Updated doc/Doxygen

doc/Doxygen/Allwmake

@@ -1,5 +1,13 @@
 #!/bin/sh
 cd ${0%/*} || exit 1    # run from this directory
+
+[ -d "$WM_PROJECT_DIR" ] || {
+    echo "Error: WM_PROJECT_DIR directory does not exist"
+    echo "    Check the OpenFOAM entries in your dot-files and source them."
+    echo "    WM_PROJECT_DIR=$WM_PROJECT_DIR"
+    exit 1
+}
+
 set -x
 
 rm -rf latex man

doc/Doxygen/Doxyfile

@@ -1,4 +1,4 @@
-# Doxyfile 1.5.3
+# Doxyfile 1.6.3
 
 # This file describes the settings to be used by the documentation system
 # doxygen (www.doxygen.org) for a project
@@ -14,11 +14,11 @@
 # Project related configuration options
 #---------------------------------------------------------------------------
 
-# 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.
 
 DOXYFILE_ENCODING      = UTF-8
 
@@ -54,10 +54,11 @@ CREATE_SUBDIRS         = NO
 # 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, Finnish, French, German, Greek, Hungarian,
-# Italian, Japanese, Japanese-en (Japanese with English messages), Korean,
-# Korean-en, Lithuanian, Norwegian, Polish, Portuguese, Romanian, Russian,
-# Serbian, Slovak, Slovene, Spanish, Swedish, and Ukrainian.
+# 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-Cyrilic, Slovak,
+# Slovene, Spanish, Swedish, Ukrainian, and Vietnamese.
 
 OUTPUT_LANGUAGE        = English
 
@@ -154,13 +155,6 @@ QT_AUTOBRIEF           = NO
 
 MULTILINE_CPP_IS_BRIEF = NO
 
-# If the DETAILS_AT_TOP tag is set to YES then Doxygen
-# will output the detailed description near the top, like JavaDoc.
-# If set to NO, the detailed description appears after the member
-# documentation.
-
-DETAILS_AT_TOP         = YES
-
 # 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.
@@ -195,14 +189,39 @@ ALIASES                =
 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.
+# 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.
 
 OPTIMIZE_OUTPUT_JAVA   = NO
 
-# 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 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.
+
+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.
+
+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, C#, 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 make the inheritance and collaboration
@@ -215,6 +234,21 @@ BUILTIN_STL_SUPPORT    = 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.
+
+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 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.
+
+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
@@ -230,6 +264,32 @@ DISTRIBUTE_GROUP_DOC   = NO
 
 SUBGROUPING            = YES
 
+# 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
+# types are typedef'ed and only the typedef is referenced, never the tag name.
+
+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 penality.
+# 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 rougly 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
+
 #---------------------------------------------------------------------------
 # Build related configuration options
 #---------------------------------------------------------------------------
@@ -264,10 +324,11 @@ EXTRACT_LOCAL_CLASSES  = YES
 
 EXTRACT_LOCAL_METHODS  = NO
 
-# 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.
+# 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.
 
 EXTRACT_ANON_NSPACES   = NO
 
@@ -327,6 +388,12 @@ HIDE_SCOPE_NAMES       = YES
 
 SHOW_INCLUDE_FILES     = 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.
+
+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.
 
@@ -346,6 +413,21 @@ SORT_MEMBER_DOCS       = 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.
+
+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.
+
+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,
@@ -407,9 +489,22 @@ SHOW_USED_FILES        = YES
 
 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.
+
+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.
+
+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
+# 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
@@ -417,6 +512,15 @@ SHOW_DIRECTORIES       = YES
 
 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
 #---------------------------------------------------------------------------
@@ -481,10 +585,18 @@ INPUT                  = $(WM_PROJECT_DIR)/src \
                          $(WM_PROJECT_DIR)/applications/utilities \
                          $(WM_PROJECT_DIR)/applications/solvers
 
-# 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.
+# limit input for testing purposes
+# INPUT                  = $(WM_PROJECT_DIR)/src/OpenFOAM/global \
+#                          $(WM_PROJECT_DIR)/src/OpenFOAM/containers \
+#                          $(WM_PROJECT_DIR)/src/OpenFOAM/primitives \
+#                          $(WM_PROJECT_DIR)/sampling \
+#                          $(WM_PROJECT_DIR)/src/finiteVolume/fvMesh
+
+# 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.
 
