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Added a test suite for module 'vaspio'

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This commit is contained in:
Oleg E. Peil 2015-02-19 14:48:45 +01:00 committed by Michel Ferrero
parent 36aadf6ff4
commit 82cc06d41e
17 changed files with 1235 additions and 0 deletions
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python/converters/vasp/test/vaspio/.gitignore vendored Normal file
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*.pyc
*.test

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python/converters/vasp/test/vaspio/DOSCAR.example Normal file
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0.530 0.0000E+00 0.0000E+00 0.0000E+00
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0.872 0.0000E+00 0.0000E+00 0.0000E+00
1.043 0.0000E+00 0.0000E+00 0.0000E+00
1.213 0.0000E+00 0.0000E+00 0.0000E+00
1.384 0.3864E-26 0.8487E-27 0.4497E-26
1.555 0.9904E-16 0.2176E-16 0.1153E-15
1.726 0.5665E-08 0.1244E-08 0.6594E-08
1.897 0.4940E-03 0.1085E-03 0.5750E-03
2.068 -0.4603E-01 -0.1011E-01 -0.5358E-01
2.238 0.1317E+01 0.2892E+00 0.1533E+01
2.409 0.1176E+00 0.2582E-01 0.1368E+00
2.580 0.6212E-02 0.1365E-02 0.7230E-02
2.751 0.2753E-05 0.6047E-06 0.3204E-05
2.922 0.8456E-09 0.1593E-08 0.8831E-08
3.093 0.5951E-04 0.1122E-03 0.6221E-03
3.263 -0.5066E-02 -0.9550E-02 -0.5296E-01
3.434 0.1306E+00 0.2462E+00 0.1365E+01
3.605 0.7168E-02 0.1351E-01 0.5448E-01
3.776 0.1498E-02 0.1115E-02 0.1449E+01
3.947 0.3581E-01 0.2981E-02 0.1090E+01
4.118 0.1593E+00 0.1326E-01 0.2235E+01
4.288 -0.3799E-02 -0.3160E-03 -0.5305E-01
4.459 0.3529E-04 0.1850E-02 0.9953E-02
4.630 0.2305E-09 -0.3490E-01 -0.2077E+00
4.801 0.1012E-11 0.9395E+00 0.7761E+01
4.972 -0.4885E-13 -0.4536E-01 0.1311E+01
5.143 0.1235E-14 0.1147E-02 0.2449E-01
5.313 0.5375E-11 0.5226E-07 0.6163E-04
5.484 0.4760E-05 0.1406E-04 0.3678E-04
5.655 0.1115E-02 0.3295E-02 0.8762E-02
5.826 0.1092E+00 0.3226E+00 0.8285E+00
5.997 0.1975E+00 0.5835E+00 0.2436E+01
6.168 -0.1863E-02 -0.5502E-02 0.3082E+00
6.338 0.2204E-04 0.6510E-04 0.5891E-02
6.509 0.7017E-10 0.2073E-09 0.1064E-04
6.680 0.9358E-23 0.1488E-18 0.8389E-11
6.851 0.1030E-21 0.3246E-10 0.6418E-09
7.022 0.3923E-16 0.1237E-04 0.2446E-03
7.193 -0.2406E-14 -0.7587E-03 -0.1500E-01
7.363 0.2299E-10 0.1331E+00 0.2633E+01
7.534 0.2215E-05 0.9189E-01 0.1819E+01
7.705 -0.2154E-03 -0.4014E-03 -0.1353E+00
7.876 0.6585E-02 0.3074E-01 0.4480E+01
8.047 0.7363E-03 0.3778E-02 0.1344E+01
8.218 0.3293E-04 0.8301E-02 0.3896E+01
8.388 0.1716E-07 0.7527E-01 0.8529E+01
8.559 0.3604E-10 0.7904E-02 0.2641E+01
8.730 0.4255E-10 0.4352E-01 0.4011E+01
8.901 -0.9775E-12 -0.9930E-03 -0.9195E-01
9.072 0.9084E-14 0.9189E-05 0.8537E-03
9.243 0.5648E-19 0.5713E-10 0.5308E-08
9.413 0.0000E+00 0.0000E+00 0.0000E+00
9.584 0.0000E+00 0.0000E+00 0.0000E+00
9.755 0.0000E+00 0.0000E+00 0.0000E+00
9.926 0.0000E+00 0.0000E+00 0.0000E+00
10.097 0.9369E-38 0.9180E-38 0.1894E-37
10.268 0.4418E-25 0.4329E-25 0.8930E-25
10.438 0.5159E-15 0.5055E-15 0.1043E-14
10.609 0.1311E-07 0.1285E-07 0.2650E-07
10.780 0.4524E-03 0.4432E-03 0.9144E-03
10.951 -0.2549E-01 -0.2498E-01 -0.5153E-01
11.122 0.5333E+00 0.5226E+00 0.1078E+01
11.293 -0.8611E-02 -0.8437E-02 -0.1741E-01
11.463 0.1436E-02 0.1407E-02 0.2902E-02
11.634 0.2049E-06 0.2008E-06 0.4142E-06
11.805 0.2993E-13 0.2933E-13 0.6050E-13
11.976 0.0000E+00 0.0000E+00 0.0000E+00
12.147 0.0000E+00 0.0000E+00 0.0000E+00
12.318 0.0000E+00 0.0000E+00 0.0000E+00
12.488 0.0000E+00 0.0000E+00 0.0000E+00
12.659 0.0000E+00 0.0000E+00 0.0000E+00
12.830 0.0000E+00 0.0000E+00 0.0000E+00
13.001 0.0000E+00 0.0000E+00 0.0000E+00
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13.684 0.0000E+00 0.0000E+00 0.0000E+00
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14.368 0.5466E-19 0.5958E-06 0.1004E-05
14.538 0.2931E-15 0.3195E-02 0.5384E-02
14.709 0.9435E-16 0.1028E-02 0.1733E-02
14.880 0.9327E-13 0.1017E+01 0.1713E+01
15.051 -0.4263E-14 -0.4647E-01 -0.7831E-01
15.222 0.6490E-16 0.7075E-03 0.1192E-02
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15.563 0.4966E-28 0.5413E-15 0.9122E-15
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16.588 0.0000E+00 0.0000E+00 0.0000E+00
16.759 0.0000E+00 0.0000E+00 0.0000E+00
16.930 0.0000E+00 0.0000E+00 0.0000E+00
17.101 0.0000E+00 0.0000E+00 0.0000E+00

