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Merged muonspin/musrfit:root6 into master

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Zaher Salman 2021-04-19 15:20:12 +02:00
commit c638456afe
12 changed files with 648 additions and 2 deletions
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6
CMakeLists.txt
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@ -5,13 +5,14 @@ if (CMAKE_VERSION GREATER_EQUAL 3.12)
cmake_policy(SET CMP0075 NEW) cmake_policy(SET CMP0075 NEW)
endif (CMAKE_VERSION GREATER_EQUAL 3.12) endif (CMAKE_VERSION GREATER_EQUAL 3.12)
project(musrfit VERSION 1.7.1 LANGUAGES C CXX) project(musrfit VERSION 1.7.2 LANGUAGES C CXX)
#--- musrfit specific options ------------------------------------------------- #--- musrfit specific options -------------------------------------------------
option(nexus "build optional NeXus support. Needed for ISIS" OFF) option(nexus "build optional NeXus support. Needed for ISIS" OFF)
option(ASlibs "build optional ASlibs" OFF) option(ASlibs "build optional ASlibs" OFF)
option(BMWlibs "build optional BMWlibs" OFF) option(BMWlibs "build optional BMWlibs" OFF)
option(BNMRlibs "build optional beta-NMR libs" OFF) option(BNMRlibs "build optional beta-NMR libs" OFF)
option(DummyUserFcn "build optional dummy user function" OFF)
option(qt_based_tools "try to install Qt based tools (musredit, musrWiz, musrStep, mupp)" ON) option(qt_based_tools "try to install Qt based tools (musredit, musrWiz, musrStep, mupp)" ON)
option(try_OpenMP "try to use OpenMP if available" ON) option(try_OpenMP "try to use OpenMP if available" ON)
# define qt_version with possible values 'auto' or version '3', '4', '5', '6' # define qt_version with possible values 'auto' or version '3', '4', '5', '6'
@ -311,6 +312,9 @@ if (BNMRlibs)
else (BNMRlibs) else (BNMRlibs)
message(" BNMRlibs : no") message(" BNMRlibs : no")
endif (BNMRlibs) endif (BNMRlibs)
if (DummyUserFcn)
message(" PDummyUserFcn : yes")
endif (DummyUserFcn)
if (qt_based_tools) if (qt_based_tools)
if (Qt6Core_FOUND) if (Qt6Core_FOUND)

14
ChangeLog
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@ -12,7 +12,19 @@ or
https://bitbucket.org/muonspin/musrfit/commits/all https://bitbucket.org/muonspin/musrfit/commits/all
Release of V1.7.0, 2021/03/30 Release of V1.7.2, 2021/04/16
=============================
add a full dummy user function class with a global part. This can be used as
a starting point to develop new polarization functions.
Currently no rge-handling present.
Release of V1.7.1, 2021/04/09
=============================
update of the docu. More version info. Dealing with the upcoming ROOT V6.24.
Release of V1.7.0, 2021/04/30
============================= =============================
Centralize the rge-handling for user functions. Centralize the rge-handling for user functions.

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doc/examples/UserFcnWithGlobal/README Normal file
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@ -0,0 +1,18 @@
/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/
Simple Example for a User Function *with* a Global Part
/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/
The source code is found under
<musrfit-dir>src/external/DummyUserFcn
For details see there.
This dummy user function implements an exp(-lambda*t)
in the global part. This is the most efficient way,
since the function time vector is only calculated once
when the parameter (lambda) changes. For all the
subsequent calls a lookup table is used to return the
value of the user function.

