Skip to content

Commit

Permalink
Merge pull request #1656 from JaGeo/master
Browse files Browse the repository at this point in the history 
Extend grosspop class
  • Loading branch information
@shyuep
shyuep committed Nov 11, 2019
2 parents 0195ee6 + a51a970 commit c0b35b0
Show file tree
Hide file tree
Showing 3 changed files with 90 additions and 0 deletions.
21 changes: 21 additions & 0 deletions pymatgen/io/lobster.py
View file
Expand Up @@ -1885,3 +1885,24 @@ def __init__(self, filename: str = "GROSSPOP.lobster"):
smalldict["Loewdin GP"][cleanline[0]] = float(cleanline[2])
if 'total' in cleanline[0]:
self.list_dict_grosspop.append(smalldict)

def get_structure_with_total_grosspop(self, structure_filename: str) -> Structure:
"""
get a Structure with Mulliken and Loewdin total grosspopulations as site properties
Args:
structure_filename (str): filename of POSCAR
Returns:
Structure Object with Mulliken and Loewdin total grosspopulations as site properties
"""

struct = Structure.from_file(structure_filename)
site_properties = {} # type: Dict[str, Any]
mullikengp = []
loewdingp = []
for grosspop in self.list_dict_grosspop:
mullikengp.append(grosspop["Mulliken GP"]["total"])
loewdingp.append(grosspop["Loewdin GP"]["total"])

site_properties = {"Total Mulliken GP": mullikengp, "Total Loewdin GP": loewdingp}
new_struct = struct.copy(site_properties=site_properties)
return new_struct
42 changes: 42 additions & 0 deletions pymatgen/io/tests/test_lobster.py
View file
Expand Up @@ -1465,6 +1465,48 @@ def testattributes(self):
self.assertAlmostEqual(self.grosspop1.list_dict_grosspop[8]["Loewdin GP"]["2s"], 1.60)
self.assertEqual(self.grosspop1.list_dict_grosspop[8]["element"], 'O')

def test_structure_with_grosspop(self):
struct_dict = {'@module': 'pymatgen.core.structure', '@class': 'Structure', 'charge': None, 'lattice': {
'matrix': [[5.021897888834907, 4.53806e-11, 0.0], [-2.5109484443388332, 4.349090983701526, 0.0],
[0.0, 0.0, 5.511929408565514]], 'a': 5.021897888834907, 'b': 5.0218974974248045,
'c': 5.511929408565514, 'alpha': 90.0, 'beta': 90.0, 'gamma': 119.99999598960493,
'volume': 120.38434608659402}, 'sites': [
{'species': [{'element': 'Si', 'occu': 1}], 'abc': [-3e-16, 0.4763431475490085, 0.6666669999999968],
'xyz': [-1.1960730853096477, 2.0716596881533986, 3.674621443020128], 'label': 'Si',
'properties': {'Total Mulliken GP': 1.64, 'Total Loewdin GP': 2.16}},
{'species': [{'element': 'Si', 'occu': 1}], 'abc': [0.5236568524509936, 0.5236568524509926, 0.0],
'xyz': [1.3148758827683875, 2.277431295571896, 0.0], 'label': 'Si',
'properties': {'Total Mulliken GP': 1.64, 'Total Loewdin GP': 2.16}},
{'species': [{'element': 'Si', 'occu': 1}], 'abc': [0.4763431475490066, -1.2e-15, 0.3333330000000032],
'xyz': [2.392146647037334, 2.1611518932482004e-11, 1.8373079655453863], 'label': 'Si',
'properties': {'Total Mulliken GP': 1.64, 'Total Loewdin GP': 2.16}},
{'species': [{'element': 'O', 'occu': 1}],
'abc': [0.1589037798059321, 0.7440031622164922, 0.4613477252144715],
'xyz': [-1.0701550264153763, 3.235737444648381, 2.5429160941844473], 'label': 'O',
'properties': {'Total Mulliken GP': 7.18, 'Total Loewdin GP': 6.92}},
{'species': [{'element': 'O', 'occu': 1}],
'abc': [0.2559968377835071, 0.4149006175894398, 0.7946807252144676],
'xyz': [0.2437959189219816, 1.8044405351020447, 4.380224059729795], 'label': 'O',
'properties': {'Total Mulliken GP': 7.18, 'Total Loewdin GP': 6.92}},
{'species': [{'element': 'O', 'occu': 1}],
'abc': [0.5850993824105679, 0.8410962201940679, 0.1280147252144683],
'xyz': [0.8263601076506712, 3.6580039876980064, 0.7056081286390611], 'label': 'O',
'properties': {'Total Mulliken GP': 7.18, 'Total Loewdin GP': 6.92}},
{'species': [{'element': 'O', 'occu': 1}],
'abc': [0.7440031622164928, 0.1589037798059326, 0.5386522747855285],
'xyz': [3.337308710918233, 0.6910869960638374, 2.969013314381067], 'label': 'O',
'properties': {'Total Mulliken GP': 7.18, 'Total Loewdin GP': 6.92}},
{'species': [{'element': 'O', 'occu': 1}], 'abc': [0.4149006175894392, 0.2559968377835, 0.2053192747855324],
'xyz': [1.4407936739605638, 1.1133535390791505, 1.13170534883572], 'label': 'O',
'properties': {'Total Mulliken GP': 7.18, 'Total Loewdin GP': 6.92}},
{'species': [{'element': 'O', 'occu': 1}],
'abc': [0.841096220194068, 0.5850993824105675, 0.8719852747855317],
'xyz': [2.754744948452184, 2.5446504486493, 4.806321279926453], 'label': 'O',
'properties': {'Total Mulliken GP': 7.18, 'Total Loewdin GP': 6.92}}]}
newstructure = self.grosspop1.get_structure_with_total_grosspop(os.path.join(test_dir, "POSCAR.SiO2"))

self.assertDictEqual(newstructure.as_dict(), struct_dict)


if __name__ == "__main__":
unittest.main()
27 changes: 27 additions & 0 deletions test_files/cohp/POSCAR.SiO2
View file
@@ -0,0 +1,27 @@
Si3 O6
1.00000000000000
5.0218978888349071 0.0000000000453806 0.0000000000000000
-2.5109484443388332 4.3490909837015259 0.0000000000000000
0.0000000000000000 0.0000000000000000 5.5119294085655142
Si O
3 6
Direct
-0.0000000000000003 0.4763431475490085 0.6666669999999968
0.5236568524509936 0.5236568524509926 0.0000000000000000
0.4763431475490066 -0.0000000000000012 0.3333330000000032
0.1589037798059321 0.7440031622164922 0.4613477252144715
0.2559968377835071 0.4149006175894398 0.7946807252144676
0.5850993824105679 0.8410962201940679 0.1280147252144683
0.7440031622164928 0.1589037798059326 0.5386522747855285
0.4149006175894392 0.2559968377835000 0.2053192747855324
0.8410962201940680 0.5850993824105675 0.8719852747855317

0.00000000E+00 0.00000000E+00 0.00000000E+00
0.00000000E+00 0.00000000E+00 0.00000000E+00
0.00000000E+00 0.00000000E+00 0.00000000E+00
0.00000000E+00 0.00000000E+00 0.00000000E+00
0.00000000E+00 0.00000000E+00 0.00000000E+00
0.00000000E+00 0.00000000E+00 0.00000000E+00
0.00000000E+00 0.00000000E+00 0.00000000E+00
0.00000000E+00 0.00000000E+00 0.00000000E+00
0.00000000E+00 0.00000000E+00 0.00000000E+00

0 comments on commit c0b35b0

Please sign in to comment.