Update ICSD drone #105

kmu · 2019-08-23T18:00:57Z

ICSD drone now reads metadata from JSON files obtained from ICSD.
ICSD drone no longer performs MongoDB operation by itself.
Abolish SNL.
Detect heavy hydrogens and replace them with H. Corresponding indices are stored in metadata.
Tests for ICSD drone.
Implicit hydrogen can be detected.

Reflect changes

kmu · 2019-08-23T18:32:19Z

@shyamd
The output looks like this:

{
  "cifmetadata": {
    "chem_name": "Aluminum oxide deuteriohydroxide - alpha",
    "chemsys": "Al-D-O",
    "elements": [
      "Al"
      "D",
      "O"
    ],
    "formula": "D8 Al8 O16",
    "formula_anonymous": "ABC2",
    "formula_reduced": "DAlO2",
    "formula_reduced_abc": "Al1 D1 O2",
    "history": [
      {
        "description": {
          "id": "5656565656"
        },
        "name": "ICSD",
        "url": "https://icsd.fiz-karlsruhe.de/"
      }
    ],
    "is_ordered": true,
    "is_valid": false,
    "nelements": 3,
    "nsites": 32,
    "pressure": 0.101325,
    "references": "@article{Pye2013,\ntitle = { Commentary: The Materials Project: A materials genome approach to accelerating materials innovation.},\nauthor = {Pye, M.F. and Birtill, J.J. and Dickens, P.G.},\njournal = {APL Materials},\nyear = {2013},\nvolume = {1},\npages = {1-1},\nASTM_id = {ACBCAR},\n}"
  },
  "metadata": {
    "AB_formula": "ABC2",
    "ICSD_version": "Version 4.2.0 (build 20190513-1424) - Data Release 2019.1",
    "NMR_data_available": false,
    "PDF_number": "01-070-0737",
    "R_value": 0.0716,
    "absolute_config_determined": false,
    "abstract": "",
    "anharmonic_temperature_factors_given": false,
    "authors": "Anubhav Jain, Shyue Ping Ong, Geoffroy Hautier, Wei Chen, William Davidson Richards, Stephen Dacek, Shreyas Cholia, Dan Gunter, David Skinner, Gerbrand Ceder, and Kristin A. Persson.",
    "calculated_PDF_number": false,
    "cell_constants_without_sd": false,
    "cell_parameters": {
      "a": 4.716,
      "alpha": 90.0,
      "b": 9.779,
      "beta": 90.0,
      "c": 2.966,
      "gamma": 90.0
    },
    "chemical_formula": "D1 Al1 O2",
    "collection_code": 5656565656,
    "comments": [],
    "consistent_composition": true,
    "correction_of_previous": false,
    "crawler_version": "0.0.3",
    "crystal_class": "mmm",
    "crystal_system": "orthorhombic",
    "data_quality": "High quality",
    "defect": false,
    "deuterium_indices": [
      0,
      1,
      2,
      3,
      4,
      5,
      6,
      7
    ],
    "disordered": false,
    "doi": "10.1063/1.4812323",
    "electron_diffraction": false,
    "experimental_PDF_number": false,
    "formula_units_per_cell": 4,
    "is_prototype_structure": false,
    "is_structure_prototype": false,
    "magnetic_structure_available": false,
    "mineral": false,
    "modulated_structure": false,
    "neutron_diffraction": false,
    "only_cell_and_structure_type": false,
    "order_disorder": false,
    "pearson": "oP16",
    "polytype": false,
    "powder": false,
    "pressure": "atmospheric",
    "publication_title": "Commentary: The Materials Project: A materials genome approach to accelerating materials innovation.",
    "references": [
      "APL Materials (2013) 1, (1) p1-p1"
    ],
    "rietveld_employed": false,
    "single_crystal": true,
    "space_group": "P b n m(62)",
    "structural_formula": "Al O (O D)",
    "structural_prototype": "AlOOH(Diaspore)",
    "synchrotron": false,
    "temperature": "room temperature",
    "temperature_factors_available": true,
    "theoretical_calculation": false,
    "tritium_indices": [],
    "twinned_crystal_data": false,
    "volume": 130.98,
    "warnings": [],
    "wyckoff_sequence": "c3",
    "x_ray": true
  },
  "structure": {
    "@class": "Structure",
    "@module": "pymatgen.core.structure",
    "@version": "2019.8.14",
    "charge": null,
    "lattice": {
      "a": 2.966,
      "alpha": 90.0,
      "b": 4.716,
      "beta": 90.0,
      "c": 9.779,
      "gamma": 90.0,
      "matrix": [
        [
          -0.0,
          -0.0,
          2.966
        ],
        [
          4.716,
          -0.0,
          2.887717152389459E-16
        ],
        [
          -5.987910524430983E-16,
          9.779,
          5.987910524430983E-16
        ]
      ],
