diff --git a/HySoP/DoxyConf/parmes.doxyfile b/HySoP/DoxyConf/parmes.doxyfile
index 3fc34f2d72df9022e0bd70641893c85df3c43605..82feb982deb021ab857610f24d295df504bcbd66 100644
--- a/HySoP/DoxyConf/parmes.doxyfile
+++ b/HySoP/DoxyConf/parmes.doxyfile
@@ -1,4 +1,4 @@
-# Doxyfile 1.7.3
+# Doxyfile 1.8.1.1
# This file describes the settings to be used by the documentation system
# doxygen (www.doxygen.org) for a project
@@ -14,21 +14,22 @@
# 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
+# 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
-# 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 sequence of words) that should
+# identify the project. Note that if you do not use Doxywizard you need
+# to put quotes around the project name if it contains spaces.
-PROJECT_NAME = ParMePy
+PROJECT_NAME = ParMeS
-# The PROJECT_NUMBER tag can be used to enter a project or revision number.
-# This could be handy for archiving the generated documentation or
+# 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 = 1.0.0
@@ -37,740 +38,796 @@ PROJECT_NUMBER = 1.0.0
# 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 = "Particular Methods simulation on hybrid architectures"
+PROJECT_BRIEF = "Particle Methods simulation on hybrid architectures"
-# 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.
+# 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 =
+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
+# 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.
OUTPUT_DIRECTORY = ../../ParmesDoc
-# 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
+# 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.
CREATE_SUBDIRS = YES
-# 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,
+# 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.
OUTPUT_LANGUAGE = English
-# 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).
+# 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.
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 (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
# brief descriptions will be completely suppressed.
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 $name file" "is" "provides" "specifies" "contains"
+# This tag implements a quasi-intelligent brief description abbreviator
+# that is used to form the text in various listings. Each string
+# in this list, if found as the leading text of the brief description, will be
+# stripped from the text and the result after processing the whole list, is
+# used as the annotated text. Otherwise, the brief description is used as-is.
+# If left blank, the following values are used ("$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"
-ABBREVIATE_BRIEF =
+ABBREVIATE_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
+# 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.
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.
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
+# 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.
-FULL_PATH_NAMES = NO
+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
+# 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 =
+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
+# 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 =
+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
+# 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.
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
+# 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.)
JAVADOC_AUTOBRIEF = YES
-# 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
+# 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.)
QT_AUTOBRIEF = NO
-# 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
+# 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.
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
+# 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.
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
+# 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.
SEPARATE_MEMBER_PAGES = NO
-# The TAB_SIZE tag can be used to set the number of spaces in a tab.
+# 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.
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:".
+# 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 =
+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
+# 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.
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
+# 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.
-OPTIMIZE_OUTPUT_JAVA = NO
+OPTIMIZE_OUTPUT_JAVA = YES
-# 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
+# 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
+# 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, 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
+# 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 =
+EXTENSION_MAPPING =
+
+# If MARKDOWN_SUPPORT is enabled (the default) 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.
-# 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
+MARKDOWN_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); v.s.
+# func(std::string) {}). This also makes the inheritance and collaboration
# diagrams that involve STL classes more complete and accurate.
BUILTIN_STL_SUPPORT = NO
-# 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.
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
+# 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 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
+# 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.
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.
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
+# 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.
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
+# 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).
+
+INLINE_GROUPED_CLASSES = NO
+
+# When the INLINE_SIMPLE_STRUCTS tag is set to YES, structs, classes, and
+# unions with only public data 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 (the default),
+# structs, classes, and unions are shown on a separate page (for HTML and Man
+# pages) or section (for LaTeX and RTF).
+
+INLINE_SIMPLE_STRUCTS = 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
# 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 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
+# 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
+# Similar to the SYMBOL_CACHE_SIZE 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 appear 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.
+
+LOOKUP_CACHE_SIZE = 0
+
#---------------------------------------------------------------------------
# Build related configuration options
#---------------------------------------------------------------------------
-# 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
+# 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
EXTRACT_ALL = YES
-# If the EXTRACT_PRIVATE tag is set to YES all private members of a class
+# If the EXTRACT_PRIVATE tag is set to YES all private members of a class
# will be included in the documentation.
EXTRACT_PRIVATE = YES
-# If the EXTRACT_STATIC tag is set to YES all static members of a file
+# If the EXTRACT_PACKAGE tag is set to YES all members with package or internal
+# scope will be included in the documentation.
+
+EXTRACT_PACKAGE = NO
+
+# If the EXTRACT_STATIC tag is set to YES all static members of a file
# will be included in the documentation.
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 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.
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.
+# 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.
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
+# 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.
EXTRACT_ANON_NSPACES = YES
-# 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.
+# 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.
-HIDE_UNDOC_MEMBERS = YES
+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
+# 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.
-HIDE_UNDOC_CLASSES = YES
+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
+# 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.
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
+# 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.
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.
+# 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.
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.
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
+# 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.
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
+# 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.
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
+# 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]
+# If the INLINE_INFO tag is set to YES (the default) then a tag [inline]
# is inserted in the documentation for inline members.
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
+# 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.
SORT_MEMBER_DOCS = NO
-# 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
+# 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.
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
+# 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 = YES
-# 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)
+# 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,
-# 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
+# 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.
SORT_BY_SCOPE_NAME = YES
# 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
+# 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
+# by doing a simple string match. By disabling STRICT_PROTO_MATCHING doxygen
# will still accept a match between prototype and implementation in such cases.
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
+# 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.
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
+# 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.
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
+# 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.
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
+# 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.
GENERATE_DEPRECATEDLIST= YES
-# The ENABLED_SECTIONS tag can be used to enable conditional
+# The ENABLED_SECTIONS tag can be used to enable conditional
# documentation sections, marked by \if sectionname ... \endif.
-ENABLED_SECTIONS =
+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
+# 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.
MAX_INITIALIZER_LINES = 39
-# 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.
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
+# 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
+# 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
-# 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
+# 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 =
+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
+# 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.
-LAYOUT_FILE =
+LAYOUT_FILE =
+
+# The CITE_BIB_FILES tag can be used to specify one or more bib files
+# containing the references data. This must be a list of .bib files. The
+# .bib extension is automatically appended if omitted. Using this command
+# 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.
+
+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
+# 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.
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
+# 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.
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
+# 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.
-WARN_IF_UNDOCUMENTED = NO
+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
+# 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.
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
+# 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.
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
+# 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
+# $version, which will be replaced by the version of the file (if it could
# be obtained via FILE_VERSION_FILTER)
WARN_FORMAT = "$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
+# 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 =
+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
+# 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.
-INPUT = ../src/main \
- ../src \
+INPUT = ../src \
../parmepy \
mainpage.doxygen
-# 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
+# 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
-# 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
+# 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
FILE_PATTERNS = *.doxygen \
*.py \
*.f90
-# 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.
+# 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.
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.
+# Note that relative paths are relative to the directory from which doxygen is
+# run.
-EXCLUDE =
+EXCLUDE = ../parmepy/unusedOrObsolet \
+ ../parmepy/particular_solvers/integrator \
+ ../parmepy/particular_solvers/interpolation \
+ ../parmepy/particular_solvers/remesh
-# 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
+# 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.
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
+# 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 = */.svn/*
-# 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,
+# 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 =
+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 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 =
+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
+# 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.
+# 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.
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_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 =
+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
+# 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 =
+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
+# 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 = *.py=/Library/Frameworks/EPD64.framework/Versions/7.1/bin/doxypy.py
+FILTER_PATTERNS = *.py=/usr/local/bin/doxypy.py
-# 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
+# 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).
FILTER_SOURCE_FILES = YES
-# 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
+# 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 =
+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
+# 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.
SOURCE_BROWSER = NO
-# Setting the INLINE_SOURCES tag to YES will include the body
+# Setting the INLINE_SOURCES tag to YES will include the body
# of functions and classes directly in the documentation.
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 (the default) will instruct
+# doxygen to hide any special comment blocks from generated source code
+# fragments. Normal C, C++ and Fortran comments will always remain visible.
STRIP_CODE_COMMENTS = YES
-# If the REFERENCED_BY_RELATION tag is set to YES
-# then for each documented function all documented
+# 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 = NO
-# If the REFERENCES_RELATION tag is set to YES
-# then for each documented function all documented entities
+# 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.
REFERENCES_RELATION = NO
-# 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
+# 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.
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
+# 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.
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
+# 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.
VERBATIM_HEADERS = YES
@@ -779,141 +836,160 @@ 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
+# 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.
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
+# 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])
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
+# 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 =
+IGNORE_PREFIX =
#---------------------------------------------------------------------------
# configuration options related to the HTML output
#---------------------------------------------------------------------------
-# If the GENERATE_HTML tag is set to YES (the default) Doxygen will
+# If the GENERATE_HTML tag is set to YES (the default) Doxygen will
# generate HTML output.
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
+# 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.
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
+# 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.
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.
+# 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 advised 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_HEADER =
+HTML_FOOTER =
-# 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.
+# 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
+# style sheet in the HTML output directory as well, or it will be erased!
-HTML_FOOTER =
+HTML_STYLESHEET =
-# 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!
+# 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_STYLESHEET =
+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 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.
# The allowed range is 0 to 359.
HTML_COLORSTYLE_HUE = 115
-# 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
+# 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 = 115
-# 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,
+# 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 = 124
-# 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
+# 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.
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
+# 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.
+
+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, 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)
+# 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
+# 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
-# When GENERATE_PUBLISHER_ID tag specifies a string that should uniquely identify
-# the documentation publisher. This should be a reverse domain-name style
+# When GENERATE_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.
DOCSET_PUBLISHER_ID = org.doxygen.Publisher
@@ -922,211 +998,215 @@ DOCSET_PUBLISHER_ID = org.doxygen.Publisher
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)
+# 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
+# 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
# written to the html output directory.
-CHM_FILE =
+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
+# 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 =
+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
+# 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).
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
+# 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 =
+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
+# 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.
BINARY_TOC = NO
-# The TOC_EXPAND flag can be set to YES to add extra items for group members
+# 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.
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
+# 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.
+# 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 =
+QCH_FILE =
-# The QHP_NAMESPACE tag specifies the namespace to use when generating
-# Qt Help Project output. For more information please see
+# 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
+# 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
+# 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 =
+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">
+# 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 =
+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">
+# 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 =
+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
+# 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 =
+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
+# 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
+# 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.
+# The DISABLE_INDEX tag can be used to turn on/off the condensed index (tabs)
+# at top of each HTML page. The value NO (the default) enables the index and
+# the value YES disables it. Since the tabs have the same information as the
+# navigation tree you can set this option to NO if you already set
+# GENERATE_TREEVIEW to YES.
DISABLE_INDEX = NO
-# This 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.
-
-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).
+# 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.
+# Since the tree basically has the same information as the tab index you
+# could consider to set DISABLE_INDEX to NO when enabling this option.
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.
+# 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.
-USE_INLINE_TREES = NO
+ENUM_VALUES_PER_LINE = 4
-# 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
+# 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
-# When the EXT_LINKS_IN_WINDOW option is set to YES doxygen will open
+# 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.
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
+# 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
-# 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
+# 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.
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
+# 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 may also need to install MathJax separately and
# configure the path to it using the MATHJAX_RELPATH option.
USE_MATHJAX = YES
-# 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 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.
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
+# The MATHJAX_EXTENSIONS tag can be used to specify one or MathJax extension
+# names that should be enabled during MathJax rendering.
+
+MATHJAX_EXTENSIONS =
+
+# 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 disadvantages are that it is more difficult to setup
+# 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.
