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Added documentation on the output file formats

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A description of the output file formats is added to the documentation.
In particular, the outline of JSON headers for projector-group (*.plog<Ng>)
and control (*.ctrl) files are given.
This commit is contained in:
Oleg E. Peil 2015-08-10 13:52:29 +02:00 committed by Michel Ferrero
parent db16a8438d
commit 4bbafa239e
71 changed files with 58 additions and 8183 deletions
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55
python/converters/vasp/doc/source/plotools.rst
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@ -72,7 +72,7 @@ Consistency with parameters
Selecting projector subsets
---------------------------
===========================
The first step of PLO processing is to select subsets of projectors
corresponding to PLO groups. Each group contains a set of shells.
@ -117,7 +117,7 @@ The class is using a helper function `select_bands()` for selecting a subset of
.. _ortho:
Orthogonalization
=================
-----------------
At the second stage the selected projectors are orthogonalized (orthonormalized).
Orthogonalization can be performed in different ways if projection is made
@ -138,3 +138,54 @@ The way the normalization of a PLO group is done is controlled by two group para
(False by default)
Storing generated projectors
****************************
After the PLOs are generated they are stored to text files which can be subsequently
converted to TRIQS h5-files (using the converter). The general format of the file
is a JSON-header containing all necessary parameters followed by a set of arrays.
There is always one (control) file containing general information (`k`-kpoints, lattice vectors etc.)
and `at least` one file containing correlated groups (one file for each group).
Control file format
===================
Filename '<namebase>.ctrl'. Contains the data shared between all shells.
The JSON-header consists of the following elements:
* *nk*: number of `k`-points
* *ns*: number of spin channels
* *nc_flag*: collinear/noncollinear case (False/True)
* *ng*: number of projector groups
* Symmetry information (list of symmetry operations)
* *efermi*: Fermi level (optional)
* Lattice information
Projector-group file format
===========================
Projector-group files have names '<namebase>.plog<Ng>'.
They essentially contain serialized objects of class 'ProjectorGroup'.
The JSON-header has, thus, the following elements:
* *shells*: list of shells
* each shell is a dictionary:
- *lshell*: orbital number `l`
- *nion*: number of ions
- *ndim*: number of orbitals/ion
- *nbmax*: maxmimum number of bands (needed for array allocations)
* *emin*, *emax*: energy window

5
python/converters/vasp/python/plotools.py
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@ -2,6 +2,9 @@
import itertools as it
import numpy as np
# 'simplejson' is supposed to be faster than 'json' in stdlib.
import simplejson as json
class Projector:
"""
Class describing a local-orbital projector.
@ -394,11 +397,13 @@ def plo_output(conf_pars, pshells, pgroups):
# Projected shells
Nshells
# Shells: <shell indices>
# Shell <1>
Shell 1
ndim
# complex arrays: plo(ns, nion, ndim, nb)
...
# Shells: <shell indices>
# Shell <2>
Shell 2
...

0
python/converters/vasp/test/inpconf/.gitignore → python/converters/vasp/test/.gitignore vendored
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20
python/converters/vasp/test/adv_example.cfg
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@ -1,20 +0,0 @@
[General]
EFERMI = -0.6
[Group 1]
SHELLS = 1 2
EMIN = -7.6
EMAX = 2.7
[Shell 1]
# Ni shell
IONS = 5 6 7 8
LSHELL = 2
RTRANSFORM =
0.0 0.0 0.0 0.0 1.0
0.0 0.0 1.0 0.0 0.0
[Shell 2]
# Oxygen shell
IONS = 9..20
LSHELL = 1

27
python/converters/vasp/test/inpconf/arraytest.py
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@ -1,27 +0,0 @@
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
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@ -1,29 +0,0 @@
[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

7
python/converters/vasp/test/inpconf/example_nogroup.cfg
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@ -1,7 +0,0 @@
[Shell 1]
LSHELL = 2
IONS = 5..8
EMIN = -7.6
EMAX = 3.0