73
doc/examples/UserFcnWithGlobal/test-histo-PSI-BIN-UserFcn.msr Normal file
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FeSe 9p4 TF100 p107apr09_sample*1p02
###############################################################
FITPARAMETER
# Nr. Name Value Step Pos_Error Boundaries
1 Asy 0.2622 -0.0014 0.0014 0 0.33
2 Rate 0.3188 -0.0044 0.0044
3 Field 97.853 -0.056 0.056 0 200
4 Phase_L 178.95 -0.41 0.41
5 Phase_R 1.75 -0.39 0.39
6 N0_L 1097.9 -1.0 1.0
7 N0_R 1159.7 -1.0 1.0
8 Bkg_L 54.47 -0.20 0.20
9 Bkg_R 46.70 -0.19 0.19
###############################################################
THEORY
asymmetry 1
userFcn libPDummyUserFcn PDummyUserFcn 2 (rate)
TFieldCos map1 fun1 (phase frequency)
###############################################################
FUNCTIONS
fun1 = par3 * gamma_mu
###############################################################
GLOBAL
fittype 0 (single histogram fit)
fit 0 8.2
packing 1
###############################################################
RUN ../data/deltat_pta_gpd_0423 PIE1 PSI PSI-BIN (name beamline institute data-file-format)
norm 6
backgr.fit 8
map 4 0 0 0 0 0 0 0 0 0
forward 1
data 165 7965
t0 162.0
RUN ../data/deltat_pta_gpd_0423 PIE1 PSI PSI-BIN (name beamline institute data-file-format)
norm 7
backgr.fit 9
map 5 0 0 0 0 0 0 0 0 0
forward 2
data 205 7965
t0 202.0
###############################################################
COMMANDS
SCALE_N0_BKG TRUE
MINIMIZE
MINOS
SAVE
###############################################################
PLOT 0 (single histo plot)
lifetimecorrection
runs 1 2
range 0.0 9.5 -0.3 0.3
view_packing 25
###############################################################
FOURIER
units Gauss # units either 'Gauss', 'Tesla', 'MHz', or 'Mc/s'
fourier_power 12
apodization NONE # NONE, WEAK, MEDIUM, STRONG
plot REAL # REAL, IMAG, REAL_AND_IMAG, POWER, PHASE
phase par4 par5
range 0.0 200.0
###############################################################
STATISTIC --- 2015-01-05 14:09:47
chisq = 663.9, NDF = 515, chisq/NDF = 1.289169

4
src/external/CMakeLists.txt vendored
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@ -29,3 +29,7 @@ if (nexus)
add_subdirectory(nexus) add_subdirectory(nexus)
endif (nexus) endif (nexus)
if (DummyUserFcn)
add_subdirectory(DummyUserFcn)
endif (DummyUserFcn)

1
src/external/DummyUserFcn/CMakeLists.txt vendored Normal file
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@ -0,0 +1 @@
add_subdirectory(src)

99
src/external/DummyUserFcn/README vendored Normal file
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@ -0,0 +1,99 @@
/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/
Simple Example for a User Function *with* a Global Part
/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/
This is a full implementation of a user function with a global part.
For a general intro to user function, please check the manual under
http://lmu.web.psi.ch/musrfit/user/html/user-manual.html#id38
The implemented user function is
exp(-lambda*t)
with lambda, being the only parameter.
Short description of the PDummyUserFcn and PDummyUserFcnGlobal classes.
PDummyUserFcn:
-------------
This class derives from the PUserFcnBase which is necessary to make this
user function available to musrfit.
The three functions:
virtual Bool_t NeedGlobalPart() const { return true; }
virtual void SetGlobalPart(std::vector<void*> &globalPart, UInt_t idx);
virtual Bool_t GlobalPartIsValid() const;
are used to bind the global part of the user function.
The method
virtual Double_t operator()(Double_t t, const std::vector<Double_t> &param) const;
is called by musrfit when evaluate the function.
The private variables:
Bool_t fValid{true};
Bool_t fInvokedGlobal{false};
Int_t fIdxGlobal;
PDummyUserFcnGlobal *fDummyUserFcnGlobal{nullptr};
have the following purpose:
fValid is a boolean variable holding the state of the user function.
If true, it means that the user function is useable. In case
something would go wrong during the initialization stage fValid
is set to false, and no calculation will take place!
fInvokedGlobal is a boolean variable which is set to true is the global
part of the user function is properly invoked.
fIdxGlobal holds the index of the global user function part.
PDummyUserFcnGlobal:
-------------------
This class holds the gloabl user function part, which handles the actual
calculation of the user function.
CalculatePol(const std::vector<Double_t> &param) const; -> carries out the
necessary calculations of this user function. This is ONLY carried
out if the parameter set has changed!
GetPolValue(const Double_t t) const; -> This is used in the operator() of
the user function to get the value of the user function (here a
value of a polarization function exp()).
mutable std::vector<Double_t> fPreviousParam; -> holds the previous
parmeter set in order to check if a parameter set has changed.
mutable std::vector<Double_t> fPol; -> lookup table for the polarization
function for the current parameter set.
How to build:
------------
When configure musrfit, there is a switch DummyUserFcn available which
needs to be enabled (default: OFF), e.g.
cmake ../ -DCMAKE_INSTALL_PREFIX=$ROOTSYS -Dnexus=1 -DDummyUserFcn=1
Files:
-----
CMakeLists.txt <- this File is needed to allow to build an install
this dummy example with the cmake build system.
inc/PDummyUserFcn.h <- header file definig the needed classes for
the user function and its globale part.
inc/PDummyUserFcnLinkDef.h <- Needed as a glue to generate the necessary
root dictionaries.
src/CMakeLists.txt <- needed for the cmake build/install process.
src/PDummyUserFcn.cpp <- source code which implements all the necessary
parts of the user function.
src/PDummyUserFcn.pc.in <- cmake input file to generate the propoer
pkg-config file for the library

