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/// \file chem5.cc
/// \brief Main program of the dna/chem5 example

// This example is provided by the Geant4-DNA collaboration
// Any report or published results obtained using the Geant4-DNA software
// shall cite the following Geant4-DNA collaboration publication:
// Med. Phys. 37 (2010) 4692-4708
// J. Comput. Phys. 274 (2014) 841-882
// Phys. Med. Biol. 63(10) (2018) 105014-12pp
// The Geant4-DNA web site is available at http://geant4-dna.org
//
//

#include "ActionInitialization.hh"
#include "CommandLineParser.hh"
#include "DetectorConstruction.hh"
#include "PhysicsList.hh"

#include "G4DNAChemistryManager.hh"
#include "G4RunManagerFactory.hh"
#include "G4UIExecutive.hh"
#include "G4UImanager.hh"
#include "G4VisExecutive.hh"

/*
 * WARNING : Geant4 was initially not intended for this kind of application
 * This code is delivered as a prototype
 * We will be happy to hear from you, do not hesitate to send your feedback and
 * communicate on the difficulties you may encounter
 * The user interface may change in the next releases since a reiteration of the
 * code has started
 */

//....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......

using namespace G4DNAPARSER;
CommandLineParser* parser(nullptr);
long seed = 0;

unsigned int noise();
void SetSeed();

void Parse(int& argc, char** argv);

//....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......

int main(int argc, char** argv)
{
  // Parse options given in commandLine
  Parse(argc, argv);
  Command* commandLine(nullptr);
  SetSeed();

  // Construct the run manager according to whether MT is activated or not
  //
  auto* runManager = G4RunManagerFactory::CreateRunManager();

  if ((commandLine = parser->GetCommandIfActive("-mt"))) {
    G4int nThreads;
    if (commandLine->GetOption() == "NMAX") {
      nThreads = G4Threading::G4GetNumberOfCores();
      G4cout<<"nThreads : "<<nThreads<<G4endl;
    }
    else {
      nThreads = G4UIcommand::ConvertToInt(commandLine->GetOption());
    }

    runManager->SetNumberOfThreads(nThreads);
  }

  G4cout << "**************************************************************"
         << "******\n===== Chem5 is started with " << runManager->GetNumberOfThreads() << " of "
         << G4Threading::G4GetNumberOfCores()
         << " available threads =====\n\n*************************************"
         << "*******************************" << G4endl;

  // Set mandatory initialization classes
  runManager->SetUserInitialization(new PhysicsList());
  runManager->SetUserInitialization(new DetectorConstruction());
  runManager->SetUserInitialization(new ActionInitialization());

  // Initialize G4 kernel
  runManager->Initialize();

  // Initialize visualization
  G4VisManager* visManager = new G4VisExecutive();
  // G4VisExecutive can take a verbosity argument - see /vis/verbose guidance.
  // G4VisManager* visManager = new G4VisExecutive("Quiet");
  visManager->Initialize();

  // Get the pointer to the User Interface manager
  G4UImanager* UImanager = G4UImanager::GetUIpointer();
  G4UIExecutive* ui = nullptr;

  // interactive mode : define UI session
  if ((commandLine = parser->GetCommandIfActive("-gui"))) {
    ui = new G4UIExecutive(argc, argv, commandLine->GetOption());

    if (ui->IsGUI()) UImanager->ApplyCommand("/control/execute gui.mac");

    if (parser->GetCommandIfActive("-novis") == nullptr) {
      // visualization is used by default
      if ((commandLine = parser->GetCommandIfActive("-vis"))) {
        // select a visualization driver if needed (e.g. HepFile)
        UImanager->ApplyCommand(G4String("/vis/open ") + commandLine->GetOption());
      }
      else {
        // by default OGL is used
        UImanager->ApplyCommand("/vis/open OGL 800x600-0+0");
      }
      UImanager->ApplyCommand("/control/execute vis.mac");
    }
  }
  else {
    // to be use visualization file (= store the visualization into
    // an external file:
    // ASCIITree ;  DAWNFILE ; HepRepFile ; VRML(1,2)FILE ; gMocrenFile ...
    if ((commandLine = parser->GetCommandIfActive("-vis"))) {
      UImanager->ApplyCommand(G4String("/vis/open ") + commandLine->GetOption());
      UImanager->ApplyCommand("/control/execute vis.mac");
    }
  }

  if ((commandLine = parser->GetCommandIfActive("-mac"))) {
    G4String command = "/control/execute ";
    UImanager->ApplyCommand(command + commandLine->GetOption());
  }
  else {
    UImanager->ApplyCommand("/control/execute beam.in");
  }

  if ((commandLine = parser->GetCommandIfActive("-gui"))) {
    ui->SessionStart();
    delete ui;
  }

