From fedd4f586c987eb9ebcfa824c3233e50b3dfad29 Mon Sep 17 00:00:00 2001
From: Jean-Matthieu Etancelin <jean-matthieu.etancelin@imag.fr>
Date: Thu, 5 Jul 2012 15:29:02 +0000
Subject: [PATCH] Clean field and domain. Fixing operator (begin). Fix
doxyfile.
---
HySoP/DoxyConf/parmes.doxyfile | 278 ++++++++++++------
HySoP/hysop/domain/box.py | 17 +-
HySoP/hysop/domain/discrete.py | 6 +-
HySoP/hysop/domain/domain.py | 11 +-
HySoP/hysop/domain/grid.py | 10 +-
HySoP/hysop/fields/analytical.py | 21 +-
HySoP/hysop/fields/continuous.py | 17 +-
HySoP/hysop/fields/discrete.py | 74 +++--
HySoP/hysop/fields/topology.py | 245 ++++++++-------
HySoP/hysop/operator/Advection.py | 15 +-
HySoP/hysop/operator/__init__.py | 14 +-
.../{AdvectionDOp.py => advection_d.py} | 9 +-
.../{ContinuousOperator.py => continuous.py} | 24 +-
.../{DiscreteOperator.py => discrete.py} | 26 +-
14 files changed, 431 insertions(+), 336 deletions(-)
rename HySoP/hysop/operator/{AdvectionDOp.py => advection_d.py} (97%)
rename HySoP/hysop/operator/{ContinuousOperator.py => continuous.py} (59%)
rename HySoP/hysop/operator/{DiscreteOperator.py => discrete.py} (70%)
diff --git a/HySoP/DoxyConf/parmes.doxyfile b/HySoP/DoxyConf/parmes.doxyfile
index 2220187f9..10e86296c 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
@@ -22,8 +22,9 @@
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
@@ -33,8 +34,8 @@ PROJECT_NAME = ParMePy
PROJECT_NUMBER = 1.0.0
-# Using the PROJECT_BRIEF tag one can provide an optional one line description
-# for a project that appears at the top of each page and should give viewer
+# Using the PROJECT_BRIEF tag one can provide an optional one line description
+# for a project that appears at the top of each page and should give viewer
# a quick idea about the purpose of the project. Keep the description short.
PROJECT_BRIEF = "Particular Methods simulation on hybrid architectures"
@@ -194,6 +195,13 @@ TAB_SIZE = 8
ALIASES =
+# This tag can be used to specify a number of word-keyword mappings (TCL only).
+# A mapping has the form "name=value". For example adding
+# "class=itcl::class" will allow you to use the command class in the
+# itcl::class meaning.
+
+TCL_SUBST =
+
# Set the OPTIMIZE_OUTPUT_FOR_C tag to YES if your project consists of C
# sources only. Doxygen will then generate output that is more tailored for C.
# For instance, some of the names that are used will be different. The list
@@ -232,6 +240,15 @@ OPTIMIZE_OUTPUT_VHDL = NO
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.
+
+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
@@ -276,6 +293,22 @@ DISTRIBUTE_GROUP_DOC = NO
SUBGROUPING = YES
+# When the INLINE_GROUPED_CLASSES tag is set to YES, classes, structs and
+# unions are shown inside the group in which they are included (e.g. using
+# @ingroup) instead of on a separate page (for HTML and Man pages) or
+# section (for LaTeX and RTF).
+
+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
@@ -298,10 +331,21 @@ TYPEDEF_HIDES_STRUCT = NO
# 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
+# 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
#---------------------------------------------------------------------------
@@ -318,6 +362,11 @@ EXTRACT_ALL = YES
EXTRACT_PRIVATE = YES
+# 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.
@@ -451,10 +500,10 @@ SORT_GROUP_NAMES = NO
SORT_BY_SCOPE_NAME = YES
-# If the STRICT_PROTO_MATCHING option is enabled and doxygen fails to
+# If the STRICT_PROTO_MATCHING option is enabled and doxygen fails to
# do proper type resolution of all parameters of a function it will reject a
-# match between the prototype and the implementation of a member function even
-# if there is only one candidate or it is obvious which candidate to choose
+# match between the prototype and the implementation of a member function even
+# if there is only one candidate or it is obvious which candidate to choose
# by doing a simple string match. By disabling STRICT_PROTO_MATCHING doxygen
# will still accept a match between prototype and implementation in such cases.
@@ -505,12 +554,6 @@ MAX_INITIALIZER_LINES = 39
SHOW_USED_FILES = YES
-# If the sources in your project are distributed over multiple directories
-# then setting the SHOW_DIRECTORIES tag to YES will show the directory hierarchy
-# in the documentation. The default is NO.
