Added License, delete old files, update README

.gitlab-ci.yml

@@ -45,7 +45,7 @@ install_and_test:
     # - apt-get -qq insall -y texlive-latex-recommended texlive-fonts-recommended tex-gyre texlive-latex-extra latexmk texlive-lang-cyrillic texlive-lang-greek cm-super texlive-xetex texlive-luatex fonts-freefont-otf xindy graphviz
     - python -m venv ipp-env
     - source ipp-env/bin/activate
-    - pip install -U pip build wheel pytest coverage 
+    - pip install -U pip build wheel pytest pytest-cov coverage 
     # - pip install -r requirements.txt
 
     # Print directory structure, but exclude virtual environment directory.
@@ -69,7 +69,6 @@ install_and_test:
     - coverage run -m pytest
     - coverage xml
     - coverage report --skip-empty
-    - coverage erase
 
     # Deploy: run deploy.
     - echo "Run deploy:"

CONTRIBUTING.md

+## Max Planck Institute for Plasma Physics
+
+* Florian Hindenlang 
+* Stefan Possanner 
+
+## TU Munich
+
+* Tin Kei Cheng

LICENSE

+Copyright 2023 (c) T.K. Cheng, F. Hindenlang, S. Possanner | Max Planck Institute for Plasma Physics
+
+Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+

README.md

 # 3D GVEC equilibria in Python
 
-Install:
+PyPI install (not yet :-):
 
 ```
 pip install gvec_to_python
 ```
-Compile kernels (for fast evaluations):
+Or from source:
+```
+git clone git@gitlab.mpcdf.mpg.de:spossann/gvec_to_python.git
+cd gvec_to_python
+pip install -e .
+```
+Compile kernels for faster evaluations:
 ```
 compile_gvec_to_python
 ```
@@ -22,7 +28,7 @@ In a second step, callables of MHD equilibrium quantities are created as methods
 ```
 from gvec_to_python import GVEC
 
-gvec = GVEC(json_file_out)
+gvec = GVEC(json_file_out, mapping='gvec', use_nfp=False, use_pyccel=False)
 ```
 Profiles can be evaluated via
 ```
@@ -31,6 +37,8 @@ gvec.profiles.profile(s, name='chi')        # poloidal flux profile
 gvec.profiles.profile(s, name='iota')       # iota profile
 gvec.profiles.profile(s, name='pressure')   # pressure profile
 ```
+![Profiles](notebooks/profiles.png "Title")
+
 The mapping and metric coefficients are called via
 ```
 gvec.f(s, a1, a2)       # mapping
@@ -41,7 +49,11 @@ gvec.g(s, a1, a2)       # metric tensor
 gvec.g_inv(s, a1, a2)   # inverse metric tensor
 ```
 Here, `s` is the radial coordinate, `a1` is the poloidal angle and `a2` denotes the toroidal angle.
-Four different mappings can be invoked by the `mapping.setter`:
+
+![Profiles](notebooks/poloidal.png "Title")
+![](notebooks/topview.png)
+
+Five different mappings can be invoked by the `mapping.setter`:
 ```
 # gvec standard coordinates
 gvec.mapping = 'gvec'
@@ -54,7 +66,14 @@ gvec.mapping = 'unit'
 
 # gvec straight-field-line with unit cube as logical domain
 gvec.mapping = 'unit_pest'
+
+# gvec without hmap
+gvec.mapping = 'wo_hmap'
 ```
+
+![](notebooks/dtheta.png)
+![](notebooks/det_df.png)
+
 The MHD quantities are called via
 ```
 gvec.p0(s, a1, a2)      # pressure as 0-form
@@ -68,8 +87,11 @@ gvec.a1(s, a1, a2)      # co-variant vector potential (1-form)
 gvec.a2(s, a1, a2)      # 2-form vector potential
 gvec.a_cart(s, a1, a2)  # Cartesian vector potential
 ```
-See the notebook `notebooks/plt_mhd_equil.ipynb` for example plots like this one:
 
-![Poloidal geometry](poloidal_grid.png "Title")
+![](notebooks/pressure.png)
+
+![](notebooks/absB.png)
+
+
 
 

build_and_test.sh

-# This script is similar to the pipeline in GitLab CI `.gitlab-ci.yml` file.
-
-# Docs: Make sphinx docs.
-echo "Make sphinx docs:"
-sphinx-apidoc -f -o ./docs/source ./src/gvec_to_python
-sphinx-build -b html ./docs/source ./public
-# cd docs/
-# make latex
-# make latexpdf
-# cd ..
-
-# Build:
-# echo "Run pyccel:"
-# cd src/ && make flags_openmp_mhd= flags_openmp_pic=--openmp && cd ..
-echo "Run python build:"
-python -m build
-ls -lah dist
-echo "Install dist:"
-pip install -U dist/gvec_to_python-*.whl # --force-reinstall
-
-# Test: run pytest.
-echo "Run pytest:"
-coverage run -m pytest 
-coverage xml 
-coverage report --skip-empty 
-coverage erase
-python test/cleanup.py
-
-# Deploy: run deploy.
-echo "Run deploy:"
-echo "Release pipeline not implemented."

