mupp: fix crash in PmuppGui::getValues plotting a variable.

getValues()/getErrors() return a std::vector by value, but the QVector was
built from begin() of one call and end() of a second call -> iterators into
two distinct temporaries -> UB and a segfault in getValues(). Bind the result
to a single local before taking begin()/end(). Same in getPosErr/getNegErr.

This surfaced reliably when plotting a <python>-generated variable added via
the GUI (the script path was unaffected as it reads getValues() only once).

Also fix check() to validate the actually selected collections
(GetCollection(idx[i]) instead of GetCollection(i)).

Co-Authored-By: Claude Opus 4.7 <noreply@anthropic.com>

.gitea/workflows/deploy-pages.yml

@@ -0,0 +1,45 @@
+name: Build and Deploy Documentation
+
+on:
+  push:
+    branches:
+      - root6
+  workflow_dispatch:
+
+jobs:
+  build-and-deploy:
+    runs-on: ubuntu-latest
+    container:
+      image: gitea.psi.ch/images/alpine-jupyterbook
+    steps:
+
+      - name: Checkout repository
+        uses: actions/checkout@v4
+
+      - name: Install system dependencies
+        run: |
+          apk add doxygen graphviz
+
+      - name: Build musrfit-tech-docu
+        run: |
+          cd doc
+          mkdir technical 
+          doxygen musrfit_dox.cfg
+          doxygen musredit_qt6_dox.cfg
+          doxygen mupp_qt6_dox.cfg
+          doxygen musrStep_qt6_dox.cfg
+          doxygen musrWiz_qt6_dox.cfg
+
+      - name: Configure Git
+        run: |
+          git config --global user.name "Gitea Actions"
+          git config --global user.email "actions@gitea.local"
+
+      - name: Push to gitea-pages branch
+        run: |
+          git checkout --orphan gitea-pages
+          git reset --hard
+          cp -r ./doc/technical/html/* .
+          git add .
+          git commit -m "Deploy site"
+          git push --verbose -f https://${{secrets.GITHUB_TOKEN}}@gitea.psi.ch/${{ github.repository }}.git gitea-pages

.gitignore

@@ -0,0 +1,2 @@
+# ignore all files generated from an in-repo build
+build/

AUTHORS

@@ -1,7 +1,5 @@
 #---------------------------------------------------------------------
 # AUTHORS
-# Andreas Suter, 2009/06/21
-# $Id: AUTHORS 4013 2009-06-21
 #---------------------------------------------------------------------
 
 Andreas Suter <andreas.suter@psi.ch>
@@ -9,8 +7,9 @@ Andreas Suter <andreas.suter@psi.ch>
 
 Bastian M. Wojek
   msr2data; initial testing; full initial documentation; BMWlibs;
-  unified building process on Linux, MacOSX and Windows (Cygwin)
-  through autotools
+
+Zaher Salman <zaher.salman@psi.ch>
+  beta-NMR and web-interface
 
 #---------------------------------------------------------------------
 # this is the end ...

CMakeLists.txt

@@ -1,38 +1,55 @@
-# - musrfit 
-cmake_minimum_required(VERSION 3.6)
+# - musrfit
+cmake_minimum_required(VERSION 3.17)
 
-project(musrfit VERSION 1.3.0 LANGUAGES C CXX)
+# cmake: use BoostConfig.cmake instead of FindBoost
+if (CMAKE_VERSION GREATER_EQUAL "3.3")
+  cmake_policy(SET CMP0167 NEW)
+endif ()  
+
+project(musrfit VERSION 1.10.0 LANGUAGES C CXX)
+
+set(CMAKE_CXX_STANDARD 17)
+set(CMAKE_CXX_STANDARD_REQUIRED ON)
+set(CMAKE_CXX_EXTENSIONS OFF)
+
+set(CMAKE_INSTALL_LIBDIR lib CACHE PATH "Object code libraries")
+include(GNUInstallDirs)
 
 #--- 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(DummyUserFcn "build optional dummy user function" 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'
+# define qt_version with possible values 'auto' or version '3', '4', '5', '6'
 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_property(CACHE qt_version PROPERTY STRINGS AUTO 3 4 5 6)
 
 #--- set a default build type if none was specified ---------------------------
 set(default_build_type "Release")
- 
-if(NOT CMAKE_BUILD_TYPE AND NOT CMAKE_CONFIGURATION_TYPES)
+
+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()
+endif ()
 
 #--- perform some checks and generate the config.h ----------------------------
+
+#--- the next two lines are needed that the math functions are found ----------
+set(CMAKE_REQUIRED_INCLUDES math.h)
+set(CMAKE_REQUIRED_LIBRARIES m)
+
 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)
@@ -59,95 +76,115 @@ endif (${LONG_DOUBLE} GREATER ${DOUBLE})
 #--- add path to my own find modules and other stuff
 set(CMAKE_MODULE_PATH ${CMAKE_CURRENT_SOURCE_DIR}/cmake)
 
+#--- check for pkg-config -----------------------------------------------------
+find_package(PkgConfig REQUIRED)
+
 #--- check for git ------------------------------------------------------------
 find_package(Git REQUIRED)
 
 #--- check for ROOT -----------------------------------------------------------
-find_package(ROOT 6.06 REQUIRED COMPONENTS Gui MathMore Minuit2 XMLParser)
+find_package(ROOT 6.18 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)
 
+#--- the next check is need to set a flag, since root 6.24 (minuit2) breaks
+#--- the backwards compatibility. ---------------------------------------------
+if (ROOT_VERSION VERSION_LESS "6.23")
+  set(ROOT_GRTEQ_24 0)
+else ()
+  set(ROOT_GRTEQ_24 1)
+endif ()
+set(ROOT_GRTEQ_24 ${ROOT_GRTEQ_24} CACHE INTERNAL "ROOT Version check")
+
 #--- check for boost ----------------------------------------------------------
-find_package(Boost REQUIRED)
+find_package(Boost QUIET)
+if (Boost_VERSION VERSION_GREATER_EQUAL "1.89")
+  find_package(Boost REQUIRED COMPONENTS filesystem)
+  set(BOOST_LINK_LIBS Boost::filesystem)
+else (Boost_VERSION VERSION_GREATER_EQUAL "1.89")
+  find_package(Boost REQUIRED COMPONENTS system filesystem)
+  set(BOOST_LINK_LIBS Boost::filesystem Boost::system)
+endif (Boost_VERSION VERSION_GREATER_EQUAL "1.89")
+message(STATUS "Boost libs: ${Boost_LIBRARIES}")
 
 #--- 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)
+if (try_OpenMP)
   find_package(OpenMP)
-  if (OpenMP_FOUND)
-    add_definitions(-DHAVE_GOMP)
+  if (OpenMP_CXX_FOUND)
+    add_compile_definitions(HAVE_GOMP)
     set(HAVE_GOMP 1 CACHE INTERNAL "Have GOMP")
-  endif (OpenMP_FOUND)
-endif (try_OpenMP AND NOT APPLE)
+  endif (OpenMP_CXX_FOUND)
+endif (try_OpenMP)
 
 #--- 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)
+    # try Qt6
+    find_package(Qt6Core QUIET)
+    if (Qt6Core_FOUND)
+      find_package(Qt6Widgets CONFIG REQUIRED)
+      find_package(Qt6Xml CONFIG REQUIRED)
+      find_package(Qt6Network CONFIG REQUIRED)
+      find_package(Qt6Svg CONFIG REQUIRED)
+      find_package(Qt6PrintSupport CONFIG REQUIRED)
+    endif (Qt6Core_FOUND)
+    # try Qt5
+    if (NOT Qt6Core_FOUND)
+      find_package(Qt5Core QUIET)
+      if (Qt5Core_FOUND)
+        find_package(Qt5Widgets CONFIG REQUIRED)
+        find_package(Qt5Xml CONFIG REQUIRED)
+        find_package(Qt5Network CONFIG REQUIRED)
+        find_package(Qt5Svg CONFIG REQUIRED)
+        find_package(Qt5PrintSupport CONFIG REQUIRED)
+      endif (Qt5Core_FOUND)
+    endif (NOT Qt6Core_FOUND)
 
-    # if Qt5 is not found, try Qt4
-    if (NOT Qt5Core_FOUND)
+    # if Qt6 and Qt5 is not found, try Qt4
+    if (NOT Qt6Core_FOUND AND NOT Qt5Core_FOUND)
       find_package(Qt4 COMPONENTS QtGui QtWebKit QtXml)
-    endif (NOT Qt5Core_FOUND)
+    endif (NOT Qt6Core_FOUND AND 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)
+    # if Qt6, Qt5 and Qt4 is not found try Qt3. Hopefully you never reach this point
+    if (NOT Qt6Core_FOUND AND NOT Qt5Core_FOUND AND Qt4_FOUND)
+      find_package(Qt3)
+    endif (NOT Qt6Core_FOUND AND NOT Qt5Core_FOUND AND Qt4_FOUND)
   endif (qt_version STREQUAL AUTO)
 
-  # check specifically for Qt5
+  # check specifically for Qt6
+  if (qt_version STREQUAL 6)
+    find_package(Qt6Core)
+    if (Qt6Core_FOUND)
+      find_package(Qt6Widgets CONFIG REQUIRED)
+      find_package(Qt6Xml CONFIG REQUIRED)
+      find_package(Qt6Network CONFIG REQUIRED)
+      find_package(Qt6Svg CONFIG REQUIRED)
+      find_package(Qt6PrintSupport CONFIG REQUIRED)
+    else (Qt6Core_FOUND)
+      message(FATAL_ERROR "Couldn't find the specifically requested Qt6 version.")
+    endif (Qt6Core_FOUND)
+  endif (qt_version STREQUAL 6)
+
+ # 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.")
@@ -171,13 +208,38 @@ if (qt_based_tools)
   endif (qt_version STREQUAL 3)
 endif (qt_based_tools)
 
-#--- if NeXus check also for HDF4, HDF5, and MXML -----------------------------
+#--- if NeXus check also for HDF4 (optional), HDF5 ----------------------------
 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)
+  find_package(HDF5 COMPONENTS CXX REQUIRED)
+  if (HAVE_HDF4)
+    #--- check for HDF4 -----------------------------------------------------------
+    # Find HDF4 manually (pkg-config often doesn't have hdf4)
+    find_path(HDF4_INCLUDE_DIR
+      NAMES mfhdf.h
+      PATH_SUFFIXES hdf
+    )
+
+    find_library(HDF4_DF_LIBRARY
+      NAMES df libdf
+    )
+
+    find_library(HDF4_MFHDF_LIBRARY
+      NAMES mfhdf libmfhdf
+    )
+
+    if (HDF4_INCLUDE_DIR AND HDF4_DF_LIBRARY AND HDF4_MFHDF_LIBRARY)
+      set(HDF4_FOUND TRUE)
+      set(HDF4_INCLUDE_DIRS ${HDF4_INCLUDE_DIR})
+      set(HDF4_LIBRARIES ${HDF4_MFHDF_LIBRARY} ${HDF4_DF_LIBRARY})
+      message(STATUS "Found HDF4: ${HDF4_INCLUDE_DIR}")
+      message(STATUS "  HDF4 libraries: ${HDF4_LIBRARIES}")
+    else()
+      message(FATAL_ERROR "HDF4 library not found. Please install libhdf4-dev or hdf-devel")
+    endif()
+
+    add_compile_definitions(HAVE_HDF4)
+  endif (HAVE_HDF4)
+  add_compile_definitions(PNEXUS_ENABLED)
 endif (nexus)
 
 #--- check for Cuba lib if BMWlibs are enabled --------------------------------
@@ -187,10 +249,65 @@ endif (nexus)
 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)
 
+#--- check if project source is a git repo ------------------------------------
+if (EXISTS "${CMAKE_SOURCE_DIR}/.git/HEAD")
+  message(STATUS "is a git repo")
+  set(IS_GIT_REPO 1)
+else ()
+  message(STATUS "is NOT a git repo")
+  set(IS_GIT_REPO 0)
+endif ()
+
+#--- start create git-revision.h ----------------------------------------------
+if (IS_GIT_REPO)
+  add_custom_target(git_revision ALL
+    COMMAND sh ${CMAKE_SOURCE_DIR}/src/git_revision.sh ${CMAKE_BINARY_DIR}/src
+    WORKING_DIRECTORY ${CMAKE_SOURCE_DIR}
+    COMMENT "Checking git revision"
+  )
+
+  set(HAVE_GIT_REV_H "-DHAVE_GIT_REV_H")
+else (IS_GIT_REPO)
+  set(HAVE_GIT_REV_H "")
+endif (IS_GIT_REPO)
+
+#--- end create git-revision.h ------------------------------------------------
+
+#--- rpath related things -----------------------------------------------------
+# use, i.e. don't skip the full RPATH for the build tree
+set(CMAKE_SKIP_BUILD_RPATH FALSE)
+
+# when building, don't use the install RPATH already
+# (but later on when installing)
+set(CMAKE_BUILD_WITH_INSTALL_RPATH FALSE)
+
+set(CMAKE_INSTALL_RPATH "${CMAKE_INSTALL_FULL_LIBDIR}")
+
+# add the automatically determined parts of the RPATH
+# which point to directories outside the build tree to the install RPATH
+set(CMAKE_INSTALL_RPATH_USE_LINK_PATH TRUE)
+
+# the RPATH to be used when installing, but only if it's not a system directory
+list(FIND CMAKE_PLATFORM_IMPLICIT_LINK_DIRECTORIES "${CMAKE_INSTALL_FULL_LIBDIR}" isSystemDir)
+if("${isSystemDir}" STREQUAL "-1")
+    set(CMAKE_INSTALL_RPATH "${CMAKE_INSTALL_FULL_LIBDIR}")
+endif("${isSystemDir}" STREQUAL "-1")
+if (UNIX)
+  set(rpath ${CMAKE_INSTALL_RPATH})
+  string(APPEND rpath ";/usr/local/lib")
+  set(CMAKE_INSTALL_RPATH "${rpath}")
+endif ()
+
 #--- propagate to the sub-directories -----------------------------------------
 add_subdirectory(src)
 
-#--- write summary of the installation 
+#--- testing ------------------------------------------------------------------
+enable_testing()
+add_subdirectory(tests)
+
+#--- write summary of the installation
+cmake_host_system_information(RESULT PROCESSOR QUERY PROCESSOR_DESCRIPTION)
+
 message("")
 message("|-----------------------------------------------------------------------|")
 message("|                                                                       |")
@@ -198,8 +315,12 @@ message("|                            Summary
 message("|                                                                       |")
 message("|-----------------------------------------------------------------------|")
 message("")
-message(" System: ${CMAKE_HOST_SYSTEM_NAME} ${CMAKE_SYSTEM_PROCESSOR} - ${CMAKE_HOST_SYSTEM_VERSION}")
-message(" -------")
+message(" System:    ${CMAKE_HOST_SYSTEM_NAME} ${CMAKE_SYSTEM_PROCESSOR} - ${CMAKE_HOST_SYSTEM_VERSION}")
+message(" Processor: ${PROCESSOR} (${CMAKE_SYSTEM_PROCESSOR})")
+message(" ----------")
+message("")
+message(" musrfit Version: ${musrfit_VERSION}")
+message(" ----------------")
 message("")
 message(" Build Type: ${CMAKE_BUILD_TYPE}")
 message(" -----------")
@@ -207,14 +328,14 @@ 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}")
+message(" FFTW3   found in ${FFTW3_INCLUDE}, Version: ${FFTW_VERSION}")
+message(" GSL     found in ${GSL_INCLUDE_DIRS}, Version: ${GSL_VERSION}")
+message(" BOOST   found in ${Boost_INCLUDE_DIRS}, Version: ${Boost_VERSION}")
+message(" LibXML2 found in ${LIBXML2_INCLUDE_DIR}, Version: ${LIBXML2_VERSION_STRING}")
+message(" ROOT    found in ${ROOT_INCLUDE_DIRS}, Version: ${ROOT_VERSION}")
 if (OpenMP_FOUND)
   if (OpenMP_CXX_VERSION)
-    message(" OpenMP  found (version ${OpenMP_CXX_VERSION})")
+    message(" OpenMP  found Version: ${OpenMP_CXX_VERSION}")
   else (OpenMP_CXX_VERSION)
     message(" OpenMP  found")
   endif (OpenMP_CXX_VERSION)
@@ -222,24 +343,31 @@ 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}") 
+  if (HAVE_HDF4)
+    message(" HDF4    found in ${HDF4_INCLUDE_DIRS}")
+  else (HAVE_HDF4)
+    message(" HDF4    not present.")	  
+  endif (HAVE_HDF4)	  
+  message(" HDF5    found in ${HDF5_INCLUDE_DIRS}, Version: ${HDF5_VERSION}")
 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)
+  if (Qt6Core_FOUND)
+    message(" Qt      found in  ${Qt6Core_INCLUDE_DIRS}, Version: ${Qt6Core_VERSION}")
+  else (Qt6Core_FOUND)
+    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 (Qt6Core_FOUND)
 endif (qt_based_tools)
 message("")
 message(" Features:")
@@ -275,27 +403,32 @@ if (BNMRlibs)
 else (BNMRlibs)
   message("   BNMRlibs                           : no")
 endif (BNMRlibs)
+if (DummyUserFcn)
+  message("   PDummyUserFcn                      : yes")
+endif (DummyUserFcn)
 
 if (qt_based_tools)
-if (Qt5Core_FOUND)
+if (Qt6Core_FOUND)
+  message("")
+  message(" Qt6 based tools:")
+  message("   musredit, musrStep, musrWiz, mupp  : yes")
+elseif (Qt5Core_FOUND)
   message("")
   message(" Qt5 based tools:")
   message("   musredit, musrStep, musrWiz, mupp  : yes")
-endif (Qt5Core_FOUND)
-if (Qt4_FOUND)
+elseif (Qt4_FOUND)
   message("")
   message(" Qt4 based tools (deprecated):")
   message("   musredit                           : yes")
-endif (Qt4_FOUND)
-if (QT_FOUND)
+else ()
   message("")
   message(" Qt3 based tools (outdated):")
   message("   musrgui                            : yes")
-endif (QT_FOUND)
-if (NOT Qt5Core_FOUND AND NOT Qt4_FOUND AND NOT QT_FOUND)
+endif ()
+if (NOT Qt6Core_FOUND AND 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)
+endif (NOT Qt6Core_FOUND AND 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")
@@ -311,4 +444,49 @@ message("")
 message("-------------------------------------------------------------------------")
 message("")
 
