493 lines
16 KiB
C++
493 lines
16 KiB
C++
/***************************************************************************
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TTrimSPDataHandler.cpp
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Author: Bastian M. Wojek
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e-mail: bastian.wojek@psi.ch
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2009/05/15
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***************************************************************************/
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/***************************************************************************
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* Copyright (C) 2009 by Bastian M. Wojek *
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* *
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* *
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* This program is free software; you can redistribute it and/or modify *
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* it under the terms of the GNU General Public License as published by *
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* the Free Software Foundation; either version 2 of the License, or *
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* (at your option) any later version. *
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* *
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* This program is distributed in the hope that it will be useful, *
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* but WITHOUT ANY WARRANTY; without even the implied warranty of *
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* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the *
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* GNU General Public License for more details. *
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* *
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* You should have received a copy of the GNU General Public License *
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* along with this program; if not, write to the *
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* Free Software Foundation, Inc., *
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* 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA. *
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***************************************************************************/
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#include "TTrimSPDataHandler.h"
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#include <iostream>
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#include <fstream>
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#include <string>
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#include <cmath>
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#include <cassert>
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#include <algorithm>
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using namespace std;
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//--------------------
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// Constructor of the TrimSPData class -- reading all available trim.SP-rge-files with a given name into std::vectors
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//--------------------
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TTrimSPData::TTrimSPData(const string &path, map<double, string> &energies, bool debug) {
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// sort the energies in ascending order - this might be useful for later applications (energy-interpolations etc.)
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// after the change from the vector to the map this is not necessary any more - since maps are always ordered!
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// sort(energies.begin(), energies.end());
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double zz(0.0), nzz(0.0);
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vector<double> vzz, vnzz;
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string word, energyStr;
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bool goodFile(false);
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for ( map<double, string>::const_iterator iter(energies.begin()); iter != energies.end(); ++iter ) {
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energyStr = path + iter->second + ".rge";
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ifstream *rgeFile = new ifstream(energyStr.c_str());
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if(! *rgeFile) {
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cerr << "TTrimSPData::TTrimSPData: file " << energyStr << " not found! Try next energy..." << endl;
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delete rgeFile;
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rgeFile = 0;
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} else {
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while(*rgeFile >> word) {
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if(word == "PARTICLES") {
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goodFile = true;
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break;
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}
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}
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if (goodFile) {
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fEnergy.push_back(iter->first);
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while(!rgeFile->eof()) {
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*rgeFile >> zz >> nzz;
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vzz.push_back(zz);
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vnzz.push_back(nzz);
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}
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fDZ.push_back(0.5*(vzz[2]-vzz[0])); // it happens that TRIM.SP uses different step sizes in one output file, therefore take the average
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while(zz < 2100.0){
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zz += fDZ.back();
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vzz.push_back(zz);
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vnzz.push_back(0.0);
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}
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fDataZ.push_back(vzz);
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fDataNZ.push_back(vnzz);
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rgeFile->close();
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delete rgeFile;
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rgeFile = 0;
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vzz.clear();
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vnzz.clear();
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goodFile = false;
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} else {
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cerr << "TTrimSPData::TTrimSPData: " << energyStr << " does not seem to be a valid unmodified TRIM.SP output file!" << endl;
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continue;
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}
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}
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}
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if (debug)
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cout << "TTrimSPData::TTrimSPData: Read in " << fDataNZ.size() << " implantation profiles in total." << endl;
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fOrigDataNZ = fDataNZ;
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for(unsigned int i(0); i<fEnergy.size();++i)
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fIsNormalized.push_back(false);
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fEnergyIter = fEnergy.end();
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}
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void TTrimSPData::UseHighResolution(double e) {
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fEnergyIter = find(fEnergy.begin(), fEnergy.end(), e);
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if(fEnergyIter != fEnergy.end()) {
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unsigned int i(fEnergyIter - fEnergy.begin());
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vector<double> vecZ;
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vector<double> vecNZ;
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for(double zz(1.); zz<2100.; zz+=1.) {
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vecZ.push_back(zz);
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vecNZ.push_back(GetNofZ(zz/10.0, e));
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}
