From ab9cdee79d7ec1e17099698fdacf91a3b165b27d Mon Sep 17 00:00:00 2001 From: Anubhav Jain Date: Tue, 4 Jun 2019 18:23:24 -0700 Subject: [PATCH] Update to v0.5.7 --- docs/_sources/changelog.rst.txt | 7 + docs/_sources/index.rst.txt | 2 + docs/_static/documentation_options.js | 2 +- docs/changelog.html | 13 +- docs/contributors.html | 6 +- docs/dataset_addition_guide.html | 6 +- docs/dataset_summary.html | 6 +- docs/example_bulkmod.html | 6 +- docs/featurizer_summary.html | 6 +- docs/genindex.html | 62 +++++-- docs/index.html | 7 +- docs/installation.html | 6 +- docs/matminer.data_retrieval.html | 183 ++++++++++++++++++++- docs/matminer.data_retrieval.tests.html | 29 +++- docs/matminer.datasets.html | 6 +- docs/matminer.datasets.tests.html | 6 +- docs/matminer.featurizers.html | 121 ++++++-------- docs/matminer.featurizers.tests.html | 12 +- docs/matminer.featurizers.utils.html | 6 +- docs/matminer.featurizers.utils.tests.html | 6 +- docs/matminer.figrecipes.html | 6 +- docs/matminer.figrecipes.tests.html | 6 +- docs/matminer.html | 10 +- docs/matminer.utils.data_files.html | 6 +- docs/matminer.utils.html | 6 +- docs/matminer.utils.tests.html | 6 +- docs/modules.html | 8 +- docs/objects.inv | Bin 7837 -> 7998 bytes docs/py-modindex.html | 16 +- docs/search.html | 6 +- docs/searchindex.js | 2 +- docs_rst/changelog.rst | 7 + matminer/__init__.py | 2 +- setup.py | 2 +- 34 files changed, 417 insertions(+), 164 deletions(-) diff --git a/docs/_sources/changelog.rst.txt b/docs/_sources/changelog.rst.txt index 15465df7b..e056043b0 100644 --- a/docs/_sources/changelog.rst.txt +++ b/docs/_sources/changelog.rst.txt @@ -5,6 +5,13 @@ matminer Changelog ================== +**v0.5.7** + +* remove SOAP normalization flag (K. Murakoa) +* fix precheck - Miedema and YangSolidSolution (Q. Wang) +* improvements to Miedema - default structure types, docs (Q. Wang) +* fix CGCNN optimizer (Q. Wang) + **v0.5.6** * add Global Instability Index featurizer (N. Wagner) diff --git a/docs/_sources/index.rst.txt b/docs/_sources/index.rst.txt index 1db85d877..8960c79fb 100644 --- a/docs/_sources/index.rst.txt +++ b/docs/_sources/index.rst.txt @@ -14,6 +14,8 @@ matminer works with the `pandas `_ data format in ord matminer is `open source `_ via a BSD-style license. +If you like matminer, you might also check out `automatminer `_ which automatically fits a machine learning pipeline to your problem using matminer descriptors. + ------------------- Installing matminer diff --git a/docs/_static/documentation_options.js b/docs/_static/documentation_options.js index d192543e9..b96ed7b6b 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: '0.5.6', + VERSION: '0.5.7', LANGUAGE: 'None', COLLAPSE_INDEX: false, FILE_SUFFIX: '.html', diff --git a/docs/changelog.html b/docs/changelog.html index e5e4e80d9..79bae7778 100644 --- a/docs/changelog.html +++ b/docs/changelog.html @@ -6,7 +6,7 @@ - MatMiner Changelog — matminer 0.5.6 documentation + MatMiner Changelog — matminer 0.5.7 documentation @@ -28,7 +28,7 @@

Navigation

  • modules |
    • -
  • matminer 0.5.6 documentation »
    • +
  • matminer 0.5.7 documentation »
    • @@ -39,6 +39,13 @@

