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Restructed test directory

Browse Source 
The names of the test suites have been prefixed with an underscore
to avoid name conflicts with corresponding modules.
Also an attempt to make a scan of all tests has been made by
creating a 'test_all.py' script that is supposed to discover all
test cases and run them. Unfortunately, this does not work as expected
because many tests use input files assumed to be found in the current
directory, which is not true if the tests are run from a different
(parent) directory.

This can be fixed by either forcing the change of directory (but it
seems that 'unittest' does not have this functionality) or
prepending input file names with the current module directory.
This commit is contained in:
Oleg E. Peil 2015-08-10 11:32:08 +02:00 committed by Michel Ferrero
parent 6ab916d2d0
commit db16a8438d
71 changed files with 8173 additions and 0 deletions
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1
python/converters/vasp/test/_inpconf/.gitignore vendored Normal file
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*.pyc

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python/converters/vasp/test/_inpconf/__init__.py Normal file
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python/converters/vasp/test/_inpconf/arraytest.py Normal file
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r"""
Module defining a custom TestCase with extra functionality.
"""
import unittest
import numpy as np
class ArrayTestCase(unittest.TestCase):
"""
Custom TestCase class supporting array equality.
"""
def __init__(self, *args, **kwargs):
"""
Initializes a custom equality function for comparing numpy arrays.
"""
super(ArrayTestCase, 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)

29
python/converters/vasp/test/_inpconf/example.cfg Normal file
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[General]
[Group 1]
SHELLS = 1 2
EMIN = -7.6
EMAX = 3.0
[Group 2]
SHELLS = 3
EMIN = -1.6
EMAX = 2.0
[Shell 1]
LSHELL = 2
IONS = 5..8
[Shell 2]
LSHELL = 1
IONS = 1..4
RTRANSFORM = 0.0 1.0 0.0
1.0 0.0 0.0
0.0 0.0 1.0
[Shell 3]
LSHELL = 3
IONS = 1..4

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python/converters/vasp/test/_inpconf/example_nogroup.cfg Normal file
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[Shell 1]
LSHELL = 2
IONS = 5..8
EMIN = -7.6
EMAX = 3.0

10
python/converters/vasp/test/_inpconf/input_test_1.cfg Normal file
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[General]
EFERMI = 0.7
[Shell 1]
LSHELL = 2
IONS = 5..8
[Shell 2]
IONS = 9..20
LSHELL = 1

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python/converters/vasp/test/_inpconf/input_test_2.cfg Normal file
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[Shell 1]
LSHELL = 2
IONS = 1..4

25
python/converters/vasp/test/_inpconf/input_test_3.cfg Normal file
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[General]
[Group 1]
SHELLS = 1 2
EMIN = -7.6
EMAX = 3.0
[Group 2]
SHELLS = 3
EMIN = -1.6
EMAX = 2.0
[Shell 1]
LSHELL = 2
IONS = 5..8
[Shell 2]
LSHELL = 1
IONS = 1..4
RTRANSFORM = 0.0 1.0 0.0
1.0 0.0 0.0
0.0 0.0 1.0

24
python/converters/vasp/test/_inpconf/input_test_4.cfg Normal file
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[General]
[Group 1]
SHELLS = 1 2
EMIN = -7.6
EMAX = 3.0
[Shell 1]
LSHELL = 2
IONS = 5..8
[Shell 2]
LSHELL = 1
IONS = 1..4
RTRANSFORM = 0.0 1.0 0.0
1.0 0.0 0.0
0.0 0.0 1.0
[Shell 3]
LSHELL = 3
IONS = 1..4

13
python/converters/vasp/test/_inpconf/parse_groups_1.cfg Normal file
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[General]
[Group 1]
SHELLS = 1 2
[Shell 1]
LSHELL = 2
IONS = 5..8
[Shell 2]
LSHELL = 1
IONS = 1..4

4
python/converters/vasp/test/_inpconf/parse_shells_1.cfg Normal file
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[General]
[Group 1]

5
python/converters/vasp/test/_inpconf/parse_shells_2.cfg Normal file
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[General]
[Group 1]
[Shell x]

7
python/converters/vasp/test/_inpconf/parse_shells_3.cfg Normal file
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[General]
[Group 1]
[Shell 1]
LSHELL = 2

17
python/converters/vasp/test/_inpconf/parse_shells_4.cfg Normal file
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[General]
[Group 1]
SHELLS = 1 2
[Shell 1]
LSHELL = 2
IONS = 5..8
[Shell 2]
LSHELL = 1
IONS = 1..4
RTRANSFORM = 0.0 1.0 0.0
1.0 0.0 0.0
0.0 0.0 1.0

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

12
python/converters/vasp/test/_inpconf/test1.cfg Normal file
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[General]
EFERMI = 0.7
[Group 1]
SHELLS = 1
[Shell 1]
LSHELL = 2
[Shell 2]
IONS = 9..20
LSHELL = 1

44
python/converters/vasp/test/_inpconf/test_groups.py Normal file
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r"""
Tests of 'parse_groups()' defined in ConfigParameters class
"""
import arraytest
import numpy as np
from inpconf import ConfigParameters
################################################################################
#
# TestParseGroups
#
################################################################################
class TestParseGroups(arraytest.ArrayTestCase):
"""
Function:
def parse_groups(self)
Scenarios:
- **if** a [Group] section does not contain all required parameters
**raise** Exception
- **if** a correct group section is defined **return** a list of dictionaries
"""
# Scenario 1
def test_gr_required(self):
conf_pars = ConfigParameters('parse_groups_1.cfg')
err_mess = "Required parameter"
with self.assertRaisesRegexp(Exception, err_mess):
conf_pars.parse_groups()
# Scenario 2
def test_example(self):
conf_pars = ConfigParameters('example.cfg')
conf_pars.parse_groups()
res = conf_pars.groups
expected = [{'index': 1, 'shells': [1, 2], 'emin': -7.6, 'emax': 3.0,
'normalize': True, 'normion': False},
{'index': 2, 'shells': [3], 'emin': -1.6, 'emax': 2.0,
'normalize': True, 'normion': False}]
self.assertListEqual(res, expected)