      "volume": 136.785288024
    },
    "sites": [
      {
        "abc": [
          0.27,
          0.0963,
          0.5869
        ],
        "label": "H",
        "properties": {},
        "species": [
          {
            "element": "H",
            "occu": 1
          }
        ],
        "xyz": [
          0.4541507999999997,
          5.7392951,
          0.8008200000000004
        ]
      },
      {
        "abc": [
          0.23,
          0.40369999999999995,
          0.0869
        ],
        "label": "H",
        "properties": {},
        "species": [
          {
            "element": "H",
            "occu": 1
          }
        ],
        "xyz": [
          1.9038491999999998,
          0.8497951,
          0.6821800000000002
        ]
      },
      {
        "abc": [
          0.77,
          0.9037,
          0.4131
        ],
        "label": "H",
        "properties": {},
        "species": [
          {
            "element": "H",
            "occu": 1
          }
        ],
        "xyz": [
          4.2618492,
          4.0397049,
          2.2838200000000013
        ]
      },
      {
        "abc": [
          0.73,
          0.5963,
          0.9131
        ],
        "label": "H",
        "properties": {},
        "species": [
          {
            "element": "H",
            "occu": 1
          }
        ],
        "xyz": [
          2.8121508,
          8.9292049,
          2.1651800000000003
        ]
      },
      {
        "abc": [
          0.7299999999999999,
          0.9037,
          0.4131
        ],
        "label": "H",
        "properties": {},
        "species": [
          {
            "element": "H",
            "occu": 1
          }
        ],
        "xyz": [
          4.2618492,
          4.0397049,
          2.1651800000000008
        ]
      },
      {
        "abc": [
          0.7700000000000002,
          0.5963,
          0.9131
        ],
        "label": "H",
        "properties": {},
        "species": [
          {
            "element": "H",
            "occu": 1
          }
        ],
        "xyz": [
          2.8121508,
          8.9292049,
          2.2838200000000013
        ]
      },
      {
        "abc": [
          0.22999999999999998,
          0.0963,
          0.5869
        ],
        "label": "H",
        "properties": {},
        "species": [
          {
            "element": "H",
            "occu": 1
          }
        ],
        "xyz": [
          0.4541507999999997,
          5.7392951,
          0.6821800000000003
        ]
      },
      {
        "abc": [
          0.27,
          0.40369999999999995,
          0.0869
        ],
        "label": "H",
        "properties": {},
        "species": [
          {
            "element": "H",
            "occu": 1
          }
        ],
        "xyz": [
          1.9038491999999998,
          0.8497951,
          0.8008200000000002
        ]
      },
      {
        "abc": [
          0.27,
          0.4288,
          0.35530000000000006
        ],
        "label": "Al3+",
        "properties": {},
        "species": [
          {
            "element": "Al",
            "occu": 1.0,
            "oxidation_state": 3.0
          }
        ],
        "xyz": [
          2.0222208,
          3.4744787000000006,
          0.8008200000000004
        ]
      },
      {
        "abc": [
          0.23,
          0.0712,
          0.8553
        ],
        "label": "Al3+",
        "properties": {},
        "species": [
          {
            "element": "Al",
            "occu": 1.0,
            "oxidation_state": 3.0
          }
        ],
        "xyz": [
          0.3357791999999995,
          8.363978699999999,
          0.6821800000000007
        ]
      },
      {
        "abc": [
          0.77,
          0.5712,
          0.6447
        ],
        "label": "Al3+",
        "properties": {},
        "species": [
          {
            "element": "Al",
            "occu": 1.0,
            "oxidation_state": 3.0
          }
        ],
        "xyz": [
          2.6937792,
          6.3045213,
          2.283820000000001
        ]
      },
      {
        "abc": [
          0.73,
          0.9288,
          0.14470000000000002
        ],
        "label": "Al3+",