    Navigation

    matminer Changelog

    +

    v0.5.7

    +
      +
    • remove SOAP normalization flag (K. Murakoa)
      • +
    • fix precheck - Miedema and YangSolidSolution (Q. Wang)
      • +
    • improvements to Miedema - default structure types, docs (Q. Wang)
      • +
    • fix CGCNN optimizer (Q. Wang)
      • +

    v0.5.6

    diff --git a/docs/contributors.html b/docs/contributors.html index b7c4fe50a..be773d5fb 100644 --- a/docs/contributors.html +++ b/docs/contributors.html @@ -6,7 +6,7 @@ - MatMiner Contributors — matminer 0.5.6 documentation + MatMiner Contributors — matminer 0.5.7 documentation @@ -28,7 +28,7 @@

    Navigation

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    • @@ -144,7 +144,7 @@

    Navigation

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  • matminer 0.5.6 documentation »
    • +
  • matminer 0.5.7 documentation »
    • diff --git a/docs/dataset_addition_guide.html b/docs/dataset_addition_guide.html index 288017662..796a74e36 100644 --- a/docs/dataset_addition_guide.html +++ b/docs/dataset_addition_guide.html @@ -6,7 +6,7 @@ - Guide to adding datasets to matminer — matminer 0.5.6 documentation + Guide to adding datasets to matminer — matminer 0.5.7 documentation @@ -28,7 +28,7 @@

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    • diff --git a/docs/dataset_summary.html b/docs/dataset_summary.html index 6213ebfb1..0afea84f0 100644 --- a/docs/dataset_summary.html +++ b/docs/dataset_summary.html @@ -6,7 +6,7 @@ - Datasets Available in Matminer — matminer 0.5.6 documentation + Datasets Available in Matminer — matminer 0.5.7 documentation @@ -28,7 +28,7 @@

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    • diff --git a/docs/example_bulkmod.html b/docs/example_bulkmod.html index 060ed06c4..665e4da77 100644 --- a/docs/example_bulkmod.html +++ b/docs/example_bulkmod.html @@ -6,7 +6,7 @@ - Predicting bulk moduli with matminer — matminer 0.5.6 documentation + Predicting bulk moduli with matminer — matminer 0.5.7 documentation @@ -28,7 +28,7 @@

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    • diff --git a/docs/featurizer_summary.html b/docs/featurizer_summary.html index ab3fac587..4f41c0b9a 100644 --- a/docs/featurizer_summary.html +++ b/docs/featurizer_summary.html @@ -6,7 +6,7 @@ - Table of Featurizers — matminer 0.5.6 documentation + Table of Featurizers — matminer 0.5.7 documentation @@ -28,7 +28,7 @@

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    • diff --git a/docs/genindex.html b/docs/genindex.html index 85eb884c2..2429ef9d3 100644 --- a/docs/genindex.html +++ b/docs/genindex.html @@ -7,7 +7,7 @@ - Index — matminer 0.5.6 documentation + Index — matminer 0.5.7 documentation @@ -29,7 +29,7 @@

    Navigation

  • modules |
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  • matminer 0.5.6 documentation »
    • +
  • matminer 0.5.7 documentation »
    • @@ -78,6 +78,10 @@

    _

  • (matminer.data_retrieval.retrieve_MDF.MDFDataRetrieval method)
  • (matminer.data_retrieval.retrieve_MP.MPDataRetrieval method) +
    • +
  • (matminer.data_retrieval.retrieve_MPDS.APIError method) +
    • +
  • (matminer.data_retrieval.retrieve_MPDS.MPDSDataRetrieval method)
  • (matminer.data_retrieval.retrieve_MongoDB.MongoDataRetrieval method)
    • @@ -286,12 +290,16 @@

    A

  • (matminer.data_retrieval.retrieve_MDF.MDFDataRetrieval method)
  • (matminer.data_retrieval.retrieve_MP.MPDataRetrieval method) +
    • +
  • (matminer.data_retrieval.retrieve_MPDS.MPDSDataRetrieval method)
  • (matminer.data_retrieval.retrieve_MongoDB.MongoDataRetrieval method)
  • get_dataframe() (matminer.data_retrieval.retrieve_base.BaseDataRetrieval method) @@ -1140,14 +1158,16 @@