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

107
python/converters/vasp/test/_inpconf/test_input.py Normal file
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r"""
Tests of 'parse_input()' defined in ConfigParameters class
"""
import arraytest
import numpy as np
from inpconf import ConfigParameters
################################################################################
#
# TestParseInput
#
################################################################################
class TestParseInput(arraytest.ArrayTestCase):
"""
Function:
def parse_input(self)
Scenarios:
- **if** no [Group] section exists and more than one [Shell] section
is given **raise** AssertionError
- **if** no [Group] section exists but the single [Shell] section
does not contain required group information **raise** KeyError
- **if** a shell referenced in a group does not exist
**raise** Exception
- **if** not all defined shells are referenced in the groups
**raise** Exception
- **if** all sections are parsed error-free check that the output
is correct
- correct example with a single shell and no explicit groups
"""
# Scenario 1
def test_no_group(self):
conf_pars = ConfigParameters('input_test_1.cfg')
err_mess = "At least one group"
with self.assertRaisesRegexp(AssertionError, err_mess):
conf_pars.parse_input()
# Scenario 2
def test_gr_required(self):
conf_pars = ConfigParameters('input_test_2.cfg')
err_mess = "One \[Shell\] section is"
with self.assertRaisesRegexp(KeyError, err_mess):
conf_pars.parse_input()
# Scenario 3
def test_no_shell(self):
conf_pars = ConfigParameters('input_test_3.cfg')
err_mess = "Shell 3 referenced in"
with self.assertRaisesRegexp(Exception, err_mess):
conf_pars.parse_input()
# Scenario 4
def test_shell_outside_groups(self):
conf_pars = ConfigParameters('input_test_4.cfg')
err_mess = "Some shells are not inside"
with self.assertRaisesRegexp(AssertionError, err_mess):
conf_pars.parse_input()
# Scenario 5
def test_example(self):
conf_pars = ConfigParameters('example.cfg')
conf_pars.parse_input()
# with open('parse_input.output.test', 'wt') as f:
# f.write("Shells:\n")
# f.write(conf_pars.shells.__repr__() + '\n\n')
# f.write("Groups:\n")
# f.write(conf_pars.groups.__repr__() + '\n')
res = "Shells:\n"
res += conf_pars.shells.__repr__() + '\n\n'
res += "Groups:\n"
res += conf_pars.groups.__repr__()
expected = r"""Shells:
[{'ion_list': array([4, 5, 6, 7]), 'user_index': 1, 'lshell': 2}, {'tmatrix': array([[ 0., 1., 0.],
[ 1., 0., 0.],
[ 0., 0., 1.]]), 'ion_list': array([0, 1, 2, 3]), 'user_index': 2, 'lshell': 1}, {'ion_list': array([0, 1, 2, 3]), 'user_index': 3, 'lshell': 3}]
Groups:
[{'normalize': True, 'index': 1, 'shells': [0, 1], 'normion': False, 'emax': 3.0, 'emin': -7.6}, {'normalize': True, 'index': 2, 'shells': [2], 'normion': False, 'emax': 2.0, 'emin': -1.6}]"""
self.assertEqual(res, expected)
# Scenario 6
def test_example_no_groups(self):
conf_pars = ConfigParameters('example_nogroup.cfg')
conf_pars.parse_input()
# with open('parse_input.output.test', 'wt') as f:
# f.write("Shells:\n")
# f.write(conf_pars.shells.__repr__() + '\n\n')
# f.write("Groups:\n")
# f.write(conf_pars.groups.__repr__() + '\n')
res = "Shells:\n"
res += conf_pars.shells.__repr__() + '\n\n'
res += "Groups:\n"
res += conf_pars.groups.__repr__()
expected = r"""Shells:
[{'ion_list': array([4, 5, 6, 7]), 'user_index': 1, 'lshell': 2}]
Groups:
[{'normalize': True, 'index': '1', 'emin': -7.6, 'emax': 3.0, 'normion': False, 'shells': [0]}]"""
self.assertEqual(res, expected)

48
python/converters/vasp/test/_inpconf/test_parameter_set.py Normal file
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r"""
Tests of 'parse_parameter_set()' defined in ConfigParameters class
"""
import arraytest
import numpy as np
from inpconf import ConfigParameters
################################################################################
#
# TestParseParameterSet
#
################################################################################
class TestParseParameterSet(arraytest.ArrayTestCase):
"""
Function:
def parse_parameter_set(self, section, param_set, excpetion=False)
Scenarios:
- **if** config-file section [Shell 1] contains 'LSHELL = 2' **and**
'lshell' and 'ions' are in `param_set` **return** a dictionary {'lshell': 2}
- **if** config-file section [Shell 1] contains 'LSHELL = 2' **and**
'lshell' and 'ions' are in `param_set` and
exception=True **raise** Exception
"""
def setUp(self):
"""
"""
# Dummy ConfigParameters object
self.cpars = ConfigParameters('test1.cfg')
# Scenario 1
def test_sh_required(self):
param_set = self.cpars.sh_required # contains 'lshell' and 'ions'
res = self.cpars.parse_parameter_set('Shell 1', param_set)
expected = {'lshell': 2}
self.assertDictEqual(res, expected)
# Scenario 2
def test_sh_required_exception(self):
section = 'Shell 1'
param_set = self.cpars.sh_required # contains 'lshell' and 'ions'
err_mess = "Required parameter" # .* in section [%s]"%(section)
with self.assertRaisesRegexp(Exception, err_mess):
self.cpars.parse_parameter_set(section, param_set, exception=True)

