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"""Check that reading and writing .con files is consistent."""
from numpy import array
import ase
import ase.io
# Error tolerance.
TOL = 1e-6
# A correct .con file.
CON_FILE = """\
10000 RANDOM NUMBER SEED
0.0000 TIME
7.2200000000 10.8760700623 14.5090868079
84.7244899634 86.0479084995 85.7006486298
0 0
0 0 0
1
96
1.0
Cu
Coordinates of Component 1
1.04833333333334 0.96500000000003 0.90250000000000 0 1
3.02000000000000 2.77000000000000 0.90250000000000 0 2
2.97833333333334 1.09000000000003 2.70750000000000 0 3
1.34000000000000 2.89500000000000 2.70750000000000 0 4
4.65833333333334 0.96500000000003 0.90250000000000 0 5
6.63000000000000 2.77000000000000 0.90250000000000 0 6
6.58833333333334 1.09000000000003 2.70750000000000 0 7
4.95000000000000 2.89500000000000 2.70750000000000 0 8
1.38166666666666 4.57499999999997 0.90250000000000 0 9
3.35333333333334 6.38000000000003 0.90250000000000 0 10
3.31166666666666 4.69999999999997 2.70750000000000 0 11
1.67333333333334 6.50500000000003 2.70750000000000 0 12
4.99166666666666 4.57499999999997 0.90250000000000 0 13
6.96333333333334 6.38000000000003 0.90250000000000 0 14
6.92166666666666 4.69999999999997 2.70750000000000 0 15
5.28333333333334 6.50500000000003 2.70750000000000 0 16
1.71500000000000 8.18500000000000 0.90250000000000 0 17
3.68666666666666 9.98999999999997 0.90250000000000 0 18
3.64500000000000 8.31000000000000 2.70750000000000 0 19
2.00666666666666 10.11499999999997 2.70750000000000 0 20
5.32500000000000 8.18500000000000 0.90250000000000 0 21
7.29666666666666 9.98999999999997 0.90250000000000 0 22
7.25500000000000 8.31000000000000 2.70750000000000 0 23
5.61666666666666 10.11499999999997 2.70750000000000 0 24
1.29833333333334 1.21500000000003 4.51250000000000 0 25
3.27000000000000 3.02000000000000 4.51250000000000 0 26
3.22833333333334 1.34000000000003 6.31750000000000 0 27
1.59000000000000 3.14500000000000 6.31750000000000 0 28
4.90833333333334 1.21500000000003 4.51250000000000 0 29
6.88000000000000 3.02000000000000 4.51250000000000 0 30
6.83833333333334 1.34000000000003 6.31750000000000 0 31
5.20000000000000 3.14500000000000 6.31750000000000 0 32
1.63166666666666 4.82499999999997 4.51250000000000 0 33
3.60333333333334 6.63000000000003 4.51250000000000 0 34
3.56166666666666 4.94999999999997 6.31750000000000 0 35
1.92333333333334 6.75500000000003 6.31750000000000 0 36
5.24166666666666 4.82499999999997 4.51250000000000 0 37
7.21333333333334 6.63000000000003 4.51250000000000 0 38
7.17166666666666 4.94999999999997 6.31750000000000 0 39
5.53333333333334 6.75500000000003 6.31750000000000 0 40
1.96500000000000 8.43500000000000 4.51250000000000 0 41
3.93666666666666 10.23999999999997 4.51250000000000 0 42
3.89500000000000 8.56000000000000 6.31750000000000 0 43
2.25666666666666 10.36499999999997 6.31750000000000 0 44
5.57500000000000 8.43500000000000 4.51250000000000 0 45