 INPUT_ENCODING         = UTF-8
 
@@ -493,9 +605,10 @@ INPUT_ENCODING         = UTF-8
 # and *.h) to filter out the source-files in the directories. If left
 # blank the following patterns are tested:
 # *.c *.cc *.cxx *.cpp *.c++ *.java *.ii *.ixx *.ipp *.i++ *.inl *.h *.hh *.hxx
-# *.hpp *.h++ *.idl *.odl *.cs *.php *.php3 *.inc *.m *.mm *.py
+# *.hpp *.h++ *.idl *.odl *.cs *.php *.php3 *.inc *.m *.mm *.py *.f90
 
-FILE_PATTERNS          = *.H *.C
+FILE_PATTERNS          = *.H \
+                         *.C
 
 # 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.
@@ -521,14 +634,14 @@ EXCLUDE_SYMLINKS       = NO
 # against the file with absolute path, so to exclude all test directories
 # for example use the pattern */test/*
 
-EXCLUDE_PATTERNS       = */lnInclude/*  \
+EXCLUDE_PATTERNS       = */lnInclude/* \
                          */t/*
 
-
 # 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
+# (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        =
 
@@ -538,7 +651,6 @@ EXCLUDE_SYMBOLS        =
 
 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
@@ -564,14 +676,17 @@ IMAGE_PATH             =
 # 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
+# to standard output.
+# If FILTER_PATTERNS is specified, this tag will be
 # ignored.
 
 INPUT_FILTER           = $(WM_PROJECT_DIR)/bin/tools/doxyFilter
 
 # 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:
+# 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, INPUT_FILTER
 # is applied to all files.
@@ -591,9 +706,7 @@ FILTER_SOURCE_FILES    = NO
 # 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. If you have enabled CALL_GRAPH or CALLER_GRAPH
-# then you must also enable this option. If you don't then doxygen will produce
-# a warning and turn it on anyway
+# VERBATIM_HEADERS is set to NO.
 
 SOURCE_BROWSER         = YES
 
@@ -608,13 +721,13 @@ INLINE_SOURCES         = NO
 
 STRIP_CODE_COMMENTS    = YES
 
-# If the REFERENCED_BY_RELATION tag is set to YES (the default)
+# If the REFERENCED_BY_RELATION tag is set to YES
 # then for each documented function all documented
 # functions referencing it will be listed.
 
 REFERENCED_BY_RELATION = YES
 
-# If the REFERENCES_RELATION tag is set to YES (the default)
+# 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.
 
@@ -623,7 +736,8 @@ 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 documentstion.
+# link to the source code.
+# Otherwise they will link to the documentation.
 
 REFERENCES_LINK_SOURCE = YES
 
@@ -655,7 +769,7 @@ ALPHABETICAL_INDEX     = YES
 # 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])
 
-COLS_IN_ALPHA_INDEX    = 4
+COLS_IN_ALPHA_INDEX    = 1
 
 # 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.
@@ -673,6 +787,11 @@ IGNORE_PREFIX          =
 
 GENERATE_HTML          = YES
 
+# If the HTML_FOOTER_DESCRIPTION tag is set to YES, Doxygen will
+# add generated date, project name and doxygen version to HTML footer.
+
+HTML_FOOTER_DESCRIPTION= NO
+
 # 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.
@@ -689,13 +808,13 @@ HTML_FILE_EXTENSION    = .html
 # each generated HTML page. If it is left blank doxygen will generate a
 # standard header.
 
-HTML_HEADER            = $(WM_PROJECT_DIR)/doc/Doxygen/FoamHeader.html
+HTML_HEADER            = $(WM_PROJECT_DIR)/doc/Doxygen/_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            = $(WM_PROJECT_DIR)/doc/Doxygen/FoamFooter.html
+HTML_FOOTER            = $(WM_PROJECT_DIR)/doc/Doxygen/_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
@@ -706,19 +825,18 @@ HTML_FOOTER            = $(WM_PROJECT_DIR)/doc/Doxygen/FoamFooter.html
 
