Changeset 1138

Timestamp:

05/18/17 17:40:03 (7 years ago)

Author:

yushan

Message:

test_remap back to work. No thread for now

Location:

XIOS/dev/branch_yushan_merged

Files:

• Doxyfile (modified) (6 diffs)
• bld.cfg (modified) (1 diff)
• extern/remap/src/mapper.cpp (modified) (3 diffs)
• extern/src_ep_dev/ep_gatherv.cpp (modified) (1 diff)
• extern/src_ep_dev/ep_memory.cpp (modified) (2 diffs)
• extern/src_ep_dev/ep_wait.cpp (modified) (2 diffs)
• src/io/inetcdf4.cpp (modified) (2 diffs)
• src/io/inetcdf4.hpp (modified) (1 diff)
• src/io/inetcdf4_decl.cpp (modified) (1 diff)
• src/io/inetcdf4_impl.hpp (modified) (1 diff)
• src/io/nc4_data_input.cpp (modified) (1 diff)
• src/io/nc4_data_input.hpp (modified) (1 diff)
• src/io/nc4_data_output.cpp (modified) (3 diffs)
• src/io/nc4_data_output.hpp (modified) (3 diffs)
• src/io/netCdfInterface.cpp (modified) (1 diff)
• src/io/netCdfInterface_decl.cpp (modified) (1 diff)
• src/io/netCdfInterface_impl.hpp (modified) (1 diff)
• src/io/netCdf_cf_constant.hpp (modified) (1 diff)
• src/io/netcdf.hpp (modified) (2 diffs)
• src/io/onetcdf4.cpp (modified) (5 diffs)
• src/io/onetcdf4.hpp (modified) (3 diffs)
• src/io/onetcdf4_decl.cpp (modified) (1 diff)
• src/io/onetcdf4_impl.hpp (modified) (1 diff)
• src/node/domain.cpp (modified) (5 diffs)
• src/node/file.cpp (modified) (2 diffs)
• src/node/transformation.hpp (modified) (2 diffs)
• src/test/test_remap.f90 (modified) (2 diffs)

XIOS/dev/branch_yushan_merged/Doxyfile

@@ -1 @@
-# Doxyfile 1.7.4
+# Doxyfile 1.8.10
 
 # This file describes the settings to be used by the documentation system
-# doxygen (www.doxygen.org) for a project
-#
-# All text after a hash (#) is considered a comment and will be ignored
+# doxygen (www.doxygen.org) for a project.
+#
+# All text after a double hash (##) is considered a comment and is placed in
+# front of the TAG it is preceding.
+#
+# All text after a single hash (#) is considered a comment and will be ignored.
 # The format is:
-#       TAG = value [value, ...]
-# For lists items can also be appended using:
-#       TAG += value [value, ...]
-# Values that contain spaces should be placed between quotes (" ")
+# TAG = value [value, ...]
+# For lists, items can also be appended using:
+# TAG += value [value, ...]
+# Values that contain spaces should be placed between quotes (\" \").
 
 #---------------------------------------------------------------------------
@@ -15 +18 @@
 #---------------------------------------------------------------------------
 
-# This tag specifies the encoding used for all characters in the config file 
-# that follow. The default is UTF-8 which is also the encoding used for all 
-# text before the first occurrence of this tag. Doxygen uses libiconv (or the 
-# iconv built into libc) for the transcoding. See 
-# http://www.gnu.org/software/libiconv for the list of possible encodings.
+# This tag specifies the encoding used for all characters in the config file
+# that follow. The default is UTF-8 which is also the encoding used for all text
+# before the first occurrence of this tag. Doxygen uses libiconv (or the iconv
+# built into libc) for the transcoding. See http://www.gnu.org/software/libiconv
+# for the list of possible encodings.
+# The default value is: UTF-8.
 
 DOXYFILE_ENCODING      = UTF-8
 
-# The PROJECT_NAME tag is a single word (or a sequence of words surrounded 
-# by quotes) that should identify the project.
+# The PROJECT_NAME tag is a single word (or a sequence of words surrounded by
+# double-quotes, unless you are using Doxywizard) that should identify the
+# project for which the documentation is generated. This name is used in the
+# title of most generated pages and in a few other places.
+# The default value is: My Project.
 
 PROJECT_NAME           = XIOS
 
-# 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.
+# The PROJECT_NUMBER tag can be used to enter a project or revision number. This
+# could be handy for archiving the generated documentation or if some version
+# control system is used.
 
 PROJECT_NUMBER         = 1.0
 
-# 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 quick idea about the purpose of the project. Keep the description short.
+# 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
+# quick idea about the purpose of the project. Keep the description short.
 
 PROJECT_BRIEF          = "Xml I/O Server"
 
-# With the PROJECT_LOGO tag one can specify an logo or icon that is 
-# included in the documentation. The maximum height of the logo should not 
-# exceed 55 pixels and the maximum width should not exceed 200 pixels. 
-# Doxygen will copy the logo to the output directory.
-
-PROJECT_LOGO           = 
-
-# The OUTPUT_DIRECTORY tag is used to specify the (relative or absolute) 
-# base path where the generated documentation will be put. 
-# If a relative path is entered, it will be relative to the location 
-# where doxygen was started. If left blank the current directory will be used.
+# With the PROJECT_LOGO tag one can specify a logo or an icon that is included
+# in the documentation. The maximum height of the logo should not exceed 55
+# pixels and the maximum width should not exceed 200 pixels. Doxygen will copy
+# the logo to the output directory.
+
+PROJECT_LOGO           =
+
+# The OUTPUT_DIRECTORY tag is used to specify the (relative or absolute) path
+# into which the generated documentation will be written. If a relative path is
+# entered, it will be relative to the location where doxygen was started. If
+# left blank the current directory will be used.
 
 OUTPUT_DIRECTORY       = ./doc
 
-# 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 will distribute the generated files over these directories. 
-# Enabling this option can be useful when feeding doxygen a huge amount of 
-# source files, where putting all generated files in the same directory would 
-# otherwise cause performance problems for the file system.
+# 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
+# will distribute the generated files over these directories. Enabling this
+# option can be useful when feeding doxygen a huge amount of source files, where
+# putting all generated files in the same directory would otherwise causes
+# performance problems for the file system.
+# The default value is: NO.
 
 CREATE_SUBDIRS         = NO
 
-# The OUTPUT_LANGUAGE tag is used to specify the language in which all 
-# documentation generated by doxygen is written. Doxygen will use this 
-# information to generate all constant output in the proper language. 
-# The default language is English, other supported languages are: 
-# Afrikaans, Arabic, Brazilian, Catalan, Chinese, Chinese-Traditional, 
-# Croatian, Czech, Danish, Dutch, Esperanto, Farsi, Finnish, French, German, 
-# Greek, Hungarian, Italian, Japanese, Japanese-en (Japanese with English 
-# messages), Korean, Korean-en, Lithuanian, Norwegian, Macedonian, Persian, 
-# Polish, Portuguese, Romanian, Russian, Serbian, Serbian-Cyrillic, Slovak, 
-# Slovene, Spanish, Swedish, Ukrainian, and Vietnamese.
+# If the ALLOW_UNICODE_NAMES tag is set to YES, doxygen will allow non-ASCII
+# characters to appear in the names of generated files. If set to NO, non-ASCII
+# characters will be escaped, for example _xE3_x81_x84 will be used for Unicode
+# U+3044.
+# The default value is: NO.
+
+ALLOW_UNICODE_NAMES    = NO
+
+# The OUTPUT_LANGUAGE tag is used to specify the language in which all
+# documentation generated by doxygen is written. Doxygen will use this
+# information to generate all constant output in the proper language.
+# Possible values are: Afrikaans, Arabic, Armenian, Brazilian, Catalan, Chinese,
+# Chinese-Traditional, Croatian, Czech, Danish, Dutch, English (United States),
+# Esperanto, Farsi (Persian), Finnish, French, German, Greek, Hungarian,
+# Indonesian, Italian, Japanese, Japanese-en (Japanese with English messages),
+# Korean, Korean-en (Korean with English messages), Latvian, Lithuanian,
+# Macedonian, Norwegian, Persian (Farsi), Polish, Portuguese, Romanian, Russian,
+# Serbian, Serbian-Cyrillic, Slovak, Slovene, Spanish, Swedish, Turkish,
+# Ukrainian and Vietnamese.
+# The default value is: English.
 
 OUTPUT_LANGUAGE        = French
 
-# If the BRIEF_MEMBER_DESC tag is set to YES (the default) Doxygen will 
-# include brief member descriptions after the members that are listed in 
-# the file and class documentation (similar to JavaDoc). 
-# Set to NO to disable this.
+# If the BRIEF_MEMBER_DESC tag is set to YES, doxygen will include brief member
+# descriptions after the members that are listed in the file and class
+# documentation (similar to Javadoc). Set to NO to disable this.
+# The default value is: YES.
 
 BRIEF_MEMBER_DESC      = YES
 
-# If the REPEAT_BRIEF tag is set to YES (the default) Doxygen will prepend 
-# the brief description of a member or function before the detailed description. 
-# Note: if both HIDE_UNDOC_MEMBERS and BRIEF_MEMBER_DESC are set to NO, the 
+# If the REPEAT_BRIEF tag is set to YES, doxygen will prepend the brief
+# description of a member or function before the detailed description
+#
+# Note: If both HIDE_UNDOC_MEMBERS and BRIEF_MEMBER_DESC are set to NO, the
 # brief descriptions will be completely suppressed.
+# The default value is: YES.
 
 REPEAT_BRIEF           = YES
 
-# This tag implements a quasi-intelligent brief description abbreviator 
-# that is used to form the text in various listings. Each string 
-# in this list, if found as the leading text of the brief description, will be 
-# stripped from the text and the result after processing the whole list, is 
-# used as the annotated text. Otherwise, the brief description is used as-is. 
-# If left blank, the following values are used ("$name" is automatically 
-# replaced with the name of the entity): "The $name class" "The $name widget" 
-# "The $name file" "is" "provides" "specifies" "contains" 
-# "represents" "a" "an" "the"
+# This tag implements a quasi-intelligent brief description abbreviator that is
+# used to form the text in various listings. Each string in this list, if found
+# as the leading text of the brief description, will be stripped from the text
+# and the result, after processing the whole list, is used as the annotated
+# text. Otherwise, the brief description is used as-is. If left blank, the
+# following values are used ($name is automatically replaced with the name of
+# the entity):The $name class, The $name widget, The $name file, is, provides,
+# specifies, contains, represents, a, an and the.
 
 ABBREVIATE_BRIEF       = "The $name class" \
@@ -112 +131 @@
                          the
 
-# If the ALWAYS_DETAILED_SEC and REPEAT_BRIEF tags are both set to YES then 
-# Doxygen will generate a detailed section even if there is only a brief 
+# If the ALWAYS_DETAILED_SEC and REPEAT_BRIEF tags are both set to YES then
+# doxygen will generate a detailed section even if there is only a brief
 # description.
+# The default value is: NO.
 
 ALWAYS_DETAILED_SEC    = NO
 
-# If the INLINE_INHERITED_MEMB tag is set to YES, doxygen will show all 
-# inherited members of a class in the documentation of that class as if those 
-# members were ordinary class members. Constructors, destructors and assignment 
+# If the INLINE_INHERITED_MEMB tag is set to YES, doxygen will show all
+# inherited members of a class in the documentation of that class as if those
+# members were ordinary class members. Constructors, destructors and assignment
 # operators of the base classes will not be shown.
+# The default value is: NO.
 
 INLINE_INHERITED_MEMB  = NO
 
-# If the FULL_PATH_NAMES tag is set to YES then Doxygen will prepend the full 
-# path before files name in the file list and in the header files. If set 
-# to NO the shortest path that makes the file name unique will be used.
+# If the FULL_PATH_NAMES tag is set to YES, doxygen will prepend the full path
+# before files name in the file list and in the header files. If set to NO the
+# shortest path that makes the file name unique will be used
+# The default value is: YES.
 
 FULL_PATH_NAMES        = YES
 
-# If the FULL_PATH_NAMES tag is set to YES then the STRIP_FROM_PATH tag 
-# can be used to strip a user-defined part of the path. Stripping is 
-# only done if one of the specified strings matches the left-hand part of 
-# the path. The tag can be used to show relative paths in the file list. 
-# If left blank the directory from which doxygen is run is used as the 
-# path to strip.
-
-STRIP_FROM_PATH        = 
-
-# The STRIP_FROM_INC_PATH tag can be used to strip a user-defined part of 
-# the path mentioned in the documentation of a class, which tells 
-# the reader which header file to include in order to use a class. 
-# If left blank only the name of the header file containing the class 
-# definition is used. Otherwise one should specify the include paths that 
-# are normally passed to the compiler using the -I flag.
-
-STRIP_FROM_INC_PATH    = 
-
-# If the SHORT_NAMES tag is set to YES, doxygen will generate much shorter 
-# (but less readable) file names. This can be useful if your file system 
-# doesn't support long names like on DOS, Mac, or CD-ROM.
+# The STRIP_FROM_PATH tag can be used to strip a user-defined part of the path.
+# Stripping is only done if one of the specified strings matches the left-hand
+# part of the path. The tag can be used to show relative paths in the file list.
+# If left blank the directory from which doxygen is run is used as the path to
+# strip.
+#
+# Note that you can specify absolute paths here, but also relative paths, which
+# will be relative from the directory where doxygen is started.
+# This tag requires that the tag FULL_PATH_NAMES is set to YES.
+
+STRIP_FROM_PATH        =
+
+# The STRIP_FROM_INC_PATH tag can be used to strip a user-defined part of the
+# path mentioned in the documentation of a class, which tells the reader which
+# header file to include in order to use a class. If left blank only the name of
+# the header file containing the class definition is used. Otherwise one should
+# specify the list of include paths that are normally passed to the compiler
+# using the -I flag.
+
+STRIP_FROM_INC_PATH    =
+
+# If the SHORT_NAMES tag is set to YES, doxygen will generate much shorter (but
+# less readable) file names. This can be useful is your file systems doesn't
+# support long names like on DOS, Mac, or CD-ROM.
+# The default value is: NO.
 
 SHORT_NAMES            = NO
 
-# If the JAVADOC_AUTOBRIEF tag is set to YES then Doxygen 
-# will interpret the first line (until the first dot) of a JavaDoc-style 
-# comment as the brief description. If set to NO, the JavaDoc 
-# comments will behave just like regular Qt-style comments 
-# (thus requiring an explicit @brief command for a brief description.)
+# If the JAVADOC_AUTOBRIEF tag is set to YES then doxygen will interpret the
+# first line (until the first dot) of a Javadoc-style comment as the brief
+# description. If set to NO, the Javadoc-style will behave just like regular Qt-
+# style comments (thus requiring an explicit @brief command for a brief
+# description.)
+# The default value is: NO.
 
 JAVADOC_AUTOBRIEF      = NO
 
-# If the QT_AUTOBRIEF tag is set to YES then Doxygen will 
-# interpret the first line (until the first dot) of a Qt-style 
-# comment as the brief description. If set to NO, the comments 
-# will behave just like regular Qt-style comments (thus requiring 
-# an explicit \brief command for a brief description.)
+# If the QT_AUTOBRIEF tag is set to YES then doxygen will interpret the first
+# line (until the first dot) of a Qt-style comment as the brief description. If
+# set to NO, the Qt-style will behave just like regular Qt-style comments (thus
+# requiring an explicit \brief command for a brief description.)
+# The default value is: NO.
 
 QT_AUTOBRIEF           = YES
 
-# The MULTILINE_CPP_IS_BRIEF tag can be set to YES to make Doxygen 
-# treat a multi-line C++ special comment block (i.e. a block of //! or /// 
-# comments) as a brief description. This used to be the default behaviour. 
-# The new default is to treat a multi-line C++ comment block as a detailed 
-# description. Set this tag to YES if you prefer the old behaviour instead.
+# The MULTILINE_CPP_IS_BRIEF tag can be set to YES to make doxygen treat a
+# multi-line C++ special comment block (i.e. a block of //! or /// comments) as
+# a brief description. This used to be the default behavior. The new default is
+# to treat a multi-line C++ comment block as a detailed description. Set this
+# tag to YES if you prefer the old behavior instead.
+#
+# Note that setting this tag to YES also means that rational rose comments are
+# not recognized any more.
+# The default value is: NO.
 
 MULTILINE_CPP_IS_BRIEF = NO
 
-# If the INHERIT_DOCS tag is set to YES (the default) then an undocumented 
-# member inherits the documentation from any documented member that it 
-# re-implements.
+# If the INHERIT_DOCS tag is set to YES then an undocumented member inherits the
+# documentation from any documented member that it re-implements.
+# The default value is: YES.
 
 INHERIT_DOCS           = YES
 
-# If the SEPARATE_MEMBER_PAGES tag is set to YES, then doxygen will produce 
-# a new page for each member. If set to NO, the documentation of a member will 
-# be part of the file/class/namespace that contains it.
+# If the SEPARATE_MEMBER_PAGES tag is set to YES then doxygen will produce a new
+# page for each member. If set to NO, the documentation of a member will be part
+# of the file/class/namespace that contains it.
+# The default value is: NO.
 
 SEPARATE_MEMBER_PAGES  = NO
 
-# The TAB_SIZE tag can be used to set the number of spaces in a tab. 
-# Doxygen uses this value to replace tabs by spaces in code fragments.
+# The TAB_SIZE tag can be used to set the number of spaces in a tab. Doxygen
+# uses this value to replace tabs by spaces in code fragments.
+# Minimum value: 1, maximum value: 16, default value: 4.
 
 TAB_SIZE               = 8
 
-# This tag can be used to specify a number of aliases that acts 
-# as commands in the documentation. An alias has the form "name=value". 
-# For example adding "sideeffect=\par Side Effects:\n" will allow you to 
-# put the command \sideeffect (or @sideeffect) in the documentation, which 
-# will result in a user-defined paragraph with heading "Side Effects:". 
-# You can put \n's in the value part of an alias to insert newlines.
-
-ALIASES                = 
-
-# Set the OPTIMIZE_OUTPUT_FOR_C tag to YES if your project consists of C 
-# sources only. Doxygen will then generate output that is more tailored for C. 
-# For instance, some of the names that are used will be different. The list 
-# of all members will be omitted, etc.
+# This tag can be used to specify a number of aliases that act as commands in
+# the documentation. An alias has the form:
+# name=value
+# For example adding
+# "sideeffect=@par Side Effects:\n"
+# will allow you to put the command \sideeffect (or @sideeffect) in the
+# documentation, which will result in a user-defined paragraph with heading
+# "Side Effects:". You can put \n's in the value part of an alias to insert
+# newlines.
+
+ALIASES                =
+
+# This tag can be used to specify a number of word-keyword mappings (TCL only).
+# A mapping has the form "name=value". For example adding "class=itcl::class"
+# will allow you to use the command class in the itcl::class meaning.
+
+TCL_SUBST              =
+
+# Set the OPTIMIZE_OUTPUT_FOR_C tag to YES if your project consists of C sources
+# only. Doxygen will then generate output that is more tailored for C. For
+# instance, some of the names that are used will be different. The list of all
+# members will be omitted, etc.
+# The default value is: NO.
 
 OPTIMIZE_OUTPUT_FOR_C  = NO
 
-# Set the OPTIMIZE_OUTPUT_JAVA tag to YES if your project consists of Java 
-# sources only. Doxygen will then generate output that is more tailored for 
-# Java. For instance, namespaces will be presented as packages, qualified 
-# scopes will look different, etc.
+# Set the OPTIMIZE_OUTPUT_JAVA tag to YES if your project consists of Java or
+# Python sources only. Doxygen will then generate output that is more tailored
+# for that language. For instance, namespaces will be presented as packages,
+# qualified scopes will look different, etc.
+# The default value is: NO.
 
 OPTIMIZE_OUTPUT_JAVA   = NO
 
-# Set the OPTIMIZE_FOR_FORTRAN tag to YES if your project consists of Fortran 
-# sources only. Doxygen will then generate output that is more tailored for 
-# Fortran.
+# Set the OPTIMIZE_FOR_FORTRAN tag to YES if your project consists of Fortran
+# sources. Doxygen will then generate output that is tailored for Fortran.
+# The default value is: NO.
 
 OPTIMIZE_FOR_FORTRAN   = NO
 
-# Set the OPTIMIZE_OUTPUT_VHDL tag to YES if your project consists of VHDL 
-# sources. Doxygen will then generate output that is tailored for 
-# VHDL.
+# Set the OPTIMIZE_OUTPUT_VHDL tag to YES if your project consists of VHDL
+# sources. Doxygen will then generate output that is tailored for VHDL.
+# The default value is: NO.
 
 OPTIMIZE_OUTPUT_VHDL   = NO
 
-# Doxygen selects the parser to use depending on the extension of the files it 
-# parses. With this tag you can assign which parser to use for a given extension. 
-# Doxygen has a built-in mapping, but you can override or extend it using this 
-# tag. The format is ext=language, where ext is a file extension, and language 
-# is one of the parsers supported by doxygen: IDL, Java, Javascript, CSharp, C, 
-# C++, D, PHP, Objective-C, Python, Fortran, VHDL, C, C++. For instance to make 
-# doxygen treat .inc files as Fortran files (default is PHP), and .f files as C 
-# (default is Fortran), use: inc=Fortran f=C. Note that for custom extensions 
-# you also need to set FILE_PATTERNS otherwise the files are not read by doxygen.
-
-EXTENSION_MAPPING      = 
-
-# If you use STL classes (i.e. std::string, std::vector, etc.) but do not want 
-# to include (a tag file for) the STL sources as input, then you should 
-# set this tag to YES in order to let doxygen match functions declarations and 
-# definitions whose arguments contain STL classes (e.g. func(std::string); v.s. 
-# func(std::string) {}). This also makes the inheritance and collaboration 
+# Doxygen selects the parser to use depending on the extension of the files it
+# parses. With this tag you can assign which parser to use for a given
+# extension. Doxygen has a built-in mapping, but you can override or extend it
+# using this tag. The format is ext=language, where ext is a file extension, and
+# language is one of the parsers supported by doxygen: IDL, Java, Javascript,
+# C#, C, C++, D, PHP, Objective-C, Python, Fortran (fixed format Fortran:
+# FortranFixed, free formatted Fortran: FortranFree, unknown formatted Fortran:
+# Fortran. In the later case the parser tries to guess whether the code is fixed
+# or free formatted code, this is the default for Fortran type files), VHDL. For
+# instance to make doxygen treat .inc files as Fortran files (default is PHP),
+# and .f files as C (default is Fortran), use: inc=Fortran f=C.
+#
+# Note: For files without extension you can use no_extension as a placeholder.
+#
+# Note that for custom extensions you also need to set FILE_PATTERNS otherwise
+# the files are not read by doxygen.
+
+EXTENSION_MAPPING      =
+
+# If the MARKDOWN_SUPPORT tag is enabled then doxygen pre-processes all comments
+# according to the Markdown format, which allows for more readable
+# documentation. See http://daringfireball.net/projects/markdown/ for details.
+# The output of markdown processing is further processed by doxygen, so you can
+# mix doxygen, HTML, and XML commands with Markdown formatting. Disable only in
+# case of backward compatibilities issues.
+# The default value is: YES.
+
+MARKDOWN_SUPPORT       = YES
+
+# When enabled doxygen tries to link words that correspond to documented
+# classes, or namespaces to their corresponding documentation. Such a link can
+# be prevented in individual cases by putting a % sign in front of the word or
+# globally by setting AUTOLINK_SUPPORT to NO.
+# The default value is: YES.
+
+AUTOLINK_SUPPORT       = YES
+
+# If you use STL classes (i.e. std::string, std::vector, etc.) but do not want
+# to include (a tag file for) the STL sources as input, then you should set this
+# tag to YES in order to let doxygen match functions declarations and
+# definitions whose arguments contain STL classes (e.g. func(std::string);
+# versus func(std::string) {}). This also make the inheritance and collaboration
 # diagrams that involve STL classes more complete and accurate.
+# The default value is: NO.
 
 BUILTIN_STL_SUPPORT    = YES
 
-# If you use Microsoft's C++/CLI language, you should set this option to YES to 
+# If you use Microsoft's C++/CLI language, you should set this option to YES to
 # enable parsing support.
+# The default value is: NO.
 
 CPP_CLI_SUPPORT        = NO
 
-# Set the SIP_SUPPORT tag to YES if your project consists of sip sources only. 
-# Doxygen will parse them like normal C++ but will assume all classes use public 
-# instead of private inheritance when no explicit protection keyword is present.
+# Set the SIP_SUPPORT tag to YES if your project consists of sip (see:
+# http://www.riverbankcomputing.co.uk/software/sip/intro) sources only. Doxygen
+# will parse them like normal C++ but will assume all classes use public instead
+# of private inheritance when no explicit protection keyword is present.
+# The default value is: NO.
 
 SIP_SUPPORT            = NO
 
-# For Microsoft's IDL there are propget and propput attributes to indicate getter 
-# and setter methods for a property. Setting this option to YES (the default) 
-# will make doxygen replace the get and set methods by a property in the 
-# documentation. This will only work if the methods are indeed getting or 
-# setting a simple type. If this is not the case, or you want to show the 
-# methods anyway, you should set this option to NO.
+# For Microsoft's IDL there are propget and propput attributes to indicate
+# getter and setter methods for a property. Setting this option to YES will make
+# doxygen to replace the get and set methods by a property in the documentation.
+# This will only work if the methods are indeed getting or setting a simple
+# type. If this is not the case, or you want to show the methods anyway, you
+# should set this option to NO.
+# The default value is: YES.
 
 IDL_PROPERTY_SUPPORT   = YES
 
-# If member grouping is used in the documentation and the DISTRIBUTE_GROUP_DOC 
-# tag is set to YES, then doxygen will reuse the documentation of the first 
-# member in the group (if any) for the other members of the group. By default 
+# If member grouping is used in the documentation and the DISTRIBUTE_GROUP_DOC
+# tag is set to YES then doxygen will reuse the documentation of the first
+# member in the group (if any) for the other members of the group. By default
 # all members of a group must be documented explicitly.
+# The default value is: NO.
 
 DISTRIBUTE_GROUP_DOC   = NO
 
-# Set the SUBGROUPING tag to YES (the default) to allow class member groups of 
-# the same type (for instance a group of public functions) to be put as a 
-# subgroup of that type (e.g. under the Public Functions section). Set it to 
-# NO to prevent subgrouping. Alternatively, this can be done per class using 
-# the \nosubgrouping command.
+# If one adds a struct or class to a group and this option is enabled, then also
+# any nested class or struct is added to the same group. By default this option
+# is disabled and one has to add nested compounds explicitly via \ingroup.
+# The default value is: NO.
+
+GROUP_NESTED_COMPOUNDS = NO
+
+# Set the SUBGROUPING tag to YES to allow class member groups of the same type
+# (for instance a group of public functions) to be put as a subgroup of that
+# type (e.g. under the Public Functions section). Set it to NO to prevent
+# subgrouping. Alternatively, this can be done per class using the
+# \nosubgrouping command.
+# The default value is: YES.
 
 SUBGROUPING            = YES
 
-# When the INLINE_GROUPED_CLASSES tag is set to YES, classes, structs and 
-# unions are shown inside the group in which they are included (e.g. using 
-# @ingroup) instead of on a separate page (for HTML and Man pages) or 
-# section (for LaTeX and RTF).
+# When the INLINE_GROUPED_CLASSES tag is set to YES, classes, structs and unions
+# are shown inside the group in which they are included (e.g. using \ingroup)
+# instead of on a separate page (for HTML and Man pages) or section (for LaTeX
+# and RTF).
+#
+# Note that this feature does not work in combination with
+# SEPARATE_MEMBER_PAGES.
+# The default value is: NO.
 
 INLINE_GROUPED_CLASSES = NO
 
-# When TYPEDEF_HIDES_STRUCT is enabled, a typedef of a struct, union, or enum 
-# is documented as struct, union, or enum with the name of the typedef. So 
-# typedef struct TypeS {} TypeT, will appear in the documentation as a struct 
-# with name TypeT. When disabled the typedef will appear as a member of a file, 
-# namespace, or class. And the struct will be named TypeS. This can typically 
-# be useful for C code in case the coding convention dictates that all compound 
+# When the INLINE_SIMPLE_STRUCTS tag is set to YES, structs, classes, and unions
+# with only public data fields or simple typedef fields will be shown inline in
+# the documentation of the scope in which they are defined (i.e. file,
+# namespace, or group documentation), provided this scope is documented. If set
+# to NO, structs, classes, and unions are shown on a separate page (for HTML and
+# Man pages) or section (for LaTeX and RTF).
+# The default value is: NO.
+
+INLINE_SIMPLE_STRUCTS  = NO
+
+# When TYPEDEF_HIDES_STRUCT tag is enabled, a typedef of a struct, union, or
+# enum is documented as struct, union, or enum with the name of the typedef. So
+# typedef struct TypeS {} TypeT, will appear in the documentation as a struct
+# with name TypeT. When disabled the typedef will appear as a member of a file,
+# namespace, or class. And the struct will be named TypeS. This can typically be
+# useful for C code in case the coding convention dictates that all compound
 # types are typedef'ed and only the typedef is referenced, never the tag name.
+# The default value is: NO.
 
 TYPEDEF_HIDES_STRUCT   = NO
 
-# The SYMBOL_CACHE_SIZE determines the size of the internal cache use to 
-# determine which symbols to keep in memory and which to flush to disk. 
-# When the cache is full, less often used symbols will be written to disk. 
-# For small to medium size projects (<1000 input files) the default value is 
-# probably good enough. For larger projects a too small cache size can cause 
-# doxygen to be busy swapping symbols to and from disk most of the time 
-# causing a significant performance penalty. 
-# If the system has enough physical memory increasing the cache will improve the 
-# performance by keeping more symbols in memory. Note that the value works on 
-# a logarithmic scale so increasing the size by one will roughly double the 
-# memory usage. The cache size is given by this formula: 
-# 2^(16+SYMBOL_CACHE_SIZE). The valid range is 0..9, the default is 0, 
-# corresponding to a cache size of 2^16 = 65536 symbols
-
-SYMBOL_CACHE_SIZE      = 0
+# The size of the symbol lookup cache can be set using LOOKUP_CACHE_SIZE. This
+# cache is used to resolve symbols given their name and scope. Since this can be
+# an expensive process and often the same symbol appears multiple times in the
+# code, doxygen keeps a cache of pre-resolved symbols. If the cache is too small
+# doxygen will become slower. If the cache is too large, memory is wasted. The
+# cache size is given by this formula: 2^(16+LOOKUP_CACHE_SIZE). The valid range
+# is 0..9, the default is 0, corresponding to a cache size of 2^16=65536
+# symbols. At the end of a run doxygen will report the cache usage and suggest
+# the optimal cache size from a speed point of view.
+# Minimum value: 0, maximum value: 9, default value: 0.
+
+LOOKUP_CACHE_SIZE      = 0
 
 #---------------------------------------------------------------------------
@@ -324 +419 @@
 #---------------------------------------------------------------------------
 
-# If the EXTRACT_ALL tag is set to YES doxygen will assume all entities in 
-# documentation are documented, even if no documentation was available. 
-# Private class members and static file members will be hidden unless 
-# the EXTRACT_PRIVATE and EXTRACT_STATIC tags are set to YES
+# If the EXTRACT_ALL tag is set to YES, doxygen will assume all entities in
+# documentation are documented, even if no documentation was available. Private
+# class members and static file members will be hidden unless the
+# EXTRACT_PRIVATE respectively EXTRACT_STATIC tags are set to YES.
+# Note: This will also disable the warnings about undocumented members that are
+# normally produced when WARNINGS is set to YES.
+# The default value is: NO.
 
 EXTRACT_ALL            = YES
 
-# If the EXTRACT_PRIVATE tag is set to YES all private members of a class 
-# will be included in the documentation.
+# If the EXTRACT_PRIVATE tag is set to YES, all private members of a class will
+# be included in the documentation.
+# The default value is: NO.
 
 EXTRACT_PRIVATE        = YES
 
-# If the EXTRACT_STATIC tag is set to YES all static members of a file 
-# will be included in the documentation.
+# If the EXTRACT_PACKAGE tag is set to YES, all members with package or internal
+# scope will be included in the documentation.
+# The default value is: NO.
+
+EXTRACT_PACKAGE        = NO
+
+# If the EXTRACT_STATIC tag is set to YES, all static members of a file will be
+# included in the documentation.
+# The default value is: NO.
 
 EXTRACT_STATIC         = YES
 
-# If the EXTRACT_LOCAL_CLASSES tag is set to YES classes (and structs) 
-# defined locally in source files will be included in the documentation. 
-# If set to NO only classes defined in header files are included.
+# If the EXTRACT_LOCAL_CLASSES tag is set to YES, classes (and structs) defined
+# locally in source files will be included in the documentation. If set to NO,
+# only classes defined in header files are included. Does not have any effect
+# for Java sources.
+# The default value is: YES.
 
