def test_get_mapping(self):
sm = StructureMatcher(ltol=0.2,
stol=0.3,
angle_tol=5,
primitive_cell=False,
scale=True,
attempt_supercell=False,
allow_subset=True)
l = Lattice.orthorhombic(1, 2, 3)
s1 = Structure(l, ['Ag', 'Si', 'Si'],
[[.7, .4, .5], [0, 0, 0.1], [0, 0, 0.2]])
s1.make_supercell([2, 1, 1])
s2 = Structure(l, ['Si', 'Si', 'Ag'],
[[0, 0.1, -0.95], [0, 0.1, 0], [-.7, .5, .375]])
shuffle = [2, 0, 1, 3, 5, 4]
s1 = Structure.from_sites([s1[i] for i in shuffle])
#test the mapping
s2.make_supercell([2, 1, 1])
#equal sizes
for i, x in enumerate(sm.get_mapping(s1, s2)):
self.assertEqual(s1[x].species_and_occu, s2[i].species_and_occu)
del s1[0]
#s1 is subset of s2
for i, x in enumerate(sm.get_mapping(s2, s1)):
self.assertEqual(s1[i].species_and_occu, s2[x].species_and_occu)
#s2 is smaller than s1
del s2[0]
del s2[1]
self.assertRaises(ValueError, sm.get_mapping, s2, s1)
def test_get_mapping(self):
sm = StructureMatcher(ltol=0.2, stol=0.3, angle_tol=5,
primitive_cell=False, scale=True,
attempt_supercell=False,
allow_subset = True)
l = Lattice.orthorhombic(1, 2, 3)
s1 = Structure(l, ['Ag', 'Si', 'Si'],
[[.7,.4,.5],[0,0,0.1],[0,0,0.2]])
s1.make_supercell([2,1,1])
s2 = Structure(l, ['Si', 'Si', 'Ag'],
[[0,0.1,-0.95],[0,0.1,0],[-.7,.5,.375]])
shuffle = [2,0,1,3,5,4]
s1 = Structure.from_sites([s1[i] for i in shuffle])
#test the mapping
s2.make_supercell([2,1,1])
#equal sizes
for i, x in enumerate(sm.get_mapping(s1, s2)):
self.assertEqual(s1[x].species_and_occu,
s2[i].species_and_occu)
del s1[0]
#s1 is subset of s2
for i, x in enumerate(sm.get_mapping(s2, s1)):
self.assertEqual(s1[i].species_and_occu,
s2[x].species_and_occu)
#s2 is smaller than s1
del s2[0]
del s2[1]
self.assertRaises(ValueError, sm.get_mapping, s2, s1)
class observer_spinel(observer_base):
def __init__(self, Asite_struct, Bspecie):
super(observer_spinel, self).__init__()
self.Asite_struct = Asite_struct
self.Bspecie = Bspecie
self.site_matcher = StructureMatcher(
ltol=0.1,
primitive_cell=False,
allow_subset=True,
comparator=FrameworkComparator(),
ignored_species=["O"],
)
def DOI(self, calc_state):
asites = self.site_matcher.get_mapping(calc_state.config.structure,
self.Asite_struct)
# print asites
# print spinel_config.structure
# print spinel_config.Asite_struct
x = 0
for i in asites:
if calc_state.config.structure.species[i] == Element(self.Bspecie):
x += 1
x /= float(len(asites))
return x
def logfunc(self, calc_state):
return calc_state.energy, self.DOI(calc_state)
def test_rms_vs_minimax(self):
# This tests that structures with adjusted RMS less than stol, but minimax
# greater than stol are treated properly
sm = StructureMatcher(ltol=0.2, stol=0.3, angle_tol=5, primitive_cell=False)
l = Lattice.orthorhombic(1, 2, 12)
sp = ["Si", "Si", "Al"]
s1 = Structure(l, sp, [[0.5, 0, 0], [0, 0, 0], [0, 0, 0.5]])
s2 = Structure(l, sp, [[0.5, 0, 0], [0, 0, 0], [0, 0, 0.6]])
self.assertArrayAlmostEqual(sm.get_rms_dist(s1, s2), (0.32 ** 0.5 / 2, 0.4))
self.assertEqual(sm.fit(s1, s2), False)
self.assertEqual(sm.fit_anonymous(s1, s2), False)
self.assertEqual(sm.get_mapping(s1, s2), None)
def test_rms_vs_minimax(self):
# This tests that structures with adjusted RMS less than stol, but minimax
# greater than stol are treated properly
# stol=0.3 gives exactly an ftol of 0.1 on the c axis
sm = StructureMatcher(ltol=0.2, stol=0.301, angle_tol=1, primitive_cell=False)
l = Lattice.orthorhombic(1, 2, 12)
sp = ["Si", "Si", "Al"]
s1 = Structure(l, sp, [[0.5, 0, 0], [0, 0, 0], [0, 0, 0.5]])
s2 = Structure(l, sp, [[0.5, 0, 0], [0, 0, 0], [0, 0, 0.6]])
self.assertArrayAlmostEqual(sm.get_rms_dist(s1, s2),
(0.32 ** 0.5 / 2, 0.4))
self.assertEqual(sm.fit(s1, s2), False)
self.assertEqual(sm.fit_anonymous(s1, s2), False)
self.assertEqual(sm.get_mapping(s1, s2), None)
def occu_from_structure(self, structure, return_mapping=False):
"""
