Geant4 Collaboration. It is provided under the terms and *
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// * conditions of the Geant4 Software License, included in the file *
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// * LICENSE and available at http://cern.ch/geant4/license . These *
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// * include a list of copyright holders. *
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// * *
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// * Neither the authors of this software system, nor their employing *
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// * institutes,nor the agencies providing financial support for this *
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// * work make any representation or warranty, express or implied, *
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// * regarding this software system or assume any liability for its *
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// * use. Please see the license in the file LICENSE and URL above *
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// * for the full disclaimer and the limitation of liability. *
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// * *
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// * This code implementation is the result of the scientific and *
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// * technical work of the GEANT4 collaboration. *
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// * By using, copying, modifying or distributing the software (or *
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// * any work based on the software) you agree to acknowledge its *
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// * use in resulting scientific publications, and indicate your *
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// * acceptance of all terms of the Geant4 Software license. *
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// ********************************************************************
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//
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//
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/// \file DetectorConstruction.cc
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/// \brief Implementation of the DetectorConstruction class
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#include "DetectorConstruction.hh"
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#include "InformationKeeper.hh"
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#include "DetectorConstructionMessenger.hh"
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#include "G4SystemOfUnits.hh"
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#include "G4Region.hh"
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#include "G4ProductionCuts.hh"
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#include "G4UserLimits.hh"
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#include "G4NistManager.hh"
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#include "G4RunManager.hh"
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#include "G4UnionSolid.hh"
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#include "G4SubtractionSolid.hh"
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#include "G4Filesystem.hh"
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RunningMode gRunMode = RunningMode::Phys;
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//....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
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DetectorConstruction::DetectorConstruction(G4double factor, G4int verbose, G4bool isVisu) :
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G4VUserDetectorConstruction(), fFactor(factor), fVerbose(verbose), fBVisu(isVisu)
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{
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fDetectorMessenger = new DetectorConstructionMessenger(this);
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fWorldBoxSizeX = fWorldBoxSizeY = fWorldBoxSizeZ = 1*nm;
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if (gRunMode == RunningMode::Chem) fChemGeoImport = std::make_unique<ChemGeoImport>();
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}
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//....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
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G4VPhysicalVolume* DetectorConstruction::Construct()
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{
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G4NistManager * man = G4NistManager::Instance();
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fWater = man->FindOrBuildMaterial("G4_WATER");
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if (gRunMode == RunningMode::Phys) ConstructFullCellNucleusGeo();
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else if (gRunMode == RunningMode::Chem) ConstructVoxelGeo();
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else {
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// only a world volume
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G4ExceptionDescription msg;
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msg <<"Only world volume is constructed."
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<<" Make sure you choose the correct running mode."
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<<" Ignore this message if you intentionally test the code.";
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G4Exception("DetectorConstruction::Construct()",
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"", JustWarning, msg);
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fSolidWorld = new G4Box("solidWorld",fWorldBoxSizeX, fWorldBoxSizeY, fWorldBoxSizeZ);
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fLogicWorld = new G4LogicalVolume(fSolidWorld, fWater, "logicWorld");
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fPhysWorld = new G4PVPlacement(0,G4ThreeVector(),"physWorld",
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fLogicWorld, 0, false, false);
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}
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return fPhysWorld;
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}
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//....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
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G4VPhysicalVolume * DetectorConstruction::ConstructFullCellNucleusGeo()
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{
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PhysGeoImport geo(fBVisu);
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geo.SetFactor(fFactor);
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std::map<G4String, G4LogicalVolume*> voxelMap;
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// Create an empty logical nucleus
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G4LogicalVolume* logicNucleus = geo.CreateNucleusLogicVolume(fCellDefFilePath);
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if (!fUsingUserDefinedSizesForWorld) {
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G4double scale = 2.0;
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fWorldBoxSizeX = scale*geo.GetNucleusSizeData()["SemiX"];
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fWorldBoxSizeY = scale*geo.GetNucleusSizeData()["SemiY"];
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fWorldBoxSizeZ = geo.GetNucleusSizeData()["SemiZ"];
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}
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G4cout<<"===>>World box sizes: SemiX = "<<G4BestUnit(fWorldBoxSizeX,"Length")<<" , SemiY = "
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<<G4BestUnit(fWorldBoxSizeY,"Length")<<", SemiZ = "
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<<G4BestUnit(fWorldBoxSizeZ,"Length")<<"<<===="<<G4endl;
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fSolidWorld = new G4Box("solidWorld",fWorldBoxSizeX, fWorldBoxSizeY, fWorldBoxSizeZ);
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fLogicWorld = new G4LogicalVolume(fSolidWorld, fWater, "logicWorld");
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fPhysWorld = new G4PVPlacement(0,G4ThreeVector(),"physWorld", fLogicWorld, 0, false, false);
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// then place cell nucleus in world
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new G4PVPlacement(0, G4ThreeVector(), logicNucleus, "nucleus_pl", fLogicWorld, false, false);
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G4LogicalVolume* logicStraightVoxel{nullptr}, *logicUpVoxel{nullptr}, *logicDownVoxel{nullptr},
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*logicLeftVoxel{nullptr},*logicRightVoxel{nullptr};
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G4LogicalVolume* logicStraightVoxel2{nullptr},*logicUpVoxel2{nullptr},*logicDownVoxel2{nullptr}