+#--- generate and install cmake package config files --------------------------
+include(CMakePackageConfigHelpers)
+
+configure_package_config_file(
+  ${CMAKE_SOURCE_DIR}/cmake/musrfitConfig.cmake.in
+  ${CMAKE_CURRENT_BINARY_DIR}/musrfitConfig.cmake
+  INSTALL_DESTINATION ${CMAKE_INSTALL_LIBDIR}/cmake/musrfit
+)
+
+write_basic_package_version_file(
+  ${CMAKE_CURRENT_BINARY_DIR}/musrfitConfigVersion.cmake
+  VERSION ${PROJECT_VERSION}
+  COMPATIBILITY AnyNewerVersion
+)
+
+install(
+  EXPORT musrfitTargets
+  FILE musrfitTargets.cmake
+  NAMESPACE musrfit::
+  DESTINATION ${CMAKE_INSTALL_LIBDIR}/cmake/musrfit
+)
+
+install(
+  FILES
+    ${CMAKE_CURRENT_BINARY_DIR}/musrfitConfig.cmake
+    ${CMAKE_CURRENT_BINARY_DIR}/musrfitConfigVersion.cmake
+  DESTINATION ${CMAKE_INSTALL_LIBDIR}/cmake/musrfit
+)
+
+#--- cpack specific info ......................................................
+file(TO_NATIVE_PATH ${PROJECT_SOURCE_DIR} PROJECT_SOURCE_DIR_NATIVE)
+file(TO_NATIVE_PATH ${PROJECT_BINARY_DIR} PROJECT_BINARY_DIR_NATIVE)
+string(REPLACE "\\" "\\\\" PROJECT_SOURCE_DIR_NATIVE_D ${PROJECT_SOURCE_DIR_NATIVE})
+string(REPLACE "\\" "\\\\" PROJECT_BINARY_DIR_NATIVE_D ${PROJECT_BINARY_DIR_NATIVE})
+
+configure_file(${CMAKE_SOURCE_DIR}/cmake/CPackOptions.cmake.in ${CMAKE_CURRENT_BINARY_DIR}/CPackOptions.cmake @ONLY)
+set (CPACK_PROJECT_CONFIG_FILE "${PROJECT_BINARY_DIR}/CPackOptions.cmake")
+#set (CPACK_GENERATOR TGZ) # not use ZIP on UNIX as problem with symlinks
+#set (CPACK_SOURCE_GENERATOR TGZ) # not use ZIP on UNIX as problem with symlinks
+if (UNIX)
+  set (CPACK_GENERATOR ${CPACK_GENERATOR};RPM)
+endif ()
+# Include of CPack must always be last
+include(CPack)
+
 #--- end ----------------------------------------------------------------------

ChangeLog

@@ -6,11 +6,188 @@ 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
+https://gitea.psi.ch/LMU/musrfit
 
 or 
 
-https://bitbucket.org/muonspin/musrfit/commits/all
+https://bitbucket.org/muonspin/musrfit
+
+Release of V1.10.0, 2026/02/21
+==============================
+
+ditch the use of the NeXus lib. NeXus files are now directly read via hdf4/5
+add deadtime correction of pulsed sources, assuming the relevant parameters are
+present in the file.
+
+Release of V1.9.10, 2026/01/16
+==============================
+
+function handling lifted from boost/spirit classic/qi to x3
+
+Release of V1.9.9, 2025/06/08
+=============================
+
+add THEORY functions for local Gaussian / global Lorentzian, and a simple F-mu-F function.
+
+Release of V1.9.8, 2025/03/24
+=============================
+
+add a user interface option to export data from a msr-file view (single- or multiple files).
+
+Release of V1.9.7, 2025/01/18
+=============================
+
+allow spaces in RUN block path-filename
+
+Release of V1.9.6, 2024/12/02
+=============================
+
+added jump to block feature in musredit.
+
+
+Release of V1.9.5, 2024/06/24
+=============================
+
+yaml export of ALL fit-parameters, as initiated by R.M.L. McFadden.
+
+Release of V1.9.4, 2024/06/08
+=============================
+
+enable OpenMP for macOS.
+
+Release of V1.9.3, 2024/04/19
+=============================
+
+fix of function string generation from AST.
+
+Release of V1.9.2, 2023/10/25
+=============================
+
+switch over to smart pointers wherever possible.
+
+Release of V1.9.1, 2023/05/16
+=============================
+
+add option [-c, --count] to dump_header which will dump the number of counts
+per detector and the total number of counts. Currently for MusrRoot data format
+only. For the other data formats it will be implement asap
+
+Release of V1.9.0, 2023/02/17
+=============================
+
+add depth profile user lib:
+A.F.A. Simões, et al.
+Muon implantation experiments in films: obtaining depth-resolved information
+Review of Scientific Instruments. 2020; 91(2): 023906 (7 pp.).
+
+
+Release of V1.8.2, 2022/12/03
+=============================
+
+add feature that mupp_plotter can show/hide lines between the data points.
+
+Release of V1.8.1, 2022/11/07
+=============================
+
+adopted to the newer Qt versions.
+
+Release of V1.8.0, 2022/05/22
+=============================
+
+new: addRun - allows to add runs and write it to file
+refactoring of Class_MuSR_PSI: (i) class variables and methods renamed according to ROOT
+rules. (ii) start to modernize to newer c++ standards.
+
+Release of V1.7.6, 2021/10/02
+=============================
+
+new: choose number of threads from the commandline for OpenMP. 
+
+Release of V1.7.5, 2021/09/22
+=============================
+
+make sure that phases stay within +-360 degrees. 
+
+Release of V1.7.4, 2021/06/16
+=============================
+
+allow in asymmetry fits #forward groups != #backward groups
+
+Release of V1.7.3, 2021/06/01
+=============================
+
+making musrfit Apple Silicon M1 ready. Currently there is still an open issue 
+with NeXus (HDF4 only).
+
+Release of V1.7.2, 2021/04/16
+=============================
+
+add a full dummy user function class with a global part. This can be used as 
+a starting point to develop new polarization functions. 
+Currently no rge-handling present.
+
+Release of V1.7.1, 2021/04/09
+=============================
+
+update of the docu. More version info. Dealing with the upcoming ROOT V6.24.
+
+Release of V1.7.0, 2021/04/30
+=============================
+
+Centralize the rge-handling for user functions.
+
+Release of V1.6.5, 2021/01/22
+=============================
+
+Add Qt6 version of musredit, mupp, etc.
+
+Release of V1.6.4, 2020/08/29
+=============================
+
+Allow to view time spectra and Fourier theory only calculated at the data points 
+via the option '-1' or '--one_to_one'.
+
+Release of V1.6.3, 2020/07/27
+=============================
+
+A single asymmetry plot allows to toggle the color of the theory function line 
+by the key 't'.
+
+Release of V1.6.2, 2020/06/17
+=============================
+
+Functions not only can use parameters and maps but now also meta data from the 
+data files like, field (B or b), energy (En or en), or temperature (T<x> pr t<x>
+where <x> is a number starting from 0, e.g. t0).
+
+Release of V1.6.1, 2020/05/25
+=============================
+
+For asymmetry fits: allow alpha, beta in the RUN block to be functions.
+
+Release of V1.6.0, 2020/05/16
+=============================
+
+Allow to transform parameter vectors of run collections for mupp. 
+This allows for instance to calculate the superfluid density directly from the
+depolarization rate and plot it.
+
+Release of V1.5.2, 2020/02/03
+=============================
+
+Implemented a SECTOR command. It allows to get chisq/maxLH information from 
+different time sector slots.
+
+Release of V1.5.0, 2019/05/15
+=============================
+
+Added beta-NMR support (thanks to Zaher Salman).
+
+Release of V1.4.2, 2019/03/08
+=============================
+
+The tool chain support for automake is removed. Only the cmake tool chain is
+supported from now one. 
 
 Release of V1.2.0, 2017/10/26
 =============================

INSTALL

@@ -2,43 +2,9 @@
 # INSTALL
 #---------------------------------------------------------------------
 
-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=$ROOTSYS             (or where ever musrfit should be installed)
-   make
-   make install                              (as superuser -- maybe)
-   /sbin/ldconfig                            (as superuser)   
-
-configure comes with a couple of options. For details either execute
-
-  ./configure --help
-
-or check under http://lmu.web.psi.ch/musrfit/user/MUSR/MusrFitSetup.html
-for a more detailed description.
-
-An example with NeXus support and BMWlibs needed would look like this
-
-   sh autogen.sh
-   ./configure --enable-NeXus --enable-BMWlibs --prefix=$ROOTSYS 
-   make 
-   make install                              (as superuser -- maybe)
-   /sbin/ldconfig                            (as superuser)
-   
-In the optimal case, everything is set up ;-)
-
 #----------------------------------
 # Install via cmake tool chain
 #----------------------------------
@@ -52,11 +18,10 @@ directory and
    cd build 
    cmake ../ -DCMAKE_INSTALL_PREFIX=$ROOTSYS (or where ever musrfit should be installed)
    cmake --build ./ --clean-first
-   make install                              (as superuser -- maybe)
+   cmake --install ./                           (as superuser -- maybe)
    /sbin/ldconfig                            (as superuser)
     
-cmake configuration allows a couple of switches.  For details check the user
-docu under 
+cmake configuration allows a couple of switches.  For details check the documentation at 
 
    http://lmu.web.psi.ch/musrfit/user/MUSR/MusrFitSetup.html
 
@@ -66,18 +31,19 @@ An example with NeXus support and BMWlibs needed would look like this
    cd build
    cmake ../ -Dnexus=1 -DBMWlibs=1 -DCMAKE_INSTALL_PREFIX=$ROOTSYS 
    cmake --build ./ --clean-first
-   make install                              (as superuser -- maybe)
+   cmake --install ./                        (as superuser -- maybe)
    /sbin/ldconfig                            (as superuser)
 
-In the optimal case, everything is set up ;-)
+In the optimal case everything is ready to be used ;-)
 
 #----------------------------------
-# Link to the docu
+# Link to the documentation
 #----------------------------------
 
-More information about the software requirements and the installation can be found at:
+More information regarding software requirements and the installation process 
+can be found here:
 
-http://lmu.web.psi.ch/musrfit/user/MUSR/MusrFitSetup.html
+   https://lmu.pages.psi.ch/musrfit-docu/setup-standard.html
 
 #---------------------------------------------------------------------
 # this is the end ...

Makefile.am

@@ -1,44 +0,0 @@
-## Process this file with automake to create Makefile.in
-
-SUBDIRS = src
-
-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 = examples \
-          examples/data \
-          examples/ASlibs \
-          examples/ASlibs/data \
-          examples/ASlibs/profiles \
-          examples/BMWlibs \
-          examples/BMWlibs/data \
-          examples/BMWlibs/profiles \
-          html/user \
-          html/user/MUSR \
-          html/user/pub/Main/SmiliesPluginPSI \
-          html/user/pub/Main/WebPreferences \
-          html/user/pub/MUSR/LibFitPofB \
-          html/user/pub/MUSR/LibZFRelaxation \
-          html/user/pub/MUSR/Msr2Data \
-          html/user/pub/MUSR/MusrFit \
-          html/user/pub/MUSR/MusrGui \
-          html/user/pub/MUSR/QuickStart \
-          html/user/pub/MUSR/TutorialSingleHisto \
-          html/user/pub/System/DocumentGraphics \
-          html/user/pub/System/HeadlinesPlugin \
-          html/user/pub/System/PatternSkin \
-          html/user/pub/System/PatternSkinTheme2009 \
-          html/user/pub/System/PsiSkin \
-          html/user/pub/System/SkinTemplates
-          #html/technical
-
-install-data-hook:
-	@$(NORMAL_INSTALL)
-	for DIR in $(DOCDIRS); do $(MKDIR_P) $(DOCDIR)/$$DIR; $(INSTALL_DATA) doc/$$DIR/*.* $(DOCDIR)/$$DIR; done
-	$(MKDIR_P) $(DOCDIR)/latex_images
-	$(INSTALL_DATA) src/musredit/latex_images/*.png $(DOCDIR)/latex_images
-
-uninstall-hook:
-	@$(NORMAL_UNINSTALL)
-	rm -rf $(DOCDIR)

README

@@ -1,35 +1,43 @@
 README
+------
 
-musrfit - muSR data analysis package
+musrfit - muSR and beta-NMR 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:
+Currently it allows the following:
 
-* 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 
+* set up most commonly used fitting functions for muSR and beta-NMR
+* fit data, including global fits
+* show the fit results and the residuals
+* show the Fourier transform of the data
+* easily extract the fit parameters and import in other programs (gnuplot, qtiplot/origin, ...)
+* generate input fitting files for follow-up runs
+* generate global input fitting files based on a single run template
+* implement more sophisticated user functions 
   (e.g. GL vortex lattice, Meissner screening including low-energy muon stopping profiles)
 
-Currently supported platforms:
+Currently supported platforms
+-----------------------------
 
 * Linux
 * Mac OS X
-* Windows - not really, only for the very brave ones
+* Windows 10 1809 or newer - current state is for the commited ones
+* Web based implementation - http://musruser.psi.ch/cgi-bin/musrfit.cgi
 
 Documentation
+-------------
 
 For a more exhaustive user documentation see:
 
-  http://lmu.web.psi.ch/musrfit/user/MUSR/WebHome.html
+  https://lmu.pages.psi.ch/musrfit-docu/index.html
 
-Contact
+Contacts
 
-<andreas.suter@psi.ch>
+  <andreas.suter@psi.ch>
+
+  For the beta-NMR related parts, please contact
+
+  <zaher.salman@psi.ch>

README.md

@@ -1,33 +1,37 @@
-# 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>
-
+# musrfit - muSR and beta-NMR data analysis package #
+
+### Contents ###
+
+This is a data analysis package to analyze time differential muSR and beta-NMR data.
+Currently it allows the following:
+
+* set up most commonly used fitting functions for muSR and beta-NMR
+* fit data, including global fits
+* show the fit results and the residuals
+* show the Fourier transform of the data
+* easily extract the fit parameters and import in other programs (gnuplot, qtiplot/origin, ...)
+* generate input fitting files for follow-up runs
+* generate global input fitting files based on a single run template
+* 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 10 1809 or newer - current state is for the commited ones
+* Web based implementation - http://musruser.psi.ch/cgi-bin/musrfit.cgi
+
+### Documentation ####
+
+For a more exhaustive user documentation see:
+
+  https://lmu.pages.psi.ch/musrfit-docu/index.html
+
+### Contacts ###
+
+<andreas.suter@psi.ch>
+
+For the beta-NMR related parts, please contact Zaher Salman
+<zaher.salman@psi.ch>
+

acinclude.m4

@@ -1,128 +0,0 @@
-dnl -*- mode: autoconf -*- 
-dnl
-dnl $Id: root.m4,v 1.3 2005/03/21 21:42:21 rdm Exp $
-dnl $Author: rdm $
-dnl $Date: 2005/03/21 21:42:21 $
-dnl
-dnl Autoconf macro to check for existence or ROOT on the system
-dnl Synopsis:
-dnl
-dnl  ROOT_PATH([MINIMUM-VERSION, [ACTION-IF-FOUND, [ACTION-IF-NOT-FOUND]]])
-dnl
-dnl Some examples: 
-dnl 
-dnl    ROOT_PATH(3.03/05, , AC_MSG_ERROR(Your ROOT version is too old))
-dnl    ROOT_PATH(, AC_DEFINE([HAVE_ROOT]))
-dnl 
-dnl The macro defines the following substitution variables
-dnl
-dnl    ROOTCONF           full path to root-config
-dnl    ROOTEXEC           full path to root
-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
-dnl    ROOTCFLAGS         Extra compiler flags
-dnl    ROOTLIBS           ROOT basic libraries 
-dnl    ROOTGLIBS          ROOT basic + GUI libraries
-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 rootcling isn't found.
-dnl
-dnl Christian Holm Christensen <cholm@nbi.dk>
-dnl
-AC_DEFUN([ROOT_PATH],
-[
-  AC_ARG_WITH([rootsys],
-              [AC_HELP_STRING([--with-rootsys],
-			      [top of the ROOT installation directory])],
-    			      [user_rootsys=$withval],
-			      [user_rootsys="none"])
-  if test ! x"$user_rootsys" = xnone; then
-    rootbin="$user_rootsys/bin"
-  elif test ! x"$ROOTSYS" = x ; then 
-    rootbin="$ROOTSYS/bin"
-  else 
-   rootbin=$PATH
-  fi
-  AC_PATH_PROG(ROOTCONF, root-config , no, $rootbin)
-  AC_PATH_PROG(ROOTEXEC, root , no, $rootbin)
-  AC_PATH_PROG(ROOTCLING, rootcling , no, $rootbin)
-	
-  if test ! x"$ROOTCONF" = "xno" && \
-     test ! x"$ROOTCLING" = "xno" ; then 
-
-    # define some variables 
-    ROOTLIBDIR=`$ROOTCONF --libdir`
-    ROOTINCDIR=`$ROOTCONF --incdir`
-    ROOTETCDIR=`$ROOTCONF --etcdir`
-    ROOTCFLAGS=`$ROOTCONF --noauxcflags --cflags` 
-    ROOTLIBS=`$ROOTCONF --noauxlibs --noldflags --libs`
-    ROOTGLIBS=`$ROOTCONF --noauxlibs --noldflags --glibs`
-    ROOTAUXCFLAGS=`$ROOTCONF --auxcflags`
-    ROOTAUXLIBS=`$ROOTCONF --auxlibs`
-    ROOTRPATH=$ROOTLIBDIR
-    ROOTVERSION=`$ROOTCONF --version`
-    ROOTSOVERSION=`dirname $ROOTVERSION`
-	
-    if test $1 ; then 
-      AC_MSG_CHECKING(whether ROOT version >= [$1])
-      vers=`$ROOTCONF --version | tr './' ' ' | awk 'BEGIN { FS = " "; } { printf "%d", ($''1 * 1000 + $''2) * 1000 + $''3;}'`
-      requ=`echo $1 | tr './' ' ' | awk 'BEGIN { FS = " "; } { printf "%d", ($''1 * 1000 + $''2) * 1000 + $''3;}'`
-      if test $vers -lt $requ ; then 
-        AC_MSG_RESULT(no)
-	no_root="yes"
-      else 
-        AC_MSG_RESULT(yes)
-      fi
-    fi
-  else
-    # otherwise, we say no_root
-    no_root="yes"
-  fi
-
-  AC_SUBST(ROOTLIBDIR)
-  AC_SUBST(ROOTINCDIR)
-  AC_SUBST(ROOTETCDIR)
-  AC_SUBST(ROOTCFLAGS)
-  AC_SUBST(ROOTLIBS)
-  AC_SUBST(ROOTGLIBS) 
-  AC_SUBST(ROOTAUXLIBS)
-  AC_SUBST(ROOTAUXCFLAGS)
-  AC_SUBST(ROOTRPATH)
-  AC_SUBST(ROOTVERSION)
-  AC_SUBST(ROOTSOVERSION)
-
-  if test "x$no_root" = "x" ; then 
-    ifelse([$2], , :, [$2])     
-  else 
-    ifelse([$3], , :, [$3])     
-  fi
-])
-
-#
-# Macro to check if ROOT has a specific feature:
-#
-#   ROOT_FEATURE(FEATURE,[ACTION_IF_HAVE,[ACTION_IF_NOT]])
-#
-# For example 
-#
-#   ROOT_FEATURE([ldap],[AC_DEFINE([HAVE_ROOT_LDAP])])
-# 
-AC_DEFUN([ROOT_FEATURE],
-[
-  AC_REQUIRE([ROOT_PATH])
-  feat=$1
-  res=`$ROOTCONF --has-$feat` 
-  if test "x$res" = "xyes" ; then 
-    ifelse([$2], , :, [$2])     
-  else 
-    ifelse([$3], , :, [$3])     
-  fi
-])
-
-#
-# EOF
-#

