adds installation of musredit as a unix app

added PyScripts/nexus_muon_validator.py to nexus.
remove obsolate test/nexus
2026-03-13 15:20:31 +01:00 · 2026-03-07 14:50:57 +01:00 · 2026-03-07 13:38:53 +01:00 · 2026-03-03 08:52:19 +01:00 · 2026-03-01 11:21:01 +01:00 · 2026-03-01 09:35:34 +01:00
155 changed files with 13536 additions and 6274 deletions
--- a/.gitea/workflows/deploy-pages.yml
+++ b/.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
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -1,4 +1,4 @@
-# - musrfit --- DKS -----------------------------------------------------------
+# - musrfit
 cmake_minimum_required(VERSION 3.17)

 # cmake: use BoostConfig.cmake instead of FindBoost
@@ -9,7 +9,6 @@ endif ()
 project(musrfit VERSION 1.10.0 LANGUAGES C CXX)

 #--- musrfit specific options -------------------------------------------------
-option(dks "build musrfit with DKS (GPU/MIC) support" ON)
 option(nexus "build optional NeXus support. Needed for ISIS" OFF)
 option(ASlibs "build optional ASlibs" OFF)
 option(BMWlibs "build optional BMWlibs" OFF)
@@ -77,7 +76,7 @@ find_package(PkgConfig REQUIRED)
 find_package(Git REQUIRED)

 #--- check for ROOT -----------------------------------------------------------
-find_package(ROOT 6.16 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)
@@ -131,42 +130,6 @@ if (try_OpenMP)
  endif (OpenMP_CXX_FOUND)
 endif (try_OpenMP)

-#--- check for CUDA and/or OpenCL followed by DKS -----------------------------
-if (dks)
-  find_package(CUDA)
-  if (CUDA_FOUND)
-    message (STATUS "CUDA include: ${CUDA_INCLUDE_DIRS}")
-    message (STATUS "CUDA libs: ${CUDA_TOOLKIT_ROOT_DIR}/lib64")
-    message (STATUS "CUDA version: ${CUDA_VERSION}")
-    add_definitions(${DKS_CMAKE_CXX_FLAGS})
-  endif (CUDA_FOUND)
-
-  if (NOT CUDA_FOUND)
-    message(STATUS "CUDA not found, looking for OpenCL")
-    find_package(OpenCL)
-    if (OpenCL_FOUND)
-      message(STATUS "OpenCL version : ${OpenCL_VERSION_STRING}")
-      message(STATUS "OpenCL include dir: ${OpenCL_INCLUDE_DIR}")
-      message(STATUS "OpenCL library dir: ${OpenCL_LIBRARY}")
-      add_definitions(-DDKS_OPENCL)
-    endif (OpenCL_FOUND)
-  endif (NOT CUDA_FOUND)
-
-  if (NOT CUDA_FOUND AND NOT OpenCL_FOUND)
-    message(WARNING ">> Neither CUDA nor OpenCL found which are required for DKS, hence disable DKS support <<")
-  else (NOT CUDA_FOUND AND NOT OpenCL_FOUND)
-    find_package(DKS "1.2.0"
-	    HINTS "/usr/local/lib/"
-	  )
- endif (NOT CUDA_FOUND AND NOT OpenCL_FOUND) 
-endif (dks)
-
-if (DKS_FOUND)
-  message(STATUS "DKS version : ${DKS_VERSION}")
-  message(STATUS "DKS include dir : ${DKS_INCLUDE_DIR}")
-  message(STATUS "DKS library : ${DKS_LIBRARY}")  
-endif (DKS_FOUND)	
-
 #--- check for Qt -------------------------------------------------------------
 if (qt_based_tools)
  # check for any Qt, i.e. AUTO
@@ -256,7 +219,7 @@ if (nexus)
    # Find HDF4 manually (pkg-config often doesn't have hdf4)
    find_path(HDF4_INCLUDE_DIR
      NAMES mfhdf.h
-      PATHS /usr/include /usr/include/hdf /usr/local/include
+      PATHS /usr/include /usr/local/include
      PATH_SUFFIXES hdf
    )

@@ -374,7 +337,6 @@ 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}")
@@ -382,21 +344,6 @@ if (OpenMP_FOUND)
    message(" OpenMP  found")
  endif (OpenMP_CXX_VERSION)
 endif (OpenMP_FOUND)
-message("")
-
-if (CUDA_FOUND)
-  message(" CUDA    found in ${CUDA_INCLUDE_DIRECTORIES} (Version: ${CUDA_VERSION})")
-endif (CUDA_FOUND)
-if (OpenCL_FOUND)
-  message(" OpenCL  found in ${OpenCL_INCLUDE_DIR} (Version: ${OpenCL_VERSION_STRING})")
-endif (OpenCL_FOUND)
-if (DKS_FOUND)
-  message(" DKS     found in ${DKS_INCLUDE_DIR} (Version: ${DKS_VERSION})")
-endif (DKS_FOUND)
-
-if (NOT CUDA_FOUND AND NOT OpenCL_FOUND AND NOT DKS_FOUND) 
-  message(" **WARNING** configured without DKS support! DKS, CUDA, OpenCL not found?")
-endif (NOT CUDA_FOUND AND NOT OpenCL_FOUND AND NOT DKS_FOUND) 

 if (nexus)
  message("")
--- a/2
+++ b/2
@@ -243,7 +243,6 @@ NEW 2016-04-28 msr2data gets a new option: paramList which allows to
               extract a subset of all the parameters of a collection
               of msr-files.
 NEW 2016-04-22 Added the theory function muMinusExpTF for mu minus fits
-NEW 2016-03-08 added a theory translator for DKS
 NEW 2016-02-23 It is now possible to export the averaged data/Fourier
 CHANGED 2016-12-18 updated the docu.
 CHANGED 2016-12-18 a couple of little improvements in musredit.
@@ -251,7 +250,6 @@ CHANGED 2016-08-10 drop NeXus support for Version < 4.4
 CHANGED 2016-04-26 start-/endTimeBin are now class members. This reduces 
               the number of recalculations.
 FIXED 2016-08-02 run lists are now properly loaded if containing nS-nE elements.
-FIXED 2016-04-14 added missing DKS selector in GetPhaseOptRealFourier.

 changes since 0.16.0
 ===================================
--- a/cmake/CPackOptions.cmake.in
+++ b/cmake/CPackOptions.cmake.in
@@ -17,7 +17,7 @@ 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")
+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")
--- a/cmake/FindHDF4.cmake
+++ b/cmake/FindHDF4.cmake
@@ -1,97 +0,0 @@
-## Process this file with cmake
-#=============================================================================
-#  NeXus - Neutron & X-ray Common Data Format
-#
-#  CMakeLists for building the NeXus library and applications.
-#
-#  Copyright (C) 2011 Stephen Rankin
-#
-#  This library is free software; you can redistribute it and/or modify it
-#  under the terms of the GNU Lesser General Public License as published by the
-#  Free Software Foundation; either version 2 of the License, or (at your
-#  option) any later version.
-#
-#  This library 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 Lesser General Public License
-#  for more details.
-#
-#  You should have received a copy of the GNU Lesser General Public License
-#  along with this library; if not, write to the Free Software Foundation,
-#  Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA
-#
-#  For further information, see <http://www.nexusformat.org>
-#
-#
-#=============================================================================
-
-
-#------------------------------------------------------------------------------
-# find the runtime binaries of the HDF4 library
-#------------------------------------------------------------------------------
-find_library(HDF4_DF_LIBRARY NAMES df hdf
-             HINTS ENV HDF4_ROOT 
-             PATH_SUFFIXES hdf)
-             
-
-if(HDF4_DF_LIBRARY MATCHES HDF4_DF_LIBRARY-NOTFOUND)
-    message(FATAL_ERROR "Could not find HDF4 DF library!")
-else()
-    get_filename_component(HDF4_LIBRARY_DIRS ${HDF4_DF_LIBRARY} PATH)
-    message(STATUS "Found HDF4 DF library: ${HDF4_DF_LIBRARY}")
-    message(STATUS "HDF4 libary path: ${HDF4_LIBRARY_DIRS}")
-endif()
-
-find_library(HDF4_MFHDF_LIBRARY NAMES mfhdf 
-             HINTS ENV HDF4_ROOT
-             PATH_SUFFIXES hdf)
-
-if(HDF4_MFHDF_LIBRARY MATCHES HDF4_MFHDF_LIBRARY-NOTFOUND)
-    message(FATAL_ERROR "Could not find HDF5 MFHDF library!")
-else()
-    message(STATUS "Found HDF4 MFHDF library: ${HDF4_MFHDF_LIBRARY}")
-endif()
-
-
-#------------------------------------------------------------------------------
-# find the HDF4 header file
-#------------------------------------------------------------------------------
-find_path(HDF4_INCLUDE_DIRS mfhdf.h 
-          HINTS ENV HDF4_ROOT 
-          PATH_SUFFIXES hdf)
-          
-if(HDF4_INCLUDE_DIRS MATCHES HDF4_INCLUDE_DIRS-NOTFOUND)
-    message(FATAL_ERROR "Could not find HDF4 header files")
-else()
-    message(STATUS "Found HDF4 header files in: ${HDF4_INCLUDE_DIRS}")
-endif()
-
-#------------------------------------------------------------------------------
-# search for additional packages required to link against HDF4
-#------------------------------------------------------------------------------
-find_package(JPEG REQUIRED)
-
-#------------------------------------------------------------------------------
-# add libraries to the link list for NAPI
-#------------------------------------------------------------------------------
-get_filename_component(LIB_EXT ${HDF4_DF_LIBRARY} EXT)
-if(LIB_EXT MATCHES .a)
-    message(STATUS "HDF4 DF library is static")
-    list(APPEND NAPI_LINK_LIBS "-Wl,-whole-archive" ${HDF4_DF_LIBRARY} "-Wl,-no-whole-archive")
-else()
-    list(APPEND NAPI_LINK_LIBS ${HDF4_DF_LIBRARY})
-endif()
-
-
-get_filename_component(LIB_EXT ${HDF4_MFHDF_LIBRARY} EXT)
-if(LIB_EXT MATCHES .a)
-    message(STATUS "HDF4 MFHDF library is static")
-    list(APPEND NAPI_LINK_LIBS "-Wl,-whole-archive" ${HDF4_MFHDF_LIBRARY} "-Wl,-no-whole-archive")
-else()
-    list(APPEND NAPI_LINK_LIBS ${HDF4_MFHDF_LIBRARY})
-endif()
-
-list(APPEND NAPI_LINK_LIBS jpeg)
-
-include_directories ( SYSTEM ${HDF4_INCLUDE_DIRS} )
-link_directories(${HDF4_LIBRARY_DIRS})
--- a/cmake/FindMXML.cmake
+++ b/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)
-
--- a/cmake/FindNEXUS.cmake
+++ b/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)
-
-
-
--- a/cmake/musredit.desktop
+++ b/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
--- a/cmake/musrfit-root6.spec.in
+++ b/cmake/musrfit-root6.spec.in
@@ -91,6 +91,8 @@ rm -rf $RPM_BUILD_ROOT
 %_prefix/lib64/*
 %license COPYING
 %doc %_prefix/share/doc/musrfit
+%{_datadir}/applications/musredit.desktop
+%{_datadir}/icons/hicolor/48x48/apps/musredit.png



--- a/cmake/post_install.sh
+++ b/cmake/post_install.sh
@@ -10,3 +10,10 @@ then
 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
--- a/cmake/post_uninstall.sh
+++ b/cmake/post_uninstall.sh
@@ -3,3 +3,11 @@
 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
--- a/doc/examples/BMWlibs/test-libGapIntegrals-ASCII.msr
+++ b/doc/examples/BMWlibs/test-libGapIntegrals-ASCII.msr
@@ -11,7 +11,7 @@ FITPARAMETER
 ###############################################################
 THEORY
 asymmetry      1
-userFcn  libGapIntegrals TGapPointPWave 2 3
+userFcn  libGapIntegrals TGapDWave 2 3 4 5

 ###############################################################
 RUN data/libGapIntegrals-test PIM3 PSI ASCII   (name beamline institute data-file-format)
--- a/doc/examples/DepthProfiles/1300Ar/depth_profile_startup.xml
+++ b/doc/examples/DepthProfiles/1300Ar/depth_profile_startup.xml
@@ -6,30 +6,6 @@
    <trim_sp>
        <data_path>./TRIMSP/</data_path>
        <rge_fln_pre>SiC_1300x_52nm_48nm_E</rge_fln_pre>
-        <energy_list>
-            <energy>1000</energy>
-            <energy>2000</energy>
-            <energy>3000</energy>
-            <energy>4000</energy>
-            <energy>5000</energy>
-            <energy>6000</energy>
-            <energy>7000</energy>
-            <energy>8000</energy>
-            <energy>9000</energy>
-            <energy>10000</energy>
-            <energy>11000</energy>
-            <energy>12000</energy>
-            <energy>13000</energy>
-            <energy>14000</energy>
-            <energy>15000</energy>
-            <energy>16000</energy>
-            <energy>17000</energy>
-            <energy>17000</energy>
-            <energy>18000</energy>
-            <energy>19000</energy>
-            <energy>20000</energy>
-            <energy>21000</energy>
-            <energy>22000</energy>
-        </energy_list>
+        <energy_vect start="1000" stop="22000" step="1000"/>
    </trim_sp>
 </depthProf>
--- a/doc/examples/DepthProfiles/1300x/depth_profile_startup.xml
+++ b/doc/examples/DepthProfiles/1300x/depth_profile_startup.xml
@@ -6,30 +6,6 @@
    <trim_sp>
        <data_path>./TRIMSP/</data_path>
        <rge_fln_pre>SiC_1300x_52nm_48nm_E</rge_fln_pre>
-        <energy_list>
-            <energy>1000</energy>
-            <energy>2000</energy>
-            <energy>3000</energy>
-            <energy>4000</energy>
-            <energy>5000</energy>
-            <energy>6000</energy>
-            <energy>7000</energy>
-            <energy>8000</energy>
-            <energy>9000</energy>
-            <energy>10000</energy>
-            <energy>11000</energy>
-            <energy>12000</energy>
-            <energy>13000</energy>
-            <energy>14000</energy>
-            <energy>15000</energy>
-            <energy>16000</energy>
-            <energy>17000</energy>
-            <energy>17000</energy>
-            <energy>18000</energy>
-            <energy>19000</energy>
-            <energy>20000</energy>
-            <energy>21000</energy>
-            <energy>22000</energy>
-        </energy_list>
+        <energy_vect start="1000" stop="22000" step="1000"/>
    </trim_sp>
 </depthProf>
--- a/doc/examples/DepthProfiles/PECVD_Si/depth_profile_startup.xml
+++ b/doc/examples/DepthProfiles/PECVD_Si/depth_profile_startup.xml
@@ -6,30 +6,6 @@
    <trim_sp>
        <data_path>./TRIMSP/</data_path>
        <rge_fln_pre>Si10_2.0_E</rge_fln_pre>
-        <energy_list>
-            <energy>1000</energy>
-            <energy>2000</energy>
-            <energy>3000</energy>
-            <energy>4000</energy>
-            <energy>5000</energy>
-            <energy>6000</energy>
-            <energy>7000</energy>
-            <energy>8000</energy>
-            <energy>9000</energy>
-            <energy>10000</energy>
-            <energy>11000</energy>
-            <energy>12000</energy>
-            <energy>13000</energy>
-            <energy>14000</energy>
-            <energy>15000</energy>
-            <energy>16000</energy>
-            <energy>17000</energy>
-            <energy>17000</energy>
-            <energy>18000</energy>
-            <energy>19000</energy>
-            <energy>20000</energy>
-            <energy>21000</energy>
-            <energy>22000</energy>
-        </energy_list>
+        <energy_vect start="1000" stop="22000" step="1000"/>
    </trim_sp>
 </depthProf>
--- a/doc/examples/DepthProfiles/PECVD_thermal_SiC/depth_profile_startup.xml
+++ b/doc/examples/DepthProfiles/PECVD_thermal_SiC/depth_profile_startup.xml
@@ -6,30 +6,6 @@
    <trim_sp>
        <data_path>./TRIMSP/</data_path>
        <rge_fln_pre>SiO2_70nm2.0_30nm2.2_SiC_E</rge_fln_pre>
-        <energy_list>
-            <energy>1000</energy>
-            <energy>2000</energy>
-            <energy>3000</energy>
-            <energy>4000</energy>
-            <energy>5000</energy>
-            <energy>6000</energy>
-            <energy>7000</energy>
-            <energy>8000</energy>
-            <energy>9000</energy>
-            <energy>10000</energy>
-            <energy>11000</energy>
-            <energy>12000</energy>
-            <energy>13000</energy>
-            <energy>14000</energy>
-            <energy>15000</energy>
-            <energy>16000</energy>
-            <energy>17000</energy>
-            <energy>17000</energy>
-            <energy>18000</energy>
-            <energy>19000</energy>
-            <energy>20000</energy>
-            <energy>21000</energy>
-            <energy>22000</energy>
-        </energy_list>
+        <energy_vect start="1000" stop="22000" step="1000"/>
    </trim_sp>
 </depthProf>
--- a/doc/examples/UserFcn/PUserFcnLinkDef.h
+++ b/doc/examples/UserFcn/PUserFcnLinkDef.h
@@ -4,7 +4,7 @@

 ***************************************************************************/

-#ifdef __CLING__
+#ifdef __CINT__

 #pragma link off all globals;
 #pragma link off all classes;
@@ -12,4 +12,4 @@

 #pragma link C++ class PUserFcn+;

-#endif //__CLING__
+#endif //__CINT__
--- a/doc/examples/test-asy-MUD.msr
+++ b/doc/examples/test-asy-MUD.msr
@@ -48,5 +48,5 @@ runs     1
 range    0   8   0   0.25

 ###############################################################
-STATISTIC --- 2026-01-21 12:33:58
+STATISTIC --- 2017-02-08 07:07:39
  chisq = 134.0, NDF = 99, chisq/NDF = 1.353150
--- a/doc/examples/test-histo-HAL9500.msr
+++ b/doc/examples/test-histo-HAL9500.msr
@@ -2,106 +2,106 @@ MnSi, FLC68.2, 50 K
 ###############################################################
 FITPARAMETER
 #      Nr. Name       Value     Step      Pos_Error Boundaries   
-        1 Rate_1      1.6686    -0.0085     0.0086      
-        2 Field_1     73089.887 -0.090      0.090       
-        3 Rate_2      1.967     -0.032      0.032       
-        4 Field_2     72289.02  -0.24       0.24        
+        1 Rate_1      1.6687    0.0086      none        
+        2 Field_1     73089.883 0.090       none        
+        3 Rate_2      1.968     0.032       none        
+        4 Field_2     72289.02  0.24        none        
        
-        5 Asym_1      0.2949    -0.0030     0.0030      
-        6 Frc_1       0.7316    -0.0058     0.0059      
-        7 Phase_1     55.61     -0.52       0.52        
-        8 N0_1        940.36    -0.54       0.54        
-        9 Bkg_1       1.524     -0.064      0.064       
+        5 Asym_1      0.2949    0.0030      none        
+        6 Frc_1       0.7316    0.0059      none        
+        7 Phase_1     55.61     0.52        none        
+        8 N0_1        940.35    0.54        none        
+        9 Bkg_1       1.523     0.064       none        

-       10 Asym_2      0.2960    -0.0030     0.0030      
-       11 Frc_2       0.7475    -0.0058     0.0059      
-       12 Phase_2     30.77     -0.50       0.50        
-       13 N0_2        961.50    -0.55       0.55        
-       14 Bkg_2       1.929     -0.065      0.065       
+       10 Asym_2      0.2960    0.0030      none        
+       11 Frc_2       0.7475    0.0059      none        
+       12 Phase_2     30.77     0.50        none        
+       13 N0_2        961.49    0.55        none        
+       14 Bkg_2       1.928     0.065       none        

-       15 Asym_3      0.3002    -0.0029     0.0029      
-       16 Frc_3       0.7462    -0.0056     0.0057      
-       17 Phase_3     18.03     -0.48       0.48        
-       18 N0_3        1024.29   -0.57       0.57        
-       19 Bkg_3       1.920     -0.067      0.067       
+       15 Asym_3      0.3002    0.0029      none        
+       16 Frc_3       0.7462    0.0056      none        
+       17 Phase_3     18.03     0.48        none        
+       18 N0_3        1024.28   0.57        none        
+       19 Bkg_3       1.919     0.067       none        

-       20 Asym_4      0.3088    -0.0029     0.0029      
-       21 Frc_4       0.7333    -0.0053     0.0054      
-       22 Phase_4     336.94    -0.48       0.47        
-       23 N0_4        1029.37   -0.57       0.57        
-       24 Bkg_4       1.865     -0.067      0.067       
+       20 Asym_4      0.3088    0.0029      none        
+       21 Frc_4       0.7333    0.0054      none        
+       22 Phase_4     336.94    0.47        none        
+       23 N0_4        1029.36   0.57        none        
+       24 Bkg_4       1.863     0.067       none        

-       25 Asym_5      0.3094    -0.0029     0.0029      
-       26 Frc_5       0.7416    -0.0054     0.0055      
-       27 Phase_5     280.33    -0.48       0.48        
-       28 N0_5        1002.70   -0.56       0.56        
-       29 Bkg_5       1.981     -0.067      0.067       
+       25 Asym_5      0.3094    0.0029      none        
+       26 Frc_5       0.7416    0.0055      none        
+       27 Phase_5     280.32    0.48        none        
+       28 N0_5        1002.69   0.56        none        
+       29 Bkg_5       1.979     0.067       none        

-       30 Asym_6      0.3153    -0.0032     0.0032      
-       31 Frc_6       0.7403    -0.0057     0.0058      
-       32 Phase_6     211.07    -0.51       0.51        
-       33 N0_6        853.44    -0.52       0.52        
-       34 Bkg_6       1.658     -0.061      0.061       
+       30 Asym_6      0.3153    0.0032      none        
+       31 Frc_6       0.7403    0.0058      none        
+       32 Phase_6     211.07    0.51        none        
+       33 N0_6        853.43    0.52        none        
+       34 Bkg_6       1.656     0.061       none        

-       35 Asym_7      0.3118    -0.0032     0.0032      
-       36 Frc_7       0.7377    -0.0058     0.0059      
-       37 Phase_7     161.75    -0.51       0.51        
-       38 N0_7        858.77    -0.52       0.52        
-       39 Bkg_7       1.595     -0.061      0.062       
+       35 Asym_7      0.3118    0.0032      none        
+       36 Frc_7       0.7378    0.0059      none        
+       37 Phase_7     161.74    0.51        none        
+       38 N0_7        858.76    0.52        none        
+       39 Bkg_7       1.594     0.061       none        

-       40 Asym_8      0.2985    -0.0031     0.0031      
-       41 Frc_8       0.7373    -0.0060     0.0061      
-       42 Phase_8     133.70    -0.53       0.53        
-       43 N0_8        871.20    -0.52       0.52        
-       44 Bkg_8       1.748     -0.062      0.062       
+       40 Asym_8      0.2985    0.0031      none        
+       41 Frc_8       0.7373    0.0061      none        
+       42 Phase_8     133.69    0.53        none        
+       43 N0_8        871.20    0.52        none        
+       44 Bkg_8       1.746     0.062       none        

-       45 Asym_9      0.2874    -0.0027     0.0027      
-       46 Frc_9       0.7340    -0.0054     0.0055      
-       47 Phase_9     158.63    -0.47       0.47        
-       48 N0_9        1184.30   -0.61       0.61        
-       49 Bkg_9       2.544     -0.073      0.073       
+       45 Asym_9      0.2874    0.0027      none        
+       46 Frc_9       0.7340    0.0054      none        
+       47 Phase_9     158.63    0.47        none        
+       48 N0_9        1184.29   0.61        none        
+       49 Bkg_9       2.542     0.073       none        

-       50 Asym_10     0.2845    -0.0027     0.0027      
-       51 Frc_10      0.7452    -0.0055     0.0055      
-       52 Phase_10    128.05    -0.47       0.47        
-       53 N0_10       1193.67   -0.61       0.61        
-       54 Bkg_10      2.396     -0.073      0.073       
+       50 Asym_10     0.2846    0.0027      none        
+       51 Frc_10      0.7453    0.0055      none        
+       52 Phase_10    128.05    0.47        none        
+       53 N0_10       1193.66   0.61        none        
+       54 Bkg_10      2.394     0.073       none        

-       55 Asym_11     0.2877    -0.0026     0.0026      
-       56 Frc_11      0.7462    -0.0052     0.0053      
-       57 Phase_11    102.42    -0.45       0.45        
-       58 N0_11       1280.01   -0.63       0.63        
-       59 Bkg_11      2.732     -0.075      0.075       
+       55 Asym_11     0.2877    0.0026      none        
+       56 Frc_11      0.7463    0.0053      none        
+       57 Phase_11    102.43    0.45        none        
+       58 N0_11       1280.00   0.63        none        
+       59 Bkg_11      2.730     0.075       none        

-       60 Asym_12     0.2919    -0.0025     0.0025      
-       61 Frc_12      0.7405    -0.0050     0.0050      
-       62 Phase_12    42.97     -0.43       0.43        
-       63 N0_12       1383.97   -0.66       0.66        
-       64 Bkg_12      2.809     -0.078      0.078       
+       60 Asym_12     0.2919    0.0025      none        
+       61 Frc_12      0.7405    0.0050      none        
+       62 Phase_12    42.97     0.43        none        
+       63 N0_12       1383.96   0.66        none        
+       64 Bkg_12      2.807     0.078       none        

-       65 Asym_13     0.2903    -0.0025     0.0025      
-       66 Frc_13      0.7493    -0.0050     0.0050      
-       67 Phase_13    350.74    -0.43       0.43        
-       68 N0_13       1393.02   -0.66       0.66        
-       69 Bkg_13      2.740     -0.078      0.079       
+       65 Asym_13     0.2903    0.0025      none        
+       66 Frc_13      0.7494    0.0050      none        
+       67 Phase_13    350.74    0.43        none        
+       68 N0_13       1393.01   0.66        none        
+       69 Bkg_13      2.738     0.078       none        

-       70 Asym_14     0.2968    -0.0025     0.0025      
-       71 Frc_14      0.7327    -0.0049     0.0050      
-       72 Phase_14    288.57    -0.43       0.43        
-       73 N0_14       1374.47   -0.66       0.66        
-       74 Bkg_14      2.771     -0.078      0.078       
+       70 Asym_14     0.2968    0.0025      none        
+       71 Frc_14      0.7327    0.0049      none        
+       72 Phase_14    288.56    0.43        none        
+       73 N0_14       1374.46   0.66        none        
+       74 Bkg_14      2.768     0.078       none        

-       75 Asym_15     0.2799    -0.0025     0.0025      
-       76 Frc_15      0.7427    -0.0052     0.0053      
-       77 Phase_15    282.56    -0.45       0.45        
-       78 N0_15       1365.99   -0.66       0.65        
-       79 Bkg_15      2.811     -0.078      0.078       
+       75 Asym_15     0.2799    0.0025      none        
+       76 Frc_15      0.7427    0.0052      none        
+       77 Phase_15    282.56    0.45        none        
+       78 N0_15       1365.97   0.65        none        
+       79 Bkg_15      2.809     0.078       none        

-       80 Asym_16     0.2771    -0.0026     0.0026      
-       81 Frc_16      0.7344    -0.0054     0.0055      
-       82 Phase_16    212.46    -0.48       0.48        
-       83 N0_16       1256.95   -0.63       0.63        
-       84 Bkg_16      2.460     -0.074      0.075       
+       80 Asym_16     0.2771    0.0026      none        
+       81 Frc_16      0.7344    0.0055      none        
+       82 Phase_16    212.46    0.48        none        
+       83 N0_16       1256.94   0.63        none        
+       84 Bkg_16      2.458     0.074       none        

 ###############################################################
 THEORY
@@ -257,12 +257,9 @@ t0              20039.0

 ###############################################################
 COMMANDS
-#OpenCL-GPU
-CUDA
 MAX_LIKELIHOOD
-#PRINT_LEVEL 2
+PRINT_LEVEL 2
 MINIMIZE
-MINOS
 SAVE

 ###############################################################
@@ -281,5 +278,5 @@ phase            par(7, 5, 16)
 range            7.1    7.5

 ###############################################################
-STATISTIC --- 2026-01-19 16:46:24
-  maxLH = 1286509.8, NDF = 1246064, maxLH/NDF = 1.032459
+STATISTIC --- 2018-10-15 15:55:36
+  maxLH = 1286508.7, NDF = 1246064, maxLH/NDF = 1.032458
--- a/doc/examples/test-histo-MusrRoot.msr
+++ b/doc/examples/test-histo-MusrRoot.msr
@@ -2,20 +2,20 @@ LSCO x=0.02 (224-227), T=12.00 (K), E=5.57 keV, WEW B=~49(G)/8.62(A), Tr=15.02 (
 ###############################################################
 FITPARAMETER
 #       No Name        Value     Step        Pos_Error   Boundaries
-        1 AsymT       0.05052   -0.00071    0.00072     0       0.33    
+        1 AsymT       0.05053   -0.00071    0.00072     0       0.33    
        2 Field       48.298    -0.094      0.095       
        3 RateT       0.129     -0.010      0.010       0       none    
        4 AsymL       0         0           none        0       0.33    
        5 RateL       0         0           none        
        6 AlphaLR     0.9784    -0.0013     0.0013      
        7 PhaseL      6.6       -1.6        1.6         -40     40      
-        8 BkgL        6.921     -0.048      0.048       
+        8 BkgL        6.920     -0.048      0.048       
        9 RelPhaseR   178.8     -1.9        1.9         150     210     
-       10 NormR       419.47    -0.40       0.40        
+       10 NormR       419.46    -0.40       0.40        
       11 BkgR        8.393     -0.050      0.050       
       12 AlphaTB     1.1025    -0.0015     0.0015      
       13 RelPhaseT   269.1     -1.9        1.9         240     300     
-       14 BkgT        7.467     -0.049      0.050       
+       14 BkgT        7.466     -0.049      0.049       
       15 NormB       393.08    -0.39       0.39        
       16 RelPhaseB   90.7      -2.0        2.0         60      120     
       17 BkgB        7.092     -0.048      0.048       
@@ -36,7 +36,7 @@ FUNCTIONS
 fun1 = par7 + map1
 fun2 = par2 * gamma_mu
 fun3 = map2 * map3
-fun4 = par4 * cos(pi / 180 * (par7 + map1))
+fun4 = par4 * cos(pi / 180.0 * (par7 + map1))

 ###############################################################
 GLOBAL
@@ -96,5 +96,5 @@ range    0   9   -0.15   0.15
 view_packing 500

 ###############################################################
-STATISTIC --- 2026-02-13 14:07:06
-  maxLH = 3971.7, NDF = 4001, maxLH/NDF = 0.992678
+STATISTIC --- 2018-11-13 07:58:56
+  maxLH = 3971.7, NDF = 4001, maxLH/NDF = 0.992668
--- a/doc/examples/test-histo-NeXus2.msr
+++ b/doc/examples/test-histo-NeXus2.msr
@@ -4,7 +4,7 @@ FITPARAMETER
 #       No Name        Value     Step        Pos_Error   Boundaries
        1 phaseL      0         0           none        
        2 field       20.3381   -0.0085     0.0085      0       none    
-        3 asym        0.23440   -0.00051    0.00052     0       0.3     
+        3 asym        0.23440   -0.00051    0.00051     0       0.3     
        4 rate        0.0234    -0.0041     0.0035      0       100     
        5 Norm_L      1151.30   -0.53       0.53        
        6 BG_L        0         0           none        0       none    
@@ -38,6 +38,7 @@ norm            5
 backgr.fit      6
 map             1    0    0    0    0    0    0    0    0    0
 forward         1-48 
+#deadtime-cor    file

 RUN data/emu00139040 XXXX ISIS NEXUS   (name beamline institute data-file-format)
 norm            7
@@ -69,8 +70,5 @@ range    0   20   -0.35   0.35
 view_packing 10

 ###############################################################
-STATISTIC --- 2026-03-02 13:44:22
+STATISTIC --- 2026-02-23 13:09:55
  maxLH = 4228.9, NDF = 3726, maxLH/NDF = 1.134977
-  expected maxLH = 4211.4, NDF = 3726, expected maxLH/NDF = 1.130285
-  run block 1: (NDF/red.maxLH/red.maxLH_e) = (1862/1.170949/1.182735)
-  run block 2: (NDF/red.maxLH/red.maxLH_e) = (1861/1.100817/1.079629)
--- a/doc/examples/test-histo-PSI-BIN.msr
+++ b/doc/examples/test-histo-PSI-BIN.msr
@@ -8,9 +8,9 @@ FITPARAMETER
        4 Phase_L     178.95    -0.41       0.41        
        5 Phase_R     1.75      -0.39       0.39        
        6 N0_L        1097.9    -1.0        1.0         
-        7 N0_R        1159.8    -1.0        1.0         
+        7 N0_R        1159.7    -1.0        1.0         
        8 Bkg_L       54.47     -0.20       0.20        
-        9 Bkg_R       46.71     -0.19       0.19        
+        9 Bkg_R       46.70     -0.19       0.19        

 ###############################################################
 THEORY
@@ -47,7 +47,6 @@ t0              202.0

 ###############################################################
 COMMANDS
-CUDA
 SCALE_N0_BKG TRUE
 MINIMIZE
 MINOS
@@ -64,11 +63,11 @@ FOURIER
 units            Gauss   # units either 'Gauss', 'Tesla', 'MHz', or 'Mc/s'
 fourier_power    12
 apodization      NONE    # NONE, WEAK, MEDIUM, STRONG
-plot             POWER   # REAL, IMAG, REAL_AND_IMAG, POWER, PHASE, PHASE_OPT_REAL
+plot             POWER   # REAL, IMAG, REAL_AND_IMAG, POWER, PHASE
 phase            8.5
 #range_for_phase_correction 50.0 70.0
-range            0    200
+range            0.0    200.0

 ###############################################################
-STATISTIC --- 2024-06-07 15:33:49
-  chisq = 663.9, NDF = 515, chisq/NDF = 1.289084
+STATISTIC --- 2015-01-05 14:09:47
+  chisq = 663.9, NDF = 515, chisq/NDF = 1.289169
--- a/doc/html/.buildinfo
+++ b/doc/html/.buildinfo
@@ -1,4 +1,4 @@
 # Sphinx build info version 1
-# This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
-config: fae482e1a3134e03efb428cbbe21a254
+# This file records the configuration used when building these files. When it is not found, a full rebuild will be done.
+config: a49a5e0b750ed752f738f66d3ddeadd4
 tags: 645f666f9bcd5a90fca523b33c5a78b7
--- a/src/musredit_qt5/mupp/mupp.dox
+++ b/src/musredit_qt5/mupp/mupp.dox
--- a/doc/mupp_qt5_dox.cfg
+++ b/doc/mupp_qt5_dox.cfg
@@ -733,9 +733,10 @@ WARN_LOGFILE           =
 # spaces.
 # Note: If this tag is empty the current directory is searched.

-INPUT                  =../src/musredit_qt5/mupp \
-                        ../src/musredit_qt5/mupp/var/include \
-                        ../src/musredit_qt5/mupp/var/src
+INPUT                  = ./ \
+                         ../src/musredit_qt5/mupp \
+                         ../src/musredit_qt5/mupp/var/include \
+                         ../src/musredit_qt5/mupp/var/src

 # This tag can be used to specify the character encoding of the source files
 # that doxygen parses. Internally doxygen uses the UTF-8 encoding. Doxygen uses
@@ -755,7 +756,7 @@ INPUT_ENCODING         = UTF-8
 # *.md, *.mm, *.dox, *.py, *.f90, *.f, *.for, *.tcl, *.vhd, *.vhdl, *.ucf,
 # *.qsf, *.as and *.js.

-FILE_PATTERNS          = *.dox *.cpp *.h *.hpp
+FILE_PATTERNS          = mupp.dox *.cpp *.h *.hpp

 # The RECURSIVE tag can be used to specify whether or not subdirectories should
 # be searched for input files as well.
@@ -1532,7 +1533,7 @@ EXTRA_SEARCH_MAPPINGS  =
 # If the GENERATE_LATEX tag is set to YES doxygen will generate LaTeX output.
 # The default value is: YES.

-GENERATE_LATEX         = YES
+GENERATE_LATEX         = NO

 # The LATEX_OUTPUT tag is used to specify where the LaTeX docs will be put. If a
 # relative path is entered the value of OUTPUT_DIRECTORY will be put in front of
--- a/doc/mupp_qt6_dox.cfg
+++ b/doc/mupp_qt6_dox.cfg
@@ -32,13 +32,13 @@ DOXYFILE_ENCODING      = UTF-8
 # title of most generated pages and in a few other places.
 # The default value is: My Project.

-PROJECT_NAME           = "musredit"
+PROJECT_NAME           = "mupp"

 # The PROJECT_NUMBER tag can be used to enter a project or revision number. This
 # could be handy for archiving the generated documentation or if some version
 # control system is used.

-PROJECT_NUMBER         = 1.0.0
+PROJECT_NUMBER         = 1.1.0

 # Using the PROJECT_BRIEF tag one can provide an optional one line description
 # for a project that appears at the top of each page and should give viewer a
@@ -58,7 +58,7 @@ PROJECT_LOGO           =
 # entered, it will be relative to the location where doxygen was started. If
 # left blank the current directory will be used.

-OUTPUT_DIRECTORY       = ./technical/html/musredit
+OUTPUT_DIRECTORY       = ./technical/html/mupp

 # If the CREATE_SUBDIRS tag is set to YES, then doxygen will create 4096 sub-
 # directories (in 2 levels) under the output directory of each output format and
@@ -733,7 +733,10 @@ WARN_LOGFILE           =
 # spaces.
 # Note: If this tag is empty the current directory is searched.

-INPUT                  =../src/musredit_qt5/musredit
+INPUT                  = ./ \
+                         ../src/musredit_qt6/mupp \
+                         ../src/musredit_qt6/mupp/var/include \
+                         ../src/musredit_qt6/mupp/var/src

 # This tag can be used to specify the character encoding of the source files
 # that doxygen parses. Internally doxygen uses the UTF-8 encoding. Doxygen uses
@@ -753,7 +756,7 @@ INPUT_ENCODING         = UTF-8
 # *.md, *.mm, *.dox, *.py, *.f90, *.f, *.for, *.tcl, *.vhd, *.vhdl, *.ucf,
 # *.qsf, *.as and *.js.

-FILE_PATTERNS          = *.dox *.cpp *.h
+FILE_PATTERNS          = mupp.dox *.cpp *.h *.hpp

 # The RECURSIVE tag can be used to specify whether or not subdirectories should
 # be searched for input files as well.
@@ -1530,7 +1533,7 @@ EXTRA_SEARCH_MAPPINGS  =
 # If the GENERATE_LATEX tag is set to YES doxygen will generate LaTeX output.
 # The default value is: YES.

-GENERATE_LATEX         = YES
+GENERATE_LATEX         = NO

 # The LATEX_OUTPUT tag is used to specify where the LaTeX docs will be put. If a
 # relative path is entered the value of OUTPUT_DIRECTORY will be put in front of
@@ -1969,7 +1972,7 @@ TAGFILES               =
 # tag file that is based on the input files it reads. See section "Linking to
 # external documentation" for more information about the usage of tag files.

