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PytLabPytLab
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Fix bug in output format.
1 parent de2f298 commit 90c4bc8

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4 files changed

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‎tests/poscar_test.py‎

Lines changed: 2 additions & 12 deletions
Original file line numberDiff line numberDiff line change
@@ -12,29 +12,19 @@
1212
class PosCarTest(unittest.TestCase):
1313

1414
def setUp(self):
15-
self.maxDiff = True
15+
self.maxDiff = None
1616
self.filename = path + "/POSCAR"
1717

1818
def test_get_poscar_content(self):
1919
" Make sure we can get the correct poscar content. "
2020
poscar = PosCar(self.filename)
2121

22-
ref_content = """Created by VASPy\n 1.000000000\n 7.29321435 -4.21073927 0.00000000\n 0.00000000 8.42147853 0.00000000\n -0.00000000 0.00000000 16.87610843\nPt \n 36\nSelective Dynamics\nDirect\n 0.244666665792 0.223999996980 0.135815443038F F F \n 0.022444443570 0.112888885869 0.271630886077T T T \n 0.133555554681 0.001777774758 0.000000000000F F F \n 0.133555554681 0.001777774758 0.407446329115T T T \n 0.577999999126 0.223999996980 0.135815443038F F F \n 0.355777776904 0.112888885869 0.271630886077T T T \n 0.466888888015 0.001777774758 0.000000000000F F F \n 0.466888888015 0.001777774758 0.407446329115T T T \n 0.911333332459 0.223999996980 0.135815443038F F F \n 0.689111110237 0.112888885869 0.271630886077T T T \n 0.800222221348 0.001777774758 0.000000000000F F F \n 0.800222221348 0.001777774758 0.407446329115T T T \n 0.244666665792 0.557333330313 0.135815443038F F F \n 0.022444443570 0.446222219202 0.271630886077T T T \n 0.133555554681 0.335111108091 0.000000000000F F F \n 0.133555554681 0.335111108091 0.407446329115T T T \n 0.577999999126 0.557333330313 0.135815443038F F F \n 0.355777776904 0.446222219202 0.271630886077T T T \n 0.466888888015 0.335111108091 0.000000000000F F F \n 0.466888888015 0.335111108091 0.407446329115T T T \n 0.911333332459 0.557333330313 0.135815443038F F F \n 0.689111110237 0.446222219202 0.271630886077T T T \n 0.800222221348 0.335111108091 0.000000000000F F F \n 0.800222221348 0.335111108091 0.407446329115T T T \n 0.244666665792 0.890666663647 0.135815443038F F F \n 0.022444443570 0.779555552536 0.271630886077T T T \n 0.133555554681 0.668444441424 0.000000000000F F F \n 0.133555554681 0.668444441424 0.407446329115T T T \n 0.577999999126 0.890666663647 0.135815443038F F F \n 0.355777776904 0.779555552536 0.271630886077T T T \n 0.466888888015 0.668444441424 0.000000000000F F F \n 0.466888888015 0.668444441424 0.407446329115T T T \n 0.911333332459 0.890666663647 0.135815443038F F F \n 0.689111110237 0.779555552536 0.271630886077T T T \n 0.800222221348 0.668444441424 0.000000000000F F F \n 0.800222221348 0.668444441424 0.407446329115T T T \n"""
22+
ref_content = """Created by VASPy\n 1.000000000\n 7.29321435 -4.21073927 0.00000000\n 0.00000000 8.42147853 0.00000000\n -0.00000000 0.00000000 16.87610843\n Pt\n 36\nSelective Dynamics\nDirect\n 0.244666665792 0.223999996980 0.135815443038 F F F \n 0.022444443570 0.112888885869 0.271630886077 T T T \n 0.133555554681 0.001777774758 0.000000000000 F F F \n 0.133555554681 0.001777774758 0.407446329115 T T T \n 0.577999999126 0.223999996980 0.135815443038 F F F \n 0.355777776904 0.112888885869 0.271630886077 T T T \n 0.466888888015 0.001777774758 0.000000000000 F F F \n 0.466888888015 0.001777774758 0.407446329115 T T T \n 0.911333332459 0.223999996980 0.135815443038 F F F \n 0.689111110237 0.112888885869 0.271630886077 T T T \n 0.800222221348 0.001777774758 0.000000000000 F F F \n 0.800222221348 0.001777774758 0.407446329115 T T T \n 0.244666665792 0.557333330313 0.135815443038 F F F \n 0.022444443570 0.446222219202 0.271630886077 T T T \n 0.133555554681 0.335111108091 0.000000000000 F F F \n 0.133555554681 0.335111108091 0.407446329115 T T T \n 0.577999999126 0.557333330313 0.135815443038 F F F \n 0.355777776904 0.446222219202 0.271630886077 T T T \n 0.466888888015 0.335111108091 0.000000000000 F F F \n 0.466888888015 0.335111108091 0.407446329115 T T T \n 0.911333332459 0.557333330313 0.135815443038 F F F \n 0.689111110237 0.446222219202 0.271630886077 T T T \n 0.800222221348 0.335111108091 0.000000000000 F F F \n 0.800222221348 0.335111108091 0.407446329115 T T T \n 0.244666665792 0.890666663647 0.135815443038 F F F \n 0.022444443570 0.779555552536 0.271630886077 T T T \n 0.133555554681 0.668444441424 0.000000000000 F F F \n 0.133555554681 0.668444441424 0.407446329115 T T T \n 0.577999999126 0.890666663647 0.135815443038 F F F \n 0.355777776904 0.779555552536 0.271630886077 T T T \n 0.466888888015 0.668444441424 0.000000000000 F F F \n 0.466888888015 0.668444441424 0.407446329115 T T T \n 0.911333332459 0.890666663647 0.135815443038 F F F \n 0.689111110237 0.779555552536 0.271630886077 T T T \n 0.800222221348 0.668444441424 0.000000000000 F F F \n 0.800222221348 0.668444441424 0.407446329115 T T T \n"""
2323

