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|
# flake8: noqa
"""Check that reading multi image .con files is consistent."""
import os
from numpy import array
import ase
import ase.io
# Error tolerance.
TOL = 1e-6
# A correct .con file.
CON_FILE = """\
0 Random Number Seed
0 Time
8.123222 5.744000 9.747867
90.000000 90.000000 90.000000
0 0
0 0 0
1
17
51.996100
Cr
Coordinates of Component 1
1.01540277999999962 0.71799999999999997 1.01540277999999984 1 0
3.04620834000000063 2.15399999999999991 1.01540277999999984 1 1
3.04620834000000063 0.71799999999999997 3.04620834000000196 1 2
1.01540277999999962 2.15399999999999991 3.04620834000000196 1 3
1.01540277999999962 3.58999999999999986 1.01540277999999984 1 4
3.04620834000000063 5.02599999999999980 1.01540277999999984 1 5
3.04620834000000063 3.58999999999999986 3.04620834000000196 1 6
1.01540277999999962 5.02599999999999980 3.04620834000000196 1 7
5.07701389999999986 0.71799999999999997 1.01540277999999984 1 8
7.10781945999998488 2.15399999999999991 1.01540277999999984 1 9
7.10781945999998488 0.71799999999999997 3.04620834000000196 1 10
5.07701389999999986 2.15399999999999991 3.04620834000000196 1 11
5.07701389999999986 3.58999999999999986 1.01540277999999984 1 12
7.10781945999998488 5.02599999999999980 1.01540277999999984 1 13
7.10781945999998488 3.58999999999999986 3.04620834000000196 1 14
5.07701389999999986 5.02599999999999980 3.04620834000000196 1 15
3.04618285858587523 2.15398224021542450 4.60622193000079427 0 16
0 Random Number Seed
0 Time
8.123222 5.744000 9.747867
90.000000 90.000000 90.000000
0 0
0 0 0
1
17
51.996100
Cr
Coordinates of Component 1
1.01540277999999962 0.71799999999999997 1.01540277999999984 1 0
3.04620834000000063 2.15399999999999991 1.01540277999999984 1 1
3.04620834000000063 0.71799999999999997 3.04620834000000196 1 2
1.01540277999999962 2.15399999999999991 3.04620834000000196 1 3
1.01540277999999962 3.58999999999999986 1.01540277999999984 1 4
3.04620834000000063 5.02599999999999980 1.01540277999999984 1 5
3.04620834000000063 3.58999999999999986 3.04620834000000196 1 6
1.01540277999999962 5.02599999999999980 3.04620834000000196 1 7
5.07701389999999986 0.71799999999999997 1.01540277999999984 1 8
7.10781945999998488 2.15399999999999991 1.01540277999999984 1 9
7.10781945999998488 0.71799999999999997 3.04620834000000196 1 10
5.07701389999999986 2.15399999999999991 3.04620834000000196 1 11
5.07701389999999986 3.58999999999999986 1.01540277999999984 1 12
7.10781945999998488 5.02599999999999980 1.01540277999999984 1 13
7.10781945999998488 3.58999999999999986 3.04620834000000196 1 14
5.07701389999999986 5.02599999999999980 3.04620834000000196 1 15
3.36369427985916092 2.20887986058760699 4.61557342394151693 0 16
0 Random Number Seed
0 Time
8.123222 5.744000 9.747867
90.000000 90.000000 90.000000
0 0
0 0 0
1
17
51.996100
Cr
Coordinates of Component 1
1.01540277999999962 0.71799999999999997 1.01540277999999984 1 0
3.04620834000000063 2.15399999999999991 1.01540277999999984 1 1
3.04620834000000063 0.71799999999999997 3.04620834000000196 1 2
1.01540277999999962 2.15399999999999991 3.04620834000000196 1 3
1.01540277999999962 3.58999999999999986 1.01540277999999984 1 4
3.04620834000000063 5.02599999999999980 1.01540277999999984 1 5
