adopt to proper version.

- Add ${HDF5_LIBRARIES} to PMusr link dependencies so HDF5 C++ symbols
  (H5::DataType, H5::PredType, etc.) used in PRunDataHandler.cpp resolve.
- Add ${FFTW3_INCLUDE} to musrRootValidation and write_musrRoot_runHeader
  include paths; both pull in PMusr.h which transitively includes fftw3.h.

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>

.gitea/workflows/deploy-pages.yml

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

CMakeLists.txt

@@ -1,4 +1,4 @@
-# - musrfit
+# - musrfit --- DKS -----------------------------------------------------------
 cmake_minimum_required(VERSION 3.17)
 
 # cmake: use BoostConfig.cmake instead of FindBoost
@@ -9,6 +9,7 @@ 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)
@@ -76,7 +77,7 @@ find_package(PkgConfig REQUIRED)
 find_package(Git REQUIRED)
 
 #--- check for ROOT -----------------------------------------------------------
-find_package(ROOT 6.18 REQUIRED COMPONENTS Gui MathMore Minuit2 XMLParser)
+find_package(ROOT 6.16 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)
@@ -130,6 +131,42 @@ 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
@@ -219,7 +256,7 @@ if (nexus)
     # Find HDF4 manually (pkg-config often doesn't have hdf4)
     find_path(HDF4_INCLUDE_DIR
       NAMES mfhdf.h
-      PATHS /usr/include /usr/local/include
+      PATHS /usr/include /usr/include/hdf /usr/local/include
       PATH_SUFFIXES hdf
     )
 
@@ -337,6 +374,7 @@ 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}")
@@ -344,6 +382,21 @@ 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("")

ChangeLog

@@ -243,6 +243,7 @@ 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.
@@ -250,6 +251,7 @@ 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
 ===================================

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;@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")
+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")
 
 # we do not have any absolute paths, so do not need DESTDIR
 set (CPACK_SET_DESTDIR "OFF")

cmake/FindHDF4.cmake

@@ -0,0 +1,97 @@
+## 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})

cmake/FindMXML.cmake

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

cmake/FindNEXUS.cmake

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

cmake/musredit.desktop

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

cmake/musrfit-root6.spec.in

@@ -91,8 +91,6 @@ 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
 
 
 

cmake/post_install.sh

@@ -10,10 +10,3 @@ 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

cmake/post_uninstall.sh

@@ -3,11 +3,3 @@
 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

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

@@ -11,7 +11,7 @@ FITPARAMETER
 ###############################################################
 THEORY
 asymmetry      1
-userFcn  libGapIntegrals TGapDWave 2 3 4 5
+userFcn  libGapIntegrals TGapPointPWave 2 3
 
 ###############################################################
 RUN data/libGapIntegrals-test PIM3 PSI ASCII   (name beamline institute data-file-format)

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

@@ -6,6 +6,30 @@
     <trim_sp>
         <data_path>./TRIMSP/</data_path>
         <rge_fln_pre>SiC_1300x_52nm_48nm_E</rge_fln_pre>
-        <energy_vect start="1000" stop="22000" step="1000"/>
+        <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>
     </trim_sp>
 </depthProf>

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

@@ -6,6 +6,30 @@
     <trim_sp>
         <data_path>./TRIMSP/</data_path>
         <rge_fln_pre>SiC_1300x_52nm_48nm_E</rge_fln_pre>
-        <energy_vect start="1000" stop="22000" step="1000"/>
+        <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>
     </trim_sp>
 </depthProf>

doc/examples/DepthProfiles/PECVD_Si/depth_profile_startup.xml

@@ -6,6 +6,30 @@
     <trim_sp>
         <data_path>./TRIMSP/</data_path>
         <rge_fln_pre>Si10_2.0_E</rge_fln_pre>
-        <energy_vect start="1000" stop="22000" step="1000"/>
+        <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>
     </trim_sp>
 </depthProf>

doc/examples/DepthProfiles/PECVD_thermal_SiC/depth_profile_startup.xml

@@ -6,6 +6,30 @@
     <trim_sp>
         <data_path>./TRIMSP/</data_path>
         <rge_fln_pre>SiO2_70nm2.0_30nm2.2_SiC_E</rge_fln_pre>
-        <energy_vect start="1000" stop="22000" step="1000"/>
+        <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>
     </trim_sp>
 </depthProf>

doc/examples/UserFcn/PUserFcnLinkDef.h

@@ -4,7 +4,7 @@
 
 ***************************************************************************/
 
-#ifdef __CINT__
+#ifdef __CLING__
 
 #pragma link off all globals;
 #pragma link off all classes;
@@ -12,4 +12,4 @@
 
 #pragma link C++ class PUserFcn+;
 
-#endif //__CINT__
+#endif //__CLING__

doc/examples/test-asy-MUD.msr

@@ -48,5 +48,5 @@ runs     1
 range    0   8   0   0.25
 
 ###############################################################
-STATISTIC --- 2017-02-08 07:07:39
+STATISTIC --- 2026-01-21 12:33:58
   chisq = 134.0, NDF = 99, chisq/NDF = 1.353150

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      1.6687    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        
+        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        
         
-        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        
+        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       
 
-       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        
+       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       
 
-       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        
+       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       
 
-       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        
+       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       
 
-       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        
+       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       
 
-       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        
+       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       
 
-       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        
+       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       
 
-       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        
+       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       
 
-       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        
+       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       
 
-       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        
+       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       
 
-       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        
+       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       
 
-       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        
+       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       
 
-       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        
+       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       
 
-       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        
+       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       
 
-       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        
+       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       
 
-       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        
+       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       
 
 ###############################################################
 THEORY
@@ -257,9 +257,12 @@ t0              20039.0
 
 ###############################################################
 COMMANDS
+#OpenCL-GPU
+CUDA
 MAX_LIKELIHOOD
-PRINT_LEVEL 2
+#PRINT_LEVEL 2
 MINIMIZE
+MINOS
 SAVE
 
 ###############################################################
@@ -278,5 +281,5 @@ phase            par(7, 5, 16)
 range            7.1    7.5
 
 ###############################################################
-STATISTIC --- 2018-10-15 15:55:36
-  maxLH = 1286508.7, NDF = 1246064, maxLH/NDF = 1.032458
+STATISTIC --- 2026-01-19 16:46:24
+  maxLH = 1286509.8, NDF = 1246064, maxLH/NDF = 1.032459

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       0.05053   -0.00071    0.00072     0       0.33    
+        1 AsymT       0.05052   -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        6.920     -0.048      0.048       
+        8 BkgL        6.921     -0.048      0.048       
         9 RelPhaseR   178.8     -1.9        1.9         150     210     
-       10 NormR       419.46    -0.40       0.40        
+       10 NormR       419.47    -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        7.466     -0.049      0.049       
+       14 BkgT        7.467     -0.049      0.050       
        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 / 180.0 * (par7 + map1))
+fun4 = par4 * cos(pi / 180 * (par7 + map1))
 
 ###############################################################
 GLOBAL
@@ -96,5 +96,5 @@ range    0   9   -0.15   0.15
 view_packing 500
 
 ###############################################################
-STATISTIC --- 2018-11-13 07:58:56
-  maxLH = 3971.7, NDF = 4001, maxLH/NDF = 0.992668
+STATISTIC --- 2026-02-13 14:07:06
+  maxLH = 3971.7, NDF = 4001, maxLH/NDF = 0.992678

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    0.00051     0       0.3     
+        3 asym        0.23440   -0.00051    0.00052     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    
@@ -38,7 +38,6 @@ 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
@@ -70,5 +69,8 @@ range    0   20   -0.35   0.35
 view_packing 10
 
 ###############################################################
-STATISTIC --- 2026-02-23 13:09:55
+STATISTIC --- 2026-03-02 13:44:22
   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)

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        1159.7    -1.0        1.0         
+        7 N0_R        1159.8    -1.0        1.0         
         8 Bkg_L       54.47     -0.20       0.20        
-        9 Bkg_R       46.70     -0.19       0.19        
+        9 Bkg_R       46.71     -0.19       0.19        
 
 ###############################################################
 THEORY
@@ -47,6 +47,7 @@ t0              202.0
 
 ###############################################################
 COMMANDS
+CUDA
 SCALE_N0_BKG TRUE
 MINIMIZE
 MINOS
@@ -63,11 +64,11 @@ 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
+plot             POWER   # REAL, IMAG, REAL_AND_IMAG, POWER, PHASE, PHASE_OPT_REAL
 phase            8.5
 #range_for_phase_correction 50.0 70.0
-range            0.0    200.0
+range            0    200
 
 ###############################################################
-STATISTIC --- 2015-01-05 14:09:47
-  chisq = 663.9, NDF = 515, chisq/NDF = 1.289169
+STATISTIC --- 2024-06-07 15:33:49
+  chisq = 663.9, NDF = 515, chisq/NDF = 1.289084

doc/html/.buildinfo

@@ -1,4 +1,4 @@
 # Sphinx build info version 1
-# This file records the configuration used when building these files. When it is not found, a full rebuild will be done.
-config: a49a5e0b750ed752f738f66d3ddeadd4
+# This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
+config: fae482e1a3134e03efb428cbbe21a254
 tags: 645f666f9bcd5a90fca523b33c5a78b7

doc/mupp_dox.cfg

@@ -733,10 +733,9 @@ 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
@@ -756,7 +755,7 @@ INPUT_ENCODING         = UTF-8
 # *.md, *.mm, *.dox, *.py, *.f90, *.f, *.for, *.tcl, *.vhd, *.vhdl, *.ucf,
 # *.qsf, *.as and *.js.
 
-FILE_PATTERNS          = mupp.dox *.cpp *.h *.hpp
+FILE_PATTERNS          = *.dox *.cpp *.h *.hpp
 
 # The RECURSIVE tag can be used to specify whether or not subdirectories should
 # be searched for input files as well.
@@ -1533,7 +1532,7 @@ EXTRA_SEARCH_MAPPINGS  =
 # If the GENERATE_LATEX tag is set to YES doxygen will generate LaTeX output.
 # The default value is: YES.
 
-GENERATE_LATEX         = NO
+GENERATE_LATEX         = YES
 
 # 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

doc/musredit_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           = "mupp"
+PROJECT_NAME           = "musredit"
 
 # 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         = 1.1.0
+PROJECT_NUMBER         = 1.0.0
 
 # 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/mupp
+OUTPUT_DIRECTORY       = ./technical/html/musredit
 
 # 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
@@ -733,10 +733,7 @@ WARN_LOGFILE           =
 # spaces.
 # Note: If this tag is empty the current directory is searched.
 
-INPUT                  = ./ \
-                         ../src/musredit_qt6/mupp \
-                         ../src/musredit_qt6/mupp/var/include \
-                         ../src/musredit_qt6/mupp/var/src
+INPUT                  =../src/musredit_qt5/musredit
 
 # 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
@@ -756,7 +753,7 @@ INPUT_ENCODING         = UTF-8
 # *.md, *.mm, *.dox, *.py, *.f90, *.f, *.for, *.tcl, *.vhd, *.vhdl, *.ucf,
 # *.qsf, *.as and *.js.
 
-FILE_PATTERNS          = mupp.dox *.cpp *.h *.hpp
+FILE_PATTERNS          = *.dox *.cpp *.h
 
 # The RECURSIVE tag can be used to specify whether or not subdirectories should
 # be searched for input files as well.
@@ -1533,7 +1530,7 @@ EXTRA_SEARCH_MAPPINGS  =
 # If the GENERATE_LATEX tag is set to YES doxygen will generate LaTeX output.
 # The default value is: YES.
 
-GENERATE_LATEX         = NO
+GENERATE_LATEX         = YES
 
 # 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
@@ -1972,7 +1969,7 @@ 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/mupp.tag
+GENERATE_TAGFILE       = dox-tags/musredit.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.

doc/musrfit.dox

@@ -16,18 +16,18 @@
 
 <p>People merely interested in the handling of the programs should check this link:
 \htmlonly
-<a href="https://lmu.pages.psi.ch/musrfit-docu/">musrfit user manual</a>
+<a href="http://lmu.web.psi.ch/musrfit/user/html/index.html">musrfit user manual</a>
 \endhtmlonly
 \latexonly
-musrfit user manual: \texttt{https://lmu.pages.psi.ch/musrfit-docu/user-manual.html}
+musrfit user manual: \texttt{http://lmu.web.psi.ch/musrfit/user/html/index.html}
 \endlatexonly 
 
 <p>People which would like to know how to install the musrfit framework, please check this link:
 \htmlonly
-<a href="https://lmu.pages.psi.ch/musrfit-docu/setup-standard.html">How to setup musrfit on different platforms</a>
+<a href="http://lmu.web.psi.ch/musrfit/user/html/setup-standard.html">How to setup musrfit on different platforms</a>
 \endhtmlonly
 \latexonly
-How to setup musrfit on different platforms: \texttt{https://lmu.pages.psi.ch/musrfit-docu/setup-standard.html}
+How to setup musrfit on different platforms: \texttt{http://lmu.web.psi.ch/musrfit/user/html/setup-standard.html}
 \endlatexonly
 
 //****************************************************************************************************
@@ -47,7 +47,12 @@ 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 
@@ -55,7 +60,8 @@ 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
-- **addRun**: allows to add runs from the command line
+- **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.
 - **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.
@@ -79,11 +85,7 @@ 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 \htmlonly
-<a href="https://bitbucket.org/muonspin/musrfit/issues">bitbucket issue tracker</a>
-\endhtmlonly
-\latexonly
-\verbatim https://bitbucket.org/muonspin/musrfit/issues \endverbatim.
-\endlatexonly 
+<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.
 
 */

src/CMakeLists.txt

@@ -81,6 +81,7 @@ 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>

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(${FFTW3_INCLUDE})
+include_directories(${FFTW3_INC})
 
 root_generate_dictionary(
   PFourierCanvasDict 
@@ -95,6 +95,7 @@ add_library(PMusr SHARED
   PFindRun.cpp
   PFitter.cpp
   PFitterFcn.cpp
+  PFitterFcnDKS.cpp
   PFourier.cpp
   PFourierCanvas.cpp
   PFourierCanvasDict.cxx
@@ -129,6 +130,7 @@ 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}>
@@ -184,6 +186,14 @@ 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})
@@ -201,6 +211,13 @@ 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})

src/classes/PFitter.cpp

@@ -31,6 +31,9 @@
 #include "config.h"
 #endif
 
+#include <sys/time.h>
+#include <sys/utsname.h>
+
 #ifdef HAVE_GOMP
 #include <omp.h>
 #endif
@@ -38,6 +41,7 @@
 #include <iostream>
 #include <iomanip>
 #include <fstream>
+#include <string>
 #include <limits>
 #include <cmath>
 
@@ -291,6 +295,7 @@ 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
@@ -336,8 +341,36 @@ PFitter::PFitter(PMsrHandler *runInfo, PRunListCollection *runListCollection, Bo
   // create phase bool array
   GetPhaseParams();
 
-  // create fit function object
-  fFitterFcn = std::make_unique<PFitterFcn>(runListCollection, fUseChi2);
+  // 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;
+    }
+  }
 }
 
 //--------------------------------------------------------------------------
@@ -658,13 +691,24 @@ Bool_t PFitter::DoFit()
       if (error[i] != 0.0)
         usedParams++;
     }
-    UInt_t ndf = static_cast<int>(fFitterFcn->GetTotalNoOfFittedBins()) - usedParams;
-    Double_t val = (*fFitterFcn)(param);
+    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);
+    }
+
     if (fUseChi2) {
       // calculate expected chisq
       Double_t totalExpectedChisq = 0.0;
       PDoubleVector expectedChisqPerRun;
-      fFitterFcn->CalcExpectedChiSquare(param, totalExpectedChisq, expectedChisqPerRun);
+      if (fDKSReady)
+        fFitterFcnDKS->CalcExpectedChiSquare(param, totalExpectedChisq, expectedChisqPerRun);
+      else
+        fFitterFcn->CalcExpectedChiSquare(param, totalExpectedChisq, expectedChisqPerRun);
       // calculate chisq per run
       std::vector<Double_t> chisqPerRun;
       for (UInt_t i=0; i<fRunInfo->GetMsrRunList()->size(); i++) {
@@ -677,14 +721,21 @@ 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++) {
-          ndf_run = fFitterFcn->GetNoOfFittedBins(i) - fRunInfo->GetNoOfFitParameters(i);
+          if (fDKSReady)
+            ndf_run = fFitterFcnDKS->GetNoOfFittedBins(i) - fRunInfo->GetNoOfFitParameters(i);
+          else
+            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++) {
-          ndf_run = fFitterFcn->GetNoOfFittedBins(i) - fRunInfo->GetNoOfFitParameters(i);
+          if (fDKSReady)
+            ndf_run = fFitterFcnDKS->GetNoOfFittedBins(i) - fRunInfo->GetNoOfFitParameters(i);
+          else
+            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 << ")";
         }
@@ -702,13 +753,20 @@ Bool_t PFitter::DoFit()
           secFitRange[0].first = fSector[k].GetTimeRangeFirst(0);
           secFitRange[0].second = fSector[k].GetTimeRangeLast();
           fRunListCollection->SetFitRange(secFitRange);
-          // calculate chisq
-          val = (*fFitterFcn)(param);
-          // calculate NDF
-          ndf = static_cast<UInt_t>(fFitterFcn->GetTotalNoOfFittedBins()) - usedParams;
+          // 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 expected chisq
           totalExpectedChisq = 0.0;
-          fFitterFcn->CalcExpectedChiSquare(param, totalExpectedChisq, expectedChisqPerRun);
+          if (fDKSReady)
+            fFitterFcnDKS->CalcExpectedChiSquare(param, totalExpectedChisq, expectedChisqPerRun);
+          else
+            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));
@@ -723,14 +781,20 @@ 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++) {
-              ndf_run = fFitterFcn->GetNoOfFittedBins(i) - fRunInfo->GetNoOfFitParameters(i);
+              if (fDKSReady)
+                ndf_run = fFitterFcnDKS->GetNoOfFittedBins(i) - fRunInfo->GetNoOfFitParameters(i);
+              else
+                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++) {
-              ndf_run = fFitterFcn->GetNoOfFittedBins(i) - fRunInfo->GetNoOfFitParameters(i);
+              if (fDKSReady)
+                ndf_run = fFitterFcnDKS->GetNoOfFittedBins(i) - fRunInfo->GetNoOfFitParameters(i);
+              else
+                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 << ")";
             }
@@ -744,7 +808,10 @@ Bool_t PFitter::DoFit()
       // calculate expected maxLH
       Double_t totalExpectedMaxLH = 0.0;
       std::vector<Double_t> expectedMaxLHPerRun;
-      fFitterFcn->CalcExpectedChiSquare(param, totalExpectedMaxLH, expectedMaxLHPerRun);
+      if (fDKSReady)
+        fFitterFcnDKS->CalcExpectedChiSquare(param, totalExpectedMaxLH, expectedMaxLHPerRun);
+      else 
+        fFitterFcn->CalcExpectedChiSquare(param, totalExpectedMaxLH, expectedMaxLHPerRun);
       // calculate maxLH per run
       std::vector<Double_t> maxLHPerRun;
       for (UInt_t i=0; i<fRunInfo->GetMsrRunList()->size(); i++) {
@@ -757,9 +824,12 @@ 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++) {
-          ndf_run = fFitterFcn->GetNoOfFittedBins(i) - fRunInfo->GetNoOfFitParameters(i);
+          if (fDKSReady)
+            ndf_run = fFitterFcnDKS->GetNoOfFittedBins(i) - fRunInfo->GetNoOfFitParameters(i);
+          else
+            ndf_run = fFitterFcn->GetNoOfFittedBins(i) - fRunInfo->GetNoOfFitParameters(i);
           if (ndf_run > 0)
-            std::cout << std::endl << ">> run block " << i+1 << ": (NDF/red.maxLH/red.maxLH_e) = (" << ndf_run << "/" << maxLHPerRun[i]/ndf_run << "/" << expectedMaxLHPerRun[i]/ndf_run << ")";
+            std::cout << std::endl << ">> run block " << i+1 << ": (NDF/maxLH.chisq/maxLH.chisq_e) = (" << ndf_run << "/" << maxLHPerRun[i]/ndf_run << "/" << expectedMaxLHPerRun[i]/ndf_run << ")";
         }
       }
 