-
-SHOW_DIRECTORIES = YES
-
# Set the SHOW_FILES tag to NO to disable the generation of the Files page.
# This will remove the Files entry from the Quick Index and from the
# Folder Tree View (if specified). The default is YES.
@@ -535,13 +578,23 @@ 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
+# 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 =
+# 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
#---------------------------------------------------------------------------
@@ -603,8 +656,9 @@ WARN_LOGFILE =
# with spaces.
INPUT = ../src/main \
- . \
- ../src
+ ../src \
+ ../parmepy \
+ ./
# 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
@@ -630,15 +684,17 @@ FILE_PATTERNS = *.doxygen \
# should be searched for input files as well. Possible values are YES and NO.
# If left blank NO is used.
-RECURSIVE = NO
+RECURSIVE = YES
-# The EXCLUDE tag can be used to specify files and/or directories that should
+# 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.
+# 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 =
-# The EXCLUDE_SYMLINKS tag can be used select whether or not files or
+# 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.
@@ -703,7 +759,7 @@ INPUT_FILTER =
# 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
@@ -737,7 +793,7 @@ 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.
+# fragments. Normal C, C++ and Fortran comments will always remain visible.
STRIP_CODE_COMMENTS = YES
@@ -820,7 +876,14 @@ 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.
+# 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 =
@@ -835,12 +898,21 @@ HTML_FOOTER =
# 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!
+# style sheet in the HTML output directory as well, or it will be erased!
HTML_STYLESHEET =
+# The HTML_EXTRA_FILES tag can be used to specify one or more extra images or
+# other source files which should be copied to the HTML output directory. Note
+# that these files will be copied to the base HTML output directory. Use the
+# $relpath$ marker in the HTML_HEADER and/or HTML_FOOTER files to load these
+# files. In the HTML_STYLESHEET file, use the file name only. Also note that
+# the files will be copied as-is; there are no commands or markers available.
+
+HTML_EXTRA_FILES =
+
# The HTML_COLORSTYLE_HUE tag controls the color of the HTML output.
-# Doxygen will adjust the colors in the stylesheet and background images
+# 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,
@@ -870,20 +942,23 @@ HTML_COLORSTYLE_GAMMA = 124
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).
+# page has loaded.
HTML_DYNAMIC_SECTIONS = NO
+# 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).
@@ -1035,33 +1110,32 @@ GENERATE_ECLIPSEHELP = NO
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).
-# Windows users are probably better off using the HTML help feature.
+# 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
@@ -1094,7 +1168,7 @@ FORMULA_TRANSPARENT = YES
# (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
+# 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
@@ -1103,13 +1177,18 @@ USE_MATHJAX = YES
# 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.
+# 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
+# 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
@@ -1183,6 +1262,13 @@ EXTRA_PACKAGES =
LATEX_HEADER =
+# The LATEX_FOOTER tag can be used to specify a personal LaTeX footer for
+# the generated latex document. The footer should contain everything after
+# the last chapter. If it is left blank doxygen will generate a
+# standard footer. Notice: only use this tag if you know what you are doing!
+
+LATEX_FOOTER =
+
# If the PDF_HYPERLINKS tag is set to YES, the LaTeX that is generated
# is prepared for conversion to pdf (using ps2pdf). The pdf file will
# contain links (just like the HTML output) instead of page references
@@ -1216,6 +1302,12 @@ LATEX_HIDE_INDICES = NO
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
#---------------------------------------------------------------------------
@@ -1247,7 +1339,7 @@ COMPACT_RTF = NO
RTF_HYPERLINKS = NO
-# Load stylesheet definitions from file. Syntax is similar to doxygen's
+# 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.
@@ -1390,7 +1482,7 @@ MACRO_EXPANSION = NO
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.
+# pointed to by INCLUDE_PATH will be searched when a #include is found.
SEARCH_INCLUDES = YES
@@ -1420,7 +1512,7 @@ PREDEFINED =
# If the MACRO_EXPANSION and EXPAND_ONLY_PREDEF tags are set to YES then
# this tag can be used to specify a list of macro names that should be expanded.
# The macro definition that is found in the sources will be used.
-# Use the PREDEFINED tag if you want to use a different macro definition that
+# 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 =
@@ -1436,20 +1528,16 @@ 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:
+# 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. 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.
+# 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 =
@@ -1517,32 +1605,30 @@ HAVE_DOT = YES
DOT_NUM_THREADS = 0
-# By default doxygen will write a font called Helvetica to the output
-# directory and reference it in all dot files that doxygen generates.
-# When you want a differently looking font you can specify the font name
-# using DOT_FONTNAME. You need to make sure dot is able to find the font,
-# which can be done by putting it in a standard location or by setting the
-# DOTFONTPATH environment variable or by setting DOT_FONTPATH to the directory
-# containing the font.
+# 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 default size is 10pt.
-DOT_FONTSIZE = 24
+DOT_FONTSIZE = 11
-# 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 =
# If the CLASS_GRAPH and HAVE_DOT tags are set to YES then doxygen
# will generate a graph for each documented class showing the direct and
# indirect inheritance relations. Setting this tag to YES will force the
-# the CLASS_DIAGRAMS tag to NO.
+# CLASS_DIAGRAMS tag to NO.
