since my automake structure is now ready for rpmbuild, the version number is increased.

added missing icons

ChangeLog

@@ -2,6 +2,45 @@
 # ChangeLog
 #---------------------------------------------------------------------
 
+The ChangeLog will describe feature changes rather than coding detail changes.
+
+For detailed information about changes have a look here:
+
+https://gitlab.psi.ch/nemu/musrfit/activity
+
+or 
+
+https://bitbucket.org/muonspin/musrfit/commits/all
+
+Release of V1.2.0, 2017/10/26
+=============================
+
+Adopted to be ready for rpm builds in a first step. This will be followed by debian style
+packages.
+
+Release of V1.1.0, 2017/10/26
+=============================
+
+Added full DKS support, i.e. additionally to CUDA also OpenCL for GPU's and CPU's in place.
+
+Release of V1.0.0, 2017/05/18
+=============================
+
+I feel that musrfit has majored enough to lift it to its first full version, i.e. V1.0.0.
+
+A lot of bug fixing went into it since 0.18.0. It is now also fully ROOT 6 compatible which
+is also the main supported version now.
+
+New features: 
+
+* musrWiz:  a wizard which will help the user to get started to generate msr-files.
+* musrStep: a little helper program which allows to reset the step size of a msr-file.
+            This is useful if you deal with a lot of detectors (e.g. HAL-9500 at PSI).
+* auto-phase correction of Fourier transforms: this is still in its early stage but will
+            eventually provide a real phase corrected Fourier transform, which will allow
+            a real Fourier detector average.
+* the startup file handling has improved substantially.        
+
 changes since 0.18.0
 ===================================
 
@@ -130,6 +169,8 @@ NEW 2015-02-13 first implementation of a standalone Fourier transform/plotter:
                A first simple minded lifetime correction is implemented as well.                
 NEW 2015-02-04 Integration of libBNMR for fitting beta-NMR relaxation data
 	       into automake of musrfit.
+NEW 2015-01-17 adding a branch for ROOT 6.x. This needs some minor adaptations due
+               to the new rootcint/rootclang and the stricter c++11.
 NEW 2014-12-18 first implementation of a GLOBAL block which allows to shorten
                a typical msr-file. Duplicate entries from the RUN blocks can be
                added here. Furthermore, the 'lifetimecorrection' flag is 

Makefile.am

@@ -6,8 +6,7 @@ EXTRA_DIST = autogen.sh acinclude.m4
 
 # The following is to install the documentation
 # It is a bit lengthy because one cannot simply install whole directories (except copying them recursively -- which also takes the .svn directories...)
-DOCDIRS = templates \
-          examples \
+DOCDIRS = examples \
           examples/data \
           examples/ASlibs \
           examples/ASlibs/data \

acinclude.m4

@@ -18,7 +18,7 @@ dnl The macro defines the following substitution variables
 dnl
 dnl    ROOTCONF           full path to root-config
 dnl    ROOTEXEC           full path to root
-dnl    ROOTCINT           full path to rootcint
+dnl    ROOTCLING          full path to rootcling
 dnl    ROOTLIBDIR         Where the ROOT libraries are 
 dnl    ROOTINCDIR         Where the ROOT headers are 
 dnl    ROOTETCDIR         Where the ROOT configuration is
@@ -29,7 +29,7 @@ dnl    ROOTAUXLIBS        Auxilary libraries and linker flags for ROOT
 dnl    ROOTAUXCFLAGS      Auxilary compiler flags 
 dnl    ROOTRPATH          Same as ROOTLIBDIR
 dnl
-dnl The macro will fail if root-config and rootcint isn't found.
+dnl The macro will fail if root-config and rootcling isn't found.
 dnl
 dnl Christian Holm Christensen <cholm@nbi.dk>
 dnl
@@ -49,10 +49,10 @@ AC_DEFUN([ROOT_PATH],
   fi
   AC_PATH_PROG(ROOTCONF, root-config , no, $rootbin)
   AC_PATH_PROG(ROOTEXEC, root , no, $rootbin)
-  AC_PATH_PROG(ROOTCINT, rootcint , no, $rootbin)
+  AC_PATH_PROG(ROOTCLING, rootcling , no, $rootbin)
 	
   if test ! x"$ROOTCONF" = "xno" && \
-     test ! x"$ROOTCINT" = "xno" ; then 
+     test ! x"$ROOTCLING" = "xno" ; then 
 
     # define some variables 
     ROOTLIBDIR=`$ROOTCONF --libdir`

configure.ac

@@ -1,7 +1,7 @@
 AC_REVISION([m4_esyscmd_s([git describe --always])])
 
 AC_PREREQ(2.63)
-AC_INIT([musrfit],[0.18.0],[andreas.suter@psi.ch])
+AC_INIT([musrfit],[1.2.0],[andreas.suter@psi.ch])
 AC_CONFIG_AUX_DIR(admin)
 AC_CANONICAL_HOST
 #AC_MSG_RESULT([${host} ${host_cpu} ${host_vendor} ${host_os}])
@@ -34,8 +34,8 @@ dnl -----------------------------------------------
 
 
 #release versioning
-MUSR_MAJOR_VERSION=0
-MUSR_MINOR_VERSION=18
+MUSR_MAJOR_VERSION=1
+MUSR_MINOR_VERSION=2
 MUSR_MICRO_VERSION=0
 
 #release versioning
@@ -421,7 +421,7 @@ dnl -----------------------------------------------
 dnl Check for ROOT
 dnl -----------------------------------------------
 
-ROOT_PATH([5.22/00], [], AC_MSG_ERROR([Either ROOT is not installed correctly or the version is too old... please check!]))
+ROOT_PATH([6.06/00], [], AC_MSG_ERROR([Either ROOT is not installed correctly or the version is too old... please check!]))
 
 ROOT_LIBS="-L${ROOTLIBDIR} ${ROOTGLIBS} ${ROOTAUXLIBS} -lMinuit2 -lMathMore -lXMLParser"
 ROOT_CFLAGS="-I${ROOTINCDIR} ${ROOTCFLAGS} ${ROOTAUXCFLAGS}"
@@ -1000,6 +1000,14 @@ if test "x$enable_editor" != "xno"; then
               [PKG_CHECK_MODULES(QT3MT, qt-mt >= 3.3.0 qt-mt < 4.0, [QT3MT_FOUND=yes], [QT3MT_FOUND=no])]
             )]
           )
+        fi        
+        if test "x${QT5_FOUND}" != "xyes"; then
+          PKG_CHECK_MODULES(QT5, Qt5WebEngine >= $QT5MINVER Qt5Xml >= $QT5MINVER, [QT5_FOUND=yes],
+            [AC_MSG_NOTICE([Qt5 (including Qt5WebEngine and Qt5Xml) not found!])
+             PKG_CHECK_MODULES(QT3, qt >= 3.3.0 qt < 4.0, [QT3_FOUND=yes],
+              [PKG_CHECK_MODULES(QT3MT, qt-mt >= 3.3.0 qt-mt < 4.0, [QT3MT_FOUND=yes], [QT3MT_FOUND=no])]
+            )]
+          )
         fi]
   )
 
@@ -1024,6 +1032,12 @@ if test "x$enable_editor" != "xno"; then
         QTEDITOR=musrgui
       fi
 
+      dnl if Qt5 but Qt5WebEngine instead of Qt5WebKit
+      if test "x$QTPATH" = "x"; then
+        QTPATH=$(pkg-config --variable=prefix Qt5WebEngine)
+        QTEDITOR=musredit_qt5
+      fi
+      
       AC_MSG_CHECKING([for qmake])
       if test "x${QTPATH}" != "xnone"; then
         if test "x$QTEDITOR" = "xmusredit_qt5"; then
@@ -1119,6 +1133,9 @@ case "${host_cpu}" in
     ;;
 esac
 
+CXXFLAGS="-std=c++11 ${CXXFLAGS}"
+AC_SUBST(CXXFLAGS)
+
 LOCAL_BIN_CXXFLAGS="${CPUFLAGS} -Wall -Wno-trigraphs"
 LOCAL_LIB_CXXFLAGS="${LOCAL_BIN_CXXFLAGS}"
 LOCAL_PSIBIN_LIB_CXXFLAGS="${LOCAL_LIB_CXXFLAGS}"
@@ -1143,7 +1160,8 @@ case "$host" in
     ;;
   *-*-darwin*)
     ARCH=DARWIN
-    LOCAL_PSIBIN_LIB_CXXFLAGS="${LOCAL_LIB_CXXFLAGS} -D__linux__"
+    LOCAL_PSIBIN_LIB_CXXFLAGS="${LOCAL_LIB_CXXFLAGS} -D_Darwin_"
+    LOCAL_BIN_LDFLAGS="${LOCAL_BIN_LDFLAGS} -Wl,-rpath ${ROOTLIBDIR}"
     ;;
   *)
     ARCH=OTHERUNIX
@@ -1194,11 +1212,24 @@ else
   INSTALLDIR="${prefix}"
 fi
 
-if test -d "${INSTALLDIR}/doc"
+dnl only define DOCDIR if not already present. This allows
+dnl to feed DOCDIR on the configure level which is useful when
+dnl for instance building a rpm. DOCDIR2 is needed for rpmbuild only
+if test "x${DOCDIR}" = "x"
 then
-  DOCDIR="${INSTALLDIR}/doc/musrfit"
+  if test -d "${INSTALLDIR}/doc"
+  then
+    DOCDIR="${INSTALLDIR}/doc/musrfit"
+  else
+    DOCDIR="${INSTALLDIR}/share/doc/musrfit"
+  fi
 else
-  DOCDIR="${INSTALLDIR}/share/doc/musrfit"
+  if test -d "${INSTALLDIR}/doc"
+  then
+    DOCDIR2="${INSTALLDIR}/doc/musrfit"
+  else
+    DOCDIR2="${INSTALLDIR}/share/doc/musrfit"
+  fi
 fi
 
 AC_SUBST(DOCDIR)
@@ -1260,8 +1291,6 @@ AC_CONFIG_FILES([Makefile \
                  src/musredit_qt5/Makefile \
                  src/musredit/Makefile \
                  src/musrgui/Makefile \
-                 src/musredit_qt5/musredit_startup.xml \
-                 src/musredit/musredit_startup.xml \
                  src/musrgui/musrgui_startup.xml])
 
 AC_OUTPUT
@@ -1422,3 +1451,24 @@ echo "   Programs:                ${INSTALLDIR}/bin"
 echo "   XML configuration files: ${HOME}/.musrfit"  
 echo "   Documentation:           ${DOCDIR}"
 echo ""
+
+dnl --------------
+dnl create header file that musredit knows at runtime where to find the documentation
+dnl the DOCDIR2 tag is used for rpmbuild only
+dnl --------------
+if test "x$enable_editor" != "xno" && test "x${QMAKEBIN}" != "x" && test "x${QTEDITOR}" = "xmusredit_qt5"; then
+  echo \#define MUSRFIT_PREFIX \"${INSTALLDIR}\" > src/musredit_qt5/musrfit-info.h
+  if test "x$DOCDIR2" = "x"; then
+    echo \#define MUSRFIT_DOC_DIR \"${DOCDIR}\" >> src/musredit_qt5/musrfit-info.h
+  else 
+    echo \#define MUSRFIT_DOC_DIR \"${DOCDIR2}\" >> src/musredit_qt5/musrfit-info.h
+  fi
+fi
+if test "x$enable_editor" != "xno" && test "x${QMAKEBIN}" != "x" && test "x${QTEDITOR}" = "xmusredit"; then
+  echo \#define MUSRFIT_PREFIX \"${INSTALLDIR}\" > src/musredit/musrfit-info.h
+  if test "x$DOCDIR2" = "x"; then
+    echo \#define MUSRFIT_DOC_DIR \"${DOCDIR}\" >> src/musredit/musrfit-info.h
+  else
+    echo \#define MUSRFIT_DOC_DIR \"${DOCDIR2}\" >> src/musredit/musrfit-info.h
+  fi
+fi

doc/examples/UserFcn/Makefile.PUserFcn

@@ -46,11 +46,11 @@ clean:; 	@rm -f $(OBJS) *Dict* core*
 $(OBJS): %.o: %.cpp
 	$(CXX) $(INCLUDES) $(CXXFLAGS) -c $<
 
-# Generate the ROOT CINT dictionary
+# Generate the ROOT CLING dictionary
 
 PUserFcnDict.cpp: PUserFcn.h PUserFcnLinkDef.h
 	@echo "Generating dictionary $@..."
-	rootcint -f $@ -c -p -I$(ROOTINCLUDE) $^
+	rootcling -f $@ -c -p -I$(ROOTINCLUDE) $^
 
 install: all
 	@echo "Installing shared lib: libTApproximation.so"

doc/examples/test-asy-LF-BaB6.msr

@@ -0,0 +1,60 @@
+BaB6 T20K LF5G                                                
+###############################################################
+FITPARAMETER
+#      Nr. Name        Value     Step      Pos_Error  Boundaries
+        1 alpha       0.7       0           none        0       none    
+        2 asy         0.2091    -0.0013     0.0013      0       0.33    
+        3 field       2.127     0           none        0       none    
+        4 width       0.5387    -0.0054     0.0055      0       100     
+        5 hopp        0.119     -0.013      0.014       0       100     
+        6 asyConst    0         0           none        
+
+###############################################################
+THEORY
+asymmetry      2
+dynGssKTLF  fun1     4     5    (frequency damping hopping-rate)
++
+asymmetry      6
+
+###############################################################
+FUNCTIONS
+fun1 = par3 * gamma_mu
+
+###############################################################
+RUN data/deltat_tdc_dolly_1020 PIE1 PSI PSI-BIN   (name beamline institute data-file-format)
+fittype         2         (asymmetry fit)
+alpha           1
+map             0    0    0    0    0    0    0    0    0    0
+forward         2 
+backward        1 
+background      15      146     13      148        # estimated bkg: 20.4846 / 4.8731
+data            170     9956    168     9110    
+t0              160.0   161.0   
+fit             0.25    10     
+packing         5
+
+###############################################################
+COMMANDS
+MINIMIZE
+MINOS
+SAVE
+
+###############################################################
+FOURIER
+units            Gauss   # units either 'Gauss', 'MHz', or 'Mc/s'
+fourier_power    12
+apodization      STRONG  # NONE, WEAK, MEDIUM, STRONG
+plot             POWER   # REAL, IMAG, REAL_AND_IMAG, POWER, PHASE
+phase            8
+#range_for_phase_correction 50.0 70.0
+range            0    800
+
+###############################################################
+PLOT 2   (asymmetry plot)
+runs     1   
+range    0   9.5   -0.15   0.3
+view_packing 150
+
+###############################################################
+STATISTIC --- 2013-07-01 20:40:44
+  chisq = 1911.7, NDF = 1905, chisq/NDF = 1.003494

doc/examples/test-asy-MUD.msr

@@ -3,7 +3,7 @@ MgB12H12 No2 ZF T=150
 FITPARAMETER
 #      Nr. Name        Value     Step      Pos_Error  Boundaries
         1 alpha       1         0           none        0       2       
-        2 asy         0.17503   -0.00082    0.00083     0       0.33    
+        2 asy         0.17503   -0.00081    0.00083     0       0.33    
         3 rate        0.1649    -0.0016     0.0016      0       none    
         4 beta        0.892     -0.016      0.016       0.5     2       
 
@@ -19,7 +19,7 @@ alpha           1
 map             0    0    0    0    0    0    0    0    0    0    0
 forward         1 
 backward        2 
-background      79      391     80      409        # estimated bkg: 21.0224 / 17.1702
+background      79      391     80      409        # estimated bkg: 21.0833 / 17.2249
 data            438     12785   436     12787   
 t0              432.0   431.0   
 fit             0       8      
@@ -34,10 +34,10 @@ SAVE
 
 ###############################################################
 FOURIER
-units            Gauss   # units either 'Gauss', 'MHz', or 'Mc/s'
+units            Gauss   # units either 'Gauss', 'Tesla', 'MHz', or 'Mc/s'
 fourier_power    12
 apodization      NONE    # NONE, WEAK, MEDIUM, STRONG
-plot             POWER   # REAL, IMAG, REAL_AND_IMAG, POWER, PHASE
+plot             POWER   # REAL, IMAG, REAL_AND_IMAG, POWER, PHASE, PHASE_OPT_REAL
 phase            8
 #range_for_phase_correction 50.0 70.0
 range            0    200
@@ -48,5 +48,5 @@ runs     1
 range    0   8   0   0.25
 
 ###############################################################
-STATISTIC --- 2012-03-20 10:11:27
-  chisq = 133.9, NDF = 99, chisq/NDF = 1.352819
+STATISTIC --- 2017-02-08 07:07:39
+  chisq = 134.0, NDF = 99, chisq/NDF = 1.353150

doc/examples/test-histo-muMinus.msr

@@ -5,11 +5,11 @@ FITPARAMETER
         1 N_0         321.0     1.4         none        
         2 tau_0       1.9066    0.0038      none        0       none    
         3 Rate_0      0.0983    0.0052      none        0       none    
-        4 Freq_0      135.53824 0.00073     none        
+        4 Freq_0      135.53823 0.00073     none        
 
         5 N_1         306.1     1.3         none        
         6 tau_1       0.7409    0.0026      none        0       none    
-        7 Rate_1      0.026     0.027       none        0       none    
+        7 Rate_1      0.027     0.031       none        0       none    
         8 Freq_1      136.8968  0.0033      none        
 
         9 Asym_F1_0   0.0490    0.0015      none        0       none    
@@ -28,7 +28,7 @@ FITPARAMETER
        20 N_bgk_F3    1.465     0.033       none        
 
        21 Asym_F4_0   0.0512    0.0015      none        0       none    
-       22 Asym_F4_1   0.0521    0.0029      none        0       none    
+       22 Asym_F4_1   0.0521    0.0030      none        0       none    
        23 Phase_F4    144.6     1.5         none        
        24 N_bgk_F4    2.311     0.034       none        
 
@@ -40,7 +40,7 @@ FITPARAMETER
        29 Asym_F6_0   0.0502    0.0015      none        0       none    
        30 Asym_F6_1   0.0517    0.0030      none        0       none    
        31 Phase_F6    232.1     1.5         none        
-       32 N_bgk_F6    1.735     0.033       none        
+       32 N_bgk_F6    1.735     0.034       none        
 
        33 Asym_F7_0   0.0488    0.0015      none        0       none    
        34 Asym_F7_1   0.0575    0.0030      none        0       none    
@@ -48,12 +48,12 @@ FITPARAMETER
        36 N_bgk_F7    1.593     0.033       none        
 
        37 Asym_F8_0   0.0547    0.0015      none        0       none    
-       38 Asym_F8_1   0.0468    0.0029      none        0       none    
+       38 Asym_F8_1   0.0468    0.0030      none        0       none    
        39 Phase_F8    321.7     1.4         none        
        40 N_bgk_F8    1.469     0.033       none        
 
        41 Asym_B1_0   0.0476    0.0015      none        0       none    
-       42 Asym_B1_1   0.0535    0.0029      none        0       none    
+       42 Asym_B1_1   0.0535    0.0030      none        0       none    
        43 Phase_B1    3.6       1.5         none        
        44 N_bgk_B1    1.378     0.033       none        
 
@@ -64,8 +64,8 @@ FITPARAMETER
 
        49 Asym_B3_0   0.0494    0.0015      none        0       none    
        50 Asym_B3_1   0.0555    0.0030      none        0       none    
-       51 Phase_B3    98.1      1.5         none        
-       52 N_bgk_B3    0.969     0.032       none        
+       51 Phase_B3    98.2      1.5         none        
+       52 N_bgk_B3    0.968     0.032       none        
 
        53 Asym_B4_0   0.0505    0.0015      none        0       none    
        54 Asym_B4_1   0.0527    0.0030      none        0       none    
@@ -78,7 +78,7 @@ FITPARAMETER
        60 N_bgk_B5    1.642     0.033       none        
 
        61 Asym_B6_0   0.0512    0.0015      none        0       none    
-       62 Asym_B6_1   0.0477    0.0029      none        0       none    
+       62 Asym_B6_1   0.0477    0.0030      none        0       none    
        63 Phase_B6    231.7     1.5         none        
        64 N_bgk_B6    1.650     0.033       none        
 
@@ -183,7 +183,7 @@ SAVE
 
 ###############################################################
 PLOT 4   (mu minus plot)
-runs        1-16
+runs        1   2   3   4   5   6   7   8   9  10  11  12  13  14  15  16
 range    0   9
 
 ###############################################################
@@ -191,9 +191,9 @@ FOURIER
 units            Tesla   # units either 'Gauss', 'Tesla', 'MHz', or 'Mc/s'
 fourier_power    14
 apodization      MEDIUM  # NONE, WEAK, MEDIUM, STRONG
-plot             POWER   # REAL, IMAG, REAL_AND_IMAG, POWER, PHASE
-range            0.8     1.2
+plot             POWER   # REAL, IMAG, REAL_AND_IMAG, POWER, PHASE, PHASE_OPT_REAL
+range            0.8    1.2
 
 ###############################################################
-STATISTIC --- 2016-04-25 17:05:56
+STATISTIC --- 2017-02-08 07:11:01
   maxLH = 238962.5, NDF = 230264, maxLH/NDF = 1.037776

doc/html/user/MUSR/BmwLibs.html

@@ -1,7 +1,7 @@
 <!DOCTYPE html><html lang="en">
 
-<!-- Mirrored from intranet.psi.ch/MUSR/BmwLibs?cover=print by HTTrack Website Copier/3.x [XR&CO'2010], Fri, 16 Dec 2016 16:01:32 GMT -->
-<!-- Added by HTTrack --><meta http-equiv="content-type" content="text/html;charset=utf-8"><!-- /Added by HTTrack -->
+<!-- Mirrored from intranet.psi.ch/MUSR/BmwLibs?cover=print by HTTrack Website Copier/3.x [XR&CO'2014], Sun, 14 May 2017 18:09:10 GMT -->
+<!-- Added by HTTrack --><meta http-equiv="content-type" content="text/html;charset=utf-8" /><!-- /Added by HTTrack -->
 <head>
 <link rel="stylesheet" href="../pub/System/HeadlinesPlugin/style.css" type="text/css" media="all" />
 <title> MUSR :: BmwLibs</title>
@@ -14,14 +14,14 @@
 <meta name="apple-mobile-web-app-status-bar-style" content="black-translucent" />
 <link rel="icon" href="../pub/Main/WebPreferences/favicon.ico" type="image/x-icon" />
 <link rel="shortcut icon" href="../pub/Main/WebPreferences/favicon.ico" type="image/x-icon" />
-<link rel="alternate" href="https://intranet.psi.ch/wiki/bin/edit/MUSR/BmwLibs?t=1481904045" type="application/x-wiki" title="edit BmwLibs" />
+<link rel="alternate" href="https://intranet.psi.ch/wiki/bin/edit/MUSR/BmwLibs?t=1494785300" type="application/x-wiki" title="edit BmwLibs" />
 <meta name="TEXT_NUM_TOPICS" content="Number of topics:" />
 <meta name="TEXT_MODIFY_SEARCH" content="Modify search" />
-<meta name="robots" content="noindex" /><link rel="alternate" type="application/rss+xml" title="RSS Feed" href="WebRsshtml.html" />
-<base  /><!--[if IE]></base><![endif]--><link class='head JQUERYPLUGIN::COMMENT' rel='stylesheet' href='../pub/System/CommentPlugin/commentf5b6.css?version=3.0' type='text/css' media='all' /><!--JQUERYPLUGIN::COMMENT-->
+<meta name="robots" content="noindex" /><link rel="alternate" type="application/rss+xml" title="RSS Feed" href="WebRss" />
+<base  /><!--[if IE]></base><![endif]--><link class='head CLASSIFICATIONPLUGIN::CSS' rel="stylesheet" href="../pub/System/ClassificationPlugin/styles.css" media="all" /><!--CLASSIFICATIONPLUGIN::CSS-->
 <link class='head FOOTNOTEPLUGIN_LINKCSS' rel="stylesheet" href="../pub/System/FootNotePlugin/styles.css" type="text/css" media="all" /><!--FOOTNOTEPLUGIN_LINKCSS-->
-<link class='head CLASSIFICATIONPLUGIN::CSS' rel="stylesheet" href="../pub/System/ClassificationPlugin/styles.css" media="all" /><!--CLASSIFICATIONPLUGIN::CSS-->
-<link class='head SMILIESPLUGIN' rel='stylesheet' href='../pub/System/SmiliesPlugin/smilies.css' type='text/css' media='all' /><!--SMILIESPLUGIN--><link rel='stylesheet' href='../pub/System/SkinTemplates/base.css' media='all' type='text/css' />
+<link class='head SMILIESPLUGIN' rel='stylesheet' href='../pub/System/SmiliesPlugin/smilies.css' type='text/css' media='all' /><!--SMILIESPLUGIN-->
+<link class='head JQUERYPLUGIN::COMMENT' rel='stylesheet' href='../pub/System/CommentPlugin/commentf5b6.css?version=3.0' type='text/css' media='all' /><!--JQUERYPLUGIN::COMMENT--><link rel='stylesheet' href='../pub/System/SkinTemplates/base.css' media='all' type='text/css' />
 <style type="text/css" media="all">
 @import url('../pub/System/PatternSkinTheme/layout.css');
 @import url('../pub/System/PatternSkinTheme2009/style.css');
@@ -149,6 +149,5 @@ Topic revision:  <span class='patternRevInfo'>03 Jul 2015, suter_a</span></div>
 
 </body>
 
-<!-- Mirrored from intranet.psi.ch/MUSR/BmwLibs?cover=print by HTTrack Website Copier/3.x [XR&CO'2010], Fri, 16 Dec 2016 16:01:33 GMT -->
-<!-- Added by HTTrack --><meta http-equiv="content-type" content="text/html;charset=utf-8"><!-- /Added by HTTrack -->
+<!-- Mirrored from intranet.psi.ch/MUSR/BmwLibs?cover=print by HTTrack Website Copier/3.x [XR&CO'2014], Sun, 14 May 2017 18:09:10 GMT -->
 </html>

doc/html/user/MUSR/CiteMusrFit.html

@@ -1,7 +1,7 @@
 <!DOCTYPE html><html lang="en">
 
-<!-- Mirrored from intranet.psi.ch/MUSR/CiteMusrFit?cover=print by HTTrack Website Copier/3.x [XR&CO'2010], Fri, 16 Dec 2016 16:01:25 GMT -->
-<!-- Added by HTTrack --><meta http-equiv="content-type" content="text/html;charset=utf-8"><!-- /Added by HTTrack -->
+<!-- Mirrored from intranet.psi.ch/MUSR/CiteMusrFit?cover=print by HTTrack Website Copier/3.x [XR&CO'2014], Sun, 14 May 2017 18:09:03 GMT -->
+<!-- Added by HTTrack --><meta http-equiv="content-type" content="text/html;charset=utf-8" /><!-- /Added by HTTrack -->
 <head>
 <link rel="stylesheet" href="../pub/System/HeadlinesPlugin/style.css" type="text/css" media="all" />
 <title> MUSR :: CiteMusrFit</title>
@@ -14,14 +14,14 @@
 <meta name="apple-mobile-web-app-status-bar-style" content="black-translucent" />
 <link rel="icon" href="../pub/Main/WebPreferences/favicon.ico" type="image/x-icon" />
 <link rel="shortcut icon" href="../pub/Main/WebPreferences/favicon.ico" type="image/x-icon" />
-<link rel="alternate" href="https://intranet.psi.ch/wiki/bin/edit/MUSR/CiteMusrFit?t=1481904044" type="application/x-wiki" title="edit CiteMusrFit" />
+<link rel="alternate" href="https://intranet.psi.ch/wiki/bin/edit/MUSR/CiteMusrFit?t=1494785299" type="application/x-wiki" title="edit CiteMusrFit" />
 <meta name="TEXT_NUM_TOPICS" content="Number of topics:" />
 <meta name="TEXT_MODIFY_SEARCH" content="Modify search" />
-<meta name="robots" content="noindex" /><link rel="alternate" type="application/rss+xml" title="RSS Feed" href="WebRsshtml.html" />
-<base  /><!--[if IE]></base><![endif]--><link class='head FOOTNOTEPLUGIN_LINKCSS' rel="stylesheet" href="../pub/System/FootNotePlugin/styles.css" type="text/css" media="all" /><!--FOOTNOTEPLUGIN_LINKCSS-->
+<meta name="robots" content="noindex" /><link rel="alternate" type="application/rss+xml" title="RSS Feed" href="WebRss" />
+<base  /><!--[if IE]></base><![endif]--><link class='head CLASSIFICATIONPLUGIN::CSS' rel="stylesheet" href="../pub/System/ClassificationPlugin/styles.css" media="all" /><!--CLASSIFICATIONPLUGIN::CSS-->
 <link class='head JQUERYPLUGIN::COMMENT' rel='stylesheet' href='../pub/System/CommentPlugin/commentf5b6.css?version=3.0' type='text/css' media='all' /><!--JQUERYPLUGIN::COMMENT-->
-<link class='head CLASSIFICATIONPLUGIN::CSS' rel="stylesheet" href="../pub/System/ClassificationPlugin/styles.css" media="all" /><!--CLASSIFICATIONPLUGIN::CSS-->
-<link class='head SMILIESPLUGIN' rel='stylesheet' href='../pub/System/SmiliesPlugin/smilies.css' type='text/css' media='all' /><!--SMILIESPLUGIN--><link rel='stylesheet' href='../pub/System/SkinTemplates/base.css' media='all' type='text/css' />
+<link class='head SMILIESPLUGIN' rel='stylesheet' href='../pub/System/SmiliesPlugin/smilies.css' type='text/css' media='all' /><!--SMILIESPLUGIN-->
+<link class='head FOOTNOTEPLUGIN_LINKCSS' rel="stylesheet" href="../pub/System/FootNotePlugin/styles.css" type="text/css" media="all" /><!--FOOTNOTEPLUGIN_LINKCSS--><link rel='stylesheet' href='../pub/System/SkinTemplates/base.css' media='all' type='text/css' />
 <style type="text/css" media="all">
 @import url('../pub/System/PatternSkinTheme/layout.css');
 @import url('../pub/System/PatternSkinTheme2009/style.css');
@@ -102,14 +102,14 @@
 <!--<![endif]-->
 <!--JQUERYPLUGIN-->
 <!--JQUERYPLUGIN::MIGRATE-->
-<!--JQUERYPLUGIN::LIVEQUERY-->
 <!--JQUERYPLUGIN::FOSWIKI-->
+<!--JQUERYPLUGIN::LIVEQUERY-->
 <!--JavascriptFiles/foswikiString-->
-<!--JavascriptFiles/foswikiPref-->
 <!--JavascriptFiles/foswikiForm-->
+<!--JavascriptFiles/foswikiPref-->
 <!--PatternSkin/pattern-->
-<!--JQUERYPLUGIN::FOSWIKI::PREFERENCES-->
-<!--JQUERYPLUGIN::COMMENT--><link class='head FOOTNOTEPLUGIN_LINKCSS' rel="stylesheet" href="../pub/System/FootNotePlugin/styles.css" type="text/css" media="all" /><!--FOOTNOTEPLUGIN_LINKCSS-->
+<!--JQUERYPLUGIN::COMMENT-->
+<!--JQUERYPLUGIN::FOSWIKI::PREFERENCES--><link class='head FOOTNOTEPLUGIN_LINKCSS' rel="stylesheet" href="../pub/System/FootNotePlugin/styles.css" type="text/css" media="all" /><!--FOOTNOTEPLUGIN_LINKCSS-->
 </head> 
 <body class="foswikiNoJs patternViewPage patternPrintPage">
 <span id="PageTop"></span><div class="foswikiPage"><div id="patternScreen">
@@ -147,6 +147,5 @@ Topic revision:  <span class='patternRevInfo'>19 Jun 2012, suter_a</span></div>
 