@@ -775,13 +845,20 @@ Bool_t PFitter::DoFit()
           secFitRange[0].first = fSector[k].GetTimeRangeFirst(0);
           secFitRange[0].second = fSector[k].GetTimeRangeLast();
           fRunListCollection->SetFitRange(secFitRange);
-          // calculate maxLH
-          val = (*fFitterFcn)(param);
-          // calculate NDF
-          ndf = static_cast<int>(fFitterFcn->GetTotalNoOfFittedBins()) - usedParams;
+          // 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 expected maxLH
           totalExpectedMaxLH = 0.0;
-          fFitterFcn->CalcExpectedChiSquare(param, totalExpectedMaxLH, expectedMaxLHPerRun);
+          if (fDKSReady)
+            fFitterFcnDKS->CalcExpectedChiSquare(param, totalExpectedMaxLH, expectedMaxLHPerRun);
+          else
+            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));
@@ -796,9 +873,12 @@ 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++) {
-              ndf_run = fFitterFcn->GetNoOfFittedBins(i) - fRunInfo->GetNoOfFitParameters(i);
+              if (fDKSReady)
+                ndf_run = fFitterFcnDKS->GetNoOfFittedBins(i) - fRunInfo->GetNoOfFitParameters(i);
+              else
+                ndf_run = fFitterFcn->GetNoOfFittedBins(i) - fRunInfo->GetNoOfFitParameters(i);
               if (ndf_run > 0)
-                std::cout << std::endl << ">> run block " << i+1 << ": (NDF/red.maxLH/red.maxLH_e) = (" << ndf_run << "/" << maxLHPerRun[i]/ndf_run << "/" << expectedMaxLHPerRun[i]/ndf_run << ")";
+                std::cout << std::endl << ">> run block " << i+1 << ": (NDF/maxLH.chisq/maxLH.chisq_e) = (" << ndf_run << "/" << maxLHPerRun[i]/ndf_run << "/" << expectedMaxLHPerRun[i]/ndf_run << ")";
             }
           }
 
@@ -977,7 +1057,15 @@ Bool_t PFitter::CheckCommands()
 
     if (line.Contains("COMMANDS", TString::kIgnoreCase)) {
       continue;
-    } else if (line.Contains("SET BATCH", TString::kIgnoreCase)) { // needed for backward compatibility
+    } 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
       continue;
     } else if (line.Contains("END RETURN", TString::kIgnoreCase)) {  // needed for backward compatibility
       continue;
@@ -1703,7 +1791,13 @@ Bool_t PFitter::ExecuteContours()
     return false;
   }
 
-  ROOT::Minuit2::MnContours contours((*fFitterFcn), *fFcnMin);
+  ROOT::Minuit2::FCNBase *fcn = nullptr;
+  if (fDKSReady)
+    fcn = fFitterFcnDKS.get();
+  else
+    fcn = fFitterFcn.get();
+
+  ROOT::Minuit2::MnContours contours((*fcn), *fFcnMin);
 
   fScanData = contours(fScanParameter[0], fScanParameter[1], fScanNoPoints);
 
@@ -1841,8 +1935,13 @@ 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((*fFitterFcn), fMnUserParams, maxfcn);
+  ROOT::Minuit2::MnUserParameterState mnState = hesse((*fcn), 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);
@@ -1853,8 +1952,8 @@ 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;
   }
 
@@ -1884,7 +1983,12 @@ Bool_t PFitter::ExecuteMigrad()
 
   // create migrad object
   // strategy is by default = 'default'
-  ROOT::Minuit2::MnMigrad migrad((*fFitterFcn), fMnUserParams, ROOT::Minuit2::MnStrategy{fStrategy});
+  ROOT::Minuit2::FCNBase *fcn = nullptr;
+  if (fDKSReady)
+    fcn = fFitterFcnDKS.get();
+  else
+    fcn = fFitterFcn.get();
+  ROOT::Minuit2::MnMigrad migrad((*fcn), fMnUserParams, ROOT::Minuit2::MnStrategy{fStrategy});
 
   // minimize
   // maxfcn is MINUIT2 Default maxfcn
@@ -1927,7 +2031,11 @@ Bool_t PFitter::ExecuteMigrad()
 
   // handle statistics
   Double_t minVal = min.Fval();
-  UInt_t ndf = fFitterFcn->GetTotalNoOfFittedBins();
+  UInt_t ndf = 0.0;
+  if (fDKSReady)
+    ndf = fFitterFcnDKS->GetTotalNoOfFittedBins();
+  else
+    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())
@@ -1960,7 +2068,12 @@ Bool_t PFitter::ExecuteMinimize()
 
   // create minimizer object
   // strategy is by default = 'default'
-  ROOT::Minuit2::MnMinimize minimize((*fFitterFcn), fMnUserParams, ROOT::Minuit2::MnStrategy{fStrategy});
+  ROOT::Minuit2::FCNBase *fcn = nullptr;
+  if (fDKSReady)
+    fcn = fFitterFcnDKS.get();
+  else
+    fcn = fFitterFcn.get();
+  ROOT::Minuit2::MnMinimize minimize((*fcn), fMnUserParams, ROOT::Minuit2::MnStrategy{fStrategy});
 
   // minimize
   // maxfcn is MINUIT2 Default maxfcn
@@ -2004,7 +2117,11 @@ Bool_t PFitter::ExecuteMinimize()
 
   // handle statistics
   Double_t minVal = min.Fval();
-  UInt_t ndf = fFitterFcn->GetTotalNoOfFittedBins();
+  UInt_t ndf = 0.0;
+  if (fDKSReady)
+    ndf = fFitterFcnDKS->GetTotalNoOfFittedBins();
+  else
+    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())
@@ -2051,8 +2168,13 @@ 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((*fFitterFcn), (*fFcnMin));
+  ROOT::Minuit2::MnMinos minos((*fcn), (*fFcnMin));
 
   for (UInt_t i=0; i<fParams.size(); i++) {
     // only try to call minos if the parameter is not fixed!!
@@ -2246,7 +2368,12 @@ Bool_t PFitter::ExecuteScan()
 {
   std::cout << ">> PFitter::ExecuteScan(): will call scan ..." << std::endl;
 
-  ROOT::Minuit2::MnScan scan((*fFitterFcn), fMnUserParams);
+  ROOT::Minuit2::FCNBase *fcn = nullptr;
+  if (fDKSReady)
+    fcn = fFitterFcnDKS.get();
+  else
+    fcn = fFitterFcn.get();
+  ROOT::Minuit2::MnScan scan((*fcn), fMnUserParams);
 
   if (fScanAll) { // not clear at the moment what to be done here
     // TO BE IMPLEMENTED
@@ -2304,9 +2431,13 @@ 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;
-  fFitterFcn->CalcExpectedChiSquare(par_r, totalExpectedChisq, expectedchisqPerRun);
+  if (fDKSReady)
+    fFitterFcnDKS->CalcExpectedChiSquare(par_r, totalExpectedChisq, expectedchisqPerRun);
+  else
+    fFitterFcn->CalcExpectedChiSquare(par_r, totalExpectedChisq, expectedchisqPerRun);
 
   // calculate chisq per run
   std::vector<Double_t> chisqPerRun;
@@ -2321,7 +2452,10 @@ 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++) {
-      ndf_run = fFitterFcn->GetNoOfFittedBins(i) - fRunInfo->GetNoOfFitParameters(i);
+      if (fDKSReady)
+        ndf_run = fFitterFcnDKS->GetNoOfFittedBins(i) - fRunInfo->GetNoOfFitParameters(i);
+      else
+        ndf_run = fFitterFcn->GetNoOfFittedBins(i) - fRunInfo->GetNoOfFitParameters(i);
       ndfPerHisto.push_back(ndf_run);
     }
 
@@ -2336,16 +2470,12 @@ 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++) {
-      ndf_run = fFitterFcn->GetNoOfFittedBins(i) - fRunInfo->GetNoOfFitParameters(i);
+      if (fDKSReady)
+        ndf_run = fFitterFcnDKS->GetNoOfFittedBins(i) - fRunInfo->GetNoOfFitParameters(i);
+      else
+        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
@@ -2386,6 +2516,43 @@ 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++) {
@@ -2784,7 +2951,12 @@ Bool_t PFitter::ExecuteSimplex()
 
   // create minimizer object
   // strategy is by default = 'default'
-  ROOT::Minuit2::MnSimplex simplex((*fFitterFcn), fMnUserParams, ROOT::Minuit2::MnStrategy{fStrategy});
+  ROOT::Minuit2::FCNBase *fcn = nullptr;
+  if (fDKSReady)
+    fcn = fFitterFcnDKS.get();
+  else
+    fcn = fFitterFcn.get();
+  ROOT::Minuit2::MnSimplex simplex((*fcn), fMnUserParams, ROOT::Minuit2::MnStrategy{fStrategy});
 
   // minimize
   // maxfcn is 10*MINUIT2 Default maxfcn
@@ -2827,7 +2999,11 @@ Bool_t PFitter::ExecuteSimplex()
 
   // handle statistics
   Double_t minVal = min.Fval();
-  UInt_t ndf = fFitterFcn->GetTotalNoOfFittedBins();
+  UInt_t ndf = 0.0;
+  if (fDKSReady)
+    fFitterFcnDKS->GetTotalNoOfFittedBins();
+  else
+    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())
@@ -2879,14 +3055,23 @@ void PFitter::PrepareSector(PDoubleVector &param, PDoubleVector &error)
       secFitRange[0].second = fSector[k].GetTimeRangeLast();
       fRunListCollection->SetFitRange(secFitRange);
       // calculate chisq
-      val = (*fFitterFcn)(param);
+      if (fDKSReady)
+        val = (*fFitterFcnDKS)(param);
+      else
+        val = (*fFitterFcn)(param);
       fSector[k].SetChisq(val);
       // calculate NDF
-      ndf = static_cast<UInt_t>(fFitterFcn->GetTotalNoOfFittedBins()) - usedParams;
+      if (fDKSReady)
+        ndf = fFitterFcnDKS->GetTotalNoOfFittedBins() - static_cast<UInt_t>(usedParams);
+      else
+        ndf = fFitterFcn->GetTotalNoOfFittedBins() - static_cast<UInt_t>(usedParams);
       fSector[k].SetNDF(ndf);
       // calculate expected chisq
       totalExpectedChisq = 0.0;
-      fFitterFcn->CalcExpectedChiSquare(param, totalExpectedChisq, expectedChisqPerRun);
+      if (fDKSReady)
+        fFitterFcnDKS->CalcExpectedChiSquare(param, totalExpectedChisq, expectedChisqPerRun);
+      else
+        fFitterFcn->CalcExpectedChiSquare(param, totalExpectedChisq, expectedChisqPerRun);
       fSector[k].SetExpectedChisq(totalExpectedChisq);
       // calculate chisq per run
       for (UInt_t i=0; i<fRunInfo->GetMsrRunList()->size(); i++) {
@@ -2898,7 +3083,10 @@ 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++) {
-          ndf_run = fFitterFcn->GetNoOfFittedBins(i) - fRunInfo->GetNoOfFitParameters(i);
+          if (fDKSReady)
+            ndf_run = fFitterFcnDKS->GetNoOfFittedBins(i) - fRunInfo->GetNoOfFitParameters(i);
+          else
+            ndf_run = fFitterFcn->GetNoOfFittedBins(i) - fRunInfo->GetNoOfFitParameters(i);
           if (ndf_run > 0) {
             fSector[k].SetNDF(ndf_run, i);
           }
@@ -2906,7 +3094,10 @@ 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++) {
-          ndf_run = fFitterFcn->GetNoOfFittedBins(i) - fRunInfo->GetNoOfFitParameters(i);
+          if (fDKSReady)
+            ndf_run = fFitterFcnDKS->GetNoOfFittedBins(i) - fRunInfo->GetNoOfFitParameters(i);
+          else
+            ndf_run = fFitterFcn->GetNoOfFittedBins(i) - fRunInfo->GetNoOfFitParameters(i);
           if (ndf_run > 0) {
             fSector[k].SetNDF(ndf_run, i);
           }
@@ -2926,14 +3117,23 @@ void PFitter::PrepareSector(PDoubleVector &param, PDoubleVector &error)
       secFitRange[0].second = fSector[k].GetTimeRangeLast();
       fRunListCollection->SetFitRange(secFitRange);
       // calculate maxLH
-      val = (*fFitterFcn)(param);
+      if (fDKSReady)
+        val = (*fFitterFcnDKS)(param);
+      else
+        val = (*fFitterFcn)(param);
       fSector[k].SetChisq(val);
       // calculate NDF
-      ndf = static_cast<UInt_t>(fFitterFcn->GetTotalNoOfFittedBins()) - usedParams;
+      if (fDKSReady)
+        ndf = fFitterFcnDKS->GetTotalNoOfFittedBins() - static_cast<UInt_t>(usedParams);
+      else
+        ndf = fFitterFcn->GetTotalNoOfFittedBins() - static_cast<UInt_t>(usedParams);
       fSector[k].SetNDF(ndf);
       // calculate expected maxLH
       totalExpectedMaxLH = 0.0;
-      fFitterFcn->CalcExpectedChiSquare(param, totalExpectedMaxLH, expectedMaxLHPerRun);
+      if (fDKSReady)
+        fFitterFcnDKS->CalcExpectedChiSquare(param, totalExpectedMaxLH, expectedMaxLHPerRun);
+      else
+        fFitterFcn->CalcExpectedChiSquare(param, totalExpectedMaxLH, expectedMaxLHPerRun);
       fSector[k].SetExpectedChisq(totalExpectedMaxLH);
       // calculate maxLH per run
       for (UInt_t i=0; i<fRunInfo->GetMsrRunList()->size(); i++) {
@@ -2945,7 +3145,10 @@ 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++) {
-          ndf_run = fFitterFcn->GetNoOfFittedBins(i) - fRunInfo->GetNoOfFitParameters(i);
+          if (fDKSReady)
+            ndf_run = fFitterFcnDKS->GetNoOfFittedBins(i) - fRunInfo->GetNoOfFitParameters(i);
+          else
+            ndf_run = fFitterFcn->GetNoOfFittedBins(i) - fRunInfo->GetNoOfFitParameters(i);
           if (ndf_run > 0) {
             fSector[k].SetNDF(ndf_run, i);
           }
@@ -3032,6 +3235,59 @@ 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)
 //--------------------------------------------------------------------------
@@ -3071,11 +3327,10 @@ PDoubleVector PFitter::ParamRound(const PDoubleVector &par, const PDoubleVector
       par_r[i] = par[i];
     }
   }
-  
+
   return par_r;
 }
 
-
 //-------------------------------------------------------------------------------------------------
 // end
 //-------------------------------------------------------------------------------------------------

src/classes/PFitterFcn.cpp

@@ -38,16 +38,14 @@
  * \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)
+PFitterFcn::PFitterFcn(PRunListCollection *runList, Bool_t useChi2) :
+  fUseChi2(useChi2),
+  fRunListCollection(runList)
 {
-  fUseChi2 = useChi2;
-
   if (fUseChi2)
     fUp = 1.0;
   else
     fUp = 0.5;
-
-  fRunListCollection = runList;
 }
 
 //--------------------------------------------------------------------------
@@ -117,6 +115,12 @@ 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++) {
@@ -124,5 +128,11 @@ 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;
+    }
   }
 }

src/classes/PFitterFcnDKS.cpp

@@ -0,0 +1,538 @@
+/***************************************************************************
+
+  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();
+}

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) :
+PFourier::PFourier(TH1F *data, Int_t unitTag, Double_t startTime, Double_t endTime, Bool_t dcCorrected, UInt_t zeroPaddingPower, Bool_t useFFTW) :
                    fData(data), fUnitTag(unitTag), fStartTime(startTime), fEndTime(endTime),
                    fDCCorrected(dcCorrected), fZeroPaddingPower(zeroPaddingPower)
 {
@@ -491,9 +491,16 @@ PFourier::PFourier(TH1F *data, Int_t unitTag, Double_t startTime, Double_t endTi
   }
 
   fValid = true;
+  fUseFFTW = true;
   fIn  = nullptr;
   fOut = nullptr;
-//as  fPhCorrectedReFT = 0;
+
+#ifdef HAVE_DKS
+  fInDKS = nullptr;
+  fOutDKS = nullptr;
+#endif
+
+  SetUseFFTW(useFFTW);
 
   fApodization = F_APODIZATION_NONE;
 
@@ -548,21 +555,71 @@ PFourier::PFourier(TH1F *data, Int_t unitTag, Double_t startTime, Double_t endTi
   }
 
   // allocate necessary memory
-  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 ((fIn == nullptr) || (fOut == nullptr)) {
-    fValid = false;
-    return;
+  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
   }
 
-  // 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) {
+  // 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
     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);
+
+    // 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
+    fValid = false;
+#endif
   }
 }
 
@@ -583,14 +640,25 @@ PFourier::PFourier(TH1F *data, Int_t unitTag, Double_t startTime, Double_t endTi
  */
 PFourier::~PFourier()
 {
-  if (fFFTwPlan)
-    fftw_destroy_plan(fFFTwPlan);
-  if (fIn)
-    fftw_free(fIn);
-  if (fOut)
-    fftw_free(fOut);
-//as  if (fPhCorrectedReFT)
-//as    delete fPhCorrectedReFT;
+  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
+  }
 }
 
 //--------------------------------------------------------------------------
@@ -636,7 +704,23 @@ void PFourier::Transform(UInt_t apodizationTag)
 
   PrepareFFTwInputData(apodizationTag);
 
-  fftw_execute(fFFTwPlan);
+  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
+  }
 
   // correct the phase for tstart != 0.0
   // find the first bin >= fStartTime
@@ -649,12 +733,42 @@ void PFourier::Transform(UInt_t apodizationTag)
   }
 
   Double_t phase, re, im;
-  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;
+  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
   }
 }
 
@@ -684,11 +798,7 @@ void PFourier::Transform(UInt_t apodizationTag)
  */
 Double_t PFourier::GetMaxFreq()
 {
-  UInt_t noOfFourierBins = 0;
-  if (fNoOfBins % 2 == 0)
-    noOfFourierBins = fNoOfBins/2;
-  else
-    noOfFourierBins = (fNoOfBins+1)/2;
+  UInt_t noOfFourierBins = fNoOfBins/2+1;
 
   return fResolution*noOfFourierBins;
 }
@@ -740,11 +850,7 @@ 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 = 0;
-  if (fNoOfBins % 2 == 0)
-    noOfFourierBins = fNoOfBins/2;
-  else
-    noOfFourierBins = (fNoOfBins+1)/2;
+  UInt_t noOfFourierBins = fNoOfBins/2+1;
 
   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) {
@@ -754,9 +860,19 @@ TH1F* PFourier::GetRealFourier(const Double_t scale)
   }
 
   // fill realFourier vector
-  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);
+  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
+    }
   }
   return realFourier;
 }
@@ -940,11 +1056,7 @@ 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 = 0;
-  if (fNoOfBins % 2 == 0)
-    noOfFourierBins = fNoOfBins/2;
-  else
-    noOfFourierBins = (fNoOfBins+1)/2;
+  UInt_t noOfFourierBins = fNoOfBins/2+1;
 
   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) {
@@ -954,11 +1066,20 @@ TH1F* PFourier::GetImaginaryFourier(const Double_t scale)
   }
 
   // fill imaginaryFourier vector
-  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);
+  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
+    }
   }
-
   return imaginaryFourier;
 }
 
@@ -1010,11 +1131,7 @@ 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 = 0;
-  if (fNoOfBins % 2 == 0)
-    noOfFourierBins = fNoOfBins/2;
-  else
-    noOfFourierBins = (fNoOfBins+1)/2;
+  UInt_t noOfFourierBins = fNoOfBins/2+1;
 
   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) {
@@ -1024,11 +1141,20 @@ TH1F* PFourier::GetPowerFourier(const Double_t scale)
   }
 