Calculates the correlation vector. Structure must be on this supercell
"""
#calculate mapping to supercell
sm_no_sc = StructureMatcher(primitive_cell=False,
attempt_supercell=False,
allow_subset=True,
comparator=OrderDisorderElementComparator(),
supercell_size=self.cluster_expansion.supercell_size,
scale=True,
ltol=self.cluster_expansion.ltol,
stol=self.cluster_expansion.stol,
angle_tol=self.cluster_expansion.angle_tol)
#print('sc:\n',self.supercell_matrix,\
# '\nstr:\n',self.cluster_expansion.supercell_matrix_from_structure(structure))
mapping = sm_no_sc.get_mapping(self.supercell, structure)
if mapping is None:
raise ValueError('Structure cannot be mapped to this supercell. Structure:{}\nSupercell:{}'.format(structure,self.supercell))
mapping = mapping.tolist()
#cs.supercell[mapping] = structure
occu = np.zeros(len(self.supercell), dtype=np.int)
for i, bit in enumerate(self.bits):
# print('i=',i)
# print('bit=', bit)
#rather than starting with all vacancies and looping
#only over mapping, explicitly loop over everything to
#catch vacancies on improper sites
if i in mapping:
sp = str(structure[mapping.index(i)].specie)
else:
sp = 'Vacancy'
occu[i] = bit.index(sp)
if not return_mapping:
return occu
else:
return occu, mapping
class config:
"""This class defines the config with lattice gas mapping"""
def __init__(
self,
base_structure,
defect_sublattices,
num_defects,
cellsize=[1, 1, 1],
perf_structure=None,
):
try:
num_defect_sublat = len(defect_sublattices)
except TypeError:
num_defect_sublat = 1
defect_sublattices = [defect_sublattices]
num_defects = [num_defects]
self.matcher_base = StructureMatcher(primitive_cell=False,
allow_subset=True)
self.matcher_frame = StructureMatcher(
stol=0.4,
primitive_cell=False,
allow_subset=True,
comparator=FrameworkComparator(),
)
self.calc_history = []
self.cellsize = cellsize
self.base_structure = base_structure
if self.base_structure.num_sites == 0:
# we need at least one site for make_supercell
self.base_structure.append("H", np.array([0, 0, 0]))
self.base_structure.make_supercell(
[cellsize[0], cellsize[1], cellsize[2]])
self.base_structure.remove_sites(
range(self.base_structure.num_sites))
else:
self.base_structure.make_supercell(
[cellsize[0], cellsize[1], cellsize[2]])
if perf_structure:
self.perf_structure = perf_structure
self.perf_structure.make_supercell(
[cellsize[0], cellsize[1], cellsize[2]])
self.supercell = self.base_structure.lattice.matrix
self.n_sublat = num_defect_sublat
invSuper = np.linalg.inv(self.supercell)
# add supercell information to defect_sites
num_sites = 0
ntot_defects = 0
sublat_id = 0
for defect_sublattice in defect_sublattices:
site_centers = defect_sublattice.site_centers
defect_sublattice.site_centers_sc = np.zeros(
(np.prod(cellsize) * site_centers.shape[0], 3), dtype=float)
idx = 0
for i in range(cellsize[0]):
for j in range(cellsize[1]):
for k in range(cellsize[2]):
for l in range(site_centers.shape[0]):
defect_sublattice.site_centers_sc[
idx] = site_centers[l] + np.array([i, j, k])
idx += 1
defect_sublattice.site_centers_sc /= np.array(cellsize)
num_sites += len(defect_sublattice.site_centers_sc)
# change cartesian coordinates to fractional
for group in defect_sublattice.groups:
for i in range(group.orientations):
for j in range(group.natoms):
group.coords[i][j] = np.dot(group.coords[i][j],
invSuper)
# fill the lattice gas representation list
latgas_rep = []
for group in num_defects[sublat_id].keys():
latgas_rep.extend(
[[group, 0] for i in range(num_defects[sublat_id][group])])
ntot_defects += num_defects[sublat_id][group]
defect_sublattice.latgas_rep = latgas_rep
sublat_id += 1
self.defect_sublattices = defect_sublattices
assert num_sites == ntot_defects
self.set_latgas()
def set_latgas(self, defect_sublattices=False):
if defect_sublattices:
self.defect_sublattices = defect_sublattices
assert len(self.defect_sublattices) == self.n_sublat