 </body>
 
-<!-- Mirrored from intranet.psi.ch/MUSR/CiteMusrFit?cover=print by HTTrack Website Copier/3.x [XR&CO'2010], Fri, 16 Dec 2016 16:01:25 GMT -->
-<!-- Added by HTTrack --><meta http-equiv="content-type" content="text/html;charset=utf-8"><!-- /Added by HTTrack -->
+<!-- Mirrored from intranet.psi.ch/MUSR/CiteMusrFit?cover=print by HTTrack Website Copier/3.x [XR&CO'2014], Sun, 14 May 2017 18:09:03 GMT -->
 </html>

doc/html/user/MUSR/LibFitPofB.html

@@ -1,7 +1,7 @@
 <!DOCTYPE html><html lang="en">
 
-<!-- Mirrored from intranet.psi.ch/MUSR/LibFitPofB?cover=print by HTTrack Website Copier/3.x [XR&CO'2010], Fri, 16 Dec 2016 16:01:26 GMT -->
-<!-- Added by HTTrack --><meta http-equiv="content-type" content="text/html;charset=utf-8"><!-- /Added by HTTrack -->
+<!-- Mirrored from intranet.psi.ch/MUSR/LibFitPofB?cover=print by HTTrack Website Copier/3.x [XR&CO'2014], Sun, 14 May 2017 18:09:04 GMT -->
+<!-- Added by HTTrack --><meta http-equiv="content-type" content="text/html;charset=utf-8" /><!-- /Added by HTTrack -->
 <head>
 <link rel="stylesheet" href="../pub/System/HeadlinesPlugin/style.css" type="text/css" media="all" />
 <title> MUSR :: LibFitPofB</title>
@@ -14,14 +14,14 @@
 <meta name="apple-mobile-web-app-status-bar-style" content="black-translucent" />
 <link rel="icon" href="../pub/Main/WebPreferences/favicon.ico" type="image/x-icon" />
 <link rel="shortcut icon" href="../pub/Main/WebPreferences/favicon.ico" type="image/x-icon" />
-<link rel="alternate" href="https://intranet.psi.ch/wiki/bin/edit/MUSR/LibFitPofB?t=1481904045" type="application/x-wiki" title="edit LibFitPofB" />
+<link rel="alternate" href="https://intranet.psi.ch/wiki/bin/edit/MUSR/LibFitPofB?t=1494785299" type="application/x-wiki" title="edit LibFitPofB" />
 <meta name="TEXT_NUM_TOPICS" content="Number of topics:" />
 <meta name="TEXT_MODIFY_SEARCH" content="Modify search" />
-<meta name="robots" content="noindex" /><link rel="alternate" type="application/rss+xml" title="RSS Feed" href="WebRsshtml.html" />
-<base  /><!--[if IE]></base><![endif]--><link class='head JQUERYPLUGIN::COMMENT' rel='stylesheet' href='../pub/System/CommentPlugin/commentf5b6.css?version=3.0' type='text/css' media='all' /><!--JQUERYPLUGIN::COMMENT-->
+<meta name="robots" content="noindex" /><link rel="alternate" type="application/rss+xml" title="RSS Feed" href="WebRss" />
+<base  /><!--[if IE]></base><![endif]--><link class='head CLASSIFICATIONPLUGIN::CSS' rel="stylesheet" href="../pub/System/ClassificationPlugin/styles.css" media="all" /><!--CLASSIFICATIONPLUGIN::CSS-->
 <link class='head FOOTNOTEPLUGIN_LINKCSS' rel="stylesheet" href="../pub/System/FootNotePlugin/styles.css" type="text/css" media="all" /><!--FOOTNOTEPLUGIN_LINKCSS-->
 <link class='head SMILIESPLUGIN' rel='stylesheet' href='../pub/System/SmiliesPlugin/smilies.css' type='text/css' media='all' /><!--SMILIESPLUGIN-->
-<link class='head CLASSIFICATIONPLUGIN::CSS' rel="stylesheet" href="../pub/System/ClassificationPlugin/styles.css" media="all" /><!--CLASSIFICATIONPLUGIN::CSS--><link rel='stylesheet' href='../pub/System/SkinTemplates/base.css' media='all' type='text/css' />
+<link class='head JQUERYPLUGIN::COMMENT' rel='stylesheet' href='../pub/System/CommentPlugin/commentf5b6.css?version=3.0' type='text/css' media='all' /><!--JQUERYPLUGIN::COMMENT--><link rel='stylesheet' href='../pub/System/SkinTemplates/base.css' media='all' type='text/css' />
 <style type="text/css" media="all">
 @import url('../pub/System/PatternSkinTheme/layout.css');
 @import url('../pub/System/PatternSkinTheme2009/style.css');
@@ -104,15 +104,15 @@
 <!--JQUERYPLUGIN::MIGRATE-->
 <!--JQUERYPLUGIN::LIVEQUERY-->
 <!--JQUERYPLUGIN::FOSWIKI-->
+<!--JavascriptFiles/foswikiString-->
+<!--JavascriptFiles/foswikiPref-->
+<!--JavascriptFiles/foswikiForm-->
+<!--PatternSkin/pattern-->
 <!--JQUERYPLUGIN::METADATA-->
+<!--JQUERYPLUGIN::COMMENT-->
 
 <!--JQUERYPLUGIN::CHILI-->
-<!--JavascriptFiles/foswikiString-->
-<!--JavascriptFiles/foswikiForm-->
-<!--JavascriptFiles/foswikiPref-->
-<!--JQUERYPLUGIN::FOSWIKI::PREFERENCES-->
-<!--JQUERYPLUGIN::COMMENT-->
-<!--PatternSkin/pattern--><link class='head FOOTNOTEPLUGIN_LINKCSS' rel="stylesheet" href="../pub/System/FootNotePlugin/styles.css" type="text/css" media="all" /><!--FOOTNOTEPLUGIN_LINKCSS-->
+<!--JQUERYPLUGIN::FOSWIKI::PREFERENCES--><link class='head FOOTNOTEPLUGIN_LINKCSS' rel="stylesheet" href="../pub/System/FootNotePlugin/styles.css" type="text/css" media="all" /><!--FOOTNOTEPLUGIN_LINKCSS-->
 </head> 
 <body class="foswikiNoJs patternViewPage patternPrintPage">
 <span id="PageTop"></span><div class="foswikiPage"><div id="patternScreen">
@@ -428,6 +428,5 @@ Topic revision:  <span class='patternRevInfo'>03 Jul 2015, suter_a</span></div>
 
 </body>
 
-<!-- Mirrored from intranet.psi.ch/MUSR/LibFitPofB?cover=print by HTTrack Website Copier/3.x [XR&CO'2010], Fri, 16 Dec 2016 16:01:32 GMT -->
-<!-- Added by HTTrack --><meta http-equiv="content-type" content="text/html;charset=utf-8"><!-- /Added by HTTrack -->
+<!-- Mirrored from intranet.psi.ch/MUSR/LibFitPofB?cover=print by HTTrack Website Copier/3.x [XR&CO'2014], Sun, 14 May 2017 18:09:10 GMT -->
 </html>

doc/html/user/MUSR/LibZFRelaxation.html

@@ -1,7 +1,7 @@
 <!DOCTYPE html><html lang="en">
 
-<!-- Mirrored from intranet.psi.ch/MUSR/LibZFRelaxation?cover=print by HTTrack Website Copier/3.x [XR&CO'2010], Fri, 16 Dec 2016 16:00:52 GMT -->
-<!-- Added by HTTrack --><meta http-equiv="content-type" content="text/html;charset=utf-8"><!-- /Added by HTTrack -->
+<!-- Mirrored from intranet.psi.ch/MUSR/LibZFRelaxation?cover=print by HTTrack Website Copier/3.x [XR&CO'2014], Sun, 14 May 2017 18:08:26 GMT -->
+<!-- Added by HTTrack --><meta http-equiv="content-type" content="text/html;charset=utf-8" /><!-- /Added by HTTrack -->
 <head>
 <link rel="stylesheet" href="../pub/System/HeadlinesPlugin/style.css" type="text/css" media="all" />
 <title> MUSR :: LibZFRelaxation</title>
@@ -14,14 +14,14 @@
 <meta name="apple-mobile-web-app-status-bar-style" content="black-translucent" />
 <link rel="icon" href="../pub/Main/WebPreferences/favicon.ico" type="image/x-icon" />
 <link rel="shortcut icon" href="../pub/Main/WebPreferences/favicon.ico" type="image/x-icon" />
-<link rel="alternate" href="https://intranet.psi.ch/wiki/bin/edit/MUSR/LibZFRelaxation?t=1481904042" type="application/x-wiki" title="edit LibZFRelaxation" />
+<link rel="alternate" href="https://intranet.psi.ch/wiki/bin/edit/MUSR/LibZFRelaxation?t=1494785294" type="application/x-wiki" title="edit LibZFRelaxation" />
 <meta name="TEXT_NUM_TOPICS" content="Number of topics:" />
 <meta name="TEXT_MODIFY_SEARCH" content="Modify search" />
-<meta name="robots" content="noindex" /><link rel="alternate" type="application/rss+xml" title="RSS Feed" href="WebRsshtml.html" />
-<base  /><!--[if IE]></base><![endif]--><link class='head SMILIESPLUGIN' rel='stylesheet' href='../pub/System/SmiliesPlugin/smilies.css' type='text/css' media='all' /><!--SMILIESPLUGIN-->
-<link class='head CLASSIFICATIONPLUGIN::CSS' rel="stylesheet" href="../pub/System/ClassificationPlugin/styles.css" media="all" /><!--CLASSIFICATIONPLUGIN::CSS-->
+<meta name="robots" content="noindex" /><link rel="alternate" type="application/rss+xml" title="RSS Feed" href="WebRss" />
+<base  /><!--[if IE]></base><![endif]--><link class='head CLASSIFICATIONPLUGIN::CSS' rel="stylesheet" href="../pub/System/ClassificationPlugin/styles.css" media="all" /><!--CLASSIFICATIONPLUGIN::CSS-->
 <link class='head FOOTNOTEPLUGIN_LINKCSS' rel="stylesheet" href="../pub/System/FootNotePlugin/styles.css" type="text/css" media="all" /><!--FOOTNOTEPLUGIN_LINKCSS-->
-<link class='head JQUERYPLUGIN::COMMENT' rel='stylesheet' href='../pub/System/CommentPlugin/commentf5b6.css?version=3.0' type='text/css' media='all' /><!--JQUERYPLUGIN::COMMENT--><link rel='stylesheet' href='../pub/System/SkinTemplates/base.css' media='all' type='text/css' />
+<link class='head JQUERYPLUGIN::COMMENT' rel='stylesheet' href='../pub/System/CommentPlugin/commentf5b6.css?version=3.0' type='text/css' media='all' /><!--JQUERYPLUGIN::COMMENT-->
+<link class='head SMILIESPLUGIN' rel='stylesheet' href='../pub/System/SmiliesPlugin/smilies.css' type='text/css' media='all' /><!--SMILIESPLUGIN--><link rel='stylesheet' href='../pub/System/SkinTemplates/base.css' media='all' type='text/css' />
 <style type="text/css" media="all">
 @import url('../pub/System/PatternSkinTheme/layout.css');
 @import url('../pub/System/PatternSkinTheme2009/style.css');
@@ -102,17 +102,17 @@
 <!--<![endif]-->
 <!--JQUERYPLUGIN-->
 <!--JQUERYPLUGIN::MIGRATE-->
-<!--JQUERYPLUGIN::FOSWIKI-->
 <!--JQUERYPLUGIN::LIVEQUERY-->
+<!--JQUERYPLUGIN::FOSWIKI-->
+<!--JQUERYPLUGIN::COMMENT-->
+<!--JQUERYPLUGIN::FOSWIKI::PREFERENCES-->
+<!--JQUERYPLUGIN::METADATA-->
+
+<!--JQUERYPLUGIN::CHILI-->
 <!--JavascriptFiles/foswikiString-->
 <!--JavascriptFiles/foswikiPref-->
 <!--JavascriptFiles/foswikiForm-->
-<!--PatternSkin/pattern-->
-<!--JQUERYPLUGIN::COMMENT-->
-<!--JQUERYPLUGIN::METADATA-->
-<!--JQUERYPLUGIN::FOSWIKI::PREFERENCES-->
-
-<!--JQUERYPLUGIN::CHILI--><link class='head FOOTNOTEPLUGIN_LINKCSS' rel="stylesheet" href="../pub/System/FootNotePlugin/styles.css" type="text/css" media="all" /><!--FOOTNOTEPLUGIN_LINKCSS-->
+<!--PatternSkin/pattern--><link class='head FOOTNOTEPLUGIN_LINKCSS' rel="stylesheet" href="../pub/System/FootNotePlugin/styles.css" type="text/css" media="all" /><!--FOOTNOTEPLUGIN_LINKCSS-->
 </head> 
 <body class="foswikiNoJs patternViewPage patternPrintPage">
 <span id="PageTop"></span><div class="foswikiPage"><div id="patternScreen">
@@ -233,6 +233,5 @@ Topic revision:  <span class='patternRevInfo'>03 Jul 2015, suter_a</span></div>
 
 </body>
 
-<!-- Mirrored from intranet.psi.ch/MUSR/LibZFRelaxation?cover=print by HTTrack Website Copier/3.x [XR&CO'2010], Fri, 16 Dec 2016 16:00:55 GMT -->
-<!-- Added by HTTrack --><meta http-equiv="content-type" content="text/html;charset=utf-8"><!-- /Added by HTTrack -->
+<!-- Mirrored from intranet.psi.ch/MUSR/LibZFRelaxation?cover=print by HTTrack Website Copier/3.x [XR&CO'2014], Sun, 14 May 2017 18:08:30 GMT -->
 </html>

doc/html/user/MUSR/Msr2Data.html

@@ -1,7 +1,7 @@
 <!DOCTYPE html><html lang="en">
 
-<!-- Mirrored from intranet.psi.ch/MUSR/Msr2Data?cover=print by HTTrack Website Copier/3.x [XR&CO'2010], Fri, 16 Dec 2016 16:01:25 GMT -->
-<!-- Added by HTTrack --><meta http-equiv="content-type" content="text/html;charset=utf-8"><!-- /Added by HTTrack -->
+<!-- Mirrored from intranet.psi.ch/MUSR/Msr2Data?cover=print by HTTrack Website Copier/3.x [XR&CO'2014], Sun, 14 May 2017 18:09:03 GMT -->
+<!-- Added by HTTrack --><meta http-equiv="content-type" content="text/html;charset=utf-8" /><!-- /Added by HTTrack -->
 <head>
 <link rel="stylesheet" href="../pub/System/HeadlinesPlugin/style.css" type="text/css" media="all" />
 <title> MUSR :: Msr2Data</title>
@@ -14,12 +14,12 @@
 <meta name="apple-mobile-web-app-status-bar-style" content="black-translucent" />
 <link rel="icon" href="../pub/Main/WebPreferences/favicon.ico" type="image/x-icon" />
 <link rel="shortcut icon" href="../pub/Main/WebPreferences/favicon.ico" type="image/x-icon" />
-<link rel="alternate" href="https://intranet.psi.ch/wiki/bin/edit/MUSR/Msr2Data?t=1481904045" type="application/x-wiki" title="edit Msr2Data" />
+<link rel="alternate" href="https://intranet.psi.ch/wiki/bin/edit/MUSR/Msr2Data?t=1494785299" type="application/x-wiki" title="edit Msr2Data" />
 <meta name="TEXT_NUM_TOPICS" content="Number of topics:" />
 <meta name="TEXT_MODIFY_SEARCH" content="Modify search" />
-<meta name="robots" content="noindex" /><link rel="alternate" type="application/rss+xml" title="RSS Feed" href="WebRsshtml.html" />
-<base  /><!--[if IE]></base><![endif]--><link class='head SMILIESPLUGIN' rel='stylesheet' href='../pub/System/SmiliesPlugin/smilies.css' type='text/css' media='all' /><!--SMILIESPLUGIN-->
-<link class='head CLASSIFICATIONPLUGIN::CSS' rel="stylesheet" href="../pub/System/ClassificationPlugin/styles.css" media="all" /><!--CLASSIFICATIONPLUGIN::CSS-->
+<meta name="robots" content="noindex" /><link rel="alternate" type="application/rss+xml" title="RSS Feed" href="WebRss" />
+<base  /><!--[if IE]></base><![endif]--><link class='head CLASSIFICATIONPLUGIN::CSS' rel="stylesheet" href="../pub/System/ClassificationPlugin/styles.css" media="all" /><!--CLASSIFICATIONPLUGIN::CSS-->
+<link class='head IMAGEPLUGIN' rel="stylesheet" href="../pub/System/ImagePlugin/style.css" type="text/css" media="all" /><!--IMAGEPLUGIN-->
 <style class='head TABLEPLUGIN_default' type="text/css" media="all">
 body .foswikiTable {border-width:1px}
 body .foswikiTable .tableSortIcon img {padding-left:.3em; vertical-align:text-bottom}
@@ -53,9 +53,9 @@ body .foswikiTable#tableMsr2Data1 tr.foswikiTableRowdataBg0 td {background-color
 body .foswikiTable#tableMsr2Data1 tr.foswikiTableRowdataBg0 td.foswikiSortedCol {background-color:#f5f5f5}
 </style><!--TABLEPLUGIN_specific-->
 <link class='head JQUERYPLUGIN::TWISTY' rel='stylesheet' href='../pub/System/TwistyPlugin/twisty327a.css?version=1.6.0' type='text/css' media='all' /><!--JQUERYPLUGIN::TWISTY: requires= missing ids: JavascriptFiles/foswikiPref-->
-<link class='head IMAGEPLUGIN' rel="stylesheet" href="../pub/System/ImagePlugin/style.css" type="text/css" media="all" /><!--IMAGEPLUGIN-->
+<link class='head FOOTNOTEPLUGIN_LINKCSS' rel="stylesheet" href="../pub/System/FootNotePlugin/styles.css" type="text/css" media="all" /><!--FOOTNOTEPLUGIN_LINKCSS-->
 <link class='head JQUERYPLUGIN::COMMENT' rel='stylesheet' href='../pub/System/CommentPlugin/commentf5b6.css?version=3.0' type='text/css' media='all' /><!--JQUERYPLUGIN::COMMENT-->
-<link class='head FOOTNOTEPLUGIN_LINKCSS' rel="stylesheet" href="../pub/System/FootNotePlugin/styles.css" type="text/css" media="all" /><!--FOOTNOTEPLUGIN_LINKCSS--><link rel='stylesheet' href='../pub/System/SkinTemplates/base.css' media='all' type='text/css' />
+<link class='head SMILIESPLUGIN' rel='stylesheet' href='../pub/System/SmiliesPlugin/smilies.css' type='text/css' media='all' /><!--SMILIESPLUGIN--><link rel='stylesheet' href='../pub/System/SkinTemplates/base.css' media='all' type='text/css' />
 <style type="text/css" media="all">
 @import url('../pub/System/PatternSkinTheme/layout.css');
 @import url('../pub/System/PatternSkinTheme2009/style.css');
@@ -135,19 +135,19 @@ body .foswikiTable#tableMsr2Data1 tr.foswikiTableRowdataBg0 td.foswikiSortedCol
 
 <!--<![endif]-->
 <!--JQUERYPLUGIN-->
-<!--JQUERYPLUGIN::MIGRATE-->
 <!--JQUERYPLUGIN::LIVEQUERY-->
 <!--JQUERYPLUGIN::FOSWIKI-->
+<!--JQUERYPLUGIN::MIGRATE-->
 <!--JavascriptFiles/foswikiString-->
 <!--JavascriptFiles/foswikiPref-->
-<!--JavascriptFiles/foswikiForm-->
-<!--PatternSkin/pattern-->
-<!--JQUERYPLUGIN::FOSWIKI::PREFERENCES-->
 <!--JQUERYPLUGIN::TWISTY-->
-<!--JQUERYPLUGIN::COMMENT-->
+<!--JavascriptFiles/foswikiForm-->
 <!--JQUERYPLUGIN::METADATA-->
 
-<!--JQUERYPLUGIN::CHILI--><link class='head FOOTNOTEPLUGIN_LINKCSS' rel="stylesheet" href="../pub/System/FootNotePlugin/styles.css" type="text/css" media="all" /><!--FOOTNOTEPLUGIN_LINKCSS-->
+<!--JQUERYPLUGIN::CHILI-->
+<!--JQUERYPLUGIN::FOSWIKI::PREFERENCES-->
+<!--JQUERYPLUGIN::COMMENT-->
+<!--PatternSkin/pattern--><link class='head FOOTNOTEPLUGIN_LINKCSS' rel="stylesheet" href="../pub/System/FootNotePlugin/styles.css" type="text/css" media="all" /><!--FOOTNOTEPLUGIN_LINKCSS-->
 </head> 
 <body class="foswikiNoJs patternViewPage patternPrintPage">
 <span id="PageTop"></span><div class="foswikiPage"><div id="patternScreen">
@@ -435,6 +435,5 @@ Topic revision:  <span class='patternRevInfo'>28 Apr 2016, <a href="https://intr
 
 </body>
 
-<!-- Mirrored from intranet.psi.ch/MUSR/Msr2Data?cover=print by HTTrack Website Copier/3.x [XR&CO'2010], Fri, 16 Dec 2016 16:01:26 GMT -->
-<!-- Added by HTTrack --><meta http-equiv="content-type" content="text/html;charset=utf-8"><!-- /Added by HTTrack -->
+<!-- Mirrored from intranet.psi.ch/MUSR/Msr2Data?cover=print by HTTrack Website Copier/3.x [XR&CO'2014], Sun, 14 May 2017 18:09:03 GMT -->
 </html>

doc/html/user/MUSR/MusrFit.html

@@ -1,7 +1,7 @@
 <!DOCTYPE html><html lang="en">
 
-<!-- Mirrored from intranet.psi.ch/MUSR/MusrFit?cover=print by HTTrack Website Copier/3.x [XR&CO'2010], Fri, 16 Dec 2016 16:01:02 GMT -->
-<!-- Added by HTTrack --><meta http-equiv="content-type" content="text/html;charset=utf-8"><!-- /Added by HTTrack -->
+<!-- Mirrored from intranet.psi.ch/MUSR/MusrFit?cover=print by HTTrack Website Copier/3.x [XR&CO'2014], Sun, 14 May 2017 18:08:39 GMT -->
+<!-- Added by HTTrack --><meta http-equiv="content-type" content="text/html;charset=utf-8" /><!-- /Added by HTTrack -->
 <head>
 <link rel="stylesheet" href="../pub/System/HeadlinesPlugin/style.css" type="text/css" media="all" />
 <title> MUSR :: MusrFit</title>
@@ -14,11 +14,14 @@
 <meta name="apple-mobile-web-app-status-bar-style" content="black-translucent" />
 <link rel="icon" href="../pub/Main/WebPreferences/favicon.ico" type="image/x-icon" />
 <link rel="shortcut icon" href="../pub/Main/WebPreferences/favicon.ico" type="image/x-icon" />
-<link rel="alternate" href="https://intranet.psi.ch/wiki/bin/edit/MUSR/MusrFit?t=1481904044" type="application/x-wiki" title="edit MusrFit" />
+<link rel="alternate" href="https://intranet.psi.ch/wiki/bin/edit/MUSR/MusrFit?t=1494785298" type="application/x-wiki" title="edit MusrFit" />
 <meta name="TEXT_NUM_TOPICS" content="Number of topics:" />
 <meta name="TEXT_MODIFY_SEARCH" content="Modify search" />
-<meta name="robots" content="noindex" /><link rel="alternate" type="application/rss+xml" title="RSS Feed" href="WebRsshtml.html" />
-<base  /><!--[if IE]></base><![endif]--><style class='head TABLEPLUGIN_default' type="text/css" media="all">
+<meta name="robots" content="noindex" /><link rel="alternate" type="application/rss+xml" title="RSS Feed" href="WebRss" />
+<base  /><!--[if IE]></base><![endif]--><link class='head FOOTNOTEPLUGIN_LINKCSS' rel="stylesheet" href="../pub/System/FootNotePlugin/styles.css" type="text/css" media="all" /><!--FOOTNOTEPLUGIN_LINKCSS-->
+<link class='head SMILIESPLUGIN' rel='stylesheet' href='../pub/System/SmiliesPlugin/smilies.css' type='text/css' media='all' /><!--SMILIESPLUGIN-->
+<link class='head JQUERYPLUGIN::COMMENT' rel='stylesheet' href='../pub/System/CommentPlugin/commentf5b6.css?version=3.0' type='text/css' media='all' /><!--JQUERYPLUGIN::COMMENT-->
+<style class='head TABLEPLUGIN_default' type="text/css" media="all">
 body .foswikiTable {border-width:1px}
 body .foswikiTable .tableSortIcon img {padding-left:.3em; vertical-align:text-bottom}
 body .foswikiTable td {border-style:solid none; vertical-align:top}
@@ -32,11 +35,8 @@ body .foswikiTable tr.foswikiTableRowdataBg0 td.foswikiSortedCol {background-col
 body .foswikiTable tr.foswikiTableRowdataBg1 td {background-color:#f7f7f6}
 body .foswikiTable tr.foswikiTableRowdataBg1 td.foswikiSortedCol {background-color:#f0f0ee}
 </style><!--TABLEPLUGIN_default-->
-<link class='head IMAGEPLUGIN' rel="stylesheet" href="../pub/System/ImagePlugin/style.css" type="text/css" media="all" /><!--IMAGEPLUGIN-->
-<link class='head FOOTNOTEPLUGIN_LINKCSS' rel="stylesheet" href="../pub/System/FootNotePlugin/styles.css" type="text/css" media="all" /><!--FOOTNOTEPLUGIN_LINKCSS-->
-<link class='head JQUERYPLUGIN::COMMENT' rel='stylesheet' href='../pub/System/CommentPlugin/commentf5b6.css?version=3.0' type='text/css' media='all' /><!--JQUERYPLUGIN::COMMENT-->
-<link class='head SMILIESPLUGIN' rel='stylesheet' href='../pub/System/SmiliesPlugin/smilies.css' type='text/css' media='all' /><!--SMILIESPLUGIN-->
-<link class='head CLASSIFICATIONPLUGIN::CSS' rel="stylesheet" href="../pub/System/ClassificationPlugin/styles.css" media="all" /><!--CLASSIFICATIONPLUGIN::CSS--><link rel='stylesheet' href='../pub/System/SkinTemplates/base.css' media='all' type='text/css' />
+<link class='head CLASSIFICATIONPLUGIN::CSS' rel="stylesheet" href="../pub/System/ClassificationPlugin/styles.css" media="all" /><!--CLASSIFICATIONPLUGIN::CSS-->
+<link class='head IMAGEPLUGIN' rel="stylesheet" href="../pub/System/ImagePlugin/style.css" type="text/css" media="all" /><!--IMAGEPLUGIN--><link rel='stylesheet' href='../pub/System/SkinTemplates/base.css' media='all' type='text/css' />
 <style type="text/css" media="all">
 @import url('../pub/System/PatternSkinTheme/layout.css');
 @import url('../pub/System/PatternSkinTheme2009/style.css');
@@ -116,18 +116,18 @@ body .foswikiTable tr.foswikiTableRowdataBg1 td.foswikiSortedCol {background-col
 
 <!--<![endif]-->
 <!--JQUERYPLUGIN-->
-<!--JQUERYPLUGIN::MIGRATE-->
-<!--JQUERYPLUGIN::FOSWIKI-->
 <!--JQUERYPLUGIN::LIVEQUERY-->
+<!--JQUERYPLUGIN::FOSWIKI-->
+<!--JQUERYPLUGIN::MIGRATE-->
 <!--JavascriptFiles/foswikiString-->
 <!--JavascriptFiles/foswikiPref-->
 <!--JavascriptFiles/foswikiForm-->
-<!--PatternSkin/pattern-->
 <!--JQUERYPLUGIN::METADATA-->
-<!--JQUERYPLUGIN::COMMENT-->
-<!--JQUERYPLUGIN::FOSWIKI::PREFERENCES-->
 
