libcpixe.c File Reference

#include <stdio.h>
#include <math.h>
#include <string.h>
#include <stdlib.h>
#include "libcpixe.h"
#include "stop96.h"
#include "compilopt.h"

Go to the source code of this file.

Functions
int	readINPUT (const char *InputFileNm, EXP_PARAM *pexppar, EXTRAINFO *pExtraInfo)
int	readEXP_PARAM (char *ExpParFileNm, EXP_PARAM *pexppar)
int	readSIM_PARAM (char *SampleParamFileNm, SIM_PARAM *simpar, char *IniMatFileNm, char *FilterFileNm, char *XYldFileNm)
int	symbol2Z (char *symbol)
int	Z2mass (int Z, double *mass, char option)
int	readCOMPOUND (FILE *f, int nelem, COMPOUND *c)
int	readsample (char *SampleDefFileNm, int *MaxZ, int *NFoil, foil **Sample)
int	createPresentElems (int MaxZ, int NFoil, const foil *MatArray, int **PresentElems)
int	readCalcFlags (const char *CalcFlagsFileNm, const int *PresentElems, int MaxZinsample, int AreasFormat, CPIXERESULTS **CalcFlags)
int	readXYld (const char *XYldFileNm, const int *PresentElems, const CPIXERESULTS *CalcFlags, int MaxZinsample, double *CalEner, XrayYield **XYldArray)
int	readFCK (char *FCKCoefFileNm, int MaxZinsample, FluorCKCoef **FCKCoefArray)
int	readAbsCoef (char *TotAbsCoefFileNm, int MaxZinsample, const int *PresentElems, const FILTER *Filter, AbsCoef **TotAbsCoefArray)
int	createSPTs (const char *path, const EXP_PARAM *pexp, int MaxZinsample, const int *PresentElems, double step, SPT **SPTArray)
double	getSP (const COMPOUND *pcmp, const SPT *SPTArray, double E)
int	initlyrarray (const EXP_PARAM *pexp, const foil *MatArray, const XrayYield *XYldArray, const AbsCoef *TotAbsCoefArray, const SPT *SPTArray, const int *PresentElems, int NFoil, int *NFoilUsed, LYR **plyrarray)
int	initlyr (const EXP_PARAM *pexp, const XrayYield *XYldArray, const AbsCoef *TotAbsCoefArray, const int *PresentElems, LYR *plyr, double *MACoef)
int	readFilter (const char *FilterDefFileNm, FILTER *Filter)
int	FilterTrans (const EXP_PARAM *pexp, const XrayYield *XYldArray, const AbsCoef *TotAbsCoefArray, const int *PresentElems, FILTER *Filter)
int	Transmission (const XrayYield *XYldArray, const AbsCoef *TotAbsCoefArray, int Z, const foil *pFoil, double geomcorr, const CalibYld *pTransOld, CalibYld *pTrans)
double	TotAbsor (const AbsCoef *TotAbsCoefArray, const COMPOUND *cmp, double Xray)
double	TotAbsor_elemental (int iener, const AbsCoef *Absco, int Z, double Xray)
int	createsublyrs (const EXP_PARAM *pexp, const foil *pMat, const SPT *SPTArray, double MajAbsCoef, LYR *plyr)
int	SSThick (const EXP_PARAM *pexp, const foil *pMat, const SPT *SPTArray, double MajAbsCoef, double LayerThickness, ESxType ESxin, ESxType *ESxfin, int *pFpos, double *thick, ESxType **ESxA)
int	integrate_Simpson (const EXP_PARAM *pexp, const AbsCoef *TotAbsCoefArray, const FluorCKCoef *FCKCoefArray, const XrayYield *XYldArray, int NFoilUsed, const FILTER *Filter, LYR *plyrarray, CalibYld *XYldSums)
int	Xprod (const AbsCoef *AbsC, const FluorCKCoef *pFCK, atomicnumber Z1, atomicnumber Z2, double M2, double ener, CalibYld *XYld)
double	PaulX (double ener, atomicnumber z)
double	PaulX_y (double MeV, atomicnumber z)
double	PaulX_lp (double x, long p)
int	ReisX (const AbsCoef *AbsC, const FluorCKCoef *pFCK, double ener, atomicnumber z, double M2, double *sigmaXL)
double	ReisX_gs (FwTipo T, int SS, double ksis)
double	ReisX_hs (FwTipo T, int SS, double ksih, double thet)
double	ReisX_En (double z, int niu)
double	ReisX_polisec (int ssind, double kz, double tz)
double	ReisX_g (int ss, atomicnumber Zg, double xi)
void	PenInteg (atomicnumber atnumb, const CalibYld *AbsFac, const ESxType *ESA, const CalibYld *YldA, const CalibYld *TrsA, const CalibYld *pTrs0, int FExlen, int NeedSFC, int AllowXEqCalc, double x0, double CosInc, CalibYld *XYld, CalibYld *XSFCr, CalibYld *XYldxmed)
double	Simps (double a, double b, double fa, double fi, double fb)
void	deNormalize (const EXP_PARAM *pexp, const AbsCoef *AbsC, const FluorCKCoef *pFCK, atomicnumber Z2, double M2, double attfraction, const CalibYld *pXYld, XrayYield *ResY, CalibYld *XYldSum)
void	freeFilter (FILTER *Filter)
void	freeReusable (int NFoils, LYR **plyrarray, foil **MatArray, CalibYld **XYldSums)
void	safefree (void **ptr)
void	fprintCALIBYLD (FILE *f, const CalibYld *pCYld)
void	fscanCALIBYLD (FILE *f, CalibYld *pCYld)

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Detailed Description

LibCPIXE is a collection of C functions which are useful for Particle Induced X-ray Emmission (PIXE) data analysis. The main objective is to produce a publicly available set of functions which can be incorporated in IBA data analysis codes.

News, documentation and latest releases can be found at: http://cpixe.sourceforge.net

A number of papers will be published and should be cited if libcpixe is used for producing scientific publications.

