/
particle.cc
1429 lines (1133 loc) · 62.6 KB
/
particle.cc
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/**
* @file particle.cc
* @author Luca Maccione, Daniele Gaggero
* @email luca.maccione@desy.de
* @email daniele.gaggero@sissa.it
* @brief Implementation of TParticle class. See the .h file
*/
#include "constants.h"
#include "geometry.h"
#include "particle.h"
#include "galaxy.h"
#include "eloss.h"
#include "xsec.h"
#include "crevolutor.h"
#include "grid.h"
#include "gas.h"
#include "input.h"
#include "spectrum.h"
#include "errorcode.h"
#include "diffusion.h"
#ifdef HAVE_ROOT
#include "TFile.h"
#include "TNtupleD.h"
#include "TString.h"
#endif
using namespace std;
vector<double> TParticle::GetEnergyGrid() const {
return _fGalaxy->GetCoordinates()->GetEk();
}
TParticle::TParticle(int A_ /**< Mass number */, int Z_ /**< Charge */, Galaxy* gal /**< A model for the galaxy */, Input* in_ /**< User input */, bool issec_, vector<TXSecBase*> xsecmodel, TNucleiList* l, int K_electron_, bool isDM_, bool isextra, bool isTPP_) :
A(A_),
Z(Z_),
uid(1000*Z_+A_),
dimz(gal->GetCoordinates()->GetDimZ()),
dimE(gal->GetCoordinates()->GetDimE()),
K_electron(K_electron_) {
in = in_;
if (in->feedback >1) cout << endl;
if (in->feedback >1) cout << "********************************************" << endl;
if (in->feedback >1) cout << "*** Welcome to the Particle constructor! ***" << endl;
if (in->feedback >1) cout << "********************************************" << endl << endl;
if (in->DiffT == Anisotropic) {
_fDiff = new TDiffusionCoefficient3D(gal->GetCoordinates(), in, gal->GetSource(), gal->GetBField(), gal->GetGeometry(), A, Z, (A==0));
vector<double> momentum = (A!=0) ? gal->GetCoordinates()->GetMomentum() : gal->GetCoordinates()->GetMomentumEl();
_fDpp = new TReaccelerationCoefficient(momentum, _fDiff, gal->GetGeometry(), in);
}
else {
_fDiff = NULL;
_fDpp = NULL;
}
isDM = isDM_;
if (in->feedback >0) cout<<"... checking IsDM? "<<isDM<<endl;
//modified
issec = issec_;
isExtra = isextra;
if (in->feedback >0) cout<<"... checking IsEXTRA? "<<isExtra<<endl;
isTPP = isTPP_;
_fGalaxy = gal;
decmode = l->GetDecayMode(uid);
lifetime = l->GetLifeTime(uid)/M_LN2;
// possible decay modes ----- DG 24.10.2013 - SK 07.11.2013 ------------------------------------------------------
if (decmode == BP) daughter = 1000*(Z-1)+A;
else if (decmode == BM) {
if ((Z == 14 && A == 32) || (Z == 18 && A ==42)) daughter = 1000*(Z+2)+A; //double beta- for these isotopes
else daughter = 1000*(Z+1)+A;
// 32Si --> 32P (14 yr) --> 32S || 42Ar(2b-)42Ca 100% Ar-K -Ca
}
else if (decmode == EC) {
if (K_electron <= 0) {
lifetime = -1.; // If the nucleus is unstable for EC the "naked" version of these isotopes does not decay
daughter = 0;
}
else { //modified
lifetime = l->GetLifeTime(uid)/M_LN2; // If the nucleus is unstable for EC the decay may happen only after it has attached an electron
daughter = 1000*(Z-1)+A;
}
}
else if (decmode == ECBM) {
if (K_electron <= 0) {
lifetime = l->GetLifeTime_naked(uid)/M_LN2;; // Beta- decay is possible for the naked nucleus
daughter = 1000*(Z+1)+A;
}
else { //modified
lifetime = l->GetLifeTime(uid)/M_LN2; // If the nucleus is unstable for EC the decay may happen only after it has attached an electron
daughter = 1000*(Z-1)+A;
}
}
else if (decmode == ECBP) {
if (K_electron <= 0) {
lifetime = l->GetLifeTime_naked(uid)/M_LN2;; // Beta+ decay is possible for the naked nucleus
daughter = 1000*(Z-1)+A;
if(Z == 28 && A == 56) daughter = 1000*(Z-2)+A; //56Ni makes a double Beta+ decay
}
else { //modified
lifetime = l->GetLifeTime(uid)/M_LN2; // If the nucleus is unstable for EC the decay may happen only after it has attached an electron
daughter = 1000*(Z-1)+A;
}
}
else daughter = 0;
//-----------------------------------------------------------------------------------------------------------------
if(!in->RDECAY){ //fk 130701
lifetime = -1; // -1 means stable!
