Deploy docs to develop by GitHub Actions triggered by 964dfce

manual/develop/en/html/.buildinfo

@@ -1,4 +1,4 @@
 # Sphinx build info version 1
 # This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
-config: 8336bb9069069badc2ccc5be38eaf940
+config: b6e3d37f03c1ca0af00ddc6b7d2e3c74
 tags: 645f666f9bcd5a90fca523b33c5a78b7

manual/develop/en/html/_sources/cif2x/basic-usage.rst.txt

@@ -16,6 +16,11 @@ Installation and basic usage
   - OpenBabel module (optional)
   - AkaiKKRPythonUtil module
 
+  For A tool to retrieve crystallographic data from databases ``getcif``, the additional library is required:
+
+  - mp-api module
+
+
 **Official pages**
 
   - `GitHub repository <https://github.com/issp-center-dev/cif2x>`_
@@ -37,7 +42,7 @@ Installation and basic usage
      $ cd ./cif2x
      $ python3 -m pip install .
 
-  The executable file ``cif2x`` will be installed.
+  The executable files ``cif2x`` and ``getcif`` will be installed.
   You may need to add ``--user`` option next to ``install`` keyword above in case you are not allowed to install packages system-wide.
 
   AkaiKKRPythonUtil module need to be installed separately. The source package is available from `the repository <https://github.com/AkaiKKRteam/AkaiKKRPythonUtil>`_. Then follow the steps below to install the module along with the required seaborn module:
@@ -86,6 +91,9 @@ Installation and basic usage
      |       |   |-- read_input.py
      |       |   |-- run_cif2kkr.py
      |       |-- utils.py
+     |   |-- getcif/
+     |       |-- __init__.py
+     |       |-- main.py
      |-- sample/
 
 

manual/develop/en/html/_sources/cif2x/index.rst.txt

@@ -13,3 +13,4 @@ Input file generator for first-principles calculations (cif2x)
    command/index
    filespec/index
    appendix/index
+   ../getcif/index

manual/develop/en/html/_sources/getcif/about/index.rst.txt

@@ -0,0 +1,5 @@
+****************************************************************
+Introduction
+****************************************************************
+
+``getcif`` is a tool to retrieve crystallographic information and other properties of materials from databases. The latest version of getcif provides access to Materials Project database. Users can search database and obtain information by specifying symmetry, composition, or physical properties of materials.

