.clang-format

+---
+Language:        Cpp
+BasedOnStyle:  Google
+AccessModifierOffset: -4
+AlignAfterOpenBracket: AlwaysBreak
+AlignConsecutiveAssignments: true
+AllowShortFunctionsOnASingleLine: None
+AllowShortIfStatementsOnASingleLine: Never
+AllowShortLambdasOnASingleLine: Empty
+AllowShortLoopsOnASingleLine: false
+BreakBeforeBinaryOperators: NonAssignment
+ColumnLimit:     100
+DerivePointerAlignment: false
+IndentWidth:     4
+IncludeBlocks: Preserve
+IndentGotoLabels: false
+NamespaceIndentation: All 
+...

.dir-locals.el

+(
+ (nil . (
+	 (indent-tabs-mode . nil)
+	 (require-final-newline . nil)
+	 )
+      )
+ (cmake-mode . (
+           (cmake-tab-width . 4)
+           )
+        )
+ 
+ (c-mode . (
+	    (c-basic-offset . 4)
+	    )
+	 )
+ (c++-mode . (
+	      (c-basic-offset . 4)
+	      )
+	   )
+ )
+

.gitignore

 .DS_Store
+.ipynb_checkpoints
+#*
 *~
 *.o
 *.a
 *.aux
+*.h5
+#*#
+*.dat
+optimizer/Tests/*.exe
 build
+data
 CMakeCache.txt
 CMakeFiles
 cmake_install.cmake
@@ -15,6 +22,7 @@ src/OPALrevision.h
 src/opal
 tests/tools/gtest
 tests/opal_unit_tests
+tests/OpalSourcePath.h
 doc/user_guide/opal_user_guide.bcf
 doc/user_guide/opal_user_guide.idx
 doc/user_guide/opal_user_guide.lof
@@ -24,4 +32,10 @@ doc/user_guide/opal_user_guide.out
 doc/user_guide/opal_user_guide.pdf
 doc/user_guide/opal_user_guide.run.xml
 doc/user_guide/opal_user_guide.synctex.gz
-doc/user_guide/opal_user_guide.toc
\ No newline at end of file
+doc/user_guide/opal_user_guide.toc
+.rtags
+init-test.sh
+init.el
+input-files/OPAL-X-STAT0.csv
+input-files/timing.dat
+build_*
\ No newline at end of file

.gitlab/issue_templates/Bug.md

+### Summary
+
+(Summarize the bug encountered concisely)
+
+
+### Steps to reproduce
+
+(How one can reproduce the issue - this is very important)
+
+
+### What is the current *bug* behavior?
+
+(What actually happens)
+
+
+### What is the expected *correct* behavior?
+
+(What you should see instead)
+
+
+### Relevant logs and/or screenshots
+
+(Paste any relevant logs - please use code blocks (```) to format console output,
+logs, and code as it's very hard to read otherwise.)
+
+
+### Possible fixes
+
+(If you can, link to the line of code that might be responsible for the problem)
+
+/label ~Bug

.gitlab/issue_templates/Feature.md

+### Summary
+
+(Summarize the feature request concisely)
+
+
+
+/label ~"Feature request"
\ No newline at end of file

.gitlab/merge_request_templates/Bug.md

+### What does this MR do?
+
+### Does this MR meet the acceptance criteria?
+
+* [ ] [Coding style guidelines](https://gitlab.psi.ch/OPAL/src/wikis/For-Developers/CodingStyle)
+* [ ] [Change to Release Notes](https://gitlab.psi.ch/OPAL/src/wikis/ReleaseNotes/ReleaseNotes)
+
+
+/label ~Bug

.gitlab/merge_request_templates/Feature.md

+### What does this MR do?
+
+### Does this MR meet the acceptance criteria?
+
+* [ ] [Coding style guidelines](https://gitlab.psi.ch/OPAL/src/wikis/For-Developers/CodingStyle)
+* [ ] [Change to Release Notes](https://gitlab.psi.ch/OPAL/src/wikis/ReleaseNotes/ReleaseNotes)
+* [ ] Documentation added
+
+
+/label ~"Feature request"

