def __init__(self,
optypes,
override_cn1=True,
cutoff_radius=8,
tol=1E-2,
cation_anion=False):
self.optypes = optypes.copy()
self.override_cn1 = override_cn1
self.cutoff_radius = cutoff_radius
self.tol = tol
self.cation_anion = cation_anion
if self.override_cn1 and self.optypes.get(1) != ["wt"]:
raise ValueError(
"If override_cn1 is True, optypes[1] must be ['wt']!")
self.ops = {}
for cn, t_list in self.optypes.items():
self.ops[cn] = []
for t in t_list:
if t == "wt":
self.ops[cn].append(t)
elif t[:4] == 'bent':
self.ops[cn].append(OrderParameters(
[t[:4]], parameters=[{'TA': float(t[4:]) / 180.0, \
'IGW_TA': 1.0 / 0.0667}]))
else:
self.ops[cn].append(OrderParameters([t]))
def featurize(self, s, pneighs=None):
"""
Calculate all sites' OPs.
Args:
s: Pymatgen Structure object.
pneighs: (dict) specification and parameters of
neighbor-finding approach (see
get_neighbors_of_site_with_index function
in Pymatgen for more details).
Returns:
opvals: (2D array of floats) OP values of all sites'
(1st dimension) order parameters (2nd dimension). 46 order
parameters are computed per site: q_cn (coordination
number), q_lin, 35 x q_bent (starting with a target angle
of 5 degrees and, increasing by 5 degrees, until 175 degrees),
q_tet, q_oct, q_bcc, q_2, q_4, q_6, q_reg_tri, q_sq, q_sq_pyr.
"""
opvals = []
ops = OrderParameters(self._types, self._paras, 100.0)
for i, site in enumerate(s.sites):
neighcent = get_neighbors_of_site_with_index(s, i, p=pneighs)
neighcent.append(site)
opvals.append(
ops.get_order_parameters(
neighcent,
len(neighcent) - 1,
indeces_neighs=[j for j in range(len(neighcent) - 1)]))
for j, opval in enumerate(opvals[i]):
if opval is None:
opvals[i][j] = 0.0
return opvals
def get_order_parameters(struct, pneighs={}, convert_none_to_zero=True):
"""
Determine the neighbors around the site that has index n in the input
Structure object struct, given a pre-defined approach. So far,
"scaled_VIRE" and "min_relative_VIRE" are implemented
(VIRE = valence-ionic radius evaluator).
Args:
struct (Structure): input structure.
pneighs (dict): specification ("approach") and parameters of
neighbor-finding approach (see
get_neighbors_of_site_with_index function
for more details; default: min_relative_VIRE,
delta_scale = 0.05, scale_cut = 4).
convert_none_to_zero (bool): flag indicating whether or not
to convert None values in OPs to zero.
Returns: ([[float]]) matrix of all sites' (1st dimension)
order parameters (2nd dimension). 46 order parameters are
computed per site: q_cn (coordination number), q_lin,
35 x q_bent (starting with a target angle of 5 degrees and,
increasing by 5 degrees, until 175 degrees), q_tet, q_oct,
q_bcc, q_2, q_4, q_6, q_reg_tri, q_sq, q_sq_pyr.
"""
if pneighs == {}:
pneighs = {
"approach": "min_relative_VIRE",
"delta_scale": 0.05,
"scale_cut": 4
}
opvals = []
optypes = ["cn", "lin"]
opparas = [[], []]
for i in range(5, 180, 5):
optypes.append("bent")
opparas.append([float(i), 0.0667])
for t in ["tet", "oct", "bcc", "q2", "q4", "q6", "reg_tri", "sq", \
"sq_pyr"]:
optypes.append(t)
opparas.append([])
ops = OrderParameters(optypes, opparas, 100.0)
for i, s in enumerate(struct.sites):
neighcent = get_neighbors_of_site_with_index(struct, i, pneighs)
neighcent.append(s)
opvals.append(
ops.get_order_parameters(
neighcent,
len(neighcent) - 1,
indeces_neighs=[j for j in range(len(neighcent) - 1)]))
if convert_none_to_zero:
for j, opval in enumerate(opvals[i]):
if opval is None:
opvals[i][j] = 0.0
return opvals
def get_order_parameters(struct, pneighs=None, convert_none_to_zero=True):
"""
Calculate all order parameters (OPs) for all sites in Structure object
struct.
Args:
struct (Structure): input structure.
pneighs (dict): specification and parameters of
neighbor-finding approach (see
get_neighbors_of_site_with_index function
for more details).
convert_none_to_zero (bool): flag indicating whether or not
to convert None values in OPs to zero.
Returns: ([[float]]) matrix of all sites' (1st dimension)
order parameters (2nd dimension). 46 order parameters are
computed per site: q_cn (coordination number), q_lin,
35 x q_bent (starting with a target angle of 5 degrees and,
increasing by 5 degrees, until 175 degrees), q_tet, q_oct,
q_bcc, q_2, q_4, q_6, q_reg_tri, q_sq, q_sq_pyr.
"""
opvals = []
optypes = ["cn", "lin"]
opparas = [[], []]
for i in range(5, 180, 5):
optypes.append("bent")
opparas.append([float(i), 0.0667])
for t in ["tet", "oct", "bcc", "q2", "q4", "q6", "reg_tri", "sq", \
"sq_pyr"]: # , "tri_bipyr"]:
optypes.append(t)
opparas.append([])
ops = OrderParameters(optypes, opparas, 100.0)
for i, s in enumerate(struct.sites):
neighcent = get_neighbors_of_site_with_index(struct, i, pneighs)
neighcent.append(s)
opvals.append(
ops.get_order_parameters(
neighcent,
len(neighcent) - 1,
indeces_neighs=[j for j in range(len(neighcent) - 1)]))
if convert_none_to_zero:
for j, opval in enumerate(opvals[i]):
if opval is None:
opvals[i][j] = 0.0
return opvals
def __init__(self,
optypes,
override_cn1=True,
cutoff_radius=8,
tol=1E-2,
cation_anion=False):
"""
Initialize the CrystalSiteFingerprint. Use the from_preset() function to
use default params.