CLASS_GRAPH = YES
@@ -1564,6 +1650,15 @@ GROUP_GRAPHS = YES
UML_LOOK = YES
+# If the UML_LOOK tag is enabled, the fields and methods are shown inside
+# the class node. If there are many fields or methods and many nodes the
+# graph may become too big to be useful. The UML_LIMIT_NUM_FIELDS
+# threshold limits the number of items for each type to make the size more
+# 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 = 0
+
# If set to YES, the inheritance and collaboration graphs will show the
# relations between templates and their instances.
@@ -1604,7 +1699,7 @@ CALLER_GRAPH = YES
GRAPHICAL_HIERARCHY = YES
-# If the DIRECTORY_GRAPH, SHOW_DIRECTORIES and HAVE_DOT tags are set to YES
+# 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.
@@ -1612,15 +1707,26 @@ GRAPHICAL_HIERARCHY = YES
DIRECTORY_GRAPH = YES
# The DOT_IMAGE_FORMAT tag can be used to set the image format of the images
-# generated by dot. Possible values are png, svg, gif or svg.
-# If left blank png will be used.
+# 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
+# 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
diff --git a/HySoP/hysop/domain/box.py b/HySoP/hysop/domain/box.py
index 530801155..6ba485a0d 100644
--- a/HySoP/hysop/domain/box.py
+++ b/HySoP/hysop/domain/box.py
@@ -4,14 +4,15 @@ 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?
+
"""
- def __init__(self,dimension=3,length=[1.0,1.0,1.0], origin=[0.,0.,0.]):
+ 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.
@@ -33,21 +34,21 @@ class Box(Domain):
self.boundaries = np.zeros((self.dimension))
self.boundaries[:] = PERIODIC
- def discretize(self,resolution):
+ def discretize(self, resolution):
"""Box discretization method.
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)
+ self.discreteDomain = CartesianGrid(resolution, self)
return self.discreteDomain
def __str__(self):
""" Doc display. """
- s = str(self.dimension)+"D box (parallelepipedic or rectangular) domain : \n"
- s += " origin : "+str(self.origin)+", maxPosition :"+str(self.max)+", lengthes :"+str(self.length)+"."
+ s = str(self.dimension) + "D box (parallelepipedic or rectangular) domain : \n"
+ s += " origin : " + str(self.origin) + ", maxPosition :" + str(self.max) + ", lengthes :" + str(self.length) + "."
return s
-
+
if __name__ == "__main__":
print __doc__
print "- Provided class : Box."
diff --git a/HySoP/hysop/domain/discrete.py b/HySoP/hysop/domain/discrete.py
index 05769bb84..e568f75bb 100644
--- a/HySoP/hysop/domain/discrete.py
+++ b/HySoP/hysop/domain/discrete.py
@@ -5,16 +5,16 @@
Physical domain discretization
"""
+from abc import ABCMeta, abstractmethod
-from abc import ABCMeta,abstractmethod
class DiscreteDomain:
""" Abstract description of a discretized physical domain. """
- __metaclass__=ABCMeta
+ __metaclass__ = ABCMeta
@abstractmethod
- def __init__(self,domain=None):
+ def __init__(self, domain=None):
"""
Constructor.
Create a DiscreteDomain with a given discretization.
diff --git a/HySoP/hysop/domain/domain.py b/HySoP/hysop/domain/domain.py
index 15935e370..2779b66d3 100644
--- a/HySoP/hysop/domain/domain.py
+++ b/HySoP/hysop/domain/domain.py
@@ -1,19 +1,20 @@
# -*- coding: utf-8 -*-
"""@package parmepy.domain.domain
-Classes for physical domains description. """
+Classes for physical domains description.
+"""
+from abc import ABCMeta, abstractmethod
-from abc import ABCMeta,abstractmethod
class Domain:
"""Abstract description of physical domain. """
- __metaclass__=ABCMeta
+ __metaclass__ = ABCMeta
@abstractmethod
def __init__(self, dimension):
"""
-
+
@param dimension integer : domain dimension.
"""
@@ -23,7 +24,7 @@ class Domain:
self.discreteDomain = None
@abstractmethod
- def discretize(self,resolution=None):
+ def discretize(self, resolution=None):
"""
@param resolution : discretization specifications.
"""
diff --git a/HySoP/hysop/domain/grid.py b/HySoP/hysop/domain/grid.py
index c6507a9ad..fe13e3149 100644
--- a/HySoP/hysop/domain/grid.py
+++ b/HySoP/hysop/domain/grid.py
@@ -7,12 +7,12 @@ Cartesian grid definition
from .discrete import DiscreteDomain
import numpy as np
+
class CartesianGrid(DiscreteDomain):
""" Discrete box representation as a cartesian grid. """
-
- def __init__(self,resolution,domain):
- DiscreteDomain.__init__(self,domain)
- assert(self.dimension==len(resolution))
+ def __init__(self, resolution, domain):
+ DiscreteDomain.__init__(self, domain)
+ assert(self.dimension == len(resolution))
self.origin = domain.origin
self.length = domain.length
self.resolution = resolution
@@ -51,7 +51,7 @@ class CartesianGrid(DiscreteDomain):
"""
ToString method.