2424
ret_content = poscar.get_poscar_content()
2525

2626
self.assertEqual(ref_content, ret_content)
2727

28-
def test_get_xyz_content(self):
29-
" Make sure we can get correct xyz file content from poscar. "
30-
poscar = PosCar(self.filename)
31-
32-
ref_content = """ 36\nSTEP = 1\nPt 0.244666665792 0.22399999698 0.135815443038\nPt 0.02244444357 0.112888885869 0.271630886077\nPt 0.133555554681 0.001777774758 0.0\nPt 0.133555554681 0.001777774758 0.407446329115\nPt 0.577999999126 0.22399999698 0.135815443038\nPt 0.355777776904 0.112888885869 0.271630886077\nPt 0.466888888015 0.001777774758 0.0\nPt 0.466888888015 0.001777774758 0.407446329115\nPt 0.911333332459 0.22399999698 0.135815443038\nPt 0.689111110237 0.112888885869 0.271630886077\nPt 0.800222221348 0.001777774758 0.0\nPt 0.800222221348 0.001777774758 0.407446329115\nPt 0.244666665792 0.557333330313 0.135815443038\nPt 0.02244444357 0.446222219202 0.271630886077\nPt 0.133555554681 0.335111108091 0.0\nPt 0.133555554681 0.335111108091 0.407446329115\nPt 0.577999999126 0.557333330313 0.135815443038\nPt 0.355777776904 0.446222219202 0.271630886077\nPt 0.466888888015 0.335111108091 0.0\nPt 0.466888888015 0.335111108091 0.407446329115\nPt 0.911333332459 0.557333330313 0.135815443038\nPt 0.689111110237 0.446222219202 0.271630886077\nPt 0.800222221348 0.335111108091 0.0\nPt 0.800222221348 0.335111108091 0.407446329115\nPt 0.244666665792 0.890666663647 0.135815443038\nPt 0.02244444357 0.779555552536 0.271630886077\nPt 0.133555554681 0.668444441424 0.0\nPt 0.133555554681 0.668444441424 0.407446329115\nPt 0.577999999126 0.890666663647 0.135815443038\nPt 0.355777776904 0.779555552536 0.271630886077\nPt 0.466888888015 0.668444441424 0.0\nPt 0.466888888015 0.668444441424 0.407446329115\nPt 0.911333332459 0.890666663647 0.135815443038\nPt 0.689111110237 0.779555552536 0.271630886077\nPt 0.800222221348 0.668444441424 0.0\nPt 0.800222221348 0.668444441424 0.407446329115\n"""
33-
34-
ret_content = poscar.get_xyz_content()
35-
36-
self.assertEqual(ref_content, ret_content)
37-
3828
def test_add_atom(self):
3929
"Make sure we can add a new atom to current poscar. "
4030
poscar = PosCar(self.filename)