 HTML_STYLESHEET        =
 
+# 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         = NO
+
 # 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 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 compressed HTML help file (.chm)
-# of the generated HTML documentation.
-
-GENERATE_HTMLHELP      = NO
-
 # 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
@@ -727,6 +845,39 @@ GENERATE_HTMLHELP      = NO
 
 HTML_DYNAMIC_SECTIONS  = NO
 
+# 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 for more
+# information.
+
+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.
+
+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.
+
+DOCSET_BUNDLE_ID       = org.doxygen.Project
+
+# 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.
+
+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
@@ -747,6 +898,12 @@ HHC_LOCATION           =
 
 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.
@@ -758,6 +915,75 @@ BINARY_TOC             = NO
 
 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.
+
+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
+
+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
+
+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.
+
+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.
+
+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.
@@ -769,29 +995,61 @@ DISABLE_INDEX          = NO
 
 ENUM_VALUES_PER_LINE   = 4
 
-# If the GENERATE_TREEVIEW tag is set to YES, a side panel will be
-# generated containing a tree-like index structure (just like the one that
+# 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 (for instance Mozilla 1.0+,
-# Netscape 6.0+, Internet explorer 5.0+, or Konqueror). Windows users are
-# probably better off using the HTML help feature.
+# 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      = NO
 
+# 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       = NO
+
 # 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.
 
 TREEVIEW_WIDTH         = 250
 
+# 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.
+
+FORMULA_FONTSIZE       = 10
+
+# 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.
+
+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 disadvances
+# is that it is more difficult to setup and does not have live searching
+# capabilities.
+
+SERVER_BASED_SEARCH    = NO
+# old default
+# SERVER_BASED_SEARCH    = YES
+
 #---------------------------------------------------------------------------
 # configuration options related to the LaTeX output
 #---------------------------------------------------------------------------
 
-# Path for OpenCFD LaTeX macros
-
-@INCLUDE_PATH = $(WM_PROJECT_DIR)/doc/Doxygen/Macros/
-
 # If the GENERATE_LATEX tag is set to YES (the default) Doxygen will
 # generate Latex output.
 
@@ -805,6 +1063,9 @@ 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.
 
 LATEX_CMD_NAME         = latex
 
@@ -864,6 +1125,12 @@ LATEX_BATCHMODE        = NO
 
 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.
+
+LATEX_SOURCE_CODE      = NO
+
 #---------------------------------------------------------------------------
 # configuration options related to the RTF output
 #---------------------------------------------------------------------------
@@ -1000,8 +1267,10 @@ GENERATE_PERLMOD       = NO
 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
+# 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.
 
@@ -1088,9 +1357,11 @@ SKIP_FUNCTION_MACROS   = YES
 # 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 ...
+#
+# TAGFILES = file1 file2 ...
 # Adding location for the tag files is done as follows:
-#   TAGFILES = file1=loc1 "file2 = loc2" ...
+#
+# 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.
@@ -1137,10 +1408,11 @@ PERL_PATH              = /usr/bin/perl
 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.
+# 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            =
 
@@ -1157,6 +1429,29 @@ HIDE_UNDOC_RELATIONS   = YES
 
 HAVE_DOT               = YES
 
+# By default doxygen will write a font called FreeSans.ttf to the output
+# directory and reference it in all dot files that doxygen generates. This font
+# does not include all possible unicode characters however, so when you need
+# these (or just want a differently looking font) you can specify the font name
+# using DOT_FONTNAME. You need 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           = FreeSans
+
+# 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
@@ -1201,19 +1496,19 @@ INCLUDE_GRAPH          = YES
 
 INCLUDED_BY_GRAPH      = YES
 
-# If the CALL_GRAPH, SOURCE_BROWSER and HAVE_DOT tags 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 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.
 
 CALL_GRAPH             = YES
 
-# If the CALLER_GRAPH, SOURCE_BROWSER 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 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.
 
 CALLER_GRAPH           = YES
 
@@ -1246,15 +1541,15 @@ DOT_PATH               =
 
 DOTFILE_DIRS           =
 
-# The MAX_DOT_GRAPH_MAX_NODES tag can be used to set the maximum number of
+# 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 if the number
-# of direct children of the root node in a graph is already larger than
-# MAX_DOT_GRAPH_NOTES then the graph will not be shown at all. Also note
+# 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.
 
