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# test read
# https://wiki.openchemistry.org/Chemical_JSON
import pytest
import numpy as np
from ase import io
ethane = """{
"chemical json": 0,
"name": "ethane",
"inchi": "1/C2H6/c1-2/h1-2H3",
"formula": "C 2 H 6",
"atoms": {
"elements": {
"number": [ 1, 6, 1, 1, 6, 1, 1, 1 ]
},
"coords": {
"3d": [ 1.185080, -0.003838, 0.987524,
0.751621, -0.022441, -0.020839,
1.166929, 0.833015, -0.569312,
1.115519, -0.932892, -0.514525,
-0.751587, 0.022496, 0.020891,
-1.166882, -0.833372, 0.568699,
-1.115691, 0.932608, 0.515082,
-1.184988, 0.004424, -0.987522 ]
}
},
"bonds": {
"connections": {
"index": [ 0, 1,
1, 2,
1, 3,
1, 4,
4, 5,
4, 6,
4, 7 ]
},
"order": [ 1, 1, 1, 1, 1, 1, 1 ]
},
"properties": {
"molecular mass": 30.0690,
"melting point": -172,
"boiling point": -88
}
}
"""
tio2 = """{
"chemicalJson": 1,
"name": "TiO2 rutile",
"formula": "Ti 2 O 4",
"unitCell": {
"a": 2.95812,
"b": 4.59373,
"c": 4.59373,
"alpha": 90.0,
"beta": 90.0,
"gamma": 90.0
},
"atoms": {
"elements": {
"number": [ 22, 22, 8, 8, 8, 8 ]
},
"coords": {
"3dFractional": [ 0.00000, 0.00000, 0.00000,
0.50000, 0.50000, 0.50000,
0.00000, 0.30530, 0.30530,
0.00000, 0.69470, 0.69470,
0.50000, 0.19470, 0.80530,
0.50000, 0.80530, 0.19470 ]
}
}
}
"""
def test_ethane():
fname = 'ethane.cml'
with open(fname, 'w') as fd:
fd.write(ethane)
atoms = io.read(fname)
assert str(atoms.symbols) == 'HCH2CH3'
def test_rutile():
fname = 'TiO2_rutile.cml'
with open(fname, 'w') as fd:
fd.write(tio2)
atoms = io.read(fname)
assert atoms.pbc.all()
cell = atoms.cell
assert str(atoms.symbols) == 'Ti2O4'
assert atoms[1].position == pytest.approx(cell.diagonal() / 2)
assert cell[1, 1] == cell[2, 2]
assert cell == pytest.approx(np.diag(cell.diagonal()))
|