manual/develop/en/html/_sources/getcif/appendix/index.rst.txt

@@ -0,0 +1,320 @@
+================================================================
+Parameter List
+================================================================
+
+Search conditions (properties)
+----------------------------------------------------------------
+
+Table :ref:`getcif-cond-table` summarizes condition terms available in the properties section.
+
+``getcif`` uses the ``mp-api`` library provided by Materials Project as a client for accessing the database via Materials Project API. The condition terms correspond to the parameters for the ``materials.summary.search`` method of MPRester class in ``mp-api``. (The content of the table is taken and reformatted from the comments of the source file in ``mpi-api``.)
+
+The types of the parameter values denote as follows:
+
+- ``str``: a string
+- ``List[str]``: a list of strings
+- ``str | List[str]``: a string or a list of strings
+- ``int``: an integer
+- ``bool``: a boolean value (``true`` or ``false``)
+- ``Tuple[float,float]``: a pair of two floating point numbers (as a list)
+- ``Tuple[int,int]``: a pair of two integers (as a list)
+- ``CrystalSystem``: a string representing the crystal system, one of the following: Triclinic, Monoclinic, Orthorhombic, Tetragonal, Trigonal, Hexagonal, Cubic
+- ``List[HasProps]``: a list of strings representing the properties defined in ``emmet.core.summary``. The available terms include:
+
+    absorption,
+    bandstructure,
+    charge_density,
+    chemenv,
+    dielectric,
+    dos,
+    elasticity,
+    electronic_structure,
+    eos,
+    grain_boundaries,
+    insertion_electrodes,
+    magnetism,
+    materials,
+    oxi_states,
+    phonon,
+    piezoelectric,
+    provenance,
+    substrates,
+    surface_properties,
+    thermo,
+    xas
+
+- ``Ordering``: a string representing the magnetic ordering, one of the following: FM, AFM, FiM, NM
+
+A list of the values is described in an indented style or in a comma-separated bracketted style in YAML notation. It is also available that it is described as a space-separated list.
+
+A ``Tuple`` is used to denote a range of values by ``min`` and ``max``. It is described by a list of two numbers, as well as by a space-separated list as ``min max``.
+The following notation is also available:
+
+  ``< max``
+    less than or equal to ``max``
+
+  ``> min``
+    more than or equal to ``min``
+
+  ``min ~ max``
+    between ``min`` and ``max``
+
+
+.. _getcif-cond-table:
+
+.. list-table:: Search criteria
+    :widths: 30 20 60
+    :header-rows: 1
+
+    * - Keyword
+      - Type
+      - Description
+    * - band_gap
+      - Tuple[float,float]
+      - Minimum and maximum band gap in eV to consider.
+    * - chemsys
+      - str | List[str]
+      - A chemical system, list of chemical systems (e.g., Li-Fe-O, Si-\*, [Si-O, Li-Fe-P]), or single formula (e.g., Fe2O3, Si\*).
+    * - crystal_system
+      - CrystalSystem
+      - Crystal system of material.
+    * - density
+      - Tuple[float,float]
+      - Minimum and maximum density to consider.
+    * - deprecated
+      - bool
+      - Whether the material is tagged as deprecated.
+    * - e_electronic
+      - Tuple[float,float]
+      - Minimum and maximum electronic dielectric constant to consider.
+    * - e_ionic
+      - Tuple[float,float]
+      - Minimum and maximum ionic dielectric constant to consider.
+    * - e_total
+      - Tuple[float,float]
+      - Minimum and maximum total dielectric constant to consider.
+    * - efermi
+      - Tuple[float,float]
+      - Minimum and maximum fermi energy in eV to consider.
+    * - elastic_anisotropy
+      - Tuple[float,float]
+      - Minimum and maximum value to consider for the elastic anisotropy.
+    * - elements
+      - List[str]
+      - A list of elements.
+    * - energy_above_hull
+      - Tuple[int,int]
+      - Minimum and maximum energy above the hull in eV/atom to consider.
+    * - equilibrium_reaction_energy
+      - Tuple[float,float]
+      - Minimum and maximum equilibrium reaction energy in eV/atom to consider.
+    * - exclude_elements
+      - List[str]
+      - List of elements to exclude.
+    * - formation_energy
+      - Tuple[int,int]
+      - Minimum and maximum formation energy in eV/atom to consider.
+    * - formula
+      - str | List[str]
+      - A formula including anonymized formula or wild cards (e.g., Fe2O3, ABO3, Si\*). A list of chemical formulas can also be passed (e.g., [Fe2O3, ABO3]).
+    * - g_reuss
+      - Tuple[float,float]
+      - Minimum and maximum value in GPa to consider for the Reuss average of the shear modulus.
+    * - g_voigt
+      - Tuple[float,float]
+      - Minimum and maximum value in GPa to consider for the Voigt average of the shear modulus.
+    * - g_vrh
+      - Tuple[float,float]
+      - Minimum and maximum value in GPa to consider for the Voigt-Reuss-Hill average of the shear modulus.
+    * - has_props
+      - List[HasProps]
+      - The calculated properties available for the material.
+    * - has_reconstructed
+      - bool
+      - Whether the entry has any reconstructed surfaces.
+    * - is_gap_direct
+      - bool
+      - Whether the material has a direct band gap.
+    * - is_metal
+      - bool
+      - Whether the material is considered a metal.
+    * - is_stable
+      - bool
+      - Whether the material lies on the convex energy hull.