"""
- s = str(self.dimension)+"D cartesian grid with resolution equal to : "+str(self.resolution)+".\n"
+ s = str(self.dimension) + "D cartesian grid with resolution equal to : " + str(self.resolution) + ".\n"
return s
if __name__ == "__main__":
diff --git a/HySoP/hysop/fields/analytical.py b/HySoP/hysop/fields/analytical.py
index a77eb886b..7e6451064 100644
--- a/HySoP/hysop/fields/analytical.py
+++ b/HySoP/hysop/fields/analytical.py
@@ -6,13 +6,14 @@
from .continuous import ContinuousField
from .discrete import DiscreteField
+
class AnalyticalField(ContinuousField):
"""
A variable (continuous) defined with an analytic formula.
"""
- def __init__(self, dimension, domain, formula=None, scalar=False, name=""):
+ def __init__(self, domain, name="", formula=None):
"""
Constructor.
Create an AnalyticalField from a formula.
@@ -21,22 +22,20 @@ class AnalyticalField(ContinuousField):
@param dimension : variable dimension.
@param formula : function defining the variable.
"""
- ContinuousField.__init__(self, dimension, domain)
+ ContinuousField.__init__(self, domain, name)
## Analytic formula.
self.formula = formula
- ## Is scalar variable
- self.scalar = scalar
- self.name = name
- def discretize(self, d_spec=None):
+ def discretize(self, topology=None):
"""
AnalyticalField discretization method.
- Create an DiscreteField.DiscreteField from given specifications.
-
- @param d_spec : discretization specifications, not used.
+ Create an DiscreteField from given topology.
"""
- if self.discreteField is None:
- self.discreteField = DiscreteField(domain=self.domain.discreteDomain, dimension=self.dimension, initialValue=self.formula, scalar=self.scalar, spec=d_spec, name=self.name)
+ self.__fieldId += 1
+ self.discreteField.append(ScalarField(self, topology, name=self.name + "_D_" + str(self.__fieldId),
+ idFromParent=self.__fieldId))
+ self.discreteField[self.__fieldId].initialize(self.formula)
+ return self.discreteField[self.__fieldId], self.__fieldId
def value(self, pos):
"""
diff --git a/HySoP/hysop/fields/continuous.py b/HySoP/hysop/fields/continuous.py
index c7557d358..09d8b5909 100644
--- a/HySoP/hysop/fields/continuous.py
+++ b/HySoP/hysop/fields/continuous.py
@@ -3,13 +3,13 @@
@package parmepy.fields.continuous
Continuous variable description
"""
-
from .discrete import ScalarField
+
class ContinuousField(object):
""" A variable defined on a physical domain """
- def __init__(self,domain,name="?"):
+ def __init__(self, domain, name="?"):
"""
Constructor.
Create a ContinuousField.
@@ -30,23 +30,24 @@ class ContinuousField(object):
## list of the various discretizations of this field
self.discreteField = []
- def discretize(self,topology=None):
+ def discretize(self, topology=None):
"""
discretization of the field on a topology
"""
self.__fieldId += 1
- self.discreteField.append(ScalarField(self,topology,name=self.name+"_D_"+str(self.__fieldId),idFromParent=self.__fieldId))
- return self.discreteField[self.__fieldId],self.__fieldId
+ self.discreteField.append(ScalarField(self, topology, name=self.name + "_D_" + str(self.__fieldId),
+ idFromParent=self.__fieldId))
+ return self.discreteField[self.__fieldId], self.__fieldId
def __str__(self):
""" Field info display """
- s = self.name + ' , ' + str(self.dimension)+'D field with the following discretizations:\n'
+ s = self.name + ' , ' + str(self.dimension) + 'D field with the following discretizations:\n'
if len(self.discreteField) != 0:
for i in range(len(self.discreteField)):
s += self.discreteField[i].__str__()
- else :
- s+="None."
+ else:
+ s += "None."
return s
diff --git a/HySoP/hysop/fields/discrete.py b/HySoP/hysop/fields/discrete.py
index 9ffe7aec6..408351a5e 100644
--- a/HySoP/hysop/fields/discrete.py
+++ b/HySoP/hysop/fields/discrete.py
@@ -3,52 +3,58 @@
@package parmepy.fields.discrete
"""
-
import numpy as np
from ..constants import *
import evtk.hl as evtk
+
class ScalarField(object):
"""
A scalar field, defined on each grid of each subdomain of the given topology.
-
+
"""
- def __init__(self,parent,topology=None,name="?",idFromParent=None):
+ def __init__(self, parent, topology=None, name="?", idFromParent=None):
if(topology is not None):
self.topology = topology
- else :
+ else:
raise NotImplementedError()
-
+
self.name = name
self.dimension = topology.domain.dimension
resolution = self.topology.mesh.resolution
- # zeros or empty???
- self.data = np.zeros((resolution),dtype=PARMES_REAL,order=ORDER)
- self.__parentField=parent
+ ## \todo is numpy array zeros or empty???
+ self.data = np.zeros((resolution), dtype=PARMES_REAL, order=ORDER)
+ self.__parentField = parent
self.__idFromParent = idFromParent
-
+
def __str__(self):
""" Display class information """
- s = '['+str(self.topology.rank)+'] '
- s += " id "+ str(self.__idFromParent)+", "
- s+= self.name+" "+str(self.dimension)+'D discrete field with resolution '
- s += str(self.data.shape)+"."