10
python/converters/vasp/test/inpconf/input_test_1.cfg
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@ -1,10 +0,0 @@
[General]
EFERMI = 0.7
[Shell 1]
LSHELL = 2
IONS = 5..8
[Shell 2]
IONS = 9..20
LSHELL = 1

3
python/converters/vasp/test/inpconf/input_test_2.cfg
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@ -1,3 +0,0 @@
[Shell 1]
LSHELL = 2
IONS = 1..4

25
python/converters/vasp/test/inpconf/input_test_3.cfg
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@ -1,25 +0,0 @@
[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
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@ -1,24 +0,0 @@
[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
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@ -1,13 +0,0 @@
[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
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@ -1,4 +0,0 @@
[General]
[Group 1]

5
python/converters/vasp/test/inpconf/parse_shells_2.cfg
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@ -1,5 +0,0 @@
[General]
[Group 1]
[Shell x]

7
python/converters/vasp/test/inpconf/parse_shells_3.cfg
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@ -1,7 +0,0 @@
[General]
[Group 1]
[Shell 1]
LSHELL = 2

17
python/converters/vasp/test/inpconf/parse_shells_4.cfg
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@ -1,17 +0,0 @@
[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
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@ -1 +0,0 @@
PYTHONPATH=../../python:../../c:$PYTHONPATH python $1

12
python/converters/vasp/test/inpconf/test1.cfg
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@ -1,12 +0,0 @@
[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
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@ -1,44 +0,0 @@
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)

9
python/converters/vasp/test/inpconf/test_inpconf.py
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@ -1,9 +0,0 @@
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
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@ -1,107 +0,0 @@
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
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@ -1,48 +0,0 @@
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
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@ -1,76 +0,0 @@
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
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@ -1,149 +0,0 @@
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)

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

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python/converters/vasp/test/plocar_io/PLOCAR.example
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python/converters/vasp/test/plocar_io/PLOCAR.example.out
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259
python/converters/vasp/test/plocar_io/PLOCAR.noprec
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@ -1,259 +0,0 @@
0000000: 0700 0000 0100 0000 0100 0000 0300 0000 ................
0000010: 0900 0000 0900 0000 0000 0000 0900 0000 ................
0000020: 0000 0000 0000 0040 c09b 42b4 952c 303e .......@..B..,0>
0000030: 0000 0000 0000 0000 876a f460 f6ec d93f .........j.`...?
0000040: 0000 0000 0000 0000 80ab 01a5 b7c9 d93f ...............?
0000050: 0000 0000 0000 0000 dc82 5188 ebf7 d93f ..........Q....?
0000060: 0000 0000 0000 0000 389e aae4 5c59 a4be ........8...\Y..
0000070: 0000 0000 0000 0000 f0cb ad9d 48d2 9bbe ............H...
0000080: 0000 0000 0000 0000 08ee b871 1214 773e ...........q..w>
0000090: 0000 0000 0000 0000 5095 ab03 b4cc 99be ........P.......
00000a0: 0000 0000 0000 0000 00e2 0cec 4018 8e3e ............@..>
00000b0: 0000 0000 0000 0000 0000 0000 0000 0040 ...............@
00000c0: 68c3 e962 e8c3 42be 0000 0000 0000 0000 h..b..B.........
00000d0: c907 d02d 79b5 c83f 0000 0000 0000 0000 ...-y..?........
00000e0: 6d5c b47d afec e4bf 0000 0000 0000 0000 m\.}............
00000f0: 8871 d914 bb3d dd3f 0000 0000 0000 0000 .q...=.?........
0000100: a09e cab7 fba1 99be 0000 0000 0000 0000 ................
0000110: 1011 02ea 4ed4 a5be 0000 0000 0000 0000 ....N...........
0000120: b8bd 64b5 faea a5be 0000 0000 0000 0000 ..d.............
0000130: 98d6 110d 5dec 733e 0000 0000 0000 0000 ....].s>........
0000140: 20bf c505 81ca 953e 0000 0000 0000 0000 ......>........
0000150: 0000 0000 0000 0040 5ede f7c4 28c9 513e .......@^...(.Q>
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BIN
python/converters/vasp/test/plocar_io/PLOCAR.trunc
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56
python/converters/vasp/test/plocar_io/mytest.py
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@ -1,56 +0,0 @@
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
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@ -1 +0,0 @@
PYTHONPATH=../../python:../../c:$PYTHONPATH python $1