The reference paper for LibCPIXE and CPIXE is: "LibCPIXE: an open-source library for PIXE simulation and Analysis", Carlos Pascual-Izarra, Nuno P. Barradas and Miguel A. Reis, To be published in Proceedings of the IBA2005 (NIMB)

A paper showing the integration of LibCPIXE into the Data Furnace code is: "Simultaneous PIXE and RBS analysis using Bayesian Inference" Carlos Pascual-Izarra, Miguel A. Reis and Nuno P. Barradas, To be published in Proceedings of the IBA2005 (NIMB)

The seed for this code is on a translation from Pascal to C of parts of the code writen by M.A. Reis for the DatPixe-v5.3 code. The Pascal code was initially translated using p2c (an automatic Pascal-to-C free translator) and afterwards heavily modified.

Definition in file libcpixe.c.

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Function Documentation

int createPresentElems (  int  MaxZ, int  NFoil, const foil *  MatArray, int **  PresentElems )

Creates an array of integer flags indicating whether an element is present in the sample (1) or not (0). The dimension of the array is that of the maximum atomic number present in the sample. For example, if the sample contains only C and Si, the array will be: PresentElems[6]= PresentElems[14]=1 (and all the other=0) Parameters: MaxZ  (I) Largest atomic number present in sample (Dimension of PresentElems). NFoil  (I) Number of target foils MatArray  (I) Array of foils defining the current sample PresentElems  (O) Pointer to array of flags indicating presence for each element Returns: Always 0 Definition at line 732 of file libcpixe.c. References foil::comp, COMPOUND::elem, COMPOUND::nelem, and ELEMENT::Z. Referenced by cpixecalib(), CPIXEMAIN(), cpixemain(), and readFilter().

int createSPTs (  const char *  path, const EXP_PARAM *  pexp, int  MaxZinsample, const int *  PresentElems, double  step, SPT **  SPTArray )

Generates the stopping force tables Returns an array of pointers referencing to one table for each element present in sample) IMPORTANT: The tables are generated in the following units: keV/(1e15at/cm2) !!! Parameters: path  (I) String containing the path to look for the data base files. (e.g. for SCOEF.95A and SCOEF95B in the case of ZBL96 stoppings) Note that the path MUST contain the last "directory separator" pexp  (I) Pointer to structure containing experimental parameters. MaxZinsample  (I) Largest atomic number present in sample. PresentElems  (I) Array of flags indicating presence for each element. See createPresentElems() step  (I) Energy step to be used (in keV) in the case of linear energy scale or the multiplicative factor in the case logarithmic energy scale. SPTArray  (O) Array of Stopping power table structs for each present element. IMPORTANT: The tables are generated in the following units: keV/(1e15at/cm2) !!! Returns: Always 0 Todo: readstopcoef assumes that the files SCOEF.95A and SCOEF.95B are located where the program is called. This must be generalized (In fact, the coefficients could be hardcoded using an include file) <For the moment, only linear Energy scale is implemented Definition at line 1290 of file libcpixe.c. References EXP_PARAM::BeamEner, SPT::dSdE, SPT::E, SPT::Emax, SPT::Estep, FILENMLENGTH, ELEMENT::IM, EXP_PARAM::ion, SPT::logmode, SPT::nrows, nuclearstopping_ZBL(), readstopcoef(), SPT::S, SPT::Smax, stop96d(), and ELEMENT::Z. Referenced by cpixecalib(), CPIXEMAIN(), and cpixemain().

int createsublyrs (  const EXP_PARAM *  pexp, const foil *  pMat, const SPT *  SPTArray, double  MajAbsCoef, LYR *  plyr )

Manages the creation of internal sublayers in each layer Parameters: pexp  (I) Pointer to structure containing experimental parameters. pMat  (I) Pointer to current foil structure. SPTArray  (I) Pointer to precalculated tables of stoppings (see createSPT() ) MajAbsCoef  (I) Maximum absorption coef for this layer. plyr  (I+O) Pointer to current layer struct. Returns: Always 0 Todo: Discuss this initialization with M.R. Definition at line 1807 of file libcpixe.c. References foil::comp, EXP_PARAM::cosInc, COMPOUND::elem, ESxType::ep, LYR::ESxArray, LYR::FESxlen, EXP_PARAM::FinalEner, LYR::FoilInEner, LYR::FoilOutEner, getSP(), foil::nfoilelm, SPT::Smax, SSThick(), ESxType::stpp, foil::thick, LYR::ThickIn, ESxType::x, COMPOUND::xn, and ELEMENT::Z. Referenced by initlyrarray().

void deNormalize (  const EXP_PARAM *  pexp, const AbsCoef *  AbsC, const FluorCKCoef *  pFCK, atomicnumber  Z2, double  M2, double  attfraction, const CalibYld *  pXYld, XrayYield *  ResY, CalibYld *  XYldSum )

Calculates the yield values using the penetration integral results, i.e. Applies all the factors such as solid angle, atomic fraction, charge,... etc See eq. (1) of "Reis et al. NIM B 109/110 (1996) 134-138" Todo: This function does not support M-lines Note: This function is only valid for 10 Z2 in range [10,99] Parameters: pexp  (I) Pointer to structure containing experimental parameters. AbsC  (I) Pointer to Absorption coef structure for element with Z2 pFCK  (I) pointer to Fluorescence and Coster-Kronig coefficients for Z2 Z2  (I) atomic number of the target element M2  (I) mass of the target element attfraction  (I) atomic fraction of the target element in the current layer pXYld  (I) Penetration integral values. ResY  (I+O) The calculated yields (in counts) for each layer will be returned in ResY->XYld XYldSum  (O) The total yield (sum for all layers processed up to this moment of ResY->XYld) is acumulated in XYldSum. Note: deNormalize() returns both the partial and the total spectra through ResY->XYld and XYldSum, respectively. Todo: do this part when the filters are supported Check hardcoded Z limits Check hardcoded Z limits Check hardcoded Z limits Support also M lines here Definition at line 2995 of file libcpixe.c. References XrayYield::atnum, SIM_PARAM::CalEner, SIM_PARAM::ColCharge, EXP_PARAM::DetColFac, SIM_PARAM::DTCC, EXP_PARAM::ion, CalibYld::K_, CalibYld::L_, CalibYld::M_, EXP_PARAM::simpar, SIM_PARAM::useFilter, Xprod(), XrayYield::XYld, and ELEMENT::Z. Referenced by integrate_Simpson().

int FilterTrans (  const EXP_PARAM *  pexp, const XrayYield *  XYldArray, const AbsCoef *  TotAbsCoefArray, const int *  PresentElems, FILTER *  Filter )

