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