autogen.sh

@@ -1,101 +0,0 @@
-#! /bin/sh
- 
-# autogen.sh
-#
-# Copyright (c) 2009  BMW
-# Copyright (c) 2002  Daniel Elstner  <daniel.elstner@gmx.net>
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU General Public License VERSION 2 as
-# published by the Free Software Foundation.  You are not allowed to
-# use any other version of the license; unless you got the explicit
-# permission from the author to do so.
-#
-# 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
-
-PATHTOAUTOCONF=$(which autoconf)
-PATHTOAUTOMAKE=$(which automake)
-PATHTOLIBTOOL=$(which libtoolize)
-PATHTOGLIBTOOL=
-if [ "$PATHTOLIBTOOL" = "" ]; then
-  PATHTOGLIBTOOL=$(which glibtoolize)
-fi
-
-if [ "$PATHTOAUTOCONF" = "" ]; then
-  echo
-  echo ">> GNU autoconf has not been found!"
-  echo ">> Please install it first and then re-run the script!"
-  echo
-  exit 1
-elif [ "$PATHTOAUTOMAKE" = "" ]; then
-  echo
-  echo ">> GNU automake has not been found!"
-  echo ">> Please install it first and then re-run the script!"
-  echo
-  exit 1
-elif [ "$PATHTOLIBTOOL" = "" ] && [ "$PATHTOGLIBTOOL" = "" ]; then
-  echo
-  echo ">> GNU libtool has not been found!"
-  echo ">> Please install it first and then re-run the script!"
-  echo
-  exit 1
-fi
-
-if [ "$PATHTOLIBTOOL" = "" ]; then
-  LIBTOOLIZE="glibtoolize"
-else
-  LIBTOOLIZE="libtoolize"
-fi
-
-dir=`echo "$0" | sed 's,[^/]*$,,'`
-test "x${dir}" = "x" && dir='.'
-
-if test "x`cd "${dir}" 2>/dev/null && pwd`" != "x`pwd`"
-then
-    echo "This script must be executed directly from the source directory!"
-    exit 1
-fi
-
-if !(test -d admin); then
-  mkdir admin
-fi
-
-rm -f config.cache
-
-if test -e admin/depcomp          && \
-   test -e admin/install-sh       && \
-   test -e admin/ltmain.sh        && \
-   test -e admin/missing          && \
-   test -e aclocal.m4
-then
-    echo ">> autoreconf"          && \
-    autoreconf                    && exit 0
-else
-    echo ""                       && \
-    echo "+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++" && \
-    echo "+ This script prepares the building environment for the configuration of    +" && \
-    echo "+ musrfit. During this process some informative messages might appear which +" && \
-    echo "+ can safely be ignored as long as they are not tagged as errors.           +" && \
-    echo "+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++" && \
-    echo ""                       && \
-    echo ">> libtoolize"          && \
-    $LIBTOOLIZE --force           && \
-    echo ">> aclocal"             && \
-    aclocal                       && \
-    echo ">> autoconf"		  && \
-    autoconf                      && \
-    echo ">> autoheader"          && \
-    autoheader			  && \
-    echo ">> automake"		  && \
-    automake --add-missing --gnu  && exit 0
-fi
-
-exit 1
-

cmake/CPackOptions.cmake.in

@@ -0,0 +1,43 @@
+# musrfit - cpack
+
+include(CPackComponent)
+
+set (CPACK_PACKAGE_NAME "musrfit-root6")
+set (CPACK_PACKAGE_VENDOR "Paul Scherrer Institute - LMU - LEM")
+set (CPACK_PACKAGE_DIRECTOR "@CMAKE_CURRENT_BINARY_DIR@/pack")
+set (CPACK_PACKAGE_VERSION_MAJOR "@PROJECT_VERSION_MAJOR@")
+set (CPACK_PACKAGE_VERSION_MINOR "@PROJECT_VERSION_MINOR@")
+set (CPACK_PACKAGE_VERSION_PATCH "@PROJECT_VERSION_PATCH@")
+set (CPACK_PACKAGE_CONTACT "<andreas.suter@psi.ch>")
+set (CPACK_PACKAGE_DESCRIPTION_FILE "@PROJECT_SOURCE_DIR@/README.md")
+set (CPACK_PACKAGE_DESCRIPTION_SUMMARY "musrfit - muSR data analysis package")
+set (CPACK_PACKAGE_HOMEPAGE_URL "http://lmu.web.psi.ch/musrfit/user/html/index.html")
+set (CPACK_PACKAGE_CHECKSUM "MD5")
+set (CPACK_RESOURCE_FILE_LICENSE "@PROJECT_SOURCE_DIR@/COPYING")
+set (CPACK_RESOURCE_FILE_README "@PROJECT_SOURCE_DIR@/README.md")
+set (CPACK_RESOURCE_FILE_WELCOME "@PROJECT_SOURCE_DIR@/cmake/welcome.txt")
+
+set (CPACK_RPM_EXCLUDE_FROM_AUTO_FILELIST_ADDITION "@CMAKE_INSTALL_PREFIX@;@CMAKE_INSTALL_PREFIX@/bin;@CMAKE_INSTALL_PREFIX@/include;@CMAKE_INSTALL_PREFIX@/share;@CMAKE_INSTALL_PREFIX@/lib64;@CMAKE_INSTALL_PREFIX@/lib;@CMAKE_INSTALL_PREFIX@/pkgconfig;@CMAKE_INSTALL_PREFIX@/share/applications;@CMAKE_INSTALL_PREFIX@/share/icons;@CMAKE_INSTALL_PREFIX@/share/icons/hicolor;@CMAKE_INSTALL_PREFIX@/share/icons/hicolor/48x48;@CMAKE_INSTALL_PREFIX@/share/icons/hicolor/48x48/apps")
+
+# we do not have any absolute paths, so do not need DESTDIR
+set (CPACK_SET_DESTDIR "OFF")
+set (CPACK_PACKAGE_RELOCATABLE "true")
+
+if (${CPACK_GENERATOR} STREQUAL "RPM")
+  set (CPACK_RPM_PACKAGE_REQUIRES "root >= 6.22.00") 
+  set (CPACK_INSTALL_PREFIX "@CMAKE_INSTALL_PREFIX@")
+  set (CPACK_PACKAGING_INSTALL_PREFIX "@CMAKE_INSTALL_PREFIX@")
+  set (CPACK_RPM_FILE_NAME "RPM-DEFAULT")
+  set (CPACK_RPM_PACKAGE_RELEASE "1")
+  # next variable for RHEL, CentOS, Fedora
+  set (CPACK_RPM_PACKAGE_RELEASE_DIST "el8")
+  set (CPACK_RPM_PACKAGE_LICENSE "GPLv2")
+  set (CPACK_RPM_PACKAGE_VENDOR "Paul Scherrer Institute - LMU - LEM")
+  set (CPACK_RPM_CHANGELOG_FILE "@PROJECT_SOURCE_DIR@/cmake/ChangeLogRPM")
+  set (CPACK_RPM_POST_INSTALL_SCRIPT_FILE "@PROJECT_SOURCE_DIR@/cmake/post_install.sh")
+  set (CPACK_RPM_POST_UNINSTALL_SCRIPT_FILE "@PROJECT_SOURCE_DIR@/cmake/post_uninstall.sh")
+endif ()
+
+if (${CPACK_GENERATOR} STREQUAL "DEB")
+  # to be populated yet
+endif ()

cmake/ChangeLogRPM

@@ -0,0 +1,4 @@
+* Mon Mar 11 2019 Andreas Suter <andreas.suter@psi.ch> - 1.4.2-2
+- minor version update
+* Mon Jan 14 2019 Andreas Suter <andreas.suter@psi.ch> - 1.4.0-1
+- first cpack/cmake version

cmake/FindFFTW3.cmake

@@ -1,7 +1,7 @@
 # - Find fftw3 library
 # Find the native FFTW3 includes and library
 # This module defines
-#  FFTW3_INCLUDE_DIR, where to find fftw3.h, etc.
+#  FFTW3_INCLUDE, 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
@@ -31,16 +31,50 @@
 #  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"
-)
+function(add_imported_library lib_name library headers)
+  add_library(FFTW3::${lib_name} UNKNOWN IMPORTED)
+  set_target_properties(FFTW3::${lib_name} PROPERTIES
+    IMPORTED_LOCATION ${library}
+    INTERFACE_INCLUDE_DIRECTORIES ${headers}
+  )
+  set(${lib_name}_FOUND 1 CACHE INTERNAL "FFTW3 ${lib_name} found" FORCE)
+  set(${lib_name}_LIBRARY ${library}
+      CACHE STRING "Path to FFTW3::${lib_name} library" FORCE)
+  set(FFTW3_INCLUDE ${headers}
+      CACHE STRING "Path to FFTW3 headers" FORCE)
+  mark_as_advanced(FORCE ${lib_name}_LIBRARY)
+  mark_as_advanced(FORCE FFTW3_INCLUDE)
+endfunction()
 
-# 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 ${substr})
-unset(substr)
+#as35 if (FFTW3_LIBRARY AND FFTW3_INCLUDE)
+#as35   add_imported_library(${FFTW3_LIBRARY} ${FFTW3_INCLUDE})
+#as35   if (FFTW3_OMP_LIBRARY AND FFTW3_INCLUDE)
+#as35     add_imported_library(${FFTW3_OMP_LIBRARY} ${FFTW3_INCLUDE})
+#as35   elseif (FFTW3_THREAD_LIBRARY AND FFTW3_INCLUDE)
+#as35     add_imported_library(${FFTW3_THRED_LIBRARY} ${FFTW3_INCLUDE})
+#as35   elseif (FFTW3L_LIBRARY AND FFTW3_INCLUDE)
+#as35     add_imported_library(${FFTW3L_LIBRARY} ${FFTW3_INCLUDE})
+#as35   elseif (FFTW3L_OMP_LIBRARY AND FFTW3_INCLUDE)
+#as35     add_imported_library(${FFTW3L_OMP_LIBRARY} ${FFTW3_INCLUDE})
+#as35   elseif (FFTW3L_THREAD_LIBRARY AND FFTW3_INCLUDE)
+#as35     add_imported_library(${FFTW3L_THRED_LIBRARY} ${FFTW3_INCLUDE})
+#as35   elseif (FFTW3F_LIBRARY AND FFTW3_INCLUDE)
+#as35     add_imported_library(${FFTW3F_LIBRARY} ${FFTW3_INCLUDE})
+#as35   elseif (FFTW3F_OMP_LIBRARY AND FFTW3_INCLUDE)
+#as35     add_imported_library(${FFTW3F_OMP_LIBRARY} ${FFTW3_INCLUDE})
+#as35   elseif (FFTW3F_THREAD_LIBRARY AND FFTW3_INCLUDE)
+#as35     add_imported_library(${FFTW3F_THRED_LIBRARY} ${FFTW3_INCLUDE})
+#as35   elseif (FFTW3Q_LIBRARY AND FFTW3_INCLUDE)
+#as35     add_imported_library(${FFTW3Q_LIBRARY} ${FFTW3_INCLUDE})
+#as35   elseif (FFTW3Q_OMP_LIBRARY AND FFTW3_INCLUDE)
+#as35     add_imported_library(${FFTW3Q_OMP_LIBRARY} ${FFTW3_INCLUDE})
+#as35   elseif (FFTW3Q_THREAD_LIBRARY AND FFTW3_INCLUDE)
+#as35     add_imported_library(${FFTW3Q_THRED_LIBRARY} ${FFTW3_INCLUDE})
+#as35   endif()
+#as35   return()
+#as35 endif()
+
+find_path(FFTW3_INCLUDE NAMES fftw3.h)
 
 find_library(FFTW3_LIBRARY fftw3)
 find_library(FFTW3_OMP_LIBRARY fftw3_omp)
@@ -58,94 +92,127 @@ 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(${CMAKE_ROOT}/Modules/FindPackageHandleStandardArgs.cmake)
+
+# FFTW3
 find_package_handle_standard_args(FFTW3
-                                  REQUIRED_VARS FFTW3_LIBRARY FFTW3_INCLUDE_DIR
-                                  VERSION_VAR "3")
+                                  DEFAULT_MSG FFTW3_LIBRARY FFTW3_INCLUDE
+                                 )
+if (FFTW3_FOUND)
+  add_imported_library("FFTW3" "${FFTW3_LIBRARY}" "${FFTW3_INCLUDE}")
+endif()
+
+# FFTW3_OMP
 find_package_handle_standard_args(FFTW3_OMP
-                                  REQUIRED_VARS FFTW3_OMP_LIBRARY FFTW3_INCLUDE_DIR
-                                  VERSION_VAR "3")
+                                  REQUIRED_VARS FFTW3_OMP_LIBRARY FFTW3_INCLUDE
+                                  HANDLE_COMPONENTS
+                                  NAME_MISMATCHED
+                                 )
+if (FFTW3_OMP_FOUND)
+  add_imported_library("FFTW3_OMP" "${FFTW3_OMP_LIBRARY}" "${FFTW3_INCLUDE}")
+endif()
+
+# FFTW3_THREAD
 find_package_handle_standard_args(FFTW3_THREAD
-                                  REQUIRED_VARS FFTW3_THREAD_LIBRARY FFTW3_INCLUDE_DIR
-                                  VERSION_VAR "3")
+                                  REQUIRED_VARS FFTW3_THREAD_LIBRARY FFTW3_INCLUDE
+                                  HANDLE_COMPONENTS
+                                  NAME_MISMATCHED
+                                 )
+if (FFTW3_THREAD_FOUND)
+  add_imported_library("FFTW3_THREAD" "${FFTW3_THREAD_LIBRARY}" "${FFTW3_INCLUDE}")
+endif()
 
+# FFTW3L
 find_package_handle_standard_args(FFTW3L
-                                  REQUIRED_VARS FFTW3L_LIBRARY FFTW3_INCLUDE_DIR
-                                  VERSION_VAR "3")
+                                  REQUIRED_VARS FFTW3L_LIBRARY FFTW3_INCLUDE
+                                  HANDLE_COMPONENTS
+                                  NAME_MISMATCHED
+                                 )
+if (FFTW3L_FOUND)
+  add_imported_library("FFTW3L" "${FFTW3L_LIBRARY}" "${FFTW3_INCLUDE}")
+endif()
+
+# FFTW3L_OMP
 find_package_handle_standard_args(FFTW3L_OMP
-                                  REQUIRED_VARS FFTW3L_OMP_LIBRARY FFTW3_INCLUDE_DIR
-                                  VERSION_VAR "3")
+                                  REQUIRED_VARS FFTW3L_OMP_LIBRARY FFTW3_INCLUDE
+                                  HANDLE_COMPONENTS
+                                  NAME_MISMATCHED
+                                 )
+if (FFTW3L_OMP_FOUND)
+  add_imported_library("FFTW3L_OMP" "${FFTW3L_OMP_LIBRARY}" "${FFTW3_INCLUDE}")
+endif()
+
+# FFTW3L_THREAD
 find_package_handle_standard_args(FFTW3L_THREAD
-                                  REQUIRED_VARS FFTW3L_THREAD_LIBRARY FFTW3_INCLUDE_DIR
-                                  VERSION_VAR "3")
+                                  REQUIRED_VARS FFTW3L_THREAD_LIBRARY FFTW3_INCLUDE
+                                  HANDLE_COMPONENTS
+                                  NAME_MISMATCHED
+                                 )
+if (FFTW3L_THREAD_FOUND)
+  add_imported_library("FFTW3L_THREAD" "${FFTW3L_THREAD_LIBRARY}" "${FFTW3_INCLUDE}")
+endif()
 
+# FFTW3F
 find_package_handle_standard_args(FFTW3F
-                                  REQUIRED_VARS FFTW3F_LIBRARY FFTW3_INCLUDE_DIR
-                                  VERSION_VAR "3")
+                                  REQUIRED_VARS FFTW3F_LIBRARY FFTW3_INCLUDE
+                                  HANDLE_COMPONENTS
+                                  NAME_MISMATCHED
+                                 )
+if (FFTW3F_FOUND)
+  add_imported_library("FFTW3F" "${FFTW3F_LIBRARY}" "${FFTW3_INCLUDE}")
+endif()
+
+# FFTW3F_OMP
 find_package_handle_standard_args(FFTW3F_OMP
-                                  REQUIRED_VARS FFTW3F_OMP_LIBRARY FFTW3_INCLUDE_DIR
-                                  VERSION_VAR "3")
+                                  REQUIRED_VARS FFTW3F_OMP_LIBRARY FFTW3_INCLUDE
+                                  HANDLE_COMPONENTS
+                                  NAME_MISMATCHED
+                                 )
+if (FFTW3F_OMP_FOUND)
+  add_imported_library("FFTW3F_OMP" "${FFTW3F_OMP_LIBRARY}" "${FFTW3_INCLUDE}")
+endif()
+
+# FFTW3F_THREAD
 find_package_handle_standard_args(FFTW3F_THREAD
-                                  REQUIRED_VARS FFTW3F_THREAD_LIBRARY FFTW3_INCLUDE_DIR
-                                  VERSION_VAR "3")
+                                  REQUIRED_VARS FFTW3F_THREAD_LIBRARY FFTW3_INCLUDE
+                                  HANDLE_COMPONENTS
+                                  NAME_MISMATCHED
+                                 )
+if (FFTW3F_THREAD_FOUND)
+  add_imported_library("FFTW3F_THREAD" "${FFTW3F_THREAD_LIBRARY}" "${FFTW3_INCLUDE}")
+endif()
 
