class TransformedStructureTest(PymatgenTest):
def setUp(self):
structure = PymatgenTest.get_structure("LiFePO4")
self.structure = structure
trans = [SubstitutionTransformation({"Li": "Na"})]
self.trans = TransformedStructure(structure, trans)
def test_append_transformation(self):
t = SubstitutionTransformation({"Fe": "Mn"})
self.trans.append_transformation(t)
self.assertEqual(
"NaMnPO4", self.trans.final_structure.composition.reduced_formula)
self.assertEqual(len(self.trans.structures), 3)
coords = list()
coords.append([0, 0, 0])
coords.append([0.75, 0.5, 0.75])
lattice = [[3.8401979337, 0.00, 0.00],
[1.9200989668, 3.3257101909, 0.00],
[0.00, -2.2171384943, 3.1355090603]]
struct = Structure(lattice, ["Si4+", "Si4+"], coords)
ts = TransformedStructure(struct, [])
ts.append_transformation(
SupercellTransformation.from_scaling_factors(2, 1, 1))
alt = ts.append_transformation(
PartialRemoveSpecieTransformation(
'Si4+',
0.5,
algo=PartialRemoveSpecieTransformation.ALGO_COMPLETE), 5)
self.assertEqual(len(alt), 2)
def test_append_filter(self):
f3 = ContainsSpecieFilter(['O2-'], strict_compare=True, AND=False)
self.trans.append_filter(f3)
def test_get_vasp_input(self):
SETTINGS["PMG_VASP_PSP_DIR"] = os.path.abspath(
os.path.join(os.path.dirname(__file__), "..", "..", "..",
"test_files"))
potcar = self.trans.get_vasp_input(MPRelaxSet)['POTCAR']
self.assertEqual("Na_pv\nFe_pv\nP\nO",
"\n".join([p.symbol for p in potcar]))
self.assertEqual(len(self.trans.structures), 2)
def test_final_structure(self):
self.assertEqual(
"NaFePO4", self.trans.final_structure.composition.reduced_formula)
def test_from_dict(self):
d = json.load(open(os.path.join(test_dir, 'transformations.json'),
'r'))
d['other_parameters'] = {'tags': ['test']}
ts = TransformedStructure.from_dict(d)
ts.other_parameters['author'] = 'Will'
ts.append_transformation(SubstitutionTransformation({"Fe": "Mn"}))
self.assertEqual("MnPO4",
ts.final_structure.composition.reduced_formula)
self.assertEqual(ts.other_parameters, {
'author': 'Will',
'tags': ['test']
})
def test_undo_and_redo_last_change(self):
trans = [
SubstitutionTransformation({"Li": "Na"}),
SubstitutionTransformation({"Fe": "Mn"})
]
ts = TransformedStructure(self.structure, trans)
self.assertEqual("NaMnPO4",
ts.final_structure.composition.reduced_formula)
ts.undo_last_change()
self.assertEqual("NaFePO4",
ts.final_structure.composition.reduced_formula)
ts.undo_last_change()
self.assertEqual("LiFePO4",
ts.final_structure.composition.reduced_formula)
self.assertRaises(IndexError, ts.undo_last_change)
ts.redo_next_change()
self.assertEqual("NaFePO4",
ts.final_structure.composition.reduced_formula)
ts.redo_next_change()
self.assertEqual("NaMnPO4",
ts.final_structure.composition.reduced_formula)
self.assertRaises(IndexError, ts.redo_next_change)
#Make sure that this works with filters.