-<!--JQUERYPLUGIN::CHILI--><link class='head FOOTNOTEPLUGIN_LINKCSS' rel="stylesheet" href="../pub/System/FootNotePlugin/styles.css" type="text/css" media="all" /><!--FOOTNOTEPLUGIN_LINKCSS-->
+<!--JQUERYPLUGIN::CHILI-->
+<!--JQUERYPLUGIN::FOSWIKI::PREFERENCES-->
+<!--JQUERYPLUGIN::COMMENT-->
+<!--PatternSkin/pattern--><link class='head FOOTNOTEPLUGIN_LINKCSS' rel="stylesheet" href="../pub/System/FootNotePlugin/styles.css" type="text/css" media="all" /><!--FOOTNOTEPLUGIN_LINKCSS-->
 </head> 
 <body class="foswikiNoJs patternViewPage patternPrintPage">
 <span id="PageTop"></span><div class="foswikiPage"><div id="patternScreen">
@@ -153,7 +153,7 @@ body .foswikiTable tr.foswikiTableRowdataBg1 td.foswikiSortedCol {background-col
 </li> <li> <a href="MusrFit.html#A_2.7_any2many"> 2.7  any2many </a>
 </li> <li> <a href="MusrFit.html#A_2.8_dump_header"> 2.8  dump_header </a>
 </li></ul> 
-</li> <li> <a href="MusrFit.html#A_3_Auxiliary_Programs"> 3  Auxiliary Programs </a>
+</li> <li> <a href="MusrFit.html#A_3_Auxiliary_Programs_40musredit_44_msr2data_41"> 3  Auxiliary Programs (musredit, msr2data) <img src="../pub/System/DocumentGraphics/updated.png" alt="UPDATED" title="UPDATED" width="55" height="16" /> </a>
 </li> <li> <a href="MusrFit.html#A_4_Description_of_the_msr_File_Format"> 4  Description of the msr File Format </a> <ul>
 <li> <a href="MusrFit.html#A_4.1_The_Title"> 4.1  The Title </a>
 </li> <li> <a href="MusrFit.html#A_4.2_The_FITPARAMETER_Block"> 4.2  The FITPARAMETER Block </a>
@@ -483,8 +483,8 @@ the same as the previous example, except that the file name is constructed via t
 Will dump the <code>LEM</code> header information of run <code>3456</code> including the content of the run summary file.
 <p></p>
 <span id="AuxiliaryPrograms"></span>
-<h1 id="A_3_Auxiliary_Programs"> 3  Auxiliary Programs </h1>
-Additionally to the programs mentioned above editor front ends called <code><a href="MusrGui.html">musrgui/musredit</a></code> and another tool named <code><a href="Msr2Data.html">msr2data</a></code> are available. The purpose of <code>msr2data</code> is to process multiple msr files with the same parameters and to summarize the fitting results either in a <strong>DB</strong> or a <strong>column ASCII</strong> file. Also, new msr files can be generated from a template. For details refer to its <a href="Msr2Data.html">manual</a>.
+<h1 id="A_3_Auxiliary_Programs_40musredit_44_msr2data_41"> 3  Auxiliary Programs (musredit, msr2data) <img src="../pub/System/DocumentGraphics/updated.png" alt="UPDATED" title="UPDATED" width="55" height="16" /> </h1>
+Additionally to the programs mentioned above editor front ends called <code><a href="MusrGui.html">musredit</a></code> and another tool named <code><a href="Msr2Data.html">msr2data</a></code> are available. The purpose of <code>msr2data</code> is to process multiple msr files with the same parameters and to summarize the fitting results either in a <strong>DB</strong> or a <strong>column ASCII</strong> file. Also, new msr files can be generated from a template. For details refer to its <a href="Msr2Data.html">manual</a>.
 <p></p>
 <strong><span class='foswikiRedFG'>Before going to use <code>musrgui</code> / <code>musredit</code> it is strongly recommended to read this manual first!</span></strong>
 <p></p>
@@ -601,7 +601,7 @@ The THEORY block is used to define the fit function. There is a set of predefine
 			<td class="foswikiTableCol1"> stg </td>
 			<td class="foswikiTableCol2"> <img alt="\sigma\,(\mu\text{s}^{-1})" class="mmpImage" src="../pub/MUSR/MusrFit/_MathModePlugin_6b6bbc4add4da0bde8220c54594658f3.png"  /> </td>
 			<td class="foswikiTableCol3"> <img alt="\frac{1}{3} + \frac{2}{3} \left&#91;1-(\sigma t)^2\right] \exp\left&#91;-\frac{1}{2}\left(\sigma t\right)^2\right]" class="mmpImage" src="../pub/MUSR/MusrFit/_MathModePlugin_1f1b2becd9ba1bee3b5d7f897bd8db7e.png"  /> </td>
-			<td class="foswikiTableCol4 foswikiLastCol"> <img class='smily' src='../pub/Main/SmiliesPluginPSI_/skull.gif' alt='dead!' title='dead!' /> </td>
+			<td class="foswikiTableCol4 foswikiLastCol"> <img class='smily' src='../pub/Main/SmiliesPluginPSI/skull.gif' alt='dead!' title='dead!' /> </td>
 		</tr>
 		<tr class="foswikiTableEven foswikiTableRowdataBgSorted0 foswikiTableRowdataBg0">
 			<td class="foswikiTableCol0 foswikiFirstCol"> statGssKTLF </td>
@@ -643,7 +643,7 @@ The THEORY block is used to define the fit function. There is a set of predefine
 			<td class="foswikiTableCol1"> lgkt </td>
 			<td class="foswikiTableCol2"> <img alt="\lambda\,(\mu\text{s}^{-1})" class="mmpImage" src="../pub/MUSR/MusrFit/_MathModePlugin_020e973cf5b1293c76cb3ecef5a269f8.png"  />, <img alt="\sigma\,(\mu\text{s}^{-1})" class="mmpImage" src="../pub/MUSR/MusrFit/_MathModePlugin_6b6bbc4add4da0bde8220c54594658f3.png"  /> </td>
 			<td class="foswikiTableCol3"> <img alt="\frac{1}{3}+\frac{2}{3}\left(1-\sigma^2 t^2-\lambda t\right)\exp\left(-\frac{\sigma^2t^2}{2}-\lambda t\right)" class="mmpImage" src="../pub/MUSR/MusrFit/_MathModePlugin_95da508ef32b516260a14999eaf14f46.png"  /> </td>
-			<td class="foswikiTableCol4 foswikiLastCol"> <img class='smily' src='../pub/Main/SmiliesPluginPSI_/skull.gif' alt='dead!' title='dead!' /> </td>
+			<td class="foswikiTableCol4 foswikiLastCol"> <img class='smily' src='../pub/Main/SmiliesPluginPSI/skull.gif' alt='dead!' title='dead!' /> </td>
 		</tr>
 		<tr class="foswikiTableEven foswikiTableRowdataBgSorted0 foswikiTableRowdataBg0">
 			<td class="foswikiTableCol0 foswikiFirstCol"> strKT </td>
@@ -657,7 +657,7 @@ The THEORY block is used to define the fit function. There is a set of predefine
 			<td class="foswikiTableCol1"> spg </td>
 			<td class="foswikiTableCol2"> <img alt="\lambda\,(\mu\text{s}^{-1})" class="mmpImage" src="../pub/MUSR/MusrFit/_MathModePlugin_020e973cf5b1293c76cb3ecef5a269f8.png"  />, <img alt="\gamma\,(\mu\text{s}^{-1})" class="mmpImage" src="../pub/MUSR/MusrFit/_MathModePlugin_8aad0e0c2c1f20995c483933a896ca0d.png"  />, <img alt="q\,(1)" class="mmpImage" src="../pub/MUSR/MusrFit/_MathModePlugin_16b8c518c1e529e6c963929287ef3a56.png"  /> </td>
 			<td class="foswikiTableCol3"> <img alt="\frac{1}{3}\exp\left(-\sqrt{\frac{4\lambda^2(1-q)t}{\gamma}}\right)+\frac{2}{3}\left(1-\frac{q\lambda^2t^2}{\sqrt{\frac{4\lambda^2(1-q)t}{\gamma}+q\lambda^2t^2}}\right)\exp\left(-\sqrt{\frac{4\lambda^2(1-q)t}{\gamma}+q\lambda^2t^2}\right)" class="mmpImage" src="../pub/MUSR/MusrFit/_MathModePlugin_e35c4217aa50607f25e6eadf9f27f874.png"  /> </td>
-			<td class="foswikiTableCol4 foswikiLastCol"> <img class='smily' src='../pub/Main/SmiliesPluginPSI_/skull.gif' alt='dead!' title='dead!' /> </td>
+			<td class="foswikiTableCol4 foswikiLastCol"> <img class='smily' src='../pub/Main/SmiliesPluginPSI/skull.gif' alt='dead!' title='dead!' /> </td>
 		</tr>
 		<tr class="foswikiTableEven foswikiTableRowdataBgSorted0 foswikiTableRowdataBg0">
 			<td class="foswikiTableCol0 foswikiFirstCol"> rdAnisoHf </td>
@@ -671,35 +671,35 @@ The THEORY block is used to define the fit function. There is a set of predefine
 			<td class="foswikiTableCol1"> tf </td>
 			<td class="foswikiTableCol2"> <img alt="\varphi\,(^{\circ})" class="mmpImage" src="../pub/MUSR/MusrFit/_MathModePlugin_61136f20673ad20f955c43e43b8cec9d.png"  />, <img alt="\nu\,(\mathrm{MHz})" class="mmpImage" src="../pub/MUSR/MusrFit/_MathModePlugin_7188605a647615e4fb92cc89274b22a0.png"  /> </td>
 			<td class="foswikiTableCol3"> <img alt="\cos\left(2\pi\nu t+\frac{\pi\varphi}{180}\right)" class="mmpImage" src="../pub/MUSR/MusrFit/_MathModePlugin_51757d805f7111ffe6e0b430b6d137c7.png"  /> </td>
-			<td class="foswikiTableCol4 foswikiLastCol"> <img class='smily' src='../pub/Main/SmiliesPluginPSI_/skull.gif' alt='dead!' title='dead!' /> </td>
+			<td class="foswikiTableCol4 foswikiLastCol"> <img class='smily' src='../pub/Main/SmiliesPluginPSI/skull.gif' alt='dead!' title='dead!' /> </td>
 		</tr>
 		<tr class="foswikiTableEven foswikiTableRowdataBgSorted0 foswikiTableRowdataBg0">
 			<td class="foswikiTableCol0 foswikiFirstCol"> internFld </td>
 			<td class="foswikiTableCol1"> if </td>
 			<td class="foswikiTableCol2"> <img alt="\alpha\,(1)" class="mmpImage" src="../pub/MUSR/MusrFit/_MathModePlugin_f266f29ff7212b8d77bf67567eac1fd3.png"  />, <img alt="\varphi\,(^{\circ})" class="mmpImage" src="../pub/MUSR/MusrFit/_MathModePlugin_61136f20673ad20f955c43e43b8cec9d.png"  />, <img alt="\nu\,(\mathrm{MHz})" class="mmpImage" src="../pub/MUSR/MusrFit/_MathModePlugin_7188605a647615e4fb92cc89274b22a0.png"  />, <img alt="\lambda&#95;{\mathrm{T}}\,(\mu\text{s}^{-1})" class="mmpImage" src="../pub/MUSR/MusrFit/_MathModePlugin_49046b617890ffeaca8bc16ae66d0dc5.png"  />, <img alt="\lambda&#95;{\mathrm{L}}\,(\mu\text{s}^{-1})" class="mmpImage" src="../pub/MUSR/MusrFit/_MathModePlugin_b0c4a8cbbcf4189b64418b381939a979.png"  /> </td>
 			<td class="foswikiTableCol3"> <img alt="\alpha\,\cos\left(2\pi\nu t+\frac{\pi\varphi}{180}\right)\exp\left(-\lambda&#95;{\mathrm{T}}t\right)+(1-\alpha)\,\exp\left(-\lambda&#95;{\mathrm{L}}t\right)" class="mmpImage" src="../pub/MUSR/MusrFit/_MathModePlugin_1582d158c5651581ca9e800ee698ce9f.png"  /> </td>
-			<td class="foswikiTableCol4 foswikiLastCol"> <img class='smily' src='../pub/Main/SmiliesPluginPSI_/skull.gif' alt='dead!' title='dead!' /> </td>
+			<td class="foswikiTableCol4 foswikiLastCol"> <img class='smily' src='../pub/Main/SmiliesPluginPSI/skull.gif' alt='dead!' title='dead!' /> </td>
 		</tr>
 		<tr class="foswikiTableOdd foswikiTableRowdataBgSorted1 foswikiTableRowdataBg1">
 			<td class="foswikiTableCol0 foswikiFirstCol"> Bessel </td>
 			<td class="foswikiTableCol1"> b </td>
 			<td class="foswikiTableCol2"> <img alt="\varphi\,(^{\circ})" class="mmpImage" src="../pub/MUSR/MusrFit/_MathModePlugin_61136f20673ad20f955c43e43b8cec9d.png"  />, <img alt="\nu\,(\mathrm{MHz})" class="mmpImage" src="../pub/MUSR/MusrFit/_MathModePlugin_7188605a647615e4fb92cc89274b22a0.png"  /> </td>
 			<td class="foswikiTableCol3"> <img alt="j&#95;0\left(2\pi\nu t+\frac{\pi\varphi}{180}\right)" class="mmpImage" src="../pub/MUSR/MusrFit/_MathModePlugin_cff60a46de8608e97a33bbae7c4e566d.png"  /> </td>
-			<td class="foswikiTableCol4 foswikiLastCol"> <img class='smily' src='../pub/Main/SmiliesPluginPSI_/skull.gif' alt='dead!' title='dead!' /> </td>
+			<td class="foswikiTableCol4 foswikiLastCol"> <img class='smily' src='../pub/Main/SmiliesPluginPSI/skull.gif' alt='dead!' title='dead!' /> </td>
 		</tr>
 		<tr class="foswikiTableEven foswikiTableRowdataBgSorted0 foswikiTableRowdataBg0">
 			<td class="foswikiTableCol0 foswikiFirstCol"> internBsl </td>
 			<td class="foswikiTableCol1"> ib </td>
 			<td class="foswikiTableCol2"> <img alt="\alpha\,(1)" class="mmpImage" src="../pub/MUSR/MusrFit/_MathModePlugin_f266f29ff7212b8d77bf67567eac1fd3.png"  />, <img alt="\varphi\,(^{\circ})" class="mmpImage" src="../pub/MUSR/MusrFit/_MathModePlugin_61136f20673ad20f955c43e43b8cec9d.png"  />, <img alt="\nu\,(\mathrm{MHz})" class="mmpImage" src="../pub/MUSR/MusrFit/_MathModePlugin_7188605a647615e4fb92cc89274b22a0.png"  />, <img alt="\lambda&#95;{\mathrm{T}}\,(\mu\text{s}^{-1})" class="mmpImage" src="../pub/MUSR/MusrFit/_MathModePlugin_49046b617890ffeaca8bc16ae66d0dc5.png"  />, <img alt="\lambda&#95;{\mathrm{L}}\,(\mu\text{s}^{-1})" class="mmpImage" src="../pub/MUSR/MusrFit/_MathModePlugin_b0c4a8cbbcf4189b64418b381939a979.png"  /> </td>
 			<td class="foswikiTableCol3"> <img alt="\alpha\,j&#95;0\left(2\pi\nu t+\frac{\pi\varphi}{180}\right)\exp\left(-\lambda&#95;{\mathrm{T}}t\right)+(1-\alpha)\,\exp\left(-\lambda&#95;{\mathrm{L}}t\right)" class="mmpImage" src="../pub/MUSR/MusrFit/_MathModePlugin_23ec8fc398b4e415b86bbd2b65f9a63c.png"  /> </td>
-			<td class="foswikiTableCol4 foswikiLastCol"> <img class='smily' src='../pub/Main/SmiliesPluginPSI_/skull.gif' alt='dead!' title='dead!' /> </td>
+			<td class="foswikiTableCol4 foswikiLastCol"> <img class='smily' src='../pub/Main/SmiliesPluginPSI/skull.gif' alt='dead!' title='dead!' /> </td>
 		</tr>
 		<tr class="foswikiTableOdd foswikiTableRowdataBgSorted1 foswikiTableRowdataBg1">
 			<td class="foswikiTableCol0 foswikiFirstCol"> abragam </td>
 			<td class="foswikiTableCol1"> ab </td>
 			<td class="foswikiTableCol2"> <img alt="\sigma\,(\mu\text{s}^{-1})" class="mmpImage" src="../pub/MUSR/MusrFit/_MathModePlugin_6b6bbc4add4da0bde8220c54594658f3.png"  />, <img alt="\gamma\,(\mathrm{MHz})" class="mmpImage" src="../pub/MUSR/MusrFit/_MathModePlugin_ebef6cda2881306e993839c1b4bcaa4c.png"  /> </td>
 			<td class="foswikiTableCol3"> <img alt="\exp\left&#91;-\frac{\sigma^2}{\gamma^2}\left(e^{-\gamma t}-1+\gamma t\right)\right]" class="mmpImage" src="../pub/MUSR/MusrFit/_MathModePlugin_e56be15b7e230ec52a9f6632e552ca4b.png"  /> </td>
-			<td class="foswikiTableCol4 foswikiLastCol"> <img class='smily' src='../pub/Main/SmiliesPluginPSI_/skull.gif' alt='dead!' title='dead!' /> </td>
+			<td class="foswikiTableCol4 foswikiLastCol"> <img class='smily' src='../pub/Main/SmiliesPluginPSI/skull.gif' alt='dead!' title='dead!' /> </td>
 		</tr>
 		<tr class="foswikiTableEven foswikiTableRowdataBgSorted0 foswikiTableRowdataBg0">
 			<td class="foswikiTableCol0 foswikiFirstCol"> skewedGss </td>
@@ -1047,7 +1047,7 @@ etc.
 addt0 t0AddRun1Forward t0AddRun1Backward
 addt0 t0AddRun2Forward t0AddRun2Backward
 etc.
-</pre> How will the background and data ranges be handled in this situation? First, the ADDRUN's will be shifted in time such that all the t0's have the same channel/bin number. Subsequently, the runs will be added. The background/data range is applied to this summed up new histogram. ADDRUN is not available for the fit type 'Non-&mu;SR Fit' (sorry <img class='smily' src='../pub/Main/SmiliesPluginPSI_/no.gif' alt='no' title='no' /> ).
+</pre> How will the background and data ranges be handled in this situation? First, the ADDRUN's will be shifted in time such that all the t0's have the same channel/bin number. Subsequently, the runs will be added. The background/data range is applied to this summed up new histogram. ADDRUN is not available for the fit type 'Non-&mu;SR Fit' (sorry <img class='smily' src='../pub/Main/SmiliesPluginPSI/no.gif' alt='no' title='no' /> ).
 <p></p>
 <span id="FitTypes"></span> <dl>
 <dt> fittype (required if not already defined in the GLOBAL block) </dt><dd> This tag is used to indicate which type of fit is wished. The supported fit types are: <dl>
@@ -1084,7 +1084,7 @@ norm            fun3
 <dt> lifetime (fit type 0) </dt><dd> Fit parameter representing the lifetime of the muon. If it is not specified the value &#964;<sub>&#956;</sub>=2.197019 &#956;s is used in the calculations.
 </dd></dl> 
 <p></p> <dl>
-<dt> lifetimecorrection (fit type 0) <img class='smily' src='../pub/Main/SmiliesPluginPSI_/eek.gif' alt='eek!' title='eek!' /> <strong>obsolete</strong> <img class='smily' src='../pub/Main/SmiliesPluginPSI_/eek.gif' alt='eek!' title='eek!' />  </dt><dd> Does not accept any arguments. If present, the output in <code>musrview</code> is corrected for the exponential decay of the muon. This item is <strong>obsolete</strong> in the RUN block and will be transferred to the <a class="foswikiCurrentTopicLink" href="#ThePlotBlock">PLOT block</a>, which allows switching between histogram view and asymmetry view much quicker.  
+<dt> lifetimecorrection (fit type 0) <img class='smily' src='../pub/Main/SmiliesPluginPSI/eek.gif' alt='eek!' title='eek!' /> <strong>obsolete</strong> <img class='smily' src='../pub/Main/SmiliesPluginPSI/eek.gif' alt='eek!' title='eek!' />  </dt><dd> Does not accept any arguments. If present, the output in <code>musrview</code> is corrected for the exponential decay of the muon. This item is <strong>obsolete</strong> in the RUN block and will be transferred to the <a class="foswikiCurrentTopicLink" href="#ThePlotBlock">PLOT block</a>, which allows switching between histogram view and asymmetry view much quicker.  
 </dd></dl> 
 <p></p> <dl>
 <dt> map </dt><dd> On this line the mapping of run-dependent parameters is done. Parameter numbers given here may be accessed through <code><b>map1</b></code>, <code><b>map2</b></code>, etc. in the THEORY and FUNCTIONS blocks (see also <a class="foswikiCurrentTopicLink" href="#MaPs">here</a>). The first ten maps are always present and have the value 0 if not used; however, the total number of maps is not restricted!
@@ -1305,8 +1305,8 @@ The PLOT block is intended to collect all the information needed for the graphic
 </dd></dl> 
 </dd> <dt> use_fit_ranges [ <i>y</i><sub>min</sub> <i>y</i><sub>max</sub>] </dt><dd> The fit ranges of the individual runs are used to present the data. Optionally, an ordinate range can be provided.
 </dd> <dt> view_packing </dt><dd> The data are presented in the packing given here rather than the binning used for the fit. <strong>WARNING</strong>: This is a global option and applies to <strong>all</strong> PLOT-blocks.
-</dd> <dt> logx </dt><dd> Will present the time axis in a logarithmic scale. So far no checking of negative and zero-valued data is performed <img class='smily' src='../pub/Main/SmiliesPluginPSI_/wink.gif' alt='wink' title='wink' />
-</dd> <dt> logy </dt><dd> Will present the axis of ordinates in a logarithmic scale. So far no checking of negative and zero-valued data is performed <img class='smily' src='../pub/Main/SmiliesPluginPSI_/wink.gif' alt='wink' title='wink' />
+</dd> <dt> logx </dt><dd> Will present the time axis in a logarithmic scale. So far no checking of negative and zero-valued data is performed <img class='smily' src='../pub/Main/SmiliesPluginPSI/wink.gif' alt='wink' title='wink' />
+</dd> <dt> logy </dt><dd> Will present the axis of ordinates in a logarithmic scale. So far no checking of negative and zero-valued data is performed <img class='smily' src='../pub/Main/SmiliesPluginPSI/wink.gif' alt='wink' title='wink' />
 </dd> <dt> rrf_packing <code>value</code> </dt><dd> In the rotating-reference-frame (RRF) representation, this will be the value for the packing. <strong>WARNING</strong>: For the time being, this is a global option and applies to <strong>all</strong> PLOT blocks.
 </dd> <dt> rrf_freq <code>value</code> <code>unit</code> </dt><dd> This entry provides the RRF "frequency" given by the <code>value</code> and the <code>unit</code> which can be: <code>kHz</code>, <code>MHz</code>, <code>Mc/s</code>, <code>G</code>, or <code>T</code>.
 </dd> <dt> rrf_phase <code>value</code> </dt><dd> A phase of the RRF can be provided, either as a value in degrees, or as a <code>parX</code>, e.g. <code>par4</code>, where <code>X</code> is supposed to be the phase parameter number in the FITPARAMETER block.
@@ -1547,7 +1547,7 @@ In case of a custom installation some paths in the Makefile might have to be cha
 <p></p>
 After installing the shared library the defined user function might be used in <code>musrfit</code> as described <a class="foswikiCurrentTopicLink" href="#UserFunctions">above</a>.
 <p></p>
-Good luck! <img class='smily' src='../pub/Main/SmiliesPluginPSI_/wink.gif' alt='wink' title='wink' />
+Good luck! <img class='smily' src='../pub/Main/SmiliesPluginPSI/wink.gif' alt='wink' title='wink' />
 <p></p>
 Finally, please be aware of the <a class="foswikiCurrentTopicLink" href="#UserFunctionRemark">remark</a> at the end of this section.
 <p></p>
@@ -1713,7 +1713,7 @@ For reporting bugs or requesting new features and improvements please use the <a
 <p></p>
 </div>
 <div class="patternInfo">This topic: MUSR<span class='foswikiSeparator'>&nbsp;&gt;&nbsp;</span><a class="foswikiCurrentWebHomeLink" href="WebHome.html">WebHome</a><span class='foswikiSeparator'>&nbsp;&gt;&nbsp;</span>MusrFit <br />
-Topic revision:  <span class='patternRevInfo'>16 Dec 2016, <a href="https://intranet.psi.ch/Main/AndreasSuter">AndreasSuter</a></span></div>
+Topic revision:  <span class='patternRevInfo'>30 Apr 2017, <a href="https://intranet.psi.ch/Main/AndreasSuter">AndreasSuter</a></span></div>
 </div>
 </div>
 </div>
@@ -1731,6 +1731,5 @@ Topic revision:  <span class='patternRevInfo'>16 Dec 2016, <a href="https://intr
 
 </body>
 
-<!-- Mirrored from intranet.psi.ch/MUSR/MusrFit?cover=print by HTTrack Website Copier/3.x [XR&CO'2010], Fri, 16 Dec 2016 16:01:25 GMT -->
-<!-- Added by HTTrack --><meta http-equiv="content-type" content="text/html;charset=utf-8"><!-- /Added by HTTrack -->
+<!-- Mirrored from intranet.psi.ch/MUSR/MusrFit?cover=print by HTTrack Website Copier/3.x [XR&CO'2014], Sun, 14 May 2017 18:09:03 GMT -->
 </html>

doc/html/user/MUSR/MusrFitAcknowledgements.html

@@ -1,7 +1,7 @@
 <!DOCTYPE html><html lang="en">
 
-<!-- Mirrored from intranet.psi.ch/MUSR/MusrFitAcknowledgements?cover=print by HTTrack Website Copier/3.x [XR&CO'2010], Fri, 16 Dec 2016 16:01:02 GMT -->
-<!-- Added by HTTrack --><meta http-equiv="content-type" content="text/html;charset=utf-8"><!-- /Added by HTTrack -->
+<!-- Mirrored from intranet.psi.ch/MUSR/MusrFitAcknowledgements?cover=print by HTTrack Website Copier/3.x [XR&CO'2014], Sun, 14 May 2017 18:08:39 GMT -->
+<!-- Added by HTTrack --><meta http-equiv="content-type" content="text/html;charset=utf-8" /><!-- /Added by HTTrack -->
 <head>
 <link rel="stylesheet" href="../pub/System/HeadlinesPlugin/style.css" type="text/css" media="all" />
 <title> MUSR :: MusrFitAcknowledgements</title>
@@ -14,12 +14,12 @@
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-<link rel="alternate" href="https://intranet.psi.ch/wiki/bin/edit/MUSR/MusrFitAcknowledgements?t=1481904044" type="application/x-wiki" title="edit MusrFitAcknowledgements" />
+<link rel="alternate" href="https://intranet.psi.ch/wiki/bin/edit/MUSR/MusrFitAcknowledgements?t=1494785298" type="application/x-wiki" title="edit MusrFitAcknowledgements" />
 <meta name="TEXT_NUM_TOPICS" content="Number of topics:" />
 <meta name="TEXT_MODIFY_SEARCH" content="Modify search" />
-<meta name="robots" content="noindex" /><link rel="alternate" type="application/rss+xml" title="RSS Feed" href="WebRsshtml.html" />
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-<link class='head CLASSIFICATIONPLUGIN::CSS' rel="stylesheet" href="../pub/System/ClassificationPlugin/styles.css" media="all" /><!--CLASSIFICATIONPLUGIN::CSS-->
+<meta name="robots" content="noindex" /><link rel="alternate" type="application/rss+xml" title="RSS Feed" href="WebRss" />
+<base  /><!--[if IE]></base><![endif]--><link class='head CLASSIFICATIONPLUGIN::CSS' rel="stylesheet" href="../pub/System/ClassificationPlugin/styles.css" media="all" /><!--CLASSIFICATIONPLUGIN::CSS-->
+<link class='head SMILIESPLUGIN' rel='stylesheet' href='../pub/System/SmiliesPlugin/smilies.css' type='text/css' media='all' /><!--SMILIESPLUGIN-->
 <link class='head JQUERYPLUGIN::COMMENT' rel='stylesheet' href='../pub/System/CommentPlugin/commentf5b6.css?version=3.0' type='text/css' media='all' /><!--JQUERYPLUGIN::COMMENT-->
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 <style type="text/css" media="all">
@@ -102,8 +102,8 @@
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 <!--JQUERYPLUGIN-->
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-<!--JQUERYPLUGIN::LIVEQUERY-->
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+<!--JQUERYPLUGIN::LIVEQUERY-->
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@@ -145,6 +145,5 @@ Topic revision:  <span class='patternRevInfo'>03 Jul 2015, suter_a</span></div>
 
 </body>
 
-<!-- Mirrored from intranet.psi.ch/MUSR/MusrFitAcknowledgements?cover=print by HTTrack Website Copier/3.x [XR&CO'2010], Fri, 16 Dec 2016 16:01:02 GMT -->
-<!-- Added by HTTrack --><meta http-equiv="content-type" content="text/html;charset=utf-8"><!-- /Added by HTTrack -->
+<!-- Mirrored from intranet.psi.ch/MUSR/MusrFitAcknowledgements?cover=print by HTTrack Website Copier/3.x [XR&CO'2014], Sun, 14 May 2017 18:08:39 GMT -->
 </html>

doc/html/user/MUSR/MusrFitSetup.html

@@ -1,7 +1,7 @@
 <!DOCTYPE html><html lang="en">
 
-<!-- Mirrored from intranet.psi.ch/MUSR/MusrFitSetup?cover=print by HTTrack Website Copier/3.x [XR&CO'2010], Fri, 16 Dec 2016 16:01:01 GMT -->
-<!-- Added by HTTrack --><meta http-equiv="content-type" content="text/html;charset=utf-8"><!-- /Added by HTTrack -->
+<!-- Mirrored from intranet.psi.ch/MUSR/MusrFitSetup?cover=print by HTTrack Website Copier/3.x [XR&CO'2014], Sun, 14 May 2017 18:08:39 GMT -->
+<!-- Added by HTTrack --><meta http-equiv="content-type" content="text/html;charset=utf-8" /><!-- /Added by HTTrack -->
 <head>
 <link rel="stylesheet" href="../pub/System/HeadlinesPlugin/style.css" type="text/css" media="all" />
 <title> MUSR :: MusrFitSetup</title>
@@ -14,13 +14,13 @@
 <meta name="apple-mobile-web-app-status-bar-style" content="black-translucent" />
 <link rel="icon" href="../pub/Main/WebPreferences/favicon.ico" type="image/x-icon" />
 <link rel="shortcut icon" href="../pub/Main/WebPreferences/favicon.ico" type="image/x-icon" />
-<link rel="alternate" href="https://intranet.psi.ch/wiki/bin/edit/MUSR/MusrFitSetup?t=1481904043" type="application/x-wiki" title="edit MusrFitSetup" />
+<link rel="alternate" href="https://intranet.psi.ch/wiki/bin/edit/MUSR/MusrFitSetup?t=1494785297" type="application/x-wiki" title="edit MusrFitSetup" />
 <meta name="TEXT_NUM_TOPICS" content="Number of topics:" />
 <meta name="TEXT_MODIFY_SEARCH" content="Modify search" />
-<meta name="robots" content="noindex" /><link rel="alternate" type="application/rss+xml" title="RSS Feed" href="WebRsshtml.html" />
-<base  /><!--[if IE]></base><![endif]--><link class='head FOOTNOTEPLUGIN_LINKCSS' rel="stylesheet" href="../pub/System/FootNotePlugin/styles.css" type="text/css" media="all" /><!--FOOTNOTEPLUGIN_LINKCSS-->
-<link class='head JQUERYPLUGIN::COMMENT' rel='stylesheet' href='../pub/System/CommentPlugin/commentf5b6.css?version=3.0' type='text/css' media='all' /><!--JQUERYPLUGIN::COMMENT-->
+<meta name="robots" content="noindex" /><link rel="alternate" type="application/rss+xml" title="RSS Feed" href="WebRss" />
+<base  /><!--[if IE]></base><![endif]--><link class='head JQUERYPLUGIN::COMMENT' rel='stylesheet' href='../pub/System/CommentPlugin/commentf5b6.css?version=3.0' type='text/css' media='all' /><!--JQUERYPLUGIN::COMMENT-->
 <link class='head SMILIESPLUGIN' rel='stylesheet' href='../pub/System/SmiliesPlugin/smilies.css' type='text/css' media='all' /><!--SMILIESPLUGIN-->
+<link class='head FOOTNOTEPLUGIN_LINKCSS' rel="stylesheet" href="../pub/System/FootNotePlugin/styles.css" type="text/css" media="all" /><!--FOOTNOTEPLUGIN_LINKCSS-->
 <link class='head CLASSIFICATIONPLUGIN::CSS' rel="stylesheet" href="../pub/System/ClassificationPlugin/styles.css" media="all" /><!--CLASSIFICATIONPLUGIN::CSS--><link rel='stylesheet' href='../pub/System/SkinTemplates/base.css' media='all' type='text/css' />
 <style type="text/css" media="all">
 @import url('../pub/System/PatternSkinTheme/layout.css');
@@ -104,12 +104,12 @@
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 <!--JQUERYPLUGIN::FOSWIKI-->
 <!--JQUERYPLUGIN::MIGRATE-->
+<!--JavascriptFiles/foswikiString-->
+<!--JavascriptFiles/foswikiPref-->
+<!--JavascriptFiles/foswikiForm-->
 <!--JQUERYPLUGIN::METADATA-->
 
