From 76a529b769055c729d62f11a419d319d8e2f838e Mon Sep 17 00:00:00 2001 From: Anubhav Jain Date: Wed, 18 May 2022 09:32:10 -0700 Subject: [PATCH] Update to v0.7.8 --- docs/_sources/dataset_summary.rst.txt | 112 +++++++++++++++- docs/_static/documentation_options.js | 2 +- docs/changelog.html | 6 +- docs/contributors.html | 6 +- docs/dataset_addition_guide.html | 6 +- docs/dataset_summary.html | 122 +++++++++++++++++- docs/example_bulkmod.html | 6 +- docs/featurizer_summary.html | 6 +- docs/genindex.html | 14 +- docs/index.html | 6 +- docs/installation.html | 6 +- docs/matminer.data_retrieval.html | 6 +- docs/matminer.data_retrieval.tests.html | 6 +- docs/matminer.datasets.html | 6 +- docs/matminer.datasets.tests.html | 16 ++- docs/matminer.featurizers.composition.html | 6 +- ...atminer.featurizers.composition.tests.html | 6 +- docs/matminer.featurizers.html | 6 +- docs/matminer.featurizers.site.html | 6 +- docs/matminer.featurizers.site.tests.html | 6 +- docs/matminer.featurizers.structure.html | 6 +- .../matminer.featurizers.structure.tests.html | 6 +- docs/matminer.featurizers.tests.html | 6 +- 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 | 6 +- docs/matminer.utils.data_files.html | 6 +- docs/matminer.utils.html | 6 +- docs/matminer.utils.tests.html | 6 +- docs/modules.html | 6 +- docs/objects.inv | Bin 8617 -> 8647 bytes docs/py-modindex.html | 6 +- docs/search.html | 6 +- docs/searchindex.js | 2 +- docs_rst/dataset_summary.rst | 112 +++++++++++++++- matminer/__init__.py | 2 +- setup.py | 2 +- 39 files changed, 453 insertions(+), 105 deletions(-) diff --git a/docs/_sources/dataset_summary.rst.txt b/docs/_sources/dataset_summary.rst.txt index ad34c84bc..40f219249 100644 --- a/docs/_sources/dataset_summary.rst.txt +++ b/docs/_sources/dataset_summary.rst.txt @@ -1,7 +1,7 @@ ================= Table of Datasets ================= -Find a table of all 43 datasets available in matminer here. +Find a table of all 45 datasets available in matminer here. .. list-table:: :align: left @@ -137,6 +137,12 @@ Find a table of all 43 datasets available in matminer here. * - :code:`superconductivity2018` - Dataset of ~16,000 experimental superconductivity records (critical temperatures) from Stanev et al., originally from the Japanese National Institute for Materials Science - 16414 + * - :code:`tholander_nitrides` + - A challenging data set for quantum machine learning containing a diverse set of 12.8k polymorphs in the Zn-Ti-N, Zn-Zr-N and Zn-Hf-N chemical systems + - 12815 + * - :code:`ucsb_thermoelectrics` + - Database of ~1,100 experimental thermoelectric materials from UCSB aggregated from 108 source publications and personal communications + - 1093 * - :code:`wolverton_oxides` - 4,914 perovskite oxides containing composition data, lattice constants, and formation + vacancy formation energies - 4914 @@ -2324,6 +2330,110 @@ https://doi.org/10.1038/s41524-018-0085-8 +------------------ +tholander_nitrides +------------------ +A challenging data set for quantum machine learning containing a diverse set of 12.8k polymorphs in the Zn-Ti-N, Zn-Zr-N and Zn-Hf-N chemical systems. The phase diagrams of the Ti-Zn-N, Zr-Zn-N, and Hf-Zn-N systems are determined using large-scale high-throughput density functional calculations (DFT-GGA) (PBE). In total 12,815 relaxed structures are shared alongside their energy calculated using the VASP DFT code. The High-Throughput Toolkit was used to manage the calculations. Data adapted and deduplicated from the original data on Zenodo at https://zenodo.org/record/5530535#.YjJ3ZhDMJLQ, published under MIT licence. Collated from separate files of chemical systems and deduplicated according to identical structures matching ht_ids. Prepared in collaboration with Rhys Goodall. + +**Number of entries:** 12815 + +.. list-table:: + :align: left + :widths: 20 80 + :header-rows: 1 + + * - Column + - Description + * - :code:`material_id` + - Human readable identifier for each material. + * - :code:`ht_id` + - Unique identifier to track the calculation in