-GENERATE_TAGFILE       = dox-tags/musredit.tag
+GENERATE_TAGFILE       = dox-tags/mupp.tag

 # If the ALLEXTERNALS tag is set to YES all external class will be listed in the
 # class index. If set to NO only the inherited external classes will be listed.
--- a/src/musredit_qt5/musredit/musredit.dox
+++ b/src/musredit_qt5/musredit/musredit.dox
--- a/doc/musredit_qt5_dox.cfg
+++ b/doc/musredit_qt5_dox.cfg
--- a/doc/musredit_qt6_dox.cfg
+++ b/doc/musredit_qt6_dox.cfg
--- a/doc/musrfit.dox
+++ b/doc/musrfit.dox
@@ -16,18 +16,18 @@

 <p>People merely interested in the handling of the programs should check this link:
 \htmlonly
-<a href="http://lmu.web.psi.ch/musrfit/user/html/index.html">musrfit user manual</a>
+<a href="https://lmu.pages.psi.ch/musrfit-docu/">musrfit user manual</a>
 \endhtmlonly
 \latexonly
-musrfit user manual: \texttt{http://lmu.web.psi.ch/musrfit/user/html/index.html}
+musrfit user manual: \texttt{https://lmu.pages.psi.ch/musrfit-docu/user-manual.html}
 \endlatexonly 

 <p>People which would like to know how to install the musrfit framework, please check this link:
 \htmlonly
-<a href="http://lmu.web.psi.ch/musrfit/user/html/setup-standard.html">How to setup musrfit on different platforms</a>
+<a href="https://lmu.pages.psi.ch/musrfit-docu/setup-standard.html">How to setup musrfit on different platforms</a>
 \endhtmlonly
 \latexonly
-How to setup musrfit on different platforms: \texttt{http://lmu.web.psi.ch/musrfit/user/html/setup-standard.html}
+How to setup musrfit on different platforms: \texttt{https://lmu.pages.psi.ch/musrfit-docu/setup-standard.html}
 \endlatexonly

 //****************************************************************************************************
@@ -47,12 +47,7 @@ under Linux, Mac OS X, and (with some more work) under Windows. The musrfit fram
     msr-files with the same parameters and summarize the fitting results either in a TRIUMF DB or a column ASCII file.
 - **msr2msr**: old WKM like msr-files can be transformed into musrfit style msr-files with this little program.
 - musrgui (obsolete): an editor to handle msr-files, calling musrfit, etc. from within the editor, based on Qt3.x. 
-<<<<<<< HEAD
-     Only bug fixing will be done on this version, and if you have >= Qt4.6 available you should use musredit instead.
- **musredit**: an editor to handle msr-files, calling musrfit, etc. from within a simple text editor, based on >= Qt4.6. A technical documentation of musredit can be found 
-=======
 - **musredit**: an editor to handle msr-files, calling musrfit, etc. from within a simple text editor, based on Qt5.x (soon being deprecated) or Qt6.x. A technical documentation of musredit can be found 
->>>>>>> 3f50462c (make the technical docu more complete by adding musrStep and musrWiz.)
 \htmlonly <a href="./musredit/html/index.html">here.</a>\endhtmlonly
 - **musrWiz** (beta): allows to create an initial msr-file by a step-by-step instruction wizard. A technical documentation of musrWiz can be found
 \htmlonly <a href="./musrWiz/html/index.html">here.</a>\endhtmlonly 
@@ -60,8 +55,7 @@ under Linux, Mac OS X, and (with some more work) under Windows. The musrfit fram
 \htmlonly <a href="./musrStep/html/index.html">here.</a>\endhtmlonly 
 - **mupp**: is the muSR parameter plotter. It allows to plot values in db- or dat-files (collections). A technical documentation of mupp can be found 
 \htmlonly <a href="./mupp/html/index.html">here.</a>\endhtmlonly
- **MuSRFit**: a graphical user interface based on PerlQt (written by Z. Salman) for an easy to use interface to the musrfit framework. 
-     Compared to the more general approach of writing msr-files, it has some limitations, though it might be easier for a first user of the musrfit framework.
+- **addRun**: allows to add runs from the command line
 - **any2many**: should be a "universal" muSR data-file-format converter.
 - **dump_header**: is a small program to dump the header information of a muSR data file to the standard output.
 - **musrRootValidation**: this is a program to validate MusrRoot files.
@@ -85,7 +79,11 @@ This two points are somewhat contradictory, and currently it is not clear which

 \section bugs How to report bugs

-<p>Bugs, unexpected features, can be reported directly to me: \verbatim andreas.suter@psi.ch, \endverbatim or entered in the bug-tracking tool at 
-bitbkucket \verbatim https://bitbucket.org/muonspin/musrfit/issues \endverbatim.
+<p>Bugs, unexpected features, can be reported directly to me: \verbatim andreas.suter@psi.ch, \endverbatim or entered in the bug-tracking tool at \htmlonly
+<a href="https://bitbucket.org/muonspin/musrfit/issues">bitbucket issue tracker</a>
+\endhtmlonly
+\latexonly
+\verbatim https://bitbucket.org/muonspin/musrfit/issues \endverbatim.
+\endlatexonly 

 */
--- a/doc/musrfit_dox.cfg
+++ b/doc/musrfit_dox.cfg
--- a/src/CMakeLists.txt
+++ b/src/CMakeLists.txt
@@ -81,7 +81,6 @@ add_executable(musrfit musrfit.cpp)
 target_compile_options(musrfit BEFORE PRIVATE "-DHAVE_CONFIG_H" "${HAVE_GIT_REV_H}")
 target_include_directories(musrfit 
  BEFORE PRIVATE 
-    $<BUILD_INTERFACE:${DKS_INCLUDE_DIR}> 
    $<BUILD_INTERFACE:${Boost_INCLUDE_DIRS}>
    $<BUILD_INTERFACE:${CMAKE_BINARY_DIR}>
    $<BUILD_INTERFACE:${CMAKE_BINARY_DIR}/src>
--- a/src/classes/CMakeLists.txt
+++ b/src/classes/CMakeLists.txt
@@ -6,7 +6,7 @@ set(MUSRFIT_INC ${CMAKE_SOURCE_DIR}/src/include)
 # Hence, target_include_directories cannot be used here because, targets are 
 # setup only afterwards.
 include_directories(${MUSRFIT_INC})
-include_directories(${FFTW3_INC})
+include_directories(${FFTW3_INCLUDE})

 root_generate_dictionary(
  PFourierCanvasDict 
@@ -95,7 +95,6 @@ add_library(PMusr SHARED
  PFindRun.cpp
  PFitter.cpp
  PFitterFcn.cpp
-  PFitterFcnDKS.cpp
  PFourier.cpp
  PFourierCanvas.cpp
  PFourierCanvasDict.cxx
@@ -130,7 +129,6 @@ add_library(PMusr SHARED
 #--- make sure that the include directory is found ----------------------------
 target_include_directories(
  PMusr BEFORE PRIVATE
-    $<BUILD_INTERFACE:${DKS_INCLUDE_DIR}> 
    $<BUILD_INTERFACE:${Boost_INCLUDE_DIRS}>
    $<BUILD_INTERFACE:${FFTW3_INCLUDE}> 
    $<BUILD_INTERFACE:${HDF4_INCLUDE_DIRS}>
@@ -186,14 +184,6 @@ if (ROOT_GRTEQ_24)
  target_compile_options(PMusr BEFORE PRIVATE "-DROOT_GRTEQ_24")
 endif(ROOT_GRTEQ_24)

-#--- add DKS compiler flags if enabled ----------------------------------------
-if (DKS_FOUND)
-  if (CUDA_FOUND)
-    set(DKS_CXX_FLAGS -DDKS_OPENCL -DDKS_CUDA  -I${CUDA_INCLUDE_DIRS} -I${DKS_INCLUDE_DIR}) 
-    target_compile_options(PMusr PUBLIC ${DKS_CXX_FLAGS})
-  endif (CUDA_FOUND)
-endif (DKS_FOUND)
-
 #--- add library dependencies -------------------------------------------------
 set(DependOnLibs ${ROOT_LIBARIES})
 #set(DependOnLibs ${DependOnLibs} ${FFTW3_LIBRARY})
@@ -211,13 +201,6 @@ endif (nexus)
 if (OpenMP_FOUND)
  set(DependOnLibs ${DependOnLibs} OpenMP::OpenMP_CXX)
 endif (OpenMP_FOUND)
-if (DKS_FOUND)
-  if (APPLE)
-    set(DependOnLibs ${DependOnLibs} "-framework OpenCL")	
-  endif (APPLE)
-  set(DependOnLibs ${DependOnLibs} "-L ${DKS_LIBRARY_DIR}")	
-  set(DependOnLibs ${DependOnLibs} ${DKS_LIBRARY})
-endif (DKS_FOUND)

 target_link_libraries(PUserFcnBase PRIVATE ${ROOT_LIBRARIES})
 target_link_libraries(PRgeHandler PRIVATE ${Boost_LIBRARIES} ${ROOT_LIBRARIES})
--- a/src/classes/PFitter.cpp
+++ b/src/classes/PFitter.cpp
@@ -31,9 +31,6 @@
 #include "config.h"
 #endif

-#include <sys/time.h>
-#include <sys/utsname.h>
-
 #ifdef HAVE_GOMP
 #include <omp.h>
 #endif
@@ -41,7 +38,6 @@
 #include <iostream>
 #include <iomanip>
 #include <fstream>
-#include <string>
 #include <limits>
 #include <cmath>

@@ -295,7 +291,6 @@ PFitter::PFitter(PMsrHandler *runInfo, PRunListCollection *runListCollection, Bo
  fChisqOnly(chisq_only), fYamlOut(yaml_out), fRunInfo(runInfo), fRunListCollection(runListCollection)
 {
  // initialize variables
-  fDKSReady = false;
  fIsScanOnly = true;
  fConverged = false;
  fUseChi2 = true; // chi^2 is the default
@@ -341,36 +336,8 @@ PFitter::PFitter(PMsrHandler *runInfo, PRunListCollection *runListCollection, Bo
  // create phase bool array
  GetPhaseParams();

-  // get the DKS tag from the commands block
-  fDKSTag = fRunInfo->GetDKSTag();
-
-  // check if the theory function can already run on the GPU
-  std::string theo = fRunInfo->GetDKSTheoryString();
-  if (fDKSTag != DKS_CPU_OPENMP) {
-    if (!theo.compare("??")) { // theory not yet DKS ready
-      std::cout << std::endl << ">> PFitter::PFitter(): **INFO** theory not yet DKS/GPU ready. Will run on the CPU." << std::endl;
-    } else {
-      fDKSReady = true;
-      std::cout << std::endl << ">> PFitter::PFitter(): **INFO** theory DKS/GPU ready. Will run on the GPU." << std::endl;
-    }
-  }
-
-  // create fit function object depending whether DKS/GPU can be used or not
-  if (fDKSReady && (fDKSTag != DKS_CPU_OPENMP)) { // run on the GPU
-    fFitterFcnDKS = std::make_unique<PFitterFcnDKS>(runListCollection, fUseChi2, fDKSTag, theo);
-    if (!fFitterFcnDKS) {
-      fIsValid = false;
-    }
-    if (!fFitterFcnDKS->IsValid()) {
-      fIsValid = false;
-    }
-  } else { // run on the CPU
-    fDKSReady = false; // needed in case dksTag == DKS_CPU_OPENMP
-    fFitterFcn = std::make_unique<PFitterFcn>(runListCollection, fUseChi2);
-    if (!fFitterFcn) {
-      fIsValid = false;
-    }
-  }
+  // create fit function object
+  fFitterFcn = std::make_unique<PFitterFcn>(runListCollection, fUseChi2);
 }

 //--------------------------------------------------------------------------
@@ -691,24 +658,13 @@ Bool_t PFitter::DoFit()
      if (error[i] != 0.0)
        usedParams++;
    }
-    UInt_t ndf = 0;
-    Double_t val = 0.0;
-    if (fDKSReady) {
-      ndf = fFitterFcnDKS->GetTotalNoOfFittedBins() - static_cast<UInt_t>(usedParams);
-      val = (*fFitterFcnDKS)(param);
-    } else {
-      ndf = fFitterFcn->GetTotalNoOfFittedBins() - static_cast<UInt_t>(usedParams);
-      val = (*fFitterFcn)(param);
-    }
-
+    UInt_t ndf = static_cast<int>(fFitterFcn->GetTotalNoOfFittedBins()) - usedParams;
+    Double_t val = (*fFitterFcn)(param);
    if (fUseChi2) {
      // calculate expected chisq
      Double_t totalExpectedChisq = 0.0;
      PDoubleVector expectedChisqPerRun;
-      if (fDKSReady)
-        fFitterFcnDKS->CalcExpectedChiSquare(param, totalExpectedChisq, expectedChisqPerRun);
-      else
-        fFitterFcn->CalcExpectedChiSquare(param, totalExpectedChisq, expectedChisqPerRun);
+      fFitterFcn->CalcExpectedChiSquare(param, totalExpectedChisq, expectedChisqPerRun);
      // calculate chisq per run
      std::vector<Double_t> chisqPerRun;
      for (UInt_t i=0; i<fRunInfo->GetMsrRunList()->size(); i++) {
@@ -721,21 +677,14 @@ Bool_t PFitter::DoFit()
        std::cout << std::endl << ">> expected chisq = " << totalExpectedChisq << ", NDF = " << ndf << ", expected chisq/NDF = " << totalExpectedChisq/ndf;
        UInt_t ndf_run = 0;
        for (UInt_t i=0; i<expectedChisqPerRun.size(); i++) {
-          if (fDKSReady)
-            ndf_run = fFitterFcnDKS->GetNoOfFittedBins(i) - fRunInfo->GetNoOfFitParameters(i);
-          else
-            ndf_run = fFitterFcn->GetNoOfFittedBins(i) - fRunInfo->GetNoOfFitParameters(i);
+          ndf_run = fFitterFcn->GetNoOfFittedBins(i) - fRunInfo->GetNoOfFitParameters(i);
          if (ndf_run > 0)
            std::cout << std::endl << ">> run block " << i+1 << ": (NDF/red.chisq/red.chisq_e) = (" << ndf_run << "/" << chisqPerRun[i]/ndf_run << "/" << expectedChisqPerRun[i]/ndf_run << ")";
        }
      } else if (chisqPerRun.size() > 0) { // in case expected chisq is not applicable like for asymmetry fits
        UInt_t ndf_run = 0;
        for (UInt_t i=0; i<chisqPerRun.size(); i++) {
-          if (fDKSReady)
-            ndf_run = fFitterFcnDKS->GetNoOfFittedBins(i) - fRunInfo->GetNoOfFitParameters(i);
-          else
-            ndf_run = fFitterFcn->GetNoOfFittedBins(i) - fRunInfo->GetNoOfFitParameters(i);
-
+          ndf_run = fFitterFcn->GetNoOfFittedBins(i) - fRunInfo->GetNoOfFitParameters(i);
          if (ndf_run > 0)
            std::cout << std::endl << ">> run block " << i+1 << ": (NDF/red.chisq) = (" << ndf_run << "/" << chisqPerRun[i]/ndf_run << ")";
        }
@@ -753,20 +702,13 @@ Bool_t PFitter::DoFit()
          secFitRange[0].first = fSector[k].GetTimeRangeFirst(0);
          secFitRange[0].second = fSector[k].GetTimeRangeLast();
          fRunListCollection->SetFitRange(secFitRange);
-          // calculate chisq and NDF
-          if (fDKSReady) {
-            ndf = fFitterFcnDKS->GetTotalNoOfFittedBins() - static_cast<UInt_t>(usedParams);
-            val = (*fFitterFcnDKS)(param);
-          } else {
-            ndf = fFitterFcn->GetTotalNoOfFittedBins() - static_cast<UInt_t>(usedParams);
-            val = (*fFitterFcn)(param);
-          }
+          // calculate chisq
+          val = (*fFitterFcn)(param);
+          // calculate NDF
+          ndf = static_cast<UInt_t>(fFitterFcn->GetTotalNoOfFittedBins()) - usedParams;
          // calculate expected chisq
          totalExpectedChisq = 0.0;
-          if (fDKSReady)
-            fFitterFcnDKS->CalcExpectedChiSquare(param, totalExpectedChisq, expectedChisqPerRun);
-          else
-            fFitterFcn->CalcExpectedChiSquare(param, totalExpectedChisq, expectedChisqPerRun);
+          fFitterFcn->CalcExpectedChiSquare(param, totalExpectedChisq, expectedChisqPerRun);
          // calculate chisq per run
          for (UInt_t i=0; i<fRunInfo->GetMsrRunList()->size(); i++) {
            chisqPerRun.push_back(fRunListCollection->GetSingleRunChisq(param, i));
@@ -781,20 +723,14 @@ Bool_t PFitter::DoFit()
            std::cout << std::endl << ">> expected chisq = " << totalExpectedChisq << ", NDF = " << ndf << ", expected chisq/NDF = " << totalExpectedChisq/ndf;
            UInt_t ndf_run = 0;
            for (UInt_t i=0; i<expectedChisqPerRun.size(); i++) {
-              if (fDKSReady)
-                ndf_run = fFitterFcnDKS->GetNoOfFittedBins(i) - fRunInfo->GetNoOfFitParameters(i);
-              else
-                ndf_run = fFitterFcn->GetNoOfFittedBins(i) - fRunInfo->GetNoOfFitParameters(i);
+              ndf_run = fFitterFcn->GetNoOfFittedBins(i) - fRunInfo->GetNoOfFitParameters(i);
              if (ndf_run > 0)
                std::cout << std::endl << ">> run block " << i+1 << ": (NDF/red.chisq/red.chisq_e) = (" << ndf_run << "/" << chisqPerRun[i]/ndf_run << "/" << expectedChisqPerRun[i]/ndf_run << ")";
            }
          } else if (chisqPerRun.size() > 0) { // in case expected chisq is not applicable like for asymmetry fits
            UInt_t ndf_run = 0;
            for (UInt_t i=0; i<chisqPerRun.size(); i++) {
-              if (fDKSReady)
-                ndf_run = fFitterFcnDKS->GetNoOfFittedBins(i) - fRunInfo->GetNoOfFitParameters(i);
-              else
-                ndf_run = fFitterFcn->GetNoOfFittedBins(i) - fRunInfo->GetNoOfFitParameters(i);
+              ndf_run = fFitterFcn->GetNoOfFittedBins(i) - fRunInfo->GetNoOfFitParameters(i);
              if (ndf_run > 0)
                std::cout << std::endl << ">> run block " << i+1 << ": (NDF/red.chisq) = (" << ndf_run << "/" << chisqPerRun[i]/ndf_run << ")";
            }
@@ -808,10 +744,7 @@ Bool_t PFitter::DoFit()
      // calculate expected maxLH
      Double_t totalExpectedMaxLH = 0.0;
      std::vector<Double_t> expectedMaxLHPerRun;
-      if (fDKSReady)
-        fFitterFcnDKS->CalcExpectedChiSquare(param, totalExpectedMaxLH, expectedMaxLHPerRun);
-      else 
-        fFitterFcn->CalcExpectedChiSquare(param, totalExpectedMaxLH, expectedMaxLHPerRun);
+      fFitterFcn->CalcExpectedChiSquare(param, totalExpectedMaxLH, expectedMaxLHPerRun);
      // calculate maxLH per run
      std::vector<Double_t> maxLHPerRun;
      for (UInt_t i=0; i<fRunInfo->GetMsrRunList()->size(); i++) {
@@ -824,12 +757,9 @@ Bool_t PFitter::DoFit()
        std::cout << std::endl << ">> expected maxLH = " << totalExpectedMaxLH << ", NDF = " << ndf << ", expected maxLH/NDF = " << totalExpectedMaxLH/ndf;
        UInt_t ndf_run = 0;
        for (UInt_t i=0; i<expectedMaxLHPerRun.size(); i++) {
-          if (fDKSReady)
-            ndf_run = fFitterFcnDKS->GetNoOfFittedBins(i) - fRunInfo->GetNoOfFitParameters(i);
-          else
-            ndf_run = fFitterFcn->GetNoOfFittedBins(i) - fRunInfo->GetNoOfFitParameters(i);
+          ndf_run = fFitterFcn->GetNoOfFittedBins(i) - fRunInfo->GetNoOfFitParameters(i);
          if (ndf_run > 0)
-            std::cout << std::endl << ">> run block " << i+1 << ": (NDF/maxLH.chisq/maxLH.chisq_e) = (" << ndf_run << "/" << maxLHPerRun[i]/ndf_run << "/" << expectedMaxLHPerRun[i]/ndf_run << ")";
+            std::cout << std::endl << ">> run block " << i+1 << ": (NDF/red.maxLH/red.maxLH_e) = (" << ndf_run << "/" << maxLHPerRun[i]/ndf_run << "/" << expectedMaxLHPerRun[i]/ndf_run << ")";
        }
      }

@@ -845,20 +775,13 @@ Bool_t PFitter::DoFit()
          secFitRange[0].first = fSector[k].GetTimeRangeFirst(0);
          secFitRange[0].second = fSector[k].GetTimeRangeLast();
          fRunListCollection->SetFitRange(secFitRange);
-          // calculate chisq and NDF
-          if (fDKSReady) {
-            ndf = static_cast<Int_t>(fFitterFcnDKS->GetTotalNoOfFittedBins()) - usedParams;
-            val = (*fFitterFcnDKS)(param);
-          } else {
-            ndf = static_cast<Int_t>(fFitterFcn->GetTotalNoOfFittedBins()) - usedParams;
-            val = (*fFitterFcn)(param);
-          }
+          // calculate maxLH
+          val = (*fFitterFcn)(param);
+          // calculate NDF
+          ndf = static_cast<int>(fFitterFcn->GetTotalNoOfFittedBins()) - usedParams;
          // calculate expected maxLH
          totalExpectedMaxLH = 0.0;
-          if (fDKSReady)
-            fFitterFcnDKS->CalcExpectedChiSquare(param, totalExpectedMaxLH, expectedMaxLHPerRun);
-          else
-            fFitterFcn->CalcExpectedChiSquare(param, totalExpectedMaxLH, expectedMaxLHPerRun);
+          fFitterFcn->CalcExpectedChiSquare(param, totalExpectedMaxLH, expectedMaxLHPerRun);
          // calculate maxLH per run
          for (UInt_t i=0; i<fRunInfo->GetMsrRunList()->size(); i++) {
            maxLHPerRun.push_back(fRunListCollection->GetSingleRunMaximumLikelihood(param, i));
@@ -873,12 +796,9 @@ Bool_t PFitter::DoFit()
            std::cout << std::endl << ">> expected maxLH = " << totalExpectedMaxLH << ", NDF = " << ndf << ", expected maxLH/NDF = " << totalExpectedMaxLH/ndf;
            UInt_t ndf_run = 0;
            for (UInt_t i=0; i<expectedMaxLHPerRun.size(); i++) {
-              if (fDKSReady)
-                ndf_run = fFitterFcnDKS->GetNoOfFittedBins(i) - fRunInfo->GetNoOfFitParameters(i);
-              else
-                ndf_run = fFitterFcn->GetNoOfFittedBins(i) - fRunInfo->GetNoOfFitParameters(i);
+              ndf_run = fFitterFcn->GetNoOfFittedBins(i) - fRunInfo->GetNoOfFitParameters(i);
              if (ndf_run > 0)
-                std::cout << std::endl << ">> run block " << i+1 << ": (NDF/maxLH.chisq/maxLH.chisq_e) = (" << ndf_run << "/" << maxLHPerRun[i]/ndf_run << "/" << expectedMaxLHPerRun[i]/ndf_run << ")";
+                std::cout << std::endl << ">> run block " << i+1 << ": (NDF/red.maxLH/red.maxLH_e) = (" << ndf_run << "/" << maxLHPerRun[i]/ndf_run << "/" << expectedMaxLHPerRun[i]/ndf_run << ")";
            }
          }

@@ -1057,15 +977,7 @@ Bool_t PFitter::CheckCommands()

    if (line.Contains("COMMANDS", TString::kIgnoreCase)) {
      continue;
-    } else if (it->fLine.Contains("OpenMP", TString::kIgnoreCase)) { // run on CPU using OpenMP
-      continue;
-    } else if (it->fLine.Contains("CUDA", TString::kIgnoreCase)) { // try to run DKS/GPU CUDA
-      continue;
-    } else if (it->fLine.Contains("OpenCL-GPU", TString::kIgnoreCase)) { // try to run DKS/GPU OpenCL
-      continue;
-    } else if (it->fLine.Contains("OpenCL-CPU", TString::kIgnoreCase)) { // try to run DKS/CPU OpenCL
-      continue;
-    } else if (it->fLine.Contains("SET BATCH", TString::kIgnoreCase)) { // needed for backward compatibility
+    } else if (line.Contains("SET BATCH", TString::kIgnoreCase)) { // needed for backward compatibility
      continue;
    } else if (line.Contains("END RETURN", TString::kIgnoreCase)) {  // needed for backward compatibility
      continue;
@@ -1791,13 +1703,7 @@ Bool_t PFitter::ExecuteContours()
    return false;
  }

-  ROOT::Minuit2::FCNBase *fcn = nullptr;
-  if (fDKSReady)
-    fcn = fFitterFcnDKS.get();
-  else
-    fcn = fFitterFcn.get();
-
-  ROOT::Minuit2::MnContours contours((*fcn), *fFcnMin);
+  ROOT::Minuit2::MnContours contours((*fFitterFcn), *fFcnMin);

  fScanData = contours(fScanParameter[0], fScanParameter[1], fScanNoPoints);

@@ -1935,13 +1841,8 @@ Bool_t PFitter::ExecuteHesse()

  // call hesse
  Double_t start=0.0, end=0.0;
-  ROOT::Minuit2::FCNBase *fcn = nullptr;
-  if (fDKSReady)
-    fcn = fFitterFcnDKS.get();
-  else
-    fcn = fFitterFcn.get();
  start=MilliTime();
-  ROOT::Minuit2::MnUserParameterState mnState = hesse((*fcn), fMnUserParams, maxfcn);
+  ROOT::Minuit2::MnUserParameterState mnState = hesse((*fFitterFcn), fMnUserParams, maxfcn);
  end=MilliTime();
  std::cout << ">> PFitter::ExecuteMinimize(): execution time for Hesse = " << std::setprecision(3) << (end-start)/1.0e3 << " sec." << std::endl;
  TString str = TString::Format("Hesse:    %.3f sec", (end-start)/1.0e3);
@@ -1952,8 +1853,8 @@ Bool_t PFitter::ExecuteHesse()
    return false;
  }
  if (!mnState.HasCovariance()) {
-    std::cerr << std::endl << ">> PFitter::ExecuteHesse(): **WARNING** Hesse encountered a problem! No covariance matrix available.";
-    std::cerr << std::endl;
+    std::cerr  << std::endl << ">> PFitter::ExecuteHesse(): **WARNING** Hesse encountered a problem! No covariance matrix available.";
+    std::cerr  << std::endl;
    return false;
  }

@@ -1983,12 +1884,7 @@ Bool_t PFitter::ExecuteMigrad()

  // create migrad object
  // strategy is by default = 'default'
-  ROOT::Minuit2::FCNBase *fcn = nullptr;
-  if (fDKSReady)
-    fcn = fFitterFcnDKS.get();
-  else
-    fcn = fFitterFcn.get();
-  ROOT::Minuit2::MnMigrad migrad((*fcn), fMnUserParams, ROOT::Minuit2::MnStrategy{fStrategy});
+  ROOT::Minuit2::MnMigrad migrad((*fFitterFcn), fMnUserParams, ROOT::Minuit2::MnStrategy{fStrategy});

  // minimize
  // maxfcn is MINUIT2 Default maxfcn
@@ -2031,11 +1927,7 @@ Bool_t PFitter::ExecuteMigrad()

  // handle statistics
  Double_t minVal = min.Fval();
-  UInt_t ndf = 0.0;
-  if (fDKSReady)
-    ndf = fFitterFcnDKS->GetTotalNoOfFittedBins();
-  else
-    ndf = fFitterFcn->GetTotalNoOfFittedBins();
+  UInt_t ndf = fFitterFcn->GetTotalNoOfFittedBins();
  // subtract number of varied parameters from total no of fitted bins -> ndf
  for (UInt_t i=0; i<fParams.size(); i++) {
    if ((min.UserState().Error(i) != 0.0) && !fMnUserParams.Parameters().at(i).IsFixed())
@@ -2068,12 +1960,7 @@ Bool_t PFitter::ExecuteMinimize()

  // create minimizer object
  // strategy is by default = 'default'
-  ROOT::Minuit2::FCNBase *fcn = nullptr;
-  if (fDKSReady)
-    fcn = fFitterFcnDKS.get();
-  else
-    fcn = fFitterFcn.get();
-  ROOT::Minuit2::MnMinimize minimize((*fcn), fMnUserParams, ROOT::Minuit2::MnStrategy{fStrategy});
+  ROOT::Minuit2::MnMinimize minimize((*fFitterFcn), fMnUserParams, ROOT::Minuit2::MnStrategy{fStrategy});

  // minimize
  // maxfcn is MINUIT2 Default maxfcn
@@ -2117,11 +2004,7 @@ Bool_t PFitter::ExecuteMinimize()

  // handle statistics
  Double_t minVal = min.Fval();
-  UInt_t ndf = 0.0;
-  if (fDKSReady)
-    ndf = fFitterFcnDKS->GetTotalNoOfFittedBins();
-  else
-    ndf = fFitterFcn->GetTotalNoOfFittedBins();
+  UInt_t ndf = fFitterFcn->GetTotalNoOfFittedBins();
  // subtract number of varied parameters from total no of fitted bins -> ndf
  for (UInt_t i=0; i<fParams.size(); i++) {
    if ((min.UserState().Error(i) != 0.0) && !fMnUserParams.Parameters().at(i).IsFixed())
@@ -2168,13 +2051,8 @@ Bool_t PFitter::ExecuteMinos()

  // make minos analysis
  Double_t start=0.0, end=0.0;
-  ROOT::Minuit2::FCNBase *fcn = nullptr;
-  if (fDKSReady)
-    fcn = fFitterFcnDKS.get();
-  else
-    fcn = fFitterFcn.get();
  start=MilliTime();
-  ROOT::Minuit2::MnMinos minos((*fcn), (*fFcnMin));
+  ROOT::Minuit2::MnMinos minos((*fFitterFcn), (*fFcnMin));

  for (UInt_t i=0; i<fParams.size(); i++) {
    // only try to call minos if the parameter is not fixed!!
@@ -2368,12 +2246,7 @@ Bool_t PFitter::ExecuteScan()
 {
  std::cout << ">> PFitter::ExecuteScan(): will call scan ..." << std::endl;

-  ROOT::Minuit2::FCNBase *fcn = nullptr;
-  if (fDKSReady)
-    fcn = fFitterFcnDKS.get();
-  else
-    fcn = fFitterFcn.get();
-  ROOT::Minuit2::MnScan scan((*fcn), fMnUserParams);
+  ROOT::Minuit2::MnScan scan((*fFitterFcn), fMnUserParams);

  if (fScanAll) { // not clear at the moment what to be done here
    // TO BE IMPLEMENTED
@@ -2431,13 +2304,9 @@ Bool_t PFitter::ExecuteSave(Bool_t firstSave)
  // CalcExpectedChiSquare handles both, chisq and mlh
  Bool_t ok;
  PDoubleVector par_r = ParamRound(param, err, ok);
-  
  if (!ok)
    par_r = param;
-  if (fDKSReady)
-    fFitterFcnDKS->CalcExpectedChiSquare(par_r, totalExpectedChisq, expectedchisqPerRun);
-  else
-    fFitterFcn->CalcExpectedChiSquare(par_r, totalExpectedChisq, expectedchisqPerRun);
+  fFitterFcn->CalcExpectedChiSquare(par_r, totalExpectedChisq, expectedchisqPerRun);

  // calculate chisq per run
  std::vector<Double_t> chisqPerRun;
@@ -2452,10 +2321,7 @@ Bool_t PFitter::ExecuteSave(Bool_t firstSave)
    // get the ndf's of the histos
    UInt_t ndf_run;
    for (UInt_t i=0; i<expectedchisqPerRun.size(); i++) {
-      if (fDKSReady)
-        ndf_run = fFitterFcnDKS->GetNoOfFittedBins(i) - fRunInfo->GetNoOfFitParameters(i);
-      else
-        ndf_run = fFitterFcn->GetNoOfFittedBins(i) - fRunInfo->GetNoOfFitParameters(i);
+      ndf_run = fFitterFcn->GetNoOfFittedBins(i) - fRunInfo->GetNoOfFitParameters(i);
      ndfPerHisto.push_back(ndf_run);
    }

@@ -2470,12 +2336,16 @@ Bool_t PFitter::ExecuteSave(Bool_t firstSave)
  } else if (chisqPerRun.size() > 1) { // in case expected chisq is not applicable like for asymmetry fits
    UInt_t ndf_run = 0;
    for (UInt_t i=0; i<chisqPerRun.size(); i++) {
-      if (fDKSReady)
-        ndf_run = fFitterFcnDKS->GetNoOfFittedBins(i) - fRunInfo->GetNoOfFitParameters(i);
-      else
-        ndf_run = fFitterFcn->GetNoOfFittedBins(i) - fRunInfo->GetNoOfFitParameters(i);
+      ndf_run = fFitterFcn->GetNoOfFittedBins(i) - fRunInfo->GetNoOfFitParameters(i);
      ndfPerHisto.push_back(ndf_run);
    }
+
+    // feed the msr-file handler
+    PMsrStatisticStructure *statistics = fRunInfo->GetMsrStatistic();
+    if (statistics) {
+      statistics->fMinPerHisto = chisqPerRun;
+      statistics->fNdfPerHisto = ndfPerHisto;
+    }
  }

  // check if sector command has been requested
@@ -2516,43 +2386,6 @@ Bool_t PFitter::ExecuteSave(Bool_t firstSave)
  fout << std::endl << "*************************************************************************";
  fout << std::endl;

-  // write CPU/GPU info
-  std::string hwInfo("??");
-  int status=0;
-  switch (fDKSTag) {
-    case DKS_CPU_OPENMP:
-      fout << std::endl << " CPU info : " << GetCPUInfo();
-#ifdef HAVE_GOMP
-      fout << std::endl << " OpenMP" << std::endl;
-#else
-      fout << std::endl << " CPU, i.e. single threaded" << std::endl;
-#endif
-      break;
-    case DKS_CPU_OPENCL:
-      if (fFitterFcnDKS)
-        status = fFitterFcnDKS->GetDeviceName(hwInfo);
-      fout << std::endl << " CPU info : " << hwInfo;
-      fout << std::endl << " OpenCL" << std::endl;
-      break;
-    case DKS_GPU_CUDA:
-      if (fFitterFcnDKS)
-        status = fFitterFcnDKS->GetDeviceName(hwInfo);
-      fout << std::endl << " GPU info : " << hwInfo;
-      fout << std::endl << " Cuda" << std::endl;
-      break;
-    case DKS_GPU_OPENCL:
-      if (fFitterFcnDKS)
-        status = fFitterFcnDKS->GetDeviceName(hwInfo);
-      fout << std::endl << " GPU info : " << hwInfo;
-      fout << std::endl << " OpenCL" << std::endl;
-      break;
-    default:
-      fout << std::endl << " CPU/GPU info : unkown" << std::endl;
-      break;
-  }
-  fout << std::endl << "*************************************************************************";
-  fout << std::endl;
-
  // write elapsed times
  fout << std::endl << " elapsed times:";
  for (UInt_t i=0; i<fElapsedTime.size(); i++) {
@@ -2951,12 +2784,7 @@ Bool_t PFitter::ExecuteSimplex()

  // create minimizer object
  // strategy is by default = 'default'
-  ROOT::Minuit2::FCNBase *fcn = nullptr;
-  if (fDKSReady)
-    fcn = fFitterFcnDKS.get();
-  else
-    fcn = fFitterFcn.get();
-  ROOT::Minuit2::MnSimplex simplex((*fcn), fMnUserParams, ROOT::Minuit2::MnStrategy{fStrategy});
+  ROOT::Minuit2::MnSimplex simplex((*fFitterFcn), fMnUserParams, ROOT::Minuit2::MnStrategy{fStrategy});

  // minimize
  // maxfcn is 10*MINUIT2 Default maxfcn
@@ -2999,11 +2827,7 @@ Bool_t PFitter::ExecuteSimplex()

  // handle statistics
  Double_t minVal = min.Fval();
-  UInt_t ndf = 0.0;
-  if (fDKSReady)
-    fFitterFcnDKS->GetTotalNoOfFittedBins();
-  else
-    fFitterFcn->GetTotalNoOfFittedBins();
+  UInt_t ndf = fFitterFcn->GetTotalNoOfFittedBins();
  // subtract number of varied parameters from total no of fitted bins -> ndf
  for (UInt_t i=0; i<fParams.size(); i++) {
    if ((min.UserState().Error(i) != 0.0) && !fMnUserParams.Parameters().at(i).IsFixed())
@@ -3055,23 +2879,14 @@ void PFitter::PrepareSector(PDoubleVector &param, PDoubleVector &error)
      secFitRange[0].second = fSector[k].GetTimeRangeLast();
      fRunListCollection->SetFitRange(secFitRange);
      // calculate chisq
-      if (fDKSReady)
-        val = (*fFitterFcnDKS)(param);
-      else
-        val = (*fFitterFcn)(param);
+      val = (*fFitterFcn)(param);
      fSector[k].SetChisq(val);
      // calculate NDF
-      if (fDKSReady)
-        ndf = fFitterFcnDKS->GetTotalNoOfFittedBins() - static_cast<UInt_t>(usedParams);
-      else
-        ndf = fFitterFcn->GetTotalNoOfFittedBins() - static_cast<UInt_t>(usedParams);
+      ndf = static_cast<UInt_t>(fFitterFcn->GetTotalNoOfFittedBins()) - usedParams;
      fSector[k].SetNDF(ndf);
      // calculate expected chisq
      totalExpectedChisq = 0.0;
-      if (fDKSReady)
-        fFitterFcnDKS->CalcExpectedChiSquare(param, totalExpectedChisq, expectedChisqPerRun);
-      else
-        fFitterFcn->CalcExpectedChiSquare(param, totalExpectedChisq, expectedChisqPerRun);
+      fFitterFcn->CalcExpectedChiSquare(param, totalExpectedChisq, expectedChisqPerRun);
      fSector[k].SetExpectedChisq(totalExpectedChisq);
      // calculate chisq per run
      for (UInt_t i=0; i<fRunInfo->GetMsrRunList()->size(); i++) {
@@ -3083,10 +2898,7 @@ void PFitter::PrepareSector(PDoubleVector &param, PDoubleVector &error)
      if (totalExpectedChisq != 0.0) {
        UInt_t ndf_run = 0;
        for (UInt_t i=0; i<expectedChisqPerRun.size(); i++) {
-          if (fDKSReady)
-            ndf_run = fFitterFcnDKS->GetNoOfFittedBins(i) - fRunInfo->GetNoOfFitParameters(i);
-          else
-            ndf_run = fFitterFcn->GetNoOfFittedBins(i) - fRunInfo->GetNoOfFitParameters(i);
+          ndf_run = fFitterFcn->GetNoOfFittedBins(i) - fRunInfo->GetNoOfFitParameters(i);
          if (ndf_run > 0) {
            fSector[k].SetNDF(ndf_run, i);
          }
@@ -3094,10 +2906,7 @@ void PFitter::PrepareSector(PDoubleVector &param, PDoubleVector &error)
      } else if (chisqPerRun.size() > 0) { // in case expected chisq is not applicable like for asymmetry fits
        UInt_t ndf_run = 0;
        for (UInt_t i=0; i<chisqPerRun.size(); i++) {
-          if (fDKSReady)
-            ndf_run = fFitterFcnDKS->GetNoOfFittedBins(i) - fRunInfo->GetNoOfFitParameters(i);
-          else
-            ndf_run = fFitterFcn->GetNoOfFittedBins(i) - fRunInfo->GetNoOfFitParameters(i);
+          ndf_run = fFitterFcn->GetNoOfFittedBins(i) - fRunInfo->GetNoOfFitParameters(i);
          if (ndf_run > 0) {
            fSector[k].SetNDF(ndf_run, i);
          }
@@ -3117,23 +2926,14 @@ void PFitter::PrepareSector(PDoubleVector &param, PDoubleVector &error)
      secFitRange[0].second = fSector[k].GetTimeRangeLast();
      fRunListCollection->SetFitRange(secFitRange);
      // calculate maxLH
-      if (fDKSReady)
-        val = (*fFitterFcnDKS)(param);
-      else
-        val = (*fFitterFcn)(param);
+      val = (*fFitterFcn)(param);
      fSector[k].SetChisq(val);
      // calculate NDF
-      if (fDKSReady)
-        ndf = fFitterFcnDKS->GetTotalNoOfFittedBins() - static_cast<UInt_t>(usedParams);
-      else
-        ndf = fFitterFcn->GetTotalNoOfFittedBins() - static_cast<UInt_t>(usedParams);
+      ndf = static_cast<UInt_t>(fFitterFcn->GetTotalNoOfFittedBins()) - usedParams;
      fSector[k].SetNDF(ndf);
      // calculate expected maxLH
      totalExpectedMaxLH = 0.0;
-      if (fDKSReady)
-        fFitterFcnDKS->CalcExpectedChiSquare(param, totalExpectedMaxLH, expectedMaxLHPerRun);
-      else
-        fFitterFcn->CalcExpectedChiSquare(param, totalExpectedMaxLH, expectedMaxLHPerRun);
+      fFitterFcn->CalcExpectedChiSquare(param, totalExpectedMaxLH, expectedMaxLHPerRun);
      fSector[k].SetExpectedChisq(totalExpectedMaxLH);
      // calculate maxLH per run
      for (UInt_t i=0; i<fRunInfo->GetMsrRunList()->size(); i++) {
@@ -3145,10 +2945,7 @@ void PFitter::PrepareSector(PDoubleVector &param, PDoubleVector &error)
      if (totalExpectedMaxLH != 0.0) {
        UInt_t ndf_run = 0;
        for (UInt_t i=0; i<expectedMaxLHPerRun.size(); i++) {
-          if (fDKSReady)
-            ndf_run = fFitterFcnDKS->GetNoOfFittedBins(i) - fRunInfo->GetNoOfFitParameters(i);
-          else
-            ndf_run = fFitterFcn->GetNoOfFittedBins(i) - fRunInfo->GetNoOfFitParameters(i);
+          ndf_run = fFitterFcn->GetNoOfFittedBins(i) - fRunInfo->GetNoOfFitParameters(i);
          if (ndf_run > 0) {
            fSector[k].SetNDF(ndf_run, i);
          }
@@ -3235,59 +3032,6 @@ Double_t PFitter::MilliTime()
  return ((Double_t)now.tv_sec * 1.0e6 + (Double_t)now.tv_usec)/1.0e3;
 }

