From 783f8f47c121b64d10af2cc29a38b2c0ad7449f4 Mon Sep 17 00:00:00 2001 From: jmmshn Date: Tue, 26 Jan 2021 15:56:02 -0500 Subject: [PATCH] Elements --- emmet-core/emmet/core/electrode.py | 4 +- tests/emmet-core/test_electrodes.py | 10 +- tests/test_files/battery_data.json | 10880 -------------------------- 3 files changed, 9 insertions(+), 10885 deletions(-) delete mode 100644 tests/test_files/battery_data.json diff --git a/emmet-core/emmet/core/electrode.py b/emmet-core/emmet/core/electrode.py index 40dbe96637..47f03a6945 100644 --- a/emmet-core/emmet/core/electrode.py +++ b/emmet-core/emmet/core/electrode.py @@ -161,7 +161,7 @@ class ConversionElectrodeDoc(ConversionVoltagePairDoc): description="Returns all the adjacent Voltage Steps", ) - working_ion: WorkingIon = Field( + working_ion: Element = Field( None, description="The working ion as an Element object", ) @@ -242,7 +242,7 @@ class StructureGroupDoc(BaseModel): None, description="The formula of the host framework." ) - working_ion: WorkingIon = Field(None, description="The working ion") + working_ion: Element = Field(None, description="The working ion") chemsys: str = Field( None, diff --git a/tests/emmet-core/test_electrodes.py b/tests/emmet-core/test_electrodes.py index c71a1ef128..0d7e6924e0 100644 --- a/tests/emmet-core/test_electrodes.py +++ b/tests/emmet-core/test_electrodes.py @@ -22,7 +22,6 @@ def insertion_elec(test_dir): """ Recycle the test cases from pymatgen - TODO: All thie can be serialized in battery_data.json after PR to pymatgen """ entry_Li = ComputedEntry("Li", -1.90753119) entry_Mg = loadfn(test_dir / "Mg_batt.json") @@ -59,7 +58,9 @@ def conversion_elec(test_dir): working_ion = "Li" elif f in ["MnO2"]: working_ion = "Mg" - c = ConversionElectrode.from_composition_and_entries(Composition(f), entries, working_ion_symbol=working_ion) + c = ConversionElectrode.from_composition_and_entries( + Composition(f), entries, working_ion_symbol=working_ion + ) conversion_eletrodes[f] = { "working_ion": working_ion, "CE": c, @@ -117,7 +118,10 @@ def test_ConversionDocs(conversion_elec): assert vp.average_voltage == sub_elec.get_average_voltage() vp = ConversionElectrodeDoc.from_composition_and_entries( - Composition(k), entries=elec["entries"], working_ion_symbol=elec["working_ion"], task_id="mp-1234", + Composition(k), + entries=elec["entries"], + working_ion_symbol=elec["working_ion"], + task_id="mp-1234", ) res_d = vp.dict() for k, v in expected.items(): diff --git a/tests/test_files/battery_data.json b/tests/test_files/battery_data.json deleted file mode 100644 index 8694c94abe..0000000000 --- a/tests/test_files/battery_data.json +++ /dev/null @@ -1,10880 +0,0 @@ -{ - 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CIF has been adopted by the International\n# Union of Crystallography as the standard for data archiving and \n# transmission.