f3 = ContainsSpecieFilter(['O2-'], strict_compare=True, AND=False)
ts.append_filter(f3)
ts.undo_last_change()
ts.redo_next_change()
def test_as_dict(self):
self.trans.set_parameter('author', 'will')
d = self.trans.as_dict()
self.assertIn('last_modified', d)
self.assertIn('history', d)
self.assertIn('version', d)
self.assertIn('author', d['other_parameters'])
self.assertEqual(Structure.from_dict(d).formula, 'Na4 Fe4 P4 O16')
def test_snl(self):
self.trans.set_parameter('author', 'will')
with warnings.catch_warnings(record=True) as w:
warnings.simplefilter("always")
snl = self.trans.to_snl([('will', '*****@*****.**')])
self.assertEqual(
len(w), 1, 'Warning not raised on type conversion '
'with other_parameters')
ts = TransformedStructure.from_snl(snl)
self.assertEqual(ts.history[-1]['@class'],
'SubstitutionTransformation')
h = ('testname', 'testURL', {'test': 'testing'})
snl = StructureNL(ts.final_structure, [('will', '*****@*****.**')],
history=[h])
snl = TransformedStructure.from_snl(snl).to_snl([('notwill',
'*****@*****.**')])
self.assertEqual(snl.history, [h])
self.assertEqual(snl.authors, [('notwill', '*****@*****.**')])
class TransformedStructureTest(unittest.TestCase):
def setUp(self):
structure_dict = {
"lattice": {
"a": 4.754150115,
"volume": 302.935463898643,
"c": 10.462573348,
"b": 6.090300362,
"matrix": [[4.754150115, 0.0, 0.0], [0.0, 6.090300362, 0.0], [0.0, 0.0, 10.462573348]],
"alpha": 90.0,
"beta": 90.0,
"gamma": 90.0,
},
"sites": [
{
"occu": 1,
"abc": [0.0, 0.0, 0.0],
"xyz": [0.0, 0.0, 0.0],
"species": [{"occu": 1, "element": "Li"}],
"label": "Li",
},
{
"occu": 1,
"abc": [0.5000010396179928, 0.0, 0.5000003178950235],
"xyz": [2.37708, 0.0, 5.23129],
"species": [{"occu": 1, "element": "Li"}],
"label": "Li",
},
{
"occu": 1,
"abc": [0.0, 0.49999997028061194, 0.0],
"xyz": [0.0, 3.04515, 0.0],
"species": [{"occu": 1, "element": "Li"}],
"label": "Li",
},
{
"occu": 1,
"abc": [0.5000010396179928, 0.49999997028061194, 0.5000003178950235],
"xyz": [2.37708, 3.04515, 5.23129],
"species": [{"occu": 1, "element": "Li"}],
"label": "Li",
},
{
"occu": 1,
"abc": [0.7885825876997996, 0.5473161916279229, 0.3339168944194627],
"xyz": [3.74904, 3.33332, 3.4936300000000005],
"species": [{"occu": 1, "element": "O"}],
"label": "O",
},
{
"occu": 1,
"abc": [0.2114173881108085, 0.452683748933301, 0.6660827855827808],
"xyz": [1.00511, 2.75698, 6.968940000000001],
"species": [{"occu": 1, "element": "O"}],
"label": "O",
},
{
"occu": 1,
"abc": [0.7114184277288014, 0.5473161916279229, 0.8339172123144861],
"xyz": [3.38219, 3.33332, 8.72492],
"species": [{"occu": 1, "element": "O"}],
"label": "O",
},
{
"occu": 1,
"abc": [0.7885825876997996, 0.9526820772587701, 0.3339168944194627],
"xyz": [3.74904, 5.8021199999999995, 3.4936300000000005],
"species": [{"occu": 1, "element": "O"}],
"label": "O",
},
{
"occu": 1,
"abc": [0.28858365150718424, 0.047317863302453654, 0.16608342347556082],
"xyz": [1.37197, 0.28818, 1.73766],
"species": [{"occu": 1, "element": "O"}],
"label": "O",
},
{
"occu": 1,
"abc": [0.7440972443925447, 0.25000080611787734, 0.09613791622232937],
"xyz": [3.537549999999999, 1.52258, 1.00585],
"species": [{"occu": 1, "element": "O"}],
"label": "O",
},
{
"occu": 1,
"abc": [0.28858365150718424, 0.452683748933301, 0.16608342347556082],
"xyz": [1.37197, 2.75698, 1.73766],
"species": [{"occu": 1, "element": "O"}],
"label": "O",
},
{
"occu": 1,
"abc": [0.2114173881108085, 0.047317863302453654, 0.6660827855827808],
"xyz": [1.00511, 0.28818, 6.968940000000001],
"species": [{"occu": 1, "element": "O"}],
"label": "O",
},
{
"occu": 1,
"abc": [0.2559006279926859, 0.7499991344433464, 0.9038627195677177],
"xyz": [1.21659, 4.56772, 9.45673],
"species": [{"occu": 1, "element": "O"}],
"label": "O",
},
{
"occu": 1,
"abc": [0.7559016676106785, 0.25000080611787734, 0.5961372783295493],
"xyz": [3.5936699999999986, 1.52258, 6.2371300000000005],
"species": [{"occu": 1, "element": "O"}],
"label": "O",
},
{
"occu": 1,
"abc": [0.7939989080466804, 0.7499991344433464, 0.5421304884886912],
"xyz": [3.77479, 4.56772, 5.67208],
"species": [{"occu": 1, "element": "O"}],
"label": "O",
},
{
"occu": 1,
"abc": [0.24409830819992942, 0.7499991344433464, 0.40386240167269416],
"xyz": [1.16048, 4.56772, 4.22544],
"species": [{"occu": 1, "element": "O"}],
"label": "O",
},
{
"occu": 1,
"abc": [0.7060021073819206, 0.7499991344433464, 0.04213017059366761],
"xyz": [3.35644, 4.56772, 0.44079000000000007],
"species": [{"occu": 1, "element": "O"}],
"label": "O",
},
{
"occu": 1,
"abc": [0.2939978684286875, 0.25000080611787734, 0.9578695094085758],
"xyz": [1.3977099999999996, 1.52258, 10.02178],
