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Added 'type_of_ion' list to class Poscar
A list 'type_of_ion' mapping ion index to their types is added to class Poscar. A corresponding test is also added.
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@ -173,7 +173,11 @@ class Poscar:
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# Read atomic positions
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self.q_types = []
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self.type_of_ion = []
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for it in xrange(self.ntypes):
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# Array mapping ion index to type
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self.type_of_ion += self.nions[it] * [it]
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q_at_it = np.zeros((self.nions[it], 3))
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for iq in xrange(self.nions[it]):
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sline = readline_remove_comments()
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28
python/converters/vasp/test/_vaspio/POSCAR.complex
Normal file
28
python/converters/vasp/test/_vaspio/POSCAR.complex
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@ -0,0 +1,28 @@
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NdNiO3
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1.0
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5.3871197701 0.0000000000 0.0000000000
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0.0000000000 5.3826699257 0.0000000000
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0.0000000000 0.0000000000 7.6093997955
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Nd Ni O
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4 4 12
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Direct
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0.995800018 0.035000000 0.250000000
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0.004199982 0.964999974 0.750000000
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0.495800018 0.465000004 0.750000000
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0.504199982 0.535000026 0.250000000
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0.500000000 0.000000000 0.000000000
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0.000000000 0.500000000 0.000000000
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0.500000000 0.000000000 0.500000000
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0.000000000 0.500000000 0.500000000
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0.069300003 0.489699990 0.250000000
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0.930700004 0.510300040 0.750000000
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0.569299996 0.010300010 0.750000000
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0.430700004 0.989699960 0.250000000
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0.716600001 0.287099987 0.039500002
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0.283399999 0.712900043 0.960500002
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0.216600001 0.212900013 0.960500002
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0.783399999 0.787099957 0.039500002
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0.283399999 0.712900043 0.539499998
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0.716600001 0.287099987 0.460500002
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0.783399999 0.787099957 0.460500002
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0.216600001 0.212900013 0.539499998
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@ -18,6 +18,7 @@ class TestPoscar(mytest.MyTestCase):
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Scenarios:
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- correct POSCAR file
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- check 'type_of_ion' array for a complex POSCAR file
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"""
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# Scenario 1
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@ -41,3 +42,12 @@ class TestPoscar(mytest.MyTestCase):
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expected = 'POSCAR.example.out'
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self.assertFileEqual(testout, expected)
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# Scenario 2
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def test_type_of_ion(self):
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filename = 'POSCAR.complex'
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poscar = Poscar()
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poscar.from_file(vasp_dir='./', poscar_filename=filename)
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test_types = 4 * [0] + 4 * [1] + 12 * [2]
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self.assertListEqual(test_types, poscar.type_of_ion)
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