Lagrange Interpolation Test.[WIP]

.gitignore

@@ -197,3 +197,4 @@ Thumbs.db
 !examples/read_and_plot_mesh/mesh/*
 !dg_maxwell/tests/mesh/*
 !dg_maxwell/tests/msh_parser/mesh/*
+!docs/quazar_logo.png

.travis.yml

@@ -7,17 +7,13 @@ python:
 
 # command to install dependencies
 before_install:
-    - ls -al
-    - pwd
     - cd ..
-    - ls -al
     - sudo apt-get update -qq
-    - sudo apt-get install -qq build-essential git cmake libfreeimage-dev cmake-curses-gui
+    - sudo apt-get install -qq build-essential git cmake3 libfreeimage-dev cmake3-curses-gui
     - sudo apt-get install -qq libopenblas-dev libfftw3-dev liblapacke-dev libboost-all-dev
     - sudo apt-get install -qq libfontconfig1-dev
-    - sudo apt-get install build-essential cmake cmake-curses-gui xorg-dev libglu1-mesa-dev libxinerama-dev libxcursor-dev
+    - sudo apt-get install build-essential xorg-dev libglu1-mesa-dev libxinerama-dev libxcursor-dev
     - grep MemTotal /proc/meminfo
-    - cat /proc/cpuinfo
     - wget https://github.com/glfw/glfw/archive/3.1.2.zip -O glfw-3.1.2.zip
     - unzip glfw-3.1.2.zip
     - cd glfw-3.1.2
@@ -41,21 +37,15 @@ before_install:
     - export AF_PATH=$PWD
     - cd lib
     - export LD_LIBRARY_PATH=$PWD:$LD_LIBRARY_PATH
-    - echo $LD_LIBRARY_PATH
     - cd ../../../../
     - cd arrayfire/build
-#    - make test
     - cd ../../
     - git clone https://github.com/amanabt/gmshtranslator.git
     - cd gmshtranslator
     - sudo pip install -e .
     - cd ..
     - pip install virtualenv
-    - pwd
-    - ls -al
     - cd DG_Maxwell
-    - pwd
-    - ls -al
     - virtualenv venv 
     - source venv/bin/activate
 
@@ -64,5 +54,5 @@ install:
 
 script:
     - python -c "import dg_maxwell"
-    - pytest
+    - pytest --verbose -r P --color=yes
 

