diff --git a/Docs/CMakeLists.txt b/Docs/CMakeLists.txt
index 60473151f172afc5ee1ee6fb3fb1a5cc36d1a9be..ac86e77bb8bda845a1149378e9ee3ad620b9dae9 100644
--- a/Docs/CMakeLists.txt
+++ b/Docs/CMakeLists.txt
@@ -22,13 +22,14 @@ include(MyTools)
# ----- CMake project setup -----
# cmake project name
-set(PROJECT_NAME "parmesdoc")
+set(PROJECT_NAME "hysopdoc")
project(${PROJECT_NAME})
# ----- Search required libraries -----
# --- Python ---
-include(PythonSetup)
+find_package(PythonFull REQUIRED)
+include(FindPythonModule)
# --- Sphinx ---
find_python_module(sphinx REQUIRED)
# --- sphinxcontrib.doxylink ---
@@ -42,6 +43,8 @@ configure_file (
"${CMAKE_CURRENT_BINARY_DIR}/sphinx_sources/conf.py"
)
+file(COPY sphinx_sources DESTINATION .)
+
set(SPHINX_EXECUTABLE sphinx-build )
set(SPHINX_PARAMETERS -b html -c ${CMAKE_CURRENT_BINARY_DIR}/sphinx_sources/)
@@ -49,4 +52,14 @@ add_custom_target(sphinx
COMMAND ${SPHINX_EXECUTABLE} ${SPHINX_PARAMETERS}
${CMAKE_CURRENT_SOURCE_DIR}/sphinx_sources
${CMAKE_CURRENT_BINARY_DIR}/sphinx_build/html
-)
+ )
+
+set(SPHINX_APIDOC sphinx-apidoc)
+set(GENERATED_DOC ${CMAKE_CURRENT_BINARY_DIR}/sphinx_sources/reference)
+set(APIDOC_PARAMETERS -e -P -o ${GENERATED_DOC})
+
+add_custom_target(apidoc
+ COMMAND ${SPHINX_APIDOC} ${APIDOC_PARAMETERS}
+ ${CMAKE_CURRENT_SOURCE_DIR}/../HySoP/hysop
+ )
+
diff --git a/Docs/sphinx_sources/_templates/indexcontent.html b/Docs/sphinx_sources/_templates/indexcontent.html
new file mode 100644
index 0000000000000000000000000000000000000000..4a6da35ced43e29235a6e9fc2624c4a738d19013
--- /dev/null
+++ b/Docs/sphinx_sources/_templates/indexcontent.html
@@ -0,0 +1,39 @@
+{% extends "defindex.html" %}
+{% block tables %}
+ <p><strong>Parts of the documentation:</strong></p>
+ <table class="contentstable" align="center"><tr>
+ <td width="50%">
+ <p class="biglink"><a class="biglink" href="{{ pathto("user_guide/index") }}">HySoP User Guide</a><br/>
+ <span class="linkdescr">start here</span></p>
+ <p class="biglink"><a class="biglink" href="{{ pathto("reference/index") }}">HySoP Reference</a><br/>
+ <span class="linkdescr">reference documentation</span></p>
+ <p class="biglink"><a class="biglink" href="{{ pathto("dev/index") }}">HySoP Developer Guide</a><br/>
+ <span class="linkdescr">contributing to NumPy</span></p>
+ </td></tr>
+ </table>
+
+ <p><strong>Indices and tables:</strong></p>
+ <table class="contentstable" align="center"><tr>
+ <td width="50%">
+ <p class="biglink"><a class="biglink" href="{{ pathto("genindex") }}">General Index</a><br/>
+ <span class="linkdescr">all functions, classes, terms</span></p>
+ <p class="biglink"><a class="biglink" href="{{ pathto("glossary") }}">Glossary</a><br/>
+ <span class="linkdescr">the most important terms explained</span></p>
+ </td><td width="50%">
+ <p class="biglink"><a class="biglink" href="{{ pathto("search") }}">Search page</a><br/>
+ <span class="linkdescr">search this documentation</span></p>
+ <p class="biglink"><a class="biglink" href="{{ pathto("contents") }}">Complete Table of Contents</a><br/>
+ <span class="linkdescr">lists all sections and subsections</span></p>
+ </td></tr>
+ </table>
+
+ <table class="contentstable" align="center"><tr>
+ <td width="50%">
+ <p class="biglink"><a class="biglink" href="{{ pathto("about") }}">About HySoP</a></p>
+ </td><td width="50%">
+ <p class="biglink"><a class="biglink" href="{{ pathto("release") }}">Release Notes</a></p>
+ <p class="biglink"><a class="biglink" href="{{ pathto("license") }}">License of HySoP</a></p>
+ </td></tr>
+ </table>
+
+{% endblock %}
diff --git a/Docs/sphinx_sources/conf.py.in b/Docs/sphinx_sources/conf.py.in
index 523742cc92ac52db138fd806a113340b63745b3f..68b40c1e84bfd32068570e03f9baf94ea50ff0d4 100644
--- a/Docs/sphinx_sources/conf.py.in
+++ b/Docs/sphinx_sources/conf.py.in
@@ -1,7 +1,7 @@
# -*- coding: utf-8 -*-
#
-# ParMeS documentation build configuration file, created by
-# sphinx-quickstart on Tue Jul 15 16:46:52 2014.
+# HySoP documentation build configuration file, created by
+# sphinx-quickstart on Tue Nov 25 11:54:57 2014.
#
# This file is execfile()d with the current directory set to its
# containing dir.
@@ -12,8 +12,6 @@
# All configuration values have a default; values that are commented out
# serve to show the default.
-import sys, os
-
# If extensions (or modules to document with autodoc) are in another directory,
# add these directories to sys.path here. If the directory is relative to the
# documentation root, use os.path.abspath to make it absolute, like shown here.
@@ -29,15 +27,25 @@ import sys, os
# ones.
extensions = [
'sphinx.ext.autodoc',
+ 'sphinx.ext.autosummary',
'sphinx.ext.doctest',
- 'sphinx.ext.intersphinx',
'sphinx.ext.todo',
'sphinx.ext.coverage',
'sphinx.ext.mathjax',
'sphinx.ext.ifconfig',
'sphinx.ext.viewcode',
- 'sphinxcontrib.doxylink',
+ 'numpydoc',
+ 'sphinx.ext.intersphinx',
]
+
+#numpydoc_class_members_toctree = True
+#autosummary_generate = True
+# -----------------------------------------------------------------------------
+# Autosummary
+# -----------------------------------------------------------------------------
+
+#import glob
+#autosummary_generate = glob.glob("@CMAKE_CURRENT_BINARY_DIR@/sphinx_source/reference/*.rst")
doxylink = {
'doxykernel':
@@ -45,6 +53,7 @@ doxylink = {
'@CMAKE_INSTALL_PREFIX@/Kernel/'),
}
+#autoclass_content = 'both'
# Add any paths that contain templates here, relative to this directory.
templates_path = ['_templates']
@@ -58,17 +67,17 @@ source_suffix = '.rst'
master_doc = 'index'
# General information about the project.
-project = u'ParMeS'
-copyright = u'2014, ParMeS development team'
+project = u'HySoP'
+copyright = u'2014, HySoP development team'
# The version info for the project you're documenting, acts as replacement for
# |version| and |release|, also used in various other places throughout the
# built documents.
#
# The short X.Y version.
-version = '1.0.0'
+version = '1.1.0'
# The full version, including alpha/beta/rc tags.
-release = '1.0.0'
+release = '1.1.0'
# The language for content autogenerated by Sphinx. Refer to documentation
# for a list of supported languages.
@@ -108,13 +117,16 @@ pygments_style = 'sphinx'
# If true, keep warnings as "system message" paragraphs in the built documents.
# keep_warnings = False
+html_additional_pages = {
+ 'index': 'indexcontent.html',
+}
# -- Options for HTML output ----------------------------------------------
# The theme to use for HTML and HTML Help pages. See the documentation for
# a list of builtin themes.
-#html_theme = 'mt_ini_gryphon' # 'default'
-html_theme = 'sphinxdoc'
+html_theme = 'agogo'
+
# Theme options are theme-specific and customize the look and feel of a theme
# further. For a list of options available for each theme, see the
# documentation.
@@ -191,8 +203,7 @@ html_static_path = ['_static']
# html_file_suffix = None
# Output file base name for HTML help builder.
-htmlhelp_basename = 'ParMeSdoc'
-
+htmlhelp_basename = 'HySoPdoc'
# -- Options for LaTeX output ---------------------------------------------
@@ -211,8 +222,8 @@ latex_elements = {
# (source start file, target name, title,
# author, documentclass [howto, manual, or own class]).
latex_documents = [
- ('index', 'ParMeS.tex', u'ParMeS Documentation',
- u'ParMeS development team', 'manual'),
+ ('index', 'HySoP.tex', u'HySoP Documentation',
+ u'HySoP development team', 'manual'),
]
# The name of an image file (relative to this directory) to place at the top of
@@ -241,8 +252,8 @@ latex_documents = [
# One entry per manual page. List of tuples
# (source start file, name, description, authors, manual section).
man_pages = [
- ('index', 'parmes', u'ParMeS Documentation',
- [u'ParMeS development team'], 1)
+ ('index', 'hysop', u'HySoP Documentation',
+ [u'HySoP development team'], 1)
]
# If true, show URL addresses after external links.
@@ -255,8 +266,8 @@ man_pages = [
# (source start file, target name, title, author,
# dir menu entry, description, category)
texinfo_documents = [
- ('index', 'ParMeS', u'ParMeS Documentation',
- u'ParMeS development team', 'ParMeS', 'One line description of project.',
+ ('index', 'HySoP', u'HySoP Documentation',
+ u'HySoP development team', 'HySoP', 'One line description of project.',
'Miscellaneous'),
]
@@ -276,10 +287,10 @@ texinfo_documents = [
# -- Options for Epub output ----------------------------------------------
# Bibliographic Dublin Core info.
-epub_title = u'ParMeS'
-epub_author = u'ParMeS development team'
-epub_publisher = u'ParMeS development team'
-epub_copyright = u'2014, ParMeS development team'
+epub_title = u'HySoP'
+epub_author = u'HySoP development team'
+epub_publisher = u'HySoP development team'
+epub_copyright = u'2014, HySoP development team'
# The basename for the epub file. It defaults to the project name.
# epub_basename = u'Siconos'
diff --git a/Docs/sphinx_sources/index.rst b/Docs/sphinx_sources/index.rst
index 22de47163a267c3de150a0541e3db357ae81cfbf..b42b619f47fa5d9daeb99cfc0eb26ac9561b5762 100644
--- a/Docs/sphinx_sources/index.rst
+++ b/Docs/sphinx_sources/index.rst
@@ -1,9 +1,9 @@
-.. ParMeS documentation master file, created by
+.. HySoP documentation master file, created by
sphinx-quickstart on Tue Jul 15 16:46:52 2014.
You can adapt this file completely to your liking, but it should at least
contain the root `toctree` directive.
-Welcome to ParMeS's documentation!
