diff --git a/docs/_images/math/de47a77e2e05505f7581a4dcf8ae4f7750fe53ad.png b/docs/_images/math/de47a77e2e05505f7581a4dcf8ae4f7750fe53ad.png new file mode 100644 index 000000000..20cbe76b9 Binary files /dev/null and b/docs/_images/math/de47a77e2e05505f7581a4dcf8ae4f7750fe53ad.png differ diff --git a/docs/_sources/changelog.rst.txt b/docs/_sources/changelog.rst.txt index bfcfd9463..42d1479ea 100644 --- a/docs/_sources/changelog.rst.txt +++ b/docs/_sources/changelog.rst.txt @@ -5,6 +5,16 @@ matminer Changelog ================== +**v0.5.3** + +* fix typo bug that got introduced in 0.5.2 pypi release + +**v0.5.2** + +* better flattening for ColoumbMatrix featurizers, making them more usable (A. Dunn) +* SOAP featurizer using the dscribe package (A. Dunn) +* DosAsymmetry featurizer (M. Dylla) + **v0.5.1** * AFLOW data retrieval (M. Dylla) diff --git a/docs/_sources/featurizer_summary.rst.txt b/docs/_sources/featurizer_summary.rst.txt index 93dca9463..cd109b22b 100644 --- a/docs/_sources/featurizer_summary.rst.txt +++ b/docs/_sources/featurizer_summary.rst.txt @@ -88,6 +88,7 @@ Name Description :code:`DOSFeaturizer` Significant character and contribution of the density of state from a `[more] `_ :code:`DopingFermi` The fermi level (w.r.t. selected reference energy) associated with a `[more] `_ :code:`Hybridization` quantify s/p/d/f orbital character and their hybridizations at band edges `[more] `_ +:code:`DosAsymmetry` `[more] `_ ===================== ================================================================================================================================================================================================================================================================================================================================================================================================================ @@ -159,7 +160,7 @@ Name Description :code:`RadialDistributionFunction` Calculate the radial distribution function (RDF) of a crystal structure. `[more] `_ :code:`PartialRadialDistributionFunction` Compute the partial radial distribution function (PRDF) of an xtal structure `[more] `_ :code:`ElectronicRadialDistributionFunction` Calculate the inherent electronic radial distribution function (ReDF) `[more] `_ -:code:`CoulombMatrix` Generate the Coulomb matrix, a representation of nuclear coulombic interaction. `[more] `_ +:code:`CoulombMatrix` The Coulomb matrix, a representation of nuclear coulombic interaction. `[more] `_ :code:`SineCoulombMatrix` A variant of the Coulomb matrix developed for periodic crystals. `[more] `_ :code:`OrbitalFieldMatrix` Representation based on the valence shell electrons of neighboring atoms. `[more] `_ :code:`MinimumRelativeDistances` Determines the relative distance of each site to its closest neighbor. `[more] `_ @@ -174,6 +175,7 @@ Name Description :code:`XRDPowderPattern` 1D array representing powder diffraction of a structure as calculated by `[more] `_ :code:`CGCNNFeaturizer` Features generated by training a Crystal Graph Convolutional Neural Network `[more] `_ :code:`JarvisCFID` Classical Force-Field Inspired Descriptors (CFID) from Jarvis-ML. `[more] `_ +:code:`SOAP` Smooth overlap of atomic positions (interface via dscribe). `[more] `_ ============================================ ================================================================================================================================================================================================================================================================================================================================================================================================================ diff --git a/docs/_static/documentation_options.js b/docs/_static/documentation_options.js index e0e95020f..9475c8e24 100644 --- a/docs/_static/documentation_options.js +++ b/docs/_static/documentation_options.js @@ -1,6 +1,6 @@ var DOCUMENTATION_OPTIONS = { URL_ROOT: document.getElementById("documentation_options").getAttribute('data-url_root'), - VERSION: '0.5.1', + VERSION: '0.5.3', LANGUAGE: 'None', COLLAPSE_INDEX: false, FILE_SUFFIX: '.html', diff --git a/docs/changelog.html b/docs/changelog.html index c346d6fc8..c22d27edb 100644 --- a/docs/changelog.html +++ b/docs/changelog.html @@ -6,7 +6,7 @@ - MatMiner Changelog — matminer 0.5.1 documentation + MatMiner Changelog — matminer 0.5.3 documentation @@ -28,7 +28,7 @@