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fDataZ[i] = vecZ;
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fDataNZ[i] = vecNZ;
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fOrigDataNZ[i] = vecNZ;
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fDZ[i] = 1.;
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fIsNormalized[i] = false;
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return;
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}
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cout << "TTrimSPData::DataZ: No implantation profile available for the specified energy... Nothing happens." << endl;
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return;
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}
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//---------------------
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// Method returning z-vector calculated by trim.SP for given energy[keV]
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//---------------------
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vector<double> TTrimSPData::DataZ(double e) const {
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fEnergyIter = find(fEnergy.begin(), fEnergy.end(), e);
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if(fEnergyIter != fEnergy.end()) {
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unsigned int i(fEnergyIter - fEnergy.begin());
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return fDataZ[i];
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}
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// default
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cout << "TTrimSPData::DataZ: No implantation profile available for the specified energy... You get back the first one." << endl;
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return fDataZ[0];
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}
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//---------------------
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// Method returning actual n(z)-vector calculated by trim.SP and
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// potentially altered by the WeightLayers- or the Normalize-method for given energy[keV]
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//---------------------
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vector<double> TTrimSPData::DataNZ(double e) const {
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fEnergyIter = find(fEnergy.begin(), fEnergy.end(), e);
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if(fEnergyIter != fEnergy.end()) {
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unsigned int i(fEnergyIter - fEnergy.begin());
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return fDataNZ[i];
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}
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// default
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cout << "TTrimSPData::DataNZ: No implantation profile available for the specified energy... You get back the first one." << endl;
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return fDataNZ[0];
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}
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//---------------------
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// Method returning original n(z)-vector calculated by trim.SP for given energy[keV]
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//---------------------
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vector<double> TTrimSPData::OrigDataNZ(double e) const {
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fEnergyIter = find(fEnergy.begin(), fEnergy.end(), e);
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if(fEnergyIter != fEnergy.end()) {
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unsigned int i(fEnergyIter - fEnergy.begin());
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return fOrigDataNZ[i];
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}
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// default
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cout << "TTrimSPData::OrigDataNZ: No implantation profile available for the specified energy... You get back the first one." << endl;
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return fOrigDataNZ[0];
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}
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//---------------------
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// Method returning fraction of muons implanted in the specified layer for a given energy[keV]
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// Parameters: Energy[keV], LayerNumber[1], Interfaces[nm]
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//---------------------
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double TTrimSPData::LayerFraction(double e, unsigned int layno, const vector<double>& interface) const {
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if(layno < 1 && layno > (interface.size()+1)) {
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cout << "TTrimSPData::LayerFraction: No such layer available according to your specified interfaces... Returning 0.0!" << endl;
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return 0.0;
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}
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fEnergyIter = find(fEnergy.begin(), fEnergy.end(), e);
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if(fEnergyIter != fEnergy.end()) {
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unsigned int i(fEnergyIter - fEnergy.begin());
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// Because we do not know if the implantation profile is normalized or not, do not care about this and calculate the fraction from the beginning
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// Total "number of muons"
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double totalNumber(0.0);
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for(unsigned int j(0); j<fDataZ[i].size(); j++)
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totalNumber += fDataNZ[i][j];
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// "number of muons" in layer layno
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double layerNumber(0.0);
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if(!(layno-1)){
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for(unsigned int j(0); j<fDataZ[i].size(); j++)
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if(fDataZ[i][j] < interface[0]*10.0)
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layerNumber += fDataNZ[i][j];
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} else if(!(layno-interface.size()-1)){
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for(unsigned int j(0); j<fDataZ[i].size(); j++)
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if(fDataZ[i][j] >= *(interface.end()-1)*10.0)
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layerNumber += fDataNZ[i][j];
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} else {
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for(unsigned int j(0); j<fDataZ[i].size(); j++)
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if(fDataZ[i][j] >= interface[layno-2]*10.0 && fDataZ[i][j] < interface[layno-1]*10.0)
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layerNumber += fDataNZ[i][j];
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}
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// fraction of muons in layer layno
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// cout << "Fraction of muons in layer " << layno << ": " << layerNumber/totalNumber << endl;
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return layerNumber/totalNumber;
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}
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// default
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cout << "TTrimSPData::LayerFraction: No implantation profile available for the specified energy... Returning 0.0" << endl;
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return 0.0;
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}
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//---------------------
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// Method putting different weight to different layers of your thin film
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// Parameters: Implantation Energy[keV], Interfaces[nm], Weights [0.0 <= w[i] <= 1.0]
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// Example: 25.0, (50, 100), (1.0, 0.33, 1.0)
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// at 25keV consider 3 layers, where the first ends after 50nm, the second after 100nm (these are NOT the layer thicknesses!!)