76
python/converters/vasp/test/_inpconf/test_shells.py Normal file
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r"""
Tests of 'parse_shells()' defined in ConfigParameters class
"""
import arraytest
import numpy as np
from inpconf import ConfigParameters
################################################################################
#
# TestParseShells
#
################################################################################
class TestParseShells(arraytest.ArrayTestCase):
"""
Function:
def parse_shells(self)
Scenarios:
- **if** config-file does not contain a valid [Shell] section
**raise** AssertionError
- **if** a [Shell] section does not contain a valid index
**raise** ValueError
- **if** a [Shell] section does not contain all required parameters
**raise** Exception
- **if** two correct [Shell] sections are defined
**return** a dictionary of shell parameters
"""
# Scenario 1
def test_no_shell(self):
conf_pars = ConfigParameters('parse_shells_1.cfg')
err_mess = "No projected shells"
with self.assertRaisesRegexp(AssertionError, err_mess):
conf_pars.parse_shells()
# Scenario 2
def test_bad_indices(self):
conf_pars = ConfigParameters('parse_shells_2.cfg')
err_mess = "Failed to extract shell indices"
with self.assertRaisesRegexp(ValueError, err_mess):
conf_pars.parse_shells()
# Scenario 3
def test_sh_required(self):
conf_pars = ConfigParameters('parse_shells_3.cfg')
err_mess = "Required parameter"
with self.assertRaisesRegexp(Exception, err_mess):
conf_pars.parse_shells()
# Scenario 4
def test_two_shells(self):
conf_pars = ConfigParameters('parse_shells_4.cfg')
conf_pars.parse_shells()
res = conf_pars.shells
expected = [{'user_index': 1, 'lshell': 2, 'ion_list': np.array([4, 5, 6, 7])},
{'user_index': 2, 'lshell': 1, 'ion_list': np.array([0, 1, 2, 3]),
'tmatrix': np.array([[ 0., 1., 0.], [ 1., 0., 0.], [ 0., 0., 1.]])}]
# ...lousy way to test equality of two dictionaries containing numpy arrays
self.assertEqual(len(res), len(expected))
arr = res[0].pop('ion_list')
arr_exp = expected[0].pop('ion_list')
self.assertEqual(arr, arr_exp)
arr = res[1].pop('ion_list')
arr_exp = expected[1].pop('ion_list')
self.assertEqual(arr, arr_exp)
arr = res[1].pop('tmatrix')
arr_exp = expected[1].pop('tmatrix')
self.assertEqual(arr, arr_exp)
self.assertListEqual(res, expected)

149
python/converters/vasp/test/_inpconf/test_special_parsers.py Normal file
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r"""
Tests of special parseres defined in ConfigParameters class
"""
import arraytest
import numpy as np
from inpconf import ConfigParameters
################################################################################
#
# TestParseStringLogical
#
################################################################################
class TestParseStringLogical(arraytest.ArrayTestCase):
"""
Function:
def parse_string_logical(self, par_str)
Scenarios:
- **if** par_str == 'True' **return** True
- **if** par_str == 'False' **return** False
- **if** par_str == '0' **raise** assertion
"""
def setUp(self):
"""
"""
# Dummy ConfigParameters object
self.cpars = ConfigParameters('test1.cfg')
# Scenario 1
def test_true(self):
res = self.cpars.parse_string_logical('True')
self.assertEqual(res, True)
# Scenario 2
def test_false(self):
res = self.cpars.parse_string_logical('False')
self.assertEqual(res, False)
# Scenario 3
def test_incorrect(self):
with self.assertRaises(AssertionError):
self.cpars.parse_string_logical('0')
################################################################################
#
# TestParseStringIonList
#
################################################################################
class TestParseStringIonList(arraytest.ArrayTestCase):
"""
Function:
def parse_string_ion_list(self, par_str)
Scenarios:
- **if** par_str == '5 6 7 8' **return** array([4, 5, 6, 7])
- **if** par_str == 'Ni' **raise** NotImplementedError
- **if** par_str == '0 1' **raise** AssertionError
- **if** par_str == '5..8' **return** array([4, 5, 6, 7])
- **if** par_str == '8..5' **raise** AssertionError
"""
def setUp(self):
"""
"""
# Dummy ConfigParameters object
self.cpars = ConfigParameters('test1.cfg')
# Scenario 1
def test_simple_list(self):
expected = np.array([4, 5, 6, 7])
res = self.cpars.parse_string_ion_list('5 6 7 8')
self.assertEqual(res, expected)
# Scenario 2
def test_atomic_symbol(self):
with self.assertRaises(NotImplementedError):
self.cpars.parse_string_ion_list('Ni')
# Scenario 3
def test_out_of_bounds(self):
err_mess = "Lowest ion index is"
with self.assertRaisesRegexp(AssertionError, err_mess):
self.cpars.parse_string_ion_list('0 1')
# Scenario 4
def test_list_range(self):
expected = np.array([4, 5, 6, 7])
res = self.cpars.parse_string_ion_list('5..8')
self.assertEqual(res, expected)
# Scenario 5
def test_range_wrong_order(self):
err_mess = "First index of the range"
with self.assertRaisesRegexp(AssertionError, err_mess):
self.cpars.parse_string_ion_list('8..5')
################################################################################
#
# TestParseStringTmatrix
#
################################################################################
class TestParseStringTmatrix(arraytest.ArrayTestCase):
"""
Function:
def parse_string_tmatrix(self, par_str)
Parses a matrix defined as a set of rows in the conf-file.
Scenarios:
- **if** number of columns is not the same **raise** AssertionError
- **if** complex matrix is read and the number of columns is odd
**raise** AssertionError
- **if** a correct matrix is given **return** an array
"""
def setUp(self):
"""
"""
# Dummy ConfigParameters object
self.cpars = ConfigParameters('test1.cfg')
# Scenario 1
def test_number_of_columns(self):
par_str = "1.0 0.0\n1.0"
err_mess = "Number of columns"
with self.assertRaisesRegexp(AssertionError, err_mess):
self.cpars.parse_string_tmatrix(par_str, real=True)
# Scenario 2
def test_complex_matrix_odd(self):
par_str = "1.0 0.0 2.0 1.0 0.0\n0.0 1.0 2.0 3.0 -1.0"
err_mess = "Complex matrix must"
with self.assertRaisesRegexp(AssertionError, err_mess):
self.cpars.parse_string_tmatrix(par_str, real=False)
# Scenario 3
def test_complex_matrix(self):
par_str = "1.0 0.0 2.0 -3.0\n0.0 1.0 -1.0 1.0"
res = self.cpars.parse_string_tmatrix(par_str, real=False)
expected = np.array([[1.0, 2.0 - 3.0j], [1.0j, -1.0 + 1.0j]])
self.assertEqual(res, expected)