50
python/converters/vasp/test/vaspio/EIGENVAL.example Normal file
View File

@ -0,0 +1,50 @@
1 1 1 1
0.1333597E+02 0.2587511E-09 0.2587511E-09 0.2587511E-09 0.5000000E-15
1.000000000000000E-004
CAR
V
11 4 9
0.0000000E+00 0.0000000E+00 0.0000000E+00 0.3703704E-01
1 -31.099965
2 -31.099965
3 -31.099965
4 -0.813470
5 5.974027
6 5.974027
7 5.974027
8 7.986328
9 7.986328
0.3333333E+00 0.0000000E+00 0.0000000E+00 0.4444444E+00
1 -31.819277
2 -31.322999
3 -31.105684
4 2.193081
5 4.784864
6 5.839340
7 7.833446
8 8.202781
9 8.589551
0.3333333E+00 0.3333333E+00 0.0000000E+00 0.2962963E+00
1 -31.750021
2 -31.750021
3 -31.217560
4 3.978315
5 4.708263
6 4.708263
7 8.262522
8 8.262522
9 14.771374
-0.3333333E+00 0.3333333E+00 0.3333333E+00 0.2222222E+00
1 -31.719893
2 -31.577292
3 -31.577292
4 3.383714
5 3.756320
6 7.355029
7 7.355029
8 8.411511
9 11.054129