"species": [{"occu": 1, "element": "O"}],
"label": "O",
},
{
"occu": 1,
"abc": [0.20600106776392774, 0.25000080611787734, 0.4578701473013559],
"xyz": [0.9793599999999998, 1.52258, 4.7905],
"species": [{"occu": 1, "element": "O"}],
"label": "O",
},
{
"occu": 1,
"abc": [0.7114184277288014, 0.9526820772587701, 0.8339172123144861],
"xyz": [3.38219, 5.8021199999999995, 8.72492],
"species": [{"occu": 1, "element": "O"}],
"label": "O",
},
{
"occu": 1,
"abc": [0.5793611756830275, 0.7499991344433464, 0.9051119342269868],
"xyz": [2.75437, 4.56772, 9.4698],
"species": [{"occu": 1, "element": "P"}],
"label": "P",
},
{
"occu": 1,
"abc": [0.9206377363201961, 0.7499991344433464, 0.40511161633196324],
"xyz": [4.37685, 4.56772, 4.23851],
"species": [{"occu": 1, "element": "P"}],
"label": "P",
},
{
"occu": 1,
"abc": [0.42063880012758065, 0.25000080611787734, 0.09488774577525667],
"xyz": [1.9997799999999994, 1.52258, 0.99277],
"species": [{"occu": 1, "element": "P"}],
"label": "P",
},
{
"occu": 1,
"abc": [0.07936223949041206, 0.25000080611787734, 0.5948880636702801],
"xyz": [0.3773, 1.52258, 6.22406],
"species": [{"occu": 1, "element": "P"}],
"label": "P",
},
{
"occu": 1,
"abc": [0.021860899947623972, 0.7499991344433464, 0.7185507570598875],
"xyz": [0.10393, 4.56772, 7.517890000000001],
"species": [{"occu": 1, "element": "Fe"}],
"label": "Fe",
},
{
"occu": 1,
"abc": [0.478135932819614, 0.7499991344433464, 0.21855043916486389],
"xyz": [2.27313, 4.56772, 2.2866],
"species": [{"occu": 1, "element": "Fe"}],
"label": "Fe",
},
{
"occu": 1,
"abc": [0.9781369724376069, 0.25000080611787734, 0.2814489229423561],
"xyz": [4.65021, 1.52258, 2.9446800000000004],
"species": [{"occu": 1, "element": "Fe"}],
"label": "Fe",
},
{
"occu": 1,
"abc": [0.5218619395656168, 0.25000080611787734, 0.7814492408373795],
"xyz": [2.48101, 1.52258, 8.17597],
"species": [{"occu": 1, "element": "Fe"}],
"label": "Fe",
},
],
}
structure = Structure.from_dict(structure_dict)
self.structure = structure
trans = [SubstitutionTransformation({"Li": "Na"})]
self.trans = TransformedStructure(structure, trans)
def test_append_transformation(self):
t = SubstitutionTransformation({"Fe": "Mn"})
self.trans.append_transformation(t)
self.assertEqual("NaMnPO4", self.trans.final_structure.composition.reduced_formula)
self.assertEqual(len(self.trans.structures), 3)
coords = list()
coords.append([0, 0, 0])
coords.append([0.75, 0.5, 0.75])
lattice = [[3.8401979337, 0.00, 0.00], [1.9200989668, 3.3257101909, 0.00], [0.00, -2.2171384943, 3.1355090603]]
struct = Structure(lattice, ["Si4+", "Si4+"], coords)
ts = TransformedStructure(struct, [])
ts.append_transformation(SupercellTransformation.from_scaling_factors(2, 1, 1))
alt = ts.append_transformation(
PartialRemoveSpecieTransformation("Si4+", 0.5, algo=PartialRemoveSpecieTransformation.ALGO_COMPLETE), 5
)
self.assertEqual(len(alt), 2)
def test_append_filter(self):
f3 = ContainsSpecieFilter(["O2-"], strict_compare=True, AND=False)
self.trans.append_filter(f3)
def test_get_vasp_input(self):
SETTINGS["VASP_PSP_DIR"] = os.path.abspath(
os.path.join(os.path.dirname(__file__), "..", "..", "..", "test_files")
)
potcar = self.trans.get_vasp_input(MPRelaxSet)["POTCAR"]
self.assertEqual("Na_pv\nFe_pv\nP\nO", "\n".join([p.symbol for p in potcar]))
self.assertEqual(len(self.trans.structures), 2)
def test_final_structure(self):
self.assertEqual("NaFePO4", self.trans.final_structure.composition.reduced_formula)
def test_from_dict(self):
d = json.load(open(os.path.join(test_dir, "transformations.json"), "r"))
d["other_parameters"] = {"tags": ["test"]}
ts = TransformedStructure.from_dict(d)
ts.other_parameters["author"] = "Will"
ts.append_transformation(SubstitutionTransformation({"Fe": "Mn"}))
self.assertEqual("MnPO4", ts.final_structure.composition.reduced_formula)
self.assertEqual(ts.other_parameters, {"author": "Will", "tags": ["test"]})
def test_undo_and_redo_last_change(self):
trans = [SubstitutionTransformation({"Li": "Na"}), SubstitutionTransformation({"Fe": "Mn"})]
ts = TransformedStructure(self.structure, trans)
self.assertEqual("NaMnPO4", ts.final_structure.composition.reduced_formula)
ts.undo_last_change()
self.assertEqual("NaFePO4", ts.final_structure.composition.reduced_formula)
ts.undo_last_change()
self.assertEqual("LiFePO4", ts.final_structure.composition.reduced_formula)
self.assertRaises(IndexError, ts.undo_last_change)
ts.redo_next_change()
self.assertEqual("NaFePO4", ts.final_structure.composition.reduced_formula)
ts.redo_next_change()
self.assertEqual("NaMnPO4", ts.final_structure.composition.reduced_formula)
self.assertRaises(IndexError, ts.redo_next_change)