-//--------------------------------------------------------------------------
-// GetCPUInfo (private)
-//--------------------------------------------------------------------------
-/**
- * <p> extract CPU information from the system.
- *
- * @return the CPU information or ?? if this was not possible.
- */
-std::string PFitter::GetCPUInfo()
-{
-  std::string cpuInfo = "??";
- 
-  // find out if linux or Mac OS X
-  struct utsname sys_info;
- 
-  uname(&sys_info);
- 
-  if (strstr(sys_info.sysname, "Linux")) {
-    char result[128];
-    strcpy(result, "??");
- 
-    char line[128], str[128], *pos;
-    bool done = false;
-    std::ifstream fin("/proc/cpuinfo", std::ifstream::in);
-    while (fin.good() && !done) {
-      fin.getline(line, 128);
-      if (strstr(line, "model name")) {
-        pos = strstr(line, ":");
-        strcpy(str, pos+2);
-        strncpy(result, str, sizeof(result));
-        done = true;
-      }
-    }
-    fin.close();
-    cpuInfo = result;
-  } else if (strstr(sys_info.sysname, "Darwin")) {
-    system("sysctl -n machdep.cpu.brand_string >> /tmp/_musrfit_cpu_info.txt");
-    sleep(1);
- 
-    char line[128], result[128];
-    std::ifstream fin("/tmp/_musrfit_cpu_info.txt", std::ifstream::in);
-    while (fin.good()) {
-      fin.getline(line, 128);
-      strncat(result, line, sizeof(result) - strlen(result) - 1);
-    }
-    fin.close();
-    system("rm /tmp/_musrfit_cpu_info.txt");
-    cpuInfo = result;
-  }
- 
-  return cpuInfo;
-}
-
 //--------------------------------------------------------------------------
 // ParamRound (private)
 //--------------------------------------------------------------------------
@@ -3327,10 +3071,11 @@ PDoubleVector PFitter::ParamRound(const PDoubleVector &par, const PDoubleVector
      par_r[i] = par[i];
    }
  }
-
+  
  return par_r;
 }

+
 //-------------------------------------------------------------------------------------------------
 // end
 //-------------------------------------------------------------------------------------------------
--- a/src/classes/PFitterFcn.cpp
+++ b/src/classes/PFitterFcn.cpp
@@ -38,14 +38,16 @@
 * \param runList run list collection
 * \param useChi2 if true, a chisq fit will be performed, otherwise a log max-likelihood fit will be carried out.
 */
-PFitterFcn::PFitterFcn(PRunListCollection *runList, Bool_t useChi2) :
-  fUseChi2(useChi2),
-  fRunListCollection(runList)
+PFitterFcn::PFitterFcn(PRunListCollection *runList, Bool_t useChi2)
 {
+  fUseChi2 = useChi2;
+
  if (fUseChi2)
    fUp = 1.0;
  else
    fUp = 0.5;
+
+  fRunListCollection = runList;
 }

 //--------------------------------------------------------------------------
@@ -115,12 +117,6 @@ void PFitterFcn::CalcExpectedChiSquare(const std::vector<Double_t> &par, Double_
      expectedChisqPerRun.push_back(value);
      totalExpectedChisq += value;
    }
-    // mu minus
-    for (UInt_t i=0; i<fRunListCollection->GetNoOfMuMinus(); i++) {
-      value = fRunListCollection->GetSingleRunChisqExpected(par, i); // calculate the expected chisq for mu minus run block 'i'
-      expectedChisqPerRun.push_back(value);
-      totalExpectedChisq += value;
-    }
  } else { // log max. likelihood
    // single histo
    for (UInt_t i=0; i<fRunListCollection->GetNoOfSingleHisto(); i++) {
@@ -128,11 +124,5 @@ void PFitterFcn::CalcExpectedChiSquare(const std::vector<Double_t> &par, Double_
      expectedChisqPerRun.push_back(value);
      totalExpectedChisq += value;
    }
-    // mu minus
-    for (UInt_t i=0; i<fRunListCollection->GetNoOfMuMinus(); i++) {
-      value = fRunListCollection->GetSingleRunMaximumLikelihoodExpected(par, i); // calculate the expected maxLH for mu minus run block 'i'
-      expectedChisqPerRun.push_back(value);
-      totalExpectedChisq += value;
-    }
  }
 }
--- a/src/classes/PFitterFcnDKS.cpp
+++ b/src/classes/PFitterFcnDKS.cpp
@@ -1,538 +0,0 @@
-/***************************************************************************
-
-  PFitterFcnDKS.cpp
-
-  Author: Andreas Suter
-  e-mail: andreas.suter@psi.ch
-
-***************************************************************************/
-
-/***************************************************************************
- *   Copyright (C) 2007-2026 by Andreas Suter                              *
- *   andreas.suter@psi.ch                                                  *
- *                                                                         *
- *   This program is free software; you can redistribute it and/or modify  *
- *   it under the terms of the GNU General Public License as published by  *
- *   the Free Software Foundation; either version 2 of the License, or     *
- *   (at your option) any later version.                                   *
- *                                                                         *
- *   This program is distributed in the hope that it will be useful,       *
- *   but WITHOUT ANY WARRANTY; without even the implied warranty of        *
- *   MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the         *
- *   GNU General Public License for more details.                          *
- *                                                                         *
- *   You should have received a copy of the GNU General Public License     *
- *   along with this program; if not, write to the                         *
- *   Free Software Foundation, Inc.,                                       *
- *   59 Temple Place - Suite 330, Boston, MA  02111-1307, USA.             *
- ***************************************************************************/
-
-#include <iostream>
-
-#include "PMusr.h"
-#include "PFitterFcnDKS.h"
-
-//--------------------------------------------------------------------------
-// Constructor
-//--------------------------------------------------------------------------
-/**
- * <p>Constructor.
- *
- * \param runList run list collection
- * \param useChi2 if true, a chisq fit will be performed, otherwise a log max-likelihood fit will be carried out.
- */
-PFitterFcnDKS::PFitterFcnDKS(PRunListCollection *runList, const Bool_t useChi2, const UInt_t dksTag,
-                             const std::string theo) :
-  fTheoStr(theo),
-  fUseChi2(useChi2),
-  fRunListCollection(runList)
-{
-  fValid = false;
-
-  if (fUseChi2)
-    fUp = 1.0;
-  else
-    fUp = 0.5;
-
-  InitDKS(dksTag);
-}
-
-//--------------------------------------------------------------------------
-// Destructor
-//--------------------------------------------------------------------------
-/**
- * <p>Destructor
- */
-PFitterFcnDKS::~PFitterFcnDKS()
-{
-//  FreeDKS();
-}
-
-//--------------------------------------------------------------------------
-// operator()
-//--------------------------------------------------------------------------
-/**
- * <p>Minuit2 interface function call routine. This is the function which should be minimized.
- *
- * \param par a vector with all the parameters of the function
- */
-Double_t PFitterFcnDKS::operator()(const std::vector<Double_t>& par) const
-{
-  Double_t value = 0.0, chisq = 0.0;
-
-  // write parameter to GPU
-  Int_t ierr = fDKS.writeParams(&par[0], par.size());
-
-  // loop over all data sets
-  PDKSParams dksp;
-  Double_t norm = 1.0;
-  // single histos
-  for (UInt_t i=0; i<fRunListCollection->GetNoOfSingleHisto(); i++) {
-    // get current values of N0, Nbkg, tau, the functions, the maps, the time resolution, the fit start time, etc.
-    ierr = fRunListCollection->GetSingleHistoParams(i, par, dksp);
-
-    // set N0, Nbkg
-    ierr += fDKS.callSetConsts(dksp.fN0, dksp.fTau, dksp.fNbkg);
-
-    // set fun values
-    if (dksp.fFun.size() == 0)
-      ierr += fDKS.writeFunctions(nullptr, 0);
-    else
-      ierr += fDKS.writeFunctions(&dksp.fFun[0], dksp.fFun.size());
-
-    // set map values
-    if (dksp.fMap.size() == 0)
-      ierr += fDKS.writeMaps(nullptr, 0);
-    else
-      ierr += fDKS.writeMaps(&dksp.fMap[0], dksp.fMap.size());
-
-    // calc chisq/log-mlh
-    chisq = 0.0;
-    ierr += fDKS.callLaunchChiSquare(FITTYPE_SINGLE_HISTO, fMemDataSingleHisto[i], fMemDataSingleHistoErr[i], dksp.fNoOfFitBins,
-                                     par.size(), dksp.fFun.size(), dksp.fMap.size(),
-                                     dksp.fStartTime , dksp.fPackedTimeResolution, chisq);
-    value += chisq;    
-
-    if (ierr != 0) {
-      std::cerr << "PFitterFcnDKS::operator(): **ERROR** Kernel launch for single histo failed!" << std::endl;
-      exit (EXIT_FAILURE);
-    }
-  }
-
-  // asymmetries
-  for (UInt_t i=0; i<fRunListCollection->GetNoOfAsymmetry(); i++) {
-    // get current values of alpha and beta, the functions, the maps, the time resolution, the fit start time, etc.
-    ierr = fRunListCollection->GetAsymmetryParams(i, par, dksp);
-
-    // set alpha and beta
-    ierr += fDKS.callSetConsts(dksp.fAlpha, dksp.fBeta);
-
-    // set fun values
-    if (dksp.fFun.size() == 0)
-      ierr += fDKS.writeFunctions(nullptr, 0);
-    else
-      ierr += fDKS.writeFunctions(&dksp.fFun[0], dksp.fFun.size());
-
-    // set map values
-    if (dksp.fMap.size() == 0)
-      ierr += fDKS.writeMaps(nullptr, 0);
-    else 
-      ierr += fDKS.writeMaps(&dksp.fMap[0], dksp.fMap.size());
-
-    // calc chisq
-    chisq = 0.0;
-    ierr += fDKS.callLaunchChiSquare(FITTYPE_ASYMMETRY, fMemDataAsymmetry[i], fMemDataAsymmetryErr[i], dksp.fNoOfFitBins,
-                                     par.size(), dksp.fFun.size(), dksp.fMap.size(),
-                                     dksp.fStartTime , dksp.fPackedTimeResolution, chisq);
-    value += chisq;
-
-    if (ierr != 0) {
-      std::cerr << "PFitterFcnDKS::operator(): **ERROR** Kernel launch for asymmetry failed!" << std::endl;
-      exit (EXIT_FAILURE);
-    }
-  }
-
-  // mu mius
-  for (UInt_t i=0; i<fRunListCollection->GetNoOfMuMinus(); i++) {
-    // get current values of N0, Nbkg, tau, the functions, the maps, the time resolution, the fit start time, etc.
-    ierr = fRunListCollection->GetMuMinusParams(i, par, dksp);
-
-    // set fun values
-    ierr += fDKS.writeFunctions(&dksp.fFun[0], dksp.fFun.size());
-
-    // set map values
-    ierr += fDKS.writeMaps(&dksp.fMap[0], dksp.fMap.size());
-
-    // calc chisq/log-mlh
-    chisq = 0.0;
-    ierr += fDKS.callLaunchChiSquare(FITTYPE_MU_MINUS, fMemDataMuMinus[i], fMemDataMuMinusErr[i], dksp.fNoOfFitBins,
-                                     par.size(), dksp.fFun.size(), dksp.fMap.size(),
-                                     dksp.fStartTime , dksp.fPackedTimeResolution, chisq);
-    value += chisq;
-
-    if (ierr != 0) {
-      std::cerr << "PFitterFcnDKS::operator(): **ERROR** Kernel launch for mu minus failed!" << std::endl;
-      exit (EXIT_FAILURE);
-    }
-  }
-
-  if (dksp.fScaleN0AndBkg)
-    norm = dksp.fPackedTimeResolution*1.0e3;
-
-  return norm*value;
-}
-
-//--------------------------------------------------------------------------
-// CalcExpectedChiSquare (public)
-//--------------------------------------------------------------------------
-/**
- * <p>Calculates the expected chisq, expected chisq per run, and chisq per run, if applicable.
- *
- * \param par
- * \param totalExpectedChisq expected chisq for all run blocks
- * \param expectedChisqPerRun expected chisq vector for all the run blocks
- */
-void PFitterFcnDKS::CalcExpectedChiSquare(const std::vector<Double_t> &par, Double_t &totalExpectedChisq, std::vector<Double_t> &expectedChisqPerRun)
-{
-  // init expected chisq related variables
-  totalExpectedChisq = 0.0;
-  expectedChisqPerRun.clear();
-
-  // only do something for chisq
-  Double_t value = 0.0;
-  if (fUseChi2) {
-    // single histo
-    for (UInt_t i=0; i<fRunListCollection->GetNoOfSingleHisto(); i++) {
-      value = fRunListCollection->GetSingleRunChisqExpected(par, i); // calculate the expected chisq for single histo run block 'i'
-      expectedChisqPerRun.push_back(value);
-      totalExpectedChisq += value;
-    }
-    // mu minus
-    for (UInt_t i=0; i<fRunListCollection->GetNoOfMuMinus(); i++) {
-      value = fRunListCollection->GetSingleRunChisqExpected(par, i); // calculate the expected chisq for mu minus run block 'i'
-      expectedChisqPerRun.push_back(value);
-      totalExpectedChisq += value;
-    }
-  } else {
-    // single histo
-    for (UInt_t i=0; i<fRunListCollection->GetNoOfSingleHisto(); i++) {
-      value = fRunListCollection->GetSingleRunMaximumLikelihoodExpected(par, i); // calculate the expected maxLH for single histo run block 'i'
-      expectedChisqPerRun.push_back(value);
-      totalExpectedChisq += value;
-    }
-    // mu minus
-    for (UInt_t i=0; i<fRunListCollection->GetNoOfMuMinus(); i++) {
-      value = fRunListCollection->GetSingleRunMaximumLikelihoodExpected(par, i); // calculate the expected maxLH for mu minus run block 'i'
-      expectedChisqPerRun.push_back(value);
-      totalExpectedChisq += value;
-    }
-  }
-}
-
-//--------------------------------------------------------------------------
-// GetDeviceName (public)
-//--------------------------------------------------------------------------
-/**
- * <p> get from DKS the device name used.
- *
- * \param devName deivce name, if status == 0
- *
- * \return 0 if OK, 1 otherwise
- */
-int PFitterFcnDKS::GetDeviceName(std::string &devName)
-{
-  int status = 1;
-  
-  devName = "??";
-  if (!fValid)
-    return status;
-  
-  status = fDKS.getDeviceName(devName);
-  
-  return status;
-}
-
-//--------------------------------------------------------------------------
-// InitDKS (private)
-//--------------------------------------------------------------------------
-/**
- * <p>initializes the DKS interface
- *
- */
-void PFitterFcnDKS::InitDKS(const UInt_t dksTag)
-{
-  Int_t ierr = 0;
-  Int_t fitType = FITTYPE_UNDEFINED;
-  Int_t startTimeBin = -1, endTimeBin = -1, length = -1;
-
-  // if any device was allocated before, free the device resources
-  FreeDKS();
-
-  // select framework
-  if (dksTag == DKS_GPU_CUDA)
-    fDKS.setAPI("Cuda");
-  else
-    fDKS.setAPI("OpenCL");
-
-  // select device
-  if (dksTag == DKS_CPU_OPENCL)
-    fDKS.setDevice("-cpu");
-  else
-    fDKS.setDevice("-gpu");
-
-  // init device
-  fDKS.initDevice();
-
-  // init chisq buffer on the GPU
-
-  // 1) calculate the maximum size for the data needed.
-  Int_t parSize = -1, mapSize = -1, funSize = -1;
-  Int_t maxSize = 0, size = -1;
-  for (UInt_t i=0; i<fRunListCollection->GetNoOfSingleHisto(); i++) {
-    size = fRunListCollection->GetNoOfBinsFitted(i);
-    if (maxSize < size)
-      maxSize = size;
-  }
-  for (UInt_t i=0; i<fRunListCollection->GetNoOfAsymmetry(); i++) {
-    size = fRunListCollection->GetNoOfBinsFitted(i);
-    if (maxSize < size)
-      maxSize = size;
-  }
-  for (UInt_t i=0; i<fRunListCollection->GetNoOfMuMinus(); i++) {
-    size = fRunListCollection->GetNoOfBinsFitted(i);
-    if (maxSize < size)
-      maxSize = size;
-  }
-  if (maxSize == 0) {
-    std::cerr << ">> PFitterFcnDKS::InitDKS: **ERROR** failed to get data size to be fitted." << std::endl;
-    fValid = false;
-    return;
-  }
-
-  // 2) get number of parameters / functions / maps
-  parSize = fRunListCollection->GetNoOfParameters();
-  if (parSize == -1) {
-    std::cerr << ">> PFitterFcnDKS::InitDKS: **ERROR** failed to get number of fit parameters." << std::endl;
-    fValid = false;
-    return;
-  }
-  funSize = fRunListCollection->GetNoOfFunctions();
-  if (funSize == -1) {
-    std::cerr << ">> PFitterFcnDKS::InitDKS: **ERROR** failed to get number of functions." << std::endl;
-    fValid = false;
-    return;
-  }
-  mapSize = fRunListCollection->GetNoOfMaps();
-  if (mapSize == -1) {
-    std::cerr << ">> PFitterFcnDKS::InitDKS: **ERROR** failed to get number of maps." << std::endl;
-    fValid = false;
-    return;
-  }
-
-  // now ready to init the chisq buffer on the GPU
-  ierr = fDKS.initChiSquare(maxSize, parSize, funSize, mapSize);
-  if (ierr != 0) {
-    std::cerr << ">> PFitterFcnDKS::InitDKS: **ERROR** failed to allocate the necessary chisq buffer on the GPU." << std::endl;
-    fValid = false;
-    return;
-  }
-
-  // allocate memory for the data on the GPU/CPU and transfer the data sets
-  PRunData *runData=0;
-
-  // single histos
-  fMemDataSingleHisto.resize(fRunListCollection->GetNoOfSingleHisto());
-  fMemDataSingleHistoErr.resize(fRunListCollection->GetNoOfSingleHisto());
-  for (UInt_t i=0; i<fRunListCollection->GetNoOfSingleHisto(); i++) {
-    runData = fRunListCollection->GetSingleHisto(i);
-    if (runData == 0) {
-      std::cerr << ">> PFitterFcnDKS::InitDKS: **ERROR** failed to get single histo data set (i=" << i << ") from fRunListCollection." << std::endl;
-      fValid = false;
-      return;
-    }
-    startTimeBin = fRunListCollection->GetStartTimeBin(MSR_FITTYPE_SINGLE_HISTO, i);
-    endTimeBin   = fRunListCollection->GetEndTimeBin(MSR_FITTYPE_SINGLE_HISTO, i);
-    length = endTimeBin-startTimeBin;
-    if (startTimeBin < 0) {
-      std::cerr << ">> PFitterFcnDKS::InitDKS: **ERROR** startTimeBin undefind (single histo fit)." << std::endl;
-      fValid = false;
-      return;
-    }
-    if (endTimeBin < 0) {
-      std::cerr << ">> PFitterFcnDKS::InitDKS: **ERROR** endTimeBin undefind (single histo fit)." << std::endl;
-      fValid = false;
-      return;
-    }
-    if (length < 0) {
-      std::cerr << ">> PFitterFcnDKS::InitDKS: **ERROR** failed for single histo data set (i=" << i << ") from fRunListCollection." << std::endl;
-      std::cerr << ">> PFitterFcnDKS::InitDKS: **ERROR** (endTimeBin=" << endTimeBin << ") < (startTimeBin=" << startTimeBin << ")." << std::endl;
-      fValid = false;
-      return;
-    }
-    fMemDataSingleHisto[i] = fDKS.allocateMemory<Double_t>(length, ierr);
-    fMemDataSingleHistoErr[i] = fDKS.allocateMemory<Double_t>(length, ierr);
-    if (ierr != 0) {
-      std::cerr << ">> PFitterFcnDKS::InitDKS: **ERROR** failed to allocated single histo data set memory (i=" << i << ") on the GPU" << std::endl;
-      fValid = false;
-      return;
-    }
-    fDKS.writeData<double>(fMemDataSingleHisto[i], &runData->GetValue()->at(startTimeBin), length);
-    fDKS.writeData<double>(fMemDataSingleHistoErr[i], &runData->GetError()->at(startTimeBin), length);
-  }
-  if (fRunListCollection->GetNoOfSingleHisto() > 0)
-    fitType = FITTYPE_SINGLE_HISTO;
-
-  // asymmetry
-  fMemDataAsymmetry.resize(fRunListCollection->GetNoOfAsymmetry());
-  fMemDataAsymmetryErr.resize(fRunListCollection->GetNoOfAsymmetry());
-  for (UInt_t i=0; i<fRunListCollection->GetNoOfAsymmetry(); i++) {
-    runData = fRunListCollection->GetAsymmetry(i);
-    if (runData == 0) {
-      std::cerr << ">> PFitterFcnDKS::InitDKS: **ERROR** failed to get asymmetry data set (i=" << i << ") from fRunListCollection." << std::endl;
-      fValid = false;
-      return;
-    }
-    startTimeBin = fRunListCollection->GetStartTimeBin(MSR_FITTYPE_ASYM, i);
-    endTimeBin   = fRunListCollection->GetEndTimeBin(MSR_FITTYPE_ASYM, i);
-    length = endTimeBin-startTimeBin;
-    if (startTimeBin < 0) {
-      std::cerr << ">> PFitterFcnDKS::InitDKS: **ERROR** startTimeBin undefind (asymmetry fit)." << std::endl;
-      fValid = false;
-      return;
-    }
-    if (endTimeBin < 0) {
-      std::cerr << ">> PFitterFcnDKS::InitDKS: **ERROR** endTimeBin undefind (asymmetry fit)." << std::endl;
-      fValid = false;
-      return;
-    }
-    if (length < 0) {
-      std::cerr << ">> PFitterFcnDKS::InitDKS: **ERROR** failed for asymmetry data set (i=" << i << ") from fRunListCollection." << std::endl;
-      std::cerr << ">> PFitterFcnDKS::InitDKS: **ERROR** (endTimeBin=" << endTimeBin << ") < (startTimeBin=" << startTimeBin << ")." << std::endl;
-      fValid = false;
-      return;
-    }
-    fMemDataAsymmetry[i] = fDKS.allocateMemory<Double_t>(length, ierr);
-    fMemDataAsymmetryErr[i] = fDKS.allocateMemory<Double_t>(length, ierr);
-    if (ierr != 0) {
-      std::cerr << ">> PFitterFcnDKS::InitDKS: **ERROR** failed to allocated asymmetry data set memory (i=" << i << ") on the GPU" << std::endl;
-      fValid = false;
-      return;
-    }
-    fDKS.writeData<double>(fMemDataAsymmetry[i], &runData->GetValue()->at(startTimeBin), length);
-    fDKS.writeData<double>(fMemDataAsymmetryErr[i], &runData->GetError()->at(startTimeBin), length);
-  }
-  if (fRunListCollection->GetNoOfAsymmetry() > 0) {
-    if (fitType == FITTYPE_UNDEFINED) {
-      fitType = FITTYPE_ASYMMETRY;
-    } else {
-      std::cerr << ">>PFitterFcnDKS::InitDKS: **ERROR** mixed fit types found. This is currently not supported!" << std::endl;
-      fValid = false;
-      return;
-    }
-  }
-
-  // mu minus
-  fMemDataMuMinus.resize(fRunListCollection->GetNoOfMuMinus());
-  fMemDataMuMinusErr.resize(fRunListCollection->GetNoOfMuMinus());
-  for (UInt_t i=0; i<fRunListCollection->GetNoOfMuMinus(); i++) {
-    runData = fRunListCollection->GetMuMinus(i);
-    if (runData == 0) {
-      std::cerr << ">> PFitterFcnDKS::InitDKS: **ERROR** failed to get mu minus data set (i=" << i << ") from fRunListCollection." << std::endl;
-      fValid = false;
-      return;
-    }
-    startTimeBin = fRunListCollection->GetStartTimeBin(MSR_FITTYPE_MU_MINUS, i);
-    endTimeBin   = fRunListCollection->GetEndTimeBin(MSR_FITTYPE_MU_MINUS, i);
-    length = endTimeBin-startTimeBin;
-    if (startTimeBin < 0) {
-      std::cerr << ">> PFitterFcnDKS::InitDKS: **ERROR** startTimeBin undefind (mu minus fit)." << std::endl;
-      fValid = false;
-      return;
-    }
-    if (endTimeBin < 0) {
-      std::cerr << ">> PFitterFcnDKS::InitDKS: **ERROR** endTimeBin undefind (mu minus fit)." << std::endl;
-      fValid = false;
-      return;
-    }
-    if (length < 0) {
-      std::cerr << ">> PFitterFcnDKS::InitDKS: **ERROR** failed for mu minus data set (i=" << i << ") from fRunListCollection." << std::endl;
-      std::cerr << ">> PFitterFcnDKS::InitDKS: **ERROR** (endTimeBin=" << endTimeBin << ") < (startTimeBin=" << startTimeBin << ")." << std::endl;
-      fValid = false;
-      return;
-    }
-    fMemDataMuMinus[i] = fDKS.allocateMemory<Double_t>(length, ierr);
-    fMemDataMuMinusErr[i] = fDKS.allocateMemory<Double_t>(length, ierr);
-    if (ierr != 0) {
-      std::cerr << ">> PFitterFcnDKS::InitDKS: **ERROR** failed to allocated mu minus data set memory (i=" << i << ") on the GPU" << std::endl;
-      fValid = false;
-      return;
-    }
-    fDKS.writeData<double>(fMemDataMuMinus[i], &runData->GetValue()->at(startTimeBin), length);
-    fDKS.writeData<double>(fMemDataMuMinusErr[i], &runData->GetError()->at(startTimeBin), length);
-  }
-  if (fRunListCollection->GetNoOfMuMinus() > 0) {
-    if (fitType == FITTYPE_UNDEFINED) {
-      fitType = FITTYPE_MU_MINUS;
-    } else {
-      std::cerr << ">>PFitterFcnDKS::InitDKS: **ERROR** mixed fit types found. This is currently not supported!" << std::endl;
-      fValid = false;
-      return;
-    }
-  }
-
-  // set the function string and compile the program
-  ierr = fDKS.callCompileProgram(fTheoStr, !fUseChi2);
-  if (ierr != 0) {
-    std::cerr << ">> PFitterFcnDKS::InitDKS: **ERROR** failed to compile theory!" << std::endl;
-    fValid = false;
-    return;
-  }
-
-  // checks device properties if openCL
-  ierr = fDKS.checkMuSRKernels(fitType);
-  if (ierr != 0) {
-    std::cerr << ">> PFitterFcnDKS::InitDKS: **ERROR** muSR kernel checks failed!" << std::endl;
-    fValid = false;
-    return;
-  }
-
-  fValid = true;
-}
-
-//--------------------------------------------------------------------------
-// FreeDKS (private)
-//--------------------------------------------------------------------------
-/**
- * <p>cleanup DKS/GPU memory
- *
- */
-void PFitterFcnDKS::FreeDKS()
-{
-  PRunData *runData=0;
-  // single histo
-  for (UInt_t i=0; i<fMemDataSingleHisto.size(); i++) {
-    runData = fRunListCollection->GetSingleHisto(i);
-    fDKS.freeMemory<Double_t>(fMemDataSingleHisto[i], runData->GetValue()->size());
-    fDKS.freeMemory<Double_t>(fMemDataSingleHistoErr[i], runData->GetValue()->size());
-  }
-  fMemDataSingleHisto.clear();
-  fMemDataSingleHistoErr.clear();
-
-  // asymmetry
-  for (UInt_t i=0; i<fMemDataAsymmetry.size(); i++) {
-    runData = fRunListCollection->GetAsymmetry(i);
-    fDKS.freeMemory<Double_t>(fMemDataAsymmetry[i], runData->GetValue()->size());
-    fDKS.freeMemory<Double_t>(fMemDataAsymmetryErr[i], runData->GetValue()->size());
-  }
-  fMemDataAsymmetry.clear();
-  fMemDataAsymmetryErr.clear();
-
-  // mu minus
-  for (UInt_t i=0; i<fMemDataMuMinus.size(); i++) {
-    runData = fRunListCollection->GetMuMinus(i);
-    fDKS.freeMemory<Double_t>(fMemDataMuMinus[i], runData->GetValue()->size());
-    fDKS.freeMemory<Double_t>(fMemDataMuMinusErr[i], runData->GetValue()->size());
-  }
-  fMemDataMuMinus.clear();
-  fMemDataMuMinusErr.clear();
-}
--- a/src/classes/PFourier.cpp
+++ b/src/classes/PFourier.cpp
@@ -479,7 +479,7 @@ double PFTPhaseCorrection::operator()(const std::vector<double> &par) const
 * @see Transform()
 * @see IsValid()
 */
-PFourier::PFourier(TH1F *data, Int_t unitTag, Double_t startTime, Double_t endTime, Bool_t dcCorrected, UInt_t zeroPaddingPower, Bool_t useFFTW) :
+PFourier::PFourier(TH1F *data, Int_t unitTag, Double_t startTime, Double_t endTime, Bool_t dcCorrected, UInt_t zeroPaddingPower) :
                   fData(data), fUnitTag(unitTag), fStartTime(startTime), fEndTime(endTime),
                   fDCCorrected(dcCorrected), fZeroPaddingPower(zeroPaddingPower)
 {
@@ -491,16 +491,9 @@ PFourier::PFourier(TH1F *data, Int_t unitTag, Double_t startTime, Double_t endTi
  }

  fValid = true;
-  fUseFFTW = true;
  fIn  = nullptr;
  fOut = nullptr;
-
-#ifdef HAVE_DKS
-  fInDKS = nullptr;
-  fOutDKS = nullptr;
-#endif
-
-  SetUseFFTW(useFFTW);
+//as  fPhCorrectedReFT = 0;

  fApodization = F_APODIZATION_NONE;

@@ -555,71 +548,21 @@ PFourier::PFourier(TH1F *data, Int_t unitTag, Double_t startTime, Double_t endTi
  }

  // allocate necessary memory
-  if (fUseFFTW) {
-    fIn  = static_cast<fftw_complex *>(fftw_malloc(sizeof(fftw_complex)*fNoOfBins));
-    fOut = static_cast<fftw_complex *>(fftw_malloc(sizeof(fftw_complex)*fNoOfBins));
-  } else { // try DKS
-#ifdef HAVE_DKS
-    fInDKS  = new double[fNoOfBins];
-    unsigned int size=fNoOfBins/2+1;
-    fOutDKS = new complex<double>[size];
-#endif
-  }
+  fIn  = static_cast<fftw_complex *>(fftw_malloc(sizeof(fftw_complex)*fNoOfBins));
+  fOut = static_cast<fftw_complex *>(fftw_malloc(sizeof(fftw_complex)*fNoOfBins));

  // check if memory allocation has been successful
-  if (fUseFFTW) {
-    if ((fIn == nullptr) || (fOut == nullptr)) {
-      fValid = false;
-      return;
-    }
-  } else { // try DKS
-#ifdef HAVE_DKS
-    if ((fInDKS == nullptr) || (fOutDKS == nullptr)) {
-      fValid = false;
-      return;
-    }
-#else
+  if ((fIn == nullptr) || (fOut == nullptr)) {
    fValid = false;
    return;
-#endif
  }

-  if (fUseFFTW) {
-    // get the FFTW3 plan (see FFTW3 manual)
-    fFFTwPlan = fftw_plan_dft_1d(fNoOfBins, fIn, fOut, FFTW_FORWARD, FFTW_ESTIMATE);
+  // get the FFTW3 plan (see FFTW3 manual)
+  fFFTwPlan = fftw_plan_dft_1d(static_cast<Int_t>(fNoOfBins), fIn, fOut, FFTW_FORWARD, FFTW_ESTIMATE);

-    // check if a valid plan has been generated
-    if (!fFFTwPlan) {
-      fValid = false;
-    }
-  } else { // try DKS
-#ifdef HAVE_DKS
-    // init DKSBase
-    fDks.setAPI("Cuda", 4);
-    fDks.setDevice("-gpu", 4);
-    fDks.initDevice();
-    int dimsize[3] = {(int)fNoOfBins, 1, 1};
-    fDks.setupFFT(1, dimsize);
-    // allocate memory on accelerator
-    int ierr;
-    unsigned int size=fNoOfBins/2+1;
-    fReal_ptr = 0;
-    fComp_ptr = 0;
-    fReal_ptr = fDks.allocateMemory<double>(fNoOfBins, ierr);
-    if (ierr > 0) {
-      cerr << ">> PFourier: **ERROR** Couldn't allocate memory for fReal_ptr." << endl;
-      fValid = false;
-    }
-    fComp_ptr = fDks.allocateMemory< complex<double> >(size, ierr);
-    if (ierr > 0) {
-      cerr << ">> PFourier: **ERROR** Couldn't allocate memory for fComp_ptr." << endl;
-      fValid = false;
-    }
-    if ((fReal_ptr==0) || (fComp_ptr==0))
-      fValid = false;
-#else
+  // check if a valid plan has been generated
+  if (!fFFTwPlan) {
    fValid = false;
-#endif
  }
 }

@@ -640,25 +583,14 @@ PFourier::PFourier(TH1F *data, Int_t unitTag, Double_t startTime, Double_t endTi
 */
 PFourier::~PFourier()
 {
-  if (fUseFFTW) {
-    if (fFFTwPlan)
-      fftw_destroy_plan(fFFTwPlan);
-    if (fIn)
-      fftw_free(fIn);
-    if (fOut)
-      fftw_free(fOut);
-  } else {
-#ifdef HAVE_DKS
-    // free accelerator memory
-    fDks.freeMemory<double>(fReal_ptr, (int)fNoOfBins);
-    int size = fNoOfBins/2+1;
-    fDks.freeMemory< complex<double> >(fComp_ptr, size);
-    if (fIn)
-      delete [] fInDKS;
-    if (fOut)
-      delete [] fOutDKS;
-#endif
-  }
+  if (fFFTwPlan)
+    fftw_destroy_plan(fFFTwPlan);
+  if (fIn)
+    fftw_free(fIn);
+  if (fOut)
+    fftw_free(fOut);
+//as  if (fPhCorrectedReFT)
+//as    delete fPhCorrectedReFT;
 }

 //--------------------------------------------------------------------------
@@ -704,23 +636,7 @@ void PFourier::Transform(UInt_t apodizationTag)

  PrepareFFTwInputData(apodizationTag);

-  if (fUseFFTW) {
-    fftw_execute(fFFTwPlan);
-  } else {
-#ifdef HAVE_DKS
-    int dimsize[3] = {(int)fNoOfBins, 1, 1};
-    int status=0, size=fNoOfBins/2+1;
-    // write data to the accelerator
-    status = fDks.writeData<double>(fReal_ptr, fInDKS, fNoOfBins);
-    // execute the FFT
-    status = fDks.callR2CFFT(fReal_ptr, fComp_ptr, 1, dimsize);
-    // read data from accelerator
-    status = fDks.readData< complex<double> >(fComp_ptr, fOutDKS, size);
-#else
-    fValid = false;
-    return;
-#endif
-  }
+  fftw_execute(fFFTwPlan);

  // correct the phase for tstart != 0.0
  // find the first bin >= fStartTime
@@ -733,42 +649,12 @@ void PFourier::Transform(UInt_t apodizationTag)
  }

  Double_t phase, re, im;
-  if (fUseFFTW) {
-    for (UInt_t i=0; i<fNoOfBins; i++) {
-      phase = 2.0*PI/(fTimeResolution*fNoOfBins) * i * shiftTime;
-      re =  fOut[i][0] * cos(phase) + fOut[i][1] * sin(phase);
-      im = -fOut[i][0] * sin(phase) + fOut[i][1] * cos(phase);
-      fOut[i][0] = re;
-      fOut[i][1] = im;
-    }
-  } else { // try DKS
-    UInt_t size=fNoOfBins/2+1;
-    for (UInt_t i=0; i<size; i++) {
-      phase = 2.0*PI/(fTimeResolution*fNoOfBins) * i * shiftTime;
-#ifdef HAVE_DKS
-      re =  fOutDKS[i].real() * cos(phase) + fOutDKS[i].imag() * sin(phase);
-      im = -fOutDKS[i].real() * sin(phase) + fOutDKS[i].imag() * cos(phase);
-      fOutDKS[i] = complex<double>(re, im);
-#endif
-    }
-  }
-}
-
-//--------------------------------------------------------------------------
-// SetUseFFTW
-//--------------------------------------------------------------------------
-/**
- * <p>Set fUseFFTW flag. Checks if DKS support is in place before setting the flag.
- */
-void PFourier::SetUseFFTW(const Bool_t flag)
-{
-  if (flag == false) {
-#ifndef HAVE_DKS
-    fUseFFTW = true;
-    std::cerr << std::endl << "PFouier::SetUseFFTW: **ERROR** DKS not in use, will fall back to FFTW" << std::endl << std::endl;
-#else
-    fUseFFTW = flag;
-#endif
+  for (UInt_t i=0; i<fNoOfBins; i++) {
+    phase = 2.0*PI/(fTimeResolution*fNoOfBins) * i * shiftTime;
+    re =  fOut[i][0] * cos(phase) + fOut[i][1] * sin(phase);
+    im = -fOut[i][0] * sin(phase) + fOut[i][1] * cos(phase);
+    fOut[i][0] = re;
+    fOut[i][1] = im;
  }
 }

@@ -798,7 +684,11 @@ void PFourier::SetUseFFTW(const Bool_t flag)
 */
 Double_t PFourier::GetMaxFreq()
 {
-  UInt_t noOfFourierBins = fNoOfBins/2+1;
+  UInt_t noOfFourierBins = 0;
+  if (fNoOfBins % 2 == 0)
+    noOfFourierBins = fNoOfBins/2;
+  else
+    noOfFourierBins = (fNoOfBins+1)/2;

  return fResolution*noOfFourierBins;
 }
@@ -850,7 +740,11 @@ TH1F* PFourier::GetRealFourier(const Double_t scale)
  snprintf(name, sizeof(name), "%s_Fourier_Re", fData->GetName());
  snprintf(title, sizeof(title), "%s_Fourier_Re", fData->GetTitle());

-  UInt_t noOfFourierBins = fNoOfBins/2+1;
+  UInt_t noOfFourierBins = 0;
+  if (fNoOfBins % 2 == 0)
+    noOfFourierBins = fNoOfBins/2;
+  else
+    noOfFourierBins = (fNoOfBins+1)/2;

  TH1F *realFourier = new TH1F(name, title, static_cast<Int_t>(noOfFourierBins), -fResolution/2.0, static_cast<Double_t>(noOfFourierBins-1)*fResolution+fResolution/2.0);
  if (realFourier == nullptr) {
@@ -860,19 +754,9 @@ TH1F* PFourier::GetRealFourier(const Double_t scale)
  }

  // fill realFourier vector
-  if (fUseFFTW) {
-    for (Int_t i=0; i<static_cast<Int_t>(noOfFourierBins); i++) {
-      realFourier->SetBinContent(i+1, scale*fOut[i][0]);
-      realFourier->SetBinError(i+1, 0.0);
-    }
-  } else {
-    for (Int_t i=0; i<static_cast<Int_t>(noOfFourierBins); i++) {
-#ifdef HAVE_DKS
-      realFourier->SetBinContent(i+1, scale*fOutDKS[i].real());
-#else
-      realFourier->SetBinContent(i+1, PMUSR_UNDEFINED);
-#endif
-    }
+  for (Int_t i=0; i<static_cast<Int_t>(noOfFourierBins); i++) {
+    realFourier->SetBinContent(i+1, scale*fOut[i][0]);
+    realFourier->SetBinError(i+1, 0.0);
  }
  return realFourier;
 }
@@ -1056,7 +940,11 @@ TH1F* PFourier::GetImaginaryFourier(const Double_t scale)
  snprintf(name, sizeof(name), "%s_Fourier_Im", fData->GetName());
  snprintf(title, sizeof(title), "%s_Fourier_Im", fData->GetTitle());