    G

  • (matminer.data_retrieval.retrieve_MDF.MDFDataRetrieval method)
  • (matminer.data_retrieval.retrieve_MP.MPDataRetrieval method) +
    • +
  • (matminer.data_retrieval.retrieve_MPDS.MPDSDataRetrieval method)
  • (matminer.data_retrieval.retrieve_MongoDB.MongoDataRetrieval method)
    • -
  • get_dataset_attribute() (in module matminer.datasets.dataset_retrieval) -
    • - +
    • matminer.featurizers.utils.tests (module)
    • matminer.featurizers.utils.tests.test_cgcnn (module) @@ -1669,6 +1695,8 @@

      M

    • maximum() (matminer.featurizers.utils.stats.PropertyStats static method)
    • MaximumPackingEfficiency (class in matminer.featurizers.structure) +
      • +
    • maxnpages (matminer.data_retrieval.retrieve_MPDS.MPDSDataRetrieval attribute)
    • MDFDataRetrieval (class in matminer.data_retrieval.retrieve_MDF)
      • @@ -1697,6 +1725,10 @@

      M

    • MPDataRetrieval (class in matminer.data_retrieval.retrieve_MP)
    • MPDataRetrievalTest (class in matminer.data_retrieval.tests.test_retrieve_MP) +
      • +
    • MPDSDataRetrieval (class in matminer.data_retrieval.retrieve_MPDS) +
      • +
    • MPDSDataRetrievalTest (class in matminer.data_retrieval.tests.test_retrieve_MPDS)
    • MultiArgs2 (class in matminer.featurizers.tests.test_base)
      • @@ -1742,6 +1774,8 @@

      O

      P

      - + + + + + + +
      @@ -43,6 +43,7 @@

      matminerpandas data format in order to make various downstream machine learning libraries and tools available to materials science applications.

      matminer is open source via a BSD-style license.

      +

      If you like matminer, you might also check out automatminer which automatically fits a machine learning pipeline to your problem using matminer descriptors.

      Installing matminer

      To install matminer, follow the short installation tutorial.

      @@ -256,7 +257,7 @@

      Navigation

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    • matminer 0.5.6 documentation »
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    • matminer 0.5.7 documentation »
      • diff --git a/docs/installation.html b/docs/installation.html index bf598a7bb..7efb8ea84 100644 --- a/docs/installation.html +++ b/docs/installation.html @@ -6,7 +6,7 @@ - Installing matminer — matminer 0.5.6 documentation + Installing matminer — matminer 0.5.7 documentation @@ -28,7 +28,7 @@

      Navigation

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      • @@ -124,7 +124,7 @@

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      • diff --git a/docs/matminer.data_retrieval.html b/docs/matminer.data_retrieval.html index f04917152..05d0d6aaf 100644 --- a/docs/matminer.data_retrieval.html +++ b/docs/matminer.data_retrieval.html @@ -6,7 +6,7 @@ - matminer.data_retrieval package — matminer 0.5.6 documentation + matminer.data_retrieval package — matminer 0.5.7 documentation @@ -28,7 +28,7 @@

      Navigation

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      • @@ -49,7 +49,7 @@

      Subpackagesmatminer.data_retrieval.tests.test_retrieve_Citrine module
    • matminer.data_retrieval.tests.test_retrieve_MDF module
    • matminer.data_retrieval.tests.test_retrieve_MP module
      • -
    • matminer.data_retrieval.tests.test_retrieve_MPDS module
      • +
    • matminer.data_retrieval.tests.test_retrieve_MPDS module
    • matminer.data_retrieval.tests.test_retrieve_MongoDB module
    • Module contents
      • @@ -402,8 +402,177 @@

      matminer.data_retrieval.retrieve_AFLOW module -

      matminer.data_retrieval.retrieve_MPDS module

      +
      +

      matminer.data_retrieval.retrieve_MPDS module

      +
      +
      +exception matminer.data_retrieval.retrieve_MPDS.APIError(msg, code=0)
      +

      Bases: Exception

      +

      Simple error handling

      +
      +
      +__init__(msg, code=0)
      +

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

      +
      + +
      + +
      +
      +class matminer.data_retrieval.retrieve_MPDS.MPDSDataRetrieval(api_key=None, endpoint=None)
      +

      Bases: matminer.data_retrieval.retrieve_base.BaseDataRetrieval

      +

      Retrieves data from Materials Platform for Data Science (MPDS). +See api_link for more information.