52
python/converters/vasp/test/vaspio/EIGENVAL.example.out Normal file
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@ -0,0 +1,52 @@
nq = 1
ispin = 1
nelect = 11
nktot = 4
nband = 9
kpts:
[[ 0. 0. 0. ]
[ 0.3333333 0. 0. ]
[ 0.3333333 0.3333333 0. ]
[-0.3333333 0.3333333 0.3333333]]
kwghts:
[ 0.03703704 0.4444444 0.2962963 0.2222222 ]
eigs:
[[[-31.099965]
[-31.099965]
[-31.099965]
[ -0.81347 ]
[ 5.974027]
[ 5.974027]
[ 5.974027]
[ 7.986328]
[ 7.986328]]
[[-31.819277]
[-31.322999]
[-31.105684]
[ 2.193081]
[ 4.784864]
[ 5.83934 ]
[ 7.833446]
[ 8.202781]
[ 8.589551]]
[[-31.750021]
[-31.750021]
[-31.21756 ]
[ 3.978315]
[ 4.708263]
[ 4.708263]
[ 8.262522]
[ 8.262522]
[ 14.771374]]
[[-31.719893]
[-31.577292]
[-31.577292]
[ 3.383714]
[ 3.75632 ]
[ 7.355029]
[ 7.355029]
[ 8.411511]
[ 11.054129]]]

122
python/converters/vasp/test/vaspio/IBZKPT.example Normal file
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@ -0,0 +1,122 @@
Automatically generated mesh
10
Reciprocal lattice
0.00000000000000 0.00000000000000 0.00000000000000 1
0.20000000000000 0.00000000000000 0.00000000000000 12
0.40000000000000 0.00000000000000 0.00000000000000 12
0.20000000000000 0.20000000000000 0.00000000000000 24
0.40000000000000 0.20000000000000 -0.00000000000000 24
0.20000000000000 0.20000000000000 0.20000000000000 8
-0.20000000000000 0.20000000000000 0.20000000000000 6
-0.40000000000000 0.40000000000000 0.20000000000000 24
-0.40000000000000 -0.40000000000000 0.20000000000000 8
-0.40000000000000 0.40000000000000 0.40000000000000 6
Tetrahedra
107 0.00133333333333
4 1 2 2 4
12 2 2 4 4
4 2 4 4 6
4 2 3 4 5
4 2 4 4 5
12 4 4 5 6
16 3 4 5 5
28 4 5 5 6
8 4 5 6 6
4 3 3 4 5
12 3 4 4 5
4 4 4 4 5
4 2 2 3 4
12 2 3 4 4
8 2 4 4 4
8 2 2 2 4
12 2 2 4 7
12 2 4 4 7
8 1 2 2 2
4 2 2 2 2
4 2 2 2 7
16 5 5 6 6
12 3 4 5 6
8 3 5 5 6
8 3 4 4 6
4 3 4 6 8
4 3 5 6 8
4 3 4 4 4
4 3 4 4 8
8 4 4 7 8
4 4 4 8 8
4 2 2 3 7
16 2 3 4 7
12 3 4 7 8
4 3 4 5 7
4 3 5 7 8
4 3 5 5 5
12 3 5 5 8
16 5 5 8 9
24 3 4 5 8
8 4 5 8 8
4 5 8 8 8
16 5 8 8 9
4 3 3 4 8
12 3 5 8 8
12 3 3 5 8
4 3 4 8 8
8 4 5 5 9
12 4 5 8 9
4 4 7 8 9
4 2 3 5 8
4 2 4 5 8
8 2 4 7 8
12 2 3 4 8
4 2 2 4 8
4 2 2 7 8
4 1 2 4 7
8 1 2 2 7
4 2 3 4 6
4 3 5 6 6
8 5 6 6 6
8 5 5 5 6
4 4 4 5 5
16 4 5 5 8
4 3 4 4 7
4 3 7 8 8
8 4 4 5 8
4 5 5 6 9
4 4 5 6 8
4 5 5 6 8
8 5 8 8 10
8 5 8 9 10
4 4 7 8 8
4 4 8 8 8
8 8 8 8 10
4 7 8 8 8
4 8 8 8 9
20 8 8 9 10
4 4 5 7 8
4 5 7 8 8
4 5 5 5 8
4 5 8 9 9
8 8 9 9 10
6 9 9 10 10
12 8 9 10 10
4 8 8 10 10
8 4 8 8 9
4 3 4 5 9
4 3 4 8 9
4 7 8 9 10
4 7 8 8 10
4 4 7 8 10
4 2 4 8 8
4 2 7 8 8
4 2 4 4 8
4 3 3 5 6
4 4 5 5 5
4 3 5 8 9
4 3 8 8 9
6 5 5 8 8
2 3 3 5 5
4 4 5 6 9
4 4 8 9 10
4 8 10 10 10
6 8 8 9 9
4 9 10 10 10
2 10 10 10 10