 EXTRACT_LOCAL_CLASSES  = YES
 
-# This flag is only useful for Objective-C code. When set to YES local 
-# methods, which are defined in the implementation section but not in 
-# the interface are included in the documentation. 
-# If set to NO (the default) only methods in the interface are included.
+# This flag is only useful for Objective-C code. If set to YES, local methods,
+# which are defined in the implementation section but not in the interface are
+# included in the documentation. If set to NO, only methods in the interface are
+# included.
+# The default value is: NO.
 
 EXTRACT_LOCAL_METHODS  = YES
 
-# If this flag is set to YES, the members of anonymous namespaces will be 
-# extracted and appear in the documentation as a namespace called 
-# 'anonymous_namespace{file}', where file will be replaced with the base 
-# name of the file that contains the anonymous namespace. By default 
-# anonymous namespaces are hidden.
+# If this flag is set to YES, the members of anonymous namespaces will be
+# extracted and appear in the documentation as a namespace called
+# 'anonymous_namespace{file}', where file will be replaced with the base name of
+# the file that contains the anonymous namespace. By default anonymous namespace
+# are hidden.
+# The default value is: NO.
 
 EXTRACT_ANON_NSPACES   = NO
 
-# If the HIDE_UNDOC_MEMBERS tag is set to YES, Doxygen will hide all 
-# undocumented members of documented classes, files or namespaces. 
-# If set to NO (the default) these members will be included in the 
-# various overviews, but no documentation section is generated. 
-# This option has no effect if EXTRACT_ALL is enabled.
+# If the HIDE_UNDOC_MEMBERS tag is set to YES, doxygen will hide all
+# undocumented members inside documented classes or files. If set to NO these
+# members will be included in the various overviews, but no documentation
+# section is generated. This option has no effect if EXTRACT_ALL is enabled.
+# The default value is: NO.
 
 HIDE_UNDOC_MEMBERS     = NO
 
-# If the HIDE_UNDOC_CLASSES tag is set to YES, Doxygen will hide all 
-# undocumented classes that are normally visible in the class hierarchy. 
-# If set to NO (the default) these classes will be included in the various 
-# overviews. This option has no effect if EXTRACT_ALL is enabled.
+# If the HIDE_UNDOC_CLASSES tag is set to YES, doxygen will hide all
+# undocumented classes that are normally visible in the class hierarchy. If set
+# to NO, these classes will be included in the various overviews. This option
+# has no effect if EXTRACT_ALL is enabled.
+# The default value is: NO.
 
 HIDE_UNDOC_CLASSES     = NO
 
-# If the HIDE_FRIEND_COMPOUNDS tag is set to YES, Doxygen will hide all 
-# friend (class|struct|union) declarations. 
-# If set to NO (the default) these declarations will be included in the 
-# documentation.
+# If the HIDE_FRIEND_COMPOUNDS tag is set to YES, doxygen will hide all friend
+# (class|struct|union) declarations. If set to NO, these declarations will be
+# included in the documentation.
+# The default value is: NO.
 
 HIDE_FRIEND_COMPOUNDS  = NO
 
-# If the HIDE_IN_BODY_DOCS tag is set to YES, Doxygen will hide any 
-# documentation blocks found inside the body of a function. 
-# If set to NO (the default) these blocks will be appended to the 
-# function's detailed documentation block.
+# If the HIDE_IN_BODY_DOCS tag is set to YES, doxygen will hide any
+# documentation blocks found inside the body of a function. If set to NO, these
+# blocks will be appended to the function's detailed documentation block.
+# The default value is: NO.
 
 HIDE_IN_BODY_DOCS      = NO
 
-# The INTERNAL_DOCS tag determines if documentation 
-# that is typed after a \internal command is included. If the tag is set 
-# to NO (the default) then the documentation will be excluded. 
-# Set it to YES to include the internal documentation.
+# The INTERNAL_DOCS tag determines if documentation that is typed after a
+# \internal command is included. If the tag is set to NO then the documentation
+# will be excluded. Set it to YES to include the internal documentation.
+# The default value is: NO.
 
 INTERNAL_DOCS          = NO
 
-# If the CASE_SENSE_NAMES tag is set to NO then Doxygen will only generate 
-# file names in lower-case letters. If set to YES upper-case letters are also 
-# allowed. This is useful if you have classes or files whose names only differ 
-# in case and if your file system supports case sensitive file names. Windows 
+# If the CASE_SENSE_NAMES tag is set to NO then doxygen will only generate file
+# names in lower-case letters. If set to YES, upper-case letters are also
+# allowed. This is useful if you have classes or files whose names only differ
+# in case and if your file system supports case sensitive file names. Windows
 # and Mac users are advised to set this option to NO.
+# The default value is: system dependent.
 
 CASE_SENSE_NAMES       = NO
 
-# If the HIDE_SCOPE_NAMES tag is set to NO (the default) then Doxygen 
-# will show members with their full class and namespace scopes in the 
-# documentation. If set to YES the scope will be hidden.
+# If the HIDE_SCOPE_NAMES tag is set to NO then doxygen will show members with
+# their full class and namespace scopes in the documentation. If set to YES, the
+# scope will be hidden.
+# The default value is: NO.
 
 HIDE_SCOPE_NAMES       = NO
 
-# If the SHOW_INCLUDE_FILES tag is set to YES (the default) then Doxygen 
-# will put a list of the files that are included by a file in the documentation 
-# of that file.
+# If the HIDE_COMPOUND_REFERENCE tag is set to NO (default) then doxygen will
+# append additional text to a page's title, such as Class Reference. If set to
+# YES the compound reference will be hidden.
+# The default value is: NO.
+
+HIDE_COMPOUND_REFERENCE= NO
+
+# If the SHOW_INCLUDE_FILES tag is set to YES then doxygen will put a list of
+# the files that are included by a file in the documentation of that file.
+# The default value is: YES.
 
 SHOW_INCLUDE_FILES     = YES
 
-# If the FORCE_LOCAL_INCLUDES tag is set to YES then Doxygen 
-# will list include files with double quotes in the documentation 
-# rather than with sharp brackets.
+# If the SHOW_GROUPED_MEMB_INC tag is set to YES then Doxygen will add for each
+# grouped member an include statement to the documentation, telling the reader
+# which file to include in order to use the member.
+# The default value is: NO.
+
+SHOW_GROUPED_MEMB_INC  = NO
+
+# If the FORCE_LOCAL_INCLUDES tag is set to YES then doxygen will list include
+# files with double quotes in the documentation rather than with sharp brackets.
+# The default value is: NO.
 
 FORCE_LOCAL_INCLUDES   = NO
 
-# If the INLINE_INFO tag is set to YES (the default) then a tag [inline] 
-# is inserted in the documentation for inline members.
+# If the INLINE_INFO tag is set to YES then a tag [inline] is inserted in the
+# documentation for inline members.
+# The default value is: YES.
 
 INLINE_INFO            = YES
 
-# If the SORT_MEMBER_DOCS tag is set to YES (the default) then doxygen 
-# will sort the (detailed) documentation of file and class members 
-# alphabetically by member name. If set to NO the members will appear in 
-# declaration order.
+# If the SORT_MEMBER_DOCS tag is set to YES then doxygen will sort the
+# (detailed) documentation of file and class members alphabetically by member
+# name. If set to NO, the members will appear in declaration order.
+# The default value is: YES.
 
 SORT_MEMBER_DOCS       = YES
 
-# If the SORT_BRIEF_DOCS tag is set to YES then doxygen will sort the 
-# brief documentation of file, namespace and class members alphabetically 
-# by member name. If set to NO (the default) the members will appear in 
-# declaration order.
+# If the SORT_BRIEF_DOCS tag is set to YES then doxygen will sort the brief
+# descriptions of file, namespace and class members alphabetically by member
+# name. If set to NO, the members will appear in declaration order. Note that
+# this will also influence the order of the classes in the class list.
+# The default value is: NO.
 
 SORT_BRIEF_DOCS        = NO
 
-# If the SORT_MEMBERS_CTORS_1ST tag is set to YES then doxygen 
-# will sort the (brief and detailed) documentation of class members so that 
-# constructors and destructors are listed first. If set to NO (the default) 
-# the constructors will appear in the respective orders defined by 
-# SORT_MEMBER_DOCS and SORT_BRIEF_DOCS. 
-# This tag will be ignored for brief docs if SORT_BRIEF_DOCS is set to NO 
-# and ignored for detailed docs if SORT_MEMBER_DOCS is set to NO.
+# If the SORT_MEMBERS_CTORS_1ST tag is set to YES then doxygen will sort the
+# (brief and detailed) documentation of class members so that constructors and
+# destructors are listed first. If set to NO the constructors will appear in the
+# respective orders defined by SORT_BRIEF_DOCS and SORT_MEMBER_DOCS.
+# Note: If SORT_BRIEF_DOCS is set to NO this option is ignored for sorting brief
+# member documentation.
+# Note: If SORT_MEMBER_DOCS is set to NO this option is ignored for sorting
+# detailed member documentation.
+# The default value is: NO.
 
 SORT_MEMBERS_CTORS_1ST = NO
 
-# If the SORT_GROUP_NAMES tag is set to YES then doxygen will sort the 
-# hierarchy of group names into alphabetical order. If set to NO (the default) 
-# the group names will appear in their defined order.
+# If the SORT_GROUP_NAMES tag is set to YES then doxygen will sort the hierarchy
+# of group names into alphabetical order. If set to NO the group names will
+# appear in their defined order.
+# The default value is: NO.
 
 SORT_GROUP_NAMES       = NO
 
-# If the SORT_BY_SCOPE_NAME tag is set to YES, the class list will be 
-# sorted by fully-qualified names, including namespaces. If set to 
-# NO (the default), the class list will be sorted only by class name, 
-# not including the namespace part. 
-# Note: This option is not very useful if HIDE_SCOPE_NAMES is set to YES. 
-# Note: This option applies only to the class list, not to the 
-# alphabetical list.
+# If the SORT_BY_SCOPE_NAME tag is set to YES, the class list will be sorted by
+# fully-qualified names, including namespaces. If set to NO, the class list will
+# be sorted only by class name, not including the namespace part.
+# Note: This option is not very useful if HIDE_SCOPE_NAMES is set to YES.
+# Note: This option applies only to the class list, not to the alphabetical
+# list.
+# The default value is: NO.
 
 SORT_BY_SCOPE_NAME     = NO
 
-# If the STRICT_PROTO_MATCHING option is enabled and doxygen fails to 
-# do proper type resolution of all parameters of a function it will reject a 
-# match between the prototype and the implementation of a member function even 
-# if there is only one candidate or it is obvious which candidate to choose 
-# by doing a simple string match. By disabling STRICT_PROTO_MATCHING doxygen 
-# will still accept a match between prototype and implementation in such cases.
+# If the STRICT_PROTO_MATCHING option is enabled and doxygen fails to do proper
+# type resolution of all parameters of a function it will reject a match between
+# the prototype and the implementation of a member function even if there is
+# only one candidate or it is obvious which candidate to choose by doing a
+# simple string match. By disabling STRICT_PROTO_MATCHING doxygen will still
+# accept a match between prototype and implementation in such cases.
+# The default value is: NO.
 
 STRICT_PROTO_MATCHING  = NO
 
-# The GENERATE_TODOLIST tag can be used to enable (YES) or 
-# disable (NO) the todo list. This list is created by putting \todo 
-# commands in the documentation.
+# The GENERATE_TODOLIST tag can be used to enable (YES) or disable (NO) the todo
+# list. This list is created by putting \todo commands in the documentation.
+# The default value is: YES.
 
 GENERATE_TODOLIST      = YES
 
-# The GENERATE_TESTLIST tag can be used to enable (YES) or 
-# disable (NO) the test list. This list is created by putting \test 
-# commands in the documentation.
+# The GENERATE_TESTLIST tag can be used to enable (YES) or disable (NO) the test
+# list. This list is created by putting \test commands in the documentation.
+# The default value is: YES.
 
 GENERATE_TESTLIST      = YES
 
-# The GENERATE_BUGLIST tag can be used to enable (YES) or 
-# disable (NO) the bug list. This list is created by putting \bug 
-# commands in the documentation.
+# The GENERATE_BUGLIST tag can be used to enable (YES) or disable (NO) the bug
+# list. This list is created by putting \bug commands in the documentation.
+# The default value is: YES.
 
 GENERATE_BUGLIST       = YES
 
-# The GENERATE_DEPRECATEDLIST tag can be used to enable (YES) or 
-# disable (NO) the deprecated list. This list is created by putting 
-# \deprecated commands in the documentation.
+# The GENERATE_DEPRECATEDLIST tag can be used to enable (YES) or disable (NO)
+# the deprecated list. This list is created by putting \deprecated commands in
+# the documentation.
+# The default value is: YES.
 
 GENERATE_DEPRECATEDLIST= YES
 
-# The ENABLED_SECTIONS tag can be used to enable conditional 
-# documentation sections, marked by \if sectionname ... \endif.
-
-ENABLED_SECTIONS       = 
-
-# The MAX_INITIALIZER_LINES tag determines the maximum number of lines 
-# the initial value of a variable or macro consists of for it to appear in 
-# the documentation. If the initializer consists of more lines than specified 
-# here it will be hidden. Use a value of 0 to hide initializers completely. 
-# The appearance of the initializer of individual variables and macros in the 
-# documentation can be controlled using \showinitializer or \hideinitializer 
-# command in the documentation regardless of this setting.
+# The ENABLED_SECTIONS tag can be used to enable conditional documentation
+# sections, marked by \if <section_label> ... \endif and \cond <section_label>
+# ... \endcond blocks.
+
+ENABLED_SECTIONS       =
+
+# The MAX_INITIALIZER_LINES tag determines the maximum number of lines that the
+# initial value of a variable or macro / define can have for it to appear in the
+# documentation. If the initializer consists of more lines than specified here
+# it will be hidden. Use a value of 0 to hide initializers completely. The
+# appearance of the value of individual variables and macros / defines can be
+# controlled using \showinitializer or \hideinitializer command in the
+# documentation regardless of this setting.
+# Minimum value: 0, maximum value: 10000, default value: 30.
 
 MAX_INITIALIZER_LINES  = 30
 
-# Set the SHOW_USED_FILES tag to NO to disable the list of files generated 
-# at the bottom of the documentation of classes and structs. If set to YES the 
+# Set the SHOW_USED_FILES tag to NO to disable the list of files generated at
+# the bottom of the documentation of classes and structs. If set to YES, the
 # list will mention the files that were used to generate the documentation.
+# The default value is: YES.
 
 SHOW_USED_FILES        = YES
 
-# If the sources in your project are distributed over multiple directories 
-# then setting the SHOW_DIRECTORIES tag to YES will show the directory hierarchy 
-# in the documentation. The default is NO.
-
-SHOW_DIRECTORIES       = YES
-
-# Set the SHOW_FILES tag to NO to disable the generation of the Files page. 
-# This will remove the Files entry from the Quick Index and from the 
-# Folder Tree View (if specified). The default is YES.
+# Set the SHOW_FILES tag to NO to disable the generation of the Files page. This
+# will remove the Files entry from the Quick Index and from the Folder Tree View
+# (if specified).
+# The default value is: YES.
 
 SHOW_FILES             = YES
 
-# Set the SHOW_NAMESPACES tag to NO to disable the generation of the 
-# Namespaces page.  This will remove the Namespaces entry from the Quick Index 
-# and from the Folder Tree View (if specified). The default is YES.
+# Set the SHOW_NAMESPACES tag to NO to disable the generation of the Namespaces
+# page. This will remove the Namespaces entry from the Quick Index and from the
+# Folder Tree View (if specified).
+# The default value is: YES.
 
 SHOW_NAMESPACES        = YES
 
-# The FILE_VERSION_FILTER tag can be used to specify a program or script that 
-# doxygen should invoke to get the current version for each file (typically from 
-# the version control system). Doxygen will invoke the program by executing (via 
-# popen()) the command <command> <input-file>, where <command> is the value of 
-# the FILE_VERSION_FILTER tag, and <input-file> is the name of an input file 
-# provided by doxygen. Whatever the program writes to standard output 
-# is used as the file version. See the manual for examples.
-
-FILE_VERSION_FILTER    = 
-
-# The LAYOUT_FILE tag can be used to specify a layout file which will be parsed 
-# by doxygen. The layout file controls the global structure of the generated 
-# output files in an output format independent way. The create the layout file 
-# that represents doxygen's defaults, run doxygen with the -l option. 
-# You can optionally specify a file name after the option, if omitted 
-# DoxygenLayout.xml will be used as the name of the layout file.
-
-LAYOUT_FILE            = 
-
-#---------------------------------------------------------------------------
-# configuration options related to warning and progress messages
-#---------------------------------------------------------------------------
-
-# The QUIET tag can be used to turn on/off the messages that are generated 
-# by doxygen. Possible values are YES and NO. If left blank NO is used.
+# The FILE_VERSION_FILTER tag can be used to specify a program or script that
+# doxygen should invoke to get the current version for each file (typically from
+# the version control system). Doxygen will invoke the program by executing (via
+# popen()) the command command input-file, where command is the value of the
+# FILE_VERSION_FILTER tag, and input-file is the name of an input file provided
+# by doxygen. Whatever the program writes to standard output is used as the file
+# version. For an example see the documentation.
+
+FILE_VERSION_FILTER    =
+
+# The LAYOUT_FILE tag can be used to specify a layout file which will be parsed
+# by doxygen. The layout file controls the global structure of the generated
+# output files in an output format independent way. To create the layout file
+# that represents doxygen's defaults, run doxygen with the -l option. You can
+# optionally specify a file name after the option, if omitted DoxygenLayout.xml
+# will be used as the name of the layout file.
+#
+# Note that if you run doxygen from a directory containing a file called
+# DoxygenLayout.xml, doxygen will parse it automatically even if the LAYOUT_FILE
+# tag is left empty.
+
+LAYOUT_FILE            =
+
+# The CITE_BIB_FILES tag can be used to specify one or more bib files containing
+# the reference definitions. This must be a list of .bib files. The .bib
+# extension is automatically appended if omitted. This requires the bibtex tool
+# to be installed. See also http://en.wikipedia.org/wiki/BibTeX for more info.
+# For LaTeX the style of the bibliography can be controlled using
+# LATEX_BIB_STYLE. To use this feature you need bibtex and perl available in the
+# search path. See also \cite for info how to create references.
+
+CITE_BIB_FILES         =
+
+#---------------------------------------------------------------------------
+# Configuration options related to warning and progress messages
+#---------------------------------------------------------------------------
+
+# The QUIET tag can be used to turn on/off the messages that are generated to
+# standard output by doxygen. If QUIET is set to YES this implies that the
+# messages are off.
+# The default value is: NO.
 
 QUIET                  = NO
 
-# The WARNINGS tag can be used to turn on/off the warning messages that are 
-# generated by doxygen. Possible values are YES and NO. If left blank 
-# NO is used.
+# The WARNINGS tag can be used to turn on/off the warning messages that are
+# generated to standard error (stderr) by doxygen. If WARNINGS is set to YES
+# this implies that the warnings are on.
+#
+# Tip: Turn warnings on while writing the documentation.
+# The default value is: YES.
 
 WARNINGS               = YES
 
-# If WARN_IF_UNDOCUMENTED is set to YES, then doxygen will generate warnings 
-# for undocumented members. If EXTRACT_ALL is set to YES then this flag will 
-# automatically be disabled.
+# If the WARN_IF_UNDOCUMENTED tag is set to YES then doxygen will generate
+# warnings for undocumented members. If EXTRACT_ALL is set to YES then this flag
+# will automatically be disabled.
+# The default value is: YES.
 
 WARN_IF_UNDOCUMENTED   = YES
 
-# If WARN_IF_DOC_ERROR is set to YES, doxygen will generate warnings for 
-# potential errors in the documentation, such as not documenting some 
-# parameters in a documented function, or documenting parameters that 
-# don't exist or using markup commands wrongly.
+# If the WARN_IF_DOC_ERROR tag is set to YES, doxygen will generate warnings for
+# potential errors in the documentation, such as not documenting some parameters
+# in a documented function, or documenting parameters that don't exist or using
+# markup commands wrongly.
+# The default value is: YES.
 
 WARN_IF_DOC_ERROR      = YES
 
-# The WARN_NO_PARAMDOC option can be enabled to get warnings for 
-# functions that are documented, but have no documentation for their parameters 
-# or return value. If set to NO (the default) doxygen will only warn about 
-# wrong or incomplete parameter documentation, but not about the absence of 
-# documentation.
+# This WARN_NO_PARAMDOC option can be enabled to get warnings for functions that
+# are documented, but have no documentation for their parameters or return
+# value. If set to NO, doxygen will only warn about wrong or incomplete
+# parameter documentation, but not about the absence of documentation.
+# The default value is: NO.
 
 WARN_NO_PARAMDOC       = YES
 
-# The WARN_FORMAT tag determines the format of the warning messages that 
-# doxygen can produce. The string should contain the $file, $line, and $text 
-# tags, which will be replaced by the file and line number from which the 
-# warning originated and the warning text. Optionally the format may contain 
-# $version, which will be replaced by the version of the file (if it could 
-# be obtained via FILE_VERSION_FILTER)
+# The WARN_FORMAT tag determines the format of the warning messages that doxygen
+# can produce. The string should contain the $file, $line, and $text tags, which
+# will be replaced by the file and line number from which the warning originated
+# and the warning text. Optionally the format may contain $version, which will
+# be replaced by the version of the file (if it could be obtained via
+# FILE_VERSION_FILTER)
+# The default value is: $file:$line: $text.
 
 WARN_FORMAT            = "$file:$line: $text"
 
-# The WARN_LOGFILE tag can be used to specify a file to which warning 
-# and error messages should be written. If left blank the output is written 
-# to stderr.
-
-WARN_LOGFILE           = 
-
-#---------------------------------------------------------------------------
-# configuration options related to the input files
-#---------------------------------------------------------------------------
-
-# The INPUT tag can be used to specify the files and/or directories that contain 
-# documented source files. You may enter file names like "myfile.cpp" or 
-# directories like "/usr/src/myproject". Separate the files or directories 
-# with spaces.
+# The WARN_LOGFILE tag can be used to specify a file to which warning and error
+# messages should be written. If left blank the output is written to standard
+# error (stderr).
+
+WARN_LOGFILE           =
+
+#---------------------------------------------------------------------------
+# Configuration options related to the input files
+#---------------------------------------------------------------------------
+
+# The INPUT tag is used to specify the files and/or directories that contain
+# documented source files. You may enter file names like myfile.cpp or
+# directories like /usr/src/myproject. Separate the files or directories with
+# spaces. See also FILE_PATTERNS and EXTENSION_MAPPING
+# Note: If this tag is empty the current directory is searched.
 
 INPUT                  = 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, which is 
-# also the default input encoding. Doxygen uses libiconv (or the iconv built 
-# into libc) for the transcoding. See http://www.gnu.org/software/libiconv for 
-# the list of possible encodings.
+# 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
+# libiconv (or the iconv built into libc) for the transcoding. See the libiconv
+# documentation (see: http://www.gnu.org/software/libiconv) for the list of
+# possible encodings.
+# The default value is: UTF-8.
 
 INPUT_ENCODING         = UTF-8
 
-# If the value of the INPUT tag contains directories, you can use the 
-# FILE_PATTERNS tag to specify one or more wildcard pattern (like *.cpp 
-# and *.h) to filter out the source-files in the directories. If left 
-# blank the following patterns are tested: 
-# *.c *.cc *.cxx *.cpp *.c++ *.d *.java *.ii *.ixx *.ipp *.i++ *.inl *.h *.hh 
-# *.hxx *.hpp *.h++ *.idl *.odl *.cs *.php *.php3 *.inc *.m *.mm *.dox *.py 
-# *.f90 *.f *.for *.vhd *.vhdl
+# If the value of the INPUT tag contains directories, you can use the
+# FILE_PATTERNS tag to specify one or more wildcard patterns (like *.cpp and
+# *.h) to filter out the source-files in the directories.
+#
+# Note that for custom extensions or not directly supported extensions you also
+# need to set EXTENSION_MAPPING for the extension otherwise the files are not
+# read by doxygen.
+#
+# If left blank the following patterns are tested:*.c, *.cc, *.cxx, *.cpp,
+# *.c++, *.java, *.ii, *.ixx, *.ipp, *.i++, *.inl, *.idl, *.ddl, *.odl, *.h,
+# *.hh, *.hxx, *.hpp, *.h++, *.cs, *.d, *.php, *.php4, *.php5, *.phtml, *.inc,
+# *.m, *.markdown, *.md, *.mm, *.dox, *.py, *.f90, *.f, *.for, *.tcl, *.vhd,
+# *.vhdl, *.ucf, *.qsf, *.as and *.js.
 
 FILE_PATTERNS          = *.cpp \
@@ -642 +805 @@
                          *.conf
 
-# The RECURSIVE tag can be used to turn specify whether or not subdirectories 
-# should be searched for input files as well. Possible values are YES and NO. 
-# If left blank NO is used.
+# The RECURSIVE tag can be used to specify whether or not subdirectories should
+# be searched for input files as well.
+# The default value is: NO.
 
 RECURSIVE              = YES
 
-# The EXCLUDE tag can be used to specify files and/or directories that should 
-# excluded from the INPUT source files. This way you can easily exclude a 
+# The EXCLUDE tag can be used to specify files and/or directories that should be
+# excluded from the INPUT source files. This way you can easily exclude a
 # subdirectory from a directory tree whose root is specified with the INPUT tag.
-
-EXCLUDE                = 
-
-# The EXCLUDE_SYMLINKS tag can be used select whether or not files or 
-# directories that are symbolic links (a Unix file system feature) are excluded 
+#
+# Note that relative paths are relative to the directory from which doxygen is
+# run.
+
+EXCLUDE                =
+
+# The EXCLUDE_SYMLINKS tag can be used to select whether or not files or
+# directories that are symbolic links (a Unix file system feature) are excluded
 # from the input.
+# The default value is: NO.
 
 EXCLUDE_SYMLINKS       = NO
 
-# If the value of the INPUT tag contains directories, you can use the 
-# EXCLUDE_PATTERNS tag to specify one or more wildcard patterns to exclude 
-# certain files from those directories. Note that the wildcards are matched 
-# against the file with absolute path, so to exclude all test directories 
-# for example use the pattern */test/*
-
-EXCLUDE_PATTERNS       = 
-
-# The EXCLUDE_SYMBOLS tag can be used to specify one or more symbol names 
-# (namespaces, classes, functions, etc.) that should be excluded from the 
-# output. The symbol name can be a fully qualified name, a word, or if the 
-# wildcard * is used, a substring. Examples: ANamespace, AClass, 
+# If the value of the INPUT tag contains directories, you can use the
+# EXCLUDE_PATTERNS tag to specify one or more wildcard patterns to exclude
+# certain files from those directories.
+#
+# Note that the wildcards are matched against the file with absolute path, so to
+# exclude all test directories for example use the pattern */test/*
+
+EXCLUDE_PATTERNS       =
+
+# The EXCLUDE_SYMBOLS tag can be used to specify one or more symbol names
+# (namespaces, classes, functions, etc.) that should be excluded from the
+# output. The symbol name can be a fully qualified name, a word, or if the
+# wildcard * is used, a substring. Examples: ANamespace, AClass,
 # AClass::ANamespace, ANamespace::*Test
-
-EXCLUDE_SYMBOLS        = 
-
-# The EXAMPLE_PATH tag can be used to specify one or more files or 
-# directories that contain example code fragments that are included (see 
-# the \include command).
-
-EXAMPLE_PATH           = 
-
-# If the value of the EXAMPLE_PATH tag contains directories, you can use the 
-# EXAMPLE_PATTERNS tag to specify one or more wildcard pattern (like *.cpp 
-# and *.h) to filter out the source-files in the directories. If left 
-# blank all files are included.
+#
+# Note that the wildcards are matched against the file with absolute path, so to
+# exclude all test directories use the pattern */test/*
+
+EXCLUDE_SYMBOLS        =
+
+# The EXAMPLE_PATH tag can be used to specify one or more files or directories
+# that contain example code fragments that are included (see the \include
+# command).
+
+EXAMPLE_PATH           =
+
+# If the value of the EXAMPLE_PATH tag contains directories, you can use the
+# EXAMPLE_PATTERNS tag to specify one or more wildcard pattern (like *.cpp and
+# *.h) to filter out the source-files in the directories. If left blank all
+# files are included.
 
 EXAMPLE_PATTERNS       = *
 
-# If the EXAMPLE_RECURSIVE tag is set to YES then subdirectories will be 
-# searched for input files to be used with the \include or \dontinclude 
-# commands irrespective of the value of the RECURSIVE tag. 
-# Possible values are YES and NO. If left blank NO is used.
+# If the EXAMPLE_RECURSIVE tag is set to YES then subdirectories will be
+# searched for input files to be used with the \include or \dontinclude commands
+# irrespective of the value of the RECURSIVE tag.
+# The default value is: NO.
 
 EXAMPLE_RECURSIVE      = NO
 
-# The IMAGE_PATH tag can be used to specify one or more files or 
-# directories that contain image that are included in the documentation (see 
-# the \image command).
-
-IMAGE_PATH             = 
-
-# The INPUT_FILTER tag can be used to specify a program that doxygen should 
-# invoke to filter for each input file. Doxygen will invoke the filter program 
-# by executing (via popen()) the command <filter> <input-file>, where <filter> 
-# is the value of the INPUT_FILTER tag, and <input-file> is the name of an 
-# input file. Doxygen will then use the output that the filter program writes 
-# to standard output.  If FILTER_PATTERNS is specified, this tag will be 
-# ignored.
-
-INPUT_FILTER           = 
-
-# The FILTER_PATTERNS tag can be used to specify filters on a per file pattern 
-# basis.  Doxygen will compare the file name with each pattern and apply the 
-# filter if there is a match.  The filters are a list of the form: 
-# pattern=filter (like *.cpp=my_cpp_filter). See INPUT_FILTER for further 
-# info on how filters are used. If FILTER_PATTERNS is empty or if 
-# non of the patterns match the file name, INPUT_FILTER is applied.
-
-FILTER_PATTERNS        = 
-
-# If the FILTER_SOURCE_FILES tag is set to YES, the input filter (if set using 
-# INPUT_FILTER) will be used to filter the input files when producing source 
-# files to browse (i.e. when SOURCE_BROWSER is set to YES).
+# The IMAGE_PATH tag can be used to specify one or more files or directories
+# that contain images that are to be included in the documentation (see the
+# \image command).
+
+IMAGE_PATH             =
+
+# The INPUT_FILTER tag can be used to specify a program that doxygen should
+# invoke to filter for each input file. Doxygen will invoke the filter program
+# by executing (via popen()) the command:
+#
+# <filter> <input-file>
+#
+# where <filter> is the value of the INPUT_FILTER tag, and <input-file> is the
+# name of an input file. Doxygen will then use the output that the filter
+# program writes to standard output. If FILTER_PATTERNS is specified, this tag
+# will be ignored.
+#
+# Note that the filter must not add or remove lines; it is applied before the
+# code is scanned, but not when the output code is generated. If lines are added
+# or removed, the anchors will not be placed correctly.
+
+INPUT_FILTER           =
+
+# The FILTER_PATTERNS tag can be used to specify filters on a per file pattern
+# basis. Doxygen will compare the file name with each pattern and apply the
+# filter if there is a match. The filters are a list of the form: pattern=filter
+# (like *.cpp=my_cpp_filter). See INPUT_FILTER for further information on how
+# filters are used. If the FILTER_PATTERNS tag is empty or if none of the
+# patterns match the file name, INPUT_FILTER is applied.
+
+FILTER_PATTERNS        =
+
+# If the FILTER_SOURCE_FILES tag is set to YES, the input filter (if set using
+# INPUT_FILTER) will also be used to filter the input files that are used for
+# producing the source files to browse (i.e. when SOURCE_BROWSER is set to YES).
+# The default value is: NO.
 
