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New API client for the Materials Project
https://materialsproject.github.io/api/
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Grain Boundaries API #58

Open mkhorton opened 4 years ago

mkhorton commented 4 years ago
image

Sample document:

{ 
    "material_id" : "mp-91", 
    "sigma" : NumberInt(3), 
    "type" : "tilt", 
    "rotation_axis" : [
        NumberInt(1), 
        NumberInt(1), 
        NumberInt(0)
    ], 
    "gb_plane" : [
        NumberInt(1), 
        NumberInt(-1), 
        NumberInt(-2)
    ], 
    "rotation_angle" : 109.47122063449069, 
    "gb_energy" : 0.6654087235291888, 
    "initial_structure" : {
        "@module" : "pymatgen.analysis.gb.grain", 
        "@class" : "GrainBoundary", 
        "charge" : null, 
        "lattice" : {
            "matrix" : [
                [
                    -1.5950455, 
                    1.5950455, 
                    -1.5950455
                ], 
                [
                    -3.1900910000000002, 
                    -3.190091, 
                    0.0
                ], 
                [
                    -12.760364000000001, 
                    12.760364000000001, 
                    25.520728
                ]
            ], 
            "a" : 2.7626998463841033, 
            "b" : 4.5114699574043495, 
            "c" : 31.256380732179725, 
            "alpha" : 90.0, 
            "beta" : 90.0, 
            "gamma" : 90.0, 
            "volume" : 389.57444585459905
        }, 
        "sites" : [
            {
                "species" : [
                    {
                        "element" : "W", 
                        "occu" : NumberInt(1)
                    }
                ], 
                "abc" : [
                    0.00000000000000004982853252972633, 
                    -0.00000000000000003062726792234917, 
                    0.25
                ], 
                "xyz" : [
                    -3.1900910000000002, 
                    3.1900910000000002, 
                    6.380182
                ], 
                "label" : "W", 
                "properties" : {
                    "grain_label" : "bottom_incident"
                }
            }, 
            {
                "species" : [
                    {
                        "element" : "W", 
                        "occu" : NumberInt(1)
                    }
                ], 
                "abc" : [
                    0.6666667, 
                    -0.00000000000000004354120932647733, 
                    0.3333333
                ], 
                "xyz" : [
                    -5.31681796115605, 
                    5.31681796115605, 
                    7.44354476280755
                ], 
                "label" : "W", 
                "properties" : {
                    "grain_label" : "bottom"
                }
            }, 
            {
                "species" : [
                    {
                        "element" : "W", 
                        "occu" : NumberInt(1)
                    }
                ], 
                "abc" : [
                    0.3333333000000007, 
                    0.00000000000000026511272849745455, 
                    0.5833332999999999
                ], 
                "xyz" : [
                    -7.975227021486352, 
                    7.97522702148635, 
                    14.355408702477247
                ], 
                "label" : "W", 
                "properties" : {
                    "grain_label" : "top"
                }
            }, 
            {
                "species" : [
                    {
                        "element" : "W", 
                        "occu" : NumberInt(1)
                    }
                ], 
                "abc" : [
                    0.00000000000000009965706505945266, 
                    -0.00000000000000006125453584469834, 
                    0.5
                ], 
                "xyz" : [
                    -6.3801820000000005, 
                    6.3801820000000005, 
                    12.760364
                ], 
                "label" : "W", 
                "properties" : {
                    "grain_label" : "top_incident"
                }
            }, 
            {
                "species" : [
                    {
                        "element" : "W", 
                        "occu" : NumberInt(1)
                    }
                ], 
                "abc" : [
                    0.3333333, 
                    -0.00000000000000003589865278611583, 
                    0.4166667
                ], 
                "xyz" : [
                    -5.84850053884395, 
                    5.84850053884395, 
                    10.10195573719245
                ], 
                "label" : "W", 
                "properties" : {
                    "grain_label" : "bottom"
                }
            }, 
            {
                "species" : [
                    {
                        "element" : "W", 
                        "occu" : NumberInt(1)
                    }
                ], 
                "abc" : [
                    0.6666667, 
                    0.49999999999999994, 
                    0.45833329999999994
                ], 
                "xyz" : [
                    -8.50690896115605, 
                    5.31681796115605, 
                    10.633635762807549
                ], 
                "label" : "W", 
                "properties" : {
                    "grain_label" : "bottom"
                }
            }, 
            {
                "species" : [
                    {
                        "element" : "W", 
                        "occu" : NumberInt(1)
                    }
                ], 
                "abc" : [
                    0.666666700000001, 