Navigation

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  • matminer 0.5.1 documentation »
    • +
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    • @@ -39,6 +39,16 @@

    Navigation

    matminer Changelog

    +

    v0.5.3

    +
      +
    • fix typo bug that got introduced in 0.5.2 pypi release
      • +
    +

    v0.5.2

    +
      +
    • better flattening for ColoumbMatrix featurizers, making them more usable (A. Dunn)
      • +
    • SOAP featurizer using the dscribe package (A. Dunn)
      • +
    • DosAsymmetry featurizer (M. Dylla)
      • +

    v0.5.1

    diff --git a/docs/contributors.html b/docs/contributors.html index 7d93c99ca..b387af28e 100644 --- a/docs/contributors.html +++ b/docs/contributors.html @@ -6,7 +6,7 @@ - MatMiner Contributors — matminer 0.5.1 documentation + MatMiner Contributors — matminer 0.5.3 documentation @@ -28,7 +28,7 @@

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    • diff --git a/docs/featurizer_summary.html b/docs/featurizer_summary.html index 71b7655bb..3e0e242b9 100644 --- a/docs/featurizer_summary.html +++ b/docs/featurizer_summary.html @@ -6,7 +6,7 @@ - Table of Featurizers — matminer 0.5.1 documentation + Table of Featurizers — matminer 0.5.3 documentation @@ -28,7 +28,7 @@

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    • @@ -188,6 +188,9 @@

    Features based on a material’s electronic density of states.Hybridization quantify s/p/d/f orbital character and their hybridizations at band edges [more] +DosAsymmetry +[more] + @@ -318,7 +321,7 @@

    Generating features based on a material’s crystal structure.[more] CoulombMatrix -Generate the Coulomb matrix, a representation of nuclear coulombic interaction. [more] +The Coulomb matrix, a representation of nuclear coulombic interaction. [more] SineCoulombMatrix A variant of the Coulomb matrix developed for periodic crystals. [more] @@ -362,6 +365,9 @@

    Generating features based on a material’s crystal structure.JarvisCFID Classical Force-Field Inspired Descriptors (CFID) from Jarvis-ML. [more] +SOAP +Smooth overlap of atomic positions (interface via dscribe). [more] + @@ -441,7 +447,7 @@

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    • @@ -136,6 +136,8 @@

    _

  • (matminer.featurizers.dos.DOSFeaturizer method)
  • (matminer.featurizers.dos.DopingFermi method) +
    • +
  • (matminer.featurizers.dos.DosAsymmetry method)
  • (matminer.featurizers.dos.Hybridization method)
    • @@ -204,6 +206,8 @@

    _

  • (matminer.featurizers.structure.PartialRadialDistributionFunction method)
  • (matminer.featurizers.structure.RadialDistributionFunction method) +
    • +
  • (matminer.featurizers.structure.SOAP method)
  • (matminer.featurizers.structure.SineCoulombMatrix method)
    • @@ -474,6 +478,8 @@

    C

  • (matminer.featurizers.structure.PartialRadialDistributionFunction method)
  • (matminer.featurizers.structure.RadialDistributionFunction method) +
    • +
  • (matminer.featurizers.structure.SOAP method)
  • (matminer.featurizers.structure.SineCoulombMatrix method)
    • @@ -554,10 +560,10 @@

    D

  • deltaH_topo() (matminer.featurizers.composition.Miedema method)
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    • @@ -943,7 +943,7 @@

    Submodules`Laws et al.<http://www.nature.com/doifinder/10.1038/ncomms9123>`_. +`Laws et al.<http://www.nature.com/doifinder/10.1038/ncomms9123>`_. The second corresponds to the packing efficiency of a system if all atoms in the alloy are simultaneously as efficiently-packed as possible.

    The packing efficiency in these models is based on the Atomic Packing @@ -955,7 +955,7 @@

    Submodules
    Features:
    -
    dist from {k} clusters |APE| < {thr} - The distance between an
    +
    dist from {k} clusters |APE| < {thr} - The distance between an
    alloy composition and the k clusters that have a packing efficiency below thr from ideal
    mean simul. packing efficiency - Mean packing efficiency of all atoms.
    @@ -3363,6 +3363,73 @@

    Submodules +
    +class matminer.featurizers.dos.DosAsymmetry(decay_length=0.5, sampling_resolution=100, gaussian_smear=0.05)
    +

    Bases: matminer.featurizers.base.BaseFeaturizer

    +

    Quantifies the asymmetry of the DOS near the Fermi level.