daughter =0;
if (in->feedback >1) cout << "Radioactive Decay is turned off so every nucleus is stable!" << endl;
}
if (in->feedback >1) cout << "Computing spectrum " << endl;
if (issec) sp = new TSpectrum(gal->GetCoordinates()); // Secondary particles
else {
if (!isDM) {
if (isExtra) sp = new TSpectrum(gal->GetCoordinates(), in, gal->GetInjSpectrum_rho(1000), gal->GetInjSpectrum_alpha(1000), in->cutoff_rig, true, true); // Standard EXTRA component particles
else {
//sp = new TSpectrum(gal->GetCoordinates(), in, gal->GetInjSpectrum(uid), gal->GetInjLowSpectrum(uid), (A==0)); // Standard particles
sp = new TSpectrum(gal->GetCoordinates(), in, gal->GetInjSpectrum_rho(uid), gal->GetInjSpectrum_alpha(uid), in->cutoff_rig, (A==0), false); // Standard particles
}
}
else {
if (in->feedback >1) cout << "Particles coming from DM. Building spectrum..." << endl;
// DM particles
if (in->DMs == EWCorrections) sp = new TSpectrum(gal->GetCoordinates(), in, int(in->mx), in->dmmode, (A==0)*151 + (A==1)*154);
else if (in->DMs == DarkSUSY || in->DMs == Delta) sp = new TSpectrum(gal->GetCoordinates(), in, (A==0)*151 + (A==1)*154);
else if (in->DMs == SelfTable) {
if (in->feedback >1) cout << "Particles coming from DM. Getting datafile with inj spectrum specified by the user... " << endl;
if (A==0) //Electrons and Positrons from DM annihilation/decay
sp = new TSpectrum(gal->GetCoordinates(), in, in->MySelfTableDMel, 0);
if (A==1 && Z==-1) //Antiprotons from DM annihilation/decay
sp = new TSpectrum(gal->GetCoordinates(), in, in->MySelfTableDMap, 0);
if (A==2 && Z==-1)
sp = new TSpectrum(gal->GetCoordinates(), in, in->MySelfTableDMdbar, 0);
}
}
}
eloss.push_back(new TIonizationLoss(gal->GetCoordinates(), gal->GetGas(), gal->GetTotalGas(), in, A, Z));
eloss.push_back(new TCoulombLoss(gal->GetCoordinates(), gal->GetGas(), in, A, Z));
if (in->feedback >1) cout << "[debug] elosses - Bremsstrahlung" << endl;
if (A == 0) {
eloss.push_back(new TBremsstrahlungLoss(gal->GetCoordinates(), gal->GetGas(), gal->GetTotalGas(), in));
if (in->feedback >1) cout << "[debug] elosses - Synchrotron" << endl;
eloss.push_back(new TSynchrotronLoss(gal->GetCoordinates(), gal->GetBField(), in));
if (in->feedback >1) cout << "[debug] elosses - Inverse Compton" << endl;
eloss.push_back(new TICSLoss(gal->GetCoordinates(), gal->GetISRF(), in));
}
if (in->feedback >0) cout<<"... energy losses done!"<<endl;
_fInXSec = new TInelasticCrossSection(gal->GetCoordinates(), in, uid, K_electron, xsecmodel); //modified
if (in->feedback >0) cout << "... inelastic Cross Sections done!" << endl;
if (in->feedback >1) cout << "End of constructor " << endl;
}
/**< The constructor normally used in DRAGON */
//modified
TParticle::TParticle(TParticle& part) :
A(part.A),
Z(part.Z),
uid(part.uid),
dimz(part.dimz),
dimE(part.dimE),
daughter(part.daughter),
lifetime(part.lifetime),
isExtra(part.isExtra),
isTPP(part.isTPP),
isDM(part.isDM),
decmode(part.decmode) {
_fGalaxy = part._fGalaxy;
_fDiff = part._fDiff;
_fDpp = part._fDpp;
_fInXSec = part._fInXSec;
eloss = part.eloss;
density = part.density;
sp = part.sp;
issec = part.issec;
K_electron = part.K_electron; //modified
in = part.in;
}
TParticle::~TParticle() {
if (sp) delete sp;
if (_fInXSec) delete _fInXSec;
for (vector<TEnergyLoss*>::iterator i = eloss.begin(); i != eloss.end(); ++i) {
if (*i) delete *i;
}
eloss.clear();
density.clear();
}
void TParticle::Evolve(vector<TParticle*> part, vector<TCREvolutorBasis*> crev_, TSpallationNetwork* spnet, vector<TXSecBase*> xsecmodel, bool isSecondIteration) {
if (isSecondIteration)
if (in->feedback >1) cout << "This is the SECOND ITERATION " << endl;
TEnergyLoss el(*(eloss.front()));
for (vector<TEnergyLoss*>::iterator i = eloss.begin()+1; i != eloss.end(); ++i) el += (*(*i));
if(!in->ELOSS) el.Set_dpdt_Zero(); //fk 130701
//modified
if (in->feedback >1) cout << "We are building the secondary source term " << endl;
const vector<double> secsource = ComputeSecondarySource(part, spnet, xsecmodel);
if (in->DiffT == Isotropic) {
for (vector<TCREvolutorBasis*>::iterator crev = crev_.begin(); crev != crev_.end(); ++crev) (*crev)->Run(density, density_previous, _fInXSec, el.GetDpdt(), secsource, sp->GetSpectrum(), double(A), double(Z), lifetime, daughter, bool(issec), K_electron, isDM, isExtra); //modified
}
else {
for (vector<TCREvolutorBasis*>::iterator crev = crev_.begin(); crev != crev_.end(); ++crev) (*crev)->Run(density, density_previous, _fInXSec, el.GetDpdt(), secsource, sp->GetSpectrum(), _fDiff, _fDpp, double(A), double(Z), lifetime, daughter, bool(issec), K_electron, isDM, isExtra, _fGalaxy); //modified
}
return ;
}
/**< The constructor normally used in DRAGON */
TParticle2D::TParticle2D(int A_ /**< Mass number */, int Z_ /**< Charge */, Galaxy* gal /**< A model for the galaxy */, Input* in /**< User input */, bool uid_prec, vector<TXSecBase*> xsecmodel, TNucleiList* l, int K_electron_, bool isDM, bool isextra,bool isTPP) :
