Added autotool-support for building musrfit - some additional tests are needed, the old Makefiles are still around

src/Makefile.am

@@ -0,0 +1,20 @@
+## Process this file with automake to create Makefile.in
+
+SUBDIRS = classes external
+
+bin_PROGRAMS = musrfit musrview musrt0 musrparam msr2msr
+musrfit_SOURCES = musrfit.cpp
+musrview_SOURCES = musrview.cpp
+musrt0_SOURCES = musrt0.cpp
+musrparam_SOURCES = musrparam.cpp
+msr2msr_SOURCES = msr2msr.cpp
+
+xmldir = $(bindir)
+xml_DATA = musrfit_startup.xml
+
+LIBADD = $(LEM_LIBS) $(PMUSR_LIBS)
+
+AM_CFLAGS = -g -O3 -Wall -Wno-trigraphs
+INCLUDES = $(PMUSR_CFLAGS) $(FFTW3_CFLAGS) $(GSL_CFLAGS) $(BOOST_CFLAGS) $(ROOT_CFLAGS)
+LIBS = $(LEM_LIBS) $(PMUSR_LIBS) $(FFTW3_LIBS) $(GSL_LIBS) $(ROOT_LIBS)
+

src/README

@@ -1,25 +0,0 @@
-#---------------------------------------------------------------------
-# README
-# Andreas Suter, 2008/01/15
-# $Id$
-#---------------------------------------------------------------------
-
-To get it all build:
-
-1) go to the subdiretory 'classes' and execute
-
-   make -f Makefile.PMusr
-   make -f Makefile.PMusr install (as root)
-   
-2) if the privous step worked execute in the current directory (in which 
-   you found this README)
-   
-   make clean
-   make 
-   make install
-   
-In the optimal case, everything is setup ;-)
-
-#---------------------------------------------------------------------
-# this is the end ...
-#---------------------------------------------------------------------

src/classes/Makefile.PMusr

@@ -44,7 +44,7 @@ endif
 
 # -- Linux
 ifeq ($(OS),LINUX)
-CXX           = g++
+CXX           = g++-4.2.4
 CXXFLAGS      = -O3 -Wall -Wno-trigraphs -fPIC
 PMUSRPATH     = ../include
 MNPATH        = $(ROOTSYS)/include
@@ -54,7 +54,7 @@ FFTW3PATH     = /usr/include
 LEMPATH       = ../external/TLemRunHeader
 PSIBINPATH    = ../external/MuSR_software/Class_MuSR_PSI
 INCLUDES      = -I$(PMUSRPATH) -I$(MNPATH) -I$(GSLPATH) -I$(BOOSTPATH) -I$(LEMPATH) -I$(PSIBINPATH) -I$(FFTW3PATH)
-LD            = g++
+LD            = g++-4.2.4
 LDFLAGS       = -O
 SOFLAGS       = -shared
 LEMLIB        = libTLemRunHeader.so

src/classes/Makefile.PUserFcn

@@ -34,10 +34,10 @@ endif
 
 # -- Linux
 ifeq ($(OS),LINUX)
-CXX           = g++
+CXX           = g++-4.3.3
 CXXFLAGS      = -Wall -Wno-trigraphs -fPIC
 INCLUDES      = -I../include
-LD            = g++
+LD            = g++-4.3.3
 LDFLAGS       = -g
 SOFLAGS       = -O -shared
 endif

