Database with pseudization parameters taken from khein table.

LICENSE

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+pseudo_dojo is free software: you can redistribute it and/or modify
+it under the terms of the GNU Lesser General Public License as published by
+the Free Software Foundation, either version 2.1 of the License, or
+(at your option) any later version.
+
+pseudo_dojo is distributed in the hope that it will be useful,
+but WITHOUT ANY WARRANTY; without even the implied warranty of
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+GNU Lesser General Public License for more details.
+
+You should have received a copy of the GNU Lesser General Public License along with pseudo_dojo.  
+If not, see <http://www.gnu.org/licenses/>.

PROJECT.rst

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+Global long-term objectives:
+----------------------------
+
+    #. To have, on the Web, sets of validated pseudopotentials, for the whole periodic table,
+       for different exchange-correlation functionals, with different possibilities of 
+       semi-core electrons (e.g. for GW), different cut-off radii (e.g. high pressure application), 
+       with an optimal cut-off energy.
+
+    #. To have a Web portal for the generation/validation of new pseudopotentials.
+
+Intermediate objectives (more and more difficult steps):
+--------------------------------------------------------
+
+    #. Robust generation of one pseudopotential, be given the atomic number
+       (for a given exchange-correlation functional, definition of semi-core electrons, 
+       definition of cut-off radii). The cut-off energy does not matter at this stage.
+
+    #. Computation of selected physical properties for selected systems, associated with one 
+       given pseudopotential (automatic computation of the cut-off energy, computation of the 
+       total energy, the interatomic distance, the lattice parameter of the elemental solid 
+       and one oxide, also dimer). Results presented on the Web.
+
+    #. Validation of pseudopotentials with respect to a reference.
+
+    #. Semi-automatic improvement of the generation of the pseudopotential:
+       more accurate physical properties, better energy cut-off.
+
+    #. Automatic generation of one set of pseudopotentials, and associated automatic procedure 
+       of calculation, validation.
+
+    #. The transfer to the Web of the different results of the objectives.
+
+Components (database):
+----------------------
+
+    #. A set of repositories (one for each atomic number). Repository is placed in the 
+       directory <Z-symbol> where Z is the atomic  number (three digits) followed by the symbol, 
+       with a dash in between, e.g. 001-H, or 092-U.
+       Each of these repository is an "ATOM repository", and will contain subdirectories of two 
+       kinds, see sections below.
+
+    #. Structuration inside one ATOM repository:
+
+         - A ReferenceData subdirectory, that is not tight to one pseudopotential.
+
+         - For each pseudopotential:  
+          /[PAW|NC|...]/num_valence_electrons/xc_type/ID , which might called a "Pseudo-atom Box" or patbox.
+
+       The num_valence_electrons might be 4e, or 22e ...
+       The xc_type might be GGA-PBE or LDA-PW91 or the libcx ID: ex. LIBXC-X001-C012.
+       ID will be a digit, e.g. 1, or 2, etc ...
+       These IDs will not have any predefined meaning. Some of the pseudo-atom boxes might be good
+       for a specific purpose (e.g. GW or High-pressure), but this will be determined from the
+       database of results for each pseudo-atom box, by a script, at the demand of one user 
+       (or for populating a Web page).
+
+    #. Content of the ReferenceData subdirectory of the "ATOM repository":
+
+        - A (xml, json?) file with the atomic configuration for each possible 
+          num_valence_electrons, and other data needed for pseudo-atom generators that are not 
+          specific to a pseudo-atom generator. Standard name: atomic_config.xml.
+
+        - Possibly, some CIF files for a elemental solid (or more than one), and for oxide(s) 
+          or hydride(s), or potassium-based compounds.
+
+        - A set of master data file (xml) containing the description of the different test systems 
+          for the specific atom. Each test system belongs to a test system class: 
+
+             - atom
+
+             - dimer
+
+             - elemental 
+
+             - oxide 
+
+             - hydride or potassium-based compound.
+
+          Within each class it is labelled with an ID (number starting from 1). 
+          This description contains insulator/metal and magnetism information, and either
+          the name of the cif file to be used, or the reference length for the dimer.
+          Standard name: <Z-symbol>.description_<class>_ID.xml
+
+    #. Content of one pseudo-atom Box:
+
+       - Subdirectories: 
+
+                - <name_of_generator>
+