+# FFTW3Q
 find_package_handle_standard_args(FFTW3Q
-                                  REQUIRED_VARS FFTW3Q_LIBRARY FFTW3_INCLUDE_DIR
-                                  VERSION_VAR "3")
+                                  REQUIRED_VARS FFTW3Q_LIBRARY FFTW3_INCLUDE
+                                  HANDLE_COMPONENTS
+                                  NAME_MISMATCHED
+                                 )
+if (FFTW3Q_FOUND)
+  add_imported_library("FFTW3Q" "${FFTW3Q_LIBRARY}" "${FFTW3_INCLUDE}")
+endif()
+
+# FFTW3Q_OMP
 find_package_handle_standard_args(FFTW3Q_OMP
-                                  REQUIRED_VARS FFTW3Q_OMP_LIBRARY FFTW3_INCLUDE_DIR
-                                  VERSION_VAR "3")
+                                  REQUIRED_VARS FFTW3Q_OMP_LIBRARY FFTW3_INCLUDE
+                                  HANDLE_COMPONENTS
+                                  NAME_MISMATCHED
+                                 )
+if (FFTW3Q_OMP_FOUND)
+  add_imported_library("FFTW3Q_OMP" "${FFTW3Q_OMP_LIBRARY}" "${FFTW3_INCLUDE}")
+endif()
+
+# FFTW3Q_THREAD
 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)
+                                  REQUIRED_VARS FFTW3Q_THREAD_LIBRARY FFTW3_INCLUDE
+                                  HANDLE_COMPONENTS
+                                  NAME_MISMATCHED
+                                 )
+if (FFTW3Q_THREAD_FOUND)
+  add_imported_library("FFTW3Q_THREAD" "${FFTW3Q_THREAD_LIBRARY}" "${FFTW3_INCLUDE}")
 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
-)
+pkg_check_modules(FFTW fftw3 QUIET)
 
 if (FFTW3_FOUND)
-  message("-- Found FFTW3: ${FFTW3_INCLUDE_DIR}")
+  message("-- Found FFTW3: ${FFTW3_INCLUDE}, Version: ${FFTW_VERSION}")
 endif (FFTW3_FOUND)

cmake/FindMXML.cmake

@@ -1,34 +0,0 @@
-# - 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

@@ -1,45 +0,0 @@
-# - 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

@@ -1,9 +1,11 @@
 // config.h
 
 #define PACKAGE_VERSION "@PROJECT_VERSION@"
+#define ROOT_VERSION_USED "@ROOT_VERSION@"
+#define BUILD_TYPE "@CMAKE_BUILD_TYPE@"
 
-// define to 1 if you have fork and it should be used 
-#cmakedefine HAVE_FORK 1
+// define to 1 if minor ROOT6 version is >= 24
+#define ROOT_GRTEQ_24 @ROOT_GRTEQ_24@
 
 // define to 1 if you have <alloca.h> and it should be used 
 #cmakedefine HAVE_ALLOCA_H 1

cmake/configure_musrfit_version_file.cmake.in

@@ -1,30 +0,0 @@
-# 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/musredit.desktop

@@ -0,0 +1,13 @@
+[Desktop Entry]
+Name=MuSRedit
+Comment=editor and launcher for the musrfit data analysis
+GenericName=musrfit editor
+Exec=musredit %F
+Icon=musredit
+Terminal=false
+Type=Application
+StartupWMClass=MuSRedit
+Categories=Science;DataEditing;
+MimeType=text/plain;
+Keywords=muSR;fitting;musrfit;physics;muon;
+StartupNotify=true

cmake/musrfit-root6.spec.in

@@ -0,0 +1,103 @@
+Name:           musrfit-root6
+Version:        1.4
+Release:        1%{?dist}
+Summary:        musrfit - muSR data analysis package
+
+License:        GPLv2
+URL:            http://lmu.web.psi.ch/musrfit/user/html/index.html
+Source0:        https://gitlab.psi.ch/nemu/musrfit/repository/%{name}-%{version}.tar.gz
+
+BuildRequires:  cmake
+BuildRequires:  libtool
+BuildRequires:  gcc
+BuildRequires:  make
+BuildRequires:  hdf-devel hdf5-devel
+BuildRequires:  mxml-devel
+BuildRequires:  fftw3-devel
+BuildRequires:  boost-devel
+BuildRequires:  gsl-devel
+BuildRequires:  libxml2-devel
+BuildRequires:  root
+BuildRequires:  root-io-xml
+BuildRequires:  root-mathmore
+BuildRequires:  root-minuit2
+BuildRequires:  qt5-qtbase-devel qt5-qtsvg-devel qt5-qtwebkit-devel
+BuildRequires:  nexus
+Requires:       hdf hdf5
+Requires:       mxml
+Requires:       fftw3
+Requires:       gsl
+Requires:       boost-devel
+Requires:       libxml2
+Requires:       root
+Requires:       root-io-xml
+Requires:       root-mathmore
+Requires:       root-minuit2
+Requires:       qt5-qtbase qt5-qtsvg qt5-qtwebkit
+Requires:       nexus
+
+%description
+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
+
+
+%prep
+%setup -q -n %{name}-%{version}
+
+
+%build
+##æs35 ./autogen.sh
+# DOCDIR is needed to be set here. BMWlibs still makes troubles
+%cmake -DASlibs=1 -DBMWlbis=1 -Dnexus=1 DOCDIR=$RPM_BUILD_ROOT/usr/share/doc/musrfit
+%cmake --build ./ --clean-first -- -j8
+##æs35 %configure --enable-ASlibs --enable-BMWlibs --enable-NeXus DOCDIR=$RPM_BUILD_ROOT/usr/share/doc/musrfit
+##æs35 %make_build
+
+
+%install
+# INSTALL_ROOT is needed for Qt applications
+rm -rf $RPM_BUILD_ROOT
+%make_install INSTALL_ROOT=%{buildroot}
+
+%files
+%_prefix/bin/any2many
+%_prefix/bin/dump_header
+%_prefix/bin/msr2data
+%_prefix/bin/msr2msr
+%_prefix/bin/mupp
+%_prefix/bin/mupp_plot
+%_prefix/bin/musredit
+%_prefix/bin/musrfit
+%_prefix/bin/musrFT
+%_prefix/bin/musrRootValidation
+%_prefix/bin/musrStep
+%_prefix/bin/musrt0
+%_prefix/bin/musrview
+%_prefix/bin/musrWiz
+%_prefix/bin/write_musrRoot_runHeader
+%_prefix/include/*
+%_prefix/lib64/*
+%license COPYING
+%doc %_prefix/share/doc/musrfit
+%{_datadir}/applications/musredit.desktop
+%{_datadir}/icons/hicolor/48x48/apps/musredit.png
+
+
+
+%changelog
+* Thu Dec 20 2018 Andreas Suter <andreas.suter@psi.ch> - 1.4-1
+- adopted to cmake 
+* Wed Oct 25 2017 Andreas Suter <andreas.suter@psi.ch> - 1.2-1
+- first spec file for musrfit-root6

cmake/musrfitConfig.cmake.in

@@ -0,0 +1,15 @@
+# musrfitConfig.cmake.in
+# CMake package configuration template for musrfit.
+# Generated by configure_package_config_file().
+
+@PACKAGE_INIT@
+
+include(CMakeFindDependencyMacro)
+
+find_dependency(ROOT REQUIRED COMPONENTS Gui MathMore Minuit2 XMLParser)
+find_dependency(Boost REQUIRED COMPONENTS filesystem)
+find_dependency(GSL REQUIRED)
+
+include("${CMAKE_CURRENT_LIST_DIR}/musrfitTargets.cmake")
+
+check_required_components(musrfit)

cmake/post_install.sh

@@ -0,0 +1,19 @@
+#!/bin/bash
+
+echo "  >> musrfit post install script started ..."
+
+# test if nemu-x86_64.conf does not exist
+if [ ! -f "/etc/ld.so.conf.d/nemu-x86_64.conf" ]
+then
+  echo "/usr/local/lib" >> /etc/ld.so.conf.d/nemu-x86_64.conf 
+  echo "/usr/local/lib64" >> /etc/ld.so.conf.d/nemu-x86_64.conf   
+fi
+/sbin/ldconfig
+
+#update .desktop and icons
+if command -v update-desktop-database &>/dev/null; then
+  update-desktop-database -q /usr/share/applications || true
+fi
+if command -v gtk-update-icon-cache &>/dev/null; then
+  gtk-update-icon-cache -q -t /usr/share/icons/hicolor || true
+fi

cmake/post_uninstall.sh

@@ -0,0 +1,13 @@
+#!/bin/bash
+
+echo "  >> musrfit post uninstall script started ..."
+
+/sbin/ldconfig
+
+#update .desktop and icons
+if command -v update-desktop-database &>/dev/null; then
+  update-desktop-database -q /usr/share/applications || true
+fi
+if command -v gtk-update-icon-cache &>/dev/null; then
+  gtk-update-icon-cache -q -t /usr/share/icons/hicolor || true
+fi

cmake/welcome.txt

@@ -0,0 +1 @@
+Welcome to the musrfit package

doc/examples/ASlibs/nonlocal_startup.xml

@@ -1,13 +1,14 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <nonlocal xmlns="http://nemu.web.psi.ch/musrfit/nonlocal">
     <comment>
-        $Id: nonlocal_startup.xml 4047 2009-07-02 13:36:18Z nemu $
+        nonlocal_startup.xml
     </comment>
     <nonlocal_par>
         <fourier_points>262144</fourier_points>
     </nonlocal_par>
-    <trim_sp_part>
-        <data_path>profiles/Sn_E</data_path>
+    <trim_sp>
+        <data_path>./profiles/</data_path>
+        <rge_fln_pre>Sn_E</rge_fln_pre>
         <energy_list>
 	    <energy>1000</energy>
 	    <energy>2000</energy>
@@ -22,5 +23,5 @@
 	    <energy>25000</energy>
 	    <energy>27300</energy>
         </energy_list>
-    </trim_sp_part>
+    </trim_sp>
 </nonlocal>

doc/examples/ASlibs/test-nonlocal.msr

@@ -4,21 +4,21 @@ FITPARAMETER
 #      Nr. Name       Value     Step      Pos_Error Boundaries   
         1 one         1         0           none        
         2 zero        0         0           none        
-        3 Asy         0.2235    -0.0066     0.0072      0       0.33    
-        4 energy      22        0           none        
+        3 Asy         0.2235    -0.0065     0.0072      0       0.33    
+        4 energy      22000     0           none        
         5 redTemp     0.8683    0           none        
         6 thickness   5000      0           none        
         7 ell         12000     0           none        
         8 xi          94        0           none        
-        9 lambdaL     52.5      -1.4        1.2         
+        9 lambdaL     52.5      -1.3        1.2         
        10 Bext        47.11     0           none        
-       11 deadLayer   0.00052   -0.00052    6.89563     0       none    
+       11 deadLayer   0.0004    0.0037      none        0       none    
        12 RateSmear   0.418     -0.015      0.015       
-       13 N0_L        301.61    0.62        none        
-       14 Bkg_L       24.442    0.076       none        
+       13 N0_L        301.6     -1.1        1.2         
+       14 Bkg_L       24.441    -0.092      0.092       
        15 Phase_L     42.0      -2.2        2.2         
-       16 Alpha_LR    1.0614    -0.0066     0.0064      
-       17 Bkg_R       27.646    -0.090      0.090       
+       16 Alpha_LR    1.0613    -0.0066     0.0064      
+       17 Bkg_R       27.646    -0.089      0.090       
        18 RelPhase_R  154.4     -1.1        1.1         
 
 ###############################################################
@@ -37,7 +37,6 @@ RUN data/lem10_his_0825 MUE4 PSI ROOT-NPP   (name beamline institute data-file-f
 fittype         0         (single histogram fit)
 norm            13
 backgr.fit      14
-lifetimecorrection
 map             1    2    0    0    0    0    0    0    0    0
 forward         1 
 data            3289    65000   
@@ -49,7 +48,6 @@ RUN data/lem10_his_0825 MUE4 PSI ROOT-NPP   (name beamline institute data-file-f
 fittype         0         (single histogram fit)
 norm            fun1
 backgr.fit      17
-lifetimecorrection
 map            16   18    0    0    0    0    0    0    0    0
 forward         3 
 data            3289    65000   
@@ -69,23 +67,27 @@ SAVE
 
 ###############################################################
 PLOT 0   (single histo plot)
+lifetimecorrection
 runs     1   2   
 range    0   9   -0.3   0.3
 view_packing 500
 
 ###############################################################
 FOURIER
-units            Gauss   # units either 'Gauss', 'MHz', or 'Mc/s'
+units            Gauss   # units either 'Gauss', 'Tesla', 'MHz', or 'Mc/s'
 fourier_power    10
 apodization      STRONG  # 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            8.5
 #range_for_phase_correction 50.0 70.0
-range            0.0    200.0
+range            0    200
 
 ###############################################################
-STATISTIC --- 2014-11-05 12:34:54
-  maxLH = 415.6, NDF = 358, maxLH/NDF = 1.160933
+STATISTIC --- 2021-03-30 15:04:30
+  maxLH = 415.6, NDF = 358, maxLH/NDF = 1.160942
+  expected maxLH = 418.1, NDF = 358, expected maxLH/NDF = 1.168011
+  run block 1: (NDF/red.maxLH/red.maxLH_e) = (177/1.072511/1.087460)
+  run block 2: (NDF/red.maxLH/red.maxLH_e) = (175/1.290186/1.289528)
 
 
 

doc/examples/BMWlibs/test-libFitPofB_Abrikosov-PSI-BIN.msr

@@ -2,23 +2,23 @@ LSCO x=0.195 single
 ###############################################################
 FITPARAMETER
 #       No Name        Value     Step        Pos_Error   Boundaries
-        1 phase       8.09      0.30        none        
-        2 field       107.08786 0.00052     none        
-        3 lambda      195.5703  0.0029      none        1       none    
+        1 phase       10.34     0.21        none        
+        2 field       112.82363 0.00033     none        
+        3 lambda      170.4570  0.0022      none        1       none    
         4 xi          4         0           none        0       10      
         
-        5 asym1       0.1980    0.0011      none        0       0.3     
-        6 rate1       0.7697    0.0063      none        
+        5 asym1       0.19219   -0.00079    0.00079     0       0.3     
+        6 rate1       0.7955    0.0043      none        
         7 asymBg      0         0           none        0       0.3     
         8 rateBg      0         0           none        0       none    
   
-        9 N01         3311.3    1.7         none        0       none    
-       10 bg1         68.70     0.30        none        0       none    
-       11 N02         3577.8    1.7         none        0       none    
-       12 bg2         69.62     0.31        none        0       none    
-       13 relphase    181.63    0.41        none        150     210     
+        9 N01         3313.6    1.2         none        0       none    
+       10 bg1         68.54     0.21        none        0       none    
+       11 N02         3575.9    1.2         none        0       none    
+       12 bg2         69.82     0.22        none        0       none    
+       13 relphase    181.46    0.29        none        150     210     
        14 zero        0         0           none        
-       15 relasy      1.0325    0.0075      none        
+       15 relasy      1.0365    0.0051      none        
        16 one         1         0           none        
 
 ###############################################################
@@ -39,52 +39,51 @@ fun3 = par5 * map2
 fun4 = par7 * map2
 
 ###############################################################
-RUN data/deltat_pta_gps_3093 PIM3 PSI PSI-BIN   (name beamline institute data-file-format)
+GLOBAL
 fittype         0         (single histogram fit)
+fit             0       8      
+packing         30
+
+
+###############################################################
+RUN data/deltat_pta_gps_3093 PIM3 PSI PSI-BIN   (name beamline institute data-file-format)
 map            14   16    0    0    0    0    0    0    0    0
 forward         3 
 norm            9
-lifetimecorrection
 backgr.fit      10
 t0              125.0   
 data            128     8001    
-fit             0       8      
-packing         30
 
 RUN data/deltat_pta_gps_3093 PIM3 PSI PSI-BIN   (name beamline institute data-file-format)
-fittype         0         (single histogram fit)
 map            13   15    0    0    0    0    0    0    0    0
 forward         4 
 norm            11
-lifetimecorrection
 backgr.fit      12
 t0              124.0   
 data            127     8000    
-fit             0       8      
-packing         30
 
 ###############################################################
 COMMANDS
+MAX_LIKELIHOOD
 MINIMIZE
-#MIGRAD
-HESSE
-#MINOS
+MINOS
 SAVE
 
 ###############################################################
 FOURIER
-units            Gauss   # units either 'Gauss', 'MHz', or 'Mc/s'
+units            Gauss   # units either 'Gauss', 'Tesla', 'MHz', or 'Mc/s'
 fourier_power    9
 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            par1
 range            0    500
 
 ###############################################################
 PLOT 0   (single histo plot)
+lifetimecorrection
 runs     1   2   
 range    0   4   -0.25   0.25
 
 ###############################################################
-STATISTIC --- 2013-05-03 09:08:20
-  chisq = 1200.8, NDF = 415, chisq/NDF = 2.893391
+STATISTIC --- 2021-02-26 14:54:47
+  maxLH = 1497.5, NDF = 415, maxLH/NDF = 3.608471

doc/examples/BMWlibs/test-libFitPofB_Meissner-ROOT-NPP.msr

@@ -4,19 +4,19 @@ FITPARAMETER
 #       No Name        Value     Step        Pos_Error   Boundaries
         1 field       94.717    0           none        
         2 deadlayer   10.5      0           none        
-        3 lambda      115.96    -0.92       0.88        
+        3 lambda      115.98    -0.65       0.63        
 
 # E = 22keV
 
         4 phase22     25.4956   0           none        
-        5 asym22      0.1047    -0.0029     0.0030      0       0.3     
-        6 rate22      0.559     -0.032      0.033       
-        7 NormL22     753.00    -0.86       0.87        
-        8 BGL22       51.08     -0.13       0.13        
-        9 NormR22     545.93    -0.77       0.76        
-       10 BGR22       38.60     -0.11       0.12        
-       11 relasyR22   1.068     -0.038      0.039       0.2     2       
-       12 relphaR22   162.8     -1.5        1.5         110     210     
+        5 asym22      0.1047    -0.0021     0.0021      0       0.3     
+        6 rate22      0.558     -0.023      0.023       
+        7 NormL22     752.98    -0.61       0.61        
+        8 BGL22       51.114    -0.094      0.094       
+        9 NormR22     545.95    -0.54       0.54        
+       10 BGR22       38.634    -0.082      0.082       
+       11 relasyR22   1.068     -0.027      0.027       0.2     2       
+       12 relphaR22   162.8     -1.1        1.1         110     210     
        13 energy22    22        0           none        
 
        14 one         1         0           none        
@@ -35,53 +35,48 @@ fun2 = map1 + map5
 fun3 = par1 * gamma_mu
 
 ###############################################################
-RUN data/lem09_his_0916 MUE4 PSI ROOT-NPP   (name beamline institute data-file-format)
+GLOBAL
 fittype         0         (single histogram fit)
-norm            7
-backgr.fit      8
-lifetimecorrection
-map             4    5    6   14   15   13    0    0    0    0
-forward         1 
-background      65000   66500   
-data            3419    63000   
-t0              3419.0  
-fit             0.15    10     
-packing         150
-
-RUN data/lem09_his_0916 MUE4 PSI ROOT-NPP   (name beamline institute data-file-format)
-fittype         0         (single histogram fit)
-norm            9
-backgr.fit      10
-lifetimecorrection
-map             4    5    6   11   12   13    0    0    0    0
-forward         3 
-background      65000   66500   
 data            3419    63000   
 t0              3419.0  
 fit             0.15    10     
 packing         150
 