+ s = '[' + str(self.topology.rank) + '] '
+ s += " id " + str(self.__idFromParent) + ", "
+ s += self.name + " " + str(self.dimension) + 'D discrete field with resolution '
+ s += str(self.data.shape) + "."
return s + "\n"
- def __getitem__(self,i):
+ def __getitem__(self, i):
""" Access to the content of the field """
return self.data.__getitem__(i)
- def __setitem__(self,i,value):
+ def __setitem__(self, i, value):
"""
Set the content of the field component at position i
Usage :
A = ScalarField(topo)
A[2,1,1] = 12.0 # Calls A.data[2,1,1] = 12.0
"""
- self.data.__setitem__(i,value)
-
+ self.data.__setitem__(i, value)
+
+ def initialize(self, formula=None):
+ """
+ Initialize values with given formula
+ \todo Ecrire l'initialisation efficace en python.
+ """
+ raise NotImplementedError("Not yet implemented")
## def init(self):
## if not self.initialValue is None:
@@ -69,41 +75,49 @@ class ScalarField(object):
## self.contains_data = True
## else:
## raise ValueError("Creating DiscreteVariable with incorrect domain dimension.")
-
- def tofile(self,filename):
- evtk.imageToVTK(filename, pointData = {"scalar" : self.data} )
+
+ def tofile(self, filename):
+ evtk.imageToVTK(filename, pointData={"scalar": self.data})
+
class VectorField(object):
"""
A vector field, defined on each grid of each subdomain of the given topology.
-
+
"""
-
- def __init__(self,topology,name=""):
+
+ def __init__(self, topology, name=""):
self.topology = topology
self.name = name
self.dimension = topology.domain.dimension
resolution = self.topology.mesh.resolution
- self.data = np.zeros((resolution),dtype=PARMES_REAL)
-
+ self.data = np.zeros((resolution), dtype=PARMES_REAL, order=ORDER)
+
def __str__(self):
""" Display class information """
- s = self.name+": "+str(self.dimension)+"D scalar field of shape " + str(self.data.shape)
+ s = self.name + ": " + str(self.dimension) + "D scalar field of shape " + str(self.data.shape)
return s + "\n"
- def __getitem__(self,i):
+ def __getitem__(self, i):
""" Access to the content of the field """
return self.data.__getitem__(i)
- def __setitem__(self,i,value):
+ def __setitem__(self, i, value):
"""
Set the content of the field component at position i
Usage :
A = ScalarField(topo)
A[2,1,1] = 12.0 # Calls A.data[2,1,1] = 12.0
"""
- self.data.__setitem__(i,value)
-
+ self.data.__setitem__(i, value)
+
+ def initialize(self, formula):
+ """
+ Initialize values with given formula
+ \todo Ecrire l'initialisation efficace en python.
+ """
+ raise NotImplementedError("Not yet implemented")
+
if __name__ == "__main__":
print __doc__
print "- Provided class : ScalarField"
diff --git a/HySoP/hysop/fields/topology.py b/HySoP/hysop/fields/topology.py
index 70f6ad4ca..0b74994e2 100644
--- a/HySoP/hysop/fields/topology.py
+++ b/HySoP/hysop/fields/topology.py
@@ -1,143 +1,142 @@
"""
@package parmepy.domain.topology
-MPI Topologies
+MPI Topologies
"""
import numpy as np
import mpi4py.MPI as MPI
from ..constants import *
+
class CartesianTopology(object):
- """
+ """
+ Define an MPI cartesian topology with an associated mesh for each sub-domain.
+ Keyword arguments :
+ - domain : the geometry; it must be a box.
+ - resolution : global resolution
+ - dim : dimension of the topology
+ - comm : MPI communicator used to create this topology
+ - periods : periodicity of the topology (in each direction)
+ - ghosts : number of poinst in the ghost layer
- Define an MPI cartesian topology with an associated mesh for each sub-domain.
- Keyword arguments :
- - domain : the geometry; it must be a box.