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, *logicLeftVoxel2{nullptr},*logicRightVoxel2{nullptr};
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for (const auto & entry : fVoxelDefFilesList) {
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G4String name="";
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auto ptemp = geo.CreateLogicVolume(entry,name);
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if (name=="voxelStraight" || name=="VoxelStraight") {
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logicStraightVoxel = ptemp;
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voxelMap["VoxelStraight"] = logicStraightVoxel;
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}
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if (name=="voxelUp" || name=="VoxelUp") {
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logicUpVoxel = ptemp;
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voxelMap["VoxelUp"] = logicUpVoxel;
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}
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if (name=="voxelDown" || name=="VoxelDown") {
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logicDownVoxel = ptemp;
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voxelMap["VoxelDown"] = logicDownVoxel;
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}
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if (name=="voxelRight" || name=="VoxelRight") {
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logicRightVoxel = ptemp;
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voxelMap["VoxelRight"] = logicRightVoxel;
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}
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if (name=="voxelLeft" || name=="VoxelLeft") {
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logicLeftVoxel = ptemp;
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voxelMap["VoxelLeft"] = logicLeftVoxel;
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}
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if (name=="voxelStraight2" || name=="VoxelStraight2") {
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logicStraightVoxel2 = ptemp;
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voxelMap["VoxelStraight2"] = logicStraightVoxel2;
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}
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if (name=="voxelUp2" || name=="VoxelUp2") {
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logicUpVoxel2 = ptemp;
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voxelMap["VoxelUp2"] = logicUpVoxel2;
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}
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if (name=="voxelDown2" || name=="VoxelDown2") {
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logicDownVoxel2 = ptemp;
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voxelMap["VoxelDown2"] = logicDownVoxel2;
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}
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if (name=="voxelRight2" || name=="VoxelRight2") {
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logicRightVoxel2 = ptemp;
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voxelMap["VoxelRight2"] = logicRightVoxel2;
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}
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if (name=="voxelLeft2" || name=="VoxelLeft2") {
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logicLeftVoxel2 = ptemp;
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voxelMap["VoxelLeft2"] = logicLeftVoxel2;
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}
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}
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// Create the voxel data table
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std::vector<Voxel>* voxelTable = geo.CreateVoxelsData(fCellDefFilePath);
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const G4int nucleusSize = voxelTable->size();
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G4cout<<"============================================================================"<<G4endl;
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G4cout<<"=====> Number of Histones in each voxel: "<<G4endl;
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for (auto [key, value] : geo.GetVoxelNbHistoneMap()) {
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G4cout<<key<<": \t\t\t"<<value<<G4endl;
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}
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G4cout<<"=====> Number of Basepairs in each voxel: "<<G4endl;
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for (auto [key, value] : geo.GetVoxelNbBpMap()) {
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G4cout<<key<<": \t\t\t"<<value<<G4endl;
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}
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G4cout <<"=====> Total Number of Histones placed in geometry: \t"
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<<geo.GetTotalNbHistonePlacedInGeo()<<G4endl;
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G4cout <<"=====> Total Number of Basepairs placed in geometry: \t"
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<<geo.GetTotalNbBpPlacedInGeo()<<G4endl;
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G4cout <<"=====> Number of each chromatin type placed in geometry: "<<G4endl;
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for (auto [key, value] : geo.GetChromatinTypeCountMap()) {
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G4String chromatinname = "Heterochromatin";
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if (key == ChromatinType::fEuchromatin) chromatinname = "Euchromatin";
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G4cout<<chromatinname<<": \t\t\t"<<value<<G4endl;
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}
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G4cout<<"============================================================================"<<G4endl;
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// Create the voxel parameterisation
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if (voxelMap.size() > 0) {
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// The following dummy declarations are nescessary for SetLogicalVolum()
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// in VoxelParameterisation to prevent from coredump
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G4double prevZpos = -fWorldBoxSizeZ;
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for (auto it = voxelMap.begin(); it != voxelMap.end(); it++) {
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G4double posX = fWorldBoxSizeX - geo.GetVoxelFullSize();
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G4double posY = fWorldBoxSizeY - geo.GetVoxelFullSize();
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G4double posZ = prevZpos + geo.GetVoxelFullSize();
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new G4PVPlacement(0, G4ThreeVector(posX,posY,posZ),
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it->second, "xx", fLogicWorld, false, 0);
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}
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// End dummy declaration
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G4int nthreads=0;
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#ifdef G4MULTITHREADED
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nthreads = G4RunManager::GetRunManager()->GetNumberOfThreads();
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#endif
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if ( (nthreads >1) && (voxelMap.size() >1)) {
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G4ExceptionDescription msg;
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msg <<"Number of thread is "<<nthreads<<" > 1; Thus, dsbandrepair will run in testing mode. "
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<<"\nThere will be no DNA constituents placed inside Cell Nucleus!!!";
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G4Exception("DetectorConstruction::ConstructFullCellNucleusGeo",
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"RunningMode", JustWarning, msg);
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} else {
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G4VPVParameterisation* voxelParam = new VoxelParameterisation(voxelMap, voxelTable);
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new G4PVParameterised("VoxelParam", voxelMap.begin()->second,
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logicNucleus, kUndefined, nucleusSize, voxelParam);
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}
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} else {
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G4ExceptionDescription msg;
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msg <<"It seems that voxel-definition files are not provided."