.local.vimrc

+set et ts=4 sw=4 sts=4
\ No newline at end of file

C++-Readme

+Expressions.h
+
+    // Template class Expression::PtrToScalar<T>.                                                                                                                                
+    // ----------------------------------------------------------------------                                                                                                    
+    /// A pointer to a scalar expression.                                                                                                                                        
+
+
+    template <class T> using PtrToScalar = std::shared_ptr<Scalar<T>>;
+    
+    template <class T> using PtrToScalar = std::unique_ptr<Scalar<T>>;
+
+
+Noe: giving up tp replace the Classic/MemoryManagement/OwnPrt.h
+
+
+
+
+
+Add new element XXX:
+
+	AbsBeamline/ElementBase.h,cpp
+    Algorithms/DefaultVisitor.h,cpp
+    Algorithms/ParallelTracker.h
+    OpalConfigure/Configure.cpp
+    Algorithms/ParallelTracker.h    
+    AbsBeamline/BeamlineVisitor.h
+
+    AbsBeamline/XXX.cpp
+	AbsBeamline/XXX.h
+    AbsBeamline/CMakeLists.txt
+    BeamlineCore/XXXRep.cpp
+	BeamlineCore/XXXRep.h
+    BeamlineCore/CMakeLists.txt
+    Elements/OpalXXX.cpp
+	Elements/OpalXXX.h
+	Elements/CMakeLists.txt
+
+    

CMakeModules/FindGSL.cmake

 #
-# Find GSL includes and library
+# Find GSL includes and libraries
 #
-# GSL
-# It can be found at:
-#     http://amas.web.psi.ch/tools/GSL/index.html
+# The FindGSL module shipped with CMake has some drawbacks. To be 
+# able to find GSL, the CMake variable GSL_ROOT_DIR *must* be set.
+# The environment variable C_INCLUDE_PATH and LIBRARY_PATH are
+# *not* taken into account.
+#
+# The following variables will be set if GSL is found:
+#
+# GSL_INCLUDE_DIR	where to find GSL include files
+# GSL_LIBRARY		GSL library to link against.
+# GSL_CBLAS_LIBRARY 	GSL CBlas library to link against
+# GSL_LIBRARIES		GSL libraries required for linking
+# GSL_FOUND		set to True if GSL was found
 #
-# GSL_INCLUDE_DIR - where to find ippl.h
-# GSL_LIBRARY     - qualified libraries to link against.
-# GSL_FOUND       - do not attempt to use if "no" or undefined.
-
-FIND_PATH(GSL_INCLUDE_DIR gsl/gsl_fft.h
-    HINTS $ENV{GSL_INCLUDE_PATH} $ENV{GSL_INCLUDE_DIR} $ENV{GSL_PREFIX}/include $ENV{GSL_DIR}/include $ENV{GSL}/include
-    PATHS ENV CPP_INCLUDE_PATH
-)
 
+if( DEFINED ENV{GSL_ROOT_DIR} )
+  set( GSL_ROOT_DIR $ENV{GSL_ROOT_DIR} )
+elseif( DEFINED ENV{GSL_DIR} )
+  set( GSL_ROOT_DIR $ENV{GSL_DIR} )
+elseif( DEFINED ENV{GSL_HOME} )
+  set( GSL_ROOT_DIR $ENV{GSL_HOME} )
+elseif( DEFINED ENV{GSL_PREFIX} )
+  set( GSL_ROOT_DIR $ENV{GSL_PREFIX} )
+elseif( DEFINED ENV{GSL} )
+  set( GSL_ROOT_DIR $ENV{GSL} )
+else()
+  set( GSL_ROOT_DIR "/usr" )
+endif()
 
-FIND_LIBRARY(GSL_LIBRARY gsl
-    HINTS $ENV{GSL_LIBRARY_PATH} $ENV{GSL_LIBRARY_DIR} $ENV{GSL_PREFIX}/lib $ENV{GSL_DIR}/lib $ENV{GSL}/lib
-    PATHS ENV LIBRARY_PATH
-)
+find_path( GSL_INCLUDE_DIR gsl/gsl_fft.h
+  HINTS ${GSL_ROOT_DIR}/include $ENV{GSL_INCLUDE_PATH} $ENV{GSL_INCLUDE_DIR}
+  PATHS ENV C_INCLUDE_PATH
+  )
 
-FIND_LIBRARY(GSL_LIBRARY_CBLAS gslcblas
-    HINTS $ENV{GSL_LIBRARY_PATH} $ENV{GSL_LIBRARY_DIR} $ENV{GSL_PREFIX}/lib $ENV{GSL_DIR}/lib $ENV{GSL}/lib
-    PATHS ENV LIBRARY_PATH
-)
+find_library( GSL_LIBRARY gsl
+  HINTS ${GSL_ROOT_DIR}/lib $ENV{GSL_LIBRARY_PATH} $ENV{GSL_LIBRARY_DIR}
+  PATHS ENV LIBRARY_PATH
+  )
 