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*.pyc
*.test

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BIN
python/converters/vasp/test/_plocar_io/PLOCAR.trunc Normal file
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56
python/converters/vasp/test/_plocar_io/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, otherwise
the data is truncated.
"""
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/_plocar_io/runtest.sh Executable file
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PYTHONPATH=../../python:../../c:$PYTHONPATH python $1

93
python/converters/vasp/test/_plocar_io/test_fileio.py Normal file
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r"""
Tests of 'read_plocar()' from module 'plocar_io.c_plocar_io'
"""
import mytest
import numpy as np
from plocar_io.c_plocar_io import read_plocar
################################################################################
#
# TestFileIO
#
################################################################################
class TestFileIO(mytest.MyTestCase):
"""
Function:
def read_plocar(filename)
Scenarios:
- **if** file PLOCAR does not exist **raise** IOError
- **if** PLOCAR is truncated **raise** IOError
- **if** the precision flag is not 4 or 8 **raise** ValueError
- **if** PLOCAR with prec=8 is read **compare** the output
- **if** PLOCAR with prec=4 is read **compare** the output
"""
# Scenario 1
def test_no_plocar(self):
err_mess = "Error opening xPLOCAR"
with self.assertRaisesRegexp(IOError, err_mess):
read_plocar('xPLOCAR')
# Scenario 2
def test_end_of_file(self):
err_mess = "End-of-file reading"
with self.assertRaisesRegexp(IOError, err_mess):
read_plocar('PLOCAR.trunc')
# Scenario 3
def test_wrong_prec(self):
err_mess = "only 'prec = 4, 8' are supported"
with self.assertRaisesRegexp(ValueError, err_mess):
read_plocar('PLOCAR.noprec')
# Scenario 4
def test_plocar_prec8(self):
pars, plo, ferw = read_plocar('PLOCAR.prec8')
nion, ns, nk, nb, nlm = plo.shape
test_file = 'PLOCAR.prec8.out.test'
with open(test_file, 'wt') as f:
f.write(" nlm =%5i\n"%(nlm))
ion = 1
isp = 1
for ik in xrange(nk):
for ib in xrange(nb):
f.write("%5i%5i%5i%5i%10.5f\n"%(ion, isp, ik+1, ib+1, ferw[0, 0, ik, ib]))
for ilm in xrange(nlm):
p = plo[0, 0, ik, ib, ilm]
f.write("%5i%15.7f%15.7f\n"%(ilm+1, p.real, p.imag))
expected_file = 'PLOCAR.prec8.out'
self.assertFileEqual(test_file, expected_file)
# Scenario 5
def test_plocar_example(self):
pars, plo, ferw = read_plocar('PLOCAR.example')
nion, ns, nk, nb, nlm = plo.shape
self.assertEqual(pars['nion'], nion)
self.assertEqual(pars['ns'], ns)
self.assertEqual(pars['nk'], nk)
self.assertEqual(pars['nb'], nb)
test_file = 'PLOCAR.example.out.test'
with open(test_file, 'wt') as f:
f.write("pars: %s\n"%(pars))
for ion in xrange(nion):
for isp in xrange(ns):
for ik in xrange(nk):
for ib in xrange(nb):
f.write("%5i%5i%5i%5i %s\n"%(ion+1, isp+1, ik+1, ib+1,
ferw[ion, isp, ik, ib]))
for ilm in xrange(nlm):
p = plo[ion, isp, ik, ib, ilm]
f.write("%5i %s\n"%(ilm+1, p))
expected_file = 'PLOCAR.example.out'
self.assertFileEqual(test_file, expected_file)

10
python/converters/vasp/test/_plocar_io/test_plocar_io.py Normal file
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@ -0,0 +1,10 @@
r"""
Test suite for module `plocar_io`.
"""
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)

2
python/converters/vasp/test/_plotools/.gitignore vendored Normal file
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@ -0,0 +1,2 @@
*.pyc
*.test

609
python/converters/vasp/test/_plotools/DOSCAR Normal file
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@ -0,0 +1,609 @@
1 1 1 0
0.1333597E+02 0.2587511E-09 0.2587511E-09 0.2587511E-09 0.5000000E-15
1.000000000000000E-004
CAR
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python/converters/vasp/test/_plotools/IBZKPT Normal file
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python/converters/vasp/test/_plotools/OUTCAR Normal file
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python/converters/vasp/test/_plotools/POSCAR Normal file
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python/converters/vasp/test/_plotools/densmat.out Normal file
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density matrix: [[[[ 2.71066432e-01 -1.07856040e-02 9.07814858e-03 -2.60324510e-01
-2.14321077e-09]
[ -1.07856040e-02 2.97099774e-01 9.52322235e-02 -1.38848431e-02
-1.97357976e-01]
[ 9.07814858e-03 9.52322235e-02 1.42730494e-01 4.53909162e-03
-4.31946315e-02]
[ -2.60324510e-01 -1.38848431e-02 4.53909162e-03 2.95736883e-01
4.02728377e-02]
[ -2.14321077e-09 -1.97357976e-01 -4.31946315e-02 4.02728377e-02
2.35328545e-01]]]]

8
python/converters/vasp/test/_plotools/example.cfg Normal file
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@ -0,0 +1,8 @@
[Shell 1]
LSHELL = 2
IONS = 1
EMIN = -15.0
EMAX = 5.0