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src/external/DummyUserFcn/inc/PDummyUserFcn.h vendored Normal file
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@ -0,0 +1,81 @@
/***************************************************************************
PDummyUserFcn.h
Author: Andreas Suter
e-mail: andreas.suter@psi.ch
***************************************************************************/
/***************************************************************************
* Copyright (C) 2013-2021 by Andreas Suter *
* andreas.suter@psi.ch *
* *
* 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. *
***************************************************************************/
#ifndef _PDUMMYUSERFNC_H_
#define _PDUMMYUSERFNC_H_
#include <vector>
#include "PUserFcnBase.h"
class PDummyUserFcnGlobal
{
public:
PDummyUserFcnGlobal();
virtual ~PDummyUserFcnGlobal();
Bool_t IsValid() { return fValid; }
virtual void CalculatePol(const std::vector<Double_t> &param) const;
virtual Double_t GetPolValue(const Double_t t) const;
private:
Bool_t fValid{true};
mutable std::vector<Double_t> fPreviousParam;
mutable Double_t fTimeStep{1.0e-3}; // time in (us), time step 1 (ns) here
mutable std::vector<Double_t> fPol;
ClassDef(PDummyUserFcnGlobal, 1)
};
class PDummyUserFcn : public PUserFcnBase
{
public:
PDummyUserFcn() {}
virtual ~PDummyUserFcn();
virtual Bool_t NeedGlobalPart() const { return true; }
virtual void SetGlobalPart(std::vector<void*> &globalPart, UInt_t idx);
virtual Bool_t GlobalPartIsValid() const;
virtual Double_t operator()(Double_t t, const std::vector<Double_t> &param) const;
private:
Bool_t fValid{true};
Bool_t fInvokedGlobal{false};
Int_t fIdxGlobal;
PDummyUserFcnGlobal *fDummyUserFcnGlobal{nullptr};
// definition of the class for the ROOT dictionary
ClassDef(PDummyUserFcn, 1)
};
#endif // _PDUMMYUSERFNC_H_

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src/external/DummyUserFcn/inc/PDummyUserFcnLinkDef.h vendored Normal file
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@ -0,0 +1,39 @@
/***************************************************************************
PDummyUserFcnLinkDef.h
Author: Andreas Suter
e-mail: andreas.suter@psi.ch
***************************************************************************/
/***************************************************************************
* Copyright (C) 2013-2021 by Andreas Suter *
* andreas.suter@psi.ch *
* *
* 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. *
***************************************************************************/
#ifdef __CINT__
#pragma link off all globals;
#pragma link off all classes;
#pragma link off all functions;
#pragma link C++ class PDummyUserFcnGlobal+;
#pragma link C++ class PDummyUserFcn+;
#endif