-set( GSL_LIBRARY
-    ${GSL_LIBRARY}
-    ${GSL_LIBRARY_CBLAS}
-)
+find_library (GSL_CBLAS_LIBRARY gslcblas
+  HINTS ${GSL_ROOT_DIR}/lib $ENV{GSL_LIBRARY_PATH} $ENV{GSL_LIBRARY_DIR}
+  PATHS ENV LIBRARY_PATH
+  )
 
-IF(GSL_INCLUDE_DIR AND GSL_LIBRARY)
-    SET( GSL_FOUND "YES" )
-ENDIF(GSL_INCLUDE_DIR AND GSL_LIBRARY)
+if( GSL_INCLUDE_DIR AND GSL_LIBRARY AND GSL_CBLAS_LIBRARY)
+  set( GSL_FOUND "YES" )
+  set( GSL_LIBRARIES ${GSL_LIBRARY},${GSL_CBLAS_LIBRARY} )
+endif()
 
-IF (GSL_FOUND)
-   IF (NOT GSL_FIND_QUIETLY)
-      MESSAGE(STATUS "Found GSL libraries: ${GSL_LIBRARY}")
-      MESSAGE(STATUS "Found GSL include dir: ${GSL_INCLUDE_DIR}")
-   ENDIF (NOT GSL_FIND_QUIETLY)
-ELSE (GSL_FOUND)
-   IF (GSL_FIND_REQUIRED)
-      MESSAGE(FATAL_ERROR "Could not find GSL!")
-   ENDIF (GSL_FIND_REQUIRED)
-ENDIF (GSL_FOUND)
+if( GSL_FOUND )
+  if( NOT GSL_FIND_QUIETLY )
+    message( STATUS "Found GSL libraries: ${GSL_LIBRARY}")
+    message( STATUS "Found GSL include dir: ${GSL_INCLUDE_DIR}")
+  endif()
+else()
+  if( GSL_FIND_REQUIRED )
+    message( FATAL_ERROR "Could not find GSL!" )
+  endif()
+endif()

CMakeModules/FindGTest.cmake

 #
 # Find gtest Google Test includes and library
 #
-# gtest
-# It can be found at:
-#     http://amas.web.psi.ch/tools/GSL/index.html
-#
-# GTEST_INCLUDE_DIRS - where to find gtest/gtest.h
+# GTEST_INCLUDE_DIR - where to find gtest/gtest.h
 # GTEST_LIBRARY     - libgtest.a path
 # GTEST_MAIN_LIBRARY     - libgtest_main.a path
 # GTEST_FOUND       - do not attempt to use if "no" or undefined.
 
-FIND_PATH(GTEST_INCLUDE_DIRS gtest/gtest.h
-    HINTS $ENV{GTEST_INCLUDE_PATH} $ENV{GTEST_INCLUDE_DIRS} $ENV{GTEST_PREFIX}/include $ENV{GTEST_ROOT}/include ${PROJECT_SOURCE_DIR}/tests/tools/gtest/include
+FIND_PATH(GTEST_INCLUDE_DIR gtest/gtest.h
+    HINTS $ENV{GTEST_INCLUDE_PATH} $ENV{GTEST_INCLUDE_DIR} $ENV{GTEST_PREFIX}/include $ENV{GTEST_ROOT}/include ${PROJECT_SOURCE_DIR}/tests/tools/gtest/include
     PATHS ENV CPP_INCLUDE_PATH
 )
 
@@ -30,14 +26,26 @@ set( GTEST_BOTH_LIBRARIES
     ${GTEST_LIBRARY_MAIN}
 )
 
-IF(GTEST_INCLUDE_DIRS AND GTEST_LIBRARY AND GTEST_LIBRARY_MAIN)
+set (GTEST_INCLUDE_DIRS
+    ${GTEST_INCLUDE_DIR}
+)
+
+set (GTEST_MAIN_LIBRARIES
+    ${GTEST_LIBRARY_MAIN}
+)
+
+set (GTEST_LIBRARIES
+    ${GTEST_LIBRARY}
+)
+
+IF(GTEST_INCLUDE_DIR AND GTEST_LIBRARY AND GTEST_LIBRARY_MAIN)
     SET( GTEST_FOUND "YES" )
-ENDIF(GTEST_INCLUDE_DIRS AND GTEST_LIBRARY AND GTEST_LIBRARY_MAIN)
+ENDIF()
 
