update of the docu.

added missing icons

CMakeLists.txt

@@ -0,0 +1,314 @@
+# - musrfit 
+cmake_minimum_required(VERSION 3.6)
+
+project(musrfit VERSION 1.3.0 LANGUAGES C CXX)
+
+#--- musrfit specific options -------------------------------------------------
+option(nexus "build optional NeXus support. Needed for ISIS" OFF)
+option(ASlibs "build optional ASlibs" OFF)
+option(BMWlibs "build optional BMWlibs" OFF)
+option(BNMRlibs "build optional beta-NMR libs" OFF)
+option(qt_based_tools "try to install Qt based tools (musredit, musrWiz, musrStep, mupp)" ON)
+option(try_OpenMP "try to use OpenMP if available" ON)
+# define qt_version with possible values 'auto' or version '3', '4', '5'
+set(qt_version AUTO CACHE STRING "provide a specific Qt version to be used.")
+set_property(CACHE qt_version PROPERTY STRINGS AUTO 3 4 5)
+
+#--- set a default build type if none was specified ---------------------------
+set(default_build_type "Release")
+ 
+if(NOT CMAKE_BUILD_TYPE AND NOT CMAKE_CONFIGURATION_TYPES)
+  message(STATUS "Setting build type to '${default_build_type}' as none was specified.")
+  set(CMAKE_BUILD_TYPE "${default_build_type}" CACHE
+      STRING "Choose the type of build." FORCE)
+  # Set the possible values of build type for cmake-gui
+  set_property(CACHE CMAKE_BUILD_TYPE PROPERTY STRINGS
+    "Debug" "Release" "MinSizeRel" "RelWithDebInfo")
+endif()
+
+#--- perform some checks and generate the config.h ----------------------------
+include(CheckTypeSize)
+include(CheckIncludeFiles)
+include(CheckFunctionExists)
+check_include_files(alloca.h HAVE_ALLOCA_H)
+check_include_files("sys/ipc.h;sys/shm.h" HAVE_SHMGET)
+check_function_exists(fork HAVE_FORK)
+check_include_files(dlfcn.h HAVE_DLFCN_H)
+check_function_exists(erf HAVE_ERF)
+check_function_exists(getloadavg HAVE_GETLOADAVG)
+check_include_files(inttypes.h HAVE_INTTYPES_H)
+check_include_files(memory.h HAVE_MEMORY_H)
+check_function_exists(powl HAVE_POWL)
+check_include_files(memory.h HAVE_MEMORY_H)
+check_include_files(stdint.h HAVE_STDINT_H)
+check_include_files(stdlib.h HAVE_STDLIB_H)
+check_include_files(string.h HAVE_STRING_H)
+check_include_files(strings.h HAVE_STRINGS_H)
+check_include_files(sys/stat.h HAVE_SYS_STAT_H)
+check_include_files(sys/types.h HAVE_SYS_TYPES_H)
+check_include_files(sys/unistd.h HAVE_UNISTD_H)
+check_type_size("long double" LONG_DOUBLE)
+check_type_size("double" DOUBLE)
+if (${LONG_DOUBLE} GREATER ${DOUBLE})
+  set(HAVE_LONG_DOUBLE 1)
+  set(HAVE_LONG_DOUBLE_WIDER 1)
+endif (${LONG_DOUBLE} GREATER ${DOUBLE})
+
+#--- check for all the needed packages ----------------------------------------
+
+#--- add path to my own find modules and other stuff
+set(CMAKE_MODULE_PATH ${CMAKE_CURRENT_SOURCE_DIR}/cmake)
+
+#--- check for git ------------------------------------------------------------
+find_package(Git REQUIRED)
+
+#--- check for ROOT -----------------------------------------------------------
+find_package(ROOT 6.06 REQUIRED COMPONENTS Gui MathMore Minuit2 XMLParser)
+if (ROOT_mathmore_FOUND)
+  execute_process(COMMAND root-config --bindir OUTPUT_VARIABLE ROOT_BINDIR)
+  string(STRIP ${ROOT_BINDIR} ROOT_BINDIR)
+  execute_process(COMMAND root-config --version OUTPUT_VARIABLE ROOT_VERSION)
+  string(STRIP ${ROOT_VERSION} ROOT_VERSION)
+  message("-- Found ROOT: ${ROOT_BINDIR} (found version: ${ROOT_VERSION})")
+  #---Define useful ROOT functions and macros (e.g. ROOT_GENERATE_DICTIONARY)
+  include(${ROOT_USE_FILE})
+endif (ROOT_mathmore_FOUND)
+
+#--- check for boost ----------------------------------------------------------
+find_package(Boost REQUIRED)
+
+#--- check for gsl ------------------------------------------------------------
+find_package(GSL REQUIRED)
+
+#--- check for fftw3 ----------------------------------------------------------
+find_package(FFTW3 REQUIRED)
+if (FFTW3_THREAD_FOUND)
+  set(HAVE_LIBFFTW3_THREADS 1 CACHE INTERNAL "fftw3_threads are available")
+endif (FFTW3_THREAD_FOUND)
+if (FFTW3F_THREAD_FOUND)
+  set(HAVE_LIBFFTW3F_THREADS 1 CACHE INTERNAL "fftw3f_threads are available")
+endif (FFTW3F_THREAD_FOUND)
+
+#--- check for libxml2 --------------------------------------------------------
+find_package(LibXml2 REQUIRED)
+
+#--- check for OpenMP ---------------------------------------------------------
+if (try_OpenMP AND NOT APPLE)
+  find_package(OpenMP)
+  if (OpenMP_FOUND)
+    add_definitions(-DHAVE_GOMP)
+    set(HAVE_GOMP 1 CACHE INTERNAL "Have GOMP")
+  endif (OpenMP_FOUND)
+endif (try_OpenMP AND NOT APPLE)
+
+#--- check for Qt -------------------------------------------------------------
+if (qt_based_tools)
+  # check for any Qt, i.e. AUTO
+  if (qt_version STREQUAL AUTO)
+    # first try Qt5
+    # Find the QtCore library
+    find_package(Qt5Core)
+    if (Qt5Core_FOUND)
+      # Find the QtWidgets library
+      find_package(Qt5Widgets CONFIG REQUIRED)
+      # Find the QtXml library
+      find_package(Qt5Xml CONFIG REQUIRED)
+      # Find the QtNetwork library
+      find_package(Qt5Network CONFIG REQUIRED)
+      # Find the QtSvg library
+      find_package(Qt5Svg CONFIG REQUIRED)
+      # Fing the QtPrintSupport
+      find_package(Qt5PrintSupport CONFIG REQUIRED)
+    endif (Qt5Core_FOUND)
+
+    # if Qt5 is not found, try Qt4
+    if (NOT Qt5Core_FOUND)
+      find_package(Qt4 COMPONENTS QtGui QtWebKit QtXml)
+    endif (NOT Qt5Core_FOUND)
+
+    # if Qt5 and Qt4 is not found try Qt3. Hopefully you never reach this point
+    if (NOT Qt5Core_FOUND)
+      if (NOT Qt4_FOUND)
+        find_package(Qt3)
+      endif (NOT Qt4_FOUND)
+    endif (NOT Qt5Core_FOUND)
+  endif (qt_version STREQUAL AUTO)
+
+  # check specifically for Qt5
+  if (qt_version STREQUAL 5)
+    # Find the QtCore library
+    find_package(Qt5Core)
+    if (Qt5Core_FOUND)
+      # Find the QtWidgets library
+      find_package(Qt5Widgets CONFIG REQUIRED)
+      # Find the QtXml library
+      find_package(Qt5Xml CONFIG REQUIRED)
+      # Find the QtNetwork library
+      find_package(Qt5Network CONFIG REQUIRED)
+      # Find the QtSvg library
+      find_package(Qt5Svg CONFIG REQUIRED)
+      # Fing the QtPrintSupport
+      find_package(Qt5PrintSupport CONFIG REQUIRED)
+    else (Qt5Core_FOUND)
+      message(FATAL_ERROR "Couldn't find the specifically requested Qt5 version.")
+    endif (Qt5Core_FOUND)
+  endif (qt_version STREQUAL 5)
+
+  # check specifically for Qt4
+  if (qt_version STREQUAL 4)
+    find_package(Qt4 COMPONENTS QtGui QtWebKit QtXml)
+    if (NOT Qt4_FOUND)
+      message(FATAL_ERROR "Couldn't find the specifically requested Qt4 version.")
+    endif (NOT Qt4_FOUND)
+  endif (qt_version STREQUAL 4)
+
+  # check specifically for Qt3
+  if (qt_version STREQUAL 3)
+    find_package(Qt3)
+    if (NOT QT_FOUND)
+      message(FATAL_ERROR "Couldn't find the specifically requested Qt3 version.")
+    endif (NOT QT_FOUND)
+  endif (qt_version STREQUAL 3)
+endif (qt_based_tools)
+
+#--- if NeXus check also for HDF4, HDF5, and MXML -----------------------------
+if (nexus)
+  find_package(HDF5 COMPONENTS CXX REQUIRED )
+#//as35 - STILL NEEDED?? -> find_package(HDF4 REQUIRED)
+  find_package(MXML REQUIRED)
+  find_package(NeXus REQUIRED)
+  add_definitions(-DPNEXUS_ENABLED)
+endif (nexus)
+
+#--- check for Cuba lib if BMWlibs are enabled --------------------------------
+#//as35 probably always stick to the internal one ...
+
+#--- all checks done -> feed config.h -----------------------------------------
+set(HAVE_CONFIG_H 1 CACHE INTERNAL "config.h is available")
+configure_file(${CMAKE_SOURCE_DIR}/cmake/config.h.in ${CMAKE_CURRENT_BINARY_DIR}/config.h)
+
+#--- propagate to the sub-directories -----------------------------------------
+add_subdirectory(src)
+
+#--- write summary of the installation 
+message("")
+message("|-----------------------------------------------------------------------|")
+message("|                                                                       |")
+message("|                            Summary                                    |")
+message("|                                                                       |")
+message("|-----------------------------------------------------------------------|")
+message("")
+message(" System: ${CMAKE_HOST_SYSTEM_NAME} ${CMAKE_SYSTEM_PROCESSOR} - ${CMAKE_HOST_SYSTEM_VERSION}")
+message(" -------")
+message("")
+message(" Build Type: ${CMAKE_BUILD_TYPE}")
+message(" -----------")
+message("")
+message(" Requirements:")
+message(" -------------")
+message("")
+message(" FFTW3   found in ${FFTW3_INCLUDE_DIR}")
+message(" GSL     found in ${GSL_INCLUDE_DIRS}")
+message(" BOOST   found in ${Boost_INCLUDE_DIRS}")
+message(" LibXML2 found in ${LIBXML2_INCLUDE_DIR}")
+message(" ROOT    found in ${ROOT_INCLUDE_DIRS}")
+if (OpenMP_FOUND)
+  if (OpenMP_CXX_VERSION)
+    message(" OpenMP  found (version ${OpenMP_CXX_VERSION})")
+  else (OpenMP_CXX_VERSION)
+    message(" OpenMP  found")
+  endif (OpenMP_CXX_VERSION)
+endif (OpenMP_FOUND)
+
+if (nexus)
+  message("")
+#//as35  message(" HDF4   found in ${HDF4_INCLUDE_DIRS}")
+  message(" HDF5    found in ${HDF5_INCLUDE_DIRS}")
+  message(" NeXus   found in ${NEXUS_INCLUDE_DIR}") 
+endif (nexus)
+
+message("")
+if (qt_based_tools)
+  if (Qt5Core_FOUND)
+    message(" Qt      found in  ${Qt5Core_INCLUDE_DIRS} (Version: ${Qt5Core_VERSION})")
+  else (Qt5Core_FOUND)
+    if (Qt4_FOUND)
+      message(" Qt      found (Version: ${QT_VERSION_MAJOR}.${QT_VERSION_MINOR}.${QT_VERSION_PATCH})")
+    else (Qt4_FOUND)
+      if (QT_FOUND)
+        message(" Qt      found (Version: ${QT_VERSION})")
+      endif (QT_FOUND)
+    endif (Qt4_FOUND)
+  endif (Qt5Core_FOUND)
+endif (qt_based_tools)
+message("")
+message(" Features:")
+message(" ---------")
+message("")
+message(" Supported muSR file formates:")
+message("   MusrRoot                           : yes")
+message("   ROOT (LEM)                         : yes")
+message("   MUD (triumf)                       : yes")
+message("   PSI-BIN                            : yes")
+message("   PSI-MDU                            : yes")
+message("   WKM (deprecated)                   : yes")
+if (nexus)
+  message("   NeXus                              : yes")
+else (nexus)
+  message("   NeXus                              : no")
+endif (nexus)
+
+message("")
+message(" External user-function libraries:")
+if (ASlibs)
+  message("   ASlibs                             : yes")
+else (ASlibs)
+  message("   ASlibs                             : no")
+endif (ASlibs)
+if (BMWlibs)
+  message("   BMWlibs                            : yes")
+else (BMWlibs)
+  message("   BMWlibs                            : no")
+endif (BMWlibs)
+if (BNMRlibs)
+  message("   BNMRlibs                           : yes")
+else (BNMRlibs)
+  message("   BNMRlibs                           : no")
+endif (BNMRlibs)
+
+if (qt_based_tools)
+if (Qt5Core_FOUND)
+  message("")
+  message(" Qt5 based tools:")
+  message("   musredit, musrStep, musrWiz, mupp  : yes")
+endif (Qt5Core_FOUND)
+if (Qt4_FOUND)
+  message("")
+  message(" Qt4 based tools (deprecated):")
+  message("   musredit                           : yes")
+endif (Qt4_FOUND)
+if (QT_FOUND)
+  message("")
+  message(" Qt3 based tools (outdated):")
+  message("   musrgui                            : yes")
+endif (QT_FOUND)
+if (NOT Qt5Core_FOUND AND NOT Qt4_FOUND AND NOT QT_FOUND)
+  message("")
+  message(" NO Qt based tools will be installed since Qt is not found or not installed on the system")
+endif (NOT Qt5Core_FOUND AND NOT Qt4_FOUND AND NOT QT_FOUND)
+else (qt_based_tools)
+  message("")
+  message(" Qt based tools (musredit, musrStep, musrWiz, mupp) have been disabled")
+endif (qt_based_tools)
+message("")
+message(" Installation directories:")
+message(" -------------------------")
+message("")
+message(" Programs                : ${CMAKE_INSTALL_PREFIX}/bin")
+message(" XML configuration files : " $ENV{HOME} "/.musrfit")
+message(" Documentation           : ${CMAKE_INSTALL_PREFIX}/share/doc/musrfit")
+message("")
+message("-------------------------------------------------------------------------")
+message("")
+
+#--- end ----------------------------------------------------------------------

ChangeLog

@@ -2,8 +2,175 @@
 # 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
+===================================
+
+changes since 0.17.0
+===================================
+NEW 2016-12-18 for maxLH it is now possible to get the per-run-block maxLH,
+               and the expected maxLH.
+NEW 2016-12-18 musrview allows no to show directly the Fourier transform,
+               and the averaged data/Fourier transform.
+NEW 2016-12-18 added a first full version of an automatic phase correction 
+               for the real part of the Fourier transform. It is based on
+               the algorithm published in JMR 158, 164 (2002).
+NEW 2016-12-18 a couple of improvements in dump_header: (i) it is not
+               only searching in the current directory, but also in all
+               default paths defined in musrfit_startup.xml. (ii) it is
+               now possible also to give only run numbers instead of the
+               full file name.
+NEW 2016-08-24 in musrview it is now possible to enable/disable a
+               crosshair cursor by pressing 'c'.
+NEW 2016-04-28 updated licence info in musredit and added paramList 
+               feature to the msr2data GUI.
+NEW 2016-04-28 msr2data gets a new option: paramList which allows to 
+               extract a subset of all the parameters of a collection
+               of msr-files.
+NEW 2016-04-22 Added the theory function muMinusExpTF for mu minus fits
+NEW 2016-02-23 It is now possible to export the averaged data/Fourier
+CHANGED 2016-12-18 updated the docu.
+CHANGED 2016-12-18 a couple of little improvements in musredit.
+CHANGED 2016-08-10 drop NeXus support for Version < 4.4
+CHANGED 2016-04-26 start-/endTimeBin are now class members. This reduces 
+               the number of recalculations.
+FIXED 2016-08-02 run lists are now properly loaded if containing nS-nE elements.
+
+changes since 0.16.0
+===================================
+NEW 2016-01-22 update of the docu which now describes the RRF option.
+CHANGED 2016-02-17 move the startup XML-files to $HOME/.musrfit
+               rather than having it within $prefix/bin. Increase
+               therefore the version number to 0.17.0
+CHANGED 2016-02-16 if the LEM file is created 2012 or later and the
+               data-file-format tag is still ROOT-NPP or ROOT-PPC, it
+               will automatically switched to MUSR-ROOT. This way red/green
+               issues should be prevented. (see MUSR-314).
+CHANGED 2016-02-16 start migrating the icons of musredit_qt5 to the breeze
+               icons (https://github.com/NitruxSA/breeze-icon-theme).
+               At the same time I start to redesign the musrfit specific
+               icons accordingly (not yet happy with it, but ...).
+
+changes since 0.15.0
+===================================
+NEW 2016-01-22 add RRF fit option. At the same time, the version has been
+               increased to 0.16.0. For details see the documentation.
+FIXED 2015-10-29 TMusrRunHeader didn't map a double vector properly into a
+                 string. The last element was a copy of the 2nd last instead
+		 if the proper last. This is now fixed. Fixed also some
+		 comment typo.
+FIXED 2015-11-11 Fixes the crash of Fourier if the maximal range given in the 
+                 Fourier block is larger than the available.
+CHANGED 2015-11-15 removed unnecessary check form musredit_qt5 msr2data interface.
+
+changes since 0.14.0
+===================================
+NEW 2015-10-26 added a first ported musredit version (Qt4 -> Qt5). At the same
+               the version has been incremented to 0.15.0.
+NEW 2015-09-24 adding a phase optimized real Fourier to musrFT. This is still VERY
+               experimental, and hence only available from within musrFT. Eventually
+               it should make its way into musrview as well. Furthermore the 
+               documentation needs to be written yet. There is only a short not in
+               the command line present.
+NEW 2015-02-23 implemented an average-per-data-set option for musrFT.
+NEW 2015-02-21 add proper Mac icon to musredit
+FIXED 2015-09-22 generating global fit msr-files including a GLOBAL block is working
+                 now as expected.
+FIXED 2015-09-17 in PMsr2Data::PrepareGlobalInputFile() there seem to be 'unmotivated'
+                 break; commands in some loops. They prevent a proper map handling.
+                 Since this is a real puzzle I contacted BMW for clarification. 
+                 2015-09-18: there is only one unmotivated break; cleaned up the code
+                 accordingly.
+FIXED 2015-09-14 any2many export of MusrRoot crashed when first histo group was != 0.
+                 This happend when exporting to PSI-BIN or WKM. This is fixed now.
+FIXED 2015-09-08 fixed error in view_packing for single histo (wrong norm of the theory).
+FIXED 2015-09-04 minor change in Fourier-block output (PMsrHandler::WriteMsrLogFile
+                 and PMsrHandler::WriteMsrLogFile) to avoid truncated range labels.
+FIXED 2015-06-30 changed setf/unsetf bug (PMsr2Data.cpp)
+FIXED 2015-05-15 another path check for HDF5 with ubuntu 15.04
+FIXED 2015-03-16 some minor correction for ASCII export in any2many
+FIXED 2015-02-26 some more bug fixing for average per data set.
+FIXED 2015-02-20 for graphical export in the batch mode, menus mustn't be set.
+CHANGED 2015-08-17 updated ChangeLog which was orphaned since V0.13.0
+CHANGED 2015-08-16 updated the docu
+CHANGED 2015-08-16 added the class PStringNumberList which allow to parse a 
+                   generic encoded list of numbers. Used this class to improve 
+                   PMsrHandler, and improved the runList feature of msr2data. 
+                   For details see the documentation of msr2data.
+CHANGED 2015-06-25 adopted the temperature dependence of the gap function 
+                   (see Eq.(8) of the memo), which breaks the self-consistency. 
+                   Makes it more flexible but requires that the user is using 
+                   his brain.
+CHANGED 2015-06-25 small correction of the skewed Gaussian for extrem parameter 
+                   values.
+CHANGED 2015-05-29 updated docu and removed an unsed variable
+CHANGED 2015-05-29 added a group histo selector in any2many for MusrRoot when 
+                   exporting to a too limited file format as PSI-BIN.
+CHANGED 2015-04-01 update of the technical docu
+CHANGED 2015-02-28 check that FOURIER block phase parameter as parX is not leading 
+                   to an error message.
+CHANGED 2015-02-24 added missing background range from msr-file (musrFT)
+CHANGED 2015-02-24 separated PSI-BIN and PSI-MDU file format
+CHANGED 2015-02-21 make sure that musrFT is found
+CHANGED 2015-02-21 needed to adopted includes for dictionary generation due to 
+                   adding fftw.h in PMusr.h
+CHANGED 2015-02-21 have now README and README.md for automake and bitbucket, 
+                   respectively.
+
 changes since 0.13.0
 ===================================
+NEW 2015-02-23 implemented an average-per-data-set option for musrFT.
+NEW 2015-02-20 add a switch to musrview that it plots initially the Fouier data rather
+               than the time domain data.
+NEW 2015-02-19 added a first preliminary user interface for musrFT within musredit.
+NEW 2015-02-16 changed the data export handling from musrview. It is now more
+               main line and follows the implementation of musrFT.
+NEW 2015-02-13 first implementation of a standalone Fourier transform/plotter: 
+               musrFT. Initially it is meant to be used for HAL-9500, 
+               i.e. Fourier transform WITHOUT lifetime correction.
+               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 

INSTALL

@@ -1,17 +1,80 @@
 #---------------------------------------------------------------------
 # INSTALL
-# AS/BMW, 2014/02/11; 2011/01/27
 #---------------------------------------------------------------------
 
-To get it all build:
+There are currently 2 wasy to build musrfit:
+
+1) via the automake tool chain (this will phase out until 2019)
+2) via the cmake tool chain (this will be the default starting from now)
+
+In the following it is assumed that the system variable ROOTSYS is already
+defined and pointing to the place where CERN/ROOT is installed.
+
+#----------------------------------
+# Install via automake tool chain
+#----------------------------------
+
+To get it build:
 
    sh autogen.sh
-   ./configure --prefix=/opt/cern/root       (or where ever musrfit should be installed)
+   ./configure --prefix=$ROOTSYS             (or where ever musrfit should be installed)
    make
    make install                              (as superuser -- maybe)
+   /sbin/ldconfig                            (as superuser)   
+
+configure comes with a couple of options. For details either execute
+
+  ./configure --help
+
+or check under http://lmu.web.psi.ch/musrfit/user/MUSR/MusrFitSetup.html
+for a more detailed description.
+
+An example with NeXus support and BMWlibs needed would look like this
+
+   sh autogen.sh
+   ./configure --enable-NeXus --enable-BMWlibs --prefix=$ROOTSYS 
+   make 
+   make install                              (as superuser -- maybe)
+   /sbin/ldconfig                            (as superuser)
    
 In the optimal case, everything is set up ;-)
 
+#----------------------------------
+# Install via cmake tool chain
+#----------------------------------
+
+cmake minimal required version is 3.6.
+
+musrfit supports only out-of-source cmake build! Hence, go to the musrfit
+directory and
+
+   mkdir build
+   cd build 
+   cmake ../ -DCMAKE_INSTALL_PREFIX=$ROOTSYS (or where ever musrfit should be installed)
+   cmake --build ./ --clean-first
+   make install                              (as superuser -- maybe)
+   /sbin/ldconfig                            (as superuser)
+    
+cmake configuration allows a couple of switches.  For details check the user
+docu under 
+
+   http://lmu.web.psi.ch/musrfit/user/MUSR/MusrFitSetup.html
+
+An example with NeXus support and BMWlibs needed would look like this
+
+   mkdir build
+   cd build
+   cmake ../ -Dnexus=1 -DBMWlibs=1 -DCMAKE_INSTALL_PREFIX=$ROOTSYS 
+   cmake --build ./ --clean-first
+   make install                              (as superuser -- maybe)
+   /sbin/ldconfig                            (as superuser)
+
+In the optimal case, everything is set up ;-)
+
+#----------------------------------
+# Link to the docu
+#----------------------------------
+
 More information about the software requirements and the installation can be found at:
 
 http://lmu.web.psi.ch/musrfit/user/MUSR/MusrFitSetup.html

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 \

README

@@ -1,33 +1,35 @@
-# musrfit - muSR data analysis package #
-
-### Contents ###
-
-This is a data analysis package to analyze time differential muSR data. 
-Currently it allows the following things:
-
-* setting up most commonly used fitting functions for muSR
-* fitting data, including global fits
-* showing the fit results and the residuals
-* showing the Fourier transform of the data
-* extracting easily the fitting parameters to be used in other programs (gnuplot, qtiplot/origin, ...)
-* allows to generate fitting input files for follow-up runs
-* allows to generate global fitting input files based on a single run template
-* allows to implement more sophisticated user functions 
-  (e.g. GL vortex lattice, Meissner screening including low-energy muon stopping profiles)
-
-### Currently supported platforms: ###
-
-* Linux
-* Mac OS X
-* Windows - not really, only for the very brave ones
-
-### Documentation ####
-
-For a more exhaustive user documentation see:
-
-  http://lmu.web.psi.ch/musrfit/user/MUSR/WebHome.html
-
-### Contact ###
-
-<andreas.suter@psi.ch>
-
+README
+
+musrfit - muSR data analysis package
+
+Contents
+--------
+
+This is a data analysis package to analyze time differential muSR and beta-NMR data. 
+Currently it allows the following things:
+
+* setting up most commonly used fitting functions for muSR and beta-NMR
+* fitting data, including global fits
+* showing the fit results and the residuals
+* showing the Fourier transform of the data
+* extracting easily the fitting parameters to be used in other programs (gnuplot, qtiplot/origin, ...)
+* allows to generate fitting input files for follow-up runs
+* allows to generate global fitting input files based on a single run template
+* allows to implement more sophisticated user functions 
+  (e.g. GL vortex lattice, Meissner screening including low-energy muon stopping profiles)
+
+Currently supported platforms:
+
+* Linux
+* Mac OS X
+* Windows - not really, only for the very brave ones
+
+Documentation
+
+For a more exhaustive user documentation see:
+
+  http://lmu.web.psi.ch/musrfit/user/MUSR/WebHome.html
+
+Contact
+
+<andreas.suter@psi.ch>

README.md

@@ -0,0 +1,33 @@
+# musrfit - muSR data analysis package #
+
+### Contents ###
+
+This is a data analysis package to analyze time differential muSR and beta-NMR data. 
+Currently it allows the following things:
+
+* setting up most commonly used fitting functions for muSR and beta-NMR
+* fitting data, including global fits
+* showing the fit results and the residuals
+* showing the Fourier transform of the data
+* extracting easily the fitting parameters to be used in other programs (gnuplot, qtiplot/origin, ...)
+* allows to generate fitting input files for follow-up runs
+* allows to generate global fitting input files based on a single run template
+* allows to implement more sophisticated user functions 
+  (e.g. GL vortex lattice, Meissner screening including low-energy muon stopping profiles)
+
+### Currently supported platforms: ###
+
+* Linux
+* Mac OS X
+* Windows - not really, only for the very brave ones
+
+### Documentation ####
+
+For a more exhaustive user documentation see:
+
+  http://lmu.web.psi.ch/musrfit/user/MUSR/WebHome.html
+
+### Contact ###
+
+<andreas.suter@psi.ch>
+

