.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

@@ -2,7 +2,10 @@
 *~
 *.o
 *.a
+*.so
 *.aux
+__pycache__
+optimizer/Tests/*.exe
 build
 CMakeCache.txt
 CMakeFiles
@@ -15,6 +18,7 @@ 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 +28,4 @@ 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

.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/issue_templates/Release.md

+**source code and binary**
+  * [ ] create branch YEAR.N
+  * [ ] create issue "Release version YEAR.N" and merge request
+  * [ ] update version string in Doxyfile
+  * [ ] update the version string in CMakeLists.txt and commit
+  * [ ] wait for approval of MR and merge
+  * [ ] tag version YEAR.N.0
+  * [ ] upload source tar-ball to `/afs/psi.ch/project/amas/webhosting/Downloads/OPAL/src`
+  * [ ] compile new binary for Linux
+  * [ ] upload Linux binary package to `/afs/psi.ch/project/amas/webhosting/Downloads/OPAL/package/`
+  * [ ] compile new binary for macOS
+  * [ ] upload macOS binary package to `/afs/psi.ch/project/amas/webhosting/Downloads/OPAL/package/`
+
+**manual/documentation**
+  * [ ] setup a new branch for the new version of the manual
+  * [ ] fix version, branches and links in `Manual.attributes`
+  * [ ] clone repository into `/afs/psi.ch/project/amas/webhosting/opal/Documentation/x.y` and checkout new branch (`git clone https://gitlab.psi.ch/OPAL/documentation/manual.git`)
+  * [ ] add links to the binaries in the wiki
+  * [ ] update https://gitlab.psi.ch/OPAL/src/wikis/For-Developers/Compile-OPAL
+  * [ ] compile the change log/release notes and publish it in the wiki: https://gitlab.psi.ch/OPAL/src/wikis/ReleaseNotes
+  * [ ] review the file `src/addToDoxygenMainPage.h`
+  * [ ] build Doxygen documentation
+  * [ ] update https://gitlab.psi.ch/OPAL/src/wikis/home
+  * [ ] update https://gitlab.psi.ch/OPAL/src/wikis/regression-tests
+
+**tracker**
+  * [ ] new milestone for `OPAL x.(y+1)`
+  * [ ] update labels and milestones in issues
+
+**regression-tests**
+
+  * [ ] create new branch x.y
+  * [ ] setup the regression-tests to run the new version on opalrunner.psi.ch
+
+**varia**
+  * [ ] PSI module
+  * [ ] write e-mail to mailing list

.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

CMakeModules/CCSEOptions.cmake

-# -*- mode: cmake -*-
-#
-# Set up defines necessary to build BoxLib-based code
-
-if(__CCSE_OPTIONS_INCLUDED)
-  return()
-endif()
-set(__CCSE_OPTIONS_INCLUDED 1)
-
-include(FortranCInterface)
-include(${FortranCInterface_BINARY_DIR}/Output.cmake)
-
-#message(STATUS "BoxLib-specific compile settings:")
-if(FortranCInterface_GLOBAL_SUFFIX STREQUAL ""  AND FortranCInterface_GLOBAL_CASE STREQUAL "UPPER")
-#    message(STATUS "   Fortran name mangling scheme to UPPERCASE (upper case, no append underscore)")
-    set(BL_FORTLINK UPPERCASE)
-elseif(FortranCInterface_GLOBAL_SUFFIX STREQUAL ""  AND FortranCInterface_GLOBAL_CASE STREQUAL "LOWER")
-#    message(STATUS "   Fortran name mangling scheme to LOWERCASE (lower case, no append underscore)")
-    set(BL_FORTLINK LOWERCASE)
-elseif(FortranCInterface_GLOBAL_SUFFIX STREQUAL "_" AND FortranCInterface_GLOBAL_CASE STREQUAL "LOWER")
-#    message(STATUS "   Fortran name mangling scheme to UNDERSCORE (lower case, append underscore)")
-    set(BL_FORTLINK "UNDERSCORE")
-#else()
-#    message(AUTHOR_WARNING "Fortran to C mangling not backward compatible with older style BoxLib code")
-endif()
-
-set(BL_MACHINE ${CMAKE_SYSTEM_NAME})
-
-set(BL_DEFINES "BL_NOLINEVALUES;BL_PARALLEL_IO;BL_SPACEDIM=3;BL_FORT_USE_${BL_FORTLINK};BL_${BL_MACHINE};BL_USE_DOUBLE;MG_USE_FBOXLIB;MG_USE_F90_SOLVERS;MG_USE_FBOXLIB")
-
-if ("${CMAKE_BUILD_TYPE}" STREQUAL "Release")
-  list(APPEND BL_DEFINES NDEBUG)
-elseif ("${CMAKE_BUILD_TYPE}" STREQUAL "RelWithDebInfo")
-  list(APPEND BL_DEFINES NDEBUG)
-elseif ("${CMAKE_BUILD_TYPE}" STREQUAL "MinSizeRel")
-  list(APPEND BL_DEFINES NDEBUG)
-endif()
-
-set(ENABLE_MPI TRUE)
-
-if (ENABLE_MPI)
-  # bandre: I think the amanzi config requires that the mpi compilers
-  # be set through the CC/CXX/FC environment variables before cmake is
-  # called. This is overwriting those values and causing the incorrect
-  # values to be used?
-  #find_package(MPI REQUIRED)
-  list(APPEND BL_DEFINES BL_USE_MPI)
-  set(CMAKE_CC_FLAGS "${CMAKE_CC_FLAGS} ${MPI_C_FLAGS}")
-  set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${MPI_CXX_FLAGS}")
-  set(CMAKE_Fortran_FLAGS "${CMAKE_Fortran_FLAGS} ${MPI_Fortran_FLAGS}")
-  set(CCSE_LIBDIR_MPI_SUFFIX .MPI)
-else()
-  set(CCSE_LIBDIR_MPI_SUFFIX)
-endif()
-
-set (ENABLE_OpenMP FALSE)
-
-if (ENABLE_OpenMP)
-  set(CCSE_LIBDIR_OMP_SUFFIX .OMP)
-else()
-  set(CCSE_LIBDIR_OMP_SUFFIX)
-endif(ENABLE_OpenMP)
-
-get_directory_property(defs COMPILE_DEFINITIONS)
-if(defs)
-  set_directory_properties(PROPERTIES COMPILE_DEFINITIONS $defs ${BL_DEFINES})
-endif()
-
-
-if(CMAKE_COMPILER_IS_GNUCXX)
-  set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -g -ftemplate-depth=512 -Wno-deprecated")
-endif(CMAKE_COMPILER_IS_GNUCXX)
-
-list(APPEND BL_DEFINES "OPAL")
-
-set_directory_properties(PROPERTIES COMPILE_DEFINITIONS "${BL_DEFINES}")