122
python/converters/vasp/test/vaspio/IBZKPT.example.out Normal file
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@ -0,0 +1,122 @@
nktot = 10
ntet = 107
volt = 0.00133333333333
kpts:
[[ 0. 0. 0. ]
[ 0.2 0. 0. ]
[ 0.4 0. 0. ]
[ 0.2 0.2 0. ]
[ 0.4 0.2 -0. ]
[ 0.2 0.2 0.2]
[-0.2 0.2 0.2]
[-0.4 0.4 0.2]
[-0.4 -0.4 0.2]
[-0.4 0.4 0.4]]
tets:
[[ 4 1 2 2 4]
[12 2 2 4 4]
[ 4 2 4 4 6]
[ 4 2 3 4 5]
[ 4 2 4 4 5]
[12 4 4 5 6]
[16 3 4 5 5]
[28 4 5 5 6]
[ 8 4 5 6 6]
[ 4 3 3 4 5]
[12 3 4 4 5]
[ 4 4 4 4 5]
[ 4 2 2 3 4]
[12 2 3 4 4]
[ 8 2 4 4 4]
[ 8 2 2 2 4]
[12 2 2 4 7]
[12 2 4 4 7]
[ 8 1 2 2 2]
[ 4 2 2 2 2]
[ 4 2 2 2 7]
[16 5 5 6 6]
[12 3 4 5 6]
[ 8 3 5 5 6]
[ 8 3 4 4 6]
[ 4 3 4 6 8]
[ 4 3 5 6 8]
[ 4 3 4 4 4]
[ 4 3 4 4 8]
[ 8 4 4 7 8]
[ 4 4 4 8 8]
[ 4 2 2 3 7]
[16 2 3 4 7]
[12 3 4 7 8]
[ 4 3 4 5 7]
[ 4 3 5 7 8]
[ 4 3 5 5 5]
[12 3 5 5 8]
[16 5 5 8 9]
[24 3 4 5 8]
[ 8 4 5 8 8]
[ 4 5 8 8 8]
[16 5 8 8 9]
[ 4 3 3 4 8]
[12 3 5 8 8]
[12 3 3 5 8]
[ 4 3 4 8 8]
[ 8 4 5 5 9]
[12 4 5 8 9]
[ 4 4 7 8 9]
[ 4 2 3 5 8]
[ 4 2 4 5 8]
[ 8 2 4 7 8]
[12 2 3 4 8]
[ 4 2 2 4 8]
[ 4 2 2 7 8]
[ 4 1 2 4 7]
[ 8 1 2 2 7]
[ 4 2 3 4 6]
[ 4 3 5 6 6]
[ 8 5 6 6 6]
[ 8 5 5 5 6]
[ 4 4 4 5 5]
[16 4 5 5 8]
[ 4 3 4 4 7]
[ 4 3 7 8 8]
[ 8 4 4 5 8]
[ 4 5 5 6 9]
[ 4 4 5 6 8]
[ 4 5 5 6 8]
[ 8 5 8 8 10]
[ 8 5 8 9 10]
[ 4 4 7 8 8]
[ 4 4 8 8 8]
[ 8 8 8 8 10]
[ 4 7 8 8 8]
[ 4 8 8 8 9]
[20 8 8 9 10]
[ 4 4 5 7 8]
[ 4 5 7 8 8]
[ 4 5 5 5 8]
[ 4 5 8 9 9]
[ 8 8 9 9 10]
[ 6 9 9 10 10]
[12 8 9 10 10]
[ 4 8 8 10 10]
[ 8 4 8 8 9]
[ 4 3 4 5 9]
[ 4 3 4 8 9]
[ 4 7 8 9 10]
[ 4 7 8 8 10]
[ 4 4 7 8 10]
[ 4 2 4 8 8]
[ 4 2 7 8 8]
[ 4 2 4 4 8]
[ 4 3 3 5 6]
[ 4 4 5 5 5]
[ 4 3 5 8 9]
[ 4 3 8 8 9]
[ 6 5 5 8 8]
[ 2 3 3 5 5]
[ 4 4 5 6 9]
[ 4 4 8 9 10]
[ 4 8 10 10 10]
[ 6 8 8 9 9]
[ 4 9 10 10 10]
[ 2 10 10 10 10]]