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src/external/DummyUserFcn/src/CMakeLists.txt vendored Normal file
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@ -0,0 +1,78 @@
# - DummyUserFcn library --------------------------------------------------------
#--- generate necessary dictionaries ------------------------------------------
set(MUSRFIT_INC ${CMAKE_SOURCE_DIR}/src/include)
set(DUMMY_USER_FUNC_INC ${CMAKE_CURRENT_SOURCE_DIR}/../inc)
# ROOT requires that the dictonary header files are found at configuration time.
# Hence, target_include_directories cannot be used here because, targets are
# setup only afterwards.
include_directories(${DUMMY_USER_FUNC_INC})
root_generate_dictionary(
PDummyUserFcnDict
PDummyUserFcn.h
OPTIONS
-I${FFTW3_INCLUDE_DIR}
-I${MUSRFIT_INC}
-I${DUMMY_USER_FUNC_INC}
-inlineInputHeader
LINKDEF ${DUMMY_USER_FUNC_INC}/PDummyUserFcnLinkDef.h
MODULE PDummyUserFcn
)
#--- create pkg-config info ---------------------------------------------------
set(prefix "${CMAKE_INSTALL_PREFIX}")
set(exec_prefix "\$\{prefix\}")
set(libdir "\$\{exec_prefix\}/lib")
set(includedir "\$\{prefix\}/include")
set(P_DUMMY_USER_FUNC_VERSION "1.0.0")
set(P_DUMMY_USER_FUNC_LIBRARY_NAME "PDummyUserFcn")
configure_file("PDummyUserFcn.pc.in" "PDummyUserFcn.pc" @ONLY)
#--- lib creation -------------------------------------------------------------
add_library(PDummyUserFcn SHARED
PDummyUserFcn.cpp
PDummyUserFcnDict.cxx
)
#--- set target properties, e.g. version --------------------------------------
set_target_properties(PDummyUserFcn
PROPERTIES
VERSION ${P_DUMMY_USER_FUNC_VERSION}
)
#--- make sure that the include directory is found ----------------------------
target_include_directories(
PDummyUserFcn BEFORE PRIVATE
$<BUILD_INTERFACE:${FFTW3_INCLUDE_DIR}>
$<BUILD_INTERFACE:${MUSRFIT_INC}>
$<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/../inc>
)
#--- add library dependencies -------------------------------------------------
target_link_libraries(PDummyUserFcn ${FFTW3_LIBRARY} ${ROOT_LIBRARIES} PUserFcnBase)
#--- install PDummyUserFcn solib -------------------------------------------------
install(TARGETS PDummyUserFcn DESTINATION lib)
#--- install root pcm's and rootmaps ------------------------------------------
install(
FILES ${CMAKE_CURRENT_BINARY_DIR}/libPDummyUserFcn_rdict.pcm
${CMAKE_CURRENT_BINARY_DIR}/libPDummyUserFcn.rootmap
DESTINATION lib
)
#--- install PDummyUserFcn header ------------------------------------------------
install(
FILES
${CMAKE_CURRENT_SOURCE_DIR}/../inc/PDummyUserFcn.h
DESTINATION
include
)
#--- install pkg-config info --------------------------------------------------
install(
FILES ${CMAKE_CURRENT_BINARY_DIR}/PDummyUserFcn.pc
DESTINATION lib/pkgconfig
)