      +

      Usage: +$>export MPDS_KEY=…

      +

      client = MPDSDataRetrieval()

      +

      dataframe = client.get_dataframe({“formula”:”SrTiO3”, “props”:”phonons”})

      +

      or +jsonobj = client.get_data(

      +
      +

      {“formula”:”SrTiO3”, “sgs”: 99, “props”:”atomic properties”}, +fields={

      +
      +
      ‘S’:[“entry”, “cell_abc”, “sg_n”, “setting”, “basis_noneq”, “els_noneq”]
      +

      }

      +
      +

      )

      +

      or +jsonobj = client.get_data({“formula”:”SrTiO3”}, fields=[])

      +

      If you use this data retrieval class, please additionally cite: +Blokhin, E., Villars, P., 2018. The PAULING FILE Project and Materials +Platform for Data Science: From Big Data Toward Materials Genome, +in: Andreoni, W., Yip, S. (Eds.), Handbook of Materials Modeling : +Methods: Theory and Modeling. Springer International Publishing, Cham, +pp. 1–26. https://doi.org/10.1007/978-3-319-42913-7_62-1

      +
      +
      +__init__(api_key=None, endpoint=None)
      +

      MPDS API consumer constructor

      +
      +
      Args:
      +
      api_key: (str) The MPDS API key, or None if the MPDS_KEY envvar is set +endpoint: (str) MPDS API gateway URL
      +
      +

      Returns: None

      +
      + +
      + +

      The link to comprehensive API documentation or data source.

      +
      +
      Returns:
      +
      (str): A link to the API documentation for this DataRetrieval class.
      +
      +
      + +
      +
      +chillouttime = 3
      +
      + +
      +
      +static compile_crystal(datarow, flavor='pmg')
      +

      Helper method for representing the MPDS crystal structures in two flavors: +either as a Pymatgen Structure object, or as an ASE Atoms object.

      +

      Attention! These two flavors are not compatible, e.g. +primitive vs. crystallographic cell is defaulted, +atoms wrapped or non-wrapped into the unit cell etc.

      +

      Note, that the crystal structures are not retrieved by default, +so one needs to specify the fields while retrieval:

      +
      +
        +
      • cell_abc
        • +
      • sg_n
        • +
      • setting
        • +
      • basis_noneq
        • +
      • els_noneq
        • +
      +
      +

      e.g. like this: {‘S’:[‘cell_abc’, ‘sg_n’, ‘setting’, ‘basis_noneq’, ‘els_noneq’]} +NB. occupancies are not considered.

      +
      +
      Args:
      +
      +
      datarow: (list) Required data to construct crystal structure:
      +
      [cell_abc, sg_n, setting, basis_noneq, els_noneq]
      +
      +

      flavor: (str) Either “pmg”, or “ase”

      +
      +
      Returns:
      +
        +
      • if flavor is pmg, returns Pymatgen Structure object
        • +
      • if flavor is ase, returns ASE Atoms object
        • +
      +
      +
      +
      + +
      +
      +default_properties = ('Phase', 'Formula', 'SG', 'Entry', 'Property', 'Units', 'Value')
      +
      + +
      +
      +endpoint = 'https://api.mpds.io/v0/download/facet'
      +
      + +
      +
      +get_data(criteria, phases=None, fields=None)
      +

      Retrieve data in JSON. +JSON is expected to be valid against the schema +at http://developer.mpds.io/mpds.schema.json

      +
      +
      Args:
      +
      +
      criteria (dict): Search query like {“categ_A”: “val_A”, “categ_B”: “val_B”},
      +

      documented at http://developer.mpds.io/#Categories +example: criteria={“elements”: “K-Ag”, “classes”: “iodide”,

      +
      +
      “props”: “heat capacity”, “lattices”: “cubic”}
      +
      +
      +

      phases (list): Phase IDs, according to the MPDS distinct phases concept +fields (dict): Data of interest for C-, S-, and P-entries,