+###############################################################
+RUN data/lem09_his_0916 MUE4 PSI ROOT-NPP   (name beamline institute data-file-format)
+norm            7
+backgr.fit      8
+map             4    5    6   14   15   13    0    0    0    0
+forward         1 
+
+RUN data/lem09_his_0916 MUE4 PSI ROOT-NPP   (name beamline institute data-file-format)
+norm            9
+backgr.fit      10
+map             4    5    6   11   12   13    0    0    0    0
+forward         3 
+
 ###############################################################
 COMMANDS
-#MAX_LIKELIHOOD
+MAX_LIKELIHOOD
 MINIMIZE
 MINOS
 SAVE
 
 ###############################################################
 FOURIER
-units            Gauss   # units either 'Gauss', 'MHz', or 'Mc/s'
+units            Gauss   # units either 'Gauss', 'Tesla', 'MHz', or 'Mc/s'
 fourier_power    10
 apodization      WEAK    # 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            par4
 range            0    200
 
 ###############################################################
 PLOT 0   (single histo plot)
-runs     1   2   
+lifetimecorrection
+runs        1   2
 range    0   4   -0.25   0.25
 
 ###############################################################
-STATISTIC --- 2013-11-12 10:25:11
-  chisq = 696.9, NDF = 663, chisq/NDF = 1.051076
+STATISTIC --- 2021-02-26 14:50:08
+  maxLH = 695.5, NDF = 663, maxLH/NDF = 1.049008

doc/examples/BNMRlibs/test-ExpRlx-hel.msr

@@ -1,21 +1,20 @@
-
-# Run Numbers: 1111
+LaAlO3,  SLR, 30G, 150K, Bias=23 kV, Ix=0A, Iy=+3A, aligned, beam on=1s
 ###############################################################
 FITPARAMETER
 ###############################################################
 #     No     Name       Value    Err     Min  Max                  
-        1 Alpha       1.11587   0.00038     none        
-        2 Asy         0.0570    0.0011      none        
+        1 Alpha       1.11592   0.00035     none        
+        2 Asy         0.05868   0.00091     none        0       0.2     
         3 T           1         0           none        
-        4 Rlx         1.015     0.023       none        
+        4 Rlx         1.142     0.023       none        0       15000   
         5 One         1         0           none        
-        6 Bet         -1.052    0.027       none        
+        6 FlHel       -1.048    0.022       none        -2      0       
 
 ###############################################################
 THEORY
 ###############################################################
 asymmetry   fun1
-userFcn  .libs/libBNMR.so ExpRlx 3 4
+userFcn  libBNMR.so ExpRlx 3 4
 
 ###############################################################
 FUNCTIONS
@@ -28,12 +27,11 @@ fittype         2         (asymmetry fit)
 alpha           1
 forward         3 
 backward        4 
-data            11      800     11      800     
-#backgr.fix 0
+data            11      910     11      910     
 background      1       9       1       9          # estimated bkg: 8.0000 / 9.6250
 t0              10.0    10.0    
 map             2    5    0    0    0    0    0    0    0    0
-fit             0.5     8      
+fit             0.2     9      
 packing         5
 
 RUN 045674 BNMR TRIUMF MUD   (name beamline institute data-file-format)
@@ -41,15 +39,13 @@ fittype         2         (asymmetry fit)
 alpha           1
 forward         5 
 backward        6 
-data            11      800     11      800     
-#backgr.fix 0
+data            11      910     11      910     
 background      1       9       1       9          # estimated bkg: 11.6250 / 15.6250
 t0              10.0    10.0    
 map             2    6    0    0    0    0    0    0    0    0
-fit             0.5     8      
+fit             0.2     9      
 packing         5
 
-
 ###############################################################
 COMMANDS
 MINIMIZE
@@ -68,9 +64,9 @@ FOURIER
 units            MHz    # units either 'Gauss', 'Tesla', 'MHz', or 'Mc/s'
 fourier_power    12
 apodization      STRONG  # 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            FRQMIN  FRQMAX
 ###############################################################
-STATISTIC --- 2015-04-14 11:00:19
-  chisq = 399.5, NDF = 290, chisq/NDF = 1.377736
+STATISTIC --- 2019-05-03 17:05:58
+  chisq = 566.6, NDF = 346, chisq/NDF = 1.637584

doc/examples/BNMRlibs/test-ExpRlx.msr

@@ -0,0 +1,53 @@
+LaAlO3,  SLR, 30G, 150K, Bias=23 kV, Ix=0A, Iy=+3A, aligned, beam on=1s
+###############################################################
+FITPARAMETER
+###############################################################
+#     No     Name       Value    Err     Min  Max                  
+        1 Alpha       1         0           none        
+        2 Asy         0.05992   0.00063     none        0       0.2     
+        3 T           1         0           none        
+        4 Rlx         1.143     0.023       none        0       100     
+
+###############################################################
+THEORY
+###############################################################
+asymmetry      2
+userFcn  libBNMR ExpRlx 3 4
+
+###############################################################
+RUN 045674 BNMR TRIUMF MUD   (name beamline institute data-file-format)
+fittype         5         (beta-NMR fit)
+alpha           1
+forward         3 5 
+backward        4 6 
+data            11      910     11      910     
+background      1       9       1       9          # estimated bkg: 8.0000 / 9.6250
+t0              10.0    10.0    10.0    10.0    
+map             0    0    0    0    0    0    0    0    0    0
+fit             0.2     9      
+packing         5
+
+###############################################################
+COMMANDS
+MINIMIZE
+HESSE
+SAVE
+
+###############################################################
+PLOT 5   (beta-NMR asymmetry plot)
+runs     1   
+use_fit_ranges
+view_packing 10
+
+
+###############################################################
+FOURIER
+units            MHz    # units either 'Gauss', 'Tesla', 'MHz', or 'Mc/s'
+fourier_power    12
+apodization      STRONG  # NONE, WEAK, MEDIUM, STRONG
+plot             POWER   # REAL, IMAG, REAL_AND_IMAG, POWER, PHASE, PHASE_OPT_REAL
+phase            8
+#range            FRQMIN  FRQMAX
+###############################################################
+STATISTIC --- 2019-05-03 17:06:29
+  chisq = 419.1, NDF = 173, chisq/NDF = 2.422357

doc/examples/BNMRlibs/test-SExpRlx-hel.msr

@@ -0,0 +1,73 @@
+LaAlO3,  SLR, 30G, 150K, Bias=23 kV, Ix=0A, Iy=+3A, aligned, beam on=1s
+###############################################################
+FITPARAMETER
+###############################################################
+#     No     Name       Value    Err     Min  Max                  
+        1 Alpha       1.11589   0.00037     none        
+        2 Asy         0.1121    0.0094      none        0       0.2     
+        3 T           1         0           none        
+        4 Rlx         4.12      0.87        none        0       15000   
+        5 Beta        0.434     0.031       none        0.3     2       
+        6 One         1         0           none        
+        7 FlHel       -1.048    0.023       none        -2      0       
+
+###############################################################
+THEORY
+###############################################################
+asymmetry   fun1
+userFcn  libBNMR SExpRlx 3 4 5
+
+###############################################################
+FUNCTIONS
+###############################################################
+fun1 = 0.5 * map1 * map2
+
+###############################################################
+RUN 045674 BNMR TRIUMF MUD   (name beamline institute data-file-format)
+fittype         2         (asymmetry fit)
+alpha           1
+forward         3 
+backward        4 
+data            11      1000    11      1000    
+background      1       9       1       9          # estimated bkg: 8.0000 / 9.6250
+t0              10.0    10.0   
+map             2    6    0    0    0    0    0    0    0    0
+fit             0.2     9      
+packing         5
+
+RUN 045674 BNMR TRIUMF MUD   (name beamline institute data-file-format)
+fittype         2         (asymmetry fit)
+alpha           1
+forward         5 
+backward        6 
+data            11      1000    11      1000    
+background      1       9       1       9          # estimated bkg: 11.6250 / 15.6250
+t0              10.0    10.0    
+map             2    7    0    0    0    0    0    0    0    0
+fit             0.2     9      
+packing         5
+
+###############################################################
+COMMANDS
+MINIMIZE
+HESSE
+SAVE
+
+###############################################################
+PLOT 2   (asymmetry plot)
+runs     1   2   
+use_fit_ranges
+view_packing 10
+
+
+###############################################################
+FOURIER
+units            MHz    # units either 'Gauss', 'Tesla', 'MHz', or 'Mc/s'
+fourier_power    12
+apodization      STRONG  # NONE, WEAK, MEDIUM, STRONG
+plot             POWER   # REAL, IMAG, REAL_AND_IMAG, POWER, PHASE, PHASE_OPT_REAL
+phase            8
+#range            FRQMIN  FRQMAX
+###############################################################
+STATISTIC --- 2019-05-01 11:29:06
+  chisq = 358.6, NDF = 345, chisq/NDF = 1.039300

doc/examples/BNMRlibs/test-SExpRlx.msr

@@ -0,0 +1,54 @@
+LaAlO3,  SLR, 30G, 150K, Bias=23 kV, Ix=0A, Iy=+3A, aligned, beam on=1s
+###############################################################
+FITPARAMETER
+###############################################################
+#     No     Name       Value    Err     Min  Max                  
+        1 Alpha       0.9       1.0         none        
+        2 Asy         0.115     0.012       none        0       0.2     
+        3 T           1         0           none        
+        4 Rlx         4.16      0.88        none        0       100     
+        5 Beta        0.433     0.031       none        0.3     2       
+
+###############################################################
+THEORY
+###############################################################
+asymmetry      2
+userFcn  libBNMR SExpRlx 3 4 5
+
+###############################################################
+RUN 045674 BNMR TRIUMF MUD   (name beamline institute data-file-format)
+fittype         5         (beta-NMR fit)
+alpha           1
+forward         3 5 
+backward        4 6 
+data            11      910    11      910    
+background      1       9       1       9          # estimated bkg: 8.0000 / 9.6250
+t0              10.0    10.0    10.0    10.0    
+map             0    0    0    0    0    0    0    0    0    0
+fit             0.2     9      
+packing         5
+
+###############################################################
+COMMANDS
+MINIMIZE
+HESSE
+SAVE
+
+###############################################################
+PLOT 5   (beta-NMR asymmetry plot)
+runs     1   
+use_fit_ranges
+view_packing 10
+
+
+###############################################################
+FOURIER
+units            MHz    # units either 'Gauss', 'Tesla', 'MHz', or 'Mc/s'
+fourier_power    12
+apodization      STRONG  # NONE, WEAK, MEDIUM, STRONG
+plot             POWER   # REAL, IMAG, REAL_AND_IMAG, POWER, PHASE, PHASE_OPT_REAL
+phase            8
+#range            FRQMIN  FRQMAX
+###############################################################
+STATISTIC --- 2019-05-03 17:07:01
+  chisq = 210.2, NDF = 171, chisq/NDF = 1.229344

doc/examples/DepthProfiles/1300Ar/1300Ar_5G_260K_asym.msr

@@ -0,0 +1,57 @@
+n/a
+###############################################################
+FITPARAMETER
+#      Nr. Name        Value     Step      Pos_Error  Boundaries    
+        1 f1          0.1531    0.0078      none        
+        2 f2          0.04051   0.00021     none        
+        3 f3          0.00447   0.00054     none        
+        4 x1          39.7      6.4         none        
+        5 x2          103.8     4.8         none        
+
+###############################################################
+THEORY
+userFcn  libPDepthProfile PDepthProfile 1 2 3 4 5
+
+###############################################################
+RUN data/1300Ar_PECVD_Escan_260K_5G_withDiaFrac MUE4 PSI DAT   (name beamline institute data-file-format)
+fittype         8         (non muSR fit)
+map             0    0    0    0    0    0    0    0    0    0
+xy-data         dataE    AsymCorrected
+fit             1       25     
+packing         1
+
+###############################################################
+COMMANDS
+MINIMIZE
+#HESSE
+MINOS
+SAVE
+
+###############################################################
+PLOT 8   (non muSR plot)
+runs     1   
+range    0   25
+
+###############################################################
+STATISTIC --- 2023-02-16 15:19:15
+  chisq = 28.6, NDF = 10, chisq/NDF = 2.856386
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+

doc/examples/DepthProfiles/1300Ar/1300Ar_5G_260K_diaFrac.msr

@@ -0,0 +1,57 @@
+n/a
+###############################################################
+FITPARAMETER
+#      Nr. Name        Value     Step      Pos_Error  Boundaries    
+        1 f1          0.379     -0.014      0.014       
+        2 f2          0.1866    -0.0034     0.0034      
+        3 f3          0.0201    -0.0024     0.0024      
+        4 x1          55.9      1.1         none        
+        5 x2          103.80    0.19        none        
+
+###############################################################
+THEORY
+userFcn  libPDepthProfile PDepthProfile 1 2 3 4 5
+
+###############################################################
+RUN data/1300Ar_PECVD_Escan_260K_5G_withDiaFrac MUE4 PSI DAT   (name beamline institute data-file-format)
+fittype         8         (non muSR fit)
+map             0    0    0    0    0    0    0    0    0    0
+xy-data         dataE    DiaFrac 
+fit             1       25     
+packing         1
+
+###############################################################
+COMMANDS
+MINIMIZE
+#HESSE
+MINOS
+SAVE
+
+###############################################################
+PLOT 8   (non muSR plot)
+runs     1   
+range    0   25
+
+###############################################################
+STATISTIC --- 2023-02-16 15:20:11
+  chisq = 28.3, NDF = 10, chisq/NDF = 2.831612
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+

doc/examples/DepthProfiles/1300Ar/TRIMSP/SiC_1300x_52nm_48nm_E1000.rge

@@ -0,0 +1,55 @@
+ DEPTH      PARTICLES
+     5.        1085
+    15.        2257
+    25.        2936
+    35.        3431
+    45.        3826
+    55.        4232
+    65.        4472
+    75.        4777
+    85.        4907
+    95.        5151
+   105.        5117
+   115.        5205
+   125.        5038
+   135.        4803
+   145.        4568
+   155.        4366
+   165.        3973
+   175.        3570
+   185.        3174
+   195.        2766
+   205.        2294
+   215.        1932
+   225.        1520
+   235.        1279
+   245.         950
+   255.         737
+   265.         503
+   275.         374
+   285.         243
+   295.         181
+   305.         126
+   315.          75
+   325.          45
+   335.          27
+   345.          15
+   355.           8
+   365.           2
+   375.           2
+   385.           0
+   395.           0
+   405.           0
+   415.           0
+   425.           0
+   435.           0
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+   455.           0
+   465.           0
+   475.           0
+   485.           0
+   495.           0
+   505.           0
+   515.           0
+   525.           0
+   535.           0

doc/examples/DepthProfiles/1300Ar/TRIMSP/SiC_1300x_52nm_48nm_E10000.rge

@@ -0,0 +1,128 @@
+ DEPTH      PARTICLES
+     5.           7
+    15.          12
+    25.          20
+    35.          19
+    45.          23
+    55.          38
+    65.          23
+    75.          29
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doc/examples/DepthProfiles/1300Ar/TRIMSP/SiC_1300x_52nm_48nm_E11000.rge

@@ -0,0 +1,137 @@
+ DEPTH      PARTICLES
+     5.           5
+    15.           5
+    25.          15
+    35.          15
+    45.          28
+    55.          23
+    65.          23
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doc/examples/DepthProfiles/1300Ar/TRIMSP/SiC_1300x_52nm_48nm_E12000.rge

@@ -0,0 +1,144 @@
+ DEPTH      PARTICLES
+     5.           1
+    15.          13
+    25.          11
+    35.           8
+    45.          18
+    55.          13
+    65.          12
+    75.          14
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doc/examples/DepthProfiles/1300Ar/TRIMSP/SiC_1300x_52nm_48nm_E13000.rge

@@ -0,0 +1,151 @@
+ DEPTH      PARTICLES
+     5.           3
+    15.           5
+    25.          10
+    35.           9
+    45.          14
+    55.          10
+    65.           5
+    75.          15
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doc/examples/DepthProfiles/1300Ar/TRIMSP/SiC_1300x_52nm_48nm_E14000.rge

@@ -0,0 +1,160 @@
+ DEPTH      PARTICLES
+     5.           4
+    15.           0
+    25.          13
+    35.          12
+    45.           3
+    55.          13
+    65.          12
+    75.          13
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doc/examples/DepthProfiles/1300Ar/TRIMSP/SiC_1300x_52nm_48nm_E15000.rge

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doc/examples/DepthProfiles/1300Ar/TRIMSP/SiC_1300x_52nm_48nm_E16000.rge

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doc/examples/DepthProfiles/1300Ar/TRIMSP/SiC_1300x_52nm_48nm_E17000.rge

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doc/examples/DepthProfiles/1300Ar/TRIMSP/SiC_1300x_52nm_48nm_E18000.rge

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doc/examples/DepthProfiles/1300Ar/TRIMSP/SiC_1300x_52nm_48nm_E19000.rge

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doc/examples/DepthProfiles/1300Ar/TRIMSP/SiC_1300x_52nm_48nm_E2000.rge

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doc/examples/DepthProfiles/1300Ar/TRIMSP/SiC_1300x_52nm_48nm_E20000.rge

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doc/examples/DepthProfiles/1300Ar/TRIMSP/SiC_1300x_52nm_48nm_E21000.rge

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doc/examples/DepthProfiles/1300Ar/TRIMSP/SiC_1300x_52nm_48nm_E22000.rge

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doc/examples/DepthProfiles/1300Ar/TRIMSP/SiC_1300x_52nm_48nm_E23000.rge

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doc/examples/DepthProfiles/1300Ar/TRIMSP/SiC_1300x_52nm_48nm_E3000.rge

@@ -0,0 +1,74 @@
+ DEPTH      PARTICLES
+     5.          91
+    15.         231
+    25.         307
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doc/examples/DepthProfiles/1300Ar/TRIMSP/SiC_1300x_52nm_48nm_E4000.rge

@@ -0,0 +1,82 @@
+ DEPTH      PARTICLES
+     5.          53
+    15.         125
+    25.         165
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+   805.           0

doc/examples/DepthProfiles/1300Ar/TRIMSP/SiC_1300x_52nm_48nm_E5000.rge

@@ -0,0 +1,91 @@
+ DEPTH      PARTICLES
+     5.          36
+    15.          86
+    25.          84
+    35.         131
+    45.         125
+    55.         157
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doc/examples/DepthProfiles/1300Ar/TRIMSP/SiC_1300x_52nm_48nm_E6000.rge

@@ -0,0 +1,99 @@
+ DEPTH      PARTICLES
+     5.          28
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doc/examples/DepthProfiles/1300Ar/TRIMSP/SiC_1300x_52nm_48nm_E7000.rge

@@ -0,0 +1,106 @@
+ DEPTH      PARTICLES
+     5.          13
+    15.          29
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+    45.          58
+    55.          86
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doc/examples/DepthProfiles/1300Ar/TRIMSP/SiC_1300x_52nm_48nm_E8000.rge

@@ -0,0 +1,113 @@
+ DEPTH      PARTICLES
+     5.          10
+    15.          26
+    25.          43
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+    55.          56
+    65.          47
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doc/examples/DepthProfiles/1300Ar/TRIMSP/SiC_1300x_52nm_48nm_E9000.rge