56
python/converters/vasp/test/_plotools/mytest.py Normal file
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@ -0,0 +1,56 @@
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))

115
python/converters/vasp/test/_plotools/projgroups.out Normal file
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pars: {'normalize': True, 'index': '1', 'emin': -15.0, 'emax': 5.0, 'normion': False, 'shells': [0]}
3 8
1 (2.5198055198e-08+0j)
2 (2.51956215891e-08+0j)
3 (-1.39707700703e-12+0j)
4 (2.51956464581e-08+0j)
5 (-9.58669992349e-14+0j)
1 (0.423249542713+0j)
2 (0.441459685564+0j)
3 (5.45383349593e-10+0j)
4 (0.441459536552+0j)
5 (-5.07696386694e-15+0j)
1 (-0.624317586422+0j)
2 (0.299283236265+0j)
3 (3.00651912255e-08+0j)
4 (0.299281418324+0j)
5 (-5.44629513472e-14+0j)
1 (-2.9753928743e-07+0j)
2 (-0.495364636183+0j)
3 (1.61749496311e-14+0j)
4 (0.495365083218+0j)
5 (2.86656725024e-08+0j)
1 (2.31630860326e-12+0j)
2 (-2.07712407274e-08+0j)
3 (6.79555596435e-05+0j)
4 (2.07689296872e-08+0j)
5 (-0.686951518059+0j)
1 (-2.55608547661e-08+0j)
2 (1.27339729872e-08+0j)
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4 (1.27377095538e-08+0j)
5 (-6.18639533059e-05+0j)
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1 (-7.42354511196e-10+0j)
2 (-0.407458901405+0j)
3 (-0.132825627923+0j)
4 (-1.12258624618e-09+0j)
5 (0.230060741305+0j)
1 (-0.529840826988+0j)
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5 (0.328566819429+0j)
1 (-5.92653073284e-08+0j)
2 (-0.511403858662+0j)
3 (0.342116594315+0j)
4 (-5.81566510505e-08+0j)
5 (-0.592563331127+0j)
1 (9.17969966707e-09+0j)
2 (3.7528921637e-10+0j)
3 (0.743389487267+0j)
4 (-7.80711495452e-09+0j)
5 (0.429196119308+0j)
1 (-0.60352396965+0j)
2 (5.06060757743e-07+0j)
3 (1.02901012156e-07+0j)
4 (-0.60352396965+0j)
5 (-1.76288821763e-07+0j)
3 7
1 (-0.157831609249+0j)
2 (0.157831639051+0j)
3 (1.93573299612e-08+0j)
4 (0.157831639051+0j)
5 (5.40782289825e-14+0j)
1 (-1.07380124348e-07+0j)
2 (-0.227066069841+0j)
3 (-1.22580686934e-07+0j)
4 (0.227065965533+0j)
5 (0.299297988415+0j)
1 (0.115845791996+0j)
2 (0.057922616601+0j)
3 (0.13223952055+0j)
4 (0.0579231306911+0j)
5 (3.36705625159e-07+0j)
1 (0.159106343985+0j)
2 (0.0795532241464+0j)
3 (-0.240490317345+0j)
4 (0.0795530825853+0j)
5 (1.18692518924e-07+0j)
1 (3.98122104173e-08+0j)
2 (-0.241537705064+0j)
3 (-6.01558127755e-08+0j)
4 (0.241537734866+0j)
5 (-0.421558618546+0j)
3 7
1 (7.91286647317e-10+0j)
2 (3.03037844818e-10+0j)
3 (0.204362645745+0j)
4 (4.89190632447e-10+0j)
5 (-0.353966474533+0j)
1 (9.13699960137e-09+0j)
2 (1.0438577086e-10+0j)
3 (-0.42577791214+0j)
4 (-6.95880419954e-09+0j)
5 (-0.245822981+0j)
1 (0.368288576603+0j)
2 (1.67113629601e-08+0j)
3 (-1.44080747333e-10+0j)
4 (0.365979760885+0j)
5 (1.25375620996e-09+0j)
1 (0.365983724594+0j)
2 (-2.74820233237e-09+0j)
3 (1.77222470032e-09+0j)
4 (-0.368292748928+0j)
5 (7.90098320103e-10+0j)
1 (-3.99936368467e-08+0j)
2 (0.546248733997+0j)
3 (-2.91795543284e-09+0j)
4 (-2.16134438347e-07+0j)
5 (1.55786352707e-08+0j)

