add dataset.rst

docs/source/_static/style.css

@@ -0,0 +1,3 @@
+.wy-nav-content {
+    max-width: 1200px !important;
+}

docs/source/_templates/layout.html

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+{% extends "!layout.html" %}
+{% block extrahead %}
+<link href="{{ pathto(" _static/style.css", True) }}" rel="stylesheet" type="text/css">
+{% endblock %}

docs/source/dataset.rst

@@ -1,4 +1,107 @@
 Dataset
 =======
 
-something here.
+Xenon.Py embed with ``elements`` and ``elements_completed`` dataset for descriptors calculation.
+These data are summarized from `mendeleev`_, `pymatgen`_, `CRC Hand Book`_ and `Magpie`_.
+
+``elements`` dataset contains 118 elements with 74 elemental features(incomplete).
+``elements_completed`` is imputed version by use multiple imputation chained equation [1]_.
+
+Because a large number of missing data in high atomic number elements lead to difficulty impute.
+The ``elements_completed`` dataset only have 94 elements from `H` to `Pu` with 58 features.
+
+.. _CRC Hand Book: http://hbcponline.com/faces/contents/ContentsSearch.xhtml
+.. _Magpie: https://bitbucket.org/wolverton/magpie
+.. _mendeleev: https://mendeleev.readthedocs.io
+.. _pymatgen: http://pymatgen.org/
+
+.. [1] `Int J Methods Psychiatr Res. 2011 Mar 1; 20(1): 40–49.`__
+            doi: `10.1002/mpr.329 <10.1002/mpr.329>`_
+
+The followig data are currently available in ``elements``:
+
+=================================   ===================================================================================
+    feature                             description
+---------------------------------   -----------------------------------------------------------------------------------
+``period``                          Period in the periodic table.
+``atomic_number``                   Number of protons found in the nucleus of an atom.
+``mendeleev_number``                Atom number in mendeleev's periodic table
+``atomic_radius``                   Atomic radius.
+``atomic_radius_rahm``              Atomic radius by Rahm et al.
+``atomic_volume``                   Atomic volume.
+``atomic_weight``                   The mass of an atom.
+``icsd_volume``                     Atom volume in ICSD database.
+``lattice_constant``                Physical dimension of unit cells in a crystal lattice.
+``vdw_radius``                      Van der Waals radiusis.
+``vdw_radius_alvarez``              Van der Waals radius according to Alvarez.
+``vdw_radius_batsanov``             Van der Waals radius according to Batsanov.
+``vdw_radius_bondi``                Van der Waals radius according to Bondi.
+``vdw_radius_dreiding``             Van der Waals radius from the DREIDING FF.
+``vdw_radius_mm3``                  Van der Waals radius from the MM3 FF.
+``vdw_radius_rt``                   Van der Waals radius according to Rowland and Taylor.
+``vdw_radius_truhlar``              Van der Waals radius according to Truhlar.
+``vdw_radius_uff``                  Van der Waals radius from the UFF.
+``covalent_radius_bragg``           Covalent radius by Bragg
+``covalent_radius_cordero``         Covalent radius by Cerdero et al.
+``covalent_radius_pyykko``          Single bond covalent radius by Pyykko et al.
+``covalent_radius_pyykko_double``   Double bond covalent radius by Pyykko et al.
+``covalent_radius_pyykko_triple``   Triple bond covalent radius by Pyykko et al.
+``covalent_radius_slater``          Covalent radius by Slater.
+``c6``                              C_6 dispersion coefficient in a.u.
+``c6_gb``                           C_6 dispersion coefficient in a.u.