  // Job termination
  // Free the store: user actions, physics_list and detector_description are
  // owned and deleted by the run manager, so they should not be deleted
  // in the main() program !
  delete visManager;
  delete runManager;
  CommandLineParser::DeleteInstance();
  return 0;
}

//....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......

bool IsBracket(char c)
{
  switch (c) {
    case '[':
    case ']':
      return true;
    default:
      return false;
  }
}

//....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......

void SetSeed()
{
  Command* commandLine(nullptr);

  if ((commandLine = parser->GetCommandIfActive("-seed"))) {
    seed = atoi(commandLine->GetOption().c_str());
  }

  if (seed == 0)  // If no seed given in argument, setup the seed
  {
    long jobID_int = 0;
    long noice = 0;

    //____________________________________
    // In case on cluster
    if ((commandLine = parser->GetCommandIfActive("-cluster"))) {
      noice = labs((long)noise());

      const char* env = std::getenv("PBS_JOBID");

      if (env) {
        G4String buffer(env);
        G4String jobID_string = buffer.substr(0, buffer.find("."));
        jobID_string.erase(std::remove_if(jobID_string.begin(), jobID_string.end(), &IsBracket),
                           jobID_string.end());
        jobID_int = atoi(jobID_string.c_str());
      }
      else {
        env = std::getenv("SGE_TASK_ID");
        if (env) jobID_int = atoi(env);
      }
    }  // end cluster

    //____________________________________
    seed = ((long)time(NULL)) + jobID_int + noice;
  }

  G4cout << "Seed used : " << seed << G4endl;
  G4Random::setTheEngine(new CLHEP::MixMaxRng());
  G4Random::setTheSeed(seed);

  // Choose the Random engine
  // CLHEP::HepRandom::setTheEngine(new CLHEP::RanecuEngine);
}

//....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......

unsigned int noise()
{
#if defined(WIN32) || defined(_WIN32) || defined(__WIN32) && !defined(__CYGWIN__)
  // TODO: MS Win
  return std::time(0);
#else
  unsigned int random_seed, random_seed_a, random_seed_b;
  std::ifstream file("/dev/urandom", std::ios::binary);
  if (file.is_open()) {
    char* memblock;
    int size = sizeof(int);
    memblock = new char[size];
    file.read(memblock, size);
    file.close();
    random_seed_a = *reinterpret_cast<int*>(memblock);
    delete[] memblock;
  }  // end if
  else {
    random_seed_a = 0;
  }
  random_seed_b = std::time(nullptr);
  random_seed = random_seed_a xor random_seed_b;
  return random_seed;
#endif
}

//....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......

void Parse(int& argc, char** argv)
{
  //////////
  // Parse options given in commandLine
  //
  parser = CommandLineParser::GetParser();

  parser->AddCommand("-gui", Command::OptionNotCompulsory,
                     "Select geant4 UI or just launch a geant4 terminal"
                     "session",
                     "qt");

  parser->AddCommand("-mac", Command::WithOption, "Give a mac file to execute", "macFile.mac");

  parser->AddCommand("-seed", Command::WithOption, "Give a seed value in argument to be tested",
                     "seed");

  parser->AddCommand("-mt", Command::WithOption,
                     "Launch in MT mode (events computed in parallel,"
                     " NOT RECOMMANDED WITH CHEMISTRY)",
                     "2");

  parser->AddCommand("-chemOFF", Command::WithoutOption, "Deactivate chemistry");

  parser->AddCommand("-vis", Command::WithOption, "Select a visualization driver",
                     "OGL 600x600-0+0");

  parser->AddCommand("-novis", Command::WithoutOption, "Deactivate visualization when using GUI");

  parser->AddCommand("-cluster", Command::WithoutOption,
                     "Launch the code on a cluster, avoid dupplicated seeds");

  //////////
  // If -h or --help is given in option : print help and exit
  //
  if (parser->Parse(argc, argv) != 0)  // help is being printed
  {
    // if you are using ROOT, create a TApplication in this condition in order
    // to print the help from ROOT as well
    CommandLineParser::DeleteInstance();
    std::exit(0);
  }

  ///////////
  // Kill application if wrong argument in command line
  //
  if (parser->CheckIfNotHandledOptionsExists(argc, argv)) {
    // if you are using ROOT, you should initialise your TApplication
    // before this condition
    std::exit(0);
  }
}