                    0.5000000000000001, 
                    0.5416667000000001
                ], 
                "xyz" : [
                    -9.570273478513654, 
                    6.380182478513652, 
                    12.76036479752275
                ], 
                "label" : "W", 
                "properties" : {
                    "grain_label" : "top"
                }
            }, 
            {
                "species" : [
                    {
                        "element" : "W", 
                        "occu" : NumberInt(1)
                    }
                ], 
                "abc" : [
                    0.0000000000000005552646838577253, 
                    0.5, 
                    0.37500000000000006
                ], 
                "xyz" : [
                    -6.380182000000002, 
                    3.190091000000002, 
                    9.570273
                ], 
                "label" : "W", 
                "properties" : {
                    "grain_label" : "bottom_incident"
                }
            }, 
            {
                "species" : [
                    {
                        "element" : "W", 
                        "occu" : NumberInt(1)
                    }
                ], 
                "abc" : [
                    0.0000000000000005322278659613053, 
                    0.4999999999999998, 
                    0.625
                ], 
                "xyz" : [
                    -9.570273, 
                    6.380182000000002, 
                    15.950454999999998
                ], 
                "label" : "W", 
                "properties" : {
                    "grain_label" : "top_incident"
                }
            }, 
            {
                "species" : [
                    {
                        "element" : "W", 
                        "occu" : NumberInt(1)
                    }
                ], 
                "abc" : [
                    0.3333333000000004, 
                    0.49999999999999994, 
                    0.2916667
                ], 
                "xyz" : [
                    -5.84850053884395, 
                    2.658409538843951, 
                    6.911864737192449
                ], 
                "label" : "W", 
                "properties" : {
                    "grain_label" : "bottom"
                }
            }, 
            {
                "species" : [
                    {
                        "element" : "W", 
                        "occu" : NumberInt(1)
                    }
                ], 
                "abc" : [
                    0.6666666999999998, 
                    0.00000000000000012691412203612193, 
                    0.66666665
                ], 
                "xyz" : [
                    -9.57027284049545, 
                    9.57027284049545, 
                    15.95045452148635
                ], 
                "label" : "W", 
                "properties" : {
                    "grain_label" : "top"
                }
            }, 
            {
                "species" : [
                    {
                        "element" : "W", 
                        "occu" : NumberInt(1)
                    }
                ], 
                "abc" : [
                    0.6666667, 
                    0.5, 
                    0.20833335
                ], 
                "xyz" : [
                    -5.31681859917425, 
                    2.12672759917425, 
                    4.25345503884395
                ], 
                "label" : "W", 
                "properties" : {
                    "grain_label" : "bottom"
                }
            }, 
            {
                "species" : [
                    {
                        "element" : "W", 
                        "occu" : NumberInt(1)
                    }
                ], 
                "abc" : [
                    0.33333329999999917, 
                    0.0000000000000003604632238599955, 
                    0.8333332999999999
                ], 
                "xyz" : [
                    -11.16531802148635, 
                    11.165318021486348, 
                    20.73559070247725
                ], 
                "label" : "W", 
                "properties" : {
                    "grain_label" : "top"
                }
            }, 
            {
                "species" : [
                    {
                        "element" : "W", 
                        "occu" : NumberInt(1)
                    }
                ], 
                "abc" : [
                    -0.0000000000000006658274716847999, 
                    -0.000000000000000022277330125063202, 
                    0.75
                ], 
                "xyz" : [
                    -9.570273, 
                    9.570273, 
                    19.140546
                ], 
                "label" : "W", 
                "properties" : {
                    "grain_label" : "top_incident"
                }
            }, 
            {
                "species" : [
                    {
                        "element" : "W", 
                        "occu" : NumberInt(1)
                    }
                ], 
                "abc" : [
                    0.0, 
                    0.0, 
                    0.0
                ], 
                "xyz" : [
                    0.0, 
                    0.0, 
                    0.0
                ], 
                "label" : "W", 
                "properties" : {
                    "grain_label" : "bottom_incident"
                }
            }, 
            {
                "species" : [
                    {
                        "element" : "W", 
                        "occu" : NumberInt(1)
                    }
                ], 