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@ -0,0 +1,227 @@
/***************************************************************************
PDummyUserFcn.cpp
Author: Andreas Suter
e-mail: andreas.suter@psi.ch
***************************************************************************/
/***************************************************************************
* Copyright (C) 2009-2021 by Andreas Suter *
* andreas.suter@psi.ch *
* *
* 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 <cassert>
#include <cmath>
#include <iostream>
#include <TMath.h>
#include "PDummyUserFcn.h"
ClassImp(PDummyUserFcnGlobal)
//--------------------------------------------------------------------------
// Constructor
//--------------------------------------------------------------------------
/**
* <p>Here would go all the stuff which will be needed by the global part.
* For instance specific information which come from a startup XML file.
* This could be case if muon-stopping information is needed for the
* calculation, or any other user function specific stuff which is not
* part of the parameters which will be propagated from the msr-file.
*/
PDummyUserFcnGlobal::PDummyUserFcnGlobal()
{
// nothing needed here for the dummy
}
//--------------------------------------------------------------------------
// Destructor
//--------------------------------------------------------------------------
/**
*
*/
PDummyUserFcnGlobal::~PDummyUserFcnGlobal()
{
fPreviousParam.clear();
fPol.clear();
}
//--------------------------------------------------------------------------
// CalculatePol (public)
//--------------------------------------------------------------------------
/**
* <p>Calculates the polarization function for the dummy user function.
* For the Dummy this is just an exp(-lambda t), where lambda is comming
* from the param.
*
* \param param the parameter for this user function
*/
void PDummyUserFcnGlobal::CalculatePol(const std::vector<Double_t> &param) const
{
// param: [0] lambda
// check that param is new and hence a calculation is needed
Bool_t newParams = false;
if (fPreviousParam.size() == 0) {
for (UInt_t i=0; i<param.size(); i++)
fPreviousParam.push_back(param[i]);
newParams = true;
} else {
assert(param.size() == fPreviousParam.size());
for (UInt_t i=0; i<param.size(); i++) {
if (param[i] != fPreviousParam[i]) {
newParams = true;
break;
}
}
}
if (!newParams)
return;
// keep parameters
for (UInt_t i=0; i<param.size(); i++)
fPreviousParam[i] = param[i];
// calculate the "polarization" in the time interval t = [0, 20] us
Double_t dt = fTimeStep, t = 0.0;
Int_t noOfPoints = 20.0 / dt;
fPol.resize(noOfPoints); // this makes sure that the polarization vector is long enough
for (Int_t i=0; i<noOfPoints; i++) {
t = i*dt;
fPol[i] = exp(-param[0] * i * dt);
}
}
//--------------------------------------------------------------------------
// GetMagneticField
//--------------------------------------------------------------------------
/**
*
*/
Double_t PDummyUserFcnGlobal::GetPolValue(const Double_t t) const
{
Double_t result = -1.0;
if (t < 0)
return 1.0;
if (t >= 20.0)
return 0.0;
Int_t idx = (Int_t)(t/fTimeStep);
if ((idx >=0) && (idx < fPol.size()))
result = fPol[idx];
return result;
}
//++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
ClassImp(PDummyUserFcn)
//--------------------------------------------------------------------------
// Destructor
//--------------------------------------------------------------------------
/**
*
*/
PDummyUserFcn::~PDummyUserFcn()
{
if ((fDummyUserFcnGlobal != nullptr) && fInvokedGlobal) {
delete fDummyUserFcnGlobal;
fDummyUserFcnGlobal = nullptr;
}
}
//--------------------------------------------------------------------------
// SetGlobalPart (public)
//--------------------------------------------------------------------------
/**
* <p>
*
* <b>return:</b>
*
* \param globalPart
* \param idx
*/
void PDummyUserFcn::SetGlobalPart(std::vector<void*> &globalPart, UInt_t idx)
{
fIdxGlobal = static_cast<Int_t>(idx);
if ((Int_t)globalPart.size() <= fIdxGlobal) {
fDummyUserFcnGlobal = new PDummyUserFcnGlobal();
if (fDummyUserFcnGlobal == nullptr) {
fValid = false;
std::cerr << std::endl << ">> PDummyUserFcn::SetGlobalPart(): **ERROR** Couldn't invoke global user function object, sorry ..." << std::endl;
} else if (!fDummyUserFcnGlobal->IsValid()) {
fValid = false;
std::cerr << std::endl << ">> PDummyUserFcn::SetGlobalPart(): **ERROR** initialization of global user function object failed, sorry ..." << std::endl;
} else {
fValid = true;
fInvokedGlobal = true;
globalPart.resize(fIdxGlobal+1);
globalPart[fIdxGlobal] = dynamic_cast<PDummyUserFcnGlobal*>(fDummyUserFcnGlobal);
}
} else {
fValid = true;
fDummyUserFcnGlobal = (PDummyUserFcnGlobal*)globalPart[fIdxGlobal];
}
}
//--------------------------------------------------------------------------
// GlobalPartIsValid (public)
//--------------------------------------------------------------------------
/**
* <p>
*
* <b>return:</b>
*/
Bool_t PDummyUserFcn::GlobalPartIsValid() const
{
return (fValid && fDummyUserFcnGlobal->IsValid());
}
//--------------------------------------------------------------------------
// operator()
//--------------------------------------------------------------------------
/**
*
*/
Double_t PDummyUserFcn::operator()(Double_t t, const std::vector<Double_t> &param) const
{
// param: [0] lambda
assert(param.size() == 1);
// for negative time return polarization == 1
if (t <= 0.0)
return 1.0;
// calculate field if parameter have changed
fDummyUserFcnGlobal->CalculatePol(param);
// return the lookup table value
return fDummyUserFcnGlobal->GetPolValue(t);
}

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@ -0,0 +1,10 @@
prefix=@prefix@
exec_prefix=@exec_prefix@
libdir=@libdir@
includedir=@includedir@
Name: PDummyUserFcn
Description: C++ shared library providing the spin valve fitter class
Version: @P_DUMMY_USER_FUNC_VERSION@
Libs: -L${libdir} -l@P_DUMMY_USER_FUNC_LIBRARY_NAME@
Cflags: -I${includedir}