-DOT_GRAPH_MAX_NODES    = 10
+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
@@ -1264,13 +1559,13 @@ DOT_GRAPH_MAX_NODES    = 10
 # 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.
 
-MAX_DOT_GRAPH_DEPTH    = 1
+MAX_DOT_GRAPH_DEPTH    = 3
 
 # Set the DOT_TRANSPARENT tag to YES to generate images with a transparent
-# background. This is disabled by default, which results in a white background.
-# 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).
+# 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).
 
 DOT_TRANSPARENT        = YES
 
@@ -1292,12 +1587,3 @@ GENERATE_LEGEND        = YES
 # the various graphs.
 
 DOT_CLEANUP            = YES
-
-#---------------------------------------------------------------------------
-# Configuration::additions related to the search engine
-#---------------------------------------------------------------------------
-
-# The SEARCHENGINE tag specifies whether or not a search engine should be
-# used. If set to NO the values of all tags below this one will be ignored.
-
-SEARCHENGINE           = YES

doc/Doxygen/Doxygen.css

@@ -1,76 +0,0 @@
-body { color: #000000 ; background: #ffffff; margin: 0px; font-family: verdana, arial, helvetica, sans-serif; text-decoration: none; font-size: 12px; }
-a:link { text-decoration: none; color: #0000ff ; }
-a:link:hover { text-decoration: none; color: #0000ff ; }
-a:visited { text-decoration: none; color: #0000ff ; }
-a:visited:hover { text-decoration: none; color: #0000ff ; }
-a:link img { border: 0; }
-a:visited img { border: 0; }
-a:active img { border: 0; }
-a.menuLefton { color: #0000ff; font-size: 12px; font-weight: bold; }
-td.leftmenu { font-family: verdana, arial, helvetica, sans-serif; text-decoration: none; background: #ddddff; text-align: left; font-size: 14px; height: 20px; width: 200px; }
-a.menuTopoff { color: #000000; font-size: 14px; }
-a.menuTopoff:visited { color: #000000; font-size: 14px; }
-a.menuTopoff:hover { color: #0000ff; font-size: 14px; }
-td.topmenu { font-family: verdana, arial, helvetica, sans-serif; background: #ddddff; text-align: center; font-size: 16px; width: 150px; font-weight: bold; }
-h1 { font-size: 18px; }
-h2 { font-size: 16px; }
-h3 { font-size: 14px; }
-
-/* formatting for member functions:
- * Since the OpenFOAM code already has nice line-breaks, wrapping the lines
- * just looks terrible.
- * Give a slightly different background to make it easier to find.
-*/
-.memitem {
-    padding: 4px;
-    background-color: #eef3f5;
-    border-width: 1px;
-    border-style: solid;
-    border-color: #dedeee;
-}
-
-.memproto {
-    background-color: #d5e1e8;
-    width: 100%;
-    border-width: 1px;
-    border-style: solid;
-    border-color: #84b0c7;
-    font-weight: bold;
-}
-
-table.memname {
-    width: 100%;
-    background: #f7f7ff;
-    white-space: nowrap;
-}
-
-
-.indexkey {
-    vertical-align: top;
-    background: #f7f7ff;
-}
-
-.indexvalue {
-    vertical-align: top;
-    background: #f7f7ff;
-}
-
-.paramkey {
-    width: 5%;
-}
-
-.memItemLeft {
-    background: #f7f7ff;
-}
-
-.memItemRight {
-    background: #f7f7ff;
-}
-
-.mdescLeft {
-    margin: 0px;
-}
-
-.mdescRight {
-    font-style: italic;
-}

doc/Doxygen/FoamFooter.html

@@ -1,5 +0,0 @@
-Copyright&nbsp;&copy;&nbsp;2000-2010&nbsp;<a href="http://www.openfoam.com/about">OpenCFD Ltd.</a>
-</td></tr>
-</table>
-</body>
-</html>