CMakeModules/FindCCSE.cmake

-# -*- mode: cmake -*-
-#
-# OPAL CCSE Find Module
-#
-# Usage:
-#    Control the search through CCSE_DIR or setting environment variable
-#    CCSE_ROOT to the ccse installation prefix.
-#
-#    This module does not search default paths!
-#
-#    Following variables are set:
-#    CCSE_FOUND            (BOOL)       Flag indicating if CCSE was found
-#    CCSE_INCLUDE_DIR      (PATH)       Path to the CCSE include file
-#    CCSE_INCLUDE_DIRS     (LIST)       List of all required include files
-#    CCSE_LIBRARY_DIR      (PATH)       Path to the CCSE library
-#    CCSE_LIBRARIES        (LIST)       List of all required CCSE libraries
-#    CCSE_PERL_DIR         (PATH)       Path to CCSE Perl scripts
-#    CCSE_EXT_LIBRARIES    (LIST)
-#    CCSE_EXT_LIBRARY_DIRS (LIST)
-#
-# #############################################################################
-# Standard CMake modules see CMAKE_ROOT/Modules
-include(FindPackageHandleStandardArgs)
-
-# OPAL CMake functions see <root>/tools/cmake for source
-
-include(CCSEOptions)
-
-MESSAGE (STATUS "IN FIND CCSE_LIBRARIES")
-
-if ( CCSE_LIBRARIES AND CCSE_INCLUDE_DIRS AND CCSE_PERL_DIR)
-
-    # Do nothing. Variables are set. No need to search again
-
-else(CCSE_LIBRARIES AND CCSE_INCLUDE_DIRS AND CCSE_PERL_DIR)
-
-    # Cache variables
-    if(CCSE_DIR)
-        set(CCSE_DIR "${CCSE_DIR}" CACHE PATH "Path to search for CCSE include and library files")
-    endif()
-
-    if(CCSE_INCLUDE_DIR)
-        set(CCSE_INCLUDE_DIR "${CCSE_INCLUDE_DIR}" CACHE PATH "Path to search for CCSE include files")
-    endif()
-
-    if(CCSE_LIBRARY_DIR)
-        set(CCSE_LIBRARY_DIR "${CCSE_LIBRARY_DIR}" CACHE PATH "Path to search for CCSE library files")
-    endif()
-
-    if(CCSE_PERL_DIR)
-        set(CCSE_PERL_DIR "${CCSE_PERL_DIR}" CACHE PATH "Path to search for CCSE perl scripts")
-    endif()
-
-
-    # Search for include files
-    # Search order preference:
-    #  (1) CCSE_INCLUDE_DIR - check existence of path AND if the include files exist
-    #  (2) CCSE_DIR/include
-    #  (3) Default CMake paths See cmake --html-help=out.html file for more information.
-    #
-    set(ccse_inc_names "BoxLib.H")
-
-    if (CCSE_INCLUDE_DIR)
-
-        if (EXISTS "${CCSE_INCLUDE_DIR}")
-
-            find_path(ccse_test_include_path
-                      NAMES ${ccse_inc_names}
-                      HINTS ${CCSE_INCLUDE_DIR}
-                      NO_DEFAULT_PATH)
-            if(NOT ccse_test_include_path)
-                message(SEND_ERROR "Cannot locate ${ccse_inc_names} in ${CCSE_INCLUDE_DIR}")
-            endif()
-            set(CCSE_INCLUDE_DIR ${ccse_test_include_path} )
-        else()
-            message(SEND_ERROR "CCSE_INCLUDE_DIR=${CCSE_INCLUDE_DIR} does not exist")
-            set(CCSE_INCLUDE_DIR "CCSE_INCLUDE_DIR-NOTFOUND")
-        endif()
-
-    else()
-
-        set(ccse_inc_suffixes "include")
-        if(CCSE_DIR)
-
-            if (EXISTS "${CCSE_DIR}" )
-
-                find_path(CCSE_INCLUDE_DIR
-                          NAMES ${ccse_inc_names}
-                          HINTS ${CCSE_DIR}
-                          PATH_SUFFIXES ${ccse_inc_suffixes}
-                          NO_DEFAULT_PATH)
-
-            else()
-                 message(SEND_ERROR "CCSE_DIR=${CCSE_DIR} does not exist")
-                 set(CCSE_INCLUDE_DIR "CCSE_INCLUDE_DIR-NOTFOUND")
-            endif()
-
-
-        else()
-
-            find_path(CCSE_INCLUDE_DIR
-                      NAMES ${ccse_inc_names}
-                      PATH_SUFFIXES ${ccse_inc_suffixes})
-
-        endif()
-
-    endif()
-
-    if ( NOT CCSE_INCLUDE_DIR )
-        message(SEND_ERROR "Cannot locate CCSE include directory")
-    else()
-        set(CCSE_INCLUDE_DIRS ${CCSE_INCLUDE_DIR})
-    endif()
-
-    # Search for libraries
-    # Search order preference:
-    #  (1) CCSE_LIBRARY_DIR - check existence of path AND if the include files exist