+``density``                         Density at 295K.
+``proton_affinity``                 Proton affinity.
+``dipole_polarizability``           Dipole polarizability.
+``electron_affinity``               Electron affinity.
+``electron_negativity``             Tendency of an atom to attract a shared pair of electronsElectron affinity.
+``en_allen``                        Allen's scale of electronegativity.
+``en_ghosh``                        Ghosh's scale of electronegativity.
+``en_pauling``                      Mulliken's scale of electronegativity.
+``gs_bandgap``                      DFT bandgap energy of T=0K ground state.
+``gs_energy``                       Estimated FCC lattice parameter based on the DFT volume.
+``gs_est_bcc_latcnt``               Estimated BCC lattice parameter based on the DFT volume.
+``gs_est_fcc_latcnt``               Estimated FCC lattice parameter based on the DFT volume.
+``gs_mag_moment``                   DFT magnetic momenet of T=0K ground state.
+``gs_volume_per``                   DFT volume per atom of T=0K ground state.
+``hhi_p``                           Herfindahl−Hirschman Index (HHI) production values
+``hhi_r``                           Herfindahl−Hirschman Index (HHI) reserves values
+``specific_heat``                   Specific heat at 20 C.
+``gas_basicity``                    Gas basicity.
+``first_ion_en``                    First ionisation energy.
+``fusion_enthalpy``                 Fusion heat.
+``heat_of_formation``               Heat of formation.
+``heat_capacity_mass``              Mass specific heat capacity.
+``heat_capacity_molar``             Molar specific heat capacity.
+``evaporation_heat``                Evaporation heat.
+``linear_expansion_coefficient``    Coefficient of linear expansion.
+``boiling_point``                   Boiling temperature.
+``brinell_hardness``                Brinell Hardness Number.
+``bulk_modulus``                    Bulk modulus.
+``melting_point``                   Melting point.
+``metallic_radius``                 Single-bond metallic radius.
+``metallic_radius_c12``             Metallic radius with 12 nearest neighbors
+``thermal_conductivity``            Thermal conductivity at 25 C.
+``sound_velocity``                  Speed of sound.
+``vickers_hardness``                Value of Vickers hardness test.
+``Polarizability``                  Ability to form instantaneous dipoles.
+``youngs_modulus``                  Young's modulus.
+``poissons_ratio``                  Poisson's ratio.
+``molar_volume``                    Molar volume.
+``num_unfilled``                    Total unfilled electron.
+``num_valance``                     Total valance electron.
+``num_d_unfilled``                  Unfilled electron in d shell.
+``num_d_valence``                   Valance electron in d shell.
+``num_f_unfilled``                  Unfilled electron in f shell.
+``num_f_valence``                   Valance electron in d shell.
+``num_p_unfilled``                  Unfilled electron in p shell.
+``num_p_valence``                   Valance electron in d shell.
+``num_s_unfilled``                  Unfilled electron in s shell.
+``num_s_valence``                   Valance electron in d shell.
+=================================   ===================================================================================
+
+
+Load dataset
+============
+
+You can use :class:`~xenonpy.utils.datatools.Loader` to load preset dataset.
+See `loader_saver sample <https://github.com/yoshida-lab/XenonPy/blob/master/samples/data_loader.ipynb>`_ for details.