Todo: Document this function Definition at line 1609 of file libcpixe.c. References FILTER::dimTrans, FILTER::foil, FILTER::geomcorr, SIM_PARAM::MaxZinsample, FILTER::nlyr, EXP_PARAM::simpar, FILTER::Trans, and Transmission(). Referenced by cpixecalib(), CPIXEMAIN(), and cpixemain().

void fprintCALIBYLD (  FILE *  f, const CalibYld *  pCYld )

Prints a CalibYld structure on a given stream Parameters: f  (I+O) Stream to which the structure is printed pCYld  (I) Structure to print Definition at line 3203 of file libcpixe.c. References CalibYld::K_, CalibYld::L_, and CalibYld::M_. Referenced by cpixecalib().

void freeFilter (  FILTER *  Filter  )

Frees all memory allocated for the filter structure. Parameters: Filter  (I+O) Pointer to filter structure. Definition at line 3122 of file libcpixe.c. References foil::comp, COMPOUND::elem, FILTER::FilterElems, FILTER::foil, FILTER::nlyr, safefree(), FILTER::Trans, COMPOUND::w, COMPOUND::X, and COMPOUND::xn. Referenced by cpixecalib(), CPIXEMAIN(), and cpixemain().

void freeReusable (  int  NFoils, LYR **  plyrarray, foil **  MatArray, CalibYld **  XYldSums )

Frees the space allocated for arrays that are to be reused in subsequent iterations Parameters: NFoils  (I) Number of target foils plyrarray  (I+O) Pointer to array of layers. Dim=NFoils+1 MatArray  (I+O) Pointer to array of foils. Dim=NFoils XYldSums  (I+O) Pointer to the Output Array of summed X-Ray Yields Definition at line 3148 of file libcpixe.c. References foil::comp, COMPOUND::elem, LYR::ESxArray, LYR::NeedSFC, LYR::ResYldArray, safefree(), LYR::SecResArray, LYR::SSTrsArray, LYR::SSYldArray, LYR::Trans, LYR::TrcAtnum, LYR::TrcUse, COMPOUND::w, COMPOUND::X, and COMPOUND::xn. Referenced by cpixecalib(), CPIXEMAIN(), and cpixemain().

void fscanCALIBYLD (  FILE *  f, CalibYld *  pCYld )

Reads a CalibYld structure from a given stream. The expected format is that as printed by fprintCALIBYLD Parameters: f  (I) Stream from which the structure is read pCYld  (O) Structure to store the read values Definition at line 3222 of file libcpixe.c. References CalibYld::K_, CalibYld::L_, and CalibYld::M_.

double getSP (  const COMPOUND *  pcmp, const SPT *  SPTArray, double  E )

Returns stopping Using previously calculated tables. Performs a linear interpolation and a Bragg adition. Parameters: pcmp  (I) Pointer to target definition SPTArray  (I) Pointer to precalculated tables of stoppings (see createSPT() ) E  (I) Energy of the ion, in keV Returns: Stopping Power, in keV/(1e15at/cm2) IMPORTANT!!! note that it's keV and ot eV Definition at line 1361 of file libcpixe.c. References SPT::dSdE, SPT::E, COMPOUND::elem, SPT::Estep, COMPOUND::nelem, SPT::S, COMPOUND::xn, and ELEMENT::Z. Referenced by createsublyrs(), and SSThick().

int initlyr (  const EXP_PARAM *  pexp, const XrayYield *  XYldArray, const AbsCoef *  TotAbsCoefArray, const int *  PresentElems, LYR *  plyr, double *  MACoef )

Initializes ONE given layer. It allocates space for various arrays and sets initial values for TrcUse, ResYldArray,... It also calculates the absorption and returns the Maximum absorption coefficient (MACoef). Note: it uses the global vars minK, maxK, minM, minL,... Parameters: pexp  (I) Pointer to structure containing experimental parameters. XYldArray  (I) Array of Xray yield coefs. See readXYld() TotAbsCoefArray  (I) Array containing a tables of Absorption Coefs (see readAbsCoef() ) plyr  (I+O) Pointer to current layer struct. PresentElems  (O) Pointer to array of flags indicating presence for each element MACoef  (I+O) Maximum absorption coefficient to be used in calcs (presently only cares about K&Lcoefs) Returns: Always 0 CAUTION: Change with respect to CDT: TrcUse now starts with index 0 CAUTION: Change with respect to CDT: NeedSFC now starts with index 0 Note: Todo: plyr->NeedSFC is just a convenience pointer to the Sample-general NeedSFC. This should be changed and not used, but for the moment it works. TODO:Check why was the following line commented out (in the Pascal Code): CAUTION: Change with respect to CDT: TrcAtnum now starts with index 0 Note: At this point in the CDT code, CalYld is defined, but it makes no sense since it is just a copy of XYldArray[].XYld (which is already there and never changing... So whenever CalYld[i] is needed, use XYldArray[i].XYld instead Definition at line 1456 of file libcpixe.c. References SRType::AbsFact, PeakArea::area, PeakArea::atnum, XrayYield::atnum, CalibYld, foil::comp, EXP_PARAM::cosDet, LYR::dimTrans, COMPOUND::elem, XrayYield::ener, CalibYld::K_, CalibYld::L_, CalibYld::M_, SIM_PARAM::MaxZinsample, LYR::NeedSFC, foil::nfoilelm, LYR::NumOfTrc, LYR::pFoil, SecResType::Pk, LYR::ResYldArray, LYR::SecResArray, EXP_PARAM::simpar, SecResType::SR, TotAbsor(), LYR::Trans, Transmission(), LYR::TrcAtnum, LYR::TrcUse, and ELEMENT::Z. Referenced by initlyrarray().

int initlyrarray (  const EXP_PARAM *  pexp, const foil *  MatArray, const XrayYield *  XYldArray, const AbsCoef *  TotAbsCoefArray, const SPT *  SPTArray, const int *  PresentElems, int  NFoil, int *  NFoilUsed, LYR **  plyrarray )