    +

    The DOS asymmetry is defined the natural logarithm of the quotient of the +total DOS above the Fermi level and the total DOS below the Fermi level. A +positive number indicates that there are more states directly above the +Fermi level than below the Fermi level. This featurizer is only meant for +metals and semi-metals.

    +
    +
    Args:
    +
    +
    decay_length (float in eV):
    +
    The dos is sampled by an exponential decay function. this parameter +sets the decay length of the exponential. Three times the decay +length corresponds to 10% sampling strength. There is a hard cutoff +at five times the decay length (1% sampling strength)
    +
    sampling_resolution (int):
    +
    Number of points to sample DOS
    +
    gaussian_smear (float in eV):
    +
    Gaussian smearing (sigma) around each sampled point in the DOS
    +
    +
    +
    +
    +
    +__init__(decay_length=0.5, sampling_resolution=100, gaussian_smear=0.05)
    +

    Initialize self. See help(type(self)) for accurate signature.

    +
    + +
    +
    +feature_labels()
    +

    Returns the labels for each of the features.

    +
    + +
    +
    +featurize(dos)
    +

    Calculates the DOS asymmetry.

    +
    +
    Args:
    +
    dos (Dos): A pymatgen Dos object.
    +
    Returns:
    +
    A float describing the asymmetry of the DOS.
    +
    +
    + +
    +
    +implementors()
    +

    List of implementors of the feature.

    +
    +
    Returns:
    +
    +
    (list) each element should either be a string with author name (e.g.,
    +
    “Anubhav Jain”) or a dictionary with required key “name” and other +keys like “email” or “institution” (e.g., {“name”: “Anubhav +Jain”, “email”: “ajain@lbl.gov”, “institution”: “LBNL”}).
    +
    +
    +
    +
    + +

    +
    class matminer.featurizers.dos.Hybridization(decay_length=0.1, sampling_resolution=100, gaussian_smear=0.05, species=None)
    @@ -4499,9 +4566,9 @@

    Submodulesself.el_list_ will be featurized. +in the self.el_list_ will be featurized. Besides, compositions of the passed structures will also be “stored” -in a dict of self.el_amt_dict_, avoiding repeated calculation of +in a dict of self.el_amt_dict_, avoiding repeated calculation of composition when featurizing multiple sites in the same structure. Args:

    @@ -5177,7 +5244,7 @@

    Submodules`

    -
    rac{sum_n {A_n |p_n - p_0|}}{sum_n {A_n}}`
    +
    rac{sum_n {A_n |p_n - p_0|}}{sum_n {A_n}}`

    where p_n is the property (e.g., atomic number) of a neighbor and p_0 is the property of a site. If signed parameter is assigned True, signed difference of the properties is returned instead of absolute @@ -5638,7 +5705,7 @@

    Submodules

    matminer.featurizers.structure module

    -class matminer.featurizers.structure.BagofBonds(coulomb_matrix=CoulombMatrix(diag_elems=True), token=' - ')
    +class matminer.featurizers.structure.BagofBonds(coulomb_matrix=SineCoulombMatrix(diag_elems=True, flatten=False), token=' - ')

    Bases: matminer.featurizers.base.BaseFeaturizer

    Compute a Bag of Bonds vector, as first described by Hansen et al. (2015).

    The Bag of Bonds approach is based creating an even-length vector from a @@ -5659,7 +5726,8 @@

    Submodules
    coulomb_matrix (BaseFeaturizer): A featurizer object containing a
    “featurize” method which returns a matrix of size nsites x nsites. -Good choices are CoulombMatrix() or SineCoulombMatrix()
    +Good choices are CoulombMatrix() or SineCoulombMatrix(), with the +flatten=False parameter set.

    token (str): The string used to separate species in a bond, including
    spaces. The token must contain at least one space and cannot have alphabetic characters in it, and should be padded by spaces. For @@ -5670,7 +5738,7 @@

    Submodules
    -__init__(coulomb_matrix=CoulombMatrix(diag_elems=True), token=' - ')
    +__init__(coulomb_matrix=SineCoulombMatrix(diag_elems=True, flatten=False), token=' - ')

    Initialize self. See help(type(self)) for accurate signature.