SERVER_BASED_SEARCH = NO
@@ -1135,154 +1215,167 @@ SERVER_BASED_SEARCH = NO
# configuration options related to the LaTeX output
#---------------------------------------------------------------------------
-# If the GENERATE_LATEX tag is set to YES (the default) Doxygen will
+# If the GENERATE_LATEX tag is set to YES (the default) Doxygen will
# generate Latex output.
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
+# 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.
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
+# 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
-# 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
+# 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.
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
+# 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.
COMPACT_LATEX = YES
-# 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
+# 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.
PAPER_TYPE = a4
-# The EXTRA_PACKAGES tag can be to specify one or more names of LaTeX
+# 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 =
+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
+# 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 =
+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!
-# 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
+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.
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, pdflatex will be used instead of
+# plain latex in the generated Makefile. Set this option to YES to get a
# higher quality PDF documentation.
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.
+# 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.
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.)
+# 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.
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
+# 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
+# The LATEX_BIB_STYLE tag can be used to specify the style to use for the
+# bibliography, e.g. plainnat, or ieeetr. The default style is "plain". See
+# http://en.wikipedia.org/wiki/BibTeX for more info.
+
+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 very pretty with
+# 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.
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
+# 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.
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
+# 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.
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.
+# 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.
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
+# Load style sheet 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 =
+RTF_STYLESHEET_FILE =
-# Set optional variables used in the generation of an rtf document.
+# Set optional variables used in the generation of an rtf document.
# Syntax is similar to doxygen's config file.
-RTF_EXTENSIONS_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
+# If the GENERATE_MAN tag is set to YES (the default) Doxygen will
# generate man pages
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
+# 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.
MAN_OUTPUT = man
-# The MAN_EXTENSION tag determines the extension that is added to
+# The MAN_EXTENSION tag determines the extension that is added to
# the generated man pages (default is the subroutine's section .3)
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
+# 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.
MAN_LINKS = NO
@@ -1291,33 +1384,33 @@ 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
+# 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.
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
+# 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.
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
+# 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 =
+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
+# 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 =
+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
+# 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.
XML_PROGRAMLISTING = YES
@@ -1326,10 +1419,10 @@ 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
+# 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.
GENERATE_AUTOGEN_DEF = NO
@@ -1338,97 +1431,97 @@ 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
+# 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.
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
+# 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.
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
+# 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.
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
+# 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 =
+PERLMOD_MAKEVAR_PREFIX =
#---------------------------------------------------------------------------
# Configuration options related to the preprocessor
#---------------------------------------------------------------------------
-# 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 (the default) Doxygen will
+# evaluate all C-preprocessor directives found in the sources and include
# 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
+# 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 = NO
-# 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
+# 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
-# in the INCLUDE_PATH (see below) will be search if a #include is found.
+# 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 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 =
+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
+# 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 =
+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
+# 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 =
+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.
+# 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 =
+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
+# 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
@@ -1437,41 +1530,37 @@ 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
+# The TAGFILES option can be used to specify one or more tagfiles. 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. 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 =
+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
+# 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
+# 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
+# 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
@@ -1480,204 +1569,222 @@ 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
+# 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
+CLASS_DIAGRAMS = NO
-# 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
+# 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 =
+MSCGEN_PATH =
-# If set to YES, the inheritance and collaboration graphs will hide
-# inheritance and usage relations if the target is undocumented
+# 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
+# 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
+# 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
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-# 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.
+# By default doxygen will use the Helvetica font for 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 DOT_FONTSIZE tag can be used to set the size of the font of dot graphs.
# The default size is 10pt.
-DOT_FONTSIZE = 24
+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.
+# By default doxygen will tell dot to use the Helvetica font.
+# If you specify a different font using DOT_FONTNAME you can use DOT_FONTPATH to
+# set the path where dot can find it.
-DOT_FONTPATH =
+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.
+# 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
+# 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
+# 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
+# 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
+# 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
+# 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
+# managable. Set this to 0 for no limit. Note that the threshold may be
+# exceeded by 50% before the limit is enforced.
+
+UML_LIMIT_NUM_FIELDS = 10
+
+# If set to YES, the inheritance and collaboration graphs will show the
# relations between templates and their instances.
TEMPLATE_RELATIONS = NO
-# 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
+# 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.
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
+# 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.
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
+# 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
+CALL_GRAPH = NO
-# 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
+# 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
+CALLER_GRAPH = NO
-# If the GRAPHICAL_HIERARCHY and HAVE_DOT tags are set to YES then doxygen
+# 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.
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
+# If the DIRECTORY_GRAPH 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.
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 png, svg, gif or svg.
-# 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. Possible values are svg, png, jpg, or gif.
+# If left blank png will be used. 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).
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. 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.
+
+INTERACTIVE_SVG = NO
+
+# The tag DOT_PATH 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 = /usr/local/bin
+DOT_PATH = /opt/local/bin
-# 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
+# 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 =
+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
+# 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 =
+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
+# 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.
-DOT_GRAPH_MAX_NODES = 3
+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.
-MAX_DOT_GRAPH_DEPTH = 7
+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
+# 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).
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)
+# 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.
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
+# 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.
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
+# 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.
DOT_CLEANUP = YES
diff --git a/HySoP/hysop/__init__.py.in b/HySoP/hysop/__init__.py.in
index dd25d5474a915edd488f75238a39c6f3049ca240..dcbbb2347440c28c2997e98c352128730c9a4e86 100755
--- a/HySoP/hysop/__init__.py.in
+++ b/HySoP/hysop/__init__.py.in
@@ -1,5 +1,5 @@
"""
-@package ParMePy
+@package parmepy
Python package dedicated to flow simulation using particular methods on hybrid architectures (MPI-GPU)
@@ -25,8 +25,8 @@ Box = domain.box.Box
## Cartesian grid
## MPI topologies and associated meshes
-import fields.topology
-CartesianTopology = fields.topology.CartesianTopology
+import domain.topology
+CartesianTopology = domain.topology.CartesianTopology
## Fields
import fields.discrete
@@ -37,10 +37,10 @@ ContinuousField = fields.continuous.ContinuousField
AnalyticalField = fields.analytical.AnalyticalField
## Operators
-import operator.Transport
-import operator.Velocity
-Transport = operator.Transport.Transport
-Velocity = operator.Velocity.Velocity
+import operator.transport
+import operator.velocity
+Transport = operator.transport.Transport
+Velocity = operator.velocity.Velocity
## Problem
import problem.problem
diff --git a/HySoP/hysop/constants.py b/HySoP/hysop/constants.py
index 434b9d86b9012fd1c4d4aae2080eac24881d0acf..891e05b580d8423d1a7ac5cbc3e6d2f9dd0656d8 100644
--- a/HySoP/hysop/constants.py
+++ b/HySoP/hysop/constants.py
@@ -1,6 +1,6 @@
-# -*- coding: utf-8 -*-
"""
@package parmepy.constants
+
Constant parameters required for the parmepy package (internal use).
"""
@@ -10,7 +10,6 @@ import math
from parmepy.particular_solvers import __path__ as solver_path
import os
-#
PI = math.pi
# Set default type for real and integer numbers
PARMES_REAL = np.float64
diff --git a/HySoP/hysop/domain/__init__.py b/HySoP/hysop/domain/__init__.py
index a698f85c8fc4f5654e3e794edf516631fd1e85b3..bf364580ec83205cc546f24797c2e9625a6946b9 100644
--- a/HySoP/hysop/domain/__init__.py
+++ b/HySoP/hysop/domain/__init__.py
@@ -1,5 +1,6 @@
"""
@package parmepy.domain
+@file parmepy/domain/__init__.py
Everything concerning physical domains, their discretizations and MPI topologies.
diff --git a/HySoP/hysop/domain/box.py b/HySoP/hysop/domain/box.py
index c2ce204a775f9d4b434126e7de26600e297fadf5..eec974a3b1e48a613062f56ee4b42fc5b10c8ab1 100644
--- a/HySoP/hysop/domain/box.py
+++ b/HySoP/hysop/domain/box.py
@@ -1,51 +1,63 @@
-# -*- coding: utf-8 -*-
+"""@package parmepy.domain.box
+
+Classes for box domains description.
+"""
from ..constants import *
from .domain import Domain
from .grid import CartesianGrid
-import numpy as np
class Box(Domain):
"""
Periodic box representation.
- Note FP : BC as parameter may be better?
-
+ @note FP : BC as parameter may be better?
+ @todo Have different BC
"""
def __init__(self, dimension=3, length=[1.0, 1.0, 1.0], origin=[0., 0., 0.]):
"""
- Constructor.
- Create a Box from a dimension, length and minimum position.
+ Create a Periodic Box from a dimension, length and origin.
Parameters dimensions must coincide. Raise ValueError in case of inconsistent parameters dimensions.
- @param length : Box length.
- @param origin : Box minimum position.
+ @par
+ By defaults, it creates a \f$[0;1]^3\f$ Box.
+
+ @param dimension : Box dimension. Default: 3
+ @param length : Box length. Default [1.0, 1.0, 1.0]
+ @param origin : Box minimum position. Default [0., 0., 0.]
"""
if not (dimension == len(length) and dimension == len(origin)):
raise ValueError("Box parameters inconsistents dimensions")
Domain.__init__(self, dimension)
- ## Box length. length = max - min.
+ ## Box length.
self.length = np.asarray(length, dtype=PARMES_REAL)
- ## Minimum Box position.
+ ## Box origin
self.origin = np.asarray(origin, dtype=PARMES_REAL)
- ## Maximum Box position.
+ ## Maximum Box position. max = origin + length
self.max = self.origin + self.length
- # Boundary conditions type :
+ ## Boundary conditions type
self.boundaries = np.zeros((self.dimension), dtype=PARMES_INTEGER)
self.boundaries[:] = PERIODIC
- self.discreteDomain = None
def discretize(self, resolution):
- """Box discretization method.
+ """
+ Box discretization method.
+ Creates a CartesianGrid from the Box and a resolution.
+
+ @param resolution : resolution of the discretization.
+ @return CartesianGrid as discretized Box.
+
Use an array for discreteDomain??? i.e to associate several discretisations for the same domain.
Or maybe this should be a member of the fields??
"""
-
self.discreteDomain = CartesianGrid(resolution, self)
return self.discreteDomain
def __str__(self):
- """ Doc display. """
+ """
+ Informations display.
+ @return Informations
+ """
s = str(self.dimension) + "D box (parallelepipedic or rectangular) domain : \n"
s += " origin : " + str(self.origin) + ", maxPosition :" + str(self.max) + ", lengthes :" + str(self.length) + "."
if self.discreteDomain is not None:
diff --git a/HySoP/hysop/domain/discrete.py b/HySoP/hysop/domain/discrete.py
index e568f75bb2c98c6247af6ca3839bb53aeb190899..cf9443864d8c1335d9ca8f87ad9e6899bb41c694 100644
--- a/HySoP/hysop/domain/discrete.py
+++ b/HySoP/hysop/domain/discrete.py
@@ -1,32 +1,27 @@
-# -*- coding: utf-8 -*-
-"""
-@package parmepy.domain.discrete
-
-Physical domain discretization
+"""@package parmepy.domain.discrete
+Classes for physical domains discretization description.
"""
from abc import ABCMeta, abstractmethod
class DiscreteDomain:
- """ Abstract description of a discretized physical domain. """
+ """ Abstract description of a discretized physical domain."""
__metaclass__ = ABCMeta
@abstractmethod
def __init__(self, domain=None):
"""
- Constructor.
Create a DiscreteDomain with a given discretization.