   // fill powerFourier vector
-  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);
+  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
+    }
   }
-
   return pwrFourier;
 }
 
@@ -1082,11 +1208,7 @@ 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 = 0;
-  if (fNoOfBins % 2 == 0)
-    noOfFourierBins = fNoOfBins/2;
-  else
-    noOfFourierBins = (fNoOfBins+1)/2;
+  UInt_t noOfFourierBins = fNoOfBins/2+1;
 
   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) {
@@ -1097,18 +1219,31 @@ 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 (fOut[i][0] == 0.0) {
-      if (fOut[i][1] >= 0.0)
+    if (re == 0) {
+      if (im >= 0.0)
         value = PI_HALF;
       else
         value = -PI_HALF;
     } else {
-      value = atan(fOut[i][1]/fOut[i][0]);
+      value = atan(re/im);
       // check sector
-      if (fOut[i][0] < 0.0) {
-        if (fOut[i][1] > 0.0)
+      if (re < 0.0) {
+        if (im > 0.0)
           value = PI + value;
         else
           value = PI - value;
@@ -1163,28 +1298,42 @@ 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 = 0;
-  if (ival >= 0) {
+  UInt_t start = 1;
+  if (ival > 0) { // start time > 0
     start = static_cast<UInt_t>(ival);
   }
 
   Double_t mean = 0.0;
   if (fDCCorrected) {
-    for (UInt_t i=0; i<fNoOfData; i++) {
-      mean += fData->GetBinContent(static_cast<Int_t>(i+start));
+    for (UInt_t i=start; i<start+fNoOfData; i++) {
+      mean += fData->GetBinContent(static_cast<Int_t>(i));
     }
     mean /= static_cast<Double_t>(fNoOfData);
-  }
+  }  
 
   // 2nd fill fIn
-  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;
+  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
+    }
   }
 
   // 3rd apodize data (if wished)
@@ -1225,6 +1374,9 @@ 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 };
@@ -1265,6 +1417,12 @@ 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));
     }
-    fIn[i][0] *= q;
+    if (fUseFFTW) {
+      fIn[i][0] *= q;
+    } else {
+#ifdef HAVE_DKS
+      fInDKS[i] *= q;
+#endif
+    }
   }
 }

src/classes/PFunctionHandler.cpp

@@ -137,6 +137,18 @@ 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;
 }
 

src/classes/PMsrHandler.cpp

@@ -3973,7 +3973,6 @@ Bool_t PMsrHandler::HandleRunEntry(PMsrLines &lines)
       }
     }
 
-
     // xy-data -----------------------------------------------
     if (line.BeginsWith("xy-data", TString::kIgnoreCase)) {
 
@@ -6450,6 +6449,14 @@ 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();
@@ -6852,6 +6859,359 @@ 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)
 //--------------------------------------------------------------------------

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;
 }
 
 //--------------------------------------------------------------------------

src/classes/PMusrCanvas.cpp

@@ -141,6 +141,8 @@ PMusrCanvas::PMusrCanvas()
 {
   fTimeout = 0;
 
+  fStartWithFourier = false;
+  fUseDKS = false;
   fScaleN0AndBkg = true;
   fValid = false;
   fAveragedView     = false;
@@ -204,10 +206,10 @@ 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) :
-    fTheoAsData(theoAsData), fStartWithFourier(fourier), fStartWithAvg(avg),
-    fBatchMode(batch), fPlotNumber(number)
+                         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)
 {
   fTimeout = 0;
   fAveragedView = false;
@@ -272,10 +274,10 @@ 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) :
-     fTheoAsData(theoAsData), fStartWithFourier(fourier), fStartWithAvg(avg), fBatchMode(batch),
-     fPlotNumber(number), fFourier(fourierDefault),
+                         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),
      fMarkerList(markerList), fColorList(colorList)
 {
   fTimeout = 0;
@@ -3390,12 +3392,17 @@ 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);
+        fourierTheory = new PFourier(fData[i].theory, fFourier.fUnits, startTime, endTime, fFourier.fDCCorrected, fFourier.fFourierPower, useFFTW);
       } else {
         Int_t powerPad = fFourier.fFourierPower+5; // +5 means 8 times more points on theo (+3) + 4 times more points in fourier (+2)
-        fourierTheory = new PFourier(fData[i].theory, fFourier.fUnits, startTime, endTime, fFourier.fDCCorrected, powerPad);
+#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);
       }
       if (!fourierTheory->IsValid()) {
         std::cerr << std::endl << ">> PMusrCanvas::HandleFourier(): **SEVERE ERROR** couldn't invoke PFourier to calculate the Fourier theory ..." << std::endl;

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];
-      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];
+      // 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 != 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))
+      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;
-    } else { // HDF4 IDF V2
-      // not yet implemented
-    }
+      }
+
+      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;
-    }
+    } 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];
+      // 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 != 2)) {
-      std::cerr << std::endl << ">> PRunDataHandler::ReadNexusFile(): a NeXus file with an invalid IDF V" << idf << std::endl;
-      return false;
-    }
+      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) { // 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

src/classes/PRunListCollection.cpp

@@ -498,6 +498,7 @@ 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
@@ -527,7 +528,6 @@ Double_t PRunListCollection::GetSingleRunChisqExpected(const std::vector<Double_
     }
   }
 
-
   // return the chisq of the single run
   switch (type) {
   case PRUN_SINGLE_HISTO:
@@ -548,9 +548,6 @@ 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;
   }
@@ -886,17 +883,17 @@ 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();
-    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++;
-    }
+  }
+
+  // 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++;
   }
 
   // return the chisq of the single run
@@ -1394,3 +1391,305 @@ 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();
+}

src/classes/PStartupHandler.cpp

@@ -291,6 +291,10 @@ 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;
 }
 
 //--------------------------------------------------------------------------
@@ -350,6 +354,8 @@ 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;
@@ -463,6 +469,11 @@ 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;
@@ -940,6 +951,8 @@ 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;

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();
+        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;
+    } 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();
     }
-    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;

src/external/BMWtools/BMWIntegrator.cpp

@@ -45,7 +45,6 @@
 #define SEED 0
 #define STATEFILE NULL
 
-
 //-----------------------------------------------------------------------------
 
 std::vector<double> TPointPWaveGapIntegralCuhre::fPar;
@@ -224,7 +223,6 @@ 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.
  *
@@ -254,7 +252,6 @@ 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.
@@ -276,11 +273,8 @@ int TDWaveGapIntegralCuhre::Integrand(const int *ndim, const double x[],
   return 0;
 }
 
-//-----------------------------------------------------------------------------
-
 std::vector<double> TCosSqDWaveGapIntegralCuhre::fPar;
 
-//-----------------------------------------------------------------------------
 /**
  * <p>Integrate the function using the Cuhre interface
  *
@@ -311,7 +305,6 @@ double TCosSqDWaveGapIntegralCuhre::IntegrateFunc()
   return integral[0];
 }
 
-//-----------------------------------------------------------------------------
 /**
  * <p>Calculate the function value for the use with Cuhre---actual implementation of the function
  *
@@ -332,11 +325,8 @@ int TCosSqDWaveGapIntegralCuhre::Integrand(const int *ndim, const double x[],
   return 0;
 }
 
-//-----------------------------------------------------------------------------
-
 std::vector<double> TSinSqDWaveGapIntegralCuhre::fPar;
 
-//-----------------------------------------------------------------------------
 /**
  * <p>Integrate the function using the Cuhre interface
  *
@@ -367,7 +357,6 @@ double TSinSqDWaveGapIntegralCuhre::IntegrateFunc()
   return integral[0];
 }
 
-//-----------------------------------------------------------------------------
 /**
  * <p>Calculate the function value for the use with Cuhre---actual implementation of the function
  *
@@ -388,11 +377,8 @@ int TSinSqDWaveGapIntegralCuhre::Integrand(const int *ndim, const double x[],
   return 0;
 }
 
-//-----------------------------------------------------------------------------
-
 std::vector<double> TAnSWaveGapIntegralCuhre::fPar;
 
-//-----------------------------------------------------------------------------
 /**
  * <p>Integrate the function using the Cuhre interface
  *
@@ -423,7 +409,6 @@ double TAnSWaveGapIntegralCuhre::IntegrateFunc()
   return integral[0];
 }
 
-//-----------------------------------------------------------------------------
 /**
  * <p>Calculate the function value for the use with Cuhre---actual implementation of the function
  *
@@ -444,11 +429,8 @@ int TAnSWaveGapIntegralCuhre::Integrand(const int *ndim, const double x[],
   return 0;
 }
 
-//-----------------------------------------------------------------------------
-
 std::vector<double> TAnSWaveGapIntegralDivonne::fPar;
 
-//-----------------------------------------------------------------------------
 /**
  * <p>Integrate the function using the Divonne interface
  *
@@ -487,7 +469,6 @@ double TAnSWaveGapIntegralDivonne::IntegrateFunc()
   return integral[0];
 }
 
-//-----------------------------------------------------------------------------
 /**
  * <p>Calculate the function value for the use with Divonne---actual implementation of the function
  *
@@ -508,11 +489,8 @@ int TAnSWaveGapIntegralDivonne::Integrand(const int *ndim, const double x[],
   return 0;
 }
 
-//-----------------------------------------------------------------------------
-
 std::vector<double> TAnSWaveGapIntegralSuave::fPar;
 
-//-----------------------------------------------------------------------------
 /**
  * <p>Integrate the function using the Suave interface
  *
@@ -545,7 +523,6 @@ double TAnSWaveGapIntegralSuave::IntegrateFunc()
   return integral[0];
 }
 
-//-----------------------------------------------------------------------------
 /**
  * <p>Calculate the function value for the use with Suave---actual implementation of the function
  *
@@ -566,11 +543,8 @@ int TAnSWaveGapIntegralSuave::Integrand(const int *ndim, const double x[],
   return 0;
 }
 
-//-----------------------------------------------------------------------------
-
 std::vector<double> TNonMonDWave1GapIntegralCuhre::fPar;
 
-//-----------------------------------------------------------------------------
 /**
  * <p>Integrate the function using the Cuhre interface
  *
@@ -601,7 +575,6 @@ double TNonMonDWave1GapIntegralCuhre::IntegrateFunc()
   return integral[0];
 }
 
-//-----------------------------------------------------------------------------
 /**
  * <p>Calculate the function value for the use with Cuhre---actual implementation of the function
  *
@@ -622,11 +595,8 @@ int TNonMonDWave1GapIntegralCuhre::Integrand(const int *ndim, const double x[],
   return 0;
 }
 
-//-----------------------------------------------------------------------------
-
 std::vector<double> TNonMonDWave2GapIntegralCuhre::fPar;
 
-//-----------------------------------------------------------------------------
 /**
  * <p>Integrate the function using the Cuhre interface
  *
@@ -657,7 +627,6 @@ double TNonMonDWave2GapIntegralCuhre::IntegrateFunc()
   return integral[0];
 }
 
-//-----------------------------------------------------------------------------
 /**
  * <p>Calculate the function value for the use with Cuhre---actual implementation of the function
  *

src/external/BMWtools/BMWIntegrator.h

@@ -48,7 +48,6 @@
 #include <vector>
 #include <memory>
 
-//-----------------------------------------------------------------------------
 /**
  * @class T2Integrator
  * @brief Alternative base class for 1D integrations using the GNU Scientific Library integrator.
@@ -71,7 +70,6 @@ class T2Integrator {
     static double FuncAtXgsl(double, void *);
 };
 
-//-----------------------------------------------------------------------------
 /**
  * <p>Method for passing the integrand function value to the integrator.
  *
@@ -87,7 +85,6 @@ 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
  *
@@ -110,7 +107,20 @@ 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.
@@ -136,7 +146,6 @@ 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
@@ -145,7 +154,6 @@ 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.
@@ -155,7 +163,6 @@ inline TIntegrator::~TIntegrator(){
   fFunc=0;
 }
 
-//-----------------------------------------------------------------------------
 /**
  * <p>Method for passing the integrand function value to the integrator.
  *
@@ -170,7 +177,6 @@ inline double TIntegrator::FuncAtXgsl(double x, void *obj)
   return ((TIntegrator*)obj)->FuncAtX(x);
 }
 
-//-----------------------------------------------------------------------------
 /**
  * <p>Calculate the integral of the function between the given boundaries
  *
@@ -186,7 +192,6 @@ 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.
@@ -213,7 +218,6 @@ 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
@@ -222,7 +226,6 @@ 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.
@@ -232,7 +235,6 @@ inline TMCIntegrator::~TMCIntegrator(){
   fFunc=0;
 }
 
-//-----------------------------------------------------------------------------
 /**
  * <p>Method for passing the integrand function value to the integrator.
  *
@@ -248,7 +250,6 @@ 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
  *
@@ -333,7 +334,6 @@ 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
@@ -355,7 +355,6 @@ 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
@@ -377,7 +376,6 @@ 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
@@ -399,7 +397,6 @@ 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
@@ -421,7 +418,6 @@ 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
@@ -443,7 +439,6 @@ 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
@@ -465,7 +460,6 @@ 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
@@ -487,7 +481,6 @@ class TNonMonDWave2GapIntegralCuhre {
     unsigned int fNDim; ///< dimension of the integral (2)
 };
 
-//-----------------------------------------------------------------------------
 /**
  * @class T2DTest
  * @brief Test class for the 2D Monte-Carlo integration.
@@ -501,7 +494,6 @@ 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
  *
@@ -595,7 +587,6 @@ class TDWaveGapIntegral : public TMCIntegrator {
     double FuncAtX(double *) const; ///< Calculate integrand at point x
 };
 
-//-----------------------------------------------------------------------------
 /**
  * <p>Calculate the function value---actual implementation of the function
  *
@@ -611,7 +602,6 @@ 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
@@ -627,7 +617,6 @@ class TAnSWaveGapIntegral : public TMCIntegrator {
     double FuncAtX(double *) const; ///< Calculate integrand at point x
 };
 
-//-----------------------------------------------------------------------------
 /**
  * <p>Calculate the function value---actual implementation of the function
  *
@@ -643,7 +632,6 @@ 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).
@@ -659,7 +647,6 @@ 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)
  *
@@ -680,7 +667,6 @@ 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).
@@ -696,7 +682,6 @@ 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)
  *
@@ -710,7 +695,6 @@ 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".
@@ -728,7 +712,6 @@ 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
  *
@@ -745,7 +728,6 @@ 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
@@ -760,7 +742,6 @@ 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)
  *
@@ -774,7 +755,6 @@ 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.
@@ -790,7 +770,6 @@ 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
  *
@@ -808,7 +787,6 @@ 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.
@@ -824,7 +802,6 @@ 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
  *

src/external/DepthProfile/src/CMakeLists.txt

@@ -6,7 +6,6 @@ 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})
 
@@ -14,7 +13,7 @@ root_generate_dictionary(
   PDepthProfileDict 
   PDepthProfile.h 
   OPTIONS 
-    -I${FFTW3_INCLUDE} 
+    -I${FFTW3_INCLUDE_DIR} 
     -I${MUSRFIT_INC}
     -I${DEPTH_PROFILE_INC}
     -inlineInputHeader
@@ -46,7 +45,7 @@ set_target_properties(PDepthProfile
 #--- make sure that the include directory is found ----------------------------
 target_include_directories(
   PDepthProfile BEFORE PRIVATE 
-    $<BUILD_INTERFACE:${FFTW3_INCLUDE}> 
+    $<BUILD_INTERFACE:${FFTW3_INCLUDE_DIR}> 
     $<BUILD_INTERFACE:${MUSRFIT_INC}>
     $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/../inc>
 )

src/external/MagProximity/PMPStartupHandlerLinkDef.h

@@ -27,7 +27,7 @@
  *   59 Temple Place - Suite 330, Boston, MA  02111-1307, USA.             *
  ***************************************************************************/
 
-#ifdef __CINT__
+#ifdef __CLING__
 
 #pragma link off all globals;
 #pragma link off all classes;

src/external/MagProximity/PMagProximityFitterLinkDef.h

@@ -27,7 +27,7 @@
  *   59 Temple Place - Suite 330, Boston, MA  02111-1307, USA.             *
  ***************************************************************************/
 
-#ifdef __CINT__
+#ifdef __CLING__
 
 #pragma link off all globals;
 #pragma link off all classes;

src/external/MusrRoot/TMusrRunHeaderLinkDef.h

@@ -27,7 +27,7 @@
  *   59 Temple Place - Suite 330, Boston, MA  02111-1307, USA.             *
  ***************************************************************************/
 
-#ifdef __CINT__
+#ifdef __CLING__
 
 #pragma link off all globals;
 #pragma link off all classes;

src/external/Nonlocal/CMakeLists.txt

@@ -54,6 +54,7 @@ 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}>
 )
 

src/external/Nonlocal/PNL_PippardFitterLinkDef.h

@@ -27,7 +27,7 @@
  *   59 Temple Place - Suite 330, Boston, MA  02111-1307, USA.             *
  ***************************************************************************/
 
-#ifdef __CINT__
+#ifdef __CLING__
 
 #pragma link off all globals;
 #pragma link off all classes;

src/external/Nonlocal/PNL_StartupHandlerLinkDef.h

@@ -27,7 +27,7 @@
  *   59 Temple Place - Suite 330, Boston, MA  02111-1307, USA.             *
  ***************************************************************************/
 
-#ifdef __CINT__
+#ifdef __CLING__
 
 #pragma link off all globals;
 #pragma link off all classes;

src/external/TLemRunHeader/TLemRunHeaderLinkDef.h

@@ -1,4 +1,4 @@
-#ifdef __CINT__
+#ifdef __CLING__
 
 #pragma link off all globals;
 #pragma link off all classes;

src/external/TLemRunHeader/TLemStatsLinkDef.h

@@ -1,4 +1,4 @@
-#ifdef __CINT__
+#ifdef __CLING__
 
 #pragma link off all globals;
 #pragma link off all classes;

src/external/libBNMR/TBNMR.h

@@ -66,7 +66,7 @@ class SExpRlx : public PUserFcnBase {
 
 public:
   // default constructor and destructor
-  SExpRlx(){}
+  SExpRlx(){sexp1.SetNpx(1000); sexp2.SetNpx(1000);}
   ~SExpRlx(){}
 
   // function operator

src/external/libBNMR/TBNMRLinkDef.h

@@ -29,7 +29,7 @@
  *   59 Temple Place - Suite 330, Boston, MA  02111-1307, USA.             *
  ***************************************************************************/
 
-#ifdef __CINT__
+#ifdef __CLING__
 
 #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 //__CINT__
+#endif //__CLING__

src/external/libCalcMeanFieldsLEM/TCalcMeanFieldsLEMLinkDef.h

@@ -27,7 +27,7 @@
  ***************************************************************************/
 
 // root dictionary stuff --------------------------------------------------
-#ifdef __CINT__
+#ifdef __CLING__
 
