Gabriele Cosmo
402 lines
12 KiB
C++
402 lines
12 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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* G4ReactionTableMessenger.cc
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*
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* Created on: Sep 14, 2015
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* Author: mkaramit
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*/
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#include <G4ReactionTableMessenger.hh>
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#include <G4DNAMolecularReactionTable.hh>
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#include <G4UIcmdWithAString.hh>
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#include <G4UIcmdWithADoubleAndUnit.hh>
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#include <G4UnitsTable.hh>
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#include <G4SystemOfUnits.hh>
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#include <G4UIcmdWithoutParameter.hh>
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//------------------------------------------------------------------------------
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G4ReactionTableMessenger::G4ReactionTableMessenger(G4DNAMolecularReactionTable* table) :
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G4UImessenger()
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{
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fpTable = table;
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fpNewDiffContReaction = new G4UIcmdWithAString("/chem/reaction/new", this);
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fpAddReaction = new G4UIcmdWithAString("/chem/reaction/add", this);
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// fpNewPartDiffContReactionByRadius =
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// new G4UIcmdWithAString("/chem/reaction/newPartDiffByRadius", this);
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//
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// fpNewPartDiffContReactionByReactionRate =
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// new G4UIcmdWithAString("/chem/reaction/newPartDiffByRate", this);
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fpPrintTable = new G4UIcmdWithoutParameter("/chem/reaction/print", this);
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}
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//------------------------------------------------------------------------------
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G4ReactionTableMessenger::~G4ReactionTableMessenger()
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{
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if(fpNewDiffContReaction) delete fpNewDiffContReaction;
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if(fpAddReaction) delete fpAddReaction;
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if(fpPrintTable) delete fpPrintTable;
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}
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//------------------------------------------------------------------------------
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void G4ReactionTableMessenger::SetNewValue(G4UIcommand* command,
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G4String newValue)
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{
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if(command == fpNewDiffContReaction)
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{
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std::istringstream iss(newValue);
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G4String species1;
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iss >> species1;
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G4String species2;
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iss >> species2;
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double reactionRate;
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iss >> reactionRate;
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// G4String reactionRateUnit;
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// iss >> reactionRateUnit;
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double dimensionedReactionRate = reactionRate * (1e-3 * m3 / (mole * s));
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// G4UIcmdWithADoubleAndUnit::ConvertToDimensionedDouble((reactionRate
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// + G4String(" ") + reactionRateUnit).c_str());
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G4DNAMolecularReactionData* reactionData =
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new G4DNAMolecularReactionData(dimensionedReactionRate,
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species1,
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species2);
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// G4String productionRate;
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// iss >> productionRate;
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//
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// if(productionRate != "" && productionRate != "X")
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// {
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// double prodRateReal = G4UIcommand::ConvertToDouble(productionRate);
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//
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// if(prodRateReal == 0 || isnan(prodRateReal))
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// {
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// G4Exception("G4ReactionTableMessenger",
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// "WRONG_PRODUCTION_RATE",
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// FatalException, "");
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// }
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//
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// double dimensionedProductionRate = prodRateReal
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// * (1e-3 * m3 / (mole * s));
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// reactionData->SetProductionRate(dimensionedProductionRate);
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// }
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while(iss.eof() == false)
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{
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G4String product;
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iss >> product;
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if(product != "")
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{
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reactionData->AddProduct(product);
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}
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else
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{
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break;
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}
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};
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fpTable->SetReaction(reactionData);
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}
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// else if(command == fpNewPartDiffContReactionByRadius)
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// {
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// std::istringstream iss(newValue);
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//
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// G4String species1;
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// iss >> species1;
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//
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// G4String species2;
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// iss >> species2;
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//
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// double reactionRate;
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// iss >> reactionRate;
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//
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//// G4String reactionRateUnit;
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//// iss >> reactionRateUnit;
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//
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//// G4String reactionRateUnit;
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//// iss >> reactionRateUnit;
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//
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// double reactionRadius;
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// iss >> reactionRadius;
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//
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//// G4String reactionRadiusUnit;
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//// iss >> reactionRadiusUnit;
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//
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// double dimensionedReactionRate = reactionRate * (1e-3 * m3 / (mole * s));
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//
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//// double dimensionedReactionRate =
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//// G4UIcmdWithADoubleAndUnit::ConvertToDimensionedDouble((reactionRate
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//// + " " + reactionRateUnit).c_str());
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//
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// double dimensionedReactionRadius = reactionRadius * nm;
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//// G4UIcmdWithADoubleAndUnit::ConvertToDimensionedDouble((reactionRadius
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//// + " " + reactionRadiusUnit).c_str());
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//
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// G4DNAMolecularReactionData* reactionData =
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// new G4DNAMolecularReactionData(dimensionedReactionRate,
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// species1,
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// species2);
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// reactionData->SetPartiallyDiffusionControlledReaction(dimensionedReactionRate,
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// dimensionedReactionRadius);
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//
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// while(iss.eof() == false)
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// {
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// G4String product;
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// iss >> product;
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//
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// if(product != "")
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// {
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// reactionData->AddProduct(product);
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// }
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// else
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// {
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// break;
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// }
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// }
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//
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// fpTable->SetReaction(reactionData);
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// }
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// else if(command == fpNewPartDiffContReactionByReactionRate)
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// {
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// std::istringstream iss(newValue);
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//
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// G4String species1;
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// iss >> species1;
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//
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// G4String species2;
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// iss >> species2;
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//
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// double reactionRate;
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// iss >> reactionRate;
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//
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// // G4String reactionRateUnit;
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// // iss >> reactionRateUnit;
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//
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// // G4String reactionRateUnit;
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// // iss >> reactionRateUnit;
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//
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// double activationRate;