 <!--JQUERYPLUGIN::CHILI-->
-<!--JavascriptFiles/foswikiString-->
-<!--JavascriptFiles/foswikiForm-->
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 <!--PatternSkin/pattern--><link class='head FOOTNOTEPLUGIN_LINKCSS' rel="stylesheet" href="../pub/System/FootNotePlugin/styles.css" type="text/css" media="all" /><!--FOOTNOTEPLUGIN_LINKCSS-->
@@ -187,7 +187,7 @@ Additionally, <span class='foswikiRedFG'>only if</span> <code>musrfit</code> sho
    $ <a href="http://www.hdfgroup.org/products/hdf4/">HDF4</a>: A library and multi-object file format for storing and managing data.
    $ <a href="http://www.hdfgroup.org/HDF5/">HDF5</a>: A data model, library, and file format for storing and managing data.
    $ <a href="http://www.minixml.org/">minixml</a>: A small <code>XML</code> library that can be used to read and write <code>XML</code> and <code>XML</code> -like data files. <em>Required version &#8805; 2.2</em>
-   $ <a href="http://www.nexusformat.org/">NeXus</a>: A common data format for neutron, x-ray, and muon science.
+   $ <a href="http://www.nexusformat.org/">NeXus</a>: A common data format for neutron, x-ray, and muon science. <em>Required version &#8805; 4.4</em>
 <p></p>
 If optionally the editor and graphical user interface <code><a href="MusrGui.html">musrgui</a></code> / <code><a href="MusrGui.html">musredit</a></code> is going to be installed there is one further requirement:
    $ <a href="http://qt.nokia.com/">Qt</a>: A cross-platform application and user interface framework. <em>Required version &#8805; 3.3 &#38; &#8810; 4.0 (<code>musrgui</code>) <strong>OR</strong> &#8805; 4.6 (<code>musredit</code>)</em> 
@@ -198,7 +198,7 @@ Each of the following sections focusing on the installation of <code>musrfit</co
 Before the further installation will be described, please note the following restrictions: <dl>
 <dt> GNU/Linux </dt><dd> No serious problems are known at the moment.
 </dd> <dt> MS Windows </dt><dd> The setup of <code>musrfit</code> (including the requirements) using <code>Visual C++</code> has not been tested. If anybody likes to do this: Just go ahead and have fun! However, not very much assistance can be expected, although it would be an interesting experiment.
-</dd> <dt> Mac OS X </dt><dd> On <code>10.6 Snow Leopard</code> <code>Qt3</code> for Mac is not supported any more since this was based on a 32-bit only API. <code>Snow Leopard</code> -users are advised to use the <code>Qt4</code> based <code>musredit</code> or to rely on the standard <code>Qt3</code> version for <code>X11</code> in order to run <code>musrgui</code>. On newer Mac OS X versions (&gt;= 10.8) you should use the <code>Qt4</code> base <code>musredit</code> only.
+</dd> <dt> Mac OS X </dt><dd> On <code>10.6 Snow Leopard</code> <code>Qt3</code> for Mac is not supported any more since this was based on a 32-bit only API. <code>Snow Leopard</code> -users are advised to use the <code>Qt4</code> based <code>musredit</code> or to rely on the standard <code>Qt3</code> version for <code>X11</code> in order to run <code>musrgui</code>. On newer Mac OS X versions (&gt;= 10.8) you should use the <code>Qt4</code> or better, if available, <code>Qt5</code> base <code>musredit</code> only.
 </dd></dl> 
 <p></p>
 <h1 id="A_3_GNU_47Linux"> 3  GNU/Linux </h1>
@@ -206,14 +206,33 @@ Before the further installation will be described, please note the following res
 <h3 id="A_3.1.1_Everything_but_61_61ROOT_61_61_and_61_61NeXus_61_61"> 3.1.1  Everything but <code><b>ROOT</b></code> and <code><b>NeXus</b></code> </h3>
 Depending on the GNU/Linux distribution chosen, the above mentioned software&mdash;except the <code>ROOT</code> system and the <code>NeXus</code> library&mdash;should be available from the distributor and could be easily installed in the form of binary packages. If done in this way there should be taken care of installing <strong>both</strong>, the libraries and the header (dev, devel) files.<br>
 On a <a href="https://www.scientificlinux.org/">Scientific Linux</a> (<a href="http://www.redhat.com/">Red Hat</a>, other RPM-package base Linux distributions) system the following command executed as superuser from the shell will do the trick (never type the '$' it is the shell prompt of your system):
+<p></p>
+For <strong>Qt4</strong>:
 <pre class="bash">
-&#36; yum install git boost-devel gsl-devel fftw-devel libxml2-devel qt-devel qtwebkit-devel
+&#36; yum install git cmake boost-devel gsl-devel fftw-devel libxml2-devel qt-devel qtwebkit-devel
 </pre> 
-When dealing with a distribution that uses the dpkg/apt package manager like <a href="http://www.debian.org/">Debian</a> or <a href="http://www.ubuntu.com/">Ubuntu</a> the installation would look like:
+<p></p>
+For <strong>Qt5</strong>:
 <pre class="bash">
-&#36; apt-get install git libboost-dev libgsl0-dev libfftw3-dev libxml2-dev libqt4-dev libqtwebkit-dev
+&#36; yum install epel-release
+&#36; yum install git cmake boost-devel gsl-devel fftw-devel libxml2-devel qt5-qtbase-devel qt5-qtsvg-devel qt5-qtwebkit-devel
+</pre> 
+<p></p>
+Depending on your distribution <strong>Qt4</strong> is still the default but is likely to be replaced by <strong>Qt5</strong> in the very near future.
+<p></p>
+When dealing with a distribution that uses the dpkg/apt package manager like <a href="http://www.debian.org/">Debian</a> or <a href="http://www.ubuntu.com/">Ubuntu</a> the installation would look like:
+<p></p>
+For <strong>Qt4</strong>:
+<pre class="bash">
+&#36; apt-get install git cmake libboost-dev libgsl0-dev libfftw3-dev libxml2-dev libqt4-dev libqtwebkit-dev
 </pre>
-Everyone should know best himself which is the way to install distribution software on the chosen distribution <img class='smily' src='../pub/Main/SmiliesPluginPSI_/wink.gif' alt='wink' title='wink' />
+<p></p>
+For <strong>Qt5</strong>:
+<pre class="bash">
+&#36; apt-get install git cmake libboost-dev libgsl0-dev libfftw3-dev libxml2-dev qt5-default qtbase5-dev libqt5svg5-dev libqt5webkit5-dev
+</pre>
+<p></p>
+Everyone should know best himself which is the way to install distribution software on the chosen distribution <img class='smily' src='../pub/Main/SmiliesPluginPSI/wink.gif' alt='wink' title='wink' />
 <p></p>
 In case the distribution does not include the required software it has to be compiled from the source files which normally means to download the source code from the corresponding website, to unpack the source tree and call the following from the shell:
 <pre class="bash">
@@ -249,9 +268,9 @@ A brief instruction how to get <code>NeXus</code> compiled from source:
 &#36; sudo make install
 </pre>
 <h3 id="A_3.1.3_61_61ROOT_61_61"> 3.1.3  <code><b>ROOT</b></code> </h3>
-<strong>Currently only ROOT 5.34/xx is support! Do NOT try to use ROOT 6.xx/yy yet!</strong>
+ROOT 5.34/xx is supported as legacy version only! <strong>The default now will be ROOT 6.xx/yy!</strong>
 <p></p>
-The <code>ROOT</code> system may or may not be part of the GNU/Linux distribution. Some distributions are packing <code>ROOT</code> in a manner incompatible with the way it is needed for <code>musrfit</code>. <strong>Therefore we advise to install <code>ROOT</code> from source</strong>. Before installing <code>ROOT</code> from source you will need to install some additional header packages. 
+The <code>ROOT</code> system may or may not be part of the GNU/Linux distribution. Some distributions are packing <code>ROOT</code> in a manner incompatible with the way it is needed for <code>musrfit</code>, though the situation is improving. If you are experienced enough you can try the packed ROOT version. Often ROOT is split in many sub-packages. Install the necessary ones (guess from the description below). <strong>One Warning</strong>: if the ROOT packages are upgraded after a <code>yum update</code> (<code>apt-get update; apt-get upgrade</code>) you might need to recompile <code>musrfit</code>. If you are not sure about all this: <strong>install <code>ROOT</code> from source</strong>. Before installing <code>ROOT</code> from source you will need to install some additional header packages. 
 <p></p>
 For RPM based systems (RedHat, Fedora, etc) this will likely to be <strong>libX11-devel</strong>, <strong>libXft-devel</strong>, <strong>libXpm-devel</strong>, and <strong>libXext-devel</strong>:
 <pre class="bash">
@@ -263,7 +282,7 @@ For a dpkg/apt based system (Debian, Ubuntu, etc) this will likely to be <strong
 &#36; apt-get install libX11-dev libxft-dev libxpm-dev libxext-dev
 </pre>
 <p></p>
-Also make sure that you have installed all required packages listed under <a class="foswikiCurrentTopicLink" href="#ReqSw">Requested Software</a> (e.g. fftw, gsl, etc).
+Also make sure that you have installed all required packages listed under <a class="foswikiCurrentTopicLink" href="#ReqSw">Required Software</a> (e.g. fftw, gsl, etc).
 <p></p>
 For the following it is assumed that <code>ROOT</code> shall be installed under <code>$HOME/Apps</code>. If you want to install it somewhere else, just systematically replace the related terms of the following description. For the following list of commands the '$' will be given, the command prompt. Do <strong>not</strong> enter it! Also some comments will be added starting with a '#' which can be omitted. They are only there to explain what is going on.
 <pre class="bash">
@@ -274,24 +293,28 @@ For the following it is assumed that <code>ROOT</code> shall be installed under
 &#36; git clone http://root.cern.ch/git/root.git
 &#36; cd root
 &#36; git tag -l
-&#36; # git tag -l will list all available tags. In the next command choose the tag v5-34-xx
-&#36; # where xx is the highest listed number, e.g. v5-34-32
-&#36; git checkout -b v5-34-32 v5-34-32
+&#36; # git tag -l will list all available tags. In the next command choose the tag v6-08-04 or the latest official release number
+&#36; git checkout -b v6-08-04 v6-08-04
 &#36; # now ROOT is ready to be configured. Below you will find the minimal ROOT configuration needed.
-&#36; ./configure --gminimal --enable-asimage --enable-mathmore --enable-minuit2 --enable-xml
+&#36; # since we are using cmake build now, first we will need to create the build directory.
+&#36; mkdir root&#95;build
+&#36; cd root&#95;build
+&#36; cmake ../ -Dgminimal&#61;ON -Dasimage&#61;ON -Dmathmore&#61;On -Dminuit2&#61;ON -Dxml&#61;ON -DCMAKE&#95;INSTALL&#95;PREFIX&#61;../root&#95;exec
 &#36; # next will be the make. If running on a multicore CPU you can speed up tremendously by calling
 &#36; # make with the option -j &#60;number&#62;, where &#60;number&#62; is the number of threads which you want to give,
 &#36; # e.g. make -j8
 &#36; make
+&#36; # as a last step of the ROOT build process we need to install it
+&#36; make install
 </pre>
 <p></p>
 What is still missing is that the system should be told where to find the <code>ROOT</code> installation, therefore the following is suggested: <ul>
 <li> As superuser create a file <strong>/etc/ld.so.conf.d/cern-root.conf</strong> where the path to the <code>lib</code> directory of <code>ROOT</code> is added and call <strong>/sbin/ldconfig</strong> afterwards. In the example mentioned above one way of doing this is (<strong>&lt;home&gt;</strong> has to be the path to your home, e.g. /home/luke_skywalker): <pre class="bash">
-&#36; echo &#34;&#60;home&#62;/Apps/root/lib&#34; &#62;&#62; /etc/ld.so.conf.d/cern-root.conf
+&#36; echo &#34;&#60;home&#62;/Apps/root/root&#95;exec/lib&#34; &#62;&#62; /etc/ld.so.conf.d/cern-root.conf
 &#36; /sbin/ldconfig
 </pre>
 </li> <li> <span class='foswikiRedFG'>Additionally</span>, as normal user one should append the following lines to the <strong>~/.bashrc</strong> and/or <strong>~/.bash_profile</strong> (<strong>~./profile</strong> on Debian like systems, and then either restart the shell or call the same commands once more from the shell) in order to change some path-setting environment variables: <pre class="bash">
-&#36; export ROOTSYS&#61;&#36;HOME/Apps/root
+&#36; export ROOTSYS&#61;&#36;HOME/Apps/root/root&#95;exec
 &#36; export PATH&#61;&#36;ROOTSYS/bin:&#36;PATH
 </pre>
 </li></ul> 
@@ -299,6 +322,7 @@ What is still missing is that the system should be told where to find the <code>
 If an update of <code>ROOT</code> is needed, simple do the following:<pre class="bash">
 &#36; cd &#36;HOME/Apps/root
 &#36; git pull
+&#36; cd root&#95;build
 &#36; make
 </pre>
 <p></p>
@@ -308,17 +332,23 @@ When all required software has been set up it can be proceeded with the <code>mu
 <pre class="bash">
 &#36; cd &#36;HOME/Apps
 &#36; git clone https://bitbucket.org/muonspin/musrfit.git
+&#36; # Only if legacy ROOT 5.xx.yy is used include the next line
+&#36; cd musrfit; git checkout root5
 </pre>
 or
 <pre class="bash">
 &#36; cd &#36;HOME/Apps
 &#36; git clone git://gitlab.psi.ch/nemu/musrfit.git
+&#36; # Only if legacy ROOT 5.xx.yy is used include the next line
+&#36; cd musrfit; git checkout root5
 </pre>
 <p></p>
-<strong>Note:</strong> musrfit has moved from svn to git. In case you still have an <em>old</em> svn version of musrfit, it is advised to remove it first. For svn users: for a smooth transition from svn to git, please check the following link: 
+<strong>Note 1:</strong> <code>musrfit</code> has moved from svn to git. In case you still have an <em>old</em> svn version of musrfit, it is advised to remove it first. For svn users: for a smooth transition from svn to git, please check the following link: 
 <a href="http://www.git-tower.com/blog/git-for-subversion-users-cheat-sheet/">Git for Subversion Users - A Cheat Sheet</a>.
 <p></p>
-If a local repository clone is already present, one can update it using:
+<strong>Note 2:</strong> after cloning the <code>musrfit</code> repo you will automatically be on the root6 branch. If you want to get legacy ROOT 5.34.xx support, you will needed to switch branches first.
+<p></p>
+If a local repository clone is already present (it needs to be newer than Dec. 2016), one can update it using:
 <pre class="bash">
 &#36; cd &#36;HOME/Apps/musrfit
 &#36; git pull
@@ -341,6 +371,7 @@ After the source-code extraction the <strong>autogen.sh</strong> script is calle
 </dd> <dt> --with-nexus </dt><dd> Set the prefix of the <code>NeXus</code> installation, e.g. /usr/local (<em>only useful in conjunction with the <code>NeXus</code> support</em>)
 </dd> <dt> --with-qt3 </dt><dd> Set the prefix of the <code>Qt3</code> installation, e.g. /usr/lib/qt-3.3 (<em>only useful in conjunction with building <code>musrgui</code></em>)
 </dd> <dt> --with-qt4 </dt><dd> Set the prefix of the <code>Qt4</code> installation, e.g. /usr/lib/qt47 (<em>only useful in conjunction with building <code>musredit</code></em>)
+</dd> <dt> --with-qt5 </dt><dd> Set the prefix of the <code>Qt5</code> installation, e.g. /usr/lib64 (<em>only useful in conjunction with building <code>musredit</code></em>)
 </dd> <dt> --enable-NeXus </dt><dd> Enable the support of <code>NeXus</code> data files (<em>requires the <code>HDF4</code>, <code>HDF5</code> and <code>NeXus</code> libraries to be installed</em>).
 </dd> <dt> --disable-editor </dt><dd> Disable the integrated building of <code>musredit</code>/<code>musrgui</code>.
 </dd> <dt> --disable-omp </dt><dd> Switches off the <a href="http://en.wikipedia.org/wiki/OpenMP">OpenMP</a> features of <code>musrfit</code> (parallelization of the &chi;<sup>2</sup> calculation when compiled with GCC &ge; 4.2)
@@ -404,7 +435,10 @@ Notes
 <h1 id="A_4_MS_Windows"> 4  MS Windows </h1>
 <span class='foswikiRedFG'> The description here is only for the very brave ones. It hasn't been tested for quite a while and therefore gives you rather a flavour of what needs to be done rather than a real instruction how to setup <code>musrfit</code>. If you just need <code>musrfit</code> to work on a MS Windows platform, it is recommended to install it via a linux virtual machine!</span>
 <p></p>
-Under Windows a native installation is not supported but there is the possibility to run <code>musrfit</code> through <a href="http://www.cygwin.com/">Cygwin</a> which has the great advantage that one gains additionally various nice <code>UNIX</code> tools also for other purposes <img class='smily' src='../pub/Main/SmiliesPluginPSI_/wink.gif' alt='wink' title='wink' /> <br>
+<span class='foswikiBlueFG'> For adventurous guys using Windows 10, there is the possibility to activate the built in Ubuntu bash-shell. It allows to install <code>musrfit</code> as described in the Linux section. 
+</span>
+<p></p>
+Under Windows a native installation is not supported but there is the possibility to run <code>musrfit</code> through <a href="http://www.cygwin.com/">Cygwin</a> which has the great advantage that one gains additionally various nice <code>UNIX</code> tools also for other purposes <img class='smily' src='../pub/Main/SmiliesPluginPSI/wink.gif' alt='wink' title='wink' /> <br>
 <span class='foswikiRedFG'>Please also be aware of the fact that the X server which is going to be installed with Cygwin has to be started (e.g. by selecting it from the "Programs" folder) before any graphical application (<code>musrview</code>, <code>musrgui</code>, etc.) is run</span>.
 <p></p>
 <span class='foswikiPinkFG'>One more advice: Please never try to install either <code>ROOT</code> or <code>musrfit</code> from or to a directory containing spaces in the absolute path or in case you do, do not wonder if some errors occur!<br>
@@ -528,6 +562,7 @@ After the source-code extraction the <strong>autogen.sh</strong> script is calle
 </dd> <dt> --with-nexus </dt><dd> Set the prefix of the <code>NeXus</code> installation, e.g. /usr/local (<em>only useful in conjunction with the <code>NeXus</code> support</em>)
 </dd> <dt> --with-qt3 </dt><dd> Set the prefix of the <code>Qt3</code> installation, e.g. /usr/lib/qt-3.3 (<em>only useful in conjunction with building <code>musrgui</code></em>)
 </dd> <dt> --with-qt4 </dt><dd> Set the prefix of the <code>Qt4</code> installation, e.g. /usr/lib/qt47 (<em>only useful in conjunction with building <code>musredit</code></em>)
+</dd> <dt> --with-qt5 </dt><dd> Set the prefix of the <code>Qt5</code> installation, e.g. /usr/lib/qt56 (<em>only useful in conjunction with building <code>musredit</code></em>)
 </dd> <dt> --enable-NeXus </dt><dd> Enable the support of <code>NeXus</code> data files (<em>requires the <code>HDF4</code>, <code>HDF5</code> and <code>NeXus</code> libraries to be installed</em>).
 </dd> <dt> --disable-editor </dt><dd> Disable the integrated building of <code>musredit</code>/<code>musrgui</code>.
 </dd> <dt> --disable-omp </dt><dd> Switches off the <a href="http://en.wikipedia.org/wiki/OpenMP">OpenMP</a> features of <code>musrfit</code> (parallelization of the &chi;<sup>2</sup> calculation when compiled with GCC &ge; 4.2)
@@ -636,23 +671,23 @@ With <code><b>qt4-mac</b></code>, <code>musredit</code> will be installed. If it
 <p></p>
 <span class='foswikiRedFG'>Only if</span> <code>musrfit</code> should support reading data files in the <code>NeXus</code> format the further <a class="foswikiCurrentTopicLink" href="#ReqSwNeXus">required</a> packages are set up:
 <pre class="bash">
-&#36; sudo port -v install jpeg6b hdf4 hdf5
+&#36; sudo port -v install hdf4 hdf5
 </pre>
 Unfortunately, the <code>minixml</code> and <code>NeXus</code> libraries have to be compiled and installed directly from the source code. Given the respective version numbers of <strong>2.9</strong> and <strong>4.4.2</strong> (which are subject to change with time, <strong>Only <code><b>NeXus</b></code> Version &gt;= 4.4 is support!</strong>) this can be achieved for example by:
 <pre class="bash">
-&#36; cd
-&#36; curl www.msweet.org/files/project3/mxml-2.9.tar.gz -G &#124; tar xz
-&#36; cd mxml-2.9
+&#36; # get and instal Mini-XML
+&#36; cd &#36;HOME/Applications
+&#36; git clone https://github.com/michaelrsweet/mxml.git
+&#36; cd mxml
 &#36; ./configure --prefix&#61;/usr/local
 &#36; make
 &#36; sudo make install
-&#36; cd &#36;HOME/Downloads
-&#36; # create a directory for the NeXus source code
-&#36; mkdir nexus
-&#36; cd nexus
+&#36; # get and install NeXus
+&#36; cd &#36;HOME/Applications
 &#36; # get the source code from the master repository
-&#36; git clone https://github.com/nexusformat/code.git
+&#36; git clone https://github.com/nexusformat/code.git nexus/code
 &#36; # next we will build NeXus out-of-source
+&#36; cd nexus
 &#36; mkdir build
 &#36; cd build
 &#36; cmake -DENABLE&#95;HDF5&#61;1 -DENABLE&#95;HDF4&#61;1 -DENABLE&#95;MXML&#61;1 ../code
@@ -660,29 +695,33 @@ Unfortunately, the <code>minixml</code> and <code>NeXus</code> libraries have to
 &#36; sudo make install
 </pre>
 <h3 id="A_5.1.3_61_61ROOT_61_61"> 5.1.3  <code><b>ROOT</b></code> </h3>
+ROOT 5.34/xx is supported as legacy version only! <strong>The default now will be ROOT 6.xx/yy!</strong>
+<p></p>
 The best way to get <code>ROOT</code> exactly the way needed for <code>musrfit</code> is to install it from source. Before describing it, please make sure that you have installed all required packages listed under <a class="foswikiCurrentTopicLink" href="#ReqSw">Requested Software</a> (e.g. fftw, gsl, etc).
 <p></p>
-For the following it is assumed that <code>ROOT</code> shall be installed under <code>$HOME/Apps</code>. If you want to install it somewhere else, just systematically replace the related terms of the following description. For the following list of commands the '$' will be given, the command prompt. Do <strong>not</strong> enter it! Also some comments will be added starting with a '#' which can be omitted. They are only there to explain what is going on.
+For the following it is assumed that <code>ROOT</code> shall be installed under <code>$HOME/Applications</code>. If you want to install it somewhere else, just systematically replace the related terms of the following description. For the following list of commands the '$' will be given, the command prompt. Do <strong>not</strong> enter it! Also some comments will be added starting with a '#' which can be omitted. They are only there to explain what is going on.
 <pre class="bash">
-&#36; cd &#36;HOME
-&#36; # creat the Apps directory if not already present
-&#36; mkdir Apps
-&#36; cd Apps
+&#36; cd &#36;HOME/Applications
 &#36; git clone http://root.cern.ch/git/root.git
 &#36; cd root
 &#36; git tag -l
-&#36; # git tag -l will list all available tags. In the next command choose the tag v5-34-xx
-&#36; # where xx is the highest listed number, e.g. v5-34-32
-&#36; git checkout -b v5-34-32 v5-34-32
+&#36; # git tag -l will list all available tags. In the next command choose the tag v6-08-xx
+&#36; # where xx is the highest listed number, e.g. v6-08-06
+&#36; git checkout -b v6-08-06 v6-08-06
 &#36; # now ROOT is ready to be configured. Below you will find the minimal ROOT configuration needed.
-&#36; ./configure --gminimal --enable-asimage --enable-mathmore --enable-minuit2 --enable-xml
+&#36; # We will use the cmake out-of-source approach here.
+&#36; mkdir root&#95;build
+&#36; cd root&#95;build
+&#36; cmake ../ -Dgminimal&#61;ON -Dasimage&#61;ON -Dmathmore&#61;ON -Dminuit2&#61;ON -Dxml&#61;ON -DCMAKE&#95;INSTALL&#95;PREFIX&#61;&#36;HOME/Applications/root/root&#95;exec
 &#36; # next will be the make. If running on a multicore CPU you can speed up tremendously by calling
 &#36; # make with the option -j &#60;number&#62;, where &#60;number&#62; is the number of threads which you want to give,
 &#36; # e.g. make -j8
 &#36; make
+&#36; # make will take quite a while
+&#36; make install
 </pre>
 <p></p>
-For further details see <a href="http://root.cern.ch/drupal/content/installing-root-source">Installing ROOT from Source</a>.
+For further details see <a href="https://root.cern.ch/building-root">Installing ROOT from Source</a>.
 <p></p>
 Since Apple in its wisdom decided that programs started from a shell are treated differently than apps if it is coming to system variables, we need to work harder compared to a Linux system.
 <p></p>
@@ -695,11 +734,11 @@ In order to finalize the <code>ROOT</code> installation and to prepare already t
 &#60;plist version&#61;&#34;1.0&#34;&#62;
 &#60;dict&#62;
         &#60;key&#62;MUSRFITPATH&#60;/key&#62;
-        &#60;string&#62;&#36;HOME/Apps/root/bin&#60;/string&#62;         (where to find the musrfit executables)
+        &#60;string&#62;&#36;HOME/Applications/root/root&#95;exec/bin&#60;/string&#62; (where to find the musrfit executables)
         &#60;key&#62;QTDIR&#60;/key&#62;
-        &#60;string&#62;/opt/local/lib/qt3mac&#60;/string&#62;       (where to find Qt3 (for musrgui) or Qt4 (for musredit))
+        &#60;string&#62;/opt/local/lib/qt3mac&#60;/string&#62;                 (where to find Qt3 (for musrgui) or Qt4 (for musredit))
         &#60;key&#62;ROOTSYS&#60;/key&#62;
-        &#60;string&#62;&#36;HOME/Apps/root&#60;/string&#62;             (where to find the ROOT system)
+        &#60;string&#62;&#36;HOME/Applications/root/root&#95;exec&#60;/string&#62;     (where to find the ROOT system)
 &#60;/dict&#62;
 &#60;/plist&#62;
 </pre>
@@ -708,7 +747,7 @@ In order to finalize the <code>ROOT</code> installation and to prepare already t
 <p></p>
 One needs to add some system variables in <strong>~/.profile</strong>:
 <pre class="bash">
-export ROOTSYS&#61;&#36;HOME/Apps/root
+export ROOTSYS&#61;&#36;HOME/Applications/root/root&#95;exec
 launchctl setenv ROOTSYS &#36;ROOTSYS
 export MUSRFITPATH&#61;&#36;ROOTSYS/bin
 launchctl setenv MUSRFITPATH &#36;MUSRFITPATH
@@ -761,16 +800,21 @@ where <strong>x_yy_z</strong> has to be substituted by the correct version numbe
 <p></p>
 Unfortunately, the <code>minixml</code> and <code>NeXus</code> libraries have to be compiled and installed directly from the source code. Given the respective version numbers of <strong>2.9</strong> and <strong>4.3.2</strong> (which are subject to change with time) this can be achieved for example by:
 <pre class="bash">
-&#36; cd
-&#36; curl www.msweet.org/files/project3/mxml-2.9.tar.gz -G &#124; tar xz
-&#36; cd mxml-2.9
+&#36; # first build Mini-XML
+&#36; cd &#36;HOME/Applications
+&#36; git clone https://github.com/michaelrsweet/mxml.git
+&#36; cd mxml
 &#36; ./configure --prefix&#61;/usr/local
 &#36; make
 &#36; sudo make install
+&#36; # second build NeXus
 &#36; cd ..
-&#36; curl http://download.nexusformat.org/kits/nexus-4.3.2-20140413svn1919.tar.gz -G &#124; tar xz
-&#36; cd nexus-4.3.2-20140413svn1919
-&#36; ./configure --prefix&#61;/usr/local
+&#36; git clone https://github.com/nexusformat/code.git nexus/code
+&#36; cd nexus
+&#36; # build NeXus out-of-source
+&#36; mkdir build
+&#36; cd build
+&#36; cmake ../code -DENABLE&#95;HDF4&#61;1 -DENABLE&#95;HDF5&#61;1 -DENABLE&#95;MXML&#61;1
 &#36; make
 &#36; sudo make install
 </pre>
@@ -778,24 +822,25 @@ Unfortunately, the <code>minixml</code> and <code>NeXus</code> libraries have to
 <h3 id="A_5.2.3_61_61ROOT_61_61"> 5.2.3  <code><b>ROOT</b></code> </h3>
 The best way to get <code>ROOT</code> exactly the way needed for <code>musrfit</code> is to install it from source. Before describing it, please make sure that you have installed all required packages listed under <a class="foswikiCurrentTopicLink" href="#ReqSw">Requested Software</a> (e.g. fftw, gsl, etc).
 <p></p>
-For the following it is assumed that <code>ROOT</code> shall be installed under <code>$HOME/Apps</code>. If you want to install it somewhere else, just systematically replace the related terms of the following description. For the following list of commands the '$' will be given, the command prompt. Do <strong>not</strong> enter it! Also some comments will be added starting with a '#' which can be omitted. They are only there to explain what is going on.
+For the following it is assumed that <code>ROOT</code> shall be installed under <code>$HOME/Applications</code>. If you want to install it somewhere else, just systematically replace the related terms of the following description. For the following list of commands the '$' will be given, the command prompt. Do <strong>not</strong> enter it! Also some comments will be added starting with a '#' which can be omitted. They are only there to explain what is going on.
 <pre class="bash">
-&#36; cd &#36;HOME
-&#36; # creat the Apps directory if not already present
-&#36; mkdir Apps
-&#36; cd Apps
+&#36; cd &#36;HOME/Applications
 &#36; git clone http://root.cern.ch/git/root.git
 &#36; cd root
 &#36; git tag -l
-&#36; # git tag -l will list all available tags. In the next command choose the tag v5-34-xx
-&#36; # where xx is the highest listed number, e.g. v5-34-32
-&#36; git checkout -b v5-34-32 v5-34-32
+&#36; # git tag -l will list all available tags. In the next command choose the tag v6-08-06
+&#36; # where xx is the highest listed number, e.g. v6-08-06
+&#36; git checkout -b v6-08-06 v6-08-06
 &#36; # now ROOT is ready to be configured. Below you will find the minimal ROOT configuration needed.
-&#36; ./configure --gminimal --enable-asimage --enable-mathmore --enable-minuit2 --enable-xml
+&#36; # the out-of-source approach will be followed
+&#36; mkdir root&#95;build
+&#36; cd root&#95;build
+&#36; cmake ../ -Dgminimal&#61;ON -Dasimage&#61;ON -Dmathmore&#61;ON -Dminuit2&#61;ON -Dxml&#61;ON -DCMAKE&#95;INSTALL&#95;PREFIX&#61;&#36;HOME/Applications/root/root&#95;exec
 &#36; # next will be the make. If running on a multicore CPU you can speed up tremendously by calling
 &#36; # make with the option -j &#60;number&#62;, where &#60;number&#62; is the number of threads which you want to give,
 &#36; # e.g. make -j8
 &#36; make
+&#36; make install
 </pre>
 <p></p>
 For further details see <a href="http://root.cern.ch/drupal/content/installing-root-source">Installing ROOT from Source</a>.
@@ -811,11 +856,11 @@ In order to finalize the <code>ROOT</code> installation and to prepare already t
 &#60;plist version&#61;&#34;1.0&#34;&#62;
 &#60;dict&#62;
         &#60;key&#62;MUSRFITPATH&#60;/key&#62;
-        &#60;string&#62;&#36;HOME/Apps/root/bin&#60;/string&#62;         (where to find the musrfit executables)
+        &#60;string&#62;&#36;HOME/Applications/root/root&#95;exec/bin&#60;/string&#62; (where to find the musrfit executables)
         &#60;key&#62;QTDIR&#60;/key&#62;
-        &#60;string&#62;/opt/local/lib/qt3mac&#60;/string&#62;       (where to find Qt3 (for musrgui) or Qt4 (for musredit))
+        &#60;string&#62;/opt/local/lib/qt3mac&#60;/string&#62;                 (where to find Qt3 (for musrgui) or Qt4 (for musredit))
         &#60;key&#62;ROOTSYS&#60;/key&#62;
-        &#60;string&#62;&#36;HOME/Apps/root&#60;/string&#62;             (where to find the ROOT system)
+        &#60;string&#62;&#36;HOME/Applications/root/root&#95;exec&#60;/string&#62;     (where to find the ROOT system)
 &#60;/dict&#62;
 &#60;/plist&#62;
 </pre>
@@ -824,23 +869,27 @@ In order to finalize the <code>ROOT</code> installation and to prepare already t
 <p></p>
 One needs to add some system variables in <strong>~/.profile</strong>:
 <pre class="bash">
-export ROOTSYS&#61;&#36;HOME/Apps/root
+export ROOTSYS&#61;&#36;HOME/Applications/root/root&#95;exec
 launchctl setenv ROOTSYS &#36;ROOTSYS
 export MUSRFITPATH&#61;&#36;ROOTSYS/bin
 launchctl setenv MUSRFITPATH &#36;MUSRFITPATH
 export PATH&#61;&#36;ROOTSYS/bin:&#36;QTDIR/bin:&#36;PATH
 </pre>
 <h2 id="A_5.3_61_61musrfit_61_61"> 5.3  <code><b>musrfit</b></code> </h2>
-First, the most recent source code should be downloaded.  First, the most recent source code should be downloaded. The preferred way of doing so is to clone the musrfit repository via git. Assuming the code should be located in ~/Apps/musrfit this is achieved most easily calling from the terminal
+First, the most recent source code should be downloaded.  First, the most recent source code should be downloaded. The preferred way of doing so is to clone the musrfit repository via git. Assuming the code should be located in ~/Applications/musrfit this is achieved most easily calling from the terminal
 <p></p>
 <pre class="bash">
-&#36; cd ~/Apps
+&#36; cd ~/Applications
 &#36; git clone https://bitbucket.org/muonspin/musrfit.git 
+&#36; # Only if legacy ROOT 5.xx.yy is used include the next line 
+&#36; cd musrfit; git checkout root5 
 </pre>
 or
 <pre class="bash">
-&#36; cd ~/Apps
+&#36; cd ~/Applications
 &#36; git clone git://gitlab.psi.ch/nemu/musrfit.git  
+&#36; # Only if legacy ROOT 5.xx.yy is used include the next line 
+&#36; cd musrfit; git checkout root5 
 </pre>
 <p></p>
 <p></p>
@@ -849,7 +898,7 @@ or
 <p></p>
 If a local repository clone is already present, one can update it using:
 <pre class="bash">
-&#36; cd ~/Apps/musrfit
+&#36; cd ~/Applications/musrfit
 &#36; git pull
 </pre>
 <p></p>
@@ -867,6 +916,7 @@ After the source-code extraction the <strong>autogen.sh</strong> script is calle
 </dd> <dt> --with-nexus </dt><dd> Set the prefix of the <code>NeXus</code> installation, e.g. /usr/local (<em>only useful in conjunction with the <code>NeXus</code> support</em>)
 </dd> <dt> --with-qt3 </dt><dd> Set the prefix of the <code>Qt3</code> installation, e.g. /opt/local/lib/qt-3.3 (<em>only useful in conjunction with building <code>musrgui</code></em>)
 </dd> <dt> --with-qt4 </dt><dd> Set the prefix of the <code>Qt4</code> installation, e.g. /opt/local/lib/qt-4.7 (<em>only useful in conjunction with building <code>musredit</code></em>)
+</dd> <dt> --with-qt5 </dt><dd> Set the prefix of the <code>Qt5</code> installation, e.g. /opt/local/libexec/qt5 (<em>only useful in conjunction with building <code>musredit</code></em>)
 </dd> <dt> --enable-NeXus </dt><dd> Enable the support of <code>NeXus</code> data files (<em>requires the <code>HDF4</code>, <code>HDF5</code> and <code>NeXus</code> libraries to be installed</em>).
 </dd> <dt> --disable-editor </dt><dd> Disable the integrated building of <code>musredit</code>/<code>musrgui</code>.
 </dd> <dt> --disable-omp </dt><dd> Switches off the <a href="http://en.wikipedia.org/wiki/OpenMP">OpenMP</a> features of <code>musrfit</code> (parallelization of the &chi;<sup>2</sup> calculation when compiled with GCC &ge; 4.2)
@@ -931,7 +981,7 @@ Notes
 In order to perform a quick test for finding out if the installation has been completed successfully, a few msr files together with the corresponding data files can be found in the <code>musrfit</code> source tree at <strong>doc/examples/</strong>.<br>
 If <code>musrgui</code> has been installed, just open one of the <strong>test-&#42;.msr</strong> files in the editor and test the <code>musrfit</code> functionalities. Otherwise, if only the terminal should be used, as an initial test for instance the following could be done:
 <pre class="bash">
-&#36; cd ~/Apps/musrfit/doc/examples
+&#36; cd ~/Applications/musrfit/doc/examples
 &#36; musrview test-histo-ROOT-NPP.msr
 </pre>
 <p></p>
@@ -940,7 +990,7 @@ If <code>musrgui</code> has been installed, just open one of the <strong>test-&#
 <p></p>
 </div>
 <div class="patternInfo">This topic: MUSR<span class='foswikiSeparator'>&nbsp;&gt;&nbsp;</span><a class="foswikiCurrentWebHomeLink" href="WebHome.html">WebHome</a> &gt; <a href="MusrFit.html">MusrFit</a><span class='foswikiSeparator'>&nbsp;&gt;&nbsp;</span>MusrFitSetup <br />
-Topic revision:  <span class='patternRevInfo'>25 Aug 2016, <a href="https://intranet.psi.ch/Main/AndreasSuter">AndreasSuter</a></span></div>
+Topic revision:  <span class='patternRevInfo'>27 Mar 2017, <a href="https://intranet.psi.ch/Main/AndreasSuter">AndreasSuter</a></span></div>
 </div>
 </div>
 </div>
@@ -958,6 +1008,5 @@ Topic revision:  <span class='patternRevInfo'>25 Aug 2016, <a href="https://intr
 
