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Metadata in json files #236

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Metadata in json files #236

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d3e1610
Added metadata to my (markus) claimed json files
mastricker Dec 3, 2019
fabb12d
add tags to structures
felixmusil Dec 4, 2019
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2 changes: 2 additions & 0 deletions reference_data/inputs/CaCrP2O7_mvc-11955_symmetrized.json
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Expand Up @@ -158,5 +158,7 @@
true
]
},
"user":"musil",
"comment":"comes from materials project id: mvc-11955",
"ids": [1],
"nextid": 2}
22 changes: 12 additions & 10 deletions reference_data/inputs/alanine-X-examples.json
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{"1": {
"cell": [[8.1, 0.0, 0.0], [0.0, 8.62, 0.0], [0.0, 0.0, 7.21]],
"ctime": 19.792880012677248,
"mtime": 19.792880012677248,
"numbers": [6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 7, 7],
"pbc": [false, false, false],
"positions": [[3.889491085, 4.97062762, 1.86077437], [3.891927665, 3.94516009, 3.0053970299999997], [2.7073416949999998, 5.93709525, 1.9835621499999998], [4.211128895, 3.6536609899999997, 5.42796568], [4.210000545, 4.67960304, 6.57156473], [5.391698695, 2.6857677099999995, 5.55687028], [3.5920354549999995, 3.2140371400000003, 0.7843498599999998], [4.828550695, 5.54957842, 1.8723012799999998], [1.758181365, 5.382449869999999, 1.9948462500000002], [2.776300025, 6.5301968, 2.90611802], [2.708255285, 6.626161099999999, 1.12917427], [4.508119535, 5.40924319, 4.35202838], [3.271190615, 3.0762157199999995, 5.4429136399999996], [6.341818634999999, 3.2387308599999995, 5.57095967], [5.318730025, 2.09561691, 6.4812020100000005], [5.392829694999999, 1.9938388999999996, 4.7049904], [3.547668225, 2.7783416499999998, 2.8106070699999997], [4.555853324999999, 5.84639344, 6.37902407], [3.839338715, 4.1980903199999995, 0.63843527], [4.261876395, 4.42509162, 4.2045273199999995]],
"unique_id": "1b5bf47287ddedc63232cd0b58101302",
"user": "markus"},
"ids": [1],
"nextid": 2}
"cell": [[8.1, 0.0, 0.0], [0.0, 8.62, 0.0], [0.0, 0.0, 7.21]],
"ctime": 19.792880012677248,
"mtime": 19.792880012677248,
"numbers": [6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 7, 7],
"pbc": [false, false, false],
"positions": [[3.889491085, 4.97062762, 1.86077437], [3.891927665, 3.94516009, 3.0053970299999997], [2.7073416949999998, 5.93709525, 1.9835621499999998], [4.211128895, 3.6536609899999997, 5.42796568], [4.210000545, 4.67960304, 6.57156473], [5.391698695, 2.6857677099999995, 5.55687028], [3.5920354549999995, 3.2140371400000003, 0.7843498599999998], [4.828550695, 5.54957842, 1.8723012799999998], [1.758181365, 5.382449869999999, 1.9948462500000002], [2.776300025, 6.5301968, 2.90611802], [2.708255285, 6.626161099999999, 1.12917427], [4.508119535, 5.40924319, 4.35202838], [3.271190615, 3.0762157199999995, 5.4429136399999996], [6.341818634999999, 3.2387308599999995, 5.57095967], [5.318730025, 2.09561691, 6.4812020100000005], [5.392829694999999, 1.9938388999999996, 4.7049904], [3.547668225, 2.7783416499999998, 2.8106070699999997], [4.555853324999999, 5.84639344, 6.37902407], [3.839338715, 4.1980903199999995, 0.63843527], [4.261876395, 4.42509162, 4.2045273199999995]],
"unique_id": "1b5bf47287ddedc63232cd0b58101302",
"user": "markus",
"comment": "alanine unit cell specifically for the examples section"},
"ids": [1],
"nextid": 2
}
22 changes: 12 additions & 10 deletions reference_data/inputs/alanine-X.json
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{"1": {