+Welcome to HySoP's documentation!
==================================
Contents:
@@ -11,11 +11,7 @@ Contents:
.. toctree::
:maxdepth: 2
- introduction
- redistribute
- parmepy.domain
- develnotes
-
+
Indices and tables
==================
diff --git a/Docs/sphinx_sources/parmepy.domain.obstacle.rst b/Docs/sphinx_sources/parmepy.domain.obstacle.rst
deleted file mode 100644
index f462b51cd4f4925a30c8835c58d8867bc9b1d1c9..0000000000000000000000000000000000000000
--- a/Docs/sphinx_sources/parmepy.domain.obstacle.rst
+++ /dev/null
@@ -1,54 +0,0 @@
-parmepy.domain.obstacle package
-===============================
-
-Submodules
-----------
-
-parmepy.domain.obstacle.controlBox module
------------------------------------------
-
-.. automodule:: parmepy.domain.obstacle.controlBox
- :members:
- :undoc-members:
- :show-inheritance:
-
-parmepy.domain.obstacle.disk module
------------------------------------
-
-.. automodule:: parmepy.domain.obstacle.disk
- :members:
- :undoc-members:
- :show-inheritance:
-
-parmepy.domain.obstacle.obstacle module
----------------------------------------
-
-.. automodule:: parmepy.domain.obstacle.obstacle
- :members:
- :undoc-members:
- :show-inheritance:
-
-parmepy.domain.obstacle.planes module
--------------------------------------
-
-.. automodule:: parmepy.domain.obstacle.planes
- :members:
- :undoc-members:
- :show-inheritance:
-
-parmepy.domain.obstacle.sphere module
--------------------------------------
-
-.. automodule:: parmepy.domain.obstacle.sphere
- :members:
- :undoc-members:
- :show-inheritance:
-
-
-Module contents
----------------
-
-.. automodule:: parmepy.domain.obstacle
- :members:
- :undoc-members:
- :show-inheritance:
diff --git a/Docs/sphinx_sources/parmepy.domain.rst b/Docs/sphinx_sources/parmepy.domain.rst
deleted file mode 100644
index 80659d3d037bd0cd82e33af967295f40bb77cce0..0000000000000000000000000000000000000000
--- a/Docs/sphinx_sources/parmepy.domain.rst
+++ /dev/null
@@ -1,25 +0,0 @@
-.. _domain:
-
-Domain and other geometries
-============================
-
-This package is used to describe the physical domain geometry
-or to define some obstacles inside this geometry.
-
-:ref:`IO_params`
-
-Base class (abstract)
------------------------
-
-.. automodule:: parmepy.domain.domain
- :members:
- :undoc-members:
- :show-inheritance:
-
-Box-shaped domain
-------------------
-
-.. automodule:: parmepy.domain.box
- :members:
- :undoc-members:
- :show-inheritance:
diff --git a/Docs/sphinx_sources/parmepy.fakef2py.fftw2py.rst b/Docs/sphinx_sources/parmepy.fakef2py.fftw2py.rst
deleted file mode 100644
index 97c3b4f9406bcb6f8df97d4f736ea9b9bb8b15e7..0000000000000000000000000000000000000000
--- a/Docs/sphinx_sources/parmepy.fakef2py.fftw2py.rst
+++ /dev/null
@@ -1,10 +0,0 @@
-parmepy.fakef2py.fftw2py package
-================================
-
-Module contents
----------------
-
-.. automodule:: parmepy.fakef2py.fftw2py
- :members:
- :undoc-members:
- :show-inheritance:
diff --git a/Docs/sphinx_sources/parmepy.fakef2py.rst b/Docs/sphinx_sources/parmepy.fakef2py.rst
deleted file mode 100644
index 76da79417d308a90ccef64fab2a3acba1a60973b..0000000000000000000000000000000000000000
--- a/Docs/sphinx_sources/parmepy.fakef2py.rst
+++ /dev/null
@@ -1,18 +0,0 @@
-parmepy.fakef2py package
-========================
-
-Subpackages
------------
-
-.. toctree::
-
- parmepy.fakef2py.fftw2py
- parmepy.fakef2py.scales2py
-
-Module contents
----------------
-
-.. automodule:: parmepy.fakef2py
- :members:
- :undoc-members:
- :show-inheritance:
diff --git a/Docs/sphinx_sources/parmepy.fakef2py.scales2py.rst b/Docs/sphinx_sources/parmepy.fakef2py.scales2py.rst
deleted file mode 100644
index f65bfc9d97336bf8f9e4e328a33905248d9feee3..0000000000000000000000000000000000000000
--- a/Docs/sphinx_sources/parmepy.fakef2py.scales2py.rst
+++ /dev/null
@@ -1,10 +0,0 @@
-parmepy.fakef2py.scales2py package
-==================================
-
-Module contents
----------------
-
-.. automodule:: parmepy.fakef2py.scales2py
- :members:
- :undoc-members:
- :show-inheritance:
diff --git a/Docs/sphinx_sources/parmepy.fields.rst b/Docs/sphinx_sources/parmepy.fields.rst
deleted file mode 100644
index 5baf08c622cec8b574922192eee0a4588cfdc243..0000000000000000000000000000000000000000
--- a/Docs/sphinx_sources/parmepy.fields.rst
+++ /dev/null
@@ -1,45 +0,0 @@
-parmepy.fields package
-======================
-
-Subpackages
------------
-
-.. toctree::
-
- parmepy.fields.tests
-
-Submodules
-----------
-
-parmepy.fields.continuous module
---------------------------------
-
-.. automodule:: parmepy.fields.continuous
- :members:
- :undoc-members:
- :show-inheritance:
-
-parmepy.fields.discrete module
-------------------------------
-
-.. automodule:: parmepy.fields.discrete
- :members:
- :undoc-members:
- :show-inheritance:
-
-parmepy.fields.variable_parameter module
-----------------------------------------
-
-.. automodule:: parmepy.fields.variable_parameter
- :members:
- :undoc-members:
- :show-inheritance:
-
-
-Module contents
----------------
-
-.. automodule:: parmepy.fields
- :members:
- :undoc-members:
- :show-inheritance:
diff --git a/Docs/sphinx_sources/parmepy.gpu.rst b/Docs/sphinx_sources/parmepy.gpu.rst
deleted file mode 100644
index 1275af6914a5f56af5017a1c75025fd8ff7a86a0..0000000000000000000000000000000000000000
--- a/Docs/sphinx_sources/parmepy.gpu.rst
+++ /dev/null
@@ -1,110 +0,0 @@
-parmepy.gpu package
-===================
-
-Subpackages
------------
-
-.. toctree::
-
- parmepy.gpu.tests
- parmepy.gpu.visu
-
-Submodules
-----------
-
-parmepy.gpu.QtRendering module
-------------------------------
-
-.. automodule:: parmepy.gpu.QtRendering
- :members:
- :undoc-members:
- :show-inheritance:
-
-parmepy.gpu.config_cayman module
---------------------------------
-
-.. automodule:: parmepy.gpu.config_cayman
- :members:
- :undoc-members:
- :show-inheritance:
-
-parmepy.gpu.config_default module
----------------------------------
-
-.. automodule:: parmepy.gpu.config_default
- :members:
- :undoc-members:
- :show-inheritance:
-
-parmepy.gpu.config_k20m module
-------------------------------
-
-.. automodule:: parmepy.gpu.config_k20m
- :members:
- :undoc-members:
- :show-inheritance:
-
-parmepy.gpu.gpu_discrete module
--------------------------------
-
-.. automodule:: parmepy.gpu.gpu_discrete
- :members:
- :undoc-members:
- :show-inheritance:
-
-parmepy.gpu.gpu_kernel module
------------------------------
-
-.. automodule:: parmepy.gpu.gpu_kernel
- :members:
- :undoc-members:
- :show-inheritance:
-
-parmepy.gpu.gpu_particle_advection module
------------------------------------------
-
-.. automodule:: parmepy.gpu.gpu_particle_advection
- :members:
- :undoc-members:
- :show-inheritance:
-
-parmepy.gpu.gpu_particle_advection_1k module
---------------------------------------------
-
-.. automodule:: parmepy.gpu.gpu_particle_advection_1k
- :members:
- :undoc-members:
- :show-inheritance:
-
-parmepy.gpu.gpu_particle_advection_2k module
---------------------------------------------
-
-.. automodule:: parmepy.gpu.gpu_particle_advection_2k
- :members:
- :undoc-members:
- :show-inheritance:
-
-parmepy.gpu.kernel_benchmark module
------------------------------------
-
-.. automodule:: parmepy.gpu.kernel_benchmark
- :members:
- :undoc-members:
- :show-inheritance:
-
-parmepy.gpu.tools module
-------------------------
-
-.. automodule:: parmepy.gpu.tools
- :members:
- :undoc-members:
- :show-inheritance:
-
-
-Module contents
----------------
-
-.. automodule:: parmepy.gpu
- :members:
- :undoc-members:
- :show-inheritance:
diff --git a/Docs/sphinx_sources/parmepy.gpu.visu.rst b/Docs/sphinx_sources/parmepy.gpu.visu.rst
deleted file mode 100644
index 00c9759659a2b4cf3c57d99cee9643fec269b001..0000000000000000000000000000000000000000
--- a/Docs/sphinx_sources/parmepy.gpu.visu.rst
+++ /dev/null
@@ -1,22 +0,0 @@
-parmepy.gpu.visu package
-========================
-
-Submodules
-----------
-
-parmepy.gpu.visu.marchingcube module
-------------------------------------
-
-.. automodule:: parmepy.gpu.visu.marchingcube
- :members:
- :undoc-members:
- :show-inheritance:
-
-
-Module contents
----------------
-
-.. automodule:: parmepy.gpu.visu
- :members:
- :undoc-members:
- :show-inheritance:
diff --git a/Docs/sphinx_sources/parmepy.mpi.rst b/Docs/sphinx_sources/parmepy.mpi.rst
deleted file mode 100644
index b3730c3808704952fbf12103d13e2f106d5c4cc1..0000000000000000000000000000000000000000
--- a/Docs/sphinx_sources/parmepy.mpi.rst
+++ /dev/null
@@ -1,61 +0,0 @@
-parmepy.mpi package
-===================
-
-Subpackages
------------
-
-.. toctree::
-
- parmepy.mpi.tests
-
-Submodules
-----------
-
-parmepy.mpi.bridge module
--------------------------
-
-.. automodule:: parmepy.mpi.bridge
- :members:
- :undoc-members:
- :show-inheritance:
-
-parmepy.mpi.main_var module
----------------------------
-
-.. automodule:: parmepy.mpi.main_var
- :members:
- :undoc-members:
- :show-inheritance:
-
-parmepy.mpi.mesh module
------------------------
-
-.. automodule:: parmepy.mpi.mesh
- :members:
- :undoc-members:
- :show-inheritance:
-
-parmepy.mpi.newBridge module
-----------------------------
-
-.. automodule:: parmepy.mpi.newBridge
- :members:
- :undoc-members:
- :show-inheritance:
-
-parmepy.mpi.topology module
----------------------------
-
-.. automodule:: parmepy.mpi.topology
- :members:
- :undoc-members:
- :show-inheritance:
-
-
-Module contents
----------------
-
-.. automodule:: parmepy.mpi
- :members:
- :undoc-members:
- :show-inheritance:
diff --git a/Docs/sphinx_sources/parmepy.numerics.integrators.rst b/Docs/sphinx_sources/parmepy.numerics.integrators.rst
deleted file mode 100644
index 4d0154954d237f0fd9daf2dc39b6f2ae1f37600a..0000000000000000000000000000000000000000
--- a/Docs/sphinx_sources/parmepy.numerics.integrators.rst
+++ /dev/null
@@ -1,54 +0,0 @@
-parmepy.numerics.integrators package
-====================================
-
-Submodules
-----------
-
-parmepy.numerics.integrators.euler module
------------------------------------------
-
-.. automodule:: parmepy.numerics.integrators.euler
- :members:
- :undoc-members:
- :show-inheritance:
-
-parmepy.numerics.integrators.odesolver module
----------------------------------------------
-
-.. automodule:: parmepy.numerics.integrators.odesolver
- :members:
- :undoc-members:
- :show-inheritance:
-
-parmepy.numerics.integrators.runge_kutta2 module
-------------------------------------------------
-
-.. automodule:: parmepy.numerics.integrators.runge_kutta2
- :members:
- :undoc-members:
- :show-inheritance:
-