- - resolution : global resolution
- - dim : dimension of the topology
- - comm : MPI communicator used to create this topology
- - periods : periodicity of the topology (in each direction)
- - ghosts : number of poinst in the ghost layer
+ """
+ def __init__(self, domain, resolution, dim=None, dims=None, comm=MPI.COMM_WORLD, periods=None, ghosts=None):
+ ## Associated domain
+ self.domain = domain
+ # Compute the "optimal" processus distribution for each direction of the grid topology
+ nbprocs = comm.Get_size()
+ if(dims is None):
+ assert(dim is not None)
+ self.dims = np.asarray(MPI.Compute_dims(nbprocs, dim))
+ # Topology dimension
+ self.dim = dim
+ else:
+ self.dims = np.asarray(dims)
+ self.dim = self.dims.size
+ # Define the topology
+ # default period status is periodic
+ if(periods is None):
+ self.periods = self.dim * (True,)
+ self.topo = comm.Create_cart(self.dims, periods=self.periods)
- """
- def __init__(self,domain,resolution,dim=None,dims=None,comm=MPI.COMM_WORLD,periods=None,ghosts=None):
+ # Size of the topology
+ self.size = self.topo.Get_size()
+ # Rank of the current process, in the new topology
+ self.rank = self.topo.Get_rank()
+ # Coordinates of the current process
+ self.coords = self.topo.Get_coords(self.rank)
+ # Neighbours
+ # self.neighbours = np.zeros((dim,2))
+ self.down, self.up = self.topo.Shift(XDIR, 1)
+ if(self.dim > 1):
+ self.west, self.east = self.topo.Shift(YDIR, 1)
+ if(self.dim > 2):
+ self.south, self.north = self.topo.Shift(ZDIR, 1)
+ # ghost layer (default = 0)
+ if(ghosts is None):
+ self.ghosts = np.zeros((self.domain.dimension))
+ # Global resolution
+ self.resolution = np.asarray(resolution)
+ nbpoints = self.resolution[:self.dim] // self.dims
+ remainingPoints = self.resolution[:self.dim] % self.dims
+ localResolution = self.resolution.copy()
+ localResolution[:self.dim] = nbpoints
+ for i in range(self.dim):
+ if(self.coords[i] == self.dims[i] - 1):
+ localResolution[i] = nbpoints[i] + remainingPoints[i]
+ start = np.zeros((domain.dimension))
+ start[:self.dim] = self.coords * nbpoints
+ self.mesh = LocalMesh(self.rank, resolution=localResolution, start=start, ghosts=self.ghosts)
- ## Associated domain
- self.domain=domain
- # Compute the "optimal" processus distribution for each direction of the grid topology
- nbprocs = comm.Get_size()
- if(dims is None):
- assert(dim is not None)
- self.dims=np.asarray(MPI.Compute_dims(nbprocs,dim))
- # Topology dimension
- self.dim=dim
- else:
- self.dims=np.asarray(dims)
- self.dim = self.dims.size
- # Define the topology
- # default period status is periodic
- if(periods is None):
- self.periods = self.dim*(True,)
- self.topo = comm.Create_cart(self.dims,periods=self.periods)
+ def __str__(self):
+ """ Topology info display """
+ s = '=======================================================\n'
+ if(self.rank == 0):
+ s += str(self.dim) + 'D cartesian Topology of size ' + str(self.dims) + '\n'
+ s += str(self.mesh)
+ s += '=======================================================\n'
+ return s
- # Size of the topology
- self.size = self.topo.Get_size()
- # Rank of the current process, in the new topology
- self.rank = self.topo.Get_rank()
- # Coordinates of the current process
- self.coords = self.topo.Get_coords(self.rank)
- # Neighbours
- # self.neighbours = np.zeros((dim,2))
- self.down,self.up=self.topo.Shift(XDIR,1)
- if(self.dim>1) :
- self.west,self.east=self.topo.Shift(YDIR,1)
- if(self.dim>2) :
- self.south,self.north=self.topo.Shift(ZDIR,1)
- # ghost layer (default = 0)
- if(ghosts is None):
- self.ghosts = np.zeros((self.domain.dimension))
- # Global resolution
- self.resolution = np.asarray(resolution)
- nbpoints = self.resolution[:self.dim]//self.dims
- remainingPoints = self.resolution[:self.dim]%self.dims
- localResolution = self.resolution.copy()
- localResolution[:self.dim] = nbpoints
- for i in range(self.dim):
- if(self.coords[i] == self.dims[i]-1):
- localResolution[i] = nbpoints[i]+remainingPoints[i]
- start = np.zeros((domain.dimension))
- start[:self.dim]=self.coords*nbpoints
- self.mesh = LocalMesh(self.rank,resolution=localResolution,start=start,ghosts=self.ghosts)
-
- def __str__(self):
- """ Topology info display """
- s ='=======================================================\n'
- if(self.rank==0):
- s += str(self.dim)+'D cartesian Topology of size '+str(self.dims)+'\n'
- s += str(self.mesh)
- s +='=======================================================\n'
- return s
class FFTTopology(object):
- """ A 2D or 3D MPI cartesian topology
-
- """
-
- def __init__(self, dim=2,comm=MPI.COMM_WORLD,nbprocs=MPI.COMM_WORLD.Get_size(),periods=3*(True,),dims=(1,1,1)):
+ """
+ A 2D or 3D MPI cartesian topology
+ """
- # Topology dimension
- self.dim=dim
- # Compute the "optimal" processus distribution for each direction of the grid topology