Initializes the lyr array Parameters: pexp  (I) Pointer to structure containing experimental parameters. MatArray  (I) Array of foils defining the current sample XYldArray  (I) Array of Xray yield coefs. See readXYld() TotAbsCoefArray  (I) Array containing a tables of Absorption Coefs (see readAbsCoef() ) SPTArray  (I) Pointer to precalculated tables of stoppings (see createSPT() ) NFoil  (I) Number of target foils PresentElems  (O) Pointer to array of flags indicating presence for each element NFoilUsed  (O) Number of foils finally used in the calcs plyrarray  (O) Pointer to the layer array. Returns: Always 0 Definition at line 1391 of file libcpixe.c. References LYR::absolutepos, EXP_PARAM::BeamEner, createsublyrs(), EXP_PARAM::FinalEner, LYR::FoilInEner, LYR::FoilOutEner, initlyr(), LYR::pFoil, and LYR::ThickIn. Referenced by cpixecalib(), CPIXEMAIN(), and cpixemain().

int integrate_Simpson (  const EXP_PARAM *  pexp, const AbsCoef *  TotAbsCoefArray, const FluorCKCoef *  FCKCoefArray, const XrayYield *  XYldArray, int  NFoilUsed, const FILTER *  Filter, LYR *  plyrarray, CalibYld *  XYldSums )

Performs Calculation of Transmission and Yields and then calculates the Penetration Integral. Uses Simpson integration method. TotAbsCoefArray XYldSums (O)is a matrix which contains, for each element, the total sum of XRayYlds for the whole sample. Todo: document this function NOTE: This function uses the global vars maxK, minM & minL Definition at line 1974 of file libcpixe.c. References SRType::AbsFact, LYR::absolutepos, SIM_PARAM::AllowXEqCalc, CalibYld, foil::comp, EXP_PARAM::cosFac, EXP_PARAM::cosInc, deNormalize(), ESxType::ep, LYR::ESxArray, LYR::FESxlen, EXP_PARAM::ion, CalibYld::K_, CalibYld::L_, CalibYld::M_, LYR::NeedSFC, LYR::NumOfTrc, PenInteg(), LYR::pFoil, LYR::ResYldArray, LYR::SecResArray, SRType::SFCr, EXP_PARAM::simpar, SecResType::SR, LYR::SSTrsArray, LYR::SSYldArray, FILTER::Trans, LYR::Trans, LYR::TrcAtnum, LYR::TrcUse, ESxType::x, SRType::Xeq, COMPOUND::xn, Xprod(), XrayYield::XYld, ELEMENT::Z, and Z2mass(). Referenced by cpixecalib(), CPIXEMAIN(), and cpixemain().

double PaulX (  double  ener, atomicnumber  z )

Parameters: ener  z  Atomic number of Target Returns: X-ray cross-section, in barn Todo: Document this function (description, units for ener & return and references) This function only works for proton beams!! Definition at line 2231 of file libcpixe.c. References PaulX_lp(), and PaulX_y(). Referenced by Xprod().

double PaulX_lp (  double  x, long  p )

Parameters: x  p  Returns: Todo: Document this function (description, units for ener & return and references) Definition at line 2327 of file libcpixe.c. Referenced by PaulX().

double PaulX_y (  double  MeV, atomicnumber  z )

Parameters: MeV  Energy of the ion, in MeV z  Atomic number of Target Returns: Todo: Document this function (description, units for ener & return and references) This function only works for proton beams!! Definition at line 2305 of file libcpixe.c. Referenced by PaulX().

void PenInteg (  atomicnumber  atnumb, const CalibYld *  AbsFac, const ESxType *  ESA, const CalibYld *  YldA, const CalibYld *  TrsA, const CalibYld *  pTrs0, int  FExlen, int  NeedSFC, int  AllowXEqCalc, double  x0, double  CosInc, CalibYld *  XYld, CalibYld *  XSFCr, CalibYld *  XYldxmed )

Calculates a normalized "Penetration Integral" for a given X-ray emission line of a given element. See "Reis et al. NIM B 109/110 (1996) 134-138" See section 1.4 of "Correccoes de Fluorescencia Secundaria em PIXE" Master Thesis by M.A. Reis It calculates the integral of eq. (4) of the cited paper except that it does not include the normalization constant "sigmaX_ij(Ep)" Parameters: atnumb  (I) Atomic number of the target element AbsFac  (I) Absorption coefficients structure for the target element ESA  (I) Pointer to Array of sublayers in the current layer. YldA  (I) Array of X-ray production cross section for the target element in each sublayer TrsA  (I) Array of Transmission coefs for the target element in each sublayer pTrs0  (I) Array of Transmission factors due tolayers over the one we are considering. FExlen  (I) Number of sublayers in this layer NeedSFC  (I) Flag indicating whether secondary fluorescence should be calculated (1) or not (0) AllowXEqCalc  (I) Flag indicating whether "equivalent thickness" should be calculated (1) or not (0) x0  (I) absolute in-going path length, in 1e15at/cm2, from sample surface (Only relevant if AllowXEqCalc=1) CosInc  Cosine of the incident angle (Only relevant if AllowXEqCalc=1) XYld  (O) Penetration integral results. XSFCr  (O) Correction factor applied due to secondary fluorescence (Only relevant if NeedSFC=1) XYldxmed  (O) Equivalent thickness results (Only relevant if AllowXEqCalc=1) Todo: IMPORTANT: check here the use of cosInc in relation with the definition of x0 Definition at line 2782 of file libcpixe.c. References ESxType::ep, CalibYld::K_, CalibYld::L_, CalibYld::M_, Simps(), ESxType::stpp, and ESxType::x. Referenced by integrate_Simpson().

int readAbsCoef (  char *  TotAbsCoefFileNm, int  MaxZinsample, const int *  PresentElems, const FILTER *  Filter, AbsCoef **  TotAbsCoefArray )