docs/Makefile

-# Minimal makefile for Sphinx documentation
-#
-
-# You can set these variables from the command line, and also
-# from the environment for the first two.
-SPHINXOPTS    ?=
-SPHINXBUILD   ?= sphinx-build
-SOURCEDIR     = source
-BUILDDIR      = build
-
-# Put it first so that "make" without argument is like "make help".
-help:
-	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
-
-.PHONY: help Makefile
-
-# Catch-all target: route all unknown targets to Sphinx using the new
-# "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
-%: Makefile
-	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)

docs/make.bat

-@ECHO OFF
-
-pushd %~dp0
-
-REM Command file for Sphinx documentation
-
-if "%SPHINXBUILD%" == "" (
-	set SPHINXBUILD=sphinx-build
-)
-set SOURCEDIR=source
-set BUILDDIR=build
-
-if "%1" == "" goto help
-
-%SPHINXBUILD% >NUL 2>NUL
-if errorlevel 9009 (
-	echo.
-	echo.The 'sphinx-build' command was not found. Make sure you have Sphinx
-	echo.installed, then set the SPHINXBUILD environment variable to point
-	echo.to the full path of the 'sphinx-build' executable. Alternatively you
-	echo.may add the Sphinx directory to PATH.
-	echo.
-	echo.If you don't have Sphinx installed, grab it from
-	echo.https://www.sphinx-doc.org/
-	exit /b 1
-)
-
-%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
-goto end
-
-:help
-%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
-
-:end
-popd

docs/source/_static/css/my_theme.css

-.wy-nav-content {
-    max-width: 1200px !important;
-}

docs/source/conf.py

-# Configuration file for the Sphinx documentation builder.
-#
-# This file only contains a selection of the most common options. For a full
-# list see the documentation:
-# https://www.sphinx-doc.org/en/master/usage/configuration.html
-
-# -- Path setup --------------------------------------------------------------
-
-# 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.
-#
-import os
-import sys
-# sys.path.insert(0, os.path.abspath('.'))
-sys.path.insert(0, os.path.abspath(os.path.join('..', '..', 'src')))
-
-import sphinx_rtd_theme
-
-
-# -- Project information -----------------------------------------------------
-
-project = 'Python Interface for GVEC Equilibria'
-copyright = '2021, Max Planck Institute for Plasma Physic'
-author = 'Tin Kei CHENG'
-
-
-# -- General configuration ---------------------------------------------------
-
-# Add any Sphinx extension module names here, as strings. They can be
-# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
-# ones.
-extensions = [
-    'sphinx.ext.duration', # https://www.sphinx-doc.org/en/master/usage/extensions/duration.html
-    'sphinx.ext.napoleon', # https://www.sphinx-doc.org/en/master/usage/extensions/napoleon.html
-    'sphinx.ext.autodoc',  # https://www.sphinx-doc.org/en/master/usage/extensions/autodoc.html
-    'sphinx.ext.mathjax',  # https://www.sphinx-doc.org/en/master/usage/extensions/math.html
-    'sphinx.ext.viewcode', # https://www.sphinx-doc.org/en/master/usage/extensions/viewcode.html
-    'sphinx.ext.graphviz', # https://www.sphinx-doc.org/en/master/usage/extensions/graphviz.html
-    'sphinx.ext.inheritance_diagram', # https://www.sphinx-doc.org/en/master/usage/extensions/inheritance.html
-    'sphinx_rtd_theme',    # https://sphinx-rtd-theme.readthedocs.io/en/stable/index.html
-]
-
-# Add any paths that contain templates here, relative to this directory.
-templates_path = ['_templates']
-
-# List of patterns, relative to source directory, that match files and
-# directories to ignore when looking for source files.
-# This pattern also affects html_static_path and html_extra_path.
-exclude_patterns = []
-
-# The language for content autogenerated by Sphinx. Refer to documentation
-# for a list of supported languages.
-#
-# This is also used if you do content translation via gettext catalogs.
-# Usually you set "language" from the command line for these cases.
-language = None
-
-
-# -- 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 = 'alabaster'
-html_theme = 'sphinx_rtd_theme'
-
-# Add any paths that contain custom static files (such as style sheets) here,
-# relative to this directory. They are copied after the builtin static files,
-# so a file named "default.css" will overwrite the builtin "default.css".
-html_static_path = ['_static']
-
-# These paths are either relative to html_static_path
-# or fully qualified paths (eg. https://...)
-html_css_files = [
-    'css/my_theme.css',
-]
-
-
-# -- Options for LaTeX output ------------------------------------------------
-
-# https://www.sphinx-doc.org/en/master/usage/builders/index.html#sphinx.builders.latex.LaTeXBuilder
-# https://www.sphinx-doc.org/en/master/usage/configuration.html#options-for-latex-output
-latex_engine = 'xelatex'