src/classes/Makefile.am

@@ -0,0 +1,90 @@
+## Process this file with automake to create Makefile.in
+
+h_sources = \
+  ../include/PFitterFcn.h \
+  ../include/PFitter.h \
+  ../include/PFourier.h \
+  ../include/PFunctionGrammar.h \
+  ../include/PFunction.h \
+  ../include/PFunctionHandler.h \
+  ../include/PMsrHandler.h \
+  ../include/PMusrCanvas.h \
+  ../include/PMusr.h \
+  ../include/PMusrT0.h \
+  ../include/PRunAsymmetry.h \
+  ../include/PRunBase.h \
+  ../include/PRunDataHandler.h \
+  ../include/PRunListCollection.h \
+  ../include/PRunNonMusr.h \
+  ../include/PRunRRF.h \
+  ../include/PRunSingleHisto.h \
+  ../include/PStartupHandler.h \
+  ../include/PTheory.h \
+  ../include/PUserFcnBase.h 
+
+h_linkdef = \
+  ../include/PMusrCanvasLinkDef.h \
+  ../include/PMusrT0LinkDef.h \
+  ../include/PStartupHandlerLinkDef.h \
+  ../include/PUserFcnBaseLinkDef.h
+
+dict_h_sources = \
+  PMusrCanvasDict.h \
+  PMusrT0Dict.h \
+  PStartupHandlerDict.h \
+  PUserFcnBaseDict.h
+
+cpp_sources = \
+  PFitter.cpp \
+  PFitterFcn.cpp \
+  PFourier.cpp \
+  PFunction.cpp \
+  PFunctionHandler.cpp \
+  PMsrHandler.cpp \
+  PMusrCanvas.cpp \
+  PMusrT0.cpp \
+  PRunAsymmetry.cpp \
+  PRunBase.cpp \
+  PRunDataHandler.cpp \
+  PRunListCollection.cpp \
+  PRunNonMusr.cpp \
+  PRunRRF.cpp \
+  PRunSingleHisto.cpp \
+  PStartupHandler.cpp \
+  PTheory.cpp \
+  PUserFcnBase.cpp
+
+dict_cpp_sources = \
+  PMusrCanvasDict.cpp \
+  PMusrT0Dict.cpp \
+  PStartupHandlerDict.cpp \
+  PUserFcnBaseDict.cpp
+
+ext_source_dir = $(top_srcdir)/src/external/MuSR_software/Class_MuSR_PSI
+ext_h_sources = $(ext_source_dir)/MuSR_td_PSI_bin.h $(ext_source_dir)/tydefs.h
+ext_cpp_sources = $(ext_source_dir)/MuSR_td_PSI_bin.cpp 
+
+include_HEADERS = $(h_sources) $(ext_h_sources)
+noinst_HEADERS = $(h_linkdef) $(dict_h_sources)
+INCLUDES = -I$(top_srcdir)/src/include -I$(ext_source_dir) $(LEM_CFLAGS) $(FFTW3_CFLAGS) $(GSL_CFLAGS) $(BOOST_CFLAGS) $(ROOT_CFLAGS)
+AM_CXXFLAGS = -g -O3 -Wall -Wno-trigraphs
+
+BUILT_SOURCES = $(dict_cpp_sources) $(dict_h_sources)
+AM_CPPFLAGS = -I@ROOTINCDIR@
+AM_LDFLAGS = -L@ROOTLIBDIR@
+CLEANFILES = *Dict.cpp *Dict.h *~ core
+
+%Dict.cpp %Dict.h: ../include/%.h ../include/%LinkDef.h
+	@ROOTCINT@ -v -f $*Dict.cpp -c -p $(INCLUDES) $(AM_CPPFLAGS) $^
+
+lib_LTLIBRARIES = libPMusr.la
+
+LIBADD = $(LEM_LIBS)
+
+libPMusr_la_SOURCES = $(h_sources) $(cpp_sources) $(dict_h_sources) $(dict_cpp_sources) $(ext_h_sources) $(ext_cpp_sources)
+libPMusr_la_LIBADD = $(FFTW3_LIBS) $(GSL_LIBS) $(ROOT_LIBS)
+libPMusr_la_LDFLAGS = -version-info $(MUSR_LIBRARY_VERSION) -release $(MUSR_RELEASE)
+
+pkgconfigdir = $(libdir)/pkgconfig
+pkgconfig_DATA = PMusr.pc
+

src/classes/PFitter.cpp

@@ -31,6 +31,7 @@
 
 #include <iostream>
 #include <fstream>
+#include <limits>
 using namespace std;
 
 #include <math.h>
@@ -408,8 +409,11 @@ bool PFitter::ExecuteHesse()
   // create the hesse object
   ROOT::Minuit2::MnHesse hesse;
 