      +
      +
      e.g. for phase diagrams: {‘C’: [‘naxes’, ‘arity’, ‘shapes’]}, +documented at http://developer.mpds.io/#JSON-schemata
      +
      +
      Returns:
      +
      List of dicts: C-, S-, and P-entries, the format is +documented at http://developer.mpds.io/#JSON-schemata
      +
      +
      + +
      +
      +get_dataframe(criteria, properties=('Phase', 'Formula', 'SG', 'Entry', 'Property', 'Units', 'Value'), **kwargs)
      +

      Retrieve data as a Pandas dataframe.

      +
      +
      Args:
      +
      criteria (dict): the same as criteria in get_data +properties ([str]): list of properties/titles to be included +**kwargs: other keyword arguments available in get_data
      +
      +

      Returns: (object) Pandas DataFrame object containing the results

      +
      + +
      +
      +maxnpages = 100
      +
      + +
      +
      +pagesize = 1000
      +
      + +
      +
      diff --git a/docs/matminer.data_retrieval.tests.html b/docs/matminer.data_retrieval.tests.html index 2bb943e69..0096a6cf9 100644 --- a/docs/matminer.data_retrieval.tests.html +++ b/docs/matminer.data_retrieval.tests.html @@ -6,7 +6,7 @@ - matminer.data_retrieval.tests package — matminer 0.5.6 documentation + matminer.data_retrieval.tests package — matminer 0.5.7 documentation @@ -28,7 +28,7 @@

      Navigation

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    • matminer 0.5.6 documentation »
      • +
    • matminer 0.5.7 documentation »
      • @@ -120,8 +120,25 @@

      matminer.data_retrieval.tests.test_retrieve_AFLOW module -

      matminer.data_retrieval.tests.test_retrieve_MPDS module

      +
      +

      matminer.data_retrieval.tests.test_retrieve_MPDS module

      +
      +
      +class matminer.data_retrieval.tests.test_retrieve_MPDS.MPDSDataRetrievalTest(methodName='runTest')
      +

      Bases: unittest.case.TestCase

      +
      +
      +setUp()
      +

      Hook method for setting up the test fixture before exercising it.

      +
      + +
      +
      +test_valid_answer()
      +
      + +
      +
      diff --git a/docs/matminer.datasets.html b/docs/matminer.datasets.html index c308e1819..d9dd02d8d 100644 --- a/docs/matminer.datasets.html +++ b/docs/matminer.datasets.html @@ -6,7 +6,7 @@ - matminer.datasets package — matminer 0.5.6 documentation + matminer.datasets package — matminer 0.5.7 documentation @@ -28,7 +28,7 @@

      Navigation

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      • @@ -692,7 +692,7 @@

      Navigation

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      • diff --git a/docs/matminer.datasets.tests.html b/docs/matminer.datasets.tests.html index e8633b584..0a5641459 100644 --- a/docs/matminer.datasets.tests.html +++ b/docs/matminer.datasets.tests.html @@ -6,7 +6,7 @@ - matminer.datasets.tests package — matminer 0.5.6 documentation + matminer.datasets.tests package — matminer 0.5.7 documentation @@ -28,7 +28,7 @@

      Navigation

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      • @@ -354,7 +354,7 @@

      Navigation

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    • matminer 0.5.6 documentation »
      • +
    • matminer 0.5.7 documentation »
      • diff --git a/docs/matminer.featurizers.html b/docs/matminer.featurizers.html index c3d33f8d8..0c55040fb 100644 --- a/docs/matminer.featurizers.html +++ b/docs/matminer.featurizers.html @@ -6,7 +6,7 @@ - matminer.featurizers package — matminer 0.5.6 documentation + matminer.featurizers package — matminer 0.5.7 documentation @@ -28,7 +28,7 @@

      Navigation

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    • matminer 0.5.6 documentation »
      • +
    • matminer 0.5.7 documentation »
      • @@ -1831,84 +1831,58 @@

      Submodules
      -class matminer.featurizers.composition.Miedema(struct_types='inter', ss_types='min', data_source='Miedema')
      +class matminer.featurizers.composition.Miedema(struct_types='all', ss_types='min', data_source='Miedema')

      Bases: matminer.featurizers.base.BaseFeaturizer

      Formation enthalpies of intermetallic compounds, from Miedema et al.