    @@ -5682,12 +5750,14 @@

    Submodules
    Args:
    -

    s (Structure): A pymatgen Structure or IStructure object. -return_baglens (bool): If True, returns the bag of bonds with as

    -
    -
    a dictionary with the number of bonds as values in place +
    +
    s (Structure): A pymatgen Structure or IStructure object. May also
    +
    work with a
    +
    return_baglens (bool): If True, returns the bag of bonds with as
    +
    a dictionary with the number of bonds as values in place of the vectors of coulomb matrix vals. If False, calculates -Coulomb matrix values and returns ‘raw’ bags.
    +Coulomb matrix values and returns ‘raw’ bags.
    +

    Returns:
    @@ -6296,27 +6366,32 @@

    Submodules
    -class matminer.featurizers.structure.CoulombMatrix(diag_elems=True)
    +class matminer.featurizers.structure.CoulombMatrix(diag_elems=True, flatten=True)

    Bases: matminer.featurizers.base.BaseFeaturizer

    -

    Generate the Coulomb matrix, a representation of nuclear coulombic interaction.

    -

    Generate the Coulomb matrix, M, of the input -structure (or molecule). The Coulomb matrix was put forward by -Rupp et al. (Phys. Rev. Lett. 108, 058301, 2012) and is defined by -off-diagonal elements M_ij = Z_i*Z_j/|R_i-R_j| -and diagonal elements 0.5*Z_i^2.4, where Z_i and R_i denote -the nuclear charge and the position of atom i, respectively.

    +

    The Coulomb matrix, a representation of nuclear coulombic interaction.

    +

    Generate the Coulomb matrix, M, of the input structure (or molecule). The +Coulomb matrix was put forward by Rupp et al. (Phys. Rev. Lett. 108, 058301, +2012) and is defined by off-diagonal elements M_ij = Z_i*Z_j/|R_i-R_j| and +diagonal elements 0.5*Z_i^2.4, where Z_i and R_i denote the nuclear charge +and the position of atom i, respectively.

    +

    Coulomb Matrix features are flattened (for ML-readiness) by default. Use +fit before featurizing to use flattened features. To return the matrix form, +set flatten=False.

    Args:
    -
    diag_elems: (bool) flag indicating whether (True, default) to use
    -
    the original definition of the diagonal elements; -if set to False, the diagonal elements are set to zero.
    +
    diag_elems (bool): flag indication whether (True, default) to use
    +
    the original definition of the diagonal elements; if set to False, +the diagonal elements are set to 0
    +
    flatten (bool): If True, returns a flattened vector based on eigenvalues
    +
    of the matrix form. Otherwise, returns a matrix object (single +feature), which will likely need to be processed further.
    -__init__(diag_elems=True)
    +__init__(diag_elems=True, flatten=True)

    Initialize self. See help(type(self)) for accurate signature.

    @@ -6356,6 +6431,19 @@

    Submodules +
    +fit(X, y=None)
    +

    Fit the Coulomb Matrix to a list of structures.

    +
    +
    Args:
    +
    X ([Structure]): A list of pymatgen structures. +y : unused (added for consistency with overridden method signature)
    +
    Returns:
    +
    self
    +
    +

    +
    implementors()
    @@ -6621,7 +6709,7 @@

    Submodulesclass matminer.featurizers.structure.EwaldEnergy(accuracy=4)

    Bases: matminer.featurizers.base.BaseFeaturizer

    Compute the energy from Coulombic interactions.

    -

    Note: The energy is computed using _charges already defined for the structure_.

    +

    Note: The energy is computed using _charges already defined for the structure_.

    Features:
    ewald_energy - Coulomb interaction energy of the structure
    @@ -7052,7 +7140,7 @@

    Submodules
    -class matminer.featurizers.structure.OrbitalFieldMatrix(period_tag=False, flatten=False)
    +class matminer.featurizers.structure.OrbitalFieldMatrix(period_tag=False, flatten=True)

    Bases: matminer.featurizers.base.BaseFeaturizer

    Representation based on the valence shell electrons of neighboring atoms.