# Make sure that this works with filters.
f3 = ContainsSpecieFilter(["O2-"], strict_compare=True, AND=False)
ts.append_filter(f3)
ts.undo_last_change()
ts.redo_next_change()
def test_as_dict(self):
self.trans.set_parameter("author", "will")
d = self.trans.as_dict()
self.assertIn("last_modified", d)
self.assertIn("history", d)
self.assertIn("version", d)
self.assertIn("author", d["other_parameters"])
self.assertEqual(Structure.from_dict(d).formula, "Na4 Fe4 P4 O16")
def test_snl(self):
self.trans.set_parameter("author", "will")
with warnings.catch_warnings(record=True) as w:
warnings.simplefilter("always")
snl = self.trans.to_snl([("will", "*****@*****.**")])
self.assertEqual(len(w), 1, "Warning not raised on type conversion " "with other_parameters")
ts = TransformedStructure.from_snl(snl)
self.assertEqual(ts.history[-1]["@class"], "SubstitutionTransformation")
h = ("testname", "testURL", {"test": "testing"})
snl = StructureNL(ts.final_structure, [("will", "*****@*****.**")], history=[h])
snl = TransformedStructure.from_snl(snl).to_snl([("notwill", "*****@*****.**")])
self.assertEqual(snl.history, [h])
self.assertEqual(snl.authors, [("notwill", "*****@*****.**")])
class TransformedStructureTest(unittest.TestCase):
def setUp(self):
structure_dict = {
"lattice": {
"a":
4.754150115,
"volume":
302.935463898643,
"c":
10.462573348,
"b":
6.090300362,
"matrix": [[4.754150115, 0.0, 0.0], [0.0, 6.090300362, 0.0],
[0.0, 0.0, 10.462573348]],
"alpha":
90.0,
"beta":
90.0,
"gamma":
90.0
},
"sites": [{
"occu": 1,
"abc": [0.0, 0.0, 0.0],
"xyz": [0.0, 0.0, 0.0],
"species": [{
"occu": 1,
"element": "Li"
}],
"label": "Li"
}, {
"occu": 1,
"abc": [0.5000010396179928, 0.0, 0.5000003178950235],
"xyz": [2.37708, 0.0, 5.23129],
"species": [{
"occu": 1,
"element": "Li"
}],
"label": "Li"
}, {
"occu": 1,
"abc": [0.0, 0.49999997028061194, 0.0],
"xyz": [0.0, 3.04515, 0.0],
"species": [{
"occu": 1,
"element": "Li"
}],
"label": "Li"
}, {
"occu":
1,
"abc":
[0.5000010396179928, 0.49999997028061194, 0.5000003178950235],
"xyz": [2.37708, 3.04515, 5.23129],
"species": [{
"occu": 1,
"element": "Li"
}],
"label":
"Li"
}, {
"occu":
1,
"abc":
[0.7885825876997996, 0.5473161916279229, 0.3339168944194627],
"xyz": [3.74904, 3.33332, 3.4936300000000005],
"species": [{
"occu": 1,
"element": "O"
}],
"label":
"O"
}, {
"occu":
1,
"abc":
[0.2114173881108085, 0.452683748933301, 0.6660827855827808],
"xyz": [1.00511, 2.75698, 6.968940000000001],
"species": [{
"occu": 1,
"element": "O"
}],
"label":
"O"
}, {
"occu":
1,
"abc":
[0.7114184277288014, 0.5473161916279229, 0.8339172123144861],
"xyz": [3.38219, 3.33332, 8.72492],
"species": [{
"occu": 1,
"element": "O"
}],
"label":
"O"
}, {
"occu":
1,
"abc":
[0.7885825876997996, 0.9526820772587701, 0.3339168944194627],
"xyz": [3.74904, 5.8021199999999995, 3.4936300000000005],
"species": [{
"occu": 1,
"element": "O"
}],
"label":
"O"
}, {
"occu":
1,
"abc": [
0.28858365150718424, 0.047317863302453654,
0.16608342347556082
],
"xyz": [1.37197, 0.28818, 1.73766],
"species": [{
"occu": 1,
"element": "O"
}],
"label":
"O"
}, {
"occu":
1,
"abc":