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`

cmake/FindFFTW3.cmake

@@ -0,0 +1,151 @@
+# - Find fftw3 library
+# Find the native FFTW3 includes and library
+# This module defines
+#  FFTW3_INCLUDE_DIR, where to find fftw3.h, etc.
+# ---
+#  FFTW3_LIBRARY, library to link against to use FFTW3
+#  FFTW3_OMP_LIBRARY, library to link against to use FFTW3_omp
+#  FFTW3_THREADS_LIBRARY, library to link against to use FFTW3_threads
+#  FFTW3_FOUND, if false, do not try to use FFTW3.
+#  FFTW3_OMP_FOUND, if false, do not try to use OpenMP FFTW3.
+#  FFTW3_THREADS_FOUND, if false, do not try to use threaded FFTW3.
+# ---
+#  FFTW3L_LIBRARY, library to link against to use FFTW3l
+#  FFTW3L_OMP_LIBRARY, library to link against to use FFTW3l_omp
+#  FFTW3L_THREADS_LIBRARY, library to link against to use FFTW3l_threads
+#  FFTW3L_FOUND, if false, do not try to use FFTW3l.
+#  FFTW3L_OMP_FOUND, if false, do not try to use OpenMP FFTW3l.
+#  FFTW3L_THREADS_FOUND, if false, do not try to use threaded FFTW3l.
+# ---
+#  FFTW3F_LIBRARY, library to link against to use FFTW3f
+#  FFTW3F_OMP_LIBRARY, library to link against to use FFTW3f_omp
+#  FFTW3F_THREADS_LIBRARY, library to link against to use FFTW3f_threads
+#  FFTW3F_FOUND, if false, do not try to use FFTW3f.
+#  FFTW3F_OMP_FOUND, if false, do not try to use OpenMP FFTW3f.
+#  FFTW3F_THREADS_FOUND, if false, do not try to use threaded FFTW3f.
+# ---
+#  FFTW3Q_LIBRARY, library to link against to use FFTW3q
+#  FFTW3Q_OMP_LIBRARY, library to link against to use FFTW3q_omp
+#  FFTW3Q_THREADS_LIBRARY, library to link against to use FFTW3q_threads
+#  FFTW3Q_FOUND, if false, do not try to use FFTW3q.
+#  FFTW3Q_OMP_FOUND, if false, do not try to use OpenMP FFTW3q.
+#  FFTW3Q_THREADS_FOUND, if false, do not try to use threaded FFTW3q.
+
+find_path(FFTW3_INCLUDE_DIR fftw3.h
+  HINTS "/usr/include" "/opt/local/include"
+)
+
+# find position of fftw3.h from the end
+string(FIND "${FFTW3_INCLUDE_DIR}" "/fftw3.h" pos REVERSE)
+# truncate the string
+string(SUBSTRING "${FFTW3_INCLUDE_DIR}" 0 ${pos} substr)
+set(FFTW3_INCLUDE_DIR ${substr})
+unset(substr)
+
+find_library(FFTW3_LIBRARY fftw3)
+find_library(FFTW3_OMP_LIBRARY fftw3_omp)
+find_library(FFTW3_THREAD_LIBRARY fftw3_threads)
+find_library(FFTW3L_LIBRARY fftw3l)
+find_library(FFTW3L_OMP_LIBRARY fftw3l_omp)
+find_library(FFTW3L_THREAD_LIBRARY fftw3l_threads)
+find_library(FFTW3F_LIBRARY fftw3f)
+find_library(FFTW3F_OMP_LIBRARY fftw3f_omp)
+find_library(FFTW3F_THREAD_LIBRARY fftw3f_threads)
+find_library(FFTW3Q_LIBRARY fftw3q)
+find_library(FFTW3Q_OMP_LIBRARY fftw3q_omp)
+find_library(FFTW3Q_THREAD_LIBRARY fftw3q_threads)
+
+# handle the QUIETLY and REQUIRED arguments and set FFTW3_FOUND to TRUE if
+# all listed variables are TRUE
+include(${CMAKE_ROOT}/Modules/FindPackageHandleStandardArgs.cmake)
+find_package_handle_standard_args(FFTW3
+                                  REQUIRED_VARS FFTW3_LIBRARY FFTW3_INCLUDE_DIR
+                                  VERSION_VAR "3")
+find_package_handle_standard_args(FFTW3_OMP
+                                  REQUIRED_VARS FFTW3_OMP_LIBRARY FFTW3_INCLUDE_DIR
+                                  VERSION_VAR "3")
+find_package_handle_standard_args(FFTW3_THREAD
+                                  REQUIRED_VARS FFTW3_THREAD_LIBRARY FFTW3_INCLUDE_DIR
+                                  VERSION_VAR "3")
+
+find_package_handle_standard_args(FFTW3L
+                                  REQUIRED_VARS FFTW3L_LIBRARY FFTW3_INCLUDE_DIR
+                                  VERSION_VAR "3")
+find_package_handle_standard_args(FFTW3L_OMP
+                                  REQUIRED_VARS FFTW3L_OMP_LIBRARY FFTW3_INCLUDE_DIR
+                                  VERSION_VAR "3")
+find_package_handle_standard_args(FFTW3L_THREAD
+                                  REQUIRED_VARS FFTW3L_THREAD_LIBRARY FFTW3_INCLUDE_DIR
+                                  VERSION_VAR "3")
+
+find_package_handle_standard_args(FFTW3F
+                                  REQUIRED_VARS FFTW3F_LIBRARY FFTW3_INCLUDE_DIR
+                                  VERSION_VAR "3")
+find_package_handle_standard_args(FFTW3F_OMP
+                                  REQUIRED_VARS FFTW3F_OMP_LIBRARY FFTW3_INCLUDE_DIR
+                                  VERSION_VAR "3")
+find_package_handle_standard_args(FFTW3F_THREAD
+                                  REQUIRED_VARS FFTW3F_THREAD_LIBRARY FFTW3_INCLUDE_DIR
+                                  VERSION_VAR "3")
+
+find_package_handle_standard_args(FFTW3Q
+                                  REQUIRED_VARS FFTW3Q_LIBRARY FFTW3_INCLUDE_DIR
+                                  VERSION_VAR "3")
+find_package_handle_standard_args(FFTW3Q_OMP
+                                  REQUIRED_VARS FFTW3Q_OMP_LIBRARY FFTW3_INCLUDE_DIR
+                                  VERSION_VAR "3")
+find_package_handle_standard_args(FFTW3Q_THREAD
+                                  REQUIRED_VARS FFTW3Q_THREAD_LIBRARY FFTW3_INCLUDE_DIR
+                                  VERSION_VAR "3")
+
+if (NOT FFTW3_FOUND)
+  unset(FFTW3_LIBRARY)
+endif()
+if (NOT FFTW3_OMP_FOUND)
+  unset(FFTW3_OMP_LIBRARY)
+endif()
+if (NOT FFTW3_THREAD_FOUND)
+  unset(FFTW3_THREAD_LIBRARY)
+endif()
+
+if (NOT FFTW3L_FOUND)
+  unset(FFTW3L_LIBRARY)
+endif()
+if (NOT FFTW3L_OMP_FOUND)
+  unset(FFTW3L_OMP_LIBRARY)
+endif()
+if (NOT FFTW3L_THREAD_FOUND)
+  unset(FFTW3L_THREAD_LIBRARY)
+endif()
+
+if (NOT FFTW3F_FOUND)
+  unset(FFTW3F_LIBRARY)
+endif()
+if (NOT FFTW3F_OMP_FOUND)
+  unset(FFTW3F_OMP_LIBRARY)
+endif()
+if (NOT FFTW3F_THREAD_FOUND)
+  unset(FFTW3F_THREAD_LIBRARY)
+endif()
+
+if (NOT FFTW3Q_FOUND)
+  unset(FFTW3Q_LIBRARY)
+endif()
+if (NOT FFTW3Q_OMP_FOUND)
+  unset(FFTW3Q_OMP_LIBRARY)
+endif()
+if (NOT FFTW3Q_THREAD_FOUND)
+  unset(FFTW3Q_THREAD_LIBRARY)
+endif()
+
+mark_as_advanced(
+  FFTW3_INCLUDE_DIR 
+  FFTW3_LIBRARY FFTW3_OMP_LIBRARY FFTW3_THREAD_LIBRARY
+  FFTW3L_LIBRARY FFTW3L_OMP_LIBRARY FFTW3L_THREAD_LIBRARY
+  FFTW3F_LIBRARY FFTW3F_OMP_LIBRARY FFTW3F_THREAD_LIBRARY
+  FFTW3Q_LIBRARY FFTW3Q_OMP_LIBRARY FFTW3Q_THREAD_LIBRARY
+)
+
+if (FFTW3_FOUND)
+  message("-- Found FFTW3: ${FFTW3_INCLUDE_DIR}")
+endif (FFTW3_FOUND)

cmake/FindMXML.cmake

@@ -0,0 +1,34 @@
+# - find MXML
+# find the MXML lib and includes
+# This module defines 
+#  LIBMXML_INCLUDE_DIR, where to find mxml.h
+#  LIBMXML_LIBRARY, library to link against
+#  LIBMXML_FOUND, if false, do not try to use the MXML lib
+
+find_path(LIBMXML_INCLUDE_DIR mxml.h
+  HINT "/usr/include"
+)
+# find position of mxml.h from the end
+string(FIND "${LIBMXML_INCLUDE_DIR}" "/mxml.h" pos REVERSE)
+# truncate the string
+string(SUBSTRING "${LIBMXML_INCLUDE_DIR}" 0 ${pos} substr)
+set(LIBMXML_INCLUDE_DIR ${substr})
+unset(substr)
+
+find_library(LIBMXML_LIBRARY mxml)
+
+# get version string
+# currently do not know from where to get it automatically
+
+# handle the QUIETLY and REQUIRED arguments and set LIBMXML_FOUND to TRUE if
+# all listed variables are TRUE
+include(${CMAKE_ROOT}/Modules/FindPackageHandleStandardArgs.cmake)
+FIND_PACKAGE_HANDLE_STANDARD_ARGS(MXML
+                                  REQUIRED_VARS LIBMXML_LIBRARY LIBMXML_INCLUDE_DIR)
+
+if (NOT LIBMXML_FOUND)
+  unset(LIBMXML_LIBRARY)
+endif()
+
+mark_as_advanced(LIBMXML_INCLUDE_DIR LIBMXML_LIBRARY)
+

cmake/FindNeXus.cmake

@@ -0,0 +1,45 @@
+# - Find NeXus library
+# Find the native NEXUS includes and library
+# This module defines
+#  NEXUS_INCLUDE_DIR, where to find NeXus.h, etc.
+#  NEXUS_LIBRARY, library to link against to use NEXUS
+#  NEXUS_FOUND, if false, do not try to use NEXUS.
+
+find_path(NEXUS_INCLUDE_DIR napi.h
+  HINTS "/usr/local/include" "/opt/nexus/include" "/usr/local/include/nexus"
+)
+# find position of napi.h from the end
+string(FIND "${NEXUS_INCLUDE_DIR}" "/napi.h" pos REVERSE)
+# truncate the string
+string(SUBSTRING "${NEXUS_INCLUDE_DIR}" 0 ${pos} substr)
+set(NEXUS_INCLUDE_DIR ${substr})
+unset(substr)
+
+find_library(NEXUS_LIBRARY NeXus 
+  HINTS "/usr/lib" "/usr/lib64" "/usr/local/lib" "/usr/local/lib64" "/opt/nexus/lib")
+
+# get version string
+if (NEXUS_INCLUDE_DIR AND EXISTS ${NEXUS_INCLUDE_DIR}/napi.h)
+  file(STRINGS "${NEXUS_INCLUDE_DIR}/napi.h" NEXUS_version_str
+       REGEX "^#define[\t ]+NEXUS_VERSION[\t ].*")
+
+  string(REGEX REPLACE "^#define[\t ]+NEXUS_VERSION[\t ]+\"([^\"]*).*"
+         "\\1" NEXUS_VERSION_STRING "${NEXUS_version_str}")
+  unset(NEXUS_version_str)
+endif()
+
+# handle the QUIETLY and REQUIRED arguments and set NEXUS_FOUND to TRUE if
+# all listed variables are TRUE
+include(${CMAKE_ROOT}/Modules/FindPackageHandleStandardArgs.cmake)
+FIND_PACKAGE_HANDLE_STANDARD_ARGS(NEXUS
+                                  REQUIRED_VARS NEXUS_LIBRARY NEXUS_INCLUDE_DIR
+                                  VERSION_VAR NEXUS_VERSION_STRING)
+
+if (NOT NEXUS_FOUND)
+  unset(NEXUS_LIBRARY)
+endif()
+
+mark_as_advanced(NEXUS_INCLUDE_DIR NEXUS_LIBRARY)
+
+
+

cmake/config.h.in

@@ -0,0 +1,67 @@
+// config.h
+
+#define PACKAGE_VERSION "@PROJECT_VERSION@"
+
+// define to 1 if you have fork and it should be used 
+#cmakedefine HAVE_FORK 1
+
+// define to 1 if you have <alloca.h> and it should be used 
+#cmakedefine HAVE_ALLOCA_H 1
+
+// Define to 1 if you have the <dlfcn.h> header file.
+#cmakedefine HAVE_DLFCN_H 1
+
+// Define to 1 if you have the `erf' function.
+#cmakedefine HAVE_ERF 1
+
+// Define to 1 if you have the `getloadavg' function.
+#cmakedefine HAVE_GETLOADAVG 1
+
+// Define to 1 if gomp is available */
+#cmakedefine HAVE_GOMP 1
+
+// Define to 1 if you have the <inttypes.h> header file.
+#cmakedefine HAVE_INTTYPES_H 1
+
+// Define to 1 if the type `long double' works and has more range or precision than `double'.
+#cmakedefine HAVE_LONG_DOUBLE 1
+
+// Define to 1 if the type `long double' works and has more range or precision than `double'.
+#cmakedefine HAVE_LONG_DOUBLE_WIDER 1
+
+// Define to 1 if fftw3f_threads are available
+#cmakedefine HAVE_LIBFFTW3F_THREADS 1
+
+// Define to 1 if fftw3_threads are available
+#cmakedefine HAVE_LIBFFTW3_THREADS 1
+
+// Define to 1 if you have the <memory.h> header file.
+#cmakedefine HAVE_MEMORY_H 1
+
+// Define to 1 if you have the `powl' function.
+#cmakedefine HAVE_POWL 1
+
+// Define to 1 if you have the `shmget' function.
+#cmakedefine HAVE_SHMGET 1
+
+// Define to 1 if you have the <stdint.h> header file.
+#cmakedefine HAVE_STDINT_H 1
+
+// Define to 1 if you have the <stdlib.h> header file.
+#cmakedefine HAVE_STDLIB_H 1
+
+// Define to 1 if you have the <string.h> header file.
+#cmakedefine HAVE_STRING_H 1
+
+// Define to 1 if you have the <strings.h> header file.
+#cmakedefine HAVE_STRINGS_H 1
+
+// Define to 1 if you have the <sys/stat.h> header file.
+#cmakedefine HAVE_SYS_STAT_H 1
+
+// Define to 1 if you have the <sys/types.h> header file.
+#cmakedefine HAVE_SYS_TYPES_H 1
+
+// Define to 1 if you have the <unistd.h> header file.
+#cmakedefine HAVE_UNISTD_H 1
+

cmake/configure_musrfit_version_file.cmake.in

@@ -0,0 +1,30 @@
+# configure_musrfit_version_file.cmake.in:
+set(SRC_DIR "@CMAKE_SOURCE_DIR@")
+set(BIN_DIR "@CMAKE_CURRENT_BINARY_DIR@")
+
+# Set variables
+set(CMAKE_INSTALL_PREFIX "@CMAKE_INSTALL_PREFIX@")
+set(MUSRFIT_VERSION "@MUSRFIT_VERSION@")
+
+# Get the current working branch
+execute_process(
+  COMMAND git rev-parse --abbrev-ref HEAD
+  WORKING_DIRECTORY ${CMAKE_SOURCE_DIR}
+  OUTPUT_VARIABLE GIT_BRANCH
+  OUTPUT_STRIP_TRAILING_WHITESPACE
+)
+
+# Get the latest abbreviated commit hash of the working branch
+execute_process(
+  COMMAND git log -1 --pretty="%h, %ci"
+  WORKING_DIRECTORY ${CMAKE_SOURCE_DIR}
+  OUTPUT_VARIABLE GIT_CURRENT_SHA1
+  OUTPUT_STRIP_TRAILING_WHITESPACE
+)
+
+configure_file(
+  ${SRC_DIR}/cmake/git-revision.h.in
+  ${BIN_DIR}/git-revision.h
+  @ONLY
+)
+# EOF

cmake/git-revision.h.in

@@ -0,0 +1,8 @@
+#ifndef GIT_VERSION_H
+#define GIT_VERSION_H
+
+#define GIT_BRANCH "@GIT_BRANCH@"
+#define GIT_CURRENT_SHA1 @GIT_CURRENT_SHA1@
+
+#endif // GIT_VERSION_H
+

cmake/musrfit-info.h.in

@@ -0,0 +1,4 @@
+//--- This file is generated by cmake -----------------------------------------
+
+#define MUSRFIT_PREFIX "@CMAKE_INSTALL_PREFIX@"
+#define MUSRFIT_DOC_DIR "@CMAKE_INSTALL_PREFIX@/share/doc/musrfit"

configure.ac

@@ -1,7 +1,7 @@
 AC_REVISION([m4_esyscmd_s([git describe --always])])
 
 AC_PREREQ(2.63)
-AC_INIT([musrfit],[0.13.0],[andreas.suter@psi.ch])
+AC_INIT([musrfit],[1.3.0],[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=13
+MUSR_MAJOR_VERSION=1
+MUSR_MINOR_VERSION=3
 MUSR_MICRO_VERSION=0
 
 #release versioning
@@ -54,7 +54,7 @@ PSIBIN_MINOR_VERSION=1
 PSIBIN_MICRO_VERSION=0
 
 #release versioning
-MUD_MAJOR_VERSION=0
+MUD_MAJOR_VERSION=1
 MUD_MINOR_VERSION=0
 MUD_MICRO_VERSION=0
 
@@ -69,7 +69,7 @@ PLUGIN_MINOR_VERSION=0
 PLUGIN_MICRO_VERSION=0
 
 #release versioning
-CUBA_MAJOR_VERSION=3
+CUBA_MAJOR_VERSION=4
 CUBA_MINOR_VERSION=2
 CUBA_MICRO_VERSION=0
 
@@ -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} ${ROOTAUXCFLAGS}"
@@ -525,6 +525,9 @@ AC_ARG_ENABLE([NeXus], [AS_HELP_STRING([--enable-NeXus],[build optional NeXus su
          elif test -r /usr/local/hdf5/include/hdf5.h; then
            HDF5_PREFIX="/usr/local/hdf5"
            AC_MSG_RESULT([${HDF5_PREFIX}])
+         elif test -r /usr/include/hdf5/serial/hdf5.h; then
+           HDF5_PREFIX="/usr/include/hdf5/serial"
+           AC_MSG_RESULT([${HDF5_PREFIX}])
          elif test -r /usr/include/hdf5.h; then
            HDF5_PREFIX="/usr"
            AC_MSG_RESULT([${HDF5_PREFIX}])
@@ -551,34 +554,31 @@ AC_ARG_ENABLE([NeXus], [AS_HELP_STRING([--enable-NeXus],[build optional NeXus su
         [AS_HELP_STRING([--with-nexus],[prefix of the NeXus installation, e.g. /usr/local])],
         [NEXUS_PREFIX=$with_nexus
          AC_MSG_CHECKING([whether NeXus can be found at the specified location])
-         if !(test -r ${NEXUS_PREFIX}/include/napi.h); then
+         if !(test -r ${NEXUS_PREFIX}/include/nexus/napi.h); then
            AC_MSG_RESULT([no])
            AC_MSG_ERROR([NeXus cannot be found at the specified path!])
          fi
          AC_MSG_RESULT([${NEXUS_PREFIX}])],
-        [PKG_CHECK_MODULES(NEXUS, nexus >= 4.1, [NEXUS_FOUND=1],
+        [PKG_CHECK_MODULES(NEXUS, nexus >= 4.4, [NEXUS_FOUND=1],
          [AC_MSG_CHECKING([whether NeXus is installed in a standard location])
-          if test -r /usr/local/include/napi.h; then
-            NEXUS_PREFIX="/usr/local"
-            AC_MSG_RESULT([${NEXUS_PREFIX}])
-         elif test -r /usr/local/nexus/include/napi.h; then
-           NEXUS_PREFIX="/usr/local/nexus"
+          if test -r /usr/local/include/nexus/napi.h; then
+           NEXUS_PREFIX="/usr/local"
            AC_MSG_RESULT([${NEXUS_PREFIX}])
-         elif test -r /usr/include/napi.h; then
-           NEXUS_PREFIX="/usr"
-           AC_MSG_RESULT([${NEXUS_PREFIX}])
-         elif test -r /sw/include/napi.h; then
+          elif test -r /sw/include/nexus/napi.h; then
            NEXUS_PREFIX="/sw"
            AC_MSG_RESULT([${NEXUS_PREFIX}])
-         elif test -r /opt/local/include/napi.h; then
+          elif test -r /opt/local/include/nexus/napi.h; then
            NEXUS_PREFIX="/opt/local"
            AC_MSG_RESULT([${NEXUS_PREFIX}])
-         else
+          elif test -r /opt/nexus/include/nexus/napi.h; then
+           NEXUS_PREFIX="/opt/nexus"
+           AC_MSG_RESULT([${NEXUS_PREFIX}])
+          else
            AC_MSG_RESULT([no])
            AC_MSG_ERROR(
-           [NeXus not found. Please call configure with the --with-nexus option.
+           [NeXus Version >= 4.4 not found. Please call configure with the --with-nexus option.
            This tells configure where to find the NeXus headers,
-           e.g. --with-nexus=/usr/local/nexus]
+           e.g. --with-nexus=/opt/nexus]
            )
          fi
         ]
@@ -586,8 +586,27 @@ AC_ARG_ENABLE([NeXus], [AS_HELP_STRING([--enable-NeXus],[build optional NeXus su
     )
     AC_SUBST(NEXUS_PREFIX)
     if test "${NEXUS_FOUND}" != "1"; then
-      NEXUS_LIBS="-L${NEXUS_PREFIX}/lib -lNeXus"
-      NEXUS_CFLAGS="-I${NEXUS_PREFIX}/include"
+      dnl get suffix for the NeXus library depending on the OS
+      AC_REQUIRE([AC_CANONICAL_HOST])
+      AS_CASE([$host_os],
+       [linux*], [NEXUS_SUFFIX="so"],
+       [darwin*], [NEXUS_SUFFIX="dylib"],
+       [*cygwin*], [NEXUS_SUFFIX="dll"],
+       [AC_MSG_ERROR([NeXus check: Your platform is not currently supported])]
+      )
+      AC_MSG_NOTICE([NeXus Suffix Result: "${NEXUS_SUFFIX}"])
+      if test -r ${NEXUS_PREFIX}/lib/libNeXus.${NEXUS_SUFFIX}; then
+        NEXUS_LIB_DIR="lib"
+      elif test -r ${NEXUS_PREFIX}/lib64/libNeXus.${NEXUS_SUFFIX}; then
+        NEXUS_LIB_DIR="lib64"
+      else
+        AC_MSG_ERROR(
+         [Couldn't find the NeXus library.]
+        )
+      fi
+
+      NEXUS_LIBS="-L${NEXUS_PREFIX}/${NEXUS_LIB_DIR} -lNeXus"
+      NEXUS_CFLAGS="-I${NEXUS_PREFIX}/include/nexus"
     fi
     AC_SUBST(NEXUS_LIBS)
     AC_SUBST(NEXUS_CFLAGS)
@@ -733,6 +752,12 @@ dnl -----------------------------------------------
 
 AC_ARG_ENABLE([ASlibs], [AS_HELP_STRING([--enable-ASlibs],[build optional AS plug-ins [default=no]])],[BUILD_AS_LIBS=1], [BUILD_AS_LIBS=0])
 
+dnl -----------------------------------------------
+dnl Ask user if BNMRlibs should be built
+dnl -----------------------------------------------
+
+AC_ARG_ENABLE([BNMRlibs], [AS_HELP_STRING([--enable-BNMRlibs],[build optional BNMR plug-ins [default=no]])],[BUILD_BNMR_LIBS=1], [BUILD_BNMR_LIBS=0])
+
 dnl -----------------------------------------------
 dnl Set some paths and flags for PMusr, MusrRoot, TLemRunHeader, Class_MuSR_PSI, mud, NeXus (if enabled), etc.
 dnl -----------------------------------------------
@@ -780,6 +805,14 @@ if test "${PNEXUS_ENABLED}" = "1"; then
   AC_SUBST(PNEXUS_CXXFLAGS)
 fi
 
+if test "${BUILD_BNMR_LIBS}" = "1"; then
+  BNMRLIBS_SRCDIR="${SRCDIR}/external/libBNMR"
+  BNMRLIBS_LIBS="${BNMRLIBS_SRCDIR}/libBNMR.la"
+  BNMRLIBS_CFLAGS="-I${BNMRLIBS_SRCDIR}"
+  AC_SUBST(BNMRLIBS_LIBS)
+  AC_SUBST(BNMRLIBS_CFLAGS)
+fi
+
 if test "${BUILD_BMW_LIBS}" = "1"; then
   BMWTOOLS_SRCDIR="${SRCDIR}/external/BMWtools"
   BMWTOOLS_LIBS="${BMWTOOLS_SRCDIR}/libBMWtools.la"
@@ -841,6 +874,8 @@ if test "x$enable_editor" != "xno"; then
 
   echo "Additional checks for musredit/musrgui ..."
 
+  QT5MINVER=5.4
+
   case "$host" in
     *-*-cygwin)
       QT4MINVER=4.5
@@ -853,6 +888,7 @@ if test "x$enable_editor" != "xno"; then
   QT3_FOUND=no
   QT3MT_FOUND=no
   QT4_FOUND=no
+  QT5_FOUND=no
   QMAKEBIN=""
   QTEDITOR=none
 
@@ -926,14 +962,66 @@ if test "x$enable_editor" != "xno"; then
         fi]
   )
 
+  AC_ARG_WITH([qt5],
+        [AS_HELP_STRING([--with-qt5],[prefix of the Qt5 installation, e.g. /usr/lib64/qt5/])],
+        [QT5_PREFIX=$with_qt5
+        AC_MSG_CHECKING([whether qmake for Qt5 can be found at the specified location])
+        for QMAKE in qmake qmake-qt5
+        do
+          if test -x "${QT5_PREFIX}/bin/${QMAKE}"; then
+            QMAKEVERSIONSTRING="$(${QT5_PREFIX}/bin/${QMAKE} -v 2>&1)"
+            for a in $QMAKEVERSIONSTRING
+            do
+              if test "$(expr "$a" : '\(..\)')" = "5."; then
+                QMAKEBIN="${QT5_PREFIX}/bin/${QMAKE}"
+                QTEDITOR=musredit_qt5
+                AC_MSG_RESULT([${QMAKEBIN}])
+                break
+              fi
+            done
+            if test "x${QMAKEBIN}" != "x"; then
+              break
+            fi
+          fi
+        done
+
+        if test "x${QMAKEBIN}" = "x"; then
+          AC_MSG_RESULT([no])
+          AC_MSG_ERROR([qmake for Qt5 cannot be found in ${QT5_PREFIX}/bin!])
+        fi
+
+        if test "x${QT4PRESENT}" = "xyes"; then
+          AC_MSG_WARN([Qt4 and Qt5 directories have been given -- only the Qt5 information will be used and only musredit will be built!])
+        fi],
+        [if test "x${QMAKEBIN}" = "x"; then
+          PKG_CHECK_MODULES(QT5, Qt5WebKit >= $QT5MINVER Qt5Xml >= $QT5MINVER, [QT5_FOUND=yes],
+            [AC_MSG_NOTICE([Qt5 (including Qt5WebKit and Qt5Xml) not found!])
+             PKG_CHECK_MODULES(QT3, qt >= 3.3.0 qt < 4.0, [QT3_FOUND=yes],
+              [PKG_CHECK_MODULES(QT3MT, qt-mt >= 3.3.0 qt-mt < 4.0, [QT3MT_FOUND=yes], [QT3MT_FOUND=no])]
+            )]
+          )
+        fi        
+        if test "x${QT5_FOUND}" != "xyes"; then
+          PKG_CHECK_MODULES(QT5, Qt5WebEngine >= $QT5MINVER Qt5Xml >= $QT5MINVER, [QT5_FOUND=yes],
+            [AC_MSG_NOTICE([Qt5 (including Qt5WebEngine and Qt5Xml) not found!])
+             PKG_CHECK_MODULES(QT3, qt >= 3.3.0 qt < 4.0, [QT3_FOUND=yes],
+              [PKG_CHECK_MODULES(QT3MT, qt-mt >= 3.3.0 qt-mt < 4.0, [QT3MT_FOUND=yes], [QT3MT_FOUND=no])]
+            )]
+          )
+        fi]
+  )
+
   if test "x${QMAKEBIN}" = "x"; then
-    if test "x${QT3_FOUND}" = "xno" && test "x${QT3MT_FOUND}" = "xno" && test "x${QT4_FOUND}" = "xno"; then
-      AC_MSG_WARN([No suitable version of either Qt4 or Qt3 has been found! musredit/musrgui will not be built in this stage!])
+    if test "x${QT3_FOUND}" = "xno" && test "x${QT3MT_FOUND}" = "xno" && test "x${QT4_FOUND}" = "xno" && test "x${Qt5_FOUND}" = "xno"; then
+      AC_MSG_WARN([No suitable version of either Qt5, Qt4 or Qt3 has been found! musredit/musrgui will not be built in this stage!])
     else
       # Check for qmake on the basis of the pkg-config information
       QTPATH=none
 
-      if test "x$QT4_FOUND" = "xyes"; then
+      if test "x$QT5_FOUND" = "xyes"; then
+        QTPATH=$(pkg-config --variable=prefix Qt5WebKit)
+        QTEDITOR=musredit_qt5
+      elif test "x$QT4_FOUND" = "xyes"; then
         QTPATH=$(pkg-config --variable=prefix QtWebKit)
         QTEDITOR=musredit
       elif test "x$QT3_FOUND" = "xyes"; then
@@ -944,9 +1032,37 @@ 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"; then
+        if test "x$QTEDITOR" = "xmusredit_qt5"; then
+          for QMAKE in qmake-qt5 qmake-qt54 qmake-qt55
+          do
+            if test -x "${QTPATH}/bin/${QMAKE}"; then
+              QMAKEBIN="${QTPATH}/bin/${QMAKE}"
+              AC_MSG_RESULT([${QMAKEBIN}])
+              break
+            fi
+          done
+          if test "x${QMAKEBIN}" = "x"; then
+            if test -x "${QTPATH}/bin/qmake"; then
+              QMAKEVERSIONSTRING="$(${QTPATH}/bin/qmake -v 2>&1)"
+              for a in $QMAKEVERSIONSTRING
+              do
+                if test "$(expr "$a" : '\(..\)')" = "5."; then
+                  QMAKEBIN="${QTPATH}/bin/qmake"
+                  AC_MSG_RESULT([${QMAKEBIN}])
+                  break
+                fi
+              done
+            fi
+          fi
+        elif test "x$QTEDITOR" = "xmusredit"; then
           for QMAKE in qmake-qt4 qmake-qt46 qmake-qt47 qmake-qt48
           do
             if test -x "${QTPATH}/bin/${QMAKE}"; then
@@ -993,13 +1109,14 @@ if test "x$enable_editor" != "xno"; then
         fi
         if test "x${QMAKEBIN}" = "x"; then
           AC_MSG_RESULT([no])
-          AC_MSG_WARN([If Qt4 or Qt3 are present but have not been detected, try using the --with-qt4 or --with-qt3 options!])
+          AC_MSG_WARN([If Qt5, Qt4 or Qt3 are present but have not been detected, try using the --with-qt5, --with-qt4 or --with-qt3 options!])
         fi
       fi
     fi
   fi
 fi
 
+AM_CONDITIONAL([BUILD_MUSREDIT_QT5], [test "x$enable_editor" != "xno" && test "x${QMAKEBIN}" != "x" && test "x${QTEDITOR}" = "xmusredit_qt5"])
 AM_CONDITIONAL([BUILD_MUSREDIT], [test "x$enable_editor" != "xno" && test "x${QMAKEBIN}" != "x" && test "x${QTEDITOR}" = "xmusredit"])
 AM_CONDITIONAL([BUILD_MUSRGUI], [test "x$enable_editor" != "xno" && test "x${QMAKEBIN}" != "x" && test "x${QTEDITOR}" = "xmusrgui"])
 
@@ -1016,6 +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}"
@@ -1040,7 +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 ${ROOTLIBDIR}"
     ;;
   *)
     ARCH=OTHERUNIX
@@ -1091,11 +1212,24 @@ else
   INSTALLDIR="${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)
@@ -1111,6 +1245,7 @@ AM_CONDITIONAL([PNEXUS_ENABLED], [test "${PNEXUS_ENABLED}" = "1"])
 AM_CONDITIONAL([BUILD_CUBALIB], [test "${BUILD_CUBA}" = "1"])
 AM_CONDITIONAL([BUILD_BMWLIBS], [test "${BUILD_BMW_LIBS}" = "1"])
 AM_CONDITIONAL([BUILD_ASLIBS], [test "${BUILD_AS_LIBS}" = "1"])
+AM_CONDITIONAL([BUILD_BNMRLIBS], [test "${BUILD_BNMR_LIBS}" = "1"])
 
 AC_CONFIG_FILES([Makefile \
                  src/Makefile \
@@ -1151,7 +1286,11 @@ AC_CONFIG_FILES([Makefile \
 		 src/external/libSpinValve/classes/Makefile \
                  src/external/libPhotoMeissner/Makefile \
                  src/external/libPhotoMeissner/classes/Makefile \
-                 src/musredit/musredit_startup.xml \
+                 src/external/libGbGLF/Makefile \
+                 src/external/libBNMR/Makefile \
+                 src/musredit_qt5/Makefile \
+                 src/musredit/Makefile \
+                 src/musrgui/Makefile \
                  src/musrgui/musrgui_startup.xml])
 
 AC_OUTPUT
@@ -1160,10 +1299,16 @@ if test "x$enable_editor" != "xno" && test "x$QMAKEBIN" != "x"; then
 
   echo "Configuring ${QTEDITOR} ..."
 