Reads from an ascii file the X-ray Absorption coefficients. The File must have the following format: Note: the index of TotAbsCoefArray starts in 1. ----------------- (any header) MAXZ [maxZ] DATA (datablocks) ----------------- The datablock for each element has the following structure: [atnum] [chemsymb] (23 coefs each one for a given standard energy (see stdtable in TotAbsor() ) [stdcoef[0]]....[stdcoef[22]] (9 triplets --1 for K, 3 for L and 5 for M-- describing absorp edges for K, L & M (1+3+5 triplets). First member of triplet is the transition ener, 2nd is abs coef for E below E_edge and 3rd is abs coef for E above E_edge ) [enr[1]] [coefenr[0][0]] [coefenr[0][1]] ... [enr[9]] [coefenr[8][0]] [coefenr[8][1]] ----------------- Todo: Note that enr indexing starts in 1 while the stdcoeffs & coefenr start in 0. A conversion from 1-->0 could be done with little work. IMPORTANT: The Absorption coeffs are tabulated using cm2/mg as unit but they need to be converted to (cm2/1e15at) Parameters: TotAbsCoefFileNm  (I) Name of the file to be read. Coefs are expected in (cm2/mg) MaxZinsample  (I) Largest atomic number present in sample. PresentElems  (I) Array of flags indicating presence for each element. See createPresentElems() Filter  (I) Pointer to filter structure. TotAbsCoefArray  (O) Pointer to array of structs containing the Absorption Coefs (in cm2/1e15at ) (see readAbsCoef() ) Returns: Always 0 Definition at line 1197 of file libcpixe.c. References AbsCoef::atnum, ChemSymb, AbsCoef::coefenr, AbsCoef::coefstd, AbsCoef::enr, FILTER::FilterElems, FILTER::MaxZ, symbol2Z(), and Z2mass(). Referenced by cpixecalib(), CPIXEMAIN(), and cpixemain().

int readCalcFlags (  const char *  CalcFlagsFileNm, const int *  PresentElems, int  MaxZinsample, int  AreasFormat, CPIXERESULTS **  CalcFlags )

Reads files containing the Calculation Flags (i.e. which lines should be calculated) or, alternativelly reads areas files from a file in the DATTPIXE Areas format. The behaviour depends on the DTAreasFlag (see below) The Format of the file is as follows: ----------------- (any header) DATA (datablocks) ----------------- if AreasFormat=1, The datablock for each element has the following structure: [ChemSymb] [Kalpha1,2] [Kbeta1] [Kbeta2] [Lalpha1,2] [Lbeta2] [Ll] [Lbeta1] [Lgamma1] [Leta] [Lbeta3] [Lbeta4] [Lgamma3] [Malpha1,2] [Mbeta] [Mgamma] Note: the flags are: 0 if not to be calculated, 1 (or >1) if should be calculated If AreasFormat=2 the datablock format is: [ChemSymb] [Kalpha1,2] [err] [Kbeta1] [err] [Kbeta2] [err] [Lalpha1,2] [err] [Lbeta2] [err] [Ll] [err] [Lbeta1] [err] [Lgamma1] [err] [Leta] [err] [Lbeta3] [err] [Lbeta4] [err] [Lgamma3] [err] [Malpha1,2] [err] [Mbeta] [err] [Mgamma] [err] Note: The information for elements not present in the sample is just ignored. Parameters: CalcFlagsFileNm  (I) Name of the input file PresentElems  (I) Array of flags indicating presence for each element. See createPresentElems() MaxZinsample  (I) Largest atomic number present in sample (dimension of PresentElems). AreasFormat  (I) Defines the format of the Areas File. 1 for raw areas format, 2 for DATTPIXE Areas Format CalcFlags  (O) Array (dimension is allocated to MaxZinsample+1) of structures containing the flags. Returns: Always 0 Definition at line 792 of file libcpixe.c. References CPIXERESULTS::atnum, ChemSymb, CPIXERESULTS::err, CalibYld::K_, CalibYld::L_, CalibYld::M_, CPIXERESULTS::simareas, and symbol2Z(). Referenced by cpixecalib(), and cpixemain().

int readCOMPOUND (  FILE *  f, int  nelem, COMPOUND *  c )

Reads a compound of 'nelem' elements from the stream f and fills with this info the the compound c This is a slightly modified version from that of hstoplib.c It fills the normalized atomic and mass concentration. Mass of the elements is obtained by calling Z2mass() The data from the stream must have the following format (repeated nelem times): [element] [atomic_concentration] ... Parameters: f  (I) Pointer to a stream from which the compound definition is read. nelem  (I) Number of elements in the compound c  (O) Pointer to structure defining the compound Returns: Maximum Atomic number read Definition at line 577 of file libcpixe.c. References ELEMENT::A, COMPOUND::elem, ELEMENT::IM, ELEMENT::M, COMPOUND::name, COMPOUND::nelem, COMPOUND::sumX, ELEMENT::symbol, symbol2Z(), COMPOUND::w, COMPOUND::X, COMPOUND::xn, ELEMENT::Z, and Z2mass(). Referenced by readFilter(), and readsample().

int readEXP_PARAM (  char *  ExpParFileNm, EXP_PARAM *  pexppar )

Fills an EXP_PARAM struct with data from a file. The file must have the following format: ------------------ BeamEner BeamCol DetColFac IncAng DetAng ------------------ Parameters: ExpParFileNm  (I) Name of the file to be read. pexppar  (O) Pointer to struct containing the experimental parameters Returns: Always 0 Todo: For the moment, only H ions are supported Definition at line 336 of file libcpixe.c. References ELEMENT::A, EXP_PARAM::BeamCol, EXP_PARAM::BeamCross, EXP_PARAM::BeamEner, EXP_PARAM::cosDet, EXP_PARAM::cosFac, EXP_PARAM::cosInc, EXP_PARAM::DetAng, EXP_PARAM::DetColFac, EXP_PARAM::FinalEner, ELEMENT::IM, EXP_PARAM::IncAng, EXP_PARAM::ion, ELEMENT::M, ELEMENT::symbol, symbol2Z(), ELEMENT::Z, and Z2mass().

int readFCK (  char *  FCKCoefFileNm, int  MaxZinsample, FluorCKCoef **  FCKCoefArray )

Reads from an ascii file the Fluorescence and Coster-Kronig coefficients. Note: the index of FCKCoefArray starts in 1. Todo: Modify to read only the present elems. Substitute the "..." by explicit labels The File must have the following format: ----------------- (any header) MAXZ [maxZ] DATA (datablocks) ----------------- The datablock for each element has the following structure: [atnum] [chemsymb] (Fluorescence Coeficients) [K] [LI] [LII] [LIII] [MI]... [f12] [f13] [f23] (Line fractions for:) [Kalpha1,2] [Kbeta1] [Kbeta2] [Lalpha1,2] [Lbeta2] [Ll] [Lbeta1] [Lgamma1] [Leta] [Lbeta3] [Lbeta4] [Lgamma3] [Malpha1,2] [Mbeta] [Mgamma] ----------------- Parameters: FCKCoefFileNm  (I) Name of the file to be read. MaxZinsample  (I) Largest atomic number present in sample. FCKCoefArray  (O) Pointer to array of structs containing Fluorescence and C-K Coefs Returns: Always 0 Definition at line 1092 of file libcpixe.c. References FluorCKCoef::atnum, ChemSymb, FluorCKCoef::ck, FluorCKCoef::k, CalibYld::K_, CalibYld::L_, CalibYld::M_, symbol2Z(), and FluorCKCoef::w. Referenced by cpixecalib(), CPIXEMAIN(), and cpixemain().