-    #  (2) CCSE_DIR/<lib,Lib>
-    #  (3) Default CMake paths See cmake --html-help=out.html file for more information.
-    #
-    set(ccse_lib_name box_c)
-    if (CCSE_LIBRARY_DIR)
-
-        if (EXISTS "${CCSE_LIBRARY_DIR}")
-
-            find_library(CCSE_LIBRARY
-                         NAMES ${ccse_lib_name}
-                         HINTS ${CCSE_LIBRARY_DIR}
-                         NO_DEFAULT_PATH)
-        else()
-            message(SEND_ERROR "CCSE_LIBRARY_DIR=${CCSE_LIBRARY_DIR} does not exist")
-            set(CCSE_LIBRARY "CCSE_LIBRARY-NOTFOUND")
-        endif()
-
-    else()
-
-        if(CCSE_DIR)
-
-            if (EXISTS "${CCSE_DIR}" )
-
-                find_library(CCSE_LIBRARY
-                             NAMES ${ccse_lib_name}
-                             HINTS ${CCSE_DIR}
-                             PATH_SUFFIXES "lib"
-                             NO_DEFAULT_PATH)
-                get_filename_component(CCSE_LIBRARY_DIR "${CCSE_LIBRARY}" PATH)
-
-            else()
-                 message(SEND_ERROR "CCSE libs not found in CCSE_DIR/lib${CCSE_LIBDIR_MPI_SUFFIX}${CCSE_LIBDIR_OMP_SUFFIX}, (CCSE_DIR=${CCSE_DIR})")
-                 set(CCSE_LIBRARY "CCSE_LIBRARY-NOTFOUND")
-            endif()
-
-        else()
-
-            find_library(CCSE_LIBRARY
-                         NAMES ${ccse_lib_name})
-
-            get_filename_component(CCSE_LIBRARY_DIR "${CCSE_LIBRARY}" PATH)
-
-        endif()
-
-    endif()
-
-    # Now, make sure the rest are in the same place
-    set(CCSE_LIBRARIES box_camrdata;cboxlib;cfboxlib;fboxlib;gslib)
-
-    foreach (L ${CCSE_LIBRARIES})
-
-            find_library(CCSE_LIBRARY
-                         NAMES ${L}
-                         HINTS ${CCSE_LIBRARY_DIR}
-                         NO_DEFAULT_PATH)
-
-            if ( NOT CCSE_LIBRARY )
-                message(SEND_ERROR "Cannot locate CCSE library: ${L}")
-            endif()
-
-    endforeach()
-    set(CCSE_LIBRARY_DIRS ${CCSE_LIBRARY_DIR})
-
-    # Search for perl scripts
-    # Search order preference:
-    #  (1) CCSE_PERL_DIR - check existence of path AND if the perl script exist
-    #  (2) CCSE_DIR/perl
-    #  (3) Default CMake paths See cmake --html-help=out.html file for more information.
-    #
-    set(ccse_perl_name strip72)
-
-    if (CCSE_PERL_DIR)
-
-        if (EXISTS "${CCSE_PERL_DIR}")
-
-            find_path(CCSE_PERL
-                      NAMES ${ccse_perl_name}
-                      HINTS ${CCSE_PERL_DIR}
-                      NO_DEFAULT_PATH)
-        else()
-            message(SEND_ERROR "CCSE_PERL_DIR=${CCSE_PERL_DIR} does not exist")
-            set(CCSE_PERL "CCSE_PERL-NOTFOUND")
-        endif()
-
-    else()
-
-        if(CCSE_DIR)
-
-            if (EXISTS "${CCSE_DIR}" )
-
-                find_path(CCSE_PERL
-                          NAMES ${ccse_perl_name}
-                          HINTS "${CCSE_DIR}/perl"
-                          NO_DEFAULT_PATH)
-
-                if ( NOT CCSE_PERL )
-                    message(SEND_ERROR "CCSE Perl scripts not in CCSE_DIR/perl=${CCSE_DIR}/perl")
-                else()
-                    set(CCSE_PERL_DIR ${CCSE_PERL})
-                endif()
-
-            else()
-
-                message(SEND_ERROR "CCSE_DIR/perl=${CCSE_DIR}/perl does not exist")
-
-            endif()
-
-        endif()
-
-    endif()
-
-
-    set(CCSE_EXT_LIBRARIES "")
-
-
-endif(CCSE_LIBRARIES AND CCSE_INCLUDE_DIRS AND CCSE_PERL_DIR)
-
-# Send useful message if everything is found
-find_package_handle_standard_args(CCSE DEFAULT_MSG
-                                  CCSE_LIBRARIES
-                                  CCSE_LIBRARY_DIRS
-                                  CCSE_INCLUDE_DIRS
-                                  CCSE_PERL_DIR)
-
-mark_as_advanced(
-  CCSE_INCLUDE_DIR
-  CCSE_INCLUDE_DIRS
-  CCSE_LIBRARIES
-  CCSE_LIBRARY_DIR
-  CCSE_LIBRARY_DIRS
-  CCSE_PERL_DIR
-)
-