+  if test "x${QTEDITOR}" = "xmusredit_qt5"; then
+    QTEDITOR_PRO="musredit"
+  else
+    QTEDITOR_PRO=${QTEDITOR}
+  fi
+
   echo "Changing directory to src/${QTEDITOR} and calling"
-  echo "${QMAKEBIN} CC=${CC} CXX=${CXX} PREFIX=${INSTALLDIR} ${QTEDITOR}.pro"
+  echo "${QMAKEBIN} CC=${CC} CXX=${CXX} PREFIX=${INSTALLDIR} ${QTEDITOR_PRO}.pro"
   cd src/${QTEDITOR}
-  ${QMAKEBIN} CC=${CC} CXX=${CXX} PREFIX=${INSTALLDIR} ${QTEDITOR}.pro
+  ${QMAKEBIN} CC=${CC} CXX=${CXX} PREFIX=${INSTALLDIR} ${QTEDITOR_PRO}.pro
   cd ../..
 
 fi
@@ -1270,6 +1415,11 @@ if test "${BUILD_AS_LIBS}" -eq 1; then
 else
   echo "     ASlibs:                              no"
 fi
+if test "${BUILD_BNMR_LIBS}" -eq 1; then
+  echo "     BNMRlibs:                            yes"
+else
+  echo "     BNMRlibs:                            no"
+fi
 if test "${BUILD_BMW_LIBS}" -eq 1; then
   echo "     BMWlibs:                             yes"
 else
@@ -1277,21 +1427,48 @@ else
 fi
 echo ""
 echo "   Qt musrfit editors:"
+if test "x$enable_editor" != "xno" && test "x${QMAKEBIN}" != "x" && test "x${QTEDITOR}" = "xmusredit_qt5"; then
+  echo "     musredit (Qt5):                      yes"
+else
+  echo "     musredit (Qt5):                      no"
+fi
 if test "x$enable_editor" != "xno" && test "x${QMAKEBIN}" != "x" && test "x${QTEDITOR}" = "xmusredit"; then
   echo "     musredit (Qt4):                      yes"
 else
   echo "     musredit (Qt4):                      no"
 fi
 if test "x$enable_editor" != "xno" && test "x${QMAKEBIN}" != "x" && test "x${QTEDITOR}" = "xmusrgui"; then
-  echo "     musrgui (Qt3):                       yes"
+  echo "     musrgui  (Qt3):                      yes"
 else
-  echo "     musrgui (Qt3):                       no"
+  echo "     musrgui  (Qt3):                      no"
 fi
 echo ""
 echo ""
 echo "   Installation directories:"
 echo "   -------------------------"
 echo ""
-echo "   Programs and XML configuration files:  ${INSTALLDIR}/bin"
-echo "   Documentation:                         ${DOCDIR}"
+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/BMWlibs/data/libGapIntegrals-test.dat

@@ -12,15 +12,25 @@ ENERGY: 4200
 # here the data will follow
 data
 # x, y, error y
-0.02, 12.0, 0.5
-0.1, 11.8, 0.8
-0.2, 9.9, 0.4
-0.33, 7.2, 0.15
-0.41, 3.8, 0.38
-0.5, 2.7, 0.5
-0.64, 1.0, 0.7
-0.7, 0.1, 0.2
-0.8, 0.0, 0.8
-0.9, 0.1, 0.5
-1.2, 0.0, 0.1
-
+0.0318411, 7.77455, 0.2
+0.0629929, 7.9869, 0.15
+0.113914, 7.64209, 0.15
+0.202492, 7.37699, 0.15
+0.302725, 7.70893, 0.12
+0.447456, 7.77565, 0.12
+0.611685, 7.45768, 0.12
+0.813613, 7.19287, 0.12
+1.00822, 7.57813, 0.12
+1.24793, 7.31343, 0.12
+1.50635, 7.16818, 0.12
+1.74591, 6.99634, 0.12
+1.99795, 6.90414, 0.12
+2.25061, 6.41393, 0.12
+2.4958, 6.66666, 0.12
+2.75514, 5.93766, 0.12
+3.00753, 5.61992, 0.12
+3.26056, 4.89091, 0.12
+3.49414, 4.52005, 0.08
+3.75356, 3.73799, 0.08
+3.99425, 2.84974, 0.08
+4.30518, 1.35139, 0.08

doc/examples/BMWlibs/test-libGapIntegrals-ASCII.msr

@@ -2,18 +2,16 @@ Test superconductor data
 ###############################################################
 FITPARAMETER
 #      Nr. Name        Value     Step      Pos_Error  Boundaries
-        1 lambdaInvSq0 11.69     0.39        none        
-        2 Tc          0.558     0.018       none        0       2       
-        3 Delta0      0.0673    0.0035      none        
-        4 aG          1         0           none        
+        1 lambdaInvSq0 7.983     -0.042      0.042       
+        2 Tc          4.470     -0.015      0.016       0       5       
+        3 Delta0      1.547     -0.026      0.027       
+        4 c0          1.468     0           none        
+        5 aG          1.33333   0           none        
 
 ###############################################################
 THEORY
 asymmetry      1
-userFcn  libGapIntegrals TGapSWave 2 3 4
-
-###############################################################
-#FUNCTIONS
+userFcn  libGapIntegrals TGapDWave 2 3 4 5
 
 ###############################################################
 RUN data/libGapIntegrals-test PIM3 PSI ASCII   (name beamline institute data-file-format)
@@ -26,15 +24,15 @@ packing         1
 ###############################################################
 COMMANDS
 MINIMIZE
-HESSE
-#MINOS
+#HESSE
+MINOS
 SAVE
 
 ###############################################################
 PLOT 8   (non muSR plot)
 runs     1   
-range    0   1.5
+range    0   6
 
 ###############################################################
-STATISTIC --- 2014-10-28 10:40:31
-  chisq = 14.3, NDF = 8, chisq/NDF = 1.790471
+STATISTIC --- 2015-06-25 08:39:03
+  chisq = 58.3, NDF = 19, chisq/NDF = 3.066272

doc/examples/UserFcn/Makefile.PUserFcn

@@ -0,0 +1,60 @@
+#---------------------------------------------------
+# get compilation flags from root-config
+
+ROOTCFLAGS    = $(shell $(ROOTSYS)/bin/root-config --cflags)
+
+#---------------------------------------------------
+
+OS            = LINUX
+CXX           = g++
+CXXFLAGS      = -O3 -Wall -Wno-trigraphs -fPIC
+LOCALINCLUDE  = .
+ROOTINCLUDE   = $(ROOTSYS)/include
+INCLUDES      = -I$(LOCALINCLUDE) -I$(ROOTINCLUDE)
+LD            = g++
+LDFLAGS       =
+SOFLAGS       = -O -shared
+
+# the output from the root-config script:
+CXXFLAGS      += $(ROOTCFLAGS)
+LDFLAGS       +=
+
+# some definitions: headers (used to generate *Dict* stuff), sources, objects,...
+OBJS =
+OBJS += PUserFcn.o PUserFcnDict.o
+
+SHLIB = libPUserFcn.so
+
+# make the shared lib:
+#
+all:  $(SHLIB)
+
+$(SHLIB): $(OBJS)
+	@echo "---> Building shared library $(SHLIB) ..."
+	/bin/rm -f $(SHLIB)
+	$(LD) $(OBJS) $(SOFLAGS) -o $(SHLIB)
+	@echo "done"
+
+# clean up: remove all object file (and core files)
+# semicolon needed to tell make there is no source
+# for this target!
+#
+clean:; 	@rm -f $(OBJS) *Dict* core*
+	@echo "---> removing $(OBJS)"
+
+#
+$(OBJS): %.o: %.cpp
+	$(CXX) $(INCLUDES) $(CXXFLAGS) -c $<
+
+# Generate the ROOT CLING dictionary
+
+PUserFcnDict.cpp: PUserFcn.h PUserFcnLinkDef.h
+	@echo "Generating dictionary $@..."
+	rootcling -f $@ -c -p -I$(ROOTINCLUDE) $^
+
+install: all
+	@echo "Installing shared lib: libTApproximation.so"
+ifeq ($(OS),LINUX)
+	cp -pv $(SHLIB) $(ROOTSYS)/lib
+	cp -pv $(LOCALINCLUDE)/*.h $(ROOTSYS)/include
+endif

doc/examples/UserFcn/PUserFcn.cpp

@@ -0,0 +1,59 @@
+/***************************************************************************
+
+  PUserFcn.cpp
+
+  Author: Andreas Suter
+  e-mail: andreas.suter@psi.ch
+
+***************************************************************************/
+
+/***************************************************************************
+ *   Copyright (C) 2007-2016 by Andreas Suter                              *
+ *   andreas.suter@psi.ch                                                  *
+ *                                                                         *
+ *   This program is free software; you can redistribute it and/or modify  *
+ *   it under the terms of the GNU General Public License as published by  *
+ *   the Free Software Foundation; either version 2 of the License, or     *
+ *   (at your option) any later version.                                   *
+ *                                                                         *
+ *   This program is distributed in the hope that it will be useful,       *
+ *   but WITHOUT ANY WARRANTY; without even the implied warranty of        *
+ *   MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the         *
+ *   GNU General Public License for more details.                          *
+ *                                                                         *
+ *   You should have received a copy of the GNU General Public License     *
+ *   along with this program; if not, write to the                         *
+ *   Free Software Foundation, Inc.,                                       *
+ *   59 Temple Place - Suite 330, Boston, MA  02111-1307, USA.             *
+ ***************************************************************************/
+
+#include <iostream>
+using namespace std;
+
+#include <cassert>
+
+#include "PUserFcn.h"
+
+ClassImp(PUserFcn)
+
+//------------------------------------------------------
+/**
+ * <p> user function example: polynome of 3rd order
+ *
+ * \f[ = \sum_{k=0}^3 c_k t^k \f]
+ *
+ * <b>meaning of paramValues:</b> \f$c_0\f$, \f$c_1\f$, \f$c_2\f$, \f$c_3\f$
+ *
+ * <b>return:</b> function value
+ *
+ * \param t time in \f$(\mu\mathrm{s})\f$, or x-axis value for non-muSR fit
+ * \param param parameter vector
+ */
+Double_t PUserFcn::operator()(Double_t t, const std::vector<Double_t> &param) const
+{
+  // expected parameters: c0, c1, c2, c3
+
+  assert(param.size() == 4);
+
+  return param[0] + param[1]*t + param[2]*t*t + param[3]*t*t*t;
+}

doc/examples/UserFcn/PUserFcn.h

@@ -0,0 +1,58 @@
+/***************************************************************************
+
+  PUserFcn.h
+
+  Author: Andreas Suter
+  e-mail: andreas.suter@psi.ch
+
+***************************************************************************/
+
+/***************************************************************************
+ *   Copyright (C) 2007-2016 by Andreas Suter                              *
+ *   andreas.suter@psi.ch                                                  *
+ *                                                                         *
+ *   This program is free software; you can redistribute it and/or modify  *
+ *   it under the terms of the GNU General Public License as published by  *
+ *   the Free Software Foundation; either version 2 of the License, or     *
+ *   (at your option) any later version.                                   *
+ *                                                                         *
+ *   This program is distributed in the hope that it will be useful,       *
+ *   but WITHOUT ANY WARRANTY; without even the implied warranty of        *
+ *   MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the         *
+ *   GNU General Public License for more details.                          *
+ *                                                                         *
+ *   You should have received a copy of the GNU General Public License     *
+ *   along with this program; if not, write to the                         *
+ *   Free Software Foundation, Inc.,                                       *
+ *   59 Temple Place - Suite 330, Boston, MA  02111-1307, USA.             *
+ ***************************************************************************/
+
+#ifndef _PUSERFCN_H_
+#define _PUSERFCN_H_
+
+#include <vector>
+
+#include "PUserFcnBase.h"
+
+/**
+ * <p>User function example class. Polynome of 3rd order.
+ */
+class PUserFcn : public PUserFcnBase
+{
+  public:
+    PUserFcn() {}
+    ~PUserFcn() {}
+
+    // global user-function-access functions, here without any functionality
+    Bool_t NeedGlobalPart() const { return false; }
+    void SetGlobalPart(vector<void*> &globalPart, UInt_t idx) { }
+    Bool_t GlobalPartIsValid() const { return true; }
+
+    // function operator
+    Double_t operator()(Double_t t, const std::vector<Double_t> &param) const;
+
+  // definition of the class for the ROOT dictionary
+  ClassDef(PUserFcn, 1)
+};
+
+#endif // _PUSERFCN_H_

doc/examples/UserFcn/PUserFcnLinkDef.h

@@ -0,0 +1,15 @@
+/***************************************************************************
+
+  PUserFcnLinkDef.h
+
+***************************************************************************/
+
+#ifdef __CINT__
+
+#pragma link off all globals;
+#pragma link off all classes;
+#pragma link off all functions;
+
+#pragma link C++ class PUserFcn+;
+
+#endif //__CINT__

doc/examples/UserFcn/README

@@ -0,0 +1,89 @@
+/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/
+
+Simple Example for a User Function without Global Part
+
+/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/
+
+Goal: define a user function which implements a polynom
+      of 3rd order.
+
+For details see: http://lmu.web.psi.ch/musrfit/user/MUSR/MusrFit.html#A_6_User_Functions
+
+Implementation:
+      3 Files are needed:
+
+      1) A header file which defines your user function
+         interface.
+ 
+         In the example here it is called PUserFcn.h
+
+         Please rename it in your case to something more
+         sensible, e.g. PMyPoly.h. At the same time also 
+         rename correspondingly the class name in your 
+         header file, i.e. PUserFcn -> PMyPoly. This will
+         be at 4 places in the header file of this example.
+
+      2) The source file which defines your user function.
+
+         In the example here it is called PUserFcn.cpp
+
+         Please rename it accordingly to the header file.
+         In case the header file is called PMyPoly.h, the
+         source file will need to be called PMyPoly.cpp.
+         As for the header file, the class names need to 
+         be adopted: PUserFcn -> PMyPoly.
+
+         In the source file change the operator implementation
+         (Double_t PUserFcn::operator()(Double_t t, 
+                   const std::vector<Double_t> &param) const)
+         to whatever you need.
+
+      3) There is another header file needed to generate
+         the necessary ROOT dictionary.
+
+         In this example it is called PUserFcnLinkDef.h
+
+         Here you only will need to find PUserFcn+ and 
+         replace it with your class name, e.g. PMyPoly+
+
+Generate Code:
+      You will find the Makefil.PUserFcn which generates
+      the needed shared library for your user function.
+
+      Again, if your user function is called PMyPoly, you
+      will need to replace things accordingly in the 
+      Makefile, i.e.
+
+      Makefile.PUserFcn -> Makefile.PMyPoly
+
+      In the Makefile:
+
+      PUserFcn.o      ->  PMyPoly.o
+      PUserFcnDict.o  ->  PMyPolyDict.o
+      libPUserFcn.so  ->  libPMyPoly.so
+
+      To create the shared library do:
+
+      make -f Makefile.PUserFcn
+
+      on the command line. This should create a file      
+      libPUserFcn.so.
+
+      Next call on the command line:
+
+      make -f Makefile.PUserFcn install
+
+      This will copy the shared library to the correct
+      place. 
+
+      You also will need to make sure that the system is
+      finding the shared library, either by setting
+      LD_LIBRARY_PATH or by calling /sbin/ldconfig as 
+      superuser/root assuming you are using linux.
+
+Example msr-file:
+      You will find an example msr-file test-asy-MUS.msr
+      which is using PUserFcn. The example is UN-PHYSICALLY
+      it is just to show how to use a user function. 
+      
+ 

doc/examples/UserFcn/test-asy-MUD.msr

@@ -0,0 +1,55 @@
+MgB12H12 No2 ZF T=150
+###############################################################
+FITPARAMETER
+#      Nr. Name        Value     Step      Pos_Error  Boundaries
+        1 alpha       1         0           none        0       2       
+        2 asy         0.1650    0.0027      none        0       0.33    
+        3 c0          1.047     0.016       none        
+        4 c1          -0.1957   0.0038      none        
+        5 c2          0.0216    0.0011      none        
+        6 c3          -0.00119  0.00011     none        
+
+###############################################################
+THEORY
+asymmetry      2
+userFcn  libPUserFcn PUserFcn 3 4 5 6
+
+###############################################################
+RUN data/000100 XXXX TRIUMF MUD   (name beamline institute data-file-format)
+fittype         2         (asymmetry fit)
+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: 21.0833 / 17.2249
+data            438     12785   436     12787   
+t0              432.0   431.0   
+fit             0       8      
+packing         100
+
+###############################################################
+COMMANDS
+MINIMIZE
+MINOS
+#HESSE
+SAVE
+
+###############################################################
+FOURIER
+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
+phase            8
+#range_for_phase_correction 50.0 70.0
+range            0    2000
+dc-corrected     true
+
+###############################################################
+PLOT 2   (asymmetry plot)
+runs     1   
+range    0   9   0   0.22
+
+###############################################################
+STATISTIC --- 2016-06-22 09:34:01
+  chisq = 152.4, NDF = 97, chisq/NDF = 1.571461

doc/examples/test-asy-HAL9500-RRF.msr

@@ -0,0 +1,178 @@
+MnSi, FLC68.2, 50 K                                           
+###############################################################
+FITPARAMETER
+#      Nr. Name       Value     Step      Pos_Error Boundaries   
+        1 rate_1      1.680     0.019       none        
+        2 field_1     1589.71   0.20        none        
+        3 rate_2      1.863     0.065       none        
+        4 field_2     788.86    0.49        none        
+
+        5 alpha_f15   1.0029    0.0015      none        
+        6 frac_f15    0.7350    0.0090      none        
+        7 asym_f15    0.2713    0.0043      none        0       none    
+        8 phase_f15   79.37     0.80        none        
+
+        9 alpha_f26   0.9996    0.0015      none        
+       10 frac_f26    0.7408    0.0085      none        
+       11 asym_f26    0.3029    0.0046      none        0       none    
+       12 phase_f26   30.22     0.73        none        
+
+       13 alpha_f37   1.0003    0.0015      none        
+       14 frac_f37    0.88      0.23        none        
+       15 asym_f37    0.0126    0.0045      none        0       none    
+       16 phase_f37   58.0      15.0        none        
+
+       17 alpha_f48   0.9999    0.0015      none        
+       18 frac_f48    0.7344    0.0084      none        
+       19 asym_f48    0.2929    0.0043      none        0       none    
+       20 phase_f48   -33.13    0.76        none        
+
+       21 alpha_b15   0.9991    0.0013      none        
+       22 frac_b15    0.7439    0.0077      none        
+       23 asym_b15    0.2807    0.0038      none        0       none    
+       24 phase_b15   164.98    0.68        none        
+
+       25 alpha_b26   1.0003    0.0013      none        
+       26 frac_b26    0.7331    0.0078      none        
+       27 asym_b26    0.2810    0.0038      none        0       none    
+       28 phase_b26   119.49    0.70        none        
+
+       29 alpha_b37   0.9989    0.0012      none        
+       30 frac_b37    0.7504    0.0078      none        
+       31 asym_b37    0.2755    0.0037      none        0       none    
+       32 phase_b37   102.07    0.69        none        
+
+       33 alpha_b48   0.9990    0.0012      none        
+       34 frac_b48    0.7391    0.0080      none        
+       35 asym_b48    0.2763    0.0039      none        0       none    
+       36 phase_b48   37.66     0.67        none        
+
+###############################################################
+THEORY
+asymmetry   fun1
+simplExpo      1          (rate)
+TFieldCos   map3  fun3       (phase frequency)
++
+asymmetry   fun2
+simplExpo      3          (rate)
+TFieldCos   map3  fun4       (phase frequency)
+
+###############################################################
+FUNCTIONS
+fun1 = map1 * map2
+fun2 = (1 - map1) * map2
+fun3 = gamma_mu * par2
+fun4 = gamma_mu * par4
+
+###############################################################
+GLOBAL
+fittype         3         (asymmetry RRF fit)
+fit             0.0005  6      
+rrf_freq        7.15     T
+rrf_packing     300     
+rrf_phase       0.00    
+
+###############################################################
+# Fw1-Fw5 +++++++
+RUN data/tdc_hifi_2014_00153 PIE3 PSI PSI-MDU   (name beamline institute data-file-format)
+alpha           5
+map             6    7    8    0    0    0    0    0    0    0    0
+forward         2 
+backward        6 
+background      500     15000   500     15000      # estimated bkg: 0.0492 / 0.0501
+data            20158   409500  20130   409500  
+t0              20108.0 20080.0 
+
+# Fw2-Fw6 +++++++
+RUN data/tdc_hifi_2014_00153 PIE3 PSI PSI-MDU   (name beamline institute data-file-format)
+alpha           9
+map            10   11   12    0    0    0    0    0    0    0    0
+forward         3 
+backward        7 
+background      500     15000   500     15000      # estimated bkg: 0.0501 / 0.0451
+data            20138   409500  20121   409500  
+t0              20088.0 20071.0 
+
+# Fw3-Fw7 +++++++
+RUN data/tdc_hifi_2014_00153 PIE3 PSI PSI-MDU   (name beamline institute data-file-format)
+alpha           13
+map            14   15   16    0    0    0    0    0    0    0    0
+forward         3 
+backward        8 
+background      500     15000   500     15000      # estimated bkg: 0.0501 / 0.0449
+data            20111   409500  20116   409500  
+t0              20061.0 20066.0 
+
+# Fw4-Fw8 +++++++
+RUN data/tdc_hifi_2014_00153 PIE3 PSI PSI-MDU   (name beamline institute data-file-format)
+alpha           17
+map            18   19   20    0    0    0    0    0    0    0    0
+forward         5 
+backward        9 
+background      500     15000   500     15000      # estimated bkg: 0.0560 / 0.0462
+data            20121   409500  20082   409500  
+t0              20071.0 20032.0 
+
+# Bw1-Bw5 +++++++
+RUN data/tdc_hifi_2014_00153 PIE3 PSI PSI-MDU   (name beamline institute data-file-format)
+alpha           21
+map            22   23   24    0    0    0    0    0    0    0    0
+forward         10 
+backward        14 
+background      500     15000   500     15000      # estimated bkg: 0.0641 / 0.0806
+data            20072   409500  20067   409500  
+t0              20022.0 20017.0 
+
+# Bw2-Bw6 +++++++
+RUN data/tdc_hifi_2014_00153 PIE3 PSI PSI-MDU   (name beamline institute data-file-format)
+alpha           25
+map            26   27   28    0    0    0    0    0    0    0    0
+forward         11 
+backward        15 
+background      500     15000   500     15000      # estimated bkg: 0.0689 / 0.0768
+data            20076   409500  20069   409500  
+t0              20026.0 20019.0 
+
+# Bw3-Bw7 +++++++
+RUN data/tdc_hifi_2014_00153 PIE3 PSI PSI-MDU   (name beamline institute data-file-format)
+alpha           29
+map            30   31   32    0    0    0    0    0    0    0    0
+forward         12 
+backward        16 
+background      500     15000   500     15000      # estimated bkg: 0.0769 / 0.0795
+data            20060   409500  20069   409500  
+t0              20010.0 20019.0 
+
+# Bw4-Bw8 +++++++
+RUN data/tdc_hifi_2014_00153 PIE3 PSI PSI-MDU   (name beamline institute data-file-format)
+alpha           33
+map            34   35   36    0    0    0    0    0    0    0    0
+forward         13 
+backward        17 
+background      500     15000   500     15000      # estimated bkg: 0.0761 / 0.0702
+data            20063   409500  20089   409500  
+t0              20013.0 20039.0 
+
+###############################################################
+COMMANDS
+#MAX_LIKELIHOOD
+PRINT_LEVEL 2
+MINIMIZE
+#MINOS
+SAVE
+
+###############################################################
+PLOT 3   (asymmetry RRF plot)
+runs     1   2   3   4   5   6   7   8   
+range    0   9.07   -0.5   0.5
+
+###############################################################
+FOURIER
+units            Gauss   # units either 'Gauss', 'Tesla', 'MHz', or 'Mc/s'
+fourier_power    11
+apodization      STRONG  # NONE, WEAK, MEDIUM, STRONG
+plot             POWER   # REAL, IMAG, REAL_AND_IMAG, POWER, PHASE
+
+###############################################################
+STATISTIC --- 2016-01-18 16:23:00
+  chisq = 7402.2, NDF = 6516, chisq/NDF = 1.135997

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-HAL9500-RRF.msr

@@ -0,0 +1,235 @@
+MnSi, FLC68.2, 50 K                                           
+###############################################################
+FITPARAMETER
+#      Nr. Name       Value     Step      Pos_Error Boundaries   
+        1 Rate_1      1.678     0.018       none        
+        2 Field_1_RRF 1589.66   0.19        none        
+        3 Rate_2      1.948     0.064       none        
+        4 Field_2_RRF 788.93    0.47        none        
+        
+        5 Asym_1      0.3102    0.0067      none        
+        6 Frc_1       0.728     0.012       none        
+        7 Phase_1     57.3      1.1         none        
+
+        8 Asym_2      0.3073    0.0066      none        
+        9 Frc_2       0.748     0.012       none        
+       10 Phase_2     30.6      1.0         none        
+
+       11 Asym_3      0.3245    0.0065      none        
+       12 Frc_3       0.728     0.011       none        
+       13 Phase_3     18.70     0.96        none        
+
+       14 Asym_4      0.3290    0.0062      none        
+       15 Frc_4       0.733     0.011       none        
+       16 Phase_4     339.27    0.96        none        
+
+       17 Asym_5      0.3213    0.0062      none        
+       18 Frc_5       0.730     0.011       none        
+       19 Phase_5     282.5     1.0         none        
+
+       20 Asym_6      0.3424    0.0072      none        
+       21 Frc_6       0.726     0.012       none        
+       22 Phase_6     211.3     1.0         none        
+
+       23 Asym_7      0.3321    0.0069      none        
+       24 Frc_7       0.731     0.012       none        
+       25 Phase_7     161.7     1.1         none        
+
+       26 Asym_8      0.3219    0.0067      none        
+       27 Frc_8       0.730     0.012       none        
+       28 Phase_8     133.7     1.1         none        
+
+       29 Asym_9      0.3030    0.0058      none        
+       30 Frc_9       0.730     0.011       none        
+       31 Phase_9     158.87    0.97        none        
+
+       32 Asym_10     0.3046    0.0057      none        
+       33 Frc_10      0.731     0.011       none        
+       34 Phase_10    129.97    0.97        none        
+
+       35 Asym_11     0.2898    0.0055      none        
+       36 Frc_11      0.754     0.011       none        
+       37 Phase_11    101.80    0.96        none        
+
+       38 Asym_12     0.3013    0.0055      none        
+       39 Frc_12      0.740     0.010       none        
+       40 Phase_12    43.00     0.88        none        
+
+       41 Asym_13     0.3009    0.0054      none        
+       42 Frc_13      0.747     0.010       none        
+       43 Phase_13    351.72    0.88        none        
+
+       44 Asym_14     0.3054    0.0053      none        
+       45 Frc_14      0.729     0.010       none        
+       46 Phase_14    289.91    0.91        none        
+
+       47 Asym_15     0.2931    0.0053      none        
+       48 Frc_15      0.740     0.010       none        
+       49 Phase_15    282.39    0.94        none        
+
+       50 Asym_16     0.2814    0.0058      none        
+       51 Frc_16      0.729     0.011       none        
+       52 Phase_16    212.89    0.99        none        
+
+###############################################################
+THEORY
+asymmetry   fun1
+simplExpo      1          (rate)
+TFieldCos   map3  fun3       (phase frequency)
++
+asymmetry   fun2
+simplExpo      3          (rate)
+TFieldCos   map3  fun4       (phase frequency)
+
+###############################################################
+FUNCTIONS
+fun1 = map1 * map2
+fun2 = map1 * (1 - map2)
+fun3 = par2 * gamma_mu
+fun4 = par4 * gamma_mu
+
+###############################################################
+GLOBAL
+fittype         1         (single histogram RRF fit)
+rrf_freq        7.15     T
+rrf_packing     300     
+rrf_phase       0.00    
+fit             0.0005  10     
+
+###############################################################
+RUN data/tdc_hifi_2014_00153 PIE3 PSI PSI-MDU   (name beamline institute data-file-format)
+map             5    6    7    0    0    0    0    0    0    0    0
+forward         2 
+background      100     18000      # estimated bkg: 0.0476
+data            20208   409500  
+t0              20108.0 
+#--------------------------------------------------------------
+RUN data/tdc_hifi_2014_00153 PIE3 PSI PSI-MDU   (name beamline institute data-file-format)
+map             8    9   10    0    0    0    0    0    0    0    0
+forward         3 
+background      100     18000      # estimated bkg: 0.0490
+data            20188   409500  
+t0              20088.0 
+#--------------------------------------------------------------
+RUN data/tdc_hifi_2014_00153 PIE3 PSI PSI-MDU   (name beamline institute data-file-format)
+map            11   12   13    0    0    0    0    0    0    0    0
+forward         4 
+background      100     18000      # estimated bkg: 0.0582
+data            20161   409500  
+t0              20061.0 
+#--------------------------------------------------------------
+RUN data/tdc_hifi_2014_00153 PIE3 PSI PSI-MDU   (name beamline institute data-file-format)
+map            14   15   16    0    0    0    0    0    0    0    0
+forward         5 
+background      100     18000      # estimated bkg: 0.0553
+data            20171   409500  
+t0              20071.0 
+#--------------------------------------------------------------
+RUN data/tdc_hifi_2014_00153 PIE3 PSI PSI-MDU   (name beamline institute data-file-format)
+map            17   18   19    0    0    0    0    0    0    0    0
+forward         6 
+background      100     18000      # estimated bkg: 0.0515
+data            20180   409500  
+t0              20080.0 
+#--------------------------------------------------------------
+RUN data/tdc_hifi_2014_00153 PIE3 PSI PSI-MDU   (name beamline institute data-file-format)
+map            20   21   22    0    0    0    0    0    0    0    0
+forward         7 
+background      100     18000      # estimated bkg: 0.0458
+data            20171   409500  
+t0              20071.0 
+#--------------------------------------------------------------
+RUN data/tdc_hifi_2014_00153 PIE3 PSI PSI-MDU   (name beamline institute data-file-format)
+map            23   24   25    0    0    0    0    0    0    0    0
+forward         8 
+background      100     18000      # estimated bkg: 0.0466
+data            20166   409500  
+t0              20066.0 
+#--------------------------------------------------------------
+RUN data/tdc_hifi_2014_00153 PIE3 PSI PSI-MDU   (name beamline institute data-file-format)
+map            26   27   28    0    0    0    0    0    0    0    0
+forward         9 
+background      100     18000      # estimated bkg: 0.0457
+data            20132   409500  
+t0              20032.0 
+#--------------------------------------------------------------
+RUN data/tdc_hifi_2014_00153 PIE3 PSI PSI-MDU   (name beamline institute data-file-format)
+map            29   30   31    0    0    0    0    0    0    0    0
+forward         10 
+background      100     18000      # estimated bkg: 0.0635
+data            20122   409500  
+t0              20022.0 
+#--------------------------------------------------------------
+RUN data/tdc_hifi_2014_00153 PIE3 PSI PSI-MDU   (name beamline institute data-file-format)
+map            32   33   34    0    0    0    0    0    0    0    0
+forward         11 
+background      100     18000      # estimated bkg: 0.0685
+data            20126   409500  
+t0              20026.0 
+#--------------------------------------------------------------
+RUN data/tdc_hifi_2014_00153 PIE3 PSI PSI-MDU   (name beamline institute data-file-format)
+map            35   36   37    0    0    0    0    0    0    0    0
+forward         12 
+background      100     18000      # estimated bkg: 0.0752
+data            20110   409500  
+t0              20010.0 
+#--------------------------------------------------------------
+RUN data/tdc_hifi_2014_00153 PIE3 PSI PSI-MDU   (name beamline institute data-file-format)
+map            38   39   40    0    0    0    0    0    0    0    0
+forward         13 
+background      100     18000      # estimated bkg: 0.0760
+data            20113   409500  
+t0              20013.0 
+#--------------------------------------------------------------
+RUN data/tdc_hifi_2014_00153 PIE3 PSI PSI-MDU   (name beamline institute data-file-format)
+map            41   42   43    0    0    0    0    0    0    0    0
+forward         14 
+background      100     18000      # estimated bkg: 0.0809
+data            20117   409500  
+t0              20017.0 
+#--------------------------------------------------------------
+RUN data/tdc_hifi_2014_00153 PIE3 PSI PSI-MDU   (name beamline institute data-file-format)
+map            44   45   46    0    0    0    0    0    0    0    0
+forward         15 
+background      100     18000      # estimated bkg: 0.0755
+data            20119   409500  
+t0              20019.0 
+#--------------------------------------------------------------
+RUN data/tdc_hifi_2014_00153 PIE3 PSI PSI-MDU   (name beamline institute data-file-format)
+map            47   48   49    0    0    0    0    0    0    0    0
+forward         16 
+background      100     18000      # estimated bkg: 0.0796
+data            20119   409500  
+t0              20019.0 
+#--------------------------------------------------------------
+RUN data/tdc_hifi_2014_00153 PIE3 PSI PSI-MDU   (name beamline institute data-file-format)
+map            50   51   52    0    0    0    0    0    0    0    0
+forward         17 
+background      100     18000      # estimated bkg: 0.0702
+data            20139   409500  
+t0              20039.0 
+
+###############################################################
+COMMANDS
+#MAX_LIKELIHOOD
+PRINT_LEVEL 2
+MINIMIZE
+#MINOS
+SAVE
+
+###############################################################
+PLOT 1   (single histo RRF plot)
+runs     1   2   3   4   5   6   7   8   9   10  11  12  13  14  15  16  
+range    0   9.07   -0.5   0.5
+
+###############################################################
+FOURIER
+units            Gauss   # units either 'Gauss', 'Tesla', 'MHz', or 'Mc/s'
+fourier_power    12
+apodization      MEDIUM  # NONE, WEAK, MEDIUM, STRONG
+plot             POWER   # REAL, IMAG, REAL_AND_IMAG, POWER, PHASE
+#range            7.1    7.5
+
+###############################################################
+STATISTIC --- 2016-01-14 13:24:36
+  chisq = 22007.6, NDF = 20700, chisq/NDF = 1.063168