Args:
optypes (dict): a dict of coordination number (int) to a list of str
representing the order parameter types
override_cn1 (bool): whether to use a special function for the single
neighbor case. Suggest to keep True.
cutoff_radius (int): radius in Angstroms for neighbor finding
tol (float): numerical tolerance (in case your site distances are
not perfect or to correct for float tolerances)
cation_anion (bool): whether to only consider cation<->anion bonds
(bonds with zero charge are also allowed)
"""
self.optypes = optypes.copy()
self.override_cn1 = override_cn1
self.cutoff_radius = cutoff_radius
self.tol = tol
self.cation_anion = cation_anion
if self.override_cn1 and self.optypes.get(1) != ["wt"]:
raise ValueError(
"If override_cn1 is True, optypes[1] must be ['wt']!")
self.ops = {}
for cn, t_list in self.optypes.items():
self.ops[cn] = []
for t in t_list:
if t == "wt":
self.ops[cn].append(t)
elif t[:4] == 'bent':
self.ops[cn].append(OrderParameters(
[t[:4]], parameters=[{'TA': float(t[4:]) / 180.0, \
'IGW_TA': 1.0 / 0.0667}]))
else:
self.ops[cn].append(OrderParameters([t]))
def featurize(self, s):
"""
Calculate all sites' local structure order parameters (LSOPs).
Args:
s: Pymatgen Structure object.
Returns:
opvals: (2D array of floats) LSOP values of all sites'
(1st dimension) order parameters (2nd dimension). 46 order
parameters are computed per site: q_cn (coordination
number), q_lin, 35 x q_bent (starting with a target angle
of 5 degrees and, increasing by 5 degrees, until 175 degrees),
q_tet, q_oct, q_bcc, q_2, q_4, q_6, q_reg_tri, q_sq, q_sq_pyr.
"""
ops = OrderParameters(self._types, self._paras, 100.0)
opvals = [[] for t in self._types]
for i, site in enumerate(s.sites):
neighcent = get_neighbors_of_site_with_index(
s, i, p=self.pneighs)
neighcent.append(site)
opvalstmp = ops.get_order_parameters(
neighcent, len(neighcent) - 1,
indeces_neighs=[j for j in range(len(neighcent) - 1)])
for j, opval in enumerate(opvalstmp):
if opval is None:
opvals[j].append(0.0)
else:
opvals[j].append(opval)
if self.stats:
opstats = []
for op in opvals:
if '_mode' in ''.join(self.stats):
modes = PropertyStats().n_numerical_modes(
op, self.nmodes, 0.01)
for stat in self.stats:
if '_mode' in stat:
opstats.append(modes[int(stat[0])-1])
else:
opstats.append(PropertyStats().calc_stat(op, stat))
return opstats
else:
return opvals
def get_ordering_for_sites(struct, sites):
"""
Gets the ordering parameter for a list of indices.
:param struct: Pymatgen Structure object
:param sites: List of sites for which we want the order parameter.
:return: Dictionary mapping ordering params to indices.
"""
bop_types = ["q4"]
paras = [[]]
cut_r = 3.0
# results = {}
results = []
bops = OrderParameters(bop_types, paras, cutoff=cut_r)
for i, s in enumerate(sites):
op = bops.get_order_parameters(struct, s)
if op[0] is not None:
results.append(op[0])
return np.array(results)
def get_order_parameters(struct, pneighs=None, convert_none_to_zero=True):
"""
Calculate all order parameters (OPs) for all sites in Structure object
struct.
Args:
struct (Structure): input structure.
pneighs (dict): specification and parameters of
neighbor-finding approach (see
get_neighbors_of_site_with_index function
for more details).
convert_none_to_zero (bool): flag indicating whether or not
to convert None values in OPs to zero.
Returns: ([[float]]) matrix of all sites' (1st dimension)
order parameters (2nd dimension). 46 order parameters are
computed per site: q_cn (coordination number), q_lin,
35 x q_bent (starting with a target angle of 5 degrees and,
increasing by 5 degrees, until 175 degrees), q_tet, q_oct,
q_bcc, q_2, q_4, q_6, q_reg_tri, q_sq, q_sq_pyr.
"""
opvals = []
optypes = ["cn", "lin"]
opparas = [[], []]
for i in range(5, 180, 5):
optypes.append("bent")
opparas.append([float(i), 0.0667])
for t in ["tet", "oct", "bcc", "q2", "q4", "q6", "reg_tri", "sq", "sq_pyr"]: # , "tri_bipyr"]:
optypes.append(t)
opparas.append([])
ops = OrderParameters(optypes, opparas, 100.0)
for i, s in enumerate(struct.sites):
neighcent = get_neighbors_of_site_with_index(struct, i, pneighs)
neighcent.append(s)
opvals.append(ops.get_order_parameters(
neighcent, len(neighcent) - 1,
indeces_neighs=[j for j in range(len(neighcent) - 1)]))
if convert_none_to_zero:
for j, opval in enumerate(opvals[i]):
if opval is None:
opvals[i][j] = 0.0
return opvals
def __init__(self,
optypes=None,
dr=0.1,
ddr=0.01,
ndr=1,
dop=0.001,
dist_exp=2,
zero_ops=True):
self.optypes = {
1: ["sgl_bd"],
2: ["bent180", "bent45", "bent90", "bent135"],
3: ["tri_plan", "tet", "T"],
4: ["sq_plan", "sq", "tet", "see_saw", "tri_pyr"],
5: ["pent_plan", "sq_pyr", "tri_bipyr"],
6: ["oct", "pent_pyr"],
7: ["hex_pyr", "pent_bipyr"],
8: ["bcc", "hex_bipyr"],
9: ["q2", "q4", "q6"],
10: ["q2", "q4", "q6"],
11: ["q2", "q4", "q6"],
12: ["cuboct", "q2", "q4", "q6"]} if optypes is None \
else optypes.copy()
self.dr = dr
self.ddr = ddr
self.ndr = ndr
self.dop = dop
self.dist_exp = dist_exp
self.zero_ops = zero_ops
self.ops = {}
for cn, t_list in self.optypes.items():
self.ops[cn] = []
for t in t_list:
if t[:4] == 'bent':
self.ops[cn].append(OrderParameters(
[t[:4]], parameters=[{'TA': float(t[4:]) / 180.0, \
'IGW_TA': 1.0 / 0.0667}]))
else:
self.ops[cn].append(OrderParameters([t]))
def test_init(self):
self.assertIsNotNone(OrderParameters(["cn"], [[]], 0.99))
def test_get_order_parameters(self):