-  UInt_t noOfFourierBins = fNoOfBins/2+1;
+  UInt_t noOfFourierBins = 0;
+  if (fNoOfBins % 2 == 0)
+    noOfFourierBins = fNoOfBins/2;
+  else
+    noOfFourierBins = (fNoOfBins+1)/2;

  TH1F* imaginaryFourier = new TH1F(name, title, static_cast<Int_t>(noOfFourierBins), -fResolution/2.0, static_cast<Double_t>(noOfFourierBins-1)*fResolution+fResolution/2.0);
  if (imaginaryFourier == nullptr) {
@@ -1066,20 +954,11 @@ TH1F* PFourier::GetImaginaryFourier(const Double_t scale)
  }

  // fill imaginaryFourier vector
-  if (fUseFFTW) {
-    for (Int_t i=0; i<static_cast<Int_t>(noOfFourierBins); i++) {
-      imaginaryFourier->SetBinContent(i+1, scale*fOut[i][1]);
-      imaginaryFourier->SetBinError(i+1, 0.0);
-    }
-  } else {
-    for (Int_t i=0; i<static_cast<Int_t>(noOfFourierBins); i++) {
-#ifdef HAVE_DKS
-      imaginaryFourier->SetBinContent(i+1, scale*fOutDKS[i].imag());
-#else
-      imaginaryFourier->SetBinContent(i+1, PMUSR_UNDEFINED);
-#endif
-    }
+  for (Int_t i=0; i<static_cast<Int_t>(noOfFourierBins); i++) {
+    imaginaryFourier->SetBinContent(i+1, scale*fOut[i][1]);
+    imaginaryFourier->SetBinError(i+1, 0.0);
  }
+
  return imaginaryFourier;
 }

@@ -1131,7 +1010,11 @@ TH1F* PFourier::GetPowerFourier(const Double_t scale)
  snprintf(name, sizeof(name), "%s_Fourier_Pwr", fData->GetName());
  snprintf(title, sizeof(title), "%s_Fourier_Pwr", fData->GetTitle());

-  UInt_t noOfFourierBins = fNoOfBins/2+1;
+  UInt_t noOfFourierBins = 0;
+  if (fNoOfBins % 2 == 0)
+    noOfFourierBins = fNoOfBins/2;
+  else
+    noOfFourierBins = (fNoOfBins+1)/2;

  TH1F* pwrFourier = new TH1F(name, title, static_cast<Int_t>(noOfFourierBins), -fResolution/2.0, static_cast<Double_t>(noOfFourierBins-1)*fResolution+fResolution/2.0);
  if (pwrFourier == nullptr) {
@@ -1141,20 +1024,11 @@ TH1F* PFourier::GetPowerFourier(const Double_t scale)
  }

  // fill powerFourier vector
-  if (fUseFFTW) {
-    for (Int_t i=0; i<static_cast<Int_t>(noOfFourierBins); i++) {
-      pwrFourier->SetBinContent(i+1, scale*sqrt(fOut[i][0]*fOut[i][0]+fOut[i][1]*fOut[i][1]));
-      pwrFourier->SetBinError(i+1, 0.0);
-    }
-  } else {
-    for (Int_t i=0; i<static_cast<Int_t>(noOfFourierBins); i++) {
-#ifdef HAVE_DKS
-      pwrFourier->SetBinContent(i+1, scale*sqrt(fOutDKS[i].real()*fOutDKS[i].real()+fOutDKS[i].imag()*fOutDKS[i].imag()));
-#else
-      pwrFourier->SetBinContent(i+1, PMUSR_UNDEFINED);
-#endif
-    }
+  for (Int_t i=0; i<static_cast<Int_t>(noOfFourierBins); i++) {
+    pwrFourier->SetBinContent(i+1, scale*sqrt(fOut[i][0]*fOut[i][0]+fOut[i][1]*fOut[i][1]));
+    pwrFourier->SetBinError(i+1, 0.0);
  }
+
  return pwrFourier;
 }

@@ -1208,7 +1082,11 @@ TH1F* PFourier::GetPhaseFourier(const Double_t scale)
  snprintf(name, sizeof(name), "%s_Fourier_Phase", fData->GetName());
  snprintf(title, sizeof(title), "%s_Fourier_Phase", fData->GetTitle());

-  UInt_t noOfFourierBins = fNoOfBins/2+1;
+  UInt_t noOfFourierBins = 0;
+  if (fNoOfBins % 2 == 0)
+    noOfFourierBins = fNoOfBins/2;
+  else
+    noOfFourierBins = (fNoOfBins+1)/2;

  TH1F* phaseFourier = new TH1F(name, title, static_cast<Int_t>(noOfFourierBins), -fResolution/2.0, static_cast<Double_t>(noOfFourierBins-1)*fResolution+fResolution/2.0);
  if (phaseFourier == nullptr) {
@@ -1219,31 +1097,18 @@ TH1F* PFourier::GetPhaseFourier(const Double_t scale)

  // fill phaseFourier vector
  Double_t value = 0.0;
-  Double_t re, im;
  for (Int_t i=0; i<static_cast<Int_t>(noOfFourierBins); i++) {
-    if (fUseFFTW) {
-      re = fOut[i][0];
-      im = fOut[i][1];
-    } else {
-#ifdef HAVE_DKS
-      re = fOutDKS[i].real();
-      im = fOutDKS[i].imag();
-#else
-      re = 1.0;
-      im = 0.0;
-#endif
-    }
    // calculate the phase
-    if (re == 0) {
-      if (im >= 0.0)
+    if (fOut[i][0] == 0.0) {
+      if (fOut[i][1] >= 0.0)
        value = PI_HALF;
      else
        value = -PI_HALF;
    } else {
-      value = atan(re/im);
+      value = atan(fOut[i][1]/fOut[i][0]);
      // check sector
-      if (re < 0.0) {
-        if (im > 0.0)
+      if (fOut[i][0] < 0.0) {
+        if (fOut[i][1] > 0.0)
          value = PI + value;
        else
          value = PI - value;
@@ -1298,42 +1163,28 @@ void PFourier::PrepareFFTwInputData(UInt_t apodizationTag)
    }
  }

-  // find the bin of the start time
  Int_t ival = static_cast<Int_t>(fStartTime/fTimeResolution) + t0bin;
-  UInt_t start = 1;
-  if (ival > 0) { // start time > 0
+  UInt_t start = 0;
+  if (ival >= 0) {
    start = static_cast<UInt_t>(ival);
  }

  Double_t mean = 0.0;
  if (fDCCorrected) {
-    for (UInt_t i=start; i<start+fNoOfData; i++) {
-      mean += fData->GetBinContent(static_cast<Int_t>(i));
+    for (UInt_t i=0; i<fNoOfData; i++) {
+      mean += fData->GetBinContent(static_cast<Int_t>(i+start));
    }
    mean /= static_cast<Double_t>(fNoOfData);
-  }  
+  }

  // 2nd fill fIn
-  if (fUseFFTW) {
-    for (UInt_t i=0; i<fNoOfData; i++) {
-      fIn[i][0] = fData->GetBinContent(static_cast<Int_t>(i+start)) - mean;
-      fIn[i][1] = 0.0;
-    }
-    for (UInt_t i=fNoOfData; i<fNoOfBins; i++) {
-      fIn[i][0] = 0.0;
-      fIn[i][1] = 0.0;
-    }
-  } else {
-    for (UInt_t i=0; i<fNoOfData; i++) {
-#ifdef HAVE_DKS
-      fInDKS[i] = fData->GetBinContent(static_cast<Int_t>(i+start)) - mean;
-#endif
-    }
-    for (UInt_t i=fNoOfData; i<fNoOfBins; i++) {
-#ifdef HAVE_DKS
-      fInDKS[i] = 0.0;
-#endif
-    }
+  for (UInt_t i=0; i<fNoOfData; i++) {
+    fIn[i][0] = fData->GetBinContent(static_cast<Int_t>(i+start)) - mean;
+    fIn[i][1] = 0.0;
+  }
+  for (UInt_t i=fNoOfData; i<fNoOfBins; i++) {
+    fIn[i][0] = 0.0;
+    fIn[i][1] = 0.0;
  }

  // 3rd apodize data (if wished)
@@ -1374,9 +1225,6 @@ void PFourier::PrepareFFTwInputData(UInt_t apodizationTag)
 */
 void PFourier::ApodizeData(Int_t apodizationTag) {

-  if (apodizationTag == F_APODIZATION_NONE)
-    return;
-
  const Double_t cweak[3]   = { 0.384093, -0.087577, 0.703484 };
  const Double_t cmedium[3] = { 0.152442, -0.136176, 0.983734 };
  const Double_t cstrong[3] = { 0.045335,  0.554883, 0.399782 };
@@ -1417,12 +1265,6 @@ void PFourier::ApodizeData(Int_t apodizationTag) {
    for (UInt_t j=1; j<5; j++) {
      q += c[j] * pow(static_cast<Double_t>(i)/static_cast<Double_t>(fNoOfData), 2.0*static_cast<Double_t>(j));
    }
-    if (fUseFFTW) {
-      fIn[i][0] *= q;
-    } else {
-#ifdef HAVE_DKS
-      fInDKS[i] *= q;
-#endif
-    }
+    fIn[i][0] *= q;
  }
 }
--- a/src/classes/PFunctionHandler.cpp
+++ b/src/classes/PFunctionHandler.cpp
@@ -137,18 +137,6 @@ Bool_t PFunctionHandler::DoParse()
    }
  }

-  // for DKS, functions must be numbered consecutive
-  if (success) {
-    for (UInt_t i=0; i<fFuncs.size(); i++) {
-      if (fFuncs[i].GetFuncNo() != i+1) {
-        std::cerr << std::endl << "**ERROR**: for DKS, the function numbers need to be consecutive, sorry.";
-        std::cerr << std::endl;
-        success = false;
-        break;
-      }
-    }
-  }
-
  return success;
 }

--- a/src/classes/PMsrHandler.cpp
+++ b/src/classes/PMsrHandler.cpp
@@ -3973,6 +3973,7 @@ Bool_t PMsrHandler::HandleRunEntry(PMsrLines &lines)
      }
    }

+
    // xy-data -----------------------------------------------
    if (line.BeginsWith("xy-data", TString::kIgnoreCase)) {

@@ -6449,14 +6450,6 @@ Bool_t PMsrHandler::CheckMaps()
    }
  }

-  if (result == true) {
-    PIntVector *map = fRuns[0].GetMap();
-    fNoOfMaps = 0;
-    for (UInt_t i=0; i<map->size(); i++)
-      if (map->at(i) != 0)
-        fNoOfMaps++;
-  }
-
  // clean up
  mapVec.clear();
  mapBlock.clear();
@@ -6859,359 +6852,6 @@ Bool_t PMsrHandler::EstimateN0()
  return fStartupOptions->estimateN0;
 }

-//--------------------------------------------------------------------------
-// GetDKSTheoryString (public)
-//--------------------------------------------------------------------------
-/**
- * <p>returns the theory string in a c++ compatible string. This is needed
- * for DKS/GPU.
- *
- * \return the theory in a c++ like string.
- */
-std::string PMsrHandler::GetDKSTheoryString()
-{
-  std::string result("");
-  PStringVector args;
-
-  TString tp = TString::Format("%.15lf", TMath::TwoPi());
-  TString ph = TString::Format("%.15lf", TMath::Pi() / 180.0);
-
-  for (UInt_t i=1; i<fTheory.size(); i++) { // start with 1, since fTheory[0].fLine == "THEORY"
-    if (i > 1) {
-      if (!fTheory[i-1].fLine.BeginsWith("+")) {
-        result += " * ";
-      }
-    }
-
-    HandleTheoryArguments(fTheory[i].fLine, args);
-
-    if (fTheory[i].fLine.BeginsWith("asymmetry ", TString::kIgnoreCase) ||
-        fTheory[i].fLine.BeginsWith("a ", TString::kIgnoreCase)) {
-      result += args[0].Data();
-    } else if (fTheory[i].fLine.BeginsWith("const ", TString::kIgnoreCase) ||
-               fTheory[i].fLine.BeginsWith("c ", TString::kIgnoreCase)) {
-      result += args[0].Data();
-    } else if (fTheory[i].fLine.BeginsWith("simplExpo ", TString::kIgnoreCase) ||
-               fTheory[i].fLine.BeginsWith("se ")) { // se -> se(t,  lambda)
-      result += "se(t, ";
-      result += args[0].Data();
-      result += ")";
-    } else if (fTheory[i].fLine.BeginsWith("generExpo ", TString::kIgnoreCase) ||
-               fTheory[i].fLine.BeginsWith("ge ")) { // ge -> ge(t, lambda, beta)
-      result += "ge(t, ";
-      result += args[0].Data();
-      result += ", ";
-      result += args[1].Data();
-      result += ")";
-    } else if (fTheory[i].fLine.BeginsWith("simpleGss ", TString::kIgnoreCase) ||
-               fTheory[i].fLine.BeginsWith("sg ")) { // sg -> sg(t, sigma)
-      result += "sg(t, ";
-      result += args[0].Data();
-      result += ")";
-    } else if (fTheory[i].fLine.BeginsWith("statGssKT ", TString::kIgnoreCase) ||
-               fTheory[i].fLine.BeginsWith("stg ")) { // stg -> stg(t, sigma)
-
-      result += "stg(t, ";
-      result += args[0].Data();
-      result += ")";
-    } else if (fTheory[i].fLine.BeginsWith("statExpKT ", TString::kIgnoreCase) ||
-               fTheory[i].fLine.BeginsWith("sekt ")) { // sekt -> sekt(t, lambda)
-
-      result += "sekt(t, ";
-      result += args[0].Data();
-      result += ")";
-    } else if (fTheory[i].fLine.BeginsWith("combiLGKT ", TString::kIgnoreCase) ||
-               fTheory[i].fLine.BeginsWith("lgkt ")) { // lgkt -> lgkt(t, lambda, sigma)
-
-      result += "lgkt(t, ";
-      result += args[0].Data();
-      result += ", ";
-      result += args[1].Data();
-      result += ")";
-    } else if (fTheory[i].fLine.BeginsWith("strKT ", TString::kIgnoreCase) ||
-               fTheory[i].fLine.BeginsWith("skt ")) { // skt -> skt(t, sigma, beta)
-
-      result += "skt(t, ";
-      result += args[0].Data();
-      result += ", ";
-      result += args[1].Data();
-      result += ")";
-    } else if (fTheory[i].fLine.BeginsWith("spinGlass ", TString::kIgnoreCase) ||
-               fTheory[i].fLine.BeginsWith("spg ")) { // spg -> spg(t, lambda, gamma, q)
-
-      result += "spg(t, ";
-      result += args[0].Data();
-      result += ", ";
-      result += args[1].Data();
-      result += ", ";
-      result += args[2].Data();
-      result += ")";
-    } else if (fTheory[i].fLine.BeginsWith("rdAnisoHf ", TString::kIgnoreCase) ||
-               fTheory[i].fLine.BeginsWith("rahf ")) { // rahf -> rahf(t, nu, lambda)
-
-      result += "rahf(t, ";
-      result += args[0].Data();
-      result += ", ";
-      result += args[1].Data();
-      result += ")";
-    } else if (fTheory[i].fLine.BeginsWith("TFieldCos ", TString::kIgnoreCase) ||
-               fTheory[i].fLine.BeginsWith("tf ")) { // tf -> tf(t, phi (°), nu (MHz))
-      result += "tf(t, ";
-      result += args[0].Data();
-      result += ", ";
-      result += args[1].Data();
-      result += ")";
-    } else if (fTheory[i].fLine.BeginsWith("internFld ", TString::kIgnoreCase) ||
-               fTheory[i].fLine.BeginsWith("if ")) { // if -> ifld(t, alpha, phi, nu, lambdaT, lambdaL)
-
-      result += "ifld(t, ";
-      result += args[0].Data();
-      result += ", ";
-      result += args[1].Data();
-      result += ", ";
-      result += args[2].Data();
-      result += ", ";
-      result += args[3].Data();
-      result += ", ";
-      result += args[4].Data();
-      result += ")";
-    } else if (fTheory[i].fLine.BeginsWith("internFldGK ", TString::kIgnoreCase) ||
-               fTheory[i].fLine.BeginsWith("ifgk ", TString::kIgnoreCase)) { // if -> ifgk(t, alpha, nu, lambdaT, lambdaL, beta)
-      result += "ifgk(t, ";
-      result += args[0].Data();
-      result += ", ";
-      result += args[1].Data();
-      result += ", ";
-      result += args[2].Data();
-      result += ", ";
-      result += args[3].Data();
-      result += ", ";
-      result += args[4].Data();
-      result += ")";
-    } else if (fTheory[i].fLine.BeginsWith("internFldLL ", TString::kIgnoreCase) ||
-               fTheory[i].fLine.BeginsWith("ifll ", TString::kIgnoreCase)) { // if -> ifll(t, alpha, nu, lambdaT, lambdaL, beta)
-      result += "ifll(t, ";
-      result += args[0].Data();
-      result += ", ";
-      result += args[1].Data();
-      result += ", ";
-      result += args[2].Data();
-      result += ", ";
-      result += args[3].Data();
-      result += ", ";
-      result += args[4].Data();
-      result += ")";
-    } else if (fTheory[i].fLine.BeginsWith("Bessel ", TString::kIgnoreCase) ||
-               fTheory[i].fLine.BeginsWith("b ")) { // b -> b(t, phi, nu)
-
-      result += "b(t, ";
-      result += args[0].Data();
-      result += ", ";
-      result += args[1].Data();
-      result += ")";
-    } else if (fTheory[i].fLine.BeginsWith("internBsl ", TString::kIgnoreCase) ||
-               fTheory[i].fLine.BeginsWith("ib ")) { // ib -> ib(t, alpha, phi, nu, lambdaT, lambdaL)
-
-      result += "ib(t, ";
-      result += args[0].Data();
-      result += ", ";
-      result += args[1].Data();
-      result += ", ";
-      result += args[2].Data();
-      result += ", ";
-      result += args[3].Data();
-      result += ", ";
-      result += args[4].Data();
-      result += ")";
-    } else if (fTheory[i].fLine.BeginsWith("abragam ", TString::kIgnoreCase) ||
-               fTheory[i].fLine.BeginsWith("ab ")) { // ab -> ab(t, sigma, gamma)
-      result += "ab(t, ";
-      result += args[0].Data();
-      result += ", ";
-      result += args[1].Data();
-      result += ")";
-    } else if (fTheory[i].fLine.BeginsWith("staticNKZF ", TString::kIgnoreCase) ||
-               fTheory[i].fLine.BeginsWith("snkzf ")) { // snkzf -> snkzf(t, Deltat0, Rb)
-      result += "snkzf(t, ";
-      result += args[0].Data();
-      result += ", ";
-      result += args[1].Data();
-      result += ")";
-    } else if (fTheory[i].fLine.BeginsWith("staticNKTF ", TString::kIgnoreCase) ||
-               fTheory[i].fLine.BeginsWith("snktf ")) { // snktf -> snktf(t, phi, nu, Delta0, Rb)
-
-      result += "snktf(t, ";
-      result += args[0].Data();
-      result += ", ";
-      result += args[1].Data();
-      result += ", ";
-      result += args[2].Data();
-      result += ", ";
-      result += args[3].Data();
-      result += ")";
-    } else if (fTheory[i].fLine.BeginsWith("dynamicNKZF ", TString::kIgnoreCase) ||
-               fTheory[i].fLine.BeginsWith("dnkzf ")) { // dnkzf -> dnkzf(t, Delta0, Rb, nu_c)
-
-      result += "dnkzf(t, ";
-      result += args[0].Data();
-      result += ", ";
-      result += args[1].Data();
-      result += ", ";
-      result += args[2].Data();
-      result += ")";
-    } else if (fTheory[i].fLine.BeginsWith("dynamicNKTF ", TString::kIgnoreCase) ||
-               fTheory[i].fLine.BeginsWith("dnktf ")) { // dnktf -> dnktf(t, phi, nu, Delta0, Rb, nu_c)
-
-      result += "dnktf(t, ";
-      result += args[0].Data();
-      result += ", ";
-      result += args[1].Data();
-      result += ", ";
-      result += args[2].Data();
-      result += ", ";
-      result += args[3].Data();
-      result += ", ";
-      result += args[4].Data();
-      result += ")";
-    } else if (fTheory[i].fLine.BeginsWith("muMinusExpTF ", TString::kIgnoreCase) ||
-               fTheory[i].fLine.BeginsWith("mmsetf ")) { // mmsetf -> mmsetf(t, N0, tau, A, lambda, phi, nu)
-
-      result += "mmsetf(t, ";
-      result += args[0].Data();
-      result += ", ";
-      result += args[1].Data();
-      result += ", ";
-      result += args[2].Data();
-      result += ", ";
-      result += args[3].Data();
-      result += ", ";
-      result += args[4].Data();
-      result += ", ";
-      result += args[5].Data();
-      result += ")";
-    } else if (fTheory[i].fLine.BeginsWith("+")) {
-      result.erase(result.end()-3, result.end()); // remove the '*' at the end
-      result += " + ";
-    } else {
-      result = std::string("??"); // not yet available in DKS
-      break;
-    }
-  }
-
-  std::cout << "debug> ++++" << std::endl;
-  std::cout << "debug> " << result << std::endl;
-  std::cout << "debug> ++++" << std::endl;
-
-  return result;
-}
-
-//--------------------------------------------------------------------------
-// GetDKSTag (public)
-//--------------------------------------------------------------------------
-/**
- * <p> Checks the COMMAND block for DKS related tags. Currently the following
- * tags are allowed:
- * (i) OpenMP: which means run on the CPU with OpenMP
- * (ii) Cuda: which means run on the GPU using Cuda
- * (iii) OpenCL-CPU: which means run on the CPU with OpenCL
- * (iv) OpenCL-GPU: which means run on the GPU with OpenCL
- *
- * @return DKS tag
- */
-UInt_t PMsrHandler::GetDKSTag()
-{
-  UInt_t count=0;
-  UInt_t tag = DKS_CPU_OPENMP;
-  TString last("");
-
-  for (UInt_t i=0; i<fCommands.size(); i++) {
-    if (fCommands[i].fLine.Contains("OpenMP", TString::kIgnoreCase)) {
-      count++;
-      tag = DKS_CPU_OPENMP;
-      last = "OpenMP";
-    } else if (fCommands[i].fLine.Contains("Cuda", TString::kIgnoreCase)) {
-      count++;
-      tag = DKS_GPU_CUDA;
-      last = "Cuda";
-    } else if (fCommands[i].fLine.Contains("OpenCL-CPU", TString::kIgnoreCase)) {
-      count++;
-      tag = DKS_CPU_OPENCL;
-      last = "OpenCL-CPU";
-    } else if (fCommands[i].fLine.Contains("OpenCL-GPU", TString::kIgnoreCase)) {
-      count++;
-      tag = DKS_GPU_OPENCL;
-      last = "OpenCL-GPU";
-    }
-  }
-
-  if (count > 1) {
-    std::cerr << ">> PMsrHandler::GetDKSTag(): **WARNING** found multiple DKS tags, will use the last one found: '" << last.Data() << "'" << std::endl;
-  }
-
-  return tag;
-}
-
-//--------------------------------------------------------------------------
-// HandleTheoryArguments (private)
-//--------------------------------------------------------------------------
-/**
- * <p>tokenizes the theory function arguments and transforms them for DKS
- *
- * \param theo
- * \param args vector of the transformed arguments
- */
-void PMsrHandler::HandleTheoryArguments(const TString theo, PStringVector &args)
-{
-  TObjArray *tok=theo.Tokenize(" \t");
-  TObjString *ostr=0;
-  TString str, argStr;
-  Int_t ival;
-
-  args.clear(); // make sure vector is empty
-
-  if (tok == 0) {
-    std::cerr << ">> PMsrHandler::HandleTheoryArguments(): **ERROR** couldn't tokensize '" << theo << "'" << std::endl;
-    return;
-  }
-
-  for (Int_t i=0; i<tok->GetEntries(); i++) {
-    ostr = dynamic_cast<TObjString*>(tok->At(i));
-    str = ostr->GetString();
-    if (str.BeginsWith("#") || str.BeginsWith("(")) { // comment or description
-      continue;
-    } else if (str.IsDigit()) { // parameter
-      ival = str.Atoi();
-      ival -= 1;
-      str = TString::Format("%d",ival);
-      argStr = "p["+ str +"]";
-      args.push_back(argStr);
-    } else if (str.BeginsWith("map", TString::kIgnoreCase)) { // map
-      str.Remove(0,3);
-      if (!str.IsDigit()) {
-        return;
-      }
-      ival = str.Atoi();
-      ival -= 1;
-      str = TString::Format("%d",ival);
-      argStr = "p[m[" + str + "]]";
-      args.push_back(argStr);
-    } else if (str.BeginsWith("fun", TString::kIgnoreCase)) { // function
-      str.Remove(0,3);
-      if (!str.IsDigit()) {
-        return;
-      }
-      ival = str.Atoi();
-      ival -= 1;
-      str = TString::Format("%d",ival);
-      argStr = "f[" + str + "]";
-      args.push_back(argStr);
-    }
-  }
-
-  // clean up
-  delete tok;
-}
-
 //--------------------------------------------------------------------------
 // NeededPrecision (private)
 //--------------------------------------------------------------------------
--- a/src/classes/PMusr.cpp
+++ b/src/classes/PMusr.cpp
@@ -733,9 +733,9 @@ PRawRunDataSet* PRawRunData::GetDataSet(const UInt_t idx, Bool_t wantHistoNo)
 */
 const Bool_t PRawRunData::DeadTimeCorrectionReady()
 {
-    if ((fNumberOfGoodFrames > 0) && (fDeadTimeParam.size() > 0))
-        return true;
-    return false;
+  if ((fNumberOfGoodFrames > 0) && (fDeadTimeParam.size() > 0))
+    return true;
+  return false;
 }

 //--------------------------------------------------------------------------
--- a/src/classes/PMusrCanvas.cpp
+++ b/src/classes/PMusrCanvas.cpp
@@ -141,8 +141,6 @@ PMusrCanvas::PMusrCanvas()
 {
  fTimeout = 0;

-  fStartWithFourier = false;
-  fUseDKS = false;
  fScaleN0AndBkg = true;
  fValid = false;
  fAveragedView     = false;
@@ -206,10 +204,10 @@ PMusrCanvas::PMusrCanvas()
 */
 PMusrCanvas::PMusrCanvas(const Int_t number, const Char_t* title,
                         Int_t wtopx, Int_t wtopy, Int_t ww, Int_t wh,
-                         const Bool_t batch, const Bool_t fourier, const Bool_t avg, 
-                         const Bool_t theoAsData, const Bool_t useDKS) :
-     fTheoAsData(theoAsData), fStartWithFourier(fourier), fStartWithAvg(avg), 
-     fUseDKS(useDKS), fBatchMode(batch), fPlotNumber(number)
+                         const Bool_t batch, const Bool_t fourier, const Bool_t avg,
+                         const Bool_t theoAsData) :
+    fTheoAsData(theoAsData), fStartWithFourier(fourier), fStartWithAvg(avg),
+    fBatchMode(batch), fPlotNumber(number)
 {
  fTimeout = 0;
  fAveragedView = false;
@@ -274,10 +272,10 @@ PMusrCanvas::PMusrCanvas(const Int_t number, const Char_t* title,
                         Int_t wtopx, Int_t wtopy, Int_t ww, Int_t wh,
                         PMsrFourierStructure fourierDefault,
                         const PIntVector markerList, const PIntVector colorList,
-                         const Bool_t batch, const Bool_t fourier, const Bool_t avg, 
-                         const Bool_t theoAsData, const Bool_t useDKS) :
-     fTheoAsData(theoAsData), fStartWithFourier(fourier), fStartWithAvg(avg), fUseDKS(useDKS),
-     fBatchMode(batch), fPlotNumber(number), fFourier(fourierDefault),
+                         const Bool_t batch, const Bool_t fourier, const Bool_t avg,
+                         const Bool_t theoAsData) :
+     fTheoAsData(theoAsData), fStartWithFourier(fourier), fStartWithAvg(avg), fBatchMode(batch),
+     fPlotNumber(number), fFourier(fourierDefault),
     fMarkerList(markerList), fColorList(colorList)
 {
  fTimeout = 0;
@@ -3392,17 +3390,12 @@ void PMusrCanvas::HandleFourier()
      fData[i].dataFourierPhase->SetMarkerStyle(fData[i].data->GetMarkerStyle());

      // calculate fourier transform of the theory
-      Bool_t useFFTW = true;
      PFourier *fourierTheory = nullptr;
      if (fTheoAsData) { // theory only at the data points
-        fourierTheory = new PFourier(fData[i].theory, fFourier.fUnits, startTime, endTime, fFourier.fDCCorrected, fFourier.fFourierPower, useFFTW);
+        fourierTheory = new PFourier(fData[i].theory, fFourier.fUnits, startTime, endTime, fFourier.fDCCorrected, fFourier.fFourierPower);
      } else {
        Int_t powerPad = fFourier.fFourierPower+5; // +5 means 8 times more points on theo (+3) + 4 times more points in fourier (+2)
-#ifdef HAVE_DKS
-        if ((powerPad >= 20) && fUseDKS)
-          useFFTW = false; // i.e. use DKS
-#endif
-        fourierTheory = new PFourier(fData[i].theory, fFourier.fUnits, startTime, endTime, fFourier.fDCCorrected, powerPad, useFFTW);
+        fourierTheory = new PFourier(fData[i].theory, fFourier.fUnits, startTime, endTime, fFourier.fDCCorrected, powerPad);
      }
      if (!fourierTheory->IsValid()) {
        std::cerr << std::endl << ">> PMusrCanvas::HandleFourier(): **SEVERE ERROR** couldn't invoke PFourier to calculate the Fourier theory ..." << std::endl;
--- a/src/classes/PRunDataHandler.cpp
+++ b/src/classes/PRunDataHandler.cpp
@@ -2193,98 +2193,98 @@ Bool_t PRunDataHandler::ReadRootFile()
 Bool_t PRunDataHandler::ReadNexusFile()
 {
 #ifdef PNEXUS_ENABLED
-    std::cout << std::endl << ">> PRunDataHandler::ReadNexusFile(): Will read nexus file " << fRunPathName.Data() << " ...";
+  std::cout << std::endl << ">> PRunDataHandler::ReadNexusFile(): Will read nexus file " << fRunPathName.Data() << " ...";

-    nxs::HDFType type = nxs::checkHDFType(fRunPathName.Data());
+  nxs::HDFType type = nxs::checkHDFType(fRunPathName.Data());

-    // check for type errors, missing enabled HDF4
-    switch (type) {
-      case nxs::HDFType::HDF4:
-        std::cout << std::endl << ">> PRunDataHandler::ReadNexusFile(): HDF4 file." << std::endl;
+  // check for type errors, missing enabled HDF4
+  switch (type) {
+    case nxs::HDFType::HDF4:
+      std::cout << std::endl << ">> PRunDataHandler::ReadNexusFile(): HDF4 file." << std::endl;
 #ifndef HAVE_HDF4
-        std::cerr << std::endl << ">> PRunDataHandler::ReadNexusFile(): **ERROR**, HDF4 is not enabled." << std::endl;
-        return false;
+      std::cerr << std::endl << ">> PRunDataHandler::ReadNexusFile(): **ERROR**, HDF4 is not enabled." << std::endl;
+      return false;
 #endif
-        break;
-      case nxs::HDFType::HDF5:
-        std::cout << std::endl << ">> PRunDataHandler::ReadNexusFile(): HDF5 file." << std::endl;
-        break;
-      case nxs::HDFType::Unknown:
-        std::cerr << std::endl << ">> PRunDataHandler::ReadNexusFile(): Not a valid NeXus file." << std::endl;
-        return false;
-    }
+      break;
+    case nxs::HDFType::HDF5:
+      std::cout << std::endl << ">> PRunDataHandler::ReadNexusFile(): HDF5 file." << std::endl;
+      break;
+    case nxs::HDFType::Unknown:
+      std::cerr << std::endl << ">> PRunDataHandler::ReadNexusFile(): Not a valid NeXus file." << std::endl;
+      return false;
+  }

-    PDoubleVector  histoData;
-    PRawRunData    runData;
-    PRawRunDataSet dataSet;
-    TString str;
-    std::string sstr;
-    Int_t ival, idf{-1};
-    Double_t dval, factor;
-    bool ok;
+  PDoubleVector  histoData;
+  PRawRunData    runData;
+  PRawRunDataSet dataSet;
+  TString str;
+  std::string sstr;
+  Int_t ival, idf{-1};
+  Double_t dval, factor;
+  bool ok;

-    if (type == nxs::HDFType::HDF4) {
+  if (type == nxs::HDFType::HDF4) {
 #ifdef HAVE_HDF4
-      std::unique_ptr<nxH4::PNeXus> nxs_file = std::make_unique<nxH4::PNeXus>(fRunPathName.Data());
-      if (nxs_file == nullptr) {
-        std::cerr << std::endl << "**ERROR** allocation of nxH4::PNeXus object failed." << std::endl;
-        return true;
-      }
+    std::unique_ptr<nxH4::PNeXus> nxs_file = std::make_unique<nxH4::PNeXus>(fRunPathName.Data());
+    if (nxs_file == nullptr) {
+      std::cerr << std::endl << "**ERROR** allocation of nxH4::PNeXus object failed." << std::endl;
+      return true;
+    }

-      // check for IDF_version
-      if (nxs_file->HasDataset("/run/IDF_version")) {
-        idf = nxs_file->GetDataset<int>("/run/IDF_version").GetData()[0];
+    // check for IDF_version
+    if (nxs_file->HasDataset("/run/IDF_version")) {
+      idf = nxs_file->GetDataset<int>("/run/IDF_version").GetData()[0];
+      std::cout << ">> PRunDataHandler::ReadNexusFile(): IDF V" << idf << std::endl;
+    }
+    if (idf == -1) { // IDF_version not found
+      if (nxs_file->HasDataset("/raw_data_1/IDF_version")) {
+        idf = nxs_file->GetDataset<int>("/raw_data_1/IDF_version").GetData()[0];
        std::cout << ">> PRunDataHandler::ReadNexusFile(): IDF V" << idf << std::endl;
      }
-      if (idf == -1) { // IDF_version not found
-        if (nxs_file->HasDataset("/raw_data_1/IDF_version")) {
-          idf = nxs_file->GetDataset<int>("/raw_data_1/IDF_version").GetData()[0];
-          std::cout << ">> PRunDataHandler::ReadNexusFile(): IDF V" << idf << std::endl;
-        }
-      }
-      if ((idf != 1) && (idf != 2)) {
-        std::cerr << std::endl << ">> PRunDataHandler::ReadNexusFile(): a NeXus file with an invalid IDF V" << idf << std::endl;
-        return false;
-      }
-
-      if (idf == 1) { // HDF4 IDF V1
-        if (!ReadNexusFileIdf1(nxs_file))
-          return false;
-      } else { // HDF4 IDF V2
-        // not yet implemented
-      }
-#endif
-    } else { // HDF5
-      std::unique_ptr<nxH5::PNeXus> nxs_file = std::make_unique<nxH5::PNeXus>(fRunPathName.Data());
-      if (nxs_file == nullptr) {
-        std::cerr << std::endl << "**ERROR** allocation of nxH5::PNeXus object failed." << std::endl;
-        return true;
-      }
-
-      // check for IDF_version
-      if (nxs_file->HasDataset("/run/IDF_version")) {
-        idf = nxs_file->GetDataset<int>("/run/IDF_version").GetData()[0];
-        std::cout << ">> PRunDataHandler::ReadNexusFile(): IDF V" << idf << std::endl;
-      }
-      if (idf == -1) { // IDF_version not found
-        if (nxs_file->HasDataset("/raw_data_1/IDF_version")) {
-          idf = nxs_file->GetDataset<int>("/raw_data_1/IDF_version").GetData()[0];
-          std::cout << ">> PRunDataHandler::ReadNexusFile(): IDF V" << idf << std::endl;
-        }
-      }
-      if ((idf != 1) && (idf != 2)) {
-        std::cerr << std::endl << ">> PRunDataHandler::ReadNexusFile(): a NeXus file with an invalid IDF V" << idf << std::endl;
-        return false;
-      }
-
-      if (idf == 1) { // HDF5 IDF V1
-        if (!ReadNexusFileIdf1(nxs_file))
-          return false;
-      } else { // HDF5 IDF V2
-        if (!ReadNexusFileIdf2(nxs_file))
-          return false;
-      }
    }
+    if ((idf != 1) && (idf != 2)) {
+      std::cerr << std::endl << ">> PRunDataHandler::ReadNexusFile(): a NeXus file with an invalid IDF V" << idf << std::endl;
+      return false;
+    }
+
+    if (idf == 1) { // HDF4 IDF V1
+      if (!ReadNexusFileIdf1(nxs_file))
+        return false;
+    } else { // HDF4 IDF V2
+      // not yet implemented
+    }
+#endif
+  } else { // HDF5
+    std::unique_ptr<nxH5::PNeXus> nxs_file = std::make_unique<nxH5::PNeXus>(fRunPathName.Data());
+    if (nxs_file == nullptr) {
+      std::cerr << std::endl << "**ERROR** allocation of nxH5::PNeXus object failed." << std::endl;
+      return true;
+    }
+
+    // check for IDF_version
+    if (nxs_file->HasDataset("/run/IDF_version")) {
+      idf = nxs_file->GetDataset<int>("/run/IDF_version").GetData()[0];
+      std::cout << ">> PRunDataHandler::ReadNexusFile(): IDF V" << idf << std::endl;
+    }
+    if (idf == -1) { // IDF_version not found
+      if (nxs_file->HasDataset("/raw_data_1/IDF_version")) {
+        idf = nxs_file->GetDataset<int>("/raw_data_1/IDF_version").GetData()[0];
+        std::cout << ">> PRunDataHandler::ReadNexusFile(): IDF V" << idf << std::endl;
+      }
+    }
+    if ((idf != 1) && (idf != 2)) {
+      std::cerr << std::endl << ">> PRunDataHandler::ReadNexusFile(): a NeXus file with an invalid IDF V" << idf << std::endl;
+      return false;
+    }
+
+    if (idf == 1) { // HDF5 IDF V1
+      if (!ReadNexusFileIdf1(nxs_file))
+        return false;
+    } else { // HDF5 IDF V2
+      if (!ReadNexusFileIdf2(nxs_file))
+        return false;
+    }
+  }
 #else
  std::cout << std::endl << ">> PRunDataHandler::ReadNexusFile(): Sorry, not enabled at configuration level, i.e. --enable-NeXus when executing configure" << std::endl << std::endl;
 #endif
@@ -4846,9 +4846,9 @@ Bool_t PRunDataHandler::WriteNexusFile(TString format, TString fln)
        // set program name
        nxs->AddDataset<std::string>("/run/program_name", {"any2many"}, {1}, nxH4::H4DataType::kCHAR8);
        str="n/a";
-#ifdef HAVE_CONFIG_H
+    #ifdef HAVE_CONFIG_H
        str = PACKAGE_VERSION;
-#endif
+    #endif
        nxs->AddDatasetAttribute<std::string>("/run/program_name", "version", str);

        // set run number
@@ -5220,9 +5220,9 @@ Bool_t PRunDataHandler::WriteNexusFile(TString format, TString fln)
        // set program name
        nxs->AddDataset<std::string>("/run/program_name", {"any2many"}, {1}, H5::StrType(H5::PredType::C_S1, H5T_VARIABLE));
        str="n/a";
-#ifdef HAVE_CONFIG_H
+    #ifdef HAVE_CONFIG_H
        str = PACKAGE_VERSION;
-#endif
+    #endif
        nxs->AddDatasetAttribute<std::string>("/run/program_name", "version", str);

        // set run number
--- a/src/classes/PRunListCollection.cpp
+++ b/src/classes/PRunListCollection.cpp
@@ -498,7 +498,6 @@ Double_t PRunListCollection::GetNonMusrChisq(const std::vector<Double_t>& par) c
 //--------------------------------------------------------------------------
 /**
 * <p>Calculates expected chi-square of the run block index idx of a msr-file.
- * Currently this is only possible for Single Histo, and Mu Minus fits.
 *
 * <b>return:</b>
 * - expected chi-square of for a single run block
@@ -528,6 +527,7 @@ Double_t PRunListCollection::GetSingleRunChisqExpected(const std::vector<Double_
    }
  }