int readFilter (  const char *  FilterDefFileNm, FILTER *  Filter )

< Todo: For the moment, the geometric correction is just initialized to 1 Definition at line 1550 of file libcpixe.c. References foil::comp, createPresentElems(), COMPOUND::elem, FILTER::FilterElems, FILTER::foil, FILTER::geomcorr, ELEMENT::M, FILTER::MaxZ, foil::nfoilelm, FILTER::nlyr, readCOMPOUND(), foil::thick, and COMPOUND::xn. Referenced by cpixecalib(), and cpixemain().

int readINPUT (  const char *  InputFileNm, EXP_PARAM *  pexppar, EXTRAINFO *  pExtraInfo )

Reads an input file consisting on a series of commands. Parameters: InputFileNm  (I) Name of the input file (no more than LONGSTRINGLENGTH characters) pexppar  (O) pointer to the experimental parameter structure pExtraInfo  (O) pointer to structure containing misc data read from input file Returns: Always 0 Todo: For the moment, only H ions are supported : SXF not supported yet : Xeq calculation not Definition at line 77 of file libcpixe.c. References ELEMENT::A, SIM_PARAM::AllowSXFCorr, SIM_PARAM::AllowXEqCalc, EXTRAINFO::AreasFileNm, EXTRAINFO::AreasFormat, EXP_PARAM::BeamCol, EXP_PARAM::BeamCross, EXP_PARAM::BeamEner, SIM_PARAM::ColCharge, EXP_PARAM::cosDet, EXP_PARAM::cosFac, EXP_PARAM::cosInc, EXTRAINFO::DBpath, EXP_PARAM::DetAng, EXP_PARAM::DetColFac, EXTRAINFO::DoCalibration, SIM_PARAM::DTCC, EXTRAINFO::FilterFileNm, EXP_PARAM::FinalEner, ELEMENT::IM, EXP_PARAM::IncAng, EXP_PARAM::ion, LONGSTRINGLENGTH, ELEMENT::M, EXTRAINFO::OutputFileNm, EXTRAINFO::SampleFileNm, EXP_PARAM::simpar, ELEMENT::symbol, symbol2Z(), EXTRAINFO::WantOutputfile, EXTRAINFO::XYldFileNm, ELEMENT::Z, and Z2mass(). Referenced by cpixecalib(), and cpixemain().

int readsample (  char *  SampleDefFileNm, int *  MaxZ, int *  NFoil, foil **  Sample )

Allocates and initializes the sample definition from a file. It also returns Number of foils and Maximum atomic number present in sample. The File must have the following format: ----------------- NUMBER_OF_FOILS [nfoils] FOIL [thickness_in_ug/cm2] [numberofelems] [symbol] [concentration] [symbol] [concentration] ... FOIL CalEner [numberofelems] [symbol] [concentration] ... ----------------- Note:Any number of foils and any number of elements are allowed. Parameters: SampleDefFileNm  (I) Name of the file to be read. MaxZ  (O) Largest atomic number present in sample (Dimension of PresentElems). NFoil  (O) Number of target foils Sample  (O) Pointer to Array of files (Dim=NFoil) Returns: Always 0 Definition at line 667 of file libcpixe.c. References foil::comp, COMPOUND::elem, ELEMENT::M, foil::nfoilelm, readCOMPOUND(), foil::thick, and COMPOUND::xn. Referenced by cpixecalib(), and cpixemain().

int readSIM_PARAM (  char *  SampleParamFileNm, SIM_PARAM *  simpar, char *  IniMatFileNm, char *  FilterFileNm, char *  XYldFileNm )

Fills a SIM_PARAM struct with data from a file. The file must have the following format: ------------------ Samplefilename absorbertype AllowSXFCorr AllowXEqCalc GenPulNumb GenInteg ColCharge ------------------ Parameters: SampleParamFileNm  (I) Name of the file to be read. simpar  (O) Pointer to struct containing the simulation parameters IniMatFileNm  (O) Name of the file defining sample FilterFileNm  (O) Name of the filter definition file XYldFileNm  (O) Name of the calibration yield file Returns: Always 0 Todo: complete here the initialization for the case when a filter is used. UPDATE: this should be managed elsewhere, probably in FilterTrans() or readFilter() Definition at line 394 of file libcpixe.c. References SIM_PARAM::AllowSXFCorr, SIM_PARAM::AllowXEqCalc, SIM_PARAM::ColCharge, SIM_PARAM::DTCC, and SIM_PARAM::useFilter.

int readXYld (  const char *  XYldFileNm, const int *  PresentElems, const CPIXERESULTS *  CalcFlags, int  MaxZinsample, double *  CalEner, XrayYield **  XYldArray )