# Set up everything.
op_types = ["cn", "bent", "bent", "tet", "oct", "bcc", "q2", "q4", \
"q6", "reg_tri", "sq", "sq_pyr_legacy", "tri_bipyr", "sgl_bd", \
"tri_plan", "sq_plan", "pent_plan", "sq_pyr", "tri_pyr", \
"pent_pyr", "hex_pyr", "pent_bipyr", "hex_bipyr", "T", "cuboct", \
"see_saw"]
op_paras = [None, {'TA': 1, 'IGW_TA': 1./0.0667}, \
{'TA': 45./180, 'IGW_TA': 1./0.0667}, None, \
None, None, None, None, None, None, None, None, None, \
None, None, None, None, None, None, None, None, None, \
None, None, None, None]
ops_044 = OrderParameters(op_types, parameters=op_paras, cutoff=0.44)
ops_071 = OrderParameters(op_types, parameters=op_paras, cutoff=0.71)
ops_087 = OrderParameters(op_types, parameters=op_paras, cutoff=0.87)
ops_099 = OrderParameters(op_types, parameters=op_paras, cutoff=0.99)
ops_101 = OrderParameters(op_types, parameters=op_paras, cutoff=1.01)
ops_501 = OrderParameters(op_types, parameters=op_paras, cutoff=5.01)
ops_voro = OrderParameters(op_types, parameters=op_paras)
# Single bond.
op_vals = ops_101.get_order_parameters(self.single_bond, 0)
self.assertAlmostEqual(int(op_vals[13] * 1000), 1000)
op_vals = ops_501.get_order_parameters(self.single_bond, 0)
self.assertAlmostEqual(int(op_vals[13] * 1000), 799)
op_vals = ops_101.get_order_parameters(self.linear, 0)
self.assertAlmostEqual(int(op_vals[13] * 1000), 0)
# Linear motif.
op_vals = ops_101.get_order_parameters(self.linear, 0)
self.assertAlmostEqual(int(op_vals[1] * 1000), 1000)
# 45 degrees-bent motif.
op_vals = ops_101.get_order_parameters(self.bent45, 0)
self.assertAlmostEqual(int(op_vals[2] * 1000), 1000)
# T-shape motif.
op_vals = ops_101.get_order_parameters(
self.T_shape, 0, indices_neighs=[1,2,3])
self.assertAlmostEqual(int(op_vals[23] * 1000), 1000)
# Cubic structure.
op_vals = ops_099.get_order_parameters(self.cubic, 0)
self.assertAlmostEqual(op_vals[0], 0.0)
self.assertIsNone(op_vals[3])
self.assertIsNone(op_vals[4])
self.assertIsNone(op_vals[5])
self.assertIsNone(op_vals[6])
self.assertIsNone(op_vals[7])
self.assertIsNone(op_vals[8])
op_vals = ops_101.get_order_parameters(self.cubic, 0)
self.assertAlmostEqual(op_vals[0], 6.0)
self.assertAlmostEqual(int(op_vals[3] * 1000), 23)
self.assertAlmostEqual(int(op_vals[4] * 1000), 1000)
self.assertAlmostEqual(int(op_vals[5] * 1000), 333)
self.assertAlmostEqual(int(op_vals[6] * 1000), 0)
self.assertAlmostEqual(int(op_vals[7] * 1000), 763)
self.assertAlmostEqual(int(op_vals[8] * 1000), 353)
# Bcc structure.
op_vals = ops_087.get_order_parameters(self.bcc, 0)
self.assertAlmostEqual(op_vals[0], 8.0)
self.assertAlmostEqual(int(op_vals[3] * 1000), 200)
self.assertAlmostEqual(int(op_vals[4] * 1000), 145)
self.assertAlmostEqual(int(op_vals[5] * 1000), 975)
self.assertAlmostEqual(int(op_vals[6] * 1000), 0)
self.assertAlmostEqual(int(op_vals[7] * 1000), 509)
self.assertAlmostEqual(int(op_vals[8] * 1000), 628)
# Fcc structure.
op_vals = ops_071.get_order_parameters(self.fcc, 0)
self.assertAlmostEqual(op_vals[0], 12.0)
self.assertAlmostEqual(int(op_vals[3] * 1000), 36)
self.assertAlmostEqual(int(op_vals[4] * 1000), 78)
self.assertAlmostEqual(int(op_vals[5] * 1000), 0)
self.assertAlmostEqual(int(op_vals[6] * 1000), 0)
self.assertAlmostEqual(int(op_vals[7] * 1000), 190)
self.assertAlmostEqual(int(op_vals[8] * 1000), 574)
# Hcp structure.
op_vals = ops_101.get_order_parameters(self.hcp, 0)
self.assertAlmostEqual(op_vals[0], 12.0)
self.assertAlmostEqual(int(op_vals[3] * 1000), 33)
self.assertAlmostEqual(int(op_vals[4] * 1000), 82)
self.assertAlmostEqual(int(op_vals[5] * 1000), -38)
self.assertAlmostEqual(int(op_vals[6] * 1000), 0)
self.assertAlmostEqual(int(op_vals[7] * 1000), 97)
self.assertAlmostEqual(int(op_vals[8] * 1000), 484)
# Diamond structure.
op_vals = ops_044.get_order_parameters(self.diamond, 0)
self.assertAlmostEqual(op_vals[0], 4.0)
self.assertAlmostEqual(int(op_vals[3] * 1000), 1000)
self.assertAlmostEqual(int(op_vals[4] * 1000), 37)
self.assertAlmostEqual(int(op_vals[5] * 1000), 727)
self.assertAlmostEqual(int(op_vals[6] * 1000), 0)
self.assertAlmostEqual(int(op_vals[7] * 1000), 509)
self.assertAlmostEqual(int(op_vals[8] * 1000), 628)
# Trigonal off-plane molecule.
op_vals = ops_044.get_order_parameters(self.trigonal_off_plane, 0)
self.assertAlmostEqual(op_vals[0], 3.0)
self.assertAlmostEqual(int(op_vals[3] * 1000), 1000)