93
python/converters/vasp/test/plocar_io/test_fileio.py
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@ -1,93 +0,0 @@
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
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@ -1,10 +0,0 @@
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
View File

@ -1,2 +0,0 @@
*.pyc
*.test

609
python/converters/vasp/test/plotools/DOSCAR
View File

@ -1,609 +0,0 @@
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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50
python/converters/vasp/test/plotools/EIGENVAL
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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

7
python/converters/vasp/test/plotools/IBZKPT
View File

@ -1,7 +0,0 @@
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

1835
python/converters/vasp/test/plotools/OUTCAR
View File

File diff suppressed because it is too large Load Diff

BIN
python/converters/vasp/test/plotools/PLOCAR
View File

Binary file not shown.

10
python/converters/vasp/test/plotools/POSCAR
View File

@ -1,10 +0,0 @@
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/plotools/densmat.out
View File

@ -1,10 +0,0 @@
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
View File

@ -1,8 +0,0 @@
[Shell 1]
LSHELL = 2
IONS = 1
EMIN = -15.0
EMAX = 5.0

56
python/converters/vasp/test/plotools/mytest.py
View File

@ -1,56 +0,0 @@
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
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@ -1,115 +0,0 @@
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)
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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)
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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
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@ -1,115 +0,0 @@
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)
1 (-5.59593660299e-09+0j)
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4 (-3.64733043767e-09+0j)
5 (0.328566819429+0j)
1 (-5.92653073284e-08+0j)
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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)
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3 (1.02901012156e-07+0j)
4 (-0.60352396965+0j)
5 (-1.76288821763e-07+0j)
3 7
1 (-0.157831609249+0j)
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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
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@ -1,115 +0,0 @@
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)
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1 (-1.07380124348e-07+0j)
2 (-0.227066069841+0j)
3 (-1.22580686934e-07+0j)
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5 (0.299297988415+0j)
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5 (3.36705625159e-07+0j)
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2 (0.0795532241464+0j)
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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
View File

@ -1 +0,0 @@
PYTHONPATH=../../python:../../c:$PYTHONPATH python $1

34
python/converters/vasp/test/plotools/test_consistency.py
View File

@ -1,34 +0,0 @@
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
View File

@ -1,10 +0,0 @@
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
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@ -1,79 +0,0 @@
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
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@ -1,86 +0,0 @@
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
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@ -1,73 +0,0 @@
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
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@ -1,2 +0,0 @@
*.pyc
*.test

609
python/converters/vasp/test/vaspio/DOSCAR.example
View File

@ -1,609 +0,0 @@
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50
python/converters/vasp/test/vaspio/EIGENVAL.example
View File

@ -1,50 +0,0 @@
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
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2 -31.322999
3 -31.105684
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1 -31.750021
2 -31.750021
3 -31.217560
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6 4.708263
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52
python/converters/vasp/test/vaspio/EIGENVAL.example.out
View File

@ -1,52 +0,0 @@
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
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@ -1,122 +0,0 @@
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
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@ -1,122 +0,0 @@
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
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@ -1,7 +0,0 @@
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
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@ -1,6 +0,0 @@
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
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@ -1,10 +0,0 @@
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
View File

@ -1,10 +0,0 @@
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
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@ -1,56 +0,0 @@
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
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@ -1 +0,0 @@
PYTHONPATH=../../python:../../c:$PYTHONPATH python $1

32
python/converters/vasp/test/vaspio/test_doscar.py
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@ -1,32 +0,0 @@
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
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@ -1,45 +0,0 @@
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
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@ -1,57 +0,0 @@
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
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@ -1,43 +0,0 @@
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
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@ -1,11 +0,0 @@
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)