-parmepy.numerics.integrators.runge_kutta3 module
-------------------------------------------------
-
-.. automodule:: parmepy.numerics.integrators.runge_kutta3
- :members:
- :undoc-members:
- :show-inheritance:
-
-parmepy.numerics.integrators.runge_kutta4 module
-------------------------------------------------
-
-.. automodule:: parmepy.numerics.integrators.runge_kutta4
- :members:
- :undoc-members:
- :show-inheritance:
-
-
-Module contents
----------------
-
-.. automodule:: parmepy.numerics.integrators
- :members:
- :undoc-members:
- :show-inheritance:
diff --git a/Docs/sphinx_sources/parmepy.numerics.rst b/Docs/sphinx_sources/parmepy.numerics.rst
deleted file mode 100644
index 3ac022afc7f490ef9320135e196949d9b2fe51d3..0000000000000000000000000000000000000000
--- a/Docs/sphinx_sources/parmepy.numerics.rst
+++ /dev/null
@@ -1,70 +0,0 @@
-parmepy.numerics package
-========================
-
-Subpackages
------------
-
-.. toctree::
-
- parmepy.numerics.integrators
- parmepy.numerics.tests
-
-Submodules
-----------
-
-parmepy.numerics.differential_operations module
------------------------------------------------
-
-.. automodule:: parmepy.numerics.differential_operations
- :members:
- :undoc-members:
- :show-inheritance:
-
-parmepy.numerics.finite_differences module
-------------------------------------------
-
-.. automodule:: parmepy.numerics.finite_differences
- :members:
- :undoc-members:
- :show-inheritance:
-
-parmepy.numerics.interpolation module
--------------------------------------
-
-.. automodule:: parmepy.numerics.interpolation
- :members:
- :undoc-members:
- :show-inheritance:
-
-parmepy.numerics.method module
-------------------------------
-
-.. automodule:: parmepy.numerics.method
- :members:
- :undoc-members:
- :show-inheritance:
-
-parmepy.numerics.remeshing module
----------------------------------
-
-.. automodule:: parmepy.numerics.remeshing
- :members:
- :undoc-members:
- :show-inheritance:
-
-parmepy.numerics.update_ghosts module
--------------------------------------
-
-.. automodule:: parmepy.numerics.update_ghosts
- :members:
- :undoc-members:
- :show-inheritance:
-
-
-Module contents
----------------
-
-.. automodule:: parmepy.numerics
- :members:
- :undoc-members:
- :show-inheritance:
diff --git a/Docs/sphinx_sources/parmepy.operator.discrete.rst b/Docs/sphinx_sources/parmepy.operator.discrete.rst
deleted file mode 100644
index 3d27c11e4e524198c6cc98b53c83b717595db052..0000000000000000000000000000000000000000
--- a/Docs/sphinx_sources/parmepy.operator.discrete.rst
+++ /dev/null
@@ -1,134 +0,0 @@
-parmepy.operator.discrete package
-=================================
-
-Submodules
-----------
-
-parmepy.operator.discrete.adapt_timestep module
------------------------------------------------
-
-.. automodule:: parmepy.operator.discrete.adapt_timestep
- :members:
- :undoc-members:
- :show-inheritance:
-
-parmepy.operator.discrete.baroclinic module
--------------------------------------------
-
-.. automodule:: parmepy.operator.discrete.baroclinic
- :members:
- :undoc-members:
- :show-inheritance:
-
-parmepy.operator.discrete.curlAndDiffusion_fft module
------------------------------------------------------
-
-.. automodule:: parmepy.operator.discrete.curlAndDiffusion_fft
- :members:
- :undoc-members:
- :show-inheritance:
-
-parmepy.operator.discrete.density module
-----------------------------------------
-
-.. automodule:: parmepy.operator.discrete.density
- :members:
- :undoc-members:
- :show-inheritance:
-
-parmepy.operator.discrete.differential module
----------------------------------------------
-
-.. automodule:: parmepy.operator.discrete.differential
- :members:
- :undoc-members:
- :show-inheritance:
-
-parmepy.operator.discrete.diffusion_fft module
-----------------------------------------------
-
-.. automodule:: parmepy.operator.discrete.diffusion_fft
- :members:
- :undoc-members:
- :show-inheritance:
-
-parmepy.operator.discrete.discrete module
------------------------------------------
-
-.. automodule:: parmepy.operator.discrete.discrete
- :members:
- :undoc-members:
- :show-inheritance:
-
-parmepy.operator.discrete.energy_enstrophy module
--------------------------------------------------
-
-.. automodule:: parmepy.operator.discrete.energy_enstrophy
- :members:
- :undoc-members:
- :show-inheritance:
-
-parmepy.operator.discrete.particle_advection module
----------------------------------------------------
-
-.. automodule:: parmepy.operator.discrete.particle_advection
- :members:
- :undoc-members:
- :show-inheritance:
-
-parmepy.operator.discrete.penalization module
----------------------------------------------
-
-.. automodule:: parmepy.operator.discrete.penalization
- :members:
- :undoc-members:
- :show-inheritance:
-
-parmepy.operator.discrete.poisson_fft module
---------------------------------------------
-
-.. automodule:: parmepy.operator.discrete.poisson_fft
- :members:
- :undoc-members:
- :show-inheritance:
-
-parmepy.operator.discrete.reprojection module
----------------------------------------------
-
-.. automodule:: parmepy.operator.discrete.reprojection
- :members:
- :undoc-members:
- :show-inheritance:
-
-parmepy.operator.discrete.scales_advection module
--------------------------------------------------
-
-.. automodule:: parmepy.operator.discrete.scales_advection
- :members:
- :undoc-members:
- :show-inheritance:
-
-parmepy.operator.discrete.stretching module
--------------------------------------------
-
-.. automodule:: parmepy.operator.discrete.stretching
- :members:
- :undoc-members:
- :show-inheritance:
-
-parmepy.operator.discrete.velocity_correction module
-----------------------------------------------------
-
-.. automodule:: parmepy.operator.discrete.velocity_correction
- :members:
- :undoc-members:
- :show-inheritance:
-
-
-Module contents
----------------
-
-.. automodule:: parmepy.operator.discrete
- :members:
- :undoc-members:
- :show-inheritance:
diff --git a/Docs/sphinx_sources/parmepy.operator.monitors.rst b/Docs/sphinx_sources/parmepy.operator.monitors.rst
deleted file mode 100644
index e99d93b7d6e478d058f9a30c5051e5e411063d0c..0000000000000000000000000000000000000000
--- a/Docs/sphinx_sources/parmepy.operator.monitors.rst
+++ /dev/null
@@ -1,54 +0,0 @@
-parmepy.operator.monitors package
-=================================
-
-Submodules
-----------
-
-parmepy.operator.monitors.compute_forces module
------------------------------------------------
-
-.. automodule:: parmepy.operator.monitors.compute_forces
- :members:
- :undoc-members:
- :show-inheritance:
-
-parmepy.operator.monitors.energy_enstrophy module
--------------------------------------------------
-
-.. automodule:: parmepy.operator.monitors.energy_enstrophy
- :members:
- :undoc-members:
- :show-inheritance:
-
-parmepy.operator.monitors.monitoring module
--------------------------------------------
-
-.. automodule:: parmepy.operator.monitors.monitoring
- :members:
- :undoc-members:
- :show-inheritance:
-
-parmepy.operator.monitors.printer module
-----------------------------------------
-
-.. automodule:: parmepy.operator.monitors.printer
- :members:
- :undoc-members:
- :show-inheritance:
-
-parmepy.operator.monitors.reader module
----------------------------------------
-
-.. automodule:: parmepy.operator.monitors.reader
- :members:
- :undoc-members:
- :show-inheritance:
-
-
-Module contents
----------------
-
-.. automodule:: parmepy.operator.monitors
- :members:
- :undoc-members:
- :show-inheritance:
diff --git a/Docs/sphinx_sources/parmepy.operator.redistribute.rst b/Docs/sphinx_sources/parmepy.operator.redistribute.rst
deleted file mode 100644
index 3d27c11e4e524198c6cc98b53c83b717595db052..0000000000000000000000000000000000000000
--- a/Docs/sphinx_sources/parmepy.operator.redistribute.rst
+++ /dev/null
@@ -1,134 +0,0 @@
-parmepy.operator.discrete package
-=================================
-
-Submodules
-----------
-
-parmepy.operator.discrete.adapt_timestep module
------------------------------------------------
-
-.. automodule:: parmepy.operator.discrete.adapt_timestep
- :members:
- :undoc-members:
- :show-inheritance:
-
-parmepy.operator.discrete.baroclinic module
--------------------------------------------
-
-.. automodule:: parmepy.operator.discrete.baroclinic
- :members:
- :undoc-members:
- :show-inheritance:
-
-parmepy.operator.discrete.curlAndDiffusion_fft module
------------------------------------------------------
-
-.. automodule:: parmepy.operator.discrete.curlAndDiffusion_fft
- :members:
- :undoc-members:
- :show-inheritance:
-
-parmepy.operator.discrete.density module
-----------------------------------------
-
-.. automodule:: parmepy.operator.discrete.density
- :members:
- :undoc-members:
- :show-inheritance:
-
-parmepy.operator.discrete.differential module
----------------------------------------------
-
-.. automodule:: parmepy.operator.discrete.differential
- :members:
- :undoc-members:
- :show-inheritance:
-
-parmepy.operator.discrete.diffusion_fft module
-----------------------------------------------
-
-.. automodule:: parmepy.operator.discrete.diffusion_fft
- :members:
- :undoc-members:
- :show-inheritance:
-
-parmepy.operator.discrete.discrete module
------------------------------------------
-
-.. automodule:: parmepy.operator.discrete.discrete
- :members:
- :undoc-members:
- :show-inheritance:
-
-parmepy.operator.discrete.energy_enstrophy module
--------------------------------------------------
-
-.. automodule:: parmepy.operator.discrete.energy_enstrophy
- :members:
- :undoc-members:
- :show-inheritance:
-
-parmepy.operator.discrete.particle_advection module
----------------------------------------------------
-
-.. automodule:: parmepy.operator.discrete.particle_advection
- :members:
- :undoc-members:
- :show-inheritance:
-
-parmepy.operator.discrete.penalization module
----------------------------------------------
-
-.. automodule:: parmepy.operator.discrete.penalization
- :members:
- :undoc-members:
- :show-inheritance:
-
-parmepy.operator.discrete.poisson_fft module
---------------------------------------------
-
-.. automodule:: parmepy.operator.discrete.poisson_fft
- :members:
- :undoc-members:
- :show-inheritance:
-
-parmepy.operator.discrete.reprojection module
----------------------------------------------
-
-.. automodule:: parmepy.operator.discrete.reprojection
- :members:
- :undoc-members:
- :show-inheritance:
-
-parmepy.operator.discrete.scales_advection module
--------------------------------------------------
-
-.. automodule:: parmepy.operator.discrete.scales_advection
