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Grain Boundaries API #58

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mkhorton opened this issue Sep 1, 2020 · 2 comments
Open

Grain Boundaries API #58

mkhorton opened this issue Sep 1, 2020 · 2 comments
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@munrojm

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@mkhorton
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mkhorton commented Sep 1, 2020 •
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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
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                "xyz" : [
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                    7.44354476280755
                ], 
                "label" : "W", 
                "properties" : {
                    "grain_label" : "bottom"
                }
            }, 
            {
                "species" : [
                    {
                        "element" : "W", 
                        "occu" : NumberInt(1)
                    }
                ], 
                "abc" : [
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                    0.5833332999999999
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                "label" : "W", 
                "properties" : {
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            {
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                "abc" : [
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                "label" : "W", 
                "properties" : {
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            }, 
            {
                "species" : [
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                "abc" : [
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                "label" : "W", 
                "properties" : {
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            {
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                "abc" : [
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                "label" : "W", 
                "properties" : {
                    "grain_label" : "top"
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            }, 
            {
                "species" : [
                    {
                        "element" : "W", 
                        "occu" : NumberInt(1)
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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" : [
                    {
                        "element" : "W", 
                        "occu" : NumberInt(1)
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                "abc" : [
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                "xyz" : [
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                    15.950454999999998
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                "label" : "W", 
                "properties" : {
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            {
                "species" : [
                    {
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                ], 
                "abc" : [
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                "xyz" : [
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                "label" : "W", 
                "properties" : {
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            {
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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" : {
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                "species" : [
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                        "element" : "W", 
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                "abc" : [
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                "label" : "W", 
                "properties" : {
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                "species" : [
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                        "occu" : NumberInt(1)
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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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            }, 
            {
                "species" : [
                    {
                        "element" : "W", 
                        "occu" : NumberInt(1)
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                ], 
                "abc" : [
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                "xyz" : [
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                    0.0
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                "label" : "W", 
                "properties" : {
                    "grain_label" : "bottom_incident"
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            }, 
            {
                "species" : [
                    {
                        "element" : "W", 
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                ], 
                "abc" : [
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                "xyz" : [
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                "label" : "W", 
                "properties" : {
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            {
                "species" : [
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                "abc" : [
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                "xyz" : [
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                "label" : "W", 
                "properties" : {
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                "species" : [
                    {
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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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                "species" : [
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                "abc" : [
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                "label" : "W", 
                "properties" : {
                    "grain_label" : "bottom"
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            {
                "species" : [
                    {
                        "element" : "W", 
                        "occu" : NumberInt(1)
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                "abc" : [
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                    0.5000000000000002, 
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                "xyz" : [
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                "label" : "W", 
                "properties" : {
                    "grain_label" : "top"
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            {
                "species" : [
                    {
                        "element" : "W", 
                        "occu" : NumberInt(1)
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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" : [
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                "label" : "W", 
                "properties" : {
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                "species" : [
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                "abc" : [
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                "label" : "W", 
                "properties" : {
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        "init_cell" : {
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            "charge" : null, 
            "lattice" : {
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                    [
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                    [
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                "a" : 2.7626998463841033, 
                "b" : 2.7626998463841033, 
                "c" : 2.7626998463841033, 
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                "beta" : 109.47122063449069, 
                "gamma" : 109.47122063449069, 
                "volume" : 16.232268577274958
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            "sites" : [
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                    "abc" : [
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                    "xyz" : [
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                    "label" : "W", 
                    "properties" : {
                        "magmom" : 0.0
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            ]
        }, 
        "rotation_axis" : [
            NumberInt(1), 
            NumberInt(1), 
            NumberInt(0)
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        "rotation_angle" : 109.47122063449069, 
        "gb_plane" : [
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            NumberInt(-1), 
            NumberInt(-2)
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        "join_plane" : [
            NumberInt(-1), 
            NumberInt(1), 
            NumberInt(-2)
        ], 
        "vacuum_thickness" : 0.0, 
        "ab_shift" : [
            0.0, 
            0.0
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        "oriented_unit_cell" : {
            "@module" : "pymatgen.core.structure", 
            "@class" : "Structure", 
            "charge" : null, 
            "lattice" : {
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                        -1.5950455
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                    [
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                        0.0
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                "a" : 2.7626998463841033, 
                "b" : 4.5114699574043495, 
                "c" : 4.5114699574043495, 
                "alpha" : 59.99999999999999, 
                "beta" : 90.0, 
                "gamma" : 90.0, 
                "volume" : 48.69680573182488
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            "sites" : [
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                            "element" : "W", 
                            "occu" : NumberInt(1)
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                    "xyz" : [
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                    "label" : "W", 
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                    "xyz" : [
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    "final_structure" : {
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                [
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                    0.0
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            "alpha" : 90.0, 
            "beta" : 89.99999894956503, 
            "gamma" : 90.0, 
            "volume" : 390.41595522357034
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        "sites" : [
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                        "element" : "W", 
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                "abc" : [
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                "xyz" : [
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                    3.214084, 
                    6.42816775
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                "label" : "W", 
                "properties" : {
                    "grain_label" : "bottom_incident"
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            {
                "species" : [
                    {
                        "element" : "W", 
                        "occu" : NumberInt(1)
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                "abc" : [
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                "xyz" : [
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                "label" : "W", 
                "properties" : {
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                "label" : "W", 
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                "xyz" : [
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                "properties" : {
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                "xyz" : [
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                "xyz" : [
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}
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munrojm commented Oct 5, 2020

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

@munrojm munrojm self-assigned this Oct 5, 2020
@munrojm munrojm closed this as completed Oct 16, 2020
@mkhorton
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mkhorton commented May 7, 2021

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

@mkhorton mkhorton reopened this May 7, 2021
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