+
  // return the chisq of the single run
  switch (type) {
  case PRUN_SINGLE_HISTO:
@@ -548,6 +548,9 @@ Double_t PRunListCollection::GetSingleRunChisqExpected(const std::vector<Double_
  case PRUN_MU_MINUS:
    expectedChisq = fRunMuMinusList[subIdx]->CalcChiSquareExpected(par);
    break;
+  case PRUN_NON_MUSR:
+    expectedChisq = fRunNonMusrList[subIdx]->CalcChiSquareExpected(par);
+    break;
  default:
    break;
  }
@@ -883,17 +886,17 @@ UInt_t PRunListCollection::GetNoOfBinsFitted(const UInt_t idx) const
    return result;
  }

+  UInt_t subIdx = 0;
  Int_t type = fMsrInfo->GetMsrRunList()->at(idx).GetFitType();
  if (type == -1) { // i.e. not found in the RUN block, try the GLOBAL block
    type = fMsrInfo->GetMsrGlobal()->GetFitType();
-  }
-
-  // count how many entries of this fit-type are present up to idx
-  UInt_t subIdx = 0;
-  for (UInt_t i=0; i<idx; i++) {
-    if ((fMsrInfo->GetMsrRunList()->at(i).GetFitType() == type) || 
-        (fMsrInfo->GetMsrRunList()->at(i).GetFitType() == -1)) // the -1 is needed if there is a global section
-      subIdx++;
+    subIdx = idx;
+  } else { // found in the RUN block
+    // count how many entries of this fit-type are present up to idx
+    for (UInt_t i=0; i<idx; i++) {
+      if (fMsrInfo->GetMsrRunList()->at(i).GetFitType() == type)
+        subIdx++;
+    }
  }

  // return the chisq of the single run
@@ -1391,305 +1394,3 @@ const Char_t* PRunListCollection::GetYAxisTitle(const TString &runName, const UI
  return result;
 }

-//--------------------------------------------------------------------------
-// GetStartTimeBin (public)
-//--------------------------------------------------------------------------
-/**
- * @brief PRunListCollection::GetStartTimeBin
- * @param fitType
- * @param idx
- * @return
- */
-Int_t PRunListCollection::GetStartTimeBin(Int_t fitType, UInt_t idx)
-{
-  Int_t result = -1;
-
-  switch (fitType) {
-  case MSR_FITTYPE_SINGLE_HISTO:
-    if (idx < fRunSingleHistoList.size())
-      result = fRunSingleHistoList[idx]->GetStartTimeBin();
-    break;
-  case MSR_FITTYPE_ASYM:
-    if (idx < fRunAsymmetryList.size())
-      result = fRunAsymmetryList[idx]->GetStartTimeBin();
-    break;
-  case MSR_FITTYPE_MU_MINUS:
-    if (idx < fRunMuMinusList.size())
-      result = fRunMuMinusList[idx]->GetStartTimeBin();
-    break;
-  default:
-    break;
-  }
-
-  return result;
-}
-
-//--------------------------------------------------------------------------
-// GetEndTimeBin (public)
-//--------------------------------------------------------------------------
-/**
- * @brief PRunListCollection::GetEndTimeBin
- * @param fitType
- * @param idx
- * @return
- */
-Int_t PRunListCollection::GetEndTimeBin(Int_t fitType, UInt_t idx)
-{
-  Int_t result = -1;
-
-  switch (fitType) {
-  case MSR_FITTYPE_SINGLE_HISTO:
-    if (idx < fRunSingleHistoList.size())
-      result = fRunSingleHistoList[idx]->GetEndTimeBin();
-    break;
-  case MSR_FITTYPE_ASYM:
-    if (idx < fRunAsymmetryList.size())
-      result = fRunAsymmetryList[idx]->GetEndTimeBin();
-    break;
-  case MSR_FITTYPE_MU_MINUS:
-    if (idx < fRunMuMinusList.size())
-      result = fRunMuMinusList[idx]->GetEndTimeBin();
-    break;
-  default:
-    break;
-  }
-
-  return result;
-}
-
-//--------------------------------------------------------------------------
-//  GetSingleHistoParams (public)
-//--------------------------------------------------------------------------
-/**
- * @brief PRunListCollection::GetSingleHistoParams
- * @param idx
- * @param par
- * @param shp
- * @return
- */
-Int_t PRunListCollection::GetSingleHistoParams(UInt_t idx, const std::vector<Double_t>& par, PDKSParams &dksp)
-{
-  Int_t ierr = 0;
-  // make sure idx is within proper bounds
-  if (idx >= fRunSingleHistoList.size())
-    return 1;
-
-  // init param
-  InitDKSParams(dksp);
-
-  // get flag if scaling of N0 and Nbkg is wished
-  dksp.fScaleN0AndBkg = fRunSingleHistoList[idx]->GetScaleN0AndBkg();
-
-  // get the meta data needed to calculate the functions
-  PMetaData metaData = fRunSingleHistoList[idx]->GetMetaData();
-
-  // check if norm is a parameter or a function
-  PMsrRunBlock runInfo = fMsrInfo->GetMsrRunList()->at(idx);
-  if (runInfo.GetNormParamNo() < MSR_PARAM_FUN_OFFSET) { // norm is a parameter
-    dksp.fN0 = par[runInfo.GetNormParamNo()-1];
-  } else { // norm is a function
-    // get function number
-    UInt_t funNo = runInfo.GetNormParamNo()-MSR_PARAM_FUN_OFFSET;
-    // evaluate function
-    dksp.fN0 = fMsrInfo->EvalFunc(funNo, *runInfo.GetMap(), par, metaData);
-  }
-
-  // get tau
-  if (runInfo.GetLifetimeParamNo() != -1)
-    dksp.fTau = par[runInfo.GetLifetimeParamNo()-1];
-  else
-    dksp.fTau = PMUON_LIFETIME;
-
-  // get background
-  if (runInfo.GetBkgFitParamNo() == -1) { // bkg not fitted
-    if (runInfo.GetBkgFix(0) == PMUSR_UNDEFINED) { // no fixed background given (background interval)
-      dksp.fNbkg = GetBackground(idx);
-    } else { // fixed bkg given
-      dksp.fNbkg = runInfo.GetBkgFix(0);
-    }
-  } else { // bkg fitted
-    dksp.fNbkg = par[runInfo.GetBkgFitParamNo()-1];
-  }
-
-  // get packed time resolution
-  dksp.fPackedTimeResolution = fRunSingleHistoList[idx]->GetData()->GetDataTimeStep();
-
-  // get start time
-  // fRunSingleHistoList[idx]->GetData()->GetDataTimeStart() : time of fgb, which is 0-bin of the fit-data-set
-  // fRunSingleHistoList[idx]->GetStartTimeBin() * dksp.fPackedTimeResolution : time-offset from fgb-time to fit start time
-  dksp.fStartTime = fRunSingleHistoList[idx]->GetData()->GetDataTimeStart() + fRunSingleHistoList[idx]->GetStartTimeBin() * dksp.fPackedTimeResolution;
-
-  // get number of bins fitted
-  dksp.fNoOfFitBins = fRunSingleHistoList[idx]->GetNoOfFitBins();
-
-  // calculate functions
-  Int_t funcNo = 0;
-  for (Int_t i=0; i<fMsrInfo->GetNoOfFuncs(); i++) {
-    funcNo = fMsrInfo->GetFuncNo(i);
-    dksp.fFun.push_back(fMsrInfo->EvalFunc(funcNo, *runInfo.GetMap(), par, metaData));
-  }
-
-  // get map vector
-  dksp.fMap = *runInfo.GetMap();
-  dksp.fMap.erase(dksp.fMap.begin()+GetNoOfMaps(), dksp.fMap.end());
-  // need to reduce map indexes by 1 since in C/C++ arrays start at 0
-  for (UInt_t i=0; i<dksp.fMap.size(); i++)
-    dksp.fMap[i] -= 1;
-
-  return ierr;
-}
-
-//--------------------------------------------------------------------------
-//  GetAsymmetryParams (public)
-//--------------------------------------------------------------------------
-/**
- * @brief PRunListCollection::GetAsymmetryParams
- * @param idx
- * @param par
- * @param shp
- * @return
- */
-Int_t PRunListCollection::GetAsymmetryParams(UInt_t idx, const std::vector<Double_t>& par, PDKSParams &dksp)
-{
-  Int_t ierr=0, ival=0;
-  // make sure idx is within proper bounds
-  if (idx >= fRunAsymmetryList.size())
-    return 1;
-
-  // init param
-  InitDKSParams(dksp);
-
-  // get the meta data needed to calculate the functions
-  PMetaData metaData = fRunAsymmetryList[idx]->GetMetaData();
-
-  // get alpha
-  PMsrRunBlock runInfo = fMsrInfo->GetMsrRunList()->at(idx);
-  ival = runInfo.GetAlphaParamNo();
-  if (ival > 0)
-    dksp.fAlpha = par[ival-1];
-
-  // get beta
-  ival = runInfo.GetBetaParamNo();
-  if (ival > 0)
-    dksp.fBeta = par[ival-1];
-
-  // get packed time resolution
-  dksp.fPackedTimeResolution = fRunAsymmetryList[idx]->GetData()->GetDataTimeStep();
-
-  // get start time
-  // fRunAsymmetryList[idx]->GetData()->GetDataTimeStart() : time of fgb, which is 0-bin of the fit-data-set
-  // fRunAsymmetryList[idx]->GetStartTimeBin() * dksp.fPackedTimeResolution : time-offset from fgb-time to fit start time
-  dksp.fStartTime = fRunAsymmetryList[idx]->GetData()->GetDataTimeStart() + fRunAsymmetryList[idx]->GetStartTimeBin() * dksp.fPackedTimeResolution;
-
-  // get number of bins fitted
-  dksp.fNoOfFitBins = fRunAsymmetryList[idx]->GetNoOfFitBins();
-
-  // calculate functions
-  Int_t funcNo = 0;
-  for (Int_t i=0; i<fMsrInfo->GetNoOfFuncs(); i++) {
-    funcNo = fMsrInfo->GetFuncNo(i);
-    dksp.fFun.push_back(fMsrInfo->EvalFunc(funcNo, *runInfo.GetMap(), par, metaData));
-  }
-
-  // get map vector
-  dksp.fMap = *runInfo.GetMap();
-  dksp.fMap.erase(dksp.fMap.begin()+GetNoOfMaps(), dksp.fMap.end());
-  // need to reduce map indexes by 1 since in C/C++ arrays start at 0
-  for (UInt_t i=0; i<dksp.fMap.size(); i++)
-    dksp.fMap[i] -= 1;
-
-  return ierr;
-}
-
-//--------------------------------------------------------------------------
-//  GetMuMinusParams (public)
-//--------------------------------------------------------------------------
-/**
- * @brief PRunListCollection::GetMuMinusParams
- * @param idx
- * @param par
- * @param shp
- * @return
- */
-Int_t PRunListCollection::GetMuMinusParams(UInt_t idx, const std::vector<Double_t>& par, PDKSParams &dksp)
-{
-  Int_t ierr = 0;
-  // make sure idx is within proper bounds
-  if (idx >= fRunMuMinusList.size())
-    return 1;
-
-  // get run block
-  PMsrRunBlock runInfo = fMsrInfo->GetMsrRunList()->at(idx);
-
-  // get the meta data needed to calculate the functions
-  PMetaData metaData = fRunMuMinusList[idx]->GetMetaData();
-
-  // init param
-  InitDKSParams(dksp);
-
-  // get packed time resolution
-  dksp.fPackedTimeResolution = fRunMuMinusList[idx]->GetData()->GetDataTimeStep();
-
-  // get start time
-  // fRunSingleHistoList[idx]->GetData()->GetDataTimeStart() : time of fgb, which is 0-bin of the fit-data-set
-  // fRunSingleHistoList[idx]->GetStartTimeBin() * dksp.fPackedTimeResolution : time-offset from fgb-time to fit start time
-  dksp.fStartTime = fRunMuMinusList[idx]->GetData()->GetDataTimeStart() + fRunMuMinusList[idx]->GetStartTimeBin() * dksp.fPackedTimeResolution;
-
-  // get number of bins fitted
-  dksp.fNoOfFitBins = fRunMuMinusList[idx]->GetNoOfFitBins();
-
-  // calculate functions
-  Int_t funcNo = 0;
-  for (Int_t i=0; i<fMsrInfo->GetNoOfFuncs(); i++) {
-    funcNo = fMsrInfo->GetFuncNo(i);
-    dksp.fFun.push_back(fMsrInfo->EvalFunc(funcNo, *runInfo.GetMap(), par, metaData));
-  }
-
-  // get map vector
-  dksp.fMap = *runInfo.GetMap();
-  dksp.fMap.erase(dksp.fMap.begin()+GetNoOfMaps(), dksp.fMap.end());
-  // need to reduce map indexes by 1 since in C/C++ arrays start at 0
-  for (UInt_t i=0; i<dksp.fMap.size(); i++)
-    dksp.fMap[i] -= 1;
-
-  return ierr;
-}
-
-//--------------------------------------------------------------------------
-//  InitDKSParams (private)
-//--------------------------------------------------------------------------
-/**
- * \brief PRunListCollection::InitDKSParams
- * \param param
- */
-void PRunListCollection::InitDKSParams(PDKSParams &param)
-{
-  param.fScaleN0AndBkg = false;
-  param.fN0   = -1.0;
-  param.fNbkg = -1.0;
-  param.fTau  = -1.0;
-  param.fAlpha = 1.0;
-  param.fBeta = 1.0;
-  param.fPackedTimeResolution = -1.0;
-  param.fStartTime = -1.0;
-  param.fNoOfFitBins = -1;
-  param.fFun.clear();
-  param.fMap.clear();
-}
-
-//--------------------------------------------------------------------------
-//  GetBackground (private)
-//--------------------------------------------------------------------------
-/**
- * @brief PRunListCollection::GetBackground
- * @param idx
- * @return
- */
-Double_t PRunListCollection::GetBackground(Int_t idx)
-{
-  // make sure idx is within proper bounds
-  if (idx >= (Int_t)fRunSingleHistoList.size())
-    return 0.0;
-
-  return fRunSingleHistoList[idx]->GetBackground();
-}
--- a/src/classes/PStartupHandler.cpp
+++ b/src/classes/PStartupHandler.cpp
@@ -291,10 +291,6 @@ void PStartupHandler::OnStartDocument()
  fFourierDefaults.fPlotRange[0] = -1.0;
  fFourierDefaults.fPlotRange[1] = -1.0;
  fFourierDefaults.fPhaseIncrement = 1.0;
-
-  fStartupOptions.writeExpectedChisq = false; // NOT defined in the XML, but initialized for later use!!
-  fStartupOptions.estimateN0 = false; // NOT defined in the XML, but initialized for later use!!
-  fStartupOptions.useDKS = false;
 }

 //--------------------------------------------------------------------------
@@ -354,8 +350,6 @@ void PStartupHandler::OnStartElement(const Char_t *str, const TList *attributes)
 {
  if (!strcmp(str, "data_path")) {
    fKey = eDataPath;
-  } else if (!strcmp(str, "use_dks")) {
-    fKey = eUseDKS;
  } else if (!strcmp(str, "run_name_template")) {
    fKey = eRunNameTemplate;
    TXMLAttr *attr;
@@ -469,11 +463,6 @@ void PStartupHandler::OnCharacters(const Char_t *str)
      // add str to the path list
      fDataPathList.push_back(str);
      break;
-    case eUseDKS:
-      tstr = TString(str);
-      if (tstr.BeginsWith("y") || tstr.BeginsWith("Y"))
-        fStartupOptions.useDKS = true;
-      break;
    case eRunNameTemplate:
      tmpl.instrument = fCurrentInstrumentName;
      tmpl.runNameTemplate = str;
@@ -951,8 +940,6 @@ Bool_t PStartupHandler::WriteDefaultStartupFile(bool reset_startup_file)
  fout << "    <comment>" << std::endl;
  fout << "        Defines default settings for the musrfit package" << std::endl;
  fout << "    </comment>" << std::endl;
-  fout << "    <!-- the use_dks flag is only for the GPU Fourier support, not the fitting -->" << std::endl;
-  fout << "    <use_dks>no</use_dks>" << std::endl;
  fout << "    <data_path>/psi.ch/group/lmu/public/data/lem/his</data_path>" << std::endl;
  fout << "    <data_path>/psi.ch/group/lmu/public/data/alc/his</data_path>" << std::endl;
  fout << "    <data_path>/psi.ch/group/lmu/public/data/dolly/his</data_path>" << std::endl;
--- a/src/dump_header.cpp
+++ b/src/dump_header.cpp
@@ -366,42 +366,42 @@ int dump_header_root(const std::string fileName, const bool summary, const bool
 int dump_header_nexus(const std::string fileName, const bool counts) {

 #ifdef PNEXUS_ENABLED
-    nxs::HDFType type = nxs::checkHDFType(fileName);
+  nxs::HDFType type = nxs::checkHDFType(fileName);

-    // check for type errors, missing enabled HDF4
-    switch (type) {
+  // check for type errors, missing enabled HDF4
+  switch (type) {
    case nxs::HDFType::HDF4:
-        std::cout << std::endl << ">> PRunDataHandler::ReadNexusFile(): HDF4 file." << std::endl;
+      std::cout << std::endl << ">> PRunDataHandler::ReadNexusFile(): HDF4 file." << std::endl;
 #ifndef HAVE_HDF4
-        std::cerr << std::endl << ">> PRunDataHandler::ReadNexusFile(): **ERROR**, HDF4 is not enabled." << std::endl;
-        return 1;
+      std::cerr << std::endl << ">> PRunDataHandler::ReadNexusFile(): **ERROR**, HDF4 is not enabled." << std::endl;
+      return 1;
 #endif
-        break;
+      break;
    case nxs::HDFType::HDF5:
-        std::cout << std::endl << ">> PRunDataHandler::ReadNexusFile(): HDF5 file." << std::endl;
-        break;
+      std::cout << std::endl << ">> PRunDataHandler::ReadNexusFile(): HDF5 file." << std::endl;
+      break;
    case nxs::HDFType::Unknown:
-        std::cerr << std::endl << ">> PRunDataHandler::ReadNexusFile(): Not a valid NeXus file." << std::endl;
-        return 1;
-    }
+      std::cerr << std::endl << ">> PRunDataHandler::ReadNexusFile(): Not a valid NeXus file." << std::endl;
+      return 1;
+  }

-    if (type == nxs::HDFType::HDF4) {
+  if (type == nxs::HDFType::HDF4) {
 #ifdef HAVE_HDF4
-        std::unique_ptr<nxH4::PNeXus> nxs_file = std::make_unique<nxH4::PNeXus>(fileName);
-        if (nxs_file == nullptr) {
-            std::cerr << std::endl << "**ERROR** allocation of nxH4::PNeXus object failed." << std::endl;
-        }
-        nxs_file->Dump();
-#endif
-    } else { // HDF5
-        std::unique_ptr<nxH5::PNeXus> nxs_file = std::make_unique<nxH5::PNeXus>(fileName);
-        if (nxs_file == nullptr) {
-            std::cerr << std::endl << "**ERROR** allocation of nxH5::PNeXus object failed." << std::endl;
-        }
-        nxs_file->Dump();
+    std::unique_ptr<nxH4::PNeXus> nxs_file = std::make_unique<nxH4::PNeXus>(fileName);
+    if (nxs_file == nullptr) {
+      std::cerr << std::endl << "**ERROR** allocation of nxH4::PNeXus object failed." << std::endl;
    }
+    nxs_file->Dump();
+#endif
+  } else { // HDF5
+    std::unique_ptr<nxH5::PNeXus> nxs_file = std::make_unique<nxH5::PNeXus>(fileName);
+    if (nxs_file == nullptr) {
+      std::cerr << std::endl << "**ERROR** allocation of nxH5::PNeXus object failed." << std::endl;
+    }
+    nxs_file->Dump();
+  }
 #else
-    std::cout << std::endl << "NeXus not enabled, hence the header information cannot be dumped." << std::endl << std::endl;
+  std::cout << std::endl << "NeXus not enabled, hence the header information cannot be dumped." << std::endl << std::endl;
 #endif

  return 0;
--- a/src/external/BMWtools/BMWIntegrator.cpp
+++ b/src/external/BMWtools/BMWIntegrator.cpp
@@ -45,6 +45,7 @@
 #define SEED 0
 #define STATEFILE NULL

+
 //-----------------------------------------------------------------------------

 std::vector<double> TPointPWaveGapIntegralCuhre::fPar;
@@ -223,6 +224,7 @@ int TLinePWaveGapIntegralCuhre::Integrand_cc(const int *ndim, const double x[],

 std::vector<double> TDWaveGapIntegralCuhre::fPar; ///< Static parameter vector for d-wave integrand

+//-----------------------------------------------------------------------------
 /**
 * @brief Integrate the function using the Cuhre interface for d-wave symmetry.
 *
@@ -252,6 +254,7 @@ double TDWaveGapIntegralCuhre::IntegrateFunc()
  return integral[0];
 }

+//-----------------------------------------------------------------------------
 /**
 * @brief Calculate the function value for the use with Cuhre---actual implementation of the function
 *        for d-wave symmetry.
@@ -273,8 +276,11 @@ int TDWaveGapIntegralCuhre::Integrand(const int *ndim, const double x[],
  return 0;
 }

+//-----------------------------------------------------------------------------
+
 std::vector<double> TCosSqDWaveGapIntegralCuhre::fPar;

+//-----------------------------------------------------------------------------
 /**
 * <p>Integrate the function using the Cuhre interface
 *
@@ -305,6 +311,7 @@ double TCosSqDWaveGapIntegralCuhre::IntegrateFunc()
  return integral[0];
 }

+//-----------------------------------------------------------------------------
 /**
 * <p>Calculate the function value for the use with Cuhre---actual implementation of the function
 *
@@ -325,8 +332,11 @@ int TCosSqDWaveGapIntegralCuhre::Integrand(const int *ndim, const double x[],
  return 0;
 }

+//-----------------------------------------------------------------------------
+
 std::vector<double> TSinSqDWaveGapIntegralCuhre::fPar;

+//-----------------------------------------------------------------------------
 /**
 * <p>Integrate the function using the Cuhre interface
 *
@@ -357,6 +367,7 @@ double TSinSqDWaveGapIntegralCuhre::IntegrateFunc()
  return integral[0];
 }

+//-----------------------------------------------------------------------------
 /**
 * <p>Calculate the function value for the use with Cuhre---actual implementation of the function
 *
@@ -377,8 +388,11 @@ int TSinSqDWaveGapIntegralCuhre::Integrand(const int *ndim, const double x[],
  return 0;
 }

+//-----------------------------------------------------------------------------
+
 std::vector<double> TAnSWaveGapIntegralCuhre::fPar;

+//-----------------------------------------------------------------------------
 /**
 * <p>Integrate the function using the Cuhre interface
 *
@@ -409,6 +423,7 @@ double TAnSWaveGapIntegralCuhre::IntegrateFunc()
  return integral[0];
 }

+//-----------------------------------------------------------------------------
 /**
 * <p>Calculate the function value for the use with Cuhre---actual implementation of the function
 *
@@ -429,8 +444,11 @@ int TAnSWaveGapIntegralCuhre::Integrand(const int *ndim, const double x[],
  return 0;
 }

+//-----------------------------------------------------------------------------
+
 std::vector<double> TAnSWaveGapIntegralDivonne::fPar;

+//-----------------------------------------------------------------------------
 /**
 * <p>Integrate the function using the Divonne interface
 *
@@ -469,6 +487,7 @@ double TAnSWaveGapIntegralDivonne::IntegrateFunc()
  return integral[0];
 }

+//-----------------------------------------------------------------------------
 /**
 * <p>Calculate the function value for the use with Divonne---actual implementation of the function
 *
@@ -489,8 +508,11 @@ int TAnSWaveGapIntegralDivonne::Integrand(const int *ndim, const double x[],
  return 0;
 }

+//-----------------------------------------------------------------------------
+
 std::vector<double> TAnSWaveGapIntegralSuave::fPar;

+//-----------------------------------------------------------------------------
 /**
 * <p>Integrate the function using the Suave interface
 *
@@ -523,6 +545,7 @@ double TAnSWaveGapIntegralSuave::IntegrateFunc()
  return integral[0];
 }

+//-----------------------------------------------------------------------------
 /**
 * <p>Calculate the function value for the use with Suave---actual implementation of the function
 *
@@ -543,8 +566,11 @@ int TAnSWaveGapIntegralSuave::Integrand(const int *ndim, const double x[],
  return 0;
 }

+//-----------------------------------------------------------------------------
+
 std::vector<double> TNonMonDWave1GapIntegralCuhre::fPar;

+//-----------------------------------------------------------------------------
 /**
 * <p>Integrate the function using the Cuhre interface
 *
@@ -575,6 +601,7 @@ double TNonMonDWave1GapIntegralCuhre::IntegrateFunc()
  return integral[0];
 }

+//-----------------------------------------------------------------------------
 /**
 * <p>Calculate the function value for the use with Cuhre---actual implementation of the function
 *
@@ -595,8 +622,11 @@ int TNonMonDWave1GapIntegralCuhre::Integrand(const int *ndim, const double x[],
  return 0;
 }

+//-----------------------------------------------------------------------------
+
 std::vector<double> TNonMonDWave2GapIntegralCuhre::fPar;

+//-----------------------------------------------------------------------------
 /**
 * <p>Integrate the function using the Cuhre interface
 *
@@ -627,6 +657,7 @@ double TNonMonDWave2GapIntegralCuhre::IntegrateFunc()
  return integral[0];
 }

+//-----------------------------------------------------------------------------
 /**
 * <p>Calculate the function value for the use with Cuhre---actual implementation of the function
 *
--- a/src/external/BMWtools/BMWIntegrator.h
+++ b/src/external/BMWtools/BMWIntegrator.h
@@ -48,6 +48,7 @@
 #include <vector>
 #include <memory>

+//-----------------------------------------------------------------------------
 /**
 * @class T2Integrator
 * @brief Alternative base class for 1D integrations using the GNU Scientific Library integrator.
@@ -70,6 +71,7 @@ class T2Integrator {
    static double FuncAtXgsl(double, void *);
 };

+//-----------------------------------------------------------------------------
 /**
 * <p>Method for passing the integrand function value to the integrator.
 *
@@ -85,6 +87,7 @@ inline double T2Integrator::FuncAtXgsl(double x, void *ptrPair)
  return pairOfPointers->first->FuncAtX(x, *(pairOfPointers->second));
 }

+//-----------------------------------------------------------------------------
 /**
 * <p>Calculate the integral of the function between the given boundaries
 *
@@ -107,20 +110,7 @@ inline double T2Integrator::IntegrateFunc(double x1, double x2, const std::vecto
  return value;
 }

-
-
-
-
-
-
-
-
-
-
-
-
-
-
+//-----------------------------------------------------------------------------
 /**
 * @class TIntegrator
 * @brief Base class for 1D integrations using the GNU Scientific Library integrator.
@@ -146,6 +136,7 @@ class TIntegrator {
    mutable double (*fFunc)(double, void *); ///< pointer to the integrand function
 };

+//-----------------------------------------------------------------------------
 /**
 * <p>Constructor of the base class for 1D integrations
 *    Allocation of memory for an integration using the adaptive 31 point Gauss-Kronrod rule
@@ -154,6 +145,7 @@ inline TIntegrator::TIntegrator() : fFunc(0) {
  fIntegrator = std::make_unique<ROOT::Math::GSLIntegrator>(ROOT::Math::Integration::kADAPTIVE,ROOT::Math::Integration::kGAUSS31);
 }

+//-----------------------------------------------------------------------------
 /**
 * <p>Destructor of the base class for 1D integrations
 *    Clean up.
@@ -163,6 +155,7 @@ inline TIntegrator::~TIntegrator(){
  fFunc=0;
 }

+//-----------------------------------------------------------------------------
 /**
 * <p>Method for passing the integrand function value to the integrator.
 *
@@ -177,6 +170,7 @@ inline double TIntegrator::FuncAtXgsl(double x, void *obj)
  return ((TIntegrator*)obj)->FuncAtX(x);
 }

+//-----------------------------------------------------------------------------
 /**
 * <p>Calculate the integral of the function between the given boundaries
 *
@@ -192,6 +186,7 @@ inline double TIntegrator::IntegrateFunc(double x1, double x2)
  return fIntegrator->Integral(fFunc, (this), x1, x2);
 }

+//-----------------------------------------------------------------------------
 /**
 * @class TMCIntegrator
 * @brief Base class for multidimensional Monte-Carlo integrations using the GNU Scientific Library integrator.
@@ -218,6 +213,7 @@ class TMCIntegrator {
    mutable double (*fFunc)(double *, size_t, void *); ///< pointer to the integrand function
 };

+//-----------------------------------------------------------------------------
 /**
 * <p>Constructor of the base class for multidimensional Monte-Carlo integrations
 *    Allocation of memory for an integration using the MISER algorithm of Press and Farrar
@@ -226,6 +222,7 @@ inline TMCIntegrator::TMCIntegrator() : fFunc(0) {
  fMCIntegrator = std::make_unique<ROOT::Math::GSLMCIntegrator>(ROOT::Math::MCIntegration::kMISER, 1.E-6, 1.E-4, 500000);
 }

+//-----------------------------------------------------------------------------
 /**
 * <p>Destructor of the base class for 1D integrations
 *    Clean up.
@@ -235,6 +232,7 @@ inline TMCIntegrator::~TMCIntegrator(){
  fFunc=0;
 }

+//-----------------------------------------------------------------------------
 /**
 * <p>Method for passing the integrand function value to the integrator.
 *
@@ -250,6 +248,7 @@ inline double TMCIntegrator::FuncAtXgsl(double *x, size_t dim, void *obj)
  return ((TMCIntegrator*)obj)->FuncAtX(x);
 }

+//-----------------------------------------------------------------------------
 /**
 * <p>Calculate the integral of the function between the given boundaries
 *
@@ -334,6 +333,7 @@ class TDWaveGapIntegralCuhre {
    unsigned int fNDim; ///< dimension of the integral (2)
 };

+//-----------------------------------------------------------------------------
 /**
 * @class TCosSqDWaveGapIntegralCuhre
 * @brief Two-dimensional integrator class for the efficient calculation of the superfluid density along the a-axis
@@ -355,6 +355,7 @@ class TCosSqDWaveGapIntegralCuhre {
    unsigned int fNDim; ///< dimension of the integral (2)
 };

+//-----------------------------------------------------------------------------
 /**
 * @class TSinSqDWaveGapIntegralCuhre
 * @brief Two-dimensional integrator class for the efficient calculation of the superfluid density along the b-axis
@@ -376,6 +377,7 @@ class TSinSqDWaveGapIntegralCuhre {
    unsigned int fNDim; ///< dimension of the integral (2)
 };

+//-----------------------------------------------------------------------------
 /**
 * @class TAnSWaveGapIntegralCuhre
 * @brief Two-dimensional integrator class for the efficient calculation of the superfluid density
@@ -397,6 +399,7 @@ class TAnSWaveGapIntegralCuhre {
    unsigned int fNDim; ///< dimension of the integral (2)
 };

+//-----------------------------------------------------------------------------
 /**
 * @class TAnSWaveGapIntegralDivonne
 * @brief Two-dimensional integrator class for the efficient calculation of the superfluid density
@@ -418,6 +421,7 @@ class TAnSWaveGapIntegralDivonne {
    unsigned int fNDim; ///< dimension of the integral (2)
 };

+//-----------------------------------------------------------------------------
 /**
 * @class TAnSWaveGapIntegralSuave
 * @brief Two-dimensional integrator class for the efficient calculation of the superfluid density
@@ -439,6 +443,7 @@ class TAnSWaveGapIntegralSuave {
    unsigned int fNDim; ///< dimension of the integral (2)
 };

+//-----------------------------------------------------------------------------
 /**
 * @class TNonMonDWave1GapIntegralCuhre
 * @brief Two-dimensional integrator class for the efficient calculation of the superfluid density
@@ -460,6 +465,7 @@ class TNonMonDWave1GapIntegralCuhre {
    unsigned int fNDim; ///< dimension of the integral (2)
 };

+//-----------------------------------------------------------------------------
 /**
 * @class TNonMonDWave2GapIntegralCuhre
 * @brief Two-dimensional integrator class for the efficient calculation of the superfluid density
@@ -481,6 +487,7 @@ class TNonMonDWave2GapIntegralCuhre {
    unsigned int fNDim; ///< dimension of the integral (2)
 };

+//-----------------------------------------------------------------------------
 /**
 * @class T2DTest
 * @brief Test class for the 2D Monte-Carlo integration.
@@ -494,6 +501,7 @@ class T2DTest : public TMCIntegrator {
    double FuncAtX(double *) const; ///< Calculate integrand x*y at point x
 };

+//-----------------------------------------------------------------------------
 /**
 * <p>Calculate the function value---actual implementation of the function x*y
 *
@@ -587,6 +595,7 @@ class TDWaveGapIntegral : public TMCIntegrator {
    double FuncAtX(double *) const; ///< Calculate integrand at point x
 };

+//-----------------------------------------------------------------------------
 /**
 * <p>Calculate the function value---actual implementation of the function
 *
@@ -602,6 +611,7 @@ inline double TDWaveGapIntegral::FuncAtX(double *x) const // x = {E, phi}, fPar
  return -1.0/(2.0*twokt*TMath::CosH(TMath::Sqrt(x[0]*x[0]+deltasq)/twokt)*TMath::CosH(TMath::Sqrt(x[0]*x[0]+deltasq)/twokt));
 }

+//-----------------------------------------------------------------------------
 /**
 * @class TAnSWaveGapIntegral
 * @brief Class for the 2D Monte-Carlo integration for the calculation of the superfluid density
@@ -617,6 +627,7 @@ class TAnSWaveGapIntegral : public TMCIntegrator {
    double FuncAtX(double *) const; ///< Calculate integrand at point x
 };

+//-----------------------------------------------------------------------------
 /**
 * <p>Calculate the function value---actual implementation of the function
 *
@@ -632,6 +643,7 @@ inline double TAnSWaveGapIntegral::FuncAtX(double *x) const // x = {E, phi}, fPa
  return -1.0/(2.0*twokt*TMath::CosH(TMath::Sqrt(x[0]*x[0]+deltasq)/twokt)*TMath::CosH(TMath::Sqrt(x[0]*x[0]+deltasq)/twokt));
 }

+//-----------------------------------------------------------------------------
 /**
 * @class TIntBesselJ0Exp
 * @brief Class for the 1D integration of j0(a*x)*exp(-b*x).
@@ -647,6 +659,7 @@ class TIntBesselJ0Exp : public T2Integrator {
    double FuncAtX(double, const std::vector<double>&) const; ///< Calculate integrand at point x
 };

+//-----------------------------------------------------------------------------
 /**
 * <p>Calculate the function value---actual implementation of the function j0(a*x)*exp(-b*x)
 *
@@ -667,6 +680,7 @@ inline double TIntBesselJ0Exp::FuncAtX(double x, const std::vector<double> &par)
  return j0 * TMath::Exp(-par[1]*x);
 }

+//-----------------------------------------------------------------------------
 /**
 * @class TIntSinGss
 * @brief Class for the 1D integration of sin(a*x)*exp(-b*x*x).
@@ -682,6 +696,7 @@ class TIntSinGss : public T2Integrator {
    double FuncAtX(double, const std::vector<double>&) const; ///< Calculate integrand at point x
 };

+//-----------------------------------------------------------------------------
 /**
 * <p>Calculate the function value---actual implementation of the function sin(a*x)*exp(-b*x*x)
 *
@@ -695,6 +710,7 @@ inline double TIntSinGss::FuncAtX(double x, const std::vector<double> &par) cons
  return TMath::Sin(TMath::TwoPi()*par[0]*x) * TMath::Exp(-0.5*par[1]*par[1]*x*x);
 }

+//-----------------------------------------------------------------------------
 /**
 * @class TIntSGInterpolation
 * @brief Class for the 1D integration of the "DeRenzi Spin Glass Interpolation Integrand".
@@ -712,6 +728,7 @@ class TIntSGInterpolation : public T2Integrator {
    double FuncAtX(double, const std::vector<double>&) const; ///< Calculate integrand at point x
 };

+//-----------------------------------------------------------------------------
 /**
 * <p>Calculate the function value---actual implementation of the function
 *
@@ -728,6 +745,7 @@ inline double TIntSGInterpolation::FuncAtX(double x, const std::vector<double> &
  return (wt*TMath::Cos(wt)-TMath::Sin(wt))/(wt*wt)*TMath::Exp(-TMath::Power(expo,par[3]))/TMath::Power(expo,(1.0-par[3]));
 }

+//-----------------------------------------------------------------------------
 /**
 * @class TGapIntegral
 * @brief Class for the 1D integration for the calculation of the superfluid density within the semi-classical model
@@ -742,6 +760,7 @@ class TGapIntegral : public TIntegrator {
    double FuncAtX(double) const; ///< Calculate integrand at energy E
 };

+//-----------------------------------------------------------------------------
 /**
 * <p>Calculate the function value---actual implementation of the function df/dE * E / sqrt(E^2 - Delta^2)
 *
@@ -755,6 +774,7 @@ inline double TGapIntegral::FuncAtX(double e) const
  return 1.0/(TMath::Power(TMath::CosH(TMath::Sqrt(e*e+fPar[1]*fPar[1])/fPar[0]),2.0));
 }

+//-----------------------------------------------------------------------------
 /**
 * @class TFirstUniaxialGssKTIntegral
 * @brief Class for the 1D integration for the calculation of the uniaxial static Gauss-Kubo-Toyabe function.
@@ -770,6 +790,7 @@ class TFirstUniaxialGssKTIntegral : public T2Integrator {
    virtual double FuncAtX(double, const std::vector<double>&) const; ///< Calculate integrand at point x
 };

+//-----------------------------------------------------------------------------
 /**
 * <p>Calculate the function value---actual implementation of the integrand in Eq. (7) of Solt's article
 *
@@ -787,6 +808,7 @@ inline double TFirstUniaxialGssKTIntegral::FuncAtX(double x, const std::vector<d
  return (1.0 - x*x)*(p - SsqTsq)/TMath::Power(p, 2.5)*TMath::Exp(-0.5*SsqTsq/p);
 }

+//-----------------------------------------------------------------------------
 /**
 * @class TSecondUniaxialGssKTIntegral
 * @brief Class for the 1D integration for the calculation of the uniaxial static Gauss-Kubo-Toyabe function.
@@ -802,6 +824,7 @@ class TSecondUniaxialGssKTIntegral : public T2Integrator {
    virtual double FuncAtX(double, const std::vector<double>&) const; ///< Calculate integrand at point x
 };

+//-----------------------------------------------------------------------------
 /**
 * <p>Calculate the function value---actual implementation of the integrand in Eq. (7) of Solt's article
 *
--- a/src/external/DepthProfile/src/CMakeLists.txt
+++ b/src/external/DepthProfile/src/CMakeLists.txt
@@ -6,6 +6,7 @@ set(DEPTH_PROFILE_INC ${CMAKE_CURRENT_SOURCE_DIR}/../inc)
 # ROOT requires that the dictonary header files are found at configuration time.
 # Hence, target_include_directories cannot be used here because, targets are 
 # setup only afterwards.
+include_directories(${FFTW3_INCLUDE})
 include_directories(${MUSRFIT_INC})
 include_directories(${DEPTH_PROFILE_INC})

@@ -13,7 +14,7 @@ root_generate_dictionary(
  PDepthProfileDict 
  PDepthProfile.h 
  OPTIONS 
-    -I${FFTW3_INCLUDE_DIR} 
+    -I${FFTW3_INCLUDE} 
    -I${MUSRFIT_INC}
    -I${DEPTH_PROFILE_INC}
    -inlineInputHeader
@@ -45,7 +46,7 @@ set_target_properties(PDepthProfile
 #--- make sure that the include directory is found ----------------------------
 target_include_directories(
  PDepthProfile BEFORE PRIVATE 
-    $<BUILD_INTERFACE:${FFTW3_INCLUDE_DIR}> 
+    $<BUILD_INTERFACE:${FFTW3_INCLUDE}> 
    $<BUILD_INTERFACE:${MUSRFIT_INC}>
    $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/../inc>
 )
--- a/src/external/MagProximity/PMPStartupHandlerLinkDef.h
+++ b/src/external/MagProximity/PMPStartupHandlerLinkDef.h
@@ -27,7 +27,7 @@
 *   59 Temple Place - Suite 330, Boston, MA  02111-1307, USA.             *
 ***************************************************************************/