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_DIR - where to find gtest/gtest.h
 # GTEST_LIBRARY     - libgtest.a path
 # GTEST_MAIN_LIBRARY     - libgtest_main.a path
@@ -30,9 +26,21 @@ set( GTEST_BOTH_LIBRARIES
     ${GTEST_LIBRARY_MAIN}
 )
 
-IF(GTEST_INCLUDE_DIR AND GTEST_LIBRARY)
+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_DIR AND GTEST_LIBRARY)
+ENDIF()
 
 IF (GTEST_FOUND)
    IF (NOT GTEST_FIND_QUIETLY)
@@ -43,6 +51,4 @@ ELSE (GTEST_FOUND)
    IF (GTest_FIND_REQUIRED)
       MESSAGE(FATAL_ERROR "Could not find GTEST!")
    ENDIF (GTest_FIND_REQUIRED)
-ENDIF (GTEST_FOUND)
-
-
+ENDIF (GTEST_FOUND)
\ No newline at end of file

CMakeModules/FindH5Hut.cmake

@@ -35,17 +35,11 @@ ELSE (H5Hut_FOUND)
 ENDIF (H5Hut_FOUND)
 
 include (CheckIncludeFile)
+SET (CMAKE_REQUIRED_INCLUDES ${H5Hut_INCLUDE_DIR})
 CHECK_INCLUDE_FILE (H5_file_attribs.h HAVE_API2_FUNCTIONS "-I${H5Hut_INCLUDE_DIR} -DPARALLEL_IO")
 
 IF (HAVE_API2_FUNCTIONS)
-    MESSAGE (STATUS "H5hut version is >= 2")
-    SET (CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -DUSE_H5HUT2")
+    MESSAGE (STATUS "H5hut version is OK")
 ELSE (HAVE_API2_FUNCTIONS)
-    MESSAGE (STATUS "H5hut version is 1.x")
+    MESSAGE (ERROR "H5hut >= 2 required")
 ENDIF (HAVE_API2_FUNCTIONS)
-
-# Local Variables:
-# mode:cmake
-# cmake-tab-width: 4
-# indent-tabs-mode:nil
-# End:
\ No newline at end of file

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/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)