 FILTER_SOURCE_FILES    = NO
 
-# The FILTER_SOURCE_PATTERNS tag can be used to specify source filters per file 
-# pattern. A pattern will override the setting for FILTER_PATTERN (if any) 
-# and it is also possible to disable source filtering for a specific pattern 
-# using *.ext= (so without naming a filter). This option only has effect when 
-# FILTER_SOURCE_FILES is enabled.
-
-FILTER_SOURCE_PATTERNS = 
-
-#---------------------------------------------------------------------------
-# configuration options related to source browsing
-#---------------------------------------------------------------------------
-
-# If the SOURCE_BROWSER tag is set to YES then a list of source files will 
-# be generated. Documented entities will be cross-referenced with these sources. 
-# Note: To get rid of all source code in the generated output, make sure also 
-# VERBATIM_HEADERS is set to NO.
+# The FILTER_SOURCE_PATTERNS tag can be used to specify source filters per file
+# pattern. A pattern will override the setting for FILTER_PATTERN (if any) and
+# it is also possible to disable source filtering for a specific pattern using
+# *.ext= (so without naming a filter).
+# This tag requires that the tag FILTER_SOURCE_FILES is set to YES.
+
+FILTER_SOURCE_PATTERNS =
+
+# If the USE_MDFILE_AS_MAINPAGE tag refers to the name of a markdown file that
+# is part of the input, its contents will be placed on the main page
+# (index.html). This can be useful if you have a project on for instance GitHub
+# and want to reuse the introduction page also for the doxygen output.
+
+USE_MDFILE_AS_MAINPAGE =
+
+#---------------------------------------------------------------------------
+# Configuration options related to source browsing
+#---------------------------------------------------------------------------
+
+# If the SOURCE_BROWSER tag is set to YES then a list of source files will be
+# generated. Documented entities will be cross-referenced with these sources.
+#
+# Note: To get rid of all source code in the generated output, make sure that
+# also VERBATIM_HEADERS is set to NO.
+# The default value is: NO.
 
 SOURCE_BROWSER         = YES
 
-# Setting the INLINE_SOURCES tag to YES will include the body 
-# of functions and classes directly in the documentation.
+# Setting the INLINE_SOURCES tag to YES will include the body of functions,
+# classes and enums directly into the documentation.
+# The default value is: NO.
 
 INLINE_SOURCES         = NO
 
-# Setting the STRIP_CODE_COMMENTS tag to YES (the default) will instruct 
-# doxygen to hide any special comment blocks from generated source code 
-# fragments. Normal C and C++ comments will always remain visible.
+# Setting the STRIP_CODE_COMMENTS tag to YES will instruct doxygen to hide any
+# special comment blocks from generated source code fragments. Normal C, C++ and
+# Fortran comments will always remain visible.
+# The default value is: YES.
 
 STRIP_CODE_COMMENTS    = YES
 
-# If the REFERENCED_BY_RELATION tag is set to YES 
-# then for each documented function all documented 
-# functions referencing it will be listed.
+# If the REFERENCED_BY_RELATION tag is set to YES then for each documented
+# function all documented functions referencing it will be listed.
+# The default value is: NO.
 
 REFERENCED_BY_RELATION = YES
 
-# If the REFERENCES_RELATION tag is set to YES 
-# then for each documented function all documented entities 
-# called/used by that function will be listed.
+# If the REFERENCES_RELATION tag is set to YES then for each documented function
+# all documented entities called/used by that function will be listed.
+# The default value is: NO.
 
 REFERENCES_RELATION    = YES
 
-# If the REFERENCES_LINK_SOURCE tag is set to YES (the default) 
-# and SOURCE_BROWSER tag is set to YES, then the hyperlinks from 
-# functions in REFERENCES_RELATION and REFERENCED_BY_RELATION lists will 
-# link to the source code.  Otherwise they will link to the documentation.
+# If the REFERENCES_LINK_SOURCE tag is set to YES and SOURCE_BROWSER tag is set
+# to YES then the hyperlinks from functions in REFERENCES_RELATION and
+# REFERENCED_BY_RELATION lists will link to the source code. Otherwise they will
+# link to the documentation.
+# The default value is: YES.
 
 REFERENCES_LINK_SOURCE = YES
 
-# If the USE_HTAGS tag is set to YES then the references to source code 
-# will point to the HTML generated by the htags(1) tool instead of doxygen 
-# built-in source browser. The htags tool is part of GNU's global source 
-# tagging system (see http://www.gnu.org/software/global/global.html). You 
-# will need version 4.8.6 or higher.
+# If SOURCE_TOOLTIPS is enabled (the default) then hovering a hyperlink in the
+# source code will show a tooltip with additional information such as prototype,
+# brief description and links to the definition and documentation. Since this
+# will make the HTML file larger and loading of large files a bit slower, you
+# can opt to disable this feature.
+# The default value is: YES.
+# This tag requires that the tag SOURCE_BROWSER is set to YES.
+
+SOURCE_TOOLTIPS        = YES
+
+# If the USE_HTAGS tag is set to YES then the references to source code will
+# point to the HTML generated by the htags(1) tool instead of doxygen built-in
+# source browser. The htags tool is part of GNU's global source tagging system
+# (see http://www.gnu.org/software/global/global.html). You will need version
+# 4.8.6 or higher.
+#
+# To use it do the following:
+# - Install the latest version of global
+# - Enable SOURCE_BROWSER and USE_HTAGS in the config file
+# - Make sure the INPUT points to the root of the source tree
+# - Run doxygen as normal
+#
+# Doxygen will invoke htags (and that will in turn invoke gtags), so these
+# tools must be available from the command line (i.e. in the search path).
+#
+# The result: instead of the source browser generated by doxygen, the links to
+# source code will now point to the output of htags.
+# The default value is: NO.
+# This tag requires that the tag SOURCE_BROWSER is set to YES.
 
 USE_HTAGS              = NO
 
-# If the VERBATIM_HEADERS tag is set to YES (the default) then Doxygen 
-# will generate a verbatim copy of the header file for each class for 
-# which an include is specified. Set to NO to disable this.
+# If the VERBATIM_HEADERS tag is set the YES then doxygen will generate a
+# verbatim copy of the header file for each class for which an include is
+# specified. Set to NO to disable this.
+# See also: Section \class.
+# The default value is: YES.
 
 VERBATIM_HEADERS       = YES
 
 #---------------------------------------------------------------------------
-# configuration options related to the alphabetical class index
-#---------------------------------------------------------------------------
-
-# If the ALPHABETICAL_INDEX tag is set to YES, an alphabetical index 
-# of all compounds will be generated. Enable this if the project 
-# contains a lot of classes, structs, unions or interfaces.
+# Configuration options related to the alphabetical class index
+#---------------------------------------------------------------------------
+
+# If the ALPHABETICAL_INDEX tag is set to YES, an alphabetical index of all
+# compounds will be generated. Enable this if the project contains a lot of
+# classes, structs, unions or interfaces.
+# The default value is: YES.
 
 ALPHABETICAL_INDEX     = YES
 
-# If the alphabetical index is enabled (see ALPHABETICAL_INDEX) then 
-# the COLS_IN_ALPHA_INDEX tag can be used to specify the number of columns 
-# in which this list will be split (can be a number in the range [1..20])
+# The COLS_IN_ALPHA_INDEX tag can be used to specify the number of columns in
+# which the alphabetical index list will be split.
+# Minimum value: 1, maximum value: 20, default value: 5.
+# This tag requires that the tag ALPHABETICAL_INDEX is set to YES.
 
 COLS_IN_ALPHA_INDEX    = 5
 
-# In case all classes in a project start with a common prefix, all 
-# classes will be put under the same header in the alphabetical index. 
-# The IGNORE_PREFIX tag can be used to specify one or more prefixes that 
-# should be ignored while generating the index headers.
-
-IGNORE_PREFIX          = 
-
-#---------------------------------------------------------------------------
-# configuration options related to the HTML output
-#---------------------------------------------------------------------------
-
-# If the GENERATE_HTML tag is set to YES (the default) Doxygen will 
-# generate HTML output.
+# In case all classes in a project start with a common prefix, all classes will
+# be put under the same header in the alphabetical index. The IGNORE_PREFIX tag
+# can be used to specify a prefix (or a list of prefixes) that should be ignored
+# while generating the index headers.
+# This tag requires that the tag ALPHABETICAL_INDEX is set to YES.
+
+IGNORE_PREFIX          =
+
+#---------------------------------------------------------------------------
+# Configuration options related to the HTML output
+#---------------------------------------------------------------------------
+
+# If the GENERATE_HTML tag is set to YES, doxygen will generate HTML output
+# The default value is: YES.
 
 GENERATE_HTML          = YES
 
-# The HTML_OUTPUT tag is used to specify where the HTML docs will be put. 
-# If a relative path is entered the value of OUTPUT_DIRECTORY will be 
-# put in front of it. If left blank `html' will be used as the default path.
+# The HTML_OUTPUT tag is used to specify where the HTML docs will be put. If a
+# relative path is entered the value of OUTPUT_DIRECTORY will be put in front of
+# it.
+# The default directory is: html.
+# This tag requires that the tag GENERATE_HTML is set to YES.
 
 HTML_OUTPUT            = html
 
-# The HTML_FILE_EXTENSION tag can be used to specify the file extension for 
-# each generated HTML page (for example: .htm,.php,.asp). If it is left blank 
-# doxygen will generate files with .html extension.
+# The HTML_FILE_EXTENSION tag can be used to specify the file extension for each
+# generated HTML page (for example: .htm, .php, .asp).
+# The default value is: .html.
+# This tag requires that the tag GENERATE_HTML is set to YES.
 
 HTML_FILE_EXTENSION    = .html
 
-# The HTML_HEADER tag can be used to specify a personal HTML header for 
-# each generated HTML page. If it is left blank doxygen will generate a 
-# standard header. Note that when using a custom header you are responsible 
-# for the proper inclusion of any scripts and style sheets that doxygen 
-# needs, which is dependent on the configuration options used. 
-# It is adviced to generate a default header using "doxygen -w html 
-# header.html footer.html stylesheet.css YourConfigFile" and then modify 
-# that header. Note that the header is subject to change so you typically 
-# have to redo this when upgrading to a newer version of doxygen or when
-# changing the value of configuration settings such as GENERATE_TREEVIEW!
-
-HTML_HEADER            = 
-
-# The HTML_FOOTER tag can be used to specify a personal HTML footer for 
-# each generated HTML page. If it is left blank doxygen will generate a 
-# standard footer.
-
-HTML_FOOTER            = 
-
-# If the HTML_TIMESTAMP tag is set to YES then the generated HTML
-# documentation will contain the timesstamp.
+# The HTML_HEADER tag can be used to specify a user-defined HTML header file for
+# each generated HTML page. If the tag is left blank doxygen will generate a
+# standard header.
+#
+# To get valid HTML the header file that includes any scripts and style sheets
+# that doxygen needs, which is dependent on the configuration options used (e.g.
+# the setting GENERATE_TREEVIEW). It is highly recommended to start with a
+# default header using
+# doxygen -w html new_header.html new_footer.html new_stylesheet.css
+# YourConfigFile
+# and then modify the file new_header.html. See also section "Doxygen usage"
+# for information on how to generate the default header that doxygen normally
+# uses.
+# Note: The header is subject to change so you typically have to regenerate the
+# default header when upgrading to a newer version of doxygen. For a description
+# of the possible markers and block names see the documentation.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+HTML_HEADER            =
+
+# The HTML_FOOTER tag can be used to specify a user-defined HTML footer for each
+# generated HTML page. If the tag is left blank doxygen will generate a standard
+# footer. See HTML_HEADER for more information on how to generate a default
+# footer and what special commands can be used inside the footer. See also
+# section "Doxygen usage" for information on how to generate the default footer
+# that doxygen normally uses.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+HTML_FOOTER            =
+
+# The HTML_STYLESHEET tag can be used to specify a user-defined cascading style
+# sheet that is used by each HTML page. It can be used to fine-tune the look of
+# the HTML output. If left blank doxygen will generate a default style sheet.
+# See also section "Doxygen usage" for information on how to generate the style
+# sheet that doxygen normally uses.
+# Note: It is recommended to use HTML_EXTRA_STYLESHEET instead of this tag, as
+# it is more robust and this tag (HTML_STYLESHEET) will in the future become
+# obsolete.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+HTML_STYLESHEET        =
+
+# The HTML_EXTRA_STYLESHEET tag can be used to specify additional user-defined
+# cascading style sheets that are included after the standard style sheets
+# created by doxygen. Using this option one can overrule certain style aspects.
+# This is preferred over using HTML_STYLESHEET since it does not replace the
+# standard style sheet and is therefore more robust against future updates.
+# Doxygen will copy the style sheet files to the output directory.
+# Note: The order of the extra style sheet files is of importance (e.g. the last
+# style sheet in the list overrules the setting of the previous ones in the
+# list). For an example see the documentation.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+HTML_EXTRA_STYLESHEET  =
+
+# The HTML_EXTRA_FILES tag can be used to specify one or more extra images or
+# other source files which should be copied to the HTML output directory. Note
+# that these files will be copied to the base HTML output directory. Use the
+# $relpath^ marker in the HTML_HEADER and/or HTML_FOOTER files to load these
+# files. In the HTML_STYLESHEET file, use the file name only. Also note that the
+# files will be copied as-is; there are no commands or markers available.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+HTML_EXTRA_FILES       =
+
+# The HTML_COLORSTYLE_HUE tag controls the color of the HTML output. Doxygen
+# will adjust the colors in the style sheet and background images according to
+# this color. Hue is specified as an angle on a colorwheel, see
+# http://en.wikipedia.org/wiki/Hue for more information. For instance the value
+# 0 represents red, 60 is yellow, 120 is green, 180 is cyan, 240 is blue, 300
+# purple, and 360 is red again.
+# Minimum value: 0, maximum value: 359, default value: 220.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+HTML_COLORSTYLE_HUE    = 224
+
+# The HTML_COLORSTYLE_SAT tag controls the purity (or saturation) of the colors
+# in the HTML output. For a value of 0 the output will use grayscales only. A
+# value of 255 will produce the most vivid colors.
+# Minimum value: 0, maximum value: 255, default value: 100.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+HTML_COLORSTYLE_SAT    = 63
+
+# The HTML_COLORSTYLE_GAMMA tag controls the gamma correction applied to the
+# luminance component of the colors in the HTML output. Values below 100
+# gradually make the output lighter, whereas values above 100 make the output
+# darker. The value divided by 100 is the actual gamma applied, so 80 represents
+# a gamma of 0.8, The value 220 represents a gamma of 2.2, and 100 does not
+# change the gamma.
+# Minimum value: 40, maximum value: 240, default value: 80.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+HTML_COLORSTYLE_GAMMA  = 152
+
+# If the HTML_TIMESTAMP tag is set to YES then the footer of each generated HTML
+# page will contain the date and time when the page was generated. Setting this
+# to YES can help to show when doxygen was last run and thus if the
+# documentation is up to date.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_HTML is set to YES.
 
 HTML_TIMESTAMP         = YES
 
-# The HTML_STYLESHEET tag can be used to specify a user-defined cascading 
-# style sheet that is used by each HTML page. It can be used to 
-# fine-tune the look of the HTML output. If the tag is left blank doxygen 
-# will generate a default style sheet. Note that doxygen will try to copy 
-# the style sheet file to the HTML output directory, so don't put your own 
-# stylesheet in the HTML output directory as well, or it will be erased!
-
-HTML_STYLESHEET        = 
-
-# The HTML_EXTRA_FILES tag can be used to specify one or more extra images or 
-# other source files which should be copied to the HTML output directory. Note 
-# that these files will be copied to the base HTML output directory. Use the 
-# $relpath$ marker in the HTML_HEADER and/or HTML_FOOTER files to load these 
-# files. In the HTML_STYLESHEET file, use the file name only. Also note that 
-# the files will be copied as-is; there are no commands or markers available.
-
-HTML_EXTRA_FILES       = 
-
-# The HTML_COLORSTYLE_HUE tag controls the color of the HTML output. 
-# Doxygen will adjust the colors in the stylesheet and background images 
-# according to this color. Hue is specified as an angle on a colorwheel, 
-# see http://en.wikipedia.org/wiki/Hue for more information. 
-# For instance the value 0 represents red, 60 is yellow, 120 is green, 
-# 180 is cyan, 240 is blue, 300 purple, and 360 is red again. 
-# The allowed range is 0 to 359.
-
-HTML_COLORSTYLE_HUE    = 224
-
-# The HTML_COLORSTYLE_SAT tag controls the purity (or saturation) of 
-# the colors in the HTML output. For a value of 0 the output will use 
-# grayscales only. A value of 255 will produce the most vivid colors.
-
-HTML_COLORSTYLE_SAT    = 63
-
-# The HTML_COLORSTYLE_GAMMA tag controls the gamma correction applied to 
-# the luminance component of the colors in the HTML output. Values below 
-# 100 gradually make the output lighter, whereas values above 100 make 
-# the output darker. The value divided by 100 is the actual gamma applied, 
-# so 80 represents a gamma of 0.8, The value 220 represents a gamma of 2.2, 
-# and 100 does not change the gamma.
-
-HTML_COLORSTYLE_GAMMA  = 152
-
-# If the HTML_TIMESTAMP tag is set to YES then the footer of each generated HTML 
-# page will contain the date and time when the page was generated. Setting 
-# this to NO can help when comparing the output of multiple runs.
-
-HTML_TIMESTAMP         = YES
-
-# If the HTML_ALIGN_MEMBERS tag is set to YES, the members of classes, 
-# files or namespaces will be aligned in HTML using tables. If set to 
-# NO a bullet list will be used.
-
-HTML_ALIGN_MEMBERS     = YES
-
-# If the HTML_DYNAMIC_SECTIONS tag is set to YES then the generated HTML 
-# documentation will contain sections that can be hidden and shown after the 
-# page has loaded. For this to work a browser that supports 
-# JavaScript and DHTML is required (for instance Mozilla 1.0+, Firefox 
-# Netscape 6.0+, Internet explorer 5.0+, Konqueror, or Safari).
+# If the HTML_DYNAMIC_SECTIONS tag is set to YES then the generated HTML
+# documentation will contain sections that can be hidden and shown after the
+# page has loaded.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_HTML is set to YES.
 
 HTML_DYNAMIC_SECTIONS  = YES
 
-# If the GENERATE_DOCSET tag is set to YES, additional index files 
-# will be generated that can be used as input for Apple's Xcode 3 
-# integrated development environment, introduced with OSX 10.5 (Leopard). 
-# To create a documentation set, doxygen will generate a Makefile in the 
-# HTML output directory. Running make will produce the docset in that 
-# directory and running "make install" will install the docset in 
-# ~/Library/Developer/Shared/Documentation/DocSets so that Xcode will find 
-# it at startup. 
-# See http://developer.apple.com/tools/creatingdocsetswithdoxygen.html 
+# With HTML_INDEX_NUM_ENTRIES one can control the preferred number of entries
+# shown in the various tree structured indices initially; the user can expand
+# and collapse entries dynamically later on. Doxygen will expand the tree to
+# such a level that at most the specified number of entries are visible (unless
+# a fully collapsed tree already exceeds this amount). So setting the number of
+# entries 1 will produce a full collapsed tree by default. 0 is a special value
+# representing an infinite number of entries and will result in a full expanded
+# tree by default.
+# Minimum value: 0, maximum value: 9999, default value: 100.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+HTML_INDEX_NUM_ENTRIES = 100
+
+# If the GENERATE_DOCSET tag is set to YES, additional index files will be
+# generated that can be used as input for Apple's Xcode 3 integrated development
+# environment (see: http://developer.apple.com/tools/xcode/), introduced with
+# OSX 10.5 (Leopard). To create a documentation set, doxygen will generate a
+# Makefile in the HTML output directory. Running make will produce the docset in
+# that directory and running make install will install the docset in
+# ~/Library/Developer/Shared/Documentation/DocSets so that Xcode will find it at
+# startup. See http://developer.apple.com/tools/creatingdocsetswithdoxygen.html
 # for more information.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_HTML is set to YES.
 
 GENERATE_DOCSET        = NO
 
-# When GENERATE_DOCSET tag is set to YES, this tag determines the name of the 
-# feed. A documentation feed provides an umbrella under which multiple 
-# documentation sets from a single provider (such as a company or product suite) 
-# can be grouped.
+# This tag determines the name of the docset feed. A documentation feed provides
+# an umbrella under which multiple documentation sets from a single provider
+# (such as a company or product suite) can be grouped.
+# The default value is: Doxygen generated docs.
+# This tag requires that the tag GENERATE_DOCSET is set to YES.
 
 DOCSET_FEEDNAME        = "Doxygen generated docs"
 
-# When GENERATE_DOCSET tag is set to YES, this tag specifies a string that 
-# should uniquely identify the documentation set bundle. This should be a 
-# reverse domain-name style string, e.g. com.mycompany.MyDocSet. Doxygen 
-# will append .docset to the name.
+# This tag specifies a string that should uniquely identify the documentation
+# set bundle. This should be a reverse domain-name style string, e.g.
+# com.mycompany.MyDocSet. Doxygen will append .docset to the name.
+# The default value is: org.doxygen.Project.
+# This tag requires that the tag GENERATE_DOCSET is set to YES.
 
 DOCSET_BUNDLE_ID       = org.doxygen.Project
 
-# When GENERATE_PUBLISHER_ID tag specifies a string that should uniquely identify 
-# the documentation publisher. This should be a reverse domain-name style 
+# The DOCSET_PUBLISHER_ID tag specifies a string that should uniquely identify
+# the documentation publisher. This should be a reverse domain-name style
 # string, e.g. com.mycompany.MyDocSet.documentation.
+# The default value is: org.doxygen.Publisher.
+# This tag requires that the tag GENERATE_DOCSET is set to YES.
 
 DOCSET_PUBLISHER_ID    = org.doxygen.Publisher
 
-# The GENERATE_PUBLISHER_NAME tag identifies the documentation publisher.
+# The DOCSET_PUBLISHER_NAME tag identifies the documentation publisher.
+# The default value is: Publisher.
+# This tag requires that the tag GENERATE_DOCSET is set to YES.
 
 DOCSET_PUBLISHER_NAME  = Publisher
 
-# If the GENERATE_HTMLHELP tag is set to YES, additional index files 
-# will be generated that can be used as input for tools like the 
-# Microsoft HTML help workshop to generate a compiled HTML help file (.chm) 
-# of the generated HTML documentation.
+# If the GENERATE_HTMLHELP tag is set to YES then doxygen generates three
+# additional HTML index files: index.hhp, index.hhc, and index.hhk. The
+# index.hhp is a project file that can be read by Microsoft's HTML Help Workshop
+# (see: http://www.microsoft.com/en-us/download/details.aspx?id=21138) on
+# Windows.
+#
+# The HTML Help Workshop contains a compiler that can convert all HTML output
+# generated by doxygen into a single compiled HTML file (.chm). Compiled HTML
+# files are now used as the Windows 98 help format, and will replace the old
+# Windows help format (.hlp) on all Windows platforms in the future. Compressed
+# HTML files also contain an index, a table of contents, and you can search for
+# words in the documentation. The HTML workshop also contains a viewer for
+# compressed HTML files.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_HTML is set to YES.
 
 GENERATE_HTMLHELP      = NO
 
-# If the GENERATE_HTMLHELP tag is set to YES, the CHM_FILE tag can 
-# be used to specify the file name of the resulting .chm file. You 
-# can add a path in front of the file if the result should not be 
+# The CHM_FILE tag can be used to specify the file name of the resulting .chm
+# file. You can add a path in front of the file if the result should not be
 # written to the html output directory.
-
-CHM_FILE               = 
-
-# If the GENERATE_HTMLHELP tag is set to YES, the HHC_LOCATION tag can 
-# be used to specify the location (absolute path including file name) of 
-# the HTML help compiler (hhc.exe). If non-empty doxygen will try to run 
-# the HTML help compiler on the generated index.hhp.
-
-HHC_LOCATION           = 
-
-# If the GENERATE_HTMLHELP tag is set to YES, the GENERATE_CHI flag 
-# controls if a separate .chi index file is generated (YES) or that 
-# it should be included in the master .chm file (NO).
+# This tag requires that the tag GENERATE_HTMLHELP is set to YES.
+
+CHM_FILE               =
+
+# The HHC_LOCATION tag can be used to specify the location (absolute path
+# including file name) of the HTML help compiler (hhc.exe). If non-empty,
+# doxygen will try to run the HTML help compiler on the generated index.hhp.
+# The file has to be specified with full path.
+# This tag requires that the tag GENERATE_HTMLHELP is set to YES.
+
+HHC_LOCATION           =
+
+# The GENERATE_CHI flag controls if a separate .chi index file is generated
+# (YES) or that it should be included in the master .chm file (NO).
+# The default value is: NO.
+# This tag requires that the tag GENERATE_HTMLHELP is set to YES.
 
 GENERATE_CHI           = NO
 
-# If the GENERATE_HTMLHELP tag is set to YES, the CHM_INDEX_ENCODING 
-# is used to encode HtmlHelp index (hhk), content (hhc) and project file 
-# content.
-
-CHM_INDEX_ENCODING     = 
-
-# If the GENERATE_HTMLHELP tag is set to YES, the BINARY_TOC flag 
-# controls whether a binary table of contents is generated (YES) or a 
-# normal table of contents (NO) in the .chm file.
+# The CHM_INDEX_ENCODING is used to encode HtmlHelp index (hhk), content (hhc)
+# and project file content.
+# This tag requires that the tag GENERATE_HTMLHELP is set to YES.
+
+CHM_INDEX_ENCODING     =
+
+# The BINARY_TOC flag controls whether a binary table of contents is generated
+# (YES) or a normal table of contents (NO) in the .chm file. Furthermore it
+# enables the Previous and Next buttons.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_HTMLHELP is set to YES.
 
 BINARY_TOC             = NO
 
-# The TOC_EXPAND flag can be set to YES to add extra items for group members 
-# to the contents of the HTML help documentation and to the tree view.
+# The TOC_EXPAND flag can be set to YES to add extra items for group members to
+# the table of contents of the HTML help documentation and to the tree view.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_HTMLHELP is set to YES.
 
 TOC_EXPAND             = NO
 
-# If the GENERATE_QHP tag is set to YES and both QHP_NAMESPACE and 
-# QHP_VIRTUAL_FOLDER are set, an additional index file will be generated 
-# that can be used as input for Qt's qhelpgenerator to generate a 
-# Qt Compressed Help (.qch) of the generated HTML documentation.
+# If the GENERATE_QHP tag is set to YES and both QHP_NAMESPACE and
+# QHP_VIRTUAL_FOLDER are set, an additional index file will be generated that
+# can be used as input for Qt's qhelpgenerator to generate a Qt Compressed Help
+# (.qch) of the generated HTML documentation.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_HTML is set to YES.
 
 GENERATE_QHP           = NO
 
-# If the QHG_LOCATION tag is specified, the QCH_FILE tag can 
-# be used to specify the file name of the resulting .qch file. 
-# The path specified is relative to the HTML output folder.
-
-QCH_FILE               = 
-
-# The QHP_NAMESPACE tag specifies the namespace to use when generating 
-# Qt Help Project output. For more information please see 
-# http://doc.trolltech.com/qthelpproject.html#namespace
+# If the QHG_LOCATION tag is specified, the QCH_FILE tag can be used to specify
+# the file name of the resulting .qch file. The path specified is relative to
+# the HTML output folder.
+# This tag requires that the tag GENERATE_QHP is set to YES.
+
+QCH_FILE               =
+
+# The QHP_NAMESPACE tag specifies the namespace to use when generating Qt Help
+# Project output. For more information please see Qt Help Project / Namespace
+# (see: http://qt-project.org/doc/qt-4.8/qthelpproject.html#namespace).
+# The default value is: org.doxygen.Project.
+# This tag requires that the tag GENERATE_QHP is set to YES.
 
 QHP_NAMESPACE          = org.doxygen.Project
 
-# The QHP_VIRTUAL_FOLDER tag specifies the namespace to use when generating 
-# Qt Help Project output. For more information please see 
-# http://doc.trolltech.com/qthelpproject.html#virtual-folders
+# The QHP_VIRTUAL_FOLDER tag specifies the namespace to use when generating Qt
+# Help Project output. For more information please see Qt Help Project / Virtual
+# Folders (see: http://qt-project.org/doc/qt-4.8/qthelpproject.html#virtual-
+# folders).
+# The default value is: doc.
+# This tag requires that the tag GENERATE_QHP is set to YES.
 
 QHP_VIRTUAL_FOLDER     = doc
 
-# If QHP_CUST_FILTER_NAME is set, it specifies the name of a custom filter to 
-# add. For more information please see 
-# http://doc.trolltech.com/qthelpproject.html#custom-filters
-
-QHP_CUST_FILTER_NAME   = 
-
-# The QHP_CUST_FILT_ATTRS tag specifies the list of the attributes of the 
-# custom filter to add. For more information please see 
-# <a href="http://doc.trolltech.com/qthelpproject.html#custom-filters"> 
-# Qt Help Project / Custom Filters</a>.
-
-QHP_CUST_FILTER_ATTRS  = 
-
-# The QHP_SECT_FILTER_ATTRS tag specifies the list of the attributes this 
-# project's 
-# filter section matches. 
-# <a href="http://doc.trolltech.com/qthelpproject.html#filter-attributes"> 
-# Qt Help Project / Filter Attributes</a>.
-
-QHP_SECT_FILTER_ATTRS  = 
-
-# If the GENERATE_QHP tag is set to YES, the QHG_LOCATION tag can 
-# be used to specify the location of Qt's qhelpgenerator. 
-# If non-empty doxygen will try to run qhelpgenerator on the generated 
-# .qhp file.
-
-QHG_LOCATION           = 
-
-# If the GENERATE_ECLIPSEHELP tag is set to YES, additional index files  
-# will be generated, which together with the HTML files, form an Eclipse help 
-# plugin. To install this plugin and make it available under the help contents 
-# menu in Eclipse, the contents of the directory containing the HTML and XML 
-# files needs to be copied into the plugins directory of eclipse. The name of 
-# the directory within the plugins directory should be the same as 
-# the ECLIPSE_DOC_ID value. After copying Eclipse needs to be restarted before 
-# the help appears.
+# If the QHP_CUST_FILTER_NAME tag is set, it specifies the name of a custom
+# filter to add. For more information please see Qt Help Project / Custom
+# Filters (see: http://qt-project.org/doc/qt-4.8/qthelpproject.html#custom-
+# filters).
+# This tag requires that the tag GENERATE_QHP is set to YES.
+
+QHP_CUST_FILTER_NAME   =
+
+# The QHP_CUST_FILTER_ATTRS tag specifies the list of the attributes of the
+# custom filter to add. For more information please see Qt Help Project / Custom
+# Filters (see: http://qt-project.org/doc/qt-4.8/qthelpproject.html#custom-
+# filters).
+# This tag requires that the tag GENERATE_QHP is set to YES.
+
+QHP_CUST_FILTER_ATTRS  =
+
+# The QHP_SECT_FILTER_ATTRS tag specifies the list of the attributes this
+# project's filter section matches. Qt Help Project / Filter Attributes (see:
+# http://qt-project.org/doc/qt-4.8/qthelpproject.html#filter-attributes).
+# This tag requires that the tag GENERATE_QHP is set to YES.
+
+QHP_SECT_FILTER_ATTRS  =
+
+# The QHG_LOCATION tag can be used to specify the location of Qt's
+# qhelpgenerator. If non-empty doxygen will try to run qhelpgenerator on the
+# generated .qhp file.
+# This tag requires that the tag GENERATE_QHP is set to YES.
+
+QHG_LOCATION           =
+
+# If the GENERATE_ECLIPSEHELP tag is set to YES, additional index files will be
+# generated, together with the HTML files, they form an Eclipse help plugin. To
+# install this plugin and make it available under the help contents menu in
+# Eclipse, the contents of the directory containing the HTML and XML files needs
+# to be copied into the plugins directory of eclipse. The name of the directory
+# within the plugins directory should be the same as the ECLIPSE_DOC_ID value.
+# After copying Eclipse needs to be restarted before the help appears.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_HTML is set to YES.
 
 GENERATE_ECLIPSEHELP   = NO
 
-# A unique identifier for the eclipse help plugin. When installing the plugin 
-# the directory name containing the HTML and XML files should also have 
-# this name.
+# A unique identifier for the Eclipse help plugin. When installing the plugin
+# the directory name containing the HTML and XML files should also have this
+# name. Each documentation set should have its own identifier.
+# The default value is: org.doxygen.Project.
+# This tag requires that the tag GENERATE_ECLIPSEHELP is set to YES.
 
 ECLIPSE_DOC_ID         = org.doxygen.Project
 
-# The DISABLE_INDEX tag can be used to turn on/off the condensed index at 
-# top of each HTML page. The value NO (the default) enables the index and 
-# the value YES disables it.
+# If you want full control over the layout of the generated HTML pages it might
+# be necessary to disable the index and replace it with your own. The
+# DISABLE_INDEX tag can be used to turn on/off the condensed index (tabs) at top
+# of each HTML page. A value of NO enables the index and the value YES disables
+# it. Since the tabs in the index contain the same information as the navigation
+# tree, you can set this option to YES if you also set GENERATE_TREEVIEW to YES.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_HTML is set to YES.
 