      Calculate the formation enthalpies of the intermetallic compound, solid solution and amorphous phase of a given composition, based on semi-empirical Miedema model (and some extensions), particularly for -transitional metal alloys. -Support elemental, binary and multicomponent alloys.

      -
      -
      For elemental/binary alloys, the formulation is based on the original +transitional metal alloys.

      +

      Support elemental, binary and multicomponent alloys. +For elemental/binary alloys, the formulation is based on the original works by Miedema et al. in 1980s; For multicomponent alloys, the formulation is basically the linear combination of sub-binary systems. This is reported to work well for -ternary alloys, but needs to be careful with quaternary alloys and more.

      +ternary alloys, but needs to be careful with quaternary alloys and more.

      Args:
      -
      struct_types (str or list of str): default=’inter’
      -
      if str, one target structure; -if list, a list of target structures. -e.g. -‘inter’: intermetallic compound -‘ss’: solid solution -‘amor’: amorphous phase -‘all’: same for [‘inter’, ‘ss’, ‘amor’] -[‘inter’, ‘ss’]: amorphous phase and solid solution, as an example
      -
      ss_types (str or list of str): only for ss, default=’min’
      -
      if str, one structure type of ss; -if list, a list of structure types of ss. -e.g. -‘fcc’: fcc solid solution -‘bcc’: bcc solid solution -‘hcp’: hcp solid solution +
      struct_types (str or [str]): default=’all’
      +
      ‘inter’: intermetallic compound; ‘ss’: solid solution +‘amor’: amorphous phase; ‘all’: same for [‘inter’, ‘ss’, ‘amor’] +[‘inter’, ‘ss’]: amorphous phase and solid solution
      +
      ss_types (str or [str]): only for ss, default=’min’
      +
      ‘fcc’: fcc solid solution; ‘bcc’: bcc solid solution +‘hcp’: hcp solid solution; ‘no_latt’: solid solution with no specific structure type ‘min’: min value of [‘fcc’, ‘bcc’, ‘hcp’, ‘no_latt’] ‘all’: same for [‘fcc’, ‘bcc’, ‘hcp’, ‘no_latt’] -[‘fcc’, ‘bcc’]: fcc and bcc solid solutions, as an example
      -
      data_source (str): default=’Miedema’, source of dataset
      -
      -
      ‘Miedema’: read from ‘Miedema.csv’
      -

      parameterized by Miedema et al. in 1980s, -containing parameters for 73 types of elements:

      -
      -
      ‘molar_volume’ -‘electron_density’ -‘electronegativity’ -‘valence_electrons’ -‘a_const’ -‘R_const’ -‘H_trans’ -‘compressibility’ -‘shear_modulus’ -‘melting_point’ -‘structural_stability’
      -
      -
      -
      +[‘fcc’, ‘bcc’]: fcc and bcc solid solutions
      +
      data_source (str): source of dataset, default=’Miedema’
      +
      ‘Miedema’: ‘Miedema.csv’ placed in “matminer/utils/data_files/” +parameterized for 73 elements by Miedema et al. in 1980s, containing +‘molar_volume’, ‘electron_density’, ‘electronegativity’ +‘valence_electrons’, ‘a_const’, ‘R_const’, ‘H_trans’ +‘compressibility’, ‘shear_modulus’, ‘melting_point’ +‘structural_stability’
      Returns:
      -
      (list of floats) Miedema formation enthalpies (per atom)
      -

      -formation_enthalpy_inter: for intermetallic compound --formation_enthalpy_ss: for solid solution, can be divided into

      +
      (list of floats) Miedema formation enthalpies (eV/atom) for input
      +

      struct_types: +-Miedema_deltaH_inter: for intermetallic compound +-Miedema_deltaH_ss: for solid solution, can include ‘fcc’, ‘bcc’,