115
python/converters/vasp/test/_plotools/projortho.out Normal file
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pars: {'normalize': True, 'index': '1', 'emin': -15.0, 'emax': 5.0, 'normion': False, 'shells': [0]}
3 8
1 (2.5198055198e-08+0j)
2 (2.51956215891e-08+0j)
3 (-1.39707700703e-12+0j)
4 (2.51956464581e-08+0j)
5 (-9.58669992349e-14+0j)
1 (0.423249542713+0j)
2 (0.441459685564+0j)
3 (5.45383349593e-10+0j)
4 (0.441459536552+0j)
5 (-5.07696386694e-15+0j)
1 (-0.624317586422+0j)
2 (0.299283236265+0j)
3 (3.00651912255e-08+0j)
4 (0.299281418324+0j)
5 (-5.44629513472e-14+0j)
1 (-2.9753928743e-07+0j)
2 (-0.495364636183+0j)
3 (1.61749496311e-14+0j)
4 (0.495365083218+0j)
5 (2.86656725024e-08+0j)
1 (2.31630860326e-12+0j)
2 (-2.07712407274e-08+0j)
3 (6.79555596435e-05+0j)
4 (2.07689296872e-08+0j)
5 (-0.686951518059+0j)
1 (-2.55608547661e-08+0j)
2 (1.27339729872e-08+0j)
3 (-0.749936163425+0j)
4 (1.27377095538e-08+0j)
5 (-6.18639533059e-05+0j)
3 8
1 (-7.42354511196e-10+0j)
2 (-0.407458901405+0j)
3 (-0.132825627923+0j)
4 (-1.12258624618e-09+0j)
5 (0.230060741305+0j)
1 (-0.529840826988+0j)
2 (1.02242869726e-09+0j)
3 (1.47169805231e-08+0j)
4 (0.529840826988+0j)
5 (8.58095106082e-09+0j)
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2 (-0.46026712656+0j)
3 (-0.189698129892+0j)
4 (-3.64733043767e-09+0j)
5 (0.328566819429+0j)
1 (-5.92653073284e-08+0j)
2 (-0.511403858662+0j)
3 (0.342116594315+0j)
4 (-5.81566510505e-08+0j)
5 (-0.592563331127+0j)
1 (9.17969966707e-09+0j)
2 (3.7528921637e-10+0j)
3 (0.743389487267+0j)
4 (-7.80711495452e-09+0j)
5 (0.429196119308+0j)
1 (-0.60352396965+0j)
2 (5.06060757743e-07+0j)
3 (1.02901012156e-07+0j)
4 (-0.60352396965+0j)
5 (-1.76288821763e-07+0j)
3 7
1 (-0.157831609249+0j)
2 (0.157831639051+0j)
3 (1.93573299612e-08+0j)
4 (0.157831639051+0j)
5 (5.40782289825e-14+0j)
1 (-1.07380124348e-07+0j)
2 (-0.227066069841+0j)
3 (-1.22580686934e-07+0j)
4 (0.227065965533+0j)
5 (0.299297988415+0j)
1 (0.115845791996+0j)
2 (0.057922616601+0j)
3 (0.13223952055+0j)
4 (0.0579231306911+0j)
5 (3.36705625159e-07+0j)
1 (0.159106343985+0j)
2 (0.0795532241464+0j)
3 (-0.240490317345+0j)
4 (0.0795530825853+0j)
5 (1.18692518924e-07+0j)
1 (3.98122104173e-08+0j)
2 (-0.241537705064+0j)
3 (-6.01558127755e-08+0j)
4 (0.241537734866+0j)
5 (-0.421558618546+0j)
3 7
1 (7.91286647317e-10+0j)
2 (3.03037844818e-10+0j)
3 (0.204362645745+0j)
4 (4.89190632447e-10+0j)
5 (-0.353966474533+0j)
1 (9.13699960137e-09+0j)
2 (1.0438577086e-10+0j)
3 (-0.42577791214+0j)
4 (-6.95880419954e-09+0j)
5 (-0.245822981+0j)
1 (0.368288576603+0j)
2 (1.67113629601e-08+0j)
3 (-1.44080747333e-10+0j)
4 (0.365979760885+0j)
5 (1.25375620996e-09+0j)
1 (0.365983724594+0j)
2 (-2.74820233237e-09+0j)
3 (1.77222470032e-09+0j)
4 (-0.368292748928+0j)
5 (7.90098320103e-10+0j)
1 (-3.99936368467e-08+0j)
2 (0.546248733997+0j)
3 (-2.91795543284e-09+0j)
4 (-2.16134438347e-07+0j)
5 (1.55786352707e-08+0j)

115
python/converters/vasp/test/_plotools/projshells.out Normal file
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pars: {'ion_list': array([0]), 'user_index': 1, 'lshell': 2}
3 8
1 (2.5198055198e-08+0j)
2 (2.51956215891e-08+0j)
3 (-1.39707700703e-12+0j)
4 (2.51956464581e-08+0j)
5 (-9.58669992349e-14+0j)
1 (0.423249542713+0j)
2 (0.441459685564+0j)
3 (5.45383349593e-10+0j)
4 (0.441459536552+0j)
5 (-5.07696386694e-15+0j)
1 (-0.624317586422+0j)
2 (0.299283236265+0j)
3 (3.00651912255e-08+0j)
4 (0.299281418324+0j)
5 (-5.44629513472e-14+0j)
1 (-2.9753928743e-07+0j)
2 (-0.495364636183+0j)
3 (1.61749496311e-14+0j)
4 (0.495365083218+0j)
5 (2.86656725024e-08+0j)
1 (2.31630860326e-12+0j)
2 (-2.07712407274e-08+0j)
3 (6.79555596435e-05+0j)
4 (2.07689296872e-08+0j)
5 (-0.686951518059+0j)
1 (-2.55608547661e-08+0j)
2 (1.27339729872e-08+0j)
3 (-0.749936163425+0j)
4 (1.27377095538e-08+0j)
5 (-6.18639533059e-05+0j)
3 8
1 (-7.42354511196e-10+0j)
2 (-0.407458901405+0j)
3 (-0.132825627923+0j)
4 (-1.12258624618e-09+0j)
5 (0.230060741305+0j)
1 (-0.529840826988+0j)
2 (1.02242869726e-09+0j)
3 (1.47169805231e-08+0j)
4 (0.529840826988+0j)
5 (8.58095106082e-09+0j)
1 (-5.59593660299e-09+0j)
2 (-0.46026712656+0j)
3 (-0.189698129892+0j)
4 (-3.64733043767e-09+0j)
5 (0.328566819429+0j)
1 (-5.92653073284e-08+0j)
2 (-0.511403858662+0j)
3 (0.342116594315+0j)
4 (-5.81566510505e-08+0j)
5 (-0.592563331127+0j)
1 (9.17969966707e-09+0j)
2 (3.7528921637e-10+0j)
3 (0.743389487267+0j)
4 (-7.80711495452e-09+0j)
5 (0.429196119308+0j)
1 (-0.60352396965+0j)
2 (5.06060757743e-07+0j)
3 (1.02901012156e-07+0j)
4 (-0.60352396965+0j)
5 (-1.76288821763e-07+0j)
3 7
1 (-0.157831609249+0j)
2 (0.157831639051+0j)
3 (1.93573299612e-08+0j)
4 (0.157831639051+0j)
5 (5.40782289825e-14+0j)
1 (-1.07380124348e-07+0j)
2 (-0.227066069841+0j)
3 (-1.22580686934e-07+0j)
4 (0.227065965533+0j)
5 (0.299297988415+0j)
1 (0.115845791996+0j)
2 (0.057922616601+0j)
3 (0.13223952055+0j)
4 (0.0579231306911+0j)
5 (3.36705625159e-07+0j)
1 (0.159106343985+0j)
2 (0.0795532241464+0j)
3 (-0.240490317345+0j)
4 (0.0795530825853+0j)
5 (1.18692518924e-07+0j)
1 (3.98122104173e-08+0j)
2 (-0.241537705064+0j)
3 (-6.01558127755e-08+0j)
4 (0.241537734866+0j)
5 (-0.421558618546+0j)
3 7
1 (7.91286647317e-10+0j)
2 (3.03037844818e-10+0j)
3 (0.204362645745+0j)
4 (4.89190632447e-10+0j)
5 (-0.353966474533+0j)
1 (9.13699960137e-09+0j)
2 (1.0438577086e-10+0j)
3 (-0.42577791214+0j)
4 (-6.95880419954e-09+0j)
5 (-0.245822981+0j)
1 (0.368288576603+0j)
2 (1.67113629601e-08+0j)
3 (-1.44080747333e-10+0j)
4 (0.365979760885+0j)
5 (1.25375620996e-09+0j)
1 (0.365983724594+0j)
2 (-2.74820233237e-09+0j)
3 (1.77222470032e-09+0j)
4 (-0.368292748928+0j)
5 (7.90098320103e-10+0j)
1 (-3.99936368467e-08+0j)
2 (0.546248733997+0j)
3 (-2.91795543284e-09+0j)
4 (-2.16134438347e-07+0j)
5 (1.55786352707e-08+0j)