- :members:
- :undoc-members:
- :show-inheritance:
-
-parmepy.operator.discrete.stretching module
--------------------------------------------
-
-.. automodule:: parmepy.operator.discrete.stretching
- :members:
- :undoc-members:
- :show-inheritance:
-
-parmepy.operator.discrete.velocity_correction module
-----------------------------------------------------
-
-.. automodule:: parmepy.operator.discrete.velocity_correction
- :members:
- :undoc-members:
- :show-inheritance:
-
-
-Module contents
----------------
-
-.. automodule:: parmepy.operator.discrete
- :members:
- :undoc-members:
- :show-inheritance:
diff --git a/Docs/sphinx_sources/parmepy.operator.rst b/Docs/sphinx_sources/parmepy.operator.rst
deleted file mode 100644
index ba97de6bf4b2f5325d63beb2c8828ce10da72b5f..0000000000000000000000000000000000000000
--- a/Docs/sphinx_sources/parmepy.operator.rst
+++ /dev/null
@@ -1,199 +0,0 @@
-parmepy.operator package
-========================
-
-Subpackages
------------
-
-.. toctree::
-
- parmepy.operator.discrete
- parmepy.operator.monitors
- parmepy.operator.tests
-
-Submodules
-----------
-
-parmepy.operator.adapt_timestep module
---------------------------------------
-
-.. automodule:: parmepy.operator.adapt_timestep
- :members:
- :undoc-members:
- :show-inheritance:
-
-parmepy.operator.advection module
----------------------------------
-
-.. automodule:: parmepy.operator.advection
- :members:
- :undoc-members:
- :show-inheritance:
-
-parmepy.operator.advectionDir module
-------------------------------------
-
-.. automodule:: parmepy.operator.advectionDir
- :members:
- :undoc-members:
- :show-inheritance:
-
-parmepy.operator.advold module
-------------------------------
-
-.. automodule:: parmepy.operator.advold
- :members:
- :undoc-members:
- :show-inheritance:
-
-parmepy.operator.analytic module
---------------------------------
-
-.. automodule:: parmepy.operator.analytic
- :members:
- :undoc-members:
- :show-inheritance:
-
-parmepy.operator.baroclinic module
-----------------------------------
-
-.. automodule:: parmepy.operator.baroclinic
- :members:
- :undoc-members:
- :show-inheritance:
-
-parmepy.operator.computational module
--------------------------------------
-
-.. automodule:: parmepy.operator.computational
- :members:
- :undoc-members:
- :show-inheritance:
-
-parmepy.operator.continuous module
-----------------------------------
-
-.. automodule:: parmepy.operator.continuous
- :members:
- :undoc-members:
- :show-inheritance:
-
-parmepy.operator.curlAndDiffusion module
-----------------------------------------
-
-.. automodule:: parmepy.operator.curlAndDiffusion
- :members:
- :undoc-members:
- :show-inheritance:
-
-parmepy.operator.density module
--------------------------------
-
-.. automodule:: parmepy.operator.density
- :members:
- :undoc-members:
- :show-inheritance:
-
-parmepy.operator.differential module
-------------------------------------
-
-.. automodule:: parmepy.operator.differential
- :members:
- :undoc-members:
- :show-inheritance:
-
-parmepy.operator.diffusion module
----------------------------------
-
-.. automodule:: parmepy.operator.diffusion
- :members:
- :undoc-members:
- :show-inheritance:
-
-parmepy.operator.energy_enstrophy module
-----------------------------------------
-
-.. automodule:: parmepy.operator.energy_enstrophy
- :members:
- :undoc-members:
- :show-inheritance:
-
-parmepy.operator.hdf_io module
-------------------------------
-
-.. automodule:: parmepy.operator.hdf_io
- :members:
- :undoc-members:
- :show-inheritance:
-
-parmepy.operator.penalization module
-------------------------------------
-
-.. automodule:: parmepy.operator.penalization
- :members:
- :undoc-members:
- :show-inheritance:
-
-parmepy.operator.poisson module
--------------------------------
-
-.. automodule:: parmepy.operator.poisson
- :members:
- :undoc-members:
- :show-inheritance:
-
-parmepy.operator.redistribute module
-------------------------------------
-
-.. automodule:: parmepy.operator.redistribute
- :members:
- :undoc-members:
- :show-inheritance:
-
-parmepy.operator.redistribute_inter module
-------------------------------------------
-
-.. automodule:: parmepy.operator.redistribute_inter
- :members:
- :undoc-members:
- :show-inheritance:
-
-parmepy.operator.redistribute_intra module
-------------------------------------------
-
-.. automodule:: parmepy.operator.redistribute_intra
- :members:
- :undoc-members:
- :show-inheritance:
-
-parmepy.operator.reprojection module
-------------------------------------
-
-.. automodule:: parmepy.operator.reprojection
- :members:
- :undoc-members:
- :show-inheritance:
-
-parmepy.operator.stretching module
-----------------------------------
-
-.. automodule:: parmepy.operator.stretching
- :members:
- :undoc-members:
- :show-inheritance:
-
-parmepy.operator.velocity_correction module
--------------------------------------------
-
-.. automodule:: parmepy.operator.velocity_correction
- :members:
- :undoc-members:
- :show-inheritance:
-
-
-Module contents
----------------
-
-.. automodule:: parmepy.operator
- :members:
- :undoc-members:
- :show-inheritance:
diff --git a/Docs/sphinx_sources/parmepy.problem.rst b/Docs/sphinx_sources/parmepy.problem.rst
deleted file mode 100644
index 92d9ff6ca2dffb7a0b41bda8ebcc1e67ba4e73ee..0000000000000000000000000000000000000000
--- a/Docs/sphinx_sources/parmepy.problem.rst
+++ /dev/null
@@ -1,69 +0,0 @@
-parmepy.problem package
-=======================
-
-Subpackages
------------
-
-.. toctree::
-
- parmepy.problem.tests
-
-Submodules
-----------
-
-parmepy.problem.navier_stokes module
-------------------------------------
-
-.. automodule:: parmepy.problem.navier_stokes
- :members:
- :undoc-members:
- :show-inheritance:
-
-parmepy.problem.problem module
-------------------------------
-
-.. automodule:: parmepy.problem.problem
- :members:
- :undoc-members:
- :show-inheritance:
-
-parmepy.problem.problem_tasks module
-------------------------------------
-
-.. automodule:: parmepy.problem.problem_tasks
- :members:
- :undoc-members:
- :show-inheritance:
-
-parmepy.problem.problem_with_GLRendering module
------------------------------------------------
-
-.. automodule:: parmepy.problem.problem_with_GLRendering
- :members:
- :undoc-members:
- :show-inheritance:
-
-parmepy.problem.simulation module
----------------------------------
-
-.. automodule:: parmepy.problem.simulation
- :members:
- :undoc-members:
- :show-inheritance:
-
-parmepy.problem.transport module
---------------------------------
-
-.. automodule:: parmepy.problem.transport
- :members:
- :undoc-members:
- :show-inheritance:
-
-
-Module contents
----------------
-
-.. automodule:: parmepy.problem
- :members:
- :undoc-members:
- :show-inheritance:
diff --git a/Docs/sphinx_sources/parmepy.rst b/Docs/sphinx_sources/parmepy.rst
deleted file mode 100644
index 95f27b689fe0f43d18bd0cbb9c0ff910862b003c..0000000000000000000000000000000000000000
--- a/Docs/sphinx_sources/parmepy.rst
+++ /dev/null
@@ -1,62 +0,0 @@
-parmepy package
-===============
-
-Subpackages
------------
-
-.. toctree::
-
- parmepy.domain
- parmepy.fakef2py
- parmepy.fields
- parmepy.gpu
- parmepy.mpi
- parmepy.numerics
- parmepy.operator
- parmepy.problem
- parmepy.test
- parmepy.tools
-
-Submodules
-----------
-
-parmepy.constants module
-------------------------
-
-.. automodule:: parmepy.constants
- :members:
- :undoc-members:
- :show-inheritance:
-
-parmepy.default_methods module
-------------------------------
-
-.. automodule:: parmepy.default_methods
- :members:
- :undoc-members:
- :show-inheritance:
-
-parmepy.methods module
-----------------------
-
-.. automodule:: parmepy.methods
- :members:
- :undoc-members:
- :show-inheritance:
-
-parmepy.methods_keys module
----------------------------
-
-.. automodule:: parmepy.methods_keys
- :members:
- :undoc-members:
- :show-inheritance:
-
-
-Module contents
----------------
-
-.. automodule:: parmepy
- :members:
- :undoc-members:
- :show-inheritance:
diff --git a/Docs/sphinx_sources/parmepy.tools.rst b/Docs/sphinx_sources/parmepy.tools.rst
deleted file mode 100644
index c71e8924d9d3d6f6b38efc1f669fce6486a21d38..0000000000000000000000000000000000000000
--- a/Docs/sphinx_sources/parmepy.tools.rst
+++ /dev/null
@@ -1,101 +0,0 @@
-parmepy.tools package
-=====================
-
-Subpackages
------------
-
-.. toctree::
-
- parmepy.tools.tests
-
-Submodules
-----------
-
-parmepy.tools.indices module
-----------------------------
-
-.. automodule:: parmepy.tools.indices
- :members:
- :undoc-members:
- :show-inheritance:
-
-parmepy.tools.io_utils module
------------------------------
-
-.. automodule:: parmepy.tools.io_utils
- :members:
- :undoc-members:
- :show-inheritance:
-
-parmepy.tools.numpywrappers module
-----------------------------------
-
-.. automodule:: parmepy.tools.numpywrappers
- :members:
- :undoc-members:
- :show-inheritance:
-
-parmepy.tools.parameters module
--------------------------------
-
-.. automodule:: parmepy.tools.parameters
- :members:
- :undoc-members:
- :show-inheritance:
-
-parmepy.tools.plotDrag module
------------------------------
-
-.. automodule:: parmepy.tools.plotDrag
- :members:
- :undoc-members:
- :show-inheritance:
-
-parmepy.tools.problem2dot module
---------------------------------
-
-.. automodule:: parmepy.tools.problem2dot
- :members:
- :undoc-members:
- :show-inheritance:
-
-parmepy.tools.profiling module
-------------------------------
-
-.. automodule:: parmepy.tools.profiling
- :members:
- :undoc-members:
- :show-inheritance:
-
-parmepy.tools.remeshing_formula_parsing module
-----------------------------------------------
-
-.. automodule:: parmepy.tools.remeshing_formula_parsing
- :members:
- :undoc-members:
- :show-inheritance:
-
-parmepy.tools.sys_utils module
-------------------------------
-
-.. automodule:: parmepy.tools.sys_utils
- :members:
- :undoc-members:
- :show-inheritance:
-
-parmepy.tools.timers module
----------------------------
-
-.. automodule:: parmepy.tools.timers
- :members:
- :undoc-members:
- :show-inheritance:
-
-
-Module contents
----------------
-
-.. automodule:: parmepy.tools
- :members:
- :undoc-members:
- :show-inheritance:
diff --git a/Docs/sphinx_sources/reference/index.rst b/Docs/sphinx_sources/reference/index.rst
new file mode 100644
index 0000000000000000000000000000000000000000..79977116df47ab4320f5ce34d5a6e679ed775453
--- /dev/null
+++ b/Docs/sphinx_sources/reference/index.rst
@@ -0,0 +1,11 @@
+.. HySoP reference (auto generated) documentation
+
+Welcome to HySoP's documentation!