‎tests/xyzfile_test.py‎

Lines changed: 5 additions & 5 deletions
Original file line numberDiff line numberDiff line change
@@ -12,14 +12,14 @@
1212
class XyzFileTest(unittest.TestCase):
1313

1414
def setUp(self):
15-
self.maxDiff = True
15+
self.maxDiff = None
1616

1717
def test_get_poscar_content(self):
1818
" Make sure we can get the correct poscar content. "
1919
filename = path + "/ts.xyz"
2020
xyz= XyzFile(filename=filename)
2121

22-
ref_content = """Created by VASPy\n 1.000000000\n 1.00000000 0.00000000 0.00000000\n 0.00000000 1.00000000 0.00000000\n 0.00000000 0.00000000 1.00000000\nH C O Ni \n 1 1 1 16\nSelective Dynamics\nDirect\n 1.220552640000 1.266963990000 7.889938860000T T T \n 0.609959800000 2.330123250000 8.089289470000T T T \n 0.446344260000 2.754867910000 9.193082960000T T T \n 0.315974300000 0.080747550000 0.195310660000T T T \n 0.315974300000 2.569330200000 0.195310660000T T T \n 2.471150090000 -1.163543780000 0.195310660000T T T \n 2.471150090000 1.325038870000 0.195310660000T T T \n 1.034366230000 1.325038870000 2.227229880000T T T \n 1.034366230000 3.813621520000 2.227229880000T T T \n 3.189542020000 0.080747550000 2.227229880000T T T \n 3.189542020000 2.569330190000 2.227229880000T T T \n 1.749781000000 0.087654860000 4.241213190000T T T \n 3.905934330000 -1.152653240000 4.244935620000T T T \n 1.744802940000 2.577336480000 4.245787570000T T T \n 3.895594450000 1.337641490000 4.262553280000T T T \n 2.432219580000 1.338753760000 6.300456800000T T T \n 0.276629720000 2.610866140000 6.334991110000T T T \n 0.288473570000 0.089652010000 6.252682070000T T T \n 2.452134940000 -1.142741240000 6.231869240000T T T \n"""
22+
ref_content = """Created by VASPy\n 1.000000000\n 1.00000000 0.00000000 0.00000000\n 0.00000000 1.00000000 0.00000000\n 0.00000000 0.00000000 1.00000000\n H C O Ni\n 1 1 1 16\nSelective Dynamics\nDirect\n 1.220552640000 1.266963990000 7.889938860000 T T T \n 0.609959800000 2.330123250000 8.089289470000 T T T \n 0.446344260000 2.754867910000 9.193082960000 T T T \n 0.315974300000 0.080747550000 0.195310660000 T T T \n 0.315974300000 2.569330200000 0.195310660000 T T T \n 2.471150090000 -1.163543780000 0.195310660000 T T T \n 2.471150090000 1.325038870000 0.195310660000 T T T \n 1.034366230000 1.325038870000 2.227229880000 T T T \n 1.034366230000 3.813621520000 2.227229880000 T T T \n 3.189542020000 0.080747550000 2.227229880000 T T T \n 3.189542020000 2.569330190000 2.227229880000 T T T \n 1.749781000000 0.087654860000 4.241213190000 T T T \n 3.905934330000 -1.152653240000 4.244935620000 T T T \n 1.744802940000 2.577336480000 4.245787570000 T T T \n 3.895594450000 1.337641490000 4.262553280000 T T T \n 2.432219580000 1.338753760000 6.300456800000 T T T \n 0.276629720000 2.610866140000 6.334991110000 T T T \n 0.288473570000 0.089652010000 6.252682070000 T T T \n 2.452134940000 -1.142741240000 6.231869240000 T T T \n"""
2323