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

34
python/converters/vasp/test/_plotools/test_consistency.py Normal file
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import vaspio
from inpconf import ConfigParameters
import mytest
################################################################################
#
# TestDataConsistency
#
################################################################################
class TestDataConsistency(mytest.MyTestCase):
"""
Function:
def read_plocar(filename)
Scenarios:
- **if** file PLOCAR does not exist **raise** IOError
- **if** PLOCAR is truncated **raise** IOError
- **if** the precision flag is not 4 or 8 **raise** ValueError
- **if** PLOCAR with prec=8 is read **compare** the output
- **if** PLOCAR with prec=4 is read **compare** the output
"""
# Scenario 1
def test_example(self):
conf_file = 'example.cfg'
pars = ConfigParameters(conf_file)
pars.parse_input()
vasp_data = vaspio.VaspData('./')
print pars.shells
print pars.groups

10
python/converters/vasp/test/_plotools/test_plotools.py Normal file
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r"""
Test suite for module `plotools`.
"""
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)

79
python/converters/vasp/test/_plotools/test_projgroups.py Normal file
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import numpy as np
import vaspio
from inpconf import ConfigParameters
from plotools import ProjectorShell, ProjectorGroup
import mytest
################################################################################
#
# TestProjectorGroup
#
################################################################################
class TestProjectorGroup(mytest.MyTestCase):
"""
Class:
ProjectorGroup(sh_pars, proj_raw)
Scenarios:
- test output for a correct input
- test the output of 'orthogonalization()' (sanity check)
"""
def setUp(self):
conf_file = 'example.cfg'
self.pars = ConfigParameters(conf_file)
self.pars.parse_input()
self.vasp_data = vaspio.VaspData('./')
efermi = self.vasp_data.doscar.efermi
eigvals = self.vasp_data.eigenval.eigs - efermi
self.shells = [ProjectorShell(self.pars.shells[0], self.vasp_data.plocar.plo)]
self.proj_gr = ProjectorGroup(self.pars.groups[0], self.shells, eigvals)
# Scenario 1
def test_example(self):
# proj_sh.select_projectors(ib_win, nb_min, nb_max)
#
testout = 'projgroups.out.test'
nion, ns, nk, nlm, nbtot = self.proj_gr.shells[0].proj_win.shape
with open(testout, 'wt') as f:
f.write("pars: %s\n"%(self.pars.groups[0]))
for ion in xrange(nion):
for isp in xrange(ns):
for ik in xrange(nk):
ib1 = self.proj_gr.ib_win[ik, 0, 0]
ib2 = self.proj_gr.ib_win[ik, 0, 1]
f.write("%i %i\n"%(ib1, ib2))
ib1w = ib1 - self.proj_gr.nb_min
ib2w = ib2 - self.proj_gr.nb_min + 1
for ib in xrange(ib1w, ib2w):
for ilm in xrange(nlm):
p = self.proj_gr.shells[0].proj_win[ion, isp, ik, ilm, ib]
f.write("%5i %s\n"%(ilm+1, p))
# Scenario 2
def test_ortho(self):
self.proj_gr.orthogonalize()
testout = 'projortho.out.test'
nion, ns, nk, nlm, nbtot = self.proj_gr.shells[0].proj_win.shape
with open(testout, 'wt') as f:
f.write("pars: %s\n"%(self.pars.groups[0]))
for ion in xrange(nion):
for isp in xrange(ns):
for ik in xrange(nk):
ib1 = self.proj_gr.ib_win[ik, 0, 0]
ib2 = self.proj_gr.ib_win[ik, 0, 1]
f.write("%i %i\n"%(ib1, ib2))
ib1w = ib1 - self.proj_gr.nb_min
ib2w = ib2 - self.proj_gr.nb_min + 1
for ib in xrange(ib1w, ib2w):
for ilm in xrange(nlm):
p = self.proj_gr.shells[0].proj_win[ion, isp, ik, ilm, ib]
f.write("%5i %s\n"%(ilm+1, p))
expected_file = 'projortho.out'
self.assertFileEqual(testout, expected_file)