-#ifdef __CLING__
+#ifdef __CINT__

 #pragma link off all globals;
 #pragma link off all classes;
--- a/src/external/MagProximity/PMagProximityFitterLinkDef.h
+++ b/src/external/MagProximity/PMagProximityFitterLinkDef.h
@@ -27,7 +27,7 @@
 *   59 Temple Place - Suite 330, Boston, MA  02111-1307, USA.             *
 ***************************************************************************/

-#ifdef __CLING__
+#ifdef __CINT__

 #pragma link off all globals;
 #pragma link off all classes;
--- a/src/external/MusrRoot/TMusrRunHeaderLinkDef.h
+++ b/src/external/MusrRoot/TMusrRunHeaderLinkDef.h
@@ -27,7 +27,7 @@
 *   59 Temple Place - Suite 330, Boston, MA  02111-1307, USA.             *
 ***************************************************************************/

-#ifdef __CLING__
+#ifdef __CINT__

 #pragma link off all globals;
 #pragma link off all classes;
--- a/src/external/Nonlocal/CMakeLists.txt
+++ b/src/external/Nonlocal/CMakeLists.txt
@@ -54,7 +54,6 @@ target_include_directories(
  PNL_PippardFitter BEFORE PRIVATE 
    $<BUILD_INTERFACE:${FFTW3_INCLUDE}> 
    $<BUILD_INTERFACE:${MUSRFIT_INC}>
-    $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}>
    $<BUILD_INTERFACE:${CMAKE_SOURCE_DIR}>
 )

--- a/src/external/Nonlocal/PNL_PippardFitterLinkDef.h
+++ b/src/external/Nonlocal/PNL_PippardFitterLinkDef.h
@@ -27,7 +27,7 @@
 *   59 Temple Place - Suite 330, Boston, MA  02111-1307, USA.             *
 ***************************************************************************/

-#ifdef __CLING__
+#ifdef __CINT__

 #pragma link off all globals;
 #pragma link off all classes;
--- a/src/external/Nonlocal/PNL_StartupHandlerLinkDef.h
+++ b/src/external/Nonlocal/PNL_StartupHandlerLinkDef.h
@@ -27,7 +27,7 @@
 *   59 Temple Place - Suite 330, Boston, MA  02111-1307, USA.             *
 ***************************************************************************/

-#ifdef __CLING__
+#ifdef __CINT__

 #pragma link off all globals;
 #pragma link off all classes;
--- a/src/external/TLemRunHeader/TLemRunHeaderLinkDef.h
+++ b/src/external/TLemRunHeader/TLemRunHeaderLinkDef.h
@@ -1,4 +1,4 @@
-#ifdef __CLING__
+#ifdef __CINT__

 #pragma link off all globals;
 #pragma link off all classes;
--- a/src/external/TLemRunHeader/TLemStatsLinkDef.h
+++ b/src/external/TLemRunHeader/TLemStatsLinkDef.h
@@ -1,4 +1,4 @@
-#ifdef __CLING__
+#ifdef __CINT__

 #pragma link off all globals;
 #pragma link off all classes;
--- a/src/external/libBNMR/TBNMR.h
+++ b/src/external/libBNMR/TBNMR.h
@@ -66,7 +66,7 @@ class SExpRlx : public PUserFcnBase {

 public:
  // default constructor and destructor
-  SExpRlx(){sexp1.SetNpx(1000); sexp2.SetNpx(1000);}
+  SExpRlx(){}
  ~SExpRlx(){}

  // function operator
--- a/src/external/libBNMR/TBNMRLinkDef.h
+++ b/src/external/libBNMR/TBNMRLinkDef.h
@@ -29,7 +29,7 @@
 *   59 Temple Place - Suite 330, Boston, MA  02111-1307, USA.             *
 ***************************************************************************/

-#ifdef __CLING__
+#ifdef __CINT__

 #pragma link off all globals;
 #pragma link off all classes;
@@ -38,4 +38,4 @@
 #pragma link C++ class ExpRlx+;
 #pragma link C++ class SExpRlx+;

-#endif //__CLING__
+#endif //__CINT__
--- a/src/external/libCalcMeanFieldsLEM/TCalcMeanFieldsLEMLinkDef.h
+++ b/src/external/libCalcMeanFieldsLEM/TCalcMeanFieldsLEMLinkDef.h
@@ -27,7 +27,7 @@
 ***************************************************************************/

 // root dictionary stuff --------------------------------------------------
-#ifdef __CLING__
+#ifdef __CINT__

 #pragma link off all globals;
 #pragma link off all classes;
@@ -39,6 +39,6 @@
 #pragma link C++ class TMeanFieldsForScTrilayer+;
 #pragma link C++ class TMeanFieldsForScTrilayerWithInsulator+;

-#endif //__CLING__
+#endif //__CINT__
 // root dictionary stuff --------------------------------------------------

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+++ b/src/external/libCuba/src/Makefile
@@ -1,912 +0,0 @@
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-install-data-am: install-includeHEADERS install-pkgconfigDATA
-
-install-dvi: install-dvi-recursive
-
-install-dvi-am:
-
-install-exec-am: install-libLTLIBRARIES
-
-install-html: install-html-recursive
-
-install-html-am:
-
-install-info: install-info-recursive
-
-install-info-am:
-
-install-man:
-
-install-pdf: install-pdf-recursive
-
-install-pdf-am:
-
-install-ps: install-ps-recursive
-
-install-ps-am:
-
-installcheck-am:
-
-maintainer-clean: maintainer-clean-recursive
-	-rm -f Makefile
-maintainer-clean-am: distclean-am maintainer-clean-generic
-
-mostlyclean: mostlyclean-recursive
-
-mostlyclean-am: mostlyclean-compile mostlyclean-generic \
-	mostlyclean-libtool
-
-pdf: pdf-recursive
-
-pdf-am:
-
-ps: ps-recursive
-
-ps-am:
-
-uninstall-am: uninstall-includeHEADERS uninstall-libLTLIBRARIES \
-	uninstall-pkgconfigDATA
-
-.MAKE: $(am__recursive_targets) install-am install-strip
-
-.PHONY: $(am__recursive_targets) CTAGS GTAGS TAGS all all-am check \
-	check-am clean clean-generic clean-libLTLIBRARIES \
-	clean-libtool cscopelist-am ctags ctags-am distclean \
-	distclean-compile distclean-generic distclean-libtool \
-	distclean-tags distdir dvi dvi-am html html-am info info-am \
-	install install-am install-data install-data-am install-dvi \
-	install-dvi-am install-exec install-exec-am install-html \
-	install-html-am install-includeHEADERS install-info \
-	install-info-am install-libLTLIBRARIES install-man install-pdf \
-	install-pdf-am install-pkgconfigDATA install-ps install-ps-am \
-	install-strip installcheck installcheck-am installdirs \
-	installdirs-am maintainer-clean maintainer-clean-generic \
-	mostlyclean mostlyclean-compile mostlyclean-generic \
-	mostlyclean-libtool pdf pdf-am ps ps-am tags tags-am uninstall \
-	uninstall-am uninstall-includeHEADERS uninstall-libLTLIBRARIES \
-	uninstall-pkgconfigDATA
-
-.PRECIOUS: Makefile
-
-
-# Tell versions [3.59,3.63) of GNU make to not export all variables.
-# Otherwise a system limit (for SysV at least) may be exceeded.
-.NOEXPORT:
--- a/src/external/libCuba/src/suave/Suave.lo
+++ b/src/external/libCuba/src/suave/Suave.lo
@@ -1,12 +0,0 @@
-# Suave.lo - a libtool object file
-# Generated by libtool (GNU libtool) 2.4.6
-#
-# Please DO NOT delete this file!
-# It is necessary for linking the library.
-
-# Name of the PIC object.
-pic_object='.libs/Suave.o'
-
-# Name of the non-PIC object
-non_pic_object=none
-
--- a/src/external/libFitPofB/include/TLondon1DLinkDef.h
+++ b/src/external/libFitPofB/include/TLondon1DLinkDef.h
@@ -27,7 +27,7 @@
 ***************************************************************************/

 // root dictionary stuff --------------------------------------------------
-#ifdef __CLING__
+#ifdef __CINT__

 #pragma link off all globals;
 #pragma link off all classes;
@@ -41,6 +41,6 @@
 #pragma link C++ class TLondon1D3LS+;
 //#pragma link C++ class TLondon1D4L+;

-#endif //__CLING__
+#endif //__CINT__
 // root dictionary stuff --------------------------------------------------

--- a/src/external/libFitPofB/include/TSkewedGssLinkDef.h
+++ b/src/external/libFitPofB/include/TSkewedGssLinkDef.h
@@ -27,7 +27,7 @@
 ***************************************************************************/

 // root dictionary stuff --------------------------------------------------
-#ifdef __CLING__
+#ifdef __CINT__

 #pragma link off all globals;
 #pragma link off all classes;
@@ -35,6 +35,6 @@

 #pragma link C++ class TSkewedGss+;

-#endif //__CLING__
+#endif //__CINT__
 // root dictionary stuff --------------------------------------------------

--- a/src/external/libFitPofB/include/TVortexLinkDef.h
+++ b/src/external/libFitPofB/include/TVortexLinkDef.h
@@ -27,7 +27,7 @@
 ***************************************************************************/

 // root dictionary stuff --------------------------------------------------
-#ifdef __CLING__
+#ifdef __CINT__

 #pragma link off all globals;
 #pragma link off all classes;
@@ -46,6 +46,6 @@
 #pragma link C++ class TBulkAnisotropicTriVortexAGL+;
 #pragma link C++ class TBulkAnisotropicTriVortexAGLGlobal+;

-#endif //__CLING__
+#endif //__CINT__
 // root dictionary stuff --------------------------------------------------

--- a/src/external/libGapIntegrals/CMakeLists.txt
+++ b/src/external/libGapIntegrals/CMakeLists.txt
@@ -41,7 +41,7 @@ add_library(GapIntegrals SHARED
 #--- set target properties, e.g. version --------------------------------------
 set_target_properties(GapIntegrals
  PROPERTIES
-    VERSION "1.0.0"
+    VERSION "1.1.0"
 )

 #--- make sure that the include directory is found ----------------------------
--- a/src/external/libGapIntegrals/TGapIntegralsLinkDef.h
+++ b/src/external/libGapIntegrals/TGapIntegralsLinkDef.h
@@ -28,7 +28,7 @@


 // root dictionary stuff --------------------------------------------------
-#ifdef __CLING__
+#ifdef __CINT__

 #pragma link off all globals;
 #pragma link off all classes;
@@ -63,6 +63,6 @@
 #pragma link C++ class TLambdaInvPowerLaw+;
 #pragma link C++ class TFilmMagnetizationDWave+;

-#endif //__CLING__
+#endif //__CINT__
 // root dictionary stuff --------------------------------------------------

--- a/src/external/libGbGLF/PGbGLFLinkDef.h
+++ b/src/external/libGbGLF/PGbGLFLinkDef.h
@@ -27,7 +27,7 @@
 ***************************************************************************/

 // root dictionary stuff --------------------------------------------------
-#ifdef __CLING__
+#ifdef __CINT__

 #pragma link off all globals;
 #pragma link off all classes;
@@ -35,6 +35,6 @@

 #pragma link C++ class PGbGLF+;

-#endif //__CLING__
+#endif //__CINT__
 // root dictionary stuff --------------------------------------------------

--- a/src/external/libLFRelaxation/TLFRelaxationLinkDef.h
+++ b/src/external/libLFRelaxation/TLFRelaxationLinkDef.h
@@ -27,7 +27,7 @@
 ***************************************************************************/

 // root dictionary stuff --------------------------------------------------
-#ifdef __CLING__
+#ifdef __CINT__

 #pragma link off all globals;
 #pragma link off all classes;
@@ -40,6 +40,6 @@
 #pragma link C++ class TLFDynSG+;
 #pragma link C++ class TLFSGInterpolation+;

-#endif //__CLING__
+#endif //__CINT__
 // root dictionary stuff --------------------------------------------------

--- a/src/external/libPhotoMeissner/include/PPhotoMeissnerLinkDef.h
+++ b/src/external/libPhotoMeissner/include/PPhotoMeissnerLinkDef.h
@@ -27,7 +27,7 @@
 *   59 Temple Place - Suite 330, Boston, MA  02111-1307, USA.             *
 ***************************************************************************/

-#ifdef __CLING__
+#ifdef __CINT__

 #pragma link off all globals;
 #pragma link off all classes;
--- a/src/external/libSpinValve/include/PSkewedLorentzianLinkDef.h
+++ b/src/external/libSpinValve/include/PSkewedLorentzianLinkDef.h
@@ -27,7 +27,7 @@
 *   59 Temple Place - Suite 330, Boston, MA  02111-1307, USA.             *
 ***************************************************************************/

-#ifdef __CLING__
+#ifdef __CINT__

 #pragma link off all globals;
 #pragma link off all classes;
--- a/src/external/libSpinValve/include/PStartupHandler_SVLinkDef.h
+++ b/src/external/libSpinValve/include/PStartupHandler_SVLinkDef.h
@@ -27,7 +27,7 @@
 *   59 Temple Place - Suite 330, Boston, MA  02111-1307, USA.             *
 ***************************************************************************/

-#ifdef __CLING__
+#ifdef __CINT__

 #pragma link off all globals;
 #pragma link off all classes;
--- a/src/external/libZFRelaxation/ZFRelaxationLinkDef.h
+++ b/src/external/libZFRelaxation/ZFRelaxationLinkDef.h
@@ -27,7 +27,7 @@
 ***************************************************************************/

 // root dictionary stuff --------------------------------------------------
-#ifdef __CLING__
+#ifdef __CINT__

 #pragma link off all globals;
 #pragma link off all classes;
@@ -37,6 +37,6 @@
 #pragma link C++ class ZFMagExp+;
 #pragma link C++ class UniaxialStatGssKT+;

-#endif //__CLING__
+#endif //__CINT__
 // root dictionary stuff --------------------------------------------------

--- a/src/external/nexus/CMakeLists.txt
+++ b/src/external/nexus/CMakeLists.txt
@@ -5,7 +5,7 @@ set(prefix "${CMAKE_INSTALL_PREFIX}")
 set(exec_prefix "\$\{prefix\}")
 set(libdir "\$\{exec_prefix\}/lib")
 set(includedir "\$\{prefix\}/include")   
-set(PNEXUS_VERSION "0.9.0")
+set(PNEXUS_VERSION "1.0.0")
 set(PNEXUS_LIBRARY_NAME "PNeXus")
 configure_file("PNeXus.pc.in" "PNeXus.pc" @ONLY)

@@ -21,11 +21,10 @@ set_target_properties(PNeXus
 )

 #--- make sure that the include directory is found ----------------------------
-target_include_directories(
-  PNeXus BEFORE PRIVATE 
-     $<BUILD_INTERFACE:${HDF4_INCLUDE_DIRS}>
-     $<BUILD_INTERFACE:${HDF5_INCLUDE_DIRS}>
-     $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}>
+target_include_directories(PNeXus 
+  BEFORE PRIVATE $<BUILD_INTERFACE:${HDF4_INCLUDE_DIRS}>
+  BEFORE PRIVATE $<BUILD_INTERFACE:${HDF5_INCLUDE_DIRS}>
+  BEFORE PRIVATE $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}>
 )

 #--- add library dependencies -------------------------------------------------
@@ -34,6 +33,7 @@ if (HAVE_HDF4)
 else (HAVE_HDF4)   
  set(HDF_LIBS ${HDF5_LIBRARIES})
 endif (HAVE_HDF4)
+message(STATUS "as35> HDF_LIBS: ${HDF_LIBS}")
 target_link_libraries(PNeXus PRIVATE ${HDF_LIBS} ${ROOT_LIBRARIES})