                "abc" : [
                    0.6666667000000003, 
                    0.000000000000000028503887416403193, 
                    0.08333330000000003
                ], 
                "xyz" : [
                    -2.126726961156051, 
                    2.126726961156051, 
                    1.0633627628075502
                ], 
                "label" : "W", 
                "properties" : {
                    "grain_label" : "bottom"
                }
            }, 
            {
                "species" : [
                    {
                        "element" : "W", 
                        "occu" : NumberInt(1)
                    }
                ], 
                "abc" : [
                    0.6666667000000001, 
                    -0.00000000000000014478531581007957, 
                    0.9166667
                ], 
                "xyz" : [
                    -12.76036447851365, 
                    12.760364478513651, 
                    22.330637797522748
                ], 
                "label" : "W", 
                "properties" : {
                    "grain_label" : "top"
                }
            }, 
            {
                "species" : [
                    {
                        "element" : "W", 
                        "occu" : NumberInt(1)
                    }
                ], 
                "abc" : [
                    -0.0000000000000002332566707829473, 
                    0.5, 
                    0.875
                ], 
                "xyz" : [
                    -12.760364000000001, 
                    9.570273, 
                    22.330637
                ], 
                "label" : "W", 
                "properties" : {
                    "grain_label" : "top_incident"
                }
            }, 
            {
                "species" : [
                    {
                        "element" : "W", 
                        "occu" : NumberInt(1)
                    }
                ], 
                "abc" : [
                    0.6666667000000005, 
                    0.5000000000000001, 
                    0.7916667000000001
                ], 
                "xyz" : [
                    -12.760364478513653, 
                    9.570273478513652, 
                    19.14054679752275
                ], 
                "label" : "W", 
                "properties" : {
                    "grain_label" : "top"
                }
            }, 
            {
                "species" : [
                    {
                        "element" : "W", 
                        "occu" : NumberInt(1)
                    }
                ], 
                "abc" : [
                    0.33333330000000005, 
                    0.5, 
                    0.0416667
                ], 
                "xyz" : [
                    -2.65840953884395, 
                    -0.5316814611560498, 
                    0.53168273719245
                ], 
                "label" : "W", 
                "properties" : {
                    "grain_label" : "bottom"
                }
            }, 
            {
                "species" : [
                    {
                        "element" : "W", 
                        "occu" : NumberInt(1)
                    }
                ], 
                "abc" : [
                    0.3333333000000014, 
                    0.5000000000000002, 
                    0.9583333
                ], 
                "xyz" : [
                    -14.355409021486354, 
                    11.165318021486353, 
                    23.92568170247725
                ], 
                "label" : "W", 
                "properties" : {
                    "grain_label" : "top"
                }
            }, 
            {
                "species" : [
                    {
                        "element" : "W", 
                        "occu" : NumberInt(1)
                    }
                ], 
                "abc" : [
                    0.000000000000000024914266264863166, 
                    0.4999999999999999, 
                    0.125
                ], 
                "xyz" : [
                    -3.190091, 
                    0.0000000000000006661338147750939, 
                    3.190091
                ], 
                "label" : "W", 
                "properties" : {
                    "grain_label" : "bottom_incident"
                }
            }, 
            {
                "species" : [
                    {
                        "element" : "W", 
                        "occu" : NumberInt(1)
                    }
                ], 
                "abc" : [
                    0.33333330000000017, 
                    -0.0000000000000000003371422756721006, 
                    0.16666665
                ], 
                "xyz" : [
                    -2.6584089008257505, 
                    2.6584089008257505, 
                    3.7217724611560494
                ], 
                "label" : "W", 
                "properties" : {
                    "grain_label" : "bottom"
                }
            }, 
            {
                "species" : [
                    {
                        "element" : "W", 
                        "occu" : NumberInt(1)
                    }
                ], 
                "abc" : [
                    0.33333330000000017, 
                    0.49999999999999994, 
                    0.70833335
                ], 
                "xyz" : [
                    -11.16531865950455, 
                    7.975227659504551, 
                    17.545500978513648
                ], 
                "label" : "W", 
                "properties" : {
                    "grain_label" : "top"
                }
            }
        ], 
        "init_cell" : {