3.04620834000000063 3.58999999999999986 3.04620834000000196 1 6
1.01540277999999962 5.02599999999999980 3.04620834000000196 1 7
5.07701389999999986 0.71799999999999997 1.01540277999999984 1 8
7.10781945999998488 2.15399999999999991 1.01540277999999984 1 9
7.10781945999998488 0.71799999999999997 3.04620834000000196 1 10
5.07701389999999986 2.15399999999999991 3.04620834000000196 1 11
5.07701389999999986 3.58999999999999986 1.01540277999999984 1 12
7.10781945999998488 5.02599999999999980 1.01540277999999984 1 13
7.10781945999998488 3.58999999999999986 3.04620834000000196 1 14
5.07701389999999986 5.02599999999999980 3.04620834000000196 1 15
3.62116697589668135 2.40183843231018113 4.63674682635805180 0 16
0 Random Number Seed
0 Time
8.123222 5.744000 9.747867
90.000000 90.000000 90.000000
0 0
0 0 0
1
17
51.996100
Cr
Coordinates of Component 1
1.01540277999999962 0.71799999999999997 1.01540277999999984 1 0
3.04620834000000063 2.15399999999999991 1.01540277999999984 1 1
3.04620834000000063 0.71799999999999997 3.04620834000000196 1 2
1.01540277999999962 2.15399999999999991 3.04620834000000196 1 3
1.01540277999999962 3.58999999999999986 1.01540277999999984 1 4
3.04620834000000063 5.02599999999999980 1.01540277999999984 1 5
3.04620834000000063 3.58999999999999986 3.04620834000000196 1 6
1.01540277999999962 5.02599999999999980 3.04620834000000196 1 7
5.07701389999999986 0.71799999999999997 1.01540277999999984 1 8
7.10781945999998488 2.15399999999999991 1.01540277999999984 1 9
7.10781945999998488 0.71799999999999997 3.04620834000000196 1 10
5.07701389999999986 2.15399999999999991 3.04620834000000196 1 11
5.07701389999999986 3.58999999999999986 1.01540277999999984 1 12
7.10781945999998488 5.02599999999999980 1.01540277999999984 1 13
7.10781945999998488 3.58999999999999986 3.04620834000000196 1 14
5.07701389999999986 5.02599999999999980 3.04620834000000196 1 15
3.83933949582109157 2.63825709178043821 4.65669727965894875 0 16
0 Random Number Seed
0 Time
8.123222 5.744000 9.747867
90.000000 90.000000 90.000000
0 0
0 0 0
1
17
51.996100
Cr
Coordinates of Component 1
1.01540277999999962 0.71799999999999997 1.01540277999999984 1 0
3.04620834000000063 2.15399999999999991 1.01540277999999984 1 1
3.04620834000000063 0.71799999999999997 3.04620834000000196 1 2
1.01540277999999962 2.15399999999999991 3.04620834000000196 1 3
1.01540277999999962 3.58999999999999986 1.01540277999999984 1 4
3.04620834000000063 5.02599999999999980 1.01540277999999984 1 5
3.04620834000000063 3.58999999999999986 3.04620834000000196 1 6
1.01540277999999962 5.02599999999999980 3.04620834000000196 1 7
5.07701389999999986 0.71799999999999997 1.01540277999999984 1 8
7.10781945999998488 2.15399999999999991 1.01540277999999984 1 9
7.10781945999998488 0.71799999999999997 3.04620834000000196 1 10
5.07701389999999986 2.15399999999999991 3.04620834000000196 1 11
5.07701389999999986 3.58999999999999986 1.01540277999999984 1 12
7.10781945999998488 5.02599999999999980 1.01540277999999984 1 13
7.10781945999998488 3.58999999999999986 3.04620834000000196 1 14
5.07701389999999986 5.02599999999999980 3.04620834000000196 1 15
4.06162234392075128 2.87141228075409316 4.66819033729618926 0 16
0 Random Number Seed
0 Time
8.123222 5.744000 9.747867