 #--- install PNeXus solib -----------------------------------------------------
--- a/src/external/nexus/PyScripts/Install.md
+++ b/src/external/nexus/PyScripts/Install.md
@@ -0,0 +1,126 @@
+# Installation
+
+## Requirements
+
+| Package | Version | Purpose |
+|---------|---------|---------|
+| Python  | ≥ 3.9   | Runtime |
+| h5py    | ≥ 3.0   | Read HDF5 files (NeXus Version 2) |
+| pyhdf      | ≥ 0.10  | Read HDF4 files (NeXus Version 1) — optional |
+| pdfplumber | ≥ 0.9   | Extract schema from instrument definition PDF (`--pdf` mode) — optional |
+
+---
+
+## Install h5py (required)
+
+h5py provides HDF5 support and is needed for all modern muon NeXus files (Version 2,
+written since ~2020).
+
+```bash
+pip install h5py
+```
+
+Or via your system package manager:
+
+```bash
+# Fedora / RHEL
+sudo dnf install python3-h5py
+
+# Ubuntu / Debian
+sudo apt install python3-h5py
+
+# macOS (Homebrew)
+brew install hdf5
+pip install h5py
+```
+
+---
+
+## Install pyhdf (optional, HDF4 / Version 1 files only)
+
+pyhdf is only needed for reading old HDF4-format files (NeXus Version 1, written
+before ~2011 by the MCS software at ISIS).  If you only work with modern HDF5 files,
+you can skip this step.
+
+pyhdf requires the HDF4 C library to be present on the system.
+
+### Linux
+
+```bash
+# Fedora / RHEL
+sudo dnf install python3-devel hdf hdf-devel
+pip install pyhdf
+
+# Ubuntu / Debian
+sudo apt install python3-dev libhdf4-dev
+pip install pyhdf
+```
+
+> **Note (GCC 14+ / Fedora 40+):** pyhdf may fail to build with a
+> `-Wincompatible-pointer-types` error. Work around it with:
+> ```bash
+> CFLAGS="-Wno-incompatible-pointer-types -Wno-discarded-qualifiers" pip install pyhdf
+> ```
+
+### macOS
+
+```bash
+brew install hdf4
+pip install pyhdf
+```
+
+### Windows
+
+Pre-built wheels are available on PyPI for some Python / Windows combinations:
+
+```bash
+pip install pyhdf
+```
+
+If no wheel is available, consider using a conda environment:
+
+```bash
+conda install -c conda-forge pyhdf
+```
+
+---
+
+## Install pdfplumber (optional, PDF-driven validation only)
+
+pdfplumber is only needed when you use the `--pdf` option to validate files against
+a specific revision of the instrument definition PDF.
+
+```bash
+pip install pdfplumber
+```
+
+Or via your system package manager (if available):
+
+```bash
+# Fedora / RHEL
+sudo dnf install python3-pdfplumber   # may not be in all repos
+
+# Ubuntu / Debian
+sudo apt install python3-pdfplumber   # may not be in all repos
+
+# macOS (Homebrew)
+pip install pdfplumber
+```
+
+---
+
+## Verify the installation
+
+```bash
+python3 -c "import h5py; print('h5py', h5py.__version__)"
+python3 -c "import pyhdf; print('pyhdf ok')"          # optional — HDF4 support
+python3 -c "import pdfplumber; print('pdfplumber ok')" # optional — PDF-driven mode
+```
+
+---
+
+## No installation needed
+
+The validator is a single self-contained script — no build step, no package
+installation of the script itself is required.  Simply place
+`nexus_muon_validator.py` anywhere on your system and run it with Python.
--- a/src/external/nexus/PyScripts/Usage.md
+++ b/src/external/nexus/PyScripts/Usage.md
@@ -0,0 +1,223 @@
+# Usage — nexus_muon_validator.py
+
+Validates muon NeXus HDF4/5 files against the ISIS Muon Instrument Definitions
+(Version 1 and Version 2 / *muonTD*).
+
+Two validation modes are available:
+
+- **Hardcoded mode** (default) — built-in rules based on the 2026 rev 11 spec.
+  No extra dependencies beyond `h5py`.
+- **PDF-driven mode** (`--pdf`) — rules are extracted live from a
+  `nexus_instrument_definitions_*.pdf` that you supply.  Requires `pdfplumber`.
+
+Reference document:
+*NeXus Instrument Definitions for Muon Data*, S. Cottrell, 21 January 2026
+(`nexus_instrument_definitions_for_muon_data_2026_rev11.pdf`)
+
+---
+
+## Basic invocation
+
+```bash
+python3 nexus_muon_validator.py <file.nxs> [<file2.nxs> ...]
+```
+
+Validate one or more files in a single call:
+
+```bash
+python3 nexus_muon_validator.py run001.nxs run002.nxs run003.nxs
+```
+
+---
+
+## Command-line options
+
+| Option | Description |
+|--------|-------------|
+| `--pdf <def.pdf>` | Parse schema from a NeXus instrument definition PDF and validate against it |
+| `--list-schema` | Print the schema extracted from `--pdf` and exit (no files needed) |
+| `-v`, `--verbose` | Also show INFO-level findings (optional fields, format info) |
+| `--errors-only` | Show only ERROR-level issues; suppress warnings |
+| `-h`, `--help` | Show built-in help and exit |
+
+---
+
+## Severity levels
+
+| Level   | Meaning |
+|---------|---------|
+| `ERROR` | A field required by the specification is missing or unreadable. |
+| `WARNING` | A field has an unexpected value, a legacy name, or a shape inconsistency. |
+| `INFO` | An optional field recommended by the specification is absent (shown only with `-v`). |
+
+---
+
+## Exit codes
+
+| Code | Meaning |
+|------|---------|
+| `0`  | Validation passed — no ERRORs found |
+| `1`  | At least one ERROR was reported |
+| `2`  | File could not be opened or is not a recognised NeXus format |
+
+---
+
+## Examples
+
+**Validate a single file (errors and warnings only):**
+```bash
+python3 nexus_muon_validator.py EMU00139040.nxs
+```
+
+**Validate a whole directory of runs:**
+```bash
+python3 nexus_muon_validator.py /data/musr/2025/*.nxs
+```
+
+**Show full detail including optional fields:**
+```bash
+python3 nexus_muon_validator.py -v EMU00139040.nxs
+```
+
+**Show only hard errors (useful in scripts):**
+```bash
+python3 nexus_muon_validator.py --errors-only EMU00139040.nxs
+echo "Exit code: $?"
+```
+
+**Use in a shell script with exit-code checking:**
+```bash
+#!/bin/bash
+python3 nexus_muon_validator.py --errors-only "$1"
+if [ $? -ne 0 ]; then
+    echo "Validation failed for $1"
+    exit 1
+fi
+```
+
+**Validate against a specific revision of the instrument definition PDF:**
+```bash
+python3 nexus_muon_validator.py \
+  --pdf nexus_instrument_definitions_for_muon_data_2026_rev11.pdf \
+  EMU00139040.nxs
+```
+
+**Inspect the schema extracted from a PDF (no files needed):**
+```bash
+python3 nexus_muon_validator.py \
+  --pdf nexus_instrument_definitions_for_muon_data_2026_rev11.pdf \
+  --list-schema
+```
+
+Example `--list-schema` output:
+```
+Parsed schema from: nexus_instrument_definitions_for_muon_data_2026_rev11.pdf …
+  → 35 NX classes found (42 version entries)
+
+  NXdata        v1  required=0  optional=8   attrs=18
+  NXdata        v2  required=2  optional=6   attrs=9
+  NXdetector    v1  required=0  optional=4   attrs=4
+  NXdetector    v2  required=4  optional=28  attrs=34
+  NXentry       v1  required=0  optional=18  attrs=1
+  NXentry       v2  required=11 optional=18  attrs=9
+  ...
+```
+
+---
+
+## What is checked
+
+### File format
+- Detects HDF5 (via `h5py`) or HDF4 (via `pyhdf`) automatically.
+- HDF4 files are Version 1 by definition; HDF5 files may be Version 1 or 2.
+- Reports an error if the format is unrecognised or the file cannot be opened.
+
+### Version detection
+The instrument definition version is detected automatically:
+
+| Condition | Detected version |
+|-----------|-----------------|
+| HDF4 file | **Version 1** (always) |
+| HDF5: entry `definition` = `muonTD` or `pulsedTD`, or `IDF_version` = 2 | **Version 2** |
+| HDF5: entry group named `run` (NXentry), no `definition` field | **Version 1** |
+
+### Version 1 checks (HDF4 or HDF5 `NXfile` / `NXentry`)
+Covers the original muon instrument definition (MCS/RAL, 2001).
+
+- Root attribute: `@NeXus_version` (WARNING if absent)
+- NXentry (`run`): `IDF_version`, `program_name`, `number`, `title`, `notes`,
+  `analysis`, `lab`, `beamline`, `start_time`, `stop_time`, `switching_states`
+- NXuser: `name`, `experiment_number`
+- NXsample: `temperature` (+`@units`), `magnetic_field` (+`@units`)
+- NXinstrument: `name`
+  - NXdetector: `number`; optional `deadtimes` (+`@units`, `@available`),
+    `angles` (+`@coordinate_system`, `@available`)
+  - NXcollimator: `type`
+  - NXbeam: `total_counts` (+`@units`)
+- NXdata (`histogram_data_1`): `counts` (+`@units`, `@signal`,
+  `@t0_bin`, `@first_good_bin`, `@last_good_bin`),
+  `resolution` (+`@units`), `time_zero` (+`@units`, `@available`),
+  `raw_time` (+`@axis`, `@primary`, `@units`)
+
+### Version 2 checks (`NXroot` / `muonTD`)
+Covers the revised muon instrument definition (ISIS, 2011–2026).
+
+- Root attributes: `@file_name` (required), `@file_time` (required)
+- At least one `raw_data_N` NXentry must be present
+- NXentry: `IDF_version` (= 2), `definition` (= `muonTD`), `run_number`,
+  `title`, `start_time`, `end_time`, `experiment_identifier`
+- NXsample: `name`
+- NXinstrument: `name`
+  - NXsource: `name`, `type`, `probe`
+  - NXdetector (`detector_*`): `counts` (+`@signal`, `@axes`, `@long_name`),
+    `raw_time` (+`@units`), `spectrum_index`
+- NXdata (`detector_*`): `counts` (+`@signal`, `@axes`), `raw_time` (+`@units`)
+- NXuser (`user_1`): `name`
+
+### Dimensional consistency checks
+- `raw_time` shape must be `(ntc,)` (bin centres) or `(ntc+1,)` (bin boundaries),
+  where `ntc` is the last dimension of `counts`.
+- `corrected_time` shape must be `(ntc,)`.
+- `spectrum_index` shape must be `(ns,)`, matching the second-to-last dimension
+  of `counts`.
+
+### Legacy / transitional handling
+The validator distinguishes real errors from known historical deviations:
+
+| Observed value | Expected (spec) | Reported as |
+|----------------|-----------------|-------------|
+| `pulsedTD` | `muonTD` | WARNING — legacy name, used in files written before rev 8 |
+| `time_of_flight` | `raw_time` | WARNING — legacy dataset name used in files before ~2020 |
+| `muons` | `positive muons` or `negative muons` | WARNING — non-specific probe label |
+| `n/a` for `type` or `probe` in NXsource | specific string | WARNING |
+
+---
+
+## Sample output
+
+```
+========================================================================
+  File: EMU00139040.nxs
+========================================================================
+  [WARNING] /raw_data_1/definition  →  Value is 'pulsedTD' (legacy name);
+                                       current spec (rev≥8) requires 'muonTD'
+========================================================================
+  Summary: 0 error(s), 1 warning(s)
+========================================================================
+```
+
+With `--verbose`:
+```
+========================================================================
+  File: EMU00139040.nxs
+========================================================================
+  [WARNING] /raw_data_1/definition  →  Value is 'pulsedTD' (legacy name); ...
+  [INFO   ] /  →  File format: HDF5
+  [INFO   ] /  →  Detected muon NeXus instrument definition version: 2
+  [INFO   ] /raw_data_1/instrument  →  Optional group 'beamline' not present
+  [INFO   ] /raw_data_1/sample  →  Optional dataset 'magnetic_field_state' not present
+  ...
+========================================================================
+  Summary: 0 error(s), 1 warning(s), 13 info(s)
+========================================================================
+```
--- a/src/external/nexus/PyScripts/nexus_muon_validator.py
+++ b/src/external/nexus/PyScripts/nexus_muon_validator.py
--- a/src/external/nexus/README.Cygwin
+++ b/src/external/nexus/README.Cygwin
@@ -1,69 +0,0 @@
-2011/04/13 -- BMW
-
-Under Cygwin of all the required libraries for NeXus only HDF5 is available.
-The packages <hdf5> and <libhdf5-devel> can be installed through the Cygwin setup.
-One should also make sure that <bison>, <flex> and a package containing "/usr/lib/librpc.a" (e.g. <sunrpc> = 4.0-3) are installed.
-
-All other libraries have to be built from the sources:
-
-* JPEG-6b
-  URL: http://www.hdfgroup.org/ftp/lib-external/jpeg/src/jpegsrc.v6b.tar.gz
-  Configure options: --prefix=/usr/local --enable-static
-
-* MXML 2.5
-  URL: http://ftp.easysw.com/pub/mxml/2.5/mxml-2.5.tar.gz
-  Configure options: --prefix=/usr/local --enable-static
-
-* HDF 4.2.5
-  URL: http://www.hdfgroup.org/ftp/HDF/HDF_Current/src/hdf-4.2.5.tar.gz 
-  Configure options: --prefix=/usr/local --enable-static --disable-fortran --with-jpeg=/usr/local
-
-* NeXus 4.2.1
-  URL: http://download.nexusformat.org/kits/nexus-4.2.1.tar.gz
-  Configure options: --prefix=/usr/local --with-hdf4=/usr/local --with-hdf5=/usr --with-xml=/usr/local
-
-The version numbers and source-code locations might of course change with time but should be easily adjustable.
-
-If one is confident enough that all requirements to build the above packages are fullfilled, one could also try to run the following lines as a script.
-However, there is absolutely no warranty that it works.
-
---
-
-#!/bin/sh
-
-cd
-mkdir nexus
-cd nexus
-curl http://www.hdfgroup.org/ftp/lib-external/jpeg/src/jpegsrc.v6b.tar.gz -G | tar xz
-cd jpeg-6b
-./configure --prefix=/usr/local --enable-static
-make
-make install
-cd ..
-curl http://ftp.easysw.com/pub/mxml/2.5/mxml-2.5.tar.gz -G | tar xz
-cd mxml-2.5
-./configure --prefix=/usr/local --enable-static
-make
-make install
-cd ..
-curl http://www.hdfgroup.org/ftp/HDF/HDF_Current/src/hdf-4.2.5.tar.gz -G | tar xz
-cd hdf-4.2.5
-./configure --prefix=/usr/local --enable-static --disable-fortran --with-jpeg=/usr/local
-make
-make install
-cd ..
-curl http://download.nexusformat.org/kits/nexus-4.2.1.tar.gz -G | tar xz
-./configure --prefix=/usr/local --with-hdf4=/usr/local --with-hdf5=/usr --with-xml=/usr/local
-make
-make install
-
---
-
-In order to obtain NeXus support in musrfit after installing the above libraries, musrfit has to be configured with the options
-"--enable-static --enable-NeXus"
-
-Further information on how to set up musrfit under Cygwin can be found here:
-https://intranet.psi.ch/MUSR/MusrFitSetup#A_4_MS_Windows
-http://lmu.web.psi.ch/facilities/software/musrfit/user/intranet.psi.ch/MUSR/MusrFitSetup.html#A_4_MS_Windows
-
-EOF
--- a/src/external/nexus/Usage.md
+++ b/src/external/nexus/Usage.md
--- a/src/external/nexus/examples/hdf4/CMakeLists.txt
+++ b/src/external/nexus/examples/hdf4/CMakeLists.txt
@@ -0,0 +1,149 @@
+# - h4nexus
+cmake_minimum_required(VERSION 3.26)
+
+project(h4nexus VERSION 0.1.0 LANGUAGES CXX)
+
+#--- set C++ standard ---------------------------------------------------------
+set(CMAKE_CXX_STANDARD 17)
+set(CMAKE_CXX_STANDARD_REQUIRED ON)
+set(CMAKE_CXX_EXTENSIONS OFF)
+
+#--- set a default build type if none was specified ---------------------------
+set(default_build_type "Release")
+
+if (NOT CMAKE_BUILD_TYPE AND NOT CMAKE_CONFIGURATION_TYPES)
+  message(STATUS "Setting build type to '${default_build_type}' as none was specified.")
+  set(CMAKE_BUILD_TYPE "${default_build_type}" CACHE
+      STRING "Choose the type of build." FORCE)
+  # Set the possible values of build type for cmake-gui
+  set_property(CACHE CMAKE_BUILD_TYPE PROPERTY STRINGS
+    "Debug" "Release" "MinSizeRel" "RelWithDebInfo")
+endif ()
+
+#--- check for pkg-config -----------------------------------------------------
+find_package(PkgConfig REQUIRED)
+
+#--- check for git ------------------------------------------------------------
+find_package(Git REQUIRED)
+
+#--- check for HDF4 -----------------------------------------------------------
+# Find HDF4 manually (pkg-config often doesn't have hdf4)
+find_path(HDF4_INCLUDE_DIR
+  NAMES mfhdf.h
+  PATHS /usr/include /usr/local/include
+  PATH_SUFFIXES hdf
+)
+
+find_library(HDF4_DF_LIBRARY
+  NAMES df libdf
+  PATHS /usr/lib64 /usr/lib /usr/local/lib64 /usr/local/lib
+)
+
+find_library(HDF4_MFHDF_LIBRARY
+  NAMES mfhdf libmfhdf
+  PATHS /usr/lib64 /usr/lib /usr/local/lib64 /usr/local/lib
+)
+
+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: ${HDF4_LIBRARIES}")
+else ()
+    message(FATAL_ERROR "HDF4 library not found. Please install libhdf4-dev or hdf-devel")
+endif ()
+
+include_directories(${HDF4_INCLUDE_DIRS})
+
+#--- check for HDF5 -----------------------------------------------------------
+find_package(HDF5 REQUIRED COMPONENTS CXX)
+if(NOT HDF5_FOUND)
+    message(FATAL_ERROR "HDF5 C++ library not found")
+endif()
+include_directories(${HDF5_INCLUDE_DIRS})
+
+#--- check for ROOT -----------------------------------------------------------
+find_package(ROOT 6.36 REQUIRED COMPONENTS Minuit2)
+if (ROOT_miniut2_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_miniut2_FOUND)
+
+#--- all checks done -> feed config.h -----------------------------------------
+set(HAVE_CONFIG_H 1 CACHE INTERNAL "config.h is available")
+configure_file(${CMAKE_SOURCE_DIR}/cmake/config.h.in ${CMAKE_CURRENT_BINARY_DIR}/config.h)
+
+#--- check if project source is a git repo ------------------------------------
+if (EXISTS "${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)
+  execute_process(COMMAND sh ${CMAKE_SOURCE_DIR}/git_revision.sh ${CMAKE_BINARY_DIR})
+
+  set(HAVE_GIT_REV_H "-DHAVE_GIT_REV_H")
+  set(GIT_REV_H "git-revision.h")
+else (IS_GIT_REPO)
+  set(HAVE_GIT_REV_H "")
+  set(GIT_REV_H "")
+endif (IS_GIT_REPO)
+
+#--- end create git-revision.h ------------------------------------------------
+
+#--- write summary of the installation
+cmake_host_system_information(RESULT PROCESSOR QUERY PROCESSOR_DESCRIPTION)
+
+message("")
+message("|-----------------------------------------------------------------------|")
+message("|                                                                       |")
+message("|                            Summary                                    |")
+message("|                                                                       |")
+message("|-----------------------------------------------------------------------|")
+message("")
+message(" System:    ${CMAKE_HOST_SYSTEM_NAME} ${CMAKE_SYSTEM_PROCESSOR} - ${CMAKE_HOST_SYSTEM_VERSION}")
+message(" Processor: ${PROCESSOR} (${CMAKE_SYSTEM_PROCESSOR})")
+message(" ----------")
+message("")
+message(" h4nexus Version: ${h4nexus_VERSION}")
+message(" ----------------")
+message("")
+message(" Build Type: ${CMAKE_BUILD_TYPE}")
+message(" -----------")
+message("")
+message(" Requirements:")
+message(" -------------")
+message("")
+message(" HDF4    found in ${HDF4_INCLUDE_DIRS}")
+message(" ROOT    found in ${ROOT_INCLUDE_DIRS}, Version: ${ROOT_VERSION}")
+message("")
+message(" Installation directories:")
+message(" -------------------------")
+message("")
+message(" Programs                : ${CMAKE_INSTALL_PREFIX}/bin")
+message("")
+message("-------------------------------------------------------------------------")
+message("")
+
+#--- h4nexus executable -------------------------------------------------------
+add_executable(h4nexus 
+               ../../PNeXus.cpp
+               main.cpp)
+target_compile_options(h4nexus BEFORE PRIVATE "-DHAVE_HDF4 -DHAVE_CONFIG_H" ${HAVE_GIT_REV_H})
+target_include_directories(h4nexus 
+  BEFORE PRIVATE
+    $<BUILD_INTERFACE:${CMAKE_SOURCE_DIR}/build>
+    $<BUILD_INTERFACE:${CMAKE_SOURCE_DIR}/../..>
+    $<BUILD_INTERFACE:${ROOT_INCLUDE_DIRS}>
+)
+target_link_libraries(h4nexus ${HDF4_LIBRARIES} ${HDF5_LIBRARIES} ${ROOT_LIBRARIES})
--- a/src/external/nexus/examples/hdf4/cmake/config.h.in
+++ b/src/external/nexus/examples/hdf4/cmake/config.h.in
@@ -0,0 +1,7 @@
+/* config.h.in.  Generated from CMakeLists.txt  */
+
+/* Define to 1 if you have the <config.h> file. */
+#cmakedefine HAVE_CONFIG_H @HAVE_CONFIG_H@
+
+/* h4nexus version */
+#define H4NEXUS_VERSION "@h4nexus_VERSION@"
--- a/src/external/nexus/examples/hdf4/docu/README.md
+++ b/src/external/nexus/examples/hdf4/docu/README.md
@@ -0,0 +1,155 @@
+# h4nexus - handle muSR-NeXus files via HDF4 only
+
+## Contents
+
+Tests and classes to handle muSR-NeXus files directly via the HDF4 C API.
+
+This project provides the same API as h5nexus but uses HDF4 instead of HDF5 for handling NeXus files.
+
+## Features
+
+- **Read and write NeXus HDF4 files** with a clean C++ API
+- **Case-insensitive path lookup** for datasets and groups
+- **Type-safe data handling** using template classes
+- **Dead time correction calculation** for muon detector data using ROOT Minuit2
+- **Compatible API with h5nexus** for easy migration
+
+## Key Classes
+
+- `nxH4::PNeXus` - Main class for reading/writing NeXus HDF4 files
+- `nxH4::PNXdata<T>` - Template class for storing dataset content with attributes
+- `nxH4::PNeXusDeadTime` - Dead time correction calculator for muon detector data
+
+## Requirements
+
+- CMake >= 3.26
+- C++17 compatible compiler
+- HDF4 library (libhdf4-dev or hdf-devel)
+- ROOT >= 6.36 with Minuit2 component
+- pkg-config
+
+## Building
+
+```bash
+mkdir build
+cd build
+cmake ..
+make
+```
+
+## Installation
+
+```bash
+make install
+```
+
+This will install:
+- Library: `libh4nexus.so` in `${CMAKE_INSTALL_PREFIX}/lib`
+- Executable: `h4nexus` in `${CMAKE_INSTALL_PREFIX}/bin`
+- Header: `PNeXus.h` in `${CMAKE_INSTALL_PREFIX}/include/h4nexus`
+
+## Usage
+
+### Command Line
+
+```bash
+# Display help
+h4nexus --help
+
+# Read and display a NeXus HDF4 file
+h4nexus --fn input.nxs
+
+# Read with debug output
+h4nexus --fn input.nxs --debug
+
+# Calculate dead time corrections
+h4nexus --fn input.nxs --dead_time_estimate
+
+# Write output file
+h4nexus --fn input.nxs --out output.nxs
+```
+
+### Programmatic Usage
+
+```cpp
+#include <h4nexus/PNeXus.h>
+
+// Read a NeXus file
+nxH4::PNeXus nexus("data.nxs");
+
+// Access datasets
+auto counts_data = nexus.GetDataset<int>("/raw_data_1/detector_1/counts");
+const auto& counts = counts_data.GetData();
+const auto& dims = counts_data.GetDimensions();
+
+// Dump file contents
+nexus.Dump();
+
+// Write to new file
+nexus.WriteNexusFile("output.nxs", 2);  // IDF version 2
+```
+
+### Creating Files from Scratch
+
+```cpp
+nxH4::PNeXus nxs_out;
+
+// Add datasets
+std::vector<int> counts(16*66000, 0);
+nxs_out.AddDataset<int>("/raw_data_1/detector_1/counts",
+                        counts, {1, 16, 66000},
+                        nxH4::H4DataType::INT32);
+
+// Add attributes
+nxs_out.AddDatasetAttribute<int>("/raw_data_1/detector_1/counts",
+                                  "units", std::string("counts"));
+
+// Add group attributes
+nxs_out.AddGroupAttribute("/raw_data_1", "NX_class", std::string("NXentry"));
+
+// Write file
+nxs_out.WriteNexusFile("output.nxs");
+```
+
+## API Compatibility with h5nexus
+
+The h4nexus API is designed to be compatible with h5nexus. The main differences are:
+
+- Namespace: `nxH4::` instead of `nxH5::`
+- Data types: `H4DataType` enum instead of `H5::DataType`
+- Dimensions: Uses `uint32_t` instead of `hsize_t`
+
+Code migration typically requires only:
+1. Changing namespace from `nxH5` to `nxH4`
+2. Changing `H5::PredType::NATIVE_INT` to `nxH4::H4DataType::INT32` (etc.)
+3. Changing dimension types from `hsize_t` to `uint32_t`
+
+## Supported Data Types
+
+- `H4DataType::INT32` - 32-bit signed integer
+- `H4DataType::FLOAT32` - 32-bit floating point
+- `H4DataType::FLOAT64` - 64-bit floating point
+- `H4DataType::CHAR8` - 8-bit character/string
+- `H4DataType::UINT32` - 32-bit unsigned integer
+- `H4DataType::INT16` - 16-bit signed integer
+- `H4DataType::UINT16` - 16-bit unsigned integer
+- `H4DataType::INT8` - 8-bit signed integer
+- `H4DataType::UINT8` - 8-bit unsigned integer
+
+## Differences from HDF5
+
+HDF4 has some limitations compared to HDF5:
+- No true hierarchical groups (simulated using naming conventions)
+- Less flexible attribute handling
+- Different maximum name lengths
+- C API instead of C++ API
+
+The h4nexus library abstracts these differences to provide a similar interface to h5nexus.
+
+## License
+
+GNU General Public License v2 (GPLv2)
+
+## Contacts
+
+Andreas Suter <andreas.suter@psi.ch>
--- a/src/external/nexus/examples/hdf4/git_revision.sh
+++ b/src/external/nexus/examples/hdf4/git_revision.sh
@@ -0,0 +1,35 @@
+#!/bin/bash
+
+# Script to create git-revision.h with current git information
+# Usage: git_revision.sh [output_directory]
+
+output_dir="${1:-.}"
+output_file="${output_dir}/git-revision.h"
+
+# Check if we're in a git repository
+if ! git rev-parse --git-dir > /dev/null 2>&1; then
+    echo "Not in a git repository, skipping git-revision.h generation"
+    exit 0
+fi
+
+# Get git information
+git_branch=$(git rev-parse --abbrev-ref HEAD 2>/dev/null)
+git_hash=$(git rev-parse --short HEAD 2>/dev/null)
+git_date=$(git log -1 --format=%cd --date=short 2>/dev/null)
+
+# Create header file
+cat > "$output_file" << EOF
+// This file is auto-generated by git_revision.sh
+// Do not edit manually
+
+#ifndef GIT_REVISION_H
+#define GIT_REVISION_H
+
+#define GIT_BRANCH "$git_branch"
+#define GIT_HASH "$git_hash"
+#define GIT_DATE "$git_date"
+
+#endif // GIT_REVISION_H
+EOF
+
+echo "Generated $output_file"
--- a/src/external/nexus/examples/hdf4/main.cpp
+++ b/src/external/nexus/examples/hdf4/main.cpp
@@ -0,0 +1,447 @@
+/***************************************************************************
+
+  main.cpp
+
+  Author: Andreas Suter
+  e-mail: andreas.suter@psi.ch
+
+***************************************************************************/
+
+/***************************************************************************
+ *   Copyright (C) 2007-2026 by Andreas Suter                              *
+ *   andreas.suter@psi.ch                                                  *
+ *                                                                         *
+ *   This program is free software; you can redistribute it and/or modify  *
+ *   it under the terms of the GNU General Public License as published by  *
+ *   the Free Software Foundation; either version 2 of the License, or     *
+ *   (at your option) any later version.                                   *
+ *                                                                         *
+ *   This program is distributed in the hope that it will be useful,       *
+ *   but WITHOUT ANY WARRANTY; without even the implied warranty of        *
+ *   MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the         *
+ *   GNU General Public License for more details.                          *
+ *                                                                         *
+ *   You should have received a copy of the GNU General Public License     *
+ *   along with this program; if not, write to the                         *
+ *   Free Software Foundation, Inc.,                                       *
+ *   59 Temple Place - Suite 330, Boston, MA  02111-1307, USA.             *
+ ***************************************************************************/
+
+/**
+ * @file main.cpp
+ * @brief Command-line interface for the h4nexus NeXus HDF4 file reader/writer
+ *
+ * This file contains the main() function and command-line interface for the
+ * h4nexus program. It provides functionality to:
+ * - Read and display NeXus HDF4 files
+ * - Write NeXus HDF4 files using the PNXdata approach
+ * - Calculate dead time corrections for muon detector data
+ *
+ * **Command-Line Options:**
+ * - --fn <file>: Input NeXus HDF4 file (required)
+ * - --out <file>: Output NeXus HDF4 file (optional)
+ * - --debug, -d: Enable debug output
+ * - --dead_time_estimate, -dt: Calculate dead time corrections
+ * - --help, -h: Display help message
+ * - --version, -v: Display version information
+ *
+ * @author Andreas Suter
+ * @date 2007-2026
+ * @copyright GNU General Public License v2
+ * @version 1.0
+ *
+ * @see nxH4::PNeXus
+ * @see nxH4::PNeXusDeadTime
+ */
+
+#include <cstring>
+#include <iostream>
+#include <string>
+#include <memory>
+#include <ctime>
+
+#include <mfhdf.h>
+
+#include "PNeXus.h"
+
+#ifdef HAVE_CONFIG_H
+#include "config.h"
+#endif
+
+#ifdef HAVE_GIT_REV_H
+#include "git-revision.h"
+#endif
+
+//-----------------------------------------------------------------------------
+/**
+ * @brief Display command-line syntax and help information
+ *
+ * Prints the usage syntax and available command-line options for the h4nexus
+ * program to stdout and exits the program.
+ */
+void h4nexus_syntax() {
+  std::cout << std::endl;
+  std::cout << "usage: h4nexus [--help | -h] |" << std::endl;
+  std::cout << "               [--version | -v] |" << std::endl;
+  std::cout << "               --fn <fln> [--debug | -d]" << std::endl;
+  std::cout << "               [--dead_time_estimate | -dt]]" << std::endl;
+  std::cout << "               [--out <fout>]" << std::endl;
+  std::cout << std::endl;
+  std::cout << "options:" << std::endl;
+  std::cout << "  --help, -h: this help." << std::endl;
+  std::cout << "  --version, -v: version of h4nexus." << std::endl;
+  std::cout << "  --fn <fln>: nexus hdf4 input file name <fn>." << std::endl;
+  std::cout << "  --dead_time_estimate, -dt: dead time estimate for the read hdf4 nexus file." << std::endl;
+  std::cout << "  --debug, -d: print additional debug information." << std::endl;
+  std::cout << "  --out <fout>: write the required datasets of a nexus hdf4 file to file " << std::endl;
+  std::cout << "                with name <fout>. Only makes sense together with the option --fn <fln>." << std::endl;
+  std::cout << std::endl;
+  exit(0);
+}
+
+//-----------------------------------------------------------------------------
+/**
+ * @brief Calculate dead time corrections for muon detector data
+ *
+ * Estimates dead time corrections for each detector in the NeXus file using
+ * the PNeXusDeadTime class and ROOT Minuit2 minimization.
+ *
+ * @param nxs Pointer to the PNeXus object containing the data
+ * @param debug If true, print additional debug information
+ *
+ * @see nxH4::PNeXusDeadTime
+ */
+void h4nexus_deadTimeEstimate(const nxH4::PNeXus *nxs, bool debug)
+{
+  if (debug) {
+    std::cout << std::endl;
+    std::cout << std::endl << "+++++++++++++++++++";
+    std::cout << std::endl << "in deadTimeEstimate";
+    std::cout << std::endl << "+++++++++++++++++++";
+    std::cout << std::endl;
+  }
+
+  nxH4::PNeXusDeadTime ndt(nxs, debug);
+  auto dims = ndt.GetDimensions();
+  for (unsigned int i=0; i<dims[1]; i++) {
+    ndt.minimize(i);
+  }
+}
+
+//-----------------------------------------------------------------------------
+/**
+ * @brief Write NeXus HDF4 file using the PNXdata approach
+ *
+ * Writes all datasets from the PNeXus data map to a new NeXus HDF4 file.
+ * This function uses the WriteNexusFile() method to create a complete
+ * NeXus file with all groups, datasets, and attributes.
+ *
+ * @param nxs Pointer to the PNeXus object containing the data to write
+ * @param outFileName Output filename for the NeXus HDF4 file
+ * @param debug If true, print additional debug information
+ *
+ * @note Currently only supports IDF version 2 files
+ *
+ * @see nxH4::PNeXus::WriteNexusFile()
+ */
+void h4nexus_writeTest(const nxH4::PNeXus *nxs, const std::string& outFileName, bool debug)
+{
+  if (debug) {
+    std::cout << std::endl;
+    std::cout << "++++++++++++++++++++" << std::endl;
+    std::cout << "Writing NeXus file" << std::endl;
+    std::cout << "++++++++++++++++++++" << std::endl;
+    std::cout << std::endl;
+  }
+
+  if (nxs->GetIdfVersion() == 1) {
+    std::cerr << "Error: IDF v1 write not yet implemented" << std::endl;
+    return;
+  }
+
+  // Write using the read object's data
+  int result = const_cast<nxH4::PNeXus*>(nxs)->WriteNexusFile(outFileName, nxs->GetIdfVersion());
+
+  if (result == 0) {
+    std::cout << "Successfully wrote: " << outFileName << std::endl;
+  } else {
+    std::cerr << "Failed to write file: " << outFileName << std::endl;
+  }
+
+  // write data from scratch
+
+  std::unique_ptr<nxH4::PNeXus> nxs_out = std::make_unique<nxH4::PNeXus>();
+
+  std::vector<int> ival;
+  std::vector<float> fval;
+  std::vector<std::string> sval;
+
+  // ----------
+  // raw_data_1
+  // ----------
+
+  // IDF version
+  ival.push_back(2);
+  nxs_out->AddDataset<int>("/raw_data_1/IDF_version", ival, {1}, nxH4::H4DataType::INT32);
+  ival.clear();
+
+  // add group attribute to '/raw_data_1'
+  nxs_out->AddGroupAttribute("/raw_data_1", "NX_class", std::string("NXentry"));
+
+  // beamline
+  sval.push_back("piE3");
+  nxs_out->AddDataset<std::string>("/raw_data_1/beamline", sval, {1}, nxH4::H4DataType::CHAR8);
+  sval.clear();
+
+  // definition
+  sval.push_back("muonTD");
+  nxs_out->AddDataset<std::string>("/raw_data_1/definition", sval, {1}, nxH4::H4DataType::CHAR8);
+  sval.clear();
+
+  // run_number
+  ival.push_back(1234);
+  nxs_out->AddDataset<int>("/raw_data_1/run_number", ival, {1}, nxH4::H4DataType::INT32);
+  ival.clear();
+
+  // title
+  sval.push_back("this is the run title.");
+  nxs_out->AddDataset<std::string>("/raw_data_1/title", sval, {1}, nxH4::H4DataType::CHAR8);
+  sval.clear();
+
+  // start time
+  sval.push_back("2026-01-01T01:02:03");
+  nxs_out->AddDataset<std::string>("/raw_data_1/start_time", sval, {1}, nxH4::H4DataType::CHAR8);
+  sval.clear();
+
+  // end time
+  sval.push_back("2026-01-01T02:03:42");
+  nxs_out->AddDataset<std::string>("/raw_data_1/end_time", sval, {1}, nxH4::H4DataType::CHAR8);
+  sval.clear();
+
+  // experiment_identifier - pgroup for PSI
+  sval.push_back("p18324");
+  nxs_out->AddDataset<std::string>("/raw_data_1/experiment_identifier", sval, {1}, nxH4::H4DataType::CHAR8);
+  sval.clear();
+
+  // -------------------
+  // detector_1 (NXdata)
+  // -------------------
+
+  // add group attribute to /raw_data_1/instrument
+  nxs_out->AddGroupAttribute("/raw_data_1/detector_1", "NX_class", std::string("NXdata"));
+
+  // counts
+  std::vector<int> counts(16*66000, 42); // data 16 histos with length 66000
+  nxs_out->AddDataset<int>("/raw_data_1/detector_1/counts", counts, {1, 16, 66000}, nxH4::H4DataType::INT32);
+
+  // attributes for counts
+  nxs_out->AddDatasetAttribute<int>("/raw_data_1/detector_1/counts", "signal", 1);
+  nxs_out->AddDatasetAttribute<int>("/raw_data_1/detector_1/counts", "axes", std::string("period_index,spectrum_index,raw_time"));
+  nxs_out->AddDatasetAttribute<int>("/raw_data_1/detector_1/counts", "long_name", std::string("positron_counts"));
+  nxs_out->AddDatasetAttribute<int>("/raw_data_1/detector_1/counts", "t0_bin", 2741);
+  nxs_out->AddDatasetAttribute<int>("/raw_data_1/detector_1/counts", "first_good_bin", 2741);
+  nxs_out->AddDatasetAttribute<int>("/raw_data_1/detector_1/counts", "last_good_bin", 66000);
+  nxs_out->AddDatasetAttribute<int>("/raw_data_1/detector_1/counts", "units", std::string("counts"));
+  nxs_out->AddDatasetAttribute<int>("/raw_data_1/detector_1/counts", "target", std::string("/raw_data_1/instrument/detector_1/counts"));
+
+  // raw_time
+  std::vector<float> raw_time(66000, 0.0);
+  for (unsigned int i=0; i<raw_time.size(); i++)
+    raw_time[i] = 0.1953125f*1.0e-3*((float)i-2741.0f+0.5f);
+  nxs_out->AddDataset<float>("/raw_data_1/detector_1/raw_time", raw_time, {66000}, nxH4::H4DataType::FLOAT32);
+
+  // attributes raw_time
+  nxs_out->AddDatasetAttribute<float>("/raw_data_1/detector_1/raw_time", "units", std::string("microseconds"));
+  nxs_out->AddDatasetAttribute<float>("/raw_data_1/detector_1/raw_time", "target", std::string("/raw_data_1/instrument/detector_1/raw_time"));
+
+
+  // ----------
+  // instrument
+  // ----------
+
+  // add group attribute to /raw_data_1/instrument
+  nxs_out->AddGroupAttribute("/raw_data_1/instrument", "NX_class", std::string("NXinstrument"));
+
+  // name
+  sval.push_back("LEM");
+  nxs_out->AddDataset<std::string>("/raw_data_1/instrument/name", sval, {1}, nxH4::H4DataType::CHAR8);
+  sval.clear();
+
+  // ------
+  // source
+  // ------
+
+  // add group attribute to /raw_data_1/instrument/source
+  nxs_out->AddGroupAttribute("/raw_data_1/instrument/source", "NX_class", std::string("NXsource"));
+
+  // name
+  sval.push_back("PSI");
+  nxs_out->AddDataset<std::string>("/raw_data_1/instrument/source/name", sval, {1}, nxH4::H4DataType::CHAR8);
+  sval.clear();
+
+  // type
+  sval.push_back("continuous muon source");
+  nxs_out->AddDataset<std::string>("/raw_data_1/instrument/source/types", sval, {1}, nxH4::H4DataType::CHAR8);
+  sval.clear();
+
+  // probe
+  sval.push_back("postive muons");
+  nxs_out->AddDataset<std::string>("/raw_data_1/instrument/source/probe", sval, {1}, nxH4::H4DataType::CHAR8);
+  sval.clear();
+
+  // -----------------------
+  // detector_1 (NXdetector)
+  // -----------------------
+
+  // add group attribute to /raw_data_1/instrument/detector_1
+  nxs_out->AddGroupAttribute("/raw_data_1/instrument/detector_1", "NX_class", std::string("NXdetector"));
+
+  // counts
+  nxs_out->AddDataset<int>("/raw_data_1/instrument/detector_1/counts", counts, {1, 16, 66000}, nxH4::H4DataType::INT32);
+
+  // attributes for counts
+  nxs_out->AddDatasetAttribute<int>("/raw_data_1/instrument/detector_1/counts", "signal", 1);
+  nxs_out->AddDatasetAttribute<int>("/raw_data_1/instrument/detector_1/counts", "axes", std::string("period_index,spectrum_index,raw_time"));
+  nxs_out->AddDatasetAttribute<int>("/raw_data_1/instrument/detector_1/counts", "long_name", std::string("positron_counts"));
+  nxs_out->AddDatasetAttribute<int>("/raw_data_1/instrument/detector_1/counts", "t0_bin", 2741);
+  nxs_out->AddDatasetAttribute<int>("/raw_data_1/instrument/detector_1/counts", "first_good_bin", 2741);
+  nxs_out->AddDatasetAttribute<int>("/raw_data_1/instrument/detector_1/counts", "last_good_bin", 66000);
+  nxs_out->AddDatasetAttribute<int>("/raw_data_1/instrument/detector_1/counts", "units", std::string("counts"));
+  nxs_out->AddDatasetAttribute<int>("/raw_data_1/instrument/detector_1/counts", "target", std::string("/raw_data_1/instrument/detector_1/counts"));
+
+  // raw_time
+  nxs_out->AddDataset<float>("/raw_data_1/instrument/detector_1/raw_time", raw_time, {66000}, nxH4::H4DataType::FLOAT32);
+
+  // attributes raw_time
+  nxs_out->AddDatasetAttribute<float>("/raw_data_1/instrument/detector_1/raw_time", "units", std::string("microseconds"));
+  nxs_out->AddDatasetAttribute<float>("/raw_data_1/instrument/detector_1/raw_time", "target", std::string("/raw_data_1/instrument/detector_1/raw_time"));
+
+  // resolution
+  fval.push_back(195.3125);
+  nxs_out->AddDataset<float>("/raw_data_1/instrument/detector_1/resolution", fval, {1}, nxH4::H4DataType::FLOAT32);
+  fval.clear();
+  nxs_out->AddDatasetAttribute<float>("/raw_data_1/instrument/detector_1/resolution",
+                                      "units", std::string("picoseconds"));
+
+  // spectrum_index
+  for (unsigned int i=0; i<16; i++)
+    ival.push_back(i+1);
+  nxs_out->AddDataset<int>("/raw_data_1/instrument/detector_1/spectrum_index", ival, {16}, nxH4::H4DataType::INT32);
+  ival.clear();
+
+  // dead_time
+  std::vector<float> deadTime(16, 0.0);
+  nxs_out->AddDataset<float>("/raw_data_1/instrument/detector_1/dead_time", deadTime, {16}, nxH4::H4DataType::FLOAT32);
+
+  // attributes dead_time
+  nxs_out->AddDatasetAttribute<float>("/raw_data_1/instrument/detector_1/dead_time", "available", 0);
+  nxs_out->AddDatasetAttribute<float>("/raw_data_1/instrument/detector_1/dead_time", "units", std::string("microseconds"));
+  nxs_out->AddDatasetAttribute<float>("/raw_data_1/instrument/detector_1/dead_time", "target", std::string("/raw_data_1/instrument/detector_1/dead_time"));
+
+  // add root attributes
+  // file name
+  nxs_out->AddRootAttribute("file_name", std::string("_test.nxs"));
+  // date-time
+  std::time_t time = std::time({});
+  char timeString[std::size("yyyy-mm-ddThh:mm:ssZ")];
+  std::strftime(std::data(timeString), std::size(timeString),
+                 "%FT%TZ", std::gmtime(&time));
+  nxs_out->AddRootAttribute("file_time", std::string(timeString));
+  // NeXus version
+  nxs_out->AddRootAttribute("NeXus_Version", std::string("4.3.0"));
+  // hdf4 version
+  nxs_out->AddRootAttribute("HDF4_Version", std::string(nxs->GetHdf4Version()));
+  // creator
+  nxs_out->AddRootAttribute("creator", std::string("h4nexus - PSI"));
+
+  nxs_out->WriteNexusFile("_test.nxs");
+}
+
+//-----------------------------------------------------------------------------
+/**
+ * @brief Main entry point for the h4nexus program
+ *
+ * Parses command-line arguments and performs the requested operations:
+ * - Read and display NeXus HDF4 file information
+ * - Write NeXus HDF4 files with modified data
+ * - Calculate dead time corrections
+ *
+ * @param argc Number of command-line arguments
+ * @param argv Array of command-line argument strings
+ *
+ * @return 0 on success, non-zero on error
+ *
+ * @see h4nexus_syntax() for available command-line options
+ */
+int main(int argc, char *argv[])
+{
+  std::string fileName{""};
+  std::string fileNameOut{""};
+  bool printDebug{false};
+  bool deadTimeEstimate{false};
+
+  if (argc == 1)
+    h4nexus_syntax();
+
+  for (int i=1; i<argc; i++) {
+    if (!strcmp(argv[i], "-h") || !strcmp(argv[i], "--help")) {
+      h4nexus_syntax();
+    } else if (!strcmp(argv[i], "-v") || !strcmp(argv[i], "--version")) {
+#ifdef HAVE_CONFIG_H
+#ifdef HAVE_GIT_REV_H
+      std::cout << std::endl << "h4nexus version: " << H4NEXUS_VERSION << ", git-branch: " << GIT_BRANCH << ", git-hash: " << GIT_HASH << std::endl << std::endl;
+#else
+      std::cout << std::endl << "h4nexus version: " << H4NEXUS_VERSION << std::endl << std::endl;
+#endif
+#else
+#ifdef HAVE_GIT_REV_H
+      std::cout << std::endl << "h4nexus git-branch: " << GIT_BRANCH << ", git-hash: " << GIT_HASH << std::endl << std::endl;
+#else
+      std::cout << std::endl << "h4nexus version: unknown." << std::endl << std::endl;
+#endif
+#endif
+      return 0;
+    } else if (!strcmp(argv[i], "--fn")) {
+      if (i+1 >= argc) {
+        std::cout << std::endl << "**ERROR** found --fn without <fln>." << std::endl;
+        h4nexus_syntax();
+      }
+      i++;
+      fileName = argv[i];
+    } else if (!strcmp(argv[i], "-dt") || !strcmp(argv[i], "--dead_time_estimate")) {
+      deadTimeEstimate = true;
+    } else if (!strcmp(argv[i], "-d") || !strcmp(argv[i], "--debug")) {
+        printDebug = true;
+    } else if (!strcmp(argv[i], "--out")) {
+      if (i+1 >= argc) {
+        std::cout << std::endl << "**ERROR** found --out without <fout>." << std::endl;
+        h4nexus_syntax();
+      }
+      i++;
+      fileNameOut = argv[i];
+    } else {
+      h4nexus_syntax();
+    }
+  }
+
+  if (fileName.empty()) {
+    std::cerr << std::endl;
+    std::cerr << "**ERROR** <fln> is missing." << std::endl;
+    std::cerr << std::endl;
+    h4nexus_syntax();
+  }
+
+  std::unique_ptr<nxH4::PNeXus> nxs = std::make_unique<nxH4::PNeXus>(fileName, printDebug);
+
+  nxs->Dump();
+
+  if (deadTimeEstimate) {
+    h4nexus_deadTimeEstimate(nxs.get(), printDebug);
+  }
+
+  if (!fileNameOut.empty()) {
+    h4nexus_writeTest(nxs.get(), fileNameOut, printDebug);
+  }
+
+  return 0;
+}
--- a/src/external/nexus/examples/hdf5/CMakeLists.txt
+++ b/src/external/nexus/examples/hdf5/CMakeLists.txt
@@ -0,0 +1,119 @@
+# - h5nexus
+cmake_minimum_required(VERSION 3.26)
+
+project(h5nexus VERSION 0.1.0 LANGUAGES CXX)
+
+#--- set C++ standard ---------------------------------------------------------
+set(CMAKE_CXX_STANDARD 17)
+set(CMAKE_CXX_STANDARD_REQUIRED ON)
+set(CMAKE_CXX_EXTENSIONS OFF)
+
+#--- set a default build type if none was specified ---------------------------
+set(default_build_type "Release")
+
+if (NOT CMAKE_BUILD_TYPE AND NOT CMAKE_CONFIGURATION_TYPES)
+  message(STATUS "Setting build type to '${default_build_type}' as none was specified.")
+  set(CMAKE_BUILD_TYPE "${default_build_type}" CACHE
+      STRING "Choose the type of build." FORCE)
+  # Set the possible values of build type for cmake-gui
+  set_property(CACHE CMAKE_BUILD_TYPE PROPERTY STRINGS
+    "Debug" "Release" "MinSizeRel" "RelWithDebInfo")
+endif ()
+
+#--- check for pkg-config -----------------------------------------------------
+find_package(PkgConfig REQUIRED)
+
+#--- check for git ------------------------------------------------------------
+find_package(Git REQUIRED)
+
+#--- check for HDF5 -----------------------------------------------------------
+find_package(HDF5 REQUIRED COMPONENTS CXX)
+if(NOT HDF5_FOUND)
+    message(FATAL_ERROR "HDF5 C++ library not found")
+endif()
+include_directories(${HDF5_INCLUDE_DIRS})
+
+#--- check for ROOT -----------------------------------------------------------
+find_package(ROOT 6.36 REQUIRED COMPONENTS Minuit2)
+if (ROOT_miniut2_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_miniut2_FOUND)
+
+#--- all checks done -> feed config.h -----------------------------------------
+set(HAVE_CONFIG_H 1 CACHE INTERNAL "config.h is available")
+configure_file(${CMAKE_SOURCE_DIR}/cmake/config.h.in ${CMAKE_CURRENT_BINARY_DIR}/config.h)
+
+#--- check if project source is a git repo ------------------------------------
+if (EXISTS "${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)
+  execute_process(COMMAND sh ${CMAKE_SOURCE_DIR}/src/git_revision.sh)
+
+  set(HAVE_GIT_REV_H "-DHAVE_GIT_REV_H")  
+  set(GIT_REV_H "git-revision.h")
+else (IS_GIT_REPO)
+  set(HAVE_GIT_REV_H "")  
+  set(GIT_REV_H "")
+endif (IS_GIT_REPO)
+
+#--- end create git-revision.h ------------------------------------------------
+
+#--- write summary of the installation
+cmake_host_system_information(RESULT PROCESSOR QUERY PROCESSOR_DESCRIPTION)
+
+message("")
+message("|-----------------------------------------------------------------------|")
+message("|                                                                       |")
+message("|                            Summary                                    |")
+message("|                                                                       |")
+message("|-----------------------------------------------------------------------|")
+message("")
+message(" System:    ${CMAKE_HOST_SYSTEM_NAME} ${CMAKE_SYSTEM_PROCESSOR} - ${CMAKE_HOST_SYSTEM_VERSION}")
+message(" Processor: ${PROCESSOR} (${CMAKE_SYSTEM_PROCESSOR})")
+message(" ----------")
+message("")
+message(" h5nexus Version: ${musrfit_VERSION}")
+message(" ----------------")
+message("")
+message(" Build Type: ${CMAKE_BUILD_TYPE}")
+message(" -----------")
+message("")
+message(" Requirements:")
+message(" -------------")
+message("")
+message(" HDF5    found in ${HDF5_INCLUDE_DIRS}, Version: ${HDF5_VERSION}")
+message(" ROOT    found in ${ROOT_INCLUDE_DIRS}, Version: ${ROOT_VERSION}")
+message("")
+message(" Installation directories:")
+message(" -------------------------")
+message("")
+message(" Programs                : ${CMAKE_INSTALL_PREFIX}/bin")
+message("")
+message("-------------------------------------------------------------------------")
+message("")
+
+#--- add executable -----------------------------------------------------------
+add_executable(h5nexus 
+               ../../PNeXus.cpp
+               main.cpp)
+target_compile_options(h5nexus BEFORE PRIVATE "-DHAVE_CONFIG_H" "${HAVE_GIT_REV_H}")
+target_include_directories(h5nexus 
+  BEFORE PRIVATE
+    $<BUILD_INTERFACE:${CMAKE_SOURCE_DIR}/build>
+    $<BUILD_INTERFACE:${CMAKE_SOURCE_DIR}/../..>
+    $<BUILD_INTERFACE:${ROOT_INCLUDE_DIRS}>
+)
+target_link_libraries(h5nexus ${HDF5_CXX_LIBRARIES} ${ROOT_LIBRARIES})
--- a/src/external/nexus/examples/hdf5/cmake/config.h.in
+++ b/src/external/nexus/examples/hdf5/cmake/config.h.in
@@ -0,0 +1,5 @@
+// config.h
+
+#define PACKAGE_VERSION "@PROJECT_VERSION@"
+#define BUILD_TYPE "@CMAKE_BUILD_TYPE@"
+
--- a/src/external/nexus/examples/hdf5/cmake/git-revision.h.in
+++ b/src/external/nexus/examples/hdf5/cmake/git-revision.h.in
@@ -0,0 +1,8 @@
+#ifndef GIT_VERSION_H
+#define GIT_VERSION_H
+
+#define GIT_BRANCH "@GIT_BRANCH@"
+#define GIT_CURRENT_SHA1 @GIT_CURRENT_SHA1@
+
+#endif // GIT_VERSION_H
+
--- a/src/external/nexus/examples/hdf5/docu/README.md
+++ b/src/external/nexus/examples/hdf5/docu/README.md
@@ -0,0 +1,55 @@
+# h5nexus Documentation
+
+This directory contains documentation for the h5nexus project.
+
+## Available Documentation
+
+- **Usage.md** - Comprehensive usage guide with detailed examples and workflow patterns
+
+## Project Structure
+
+The h5nexus example project has the following structure:
+
+```
+h5nexus/
+├── CMakeLists.txt          - Build configuration
+├── main.cpp                - Main program source
+├── git_revision.sh         - Git revision header generator
+├── cmake/
+│   ├── config.h.in         - CMake config template
+│   └── git-revision.h.in   - Git revision template
+└── docu/
+    ├── README.md           - This file
+    └── Usage.md            - Detailed usage documentation
+```
+
+## Building
+
+```bash
+mkdir build
+cd build
+cmake ..
+make
+```
+
+### Prerequisites
+
+- CMake >= 3.26
+- C++17 compatible compiler
+- HDF5 C++ library
+- ROOT >= 6.36 with Minuit2
+
+## Key Classes
+
+The h5nexus example uses the PNeXus library which provides:
+
+- `nxH5::PNeXus` - Main NeXus file reader/writer class
+- `nxH5::PNXdata<T>` - Template class for dataset storage
+- `nxH5::PNeXusDeadTime` - Dead time correction calculator
+- `nxs::checkHDFType()` - File format detection
+
+## Additional Resources
+
+- [Doxygen Manual](https://www.doxygen.nl/manual/)
+- [HDF5 Documentation](https://portal.hdfgroup.org/documentation/)
+- [NeXus Format](https://www.nexusformat.org/)
--- a/src/external/nexus/examples/hdf5/docu/Usage.md
+++ b/src/external/nexus/examples/hdf5/docu/Usage.md
--- a/src/external/nexus/examples/hdf5/git_revision.sh
+++ b/src/external/nexus/examples/hdf5/git_revision.sh
@@ -0,0 +1,27 @@
+#!/bin/bash
+
+echo "-- Generating header for git hash"
+GIT_HEADER="git-revision.h"
+[ -d src ] || mkdir src
+
+GIT_BRANCH=`git rev-parse --abbrev-ref HEAD`
+
+GIT_VERSION=`git log -n 1 --pretty=format:"%ad - %h"`
+if [ "$(grep -ics "$GIT_VERSION" $GIT_HEADER)" = 1 ] 
+then
+   echo "-- No need to generate new $GIT_HEADER - git hash is unchanged"
+   exit 0;
+fi
+
+echo "-- git branch is  : " $GIT_BRANCH
+echo "-- git version is : " $GIT_VERSION
+
+echo "#ifndef GIT_VERSION_H" > $GIT_HEADER
+echo "#define GIT_VERSION_H" >> $GIT_HEADER
+echo "" >> $GIT_HEADER
+echo "#define GIT_BRANCH \"$GIT_BRANCH\"" >> $GIT_HEADER
+echo "#define GIT_CURRENT_SHA1 \"$GIT_VERSION\"" >> $GIT_HEADER
+echo "" >> $GIT_HEADER
+echo "#endif //GIT_VERSION_H" >> $GIT_HEADER
+
+echo "-- file is generated into" $GIT_HEADER
--- a/src/external/nexus/examples/hdf5/main.cpp
+++ b/src/external/nexus/examples/hdf5/main.cpp
@@ -0,0 +1,572 @@
+/***************************************************************************
+
+  main.cpp
+
+  Author: Andreas Suter
+  e-mail: andreas.suter@psi.ch
+
+***************************************************************************/
+
+/***************************************************************************
+ *   Copyright (C) 2007-2026 by Andreas Suter                              *
+ *   andreas.suter@psi.ch                                                  *
+ *                                                                         *
+ *   This program is free software; you can redistribute it and/or modify  *
+ *   it under the terms of the GNU General Public License as published by  *
+ *   the Free Software Foundation; either version 2 of the License, or     *
+ *   (at your option) any later version.                                   *
+ *                                                                         *
+ *   This program is distributed in the hope that it will be useful,       *
+ *   but WITHOUT ANY WARRANTY; without even the implied warranty of        *
+ *   MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the         *
+ *   GNU General Public License for more details.                          *
+ *                                                                         *
+ *   You should have received a copy of the GNU General Public License     *
+ *   along with this program; if not, write to the                         *
+ *   Free Software Foundation, Inc.,                                       *
+ *   59 Temple Place - Suite 330, Boston, MA  02111-1307, USA.             *
+ ***************************************************************************/
+
+/**
+ * @file main.cpp
+ * @brief Command-line interface for the h5nexus NeXus HDF5 file reader/writer
+ *
+ * This file contains the main() function and command-line interface for the
+ * h5nexus program. It provides functionality to:
+ * - Read and display NeXus HDF5 files
+ * - Write NeXus HDF5 files using the PNXdata approach
+ * - Calculate dead time corrections for muon detector data
+ *
+ * **Command-Line Options:**
+ * - --fn <file>: Input NeXus HDF5 file (required)
+ * - --out <file>: Output NeXus HDF5 file (optional)
+ * - --debug, -d: Enable debug output
+ * - --dead_time_estimate, -dt: Calculate dead time corrections
+ * - --help, -h: Display help message
+ * - --version, -v: Display version information
+ *
+ * @author Andreas Suter
+ * @date 2007-2026
+ * @copyright GNU General Public License v2
+ * @version 1.0
+ *
+ * @see nxH5::PNeXus
+ * @see nxH5::PNeXusDeadTime
+ */
+
+#include <cstring>
+#include <iostream>
+#include <string>
+#include <memory>
+#include <ctime>
+#include <fstream>
+
+#include "hdf5.h"
+
+#include "PNeXus.h"
+
+#ifdef HAVE_CONFIG_H
+#include "config.h"
+#endif
+
+#ifdef HAVE_GIT_REV_H
+#include "git-revision.h"
+#endif
+
+//-----------------------------------------------------------------------------
+/**
+ * @brief Display command-line syntax and help information
+ *
+ * Prints the usage syntax and available command-line options for the h5nexus
+ * program to stdout and exits the program.
+ */
+void h5nexus_syntax() {
+  std::cout << std::endl;
+  std::cout << "usage: h5nexus [--help | -h] |" << std::endl;
+  std::cout << "               [--version | -v] |" << std::endl;
+  std::cout << "               --fn <fln> [--debug | -d]" << std::endl;
+  std::cout << "               [--dead_time_estimate | -dt]]" << std::endl;
+  std::cout << "               [--out <fout>]" << std::endl;
+  std::cout << "               [--data idx <dout>]" << std::endl;
+  std::cout << std::endl;
+  std::cout << "options:" << std::endl;
+  std::cout << "  --help, -h: this help." << std::endl;
+  std::cout << "  --version, -v: version of h5nexus." << std::endl;
+  std::cout << "  --fn <fln>: nexus hdf5 input file name <fn>." << std::endl;
+  std::cout << "  --dead_time_estimate, -dt: dead time estimate for the read hdf5 nexus file." << std::endl;
+  std::cout << "  --debug, -d: print additional debug information." << std::endl;
+  std::cout << "  --out <fout>: write the required datasets of a nexus hdf5 file to file " << std::endl;
+  std::cout << "                with name <fout>. Only makes sense together with the option --fn <fln>." << std::endl;
+  std::cout << "  --data idx <dout>: write a single ascii data set with idx to <dout>." << std::endl;
+  std::cout << "                Only makes sense together with the option --fn <fln>." << std::endl;
+  std::cout << std::endl;
+  exit(0);
+}
+
+//-----------------------------------------------------------------------------
+/**
+ * @brief Calculate dead time corrections for muon detector data
+ *
+ * Estimates dead time corrections for each detector in the NeXus file using
+ * the PNeXusDeadTime class and ROOT Minuit2 minimization.
+ *
+ * @param nxs Pointer to the PNeXus object containing the data
+ * @param debug If true, print additional debug information
+ *
+ * @see nxH5::PNeXusDeadTime
+ */
+std::vector<float> h5nexus_deadTimeEstimate(const nxH5::PNeXus *nxs, bool debug)
+{
+  if (debug) {
+    std::cout << std::endl;
+    std::cout << std::endl << "+++++++++++++++++++";
+    std::cout << std::endl << "in deadTimeEstimate";
+    std::cout << std::endl << "+++++++++++++++++++";
+    std::cout << std::endl;
+  }
+
+  nxH5::PNeXusDeadTime ndt(nxs, debug);
+  auto dims = ndt.GetDimensions();
+  for (unsigned int i=0; i<dims[1]; i++) {
+    ndt.minimize(i);
+  }
+
+  return ndt.GetDeadTimeEstimated();
+}
+
+//-----------------------------------------------------------------------------
+void h5nexus_writeData(const nxH5::PNeXus *nxs, const std::string& fln, const std::string& dataOutFln, const int idx, const std::vector<float> dte)
+{
+  std::cout << std::endl << "as35> in h5nexus_writeData: idf version: " << nxs->GetIdfVersion();
+  std::vector<int> counts;
+  std::vector<float> dt;
+  std::vector<long long unsigned int> dims;
+  float resolution{0.0};
+  int good_frames{0};
+
+  if (nxs->GetIdfVersion() == 1) {
+    if (nxs->HasDataset("/run/histogram_data_1/counts")) {
+      std::cout << std::endl << "as35> found counts in idf version 1";
+    }
+  } else {
+    auto dataMap = nxs->GetDataMap();
+    if (nxs->HasDataset("/raw_data_1/detector_1/counts")) {
+        std::cout << std::endl << "as35> found counts in idf version 2";
+      auto counts_data = std::any_cast<nxH5::PNXdata<int>>(dataMap["/raw_data_1/detector_1/counts"]);
+      counts = counts_data.GetData();
+      auto dd = counts_data.GetDimensions();
+      for (auto i=0; i<dd.size(); i++)
+        dims.push_back(dd[i]);
+
+      std::cout << std::endl << "as35> dims: " << dims.size() << ": ";
+      for (auto i=0; i<dims.size(); i++)
+        std::cout << dims[i] << ", ";
+    }
+    if (idx >= dims[1]) {
+      std::cerr << std::endl << "**ERROR** idx=" << idx << " is >= number of dataset=" << dims[1] << std::endl;
+      return;
+    }
+    if (nxs->HasDataset("/raw_data_1/detector_1/dead_time")) {
+      std::cout << std::endl << "as35> found dead_time in idf version 2";
+      auto dt_data = std::any_cast<nxH5::PNXdata<float>>(dataMap["/raw_data_1/detector_1/dead_time"]);
+      dt = dt_data.GetData();
+    }
+    if (nxs->HasDataset("/raw_data_1/instrument/detector_1/resolution")) {
+      std::cout << std::endl << "as35> found resolution in idf version 2";
+      auto r_data = std::any_cast<nxH5::PNXdata<int>>(dataMap["/raw_data_1/instrument/detector_1/resolution"]);
+      auto rr = r_data.GetData();
+      resolution = (float)rr[0];
+      if (r_data.HasAttribute("units")) {
+        std::string units = std::any_cast<std::string>(r_data.GetAttribute("units"));
+        if (units == "picoseconds")
+          resolution *= 1.0e-6;
+        else if (units == "nanoseconds")
+          resolution *= 1.0e-3;
+      }
+    }
+    if (nxs->HasDataset("/raw_data_1/good_frames")) {
+      std::cout << std::endl << "as35> found good_frames in idf version 2";
+      auto gf_data = std::any_cast<nxH5::PNXdata<int>>(dataMap["/raw_data_1/good_frames"]);
+      good_frames = gf_data.GetData()[0];
+    }
+  }
+  std::cout << std::endl;
+
+  float dtei;
+  if (dte.size() > idx)
+    dtei = dte[idx];
+
+  // write dataset
+  std::ofstream fout(dataOutFln);
+  fout << "# NeXus fln: " << fln << std::endl;
+  fout << "# idx=" << idx << std::endl;
+  fout << "# resolution  : " << resolution << " (us)" << std::endl;
+  fout << "# good_frames : " << good_frames << std::endl;
+  fout << "# dead_time   : " << dt[idx] << " (us) : from file" << std::endl;
+  fout << "# dead_time   : " << dtei << " (us) : from estimater" << std::endl;
+  fout << "# ------" << std::endl;
+  fout << "# raw counts, dead time corrected counts (file), dead time corrected counts (estimated)" << std::endl;
+  int cc{0}, dtcc{0}, dtecc{0};
+  // see https://docs.mantidproject.org/v3.9.0/algorithms/ApplyDeadTimeCorr-v1.html#algm-applydeadtimecorr
+  for (auto i=0; i<dims[2]; i++) {
+    cc = counts[i + idx*dims[2]];
+    dtcc = (int)((float)cc / (1.0 - (float)cc * (dt[idx]/(resolution*(float)good_frames))));
+    dtecc = (int)((float)cc / (1.0 - (float)cc * (dtei/(resolution*(float)good_frames))));
+    fout << cc << ", " << dtcc << ", " << dtecc << std::endl;
+  }
+  fout.close();
+}
+
+//-----------------------------------------------------------------------------
+/**
+ * @brief Write NeXus HDF5 file using the PNXdata approach
+ *
+ * Writes all datasets from the PNeXus data map to a new NeXus HDF5 file.
+ * This function uses the WriteNexusFile() method to create a complete
+ * NeXus file with all groups, datasets, and attributes.
+ *
+ * @param nxs Pointer to the PNeXus object containing the data to write
+ * @param outFileName Output filename for the NeXus HDF5 file
+ * @param debug If true, print additional debug information
+ *
+ * @note Currently only supports IDF version 2 files
+ *
+ * @see nxH5::PNeXus::WriteNexusFile()
+ */
+void h5nexus_writeTest(const nxH5::PNeXus *nxs, const std::string& outFileName, bool debug)
+{
+  if (debug) {
+    std::cout << std::endl;
+    std::cout << "++++++++++++++++++++" << std::endl;
+    std::cout << "Writing NeXus file" << std::endl;
+    std::cout << "++++++++++++++++++++" << std::endl;
+    std::cout << std::endl;
+  }
+
+  if (nxs->GetIdfVersion() == 1) {
+    std::cerr << "Error: IDF v1 write not yet implemented" << std::endl;
+    return;
+  }
+
+  // Write using the read object's data
+  int result = const_cast<nxH5::PNeXus*>(nxs)->WriteNexusFile(outFileName, nxs->GetIdfVersion());
+
+  if (result == 0) {
+    std::cout << "Successfully wrote: " << outFileName << std::endl;
+  } else {
+    std::cerr << "Failed to write file: " << outFileName << std::endl;
+  }
+
+  // write data from scratch
+
+  std::unique_ptr<nxH5::PNeXus> nxs_out = std::make_unique<nxH5::PNeXus>();
+
+  std::vector<int> ival;
+  std::vector<float> fval;
+  std::vector<std::string> sval;
+
+  H5::StrType strType(H5::PredType::C_S1, H5T_VARIABLE);
+
+  // ----------
+  // raw_data_1
+  // ----------
+
+  // IDF version
+  ival.push_back(2);
+  nxs_out->AddDataset<int>("/raw_data_1/IDF_version", ival, {1}, H5::PredType::NATIVE_INT);
+  ival.clear();
+
+  // add group attribute to '/raw_data_1'
+  nxs_out->AddGroupAttribute("/raw_data_1", "NX_class", std::string("NXentry"));
+
+  // beamline
+  sval.push_back("piE3");
+  nxs_out->AddDataset<std::string>("/raw_data_1/beamline", sval, {1}, strType);
+  sval.clear();
+
+  // definition
+  sval.push_back("muonTD");
+  nxs_out->AddDataset<std::string>("/raw_data_1/definition", sval, {1}, strType);
+  sval.clear();
+
+  // run_number
+  ival.push_back(1234);
+  nxs_out->AddDataset<int>("/raw_data_1/run_number", ival, {1}, H5::PredType::NATIVE_INT);
+  ival.clear();
+
+  // title
+  sval.push_back("this is the run title.");
+  nxs_out->AddDataset<std::string>("/raw_data_1/title", sval, {1}, strType);
+  sval.clear();
+
+  // start time
+  sval.push_back("2026-01-01T01:02:03");
+  nxs_out->AddDataset<std::string>("/raw_data_1/start_time", sval, {1}, strType);
+  sval.clear();
+
+  // end time
+  sval.push_back("2026-01-01T02:03:42");
+  nxs_out->AddDataset<std::string>("/raw_data_1/end_time", sval, {1}, strType);
+  sval.clear();
+
+  // experiment_identifier - pgroup for PSI
+  sval.push_back("p18324");
+  nxs_out->AddDataset<std::string>("/raw_data_1/experiment_identifier", sval, {1}, strType);
+  sval.clear();
+
+  // -------------------
+  // detector_1 (NXdata)
+  // -------------------
+
+  // add group attribute to /raw_data_1/instrument
+  nxs_out->AddGroupAttribute("/raw_data_1/detector_1", "NX_class", std::string("NXdata"));
+
+  // counts
+  std::vector<int> counts(16*66000, 42); // data 16 histos with length 66000
+  nxs_out->AddDataset<int>("/raw_data_1/detector_1/counts", counts, {1, 16, 66000}, H5::PredType::NATIVE_INT);
+
+  // attributes for counts
+  nxs_out->AddDatasetAttribute<int>("/raw_data_1/detector_1/counts", "signal", 1);
+  nxs_out->AddDatasetAttribute<int>("/raw_data_1/detector_1/counts", "axes", std::string("period_index,spectrum_index,raw_time"));
+  nxs_out->AddDatasetAttribute<int>("/raw_data_1/detector_1/counts", "long_name", std::string("positron_counts"));
+  nxs_out->AddDatasetAttribute<int>("/raw_data_1/detector_1/counts", "t0_bin", 2741);
+  nxs_out->AddDatasetAttribute<int>("/raw_data_1/detector_1/counts", "first_good_bin", 2741);
+  nxs_out->AddDatasetAttribute<int>("/raw_data_1/detector_1/counts", "last_good_bin", 66000);
+  nxs_out->AddDatasetAttribute<int>("/raw_data_1/detector_1/counts", "units", std::string("counts"));
+  nxs_out->AddDatasetAttribute<int>("/raw_data_1/detector_1/counts", "target", std::string("/raw_data_1/instrument/detector_1/counts"));
+
+  // raw_time
+  std::vector<float> raw_time(66000, 0.0);
+  for (unsigned int i=0; i<raw_time.size(); i++)
+    raw_time[i] = 0.1953125f*1.0e-3*((float)i-2741.0f+0.5f);
+  nxs_out->AddDataset<float>("/raw_data_1/detector_1/raw_time", raw_time, {66000}, H5::PredType::NATIVE_FLOAT);
+
+  // attributes raw_time
+  nxs_out->AddDatasetAttribute<float>("/raw_data_1/detector_1/raw_time", "units", std::string("microseconds"));
+  nxs_out->AddDatasetAttribute<float>("/raw_data_1/detector_1/raw_time", "target", std::string("/raw_data_1/instrument/detector_1/raw_time"));
+
+
+  // ----------
+  // instrument
+  // ----------
+
+  // add group attribute to /raw_data_1/instrument
+  nxs_out->AddGroupAttribute("/raw_data_1/instrument", "NX_class", std::string("NXinstrument"));
+
+  // name
+  sval.push_back("LEM");
+  nxs_out->AddDataset<std::string>("/raw_data_1/instrument/name", sval, {1}, strType);
+  sval.clear();
+
+  // ------
+  // source
+  // ------
+
+  // add group attribute to /raw_data_1/instrument/source
+  nxs_out->AddGroupAttribute("/raw_data_1/instrument/source", "NX_class", std::string("NXsource"));
+
+  // name
+  sval.push_back("PSI");
+  nxs_out->AddDataset<std::string>("/raw_data_1/instrument/source/name", sval, {1}, strType);
+  sval.clear();
+
+  // type
+  sval.push_back("continuous muon source");
+  nxs_out->AddDataset<std::string>("/raw_data_1/instrument/source/types", sval, {1}, strType);
+  sval.clear();
+
+  // probe
+  sval.push_back("postive muons");
+  nxs_out->AddDataset<std::string>("/raw_data_1/instrument/source/probe", sval, {1}, strType);
+  sval.clear();
+
+  // -----------------------
+  // detector_1 (NXdetector)
+  // -----------------------
+
+  // add group attribute to /raw_data_1/instrument/detector_1
+  nxs_out->AddGroupAttribute("/raw_data_1/instrument/detector_1", "NX_class", std::string("NXdetector"));
+
+  // counts
+  nxs_out->AddDataset<int>("/raw_data_1/instrument/detector_1/counts", counts, {1, 16, 66000}, H5::PredType::NATIVE_INT);
+
+  // attributes for counts
+  nxs_out->AddDatasetAttribute<int>("/raw_data_1/instrument/detector_1/counts", "signal", 1);
+  nxs_out->AddDatasetAttribute<int>("/raw_data_1/instrument/detector_1/counts", "axes", std::string("period_index,spectrum_index,raw_time"));
+  nxs_out->AddDatasetAttribute<int>("/raw_data_1/instrument/detector_1/counts", "long_name", std::string("positron_counts"));
+  nxs_out->AddDatasetAttribute<int>("/raw_data_1/instrument/detector_1/counts", "t0_bin", 2741);
+  nxs_out->AddDatasetAttribute<int>("/raw_data_1/instrument/detector_1/counts", "first_good_bin", 2741);
+  nxs_out->AddDatasetAttribute<int>("/raw_data_1/instrument/detector_1/counts", "last_good_bin", 66000);
+  nxs_out->AddDatasetAttribute<int>("/raw_data_1/instrument/detector_1/counts", "units", std::string("counts"));
+  nxs_out->AddDatasetAttribute<int>("/raw_data_1/instrument/detector_1/counts", "target", std::string("/raw_data_1/instrument/detector_1/counts"));
+
+  // raw_time
+  nxs_out->AddDataset<float>("/raw_data_1/instrument/detector_1/raw_time", raw_time, {66000}, H5::PredType::NATIVE_FLOAT);
+
+  // attributes raw_time
+  nxs_out->AddDatasetAttribute<float>("/raw_data_1/instrument/detector_1/raw_time", "units", std::string("microseconds"));
+  nxs_out->AddDatasetAttribute<float>("/raw_data_1/instrument/detector_1/raw_time", "target", std::string("/raw_data_1/instrument/detector_1/raw_time"));
+
+  // resolution
+  fval.push_back(195.3125);
+  nxs_out->AddDataset<float>("/raw_data_1/instrument/detector_1/resolution", fval, {1}, H5::PredType::NATIVE_FLOAT);
+  fval.clear();
+  nxs_out->AddDatasetAttribute<float>("/raw_data_1/instrument/detector_1/resolution",
+                                      "units", std::string("picoseconds"));
+
+  // spectrum_index
+  for (unsigned int i=0; i<16; i++)
+    ival.push_back(i+1);
+  nxs_out->AddDataset<int>("/raw_data_1/instrument/detector_1/spectrum_index", ival, {16}, H5::PredType::NATIVE_INT);
+  ival.clear();
+
+  // dead_time
+  std::vector<float> deadTime(16, 0.0);
+  nxs_out->AddDataset<float>("/raw_data_1/instrument/detector_1/dead_time", deadTime, {16}, H5::PredType::NATIVE_FLOAT);
+
+  // attributes dead_time
+  nxs_out->AddDatasetAttribute<float>("/raw_data_1/instrument/detector_1/dead_time", "available", 0);
+  nxs_out->AddDatasetAttribute<float>("/raw_data_1/instrument/detector_1/dead_time", "units", std::string("microseconds"));
+  nxs_out->AddDatasetAttribute<float>("/raw_data_1/instrument/detector_1/dead_time", "target", std::string("/raw_data_1/instrument/detector_1/dead_time"));
+
+  // add root attributes
+  // file name
+  nxs_out->AddRootAttribute("file_name", std::string("_test.nxs"));
+  // date-time
+  std::time_t time = std::time({});
+  char timeString[std::size("yyyy-mm-ddThh:mm:ssZ")];
+  std::strftime(std::data(timeString), std::size(timeString),
+                 "%FT%TZ", std::gmtime(&time));
+  nxs_out->AddRootAttribute("file_time", std::string(timeString));
+  // NeXus version
+  nxs_out->AddRootAttribute("NeXus_Version", std::string("4.3.0"));
+  // hdf5 version
+  nxs_out->AddRootAttribute("HDF5_Version", std::string(nxs->GetHdf5Version()));
+  // creator
+  nxs_out->AddRootAttribute("creator", std::string("h5nexus - PSI"));
+
+  nxs_out->WriteNexusFile("_test.nxs");
+}
+
+//-----------------------------------------------------------------------------
+/**
+ * @brief Main entry point for the h5nexus program
+ *
+ * Parses command-line arguments and performs the requested operations:
+ * - Read and display NeXus HDF5 file information
+ * - Write NeXus HDF5 files with modified data
+ * - Calculate dead time corrections
+ *
+ * @param argc Number of command-line arguments
+ * @param argv Array of command-line argument strings
+ *
+ * @return 0 on success, non-zero on error
+ *
+ * @see h5nexus_syntax() for available command-line options
+ */
+int main(int argc, char *argv[])
+{
+  std::string fileName{""};
+  std::string fileNameOut{""};
+  std::string dataNameOut{""};
+  int idx{-1};
+  bool printDebug{false};
+  bool deadTimeEstimate{false};
+
+  if (argc == 1)
+    h5nexus_syntax();
+
+  for (int i=1; i<argc; i++) {
+    if (!strcmp(argv[i], "-h") || !strcmp(argv[i], "--help")) {
+      h5nexus_syntax();
+    } else if (!strcmp(argv[i], "-v") || !strcmp(argv[i], "--version")) {
+#ifdef HAVE_CONFIG_H
+#ifdef HAVE_GIT_REV_H
+      std::cout << std::endl << "h5nexus version: " << PACKAGE_VERSION << ", git-branch: " << GIT_BRANCH << ", git-rev: " << GIT_CURRENT_SHA1 << " (" << BUILD_TYPE << ")" << std::endl << std::endl;
+#else
+      std::cout << std::endl << "h5nexus version: " << PACKAGE_VERSION << " (" << BUILD_TYPE << ")" << std::endl << std::endl;
+#endif
+#else
+#ifdef HAVE_GIT_REV_H
+      std::cout << std::endl << "h5nexus git-branch: " << GIT_BRANCH << ", git-rev: " << GIT_CURRENT_SHA1 << std::endl << std::endl;
+#else
+      std::cout << std::endl << "h5nexus version: unkown." << std::endl << std::endl;
+#endif
+#endif
+      return 0;
+    } else if (!strcmp(argv[i], "--fn")) {
+      if (i+1 >= argc) {
+        std::cout << std::endl << "**ERROR** found --fn without <fln>." << std::endl;
+        h5nexus_syntax();
+      }
+      i++;
+      fileName = argv[i];
+    } else if (!strcmp(argv[i], "-dt") || !strcmp(argv[i], "--dead_time_estimate")) {
+      deadTimeEstimate = true;
+    } else if (!strcmp(argv[i], "-d") || !strcmp(argv[i], "--debug")) {
+        printDebug = true;
+    } else if (!strcmp(argv[i], "--data")) {
+      if (i+2 >= argc) {
+        std::cout << std::endl << "**ERROR** in --data idx <dout>." << std::endl;
+        h5nexus_syntax();
+      }
+      int ii;
+      try {
+        ii = std::stoi(argv[i+1]);
+      } catch (const std::invalid_argument& ia) {
+        std::cout << std::endl << "**ERROR** couldn't convert idx from arguments given." << std::endl;
+        h5nexus_syntax();
+      }
+      if (ii < 0) {
+        std::cout << std::endl << "**ERROR** found idx < 0, namely " << ii << std::endl;
+        h5nexus_syntax();
+      }
+      idx = ii;
+      dataNameOut = argv[i+2];
+      i += 2;
+    } else if (!strcmp(argv[i], "--out")) {
+      if (i+1 >= argc) {
+        std::cout << std::endl << "**ERROR** found --out without <fout>." << std::endl;
+        h5nexus_syntax();
+      }
+      i++;
+      fileNameOut = argv[i];
+    } else {
+      h5nexus_syntax();
+    }
+  }
+  
+  if (fileName.empty()) {
+    std::cerr << std::endl;
+    std::cerr << "**ERROR** <fln> is missing." << std::endl;
+    std::cerr << std::endl;
+    h5nexus_syntax();
+  }
+
+  if (printDebug) {
+    std::cout << std::endl;
+    std::cout << ">> fln  = '" << fileName << "'" << std::endl;
+    std::cout << ">> fout = '" << fileNameOut << "'" << std::endl;
+    std::cout << ">> dout = '" << dataNameOut << "', idx=" << idx << std::endl;
+    std::cout << std::endl;
+  }
+
+  std::unique_ptr<nxH5::PNeXus> nxs = std::make_unique<nxH5::PNeXus>(fileName, printDebug);
+
+  nxs->Dump();
+
+  std::vector<float> dte;
+  if (deadTimeEstimate) {
+    dte = h5nexus_deadTimeEstimate(nxs.get(), printDebug);
+  }
+
+  if (!fileNameOut.empty()) {
+    h5nexus_writeTest(nxs.get(), fileNameOut, printDebug);
+  }
+
+  if (!dataNameOut.empty()) {
+    h5nexus_writeData(nxs.get(), fileName, dataNameOut, idx, dte);
+  }
+
+  return 0;
+}
--- a/src/external/nexus/nexus_definitions/NeXus-Def-V2-Rev10.pdf
+++ b/src/external/nexus/nexus_definitions/NeXus-Def-V2-Rev10.pdf
--- a/src/include/PFitter.h
+++ b/src/include/PFitter.h
@@ -32,8 +32,6 @@