            "@module" : "pymatgen.core.structure", 
            "@class" : "Structure", 
            "charge" : null, 
            "lattice" : {
                "matrix" : [
                    [
                        1.5950455, 
                        1.5950455, 
                        1.5950455
                    ], 
                    [
                        1.5950455, 
                        -1.5950455, 
                        -1.5950455
                    ], 
                    [
                        -1.5950455, 
                        1.5950455, 
                        -1.5950455
                    ]
                ], 
                "a" : 2.7626998463841033, 
                "b" : 2.7626998463841033, 
                "c" : 2.7626998463841033, 
                "alpha" : 109.47122063449069, 
                "beta" : 109.47122063449069, 
                "gamma" : 109.47122063449069, 
                "volume" : 16.232268577274958
            }, 
            "sites" : [
                {
                    "species" : [
                        {
                            "element" : "W", 
                            "occu" : NumberInt(1)
                        }
                    ], 
                    "abc" : [
                        0.0, 
                        0.0, 
                        0.0
                    ], 
                    "xyz" : [
                        0.0, 
                        0.0, 
                        0.0
                    ], 
                    "label" : "W", 
                    "properties" : {
                        "magmom" : 0.0
                    }
                }
            ]
        }, 
        "rotation_axis" : [
            NumberInt(1), 
            NumberInt(1), 
            NumberInt(0)
        ], 
        "rotation_angle" : 109.47122063449069, 
        "gb_plane" : [
            NumberInt(1), 
            NumberInt(-1), 
            NumberInt(-2)
        ], 
        "join_plane" : [
            NumberInt(-1), 
            NumberInt(1), 
            NumberInt(-2)
        ], 
        "vacuum_thickness" : 0.0, 
        "ab_shift" : [
            0.0, 
            0.0
        ], 
        "oriented_unit_cell" : {
            "@module" : "pymatgen.core.structure", 
            "@class" : "Structure", 
            "charge" : null, 
            "lattice" : {
                "matrix" : [
                    [
                        -1.5950455, 
                        1.5950455, 
                        -1.5950455
                    ], 
                    [
                        -3.1900910000000002, 
                        -3.190091, 
                        0.0
                    ], 
                    [
                        -3.1900910000000002, 
                        0.0, 
                        3.190091
                    ]
                ], 
                "a" : 2.7626998463841033, 
                "b" : 4.5114699574043495, 
                "c" : 4.5114699574043495, 
                "alpha" : 59.99999999999999, 
                "beta" : 90.0, 
                "gamma" : 90.0, 
                "volume" : 48.69680573182488
            }, 
            "sites" : [
                {
                    "species" : [
                        {
                            "element" : "W", 
                            "occu" : NumberInt(1)
                        }
                    ], 
                    "abc" : [
                        0.3333333, 
                        0.6666667, 
                        0.6666667
                    ], 
                    "xyz" : [
                        -4.78513665950455, 
                        -1.5950456595045497, 
                        1.5950456595045497
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                    "label" : "W", 
                    "properties" : {
                        "magmom" : 0.0
                    }
                }, 
                {
                    "species" : [
                        {
                            "element" : "W", 
                            "occu" : NumberInt(1)
                        }
                    ], 
                    "abc" : [
                        0.6666667, 
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                        0.3333333
                    ], 
                    "xyz" : [
                        -3.19009084049545, 
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                        -0.00000015950454985918036
                    ], 
                    "label" : "W", 
                    "properties" : {
                        "magmom" : 0.0
                    }
                }, 
                {
                    "species" : [
                        {
                            "element" : "W", 
                            "occu" : NumberInt(1)
                        }
                    ], 
                    "abc" : [
                        0.0, 
                        0.0, 
                        0.0
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                    "xyz" : [
                        0.0, 
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                        0.0
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                    "label" : "W", 
                    "properties" : {
                        "magmom" : 0.0
                    }
                }
            ]
        }
    }, 
    "final_structure" : {
        "@module" : "pymatgen.analysis.gb.grain", 
        "@class" : "GrainBoundary", 
        "charge" : null, 
        "lattice" : {
            "matrix" : [
                [
                    -1.591016, 
                    1.591016, 
                    -1.591016
                ], 
                [
                    -3.181153, 
                    -3.181153, 