90.000000 90.000000 90.000000
0 0
0 0 0
1
17
51.996100
Cr
Coordinates of Component 1
1.01540277999999962 0.71799999999999997 1.01540277999999984 1 0
3.04620834000000063 2.15399999999999991 1.01540277999999984 1 1
3.04620834000000063 0.71799999999999997 3.04620834000000196 1 2
1.01540277999999962 2.15399999999999991 3.04620834000000196 1 3
1.01540277999999962 3.58999999999999986 1.01540277999999984 1 4
3.04620834000000063 5.02599999999999980 1.01540277999999984 1 5
3.04620834000000063 3.58999999999999986 3.04620834000000196 1 6
1.01540277999999962 5.02599999999999980 3.04620834000000196 1 7
5.07701389999999986 0.71799999999999997 1.01540277999999984 1 8
7.10781945999998488 2.15399999999999991 1.01540277999999984 1 9
7.10781945999998488 0.71799999999999997 3.04620834000000196 1 10
5.07701389999999986 2.15399999999999991 3.04620834000000196 1 11
5.07701389999999986 3.58999999999999986 1.01540277999999984 1 12
7.10781945999998488 5.02599999999999980 1.01540277999999984 1 13
7.10781945999998488 3.58999999999999986 3.04620834000000196 1 14
5.07701389999999986 5.02599999999999980 3.04620834000000196 1 15
4.28380999862949441 3.10482201783771883 4.65660558580467221 0 16
0 Random Number Seed
0 Time
8.123222 5.744000 9.747867
90.000000 90.000000 90.000000
0 0
0 0 0
1
17
51.996100
Cr
Coordinates of Component 1
1.01540277999999962 0.71799999999999997 1.01540277999999984 1 0
3.04620834000000063 2.15399999999999991 1.01540277999999984 1 1
3.04620834000000063 0.71799999999999997 3.04620834000000196 1 2
1.01540277999999962 2.15399999999999991 3.04620834000000196 1 3
1.01540277999999962 3.58999999999999986 1.01540277999999984 1 4
3.04620834000000063 5.02599999999999980 1.01540277999999984 1 5
3.04620834000000063 3.58999999999999986 3.04620834000000196 1 6
1.01540277999999962 5.02599999999999980 3.04620834000000196 1 7
5.07701389999999986 0.71799999999999997 1.01540277999999984 1 8
7.10781945999998488 2.15399999999999991 1.01540277999999984 1 9
7.10781945999998488 0.71799999999999997 3.04620834000000196 1 10
5.07701389999999986 2.15399999999999991 3.04620834000000196 1 11
5.07701389999999986 3.58999999999999986 1.01540277999999984 1 12
7.10781945999998488 5.02599999999999980 1.01540277999999984 1 13
7.10781945999998488 3.58999999999999986 3.04620834000000196 1 14
5.07701389999999986 5.02599999999999980 3.04620834000000196 1 15
4.50188452903429326 3.34154720502221236 4.63664894132718874 0 16
0 Random Number Seed
0 Time
8.123222 5.744000 9.747867
90.000000 90.000000 90.000000
0 0
0 0 0
1
17
51.996100
Cr
Coordinates of Component 1
1.01540277999999962 0.71799999999999997 1.01540277999999984 1 0
3.04620834000000063 2.15399999999999991 1.01540277999999984 1 1
3.04620834000000063 0.71799999999999997 3.04620834000000196 1 2
1.01540277999999962 2.15399999999999991 3.04620834000000196 1 3
1.01540277999999962 3.58999999999999986 1.01540277999999984 1 4
3.04620834000000063 5.02599999999999980 1.01540277999999984 1 5
3.04620834000000063 3.58999999999999986 3.04620834000000196 1 6
1.01540277999999962 5.02599999999999980 3.04620834000000196 1 7
5.07701389999999986 0.71799999999999997 1.01540277999999984 1 8
7.10781945999998488 2.15399999999999991 1.01540277999999984 1 9
7.10781945999998488 0.71799999999999997 3.04620834000000196 1 10