 </body>
 
-<!-- Mirrored from intranet.psi.ch/MUSR/MusrFitSetup?cover=print by HTTrack Website Copier/3.x [XR&CO'2010], Fri, 16 Dec 2016 16:01:02 GMT -->
-<!-- Added by HTTrack --><meta http-equiv="content-type" content="text/html;charset=utf-8"><!-- /Added by HTTrack -->
+<!-- Mirrored from intranet.psi.ch/MUSR/MusrFitSetup?cover=print by HTTrack Website Copier/3.x [XR&CO'2014], Sun, 14 May 2017 18:08:39 GMT -->
 </html>

doc/html/user/MUSR/MusrGui.html

@@ -1,7 +1,7 @@
 <!DOCTYPE html><html lang="en">
 
-<!-- Mirrored from intranet.psi.ch/MUSR/MusrGui?cover=print by HTTrack Website Copier/3.x [XR&CO'2010], Fri, 16 Dec 2016 16:00:59 GMT -->
-<!-- Added by HTTrack --><meta http-equiv="content-type" content="text/html;charset=utf-8"><!-- /Added by HTTrack -->
+<!-- Mirrored from intranet.psi.ch/MUSR/MusrGui?cover=print by HTTrack Website Copier/3.x [XR&CO'2014], Sun, 14 May 2017 18:08:33 GMT -->
+<!-- Added by HTTrack --><meta http-equiv="content-type" content="text/html;charset=utf-8" /><!-- /Added by HTTrack -->
 <head>
 <link rel="stylesheet" href="../pub/System/HeadlinesPlugin/style.css" type="text/css" media="all" />
 <title> MUSR :: MusrGui</title>
@@ -14,14 +14,11 @@
 <meta name="apple-mobile-web-app-status-bar-style" content="black-translucent" />
 <link rel="icon" href="../pub/Main/WebPreferences/favicon.ico" type="image/x-icon" />
 <link rel="shortcut icon" href="../pub/Main/WebPreferences/favicon.ico" type="image/x-icon" />
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+<link rel="alternate" href="https://intranet.psi.ch/wiki/bin/edit/MUSR/MusrGui?t=1494785296" type="application/x-wiki" title="edit MusrGui" />
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-<h1 id="A_61_61musredit_47_40musrgui_41_61_61">  <code><b>musredit / (musrgui)</b></code> </h1>
+<h1 id="A_61_61musredit_47_40musrgui_41_61_61">  <code><b>musredit / (musrgui)</b></code>  </h1>
 <p></p>
 <div class="foswikiToc" id="foswikiTOC"> <ul>
 <li> <a href="MusrGui.html#A_61_61musredit_47_40musrgui_41_61_61"> musredit / (musrgui) </a>
@@ -168,14 +167,23 @@ body .foswikiTable#tableMusrGui1 tr.foswikiTableRowdataBg0 td.foswikiSortedCol {
 </li> <li> <a href="MusrGui.html#A_2.2_musredit_startup.xml_47_musrgui_startup.xml"> 2.2  musredit_startup.xml / musrgui_startup.xml </a>
 </li></ul> 
 </li> <li> <a href="MusrGui.html#A_3_61_61musrfit_61_61_Features"> 3  musrfit Features </a>
-</li> <li> <a href="MusrGui.html#A_4_Editor_Features"> 4  Editor Features </a>
-</li> <li> <a href="MusrGui.html#A_5_Bugtracking"> 5  Bugtracking </a>
+</li> <li> <a href="MusrGui.html#A_4_musrWiz"> 4  musrWiz </a> <ul>
+<li> <a href="MusrGui.html#A_4.1_musrWiz_45_Introduction"> 4.1  musrWiz - Introduction </a>
+</li> <li> <a href="MusrGui.html#A_4.2_musrWiz_45_Theory"> 4.2  musrWiz - Theory </a>
+</li> <li> <a href="MusrGui.html#A_4.3_musrWiz_45_Functions"> 4.3  musrWiz - Functions </a>
+</li> <li> <a href="MusrGui.html#A_4.4_musrWiz_45_Maps"> 4.4  musrWiz - Maps </a>
+</li> <li> <a href="MusrGui.html#A_4.5_musrWiz_45_Fit_Parameters"> 4.5  musrWiz - Fit Parameters </a>
+</li> <li> <a href="MusrGui.html#A_4.6_musrWiz_45_Fit_Info"> 4.6  musrWiz - Fit Info </a>
+</li> <li> <a href="MusrGui.html#A_4.7_musrWiz_45_Create"> 4.7  musrWiz - Create </a>
+</li></ul> 
+</li> <li> <a href="MusrGui.html#A_5_musrStep"> 5  musrStep </a>
+</li> <li> <a href="MusrGui.html#A_6_Bugtracking"> 6  Bugtracking </a>
 </li></ul> 
 </div>
 <p></p>
 <h1 id="A_1_Introduction"> 1  Introduction </h1>
-<code>musredit</code> and <code>musrgui</code> are editors which also provide a graphical user interface to the programs contained in the <code><a href="MusrFit.html">musrfit</a></code> suite and are intended to help the user handle <code>musrfit</code> msr files. They are implemented in <code>C++</code> and use the <a href="http://qt.nokia.com/">Qt</a> framework. Principally, <code>musrgui</code> and <code>musredit</code> are doing the same, but are based on different Qt versions. <code>musrgui</code> is based on Qt 3.x and will only be maintained on bug-fixing level since the Qt 3.x licensing is less straight forward than the Qt 4.x one. <code>musredit</code> is based on Qt 4.6 (or above) and this is the program which will be developed further.<br>
-On this documentation page only the features related to <code>musrfit</code> are described&mdash;the basic editor functions which should be self-explanatory are not.
+<code>musredit</code> and <code>musrgui</code> are editors which also provide a graphical user interface to the programs contained in the <code><a href="MusrFit.html">musrfit</a></code> suite and are intended to help the user handle <code>musrfit</code> msr files. They are implemented in <code>C++</code> and use the <a href="http://qt.nokia.com/">Qt</a> framework. Principally, <code>musrgui</code> and <code>musredit</code> are doing the same, but are based on different Qt versions. <code>musrgui</code> is based on Qt 3.x and will only be maintained on bug-fixing level since the Qt 3.x licensing is less straight forward than the Qt 4.x one. <code>musredit</code> is based on Qt 4.6 or Qt 5.6 (or above). The Qt 5.6 version of <code>musredit</code> will be actively developed, whereas the Qt 4.x version will only get bug fixing and eventually will be droped.<br>
+On this documentation page only the features related to <code>musrfit</code> are described&mdash;the basic editor functions which should be self-explanatory are not.<br>
 <strong><span class='foswikiRedFG'>Before going on using <code>musrgui</code> / <code>musredit</code> it is strongly recommended to read the <a href="MusrFit.html">manual</a> of <code>musrfit</code> first!</span></strong>
 <p></p>
 <h1 id="A_2_Available_Executables_44_Configuration_Files_and_their_Basic_Usage"> 2  Available Executables, Configuration Files and their Basic Usage </h1>
@@ -196,9 +204,16 @@ If called without any parameters an empty editor window opens.
 In this file the following XML tags are allowed to define settings and might proof useful for all users of <code>musredit</code> / <code>musrgui</code>: <dl>
 <dt> &lt;general&gt;&lt;/general&gt; </dt><dd> set the default paths to executables and files in this environment <dl>
 <dt> &lt;exec_path&gt;PATH_TO_EXEC&lt;/exec_path&gt; </dt><dd> set the path <strong>PATH_TO_EXEC</strong> where the executables <code>musrfit</code>, <code>musrview</code>, <code>musrt0</code>, etc. can be found (inside the &lt;general&gt; environment)
-</dd> <dt> &lt;default_save_path&gt;SAV_PATH&lt;/default_save_path&gt; </dt><dd> specify the path <strong>SAV_PATH</strong> where <code>musrgui</code> / <code>musredit</code> point by default when opening and saving msr files (inside the &lt;general&gt; environment)
+</dd> <dt> &lt;default_save_path&gt;SAV_PATH&lt;/default_save_path&gt; </dt><dd> specify the path <strong>SAV_PATH</strong> where <code>musrgui</code> / <code>musredit</code> point by default when opening and saving msr files (inside the &lt;general&gt; environment). Default is the current directory.
 </dd> <dt> &lt;msr_default_file_path&gt;MSR_DEF_PATH&lt;/msr_default_file_path&gt; </dt><dd> set the path <strong>MSR_DEF_PATH</strong> where the <a class="foswikiCurrentTopicLink" href="#MusrfitFeatures">default msr files provided by</a> <code>musrgui</code> are stored (inside the &lt;general&gt; environment)
+</dd> <dt> &lt;timeout&gt;3600&lt;/timeout&gt; </dt><dd> timeout in seconds after which musrview canvas will automatically quit. A value of 0 or a negative number will keep the musrview canvas open without self-determination.
+</dd> <dt> &lt;keep_minuit2_output&gt;y/n&lt;/keep_minuit2_output&gt; </dt><dd> flag indicating if the <code>MINUIT2</code> output shall be kept per msr-file ('y') or only for the current msr-file ('n').
+</dd> <dt> &lt;dump_ascii&gt;y/n&lt;/dump_ascii&gt; </dt><dd> flag indicating if musrfit shall dump fit data into ascii format. See help of musrfit. 
+</dd> <dt> &lt;dump_root&gt;y/n&lt;/dump_root&gt; </dt><dd> flag indicating if musrfit shall dump fit data into root format. See help of musrfit. 
 </dd> <dt> &lt;title_from_data_file&gt;y/n&lt;/title_from_data_file&gt; </dt><dd> specify if <code>musrfit</code> should be called with the <a href="MusrFit.html#MusrFit">-t option</a> by default (inside the &lt;general&gt; environment)
+</dd> <dt> &lt;chisq_pre_run_block&gt;y/n&lt;/chisq_pre_run_block&gt; </dt><dd> flag indicating if per-run chisq shall be written into the msr-output-file.      $ &lt;estimate_n0&gt;y/n&lt;/estimate_n0&gt; flag indicating if for a single histogram fit N0 shall be estimated before the fit procedure starts.
+</dd> <dt> &lt;musrview_show_fourier&gt;y/n&lt;/musrview_show_fourier&gt; </dt><dd> flag indicating if musrview will directly present the Fourier transform rather than the time domain data.
+</dd> <dt> &lt;musrview_show_avg&gt;y/n&lt;/musrview_show_avg&gt; </dt><dd> flag indicating if musrview will directly present averaged data, typically used for Fourier power spectra.
 </dd> <dt> &lt;enable_musrt0&gt;y/n&lt;/enable_musrt0&gt; </dt><dd> specify if <code><a href="MusrFit.html#MusrT0">musrt0</a></code> can be called from within <code>musrgui</code> / <code>musredit</code> (inside the &lt;general&gt; environment)
 </dd></dl> 
 </dd> <dt> &lt;font_settings&gt;&lt;/font_settings&gt; </dt><dd> set the default font in this environment <dl>
@@ -308,45 +323,167 @@ An example of the <code><b>musrgui_startup.xml</b></code> looks like:
 <p></p>
 <span id="MusrfitFeatures"></span>
 <h1 id="A_3_61_61musrfit_61_61_Features"> 3  <code><b>musrfit</b></code> Features </h1>
-The features of <code>musrfit</code> which can be accessed by the graphical front ends <code>musrgui</code> / <code>musredit</code> are described in the following. All functions can either be called by choosing them from the MusrFit menu, by clicking the respective button in the MusrFit bar, or by using a keyboard shortcut.
+The features of <code>musrfit</code> which can be accessed by the graphical front ends <code>musredit</code> / (<code>musrgui</code>) are described in the following. All functions can either be called by choosing them from the MusrFit menu, by clicking the respective button in the MusrFit bar, or by using a keyboard shortcut.
 <p></p>
-   $ <img alt="musrasym.png" src="../pub/MUSR/MusrGui/musrasym.png" /> Asymmetry Default (Alt+a): Generate a full msr file suitable for the <a href="MusrFit.html#FitTypes">fit type</a> <strong>2</strong> of <code>musrfit</code> from defaults. Calling this function opens a window where the relative path and file name to a data file as well as the file format that should be used have to be specified. For instance if the data file <code><b>/path-to-datadir/2007/lem07_his_8472.root</b></code> should be used and <code><b>/path-to-datadir</b></code> is on the path where <code>musrfit</code> <a href="MusrFit.html#PathToDataFiles">looks for data files</a> then the file name would be <code><b>2007/lem07_his_8472</b></code> and the file format either <strong>ROOT-NPP</strong> or <strong>ROOT-PPC</strong>.
+   <img alt="musrWiz-32x32.png" src="../pub/MUSR/MusrGui/musrWiz-32x32.png" /> musrWiz is a helper programs which allows to create a msr-file from scratch without too much a priori knowledge. For details see <a class="foswikiCurrentTopicLink" href="#MusrWiz">musrWiz</a>.
 <p></p>
-   $ <img alt="musrsinglehisto.png" src="../pub/MUSR/MusrGui/musrsinglehisto.png" /> Single-Histogram Default (Alt+h): Generate a full msr file suitable for the <a href="MusrFit.html#FitTypes">fit type</a> <strong>0</strong> of <code>musrfit</code> from defaults. Calling this function opens a window where the relative path and file name to a data file as well as the file format that should be used have to be specified. For instance if the data file <code><b>/path-to-datadir/d2007/deltat_pta_gps_8472.bin</b></code> should be used and <code><b>/path-to-datadir</b></code> is on the path where <code>musrfit</code> <a href="MusrFit.html#PathToDataFiles">looks for data files</a> then the file name would be <code><b>d2007/deltat_pta_gps_8472</b></code> and the file format <strong>PSI-BIN</strong>.
+   <img alt="musrchisq-plain.png" src="../pub/MUSR/MusrGui/musrchisq-plain.png" /> Calculate Chisq (Alt+c): <pre class="bash">musrfit &#60;msr&#95;file&#62; --chisq-only</pre> is called for the <strong>&lt;msr_file&gt;</strong> selected in the editor. For further information refer to the <a href="MusrFit.html#MusrFit">manual</a> of <code>musrfit</code>.
 <p></p>
-   $ <img alt="musrcalcchisq.png" src="../pub/MUSR/MusrGui/musrcalcchisq.png" /> Calculate Chisq (Alt+c): <pre class="bash">musrfit &#60;msr&#95;file&#62; --chisq-only</pre> is called for the <strong>&lt;msr_file&gt;</strong> selected in the editor. For further information refer to the <a href="MusrFit.html#MusrFit">manual</a> of <code>musrfit</code>.
+   <img alt="musrfit-plain.png" src="../pub/MUSR/MusrGui/musrfit-plain.png" /> Fit (Alt+f): <pre class="bash">musrfit &#60;msr&#95;file&#62; &#91;optional parameters&#93;</pre> is called for the <strong>&lt;msr_file&gt;</strong> selected in the editor. The optional parameters may be chosen under <a class="foswikiCurrentTopicLink" href="#MusrPrefs">Preferences</a>. For further information refer to the <a href="MusrFit.html#MusrFit">manual</a> of <code>musrfit</code>.
 <p></p>
-   $ <img alt="musrfit.png" src="../pub/MUSR/MusrGui/musrfit.png" /> Fit (Alt+f): <pre class="bash">musrfit &#60;msr&#95;file&#62; &#91;optional parameters&#93;</pre> is called for the <strong>&lt;msr_file&gt;</strong> selected in the editor. The optional parameters may be chosen under <a class="foswikiCurrentTopicLink" href="#MusrPrefs">Preferences</a>. For further information refer to the <a href="MusrFit.html#MusrFit">manual</a> of <code>musrfit</code>.
+   <img alt="musrswap-plain.png" src="../pub/MUSR/MusrGui/musrswap-plain.png" /> Swap Msr &#8596; Mlog (Alt+s): Swap the msr and mlog files. E.g., for a file called <code><b>8472_zf.msr</b></code>, this is copied to <code><b>8472_zf.mlog</b></code> and vice versa.
 <p></p>
-   $ <img alt="musrswap.png" src="../pub/MUSR/MusrGui/musrswap.png" /> Swap Msr &#8596; Mlog (Alt+s): Swap the msr and mlog files. E.g., for a file called <code><b>8472_zf.msr</b></code>, this is copied to <code><b>8472_zf.mlog</b></code> and vice versa.
+   <img alt="musrStep-32x32.png" src="../pub/MUSR/MusrGui/musrStep-32x32.png" /> musrStep
 <p></p>
-   $ <img alt="musrmsr2data.png" src="../pub/MUSR/MusrGui/musrmsr2data.png" /> Msr2data (Alt+m): Opens a graphical interface to the <code>msr2data</code> program described in detail in its own <a href="Msr2Data.html#MusrGuiInterface">manual</a>.
+   <img alt="msr2data-plain.png" src="../pub/MUSR/MusrGui/msr2data-plain.png" /> Msr2data (Alt+m): Opens a graphical interface to the <code>msr2data</code> program described in detail in its own <a href="Msr2Data.html#MusrGuiInterface">manual</a>.
 <p></p>
-   $ <img alt="musrview.png" src="../pub/MUSR/MusrGui/musrview.png" /> View (Alt+v): <pre class="bash">musrview &#60;msr&#95;file&#62;</pre> is called for the <strong>&lt;msr_file&gt;</strong> selected in the editor. For further information refer to the <a href="MusrFit.html#MusrView">manual</a> of <code>musrfit</code>.
+   <img alt="musrview-plain.png" src="../pub/MUSR/MusrGui/musrview-plain.png" /> View (Alt+v): <pre class="bash">musrview &#60;msr&#95;file&#62;</pre> is called for the <strong>&lt;msr_file&gt;</strong> selected in the editor. For further information refer to the <a href="MusrFit.html#MusrView">manual</a> of <code>musrfit</code>.
 <p></p>
-   $ <img alt="musrt0.png" src="../pub/MUSR/MusrGui/musrt0.png" /> T0 (Alt+t): <pre class="bash">musrt0 &#60;msr&#95;file&#62;</pre> is called for the <strong>&lt;msr_file&gt;</strong> selected in the editor. For further information refer to the <a href="MusrFit.html#MusrT0">manual</a> of <code>musrfit</code>.
+   <img alt="musrt0-plain.png" src="../pub/MUSR/MusrGui/musrt0-plain.png" /> T0 (Alt+t): <pre class="bash">musrt0 &#60;msr&#95;file&#62;</pre> is called for the <strong>&lt;msr_file&gt;</strong> selected in the editor. For further information refer to the <a href="MusrFit.html#MusrT0">manual</a> of <code>musrfit</code>.
 <p></p>
-   $ <img alt="musrFT.png" src="../pub/MUSR/MusrGui/musrFT.png" /> Raw Fourier: <code>musrFT &lt;with-many-options&gt;</code> is called. For a proper documentation of it, check the <a href="MusrFit.html#MusrFT">manual</a> of <code>musrFT</code>.
+   <img alt="musrFT-plain.png" src="../pub/MUSR/MusrGui/musrFT-plain.png" /> Raw Fourier: <code>musrFT &lt;with-many-options&gt;</code> is called. For a proper documentation of it, check the <a href="MusrFit.html#MusrFT">manual</a> of <code>musrFT</code>.
 <p></p>
 <span id="MusrPrefs"></span>
-   $ <img alt="musrprefs.png" src="../pub/MUSR/MusrGui/musrprefs.png" /> Preferences (Alt+p): Opens a window in which the optional parameters that should be passed to <code>musrfit</code> can be chosen. These options are <code><b>--keep-mn2-output</b></code>, <code><b>--dump ascii</b></code>, <code><b>--dump root</b></code>, and <code><b>--title-from-data-file</b></code>. For further information refer to the <a href="MusrFit.html#MusrFit">manual</a> of <code>musrfit</code>. Additionally, the access to <code>musrt0</code> can be enabled temporarily.
+   <img alt="musrprefs-plain.png" src="../pub/MUSR/MusrGui/musrprefs-plain.png" /> Preferences (Alt+p): Opens a window in which the optional parameters that should be passed to <code>musrfit</code> can be chosen. These options are <code><b>--keep-mn2-output</b></code>, <code><b>--dump ascii</b></code>, <code><b>--dump root</b></code>, and <code><b>--title-from-data-file</b></code>. For further information refer to the <a href="MusrFit.html#MusrFit">manual</a> of <code>musrfit</code>. Additionally, the access to <code>musrt0</code> can be enabled temporarily.
 <p></p>
-   $ <img alt="musrdump.png" src="../pub/MUSR/MusrGui/musrdump.png" /> Dump Header: Opens a file dialog which allows to select a &mu;SR data file. When this file can be read, the run header info is dumped into a dialog window. Essentially this calls <code><b>dump_header</b></code> internally.
+   <img alt="musrdump-plain.png" src="../pub/MUSR/MusrGui/musrdump-plain.png" /> Dump Header: Opens a file dialog which allows to select a &mu;SR data file. When this file can be read, the run header info is dumped into a dialog window. Essentially this calls <code><b>dump_header</b></code> internally.
 <p></p>
-<span id="EditorFeatures"></span>
-<h1 id="A_4_Editor_Features"> 4  Editor Features </h1>
-Besides the functions described above and which are mostly interfacing <code>musrfit/msr2data</code> the editors of <code>musrgui</code> / <code>musredit</code> offer various functions for manipulating especially <code>musrfit</code> msr files:
-<img class='imagePlain imagePlain_right ' src='../pub/MUSR/MusrGui/igp_4e5811420d6b5b31cac70e88b8477a14_musrgui-editor-v0.png' alt='musrgui editor features' title='musrgui-editor-v0.png' width='415' height='566'   style='' /> <ul>
-<li> Upon right-clicking an open msr file a menu as shown to the right is displayed which offers the addition of any valid msr file block or theory function. In case a simple theory function is chosen, the function will be inserted into the THEORY block using the <a href="MusrFit.html#TheoryTable">correct syntax</a>. If one chooses to add a whole block to the file a dialog opens in which the necessary information for each block as described in the <a href="MusrFit.html#DescriptionOfTheMsrFileFormat">manual</a> of <code>musrfit</code> can be supplied. <span class='foswikiBlueFG'>This feature is available only in <code>musrgui</code>. In <code>musredit</code> the respective functions can be accessed through the <em>Edit</em> menu.</span>
-</li> <li> In order to comment or uncomment lines in a msr file select the according lines and apply <strong>Edit &rarr; (Un)Comment</strong> or use the keyboard shortcut <strong>Ctrl+(Shift)+m</strong>.
-</li></ul> 
+<span id="MusrWiz"></span>
+<h1 id="A_4_musrWiz"> 4  musrWiz </h1>
+<p></p>
+musrWiz is a helper program which allows to easily create the necessary msr-file needed as the input for musrfit. musrWiz is still in it's early stage; not all options are already implemented and here and there you will likely find some bugs. 
+From musredit it can be accessed via the MusrFit menu or the wand
+<p></p>
+<img alt="musredit-main_0.png" src="../pub/MUSR/MusrGui/musredit-main_0.png" />
+<p></p>
+The musrWiz GUI is organized in a couple of different dialogues which some information needs to be provided by the user. In the following these different dialogues will be discussed briefly.
+<p></p>
+<span id="MusrWizIntroduction"></span>
+<h2 id="A_4.1_musrWiz_45_Introduction"> 4.1  musrWiz - Introduction </h2>
+<p></p>
+The introduction dialogue 
+<p></p>
+<img alt="musrWiz-Introduction_0.png" src="../pub/MUSR/MusrGui/musrWiz-Introduction_0.png" />
+<p></p> <ol>
+<li> an explicit msr-file name can be provided here. More often the msr-file name is generated out of the run number.
+</li> <li> year of the run data.
+</li> <li> run number. If no explicit msr-file is provided, the run number together with fit type and type of measurement will be used to generate the msr-file name.
+</li> <li> from the pull down menu the institute (for which a necessary xml-file is provided) has to be choosen.
+</li> <li> from the pull down menu the the instrument can be chosen.
+</li> <li> the fit type has to be chosen. Possible fit types are: <code>Single Histo</code> / <code>Single Histo RRF</code> / <code>Asymmetry</code> / <code>Asymmetry RRF</code> / <code>Mu Minus</code> / <code>None muSR</code>
+</li> <li> type of measurement is essentially needed for the grouping of the detectors. Possible are: <code>ZF</code> for zero field measurements / <code>TF</code> for transverse field measurements / <code>LF</code> for longitudinal field measurements. Depending on the choice and instrument some additional question might be asked, e.g. which magnet has been used.
+</li> <li> T0's: this last menu defines from where to get the t0's. The options are: ' <code>from data file</code> ', i.e. the t0 are assumed to be correctly set in the provided data file ' <code>call musrT0</code> ', i.e. after the msr-file is generated, musrt0 will be called which allows the user to find the proper t0 from the prompt peak ' <code>enter here</code> ' will provide a pop-up menu where the t0 parameter can be given explicitly. 
+</li></ol> 
+<p></p>
+If all this information have been provided ' <code>Next&gt;</code> ' will lead you the the theory dialogue. 
+<p></p>
+<span id="MusrWizTheory"></span>
+<h2 id="A_4.2_musrWiz_45_Theory"> 4.2  musrWiz - Theory </h2>
+<p></p>
+The theory dialogue is used to define the fitting function. There are two ways of using it: <ol>
+<li> choose a template theory function. This option has the advantage that the next steps will be very easy because within the template almost everything is already pre-defined. The disadvantage is that you are not free in setting up your theory function as you would like to have.
+</li> <li> freely write your theory function. The advantage here is that you can customize your theory function as you would like to have it. This will come at the cost that you also will need to define maps, functions, etc. yourself. The good thing though is that at the very end you can save this as a template for future re-use.
+</li></ol> 
+<p></p>
+First the template path will be described. The theory dialogue looks like this
+<p></p>
+<img alt="musrWiz-Theory-1_0.png" src="../pub/MUSR/MusrGui/musrWiz-Theory-1_0.png" />
+<p></p> <ol>
+<li> This is a text edit field were you can enter the theory fit function as you would like to have it.
+</li> <li> The ' <code>Clear All</code> ' button will clear whatever you entered in the text field above
+</li> <li> This pull-down menu allows to select a theory function which will be added to the text field above by pressing the ' <code>Add</code> ' button. Pre defined theory function starting with a 'T' are templates rather than only theory function strings.
+</li> <li> The ' <code>Add</code> ' button is used to add the chosen theory function / template from the pull-down menu to its left.
+</li> <li> The ' <code>Check</code> ' button is used to make a syntactical check of whatever is written in the text edit field.
+</li></ol> 
+<p></p>
+Let's assume you would like to chose a template of an exponentially damped cosine (likely a TF measurement with dilute nuclear damping), do the following: Select ' <code>T: 1 [exp x cos](TF)</code> ' from the pull-down menu and than press the ' <code>Add</code> ' button. You will see that the theory fit function will be entered in the text edit field. After this just press the ' <code>Next&gt;</code> ' button which will bring you to <code>Functions</code> dialogue.
+<p></p>
+<span id="MusrWizFunctions"></span>
+<h2 id="A_4.3_musrWiz_45_Functions"> 4.3  musrWiz - Functions </h2>
+<p></p>
+In the <code>Functions</code> dialogue all the necessary functions can be entered. A function operates <strong>only</strong> on fitting parameters. This is different to the theory function which operates on the fitting parameters <strong>and</strong> the time.
+The dialogue looks like this
+<p></p>
+<img alt="musrWiz-Functions-1_0.png" src="../pub/MUSR/MusrGui/musrWiz-Functions-1_0.png" />
+<p></p> <ol>
+<li> a text edit field in which the various needed functions can be entered. In case a template theory is used, the appropriate function should be shown here and <strong>no</strong> editing will be needed here.
+</li> <li> pressing ' <code>Show Theory</code> ' button  will pop-up a little window showing the previously entered theory function. This is handy when defining its own theory, i.e. not working with a template.
+</li></ol> 
+<p></p>
+<img alt="musrWiz-Functions-2_0.png" src="../pub/MUSR/MusrGui/musrWiz-Functions-2_0.png" />
+<p></p>
+<span id="MusrWizMaps"></span>
+<h2 id="A_4.4_musrWiz_45_Maps"> 4.4  musrWiz - Maps </h2>
+<p></p>
+<img alt="musrWiz-Maps-1_0.png" src="../pub/MUSR/MusrGui/musrWiz-Maps-1_0.png" />
+<p></p>
+The map dialogue will list the maps previously used in the theory and functions blocks/dialogues before. Again, if a template is used, nothing needs to be entered here.
+<p></p> <ol>
+<li> The ' <code>Show Theory</code> ' button allows to show the currently defined theory and the functions.
+</li></ol> 
+<p></p>
+<span id="MusrWizFitParameters"></span>
+<h2 id="A_4.5_musrWiz_45_Fit_Parameters"> 4.5  musrWiz - Fit Parameters </h2>
+<p></p>
+<img alt="musrWiz-FitParameters-1_0.png" src="../pub/MUSR/MusrGui/musrWiz-FitParameters-1_0.png" />
+<p></p> <ol>
+<li> The ' <code>Show Theory</code> ' button allows to show the currently defined theory and the functions.
+</li></ol> 
+<p></p>
+In the fit parameter dialogue all parameter names can be defined. Furthermore the starting values for the parameters, the step (initial step size for the parameter fit), and any boundaries can be defined here.
+<p></p>
+<span id="MusrWizFitInfo"></span>
+<h2 id="A_4.6_musrWiz_45_Fit_Info"> 4.6  musrWiz - Fit Info </h2>
+<p></p>
+<img alt="musrWiz-FitInfo-1_0.png" src="../pub/MUSR/MusrGui/musrWiz-FitInfo-1_0.png" />
+<p></p> <ol>
+<li> allows to define the time fit range (start time, end time).
+</li> <li> packing defines how many bins of the original data shall be combined (added, also called re-binning).
+</li> <li> In this text field to fitting commands are given (see the <code>MINUIT</code> and <code>musrfit</code> manual for details).
+</li></ol> 
+<p></p>
+<span id="MusrWizCreate"></span>
+<h2 id="A_4.7_musrWiz_45_Create"> 4.7  musrWiz - Create </h2>
+<p></p>
+<img alt="musrWiz-Create-1_0.png" src="../pub/MUSR/MusrGui/musrWiz-Create-1_0.png" />
+<p></p> <ol>
+<li> shows the path where the msr-file will be saved. If you would like to save it somewhere else press the ' <code>Save As (msr-file path)</code> button.
+</li> <li> pressing this button will allow you to find the path where to save the msr-file.
+</li> <li> pressing this button will save to current configuration as a template for future re-use.
+</li></ol> 
+<p></p>
+<span id="MusrStep"></span>
+<h1 id="A_5_musrStep"> 5  musrStep </h1>
+<p></p>
+musrStep is a little helper program which allows to reset the initial step size. This sometimes comes very handy if working on an instrument with many detectors after a fit slightly went wrong leaving you with a far too small initial step size for further iterations. To edit all the steps individually is tedious and error prone. Here musrStep can help. 
+<p></p>
+<img alt="musrStep_0_0.png" src="../pub/MUSR/MusrGui/musrStep_0_0.png" />
+<p></p>
+When invoking musrStep the above dialogue will popup <ol>
+<li> shows the relevant parts of the <code>FITPARAMETER</code> block. The only editable column is <code>step</code>.
+</li> <li> ' <code>Check Specific</code> ' will popup a dialogue where a template string can be entered, e.g. <code>Asym</code>. As a result all fit parameters containing the template string will be selected.
+</li> <li> ' <code>Check All</code> ' will select <em>all</em> fit parameters.
+</li> <li> ' <code>Uncheck All</code> ' will unselect <em>all</em> fir parameters.
+</li> <li> ' <code>Modify Automatic</code> ' will change all the step values automatically. It basically sets all the step sizes to 1% of the corresponding fit parameter value, except the phases where the step will be set to a value of 5 degrees.
+</li> <li> ' <code>Modify Selected</code> ' will start the dialogue shown beneath. Follow the description there.
+</li> <li> ' <code>Save&amp;Quit</code> ' will save the current step values, close the dialogue and reload the modified msr-file.
+</li> <li> ' <code>Cancel</code> ' will cancel the musrStep dialogue without modifying anything. 
+</li></ol> 
+<p></p>
+<img alt="musrStep_1_0.png" src="../pub/MUSR/MusrGui/musrStep_1_0.png" />
+<p></p>
+When clicking on ' <code>Modify Selected</code> ' the above dialogue will be presented. It allows to manipulate all selected fir parameter step values according to the following rules <ol>
+<li> ' <code>Scale by Factor</code> ' will scale the step value by the factor given in the field (2). If the ' <code>Absolute Value</code> ' check box is selected, rather than scaling the factor value will be used to modify the step value.
+</li> <li> Scaling factor or absolute value to modify the step values of the selected fit parameters.
+</li> <li> checking the ' <code>Absolute Value</code> ' check box will change the meaning from <code>Scale by Factor</code> to <code>Copy Factor Value</code>.
+</li> <li> ' <code>Scale Automatically</code> ' will modify the step values of the selected fit parameters according to the rules described before.
+</li> <li> ' <code>Cancel</code> ' will cancel the dialogue.
+</li></ol> 
 <p></p>
 <span id="BugTracking"></span>
-<h1 id="A_5_Bugtracking"> 5  Bugtracking </h1>
+<h1 id="A_6_Bugtracking"> 6  Bugtracking </h1>
 <p></p>
-For reporting bugs or requesting new features and improvements please use the <a href="https://bitbucket.org/muonspin/musrfit/issues">Bitbucket Tracker</a>,  <a href="https://tracker.psi.ch/jira/browse/MUSR/">PSI Tracker</a> (PSI account needed) or send an e-mail to A. Suter.
-<p></p>
---  <a href="http://www.psi.ch/low-energy-muons/people">AS</a> &amp; <a href="http://www.fsf.org/register_form?referrer=8369">BMW</a></div>
+For reporting bugs or requesting new features and improvements please use the <a href="https://bitbucket.org/muonspin/musrfit/issues">Bitbucket Tracker</a>,  <a href="https://tracker.psi.ch/jira/browse/MUSR/">PSI Tracker</a> (PSI account needed) or send an e-mail to A. Suter.</div>
 <p></p>
 <p></p>
 <br class="imageClear" clear="all"/><div class="foswikiAttachments">
@@ -376,7 +513,7 @@ For reporting bugs or requesting new features and improvements please use the <a
 	</tbody></table>
 </div></div></div></div>
 <div class="patternInfo">This topic: MUSR<span class='foswikiSeparator'>&nbsp;&gt;&nbsp;</span><a class="foswikiCurrentWebHomeLink" href="WebHome.html">WebHome</a> &gt; <a href="MusrFit.html">MusrFit</a><span class='foswikiSeparator'>&nbsp;&gt;&nbsp;</span>MusrGui <br />
-Topic revision:  <span class='patternRevInfo'>19 Feb 2015, suter_a</span></div>
+Topic revision:  <span class='patternRevInfo'>14 May 2017, <a href="https://intranet.psi.ch/Main/AndreasSuter">AndreasSuter</a></span></div>
 </div>
 </div>
 </div>
@@ -394,6 +531,5 @@ Topic revision:  <span class='patternRevInfo'>19 Feb 2015, suter_a</span></div>
 