    Each atom is described by a 32-element vector (or 39-element vector, see @@ -7085,7 +7173,7 @@

    Submodules
    -__init__(period_tag=False, flatten=False)
    +__init__(period_tag=False, flatten=True)

    Initialize the featurizer

    Args:
    @@ -7446,9 +7534,144 @@

    Submodules +
    +class matminer.featurizers.structure.SOAP(r_cut=3.0, n_max=4, l_max=2, **soap_kwargs)
    +

    Bases: matminer.featurizers.base.BaseFeaturizer

    +

    Smooth overlap of atomic positions (interface via dscribe).

    +

    The smooth overlap of atomic positions descriptors provided by dscribe and +SOAPLite. This implementation uses orthogonalized spherical primitive +gaussian-type orbitals as the radial basis set to reach a fast analytical +solution. Please see the dscribe SOAP documentation for more details.

    +

    Based originally on the following publications:

    +
    +
    “On representing chemical environments, Albert P. Bartók, Risi
    +
    Kondor, and Gábor Csányi, Phys. Rev. B 87, 184115, (2013), +https://doi.org/10.1103/PhysRevB.87.184115
    +
    “Comparing molecules and solids across structural and alchemical
    +
    space”, Sandip De, Albert P. Bartók, Gábor Csányi and Michele Ceriotti, +Phys. Chem. Chem. Phys. 18, 13754 (2016), +https://doi.org/10.1039/c6cp00415f
    +
    +

    Implementation (and some documentation) originally based on dscribe: +https://github.com/SINGROUP/dscribe. Please see their page for the latest +updates.

    +
    +
    Args:
    +

    r_cut (float): Cutoff radius (>1) for local region, in angstrom. +n_max (int): Number of basis functions to be used. +l_max (int): Number of l’s to be used (spherical harmonic)

    +
    +
    **soap_kwargs: (from dscribe docs)
    +
    +
    periodic (bool): Determines whether the system is considered to
    +
    be periodic.
    +
    sigma (float): The standard deviation of the gaussians used to
    +
    expand the atomic density.
    +
    rbf (str): The radial basis functions to use. The available
    +
    +
    options are:
    +
      +
    • +
      “gto”: Spherical gaussian type orbitals defined as
      +
      \phi(r) = \beta r^l e^{-\alpha r^2}
      +
      +
      • +
    +
    +
    +
    +
    crossover (bool): Default True, if crossover of atomic types
    +
    should be included in the power spectrum.
    +
    average (bool): Whether to build an average output for all
    +
    selected positions. Before averaging the outputs for +individual atoms are normalized.
    +
    +

    normalize (bool): Whether to normalize the final output. +sparse (bool): Whether the output should be a sparse matrix or a

    +
    +
    dense numpy array.
    +
    +
    +
    +
    +
    +
    +__init__(r_cut=3.0, n_max=4, l_max=2, **soap_kwargs)
    +

    Initialize self. See help(type(self)) for accurate signature.

    +
    + +
    +
    +citations()
    +

    Citation(s) and reference(s) for this feature.

    +
    +
    Returns:
    +
    +
    (list) each element should be a string citation,
    +
    ideally in BibTeX format.
    +
    +
    +
    +
    + +
    +
    +feature_labels()
    +

    Generate attribute names.

    +
    +
    Returns:
    +
    ([str]) attribute labels.
    +
    +
    + +
    +
    +featurize(s)
    +

    Main featurizer function, which has to be implemented +in any derived featurizer subclass.

    +
    +
    Args:
    +
    x: input data to featurize (type depends on featurizer).
    +
    Returns:
    +
    (list) one or more features.
    +
    +
    + +
    +
    +fit(X, y=None)
    +

    Fit the SOAP structure featurizer to a dataframe.

    +
    +
    Args:
    +
    X ([SiteCollection]): For example, a list of pymatgen Structures. +y : unused (added for consistency with overridden method signature)
    +
    Returns:
    +
    self
    +
    +
    + +
    +
    +implementors()
    +

    List of implementors of the feature.

    +
    +
    Returns:
    +
    +
    (list) each element should either be a string with author name (e.g.,
    +
    “Anubhav Jain”) or a dictionary with required key “name” and other +keys like “email” or “institution” (e.g., {“name”: “Anubhav +Jain”, “email”: “ajain@lbl.gov”, “institution”: “LBNL”}).
    +
    +
    +
    +
    + +

    +
    -class matminer.featurizers.structure.SineCoulombMatrix(diag_elems=True)
    +class matminer.featurizers.structure.SineCoulombMatrix(diag_elems=True, flatten=True)

    Bases: matminer.featurizers.base.BaseFeaturizer

    A variant of the Coulomb matrix developed for periodic crystals.