+==================================
+
+Contents:
+
+.. toctree::
+ :maxdepth: 2
+
+ modules
diff --git a/Docs/sphinx_sources/develnotes.rst b/Docs/sphinx_sources/user_guide/develnotes.rst
similarity index 100%
rename from Docs/sphinx_sources/develnotes.rst
rename to Docs/sphinx_sources/user_guide/develnotes.rst
diff --git a/Docs/sphinx_sources/forces.rst b/Docs/sphinx_sources/user_guide/forces.rst
similarity index 100%
rename from Docs/sphinx_sources/forces.rst
rename to Docs/sphinx_sources/user_guide/forces.rst
diff --git a/Docs/sphinx_sources/user_guide/index.rst b/Docs/sphinx_sources/user_guide/index.rst
new file mode 100644
index 0000000000000000000000000000000000000000..54ce631d5b093daba8d0acdc4598145b25366b12
--- /dev/null
+++ b/Docs/sphinx_sources/user_guide/index.rst
@@ -0,0 +1,25 @@
+.. HySoP documentation master file, created by
+ sphinx-quickstart on Tue Jul 15 16:46:52 2014.
+ You can adapt this file completely to your liking, but it should at least
+ contain the root `toctree` directive.
+
+Welcome to HySoP's documentation!
+==================================
+
+Contents:
+
+.. toctree::
+ :maxdepth: 2
+
+ introduction
+ redistribute
+ develnotes
+ memo_sphinx
+
+
+Indices and tables
+==================
+
+* :ref:`genindex`
+* :ref:`modindex`
+* :ref:`search`
diff --git a/Docs/sphinx_sources/introduction.rst b/Docs/sphinx_sources/user_guide/introduction.rst
similarity index 83%
rename from Docs/sphinx_sources/introduction.rst
rename to Docs/sphinx_sources/user_guide/introduction.rst
index 6fa19c60d3b4a00f6c8bc66dab77bc176ea6402e..af16a0cb11dac0c77eaa22ae69b3caf9c97229d8 100644
--- a/Docs/sphinx_sources/introduction.rst
+++ b/Docs/sphinx_sources/user_guide/introduction.rst
@@ -3,8 +3,8 @@
Introduction
============
-ParMepy (Particular Methods Software) is a library dedicated to
-flow simulation based on particular methods,
+HySoP (Hybrid SimulatiOn with Particles) is a library dedicated to
+flow simulation based on particles methods,
on hybrid (multi CPU-GPU) architecture.
It is written in Python (high level functionnalities) and Fortran.
diff --git a/Docs/sphinx_sources/user_guide/memo_sphinx.rst b/Docs/sphinx_sources/user_guide/memo_sphinx.rst
new file mode 100644
index 0000000000000000000000000000000000000000..2b26176637ec970bc3fa88b3fa47d3136241c5ba
--- /dev/null
+++ b/Docs/sphinx_sources/user_guide/memo_sphinx.rst
@@ -0,0 +1,28 @@
+.. _memo_sphinx:
+
+Reminder for sphinx utilities
+=============================
+
+To print source Code::
+
+ for i in xrange(3):
+ do un_truc()
+
+Hyperlinks `HySoP Web`_.
+
+.. _Hysop Web: https://forge.imag.fr
+
+.. math::
+ \begin{eqnarray}
+ a &=& \frac{1}{2}\\
+ \alpha &=& 3 \times \nabla \omega
+ \end{eqnarray}
+
+To print a link to some HySoP object:
+
+.. currentmodule:: hysop.operator.discrete
+
+An example of a discrete operator, :class:`stretching.Conservative`, used to represent the
+stretching part of NS.
+
+
diff --git a/Docs/sphinx_sources/modules.rst b/Docs/sphinx_sources/user_guide/modules.rst
similarity index 67%
rename from Docs/sphinx_sources/modules.rst
rename to Docs/sphinx_sources/user_guide/modules.rst
index 3aff027fde3d9902352c96354210099d5b6a3718..6845fe56470ff697e18a2893e11f94c150b85c9f 100644
--- a/Docs/sphinx_sources/modules.rst
+++ b/Docs/sphinx_sources/user_guide/modules.rst
@@ -1,7 +1,7 @@
-parmepy
+hysop
=======
.. toctree::
:maxdepth: 4
- parmepy
+ hysop
diff --git a/Docs/sphinx_sources/redistribute.rst b/Docs/sphinx_sources/user_guide/redistribute.rst
similarity index 100%
rename from Docs/sphinx_sources/redistribute.rst
rename to Docs/sphinx_sources/user_guide/redistribute.rst
diff --git a/Examples/TaylorGreen3D_debug.py b/Examples/TaylorGreen3D_debug.py
index 5a04498d91d0fcda2b67ee6121e466352d632729..7f7eef8871b06252c7237355f9076f1d8884fa25 100644
--- a/Examples/TaylorGreen3D_debug.py
+++ b/Examples/TaylorGreen3D_debug.py
@@ -11,7 +11,6 @@ from hysop import Box
from hysop.f2py import fftw2py
import numpy as np
from hysop.fields.continuous import Field
-from hysop.fields.variable_parameter import VariableParameter
from hysop.operator.advection import Advection
from hysop.operator.stretching import Stretching
from hysop.operator.poisson import Poisson
@@ -69,8 +68,6 @@ velo = Field(domain=box, formula=computeVel,
vorti = Field(domain=box, formula=computeVort,
name='Vorticity', isVector=True)
-# ======= Parameter Variable (adaptative timestep) =======
-dt = VariableParameter(data=0.0125, name='dt')
# ========= Simulation setup =========
simu = Simulation(tinit=0.0, tend=10.0, timeStep=0.0125, iterMax=50)
diff --git a/HySoP/hysop/domain/box.py b/HySoP/hysop/domain/box.py
index 0a22d36ce795cfd1beea7f6bf887ec908aff4500..b67c20794e30d513b349af7b91476146c539b62a 100644
--- a/HySoP/hysop/domain/box.py
+++ b/HySoP/hysop/domain/box.py
@@ -19,18 +19,18 @@ class Box(Domain):
def __init__(self, length=None, origin=None, **kwds):
"""
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. Default [1.0, ...]
@param origin : Box minimum position. Default [0., ...]
- \code
+
+ Example:
+
>>> import hysop as pp
>>> import numpy as np
>>> b = pp.Box()
>>> (b.end == np.asarray([1.0, 1.0, 1.0])).all()
True
- \endcode
"""
if 'dimension' not in kwds:
if length is not None or origin is not None:
diff --git a/HySoP/hysop/gpu/tests/test_advection_nullVelocity.py b/HySoP/hysop/gpu/tests/test_advection_nullVelocity.py
index de2f58dbd1328b51a623c1996c912e4c0a3f3a68..3e73d98bcdf1fbce023289ec16691779a37eab59 100644
--- a/HySoP/hysop/gpu/tests/test_advection_nullVelocity.py
+++ b/HySoP/hysop/gpu/tests/test_advection_nullVelocity.py
@@ -42,11 +42,13 @@ def assertion_2D(scal, velo, advec):
scal_init = scal_d.data[0].copy()
scal_d.toDevice()
velo_d.toDevice()
-
+ scal_d.wait()
+ velo_d.wait()
+
advec.apply(Simulation(tinit=0., tend=0.01, nbIter=1))
scal_d.toHost()
-
+ scal_d.wait()
advec.finalize()
return np.allclose(scal_init, scal_d.data[0])
@@ -59,17 +61,21 @@ def assertion_2D_withPython(scal, velo, advec, advec_py):
scal_d = scal.discreteFields.values()[0]
velo_d = velo.discreteFields.values()[0]
- scal_d.data[0][...] = npw.asrealarray(np.random.random(scal_d.data[0].shape))
- velo_d.data[0][...] = npw.zeros_like(scal_d.data[0])
- velo_d.data[1][...] = npw.zeros_like(scal_d.data[0])
+ scal_d.data[0][...] = npw.asrealarray(
+ np.random.random(scal_d.data[0].shape))
+ velo_d.data[0][...] = npw.zeros(scal_d.data[0].shape)
+ velo_d.data[1][...] = npw.zeros(scal_d.data[0].shape)
scal_d.toDevice()
velo_d.toDevice()
+ scal_d.wait()
+ velo_d.wait()
advec_py.apply(Simulation(tinit=0., tend=0.01, nbIter=1))
advec.apply(Simulation(tinit=0., tend=0.01, nbIter=1))
py_res = scal_d.data[0].copy()
scal_d.toHost()
+ scal_d.wait()
advec.finalize()
print py_res, scal_d.data[0]
@@ -90,10 +96,13 @@ def assertion_3D(scal, velo, advec):
scal_init = scal_d.data[0].copy()
scal_d.toDevice()
velo_d.toDevice()
+ scal_d.wait()
+ velo_d.wait()
advec.apply(Simulation(tinit=0., tend=0.01, nbIter=1))
scal_d.toHost()
+ scal_d.wait()
advec.finalize()
return np.allclose(scal_init, scal_d.data[0])
@@ -113,12 +122,15 @@ def assertion_3D_withPython(scal, velo, advec, advec_py):
velo_d.data[2][...] = npw.zeros_like(scal_d.data[0])
scal_d.toDevice()
velo_d.toDevice()
+ scal_d.wait()
+ velo_d.wait()
advec_py.apply(Simulation(tinit=0., tend=0.01, nbIter=1))
advec.apply(Simulation(tinit=0., tend=0.01, nbIter=1))
py_res = scal_d.data[0].copy()
scal_d.toHost()
+ scal_d.wait()
advec.finalize()
return np.allclose(py_res, scal_d.data[0])
@@ -130,7 +142,7 @@ d3d = Discretization([17, 17, 17])
# M6 tests
def test_2D_m6_1k():
"""
- Testing M6 remeshing formula in 2D, 1 kernel, simple precision,
+ Testing M6 remeshing formula in 2D, 1 kernel,
o2 splitting.