@@ -0,0 +1,120 @@
+ DEPTH      PARTICLES
+     5.           9
+    15.          14
+    25.          24
+    35.          22
+    45.          36
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doc/examples/DepthProfiles/1300Ar/data/1300Ar_PECVD_Escan_260K_5G_withDiaFrac.dat

@@ -0,0 +1,16 @@
+dataT   dataTErr   dataB   dataE   dataTr   dataRALRAR   dataRATRAB   dataSpinRot   Asym_Mu   Asym_MuPosErr   Asym_MuNegErr   Lambda_Mu   Lambda_MuPosErr   Lambda_MuNegErr   freq_Mu1   freq_Mu1PosErr   freq_Mu1NegErr   Asym_muon   Asym_muonPosErr   Asym_muonNegErr   Sigma_muon   Sigma_muonPosErr   Sigma_muonNegErr   field   fieldPosErr   fieldNegErr   ph_LR   ph_LRPosErr   ph_LRNegErr   Alpha_LR   Alpha_LRPosErr   Alpha_LRNegErr   relph_TB   relph_TBPosErr   relph_TBNegErr   relph_TB_Mu   relph_TB_MuPosErr   relph_TB_MuNegErr   Alpha_TB   Alpha_TBPosErr   Alpha_TBNegErr   Zero   ZeroPosErr   ZeroNegErr   freqMu2   freqMu2PosErr   freqMu2NegErr   Asym_MuSiO2   Asym_MuSiO2PosErr   Asym_MuSiO2NegErr   Lambda_MuSiO2   Lambda_MuSiO2PosErr   Lambda_MuSiO2NegErr   freqMuSiO2   freqMuSiO2PosErr   freqMuSiO2NegErr   CHISQ   NDF   CHISQred   RUN   AsymCorrected   AsymCorrectedErr   AsymAg   DiaFrac   DiaFracErr
+  260.0000     0.0060     4.4400     6.9980    16.4946    -0.0100    -0.0090   -10.0000     0.0000     0.0000     0.0000     0.0000     0.0000     0.0000     9.2100     0.0000     0.0000     0.0730     0.0012     0.0011     0.1359     0.0079     0.0080     7.0900     0.0270     0.0310   363.4600     0.8000     0.7800     1.0099     0.0019     0.0019   -90.0000     0.0000     0.0000    90.0000     0.0000     0.0000     0.9959     0.0017     0.0017     0.0000     0.0000     0.0000    10.8000     0.0000     0.0000     0.0813     0.0102     0.0090     2.1300     0.3700     0.3200     0.0000     0.0000     0.0000  2320.3999  2224.0000     1.0433  3817.0000     0.0565     0.0012     0.2019     0.2797     0.0059
+  260.0000     0.0050     4.4500     8.9961    16.4946    -0.0100    -0.0090   -10.0000     0.0000     0.0000     0.0000     0.0000     0.0000     0.0000     9.2100     0.0000     0.0000     0.0608     0.0011     0.0011     0.1190     0.0097     0.0100     7.1670     0.0110     0.0120   359.4000     0.7900     0.7900     1.0072     0.0018     0.0018   -90.0000     0.0000     0.0000    90.0000     0.0000     0.0000     0.9898     0.0016     0.0016     0.0000     0.0000     0.0000    10.8000     0.0000     0.0000     0.0765     0.0058     0.0055     1.1400     0.1400     0.1300     0.0000     0.0000     0.0000  2366.3999  2224.0000     1.0640  3818.0000     0.0462     0.0011     0.2110     0.2190     0.0052
+  260.0000     0.0060     4.4510     9.9949    16.4946    -0.0100    -0.0090   -10.0000     0.0000     0.0000     0.0000     0.0000     0.0000     0.0000     9.2100     0.0000     0.0000     0.0586     0.0011     0.0011     0.1100     0.0110     0.0110     7.1628     0.0096     0.0101   358.3500     0.8000     0.8000     1.0097     0.0018     0.0018   -90.0000     0.0000     0.0000    90.0000     0.0000     0.0000     0.9877     0.0016     0.0016     0.0000     0.0000     0.0000    10.8000     0.0000     0.0000     0.0781     0.0054     0.0051     1.1600     0.1200     0.1100     0.0000     0.0000     0.0000  2404.7000  2224.0000     1.0812  3819.0000     0.0445     0.0011     0.2139     0.2080     0.0051
+  260.0000     0.0050     4.4480    10.9940    16.4946    -0.0100    -0.0090   -10.0000     0.0000     0.0000     0.0000     0.0000     0.0000     0.0000     9.2100     0.0000     0.0000     0.0565     0.0011     0.0011     0.1060     0.0110     0.0110     7.0730     0.0200     0.0210   358.7500     0.9000     0.9000     1.0121     0.0018     0.0018   -90.0000     0.0000     0.0000    90.0000     0.0000     0.0000     0.9882     0.0016     0.0016     0.0000     0.0000     0.0000    10.8000     0.0000     0.0000     0.0910     0.0081     0.0075     1.9600     0.2400     0.2100     0.0000     0.0000     0.0000  2387.1001  2224.0000     1.0733  3820.0000     0.0427     0.0011     0.2161     0.1977     0.0051
+  260.0000     0.0050     4.4500    11.9930    16.4946    -0.0090    -0.0090   -10.0000     0.0000     0.0000     0.0000     0.0000     0.0000     0.0000     9.2100     0.0000     0.0000     0.0548     0.0011     0.0011     0.1210     0.0100     0.0110     7.1610     0.0140     0.0160   358.4900     0.8800     0.8700     1.0151     0.0018     0.0018   -90.0000     0.0000     0.0000    90.0000     0.0000     0.0000     0.9912     0.0016     0.0016     0.0000     0.0000     0.0000    10.8000     0.0000     0.0000     0.0470     0.0053     0.0048     1.0500     0.2000     0.1600     0.0000     0.0000     0.0000  2299.3000  2224.0000     1.0339  3821.0000     0.0412     0.0011     0.2178     0.1893     0.0051
+  260.0000     0.0060     4.4500    12.9921    16.4946    -0.0090    -0.0090   -10.0000     0.0237     0.0039     0.0037     0.7300     0.1600     0.1400     0.0000     0.0000     0.0000     0.0432     0.0013     0.0013     0.1090     0.0150     0.0160     6.6470     0.0520     0.0520   362.9000     1.5000     1.5000     1.0200     0.0022     0.0022   -90.0000     0.0000     0.0000    90.0000     0.0000     0.0000     0.9875     0.0018     0.0018     0.0000     0.0000     0.0000     9.9840     0.0260     0.0270     0.0650     0.0180     0.0140     3.5200     0.9800     0.7700     0.0000     0.0000     0.0000  2256.7000  2221.0000     1.0161  3822.0000     0.0298     0.0013     0.2191     0.1358     0.0059
+  260.0000     0.0050     4.4520    13.9909    16.4946    -0.0100    -0.0090   -10.0000     0.0320     0.0058     0.0049     2.0300     0.6100     0.4500     9.1330     0.0770     0.0820     0.0375     0.0011     0.0010     0.0950     0.0170     0.0190     7.5000     0.0000     0.0000    -5.9000     1.1000     1.1000     1.0125     0.0017     0.0017   -90.0000     0.0000     0.0000    90.0000     0.0000     0.0000     0.9840     0.0015     0.0015     0.0000     0.0000     0.0000     9.9900     0.0530     0.0610     0.0000     0.0000     0.0000     0.0000     0.0000     0.0000     0.0000     0.0000     0.0000  2252.0000  2223.0000     1.0130  3823.0000     0.0241     0.0011     0.2200     0.1097     0.0050
+  260.0000     0.0050     4.4500    14.9898    16.4946    -0.0100    -0.0090   -10.0000     0.0550     0.0160     0.0110     4.2000     1.6000     1.0000     9.1090     0.0940     0.1010     0.0329     0.0011     0.0011     0.1240     0.0170     0.0180     7.5000     0.0000     0.0000    -4.6000     1.4000     1.3000     1.0149     0.0017     0.0017   -90.0000     0.0000     0.0000    90.0000     0.0000     0.0000     0.9859     0.0015     0.0015     0.0000     0.0000     0.0000    10.1400     0.1000     0.1300     0.0000     0.0000     0.0000     0.0000     0.0000     0.0000     0.0000     0.0000     0.0000  2219.8000  2223.0000     0.9986  3824.0000     0.0196     0.0011     0.2208     0.0888     0.0050
+  260.0000     0.0060     4.4500    15.9972    16.4946    -0.0100    -0.0090   -10.0000     0.0240     0.0050     0.0040     1.6400     0.5900     0.3800     9.0870     0.0610     0.0620     0.0293     0.0011     0.0011     0.1460     0.0190     0.0200     7.5000     0.0000     0.0000    -8.4000     1.6000     1.6000     1.0168     0.0019     0.0018   -90.0000     0.0000     0.0000    90.0000     0.0000     0.0000     0.9807     0.0015     0.0015     0.0000     0.0000     0.0000    10.0240     0.0520     0.0600     0.0000     0.0000     0.0000     0.0000     0.0000     0.0000     0.0000     0.0000     0.0000  2290.2000  2223.0000     1.0302  3825.0000     0.0160     0.0011     0.2214     0.0724     0.0050
+  260.0000     0.0060     4.4600    16.9959    16.4946    -0.0100    -0.0090   -10.0000     0.0455     0.0110     0.0081     2.8000     1.0000     0.7200     0.0000     0.0000     0.0000     0.0212     0.0011     0.0011     0.0770     0.0320     0.0500     7.5000     0.0000     0.0000   -12.3000     2.2000     2.2000     1.0182     0.0019     0.0018   -90.0000     0.0000     0.0000    90.0000     0.0000     0.0000     0.9827     0.0014     0.0014     0.0000     0.0000     0.0000     9.2480     0.0670     0.0590     0.0000     0.0000     0.0000     0.0000     0.0000     0.0000     0.0000     0.0000     0.0000  2312.0000  2224.0000     1.0396  3826.0000     0.0080     0.0011     0.2218     0.0359     0.0050
+  260.0000     0.0060     4.4590    17.9950    16.4946    -0.0090    -0.0090   -10.0000     0.0850     0.0250     0.0190     7.0000     1.7000     1.4000     0.0000     0.0000     0.0000     0.0194     0.0013     0.0012     0.0950     0.0320     0.0420     6.9900     0.3200     0.3400   355.5000     5.2000     5.0000     1.0173     0.0019     0.0019   -90.0000     0.0000     0.0000    90.0000     0.0000     0.0000     0.9846     0.0023     0.0021     0.0000     0.0000     0.0000     9.5800     0.1700     0.1700     0.0000     0.0000     0.0000     0.0000     0.0000     0.0000     0.0000     0.0000     0.0000  2096.3999  2223.0000     0.9431  3827.0000     0.0062     0.0013     0.2221     0.0278     0.0059
+  260.0000     0.0060     4.4600    18.9939    16.4946    -0.0100    -0.0090   -10.0000     0.0540     0.0250     0.0160     5.3000     2.4000     1.7000     0.0000     0.0000     0.0000     0.0205     0.0020     0.0017     0.1080     0.0400     0.0490     6.6700     0.4100     0.4500   358.4000     6.6000     6.3000     1.0209     0.0027     0.0025   -90.0000     0.0000     0.0000    90.0000     0.0000     0.0000     0.9832     0.0033     0.0028     0.0000     0.0000     0.0000     9.1400     0.2100     0.1900     0.0000     0.0000     0.0000     0.0000     0.0000     0.0000     0.0000     0.0000     0.0000  2133.8000  2223.0000     0.9599  3828.0000     0.0073     0.0020     0.2224     0.0327     0.0090
+  260.0000     0.0040     4.4500    19.9932    16.4946    -0.0100    -0.0090   -10.0000     0.0920     0.0550     0.0330     8.7000     3.5000     2.9000     0.0000     0.0000     0.0000     0.0173     0.0014     0.0014     0.1050     0.0420     0.0570     7.1600     0.0000     0.0000    -9.5000     3.4000     3.4000     1.0189     0.0024     0.0023   -90.0000     0.0000     0.0000    90.0000     0.0000     0.0000     0.9887     0.0018     0.0018     0.0000     0.0000     0.0000     9.3800     0.2100     0.2000     0.0000     0.0000     0.0000     0.0000     0.0000     0.0000     0.0000     0.0000     0.0000  2261.3999  2224.0000     1.0168  3829.0000     0.0041     0.0014     0.2226     0.0184     0.0063
+  260.0000     0.0040     4.4500    20.9920    16.4946    -0.0090    -0.0090   -10.0000     0.0292     0.0101     0.0076     2.0900     0.9000     0.6500     9.0670     0.0830     0.0790     0.0199     0.0015     0.0014     0.1640     0.0380     0.0370     7.1600     0.0000     0.0000   -12.2000     2.7000     2.7000     1.0147     0.0024     0.0022   -90.0000     0.0000     0.0000    90.0000     0.0000     0.0000     0.9891     0.0018     0.0018     0.0000     0.0000     0.0000    10.8640     0.0700     0.0610     0.0000     0.0000     0.0000     0.0000     0.0000     0.0000     0.0000     0.0000     0.0000  2157.5000  2223.0000     0.9705  3830.0000     0.0067     0.0015     0.2228     0.0300     0.0067
+  260.0000     0.0060     4.4490    21.9912    16.4946    -0.0090    -0.0090   -10.0000     0.0364     0.0094     0.0090     2.7000     0.8300     0.8000     9.1320     0.0840     0.0800     0.0193     0.0014     0.0013     0.1550     0.0350     0.0350     7.1600     0.0000     0.0000    -7.6000     2.7000     2.7000     1.0140     0.0022     0.0021   -90.0000     0.0000     0.0000    90.0000     0.0000     0.0000     0.9907     0.0017     0.0017     0.0000     0.0000     0.0000    10.8540     0.0830     0.1010     0.0000     0.0000     0.0000     0.0000     0.0000     0.0000     0.0000     0.0000     0.0000  2162.2000  2223.0000     0.9726  3831.0000     0.0061     0.0014     0.2229     0.0273     0.0063

doc/examples/DepthProfiles/1300Ar/depth_profile_startup.xml

@@ -0,0 +1,11 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<depthProf xmlns="http://nemu.web.psi.ch/musrfit/depthProf">
+    <comment>
+        TrimSp information
+    </comment>
+    <trim_sp>
+        <data_path>./TRIMSP/</data_path>
+        <rge_fln_pre>SiC_1300x_52nm_48nm_E</rge_fln_pre>
+        <energy_vect start="1000" stop="22000" step="1000"/>
+    </trim_sp>
+</depthProf>

doc/examples/DepthProfiles/1300x/1300x_100G_260K_diaFrac.msr

@@ -0,0 +1,57 @@
+n/a
+###############################################################
+FITPARAMETER
+#      Nr. Name        Value     Step      Pos_Error  Boundaries    
+        1 f1          0.4157    0.0029      none        0       1       
+        2 f2          0.22821   0.00058     none        0       1       
+        3 f3          0.02658   0.00045     none        0       1       
+        4 x1          42.3      1.0         none        
+        5 x2          99.5008   0.0029      none        
+
+###############################################################
+THEORY
+userFcn  libPDepthProfile PDepthProfile 1 2 3 4 5
+
+###############################################################
+RUN data/1300x_PECVD_Escan_260K_100G_withDiaFrac MUE4 PSI DAT   (name beamline institute data-file-format)
+fittype         8         (non muSR fit)
+map             0    0    0    0    0    0    0    0    0    0
+xy-data         dataE    DiaFrac 
+fit             1       22     
+packing         1
+
+###############################################################
+COMMANDS
+MINIMIZE
+#HESSE
+MINOS
+SAVE
+
+###############################################################
+PLOT 8   (non muSR plot)
+runs     1   
+range    2.5   22
+
+###############################################################
+STATISTIC --- 2023-01-31 11:22:41
+  chisq = 122.1, NDF = 14, chisq/NDF = 8.723769
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+

doc/examples/DepthProfiles/1300x/1300x_5G_260K_asym.msr

@@ -0,0 +1,57 @@
+n/a
+###############################################################
+FITPARAMETER
+#      Nr. Name        Value     Step      Pos_Error  Boundaries    
+        1 f1          0.07038   0.00053     none        
+        2 f2          0.03252   0.00055     none        -0.5    1       
+        3 x1          86.7      10.8        none        
+
+###############################################################
+THEORY
+userFcn  libPDepthProfile PDepthProfile 1 2 3
+
+###############################################################
+RUN data/1300x_PECVD_Escan_260K_5G_noDiaFrac MUE4 PSI DAT   (name beamline institute data-file-format)
+fittype         8         (non muSR fit)
+map             0    0    0    0    0    0    0    0    0    0
+xy-data         dataE    Asym_muon
+fit             1       22     
+packing         1
+
+###############################################################
+COMMANDS
+MINIMIZE
+#HESSE
+MINOS
+SAVE
+
+###############################################################
+PLOT 8   (non muSR plot)
+runs     1   
+range    0   22
+
+
+
+###############################################################
+STATISTIC --- 2023-02-16 15:29:27
+  chisq = 42.1, NDF = 6, chisq/NDF = 7.024748
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+

doc/examples/DepthProfiles/1300x/TRIMSP/SiC_1300x_52nm_48nm_E1000.rge

@@ -0,0 +1,55 @@
+ DEPTH      PARTICLES
+     5.        1085
+    15.        2257
+    25.        2936
+    35.        3431
+    45.        3826
+    55.        4232
+    65.        4472
+    75.        4777
+    85.        4907
+    95.        5151
+   105.        5117
+   115.        5205
+   125.        5038
+   135.        4803
+   145.        4568
+   155.        4366
+   165.        3973
+   175.        3570
+   185.        3174
+   195.        2766
+   205.        2294
+   215.        1932
+   225.        1520
+   235.        1279
+   245.         950
+   255.         737
+   265.         503
+   275.         374
+   285.         243
+   295.         181
+   305.         126
+   315.          75
+   325.          45
+   335.          27
+   345.          15
+   355.           8
+   365.           2
+   375.           2
+   385.           0
+   395.           0
+   405.           0
+   415.           0
+   425.           0
+   435.           0
+   445.           0
+   455.           0
+   465.           0
+   475.           0
+   485.           0
+   495.           0
+   505.           0
+   515.           0
+   525.           0
+   535.           0