 #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 //__CINT__
+#endif //__CLING__
 // root dictionary stuff --------------------------------------------------
 

src/external/libCuba/src/Makefile

@@ -0,0 +1,912 @@
+# Makefile.in generated by automake 1.16.1 from Makefile.am.
+# src/external/libCuba/src/Makefile.  Generated from Makefile.in by configure.
+
+# Copyright (C) 1994-2018 Free Software Foundation, Inc.
+
+# This Makefile.in is free software; the Free Software Foundation
+# gives unlimited permission to copy and/or distribute it,
+# with or without modifications, as long as this notice is preserved.
+
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY, to the extent permitted by law; without
+# even the implied warranty of MERCHANTABILITY or FITNESS FOR A
+# PARTICULAR PURPOSE.
+
+
+
+
+
+
+am__is_gnu_make = { \
+  if test -z '$(MAKELEVEL)'; then \
+    false; \
+  elif test -n '$(MAKE_HOST)'; then \
+    true; \
+  elif test -n '$(MAKE_VERSION)' && test -n '$(CURDIR)'; then \
+    true; \
+  else \
+    false; \
+  fi; \
+}
+am__make_running_with_option = \
+  case $${target_option-} in \
+      ?) ;; \
+      *) echo "am__make_running_with_option: internal error: invalid" \
+              "target option '$${target_option-}' specified" >&2; \
+         exit 1;; \
+  esac; \
+  has_opt=no; \
+  sane_makeflags=$$MAKEFLAGS; \
+  if $(am__is_gnu_make); then \
+    sane_makeflags=$$MFLAGS; \
+  else \
+    case $$MAKEFLAGS in \
+      *\\[\ \	]*) \
+        bs=\\; \
+        sane_makeflags=`printf '%s\n' "$$MAKEFLAGS" \
+          | sed "s/$$bs$$bs[$$bs $$bs	]*//g"`;; \
+    esac; \
+  fi; \
+  skip_next=no; \
+  strip_trailopt () \
+  { \
+    flg=`printf '%s\n' "$$flg" | sed "s/$$1.*$$//"`; \
+  }; \
+  for flg in $$sane_makeflags; do \
+    test $$skip_next = yes && { skip_next=no; continue; }; \
+    case $$flg in \
+      *=*|--*) continue;; \
+        -*I) strip_trailopt 'I'; skip_next=yes;; \
+      -*I?*) strip_trailopt 'I';; \
+        -*O) strip_trailopt 'O'; skip_next=yes;; \
+      -*O?*) strip_trailopt 'O';; \
+        -*l) strip_trailopt 'l'; skip_next=yes;; \
+      -*l?*) strip_trailopt 'l';; \
+      -[dEDm]) skip_next=yes;; \
+      -[JT]) skip_next=yes;; \
+    esac; \
+    case $$flg in \
+      *$$target_option*) has_opt=yes; break;; \
+    esac; \
+  done; \
+  test $$has_opt = yes
+am__make_dryrun = (target_option=n; $(am__make_running_with_option))
+am__make_keepgoing = (target_option=k; $(am__make_running_with_option))
+pkgdatadir = $(datadir)/musrfit
+pkgincludedir = $(includedir)/musrfit
+pkglibdir = $(libdir)/musrfit
+pkglibexecdir = $(libexecdir)/musrfit
+am__cd = CDPATH="$${ZSH_VERSION+.}$(PATH_SEPARATOR)" && cd
+install_sh_DATA = $(install_sh) -c -m 644
+install_sh_PROGRAM = $(install_sh) -c
+install_sh_SCRIPT = $(install_sh) -c
+INSTALL_HEADER = $(INSTALL_DATA)
+transform = $(program_transform_name)
+NORMAL_INSTALL = :
+PRE_INSTALL = :
+POST_INSTALL = :
+NORMAL_UNINSTALL = :
+PRE_UNINSTALL = :
+POST_UNINSTALL = :
+build_triplet = x86_64-apple-darwin17.5.0
+host_triplet = x86_64-apple-darwin17.5.0
+subdir = src/external/libCuba/src
+ACLOCAL_M4 = $(top_srcdir)/aclocal.m4
+am__aclocal_m4_deps = $(top_srcdir)/acinclude.m4 \
+	$(top_srcdir)/configure.ac
+am__configure_deps = $(am__aclocal_m4_deps) $(CONFIGURE_DEPENDENCIES) \
+	$(ACLOCAL_M4)
+DIST_COMMON = $(srcdir)/Makefile.am $(include_HEADERS) \
+	$(am__DIST_COMMON)
+mkinstalldirs = $(install_sh) -d
+CONFIG_HEADER = $(top_builddir)/config.h
+CONFIG_CLEAN_FILES = cuba.pc
+CONFIG_CLEAN_VPATH_FILES =
+am__vpath_adj_setup = srcdirstrip=`echo "$(srcdir)" | sed 's|.|.|g'`;
+am__vpath_adj = case $$p in \
+    $(srcdir)/*) f=`echo "$$p" | sed "s|^$$srcdirstrip/||"`;; \
+    *) f=$$p;; \
+  esac;
+am__strip_dir = f=`echo $$p | sed -e 's|^.*/||'`;
+am__install_max = 40
+am__nobase_strip_setup = \
+  srcdirstrip=`echo "$(srcdir)" | sed 's/[].[^$$\\*|]/\\\\&/g'`
+am__nobase_strip = \
+  for p in $$list; do echo "$$p"; done | sed -e "s|$$srcdirstrip/||"
+am__nobase_list = $(am__nobase_strip_setup); \
+  for p in $$list; do echo "$$p $$p"; done | \
+  sed "s| $$srcdirstrip/| |;"' / .*\//!s/ .*/ ./; s,\( .*\)/[^/]*$$,\1,' | \
+  $(AWK) 'BEGIN { files["."] = "" } { files[$$2] = files[$$2] " " $$1; \
+    if (++n[$$2] == $(am__install_max)) \
+      { print $$2, files[$$2]; n[$$2] = 0; files[$$2] = "" } } \
+    END { for (dir in files) print dir, files[dir] }'
+am__base_list = \
+  sed '$$!N;$$!N;$$!N;$$!N;$$!N;$$!N;$$!N;s/\n/ /g' | \
+  sed '$$!N;$$!N;$$!N;$$!N;s/\n/ /g'
+am__uninstall_files_from_dir = { \
+  test -z "$$files" \
+    || { test ! -d "$$dir" && test ! -f "$$dir" && test ! -r "$$dir"; } \
+    || { echo " ( cd '$$dir' && rm -f" $$files ")"; \
+         $(am__cd) "$$dir" && rm -f $$files; }; \
+  }
+am__installdirs = "$(DESTDIR)$(libdir)" "$(DESTDIR)$(pkgconfigdir)" \
+	"$(DESTDIR)$(includedir)"
+LTLIBRARIES = $(lib_LTLIBRARIES)
+libcuba_la_DEPENDENCIES = common/libcommon.la cuhre/libcuhre.la \
+	divonne/libdivonne.la suave/libsuave.la vegas/libvegas.la
+am_libcuba_la_OBJECTS =
+libcuba_la_OBJECTS = $(am_libcuba_la_OBJECTS)
+AM_V_lt = $(am__v_lt_$(V))
+am__v_lt_ = $(am__v_lt_$(AM_DEFAULT_VERBOSITY))
+am__v_lt_0 = --silent
+am__v_lt_1 = 
+libcuba_la_LINK = $(LIBTOOL) $(AM_V_lt) --tag=CC $(AM_LIBTOOLFLAGS) \
+	$(LIBTOOLFLAGS) --mode=link $(CCLD) $(AM_CFLAGS) $(CFLAGS) \
+	$(libcuba_la_LDFLAGS) $(LDFLAGS) -o $@
+AM_V_P = $(am__v_P_$(V))
+am__v_P_ = $(am__v_P_$(AM_DEFAULT_VERBOSITY))
+am__v_P_0 = false
+am__v_P_1 = :
+AM_V_GEN = $(am__v_GEN_$(V))
+am__v_GEN_ = $(am__v_GEN_$(AM_DEFAULT_VERBOSITY))
+am__v_GEN_0 = @echo "  GEN     " $@;
+am__v_GEN_1 = 
+AM_V_at = $(am__v_at_$(V))
+am__v_at_ = $(am__v_at_$(AM_DEFAULT_VERBOSITY))
+am__v_at_0 = @
+am__v_at_1 = 
+DEFAULT_INCLUDES = -I. -I$(top_builddir)
+COMPILE = $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) \
+	$(CPPFLAGS) $(AM_CFLAGS) $(CFLAGS)
+LTCOMPILE = $(LIBTOOL) $(AM_V_lt) --tag=CC $(AM_LIBTOOLFLAGS) \
+	$(LIBTOOLFLAGS) --mode=compile $(CC) $(DEFS) \
+	$(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) \
+	$(AM_CFLAGS) $(CFLAGS)
+AM_V_CC = $(am__v_CC_$(V))
+am__v_CC_ = $(am__v_CC_$(AM_DEFAULT_VERBOSITY))
+am__v_CC_0 = @echo "  CC      " $@;
+am__v_CC_1 = 
+CCLD = $(CC)
+LINK = $(LIBTOOL) $(AM_V_lt) --tag=CC $(AM_LIBTOOLFLAGS) \
+	$(LIBTOOLFLAGS) --mode=link $(CCLD) $(AM_CFLAGS) $(CFLAGS) \
+	$(AM_LDFLAGS) $(LDFLAGS) -o $@
+AM_V_CCLD = $(am__v_CCLD_$(V))
+am__v_CCLD_ = $(am__v_CCLD_$(AM_DEFAULT_VERBOSITY))
+am__v_CCLD_0 = @echo "  CCLD    " $@;
+am__v_CCLD_1 = 
+SOURCES = $(libcuba_la_SOURCES)
+DIST_SOURCES = $(libcuba_la_SOURCES)
+RECURSIVE_TARGETS = all-recursive check-recursive cscopelist-recursive \
+	ctags-recursive dvi-recursive html-recursive info-recursive \
+	install-data-recursive install-dvi-recursive \
+	install-exec-recursive install-html-recursive \
+	install-info-recursive install-pdf-recursive \
+	install-ps-recursive install-recursive installcheck-recursive \
+	installdirs-recursive pdf-recursive ps-recursive \
+	tags-recursive uninstall-recursive
+am__can_run_installinfo = \
+  case $$AM_UPDATE_INFO_DIR in \
+    n|no|NO) false;; \
+    *) (install-info --version) >/dev/null 2>&1;; \
+  esac
+DATA = $(pkgconfig_DATA)
+HEADERS = $(include_HEADERS)
+RECURSIVE_CLEAN_TARGETS = mostlyclean-recursive clean-recursive	\
+  distclean-recursive maintainer-clean-recursive
+am__recursive_targets = \
+  $(RECURSIVE_TARGETS) \
+  $(RECURSIVE_CLEAN_TARGETS) \
+  $(am__extra_recursive_targets)
+AM_RECURSIVE_TARGETS = $(am__recursive_targets:-recursive=) TAGS CTAGS \
+	distdir distdir-am
+am__tagged_files = $(HEADERS) $(SOURCES) $(TAGS_FILES) $(LISP)
+# Read a list of newline-separated strings from the standard input,
+# and print each of them once, without duplicates.  Input order is
+# *not* preserved.
+am__uniquify_input = $(AWK) '\
+  BEGIN { nonempty = 0; } \
+  { items[$$0] = 1; nonempty = 1; } \
+  END { if (nonempty) { for (i in items) print i; }; } \
+'
+# Make sure the list of sources is unique.  This is necessary because,
+# e.g., the same source file might be shared among _SOURCES variables
+# for different programs/libraries.
+am__define_uniq_tagged_files = \
+  list='$(am__tagged_files)'; \
+  unique=`for i in $$list; do \
+    if test -f "$$i"; then echo $$i; else echo $(srcdir)/$$i; fi; \
+  done | $(am__uniquify_input)`
+ETAGS = etags
+CTAGS = ctags
+DIST_SUBDIRS = $(SUBDIRS)
+am__DIST_COMMON = $(srcdir)/Makefile.in $(srcdir)/cuba.pc.in
+DISTFILES = $(DIST_COMMON) $(DIST_SOURCES) $(TEXINFOS) $(EXTRA_DIST)
+am__relativize = \
+  dir0=`pwd`; \
+  sed_first='s,^\([^/]*\)/.*$$,\1,'; \
+  sed_rest='s,^[^/]*/*,,'; \
+  sed_last='s,^.*/\([^/]*\)$$,\1,'; \
+  sed_butlast='s,/*[^/]*$$,,'; \
+  while test -n "$$dir1"; do \
+    first=`echo "$$dir1" | sed -e "$$sed_first"`; \
+    if test "$$first" != "."; then \
+      if test "$$first" = ".."; then \
+        dir2=`echo "$$dir0" | sed -e "$$sed_last"`/"$$dir2"; \
+        dir0=`echo "$$dir0" | sed -e "$$sed_butlast"`; \
+      else \
+        first2=`echo "$$dir2" | sed -e "$$sed_first"`; \
+        if test "$$first2" = "$$first"; then \
+          dir2=`echo "$$dir2" | sed -e "$$sed_rest"`; \
+        else \
+          dir2="../$$dir2"; \
+        fi; \
+        dir0="$$dir0"/"$$first"; \
+      fi; \
+    fi; \
+    dir1=`echo "$$dir1" | sed -e "$$sed_rest"`; \
+  done; \
+  reldir="$$dir2"
+ACLOCAL = ${SHELL} /Users/suter_a/Applications/musrfit-root6/admin/missing aclocal-1.16
+ALLOCA = 
+AMTAR = $${TAR-tar}
+AM_DEFAULT_VERBOSITY = 1
+AR = ar
+AUTOCONF = ${SHELL} /Users/suter_a/Applications/musrfit-root6/admin/missing autoconf
+AUTOHEADER = ${SHELL} /Users/suter_a/Applications/musrfit-root6/admin/missing autoheader
+AUTOMAKE = ${SHELL} /Users/suter_a/Applications/musrfit-root6/admin/missing automake-1.16
+AWK = awk
+BMWTOOLS_CFLAGS = -I/Users/suter_a/Applications/musrfit-root6/src/external/BMWtools
+BMWTOOLS_LIBS = /Users/suter_a/Applications/musrfit-root6/src/external/BMWtools/libBMWtools.la
+BNMRLIBS_CFLAGS = 
+BNMRLIBS_LIBS = 
+BOOST_CFLAGS = -I/opt/local/include
+BOOST_INCLUDE = /opt/local/include
+BOOST_LIBS = 
+CC = gcc
+CCDEPMODE = depmode=gcc3
+CFLAGS = 
+CPP = gcc -E
+CPPFLAGS = 
+CUBA_API_VERSION = 4.2
+CUBA_CFLAGS = -I/Users/suter_a/Applications/musrfit-root6/src/external/libCuba/src
+CUBA_LIBRARY_NAME = cuba
+CUBA_LIBRARY_VERSION = 4:2:0
+CUBA_LIBS = /Users/suter_a/Applications/musrfit-root6/src/external/libCuba/src/libcuba.la
+CUBA_PREFIX = 
+CUBA_RELEASE = 4.2
+CUBA_VERSION = 4.2.0
+CXX = g++
+CXXCPP = g++ -E
+CXXDEPMODE = depmode=gcc3
+CXXFLAGS = -std=c++11 -g -O2
+CYGPATH_W = echo
+DEFS = -DHAVE_CONFIG_H
+DEPDIR = .deps
+DLLTOOL = false
+DOCDIR = /Users/suter_a/Applications/root/root_exec/share/doc/musrfit
+DSYMUTIL = dsymutil
+DUMPBIN = 
+ECHO_C = \c
+ECHO_N = 
+ECHO_T = 
+EGREP = /usr/bin/grep -E
+EXEEXT = 
+FFTW3_CFLAGS = -I/opt/local/include
+FFTW3_LIBS = -L/opt/local/lib -lfftw3 -lfftw3_threads -lpthread -lfftw3f -lfftw3f_threads -lpthread
+FFTW3_PREFIX = 
+FGREP = /usr/bin/grep -F
+FITPOFB_CFLAGS = -I/Users/suter_a/Applications/musrfit-root6/src/external/libFitPofB/include
+FITPOFB_LIBS = /Users/suter_a/Applications/musrfit-root6/src/external/libFitPofB/classes/libFitPofB.la
+GREP = /usr/bin/grep
+GSL_CFLAGS = -I/opt/local/include
+GSL_LIBS = -L/opt/local/lib -lgsl -lgslcblas -lm
+GSL_PREFIX = 
+INSTALL = /usr/bin/install -c
+INSTALL_DATA = ${INSTALL} -m 644
+INSTALL_PROGRAM = ${INSTALL}
+INSTALL_SCRIPT = ${INSTALL}
+INSTALL_STRIP_PROGRAM = $(install_sh) -c -s
+LD = /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ld
+LDFLAGS = 
+LEM_API_VERSION = 1.5
+LEM_CFLAGS = -I/Users/suter_a/Applications/musrfit-root6/src/external/TLemRunHeader
+LEM_LIBRARY_NAME = TLemRunHeader
+LEM_LIBRARY_VERSION = 1:5:0
+LEM_LIBS = /Users/suter_a/Applications/musrfit-root6/src/external/TLemRunHeader/libTLemRunHeader.la
+LEM_RELEASE = 1.5
+LEM_VERSION = 1.5.0
+LIBOBJS = 
+LIBS = 
+LIBTOOL = $(SHELL) $(top_builddir)/libtool
+LIBXML2_CFLAGS = -I/usr/include/libxml2
+LIBXML2_LIBS = -L/usr/include/lib -lxml2
+LIBXML2_PREFIX = /usr/include
+LIPO = lipo
+LN_S = ln -s
+LOCAL_BIN_CXXFLAGS = -m64 -fPIC -DPIC -Wall -Wno-trigraphs
+LOCAL_BIN_LDFLAGS =  -Wl,-rpath /Users/suter_a/Applications/root/root_exec/lib
+LOCAL_CUBA_LIB_CFLAGS = -m64 -fPIC -DPIC -Wall -Wno-trigraphs -O3 -fomit-frame-pointer -ffast-math
+LOCAL_LIB_CXXFLAGS = -m64 -fPIC -DPIC -Wall -Wno-trigraphs
+LOCAL_LIB_LDFLAGS = 
+LOCAL_MUD_LIB_CFLAGS = -m64 -fPIC -DPIC -Wall -Wno-trigraphs -g -O2
+LOCAL_PNEXUS_LIB_CXXFLAGS = -m64 -fPIC -DPIC -Wall -Wno-trigraphs
+LOCAL_PSIBIN_LIB_CXXFLAGS = -m64 -fPIC -DPIC -Wall -Wno-trigraphs -D_Darwin_
+LTLIBOBJS = 
+LT_SYS_LIBRARY_PATH = 
+MAKEINFO = ${SHELL} /Users/suter_a/Applications/musrfit-root6/admin/missing makeinfo
+MANIFEST_TOOL = :
+MKDIR_P = ../../../../admin/install-sh -c -d
+MUD_API_VERSION = 0.0
+MUD_CFLAGS = -I/Users/suter_a/Applications/musrfit-root6/src/external/mud/src
+MUD_LIBRARY_NAME = mud
+MUD_LIBRARY_VERSION = 0:0:0
+MUD_LIBS = /Users/suter_a/Applications/musrfit-root6/src/external/mud/src/libmud.la
+MUD_RELEASE = 0.0
+MUD_VERSION = 0.0.0
+MUSR_API_VERSION = 1.2
+MUSR_LIBRARY_NAME = PMusr
+MUSR_LIBRARY_VERSION = 1:2:1
+MUSR_RELEASE = 1.2
+MUSR_ROOT_API_VERSION = 1.0
+MUSR_ROOT_CFLAGS = -I/Users/suter_a/Applications/musrfit-root6/src/external/MusrRoot
+MUSR_ROOT_LIBRARY_NAME = TMusrRunHeader
+MUSR_ROOT_LIBRARY_VERSION = 1:0:0
+MUSR_ROOT_LIBS = /Users/suter_a/Applications/musrfit-root6/src/external/MusrRoot/libTMusrRunHeader.la
+MUSR_ROOT_RELEASE = 1.0
+MUSR_ROOT_VERSION = 1.0.0
+MUSR_VERSION = 1.2.1
+NEXUS_CFLAGS = 
+NEXUS_LIBS = 
+NEXUS_PREFIX = 
+NM = /opt/local/bin/nm -B
+NMEDIT = nmedit
+OBJDUMP = objdump
+OBJEXT = o
+OTOOL = otool
+OTOOL64 = :
+PACKAGE = musrfit
+PACKAGE_BUGREPORT = andreas.suter@psi.ch
+PACKAGE_NAME = musrfit
+PACKAGE_STRING = musrfit 1.2.1
+PACKAGE_TARNAME = musrfit
+PACKAGE_URL = 
+PACKAGE_VERSION = 1.2.1
+PATH_SEPARATOR = :
+PKG_CONFIG = /opt/local/bin/pkg-config
+PKG_CONFIG_LIBDIR = 
+PKG_CONFIG_PATH = 
+PLUGIN_API_VERSION = 1.0
+PLUGIN_LIBRARY_VERSION = 1:0:0
+PLUGIN_MAJOR_VERSION = 1
+PLUGIN_MINOR_VERSION = 0
+PLUGIN_RELEASE = 1.0
+PLUGIN_VERSION = 1.0.0
+PMUSR_CFLAGS = -I/Users/suter_a/Applications/musrfit-root6/src/include
+PMUSR_LIBS = /Users/suter_a/Applications/musrfit-root6/src/classes/libPMusr.la
+PNEXUS_API_VERSION = 0.9
+PNEXUS_CXXFLAGS = 
+PNEXUS_LIBRARY_NAME = PNeXus
+PNEXUS_LIBRARY_VERSION = 0:9:0
+PNEXUS_LIBS = 
+PNEXUS_RELEASE = 0.9
+PNEXUS_VERSION = 0.9.0
+PSIBIN_API_VERSION = 0.1
+PSIBIN_CFLAGS = -I/Users/suter_a/Applications/musrfit-root6/src/external/MuSR_software/Class_MuSR_PSI
+PSIBIN_LIBRARY_NAME = Class_MuSR_PSI
+PSIBIN_LIBRARY_VERSION = 0:1:0
+PSIBIN_LIBS = /Users/suter_a/Applications/musrfit-root6/src/external/MuSR_software/Class_MuSR_PSI/libClass_MuSR_PSI.la
+PSIBIN_RELEASE = 0.1
+PSIBIN_VERSION = 0.1.0
+QT3MT_CFLAGS = 
+QT3MT_LIBS = 
+QT3_CFLAGS = 
+QT3_LIBS = 
+QT4_CFLAGS = 
+QT4_LIBS = 
+QT5_CFLAGS = 
+QT5_LIBS = 
+RANLIB = ranlib
+ROOTAUXCFLAGS = -pthread -stdlib=libc++ -std=c++11 -m64
+ROOTAUXLIBS = -lpthread -stdlib=libc++ -lm -ldl
+ROOTCFLAGS = -I/Users/suter_a/Applications/root/root_exec/include
+ROOTCLING = /Users/suter_a/Applications/root/root_exec/bin/rootcling
+ROOTCONF = /Users/suter_a/Applications/root/root_exec/bin/root-config