    This function generates a variant of the Coulomb matrix developed @@ -7457,18 +7680,24 @@

    Submodules
    Args:
    diag_elems (bool): flag indication whether (True, default) to use
    -
    the original definition of the diagonal elements; -if set to False, the diagonal elements are set to 0
    +
    the original definition of the diagonal elements; if set to False, +the diagonal elements are set to 0
    +
    flatten (bool): If True, returns a flattened vector based on eigenvalues
    +
    of the matrix form. Otherwise, returns a matrix object (single +feature), which will likely need to be processed further.

    -__init__(diag_elems=True)
    +__init__(diag_elems=True, flatten=True)

    Initialize self. See help(type(self)) for accurate signature.

    @@ -7503,7 +7732,20 @@

    Submodules +
    +fit(X, y=None)
    +

    Fit the Sine Coulomb Matrix to a list of structures.

    +
    +
    Args:
    +
    X ([Structure]): A list of pymatgen structures. +y : unused (added for consistency with overridden method signature)
    +
    Returns:
    +
    self

    @@ -7553,7 +7795,7 @@

    Submodules*Note for nth mode, stat must be ‘n*_mode’; e.g. stat=‘2nd_mode’ +*Note for nth mode, stat must be ‘n*_mode’; e.g. stat=‘2nd_mode’
    min_oxi (int): minimum site oxidation state for inclusion (e.g.,
    zero means metals/cations only)
    @@ -7844,7 +8086,7 @@

    Submodules -
    **kwargs: any other arguments to pass into pymatgen’s XRDCalculator,
    +
    **kwargs: any other arguments to pass into pymatgen’s XRDCalculator,
    such as the type of radiation.