TParticle(A_, Z_, gal, in, uid_prec, xsecmodel, l, K_electron_, isDM, isextra,isTPP),
dimr(gal->GetCoordinates()->GetDimR()) {
density = vector<double>(dimr*dimz*dimE, 0.0);
}
double TParticle2D::FindNormalization(const double& normrig, const double& normval) {
if (!(uid == 1001 || uid == -1000)) {
cerr << "Asking for normalization but no protons nor primary electrons found" << endl;
exit(NOPROTELNORM);
}
vector<double> r = _fGalaxy->GetCoordinates()->GetR();
unsigned int irsun = (unsigned int) ((in->robs-r.front())/(r.back()-r.front())*(double)(dimr-1));
vector<double> z = _fGalaxy->GetCoordinates()->GetZ();
vector<double> Ek = _fGalaxy->GetCoordinates()->GetEk();
unsigned int izsun = (unsigned int) ((in->zobs-z.front())/(z.back()-z.front())*(double)(dimz-1));
if (in->feedback >1) cout << "irsun = " << irsun << " izsun = " << izsun << endl;
for (int ind = 0; ind < Ek.size(); ind++)
if (in->feedback >1) cout << "spectrum at irsun, izsun = " << density[TParticle::index(irsun,izsun,ind)] << endl;
double r1 = (r[irsun+1]-in->robs)/(r[irsun+1]-r[irsun]);
double r2 = (in->robs-r[irsun])/(r[irsun+1]-r[irsun]);
int ilow = int(log(normrig/Ek[0])/log(Ek[1]/Ek[0]));
if (in->feedback >1) cout << "energy index = " << ilow << endl;
double valuelow = log10( (density[TParticle::index(irsun,izsun,ilow)]*r1+density[TParticle::index(irsun+1,izsun,ilow)]*r2) );
double valuehigh = log10( (density[TParticle::index(irsun,izsun,ilow+1)]*r1+density[TParticle::index(irsun+1,izsun,ilow+1)]*r2) );
if (in->feedback >1) cout << "valuelow and valuehigh " << valuelow << " " << valuehigh << endl;
double e1 = log(Ek[ilow+1]/normrig)/log(Ek[ilow+1]/Ek[ilow]);
double e2 = log(normrig/Ek[ilow])/log(Ek[ilow+1]/Ek[ilow]);
double value = pow(10,valuelow*e1 + valuehigh*e2);
double factor = normval/value;
//cout << value << " " << inp->spect_norm << endl;
//cout << factor << " " << factorint << " comparison of interpolation." << endl;
//cout << "Normalization required in the xml: " << inp->spect_norm << endl;
if (in->feedback >1) cout << "Reference value in arbitrary units = " << value << "; Normalization factor = " << factor << endl << endl;
return factor;
}
vector<double> TParticle2D::ComputeSecondarySource(vector<TParticle*> part, TSpallationNetwork* spnet, vector<TXSecBase*> xsecmodel) {
/**< Here also inverse beta-decay (K-electron capture) must be taken into account */
vector<double> result(density.size(), 0.0);
// If it is the only particle to be propagated, or if it is primary electrons, or if it is DM, do not add secondary contribution
if (part.size() == 1 || (uid == -1000 && !issec) || isDM) return result;
TGas* totalgas = _fGalaxy->GetTotalGas();
TGrid* coord = _fGalaxy->GetCoordinates();
#undef DEBUG
#ifdef DEBUG
vector<double> Ek = coord->GetEk();
#endif
if (issec && fabs(uid) != 1000) { // Secondary protons or tertiary antiprotons or tertiary antideuterons: they are next to their primary brothers...
vector<double> Ek(coord->GetEk());
if (in->spallationxsec != Fluka) {
if (uid == 1001 && issec)
cout << "... secondary protons!" << endl;
if (uid == -999 && issec)
cout << "... tertiary antiprotons!" << endl;
vector<TParticle*>::iterator iprim = part.end()-2; // Primary species
vector<double> beta(coord->GetBeta());
vector<double> spall_spectrum( spnet->GetXSec(uid, uid) );
for (int k = 0; k < dimr; ++k) {
for (int l = 0; l < dimz; ++l) {
int indspat = coord->index(k,l);
double gasdensity = totalgas->GetGas(indspat);
for (int i = 0; i < dimE; ++i) {
double betaigasdensity = beta[i]*gasdensity;
int ind = indspat*dimE+i;
//if (k==0 && l==0) cout << "E= " << Ek[i] << " spall xsec from p = " << spall_spectrum[i] << endl;
for (int ii = i; ii < dimE; ++ii) result[ind] += (*iprim)->GetDensity(indspat*dimE+ii) * betaigasdensity * spall_spectrum[ii];
}
}
}
//cout << "*** End of spallation cross section: ***" << endl;
} else { //Fluka model
if (uid == 1001 && issec)
cout << "Secondary protons!" << endl;
if (uid == -999 && issec)
cout << "Tertiary antiprotons" << endl;
cout << "*** Fluka cross sections! " << endl;
pair<int,int> coupleppr(1001,1001); // Secondary protons, from prim. protons
pair<int,int> couplepHe(2004,1001); // Secondary protons, from Helium
pair<int,int> coupleapap(-999, -999); // Tertiary antiprotons, from sec. antiprotons
cout << "*** Spallation cross section: ***" << endl;
//loop over the parent particles. Only p and He are relevant
for (vector<TParticle*>::iterator ipart = part.begin(); ipart != part.end()-1; ++ipart) {
if ((*ipart)->GetUid() > 2004 || (*ipart)->GetUid() < 0) continue;
for (int i = 0; i < dimE; i++) {
vector<double> spall_spectrum( spnet->GetXSecApEl((*ipart)->GetUid(), uid, i) );
if (spall_spectrum.size() == dimE) {
for (int k = 0; k < dimr; k++) {
for (int l = 0; l < dimz; l++) {
int indspat = coord->index(k,l);
double gasdensity = totalgas->GetGas(indspat);
int ind = indspat*dimE+i;
// ENERGY INTEGRAL
for (int ii=0; ii < dimE; ii++) {