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// the first and last layers get the full n(z), where only one third of the muons in the second layer will be taken into account
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//---------------------
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void TTrimSPData::WeightLayers(double e, const vector<double>& interface, const vector<double>& weight) const {
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if(weight.size()-interface.size()-1) {
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cout << "TTrimSPData::WeightLayers: For the weighting the number of interfaces has to be one less than the number of weights!" << endl;
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cout << "TTrimSPData::WeightLayers: No weighting of the implantation profile will be done unless you take care of that!" << endl;
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return;
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}
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for(unsigned int i(0); i<interface.size(); i++) {
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if (interface[i]<0.0) {
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cout << "TTrimSPData::WeightLayers: One of your layer interfaces has a negative coordinate! - No weighting will be done!" << endl;
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return;
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}
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else if (i>1) {
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if (interface[i]<interface[i-1]) {
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cout << "TTrimSPData::WeightLayers: The specified interfaces appear to be not in ascending order! - No weighting will be done!" << endl;
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return;
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}
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}
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}
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for(unsigned int i(0); i<weight.size(); i++) {
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if (weight[i]>1.0 || weight[i]<0.0) {
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cout << "TTrimSPData::WeightLayers: At least one of the specified weights is out of range - no weighting will be done!" << endl;
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return;
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}
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}
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fEnergyIter = find(fEnergy.begin(), fEnergy.end(), e);
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// If all weights are equal to one, use the original n(z) vector
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for(unsigned int i(0); i<weight.size(); i++) {
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if(weight[i]-1.0)
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break;
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if(i == weight.size() - 1) {
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if(fEnergyIter != fEnergy.end()) {
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unsigned int j(fEnergyIter - fEnergy.begin());
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fDataNZ[j] = fOrigDataNZ[j];
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fIsNormalized[j] = false;
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return;
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}
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}
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}
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if(fEnergyIter != fEnergy.end()) {
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unsigned int i(fEnergyIter - fEnergy.begin());
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unsigned int k(0);
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for(unsigned int j(0); j<fDataZ[i].size(); j++) {
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if(k<interface.size()) {
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if(fDataZ[i][j] < interface[k]*10.0)
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fDataNZ[i][j] = fOrigDataNZ[i][j]*weight[k];
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else {
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k++;
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fDataNZ[i][j] = fOrigDataNZ[i][j]*weight[k];
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}
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}
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else
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fDataNZ[i][j] = fOrigDataNZ[i][j]*weight[k];
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}
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fIsNormalized[i] = false;
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return;
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}
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cout << "TTrimSPData::WeightLayers: No implantation profile available for the specified energy... No weighting done." << endl;
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return;
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}
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//---------------------
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// Method returning n(z) for given z[nm] and energy[keV]
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//---------------------
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double TTrimSPData::GetNofZ(double zz, double e) const {
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vector<double> z, nz;
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fEnergyIter = find(fEnergy.begin(), fEnergy.end(), e);
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if(fEnergyIter != fEnergy.end()) {
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unsigned int i(fEnergyIter - fEnergy.begin());
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z = fDataZ[i];
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nz = fDataNZ[i];
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} else {
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cout << "TTrimSPData::GetNofZ: No implantation profile available for the specified energy... Quitting!" << endl;
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exit(-1);
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}
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if(zz < 0)
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return 0.0;
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bool found = false;
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unsigned int i;
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for (i=0; i<z.size(); i++) {
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if (z[i]/10.0 >= zz) {
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found = true;
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break;
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}
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}
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if (!found)
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return 0.0;
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if (i == 0)
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return nz[0]*10.0*zz/z[0];
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return fabs(nz[i-1]+(nz[i]-nz[i-1])*(10.0*zz-z[i-1])/(z[i]-z[i-1]));
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}
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//---------------------
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// Method normalizing the n(z)-vector calculated by trim.SP for a given energy[keV]
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//---------------------
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void TTrimSPData::Normalize(double e) const {
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fEnergyIter = find(fEnergy.begin(), fEnergy.end(), e);
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if(fEnergyIter != fEnergy.end()) {