+ @param domain : Domain to discretize
"""
+ ## Domain to discretize
self.domain = domain
if(domain is not None):
+ ## Domain dimension
self.dimension = domain.dimension
- ## Discretization specifications. Discrete elements number.
- #self.elementNumber = None
- ## Discretization specifications. Discrete elements size.
- #self.elementSize = None
if __name__ == "__main__":
print __doc__
diff --git a/HySoP/hysop/domain/domain.py b/HySoP/hysop/domain/domain.py
index 2779b66d38b75caf37b7d58362dd500633020c3b..670d0fea5b872419ba2d2d5438e1295a3a2eafe3 100644
--- a/HySoP/hysop/domain/domain.py
+++ b/HySoP/hysop/domain/domain.py
@@ -1,4 +1,3 @@
-# -*- coding: utf-8 -*-
"""@package parmepy.domain.domain
Classes for physical domains description.
@@ -13,10 +12,8 @@ class Domain:
@abstractmethod
def __init__(self, dimension):
- """
-
+ """ Constructor
@param dimension integer : domain dimension.
-
"""
## Domain dimension.
self.dimension = dimension
diff --git a/HySoP/hysop/domain/grid.py b/HySoP/hysop/domain/grid.py
index 18e284859066dff8b21c43b7cd94f5e237df2103..e1bdcb5fa32320036a920439c0863f26b2f26bf2 100644
--- a/HySoP/hysop/domain/grid.py
+++ b/HySoP/hysop/domain/grid.py
@@ -1,16 +1,21 @@
-# -*- coding: utf-8 -*-
-"""
-@package parmepy.domain.grid
+"""@package parmepy.domain.grid
-Cartesian grid definition
+Cartesian grid definition.
"""
+from ..constants import *
from .discrete import DiscreteDomain
-import numpy as np
class CartesianGrid(DiscreteDomain):
- """ Discrete box representation as a cartesian grid. """
+ """ Discrete box representation as a cartesian grid."""
+
def __init__(self, resolution, domain):
+ """
+ Creates a CartesianGrid.
+
+ @param resolution : resolution used
+ @param domain : Domain to discretize
+ """
DiscreteDomain.__init__(self, domain)
assert(self.dimension == len(resolution))
## lowest point of the grid
@@ -20,24 +25,11 @@ class CartesianGrid(DiscreteDomain):
## number of points in each direction
self.resolution = resolution
## space step size
- self.step = self.length/(self.resolution-1)
- ## self.axes = [np.asarray(np.arange(self.min[i], self.max[i], self.elementSize[i]), dtype=dtype_real, order=order) for i in xrange(self.dimension)]
+ self.step = self.length / (self.resolution - 1)
def update(start):
self.start = start
- def applyConditions(self, pos, dir):
- """
- Apply periodic boundary conditions of the periodic domain.
-
- @param pos position : position to check.
- @return position inside the box boundary.
- """
- ## ------------------- NumPy Optimisation
- pos[..., dir] = np.where(pos[..., dir] >= self.max[dir], pos[..., dir] - self.max[dir] + self.min[dir], pos[..., dir])
- pos[..., dir] = np.where(pos[..., dir] < self.min[dir], pos[..., dir] + self.max[dir] - self.min[dir], pos[..., dir])
- ## -------------------
-
def __getitem__(self, index):
"""
Get iter overriding
diff --git a/HySoP/hysop/fields/topology.py b/HySoP/hysop/domain/topology.py
similarity index 95%
rename from HySoP/hysop/fields/topology.py
rename to HySoP/hysop/domain/topology.py
index d993b7197289188d102b7fcf84e1612f26bdb391..d99ece672f73396be2c2ef59027de2fc4cef3685 100644
--- a/HySoP/hysop/fields/topology.py
+++ b/HySoP/hysop/domain/topology.py
@@ -2,7 +2,6 @@
@package parmepy.domain.topology
MPI Topologies
"""
-import numpy as np
import mpi4py.MPI as MPI
from ..constants import *
@@ -65,7 +64,12 @@ class CartesianTopology(object):
localResolution[i] = nbpoints[i] + remainingPoints[i]
start = np.zeros((domain.dimension), dtype=PARMES_INTEGER)
start[:self.dim] = self.coords * nbpoints
- self.mesh = LocalMesh(self.rank, resolution=localResolution, start=start, dom_size=self.domain.length / self.resolution,dom_origin=self.domain.origin, ghosts=self.ghosts)
+ self.mesh = LocalMesh(self.rank,
+ resolution=localResolution,
+ start=start,
+ dom_size=self.domain.length / self.resolution,
+ dom_origin=self.domain.origin,
+ ghosts=self.ghosts)
def __str__(self):
""" Topology info display """
diff --git a/HySoP/hysop/fields/__init__.py b/HySoP/hysop/fields/__init__.py
index cee2ba565939f0122501e45c1c3e6e89502736f4..3ae374d3bc7dc977e39288ab8c6dd0930c993659 100644
--- a/HySoP/hysop/fields/__init__.py
+++ b/HySoP/hysop/fields/__init__.py
@@ -2,5 +2,4 @@
@package parmepy.fields
Everything concerning Fields.
-
"""
diff --git a/HySoP/hysop/fields/analytical.py b/HySoP/hysop/fields/analytical.py
index 2b1dcc35320caf65e03ad2b46d357a76e3d3527c..b8c04f6c8fb0d510c1ec89b3f9445e09a8e2f55b 100644
--- a/HySoP/hysop/fields/analytical.py
+++ b/HySoP/hysop/fields/analytical.py
@@ -1,7 +1,7 @@
-# -*- coding: utf-8 -*-
"""
@package parmepy.fields.analytical
+Continuous variable description defined with an analytic formula.
"""
from .continuous import ContinuousField
from .discrete import ScalarField
@@ -16,12 +16,14 @@ class AnalyticalField(ContinuousField):
def __init__(self, domain, formula, name="", vector=False):
"""
- Constructor.
Create an AnalyticalField from a formula.
- @param domain : application domain of the variable.
- @param dimension : variable dimension.
- @param formula : function defining the variable.
+ @param domain : variable application domain.
+ @param formula : python function
+ @param name : name of the variable (used for vtk output).
+ @param vector : is variable is a vector.
+
+ @note formula is used in ScalarField or VectorField as vectorized function by numpy.
"""
ContinuousField.__init__(self, domain, name, vector)
## Analytic formula.
@@ -32,7 +34,7 @@ class AnalyticalField(ContinuousField):
Evaluation of the variable at a given position.
@param pos : Position to evaluate.
- @return : value of the formula at the given position.
+ @return formula(pos): value of the formula at the given position.
"""
return self.formula(*pos)
diff --git a/HySoP/hysop/fields/continuous.py b/HySoP/hysop/fields/continuous.py
index aa088c6a2f2ef500acc87cf2a930768ab2741c92..75f0925b23815dbb9883bd00519d881a114e349b 100644
--- a/HySoP/hysop/fields/continuous.py
+++ b/HySoP/hysop/fields/continuous.py
@@ -1,6 +1,6 @@
-# -*- coding: utf-8 -*-
"""
@package parmepy.fields.continuous
+
Continuous variable description
"""
from .discrete import ScalarField
@@ -12,11 +12,11 @@ class ContinuousField(object):
def __init__(self, domain, name="?", vector=False):
"""
- Constructor.
Create a ContinuousField.
- @param domain : variable application domain.
- @param name : name of the variable (used for vtk output).
+ @param domain : variable application domain.
+ @param name : name of the variable (used for vtk output).
+ @param vector : is variable is a vector.
"""
## Application domain of the variable.
self.domain = domain
@@ -26,17 +26,18 @@ class ContinuousField(object):
self.discreteField = None
## Name of this field
self.name = name
- # number of different discretizations
+ # Number of different discretizations
self._fieldId = -1
- ## list of the various discretizations of this field
+ ## List of the various discretizations of this field
self.discreteField = []
- ## is field is a vector field
+ ## Is field is a vector field
self.vector = vector
def discretize(self, topology=None):
"""
- discretization of the field on a topology
-
+ Discretization of the field on a topology
+ @param topology : Topology definition to use
+ @return discrete field and its index
"""
self._fieldId += 1
if self.vector:
@@ -50,12 +51,17 @@ class ContinuousField(object):
return self.discreteField[self._fieldId], self._fieldId
def initialize(self):
+ """
+ Initialize a field.
+ @see VectorField.initialize
+ @see ScalarField.initialize
+ """
if self._fieldId == -1:
raise ValueError("Cannot initialise analytical field non discretized.")
print self.name,
for dF in self.discreteField:
dF.initialize()
- print "Done"
+ print " .Done"
def __str__(self):
""" Field info display """
diff --git a/HySoP/hysop/fields/discrete.py b/HySoP/hysop/fields/discrete.py
index a47e5440fe6a67d3f02ec3341be1d6e0d1071e4e..c267afaaa174db7b94f83085c0a2f2d9ba5852dd 100644
--- a/HySoP/hysop/fields/discrete.py
+++ b/HySoP/hysop/fields/discrete.py
@@ -1,7 +1,7 @@
-# -*- coding: utf-8 -*-
"""
@package parmepy.fields.discrete
+Discretes variables (scalar and vectors) descriptions.
"""
import numpy as np
from ..constants import *
@@ -15,25 +15,42 @@ class ScalarField(object):
"""
def __init__(self, parent, topology=None, name="?", idFromParent=None):
+ """
+ Creates a ScalaField.
+
+ @param parent : Continuous field.
+ @param topology : Topology informations
+ @param name : Field name
+ @param idFromParent : Index in the parent's discrete fields
+ """
if(topology is not None):
+ ## Topology informations.
self.topology = topology
else:
raise NotImplementedError()
-
+ ## Field name.
self.name = name
+ ## Field dimension.
self.dimension = topology.domain.dimension
+ ## Field resolution.
self.resolution = self.topology.mesh.resolution
- ## \todo is numpy array zeros or empty???
+ ## Field data numpy array. \todo is numpy array zeros or empty???
self.data = np.zeros((self.resolution), dtype=PARMES_REAL, order=ORDER)
+ ## Pointer to gpu data array if needed.
self.gpu_data = None
+ ## @private Continuous field
self.__parentField = parent
+ ## @private Index in parent's field discrete fields
self.__idFromParent = idFromParent
+ ## Application domain of the variable.
self.domain = self.__parentField.domain.discreteDomain
+ ## Is self.data contains data
self.contains_data = False
+ ## Scalar is not vector
self.vector = False
def __str__(self):
- """ Display class information """
+ """ Display class information. """
s = '[' + str(self.topology.rank) + '] '
s += " id " + str(self.__idFromParent) + ", "
s += self.name + " " + str(self.dimension) + 'D discrete field with resolution '
@@ -41,21 +58,36 @@ class ScalarField(object):
return s + "\n"
def __getitem__(self, i):
- """ Access to the content of the field """
+ """
+ Access to the content of the field.
+ @param i : requested index.
+ @return data[i].
+ """
return self.data.__getitem__(i)
def __setitem__(self, i, value):
"""
- Set the content of the field component at position i
- Usage :
- A = ScalarField(topo)
+ Set the content of the field component at position i.
+
+ @param i : requested index.
+ @param value : value to set.
+
+ Usage :\n
+ A = ScalarField(topo)\n
A[2,1,1] = 12.0 # Calls A.data[2,1,1] = 12.0
"""
self.data.__setitem__(i, value)
def initialize(self, formula=None):
"""
- Initialize values with given formula
+ Initialize values with given formula.
+
+ @param formula : formula to apply on coordinates.
+
+ Formula need to be vectorized by numpy. Therefore formula must have the following signature:
+ @li 3D : float formula(float x, float y, float z)
+ @li 2D : float formula(float x, float y)
+ where x,y,z are point coordinates.