result[ind] += (*ipart)->GetDensity(indspat*dimE+ii) * gasdensity * spall_spectrum[ii];
if ((*ipart)->GetUid() == 1001 && uid==1001 && k==0 && l==0)
cout << " E_parent= " << Ek[i] << " E_daughter= " << Ek[ii] << " spall xsec from p = " << spall_spectrum[ii] << endl;
}
}
}
}
}
}
cout << "*** End of spallation cross section: ***" << endl;
}
} // if (issec && uid != -1000)
else if (uid > 1000) { // nuclei spallation
//modified
vector<double> gamma(coord->GetGamma());
vector<double> beta(coord->GetBeta());
vector<double> energy(coord->GetEk());
//modified
//if K_capture is present, the source term due to electron attachment/stripping is computed
if (K_electron > 0) {
double factor = 1.e-27*Clight;
TParticle* naked_nucleus;
if (part.size() > 1) naked_nucleus = part[part.size()-2];
if (in->feedback >1) cout << "Computing source term for dressed nucleus " << endl;
//cout << "source term coming from nucleus with A = " << naked_nucleus->GetA() << "; Z = " << naked_nucleus->GetZ() << endl;
for (int k = 0; k < dimr; ++k) {
for (int l = 0; l < dimz; ++l) {
int indspat = coord->index(k,l);
double Gasdensity = totalgas->GetGas(indspat);
for (int i = 0; i < dimE; ++i) {
int ind = indspat*dimE+i;
double attach_H=0., attach_He=0., strip_H=0., strip_He=0.;
xsecmodel[0]->Kcapture_cs(energy[i],naked_nucleus->GetZ(),1,&attach_H,&strip_H);
xsecmodel[0]->Kcapture_cs(energy[i],naked_nucleus->GetZ(),2,&attach_He,&strip_He);
result[ind] = Gasdensity * (attach_H + He_abundance*attach_He) * factor * beta[i] * naked_nucleus->GetDensity(ind);
}
}
}
}
//modified
//if K_capture is present and K_electron == 1, the source term ends here: it only contains contribution from the corresponding naked nucleus
else { // if K_capture is present and K_electron == 0, the source term must contain also the spallation and decay contribution from heavier nuclei
for (vector<TParticle*>::iterator ipart = part.begin(); ipart != part.end()-1; ++ipart) { // // //
if ((*ipart)->GetDaughter() == uid && in->feedback >1)
cout << "---> Nucleus " << ((*ipart))->GetUid() << " decays into current particle " << uid << endl;
vector<double> spall_spectrum( spnet->GetXSec( (*ipart)->GetUid(), uid ) );
if (spall_spectrum.size() == dimE || (*ipart)->GetDaughter() == uid) {
double Afactor = double((*ipart)->GetA())/double(A); // To convert between kinetic energy per nucleon (which is approx. constant) to momentum
for (int k = 0; k < dimr; ++k) {
for (int l = 0; l < dimz; ++l) {
int indspat = coord->index(k,l);
double Afactorgasdensity = Afactor*totalgas->GetGas(indspat);
for (int i = 0; i < dimE; ++i) {
int ind = indspat*dimE+i;
if (spall_spectrum.size() == dimE) result[ind] += Afactorgasdensity * spall_spectrum[i] * (*ipart)->GetDensity(ind); // spallation
if ((*ipart)->GetDaughter() == uid) result[ind] += (*ipart)->GetDensity(ind)/(*ipart)->GetLifetime()/gamma[i]; // decay
}
}
}
}
}
} // if (K_electron == 0)
} // else if (uid > 1000)
else { // Secondary antiprotons, electrons and positrons, antideuterons, positrons from TPP
if (!isTPP) {
// ofstream outfile("prova_Pohl.dat", ios::out);
for (vector<TParticle*>::iterator ipart = part.begin(); ipart != part.end()-1; ++ipart) {
if ((*ipart)->GetUid() > 2004 || (*ipart)->GetUid() < 0) continue;
for (int i = 0; i < dimE; i++) {
vector<double> spall_spectrum( spnet->GetXSecApEl((*ipart)->GetUid(), uid, i) );
if (spall_spectrum.size() == dimE) {
for (int k = 0; k < dimr; k++) {
for (int l = 0; l < dimz; l++) {
int indspat = coord->index(k,l);
double gasdensity = totalgas->GetGas(indspat);
int ind = indspat*dimE+i;
// ENERGY INTEGRAL
for (int ii=0; ii < dimE; ii++) { result[ind] += (*ipart)->GetDensity(indspat*dimE+ii) * gasdensity * spall_spectrum[ii];
#ifdef DEBUG
if ((*ipart)->GetUid() == 1001 && uid==1000) outfile << Ek[i] << Ek[ii] << spall_spectrum[ii] << endl;
#endif
}
}
}
}
}
}
// outfile.close();
}
else { //TPP: Secondary positrons coming from TPP -- implemented by D.Gaggero -- november 2011
// if (uid == 1000 && issec) { //TPP: Secondary positrons coming from TPP
if (in->feedback >1) cout << "Building source term for TPP positrons..." << endl;
vector<double> energy(coord->GetEk());
vector<double> R_vec(coord->GetR());
vector<double> z_vec(coord->GetZ());
double DlogE = coord->GetDeltaE();
TISRF* Gal_ISRF = _fGalaxy->GetISRF();
vector <double> nu_vector = Gal_ISRF->GetNuArray();
double DlogNu = Gal_ISRF->GetDnu();
int dimNu = nu_vector.size();
double hPlanck = 4.135667e-15; // eV/Hz
vector <double> ISRF_vector = Gal_ISRF->GetISRF(); // nu U_nu; units: Hz eV cm^-3 Hz^-1
for (vector<TParticle*>::iterator ipart=part.begin(); ipart!=part.end()-1; ++ipart) {
if ((*ipart)->GetUid() == -1000) { //TPP positrons only come from (primary and secondary) electrons
if (in->feedback >1) cout << "Calculating TPP cross section..." << endl;
vector<double> TPP_cross_section(spnet->GetXSecTPP(nu_vector));
if (in->feedback >1) cout << "TPP cross section calculated" << endl;