7
python/converters/vasp/test/vaspio/IBZKPT.notet Normal file
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Automatically generated mesh
4
Reciprocal lattice
0.00000000000000 0.00000000000000 0.00000000000000 1
0.33333333333333 0.00000000000000 0.00000000000000 12
0.33333333333333 0.33333333333333 0.00000000000000 8
-0.33333333333333 0.33333333333333 0.33333333333333 6

6
python/converters/vasp/test/vaspio/IBZKPT.notet.out Normal file
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nktot = 4
kpts:
[[ 0. 0. 0. ]
[ 0.33333333 0. 0. ]
[ 0.33333333 0.33333333 0. ]
[-0.33333333 0.33333333 0.33333333]]

10
python/converters/vasp/test/vaspio/POSCAR.example Normal file
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V SF test
2.9878
-0.5 0.5 0.5
0.5 -0.5 0.5
0.5 0.5 -0.5
V
1
Direct
0.0 0.0 0.0

10
python/converters/vasp/test/vaspio/POSCAR.example.out Normal file
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nq = 1
ntypes = 1
nions = [1]
el_names = ['V']
a_brav:
[[-1. 1. 1.]
[ 1. -1. 1.]
[ 1. 1. -1.]]
q_types:
[array([[ 0., 0., 0.]])]

56
python/converters/vasp/test/vaspio/mytest.py Normal file
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r"""
Module defining a custom TestCase with extra functionality.
"""
import unittest
import numpy as np
import difflib
class MyTestCase(unittest.TestCase):
"""
Custom TestCase class supporting additional equality checks:
- numpy array equality
- file equality
"""
def __init__(self, *args, **kwargs):
"""
Initializes a custom equality function for comparing numpy arrays.
"""
super(MyTestCase, self).__init__(*args, **kwargs)
self.addTypeEqualityFunc(np.ndarray, self.is_arrays_equal)
def is_arrays_equal(self, arr1, arr2, msg=None):
"""
Raises self.failureException is arrays arr1 and arr2
are not equal.
"""
if not np.allclose(arr1, arr2):
raise self.failureException(msg)
def assertFileEqual(self, file1, file2):
"""
Compares two files using difflib.
Empty lines are ignored.
Files are assumed to be relatively small;
the data is truncated for files larger than MAX_SIZE bytes.
"""
MAX_SIZE = 100000
with open(file1, 'r') as f1:
str1 = f1.read(MAX_SIZE)
with open(file2, 'r') as f2:
str2 = f2.read(MAX_SIZE)
#
# Make a diff
#
# Remove empty lines
lstr1 = filter(lambda s: s.strip() != '', str1.splitlines(True))
lstr2 = filter(lambda s: s.strip() != '', str2.splitlines(True))
# diff
delta = difflib.unified_diff(lstr1, lstr2)
# combine delta's to a string
diff = ''.join(delta)
# if 'diff' is non-empty, files are different
if diff:
return self.fail("Files '%s' and '%s' differ"%(file1, file2))

1
python/converters/vasp/test/vaspio/runtest.sh Executable file
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PYTHONPATH=../../python:../../c:$PYTHONPATH python $1

32
python/converters/vasp/test/vaspio/test_doscar.py Normal file
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r"""
Tests for class 'Doscar' from module 'vaspio'
"""
import mytest
import numpy as np
from vaspio import Doscar
################################################################################
#
# TestDoscar
#
################################################################################
class TestDoscar(mytest.MyTestCase):
"""
Function:
def Doscar.from_file(vasp_dir, dos_filename)
Scenarios:
- correct DOSCAR file
"""
# Scenario 1
def test_example(self):
filename = 'DOSCAR.example'
doscar = Doscar()
doscar.from_file(vasp_dir='./', dos_filename=filename)
test_efermi = doscar.efermi
expected = 5.84395237
self.assertAlmostEqual(test_efermi, expected)