httk + * - :code:`initial_structure` + - A pymatgen structure object representing the structure before relaxation. + * - :code:`final_structure` + - A pymatgen structure object representing the structure after relaxation. + * - :code:`E_vasp_per_atom` + - The VASP calculated energy per atom for the final structure, in eV/atom + * - :code:`chemical_system` + - The chemical system represented by the atoms actually contained in the structure + + + +**Reference** + +https://zenodo.org/record/5530535#.YjJ3ZhDMJLQ + + + +**Bibtex Formatted Citations** + +.. code-block:: text + + + @article{tholander2016strong, title={Strong piezoelectric response in stable TiZnN2, ZrZnN2, and HfZnN2 found by ab initio high-throughput approach}, author={Tholander, Christopher and Andersson, CBA and Armiento, Rickard and Tasnadi, Ferenc and Alling, Bj{\"o}rn}, journal={Journal of Applied Physics}, volume={120}, number={22}, pages={225102}, year={2016}, publisher={AIP Publishing LLC} } + + + + +-------------------- +ucsb_thermoelectrics +-------------------- +Database of ~1,100 experimental thermoelectric materials from UCSB aggregated from 108 source publications and personal communications. Downloaded from Citrine. Source UCSB webpage is http://www.mrl.ucsb.edu:8080/datamine/thermoelectric.jsp. See reference for more information on original data aggregation. No duplicate entries are present, but each src may result in multiple measurements of the same materials' properties at different temperatures or conditions. + +**Number of entries:** 1093 + +.. list-table:: + :align: left + :widths: 20 80 + :header-rows: 1 + + * - Column + - Description + * - :code:`composition` + - Chemical formula. + * - :code:`crystallinity` + - Either single crystal, polycrystalline, or nanoparticles. + * - :code:`synthesis` + - Brief string describing the synthesis method + * - :code:`spacegroup` + - Spacegroup number, if available + * - :code:`rho (ohm.cm)` + - Electrical resistivity, in ohm.cm + * - :code:`S [muV/K]` + - Seebeck coefficient, in microVolts/K, if available + * - :code:`PF [W/mK^2]` + - Thermoelectric power factor, conductivity * Seebeck^2, in [W/mK^2] if available + * - :code:`zT` + - Thermoelectric figure of merit, PF * T/K, unitless, if available + * - :code:`kappa [W/mK]` + - Thermal conductivity in Watt/ meter * Kelvin, if available + * - :code:`sigma [S/cm]` + - Electrical conductivity, in Siemens/cm, if available + * - :code:`T [K]` + - Temperature in Kelvin at which these properties were obtained, if available + * - :code:`src` + - Original source of the recording. To cite the aggregator of the data, see the bibtext_refs section of this metadata. + + + +**Reference** + +https://citrination.com/datasets/150557/ + + + +**Bibtex Formatted Citations** + +.. code-block:: text + + + @article{Gaultois2013, doi = {10.1021/cm400893e}, url = {https://doi.org/10.1021/cm400893e}, year = {2013}, month = may, publisher = {American Chemical Society ({ACS})}, volume = {25}, number = {15}, pages = {2911--2920}, author = {Michael W. Gaultois and Taylor D. Sparks and Christopher K. H. Borg and Ram Seshadri and William D. Bonificio and David R. Clarke}, title = {Data-Driven Review of Thermoelectric Materials: Performance and Resource Considerations}, journal = {Chemistry of Materials} } + + @misc{Citrine Informatics, title = {UCSB Thermoelectrics Database}, howpublished = {\url{https://citrination.com/datasets/150557/}, } + + + + ---------------- wolverton_oxides ---------------- diff --git a/docs/_static/documentation_options.js b/docs/_static/documentation_options.js index 8eb2f5e42..ad801d555 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: '0.7.6', + VERSION: '0.7.8', LANGUAGE: 'None', COLLAPSE_INDEX: false, BUILDER: 'html', diff --git a/docs/changelog.html b/docs/changelog.html index 36953da53..a09a4f637 100644 --- a/docs/changelog.html +++ b/docs/changelog.html @@ -5,7 +5,7 @@ - MatMiner Changelog — matminer 0.7.6 documentation + MatMiner Changelog — matminer 0.7.8 documentation @@ -28,7 +28,7 @@