- dims=MPI.Compute_dims(nbprocs,dim)
- self.dims=np.ones((dim+1))
- self.dims[0:dim] = np.asarray(dims)
- # Define the topology
- self.topo = comm.Create_cart(self.dims,periods=periods[0:dim+1])
- # Size of the topology
- sizeT = self.topo.Get_size()
- # Rank of the current process
- self.rank = self.topo.Get_rank()
- # Coordinates of the current process
- self.coords = self.topo.Get_coords(self.rank)
- # Neighbours
- # self.neighbours = np.zeros((dim,2))
- self.down,self.up=self.topo.Shift(XDIR,1)
- if(dim>1) :
- self.west,self.east=self.topo.Shift(YDIR,1)
- if(dim>2) :
- self.south,self.north=self.topo.Shift(ZDIR,1)
+ def __init__(self, dim=2, comm=MPI.COMM_WORLD, nbprocs=MPI.COMM_WORLD.Get_size(), periods=3 * (True,), dims=(1, 1, 1)):
+ # Topology dimension
+ self.dim = dim
+ # Compute the "optimal" processus distribution for each direction of the grid topology
+ dims = MPI.Compute_dims(nbprocs, dim)
+ self.dims = np.ones((dim + 1))
+ self.dims[0:dim] = np.asarray(dims)
+ # Define the topology
+ self.topo = comm.Create_cart(self.dims, periods=periods[0:dim + 1])
+ # Size of the topology
+ sizeT = self.topo.Get_size()
+ # Rank of the current process
+ self.rank = self.topo.Get_rank()
+ # Coordinates of the current process
+ self.coords = self.topo.Get_coords(self.rank)
+ # Neighbours
+ # self.neighbours = np.zeros((dim,2))
+ self.down, self.up = self.topo.Shift(XDIR, 1)
+ if(dim > 1):
+ self.west, self.east = self.topo.Shift(YDIR, 1)
+ if(dim > 2):
+ self.south, self.north = self.topo.Shift(ZDIR, 1)
+
+ def __str__(self):
+ """ Topology info display """
+ s = '======================================================='
+ s += str(self.dim) + 'D FFT Topology of size ' + str(self.dims)
+ s += self.mesh.__str__
+ s += '======================================================='
+ return s
- def __str__(self):
- """ Topology info display """
- s ='======================================================='
- s += str(self.dim)+'D FFT Topology of size '+str(self.dims)
- s+=self.mesh.__str__
- s+='======================================================='
- return s
class LocalMesh(object):
- """
- """
+ """
+ """
+ def __init__(self, rank, resolution, start, ghosts=np.zeros((3))):
+ # Current process rank in the topology that owns this mesh
+ self.rank = rank
+ # Local resolution
+ self.resolution = resolution.copy() + 2 * ghosts
+ # index of the lower point (in each dir) in the global mesh
+ self.start = start
+ # index of the upper point (in each dir), global mesh
+ self.end = self.start + self.resolution - 1
+ # Mesh step size
+
+ def __str__(self):
+ """ Local mesh display """
+ s = '[' + str(self.rank) + '] Local mesh resolution :' + str(self.resolution) + '\n'
+ s += 'Global indices :' + str(self.start) + '\n'
+ return s
- def __init__(self,rank,resolution,start,ghosts=np.zeros((3))) :
- # Current process rank in the topology that owns this mesh
- self.rank = rank
- # Local resolution
- self.resolution = resolution.copy()+2*ghosts
- # index of the lower point (in each dir) in the global mesh
- self.start = start
- # index of the upper point (in each dir), global mesh
- self.end = self.start + self.resolution - 1
- # Mesh step size
- def __str__(self):
- """ Local mesh display """
- s = '['+str(self.rank)+'] Local mesh resolution :'+str(self.resolution)+'\n'
- s+= 'Global indices :'+str(self.start)+'\n'
- return s
-
-
-if __name__ == "__main__" :
- print "This module defines the following classes:"
- print "- CartesianTopology: ", CartesianTopology.__doc__
- print "- FFTTopology: ", FFTTopology.__doc__
- print "- LocalMesh: ", LocalMesh.__doc__
+if __name__ == "__main__":
+ print "This module defines the following classes:"
+ print "- CartesianTopology: ", CartesianTopology.__doc__
+ print "- FFTTopology: ", FFTTopology.__doc__
+ print "- LocalMesh: ", LocalMesh.__doc__
diff --git a/HySoP/hysop/operator/Advection.py b/HySoP/hysop/operator/Advection.py
index 1649f1016..144b51902 100644
--- a/HySoP/hysop/operator/Advection.py
+++ b/HySoP/hysop/operator/Advection.py
@@ -1,11 +1,11 @@
# -*- coding: utf-8 -*-
"""
-@package Operator
-Operator representation
+@package parmepy.operator.Advection
+
+Advection operator representation
"""
-from ..Param import *
-from ContinuousOperator import ContinuousOperator
-from AdvectionDOp import AdvectionDOp
+from .continuous import ContinuousOperator
+from .advection_d import AdvectionDOp
class Advection(ContinuousOperator):
@@ -18,15 +18,14 @@ class Advection(ContinuousOperator):
Constructor.
Create an Advection operator from given variables velocity and scalar.
- @param velocity ContinuousVariable.ContinuousVariable : velocity variable.
- @param scalar ContinuousVariable.ContinuousVariable : scalar variable.
+ @param velocity ContinuousField : velocity variable.
+ @param scalar ContinuousField : scalar variable.