"cell": [[8.1, 0.0, 0.0], [0.0, 8.62, 0.0], [0.0, 0.0, 7.21]],
"ctime": 18.407640453530774,
"mtime": 18.407640453530774,
"numbers": [6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 7, 7],
"pbc": [false, false, false],
"positions": [[-0.1613651, 0.65906786, -1.97824041], [-0.15892852, -0.36639967, -0.83361775], [-1.34351449, 1.62553549, -1.85545263], [0.16027271, -0.65789877, 1.5889509], [0.15914436, 0.36804328, 2.73254995], [1.34084251, -1.62579205, 1.7178555], [-0.45882073, -1.09752262, -3.05466492], [0.77769451, 1.23801866, -1.9667135], [-2.29267482, 1.07089011, -1.84416853], [-1.27455616, 2.21863704, -0.93289676], [-1.3426009, 2.31460134, -2.70984051], [0.45726335, 1.09768343, 0.5130136], [-0.77966557, -1.23534404, 1.60389886], [2.29096245, -1.0728289, 1.73194489], [1.26787384, -2.21594285, 2.64218723], [1.34197351, -2.31772086, 0.86597562], [-0.50318796, -1.53321811, -1.02840771], [0.50499714, 1.53483368, 2.54000929], [-0.21151747, -0.11346944, -3.20057951], [0.21102021, 0.11353186, 0.36551254]],
"unique_id": "e3fc0a6b5a2f88b7e05a78a383f1ed40",
"user": "markus"},
"ids": [1],
"nextid": 2}
"cell": [[8.1, 0.0, 0.0], [0.0, 8.62, 0.0], [0.0, 0.0, 7.21]],
"ctime": 18.407640453530774,
"mtime": 18.407640453530774,
"numbers": [6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 7, 7],
"pbc": [false, false, false],
"positions": [[-0.1613651, 0.65906786, -1.97824041], [-0.15892852, -0.36639967, -0.83361775], [-1.34351449, 1.62553549, -1.85545263], [0.16027271, -0.65789877, 1.5889509], [0.15914436, 0.36804328, 2.73254995], [1.34084251, -1.62579205, 1.7178555], [-0.45882073, -1.09752262, -3.05466492], [0.77769451, 1.23801866, -1.9667135], [-2.29267482, 1.07089011, -1.84416853], [-1.27455616, 2.21863704, -0.93289676], [-1.3426009, 2.31460134, -2.70984051], [0.45726335, 1.09768343, 0.5130136], [-0.77966557, -1.23534404, 1.60389886], [2.29096245, -1.0728289, 1.73194489], [1.26787384, -2.21594285, 2.64218723], [1.34197351, -2.31772086, 0.86597562], [-0.50318796, -1.53321811, -1.02840771], [0.50499714, 1.53483368, 2.54000929], [-0.21151747, -0.11346944, -3.20057951], [0.21102021, 0.11353186, 0.36551254]],
"unique_id": "e3fc0a6b5a2f88b7e05a78a383f1ed40",
"user": "markus",
"comment": "generic polyalanine geometry for testing different elements"},
"ids": [1],
"nextid": 2
}
28 changes: 15 additions & 13 deletions reference_data/inputs/alanine-center-select.json
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@@ -1,14 +1,16 @@
{"1": {
"cell": [[8.1, 0.0, 0.0], [0.0, 8.62, 0.0], [0.0, 0.0, 7.21]],
"ctime": 19.792880012677248,
"mtime": 19.792880012677248,
"numbers": [6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 7, 7],
"center_atoms_mask": [true, true, true, true, true, true, false, false, false,
false, false, false, false, false, false, false, true,
true, true, true],
"pbc": [false, false, false],
"positions": [[3.889491085, 4.97062762, 1.86077437], [3.891927665, 3.94516009, 3.0053970299999997], [2.7073416949999998, 5.93709525, 1.9835621499999998], [4.211128895, 3.6536609899999997, 5.42796568], [4.210000545, 4.67960304, 6.57156473], [5.391698695, 2.6857677099999995, 5.55687028], [3.5920354549999995, 3.2140371400000003, 0.7843498599999998], [4.828550695, 5.54957842, 1.8723012799999998], [1.758181365, 5.382449869999999, 1.9948462500000002], [2.776300025, 6.5301968, 2.90611802], [2.708255285, 6.626161099999999, 1.12917427], [4.508119535, 5.40924319, 4.35202838], [3.271190615, 3.0762157199999995, 5.4429136399999996], [6.341818634999999, 3.2387308599999995, 5.57095967], [5.318730025, 2.09561691, 6.4812020100000005], [5.392829694999999, 1.9938388999999996, 4.7049904], [3.547668225, 2.7783416499999998, 2.8106070699999997], [4.555853324999999, 5.84639344, 6.37902407], [3.839338715, 4.1980903199999995, 0.63843527], [4.261876395, 4.42509162, 4.2045273199999995]],
