本文整理汇总了Python中pymatgen.alchemy.materials.TransformedStructure类的典型用法代码示例。如果您正苦于以下问题：Python TransformedStructure类的具体用法？Python TransformedStructure怎么用？Python TransformedStructure使用的例子？那么恭喜您, 这里精选的类代码示例或许可以为您提供帮助。
在下文中一共展示了TransformedStructure类的15个代码示例，这些例子默认根据受欢迎程度排序。您可以为喜欢或者感觉有用的代码点赞，您的评价将有助于系统推荐出更棒的Python代码示例。
示例1: test_snl
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", "[email protected]")])
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", "[email protected]")], history=[h])
snl = TransformedStructure.from_snl(snl).to_snl([("notwill", "[email protected]")])
self.assertEqual(snl.history, [h])
self.assertEqual(snl.authors, [("notwill", "[email protected]")])示例2: test_append_transformation
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)示例3: setUp
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)示例4: __init__
def __init__(self, cif_string, transformations=None, primitive=True,
extend_collection=False):
"""
Generates a Transmuter from a cif string, possibly
containing multiple structures.
Args:
cif_string:
A string containing a cif or a series of cifs
transformations:
New transformations to be applied to all structures
primitive:
Whether to generate the primitive cell from the cif.
extend_collection:
Whether to use more than one output structure from one-to-many
transformations.
"""
transformed_structures = []
lines = cif_string.split("\n")
structure_data = []
read_data = False
for line in lines:
if re.match("^\s*data", line):
structure_data.append([])
read_data = True
if read_data:
structure_data[-1].append(line)
for data in structure_data:
tstruct = TransformedStructure.from_cif_string("\n".join(data), [],
primitive)
transformed_structures.append(tstruct)
StandardTransmuter.__init__(self, transformed_structures,
transformations, extend_collection)示例5: test_snl
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', '[email protected]')])
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', '[email protected]')],
history = [h])
snl = TransformedStructure.from_snl(snl).to_snl([('notwill',
'[email protected]')])
self.assertEqual(snl.history, [h])
self.assertEqual(snl.authors, [('notwill', '[email protected]')])示例6: test_from_dict
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"]})示例7: test_from_dict
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.set_parameter('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']})示例8: test_undo_last_transformation_and_redo
def test_undo_last_transformation_and_redo(self):
trans = []
trans.append(SubstitutionTransformation({"Li":"Na"}))
trans.append(SubstitutionTransformation({"Fe":"Mn"}))
ts = TransformedStructure(self.structure, trans)
self.assertEqual("NaMnPO4", ts.final_structure.composition.reduced_formula)
ts.undo_last_transformation()
self.assertEqual("NaFePO4", ts.final_structure.composition.reduced_formula)
ts.undo_last_transformation()
self.assertEqual("LiFePO4", ts.final_structure.composition.reduced_formula)
self.assertRaises(IndexError, ts.undo_last_transformation)
ts.redo_next_transformation()
self.assertEqual("NaFePO4", ts.final_structure.composition.reduced_formula)
ts.redo_next_transformation()
self.assertEqual("NaMnPO4", ts.final_structure.composition.reduced_formula)
self.assertRaises(IndexError, ts.redo_next_transformation)示例9: convert_fmt
def convert_fmt(args):
iformat = args.input_format[0]
oformat = args.output_format[0]
filename = args.input_filename[0]
out_filename = args.output_filename[0]
try:
if iformat == "smart":
structure = read_structure(filename)
if iformat == "POSCAR":
p = Poscar.from_file(filename)
structure = p.structure
elif iformat == "CIF":
r = CifParser(filename)
structure = r.get_structures()[0]
elif iformat == "CSSR":
structure = Cssr.from_file(filename).structure
if oformat == "smart":
write_structure(structure, out_filename)
elif oformat == "POSCAR":
p = Poscar(structure)
p.write_file(out_filename)
elif oformat == "CIF":
w = CifWriter(structure)
w.write_file(out_filename)
elif oformat == "CSSR":
c = Cssr(structure)
c.write_file(out_filename)
elif oformat == "VASP":
input_set = MPVaspInputSet()
ts = TransformedStructure(
structure,
[],
history=[
{"source": "file", "datetime": str(datetime.datetime.now()), "original_file": open(filename).read()}
],
)
ts.write_vasp_input(input_set, output_dir=out_filename)
elif oformat == "MITVASP":
input_set = MITVaspInputSet()
ts = TransformedStructure(
structure,
[],
history=[
{"source": "file", "datetime": str(datetime.datetime.now()), "original_file": open(filename).read()}
],
)
ts.write_vasp_input(input_set, output_dir=out_filename)
except Exception as ex:
print "Error converting file. Are they in the right format?"
print str(ex)示例10: __init__
def __init__(self, poscar_string, transformations=[], extend_collection=False):
"""
Generates a transmuter from a sequence of POSCARs.
Args:
poscar_string:
List of POSCAR strings
transformations:
New transformations to be applied to all structures.
primitive:
Whether to generate the primitive cell from the cif.
extend_collection:
Whether to use more than one output structure from one-to-many
transformations.
"""
transformed_structures = []
transformed_structures.append(TransformedStructure.from_poscar_string(poscar_string, []))
StandardTransmuter.__init__(self, transformed_structures, transformations, extend_collection=extend_collection)示例11: __init__
def __init__(self, poscar_string, transformations=None,
extend_collection=False):
tstruct = TransformedStructure.from_poscar_string(poscar_string, [])
StandardTransmuter.__init__(self, [tstruct], transformations,
extend_collection=extend_collection)示例12: TransformedStructureTest
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,
#.........这里部分代码省略.........
示例13: from_filenames
def from_filenames(poscar_filenames, transformations=[], extend_collection=False):
transformed_structures = []
for filename in poscar_filenames:
with open(filename, "r") as f:
transformed_structures.append(TransformedStructure.from_poscar_string(f.read(), []))
return StandardTransmuter(transformed_structures, transformations, extend_collection=extend_collection)示例14: test_undo_and_redo_last_change
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()示例15: CifParser
excluded_bonding_elements = args.exclude_bonding[0].split(',') if args.exclude_bonding else []
file_format = args.format
filename = args.input_file[0]
s = None
if filename.endswith(".cif"):
file_format = "cif"
elif filename.startswith("POSCAR"):
file_format = "poscar"
elif re.search('\.json', filename):
file_format = 'mpjson'
if file_format == 'poscar':
p = Poscar.from_file(filename)
s = p.struct
elif file_format == 'cif':
r = CifParser(filename)
s = r.get_structures(False)[0]
else:
d = json.load(file_open_zip_aware(filename))
ts = TransformedStructure.from_dict(d)
s = ts.final_structure
if s:
vis = StructureVis(excluded_bonding_elements=excluded_bonding_elements)
vis.set_structure(s)
vis.show()