Reads from an ascii file the calibration yields and also returns CalEner. Todo: Modify to read only the present elems. Note: the index of XYldArray starts in 1. The File must have the following format: ----------------- (any header) CALENER [calener] MAXZ [maxZ] DATA (datablocks) ----------------- The datablock for each element has the following structure: [AtNum] [ChemSymb] [Kalpha1,2] [Kbeta1] [Kbeta2] <----Energies [Kalpha1,2] [Kbeta1] [Kbeta2] <----Yields [Lalpha1,2] [Lbeta2] [Ll] <---------Energies [Lalpha1,2] [Lbeta2] [Ll] <---------Yields [Lbeta1] [Lgamma1] [Leta] <--------Energies [Lbeta1] [Lgamma1] [Leta] <--------Yields [Lbeta3] [Lbeta4] [Lgamma3] <----Energies [Lbeta3] [Lbeta4] [Lgamma3] <----Yields [Malpha1,2] [Mbeta] [Mgamma] <-----Energies [Malpha1,2] [Mbeta] [Mgamma] <-----Yields ----------------- Parameters: XYldFileNm  (I) Name of the file to be read. PresentElems  (I) Array of flags indicating presence for each element. See createPresentElems() CalcFlags  (I) array of structures indicating which lines are to be calculated (simareas values>0) and which not (simareas values=-1). See readCalcFlags() MaxZinsample  (I) Largest atomic number present in sample (dimension of PresentElems). CalEner  (O) Energy at which the calibration was performed XYldArray  (O) Pointer to array of structs containing the efficiencies for each element Returns: Always 0 NOTE that the calib yield files from DT are in (cm2/ug)/uC and should be passed to (cm2/1e15at)/uC Definition at line 934 of file libcpixe.c. References XrayYield::atnum, CPIXERESULTS::atnum, ChemSymb, XrayYield::ener, CalibYld::K_, CalibYld::L_, CalibYld::M_, CPIXERESULTS::simareas, XrayYield::symb, symbol2Z(), XrayYield::XYld, and Z2mass(). Referenced by cpixecalib(), CPIXEMAIN(), and cpixemain().

int ReisX (  const AbsCoef *  AbsC, const FluorCKCoef *  pFCK, double  ener, atomicnumber  z, double  M2, double *  sigmaXL )

Returns X-ray fluorescence cross-sections for L lines. See paper ??? Todo: (cite M.Reis paper named ???) This function is only for proton beams!! Parameters: AbsC  (I) Pointer to Absorption coef structure for element with Z2 pFCK  (I) Pointer to structure containing the Fluorescence and Coster-Kronig coefs ener  (I) Proton energy, in keV z  (I) Atomic number of Target M2  (I) Atomic mass of Target (in amu) sigmaXL  (O) X-ray cross sections, in barn Returns: Always 0 Todo: What is Hr ??? What is cau ??? What is a02 ??? U.Atomicas de massa * U.Atomicas * parametro de correccao de polarizacao-ligacao * correccao de defleccao Coulombiana * Definition at line 2371 of file libcpixe.c. References FluorCKCoef::ck, AbsCoef::enr, FwTipo, ReisX_En(), ReisX_g(), ReisX_gs(), ReisX_hs(), ReisX_polisec(), SecXL, and FluorCKCoef::w. Referenced by Xprod().

double ReisX_En (  double  z, int  niu )

Auxiliar function to ReisX() Parameters: z  niu  Returns: Todo: check that the units of the hardcoded constants are appropriate document this function aproximation for niu>> * vide Abramowitz & Stegun , Dover 1Ed. 1965 * Definition at line 2599 of file libcpixe.c. Referenced by ReisX().

double ReisX_g (  int  ss, atomicnumber  Zg, double  xi )

Auxiliar function to ReisX() Parameters: ss  Zg  xi  Returns: Todo: check that the units of the hardcoded constants are appropriate document this function Definition at line 2712 of file libcpixe.c. Referenced by ReisX().

double ReisX_gs (  FwTipo  T, int  SS, double  ksis )

Auxiliar function to ReisX() Parameters: T  SS  ksis  Returns: Todo: check that the units of the hardcoded constants are appropriate document this function ref. Brandt and Lapicki,Phys.Rev.,A20(1979)465 * Definition at line 2474 of file libcpixe.c. References K, and L. Referenced by ReisX().

double ReisX_hs (  FwTipo  T, int  SS, double  ksih, double  thet )

Auxiliar function to ReisX() Parameters: T  SS  ksih  thet  Returns: Todo: check that the units of the hardcoded constants are appropriate document this function Definition at line 2550 of file libcpixe.c. References K, and L. Referenced by ReisX().

double ReisX_polisec (  int  ssind, double  kz, double  tz )

Auxiliar function to ReisX() Parameters: ssind  kz  tz  Returns: Todo: check that the units of the hardcoded constants are appropriate document this function Definition at line 2631 of file libcpixe.c. Referenced by ReisX().

void safefree (  void **  ptr  )

Frees memory only if *ptr is not NULL Parameters: ptr  (I+O) Pointer to array to be freed Definition at line 3188 of file libcpixe.c. Referenced by CPIXEMAIN(), freeFilter(), and freeReusable().

double Simps (  double  a, double  b, double  fa, double  fi, double  fb )

Returns area of trapezoid, useful for Simpson Integration. See "Corrected Trapezoidal Rule" in Conte & de Boor "Elementar Numerical Analysis" 3rd Ed. McGraw-Hill,1980,,p309 ExpCTR:=(b-a)/2*(fa+fb) Parameters: a  First point of the trapezoid base b  Second point of the Trapezoid base fa  fi  fb  Returns: Todo: IMPORTANT: Why the 6 and the 4??????? Has something to do with exponential function integration? If not, it should be rather: return( (b-a)/4 * (fa+2*fi+fb) ) UPDATE: This has to do with the line in SSthick where "thick" is calculated. document this function Definition at line 2964 of file libcpixe.c. Referenced by PenInteg().

int SSThick (  const EXP_PARAM *  pexp, const foil *  pMat, const SPT *  SPTArray, double  MajAbsCoef, double  LayerThickness, ESxType  ESxin, ESxType *  ESxfin, int *  pFpos, double *  thick, ESxType **  ESxA )

Recursive function which divides a sublayer in two if either energy loss or absorption are too large Parameters: pexp  (I) Pointer to structure containing experimental parameters. pMat  (I) Pointer to current foil structure. SPTArray  (I) Pointer to precalculated tables of stoppings (see createSPT() ) MajAbsCoef  (I) Maximum absorption coef for this layer. LayerThickness  (I) Effective Thickness (in-going path) for the layer containing this sublayer. ESxin  (I) Struct of energy, stopping and depth (ESx) for first half of this sublayer ESxfin  (I+O) Pointer to struct of energy, stopping and depth (ESx) for 2nd half of this sublayer pFpos  (I+O) Pointer to index of sublayer position into the layer. thick  (O) Pointer to thickness of current sublayer. ESxA  (O) Pointer to Array of sublayers in the current layer. Returns: always 0. Todo: : check if the thressholds of these conditions are reasonable or should be more conservative. The reallocation of ESxArray could be done inteligently in increments larger than 2, thus sacrificing some memory to speed up the process. Some extra variable would also be needed to remember the actual dimension of the matrix and comparing it with pFpos. Definition at line 1884 of file libcpixe.c. References EXP_PARAM::BeamEner, foil::comp, EXP_PARAM::cosFac, ESxType::ep, getSP(), ESxType::stpp, and ESxType::x. Referenced by createsublyrs().