"""
if formula is not None:
print "...",
@@ -73,9 +105,6 @@ class ScalarField(object):
else:
print "No formula",
- def tofile(self, filename):
- evtk.imageToVTK(filename, pointData={self.name: self.data})
-
class VectorField(object):
"""
@@ -84,21 +113,38 @@ class VectorField(object):
"""
def __init__(self, parent, topology=None, name="?", idFromParent=None):
+ """
+ Creates a VectorField.
+
+ @param parent : Continuous field.
+ @param topology : Topology informations
+ @param name : Field name
+ @param idFromParent : Index in the parent's discrete fields
+ """
if(topology is not None):
+ ## Topology informations.
self.topology = topology
else:
raise NotImplementedError()
-
+ ## Field name.
self.name = name
+ ## Field dimension.
self.dimension = topology.domain.dimension
+ ## Field resolution.
self.resolution = self.topology.mesh.resolution
- ## \todo is numpy array zeros or empty???
+ ## Field data numpy array. \todo is numpy array zeros or empty???
self.data = [np.zeros((self.resolution), dtype=PARMES_REAL, order=ORDER) for d in xrange(self.dimension)]
+ ## Pointer to gpu data arrays if needed.
self.gpu_data = [None for d in xrange(self.dimension)]
+ ## @private Continuous field
self.__parentField = parent
+ ## @private Index in parent's field discrete fields
self.__idFromParent = idFromParent
+ ## Application domain of the variable.
self.domain = self.__parentField.domain.discreteDomain
+ ## Is self.data contains data
self.contains_data = False
+ ## Scalar is not vector
self.vector = True
def __str__(self):
@@ -110,12 +156,17 @@ class VectorField(object):
return s + "\n"
def __getitem__(self, i):
- """ Access to the content of the field
- Usage (3D): A = VectorField(...), We have 3 components len(a.data) == 3.
+ """ Access to the content of the field.
+
+ @param i : requested index.
+ @return data[i] depending on i.
+
+ Usage (3D): \n
+ A = VectorField(...), We have 3 components len(a.data) == 3. \n
Following instructions access to index 2,1,1 of y component:
- A[2,1,1,1]
- A[1][2,1,1]
- Access to whole vector of index 2,1,1: A[2,1,1]
+ @li A[2,1,1,1]
+ @li A[1][2,1,1]
+ @li Access to whole vector of index 2,1,1: A[2,1,1]
"""
try:
if len(i) == len(self.data):
@@ -127,11 +178,15 @@ class VectorField(object):
def __setitem__(self, i, value):
"""
- Set the content of the vector field component at position i
- Usage :
- A = VectorField(topo)
- A[2,1,1] = 12.0 # Calls A.data[d][2,1,1] = 12.0 for all components d.
- A[2,1,1] = [12.0, 13.0, 14.0] # Calls A.data[0][2,1,1] = 12.0, A.data[1][2,1,1] = 13.0 and A.data[2][2,1,1] = 14.0
+ Set the content of the vector field component at position i.
+
+ @param i : requested index.
+ @param value : value to set.
+
+ Usage :\n
+ A = VectorField(topo)\n
+ A[2,1,1] = 12.0 # Calls A.data[d][2,1,1] = 12.0 for all components d.\n
+ A[2,1,1] = [12.0, 13.0, 14.0] # Calls A.data[0][2,1,1] = 12.0, A.data[1][2,1,1] = 13.0 and A.data[2][2,1,1] = 14.0\n
A[1][2,1,1] = 13.0 # Calls A.data[1][2,1,1] = 12.0
"""
if len(i) == len(self.data):
@@ -144,9 +199,15 @@ class VectorField(object):
def initialize(self, formula=None):
"""
- Initialize values with given formula
+ Initialize values with given formula.
+
+ @param formula : formula to apply on coordinates.
+
+ Formula need to be vectorized by numpy. Therefore formula must have the following signature:
+ @li 3D : float, float, float formula(float x, float y, float z)
+ @li 2D : float, float formula(float x, float y)
+ where x,y,z are point coordinates.
"""
- #print self.topology.mesh.coords
if formula is not None:
print "...",
v_formula = np.vectorize(formula)
@@ -163,5 +224,5 @@ class VectorField(object):
if __name__ == "__main__":
print __doc__
- print "- Provided class : ScalarField"
+ print "- Provided class : ScalarField, VectorField"
print ScalarField.__doc__
diff --git a/HySoP/hysop/operator/__init__.py b/HySoP/hysop/operator/__init__.py
index b6378e5b42d3b51a1c8a1bd69ea4401b5d394294..430a206ea3619dd4a0923cf131408ed6e1825a44 100644
--- a/HySoP/hysop/operator/__init__.py
+++ b/HySoP/hysop/operator/__init__.py
@@ -2,5 +2,4 @@
@package parmepy.operator
Everything concerning operators.
-
"""
diff --git a/HySoP/hysop/operator/continuous.py b/HySoP/hysop/operator/continuous.py
index 0375e3ec60f3f6cbcebc64273666608c55bf0f1c..f3500bb2ade1e0ebe95b6818ef3e900f6dd4a4c8 100644
--- a/HySoP/hysop/operator/continuous.py
+++ b/HySoP/hysop/operator/continuous.py
@@ -1,8 +1,7 @@
-# -*- coding: utf-8 -*-
"""
@package parmepy.operator.continuous
-Operator representation
+Operator representation.
"""
from abc import ABCMeta, abstractmethod
@@ -17,47 +16,58 @@ class ContinuousOperator:
@abstractmethod
def __init__(self):
"""
- Constructor.
Create a ContinuousOperator.
"""
## Variables
self.variables = []
## Operator discretization.
self.discreteOperator = None
+ ## Is need to split operator
+ self.needSplitting = False
def addVariable(self, cVariable):
"""
Add an continuous variables to the operator.
- Also add variables' domains to the operator.
- @param cVariable ContinuousVariable.ContinuousVariable : variables to add.
+ @param cVariable : list of variables to add.
"""
for v in cVariable:
if self.variables.count(v) == 0:
self.variables.append(v)
def apply(self, *args):
+ """
+ Apply operator.
+
+ @param *args : Operator arguments.
+ @return computing time.
+ """
return self.discreteOperator.apply(*args)
def setMethod(self, method):
+ """
+ Sets method to use in apply method.
+ @param method : the method to use.
+ """
if self.discreteOperator is not None:
self.discreteOperator.setMethod(method)
else:
raise ValueError("Cannot set mumerical method to non discretized operator")
def printComputeTime(self):
+ """Displays compute time for operator."""
if self.discreteOperator is not None:
self.discreteOperator.printComputeTime()
else:
raise ValueError("Cannot print compute time of a non discretized operator")
@abstractmethod
- def discretize(self, spec=None):
+ def discretize(self, *spec):
"""
Abstract method.
Must be implemented by sub-class.
- @param spec : discretization specifications.
+ @param *spec : discretization specifications.
"""
raise NotImplementedError("Need to override method in a subclass of " + providedClass)
diff --git a/HySoP/hysop/operator/discrete.py b/HySoP/hysop/operator/discrete.py
index 600b1833f9a140c707422c26adc08850ee0883ae..bcdeb809b9d20d29a863bd761bb7b949f9cd0cc8 100644
--- a/HySoP/hysop/operator/discrete.py
+++ b/HySoP/hysop/operator/discrete.py
@@ -1,7 +1,7 @@
-# -*- coding: utf-8 -*-
"""
-@package operator
-Discrete operator representation
+@package parmepy.operator.discrete
+
+Discrete operator representation.
"""
from abc import ABCMeta, abstractmethod
@@ -16,19 +16,22 @@ class DiscreteOperator:
@abstractmethod
def __init__(self):
"""
- Constructor.
Create an empty discrete operator.
"""
- self.input, self.output = None, None
+ ## Input variables
+ self.input = None
+ ## Output variables
+ self.output = None
## variables
self.variables = []
## Operator numerical method.
- self.numMethod = []
- self.needSplitting = False
- self.gpu_kernel = None
- self.gpu_kernel_name = ""
+ self.numMethod = None
+ ## DiscreteOperator is a discrete operator
self.discreteOperator = self
+ ## Total compute time
self.total_time = 0.
+ ## Operator name
+ self.name = "?"
def setMethod(self, method):
"""
@@ -41,9 +44,8 @@ class DiscreteOperator:
def addVariable(self, cVariable):
"""
Add an continuous variables to the operator.
- Also add variables' domains to the operator.
- @param cVariable ContinuousVariable.ContinuousVariable : variables to add.
+ @param cVariable : list of variables to add.
"""
for v in cVariable:
if self.variables.count(v) == 0:
@@ -51,9 +53,7 @@ class DiscreteOperator:
@abstractmethod
def printComputeTime(self):
- """
- Print total computing time
- """
+ """Print total computing time."""
raise NotImplementedError("Need to override method in a subclass of " + providedClass)
@abstractmethod
@@ -61,8 +61,6 @@ class DiscreteOperator:
"""
Abstract method, apply operaton on a variable.
Must be implemented by sub-class.
-
- @param point DiscreteVariable : apply operator on this point.
"""
raise NotImplementedError("Need to override method in a subclass of " + providedClass)
diff --git a/HySoP/hysop/operator/remeshing.py b/HySoP/hysop/operator/remeshing.py
index 2b84c868cd632c9f2ab57ea86a5dbd5aaf3fb44c..af65a15168c89212e1d1e030fa14cd4b9ba5c2a6 100644
--- a/HySoP/hysop/operator/remeshing.py
+++ b/HySoP/hysop/operator/remeshing.py
@@ -1,7 +1,7 @@
-# -*- coding: utf-8 -*-
"""
-@package Operator
-Operator representation
+@package parmepy.operator.remeshing
+
+Discrete remeshing representation
"""
from .discrete import DiscreteOperator
from ..constants import *
@@ -12,20 +12,16 @@ import time
class Remeshing(DiscreteOperator):
"""
Remeshing operator representation.
- DiscreteOperator.DiscreteOperator specialization.
"""
- def __init__(self, partPositions, partScalar, resscal, method):
+ def __init__(self, partPositions, partScalar, resscal, method=None):
"""
- Constructor.
- Create a Remeshing operator on a given discrete domain.
- Work with a particle field (positions, scalar, type and tag) to set scalar on a grid.
+ Create a Remeshing operator.
@param partPositions : particles positions.
@param partScalar : particles scalar.
- @param partBloc : particles bloc number.
- @param partTag : particle tag number.
- @param resscal DiscreteVariable.DiscreteVariable : new grid scalar values.
+ @param resscal : result grid scalar values.
+ @param method : the method to use.
"""
DiscreteOperator.__init__(self)
## Particles positions.
@@ -35,18 +31,25 @@ class Remeshing(DiscreteOperator):
## Result scalar
self.res_scalar = resscal
self.addVariable([self.ppos, self.pscal, self.res_scalar])
- self.numMethod = method
- ## input fields
self.input = [self.ppos, self.pscal]
- ## output fields
self.output = [self.res_scalar]
- self.needSplitting = True
+ self.method = method
+ ## Compute time detailed per directions
self.compute_time = [0., 0., 0.]
self.name = "remeshing"
def apply(self, t, dt, splittingDirection):
"""
Apply Remeshing operator.
+
+ @param t : current time.
+ @param dt : time step.
+ @param splittingDirection : Direction of splitting.
+
+ Remeshing algorithm:
+ @li 1. Remesh particles on grid
+ - Use a M'6 formula
+ @li 2. Profile timings of OpenCL kernels.