5.07701389999999986 2.15399999999999991 3.04620834000000196 1 11
5.07701389999999986 3.58999999999999986 1.01540277999999984 1 12
7.10781945999998488 5.02599999999999980 1.01540277999999984 1 13
7.10781945999998488 3.58999999999999986 3.04620834000000196 1 14
5.07701389999999986 5.02599999999999980 3.04620834000000196 1 15
4.75928919917819293 3.53496190773495211 4.61566200013953409 0 16
0 Random Number Seed
0 Time
8.123222 5.744000 9.747867
90.000000 90.000000 90.000000
0 0
0 0 0
1
17
51.996100
Cr
Coordinates of Component 1
1.01540277999999962 0.71799999999999997 1.01540277999999984 1 0
3.04620834000000063 2.15399999999999991 1.01540277999999984 1 1
3.04620834000000063 0.71799999999999997 3.04620834000000196 1 2
1.01540277999999962 2.15399999999999991 3.04620834000000196 1 3
1.01540277999999962 3.58999999999999986 1.01540277999999984 1 4
3.04620834000000063 5.02599999999999980 1.01540277999999984 1 5
3.04620834000000063 3.58999999999999986 3.04620834000000196 1 6
1.01540277999999962 5.02599999999999980 3.04620834000000196 1 7
5.07701389999999986 0.71799999999999997 1.01540277999999984 1 8
7.10781945999998488 2.15399999999999991 1.01540277999999984 1 9
7.10781945999998488 0.71799999999999997 3.04620834000000196 1 10
5.07701389999999986 2.15399999999999991 3.04620834000000196 1 11
5.07701389999999986 3.58999999999999986 1.01540277999999984 1 12
7.10781945999998488 5.02599999999999980 1.01540277999999984 1 13
7.10781945999998488 3.58999999999999986 3.04620834000000196 1 14
5.07701389999999986 5.02599999999999980 3.04620834000000196 1 15
5.07701160164306042 3.58998956883621734 4.60626159988447537 0 16
"""
# The corresponding data for the second to last image as an ASE Atoms object.
data = ase.Atoms('Cr17',cell = array([[8.123222, 0, 0],
[0, 5.744000, 0],
[0, 0, 9.747867]]),
positions = array([ [1.01540277999999962, 0.71799999999999997, 1.01540277999999984],
[3.04620834000000063, 2.15399999999999991, 1.01540277999999984],
[3.04620834000000063, 0.71799999999999997, 3.04620834000000196],
[1.01540277999999962, 2.15399999999999991, 3.04620834000000196],
[1.01540277999999962, 3.58999999999999986, 1.01540277999999984],
[3.04620834000000063, 5.02599999999999980, 1.01540277999999984],
[3.04620834000000063, 3.58999999999999986, 3.04620834000000196],
[1.01540277999999962, 5.02599999999999980, 3.04620834000000196],
[5.07701389999999986, 0.71799999999999997, 1.01540277999999984],
[7.10781945999998488, 2.15399999999999991, 1.01540277999999984],
[7.10781945999998488, 0.71799999999999997, 3.04620834000000196],
[5.07701389999999986, 2.15399999999999991, 3.04620834000000196],
[5.07701389999999986, 3.58999999999999986, 1.01540277999999984],
[7.10781945999998488, 5.02599999999999980, 1.01540277999999984],
[7.10781945999998488, 3.58999999999999986, 3.04620834000000196],
[5.07701389999999986, 5.02599999999999980, 3.04620834000000196],
[4.75928919917819293, 3.53496190773495211, 4.61566200013953409]]),
pbc=(True, True, True))
def test_eon():
# First, write a correct .con file and try to read it.
con_file = 'neb.con'
with open(con_file, 'w') as f:
f.write(CON_FILE)
images = ase.io.read(con_file, format='eon', index =':')
box = images[-2]
# 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
|