86
python/converters/vasp/test/_plotools/test_projshells.py Normal file
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@ -0,0 +1,86 @@
import numpy as np
import vaspio
import elstruct
from inpconf import ConfigParameters
from plotools import select_bands, ProjectorShell
import mytest
################################################################################
#
# TestProjectorShell
#
################################################################################
class TestProjectorShell(mytest.MyTestCase):
"""
Class:
ProjectorShell(sh_pars, proj_raw)
Scenarios:
- compare output for a correct input
- test density matrix
"""
# Scenario 1
def test_example(self):
conf_file = 'example.cfg'
pars = ConfigParameters(conf_file)
pars.parse_input()
vasp_data = vaspio.VaspData('./')
efermi = vasp_data.doscar.efermi
eigvals = vasp_data.eigenval.eigs - efermi
emin = pars.groups[0]['emin']
emax = pars.groups[0]['emax']
ib_win, nb_min, nb_max = select_bands(eigvals, emin, emax)
proj_sh = ProjectorShell(pars.shells[0], vasp_data.plocar.plo)
proj_sh.select_projectors(ib_win, nb_min, nb_max)
testout = 'projshells.out.test'
nion, ns, nk, nlm, nbtot = proj_sh.proj_win.shape
with open(testout, 'wt') as f:
f.write("pars: %s\n"%(pars.shells[0]))
for ion in xrange(nion):
for isp in xrange(ns):
for ik in xrange(nk):
ib1 = ib_win[ik, 0, 0]
ib2 = ib_win[ik, 0, 1]
f.write("%i %i\n"%(ib1, ib2))
for ib in xrange(ib2 - nb_min + 1):
for ilm in xrange(nlm):
p = proj_sh.proj_win[ion, isp, ik, ilm, ib]
f.write("%5i %s\n"%(ilm+1, p))
expected_file = 'projshells.out'
self.assertFileEqual(testout, expected_file)
# Scenario 2
def test_dens_mat(self):
conf_file = 'example.cfg'
pars = ConfigParameters(conf_file)
pars.parse_input()
vasp_data = vaspio.VaspData('./')
el_struct = elstruct.ElectronicStructure(vasp_data)
efermi = el_struct.efermi
eigvals = el_struct.eigvals - efermi
emin = pars.groups[0]['emin']
emax = pars.groups[0]['emax']
ib_win, nb_min, nb_max = select_bands(eigvals, emin, emax)
proj_sh = ProjectorShell(pars.shells[0], vasp_data.plocar.plo)
proj_sh.select_projectors(ib_win, nb_min, nb_max)
dens_mat = proj_sh.density_matrix(el_struct)
print dens_mat
testout = 'densmat.out.test'
with open(testout, 'wt') as f:
f.write("density matrix: %s\n"%(dens_mat))
expected_file = 'densmat.out'
self.assertFileEqual(testout, expected_file)

73
python/converters/vasp/test/_plotools/test_select_bands.py Normal file
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import numpy as np
import vaspio
from inpconf import ConfigParameters
from plotools import select_bands
import mytest
################################################################################
#
# TestSelectBands
#
################################################################################
class TestSelectBands(mytest.MyTestCase):
"""
Function:
def select_bands(eigvals, emin, emax)
Scenarios:
- compare output for a correct input
- **if** emin > max(eigvals) **raise** Exception
- **if** emax > min(eigvals) **raise** Exception
"""
# Scenario 1
def test_example(self):
conf_file = 'example.cfg'
pars = ConfigParameters(conf_file)
pars.parse_input()
vasp_data = vaspio.VaspData('./')
efermi = vasp_data.doscar.efermi
eigvals = vasp_data.eigenval.eigs - efermi
emin = pars.groups[0]['emin']
emax = pars.groups[0]['emax']
ib_win, nb_min, nb_max = select_bands(eigvals, emin, emax)
nb_min_exp = 3
nb_max_exp = 8
ib_win_exp = np.array([[[3, 8]], [[3, 8]], [[3, 7]], [[3, 7]]])
self.assertEqual(nb_min, nb_min_exp)
self.assertEqual(nb_max, nb_max_exp)
self.assertEqual(ib_win, ib_win_exp)
# Scenario 2
def test_emin_too_large(self):
conf_file = 'example.cfg'
pars = ConfigParameters(conf_file)
pars.parse_input()
vasp_data = vaspio.VaspData('./')
efermi = vasp_data.doscar.efermi
eigvals = vasp_data.eigenval.eigs - efermi
emin = 20.0
emax = 25.0
with self.assertRaisesRegexp(Exception, "Energy window does not overlap"):
ib_win, nb_min, nb_max = select_bands(eigvals, emin, emax)
# Scenario 3
def test_emax_too_small(self):
conf_file = 'example.cfg'
pars = ConfigParameters(conf_file)
pars.parse_input()
vasp_data = vaspio.VaspData('./')
efermi = vasp_data.doscar.efermi
eigvals = vasp_data.eigenval.eigs - efermi
emin = -50.0
emax = -55.0
with self.assertRaisesRegexp(Exception, "Energy window does not overlap"):
ib_win, nb_min, nb_max = select_bands(eigvals, emin, emax)

2
python/converters/vasp/test/_vaspio/.gitignore vendored Normal file
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*.pyc
*.test

609
python/converters/vasp/test/_vaspio/DOSCAR.example Normal file
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50
python/converters/vasp/test/_vaspio/EIGENVAL.example Normal file
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52
python/converters/vasp/test/_vaspio/EIGENVAL.example.out Normal file
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nktot = 4
nband = 9
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kwghts:
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eigs:
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[ -0.81347 ]
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[ 3.978315]
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122
python/converters/vasp/test/_vaspio/IBZKPT.example Normal file
View File

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Automatically generated mesh
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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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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)

1
python/converters/vasp/test/run_all.sh Executable file
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PYTHONPATH=$HOME/Codes/vasp/vasp5.3/plo_vasp/plovasp/python:$HOME/Codes/vasp/vasp5.3/plo_vasp/plovasp/c:$PYTHONPATH python test_all.py

10
python/converters/vasp/test/test_all.py Normal file
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r"""
Searches and runs all available test suites.
"""
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)