    @@ -7969,7 +8211,7 @@

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    @@ -443,6 +448,11 @@

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\ No newline at end of file diff --git a/docs_rst/changelog.rst b/docs_rst/changelog.rst index 72e47b47e..42d1479ea 100644 --- a/docs_rst/changelog.rst +++ b/docs_rst/changelog.rst @@ -5,6 +5,10 @@ matminer Changelog ================== +**v0.5.3** + +* fix typo bug that got introduced in 0.5.2 pypi release + **v0.5.2** * better flattening for ColoumbMatrix featurizers, making them more usable (A. Dunn) diff --git a/docs_rst/featurizer_summary.rst b/docs_rst/featurizer_summary.rst index e69de29bb..cd109b22b 100644 --- a/docs_rst/featurizer_summary.rst +++ b/docs_rst/featurizer_summary.rst @@ -0,0 +1,182 @@ +==================== +Table of Featurizers +==================== + +Below, you will find a description of each featurizer, listed in tables grouped by module. + + +------------- +bandstructure +------------- +Features derived from a material's electronic bandstructure. +------------------------------------------------------------- + +(matminer.featurizers.bandstructure) + +========================= ================================================================================================================================================================================================================================================================================================================================================================================================================ +Name Description +========================= ================================================================================================================================================================================================================================================================================================================================================================================================================ +:code:`BranchPointEnergy` Branch point energy and absolute band edge position. `[more] `_ +:code:`BandFeaturizer` Featurizes a pymatgen band structure object. `[more] `_ +========================= ================================================================================================================================================================================================================================================================================================================================================================================================================ + + + + +---- +base +---- +Parent classes and meta-featurizers. +------------------------------------- + +(matminer.featurizers.base) + +========================== ================================================================================================================================================================================================================================================================================================================================================================================================================ +Name Description +========================== ================================================================================================================================================================================================================================================================================================================================================================================================================ +:code:`MultipleFeaturizer` Class to run multiple featurizers on the same input data. `[more] `_ +:code:`StackedFeaturizer` Use the output of a machine learning model as features `[more] `_ +:code:`BaseFeaturizer` Abstract class to calculate features from raw materials input data `[more] `_ +========================== ================================================================================================================================================================================================================================================================================================================================================================================================================ + + + + +----------- +composition +----------- +Features based on a material's composition. +-------------------------------------------- + +(matminer.featurizers.composition) + +=============================== ================================================================================================================================================================================================================================================================================================================================================================================================================ +Name Description +=============================== ================================================================================================================================================================================================================================================================================================================================================================================================================ +:code:`ElementProperty` Class to calculate elemental property attributes. `[more] `_ +:code:`OxidationStates` Statistics about the oxidation states for each specie. `[more] `_ +:code:`AtomicOrbitals` Determine HOMO/LUMO features based on a composition. `[more] `_ +:code:`BandCenter` Estimation of absolute position of band center using electronegativity. `[more] `_ +:code:`ElectronegativityDiff` Features from electronegativity differences between anions and cations. `[more] `_ +:code:`ElectronAffinity` Calculate average electron affinity times formal charge of anion elements. `[more] `_ +:code:`Stoichiometry` Calculate norms of stoichiometric attributes. `[more] `_ +:code:`ValenceOrbital` Attributes of valence orbital shells `[more] `_ +:code:`IonProperty` Ionic property attributes. Similar to ElementProperty. `[more] `_ +:code:`ElementFraction` Class to calculate the atomic fraction of each element in a composition. `[more] `_ +:code:`TMetalFraction` Class to calculate fraction of magnetic transition metals in a composition. `[more] `_ +:code:`CohesiveEnergy` Cohesive energy per atom using elemental cohesive energies and `[more] `_ +:code:`Miedema` Formation enthalpies of intermetallic compounds, from Miedema et al. `[more] `_ +:code:`YangSolidSolution` Mixing thermochemistry and size mismatch terms of Yang and Zhang (2012) `[more] `_ +:code:`AtomicPackingEfficiency` Packing efficiency based on a geometric theory of the amorphous packing `[more] `_ +=============================== ================================================================================================================================================================================================================================================================================================================================================================================================================ + + + + +--- +dos +--- +Features based on a material's electronic density of states. +------------------------------------------------------------- + +(matminer.featurizers.dos) + +===================== ================================================================================================================================================================================================================================================================================================================================================================================================================ +Name Description +===================== ================================================================================================================================================================================================================================================================================================================================================================================================================ +:code:`SiteDOS` report the fractional s/p/d/f dos for a particular site. a CompleteDos `[more] `_ +:code:`DOSFeaturizer` Significant character and contribution of the density of state from a `[more] `_ +:code:`DopingFermi` The fermi level (w.r.t. selected reference energy) associated with a `[more] `_ +:code:`Hybridization` quantify s/p/d/f orbital character and their hybridizations at band edges `[more] `_ +:code:`DosAsymmetry` `[more] `_ +===================== ================================================================================================================================================================================================================================================================================================================================================================================================================ + + + + +-------- +function +-------- +Classes for expanding