+ROOTETCDIR = /Users/suter_a/Applications/root/root_exec/etc
+ROOTEXEC = /Users/suter_a/Applications/root/root_exec/bin/root
+ROOTGLIBS = -lGui -lCore -lImt -lRIO -lNet -lHist -lGraf -lGraf3d -lGpad -lTree -lTreePlayer -lRint -lPostscript -lMatrix -lPhysics -lMathCore -lThread -lMultiProc
+ROOTINCDIR = /Users/suter_a/Applications/root/root_exec/include
+ROOTLIBDIR = /Users/suter_a/Applications/root/root_exec/lib
+ROOTLIBS = -lCore -lImt -lRIO -lNet -lHist -lGraf -lGraf3d -lGpad -lTree -lTreePlayer -lRint -lPostscript -lMatrix -lPhysics -lMathCore -lThread -lMultiProc
+ROOTRPATH = /Users/suter_a/Applications/root/root_exec/lib
+ROOTSOVERSION = 6.13
+ROOTVERSION = 6.13/02
+ROOT_CFLAGS = -I/Users/suter_a/Applications/root/root_exec/include -I/Users/suter_a/Applications/root/root_exec/include -pthread -stdlib=libc++ -std=c++11 -m64
+ROOT_LIBS = -L/Users/suter_a/Applications/root/root_exec/lib -lGui -lCore -lImt -lRIO -lNet -lHist -lGraf -lGraf3d -lGpad -lTree -lTreePlayer -lRint -lPostscript -lMatrix -lPhysics -lMathCore -lThread -lMultiProc -lpthread -stdlib=libc++ -lm -ldl -lMinuit2 -lMathMore -lXMLParser
+SED = /usr/bin/sed
+SET_MAKE = 
+SHELL = /bin/sh
+STRIP = strip
+USERFCN_LIBRARY_NAME = PUserFcnBase
+USERFCN_LIBS = /Users/suter_a/Applications/musrfit-root6/src/classes/libPUserFcnBase.la
+VERSION = 1.2.1
+abs_builddir = /Users/suter_a/Applications/musrfit-root6/src/external/libCuba/src
+abs_srcdir = /Users/suter_a/Applications/musrfit-root6/src/external/libCuba/src
+abs_top_builddir = /Users/suter_a/Applications/musrfit-root6
+abs_top_srcdir = /Users/suter_a/Applications/musrfit-root6
+ac_ct_AR = ar
+ac_ct_CC = gcc
+ac_ct_CXX = g++
+ac_ct_DUMPBIN = 
+am__include = include
+am__leading_dot = .
+am__quote = 
+am__tar = $${TAR-tar} chof - "$$tardir"
+am__untar = $${TAR-tar} xf -
+bindir = ${exec_prefix}/bin
+build = x86_64-apple-darwin17.5.0
+build_alias = 
+build_cpu = x86_64
+build_os = darwin17.5.0
+build_vendor = apple
+builddir = .
+datadir = ${datarootdir}
+datarootdir = ${prefix}/share
+docdir = ${datarootdir}/doc/${PACKAGE_TARNAME}
+dvidir = ${docdir}
+exec_prefix = ${prefix}
+host = x86_64-apple-darwin17.5.0
+host_alias = 
+host_cpu = x86_64
+host_os = darwin17.5.0
+host_vendor = apple
+htmldir = ${docdir}
+includedir = ${prefix}/include
+infodir = ${datarootdir}/info
+install_sh = ${SHELL} /Users/suter_a/Applications/musrfit-root6/admin/install-sh
+libdir = ${exec_prefix}/lib
+libexecdir = ${exec_prefix}/libexec
+localedir = ${datarootdir}/locale
+localstatedir = ${prefix}/var
+mandir = ${datarootdir}/man
+mkdir_p = $(MKDIR_P)
+oldincludedir = /usr/include
+pdfdir = ${docdir}
+prefix = /Users/suter_a/Applications/root/root_exec
+program_transform_name = s,x,x,
+psdir = ${docdir}
+sbindir = ${exec_prefix}/sbin
+sharedstatedir = ${prefix}/com
+srcdir = .
+sysconfdir = ${prefix}/etc
+target_alias = 
+top_build_prefix = ../../../../
+top_builddir = ../../../..
+top_srcdir = ../../../..
+SUBDIRS = cuhre divonne suave vegas common
+include_HEADERS = cuba.h
+AM_LDFLAGS = $(LOCAL_LIB_LDFLAGS)
+CLEANFILES = common/*~ cuhre/*~ divonne/*~ suave/*~ vegas/*~ *~ core
+lib_LTLIBRARIES = libcuba.la
+libcuba_la_SOURCES = 
+libcuba_la_LIBADD = common/libcommon.la cuhre/libcuhre.la divonne/libdivonne.la suave/libsuave.la vegas/libvegas.la -lm
+libcuba_la_LDFLAGS = -version-info $(CUBA_LIBRARY_VERSION) -release $(CUBA_RELEASE) $(AM_LDFLAGS)
+pkgconfigdir = $(libdir)/pkgconfig
+pkgconfig_DATA = cuba.pc
+all: all-recursive
+
+.SUFFIXES:
+$(srcdir)/Makefile.in:  $(srcdir)/Makefile.am  $(am__configure_deps)
+	@for dep in $?; do \
+	  case '$(am__configure_deps)' in \
+	    *$$dep*) \
+	      ( cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh ) \
+	        && { if test -f $@; then exit 0; else break; fi; }; \
+	      exit 1;; \
+	  esac; \
+	done; \
+	echo ' cd $(top_srcdir) && $(AUTOMAKE) --gnu src/external/libCuba/src/Makefile'; \
+	$(am__cd) $(top_srcdir) && \
+	  $(AUTOMAKE) --gnu src/external/libCuba/src/Makefile
+Makefile: $(srcdir)/Makefile.in $(top_builddir)/config.status
+	@case '$?' in \
+	  *config.status*) \
+	    cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh;; \
+	  *) \
+	    echo ' cd $(top_builddir) && $(SHELL) ./config.status $(subdir)/$@ $(am__maybe_remake_depfiles)'; \
+	    cd $(top_builddir) && $(SHELL) ./config.status $(subdir)/$@ $(am__maybe_remake_depfiles);; \
+	esac;
+
+$(top_builddir)/config.status: $(top_srcdir)/configure $(CONFIG_STATUS_DEPENDENCIES)
+	cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh
+
+$(top_srcdir)/configure:  $(am__configure_deps)
+	cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh
+$(ACLOCAL_M4):  $(am__aclocal_m4_deps)
+	cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh
+$(am__aclocal_m4_deps):
+cuba.pc: $(top_builddir)/config.status $(srcdir)/cuba.pc.in
+	cd $(top_builddir) && $(SHELL) ./config.status $(subdir)/$@
+
+install-libLTLIBRARIES: $(lib_LTLIBRARIES)
+	@$(NORMAL_INSTALL)
+	@list='$(lib_LTLIBRARIES)'; test -n "$(libdir)" || list=; \
+	list2=; for p in $$list; do \
+	  if test -f $$p; then \
+	    list2="$$list2 $$p"; \
+	  else :; fi; \
+	done; \
+	test -z "$$list2" || { \
+	  echo " $(MKDIR_P) '$(DESTDIR)$(libdir)'"; \
+	  $(MKDIR_P) "$(DESTDIR)$(libdir)" || exit 1; \
+	  echo " $(LIBTOOL) $(AM_LIBTOOLFLAGS) $(LIBTOOLFLAGS) --mode=install $(INSTALL) $(INSTALL_STRIP_FLAG) $$list2 '$(DESTDIR)$(libdir)'"; \
+	  $(LIBTOOL) $(AM_LIBTOOLFLAGS) $(LIBTOOLFLAGS) --mode=install $(INSTALL) $(INSTALL_STRIP_FLAG) $$list2 "$(DESTDIR)$(libdir)"; \
+	}
+
+uninstall-libLTLIBRARIES:
+	@$(NORMAL_UNINSTALL)
+	@list='$(lib_LTLIBRARIES)'; test -n "$(libdir)" || list=; \
+	for p in $$list; do \
+	  $(am__strip_dir) \
+	  echo " $(LIBTOOL) $(AM_LIBTOOLFLAGS) $(LIBTOOLFLAGS) --mode=uninstall rm -f '$(DESTDIR)$(libdir)/$$f'"; \
+	  $(LIBTOOL) $(AM_LIBTOOLFLAGS) $(LIBTOOLFLAGS) --mode=uninstall rm -f "$(DESTDIR)$(libdir)/$$f"; \
+	done
+
+clean-libLTLIBRARIES:
+	-test -z "$(lib_LTLIBRARIES)" || rm -f $(lib_LTLIBRARIES)
+	@list='$(lib_LTLIBRARIES)'; \
+	locs=`for p in $$list; do echo $$p; done | \
+	      sed 's|^[^/]*$$|.|; s|/[^/]*$$||; s|$$|/so_locations|' | \
+	      sort -u`; \
+	test -z "$$locs" || { \
+	  echo rm -f $${locs}; \
+	  rm -f $${locs}; \
+	}
+
+libcuba.la: $(libcuba_la_OBJECTS) $(libcuba_la_DEPENDENCIES) $(EXTRA_libcuba_la_DEPENDENCIES) 
+	$(AM_V_CCLD)$(libcuba_la_LINK) -rpath $(libdir) $(libcuba_la_OBJECTS) $(libcuba_la_LIBADD) $(LIBS)
+
+mostlyclean-compile:
+	-rm -f *.$(OBJEXT)
+
+distclean-compile:
+	-rm -f *.tab.c
+
+mostlyclean-libtool:
+	-rm -f *.lo
+
+clean-libtool:
+	-rm -rf .libs _libs
+install-pkgconfigDATA: $(pkgconfig_DATA)
+	@$(NORMAL_INSTALL)
+	@list='$(pkgconfig_DATA)'; test -n "$(pkgconfigdir)" || list=; \
+	if test -n "$$list"; then \
+	  echo " $(MKDIR_P) '$(DESTDIR)$(pkgconfigdir)'"; \
+	  $(MKDIR_P) "$(DESTDIR)$(pkgconfigdir)" || exit 1; \
+	fi; \
+	for p in $$list; do \
+	  if test -f "$$p"; then d=; else d="$(srcdir)/"; fi; \
+	  echo "$$d$$p"; \
+	done | $(am__base_list) | \
+	while read files; do \
+	  echo " $(INSTALL_DATA) $$files '$(DESTDIR)$(pkgconfigdir)'"; \
+	  $(INSTALL_DATA) $$files "$(DESTDIR)$(pkgconfigdir)" || exit $$?; \
+	done
+
+uninstall-pkgconfigDATA:
+	@$(NORMAL_UNINSTALL)
+	@list='$(pkgconfig_DATA)'; test -n "$(pkgconfigdir)" || list=; \
+	files=`for p in $$list; do echo $$p; done | sed -e 's|^.*/||'`; \
+	dir='$(DESTDIR)$(pkgconfigdir)'; $(am__uninstall_files_from_dir)
+install-includeHEADERS: $(include_HEADERS)
+	@$(NORMAL_INSTALL)
+	@list='$(include_HEADERS)'; test -n "$(includedir)" || list=; \
+	if test -n "$$list"; then \
+	  echo " $(MKDIR_P) '$(DESTDIR)$(includedir)'"; \
+	  $(MKDIR_P) "$(DESTDIR)$(includedir)" || exit 1; \
+	fi; \
+	for p in $$list; do \
+	  if test -f "$$p"; then d=; else d="$(srcdir)/"; fi; \
+	  echo "$$d$$p"; \
+	done | $(am__base_list) | \
+	while read files; do \
+	  echo " $(INSTALL_HEADER) $$files '$(DESTDIR)$(includedir)'"; \
+	  $(INSTALL_HEADER) $$files "$(DESTDIR)$(includedir)" || exit $$?; \
+	done
+
+uninstall-includeHEADERS:
+	@$(NORMAL_UNINSTALL)
+	@list='$(include_HEADERS)'; test -n "$(includedir)" || list=; \
+	files=`for p in $$list; do echo $$p; done | sed -e 's|^.*/||'`; \
+	dir='$(DESTDIR)$(includedir)'; $(am__uninstall_files_from_dir)
+
+# This directory's subdirectories are mostly independent; you can cd
+# into them and run 'make' without going through this Makefile.
+# To change the values of 'make' variables: instead of editing Makefiles,
+# (1) if the variable is set in 'config.status', edit 'config.status'
+#     (which will cause the Makefiles to be regenerated when you run 'make');
+# (2) otherwise, pass the desired values on the 'make' command line.
+$(am__recursive_targets):
+	@fail=; \
+	if $(am__make_keepgoing); then \
+	  failcom='fail=yes'; \
+	else \
+	  failcom='exit 1'; \
+	fi; \
+	dot_seen=no; \
+	target=`echo $@ | sed s/-recursive//`; \
+	case "$@" in \
+	  distclean-* | maintainer-clean-*) list='$(DIST_SUBDIRS)' ;; \
+	  *) list='$(SUBDIRS)' ;; \
+	esac; \
+	for subdir in $$list; do \
+	  echo "Making $$target in $$subdir"; \
+	  if test "$$subdir" = "."; then \
+	    dot_seen=yes; \
+	    local_target="$$target-am"; \
+	  else \
+	    local_target="$$target"; \
+	  fi; \
+	  ($(am__cd) $$subdir && $(MAKE) $(AM_MAKEFLAGS) $$local_target) \
+	  || eval $$failcom; \
+	done; \
+	if test "$$dot_seen" = "no"; then \
+	  $(MAKE) $(AM_MAKEFLAGS) "$$target-am" || exit 1; \
+	fi; test -z "$$fail"
+
+ID: $(am__tagged_files)
+	$(am__define_uniq_tagged_files); mkid -fID $$unique
+tags: tags-recursive
+TAGS: tags
+
+tags-am: $(TAGS_DEPENDENCIES) $(am__tagged_files)
+	set x; \
+	here=`pwd`; \
+	if ($(ETAGS) --etags-include --version) >/dev/null 2>&1; then \
+	  include_option=--etags-include; \
+	  empty_fix=.; \
+	else \
+	  include_option=--include; \
+	  empty_fix=; \
+	fi; \
+	list='$(SUBDIRS)'; for subdir in $$list; do \
+	  if test "$$subdir" = .; then :; else \
+	    test ! -f $$subdir/TAGS || \
+	      set "$$@" "$$include_option=$$here/$$subdir/TAGS"; \
+	  fi; \
+	done; \
+	$(am__define_uniq_tagged_files); \
+	shift; \
+	if test -z "$(ETAGS_ARGS)$$*$$unique"; then :; else \
+	  test -n "$$unique" || unique=$$empty_fix; \
+	  if test $$# -gt 0; then \
+	    $(ETAGS) $(ETAGSFLAGS) $(AM_ETAGSFLAGS) $(ETAGS_ARGS) \
+	      "$$@" $$unique; \
+	  else \
+	    $(ETAGS) $(ETAGSFLAGS) $(AM_ETAGSFLAGS) $(ETAGS_ARGS) \
+	      $$unique; \
+	  fi; \
+	fi
+ctags: ctags-recursive
+
+CTAGS: ctags
+ctags-am: $(TAGS_DEPENDENCIES) $(am__tagged_files)
+	$(am__define_uniq_tagged_files); \
+	test -z "$(CTAGS_ARGS)$$unique" \
+	  || $(CTAGS) $(CTAGSFLAGS) $(AM_CTAGSFLAGS) $(CTAGS_ARGS) \
+	     $$unique
+
+GTAGS:
+	here=`$(am__cd) $(top_builddir) && pwd` \
+	  && $(am__cd) $(top_srcdir) \
+	  && gtags -i $(GTAGS_ARGS) "$$here"
+cscopelist: cscopelist-recursive
+
+cscopelist-am: $(am__tagged_files)
+	list='$(am__tagged_files)'; \
+	case "$(srcdir)" in \
+	  [\\/]* | ?:[\\/]*) sdir="$(srcdir)" ;; \
+	  *) sdir=$(subdir)/$(srcdir) ;; \
+	esac; \
+	for i in $$list; do \
+	  if test -f "$$i"; then \
+	    echo "$(subdir)/$$i"; \
+	  else \
+	    echo "$$sdir/$$i"; \
+	  fi; \
+	done >> $(top_builddir)/cscope.files
+
+distclean-tags:
+	-rm -f TAGS ID GTAGS GRTAGS GSYMS GPATH tags
+
+distdir: $(BUILT_SOURCES)
+	$(MAKE) $(AM_MAKEFLAGS) distdir-am
+
+distdir-am: $(DISTFILES)
+	@srcdirstrip=`echo "$(srcdir)" | sed 's/[].[^$$\\*]/\\\\&/g'`; \
+	topsrcdirstrip=`echo "$(top_srcdir)" | sed 's/[].[^$$\\*]/\\\\&/g'`; \
+	list='$(DISTFILES)'; \
+	  dist_files=`for file in $$list; do echo $$file; done | \
+	  sed -e "s|^$$srcdirstrip/||;t" \
+	      -e "s|^$$topsrcdirstrip/|$(top_builddir)/|;t"`; \
+	case $$dist_files in \
+	  */*) $(MKDIR_P) `echo "$$dist_files" | \
+			   sed '/\//!d;s|^|$(distdir)/|;s,/[^/]*$$,,' | \
+			   sort -u` ;; \
+	esac; \
+	for file in $$dist_files; do \
+	  if test -f $$file || test -d $$file; then d=.; else d=$(srcdir); fi; \
+	  if test -d $$d/$$file; then \
+	    dir=`echo "/$$file" | sed -e 's,/[^/]*$$,,'`; \
+	    if test -d "$(distdir)/$$file"; then \
+	      find "$(distdir)/$$file" -type d ! -perm -700 -exec chmod u+rwx {} \;; \
+	    fi; \
+	    if test -d $(srcdir)/$$file && test $$d != $(srcdir); then \
+	      cp -fpR $(srcdir)/$$file "$(distdir)$$dir" || exit 1; \
+	      find "$(distdir)/$$file" -type d ! -perm -700 -exec chmod u+rwx {} \;; \
+	    fi; \
+	    cp -fpR $$d/$$file "$(distdir)$$dir" || exit 1; \
+	  else \
+	    test -f "$(distdir)/$$file" \
+	    || cp -p $$d/$$file "$(distdir)/$$file" \
+	    || exit 1; \
+	  fi; \
+	done
+	@list='$(DIST_SUBDIRS)'; for subdir in $$list; do \
+	  if test "$$subdir" = .; then :; else \
+	    $(am__make_dryrun) \
+	      || test -d "$(distdir)/$$subdir" \
+	      || $(MKDIR_P) "$(distdir)/$$subdir" \
+	      || exit 1; \
+	    dir1=$$subdir; dir2="$(distdir)/$$subdir"; \
+	    $(am__relativize); \
+	    new_distdir=$$reldir; \
+	    dir1=$$subdir; dir2="$(top_distdir)"; \
+	    $(am__relativize); \
+	    new_top_distdir=$$reldir; \
+	    echo " (cd $$subdir && $(MAKE) $(AM_MAKEFLAGS) top_distdir="$$new_top_distdir" distdir="$$new_distdir" \\"; \
+	    echo "     am__remove_distdir=: am__skip_length_check=: am__skip_mode_fix=: distdir)"; \
+	    ($(am__cd) $$subdir && \
+	      $(MAKE) $(AM_MAKEFLAGS) \
+	        top_distdir="$$new_top_distdir" \
+	        distdir="$$new_distdir" \
+		am__remove_distdir=: \
+		am__skip_length_check=: \
+		am__skip_mode_fix=: \
+	        distdir) \
+	      || exit 1; \
+	  fi; \
+	done
+check-am: all-am
+check: check-recursive
+all-am: Makefile $(LTLIBRARIES) $(DATA) $(HEADERS)
+installdirs: installdirs-recursive
+installdirs-am:
+	for dir in "$(DESTDIR)$(libdir)" "$(DESTDIR)$(pkgconfigdir)" "$(DESTDIR)$(includedir)"; do \
+	  test -z "$$dir" || $(MKDIR_P) "$$dir"; \
+	done
+install: install-recursive
+install-exec: install-exec-recursive
+install-data: install-data-recursive
+uninstall: uninstall-recursive
+
+install-am: all-am
+	@$(MAKE) $(AM_MAKEFLAGS) install-exec-am install-data-am
+
+installcheck: installcheck-recursive
+install-strip:
+	if test -z '$(STRIP)'; then \
+	  $(MAKE) $(AM_MAKEFLAGS) INSTALL_PROGRAM="$(INSTALL_STRIP_PROGRAM)" \
+	    install_sh_PROGRAM="$(INSTALL_STRIP_PROGRAM)" INSTALL_STRIP_FLAG=-s \
+	      install; \
+	else \
+	  $(MAKE) $(AM_MAKEFLAGS) INSTALL_PROGRAM="$(INSTALL_STRIP_PROGRAM)" \
+	    install_sh_PROGRAM="$(INSTALL_STRIP_PROGRAM)" INSTALL_STRIP_FLAG=-s \
+	    "INSTALL_PROGRAM_ENV=STRIPPROG='$(STRIP)'" install; \
+	fi
+mostlyclean-generic:
+
+clean-generic:
+	-test -z "$(CLEANFILES)" || rm -f $(CLEANFILES)
+
+distclean-generic:
+	-test -z "$(CONFIG_CLEAN_FILES)" || rm -f $(CONFIG_CLEAN_FILES)
+	-test . = "$(srcdir)" || test -z "$(CONFIG_CLEAN_VPATH_FILES)" || rm -f $(CONFIG_CLEAN_VPATH_FILES)
+
+maintainer-clean-generic:
+	@echo "This command is intended for maintainers to use"
+	@echo "it deletes files that may require special tools to rebuild."
+clean: clean-recursive
+
+clean-am: clean-generic clean-libLTLIBRARIES clean-libtool \
+	mostlyclean-am
+
+distclean: distclean-recursive
+	-rm -f Makefile
+distclean-am: clean-am distclean-compile distclean-generic \
+	distclean-tags
+
+dvi: dvi-recursive
+
+dvi-am:
+
+html: html-recursive
+
+html-am:
+
+info: info-recursive
+
+info-am:
+
+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:

src/external/libCuba/src/Makefile.in

@@ -0,0 +1,912 @@
+# Makefile.in generated by automake 1.16.1 from Makefile.am.
+# @configure_input@
+
+# Copyright (C) 1994-2018 Free Software Foundation, Inc.
+
+# This Makefile.in is free software; the Free Software Foundation
+# gives unlimited permission to copy and/or distribute it,
+# with or without modifications, as long as this notice is preserved.
+
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY, to the extent permitted by law; without
+# even the implied warranty of MERCHANTABILITY or FITNESS FOR A
+# PARTICULAR PURPOSE.
+
+@SET_MAKE@
+
+
+
+VPATH = @srcdir@
+am__is_gnu_make = { \
+  if test -z '$(MAKELEVEL)'; then \
+    false; \
+  elif test -n '$(MAKE_HOST)'; then \
+    true; \
+  elif test -n '$(MAKE_VERSION)' && test -n '$(CURDIR)'; then \
+    true; \
+  else \
+    false; \
+  fi; \
+}
+am__make_running_with_option = \
+  case $${target_option-} in \
+      ?) ;; \
+      *) echo "am__make_running_with_option: internal error: invalid" \
+              "target option '$${target_option-}' specified" >&2; \
+         exit 1;; \
+  esac; \
+  has_opt=no; \
+  sane_makeflags=$$MAKEFLAGS; \
+  if $(am__is_gnu_make); then \
+    sane_makeflags=$$MFLAGS; \
+  else \
+    case $$MAKEFLAGS in \
+      *\\[\ \	]*) \
+        bs=\\; \
+        sane_makeflags=`printf '%s\n' "$$MAKEFLAGS" \
+          | sed "s/$$bs$$bs[$$bs $$bs	]*//g"`;; \
+    esac; \
+  fi; \
+  skip_next=no; \
+  strip_trailopt () \
+  { \
+    flg=`printf '%s\n' "$$flg" | sed "s/$$1.*$$//"`; \
+  }; \
+  for flg in $$sane_makeflags; do \
+    test $$skip_next = yes && { skip_next=no; continue; }; \
+    case $$flg in \
+      *=*|--*) continue;; \
+        -*I) strip_trailopt 'I'; skip_next=yes;; \
+      -*I?*) strip_trailopt 'I';; \
+        -*O) strip_trailopt 'O'; skip_next=yes;; \
+      -*O?*) strip_trailopt 'O';; \
+        -*l) strip_trailopt 'l'; skip_next=yes;; \
+      -*l?*) strip_trailopt 'l';; \
+      -[dEDm]) skip_next=yes;; \
+      -[JT]) skip_next=yes;; \
+    esac; \
+    case $$flg in \
+      *$$target_option*) has_opt=yes; break;; \
+    esac; \
+  done; \
+  test $$has_opt = yes
+am__make_dryrun = (target_option=n; $(am__make_running_with_option))
+am__make_keepgoing = (target_option=k; $(am__make_running_with_option))
+pkgdatadir = $(datadir)/@PACKAGE@
+pkgincludedir = $(includedir)/@PACKAGE@
+pkglibdir = $(libdir)/@PACKAGE@
+pkglibexecdir = $(libexecdir)/@PACKAGE@
+am__cd = CDPATH="$${ZSH_VERSION+.}$(PATH_SEPARATOR)" && cd
+install_sh_DATA = $(install_sh) -c -m 644
+install_sh_PROGRAM = $(install_sh) -c
+install_sh_SCRIPT = $(install_sh) -c
+INSTALL_HEADER = $(INSTALL_DATA)
+transform = $(program_transform_name)
+NORMAL_INSTALL = :
+PRE_INSTALL = :
+POST_INSTALL = :
+NORMAL_UNINSTALL = :
+PRE_UNINSTALL = :
+POST_UNINSTALL = :
+build_triplet = @build@
+host_triplet = @host@
+subdir = src/external/libCuba/src
+ACLOCAL_M4 = $(top_srcdir)/aclocal.m4
+am__aclocal_m4_deps = $(top_srcdir)/acinclude.m4 \
+	$(top_srcdir)/configure.ac
+am__configure_deps = $(am__aclocal_m4_deps) $(CONFIGURE_DEPENDENCIES) \
+	$(ACLOCAL_M4)
+DIST_COMMON = $(srcdir)/Makefile.am $(include_HEADERS) \
+	$(am__DIST_COMMON)
+mkinstalldirs = $(install_sh) -d
+CONFIG_HEADER = $(top_builddir)/config.h
+CONFIG_CLEAN_FILES = cuba.pc
+CONFIG_CLEAN_VPATH_FILES =
+am__vpath_adj_setup = srcdirstrip=`echo "$(srcdir)" | sed 's|.|.|g'`;
+am__vpath_adj = case $$p in \
+    $(srcdir)/*) f=`echo "$$p" | sed "s|^$$srcdirstrip/||"`;; \
+    *) f=$$p;; \
+  esac;
+am__strip_dir = f=`echo $$p | sed -e 's|^.*/||'`;
+am__install_max = 40
+am__nobase_strip_setup = \
+  srcdirstrip=`echo "$(srcdir)" | sed 's/[].[^$$\\*|]/\\\\&/g'`
+am__nobase_strip = \
+  for p in $$list; do echo "$$p"; done | sed -e "s|$$srcdirstrip/||"
+am__nobase_list = $(am__nobase_strip_setup); \
+  for p in $$list; do echo "$$p $$p"; done | \
+  sed "s| $$srcdirstrip/| |;"' / .*\//!s/ .*/ ./; s,\( .*\)/[^/]*$$,\1,' | \
+  $(AWK) 'BEGIN { files["."] = "" } { files[$$2] = files[$$2] " " $$1; \
+    if (++n[$$2] == $(am__install_max)) \
+      { print $$2, files[$$2]; n[$$2] = 0; files[$$2] = "" } } \
+    END { for (dir in files) print dir, files[dir] }'
+am__base_list = \
+  sed '$$!N;$$!N;$$!N;$$!N;$$!N;$$!N;$$!N;s/\n/ /g' | \
+  sed '$$!N;$$!N;$$!N;$$!N;s/\n/ /g'
+am__uninstall_files_from_dir = { \
+  test -z "$$files" \
+    || { test ! -d "$$dir" && test ! -f "$$dir" && test ! -r "$$dir"; } \
+    || { echo " ( cd '$$dir' && rm -f" $$files ")"; \
+         $(am__cd) "$$dir" && rm -f $$files; }; \
+  }
+am__installdirs = "$(DESTDIR)$(libdir)" "$(DESTDIR)$(pkgconfigdir)" \
+	"$(DESTDIR)$(includedir)"
+LTLIBRARIES = $(lib_LTLIBRARIES)
+libcuba_la_DEPENDENCIES = common/libcommon.la cuhre/libcuhre.la \
+	divonne/libdivonne.la suave/libsuave.la vegas/libvegas.la
+am_libcuba_la_OBJECTS =
+libcuba_la_OBJECTS = $(am_libcuba_la_OBJECTS)
+AM_V_lt = $(am__v_lt_@AM_V@)
+am__v_lt_ = $(am__v_lt_@AM_DEFAULT_V@)
+am__v_lt_0 = --silent
+am__v_lt_1 = 
+libcuba_la_LINK = $(LIBTOOL) $(AM_V_lt) --tag=CC $(AM_LIBTOOLFLAGS) \
+	$(LIBTOOLFLAGS) --mode=link $(CCLD) $(AM_CFLAGS) $(CFLAGS) \
+	$(libcuba_la_LDFLAGS) $(LDFLAGS) -o $@
+AM_V_P = $(am__v_P_@AM_V@)
+am__v_P_ = $(am__v_P_@AM_DEFAULT_V@)
+am__v_P_0 = false
+am__v_P_1 = :
+AM_V_GEN = $(am__v_GEN_@AM_V@)
+am__v_GEN_ = $(am__v_GEN_@AM_DEFAULT_V@)
+am__v_GEN_0 = @echo "  GEN     " $@;
+am__v_GEN_1 = 
+AM_V_at = $(am__v_at_@AM_V@)
+am__v_at_ = $(am__v_at_@AM_DEFAULT_V@)
+am__v_at_0 = @
+am__v_at_1 = 
+DEFAULT_INCLUDES = -I.@am__isrc@ -I$(top_builddir)
+COMPILE = $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) \
+	$(CPPFLAGS) $(AM_CFLAGS) $(CFLAGS)
+LTCOMPILE = $(LIBTOOL) $(AM_V_lt) --tag=CC $(AM_LIBTOOLFLAGS) \
+	$(LIBTOOLFLAGS) --mode=compile $(CC) $(DEFS) \
+	$(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) \
+	$(AM_CFLAGS) $(CFLAGS)
+AM_V_CC = $(am__v_CC_@AM_V@)
+am__v_CC_ = $(am__v_CC_@AM_DEFAULT_V@)
+am__v_CC_0 = @echo "  CC      " $@;
+am__v_CC_1 = 
+CCLD = $(CC)
+LINK = $(LIBTOOL) $(AM_V_lt) --tag=CC $(AM_LIBTOOLFLAGS) \
+	$(LIBTOOLFLAGS) --mode=link $(CCLD) $(AM_CFLAGS) $(CFLAGS) \
+	$(AM_LDFLAGS) $(LDFLAGS) -o $@
+AM_V_CCLD = $(am__v_CCLD_@AM_V@)
+am__v_CCLD_ = $(am__v_CCLD_@AM_DEFAULT_V@)
+am__v_CCLD_0 = @echo "  CCLD    " $@;
+am__v_CCLD_1 = 
+SOURCES = $(libcuba_la_SOURCES)
+DIST_SOURCES = $(libcuba_la_SOURCES)
+RECURSIVE_TARGETS = all-recursive check-recursive cscopelist-recursive \
+	ctags-recursive dvi-recursive html-recursive info-recursive \
+	install-data-recursive install-dvi-recursive \
+	install-exec-recursive install-html-recursive \
+	install-info-recursive install-pdf-recursive \
+	install-ps-recursive install-recursive installcheck-recursive \
+	installdirs-recursive pdf-recursive ps-recursive \
+	tags-recursive uninstall-recursive
+am__can_run_installinfo = \
+  case $$AM_UPDATE_INFO_DIR in \
+    n|no|NO) false;; \
+    *) (install-info --version) >/dev/null 2>&1;; \
+  esac
+DATA = $(pkgconfig_DATA)
+HEADERS = $(include_HEADERS)
+RECURSIVE_CLEAN_TARGETS = mostlyclean-recursive clean-recursive	\
+  distclean-recursive maintainer-clean-recursive
+am__recursive_targets = \
+  $(RECURSIVE_TARGETS) \
+  $(RECURSIVE_CLEAN_TARGETS) \
+  $(am__extra_recursive_targets)
+AM_RECURSIVE_TARGETS = $(am__recursive_targets:-recursive=) TAGS CTAGS \
+	distdir distdir-am
+am__tagged_files = $(HEADERS) $(SOURCES) $(TAGS_FILES) $(LISP)
+# Read a list of newline-separated strings from the standard input,
+# and print each of them once, without duplicates.  Input order is
+# *not* preserved.
+am__uniquify_input = $(AWK) '\
+  BEGIN { nonempty = 0; } \
+  { items[$$0] = 1; nonempty = 1; } \
+  END { if (nonempty) { for (i in items) print i; }; } \
+'
+# Make sure the list of sources is unique.  This is necessary because,
+# e.g., the same source file might be shared among _SOURCES variables
+# for different programs/libraries.
+am__define_uniq_tagged_files = \
+  list='$(am__tagged_files)'; \
+  unique=`for i in $$list; do \
+    if test -f "$$i"; then echo $$i; else echo $(srcdir)/$$i; fi; \
+  done | $(am__uniquify_input)`
+ETAGS = etags
+CTAGS = ctags
+DIST_SUBDIRS = $(SUBDIRS)
+am__DIST_COMMON = $(srcdir)/Makefile.in $(srcdir)/cuba.pc.in
+DISTFILES = $(DIST_COMMON) $(DIST_SOURCES) $(TEXINFOS) $(EXTRA_DIST)
+am__relativize = \
+  dir0=`pwd`; \
+  sed_first='s,^\([^/]*\)/.*$$,\1,'; \
+  sed_rest='s,^[^/]*/*,,'; \
+  sed_last='s,^.*/\([^/]*\)$$,\1,'; \
+  sed_butlast='s,/*[^/]*$$,,'; \
+  while test -n "$$dir1"; do \
+    first=`echo "$$dir1" | sed -e "$$sed_first"`; \
+    if test "$$first" != "."; then \
+      if test "$$first" = ".."; then \
+        dir2=`echo "$$dir0" | sed -e "$$sed_last"`/"$$dir2"; \
+        dir0=`echo "$$dir0" | sed -e "$$sed_butlast"`; \
+      else \
+        first2=`echo "$$dir2" | sed -e "$$sed_first"`; \
+        if test "$$first2" = "$$first"; then \
+          dir2=`echo "$$dir2" | sed -e "$$sed_rest"`; \
+        else \
+          dir2="../$$dir2"; \
+        fi; \
+        dir0="$$dir0"/"$$first"; \
+      fi; \
+    fi; \
+    dir1=`echo "$$dir1" | sed -e "$$sed_rest"`; \
+  done; \
+  reldir="$$dir2"
+ACLOCAL = @ACLOCAL@
+ALLOCA = @ALLOCA@
+AMTAR = @AMTAR@
+AM_DEFAULT_VERBOSITY = @AM_DEFAULT_VERBOSITY@
+AR = @AR@
+AUTOCONF = @AUTOCONF@
+AUTOHEADER = @AUTOHEADER@
+AUTOMAKE = @AUTOMAKE@
+AWK = @AWK@
+BMWTOOLS_CFLAGS = @BMWTOOLS_CFLAGS@
+BMWTOOLS_LIBS = @BMWTOOLS_LIBS@
+BNMRLIBS_CFLAGS = @BNMRLIBS_CFLAGS@
+BNMRLIBS_LIBS = @BNMRLIBS_LIBS@
+BOOST_CFLAGS = @BOOST_CFLAGS@
+BOOST_INCLUDE = @BOOST_INCLUDE@
+BOOST_LIBS = @BOOST_LIBS@
+CC = @CC@
+CCDEPMODE = @CCDEPMODE@
+CFLAGS = @CFLAGS@
+CPP = @CPP@
+CPPFLAGS = @CPPFLAGS@
+CUBA_API_VERSION = @CUBA_API_VERSION@
+CUBA_CFLAGS = @CUBA_CFLAGS@
+CUBA_LIBRARY_NAME = @CUBA_LIBRARY_NAME@
+CUBA_LIBRARY_VERSION = @CUBA_LIBRARY_VERSION@
+CUBA_LIBS = @CUBA_LIBS@
+CUBA_PREFIX = @CUBA_PREFIX@
+CUBA_RELEASE = @CUBA_RELEASE@
+CUBA_VERSION = @CUBA_VERSION@
+CXX = @CXX@
+CXXCPP = @CXXCPP@
+CXXDEPMODE = @CXXDEPMODE@
+CXXFLAGS = @CXXFLAGS@
+CYGPATH_W = @CYGPATH_W@
+DEFS = @DEFS@
+DEPDIR = @DEPDIR@
+DLLTOOL = @DLLTOOL@
+DOCDIR = @DOCDIR@
+DSYMUTIL = @DSYMUTIL@
+DUMPBIN = @DUMPBIN@
+ECHO_C = @ECHO_C@
+ECHO_N = @ECHO_N@
+ECHO_T = @ECHO_T@
+EGREP = @EGREP@
+EXEEXT = @EXEEXT@
+FFTW3_CFLAGS = @FFTW3_CFLAGS@
+FFTW3_LIBS = @FFTW3_LIBS@
+FFTW3_PREFIX = @FFTW3_PREFIX@
+FGREP = @FGREP@
+FITPOFB_CFLAGS = @FITPOFB_CFLAGS@
+FITPOFB_LIBS = @FITPOFB_LIBS@
+GREP = @GREP@
+GSL_CFLAGS = @GSL_CFLAGS@
+GSL_LIBS = @GSL_LIBS@
+GSL_PREFIX = @GSL_PREFIX@
+INSTALL = @INSTALL@
+INSTALL_DATA = @INSTALL_DATA@
+INSTALL_PROGRAM = @INSTALL_PROGRAM@
+INSTALL_SCRIPT = @INSTALL_SCRIPT@
+INSTALL_STRIP_PROGRAM = @INSTALL_STRIP_PROGRAM@
+LD = @LD@
+LDFLAGS = @LDFLAGS@
+LEM_API_VERSION = @LEM_API_VERSION@
+LEM_CFLAGS = @LEM_CFLAGS@
+LEM_LIBRARY_NAME = @LEM_LIBRARY_NAME@
+LEM_LIBRARY_VERSION = @LEM_LIBRARY_VERSION@
+LEM_LIBS = @LEM_LIBS@
+LEM_RELEASE = @LEM_RELEASE@
+LEM_VERSION = @LEM_VERSION@
+LIBOBJS = @LIBOBJS@
+LIBS = @LIBS@
+LIBTOOL = @LIBTOOL@
+LIBXML2_CFLAGS = @LIBXML2_CFLAGS@
+LIBXML2_LIBS = @LIBXML2_LIBS@
+LIBXML2_PREFIX = @LIBXML2_PREFIX@
+LIPO = @LIPO@
+LN_S = @LN_S@
+LOCAL_BIN_CXXFLAGS = @LOCAL_BIN_CXXFLAGS@
+LOCAL_BIN_LDFLAGS = @LOCAL_BIN_LDFLAGS@
+LOCAL_CUBA_LIB_CFLAGS = @LOCAL_CUBA_LIB_CFLAGS@
+LOCAL_LIB_CXXFLAGS = @LOCAL_LIB_CXXFLAGS@
+LOCAL_LIB_LDFLAGS = @LOCAL_LIB_LDFLAGS@
+LOCAL_MUD_LIB_CFLAGS = @LOCAL_MUD_LIB_CFLAGS@
+LOCAL_PNEXUS_LIB_CXXFLAGS = @LOCAL_PNEXUS_LIB_CXXFLAGS@
+LOCAL_PSIBIN_LIB_CXXFLAGS = @LOCAL_PSIBIN_LIB_CXXFLAGS@
+LTLIBOBJS = @LTLIBOBJS@
+LT_SYS_LIBRARY_PATH = @LT_SYS_LIBRARY_PATH@
+MAKEINFO = @MAKEINFO@
+MANIFEST_TOOL = @MANIFEST_TOOL@
+MKDIR_P = @MKDIR_P@
+MUD_API_VERSION = @MUD_API_VERSION@
+MUD_CFLAGS = @MUD_CFLAGS@
+MUD_LIBRARY_NAME = @MUD_LIBRARY_NAME@
+MUD_LIBRARY_VERSION = @MUD_LIBRARY_VERSION@
+MUD_LIBS = @MUD_LIBS@
+MUD_RELEASE = @MUD_RELEASE@
+MUD_VERSION = @MUD_VERSION@
+MUSR_API_VERSION = @MUSR_API_VERSION@
+MUSR_LIBRARY_NAME = @MUSR_LIBRARY_NAME@
+MUSR_LIBRARY_VERSION = @MUSR_LIBRARY_VERSION@
+MUSR_RELEASE = @MUSR_RELEASE@
+MUSR_ROOT_API_VERSION = @MUSR_ROOT_API_VERSION@
+MUSR_ROOT_CFLAGS = @MUSR_ROOT_CFLAGS@
+MUSR_ROOT_LIBRARY_NAME = @MUSR_ROOT_LIBRARY_NAME@
+MUSR_ROOT_LIBRARY_VERSION = @MUSR_ROOT_LIBRARY_VERSION@
+MUSR_ROOT_LIBS = @MUSR_ROOT_LIBS@
+MUSR_ROOT_RELEASE = @MUSR_ROOT_RELEASE@
+MUSR_ROOT_VERSION = @MUSR_ROOT_VERSION@
+MUSR_VERSION = @MUSR_VERSION@
+NEXUS_CFLAGS = @NEXUS_CFLAGS@
+NEXUS_LIBS = @NEXUS_LIBS@
+NEXUS_PREFIX = @NEXUS_PREFIX@
+NM = @NM@
+NMEDIT = @NMEDIT@
+OBJDUMP = @OBJDUMP@
+OBJEXT = @OBJEXT@
+OTOOL = @OTOOL@
+OTOOL64 = @OTOOL64@
+PACKAGE = @PACKAGE@
+PACKAGE_BUGREPORT = @PACKAGE_BUGREPORT@
+PACKAGE_NAME = @PACKAGE_NAME@
+PACKAGE_STRING = @PACKAGE_STRING@
+PACKAGE_TARNAME = @PACKAGE_TARNAME@
+PACKAGE_URL = @PACKAGE_URL@
+PACKAGE_VERSION = @PACKAGE_VERSION@
+PATH_SEPARATOR = @PATH_SEPARATOR@
+PKG_CONFIG = @PKG_CONFIG@
+PKG_CONFIG_LIBDIR = @PKG_CONFIG_LIBDIR@
+PKG_CONFIG_PATH = @PKG_CONFIG_PATH@
+PLUGIN_API_VERSION = @PLUGIN_API_VERSION@
+PLUGIN_LIBRARY_VERSION = @PLUGIN_LIBRARY_VERSION@
+PLUGIN_MAJOR_VERSION = @PLUGIN_MAJOR_VERSION@
+PLUGIN_MINOR_VERSION = @PLUGIN_MINOR_VERSION@
+PLUGIN_RELEASE = @PLUGIN_RELEASE@
+PLUGIN_VERSION = @PLUGIN_VERSION@
+PMUSR_CFLAGS = @PMUSR_CFLAGS@
+PMUSR_LIBS = @PMUSR_LIBS@
+PNEXUS_API_VERSION = @PNEXUS_API_VERSION@
+PNEXUS_CXXFLAGS = @PNEXUS_CXXFLAGS@
+PNEXUS_LIBRARY_NAME = @PNEXUS_LIBRARY_NAME@
+PNEXUS_LIBRARY_VERSION = @PNEXUS_LIBRARY_VERSION@
+PNEXUS_LIBS = @PNEXUS_LIBS@
+PNEXUS_RELEASE = @PNEXUS_RELEASE@
+PNEXUS_VERSION = @PNEXUS_VERSION@
+PSIBIN_API_VERSION = @PSIBIN_API_VERSION@
+PSIBIN_CFLAGS = @PSIBIN_CFLAGS@
+PSIBIN_LIBRARY_NAME = @PSIBIN_LIBRARY_NAME@
+PSIBIN_LIBRARY_VERSION = @PSIBIN_LIBRARY_VERSION@
+PSIBIN_LIBS = @PSIBIN_LIBS@
+PSIBIN_RELEASE = @PSIBIN_RELEASE@
+PSIBIN_VERSION = @PSIBIN_VERSION@
+QT3MT_CFLAGS = @QT3MT_CFLAGS@
+QT3MT_LIBS = @QT3MT_LIBS@
+QT3_CFLAGS = @QT3_CFLAGS@
+QT3_LIBS = @QT3_LIBS@
+QT4_CFLAGS = @QT4_CFLAGS@
+QT4_LIBS = @QT4_LIBS@
+QT5_CFLAGS = @QT5_CFLAGS@
+QT5_LIBS = @QT5_LIBS@
+RANLIB = @RANLIB@
+ROOTAUXCFLAGS = @ROOTAUXCFLAGS@
+ROOTAUXLIBS = @ROOTAUXLIBS@
+ROOTCFLAGS = @ROOTCFLAGS@
+ROOTCLING = @ROOTCLING@
+ROOTCONF = @ROOTCONF@
+ROOTETCDIR = @ROOTETCDIR@