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-<!-- Added by HTTrack --><meta http-equiv="content-type" content="text/html;charset=utf-8"><!-- /Added by HTTrack -->
+<!-- Mirrored from intranet.psi.ch/MUSR/MusrGui?cover=print by HTTrack Website Copier/3.x [XR&CO'2014], Sun, 14 May 2017 18:08:38 GMT -->
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doc/html/user/MUSR/MusrRoot.html

@@ -1,7 +1,7 @@
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-<!-- Mirrored from intranet.psi.ch/MUSR/MusrRoot?cover=print by HTTrack Website Copier/3.x [XR&CO'2010], Fri, 16 Dec 2016 16:00:46 GMT -->
-<!-- Added by HTTrack --><meta http-equiv="content-type" content="text/html;charset=utf-8"><!-- /Added by HTTrack -->
+<!-- Mirrored from intranet.psi.ch/MUSR/MusrRoot?cover=print by HTTrack Website Copier/3.x [XR&CO'2014], Sun, 14 May 2017 18:08:20 GMT -->
+<!-- Added by HTTrack --><meta http-equiv="content-type" content="text/html;charset=utf-8" /><!-- /Added by HTTrack -->
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@@ -14,11 +14,14 @@
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-<link rel="alternate" href="https://intranet.psi.ch/wiki/bin/edit/MUSR/MusrRoot?t=1481904041" type="application/x-wiki" title="edit MusrRoot" />
+<link rel="alternate" href="https://intranet.psi.ch/wiki/bin/edit/MUSR/MusrRoot?t=1494785293" type="application/x-wiki" title="edit MusrRoot" />
 <meta name="TEXT_NUM_TOPICS" content="Number of topics:" />
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+<meta name="robots" content="noindex" /><link rel="alternate" type="application/rss+xml" title="RSS Feed" href="WebRss" />
+<base  /><!--[if IE]></base><![endif]--><link class='head SMILIESPLUGIN' rel='stylesheet' href='../pub/System/SmiliesPlugin/smilies.css' type='text/css' media='all' /><!--SMILIESPLUGIN-->
+<link class='head JQUERYPLUGIN::COMMENT' rel='stylesheet' href='../pub/System/CommentPlugin/commentf5b6.css?version=3.0' type='text/css' media='all' /><!--JQUERYPLUGIN::COMMENT-->
+<link class='head FOOTNOTEPLUGIN_LINKCSS' rel="stylesheet" href="../pub/System/FootNotePlugin/styles.css" type="text/css" media="all" /><!--FOOTNOTEPLUGIN_LINKCSS-->
+<link class='head JQUERYPLUGIN::TWISTY' rel='stylesheet' href='../pub/System/TwistyPlugin/twisty327a.css?version=1.6.0' type='text/css' media='all' /><!--JQUERYPLUGIN::TWISTY: requires= missing ids: JavascriptFiles/foswikiPref-->
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+<link class='head CLASSIFICATIONPLUGIN::CSS' rel="stylesheet" href="../pub/System/ClassificationPlugin/styles.css" media="all" /><!--CLASSIFICATIONPLUGIN::CSS-->
+<link class='head IMAGEPLUGIN' rel="stylesheet" href="../pub/System/ImagePlugin/style.css" type="text/css" media="all" /><!--IMAGEPLUGIN--><link rel='stylesheet' href='../pub/System/SkinTemplates/base.css' media='all' type='text/css' />
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-<!-- Added by HTTrack --><meta http-equiv="content-type" content="text/html;charset=utf-8"><!-- /Added by HTTrack -->
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doc/html/user/MUSR/QuickStart.html

@@ -1,7 +1,7 @@
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-<!-- Mirrored from intranet.psi.ch/MUSR/QuickStart?cover=print by HTTrack Website Copier/3.x [XR&CO'2010], Fri, 16 Dec 2016 16:00:58 GMT -->
-<!-- Added by HTTrack --><meta http-equiv="content-type" content="text/html;charset=utf-8"><!-- /Added by HTTrack -->
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+<!-- Added by HTTrack --><meta http-equiv="content-type" content="text/html;charset=utf-8" /><!-- /Added by HTTrack -->
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-<link rel="alternate" href="https://intranet.psi.ch/wiki/bin/edit/MUSR/QuickStart?t=1481904043" type="application/x-wiki" title="edit QuickStart" />
+<link rel="alternate" href="https://intranet.psi.ch/wiki/bin/edit/MUSR/QuickStart?t=1494785296" type="application/x-wiki" title="edit QuickStart" />
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+<base  /><!--[if IE]></base><![endif]--><link class='head SMILIESPLUGIN' rel='stylesheet' href='../pub/System/SmiliesPlugin/smilies.css' type='text/css' media='all' /><!--SMILIESPLUGIN-->
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-<link class='head FOOTNOTEPLUGIN_LINKCSS' rel="stylesheet" href="../pub/System/FootNotePlugin/styles.css" type="text/css" media="all" /><!--FOOTNOTEPLUGIN_LINKCSS--><link rel='stylesheet' href='../pub/System/SkinTemplates/base.css' media='all' type='text/css' />
+<link class='head FOOTNOTEPLUGIN_LINKCSS' rel="stylesheet" href="../pub/System/FootNotePlugin/styles.css" type="text/css" media="all" /><!--FOOTNOTEPLUGIN_LINKCSS-->
+<link class='head CLASSIFICATIONPLUGIN::CSS' rel="stylesheet" href="../pub/System/ClassificationPlugin/styles.css" media="all" /><!--CLASSIFICATIONPLUGIN::CSS--><link rel='stylesheet' href='../pub/System/SkinTemplates/base.css' media='all' type='text/css' />
 <style type="text/css" media="all">
 @import url('../pub/System/PatternSkinTheme/layout.css');
 @import url('../pub/System/PatternSkinTheme2009/style.css');
@@ -104,11 +104,11 @@
 <!--JQUERYPLUGIN::MIGRATE-->
 <!--JQUERYPLUGIN::LIVEQUERY-->
 <!--JQUERYPLUGIN::FOSWIKI-->
-<!--JavascriptFiles/foswikiString-->
-<!--JavascriptFiles/foswikiForm-->
 <!--JQUERYPLUGIN::COMMENT-->
 <!--JQUERYPLUGIN::FOSWIKI::PREFERENCES-->
+<!--JavascriptFiles/foswikiString-->
 <!--JavascriptFiles/foswikiPref-->
+<!--JavascriptFiles/foswikiForm-->
 <!--PatternSkin/pattern--><link class='head FOOTNOTEPLUGIN_LINKCSS' rel="stylesheet" href="../pub/System/FootNotePlugin/styles.css" type="text/css" media="all" /><!--FOOTNOTEPLUGIN_LINKCSS-->
 </head> 
 <body class="foswikiNoJs patternViewPage patternPrintPage">
@@ -285,6 +285,5 @@ Topic revision:  <span class='patternRevInfo'>10 Jul 2011, wojek</span></div>
 
 </body>
 
-<!-- Mirrored from intranet.psi.ch/MUSR/QuickStart?cover=print by HTTrack Website Copier/3.x [XR&CO'2010], Fri, 16 Dec 2016 16:00:59 GMT -->
-<!-- Added by HTTrack --><meta http-equiv="content-type" content="text/html;charset=utf-8"><!-- /Added by HTTrack -->
+<!-- Mirrored from intranet.psi.ch/MUSR/QuickStart?cover=print by HTTrack Website Copier/3.x [XR&CO'2014], Sun, 14 May 2017 18:08:33 GMT -->
 </html>

doc/html/user/MUSR/TutorialSingleHisto.html

@@ -1,7 +1,7 @@
 <!DOCTYPE html><html lang="en">
 
-<!-- Mirrored from intranet.psi.ch/MUSR/TutorialSingleHisto?cover=print by HTTrack Website Copier/3.x [XR&CO'2010], Fri, 16 Dec 2016 16:00:55 GMT -->
-<!-- Added by HTTrack --><meta http-equiv="content-type" content="text/html;charset=utf-8"><!-- /Added by HTTrack -->
+<!-- Mirrored from intranet.psi.ch/MUSR/TutorialSingleHisto?cover=print by HTTrack Website Copier/3.x [XR&CO'2014], Sun, 14 May 2017 18:08:30 GMT -->
+<!-- Added by HTTrack --><meta http-equiv="content-type" content="text/html;charset=utf-8" /><!-- /Added by HTTrack -->
 <head>
 <link rel="stylesheet" href="../pub/System/HeadlinesPlugin/style.css" type="text/css" media="all" />
 <title> MUSR :: TutorialSingleHisto</title>
@@ -14,10 +14,10 @@
 <meta name="apple-mobile-web-app-status-bar-style" content="black-translucent" />
 <link rel="icon" href="../pub/Main/WebPreferences/favicon.ico" type="image/x-icon" />
 <link rel="shortcut icon" href="../pub/Main/WebPreferences/favicon.ico" type="image/x-icon" />
-<link rel="alternate" href="https://intranet.psi.ch/wiki/bin/edit/MUSR/TutorialSingleHisto?t=1481904042" type="application/x-wiki" title="edit TutorialSingleHisto" />
+<link rel="alternate" href="https://intranet.psi.ch/wiki/bin/edit/MUSR/TutorialSingleHisto?t=1494785295" type="application/x-wiki" title="edit TutorialSingleHisto" />
 <meta name="TEXT_NUM_TOPICS" content="Number of topics:" />
 <meta name="TEXT_MODIFY_SEARCH" content="Modify search" />
-<meta name="robots" content="noindex" /><link rel="alternate" type="application/rss+xml" title="RSS Feed" href="WebRsshtml.html" />
+<meta name="robots" content="noindex" /><link rel="alternate" type="application/rss+xml" title="RSS Feed" href="WebRss" />
 <base  /><!--[if IE]></base><![endif]--><style class='head TABLEPLUGIN_default' type="text/css" media="all">
 body .foswikiTable {border-width:1px}
 body .foswikiTable .tableSortIcon img {padding-left:.3em; vertical-align:text-bottom}
@@ -32,8 +32,6 @@ body .foswikiTable tr.foswikiTableRowdataBg0 td.foswikiSortedCol {background-col
 body .foswikiTable tr.foswikiTableRowdataBg1 td {background-color:#f7f7f6}
 body .foswikiTable tr.foswikiTableRowdataBg1 td.foswikiSortedCol {background-color:#f0f0ee}
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-<link class='head CLASSIFICATIONPLUGIN::CSS' rel="stylesheet" href="../pub/System/ClassificationPlugin/styles.css" media="all" /><!--CLASSIFICATIONPLUGIN::CSS-->
 <style class='head TABLEPLUGIN_specific' type="text/css" media="all">
 body .foswikiTable#tableTutorialSingleHisto1 td {vertical-align:middle; vertical-align:top}
 body .foswikiTable#tableTutorialSingleHisto1 td.foswikiTableCol0 {text-align:left}
@@ -52,10 +50,12 @@ body .foswikiTable#tableTutorialSingleHisto1 th.foswikiSortedCol {background-col
 body .foswikiTable#tableTutorialSingleHisto1 tr.foswikiTableRowdataBg0 td {background-color:#ffffff}
 body .foswikiTable#tableTutorialSingleHisto1 tr.foswikiTableRowdataBg0 td.foswikiSortedCol {background-color:#f5f5f5}
 </style><!--TABLEPLUGIN_specific-->
-<link class='head JQUERYPLUGIN::TWISTY' rel='stylesheet' href='../pub/System/TwistyPlugin/twisty327a.css?version=1.6.0' type='text/css' media='all' /><!--JQUERYPLUGIN::TWISTY: requires= missing ids: JavascriptFiles/foswikiPref-->
 <link class='head IMAGEPLUGIN' rel="stylesheet" href="../pub/System/ImagePlugin/style.css" type="text/css" media="all" /><!--IMAGEPLUGIN-->
-<link class='head JQUERYPLUGIN::COMMENT' rel='stylesheet' href='../pub/System/CommentPlugin/commentf5b6.css?version=3.0' type='text/css' media='all' /><!--JQUERYPLUGIN::COMMENT-->
-<link class='head FOOTNOTEPLUGIN_LINKCSS' rel="stylesheet" href="../pub/System/FootNotePlugin/styles.css" type="text/css" media="all" /><!--FOOTNOTEPLUGIN_LINKCSS--><link rel='stylesheet' href='../pub/System/SkinTemplates/base.css' media='all' type='text/css' />
+<link class='head CLASSIFICATIONPLUGIN::CSS' rel="stylesheet" href="../pub/System/ClassificationPlugin/styles.css" media="all" /><!--CLASSIFICATIONPLUGIN::CSS-->
+<link class='head JQUERYPLUGIN::TWISTY' rel='stylesheet' href='../pub/System/TwistyPlugin/twisty327a.css?version=1.6.0' type='text/css' media='all' /><!--JQUERYPLUGIN::TWISTY: requires= missing ids: JavascriptFiles/foswikiPref-->
+<link class='head FOOTNOTEPLUGIN_LINKCSS' rel="stylesheet" href="../pub/System/FootNotePlugin/styles.css" type="text/css" media="all" /><!--FOOTNOTEPLUGIN_LINKCSS-->
+<link class='head SMILIESPLUGIN' rel='stylesheet' href='../pub/System/SmiliesPlugin/smilies.css' type='text/css' media='all' /><!--SMILIESPLUGIN-->
+<link class='head JQUERYPLUGIN::COMMENT' rel='stylesheet' href='../pub/System/CommentPlugin/commentf5b6.css?version=3.0' type='text/css' media='all' /><!--JQUERYPLUGIN::COMMENT--><link rel='stylesheet' href='../pub/System/SkinTemplates/base.css' media='all' type='text/css' />
 <style type="text/css" media="all">
 @import url('../pub/System/PatternSkinTheme/layout.css');
 @import url('../pub/System/PatternSkinTheme2009/style.css');
@@ -138,12 +138,12 @@ body .foswikiTable#tableTutorialSingleHisto1 tr.foswikiTableRowdataBg0 td.foswik
 <!--JQUERYPLUGIN::MIGRATE-->
 <!--JQUERYPLUGIN::LIVEQUERY-->
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-<!--JQUERYPLUGIN::FOSWIKI::PREFERENCES-->
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 <!--JavascriptFiles/foswikiPref-->
 <!--JQUERYPLUGIN::TWISTY-->
-<!--JQUERYPLUGIN::COMMENT-->
 <!--JavascriptFiles/foswikiForm-->
+<!--JQUERYPLUGIN::COMMENT-->
+<!--JQUERYPLUGIN::FOSWIKI::PREFERENCES-->
 <!--PatternSkin/pattern--><link class='head FOOTNOTEPLUGIN_LINKCSS' rel="stylesheet" href="../pub/System/FootNotePlugin/styles.css" type="text/css" media="all" /><!--FOOTNOTEPLUGIN_LINKCSS-->
 </head> 
 <body class="foswikiNoJs patternViewPage patternPrintPage">
@@ -270,7 +270,7 @@ STATISTIC --- 2011-07-09 10:58:44
 </li></ul> 
 <p></p>
 <h1 id="A_2_Determine_t0_and_the_data_range_using_61musrt0_61"> 2  Determine <i>t</i><sub>0</sub> and the data range using <code>musrt0</code> </h1>
-Before the given model can be fitted to the data, the data ranges and time zeros of the different RUN blocks have to be set correctly. This can be achieved using <code><a href="MusrFit.html#MusrT0">musrt0</a></code>. Starting this program by selecting the <img alt="musrt0.png" src="../pub/MUSR/MusrGui/musrt0.png" /> button in <code>musredit</code> or calling from a terminal <pre>musrt0 3110&#95;tutorial.msr</pre> opens an interactive window plotting the data of the first RUN block:<br />
+Before the given model can be fitted to the data, the data ranges and time zeros of the different RUN blocks have to be set correctly. This can be achieved using <code><a href="MusrFit.html#MusrT0">musrt0</a></code>. Starting this program by selecting the <img alt="musrt0.png" src="../pub/MUSR/MusrGui/musrt0.html" /> button in <code>musredit</code> or calling from a terminal <pre>musrt0 3110&#95;tutorial.msr</pre> opens an interactive window plotting the data of the first RUN block:<br />
 <img class='imagePlain imagePlain_center ' src='../pub/MUSR/TutorialSingleHisto/musrt0-1.png' alt='musrt0-1' title='musrt0-1.png' width='708' height='529'   style='' /><br />
 The green line (at bin 1) represents time zero, the blue lines the start (at bin 1) and end (at bin 8000) of the data range and the optional red lines give the limits of the background range (if the background shall not be determined by the fit). All lines can be either dragged to reasonable locations or set by pressing the corresponding keyboard shortcuts. In the example the time zero can be set by pressing <strong>T</strong> (which moves the green line to the bin containing the maximum number of counts), the start of the data range should be set to about five bins later by zooming into the graph around bin 250 and pressing <strong>d</strong> when the cursor is found at a suitable location:<br />
 <img class='imagePlain imagePlain_center ' src='../pub/MUSR/TutorialSingleHisto/igp_9c0f9b31d4414f37be0d3d171836fe63_musrt0-2.png' alt='musrt0-2' title='musrt0-2.png' width='688' height='529'   style='' /><br />
@@ -278,7 +278,7 @@ After all lines have been adjusted for the first histogram, one can go on to the
 A full description of <code>musrt0</code> can be found <a href="MusrFit.html#MusrT0">here</a>.
 <p></p>
 <h1 id="A_3_Fit_the_model_to_the_data_using_61musrfit_61"> 3  Fit the model to the data using <code>musrfit</code> </h1>
-Now that the basics of the <code>msr</code> file have been introduced and the necessary adjustments have been done one can proceed with fitting the specified model to the data. This is done by selecting the <img alt="musrfit.png" src="../pub/MUSR/MusrGui/musrfit.png" /> button in <code>musredit</code> or calling from a terminal <pre>musrfit 3110&#95;tutorial.msr</pre>
+Now that the basics of the <code>msr</code> file have been introduced and the necessary adjustments have been done one can proceed with fitting the specified model to the data. This is done by selecting the <img alt="musrfit.png" src="../pub/MUSR/MusrGui/musrfit.html" /> button in <code>musredit</code> or calling from a terminal <pre>musrfit 3110&#95;tutorial.msr</pre>
 <p></p>
 After the fitting procedure has finished the <code>msr</code> file is updated and contains the newly determined values of the fit parameters.
 <p></p>
@@ -298,7 +298,7 @@ Assuming the successive runs <strong>3111</strong> through <strong>3114</strong>
 From the terminal this would be done as follows:<pre>
 msr2data 3110 3114 &#95;tutorial fit-3110 -o tutorial-T-dependence.dat data
 </pre>
-To achieve the same in <code>musredit</code> one selects <img alt="musrmsr2data.png" src="../pub/MUSR/MusrGui/musrmsr2data.png" /> and fills the form accordingly:<br />
+To achieve the same in <code>musredit</code> one selects <img alt="musrmsr2data.png" src="../pub/MUSR/MusrGui/musrmsr2data.html" /> and fills the form accordingly:<br />
 <img class='imagePlain imagePlain_center ' src='../pub/MUSR/TutorialSingleHisto/msr2data.png' alt='msr2data' title='msr2data.png' width='612' height='605'   style='' />
 <p></p>
 <h1 id="A_6_Further_reading"> 6  Further reading </h1>
@@ -401,6 +401,5 @@ Topic revision:  <span class='patternRevInfo'>02 Sep 2011, wojek</span></div>
 