"""
ContinuousOperator.__init__(self)
## advection velocity variable
self.velocity = velocity
## advected scalar variable
self.scalar = scalar
- self.addVariable([self.velocity, self.scalar])
def discretize(self, spec=None):
"""
diff --git a/HySoP/hysop/operator/__init__.py b/HySoP/hysop/operator/__init__.py
index f1513ea05..b6378e5b4 100644
--- a/HySoP/hysop/operator/__init__.py
+++ b/HySoP/hysop/operator/__init__.py
@@ -1,8 +1,6 @@
-from ContinuousOperator import ContinuousOperator
-from Advection import Advection
-from DiscreteOperator import DiscreteOperator
-from AdvectionDOp import AdvectionDOp
-from InterpolationDOp import InterpolationDOp
-from RemeshingDOp import RemeshingDOp
-from TagDOp import TagDOp
-from VelocityOp import VelocityOp
+"""
+@package parmepy.operator
+
+Everything concerning operators.
+
+"""
diff --git a/HySoP/hysop/operator/AdvectionDOp.py b/HySoP/hysop/operator/advection_d.py
similarity index 97%
rename from HySoP/hysop/operator/AdvectionDOp.py
rename to HySoP/hysop/operator/advection_d.py
index c13f0d61c..8aaab8ea2 100644
--- a/HySoP/hysop/operator/AdvectionDOp.py
+++ b/HySoP/hysop/operator/advection_d.py
@@ -1,15 +1,12 @@
# -*- coding: utf-8 -*-
"""
-@package Operator
-Operator representation
+@package operator
+Discrete advection representation
"""
-from ..Param import *
-from DiscreteOperator import DiscreteOperator
+from .discrete import DiscreteOperator
import pyopencl as cl
import time
-providedClass = "AdvectionDOp"
-
class AdvectionDOp(DiscreteOperator):
"""
diff --git a/HySoP/hysop/operator/ContinuousOperator.py b/HySoP/hysop/operator/continuous.py
similarity index 59%
rename from HySoP/hysop/operator/ContinuousOperator.py
rename to HySoP/hysop/operator/continuous.py
index a5b83bda1..6241f5617 100644
--- a/HySoP/hysop/operator/ContinuousOperator.py
+++ b/HySoP/hysop/operator/continuous.py
@@ -1,9 +1,10 @@
# -*- coding: utf-8 -*-
"""
-@package Operator
+@package parmepy.operator.continuous
+
Operator representation
"""
-from ..Param import *
+from abc import ABCMeta, abstractmethod
class ContinuousOperator:
@@ -11,6 +12,9 @@ class ContinuousOperator:
Continuous operator abstract description.
"""
+ __metaclass__ = ABCMeta
+
+ @abstractmethod
def __init__(self):
"""
Constructor.
@@ -18,24 +22,10 @@ class ContinuousOperator:
"""
## Application domains of the variables.
self.domains = []
- ## Variables
- self.variables = []
## Operator discretization.
self.discreteOperator = None
- 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.
- """
- for v in cVariable:
- if self.variables.count(v) == 0:
- self.variables.append(v)
- if self.domains.count(v.domain) == 0:
- self.domains.append(v.domain)
-
+ @abstractmethod
def discretize(self, spec=None):
"""
Abstract method.
diff --git a/HySoP/hysop/operator/DiscreteOperator.py b/HySoP/hysop/operator/discrete.py
similarity index 70%
rename from HySoP/hysop/operator/DiscreteOperator.py
rename to HySoP/hysop/operator/discrete.py
index c95859de8..d816c828b 100644
--- a/HySoP/hysop/operator/DiscreteOperator.py
+++ b/HySoP/hysop/operator/discrete.py
@@ -1,9 +1,9 @@
# -*- coding: utf-8 -*-
"""
-@package Operator
-Operator representation
+@package operator
+Discrete operator representation
"""
-from ..Param import *
+from abc import ABCMeta, abstractmethod
class DiscreteOperator:
@@ -11,6 +11,9 @@ class DiscreteOperator:
Abstract description of a discretized operator.
"""
+ __metaclass__ = ABCMeta
+
+ @abstractmethod
def __init__(self):
"""
Constructor.
@@ -18,27 +21,12 @@ class DiscreteOperator:
"""
## Application domains of the variables.
self.domains = []
- ## Variables
- self.variables = []
## Operator numerical method.
self.numMethod = []
self.is_splittable = True
self.gpu_kernel = None
self.gpu_kernel_name = ""
- def addVariable(self, cVariable):
- """
- Add an discrete variables to the operator.
- Also add variables' domains to the operator.
-
- @param cVariable DiscreteVariable.DiscreteVariable : variables to add.
- """
- for v in cVariable:
- if self.variables.count(v) == 0:
- self.variables.append(v)
- if self.domains.count(v.domain) == 0:
- self.domains.append(v.domain)
-
def setMethod(self, method):
"""
Set the numerical method used by operator when calling applyOperator.
@@ -47,6 +35,7 @@ class DiscreteOperator:
"""
self.numMethod = method
+ @abstractmethod
def setResultVariable(self):
"""
Abstract method, apply operaton on a variable.
@@ -54,6 +43,7 @@ class DiscreteOperator:
"""
raise NotImplementedError("Need to override method in a subclass of " + providedClass)
+ @abstractmethod
def applyOperator(self):
"""
Abstract method, apply operaton on a variable.
--
GitLab