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<<" There will be no DNA constituents placed inside Cell Nucleus!!!";
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G4Exception("DetectorConstruction::ConstructFullCellNucleusGeo",
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"Geo_InputFile_NoFile", JustWarning, msg);
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}
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InformationKeeper::Instance()->RecordVoxelDefFilesList(fVoxelDefFilesList);
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InformationKeeper::Instance()->SetTotalNbBpPlacedInGeo(geo.GetTotalNbBpPlacedInGeo());
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InformationKeeper::Instance()->SetTotalNbHistonePlacedInGeo(geo.GetTotalNbHistonePlacedInGeo());
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InformationKeeper::Instance()->SetNucleusVolume(geo.GetNucleusVolume());
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InformationKeeper::Instance()->SetNucleusMassDensity(
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logicNucleus->GetMaterial()->GetDensity()/(kg/m3)); // density in kg/m3;
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return fPhysWorld;
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}
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//....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
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G4VPhysicalVolume *DetectorConstruction::ConstructVoxelGeo()
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{
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if (fWorldBoxSizeX < fVoxelHalfSizeXYZ) {
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fWorldBoxSizeX = fWorldBoxSizeY = fWorldBoxSizeZ = fVoxelHalfSizeXYZ*1.1;
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}
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fSolidWorld = new G4Box("solidWorld", fWorldBoxSizeX, fWorldBoxSizeY, fWorldBoxSizeZ);
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fLogicWorld = new G4LogicalVolume(fSolidWorld, fWater, "logicWorld");
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fPhysWorld = new G4PVPlacement(0,G4ThreeVector(),"physWorld", fLogicWorld, 0, false, 0);
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if (fVoxelHalfSizeXYZ>0) {
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G4cout<<"=====> Construct voxel ........"<<G4endl;
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G4Box* solidVoxel = new G4Box("solidVoxel", fVoxelHalfSizeXYZ, fVoxelHalfSizeXYZ, fVoxelHalfSizeXYZ );
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G4LogicalVolume* logicVoxel = new G4LogicalVolume(solidVoxel, fWater, "logicVoxel");
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new G4PVPlacement(0, G4ThreeVector(), logicVoxel, "physVoxel", fLogicWorld, false, 0);
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}
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return fPhysWorld;
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}
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//....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
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void DetectorConstruction::SetCellDefFilePath(const G4String finput)
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{
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const G4fs::path thisP{std::string(finput)};
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G4fs::file_status fst = G4fs::file_status{};
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auto isExist = G4fs::status_known(fst) ? G4fs::exists(fst) : G4fs::exists(thisP);
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if (! isExist) {
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G4String msg = "File " + finput + "does not exist !!! ";
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G4Exception("DetectorConstruction::SetNucleusDefFilePath()",
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"Geo_InputFileNotOpened", FatalException, msg);
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} else {
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fCellDefFilePath = finput;
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InformationKeeper::Instance()->RecordCellDefFiliePath(fCellDefFilePath);
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}
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}
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//....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
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void DetectorConstruction::AddVoxelDefFile(const G4String finput)
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{
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const G4fs::path thisP{std::string(finput)};
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G4fs::file_status fst = G4fs::file_status{};
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auto isExist = G4fs::status_known(fst) ? G4fs::exists(fst) : G4fs::exists(thisP);
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if (! isExist) {
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G4String msg = "File " + finput + "does not exist !!! ";
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G4Exception("DetectorConstruction::AddVoxelDefFile()",
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"Geo_InputFileNotOpened", FatalException, msg);
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} else {
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fVoxelDefFilesList.insert(finput);
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}
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}
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//....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
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void DetectorConstruction::SetWorldBoxSizes(G4ThreeVector v)
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{
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G4double sizex = v.getX();
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G4double sizey = v.getY();
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G4double sizez = v.getZ();
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if (sizex > 0. && sizey > 0. && sizez > 0.) {
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fWorldBoxSizeX = sizex;
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fWorldBoxSizeY = sizey;
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fWorldBoxSizeZ = sizez;
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fUsingUserDefinedSizesForWorld = true;
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} else {
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G4ExceptionDescription msg ;
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msg << " Check your setting? One world dimensions is <= 0 !!! ";
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G4Exception("DetectorConstruction::SetWorldBoxSizes",
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"Geo_WorldSizes", FatalException, msg);
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}
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}
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//....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
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void DetectorConstruction::ParseGeoFileForChemMode(const G4String fn)
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{
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fChemGeoImport->ParseFiles(fn);
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fVoxelHalfSizeXYZ = fChemGeoImport->GetSize()/2.;
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} |