vector<double> parent_particle_density (dimE*dimr*dimz);
for (int k = 0; k < dimr; k++) {
for (int l = 0; l < dimz; l++) {
for (int ii = 0; ii < dimE; ii++) {
int indspat = coord->index(k,l);
parent_particle_density[indspat*dimE+ii] = (*ipart)->GetDensity(indspat*dimE+ii);
}
}
}
for (int i = 0; i < dimE; i++) {
for (int k = 0; k < dimr; k++) {
for (int l = 0; l < dimz; l++) {
int indspat = coord->index(k,l);
int ind = indspat*dimE+i;
for (int inu = 0; inu<dimNu; inu++) { // integral over frequency_vector of ISRF
double photon_density = ISRF_vector[(inu*dimr+k)*dimz+l] / ((hPlanck * nu_vector[inu])*nu_vector[inu]); // rho_nu; units: cm^-3 Hz^-1
double energy_integral = 0.;
for (int ii=0; ii < dimE; ii++) { // integral over energy of parent particle
double contrib = parent_particle_density[indspat*dimE+ii] * TPP_cross_section[(i*dimNu + inu)*dimE +ii] * DlogE; // cm^-3 * cm^3/Myr DeltalogE:adimensional
energy_integral += contrib;
}
double contrib_2 = photon_density * energy_integral * nu_vector[inu] * DlogNu; // cm^-3 * 1/Myr Deltalognu: adimensional
result[ind] += contrib_2;
}
} //for l = 0,dimz
} // for k = 0,dimr
} //for i=0,dimE
}
if (in->feedback >1) cout << "Building source term for TPP positrons succeeded." << endl;
}
}
} // else
return result;
}
void TParticle2D::Print(fitsfile* output_ptr, double norm) { /**< Print all the information relevant to that nucleus: charge, mass, source abundance, injection spectrum and propagated density. */
int status = 0;
const long naxis = 3;
long size_axes[naxis] = {dimE,dimr,dimz};
long nelements = size_axes[0]*size_axes[1]*size_axes[2];
long fpixel = 1;
int bitpix = FLOAT_IMG;
if (fits_create_img(output_ptr, bitpix, naxis, size_axes, &status)) fits_report_error(stderr, status);
double sab = _fGalaxy->GetSourceAbundance(uid);
if (fits_write_key(output_ptr, TINT, (char*) "Z_", &Z, NULL, &status)) fits_report_error(stderr, status);
if (fits_write_key(output_ptr, TINT, (char*) "A", &A, NULL, &status)) fits_report_error(stderr, status);
if (fits_write_key(output_ptr, TINT, (char*) "Sec", &issec, NULL, &status)) fits_report_error(stderr, status);
if (fits_write_key(output_ptr, TINT, (char*) "DM", &isDM, NULL, &status)) fits_report_error(stderr, status);
if (fits_write_key(output_ptr, TINT, (char*) "EXTRA", &isExtra, NULL, &status)) fits_report_error(stderr, status);
if (fits_write_key(output_ptr, TINT, (char*) "TPP", &isTPP, NULL, &status)) fits_report_error(stderr, status);
if (fits_write_key(output_ptr, TDOUBLE, (char*) "S_Ab", &sab, NULL, &status)) fits_report_error(stderr, status);
int counter = 0;
float* array = new float[nelements];
double weight = 1;
if (A != 0) weight = double(A);
for (int l = 0; l < dimz; ++l) {
for (int k = 0; k < dimr; ++k) {
for (int j = 0; j < dimE; ++j) {
array[counter] = float(weight*density[TParticle::index(k,l,j)]*norm);
counter++;
}
}
}
if (fits_write_img(output_ptr, TFLOAT, fpixel, nelements, array, &status)) fits_report_error(stderr, status);
delete [] array;
return ;
}
void TParticle2D::PrintSpectrum(fitsfile* output_ptr, double norm) { /**< Print all the information relevant to that nucleus: charge, mass, source abundance, injection spectrum and propagated spectrum at Sun position. */
int status = 0;
const long naxis = 1;
long size_axes[naxis] = {dimE};
long nelements = size_axes[0];
long fpixel = 1;
int bitpix = FLOAT_IMG;
if (fits_create_img(output_ptr, bitpix, naxis, size_axes, &status)) fits_report_error(stderr, status);
double sab = (!issec) ? _fGalaxy->GetSourceAbundance(uid) : 0.0;
if (fits_write_key(output_ptr, TINT, (char*) "Z_", &Z, NULL, &status)) fits_report_error(stderr, status);
if (fits_write_key(output_ptr, TINT, (char*) "A", &A, NULL, &status)) fits_report_error(stderr, status);
if (fits_write_key(output_ptr, TINT, (char*) "Sec", &issec, NULL, &status)) fits_report_error(stderr, status);
if (fits_write_key(output_ptr, TINT, (char*) "DM", &isDM, NULL, &status)) fits_report_error(stderr, status);
if (fits_write_key(output_ptr, TINT, (char*) "EXTRA", &isExtra, NULL, &status)) fits_report_error(stderr, status);
if (fits_write_key(output_ptr, TINT, (char*) "TPP", &isTPP, NULL, &status)) fits_report_error(stderr, status);
if (fits_write_key(output_ptr, TDOUBLE, (char*) "S_Ab", &sab, NULL, &status)) fits_report_error(stderr, status);
float* array = new float[nelements];
double weight = 1;
vector<double> r = _fGalaxy->GetCoordinates()->GetR();
vector<double> z = _fGalaxy->GetCoordinates()->GetZ();
vector<double> Ek =_fGalaxy->GetCoordinates()->GetEk();
unsigned int irsun = (unsigned int) ((in->robs-r.front())/(r.back()-r.front())*(double)(dimr-1));
unsigned int izsun = (unsigned int) ((in->zobs-z.front())/(2.0*z.back())*(double)(dimz-1));
double r1 = (r[irsun+1]-in->robs)/(r[irsun+1]-r[irsun]);
double r2 = (in->robs-r[irsun])/(r[irsun+1]-r[irsun]);
if (A != 0) weight = double(A);
if (isDM && in->feedback >1)
cout << "**** particle originating from DARK MATTER *****" << endl;