+                - atom_X, dimer_X
+
+                - elemental_X, oxide_X
+
+                - possibly hydride_X or K_X . 
+
+         Where <name_of_generator> might be atompaw, or ape, or fhi98pp, or ...
+         And where X is the ID defined in D3c.
+
+        - A (xml) summary file containing metadata concerning this pseudo-atom box, obtained by 
+          running the applications in the different subdirectories, and also describing the 
+          validation criteria (this implies a set of runs).
+          Standard name: <Z-symbol>.summary.[PAW|NC|...].#valence_electrons.<xc_type>.ID.xml
+
+    #. Content of the <name_of_generator> subdirectory of the pseudo-atom Box:
+
+       - Optionally, the specific input data needed for the generator (PAW or NC), to complement 
+         the content of the atomic_config file. Typically cut-off radii.
+         Standard name atomic_data_<name_of_generator>.xml, e.g. atomic_data_atompaw.xml
+
+       - A pseudo-atom data generator input file (PAW or NC) - might have been automatically generated
+         from atomc_config and the file in D5a. Standard name <name_of_generator>.in
+
+       - A pseudo-atom data file (PAW or NC) - has been automatically generated (output of the atomic generator).
+         Standard name <Z-symbol>.pseudoatom.[PAW|NC|...].#valence_electrons.<xc_type>.ID. 
+
+       - <standard_postfix_for_the_generator>
+         This is the pseudopotential file, or the PAW atomic data file.
+         The <standard_postfix_for_the_generator> might be .fhi or .pawps , or other postfix.
+
+    #. Content of the <class>_X (where class is atom, dimer, elemental, oxide, hydride ...)
+       D6a Subdirectories abinit_runY and elk_runY, where Y is an integer starting from 1.
+
+    #. Content of the abinit_runY directory
+       D7a This is a working directory for one abinit run. It contains an ABINIT input file 
+       usually automatically generated from D3c, specialized for the pseudo-atom box and the system.
+       D7b For Y=1 : determination of a basic k point grid, using kptrlen and prtkpt. 
+       Can be used by elk, see elk_1.
+       D7c For Y=2 : computation of total energy as a function of ecut, for basic k point grid, 
+       and, for metals, using the tsmear determined by elk_1.
+
+    #. Content of the elk_runY subdirectory:
+
+       - This is a working directory for one elk run. It contains an ELK input file 
+         usually automatically generated from D3c, specialized for the pseudo-atom box 
+         and the system, and using the k point grid determined by D7b .
+
+       - For Y=1, determination of the tsmear.
+
+Components (software).
+----------------------
+
+They should be placed inside ABINIT package psps/script, for testing/coherency purposes 
+across the different <Z-symbol> directories.
+
+   #. A "pseudo-atom box" creator (init_patbox.py), to be called inside the psps/<Z-symbol> directory.
+      (propose options for the path described in D2, then create the path, 
+      and the directories of the pseudo-atom box, and also bzr add the dirs)
+
+   #. A cif2cml translator, to go from D3b to D3c.
+
+   #. A script to initialize the file <name_of_generator>.in mentioned in D5b from D3a 
+      atomic_config.xml and D5a atomic_data_<name_of_generator>.xml
+
+   #. A pseudopotential generator, e.g. ATOMPAW  (already placed inside the ABINIT package)
+
+   #. A driver of abinit: generation of abinit input files, running of abinit, gathering of the data in D4b. 
+      ACTUALLY NEED A LIST OF TASKS / VALIDATION CRITERIA /  to be defined.
+
+   #. A driver of elk, and a binary for elk.
+
+   #. A validator.
+
+   #. More scripts to be added ...
+
+Miscellaneous
+-------------
+
+  #. Reference oxygen PAW data files for different XC functionals, reference hydrogen PAW data files
+     for different XC functionals.  Placed in the abinit/psps/RefPseudoAtoms subdirectory of 
+     the ABINIT package. And to be copied in the patbox at init time.
+
+Strategy
+--------
+
+   - Work component by component, by placing these components under version management and 
+     automatic testing, with appropriate hardware.
+
+   - Define the files and their format (including metadata) in an iterative way, with possibilities 
+     to regenerate them in an automatic way
+
+   - Gradual understanding of the CPU constraints, memory constraint, and human time needed.
+
+   - Adjust the objectives to stay realist.
+
+TO BE KEPT IN MIND FOR FURTHER SPECIFICATION
+--------------------------------------------
+
+   - set up of a bot (on the machine nazgul): be given the ABINIT branch, and the pseudopotentials =>
+     computation of the physical characteristics of this pseudopotential
+
+   - set up of the corresponding "on-demand" mechanism
+
+   - set up a new waterfall: the list of files that will be provided will be quite different 
+     from the usual bots
+
+   - set up of a new Web window to visualize the files (to be discussed).
+

