def get_prim_host(struct):
"""
Get the primitive structure with all of the lithiums removed
"""
structure = struct.copy()
structure.remove_species([self.working_ion])
prim = PrimitiveCellTransformation()
return prim.apply_transformation(structure)
def abi_sanitize(self, symprec=1e-3, primitive=True):
"""
Returns a new structure in which:
* Oxidation states are removed.
* Structure is refined.
* Reduced to primitive settings.
* Lattice vectors are exchanged if the triple product is negative
Args:
symprec: Symmetry precision used to refine the structure.
if `symprec` is None, so structure refinement is peformed.
primitive (bool): Whether to convert to a primitive cell.
"""
from pymatgen.transformations.standard_transformations import OxidationStateRemovalTransformation, \
PrimitiveCellTransformation, SupercellTransformation
# Remove oxidation states.
remove_ox = OxidationStateRemovalTransformation()
structure = remove_ox.apply_transformation(self)
# Refine structure
if symprec is not None:
sym_finder = SpacegroupAnalyzer(structure=structure,
symprec=symprec)
structure = sym_finder.get_refined_structure()
# Convert to primitive structure.
if primitive:
get_prim = PrimitiveCellTransformation()
structure = get_prim.apply_transformation(structure)
# Exchange last two lattice vectors if triple product is negative.
m = structure.lattice.matrix
x_prod = np.dot(np.cross(m[0], m[1]), m[2])
if x_prod < 0:
trans = SupercellTransformation(((1, 0, 0), (0, 0, 1), (0, 1, 0)))
structure = trans.apply_transformation(structure)
m = structure.lattice.matrix
x_prod = np.dot(np.cross(m[0], m[1]), m[2])
if x_prod < 0: raise RuntimeError("x_prod is still negative!")
return structure
def refine_structure(structure, symprec=1e-3):
remove_ox = OxidationStateRemovalTransformation()
structure = remove_ox.apply_transformation(structure)
sym_finder = SpacegroupAnalyzer(structure=structure, symprec=symprec)
structure = sym_finder.get_refined_structure()
get_prim = PrimitiveCellTransformation()
structure = get_prim.apply_transformation(structure)
m = structure.lattice.matrix
x_prod = np.dot(np.cross(m[0], m[1]), m[2])
if x_prod < 0:
print(x_prod)
trans = SupercellTransformation(((1, 0, 0), (0, 0, 1), (0, 1, 0)))
structure = trans.apply_transformation(structure)
m = structure.lattice.matrix
x_prod = np.dot(np.cross(m[0], m[1]), m[2])
print(x_prod)
if x_prod < 0:
raise RuntimeError
return structure
def abi_sanitize(self, symprec=1e-3, angle_tolerance=5, primitive=True, primitive_standard=False):
"""
Returns a new structure in which:
* Structure is refined.
* Reduced to primitive settings.
* Lattice vectors are exchanged if the triple product is negative
Args:
symprec: Symmetry precision used to refine the structure.
if `symprec` is None, so structure refinement is peformed.
primitive (bool): Whether to convert to a primitive cell.
"""
from pymatgen.transformations.standard_transformations import PrimitiveCellTransformation, SupercellTransformation
structure = self.__class__.from_sites(self)
# Refine structure
if symprec is not None and angle_tolerance is not None:
sym_finder = SpacegroupAnalyzer(structure=structure, symprec=symprec, angle_tolerance=angle_tolerance)
structure = sym_finder.get_refined_structure()
# Convert to primitive structure.
if primitive:
if primitive_standard:
sym_finder_prim = SpacegroupAnalyzer(structure=structure, symprec=symprec, angle_tolerance=angle_tolerance)
structure = sym_finder_prim.get_primitive_standard_structure()
else:
get_prim = PrimitiveCellTransformation()
structure = get_prim.apply_transformation(structure)
# Exchange last two lattice vectors if triple product is negative.
m = structure.lattice.matrix
x_prod = np.dot(np.cross(m[0], m[1]), m[2])
if x_prod < 0:
trans = SupercellTransformation(((1, 0, 0), (0, 0, 1), (0, 1, 0)))
structure = trans.apply_transformation(structure)
m = structure.lattice.matrix
x_prod = np.dot(np.cross(m[0], m[1]), m[2])
if x_prod < 0: raise RuntimeError("x_prod is still negative!")
return structure
def refine_structure(structure, symprec=1e-3):
remove_ox = OxidationStateRemovalTransformation()
structure = remove_ox.apply_transformation(structure)
sym_finder = SpacegroupAnalyzer(structure=structure, symprec=symprec)
structure = sym_finder.get_refined_structure()
get_prim = PrimitiveCellTransformation()
structure = get_prim.apply_transformation(structure)
m = structure.lattice.matrix
x_prod = np.dot(np.cross(m[0], m[1]), m[2])
if x_prod < 0:
print(x_prod)
trans = SupercellTransformation(((1, 0, 0), (0, 0, 1), (0, 1, 0)))
structure = trans.apply_transformation(structure)
m = structure.lattice.matrix
x_prod = np.dot(np.cross(m[0], m[1]), m[2])
print(x_prod)
if x_prod < 0:
raise RuntimeError
return structure
def test_apply_transformation(self):
t = PrimitiveCellTransformation()
coords = []
coords.append([0, 0, 0])
coords.append([0.375, 0.375, 0.375])
coords.append([0.5, 0.5, 0.5])
coords.append([0.875, 0.875, 0.875])
coords.append([0.125, 0.125, 0.125])
coords.append([0.25, 0.25, 0.25])
coords.append([0.625, 0.625, 0.625])
coords.append([0.75, 0.75, 0.75])
lattice = Lattice([
[3.8401979337, 0.00, 0.00],
[1.9200989668, 3.3257101909, 0.00],
[0.00, -2.2171384943, 3.1355090603],
])
struct = Structure(
lattice, ["Li+", "Li+", "Li+", "Li+", "O2-", "O2-", "O2-", "O2-"],
coords)
s = t.apply_transformation(struct)
self.assertEqual(len(s), 4)
with open(os.path.join(PymatgenTest.TEST_FILES_DIR,
"TiO2_super.json")) as f:
s = json.load(f, cls=MontyDecoder)
prim = t.apply_transformation(s)
self.assertEqual(prim.formula, "Ti4 O8")
d = t.as_dict()
self.assertEqual(type(PrimitiveCellTransformation.from_dict(d)),
PrimitiveCellTransformation)