        "properties": {},
        "species": [
          {
            "element": "Al",
            "occu": 1.0,
            "oxidation_state": 3.0
          }
        ],
        "xyz": [
          4.3802208,
          1.4150213000000003,
          2.1651800000000003
        ]
      },
      {
        "abc": [
          0.7299999999999999,
          0.5712,
          0.6447
        ],
        "label": "Al3+",
        "properties": {},
        "species": [
          {
            "element": "Al",
            "occu": 1.0,
            "oxidation_state": 3.0
          }
        ],
        "xyz": [
          2.6937792,
          6.3045213,
          2.1651800000000003
        ]
      },
      {
        "abc": [
          0.7700000000000001,
          0.9288,
          0.14470000000000002
        ],
        "label": "Al3+",
        "properties": {},
        "species": [
          {
            "element": "Al",
            "occu": 1.0,
            "oxidation_state": 3.0
          }
        ],
        "xyz": [
          4.3802208,
          1.4150213000000003,
          2.283820000000001
        ]
      },
      {
        "abc": [
          0.23,
          0.4288,
          0.35530000000000006
        ],
        "label": "Al3+",
        "properties": {},
        "species": [
          {
            "element": "Al",
            "occu": 1.0,
            "oxidation_state": 3.0
          }
        ],
        "xyz": [
          2.0222208,
          3.4744787000000006,
          0.6821800000000005
        ]
      },
      {
        "abc": [
          0.27,
          0.0712,
          0.8553
        ],
        "label": "Al3+",
        "properties": {},
        "species": [
          {
            "element": "Al",
            "occu": 1.0,
            "oxidation_state": 3.0
          }
        ],
        "xyz": [
          0.3357791999999995,
          8.363978699999999,
          0.8008200000000006
        ]
      },
      {
        "abc": [
          0.27,
          0.798,
          0.6973
        ],
        "label": "O2-",
        "properties": {},
        "species": [
          {
            "element": "O",
            "occu": 1.0,
            "oxidation_state": -2.0
          }
        ],
        "xyz": [
          3.763368,
          6.8188967,
          0.8008200000000008
        ]
      },
      {
        "abc": [
          0.23,
          0.702,
          0.19730000000000003
        ],
        "label": "O2-",
        "properties": {},
        "species": [
          {
            "element": "O",
            "occu": 1.0,
            "oxidation_state": -2.0
          }
        ],
        "xyz": [
          3.310632,
          1.9293967000000003,
          0.6821800000000005
        ]
      },
      {
        "abc": [
          0.7700000000000001,
          0.20199999999999993,
          0.30269999999999997
        ],
        "label": "O2-",
        "properties": {},
        "species": [
          {
            "element": "O",
            "occu": 1.0,
            "oxidation_state": -2.0
          }
        ],
        "xyz": [
          0.9526319999999995,
          2.9601032999999997,
          2.2838200000000004
        ]
      },
      {
        "abc": [
          0.7299999999999999,
          0.29800000000000004,
          0.8027000000000001
        ],
        "label": "O2-",
        "properties": {},
        "species": [
          {
            "element": "O",
            "occu": 1.0,
            "oxidation_state": -2.0
          }
        ],
        "xyz": [
          1.4053679999999997,
          7.849603300000001,
          2.1651800000000003
        ]
      },
      {
        "abc": [
          0.73,
          0.20199999999999993,
          0.30269999999999997
        ],
        "label": "O2-",
        "properties": {},
        "species": [
          {
            "element": "O",
            "occu": 1.0,
            "oxidation_state": -2.0
          }
        ],
        "xyz": [
          0.9526319999999995,
          2.9601032999999997,
          2.16518
        ]
      },
      {
        "abc": [
          0.77,
          0.29800000000000004,
          0.8027000000000001
        ],
        "label": "O2-",
        "properties": {},
        "species": [
          {
            "element": "O",
            "occu": 1.0,