if (in->feedback >1) cout << "************************************************" << endl;
if (in->feedback >1) cout << "***Writing spectrum at Solar System position... " << endl;
if (in->feedback >1) cout << "************************************************" << endl;
if (in->feedback >1) cout << "A = " << A << " Z = " << Z << " issec = " << issec << endl;
if (in->feedback >1) cout << "************************************************" << endl;
if (in->feedback >1) cout << "Energy -- Normalized flux " << endl;
for (int j = 0; j < dimE; ++j){
array[j] = float(weight*norm*( density[TParticle::index(irsun,izsun,j)]*r1 + density[TParticle::index(irsun+1,izsun,j)]*r2 ));
if (in->feedback >1) cout << Ek[j] << " " << array[j] << endl;
}
if (in->feedback >1) cout << endl;
if (fits_write_img(output_ptr, TFLOAT, fpixel, nelements, array, &status)) fits_report_error(stderr, status);
delete [] array;
return;
}
vector<double> TParticle2D::GetSpectrumAtSunPosition() {
vector<double> result(dimE);
vector<double> r = _fGalaxy->GetCoordinates()->GetR();
vector<double> z = _fGalaxy->GetCoordinates()->GetZ();
vector<double> Ek = _fGalaxy->GetCoordinates()->GetEk();
unsigned int irsun = (unsigned int) ((in->robs-r.front())/(r.back()-r.front())*(double)(dimr-1));
unsigned int izsun = (unsigned int) ((in->zobs-z.front())/(2.0*z.back())*(double)(dimz-1));
double r1 = (r[irsun+1]-in->robs)/(r[irsun+1]-r[irsun]);
double r2 = (in->robs-r[irsun])/(r[irsun+1]-r[irsun]);
double weight = 1;
if (A != 0) weight = double(A);
for (int j = 0; j < dimE; ++j)
result[j] = weight*(density[TParticle::index(irsun,izsun,j)]*r1 + density[TParticle::index(irsun+1,izsun,j)]*r2);
return result;
}
double TParticle2D::GetFluxAtSunPosition(int j) {
vector<double> r = _fGalaxy->GetCoordinates()->GetX();
vector<double> z = _fGalaxy->GetCoordinates()->GetZ();
vector<double> Ek = _fGalaxy->GetCoordinates()->GetEk();
unsigned int irsun = (unsigned int) ((in->robs-r.front())/(r.back()-r.front())*(double)(dimr-1));
unsigned int izsun = (unsigned int) ((in->zobs-z.front())/(2.0*z.back())*(double)(dimz-1));
double r1 = (r[irsun+1]-in->robs)/(r[irsun+1]-r[irsun]);
double r2 = (in->robs-r[irsun])/(r[irsun+1]-r[irsun]);
double weight = 1;
if (A != 0) weight = double(A);
return density[TParticle::index(irsun,izsun,j)]*r1 + density[TParticle::index(irsun+1,izsun,j)]*r2;
}
TParticle3D::TParticle3D(int A_ /**< Mass number */, int Z_ /**< Charge */, Galaxy* gal /**< A model for the galaxy */, Input* in /**< User input */, bool uid_prec, vector<TXSecBase*> xsecmodel, TNucleiList* l, int K_electron_, bool isDM, bool isextra, bool isTPP) :
TParticle(A_, Z_, gal, in, uid_prec, xsecmodel, l, K_electron_, isDM, isextra, isTPP),
dimx(gal->GetCoordinates()->GetDimX()),
dimy(gal->GetCoordinates()->GetDimY()) {
cout << "Welcome to the Particle 3D constructor! " << endl;
int dimz = (gal->GetCoordinates()->GetDimZ());
vector<double> x = (gal->GetCoordinates()->GetX());
vector<double> y = (gal->GetCoordinates()->GetY());
vector<double> z = (gal->GetCoordinates()->GetZ());
//MW130620: What are these deltas used for? -- for now, set them equidistantially
double deltax = ( (x.back() - x.front()) / (dimx-1) );
double deltay = ( (y.back() - y.front()) / (dimy-1) );
double deltaz = ( (z.back() - z.front()) / (dimz-1) );
cout << "Initializing the density vector... " << endl;
density = vector<double>(dimx*dimy*dimz*dimE, 0.0);
density_previous = vector<double>(dimx*dimy*dimz*dimE, 0.0);
if (gal->GetTestMode() == true) {
cout << "Initializing to a gaussian... " << endl;
//double delta_ = deltax * 2.;
double delta_ = deltax/100.;
cout << "Amplitude of initial gaussian = " << delta_ << endl;
double init_value = 0.;
double x1 = 0.;
double x2 = 0.;
double norm1 = 1.;
double norm2 = 0.;
//double x3 = -10;
for (int ix=0; ix<dimx; ix++) {
for (int iy=0; iy<dimy; iy++) {
for (int iz=0; iz<dimz; iz++) {
for (int ip=0; ip<dimE; ip++) {
// double x1 = -20.;
// double x2 = 20.;
if ( gal->IsSourceMoving() == false) {
init_value = norm1 * (1./(sqrt(3.14)*delta_)) * exp( -((x[ix]-x1)*(x[ix]-x1))/(delta_*delta_) - (y[iy]*y[iy])/(delta_*delta_) - (z[iz]*z[iz])/(delta_*delta_) );
init_value += norm2 * (1./(sqrt(3.14)*delta_)) * exp( -((x[ix]-x2)*(x[ix]-x2))/(delta_*delta_) - (y[iy]*y[iy])/(delta_*delta_) - (z[iz]*z[iz])/(delta_*delta_) );
}
else {
init_value = 0.; // (1./(sqrt(3.14)*delta_)) * exp( -((x[ix]-x3)*(x[ix]-x3))/(delta_*delta_) - (y[iy]*y[iy])/(delta_*delta_) - (z[iz]*z[iz])/(delta_*delta_) );
}
// if (ip == 0 && iz == dimz/2 && init_value > 1.e-1)
// cout << " x = " << x[ix] << " y = " << y[iy] << " z = " << z[iz] << " value = " << init_value << endl;
density[index(ix,iy,iz,ip)] = init_value; //initialization ot a Gaussian centered on the origin in order to compare with the analytical solution
}
}
}
}
}
}
//******************************************************************************************************************************************************