"""
c_time = 0.
if self.numMethod is not None:
@@ -58,6 +61,7 @@ class Remeshing(DiscreteOperator):
PARMES_REAL_GPU(self.res_scalar.domain.step[splittingDirection]))
for df in self.output:
df.contains_data = False
+ # Get timpings from OpenCL events
self.numMethod.queue.finish()
c_time += (evt.profile.end - evt.profile.start) * 1e-9
self.compute_time[splittingDirection] += c_time
diff --git a/HySoP/hysop/operator/splitting.py b/HySoP/hysop/operator/splitting.py
index c904e54d80a982e4ba144ac2bdee8e174bb0836f..21908dff60369348a0eaa99f8de2841aed8fe1fd 100644
--- a/HySoP/hysop/operator/splitting.py
+++ b/HySoP/hysop/operator/splitting.py
@@ -1,7 +1,7 @@
-# -*- coding: utf-8 -*-
"""
-@package Operator
-Operator representation
+@package parmepy.operator.splitting
+
+Splitting operator representation
"""
from .discrete import DiscreteOperator
import time
@@ -10,18 +10,33 @@ import time
class Splitting(DiscreteOperator):
"""
Splitting operator representation.
- DiscreteOperator.DiscreteOperator specialization.
+
+ Operator of operators applying in a Strang splitting.
+
+ Implements a 2nd order splitting in 3D:
+ @li X-dir, half time step
+ @li Y-dir, half time step
+ @li Z-dir, full time step
+ @li Y-dir, half time step
+ @li X-dir, half time step
+ \n
+ Implements a 2nd order splitting in 2D:
+ @li X-dir, half time step
+ @li Y-dir, full time step
+ @li X-dir, half time step
"""
def __init__(self, operators=[], dim=3):
"""
- Constructor.
- Create a Splittinf operator on a given discrete domain.
- Work with a particle field (positions, scalar, type and tag) to set scalar on a grid.
+ Create a Splitting operator on a given list of operators and a dimension.
+ @param operators : list of operators to split.
+ @param dim : problem dimension.
"""
DiscreteOperator.__init__(self)
+ ## Operators to split
self.operators = operators
+ ## Splitting at 2nd order.
self.splitting = []
## Half timestep in all directions
# [self.splitting.append((i, 0.5)) for i in xrange(dim)]
@@ -30,12 +45,16 @@ class Splitting(DiscreteOperator):
[self.splitting.append((i, 0.5)) for i in xrange(dim - 1)]
self.splitting.append((dim - 1, 1.))
[self.splitting.append((dim - 2 - i, 0.5)) for i in xrange(dim - 1)]
+ ## Compute time detailed per directions and per operators
self.compute_time_details = [[0. for i in xrange(dim)] for op in self.operators]
self.name = "splitting"
def apply(self, t, dt):
"""
Apply Remeshing operator.
+
+ @param t : current time.
+ @param dt : time step.
"""
c_time = 0.
for split in self.splitting:
@@ -66,5 +85,5 @@ class Splitting(DiscreteOperator):
if __name__ == "__main__":
print __doc__
- print "- Provided class : RemeshingDOp"
+ print "- Provided class : Splitting"
print RemeshingDOp.__doc__
diff --git a/HySoP/hysop/operator/Transport.py b/HySoP/hysop/operator/transport.py
similarity index 51%
rename from HySoP/hysop/operator/Transport.py
rename to HySoP/hysop/operator/transport.py
index 0490eb21b22354dd80e835deca2b45ac5e2de75f..4879d1799ccf49f4f2395705ab8abf287c25b075 100644
--- a/HySoP/hysop/operator/Transport.py
+++ b/HySoP/hysop/operator/transport.py
@@ -1,42 +1,45 @@
-# -*- coding: utf-8 -*-
"""
-@package parmepy.operator.Advection
+@package parmepy.operator.transport
-Advection operator representation
+Transport operator representation.
"""
from .continuous import ContinuousOperator
-from .advection_d import Advection_P
+from .transport_d import Transport_d
class Transport(ContinuousOperator):
"""
- Advection operator representation
+ Transport operator representation.
"""
def __init__(self, velocity, scalar):
"""
- Constructor.
- Create an Advection operator from given variables velocity and scalar.
+ Create an Transport operator from given variables velocity and scalar.
- @param velocity ContinuousField : velocity variable.
- @param scalar ContinuousField : scalar variable.
+ @param velocity : velocity variable.
+ @param scalar : scalar variable.
"""
ContinuousOperator.__init__(self)
- ## advection velocity variable
+ ## Transport velocity
self.velocity = velocity
- ## advected scalar variable
+ ## Transported scalar
self.scalar = scalar
+ self.needSplitting = True
self.addVariable([velocity, scalar])
def discretize(self, idVelocityD=0, idScalarD=0, result_position=None, result_scalar=None, method=None):
"""
- Advection operator discretization method.
- Create an AdvectionDOp.AdvectionDOp from given specifications.
-
- @param spec : discretization specifications, not used.
+ Transport operator discretization method.
+ Create an discrete Transport operator from given specifications.
+
+ @param idVelocityD : Index of velocity discretisation to use.
+ @param idScalarD : Index of scalar discretisation to use.
+ @param result_position : result position.
+ @param result_scalar : result scalar.
+ @param method : the method to use.
"""
if self.discreteOperator is None:
- self.discreteOperator = Advection_P(self, idVelocityD, idScalarD, result_position, result_scalar)
+ self.discreteOperator = Transport_d(self, idVelocityD, idScalarD, result_position, result_scalar, method)
def __str__(self):
"""ToString method"""
diff --git a/HySoP/hysop/operator/advection_d.py b/HySoP/hysop/operator/transport_d.py
similarity index 71%
rename from HySoP/hysop/operator/advection_d.py
rename to HySoP/hysop/operator/transport_d.py
index a291e6673ac05afe78e908e56a1831d7fe68364e..1ae5de69a8c7873c2df64defaf5b5a7e477b370a 100644
--- a/HySoP/hysop/operator/advection_d.py
+++ b/HySoP/hysop/operator/transport_d.py
@@ -1,28 +1,31 @@
-# -*- coding: utf-8 -*-
"""
-@package operator
-Discrete advection representation
+@package parmepy.operator.transport_d
+
+Discrete transport representation
"""
from ..constants import *
from .discrete import DiscreteOperator
import pyopencl as cl
-import numpy as np
import time
-class Advection_P(DiscreteOperator):
+class Transport_d(DiscreteOperator):
"""
- Particle avection operator representation.
- DiscreteOperator.DiscreteOperator specialization.
+ Particle transport operator representation.
+
"""
def __init__(self, advec, idVelocityD=0, idScalarD=0, result_position=None, result_scalar=None, method=None):
"""
- Constructor.
- Create a Advection operator on a given continuous domain.
+ Create a Advection operator.
Work on a given scalar at a given velocity to produce scalar distribution at new positions.
- @param advec : Advection operator.
+ @param advec : Transport operator
+ @param idVelocityD : Index of velocity discretisation to use.
+ @param idScalarD : Index of scalar discretisation to use.
+ @param result_position : result position.
+ @param result_scalar : result scalar.
+ @param method : the method to use.
"""
DiscreteOperator.__init__(self)
## Velocity.
@@ -33,21 +36,37 @@ class Advection_P(DiscreteOperator):
self.res_position = result_position.discreteField[0]
## Result scalar
self.res_scalar = result_scalar.discreteField[0]
- ## input fields
self.input = [self.velocity, self.scalar]
- ## output fields
self.output = [self.res_position, self.res_scalar]
- self.numMethod = method
- self.needSplitting = True
+ self.method = method
+ ## Previous splitting direction
self.old_splitting_direction = None
+ ## Compute time detailed per directions
self.compute_time = [0., 0., 0.]
+ ## Compute time for copy detailed per directions
self.compute_time_copy = [0., 0., 0.]
+ ## Compute time for transposition detailed per directions
self.compute_time_transpose = [0., 0., 0.]
self.name = "advection"
def apply(self, t, dt, splittingDirection):
+ """
+ Apply advection operator.
+
+ @param t : current time.
+ @param dt : time step.
+ @param splittingDirection : Direction of splitting.
+
+ Advection algorithm:
+ @li 1. Particle initialization : \n
+ - by copy scalar from grid to particles if previous splitting direction equals current splitting direction.\n
+ - by transposition of scalar from grid to particle.
+ @li 2. Particle advection :\n
+ - compute particle position in splitting direction as a scalar. Performs a RK2 resolution of dx_p/dt = a_p.
+ @li 3. Profile timings of OpenCL kernels.
+ """
c_time, c_time_init = 0., 0.
- if self.numMethod is not None:
+ if self.numMethod is not None and self.init_transpose is not None and self.init_copy is not None:
# Particle init
if (self.old_splitting_direction == splittingDirection) or self.old_splitting_direction is None:
evt_init = self.init_copy.launch(self.scalar.gpu_data,
@@ -73,6 +92,7 @@ class Advection_P(DiscreteOperator):
PARMES_REAL_GPU(self.scalar.domain.step[splittingDirection]))
for df in self.output:
df.contains_data = False
+ # Get timpings from OpenCL events
self.numMethod.queue.finish()
c_time_init = (evt_init.profile.end - evt_init.profile.start) * 1e-9
c_time = (evt.profile.end - evt.profile.start) * 1e-9
@@ -97,5 +117,5 @@ class Advection_P(DiscreteOperator):
if __name__ == "__main__":
print __doc__
- print "- Provided class : AdvectionDOp"
+ print "- Provided class : Transport_d"
print AdvectionDOp.__doc__
diff --git a/HySoP/hysop/operator/Velocity.py b/HySoP/hysop/operator/velocity.py
similarity index 72%
rename from HySoP/hysop/operator/Velocity.py
rename to HySoP/hysop/operator/velocity.py
index f03384b5a64498361ef9ed57d64c65336a835d95..00e9c7e2ac314f1fe42897df56c68c0efbfe0dd1 100644
--- a/HySoP/hysop/operator/Velocity.py
+++ b/HySoP/hysop/operator/velocity.py
@@ -1,8 +1,7 @@
-# -*- coding: utf-8 -*-
"""
-@package parmepy.operator.Advection
+@package parmepy.operator.velocity
-Advection operator representation
+Velocity operator representation.
"""
from .continuous import ContinuousOperator
from .velocity_d import Velocity_P
@@ -10,16 +9,14 @@ from .velocity_d import Velocity_P
class Velocity(ContinuousOperator):
"""
- Velocity operator representation
+ Velocity operator representation.
"""
def __init__(self, velocity):
"""
- Constructor.
- Create an Advection operator from given variables velocity and scalar.
+ Create an operator for computing analyically a velocity field.
- @param velocity ContinuousField : velocity variable.
- @param scalar ContinuousField : scalar variable.
+ @param velocity : velocity variable.
"""
ContinuousOperator.__init__(self)
## velocity variable
@@ -31,10 +28,11 @@ class Velocity(ContinuousOperator):
Advection operator discretization method.
Create an AdvectionDOp.AdvectionDOp from given specifications.
- @param spec : discretization specifications, not used.
+ @param idVelocityD : Index of velocity discretisation to use.
+ @param method : the method to use.
"""
if self.discreteOperator is None:
- self.discreteOperator = Velocity_P(self, idVelocityD)
+ self.discreteOperator = Velocity_P(self, idVelocityD, method)
def __str__(self):
"""ToString method"""
diff --git a/HySoP/hysop/operator/velocity_d.py b/HySoP/hysop/operator/velocity_d.py
index 2af16d6aee2524b3b602f8fce7ea9e95bd618623..7885f55c027d95331eace964c92118d2a7132b63 100644
--- a/HySoP/hysop/operator/velocity_d.py
+++ b/HySoP/hysop/operator/velocity_d.py
@@ -1,37 +1,34 @@
-# -*- coding: utf-8 -*-
"""
-@package operator
-Discrete velocity
+@package parmepy.operator.velocity_d
+
+Velocity operator representation.