 DISABLE_INDEX          = NO
 
-# The ENUM_VALUES_PER_LINE tag can be used to set the number of enum values 
-# (range [0,1..20]) that doxygen will group on one line in the generated HTML 
-# documentation. Note that a value of 0 will completely suppress the enum 
-# values from appearing in the overview section.
+# The GENERATE_TREEVIEW tag is used to specify whether a tree-like index
+# structure should be generated to display hierarchical information. If the tag
+# value is set to YES, a side panel will be generated containing a tree-like
+# index structure (just like the one that is generated for HTML Help). For this
+# to work a browser that supports JavaScript, DHTML, CSS and frames is required
+# (i.e. any modern browser). Windows users are probably better off using the
+# HTML help feature. Via custom style sheets (see HTML_EXTRA_STYLESHEET) one can
+# further fine-tune the look of the index. As an example, the default style
+# sheet generated by doxygen has an example that shows how to put an image at
+# the root of the tree instead of the PROJECT_NAME. Since the tree basically has
+# the same information as the tab index, you could consider setting
+# DISABLE_INDEX to YES when enabling this option.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+GENERATE_TREEVIEW      = YES
+
+# The ENUM_VALUES_PER_LINE tag can be used to set the number of enum values that
+# doxygen will group on one line in the generated HTML documentation.
+#
+# Note that a value of 0 will completely suppress the enum values from appearing
+# in the overview section.
+# Minimum value: 0, maximum value: 20, default value: 4.
+# This tag requires that the tag GENERATE_HTML is set to YES.
 
 ENUM_VALUES_PER_LINE   = 4
 
-# The GENERATE_TREEVIEW tag is used to specify whether a tree-like index 
-# structure should be generated to display hierarchical information. 
-# If the tag value is set to YES, a side panel will be generated 
-# containing a tree-like index structure (just like the one that 
-# is generated for HTML Help). For this to work a browser that supports 
-# JavaScript, DHTML, CSS and frames is required (i.e. any modern browser). 
-# Windows users are probably better off using the HTML help feature.
-
-GENERATE_TREEVIEW      = YES
-
-# By enabling USE_INLINE_TREES, doxygen will generate the Groups, Directories, 
-# and Class Hierarchy pages using a tree view instead of an ordered list.
-
-USE_INLINE_TREES       = YES
-
-# If the treeview is enabled (see GENERATE_TREEVIEW) then this tag can be 
-# used to set the initial width (in pixels) of the frame in which the tree 
-# is shown.
+# If the treeview is enabled (see GENERATE_TREEVIEW) then this tag can be used
+# to set the initial width (in pixels) of the frame in which the tree is shown.
+# Minimum value: 0, maximum value: 1500, default value: 250.
+# This tag requires that the tag GENERATE_HTML is set to YES.
 
 TREEVIEW_WIDTH         = 250
 
-# When the EXT_LINKS_IN_WINDOW option is set to YES doxygen will open 
-# links to external symbols imported via tag files in a separate window.
+# If the EXT_LINKS_IN_WINDOW option is set to YES, doxygen will open links to
+# external symbols imported via tag files in a separate window.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_HTML is set to YES.
 
 EXT_LINKS_IN_WINDOW    = NO
 
-# Use this tag to change the font size of Latex formulas included 
-# as images in the HTML documentation. The default is 10. Note that 
-# when you change the font size after a successful doxygen run you need 
-# to manually remove any form_*.png images from the HTML output directory 
-# to force them to be regenerated.
+# Use this tag to change the font size of LaTeX formulas included as images in
+# the HTML documentation. When you change the font size after a successful
+# doxygen run you need to manually remove any form_*.png images from the HTML
+# output directory to force them to be regenerated.
+# Minimum value: 8, maximum value: 50, default value: 10.
+# This tag requires that the tag GENERATE_HTML is set to YES.
 
 FORMULA_FONTSIZE       = 10
 
-# Use the FORMULA_TRANPARENT tag to determine whether or not the images 
-# generated for formulas are transparent PNGs. Transparent PNGs are 
-# not supported properly for IE 6.0, but are supported on all modern browsers. 
-# Note that when changing this option you need to delete any form_*.png files 
-# in the HTML output before the changes have effect.
+# Use the FORMULA_TRANPARENT tag to determine whether or not the images
+# generated for formulas are transparent PNGs. Transparent PNGs are not
+# supported properly for IE 6.0, but are supported on all modern browsers.
+#
+# Note that when changing this option you need to delete any form_*.png files in
+# the HTML output directory before the changes have effect.
+# The default value is: YES.
+# This tag requires that the tag GENERATE_HTML is set to YES.
 
 FORMULA_TRANSPARENT    = YES
 
-# Enable the USE_MATHJAX option to render LaTeX formulas using MathJax 
-# (see http://www.mathjax.org) which uses client side Javascript for the 
-# rendering instead of using prerendered bitmaps. Use this if you do not 
-# have LaTeX installed or if you want to formulas look prettier in the HTML 
-# output. When enabled you also need to install MathJax separately and 
-# configure the path to it using the MATHJAX_RELPATH option.
+# Enable the USE_MATHJAX option to render LaTeX formulas using MathJax (see
+# http://www.mathjax.org) which uses client side Javascript for the rendering
+# instead of using pre-rendered bitmaps. Use this if you do not have LaTeX
+# installed or if you want to formulas look prettier in the HTML output. When
+# enabled you may also need to install MathJax separately and configure the path
+# to it using the MATHJAX_RELPATH option.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_HTML is set to YES.
 
 USE_MATHJAX            = NO
 
-# When MathJax is enabled you need to specify the location relative to the 
-# HTML output directory using the MATHJAX_RELPATH option. The destination 
-# directory should contain the MathJax.js script. For instance, if the mathjax 
-# directory is located at the same level as the HTML output directory, then 
-# MATHJAX_RELPATH should be ../mathjax. The default value points to the 
-# mathjax.org site, so you can quickly see the result without installing 
-# MathJax, but it is strongly recommended to install a local copy of MathJax 
-# before deployment.
+# When MathJax is enabled you can set the default output format to be used for
+# the MathJax output. See the MathJax site (see:
+# http://docs.mathjax.org/en/latest/output.html) for more details.
+# Possible values are: HTML-CSS (which is slower, but has the best
+# compatibility), NativeMML (i.e. MathML) and SVG.
+# The default value is: HTML-CSS.
+# This tag requires that the tag USE_MATHJAX is set to YES.
+
+MATHJAX_FORMAT         = HTML-CSS
+
+# When MathJax is enabled you need to specify the location relative to the HTML
+# output directory using the MATHJAX_RELPATH option. The destination directory
+# should contain the MathJax.js script. For instance, if the mathjax directory
+# is located at the same level as the HTML output directory, then
+# MATHJAX_RELPATH should be ../mathjax. The default value points to the MathJax
+# Content Delivery Network so you can quickly see the result without installing
+# MathJax. However, it is strongly recommended to install a local copy of
+# MathJax from http://www.mathjax.org before deployment.
+# The default value is: http://cdn.mathjax.org/mathjax/latest.
+# This tag requires that the tag USE_MATHJAX is set to YES.
 
 MATHJAX_RELPATH        = http://www.mathjax.org/mathjax
 
-# When the SEARCHENGINE tag is enabled doxygen will generate a search box 
-# for the HTML output. The underlying search engine uses javascript 
-# and DHTML and should work on any modern browser. Note that when using 
-# HTML help (GENERATE_HTMLHELP), Qt help (GENERATE_QHP), or docsets 
-# (GENERATE_DOCSET) there is already a search function so this one should 
-# typically be disabled. For large projects the javascript based search engine 
-# can be slow, then enabling SERVER_BASED_SEARCH may provide a better solution.
+# The MATHJAX_EXTENSIONS tag can be used to specify one or more MathJax
+# extension names that should be enabled during MathJax rendering. For example
+# MATHJAX_EXTENSIONS = TeX/AMSmath TeX/AMSsymbols
+# This tag requires that the tag USE_MATHJAX is set to YES.
+
+MATHJAX_EXTENSIONS     =
+
+# The MATHJAX_CODEFILE tag can be used to specify a file with javascript pieces
+# of code that will be used on startup of the MathJax code. See the MathJax site
+# (see: http://docs.mathjax.org/en/latest/output.html) for more details. For an
+# example see the documentation.
+# This tag requires that the tag USE_MATHJAX is set to YES.
+
+MATHJAX_CODEFILE       =
+
+# When the SEARCHENGINE tag is enabled doxygen will generate a search box for
+# the HTML output. The underlying search engine uses javascript and DHTML and
+# should work on any modern browser. Note that when using HTML help
+# (GENERATE_HTMLHELP), Qt help (GENERATE_QHP), or docsets (GENERATE_DOCSET)
+# there is already a search function so this one should typically be disabled.
+# For large projects the javascript based search engine can be slow, then
+# enabling SERVER_BASED_SEARCH may provide a better solution. It is possible to
+# search using the keyboard; to jump to the search box use <access key> + S
+# (what the <access key> is depends on the OS and browser, but it is typically
+# <CTRL>, <ALT>/<option>, or both). Inside the search box use the <cursor down
+# key> to jump into the search results window, the results can be navigated
+# using the <cursor keys>. Press <Enter> to select an item or <escape> to cancel
+# the search. The filter options can be selected when the cursor is inside the
+# search box by pressing <Shift>+<cursor down>. Also here use the <cursor keys>
+# to select a filter and <Enter> or <escape> to activate or cancel the filter
+# option.
+# The default value is: YES.
+# This tag requires that the tag GENERATE_HTML is set to YES.
 
 SEARCHENGINE           = YES
 
-# When the SERVER_BASED_SEARCH tag is enabled the search engine will be 
-# implemented using a PHP enabled web server instead of at the web client 
-# using Javascript. Doxygen will generate the search PHP script and index 
-# file to put on the web server. The advantage of the server 
-# based approach is that it scales better to large projects and allows 
-# full text search. The disadvantages are that it is more difficult to setup 
-# and does not have live searching capabilities.
+# When the SERVER_BASED_SEARCH tag is enabled the search engine will be
+# implemented using a web server instead of a web client using Javascript. There
+# are two flavors of web server based searching depending on the EXTERNAL_SEARCH
+# setting. When disabled, doxygen will generate a PHP script for searching and
+# an index file used by the script. When EXTERNAL_SEARCH is enabled the indexing
+# and searching needs to be provided by external tools. See the section
+# "External Indexing and Searching" for details.
+# The default value is: NO.
+# This tag requires that the tag SEARCHENGINE is set to YES.
 
 SERVER_BASED_SEARCH    = NO
 
-#---------------------------------------------------------------------------
-# configuration options related to the LaTeX output
-#---------------------------------------------------------------------------
-
-# If the GENERATE_LATEX tag is set to YES (the default) Doxygen will 
-# generate Latex output.
+# When EXTERNAL_SEARCH tag is enabled doxygen will no longer generate the PHP
+# script for searching. Instead the search results are written to an XML file
+# which needs to be processed by an external indexer. Doxygen will invoke an
+# external search engine pointed to by the SEARCHENGINE_URL option to obtain the
+# search results.
+#
+# Doxygen ships with an example indexer (doxyindexer) and search engine
+# (doxysearch.cgi) which are based on the open source search engine library
+# Xapian (see: http://xapian.org/).
+#
+# See the section "External Indexing and Searching" for details.
+# The default value is: NO.
+# This tag requires that the tag SEARCHENGINE is set to YES.
+
+EXTERNAL_SEARCH        = NO
+
+# The SEARCHENGINE_URL should point to a search engine hosted by a web server
+# which will return the search results when EXTERNAL_SEARCH is enabled.
+#
+# Doxygen ships with an example indexer (doxyindexer) and search engine
+# (doxysearch.cgi) which are based on the open source search engine library
+# Xapian (see: http://xapian.org/). See the section "External Indexing and
+# Searching" for details.
+# This tag requires that the tag SEARCHENGINE is set to YES.
+
+SEARCHENGINE_URL       =
+
+# When SERVER_BASED_SEARCH and EXTERNAL_SEARCH are both enabled the unindexed
+# search data is written to a file for indexing by an external tool. With the
+# SEARCHDATA_FILE tag the name of this file can be specified.
+# The default file is: searchdata.xml.
+# This tag requires that the tag SEARCHENGINE is set to YES.
+
+SEARCHDATA_FILE        = searchdata.xml
+
+# When SERVER_BASED_SEARCH and EXTERNAL_SEARCH are both enabled the
+# EXTERNAL_SEARCH_ID tag can be used as an identifier for the project. This is
+# useful in combination with EXTRA_SEARCH_MAPPINGS to search through multiple
+# projects and redirect the results back to the right project.
+# This tag requires that the tag SEARCHENGINE is set to YES.
+
+EXTERNAL_SEARCH_ID     =
+
+# The EXTRA_SEARCH_MAPPINGS tag can be used to enable searching through doxygen
+# projects other than the one defined by this configuration file, but that are
+# all added to the same external search index. Each project needs to have a
+# unique id set via EXTERNAL_SEARCH_ID. The search mapping then maps the id of
+# to a relative location where the documentation can be found. The format is:
+# EXTRA_SEARCH_MAPPINGS = tagname1=loc1 tagname2=loc2 ...
+# This tag requires that the tag SEARCHENGINE is set to YES.
+
+EXTRA_SEARCH_MAPPINGS  =
+
+#---------------------------------------------------------------------------
+# Configuration options related to the LaTeX output
+#---------------------------------------------------------------------------
+
+# If the GENERATE_LATEX tag is set to YES, doxygen will generate LaTeX output.
+# The default value is: YES.
 
 GENERATE_LATEX         = NO
 
-# The LATEX_OUTPUT tag is used to specify where the LaTeX docs will be put. 
-# If a relative path is entered the value of OUTPUT_DIRECTORY will be 
-# put in front of it. If left blank `latex' will be used as the default path.
+# 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
+# it.
+# The default directory is: latex.
+# This tag requires that the tag GENERATE_LATEX is set to YES.
 
 LATEX_OUTPUT           = latex
 
-# The LATEX_CMD_NAME tag can be used to specify the LaTeX command name to be 
-# invoked. If left blank `latex' will be used as the default command name. 
-# Note that when enabling USE_PDFLATEX this option is only used for 
-# generating bitmaps for formulas in the HTML output, but not in the 
-# Makefile that is written to the output directory.
+# The LATEX_CMD_NAME tag can be used to specify the LaTeX command name to be
+# invoked.
+#
+# Note that when enabling USE_PDFLATEX this option is only used for generating
+# bitmaps for formulas in the HTML output, but not in the Makefile that is
+# written to the output directory.
+# The default file is: latex.
+# This tag requires that the tag GENERATE_LATEX is set to YES.
 
 LATEX_CMD_NAME         = latex
 
-# The MAKEINDEX_CMD_NAME tag can be used to specify the command name to 
-# generate index for LaTeX. If left blank `makeindex' will be used as the 
-# default command name.
+# The MAKEINDEX_CMD_NAME tag can be used to specify the command name to generate
+# index for LaTeX.
+# The default file is: makeindex.
+# This tag requires that the tag GENERATE_LATEX is set to YES.
 
 MAKEINDEX_CMD_NAME     = makeindex
 
-# If the COMPACT_LATEX tag is set to YES Doxygen generates more compact 
-# LaTeX documents. This may be useful for small projects and may help to 
-# save some trees in general.
+# If the COMPACT_LATEX tag is set to YES, doxygen generates more compact LaTeX
+# documents. This may be useful for small projects and may help to save some
+# trees in general.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_LATEX is set to YES.
 
 COMPACT_LATEX          = NO
 
-# The PAPER_TYPE tag can be used to set the paper type that is used 
-# by the printer. Possible values are: a4, letter, legal and 
-# executive. If left blank a4wide will be used.
+# The PAPER_TYPE tag can be used to set the paper type that is used by the
+# printer.
+# Possible values are: a4 (210 x 297 mm), letter (8.5 x 11 inches), legal (8.5 x
+# 14 inches) and executive (7.25 x 10.5 inches).
+# The default value is: a4.
+# This tag requires that the tag GENERATE_LATEX is set to YES.
 
 PAPER_TYPE             = a4
 
-# The EXTRA_PACKAGES tag can be to specify one or more names of LaTeX 
-# packages that should be included in the LaTeX output.
-
-EXTRA_PACKAGES         = 
-
-# The LATEX_HEADER tag can be used to specify a personal LaTeX header for 
-# the generated latex document. The header should contain everything until 
-# the first chapter. If it is left blank doxygen will generate a 
-# standard header. Notice: only use this tag if you know what you are doing!
-
-LATEX_HEADER           = 
-
-# The LATEX_FOOTER tag can be used to specify a personal LaTeX footer for 
-# the generated latex document. The footer should contain everything after 
-# the last chapter. If it is left blank doxygen will generate a 
-# standard footer. Notice: only use this tag if you know what you are doing!
-
-LATEX_FOOTER           = 
-
-# If the PDF_HYPERLINKS tag is set to YES, the LaTeX that is generated 
-# is prepared for conversion to pdf (using ps2pdf). The pdf file will 
-# contain links (just like the HTML output) instead of page references 
-# This makes the output suitable for online browsing using a pdf viewer.
+# The EXTRA_PACKAGES tag can be used to specify one or more LaTeX package names
+# that should be included in the LaTeX output. The package can be specified just
+# by its name or with the correct syntax as to be used with the LaTeX
+# \usepackage command. To get the times font for instance you can specify :
+# EXTRA_PACKAGES=times or EXTRA_PACKAGES={times}
+# To use the option intlimits with the amsmath package you can specify:
+# EXTRA_PACKAGES=[intlimits]{amsmath}
+# If left blank no extra packages will be included.
+# This tag requires that the tag GENERATE_LATEX is set to YES.
+
+EXTRA_PACKAGES         =
+
+# The LATEX_HEADER tag can be used to specify a personal LaTeX header for the
+# generated LaTeX document. The header should contain everything until the first
+# chapter. If it is left blank doxygen will generate a standard header. See
+# section "Doxygen usage" for information on how to let doxygen write the
+# default header to a separate file.
+#
+# Note: Only use a user-defined header if you know what you are doing! The
+# following commands have a special meaning inside the header: $title,
+# $datetime, $date, $doxygenversion, $projectname, $projectnumber,
+# $projectbrief, $projectlogo. Doxygen will replace $title with the empty
+# string, for the replacement values of the other commands the user is referred
+# to HTML_HEADER.
+# This tag requires that the tag GENERATE_LATEX is set to YES.
+
+LATEX_HEADER           =
+
+# The LATEX_FOOTER tag can be used to specify a personal LaTeX footer for the
+# generated LaTeX document. The footer should contain everything after the last
+# chapter. If it is left blank doxygen will generate a standard footer. See
+# LATEX_HEADER for more information on how to generate a default footer and what
+# special commands can be used inside the footer.
+#
+# Note: Only use a user-defined footer if you know what you are doing!
+# This tag requires that the tag GENERATE_LATEX is set to YES.
+
+LATEX_FOOTER           =
+
+# The LATEX_EXTRA_STYLESHEET tag can be used to specify additional user-defined
+# LaTeX style sheets that are included after the standard style sheets created
+# by doxygen. Using this option one can overrule certain style aspects. Doxygen
+# will copy the style sheet files to the output directory.
+# Note: The order of the extra style sheet files is of importance (e.g. the last
+# style sheet in the list overrules the setting of the previous ones in the
+# list).
+# This tag requires that the tag GENERATE_LATEX is set to YES.
+
+LATEX_EXTRA_STYLESHEET =
+
+# The LATEX_EXTRA_FILES tag can be used to specify one or more extra images or
+# other source files which should be copied to the LATEX_OUTPUT output
+# directory. Note that the files will be copied as-is; there are no commands or
+# markers available.
+# This tag requires that the tag GENERATE_LATEX is set to YES.
+
+LATEX_EXTRA_FILES      =
+
+# If the PDF_HYPERLINKS tag is set to YES, the LaTeX that is generated is
+# prepared for conversion to PDF (using ps2pdf or pdflatex). The PDF file will
+# contain links (just like the HTML output) instead of page references. This
+# makes the output suitable for online browsing using a PDF viewer.
+# The default value is: YES.
+# This tag requires that the tag GENERATE_LATEX is set to YES.
 
 PDF_HYPERLINKS         = YES
 
-# If the USE_PDFLATEX tag is set to YES, pdflatex will be used instead of 
-# plain latex in the generated Makefile. Set this option to YES to get a 
+# If the USE_PDFLATEX tag is set to YES, doxygen will use pdflatex to generate
+# the PDF file directly from the LaTeX files. Set this option to YES, to get a
 # higher quality PDF documentation.
+# The default value is: YES.
+# This tag requires that the tag GENERATE_LATEX is set to YES.
 
 USE_PDFLATEX           = YES
 
-# If the LATEX_BATCHMODE tag is set to YES, doxygen will add the \\batchmode. 
-# command to the generated LaTeX files. This will instruct LaTeX to keep 
-# running if errors occur, instead of asking the user for help. 
-# This option is also used when generating formulas in HTML.
+# If the LATEX_BATCHMODE tag is set to YES, doxygen will add the \batchmode
+# command to the generated LaTeX files. This will instruct LaTeX to keep running
+# if errors occur, instead of asking the user for help. This option is also used
+# when generating formulas in HTML.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_LATEX is set to YES.
 
 LATEX_BATCHMODE        = NO
 
-# If LATEX_HIDE_INDICES is set to YES then doxygen will not 
-# include the index chapters (such as File Index, Compound Index, etc.) 
-# in the output.
+# If the LATEX_HIDE_INDICES tag is set to YES then doxygen will not include the
+# index chapters (such as File Index, Compound Index, etc.) in the output.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_LATEX is set to YES.
 
 LATEX_HIDE_INDICES     = NO
 
-# If LATEX_SOURCE_CODE is set to YES then doxygen will include 
-# source code with syntax highlighting in the LaTeX output. 
-# Note that which sources are shown also depends on other settings 
-# such as SOURCE_BROWSER.
+# If the LATEX_SOURCE_CODE tag is set to YES then doxygen will include source
+# code with syntax highlighting in the LaTeX output.
+#
+# Note that which sources are shown also depends on other settings such as
+# SOURCE_BROWSER.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_LATEX is set to YES.
 
 LATEX_SOURCE_CODE      = NO
 
-#---------------------------------------------------------------------------
-# configuration options related to the RTF output
-#---------------------------------------------------------------------------
-
-# If the GENERATE_RTF tag is set to YES Doxygen will generate RTF output 
-# The RTF output is optimized for Word 97 and may not look very pretty with 
-# other RTF readers or editors.
+# The LATEX_BIB_STYLE tag can be used to specify the style to use for the
+# bibliography, e.g. plainnat, or ieeetr. See
+# http://en.wikipedia.org/wiki/BibTeX and \cite for more info.
+# The default value is: plain.
+# This tag requires that the tag GENERATE_LATEX is set to YES.
+
+LATEX_BIB_STYLE        = plain
+
+#---------------------------------------------------------------------------
+# Configuration options related to the RTF output
+#---------------------------------------------------------------------------
+
+# If the GENERATE_RTF tag is set to YES, doxygen will generate RTF output. The
+# RTF output is optimized for Word 97 and may not look too pretty with other RTF
+# readers/editors.
+# The default value is: NO.
 
 GENERATE_RTF           = NO
 
-# The RTF_OUTPUT tag is used to specify where the RTF docs will be put. 
-# If a relative path is entered the value of OUTPUT_DIRECTORY will be 
-# put in front of it. If left blank `rtf' will be used as the default path.
+# The RTF_OUTPUT tag is used to specify where the RTF docs will be put. If a
+# relative path is entered the value of OUTPUT_DIRECTORY will be put in front of
+# it.
+# The default directory is: rtf.
+# This tag requires that the tag GENERATE_RTF is set to YES.
 
 RTF_OUTPUT             = rtf
 
-# If the COMPACT_RTF tag is set to YES Doxygen generates more compact 
-# RTF documents. This may be useful for small projects and may help to 
-# save some trees in general.
+# If the COMPACT_RTF tag is set to YES, doxygen generates more compact RTF
+# documents. This may be useful for small projects and may help to save some
+# trees in general.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_RTF is set to YES.
 
 COMPACT_RTF            = NO
 
-# If the RTF_HYPERLINKS tag is set to YES, the RTF that is generated 
-# will contain hyperlink fields. The RTF file will 
-# contain links (just like the HTML output) instead of page references. 
-# This makes the output suitable for online browsing using WORD or other 
-# programs which support those fields. 
-# Note: wordpad (write) and others do not support links.
+# If the RTF_HYPERLINKS tag is set to YES, the RTF that is generated will
+# contain hyperlink fields. The RTF file will contain links (just like the HTML
+# output) instead of page references. This makes the output suitable for online
+# browsing using Word or some other Word compatible readers that support those
+# fields.
+#
+# Note: WordPad (write) and others do not support links.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_RTF is set to YES.
 
 RTF_HYPERLINKS         = NO
 
-# Load stylesheet definitions from file. Syntax is similar to doxygen's 
-# config file, i.e. a series of assignments. You only have to provide 
-# replacements, missing definitions are set to their default value.
-
-RTF_STYLESHEET_FILE    = 
-
-# Set optional variables used in the generation of an rtf document. 
-# Syntax is similar to doxygen's config file.
-
-RTF_EXTENSIONS_FILE    = 
-
-#---------------------------------------------------------------------------
-# configuration options related to the man page output
-#---------------------------------------------------------------------------
-
-# If the GENERATE_MAN tag is set to YES (the default) Doxygen will 
-# generate man pages
+# Load stylesheet definitions from file. Syntax is similar to doxygen's config
+# file, i.e. a series of assignments. You only have to provide replacements,
+# missing definitions are set to their default value.
+#
+# See also section "Doxygen usage" for information on how to generate the
+# default style sheet that doxygen normally uses.
+# This tag requires that the tag GENERATE_RTF is set to YES.
+
+RTF_STYLESHEET_FILE    =
+
+# Set optional variables used in the generation of an RTF document. Syntax is
+# similar to doxygen's config file. A template extensions file can be generated
+# using doxygen -e rtf extensionFile.
+# This tag requires that the tag GENERATE_RTF is set to YES.
+
+RTF_EXTENSIONS_FILE    =
+
+# If the RTF_SOURCE_CODE tag is set to YES then doxygen will include source code
+# with syntax highlighting in the RTF output.
+#
+# Note that which sources are shown also depends on other settings such as
+# SOURCE_BROWSER.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_RTF is set to YES.
+
+RTF_SOURCE_CODE        = NO
+
+#---------------------------------------------------------------------------
+# Configuration options related to the man page output
+#---------------------------------------------------------------------------
+
+# If the GENERATE_MAN tag is set to YES, doxygen will generate man pages for
+# classes and files.
+# The default value is: NO.
 
 GENERATE_MAN           = NO
 
-# The MAN_OUTPUT tag is used to specify where the man pages will be put. 
-# If a relative path is entered the value of OUTPUT_DIRECTORY will be 
-# put in front of it. If left blank `man' will be used as the default path.
+# The MAN_OUTPUT tag is used to specify where the man pages will be put. If a
+# relative path is entered the value of OUTPUT_DIRECTORY will be put in front of
+# it. A directory man3 will be created inside the directory specified by
+# MAN_OUTPUT.
+# The default directory is: man.
+# This tag requires that the tag GENERATE_MAN is set to YES.
 
 MAN_OUTPUT             = man
 
-# The MAN_EXTENSION tag determines the extension that is added to 
-# the generated man pages (default is the subroutine's section .3)
+# The MAN_EXTENSION tag determines the extension that is added to the generated
+# man pages. In case the manual section does not start with a number, the number
+# 3 is prepended. The dot (.) at the beginning of the MAN_EXTENSION tag is
+# optional.
+# The default value is: .3.
+# This tag requires that the tag GENERATE_MAN is set to YES.
 
 MAN_EXTENSION          = .3
 
-# If the MAN_LINKS tag is set to YES and Doxygen generates man output, 
-# then it will generate one additional man file for each entity 
-# documented in the real man page(s). These additional files 
-# only source the real man page, but without them the man command 
-# would be unable to find the correct page. The default is NO.
+# The MAN_SUBDIR tag determines the name of the directory created within
+# MAN_OUTPUT in which the man pages are placed. If defaults to man followed by
+# MAN_EXTENSION with the initial . removed.
+# This tag requires that the tag GENERATE_MAN is set to YES.
+
+MAN_SUBDIR             =
+
+# If the MAN_LINKS tag is set to YES and doxygen generates man output, then it
+# will generate one additional man file for each entity documented in the real
+# man page(s). These additional files only source the real man page, but without
+# them the man command would be unable to find the correct page.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_MAN is set to YES.
 
 MAN_LINKS              = NO
 
 #---------------------------------------------------------------------------
-# configuration options related to the XML output
-#---------------------------------------------------------------------------
-
-# If the GENERATE_XML tag is set to YES Doxygen will 
-# generate an XML file that captures the structure of 
-# the code including all documentation.
+# Configuration options related to the XML output
+#---------------------------------------------------------------------------
+
+# If the GENERATE_XML tag is set to YES, doxygen will generate an XML file that
+# captures the structure of the code including all documentation.
+# The default value is: NO.
 
 GENERATE_XML           = NO
 
-# The XML_OUTPUT tag is used to specify where the XML pages will be put. 
-# If a relative path is entered the value of OUTPUT_DIRECTORY will be 
-# put in front of it. If left blank `xml' will be used as the default path.
+# The XML_OUTPUT tag is used to specify where the XML pages will be put. If a
+# relative path is entered the value of OUTPUT_DIRECTORY will be put in front of
+# it.
+# The default directory is: xml.
+# This tag requires that the tag GENERATE_XML is set to YES.
 
 XML_OUTPUT             = xml
 
-# The XML_SCHEMA tag can be used to specify an XML schema, 
-# which can be used by a validating XML parser to check the 
-# syntax of the XML files.
-
-XML_SCHEMA             = 
-
-# The XML_DTD tag can be used to specify an XML DTD, 
-# which can be used by a validating XML parser to check the 
-# syntax of the XML files.
-
-XML_DTD                = 
-
-# If the XML_PROGRAMLISTING tag is set to YES Doxygen will 
-# dump the program listings (including syntax highlighting 
-# and cross-referencing information) to the XML output. Note that 
-# enabling this will significantly increase the size of the XML output.
+# If the XML_PROGRAMLISTING tag is set to YES, doxygen will dump the program
+# listings (including syntax highlighting and cross-referencing information) to
+# the XML output. Note that enabling this will significantly increase the size
+# of the XML output.
+# The default value is: YES.
+# This tag requires that the tag GENERATE_XML is set to YES.
 
 XML_PROGRAMLISTING     = YES
 
 #---------------------------------------------------------------------------
-# configuration options for the AutoGen Definitions output
-#---------------------------------------------------------------------------
-
-# If the GENERATE_AUTOGEN_DEF tag is set to YES Doxygen will 
-# generate an AutoGen Definitions (see autogen.sf.net) file 
-# that captures the structure of the code including all 
-# documentation. Note that this feature is still experimental 
-# and incomplete at the moment.
+# Configuration options related to the DOCBOOK output
+#---------------------------------------------------------------------------
+
+# If the GENERATE_DOCBOOK tag is set to YES, doxygen will generate Docbook files
+# that can be used to generate PDF.
+# The default value is: NO.
+
+GENERATE_DOCBOOK       = NO
+
+# The DOCBOOK_OUTPUT tag is used to specify where the Docbook pages will be put.
+# If a relative path is entered the value of OUTPUT_DIRECTORY will be put in
+# front of it.
+# The default directory is: docbook.
+# This tag requires that the tag GENERATE_DOCBOOK is set to YES.
+
+DOCBOOK_OUTPUT         = docbook
+
+# If the DOCBOOK_PROGRAMLISTING tag is set to YES, doxygen will include the
+# program listings (including syntax highlighting and cross-referencing
+# information) to the DOCBOOK output. Note that enabling this will significantly
+# increase the size of the DOCBOOK output.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_DOCBOOK is set to YES.
+
+DOCBOOK_PROGRAMLISTING = NO
+
+#---------------------------------------------------------------------------
+# Configuration options for the AutoGen Definitions output
+#---------------------------------------------------------------------------
+
+# If the GENERATE_AUTOGEN_DEF tag is set to YES, doxygen will generate an
+# AutoGen Definitions (see http://autogen.sf.net) file that captures the
+# structure of the code including all documentation. Note that this feature is
+# still experimental and incomplete at the moment.
+# The default value is: NO.
 
 GENERATE_AUTOGEN_DEF   = NO
 
 #---------------------------------------------------------------------------
-# configuration options related to the Perl module output
-#---------------------------------------------------------------------------
-
-# If the GENERATE_PERLMOD tag is set to YES Doxygen will 
-# generate a Perl module file that captures the structure of 
-# the code including all documentation. Note that this 
-# feature is still experimental and incomplete at the 
-# moment.
+# Configuration options related to the Perl module output
+#---------------------------------------------------------------------------
+
+# If the GENERATE_PERLMOD tag is set to YES, doxygen will generate a Perl module
+# file that captures the structure of the code including all documentation.
+#
+# Note that this feature is still experimental and incomplete at the moment.
+# The default value is: NO.
 