"""
scal, velo = setup_2D()
@@ -156,7 +168,7 @@ def test_2D_m6_1k():
def test_2D_m6_2k():
"""
- Testing M6 remeshing formula in 2D, 2 kernel, simple precision,
+ Testing M6 remeshing formula in 2D, 2 kernel,
o2 splitting.
"""
scal, velo = setup_2D()
@@ -174,7 +186,7 @@ def test_2D_m6_2k():
def test_2D_m6_1k_sFH():
"""
- Testing M6 remeshing formula in 2D, 1 kernel, simple precision,
+ Testing M6 remeshing formula in 2D, 1 kernel,
o2_FullHalf splitting.
"""
scal, velo = setup_2D()
@@ -192,7 +204,7 @@ def test_2D_m6_1k_sFH():
def test_2D_m6_2k_sFH():
"""
- Testing M6 remeshing formula in 2D, 2 kernel, simple precision,
+ Testing M6 remeshing formula in 2D, 2 kernel,
o2_FullHalf splitting.
"""
scal, velo = setup_2D()
@@ -210,7 +222,7 @@ def test_2D_m6_2k_sFH():
def test_3D_m6_1k():
"""
- Testing M6 remeshing formula in 3D, 1 kernel, simple precision,
+ Testing M6 remeshing formula in 3D, 1 kernel,
o2 splitting.
"""
scal, velo = setup_3D()
@@ -228,7 +240,7 @@ def test_3D_m6_1k():
def test_3D_m6_2k():
"""
- Testing M6 remeshing formula in 3D, 2 kernel, simple precision,
+ Testing M6 remeshing formula in 3D, 2 kernel,
o2 splitting.
"""
scal, velo = setup_3D()
@@ -246,7 +258,7 @@ def test_3D_m6_2k():
def test_3D_m6_1k_sFH():
"""
- Testing M6 remeshing formula in 3D, 1 kernel, simple precision,
+ Testing M6 remeshing formula in 3D, 1 kernel,
o2_FullHalf splitting.
"""
scal, velo = setup_3D()
@@ -264,7 +276,7 @@ def test_3D_m6_1k_sFH():
def test_3D_m6_2k_sFH():
"""
- Testing M6 remeshing formula in 3D, 2 kernel, simple precision,
+ Testing M6 remeshing formula in 3D, 2 kernel,
o2_FullHalf splitting.
"""
scal, velo = setup_3D()
@@ -283,7 +295,7 @@ def test_3D_m6_2k_sFH():
# M4 testing
def test_2D_m4_1k():
"""
- Testing M4 remeshing formula in 2D, 1 kernel, simple precision,
+ Testing M4 remeshing formula in 2D, 1 kernel,
o2 splitting.
"""
scal, velo = setup_2D()
@@ -308,7 +320,7 @@ def test_2D_m4_1k():
def test_2D_m4_2k():
"""
- Testing M4 remeshing formula in 2D, 2 kernel, simple precision,
+ Testing M4 remeshing formula in 2D, 2 kernel,
o2 splitting.
"""
scal, velo = setup_2D()
@@ -334,7 +346,7 @@ def test_2D_m4_2k():
def test_2D_m4_1k_sFH():
"""
- Testing M4 remeshing formula in 2D, 1 kernel, simple precision,
+ Testing M4 remeshing formula in 2D, 1 kernel,
o2_FullHalf splitting.
"""
scal, velo = setup_2D()
@@ -359,7 +371,7 @@ def test_2D_m4_1k_sFH():
def test_2D_m4_2k_sFH():
"""
- Testing M4 remeshing formula in 2D, 2 kernel, simple precision,
+ Testing M4 remeshing formula in 2D, 2 kernel,
o2_FullHalf splitting.
"""
scal, velo = setup_2D()
@@ -383,7 +395,7 @@ def test_2D_m4_2k_sFH():
def test_3D_m4_1k():
"""
- Testing M4 remeshing formula in 3D, 1 kernel, simple precision,
+ Testing M4 remeshing formula in 3D, 1 kernel,
o2 splitting.
"""
scal, velo = setup_3D()
@@ -407,7 +419,7 @@ def test_3D_m4_1k():
def test_3D_m4_2k():
"""
- Testing M4 remeshing formula in 3D, 2 kernel, simple precision,
+ Testing M4 remeshing formula in 3D, 2 kernel,
o2 splitting.
"""
scal, velo = setup_3D()
@@ -431,7 +443,7 @@ def test_3D_m4_2k():
def test_3D_m4_1k_sFH():
"""
- Testing M4 remeshing formula in 3D, 1 kernel, simple precision,
+ Testing M4 remeshing formula in 3D, 1 kernel,
o2_FullHalf splitting.
"""
scal, velo = setup_3D()
@@ -454,7 +466,7 @@ def test_3D_m4_1k_sFH():
def test_3D_m4_2k_sFH():
"""
- Testing M4 remeshing formula in 3D, 2 kernel, simple precision,
+ Testing M4 remeshing formula in 3D, 2 kernel,
o2_FullHalf splitting.
"""
scal, velo = setup_3D()
@@ -479,7 +491,7 @@ def test_3D_m4_2k_sFH():
# M8 testing
def test_2D_m8_1k():
"""
- Testing M8 remeshing formula in 2D, 1 kernel, simple precision,
+ Testing M8 remeshing formula in 2D, 1 kernel,
o2 splitting.
"""
scal, velo = setup_2D()
@@ -503,7 +515,7 @@ def test_2D_m8_1k():
def test_2D_m8_2k():
"""
- Testing M8 remeshing formula in 2D, 2 kernel, simple precision,
+ Testing M8 remeshing formula in 2D, 2 kernel,
o2 splitting.
"""
scal, velo = setup_2D()
@@ -527,12 +539,12 @@ def test_2D_m8_2k():
def test_2D_m8_1k_sFH():
"""
- Testing M8 remeshing formula in 2D, 1 kernel, simple precision,
+ Testing M8 remeshing formula in 2D, 1 kernel,
o2_FullHalf splitting.
"""
scal, velo = setup_2D()
- advec = Advection(velo, scal,discretization=d2d,
+ advec = Advection(velo, scal, discretization=d2d,
method={TimeIntegrator: RK2,
Interpolation: Linear,
Remesh: M8Prime,
@@ -551,7 +563,7 @@ def test_2D_m8_1k_sFH():
def test_2D_m8_2k_sFH():
"""
- Testing M8 remeshing formula in 2D, 2 kernel, simple precision,
+ Testing M8 remeshing formula in 2D, 2 kernel,
o2_FullHalf splitting.
"""
scal, velo = setup_2D()
@@ -575,7 +587,7 @@ def test_2D_m8_2k_sFH():
def test_3D_m8_1k():
"""
- Testing M8 remeshing formula in 3D, 1 kernel, simple precision,
+ Testing M8 remeshing formula in 3D, 1 kernel,
o2 splitting.
"""
scal, velo = setup_3D()
@@ -599,7 +611,7 @@ def test_3D_m8_1k():
def test_3D_m8_2k():
"""
- Testing M8 remeshing formula in 3D, 2 kernel, simple precision,
+ Testing M8 remeshing formula in 3D, 2 kernel,
o2 splitting.
"""
scal, velo = setup_3D()
@@ -623,7 +635,7 @@ def test_3D_m8_2k():
def test_3D_m8_1k_sFH():
"""
- Testing M8 remeshing formula in 3D, 1 kernel, simple precision,
+ Testing M8 remeshing formula in 3D, 1 kernel,
o2_FullHalf splitting.
"""
scal, velo = setup_3D()
@@ -647,7 +659,7 @@ def test_3D_m8_1k_sFH():
def test_3D_m8_2k_sFH():
"""
- Testing M8 remeshing formula in 3D, 2 kernel, simple precision,
+ Testing M8 remeshing formula in 3D, 2 kernel,
o2_FullHalf splitting.
"""
scal, velo = setup_3D()
@@ -671,7 +683,7 @@ def test_3D_m8_2k_sFH():
def test_2D_l6_2k():
"""
- Testing Lambda6star remeshing formula in 2D, 2 kernel, simple precision,
+ Testing Lambda6star remeshing formula in 2D, 2 kernel,
o2 splitting.
"""
scal, velo = setup_2D()
@@ -688,7 +700,7 @@ def test_2D_l6_2k():
def test_2D_l6_1k_sFH():
"""
- Testing Lambda6star remeshing formula in 2D, 1 kernel, simple precision,
+ Testing Lambda6star remeshing formula in 2D, 1 kernel,
o2_FullHalf splitting.
"""
scal, velo = setup_2D()
@@ -705,7 +717,7 @@ def test_2D_l6_1k_sFH():
def test_2D_l6_2k_sFH():
"""
- Testing Lambda6star remeshing formula in 2D, 2 kernel, simple precision,
+ Testing Lambda6star remeshing formula in 2D, 2 kernel,
o2_FullHalf splitting.
"""
scal, velo = setup_2D()
@@ -722,7 +734,7 @@ def test_2D_l6_2k_sFH():
def test_3D_l6_1k():
"""
- Testing Lambda6star remeshing formula in 3D, 1 kernel, simple precision,
+ Testing Lambda6star remeshing formula in 3D, 1 kernel,
o2 splitting.
"""
scal, velo = setup_3D()
@@ -739,7 +751,7 @@ def test_3D_l6_1k():
def test_3D_l6_2k():
"""
- Testing Lambda6star remeshing formula in 3D, 2 kernel, simple precision,
+ Testing Lambda6star remeshing formula in 3D, 2 kernel,
o2 splitting.
"""
scal, velo = setup_3D()
@@ -756,7 +768,7 @@ def test_3D_l6_2k():
def test_3D_l6_1k_sFH():
"""
- Testing Lambda6star remeshing formula in 3D, 1 kernel, simple precision,
+ Testing Lambda6star remeshing formula in 3D, 1 kernel,
o2_FullHalf splitting.
"""
scal, velo = setup_3D()
@@ -773,7 +785,7 @@ def test_3D_l6_1k_sFH():
def test_3D_l6_2k_sFH():
"""
- Testing Lambda6star remeshing formula in 3D, 2 kernel, simple precision,
+ Testing Lambda6star remeshing formula in 3D, 2 kernel,
o2_FullHalf splitting.