+ROOTEXEC = @ROOTEXEC@
+ROOTGLIBS = @ROOTGLIBS@
+ROOTINCDIR = @ROOTINCDIR@
+ROOTLIBDIR = @ROOTLIBDIR@
+ROOTLIBS = @ROOTLIBS@
+ROOTRPATH = @ROOTRPATH@
+ROOTSOVERSION = @ROOTSOVERSION@
+ROOTVERSION = @ROOTVERSION@
+ROOT_CFLAGS = @ROOT_CFLAGS@
+ROOT_LIBS = @ROOT_LIBS@
+SED = @SED@
+SET_MAKE = @SET_MAKE@
+SHELL = @SHELL@
+STRIP = @STRIP@
+USERFCN_LIBRARY_NAME = @USERFCN_LIBRARY_NAME@
+USERFCN_LIBS = @USERFCN_LIBS@
+VERSION = @VERSION@
+abs_builddir = @abs_builddir@
+abs_srcdir = @abs_srcdir@
+abs_top_builddir = @abs_top_builddir@
+abs_top_srcdir = @abs_top_srcdir@
+ac_ct_AR = @ac_ct_AR@
+ac_ct_CC = @ac_ct_CC@
+ac_ct_CXX = @ac_ct_CXX@
+ac_ct_DUMPBIN = @ac_ct_DUMPBIN@
+am__include = @am__include@
+am__leading_dot = @am__leading_dot@
+am__quote = @am__quote@
+am__tar = @am__tar@
+am__untar = @am__untar@
+bindir = @bindir@
+build = @build@
+build_alias = @build_alias@
+build_cpu = @build_cpu@
+build_os = @build_os@
+build_vendor = @build_vendor@
+builddir = @builddir@
+datadir = @datadir@
+datarootdir = @datarootdir@
+docdir = @docdir@
+dvidir = @dvidir@
+exec_prefix = @exec_prefix@
+host = @host@
+host_alias = @host_alias@
+host_cpu = @host_cpu@
+host_os = @host_os@
+host_vendor = @host_vendor@
+htmldir = @htmldir@
+includedir = @includedir@
+infodir = @infodir@
+install_sh = @install_sh@
+libdir = @libdir@
+libexecdir = @libexecdir@
+localedir = @localedir@
+localstatedir = @localstatedir@
+mandir = @mandir@
+mkdir_p = @mkdir_p@
+oldincludedir = @oldincludedir@
+pdfdir = @pdfdir@
+prefix = @prefix@
+program_transform_name = @program_transform_name@
+psdir = @psdir@
+sbindir = @sbindir@
+sharedstatedir = @sharedstatedir@
+srcdir = @srcdir@
+sysconfdir = @sysconfdir@
+target_alias = @target_alias@
+top_build_prefix = @top_build_prefix@
+top_builddir = @top_builddir@
+top_srcdir = @top_srcdir@
+SUBDIRS = cuhre divonne suave vegas common
+include_HEADERS = cuba.h
+AM_LDFLAGS = $(LOCAL_LIB_LDFLAGS)
+CLEANFILES = common/*~ cuhre/*~ divonne/*~ suave/*~ vegas/*~ *~ core
+lib_LTLIBRARIES = libcuba.la
+libcuba_la_SOURCES = 
+libcuba_la_LIBADD = common/libcommon.la cuhre/libcuhre.la divonne/libdivonne.la suave/libsuave.la vegas/libvegas.la -lm
+libcuba_la_LDFLAGS = -version-info $(CUBA_LIBRARY_VERSION) -release $(CUBA_RELEASE) $(AM_LDFLAGS)
+pkgconfigdir = $(libdir)/pkgconfig
+pkgconfig_DATA = cuba.pc
+all: all-recursive
+
+.SUFFIXES:
+$(srcdir)/Makefile.in:  $(srcdir)/Makefile.am  $(am__configure_deps)
+	@for dep in $?; do \
+	  case '$(am__configure_deps)' in \
+	    *$$dep*) \
+	      ( cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh ) \
+	        && { if test -f $@; then exit 0; else break; fi; }; \
+	      exit 1;; \
+	  esac; \
+	done; \
+	echo ' cd $(top_srcdir) && $(AUTOMAKE) --gnu src/external/libCuba/src/Makefile'; \
+	$(am__cd) $(top_srcdir) && \
+	  $(AUTOMAKE) --gnu src/external/libCuba/src/Makefile
+Makefile: $(srcdir)/Makefile.in $(top_builddir)/config.status
+	@case '$?' in \
+	  *config.status*) \
+	    cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh;; \
+	  *) \
+	    echo ' cd $(top_builddir) && $(SHELL) ./config.status $(subdir)/$@ $(am__maybe_remake_depfiles)'; \
+	    cd $(top_builddir) && $(SHELL) ./config.status $(subdir)/$@ $(am__maybe_remake_depfiles);; \
+	esac;
+
+$(top_builddir)/config.status: $(top_srcdir)/configure $(CONFIG_STATUS_DEPENDENCIES)
+	cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh
+
+$(top_srcdir)/configure:  $(am__configure_deps)
+	cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh
+$(ACLOCAL_M4):  $(am__aclocal_m4_deps)
+	cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh
+$(am__aclocal_m4_deps):
+cuba.pc: $(top_builddir)/config.status $(srcdir)/cuba.pc.in
+	cd $(top_builddir) && $(SHELL) ./config.status $(subdir)/$@
+
+install-libLTLIBRARIES: $(lib_LTLIBRARIES)
+	@$(NORMAL_INSTALL)
+	@list='$(lib_LTLIBRARIES)'; test -n "$(libdir)" || list=; \
+	list2=; for p in $$list; do \
+	  if test -f $$p; then \
+	    list2="$$list2 $$p"; \
+	  else :; fi; \
+	done; \
+	test -z "$$list2" || { \
+	  echo " $(MKDIR_P) '$(DESTDIR)$(libdir)'"; \
+	  $(MKDIR_P) "$(DESTDIR)$(libdir)" || exit 1; \
+	  echo " $(LIBTOOL) $(AM_LIBTOOLFLAGS) $(LIBTOOLFLAGS) --mode=install $(INSTALL) $(INSTALL_STRIP_FLAG) $$list2 '$(DESTDIR)$(libdir)'"; \
+	  $(LIBTOOL) $(AM_LIBTOOLFLAGS) $(LIBTOOLFLAGS) --mode=install $(INSTALL) $(INSTALL_STRIP_FLAG) $$list2 "$(DESTDIR)$(libdir)"; \
+	}
+
+uninstall-libLTLIBRARIES:
+	@$(NORMAL_UNINSTALL)
+	@list='$(lib_LTLIBRARIES)'; test -n "$(libdir)" || list=; \
+	for p in $$list; do \
+	  $(am__strip_dir) \
+	  echo " $(LIBTOOL) $(AM_LIBTOOLFLAGS) $(LIBTOOLFLAGS) --mode=uninstall rm -f '$(DESTDIR)$(libdir)/$$f'"; \
+	  $(LIBTOOL) $(AM_LIBTOOLFLAGS) $(LIBTOOLFLAGS) --mode=uninstall rm -f "$(DESTDIR)$(libdir)/$$f"; \
+	done
+
+clean-libLTLIBRARIES:
+	-test -z "$(lib_LTLIBRARIES)" || rm -f $(lib_LTLIBRARIES)
+	@list='$(lib_LTLIBRARIES)'; \
+	locs=`for p in $$list; do echo $$p; done | \
+	      sed 's|^[^/]*$$|.|; s|/[^/]*$$||; s|$$|/so_locations|' | \
+	      sort -u`; \
+	test -z "$$locs" || { \
+	  echo rm -f $${locs}; \
+	  rm -f $${locs}; \
+	}
+
+libcuba.la: $(libcuba_la_OBJECTS) $(libcuba_la_DEPENDENCIES) $(EXTRA_libcuba_la_DEPENDENCIES) 
+	$(AM_V_CCLD)$(libcuba_la_LINK) -rpath $(libdir) $(libcuba_la_OBJECTS) $(libcuba_la_LIBADD) $(LIBS)
+
+mostlyclean-compile:
+	-rm -f *.$(OBJEXT)
+
+distclean-compile:
+	-rm -f *.tab.c
+
+mostlyclean-libtool:
+	-rm -f *.lo
+
+clean-libtool:
+	-rm -rf .libs _libs
+install-pkgconfigDATA: $(pkgconfig_DATA)
+	@$(NORMAL_INSTALL)
+	@list='$(pkgconfig_DATA)'; test -n "$(pkgconfigdir)" || list=; \
+	if test -n "$$list"; then \
+	  echo " $(MKDIR_P) '$(DESTDIR)$(pkgconfigdir)'"; \
+	  $(MKDIR_P) "$(DESTDIR)$(pkgconfigdir)" || exit 1; \
+	fi; \
+	for p in $$list; do \
+	  if test -f "$$p"; then d=; else d="$(srcdir)/"; fi; \
+	  echo "$$d$$p"; \
+	done | $(am__base_list) | \
+	while read files; do \
+	  echo " $(INSTALL_DATA) $$files '$(DESTDIR)$(pkgconfigdir)'"; \
+	  $(INSTALL_DATA) $$files "$(DESTDIR)$(pkgconfigdir)" || exit $$?; \
+	done
+
+uninstall-pkgconfigDATA:
+	@$(NORMAL_UNINSTALL)
+	@list='$(pkgconfig_DATA)'; test -n "$(pkgconfigdir)" || list=; \
+	files=`for p in $$list; do echo $$p; done | sed -e 's|^.*/||'`; \
+	dir='$(DESTDIR)$(pkgconfigdir)'; $(am__uninstall_files_from_dir)
+install-includeHEADERS: $(include_HEADERS)
+	@$(NORMAL_INSTALL)
+	@list='$(include_HEADERS)'; test -n "$(includedir)" || list=; \
+	if test -n "$$list"; then \
+	  echo " $(MKDIR_P) '$(DESTDIR)$(includedir)'"; \
+	  $(MKDIR_P) "$(DESTDIR)$(includedir)" || exit 1; \
+	fi; \
+	for p in $$list; do \
+	  if test -f "$$p"; then d=; else d="$(srcdir)/"; fi; \
+	  echo "$$d$$p"; \
+	done | $(am__base_list) | \
+	while read files; do \
+	  echo " $(INSTALL_HEADER) $$files '$(DESTDIR)$(includedir)'"; \
+	  $(INSTALL_HEADER) $$files "$(DESTDIR)$(includedir)" || exit $$?; \
+	done
+
+uninstall-includeHEADERS:
+	@$(NORMAL_UNINSTALL)
+	@list='$(include_HEADERS)'; test -n "$(includedir)" || list=; \
+	files=`for p in $$list; do echo $$p; done | sed -e 's|^.*/||'`; \
+	dir='$(DESTDIR)$(includedir)'; $(am__uninstall_files_from_dir)
+
+# This directory's subdirectories are mostly independent; you can cd
+# into them and run 'make' without going through this Makefile.
+# To change the values of 'make' variables: instead of editing Makefiles,
+# (1) if the variable is set in 'config.status', edit 'config.status'
+#     (which will cause the Makefiles to be regenerated when you run 'make');
+# (2) otherwise, pass the desired values on the 'make' command line.
+$(am__recursive_targets):
+	@fail=; \
+	if $(am__make_keepgoing); then \
+	  failcom='fail=yes'; \
+	else \
+	  failcom='exit 1'; \
+	fi; \
+	dot_seen=no; \
+	target=`echo $@ | sed s/-recursive//`; \
+	case "$@" in \
+	  distclean-* | maintainer-clean-*) list='$(DIST_SUBDIRS)' ;; \
+	  *) list='$(SUBDIRS)' ;; \
+	esac; \
+	for subdir in $$list; do \
+	  echo "Making $$target in $$subdir"; \
+	  if test "$$subdir" = "."; then \
+	    dot_seen=yes; \
+	    local_target="$$target-am"; \
+	  else \
+	    local_target="$$target"; \
+	  fi; \
+	  ($(am__cd) $$subdir && $(MAKE) $(AM_MAKEFLAGS) $$local_target) \
+	  || eval $$failcom; \
+	done; \
+	if test "$$dot_seen" = "no"; then \
+	  $(MAKE) $(AM_MAKEFLAGS) "$$target-am" || exit 1; \
+	fi; test -z "$$fail"
+
+ID: $(am__tagged_files)
+	$(am__define_uniq_tagged_files); mkid -fID $$unique
+tags: tags-recursive
+TAGS: tags
+
+tags-am: $(TAGS_DEPENDENCIES) $(am__tagged_files)
+	set x; \
+	here=`pwd`; \
+	if ($(ETAGS) --etags-include --version) >/dev/null 2>&1; then \
+	  include_option=--etags-include; \
+	  empty_fix=.; \
+	else \
+	  include_option=--include; \
+	  empty_fix=; \
+	fi; \
+	list='$(SUBDIRS)'; for subdir in $$list; do \
+	  if test "$$subdir" = .; then :; else \
+	    test ! -f $$subdir/TAGS || \
+	      set "$$@" "$$include_option=$$here/$$subdir/TAGS"; \
+	  fi; \
+	done; \
+	$(am__define_uniq_tagged_files); \
+	shift; \
+	if test -z "$(ETAGS_ARGS)$$*$$unique"; then :; else \
+	  test -n "$$unique" || unique=$$empty_fix; \
+	  if test $$# -gt 0; then \
+	    $(ETAGS) $(ETAGSFLAGS) $(AM_ETAGSFLAGS) $(ETAGS_ARGS) \
+	      "$$@" $$unique; \
+	  else \
+	    $(ETAGS) $(ETAGSFLAGS) $(AM_ETAGSFLAGS) $(ETAGS_ARGS) \
+	      $$unique; \
+	  fi; \
+	fi
+ctags: ctags-recursive
+
+CTAGS: ctags
+ctags-am: $(TAGS_DEPENDENCIES) $(am__tagged_files)
+	$(am__define_uniq_tagged_files); \
+	test -z "$(CTAGS_ARGS)$$unique" \
+	  || $(CTAGS) $(CTAGSFLAGS) $(AM_CTAGSFLAGS) $(CTAGS_ARGS) \
+	     $$unique
+
+GTAGS:
+	here=`$(am__cd) $(top_builddir) && pwd` \
+	  && $(am__cd) $(top_srcdir) \
+	  && gtags -i $(GTAGS_ARGS) "$$here"
+cscopelist: cscopelist-recursive
+
+cscopelist-am: $(am__tagged_files)
+	list='$(am__tagged_files)'; \
+	case "$(srcdir)" in \
+	  [\\/]* | ?:[\\/]*) sdir="$(srcdir)" ;; \
+	  *) sdir=$(subdir)/$(srcdir) ;; \
+	esac; \
+	for i in $$list; do \
+	  if test -f "$$i"; then \
+	    echo "$(subdir)/$$i"; \
+	  else \
+	    echo "$$sdir/$$i"; \
+	  fi; \
+	done >> $(top_builddir)/cscope.files
+
+distclean-tags:
+	-rm -f TAGS ID GTAGS GRTAGS GSYMS GPATH tags
+
+distdir: $(BUILT_SOURCES)
+	$(MAKE) $(AM_MAKEFLAGS) distdir-am
+
+distdir-am: $(DISTFILES)
+	@srcdirstrip=`echo "$(srcdir)" | sed 's/[].[^$$\\*]/\\\\&/g'`; \
+	topsrcdirstrip=`echo "$(top_srcdir)" | sed 's/[].[^$$\\*]/\\\\&/g'`; \
+	list='$(DISTFILES)'; \
+	  dist_files=`for file in $$list; do echo $$file; done | \
+	  sed -e "s|^$$srcdirstrip/||;t" \
+	      -e "s|^$$topsrcdirstrip/|$(top_builddir)/|;t"`; \
+	case $$dist_files in \
+	  */*) $(MKDIR_P) `echo "$$dist_files" | \
+			   sed '/\//!d;s|^|$(distdir)/|;s,/[^/]*$$,,' | \
+			   sort -u` ;; \
+	esac; \
+	for file in $$dist_files; do \
+	  if test -f $$file || test -d $$file; then d=.; else d=$(srcdir); fi; \
+	  if test -d $$d/$$file; then \
+	    dir=`echo "/$$file" | sed -e 's,/[^/]*$$,,'`; \
+	    if test -d "$(distdir)/$$file"; then \
+	      find "$(distdir)/$$file" -type d ! -perm -700 -exec chmod u+rwx {} \;; \
+	    fi; \
+	    if test -d $(srcdir)/$$file && test $$d != $(srcdir); then \
+	      cp -fpR $(srcdir)/$$file "$(distdir)$$dir" || exit 1; \
+	      find "$(distdir)/$$file" -type d ! -perm -700 -exec chmod u+rwx {} \;; \
+	    fi; \
+	    cp -fpR $$d/$$file "$(distdir)$$dir" || exit 1; \
+	  else \
+	    test -f "$(distdir)/$$file" \
+	    || cp -p $$d/$$file "$(distdir)/$$file" \
+	    || exit 1; \
+	  fi; \
+	done
+	@list='$(DIST_SUBDIRS)'; for subdir in $$list; do \
+	  if test "$$subdir" = .; then :; else \
+	    $(am__make_dryrun) \
+	      || test -d "$(distdir)/$$subdir" \
+	      || $(MKDIR_P) "$(distdir)/$$subdir" \
+	      || exit 1; \
+	    dir1=$$subdir; dir2="$(distdir)/$$subdir"; \
+	    $(am__relativize); \
+	    new_distdir=$$reldir; \
+	    dir1=$$subdir; dir2="$(top_distdir)"; \
+	    $(am__relativize); \
+	    new_top_distdir=$$reldir; \
+	    echo " (cd $$subdir && $(MAKE) $(AM_MAKEFLAGS) top_distdir="$$new_top_distdir" distdir="$$new_distdir" \\"; \
+	    echo "     am__remove_distdir=: am__skip_length_check=: am__skip_mode_fix=: distdir)"; \
+	    ($(am__cd) $$subdir && \
+	      $(MAKE) $(AM_MAKEFLAGS) \
+	        top_distdir="$$new_top_distdir" \
+	        distdir="$$new_distdir" \
+		am__remove_distdir=: \
+		am__skip_length_check=: \
+		am__skip_mode_fix=: \
+	        distdir) \
+	      || exit 1; \
+	  fi; \
+	done
+check-am: all-am
+check: check-recursive
+all-am: Makefile $(LTLIBRARIES) $(DATA) $(HEADERS)
+installdirs: installdirs-recursive
+installdirs-am:
+	for dir in "$(DESTDIR)$(libdir)" "$(DESTDIR)$(pkgconfigdir)" "$(DESTDIR)$(includedir)"; do \
+	  test -z "$$dir" || $(MKDIR_P) "$$dir"; \
+	done
+install: install-recursive
+install-exec: install-exec-recursive
+install-data: install-data-recursive
+uninstall: uninstall-recursive
+
+install-am: all-am
+	@$(MAKE) $(AM_MAKEFLAGS) install-exec-am install-data-am
+
+installcheck: installcheck-recursive
+install-strip:
+	if test -z '$(STRIP)'; then \
+	  $(MAKE) $(AM_MAKEFLAGS) INSTALL_PROGRAM="$(INSTALL_STRIP_PROGRAM)" \
+	    install_sh_PROGRAM="$(INSTALL_STRIP_PROGRAM)" INSTALL_STRIP_FLAG=-s \
+	      install; \
+	else \
+	  $(MAKE) $(AM_MAKEFLAGS) INSTALL_PROGRAM="$(INSTALL_STRIP_PROGRAM)" \
+	    install_sh_PROGRAM="$(INSTALL_STRIP_PROGRAM)" INSTALL_STRIP_FLAG=-s \
+	    "INSTALL_PROGRAM_ENV=STRIPPROG='$(STRIP)'" install; \
+	fi
+mostlyclean-generic:
+
+clean-generic:
+	-test -z "$(CLEANFILES)" || rm -f $(CLEANFILES)
+
+distclean-generic:
+	-test -z "$(CONFIG_CLEAN_FILES)" || rm -f $(CONFIG_CLEAN_FILES)
+	-test . = "$(srcdir)" || test -z "$(CONFIG_CLEAN_VPATH_FILES)" || rm -f $(CONFIG_CLEAN_VPATH_FILES)
+
+maintainer-clean-generic:
+	@echo "This command is intended for maintainers to use"
+	@echo "it deletes files that may require special tools to rebuild."
+clean: clean-recursive
+
+clean-am: clean-generic clean-libLTLIBRARIES clean-libtool \
+	mostlyclean-am
+
+distclean: distclean-recursive
+	-rm -f Makefile
+distclean-am: clean-am distclean-compile distclean-generic \
+	distclean-tags
+
+dvi: dvi-recursive
+
+dvi-am:
+
+html: html-recursive
+
+html-am:
+
+info: info-recursive
+
+info-am:
+
+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:

src/external/libCuba/src/suave/Suave.lo

@@ -0,0 +1,12 @@
+# 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
+

src/external/libFitPofB/include/TLondon1DLinkDef.h

@@ -27,7 +27,7 @@
  ***************************************************************************/
 
 // root dictionary stuff --------------------------------------------------
-#ifdef __CINT__
+#ifdef __CLING__
 
 #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 //__CINT__
+#endif //__CLING__
 // root dictionary stuff --------------------------------------------------
 

src/external/libFitPofB/include/TSkewedGssLinkDef.h

@@ -27,7 +27,7 @@
  ***************************************************************************/
 
 // root dictionary stuff --------------------------------------------------
-#ifdef __CINT__
+#ifdef __CLING__
 
 #pragma link off all globals;
 #pragma link off all classes;
@@ -35,6 +35,6 @@
 
 #pragma link C++ class TSkewedGss+;
 
-#endif //__CINT__
+#endif //__CLING__
 // root dictionary stuff --------------------------------------------------
 

src/external/libFitPofB/include/TVortexLinkDef.h

@@ -27,7 +27,7 @@
  ***************************************************************************/
 
 // root dictionary stuff --------------------------------------------------
-#ifdef __CINT__
+#ifdef __CLING__
 
 #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 //__CINT__
+#endif //__CLING__
 // root dictionary stuff --------------------------------------------------
 

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 "1.1.0"
+    VERSION "1.0.0"
 )
 
 #--- make sure that the include directory is found ----------------------------

src/external/libGapIntegrals/TGapIntegralsLinkDef.h

@@ -28,7 +28,7 @@
 
 
 // root dictionary stuff --------------------------------------------------
-#ifdef __CINT__
+#ifdef __CLING__
 
 #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 //__CINT__
+#endif //__CLING__
 // root dictionary stuff --------------------------------------------------
 

src/external/libGbGLF/PGbGLFLinkDef.h

@@ -27,7 +27,7 @@
  ***************************************************************************/
 
 // root dictionary stuff --------------------------------------------------
-#ifdef __CINT__
+#ifdef __CLING__
 
 #pragma link off all globals;
 #pragma link off all classes;
@@ -35,6 +35,6 @@
 
 #pragma link C++ class PGbGLF+;
 
-#endif //__CINT__
+#endif //__CLING__
 // root dictionary stuff --------------------------------------------------
 

src/external/libLFRelaxation/TLFRelaxationLinkDef.h

@@ -27,7 +27,7 @@
  ***************************************************************************/
 
 // root dictionary stuff --------------------------------------------------
-#ifdef __CINT__
+#ifdef __CLING__
 
 #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 //__CINT__
+#endif //__CLING__
 // root dictionary stuff --------------------------------------------------
 

src/external/libPhotoMeissner/include/PPhotoMeissnerLinkDef.h

@@ -27,7 +27,7 @@
  *   59 Temple Place - Suite 330, Boston, MA  02111-1307, USA.             *
  ***************************************************************************/
 
-#ifdef __CINT__
+#ifdef __CLING__
 
 #pragma link off all globals;
 #pragma link off all classes;

src/external/libSpinValve/include/PSkewedLorentzianLinkDef.h

@@ -27,7 +27,7 @@
  *   59 Temple Place - Suite 330, Boston, MA  02111-1307, USA.             *
  ***************************************************************************/
 
-#ifdef __CINT__
+#ifdef __CLING__
 
 #pragma link off all globals;
 #pragma link off all classes;

src/external/libSpinValve/include/PStartupHandler_SVLinkDef.h

@@ -27,7 +27,7 @@
  *   59 Temple Place - Suite 330, Boston, MA  02111-1307, USA.             *
  ***************************************************************************/
 
-#ifdef __CINT__
+#ifdef __CLING__
 
 #pragma link off all globals;
 #pragma link off all classes;

src/external/libZFRelaxation/ZFRelaxationLinkDef.h

@@ -27,7 +27,7 @@
  ***************************************************************************/
 
 // root dictionary stuff --------------------------------------------------
-#ifdef __CINT__
+#ifdef __CLING__
 
 #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 //__CINT__
+#endif //__CLING__
 // root dictionary stuff --------------------------------------------------
 

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 "1.0.0")
+set(PNEXUS_VERSION "0.9.0")
 set(PNEXUS_LIBRARY_NAME "PNeXus")
 configure_file("PNeXus.pc.in" "PNeXus.pc" @ONLY)
 
@@ -21,10 +21,11 @@ set_target_properties(PNeXus
 )
 
 #--- make sure that the include directory is found ----------------------------
-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}>
+target_include_directories(
+  PNeXus BEFORE PRIVATE 
+     $<BUILD_INTERFACE:${HDF4_INCLUDE_DIRS}>
+     $<BUILD_INTERFACE:${HDF5_INCLUDE_DIRS}>
+     $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}>
 )
 
 #--- add library dependencies -------------------------------------------------
@@ -33,7 +34,6 @@ 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 -----------------------------------------------------

src/external/nexus/PyScripts/Install.md

@@ -1,126 +0,0 @@
-# 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.

src/external/nexus/PyScripts/Usage.md

@@ -1,223 +0,0 @@
-# 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)
-========================================================================
-```

src/external/nexus/README.Cygwin

@@ -0,0 +1,69 @@
+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

src/external/nexus/examples/hdf4/CMakeLists.txt

@@ -1,149 +0,0 @@
-# - 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})

src/external/nexus/examples/hdf4/cmake/config.h.in

@@ -1,7 +0,0 @@
-/* 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@"

src/external/nexus/examples/hdf4/docu/README.md

@@ -1,155 +0,0 @@
-# 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>

src/external/nexus/examples/hdf4/git_revision.sh

@@ -1,35 +0,0 @@
-#!/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"

src/external/nexus/examples/hdf4/main.cpp

@@ -1,447 +0,0 @@
-/***************************************************************************
-
-  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;
-}

src/external/nexus/examples/hdf5/CMakeLists.txt

@@ -1,119 +0,0 @@
-# - 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})

src/external/nexus/examples/hdf5/cmake/config.h.in

@@ -1,5 +0,0 @@
-// config.h
-
-#define PACKAGE_VERSION "@PROJECT_VERSION@"
-#define BUILD_TYPE "@CMAKE_BUILD_TYPE@"
-

src/external/nexus/examples/hdf5/cmake/git-revision.h.in

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

src/external/nexus/examples/hdf5/docu/README.md

@@ -1,55 +0,0 @@
-# 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/)

src/external/nexus/examples/hdf5/git_revision.sh

@@ -1,27 +0,0 @@
-#!/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

src/external/nexus/examples/hdf5/main.cpp

@@ -1,572 +0,0 @@
-/***************************************************************************
-
-  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;
-}

src/include/PFitter.h

@@ -32,6 +32,8 @@
 
 #include <memory>
 
+#include "TString.h"
+
 #include "Minuit2/MnUserParameters.h"
 #include "Minuit2/FunctionMinimum.h"
 
@@ -39,6 +41,7 @@
 #include "PMsrHandler.h"
 #include "PRunListCollection.h"
 #include "PFitterFcn.h"
+#include "PFitterFcnDKS.h"
 
 //-------------------------------------------------------------
 /**
@@ -292,6 +295,8 @@ 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
@@ -312,6 +317,7 @@ 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
@@ -580,6 +586,7 @@ class PFitter
      * @return Rounded parameter values
      */
     PDoubleVector ParamRound(const PDoubleVector &par, const PDoubleVector &err, Bool_t &ok);
+    std::string GetCPUInfo();
 };
 
 #endif // _PFITTER_H_

src/include/PFitterFcn.h

@@ -61,6 +61,7 @@
  *
  * @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
 {

src/include/PFitterFcnDKS.h

@@ -0,0 +1,85 @@
+/***************************************************************************
+
+  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_

src/include/PFourier.h

@@ -32,7 +32,16 @@
 
 #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>
 
@@ -213,7 +222,8 @@ 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 dcCorrected = false, UInt_t zeroPaddingPower = 0,
+             Bool_t useFFTW = true);
 
     virtual ~PFourier();
 
@@ -225,7 +235,9 @@ class PFourier
      *
      * @param apodizationTag Apodization strength (0/1=none, 2=weak, 3=medium, 4=strong)
      */
-    virtual void Transform(UInt_t apodizationTag = 0);
+    virtual void Transform(UInt_t apodizationTag = F_APODIZATION_NONE);
+
+    virtual void SetUseFFTW(const Bool_t flag);
 
     /// Returns the original data histogram title
     /// @return Title string
@@ -301,12 +313,14 @@ 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
 
@@ -319,11 +333,18 @@ 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
 
-//as    PFTPhaseCorrection *fPhCorrectedReFT;
+    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
+
+#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
 
     virtual void PrepareFFTwInputData(UInt_t apodizationTag);
     virtual void ApodizeData(Int_t apodizationTag);

src/include/PFourierCanvasLinkDef.h

@@ -27,7 +27,7 @@
  *   59 Temple Place - Suite 330, Boston, MA  02111-1307, USA.             *
  ***************************************************************************/
 
-#ifdef __CINT__
+#ifdef __CLING__
 
 #pragma link off all globals;
 #pragma link off all classes;

src/include/PMsrHandler.h

@@ -30,6 +30,7 @@
 #ifndef _PMSRHANDLER_H_
 #define _PMSRHANDLER_H_
 
+#include <string>
 #include <memory>
 #include <sstream>
 #include <string>
@@ -373,6 +374,10 @@ 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
@@ -398,6 +403,8 @@ 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
@@ -466,6 +473,8 @@ 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_

src/include/PMusr.h

@@ -348,6 +348,13 @@
  */
 #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.
@@ -923,44 +930,44 @@ class PRawRunData {
     PNonMusrRawRunData fDataNonMusr; ///< keeps all ascii- or db-file info in case of nonMusr fit
 
   private:
-    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
+    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
     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.
 };
 
 //-------------------------------------------------------------
@@ -1222,7 +1229,7 @@ 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)
 
@@ -1378,6 +1385,7 @@ 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)
 };
 
 //-------------------------------------------------------------

src/include/PMusrCanvas.h

@@ -290,7 +290,8 @@ 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 fourier=false, const Bool_t avg=false, const Bool_t theoAsData=false, 
+                const Bool_t useDKS=false);
 
     //----------------------------------------------------------------------
     /**
@@ -314,7 +315,8 @@ 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 fourier=false, const Bool_t avg=false, const Bool_t theoAsData=false, 
+                const Bool_t useDKS=false);
 
     /// Destructor - cleans up all histograms, graphs, and ROOT objects
     virtual ~PMusrCanvas();
@@ -358,6 +360,7 @@ 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

src/include/PMusrCanvasLinkDef.h

@@ -27,7 +27,7 @@
  *   59 Temple Place - Suite 330, Boston, MA  02111-1307, USA.             *
  ***************************************************************************/
 
-#ifdef __CINT__
+#ifdef __CLING__
 
 #pragma link off all globals;
 #pragma link off all classes;

src/include/PMusrT0LinkDef.h

@@ -27,7 +27,7 @@
  *   59 Temple Place - Suite 330, Boston, MA  02111-1307, USA.             *
  ***************************************************************************/
 
-#ifdef __CINT__
+#ifdef __CLING__
 
 #pragma link off all globals;
 #pragma link off all classes;