# Trigonal-planar motif.
op_vals = ops_101.get_order_parameters(self.trigonal_planar, 0)
self.assertEqual(int(op_vals[0] + 0.5), 3)
self.assertAlmostEqual(int(op_vals[14] * 1000 + 0.5), 1000)
# Regular triangle motif.
op_vals = ops_101.get_order_parameters(self.regular_triangle, 0)
self.assertAlmostEqual(int(op_vals[9] * 1000), 999)
# Square-planar motif.
op_vals = ops_101.get_order_parameters(self.square_planar, 0)
self.assertAlmostEqual(int(op_vals[15] * 1000 + 0.5), 1000)
# Square motif.
op_vals = ops_101.get_order_parameters(self.square, 0)
self.assertAlmostEqual(int(op_vals[10] * 1000), 1000)
# Pentagonal planar.
op_vals = ops_101.get_order_parameters(
self.pentagonal_planar.sites, 0, indices_neighs=[1,2,3,4,5])
self.assertAlmostEqual(int(op_vals[12] * 1000 + 0.5), 33)
self.assertAlmostEqual(int(op_vals[16] * 1000 + 0.5), 1000)
# Trigonal pyramid motif.
op_vals = ops_101.get_order_parameters(
self.trigonal_pyramid, 0, indices_neighs=[1,2,3,4])
self.assertAlmostEqual(int(op_vals[18] * 1000 + 0.5), 1000)
# Square pyramid motif.
op_vals = ops_101.get_order_parameters(self.square_pyramid, 0)
self.assertAlmostEqual(int(op_vals[11] * 1000 + 0.5), 1000)
self.assertAlmostEqual(int(op_vals[12] * 1000 + 0.5), 375)
self.assertAlmostEqual(int(op_vals[17] * 1000 + 0.5), 1000)
# Pentagonal pyramid motif.
op_vals = ops_101.get_order_parameters(
self.pentagonal_pyramid, 0, indices_neighs=[1,2,3,4,5,6])
self.assertAlmostEqual(int(op_vals[19] * 1000 + 0.5), 1000)
# Hexagonal pyramid motif.
op_vals = ops_101.get_order_parameters(
self.hexagonal_pyramid, 0, indices_neighs=[1,2,3,4,5,6,7])
self.assertAlmostEqual(int(op_vals[20] * 1000 + 0.5), 1000)
# Trigonal bipyramidal.
op_vals = ops_101.get_order_parameters(
self.trigonal_bipyramidal.sites, 0, indices_neighs=[1,2,3,4,5])
self.assertAlmostEqual(int(op_vals[12] * 1000 + 0.5), 1000)
# Pentagonal bipyramidal.
op_vals = ops_101.get_order_parameters(
self.pentagonal_bipyramid.sites, 0,
indices_neighs=[1,2,3,4,5,6,7])
self.assertAlmostEqual(int(op_vals[21] * 1000 + 0.5), 1000)
# Hexagonal bipyramid motif.
op_vals = ops_101.get_order_parameters(
self.hexagonal_bipyramid, 0, indices_neighs=[1,2,3,4,5,6,7,8])
self.assertAlmostEqual(int(op_vals[22] * 1000 + 0.5), 1000)
# Cuboctahedral motif.
op_vals = ops_101.get_order_parameters(
self.cuboctahedron, 0, indices_neighs=[i for i in range(1, 13)])
self.assertAlmostEqual(int(op_vals[24] * 1000 + 0.5), 1000)
# See-saw motif.
op_vals = ops_101.get_order_parameters(
self.see_saw, 0, indices_neighs=[i for i in range(1, 5)])
self.assertAlmostEqual(int(op_vals[25] * 1000 + 0.5), 1000)
# Test providing explicit neighbor lists.
op_vals = ops_101.get_order_parameters(self.bcc, 0, indices_neighs=[1])
self.assertIsNotNone(op_vals[0])
self.assertIsNone(op_vals[3])
with self.assertRaises(ValueError):
ops_101.get_order_parameters(self.bcc, 0, indices_neighs=[2])
def test_init(self):
self.assertIsNotNone(
OrderParameters(["cn"], parameters=None, cutoff=0.99))
def test_get_order_parameters(self):
# Set up everything.
op_types = ["cn", "tet", "oct", "bcc", "q2", "q4", "q6"]
op_paras = [[], [], [], [], [], [], []]
ops_044 = OrderParameters(op_types, op_paras, 0.44)
ops_071 = OrderParameters(op_types, op_paras, 0.71)
ops_087 = OrderParameters(op_types, op_paras, 0.87)
ops_099 = OrderParameters(op_types, op_paras, 0.99)
ops_101 = OrderParameters(op_types, op_paras, 1.01)
ops_voro = OrderParameters(op_types, op_paras)
# Cubic structure.
op_vals = ops_099.get_order_parameters(self.cubic, 0)
self.assertAlmostEqual(op_vals[0], 0.0)
self.assertIsNone(op_vals[1])
self.assertIsNone(op_vals[2])
self.assertIsNone(op_vals[3])
self.assertIsNone(op_vals[4])
self.assertIsNone(op_vals[5])
self.assertIsNone(op_vals[6])
op_vals = ops_101.get_order_parameters(self.cubic, 0)
self.assertAlmostEqual(op_vals[0], 6.0)
self.assertAlmostEqual(int(op_vals[1] * 1000), -72)
self.assertAlmostEqual(int(op_vals[2] * 1000), 1000)
self.assertAlmostEqual(int(op_vals[3] * 1000), 125)
self.assertAlmostEqual(int(op_vals[4] * 1000), 0)
self.assertAlmostEqual(int(op_vals[5] * 1000), 763)
self.assertAlmostEqual(int(op_vals[6] * 1000), 353)
# Bcc structure.
op_vals = ops_087.get_order_parameters(self.bcc, 0)
self.assertAlmostEqual(op_vals[0], 8.0)
self.assertAlmostEqual(int(op_vals[1] * 1000),
1968) # 1.9688949183589557
self.assertAlmostEqual(int(op_vals[2] * 1000),
125) # 0.12540815310925768
self.assertAlmostEqual(int(op_vals[3] * 1000),
975) # 0.9753713330608598
self.assertAlmostEqual(int(op_vals[4] * 1000), 0)