 GENERATE_PERLMOD       = NO
 
-# If the PERLMOD_LATEX tag is set to YES Doxygen will generate 
-# the necessary Makefile rules, Perl scripts and LaTeX code to be able 
-# to generate PDF and DVI output from the Perl module output.
+# If the PERLMOD_LATEX tag is set to YES, doxygen will generate the necessary
+# Makefile rules, Perl scripts and LaTeX code to be able to generate PDF and DVI
+# output from the Perl module output.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_PERLMOD is set to YES.
 
 PERLMOD_LATEX          = NO
 
-# If the PERLMOD_PRETTY tag is set to YES the Perl module output will be 
-# nicely formatted so it can be parsed by a human reader.  This is useful 
-# if you want to understand what is going on.  On the other hand, if this 
-# tag is set to NO the size of the Perl module output will be much smaller 
-# and Perl will parse it just the same.
+# If the PERLMOD_PRETTY tag is set to YES, the Perl module output will be nicely
+# formatted so it can be parsed by a human reader. This is useful if you want to
+# understand what is going on. On the other hand, if this tag is set to NO, the
+# size of the Perl module output will be much smaller and Perl will parse it
+# just the same.
+# The default value is: YES.
+# This tag requires that the tag GENERATE_PERLMOD is set to YES.
 
 PERLMOD_PRETTY         = YES
 
-# The names of the make variables in the generated doxyrules.make file 
-# are prefixed with the string contained in PERLMOD_MAKEVAR_PREFIX. 
-# This is useful so different doxyrules.make files included by the same 
-# Makefile don't overwrite each other's variables.
-
-PERLMOD_MAKEVAR_PREFIX = 
+# The names of the make variables in the generated doxyrules.make file are
+# prefixed with the string contained in PERLMOD_MAKEVAR_PREFIX. This is useful
+# so different doxyrules.make files included by the same Makefile don't
+# overwrite each other's variables.
+# This tag requires that the tag GENERATE_PERLMOD is set to YES.
+
+PERLMOD_MAKEVAR_PREFIX =
 
 #---------------------------------------------------------------------------
@@ -1414 +1956 @@
 #---------------------------------------------------------------------------
 
-# If the ENABLE_PREPROCESSING tag is set to YES (the default) Doxygen will 
-# evaluate all C-preprocessor directives found in the sources and include 
+# If the ENABLE_PREPROCESSING tag is set to YES, doxygen will evaluate all
+# C-preprocessor directives found in the sources and include files.
+# The default value is: YES.
+
+ENABLE_PREPROCESSING   = YES
+
+# If the MACRO_EXPANSION tag is set to YES, doxygen will expand all macro names
+# in the source code. If set to NO, only conditional compilation will be
+# performed. Macro expansion can be done in a controlled way by setting
+# EXPAND_ONLY_PREDEF to YES.
+# The default value is: NO.
+# This tag requires that the tag ENABLE_PREPROCESSING is set to YES.
+
+MACRO_EXPANSION        = YES
+
+# If the EXPAND_ONLY_PREDEF and MACRO_EXPANSION tags are both set to YES then
+# the macro expansion is limited to the macros specified with the PREDEFINED and
+# EXPAND_AS_DEFINED tags.
+# The default value is: NO.
+# This tag requires that the tag ENABLE_PREPROCESSING is set to YES.
+
+EXPAND_ONLY_PREDEF     = NO
+
+# If the SEARCH_INCLUDES tag is set to YES, the include files in the
+# INCLUDE_PATH will be searched if a #include is found.
+# The default value is: YES.
+# This tag requires that the tag ENABLE_PREPROCESSING is set to YES.
+
+SEARCH_INCLUDES        = YES
+
+# The INCLUDE_PATH tag can be used to specify one or more directories that
+# contain include files that are not input files but should be processed by the
+# preprocessor.
+# This tag requires that the tag SEARCH_INCLUDES is set to YES.
+
+INCLUDE_PATH           =
+
+# You can use the INCLUDE_FILE_PATTERNS tag to specify one or more wildcard
+# patterns (like *.h and *.hpp) to filter out the header-files in the
+# directories. If left blank, the patterns specified with FILE_PATTERNS will be
+# used.
+# This tag requires that the tag ENABLE_PREPROCESSING is set to YES.
+
+INCLUDE_FILE_PATTERNS  =
+
+# The PREDEFINED tag can be used to specify one or more macro names that are
+# defined before the preprocessor is started (similar to the -D option of e.g.
+# gcc). The argument of the tag is a list of macros of the form: name or
+# name=definition (no spaces). If the definition and the "=" are omitted, "=1"
+# is assumed. To prevent a macro definition from being undefined via #undef or
+# recursively expanded use the := operator instead of the = operator.
+# This tag requires that the tag ENABLE_PREPROCESSING is set to YES.
+
+PREDEFINED             =
+
+# If the MACRO_EXPANSION and EXPAND_ONLY_PREDEF tags are set to YES then this
+# tag can be used to specify a list of macro names that should be expanded. The
+# macro definition that is found in the sources will be used. Use the PREDEFINED
+# tag if you want to use a different macro definition that overrules the
+# definition found in the source code.
+# This tag requires that the tag ENABLE_PREPROCESSING is set to YES.
+
+EXPAND_AS_DEFINED      =
+
+# If the SKIP_FUNCTION_MACROS tag is set to YES then doxygen's preprocessor will
+# remove all references to function-like macros that are alone on a line, have
+# an all uppercase name, and do not end with a semicolon. Such function macros
+# are typically used for boiler-plate code, and will confuse the parser if not
+# removed.
+# The default value is: YES.
+# This tag requires that the tag ENABLE_PREPROCESSING is set to YES.
+
+SKIP_FUNCTION_MACROS   = YES
+
+#---------------------------------------------------------------------------
+# Configuration options related to external references
+#---------------------------------------------------------------------------
+
+# The TAGFILES tag can be used to specify one or more tag files. For each tag
+# file the location of the external documentation should be added. The format of
+# a tag file without this location is as follows:
+# TAGFILES = file1 file2 ...
+# Adding location for the tag files is done as follows:
+# TAGFILES = file1=loc1 "file2 = loc2" ...
+# where loc1 and loc2 can be relative or absolute paths or URLs. See the
+# section "Linking to external documentation" for more information about the use
+# of tag files.
+# Note: Each tag file must have a unique name (where the name does NOT include
+# the path). If a tag file is not located in the directory in which doxygen is
+# run, you must also specify the path to the tagfile here.
+
+TAGFILES               =
+
+# When a file name is specified after GENERATE_TAGFILE, doxygen will create a
+# 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       =
+
+# 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.
+# The default value is: NO.
+
+ALLEXTERNALS           = NO
+
+# If the EXTERNAL_GROUPS tag is set to YES, all external groups will be listed
+# in the modules index. If set to NO, only the current project's groups will be
+# listed.
+# The default value is: YES.
+
+EXTERNAL_GROUPS        = YES
+
+# If the EXTERNAL_PAGES tag is set to YES, all external pages will be listed in
+# the related pages index. If set to NO, only the current project's pages will
+# be listed.
+# The default value is: YES.
+
+EXTERNAL_PAGES         = YES
+
+# The PERL_PATH should be the absolute path and name of the perl script
+# interpreter (i.e. the result of 'which perl').
+# The default file (with absolute path) is: /usr/bin/perl.
+
+PERL_PATH              = /usr/bin/perl
+
+#---------------------------------------------------------------------------
+# Configuration options related to the dot tool
+#---------------------------------------------------------------------------
+
+# If the CLASS_DIAGRAMS tag is set to YES, doxygen will generate a class diagram
+# (in HTML and LaTeX) for classes with base or super classes. Setting the tag to
+# NO turns the diagrams off. Note that this option also works with HAVE_DOT
+# disabled, but it is recommended to install and use dot, since it yields more
+# powerful graphs.
+# The default value is: YES.
+
+CLASS_DIAGRAMS         = YES
+
+# You can define message sequence charts within doxygen comments using the \msc
+# command. Doxygen will then run the mscgen tool (see:
+# http://www.mcternan.me.uk/mscgen/)) to produce the chart and insert it in the
+# documentation. The MSCGEN_PATH tag allows you to specify the directory where
+# the mscgen tool resides. If left empty the tool is assumed to be found in the
+# default search path.
+
+MSCGEN_PATH            =
+
+# You can include diagrams made with dia in doxygen documentation. Doxygen will
+# then run dia to produce the diagram and insert it in the documentation. The
+# DIA_PATH tag allows you to specify the directory where the dia binary resides.
+# If left empty dia is assumed to be found in the default search path.
+
+DIA_PATH               =
+
+# If set to YES the inheritance and collaboration graphs will hide inheritance
+# and usage relations if the target is undocumented or is not a class.
+# The default value is: YES.
+
+HIDE_UNDOC_RELATIONS   = YES
+
+# If you set the HAVE_DOT tag to YES then doxygen will assume the dot tool is
+# available from the path. This tool is part of Graphviz (see:
+# http://www.graphviz.org/), a graph visualization toolkit from AT&T and Lucent
+# Bell Labs. The other options in this section have no effect if this option is
+# set to NO
+# The default value is: NO.
+
+HAVE_DOT               = YES
+
+# The DOT_NUM_THREADS specifies the number of dot invocations doxygen is allowed
+# to run in parallel. When set to 0 doxygen will base this on the number of
+# processors available in the system. You can set it explicitly to a value
+# larger than 0 to get control over the balance between CPU load and processing
+# speed.
+# Minimum value: 0, maximum value: 32, default value: 0.
+# This tag requires that the tag HAVE_DOT is set to YES.
+
+DOT_NUM_THREADS        = 0
+
+# When you want a differently looking font in the dot files that doxygen
+# generates you can specify the font name using DOT_FONTNAME. You need to make
+# sure dot is able to find the font, which can be done by putting it in a
+# standard location or by setting the DOTFONTPATH environment variable or by
+# setting DOT_FONTPATH to the directory containing the font.
+# The default value is: Helvetica.
+# This tag requires that the tag HAVE_DOT is set to YES.
+
+DOT_FONTNAME           = Helvetica
+
+# The DOT_FONTSIZE tag can be used to set the size (in points) of the font of
+# dot graphs.
+# Minimum value: 4, maximum value: 24, default value: 10.
+# This tag requires that the tag HAVE_DOT is set to YES.
+
+DOT_FONTSIZE           = 10
+
+# By default doxygen will tell dot to use the default font as specified with
+# DOT_FONTNAME. If you specify a different font using DOT_FONTNAME you can set
+# the path where dot can find it using this tag.
+# This tag requires that the tag HAVE_DOT is set to YES.
+
+DOT_FONTPATH           =
+
+# If the CLASS_GRAPH tag is set to YES then doxygen will generate a graph for
+# each documented class showing the direct and indirect inheritance relations.
+# Setting this tag to YES will force the CLASS_DIAGRAMS tag to NO.
+# The default value is: YES.
+# This tag requires that the tag HAVE_DOT is set to YES.
+
+CLASS_GRAPH            = YES
+
+# If the COLLABORATION_GRAPH tag is set to YES then doxygen will generate a
+# graph for each documented class showing the direct and indirect implementation
+# dependencies (inheritance, containment, and class references variables) of the
+# class with other documented classes.
+# The default value is: YES.
+# This tag requires that the tag HAVE_DOT is set to YES.
+
+COLLABORATION_GRAPH    = YES
+
+# If the GROUP_GRAPHS tag is set to YES then doxygen will generate a graph for
+# groups, showing the direct groups dependencies.
+# The default value is: YES.
+# This tag requires that the tag HAVE_DOT is set to YES.
+
+GROUP_GRAPHS           = YES
+
+# If the UML_LOOK tag is set to YES, doxygen will generate inheritance and
+# collaboration diagrams in a style similar to the OMG's Unified Modeling
+# Language.
+# The default value is: NO.
+# This tag requires that the tag HAVE_DOT is set to YES.
+
+UML_LOOK               = YES
+
+# If the UML_LOOK tag is enabled, the fields and methods are shown inside the
+# class node. If there are many fields or methods and many nodes the graph may
+# become too big to be useful. The UML_LIMIT_NUM_FIELDS threshold limits the
+# number of items for each type to make the size more manageable. Set this to 0
+# for no limit. Note that the threshold may be exceeded by 50% before the limit
+# is enforced. So when you set the threshold to 10, up to 15 fields may appear,
+# but if the number exceeds 15, the total amount of fields shown is limited to
+# 10.
+# Minimum value: 0, maximum value: 100, default value: 10.
+# This tag requires that the tag HAVE_DOT is set to YES.
+
+UML_LIMIT_NUM_FIELDS   = 10
+
+# If the TEMPLATE_RELATIONS tag is set to YES then the inheritance and
+# collaboration graphs will show the relations between templates and their
+# instances.
+# The default value is: NO.
+# This tag requires that the tag HAVE_DOT is set to YES.
+
+TEMPLATE_RELATIONS     = YES
+
+# If the INCLUDE_GRAPH, ENABLE_PREPROCESSING and SEARCH_INCLUDES tags are set to
+# YES then doxygen will generate a graph for each documented file showing the
+# direct and indirect include dependencies of the file with other documented
 # files.
-
-ENABLE_PREPROCESSING   = YES
-
-# If the MACRO_EXPANSION tag is set to YES Doxygen will expand all macro 
-# names in the source code. If set to NO (the default) only conditional 
-# compilation will be performed. Macro expansion can be done in a controlled 
-# way by setting EXPAND_ONLY_PREDEF to YES.
-
-MACRO_EXPANSION        = YES
-
-# If the EXPAND_ONLY_PREDEF and MACRO_EXPANSION tags are both set to YES 
-# then the macro expansion is limited to the macros specified with the 
-# PREDEFINED and EXPAND_AS_DEFINED tags.
-
-EXPAND_ONLY_PREDEF     = NO
-
-# If the SEARCH_INCLUDES tag is set to YES (the default) the includes files 
-# pointed to by INCLUDE_PATH will be searched when a #include is found.
-
-SEARCH_INCLUDES        = YES
-
-# The INCLUDE_PATH tag can be used to specify one or more directories that 
-# contain include files that are not input files but should be processed by 
-# the preprocessor.
-
-INCLUDE_PATH           = 
-
-# You can use the INCLUDE_FILE_PATTERNS tag to specify one or more wildcard 
-# patterns (like *.h and *.hpp) to filter out the header-files in the 
-# directories. If left blank, the patterns specified with FILE_PATTERNS will 
-# be used.
-
-INCLUDE_FILE_PATTERNS  = 
-
-# The PREDEFINED tag can be used to specify one or more macro names that 
-# are defined before the preprocessor is started (similar to the -D option of 
-# gcc). The argument of the tag is a list of macros of the form: name 
-# or name=definition (no spaces). If the definition and the = are 
-# omitted =1 is assumed. To prevent a macro definition from being 
-# undefined via #undef or recursively expanded use the := operator 
-# instead of the = operator.
-
-PREDEFINED             = 
-
-# If the MACRO_EXPANSION and EXPAND_ONLY_PREDEF tags are set to YES then 
-# this tag can be used to specify a list of macro names that should be expanded. 
-# The macro definition that is found in the sources will be used. 
-# Use the PREDEFINED tag if you want to use a different macro definition that 
-# overrules the definition found in the source code.
-
-EXPAND_AS_DEFINED      = 
-
-# If the SKIP_FUNCTION_MACROS tag is set to YES (the default) then 
-# doxygen's preprocessor will remove all references to function-like macros 
-# that are alone on a line, have an all uppercase name, and do not end with a 
-# semicolon, because these will confuse the parser if not removed.
-
-SKIP_FUNCTION_MACROS   = YES
-
-#---------------------------------------------------------------------------
-# Configuration::additions related to external references
-#---------------------------------------------------------------------------
-
-# The TAGFILES option can be used to specify one or more tagfiles. 
-# Optionally an initial location of the external documentation 
-# can be added for each tagfile. The format of a tag file without 
-# this location is as follows: 
-#   TAGFILES = file1 file2 ... 
-# Adding location for the tag files is done as follows: 
-#   TAGFILES = file1=loc1 "file2 = loc2" ... 
-# where "loc1" and "loc2" can be relative or absolute paths or 
-# URLs. If a location is present for each tag, the installdox tool 
-# does not have to be run to correct the links. 
-# Note that each tag file must have a unique name 
-# (where the name does NOT include the path) 
-# If a tag file is not located in the directory in which doxygen 
-# is run, you must also specify the path to the tagfile here.
-
-TAGFILES               = 
-
-# When a file name is specified after GENERATE_TAGFILE, doxygen will create 
-# a tag file that is based on the input files it reads.
-
-GENERATE_TAGFILE       = 
-
-# If the ALLEXTERNALS tag is set to YES all external classes will be listed 
-# in the class index. If set to NO only the inherited external classes 
-# will be listed.
-
-ALLEXTERNALS           = NO
-
-# If the EXTERNAL_GROUPS tag is set to YES all external groups will be listed 
-# in the modules index. If set to NO, only the current project's groups will 
-# be listed.
-
-EXTERNAL_GROUPS        = YES
-
-# The PERL_PATH should be the absolute path and name of the perl script 
-# interpreter (i.e. the result of `which perl').
-
-PERL_PATH              = /usr/bin/perl
-
-#---------------------------------------------------------------------------
-# Configuration options related to the dot tool
-#---------------------------------------------------------------------------
-
-# If the CLASS_DIAGRAMS tag is set to YES (the default) Doxygen will 
-# generate a inheritance diagram (in HTML, RTF and LaTeX) for classes with base 
-# or super classes. Setting the tag to NO turns the diagrams off. Note that 
-# this option also works with HAVE_DOT disabled, but it is recommended to 
-# install and use dot, since it yields more powerful graphs.
-
-CLASS_DIAGRAMS         = YES
-
-# You can define message sequence charts within doxygen comments using the \msc 
-# command. Doxygen will then run the mscgen tool (see 
-# http://www.mcternan.me.uk/mscgen/) to produce the chart and insert it in the 
-# documentation. The MSCGEN_PATH tag allows you to specify the directory where 
-# the mscgen tool resides. If left empty the tool is assumed to be found in the 
-# default search path.
-
-MSCGEN_PATH            = 
-
-# If set to YES, the inheritance and collaboration graphs will hide 
-# inheritance and usage relations if the target is undocumented 
-# or is not a class.
-
-HIDE_UNDOC_RELATIONS   = YES
-
-# If you set the HAVE_DOT tag to YES then doxygen will assume the dot tool is 
-# available from the path. This tool is part of Graphviz, a graph visualization 
-# toolkit from AT&T and Lucent Bell Labs. The other options in this section 
-# have no effect if this option is set to NO (the default)
-
-HAVE_DOT               = YES
-
-# The DOT_NUM_THREADS specifies the number of dot invocations doxygen is 
-# allowed to run in parallel. When set to 0 (the default) doxygen will 
-# base this on the number of processors available in the system. You can set it 
-# explicitly to a value larger than 0 to get control over the balance 
-# between CPU load and processing speed.
-
-DOT_NUM_THREADS        = 0
-
-# By default doxygen will write a font called Helvetica to the output 
-# directory and reference it in all dot files that doxygen generates. 
-# When you want a differently looking font you can specify the font name 
-# using DOT_FONTNAME. You need to make sure dot is able to find the font, 
-# which can be done by putting it in a standard location or by setting the 
-# DOTFONTPATH environment variable or by setting DOT_FONTPATH to the directory 
-# containing the font.
-
-DOT_FONTNAME           = Helvetica
-
-# The DOT_FONTSIZE tag can be used to set the size of the font of dot graphs. 
-# The default size is 10pt.
-
-DOT_FONTSIZE           = 10
-
-# By default doxygen will tell dot to use the output directory to look for the 
-# FreeSans.ttf font (which doxygen will put there itself). If you specify a 
-# different font using DOT_FONTNAME you can set the path where dot 
-# can find it using this tag.
-
-DOT_FONTPATH           = 
-
-# If the CLASS_GRAPH and HAVE_DOT tags are set to YES then doxygen 
-# will generate a graph for each documented class showing the direct and 
-# indirect inheritance relations. Setting this tag to YES will force the 
-# the CLASS_DIAGRAMS tag to NO.
-
-CLASS_GRAPH            = YES
-
-# If the COLLABORATION_GRAPH and HAVE_DOT tags are set to YES then doxygen 
-# will generate a graph for each documented class showing the direct and 
-# indirect implementation dependencies (inheritance, containment, and 
-# class references variables) of the class with other documented classes.
-
-COLLABORATION_GRAPH    = YES
-
-# If the GROUP_GRAPHS and HAVE_DOT tags are set to YES then doxygen 
-# will generate a graph for groups, showing the direct groups dependencies
-
-GROUP_GRAPHS           = YES
-
-# If the UML_LOOK tag is set to YES doxygen will generate inheritance and 
-# collaboration diagrams in a style similar to the OMG's Unified Modeling 
-# Language.
-
-UML_LOOK               = YES
-
-# If set to YES, the inheritance and collaboration graphs will show the 
-# relations between templates and their instances.
-
-TEMPLATE_RELATIONS     = YES
-
-# If the ENABLE_PREPROCESSING, SEARCH_INCLUDES, INCLUDE_GRAPH, and HAVE_DOT 
-# tags are set to YES then doxygen will generate a graph for each documented 
-# file showing the direct and indirect include dependencies of the file with 
-# other documented files.
+# The default value is: YES.
+# This tag requires that the tag HAVE_DOT is set to YES.
 
 INCLUDE_GRAPH          = YES
 
-# If the ENABLE_PREPROCESSING, SEARCH_INCLUDES, INCLUDED_BY_GRAPH, and 
-# HAVE_DOT tags are set to YES then doxygen will generate a graph for each 
-# documented header file showing the documented files that directly or 
-# indirectly include this file.
+# If the INCLUDED_BY_GRAPH, ENABLE_PREPROCESSING and SEARCH_INCLUDES tags are
+# set to YES then doxygen will generate a graph for each documented file showing
+# the direct and indirect include dependencies of the file with other documented
+# files.
+# The default value is: YES.
+# This tag requires that the tag HAVE_DOT is set to YES.
 
 INCLUDED_BY_GRAPH      = YES
 
-# If the CALL_GRAPH and HAVE_DOT options are set to YES then 
-# doxygen will generate a call dependency graph for every global function 
-# or class method. Note that enabling this option will significantly increase 
-# the time of a run. So in most cases it will be better to enable call graphs 
-# for selected functions only using the \callgraph command.
+# If the CALL_GRAPH tag is set to YES then doxygen will generate a call
+# dependency graph for every global function or class method.
+#
+# Note that enabling this option will significantly increase the time of a run.
+# So in most cases it will be better to enable call graphs for selected
+# functions only using the \callgraph command. Disabling a call graph can be
+# accomplished by means of the command \hidecallgraph.
+# The default value is: NO.
+# This tag requires that the tag HAVE_DOT is set to YES.
 
 CALL_GRAPH             = YES
 
-# If the CALLER_GRAPH and HAVE_DOT tags are set to YES then 
-# doxygen will generate a caller dependency graph for every global function 
-# or class method. Note that enabling this option will significantly increase 
-# the time of a run. So in most cases it will be better to enable caller 
-# graphs for selected functions only using the \callergraph command.
+# If the CALLER_GRAPH tag is set to YES then doxygen will generate a caller
+# dependency graph for every global function or class method.
+#
+# Note that enabling this option will significantly increase the time of a run.
+# So in most cases it will be better to enable caller graphs for selected
+# functions only using the \callergraph command. Disabling a caller graph can be
+# accomplished by means of the command \hidecallergraph.
+# The default value is: NO.
+# This tag requires that the tag HAVE_DOT is set to YES.
 
 CALLER_GRAPH           = YES
 
-# If the GRAPHICAL_HIERARCHY and HAVE_DOT tags are set to YES then doxygen 
-# will generate a graphical hierarchy of all classes instead of a textual one.
+# If the GRAPHICAL_HIERARCHY tag is set to YES then doxygen will graphical
+# hierarchy of all classes instead of a textual one.
+# The default value is: YES.
+# This tag requires that the tag HAVE_DOT is set to YES.
 
 GRAPHICAL_HIERARCHY    = YES
 
-# If the DIRECTORY_GRAPH, SHOW_DIRECTORIES and HAVE_DOT tags are set to YES 
-# then doxygen will show the dependencies a directory has on other directories 
-# in a graphical way. The dependency relations are determined by the #include 
-# relations between the files in the directories.
+# If the DIRECTORY_GRAPH tag is set to YES then doxygen will show the
+# dependencies a directory has on other directories in a graphical way. The
+# dependency relations are determined by the #include relations between the
+# files in the directories.
+# The default value is: YES.
+# This tag requires that the tag HAVE_DOT is set to YES.
 
 DIRECTORY_GRAPH        = YES
 
-# The DOT_IMAGE_FORMAT tag can be used to set the image format of the images 
-# generated by dot. Possible values are svg, png, jpg, or gif. 
-# If left blank png will be used.
+# The DOT_IMAGE_FORMAT tag can be used to set the image format of the images
+# generated by dot. For an explanation of the image formats see the section
+# output formats in the documentation of the dot tool (Graphviz (see:
+# http://www.graphviz.org/)).
+# Note: If you choose svg you need to set HTML_FILE_EXTENSION to xhtml in order
+# to make the SVG files visible in IE 9+ (other browsers do not have this
+# requirement).
+# Possible values are: png, jpg, gif, svg, png:gd, png:gd:gd, png:cairo,
+# png:cairo:gd, png:cairo:cairo, png:cairo:gdiplus, png:gdiplus and
+# png:gdiplus:gdiplus.
+# The default value is: png.
+# This tag requires that the tag HAVE_DOT is set to YES.
 
 DOT_IMAGE_FORMAT       = png
 
-# The tag DOT_PATH can be used to specify the path where the dot tool can be 
+# If DOT_IMAGE_FORMAT is set to svg, then this option can be set to YES to
+# enable generation of interactive SVG images that allow zooming and panning.
+#
+# Note that this requires a modern browser other than Internet Explorer. Tested
+# and working are Firefox, Chrome, Safari, and Opera.
+# Note: For IE 9+ you need to set HTML_FILE_EXTENSION to xhtml in order to make
+# the SVG files visible. Older versions of IE do not have SVG support.
+# The default value is: NO.
+# This tag requires that the tag HAVE_DOT is set to YES.
+
+INTERACTIVE_SVG        = NO
+
+# The DOT_PATH tag can be used to specify the path where the dot tool can be
 # found. If left blank, it is assumed the dot tool can be found in the path.
-
-DOT_PATH               = 
-
-# The DOTFILE_DIRS tag can be used to specify one or more directories that 
-# contain dot files that are included in the documentation (see the 
-# \dotfile command).
-
-DOTFILE_DIRS           = 
-
-# The MSCFILE_DIRS tag can be used to specify one or more directories that 
-# contain msc files that are included in the documentation (see the 
-# \mscfile command).
-
-MSCFILE_DIRS           = 
-
-# The DOT_GRAPH_MAX_NODES tag can be used to set the maximum number of 
-# nodes that will be shown in the graph. If the number of nodes in a graph 
-# becomes larger than this value, doxygen will truncate the graph, which is 
-# visualized by representing a node as a red box. Note that doxygen if the 
-# number of direct children of the root node in a graph is already larger than 
-# DOT_GRAPH_MAX_NODES then the graph will not be shown at all. Also note 
-# that the size of a graph can be further restricted by MAX_DOT_GRAPH_DEPTH.
+# This tag requires that the tag HAVE_DOT is set to YES.
+
+DOT_PATH               =
+
+# The DOTFILE_DIRS tag can be used to specify one or more directories that
+# contain dot files that are included in the documentation (see the \dotfile
+# command).
+# This tag requires that the tag HAVE_DOT is set to YES.
+
+DOTFILE_DIRS           =
+
+# The MSCFILE_DIRS tag can be used to specify one or more directories that
+# contain msc files that are included in the documentation (see the \mscfile
+# command).
+
+MSCFILE_DIRS           =
+
+# The DIAFILE_DIRS tag can be used to specify one or more directories that
+# contain dia files that are included in the documentation (see the \diafile
+# command).
+
+DIAFILE_DIRS           =
+
+# When using plantuml, the PLANTUML_JAR_PATH tag should be used to specify the
+# path where java can find the plantuml.jar file. If left blank, it is assumed
+# PlantUML is not used or called during a preprocessing step. Doxygen will
+# generate a warning when it encounters a \startuml command in this case and
+# will not generate output for the diagram.
+
+PLANTUML_JAR_PATH      =
+
+# When using plantuml, the specified paths are searched for files specified by
+# the !include statement in a plantuml block.
+
+PLANTUML_INCLUDE_PATH  =
+
+# The DOT_GRAPH_MAX_NODES tag can be used to set the maximum number of nodes
+# that will be shown in the graph. If the number of nodes in a graph becomes
+# larger than this value, doxygen will truncate the graph, which is visualized
+# by representing a node as a red box. Note that doxygen if the number of direct
+# children of the root node in a graph is already larger than
+# DOT_GRAPH_MAX_NODES then the graph will not be shown at all. Also note that
+# the size of a graph can be further restricted by MAX_DOT_GRAPH_DEPTH.
+# Minimum value: 0, maximum value: 10000, default value: 50.
+# This tag requires that the tag HAVE_DOT is set to YES.
 
 DOT_GRAPH_MAX_NODES    = 50
 
-# The MAX_DOT_GRAPH_DEPTH tag can be used to set the maximum depth of the 
-# graphs generated by dot. A depth value of 3 means that only nodes reachable 
-# from the root by following a path via at most 3 edges will be shown. Nodes 
-# that lay further from the root node will be omitted. Note that setting this 
-# option to 1 or 2 may greatly reduce the computation time needed for large 
-# code bases. Also note that the size of a graph can be further restricted by 
+# The MAX_DOT_GRAPH_DEPTH tag can be used to set the maximum depth of the graphs
+# generated by dot. A depth value of 3 means that only nodes reachable from the
+# root by following a path via at most 3 edges will be shown. Nodes that lay
+# further from the root node will be omitted. Note that setting this option to 1
+# or 2 may greatly reduce the computation time needed for large code bases. Also
+# note that the size of a graph can be further restricted by
 # DOT_GRAPH_MAX_NODES. Using a depth of 0 means no depth restriction.
+# Minimum value: 0, maximum value: 1000, default value: 0.
+# This tag requires that the tag HAVE_DOT is set to YES.
 
 MAX_DOT_GRAPH_DEPTH    = 0
 
-# Set the DOT_TRANSPARENT tag to YES to generate images with a transparent 
-# background. This is disabled by default, because dot on Windows does not 
-# seem to support this out of the box. Warning: Depending on the platform used, 
-# enabling this option may lead to badly anti-aliased labels on the edges of 
-# a graph (i.e. they become hard to read).
+# Set the DOT_TRANSPARENT tag to YES to generate images with a transparent
+# background. This is disabled by default, because dot on Windows does not seem
+# to support this out of the box.
+#
+# Warning: Depending on the platform used, enabling this option may lead to
+# badly anti-aliased labels on the edges of a graph (i.e. they become hard to
+# read).
+# The default value is: NO.
+# This tag requires that the tag HAVE_DOT is set to YES.
 
 DOT_TRANSPARENT        = NO
 
-# Set the DOT_MULTI_TARGETS tag to YES allow dot to generate multiple output 
-# files in one run (i.e. multiple -o and -T options on the command line). This 
-# makes dot run faster, but since only newer versions of dot (>1.8.10) 
-# support this, this feature is disabled by default.
+# Set the DOT_MULTI_TARGETS tag to YES to allow dot to generate multiple output
+# files in one run (i.e. multiple -o and -T options on the command line). This
+# makes dot run faster, but since only newer versions of dot (>1.8.10) support
+# this, this feature is disabled by default.
+# The default value is: NO.
+# This tag requires that the tag HAVE_DOT is set to YES.
 
 DOT_MULTI_TARGETS      = NO
 
-# If the GENERATE_LEGEND tag is set to YES (the default) Doxygen will 
-# generate a legend page explaining the meaning of the various boxes and 
-# arrows in the dot generated graphs.
+# If the GENERATE_LEGEND tag is set to YES doxygen will generate a legend page
+# explaining the meaning of the various boxes and arrows in the dot generated
+# graphs.
+# The default value is: YES.
+# This tag requires that the tag HAVE_DOT is set to YES.
 
 GENERATE_LEGEND        = YES
 
-# If the DOT_CLEANUP tag is set to YES (the default) Doxygen will 
-# remove the intermediate dot files that are used to generate 
-# the various graphs.
+# If the DOT_CLEANUP tag is set to YES, doxygen will remove the intermediate dot
+# files that are used to generate the various graphs.
+# The default value is: YES.
+# This tag requires that the tag HAVE_DOT is set to YES.
 