doc/Doxygen/FoamHeader.html

@@ -1,73 +0,0 @@
-<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN"
-  "http://www.w3.org/TR/html4/loose.dtd">
-<html>
-<head>
-   <title> OpenFOAM programmer's C++ documentation </title>
-<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1">
-<!-- html,info -->
-<link rel="stylesheet" type="text/css" href="../Doxygen.css">
-<link rel="stylesheet" type="text/css" href="../tabs.css">
-<link href="../OpenFOAMicon.png" type="image/png" rel="icon" />
-<meta name="keywords" content="computational fluid dynamics, CFD, OpenCFD, OpenFOAM, open source CFD, open source">
-<meta name="description" content="OpenCFD Ltd, leaders in open source Computational Fluid Dynamics (CFD), the developers and maintainers of OpenFOAM: the open source CFD toolbox. We supply support and contracted developments for OpenFOAM">
-</head>
-<body>
-<a id="openfoam"> </a>
-<!-- Top banner -->
-<table
-    style="border-width: 0px; width: 800px; background: #ddddff;"
-    cellspacing="0" cellpadding="0">
-<tr>
-<td style="width: 9px; height:54px"></td>
-<td style="width: 250px; height:54px; vertical-align:middle;
-    horizontal-align: left;">
-<img alt="OpenFOAM logo" src="../OpenFOAMlogo.jpg"> </td>
-<td style="width:350px; height:54px; vertical-align:middle;
-horizontal-align: left; ">
-    <table>
-    <tr>
-    <td><img alt="The Open Source CFD Toolbox" src="../OpenSourceToolbox.jpg"></td>
-    </tr>
-    </table>
-</td>
-</tr>
-</table>
-<!-- Button banner -->
-<table
-    style="border-width: 0px; width: 800px; background: #ffffff;"
-    cellspacing="0" cellpadding="0">
-<tr>
-<td valign="top">
-    <table width="801" border="0" cellspacing="1" cellpadding="0" bgcolor="#ffffff">
-    <tr>
-    <td class="leftmenu">&nbsp;
-        <a href="http://foam.sourceforge.net/doc/Doxygen/html"
-            class="menuLefton">Source Guide</a>
-    </td>
-    <td class="topmenu">
-        <a href="http://www.openfoam.com/about/"
-            class="menuTopoff">OpenCFD</a>
-    </td>
-    <td class="topmenu">
-        <a href="http://www.openfoam.com/features/"
-            class="menuTopoff">Features</a>
-    </td>
-    <td class="topmenu">
-        <a href="http://www.openfoam.com/contact/"
-            class="menuTopoff">Contact</a>
-    </td>
-    <td class="topmenu">
-        <a href="http://www.openfoam.com/"
-            class="menuTopoff">OpenFOAM</a>
-    </td>
-    </tr>
-    <tr><td></td></tr>
-    </table>
-</td>
-</tr>
-</table>
-<table
-    style="border-width: 0px; width: 800px; background: #ffffff;"
-    cellspacing="5" cellpadding="0">
-<tr>
-<td>