Navigation

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    Navigation

    Table of Datasets

    -

    Find a table of all 43 datasets available in matminer here.

    +

    Find a table of all 45 datasets available in matminer here.

    @@ -222,6 +222,14 @@

    Table of Datasets

    + + + + + + + @@ -2361,6 +2369,110 @@

    superconductivity2018 +
    +

    tholander_nitrides

    +

    A challenging data set for quantum machine learning containing a diverse set of 12.8k polymorphs in the Zn-Ti-N, Zn-Zr-N and Zn-Hf-N chemical systems. The phase diagrams of the Ti-Zn-N, Zr-Zn-N, and Hf-Zn-N systems are determined using large-scale high-throughput density functional calculations (DFT-GGA) (PBE). In total 12,815 relaxed structures are shared alongside their energy calculated using the VASP DFT code. The High-Throughput Toolkit was used to manage the calculations. Data adapted and deduplicated from the original data on Zenodo at https://zenodo.org/record/5530535#.YjJ3ZhDMJLQ, published under MIT licence. Collated from separate files of chemical systems and deduplicated according to identical structures matching ht_ids. Prepared in collaboration with Rhys Goodall.

    +

    Number of entries: 12815

    +

    tholander_nitrides

    A challenging data set for quantum machine learning containing a diverse set of 12.8k polymorphs in the Zn-Ti-N, Zn-Zr-N and Zn-Hf-N chemical systems

    12815

    ucsb_thermoelectrics

    Database of ~1,100 experimental thermoelectric materials from UCSB aggregated from 108 source publications and personal communications

    1093

    wolverton_oxides

    4,914 perovskite oxides containing composition data, lattice constants, and formation + vacancy formation energies

    4914

    ++++ + + + + + + + + + + + + + + + + + + + + + + + + + +

    Column

    Description

    material_id

    Human readable identifier for each material.

    ht_id

    Unique identifier to track the calculation in httk

    initial_structure

    A pymatgen structure object representing the structure before relaxation.

    final_structure

    A pymatgen structure object representing the structure after relaxation.

    E_vasp_per_atom

    The VASP calculated energy per atom for the final structure, in eV/atom

    chemical_system

    The chemical system represented by the atoms actually contained in the structure

    +

    Reference

    +

    https://zenodo.org/record/5530535#.YjJ3ZhDMJLQ

    +

    Bibtex Formatted Citations

    +
    @article{tholander2016strong,   title={Strong piezoelectric response in stable TiZnN2, ZrZnN2, and HfZnN2 found by ab initio high-throughput approach},   author={Tholander, Christopher and Andersson, CBA and Armiento, Rickard and Tasnadi, Ferenc and Alling, Bj{\"o}rn},   journal={Journal of Applied Physics},   volume={120},   number={22},   pages={225102},   year={2016},   publisher={AIP Publishing LLC} }
+
    +
    +
    +
    +

    ucsb_thermoelectrics

    +

    Database of ~1,100 experimental thermoelectric materials from UCSB aggregated from 108 source publications and personal communications. Downloaded from Citrine. Source UCSB webpage is http://www.mrl.ucsb.edu:8080/datamine/thermoelectric.jsp. See reference for more information on original data aggregation. No duplicate entries are present, but each src may result in multiple measurements of the same materials’ properties at different temperatures or conditions.

    +

    Number of entries: 1093

    + ++++ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +

    Column

    Description

    composition

    Chemical formula.

    crystallinity

    Either single crystal, polycrystalline, or nanoparticles.

    synthesis

    Brief string describing the synthesis method

    spacegroup

    Spacegroup number, if available

    rho (ohm.cm)

    Electrical resistivity, in ohm.cm

    S [muV/K]

    Seebeck coefficient, in microVolts/K, if available

    PF [W/mK^2]

    Thermoelectric power factor, conductivity * Seebeck^2, in [W/mK^2] if available

    zT

    Thermoelectric figure of merit, PF * T/K, unitless, if available

    kappa [W/mK]

    Thermal conductivity in Watt/ meter * Kelvin, if available

    sigma [S/cm]

    Electrical conductivity, in Siemens/cm, if available

    T [K]

    Temperature in Kelvin at which these properties were obtained, if available

    src

    Original source of the recording. To cite the aggregator of the data, see the bibtext_refs section of this metadata.