self.assertAlmostEqual(int(op_vals[5] * 1000),
509) # 0.5091750772173156
self.assertAlmostEqual(int(op_vals[6] * 1000),
628) # 0.6285393610547088
# Fcc structure.
op_vals = ops_071.get_order_parameters(self.fcc, 0)
self.assertAlmostEqual(op_vals[0], 12.0)
self.assertAlmostEqual(int(op_vals[1] * 1000),
-998) # -0.9989621462333275
self.assertAlmostEqual(int(op_vals[2] * 1000),
-1012) # -1.0125484381377454
self.assertAlmostEqual(int(op_vals[3] * 1000),
0) # -0.0007417813723164877
self.assertAlmostEqual(int(op_vals[4] * 1000), 0)
self.assertAlmostEqual(int(op_vals[5] * 1000),
190) # 0.1909406539564932
self.assertAlmostEqual(int(op_vals[6] * 1000), 574) # 0.57452425971407
# Hcp structure.
op_vals = ops_101.get_order_parameters(self.hcp, 0)
self.assertAlmostEqual(op_vals[0], 12.0)
self.assertAlmostEqual(int(op_vals[1] * 1000), -455)
self.assertAlmostEqual(int(op_vals[2] * 1000), -735)
self.assertAlmostEqual(int(op_vals[3] * 1000), -155)
self.assertAlmostEqual(int(op_vals[4] * 1000), 0)
self.assertAlmostEqual(int(op_vals[5] * 1000), 97)
self.assertAlmostEqual(int(op_vals[6] * 1000), 484)
# Diamond structure.
op_vals = ops_044.get_order_parameters(self.diamond, 0)
self.assertAlmostEqual(op_vals[0], 4.0)
self.assertAlmostEqual(int(op_vals[1] * 1000), 1000)
self.assertAlmostEqual(int(op_vals[2] * 1000), -8)
self.assertAlmostEqual(int(op_vals[3] * 1000), 80)
self.assertAlmostEqual(int(op_vals[4] * 1000), 0)
self.assertAlmostEqual(int(op_vals[5] * 1000), 509)
self.assertAlmostEqual(int(op_vals[6] * 1000), 628)
# Test providing explicit neighbor lists.
op_vals = ops_101.get_order_parameters(self.bcc, 0, indeces_neighs=[1])
self.assertIsNotNone(op_vals[0])
self.assertIsNone(op_vals[1])
with self.assertRaises(ValueError):
ops_101.get_order_parameters(self.bcc, 0, indeces_neighs=[2])
def test_get_order_parameters(self):
# Set up everything.
op_types = ["cn", "tet", "oct", "bcc", "q2", "q4", "q6"]
op_paras = [[], [], [], [], [], [], []]
ops_044 = OrderParameters(op_types, op_paras, 0.44)
ops_071 = OrderParameters(op_types, op_paras, 0.71)
ops_087 = OrderParameters(op_types, op_paras, 0.87)
ops_099 = OrderParameters(op_types, op_paras, 0.99)
ops_101 = OrderParameters(op_types, op_paras, 1.01)
ops_voro = OrderParameters(op_types, op_paras)
# Cubic structure.
op_vals = ops_099.get_order_parameters(self.cubic, 0)
self.assertAlmostEqual(op_vals[0], 0.0)
self.assertIsNone(op_vals[1])
self.assertIsNone(op_vals[2])
self.assertIsNone(op_vals[3])
self.assertIsNone(op_vals[4])
self.assertIsNone(op_vals[5])
self.assertIsNone(op_vals[6])
op_vals = ops_101.get_order_parameters(self.cubic, 0)
self.assertAlmostEqual(op_vals[0], 6.0)
self.assertAlmostEqual(int(op_vals[1] * 1000), -72)
self.assertAlmostEqual(int(op_vals[2] * 1000), 1000)
self.assertAlmostEqual(int(op_vals[3] * 1000), 125)
self.assertAlmostEqual(int(op_vals[4] * 1000), 0)
self.assertAlmostEqual(int(op_vals[5] * 1000), 763)
self.assertAlmostEqual(int(op_vals[6] * 1000), 353)
# Bcc structure.
op_vals = ops_087.get_order_parameters(self.bcc, 0)
self.assertAlmostEqual(op_vals[0], 8.0)
self.assertAlmostEqual(int(op_vals[1] * 1000),
1968) # 1.9688949183589557
self.assertAlmostEqual(int(op_vals[2] * 1000),
125) # 0.12540815310925768
self.assertAlmostEqual(int(op_vals[3] * 1000),
975) # 0.9753713330608598
self.assertAlmostEqual(int(op_vals[4] * 1000), 0)
self.assertAlmostEqual(int(op_vals[5] * 1000),
509) # 0.5091750772173156
self.assertAlmostEqual(int(op_vals[6] * 1000),
628) # 0.6285393610547088
# Fcc structure.
op_vals = ops_071.get_order_parameters(self.fcc, 0)
self.assertAlmostEqual(op_vals[0], 12.0)
self.assertAlmostEqual(int(op_vals[1] * 1000),
-998) # -0.9989621462333275
self.assertAlmostEqual(int(op_vals[2] * 1000),
-1012) # -1.0125484381377454
self.assertAlmostEqual(int(op_vals[3] * 1000),
0) # -0.0007417813723164877
self.assertAlmostEqual(int(op_vals[4] * 1000), 0)
self.assertAlmostEqual(int(op_vals[5] * 1000),
190) # 0.1909406539564932
self.assertAlmostEqual(int(op_vals[6] * 1000), 574) # 0.57452425971407
# Hcp structure.
op_vals = ops_101.get_order_parameters(self.hcp, 0)
self.assertAlmostEqual(op_vals[0], 12.0)
self.assertAlmostEqual(int(op_vals[1] * 1000), -455)
self.assertAlmostEqual(int(op_vals[2] * 1000), -735)
self.assertAlmostEqual(int(op_vals[3] * 1000), -155)
self.assertAlmostEqual(int(op_vals[4] * 1000), 0)
self.assertAlmostEqual(int(op_vals[5] * 1000), 97)
self.assertAlmostEqual(int(op_vals[6] * 1000), 484)