CONTRIBUTING.md

@@ -0,0 +1,122 @@
+# Contributing to DG Maxwell
+You can contribute to this project by testing, raising issues
+and making code contributions. A certain set of guidelines needs
+to be followed for cotributing to the project.
+
+## Code Guidelines
+This project is mostly written in `Python3`, we follow a certain
+set of code guidelines for writing `Python3` code. This project
+follows the code guidelines set by the master organization
+[Quazar Technologies](https://github.com/quazartech). You may
+find the latest code guidelines on this
+[link](https://github.com/QuazarTech/Style-Guidelines/blob/master/code_guidelines/python.md).
+
+## Documentation Guidelines
+This project uses [Sphinx](http://www.sphinx-doc.org/en/stable/)
+to build it's documentation. The documentation lies in the
+`docs` directory of the repository. In this project,
+python `docstrings` are used to document all the member functions
+of a module. Sphinx uses `autodoc` to read this docstring and
+convert it into beautiful `html` pages. We follow a
+certain set of guidelines for writing the `docstrings` as explained
+below.
+
+- Use `reST` syntax to write the documentation. Refer to these links,
+  [reST](http://www.sphinx-doc.org/en/stable/rest.html#rst-primer) and
+  [Sphinx Markup Constructs](http://www.sphinx-doc.org/en/stable/markup/index.html#sphinxmarkup)
+  to write the documentation for `Sphinx`.
+- This project uses `numpydoc` for it's documentation. See how to use it
+  on this [link](https://github.com/numpy/numpy/blob/master/doc/HOWTO_DOCUMENT.rst.txt).
+- Give a short description of what the function does.
+- Mathematical variables should be written in LaTeX. See
+  [Math support in Sphinx](http://www.sphinx-doc.org/en/stable/ext/math.html#math-support).
+- When using the special LaTeX symbols, use double "\\\\" instead of a
+    single "\\". For eg, for writing the math symbol
+    ![xi](.svgs/xi.svg), write "\\\\xi" instead of "\\xi".
+- If the function implements some mathematical equation, state that
+    equation and describe the terms occuring in the equation.
+- If the algorithm is non-trivial, explain it in the documentation.
+- If the algorithm is very lengthy and complicated,
+    write a LaTeX file explaining the algorithm and state it in the documentation.
+    Here is an example for stating the link `Full description of the algorithm can
+    be found here < link >`
+- In case you want to insert the URL in the documentation and the URL is
+    exceeding the 80 characters limit, shorten the URL using
+    the [Google URL shortener](https://goo.gl/).
+- Don't use personal pronouns in the documentation.
+- Do not exceed the 80 characters per line limit.
+
+Shown below is an example for documentation of a function
+```python
+def isoparam_1D(x_nodes, xi):
+    '''
+    Maps points in :math:`\\xi` space to :math:`x` space using the formula
+    :math:`x = \\frac{1 - \\xi}{2} x_0 + \\frac{1 + \\xi}{2} x_1`
+
+    Parameters
+    ----------
+
+    x_nodes : arrayfire.Array [2 1 1 1]
+              Element nodes.
+
+    xi      : arrayfire.Array [N 1 1 1]
+              Value of :math:`\\xi` coordinate for which the corresponding
+              :math:`x` coordinate is to be found.
+
+    Returns
+    -------
+    x : arrayfire.Array
+        :math:`x` value in the element corresponding to :math:`\\xi`.
+    '''    '''
+```
+
+## Documentation Hosting
+The documentations for the code is hosted on
+[readthedocs(rtd)](https://readthedocs.org). This platform uses the `makefile`
+in the `docs` directory to build a documentation and host it on the web if the
+documentation build is successful. So, it's necessary to always make sure that
+rtd is able to build the documentation successfully. Here are some things to
+keep in mind when using rtd to host the documentation.
+1.This project uses Sphinx `autodoc` extension to generate
+  the documentation from the `doc-strings`. But, in doing so, it imports the
+  actual modules. Those modules often contain some other 3rd party imports.
+  Sphinx fails if that dependency is not satisfied. So, to avoid that situation,
+  this project uses `unittest.mock.MagicMock`. This was you can use mock imports.
+  This code snippet is added in `docs/conf.py`.
+  ```python
+  from unittest.mock import MagicMock
+
+  class Mock(MagicMock):
+      @classmethod
+      def __getattr__(cls, name):
+              return MagicMock()
+
+  MOCK_MODULES = ['gmshtranslator', 'gmshtranslator.gmshtranslator', 'arrayfire',
+                  'lagrange', 'scipy', 'numpy', 'matplotlib', 'matplotlib.lines',
+                  'dg_maxwell.params', 'tqdm']
+  sys.modules.update((mod_name, Mock()) for mod_name in MOCK_MODULES)
+  ```
+  If you want to add a mock import, add that import name in the `MOCK_MODULES`
+  list.
+
+## Continuous Integration
+This project uses [Travis CI](https://travis-ci.org/) for automatically checking
+the `build` and the unit tests.
+
+## Code Quality
+This project uses [CODACY](https://www.codacy.com/) to automatically check the
+code quality.
+
+## Pull Request Process
+This project follows the guidelines set by Quazar Technologies for giving
+a pull request. You may find the link to the pull request
+[here](https://github.com/QuazarTech/Style-Guidelines/blob/master/github/PR_guidelines.md).
+Here are few additional guidelines to be followed when giving a pull request
+- Before asking to merge the pull request, make sure that the documentation
+  build is passing on `rtd`. You may do this by hosting your fork documentation on
+  `rtd`. Make sure that there are no errors by checking the build log and also
+  check your documentation on the `rtd` website and make sure to check the
+  hosted documentation of your fork.
+- Make sure that the build is successfull and all the unit tests are passing on
+  `Travis CI`.
+- Check the code quality of your fork with CODACY.