docs/source/index.rst

-.. Python Interface for GVEC Equilibria documentation master file, created by
-   sphinx-quickstart on Thu Nov  4 11:55:49 2021.
-   You can adapt this file completely to your liking, but it should at least
-   contain the root `toctree` directive.
-
-Welcome to Python Interface for GVEC Equilibria's documentation!
-================================================================
-
-`STRUcture-Preserving HYbrid code (STRUPHY) <https://gitlab.mpcdf.mpg.de/clapp/hylife>`_ is a code base for kinetic-fluid plasma simulations developed at the `Max Planck Institute for Plasma Physics in Garching <https://www.ipp.mpg.de/17301/garching>`_.
-In this package we add to STRUPHY several general Python interfaces for reading magneto-hydrodynamic (MHD) equilibrium data for Tokamaks and Stellarators.
-In particular, interfaces to the equilibrium code `Galerkin Variational Equilibrium Code (GVEC) <https://gitlab.mpcdf.mpg.de/gvec-group/gvec>`_ (and in the future, to the ``eqdsk`` file format) are provided.
-From the data, a flux-aligned coordinate system is created, and the MHD quantities are transformed into differential forms for the use in STRUPHY.
-
-.. toctree::
-   :maxdepth: 3
-   :caption: Contents:
-
-   modules
-
-..
-   Below is a comment.
-   .. inheritance-diagram:: gvec_to_python.GVEC_functions.GVEC
-
-
-How to use
-==========
-
-First and foremost, one need to setup the package.
-It can be accomplished as simple as a ``pip install -e ./``.
-
-..
-   See Section "Build and install" below for detailed instructions.
-
-This code needs to read in a GVEC MHD equilibrium in JSON format.
-Therefore, the `.dat` GVEC output data has to be converted into ``.json`` using a utility as demonstrated below.
-This only needs to be done once, per GVEC equilibrium.
-
-.. code-block:: python
-
-   from  gvec_to_python.reader.gvec_reader import GVEC_Reader
-
-   # Spline coefficients are not provided by GVEC by default.
-   read_filepath = 'GVEC/testcases/circ_tok/'
-   read_filename = 'CIRC_TOK_State_0000_00010000.dat'
-   save_filepath = 'GVEC/testcases/circ_tok/'
-   save_filename = 'CIRC_TOK_State_0000_00010000.json'
-   reader = GVEC_Reader(read_filepath, read_filename, save_filepath, save_filename, with_spl_coef=False)
-
-   # Special case with spline coefficients.
-   read_filepath = 'GVEC/testcases/ellipstell/'
-   read_filename = 'GVEC_ellipStell_profile_update_State_0000_00010000.dat'
-   save_filepath = 'GVEC/testcases/ellipstell/'
-   save_filename = 'GVEC_ellipStell_profile_update_State_0000_00010000.json'
-   reader = GVEC_Reader(read_filepath, read_filename, save_filepath, save_filename, with_spl_coef=True)
-
-The main features can then be used simply as follows:
-
-.. code-block:: python
-   :emphasize-lines: 6,24,25,26,27,28
-
-   import numpy as np
-   from gvec_to_python import GVEC, Form, Variable
-
-   gvec_data_filepath = 'GVEC/testcases/ellipstell/'
-   gvec_data_filename = 'GVEC_ellipStell_profile_update_State_0000_00010000.json'
-   gvec = GVEC(gvec_data_filepath, gvec_data_filename)
-
-   # The functions can accept various types of inputs:
-   # - Individual point in logical coordinates.
-   (s, u, v) = (0.1, 0.2, 0.3)
-   # - 1D arrays of a grid.
-   s_range = np.linspace(0, 1, 11)
-   u_range = np.linspace(0, 1, 21)
-   v_range = np.linspace(0, 1, 31)
-   # - A sparse 3D meshgrid.
-   s_sparse, u_sparse, v_sparse = np.meshgrid(s_range, u_range, v_range, indexing='ij', sparse=True)
-   # - A dense 3D meshgrid.
-   s_dense,  u_dense,  v_dense  = np.meshgrid(s_range, u_range, v_range, indexing='ij', sparse=False)
-
-   # Function parameters can either be floats gvec.F(s, u, v), 
-   # or 1D arrays gvec.F(s_range, u_range, v_range), 
-   # or 3D arrays from sparse meshgrid gvec.F(s_sparse, u_sparse, v_sparse), 
-   # or dense meshgrid gvec.F(s_dense, u_dense, v_dense).
-   (x, y, z) = gvec.F(s, u, v)
-   jacobian  = gvec.DF(s, u, v)
-   pressure  = gvec.get_variable(s, u, v, variable=Variable.PRESSURE, form=Form.ZERO)
-   pressure  = gvec.P(s, u, v) # Alternatively, a shorthand is available.
-   p_3       = gvec.P_3(s, u, v) # 3-form pressure.
-
-Caveat: The mapping function ``F()`` returns in the shape ``(3, #s, #u, #v)`` so that we can do ``(x, y, z) = gvec.F(s, u, v)``, but the Jacobian function ``DF()`` returns in the shape ``(#s, #u, #v, 3, 3)`` in order to comply with numpy's convention.
-
-
-
-Indices and tables
-==================
-
-* :ref:`genindex`
-* :ref:`modindex`
-* :ref:`search`

logs/.gitignore

-# Ignore everything in this directory
-*
-# Except this file
-!.gitignore
\ No newline at end of file