doc/Doxygen/Macros/tensorOperator.sty

@@ -1,128 +0,0 @@
-%-----------------------------------------------------------------------------
-% =========                 |
-% \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
-%  \\    /   O peration     |
-%   \\  /    A nd           | Copyright (C) 2004-2010 OpenCFD Ltd.
-%    \\/     M anipulation  |
-%------------------------------------------------------------------------------
-% License
-%     This file is part of OpenFOAM.
-%
-%     OpenFOAM is free software: you can redistribute it and/or modify it
-%     under the terms of the GNU General Public License as published by
-%     the Free Software Foundation, either version 3 of the License, or
-%     (at your option) any later version.
-%
-%     OpenFOAM is distributed in the hope that it will be useful, but WITHOUT
-%     ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
-%     FITNESS FOR A PARTICULAR PURPOSE.  See the GNU General Public License
-%     for more details.
-%
-%     You should have received a copy of the GNU General Public License
-%     along with OpenFOAM.  If not, see <http://www.gnu.org/licenses/>.
-%
-% LaTeX Style file
-%     tensorOperator.sty
-%
-% Description
-%     Standard OpenCFD LaTeX macros for typesetting tensor algebra.
-%
-%------------------------------------------------------------------------------
-
-% tensor style
-% ~~~~~~~~~~~~
-\renewcommand{\vec}[1] {\ensuremath{\mathbf #1}}
-\newcommand{\gvec}[1] {\ensuremath{\mbox{\boldmath$\bf#1$}}}
-
-% products
-% ~~~~~~~~
-\newcommand{\anyprod}{\star}
-\newcommand{\cprod} {\times}
-\newcommand{\dprod} {\,{\scriptscriptstyle \stackrel{\bullet}{{}}}\,}
-\newcommand{\ddprod} {\,{\scriptscriptstyle \stackrel{\bullet}{\bullet}}\,}
-\newcommand{\tdprod} {\,{\scriptscriptstyle \stackrel{3}{\bullet}}\,}
-\newcommand{\tprod} {\,{\scriptscriptstyle \stackrel{\otimes}{{}}}\,}
-
-% operations
-% ~~~~~~~~~~
-\newcommand{\adj} {\ensuremath{\operatorname{adj}}}
-\newcommand{\cof} {\ensuremath{\operatorname{cof}}}
-\newcommand{\diag} {\ensuremath{\operatorname{diag}}}
-\newcommand{\dev} {\ensuremath{\operatorname{dev}}}
-
-\newcommand{\Hodge} {\ensuremath{\operatorname{\stackrel{\displaystyle \ast}{}}}}
-\newcommand{\hyd} {\ensuremath{\operatorname{hyd}}}
-\renewcommand{\max} {\ensuremath{\operatorname{max}}}
-\renewcommand{\min} {\ensuremath{\operatorname{min}}}
-\newcommand{\inv} {\ensuremath{\operatorname{inv}}}
-\newcommand{\sym} {\ensuremath{\operatorname{symm}}}    % symm ?
-\newcommand{\skw} {\ensuremath{\operatorname{skew}}}    % skew already defined
-\newcommand{\tr} {\ensuremath{\operatorname{tr}}}
-\newcommand{\trans}[1] {\ensuremath{#1^{\operatorname{T}}}}
-
-% alternative tensor operators for hypersonics etc.
-% ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-\newcommand{\devs}[1] {\overset{\scriptscriptstyle\circ}{#1}}
-%\newcommand{\trans}[1] {\ensuremath{#1^{\operatorname{T}}}}
-\newcommand{\symms}[1] {\overleftrightarrow{#1}}
-\newlength{\skewslength}
-\newlength{\skewsheight}
-\newcommand{\skews}[1]{
-    \settowidth{\skewslength}{#1}%
-    \settoheight{\skewsheight}{#1}%
-    \addtolength{\skewsheight}{0.4mm}%
-    {\overleftrightarrow{#1}\hspace{-.5\skewslength}%
-    \rule[\skewsheight]{.4pt}{1.4mm}
-    \hspace{.5\skewslength}%
-}}
-%\newcommand{\skew}[1] {\ensuremath{#1^{\operatorname{A}}}}
-
-% spatial derivatives
-% ~~~~~~~~~~~~~~~~~~~
-\newcommand{\curl}{\ensuremath{\nabla\cprod}}
-\renewcommand{\div} {\ensuremath{\nabla\dprod}}
-\newcommand{\grad}{\ensuremath{\nabla}}
-\newcommand{\laplacian}{\ensuremath{\nabla^{2}}}
-
-% temporal derivatives
-% ~~~~~~~~~~~~~~~~~~~~
-\newcommand{\ddt}[1] {\ensuremath{\frac{\partial #1}{\partial t }}}
-\newcommand{\DDt}[1] {\ensuremath{\frac{D #1}{D t}}}
-\newcommand{\DpDt}[2] {\ensuremath{\frac{d_{#1} #2}{d t }}}
-\newcommand{\dsdts}[1] {\ensuremath{\frac{\partial ^2 #1}{\partial t^2}}}
-\newcommand{\rate}[1] {\ensuremath{\dot{#1}}}
-
-\newcommand{\genDer}{\mathcal{L}}
-
-% time average symbols
-% ~~~~~~~~~~~~~~~~~~~~
-\newcommand{\av}[1] {\ensuremath{\overline{#1}}}
-\newcommand{\corrtwo}[2] {{\dwea{\dprime{#1} \dprime{#2}}}}
-\newcommand{\curly}[1] {{\cal #1}}
-\newcommand{\dprime}[1] {\ensuremath{{#1}^{^{\prime \prime}}}}
-\newcommand{\dwea}[1] {\ensuremath{\widetilde{#1}}}
-\newcommand{\dweafluc}[1] {\ensuremath{\dprime{#1}}}
-\newcommand{\fluc}[1] {\ensuremath{#1^{\prime}}}
-
-% index style
-% ~~~~~~~~~~~
-\newcommand{\veci}[2][i] {\ensuremath{#2_{#1}}}
-\newcommand{\teni}[2][ij] {\ensuremath{#2_{#1}}}
-\newcommand{\tenTi}[2][ji] {\ensuremath{#2_{#1}}}
-
-% index operations
-% ~~~~~~~~~~~~~~~~
-\newcommand{\deltai}[1] {\ensuremath{\partial_{#1}}}
-
-% Sub-subscripts
-% ~~~~~~~~~~~~~~
-\newcommand{\eff} {{\scriptscriptstyle e\!f\!\!f\!}}
-
-% unknown use
-% ~~~~~~~~~~~
-%\font\bigtenrm=cmr12 scaled 1200
-%\newcommand{\eexp}[1]{{\hbox{$\textfont1=\bigtenrm e$}}^{\raise3pt
-%\hbox{$#1$}}}
-
-
-% ------------------------------------------------------------------------------