+  // specify maximal number of function calls
+  unsigned int maxfcn = numeric_limits<unsigned int>::max();
+
   // call hesse
-  ROOT::Minuit2::MnUserParameterState mnState = hesse((*fFitterFcn), fMnUserParams);
+  ROOT::Minuit2::MnUserParameterState mnState = hesse((*fFitterFcn), fMnUserParams, maxfcn);
 
   if (!mnState.IsValid()) {
     cout << endl << "**WARNING** PFitter::ExecuteHesse(): Hesse encountered some problems!";
@@ -453,7 +457,7 @@ bool PFitter::ExecuteMigrad()
 
   // minimize
   // maxfcn is MINUIT2 Default maxfcn
-  unsigned int maxfcn = (200 + 100*fParams.size() + 5*fParams.size()*fParams.size());
+  unsigned int maxfcn = numeric_limits<unsigned int>::max();
   // tolerance = MINUIT2 Default tolerance
   double tolerance = 0.1;
   ROOT::Minuit2::FunctionMinimum min = migrad(maxfcn, tolerance);
@@ -521,7 +525,7 @@ bool PFitter::ExecuteMinimize()
 
   // minimize
   // maxfcn is MINUIT2 Default maxfcn
-  unsigned int maxfcn = (200 + 100*fParams.size() + 5*fParams.size()*fParams.size());
+  unsigned int maxfcn = numeric_limits<unsigned int>::max();
 //cout << endl << "maxfcn=" << maxfcn << endl;
   // tolerance = MINUIT2 Default tolerance
   double tolerance = 0.1;
@@ -896,7 +900,7 @@ bool PFitter::ExecuteSimplex()
 
   // minimize
   // maxfcn is 10*MINUIT2 Default maxfcn
-  unsigned int maxfcn = 10*(200 + 100*fParams.size() + 5*fParams.size()*fParams.size());
+  unsigned int maxfcn = numeric_limits<unsigned int>::max();
   // tolerance = MINUIT2 Default tolerance
   double tolerance = 0.1;
   ROOT::Minuit2::FunctionMinimum min = simplex(maxfcn, tolerance);

src/classes/PMusr.pc.in

@@ -0,0 +1,10 @@
+prefix=@prefix@
+exec_prefix=@exec_prefix@
+libdir=@libdir@
+includedir=@includedir@
+
+Name: PMusr
+Description: C++ shared library providing musr classes
+Version: @VERSION@
+Libs: -L${libdir} -l@GENERIC_LIBRARY_NAME@
+Cflags: -I${includedir}/@GENERIC_LIBRARY_NAME@ -I${libdir}/include

src/external/Makefile.am

@@ -0,0 +1 @@
+SUBDIRS = TLemRunHeader scripts

src/external/TFitPofB-lib/classes/TBofZCalc.cpp

@@ -152,11 +152,16 @@ TLondon1D_1L::TLondon1D_1L(const vector<double> &param, unsigned int steps)
   fMinB = -1.0;
 
 // thicknesses have to be greater or equal to zero
-  for(unsigned int i(1); i<3; i++)
-    assert(param[i]>=0.);
+  for(unsigned int i(1); i<3; i++){
+    if(param[i] < 0.){
+      fParam[i] = 0.;
+    }
+  }
 
 // lambdas have to be greater than zero
-    assert(param[3]!=0.);
+  if(param[3] < 0.1){
+    fParam[3] = 0.1;
+  }
 
 // Calculate the coefficients of the exponentials
   double N0(param[0]/(1.0+exp(param[2]/param[3])));
@@ -194,7 +199,10 @@ double TLondon1D_1L::GetBmin() const
 void TLondon1D_1L::SetBmin()
 {
   double b_a(fCoeff[1]/fCoeff[0]);
-  assert (b_a>0.);
+// assert(b_a>0.);
+  if(b_a<10E-7){
+    b_a = 10E-7;
+  }
 
   double minZ;
   // check if the minimum is in the first layer
@@ -205,7 +213,14 @@ void TLondon1D_1L::SetBmin()
     return;
   }
 
-  assert(fMinZ > 0. && fMinB > 0.);
+//  assert(fMinZ > 0. && fMinB > 0.);
+  if(fMinZ <= 0.){
+    fMinZ = 0.;
+  }
+  if(fMinB <= 0.){
+    fMinB = 0.;
+  }
+
   return;
 }
 

src/external/TFitPofB-lib/classes/TLondon1D.cpp

@@ -204,6 +204,8 @@ double TLondon1DHS::operator()(double t, const vector<double> &par) const {
   if(t<0.0)
     return cos(par[0]*0.017453293);
 