[0.7440972443925447, 0.25000080611787734, 0.09613791622232937],
"xyz": [3.537549999999999, 1.52258, 1.00585],
"species": [{
"occu": 1,
"element": "O"
}],
"label":
"O"
}, {
"occu":
1,
"abc":
[0.28858365150718424, 0.452683748933301, 0.16608342347556082],
"xyz": [1.37197, 2.75698, 1.73766],
"species": [{
"occu": 1,
"element": "O"
}],
"label":
"O"
}, {
"occu":
1,
"abc":
[0.2114173881108085, 0.047317863302453654, 0.6660827855827808],
"xyz": [1.00511, 0.28818, 6.968940000000001],
"species": [{
"occu": 1,
"element": "O"
}],
"label":
"O"
}, {
"occu":
1,
"abc":
[0.2559006279926859, 0.7499991344433464, 0.9038627195677177],
"xyz": [1.21659, 4.56772, 9.45673],
"species": [{
"occu": 1,
"element": "O"
}],
"label":
"O"
}, {
"occu":
1,
"abc":
[0.7559016676106785, 0.25000080611787734, 0.5961372783295493],
"xyz": [3.5936699999999986, 1.52258, 6.2371300000000005],
"species": [{
"occu": 1,
"element": "O"
}],
"label":
"O"
}, {
"occu":
1,
"abc":
[0.7939989080466804, 0.7499991344433464, 0.5421304884886912],
"xyz": [3.77479, 4.56772, 5.67208],
"species": [{
"occu": 1,
"element": "O"
}],
"label":
"O"
}, {
"occu":
1,
"abc":
[0.24409830819992942, 0.7499991344433464, 0.40386240167269416],
"xyz": [1.16048, 4.56772, 4.22544],
"species": [{
"occu": 1,
"element": "O"
}],
"label":
"O"
}, {
"occu":
1,
"abc":
[0.7060021073819206, 0.7499991344433464, 0.04213017059366761],
"xyz": [3.35644, 4.56772, 0.44079000000000007],
"species": [{
"occu": 1,
"element": "O"
}],
"label":
"O"
}, {
"occu":
1,
"abc":
[0.2939978684286875, 0.25000080611787734, 0.9578695094085758],
"xyz": [1.3977099999999996, 1.52258, 10.02178],
"species": [{
"occu": 1,
"element": "O"
}],
"label":
"O"
}, {
"occu":
1,
"abc":
[0.20600106776392774, 0.25000080611787734, 0.4578701473013559],
"xyz": [0.9793599999999998, 1.52258, 4.7905],
"species": [{
"occu": 1,
"element": "O"
}],
"label":
"O"
}, {
"occu":
1,
"abc":
[0.7114184277288014, 0.9526820772587701, 0.8339172123144861],
"xyz": [3.38219, 5.8021199999999995, 8.72492],
"species": [{
"occu": 1,
"element": "O"
}],
"label":
"O"
}, {
"occu":
1,
"abc":
[0.5793611756830275, 0.7499991344433464, 0.9051119342269868],
"xyz": [2.75437, 4.56772, 9.4698],
"species": [{
"occu": 1,
"element": "P"
}],
"label":
"P"
}, {
"occu":
1,
"abc":
[0.9206377363201961, 0.7499991344433464, 0.40511161633196324],
"xyz": [4.37685, 4.56772, 4.23851],
"species": [{
"occu": 1,
"element": "P"
}],
"label":
"P"
}, {
"occu":
1,
"abc": [
0.42063880012758065, 0.25000080611787734,
0.09488774577525667
],
"xyz": [1.9997799999999994, 1.52258, 0.99277],
"species": [{
"occu": 1,
"element": "P"
}],
"label":
"P"
}, {
"occu":
1,
"abc":
[0.07936223949041206, 0.25000080611787734, 0.5948880636702801],
"xyz": [0.3773, 1.52258, 6.22406],
"species": [{
"occu": 1,
"element": "P"
}],
"label":
"P"
}, {
"occu":
1,
"abc":
[0.021860899947623972, 0.7499991344433464, 0.7185507570598875],
"xyz": [0.10393, 4.56772, 7.517890000000001],
"species": [{
"occu": 1,
"element": "Fe"
}],
"label":
"Fe"
}, {
"occu":
1,
"abc":
[0.478135932819614, 0.7499991344433464, 0.21855043916486389],
"xyz": [2.27313, 4.56772, 2.2866],