"unique_id": "1b5bf47287ddedc63232cd0b58101302",
"user": "markus"},
"ids": [1],
"nextid": 2}
"cell": [[8.1, 0.0, 0.0], [0.0, 8.62, 0.0], [0.0, 0.0, 7.21]],
"ctime": 19.792880012677248,
"mtime": 19.792880012677248,
"numbers": [6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 7, 7],
"center_atoms_mask": [true, true, true, true, true, true, false, false, false,
false, false, false, false, false, false, false, true,
true, true, true],
"pbc": [false, false, false],
"positions": [[3.889491085, 4.97062762, 1.86077437], [3.891927665, 3.94516009, 3.0053970299999997], [2.7073416949999998, 5.93709525, 1.9835621499999998], [4.211128895, 3.6536609899999997, 5.42796568], [4.210000545, 4.67960304, 6.57156473], [5.391698695, 2.6857677099999995, 5.55687028], [3.5920354549999995, 3.2140371400000003, 0.7843498599999998], [4.828550695, 5.54957842, 1.8723012799999998], [1.758181365, 5.382449869999999, 1.9948462500000002], [2.776300025, 6.5301968, 2.90611802], [2.708255285, 6.626161099999999, 1.12917427], [4.508119535, 5.40924319, 4.35202838], [3.271190615, 3.0762157199999995, 5.4429136399999996], [6.341818634999999, 3.2387308599999995, 5.57095967], [5.318730025, 2.09561691, 6.4812020100000005], [5.392829694999999, 1.9938388999999996, 4.7049904], [3.547668225, 2.7783416499999998, 2.8106070699999997], [4.555853324999999, 5.84639344, 6.37902407], [3.839338715, 4.1980903199999995, 0.63843527], [4.261876395, 4.42509162, 4.2045273199999995]],
"unique_id": "1b5bf47287ddedc63232cd0b58101302",
"user": "markus",
"comment": "example molecule for dihedral angles including a mask for center atoms for testing"},
"ids": [1],
"nextid": 2
}
8 changes: 5 additions & 3 deletions reference_data/inputs/crystal_structure.json
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Expand Up @@ -46,6 +46,8 @@
[8.69635908, -22.91214366, 47.04070713],
[3.47854363, -24.48756343, 49.71844700]],
"unique_id": "a0ias0d",
"user": "markus stricker"},
"ids": [1],
"nextid": 2}
"user": "markus stricker",
"comment": "hcp Magnesium structure from a stacking fault calculation"},
"ids": [1],
"nextid": 2
}
1 change: 1 addition & 0 deletions reference_data/inputs/dummy_structure.json
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"positions": [[6.03082510917271, -2.913100950849861, -1.4110821617697935], [7.030973863685865, -3.9442545913417115, 7.975299746380401], [7.510589457284684, -1.0048832736406603, 0.6507593684212125], [8.606901396586432, -0.8040071549228305, 9.304703596048965], [-2.914845713471, -1.1230526607765916, -0.5388356363489741], [3.6769411844653135, 8.932319785127099, 2.0360098626537777], [-3.2790995230230258, 6.9653701020480305, -2.1893609120406996], [-4.981994061617974, -3.9631171819320636, 2.9671084697147574], [5.550149395141625, 8.179110963564593, 1.8162513380958059], [7.301136575640884, 9.119717390418975, 0.15305376319016695]],
"unique_id": "74caf9bd73247664c6d32acf24402306",
"user": "musil"},
"comment": "hand made structure for testing",
"ids": [1],
"nextid": 2}
1 change: 1 addition & 0 deletions reference_data/inputs/dummy_structure_wrapped.json