doc/examples/DepthProfiles/1300x/TRIMSP/SiC_1300x_52nm_48nm_E10000.rge

@@ -0,0 +1,128 @@
+ DEPTH      PARTICLES
+     5.           7
+    15.          12
+    25.          20
+    35.          19
+    45.          23
+    55.          38
+    65.          23
+    75.          29
+    85.          33
+    95.          34
+   105.          33
+   115.          48
+   125.          38
+   135.          64
+   145.          47
+   155.          60
+   165.          48
+   175.          58
+   185.          65
+   195.          83
+   205.          80
+   215.          72
+   225.          74
+   235.          84
+   245.          87
+   255.         108
+   265.          90
+   275.         115
+   285.         126
+   295.         104
+   305.         163
+   315.         153
+   325.         150
+   335.         158
+   345.         142
+   355.         195
+   365.         204
+   375.         183
+   385.         208
+   395.         211
+   405.         251
+   415.         245
+   425.         291
+   435.         294
+   445.         340
+   455.         338
+   465.         382
+   475.         398
+   485.         420
+   495.         475
+   505.         480
+   515.         505
+   525.         578
+   535.         637
+   545.         677
+   555.         752
+   565.         746
+   575.         816
+   585.         879
+   595.        1020
+   605.        1000
+   615.        1153
+   625.        1192
+   635.        1417
+   645.        1402
+   655.        1478
+   665.        1644
+   675.        1717
+   685.        1749
+   695.        1958
+   705.        2029
+   715.        2156
+   725.        2277
+   735.        2460
+   745.        2549
+   755.        2666
+   765.        2914
+   775.        2952
+   785.        3034
+   795.        3217
+   805.        3201
+   815.        3337
+   825.        3326
+   835.        3339
+   845.        3243
+   855.        3202
+   865.        3113
+   875.        3013
+   885.        2849
+   895.        2628
+   905.        2448
+   915.        2155
+   925.        1858
+   935.        1584
+   945.        1306
+   955.        1036
+   965.         854
+   975.         626
+   985.         437
+   995.         324
+  1005.         307
+  1015.         165
+  1025.          77
+  1035.          27
+  1045.           5
+  1055.           2
+  1065.           0
+  1075.           0
+  1085.           0
+  1095.           0
+  1105.           0
+  1115.           0
+  1125.           0
+  1135.           0
+  1145.           0
+  1155.           0
+  1165.           0
+  1175.           0
+  1185.           0
+  1195.           0
+  1205.           0
+  1215.           0
+  1225.           0
+  1235.           0
+  1245.           0
+  1255.           0
+  1265.           0

doc/examples/DepthProfiles/1300x/TRIMSP/SiC_1300x_52nm_48nm_E11000.rge

@@ -0,0 +1,137 @@
+ DEPTH      PARTICLES
+     5.           5
+    15.           5
+    25.          15
+    35.          15
+    45.          28
+    55.          23
+    65.          23
+    75.          27
+    85.          21
+    95.          37
+   105.          24
+   115.          29
+   125.          28
+   135.          44
+   145.          48
+   155.          46
+   165.          44
+   175.          45
+   185.          50
+   195.          53
+   205.          48
+   215.          59
+   225.          67
+   235.          51
+   245.          73
+   255.          85
+   265.          67
+   275.          79
+   285.          73
+   295.          95
+   305.          84
+   315.          88
+   325.         101
+   335.         107
+   345.         100
+   355.         126
+   365.         144
+   375.         120
+   385.         171
+   395.         146
+   405.         147
+   415.         175
+   425.         184
+   435.         205
+   445.         232
+   455.         238
+   465.         218
+   475.         237
+   485.         265
+   495.         279
+   505.         322
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doc/examples/DepthProfiles/1300x/TRIMSP/SiC_1300x_52nm_48nm_E12000.rge

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doc/examples/DepthProfiles/1300x/TRIMSP/SiC_1300x_52nm_48nm_E13000.rge

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doc/examples/DepthProfiles/1300x/TRIMSP/SiC_1300x_52nm_48nm_E14000.rge

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doc/examples/DepthProfiles/1300x/TRIMSP/SiC_1300x_52nm_48nm_E15000.rge

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doc/examples/DepthProfiles/1300x/TRIMSP/SiC_1300x_52nm_48nm_E16000.rge

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doc/examples/DepthProfiles/1300x/TRIMSP/SiC_1300x_52nm_48nm_E17000.rge

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doc/examples/DepthProfiles/1300x/TRIMSP/SiC_1300x_52nm_48nm_E18000.rge

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doc/examples/DepthProfiles/1300x/TRIMSP/SiC_1300x_52nm_48nm_E19000.rge

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doc/examples/DepthProfiles/1300x/TRIMSP/SiC_1300x_52nm_48nm_E2000.rge

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doc/examples/DepthProfiles/1300x/TRIMSP/SiC_1300x_52nm_48nm_E20000.rge

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doc/examples/DepthProfiles/1300x/TRIMSP/SiC_1300x_52nm_48nm_E21000.rge

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doc/examples/DepthProfiles/1300x/TRIMSP/SiC_1300x_52nm_48nm_E22000.rge

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doc/examples/DepthProfiles/1300x/TRIMSP/SiC_1300x_52nm_48nm_E23000.rge

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doc/examples/DepthProfiles/1300x/TRIMSP/SiC_1300x_52nm_48nm_E3000.rge

@@ -0,0 +1,74 @@
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doc/examples/DepthProfiles/1300x/TRIMSP/SiC_1300x_52nm_48nm_E4000.rge

@@ -0,0 +1,82 @@
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doc/examples/DepthProfiles/1300x/TRIMSP/SiC_1300x_52nm_48nm_E5000.rge

@@ -0,0 +1,91 @@
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doc/examples/DepthProfiles/1300x/TRIMSP/SiC_1300x_52nm_48nm_E6000.rge

@@ -0,0 +1,99 @@
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doc/examples/DepthProfiles/1300x/TRIMSP/SiC_1300x_52nm_48nm_E7000.rge

@@ -0,0 +1,106 @@
+ DEPTH      PARTICLES
+     5.          13
+    15.          29
+    25.          37
+    35.          50
+    45.          58
+    55.          86
+    65.          56
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doc/examples/DepthProfiles/1300x/TRIMSP/SiC_1300x_52nm_48nm_E8000.rge

@@ -0,0 +1,113 @@
+ DEPTH      PARTICLES
+     5.          10
+    15.          26
+    25.          43
+    35.          41
+    45.          43
+    55.          56
+    65.          47
+    75.          59
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+   465.        1087
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+   485.        1085
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+   505.        1377
+   515.        1394
+   525.        1587
+   535.        1745
+   545.        1874
+   555.        2016
+   565.        2219
+   575.        2251
+   585.        2383
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+   645.        3266
+   655.        3327
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doc/examples/DepthProfiles/1300x/TRIMSP/SiC_1300x_52nm_48nm_E9000.rge

@@ -0,0 +1,120 @@
+ DEPTH      PARTICLES
+     5.           9
+    15.          14
+    25.          24
+    35.          22
+    45.          36
+    55.          35
+    65.          39
+    75.          43
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doc/examples/DepthProfiles/1300x/data/1300x_PECVD_Escan_260K_100G_withDiaFrac.dat

@@ -0,0 +1,20 @@
+dataT   dataTErr   dataB   dataE   dataTr   dataRALRAR   dataRATRAB   dataSpinRot   Asy   AsyPosErr   AsyNegErr   Sigma   SigmaPosErr   SigmaNegErr   Ph   PhPosErr   PhNegErr   Field   FieldPosErr   FieldNegErr   RelPh_L   RelPh_LPosErr   RelPh_LNegErr   N0_L   N0_LPosErr   N0_LNegErr   N_bkg_L   N_bkg_LPosErr   N_bkg_LNegErr   RelPh_T   RelPh_TPosErr   RelPh_TNegErr   N0_T   N0_TPosErr   N0_TNegErr   N_bkg_T   N_bkg_TPosErr   N_bkg_TNegErr   RelPh_R   RelPh_RPosErr   RelPh_RNegErr   alpha_LR   alpha_LRPosErr   alpha_LRNegErr   N_bkg_R   N_bkg_RPosErr   N_bkg_RNegErr   RelPh_B   RelPh_BPosErr   RelPh_BNegErr   alpha_TB   alpha_TBPosErr   alpha_TBNegErr   N_bkg_B   N_bkg_BPosErr   N_bkg_BNegErr   maxLH   NDF   maxLHred   RUN   AsymCorrected   AsymCorrectedErr   AsymAg   DiaFrac   DiaFracErr
+  259.9980     0.0050    99.4870    21.9908    16.4943    -0.0090    -0.0090   -10.0000     0.0189     0.0009     0.0009     0.2110     0.0370     0.0380     6.9000     3.3000     3.3000   102.0700     0.3500     0.3600     0.0000     0.0000     0.0000   307.1100     0.3400     0.3500     6.4110     0.0520     0.0520   -90.0000     0.0000     0.0000   318.1600     0.3500     0.3400     6.6130     0.0520     0.0530   180.0000     0.0000     0.0000     0.9960     0.0016     0.0016     6.6640     0.0530     0.0520    90.0000     0.0000     0.0000     0.9709     0.0015     0.0015     6.4340     0.0520     0.0520  3626.0000  3648.0000     0.9940  1768.0000     0.0056     0.0009     0.2229     0.0253     0.0041
+  260.0010     0.0050    99.4860    20.9917    16.4944    -0.0100    -0.0090   -10.0000     0.0173     0.0008     0.0008     0.1150     0.0380     0.0480    14.6000     3.3000     3.3000   101.5700     0.2900     0.2900     0.0000     0.0000     0.0000   307.7100     0.3400     0.3400     6.2450     0.0520     0.0520   -90.0000     0.0000     0.0000   319.7600     0.3500     0.3500     6.4440     0.0530     0.0530   180.0000     0.0000     0.0000     0.9888     0.0016     0.0016     6.6200     0.0520     0.0520    90.0000     0.0000     0.0000     0.9675     0.0015     0.0015     6.2600     0.0520     0.0520  3534.0000  3648.0000     0.9688  1769.0000     0.0041     0.0008     0.2228     0.0186     0.0036
+  259.9990     0.0040    99.4850    19.9929    16.4944    -0.0090    -0.0090   -10.0000     0.0189     0.0008     0.0008     0.1850     0.0310     0.0320    12.8000     3.2000     3.2000   101.5500     0.3300     0.3300     0.0000     0.0000     0.0000   307.4900     0.3400     0.3400     6.1700     0.0520     0.0510   -90.0000     0.0000     0.0000   318.8100     0.3500     0.3500     6.4530     0.0520     0.0530   180.0000     0.0000     0.0000     0.9956     0.0016     0.0016     6.5020     0.0520     0.0520    90.0000     0.0000     0.0000     0.9658     0.0015     0.0015     6.3610     0.0520     0.0520  3714.3000  3648.0000     1.0182  1770.0000     0.0057     0.0008     0.2226     0.0257     0.0038
+  260.0000     0.0040    99.4800    18.9936    16.4944    -0.0090    -0.0090   -10.0000     0.0224     0.0009     0.0009     0.1440     0.0310     0.0350    11.3000     2.5000     2.5000   101.4700     0.2400     0.2400     0.0000     0.0000     0.0000   309.8000     0.3400     0.3400     6.1220     0.0520     0.0520   -90.0000     0.0000     0.0000   320.2200     0.3500     0.3500     6.4730     0.0530     0.0530   180.0000     0.0000     0.0000     0.9840     0.0016     0.0015     6.5210     0.0520     0.0520    90.0000     0.0000     0.0000     0.9671     0.0015     0.0015     6.3290     0.0520     0.0520  3693.7000  3648.0000     1.0125  1771.0000     0.0091     0.0009     0.2224     0.0411     0.0038
+  260.0000     0.0040    99.4840    17.9948    16.4944    -0.0090    -0.0090   -10.0000     0.0227     0.0008     0.0008     0.1160     0.0280     0.0330     7.8000     2.6000     2.6000   101.5600     0.2300     0.2300     0.0000     0.0000     0.0000   309.8600     0.3400     0.3400     6.2460     0.0520     0.0520   -90.0000     0.0000     0.0000   318.6400     0.3500     0.3500     6.5590     0.0530     0.0530   180.0000     0.0000     0.0000     0.9908     0.0016     0.0016     6.5410     0.0520     0.0520    90.0000     0.0000     0.0000     0.9674     0.0015     0.0015     6.2850     0.0520     0.0520  3799.8999  3648.0000     1.0416  1772.0000     0.0094     0.0008     0.2221     0.0425     0.0036
+  259.9990     0.0030    99.4800    16.9956    16.4944    -0.0090    -0.0090   -10.0000     0.0245     0.0008     0.0008     0.0550     0.0350     0.0550     9.7000     2.3000     2.3000   101.5300     0.1900     0.1900     0.0000     0.0000     0.0000   310.9500     0.3400     0.3400     6.1020     0.0520     0.0520   -90.0000     0.0000     0.0000   319.5300     0.3500     0.3500     6.3210     0.0530     0.0520   180.0000     0.0000     0.0000     0.9998     0.0016     0.0016     6.5870     0.0530     0.0520    90.0000     0.0000     0.0000     0.9641     0.0015     0.0015     6.2840     0.0520     0.0520  3579.0000  3648.0000     0.9811  1773.0000     0.0112     0.0008     0.2218     0.0507     0.0034
+  260.0010     0.0050    99.4830    15.9969    16.4944    -0.0090    -0.0100   -10.0000     0.0270     0.0008     0.0008     0.0940     0.0250     0.0310    18.5000     2.1000     2.1000   101.0900     0.1800     0.1800     0.0000     0.0000     0.0000   310.8400     0.3400     0.3400     6.1600     0.0520     0.0520   -90.0000     0.0000     0.0000   319.8000     0.3500     0.3500     6.4640     0.0530     0.0530   180.0000     0.0000     0.0000     0.9856     0.0016     0.0015     6.6430     0.0520     0.0520    90.0000     0.0000     0.0000     0.9620     0.0015     0.0015     6.2280     0.0520     0.0520  3668.1001  3648.0000     1.0055  1774.0000     0.0138     0.0008     0.2214     0.0622     0.0035
+  260.0000     0.0050    99.4800    14.9896    16.4944    -0.0090    -0.0100   -10.0000     0.0321     0.0008     0.0008     0.1090     0.0210     0.0240    21.3000     1.8000     1.8000   100.6400     0.1500     0.1600     0.0000     0.0000     0.0000   310.5100     0.3400     0.3400     6.0220     0.0520     0.0510   -90.0000     0.0000     0.0000   320.0000     0.3500     0.3500     6.3740     0.0520     0.0530   180.0000     0.0000     0.0000     0.9995     0.0016     0.0016     6.5310     0.0520     0.0520    90.0000     0.0000     0.0000     0.9638     0.0015     0.0015     6.2240     0.0520     0.0520  3688.7000  3648.0000     1.0112  1775.0000     0.0188     0.0008     0.2208     0.0852     0.0036
+  259.9990     0.0070    99.4840    13.9908    16.4944    -0.0100    -0.0100   -10.0000     0.0378     0.0008     0.0008     0.1390     0.0160     0.0170    13.9000     1.6000     1.6000   101.2900     0.1500     0.1500     0.0000     0.0000     0.0000   309.9200     0.3400     0.3500     6.2450     0.0520     0.0520   -90.0000     0.0000     0.0000   319.7900     0.3500     0.3500     6.3790     0.0520     0.0530   180.0000     0.0000     0.0000     1.0024     0.0016     0.0016     6.5540     0.0520     0.0520    90.0000     0.0000     0.0000     0.9592     0.0015     0.0015     6.2040     0.0520     0.0510  3584.0000  3648.0000     0.9825  1776.0000     0.0244     0.0008     0.2200     0.1109     0.0036
+  260.0010     0.0070    99.4800    12.9921    16.4944    -0.0090    -0.0100   -10.0000     0.0438     0.0008     0.0008     0.1140     0.0140     0.0150    11.7000     1.3000     1.3000   101.6000     0.1200     0.1200     0.0000     0.0000     0.0000   312.5200     0.3400     0.3500     6.1510     0.0520     0.0520   -90.0000     0.0000     0.0000   320.1200     0.3500     0.3400     6.3970     0.0520     0.0530   180.0000     0.0000     0.0000     0.9942     0.0016     0.0015     6.4640     0.0520     0.0520    90.0000     0.0000     0.0000     0.9622     0.0015     0.0015     6.1950     0.0520     0.0520  3427.6001  3648.0000     0.9396  1777.0000     0.0303     0.0008     0.2191     0.1385     0.0036
+  259.9980     0.0050    99.4800    11.9928    16.4945    -0.0090    -0.0090   -10.0000     0.0517     0.0008     0.0008     0.0930     0.0140     0.0160    14.3000     1.1000     1.1000   101.3650     0.0930     0.0930     0.0000     0.0000     0.0000   311.7100     0.3400     0.3500     6.0330     0.0520     0.0510   -90.0000     0.0000     0.0000   318.4700     0.3500     0.3400     6.3530     0.0520     0.0530   180.0000     0.0000     0.0000     0.9945     0.0016     0.0015     6.6250     0.0530     0.0520    90.0000     0.0000     0.0000     0.9632     0.0015     0.0015     6.0950     0.0520     0.0510  3576.7000  3648.0000     0.9805  1778.0000     0.0381     0.0008     0.2178     0.1751     0.0036
+  260.0020     0.0070    99.4760    10.9941    16.4945    -0.0100    -0.0090   -10.0000     0.0588     0.0008     0.0008     0.1200     0.0110     0.0110    15.0300     0.9900     0.9900   101.3480     0.0880     0.0880     0.0000     0.0000     0.0000   310.9300     0.3400     0.3400     6.2370     0.0520     0.0520   -90.0000     0.0000     0.0000   318.9400     0.3500     0.3400     6.3220     0.0520     0.0530   180.0000     0.0000     0.0000     0.9972     0.0016     0.0016     6.5920     0.0520     0.0520    90.0000     0.0000     0.0000     0.9630     0.0015     0.0015     6.1340     0.0520     0.0520  3697.3999  3648.0000     1.0135  1779.0000     0.0451     0.0008     0.2161     0.2085     0.0037
+  259.9990     0.0040    99.4780     9.9949    16.4944    -0.0090    -0.0090   -10.0000     0.0637     0.0008     0.0008     0.0840     0.0120     0.0130    18.0300     0.9000     0.8900   101.1790     0.0750     0.0760     0.0000     0.0000     0.0000   309.4700     0.3400     0.3400     6.1330     0.0520     0.0510   -90.0000     0.0000     0.0000   319.3200     0.3500     0.3500     6.2810     0.0520     0.0530   180.0000     0.0000     0.0000     1.0038     0.0016     0.0016     6.6150     0.0520     0.0530    90.0000     0.0000     0.0000     0.9603     0.0015     0.0015     6.0590     0.0520     0.0510  3728.6001  3648.0000     1.0221  1780.0000     0.0497     0.0008     0.2139     0.2321     0.0036
+  260.0010     0.0060    99.4820     8.9960    16.4945    -0.0090    -0.0090   -10.0000     0.0665     0.0008     0.0008     0.1030     0.0100     0.0110    18.6200     0.8600     0.8600   101.2670     0.0740     0.0740     0.0000     0.0000     0.0000   310.4800     0.3400     0.3500     5.9660     0.0520     0.0510   -90.0000     0.0000     0.0000   318.5100     0.3500     0.3400     6.3040     0.0520     0.0530   180.0000     0.0000     0.0000     0.9986     0.0016     0.0015     6.6620     0.0520     0.0530    90.0000     0.0000     0.0000     0.9627     0.0015     0.0015     6.1230     0.0520     0.0510  3587.3000  3648.0000     0.9834  1781.0000     0.0519     0.0008     0.2110     0.2462     0.0037
+  259.9990     0.0090    99.4800     6.9982    16.4945    -0.0090    -0.0090   -10.0000     0.0715     0.0008     0.0008     0.1211     0.0086     0.0091    17.1600     0.8200     0.8200   101.1230     0.0720     0.0730     0.0000     0.0000     0.0000   313.3200     0.3400     0.3500     5.9760     0.0520     0.0520   -90.0000     0.0000     0.0000   320.7800     0.3500     0.3500     6.2370     0.0520     0.0530   180.0000     0.0000     0.0000     0.9914     0.0016     0.0015     6.5660     0.0520     0.0520    90.0000     0.0000     0.0000     0.9568     0.0015     0.0015     6.0440     0.0520     0.0510  3532.3000  3648.0000     0.9683  1782.0000     0.0549     0.0008     0.2019     0.2721     0.0039
+  260.0010     0.0070    99.4800     5.0084    11.9989    -0.0080    -0.0080   -10.0000     0.0687     0.0008     0.0008     0.1333     0.0090     0.0093    19.4000     0.8400     0.8400   101.1300     0.0760     0.0760     0.0000     0.0000     0.0000   312.8000     0.3400     0.3500     5.6030     0.0510     0.0510   -90.0000     0.0000     0.0000   315.9700     0.3500     0.3400     5.8100     0.0510     0.0520   180.0000     0.0000     0.0000     1.0046     0.0016     0.0015     6.1330     0.0520     0.0520    90.0000     0.0000     0.0000     0.9559     0.0015     0.0015     5.5120     0.0510     0.0500  3703.7000  3648.0000     1.0153  1786.0000     0.0564     0.0008     0.1714     0.3291     0.0047
+  259.9990     0.0040    99.4800     4.0095    11.9989    -0.0080    -0.0080   -10.0000     0.0726     0.0008     0.0008     0.1520     0.0079     0.0080    18.6900     0.8300     0.8300   101.2350     0.0780     0.0780     0.0000     0.0000     0.0000   305.7300     0.3400     0.3400     5.5080     0.0510     0.0500   -90.0000     0.0000     0.0000   317.1300     0.3500     0.3400     5.8440     0.0520     0.0520   180.0000     0.0000     0.0000     1.0351     0.0016     0.0016     6.3320     0.0520     0.0520    90.0000     0.0000     0.0000     0.9532     0.0015     0.0015     5.7120     0.0510     0.0510  3675.3999  3648.0000     1.0075  1785.0000     0.0582     0.0008     0.1632     0.3564     0.0049
+  260.0000     0.0060    99.4800     3.0103    11.9989    -0.0080    -0.0080   -10.0000     0.0790     0.0008     0.0008     0.1489     0.0072     0.0073    18.9800     0.7500     0.7500   101.2100     0.0700     0.0700     0.0000     0.0000     0.0000   305.8800     0.3300     0.3400     4.7740     0.0500     0.0490   -90.0000     0.0000     0.0000   321.4400     0.3500     0.3400     5.1770     0.0510     0.0510   180.0000     0.0000     0.0000     1.0492     0.0016     0.0016     5.5870     0.0520     0.0510    90.0000     0.0000     0.0000     0.9542     0.0015     0.0015     4.9270     0.0500     0.0500  3820.3000  3648.0000     1.0472  1784.0000     0.0596     0.0008     0.1505     0.3960     0.0052
+  260.0010     0.0050    99.4800     2.0117    11.9990    -0.0080    -0.0080   -10.0000     0.0876     0.0008     0.0008     0.1596     0.0066     0.0068    20.6200     0.6800     0.6800   100.8890     0.0650     0.0650     0.0000     0.0000     0.0000   303.6100     0.3400     0.3400     5.4660     0.0510     0.0500   -90.0000     0.0000     0.0000   318.3500     0.3500     0.3400     5.7660     0.0510     0.0520   180.0000     0.0000     0.0000     1.0639     0.0017     0.0016     6.2660     0.0530     0.0530    90.0000     0.0000     0.0000     0.9477     0.0015     0.0015     5.6210     0.0510     0.0500  3815.1001  3648.0000     1.0458  1783.0000     0.0568     0.0008     0.1291     0.4397     0.0063