"species": [{
"occu": 1,
"element": "Fe"
}],
"label":
"Fe"
}, {
"occu":
1,
"abc":
[0.9781369724376069, 0.25000080611787734, 0.2814489229423561],
"xyz": [4.65021, 1.52258, 2.9446800000000004],
"species": [{
"occu": 1,
"element": "Fe"
}],
"label":
"Fe"
}, {
"occu":
1,
"abc":
[0.5218619395656168, 0.25000080611787734, 0.7814492408373795],
"xyz": [2.48101, 1.52258, 8.17597],
"species": [{
"occu": 1,
"element": "Fe"
}],
"label":
"Fe"
}]
}
structure = Structure.from_dict(structure_dict)
self.structure = structure
trans = [SubstitutionTransformation({"Li": "Na"})]
self.trans = TransformedStructure(structure, trans)
def test_append_transformation(self):
t = SubstitutionTransformation({"Fe": "Mn"})
self.trans.append_transformation(t)
self.assertEqual(
"NaMnPO4", self.trans.final_structure.composition.reduced_formula)
self.assertEqual(len(self.trans.structures), 3)
coords = list()
coords.append([0, 0, 0])
coords.append([0.75, 0.5, 0.75])
lattice = [[3.8401979337, 0.00, 0.00],
[1.9200989668, 3.3257101909, 0.00],
[0.00, -2.2171384943, 3.1355090603]]
struct = Structure(lattice, ["Si4+", "Si4+"], coords)
ts = TransformedStructure(struct, [])
ts.append_transformation(
SupercellTransformation.from_scaling_factors(2, 1, 1))
alt = ts.append_transformation(
PartialRemoveSpecieTransformation(
'Si4+',
0.5,
algo=PartialRemoveSpecieTransformation.ALGO_COMPLETE), 5)
self.assertEqual(len(alt), 2)
def test_append_filter(self):
f3 = ContainsSpecieFilter(['O2-'], strict_compare=True, AND=False)
self.trans.append_filter(f3)
def test_get_vasp_input(self):
vaspis = MPVaspInputSet()
self.assertEqual(
"Na_pv\nFe_pv\nP\nO",
self.trans.get_vasp_input(vaspis, False)['POTCAR.spec'])
self.assertEqual(len(self.trans.structures), 2)
def test_final_structure(self):
self.assertEqual(
"NaFePO4", self.trans.final_structure.composition.reduced_formula)
def test_from_dict(self):
d = json.load(open(os.path.join(test_dir, 'transformations.json'),
'r'))
d['other_parameters'] = {'tags': ['test']}
ts = TransformedStructure.from_dict(d)
ts.other_parameters['author'] = 'Will'
ts.append_transformation(SubstitutionTransformation({"Fe": "Mn"}))
self.assertEqual("MnPO4",
ts.final_structure.composition.reduced_formula)
self.assertEqual(ts.other_parameters, {
'author': 'Will',
'tags': ['test']
})
def test_undo_and_redo_last_change(self):
trans = [
SubstitutionTransformation({"Li": "Na"}),
SubstitutionTransformation({"Fe": "Mn"})
]
ts = TransformedStructure(self.structure, trans)
self.assertEqual("NaMnPO4",
ts.final_structure.composition.reduced_formula)
ts.undo_last_change()
self.assertEqual("NaFePO4",
ts.final_structure.composition.reduced_formula)
ts.undo_last_change()
self.assertEqual("LiFePO4",
ts.final_structure.composition.reduced_formula)
self.assertRaises(IndexError, ts.undo_last_change)
ts.redo_next_change()
self.assertEqual("NaFePO4",
ts.final_structure.composition.reduced_formula)
ts.redo_next_change()
self.assertEqual("NaMnPO4",
ts.final_structure.composition.reduced_formula)
self.assertRaises(IndexError, ts.redo_next_change)
#Make sure that this works with filters.