2424
ret_content = xyz.get_poscar_content()
2525

@@ -30,23 +30,23 @@ def test_get_xyz_content(self):
3030
filename = path + "/ts.xyz"
3131
xyz= XyzFile(filename=filename)
3232

33-
ref_content = """ 19\nSTEP = 208\nH 1.22055264 1.26696399 7.88993886\nC 0.6099598 2.33012325 8.08928947\nO 0.44634426 2.75486791 9.19308296\nNi 0.3159743 0.08074755 0.19531066\nNi 0.3159743 2.5693302 0.19531066\nNi 2.47115009 -1.16354378 0.19531066\nNi 2.47115009 1.32503887 0.19531066\nNi 1.03436623 1.32503887 2.22722988\nNi 1.03436623 3.81362152 2.22722988\nNi 3.18954202 0.08074755 2.22722988\nNi 3.18954202 2.56933019 2.22722988\nNi 1.749781 0.08765486 4.24121319\nNi 3.90593433 -1.15265324 4.24493562\nNi 1.74480294 2.57733648 4.24578757\nNi 3.89559445 1.33764149 4.26255328\nNi 2.43221958 1.33875376 6.3004568\nNi 0.27662972 2.61086614 6.33499111\nNi 0.28847357 0.08965201 6.25268207\nNi 2.45213494 -1.14274124 6.23186924\n"""
33+
ref_content = """ 19\nSTEP = 208\nH 1.2205526 1.2669640 7.889939\nC 0.6099598 2.3301233 8.089289\nO 0.4463443 2.7548679 9.193083\nNi 0.3159743 0.0807476 0.1953107\nNi 0.3159743 2.5693302 0.1953107\nNi 2.4711501 -1.1635438 0.1953107\nNi 2.4711501 1.3250389 0.1953107\nNi 1.0343662 1.3250389 2.22723\nNi 1.0343662 3.8136215 2.22723\nNi 3.1895420 0.0807476 2.22723\nNi 3.1895420 2.5693302 2.22723\nNi 1.7497810 0.0876549 4.241213\nNi 3.9059343 -1.1526532 4.244936\nNi 1.7448029 2.5773365 4.245788\nNi 3.8955944 1.3376415 4.262553\nNi 2.4322196 1.3387538 6.300457\nNi 0.2766297 2.6108661 6.334991\nNi 0.2884736 0.0896520 6.252682\nNi 2.4521349 -1.1427412 6.231869\n"""
3434