 </body>
 
-<!-- Mirrored from intranet.psi.ch/MUSR/TutorialSingleHisto?cover=print by HTTrack Website Copier/3.x [XR&CO'2010], Fri, 16 Dec 2016 16:00:58 GMT -->
-<!-- Added by HTTrack --><meta http-equiv="content-type" content="text/html;charset=utf-8"><!-- /Added by HTTrack -->
+<!-- Mirrored from intranet.psi.ch/MUSR/TutorialSingleHisto?cover=print by HTTrack Website Copier/3.x [XR&CO'2014], Sun, 14 May 2017 18:08:33 GMT -->
 </html>

doc/html/user/MUSR/WebHome.html

@@ -1,7 +1,7 @@
 <!DOCTYPE html><html lang="en">
 
-<!-- Mirrored from intranet.psi.ch/MUSR/WebHome?cover=print by HTTrack Website Copier/3.x [XR&CO'2010], Fri, 16 Dec 2016 16:01:33 GMT -->
-<!-- Added by HTTrack --><meta http-equiv="content-type" content="text/html;charset=utf-8"><!-- /Added by HTTrack -->
+<!-- Mirrored from intranet.psi.ch/MUSR/WebHome?cover=print by HTTrack Website Copier/3.x [XR&CO'2014], Sun, 14 May 2017 18:09:10 GMT -->
+<!-- Added by HTTrack --><meta http-equiv="content-type" content="text/html;charset=utf-8" /><!-- /Added by HTTrack -->
 <head>
 <link rel="stylesheet" href="../pub/System/HeadlinesPlugin/style.css" type="text/css" media="all" />
 <title> MUSR :: MUSR</title>
@@ -14,14 +14,14 @@
 <meta name="apple-mobile-web-app-status-bar-style" content="black-translucent" />
 <link rel="icon" href="../pub/Main/WebPreferences/favicon.ico" type="image/x-icon" />
 <link rel="shortcut icon" href="../pub/Main/WebPreferences/favicon.ico" type="image/x-icon" />
-<link rel="alternate" href="https://intranet.psi.ch/wiki/bin/edit/MUSR/WebHome?t=1481904045" type="application/x-wiki" title="edit WebHome" />
+<link rel="alternate" href="https://intranet.psi.ch/wiki/bin/edit/MUSR/WebHome?t=1494785300" type="application/x-wiki" title="edit WebHome" />
 <meta name="TEXT_NUM_TOPICS" content="Number of topics:" />
 <meta name="TEXT_MODIFY_SEARCH" content="Modify search" />
-<meta name="robots" content="noindex" /><link rel="alternate" type="application/rss+xml" title="RSS Feed" href="WebRsshtml.html" />
+<meta name="robots" content="noindex" /><link rel="alternate" type="application/rss+xml" title="RSS Feed" href="WebRss" />
 <base  /><!--[if IE]></base><![endif]--><link class='head CLASSIFICATIONPLUGIN::CSS' rel="stylesheet" href="../pub/System/ClassificationPlugin/styles.css" media="all" /><!--CLASSIFICATIONPLUGIN::CSS-->
-<link class='head SMILIESPLUGIN' rel='stylesheet' href='../pub/System/SmiliesPlugin/smilies.css' type='text/css' media='all' /><!--SMILIESPLUGIN-->
+<link class='head FOOTNOTEPLUGIN_LINKCSS' rel="stylesheet" href="../pub/System/FootNotePlugin/styles.css" type="text/css" media="all" /><!--FOOTNOTEPLUGIN_LINKCSS-->
 <link class='head JQUERYPLUGIN::COMMENT' rel='stylesheet' href='../pub/System/CommentPlugin/commentf5b6.css?version=3.0' type='text/css' media='all' /><!--JQUERYPLUGIN::COMMENT-->
-<link class='head FOOTNOTEPLUGIN_LINKCSS' rel="stylesheet" href="../pub/System/FootNotePlugin/styles.css" type="text/css" media="all" /><!--FOOTNOTEPLUGIN_LINKCSS--><link rel='stylesheet' href='../pub/System/SkinTemplates/base.css' media='all' type='text/css' />
+<link class='head SMILIESPLUGIN' rel='stylesheet' href='../pub/System/SmiliesPlugin/smilies.css' type='text/css' media='all' /><!--SMILIESPLUGIN--><link rel='stylesheet' href='../pub/System/SkinTemplates/base.css' media='all' type='text/css' />
 <style type="text/css" media="all">
 @import url('../pub/System/PatternSkinTheme/layout.css');
 @import url('../pub/System/PatternSkinTheme2009/style.css');
@@ -101,14 +101,14 @@
 
 <!--<![endif]-->
 <!--JQUERYPLUGIN-->
-<!--JQUERYPLUGIN::MIGRATE-->
 <!--JQUERYPLUGIN::LIVEQUERY-->
 <!--JQUERYPLUGIN::FOSWIKI-->
+<!--JQUERYPLUGIN::MIGRATE-->
 <!--JavascriptFiles/foswikiString-->
 <!--JavascriptFiles/foswikiPref-->
+<!--JavascriptFiles/foswikiForm-->
 <!--JQUERYPLUGIN::FOSWIKI::PREFERENCES-->
 <!--JQUERYPLUGIN::COMMENT-->
-<!--JavascriptFiles/foswikiForm-->
 <!--PatternSkin/pattern--><link class='head FOOTNOTEPLUGIN_LINKCSS' rel="stylesheet" href="../pub/System/FootNotePlugin/styles.css" type="text/css" media="all" /><!--FOOTNOTEPLUGIN_LINKCSS-->
 </head> 
 <body class="foswikiNoJs patternViewPage patternPrintPage">
@@ -122,12 +122,12 @@
 <div class="patternContent"><div class="foswikiTopic"> <h1 id="Welcome_to_the_MUSR_web">  Welcome to the MUSR web </h1>
 <p></p>
 <h2 id="Documentation_of_the_SR_data_analysis_suite_61musrfit_61">  Documentation of the &#956;SR data analysis suite <code>musrfit</code> </h2> <ul>
-<li> <a href="CiteMusrFit.html">How to cite <code>musrfit</code>? <img class='smily' src='../pub/Main/SmiliesPluginPSI_/yes.gif' alt='yes' title='yes' /> </a>
+<li> <a href="CiteMusrFit.html">How to cite <code>musrfit</code>? <img class='smily' src='../pub/Main/SmiliesPluginPSI/yes.gif' alt='yes' title='yes' /> </a>
 </li> <li> <a href="TutorialSingleHisto.html">Single-histogram-fit tutorial for <code>musrfit</code> introducing the basic features of the programs and <code>msr</code> files</a> 
 </li> <li> <a href="MusrFit.html">User manual of the &#956;SR data analysis software <code>musrfit</code> </a>
-</li> <li> <a href="MusrFitSetup.html">Setting up <code>musrfit</code> on Different Platforms</a>
+</li> <li> <a href="MusrFitSetup.html">Setting up <code>musrfit</code> on Different Platforms <img src="../pub/System/DocumentGraphics/new.png" alt="NEW" title="NEW" width="30" height="16" /> <strong><span class='foswikiRedFG'>ROOT6!</span></strong></a>
 </li> <li> <a href="QuickStart.html">Quick start page for <code>WKM</code> users</a>
-</li> <li> <a href="MusrGui.html">Documentation of <code>musrgui</code>/<code>musredit</code>&mdash;editors interfacing <code>musrfit</code> </a>
+</li> <li> <a href="MusrGui.html">Documentation of <code>musrgui</code>/<code>musredit</code>&mdash;editors interfacing <code>musrfit</code> <img src="../pub/System/DocumentGraphics/updated.png" alt="UPDATED" title="UPDATED" width="55" height="16" /></a>
 </li> <li> <a href="Msr2Data.html">Documentation of <code>msr2data</code>&mdash;a program for automatically processing multiple musrfit <code>msr</code> files</a>
 </li> <li> <a href="MusrFit.html#Any2Many"><code>any2many</code>&mdash;a universal &#956;SR-file-format converter</a> 
 </li> <li> <a href="MusrRoot.html"><code>MusrRoot</code>: an extensible open file format for &#956;SR</a>
@@ -138,12 +138,12 @@
 </li> <li> <a href="MusrFitAcknowledgements.html">Acknowledgements</a>
 </li></ul> 
 <p></p>
---  <a href="http://www.psi.ch/low-energy-muons/people">AS</a> &amp; (<a href="http://www.fsf.org/register_form?referrer=8369">BMW</a>) - last update Dec 15, 2016</div>
+--  <a href="http://www.psi.ch/low-energy-muons/people">AS</a> &amp; (<a href="http://www.fsf.org/register_form?referrer=8369">BMW</a>) - last update May 14, 2017</div>
 <p></p>
 <p></p>
 </div>
 <div class="patternInfo">This topic: MUSR<span class='foswikiSeparator'>&nbsp;&gt;&nbsp;</span>WebHome <br />
-Topic revision:  <span class='patternRevInfo'>15 Dec 2016, <a href="https://intranet.psi.ch/Main/AndreasSuter">AndreasSuter</a></span></div>
+Topic revision:  <span class='patternRevInfo'>14 May 2017, <a href="https://intranet.psi.ch/Main/AndreasSuter">AndreasSuter</a></span></div>
 </div>
 </div>
 </div>
@@ -161,6 +161,5 @@ Topic revision:  <span class='patternRevInfo'>15 Dec 2016, <a href="https://intr
 
 </body>
 
-<!-- Mirrored from intranet.psi.ch/MUSR/WebHome?cover=print by HTTrack Website Copier/3.x [XR&CO'2010], Fri, 16 Dec 2016 16:01:34 GMT -->
-<!-- Added by HTTrack --><meta http-equiv="content-type" content="text/html;charset=utf-8"><!-- /Added by HTTrack -->
+<!-- Mirrored from intranet.psi.ch/MUSR/WebHome?cover=print by HTTrack Website Copier/3.x [XR&CO'2014], Sun, 14 May 2017 18:09:12 GMT -->
 </html>

doc/html/user/pub/MUSR/MusrGui/musrfit.html

@@ -0,0 +1,2 @@
+Ihr Aufruf ist nicht korrekt. <br>
+Hier geht es zum <a href="https://intranet.psi.ch/">PSI Intranet</a>.

doc/html/user/pub/MUSR/MusrGui/musrmsr2data.html

@@ -0,0 +1,2 @@
+Ihr Aufruf ist nicht korrekt. <br>
+Hier geht es zum <a href="https://intranet.psi.ch/">PSI Intranet</a>.

doc/html/user/pub/MUSR/MusrGui/musrt0.html

@@ -0,0 +1,2 @@
+Ihr Aufruf ist nicht korrekt. <br>
+Hier geht es zum <a href="https://intranet.psi.ch/">PSI Intranet</a>.

doc/musrfit_dox.cfg

@@ -23,7 +23,7 @@ PROJECT_NAME           = musrfit
 # This could be handy for archiving the generated documentation or 
 # if some version control system is used.
 
-PROJECT_NUMBER         = 0.14.0
+PROJECT_NUMBER         = 1.1.0
 
 # The OUTPUT_DIRECTORY tag is used to specify the (relative or absolute) 
 # base path where the generated documentation will be put. 
@@ -462,8 +462,9 @@ WARN_LOGFILE           =
 INPUT                  = musrfit.dox \
                          ../src/include/PFitterFcn.h \
                          ../src/include/PFitter.h \
-                         ../src/include/PFourier.h \
                          ../src/include/PFourierCanvas.h \
+                         ../src/include/PFourierCanvasLinkDef.h \
+                         ../src/include/PFourier.h \
                          ../src/include/PFunctionGrammar.h \
                          ../src/include/PFunction.h \
                          ../src/include/PFunctionHandler.h \
@@ -476,12 +477,14 @@ INPUT                  = musrfit.dox \
                          ../src/include/PMusrT0LinkDef.h \
                          ../src/include/PPrepFourier.h \
                          ../src/include/PRunAsymmetry.h \
+                         ../src/include/PRunAsymmetryRRF.h \
                          ../src/include/PRunBase.h \
                          ../src/include/PRunDataHandler.h \
                          ../src/include/PRunListCollection.h \
                          ../src/include/PRunMuMinus.h \
                          ../src/include/PRunNonMusr.h \
                          ../src/include/PRunSingleHisto.h \
+                         ../src/include/PRunSingleHistoRRF.h \
                          ../src/include/PStartupHandler.h \
                          ../src/include/PStartupHandlerLinkDef.h \
                          ../src/include/PTheory.h \
@@ -490,8 +493,8 @@ INPUT                  = musrfit.dox \
                          ../src/include/PUserFcn.h \
                          ../src/classes/PFitter.cpp \
                          ../src/classes/PFitterFcn.cpp \
-                         ../src/classes/PFourier.cpp \
                          ../src/classes/PFourierCanvas.cpp \
+                         ../src/classes/PFourier.cpp \
                          ../src/classes/PFunction.cpp \
                          ../src/classes/PFunctionHandler.cpp \
 			 ../src/classes/PMsr2Data.cpp \
@@ -501,12 +504,14 @@ INPUT                  = musrfit.dox \
 			 ../src/classes/PMusrT0.cpp \
                          ../src/classes/PPrepFourier.cpp \
                          ../src/classes/PRunAsymmetry.cpp \
+                         ../src/classes/PRunAsymmetryRRF.cpp \
                          ../src/classes/PRunBase.cpp \
                          ../src/classes/PRunDataHandler.cpp \
                          ../src/classes/PRunListCollection.cpp \
                          ../src/classes/PRunMuMinus.cpp \
                          ../src/classes/PRunNonMusr.cpp \
                          ../src/classes/PRunSingleHisto.cpp \
+                         ../src/classes/PRunSingleHistoRRF.cpp \
                          ../src/classes/PStartupHandler.cpp \
                          ../src/classes/PTheory.cpp \
                          ../src/classes/PUserFcnBase.cpp \

doc/templates/asymDefault.msr

@@ -1,59 +0,0 @@
-TITLE
-###############################################################
-FITPARAMETER
-#      Nr. Name        Value     Step      Pos_Error  Boundaries
-         1 alpha       0.989765  1.0       none       0         none      
-         2 asy         0.26      0.1       none       0         0.33     
-         3 phase       8.5       1.0       none
-         4 field       100.0     0.1       none       0         none
-         5 rate        0.36      0.02      none       0         100
-
-###############################################################
-THEORY
-asymmetry     2
-TFieldCos     3  fun1                 (phase frequency)
-simplExpo     5
-
-###############################################################
-FUNCTIONS
-fun1 = par4 * gamma_mu
-
-###############################################################
-RUN lem07_his_0147 MUE4 PSI ROOT-NPP        (name beamline institute data-file-format)
-fittype         2               (asymmetry fit)
-alpha           1
-map             0    0    0    0    0    0    0    0    0    0
-forward         1
-backward        3
-background  65000  66500  65000  66500
-data         3413  63000   3413  63000
-t0           3413   3413
-fit          0.00   8.00          (fw bw)
-packing        75
-
-###############################################################
-COMMANDS
-SET BATCH
-MINIMIZE
-MINOS
-SAVE
-END RETURN
-
-###############################################################
-FOURIER
-units   Gauss  # fourier in field units
-fourier_power 12
-apodization NONE # NONE, WEAK, MEDIUM, STRONG
-plot power
-phase   8.5
-#range_for_phase_correction 50.0 70.0
-range   0.0  200.0
-
-###############################################################
-PLOT 2   (asymmetry plot)
-runs     1
-range    0.00    8.00   -0.30    0.30
-
-###############################################################
-STATISTIC --- 2008-04-04 07:44:31
-  chisq = 569.50931, NDF = 542, chisq/NDF = 1.05075518

doc/templates/singleHistoDefault.msr

@@ -1,60 +0,0 @@
-TITLE
-###############################################################
-FITPARAMETER
-#      Nr. Name       Value     Step      Pos_Error Boundaries   
-        1 Asy         0.26      0.01      none      0       0.33    
-        2 Rate        0.36      0.01      none
-        3 Field       100.0     1.0       none      0       200     
-        4 N0_L        150.0     0.01      none   
-        5 Bkg_L       4.9       0.01      none
-        6 Phase_L     7.0       1.5       none     -50     50      
-
-###############################################################
-THEORY
-asymmetry      1
-simplExpo      2                   (rate)
-TFieldCos   map1  fun1             (phase frequency)
-
-###############################################################
-FUNCTIONS
-fun1 = par3 * gamma_mu
-
-###############################################################
-RUN lem07_his_0111 MUE4 PSI ROOT-NPP   (name beamline institute data-file-format)
-fittype         0         (single histogram fit)
-norm            4
-backgr.fit      5
-lifetimecorrection
-map             6    0    0    0    0    0    0    0    0    0
-forward         1
-data            3413    65000   
-t0              3413    
-fit             0.20    8.2
-packing         50
-
-###############################################################
-COMMANDS
-SET BATCH
-MINIMIZE
-MINOS
-SAVE
-END RETURN
-
-###############################################################
-PLOT 0   (single histo plot)
-runs     1 
-range    0.00   7.00   -0.30   0.30
-
-###############################################################
-FOURIER
-units   Gauss  # fourier in field units
-fourier_power 12
-apodization NONE # NONE, WEAK, MEDIUM, STRONG
-plot power
-phase   8.5
-#range_for_phase_correction 50.0 70.0
-range   0.0  200.0
-
-###############################################################
-STATISTIC --- 2008-06-09 14:09:39
-  chisq = 1446.93547, NDF = 1377, chisq/NDF = 1.05078829

src/Makefile.am

@@ -2,7 +2,7 @@
 
 BUILT_SOURCES = git-revision.h
 git-revision.h : Makefile
-	echo \#define GIT_REVISION \"`git log -n 1 --pretty=format:"%ad - %h"`\" > include/git-revision.h
+	sh git_revision.sh ./include git-revision.h
 
 if PNEXUS_ENABLED
   PNEXUSDIRS = external/nexus
@@ -60,9 +60,6 @@ write_musrRoot_runHeader_SOURCES = write_musrRoot_runHeader.cpp
 musrRootValidation_SOURCES = musrRootValidation.cpp
 dump_header_SOURCES = dump_header.cpp
 
-xmldir = $(HOME)/.musrfit
-xml_DATA = musrfit_startup.xml
-
 LIBADD = $(PMUSR_LIBS) $(MUSR_ROOT_LIBS) $(LEM_LIBS) $(PSIBIN_LIBS) $(MUD_LIBS) $(PNEXUS_LIBS)
 
 AM_CXXFLAGS = $(LOCAL_BIN_CXXFLAGS)
@@ -75,42 +72,3 @@ endif
 
 LIBS = $(PMUSR_LIBS) $(USERFCN_LIBS) $(MUSR_ROOT_LIBS) $(LEM_LIBS) $(PSIBIN_LIBS) $(MUD_LIBS) $(PNEXUS_LIBS) \
        $(FFTW3_LIBS) $(GSL_LIBS) $(ROOT_LIBS) $(LIBXML2_LIBS)
-
-install-xmlDATA: $(xml_DATA)
-	test -z "$(xmldir)" || $(mkdir_p) "$(DESTDIR)$(xmldir)"
-	@if test -e "$(DESTDIR)$(xmldir)/$(xml_DATA)"; then \
-	  DIFF="$$(diff "$(DESTDIR)$(xmldir)/$(xml_DATA)" "$(xml_DATA)" 2>&1)"; \
-	  if test "x$$DIFF" != "x"; then \
-	    echo "   " && \
-	    echo "   musrfit_startup.xml in $(xmldir)" && \
-	    echo "   is different from the distribution's version." && \
-	    echo "   Do you want to overwrite it? [y/N]" && \
-	    read OVERWRITE && \
-	    if test "$$OVERWRITE" = "y" || test "$$OVERWRITE" = "Y"; then \
-	      echo "$(INSTALL_DATA) '$(xml_DATA)' '$(DESTDIR)$(xmldir)'" && \
-	      $(INSTALL_DATA) '$(xml_DATA)' '$(DESTDIR)$(xmldir)'; \
-	    fi; \
-	  fi; \
-	else \
-	  echo "$(INSTALL_DATA) '$(xml_DATA)' '$(DESTDIR)$(xmldir)'" && \
-	  $(INSTALL_DATA) '$(xml_DATA)' '$(DESTDIR)$(xmldir)'; \
-	fi
-
-uninstall-xmlDATA:
-	@if test -e "$(DESTDIR)$(xmldir)/$(xml_DATA)"; then \
-	  DIFF="$$(diff "$(DESTDIR)$(xmldir)/$(xml_DATA)" "$(xml_DATA)" 2>&1)"; \
-	  if test "x$$DIFF" != "x"; then \
-	    echo "   " && \
-	    echo "   musrfit_startup.xml in $(xmldir)" && \
-	    echo "   is different from the distribution's version." && \
-	    echo "   Do you want to remove it? [y/N]" && \
-	    read REMOVE && \
-	    if test "$$REMOVE" = "y" || test "$$REMOVE" = "Y"; then \
-	      echo "$(RM) '$(DESTDIR)$(xmldir)/$(xml_DATA)'" && \
-	      $(RM) "$(DESTDIR)$(xmldir)/$(xml_DATA)"; \
-	    fi; \
-	  else \
-	    echo "$(RM) '$(DESTDIR)$(xmldir)/$(xml_DATA)'" && \
-	    $(RM) "$(DESTDIR)$(xmldir)/$(xml_DATA)"; \
-	  fi; \
-	fi

src/any2many.cpp

@@ -198,9 +198,9 @@ int main(int argc, char *argv[])
       any2many_syntax();
     else if (strstr(argv[1], "--v")) {
 #ifdef HAVE_CONFIG_H
-      cout << endl << "any2many version: " << PACKAGE_VERSION << ", git-rev: " << GIT_REVISION << endl << endl;
+      cout << endl << "any2many version: " << PACKAGE_VERSION << ", git-branch: " << GIT_BRANCH << ", git-rev: " << GIT_CURRENT_SHA1 << endl << endl;
 #else
-      cout << endl << "any2many git-rev: " << GIT_REVISION << endl << endl;
+      cout << endl << "any2many git-branch: " << GIT_BRANCH << ", git-rev: " << GIT_CURRENT_SHA1 << endl << endl;
 #endif
     } else {
       any2many_syntax();

src/classes/Makefile.PMusr

@@ -202,27 +202,27 @@ $(EXTOBJS): ../external/MuSR_software/Class_MuSR_PSI/MuSR_td_PSI_bin.cpp
 
 TLemRunHeaderDict.cxx: ../external/TLemRunHeader/TLemRunHeader.h ../external/TLemRunHeader/TLemRunHeaderLinkDef.h
 	@echo "Generating dictionary $@..."
-	rootcint -f $@ -c -p $^
+	rootcling -f $@ -c -p $^
 
 TLemStatsDict.cxx: ../external/TLemRunHeader/TLemStats.h ../external/TLemRunHeader/TLemStatsLinkDef.h
 	@echo "Generating dictionary $@..."
-	rootcint -f $@ -c -p $^
+	rootcling -f $@ -c -p $^
 
 PStartupHandlerDict.cpp: ../include/PStartupHandler.h ../include/PStartupHandlerLinkDef.h
 	@echo "Generating dictionary $@..."
-	rootcint -f $@ -c -p $^
+	rootcling -f $@ -c -p $^
 
 PMusrCanvasDict.cpp: ../include/PMusrCanvas.h ../include/PMusrCanvasLinkDef.h
 	@echo "Generating dictionary $@..."
-	rootcint -v -f $@ -c -p $^
+	rootcling -v -f $@ -c -p $^
 
 PMusrT0Dict.cpp: ../include/PMusrT0.h ../include/PMusrT0LinkDef.h
 	@echo "Generating dictionary $@..."
-	rootcint -v -f $@ -c -p $^
+	rootcling -v -f $@ -c -p $^
 
 PUserFcnBaseDict.cpp: ../include/PUserFcnBase.h ../include/PUserFcnBaseLinkDef.h
 	@echo "Generating dictionary $@..."
-	rootcint -v -f $@ -c -p $^
+	rootcling -v -f $@ -c -p $^
 
 install: leminstall musrinstall
 

src/classes/Makefile.PUserFcn

@@ -89,7 +89,7 @@ $(OBJS): %.o: %.cpp
 
 PUserFcnDict.cpp: ../include/PUserFcn.h ../include/PUserFcnLinkDef.h
 	@echo "Generating dictionary $@..."
-	rootcint -f $@ -c -p $^
+	rootcling -f $@ -c -p $^
 
 install: all
 	@echo "Installing shared lib: libPUserFcn.so ( you must be root ;-) )"

src/classes/Makefile.am

@@ -84,6 +84,14 @@ dict_cpp_sources = \
 dict_cpp_sources_userFcn = \
   PUserFcnBaseDict.cpp
 
+pcmdir = $(libdir)
+pcm_DATA = \
+  PFourierCanvasDict_rdict.pcm \
+  PMusrCanvasDict_rdict.pcm \
+  PMusrT0Dict_rdict.pcm \
+  PStartupHandlerDict_rdict.pcm \
+  PUserFcnBaseDict_rdict.pcm
+
 include_HEADERS = $(h_sources) $(h_sources_userFcn)
 noinst_HEADERS = $(h_linkdef) $(dict_h_sources) $(h_linkdef_userFcn) $(dict_h_sources_userFcn)
 
@@ -92,10 +100,10 @@ AM_CXXFLAGS = $(LOCAL_LIB_CXXFLAGS)
 
 BUILT_SOURCES = $(dict_cpp_sources) $(dict_h_sources) $(dict_cpp_sources_userFcn) $(dict_h_sources_userFcn)
 AM_LDFLAGS = $(LOCAL_LIB_LDFLAGS) -L@ROOTLIBDIR@
-CLEANFILES = *Dict.cpp *Dict.h *~ core
+CLEANFILES = *Dict.cpp *Dict.h *Dict* *~ core
 
 %Dict.cpp %Dict.h: ../include/%.h ../include/%LinkDef.h
-	@ROOTCINT@ -v -f $*Dict.cpp -c -p $(AM_CPPFLAGS) $^
+	@ROOTCLING@ -v -f $*Dict.cpp -c -p $(AM_CPPFLAGS) $^
 
 lib_LTLIBRARIES = libPUserFcnBase.la libPMusr.la
 

src/classes/PFitter.cpp

@@ -1343,6 +1343,8 @@ Bool_t PFitter::ExecuteMinos()
     // the 2nd condition is from an all together unused variable
     // the 3rd condition is a variable fixed via the FIX command
     if ((fMnUserParams.Error(i) != 0.0) && (fRunInfo->ParameterInUse(i) != 0) && (!fMnUserParams.Parameters().at(i).IsFixed())) {
+      cout << ">> PFitter::ExecuteMinos(): calculate errors for " << fParams[i].fName << endl;
+
       // 1-sigma MINOS errors
       ROOT::Minuit2::MinosError err = minos.Minos(i);
 

src/classes/PFourier.cpp

@@ -507,7 +507,7 @@ TH1F* PFourier::GetPhaseOptRealFourier(const TH1F *re, const TH1F *im, vector<Do
 
   phase.resize(2); // c0, c1
 
-  TAxis *axis = re->GetXaxis();
+  const TAxis *axis = re->GetXaxis();
 
   Int_t minBin = 1;
   Int_t maxBin = axis->GetNbins();

src/classes/PMsrHandler.cpp

@@ -6094,22 +6094,6 @@ Bool_t PMsrHandler::EstimateN0()
   return fStartupOptions->estimateN0;
 }
 
-//--------------------------------------------------------------------------
-// GetAlphaEstimateN0 (public)
-//--------------------------------------------------------------------------
-/**
- * <p>returns alpha to estimate N0
- */
-/*as
-Double_t PMsrHandler::GetAlphaEstimateN0()
-{
-  if (fStartupOptions == 0)
-    return 0.0;
-
-  return fStartupOptions->alphaEstimateN0;
-}
-*/
-
 //--------------------------------------------------------------------------
 // NeededPrecision (private)
 //--------------------------------------------------------------------------

src/classes/PMusrCanvas.cpp

@@ -1582,7 +1582,9 @@ void PMusrCanvas::ExportData(const Char_t *fileName)
 
   switch (fPlotType) {
     case MSR_PLOT_SINGLE_HISTO:
+    case MSR_PLOT_SINGLE_HISTO_RRF:
     case MSR_PLOT_ASYM:
+    case MSR_PLOT_ASYM_RRF:
     case MSR_PLOT_MU_MINUS:
       if (fDifferenceView) { // difference view plot
         switch (fCurrentPlotView) {
@@ -4593,14 +4595,8 @@ void PMusrCanvas::PlotData(Bool_t unzoom)
               dataYmax = GetMaximum(fData[i].data, dataXmin, dataXmax);
           }
           Double_t dd = 0.05*fabs(dataYmax-dataYmin);
-          if (!fMsrHandler->GetMsrPlotList()->at(fPlotNumber).fLogY) {
-            dataYmin -= dd;
-            dataYmax += dd;
-          } else {
-            if (dataYmin < 0)
-              dataYmin = 0.1;
-            dataYmax += dd;
-          }
+          dataYmin -= dd;
+          dataYmax += dd;
         }
       } else { // set the x-/y-range to the previous fHistoFrame range
         dataXmin = xmin;
@@ -4618,16 +4614,13 @@ void PMusrCanvas::PlotData(Bool_t unzoom)
               dataYmax = GetMaximum(fData[i].data, dataXmin, dataXmax);
           }
           Double_t dd = 0.05*fabs(dataYmax-dataYmin);
-          if (!fMsrHandler->GetMsrPlotList()->at(fPlotNumber).fLogY) {
-            dataYmin -= dd;
-            dataYmax += dd;
-          } else {
-            if (dataYmin < 0)
-              dataYmin = 0.1;
-            dataYmax += dd;
-          }
+          dataYmin -= dd;
+          dataYmax += dd;
         }
       }
+      if (fMsrHandler->GetMsrPlotList()->at(fPlotNumber).fLogY) {
+        dataYmin = 1.0e-4 * dataYmax;
+      }
 
       // create histo frame in order to plot histograms possibly with different x-frames
       fHistoFrame = fDataTheoryPad->DrawFrame(dataXmin, dataYmin, dataXmax, dataYmax);
@@ -4749,14 +4742,8 @@ void PMusrCanvas::PlotData(Bool_t unzoom)
               dataYmax = GetMaximum(fNonMusrData[i].data, dataXmin, dataXmax);
           }
           Double_t dd = 0.05*fabs(dataYmax-dataYmin);
-          if (!fMsrHandler->GetMsrPlotList()->at(fPlotNumber).fLogY) {
-            dataYmin -= dd;
-            dataYmax += dd;
-          } else {
-            if (dataYmin < 0)
-              dataYmin = 0.1;
-            dataYmax += dd;
-          }
+          dataYmin -= dd;
+          dataYmax += dd;
         }
       } else { // set the x-/y-range to the previous fHistoFrame range
         dataXmin = xmin;
@@ -4774,16 +4761,14 @@ void PMusrCanvas::PlotData(Bool_t unzoom)
               dataYmax = GetMaximum(fNonMusrData[i].data, dataXmin, dataXmax);
           }
           Double_t dd = 0.05*fabs(dataYmax-dataYmin);
-          if (!fMsrHandler->GetMsrPlotList()->at(fPlotNumber).fLogY) {
-            dataYmin -= dd;
-            dataYmax += dd;
-          } else {
-            if (dataYmin < 0)
-              dataYmin = 0.1;
-            dataYmax += dd;
-          }
+          dataYmin -= dd;
+          dataYmax += dd;
         }
       }
+      if (fMsrHandler->GetMsrPlotList()->at(fPlotNumber).fLogY) {
+        if (dataYmin <= 0.0)
+          dataYmin = 1.0e-4 * dataYmax;
+      }
 