doc/examples/test-histo-muMinus.msr

@@ -0,0 +1,199 @@
+07770 - test
+###############################################################
+FITPARAMETER
+#      Nr. Name       Value     Step      Pos_Error Boundaries   
+        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      135.53823 0.00073     none        
+
+        5 N_1         306.1     1.3         none        
+        6 tau_1       0.7409    0.0026      none        0       none    
+        7 Rate_1      0.027     0.031       none        0       none    
+        8 Freq_1      136.8968  0.0033      none        
+
+        9 Asym_F1_0   0.0490    0.0015      none        0       none    
+       10 Asym_F1_1   0.0501    0.0029      none        0       none    
+       11 Phase_F1    4.9       1.5         none        
+       12 N_bgk_F1    1.880     0.034       none        
+        
+       13 Asym_F2_0   0.0496    0.0015      none        0       none    
+       14 Asym_F2_1   0.0581    0.0030      none        0       none    
+       15 Phase_F2    52.4      1.5         none        
+       16 N_bgk_F2    1.508     0.033       none        
+
+       17 Asym_F3_0   0.0486    0.0015      none        0       none    
+       18 Asym_F3_1   0.0593    0.0030      none        0       none    
+       19 Phase_F3    95.2      1.5         none        
+       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    0.0030      none        0       none    
+       23 Phase_F4    144.6     1.5         none        
+       24 N_bgk_F4    2.311     0.034       none        
+
+       25 Asym_F5_0   0.0542    0.0015      none        0       none    
+       26 Asym_F5_1   0.0537    0.0030      none        0       none    
+       27 Phase_F5    188.4     1.4         none        
+       28 N_bgk_F5    1.799     0.033       none        
+
+       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     0.034       none        
+
+       33 Asym_F7_0   0.0488    0.0015      none        0       none    
+       34 Asym_F7_1   0.0575    0.0030      none        0       none    
+       35 Phase_F7    273.0     1.5         none        
+       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    0.0030      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    0.0030      none        0       none    
+       43 Phase_B1    3.6       1.5         none        
+       44 N_bgk_B1    1.378     0.033       none        
+
+       45 Asym_B2_0   0.0524    0.0015      none        0       none    
+       46 Asym_B2_1   0.0495    0.0030      none        0       none    
+       47 Phase_B2    53.7      1.5         none        
+       48 N_bgk_B2    1.272     0.032       none        
+
+       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    98.2      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    
+       55 Phase_B4    141.8     1.5         none        
+       56 N_bgk_B4    1.233     0.032       none        
+
+       57 Asym_B5_0   0.0515    0.0015      none        0       none    
+       58 Asym_B5_1   0.0584    0.0030      none        0       none    
+       59 Phase_B5    182.2     1.4         none        
+       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    0.0030      none        0       none    
+       63 Phase_B6    231.7     1.5         none        
+       64 N_bgk_B6    1.650     0.033       none        
+
+       65 Asym_B7_0   0.0514    0.0015      none        0       none    
+       66 Asym_B7_1   0.0539    0.0030      none        0       none    
+       67 Phase_B7    275.2     1.5         none        
+       68 N_bgk_B7    1.729     0.033       none        
+
+       69 Asym_B8_0   0.0541    0.0015      none        0       none    
+       70 Asym_B8_1   0.0444    0.0030      none        0       none    
+       71 Phase_B8    321.0     1.5         none        
+       72 N_bgk_B8    1.136     0.032       none        
+
+###############################################################
+THEORY
+muMinusExpTF     1     2  map1     3  map3     4 (N0 tau A lambda phase nu)
++
+muMinusExpTF     5     6  map2     7  map3     8 (N0 tau A lambda phase nu)
++
+asymmetry   map4
+
+###############################################################
+GLOBAL
+fittype         4         (mu minus fit)
+t0              20000.0 
+data            20100   409500  
+fit             0.0005  9      
+packing         25
+
+###############################################################
+RUN data/07770 PIE3 PSI MUSR-ROOT   (name beamline institute data-file-format)
+map             9   10   11   12    0    0    0    0    0    0    0    0
+forward         1 
+#--------------------------------------------------------------
+RUN data/07770 PIE3 PSI MUSR-ROOT   (name beamline institute data-file-format)
+map            13   14   15   16    0    0    0    0    0    0    0    0
+forward         2 
+#--------------------------------------------------------------
+RUN data/07770 PIE3 PSI MUSR-ROOT   (name beamline institute data-file-format)
+map            17   18   19   20    0    0    0    0    0    0    0    0
+forward         3 
+#--------------------------------------------------------------
+RUN data/07770 PIE3 PSI MUSR-ROOT   (name beamline institute data-file-format)
+map            21   22   23   24    0    0    0    0    0    0    0    0
+forward         4 
+#--------------------------------------------------------------
+RUN data/07770 PIE3 PSI MUSR-ROOT   (name beamline institute data-file-format)
+map            25   26   27   28    0    0    0    0    0    0    0    0
+forward         5 
+#--------------------------------------------------------------
+RUN data/07770 PIE3 PSI MUSR-ROOT   (name beamline institute data-file-format)
+map            29   30   31   32    0    0    0    0    0    0    0    0
+forward         6 
+#--------------------------------------------------------------
+RUN data/07770 PIE3 PSI MUSR-ROOT   (name beamline institute data-file-format)
+map            33   34   35   36    0    0    0    0    0    0    0    0
+forward         7 
+#--------------------------------------------------------------
+RUN data/07770 PIE3 PSI MUSR-ROOT   (name beamline institute data-file-format)
+map            37   38   39   40    0    0    0    0    0    0    0    0
+forward         8 
+#--------------------------------------------------------------
+RUN data/07770 PIE3 PSI MUSR-ROOT   (name beamline institute data-file-format)
+map            41   42   43   44    0    0    0    0    0    0    0    0
+forward         9 
+#--------------------------------------------------------------
+RUN data/07770 PIE3 PSI MUSR-ROOT   (name beamline institute data-file-format)
+map            45   46   47   48    0    0    0    0    0    0    0    0
+forward         10 
+#--------------------------------------------------------------
+RUN data/07770 PIE3 PSI MUSR-ROOT   (name beamline institute data-file-format)
+map            49   50   51   52    0    0    0    0    0    0    0    0
+forward         11 
+#--------------------------------------------------------------
+RUN data/07770 PIE3 PSI MUSR-ROOT   (name beamline institute data-file-format)
+map            53   54   55   56    0    0    0    0    0    0    0    0
+forward         12 
+#--------------------------------------------------------------
+RUN data/07770 PIE3 PSI MUSR-ROOT   (name beamline institute data-file-format)
+map            57   58   59   60    0    0    0    0    0    0    0    0
+forward         13 
+#--------------------------------------------------------------
+RUN data/07770 PIE3 PSI MUSR-ROOT   (name beamline institute data-file-format)
+map            61   62   63   64    0    0    0    0    0    0    0    0
+forward         14 
+#--------------------------------------------------------------
+RUN data/07770 PIE3 PSI MUSR-ROOT   (name beamline institute data-file-format)
+map            65   66   67   68    0    0    0    0    0    0    0    0
+forward         15 
+#--------------------------------------------------------------
+RUN data/07770 PIE3 PSI MUSR-ROOT   (name beamline institute data-file-format)
+map            69   70   71   72    0    0    0    0    0    0    0    0
+forward         16 
+
+###############################################################
+COMMANDS
+MAX_LIKELIHOOD
+PRINT_LEVEL 2
+MINIMIZE
+#MINOS
+SAVE
+
+###############################################################
+PLOT 4   (mu minus plot)
+runs        1   2   3   4   5   6   7   8   9  10  11  12  13  14  15  16
+range    0   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, PHASE_OPT_REAL
+range            0.8    1.2
+
+###############################################################
+STATISTIC --- 2017-02-08 07:11:01
+  maxLH = 238962.5, NDF = 230264, maxLH/NDF = 1.037776

doc/html/user/MUSR/BmwLibs.html

@@ -1,35 +1,38 @@
-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd"><html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en_US" lang="en_US">
+<!DOCTYPE html><html lang="en">
 
-<!-- Mirrored from intranet.psi.ch/MUSR/BmwLibs?cover=print by HTTrack Website Copier/3.x [XR&CO'2010], Thu, 18 Dec 2014 13:46:44 GMT -->
-<!-- Added by HTTrack --><meta http-equiv="content-type" content="text/html;charset=iso-8859-1"><!-- /Added by HTTrack -->
+<!-- Mirrored from intranet.psi.ch/MUSR/BmwLibs?cover=print by HTTrack Website Copier/3.x [XR&CO'2014], Fri, 08 Jun 2018 13:42:27 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>
-<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1" />
+<title> MUSR :: BmwLibs</title>
+<meta http-equiv="X-UA-Compatible" content="IE=edge" />
+<meta charset="utf-8" />
+<meta name="viewport" content="width=device-width, initial-scale=1, maximum-scale=1.5, user-scalable=yes" />
+<meta name="mobile-web-app-capable" content="yes" />
+<meta name="mobile-web-app-status-bar-style" content="black-translucent" />
+<meta name="apple-mobile-web-app-capable" content="yes" />
+<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=1418910336" type="application/x-wiki" title="edit BmwLibs" />
+<link rel="alternate" href="https://intranet.psi.ch/wiki/bin/edit/MUSR/BmwLibs?t=1528465298" 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 rel='stylesheet' href='../pub/System/ImagePlugin/style.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 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/SkinTemplates/base.css');
-</style>
-<style type="text/css" media="all">
-@import url('../pub/System/PatternSkinTheme2009/layout.css');
+@import url('../pub/System/PatternSkinTheme/layout.css');
 @import url('../pub/System/PatternSkinTheme2009/style.css');
 @import url('../pub/System/PatternSkinTheme2009/colors.css');
 </style>
-<style type="text/css" media="all">
-@import url('../pub/System/PatternSkinTheme2009/column_left.css');
-@import url('../pub/System/PatternSkinTheme2009/variant_twiki.css');
-</style><style type="text/css" media="all">
+<link rel='stylesheet' href='../pub/System/PatternSkinTheme2009/column_left.css' media='all' type='text/css' />
+<link rel='stylesheet' href='../pub/System/PatternSkinTheme2009/variant_twiki.css' media='all' type='text/css' /><style type="text/css" media="all">
 	/* Styles that are set using variables */
 	.patternBookView .foswikiTopRow,
-	.patternWebIndicator a img,
-	.patternWebIndicator a:hover img {
+	.patternWebIndicator,
+	.patternWebIndicator a {
 		background-color:#D0D0D0;
 	}
 	#patternTopBarContents { background-image:url(../pub/System/PatternSkin/header5.gif); background-repeat:repeat-x;}
@@ -50,14 +53,8 @@
 	
 
 
-<style type="text/css" media="all">
-	@import url("../pub/System/PatternSkin/print.css");
-</style>
-<!--[if IE]><style type="text/css" media="screen">
-pre {
-	height:1%;
-	overflow-x:auto;
-}
+<link rel='stylesheet' href='../pub/System/PatternSkin/print.css' media='all' type='text/css' />
+<!--[if IE 7 ]><style type="text/css" media="screen">
 .foswikiAttachments,
 .foswikiForm,
 .foswikiHelp,
@@ -79,7 +76,17 @@ pre {
 .foswikiFormStep {
 	height:100%;
 }
-#foswikiLogin,
+#foswikiLogin {
+	 margin-left: 25%;
+	 margin-right: 25%;
+}
+#foswikiLogin .foswikiFormSteps {
+	 width:auto;
+}
+#foswikiLogin input[type="text"],
+#foswikiLogin input[type="password"] {
+	 width: auto;
+}
 .patternShadow {
 	border:10px solid #fff;
 	margin-top:10px;
@@ -87,118 +94,60 @@ pre {
 	border:2px solid #ccc;
 }
 </style><![endif]-->
-<!--[if gt IE 8 ]><style type="text/css" media="screen">
-#foswikiLogin,
-.patternShadow {
-	border:10px solid #fff;
-	margin-top:10px;
-	margin-bottom:10px;
-	box-shadow: 0 0 10px #ccc;
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-</style><![endif]-->
-<link rel="stylesheet" href="../pub/System/FootNotePlugin/styles.css" type="text/css" media="all" /><!--FOOTNOTEPLUGIN_LINKCSS-->
-</head>
-<body class="foswikiNoJs patternViewPage">
-<a name="PageTop"></a><div class="foswikiPage"><div id="patternScreen">
+<!--[if lte IE 9]>
+
+<![endif]-->
+<!--[if gt IE 9]><!-->
+
+<!--<![endif]-->
+<!--JQUERYPLUGIN-->
+<!--JQUERYPLUGIN::MIGRATE-->
+<!--JQUERYPLUGIN::LIVEQUERY-->
+<!--JQUERYPLUGIN::FOSWIKI-->
+<!--JavascriptFiles/foswikiString-->
+<!--JavascriptFiles/foswikiPref-->
+<!--JQUERYPLUGIN::COMMENT-->
+<!--JQUERYPLUGIN::FOSWIKI::PREFERENCES-->
+<!--JavascriptFiles/foswikiForm-->
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-<h1><a name="BMWlibs_for_61musrfit_61"></a>  BMWlibs for <code>musrfit</code> </h1> <ul>
+<h1 id="BMWlibs_for_61musrfit_61">  BMWlibs for <code>musrfit</code> </h1> <ul>
 <li> <a href="LibFitPofB.html"> <code>libFitPofB</code>: routines for calculating transverse-field muon-spin depolarization functions from various static field distributions in superconductors</a>
 </li> <li> <a href="LibZFRelaxation.html"> <code>libZFRelaxation</code>: routines for calculating zero-field muon-spin depolarization functions from various static field distributions</a>
 </li></ul> 
 <p></p>
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+<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>BmwLibs <br />
+Topic revision:  <span class='patternRevInfo'>03 Jul 2015, suter_a</span></div>
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doc/html/user/MUSR/CiteMusrFit.html

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 <p></p>
 Since quite some effort is going into the development and maintenance of the <code>musrfit</code> package, you should at least acknowledge it in your publication if you have used it to analyze your data. Even better of course is to cite it properly by the reference given beneath 
 <p></p> <ul>
-<li>  <a href="http://dx.doi.org/10.1016/j.phpro.2012.04.042" target="_top">A. Suter, B.M. Wojek, "Musrfit: A Free Platform-Independent Framework for &mu;SR Data Analysis", Physics Procedia 30, 69 (2012).</a>
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+<li>  <a href="http://dx.doi.org/10.1016/j.phpro.2012.04.042">A. Suter, B.M. Wojek, "Musrfit: A Free Platform-Independent Framework for &mu;SR Data Analysis", Physics Procedia <strong>30</strong>, 69 (2012).</a>
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+The GPU high speed <code>musrfit</code> version is utilizing <code>DKS</code>. In case you are using this version, please also add the following citations
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+<li>  <a href="https://doi.org/10.1016/j.cpc.2016.05.013">A. Adelmann, U. Locans, A. Suter, "The Dynamic Kernel Scheduler&mdash;Part 1", Computer Physics Communications <strong>207</strong>, 83 (2016).</a>
+</li> <li>  <a href="https://doi.org/10.1016/j.cpc.2017.02.007">U. Locans, <strong><em>et al.</em></strong>, "Real-time computation of parameter fitting and image reconstruction using graphical processing units", Computer Physics Communications <strong>215</strong>, 71 (2017).</a>
+</li></ul> </div>
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+Topic revision:  <span class='patternRevInfo'>22 Aug 2017, <a href="https://intranet.psi.ch/Main/AndreasSuter">AndreasSuter</a></span></div>
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+<title> MUSR :: LibFitPofB</title>
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-<h1><a name="libFitPofB"></a>  libFitPofB </h1>
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+<h1 id="libFitPofB">  libFitPofB </h1>
+<div class="foswikiToc" id="foswikiTOC"> <ul>
 <li> <a href="LibFitPofB.html#libFitPofB"> libFitPofB </a>
 </li> <li> <a href="LibFitPofB.html#A_1_Introduction"> 1  Introduction </a>
 </li> <li> <a href="LibFitPofB.html#A_2_LE_45SR"> 2  LE-&mu;SR </a> <ul>
@@ -130,28 +137,28 @@ pre {
 </li> <li> <a href="LibFitPofB.html#A_4_The_XML_startup_file"> 4  The XML startup file </a>
 </li></ul> 
 </div>
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-<h1><a name="A_1_Introduction"></a> 1  Introduction </h1>
+<span id="IntroDuction"></span>
+<h1 id="A_1_Introduction"> 1  Introduction </h1>
 <p></p>
 <code>libFitPofB</code> is a collection of <code>C++</code> classes using the <code><a href="MusrFit.html">musrfit</a></code> <code><a href="MusrFit.html#UserFunctions1">user-function interface</a></code> in order to facilitate the usage in conjunction with <code>musrfit</code>. The classes contained in this library generally implement calculations of one-dimensional static magnetic field distributions <img alt="P(B)" class="mmpImage" src="../pub/MUSR/LibFitPofB/_MathModePlugin_9cc0fd47eedada7247b14775bd308deb.png" title="PofB" /> which lead to muon-spin depolarization functions
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-At the moment the only available implementations deal with field distributions measured in local isotropic superconductors, either by means of <a href="http://lmu.web.psi.ch/lem/" target="_top">low-energy &mu;SR</a> in the Meissner state or by conventional &mu;SR in the mixed state. In the following the basic usage of the library in <code>musrfit</code> is explained&mdash;the calculations by themselves are only outlined. For further information please refer to the original literature and/or the source code of the implementation.
+At the moment the only available implementations deal with field distributions measured in local isotropic superconductors, either by means of <a href="http://lmu.web.psi.ch/lem/">low-energy &mu;SR</a> in the Meissner state or by conventional &mu;SR in the mixed state. In the following the basic usage of the library in <code>musrfit</code> is explained&mdash;the calculations by themselves are only outlined. For further information please refer to the original literature and/or the source code of the implementation.
 <p></p>
 <hr />
-<strong><span class='foswikiBlackFG'>Remark 1:</span></strong> In order to supply certain information needed for the calculations but not suited to be stored in the <code>musrfit</code> msr files an XML configuration file in the working directory is used. For details, see <a href="#XmlFile" class="foswikiCurrentTopicLink">below</a>.
+<strong><span class='foswikiBlackFG'>Remark 1:</span></strong> In order to supply certain information needed for the calculations but not suited to be stored in the <code>musrfit</code> msr files an XML configuration file in the working directory is used. For details, see <a class="foswikiCurrentTopicLink" href="#XmlFile">below</a>.
 <p></p>
-<strong><span class='foswikiBlackFG'>Remark 2:</span></strong> The implementations in this library heavily rely on <code><a href="http://www.fftw.org/" target="_top">FFTW3</a></code>. In principle, it always checks what is the best way to do efficient Fourier transforms for a given machine before the transforms are actually done. If repeatedly Fourier transforms of the same (sizable) length should be done, it might be worth storing the once obtained information in an external file and just load it the next time this information is needed (<a href="http://fftw.org/fftw3_doc/Wisdom.html" target="_top">"wisdom handling"</a>). In case this feature shall be used, a valid wisdom file has to be specified in the <a href="#XmlFile" class="foswikiCurrentTopicLink">XML file</a>.
+<strong><span class='foswikiBlackFG'>Remark 2:</span></strong> The implementations in this library heavily rely on <code><a href="http://www.fftw.org/">FFTW3</a></code>. In principle, it always checks what is the best way to do efficient Fourier transforms for a given machine before the transforms are actually done. If repeatedly Fourier transforms of the same (sizable) length should be done, it might be worth storing the once obtained information in an external file and just load it the next time this information is needed (<a href="http://fftw.org/fftw3_doc/Wisdom.html">"wisdom handling"</a>). In case this feature shall be used, a valid wisdom file has to be specified in the <a class="foswikiCurrentTopicLink" href="#XmlFile">XML file</a>.
 <p></p>
 <strong><span class='foswikiBlackFG'>Remark 3:</span></strong> The model functions described in the following do generally not behave nicely in conjunction with <code>MINUIT</code> function minimizations (or maximizations). The analysis process at the moment in most cases involves some tedious <em>trial-and-error</em> procedure, where the displayed <code>MINUIT</code> information as always deserves attention. This is especially true if small effects should be analyzed (e.g. small diamagnetic shifts in superconductors). The parameter uncertainty in many cases has to be estimated independently. Due to these limitations, also the use of the fit option of <code><a href="Msr2Data.html">msr2data</a></code> cannot be advised.
 <p></p>
 <strong><span class='foswikiBlackFG'>Remark 4:</span></strong> If these classes still prove useful and results obtained through them are part of scientific publications,
 an acknowledgement of the use of the library is appreciated.
 <p></p>
-<h1><a name="A_2_LE_45SR"></a> 2  LE-&mu;SR </h1>
-<h2><a name="A_2.1_One_45dimensional_London_model_for_the_Meissner_state_of_isotropic_superconductors"></a> 2.1  One-dimensional London model for the Meissner state of isotropic superconductors </h2>
+<h1 id="A_2_LE_45SR"> 2  LE-&mu;SR </h1>
+<h2 id="A_2.1_One_45dimensional_London_model_for_the_Meissner_state_of_isotropic_superconductors"> 2.1  One-dimensional London model for the Meissner state of isotropic superconductors </h2>
 <p></p>
 The models for analyzing LE-&mu;SR data assume the magnetic induction <img alt="B(z)" class="mmpImage" src="../pub/MUSR/LibFitPofB/_MathModePlugin_532f98969690650ac4d127919a0eda38.png" title="BofZ" /> to vary only in the dimension parallel to the momentum of the incident muons. In such a case the magnetic field distribution is given by
 <p style="text-align:center">
@@ -163,7 +170,7 @@ Assuming an array of <img alt="N" class="mmpImage" src="../pub/MUSR/LibFitPofB/_
 <p style="text-align:center">
 <img alt="\frac{\partial^2}{\partial z^2}B&#95;i(z) &#61; \frac{1}{\lambda&#95;i^2}B&#95;i(z)" class="mmpImage" src="../pub/MUSR/LibFitPofB/_MathModePlugin_dfd02951094e1cb98f48e3f6d4562f38.png" title="London-eq" />