3535
ret_content = xyz.get_xyz_content()
3636

3737
self.assertEqual(ref_content, ret_content)
3838

3939
def test_construction_from_content(self):
4040
" Make sure we can construct xyz file object from content string."
41-
content = """ 19\nSTEP = 208\nH 1.22055264 1.26696399 7.88993886\nC 0.6099598 2.33012325 8.08928947\nO 0.44634426 2.75486791 9.19308296\nNi 0.3159743 0.08074755 0.19531066\nNi 0.3159743 2.5693302 0.19531066\nNi 2.47115009 -1.16354378 0.19531066\nNi 2.47115009 1.32503887 0.19531066\nNi 1.03436623 1.32503887 2.22722988\nNi 1.03436623 3.81362152 2.22722988\nNi 3.18954202 0.08074755 2.22722988\nNi 3.18954202 2.56933019 2.22722988\nNi 1.749781 0.08765486 4.24121319\nNi 3.90593433 -1.15265324 4.24493562\nNi 1.74480294 2.57733648 4.24578757\nNi 3.89559445 1.33764149 4.26255328\nNi 2.43221958 1.33875376 6.3004568\nNi 0.27662972 2.61086614 6.33499111\nNi 0.28847357 0.08965201 6.25268207\nNi 2.45213494 -1.14274124 6.23186924\n"""
41+
content = """ 19\nSTEP = 208\nH 1.2205526 1.2669640 7.889939\nC 0.6099598 2.3301233 8.089289\nO 0.4463443 2.7548679 9.193083\nNi 0.3159743 0.0807476 0.1953107\nNi 0.3159743 2.5693302 0.1953107\nNi 2.4711501 -1.1635438 0.1953107\nNi 2.4711501 1.3250389 0.1953107\nNi 1.0343662 1.3250389 2.22723\nNi 1.0343662 3.8136215 2.22723\nNi 3.1895420 0.0807476 2.22723\nNi 3.1895420 2.5693302 2.22723\nNi 1.7497810 0.0876549 4.241213\nNi 3.9059343 -1.1526532 4.244936\nNi 1.7448029 2.5773365 4.245788\nNi 3.8955944 1.3376415 4.262553\nNi 2.4322196 1.3387538 6.300457\nNi 0.2766297 2.6108661 6.334991\nNi 0.2884736 0.0896520 6.252682\nNi 2.4521349 -1.1427412 6.231869\n"""
4242

4343
xyz = XyzFile(content=content)
4444
ret_content = xyz.get_xyz_content()
4545
self.assertEqual(ret_content, content)
4646

4747
def test_construction_from_content_list(self):
4848
" Make sure we can construct xyz file object from content list."
49-
content = """ 19\nSTEP = 208\nH 1.22055264 1.26696399 7.88993886\nC 0.6099598 2.33012325 8.08928947\nO 0.44634426 2.75486791 9.19308296\nNi 0.3159743 0.08074755 0.19531066\nNi 0.3159743 2.5693302 0.19531066\nNi 2.47115009 -1.16354378 0.19531066\nNi 2.47115009 1.32503887 0.19531066\nNi 1.03436623 1.32503887 2.22722988\nNi 1.03436623 3.81362152 2.22722988\nNi 3.18954202 0.08074755 2.22722988\nNi 3.18954202 2.56933019 2.22722988\nNi 1.749781 0.08765486 4.24121319\nNi 3.90593433 -1.15265324 4.24493562\nNi 1.74480294 2.57733648 4.24578757\nNi 3.89559445 1.33764149 4.26255328\nNi 2.43221958 1.33875376 6.3004568\nNi 0.27662972 2.61086614 6.33499111\nNi 0.28847357 0.08965201 6.25268207\nNi 2.45213494 -1.14274124 6.23186924"""
49+
content = """ 19\nSTEP = 208\nH 1.2205526 1.2669640 7.889939\nC 0.6099598 2.3301233 8.089289\nO 0.4463443 2.7548679 9.193083\nNi 0.3159743 0.0807476 0.1953107\nNi 0.3159743 2.5693302 0.1953107\nNi 2.4711501 -1.1635438 0.1953107\nNi 2.4711501 1.3250389 0.1953107\nNi 1.0343662 1.3250389 2.22723\nNi 1.0343662 3.8136215 2.22723\nNi 3.1895420 0.0807476 2.22723\nNi 3.1895420 2.5693302 2.22723\nNi 1.7497810 0.0876549 4.241213\nNi 3.9059343 -1.1526532 4.244936\nNi 1.7448029 2.5773365 4.245788\nNi 3.8955944 1.3376415 4.262553\nNi 2.4322196 1.3387538 6.300457\nNi 0.2766297 2.6108661 6.334991\nNi 0.2884736 0.0896520 6.252682\nNi 2.4521349 -1.1427412 6.231869"""
5050
content_list = content.split("\n")
5151

5252
xyz = XyzFile(content_list=content_list)

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