            "oxidation_state": -2.0
          }
        ],
        "xyz": [
          1.4053679999999997,
          7.849603300000001,
          2.283820000000001
        ]
      },
      {
        "abc": [
          0.23,
          0.798,
          0.6973
        ],
        "label": "O2-",
        "properties": {},
        "species": [
          {
            "element": "O",
            "occu": 1.0,
            "oxidation_state": -2.0
          }
        ],
        "xyz": [
          3.763368,
          6.8188967,
          0.6821800000000008
        ]
      },
      {
        "abc": [
          0.27,
          0.702,
          0.19730000000000003
        ],
        "label": "O2-",
        "properties": {},
        "species": [
          {
            "element": "O",
            "occu": 1.0,
            "oxidation_state": -2.0
          }
        ],
        "xyz": [
          3.310632,
          1.9293967000000003,
          0.8008200000000004
        ]
      },
      {
        "abc": [
          0.27,
          0.30529999999999996,
          0.5746
        ],
        "label": "O2-",
        "properties": {},
        "species": [
          {
            "element": "O",
            "occu": 1.0,
            "oxidation_state": -2.0
          }
        ],
        "xyz": [
          1.4397947999999994,
          5.6190134,
          0.8008200000000005
        ]
      },
      {
        "abc": [
          0.23,
          0.19469999999999998,
          0.0746
        ],
        "label": "O2-",
        "properties": {},
        "species": [
          {
            "element": "O",
            "occu": 1.0,
            "oxidation_state": -2.0
          }
        ],
        "xyz": [
          0.9182051999999999,
          0.7295134,
          0.6821800000000002
        ]
      },
      {
        "abc": [
          0.7700000000000001,
          0.6946999999999999,
          0.4254
        ],
        "label": "O2-",
        "properties": {},
        "species": [
          {
            "element": "O",
            "occu": 1.0,
            "oxidation_state": -2.0
          }
        ],
        "xyz": [
          3.2762051999999993,
          4.1599866,
          2.283820000000001
        ]
      },
      {
        "abc": [
          0.73,
          0.8053,
          0.9254
        ],
        "label": "O2-",
        "properties": {},
        "species": [
          {
            "element": "O",
            "occu": 1.0,
            "oxidation_state": -2.0
          }
        ],
        "xyz": [
          3.7977947999999997,
          9.0494866,
          2.1651800000000008
        ]
      },
      {
        "abc": [
          0.73,
          0.6946999999999999,
          0.4254
        ],
        "label": "O2-",
        "properties": {},
        "species": [
          {
            "element": "O",
            "occu": 1.0,
            "oxidation_state": -2.0
          }
        ],
        "xyz": [
          3.2762051999999993,
          4.1599866,
          2.1651800000000003
        ]
      },
      {
        "abc": [
          0.7700000000000002,
          0.8053,
          0.9254
        ],
        "label": "O2-",
        "properties": {},
        "species": [
          {
            "element": "O",
            "occu": 1.0,
            "oxidation_state": -2.0
          }
        ],
        "xyz": [
          3.7977947999999997,
          9.0494866,
          2.2838200000000017
        ]
      },
      {
        "abc": [
          0.23,
          0.30529999999999996,
          0.5746
        ],
        "label": "O2-",
        "properties": {},
        "species": [
          {
            "element": "O",
            "occu": 1.0,
            "oxidation_state": -2.0
          }
        ],
        "xyz": [
          1.4397947999999994,
          5.6190134,
          0.6821800000000006
        ]
      },
      {
        "abc": [
          0.27,
          0.19469999999999998,
          0.0746
        ],
        "label": "O2-",
        "properties": {},
        "species": [
          {
            "element": "O",
            "occu": 1.0,
            "oxidation_state": -2.0
          }
        ],
        "xyz": [
          0.9182051999999999,
          0.7295134,
          0.8008200000000002
        ]
      }
    ]
  }
}