 </p>
-for each layer <img alt="i" class="mmpImage" src="../pub/MUSR/LibFitPofB/_MathModePlugin_c465118a8d86d5f25bba37cc1dcb38a0.png" title="i" /> taking into account the boundary conditions<a name="FootNote1text"></a><span class='FootNoteTextLink' title='F. London, Superfluids: Macroscopic Theory of Superconductivity, Dover (1961), p. 34'><a href="#FootNote1note" class="foswikiCurrentTopicLink">(1)</a></span>
+for each layer <img alt="i" class="mmpImage" src="../pub/MUSR/LibFitPofB/_MathModePlugin_c465118a8d86d5f25bba37cc1dcb38a0.png" title="i" /> taking into account the boundary conditions<a name="FootNote1text"></a><span class="FootNoteTextLink" title="F&#46; London&#44; Superfluids&#58; Macroscopic Theory of Superconductivity&#44; Dover &#40;1961&#41;&#44; p&#46; 34"><a class="foswikiCurrentTopicLink" href="#FootNote1note">(1)</a></span>
 <p style="text-align:center">
 <img alt="B&#95;1(0) &#61; B&#95;N(d) &#61; \mu&#95;0H" class="mmpImage" src="../pub/MUSR/LibFitPofB/_MathModePlugin_432d7664e0756ded77e7423dd256c122.png" title="cond1" />
 </p>
@@ -182,19 +189,19 @@ userFcn  libFitPofB TLondon1DHS 1 2 3 4 5
 </dd></dl> 
 The parameters are: <ol>
 <li> phase (deg)
-</li> <li> muon implantation energy as specified in the <a href="#XmlFile" class="foswikiCurrentTopicLink">XML startup file</a> (keV)
+</li> <li> muon implantation energy as specified in the <a class="foswikiCurrentTopicLink" href="#XmlFile">XML startup file</a> (keV)
 </li> <li> applied field (G)
 </li> <li> thickness of the dead layer (nm)
 </li> <li> magnetic field penetration depth (nm) 
 </li></ol> 
 <p></p> <dl>
 <dt> Superconducting thin film (one layer) </dt><dd> <pre>
-userFcn  libFitPofB TLondon1D1L 1 2 3 4 5 6 &#91;a b]
+userFcn  libFitPofB TLondon1D1L 1 2 3 4 5 6 &#91;a b&#93;
 </pre>
 </dd></dl> 
 The mandatory parameters are: <ol>
 <li> phase (deg)
-</li> <li> muon implantation energy as specified in the <a href="#XmlFile" class="foswikiCurrentTopicLink">XML startup file</a> (keV)
+</li> <li> muon implantation energy as specified in the <a class="foswikiCurrentTopicLink" href="#XmlFile">XML startup file</a> (keV)
 </li> <li> applied field (G)
 </li> <li> thickness of the dead layer (nm)
 </li> <li> thickness of the actually superconducting layer (nm)
@@ -202,17 +209,17 @@ The mandatory parameters are: <ol>
 </li></ol> 
 <p></p>
 The optional parameters are: <ol>
-<li type="a"> fraction <i>f</i><sub>1</sub> of muons in the thin film contributing to the signal (0 &le; <i>f</i><sub>1</sub> &le; 1)
-</li> <li type="a"> fraction <i>f</i><sub>s</sub> of muons in the substrate contributing to the signal (0 &le; <i>f</i><sub>s</sub> &le; 1)
+<li style="list-style-type:lower-alpha"> fraction <i>f</i><sub>1</sub> of muons in the thin film contributing to the signal (0 &le; <i>f</i><sub>1</sub> &le; 1)
+</li> <li style="list-style-type:lower-alpha"> fraction <i>f</i><sub>s</sub> of muons in the substrate contributing to the signal (0 &le; <i>f</i><sub>s</sub> &le; 1)
 </li></ol> 
 <p></p> <dl>
 <dt> Superconducting thin-film bilayer heterostructure </dt><dd> <pre>
-userFcn  libFitPofB TLondon1D2L 1 2 3 4 5 6 7 8 &#91;a b c]
+userFcn  libFitPofB TLondon1D2L 1 2 3 4 5 6 7 8 &#91;a b c&#93;
 </pre>
 </dd></dl> 
 The mandatory parameters are: <ol>
 <li> phase (deg)
-</li> <li> muon implantation energy as specified in the <a href="#XmlFile" class="foswikiCurrentTopicLink">XML startup file</a> (keV)
+</li> <li> muon implantation energy as specified in the <a class="foswikiCurrentTopicLink" href="#XmlFile">XML startup file</a> (keV)
 </li> <li> applied field (G)
 </li> <li> thickness of the dead layer (nm)
 </li> <li> thickness of the actually superconducting first layer (nm)
@@ -222,18 +229,18 @@ The mandatory parameters are: <ol>
 </li></ol> 
 <p></p>
 The optional parameters are: <ol>
-<li type="a"> fraction <i>f</i><sub>1</sub> of muons in the dead and first layer contributing to the signal (0 &le; <i>f</i><sub>1</sub> &le; 1)
-</li> <li type="a"> fraction <i>f</i><sub>2</sub> of muons in the second layer contributing to the signal (0 &le; <i>f</i><sub>2</sub> &le; 1)
-</li> <li type="a"> fraction <i>f</i><sub>s</sub> of muons in the substrate contributing to the signal (0 &le; <i>f</i><sub>s</sub> &le; 1)
+<li style="list-style-type:lower-alpha"> fraction <i>f</i><sub>1</sub> of muons in the dead and first layer contributing to the signal (0 &le; <i>f</i><sub>1</sub> &le; 1)
+</li> <li style="list-style-type:lower-alpha"> fraction <i>f</i><sub>2</sub> of muons in the second layer contributing to the signal (0 &le; <i>f</i><sub>2</sub> &le; 1)
+</li> <li style="list-style-type:lower-alpha"> fraction <i>f</i><sub>s</sub> of muons in the substrate contributing to the signal (0 &le; <i>f</i><sub>s</sub> &le; 1)
 </li></ol> 
 <p></p> <dl>
 <dt> Superconducting thin-film trilayer heterostructure </dt><dd> <pre>
-userFcn  libFitPofB TLondon1D3L 1 2 3 4 5 6 7 8 9 10 &#91;a b c d]
+userFcn  libFitPofB TLondon1D3L 1 2 3 4 5 6 7 8 9 10 &#91;a b c d&#93;
 </pre>
 </dd></dl> 
 The mandatory parameters are: <ol>
 <li> phase (deg)
-</li> <li> muon implantation energy as specified in the <a href="#XmlFile" class="foswikiCurrentTopicLink">XML startup file</a> (keV)
+</li> <li> muon implantation energy as specified in the <a class="foswikiCurrentTopicLink" href="#XmlFile">XML startup file</a> (keV)
 </li> <li> applied field (G)
 </li> <li> thickness of the dead layer (nm)
 </li> <li> thickness of the actually superconducting first layer (nm)
@@ -245,39 +252,39 @@ The mandatory parameters are: <ol>
 </li></ol> 
 <p></p>
 The optional parameters are: <ol>
-<li type="a"> fraction <i>f</i><sub>1</sub> of muons in the dead and first layer contributing to the signal (0 &le; <i>f</i><sub>1</sub> &le; 1)
-</li> <li type="a"> fraction <i>f</i><sub>2</sub> of muons in the second layer contributing to the signal (0 &le; <i>f</i><sub>2</sub> &le; 1)
-</li> <li type="a"> fraction <i>f</i><sub>3</sub> of muons in the third layer contributing to the signal (0 &le; <i>f</i><sub>3</sub> &le; 1)
-</li> <li type="a"> fraction <i>f</i><sub>s</sub> of muons in the substrate contributing to the signal (0 &le; <i>f</i><sub>s</sub> &le; 1)
+<li style="list-style-type:lower-alpha"> fraction <i>f</i><sub>1</sub> of muons in the dead and first layer contributing to the signal (0 &le; <i>f</i><sub>1</sub> &le; 1)
+</li> <li style="list-style-type:lower-alpha"> fraction <i>f</i><sub>2</sub> of muons in the second layer contributing to the signal (0 &le; <i>f</i><sub>2</sub> &le; 1)
+</li> <li style="list-style-type:lower-alpha"> fraction <i>f</i><sub>3</sub> of muons in the third layer contributing to the signal (0 &le; <i>f</i><sub>3</sub> &le; 1)
+</li> <li style="list-style-type:lower-alpha"> fraction <i>f</i><sub>s</sub> of muons in the substrate contributing to the signal (0 &le; <i>f</i><sub>s</sub> &le; 1)
 </li></ol> 
 <p></p>
 <p></p>
 <p></p>
 Notes
 <p></p>
-<a name="FootNote1note"></a><span class="FootNoteLabel"><a href="#FootNote1text" class="foswikiCurrentTopicLink"> <strong>1</strong> </a></span>: <span class="FootNote">F. London, Superfluids: Macroscopic Theory of Superconductivity, Dover (1961), p. 34</span> 
+<a name="FootNote1note"></a><span class="FootNoteLabel"><a href="#FootNote1text"><b>1</b></a></span>: <span class="FootNote">F. London, Superfluids: Macroscopic Theory of Superconductivity, Dover (1961), p. 34</span> 
 <p></p>
 <p></p>
 <p></p>
 <hr />
 <p></p>
-<h1><a name="A_3_Conventional_40bulk_41_SR"></a> 3  Conventional (bulk) &mu;SR </h1>
-<h2><a name="A_3.1_Field_distributions_in_the_mixed_state_of_isotropic_superconductors"></a> 3.1  Field distributions in the mixed state of isotropic superconductors </h2>
+<h1 id="A_3_Conventional_40bulk_41_SR"> 3  Conventional (bulk) &mu;SR </h1>
+<h2 id="A_3.1_Field_distributions_in_the_mixed_state_of_isotropic_superconductors"> 3.1  Field distributions in the mixed state of isotropic superconductors </h2>
 <p></p>
 When investigating superconductors in the mixed state by means of conventional &mu;SR a two-dimensional flux-line lattice is probed randomly by the muons. The spatial field distributions within such an ordered lattice are modeled using the Fourier series
 <p style="text-align:center">
 <img alt="B(\mathbf{r}) &#61; \langle B \rangle \sum\limits&#95;{\mathbf{K}}B&#95;{\mathbf{K}}\exp(-\imath\mathbf{K}\mathbf{r})," class="mmpImage" src="../pub/MUSR/LibFitPofB/_MathModePlugin_c25933e91d56089992506f463d71de8f.png" title="spatialB" />
 </p>
 where <img alt="\mathbf{r}&#61;(x,y)" class="mmpImage" src="../pub/MUSR/LibFitPofB/_MathModePlugin_e47f33589d28eaa3f9baccb7a80fdbaa.png" title="r" />, <img alt="\mathbf{K}" class="mmpImage" src="../pub/MUSR/LibFitPofB/_MathModePlugin_e6688a12ee4e821abc31b4c1dd511539.png" title="K" /> are the reciprocal lattice vectors of a two-dimensional vortex lattice and the <img alt="B&#95;{\mathbf{K}}" class="mmpImage" src="../pub/MUSR/LibFitPofB/_MathModePlugin_8fa3ac8f18b7bc49eb89163d6528684c.png" title="Bk" /> are the Fourier coefficients depending on the magnetic penetration depth <img alt="\lambda" class="mmpImage" src="../pub/MUSR/LibFitPofB/_MathModePlugin_28f3ed750a4819b4256c2f9be649f594.png" title="lambda" /> and the superconducting coherence length <img alt="\xi" class="mmpImage" src="../pub/MUSR/LibFitPofB/_MathModePlugin_e8414d477977d226317c020980b7d34f.png" title="xi" />. The <img alt="B&#95;{\mathbf{K}}" class="mmpImage" src="../pub/MUSR/LibFitPofB/_MathModePlugin_8fa3ac8f18b7bc49eb89163d6528684c.png" title="Bk" /> for some specific models are as follows: <dl>
-<dt> London model with Gaussian cutoff<a name="FootNote2text"></a><span class='FootNoteTextLink' title='E.H. Brandt, <a href="http://dx.doi.org/10.1007/BF00683568" target="_top">J. Low Temp. Phys. <strong>73</strong>, 355 (1988)</a>.'><a href="#FootNote2note" class="foswikiCurrentTopicLink">(2)</a></span> </dt><dd> <p style="text-align:center"><img alt="B&#95;{\mathbf{K}} &#61; \frac{\exp\left({-K^2\xi^2/2}\right)}{1 + K^2\lambda^2}" class="mmpImage" src="../pub/MUSR/LibFitPofB/_MathModePlugin_469d5d1b83125e4915e2f073d8150b12.png" title="BkLondon" /></p>
-</dd> <dt> Modified London model<a name="FootNote3text"></a><span class='FootNoteTextLink' title='T.M. Riseman <em>et al.</em>, <a href="http://dx.doi.org/10.1103/PhysRevB.52.10569" target="_top">Phys. Rev. B <strong>52</strong>, 10569 (1995)</a>.'><a href="#FootNote3note" class="foswikiCurrentTopicLink">(3)</a></span> </dt><dd> <p style="text-align:center"><img alt="B&#95;{\mathbf{K}} &#61; \frac{\exp\left({-K^2\xi^2/2(1-b)}\right)}{1 + K^2\lambda^2/(1-b)}," class="mmpImage" src="../pub/MUSR/LibFitPofB/_MathModePlugin_b6719fad8e30208538b34bc94040b7a5.png" title="BkML" /></p> where <img alt="b &#61; \langle B \rangle/\mu&#95;0H&#95;{\mathrm{c}2}." class="mmpImage" src="../pub/MUSR/LibFitPofB/_MathModePlugin_039b3b38df7c6f284089c14f1efdf643.png" title="b" />
-</dd> <dt> Analytical Ginzburg-Landau model<a name="FootNote4text"></a><span class='FootNoteTextLink' title='A. Yaouanc, P. Dalmas de R&eacute;otier and E.H. Brandt, <a href="http://dx.doi.org/10.1103/PhysRevB.55.11107" target="_top">Phys. Rev. B <strong>55</strong>, 11107 (1997)</a>.'><a href="#FootNote4note" class="foswikiCurrentTopicLink">(4)</a></span> </dt><dd> <p style="text-align:center"><img alt="B&#95;{\mathbf{K}} &#61; \frac{f&#95;{\infty}K&#95;1\left(\frac{\xi&#95;v}{\lambda}\sqrt{f&#95;{\infty}^2+\lambda^2K^2}\right)}{K&#95;1\left(\frac{\xi&#95;v}{\lambda}f&#95;{\infty}\right)\sqrt{f&#95;{\infty}^2+\lambda^2K^2}}," class="mmpImage" src="../pub/MUSR/LibFitPofB/_MathModePlugin_3146cb17887e3a20cc2078f103605af5.png" title="BkAGL" /></p> where <img alt="f&#95;{\infty} &#61; 1 - b^4,~\xi&#95;v &#61; \xi\left(\sqrt{2}-{3\xi}/\left({4\lambda}\right)\right)\sqrt{(1+b^4)(1-2b(1-b)^2)}" class="mmpImage" src="../pub/MUSR/LibFitPofB/_MathModePlugin_e0b0e98f9a3974249b42b6910523c8a4.png" title="f_inf_and_xi_v" /> and <img alt="K&#95;1" class="mmpImage" src="../pub/MUSR/LibFitPofB/_MathModePlugin_3cee3cc69dbe918398ec39a72a465014.png" title="K1" /> is a modified Bessel function.
+<dt> London model with Gaussian cutoff<a name="FootNote2text"></a><span class="FootNoteTextLink" title="E&#46;H&#46; Brandt&#44; &#91;&#91;http&#58;&#47;&#47;dx&#46;doi&#46;org&#47;10&#46;1007&#47;BF00683568&#93;&#91;J&#46; Low Temp&#46; Phys&#46; &#42;73&#42;&#44; 355 &#40;1988&#41;&#93;&#93;&#46;"><a class="foswikiCurrentTopicLink" href="#FootNote2note">(2)</a></span> </dt><dd> <p style="text-align:center"><img alt="B&#95;{\mathbf{K}} &#61; \frac{\exp\left({-K^2\xi^2/2}\right)}{1 + K^2\lambda^2}" class="mmpImage" src="../pub/MUSR/LibFitPofB/_MathModePlugin_469d5d1b83125e4915e2f073d8150b12.png" title="BkLondon" /></p>
+</dd> <dt> Modified London model<a name="FootNote3text"></a><span class="FootNoteTextLink" title="T&#46;M&#46; Riseman _et al&#46;_&#44; &#91;&#91;http&#58;&#47;&#47;dx&#46;doi&#46;org&#47;10&#46;1103&#47;PhysRevB&#46;52&#46;10569&#93;&#91;Phys&#46; Rev&#46; B &#42;52&#42;&#44; 10569 &#40;1995&#41;&#93;&#93;&#46;"><a class="foswikiCurrentTopicLink" href="#FootNote3note">(3)</a></span> </dt><dd> <p style="text-align:center"><img alt="B&#95;{\mathbf{K}} &#61; \frac{\exp\left({-K^2\xi^2/2(1-b)}\right)}{1 + K^2\lambda^2/(1-b)}," class="mmpImage" src="../pub/MUSR/LibFitPofB/_MathModePlugin_b6719fad8e30208538b34bc94040b7a5.png" title="BkML" /></p> where <img alt="b &#61; \langle B \rangle/\mu&#95;0H&#95;{\mathrm{c}2}." class="mmpImage" src="../pub/MUSR/LibFitPofB/_MathModePlugin_039b3b38df7c6f284089c14f1efdf643.png" title="b" />
+</dd> <dt> Analytical Ginzburg-Landau model<a name="FootNote4text"></a><span class="FootNoteTextLink" title="A&#46; Yaouanc&#44; P&#46; Dalmas de R&#38;eacute&#59;otier and E&#46;H&#46; Brandt&#44; &#91;&#91;http&#58;&#47;&#47;dx&#46;doi&#46;org&#47;10&#46;1103&#47;PhysRevB&#46;55&#46;11107&#93;&#91;Phys&#46; Rev&#46; B &#42;55&#42;&#44; 11107 &#40;1997&#41;&#93;&#93;&#46;"><a class="foswikiCurrentTopicLink" href="#FootNote4note">(4)</a></span> </dt><dd> <p style="text-align:center"><img alt="B&#95;{\mathbf{K}} &#61; \frac{f&#95;{\infty}K&#95;1\left(\frac{\xi&#95;v}{\lambda}\sqrt{f&#95;{\infty}^2+\lambda^2K^2}\right)}{K&#95;1\left(\frac{\xi&#95;v}{\lambda}f&#95;{\infty}\right)\sqrt{f&#95;{\infty}^2+\lambda^2K^2}}," class="mmpImage" src="../pub/MUSR/LibFitPofB/_MathModePlugin_3146cb17887e3a20cc2078f103605af5.png" title="BkAGL" /></p> where <img alt="f&#95;{\infty} &#61; 1 - b^4,~\xi&#95;v &#61; \xi\left(\sqrt{2}-{3\xi}/\left({4\lambda}\right)\right)\sqrt{(1+b^4)(1-2b(1-b)^2)}" class="mmpImage" src="../pub/MUSR/LibFitPofB/_MathModePlugin_e0b0e98f9a3974249b42b6910523c8a4.png" title="f_inf_and_xi_v" /> and <img alt="K&#95;1" class="mmpImage" src="../pub/MUSR/LibFitPofB/_MathModePlugin_3cee3cc69dbe918398ec39a72a465014.png" title="K1" /> is a modified Bessel function.
 </dd></dl> 
-Apart from the mentioned analytical models the <strong>numerical Ginzburg-Landau model</strong> <a name="FootNote5text"></a><span class='FootNoteTextLink' title='E.H. Brandt, <a href="http://dx.doi.org/10.1103/PhysRevB.68.054506" target="_top">Phys. Rev. B <strong>68</strong>, 054506 (2003)</a>.'><a href="#FootNote5note" class="foswikiCurrentTopicLink">(5)</a></span> is available. In this case <img alt="B(\mathbf{r})" class="mmpImage" src="../pub/MUSR/LibFitPofB/_MathModePlugin_373e9bf1fc97e2c6aacf93bcc090402c.png" title="BofR" /> is obtained by an iterative minimization of the free energy of the vortex lattice.
+Apart from the mentioned analytical models the <strong>numerical Ginzburg-Landau model</strong> <a name="FootNote5text"></a><span class="FootNoteTextLink" title="E&#46;H&#46; Brandt&#44; &#91;&#91;http&#58;&#47;&#47;dx&#46;doi&#46;org&#47;10&#46;1103&#47;PhysRevB&#46;68&#46;054506&#93;&#91;Phys&#46; Rev&#46; B &#42;68&#42;&#44; 054506 &#40;2003&#41;&#93;&#93;&#46;"><a class="foswikiCurrentTopicLink" href="#FootNote5note">(5)</a></span> is available. In this case <img alt="B(\mathbf{r})" class="mmpImage" src="../pub/MUSR/LibFitPofB/_MathModePlugin_373e9bf1fc97e2c6aacf93bcc090402c.png" title="BofR" /> is obtained by an iterative minimization of the free energy of the vortex lattice.
 <p></p>
 <span class='foswikiRedFG'>Concerning the applicability (e.g. field regions) of each of the mentioned models please refer to the original publications!</span>
 <p></p>
-At the moment, the calculation of the field distribution has been implemented for triangular flux-line lattices. The number of grid lines in which the inter-vortex distance is divided for the calculations to be specified through the <a href="#XmlFile" class="foswikiCurrentTopicLink">XML file</a>.<br>The muon-spin depolarization functions finally are calculated using the following lines in the THEORY block of a <code>musrfit</code> msr file: <dl>
+At the moment, the calculation of the field distribution has been implemented for triangular flux-line lattices. The number of grid lines in which the inter-vortex distance is divided for the calculations to be specified through the <a class="foswikiCurrentTopicLink" href="#XmlFile">XML file</a>.<br>The muon-spin depolarization functions finally are calculated using the following lines in the THEORY block of a <code>musrfit</code> msr file: <dl>
 <dt> 2D triangular vortex lattice, London model with Gaussian cutoff </dt><dd> <pre>
 userFcn  libFitPofB TBulkTriVortexLondon 1 2 3 4
 </pre>
@@ -336,23 +343,23 @@ SAVE
 <p></p>
 Notes
 <p></p>
-<a name="FootNote2note"></a><span class="FootNoteLabel"><a href="#FootNote2text" class="foswikiCurrentTopicLink"> <strong>2</strong> </a></span>: <span class="FootNote">E.H. Brandt, <a href="http://dx.doi.org/10.1007/BF00683568" target="_top">J. Low Temp. Phys. <strong>73</strong>, 355 (1988)</a>.</span> 
+<a name="FootNote2note"></a><span class="FootNoteLabel"><a href="#FootNote2text"><b>2</b></a></span>: <span class="FootNote">E.H. Brandt, <a href="http://dx.doi.org/10.1007/BF00683568">J. Low Temp. Phys. <strong>73</strong>, 355 (1988)</a>.</span> 
 <p></p>
-<a name="FootNote3note"></a><span class="FootNoteLabel"><a href="#FootNote3text" class="foswikiCurrentTopicLink"> <strong>3</strong> </a></span>: <span class="FootNote">T.M. Riseman <em>et al.</em>, <a href="http://dx.doi.org/10.1103/PhysRevB.52.10569" target="_top">Phys. Rev. B <strong>52</strong>, 10569 (1995)</a>.</span> 
+<a name="FootNote3note"></a><span class="FootNoteLabel"><a href="#FootNote3text"><b>3</b></a></span>: <span class="FootNote">T.M. Riseman <em>et al.</em>, <a href="http://dx.doi.org/10.1103/PhysRevB.52.10569">Phys. Rev. B <strong>52</strong>, 10569 (1995)</a>.</span> 
 <p></p>
-<a name="FootNote4note"></a><span class="FootNoteLabel"><a href="#FootNote4text" class="foswikiCurrentTopicLink"> <strong>4</strong> </a></span>: <span class="FootNote">A. Yaouanc, P. Dalmas de R&eacute;otier and E.H. Brandt, <a href="http://dx.doi.org/10.1103/PhysRevB.55.11107" target="_top">Phys. Rev. B <strong>55</strong>, 11107 (1997)</a>.</span> 
+<a name="FootNote4note"></a><span class="FootNoteLabel"><a href="#FootNote4text"><b>4</b></a></span>: <span class="FootNote">A. Yaouanc, P. Dalmas de R&eacute;otier and E.H. Brandt, <a href="http://dx.doi.org/10.1103/PhysRevB.55.11107">Phys. Rev. B <strong>55</strong>, 11107 (1997)</a>.</span> 
 <p></p>
-<a name="FootNote5note"></a><span class="FootNoteLabel"><a href="#FootNote5text" class="foswikiCurrentTopicLink"> <strong>5</strong> </a></span>: <span class="FootNote">E.H. Brandt, <a href="http://dx.doi.org/10.1103/PhysRevB.68.054506" target="_top">Phys. Rev. B <strong>68</strong>, 054506 (2003)</a>.</span> 
+<a name="FootNote5note"></a><span class="FootNoteLabel"><a href="#FootNote5text"><b>5</b></a></span>: <span class="FootNote">E.H. Brandt, <a href="http://dx.doi.org/10.1103/PhysRevB.68.054506">Phys. Rev. B <strong>68</strong>, 054506 (2003)</a>.</span> 
 <p></p>
 <p></p>
 <p></p>
 <hr />
 <p></p>
-<a name="XmlFile"></a>
-<h1><a name="A_4_The_XML_startup_file"></a> 4  The XML startup file </h1>
+<span id="XmlFile"></span>
+<h1 id="A_4_The_XML_startup_file"> 4  The XML startup file </h1>
 <code><b>BMW_startup.xml</b></code> is a configuration file located in the working directory. In this file some settings like the time and field resolution of the calculations as well as the present muon implantation profiles for a LE-&mu;SR analysis have to be defined. The following XML tags are allowed to define settings: <dl>
 <dt> &lt;debug&gt;ONE_OR_ZERO&lt;/debug&gt; </dt><dd> activate the debugging output of the settings read from the XML file by setting <strong>1</strong>, deactivate it with <strong>0</strong>
-</dd> <dt> &lt;wisdom&gt;PATH_TO_FILE&lt;/wisdom&gt; </dt><dd> specify the <strong>PATH_TO_FILE</strong> to an <a href="http://fftw.org/fftw3_doc/Wisdom.html#Wisdom" target="_top">FFTW3 wisdom file</a> that should be used; if the <strong>PATH_TO_FILE</strong> is invalid, no FFTW3 wisdom will be used
+</dd> <dt> &lt;wisdom&gt;PATH_TO_FILE&lt;/wisdom&gt; </dt><dd> specify the <strong>PATH_TO_FILE</strong> to an <a href="http://fftw.org/fftw3_doc/Wisdom.html#Wisdom">FFTW3 wisdom file</a> that should be used; if the <strong>PATH_TO_FILE</strong> is invalid, no FFTW3 wisdom will be used
 </dd> <dt> &lt;delta_t&gt;ResT&lt;/delta_t&gt; </dt><dd> set the time resolution <strong>ResT</strong> for the calculated depolarization function in <strong>microseconds</strong>
 </dd> <dt> &lt;delta_B&gt;ResB&lt;/delta_B&gt; </dt><dd> set the field resolution <strong>ResB</strong> for the calculated field distribution in <strong>Gauss</strong>
 </dd> <dt> &lt;VortexLattice&gt;&lt;/VortexLattice&gt; </dt><dd> set the parameters used for the calculation of the spatial field distribution of a vortex lattice <dl>
@@ -398,83 +405,28 @@ An example XML file looks as follows:
 &#60;/BMW&#62;
 </pre>
 <p></p>
--- <a href="http://www.fsf.org/register_form?referrer=8369" target="_top">BMW</a> &amp; <a href="http://lmu.web.psi.ch/lem/group.html" target="_top">AS</a> </div>
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+-- <a href="http://www.fsf.org/register_form?referrer=8369">BMW</a> &amp; <a href="http://www.psi.ch/low-energy-muons/people">AS</a></div>
+<p></p>
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+<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> &gt; <a href="BmwLibs.html">BmwLibs</a><span class='foswikiSeparator'>&nbsp;&gt;&nbsp;</span>LibFitPofB <br />
+Topic revision:  <span class='patternRevInfo'>03 Jul 2015, suter_a</span></div>
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+</div>
+</div>
+</div>
+</div></div><!-- /endWrap -->
 <p></p>
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+<!-- Mirrored from intranet.psi.ch/MUSR/LibFitPofB?cover=print by HTTrack Website Copier/3.x [XR&CO'2014], Fri, 08 Jun 2018 13:42:26 GMT -->
+</html>