"""
scal, velo = setup_3D()
diff --git a/HySoP/hysop/numerics/integrators/euler.py b/HySoP/hysop/numerics/integrators/euler.py
index c65192afc17d0468a09a8fdf3e82cf324eac9693..4151970e0fdfcee63d85605a101fe49973d0a236 100755
--- a/HySoP/hysop/numerics/integrators/euler.py
+++ b/HySoP/hysop/numerics/integrators/euler.py
@@ -51,7 +51,7 @@ class Euler(ODESolver):
# result = y + dt * work0
# result = y + work0
- [np.add(y[i], self.work[i] * dt, result[i])
+ [np.add(y[i], self.work[i] * dt, result[i])
for i in xrange(self._nbComponents)]
return result
diff --git a/HySoP/hysop/operator/discrete/drag_and_lift.py b/HySoP/hysop/operator/discrete/drag_and_lift.py
index 7782cf0056127a1b600703ecb2eb9af0f4f88690..ebe521df43a3008709ee5cbbdbe1e6dfc7ae942e 100644
--- a/HySoP/hysop/operator/discrete/drag_and_lift.py
+++ b/HySoP/hysop/operator/discrete/drag_and_lift.py
@@ -179,6 +179,7 @@ class MomentumForces(Forces):
for d in xrange(nbc)]
self.force[...] = 1. / dt * (self._buffer - self._previous)
# Update previous for next time step ...
+ # Which value must we choose for previous??
self._previous[...] = self._buffer[...]
@@ -593,18 +594,18 @@ class NocaIII(NocaForces):
dsurf = npw.prod(self._topology.mesh.space_step[i_t])
self._buffer[...] = 0.0
# First, part relative to "du/dt"
- self._compute_gamma_impulse(dt, s_x0, -1, 2 * d, self._buffer)
+ self._compute_gamma_flux(dt, s_x0, -1, 2 * d, self._buffer)
self._compute_gamma_common(s_x0, -1, 2 * d, self._buffer)
self.force += self._buffer * dsurf
self._buffer[...] = 0.0
- self._compute_gamma_impulse(dt, s_xn, 1, 2 * d + 1, self._buffer)
+ self._compute_gamma_flux(dt, s_xn, 1, 2 * d + 1, self._buffer)
self._compute_gamma_common(s_xn, 1, 2 * d + 1, self._buffer)
self.force += self._buffer * dsurf
self.force *= self._normalization
self._update_buffers()
- def _compute_gamma_impulse(self, dt, surf, normal, s_id, res):
+ def _compute_gamma_flux(self, dt, surf, normal, s_id, res):
# i_n : normal dir
# i_t : other dirs
i_n = surf.n_dir
diff --git a/HySoP/hysop/operator/discrete/penalization_and_curl.py b/HySoP/hysop/operator/discrete/penalize_vorticity.py
similarity index 87%
rename from HySoP/hysop/operator/discrete/penalization_and_curl.py
rename to HySoP/hysop/operator/discrete/penalize_vorticity.py
index e4830a206ffd502acbe747d428bbbe1c4e786c40..f0fa15ddf5d60fd51be889e724134909b7b20a03 100644
--- a/HySoP/hysop/operator/discrete/penalization_and_curl.py
+++ b/HySoP/hysop/operator/discrete/penalize_vorticity.py
@@ -7,7 +7,7 @@ from hysop.constants import debug
from hysop.operator.discrete.penalization import Penalization
-class PenalizationAndCurl(Penalization):
+class PenalizeVorticity(Penalization):
"""
Discretized penalisation operator.
See details in hysop.operator.penalization
@@ -21,7 +21,7 @@ class PenalizationAndCurl(Penalization):
somebuffer = curl(penalized vorticity)
"""
assert 'variables' not in kwds, 'variables parameter is useless.'
- super(PenalizationAndCurl, self).__init__(variables=[vorticity,
+ super(PenalizeVorticity, self).__init__(variables=[vorticity,
curl.invar],
**kwds)
self.velocity = curl.invar
@@ -33,10 +33,11 @@ class PenalizationAndCurl(Penalization):
def _apply_single_coeff(self, dt):
coeff = -dt * self._coeff / (1.0 + dt * self._coeff)
+ print coeff
self._penalize(self.velocity, coeff, self._cond)
self._curl.apply()
for d in xrange(self.vorticity.nbComponents):
- self.vorticity[d][...] += self._curl.invar[d]
+ self.vorticity[d][self._cond] += self._curl.outvar[d][self._cond]
coeff = -1. / (dt * self._coeff)
self._penalize(self.velocity, coeff, self._cond)
@@ -47,7 +48,7 @@ class PenalizationAndCurl(Penalization):
self._penalize(self.velocity, coeff, cond)
self._curl.apply()
for d in xrange(self.vorticity.nbComponents):
- self.vorticity[d][...] += self._curl.invar[d]
+ self.vorticity[d][self._cond] += self._curl.outvar[d][self._cond]
for i in xrange(len(self._cond)):
coeff = -1. / dt * self._coeff[i]
cond = self._cond[i]
diff --git a/HySoP/hysop/operator/discrete/stretching.py b/HySoP/hysop/operator/discrete/stretching.py
index 66236a7cc4c88191144d040ea883db7801a0ed16..38f6e52f2d994b63c21d073c05322881c9ce539e 100755
--- a/HySoP/hysop/operator/discrete/stretching.py
+++ b/HySoP/hysop/operator/discrete/stretching.py
@@ -2,7 +2,7 @@
"""
@file operator/discrete/stretching.py
-Discretisation of the stretching operator for two different formulations.
+Discretisation of the stretching operator for different formulations.
"""
from hysop.constants import debug, WITH_GUESS
@@ -25,9 +25,10 @@ ceil = math.ceil
class Stretching(DiscreteOperator):
"""
Abstract interface to stretching discrete operators.
- Two formulations are available:
+ Three formulations are available:
- conservative, see operator.discrete.stretching.Conservative
- 'Grad(UxW), see operator.discrete.stretching.GradUW
+ - Symmetric, see operator.discrete.stretching.Symmetric
"""
__metaclass__ = ABCMeta
@@ -242,3 +243,49 @@ class GradUW(Stretching):
subdt[:] = dt_stab
subdt[-1] = dt - (nb_cycles - 1) * dt_stab
return nb_cycles, subdt
+
+
+class Symmetric(Stretching):
+ """
+ Discretisation of the following problem :
+ \f{eqnarray*} \frac{\partial\omega}{\partial t} = \frac{1}{2}(\nabla(v) + \nabla(v)^T)\omega \f}
+ """
+ def __init__(self, **kwds):
+ super(Symmetric, self).__init__(formulation=diff_op.DivWV, **kwds)
+
+ # Time integration scheme.
+ def rhs(t, y, result):
+ result = self.strFunc(y, self.velocity.data, result)
+ return result
+
+ # Create the time integrator
+ self.timeIntegrator = \
+ self.method[TimeIntegrator](self.nbComponents,
+ self._ti_work,
+ self.velocity.topology,
+ f=rhs,
+ optim=WITH_GUESS)
+
+ @debug
+ @profile
+ def apply(self, simulation=None):
+ assert simulation is not None, \
+ "Missing simulation value for computation."
+
+ # time step
+ dt = simulation.timeStep
+ # current time
+ t = simulation.time
+ # Synchronize ghost points of velocity and vorticity
+ self._synchronize(self.velocity.data + self.vorticity.data)
+ # - Call time integrator -
+ # Init workspace with a first evaluation of the
+ # rhs of the integrator
+ self._ti_work[:self.nbComponents] = \
+ self.timeIntegrator.f(t, self.vorticity.data,
+ self._ti_work[:self.nbComponents])
+ # perform integration and save result in-place
+ self.vorticity.data = self.timeIntegrator(t, self.vorticity.data, dt,
+ result=self.vorticity.data)
+
+
diff --git a/HySoP/hysop/operator/penalization_and_curl.py b/HySoP/hysop/operator/penalize_vorticity.py
similarity index 90%
rename from HySoP/hysop/operator/penalization_and_curl.py
rename to HySoP/hysop/operator/penalize_vorticity.py
index 2bdccc7a34646ac4503dbcb7152c3d9fa6eba83c..1cd39ab43f03cd606eba48b3c62ec6130443c8ac 100644
--- a/HySoP/hysop/operator/penalization_and_curl.py
+++ b/HySoP/hysop/operator/penalize_vorticity.py
@@ -5,8 +5,8 @@
Compute the vorticity field from velocity using penalization.
"""
from hysop.operator.penalization import Penalization
-from hysop.operator.discrete.penalization_and_curl\
- import PenalizationAndCurl as PAC
+from hysop.operator.discrete.penalize_vorticity\
+ import PenalizeVorticity as PW
from hysop.constants import debug
from hysop.operator.continuous import opsetup
import hysop.default_methods as default
@@ -17,7 +17,7 @@ from hysop.operator.differential import Curl
from hysop.fields.continuous import Field
-class PenalizationAndCurl(Penalization):
+class PenalizeVorticity(Penalization):
"""
Solve
\f{eqnarray*}
@@ -33,7 +33,7 @@ class PenalizationAndCurl(Penalization):
@param[in,out] vorticity : vorticity field
"""
assert 'variables' not in kwds, 'variables parameter is useless.'
- super(PenalizationAndCurl, self).__init__(variables=[velocity,
+ super(PenalizeVorticity, self).__init__(variables=[velocity,
vorticity],
**kwds)
## velocity field
@@ -57,7 +57,7 @@ class PenalizationAndCurl(Penalization):
else:
raise ValueError("Unknown method for space discretization of the\
differential operator in penalization.")
- super(PenalizationAndCurl, self)._standard_discretize(nbGhosts)
+ super(PenalizeVorticity, self)._standard_discretize(nbGhosts)
# all variables must have the same resolution
assert self._single_topo, 'multi-resolution case not allowed.'