doc/examples/DepthProfiles/1300x/data/1300x_PECVD_Escan_260K_5G_noDiaFrac.dat

@@ -0,0 +1,10 @@
+dataT   dataTErr   dataB   dataE   dataTr   dataRALRAR   dataRATRAB   dataSpinRot   Asym_Mu   Asym_MuPosErr   Asym_MuNegErr   Lambda_Mu   Lambda_MuPosErr   Lambda_MuNegErr   freq_Mu1   freq_Mu1PosErr   freq_Mu1NegErr   Asym_muon   Asym_muonPosErr   Asym_muonNegErr   Sigma_muon   Sigma_muonPosErr   Sigma_muonNegErr   field   fieldPosErr   fieldNegErr   ph_LR   ph_LRPosErr   ph_LRNegErr   Alpha_LR   Alpha_LRPosErr   Alpha_LRNegErr   relph_TB   relph_TBPosErr   relph_TBNegErr   relph_TB_Mu   relph_TB_MuPosErr   relph_TB_MuNegErr   Alpha_TB   Alpha_TBPosErr   Alpha_TBNegErr   Zero   ZeroPosErr   ZeroNegErr   freqMu2   freqMu2PosErr   freqMu2NegErr   Asym_MuSiO2   Asym_MuSiO2PosErr   Asym_MuSiO2NegErr   Lambda_MuSiO2   Lambda_MuSiO2PosErr   Lambda_MuSiO2NegErr   freqMuSiO2   freqMuSiO2PosErr   freqMuSiO2NegErr   CHISQ   NDF   CHISQred   RUN
+259.999   0.006   4.48   21.9909   16.4945   -0.009   -0.009   -10   0.055   0.064   -0.021   7.2   5.8   -2.7   8.858   0.075   0.084   0.0282   0.0016   -0.0015   0.108   0.025   -0.028   6.03   0.17   0.18   -11.5   2.9   -2.9   0.9996   0.0026   -0.0025   -90   0   0   90   0   0   1.0013   0.0024   -0.0023   0   0   0   10.314   0.094   0.11   0   0   0   0   0   0   0   0   0   8745.7   8897   0.982994   1793
+260   0.009   4.48   19.9929   16.4945   -0.009   -0.009   -10   0.037   0.02   -0.011   4.7   2.9   -1.5   8.858   0.075   0.084   0.0306   0.0019   -0.0017   0.137   0.027   -0.028   6.03   0.17   0.18   -11   3   -2.9   1.0026   0.0033   -0.003   -90   0   0   90   0   0   1.0027   0.0025   -0.0024   0   0   0   10.314   0.094   0.11   0   0   0   0   0   0   0   0   0   8745.7   8897   0.982994   1794
+260   0.006   4.473   17.9949   16.4945   -0.009   -0.01   -10   0.046   0.017   -0.01   4.7   2   -1.2   8.858   0.075   0.084   0.0341   0.0018   -0.0017   0.212   0.022   -0.02   6.03   0.17   0.18   -13.3   2.4   -2.4   1.0115   0.0031   -0.0029   -90   0   0   90   0   0   0.9954   0.0021   -0.0021   0   0   0   10.314   0.094   0.11   0   0   0   0   0   0   0   0   0   8745.7   8897   0.982994   1795
+260   0.007   4.475   15.997   16.4945   -0.009   -0.01   -10   0.0455   0.0104   -0.0083   3.7   1   -0.76   8.858   0.075   0.084   0.036   0.0019   -0.0018   0.21   0.023   -0.022   6.03   0.17   0.18   -6.1   2.4   -2.3   1.0039   0.0033   -0.0031   -90   0   0   90   0   0   1.0009   0.0022   -0.0021   0   0   0   10.314   0.094   0.11   0   0   0   0   0   0   0   0   0   8745.7   8897   0.982994   1796
+260   0.007   4.476   13.9907   16.4945   -0.01   -0.01   -10   0.0258   0.0126   0.0087   2   1.4   0.87   10.16   0.12   0.1   0.0404   0.0039   0.0032   0.181   0.032   0.03   6.05   0.41   0.46   -0.6   4.5   4.4   0.9992   0.0061   0.0047   -90   0   0   90   0   0   1.0043   0.0052   0.0047   0   0   0   8.91   0.1   0.165   0   0   0   0   0   0   0   0   0   2038.1   2222   0.9172   1797
+260   0.007   4.479   11.9929   16.4945   -0.009   -0.009   -10   0   0   0   0   0   0   9.2   9.9   9.9   0.0499   0.0008   0.0008   0.1606   0.0092   0.0092   7.0309   0.0077   0.0077   -7.81   0.57   0.57   0.995   0.0015   0.0015   -90   0   0   90   0   0   0.9879   0.0009   0.0009   0   0   0   -77.1   33.7   33.7   0.053   0.013   0.013   1.63   0.53   0.53   0   0   0   2197.2   2222   0.9888   1798
+260   0.008   4.477   9.995   16.4945   -0.009   -0.009   -10   0   0   0   0   0   0   8.4   2.1   8.4   0.0589   0.0011   0.0011   0.119   0.01   0.01   7.004   0.013   0.014   -5   0.83   0.83   0.989   0.0018   0.0018   -90   0   0   90   0   0   0.9878   0.0016   0.0016   0   0   0   9.2   1.4   1.4   0.0855   0.0073   0.0067   1.53   0.2   0.17   0   0   0   2299.1001   2222   1.0347   1799
+260   0.006   4.472   8.9961   16.4945   -0.01   -0.009   -10   0   0   0   0   0   0   10.214   0   0   0.0701   0.0011   0.001   0.0972   0.0091   0.0097   7.327   0.011   0.011   -3.59   0.67   0.67   0.9619   0.0017   0.0017   -90   0   0   90   0   0   0.988   0.0016   0.0016   0   0   0   6.764   0   0   0.0732   0.0055   0.0052   1.25   0.14   0.13   0   0   0   2343.2   2224   1.0536   1788
+260   0.006   4.468   6.9983   16.4945   -0.01   -0.009   -10   0   0   0   0   0   0   10.214   0   0   0.0708   0.0011   0.0011   0.106   0.0086   0.009   7.295   0.016   0.017   -0.84   0.69   0.69   0.9535   0.0017   0.0017   -90   0   0   90   0   0   0.9884   0.0016   0.0016   0   0   0   6.764   0   0   0.0681   0.0064   0.0059   1.6   0.2   0.18   0   0   0   2271.8   2224   1.0215   1787

doc/examples/DepthProfiles/1300x/depth_profile_startup.xml

@@ -0,0 +1,11 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<depthProf xmlns="http://nemu.web.psi.ch/musrfit/depthProf">
+    <comment>
+        TrimSp information
+    </comment>
+    <trim_sp>
+        <data_path>./TRIMSP/</data_path>
+        <rge_fln_pre>SiC_1300x_52nm_48nm_E</rge_fln_pre>
+        <energy_vect start="1000" stop="22000" step="1000"/>
+    </trim_sp>
+</depthProf>

doc/examples/DepthProfiles/PECVD_Si/Si_PECVD_100G_260K_asym.msr

@@ -0,0 +1,55 @@
+n/a
+###############################################################
+FITPARAMETER
+#      Nr.   Name        Value     Step      Pos_Error  Boundaries    
+        1 f1          0.11295   -0.00071    0.00071     0       1       
+        2 f2          0.06790   -0.00078    0.00078     
+        3 x1          107.83    0.17        none        
+
+###############################################################
+THEORY
+userFcn  libPDepthProfile PDepthProfile 1 2 3
+
+###############################################################
+RUN data/Si10_260K_Escan_100GTF_withDiaFrac MUE4 PSI DAT   (name beamline institute data-file-format)
+fittype         8         (non muSR fit)
+map             0    0    0    0    0    0    0    0    0    0
+xy-data         dataE    Asy     
+fit             5       22     
+packing         1
+
+###############################################################
+COMMANDS
+MINIMIZE
+#HESSE
+MINOS
+SAVE
+
+###############################################################
+PLOT 8   (non muSR plot)
+runs     1   
+range    5   25
+
+###############################################################
+STATISTIC --- 2023-02-16 15:35:37
+  chisq = 18.8, NDF = 8, chisq/NDF = 2.354740
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+

doc/examples/DepthProfiles/PECVD_Si/Si_PECVD_100G_260K_diaFrac.msr

@@ -0,0 +1,55 @@
+n/a
+###############################################################
+FITPARAMETER
+#      Nr.   Name        Value     Step      Pos_Error  Boundaries    
+        1 f1          0.49635   0.00035     none        0       1       
+        2 f2          0.26714   0.00057     none        
+        3 x1          107.4     3.3         none        
+
+###############################################################
+THEORY
+userFcn  libPDepthProfile PDepthProfile 1 2 3
+
+###############################################################
+RUN data/Si10_260K_Escan_100GTF_withDiaFrac MUE4 PSI DAT   (name beamline institute data-file-format)
+fittype         8         (non muSR fit)
+map             0    0    0    0    0    0    0    0    0    0
+xy-data         dataE    DiaFrac 
+fit             5       22     
+packing         1
+
+###############################################################
+COMMANDS
+MINIMIZE
+#HESSE
+MINOS
+SAVE
+
+###############################################################
+PLOT 8   (non muSR plot)
+runs     1   
+range    0   25
+
+###############################################################
+STATISTIC --- 2023-02-16 15:47:33
+  chisq = 13.2, NDF = 8, chisq/NDF = 1.645757
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+

doc/examples/DepthProfiles/PECVD_Si/TRIMSP/Si10_2.0_E1000.rge

@@ -0,0 +1,54 @@
+ DEPTH      PARTICLES
+     5.          99
+    15.         225
+    25.         275
+    35.         306
+    45.         345
+    55.         396
+    65.         419
+    75.         480
+    85.         478
+    95.         478
+   105.         510
+   115.         501
+   125.         505
+   135.         487
+   145.         456
+   155.         425
+   165.         389
+   175.         400
+   185.         330
+   195.         299
+   205.         252
+   215.         218
+   225.         191
+   235.         144
+   245.         112
+   255.          84
+   265.          76
+   275.          53
+   285.          36
+   295.          25
+   305.          24
+   315.          11
+   325.           6
+   335.           4
+   345.           3
+   355.           0
+   365.           0
+   375.           1
+   385.           0
+   395.           0
+   405.           0
+   415.           0
+   425.           0
+   435.           0
+   445.           0
+   455.           0
+   465.           0
+   475.           0
+   485.           0
+   495.           0
+   505.           0
+   515.           0
+   525.           0

doc/examples/DepthProfiles/PECVD_Si/TRIMSP/Si10_2.0_E10000.rge

@@ -0,0 +1,135 @@
+ DEPTH      PARTICLES
+     5.           1
+    15.           2
+    25.           2
+    35.           0
+    45.           1
+    55.           0
+    65.           3
+    75.           3
+    85.           4
+    95.           7
+   105.           5
+   115.           4
+   125.           2
+   135.           3
+   145.           3
+   155.           7
+   165.           9
+   175.           4
+   185.           7
+   195.           4
+   205.           5
+   215.           9
+   225.           5
+   235.           8
+   245.           6
+   255.           6
+   265.           7
+   275.          13
+   285.          11
+   295.          12
+   305.          15
+   315.          10
+   325.          11
+   335.          13
+   345.          18
+   355.          16
+   365.          13
+   375.          21
+   385.          21
+   395.          21
+   405.          18
+   415.          18
+   425.          20
+   435.          18
+   445.          25
+   455.          25
+   465.          28
+   475.          38
+   485.          32
+   495.          38
+   505.          33
+   515.          47
+   525.          33
+   535.          36
+   545.          67
+   555.          52
+   565.          49
+   575.          59
+   585.          69
+   595.          88
+   605.          73
+   615.          85
+   625.          84
+   635.          92
+   645.          81
+   655.         102
+   665.         129
+   675.         132
+   685.         131
+   695.         137
+   705.         143
+   715.         153
+   725.         166
+   735.         157
+   745.         193
+   755.         210
+   765.         203
+   775.         205
+   785.         208
+   795.         241
+   805.         249
+   815.         227
+   825.         255
+   835.         278
+   845.         277
+   855.         267
+   865.         303
+   875.         297
+   885.         267
+   895.         316
+   905.         325
+   915.         303
+   925.         283
+   935.         257
+   945.         296
+   955.         254
+   965.         212
+   975.         221
+   985.         167
+   995.         178
+  1005.         145
+  1015.         145
+  1025.          98
+  1035.          71
+  1045.          76
+  1055.          45
+  1065.          37
+  1075.          26
+  1085.          12
+  1095.          12
+  1105.           3
+  1115.           4
+  1125.           1
+  1135.           1
+  1145.           0
+  1155.           1
+  1165.           0
+  1175.           0
+  1185.           0
+  1195.           0
+  1205.           0
+  1215.           0
+  1225.           0
+  1235.           0
+  1245.           0
+  1255.           0
+  1265.           0
+  1275.           0
+  1285.           0
+  1295.           0
+  1305.           0
+  1315.           0
+  1325.           0
+  1335.           0

doc/examples/DepthProfiles/PECVD_Si/TRIMSP/Si10_2.0_E11000.rge

@@ -0,0 +1,144 @@
+ DEPTH      PARTICLES
+     5.           1
+    15.           4
+    25.           1
+    35.           2
+    45.           3
+    55.           2
+    65.           2
+    75.           5
+    85.           3
+    95.           4
+   105.           1
+   115.           1
+   125.           1
+   135.           3
+   145.           3
+   155.           3
+   165.           4
+   175.           6
+   185.           5
+   195.           4
+   205.           3
+   215.           1
+   225.           3
+   235.           7
+   245.           6
+   255.           8
+   265.           7
+   275.           7
+   285.           5
+   295.           3
+   305.          11
+   315.          11
+   325.           6
+   335.           8
+   345.          15
+   355.          15
+   365.          13
+   375.          10
+   385.          11
+   395.          17
+   405.          18
+   415.          17
+   425.          14
+   435.          19
+   445.          15
+   455.          17
+   465.          17
+   475.          22
+   485.          18
+   495.          31
+   505.          27
+   515.          33
+   525.          30
+   535.          33
+   545.          21
+   555.          31
+   565.          43
+   575.          38
+   585.          36
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doc/examples/DepthProfiles/PECVD_Si/TRIMSP/Si10_2.0_E12000.rge

@@ -0,0 +1,151 @@
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doc/examples/DepthProfiles/PECVD_Si/TRIMSP/Si10_2.0_E13000.rge

@@ -0,0 +1,159 @@
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