Fix format bug in POSCAR/CONTCAR tofile method/

Author: PytLab

tests/poscar_test.py

@@ -19,7 +19,7 @@ def test_get_poscar_content(self):
         " Make sure we can get the correct poscar content. "
         poscar = PosCar(self.filename)
 
-        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"""
+        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"""
 
         ret_content = poscar.get_poscar_content()
 

tests/xyzfile_test.py

@@ -19,7 +19,7 @@ def test_get_poscar_content(self):
         filename = path + "/ts.xyz"
         xyz= XyzFile(filename=filename)
 
-        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"""
+        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"""
 
         ret_content = xyz.get_poscar_content()
 

vaspy/atomco.py

@@ -170,7 +170,7 @@ def get_poscar_content(self, **kwargs):
             tf = kwargs.get("tf", default_tf)
         data_tf = ''
         for data, tf in zip(self.data.tolist(), tf.tolist()):
-            data_tf += ("{:18.12f}"*3 + " " + "{:5s}"*3 + "\n").format(*(data+tf))
+            data_tf += ("{:18.12f}"*3 + "{:>5s}"*3 + "\n").format(*(data+tf))
 
         # merge all strings
         content += (bases_const + bases + atom_types + atom_numbers +