 DOT_CLEANUP            = YES

XIOS/dev/branch_yushan_merged/bld.cfg

@@ -33 +33 @@
 #bld::target libxios.a 
 #bld::target generate_fortran_interface.exe 
-#bld::target xios_server.exe 
-#bld::target test_remap.exe
+bld::target xios_server.exe 
+bld::target test_remap.exe
 #bld::target test_regular.exe
 #bld::target test_expand_domain.exe
 #bld::target test_new_features.exe test_unstruct_complete.exe 
 bld::target test_omp.exe test_complete_omp.exe
-bld::target test_client.exe test_complete.exe test_xios2_cmip6.exe
+bld::target test_client.exe test_complete.exe #test_xios2_cmip6.exe
 #bld::target test_connectivity_expand.exe
 #bld::target toy_cmip6.exe

XIOS/dev/branch_yushan_merged/extern/remap/src/mapper.cpp

@@ -65 +65 @@
 void Mapper::setTargetMesh(const double* boundsLon, const double* boundsLat, int nVertex, int nbCells, const double* pole, const long int* globalId)
 {
-  tgtGrid.pole = Coord(pole[0], pole[1], pole[2]);
-
-        int mpiRank, mpiSize;
-        MPI_Comm_rank(communicator, &mpiRank);
-        MPI_Comm_size(communicator, &mpiSize);
-
-        targetElements.reserve(nbCells);
-        targetMesh.reserve(nbCells);
-
-  targetGlobalId.resize(nbCells) ;
-  if (globalId==NULL)
-  {
-    long int offset ;
-    long int nb=nbCells ;
-    MPI_Scan(&nb,&offset,1,MPI_LONG,MPI_SUM,communicator) ;
-    offset=offset-nb ;
-    for(int i=0;i<nbCells;i++) targetGlobalId[i]=offset+i ;
-  }
-  else targetGlobalId.assign(globalId,globalId+nbCells);
-
-        for (int i = 0; i < nbCells; i++)
-        {
-                int offs = i*nVertex;
-                Elt elt(boundsLon + offs, boundsLat + offs, nVertex);
-                targetElements.push_back(elt);
-                targetMesh.push_back(Node(elt.x, cptRadius(elt), &sourceElements.back()));
-                cptEltGeom(targetElements[i], Coord(pole[0], pole[1], pole[2]));
-        }
+    tgtGrid.pole = Coord(pole[0], pole[1], pole[2]);
+
+    int mpiRank, mpiSize;
+    MPI_Comm_rank(communicator, &mpiRank);
+    MPI_Comm_size(communicator, &mpiSize);
+
+    targetElements.reserve(nbCells);
+    targetMesh.reserve(nbCells);
+
+    targetGlobalId.resize(nbCells) ;
+    if (globalId==NULL)
+    {
+        long int offset ;
+        long int nb=nbCells ;
+        MPI_Scan(&nb,&offset,1,MPI_LONG,MPI_SUM,communicator) ;
+        offset=offset-nb ;
+        for(int i=0;i<nbCells;i++) targetGlobalId[i]=offset+i ;
+    }
+    else targetGlobalId.assign(globalId,globalId+nbCells);
+
+    for (int i = 0; i < nbCells; i++)
+    {
+        int offs = i*nVertex;
+        Elt elt(boundsLon + offs, boundsLat + offs, nVertex);
+        targetElements.push_back(elt);
+        targetMesh.push_back(Node(elt.x, cptRadius(elt), &sourceElements.back()));
+        cptEltGeom(targetElements[i], Coord(pole[0], pole[1], pole[2]));
+    }
 
 
@@ -99 +99 @@
 void Mapper::setSourceValue(const double* val)
 {
-  int size=sourceElements.size() ;
-  for(int i=0;i<size;++i) sourceElements[i].val=val[i] ;
+    int size=sourceElements.size() ;
+    for(int i=0;i<size;++i) sourceElements[i].val=val[i] ;
 }
 
 void Mapper::getTargetValue(double* val)
 {
-  int size=targetElements.size() ;
-  for(int i=0;i<size;++i) val[i]=targetElements[i].val ;
+    int size=targetElements.size() ;
+    for(int i=0;i<size;++i) val[i]=targetElements[i].val ;
 }
 
 vector<double> Mapper::computeWeights(int interpOrder, bool renormalize, bool quantity)
 {
-        vector<double> timings;
-        int mpiSize, mpiRank;
-        MPI_Comm_size(communicator, &mpiSize);
-        MPI_Comm_rank(communicator, &mpiRank);
-
-  this->buildSSTree(sourceMesh, targetMesh);
-
-        if (mpiRank == 0 && verbose) cout << "Computing intersections ..." << endl;
-        double tic = cputime();
-        computeIntersection(&targetElements[0], targetElements.size());
-        timings.push_back(cputime() - tic);
-
-        tic = cputime();
-        if (interpOrder == 2) {
-                if (mpiRank == 0 && verbose) cout << "Computing grads ..." << endl;
-                buildMeshTopology();
-                computeGrads();
-        }
-        timings.push_back(cputime() - tic);
-
-        /* Prepare computation of weights */
-        /* compute number of intersections which for the first order case
-           corresponds to the number of edges in the remap matrix */
-        int nIntersections = 0;
-        for (int j = 0; j < targetElements.size(); j++)
-        {
-                Elt &elt = targetElements[j];
-                for (list<Polyg*>::iterator it = elt.is.begin(); it != elt.is.end(); it++)
-                        nIntersections++;
-        }
-        /* overallocate for NMAX neighbours for each elements */
-        remapMatrix = new double[nIntersections*NMAX];
-        srcAddress = new int[nIntersections*NMAX];
-        srcRank = new int[nIntersections*NMAX];
-        dstAddress = new int[nIntersections*NMAX];
-  sourceWeightId =new long[nIntersections*NMAX];
-  targetWeightId =new long[nIntersections*NMAX];
-
-
-        if (mpiRank == 0 && verbose) cout << "Remapping..." << endl;
-        tic = cputime();
-        nWeights = remap(&targetElements[0], targetElements.size(), interpOrder, renormalize, quantity);
-        timings.push_back(cputime() - tic);
-
-  for (int i = 0; i < targetElements.size(); i++) targetElements[i].delete_intersections();
-
-        return timings;
+    vector<double> timings;
+    int mpiSize, mpiRank;
+    MPI_Comm_size(communicator, &mpiSize);
+    MPI_Comm_rank(communicator, &mpiRank);
+
+    this->buildSSTree(sourceMesh, targetMesh);
+
+    if (mpiRank == 0 && verbose) cout << "Computing intersections ..." << endl;
+    double tic = cputime();
+    computeIntersection(&targetElements[0], targetElements.size());
+    timings.push_back(cputime() - tic);
+
+    tic = cputime();
+    if (interpOrder == 2) {
+        if (mpiRank == 0 && verbose) cout << "Computing grads ..." << endl;
+        buildMeshTopology();
+        computeGrads();
+    }
+    timings.push_back(cputime() - tic);
+
+    /* Prepare computation of weights */
+    /* compute number of intersections which for the first order case
+       corresponds to the number of edges in the remap matrix */
+    int nIntersections = 0;
+    for (int j = 0; j < targetElements.size(); j++)
+    {
+        Elt &elt = targetElements[j];
+        for (list<Polyg*>::iterator it = elt.is.begin(); it != elt.is.end(); it++)
+            nIntersections++;
+    }
+    /* overallocate for NMAX neighbours for each elements */
+    remapMatrix = new double[nIntersections*NMAX];
+    srcAddress = new int[nIntersections*NMAX];
+    srcRank = new int[nIntersections*NMAX];
+    dstAddress = new int[nIntersections*NMAX];
+    sourceWeightId =new long[nIntersections*NMAX];
+    targetWeightId =new long[nIntersections*NMAX];
+
+
+    if (mpiRank == 0 && verbose) cout << "Remapping..." << endl;
+    tic = cputime();
+    nWeights = remap(&targetElements[0], targetElements.size(), interpOrder, renormalize, quantity);
+    timings.push_back(cputime() - tic);
+
+    for (int i = 0; i < targetElements.size(); i++) targetElements[i].delete_intersections();
+
+    return timings;
 }
 
 /**
-   @param elements are cells of the target grid that are distributed over CPUs
-          indepentently of the distribution of the SS-tree.
-   @param nbElements is the size of the elements array.
-   @param order is the order of interpolaton (must be 1 or 2).
-*/
+  @param elements are cells of the target grid that are distributed over CPUs
+  indepentently of the distribution of the SS-tree.
+  @param nbElements is the size of the elements array.
+  @param order is the order of interpolaton (must be 1 or 2).
+  */
 int Mapper::remap(Elt *elements, int nbElements, int order, bool renormalize, bool quantity)
 {
-        int mpiSize, mpiRank;
-        MPI_Comm_size(communicator, &mpiSize);
-        MPI_Comm_rank(communicator, &mpiRank);
-
-        /* create list of intersections (super mesh elements) for each rank */
-        multimap<int, Polyg *> *elementList = new multimap<int, Polyg *>[mpiSize];
-        for (int j = 0; j < nbElements; j++)
-        {
-                Elt& e = elements[j];
-                for (list<Polyg *>::iterator it = e.is.begin(); it != e.is.end(); it++)
-                        elementList[(*it)->id.rank].insert(pair<int, Polyg *>((*it)->id.ind, *it));
-        }
-
-        int *nbSendElement = new int[mpiSize];
-        int **sendElement = new int*[mpiSize]; /* indices of elements required from other rank */
-        double **recvValue = new double*[mpiSize];
-        double **recvArea = new double*[mpiSize];
-        Coord **recvGrad = new Coord*[mpiSize];
-        GloId **recvNeighIds = new GloId*[mpiSize]; /* ids of the of the source neighbours which also contribute through gradient */
-        for (int rank = 0; rank < mpiSize; rank++)
-        {
-                /* get size for allocation */
-                int last = -1; /* compares unequal to any index */
-                int index = -1; /* increased to starting index 0 in first iteration */
-                for (multimap<int, Polyg *>::iterator it = elementList[rank].begin(); it != elementList[rank].end(); ++it)
-                {
-                        if (last != it->first)
-                                index++;
-                        (it->second)->id.ind = index;
-                        last = it->first;
-                }
-                nbSendElement[rank] = index + 1;
-
-                /* if size is non-zero allocate and collect indices of elements on other ranks that we intersect */
-                if (nbSendElement[rank] > 0)
-                {
-                        sendElement[rank] = new int[nbSendElement[rank]];
-                        recvValue[rank]   = new double[nbSendElement[rank]];
-                        recvArea[rank]    = new double[nbSendElement[rank]];
-                        if (order == 2)
-                        {
-                                recvNeighIds[rank] = new GloId[nbSendElement[rank]*(NMAX+1)];
-                                recvGrad[rank]    = new Coord[nbSendElement[rank]*(NMAX+1)];
-                        }
-                        else
-                                recvNeighIds[rank] = new GloId[nbSendElement[rank]];
-
-                        last = -1;
-                        index = -1;
-                        for (multimap<int, Polyg *>::iterator it = elementList[rank].begin(); it != elementList[rank].end(); ++it)
-                        {
-                                if (last != it->first)
-                                        index++;
-                                sendElement[rank][index] = it->first;
-                                last = it->first;
-                        }
-                }
-        }
-
-        /* communicate sizes of source elements to be sent (index lists and later values and gradients) */
-        int *nbRecvElement = new int[mpiSize];
-        MPI_Alltoall(nbSendElement, 1, MPI_INT, nbRecvElement, 1, MPI_INT, communicator);
-
-        /* communicate indices of source elements on other ranks whoes value and gradient we need (since intersection) */
-        int nbSendRequest = 0;
-        int nbRecvRequest = 0;
-        int **recvElement = new int*[mpiSize];
-        double **sendValue = new double*[mpiSize];
-        double **sendArea = new double*[mpiSize];
-        Coord **sendGrad = new Coord*[mpiSize];
-        GloId **sendNeighIds = new GloId*[mpiSize];
-        MPI_Request *sendRequest = new MPI_Request[3*mpiSize];
-        MPI_Request *recvRequest = new MPI_Request[3*mpiSize];
-        for (int rank = 0; rank < mpiSize; rank++)
-        {
-                if (nbSendElement[rank] > 0)
-                {
-                        MPI_Issend(sendElement[rank], nbSendElement[rank], MPI_INT, rank, 0, communicator, &sendRequest[nbSendRequest]);
-                        nbSendRequest++;
-                }
-
-                if (nbRecvElement[rank] > 0)
-                {
-                        recvElement[rank] = new int[nbRecvElement[rank]];
-                        sendValue[rank]   = new double[nbRecvElement[rank]];
-                        sendArea[rank]   = new double[nbRecvElement[rank]];
-                        if (order == 2)
-                        {
-                                sendNeighIds[rank] = new GloId[nbRecvElement[rank]*(NMAX+1)];
-                                sendGrad[rank]    = new Coord[nbRecvElement[rank]*(NMAX+1)];
-                        }
-                        else
-                        {
-                                sendNeighIds[rank] = new GloId[nbRecvElement[rank]];
-                        }
-                        MPI_Irecv(recvElement[rank], nbRecvElement[rank], MPI_INT, rank, 0, communicator, &recvRequest[nbRecvRequest]);
-                        nbRecvRequest++;
-                }
-        }
-        MPI_Status *status = new MPI_Status[3*mpiSize];
-        MPI_Waitall(nbRecvRequest, recvRequest, status);
-        MPI_Waitall(nbSendRequest, sendRequest, status);
-
-        /* for all indices that have been received from requesting ranks: pack values and gradients, then send */
-        nbSendRequest = 0;
-        nbRecvRequest = 0;
-        for (int rank = 0; rank < mpiSize; rank++)
-        {
-                if (nbRecvElement[rank] > 0)
-                {
-                        int jj = 0; // jj == j if no weight writing
-                        for (int j = 0; j < nbRecvElement[rank]; j++)
-                        {
-                                sendValue[rank][j] = sstree.localElements[recvElement[rank][j]].val;
-                                sendArea[rank][j] = sstree.localElements[recvElement[rank][j]].area;
-                                if (order == 2)
-                                {
-                                        sendGrad[rank][jj] = sstree.localElements[recvElement[rank][j]].grad;
-//          cout<<"grad  "<<jj<<"  "<<recvElement[rank][j]<<"  "<<sendGrad[rank][jj]<<" "<<sstree.localElements[recvElement[rank][j]].grad<<endl ;
-                                        sendNeighIds[rank][jj] = sstree.localElements[recvElement[rank][j]].src_id;
-                                        jj++;
-                                        for (int i = 0; i < NMAX; i++)
-                                        {
-                                                sendGrad[rank][jj] = sstree.localElements[recvElement[rank][j]].gradNeigh[i];
-//            cout<<"grad  "<<jj<<"  "<<sendGrad[rank][jj]<<" "<<sstree.localElements[recvElement[rank][j]].grad<<endl ;
-            sendNeighIds[rank][jj] = sstree.localElements[recvElement[rank][j]].neighId[i];
-                                                jj++;
-                                        }
-                                }
-                                else
-                                        sendNeighIds[rank][j] = sstree.localElements[recvElement[rank][j]].src_id;
-                        }
-                        MPI_Issend(sendValue[rank],  nbRecvElement[rank], MPI_DOUBLE, rank, 0, communicator, &sendRequest[nbSendRequest]);
-                        nbSendRequest++;
-                        MPI_Issend(sendArea[rank],  nbRecvElement[rank], MPI_DOUBLE, rank, 0, communicator, &sendRequest[nbSendRequest]);
-                        nbSendRequest++;
-                        if (order == 2)
-                        {
-                                MPI_Issend(sendGrad[rank], 3*nbRecvElement[rank]*(NMAX+1),
-                                                                MPI_DOUBLE, rank, 0, communicator, &sendRequest[nbSendRequest]);
-                                nbSendRequest++;
-                                MPI_Issend(sendNeighIds[rank], 4*nbRecvElement[rank]*(NMAX+1), MPI_INT, rank, 0, communicator, &sendRequest[nbSendRequest]);
-//ym  --> attention taille GloId
-                                nbSendRequest++;
-                        }
-                        else
-                        {
-                                MPI_Issend(sendNeighIds[rank], 4*nbRecvElement[rank], MPI_INT, rank, 0, communicator, &sendRequest[nbSendRequest]);
-//ym  --> attention taille GloId
-                                nbSendRequest++;
-                        }
-                }
-                if (nbSendElement[rank] > 0)
-                {
-                        MPI_Irecv(recvValue[rank],  nbSendElement[rank], MPI_DOUBLE, rank, 0, communicator, &recvRequest[nbRecvRequest]);
-                        nbRecvRequest++;
-                        MPI_Irecv(recvArea[rank],  nbSendElement[rank], MPI_DOUBLE, rank, 0, communicator, &recvRequest[nbRecvRequest]);
-                        nbRecvRequest++;
-                        if (order == 2)
-                        {
-                                MPI_Irecv(recvGrad[rank], 3*nbSendElement[rank]*(NMAX+1),
-                                                MPI_DOUBLE, rank, 0, communicator, &recvRequest[nbRecvRequest]);
-                                nbRecvRequest++;
-                                MPI_Irecv(recvNeighIds[rank], 4*nbSendElement[rank]*(NMAX+1), MPI_INT, rank, 0, communicator, &recvRequest[nbRecvRequest]);
-//ym  --> attention taille GloId
-                                nbRecvRequest++;
-                        }
-                        else
-                        {
-                                MPI_Irecv(recvNeighIds[rank], 4*nbSendElement[rank], MPI_INT, rank, 0, communicator, &recvRequest[nbRecvRequest]);
-//ym  --> attention taille GloId
-                                nbRecvRequest++;
-                        }
-                }
-        }
-        MPI_Waitall(nbRecvRequest, recvRequest, status);
-        MPI_Waitall(nbSendRequest, sendRequest, status);
-
-        /* now that all values and gradients are available use them to computed interpolated values on target
-           and also to compute weights */
-        int i = 0;
-        for (int j = 0; j < nbElements; j++)
-        {
-                Elt& e = elements[j];
-
-                /* since for the 2nd order case source grid elements can contribute to a destination grid element over several "paths"
-                   (step1: gradient is computed using neighbours on same grid, step2: intersection uses several elements on other grid)
-                   accumulate them so that there is only one final weight between two elements */
-                map<GloId,double> wgt_map;
-
-                /* for destination element `e` loop over all intersetions/the corresponding source elements */
-                for (list<Polyg *>::iterator it = e.is.begin(); it != e.is.end(); it++)
-                {
-                        /* it is the intersection element, so it->x and it->area are barycentre and area of intersection element (super mesh)
-                        but it->id is id of the source element that it intersects */
-                        int n1 = (*it)->id.ind;
-                        int rank = (*it)->id.rank;
-                        double fk = recvValue[rank][n1];
-                        double srcArea = recvArea[rank][n1];
-                        double w = (*it)->area;
-                        if (quantity) w/=srcArea ;
-
-                        /* first order: src value times weight (weight = supermesh area), later divide by target area */
-                        int kk = (order == 2) ? n1 * (NMAX + 1) : n1;
-                        GloId neighID = recvNeighIds[rank][kk];
-                        wgt_map[neighID] += w;
-
-                        if (order == 2)
-                        {
-                                for (int k = 0; k < NMAX+1; k++)
-                                {
-                                        int kk = n1 * (NMAX + 1) + k;
-                                        GloId neighID = recvNeighIds[rank][kk];
-                                        if (neighID.ind != -1)  wgt_map[neighID] += w * scalarprod(recvGrad[rank][kk], (*it)->x);
-                                }
-
-                        }
-                }
-
-    double renorm=0;
-    if (renormalize) 
-      for (map<GloId,double>::iterator it = wgt_map.begin(); it != wgt_map.end(); it++) renorm+=it->second / e.area;
-    else renorm=1. ;
-
-    for (map<GloId,double>::iterator it = wgt_map.begin(); it != wgt_map.end(); it++)
-                {
-      if (quantity)  this->remapMatrix[i] = (it->second ) / renorm;
-                        else this->remapMatrix[i] = (it->second / e.area) / renorm;
-                        this->srcAddress[i] = it->first.ind;
-                        this->srcRank[i] = it->first.rank;
-                        this->dstAddress[i] = j;
-      this->sourceWeightId[i]= it->first.globalId ;
-      this->targetWeightId[i]= targetGlobalId[j] ;
-                        i++;
-                }
-        }
-
-        /* free all memory allocated in this function */
-        for (int rank = 0; rank < mpiSize; rank++)
-        {
-                if (nbSendElement[rank] > 0)
-                {
-                        delete[] sendElement[rank];
-                        delete[] recvValue[rank];
-                        delete[] recvArea[rank];
-                        if (order == 2)
-                        {
-                                delete[] recvGrad[rank];
-                        }
-                        delete[] recvNeighIds[rank];
-                }
-                if (nbRecvElement[rank] > 0)
-                {
-                        delete[] recvElement[rank];
-                        delete[] sendValue[rank];
-                        delete[] sendArea[rank];
-                        if (order == 2)
-                                delete[] sendGrad[rank];
-                        delete[] sendNeighIds[rank];
-                }
-        }
-        delete[] status;
-        delete[] sendRequest;
-        delete[] recvRequest;
-        delete[] elementList;
-        delete[] nbSendElement;
-        delete[] nbRecvElement;
-        delete[] sendElement;
-        delete[] recvElement;
-        delete[] sendValue;
-        delete[] recvValue;
-        delete[] sendGrad;
-        delete[] recvGrad;
-        delete[] sendNeighIds;
-        delete[] recvNeighIds;
-        return i;
+    int mpiSize, mpiRank;
+    MPI_Comm_size(communicator, &mpiSize);
+    MPI_Comm_rank(communicator, &mpiRank);
+
+    /* create list of intersections (super mesh elements) for each rank */
+    multimap<int, Polyg *> *elementList = new multimap<int, Polyg *>[mpiSize];
+    for (int j = 0; j < nbElements; j++)
+    {
+        Elt& e = elements[j];
+        for (list<Polyg *>::iterator it = e.is.begin(); it != e.is.end(); it++)
+            elementList[(*it)->id.rank].insert(pair<int, Polyg *>((*it)->id.ind, *it));
+    }
+
+    int *nbSendElement = new int[mpiSize];
+    int **sendElement = new int*[mpiSize]; /* indices of elements required from other rank */
+    double **recvValue = new double*[mpiSize];
+    double **recvArea = new double*[mpiSize];
+    Coord **recvGrad = new Coord*[mpiSize];
+    GloId **recvNeighIds = new GloId*[mpiSize]; /* ids of the of the source neighbours which also contribute through gradient */
+    for (int rank = 0; rank < mpiSize; rank++)
+    {
+        /* get size for allocation */
+        int last = -1; /* compares unequal to any index */
+        int index = -1; /* increased to starting index 0 in first iteration */
+        for (multimap<int, Polyg *>::iterator it = elementList[rank].begin(); it != elementList[rank].end(); ++it)
+        {
+            if (last != it->first)
+                index++;
+            (it->second)->id.ind = index;
+            last = it->first;
+        }
+        nbSendElement[rank] = index + 1;
+
+        /* if size is non-zero allocate and collect indices of elements on other ranks that we intersect */
+        if (nbSendElement[rank] > 0)
+        {
+            sendElement[rank] = new int[nbSendElement[rank]];
+            recvValue[rank]   = new double[nbSendElement[rank]];
+            recvArea[rank]    = new double[nbSendElement[rank]];
+            if (order == 2)
+            {
+                recvNeighIds[rank] = new GloId[nbSendElement[rank]*(NMAX+1)];
+                recvGrad[rank]    = new Coord[nbSendElement[rank]*(NMAX+1)];
+            }
+            else
+                recvNeighIds[rank] = new GloId[nbSendElement[rank]];
+
+            last = -1;
+            index = -1;
+            for (multimap<int, Polyg *>::iterator it = elementList[rank].begin(); it != elementList[rank].end(); ++it)
+            {
+                if (last != it->first)
+                    index++;
+                sendElement[rank][index] = it->first;
+                last = it->first;
+            }
+        }
+    }
+
+    /* communicate sizes of source elements to be sent (index lists and later values and gradients) */
+    int *nbRecvElement = new int[mpiSize];
+    MPI_Alltoall(nbSendElement, 1, MPI_INT, nbRecvElement, 1, MPI_INT, communicator);
+
+    /* communicate indices of source elements on other ranks whoes value and gradient we need (since intersection) */
+    int nbSendRequest = 0;
+    int nbRecvRequest = 0;
+    int **recvElement = new int*[mpiSize];
+    double **sendValue = new double*[mpiSize];
+    double **sendArea = new double*[mpiSize];
+    Coord **sendGrad = new Coord*[mpiSize];
+    GloId **sendNeighIds = new GloId*[mpiSize];
+    MPI_Request *sendRequest = new MPI_Request[4*mpiSize];
+    MPI_Request *recvRequest = new MPI_Request[4*mpiSize];
+    for (int rank = 0; rank < mpiSize; rank++)
+    {
+        if (nbSendElement[rank] > 0)
+        {
+            MPI_Issend(sendElement[rank], nbSendElement[rank], MPI_INT, rank, 0, communicator, &sendRequest[nbSendRequest]);
+            nbSendRequest++;
+        }
+
+        if (nbRecvElement[rank] > 0)
+        {
+            recvElement[rank] = new int[nbRecvElement[rank]];
+            sendValue[rank]   = new double[nbRecvElement[rank]];
+            sendArea[rank]   = new double[nbRecvElement[rank]];
+            if (order == 2)
+            {
+                sendNeighIds[rank] = new GloId[nbRecvElement[rank]*(NMAX+1)];
+                sendGrad[rank]    = new Coord[nbRecvElement[rank]*(NMAX+1)];
+            }
+            else
+            {
+                sendNeighIds[rank] = new GloId[nbRecvElement[rank]];
+            }
+            MPI_Irecv(recvElement[rank], nbRecvElement[rank], MPI_INT, rank, 0, communicator, &recvRequest[nbRecvRequest]);
+            nbRecvRequest++;
+        }
+    }
+
+    MPI_Status *status = new MPI_Status[4*mpiSize];
+    
+    MPI_Waitall(nbSendRequest, sendRequest, status);
+    MPI_Waitall(nbRecvRequest, recvRequest, status);
+
+    /* for all indices that have been received from requesting ranks: pack values and gradients, then send */
+    nbSendRequest = 0;
+    nbRecvRequest = 0;
+    for (int rank = 0; rank < mpiSize; rank++)
+    {
+        if (nbRecvElement[rank] > 0)
+        {
+            int jj = 0; // jj == j if no weight writing
+            for (int j = 0; j < nbRecvElement[rank]; j++)
+            {
+                sendValue[rank][j] = sstree.localElements[recvElement[rank][j]].val;
+                sendArea[rank][j] = sstree.localElements[recvElement[rank][j]].area;
+                if (order == 2)
+                {
+                    sendGrad[rank][jj] = sstree.localElements[recvElement[rank][j]].grad;
+                    sendNeighIds[rank][jj] = sstree.localElements[recvElement[rank][j]].src_id;
+                    jj++;
+                    for (int i = 0; i < NMAX; i++)
+                    {
+                        sendGrad[rank][jj] = sstree.localElements[recvElement[rank][j]].gradNeigh[i];
+                        sendNeighIds[rank][jj] = sstree.localElements[recvElement[rank][j]].neighId[i];
+                        jj++;
+                    }
+                }
+                else
+                    sendNeighIds[rank][j] = sstree.localElements[recvElement[rank][j]].src_id;
+            }
+            MPI_Issend(sendValue[rank],  nbRecvElement[rank], MPI_DOUBLE, rank, 0, communicator, &sendRequest[nbSendRequest]);
+            nbSendRequest++;
+            MPI_Issend(sendArea[rank],  nbRecvElement[rank], MPI_DOUBLE, rank, 0, communicator, &sendRequest[nbSendRequest]);
+            nbSendRequest++;
+            if (order == 2)
+            {
+                MPI_Issend(sendGrad[rank], 3*nbRecvElement[rank]*(NMAX+1),
+                        MPI_DOUBLE, rank, 0, communicator, &sendRequest[nbSendRequest]);
+                nbSendRequest++;
+                MPI_Issend(sendNeighIds[rank], 4*nbRecvElement[rank]*(NMAX+1), MPI_INT, rank, 0, communicator, &sendRequest[nbSendRequest]);
+                //ym  --> attention taille GloId
+                nbSendRequest++;
+            }
+            else
+            {
+                MPI_Issend(sendNeighIds[rank], 4*nbRecvElement[rank], MPI_INT, rank, 0, communicator, &sendRequest[nbSendRequest]);
+                //ym  --> attention taille GloId
+                nbSendRequest++;
+                
+            }
+        }
+        if (nbSendElement[rank] > 0)
+        {
+            MPI_Irecv(recvValue[rank],  nbSendElement[rank], MPI_DOUBLE, rank, 0, communicator, &recvRequest[nbRecvRequest]);
+            nbRecvRequest++;
+            MPI_Irecv(recvArea[rank],  nbSendElement[rank], MPI_DOUBLE, rank, 0, communicator, &recvRequest[nbRecvRequest]);
+            nbRecvRequest++;
+            if (order == 2)
+            {
+                MPI_Irecv(recvGrad[rank], 3*nbSendElement[rank]*(NMAX+1),
+                        MPI_DOUBLE, rank, 0, communicator, &recvRequest[nbRecvRequest]);
+                nbRecvRequest++;
+                MPI_Irecv(recvNeighIds[rank], 4*nbSendElement[rank]*(NMAX+1), MPI_INT, rank, 0, communicator, &recvRequest[nbRecvRequest]);
+                //ym  --> attention taille GloId
+                nbRecvRequest++;
+            }
+            else
+            {
+                MPI_Irecv(recvNeighIds[rank], 4*nbSendElement[rank], MPI_INT, rank, 0, communicator, &recvRequest[nbRecvRequest]);
+                //ym  --> attention taille GloId
+                nbRecvRequest++;
+            }
+        }
+    }
+    
+    MPI_Waitall(nbSendRequest, sendRequest, status);
+    MPI_Waitall(nbRecvRequest, recvRequest, status);
+
+    /* now that all values and gradients are available use them to computed interpolated values on target
+       and also to compute weights */
+    int i = 0;
+    for (int j = 0; j < nbElements; j++)
+    {
+        Elt& e = elements[j];
+
+        /* since for the 2nd order case source grid elements can contribute to a destination grid element over several "paths"
+           (step1: gradient is computed using neighbours on same grid, step2: intersection uses several elements on other grid)
+           accumulate them so that there is only one final weight between two elements */
+        map<GloId,double> wgt_map;
+
+        /* for destination element `e` loop over all intersetions/the corresponding source elements */
+        for (list<Polyg *>::iterator it = e.is.begin(); it != e.is.end(); it++)
+        {
+            /* it is the intersection element, so it->x and it->area are barycentre and area of intersection element (super mesh)
+               but it->id is id of the source element that it intersects */
+            int n1 = (*it)->id.ind;
+            int rank = (*it)->id.rank;
+            double fk = recvValue[rank][n1];
+            double srcArea = recvArea[rank][n1];
+            double w = (*it)->area;
+            if (quantity) w/=srcArea ;
+
+            /* first order: src value times weight (weight = supermesh area), later divide by target area */
+            int kk = (order == 2) ? n1 * (NMAX + 1) : n1;
+            GloId neighID = recvNeighIds[rank][kk];
+            wgt_map[neighID] += w;
+
+            if (order == 2)
+            {
+                for (int k = 0; k < NMAX+1; k++)
+                {
+                    int kk = n1 * (NMAX + 1) + k;
+                    GloId neighID = recvNeighIds[rank][kk];
+                    if (neighID.ind != -1)  wgt_map[neighID] += w * scalarprod(recvGrad[rank][kk], (*it)->x);
+                }
+
+            }
+        }
+
+        double renorm=0;
+        if (renormalize) 
+            for (map<GloId,double>::iterator it = wgt_map.begin(); it != wgt_map.end(); it++) renorm+=it->second / e.area;
+        else renorm=1. ;
+
+        for (map<GloId,double>::iterator it = wgt_map.begin(); it != wgt_map.end(); it++)
+        {
+            if (quantity)  this->remapMatrix[i] = (it->second ) / renorm;
+            else this->remapMatrix[i] = (it->second / e.area) / renorm;
+            this->srcAddress[i] = it->first.ind;
+            this->srcRank[i] = it->first.rank;
+            this->dstAddress[i] = j;
+            this->sourceWeightId[i]= it->first.globalId ;
+            this->targetWeightId[i]= targetGlobalId[j] ;
+            i++;
+        }
+    }
+
+    /* free all memory allocated in this function */
+    for (int rank = 0; rank < mpiSize; rank++)
+    {
+        if (nbSendElement[rank] > 0)
+        {
+            delete[] sendElement[rank];
+            delete[] recvValue[rank];
+            delete[] recvArea[rank];
+            if (order == 2)
+            {
+                delete[] recvGrad[rank];
+            }
+            delete[] recvNeighIds[rank];
+        }
+        if (nbRecvElement[rank] > 0)
+        {
+            delete[] recvElement[rank];
+            delete[] sendValue[rank];
+            delete[] sendArea[rank];
+            if (order == 2)
+                delete[] sendGrad[rank];
+            delete[] sendNeighIds[rank];
+        }
+    }
+    delete[] status;
+    delete[] sendRequest;
+    delete[] recvRequest;
+    delete[] elementList;
+    delete[] nbSendElement;
+    delete[] nbRecvElement;
+    delete[] sendElement;
+    delete[] recvElement;
+    delete[] sendValue;
+    delete[] recvValue;
+    delete[] sendGrad;
+    delete[] recvGrad;
+    delete[] sendNeighIds;
+    delete[] recvNeighIds;
+    return i;
 }
 
 void Mapper::computeGrads()
 {
-        /* array of pointers to collect local elements and elements received from other cpu */
-        vector<Elt*> globalElements(sstree.nbLocalElements + nbNeighbourElements);
-        int index = 0;
-        for (int i = 0; i < sstree.nbLocalElements; i++, index++)
-                globalElements[index] = &(sstree.localElements[i]);
-        for (int i = 0; i < nbNeighbourElements; i++, index++)
-                globalElements[index] = &neighbourElements[i];
-
-        update_baryc(sstree.localElements, sstree.nbLocalElements);
-        computeGradients(&globalElements[0], sstree.nbLocalElements);
+    /* array of pointers to collect local elements and elements received from other cpu */
+    vector<Elt*> globalElements(sstree.nbLocalElements + nbNeighbourElements);
+    int index = 0;
+    for (int i = 0; i < sstree.nbLocalElements; i++, index++)
+        globalElements[index] = &(sstree.localElements[i]);
+    for (int i = 0; i < nbNeighbourElements; i++, index++)
+        globalElements[index] = &neighbourElements[i];
+
+    update_baryc(sstree.localElements, sstree.nbLocalElements);
+    computeGradients(&globalElements[0], sstree.nbLocalElements);
 }
 