+    * - k_reuss
+      - Tuple[float,float]
+      - Minimum and maximum value in GPa to consider for the Reuss average of the bulk modulus.
+    * - k_voigt
+      - Tuple[float,float]
+      - Minimum and maximum value in GPa to consider for the Voigt average of the bulk modulus.
+    * - k_vrh
+      - Tuple[float,float]
+      - Minimum and maximum value in GPa to consider for the Voigt-Reuss-Hill average of the bulk modulus.
+    * - magnetic_ordering
+      - Ordering
+      - Magnetic ordering of the material.
+    * - material_ids
+      - List[str]
+      - List of Materials Project IDs to return data for.
+    * - n
+      - Tuple[float,float]
+      - Minimum and maximum refractive index to consider.
+    * - num_elements
+      - Tuple[int,int]
+      - Minimum and maximum number of elements to consider.
+    * - num_sites
+      - Tuple[int,int]
+      - Minimum and maximum number of sites to consider.
+    * - num_magnetic_sites
+      - Tuple[int,int]
+      - Minimum and maximum number of magnetic sites to consider.
+    * - num_unique_magnetic_sites
+      - Tuple[int,int]
+      - Minimum and maximum number of unique magnetic sites to consider.
+    * - piezoelectric_modulus
+      - Tuple[float,float]
+      - Minimum and maximum piezoelectric modulus to consider.
+    * - poisson_ratio
+      - Tuple[float,float]
+      - Minimum and maximum value to consider for Poisson's ratio.
+    * - possible_species
+      - List[str]
+      - List of element symbols appended with oxidation states. (e.g. Cr2+,O2-)
+    * - shape_factor
+      - Tuple[float,float]
+      - Minimum and maximum shape factor values to consider.
+    * - spacegroup_number
+      - int
+      - Space group number of material.
+    * - spacegroup_symbol
+      - str
+      - Space group symbol of the material in international short symbol notation.
+    * - surface_energy_anisotropy
+      - Tuple[float,float]
+      - Minimum and maximum surface energy anisotropy values to consider.
+    * - theoretical
+      - bool
+      - Whether the material is theoretical.
+    * - total_energy
+      - Tuple[int,int]
+      - Minimum and maximum corrected total energy in eV/atom to consider.
+    * - total_magnetization
+      - Tuple[float,float]
+      - Minimum and maximum total magnetization values to consider.
+    * - total_magnetization_normalized_formula_units
+      - Tuple[float,float]
+      - Minimum and maximum total magnetization values normalized by formula units to consider.
+    * - total_magnetization_normalized_vol
+      - Tuple[float,float]
+      - Minimum and maximum total magnetization values normalized by volume to consider.
+    * - uncorrected_energy
+      - Tuple[int,int]
+      - Minimum and maximum uncorrected total energy in eV/atom to consider.
+    * - volume
+      - Tuple[float,float]
+      - Minimum and maximum volume to consider.
+    * - weighted_surface_energy
+      - Tuple[float,float]
+      - Minimum and maximum weighted surface energy in J/:math:`m^2` to consider.
+    * - weighted_work_function
+      - Tuple[float,float]
+      - Minimum and maximum weighted work function in eV to consider.
+
+..
+.. .. list-table:: Unsupported search criteria for the properties section
+..     :widths: 30 20 60
+..    :header-rows: 1
+..
+..    * - Keyword
+..      - Type
+..      - Description
+..    * - num_chunks
+..      - int
+..      - Maximum number of chunks of data to yield. None will yield all possible.
+..    * - chunk_size
+..      - int
+..      - Number of data entries per chunk.
+..    * - all_fields
+..      - bool
+..      - Whether to return all fields in the document. Defaults to True.
+..    * - fields
+..      - List[str]
+..      - List of fields in SearchDoc to return data for. Default is material_id if all_fields is False.
+..    
+    
+Data to retrive (fields)
+----------------------------------------------------------------
+
+The items available for the ``fields`` section for retrieving from the database are listed below.
+
+.. code:: text
+
+    band_gap
+    bandstructure
+    builder_meta
+    bulk_modulus
+    cbm
+    chemsys
+    composition
+    composition_reduced
+    database_IDs
+    decomposes_to
+    density
+    density_atomic
+    deprecated
+    deprecation_reasons
+    dos
+    dos_energy_down
+    dos_energy_up
+    e_electronic
+    e_ij_max
+    e_ionic
+    e_total
+    efermi
+    elements
+    energy_above_hull
+    energy_per_atom
+    equilibrium_reaction_energy_per_atom
+    es_source_calc_id
+    formation_energy_per_atom
+    formula_anonymous
+    formula_pretty
+    grain_boundaries
+    has_props
+    has_reconstructed
+    homogeneous_poisson
+    is_gap_direct
+    is_magnetic
+    is_metal
+    is_stable
+    last_updated
+    material_id
+    n
+    nelements
+    nsites
+    num_magnetic_sites
+    num_unique_magnetic_sites
+    ordering
+    origins
+    possible_species
+    property_name
+    shape_factor
+    shear_modulus
+    structure
+    surface_anisotropy
+    symmetry
+    task_ids
+    theoretical
+    total_magnetization
+    total_magnetization_normalized_formula_units
+    total_magnetization_normalized_vol
+    types_of_magnetic_species
+    uncorrected_energy_per_atom
+    universal_anisotropy
+    vbm
+    volume
+    warnings
+    weighted_surface_energy
+    weighted_surface_energy_EV_PER_ANG2
+    weighted_work_function
+    xas