+  bool dead_layer_changed(false);
+
   // check if the function is called the first time and if yes, read in parameters
 
   if(fFirstCall){
@@ -217,7 +219,8 @@ double TLondon1DHS::operator()(double t, const vector<double> &par) const {
       fParForBofZ.push_back(fPar[i]);
 //      cout << "fParForBofZ[" << i-2 << "] = " << fParForBofZ[i-2] << endl;
     }
-    fFirstCall=false;
+    fFirstCall = false;
+    dead_layer_changed = true;
 //  cout << this << endl;
   }
 
@@ -232,11 +235,11 @@ double TLondon1DHS::operator()(double t, const vector<double> &par) const {
       par_changed = true;
       if (i == 0) {
         only_phase_changed = true;
-      } else if (i == 3) {
-        fDeadLayerChanged = true;
-        only_phase_changed = false;
       } else {
         only_phase_changed = false;
+        if (i == 3) {
+          dead_layer_changed = true;
+        }
       }
     }
   }
@@ -261,12 +264,11 @@ double TLondon1DHS::operator()(double t, const vector<double> &par) const {
       fParForPofB[3] = par[2]; // Bkg-Field
       //fParForPofB[4] = 0.005; // Bkg-width (in principle zero)
 
-      if(fDeadLayerChanged){
+      if(dead_layer_changed){
         vector<double> interfaces;
         interfaces.push_back(par[3]);// dead layer
         fParForPofB[5] = fImpProfile->LayerFraction(par[1], 1, interfaces); // Fraction of muons in the deadlayer
         interfaces.clear();
-        fDeadLayerChanged = false;
       }
 
       TLondon1D_HS BofZ(fParForBofZ);
@@ -615,7 +617,9 @@ TProximity1D1LHS::TProximity1D1LHS() : fCalcNeeded(true), fFirstCall(true) {
     fParForPofB.push_back(startupHandler->GetDeltat());
     fParForPofB.push_back(startupHandler->GetDeltaB());
     fParForPofB.push_back(0.0);
-//    fParForPofB.push_back(0.0);
+    fParForPofB.push_back(0.0); // Bkg-Field
+    fParForPofB.push_back(0.005); // Bkg-width
+    fParForPofB.push_back(0.0); // Bkg-weight
 
     TTrimSPData *x = new TTrimSPData(rge_path, energy_vec);
     fImpProfile = x;
@@ -652,6 +656,7 @@ double TProximity1D1LHS::operator()(double t, const vector<double> &par) const {
   // check if the function is called the first time and if yes, read in parameters
 
   bool width_changed(false);
+  bool dead_layer_changed(false);
 
   if(fFirstCall){
     fPar = par;
@@ -666,6 +671,7 @@ double TProximity1D1LHS::operator()(double t, const vector<double> &par) const {
     }
     fFirstCall=false;
     width_changed = true;
+    dead_layer_changed = true;
 //  cout << this << endl;
   }
 
@@ -685,6 +691,9 @@ double TProximity1D1LHS::operator()(double t, const vector<double> &par) const {
         if (i == 7){
           width_changed = true;
         }
+        if (i == 4){
+          dead_layer_changed = true;
+        }
       }
     }
   }
@@ -705,11 +714,19 @@ double TProximity1D1LHS::operator()(double t, const vector<double> &par) const {
       for (unsigned int i(2); i<fPar.size(); i++)
         fParForBofZ[i-2] = par[i];
 
-      fParForPofB[2] = par[1]; // energy
-
       if(width_changed) { // Convolution of the implantation profile with Gaussian
         fImpProfile->ConvolveGss(par[7], par[1]);
-        width_changed = false;
+      }
+
+      fParForPofB[2] = par[1]; // energy
+      fParForPofB[3] = par[2]; // Bkg-Field
+      //fParForPofB[4] = 0.005; // Bkg-width (in principle zero)
+
+      if(dead_layer_changed){
+        vector<double> interfaces;
+        interfaces.push_back(par[4]);// dead layer
+        fParForPofB[5] = fImpProfile->LayerFraction(par[1], 1, interfaces); // Fraction of muons in the deadlayer
+        interfaces.clear();
       }
 