f3 = ContainsSpecieFilter(['O2-'], strict_compare=True, AND=False)
ts.append_filter(f3)
ts.undo_last_change()
ts.redo_next_change()
def test_as_dict(self):
self.trans.set_parameter('author', 'will')
d = self.trans.as_dict()
self.assertIn('last_modified', d)
self.assertIn('history', d)
self.assertIn('version', d)
self.assertIn('author', d['other_parameters'])
self.assertEqual(Structure.from_dict(d).formula, 'Na4 Fe4 P4 O16')
def test_snl(self):
self.trans.set_parameter('author', 'will')
with warnings.catch_warnings(record=True) as w:
warnings.simplefilter("always")
snl = self.trans.to_snl([('will', '*****@*****.**')])
self.assertEqual(
len(w), 1, 'Warning not raised on type conversion '
'with other_parameters')
ts = TransformedStructure.from_snl(snl)
self.assertEqual(ts.history[-1]['name'], 'SubstitutionTransformation')
h = ('testname', 'testURL', {'test': 'testing'})
snl = StructureNL(ts.final_structure, [('will', '*****@*****.**')],
history=[h])
snl = TransformedStructure.from_snl(snl).to_snl([('notwill',
'*****@*****.**')])
self.assertEqual(snl.history, [h])
self.assertEqual(snl.authors, [('notwill', '*****@*****.**')])
class TransformedStructureTest(PymatgenTest):
def setUp(self):
structure = PymatgenTest.get_structure("LiFePO4")
self.structure = structure
trans = [SubstitutionTransformation({"Li": "Na"})]
self.trans = TransformedStructure(structure, trans)
def test_append_transformation(self):
t = SubstitutionTransformation({"Fe": "Mn"})
self.trans.append_transformation(t)
self.assertEqual("NaMnPO4",
self.trans.final_structure.composition
.reduced_formula)
self.assertEqual(len(self.trans.structures), 3)
coords = list()
coords.append([0, 0, 0])
coords.append([0.75, 0.5, 0.75])
lattice = [[3.8401979337, 0.00, 0.00],
[1.9200989668, 3.3257101909, 0.00],
[0.00, -2.2171384943, 3.1355090603]]
struct = Structure(lattice, ["Si4+", "Si4+"], coords)
ts = TransformedStructure(struct, [])
ts.append_transformation(SupercellTransformation
.from_scaling_factors(2, 1, 1))
alt = ts.append_transformation(
PartialRemoveSpecieTransformation(
'Si4+', 0.5,
algo=PartialRemoveSpecieTransformation.ALGO_COMPLETE), 5)
self.assertEqual(len(alt), 2)
def test_append_filter(self):
f3 = ContainsSpecieFilter(['O2-'], strict_compare=True, AND=False)
self.trans.append_filter(f3)
def test_get_vasp_input(self):
SETTINGS["PMG_VASP_PSP_DIR"] = os.path.abspath(
os.path.join(os.path.dirname(__file__), "..", "..", "..",
"test_files"))
potcar = self.trans.get_vasp_input(MPRelaxSet)['POTCAR']
self.assertEqual("Na_pv\nFe_pv\nP\nO",
"\n".join([p.symbol for p in potcar]))
self.assertEqual(len(self.trans.structures), 2)
def test_final_structure(self):
self.assertEqual("NaFePO4", self.trans.final_structure.composition
.reduced_formula)
def test_from_dict(self):
d = json.load(open(os.path.join(test_dir, 'transformations.json'),
'r'))
d['other_parameters'] = {'tags': ['test']}
ts = TransformedStructure.from_dict(d)
ts.other_parameters['author'] = 'Will'
ts.append_transformation(SubstitutionTransformation({"Fe": "Mn"}))
self.assertEqual("MnPO4",
ts.final_structure.composition.reduced_formula)
self.assertEqual(ts.other_parameters, {'author': 'Will',
'tags': ['test']})
def test_undo_and_redo_last_change(self):
trans = [SubstitutionTransformation({"Li": "Na"}),
SubstitutionTransformation({"Fe": "Mn"})]
ts = TransformedStructure(self.structure, trans)
self.assertEqual("NaMnPO4",
ts.final_structure.composition.reduced_formula)
ts.undo_last_change()
self.assertEqual("NaFePO4",
ts.final_structure.composition.reduced_formula)
ts.undo_last_change()
self.assertEqual("LiFePO4",
ts.final_structure.composition.reduced_formula)
self.assertRaises(IndexError, ts.undo_last_change)
ts.redo_next_change()
self.assertEqual("NaFePO4",
ts.final_structure.composition.reduced_formula)
ts.redo_next_change()
self.assertEqual("NaMnPO4",
ts.final_structure.composition.reduced_formula)
self.assertRaises(IndexError, ts.redo_next_change)
#Make sure that this works with filters.