sets of features calculated with other featurizers. +-------------------------------------------------------------------------- + +(matminer.featurizers.function) + +========================== ================================================================================================================================================================================================================================================================================================================================================================================================================ +Name Description +========================== ================================================================================================================================================================================================================================================================================================================================================================================================================ +:code:`FunctionFeaturizer` Features from functions applied to existing features, e.g. "1/x" `[more] `_ +========================== ================================================================================================================================================================================================================================================================================================================================================================================================================ + + + + +---- +site +---- +Features from individual sites in a material's crystal structure. +------------------------------------------------------------------ + +(matminer.featurizers.site) + +============================================= ================================================================================================================================================================================================================================================================================================================================================================================================================ +Name Description +============================================= ================================================================================================================================================================================================================================================================================================================================================================================================================ +:code:`AGNIFingerprints` Product integral of RDF and Gaussian window function, from Botu et al. `[more] `_ +:code:`OPSiteFingerprint` Local structure order parameters computed from a site's neighbor env. `[more] `_ +:code:`CrystalNNFingerprint` A local order parameter fingerprint for periodic crystals. `[more] `_ +:code:`VoronoiFingerprint` Voronoi tessellation-based features around target site. `[more] `_ +:code:`ChemicalSRO` Chemical short range ordering, deviation of local site and nominal structure compositions `[more] `_ +:code:`GaussianSymmFunc` Gaussian symmetry function features suggested by Behler et al. `[more] `_ +:code:`EwaldSiteEnergy` Compute site energy from Coulombic interactions `[more] `_ +:code:`ChemEnvSiteFingerprint` Resemblance of given sites to ideal environments `[more] `_ +:code:`CoordinationNumber` Number of first nearest neighbors of a site. `[more] `_ +:code:`GeneralizedRadialDistributionFunction` Compute the general radial distribution function (GRDF) for a site. `[more] `_ +:code:`AngularFourierSeries` Compute the angular Fourier series (AFS), including both angular and radial info `[more] `_ +:code:`LocalPropertyDifference` Differences in elemental properties between site and its neighboring sites. `[more] `_ +:code:`BondOrientationalParameter` Averages of spherical harmonics of local neighbors `[more] `_ +:code:`SiteElementalProperty` Elemental properties of atom on a certain site `[more] `_ +:code:`AverageBondLength` Determines the average bond length between one specific site `[more] `_ +:code:`AverageBondAngle` Determines the average bond angles of a specific site with `[more] `_ +============================================= ================================================================================================================================================================================================================================================================================================================================================================================================================ + + + + +--------- +structure +--------- +Generating features based on a material's crystal structure. +------------------------------------------------------------- + +(matminer.featurizers.structure) + +============================================ ================================================================================================================================================================================================================================================================================================================================================================================================================ +Name Description +============================================ ================================================================================================================================================================================================================================================================================================================================================================================================================ +:code:`DensityFeatures` Calculates density and density-like features `[more] `_ +:code:`GlobalSymmetryFeatures` Determines symmetry features, e.g. spacegroup number and crystal system `[more] `_ +:code:`Dimensionality` Returns dimensionality of structure: 1 means linear chains of atoms OR `[more] `_ +:code:`RadialDistributionFunction` Calculate the radial distribution function (RDF) of a crystal structure. `[more] `_ +:code:`PartialRadialDistributionFunction` Compute the partial radial distribution function (PRDF) of an xtal structure `[more] `_ +:code:`ElectronicRadialDistributionFunction` Calculate the inherent electronic radial distribution function (ReDF) `[more] `_ +:code:`CoulombMatrix` The Coulomb matrix, a representation of nuclear coulombic interaction. `[more] `_ +:code:`SineCoulombMatrix` A variant of the Coulomb matrix developed for periodic crystals. `[more] `_ +:code:`OrbitalFieldMatrix` Representation based on the valence shell electrons of neighboring atoms. `[more] `_ +:code:`MinimumRelativeDistances` Determines the relative distance of each site to its closest neighbor. `[more] `_ +:code:`SiteStatsFingerprint` Computes statistics of properties across all sites in a structure. `[more] `_ +:code:`EwaldEnergy` Compute the energy from Coulombic interactions. `[more] `_ +:code:`BondFractions` Compute the fraction of each bond in a structure, based on NearestNeighbors. `[more] `_ +:code:`BagofBonds` Compute a Bag of Bonds vector, as first described by Hansen et al. (2015). `[more] `_ +:code:`StructuralHeterogeneity` Variance in the bond lengths and atomic volumes in a structure `[more] `_ +:code:`MaximumPackingEfficiency` Maximum possible packing efficiency of this structure `[more] `_ +:code:`ChemicalOrdering` How much the ordering of species in the structure differs from random `[more] `_ +:code:`StructureComposition` Features related to the composition of a structure `[more] `_ +:code:`XRDPowderPattern` 1D array representing powder diffraction of a structure as calculated by `[more] `_ +:code:`CGCNNFeaturizer` Features generated by training a Crystal Graph Convolutional Neural Network `[more] `_ +:code:`JarvisCFID` Classical Force-Field Inspired Descriptors (CFID) from Jarvis-ML. `[more] `_ +:code:`SOAP` Smooth overlap of atomic positions (interface via dscribe). `[more] `_ +============================================ ================================================================================================================================================================================================================================================================================================================================================================================================================ + + + diff --git a/matminer/__init__.py b/matminer/__init__.py index 6bf6aaa1e..ca2a190de 100644 --- a/matminer/__init__.py +++ b/matminer/__init__.py @@ -1,3 +1,3 @@ -__version__ = '0.5.2' +__version__ = '0.5.3' from matminer.figrecipes.plot import PlotlyFig diff --git a/setup.py b/setup.py index 649f085ba..561f60fd5 100644 --- a/setup.py +++ b/setup.py @@ -22,7 +22,7 @@ if __name__ == "__main__": setup( name='matminer', - version='0.5.2', + version='0.5.3', description='matminer is a library that contains tools for data ' 'mining in Materials Science', long_description=open(os.path.join(module_dir, 'README.md')).read(),