self.structure = copy.deepcopy(self.base_structure)
for defect_sublattice in self.defect_sublattices:
latgas_rep = defect_sublattice.latgas_rep
assert len(latgas_rep) == len(defect_sublattice.site_centers_sc)
for isite in range(len(latgas_rep)):
grp_name = latgas_rep[isite][0]
orr = latgas_rep[isite][1]
group = defect_sublattice.group_dict[grp_name]
for j in range(group.natoms):
self.structure.append(
group.species[j], group.coords[orr][j] +
defect_sublattice.site_centers_sc[isite]
# properties={"velocities":[0,0,0]}
)
def shuffle(self):
for defect_sublattice in self.defect_sublattices:
latgas_rep = defect_sublattice.latgas_rep
rand.shuffle(latgas_rep)
for site in latgas_rep:
group = defect_sublattice.group_dict[site[0]]
norr = group.orientations
site[1] = rand.randrange(norr)
# print(latgas_rep)
self.set_latgas()
def count(self, group_name, orientation):
num_grp = []
for defect_sublattice in self.defect_sublattices:
num_grp.append(
defect_sublattice.latgas_rep.count([group_name, orientation]))
return num_grp
def update_basestruct(self):
basesites = self.matcher_base.get_mapping(self.structure,
self.base_structure)
idx = 0
for i in basesites:
self.base_structure[idx] = self.structure[i]
idx += 1
def defect_sublattice_structure(self, sublat_id):
assert sublat_id < self.n_sublat
sublattice_structure = self.structure.copy()
base_sites = self.matcher_base.get_mapping(self.structure,
self.base_structure)
sublattice_structure.remove_sites(base_sites)
return sublattice_structure
@property
def vacancy_structure(self):
filledsites = self.matcher_frame.get_mapping(self.perf_structure,
self.structure)
# print(self.perf_structure)
# print(self.structure)
# print(filledsites)
vac_structure = self.perf_structure.copy()
vac_structure.remove_sites(filledsites)
return vac_structure
for site in Vacsites:
structure.pop(site)
structure_Osite = structure.copy()
structure_Osite.remove_species(["Pt", "Zr"])
matcher_site = StructureMatcher(
ltol=ltol,
primitive_cell=False,
allow_subset=True,
comparator=FrameworkComparator(),
ignored_species=["Pt"],
)
# Figure out where the vacancies are by comparing with base_structure
filled_sites = matcher_site.get_mapping(base_Osite, structure_Osite)
print(filled_sites)
vac_struct = base_Osite.copy()
vac_struct.remove_sites(filled_sites)
print(vac_struct)
# assert len(vac_struct) == 10
# choose one vacancy and one O atom randomly and flip
vac_flip = rand.choice(vac_struct)
Osites = structure.indices_from_symbol("O")
O_flip = rand.choice(Osites)
del structure[O_flip]
print(vac_flip.frac_coords)
class config:
"""This class defines the config with lattice gas mapping"""
def __init__(
self,
base_structure,
defect_sublattices,
num_defects,
cellsize=[1, 1, 1],
perfect_structure=None,
):
"""
Parameters
----------
base_structure : pymatgen.Structure
Structure of base sites (unsampled sites)
defect_sublattices : defect_sublattice
Structure of defects (sampled sites)
num_defects : dict
{group name: number of defects}
cellsize : list, optional
Cell size, by default [1, 1, 1]
perfect_structure : pymatgen.Structure, optional
Strucure of all sites (union of base and defect), by default None
"""
try:
num_defect_sublat = len(defect_sublattices)
except TypeError:
num_defect_sublat = 1
defect_sublattices = [defect_sublattices]
num_defects = [num_defects]
self.matcher_base = StructureMatcher(primitive_cell=False,
allow_subset=True)
self.matcher_frame = StructureMatcher(
stol=0.4,
primitive_cell=False,
allow_subset=True,
comparator=FrameworkComparator(),
)
self.calc_history = []
self.cellsize = cellsize
self.base_structure = base_structure
if self.base_structure.num_sites == 0:
# we need at least one site for make_supercell
self.base_structure.append("H", np.array([0, 0, 0]))
self.base_structure.make_supercell(
[cellsize[0], cellsize[1], cellsize[2]])
self.base_structure.remove_sites(