7.54666666666666 10.23999999999997 4.51250000000000 0 46
7.50500000000000 8.56000000000000 6.31750000000000 0 47
5.86666666666666 10.36499999999997 6.31750000000000 0 48
1.54833333333334 1.46500000000003 8.12250000000000 0 49
3.52000000000000 3.27000000000000 8.12250000000000 0 50
3.47833333333334 1.59000000000003 9.92750000000000 0 51
1.84000000000000 3.39500000000000 9.92750000000000 0 52
5.15833333333334 1.46500000000003 8.12250000000000 0 53
7.13000000000000 3.27000000000000 8.12250000000000 0 54
7.08833333333334 1.59000000000003 9.92750000000000 0 55
5.45000000000000 3.39500000000000 9.92750000000000 0 56
1.88166666666666 5.07499999999997 8.12250000000000 0 57
3.85333333333334 6.88000000000003 8.12250000000000 0 58
3.81166666666666 5.19999999999997 9.92750000000000 0 59
2.17333333333334 7.00500000000003 9.92750000000000 0 60
5.49166666666666 5.07499999999997 8.12250000000000 0 61
7.46333333333334 6.88000000000003 8.12250000000000 0 62
7.42166666666666 5.19999999999997 9.92750000000000 0 63
5.78333333333334 7.00500000000003 9.92750000000000 0 64
2.21500000000000 8.68500000000000 8.12250000000000 0 65
4.18666666666666 10.48999999999997 8.12250000000000 0 66
4.14500000000000 8.81000000000000 9.92750000000000 0 67
2.50666666666666 10.61499999999997 9.92750000000000 0 68
5.82500000000000 8.68500000000000 8.12250000000000 0 69
7.79666666666666 10.48999999999997 8.12250000000000 0 70
7.75500000000000 8.81000000000000 9.92750000000000 0 71
6.11666666666666 10.61499999999997 9.92750000000000 0 72
1.79833333333334 1.71500000000003 11.73250000000000 0 73
3.77000000000000 3.52000000000000 11.73250000000000 0 74
3.72833333333334 1.84000000000003 13.53750000000000 0 75
2.09000000000000 3.64500000000000 13.53750000000000 0 76
5.40833333333334 1.71500000000003 11.73250000000000 0 77
7.38000000000000 3.52000000000000 11.73250000000000 0 78
7.33833333333334 1.84000000000003 13.53750000000000 0 79
5.70000000000000 3.64500000000000 13.53750000000000 0 80
2.13166666666666 5.32499999999997 11.73250000000000 0 81
4.10333333333334 7.13000000000003 11.73250000000000 0 82
4.06166666666666 5.44999999999997 13.53750000000000 0 83
2.42333333333334 7.25500000000003 13.53750000000000 0 84
5.74166666666666 5.32499999999997 11.73250000000000 0 85
7.71333333333334 7.13000000000003 11.73250000000000 0 86
7.67166666666666 5.44999999999997 13.53750000000000 0 87
6.03333333333334 7.25500000000003 13.53750000000000 0 88
2.46500000000000 8.93500000000000 11.73250000000000 0 89
4.43666666666666 10.73999999999997 11.73250000000000 0 90
4.39500000000000 9.06000000000000 13.53750000000000 0 91
2.75666666666666 10.86499999999997 13.53750000000000 0 92
6.07500000000000 8.93500000000000 11.73250000000000 0 93
8.04666666666666 10.73999999999997 11.73250000000000 0 94
8.00500000000000 9.06000000000000 13.53750000000000 0 95
6.36666666666666 10.86499999999997 13.53750000000000 0 96
"""