                    0.0
                ], 
                [
                    -12.856336, 
                    12.856336, 
                    25.712671
                ]
            ], 
            "a" : 2.7557205476550046, 
            "b" : 4.498829716583859, 
            "c" : 31.491462345277537, 
            "alpha" : 90.0, 
            "beta" : 89.99999894956503, 
            "gamma" : 90.0, 
            "volume" : 390.41595522357034
        }, 
        "sites" : [
            {
                "species" : [
                    {
                        "element" : "W", 
                        "occu" : NumberInt(1)
                    }
                ], 
                "abc" : [
                    0.0, 
                    0.0, 
                    0.25
                ], 
                "xyz" : [
                    -3.214084, 
                    3.214084, 
                    6.42816775
                ], 
                "label" : "W", 
                "properties" : {
                    "grain_label" : "bottom_incident"
                }
            }, 
            {
                "species" : [
                    {
                        "element" : "W", 
                        "occu" : NumberInt(1)
                    }
                ], 
                "abc" : [
                    0.665252, 
                    0.0, 
                    0.332944
                ], 
                "xyz" : [
                    -5.338866509216, 
                    5.338866509216, 
                    7.502452957392
                ], 
                "label" : "W", 
                "properties" : {
                    "grain_label" : "bottom"
                }
            }, 
            {
                "species" : [
                    {
                        "element" : "W", 
                        "occu" : NumberInt(1)
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                ], 
                "abc" : [
                    0.333021, 
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                "xyz" : [
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                "label" : "W", 
                "properties" : {
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            {
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                "abc" : [
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                "xyz" : [
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                "label" : "W", 
                "properties" : {
                    "grain_label" : "top_incident"
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                "xyz" : [
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                "label" : "W", 
                "properties" : {
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                "abc" : [
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                "xyz" : [
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                "label" : "W", 
                "properties" : {
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                "abc" : [
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                "xyz" : [
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                "label" : "W", 
                "properties" : {
                    "grain_label" : "top"
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            {
                "species" : [
                    {
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                ], 
                "abc" : [
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                "xyz" : [
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                "label" : "W", 
                "properties" : {
                    "grain_label" : "bottom_incident"
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            }, 
            {
                "species" : [
                    {
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                "abc" : [
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                "xyz" : [
                    -11.223359648384, 
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                "label" : "W", 
                "properties" : {
                    "grain_label" : "top_incident"
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            }, 
            {
                "species" : [
                    {
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                "abc" : [
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                "xyz" : [
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                "label" : "W", 
                "properties" : {
                    "grain_label" : "bottom"
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            }, 
            {
                "species" : [
                    {
                        "element" : "W", 
                        "occu" : NumberInt(1)
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}
munrojm commented 3 years ago

Grain boundary endpoint added with client. Docs moved over to atlas.

mkhorton commented 3 years ago

Some issues I've noticed using this as an end-user:

  1. Grain boundary docs are missing a primary key, so you can't request a specific grain boundary. Perhaps it would be good practice to ensure all end-points have a primary key?
  2. Inconsistency with surface_properties since surfaces returns all surface information as a single doc for a given mpid, whereas grain_boundaries returns many docs for a given mpid -- for this, I think the grain boundary way makes more sense, since it makes it possible to request just a single grain boundary Structure, whereas for the surfaces you have to request all the surface Structures for a given mpid even if you only want one