 IF (GTEST_FOUND)
    IF (NOT GTEST_FIND_QUIETLY)
       MESSAGE(STATUS "Found gtest libraries: ${GTEST_BOTH_LIBRARIES}")
-      MESSAGE(STATUS "Found gtest include dir: ${GTEST_INCLUDE_DIRS}")
+      MESSAGE(STATUS "Found gtest include dir: ${GTEST_INCLUDE_DIR}")
    ENDIF (NOT GTEST_FIND_QUIETLY)
 ELSE (GTEST_FOUND)
    IF (GTest_FIND_REQUIRED)

CMakeModules/FindH5Hut.cmake

@@ -43,9 +43,3 @@ IF (HAVE_API2_FUNCTIONS)
 ELSE (HAVE_API2_FUNCTIONS)
     MESSAGE (ERROR "H5hut >= 2 required")
 ENDIF (HAVE_API2_FUNCTIONS)
-
-# Local Variables:
-# mode:cmake
-# cmake-tab-width: 4
-# indent-tabs-mode:nil
-# End:

CMakeModules/FindHDF5.cmake

-#
-# Find HDF5 includes and library
-#
-# HDF5
-# It can be found at:
-#     http://amas.web.psi.ch/tools/HDF5/index.html
-#
-# HDF5_INCLUDE_DIR - where to find hdf5.h
-# HDF5_LIBRARY     - qualified libraries to link against.
-# HDF5_FOUND       - do not attempt to use if "no" or undefined.
-
-SET(CMAKE_FIND_LIBRARY_SUFFIXES .lib .a ${CMAKE_FIND_LIBRARY_SUFFIXES})
-
-FIND_PATH(HDF5_INCLUDE_DIR hdf5.h
-    HINTS $ENV{HDF5_INCLUDE_PATH} $ENV{HDF5_INCLUDE_DIR} $ENV{HDF5_PREFIX}/include $ENV{HDF5_DIR}/include $ENV{HDF5}/include
-    PATHS ENV C_INCLUDE_PATH
-)
-
-FIND_LIBRARY(HDF5_LIBRARY libhdf5.a
-    HINTS $ENV{HDF5_LIBRARY_PATH} $ENV{HDF5_LIBRARY_DIR} $ENV{HDF5_PREFIX}/lib $ENV{HDF5_DIR}/lib $ENV{HDF5}/lib
-    PATHS ENV LIBRARY_PATH
-)
-
-
-IF(HDF5_INCLUDE_DIR AND HDF5_LIBRARY)
-    SET( HDF5_FOUND "YES" )
-ENDIF(HDF5_INCLUDE_DIR AND HDF5_LIBRARY)
-
-IF (HDF5_FOUND)
-   IF (NOT HDF5_FIND_QUIETLY)
-      MESSAGE(STATUS "Found HDF5 library: ${HDF5_LIBRARY}")
-      MESSAGE(STATUS "Found HDF5 include dir: ${HDF5_INCLUDE_DIR}")
-   ENDIF (NOT HDF5_FIND_QUIETLY)
-ELSE (HDF5_FOUND)
-   IF (HDF5_FIND_REQUIRED)
-      MESSAGE(FATAL_ERROR "Could not find HDF5!")
-   ENDIF (HDF5_FIND_REQUIRED)
-ENDIF (HDF5_FOUND)