doc/html/user/MUSR/LibZFRelaxation.html

@@ -1,35 +1,38 @@
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+<!DOCTYPE html><html lang="en">
 
-<!-- Mirrored from intranet.psi.ch/MUSR/LibZFRelaxation?cover=print by HTTrack Website Copier/3.x [XR&CO'2010], Thu, 18 Dec 2014 13:45:53 GMT -->
-<!-- Added by HTTrack --><meta http-equiv="content-type" content="text/html;charset=iso-8859-1"><!-- /Added by HTTrack -->
+<!-- Mirrored from intranet.psi.ch/MUSR/LibZFRelaxation?cover=print by HTTrack Website Copier/3.x [XR&CO'2014], Fri, 08 Jun 2018 13:41:45 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>
-<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1" />
+<title> MUSR :: LibZFRelaxation</title>
+<meta http-equiv="X-UA-Compatible" content="IE=edge" />
+<meta charset="utf-8" />
+<meta name="viewport" content="width=device-width, initial-scale=1, maximum-scale=1.5, user-scalable=yes" />
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+<meta name="apple-mobile-web-app-capable" content="yes" />
+<meta name="apple-mobile-web-app-status-bar-style" content="black-translucent" />
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+<link rel="alternate" href="https://intranet.psi.ch/wiki/bin/edit/MUSR/LibZFRelaxation?t=1528465295" type="application/x-wiki" title="edit LibZFRelaxation" />
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+<meta name="robots" content="noindex" /><link rel="alternate" type="application/rss+xml" title="RSS Feed" href="WebRss" />
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-@import url('../pub/System/PatternSkinTheme2009/layout.css');
+@import url('../pub/System/PatternSkinTheme/layout.css');
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-@import url('../pub/System/PatternSkinTheme2009/variant_twiki.css');
-</style><style type="text/css" media="all">
+<link rel='stylesheet' href='../pub/System/PatternSkinTheme2009/column_left.css' media='all' type='text/css' />
+<link rel='stylesheet' href='../pub/System/PatternSkinTheme2009/variant_twiki.css' media='all' type='text/css' /><style type="text/css" media="all">
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+<link rel='stylesheet' href='../pub/System/PatternSkin/print.css' media='all' type='text/css' />
+<!--[if IE 7 ]><style type="text/css" media="screen">
 .foswikiAttachments,
 .foswikiForm,
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-<h1><a name="libZFRelaxation"></a>  libZFRelaxation </h1>
-<a name="foswikiTOC"></a><div class="foswikiToc"> <ul>
+<div id="patternMain">
+<div id="patternMainContents">
+<div class="patternContent"><div class="foswikiTopic"> 
+<span id="TopIc"></span>
+<h1 id="libZFRelaxation">  libZFRelaxation </h1>
+<div class="foswikiToc" id="foswikiTOC"> <ul>
 <li> <a href="LibZFRelaxation.html#libZFRelaxation"> libZFRelaxation </a>
 </li> <li> <a href="LibZFRelaxation.html#A_1_Introduction"> 1  Introduction </a>
 </li> <li> <a href="LibZFRelaxation.html#A_2_Isotropic_static_Gaussian_broadened_randomly_oriented_internal_fields"> 2  Isotropic static Gaussian broadened randomly oriented internal fields </a>
@@ -126,8 +133,8 @@ pre {
 </li> <li> <a href="LibZFRelaxation.html#A_4_Static_Gaussian_distributed_fields_with_uniaxial_anisotropy"> 4  Static Gaussian distributed fields with uniaxial anisotropy </a>
 </li></ul> 
 </div>
-<a name="IntroDuction"></a>
-<h1><a name="A_1_Introduction"></a> 1  Introduction </h1>
+<span id="IntroDuction"></span>
+<h1 id="A_1_Introduction"> 1  Introduction </h1>
 <p></p>
 <code>libZFRelaxation</code> is a collection of <code>C++</code> classes using the <code><a href="MusrFit.html">musrfit</a></code> <code><a href="MusrFit.html#UserFunctions1">user-function interface</a></code> in order to facilitate the usage in conjunction with <code>musrfit</code>. The classes contained in this library implement the calculation of some additional zero-field &mu;SR relaxation functions which are not built-in into <code>musrfit</code>.
 <p></p>
@@ -136,9 +143,9 @@ In the following the use of the implemented functions is shortly introduced&mdas
 If these classes prove useful and results obtained through them are part of scientific publications,
 an acknowledgement of the use of the library is appreciated.
 <p></p>
-<h1><a name="A_2_Isotropic_static_Gaussian_broadened_randomly_oriented_internal_fields"></a> 2  Isotropic static Gaussian broadened randomly oriented internal fields </h1>
+<h1 id="A_2_Isotropic_static_Gaussian_broadened_randomly_oriented_internal_fields"> 2  Isotropic static Gaussian broadened randomly oriented internal fields </h1>
 <p></p>
-E. I. Kornilov and V. Yu. Pomjakushin, Phys. Lett. A <b>153</b>, 364&#150;367 (1991), doi: <a href="http://dx.doi.org/10.1016/0375-9601(91)90959-C" target="_top">10.1016/0375-9601(91)90959-C</a>
+E. I. Kornilov and V. Yu. Pomjakushin, Phys. Lett. A <b>153</b>, 364&#150;367 (1991), doi: <a href="http://dx.doi.org/10.1016/0375-9601(91)90959-C">10.1016/0375-9601(91)90959-C</a>
 <p></p>
 <p style="text-align:center">
 <img alt="\mathcal{P}(t) &#61; \left(1-\alpha\right)\exp\left(-\frac{\sigma&#95;{\mathrm{L}}^2t^2}{2}\right)+\alpha\left(\cos\left(2\pi\nu t\right)-\frac{\sigma&#95;{\mathrm{T}}^2t}{2\pi\nu}\sin\left(2\pi\nu t\right)\right)\exp\left(-\frac{\sigma&#95;{\mathrm{T}}^2t^2}{2}\right)" class="mmpImage" src="../pub/MUSR/LibZFRelaxation/_MathModePlugin_fca91646b118061038b53ada5563c17c.png" title="ZFMagGss" />
@@ -154,9 +161,9 @@ The parameters are: <ol>
 </li> <li> the "longitudinal depolarization rate" &sigma;<sub>L</sub> (&mu;s<sup>-1</sup>) (= 0 in the article).
 </li></ol> 
 <p></p>
-<h1><a name="A_3_Isotropic_static_Lorentzian_broadened_randomly_oriented_internal_fields"></a> 3  Isotropic static Lorentzian broadened randomly oriented internal fields </h1>
+<h1 id="A_3_Isotropic_static_Lorentzian_broadened_randomly_oriented_internal_fields"> 3  Isotropic static Lorentzian broadened randomly oriented internal fields </h1>
 <p></p>
-M. I. Larkin, Y. Fudamoto, I. M. Gat, A. Kinkhabwala, K. M. Kojima, G. M. Luke, J. Merrin, B. Nachumi, Y. J. Uemura, M. Azuma, T. Saito, and M. Takano, Physica B <b>289&#150;290</b>, 153&#150;156 (2000), doi: <a href="http://dx.doi.org/10.1016/S0921-4526(00)00337-9"" target="_top">10.1016/S0921-4526(00)00337-9</a>
+M. I. Larkin, Y. Fudamoto, I. M. Gat, A. Kinkhabwala, K. M. Kojima, G. M. Luke, J. Merrin, B. Nachumi, Y. J. Uemura, M. Azuma, T. Saito, and M. Takano, Physica B <b>289&#150;290</b>, 153&#150;156 (2000), doi: <a href="http://dx.doi.org/10.1016/S0921-4526(00)00337-9"">10.1016/S0921-4526(00)00337-9</a>
 <p></p>
 <p style="text-align:center">
 <img alt="\mathcal{P}(t) &#61; \left(1-\alpha\right)\exp\left(-a&#95;{\mathrm{L}}t\right) + \alpha\left(\cos\left(2\pi\nu t\right)-\frac{a&#95;{\mathrm{T}}}{2\pi\nu}\sin\left(2\pi\nu t\right)\right)\exp\left(-a&#95;{\mathrm{T}}t\right)" class="mmpImage" src="../pub/MUSR/LibZFRelaxation/_MathModePlugin_975f948b57199037b2b8bfb5e986b6a9.png" title="ZFMagExp" />
@@ -172,9 +179,9 @@ The parameters are: <ol>
 </li> <li> the "longitudinal depolarization rate" a<sub>L</sub> (&mu;s<sup>-1</sup>) (= 0 in the article).
 </li></ol> 
 <p></p>
-<h1><a name="A_4_Static_Gaussian_distributed_fields_with_uniaxial_anisotropy"></a> 4  Static Gaussian distributed fields with uniaxial anisotropy </h1>
+<h1 id="A_4_Static_Gaussian_distributed_fields_with_uniaxial_anisotropy"> 4  Static Gaussian distributed fields with uniaxial anisotropy </h1>
 <p></p>
-G. Solt, Hyperfine Interactions <b>96</b>, 167&#150;175 (1995), doi: <a href="http://dx.doi.org/10.1007/BF02066280" target="_top">10.1007/BF02066280</a>
+G. Solt, Hyperfine Interactions <b>96</b>, 167&#150;175 (1995), doi: <a href="http://dx.doi.org/10.1007/BF02066280">10.1007/BF02066280</a>
 <p></p>
 <p style="text-align:center">
 <img alt="\mathcal{P}(t) &#61; \frac{1}{2}\sin^2\Theta + \left(\frac{3}{2}\cos^2\Theta-\frac{1}{2}\right)f&#95;1\left(\epsilon\right) + \sin^2\Theta f&#95;2(\epsilon, \sigma&#95;1, t) + \left(\frac{3}{2}\cos^2\Theta-\frac{1}{2}\right)f&#95;3\left(\epsilon, \sigma&#95;1, t\right)," class="mmpImage" src="../pub/MUSR/LibZFRelaxation/_MathModePlugin_4611c56f1556464dd8a6eaabbe070c05.png" title="UniaxialStatGssKT" />
@@ -203,83 +210,28 @@ The parameters are: <ol>
 </li> <li> &Theta; (&deg;).
 </li></ol> 
 <p></p>
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+<link rel='stylesheet' href='../pub/System/PatternSkinTheme2009/column_left.css' media='all' type='text/css' />
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-<div id="patternMainContents"><div class="patternTop"><span class="patternHomePath foswikiLeft"></span><span class="patternToolBar foswikiRight"><span><a href='Msr2Datac99a.html?cover=print;cover=print' rel='nofollow' title='Printable version of this topic' accesskey='p'><span class='foswikiAccessKey'>P</span>rint version</a></span><a href="https://intranet.psi.ch/MUSR/Msr2Data?restrictions=on" id="restriction_link"><img src='../pub/System/PsiSkin/lock_open.png' class='lock' height='16' width='23' title='open in PSI - click for more information'/></a></span><div class="foswikiClear"></div></div><div class="foswikiContentHeader">
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+<h1 id="A_61_61msr2data_61_61">  <code><b>msr2data</b></code> </h1>
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-<h1><a name="A_61_61msr2data_61_61"></a>  <code><b>msr2data</b></code> </h1>
-<p></p>
-<a name="foswikiTOC"></a><div class="foswikiToc"> <ul>
+<div class="foswikiToc" id="foswikiTOC"> <ul>
 <li> <a href="Msr2Data.html#A_61_61msr2data_61_61"> msr2data </a>
 </li> <li> <a href="Msr2Data.html#A_1_Introduction"> 1  Introduction </a>
 </li> <li> <a href="Msr2Data.html#A_2_Basic_Types_of_Usage"> 2  Basic Types of Usage </a>
@@ -134,70 +176,72 @@ pre {
 </li></ul> 
 </div>
 <p></p>
-<a name="IntroDuction"></a>
-<h1><a name="A_1_Introduction"></a> 1  Introduction </h1>
-<code>msr2data</code> (originally written by B. M. Wojek) is a program implemented in <code>C++</code>. Its purpose is to process multiple <code><a href="MusrFit.html">musrfit</a></code> msr files with the same parameters and summarize the fitting results either in a TRIUMF <strong>DB</strong> <a name="FootNote1text"></a><span class='FootNoteTextLink' title=' For an abridged description of this format see <a href="http://musr.org/xyfit/dbformat.html" target="_top">here</a>. The <strong>DB</strong> files produced by <code>msr2data</code> can be viewed for instance with <a href="http://musr.org/muview/" target="_top">&mu;View</a>, however, they are <em>not completely</em> backward-compatible to the original "db language" since the parameter names can be longer than five or six characters! In order to establish this backward compatibility (if needed) the user has to ensure the correct length of the parameter names in the msr files!'><a href="#FootNote1note" class="foswikiCurrentTopicLink">(1)</a></span> or a <strong>column ASCII</strong> file. It evolved from a script called <code>mlog2db</code> which has been written only for collecting fit results of <a href="http://lmu.web.psi.ch/lem/" target="_top">LEM</a> data stored in mlog files generated by <code>musrfit</code> and putting them together in a file with the <strong>DB</strong> format for further analysis. Therefore, any peculiarities, e.g. in supplying options to <code>msr2data</code> are owed its original purpose.
-<code>msr2data</code> is <a href="http://www.gnu.org/philosophy/free-sw.html" target="_top">free software</a> and licensed under the <a href="http://www.gnu.org/licenses/old-licenses/gpl-2.0.html" target="_top">GNU GPL version 2</a> or any later version (at your option).
+<span id="IntroDuction"></span>
+<h1 id="A_1_Introduction"> 1  Introduction </h1>
+<code>msr2data</code> (originally written by B. M. Wojek) is a program implemented in <code>C++</code>. Its purpose is to process multiple <code><a href="MusrFit.html">musrfit</a></code> msr files with the same parameters and summarize the fitting results either in a TRIUMF <strong>DB</strong> <a name="FootNote1text"></a><span class="FootNoteTextLink" title=" For an abridged description of this format see &#91;&#91;http&#58;&#47;&#47;musr&#46;org&#47;xyfit&#47;dbformat&#46;html&#93;&#91;here&#93;&#93;&#46; The &#42;DB&#42; files produced by &#61;msr2data&#61; can be viewed for instance with &#91;&#91;http&#58;&#47;&#47;musr&#46;org&#47;muview&#47;&#93;&#91;&#38;mu&#59;View&#93;&#93;&#44; however&#44; they are <em>not completely</em> backward&#45;compatible to the original &#34;db language&#34; since the parameter names can be longer than five or six characters&#33; In order to establish this backward compatibility &#40;if needed&#41; the user has to ensure the correct length of the parameter names in the msr files&#33;"><a class="foswikiCurrentTopicLink" href="#FootNote1note">(1)</a></span> or a <strong>column ASCII</strong> file. It evolved from a script called <code>mlog2db</code> which has been written only for collecting fit results of <a href="http://lmu.web.psi.ch/lem/">LEM</a> data stored in mlog files generated by <code>musrfit</code> and putting them together in a file with the <strong>DB</strong> format for further analysis. Therefore, any peculiarities, e.g. in supplying options to <code>msr2data</code> are owed its original purpose.
+<code>msr2data</code> is <a href="http://www.gnu.org/philosophy/free-sw.html">free software</a> and licensed under the <a href="http://www.gnu.org/licenses/old-licenses/gpl-2.0.html">GNU GPL version 2</a> or any later version (at your option).
 <p></p>
 Before the usage of msr2data will be explained in greater detail first be aware of the following:
 <p></p>
-<strong><span class='foswikiRedFG'>If using msr2data always bear in mind <a href="#KnownLimitations" class="foswikiCurrentTopicLink">its limitations</a>!</span></strong>
+<strong><span class='foswikiRedFG'>If using msr2data always bear in mind <a class="foswikiCurrentTopicLink" href="#KnownLimitations">its limitations</a>!</span></strong>
 <p></p>
 <p></p>
 <p></p>
 Notes
 <p></p>
-<a name="FootNote1note"></a><span class="FootNoteLabel"><a href="#FootNote1text" class="foswikiCurrentTopicLink"> <strong>1</strong> </a></span>: <span class="FootNote"> For an abridged description of this format see <a href="http://musr.org/xyfit/dbformat.html" target="_top">here</a>. The <strong>DB</strong> files produced by <code>msr2data</code> can be viewed for instance with <a href="http://musr.org/muview/" target="_top">&mu;View</a>, however, they are <em>not completely</em> backward-compatible to the original "db language" since the parameter names can be longer than five or six characters! In order to establish this backward compatibility (if needed) the user has to ensure the correct length of the parameter names in the msr files!</span> 
+<a name="FootNote1note"></a><span class="FootNoteLabel"><a href="#FootNote1text"><b>1</b></a></span>: <span class="FootNote"> For an abridged description of this format see <a href="http://musr.org/xyfit/dbformat.html">here</a>. The <strong>DB</strong> files produced by <code>msr2data</code> can be viewed for instance with <a href="http://musr.org/muview/">&mu;View</a>, however, they are <em>not completely</em> backward-compatible to the original "db language" since the parameter names can be longer than five or six characters! In order to establish this backward compatibility (if needed) the user has to ensure the correct length of the parameter names in the msr files!</span> 
 <p></p>
 <p></p>
 <p></p>
 <hr />
 <p></p>
-<a name="BasicTypesOfUsage"></a>
-<h1><a name="A_2_Basic_Types_of_Usage"></a> 2  Basic Types of Usage </h1>
-Apart from numerous <a href="#OptionalParameters" class="foswikiCurrentTopicLink">optional parameters</a> that might be set or not, in principle there are four different ways of calling <code>msr2data</code>. These differ in how the list of runs which should be processed is supplied: <dl>
+<span id="BasicTypesOfUsage"></span>
+<h1 id="A_2_Basic_Types_of_Usage"> 2  Basic Types of Usage </h1>
+Apart from numerous <a class="foswikiCurrentTopicLink" href="#OptionalParameters">optional parameters</a> that might be set or not, in principle there are four different ways of calling <code>msr2data</code>. These differ in how the list of runs which should be processed is supplied: <dl>
 <dt> msr2data &lt;run&gt; &lt;extension&gt; [optional parameters] </dt><dd> A single run number.
 </dd> <dt> msr2data &lt;firstRunNo&gt; &lt;lastRunNo&gt; &lt;extension&gt; [optional parameters] </dt><dd> An interval of run numbers is specified through the first and the last run number. The condition <strong>&lt;firstRunNo&gt;  &lt; &lt;lastRunNo&gt;</strong> is <em>not</em> necessary.
-</dd> <dt> msr2data \[&lt;run1&gt; &lt;run2&gt; ... &lt;runN&gt; \] &lt;extension&gt; [optional parameters] </dt><dd> A space separated list of run numbers can be enclosed in <strong>[</strong> and <strong>]</strong>. Every run that should be processed has to be specified explicitly by its run number.
-</dd> <dt> msr2data &lt;runListFileName&gt; &lt;extension&gt; [optional parameters] </dt><dd> An ASCII file containing a list of run numbers and optional external parameters is passed to <code>msr2data</code>. For the structure of the ASCII file see <a href="#RunListStructure" class="foswikiCurrentTopicLink">below</a>.
+</dd> <dt> msr2data \[ &lt;runList&gt; \] &lt;extension&gt; [optional parameters] </dt><dd> Where &lt;runList&gt; is one or a combination of the following:(i) <strong>&lt;run0&gt;, &lt;run1&gt;, &lt;run2&gt;, ... &lt;runN&gt;</strong> : run numbers, e.g. 123 124, (ii)  <strong>&lt;run0&gt;-&lt;runN&gt;</strong> : a range, e.g. 123-125 -&gt; 123 124 125, (iii) <strong>&lt;run0&gt;:&lt;runN&gt;:&lt;step&gt;</strong> : a sequence, e.g. 123:127:2 -&gt; 123 125 127. &lt;step&gt; has to be a <strong>positive</strong> integer. A &lt;runList&gt; can also combine (i)-(iii), e.g. 123 128-130 133, etc.    
+</dd> <dt> msr2data &lt;runListFileName&gt; &lt;extension&gt; [optional parameters] </dt><dd> An ASCII file containing a list of run numbers and optional external parameters is passed to <code>msr2data</code>. For the structure of the ASCII file see <a class="foswikiCurrentTopicLink" href="#RunListStructure">below</a>.
 </dd></dl> 
 <p></p>
 All four basic types of calling <code>msr2data</code> contain the <em>mandatory</em> file-name <strong>&lt;extension&gt;</strong> passed right after the list of runs. The meaning of this <strong>&lt;extension&gt;</strong> should become clear after giving examples for all four cases:
-<pre class="bash">msr2data 8472 &#95;tf&#95;h13</pre> generates the <strong>DB</strong> file <code><b>out.db</b></code> (can be changed by using <a href="#OptionalParameters" class="foswikiCurrentTopicLink">the -o option</a>) from <code><b>8472_tf_h13.msr</b></code>.
-<pre class="bash">msr2data 8472 8474 &#95;tf&#95;h13</pre> generates the <strong>DB</strong> file <code><b>out.db</b></code> (can be changed by using <a href="#OptionalParameters" class="foswikiCurrentTopicLink">the -o option</a>) from <code><b>8472_tf_h13.msr</b></code>, <code><b>8473_tf_h13.msr</b></code>, and <code><b>8474_tf_h13.msr</b></code>.
-<pre class="bash">msr2data &#91;8472 8470] &#95;tf&#95;h13</pre> generates the <strong>DB</strong> file <code><b>out.db</b></code> (can be changed by using <a href="#OptionalParameters" class="foswikiCurrentTopicLink">the -o option</a>) from <code><b>8472_tf_h13.msr</b></code> and <code><b>8470_tf_h13.msr</b></code>.
-<pre class="bash">msr2data run.list &#95;tf&#95;h13</pre> generates the <strong>DB</strong> file <code><b>out.db</b></code> (can be changed by using <a href="#OptionalParameters" class="foswikiCurrentTopicLink">the -o option</a>) from all runs listed in the ASCII file <code><b>run.list</b></code> in the working directory. In this file it is also possible to include external parameters which should be put in the resulting <strong>DB</strong> file. The structure of the <code><b>run.list</b></code> is the following:
-<a name="RunListStructure"></a>
+<pre class="bash">msr2data 8472 &#95;tf&#95;h13</pre> generates the <strong>DB</strong> file <code><b>out.db</b></code> (can be changed by using <a class="foswikiCurrentTopicLink" href="#OptionalParameters">the -o option</a>) from <code><b>8472_tf_h13.msr</b></code>.
+<pre class="bash">msr2data 8472 8474 &#95;tf&#95;h13</pre> generates the <strong>DB</strong> file <code><b>out.db</b></code> (can be changed by using <a class="foswikiCurrentTopicLink" href="#OptionalParameters">the -o option</a>) from <code><b>8472_tf_h13.msr</b></code>, <code><b>8473_tf_h13.msr</b></code>, and <code><b>8474_tf_h13.msr</b></code>.
+<pre class="bash">msr2data &#91;8472 8470&#93; &#95;tf&#95;h13</pre> generates the <strong>DB</strong> file <code><b>out.db</b></code> (can be changed by using <a class="foswikiCurrentTopicLink" href="#OptionalParameters">the -o option</a>) from <code><b>8472_tf_h13.msr</b></code> and <code><b>8470_tf_h13.msr</b></code>.
+<pre class="bash">msr2data &#91;8470:8474:2&#93; &#95;tf&#95;h13</pre> generates the <strong>DB</strong> file <code><b>out.db</b></code> (can be changed by using <a class="foswikiCurrentTopicLink" href="#OptionalParameters">the -o option</a>) from <code><b>8470_tf_h13.msr</b></code>, <code><b>8472_tf_h13.msr</b></code>, and <code><b>8474_tf_h13.msr</b></code>.
+<pre class="bash">msr2data run.list &#95;tf&#95;h13</pre> generates the <strong>DB</strong> file <code><b>out.db</b></code> (can be changed by using <a class="foswikiCurrentTopicLink" href="#OptionalParameters">the -o option</a>) from all runs listed in the ASCII file <code><b>run.list</b></code> in the working directory. In this file it is also possible to include external parameters which should be put in the resulting <strong>DB</strong> file. The structure of the <code><b>run.list</b></code> is the following:
+<span id="RunListStructure"></span>
 <pre>
 RUN VAR1 VAR2 VAR3 ...
 8460 200 27.1 46.2 ...
 8472 205 27.1 46.3 ...
 8453 210 27.2 45.9 ...
-<EFBFBD>     <EFBFBD>    <EFBFBD>    <EFBFBD>
-<EFBFBD>     <EFBFBD>    <EFBFBD>    <EFBFBD>
-<EFBFBD>     <EFBFBD>    <EFBFBD>    <EFBFBD>
+·     ·    ·    ·
+·     ·    ·    ·
+·     ·    ·    ·
 </pre>
 <span class='foswikiRedFG'>The first not commented and not empty line determines the parameter names and labels and has to be present!</span><br/>
 It is allowed to add comments (with a preceding <strong>#</strong>) or empty lines to the run-list file. 
 <p></p>
 The following should be mentioned together with the above examples: <ul>
 <li> The output files in the examples above are only newly created if they did not exist before invoking <strong>msr2data</strong>. If the files were already present the msr-file data would be appended!
-</li> <li> If the files have been newly created, also the <strong>DB</strong> file header is written. If the files were present before, only the data blocks are appended. The output of the header can either be forced or completely suppressed with the <a href="#OptionalParameters" class="foswikiCurrentTopicLink">header and noheader options</a> as shall be seen later.
+</li> <li> If the files have been newly created, also the <strong>DB</strong> file header is written. If the files were present before, only the data blocks are appended. The output of the header can either be forced or completely suppressed with the <a class="foswikiCurrentTopicLink" href="#OptionalParameters">header and noheader options</a> as shall be seen later.
 </li></ul> 
-<a name="NoExtension"></a> <ul>
+<span id="NoExtension"></span> <ul>
 <li> <span class='foswikiRedFG'>If the <code>musrfit</code> output files do not have an &lt;extension&gt; as specified above like <code><b>8472.msr</b></code> one has to call <code>msr2data</code> like in the following example:</span> <pre class="bash">
 msr2data 8472 8460 &#34;&#34;
 </pre>
 </li></ul> 
 <p></p>
-<a name="OptionalParameters"></a>
-<h1><a name="A_3_Optional_Parameters"></a> 3  Optional Parameters </h1>
+<span id="OptionalParameters"></span>
+<h1 id="A_3_Optional_Parameters"> 3  Optional Parameters </h1>
 As mentioned already above there are some optional parameters which change the behavior of <code>msr2data</code> and can be passed in any order. Here is a complete list: <dl>
 <dt> data </dt><dd> The output file format is changed to a simple column ASCII file (default output file name: <code><b>out.dat</b></code>).
 </dd> <dt> new </dt><dd> An existing output file is deleted before new information is written to it.
 </dd> <dt> header </dt><dd> Force the output of the file header&#151;even if the output file was present before.
 </dd> <dt> noheader </dt><dd> The output of the file header is suppressed&#151;also if the output file is newly created.<br>If either both or none of the header options are given, <code>msr2data</code> writes the file header only to new files and it solely appends the data blocks to an existing output file assuming that the header is present already.
 </dd> <dt> nosummary </dt><dd> There will be no attempt to read additional information like the temperature or the applied magnetic field from the data files even if these information were present there.
+</dd> <dt> paramList &lt;param&gt; </dt><dd> option used to select the parameters which shall be exported. &lt;param&gt; is a list of parameter numbers to be exported. Allowed lists are: &lt;startNo&gt;-&lt;endNo&gt;, e.g. 1-16 will export parameters 1 to 16. Space separated numbers, e.g.: 1 3 5. A combination of both is possible, e.g. 1-16 19 31 62, and so on. 
 </dd> <dt> -o&lt;outputFileName&gt;, -o &lt;outputFileName&gt; </dt><dd> The processed data will be written to the file <strong>&lt;outputFileName&gt;</strong> instead of the default <code><b>out.db</b></code> or <code><b>out.dat</b></code>. If <strong>&lt;outputFileName&gt;</strong> is equal to <strong>none</strong> (case-insensitive) the parameter data are <em>not appended</em> to any output file.
 </dd> <dt> fit </dt><dd> Additionally to the final data collection <code>msr2data</code> will invoke musrfit to fit the specified runs. All msr files are assumed to be present, none is newly generated!
 </dd> <dt> fit-&lt;template&gt;[!] </dt><dd> Additionally to the final data collection <code>msr2data</code> will generate msr files for the runs specified in the list of runs and invoke <code>musrfit</code> for performing fits of the data. As template for the first run the file <code><b>&lt;template&gt;&lt;extension&gt;.msr</b></code> (or if not available: <code><b>&lt;template&gt;&lt;extension&gt;.mlog</b></code>) is used; the subsequent input files will be created using the msr output of the last processed runs ("chain fit"). However, if for <em>all</em> runs only the given template should be used one has to append an exclamation mark (<strong>!</strong>) to the <strong>&lt;template&gt;</strong>.
@@ -212,9 +256,9 @@ msr2data 8400 8460 &#95;tf&#95;h13 -oABC.db fit-8472
 </pre>
 Using <code><b>8472_tf_h13.msr</b></code> as first template, <code>msr2data</code> generates subsequent msr input files <code><b>8400_tf_h13.msr</b></code> through <code><b>8460_tf_h13.msr</b></code>, calls <code>musrfit</code> to perform a fit of these files and collects the results of the fits together with the <strong>DB</strong> header in the new file <code><b>ABC.db</b></code>. Additionally, some information about external parameters like the temperature will be passed to <code><b>ABC.db</b></code> if it is present in the data files.
 <pre class="bash">
-msr2data &#91;8500 8505] &#95;zf fit-8472 noheader nosummary -o DEF.db 
+msr2data &#91;8500 8502-8504 8507&#93; &#95;zf fit-8472 noheader nosummary -o DEF.db 
 </pre>
-Using <code><b>8472_zf.msr</b></code> as first template, <code>msr2data</code> generates subsequent msr input files <code><b>8500_zf.msr</b></code> and <code><b>8505_zf.msr</b></code>, calls <code>musrfit</code> to perform a fit of these files and collects the results of the fits in the file <code><b>DEF.db</b></code> without writing the <strong>DB</strong> file header or attempting to read additional information from the data files.
+Using <code><b>8472_zf.msr</b></code> as first template, <code>msr2data</code> generates subsequent msr input files <code><b>8500_zf.msr</b></code>, <code><b>8502_zf.msr</b></code>, <code><b>8503_zf.msr</b></code>, <code><b>8504_zf.msr</b></code> and <code><b>8507_zf.msr</b></code>, calls <code>musrfit</code> to perform a fit of these files and collects the results of the fits in the file <code><b>DEF.db</b></code> without writing the <strong>DB</strong> file header or attempting to read additional information from the data files.
 <pre class="bash">
 msr2data 8595 8585 &#34;&#34; noheader fit-8472! -oGHI.dat data nosummary -k 
 </pre>
@@ -227,13 +271,19 @@ Take the <strong>given</strong> msr files <code><b>8472.msr</b></code> through <
 msr2data 8472 8475 &#95;tf&#95;h13 msr-8471!
 </pre>
 Using <code><b>8471_tf_h13.msr</b></code> as template for <em>all</em> runs, <code>msr2data</code> generates the msr input files <code><b>8472_tf_h13.msr</b></code> through <code><b>8475_tf_h13.msr</b></code>. <span class='foswikiRedFG'>No fitting will be performed and no DB or ASCII output will be generated!</span>
+<pre class="bash">
+msr2data &#91;8472 8475-8479&#93; &#95;tf&#95;h13 paramList 1-16 data -o bestData.dat
+</pre>
+Will collect the parameters 1 to 16 from the msr-files <code><b>8472_tf_h13.msr</b></code>, <code><b>8475_tf_h13.msr</b></code>, <code><b>8476_tf_h13.msr</b></code>, <code><b>8477_tf_h13.msr</b></code>, <code><b>8478_tf_h13.msr</b></code>, and <code><b>8479_tf_h13.msr</b></code> and write these parameters into a column like output file <code><b>bestData.dat</b></code>.
 <p></p>
-<a name="TheGlobalMode"></a>
-<h1><a name="A_4_The_Global_Mode"></a> 4  The Global Mode </h1>
-Apart from all the options described <a href="#OptionalParameters" class="foswikiCurrentTopicLink">above</a> there is another program option: <strong>global</strong>. This option changes the general behavior of <code>msr2data</code> in that way that instead of processing one msr file for each run it combines all specified runs in one single msr file with the possibility to define common parameters for all runs as well as run-specific parameters. When writing the obtained parameters to a DB file or a column-structured ASCII file that single msr file is read and the parameters valid for each run are extracted. The <strong>global</strong> option can be used in conjunction with any of the described <a href="#BasicTypesOfUsage" class="foswikiCurrentTopicLink">invocations</a> of <code>msr2data</code> and together with all options stated <a href="#OptionalParameters" class="foswikiCurrentTopicLink">above</a>.
 <p></p>
-<a name="GlobalFileGeneration"></a>
-<h2><a name="A_4.1_File_Generation"></a> 4.1  File Generation </h2>
+<p></p>
+<span id="TheGlobalMode"></span>
+<h1 id="A_4_The_Global_Mode"> 4  The Global Mode </h1>
+Apart from all the options described <a class="foswikiCurrentTopicLink" href="#OptionalParameters">above</a> there is another program option: <strong>global</strong>. This option changes the general behavior of <code>msr2data</code> in that way that instead of processing one msr file for each run it combines all specified runs in one single msr file with the possibility to define common parameters for all runs as well as run-specific parameters. When writing the obtained parameters to a DB file or a column-structured ASCII file that single msr file is read and the parameters valid for each run are extracted. The <strong>global</strong> option can be used in conjunction with any of the described <a class="foswikiCurrentTopicLink" href="#BasicTypesOfUsage">invocations</a> of <code>msr2data</code> and together with all options stated <a class="foswikiCurrentTopicLink" href="#OptionalParameters">above</a>.
+<p></p>
+<span id="GlobalFileGeneration"></span>
+<h2 id="A_4.1_File_Generation"> 4.1  File Generation </h2>
 The general idea of this mode is to generate a global msr file on the basis of a working single-run msr file. For this purpose a single-run template containing information about common and run-specific parameters should be created. These parameters are identified through their parameter names: <dl>
 <dt> run-specific parameters </dt><dd> these parameters are tagged with the current run number in the format <strong>%0Xu</strong>, i.e. <strong>X</strong> digits with leading zeros, at the end of the parameter name, e.g. for a 4-digit-formatted run number <strong>alpha0123</strong> if the run number was <strong>123</strong> or for a 8-digit-formatted run number <strong>alpha00123456</strong> if the run number was <strong>123456</strong>. <strong>X</strong> has to be at least 4.
 </dd> <dt> common parameters </dt><dd> all parameters that are not run specific
@@ -278,32 +328,32 @@ During this reorganization all the affected parameter occurrences are changed ac
 <p></p>
 <span class='foswikiRedFG'>Please be aware of the fact that comments in the template msr file are <em>not</em> propagated to the newly generated global msr file!</span>
 <p></p>
-<h2><a name="A_4.2_Parameter_Extraction"></a> 4.2  Parameter Extraction </h2>
-After fitting some model to the specified data the fit parameters can be extracted from the global msr file to a <strong>DB</strong> or column-structured ASCII file&mdash;as usual this includes also parameters stored in the run data files or externally specified parameters given in a <a href="#RunListStructure" class="foswikiCurrentTopicLink">run-list file</a>.
+<h2 id="A_4.2_Parameter_Extraction"> 4.2  Parameter Extraction </h2>
+After fitting some model to the specified data the fit parameters can be extracted from the global msr file to a <strong>DB</strong> or column-structured ASCII file&mdash;as usual this includes also parameters stored in the run data files or externally specified parameters given in a <a class="foswikiCurrentTopicLink" href="#RunListStructure">run-list file</a>.
 In order to reach this goal the global msr file has to obey certain rules: <ul>
-<li> The order of the parameters has to match the one described <a href="#GlobalFileGeneration" class="foswikiCurrentTopicLink">above</a>, meaning the common parameters are listed first followed by the same number of parameters specific to each run tagged by the according run numbers at the end of the parameter names and having the same order as the specified list of runs.
+<li> The order of the parameters has to match the one described <a class="foswikiCurrentTopicLink" href="#GlobalFileGeneration">above</a>, meaning the common parameters are listed first followed by the same number of parameters specific to each run tagged by the according run numbers at the end of the parameter names and having the same order as the specified list of runs.
 </li> <li> The RUN blocks have to be ordered according to the list of runs to be processed.
 </li></ul> 
-Following these rules&mdash;which is achieved most easily by generating the global msr file using <code>msr2data</code> as shown <a href="#GlobalFileGeneration" class="foswikiCurrentTopicLink">above</a>&mdash;the parameters can be extracted e.g. like <pre class="bash">
+Following these rules&mdash;which is achieved most easily by generating the global msr file using <code>msr2data</code> as shown <a class="foswikiCurrentTopicLink" href="#GlobalFileGeneration">above</a>&mdash;the parameters can be extracted e.g. like <pre class="bash">
 msr2data 8471 8470 &#95;example global data -o globalFit.dat
 </pre>
 This will read in the file <code><b>8471+global_example.msr</b></code>, extract for each run all relevant parameters from the msr file as well as from the according data files (if available) and append all of them in columns to the ASCII file <code><b>globalFit.dat</b></code>.
 <p></p>
-<a name="GlobalPlus"></a>
-<h2><a name="A_4.3_The_Extended_Global_Mode"></a> 4.3  The Extended Global Mode </h2>
+<span id="GlobalPlus"></span>
+<h2 id="A_4.3_The_Extended_Global_Mode"> 4.3  The Extended Global Mode </h2>
 If a new global input file is generated, it is also possible to do an automatic pre-analysis for each single run using the specified template first; afterwards the run-specific parameters of these single-run msr files are collected in the global msr file. In special cases this might be useful to obtain a better set of starting values for the parameters, however, in most cases it will not replace the "manual review" of the generated global input file. The option is activated by choosing the keyword <strong>global+</strong>. For example <pre class="bash">
 msr2data 8471 8470 &#95;example global+ msr-8472
 </pre>
 Here, <code><b>8472_example.msr</b></code> is first used as template to generate the file <code><b>8471-OneRunFit_example.msr</b></code>, then <code>musrfit</code> is called for it, the result is used to generate <code><b>8470-OneRunFit_example.msr</b></code> and <code>musrfit</code> is called for that file. Finally, the global fit file <code><b>8471+global_example.msr</b></code> is produced&mdash;including the fit results of the OneRunFit files for the run-specific parameters.<br>
-By appending an exclamation mark <strong>!</strong> to the <strong>global+</strong> option, the given template will be used for every new file generation (similar to the <strong>fit</strong> option explained <a href="#OptionalParameters" class="foswikiCurrentTopicLink">before</a>). The <strong>+[!]</strong> extension will be ignored, if no new global input file is generated.<br>
+By appending an exclamation mark <strong>!</strong> to the <strong>global+</strong> option, the given template will be used for every new file generation (similar to the <strong>fit</strong> option explained <a class="foswikiCurrentTopicLink" href="#OptionalParameters">before</a>). The <strong>+[!]</strong> extension will be ignored, if no new global input file is generated.<br>
 The single run msr files are not deleted at the moment. The information contained in them might be useful for some people. Of course the data can also be collected by <code>msr2data</code>. E.g. in order to produce a <strong>DB</strong> file <code><b>OneRunFits.db</b></code> one could call <pre class="bash">
 msr2data 8471 8470 -OneRunFit&#95;example -o OneRunFits.db
 </pre>
 <p></p>
 <span class='foswikiRedFG'>Please be aware that the program in this mode always generates new single-run msr files and always calls <code>musrfit</code> for them. In case there are already single-run fits present, these cannot be used in conjunction with this option. The program on purpose behaves in this way in order to ensure the file integrity and correct parameter order within these files.</span>
 <p></p>
-<a name="KnownLimitations"></a>
-<h1><a name="A_5_Known_Limitations"></a> 5  Known Limitations </h1> <ul>
+<span id="KnownLimitations"></span>
+<h1 id="A_5_Known_Limitations"> 5  Known Limitations </h1> <ul>
 <li> The indexing run number of the msr file has to be at the begin of every filename.
 </li> <li> Within the data file name the <strong>RUN#</strong> has the format <strong>%0Xu</strong>, i.e. <strong>X</strong> digits with leading zeros, and has to be the rightmost number given in this format in the file name. <strong>X</strong> has to be at least 4. The highest treatable run number is 2<sup>32</sup>-1 = 4294967295.
 </li> <li> In order to keep <code>msr2data</code> working properly the msr files should only contain <em><span class='foswikiRedFG'>one</span> STATISTIC block at the end of the file</em> and <i><span class='foswikiRedFG'>one</span> FITPARAMETER block right after the TITLE</i>&mdash;<code>musrfit</code> itself allows to have more creative msr files...
@@ -311,12 +361,12 @@ msr2data 8471 8470 -OneRunFit&#95;example -o OneRunFits.db
 </li> <li> <code>msr2data</code> will write only up to <em>two successive</em> empty lines in newly generated msr files. In case more subsequent empty lines are encountered in a template file, these are <em>not</em> copied! Actually, this measure is not a limitation but has been introduced to keep the msr files in a reasonable shape.
 </li></ul> 
 <p></p>
-<a name="MusrGuiInterface"></a>
-<h1><a name="A_6_The_Graphical_User_Interface_Provided_by_61_61musrgui_61_61_47_61_61musredit_61_61"></a> 6  The Graphical User Interface Provided by <code><b>musrgui</b></code> / <code><b>musredit</b></code> </h1>
+<span id="MusrGuiInterface"></span>
+<h1 id="A_6_The_Graphical_User_Interface_Provided_by_61_61musrgui_61_61_47_61_61musredit_61_61"> 6  The Graphical User Interface Provided by <code><b>musrgui</b></code> / <code><b>musredit</b></code> </h1>
 <code><a href="MusrGui.html">musrgui/musredit</a></code>, editors designed especially for the manipulation of <code>musrfit</code> msr files and graphical front ends to <code><a href="MusrFit.html">musrfit</a></code>, offer an almost self-explanatory graphical user interface to <code>msr2data</code> depicted below:<br>
-<img src="../pub/MUSR/Msr2Data/msr2data-input-tabs.png" alt="msr2data-input-tabs.png" width='612' height='605' align="right" /> <dl>
-<dt> <span class='foswikiRedFG'>1&ndash;3</span> </dt><dd> Choose one of the <a href="#BasicTypesOfUsage" class="foswikiCurrentTopicLink">ways</a> to specify your list of runs.
-</dd> <dt> <span class='foswikiRedFG'>4</span> </dt><dd> Give the file extension here, e.g. <strong>_zf</strong> for files like <code><b>8472_zf.msr</b></code>. If the files do not have an extension this field stays empty. <code>musrgui</code> / <code>musredit</code> take care of passing the <strong>""</strong> to <code>msr2data</code> as mentioned <a href="#NoExtension" class="foswikiCurrentTopicLink">above</a>.
+<img class='imagePlain imagePlain_right ' src='../pub/MUSR/Msr2Data/igp_589e1dc22ab7bf8fd9d5889da6e407f1_msr2data-input-tabs.png' alt='msr2data-input-tabs.png' title='msr2data-input-tabs.png' width='612' height='605'   style='' /> <dl>
+<dt> <span class='foswikiRedFG'>1&ndash;3</span> </dt><dd> Choose one of the <a class="foswikiCurrentTopicLink" href="#BasicTypesOfUsage">ways</a> to specify your list of runs.
+</dd> <dt> <span class='foswikiRedFG'>4</span> </dt><dd> Give the file extension here, e.g. <strong>_zf</strong> for files like <code><b>8472_zf.msr</b></code>. If the files do not have an extension this field stays empty. <code>musrgui</code> / <code>musredit</code> take care of passing the <strong>""</strong> to <code>msr2data</code> as mentioned <a class="foswikiCurrentTopicLink" href="#NoExtension">above</a>.
 </dd> <dt> <span class='foswikiRedFG'>5</span> </dt><dd> Activates the <strong>fit-&lt;template&gt;</strong> option if <strong>&lt;template&gt;</strong> is entered. In case the option "Chain Fit" is <em>not</em> set the given template will be used for the input-file generation for <em>all</em> runs to be fitted&mdash;otherwise the output of the first fit serves as template for the second and so on. The template field stays empty if no fits should be performed!
 </dd> <dt> <span class='foswikiRedFG'>6</span> </dt><dd> Activates the <strong>-o&lt;outputFileName&gt;</strong> option if <strong>&lt;outputFileName&gt;</strong> is entered. If nothing is entered the default output file <code><b>out.db</b></code> or <code><b>out.dat</b></code> is used.
 </dd> <dt> <span class='foswikiRedFG'>7</span> </dt><dd> If <em>not</em> set, the <strong>noheader</strong> option is passed to <code>msr2data</code>.
@@ -328,104 +378,62 @@ msr2data 8471 8470 -OneRunFit&#95;example -o OneRunFits.db
 </dd> <dt> <span class='foswikiRedFG'>13</span> </dt><dd> If set, the <strong>-t</strong> option is passed to <code>msr2data</code>.
 </dd> <dt> <span class='foswikiRedFG'>14</span> </dt><dd> If set, <code>msr2data</code> is called with the option <strong>msr-&lt;template&gt;</strong> (instead of <strong>fit-&lt;template&gt;</strong>) and hence is only producing the msr input files without any fitting.
 </dd> <dt> <span class='foswikiRedFG'>15</span> </dt><dd> If set, <code>msr2data</code> is called with the option <strong>fit</strong>, i.e. no template will be used to generate new msr input files; only existing files are fed to <code>musrfit</code>.
-</dd> <dt> <span class='foswikiRedFG'>16</span> </dt><dd> If set, <code>msr2data</code> is operating in the <a href="#TheGlobalMode" class="foswikiCurrentTopicLink">global mode</a>.
-</dd> <dt> <span class='foswikiRedFG'>17</span> </dt><dd> If set, <code>msr2data</code> is operating in the <a href="#GlobalPlus" class="foswikiCurrentTopicLink">extended global mode</a>.
+</dd> <dt> <span class='foswikiRedFG'>16</span> </dt><dd> If set, <code>msr2data</code> is operating in the <a class="foswikiCurrentTopicLink" href="#TheGlobalMode">global mode</a>.
+</dd> <dt> <span class='foswikiRedFG'>17</span> </dt><dd> If set, <code>msr2data</code> is operating in the <a class="foswikiCurrentTopicLink" href="#GlobalPlus">extended global mode</a>.
 </dd></dl> 
 <p></p>
-<a name="BugTracking"></a>
-<h1><a name="A_7_Bugtracking"></a> 7  Bugtracking </h1>
+<span id="BugTracking"></span>
+<h1 id="A_7_Bugtracking"> 7  Bugtracking </h1>
 <p></p>
-For reporting bugs or requesting new features and improvements please use the <a href="https://tracker.intranet.psi.ch/jira/browse/MUSR" target="_top">PSI Tracker</a> or send an e-mail to A. Suter.
+For reporting bugs or requesting new features and improvements please use the <a href="https://bitbucket.org/muonspin/musrfit/issues?status=new&amp;status=open">Bitbucket Issues</a>, <a href="https://tracker.psi.ch/jira/browse/MUSR">PSI Tracker</a> or send an e-mail to A. Suter.
 <p></p>
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-<li> <span class="foswikiIcon"><img src="../pub/System/DocumentGraphics/psi.png" width="16" height="16" alt="psi" /></span> <a href="https://intranet.psi.ch/Main/WebHome">Main</a>
-</li> <li> <span class="foswikiIcon"><img src="../pub/System/DocumentGraphics/psi.png" width="16" height="16" alt="psi" /></span> <a href="https://intranet.psi.ch/Main/WebList">weitere Webs</a>
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+			<th class="foswikiTableCol4"> <a href="https://intranet.psi.ch/MUSR/Msr2Data?cover=print;sortcol=4;table=1;up=0#sorted_table" rel="nofollow" title="Sort by this column">Date</a> </th>
+			<th class="foswikiTableCol5"> <a href="https://intranet.psi.ch/MUSR/Msr2Data?cover=print;sortcol=5;table=1;up=0#sorted_table" rel="nofollow" title="Sort by this column">Who</a> </th>
+			<th class="foswikiTableCol6 foswikiLastCol"> <a href="https://intranet.psi.ch/MUSR/Msr2Data?cover=print;sortcol=6;table=1;up=0#sorted_table" rel="nofollow" title="Sort by this column">Comment</a> </th>
+		</tr>
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+			<td class="foswikiTableCol1 foswikiLast"> <a href="../pub/MUSR/Msr2Data/msr2data-input-tabs.png">msr2data-input-tabs.png</a> </td>
+			<td class="foswikiTableCol2 foswikiLast"> <a href="https://intranet.psi.ch/wiki/bin/attach/MUSR/Msr2Data?filename=msr2data-input-tabs.png;revInfo=1" title="change, update, previous revisions, move, delete..." rel="nofollow">manage</a> </td>
+			<td class="foswikiTableCol3 foswikiLast" style="text-align:right"> 36 K </td>
+			<td class="foswikiTableCol4 foswikiLast"> <span class="foswikiNoBreak">20 Jul 2011 - 12:13</span> </td>
+			<td class="foswikiTableCol5 foswikiLast"> <a href="https://intranet.psi.ch/Main/UnknownUser">UnknownUser</a> </td>
+			<td class="foswikiTableCol6 foswikiLastCol foswikiLast"> graphical interface to msr2data </td>
+		</tr>
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+<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>Msr2Data <br />
+Topic revision:  <span class='patternRevInfo'>28 Apr 2016, <a href="https://intranet.psi.ch/Main/AndreasSuter">AndreasSuter</a></span></div>
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doc/html/user/MUSR/MusrFitAcknowledgements.html