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// iss >> activationRate;
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//
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// // G4String reactionRadiusUnit;
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// // iss >> reactionRadiusUnit;
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//
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// double dimensionedReactionRate = reactionRate * (1e-3 * m3 / (mole * s));
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//
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// double dimensionedActivationRate = activationRate
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// * (1e-3 * m3 / (mole * s));
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//
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// G4DNAMolecularReactionData* reactionData =
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// new G4DNAMolecularReactionData(dimensionedReactionRate,
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// species1,
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// species2);
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// reactionData->
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// SetPartiallyDiffusionControlledReactionByActivation(dimensionedReactionRate,
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// dimensionedActivationRate);
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//
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// while(iss.eof() == false)
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// {
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// G4String product;
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// iss >> product;
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//
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// if(product != "")
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// {
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// reactionData->AddProduct(product);
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// }
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// else
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// {
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// break;
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// }
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// }
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//
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// fpTable->SetReaction(reactionData);
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// }
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else if(command == fpPrintTable)
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{
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fpTable->PrintTable();
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}
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else if(command == fpAddReaction)
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{
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std::istringstream iss(newValue);
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//--------------------------------------------------------------------------
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// Reactants definition
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G4String species1;
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iss >> species1;
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G4String marker;
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iss >> marker; // peut etre +, ->, |
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G4String species2;
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if(marker == "+")
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{
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iss >> species2;
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iss >> marker; // peut etre ->, |
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}
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//--------------------------------------------------------------------------
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G4DNAMolecularReactionData* reactionData =
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new G4DNAMolecularReactionData(0,
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species1,
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species2);
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//fpTable->SetReaction(reactionData);
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//--------------------------------------------------------------------------
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// Add products
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if(marker == "->")
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{
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iss >> marker; // doit etre = species name
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while(marker!="|"
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//&& marker!=""
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&& iss.eof() == false
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)
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{
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G4cout << marker << G4endl;
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if(marker == "+")
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{
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iss >> marker; // doit etre species name
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continue;
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}
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reactionData->AddProduct(marker);
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iss >> marker; // peut etre species name, +, |
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};
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}
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// G4cout << "out of 1st loop" << G4endl;
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//--------------------------------------------------------------------------
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// Add reaction rate method
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G4String rateconst_method;
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iss >> rateconst_method;
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if(rateconst_method == "Fix")
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{
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iss >> marker; // must be |
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double reactionRate;
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iss >> reactionRate;
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double dimensionedReactionRate = reactionRate * (1e-3 * m3 / (mole * s));
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reactionData->SetObservedReactionRateConstant(dimensionedReactionRate);
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// G4String productionRate;
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// iss >> productionRate;
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//
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// if(productionRate != "" && productionRate != "X")
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// {
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// double prodRateReal = G4UIcommand::ConvertToDouble(productionRate);
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//
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// if(prodRateReal == 0 || isnan(prodRateReal))
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// {
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// G4Exception("G4ReactionTableMessenger",
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// "WRONG_PRODUCTION_RATE",
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// FatalException,
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// "");
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// }
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//
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// double dimensionedProductionRate = prodRateReal
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// * (1e-3 * m3 / (mole * s));
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// reactionData->SetProductionRate(dimensionedProductionRate);
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// }
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}
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else if(rateconst_method == "Arr")
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{
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iss >> marker; // must be |
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double A0 = 0;
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double E_R = 0;
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iss >> A0;
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iss >> E_R;
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reactionData->SetArrehniusParameterization(A0, E_R);
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}
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else if(rateconst_method == "Pol")
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{
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iss >> marker; // must be |
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std::vector<double> P = {0, 0, 0, 0, 0};
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size_t i = 0;
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while(i < 4) // could be changed to 5 only if marker is used as delimiter
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{
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double tmp;
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iss >> tmp;
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P[i] = tmp;
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// G4cout << newValue << G4endl;
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// G4cout << tmp << G4endl;
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// G4cout << P[i] << G4endl;
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++i;
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};
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reactionData->SetPolynomialParameterization(P);
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}
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else if(rateconst_method == "Scale")
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{
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iss >> marker; // must be |
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double temp_K;
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iss >> temp_K;
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double reactionRateCste;
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iss >> reactionRateCste;
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double dimensionedReactionRate = reactionRateCste * (1e-3 * m3 / (mole * s));
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reactionData->SetObservedReactionRateConstant(dimensionedReactionRate);
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reactionData->SetScaledParameterization(temp_K, dimensionedReactionRate);
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}
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// if(iss.eof() == false)
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// {
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// iss >> marker;
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//
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// if(marker == "|")
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// {
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// G4String productionRate ;
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// iss >> productionRate;
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//
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//// G4cout << productionRate << G4endl;
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//
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// double dimProductionRate = G4UIcommand::ConvertToDouble(productionRate)* (1e-3 * m3 / (mole * s));
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//
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// G4cout << " DIM PROD RATE = " << reactionData->GetReactant1()->GetName()
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// << " + " << reactionData->GetReactant2()->GetName() << " = " << dimProductionRate << G4endl;
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//
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// reactionData->SetProductionRate(dimProductionRate);
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// }
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// }
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fpTable->SetReaction(reactionData);
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// G4cout << "Reaction " << species1 << " + " << species2 << " added" << G4endl;
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}
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}
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