      -
      -
      ‘min’, ‘fcc’, ‘bcc’, ‘hcp’, ‘no_latt’
      -
      for different lattice_types
      -
      -
      -

      -formation_enthalpy_amor: for amorphous phase

      +
      ‘hcp’, ‘no_latt’, ‘min’ based on input ss_types
      +

      -Miedema_deltaH_amor: for amorphous phase

      -__init__(struct_types='inter', ss_types='min', data_source='Miedema')
      +__init__(struct_types='all', ss_types='min', data_source='Miedema')

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

      @@ -2480,9 +2454,22 @@

      Submodules
      Args:
      -
      comp - (Composition) Composition to check
      +
      comp (Composition): Composition to check
      +
      Returns:
      +
      (boolean) Whether this composition object contains oxidation states
      + + + +
      +
      +matminer.featurizers.composition.is_ionic(comp)
      +

      Determines whether a compound is an ionic compound.

      +

      Looks at the oxidation states of each site and checks if both anions and cations exist

      +
      +
      Args:
      +
      comp (Composition): Composition to check
      Returns:
      -
      (Boolean) Whether this composition object contains oxidation states
      +
      (bool) Whether the composition describes an ionic compound
      @@ -6882,18 +6869,18 @@

      Submodulesclass matminer.featurizers.structure.GlobalInstabilityIndex(r_cut=4.0, disordered_pymatgen=False)

      Bases: matminer.featurizers.base.BaseFeaturizer

      The global instability index of a structure.

      -

      The default is to use IUCr 2016 bond valence parameters for computing -bond valence sums. If the structure has disordered site occupancies -or non-integer valences on sites, pymatgen’s bond valence sum method +

      The default is to use IUCr 2016 bond valence parameters for computing +bond valence sums. If the structure has disordered site occupancies +or non-integer valences on sites, pymatgen’s bond valence sum method can be used instead.

      -

      Note that pymatgen’s bond valence sum method is prone to error unless -the correct scale factor is supplied. A scale factor based on testing +

      Note that pymatgen’s bond valence sum method is prone to error unless +the correct scale factor is supplied. A scale factor based on testing with perovskites is used here. TODO: Use scipy to optimize scale factor for minimizing GII

      Based on the following publication:

      -
      ‘Structural characterization of R2BaCuO5 (R = Y, Lu, Yb, Tm, Er, Ho,
      -
      Dy, Gd, Eu and Sm) oxides by X-ray and neutron diffraction’, +
      ‘Structural characterization of R2BaCuO5 (R = Y, Lu, Yb, Tm, Er, Ho,
      +
      Dy, Gd, Eu and Sm) oxides by X-ray and neutron diffraction’, A.Salinas-Sanchez, J.L.Garcia-Muñoz, J.Rodriguez-Carvajal, R.Saez-Puche, and J.L.Martinez, Journal of Solid State Chemistry, 100, 201-211 (1992), @@ -6906,8 +6893,8 @@

      Submodules -
      The global instability index is the square root of the sum of squared
      -
      differences of the bond valence sums from the formal valences +
      The global instability index is the square root of the sum of squared
      +
      differences of the bond valence sums from the formal valences averaged over all atoms in the unit cell.

      @@ -8468,7 +8455,7 @@

      Navigation

    • modules |
      • -
    • matminer 0.5.6 documentation »
      • +
    • matminer 0.5.7 documentation »
      • diff --git a/docs/matminer.featurizers.tests.html b/docs/matminer.featurizers.tests.html index 2543296c0..c32426c45 100644 --- a/docs/matminer.featurizers.tests.html +++ b/docs/matminer.featurizers.tests.html @@ -6,7 +6,7 @@ - matminer.featurizers.tests package — matminer 0.5.6 documentation + matminer.featurizers.tests package — matminer 0.5.7 documentation @@ -28,7 +28,7 @@

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      • -
    • matminer 0.5.6 documentation »
      • +
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      • @@ -689,6 +689,12 @@

      Submodulestest_ionic()
      +
      +
      +test_is_ionic()
      +

      Test checking whether a compound is ionic

      +
      +
      test_miedema_all()
      @@ -1185,7 +1191,7 @@

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      • @@ -180,7 +180,7 @@

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      Navigation

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    • matminer 0.5.6 documentation »
      • +
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      • @@ -51,7 +51,7 @@