CMakeModules/FindIppl.cmake

+#
+# Find IPPL package
+# https://
+#
+# IPPL_INCLUDE_DIR
+# IPPL_LIBRARY_DIR
+# IPPL_FOUND
+
+#message (STATUS "Hint IPPL include dir: ${IPPL_DIR}")
+
+find_path (IPPL_INCLUDE_DIR Ippl.h
+    HINTS ${IPPL_DIR}/include 
+    PATHS ENV C_INCLUDE_PATH 
+)
+#message (STATUS "From find_path IPPL_INCLUDE_DIR: ${IPPL_INCLUDE_DIR}")
+
+find_path (IPPL_LIBRARY_DIR libippl.a
+    HINTS ${IPPL_DIR}/lib 
+    PATHS ENV LIBRARY_PATH
+)
+#message (STATUS "From find_path IPPL_LIBRARY_DIR: ${IPPL_LIBRARY_DIR}")
+
+
+if (IPPL_INCLUDE_DIR AND IPPL_LIBRARY_DIR)
+    set (IPPL_FOUND "YES")
+endif ()
+
+if (IPPL_FOUND)
+    if (NOT IPPL_FIND_QUIETLY)
+        message (STATUS "Found IPPL include dir: ${IPPL_INCLUDE_DIR}")
+        message (STATUS "Found IPPL library dir: ${IPPL_LIBRARY_DIR}")
+        set (IPPL_LIBRARIES libippl.a)
+        endif ()
+else (IPPL_FOUND)
+    if (IPPL_FIND_REQUIRED)
+        if (NOT IPPL_INCLUDE_DIR)
+            message (WARNING 
+                "IPPL include directory was not found! "
+                "Make sure that IPPL is compiled and that "
+                "the directory ippl/include/ippl has been automatically created. "
+                "Also make sure that at least one of the following "
+                "environment variables is set: "
+                "IPPL_INCLUDE_DIR, IPPL_INCLUDE_PATH, IPPL_PREFIX, or IPPL.")
+        endif ()
+        if (NOT IPPL_LIBRARY_DIR)
+            message (WARNING 
+                "IPPL library was not found! "
+                "Make sure that IPPL is compiled and that "
+                "the directory ippl/lib has been automatically created. "
+                "Also make sure that at least one of the following "
+                "environment variables is set: "
+                "IPPL_LIBRARY_DIR, IPPL_LIBRARY_PATH, IPPL_PREFIX, or IPPL.")
+        endif ()
+        message (STATUS "IPPL can be downloaded and compiled from https://xxxx")
+        message (FATAL_ERROR "Could not find IPPL!")
+    endif (IPPL_FIND_REQUIRED)
+endif (IPPL_FOUND)
+
+
+include (CheckIncludeFile)
+SET (CMAKE_REQUIRED_INCLUDES ${IPPL_INCLUDE_DIR})
+CHECK_INCLUDE_FILE (Ippl.h HAVE_API2_FUNCTIONS "-I${IPPL_INCLUDE_DIR} -DPARALLEL_IO")
+
+IF (HAVE_API2_FUNCTIONS)
+    MESSAGE (STATUS "IPPL version is OK")
+ELSE (HAVE_API2_FUNCTIONS)
+   MESSAGE (ERROR "IPPL >= 2 required")
+ENDIF (HAVE_API2_FUNCTIONS)
\ No newline at end of file

CMakeModules/FindMITHRA.cmake

+#
+# Find MITHRA package
+# https://github.com/aryafallahi/mithra
+#
+# MITHRA_INCLUDE_DIR
+# MITHRA_LIBRARY_DIR
+# MITHRA_FOUND
+
+find_path (MITHRA_INCLUDE_DIR mithra/classes.h
+    HINTS $ENV{MITHRA_INCLUDE_DIR} $ENV{MITHRA_INCLUDE_PATH} $ENV{MITHRA_PREFIX}/include $ENV{MITHRA}/include
+)
+
+find_path (MITHRA_LIBRARY_DIR libmithra.a
+    HINTS $ENV{MITHRA_LIBRARY_DIR} $ENV{MITHRA_LIBRARY_PATH} $ENV{MITHRA_PREFIX}/lib $ENV{MITHRA}/lib
+)
+
+if (MITHRA_INCLUDE_DIR AND MITHRA_LIBRARY_DIR)
+    set (MITHRA_FOUND "YES")
+endif ()
+
+if (MITHRA_FOUND)
+    if (NOT MITHRA_FIND_QUIETLY)
+        message (STATUS "Found MITHRA include dir: ${MITHRA_INCLUDE_DIR}")
+        message (STATUS "Found MITHRA library dir: ${MITHRA_LIBRARY_DIR}")
+    endif ()
+else (MITHRA_FOUND)
+    if (MITHRA_FIND_REQUIRED)
+        if (NOT MITHRA_INCLUDE_DIR)
+            message (WARNING 
+                "MITHRA include directory was not found! "
+                "Make sure that MITHRA is compiled and that "
+                "the directory mithra/include/mithra has been automatically created. "
+                "Also make sure that at least one of the following "
+                "environment variables is set: "
+                "MITHRA_INCLUDE_DIR, MITHRA_INCLUDE_PATH, MITHRA_PREFIX, or MITHRA.")
+        endif ()
+        if (NOT MITHRA_LIBRARY_DIR)
+            message (WARNING 
+                "MITHRA library was not found! "
+                "Make sure that MITHRA is compiled and that "
+                "the directory mithra/lib has been automatically created. "
+                "Also make sure that at least one of the following "
+                "environment variables is set: "
+                "MITHRA_LIBRARY_DIR, MITHRA_LIBRARY_PATH, MITHRA_PREFIX, or MITHRA.")
+        endif ()
+        message (STATUS "MITHRA can be downloaded and compiled from https://github.com/aryafallahi/mithra.git")
+        message (FATAL_ERROR "Could not find MITHRA!")
+    endif (MITHRA_FIND_REQUIRED)
+endif (MITHRA_FOUND)

LICENSE

+LICENSES/OPAL/LICENSE
\ No newline at end of file