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unsigned int i(fEnergyIter - fEnergy.begin());
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double nZsum = 0.0;
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for (unsigned int j(0); j<fDataZ[i].size(); j++)
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nZsum += fDataNZ[i][j];
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nZsum *= fDZ[i];
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for (unsigned int j(0); j<fDataZ[i].size(); j++)
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fDataNZ[i][j] /= nZsum;
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fIsNormalized[i] = true;
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return;
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}
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// default
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cout << "TTrimSPData::Normalize: No implantation profile available for the specified energy... No normalization done." << endl;
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return;
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}
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//---------------------
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// Method telling you if the n(z)-vector calculated by trim.SP for a given energy [keV] has been normalized
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//---------------------
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bool TTrimSPData::IsNormalized(double e) const {
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fEnergyIter = find(fEnergy.begin(), fEnergy.end(), e);
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if(fEnergyIter != fEnergy.end()) {
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unsigned int i(fEnergyIter - fEnergy.begin());
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return fIsNormalized[i];
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}
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cout << "TTrimSPData::IsNormalized: No implantation profile available for the specified energy... Returning false! Check your code!" << endl;
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return false;
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}
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//---------------------
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// Calculate the mean range in (nm) for a given energy e
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//---------------------
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double TTrimSPData::MeanRange(double e) const {
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fEnergyIter = find(fEnergy.begin(), fEnergy.end(), e);
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if(fEnergyIter != fEnergy.end()) {
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unsigned int i(fEnergyIter - fEnergy.begin());
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if (!fIsNormalized[i])
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Normalize(e);
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double mean(0.0);
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for(unsigned int j(0); j<fDataNZ[i].size(); j++){
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mean += fDataNZ[i][j]*fDataZ[i][j];
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}
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mean *= fDZ[i]/10.0;
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return mean;
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}
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cout << "TTrimSPData::MeanRange: No implantation profile available for the specified energy... Returning -1! Check your code!" << endl;
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return -1.;
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}
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//---------------------
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// Find the peak range in (nm) for a given energy e
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//---------------------
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double TTrimSPData::PeakRange(double e) const {
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fEnergyIter = find(fEnergy.begin(), fEnergy.end(), e);
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if(fEnergyIter != fEnergy.end()) {
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unsigned int i(fEnergyIter - fEnergy.begin());
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vector<double>::const_iterator nziter;
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nziter = max_element(fDataNZ[i].begin(),fDataNZ[i].end());
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if(nziter != fDataNZ[i].end()){
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unsigned int j(nziter - fDataNZ[i].begin());
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return fDataZ[i][j]/10.0;
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}
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cout << "TTrimSPData::PeakRange: No maximum found in the implantation profile... Returning -1! Please check the profile!" << endl;
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return -1.;
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}
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cout << "TTrimSPData::PeakRange: No implantation profile available for the specified energy... Returning -1! Check your code!" << endl;
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return -1.;
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}
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//---------------------
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// Convolve the n(z)-vector calculated by trim.SP for a given energy e [keV] with a gaussian exp(-z^2/(2*w^2))
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// No normalization is done!
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//---------------------
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void TTrimSPData::ConvolveGss(double w, double e) const {
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if(!w)
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return;
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vector<double> z, nz, gss;
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double nn;
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fEnergyIter = find(fEnergy.begin(), fEnergy.end(), e);
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if(fEnergyIter != fEnergy.end()) {
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unsigned int i(fEnergyIter - fEnergy.begin());
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z = fDataZ[i];
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nz = fOrigDataNZ[i];
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for(unsigned int k(0); k<z.size(); k++) {
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gss.push_back(exp(-z[k]*z[k]/200.0/w/w));
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}
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for(unsigned int k(0); k<nz.size(); k++) {
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nn = 0.0;
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for(unsigned int j(0); j<nz.size(); j++) {
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nn += nz[j]*gss[abs(int(k)-int(j))];
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}
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fDataNZ[i][k] = nn;
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}
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fIsNormalized[i] = false;
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return;
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}
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cout << "TTrimSPData::ConvolveGss: No implantation profile available for the specified energy... No convolution done!" << endl;
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return;
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}
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