      Subpackagesmatminer.data_retrieval.tests.test_retrieve_Citrine module
    • matminer.data_retrieval.tests.test_retrieve_MDF module
    • matminer.data_retrieval.tests.test_retrieve_MP module
      • -
    • matminer.data_retrieval.tests.test_retrieve_MPDS module
      • +
    • matminer.data_retrieval.tests.test_retrieve_MPDS module
    • matminer.data_retrieval.tests.test_retrieve_MongoDB module
    • Module contents
      • @@ -63,7 +63,7 @@

      Subpackagesmatminer.data_retrieval.retrieve_Citrine module
    • matminer.data_retrieval.retrieve_MDF module
    • matminer.data_retrieval.retrieve_MP module
      • -
    • matminer.data_retrieval.retrieve_MPDS module
      • +
    • matminer.data_retrieval.retrieve_MPDS module
    • matminer.data_retrieval.retrieve_MongoDB module
    • matminer.data_retrieval.retrieve_base module
    • Module contents
      • @@ -241,7 +241,7 @@

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      Navigation

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      • @@ -98,7 +98,7 @@

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      Navigation

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      • @@ -813,7 +813,7 @@

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      Navigation

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      • diff --git a/docs/modules.html b/docs/modules.html index ba56ef5af..b6729c9bc 100644 --- a/docs/modules.html +++ b/docs/modules.html @@ -6,7 +6,7 @@ - matminer — matminer 0.5.6 documentation + matminer — matminer 0.5.7 documentation @@ -28,7 +28,7 @@

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      • @@ -50,7 +50,7 @@

      matminermatminer.data_retrieval.retrieve_Citrine module
    • matminer.data_retrieval.retrieve_MDF module
    • matminer.data_retrieval.retrieve_MP module
      • -
    • matminer.data_retrieval.retrieve_MPDS module
      • +
    • matminer.data_retrieval.retrieve_MPDS module
    • matminer.data_retrieval.retrieve_MongoDB module
    • matminer.data_retrieval.retrieve_base module
    • Module contents
      • @@ -148,7 +148,7 @@

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    • matminer 0.5.7 documentation »
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    • matminer 0.5.6 documentation »
      • +
    • matminer 0.5.7 documentation »
      • @@ -87,6 +87,11 @@

      Python Module Index

      		    matminer.data_retrieval.retrieve_MP
          + matminer.data_retrieval.retrieve_MPDS +
          @@ -112,6 +117,11 @@

      Python Module Index

      		    matminer.data_retrieval.tests.test_retrieve_MP
          + matminer.data_retrieval.tests.test_retrieve_MPDS +
          @@ -435,7 +445,7 @@

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    • matminer 0.5.6 documentation »
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\ No newline at end of file diff --git a/docs_rst/changelog.rst b/docs_rst/changelog.rst index 15465df7b..e056043b0 100644 --- a/docs_rst/changelog.rst +++ b/docs_rst/changelog.rst @@ -5,6 +5,13 @@ matminer Changelog ================== +**v0.5.7** + +* remove SOAP normalization flag (K. Murakoa) +* fix precheck - Miedema and YangSolidSolution (Q. Wang) +* improvements to Miedema - default structure types, docs (Q. Wang) +* fix CGCNN optimizer (Q. Wang) + **v0.5.6** * add Global Instability Index featurizer (N. Wagner) diff --git a/matminer/__init__.py b/matminer/__init__.py index 1fc9997c6..0c10c2230 100644 --- a/matminer/__init__.py +++ b/matminer/__init__.py @@ -1,3 +1,3 @@ -__version__ = '0.5.6' +__version__ = '0.5.7' from matminer.figrecipes.plot import PlotlyFig diff --git a/setup.py b/setup.py index ccab75b64..200419b39 100644 --- a/setup.py +++ b/setup.py @@ -22,7 +22,7 @@ if __name__ == "__main__": setup( name='matminer', - version='0.5.6', + version='0.5.7', 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(),