\n#\n# For information on this file format, follow the CIF links at\n# http://www.iucr.org\n##########################################################################\n\ndata_Mg\n_symmetry_space_group_name_H-M 'P 1'\n_cell_length_a 3.18377279\n_cell_length_b 3.18377279595\n_cell_length_c 5.24943967\n_cell_angle_alpha 90.0\n_cell_angle_beta 90.0\n_cell_angle_gamma 120.000000042\n_chemical_name_systematic 'Generated by pymatgen'\n_symmetry_Int_Tables_number 1\n_chemical_formula_structural Mg\n_chemical_formula_sum Mg2\n_cell_volume 46.0816174934\n_cell_formula_units_Z 2\nloop_\n _symmetry_equiv_pos_site_id\n _symmetry_equiv_pos_as_xyz\n 1 'x, y, z'\n \nloop_\n _atom_site_type_symbol\n _atom_site_label\n _atom_site_symmetry_multiplicity\n _atom_site_fract_x\n _atom_site_fract_y\n _atom_site_fract_z\n _atom_site_attached_hydrogens\n _atom_site_B_iso_or_equiv\n _atom_site_occupancy\n Mg Mg1 1 0.333333 0.666667 0.250000 0 . 1\n Mg Mg2 1 0.666667 0.333333 0.750000 0 . 1\n \n", - "e_above_hull": 0, - "nelements": 1, - "pretty_formula": "Mg", - "energy": -3.18719007, - "hubbards": {}, - "nsites": 2, - "material_id": "mp-153", - "unit_cell_formula": { - "Mg": 2.0 - }, - "volume": 46.081617493391995, - "is_compatible": true, - "total_magnetization": 0.0, - "is_hubbard": false, - "task_ids": [ - "mp-153" - ], - "spacegroup": { - "symbol": "P6_3/mmc", - "number": 194, - "point_group": "6/mmm", - "source": "spglib", - "crystal_system": "hexagonal", - "hall": "-P 6c 2c" - }, - "energy_per_atom": -1.593595035, - "density": 1.75164851714211, - "icsd_id": [ - 181728, - 76259, - 52260, - 181254, - 53767, - 76748, - 162414, - 642653, - 76145, - 77908, - 170902, - 654648, - 166868, - 642651, - 168829, - 642655 - ] - }, - "entry_id": "mp-153", - "correction": 0.0, - "structure": { - "@module": "pymatgen.core.structure", - "@class": "Structure", - "charge": null, - "lattice": { - "matrix": [ - [ - 3.18377279, - 0.0, - 0.0 - ], - [ - -1.5918864, - 2.75722812, - 0.0 - ], - [ - 0.0, - 0.0, - 5.24943967 - ] - ], - "a": 3.18377279, - "b": 3.183772795948809, - "c": 5.24943967, - "alpha": 90.0, - "beta": 90.0, - "gamma": 120.0000000420923, - "volume": 46.081617493391995 - }, - "sites": [ - { - "species": [ - { - "element": "Mg", - "occu": 1 - } - ], - "abc": [ - 0.33333333, - 0.66666667, - 0.25 - ], - "xyz": [ - -1.925219716980564e-08, - 1.8381520891907606, - 1.3123599175 - ], - "label": "Mg", - "properties": { - "coordination_no": 12, - "forces": [ - 0.0, - 0.0, - 0.0 - ] - } - }, - { - "species": [ - { - "element": "Mg", - "occu": 1 - } - ], - "abc": [ - 0.66666667, - 0.33333333, - 0.75 - ], - "xyz": [ - 1.5918864092521976, - 0.9190760308092396, - 3.9370797525 - ], - "label": "Mg", - "properties": { - "coordination_no": 12, - "forces": [ - 0.0, - 0.0, - 0.0 - ] - } - } - ] - } - }, - "_framework_formula": "VO2", - "entry_charge": { - "@module": "pymatgen.entries.computed_entries", - "@class": "ComputedStructureEntry", - "energy": -90.23356258, - "composition": { - "O": 8.0, - "V": 4.0 - }, - "energy_adjustments": [ - { - "@module": "pymatgen.entries.computed_entries", - "@class": "ManualEnergyAdjustment", - "@version": "2020.12.3", - "value": -6.728 - } - ], - "parameters": { - "run_type": "GGA+U", - "hubbards": { - "O": 0.0, - "V": 3.25 - }, - "potcar_symbols": [ - "pbe O", - "pbe V_pv" - ], - "is_hubbard": true - }, - "data": { - "formation_energy_per_atom": -2.2322343254933323, - "elements": [ - "O", - "V" - ], - "band_gap": 0, - "cif": "#\\#CIF1.1\n##########################################################################\n# Crystallographic Information Format file \n# Produced by PyCifRW module\n# \n# This is a CIF file. 