double TParticle3D::FindNormalization(const double& sp_ref_rig_norm, const double& spect_norm) {
if (!(uid == 1001 || uid == -1000)) {
cerr << "Asking for normalization but no protons nor primary electrons found" << endl;
exit(NOPROTELNORM);
}
cout << "3D normalization " << endl;
cout << "Observer position: " << in->xobs << " " << in->yobs << " " << in->zobs << endl;
// Matze: rewrite stuff for nonequidistant grid
vector <double> x = _fGalaxy->GetCoordinates()->GetX();
vector <double> y = _fGalaxy->GetCoordinates()->GetY();
vector <double> z = _fGalaxy->GetCoordinates()->GetZ();
vector <double> Ek = _fGalaxy->GetCoordinates()->GetEk();
unsigned int ixsun = 0;
while(x[++ixsun] <= in->xobs){}
ixsun--;
unsigned int iysun = 0;
while(y[++iysun] <= in->yobs){}
iysun--;
unsigned int izsun = 0;
while(z[++izsun] <= in->zobs){}
izsun--;
double rx1 = (x[ixsun+1]-in->xobs)/(x[ixsun+1]-x[ixsun]);
double ry1 = (y[iysun+1]-in->yobs)/(y[iysun+1]-y[iysun]);
double rz1 = (z[izsun+1]-in->zobs)/(z[izsun+1]-z[izsun]);
double rx2 = 1-rx1;
double ry2 = 1-ry1;
double rz2 = 1-rz1;
cout << rx1 << " = rx1; rx2 = " << rx2 << endl;
cout << ry1 << " = ry1; ry2 = " << ry2 << endl;
cout << rz1 << " = rz1; rz2 = " << rz2 << endl;
//double sp_ref_rig_norm, spect_norm;
//sp_ref_rig_norm = (uid == 1001) ? inp->sp_ref_rig_norm : inp->sp_ref_rig_el;
//spect_norm = (uid == 1001) ? inp->spect_norm : inp->spect_norm_el;
int ilow = int(log(sp_ref_rig_norm/Ek[0])/log(Ek[1]/Ek[0]));
cout << "ilow, i.e. energy index " << ilow << endl;
cout << "Ek[ilow] = " << Ek[ilow] << endl;
cout << "Sun coordinates: " << ixsun << " " << iysun << " " << izsun << endl;
cout << "+++ Propagated spectrum at Sun +++" << endl;
for (int i=0; i < Ek.size(); i++)
cout << density[index(ixsun, iysun, izsun, i)] << " " ;
cout << "+++ End of propagated spectrum +++" << endl;
double valuelow = log10( (density[index(ixsun, iysun, izsun, ilow)]*rx1*ry1
+ density[index(ixsun, iysun+1,izsun, ilow)]*rx1*ry2
+ density[index(ixsun+1,iysun, izsun, ilow)]*rx2*ry1
+ density[index(ixsun+1,iysun+1,izsun, ilow)]*rx2*ry2)*rz1
+(density[index(ixsun, iysun, izsun+1,ilow)]*rx1*ry1
+ density[index(ixsun, iysun+1,izsun+1,ilow)]*rx1*ry2
+ density[index(ixsun+1,iysun, izsun+1,ilow)]*rx2*ry1
+ density[index(ixsun+1,iysun+1,izsun+1,ilow)]*rx2*ry2)*rz2);
if (in->feedback >1) cout << "10^valuelow i.e. density at sun pos., ilow energy = " << pow(10,valuelow) << endl;
double valuehigh = log10((density[index(ixsun, iysun, izsun ,ilow+1)]*rx1*ry1
+ density[index(ixsun, iysun+1,izsun ,ilow+1)]*rx1*ry2
+ density[index(ixsun+1,iysun, izsun ,ilow+1)]*rx2*ry1
+ density[index(ixsun+1,iysun+1,izsun ,ilow+1)]*rx2*ry2)*rz1
+(density[index(ixsun, iysun, izsun+1,ilow+1)]*rx1*ry1
+ density[index(ixsun, iysun+1,izsun+1,ilow+1)]*rx1*ry2
+ density[index(ixsun+1,iysun, izsun+1,ilow+1)]*rx2*ry1
+ density[index(ixsun+1,iysun+1,izsun+1,ilow+1)]*rx2*ry2)*rz2);
if (in->feedback >1) cout << "10^valuehigh i.e. density at sun pos., ihigh energy = " << pow(10,valuehigh) << endl;
double e1 = log(Ek[ilow+1]/sp_ref_rig_norm)/log(Ek[ilow+1]/Ek[ilow]);
double e2 = log(sp_ref_rig_norm/Ek[ilow])/log(Ek[ilow+1]/Ek[ilow]);
if (in->feedback >1) cout << e1 << " = e1; e2 = " << e2 << endl;
double value = pow(10,valuelow*e1 + valuehigh*e2);
if (in->feedback >1) cout << "10^(valuelow*e1 + valuehigh*e2) = " << value << endl;
double factor = spect_norm/value;
if (in->feedback >1) cout << "normalization required in the xml: " << spect_norm << endl;
if (in->feedback >1) cout << "interpolated value at ixsun, ixsun+1, iysun, iysun+1, ilow, ilow+1: " << value << endl;
if (in->feedback >1) cout << "normalization factor = norm/value: " << factor << endl;
if (in->feedback >1){
cout << "+++ Propagated NORMALIZED spectrum at Sun +++" << endl;
for (int i=0; i < Ek.size(); i++)
cout << density[index(ixsun, iysun, izsun, i)]*factor << " " ;
cout << "+++ End of propagated spectrum +++" << endl;
}
int dimx = x.size();
int dimy = y.size();
int dimz = z.size();
if (in->feedback >1){
cout << "+++ Propagated NORMALIZED spectrum at the Gal.center +++" << endl;
for (int i=0; i < Ek.size(); i++)
cout << density[index(dimx/2+1, dimy/2+1, izsun, i)]*factor << " " ;
cout << "+++ End of propagated spectrum +++" << endl;
cout << "+++ Propagated NORMALIZED spectrum at intermediate latitude +++" << endl;
for (int i=0; i < Ek.size(); i++)
cout << density[index(ixsun-1, iysun-1, (dimz+izsun)/2, i)]*factor << " " ;
cout << "+++ End of propagated spectrum +++" << endl;
}
return factor;
}
/*
double TParticle3D::FindNormalization(TParticle* electrons, const double& normel) {
//To be used for the extra component
if (!(uid == -1000)) {
cerr << "Asking for normalization of the extra component but no primary electrons found" << endl;
exit(NOPROTELNORM);
}
// Matze: rewrite what needed to be revised,
// 10/12/12: copied that from above
// To Be Improved!! Now it is only a copy of the previous routine!!