"""
from ..constants import *
from .discrete import DiscreteOperator
import pyopencl as cl
-import numpy as np
import time
class Velocity_P(DiscreteOperator):
"""
- Velocity computation
- DiscreteOperator.DiscreteOperator specialization.
+ Velocity computation from analytical expression.x
"""
- def __init__(self, advec, idVelocityD=0, method=None):
+ def __init__(self, velocity_Op, idVelocityD=0, method=None):
"""
- Constructor.
- Create a Velocity operator on a given continuous domain.
+ Create a Velocity operator.
+ @param velocity_Op : Velocity operator.
+ @param idVelocityD : Index of velocity discretisation to use.
+ @param method : the method to use.
"""
DiscreteOperator.__init__(self)
## Velocity.
- self.velocity = advec.velocity.discreteField[idVelocityD]
- ## input fields
+ self.velocity = velocity_Op.velocity.discreteField[idVelocityD]
self.input = [self.velocity]
- ## output fields
self.output = [self.velocity]
- self.numMethod = method
+ self.method = method
self.needSplitting = False
- self.old_splitting_direction = None
self.compute_time = 0.
self.name = "velocity"
diff --git a/HySoP/hysop/particular_solvers/__init__.py b/HySoP/hysop/particular_solvers/__init__.py
index 6324d880212a0d964c61e0731382bc8f4d2f37c4..8a853e394e565707c4ae5d64b74ec2542117ae39 100644
--- a/HySoP/hysop/particular_solvers/__init__.py
+++ b/HySoP/hysop/particular_solvers/__init__.py
@@ -1,5 +1,5 @@
"""
-@package parmepy.ParticularSolvers
+@package parmepy.particular_solvers
Everything concerning particle solvers.
diff --git a/HySoP/hysop/particular_solvers/basic.py b/HySoP/hysop/particular_solvers/basic.py
index 4cdb74de87f6656a00a9558ee220075c17572ce6..f1da47c3173650da477ed913bde5dc2a6280c9df 100644
--- a/HySoP/hysop/particular_solvers/basic.py
+++ b/HySoP/hysop/particular_solvers/basic.py
@@ -1,11 +1,11 @@
-# -*- coding: utf-8 -*-
"""
-@package Utils
+@package parmepy.particular_solvers.basic
+
Particular solver description.
"""
from solver import Solver
from ..fields.continuous import ContinuousField
-from ..operator.Transport import Transport
+from ..operator.transport import Transport
from ..operator.remeshing import Remeshing
from ..operator.splitting import Splitting
from ..tools.timer import Timer
@@ -15,6 +15,7 @@ from ..tools.printer import Printer
class ParticleSolver(Solver):
"""
Particular solver description.
+
Link with differents numericals methods used.
"""
def __init__(self, problem, t_end, dt,
@@ -25,11 +26,22 @@ class ParticleSolver(Solver):
timer=None,
io=None):
"""
- Constructor.
Create a solver description.
+
+ @param problem : problen that solve this solver.
+ @param t_end : Simulation final time.
+ @param dt : Simulation time step.
+ @param ODESolver : ODE solver method.
+ @param InterpolationMethod : Interpolation method.
+ @param RemeshingMethod : Remeshing method.
+ @param splittingMethod : Splitting type.
+ @param timer : Simulation time step manager.
+ @param io : Simulation io manager.
"""
Solver.__init__(self, problem)
+ ## Problem to solve
self.problem = problem
+ ## Advection operator of the problem. Advection need special treatment in particle methods.
self.advection = None
## ODE Solver method.
self.ODESolver = ODESolver
@@ -39,6 +51,7 @@ class ParticleSolver(Solver):
self.RemeshingMethod = RemeshingMethod
## Splitting Method
self.splittingMethod = splittingMethod
+ ## Is solver initialized
self.isInitialized = False
if timer is None:
self.problem.setTimer(Timer(t_end, dt))
@@ -56,9 +69,8 @@ class ParticleSolver(Solver):
def initialize(self):
"""
- Solver initialisation for a given DiscreteProblem.DiscreteProblem.
-
- @param discreteProblem : Problem to initialize.
+ Solver initialisation.
+ Initialize a particle method solver regarding the problem.
"""
self.p_position = ContinuousField(domain=self.problem.domains[0], name='ParticlePosition')
self.p_scalar = ContinuousField(domain=self.problem.domains[0], name='ParticleScalar')
@@ -85,7 +97,7 @@ class ParticleSolver(Solver):
resscal=self.advection.discreteOperator.scalar,
method=self.RemeshingMethod)
for op in self.problem.operators:
- if op.discreteOperator.needSplitting:
+ if op.needSplitting:
if op is self.advection:
index = self.problem.operators.index(op)
self.problem.operators[index] = Splitting([op, self.remeshing], dim=self.problem.topology.dim)
diff --git a/HySoP/hysop/particular_solvers/gpu.py b/HySoP/hysop/particular_solvers/gpu.py
index 80f60c296b2cc810523805d83a3e87b0273399d3..f35c66ede44fed07b778d53acf6fe499e0312bad 100644
--- a/HySoP/hysop/particular_solvers/gpu.py
+++ b/HySoP/hysop/particular_solvers/gpu.py
@@ -1,7 +1,7 @@
-# -*- coding: utf-8 -*-
"""
-@package Utils
-GPU Particular solver description.
+@package parmepy.particular_solvers.gpu
+
+Particular solver description. Computations are performed on GPU device.
"""
from ..constants import *
from basic import ParticleSolver
@@ -19,6 +19,7 @@ from ..tools.gpu_data_transfer import deviceToHost
class GPUParticleSolver(ParticleSolver):
"""
GPU Particular solver description.
+
Link with differents numericals methods used. Prepare GPU side (memory, kernels, ...)
"""
def __init__(self, problem, t_end, dt,
@@ -32,8 +33,13 @@ class GPUParticleSolver(ParticleSolver):
device_type='gpu',
src=None):
"""
- Constructor.
- Create a solver description.
+ @copydoc ParticleSolver.__init__()
+ @param platform_id : OpenCL platform id to use.
+ @param device_id : OpenCL device id to use.
+ @param device_type='gpu' : OpenCL device type to use.
+ @param src : OpenCL kernel sources given by user.
+
+ Discover OpenCL environment.
"""
ParticleSolver.__init__(self, problem, t_end, dt,
ODESolver=ODESolver,
@@ -42,10 +48,12 @@ class GPUParticleSolver(ParticleSolver):
splittingMethod=splittingMethod,
timer=timer,
io=io)
+ ## User kernel sources filename
self.user_gpu_src = src
print "=== OpenCL environment ==="
#Get platform.
try:
+ ## OpenCL platform
self.platform = cl.get_platforms()[platform_id]
except IndexError:
print " Incorrect platform_id :", platform_id, ".",
@@ -57,6 +65,7 @@ class GPUParticleSolver(ParticleSolver):
print " - Version :", self.platform.version
#Get device.
try:
+ ## OpenCL device
self.device = self.platform.get_devices(eval("cl.device_type." + device_type.upper()))[device_id]
except cl.RuntimeError as e:
print "RuntimeError:", e
@@ -71,21 +80,26 @@ class GPUParticleSolver(ParticleSolver):
print " - Global mem size :", self.device.global_mem_size / (1024 ** 3), "GB"
print "===\n"
#Creates GPU Context
+ ## OpenCL context
self.ctx = cl.Context([self.device])
#Create CommandQueue on the GPU Context
+ ## OpenCL command queue
self.queue = cl.CommandQueue(self.ctx, properties=cl.command_queue_properties.PROFILING_ENABLE)
def initialize(self):
"""
- Solver initialisation for a given DiscreteProblem.DiscreteProblem.
-
- @param discreteProblem : Problem to initialize.
+ @copydoc ParticleSolver.initialize(self)
+ Compile kernel sources. \n
+ Allocate device memory as OpenCL Buffers.\n
+ Initialize memory on device. \n
+ Link kernels ans parmepy.operators.
"""
ParticleSolver.initialize(self)
- ## kernels compilation
+ # kernels compilation
print "=== Kernel sources compiling ==="
print "Sources files (default): ", GPU_SRC
f = open(GPU_SRC, 'r')
+ ## OpenCL kernel sources
self.gpu_src = "".join(f.readlines())
f.close()
if self.user_gpu_src is not None:
@@ -102,7 +116,7 @@ class GPUParticleSolver(ParticleSolver):
f.close()
workItemNumber = int(min(64, min(self.problem.domains[0].discreteDomain.resolution)))
padding = 32
- ## Enabling optimisations regarding problem size
+ # Enabling optimisations regarding problem size
float4_enable = True
if min(self.problem.domains[0].discreteDomain.resolution) < 4 * workItemNumber:
float4_enable = False
@@ -113,12 +127,13 @@ class GPUParticleSolver(ParticleSolver):
build_options += " -D PADDING=" + str(padding)
if not float4_enable:
build_options += " -D BASIC=1"
+ ## OpenCL program
self.prg = cl.Program(self.ctx, self.gpu_src).build(build_options)
print self.prg.get_build_info(self.device, cl.program_build_info.LOG)
print self.prg.get_build_info(self.device, cl.program_build_info.OPTIONS)
print self.prg.get_build_info(self.device, cl.program_build_info.STATUS)
print "===\n"
- ## Pad the particle scalar (for transposition efficiency)
+ # Pad the particle scalar (for transposition efficiency)
if len(self.p_scalar.discreteField[0].data.shape) == 2:
new_shape = (self.p_scalar.discreteField[0].data.shape[0] + padding,
self.p_scalar.discreteField[0].data.shape[1] + padding)
@@ -128,7 +143,7 @@ class GPUParticleSolver(ParticleSolver):
self.p_scalar.discreteField[0].data.shape[1] + padding,
self.p_scalar.discreteField[0].data.shape[2] + padding)
self.p_scalar.discreteField[0].data = np.resize(self.p_scalar.discreteField[0].data, new_shape)
- ## Convert fields to simple precision floats (PARMES_REAL_GPU) and ensure order
+ # Convert fields to simple precision floats (PARMES_REAL_GPU) and ensure order
for f in self.problem.variables:
for df in f.discreteField:
if f.vector:
@@ -136,7 +151,7 @@ class GPUParticleSolver(ParticleSolver):
df.data[d] = np.asarray(df.data[d], dtype=PARMES_REAL_GPU, order='F')
else:
df.data = np.asarray(df.data, dtype=PARMES_REAL_GPU, order='F')
- ## Create OpenCL Buffers from fields
+ # Create OpenCL Buffers from fields
print "=== OpenCL Buffer allocations ==="
total_mem_used = 0
for f in self.problem.variables:
@@ -222,21 +237,24 @@ class GPUParticleSolver(ParticleSolver):
print "Total Transfers : ", data, "Bytes transfered at {0:.3f} GBytes/sec".format((data * 1e-9) / transfer_time)
if compute_time > 0.:
print "Total Computing : ", compute_time, "sec"
- ## Setting advection and remeshing kernels:
+ print "===\n"
+ # Setting advection and remeshing kernels:
+ print "=== OpenCL Kernels setting ==="
for op in self.problem.operators:
if op.discreteOperator.name == "splitting":
for sop in op.operators:
- print sop.discreteOperator.name
- sop.setMethod(KernelLauncher(eval("self.prg."+sop.discreteOperator.name),
+ print sop.discreteOperator.name,
+ sop.setMethod(KernelLauncher(eval("self.prg." + sop.discreteOperator.name),
self.queue,
global_wg,
local_wg))
else:
- print op.discreteOperator.name
- op.setMethod(KernelLauncher(eval("self.prg."+op.discreteOperator.name),
+ print op.discreteOperator.name,
+ op.setMethod(KernelLauncher(eval("self.prg." + op.discreteOperator.name),
self.queue,
global_wg,
local_wg))
+ print self.advection.discreteOperator.name,
self.advection.discreteOperator.init_copy = KernelLauncher(self.prg.advec_init_copy,
self.queue,
global_wg,
@@ -247,6 +265,7 @@ class GPUParticleSolver(ParticleSolver):
# The problem size becomes (nb, nb/16) to let workGroup deal with internal loop
# workGroup size (32,2) is rearranged in (64,1)
# Problem size (nb, nb/16) is is rearranged in (nb*2,nb/(16*2))
+ print self.advection.discreteOperator.name,
self.advection.discreteOperator.init_transpose = KernelLauncher(self.prg.advec_init_transpose_2D,
self.queue,
(2 * int(resolution[0]),
@@ -263,6 +282,7 @@ class GPUParticleSolver(ParticleSolver):
# The problem size becomes (nb, nb, nb/16) to let workGroup deal with internal loop
# workGroup size (32,1,2) is rearranged in (64,1,1)
# Problem size (nb, nb, nb) is is rearranged in (nb*2,nb,nb/(16*2))
+ print self.advection.discreteOperator.name,
self.advection.discreteOperator.init_transpose = KernelListLauncher([self.prg.advec_init_transpose_3D_01,
self.prg.advec_init_transpose_3D_02],
self.queue,
@@ -279,6 +299,7 @@ class GPUParticleSolver(ParticleSolver):
print "===\n"
def get_data_from_device(self, field):
+ """Data collect method."""