range(self.base_structure.num_sites))
else:
self.base_structure.make_supercell(
[cellsize[0], cellsize[1], cellsize[2]])
if perfect_structure:
self.perfect_structure = perfect_structure
self.perfect_structure.make_supercell(
[cellsize[0], cellsize[1], cellsize[2]])
self.supercell = self.base_structure.lattice.matrix
self.n_sublat = num_defect_sublat
invSuper = np.linalg.inv(self.supercell)
# add supercell information to defect_sites
num_sites = 0
ntot_defects = 0
sublat_id = 0
for defect_sublattice in defect_sublattices:
site_centers = defect_sublattice.site_centers
defect_sublattice.site_centers_sc = np.zeros(
(np.prod(cellsize) * site_centers.shape[0], 3), dtype=float)
idx = 0
for (idx, (i, j, k, l)) in enumerate(
product(
range(cellsize[0]),
range(cellsize[1]),
range(cellsize[2]),
range(site_centers.shape[0]),
)):
defect_sublattice.site_centers_sc[
idx] = site_centers[l] + np.array([i, j, k])
idx += 1
defect_sublattice.site_centers_sc /= np.array(cellsize)
num_sites += len(defect_sublattice.site_centers_sc)
# change cartesian coordinates to fractional
for group in defect_sublattice.groups:
for i in range(group.orientations):
for j in range(group.natoms):
group.coords[i][j] = np.dot(group.coords[i][j],
invSuper)
# fill the lattice gas representation list
latgas_rep = []
for group in num_defects[sublat_id].keys():
latgas_rep.extend(
[[group, 0] for i in range(num_defects[sublat_id][group])])
ntot_defects += num_defects[sublat_id][group]
defect_sublattice.latgas_rep = latgas_rep
sublat_id += 1
self.defect_sublattices = defect_sublattices
assert num_sites == ntot_defects
self.set_latgas()
def set_latgas(self, defect_sublattices=False):
"""
Parameters
----------
defect_sublattices: pymatgen.Structure
"""
if defect_sublattices:
self.defect_sublattices = defect_sublattices
assert len(self.defect_sublattices) == self.n_sublat
self.structure = copy.deepcopy(self.base_structure)
for defect_sublattice in self.defect_sublattices:
latgas_rep = defect_sublattice.latgas_rep
assert len(latgas_rep) == len(defect_sublattice.site_centers_sc)
for isite in range(len(latgas_rep)):
grp_name = latgas_rep[isite][0]
orr = latgas_rep[isite][1]
group = defect_sublattice.group_dict[grp_name]
for j in range(group.natoms):
self.structure.append(
group.species[j],
group.coords[orr][j] +
defect_sublattice.site_centers_sc[isite],
properties={
"seldyn": group.relaxations[j, :],
"magnetization": group.magnetizations[j],
},
)
def shuffle(self):
for defect_sublattice in self.defect_sublattices:
latgas_rep = defect_sublattice.latgas_rep
rand.shuffle(latgas_rep)
for site in latgas_rep:
group = defect_sublattice.group_dict[site[0]]
norr = group.orientations
site[1] = rand.randint(norr)
self.set_latgas()
def count(self, group_name, orientation):
"""
Parameters
----------
group_name: str
The name of the group
orientation:
Returns
-------
"""
num_grp = []
for defect_sublattice in self.defect_sublattices:
num_grp.append(
defect_sublattice.latgas_rep.count([group_name, orientation]))
return num_grp
def update_basestruct(self):
basesites = self.matcher_base.get_mapping(self.structure,
self.base_structure)
idx = 0
for i in basesites:
self.base_structure[idx] = self.structure[i]
idx += 1
def defect_sublattice_structure(self, sublat_id):
"""
Parameters
----------
sublat_id: int
index of sublattice
Returns
-------
sublattice_structure: pymatgen.Structure
sublattice structure object
"""
assert sublat_id < self.n_sublat
sublattice_structure = self.structure.copy()
base_sites = self.matcher_base.get_mapping(self.structure,
self.base_structure)
sublattice_structure.remove_sites(base_sites)
return sublattice_structure
@property
def vacancy_structure(self):
filledsites = self.matcher_frame.get_mapping(self.perfect_structure,
self.structure)
vac_structure = self.perfect_structure.copy()
vac_structure.remove_sites(filledsites)
return vac_structure