doc/Doxygen/tabs.css

@@ -1,100 +0,0 @@
-/* tabs styles, based on http://www.alistapart.com/articles/slidingdoors */
-
-div.tabs
-{
-    float           : left;
-    width           : 100%;
-    margin-bottom   : 2px;
-    padding-bottom  : 6px;
-}
-
-div.tabs ul
-{
-    margin          : 0px;
-    padding-left    : 0px;
-    border-right    : 1px solid #84B0C7;
-    list-style      : none;
-}
-
-div.tabs li, div.tabs form
-{
-    display         : inline;
-    margin          : 0px;
-    padding         : 0px;
-}
-
-div.tabs form
-{
-    float           : left;
-    padding         : 0px 9px;
-}
-
-div.tabs a
-{
-    float           : left;
-    font-size       : 12px;
-    font-weight     : bold;
-    text-decoration : none;
-    border-right    : 1px solid #000000;
-}
-
-div.tabs a:hover
-{
-    background-position: 100% -150px;
-}
-
-div.tabs a:link, div.tabs a:visited, div.tabs a:active, div.tabs a:hover
-{
-    color           : #000000;
-}
-
-div.tabs span
-{
-    float           : left;
-    display         : block;
-    padding         : 0px 9px;
-    white-space     : nowrap;
-}
-
-div.tabs input
-{
-    float           : right;
-    display         : inline;
-    font-size       : 12px;
-}
-
-div.tabs td
-{
-    font-size       : 12px;
-    font-weight     : bold;
-    text-decoration : none;
-}
-
-/* Commented backslash hack hides rule from IE5-Mac \*/
-div.tabs span { float : none; }
-/* End IE5-Mac hack */
-
-div.tabs a:hover span
-{
-    background-position: 0% -150px;
-}
-
-div.tabs li#current a
-{
-    border-width    : 0px;
-    border-right    : 1px solid #000000;
-    color           : #0000ff;
-}
-
-div.tabs li#current span
-{
-    padding-bottom  : 0px;
-}
-
-div.nav
-{
-    background      : none;
-    border          : none;
-    border-bottom   : 1px solid #000000;
-}
-

doc/doxygen/Allwmake

@@ -1,30 +0,0 @@
-#!/bin/sh
-cd ${0%/*} || exit 1    # run from this directory
-
-[ -d "$WM_PROJECT_DIR" ] || {
-    echo "Error: WM_PROJECT_DIR directory does not exist"
-    echo "    Check the OpenFOAM entries in your dot-files and source them."
-    echo "    WM_PROJECT_DIR=$WM_PROJECT_DIR"
-    exit 1
-}
-
-set -x
-
-rm -rf latex man
-
-# remove html directory in background
-mv html html-stagedRemove$$ 2> /dev/null
-rm -rf html-stagedRemove$$ >/dev/null 2>&1 &
-
-# ensure that created files are readable by everyone
-umask 22
-doxygen
-
-# fix permissions (NB: '+X' and not '+x'!)
-chmod -R a+rX html latex man 2>/dev/null
-
-echo
-echo "Done doxygen"
-echo
-
-# ----------------------------------------------------------------- end-of-file