       TProximity1D_1LHS BofZ(fParForBofZ);

src/external/TFitPofB-lib/classes/TPofBCalc.cpp

@@ -186,7 +186,8 @@ TPofBCalc::TPofBCalc( const TBofZCalcInverse &BofZ, const TTrimSPData &dataTrimS
   for (unsigned int i(firstZerosEnd); i<lastZerosStart; i++)
     fPB[i] /= pBsum;
 
-  AddBackground(para[3], para[4], para[5]);
+  if(para.size() == 6)
+    AddBackground(para[3], para[4], para[5]);
 
 }
 

src/external/TFitPofB-lib/include/TLondon1D.h

@@ -30,7 +30,6 @@ private:
   TPofTCalc *fPofT;
   mutable bool fCalcNeeded;
   mutable bool fFirstCall;
-  mutable bool fDeadLayerChanged;
   mutable vector<double> fParForPofT;
   mutable vector<double> fParForBofZ;
   mutable vector<double> fParForPofB;

src/external/TLemRunHeader/Makefile.am

@@ -0,0 +1,43 @@
+## Process this file with automake to create Makefile.in
+
+h_sources = \
+  TLemStats.h \
+  TLemRunHeader.h
+
+h_linkdef = \
+  TLemStatsLinkDef.h \
+  TLemRunHeaderLinkDef.h
+
+dict_h_sources = \
+  TLemStatsDict.h \
+  TLemRunHeaderDict.h
+
+cpp_sources = \
+  TLemStats.cxx \
+  TLemRunHeader.cxx
+
+dict_cpp_sources = \
+  TLemStatsDict.cxx \
+  TLemRunHeaderDict.cxx
+
+include_HEADERS = $(h_sources)
+noinst_HEADERS = $(h_linkdef) $(dict_h_sources)
+INCLUDES = -I. $(ROOT_CFLAGS)
+
+BUILT_SOURCES = $(dict_cpp_sources) $(dist_h_sources)
+AM_CPPFLAGS = -I@ROOTINCDIR@
+AM_LDFLAGS = -L@ROOTLIBDIR@
+CLEANFILES = *Dict.cxx *Dict.h *~ core
+
+%Dict.cxx %Dict.h: %.h %LinkDef.h
+	@ROOTCINT@ -v -f $*Dict.cxx -c -p $(INCLUDES) $(AM_CPPFLAGS) $^
+
+lib_LTLIBRARIES = libTLemRunHeader.la
+
+libTLemRunHeader_la_SOURCES = $(h_sources) $(cpp_sources) $(dict_h_sources) $(dict_cpp_sources)
+libTLemRunHeader_la_LIBADD = $(ROOT_LIBS)
+libTLemRunHeader_la_LDFLAGS = -version-info $(LEM_LIBRARY_VERSION) -release $(LEM_RELEASE)
+
+pkgconfigdir = $(libdir)/pkgconfig
+pkgconfig_DATA = TLemRunHeader.pc
+

src/external/TLemRunHeader/TLemRunHeader.pc.in

@@ -0,0 +1,10 @@
+prefix=@prefix@
+exec_prefix=@exec_prefix@
+libdir=@libdir@
+includedir=@includedir@
+
+Name: TLemRunHeader
+Description: C++ shared library providing the LEM Run Header class
+Version: @VERSION@
+Libs: -L${libdir} -l@GENERIC_LIBRARY_NAME@
+Cflags: -I${includedir}

src/external/scripts/Makefile.am

@@ -0,0 +1 @@
+bin_SCRIPTS = msr2data

src/musrgui/musrgui.pro

@@ -9,8 +9,8 @@ exists( /usr/bin/cygwin1.dll ) {
 }
 
 INSTALLS += target
-QMAKE_CC = gcc
-QMAKE_CXX = g++
+QMAKE_CC = gcc-4.2.4
+QMAKE_CXX = g++-4.2.4
 
 # install path for the XML configuration file
 unix:xml.path = $(ROOTSYS)/bin/