int symbol2Z (  char *  symbol  )

Returns the atomic number for a certain element (up to Z=109) This is a faster version than that of hstoplib.c because it does not access any file. Parameters: symbol  (I) Chemical symbol of the element (case insensitive) Returns: Atomic Number Array containing the chemical symbols from H(Z=1) to Mt(Z=109) Definition at line 469 of file libcpixe.c. References ChemSymb. Referenced by readAbsCoef(), readCalcFlags(), readCOMPOUND(), readEXP_PARAM(), readFCK(), readINPUT(), and readXYld().

double TotAbsor (  const AbsCoef *  TotAbsCoefArray, const COMPOUND *  cmp, double  Xray )

Calculates the total absoption (it returns it as a double) for a given X-ray line in a given compound Parameters: TotAbsCoefArray  (I) Array containing a tables of Absorption Coefs (see readAbsCoef() ) cmp  (I) Definition of the absorber material. Xray  (I) Energy of the X-ray, in keV Returns: Total absorption coefficient < Todo: This function returns 0 if the Xray energy is not in the range covered by stdener. Maybe an error (and exit) should be triggered instead. Moreover: Is this absolutely general? I think this limits the generality of the program since elements below Na cannot be treated (and this is not desirable from a generalistic point of view). Therefore, these limits should be coded as variables just as minK, maxK,... UPDATE 1: The limits can be expanded, but the X-absorption data table should be altered accordingly (and dimstdener too). UPDATE 2: Better to show a warning than to exit in case that the limits are violated (TODO). Definition at line 1698 of file libcpixe.c. References COMPOUND::elem, COMPOUND::nelem, TotAbsor_elemental(), COMPOUND::xn, and ELEMENT::Z. Referenced by initlyr(), and Transmission().

double TotAbsor_elemental (  int  iener, const AbsCoef *  Absco, int  Z, double  Xray )

Calculates the total absoption coefficient (it returns it as a double) for a given X-ray line in a given element. Parameters: iener  (I) Index of the absorption line to be considered Absco  (I) Pointer to structure of Absorption Coefs for the absorber element Z  (I) Atomic number of the absorber element Xray  (I) Energy of the X-ray, in keV Returns: Total absorption coefficient Todo: This function returns 0 if the Xray energy is not in the 1-30 range. Maybe an error (and exit) should be triggered instead. Moreover: Is this absolutely general? I think this limits the generality of the program since elements below Na cannot be treated (and this is not desirable from a generalistic point of view). Therefore, these limits should be coded as variables just as minK, maxK,... UPDATE 1: The limits can be expanded, but the X-absorption data table should be altered accordingly. UPDATE 2: Better to show a warning than to exit in case that the limits are violated (TODO). Definition at line 1742 of file libcpixe.c. References AbsCoef::coefenr, AbsCoef::coefstd, and AbsCoef::enr. Referenced by sigmaphoto(), and TotAbsor().

int Transmission (  const XrayYield *  XYldArray, const AbsCoef *  TotAbsCoefArray, int  Z, const foil *  pFoil, double  geomcorr, const CalibYld *  pTransOld, CalibYld *  pTrans )

Calculates the Transmission coefficients for a given foil (whith effective thickness calculated using a geometric correction). Parameters: XYldArray  (I) Array of Xray yield coefs. See readXYld() TotAbsCoefArray  (I) Array containing a tables of Absorption Coefs (see readAbsCoef() ) Z  (I) Atomic number of the element for whose lines the transmission is calculated pFoil  (I) pointer to the current foil definition geomcorr  (I) geometric correction to the foil thickness (allows tiltings) pTransOld  (I) If this pointer is not null, pTrans will be multiplied by it line-by-line. pTrans  (O) Structure where the transmission coefs for each line are returned. Returns: Always 0 Definition at line 1655 of file libcpixe.c. References foil::comp, XrayYield::ener, CalibYld::K_, CalibYld::L_, CalibYld::M_, foil::thick, and TotAbsor(). Referenced by FilterTrans(), and initlyr().

int Xprod (  const AbsCoef *  AbsC, const FluorCKCoef *  pFCK, atomicnumber  Z1, atomicnumber  Z2, double  M2, double  ener, CalibYld *  XYld )

Calculates X-Ray production efficiency for a given beam and target, in cm2/(1e15at). Parameters: AbsC  (I) pointer to Absorption coef structure for Z2 pFCK  (I) pointer to Fluorescence and Coster-Kronig coefficients for Z2 Z1  (I) atomic number of the ion (note: currently only Z1=1 is supported) Z2  (I) atomic number of the target M2  (I) mass of the target atom ener  (I) energy of the incident ion, in keV XYld  (O) Pointer to return the X-ray production efficiency, in cm2/(1e15at) Returns: Always 0 Todo: This function only works for proton beams!! Todo: Check hardcoded Z limits Check hardcoded Z limits Check hardcoded Z limits Definition at line 2151 of file libcpixe.c. References FluorCKCoef::k, CalibYld::K_, CalibYld::L_, PaulX(), ReisX(), and SecXL. Referenced by cpixecalib(), deNormalize(), and integrate_Simpson().

int Z2mass (  int  Z, double *  mass, char  option )

Returns mass information for a given element (specified by its atomic number). Currently the range is limited from Z=1 (H) to Z=92 (U). It provides the Natural (average) weight, Most Abundant Isotope (MAI) weight and Most Abundant Isotope number of nucleons Parameters: Z  (I) Atomic number mass  (O) mass in amu. See also the "option" argument. option  (I) Either 'n' or 'm' to select "Natural" or "MAI" mass, respectively Returns: Number of nucleons of the Most Abundant Isotope Array containing the chemical symbols from H(Z=1) to Es(Z=99) Definition at line 500 of file libcpixe.c. Referenced by cpixecalib(), integrate_Simpson(), readAbsCoef(), readCOMPOUND(), readEXP_PARAM(), readINPUT(), readXYld(), translatesample(), and translatesample2().

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