README.rst

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+
+Pseudo_dojo is a open-source Python framework for generaring and validating  pseudo potentials.
+
+pseudo_dojo is free to use. However, we also welcome your help to improve this
+library by making your own contributions.  These contributions can be in the
+form of additional tools or modules you develop, or even simple things such
+as bug reports. Please report any bugs and issues at pseudo_dojo's `Github page
+<https://github.com/gmatteo/pseudo_dojo>`_. 
+
+Getting pseudo_dojo
+================
+
+Stable version
+--------------
+
+The version at the Python Package Index (PyPI) is always the latest stable
+release that will be hopefully, be relatively bug-free. The easiest way to
+install pseudo_dojo on any system is to use easy_install or pip, as follows::
+
+    easy_install pseudo_dojo
+
+or::
+
+    pip install pseudo_dojo
+
+Developmental version
+---------------------
+
+The developmental version is at the pseudo_dojo's `Github repo <https://github.com/gmatteo/pseudo_dojo>`_. 
+After cloning the source, you can type::
+
+    python setup.py install
+
+or to install the package in developmental mode::
+
+    python setup.py develop
+
+Requirements
+============
+
+All required dependencies should be automatically taken care of if you
+install pseudo_dojo using easy_install or pip. Otherwise, these packages should
+be available on `PyPI <http://pypi.python.org>`_.
+
+1. Python 2.7+ required. 
+2. numpy 
+3. scipy 0.10+ 
+4. matplotlib 1.1+ 
+5. periodictable
+
+Using pseudo_dojo
+=================
+
+Basic usage
+-----------
+
+Useful aliases for commonly used objects are now provided, similar in style to
+numpy. Supported objects include Element, Composition, Structure, Molecule,
+Spin and Orbital. Here are some quick examples of the core capabilities and
+objects:
+
+.. code-block:: pycon
+
+    >>> import pseudo_dojo as mg
+    >>>
+    >>> si = mg.Element("Si")
+    >>> si.atomic_mass
+    28.0855
+    >>> si.melting_point
+    u'1687 K'
+    >>>
+    >>> comp = mg.Composition("Fe2O3")
+    >>> comp.weight
+    159.6882
+    >>> #Note that Composition conveniently allows strings to be treated just
+    >>> #like an Element object.
+    >>> comp["Fe"]
+    2.0
+    >>> comp.get_atomic_fraction("Fe")
+    0.4
+    >>> lattice = mg.Lattice.cubic(4.2)
+    >>> structure = mg.Structure(lattice, ["Cs", "Cl"],
+    ...                          [[0, 0, 0], [0.5, 0.5, 0.5]])
+    >>> structure.volume
+    74.088000000000008
+    >>> structure[0]
+    PeriodicSite: Cs (0.0000, 0.0000, 0.0000) [0.0000, 0.0000, 0.0000]
+    >>>
+    >>> #Integrated symmetry tools from spglib.
+    >>> from pseudo_dojo.symmetry.finder import SymmetryFinder
+    >>> finder = SymmetryFinder(structure)
+    >>> finder.get_spacegroup_symbol()
+    'Pm-3m'
+    >>>
+    >>> #Writing out a POSCAR file for VASP calculations.
+    >>> poscar = Poscar(structure)
+    >>> mg.write_structure(structure, "POSCAR")
+    >>>
+    >>> #Reading a structure from a file.
+    >>> structure = mg.read_structure("POSCAR")
+
+The above illustrates only the most basic capabilities of pseudo_dojo.
+
+.. note:: Examples
+
+    A good way to explore the functionality of pseudo_dojo is to look at examples.
+    We have created a `Github wiki page
+    <https://github.com/materialsproject/pseudo_dojo/wiki>`_ to allow users to
+    share their Github gists (essentially mini git repos of scripts)
+    performing various kinds of functions with pseudo_dojo. Please feel free to
+    check them out and we welcome your contributions as well!
+
+===============================
+Project PseudoDojo: global view
+===============================
+
+.. include:: PROJECT.rst
+
+License
+=======
+
+pseudo_dojo is released under the GPL License. The terms of the license are as follows:
+
+.. literalinclude:: LICENSE
+