# The corresponding data as an ASE Atoms object.
data = ase.Atoms('Cu96',
cell=array([[7.22, 0, 0],
[1, 10.83, 0],
[1, 1, 14.44]]),
positions=array([[1.04833333, 0.965, 0.9025],
[3.02, 2.77, 0.9025],
[2.97833333, 1.09, 2.7075],
[1.34, 2.895, 2.7075],
[4.65833333, 0.965, 0.9025],
[6.63, 2.77, 0.9025],
[6.58833333, 1.09, 2.7075],
[4.95, 2.895, 2.7075],
[1.38166667, 4.575, 0.9025],
[3.35333333, 6.38, 0.9025],
[3.31166667, 4.7, 2.7075],
[1.67333333, 6.505, 2.7075],
[4.99166667, 4.575, 0.9025],
[6.96333333, 6.38, 0.9025],
[6.92166667, 4.7, 2.7075],
[5.28333333, 6.505, 2.7075],
[1.715, 8.185, 0.9025],
[3.68666667, 9.99, 0.9025],
[3.645, 8.31, 2.7075],
[2.00666667, 10.115, 2.7075],
[5.325, 8.185, 0.9025],
[7.29666667, 9.99, 0.9025],
[7.255, 8.31, 2.7075],
[5.61666667, 10.115, 2.7075],
[1.29833333, 1.215, 4.5125],
[3.27, 3.02, 4.5125],
[3.22833333, 1.34, 6.3175],
[1.59, 3.145, 6.3175],
[4.90833333, 1.215, 4.5125],
[6.88, 3.02, 4.5125],
[6.83833333, 1.34, 6.3175],
[5.2, 3.145, 6.3175],
[1.63166667, 4.825, 4.5125],
[3.60333333, 6.63, 4.5125],
[3.56166667, 4.95, 6.3175],
[1.92333333, 6.755, 6.3175],
[5.24166667, 4.825, 4.5125],
[7.21333333, 6.63, 4.5125],
[7.17166667, 4.95, 6.3175],
[5.53333333, 6.755, 6.3175],
[1.965, 8.435, 4.5125],
[3.93666667, 10.24, 4.5125],
[3.895, 8.56, 6.3175],
[2.25666667, 10.365, 6.3175],
[5.575, 8.435, 4.5125],
[7.54666667, 10.24, 4.5125],
[7.505, 8.56, 6.3175],
[5.86666667, 10.365, 6.3175],
[1.54833333, 1.465, 8.1225],
[3.52, 3.27, 8.1225],
[3.47833333, 1.59, 9.9275],
[1.84, 3.395, 9.9275],
[5.15833333, 1.465, 8.1225],
[7.13, 3.27, 8.1225],
[7.08833333, 1.59, 9.9275],
[5.45, 3.395, 9.9275],
[1.88166667, 5.075, 8.1225],
[3.85333333, 6.88, 8.1225],
[3.81166667, 5.2, 9.9275],
[2.17333333, 7.005, 9.9275],
[5.49166667, 5.075, 8.1225],
[7.46333333, 6.88, 8.1225],
[7.42166667, 5.2, 9.9275],
[5.78333333, 7.005, 9.9275],
[2.215, 8.685, 8.1225],
[4.18666667, 10.49, 8.1225],
[4.145, 8.81, 9.9275],
[2.50666667, 10.615, 9.9275],
[5.825, 8.685, 8.1225],
[7.79666667, 10.49, 8.1225],
[7.755, 8.81, 9.9275],
[6.11666667, 10.615, 9.9275],
[1.79833333, 1.715, 11.7325],
[3.77, 3.52, 11.7325],
[3.72833333, 1.84, 13.5375],
[2.09, 3.645, 13.5375],
[5.40833333, 1.715, 11.7325],
[7.38, 3.52, 11.7325],
[7.33833333, 1.84, 13.5375],
[5.7, 3.645, 13.5375],
[2.13166667, 5.325, 11.7325],
[4.10333333, 7.13, 11.7325],
[4.06166667, 5.45, 13.5375],
[2.42333333, 7.255, 13.5375],
[5.74166667, 5.325, 11.7325],
[7.71333333, 7.13, 11.7325],
[7.67166667, 5.45, 13.5375],
[6.03333333, 7.255, 13.5375],
[2.465, 8.935, 11.7325],
[4.43666667, 10.74, 11.7325],
[4.395, 9.06, 13.5375],
[2.75666667, 10.865, 13.5375],
[6.075, 8.935, 11.7325],
[8.04666667, 10.74, 11.7325],
[8.005, 9.06, 13.5375],
[6.36666667, 10.865, 13.5375]]),
pbc=(True, True, True))
def test_eon_readwrite():
# First, write a correct .con file and try to read it.
con_file = 'pos.con'
with open(con_file, 'w') as f:
f.write(CON_FILE)
box = ase.io.read(con_file, format='eon')
# Check cell vectors.
assert (abs(box.cell - data.cell)).sum() < TOL # read: cell vector check
# Check atom positions.
# read: position check
assert (abs(box.positions - data.positions)).sum() < TOL
# Now that we know that reading a .con file works, we will write
# one and read it back in.
out_file = 'out.con'
ase.io.write(out_file, data, format='eon')
data2 = ase.io.read(out_file, format='eon')
# Check cell vectors.
# write: cell vector check
assert (abs(data2.cell - data.cell)).sum() < TOL
# Check atom positions.
# write: position check
assert (abs(data2.positions - data.positions)).sum() < TOL
|