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"positions": [[0.030825109172710086, 0.5510006642878933, 0.5889178382302064], [-0.9690261363141339, 1.2518978313649192, 1.9752997463804005], [-0.4894105427153157, 0.7271675339282166, 0.6507593684212125], [-1.393098603413569, 0.9280436526460467, 1.3047035960489655], [-0.9148457134710007, 0.6089981467922854, 1.461164363651026], [-0.32305881553468885, 0.2720657472827135, 0.03600986265377782], [0.7209004769769732, 0.03716687177252341, 1.8106390879593006], [-0.9819940616179721, 1.2330352407745677, 0.9671084697147575], [-2.449850604858379, 1.2509077332890859, 1.8162513380958059], [-0.6988634243591202, 0.4594633525745903, 0.15305376319016695]],
"unique_id": "d3185d2d5a94a8bee9f48b38eb058871",
"user": "musil"},
"comment": "hand made structure for testing",
"ids": [1],
"nextid": 2}
2 changes: 2 additions & 0 deletions reference_data/inputs/molecular_crystal.json
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Expand Up @@ -1179,6 +1179,8 @@
true
]
},
"user": "musil",
"comment": "first structure of the CSD 500 molecular crystals dataset",
"nextid": 2,
"ids": [
0
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20 changes: 11 additions & 9 deletions reference_data/inputs/polyalanine.json
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{"1": {
"cell": [[8.1, 0.0, 0.0], [0.0, 8.62, 0.0], [0.0, 0.0, 7.21]],
"ctime": 18.407640453530774,
"mtime": 18.407640453530774,
"numbers": [6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 7, 7],
"pbc": [false, false, false],
"cell": [[8.1, 0.0, 0.0], [0.0, 8.62, 0.0], [0.0, 0.0, 7.21]],
"ctime": 18.407640453530774,
"mtime": 18.407640453530774,
"numbers": [6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 7, 7],
"pbc": [false, false, false],
"positions": [[-0.1613651, 0.65906786, -1.97824041],
[-0.15892852, -0.36639967, -0.83361775],
[-1.34351449, 1.62553549, -1.85545263],
Expand All @@ -24,7 +24,9 @@
[0.50499714, 1.53483368, 2.54000929],
[-0.21151747, -0.11346944, -3.20057951],
[0.21102021, 0.11353186, 0.36551254]],
"unique_id": "e3fc0a6b5a2f88b7e05a78a383f1ed40",
"user": "markus stricker"},
"ids": [1],
"nextid": 2}
"unique_id": "e3fc0a6b5a2f88b7e05a78a383f1ed40",
"user": "markus stricker",
"comment": "example molecule for dihedral angles testing"},
"ids": [1],
"nextid": 2
}
10 changes: 6 additions & 4 deletions reference_data/inputs/simple_cubic_8.json
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[1.5, 0.5, 1.5],
[0.5, 1.5, 1.5],
[1.5, 1.5, 1.8]
]
},
"ids": [1],
"nextid": 2}
],
"user": "markus",
"comment": "custom structure with simple geometry for testing neighbourlists"},
"ids": [1],
"nextid": 2
}
3 changes: 2 additions & 1 deletion reference_data/inputs/simple_cubic_9.json
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Expand Up @@ -16,7 +16,8 @@
[1.5, 1.5, 1.8]
],
"unique_id": "abcdef",
"user": "markus"},
"user": "markus",
"comment": "custom structure with 9 atoms and simple geometry for testing neighbourlists"},
"ids": [1],
"nextid": 2
}
2 changes: 2 additions & 0 deletions reference_data/inputs/small_molecule.json
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Expand Up @@ -96,5 +96,7 @@
"ids": [
0
],
"user": "musil",
"comment": "molecule taken from the QM9 dataset",
"nextid": 2
}
2 changes: 2 additions & 0 deletions reference_data/inputs/small_molecule_no_cell.json
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"ids": [
0
],
"user": "musil",
"comment": "molecule taken from the QM9 dataset",
"nextid": 2
}
3 changes: 2 additions & 1 deletion reference_data/unused/behler_parinello_pair_hypers.json
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Expand Up @@ -172,5 +172,6 @@
"bias_weight": 16840.8752
}
]
]
],
"comment": "example input file for defining the hyper parameters in a Behler-Parinello style Neural Network potential"
}
16 changes: 0 additions & 16 deletions reference_data/unused/simple_cubic_3.json
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