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Added several tests

Browse Source 
Tests for 'select_bands()' and class 'ProjectorShell' have been added.
The function and class methods have been fixed accordingly to pass
the tests.
This commit is contained in:
Oleg E. Peil 2015-02-19 16:18:01 +01:00 committed by Michel Ferrero
parent 90c93c4693
commit 5c3b3d0b8d
17 changed files with 2881 additions and 5 deletions
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18
python/converters/vasp/python/plotools.py
View File

@ -93,7 +93,13 @@ def select_bands(eigvals, emin, emax):
ib_win, nb_min, nb_max :
"""
# Sanity check
if emin > eigvals.max() or emax < eigvals.min():
raise Exception("Energy window does not overlap with the band structure")
nk, nband, ns_band = eigvals.shape
print nk, nband, ns_band
print emin, emax
ib_win = np.zeros((nk, ns_band, 2), dtype=np.int32)
nb_min = 10000000
@ -105,11 +111,14 @@ def select_bands(eigvals, emin, emax):
if en >= emin:
break
ib1 = ib
for ib in xrange(ib1, nb_max):
for ib in xrange(ib1, nband):
en = eigvals[ik, ib, isp]
if en <= emax:
if en > emax:
break
ib2 = ib
else:
# If we reached the last band add 1 to get the correct bound
ib += 1
ib2 = ib - 1
ib_win[ik, isp, 0] = ib1
ib_win[ik, isp, 1] = ib2
@ -248,7 +257,7 @@ class ProjectorShell:
self.lm2 = (self.lorb+1)**2
# Pre-select a subset of projectors (this should be an array view => no memory is wasted)
self.proj_arr = proj_raw[self.ion_list, :, :, :, lm1:lm2]
self.proj_arr = proj_raw[self.ion_list, :, :, :, self.lm1:self.lm2]
################################################################################
#
@ -282,6 +291,7 @@ class ProjectorShell:
self.proj_win[:, isp, ik, ib1_win:ib2_win, :] = self.proj_arr[:, isp, ik, ib1:ib2, :]
# !!! This sucks but I have to change the order of 'ib' and 'ilm' indices here
# This should perhaps be done right after the projector array is read from PLOCAR
self.proj_win.transpose((0, 1, 2, 4, 3))

2
python/converters/vasp/python/vaspio.py
View File

@ -271,7 +271,7 @@ class Kpoints:
line = ibz_file.next()
self.itet[it, :] = map(int, line.split()[:5])
except StopIteration, ValueError:
print " Error reading tetrahedra. No tetrahedron data is used"
print " No tetrahedron data found in %s. Skipping..."%(ibz_filename)
self.ntet = 0
# data = { 'nktot': nktot,

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
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python/converters/vasp/test/plotools/EIGENVAL Normal file
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@ -0,0 +1,50 @@
1 1 1 1
0.1333597E+02 0.2587511E-09 0.2587511E-09 0.2587511E-09 0.5000000E-15
1.000000000000000E-004
CAR
V
11 4 9
0.0000000E+00 0.0000000E+00 0.0000000E+00 0.3703704E-01
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0.3333333E+00 0.0000000E+00 0.0000000E+00 0.4444444E+00
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0.3333333E+00 0.3333333E+00 0.0000000E+00 0.2962963E+00
1 -31.750021
2 -31.750021
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7
python/converters/vasp/test/plotools/IBZKPT Normal file
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Automatically generated mesh
4
Reciprocal lattice
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0.33333333333333 0.00000000000000 0.00000000000000 12
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1835
python/converters/vasp/test/plotools/OUTCAR Normal file
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BIN
python/converters/vasp/test/plotools/PLOCAR Normal file
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10
python/converters/vasp/test/plotools/POSCAR Normal file
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@ -0,0 +1,10 @@
V SF test
2.9878
-0.5 0.5 0.5
0.5 -0.5 0.5
0.5 0.5 -0.5
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Direct
0.0 0.0 0.0

8
python/converters/vasp/test/plotools/example.cfg Normal file
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[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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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/projshells.out Normal file
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@ -0,0 +1,115 @@
pars: {'ion_list': array([0]), 'user_index': 1, 'lshell': 2}
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3 (-1.39707700703e-12+0j)
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5 (-9.58669992349e-14+0j)
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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)

56
python/converters/vasp/test/plotools/test_projshells.py Normal file
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import numpy as np
import vaspio
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
"""
# 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, nbtot, nlm = 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, ib, ilm]
f.write("%5i %s\n"%(ilm+1, p))
expected_file = 'projshells.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)