# Diamond structure.
op_vals = ops_044.get_order_parameters(self.diamond, 0)
self.assertAlmostEqual(op_vals[0], 4.0)
self.assertAlmostEqual(int(op_vals[1] * 1000), 1000)
self.assertAlmostEqual(int(op_vals[2] * 1000), -8)
self.assertAlmostEqual(int(op_vals[3] * 1000), 80)
self.assertAlmostEqual(int(op_vals[4] * 1000), 0)
self.assertAlmostEqual(int(op_vals[5] * 1000), 509)
self.assertAlmostEqual(int(op_vals[6] * 1000), 628)
# Test providing explicit neighbor lists.
op_vals = ops_101.get_order_parameters(self.bcc, 0, indeces_neighs=[1])
self.assertIsNotNone(op_vals[0])
self.assertIsNone(op_vals[1])
with self.assertRaises(ValueError):
ops_101.get_order_parameters(self.bcc, 0, indeces_neighs=[2])
def site_is_of_motif_type(struct, n, approach="min_dist", delta=0.1, \
cutoff=10.0, thresh=None):
"""
Returns the motif type of the site with index n in structure struct;
currently featuring "tetrahedral", "octahedral", "bcc", and "cp"
(close-packed: fcc and hcp) as well as "square pyramidal" and
"trigonal bipyramidal". If the site is not recognized,
"unrecognized" is returned. If a site should be assigned to two
different motifs, "multiple assignments" is returned.
Args:
struct (Structure): input structure.
n (int): index of site in Structure object for which motif type
is to be determined.
approach (str): type of neighbor-finding approach, where
"min_dist" will use the MinimumDistanceNN class,
"voronoi" the VoronoiNN class, "min_OKeeffe" the
MinimumOKeeffe class, and "min_VIRE" the MinimumVIRENN class.
delta (float): tolerance involved in neighbor finding.
cutoff (float): (large) radius to find tentative neighbors.
thresh (dict): thresholds for motif criteria (currently, required
keys and their default values are "qtet": 0.5,
"qoct": 0.5, "qbcc": 0.5, "q6": 0.4).
Returns: motif type (str).
"""
if thresh is None:
thresh = {
"qtet": 0.5, "qoct": 0.5, "qbcc": 0.5, "q6": 0.4,
"qtribipyr": 0.8, "qsqpyr": 0.8}
ops = OrderParameters([
"cn", "tet", "oct", "bcc", "q6", "sq_pyr", "tri_bipyr"])
neighs_cent = get_neighbors_of_site_with_index(
struct, n, approach=approach, delta=delta, cutoff=cutoff)
neighs_cent.append(struct.sites[n])
opvals = ops.get_order_parameters(
neighs_cent, len(neighs_cent)-1, indices_neighs=[
i for i in range(len(neighs_cent)-1)])
cn = int(opvals[0] + 0.5)
motif_type = "unrecognized"
nmotif = 0
if cn == 4 and opvals[1] > thresh["qtet"]:
motif_type = "tetrahedral"
nmotif += 1
if cn == 5 and opvals[5] > thresh["qsqpyr"]:
motif_type = "square pyramidal"
nmotif += 1
if cn == 5 and opvals[6] > thresh["qtribipyr"]:
motif_type = "trigonal bipyramidal"
nmotif += 1
if cn == 6 and opvals[2] > thresh["qoct"]:
motif_type = "octahedral"
nmotif += 1
if cn == 8 and (opvals[3] > thresh["qbcc"] and opvals[1] < thresh["qtet"]):
motif_type = "bcc"
nmotif += 1
if cn == 12 and (opvals[4] > thresh["q6"] and opvals[1] < thresh["q6"] and \
opvals[2] < thresh["q6"] and opvals[3] < thresh["q6"]):
motif_type = "cp"
nmotif += 1
if nmotif > 1:
motif_type = "multiple assignments"
return motif_type
def test_get_order_parameters(self):
# Set up everything.
op_types = ["cn", "lin", "bent", "tet", "oct", "bcc", "q2", "q4", \
"q6", "reg_tri", "sq", "sq_pyr", "tri_bipyr"]
op_paras = [[], [], [], [], [], [], [], [], [], [], [], [], []]
op_paras = [[], [], [45.0, 0.0667], [], [], [], [], [], [], [], [], [],
[]]
ops_044 = OrderParameters(op_types, op_paras, 0.44)
ops_071 = OrderParameters(op_types, op_paras, 0.71)
ops_087 = OrderParameters(op_types, op_paras, 0.87)
ops_099 = OrderParameters(op_types, op_paras, 0.99)
ops_101 = OrderParameters(op_types, op_paras, 1.01)
ops_voro = OrderParameters(op_types, op_paras)
# Linear motif.
op_vals = ops_101.get_order_parameters(self.linear, 0)
self.assertAlmostEqual(int(op_vals[1] * 1000), 1000)
# 45 degrees-bent motif.
op_vals = ops_101.get_order_parameters(self.bent45, 0)
self.assertAlmostEqual(int(op_vals[2] * 1000), 1000)
# Cubic structure.
op_vals = ops_099.get_order_parameters(self.cubic, 0)
self.assertAlmostEqual(op_vals[0], 0.0)
self.assertIsNone(op_vals[3])
self.assertIsNone(op_vals[4])
self.assertIsNone(op_vals[5])
self.assertIsNone(op_vals[6])
self.assertIsNone(op_vals[7])
self.assertIsNone(op_vals[8])
op_vals = ops_101.get_order_parameters(self.cubic, 0)
self.assertAlmostEqual(op_vals[0], 6.0)
self.assertAlmostEqual(int(op_vals[3] * 1000), -14)
self.assertAlmostEqual(int(op_vals[4] * 1000), 1000)
self.assertAlmostEqual(int(op_vals[5] * 1000), 333)
self.assertAlmostEqual(int(op_vals[6] * 1000), 0)
self.assertAlmostEqual(int(op_vals[7] * 1000), 763)
self.assertAlmostEqual(int(op_vals[8] * 1000), 353)
# Bcc structure.
op_vals = ops_087.get_order_parameters(self.bcc, 0)
self.assertAlmostEqual(op_vals[0], 8.0)
self.assertAlmostEqual(int(op_vals[3] * 1000), 140)
self.assertAlmostEqual(int(op_vals[4] * 1000), 42)
self.assertAlmostEqual(int(op_vals[5] * 1000), 975)
self.assertAlmostEqual(int(op_vals[6] * 1000), 0)
self.assertAlmostEqual(int(op_vals[7] * 1000), 509)
self.assertAlmostEqual(int(op_vals[8] * 1000), 628)