LICENSE

@@ -654,7 +654,7 @@ Also add information on how to contact you by electronic and paper mail.
 notice like this when it starts in an interactive mode:
 
     {DG_Maxwell}  Copyright (C) {Research Division, Quazar Technologies, Delhi}{2017}
-                                {Shyam Sundar Sankaran, Mani Chandra}
+                                {Balavarun P, Aman Abhishek Tiwari, Mani Chandra}
     This program comes with ABSOLUTELY NO WARRANTY; for details type `show w'.
     This is free software, and you are welcome to redistribute it
     under certain conditions; type `show c' for details.

README.md

@@ -82,9 +82,9 @@ The unit tests are located in the
 
 ### Running Unit Tests
 To run the unit tests, enter the following commands
-```
+```bash
 $ cd path/to/the/DG_Maxwell/repo
-$ pytest
+$ pytest --verbose -r P --color=yes
 ```
 * The parameters of the simulation are stored in params.py in
   the app folder, These can be changed accordingly.

dg_maxwell/params.py

@@ -12,13 +12,13 @@
 
 
 # The domain of the function.
-x_nodes    = af.np_to_af_array(np.array([-1., 1.]))
+x_nodes    = af.np_to_af_array(np.array([0, 1.]))
 
 # The number of LGL points into which an element is split.
 N_LGL      = 8
 
 # Number of elements the domain is to be divided into.
-N_Elements = 10
+N_Elements = 8
 
 # The scheme to be used for integration. Values are either
 # 'gauss_quadrature' or 'lobatto_quadrature'
@@ -133,6 +133,7 @@
 
 
 # Initializing the amplitudes. Change u_init to required initial conditions.
+u_init     = af.sin(2 * np.pi * element_LGL)
 u          = af.constant(0, N_LGL, N_Elements, time.shape[0],\
                                  dtype = af.Dtype.f64)
 u[:, :, 0] = u_init

dg_maxwell/wave_equation.py

@@ -236,7 +236,7 @@ def volume_integral_flux(u_n, t_n):
 
     if(params.volume_integral_scheme == 'lobatto_quadrature'\
         and params.N_quad == params.N_LGL):
-
+        print('option1')
         # Flux using u_n, reordered to 1 X N_LGL X N_Elements array.
         F_u_n                  = af.reorder(flux_x(u_n), 2, 0, 1)
 
@@ -265,6 +265,7 @@ def volume_integral_flux(u_n, t_n):
 
 
     else:
+        print('option3')
         # Obtaining the u_n in polynomial form using the value at LGL points.
         analytical_form_flux       = flux_x(lagrange.\
                                             wave_equation_lagrange(u_n))

docs/conf.py

@@ -149,7 +149,7 @@ def __getattr__(cls, name):
 
 # The name of an image file (relative to this directory) to place at the top
 # of the sidebar.
-html_logo = "docs/quazar_logo.png"
+html_logo = "quazar_logo.png"
 
 # The name of an image file (relative to this directory) to use as a favicon of
 # the docs.  This file should be a Windows icon file (.ico) being 16x16 or 32x32

examples/README.md

@@ -0,0 +1,31 @@
+# DG Maxwell examples.
+
+This directory contains the examples demonstrating the usage of
+some of the `dg_maxwell` library functions.
+
+## Dependencies
+The examples are written in Jupyter notebooks. So, apart from
+installation of the main `dg_maxwell` dependencies shown
+[here](../README.md), [Jupyter](http://jupyter.org/) also needs
+to be installed to run the examples.
+
+## Running Examples
+First, a Jupyter server needs to started by entering this command in
+a terminal,
+
+```bash
+$ jupyter-notebook
+```
+
+Among the outputs of the above command, there will be an link on which
+jupyter server is hosted, it will look something like this
+```bash
+  http://localhost:8888/?token=58ec8707ab7b1fade9667b783455f4ccc9af5aa95dd6a65e
+```
+
+Open the link in your browser. The website will show the local directories.
+Navigate to the `DG_Maxwell/examples` directory on that web page and locate
+the example you want to run. Click on the file to open the example.
+
+Read [Jupyter Documentation](https://jupyter.readthedocs.io/en/latest/index.html)
+for helo with issues regarding Jupyter.