kmu · 2019-08-23T21:15:22Z

WIP:

implicit hydrogens
data parsed from atomate -> root level

kmu · 2019-08-23T21:54:31Z

Updated output:

{
  "chemsys": "Al-D-O",
  "cifmetadata": {
    "chem_name": "Aluminum oxide deuteriohydroxide - alpha",
    "history": [
      {
        "description": {
          "id": "5656565656"
        },
        "name": "ICSD",
        "url": "https://icsd.fiz-karlsruhe.de/"
      }
    ],
    "pressure": 0.101325,
    "references": "@article{Pye2013,\ntitle = { Commentary: The Materials Project: A materials genome approach to accelerating materials innovation.},\nauthor = {Pye, M.F. and Birtill, J.J. and Dickens, P.G.},\njournal = {APL Materials},\nyear = {2013},\nvolume = {1},\npages = {1-1},\nASTM_id = {ACBCAR},\n}"
  },
  "elements": [
    "Al",
    "D",
    "O"
  ],
  "formula": "D8 Al8 O16",
  "formula_anonymous": "ABC2",
  "formula_pretty": "DAlO2",
  "formula_reduced_abc": "Al1 D1 O2",
  "is_ordered": true,
  "is_valid": false,
  "metadata": {
    "AB_formula": "ABC2",
    "ICSD_version": "Version 4.2.0 (build 20190513-1424) - Data Release 2019.1",
    "NMR_data_available": false,
    "PDF_number": "01-070-0737",
    "R_value": 0.0716,
    "absolute_config_determined": false,
    "abstract": "",
    "anharmonic_temperature_factors_given": false,
    "authors": "Anubhav Jain, Shyue Ping Ong, Geoffroy Hautier, Wei Chen, William Davidson Richards, Stephen Dacek, Shreyas Cholia, Dan Gunter, David Skinner, Gerbrand Ceder, and Kristin A. Persson.",
    "calculated_PDF_number": false,
    "cell_constants_without_sd": false,
    "cell_parameters": {
      "a": 4.716,
      "alpha": 90.0,
      "b": 9.779,
      "beta": 90.0,
      "c": 2.966,
      "gamma": 90.0
    },
    "chemical_formula": "D1 Al1 O2",
    "collection_code": 5656565656,
    "comments": [],
    "consistent_composition": true,
    "correction_of_previous": false,
    "crawler_version": "0.0.3",
    "crystal_class": "mmm",
    "crystal_system": "orthorhombic",
    "data_quality": "High quality",
    "defect": false,
    "deuterium_indices": [
      0,
      1,
      2,
      3,
      4,
      5,
      6,
      7
    ],
    "disordered": false,
    "doi": "10.1063/1.4812323",
    "electron_diffraction": false,
    "experimental_PDF_number": false,
    "formula_units_per_cell": 4,
    "implicit_hydrogen": false,
    "is_prototype_structure": false,
    "is_structure_prototype": false,
    "magnetic_structure_available": false,
    "mineral": false,
    "modulated_structure": false,
    "neutron_diffraction": false,
    "only_cell_and_structure_type": false,
    "order_disorder": false,
    "pearson": "oP16",
    "polytype": false,
    "powder": false,
    "pressure": "atmospheric",
    "publication_title": "Commentary: The Materials Project: A materials genome approach to accelerating materials innovation.",
    "references": [
      "APL Materials (2013) 1, (1) p1-p1"
    ],
    "rietveld_employed": false,
    "single_crystal": true,
    "space_group": "P b n m(62)",
    "structural_formula": "Al O (O D)",
    "structural_prototype": "AlOOH(Diaspore)",
    "synchrotron": false,
    "temperature": "room temperature",
    "temperature_factors_available": true,
    "theoretical_calculation": false,
    "tritium_indices": [],
    "twinned_crystal_data": false,
    "volume": 130.98,
    "warnings": [],
    "wyckoff_sequence": "c3",
    "x_ray": true
  },
  "nelements": 3,
  "nsites": 32,
  "structure": {
    "@class": "Structure",
    "@module": "pymatgen.core.structure",
    "@version": "2019.8.23",
    "charge": null,
    "lattice": {
      "a": 2.966,
      "alpha": 90.0,
      "b": 4.716,
      "beta": 90.0,
      "c": 9.779,
      "gamma": 90.0,
      "matrix": [
        [
          -0.0,
          -0.0,
          2.966
        ],
        [
          4.716,
          -0.0,
          2.887717152389459E-16
        ],
        [
          -5.987910524430983E-16,
          9.779,
          5.987910524430983E-16
        ]
      ],
      "volume": 136.785288024
    },
    "sites": [
      {
        "abc": [
          0.27,
          0.0963,
          0.5869
        ],
        "label": "H",
        "properties": {},
        "species": [
          {
            "element": "H",
            "occu": 1
          }
        ],
        "xyz": [
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}