f3 = ContainsSpecieFilter(['O2-'], strict_compare=True, AND=False)
ts.append_filter(f3)
ts.undo_last_change()
ts.redo_next_change()
def test_as_dict(self):
self.trans.set_parameter('author', 'will')
d = self.trans.as_dict()
self.assertIn('last_modified', d)
self.assertIn('history', d)
self.assertIn('version', d)
self.assertIn('author', d['other_parameters'])
self.assertEqual(Structure.from_dict(d).formula, 'Na4 Fe4 P4 O16')
def test_snl(self):
self.trans.set_parameter('author', 'will')
with warnings.catch_warnings(record=True) as w:
warnings.simplefilter("always")
snl = self.trans.to_snl([('will', '*****@*****.**')])
self.assertEqual(len(w), 1, 'Warning not raised on type conversion '
'with other_parameters')
ts = TransformedStructure.from_snl(snl)
self.assertEqual(ts.history[-1]['@class'], 'SubstitutionTransformation')
h = ('testname', 'testURL', {'test' : 'testing'})
snl = StructureNL(ts.final_structure,[('will', '*****@*****.**')],
history = [h])
snl = TransformedStructure.from_snl(snl).to_snl([('notwill',
'*****@*****.**')])
self.assertEqual(snl.history, [h])
self.assertEqual(snl.authors, [('notwill', '*****@*****.**')])
class TransformedStructureTest(PymatgenTest):
def setUp(self):
structure = PymatgenTest.get_structure("LiFePO4")
self.structure = structure
trans = [SubstitutionTransformation({"Li": "Na"})]
self.trans = TransformedStructure(structure, trans)
def test_append_transformation(self):
t = SubstitutionTransformation({"Fe": "Mn"})
self.trans.append_transformation(t)
self.assertEqual("NaMnPO4", self.trans.final_structure.composition.reduced_formula)
self.assertEqual(len(self.trans.structures), 3)
coords = list()
coords.append([0, 0, 0])
coords.append([0.75, 0.5, 0.75])
lattice = [
[3.8401979337, 0.00, 0.00],
[1.9200989668, 3.3257101909, 0.00],
[0.00, -2.2171384943, 3.1355090603],
]
struct = Structure(lattice, ["Si4+", "Si4+"], coords)
ts = TransformedStructure(struct, [])
ts.append_transformation(SupercellTransformation.from_scaling_factors(2, 1, 1))
alt = ts.append_transformation(
PartialRemoveSpecieTransformation("Si4+", 0.5, algo=PartialRemoveSpecieTransformation.ALGO_COMPLETE),
5,
)
self.assertEqual(len(alt), 2)
def test_append_filter(self):
f3 = ContainsSpecieFilter(["O2-"], strict_compare=True, AND=False)
self.trans.append_filter(f3)
def test_get_vasp_input(self):
SETTINGS["PMG_VASP_PSP_DIR"] = os.path.abspath(
os.path.join(os.path.dirname(__file__), "..", "..", "..", "test_files")
)
potcar = self.trans.get_vasp_input(MPRelaxSet)["POTCAR"]
self.assertEqual("Na_pv\nFe_pv\nP\nO", "\n".join([p.symbol for p in potcar]))
self.assertEqual(len(self.trans.structures), 2)
def test_final_structure(self):
self.assertEqual("NaFePO4", self.trans.final_structure.composition.reduced_formula)
def test_from_dict(self):
d = json.load(open(os.path.join(PymatgenTest.TEST_FILES_DIR, "transformations.json"), "r"))
d["other_parameters"] = {"tags": ["test"]}
ts = TransformedStructure.from_dict(d)
ts.other_parameters["author"] = "Will"
ts.append_transformation(SubstitutionTransformation({"Fe": "Mn"}))
self.assertEqual("MnPO4", ts.final_structure.composition.reduced_formula)
self.assertEqual(ts.other_parameters, {"author": "Will", "tags": ["test"]})
def test_undo_and_redo_last_change(self):
trans = [
SubstitutionTransformation({"Li": "Na"}),
SubstitutionTransformation({"Fe": "Mn"}),
]
ts = TransformedStructure(self.structure, trans)
self.assertEqual("NaMnPO4", ts.final_structure.composition.reduced_formula)
ts.undo_last_change()
self.assertEqual("NaFePO4", ts.final_structure.composition.reduced_formula)
ts.undo_last_change()
self.assertEqual("LiFePO4", ts.final_structure.composition.reduced_formula)
self.assertRaises(IndexError, ts.undo_last_change)
ts.redo_next_change()
self.assertEqual("NaFePO4", ts.final_structure.composition.reduced_formula)
ts.redo_next_change()
self.assertEqual("NaMnPO4", ts.final_structure.composition.reduced_formula)
self.assertRaises(IndexError, ts.redo_next_change)
# Make sure that this works with filters.
f3 = ContainsSpecieFilter(["O2-"], strict_compare=True, AND=False)
ts.append_filter(f3)
ts.undo_last_change()
ts.redo_next_change()
def test_as_dict(self):
self.trans.set_parameter("author", "will")
d = self.trans.as_dict()
self.assertIn("last_modified", d)
self.assertIn("history", d)
self.assertIn("author", d["other_parameters"])
self.assertEqual(Structure.from_dict(d).formula, "Na4 Fe4 P4 O16")
def test_snl(self):
self.trans.set_parameter("author", "will")
with warnings.catch_warnings(record=True) as w:
warnings.simplefilter("always")
snl = self.trans.to_snl([("will", "*****@*****.**")])
self.assertEqual(
len(w),
1,
"Warning not raised on type conversion " "with other_parameters",
)
ts = TransformedStructure.from_snl(snl)
self.assertEqual(ts.history[-1]["@class"], "SubstitutionTransformation")
h = ("testname", "testURL", {"test": "testing"})
snl = StructureNL(ts.final_structure, [("will", "*****@*****.**")], history=[h])
snl = TransformedStructure.from_snl(snl).to_snl([("notwill", "*****@*****.**")])
self.assertEqual(snl.history, [h])
self.assertEqual(snl.authors, [("notwill", "*****@*****.**")])
