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Added 'type_of_ion' list to class Poscar

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A list 'type_of_ion' mapping ion index to their types is added
to class Poscar. A corresponding test is also added.
This commit is contained in:
Oleg E. Peil 2015-09-16 11:02:30 +02:00 committed by Michel Ferrero
parent 529c7bc9d5
commit 0cec37f3fc
3 changed files with 42 additions and 0 deletions
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4
python/converters/vasp/python/vaspio.py
View File

@ -173,7 +173,11 @@ class Poscar:
# Read atomic positions # Read atomic positions
self.q_types = [] self.q_types = []
self.type_of_ion = []
for it in xrange(self.ntypes): for it in xrange(self.ntypes):
# Array mapping ion index to type
self.type_of_ion += self.nions[it] * [it]
q_at_it = np.zeros((self.nions[it], 3)) q_at_it = np.zeros((self.nions[it], 3))
for iq in xrange(self.nions[it]): for iq in xrange(self.nions[it]):
sline = readline_remove_comments() sline = readline_remove_comments()

28
python/converters/vasp/test/_vaspio/POSCAR.complex Normal file
View File

@ -0,0 +1,28 @@
NdNiO3
1.0
5.3871197701 0.0000000000 0.0000000000
0.0000000000 5.3826699257 0.0000000000
0.0000000000 0.0000000000 7.6093997955
Nd Ni O
4 4 12
Direct
0.995800018 0.035000000 0.250000000
0.004199982 0.964999974 0.750000000
0.495800018 0.465000004 0.750000000
0.504199982 0.535000026 0.250000000
0.500000000 0.000000000 0.000000000
0.000000000 0.500000000 0.000000000
0.500000000 0.000000000 0.500000000
0.000000000 0.500000000 0.500000000
0.069300003 0.489699990 0.250000000
0.930700004 0.510300040 0.750000000
0.569299996 0.010300010 0.750000000
0.430700004 0.989699960 0.250000000
0.716600001 0.287099987 0.039500002
0.283399999 0.712900043 0.960500002
0.216600001 0.212900013 0.960500002
0.783399999 0.787099957 0.039500002
0.283399999 0.712900043 0.539499998
0.716600001 0.287099987 0.460500002
0.783399999 0.787099957 0.460500002
0.216600001 0.212900013 0.539499998

10
python/converters/vasp/test/_vaspio/test_poscar.py
View File

@ -18,6 +18,7 @@ class TestPoscar(mytest.MyTestCase):
Scenarios: Scenarios:
- correct POSCAR file - correct POSCAR file
- check 'type_of_ion' array for a complex POSCAR file
""" """
# Scenario 1 # Scenario 1
@ -41,3 +42,12 @@ class TestPoscar(mytest.MyTestCase):
expected = 'POSCAR.example.out' expected = 'POSCAR.example.out'
self.assertFileEqual(testout, expected) self.assertFileEqual(testout, expected)
# Scenario 2
def test_type_of_ion(self):
filename = 'POSCAR.complex'
poscar = Poscar()
poscar.from_file(vasp_dir='./', poscar_filename=filename)
test_types = 4 * [0] + 4 * [1] + 12 * [2]
self.assertListEqual(test_types, poscar.type_of_ion)