…it-2.1.1 Bump pre-commit from 2.0.1 to 2.1.1

kmu added 24 commits August 21, 2019 16:41

update path to StructureNL

4b101aa

Merge remote-tracking branch 'upstream/master' into snl_path

c2c95ec

Add missing self

d971a10

Pymatgen needs networkx==2.2

b42816d

Reflect atomate's new name convention

6c19291

Keep legacy name

5840bea

Store mongo on demand for icsdDrone

1e9dbd1

Test files for icsdDrone

6aaaa06

Uses jsonschema

16db80c

Merge pull request #1 from kmu/snl_path

97d4861

Reflect changes

Abolish mongo operation from icsdDrone

f561ac7

Refactoring

a575e2a

Rename test files

181f759

Do not import mongo staff

9f8cc3f

Divide assimilate methods into cif parser and json parser

b6cdb06

Abolish SNL and authors from LBL

d8d2adc

Fix tests

a498a51

Verify composition

7cce825

Fix typo

742476d

Add dummy data for D

3da7aae

Fix dummy cif

b251d1b

Logic to detect D and T

01e24fc

Refactoring

0810a09

Read json if it exists

be9f5a3

kmu changed the title ~~Update ICSD drone~~ [WIP] Update ICSD drone Aug 23, 2019

kmu added 3 commits August 23, 2019 14:25

Move atomate metadata to root

84bca5a

Do not dump json

21d9099

Helper method to detect implicit H

422822b

Fix test data

ccfe358

kmu changed the title ~~[WIP] Update ICSD drone~~ Update ICSD drone Aug 23, 2019

kmu added 2 commits August 25, 2019 18:27

Merge remote-tracking branch 'origin/master' into icsd_drone

9ab74ff

Merge remote-tracking branch 'upstream/master' into icsd_drone

b469de8

shyamd merged commit 713fc8b into materialsproject:master Aug 27, 2019

utf referenced this pull request in utf/emmet May 8, 2021

Merge pull request #105 from materialsproject/dependabot/pip/pre-comm…

d2ed96e

…it-2.1.1 Bump pre-commit from 2.0.1 to 2.1.1

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