45
python/converters/vasp/test/vaspio/test_eigenval.py Normal file
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r"""
Tests for class 'Eigneval' from module 'vaspio'
"""
import mytest
import numpy as np
from vaspio import Eigenval
################################################################################
#
# TestEigenval
#
################################################################################
class TestEigenval(mytest.MyTestCase):
"""
Function:
def Eigenval.from_file(vasp_dir, eig_filename)
Scenarios:
- correct EIGENVAL file
"""
# Scenario 1
def test_example(self):
filename = 'EIGENVAL.example'
eigenval = Eigenval()
eigenval.from_file(vasp_dir='./', eig_filename=filename)
testout = 'EIGENVAL.example.out.test'
with open(testout, 'w') as f:
writeline = lambda s: f.write(s + '\n')
writeprop = lambda pname: writeline("%s = %s"%(pname, eigenval.__dict__[pname]))
writeprop('nq')
writeprop('ispin')
writeprop('nelect')
writeprop('nktot')
writeprop('nband')
writeline("kpts:\n%s"%(eigenval.kpts))
writeline("kwghts:\n%s"%(eigenval.kwghts))
writeline("eigs:\n%s"%(eigenval.eigs))
expected = 'EIGENVAL.example.out'
self.assertFileEqual(testout, expected)

57
python/converters/vasp/test/vaspio/test_kpoints.py Normal file
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r"""
Tests for class 'Ibzkpt' from module 'vaspio'
"""
import mytest
import numpy as np
from vaspio import Kpoints
################################################################################
#
# TestIbzkpt
#
################################################################################
class TestIbzkpt(mytest.MyTestCase):
"""
Function:
def read_plocar(filename)
Scenarios:
- full IBZKPT file with tetrahedra
- partial IBZKPT file with k-points only
"""
# Scenario 1
def test_example(self):
ibz_file = 'IBZKPT.example'
kpoints = Kpoints()
kpoints.from_file(vasp_dir='./', ibz_filename=ibz_file)
testout = 'IBZKPT.example.out.test'
with open(testout, 'w') as f:
writeline = lambda s: f.write(s + '\n')
writeline("nktot = %s"%(kpoints.nktot))
writeline("ntet = %s"%(kpoints.ntet))
writeline("volt = %s"%(kpoints.volt))
writeline("kpts:\n%s"%(kpoints.kpts))
writeline("tets:\n%s"%(kpoints.itet))
expected = 'IBZKPT.example.out'
self.assertFileEqual(testout, expected)
# Scenario 2
def test_notet(self):
ibz_file = 'IBZKPT.notet'
kpoints = Kpoints()
kpoints.from_file(vasp_dir='./', ibz_filename=ibz_file)
testout = 'IBZKPT.notet.out.test'
with open(testout, 'w') as f:
writeline = lambda s: f.write(s + '\n')
writeline("nktot = %s"%(kpoints.nktot))
writeline("kpts:\n%s"%(kpoints.kpts))
expected = 'IBZKPT.notet.out'
self.assertFileEqual(testout, expected)

43
python/converters/vasp/test/vaspio/test_poscar.py Normal file
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r"""
Tests for class 'Poscar' from module 'vaspio'
"""
import mytest
import numpy as np
from vaspio import Poscar
################################################################################
#
# TestPoscar
#
################################################################################
class TestPoscar(mytest.MyTestCase):
"""
Function:
def Poscar.from_file(vasp_dir, poscar_filename)
Scenarios:
- correct POSCAR file
"""
# Scenario 1
def test_example(self):
filename = 'POSCAR.example'
poscar = Poscar()
poscar.from_file(vasp_dir='./', poscar_filename=filename)
testout = 'POSCAR.example.out.test'
with open(testout, 'w') as f:
writeline = lambda s: f.write(s + '\n')
writeprop = lambda pname: writeline("%s = %s"%(pname, poscar.__dict__[pname]))
writeprop('nq')
writeprop('ntypes')
writeprop('nions')
writeprop('el_names')
writeline("a_brav:\n%s"%(poscar.a_brav))
writeline("q_types:\n%s"%(poscar.q_types))
expected = 'POSCAR.example.out'
self.assertFileEqual(testout, expected)

11
python/converters/vasp/test/vaspio/test_vaspio.py Normal file
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r"""
Test suite for module `vaspio`.
"""
import unittest
if __name__ == '__main__':
suite = unittest.TestLoader().discover('./')
unittest.TextTestRunner(verbosity=2, buffer=True).run(suite)
# unittest.TextTestRunner(verbosity=2, buffer=False).run(suite)