 /** for each element of the source grid, finds all the neighbouring elements that share an edge
-    (filling array neighbourElements). This is used later to compute gradients */
+  (filling array neighbourElements). This is used later to compute gradients */
 void Mapper::buildMeshTopology()
 {
-        int mpiSize, mpiRank;
-        MPI_Comm_size(communicator, &mpiSize);
-        MPI_Comm_rank(communicator, &mpiRank);
-
-        vector<Node> *routingList = new vector<Node>[mpiSize];
-        vector<vector<int> > routes(sstree.localTree.leafs.size());
-
-        sstree.routeIntersections(routes, sstree.localTree.leafs);
-
-        for (int i = 0; i < routes.size(); ++i)
-                for (int k = 0; k < routes[i].size(); ++k)
-                        routingList[routes[i][k]].push_back(sstree.localTree.leafs[i]);
-        routingList[mpiRank].clear();
-
-
-        CMPIRouting mpiRoute(communicator);
-        mpiRoute.init(routes);
-        int nRecv = mpiRoute.getTotalSourceElement();
-// cout << mpiRank << " NRECV " << nRecv << "(" << routes.size() << ")"<< endl;
-
-        int *nbSendNode = new int[mpiSize];
-        int *nbRecvNode = new int[mpiSize];
-        int *sendMessageSize = new int[mpiSize];
-        int *recvMessageSize = new int[mpiSize];
-
-        for (int rank = 0; rank < mpiSize; rank++)
-        {
-                nbSendNode[rank] = routingList[rank].size();
-                sendMessageSize[rank] = 0;
-                for (size_t j = 0; j < routingList[rank].size(); j++)
-                {
-                        Elt *elt = (Elt *) (routingList[rank][j].data);
-                        sendMessageSize[rank] += packedPolygonSize(*elt);
-                }
-        }
-
-        MPI_Alltoall(nbSendNode, 1, MPI_INT, nbRecvNode, 1, MPI_INT, communicator);
-        MPI_Alltoall(sendMessageSize, 1, MPI_INT, recvMessageSize, 1, MPI_INT, communicator);
-
-        char **sendBuffer = new char*[mpiSize];
-        char **recvBuffer = new char*[mpiSize];
-        int *pos = new int[mpiSize];
-
-        for (int rank = 0; rank < mpiSize; rank++)
-        {
-                if (nbSendNode[rank] > 0) sendBuffer[rank] = new char[sendMessageSize[rank]];
-                if (nbRecvNode[rank] > 0) recvBuffer[rank] = new char[recvMessageSize[rank]];
-        }
-
-        for (int rank = 0; rank < mpiSize; rank++)
-        {
-                pos[rank] = 0;
-                for (size_t j = 0; j < routingList[rank].size(); j++)
-                {
-                        Elt *elt = (Elt *) (routingList[rank][j].data);
-                        packPolygon(*elt, sendBuffer[rank], pos[rank]);
-                }
-        }
-        delete [] routingList;
-
-
-        int nbSendRequest = 0;
-        int nbRecvRequest = 0;
-        MPI_Request *sendRequest = new MPI_Request[mpiSize];
-        MPI_Request *recvRequest = new MPI_Request[mpiSize];
-        MPI_Status  *status      = new MPI_Status[mpiSize];
-
-        for (int rank = 0; rank < mpiSize; rank++)
-        {
-                if (nbSendNode[rank] > 0)
-                {
-                        MPI_Issend(sendBuffer[rank], sendMessageSize[rank], MPI_CHAR, rank, 0, communicator, &sendRequest[nbSendRequest]);
-                        nbSendRequest++;
-                }
-                if (nbRecvNode[rank] > 0)
-                {
-                        MPI_Irecv(recvBuffer[rank], recvMessageSize[rank], MPI_CHAR, rank, 0, communicator, &recvRequest[nbRecvRequest]);
-                        nbRecvRequest++;
-                }
-        }
-
-        MPI_Waitall(nbRecvRequest, recvRequest, status);
-        MPI_Waitall(nbSendRequest, sendRequest, status);
-
-        for (int rank = 0; rank < mpiSize; rank++)
-                if (nbSendNode[rank] > 0) delete [] sendBuffer[rank];
-        delete [] sendBuffer;
-
-        char **sendBuffer2 = new char*[mpiSize];
-        char **recvBuffer2 = new char*[mpiSize];
-
-        for (int rank = 0; rank < mpiSize; rank++)
-        {
-                nbSendNode[rank] = 0;
-                sendMessageSize[rank] = 0;
-
-                if (nbRecvNode[rank] > 0)
-                {
-                        set<NodePtr> neighbourList;
-                        pos[rank] = 0;
-                        for (int j = 0; j < nbRecvNode[rank]; j++)
-                        {
-                                Elt elt;
-                                unpackPolygon(elt, recvBuffer[rank], pos[rank]);
-                                Node node(elt.x, cptRadius(elt), &elt);
-                                findNeighbour(sstree.localTree.root, &node, neighbourList);
-                        }
-                        nbSendNode[rank] = neighbourList.size();
-                        for (set<NodePtr>::iterator it = neighbourList.begin(); it != neighbourList.end(); it++)
-                        {
-                                Elt *elt = (Elt *) ((*it)->data);
-                                sendMessageSize[rank] += packedPolygonSize(*elt);
-                        }
-
-                        sendBuffer2[rank] = new char[sendMessageSize[rank]];
-                        pos[rank] = 0;
-
-                        for (set<NodePtr>::iterator it = neighbourList.begin(); it != neighbourList.end(); it++)
-                        {
-                                Elt *elt = (Elt *) ((*it)->data);
-                                packPolygon(*elt, sendBuffer2[rank], pos[rank]);
-                        }
-                }
-        }
-        for (int rank = 0; rank < mpiSize; rank++)
-                if (nbRecvNode[rank] > 0) delete [] recvBuffer[rank];
-        delete [] recvBuffer;
-
-
-        MPI_Barrier(communicator);
-        MPI_Alltoall(nbSendNode, 1, MPI_INT, nbRecvNode, 1, MPI_INT, communicator);
-        MPI_Alltoall(sendMessageSize, 1, MPI_INT, recvMessageSize, 1, MPI_INT, communicator);
-
-        for (int rank = 0; rank < mpiSize; rank++)
-                if (nbRecvNode[rank] > 0) recvBuffer2[rank] = new char[recvMessageSize[rank]];
-
-        nbSendRequest = 0;
-        nbRecvRequest = 0;
-
-        for (int rank = 0; rank < mpiSize; rank++)
-        {
-                if (nbSendNode[rank] > 0)
-                {
-                        MPI_Issend(sendBuffer2[rank], sendMessageSize[rank], MPI_CHAR, rank, 0, communicator, &sendRequest[nbSendRequest]);
-                        nbSendRequest++;
-                }
-                if (nbRecvNode[rank] > 0)
-                {
-                        MPI_Irecv(recvBuffer2[rank], recvMessageSize[rank], MPI_CHAR, rank, 0, communicator, &recvRequest[nbRecvRequest]);
-                        nbRecvRequest++;
-                }
-        }
-
-        MPI_Waitall(nbRecvRequest, recvRequest, status);
-        MPI_Waitall(nbSendRequest, sendRequest, status);
-
-        int nbNeighbourNodes = 0;
-        for (int rank = 0; rank < mpiSize; rank++)
-                nbNeighbourNodes += nbRecvNode[rank];
-
-        neighbourElements = new Elt[nbNeighbourNodes];
-        nbNeighbourElements = nbNeighbourNodes;
-
-        int index = 0;
-        for (int rank = 0; rank < mpiSize; rank++)
-        {
-                pos[rank] = 0;
-                for (int j = 0; j < nbRecvNode[rank]; j++)
-                {
-                        unpackPolygon(neighbourElements[index], recvBuffer2[rank], pos[rank]);
-                        neighbourElements[index].id.ind = sstree.localTree.leafs.size() + index;
-                        index++;
-                }
-        }
-        for (int rank = 0; rank < mpiSize; rank++)
-        {
-                if (nbRecvNode[rank] > 0) delete [] recvBuffer2[rank];
-                if (nbSendNode[rank] > 0) delete [] sendBuffer2[rank];
-        }
-        delete [] recvBuffer2;
-        delete [] sendBuffer2;
-        delete [] sendMessageSize;
-        delete [] recvMessageSize;
-        delete [] nbSendNode;
-        delete [] nbRecvNode;
-        delete [] sendRequest;
-        delete [] recvRequest;
-        delete [] status;
-        delete [] pos;
-
-        /* re-compute on received elements to avoid having to send this information */
-        neighbourNodes.resize(nbNeighbourNodes);
-        setCirclesAndLinks(neighbourElements, neighbourNodes);
-        cptAllEltsGeom(neighbourElements, nbNeighbourNodes, srcGrid.pole);
-
-        /* the local SS tree must include nodes from other cpus if they are potential
-           intersector of a local node */
-        sstree.localTree.insertNodes(neighbourNodes);
-
-        /* for every local element,
-           use the SS-tree to find all elements (including neighbourElements)
-           who are potential neighbours because their circles intersect,
-           then check all canditates for common edges to build up connectivity information
-        */
-        for (int j = 0; j < sstree.localTree.leafs.size(); j++)
-        {
-                Node& node = sstree.localTree.leafs[j];
-
-                /* find all leafs whoes circles that intersect node's circle and save into node->intersectors */
-                node.search(sstree.localTree.root);
-
-                Elt *elt = (Elt *)(node.data);
-
-                for (int i = 0; i < elt->n; i++) elt->neighbour[i] = NOT_FOUND;
-
-                /* for element `elt` loop through all nodes in the SS-tree
-                   whoes circles intersect with the circle around `elt` (the SS intersectors)
-                   and check if they are neighbours in the sense that the two elements share an edge.
-                   If they do, save this information for elt */
-                for (list<NodePtr>::iterator it = (node.intersectors).begin(); it != (node.intersectors).end(); ++it)
-                {
-                        Elt *elt2 = (Elt *)((*it)->data);
-                        set_neighbour(*elt, *elt2);
-                }
-
-/*
-                for (int i = 0; i < elt->n; i++)
-                {
-                        if (elt->neighbour[i] == NOT_FOUND)
-                                error_exit("neighbour not found");
-                }
-*/
-        }
+    int mpiSize, mpiRank;
+    MPI_Comm_size(communicator, &mpiSize);
+    MPI_Comm_rank(communicator, &mpiRank);
+
+    vector<Node> *routingList = new vector<Node>[mpiSize];
+    vector<vector<int> > routes(sstree.localTree.leafs.size());
+
+    sstree.routeIntersections(routes, sstree.localTree.leafs);
+
+    for (int i = 0; i < routes.size(); ++i)
+        for (int k = 0; k < routes[i].size(); ++k)
+            routingList[routes[i][k]].push_back(sstree.localTree.leafs[i]);
+    routingList[mpiRank].clear();
+
+
+    CMPIRouting mpiRoute(communicator);
+    mpiRoute.init(routes);
+    int nRecv = mpiRoute.getTotalSourceElement();
+    // cout << mpiRank << " NRECV " << nRecv << "(" << routes.size() << ")"<< endl;
+
+    int *nbSendNode = new int[mpiSize];
+    int *nbRecvNode = new int[mpiSize];
+    int *sendMessageSize = new int[mpiSize];
+    int *recvMessageSize = new int[mpiSize];
+
+    for (int rank = 0; rank < mpiSize; rank++)
+    {
+        nbSendNode[rank] = routingList[rank].size();
+        sendMessageSize[rank] = 0;
+        for (size_t j = 0; j < routingList[rank].size(); j++)
+        {
+            Elt *elt = (Elt *) (routingList[rank][j].data);
+            sendMessageSize[rank] += packedPolygonSize(*elt);
+        }
+    }
+
+    MPI_Alltoall(nbSendNode, 1, MPI_INT, nbRecvNode, 1, MPI_INT, communicator);
+    MPI_Alltoall(sendMessageSize, 1, MPI_INT, recvMessageSize, 1, MPI_INT, communicator);
+
+    char **sendBuffer = new char*[mpiSize];
+    char **recvBuffer = new char*[mpiSize];
+    int *pos = new int[mpiSize];
+
+    for (int rank = 0; rank < mpiSize; rank++)
+    {
+        if (nbSendNode[rank] > 0) sendBuffer[rank] = new char[sendMessageSize[rank]];
+        if (nbRecvNode[rank] > 0) recvBuffer[rank] = new char[recvMessageSize[rank]];
+    }
+
+    for (int rank = 0; rank < mpiSize; rank++)
+    {
+        pos[rank] = 0;
+        for (size_t j = 0; j < routingList[rank].size(); j++)
+        {
+            Elt *elt = (Elt *) (routingList[rank][j].data);
+            packPolygon(*elt, sendBuffer[rank], pos[rank]);
+        }
+    }
+    delete [] routingList;
+
+
+    int nbSendRequest = 0;
+    int nbRecvRequest = 0;
+    MPI_Request *sendRequest = new MPI_Request[mpiSize];
+    MPI_Request *recvRequest = new MPI_Request[mpiSize];
+    MPI_Status  *status      = new MPI_Status[mpiSize];
+
+    for (int rank = 0; rank < mpiSize; rank++)
+    {
+        if (nbSendNode[rank] > 0)
+        {
+            MPI_Issend(sendBuffer[rank], sendMessageSize[rank], MPI_CHAR, rank, 0, communicator, &sendRequest[nbSendRequest]);
+            nbSendRequest++;
+        }
+        if (nbRecvNode[rank] > 0)
+        {
+            MPI_Irecv(recvBuffer[rank], recvMessageSize[rank], MPI_CHAR, rank, 0, communicator, &recvRequest[nbRecvRequest]);
+            nbRecvRequest++;
+        }
+    }
+
+    MPI_Waitall(nbRecvRequest, recvRequest, status);
+    MPI_Waitall(nbSendRequest, sendRequest, status);
+
+    for (int rank = 0; rank < mpiSize; rank++)
+        if (nbSendNode[rank] > 0) delete [] sendBuffer[rank];
+    delete [] sendBuffer;
+
+    char **sendBuffer2 = new char*[mpiSize];
+    char **recvBuffer2 = new char*[mpiSize];
+
+    for (int rank = 0; rank < mpiSize; rank++)
+    {
+        nbSendNode[rank] = 0;
+        sendMessageSize[rank] = 0;
+
+        if (nbRecvNode[rank] > 0)
+        {
+            set<NodePtr> neighbourList;
+            pos[rank] = 0;
+            for (int j = 0; j < nbRecvNode[rank]; j++)
+            {
+                Elt elt;
+                unpackPolygon(elt, recvBuffer[rank], pos[rank]);
+                Node node(elt.x, cptRadius(elt), &elt);
+                findNeighbour(sstree.localTree.root, &node, neighbourList);
+            }
+            nbSendNode[rank] = neighbourList.size();
+            for (set<NodePtr>::iterator it = neighbourList.begin(); it != neighbourList.end(); it++)
+            {
+                Elt *elt = (Elt *) ((*it)->data);
+                sendMessageSize[rank] += packedPolygonSize(*elt);
+            }
+
+            sendBuffer2[rank] = new char[sendMessageSize[rank]];
+            pos[rank] = 0;
+
+            for (set<NodePtr>::iterator it = neighbourList.begin(); it != neighbourList.end(); it++)
+            {
+                Elt *elt = (Elt *) ((*it)->data);
+                packPolygon(*elt, sendBuffer2[rank], pos[rank]);
+            }
+        }
+    }
+    for (int rank = 0; rank < mpiSize; rank++)
+        if (nbRecvNode[rank] > 0) delete [] recvBuffer[rank];
+    delete [] recvBuffer;
+
+
+    MPI_Barrier(communicator);
+    MPI_Alltoall(nbSendNode, 1, MPI_INT, nbRecvNode, 1, MPI_INT, communicator);
+    MPI_Alltoall(sendMessageSize, 1, MPI_INT, recvMessageSize, 1, MPI_INT, communicator);
+
+    for (int rank = 0; rank < mpiSize; rank++)
+        if (nbRecvNode[rank] > 0) recvBuffer2[rank] = new char[recvMessageSize[rank]];
+
+    nbSendRequest = 0;
+    nbRecvRequest = 0;
+
+    for (int rank = 0; rank < mpiSize; rank++)
+    {
+        if (nbSendNode[rank] > 0)
+        {
+            MPI_Issend(sendBuffer2[rank], sendMessageSize[rank], MPI_CHAR, rank, 0, communicator, &sendRequest[nbSendRequest]);
+            nbSendRequest++;
+        }
+        if (nbRecvNode[rank] > 0)
+        {
+            MPI_Irecv(recvBuffer2[rank], recvMessageSize[rank], MPI_CHAR, rank, 0, communicator, &recvRequest[nbRecvRequest]);
+            nbRecvRequest++;
+        }
+    }
+
+    MPI_Waitall(nbRecvRequest, recvRequest, status);
+    MPI_Waitall(nbSendRequest, sendRequest, status);
+
+    int nbNeighbourNodes = 0;
+    for (int rank = 0; rank < mpiSize; rank++)
+        nbNeighbourNodes += nbRecvNode[rank];
+
+    neighbourElements = new Elt[nbNeighbourNodes];
+    nbNeighbourElements = nbNeighbourNodes;
+
+    int index = 0;
+    for (int rank = 0; rank < mpiSize; rank++)
+    {
+        pos[rank] = 0;
+        for (int j = 0; j < nbRecvNode[rank]; j++)
+        {
+            unpackPolygon(neighbourElements[index], recvBuffer2[rank], pos[rank]);
+            neighbourElements[index].id.ind = sstree.localTree.leafs.size() + index;
+            index++;
+        }
+    }
+    for (int rank = 0; rank < mpiSize; rank++)
+    {
+        if (nbRecvNode[rank] > 0) delete [] recvBuffer2[rank];
+        if (nbSendNode[rank] > 0) delete [] sendBuffer2[rank];
+    }
+    delete [] recvBuffer2;
+    delete [] sendBuffer2;
+    delete [] sendMessageSize;
+    delete [] recvMessageSize;
+    delete [] nbSendNode;
+    delete [] nbRecvNode;
+    delete [] sendRequest;
+    delete [] recvRequest;
+    delete [] status;
+    delete [] pos;
+
+    /* re-compute on received elements to avoid having to send this information */
+    neighbourNodes.resize(nbNeighbourNodes);
+    setCirclesAndLinks(neighbourElements, neighbourNodes);
+    cptAllEltsGeom(neighbourElements, nbNeighbourNodes, srcGrid.pole);
+
+    /* the local SS tree must include nodes from other cpus if they are potential
+       intersector of a local node */
+    sstree.localTree.insertNodes(neighbourNodes);
+
+    /* for every local element,
+       use the SS-tree to find all elements (including neighbourElements)
+       who are potential neighbours because their circles intersect,
+       then check all canditates for common edges to build up connectivity information
+       */
+    for (int j = 0; j < sstree.localTree.leafs.size(); j++)
+    {
+        Node& node = sstree.localTree.leafs[j];
+
+        /* find all leafs whoes circles that intersect node's circle and save into node->intersectors */
+        node.search(sstree.localTree.root);
+
+        Elt *elt = (Elt *)(node.data);
+
+        for (int i = 0; i < elt->n; i++) elt->neighbour[i] = NOT_FOUND;
+
+        /* for element `elt` loop through all nodes in the SS-tree
+           whoes circles intersect with the circle around `elt` (the SS intersectors)
+           and check if they are neighbours in the sense that the two elements share an edge.
+           If they do, save this information for elt */
+        for (list<NodePtr>::iterator it = (node.intersectors).begin(); it != (node.intersectors).end(); ++it)
+        {
+            Elt *elt2 = (Elt *)((*it)->data);
+            set_neighbour(*elt, *elt2);
+        }
+
+        /*
+           for (int i = 0; i < elt->n; i++)
+           {
+           if (elt->neighbour[i] == NOT_FOUND)
+           error_exit("neighbour not found");
+           }
+           */
+    }
 }
 
@@ -702 +704 @@
 void Mapper::computeIntersection(Elt *elements, int nbElements)
 {
-        int mpiSize, mpiRank;
-        MPI_Comm_size(communicator, &mpiSize);
-        MPI_Comm_rank(communicator, &mpiRank);
-
-        MPI_Barrier(communicator);
-
-        vector<Node> *routingList = new vector<Node>[mpiSize];
-
-        vector<Node> routeNodes;  routeNodes.reserve(nbElements);
-        for (int j = 0; j < nbElements; j++)
-        {
-                elements[j].id.ind = j;
-                elements[j].id.rank = mpiRank;
-                routeNodes.push_back(Node(elements[j].x, cptRadius(elements[j]), &elements[j]));
-        }
-
-        vector<vector<int> > routes(routeNodes.size());
-        sstree.routeIntersections(routes, routeNodes);
-        for (int i = 0; i < routes.size(); ++i)
-                for (int k = 0; k < routes[i].size(); ++k)
-                        routingList[routes[i][k]].push_back(routeNodes[i]);
-
-        if (verbose >= 2)
-        {
-                cout << " --> rank  " << mpiRank << " nbElements " << nbElements << " : ";
-                for (int rank = 0; rank < mpiSize; rank++)
-                        cout << routingList[rank].size() << "   ";
-                cout << endl;
-        }
-        MPI_Barrier(communicator);
-
-        int *nbSendNode = new int[mpiSize];
-        int *nbRecvNode = new int[mpiSize];
-        int *sentMessageSize = new int[mpiSize];
-        int *recvMessageSize = new int[mpiSize];
-
-        for (int rank = 0; rank < mpiSize; rank++)
-        {
-                nbSendNode[rank] = routingList[rank].size();
-                sentMessageSize[rank] = 0;
-                for (size_t j = 0; j < routingList[rank].size(); j++)
-                {
-                        Elt *elt = (Elt *) (routingList[rank][j].data);
-                        sentMessageSize[rank] += packedPolygonSize(*elt);
-                }
-        }
-
-        MPI_Alltoall(nbSendNode, 1, MPI_INT, nbRecvNode, 1, MPI_INT, communicator);
-        MPI_Alltoall(sentMessageSize, 1, MPI_INT, recvMessageSize, 1, MPI_INT, communicator);
-
-        int total = 0;
-
-        for (int rank = 0; rank < mpiSize; rank++)
-        {
-                total = total + nbRecvNode[rank];
-        }
-
-        if (verbose >= 2) cout << "---> rank " << mpiRank << " : compute intersection : total received nodes  " << total << endl;
-        char **sendBuffer = new char*[mpiSize];
-        char **recvBuffer = new char*[mpiSize];
-        int *pos = new int[mpiSize];
-
-        for (int rank = 0; rank < mpiSize; rank++)
-        {
-                if (nbSendNode[rank] > 0) sendBuffer[rank] = new char[sentMessageSize[rank]];
-                if (nbRecvNode[rank] > 0) recvBuffer[rank] = new char[recvMessageSize[rank]];
-        }
-
-        for (int rank = 0; rank < mpiSize; rank++)
-        {
-                pos[rank] = 0;
-                for (size_t j = 0; j < routingList[rank].size(); j++)
-                {
-                        Elt* elt = (Elt *) (routingList[rank][j].data);
-                        packPolygon(*elt, sendBuffer[rank], pos[rank]);
-                }
-        }
-        delete [] routingList;
-
-        int nbSendRequest = 0;
-        int nbRecvRequest = 0;
-        MPI_Request *sendRequest = new MPI_Request[mpiSize];
-        MPI_Request *recvRequest = new MPI_Request[mpiSize];
-        MPI_Status   *status = new MPI_Status[mpiSize];
-
-        for (int rank = 0; rank < mpiSize; rank++)
-        {
-                if (nbSendNode[rank] > 0)
-                {
-                        MPI_Issend(sendBuffer[rank], sentMessageSize[rank], MPI_CHAR, rank, 0, communicator, &sendRequest[nbSendRequest]);
-                        nbSendRequest++;
-                }
-                if (nbRecvNode[rank] > 0)
-                {
-                        MPI_Irecv(recvBuffer[rank], recvMessageSize[rank], MPI_CHAR, rank, 0, communicator, &recvRequest[nbRecvRequest]);
-                        nbRecvRequest++;
-                }
-        }
-
-        MPI_Waitall(nbRecvRequest, recvRequest, status);
-        MPI_Waitall(nbSendRequest, sendRequest, status);
-        char **sendBuffer2 = new char*[mpiSize];
-        char **recvBuffer2 = new char*[mpiSize];
-
-        double tic = cputime();
-        for (int rank = 0; rank < mpiSize; rank++)
-        {
-                sentMessageSize[rank] = 0;
-
-                if (nbRecvNode[rank] > 0)
-                {
-                        Elt *recvElt = new Elt[nbRecvNode[rank]];
-                        pos[rank] = 0;
-                        for (int j = 0; j < nbRecvNode[rank]; j++)
-                        {
-                                unpackPolygon(recvElt[j], recvBuffer[rank], pos[rank]);
-                                cptEltGeom(recvElt[j], tgtGrid.pole);
-                                Node recvNode(recvElt[j].x, cptRadius(recvElt[j]), &recvElt[j]);
-                                recvNode.search(sstree.localTree.root);
-                                /* for a node holding an element of the target, loop throught candidates for intersecting source */
-                                for (list<NodePtr>::iterator it = (recvNode.intersectors).begin(); it != (recvNode.intersectors).end(); ++it)
-                                {
-                                        Elt *elt2 = (Elt *) ((*it)->data);
-                                        /* recvElt is target, elt2 is source */
-//                                      intersect(&recvElt[j], elt2);
-                                        intersect_ym(&recvElt[j], elt2);
-                                }
-
-                                if (recvElt[j].is.size() > 0) sentMessageSize[rank] += packIntersectionSize(recvElt[j]);
-
-                                // here recvNode goes out of scope
-                        }
-
-                        if (sentMessageSize[rank] > 0)
-                        {
-                                sentMessageSize[rank] += sizeof(int);
-                                sendBuffer2[rank] = new char[sentMessageSize[rank]];
-                                *((int *) sendBuffer2[rank]) = 0;
-                                pos[rank] = sizeof(int);
-                                for (int j = 0; j < nbRecvNode[rank]; j++)
-                                {
-                                        packIntersection(recvElt[j], sendBuffer2[rank], pos[rank]);
-                                        //FIXME should be deleted: recvElt[j].delete_intersections(); // intersection areas have been packed to buffer and won't be used any more
-                                }
-                        }
-                        delete [] recvElt;
-
-                }
-        }
-        delete [] pos;
-
-        for (int rank = 0; rank < mpiSize; rank++)
-        {
-                if (nbSendNode[rank] > 0) delete [] sendBuffer[rank];
-                if (nbRecvNode[rank] > 0) delete [] recvBuffer[rank];
-                nbSendNode[rank] = 0;
-        }
-
-        if (verbose >= 2) cout << "Rank " << mpiRank << "  Compute (internal) intersection " << cputime() - tic << " s" << endl;
-        MPI_Alltoall(sentMessageSize, 1, MPI_INT, recvMessageSize, 1, MPI_INT, communicator);
-
-        for (int rank = 0; rank < mpiSize; rank++)
-                if (recvMessageSize[rank] > 0)
-                        recvBuffer2[rank] = new char[recvMessageSize[rank]];
-
-        nbSendRequest = 0;
-        nbRecvRequest = 0;
-
-        for (int rank = 0; rank < mpiSize; rank++)
-        {
-                if (sentMessageSize[rank] > 0)
-                {
-                        MPI_Issend(sendBuffer2[rank], sentMessageSize[rank], MPI_CHAR, rank, 0, communicator, &sendRequest[nbSendRequest]);
-                        nbSendRequest++;
-                }
-                if (recvMessageSize[rank] > 0)
-                {
-                        MPI_Irecv(recvBuffer2[rank], recvMessageSize[rank], MPI_CHAR, rank, 0, communicator, &recvRequest[nbRecvRequest]);
-                        nbRecvRequest++;
-                }
-        }
-
-        MPI_Waitall(nbRecvRequest, recvRequest, status);
-        MPI_Waitall(nbSendRequest, sendRequest, status);
-
-        delete [] sendRequest;
-        delete [] recvRequest;
-        delete [] status;
-        for (int rank = 0; rank < mpiSize; rank++)
-        {
-                if (nbRecvNode[rank] > 0)
-                {
-                        if (sentMessageSize[rank] > 0)
-                                delete [] sendBuffer2[rank];
-                }
-
-                if (recvMessageSize[rank] > 0)
-                {
-                        unpackIntersection(elements, recvBuffer2[rank]);
-                        delete [] recvBuffer2[rank];
-                }
-        }
-        delete [] sendBuffer2;
-        delete [] recvBuffer2;
-        delete [] sendBuffer;
-        delete [] recvBuffer;
-
-        delete [] nbSendNode;
-        delete [] nbRecvNode;
-        delete [] sentMessageSize;
-        delete [] recvMessageSize;
+    int mpiSize, mpiRank;
+    MPI_Comm_size(communicator, &mpiSize);
+    MPI_Comm_rank(communicator, &mpiRank);
+
+    MPI_Barrier(communicator);
+
+    vector<Node> *routingList = new vector<Node>[mpiSize];
+
+    vector<Node> routeNodes;  routeNodes.reserve(nbElements);
+    for (int j = 0; j < nbElements; j++)
+    {
+        elements[j].id.ind = j;
+        elements[j].id.rank = mpiRank;
+        routeNodes.push_back(Node(elements[j].x, cptRadius(elements[j]), &elements[j]));
+    }
+
+    vector<vector<int> > routes(routeNodes.size());
+    sstree.routeIntersections(routes, routeNodes);
+    for (int i = 0; i < routes.size(); ++i)
+        for (int k = 0; k < routes[i].size(); ++k)
+            routingList[routes[i][k]].push_back(routeNodes[i]);
+
+    if (verbose >= 2)
+    {
+        cout << " --> rank  " << mpiRank << " nbElements " << nbElements << " : ";
+        for (int rank = 0; rank < mpiSize; rank++)
+            cout << routingList[rank].size() << "   ";
+        cout << endl;
+    }
+    MPI_Barrier(communicator);
+
+    int *nbSendNode = new int[mpiSize];
+    int *nbRecvNode = new int[mpiSize];
+    int *sentMessageSize = new int[mpiSize];
+    int *recvMessageSize = new int[mpiSize];
+
+    for (int rank = 0; rank < mpiSize; rank++)
+    {
+        nbSendNode[rank] = routingList[rank].size();
+        sentMessageSize[rank] = 0;
+        for (size_t j = 0; j < routingList[rank].size(); j++)
+        {
+            Elt *elt = (Elt *) (routingList[rank][j].data);
+            sentMessageSize[rank] += packedPolygonSize(*elt);
+        }
+    }
+
+    MPI_Alltoall(nbSendNode, 1, MPI_INT, nbRecvNode, 1, MPI_INT, communicator);
+    MPI_Alltoall(sentMessageSize, 1, MPI_INT, recvMessageSize, 1, MPI_INT, communicator);
+
+    int total = 0;
+
+    for (int rank = 0; rank < mpiSize; rank++)
+    {
+        total = total + nbRecvNode[rank];
+    }
+
+    if (verbose >= 2) cout << "---> rank " << mpiRank << " : compute intersection : total received nodes  " << total << endl;
+    char **sendBuffer = new char*[mpiSize];
+    char **recvBuffer = new char*[mpiSize];
+    int *pos = new int[mpiSize];
+
+    for (int rank = 0; rank < mpiSize; rank++)
+    {
+        if (nbSendNode[rank] > 0) sendBuffer[rank] = new char[sentMessageSize[rank]];
+        if (nbRecvNode[rank] > 0) recvBuffer[rank] = new char[recvMessageSize[rank]];
+    }
+
+    for (int rank = 0; rank < mpiSize; rank++)
+    {
+        pos[rank] = 0;
+        for (size_t j = 0; j < routingList[rank].size(); j++)
+        {
+            Elt* elt = (Elt *) (routingList[rank][j].data);
+            packPolygon(*elt, sendBuffer[rank], pos[rank]);
+        }
+    }
+    delete [] routingList;
+
+    int nbSendRequest = 0;
+    int nbRecvRequest = 0;
+    MPI_Request *sendRequest = new MPI_Request[mpiSize];
+    MPI_Request *recvRequest = new MPI_Request[mpiSize];
+    MPI_Status   *status = new MPI_Status[mpiSize];
+
+    for (int rank = 0; rank < mpiSize; rank++)
+    {
+        if (nbSendNode[rank] > 0)
+        {
+            MPI_Issend(sendBuffer[rank], sentMessageSize[rank], MPI_CHAR, rank, 0, communicator, &sendRequest[nbSendRequest]);
+            nbSendRequest++;
+        }
+        if (nbRecvNode[rank] > 0)
+        {
+            MPI_Irecv(recvBuffer[rank], recvMessageSize[rank], MPI_CHAR, rank, 0, communicator, &recvRequest[nbRecvRequest]);
+            nbRecvRequest++;
+        }
+    }
+
+    MPI_Waitall(nbRecvRequest, recvRequest, status);
+    MPI_Waitall(nbSendRequest, sendRequest, status);
+    char **sendBuffer2 = new char*[mpiSize];
+    char **recvBuffer2 = new char*[mpiSize];
+
+    double tic = cputime();
+    for (int rank = 0; rank < mpiSize; rank++)
+    {
+        sentMessageSize[rank] = 0;
+
+        if (nbRecvNode[rank] > 0)
+        {
+            Elt *recvElt = new Elt[nbRecvNode[rank]];
+            pos[rank] = 0;
+            for (int j = 0; j < nbRecvNode[rank]; j++)
+            {
+                unpackPolygon(recvElt[j], recvBuffer[rank], pos[rank]);
+                cptEltGeom(recvElt[j], tgtGrid.pole);
+                Node recvNode(recvElt[j].x, cptRadius(recvElt[j]), &recvElt[j]);
+                recvNode.search(sstree.localTree.root);
+                /* for a node holding an element of the target, loop throught candidates for intersecting source */
+                for (list<NodePtr>::iterator it = (recvNode.intersectors).begin(); it != (recvNode.intersectors).end(); ++it)
+                {
+                    Elt *elt2 = (Elt *) ((*it)->data);
+                    /* recvElt is target, elt2 is source */
+                    //                                  intersect(&recvElt[j], elt2);
+                    intersect_ym(&recvElt[j], elt2);
+                }
+
+                if (recvElt[j].is.size() > 0) sentMessageSize[rank] += packIntersectionSize(recvElt[j]);
+
+                // here recvNode goes out of scope
+            }
+
+            if (sentMessageSize[rank] > 0)
+            {
+                sentMessageSize[rank] += sizeof(int);
+                sendBuffer2[rank] = new char[sentMessageSize[rank]];
+                *((int *) sendBuffer2[rank]) = 0;
+                pos[rank] = sizeof(int);
+                for (int j = 0; j < nbRecvNode[rank]; j++)
+                {
+                    packIntersection(recvElt[j], sendBuffer2[rank], pos[rank]);
+                    //FIXME should be deleted: recvElt[j].delete_intersections(); // intersection areas have been packed to buffer and won't be used any more
+                }
+            }
+            delete [] recvElt;
+
+        }
+    }
+    delete [] pos;
+
+    for (int rank = 0; rank < mpiSize; rank++)
+    {
+        if (nbSendNode[rank] > 0) delete [] sendBuffer[rank];
+        if (nbRecvNode[rank] > 0) delete [] recvBuffer[rank];
+        nbSendNode[rank] = 0;
+    }
+
+    if (verbose >= 2) cout << "Rank " << mpiRank << "  Compute (internal) intersection " << cputime() - tic << " s" << endl;
+    MPI_Alltoall(sentMessageSize, 1, MPI_INT, recvMessageSize, 1, MPI_INT, communicator);
+
+    for (int rank = 0; rank < mpiSize; rank++)
+        if (recvMessageSize[rank] > 0)
+            recvBuffer2[rank] = new char[recvMessageSize[rank]];
+
+    nbSendRequest = 0;
+    nbRecvRequest = 0;
+
+    for (int rank = 0; rank < mpiSize; rank++)
+    {
+        if (sentMessageSize[rank] > 0)
+        {
+            MPI_Issend(sendBuffer2[rank], sentMessageSize[rank], MPI_CHAR, rank, 0, communicator, &sendRequest[nbSendRequest]);
+            nbSendRequest++;
+        }
+        if (recvMessageSize[rank] > 0)
+        {
+            MPI_Irecv(recvBuffer2[rank], recvMessageSize[rank], MPI_CHAR, rank, 0, communicator, &recvRequest[nbRecvRequest]);
+            nbRecvRequest++;
+        }
+    }
+
+    MPI_Waitall(nbRecvRequest, recvRequest, status);
+    MPI_Waitall(nbSendRequest, sendRequest, status);
+
+    delete [] sendRequest;
+    delete [] recvRequest;
+    delete [] status;
+    for (int rank = 0; rank < mpiSize; rank++)
+    {
+        if (nbRecvNode[rank] > 0)
+        {
+            if (sentMessageSize[rank] > 0)
+                delete [] sendBuffer2[rank];
+        }
+
+        if (recvMessageSize[rank] > 0)
+        {
+            unpackIntersection(elements, recvBuffer2[rank]);
+            delete [] recvBuffer2[rank];
+        }
+    }
+    delete [] sendBuffer2;
+    delete [] recvBuffer2;
+    delete [] sendBuffer;
+    delete [] recvBuffer;
+
+    delete [] nbSendNode;
+    delete [] nbRecvNode;
+    delete [] sentMessageSize;
+    delete [] recvMessageSize;
 }
 