    +

    Reference

    +

    https://citrination.com/datasets/150557/

    +

    Bibtex Formatted Citations

    +
    @article{Gaultois2013,   doi = {10.1021/cm400893e},   url = {https://doi.org/10.1021/cm400893e},   year = {2013},   month = may,   publisher = {American Chemical Society ({ACS})},   volume = {25},   number = {15},   pages = {2911--2920},   author = {Michael W. Gaultois and Taylor D. Sparks and Christopher K. H. Borg and Ram Seshadri and William D. Bonificio and David R. Clarke},   title = {Data-Driven Review of Thermoelectric Materials: Performance and Resource Considerations},   journal = {Chemistry of Materials} }
+
+@misc{Citrine Informatics, title = {UCSB Thermoelectrics Database}, howpublished = {\url{https://citrination.com/datasets/150557/}, }
+
    +
    +

    wolverton_oxides

    4,914 perovskite oxides containing composition data, lattice constants, and formation + vacancy formation energies. All perovskites are of the form ABO3. Adapted from a dataset presented by Emery and Wolverton.

    @@ -2491,6 +2603,8 @@

    Table of Contents

  • ricci_boltztrap_mp_tabular
  • steel_strength
  • superconductivity2018
    • +
  • tholander_nitrides
    • +
  • ucsb_thermoelectrics
  • wolverton_oxides
    • @@ -2526,7 +2640,7 @@

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    T

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    • @@ -296,6 +296,16 @@

    Submodulestest_superconductivity2018()
    +
    +
    +test_tholander_nitrides_e_form()
    +
    + +
    +
    +test_ucsb_thermoelectrics()
    +
    +
    test_wolverton_oxides()
    @@ -399,7 +409,7 @@