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"value": -6.728 - } - ], - "parameters": { - "run_type": "GGA+U", - "hubbards": { - "Mg": 0.0, - "O": 0.0, - "V": 3.25 - }, - "potcar_symbols": [ - "pbe O", - "pbe Mg_pv", - "pbe V_pv" - ], - "is_hubbard": true - }, - "data": { - "formation_energy_per_atom": -2.6315631139942863, - "elements": [ - "Mg", - "O", - "V" - ], - "band_gap": 0, - "cif": "#\\#CIF1.1\n##########################################################################\n# Crystallographic Information Format file \n# Produced by PyCifRW module\n# \n# This is a CIF file. CIF has been adopted by the International\n# Union of Crystallography as the standard for data archiving and \n# transmission.\n#\n# For information on this file format, follow the CIF links at\n# http://www.iucr.org\n##########################################################################\n\ndata_MgV2O4\n_symmetry_space_group_name_H-M 'P 1'\n_cell_length_a 6.03426766278\n_cell_length_b 6.03426766619\n_cell_length_c 6.03426767\n_cell_angle_alpha 60.000000034\n_cell_angle_beta 60.0000000152\n_cell_angle_gamma 60.0000000289\n_chemical_name_systematic 'Generated by pymatgen'\n_symmetry_Int_Tables_number 1\n_chemical_formula_structural MgV2O4\n_chemical_formula_sum 'Mg2 V4 O8'\n_cell_volume 155.366976453\n_cell_formula_units_Z 2\nloop_\n _symmetry_equiv_pos_site_id\n _symmetry_equiv_pos_as_xyz\n 1 'x, y, z'\n \nloop_\n _atom_site_type_symbol\n _atom_site_label\n _atom_site_symmetry_multiplicity\n _atom_site_fract_x\n _atom_site_fract_y\n _atom_site_fract_z\n _atom_site_attached_hydrogens\n _atom_site_B_iso_or_equiv\n _atom_site_occupancy\n O O1 1 0.740511 0.740510 0.740512 0 . 1\n O O2 1 0.259489 0.259489 0.721533 0 . 1\n O O3 1 0.259490 0.721531 0.259490 0 . 1\n O O4 1 0.721533 0.259489 0.259490 0 . 1\n O O5 1 0.740510 0.278468 0.740510 0 . 1\n O O6 1 0.278468 0.740510 0.740510 0 . 1\n O O7 1 0.259489 0.259489 0.259490 0 . 1\n O O8 1 0.740511 0.740510 0.278467 0 . 1\n Mg Mg9 1 0.875000 0.874999 0.875000 0 . 1\n Mg Mg10 1 0.125000 0.125000 0.125000 0 . 1\n V V11 1 0.500001 0.500000 0.500000 0 . 1\n V V12 1 0.500001 0.500000 1.000000 0 . 1\n V V13 1 0.000000 0.500000 0.500000 0 . 1\n V V14 1 0.500001 0.000000 0.500000 0 . 1\n \n", - "e_above_hull": 0.0469839557142846, - "nelements": 3, - "pretty_formula": "MgV2O4", - "energy": -103.47582434, - "hubbards": { - "Mg": 0.0, - "O": 0.0, - "V": 3.25 - }, - "nsites": 14, - "material_id": "mp-18900", - "unit_cell_formula": { - "Mg": 2.0, - "O": 8.0, - "V": 4.0 - }, - "volume": 155.3669764533744, - "is_compatible": true, - "total_magnetization": 8.0000016, - "is_hubbard": true, - "task_ids": [ - "mp-636207", - "mp-18900" - ], - "spacegroup": { - "symbol": "Fd-3m", - "number": 227, - "point_group": "m-3m", - "source": "spglib", - "crystal_system": "cubic", - "hall": "-F 4vw 2vw 3" - }, - "energy_per_atom": -7.39113031, - "density": 4.0653502851490755, - "icsd_id": [ - 76979, - 60412, - 56283 - ], - "muO2": [ - { - "reaction": "2 MgV2O4 + 2 O2 -> 2 MgV2O6", - "chempot": -4.93552791875, - "evolution": 3.9999999999999982 - }, - { - "reaction": "2 MgV2O4 + 1.833 O2 -> 0.6667 V3O7 + Mg2V2O7", - "chempot": -5.893613010000022, - "evolution": 3.6666666666666705 - }, - { - "reaction": "2 MgV2O4 + 1.5 O2 -> 2 VO2 + Mg2V2O7", - 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