 Mapper::~Mapper()
 {
-        delete [] remapMatrix;
-        delete [] srcAddress;
-        delete [] srcRank;
-        delete [] dstAddress;
-        if (neighbourElements) delete [] neighbourElements;
-}
-
-}
+    delete [] remapMatrix;
+    delete [] srcAddress;
+    delete [] srcRank;
+    delete [] dstAddress;
+    if (neighbourElements) delete [] neighbourElements;
+}
+
+}

XIOS/dev/branch_yushan_merged/extern/src_ep_dev/ep_gatherv.cpp

@@ -484 +484 @@
     mpi_size = comm.ep_comm_ptr->size_rank_info[2].second;
     
-
-    assert(accumulate(recvcounts, recvcounts+ep_size-1, 0) == displs[ep_size-1]); // Only for continuous gather.
+    if(ep_size == mpi_size) 
+      return ::MPI_Allgatherv(sendbuf, sendcount, static_cast< ::MPI_Datatype>(datatype), recvbuf, recvcounts, displs,
+                              static_cast< ::MPI_Datatype>(datatype), static_cast< ::MPI_Comm>(comm.mpi_comm));
+    
+
+    assert(accumulate(recvcounts, recvcounts+ep_size-1, 0) >= displs[ep_size-1]); // Only for continuous gather.
 
 

XIOS/dev/branch_yushan_merged/extern/src_ep_dev/ep_memory.cpp

@@ -10 +10 @@
   int MPI_Alloc_mem(MPI_Aint size, MPI_Info info, void *baseptr)
   {
-    ::MPI_Alloc_mem(size.mpi_aint, static_cast< ::MPI_Info>(info.mpi_info), baseptr);
+    //::MPI_Alloc_mem(size.mpi_aint, static_cast< ::MPI_Info>(info.mpi_info), baseptr);
+    ::MPI_Alloc_mem(size.mpi_aint, MPI_INFO_NULL_STD, baseptr);
     return 0;
    }
@@ -16 +17 @@
   int MPI_Alloc_mem(unsigned long size, MPI_Info info, void *baseptr)
   {
-    ::MPI_Alloc_mem(size, static_cast< ::MPI_Info>(info.mpi_info), baseptr);
+    //::MPI_Alloc_mem(size, static_cast< ::MPI_Info>(info.mpi_info), baseptr);
+    ::MPI_Alloc_mem(size, MPI_INFO_NULL_STD, baseptr);
     return 0;
   }

XIOS/dev/branch_yushan_merged/extern/src_ep_dev/ep_wait.cpp

@@ -1 +1 @@
 /*!
-   \file ep_wait.cpp
-   \since 2 may 2016
+  \file ep_wait.cpp
+  \since 2 may 2016
 
-   \brief Definitions of MPI wait function: MPI_Wait, MPI_Waitall, MPI_Waitsome, MPI_Waitany
- */
+  \brief Definitions of MPI wait function: MPI_Wait, MPI_Waitall, MPI_Waitsome, MPI_Waitany
+  */
 
 #include "ep_lib.hpp"
@@ -16 +16 @@
 namespace ep_lib {      
 
-        int MPI_Wait(MPI_Request *request, MPI_Status *status)
-        {
+    int MPI_Wait(MPI_Request *request, MPI_Status *status)
+    {
 
-    if(request->type == 1)
-    {
-      ::MPI_Request mpi_request = static_cast< ::MPI_Request >(request->mpi_request);
-      ::MPI_Status mpi_status;
-      ::MPI_Wait(&mpi_request, &mpi_status);
-
-
-      
-      status->mpi_status = &mpi_status;
-      status->ep_src = request->ep_src;
-      status->ep_tag = request->ep_tag;
-      status->ep_datatype = request->ep_datatype;
-
-      return 0;
-    }
-
-    if(request->type == 2)
-    {
-      int flag = false;
-      MPI_Message message;
-
-      while(!flag)
-      {
-        Message_Check(request->comm);
-        #pragma omp flush
-        MPI_Improbe(request->ep_src, request->ep_tag, request->comm, &flag, &message, status);
-      }
-
-      int count;
-      MPI_Get_count(status, request->ep_datatype, &count);
-      MPI_Mrecv(request->buf, count, request->ep_datatype, &message, status);
-      status->ep_datatype = request->ep_datatype;
-
-      //check_sum_recv(request->buf, count, request->ep_datatype, request->ep_src, request->ep_tag, request->comm, 2);
-
-      return 0;
-    }
-
-    if(request->type == 3)
-    {
-      ::MPI_Request mpi_request = static_cast< ::MPI_Request >(request->mpi_request);
-      ::MPI_Status mpi_status;
-      ::MPI_Wait(&mpi_request, &mpi_status);
-      
-      status->mpi_status = new ::MPI_Status(mpi_status);
-      status->ep_src = request->ep_src;
-      status->ep_tag = request->ep_tag;
-      status->ep_datatype = request->ep_datatype;
-
-      //int count;
-      //MPI_Get_count(status, request->ep_datatype, &count);
-      //check_sum_recv(request->buf, count, request->ep_datatype, request->ep_src, request->ep_tag, request->comm, 2);
-    }
-          return MPI_SUCCESS;
-        }
+        if(request->type == 1)
+        {
+            ::MPI_Request mpi_request = static_cast< ::MPI_Request >(request->mpi_request);
+            ::MPI_Status mpi_status;
+            ::MPI_Wait(&mpi_request, &mpi_status);
 
 
 
-        
+            status->mpi_status = &mpi_status;
+            status->ep_src = request->ep_src;
+            status->ep_tag = request->ep_tag;
+            status->ep_datatype = request->ep_datatype;
+
+            return 0;
+        }
+
+        if(request->type == 2)
+        {
+            int flag = false;
+            MPI_Message message;
+
+            while(!flag)
+            {
+                Message_Check(request->comm);
+#pragma omp flush
+                MPI_Improbe(request->ep_src, request->ep_tag, request->comm, &flag, &message, status);
+            }
+
+            int count;
+            MPI_Get_count(status, request->ep_datatype, &count);
+            MPI_Mrecv(request->buf, count, request->ep_datatype, &message, status);
+            status->ep_datatype = request->ep_datatype;
+
+            //check_sum_recv(request->buf, count, request->ep_datatype, request->ep_src, request->ep_tag, request->comm, 2);
+
+            return 0;
+        }
+
+        if(request->type == 3)
+        {
+            ::MPI_Request mpi_request = static_cast< ::MPI_Request >(request->mpi_request);
+            ::MPI_Status mpi_status;
+            ::MPI_Wait(&mpi_request, &mpi_status);
+
+            status->mpi_status = new ::MPI_Status(mpi_status);
+            status->ep_src = request->ep_src;
+            status->ep_tag = request->ep_tag;
+            status->ep_datatype = request->ep_datatype;
+
+            //int count;
+            //MPI_Get_count(status, request->ep_datatype, &count);
+            //check_sum_recv(request->buf, count, request->ep_datatype, request->ep_src, request->ep_tag, request->comm, 2);
+        }
+        return MPI_SUCCESS;
+    }
 
 
-        int MPI_Waitall(int count, MPI_Request *array_of_requests, MPI_Status *array_of_statuses)
-        {
-    int dest_rank;
-    MPI_Comm_rank(MPI_COMM_WORLD, &dest_rank);
-    
-    int finished = 0;
-    bool finished_index[count];
 
-          for(int i=0; i<count; i++)
+
+
+
+    int MPI_Waitall(int count, MPI_Request *array_of_requests, MPI_Status *array_of_statuses)
     {
-      finished_index[i] = false;
+        int dest_rank;
+        MPI_Comm_rank(MPI_COMM_WORLD, &dest_rank);
+
+        int finished = 0;
+        bool finished_index[count];
+
+        for(int i=0; i<count; i++)
+        {
+            finished_index[i] = false;
+        }
+
+        while(finished < count)
+        {
+            for(int i=0; i<count; i++)
+            {
+                if(finished_index[i] == false) // this request has not been tested.
+                {
+                    if(array_of_requests[i].type != 2) // isend or imrecv
+                    {      
+                        MPI_Wait(&array_of_requests[i], &array_of_statuses[i]);
+                        if(array_of_requests[i].type == 3)
+                        {
+                            //int check_count;
+                            //MPI_Get_count(&array_of_statuses[i], array_of_requests[i].ep_datatype, &check_count);
+                            //check_sum_recv(array_of_requests[i].buf, count, array_of_requests[i].ep_datatype, array_of_requests[i].ep_src, array_of_requests[i].ep_tag, array_of_requests[i].comm, 2);
+                        }
+                        finished++;
+                        finished_index[i] = true;
+                    }
+                    else // irecv
+                    {
+                        int flag = false;
+                        MPI_Message message;
+
+                        MPI_Improbe(array_of_requests[i].ep_src, array_of_requests[i].ep_tag, array_of_requests[i].comm, &flag, &message, &array_of_statuses[i]);
+
+                        if(flag)
+                        {
+                            //printf("dest_rank = %d, Waiting one message with src = %d, tag = %d, buf = %p\n", dest_rank, array_of_requests[i].ep_src, array_of_requests[i].ep_tag, array_of_requests[i].buf);
+                            int recv_count;
+                            MPI_Get_count(&array_of_statuses[i], array_of_requests[i].ep_datatype, &recv_count);
+                            MPI_Mrecv(array_of_requests[i].buf, recv_count, array_of_requests[i].ep_datatype, &message, &array_of_statuses[i]);
+                            //check_sum_recv(array_of_requests[i].buf, recv_count, array_of_requests[i].ep_datatype, array_of_requests[i].ep_src, array_of_requests[i].ep_tag, array_of_requests[i].comm, 2);
+
+                            finished++;
+                            finished_index[i] = true;
+                        }
+                    }
+                }
+            }    
+        }
+        return MPI_SUCCESS;
     }
-
-    while(finished < count)
-    {
-      for(int i=0; i<count; i++)
-      {
-        if(finished_index[i] == false) // this request has not been tested.
-        {
-          if(array_of_requests[i].type != 2) // isend or imrecv
-          {      
-            MPI_Wait(&array_of_requests[i], &array_of_statuses[i]);
-            if(array_of_requests[i].type == 3)
-            {
-              //int check_count;
-              //MPI_Get_count(&array_of_statuses[i], array_of_requests[i].ep_datatype, &check_count);
-              //check_sum_recv(array_of_requests[i].buf, count, array_of_requests[i].ep_datatype, array_of_requests[i].ep_src, array_of_requests[i].ep_tag, array_of_requests[i].comm, 2);
-            }
-            finished++;
-            finished_index[i] = true;
-          }
-          else // irecv
-          {
-            int flag = false;
-            MPI_Message message;
-            
-            MPI_Improbe(array_of_requests[i].ep_src, array_of_requests[i].ep_tag, array_of_requests[i].comm, &flag, &message, &array_of_statuses[i]);
-            
-            if(flag)
-            {
-              //printf("dest_rank = %d, Waiting one message with src = %d, tag = %d, buf = %p\n", dest_rank, array_of_requests[i].ep_src, array_of_requests[i].ep_tag, array_of_requests[i].buf);
-              int recv_count;
-              MPI_Get_count(&array_of_statuses[i], array_of_requests[i].ep_datatype, &recv_count);
-              MPI_Mrecv(array_of_requests[i].buf, recv_count, array_of_requests[i].ep_datatype, &message, &array_of_statuses[i]);
-              //check_sum_recv(array_of_requests[i].buf, recv_count, array_of_requests[i].ep_datatype, array_of_requests[i].ep_src, array_of_requests[i].ep_tag, array_of_requests[i].comm, 2);
-
-              finished++;
-              finished_index[i] = true;
-            }
-          }
-        }
-      }    
-    }
-          return MPI_SUCCESS;
-        }
 
 

XIOS/dev/branch_yushan_merged/src/io/inetcdf4.cpp

@@ -4 +4 @@
 
 #include <boost/algorithm/string.hpp>
+// mpi_std.hpp
+#ifdef _usingEP
+#include "ep_declaration.hpp"
+#endif
 
 namespace xios
@@ -18 +22 @@
     }
     mpi = comm && !multifile;
-    MPI_Info m_info;
+    MPI_Info m_info = MPI_INFO_NULL_STD;
 
     // The file format will be detected automatically by NetCDF, it is safe to always set NC_MPIIO

XIOS/dev/branch_yushan_merged/src/io/inetcdf4.hpp

@@ -13 +13 @@
 #define UNLIMITED_DIM (size_t)(-1)
 #endif  // UNLIMITED_DIM
+
 
 namespace xios

XIOS/dev/branch_yushan_merged/src/io/inetcdf4_decl.cpp

@@ -1 +1 @@
 #include "inetcdf4_impl.hpp"
+// mpi_std.hpp
 
 namespace xios

XIOS/dev/branch_yushan_merged/src/io/inetcdf4_impl.hpp

@@ -4 +4 @@
 #include "inetcdf4.hpp"
 #include "netCdfInterface.hpp"
+// mpi_std.hpp
 
 namespace xios

XIOS/dev/branch_yushan_merged/src/io/nc4_data_input.cpp

@@ -8 +8 @@
 #include "scalar.hpp"
 
+// mpi.hpp
+
 namespace xios
 {
-  CNc4DataInput::CNc4DataInput(const StdString& filename, MPI_Comm comm_file, bool multifile, bool isCollective /*= true*/, const StdString& timeCounterName /*= "time_counter"*/)
+  CNc4DataInput::CNc4DataInput(const StdString& filename, ::MPI_Comm comm_file, bool multifile, bool isCollective /*= true*/, const StdString& timeCounterName /*= "time_counter"*/)
     : SuperClass()
     , SuperClassWriter(filename, &comm_file, multifile, timeCounterName)

XIOS/dev/branch_yushan_merged/src/io/nc4_data_input.hpp

@@ -6 +6 @@
 #include "data_input.hpp"
 #include "inetcdf4.hpp"
+// mpi_std.hpp
 
 namespace xios

XIOS/dev/branch_yushan_merged/src/io/nc4_data_output.cpp

@@ -12 +12 @@
 #include "exception.hpp"
 #include "uuid.hpp"
+// mpi.hpp
 
 namespace xios
@@ -28 +29 @@
       CNc4DataOutput::CNc4DataOutput
          (CFile* file, const StdString & filename, bool exist, bool useClassicFormat, bool useCFConvention,
-          ep_lib::MPI_Comm comm_file, bool multifile, bool isCollective, const StdString& timeCounterName)
+          ::MPI_Comm comm_file, bool multifile, bool isCollective, const StdString& timeCounterName)
             : SuperClass()
             , SuperClassWriter(filename, exist, useClassicFormat, useCFConvention, &comm_file, multifile, timeCounterName)
@@ -463 +464 @@
       StdString domainName = domain->name;
       domain->assignMesh(domainName, domain->nvertex);
-      domain->mesh->createMeshEpsilon(static_cast<MPI_Comm>(server->intraComm.mpi_comm), domain->lonvalue_srv, domain->latvalue_srv, domain->bounds_lon_srv, domain->bounds_lat_srv);
+      domain->mesh->createMeshEpsilon(static_cast< ::MPI_Comm >(server->intraComm.mpi_comm), domain->lonvalue_srv, domain->latvalue_srv, domain->bounds_lon_srv, domain->bounds_lat_srv);
 
       StdString node_x = domainName + "_node_x";

XIOS/dev/branch_yushan_merged/src/io/nc4_data_output.hpp

@@ -6 +6 @@
 #include "onetcdf4.hpp"
 #include "data_output.hpp"
+// mpi_std.hpp
 
 namespace xios
@@ -26 +27 @@
             CNc4DataOutput
                (CFile* file, const StdString & filename, bool exist, bool useClassicFormat,
-                bool useCFConvention,
-                ep_lib::MPI_Comm comm_file, bool multifile, bool isCollective = true,
-                const StdString& timeCounterName = "time_counter");
+                bool useCFConvention, MPI_Comm comm_file, bool multifile, 
+                bool isCollective = true, const StdString& timeCounterName = "time_counter");
 
             CNc4DataOutput(const CNc4DataOutput & dataoutput);       // Not implemented.
@@ -116 +116 @@
 
             /// Propriétés privées ///
-            ep_lib::MPI_Comm comm_file;
+            MPI_Comm comm_file;
             const StdString filename;
             std::map<Time, StdSize> timeToRecordCache;

XIOS/dev/branch_yushan_merged/src/io/netCdfInterface.cpp

@@ -10 +10 @@
 #include "netCdfInterface.hpp"
 #include "netCdfException.hpp"
+// mpi_std.hpp
 
 namespace xios

XIOS/dev/branch_yushan_merged/src/io/netCdfInterface_decl.cpp

@@ -9 +9 @@
 
 #include "netCdfInterface_impl.hpp"
+// mpi_std.hpp
 
 namespace xios

XIOS/dev/branch_yushan_merged/src/io/netCdfInterface_impl.hpp

@@ -13 +13 @@
 #include "netCdfInterface.hpp"
 #include "netCdfException.hpp"
+// mpi_std.hpp
 
 namespace xios

XIOS/dev/branch_yushan_merged/src/io/netCdf_cf_constant.hpp

@@ -4 +4 @@
 #include "inetcdf4.hpp"
 #include "netCdfInterface.hpp"
+
+// mpi_std.hpp
 
 namespace xios

XIOS/dev/branch_yushan_merged/src/io/netcdf.hpp

@@ -30 +30 @@
 namespace xios
 {
-  inline int nc_create_par(const char *path, int cmode, ep_lib::MPI_Comm comm, MPI_Info info,int *ncidp)
+  inline int nc_create_par(const char *path, int cmode, MPI_Comm comm, MPI_Info info,int *ncidp)
   {
 #if defined(USING_NETCDF_PAR)
-    return ::nc_create_par(path, cmode, static_cast<MPI_Comm>(comm.mpi_comm), info, ncidp) ;
+    return ::nc_create_par(path, cmode, comm, info, ncidp) ;
 #else
     ERROR("int nc_create_par(const char *path, int cmode, MPI_Comm comm, MPI_Info info,int *ncidp)",
@@ -41 +41 @@
   }
 
-  inline int nc_open_par(const char *path, int mode, ep_lib::MPI_Comm comm, MPI_Info info,int *ncidp)
+  inline int nc_open_par(const char *path, int mode, MPI_Comm comm, MPI_Info info,int *ncidp)
   {
 #if defined(USING_NETCDF_PAR)
-    return ::nc_open_par(path, mode, static_cast<MPI_Comm>(comm.mpi_comm), info, ncidp) ;
+    return ::nc_open_par(path, mode, comm, info, ncidp) ;
 #else
     ERROR("int nc_open_par(const char *path, int mode, MPI_Comm comm, MPI_Info info,int *ncidp)",

XIOS/dev/branch_yushan_merged/src/io/onetcdf4.cpp

@@ -6 +6 @@
 #include "netCdfInterface.hpp"
 #include "netCdfException.hpp"
+// mpi_std.hpp
 
 namespace xios
@@ -12 +13 @@
 
       CONetCDF4::CONetCDF4(const StdString& filename, bool append, bool useClassicFormat, bool useCFConvention, 
-                           const ep_lib::MPI_Comm* comm, bool multifile, const StdString& timeCounterName)
+                           const MPI_Comm* comm, bool multifile, const StdString& timeCounterName)
         : path()
         , wmpi(false)
@@ -30 +31 @@
 
       void CONetCDF4::initialize(const StdString& filename, bool append, bool useClassicFormat, bool useCFConvention, 
-                                 const ep_lib::MPI_Comm* comm, bool multifile, const StdString& timeCounterName)
+                                 const MPI_Comm* comm, bool multifile, const StdString& timeCounterName)
       {
          this->useClassicFormat = useClassicFormat;
@@ -54 +55 @@
          {
             if (wmpi)
-               CNetCdfInterface::createPar(filename, mode, static_cast<MPI_Comm>(comm->mpi_comm), MPI_INFO_NULL_STD, this->ncidp);           
+               //CNetCdfInterface::createPar(filename, mode, static_cast<MPI_Comm>(comm->mpi_comm), MPI_INFO_NULL_STD, this->ncidp);           
+               CNetCdfInterface::createPar(filename, mode, *comm, MPI_INFO_NULL_STD, this->ncidp);           
             else
                CNetCdfInterface::create(filename, mode, this->ncidp);
@@ -64 +66 @@
             mode |= NC_WRITE;
             if (wmpi)
-               CNetCdfInterface::openPar(filename, mode, static_cast<MPI_Comm>(comm->mpi_comm), MPI_INFO_NULL_STD, this->ncidp);
+               //CNetCdfInterface::openPar(filename, mode, static_cast<MPI_Comm>(comm->mpi_comm), MPI_INFO_NULL_STD, this->ncidp);
+               CNetCdfInterface::openPar(filename, mode, *comm, MPI_INFO_NULL_STD, this->ncidp);
             else
                CNetCdfInterface::open(filename, mode, this->ncidp);

XIOS/dev/branch_yushan_merged/src/io/onetcdf4.hpp

@@ -14 +14 @@
 #endif  //UNLIMITED_DIM
 
+// mpi_std.hpp
+
 namespace xios
 {
@@ -28 +30 @@
             CONetCDF4(const StdString& filename, bool append, bool useClassicFormat = false,
                           bool useCFConvention = true,
-                      const ep_lib::MPI_Comm* comm = NULL, bool multifile = true,
+                      const MPI_Comm* comm = NULL, bool multifile = true,
                       const StdString& timeCounterName = "time_counter");
 
@@ -37 +39 @@
             /// Initialisation ///
             void initialize(const StdString& filename, bool append, bool useClassicFormat, bool useCFConvention,
-                            const ep_lib::MPI_Comm* comm, bool multifile, const StdString& timeCounterName);
+                            const MPI_Comm* comm, bool multifile, const StdString& timeCounterName);
             void close(void);
             void sync(void);

XIOS/dev/branch_yushan_merged/src/io/onetcdf4_decl.cpp

@@ -1 +1 @@
 #include "onetcdf4_impl.hpp"
+// mpi_std.hpp
 
 namespace xios

XIOS/dev/branch_yushan_merged/src/io/onetcdf4_impl.hpp

@@ -4 +4 @@
 #include "onetcdf4.hpp"
 #include "netCdfInterface.hpp"
+
+// mpi_std.hpp
 
 namespace xios

XIOS/dev/branch_yushan_merged/src/node/domain.cpp

@@ -26 +26 @@
 namespace xios {
 
-   /// ////////////////////// Définitions ////////////////////// ///
+   /// ////////////////////// Dfinitions ////////////////////// ///
 
    CDomain::CDomain(void)
@@ -1495 +1495 @@
 
       if (context->hasClient)
-      { // CÎté client uniquement
+      { // Ct client uniquement
          this->checkMask();
          this->checkDomainData();
@@ -1502 +1502 @@
       }
       else
-      { // CÎté serveur uniquement
+      { // Ct serveur uniquement
       }
 
@@ -1535 +1535 @@
 
       if (context->hasClient)
-      { // CÎté client uniquement
+      { // Ct client uniquement
          this->checkMask();
          this->checkDomainData();
@@ -1543 +1543 @@
       }
       else
-      { // CÎté serveur uniquement
+      { // Ct serveur uniquement
       }
 

XIOS/dev/branch_yushan_merged/src/node/file.cpp

@@ -465 +465 @@
 
         data_out = shared_ptr<CDataOutput>(new CNc4DataOutput(this, oss.str(), append, useClassicFormat, useCFConvention,
-                                                              fileComm, multifile, isCollective, time_counter_name));
+                                                              static_cast< ::MPI_Comm >(fileComm.mpi_comm), multifile, isCollective, time_counter_name));
         isOpen = true;
 
@@ -579 +579 @@
 
       if (isOpen) data_out->closeFile();
-      if (time_counter_name.isEmpty()) data_in = shared_ptr<CDataInput>(new CNc4DataInput(oss.str(), static_cast<MPI_Comm>(fileComm.mpi_comm), multifile, isCollective));
-      else data_in = shared_ptr<CDataInput>(new CNc4DataInput(oss.str(), static_cast<MPI_Comm>(fileComm.mpi_comm), multifile, isCollective, time_counter_name));
+      if (time_counter_name.isEmpty()) data_in = shared_ptr<CDataInput>(new CNc4DataInput(oss.str(), static_cast< ::MPI_Comm >(fileComm.mpi_comm), multifile, isCollective));
+      else data_in = shared_ptr<CDataInput>(new CNc4DataInput(oss.str(), static_cast< ::MPI_Comm >(fileComm.mpi_comm), multifile, isCollective, time_counter_name));
       isOpen = true;
     }

XIOS/dev/branch_yushan_merged/src/node/transformation.hpp

@@ -35 +35 @@
       typedef std::map<ETranformationType, CreateTransformationCallBack> CallBackMap;
       static CallBackMap* transformationCreationCallBacks_;
+      //#pragma omp threadprivate(transformationCreationCallBacks_)
 
       static bool registerTransformation(ETranformationType transType, CreateTransformationCallBack createFn);
@@ -65 +66 @@
     if (0 == transformationCreationCallBacks_)
       transformationCreationCallBacks_ = new CallBackMap();
-
     return (*transformationCreationCallBacks_).insert(make_pair(transType, createFn)).second;
   }

XIOS/dev/branch_yushan_merged/src/test/test_remap.f90

@@ -42 +42 @@
   CALL MPI_INIT(ierr)
   CALL init_wait
+  
+  CALL MPI_COMM_RANK(MPI_COMM_WORLD,rank,ierr)
+  if(rank < 2) then
 
 !!! XIOS Initialization (get the local communicator)
@@ -228 +231 @@
 
   CALL xios_finalize()
+  
+  print *, "Client : xios_finalize "
+
+    else
+
+    CALL xios_init_server
+    print *, "Server : xios_finalize "
+  
+    endif
 
   CALL MPI_FINALIZE(ierr)