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+<div class="patternContent"><div class="foswikiTopic"> <h1 id="Acknowledgements_45_61_61musrfit_61_61">  Acknowledgements - <code><b>musrfit</b></code> </h1>
 <p></p> <dl>
-<dt> Bastian M. Wojek </dt><dd> I am very much indebted to <a href="http://www.fsf.org/register_form?referrer=8369" target="_top">BMW</a> for his rigorous testing of <code><a href="MusrFit.html">musrfit</a></code>, his many useful suggestions, contributions, and for the largest part of the <a href="WebHome.html" class="foswikiCurrentWebHomeLink">user manual of <code>musrfit</code></a> which makes it accessible to a broader audience! Many thanks Bastian!
+<dt> Bastian M. Wojek </dt><dd> I am very much indebted to <a href="http://www.fsf.org/register_form?referrer=8369">BMW</a> for his rigorous testing of <code><a href="MusrFit.html">musrfit</a></code>, his many useful suggestions, contributions, and for the largest part of the <a class="foswikiCurrentWebHomeLink" href="WebHome.html">user manual of <code>musrfit</code></a> which makes it accessible to a broader audience! Many thanks Bastian!
 </dd></dl> 
+<p></p> <dl>
+<dt> Uldis Locans </dt><dd> I am very much indebted to Uldis work on <a href="CiteMusrFit.html">DKS</a> enabling the GPU support for <code><a href="MusrFit.html">musrfit</a></code>. His kind, calm, and extremely competent way to deal with his projects as well as to deal with the chaos of physicists way to think is admirable. Many thanks Uldis!
+</dd></dl> </div>
+<p></p>
 <p></p>
--- <a href="http://www.fsf.org/register_form?referrer=8369" target="_top">BMW</a> &amp; <a href="http://lmu.web.psi.ch/lem/group.html" target="_top">AS</a> </div>
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+<div class="patternContent"><div class="foswikiTopic"> <h1 id="Setting_up_61musrfit_61_47_61DKS_61:_high_speed_fitting_with_GPU_39s">  Setting up <code>musrfit</code> / <code>DKS</code>: high speed fitting with GPU's </h1>
+<p></p>
+<div class="foswikiToc" id="foswikiTOC"> <ul>
+<li> <a href="MusrFitSetupDKS.html#Setting_up_61musrfit_61_47_61DKS_61:_high_speed_fitting_with_GPU_39s"> Setting up musrfit / DKS: high speed fitting with GPU's </a>
+</li> <li> <a href="MusrFitSetupDKS.html#A_1_Setting_up_61_61musrfit_47DKS_61_61_for_a_Tesla_K40c_40NVIDIA_41"> 1  Setting up musrfit/DKS for a Tesla K40c (NVIDIA) </a> <ul>
+<li> <a href="MusrFitSetupDKS.html#A_1.1_Driver_Installation_for_the_Tesla_K40c"> 1.1  Driver Installation for the Tesla K40c </a>
+</li> <li> <a href="MusrFitSetupDKS.html#A_1.2_Installation_of_CUDA"> 1.2  Installation of CUDA </a>
+</li> <li> <a href="MusrFitSetupDKS.html#A_1.3_Installation_of_DKS"> 1.3  Installation of DKS </a>
+</li> <li> <a href="MusrFitSetupDKS.html#A_1.4_Installation_of_61musrfit_61_for_DKS"> 1.4  Installation of musrfit for DKS </a> <ul>
+<li> <a href="MusrFitSetupDKS.html#A_1.4.1_Install_via_61_61automake_61_61"> 1.4.1  Install via automake </a>
+</li> <li> <a href="MusrFitSetupDKS.html#A_1.4.2_Install_via_61_61cmake_61_61"> 1.4.2  Install via cmake </a>
+</li></ul> 
+</li></ul> 
+</li> <li> <a href="MusrFitSetupDKS.html#A_2_Setting_up_61_61musrfit_47DKS_61_61_for_a_AMD_Graphic_Card_40Radeon_R9_390X_41"> 2  Setting up musrfit/DKS for a AMD Graphic Card (Radeon R9 390X) </a> <ul>
+<li> <a href="MusrFitSetupDKS.html#A_2.1_Driver_Installation_for_an_AMD_Graphic_Card_44_e.g._Radeon_R9_390X"> 2.1  Driver Installation for an AMD Graphic Card, e.g. Radeon R9 390X </a>
+</li> <li> <a href="MusrFitSetupDKS.html#A_2.2_AMD_APP_Software_Development_Kit_40SDK_41_to_enable_OpenCL_support"> 2.2 AMD APP Software Development Kit (SDK) to enable OpenCL support </a>
+</li> <li> <a href="MusrFitSetupDKS.html#A_2.3_Installation_of_DKS_and_61musrfit_61"> 2.3  Installation of DKS and musrfit </a>
+</li></ul> 
+</li> <li> <a href="MusrFitSetupDKS.html#A_3_Setting_up_61_61musrfit_47DKS_61_61_for_macOS_for_OpenCL_support"> 3  Setting up musrfit/DKS for macOS for OpenCL support </a>
+</li></ul> 
+</div>
+<p></p>
+In the years 2016/2017 we explored ways to speed up current fitting frameworks, especially <code>musrfit</code>. This allows now to analyze histogram sets of high field spectrometers like HAL-9500 at PSI without the error-prone RRF fitting (see U. Locans and A. Suter, " <code>musrfit</code> - Real Time Parameter Fitting Using GPUs", accepted for the proceedings of the muSR2017 conference in Sapporo, and the Memo from A. Suter, "Rotating Reference Frame Fits", in the <code>musrfit</code> source code). At the same time it can help to speed-up elaborate global fits tremendously, and dealing properly with muonium. It also allows Apple Mac users to speed up their fitting code on the CPU. Currently it is not straight forward to get <code>musrfit</code> multi-threaded under macOS since Apple doesn't be default support OpenMP. DKS enables <code>musrfit</code> to utilize OpenCL instead which is present on macOS by default.
+<p></p>
+<strong>Warning</strong>: before you run into the shop to buy a gamer graphic card or a Tesla card, make sure that you have an appropriate server with a sufficiently strong power supply!
+<p></p>
+<strong>However, the current <code>musrfit/DKS</code> version doesn't yet support all theory functions on the GPU.</strong> In case the theory function is not yet available for the GPU, <code>musrfit</code> will fall back to the CPU implementation.
+<p></p>
+Conceptually the setup of <code>musrfit/DKS</code> is as following: <ol>
+<li> install the latest hardware driver for your graphic card.
+</li> <li> install the GPU SDK which enables number crunching (CUDA for NVIDIA, OpenCL for AMD)
+</li> <li> install DKS
+</li> <li> install the musrfit version which is DKS ready
+</li></ol> 
+<p></p>
+In the following the description for the installation of <code>musrfit/DKS</code> for the following systems will be discussed in some more detail: <ul>
+<li> NVIDIA Tesla K40c 
+</li> <li> AMD Graphic Card (Radeon R9 390X)
+</li> <li> macOS in order to get OpenCL support
+</li></ul> 
+<p></p>
+The <strong>usage</strong> of <code>musrfit</code> with GPU acceleration and OpenCL support is described in the <a href="MusrFit.html">'User manual of the &#956;SR data analysis software <code>musrfit</code> '</a>. The additional <code>musrfit</code> / DKS commands are labelled in <span class='foswikiMaroonFG'> <strong>MAROON</strong> </span>.
+<p></p>
+<h1 id="A_1_Setting_up_61_61musrfit_47DKS_61_61_for_a_Tesla_K40c_40NVIDIA_41"> 1  Setting up <code><b>musrfit/DKS</b></code> for a Tesla K40c (NVIDIA) </h1>
+<p></p>
+It is assumed that the Tesla K40c is already physically installed on your system. For now I only will discuss to set it up for a Linux based system. In order to check that your operating systems see the card, enter the following command in the terminal:
+<p></p>
+<pre class="bash">
+&#36; lspci &#124; grep NVIDIA
+</pre>
+<p></p>
+On the response you should find something like
+<p></p>
+<pre class="bash">
+05:00.0 3D controller: NVIDIA Corporation GK110BGL &#91;Tesla K40c&#93; (rev a1)
+</pre>
+<p></p>
+which means that the OS physically recognises your card. 
+<p></p>
+<h2 id="A_1.1_Driver_Installation_for_the_Tesla_K40c"> 1.1  Driver Installation for the Tesla K40c </h2>
+<p></p>
+Next, you will need to download and install the driver for your card. Select the proper operating system, card, etc. from the <a href="http://www.nvidia.com/Download/index.aspx?lang=en-us">NVIDIA download center</a>. At PSI we are running currently Red Hat Enterprise Linux 7.x (RHEL) for which we will get a rpm (something like <code>nvidia-diag-driver-local-repo-rhel7-375.66-1.x86_64.rpm</code>). Install it and make sure there is no conflict with the nouveau driver of the system.
+<p></p>
+<h2 id="A_1.2_Installation_of_CUDA"> 1.2  Installation of CUDA </h2>
+<p></p>
+Download the <a href="https://developer.nvidia.com/cuda-downloads">CUDA SDK</a> form NVIDIA for your system. Again, for the RHEL 7.x this is an rpm. After the installation of the rpm you should reboot your machine. Afterwards you are ready for the installation of DKS.
+<p></p>
+<span id="DksInstall"></span>
+<h2 id="A_1.3_Installation_of_DKS"> 1.3  Installation of DKS </h2>
+<p></p>
+For the following list of commands the '$' will be given as the command prompt. Do not enter it! Also some comments will be added starting with a '#' which can be omitted. They are only there to explain what is going on. 
+<code>DKS</code> stands for Dynamical Kernel Scheduler and provides a thin interface allowing host applications to incorporate GPU's and other hardware accelerators.
+<p></p>
+Details can be found in the papers listed <a href="CiteMusrFit.html">here</a>, or on the <a href="https://gitlab.psi.ch/uldis_l/DKS/wikis/home">DKS wiki page</a>.
+<p></p>
+In brief the installation should be something like this:<pre class="bash">
+# go to whatever directory you would like to clone/install DKS
+# For macOS DKS will likely to got to &#36;HOME/Applications to be consistent with the musrfit docu for macOS
+&#36; cd &#36;HOME/Apps
+&#36; git clone https://gitlab.psi.ch/uldis&#95;l/DKS.git
+&#36; cd DKS
+&#36; mkdir build
+&#36; cd build
+&#36; cmake ../ -DENABLE&#95;MUSR&#61;1 -DCMAKE&#95;INSTALL&#95;PREFIX&#61;../exec
+&#36; cmake --build ./ --clean-first
+&#36; make install
+</pre>
+<p></p>
+Since <code>DKS</code> is installed in a non-standard path, a couple of additional small steps are required. This will be different for Linux compared to macOS.
+<p></p>
+For <strong>Linux</strong>:
+<p></p>
+add the <code>DKS</code> library path to <code>/etc/ld.so.conf.d/musrfit-x86_64.conf</code> and execute as super user
+<p></p>
+<pre class="bash">
+&#36; /sbin/ldconfig
+</pre>
+<p></p>
+For <strong>macOS</strong>:
+<p></p>
+add the <code>DKS</code> path to <code>$HOME/.profile</code>:
+<p></p>
+<pre class="bash">
+export DKS&#61;&#36;HOME/Applications/DKS/exec
+export LD&#95;LIBRARY&#95;PATH&#61;&#36;DKS/lib:&#36;LD&#95;LIBRARY&#95;PATH
+
+launchctl setenv DKS &#36;DKS
+launchctl setenv LD&#95;LIBRARY&#95;PATH &#36;LD&#95;LIBRARY&#95;PATH
+</pre>
+<p></p>
+<h2 id="A_1.4_Installation_of_61musrfit_61_for_DKS"> 1.4  Installation of <code>musrfit</code> for DKS </h2>
+<p></p>
+Most of the installation steps are the same as described for <a href="MusrFitSetup.html"><code>musrfit</code></a> without GPU support.
+Here only the differences are explained. First checkout <code>musrfit</code>, then you will need to switch the working branch which is done by<pre class="bash">
+&#36; cd &#36;HOME/Apps/musrfit
+&#36; git checkout dks6
+</pre>
+<p></p>
+<h3 id="A_1.4.1_Install_via_61_61automake_61_61"> 1.4.1  Install via <code><b>automake</b></code> </h3>
+<p></p>
+The configure script for <code>musrfit</code> has now a couple of more tags/options, which are: <dl>
+<dt> <code><b>--enable-dks</b></code> </dt><dd> by default this is set to <code><b>no</b></code>, hence if you want to have GPU support you need to enable it.
+</dd> <dt> <code><b>--with-cuda</b></code> </dt><dd> with this tag you tell the configure script where it can find CUDA
+</dd> <dt> <code><b>--with-opencl</b></code> </dt><dd> with this tag you tell the configure script where it can find OpenCL
+</dd> <dt> <code><b>--with-dks</b></code> </dt><dd> with this tag you tell the configure script where it can find <code>DKS</code> 
+</dd></dl> 
+<p></p>
+For a typical setup on a RHEL system it could look like this
+<pre class="bash">
+&#36; ./configure --enable-ASlibs --enable-BMWlibs --enable-NeXus --with-dks&#61;&#36;HOME/Apps/DKS/exec --enable-dks --prefix&#61;&#36;ROOTSYS
+</pre>
+whereas for macOS it would typically look like this
+<pre class="bash">
+&#36; ./configure --enable-ASlibs --enable-BMWlibs --enable-NeXus --with-dks&#61;&#36;HOME/Applications/DKS/exec --enable-dks --prefix&#61;&#36;ROOTSYS
+</pre>
+After
+<pre class="bash">
+&#36; make
+&#36; make install
+</pre>
+and updating the shared library lookup table (only needed for Linux)
+<pre class="bash">
+/sbin/ldconfig # as superuser / root
+</pre>
+you are done with the setup.
+<p></p>
+<h3 id="A_1.4.2_Install_via_61_61cmake_61_61"> 1.4.2  Install via <code><b>cmake</b></code> </h3>
+<p></p>
+There is on more configuration switch 
+<p></p> <dl>
+<dt> <code>-Ddks=&lt;value&gt; </dt><dd> it allows to enable/disable =DKS</code> support. The default is &lt;value&gt;=1, i.e. <strong>enabled</strong>. To disable use &lt;value&gt;=0. 
+</dd></dl> 
+<p></p>
+For a typical setup on a RHEL system it could look like this
+<pre class="bash">
+&#36; cmake ../ -DCMAKE&#95;INSTALL&#95;PREFIX&#61;&#36;ROOTSYS -DASlibs&#61;1 -DBMWlibs&#61;1 -Dnexus&#61;1
+</pre>
+whereas for macOS it would typically look like this
+<pre class="bash">
+&#36; cmake ../ -DCMAKE&#95;INSTALL&#95;PREFIX&#61;&#36;ROOTSYS -DASlibs&#61;1 -DBMWlibs&#61;1 -Dnexus&#61;1
+</pre>
+<p></p>
+After
+<pre class="bash">
+&#36; cmake --build ./ --clean-first
+&#36; make install
+</pre>
+and updating the shared library lookup table (only needed for Linux)
+<pre class="bash">
+/sbin/ldconfig # as superuser / root
+</pre>
+you are done with the setup.
+<p></p>
+<h1 id="A_2_Setting_up_61_61musrfit_47DKS_61_61_for_a_AMD_Graphic_Card_40Radeon_R9_390X_41"> 2  Setting up <code><b>musrfit/DKS</b></code> for a AMD Graphic Card (Radeon R9 390X) </h1>
+<p></p>
+<h2 id="A_2.1_Driver_Installation_for_an_AMD_Graphic_Card_44_e.g._Radeon_R9_390X"> 2.1  Driver Installation for an AMD Graphic Card, e.g. Radeon R9 390X </h2>
+<p></p>
+This will depend slightly on the AMD Card and operating system. Here I will summaries how it was done on a RHEL (Linux) system using a Radeon R9 390X.
+<p></p>
+It is assumed that the Radeon R9 390X is already physically installed on your system. For now I only will discuss to set it up for a Linux based system. In order to check that your operating systems see the card, enter the following command in the terminal:
+<p></p>
+<pre class="bash">
+&#36; lspci &#124; grep NVIDIA 
+</pre>
+<p></p>
+On the response you should find something like
+<pre class="bash">
+84:00.0 VGA compatible controller: Advanced Micro Devices, Inc. &#91;AMD/ATI&#93; Hawaii XT / Grenada XT &#91;Radeon R9 290X/390X&#93; (rev 80)
+</pre>
+which means that the OS physically recognises your card. 
+<p></p>
+For RHEL7.x the AMDGPU-PRO driver should be used. It can be downloaded from <a href="http://support.amd.com/en-us/kb-articles/Pages/AMDGPU-PRO-RedHat-Install.aspx">here</a>.
+Unpack the driver
+<pre class="bash">
+&#36; tar -Jxvf amdgpu-pro-17.10-414273.tar.xz
+&#36; cd amdgpu-pro-17.10-414273
+</pre>
+<p></p>
+Install the driver as root
+<pre class="bash">
+&#36; ./amdgpu-pro-install --compute -y
+</pre>
+<p></p>
+Here I assume that the AMD graphic card is only used for computation. You need to add the following command in order that the user 'blabla' (chance this to the appropriate user name) can access the GPU (otherwise only root works):
+<pre class="bash">
+&#36; /sbin/usermod -a -G video blabla
+</pre>
+<p></p>
+Reboot the machine.
+<p></p>
+<h2 id="A_2.2_AMD_APP_Software_Development_Kit_40SDK_41_to_enable_OpenCL_support"> 2.2  AMD APP Software Development Kit (SDK) to enable OpenCL support  </h2>
+<p></p>
+The AMD APP Software Development Kit (SDK) is a complete development platform created by AMD to allow you to quickly and easily develop applications accelerated by AMD APP technology. The SDK provides samples, documentation, and other materials to quickly get you started leveraging accelerated compute using OpenCL or <code>C++ AMP</code> in your <code>C/C++</code> applications.
+<p></p>
+Download the AMD APP SDK 3.0 from <a href="http://developer.amd.com/tools-and-sdks/opencl-zone/amd-accelerated-parallel-processing-app-sdk/">here</a>.
+<p></p>
+Extract the installer
+<pre class="bash">
+&#36; tar -xvjf AMD-APP-SDKInstaller-v3.0.130.136-GA-linux64.tar.bz2
+</pre>
+<p></p>
+Run the installer
+<pre class="bash">
+&#36; ./AMD-APP-SDK-v3.0.130.136-GA-linux64.sh
+</pre>
+<p></p>
+This will install the AMD APP SDK to /opt/AMDAPPSDK-3.0/ where you can find the OpenCL include and library files, as well as documentation and sample code.
+The install guide for AMD OpenCL SDK can be found <a href="http://developer.amd.com/wordpress/media/2012/10/AMD_APP_SDK_InstallationNotes.pdf">here</a>.
+<p></p>
+<h2 id="A_2.3_Installation_of_DKS_and_61musrfit_61"> 2.3  Installation of DKS and <code>musrfit</code> </h2>
+<p></p>
+To install DKS and <code>musrfit</code> follow the instructions <a class="foswikiCurrentTopicLink" href="#DksInstall">here</a>.
+<p></p>
+<h1 id="A_3_Setting_up_61_61musrfit_47DKS_61_61_for_macOS_for_OpenCL_support"> 3  Setting up <code><b>musrfit/DKS</b></code> for macOS for OpenCL support </h1>
+<p></p>
+Since Apple is not providing an out-of-the-box OpenMP support on their macOS compiler framework (Xcode), typically <code>musrfit</code> is just running single threaded. Here DKS can help since it delivers OpenCL support which is present on macOS. Hence, if you would like to run <code>musrfit</code> multi-threaded the easiest way is to use DKS.
+<p></p>
+Since there is no graphic card involved, you do not need any graphic card driver of additional SDK. The only thing you need DKS and the proper <code>musrfit</code> version.
+<p></p>
+The installation instruction for DKS / <code>musrfit</code> can be found <a class="foswikiCurrentTopicLink" href="#DksInstall">here</a>.
+<p></p>
+-- <a href="https://intranet.psi.ch/Main/AndreasSuter">AndreasSuter</a> - June 8, 2018</div>
+<p></p>
+<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>MusrFitSetupDKS <br />
+Topic revision:  <span class='patternRevInfo'>08 Jun 2018, <a href="https://intranet.psi.ch/Main/AndreasSuter">AndreasSuter</a></span></div>
+</div>
+</div>
+</div>
+</div><div id="patternBottomBar"><div id="patternBottomBarContents"><div id="patternWebBottomBar"><span class="foswikiRight"> <a href="http://foswiki.org/"><img src="../pub/System/ProjectLogos/foswiki-badge.png" alt="This site is powered by Foswiki" title="This site is powered by Foswiki" /></a></span>Copyright &copy; by the contributing authors. All material on this collaboration platform is the property of the contributing authors. <br /> Ideas, requests, problems regarding PSI Wiki? <a href='mailto:thomas.buecklers@psi.ch?subject=PSI Wiki %20Feedback%20on%20MUSR.MusrFitSetupDKS'>Send feedback</a></div></div></div>
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+<h1 id="A_61_61musredit_47_40musrgui_41_61_61">  <code><b>musredit / (musrgui)</b></code>  </h1>
 <p></p>
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-      	
-      	
-      	
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-<h1><a name="A_61_61musrgui_47_musredit_61_61"></a>  <code><b>musrgui / musredit</b></code> </h1>
-<p></p>
-<a name="foswikiTOC"></a><div class="foswikiToc"> <ul>
-<li> <a href="MusrGui.html#A_61_61musrgui_47_musredit_61_61"> musrgui / musredit </a>
+<div class="foswikiToc" id="foswikiTOC"> <ul>
+<li> <a href="MusrGui.html#A_61_61musredit_47_40musrgui_41_61_61"> musredit / (musrgui) </a>
 </li> <li> <a href="MusrGui.html#A_1_Introduction"> 1  Introduction </a>
 </li> <li> <a href="MusrGui.html#A_2_Available_Executables_44_Configuration_Files_and_their_Basic_Usage"> 2  Available Executables, Configuration Files and their Basic Usage </a> <ul>
-<li> <a href="MusrGui.html#A_2.1_musrgui_47_musredit"> 2.1  musrgui / musredit </a>
-</li> <li> <a href="MusrGui.html#A_2.2_musrgui_startup.xml_47_musredit_startup.xml"> 2.2  musrgui_startup.xml / musredit_startup.xml </a>
+<li> <a href="MusrGui.html#A_2.1_musredit_47_40musrgui_41"> 2.1  musredit / (musrgui) </a>
+</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><a name="A_1_Introduction"></a> 1  Introduction </h1>
-<code>musrgui</code> and <code>musredit</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/" target="_top">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.
+<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 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><a name="A_2_Available_Executables_44_Configuration_Files_and_their_Basic_Usage"></a> 2  Available Executables, Configuration Files and their Basic Usage </h1>
-<a name="MusrEdit"></a>
-<h2><a name="A_2.1_musrgui_47_musredit"></a> 2.1  musrgui / musredit </h2>
-<code>musrgui</code> / <code>musredit</code> are the editor executables. If called from within a shell they accept a few optional parameters: <dl>
+<h1 id="A_2_Available_Executables_44_Configuration_Files_and_their_Basic_Usage"> 2  Available Executables, Configuration Files and their Basic Usage </h1>
+<span id="MusrEdit"></span>
+<h2 id="A_2.1_musredit_47_40musrgui_41"> 2.1  musredit / (musrgui) </h2>
+<code>musredit</code> / <code>musrgui</code> are the editor executables. If called from within a shell they accept a few optional parameters: <dl>
 <dt> &lt;msr_files&gt; </dt><dd> file names of the msr files that should be opened in separate editor tabs on startup of <code>musrgui</code> / <code>musredit</code>.
 </dd> <dt> --help </dt><dd> displays a small help notice in the shell explaining the basic usage of the program
 </dd> <dt> --version </dt><dd> prints the version number of <code>musrgui</code> / <code>musredit</code>
@@ -147,16 +197,23 @@ On this documentation page only the features related to <code>musrfit</code> are
 <p></p>
 If called without any parameters an empty editor window opens.
 <p></p>
-<a name="MusreditStartupXml"></a>
-<h2><a name="A_2.2_musrgui_startup.xml_47_musredit_startup.xml"></a> 2.2  musrgui_startup.xml / musredit_startup.xml </h2>
-<code><b>musrgui_startup.xml</b></code> / <code><b>musredit_startup.xml</b></code> are configuration files located at the <code>musrgui</code> / <code>musredit</code> binary path. It is also possible to have another version of this file in the working directory which then will be used!
+<span id="MusreditStartupXml"></span>
+<h2 id="A_2.2_musredit_startup.xml_47_musrgui_startup.xml"> 2.2  musredit_startup.xml / musrgui_startup.xml </h2>
+<code><b>musredit_startup.xml</b></code> / <code><b>musrgui_startup.xml</b></code> are configuration files located at the <code>musredit</code> / <code>musrgui</code> binary path. It is also possible to have another version of this file in the working directory which then will be used!
 <p></p>
-In this file the following XML tags are allowed to define settings and might proof useful for all users of <code>musrgui</code> / <code>musredit</code>: <dl>
+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;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 href="#MusrfitFeatures" class="foswikiCurrentTopicLink">default msr files provided by</a> <code>musrgui</code> are stored (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>
@@ -264,143 +321,215 @@ An example of the <code><b>musrgui_startup.xml</b></code> looks like:
 &#60;/musrgui&#95;startup&#62;
 </pre>
 <p></p>
-<a name="MusrfitFeatures"></a>
-<h1><a name="A_3_61_61musrfit_61_61_Features"></a> 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.
-<p></p> <dl>
-<dt> <img alt="musrasym.png" src="../pub/MUSR/MusrGui/musrasym.png" /> Asymmetry Default (Alt+a) </dt><dd> 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>.
-</dd></dl> 
-<p></p> <dl>
-<dt> <img alt="musrsinglehisto.png" src="../pub/MUSR/MusrGui/musrsinglehisto.png" /> Single-Histogram Default (Alt+h) </dt><dd> 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>.
-</dd></dl> 
-<p></p> <dl>
-<dt> <img alt="musrcalcchisq.png" src="../pub/MUSR/MusrGui/musrcalcchisq.png" /> Calculate Chisq (Alt+c) </dt><dd> <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>.
-</dd></dl> 
-<p></p> <dl>
-<dt> <img alt="musrfit.png" src="../pub/MUSR/MusrGui/musrfit.png" /> Fit (Alt+f) </dt><dd> <pre class="bash">musrfit &#60;msr&#95;file&#62; &#91;optional parameters]</pre> is called for the <strong>&lt;msr_file&gt;</strong> selected in the editor. The optional parameters may be chosen under <a href="#MusrPrefs" class="foswikiCurrentTopicLink">Preferences</a>. For further information refer to the <a href="MusrFit.html#MusrFit">manual</a> of <code>musrfit</code>.
-</dd></dl> 
-<p></p> <dl>
-<dt> <img alt="musrswap.png" src="../pub/MUSR/MusrGui/musrswap.png" /> Swap Msr &#8596; Mlog (Alt+s) </dt><dd> 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.
-</dd></dl> 
-<p></p> <dl>
-<dt> <img alt="musrmsr2data.png" src="../pub/MUSR/MusrGui/musrmsr2data.png" /> Msr2data (Alt+m) </dt><dd> Opens a graphical interface to the <code>msr2data</code> program described in detail in its own <a href="Msr2Data.html#MusrGuiInterface">manual</a>.
-</dd></dl> 
-<p></p> <dl>
-<dt> <img alt="musrview.png" src="../pub/MUSR/MusrGui/musrview.png" /> View (Alt+v) </dt><dd> <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>.
-</dd></dl> 
-<p></p> <dl>
-<dt> <img alt="musrt0.png" src="../pub/MUSR/MusrGui/musrt0.png" /> T0 (Alt+t) </dt><dd> <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>.
-</dd></dl> 
+<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>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>
-<a name="MusrPrefs"></a> <dl>
-<dt> <img alt="musrprefs.png" src="../pub/MUSR/MusrGui/musrprefs.png" /> Preferences (Alt+p) </dt><dd> 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.
-</dd></dl> 
-<p></p> <dl>
-<dt> <img alt="musrdump.png" src="../pub/MUSR/MusrGui/musrdump.png" /> Dump Header </dt><dd> 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.
-</dd></dl> 
+   <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>
-<a name="EditorFeatures"></a>
-<h1><a name="A_4_Editor_Features"></a> 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 src="../pub/MUSR/MusrGui/musrgui-editor-v0.png" alt="musrgui editor features" width='415' height='566' align="right" /> <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> 
+   <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>
-<a name="BugTracking"></a>
-<h1><a name="A_5_Bugtracking"></a> 5  Bugtracking </h1>
+   <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>
-For reporting bugs or requesting new features and improvements please use the <a href="https://tracker.intranet.psi.ch/jira/browse/MUSR" target="_top">PSI Tracker</a> or send an e-mail to A. Suter.
+   <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>
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+   <img alt="musrStep-32x32.png" src="../pub/MUSR/MusrGui/musrStep-32x32.png" /> musrStep
+<p></p>
+   <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-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-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-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-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-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="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_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.</div>
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+			<th class="foswikiTableCol5"> <a href="https://intranet.psi.ch/MUSR/MusrGui?cover=print;sortcol=5;table=1;up=0#sorted_table" rel="nofollow" title="Sort by this column">Who</a> </th>
+			<th class="foswikiTableCol6 foswikiLastCol"> <a href="https://intranet.psi.ch/MUSR/MusrGui?cover=print;sortcol=6;table=1;up=0#sorted_table" rel="nofollow" title="Sort by this column">Comment</a> </th>
+		</tr>
+	</thead>
+	<tbody>
+		<tr class="foswikiTableEven foswikiTableRowdataBgSorted0 foswikiTableRowdataBg0">
+			<td class="foswikiTableCol0 foswikiFirstCol foswikiLast"> <span class='foswikiIcon'><img src='../pub/System/DocumentGraphics/png.png' width='16' height='16' alt='musrgui-editor-v0.png' /></span><span class="foswikiHidden">png</span> </td>
+			<td class="foswikiTableCol1 foswikiLast"> <a href="../pub/MUSR/MusrGui/musrgui-editor-v0.png">musrgui-editor-v0.png</a> </td>
+			<td class="foswikiTableCol2 foswikiLast"> <a href="https://intranet.psi.ch/wiki/bin/attach/MUSR/MusrGui?filename=musrgui-editor-v0.png;revInfo=1" title="change, update, previous revisions, move, delete..." rel="nofollow">manage</a> </td>
+			<td class="foswikiTableCol3 foswikiLast" style="text-align:right"> 37 K </td>
+			<td class="foswikiTableCol4 foswikiLast"> <span class="foswikiNoBreak">10 Apr 2009 - 14:53</span> </td>
+			<td class="foswikiTableCol5 foswikiLast"> <a href="https://intranet.psi.ch/Main/UnknownUser">UnknownUser</a> </td>
+			<td class="foswikiTableCol6 foswikiLastCol foswikiLast"> musrgui options available upon right clicking a open msr-file </td>
+		</tr>
+	</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'>14 May 2017, <a href="https://intranet.psi.ch/Main/AndreasSuter">AndreasSuter</a></span></div>
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doc/html/user/MUSR/QuickStart.html