topo = self.variables[self.velocity]
@@ -78,7 +78,7 @@ class PenalizationAndCurl(Penalization):
@opsetup
def setup(self, rwork=None, iwork=None):
self._curl.setup(rwork, iwork)
- self.discrete_op = PAC(
+ self.discrete_op = PW(
vorticity=self.discreteFields[self.vorticity],
curl=self._curl.discrete_op,
obstacles=self.obstacles,
diff --git a/HySoP/hysop/operator/tests/Testing/Temporary/CTestCostData.txt b/HySoP/hysop/operator/tests/Testing/Temporary/CTestCostData.txt
deleted file mode 100644
index ed97d539c095cf1413af30cc23dea272095b97dd..0000000000000000000000000000000000000000
--- a/HySoP/hysop/operator/tests/Testing/Temporary/CTestCostData.txt
+++ /dev/null
@@ -1 +0,0 @@
----
diff --git a/HySoP/hysop/operator/tests/Testing/Temporary/LastTest.log b/HySoP/hysop/operator/tests/Testing/Temporary/LastTest.log
deleted file mode 100644
index b448b0555ed69bab888caa8f66c3534ccd6779ed..0000000000000000000000000000000000000000
--- a/HySoP/hysop/operator/tests/Testing/Temporary/LastTest.log
+++ /dev/null
@@ -1,3 +0,0 @@
-Start testing: Mar 12 09:26 CET
-----------------------------------------------------------
-End testing: Mar 12 09:26 CET
diff --git a/HySoP/hysop/operator/tests/parmesfftw.log b/HySoP/hysop/operator/tests/parmesfftw.log
deleted file mode 100644
index e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
diff --git a/HySoP/hysop/operator/tests/ref_files/p1/penal_vort_2d_sphere_00000.h5 b/HySoP/hysop/operator/tests/ref_files/p1/penal_vort_2d_sphere_00000.h5
index d0779a1c34acf4208bcfbe548bcd0590d303e055..19a24964eface15840a192db6f330388f07117dc 100644
Binary files a/HySoP/hysop/operator/tests/ref_files/p1/penal_vort_2d_sphere_00000.h5 and b/HySoP/hysop/operator/tests/ref_files/p1/penal_vort_2d_sphere_00000.h5 differ
diff --git a/HySoP/hysop/operator/tests/ref_files/p1/penal_vort_3d_sphere_00000.h5 b/HySoP/hysop/operator/tests/ref_files/p1/penal_vort_3d_sphere_00000.h5
index f24b078890d67f888944759308dccf7f3bce961d..c0287248cf6f7a0591091629dc0792362aef4b2b 100644
Binary files a/HySoP/hysop/operator/tests/ref_files/p1/penal_vort_3d_sphere_00000.h5 and b/HySoP/hysop/operator/tests/ref_files/p1/penal_vort_3d_sphere_00000.h5 differ
diff --git a/HySoP/hysop/operator/tests/ref_files/p8/penal_vort_2d_sphere_00000.h5 b/HySoP/hysop/operator/tests/ref_files/p8/penal_vort_2d_sphere_00000.h5
index 4498067bae1dd707b895bf3d0a014eac1ca34afe..4cda70e51b59a4f2140fa3249bd81aaafdcf0179 100644
Binary files a/HySoP/hysop/operator/tests/ref_files/p8/penal_vort_2d_sphere_00000.h5 and b/HySoP/hysop/operator/tests/ref_files/p8/penal_vort_2d_sphere_00000.h5 differ
diff --git a/HySoP/hysop/operator/tests/ref_files/p8/penal_vort_3d_sphere_00000.h5 b/HySoP/hysop/operator/tests/ref_files/p8/penal_vort_3d_sphere_00000.h5
index 37f3155499a58ba5a077b0aa8665f4b079c6b806..adaff3819b40dd732f71a244602e4b6cd72a8890 100644
Binary files a/HySoP/hysop/operator/tests/ref_files/p8/penal_vort_3d_sphere_00000.h5 and b/HySoP/hysop/operator/tests/ref_files/p8/penal_vort_3d_sphere_00000.h5 differ
diff --git a/HySoP/hysop/operator/tests/test_drag_and_lift.py b/HySoP/hysop/operator/tests/test_drag_and_lift.py
index cebb1eb2c8589f6b9435120cca42379539d97247..dbce593d3384346ec70e3bf27c9068be35974bf3 100644
--- a/HySoP/hysop/operator/tests/test_drag_and_lift.py
+++ b/HySoP/hysop/operator/tests/test_drag_and_lift.py
@@ -1,7 +1,6 @@
# -*- coding: utf-8 -*-
from hysop.domain.subsets.sphere import Sphere
-from hysop.operator.penalization import Penalization
-from hysop.operator.penalization_and_curl import PenalizationAndCurl
+from hysop.operator.penalize_vorticity import PenalizeVorticity
from hysop.problem.simulation import Simulation
from hysop.tools.parameters import Discretization, IO_params
from hysop.mpi.topology import Cartesian
@@ -104,9 +103,9 @@ def test_momentum_forces_3D():
vorti = Field(domain=topo.domain, formula=v3d, name='Vorti', isVector=True)
velo = Field(domain=topo.domain, formula=v3d, name='Velo', isVector=True)
hsphere = Sphere(parent=topo.domain, origin=xpos, radius=rd)
- penal = PenalizationAndCurl(velocity=velo, vorticity=vorti,
- discretization=topo,
- obstacles=[hsphere], coeff=1e8)
+ penal = PenalizeVorticity(velocity=velo, vorticity=vorti,
+ discretization=topo,
+ obstacles=[hsphere], coeff=1e8)
penal.discretize()
penal.setup()
diff --git a/HySoP/hysop/operator/tests/test_hdf5/testIO_scal.xmf b/HySoP/hysop/operator/tests/test_hdf5/testIO_scal.xmf
deleted file mode 100644
index 167c44c016c1bae9db38c54b879c7400eaa3d5f1..0000000000000000000000000000000000000000
--- a/HySoP/hysop/operator/tests/test_hdf5/testIO_scal.xmf
+++ /dev/null
@@ -1,42 +0,0 @@
-<?xml version="1.0" ?>
-<!DOCTYPE Xdmf SYSTEM "Xdmf.dtd">
-<Xdmf Version="2.0">
- <Domain>
- <Grid Name="CellTime" GridType="Collection" CollectionType="Temporal">
- <Grid Name="Iteration 000" GridType="Uniform">
- <Time Value="0.0" />
- <Topology TopologyType="3DCORECTMesh" NumberOfElements="64 64 64 "/>
- <Geometry GeometryType="ORIGIN_DXDYDZ">
- <DataItem Dimensions="3 " NumberType="Float" Precision="4" Format="XML">
- -1.0 -1.0 -1.0
- </DataItem>
- <DataItem Dimensions="3 " NumberType="Float" Precision="8" Format="XML">
- 0.03125 0.03125 0.03125
- </DataItem>
- </Geometry>
- <Attribute Name="ScalRef3D_0_X" AttributeType="Scalar" Center="Node">
- <DataItem Dimensions="64 64 64 " NumberType="Float" Precision="8" Format="HDF" Compression="Raw">
- testIO_scal_00000.h5:/ScalRef3D_0_X
- </DataItem>
- </Attribute>
- </Grid>
- <Grid Name="Iteration 001" GridType="Uniform">
- <Time Value="0.3" />
- <Topology TopologyType="3DCORECTMesh" NumberOfElements="64 64 64 "/>
- <Geometry GeometryType="ORIGIN_DXDYDZ">
- <DataItem Dimensions="3 " NumberType="Float" Precision="4" Format="XML">
- -1.0 -1.0 -1.0
- </DataItem>
- <DataItem Dimensions="3 " NumberType="Float" Precision="8" Format="XML">
- 0.03125 0.03125 0.03125
- </DataItem>
- </Geometry>
- <Attribute Name="ScalRef3D_0_X" AttributeType="Scalar" Center="Node">
- <DataItem Dimensions="64 64 64 " NumberType="Float" Precision="8" Format="HDF" Compression="Raw">
- testIO_scal_00001.h5:/ScalRef3D_0_X
- </DataItem>
- </Attribute>
- </Grid>
- </Grid>
- </Domain>
-</Xdmf>
diff --git a/HySoP/hysop/operator/tests/test_hdf5/testIO_scal_00000.h5 b/HySoP/hysop/operator/tests/test_hdf5/testIO_scal_00000.h5
deleted file mode 100644
index 3a2446225bd61bbf04a60851a154984eae08d2fc..0000000000000000000000000000000000000000
Binary files a/HySoP/hysop/operator/tests/test_hdf5/testIO_scal_00000.h5 and /dev/null differ
diff --git a/HySoP/hysop/operator/tests/test_hdf5/testIO_scal_00001.h5 b/HySoP/hysop/operator/tests/test_hdf5/testIO_scal_00001.h5
deleted file mode 100644
index 3a2446225bd61bbf04a60851a154984eae08d2fc..0000000000000000000000000000000000000000
Binary files a/HySoP/hysop/operator/tests/test_hdf5/testIO_scal_00001.h5 and /dev/null differ
diff --git a/HySoP/hysop/operator/tests/test_penalization.py b/HySoP/hysop/operator/tests/test_penalization.py
index 8c94c52928a2b375c0bbebe5dc1b01a56e6c676e..d85d72d04de9a09f2529238e73f8531c2ef4b825 100644
--- a/HySoP/hysop/operator/tests/test_penalization.py
+++ b/HySoP/hysop/operator/tests/test_penalization.py
@@ -3,7 +3,7 @@ from hysop.domain.subsets.sphere import HemiSphere, Sphere
from hysop.domain.subsets.cylinder import Cylinder
from hysop.domain.subsets.porous import Porous
from hysop.operator.penalization import Penalization
-from hysop.operator.penalization_and_curl import PenalizationAndCurl
+from hysop.operator.penalize_vorticity import PenalizeVorticity
from hysop.problem.simulation import Simulation
from hysop.tools.parameters import Discretization, IO_params
from hysop.mpi.topology import Cartesian
@@ -275,14 +275,13 @@ def check_penal_vort(penal, wref, vref, vorti, velo):
velo.initialize(topo=topo)
vd = velo.discretize(topo)
wd = vorti.discretize(topo)
- simu = Simulation(nbIter=3)
- penal.apply(simu)
ind = topo.mesh.iCompute
+
+ simu = Simulation(nbIter=200)
+ penal.apply(simu)
for d in xrange(vd.nbComponents):
- print np.max(np.abs(vd.data[d][ind]- vref.data[d][ind])),np.max(np.abs((vd.data[d][ind]- vref.data[d][ind])/vd.data[d][ind]))
assert np.allclose(vd.data[d][ind], vref.data[d][ind])
for d in xrange(wd.nbComponents):
- print np.max(np.abs(wd.data[d][ind]- wref.data[d][ind])),np.max(np.abs((wd.data[d][ind]- wref.data[d][ind])/wd.data[d][ind]))
assert np.allclose(wd.data[d][ind], wref.data[d][ind])
@@ -299,9 +298,9 @@ def test_penal_vort_2D():
vorti = Field(domain=topo.domain, formula=s2d, name='Vorti')
velo = Field(domain=topo.domain, formula=v2d, name='Velo', isVector=True)
hsphere = HemiSphere(parent=topo.domain, origin=xpos[:2], radius=rd)
- penal = PenalizationAndCurl(velocity=velo, vorticity=vorti,
- discretization=topo,
- obstacles=[hsphere], coeff=1e8)
+ penal = PenalizeVorticity(velocity=velo, vorticity=vorti,
+ discretization=topo,
+ obstacles=[hsphere], coeff=1e8)
hsphere.discretize(topo)
check_penal_vort(penal, wref, vref, vorti, velo)
@@ -319,9 +318,9 @@ def test_penal_vort_3D():
vorti = Field(domain=topo.domain, formula=v3d, name='Vorti', isVector=True)
velo = Field(domain=topo.domain, formula=v3d, name='Velo', isVector=True)
hsphere = HemiSphere(parent=topo.domain, origin=xpos, radius=rd)
- penal = PenalizationAndCurl(velocity=velo, vorticity=vorti,
- discretization=topo,
- obstacles=[hsphere], coeff=1e8)
+ penal = PenalizeVorticity(velocity=velo, vorticity=vorti,
+ discretization=topo,
+ obstacles=[hsphere], coeff=1e8)
check_penal_vort(penal, wref, vref, vorti, velo)