       // create fMultiGraphData, and add all data and theory
       fMultiGraphData = new TMultiGraph();

src/classes/PRunAsymmetry.cpp

@@ -757,8 +757,8 @@ Bool_t PRunAsymmetry::SubtractEstimatedBkg()
     beamPeriod = 0.0;
 
   // check if start and end are in proper order
-  UInt_t start[2] = {fRunInfo->GetBkgRange(0), fRunInfo->GetBkgRange(2)};
-  UInt_t end[2]   = {fRunInfo->GetBkgRange(1), fRunInfo->GetBkgRange(3)};
+  Int_t start[2] = {fRunInfo->GetBkgRange(0), fRunInfo->GetBkgRange(2)};
+  Int_t end[2]   = {fRunInfo->GetBkgRange(1), fRunInfo->GetBkgRange(3)};
   for (UInt_t i=0; i<2; i++) {
     if (end[i] < start[i]) {
       cout << endl << "PRunAsymmetry::SubtractEstimatedBkg(): end = " << end[i] << " > start = " << start[i] << "! Will swap them!";

src/classes/PRunAsymmetryRRF.cpp

@@ -746,8 +746,8 @@ Bool_t PRunAsymmetryRRF::SubtractEstimatedBkg()
     beamPeriod = 0.0;
 
   // check if start and end are in proper order
-  UInt_t start[2] = {fRunInfo->GetBkgRange(0), fRunInfo->GetBkgRange(2)};
-  UInt_t end[2]   = {fRunInfo->GetBkgRange(1), fRunInfo->GetBkgRange(3)};
+  UInt_t start[2] = {(UInt_t)fRunInfo->GetBkgRange(0), (UInt_t)fRunInfo->GetBkgRange(2)};
+  UInt_t end[2]   = {(UInt_t)fRunInfo->GetBkgRange(1), (UInt_t)fRunInfo->GetBkgRange(3)};
   for (UInt_t i=0; i<2; i++) {
     if (end[i] < start[i]) {
       cout << endl << "PRunAsymmetryRRF::SubtractEstimatedBkg(): end = " << end[i] << " > start = " << start[i] << "! Will swap them!";

src/classes/PRunDataHandler.cpp

@@ -6154,7 +6154,7 @@ bool PRunDataHandler::DateToISO8601(string inDate, string &iso8601Date)
     return false;
 
   TString str("");
-  str.Form("%04d-%02d-%02d", 1900+tm.tm_year, tm.tm_mon, tm.tm_mday);
+  str.Form("%04d-%02d-%02d", 1900+tm.tm_year, tm.tm_mon+1, tm.tm_mday);
 
   iso8601Date = str.Data();
 
@@ -6187,7 +6187,7 @@ void PRunDataHandler::SplitTimeDate(TString timeData, TString &time, TString &da
   }
 
   time = TString::Format("%02d:%02d:%02d", tm.tm_hour, tm.tm_min, tm.tm_sec);
-  date = TString::Format("%04d-%02d-%02d", tm.tm_year+1900, tm.tm_mon, tm.tm_mday);
+  date = TString::Format("%04d-%02d-%02d", tm.tm_year+1900, tm.tm_mon+1, tm.tm_mday);
 }
 
 //--------------------------------------------------------------------------

src/classes/PStartupHandler.cpp

@@ -27,6 +27,9 @@
  *   59 Temple Place - Suite 330, Boston, MA  02111-1307, USA.             *
  ***************************************************************************/
 
+#include <sys/types.h>
+#include <sys/stat.h>
+
 #include <cstdlib>
 #include <iostream>
 #include <fstream>
@@ -140,6 +143,23 @@ PStartupHandler::PStartupHandler()
       }
     }
   }
+
+  // if musrfit_startup.xml is still not found, will create a default one
+  if (!fStartupFileFound) {
+    cout << endl << "**INFO** no musrfit_startup.xml file found, will write a default one." << endl;
+    if (!WriteDefaultStartupFile()) {
+      cerr << endl << "**ERROR** couldn't write default musrfit_startup.xml." << endl;
+    } else {
+      home = getenv("HOME");
+      if (home != 0) {
+        sprintf(startup_path_name, "%s/.musrfit/musrfit_startup.xml", home);
+        if (StartupFileExists(startup_path_name)) {
+          fStartupFilePath = TString(startup_path_name);
+          fStartupFileFound = true;
+        }
+      }
+    }
+  }
 }
 
 //--------------------------------------------------------------------------
@@ -566,6 +586,105 @@ Bool_t PStartupHandler::StartupFileExists(Char_t *fln)
   return result;
 }
 
+//--------------------------------------------------------------------------
+// WriteDefaultStartupFile
+//--------------------------------------------------------------------------
+Bool_t PStartupHandler::WriteDefaultStartupFile()
+{
+  // get home
+  Char_t startup_path_name[256];
+  Char_t *home=0;
+  home = getenv("HOME");
+  if (home == 0) {
+    cerr << endl << "**ERROR** couldn't obtain $HOME." << endl;
+    return false;
+  }
+
+  // first check that $HOME/.musrfit exists and if NOT create it
+  struct stat info;
+
+  sprintf(startup_path_name, "%s/.musrfit", home);
+  if (!stat(startup_path_name, &info)) {
+    if (!(info.st_mode & S_IFDIR))
+      return false;
+  } else {
+    if (mkdir(startup_path_name, 0777)) {
+      cerr << endl << "**ERROR** couldn't create '" << startup_path_name << "'" << endl;
+      return false;
+    }
+  }
+
+  // set path-name for musrfit_startup.xml
+  sprintf(startup_path_name, "%s/.musrfit/musrfit_startup.xml", home);
+
+  ofstream fout(startup_path_name, ofstream::out);
+  if (!fout.is_open()) {
+    cerr << endl << "**ERROR** couldn't open '" << startup_path_name << "' for writing." << endl;
+    return false;
+  }
+
+  // write default musrfit_startup.xml
+  fout << "<?xml version=\"1.0\" encoding=\"UTF-8\"?>" << endl;
+  fout << "<musrfit xmlns=\"http://lmu.web.psi.ch/musrfit/user/MUSR/WebHome.html\">" << endl;
+  fout << "    <comment>" << endl;
+  fout << "        Defines default settings for the musrfit package" << endl;
+  fout << "    </comment>" << endl;
+  fout << "    <data_path>/afs/psi.ch/project/nemu/data/his</data_path>" << endl;
+  fout << "    <data_path>/afs/psi.ch/project/nemu/data/wkm</data_path>" << endl;
+  fout << "    <data_path>/afs/psi.ch/project/bulkmusr/data/gps</data_path>" << endl;
+  fout << "    <data_path>/afs/psi.ch/project/bulkmusr/data/dolly</data_path>" << endl;
+  fout << "    <data_path>/afs/psi.ch/project/bulkmusr/data/gpd</data_path>" << endl;
+  fout << "    <data_path>/afs/psi.ch/project/bulkmusr/data/ltf</data_path>" << endl;
+  fout << "    <data_path>/afs/psi.ch/project/bulkmusr/data/alc</data_path>" << endl;
+  fout << "    <data_path>/afs/psi.ch/project/bulkmusr/data/hifi</data_path>" << endl;
+  fout << "    <data_path>/afs/psi.ch/project/bulkmusr/data/lem</data_path>" << endl;
+  fout << "    <fourier_settings>" << endl;
+  fout << "        <units>Gauss</units>" << endl;
+  fout << "        <fourier_power>0</fourier_power>" << endl;
+  fout << "        <apodization>none</apodization>" << endl;
+  fout << "        <plot>real_and_imag</plot>" << endl;
+  fout << "        <phase>0.0</phase>" << endl;
+  fout << "        <phase_increment>1.0</phase_increment>" << endl;
+  fout << "    </fourier_settings>" << endl;
+  fout << "    <root_settings>" << endl;
+  fout << "        <marker_list>" << endl;
+  fout << "            <!-- Root marker numbers -->" << endl;
+  fout << "            <marker>24</marker> <!-- open circle -->" << endl;
+  fout << "            <marker>25</marker> <!-- open square -->" << endl;
+  fout << "            <marker>26</marker> <!-- open triangle -->" << endl;
+  fout << "            <marker>27</marker> <!-- open diamond -->" << endl;
+  fout << "            <marker>28</marker> <!-- open cross -->" << endl;
+  fout << "            <marker>29</marker> <!-- full star -->" << endl;
+  fout << "            <marker>30</marker> <!-- open star -->" << endl;
+  fout << "            <marker>20</marker> <!-- full circle -->" << endl;
+  fout << "            <marker>21</marker> <!-- full square -->" << endl;
+  fout << "            <marker>22</marker> <!-- full triangle -->" << endl;
+  fout << "            <marker>23</marker> <!-- full triangle down -->" << endl;
+  fout << "            <marker>2</marker>  <!-- thin cross -->" << endl;
+  fout << "            <marker>3</marker>  <!-- thin star -->" << endl;
+  fout << "            <marker>5</marker>  <!-- thin x -->" << endl;
+  fout << "        </marker_list>" << endl;
+  fout << "        <color_list>" << endl;
+  fout << "            <!-- Color as RGB coded string -->" << endl;
+  fout << "            <color>0,0,0</color>      <!-- kBlack -->" << endl;
+  fout << "            <color>255,0,0</color>    <!-- kRed -->" << endl;
+  fout << "            <color>0,255,0</color>    <!-- kGreen -->" << endl;
+  fout << "            <color>0,0,255</color>    <!-- kBlue -->" << endl;
+  fout << "            <color>255,0,255</color>  <!-- kMagenta -->" << endl;
+  fout << "            <color>0,255,255</color>  <!-- kCyan -->" << endl;
+  fout << "            <color>153,0,255</color>  <!-- kViolet-3 -->" << endl;
+  fout << "            <color>102,102,51</color> <!-- kYellow-1 -->" << endl;
+  fout << "            <color>51,102,51</color>  <!-- kGreen-1 -->" << endl;
+  fout << "            <color>153,0,0</color>    <!-- kRed+2 -->" << endl;
+  fout << "        </color_list>" << endl;
+  fout << "    </root_settings>" << endl;
+  fout << "</musrfit>" << endl;
+
+  fout.close();
+
+  return true;
+}
+
 // -------------------------------------------------------------------------
 // end
 // -------------------------------------------------------------------------

src/classes/PTheory.cpp

@@ -2687,14 +2687,16 @@ void PTheory::CalculateGaussLFIntegral(const Double_t *val) const
   fLFIntegral.push_back(0.0); // start value of the integral
 
   ft = 0.0;
-  Double_t step = 0.0;
+  Double_t step = 0.0, lastft = 1.0, diff = 0.0;
   do {
     t  += dt;
     step = 0.5*dt*preFactor*(exp(-0.5*pow(Delta * (t-dt), 2.0))*sin(w0*(t-dt))+
                              exp(-0.5*pow(Delta * t, 2.0))*sin(w0*t));
     ft += step;
+    diff = fabs(fabs(lastft)-fabs(ft));
+    lastft = ft;
     fLFIntegral.push_back(ft);
-  } while ((t <= 20.0) && (fabs(step) > 1.0e-10));
+  } while ((t <= 20.0) && (diff > 1.0e-10));
 }
 
 //--------------------------------------------------------------------------
@@ -2760,13 +2762,15 @@ void PTheory::CalculateLorentzLFIntegral(const Double_t *val) const
   ft += 0.5*dt*preFactor*(1.0+sin(w0*t)/(w0*t)*exp(-a*t));
   fLFIntegral.push_back(ft);
   // calculate all the other integral bin values
-  Double_t step = 0.0;
+  Double_t step = 0.0, lastft = 1.0, diff = 0.0;
   do {
     t  += dt;
     step = 0.5*dt*preFactor*(sin(w0*(t-dt))/(w0*(t-dt))*exp(-a*(t-dt))+sin(w0*t)/(w0*t)*exp(-a*t));
     ft += step;
+    diff = fabs(fabs(lastft)-fabs(ft));
+    lastft = ft;
     fLFIntegral.push_back(ft);
-  } while ((t <= 20.0) && (fabs(step) > 1.0e-10));
+  } while ((t <= 20.0) && (diff > 1.0e-10));
 }
 
 
@@ -2788,7 +2792,7 @@ Double_t PTheory::GetLFIntegralValue(const Double_t t) const
   if (idx + 2 > fLFIntegral.size())
     return fLFIntegral.back();
 
-  // linearly interpolate between the two relvant function bins
+  // linearly interpolate between the two relevant function bins
   Double_t df = (fLFIntegral[idx+1]-fLFIntegral[idx])*(t/fSamplingTime-static_cast<Double_t>(idx));
 
   return fLFIntegral[idx]+df;

src/dump_header.cpp

@@ -762,9 +762,9 @@ int main(int argc, char *argv[])
       return 0;
     } else if (!strcmp(argv[i], "--version") || !strcmp(argv[i], "-v")) {
 #ifdef HAVE_CONFIG_H
-      cout << endl << "dump_header: version " << PACKAGE_VERSION << ", git-rev: " << GIT_REVISION << endl << endl;
+      cout << endl << "dump_header version: " << PACKAGE_VERSION << ", git-branch: " << GIT_BRANCH << ", git-rev: " << GIT_CURRENT_SHA1 << endl << endl;
 #else
-      cout << endl << "dump_header: git-rev: " << GIT_REVISION << endl << endl;
+      cout << endl << "dump_header git-branch: " << GIT_BRANCH << ", git-rev: " << GIT_CURRENT_SHA1 << endl << endl;
 #endif
       return 0;
     } else if (!strcmp(argv[i], "-rn") || !strcmp(argv[i], "--runNo")) {
@@ -929,13 +929,20 @@ int main(int argc, char *argv[])
   }
 
   bool found_fln = false;
-  // 1st check if the file name is found in the current directory
   string pathFln("");
-  pathFln = "./" + fileName;
+  // 1st check if the file name is the full path-file name and the file exists
+  pathFln = fileName;
   if (dump_file_exists(pathFln))
     found_fln = true;
 
-  // 2nd check if file name is found in any default search paths if not already found in the current directory
+  // 2nd check if the file name is found in the current directory
+  if (!found_fln) {
+    pathFln = "./" + fileName;
+    if (dump_file_exists(pathFln))
+      found_fln = true;
+  }
+
+  // 3rd check if file name is found in any default search paths if not already found in the current directory
   if (!found_fln) {
     PStringVector pathList = startupHandler->GetDataPathList();
     for (unsigned int i=0; i<pathList.size(); i++) {

src/external/BMWtools/BMWStartupHandlerLinkDef.h

@@ -4,8 +4,6 @@
 
   Author: Bastian M. Wojek
 
-  $Id$
-
 ***************************************************************************/
 
 /***************************************************************************

src/external/BMWtools/Makefile.am

@@ -19,6 +19,9 @@ cpp_sources = \
 dict_cpp_sources = \
   BMWStartupHandlerDict.cpp
 
+pcmdir = $(libdir)
+pcm_DATA = BMWStartupHandlerDict_rdict.pcm
+
 include_HEADERS = $(h_sources)
 noinst_HEADERS = $(h_linkdef) $(dict_h_sources)
 
@@ -27,10 +30,10 @@ AM_CXXFLAGS = $(LOCAL_LIB_CXXFLAGS)
 
 BUILT_SOURCES = $(dict_cpp_sources) $(dict_h_sources)
 AM_LDFLAGS = $(LOCAL_LIB_LDFLAGS) -L@ROOTLIBDIR@
-CLEANFILES = *Dict.cpp *Dict.h *~ core
+CLEANFILES = *Dict.cpp *Dict.h *Dict* *~ core
 
 %Dict.cpp %Dict.h: %.h %LinkDef.h
-	@ROOTCINT@ -v -f $*Dict.cpp -c -p $(INCLUDES) $^
+	@ROOTCLING@ -v -f $*Dict.cpp -c -p $(INCLUDES) $^
 
 lib_LTLIBRARIES = libBMWtools.la
 

src/external/MagProximity/Makefile.am

@@ -23,6 +23,11 @@ dict_cpp_sources = \
   PMagProximityFitterDict.cpp \
   PMPStartupHandlerDict.cpp
 
+pcmdir = $(libdir)
+pcm_DATA = \
+  PMagProximityFitterDict_rdict.pcm \
+  PMPStartupHandlerDict_rdict.pcm
+
 include_HEADERS = $(h_sources)
 noinst_HEADERS = $(h_linkdef) $(dict_h_sources)
 
@@ -31,10 +36,10 @@ AM_CXXFLAGS = $(LOCAL_LIB_CXXFLAGS)
 
 BUILT_SOURCES = $(dict_cpp_sources) $(dict_h_sources)
 AM_LDFLAGS = $(LOCAL_LIB_LDFLAGS) -L@ROOTLIBDIR@
-CLEANFILES = *Dict.cpp *Dict.h *~ core
+CLEANFILES = *Dict.cpp *Dict.h *Dict* *~ core
 
 %Dict.cpp %Dict.h: %.h %LinkDef.h
-	@ROOTCINT@ -v -f $*Dict.cpp -c -p $(AM_CPPFLAGS) $^
+	@ROOTCLING@ -v -f $*Dict.cpp -c -p $(AM_CPPFLAGS) $^
 
 lib_LTLIBRARIES = libPMagProximityFitter.la
 

src/external/MuSRFitGUI/MuSRFit4.pl

@@ -0,0 +1,17 @@
+#!/usr/bin/perl
+
+use strict;
+use warnings;
+
+use QtCore4;
+use QtGui4;
+use MuSRFit4;
+
+sub main {
+    my $app = Qt::Application(\@ARGV);
+    my $musrfit = MuSRFit4();
+    $musrfit->show();
+    exit $app->exec();
+}
+
+main();

src/external/MuSR_software/Class_MuSR_PSI/Makefile.am

@@ -1,5 +1,4 @@
 ## Process this file with automake to create Makefile.in
-## $Id$
 
 h_sources = MuSR_td_PSI_bin.h
 cpp_sources = MuSR_td_PSI_bin.cpp 

src/external/MuSR_software/Class_MuSR_PSI/MuSR_td_PSI_bin.cpp

@@ -205,7 +205,7 @@ typedef            long int      Int32;
 #else /* other operating system */
 
 /* 32 bit word length */
-#if (defined(_WIN32) || defined(__linux__) || defined(_WIN32GCC))
+#if (defined(_WIN32) || defined(__linux__) || defined(_Darwin_) || defined(_WIN32GCC))
 typedef                 short    Int16;
 typedef                 int      Int32;
 #else

src/external/MusrRoot/Makefile.am

@@ -15,6 +15,9 @@ cpp_sources = \
 dict_cpp_sources = \
   TMusrRunHeaderDict.cpp 
 
+pcmdir = $(libdir)
+pcm_DATA = TMusrRunHeaderDict_rdict.pcm
+
 include_HEADERS = $(h_sources)
 noinst_HEADERS = $(h_linkdef) $(dict_h_sources)
 
@@ -23,10 +26,10 @@ AM_CXXFLAGS = $(LOCAL_LIB_CXXFLAGS)
 
 BUILT_SOURCES = $(dict_cpp_sources) $(dist_h_sources)
 AM_LDFLAGS = $(LOCAL_LIB_LDFLAGS) -L@ROOTLIBDIR@
-CLEANFILES = *Dict.cpp *Dict.h *~ core
+CLEANFILES = *Dict.cpp *Dict.h *Dict* *~ core
 
 %Dict.cpp %Dict.h: %.h %LinkDef.h
-	@ROOTCINT@ -v -f $*Dict.cpp -c -p $(INCLUDES) $^
+	@ROOTCLING@ -v -f $*Dict.cpp -c -p $(INCLUDES) $^
 
 lib_LTLIBRARIES = libTMusrRunHeader.la
 

src/external/Nonlocal/Makefile.am

@@ -23,6 +23,11 @@ dict_cpp_sources = \
   PNL_PippardFitterDict.cpp \
   PNL_StartupHandlerDict.cpp
 
+pcmdir = $(libdir)
+pcm_DATA = \
+  PNL_PippardFitterDict_rdict.pcm \
+  PNL_StartupHandlerDict_rdict.pcm
+
 include_HEADERS = $(h_sources)
 noinst_HEADERS = $(h_linkdef) $(dict_h_sources)
 
@@ -31,10 +36,10 @@ AM_CXXFLAGS = $(LOCAL_LIB_CXXFLAGS)
 
 BUILT_SOURCES = $(dict_cpp_sources) $(dict_h_sources)
 AM_LDFLAGS = $(LOCAL_LIB_LDFLAGS) -L@ROOTLIBDIR@
-CLEANFILES = *Dict.cpp *Dict.h *~ core
+CLEANFILES = *Dict.cpp *Dict.h *Dict* *~ core
 
 %Dict.cpp %Dict.h: %.h %LinkDef.h
-	@ROOTCINT@ -v -f $*Dict.cpp -c -p $(AM_CPPFLAGS) $^
+	@ROOTCLING@ -v -f $*Dict.cpp -c -p $(AM_CPPFLAGS) $^
 
 lib_LTLIBRARIES = libPNL_PippardFitter.la
 
@@ -63,12 +68,3 @@ uninstall-hook:
 	rm -f $(libdir)/libPNL_PippardFitter.so
 endif
 
-xmldir = $(HOME)/.musrfit/external
-xml_DATA = nonlocal_startup.xml
-
-install-xml_DATA: $(xml_DATA)
-	$(INSTALL_DATA) '$(xml_DATA)' '$xmldir'
-
-uninstall-xml_DATA: $(xml_DATA)
-	$(RM) '$(xml_DATA)' '$xmldir'
-

src/external/Nonlocal/PNL_PippardFitter.h

@@ -31,9 +31,9 @@
 #define _PNL_PIPPARDFITTER_H_
 
 // the following ifdef is needed for GCC 4.6 or higher, fftw 3.3 or higher and root 5.30.03 or lower
-#ifdef __CINT__
-typedef struct { char a[7]; } __float128; // needed since cint doesn't know it
-#endif
+//#ifdef __CINT__
+//typedef struct { char a[7]; } __float128; // needed since cint doesn't know it
+//#endif
 #include <fftw3.h>
 
 #include "PUserFcnBase.h"

src/external/Nonlocal/PNL_StartupHandlerLinkDef.h

@@ -5,8 +5,6 @@
   Author: Andreas Suter
   e-mail: andreas.suter@psi.ch
 
-  $Id$
-
 ***************************************************************************/
 
 /***************************************************************************

src/external/TLemRunHeader/Makefile.am

@@ -20,6 +20,11 @@ dict_cpp_sources = \
   TLemStatsDict.cxx \
   TLemRunHeaderDict.cxx
 
+pcmdir = $(libdir)
+pcm_DATA = \
+  TLemStatsDict_rdict.pcm \
+  TLemRunHeaderDict_rdict.pcm
+
 include_HEADERS = $(h_sources)
 noinst_HEADERS = $(h_linkdef) $(dict_h_sources)
 
@@ -28,10 +33,10 @@ AM_CXXFLAGS = $(LOCAL_LIB_CXXFLAGS)
 
 BUILT_SOURCES = $(dict_cpp_sources) $(dist_h_sources)
 AM_LDFLAGS = $(LOCAL_LIB_LDFLAGS) -L@ROOTLIBDIR@
-CLEANFILES = *Dict.cxx *Dict.h *~ core
+CLEANFILES = *Dict.cxx *Dict.h *Dict* *~ core
 
 %Dict.cxx %Dict.h: %.h %LinkDef.h
-	@ROOTCINT@ -v -f $*Dict.cxx -c -p $(INCLUDES) $^
+	@ROOTCLING@ -v -f $*Dict.cxx -c -p $(INCLUDES) $^
 
 lib_LTLIBRARIES = libTLemRunHeader.la
 

src/external/libBNMR/Makefile.am

@@ -26,7 +26,7 @@ AM_LDFLAGS = $(LOCAL_LIB_LDFLAGS) -L@ROOTLIBDIR@
 CLEANFILES = *Dict.cpp *Dict.h *~ core
 
 %Dict.cpp %Dict.h: %.h %LinkDef.h
-	@ROOTCINT@ -v -f $*Dict.cpp -c -p $(AM_CPPFLAGS) $^
+	@ROOTCLING@ -v -f $*Dict.cpp -c -p $(AM_CPPFLAGS) $^
 
 lib_LTLIBRARIES = libBNMR.la
 

src/external/libBNMR/Makefile.libBNMR

@@ -46,11 +46,11 @@ clean:; 	@rm -f $(OBJS) *Dict* core*
 $(OBJS): %.o: %.cpp
 	$(CXX) $(INCLUDES) $(CXXFLAGS) -c $<
 
-# Generate the ROOT CINT dictionary
+# Generate the ROOT CLING dictionary
 
 TlibBNMRDict.cpp: TBNMR.h TBNMRLinkDef.h
 	@echo "Generating dictionary $@..."
-	rootcint -f $@ -c -p -I$(ROOTINCLUDE) $^
+	rootcling -f $@ -c -p -I$(ROOTINCLUDE) $^
 
 install: all
 	@echo "Installing shared lib: libTApproximation.so"

src/external/libCalcMeanFieldsLEM/Makefile.am

@@ -15,6 +15,9 @@ cpp_sources = \
 dict_cpp_sources = \
   TCalcMeanFieldsLEMDict.cpp
 
+pcmdir = $(libdir)
+pcm_DATA = TCalcMeanFieldsLEMDict_rdict.pcm
+
 include_HEADERS = $(h_sources)
 noinst_HEADERS = $(h_linkdef) $(dict_h_sources)
 
@@ -23,10 +26,10 @@ AM_CXXFLAGS = $(LOCAL_LIB_CXXFLAGS)
 
 BUILT_SOURCES = $(dict_cpp_sources) $(dict_h_sources)
 AM_LDFLAGS = $(LOCAL_LIB_LDFLAGS) -L@ROOTLIBDIR@
-CLEANFILES = *Dict.cpp *Dict.h *~ core
+CLEANFILES = *Dict.cpp *Dict.h *Dict* *~ core
 
 %Dict.cpp %Dict.h: %.h %LinkDef.h
-	@ROOTCINT@ -v -f $*Dict.cpp -c -p $(AM_CPPFLAGS) $^
+	@ROOTCLING@ -v -f $*Dict.cpp -c -p $(AM_CPPFLAGS) $^
 
 lib_LTLIBRARIES = libCalcMeanFieldsLEM.la
 

src/external/libFitPofB/classes/Makefile.am

@@ -33,6 +33,12 @@ dict_cpp_sources = \
   TSkewedGssDict.cpp \
   TVortexDict.cpp
 
+pcmdir = $(libdir)
+pcm_DATA = \
+  TLondon1DDict_rdict.pcm \
+  TSkewedGssDict_rdict.pcm \
+  TVortexDict_rdict.pcm
+
 include_HEADERS = $(h_sources)
 noinst_HEADERS = $(h_linkdef) $(dict_h_sources)
 
@@ -41,10 +47,10 @@ AM_CXXFLAGS = $(LOCAL_LIB_CXXFLAGS)
 
 BUILT_SOURCES = $(dict_cpp_sources) $(dict_h_sources)
 AM_LDFLAGS = $(LOCAL_LIB_LDFLAGS) -L@ROOTLIBDIR@
-CLEANFILES = *Dict.cpp *Dict.h *~ ../include/*~ core
+CLEANFILES = *Dict.cpp *Dict.h *Dict* *~ ../include/*~ core
 
 %Dict.cpp %Dict.h: ../include/%.h ../include/%LinkDef.h
-	@ROOTCINT@ -v -f $*Dict.cpp -c -p $(AM_CPPFLAGS) $^
+	@ROOTCLING@ -v -f $*Dict.cpp -c -p $(AM_CPPFLAGS) $^
 
 lib_LTLIBRARIES = libFitPofB.la
 

src/external/libFitPofB/include/TBulkTriVortexFieldCalc.h

@@ -34,9 +34,9 @@
 using namespace std;
 
 // the following ifdef is needed for GCC 4.6 or higher, fftw 3.3 or higher and root 5.30.03 or lower
-#ifdef __CINT__
-typedef struct { char a[7]; } __float128; // needed since cint doesn't know it
-#endif
+//#ifdef __CINT__
+//typedef struct { char a[7]; } __float128; // needed since cint doesn't know it
+//#endif
 #include "fftw3.h"
 
 /**

src/external/libFitPofB/include/TFilmTriVortexFieldCalc.h

@@ -35,9 +35,9 @@
 using namespace std;
 
 // the following ifdef is needed for GCC 4.6 or higher, fftw 3.3 or higher and root 5.30.03 or lower
-#ifdef __CINT__
-typedef struct { char a[7]; } __float128; // needed since cint doesn't know it
-#endif
+//#ifdef __CINT__
+//typedef struct { char a[7]; } __float128; // needed since cint doesn't know it
+//#endif
 #include "fftw3.h"
 
 //--------------------

src/external/libFitPofB/include/TPofTCalc.h

@@ -32,9 +32,9 @@
 #include "TPofBCalc.h"
 
 // the following ifdef is needed for GCC 4.6 or higher, fftw 3.3 or higher and root 5.30.03 or lower
-#ifdef __CINT__
-typedef struct { char a[7]; } __float128; // needed since cint doesn't know it
-#endif
+//#ifdef __CINT__
+//typedef struct { char a[7]; } __float128; // needed since cint doesn't know it
+//#endif
 #include "fftw3.h"
 #include <string>
 

src/external/libGapIntegrals/Makefile.am

@@ -15,6 +15,9 @@ cpp_sources = \
 dict_cpp_sources = \
   TGapIntegralsDict.cpp
 
+pcmdir = $(libdir)
+pcm_DATA = TGapIntegralsDict_rdict.pcm
+
 include_HEADERS = $(h_sources)
 noinst_HEADERS = $(h_linkdef) $(dict_h_sources)
 
@@ -23,10 +26,10 @@ AM_CXXFLAGS = $(LOCAL_LIB_CXXFLAGS)
 
 BUILT_SOURCES = $(dict_cpp_sources) $(dict_h_sources)
 AM_LDFLAGS = $(LOCAL_LIB_LDFLAGS) -L@ROOTLIBDIR@
-CLEANFILES = *Dict.cpp *Dict.h *~ core
+CLEANFILES = *Dict.cpp *Dict.h *Dict* *~ core
 
 %Dict.cpp %Dict.h: %.h %LinkDef.h
-	@ROOTCINT@ -v -f $*Dict.cpp -c -p $(AM_CPPFLAGS) $^
+	@ROOTCLING@ -v -f $*Dict.cpp -c -p $(AM_CPPFLAGS) $^
 
 lib_LTLIBRARIES = libGapIntegrals.la
 

src/external/libGbGLF/Makefile.am

@@ -26,7 +26,7 @@ AM_LDFLAGS = $(LOCAL_LIB_LDFLAGS) -L@ROOTLIBDIR@
 CLEANFILES = *Dict.cpp *Dict.h *~ core
 
 %Dict.cpp %Dict.h: %.h %LinkDef.h
-	@ROOTCINT@ -v -f $*Dict.cpp -c -p $(AM_CPPFLAGS) $^
+	@ROOTCLING@ -v -f $*Dict.cpp -c -p $(AM_CPPFLAGS) $^
 
 lib_LTLIBRARIES = libGbGLF.la