vector <double> x = _fGalaxy->GetCoordinates()->GetX();
vector <double> y = _fGalaxy->GetCoordinates()->GetY();
vector<double> z = _fGalaxy->GetCoordinates()->GetZ();
vector<double> Ek = _fGalaxy->GetCoordinates()->GetEk();
unsigned int ixsun = 0;
unsigned int iysun = 0;
unsigned int izsun = 0;
while(x[++ixsun] <= xobs){}
ixsun--;
while(y[++iysun] <= yobs){}
iysun--;
while(z[++izsun] <= zobs){}
izsun--;
double rx1 = (x[ixsun+1]-xobs)/(x[ixsun+1]-x[ixsun]);
double ry1 = (y[iysun+1]-yobs)/(y[iysun+1]-y[iysun]);
double rz1 = (z[izsun+1]-zobs)/(z[izsun+1]-z[izsun]);
double rx2 = 1-rx1;
double ry2 = 1-ry1;
double rz2 = 1-rz1;
cout << rx1 << " = rx1; rx2 = " << rx2 << endl;
cout << ry1 << " = ry1; ry2 = " << ry2 << endl;
cout << rz1 << " = rz1; rz2 = " << rz2 << endl;
double sp_ref_rig_norm, spect_norm;
sp_ref_rig_norm = (uid == 1001) ? inp->sp_ref_rig_norm : inp->sp_ref_rig_el_extra;
spect_norm = (uid == 1001) ? inp->spect_norm : inp->spect_norm_el_extra;
int ilow = int(log(sp_ref_rig_norm/Ek[0])/log(Ek[1]/Ek[0]));
cout << "ilow, i.e. energy index " << ilow << endl;
// To be checked
cout << "sun coordinates (for electrons): " << ixsun << " " << iysun << " " << izsun << endl;
double valuelow = log10( (density[index(ixsun,iysun,izsun,ilow)]*rx1*ry1
+ density[index(ixsun,iysun+1,izsun,ilow)]*rx1*ry2
+ density[index(ixsun+1,iysun,izsun,ilow)]*rx2*ry1
+ density[index(ixsun+1,izsun+1,izsun,ilow)]*rx2*ry2)*rz1
+ (density[index(ixsun,iysun,izsun+1,ilow)]*rx1*ry1
+ density[index(ixsun,iysun+1,izsun+1,ilow)]*rx1*ry2
+ density[index(ixsun+1,iysun,izsun+1,ilow)]*rx2*ry1
+ density[index(ixsun+1,izsun+1,izsun+1,ilow)]*rx2*ry2)*rz2);
cout << "valuelow = " << pow(10,valuelow) << endl;
double valuehigh = log10( (density[index(ixsun,iysun,izsun,ilow+1)]*rx1*ry1
+ density[index(ixsun,iysun+1,izsun,ilow+1)]*rx1*ry2
+ density[index(ixsun+1,iysun,izsun,ilow+1)]*rx2*ry1
+ density[index(ixsun+1,izsun+1,izsun,ilow+1)]*rx2*ry2)*rz1
+ (density[index(ixsun,iysun,izsun+1,ilow+1)]*rx1*ry1
+ density[index(ixsun,iysun+1,izsun+1,ilow+1)]*rx1*ry2
+ density[index(ixsun+1,iysun,izsun+1,ilow+1)]*rx2*ry1
+ density[index(ixsun+1,izsun+1,izsun+1,ilow+1)]*rx2*ry2)*rz2);
cout << "valuehigh = " << pow(10,valuehigh) << endl;
double e1 = log(Ek[ilow+1]/sp_ref_rig_norm)/log(Ek[ilow+1]/Ek[ilow]);
double e2 = log(sp_ref_rig_norm/Ek[ilow])/log(Ek[ilow+1]/Ek[ilow]);
cout << e1 << " = e1; e2 = " << e2 << endl;
double value = pow(10,valuelow*e1 + valuehigh*e2);
double factor = spect_norm/value;
cout << "normalization required in the xml: " << spect_norm << endl;
cout << "interpolated value at ixsun, ixsun+1, iysun, iysun+1, ilow, ilow+1: " << value << endl;
cout << "normalization factor = norm/value: " << factor << endl << endl;
return factor;
}
*/
//******************************************************************************************************************************************************
vector<double> TParticle3D::ComputeSecondarySource(vector<TParticle*> part, TSpallationNetwork* spnet, vector<TXSecBase*> xsecmodel) {
/**< Here also inverse beta-decay (K-electron capture) must be taken into account */
cout << "We are starting the 3D computation of the secondary source " << endl;
vector<double> result(density.size(), 0.0);
// If it is the only particle to be propagated, or if it is primary electrons, do not add secondary contribution
if (part.size() == 1 || (uid == -1000 && !issec) || isDM || isExtra) return result;
TGas* totalgas = _fGalaxy->GetTotalGas();
TGrid* coord = _fGalaxy->GetCoordinates();
if (issec && fabs(uid) != 1000) { // Secondary protons or tertiary antiprotons or tertiary antideuterons: they are next to their primary brothers...
vector<TParticle*>::iterator iprim = part.end()-2; // Primary species
vector<double> beta(coord->GetBeta());
vector<double> spall_spectrum( spnet->GetXSec(uid, uid) );
cout << "Sec. proton or tert. antiproton/antideuteron: " << uid << " "<< issec << endl;
for (int k = 0; k < dimx; ++k) {
for (int j = 0; j < dimy; ++j) {
for (int l = 0; l < dimz; ++l) {
int indspat = coord->indexD(k,j,l);
double gasdensity = totalgas->GetGas(indspat);
//if (l == dimz/2 && j==0)
// cout << k << " " << j << " " << gasdensity << endl;
//if (l == dimz/2 && j==dimy/2)
// cout << k << " " << j << " " << gasdensity << endl;
for (int i = 0; i < dimE; ++i) {
double betaigasdensity = beta[i]*gasdensity;
int ind = indspat*dimE+i;
for (int ii = i+1; ii < dimE; ++ii) result[ind] += (*iprim)->GetDensity(indspat*dimE+ii) * betaigasdensity * spall_spectrum[ii];
}
}
}
}
} // if (issec && uid != -1000)
else if (uid > 1000) { // nuclei spallation
//modified
vector<double> gamma(coord->GetGamma());
vector<double> beta(coord->GetBeta());
vector<double> energy(coord->GetEk());
//modified
//if K_capture is present, the source term due to electron attachment/stripping is computed
if (K_electron > 0) {
double factor = 1.e-27*Clight;