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\ No newline at end of file diff --git a/docs_rst/dataset_summary.rst b/docs_rst/dataset_summary.rst index ad34c84bc..40f219249 100644 --- a/docs_rst/dataset_summary.rst +++ b/docs_rst/dataset_summary.rst @@ -1,7 +1,7 @@ ================= Table of Datasets ================= -Find a table of all 43 datasets available in matminer here. +Find a table of all 45 datasets available in matminer here. .. list-table:: :align: left @@ -137,6 +137,12 @@ Find a table of all 43 datasets available in matminer here. * - :code:`superconductivity2018` - Dataset of ~16,000 experimental superconductivity records (critical temperatures) from Stanev et al., originally from the Japanese National Institute for Materials Science - 16414 + * - :code:`tholander_nitrides` + - A challenging data set for quantum machine learning containing a diverse set of 12.8k polymorphs in the Zn-Ti-N, Zn-Zr-N and Zn-Hf-N chemical systems + - 12815 + * - :code:`ucsb_thermoelectrics` + - Database of ~1,100 experimental thermoelectric materials from UCSB aggregated from 108 source publications and personal communications + - 1093 * - :code:`wolverton_oxides` - 4,914 perovskite oxides containing composition data, lattice constants, and formation + vacancy formation energies - 4914 @@ -2324,6 +2330,110 @@ https://doi.org/10.1038/s41524-018-0085-8 +------------------ +tholander_nitrides +------------------ +A challenging data set for quantum machine learning containing a diverse set of 12.8k polymorphs in the Zn-Ti-N, Zn-Zr-N and Zn-Hf-N chemical systems. The phase diagrams of the Ti-Zn-N, Zr-Zn-N, and Hf-Zn-N systems are determined using large-scale high-throughput density functional calculations (DFT-GGA) (PBE). In total 12,815 relaxed structures are shared alongside their energy calculated using the VASP DFT code. The High-Throughput Toolkit was used to manage the calculations. Data adapted and deduplicated from the original data on Zenodo at https://zenodo.org/record/5530535#.YjJ3ZhDMJLQ, published under MIT licence. Collated from separate files of chemical systems and deduplicated according to identical structures matching ht_ids. Prepared in collaboration with Rhys Goodall. + +**Number of entries:** 12815 + +.. list-table:: + :align: left + :widths: 20 80 + :header-rows: 1 + + * - Column + - Description + * - :code:`material_id` + - Human readable identifier for each material. + * - :code:`ht_id` + - Unique identifier to track the calculation in httk + * - :code:`initial_structure` + - A pymatgen structure object representing the structure before relaxation. + * - :code:`final_structure` + - A pymatgen structure object representing the structure after relaxation. + * - :code:`E_vasp_per_atom` + - The VASP calculated energy per atom for the final structure, in eV/atom + * - :code:`chemical_system` + - The chemical system represented by the atoms actually contained in the structure + + + +**Reference** + +https://zenodo.org/record/5530535#.YjJ3ZhDMJLQ + + + +**Bibtex Formatted Citations** + +.. code-block:: text + + + @article{tholander2016strong, title={Strong piezoelectric response in stable TiZnN2, ZrZnN2, and HfZnN2 found by ab initio high-throughput approach}, author={Tholander, Christopher and Andersson, CBA and Armiento, Rickard and Tasnadi, Ferenc and Alling, Bj{\"o}rn}, journal={Journal of Applied Physics}, volume={120}, number={22}, pages={225102}, year={2016}, publisher={AIP Publishing LLC} } + + + + +-------------------- +ucsb_thermoelectrics +-------------------- +Database of ~1,100 experimental thermoelectric materials from UCSB aggregated from 108 source publications and personal communications. Downloaded from Citrine. Source UCSB webpage is http://www.mrl.ucsb.edu:8080/datamine/thermoelectric.jsp. See reference for more information on original data aggregation. No duplicate entries are present, but each src may result in multiple measurements of the same materials' properties at different temperatures or conditions. + +**Number of entries:** 1093 + +.. list-table:: + :align: left + :widths: 20 80 + :header-rows: 1 + + * - Column + - Description + * - :code:`composition` + - Chemical formula. + * - :code:`crystallinity` + - Either single crystal, polycrystalline, or nanoparticles. + * - :code:`synthesis` + - Brief string describing the synthesis method + * - :code:`spacegroup` + - Spacegroup number, if available + * - :code:`rho (ohm.cm)` + - Electrical resistivity, in ohm.cm + * - :code:`S [muV/K]` + - Seebeck coefficient, in microVolts/K, if available + * - :code:`PF [W/mK^2]` + - Thermoelectric power factor, conductivity * Seebeck^2, in [W/mK^2] if available + * - :code:`zT` + - Thermoelectric figure of merit, PF * T/K, unitless, if available + * - :code:`kappa [W/mK]` + - Thermal conductivity in Watt/ meter * Kelvin, if available + * - :code:`sigma [S/cm]` + - Electrical conductivity, in Siemens/cm, if available + * - :code:`T [K]` + - Temperature in Kelvin at which these properties were obtained, if available + * - :code:`src` + - Original source of the recording. To cite the aggregator of the data, see the bibtext_refs section of this metadata. + + + +**Reference** + +https://citrination.com/datasets/150557/ + + + +**Bibtex Formatted Citations** + +.. code-block:: text + + + @article{Gaultois2013, doi = {10.1021/cm400893e}, url = {https://doi.org/10.1021/cm400893e}, year = {2013}, month = may, publisher = {American Chemical Society ({ACS})}, volume = {25}, number = {15}, pages = {2911--2920}, author = {Michael W. Gaultois and Taylor D. Sparks and Christopher K. H. Borg and Ram Seshadri and William D. Bonificio and David R. Clarke}, title = {Data-Driven Review of Thermoelectric Materials: Performance and Resource Considerations}, journal = {Chemistry of Materials} } + + @misc{Citrine Informatics, title = {UCSB Thermoelectrics Database}, howpublished = {\url{https://citrination.com/datasets/150557/}, } + + + + ---------------- wolverton_oxides ---------------- diff --git a/matminer/__init__.py b/matminer/__init__.py index aed57348c..894cebca0 100644 --- a/matminer/__init__.py +++ b/matminer/__init__.py @@ -1 +1 @@ -__version__ = "0.7.6" +__version__ = "0.7.8" diff --git a/setup.py b/setup.py index 3a2a11782..a99349193 100644 --- a/setup.py +++ b/setup.py @@ -28,7 +28,7 @@ if __name__ == "__main__": setup( name='matminer', - version='0.7.6', + version='0.7.8', 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(),