# Fcc structure.
op_vals = ops_071.get_order_parameters(self.fcc, 0)
self.assertAlmostEqual(op_vals[0], 12.0)
self.assertAlmostEqual(int(op_vals[3] * 1000), -18)
self.assertAlmostEqual(int(op_vals[4] * 1000), -81)
self.assertAlmostEqual(int(op_vals[5] * 1000), 0)
self.assertAlmostEqual(int(op_vals[6] * 1000), 0)
self.assertAlmostEqual(int(op_vals[7] * 1000), 190)
self.assertAlmostEqual(int(op_vals[8] * 1000), 574)
# Hcp structure.
op_vals = ops_101.get_order_parameters(self.hcp, 0)
self.assertAlmostEqual(op_vals[0], 12.0)
self.assertAlmostEqual(int(op_vals[3] * 1000), -8)
self.assertAlmostEqual(int(op_vals[4] * 1000), -59)
self.assertAlmostEqual(int(op_vals[5] * 1000), -38)
self.assertAlmostEqual(int(op_vals[6] * 1000), 0)
self.assertAlmostEqual(int(op_vals[7] * 1000), 97)
self.assertAlmostEqual(int(op_vals[8] * 1000), 484)
# Diamond structure.
op_vals = ops_044.get_order_parameters(self.diamond, 0)
self.assertAlmostEqual(op_vals[0], 4.0)
self.assertAlmostEqual(int(op_vals[3] * 1000), 1000)
self.assertAlmostEqual(int(op_vals[4] * 1000), -39)
self.assertAlmostEqual(int(op_vals[5] * 1000), 727)
self.assertAlmostEqual(int(op_vals[6] * 1000), 0)
self.assertAlmostEqual(int(op_vals[7] * 1000), 509)
self.assertAlmostEqual(int(op_vals[8] * 1000), 628)
# Regular triangle motif.
op_vals = ops_101.get_order_parameters(self.regular_triangle, 0)
self.assertAlmostEqual(int(op_vals[9] * 1000), 999)
# Square motif.
op_vals = ops_101.get_order_parameters(self.square, 0)
self.assertAlmostEqual(int(op_vals[10] * 1000), 1000)
# Pentagonal planar.
op_vals = ops_101.get_order_parameters(self.pentagonal_planar.sites,
0,
indeces_neighs=[1, 2, 3, 4, 5])
self.assertAlmostEqual(int(op_vals[12] * 1000), 100)
# Square pyramid motif.
op_vals = ops_101.get_order_parameters(self.square_pyramid, 0)
self.assertAlmostEqual(int(op_vals[11] * 1000 + 0.5), 1000)
self.assertAlmostEqual(int(op_vals[12] * 1000 + 0.5), 500)
# Trigonal bipyramidal.
op_vals = ops_101.get_order_parameters(self.trigonal_bipyramidal.sites,
0,
indeces_neighs=[1, 2, 3, 4, 5])
self.assertAlmostEqual(int(op_vals[12] * 1000 + 0.5), 1000)
# Test providing explicit neighbor lists.
op_vals = ops_101.get_order_parameters(self.bcc, 0, indeces_neighs=[1])
self.assertIsNotNone(op_vals[0])
self.assertIsNone(op_vals[3])
with self.assertRaises(ValueError):
ops_101.get_order_parameters(self.bcc, 0, indeces_neighs=[2])
def site_is_of_motif_type(struct, n, approach="min_dist", delta=0.1, \
cutoff=10.0, thresh=None):
"""
Returns the motif type of the site with index n in structure struct;
currently featuring "tetrahedral", "octahedral", "bcc", and "cp"
(close-packed: fcc and hcp) as well as "square pyramidal" and
"trigonal bipyramidal". If the site is not recognized,
"unrecognized" is returned. If a site should be assigned to two
different motifs, "multiple assignments" is returned.
Args:
struct (Structure): input structure.
n (int): index of site in Structure object for which motif type
is to be determined.
approach (str): type of neighbor-finding approach, where
"min_dist" will use the MinimumDistanceNN class,
"voronoi" the VoronoiNN class, "min_OKeeffe" the
MinimumOKeeffe class, and "min_VIRE" the MinimumVIRENN class.
delta (float): tolerance involved in neighbor finding.
cutoff (float): (large) radius to find tentative neighbors.
thresh (dict): thresholds for motif criteria (currently, required
keys and their default values are "qtet": 0.5,
"qoct": 0.5, "qbcc": 0.5, "q6": 0.4).
Returns: motif type (str).
"""
if thresh is None:
thresh = {
"qtet": 0.5, "qoct": 0.5, "qbcc": 0.5, "q6": 0.4,
"qtribipyr": 0.8, "qsqpyr": 0.8}
ops = OrderParameters([
"cn", "tet", "oct", "bcc", "q6", "sq_pyr", "tri_bipyr"])
neighs_cent = get_neighbors_of_site_with_index(
struct, n, approach=approach, delta=delta, cutoff=cutoff)
neighs_cent.append(struct.sites[n])
opvals = ops.get_order_parameters(
neighs_cent, len(neighs_cent)-1, indeces_neighs=[
i for i in range(len(neighs_cent)-1)])
cn = int(opvals[0] + 0.5)
motif_type = "unrecognized"
nmotif = 0
if cn == 4 and opvals[1] > thresh["qtet"]:
motif_type = "tetrahedral"
nmotif += 1
if cn == 5 and opvals[5] > thresh["qsqpyr"]:
motif_type = "square pyramidal"
nmotif += 1
if cn == 5 and opvals[6] > thresh["qtribipyr"]:
motif_type = "trigonal bipyramidal"
nmotif += 1
if cn == 6 and opvals[2] > thresh["qoct"]:
motif_type = "octahedral"
nmotif += 1
if cn == 8 and (opvals[3] > thresh["qbcc"] and opvals[1] < thresh["qtet"]):
motif_type = "bcc"
nmotif += 1
if cn == 12 and (opvals[4] > thresh["q6"] and opvals[1] < thresh["q6"] and \
opvals[2] < thresh["q6"] and opvals[3] < thresh["q6"]):
motif_type = "cp"
nmotif += 1
if nmotif > 1:
motif_type = "multiple assignments"
return motif_type
def test_get_order_parameters(self):