deviceToHost(self.queue, field)
def __str__(self):
@@ -294,23 +315,56 @@ if __name__ == "__main__":
class KernelListLauncher:
"""
- kernel launcher
+ OpenCL kernel list launcher.
+
+ Manage launching of OpenCL kernels as a list.
"""
def __init__(self, kernel, queue, gsize=None, lsize=None):
+ """
+ Create a kernel list launcher.
+ @param kernel : kernel list.
+ @param queue : OpenCL command queue.
+ @param gsize : OpenCL global size index.
+ @param lsize : OpenCL local size index.
+ """
+ ## OpenCL Kernel list
self.kernel = kernel
+ print [k.function_name for k in self.kernel]
+ ## OpenCL command queue
self.queue = queue
+ ## OpenCL global size index.
self.global_size = gsize
+ ## OpenCL local size index.
self.local_size = lsize
def launch(self, d, *args):
+ """
+ Launch a kernel.
+
+ @param d : kernel index in kernel list.
+ @param args : kernel arguments.
+ @return OpenCL Event
+
+ OpenCL global size and local sizes are not given in args. Class member are used.
+ """
return KernelListLauncher.launch_sizes_in_args(self, d, self.global_size[d], self.local_size[d], *args)
def launch_sizes_in_args(self, d, *args):
+ """
+ Launch a kernel.
+
+ @param d : kernel index in kernel list.
+ @param args : kernel arguments.
+ @return OpenCL Event.
+
+ Opencl global and local sizes are given in args.
+ """
#print self.kernel[d].function_name, args[0], args[1]
evt = self.kernel[d](self.queue, *args)
return evt
def function_name(self, d=None):
+ """Prints OpenCL Kernels function names informations"""
if d is not None:
return self.kernel[d].get_info(cl.kernel_info.FUNCTION_NAME)
else:
@@ -319,17 +373,46 @@ class KernelListLauncher:
class KernelLauncher(KernelListLauncher):
"""
- kernel launcher
+ OpenCL kernel launcher.
+
+ Manage launching of one OpenCL kernel as a KernelListLauncher with a list of one kernel.
"""
def __init__(self, kernel, queue, gsize, lsize):
+ """
+ Create a KernelLauncher.
+
+ @param kernel : kernel.
+ @param queue : OpenCL command queue.
+ @param gsize : OpenCL global size index.
+ @param lsize : OpenCL local size index.
+
+ Create a KernelListLauncher with a list of one kernel.
+ """
KernelListLauncher.__init__(self, [kernel], queue, [gsize], [lsize])
def launch_sizes_in_args(self, *args):
+ """
+ Launch the kernel.
+
+ @param args : kernel arguments.
+ @return OpenCL Event.
+
+ Opencl global and local sizes are given in args.
+ """
return KernelListLauncher.launch_sizes_in_args(self, 0, *args)
def launch(self, *args):
+ """
+ Launch the kernel.
+
+ @param args : kernel arguments.
+ @return OpenCL Event
+
+ OpenCL global size and local sizes are not given in args. Class member are used.
+ """
return KernelListLauncher.launch(self, 0, *args)
def function_name(self):
+ """Prints OpenCL Kernel function name informations"""
res = KernelListLauncher.function_name(self, 0)
return res
diff --git a/HySoP/hysop/particular_solvers/solver.py b/HySoP/hysop/particular_solvers/solver.py
index 0f133c266ad682e114229f961b98701c7314f4cb..1f201f19354e635914248e2343f8aa57974b43cd 100644
--- a/HySoP/hysop/particular_solvers/solver.py
+++ b/HySoP/hysop/particular_solvers/solver.py
@@ -1,7 +1,7 @@
-# -*- coding: utf-8 -*-
"""
-@package solver
-Solver interface.
+@package parmepy.particular_solvers.solver
+
+Solver class interface.
"""
from abc import ABCMeta, abstractmethod
diff --git a/HySoP/hysop/problem/problem.py b/HySoP/hysop/problem/problem.py
index 15a4284d10f106bdd5bd973184d5c0a8e623b50b..c6a0c659f9bb6dbfdbdd7d70bff16759a3193ec1 100644
--- a/HySoP/hysop/problem/problem.py
+++ b/HySoP/hysop/problem/problem.py
@@ -1,7 +1,7 @@
-# -*- coding: utf-8 -*-
"""
-@package Problem
-Problem representation
+@package parmepy.problem.problem
+
+Problem representation.
"""
from ..particular_solvers.basic import ParticleSolver
from ..particular_solvers.gpu import GPUParticleSolver
@@ -10,33 +10,62 @@ from ..particular_solvers.gpu import GPUParticleSolver
class Problem():
"""
Problem representation.
+
+ Contains several operators that apply on variables. Variables are defined on different domains.\n
+ The problem contains a solver that define how the problem is solved.\n
+ A problem is based on a topology that deploys its resolution over MPI processus.\n
+ Finally, the problem handle outputs thanks to a io object.
"""
def __init__(self, topology, operators, params=None):
"""
- Constructor.
Create a transport problem instance.
+ @param topology : underlying topology. \todo make topology transparent to user.
+ @param operators : list of operators.
+ @param params : unused.
"""
+ ## Problem domains
self.domains = []
+ ## Prolem variables
self.variables = []
+ ## Problem operators
self.operators = operators
- for op in self.operators:
- self.addVariable(op.variables)
- for v in self.variables:
- self.addDomain(v.domain)
+ ## Problem topology
self.topology = topology
+ ## Solver for problem
self.solver = None
+ ## Computes time step and manage iterations
self.timer = None
+ ## IO manager
self.io = None
+ for op in self.operators:
+ self.addVariable(op.variables)
+ for v in self.variables:
+ self.addDomain(v.domain)
def setTimer(self, t):
+ """
+ Set timer.
+ @param t : timer.
+ """
self.timer = t
def setIO(self, io):
+ """
+ Set IO.
+ @param io : io interface.
+ """
self.io = io
- def setSolver(self, t_end, dt, solver_type='basic', **kwargs):
+ def setSolver(self, t_end, dt, solver_type='gpu', **kwargs):
+ """
+ Set solver.
+ @param t_end : simulation final time.
+ @param dt : simulation time step.
+ @param solver_type : type of solver to use. Default : gpu solver.
+ @param **kwargs : dynamic dictionary of arguments specific to solver.
+ """
if solver_type == 'basic':
self.solver = ParticleSolver(self, t_end, dt, **kwargs)
elif solver_type == 'gpu':
@@ -45,10 +74,18 @@ class Problem():
raise ValueError("Unknown solver type : " + str(solver_type))
def initSolver(self):
+ """Initialize solver."""
if self.solver is not None:
self.solver.initialize()
def solve(self):
+ """
+ Solve problem.
+
+ Performs simulations iterations by calling each operators of the list until timer end.\n
+ At end of time step, call an io step.\n
+ Displays timings at simulation end.
+ """
print "\n\n Start solving ..."
if not self.solver.isInitialized:
self.initSolver()
@@ -96,9 +133,17 @@ class Problem():
self.domains.append(cDomain)
def addOperator(self, op, index=None):
- if index is None:
- if not op in self.operators:
+ """
+ Add operator to problem.
+
+ @param op : operator.
+ @param index : operator index.
+ """
+ if not op in self.operators:
+ if index is None:
self.operators.append(op)
+ else:
+ self.operators.insert(index, op)
def __str__(self):
"""ToString method"""
@@ -119,5 +164,5 @@ class Problem():
if __name__ == "__main__":
print __doc__
- print "- Provided class : ContinuousTransportProblem"
+ print "- Provided class : Problem"
print ContinuousTransportProblem.__doc__
diff --git a/HySoP/hysop/tools/gpu_data_transfer.py b/HySoP/hysop/tools/gpu_data_transfer.py
index 026015a251e7ce631d78651e9a0c4c89dfe76a49..bcb706532e9f856af7fb3b0e19153db2fd098339 100644
--- a/HySoP/hysop/tools/gpu_data_transfer.py
+++ b/HySoP/hysop/tools/gpu_data_transfer.py
@@ -1,14 +1,26 @@
-# -*- coding: utf-8 -*-
"""
-@package tools
-GPU Memory transfering methods
+@package parmepy.tools.gpu_data_transfer
+
+GPU Memory transfering methods.
"""
from ..constants import *
import pyopencl as cl
-import numpy as np
def hostToDevice(queue, discreteField):
+ """
+ Host to device method.
+
+ @param queue : OpenCL queue.
+ @param discreteField : Variable to transfer.
+
+ Performs a direct OpenCL copy from numpy arrays to OpenCL Buffers.\n
+ Arrange memory on device so that vector components are contiguous in the direction of the component.\n
+ Example : A 3D vector field F(x,y,z) is made up of 3 OpenCL Buffers Fx, Fy, Fz. The memory layout is :
+ - Fx : x-major ordering. On device, Fx[i + j*WIDTH + k*WIDTH*HEIGHT] access to Fx(i,j,k)
+ - Fy : y-major ordering. On device, Fy[i + j*WIDTH + k*WIDTH*HEIGHT] access to Fy(j,i,k)
+ - Fz : z-major ordering. On device, Fz[i + j*WIDTH + k*WIDTH*HEIGHT] access to Fz(k,i,j)
+ """
print "host->device :",
data = 0
time = 0.
@@ -36,6 +48,15 @@ def hostToDevice(queue, discreteField):
def deviceToHost(queue, discreteField):
+ """
+ Device to host method.
+
+ @param queue : OpenCL queue.
+ @param discreteField : Variable to transfer.
+
+ Performs a direct OpenCL copy from OpenCL Buffers to numpy arrays.\n
+ As memory layout is arranged on device, not only a copy is performed but also transpositions to have numpy arrays consistent to each other.