docs/source/index.rst

@@ -34,14 +34,21 @@ Xenon.Py is a open source project https://github.com/yoshida-lab/XenonPy.
 Why this name
 =============
 
+Xenon.Py named from element Xenon_.
+We did a `Graphical Lasso` calculation with our elemental descriptor to find the relationship between elements.
+In Bonacich’s centrality calculation, Xenon_ got the lowest score which the means most isolated element.
+This is especially interesting because the element's name xenon from the Greek word also meaning 'foreign(er)', 'strange(r)', or 'guest'!
+
+.. figure:: _static/glasso.png
+    :alt: Graphical Lasso`
 
 Overview
 ========
 Xenon.Py is built on top of pandas_ and PyTorch_ in order to make various downstream machine learning libraries and high-performance NN training.
-Use Xenon.Py you can:
+By use Xenon.Py(v0.1.0pre-alpha) you can:
 
 * Turn a compound's composition into arrays of numbers representing things such as ``atomic_radius``, ``melting_point`` etc.
-* Calculate pair distribution from compound's structure
+* Calculate pair distribution from compound's structure.
 
 
 .. _user-doc:
@@ -70,4 +77,4 @@ Released under the `BSD-3 license`_.
 .. _pandas: https://pandas.pydata.org
 .. _PyTorch: http://pytorch.org/
 .. _BSD-3 license: https://opensource.org/licenses/BSD-3-Clause
-
+.. _Xenon: https://en.wikipedia.org/wiki/Xenon

docs/source/installation.rst

@@ -7,79 +7,81 @@ For some legacy clusters which only come with Python 2.x, a possibility approach
 
 There are many ways to install Xenon.Py:
 
-Via anaconda (recommended)
+via anaconda (recommended)
 --------------------------
-The easiest way to install Xenon.Py is using `conda <http://conda.pydata.org>`_.
-We created a The
-`Materials Virtual Lab`_ has started `materials.sh <http://materials.sh>`_,
-a community initiative to build a comprehensive collection of materials science
-software, where pymatgen is available. If you already have conda installed,
-pymatgen can be installed from the `matsci channel on Anaconda cloud
-<https://anaconda.org/matsci>`_ using the following one line command:
+The easiest way to install Xenon.Py is using `conda`_.
+We created a channel to build a collection of our materials science software,
+If you already have conda installed, Xenon.Py can be installed from the `yoshida-lab channel`_
+using the following one line command:
 
 .. code-block:: bash
 
-   $ conda install --channel yoshida-lab pymatgen
+   $ conda install --channel yoshida-lab xenonpy
 
 
 Pymatgen is under active development, and new features are added regularly. To
 upgrade pymatgen to the latest version, use the following command:
 
 .. code-block:: bash
 
-   $ conda upgrade pymatgen
+   $ conda upgrade xenonpy
 
-Step-by-step instructions for all platforms are available at the
-:ref:`step-by-step`.
+.. Step-by-step instructions for all platforms are available at the :ref:`step-by-step`.
 
 
 
-Via pip
+via pip
 --------------------------
 
-If you have installed pip, simply run the command in a bash terminal:
+If you don't/can't install conda_. A common way is to use pip_.
+Simply run the command in a bash terminal:
 
 .. code-block:: bash
 
     $ pip install xenonpy
 
-or, to install matminer in your user home folder, run the command:
+or, to install Xenon.Py in your user home folder, run the command:
 
 .. code-block:: bash
 
-    $ pip install xenon --user
+    $ pip install xenonpy --user
+
+To update, simply type ``pip install --upgrade xenonpy``.
+
 
-To update matminer, simply type ``pip install --upgrade matminer``.
 
 Install in development mode
 -----------------------------
 
-To install from the latest source of the matminer code in developmental mode, clone the Git source:
+To install from the latest source code of the Xenon.Py from our `Github repository`_, clone the Git source:
 
 .. code-block:: bash
 
-    $ git clone https://github.com/hackingmaterials/matminer.git
+    $ git clone https://github.com/yoshida-lab/XenonPy.git
 
 and then enter the cloned repository/folder to install in developer mode:
 
 .. code-block:: bash
 
-    $ cd matminer
-    $ python setup.py develop
+    $ cd XenonPy
+    $ pip install -e .
 
-To update matminer, enter your cloned folder and type ``git pull`` followed by ``python setup.py develop``.
+To update Xenon.Py, enter your cloned folder and type ``git pull`` then ``pip install -e``.
 
 
 Troubleshooting/Issues
 ----------------------
 
-Having issues installing? Open up an issue on our `forum <https://groups.google.com/forum/#!forum/matminer>`_  describing your problem in full (including your system specifications, Python version information, and input/output log).
+Having issues installing? Contract us with issues_ and Gitter_.
 
------------------------------------------------------------------------------------------------------------
+When open issues, please describing your problem in full
+(including your system specifications, Python version information, and input/output log).
 
-.. _step-by-step:
+-----------------------------------------------------------------------------------------------------------
 
-=========================
-Step-by-step installation
-=========================
-sdf
+.. _conda: http://conda.pydata.org
+.. _yoshida-lab channel: https://anaconda.org/yoshida
+.. _pip: https://pip.pypa.io
+.. _Github repository: https://github.com/yoshida-lab/XenonPy
+.. _issues: https://github.com/yoshida-lab/XenonPy/issues
+.. _Gitter: https://gitter.im/yoshida-lab/XenonPy