@@ -1,35 +1,38 @@
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+<!DOCTYPE html><html lang="en">
 
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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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-<title>   MUSR :: QuickStart</title>
-<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1" />
+<title> MUSR :: QuickStart</title>
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+<meta name="apple-mobile-web-app-capable" content="yes" />
+<meta name="apple-mobile-web-app-status-bar-style" content="black-translucent" />
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-<link rel="alternate" href="https://intranet.psi.ch/wiki/bin/edit/MUSR/QuickStart?t=1418910326" type="application/x-wiki" title="edit QuickStart" />
+<link rel="alternate" href="https://intranet.psi.ch/wiki/bin/edit/MUSR/QuickStart?t=1528465296" type="application/x-wiki" title="edit QuickStart" />
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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 CLASSIFICATIONPLUGIN::CSS' rel="stylesheet" href="../pub/System/ClassificationPlugin/styles.css" media="all" /><!--CLASSIFICATIONPLUGIN::CSS-->
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+@import url('../pub/System/PatternSkinTheme/layout.css');
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+<link rel='stylesheet' href='../pub/System/PatternSkinTheme2009/column_left.css' media='all' type='text/css' />
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@@ -50,14 +53,8 @@
 	
 
 
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-<!--[if IE]><style type="text/css" media="screen">
-pre {
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+<link rel='stylesheet' href='../pub/System/PatternSkin/print.css' media='all' type='text/css' />
+<!--[if IE 7 ]><style type="text/css" media="screen">
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@@ -79,7 +76,17 @@ pre {
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-</div><div class="patternContent"><div class="foswikiTopic"><h1><a name="Quickstart_for_61_61WKM_61_61_users"></a>  Quickstart for <code><b>WKM</b></code> users </h1>
-<a name="foswikiTOC"></a><div class="foswikiToc"> <ul>
+<div id="patternMain">
+<div id="patternMainContents">
+<div class="patternContent"><div class="foswikiTopic"> <h1 id="Quickstart_for_61_61WKM_61_61_users">  Quickstart for <code><b>WKM</b></code> users </h1>
+<div class="foswikiToc" id="foswikiTOC"> <ul>
 <li> <a href="QuickStart.html#Quickstart_for_61_61WKM_61_61_users"> Quickstart for WKM users </a> <ul>
 <li> <a href="QuickStart.html#Introduction"> Introduction </a>
 </li> <li> <a href="QuickStart.html#Differences_between_61WKM_61_and_61musrfit_61_msr_files"> Differences between WKM and musrfit msr files </a>
@@ -124,16 +128,16 @@ pre {
 </li></ul> 
 </li></ul> 
 </div>
-<h2><a name="Introduction"></a>  Introduction </h2>
+<h2 id="Introduction">  Introduction </h2>
 <p></p>
-<code>musrfit</code> is a program suite for analyzing &mu;SR data. It is implemented in <code>C++/<a href="http://root.cern.ch/" target="_top">ROOT</a></code> and uses the <a href="http://www.cern.ch/minuit/" target="_top">MINUIT2</a> libraries developed at <a href="http://www.cern.ch/" target="_top">CERN</a> for fitting data.
+<code>musrfit</code> is a program suite for analyzing &mu;SR data. It is implemented in <code>C++/<a href="http://root.cern.ch/">ROOT</a></code> and uses the <a href="http://www.cern.ch/minuit/">MINUIT2</a> libraries developed at <a href="http://www.cern.ch/">CERN</a> for fitting data.
 Installation instructions for Linux, MS Windows, and Mac OS X can be found <a href="MusrFitSetup.html">here</a>. The full user manual is available <a href="MusrFit.html">here</a>.<br>
 In principle the programs can be used in the same fashion as <code>WKM</code> (<code>wkmfit, wkmview</code>).
 E.g., for fitting data as defined in the input file <code><b>8472.msr</b></code> one types:<pre>musrfit 8472.msr</pre> for plotting data and the corresponding 
 fit one calls:<pre>musrview 8472.msr</pre>
 Additionally, there are editors called <code><a href="MusrGui.html">musrgui/musredit</a></code> available which can do everything the <code>emacs</code> plug-in for <code>WKM</code> is capable of and even more. <strong><span class='foswikiRedFG'>However, before going to use only <code>musrgui</code> / <code>musredit</code> it is strongly recommended to read at least this "Quickstart" since there are a few differences between the programs as well as new features which are partially described in the following.</span></strong>
 <p></p>
-<h2><a name="Differences_between_61WKM_61_and_61musrfit_61_msr_files"></a>  Differences between <code>WKM</code> and <code>musrfit</code> msr files </h2>
+<h2 id="Differences_between_61WKM_61_and_61musrfit_61_msr_files">  Differences between <code>WKM</code> and <code>musrfit</code> msr files </h2>
 <p></p>
 The msr file format of <code>WKM</code> has some weaknesses and has therefore been extended for the use with <code>musrfit</code>. Existing <code>WKM</code> files can be converted using the <a href="MusrFit.html#Msr2Msr">small utility</a> <code>msr2msr</code>. The changes are: <ul>
 <li> The <code>musrfit</code> msr and mlog files contain an additional column in the FITPARAMETER block for the representation of positive uncertainties if <code>MINOS</code> was called during fitting. In that case the <strong>Step</strong> column holds the negative uncertainties. If there has not been performed an error analysis using <code>MINOS</code>, the symmetric error can be found in the <strong>Step</strong> column, whereas the <strong>Pos_Error</strong> column contains only <strong>none</strong> entries. The beginning of the FITPARAMETER block then might look like this <pre>
@@ -170,7 +174,7 @@ RUN 2008/lem08&#95;his&#95;8472 MUE4 PSI ROOT-NPP   (name beamline institute dat
 </li> <li> The commands <strong>SET BATCH</strong> and <strong>END RETURN</strong> may be omitted in the COMMANDS block.
 </li></ul> 
 <p></p>
-<h2><a name="Selected_new_features_in_61musrfit_61"></a>  Selected new features in <code>musrfit</code> </h2> <ul>
+<h2 id="Selected_new_features_in_61musrfit_61">  Selected new features in <code>musrfit</code> </h2> <ul>
 <li> If single-histogram fits are done, the normalization and background constants are given either "per nanosecond" or "per rebinned bin". The nanosecond normalization allows to change the binning without the need of re-doing the fit to the data.
 </li> <li> The use of functions in the RUN block is now possible for the normalization parameter, e.g. for the definition of an &alpha; parameter in simultaneous single-histogram fits of two histograms.
 </li> <li> Apart from the default &chi;<sup>2</sup> minimization, when doing single-histogram fits (fit type <strong>0</strong>) in <code>musrfit</code> there is also the possibility to do a log-likelihood maximization instead. For switching, just put <strong>MAX_LIKELIHOOD</strong> in the COMMANDS block.
@@ -200,7 +204,7 @@ RUN 2008/lem08&#95;his&#95;8472 MUE4 PSI ROOT-NPP   (name beamline institute dat
 <li> <strong>gamma_mu</strong> = &gamma;<sub>&mu;</sub>/2&pi; = 0.0135538817 MHz/G
 </li> <li> <strong>pi</strong> = &pi; = 3.14159265358979323846
 </li></ul> 
-</li> <li> As theory function also the so called skewed Gaussian can be chosen. The properties of this function are summarized in <a href="http://nemu.web.psi.ch/doc/LEM_Memo/skewedGaussian/skewedGaussian.pdf" target="_top">a memo</a> <span class="foswikiIcon"><img src="../pub/System/DocumentGraphics/pdf.png" width="16" height="16" alt="pdf" /></span>. The function is called in the THEORY block as follows: <pre>
+</li> <li> As theory function also the so called skewed Gaussian can be chosen. The properties of this function are summarized in <a href="http://nemu.web.psi.ch/doc/LEM_Memo/skewedGaussian/skewedGaussian.pdf">a memo</a> <span class='foswikiIcon'><img src='../pub/System/DocumentGraphics/pdf.png' width='16' height='16' alt='pdf' /></span>. The function is called in the THEORY block as follows: <pre>
    skewedGss   1  2  3  4 (phase frequency rate&#95;m rate&#95;p)
 </pre>
 </li> <li> After fitting it is possible to keep the <code>MINUIT2</code> output including the correlation matrix of the parameters. Calling <code>musrfit</code> with the <strong>--keep-mn2-ouput</strong> or <strong>-k</strong> option will provide you an ASCII and a ROOT file with the complete output, e.g. <pre>musrfit 8472.msr --keep-mn2-ouput</pre> generates <code><b>8472-mn2.output</b></code> and <code><b>8472-mn2.root</b></code> (and of course <code><b>8472.mlog</b></code>).
@@ -258,83 +262,28 @@ RUN 2008/lem08&#95;his&#95;8472 MUE4 PSI ROOT-NPP   (name beamline institute dat
 </pre> In the above example <code>musrfit</code> reads the data from the file <code><b>superconductor-data.db</b></code>; the <i>x</i> and <i>y</i> data are specified by the <strong>DB</strong> parameter names <code><b>range</b></code> and <code><b>field</b></code>. An alternative specification of the <i>x</i> and <i>y</i> data by the parameter number in the <strong>DB</strong> file is also possible!
 </li></ul> 
 <p></p>
--- <a href="http://www.fsf.org/register_form?referrer=8369" target="_top">BMW</a> &amp; <a href="http://lmu.web.psi.ch/lem/group.html" target="_top">AS</a> </div>
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+-- <a href="http://www.fsf.org/register_form?referrer=8369">BMW</a> &amp; <a href="http://lmu.web.psi.ch/lem/group.html">AS</a></div>
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 <p></p>
 The &mu;SR-data-analysis process using <code>musrfit</code> is based on so-called <code>msr</code> files. These files contain all information needed for the analysis such as names of the data files, a theory function, fit and plot parameters, and so on. It is the idea of this page to explain the basic use of an <code>msr</code> file and the different programs of the <code>musrfit</code> suite using the example of a single-histogram fit to time-differential transverse-field &mu;SR data. For a complete description of all options please refer to the <a href="MusrFit.html">manual</a>.
 <p></p>
-The example deals with a diamagnetic sample that has been measured in an applied field of approximately 150 G in the <a href="http://lmu.web.psi.ch/facilities/gps/gps.html" target="_top">GPS spectrometer</a> at <a href="http://www.psi.ch/" target="_top">PSI</a> using the "transverse geometry". In this geometry the muon spin is rotated about 50&#176; up and the field is applied parallel to the muon momentum. Hence, the relevant positron counters (to detect the spin precession) are placed above (histogram 3), below (histogram 4) and right of (histogram 5) the sample. The run numbers start from 3110.
+The example deals with a diamagnetic sample that has been measured in an applied field of approximately 150 G in the <a href="http://lmu.web.psi.ch/facilities/gps/gps.html">GPS spectrometer</a> at <a href="http://www.psi.ch/">PSI</a> using the "transverse geometry". In this geometry the muon spin is rotated about 50&#176; up and the field is applied parallel to the muon momentum. Hence, the relevant positron counters (to detect the spin precession) are placed above (histogram 3), below (histogram 4) and right of (histogram 5) the sample. The run numbers start from 3110.
 <p></p>
 To analyze these data (in a simple way) one starts out from the <code>msr</code> file <strong>3110_tutorial.msr</strong> provided together with the source-code distribution in the sub-directory <strong>doc/examples/</strong>. This ASCII file can be edited using any text editor. For convenience the editors <code>musredit</code>/<code>musrgui</code> are provided which offer some <code>msr</code>-file-specific functionalities and additionally serve as front ends to the underlying programs. In the following it is assumed that the file is open within <code>musredit</code>.
 <p></p>
-<h1><a name="A_1_The_61msr_61_file"></a> 1  The <code>msr</code> file </h1>
+<h1 id="A_1_The_61msr_61_file"> 1  The <code>msr</code> file </h1>
 <p></p>
 The <code>msr</code> file itself is divided into different blocks&mdash;a full description of the format can be found <a href="MusrFit.html#DescriptionOfTheMsrFileFormat">here</a>.
 In the file <strong>3110_tutorial.msr</strong> these blocks are successively: <ul>
@@ -230,134 +269,137 @@ STATISTIC --- 2011-07-09 10:58:44
 </pre> This block is the last block of a <code>msr</code> file. It contains some information on the fit: the date and time as well as the absolute and normalized values of &#967;<sup>2</sup> and the number of degrees of freedom in the fit.<br>   These information only have a meaning if the fitting procedure has been executed at least once and the fit has converged!
 </li></ul> 
 <p></p>
-<h1><a name="A_2_Determine_t0_and_the_data_range_using_61musrt0_61"></a> 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 />
-<img src="../pub/MUSR/TutorialSingleHisto/musrt0-1.png" alt="musrt0-1" align="center" /><br />
+<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.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 src="../pub/MUSR/TutorialSingleHisto/musrt0-2.png" alt="musrt0-2" width='708' height='529' align="center" /><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 />
 After all lines have been adjusted for the first histogram, one can go on to the second by pressing <strong>q</strong>. This procedure is repeated until all ranges have been set correctly. When finished with the last histogram the new <i>t</i><sub>0</sub> and data-range values will be written to the <code>msr</code> file.
 A full description of <code>musrt0</code> can be found <a href="MusrFit.html#MusrT0">here</a>.
 <p></p>
-<h1><a name="A_3_Fit_the_model_to_the_data_using_61musrfit_61"></a> 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>
+<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.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>
-<h1><a name="A_4_View_the_data_and_the_fit_using_61musrview_61"></a> 4  View the data and the fit using <code>musrview</code> </h1>
+<h1 id="A_4_View_the_data_and_the_fit_using_61musrview_61"> 4  View the data and the fit using <code>musrview</code> </h1>
 The data and the corresponding fit can be visualized by choosing <img alt="musrview.png" src="../pub/MUSR/MusrGui/musrview.png" /> in <code>musredit</code> or calling from a terminal <pre>musrview 3110&#95;tutorial.msr</pre> This creates the windows according to the given PLOT blocks in the <code>msr</code> file:<br />
-<img src="../pub/MUSR/TutorialSingleHisto/musrview-1.png" alt="musrview-1" align="center" /><br />
-<img src="../pub/MUSR/TutorialSingleHisto/musrview-2.png" alt="musrview-2" align="center" /><br />
+<img class='imagePlain imagePlain_center ' src='../pub/MUSR/TutorialSingleHisto/musrview-1.png' alt='musrview-1' title='musrview-1.png' width='808' height='629'   style='' /><br />
+<img class='imagePlain imagePlain_center ' src='../pub/MUSR/TutorialSingleHisto/musrview-2.png' alt='musrview-2' title='musrview-2.png' width='808' height='629'   style='' /><br />
 The basic features of <code>musrview</code> can be found in the Musrfit menu. They include: <ul>
 <li> export the shown data and the model to an ASCII file with comma-separated values   
 </li> <li> presenting the difference between the shown data and the model (keyboard shortcut: <strong>d</strong>)
-</li> <li> calculate and show the Fourier transform of the shown data (keyboard shortcut: <strong>f</strong>), e.g. for the asymmetry of the "Up" and "Down" detectors:<br />   <img src="../pub/MUSR/TutorialSingleHisto/musrview-3.png" alt="musrview-3" align="center" /><br />
+</li> <li> calculate and show the Fourier transform of the shown data (keyboard shortcut: <strong>f</strong>), e.g. for the asymmetry of the "Up" and "Down" detectors:<br />   <img class='imagePlain imagePlain_center ' src='../pub/MUSR/TutorialSingleHisto/musrview-3.png' alt='musrview-3' title='musrview-3.png' width='808' height='629'   style='' /><br />
 </li></ul> 
 <p></p>
-<h1><a name="A_5_Process_multiple_61msr_61_files_using_61msr2data_61"></a> 5  Process multiple <code>msr</code> files using <code>msr2data</code> </h1>
+<h1 id="A_5_Process_multiple_61msr_61_files_using_61msr2data_61"> 5  Process multiple <code>msr</code> files using <code>msr2data</code> </h1>
 This short introduction is concluded by calling attention to the program <code><a href="Msr2Data.html">msr2data</a></code>. As the name indicates the main purpose of this program is to extract the FITPARAMETER-block information from multiple <code>msr</code> files with the same structure and to summarize them in a single ASCII file (either in TRIUMF DB format or simple columns). However, as described in detail in the <code><a href="Msr2Data.html">manual</a></code>, it is not only possible to collect data from <code>msr</code> files but also to create new <code>msr</code> files from a template and to process these files using <code>musrfit</code> on the fly.<br>
 Assuming the successive runs <strong>3111</strong> through <strong>3114</strong> can be analyzed using the same model introduced above for run <strong>3110</strong> (e.g. in the case one has done measurements at different temperatures) one can use the file <strong>3110_tutorial.msr</strong> as template, generate the files <strong>3111_tutorial.msr</strong> through <strong>3114_tutorial.msr</strong> with the corresponding updates in the RUN blocks, call for each one <code>musrfit</code> and finally summarize the FITPARAMETER-block information of all processed files in an ASCII output file <strong>tutorial-T-dependence.dat</strong> (simple columns). If further information on the temperature or the applied field is available in the data files these will be included as well in the resulting ASCII file.<br>
 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 />
-<img src="../pub/MUSR/TutorialSingleHisto/msr2data.png" alt="msr2data" align="center" />
+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><a name="A_6_Further_reading"></a> 6  Further reading </h1>
+<h1 id="A_6_Further_reading"> 6  Further reading </h1>
 This page only summarizes the very basic features and options of the programs contained in the <code>musrfit</code> suite. For a complete description please refer to the manuals of <ul>
 <li> <code><a href="MusrFit.html">musrfit</a></code> (including <code><a href="MusrFit.html#MusrFit">musrfit</a></code>, <code><a href="MusrFit.html#MusrView">musrview</a></code>, <code><a href="MusrFit.html#MusrT0">musrt0</a></code> and the full description of the <a href="MusrFit.html#DescriptionOfTheMsrFileFormat"><code>msr</code>-file format</a>)
 </li> <li> <code><a href="MusrGui.html">musredit</a></code>
 </li> <li> <code><a href="Msr2Data.html">msr2data</a></code>.
 </li></ul> 
 <p></p>
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+	<tbody>
+		<tr class="foswikiTableEven foswikiTableRowdataBgSorted0 foswikiTableRowdataBg0">
+			<td class="foswikiTableCol0 foswikiFirstCol"> <span class='foswikiIcon'><img src='../pub/System/DocumentGraphics/png.png' width='16' height='16' alt='msr2data.png' /></span><span class="foswikiHidden">png</span> </td>
+			<td class="foswikiTableCol1"> <a href="../pub/MUSR/TutorialSingleHisto/msr2data.png">msr2data.png</a> </td>
+			<td class="foswikiTableCol2"> <a href="https://intranet.psi.ch/wiki/bin/attach/MUSR/TutorialSingleHisto?filename=msr2data.png;revInfo=1" title="change, update, previous revisions, move, delete..." rel="nofollow">manage</a> </td>
+			<td class="foswikiTableCol3" style="text-align:right"> 34 K </td>
+			<td class="foswikiTableCol4"> <span class="foswikiNoBreak">20 Jul 2011 - 13:34</span> </td>
+			<td class="foswikiTableCol5"> <a href="https://intranet.psi.ch/Main/UnknownUser">UnknownUser</a> </td>
+			<td class="foswikiTableCol6 foswikiLastCol"> &nbsp; </td>
+		</tr>
+		<tr class="foswikiTableOdd foswikiTableRowdataBgSorted0 foswikiTableRowdataBg0">
+			<td class="foswikiTableCol0 foswikiFirstCol"> <span class='foswikiIcon'><img src='../pub/System/DocumentGraphics/png.png' width='16' height='16' alt='musrt0-1.png' /></span><span class="foswikiHidden">png</span> </td>
+			<td class="foswikiTableCol1"> <a href="../pub/MUSR/TutorialSingleHisto/musrt0-1.png">musrt0-1.png</a> </td>
+			<td class="foswikiTableCol2"> <a href="https://intranet.psi.ch/wiki/bin/attach/MUSR/TutorialSingleHisto?filename=musrt0-1.png;revInfo=1" title="change, update, previous revisions, move, delete..." rel="nofollow">manage</a> </td>
+			<td class="foswikiTableCol3" style="text-align:right"> 19 K </td>
+			<td class="foswikiTableCol4"> <span class="foswikiNoBreak">20 Jul 2011 - 13:38</span> </td>
+			<td class="foswikiTableCol5"> <a href="https://intranet.psi.ch/Main/UnknownUser">UnknownUser</a> </td>
+			<td class="foswikiTableCol6 foswikiLastCol"> &nbsp; </td>
+		</tr>
+		<tr class="foswikiTableEven foswikiTableRowdataBgSorted0 foswikiTableRowdataBg0">
+			<td class="foswikiTableCol0 foswikiFirstCol"> <span class='foswikiIcon'><img src='../pub/System/DocumentGraphics/png.png' width='16' height='16' alt='musrt0-2.png' /></span><span class="foswikiHidden">png</span> </td>
+			<td class="foswikiTableCol1"> <a href="../pub/MUSR/TutorialSingleHisto/musrt0-2.png">musrt0-2.png</a> </td>
+			<td class="foswikiTableCol2"> <a href="https://intranet.psi.ch/wiki/bin/attach/MUSR/TutorialSingleHisto?filename=musrt0-2.png;revInfo=1" title="change, update, previous revisions, move, delete..." rel="nofollow">manage</a> </td>
+			<td class="foswikiTableCol3" style="text-align:right"> 19 K </td>
+			<td class="foswikiTableCol4"> <span class="foswikiNoBreak">09 Jul 2011 - 15:17</span> </td>
+			<td class="foswikiTableCol5"> <a href="https://intranet.psi.ch/Main/UnknownUser">UnknownUser</a> </td>
+			<td class="foswikiTableCol6 foswikiLastCol"> &nbsp; </td>
+		</tr>
+		<tr class="foswikiTableOdd foswikiTableRowdataBgSorted0 foswikiTableRowdataBg0">
+			<td class="foswikiTableCol0 foswikiFirstCol"> <span class='foswikiIcon'><img src='../pub/System/DocumentGraphics/png.png' width='16' height='16' alt='musrview-1.png' /></span><span class="foswikiHidden">png</span> </td>
+			<td class="foswikiTableCol1"> <a href="../pub/MUSR/TutorialSingleHisto/musrview-1.png">musrview-1.png</a> </td>
+			<td class="foswikiTableCol2"> <a href="https://intranet.psi.ch/wiki/bin/attach/MUSR/TutorialSingleHisto?filename=musrview-1.png;revInfo=1" title="change, update, previous revisions, move, delete..." rel="nofollow">manage</a> </td>
+			<td class="foswikiTableCol3" style="text-align:right"> 45 K </td>
+			<td class="foswikiTableCol4"> <span class="foswikiNoBreak">09 Jul 2011 - 15:48</span> </td>
+			<td class="foswikiTableCol5"> <a href="https://intranet.psi.ch/Main/UnknownUser">UnknownUser</a> </td>
+			<td class="foswikiTableCol6 foswikiLastCol"> &nbsp; </td>
+		</tr>
+		<tr class="foswikiTableEven foswikiTableRowdataBgSorted0 foswikiTableRowdataBg0">
+			<td class="foswikiTableCol0 foswikiFirstCol"> <span class='foswikiIcon'><img src='../pub/System/DocumentGraphics/png.png' width='16' height='16' alt='musrview-2.png' /></span><span class="foswikiHidden">png</span> </td>
+			<td class="foswikiTableCol1"> <a href="../pub/MUSR/TutorialSingleHisto/musrview-2.png">musrview-2.png</a> </td>
+			<td class="foswikiTableCol2"> <a href="https://intranet.psi.ch/wiki/bin/attach/MUSR/TutorialSingleHisto?filename=musrview-2.png;revInfo=1" title="change, update, previous revisions, move, delete..." rel="nofollow">manage</a> </td>
+			<td class="foswikiTableCol3" style="text-align:right"> 36 K </td>
+			<td class="foswikiTableCol4"> <span class="foswikiNoBreak">09 Jul 2011 - 15:48</span> </td>
+			<td class="foswikiTableCol5"> <a href="https://intranet.psi.ch/Main/UnknownUser">UnknownUser</a> </td>
+			<td class="foswikiTableCol6 foswikiLastCol"> &nbsp; </td>
+		</tr>
+		<tr class="foswikiTableOdd foswikiTableRowdataBgSorted0 foswikiTableRowdataBg0">
+			<td class="foswikiTableCol0 foswikiFirstCol foswikiLast"> <span class='foswikiIcon'><img src='../pub/System/DocumentGraphics/png.png' width='16' height='16' alt='musrview-3.png' /></span><span class="foswikiHidden">png</span> </td>
+			<td class="foswikiTableCol1 foswikiLast"> <a href="../pub/MUSR/TutorialSingleHisto/musrview-3.png">musrview-3.png</a> </td>
+			<td class="foswikiTableCol2 foswikiLast"> <a href="https://intranet.psi.ch/wiki/bin/attach/MUSR/TutorialSingleHisto?filename=musrview-3.png;revInfo=1" title="change, update, previous revisions, move, delete..." rel="nofollow">manage</a> </td>
+			<td class="foswikiTableCol3 foswikiLast" style="text-align:right"> 42 K </td>
+			<td class="foswikiTableCol4 foswikiLast"> <span class="foswikiNoBreak">09 Jul 2011 - 16:01</span> </td>
+			<td class="foswikiTableCol5 foswikiLast"> <a href="https://intranet.psi.ch/Main/UnknownUser">UnknownUser</a> </td>
+			<td class="foswikiTableCol6 foswikiLastCol foswikiLast"> &nbsp; </td>
+		</tr>
+	</tbody></table>
+</div></div></div></div>
+<div class="patternInfo">This topic: MUSR<span class='foswikiSeparator'>&nbsp;&gt;&nbsp;</span>TutorialSingleHisto <br />
+Topic revision:  <span class='patternRevInfo'>02 Sep 2011, wojek</span></div>
 </div>
 </div>
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+<!DOCTYPE html><html lang="en">
 
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-<!-- Added by HTTrack --><meta http-equiv="content-type" content="text/html;charset=iso-8859-1"><!-- /Added by HTTrack -->
+<!-- Mirrored from intranet.psi.ch/MUSR/WebHome?cover=print by HTTrack Website Copier/3.x [XR&CO'2014], Fri, 08 Jun 2018 13:42:27 GMT -->
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-<title>   MUSR :: MUSR</title>
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+<title> MUSR :: MUSR</title>
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+<meta name="viewport" content="width=device-width, initial-scale=1, maximum-scale=1.5, user-scalable=yes" />
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+<link rel='stylesheet' href='../pub/System/PatternSkinTheme2009/column_left.css' media='all' type='text/css' />
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-<h2><a name="Documentation_of_the_SR_data_analysis_suite_61musrfit_61"></a>  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 src="../pub/Main/SmiliesPluginPSI/yes.gif" alt="yes" title="yes" border="0" /> </a>
+<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> <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="MusrFitSetupDKS.html">Setting up <code>musrfit</code> / <code>DKS</code>: high speed fitting with GPU's</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></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> <img src="../pub/System/DocumentGraphics/new.png" width="30" height="16" alt="New" border="0" /> 
+</li> <li> <a href="MusrRoot.html"><code>MusrRoot</code>: an extensible open file format for &#956;SR</a>
 </li> <li> Documentation of user libs (user functions) <ul>
 <li> <a href="BmwLibs.html">Meissner-Profiles / Vortex-Lattice related functions (BMW libs)</a>
 </li> <li> Nonlocal superconductivity related Meissner screening functions (AS libs)
@@ -134,83 +139,28 @@ pre {
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 <p></p>
---  <a href="http://lmu.web.psi.ch/lem/group.html" target="_top">AS</a> &amp; (<a href="http://www.fsf.org/register_form?referrer=8369" target="_top">BMW</a>) - last update Dec 18, 2014 </div>
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+--  <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 June 8, 2018</div>
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+<div class="patternInfo">This topic: MUSR<span class='foswikiSeparator'>&nbsp;&gt;&nbsp;</span>WebHome <br />
+Topic revision:  <span class='patternRevInfo'>08 Jun 2018, <a href="https://intranet.psi.ch/Main/AndreasSuter">AndreasSuter</a></span></div>
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doc/html/user/pub/MUSR/MusrFit/Makefile.html

@@ -0,0 +1,60 @@
+#---------------------------------------------------
+# get compilation flags from root-config
+
+ROOTCFLAGS    = $(shell $(ROOTSYS)/bin/root-config --cflags)
+
+#---------------------------------------------------
+
+OS            = LINUX
+CXX           = g++
+CXXFLAGS      = -O3 -Wall -Wno-trigraphs -fPIC
+LOCALINCLUDE  = .
+ROOTINCLUDE   = $(ROOTSYS)/include
+INCLUDES      = -I$(LOCALINCLUDE) -I$(ROOTINCLUDE)
+LD            = g++
+LDFLAGS       =
+SOFLAGS       = -O -shared
+
+# the output from the root-config script:
+CXXFLAGS      += $(ROOTCFLAGS)
+LDFLAGS       +=
+
+# some definitions: headers (used to generate *Dict* stuff), sources, objects,...
+OBJS =
+OBJS += TMyFunction.o TMyLibraryDict.o
+
+SHLIB = libTMyLibrary.so
+
+# make the shared lib:
+#
+all:  $(SHLIB)
+
+$(SHLIB): $(OBJS)
+	@echo "---> Building shared library $(SHLIB) ..."
+	/bin/rm -f $(SHLIB)
+	$(LD) $(OBJS) $(SOFLAGS) -o $(SHLIB)
+	@echo "done"
+
+# clean up: remove all object file (and core files)
+# semicolon needed to tell make there is no source
+# for this target!
+#
+clean:; 	@rm -f $(OBJS) *Dict* core*
+	@echo "---> removing $(OBJS)"
+
+#
+$(OBJS): %.o: %.cpp
+	$(CXX) $(INCLUDES) $(CXXFLAGS) -c $<
+
+# Generate the ROOT CINT dictionary
+
+TMyLibraryDict.cpp: TMyFunction.h TMyLibraryLinkDef.h
+	@echo "Generating dictionary $@..."
+	rootcint -f $@ -c -p -I$(ROOTINCLUDE) $^
+
+install: all
+	@echo "Installing shared lib: libTApproximation.so"
+ifeq ($(OS),LINUX)
+	cp -pv $(SHLIB) $(ROOTSYS)/lib
+	cp -pv $(LOCALINCLUDE)/*.h $(ROOTSYS)/include
+endif

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>.