+ """
print "device->host :",
data = 0
time = 0.
diff --git a/HySoP/hysop/tools/printer.py b/HySoP/hysop/tools/printer.py
index fcde53e327274624f60c1ef9f851e454857eb0c5..fe481fa82d588ceb6d25a3c4b51fc9ec216e6e25 100644
--- a/HySoP/hysop/tools/printer.py
+++ b/HySoP/hysop/tools/printer.py
@@ -1,7 +1,7 @@
-# -*- coding: utf-8 -*-
"""
-@package Utils
-Results Printer
+@package parmepy.tools.printer
+
+Classes for handling ouputs.
"""
from ..constants import *
import evtk.hl as evtk
@@ -10,30 +10,39 @@ import time
class Printer():
"""
- Results printer.
+ Basic printer.
+
+ Performs outputs in VTK images.
"""
def __init__(self, fields=[], frequency=0, outputPrefix='./out_'):
"""
- Constructor.
- Create a results printer from a ContinuousProblem.ContinuousProblem with a given output prefix (relative path) and an output frequency.
+ Create a results printer for given fields, filename prefix (relative path) and an output frequency.
+ @param fields : Fields to output.
@param frequency : output file producing frequency.
@param outputPrefix : file name prefix, contains relative path.
- @param probem : ContinuousProblem.ContinuousProblem to print results.
"""
+ ## Printer frequency
self.freq = frequency
+ ## Filename prefix
self.outputPrefix = outputPrefix
+ ## Fields to output
self.fields = fields
+ ## Iterations counter
self.ite = 0
+ ## Method to collect data in case of distributed data
self.get_data_method = None
if self.freq != 0:
+ ## Printer core method
self.step = self._printStep
else:
self.step = self._passStep
+ ## Printing compute time
self.compute_time = 0.
def _build_vtk_dict(self):
+ """Build a dictionary from fields to VTK image."""
res = {}
for f in self.fields:
for df in f.discreteField:
@@ -51,15 +60,23 @@ class Printer():
return res
def set_get_data_method(self, method):
+ """Set data collect method."""
if callable(method):
self.get_data_method = method
else:
raise ValueError("Cannot set non callable method to get data to print. Given method : " + str(method))
def _passStep(self):
+ """A code method that do nothing."""
pass
def _printStep(self):
+ """
+ Printer core method.
+
+ Write fields data to file on necessary.\n
+ VTK images are writed. If fails, classical ascii output is performed.
+ """
t = time.time()
if (self.ite % self.freq) == 0:
print "== IO"
@@ -71,7 +88,7 @@ class Printer():
self.get_data_method(df)
filename = self.outputPrefix + "results_{0:05d}.dat".format(self.ite)
print "Print file : " + filename
- ## VTK output \TODO: Need fix in 2D, getting an IOError.
+ ## VTK output \todo: Need fix in 2D, getting an IOError.
try:
evtk.imageToVTK(filename, pointData=self._build_vtk_dict())
except IOError:
diff --git a/HySoP/hysop/tools/profiling.py b/HySoP/hysop/tools/profiling.py
index 399f5a4b7ff46452b55a4c8ee8dc9dff2bb12691..9bde5d032e550d43d20f768539194277432588dc 100644
--- a/HySoP/hysop/tools/profiling.py
+++ b/HySoP/hysop/tools/profiling.py
@@ -1,4 +1,8 @@
-# -*- coding: utf-8 -*-
+"""
+@package parmepy.tools.profiling
+
+External tool to profile parmepy problem solving.
+"""
import argparse
import cProfile
import pstats
diff --git a/HySoP/hysop/tools/timer.py b/HySoP/hysop/tools/timer.py
index 8d8c0ba9f328e73ec234f884c0381b73e083f201..d3013a3cbafdcc77b69ecdf61fa30542b2025d48 100644
--- a/HySoP/hysop/tools/timer.py
+++ b/HySoP/hysop/tools/timer.py
@@ -1,31 +1,39 @@
-# -*- coding: utf-8 -*-
"""
-@package Operator
-Operator representation
+@package parmepy.tools.timer
+
+Time steps manager.
"""
import time
class Timer:
"""
- Timer. Manage time steps
- DiscreteOperator.DiscreteOperator specialization.
+ Manage time steps and simulation end.
+
"""
def __init__(self, t_end, dt, t_init=0.):
"""
- Constructor.
+ Creates a Timer.
+ @param t_end : Simulation final time.
+ @param dt : Time step.
+ @param t_init : Simulation starting time.
"""
+ ## Simulation final time
self.t_end = t_end
+ ## Simulation time step
self.dt = dt
+ ## Simulation current time
self.t = t_init
+ ## Is simulation is terminated
self.end = False
+ ## Iteration counter
self.ite = 0
def step(self):
"""
- Apply Remeshing operator.
+ Update current time.
"""
if self.t < self.t_end:
self.ite += 1
diff --git a/HySoP/hysop/problem/DiscreteTransportProblem.py b/HySoP/hysop/unusedOrObsolet/DiscreteTransportProblem.py
similarity index 100%
rename from HySoP/hysop/problem/DiscreteTransportProblem.py
rename to HySoP/hysop/unusedOrObsolet/DiscreteTransportProblem.py
diff --git a/HySoP/hysop/particular_solvers/GPUParticularSolver.py b/HySoP/hysop/unusedOrObsolet/GPUParticularSolver.py
similarity index 100%
rename from HySoP/hysop/particular_solvers/GPUParticularSolver.py
rename to HySoP/hysop/unusedOrObsolet/GPUParticularSolver.py
diff --git a/HySoP/hysop/particular_solvers/GPUParticularSolver_GLRender.py b/HySoP/hysop/unusedOrObsolet/GPUParticularSolver_GLRender.py
similarity index 100%
rename from HySoP/hysop/particular_solvers/GPUParticularSolver_GLRender.py
rename to HySoP/hysop/unusedOrObsolet/GPUParticularSolver_GLRender.py
diff --git a/HySoP/hysop/operator/InterpolationDOp.py b/HySoP/hysop/unusedOrObsolet/InterpolationDOp.py
similarity index 100%
rename from HySoP/hysop/operator/InterpolationDOp.py
rename to HySoP/hysop/unusedOrObsolet/InterpolationDOp.py
diff --git a/HySoP/hysop/operator/TagDOp.py b/HySoP/hysop/unusedOrObsolet/TagDOp.py
similarity index 100%
rename from HySoP/hysop/operator/TagDOp.py
rename to HySoP/hysop/unusedOrObsolet/TagDOp.py
diff --git a/HySoP/hysop/operator/VelocityDOp.py b/HySoP/hysop/unusedOrObsolet/VelocityDOp.py
similarity index 100%
rename from HySoP/hysop/operator/VelocityDOp.py
rename to HySoP/hysop/unusedOrObsolet/VelocityDOp.py
diff --git a/HySoP/hysop/operator/VelocityOp.py b/HySoP/hysop/unusedOrObsolet/VelocityOp.py
similarity index 100%
rename from HySoP/hysop/operator/VelocityOp.py
rename to HySoP/hysop/unusedOrObsolet/VelocityOp.py
diff --git a/HySoP/hysop/operator/VolumeDOp.py b/HySoP/hysop/unusedOrObsolet/VolumeDOp.py
similarity index 100%
rename from HySoP/hysop/operator/VolumeDOp.py
rename to HySoP/hysop/unusedOrObsolet/VolumeDOp.py
diff --git a/HySoP/hysop/problem/continuous.py b/HySoP/hysop/unusedOrObsolet/continuous.py
similarity index 79%
rename from HySoP/hysop/problem/continuous.py
rename to HySoP/hysop/unusedOrObsolet/continuous.py
index 125e630059466064410d65ab4b40749e90da2815..9f7b5f11d2eea3097ae62d40f2a2fd464e17f94b 100644
--- a/HySoP/hysop/problem/continuous.py
+++ b/HySoP/hysop/unusedOrObsolet/continuous.py
@@ -1,7 +1,7 @@
-# -*- coding: utf-8 -*-
"""
-@package Problem
-Problem representation
+@package parmepy.problem.continuous
+
+Abstract problem representation.
"""
from abc import ABCMeta, abstractmethod
@@ -16,9 +16,9 @@ class ContinuousProblem:
@abstractmethod
def __init__(self):
"""
- Constructor.
Create an empty problem.
"""
+ print "CONTINUOUS PROBLEM"
## Operators of the problem.
self.operators = []
## Discretization of the problem.
@@ -30,9 +30,7 @@ class ContinuousProblem:
Abstract method.
Must be implemented by sub-class.
- @param dSpec list : ContinuousDomain.ContinuousDomain discretization specifications
- @param vSpec list : ContinuousVariable.ContinuousVariable discretization specifications
- @param oSpec list : ContinuousOperator.ContinuousOperator discretization specifications
+ @param spec : discretization specifications
"""
raise NotImplementedError("Need to override method in a subclass")
@@ -42,7 +40,7 @@ class ContinuousProblem:
Set solver for the discrete problem.
It must have a discrete Problem.
- @param solver : Solver.Solver to use.
+ @param solver : solver to use.
"""
if self.discreteProblem == None:
raise NotImplementedError("Cannot set solver on a non discretized problem ")
@@ -54,7 +52,7 @@ class ContinuousProblem:
Set result printer.
It must have a discrete Problem.
- @param printer : Printer.Printer to use.
+ @param printer : printer to use.
"""
if self.discreteProblem == None:
raise NotImplementedError("Cannot set printer on a non discretized problem ")
diff --git a/HySoP/hysop/problem/discrete.py b/HySoP/hysop/unusedOrObsolet/discrete.py
similarity index 93%
rename from HySoP/hysop/problem/discrete.py
rename to HySoP/hysop/unusedOrObsolet/discrete.py
index 666f3e7bee696c95748157fdda667ebfba12c4cf..6023b35c7e682262f383b20ec778e7fff8c565c9 100644
--- a/HySoP/hysop/problem/discrete.py
+++ b/HySoP/hysop/unusedOrObsolet/discrete.py
@@ -1,7 +1,7 @@
-# -*- coding: utf-8 -*-
"""
-@package Problem
-Problem representation
+@package parmepy.problem.discrete
+
+Problem representation.
"""
from ..Param import *
@@ -13,9 +13,9 @@ class DiscreteProblem:
def __init__(self):
"""
- Constructor.
Create an empty discerte problem.
"""
+ print "DISCRETE PROBLEM"
## Domains of the problem.
self.domains = []
## Variables of the problem.
@@ -33,6 +33,7 @@ class DiscreteProblem:
@param cDomain DiscreteDomain.DiscreteDomain : list of domains to add.
"""
+ print "Add domain"
for d in cDomain:
if self.domains.count(d) == 0:
self.domains.append(d)
@@ -44,6 +45,7 @@ class DiscreteProblem:
@param cVariable DiscreteVariable.DiscreteVariable : list of variables to add.
"""
+ print "add variable"
for v in cVariable:
if self.variables.count(v) == 0:
self.variables.append(v)
@@ -57,6 +59,7 @@ class DiscreteProblem:
@param cOperator DiscreteOperator.DiscreteOperator : list od operators to add.
"""
+ print "add operator"
if isinstance(cOperator, list):
for i,o in enumerate(cOperator):
if self.operators.count(o) == 0:
@@ -88,6 +91,7 @@ class DiscreteProblem:
@param solver : Solver.Solver to use.
"""
+ print "set solver"
self.solver = solver
self.solver.initialize()
@@ -97,6 +101,7 @@ class DiscreteProblem:
@param printer : Printer.Printer to use.
"""
+ print "set printer"
self.printer = printer
def solve(self, T, dt):