 #include <memory>

-#include "TString.h"
-
 #include "Minuit2/MnUserParameters.h"
 #include "Minuit2/FunctionMinimum.h"

@@ -41,7 +39,6 @@
 #include "PMsrHandler.h"
 #include "PRunListCollection.h"
 #include "PFitterFcn.h"
-#include "PFitterFcnDKS.h"

 //-------------------------------------------------------------
 /**
@@ -295,8 +292,6 @@ class PFitter

  private:
    // State flags
-    Bool_t fDKSReady;    ///< flag. true: fit via DKS/GPU. false: fit on CPU
-    Int_t  fDKSTag;      ///< tag.  holding more detailed information about the DKS/CPU/GPU request
    Bool_t fIsValid;     ///< Overall validity flag: true if fitter initialized successfully
    Bool_t fIsScanOnly;  ///< Scan mode flag: true if only parameter scans requested (no minimization)
    Bool_t fConverged;   ///< Convergence flag: true if fit converged to a valid minimum
@@ -317,7 +312,6 @@ class PFitter
    PIntPairVector fCmdList;  ///< Parsed commands: first=command ID, second=line number

    std::unique_ptr<PFitterFcn> fFitterFcn; ///< Objective function for Minuit2 minimization
-    std::unique_ptr<PFitterFcnDKS> fFitterFcnDKS; ///< Pointer to the DKS fitter function object

    ROOT::Minuit2::MnUserParameters fMnUserParams; ///< Minuit2 parameter state (values, errors, limits)
    std::unique_ptr<ROOT::Minuit2::FunctionMinimum> fFcnMin; ///< Minuit2 function minimum result
@@ -586,7 +580,6 @@ class PFitter
     * @return Rounded parameter values
     */
    PDoubleVector ParamRound(const PDoubleVector &par, const PDoubleVector &err, Bool_t &ok);
-    std::string GetCPUInfo();
 };

 #endif // _PFITTER_H_
--- a/src/include/PFitterFcn.h
+++ b/src/include/PFitterFcn.h
@@ -61,7 +61,6 @@
 *
 * @see PFitter, PRunListCollection
 * @see ROOT::Minuit2::FCNBase in ROOT Minuit2 documentation
->>>>>>> 25024aae (improve the doxygen docu with the help of Claude AI.)
 */
 class PFitterFcn : public ROOT::Minuit2::FCNBase
 {
--- a/src/include/PFitterFcnDKS.h
+++ b/src/include/PFitterFcnDKS.h
@@ -1,85 +0,0 @@
-/***************************************************************************
-
-  PFitterFcnDKS.h
-
-  Author: Andreas Suter
-  e-mail: andreas.suter@psi.ch
-
-***************************************************************************/
-
-/***************************************************************************
- *   Copyright (C) 2007-2026 by Andreas Suter                              *
- *   andreas.suter@psi.ch                                                  *
- *                                                                         *
- *   This program is free software; you can redistribute it and/or modify  *
- *   it under the terms of the GNU General Public License as published by  *
- *   the Free Software Foundation; either version 2 of the License, or     *
- *   (at your option) any later version.                                   *
- *                                                                         *
- *   This program is distributed in the hope that it will be useful,       *
- *   but WITHOUT ANY WARRANTY; without even the implied warranty of        *
- *   MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the         *
- *   GNU General Public License for more details.                          *
- *                                                                         *
- *   You should have received a copy of the GNU General Public License     *
- *   along with this program; if not, write to the                         *
- *   Free Software Foundation, Inc.,                                       *
- *   59 Temple Place - Suite 330, Boston, MA  02111-1307, USA.             *
- ***************************************************************************/
-
-#ifndef _PFITTERFCNDKS_H_
-#define _PFITTERFCNDKS_H_
-
-#include <vector>
-#include <string>
-#include "Minuit2/FCNBase.h"
-#include "DKSBaseMuSR.h"
-#include "PRunListCollection.h"
-
-typedef struct {
-  UInt_t fN0;   ///< N0 parameter index
-  UInt_t fNbkg; ///< Nbkg parameter index
-} PNidx;
-
-/**
- * <p>This is the minuit2 interface function class providing the function to be optimized (chisq or log max-likelihood).
- */
-class PFitterFcnDKS : public ROOT::Minuit2::FCNBase
-{
-  public:
-    PFitterFcnDKS(PRunListCollection *runList, const Bool_t useChi2, const UInt_t dksTag, const std::string theo);
-    virtual ~PFitterFcnDKS();
-
-    virtual Bool_t IsValid() { return fValid; }
-
-    virtual Double_t Up() const { return fUp; }
-    virtual Double_t operator()(const std::vector<Double_t> &par) const;
-
-    virtual UInt_t GetTotalNoOfFittedBins() { return fRunListCollection->GetTotalNoOfBinsFitted(); }
-    virtual UInt_t GetNoOfFittedBins(const UInt_t idx) { return fRunListCollection->GetNoOfBinsFitted(idx); }
-    virtual void CalcExpectedChiSquare(const std::vector<Double_t> &par, Double_t &totalExpectedChisq, std::vector<Double_t> &expectedChisqPerRun);
-  
-    virtual int GetDeviceName(std::string &devName);
-
-  private:
-    Bool_t fValid; ///< flag needed to ensure a valid state
-    std::string fTheoStr; ///< theory string for DKS compilation
-    Double_t fUp;     ///< for chisq == 1.0, i.e. errors are 1 std. deviation errors. for log max-likelihood == 0.5, i.e. errors are 1 std. deviation errors (for details see the minuit2 user manual).
-    Bool_t fUseChi2;  ///< true = chisq fit, false = log max-likelihood fit
-    PRunListCollection *fRunListCollection; ///< pre-processed data to be fitted
-
-    mutable DKSBaseMuSR fDKS;
-
-    std::vector<void *> fMemDataSingleHisto;    ///< vector holding the initial addresses of the single histo data sets on the GPU
-    std::vector<void *> fMemDataSingleHistoErr; ///< vector holding the initial addresses of the single histo error sets on the GPU
-    std::vector<void *> fMemDataAsymmetry;      ///< vector holding the initial addresses of the asymmetry data sets on the GPU
-    std::vector<void *> fMemDataAsymmetryErr;   ///< vector holding the initial addresses of the asymmetry error sets on the GPU
-    std::vector<void *> fMemDataMuMinus;        ///< vector holding the initial addresses of the mu minus data sets on the GPU
-    std::vector<void *> fMemDataMuMinusErr;     ///< vector holding the initial addresses of the mu minus error sets on the GPU
-    std::vector<PNidx>  fNidx;    ///< N0 / Nbkg parameter index vector
-
-    virtual void InitDKS(const UInt_t dksTag);
-    virtual void FreeDKS();
-};
-
-#endif // _PFITTERFCNDKS_H_
--- a/src/include/PFourier.h
+++ b/src/include/PFourier.h
@@ -32,16 +32,7 @@

 #include <vector>

-#ifndef HAVE_DKS
-#include <vector>
 #include "fftw3.h"
-#else
-#include <complex>
-#include "DKSBase.h"
-#include "DKSFFT.h"
-#endif
-
-#include <TH1F.h>

 #include <TH1F.h>

@@ -222,8 +213,7 @@ class PFourier
     */
    PFourier(TH1F *data, Int_t unitTag,
             Double_t startTime = 0.0, Double_t endTime = 0.0,
-             Bool_t dcCorrected = false, UInt_t zeroPaddingPower = 0,
-             Bool_t useFFTW = true);
+             Bool_t dcCorrected = false, UInt_t zeroPaddingPower = 0);

    virtual ~PFourier();

@@ -235,9 +225,7 @@ class PFourier
     *
     * @param apodizationTag Apodization strength (0/1=none, 2=weak, 3=medium, 4=strong)
     */
-    virtual void Transform(UInt_t apodizationTag = F_APODIZATION_NONE);
-
-    virtual void SetUseFFTW(const Bool_t flag);
+    virtual void Transform(UInt_t apodizationTag = 0);

    /// Returns the original data histogram title
    /// @return Title string
@@ -313,14 +301,12 @@ class PFourier
    /// Returns true if Fourier transform is ready
    /// @return Validity status
    virtual Bool_t IsValid() { return fValid; }
-    virtual Bool_t IsUseFFTW() { return fUseFFTW; }

  private:
    TH1F *fData; ///< data histogram to be Fourier transformed.

    Bool_t fValid; ///< true = all boundary conditions fullfilled and hence a Fourier transform can be performed.
    Int_t  fUnitTag; ///< 1=Field Units (G), 2=Field Units (T), 3=Frequency Units (MHz), 4=Angular Frequency Units (Mc/s)
-    Bool_t fUseFFTW; ///< true = use FFTW, otherwise use DKS if present

    Int_t fApodization; ///< 0=none, 1=weak, 2=medium, 3=strong

@@ -333,18 +319,11 @@ class PFourier

    UInt_t fNoOfData; ///< number of bins in the time interval between fStartTime and fStopTime
    UInt_t fNoOfBins; ///< number of bins to be Fourier transformed. Might be different to fNoOfData due to zero padding
-
    fftw_plan fFFTwPlan; ///< fftw plan (see FFTW3 User Manual)
-    fftw_complex *fIn;   ///< real part of the Fourier transform
-    fftw_complex *fOut;  ///< imaginary part of the Fourier transform
+    fftw_complex *fIn; ///< real part of the Fourier transform
+    fftw_complex *fOut; ///< imaginary part of the Fourier transform

-#ifdef HAVE_DKS
-    double *fInDKS; ///< real part of the Fourier transform
-    std::complex<double> *fOutDKS; ///< imaginary part of the Fourier transform
-    DKSFFT fDks; ///< Dynamic Kernel Scheduler
-    void *fReal_ptr; ///< real part of the Fourier on accelartor
-    void *fComp_ptr; ///< imaginary part of the Fourier on the acclerator
-#endif
+//as    PFTPhaseCorrection *fPhCorrectedReFT;

    virtual void PrepareFFTwInputData(UInt_t apodizationTag);
    virtual void ApodizeData(Int_t apodizationTag);
--- a/src/include/PFourierCanvasLinkDef.h
+++ b/src/include/PFourierCanvasLinkDef.h
@@ -27,7 +27,7 @@
 *   59 Temple Place - Suite 330, Boston, MA  02111-1307, USA.             *
 ***************************************************************************/

-#ifdef __CLING__
+#ifdef __CINT__

 #pragma link off all globals;
 #pragma link off all classes;
--- a/src/include/PMsrHandler.h
+++ b/src/include/PMsrHandler.h
@@ -30,7 +30,6 @@
 #ifndef _PMSRHANDLER_H_
 #define _PMSRHANDLER_H_

-#include <string>
 #include <memory>
 #include <sstream>
 #include <string>
@@ -374,10 +373,6 @@ class PMsrHandler
    /// @return Error message string
    virtual std::string GetLastErrorMsg() { return fLastErrorMsg.str(); }

-    virtual std::string GetDKSTheoryString();
-    virtual UInt_t GetDKSTag();
-    virtual Int_t GetNoOfMaps() { return fNoOfMaps; }
-
  private:
    Bool_t                 fFourierOnly; ///< Flag indicating Fourier transform only mode (for musrFT)
    PStartupOptions       *fStartupOptions; ///< Pointer to startup options from musrfit_startup.xml
@@ -403,8 +398,6 @@ class PMsrHandler

    Bool_t fCopyStatisticsBlock; ///< If true, copy old statistics block (musrt0); if false, write new one (musrfit)

-    Int_t fNoOfMaps;
-
    std::stringstream fLastErrorMsg; ///< Stream accumulating error messages during parsing

    /// Parses FITPARAMETER block entries
@@ -473,8 +466,6 @@ class PMsrHandler
    virtual Bool_t CheckRealFFT();
    /// Validates maximum likelihood fit settings
    virtual void CheckMaxLikelihood();
-
-    virtual void HandleTheoryArguments(const TString theo, PStringVector &args);
 };

 #endif // _PMSRHANDLER_H_
--- a/src/include/PMusr.h
+++ b/src/include/PMusr.h
@@ -348,13 +348,6 @@
 */
 #define RRF_FREQ_UNDEF  1.0e10

-//-------------------------------------------------------------
-// DKS related tags
-#define DKS_CPU_OPENMP 0
-#define DKS_CPU_OPENCL 1
-#define DKS_GPU_OPENCL 2
-#define DKS_GPU_CUDA   3
-
 //-------------------------------------------------------------
 /**
 * <p>typedef to make to code more readable. Definition of a bool vector.
@@ -930,44 +923,44 @@ class PRawRunData {
    PNonMusrRawRunData fDataNonMusr; ///< keeps all ascii- or db-file info in case of nonMusr fit

  private:
-    TString fVersion;                ///< keeps the version information of the data file
-    TString fGenericValidatorURL;    ///< keeps the generic validator MusrRoot URL
-    TString fSpecificValidatorURL;   ///< keeps the instrument specific validator MusrRoot URL
-    TString fGenerator;              ///< keeps the data file generator name
-    TString fComment;                ///< keeps the data file comment
-    TString fFileName;               ///< keeps the name of the original data file
-    TString fLaboratory;             ///< keeps the name of the laboratory, e.g. PSI, ISIS, TRIUMF, JPARC
-    TString fBeamline;               ///< keeps the name of the be beamline, e.g. muE4, piM3.1, ...
-    TString fInstrument;             ///< keeps the name of the instrument, e.g. LEM, GPS, MUSR, EMU, ...
-    TString fMuonSource;             ///< keeps the type of muon source, e.g. continous surface beam, pulsed beam, low energy muon beam
-    TString fMuonSpecies;            ///< positive muon or negative muon
-    Double_t fMuonBeamMomentum;      ///< given in MeV/c, for LEM this is the momentum of the secondary beamline and NOT the momentum of the low energy beam
-    Double_t fMuonSpinAngle;         ///< gives the muon spin angle in degrees (reference frame depends on the instrument)
-    TString fRunName;                ///< name of the run as found in the msr-file
-    Int_t   fRunNumber;              ///< run number
-    TString fRunTitle;               ///< run title
-    TString fSetup;                  ///< description of the setup of this run
-    TString fStartTime;              ///< start time of the run
-    TString fStartDate;              ///< start date of the run
-    time_t fStartDateTimeSec;        ///< start run given as time_t object
-    TString fStopTime;               ///< stop time of the run
-    TString fStopDate;               ///< stop date of the run
-    time_t fStopDateTimeSec;         ///< stop run given as time_t object
-    TString fCryo;                   ///< name of the cryo
-    TString fSample;                 ///< description of the sample
-    TString fOrientation;            ///< description of the orientation
-    TString fMagnet;                 ///< name of the sample magnet
-    Double_t fField;                 ///< magnetic field value in (G)
-    PDoublePairVector fTemp;         ///< measured temperatures and standard deviations during the run
-    Double_t fEnergy;                ///< implantation energy of the muon
-    Double_t fTransport;             ///< LEM transport settings (Moderator HV)
-    PDoubleVector fRingAnode;        ///< LEM ring anode HVs (L,R[,T,B])
-    Double_t fTimeResolution;        ///< time resolution of the run in (ns)
-    PIntVector fRedGreenOffset;      ///< keeps the Red/Green offsets
+    TString fVersion{"n/a"};                ///< keeps the version information of the data file
+    TString fGenericValidatorURL{"n/a"};    ///< keeps the generic validator MusrRoot URL
+    TString fSpecificValidatorURL{"n/a"};   ///< keeps the instrument specific validator MusrRoot URL
+    TString fGenerator{"n/a"};              ///< keeps the data file generator name
+    TString fComment{"n/a"};                ///< keeps the data file comment
+    TString fFileName{"n/a"};               ///< keeps the name of the original data file
+    TString fLaboratory{"n/a"};             ///< keeps the name of the laboratory, e.g. PSI, ISIS, TRIUMF, JPARC
+    TString fBeamline{"n/a"};               ///< keeps the name of the be beamline, e.g. muE4, piM3.1, ...
+    TString fInstrument{"n/a"};             ///< keeps the name of the instrument, e.g. LEM, GPS, MUSR, EMU, ...
+    TString fMuonSource{"n/a"};             ///< keeps the type of muon source, e.g. continous surface beam, pulsed beam, low energy muon beam
+    TString fMuonSpecies{"n/a"};            ///< positive muon or negative muon
+    Double_t fMuonBeamMomentum{PMUSR_UNDEFINED}; ///< given in MeV/c, for LEM this is the momentum of the secondary beamline and NOT the momentum of the low energy beam
+    Double_t fMuonSpinAngle{PMUSR_UNDEFINED};    ///< gives the muon spin angle in degrees (reference frame depends on the instrument)
+    TString fRunName{"n/a"};                ///< name of the run as found in the msr-file
+    Int_t   fRunNumber{-1};                 ///< run number
+    TString fRunTitle{"n/a"};               ///< run title
+    TString fSetup{"n/a"};                  ///< description of the setup of this run
+    TString fStartTime{"n/a"};              ///< start time of the run
+    TString fStartDate{"n/a"};              ///< start date of the run
+    time_t fStartDateTimeSec{0};            ///< start run given as time_t object
+    TString fStopTime{"n/a"};               ///< stop time of the run
+    TString fStopDate{"n/a"};               ///< stop date of the run
+    time_t fStopDateTimeSec{0};             ///< stop run given as time_t object
+    TString fCryo{"n/a"};                   ///< name of the cryo
+    TString fSample{"n/a"};                 ///< description of the sample
+    TString fOrientation{"n/a"};            ///< description of the orientation
+    TString fMagnet{"n/a"};                 ///< name of the sample magnet
+    Double_t fField{PMUSR_UNDEFINED};       ///< magnetic field value in (G)
+    PDoublePairVector fTemp;                ///< measured temperatures and standard deviations during the run
+    Double_t fEnergy{PMUSR_UNDEFINED};      ///< implantation energy of the muon
+    Double_t fTransport{PMUSR_UNDEFINED};   ///< LEM transport settings (Moderator HV)
+    PDoubleVector fRingAnode;               ///< LEM ring anode HVs (L,R[,T,B])
+    Double_t fTimeResolution{PMUSR_UNDEFINED}; ///< time resolution of the run in (ns)
+    PIntVector fRedGreenOffset;             ///< keeps the Red/Green offsets
    std::vector<float> fDeadTimeParam;      ///< dead time parameter vector needed for pulsed sources
    Int_t fNumberOfGoodFrames{0};           ///< needed to correct dead times at pulsed sources

-    PRawRunDataVector fData;         ///< keeps the histos together with the histo related properties such as T0, first good bin, etc.
+    PRawRunDataVector fData;                ///< keeps the histos together with the histo related properties such as T0, first good bin, etc.
 };

 //-------------------------------------------------------------
@@ -1229,7 +1222,7 @@ class PMsrRunBlock {
    Int_t fFitRangeOffset[2];       ///< if fit range is given in bins it can have the form fit fgb+n0 lgb-n1. This variable holds the n0 and n1.
    Double_t fAlpha;                ///< estimated alpha value from F/B counts
    Int_t fPacking;                 ///< packing/rebinning
-    TString fDeadTimeCorrection;    ///< tells if deadtime correction (pulsed sources) should be applied. Possible value: 'no' (default), 'file', 'estimate'
+    TString fDeadTimeCorrection; ///< tells if deadtime correction (pulsed sources) should be applied. Possible value: 'no' (default), 'file', 'estimate'
    Int_t fXYDataIndex[2];          ///< used to get the data indices when using db-files (fit type 8)
    TString fXYDataLabel[2];        ///< used to get the indices via labels when using db-files  (fit type 8)

@@ -1385,7 +1378,6 @@ struct PAny2ManyInfo {
 struct PStartupOptions {
  Bool_t writeExpectedChisq; ///< if set to true, expected chisq and chisq per block will be written
  Bool_t estimateN0;         ///< if set to true, for single histogram fits N0 will be estimated
-  Bool_t useDKS;             ///< if set to true, use DKS if present and "sensible" (from xml)
 };

 //-------------------------------------------------------------
--- a/src/include/PMusrCanvas.h
+++ b/src/include/PMusrCanvas.h
@@ -290,8 +290,7 @@ class PMusrCanvas : public TObject, public TQObject
     */
    PMusrCanvas(const Int_t number, const Char_t* title,
                Int_t wtopx, Int_t wtopy, Int_t ww, Int_t wh, const Bool_t batch,
-                const Bool_t fourier=false, const Bool_t avg=false, const Bool_t theoAsData=false, 
-                const Bool_t useDKS=false);
+                const Bool_t fourier=false, const Bool_t avg=false, const Bool_t theoAsData=false);

    //----------------------------------------------------------------------
    /**
@@ -315,8 +314,7 @@ class PMusrCanvas : public TObject, public TQObject
                Int_t wtopx, Int_t wtopy, Int_t ww, Int_t wh,
                PMsrFourierStructure fourierDefault,
                const PIntVector markerList, const PIntVector colorList, const Bool_t batch,
-                const Bool_t fourier=false, const Bool_t avg=false, const Bool_t theoAsData=false, 
-                const Bool_t useDKS=false);
+                const Bool_t fourier=false, const Bool_t avg=false, const Bool_t theoAsData=false);

    /// Destructor - cleans up all histograms, graphs, and ROOT objects
    virtual ~PMusrCanvas();
@@ -360,7 +358,6 @@ class PMusrCanvas : public TObject, public TQObject
    Bool_t fTheoAsData;       ///< flag if true, calculate theory points only at the data points
    Bool_t fStartWithFourier; ///< flag if true, the Fourier transform will be presented bypassing the time domain representation
    Bool_t fStartWithAvg;     ///< flag if true, the averaged data/Fourier will be presented
-    Bool_t fUseDKS;           ///< flag if true, use DKS if it is enabled
    Int_t  fTimeout;          ///< timeout after which the Done signal should be emited. If timeout <= 0, no timeout is taking place
    Bool_t fScaleN0AndBkg;    ///< true=N0 and background is scaled to (1/ns), otherwise (1/bin) for the single histogram case
    Bool_t fBatchMode;        ///< musrview in ROOT batch mode
--- a/Show More
+++ b/Show More