# Set up everything.
op_types = ["cn", "lin", "bent", "tet", "oct", "bcc", "q2", "q4", \
"q6", "reg_tri", "sq", "sq_pyr", "tri_bipyr"]
op_paras = [[], [], [], [], [], [], [], [], [], [], [], [], []]
op_paras = [[], [], [45.0, 0.0667], [], [], [], [], [], [], [], [], [], []]
ops_044 = OrderParameters(op_types, op_paras, 0.44)
ops_071 = OrderParameters(op_types, op_paras, 0.71)
ops_087 = OrderParameters(op_types, op_paras, 0.87)
ops_099 = OrderParameters(op_types, op_paras, 0.99)
ops_101 = OrderParameters(op_types, op_paras, 1.01)
ops_voro = OrderParameters(op_types, op_paras)
# Linear motif.
op_vals = ops_101.get_order_parameters(self.linear, 0)
self.assertAlmostEqual(int(op_vals[1] * 1000), 1000)
# 45 degrees-bent motif.
op_vals = ops_101.get_order_parameters(self.bent45, 0)
self.assertAlmostEqual(int(op_vals[2] * 1000), 1000)
# Cubic structure.
op_vals = ops_099.get_order_parameters(self.cubic, 0)
self.assertAlmostEqual(op_vals[0], 0.0)
self.assertIsNone(op_vals[3])
self.assertIsNone(op_vals[4])
self.assertIsNone(op_vals[5])
self.assertIsNone(op_vals[6])
self.assertIsNone(op_vals[7])
self.assertIsNone(op_vals[8])
op_vals = ops_101.get_order_parameters(self.cubic, 0)
self.assertAlmostEqual(op_vals[0], 6.0)
self.assertAlmostEqual(int(op_vals[3] * 1000), 14)
self.assertAlmostEqual(int(op_vals[4] * 1000), 1000)
self.assertAlmostEqual(int(op_vals[5] * 1000), 333)
self.assertAlmostEqual(int(op_vals[6] * 1000), 0)
self.assertAlmostEqual(int(op_vals[7] * 1000), 763)
self.assertAlmostEqual(int(op_vals[8] * 1000), 353)
# Bcc structure.
op_vals = ops_087.get_order_parameters(self.bcc, 0)
self.assertAlmostEqual(op_vals[0], 8.0)
self.assertAlmostEqual(int(op_vals[3] * 1000), 142)
self.assertAlmostEqual(int(op_vals[4] * 1000), 145)
self.assertAlmostEqual(int(op_vals[5] * 1000), 975)
self.assertAlmostEqual(int(op_vals[6] * 1000), 0)
self.assertAlmostEqual(int(op_vals[7] * 1000), 509)
self.assertAlmostEqual(int(op_vals[8] * 1000), 628)
# Fcc structure.
op_vals = ops_071.get_order_parameters(self.fcc, 0)
self.assertAlmostEqual(op_vals[0], 12.0)
self.assertAlmostEqual(int(op_vals[3] * 1000), 30)
self.assertAlmostEqual(int(op_vals[4] * 1000), 78)
self.assertAlmostEqual(int(op_vals[5] * 1000), 0)
self.assertAlmostEqual(int(op_vals[6] * 1000), 0)
self.assertAlmostEqual(int(op_vals[7] * 1000), 190)
self.assertAlmostEqual(int(op_vals[8] * 1000), 574)
# Hcp structure.
op_vals = ops_101.get_order_parameters(self.hcp, 0)
self.assertAlmostEqual(op_vals[0], 12.0)
self.assertAlmostEqual(int(op_vals[3] * 1000), 30)
self.assertAlmostEqual(int(op_vals[4] * 1000), 89)
self.assertAlmostEqual(int(op_vals[5] * 1000), -38)
self.assertAlmostEqual(int(op_vals[6] * 1000), 0)
self.assertAlmostEqual(int(op_vals[7] * 1000), 97)
self.assertAlmostEqual(int(op_vals[8] * 1000), 484)
# Diamond structure.
op_vals = ops_044.get_order_parameters(self.diamond, 0)
self.assertAlmostEqual(op_vals[0], 4.0)
self.assertAlmostEqual(int(op_vals[3] * 1000), 1000)
self.assertAlmostEqual(int(op_vals[4] * 1000), 45)
self.assertAlmostEqual(int(op_vals[5] * 1000), 727)
self.assertAlmostEqual(int(op_vals[6] * 1000), 0)
self.assertAlmostEqual(int(op_vals[7] * 1000), 509)
self.assertAlmostEqual(int(op_vals[8] * 1000), 628)
# Regular triangle motif.
op_vals = ops_101.get_order_parameters(self.regular_triangle, 0)
self.assertAlmostEqual(int(op_vals[9] * 1000), 999)
# Square motif.
op_vals = ops_101.get_order_parameters(self.square, 0)
self.assertAlmostEqual(int(op_vals[10] * 1000), 1000)
# Pentagonal planar.
op_vals = ops_101.get_order_parameters(
self.pentagonal_planar.sites, 0, indeces_neighs=[1,2,3,4,5])
self.assertAlmostEqual(int(op_vals[12] * 1000), 100)
# Square pyramid motif.
op_vals = ops_101.get_order_parameters(self.square_pyramid, 0)
self.assertAlmostEqual(int(op_vals[11] * 1000 + 0.5), 1000)
self.assertAlmostEqual(int(op_vals[12] * 1000 + 0.5), 500)
# Trigonal bipyramidal.
op_vals = ops_101.get_order_parameters(
self.trigonal_bipyramidal.sites, 0, indeces_neighs=[1,2,3,4,5])
self.assertAlmostEqual(int(op_vals[12] * 1000 + 0.5), 1000)
# Test providing explicit neighbor lists.
op_vals = ops_101.get_order_parameters(self.bcc, 0, indeces_neighs=[1])
self.assertIsNotNone(op_vals[0])
self.assertIsNone(op_vals[3])
with self.assertRaises(ValueError):
ops_101.get_order_parameters(self.bcc, 0, indeces_neighs=[2])