def _get_graphs(cutoff, ordered_structures):
"""
Generate graph representations of magnetic structures with nearest
neighbor bonds. Right now this only works for MinimumDistanceNN.
Args:
cutoff (float): Cutoff in Angstrom for nearest neighbor search.
ordered_structures (list): Structure objects.
Returns:
sgraphs (list): StructureGraph objects.
"""
# Strategy for finding neighbors
if cutoff:
strategy = MinimumDistanceNN(cutoff=cutoff, get_all_sites=True)
else:
strategy = MinimumDistanceNN() # only NN
# Generate structure graphs
sgraphs = [
StructureGraph.with_local_env_strategy(s, strategy=strategy)
for s in ordered_structures
]
return sgraphs
def test_get_local_order_params(self):
nn = MinimumDistanceNN()
ops = nn.get_local_order_parameters(self.diamond, 0)
self.assertAlmostEqual(ops['tetrahedral'], 0.9999934389036574)
ops = nn.get_local_order_parameters(self.nacl, 0)
self.assertAlmostEqual(ops['octahedral'], 0.9999995266669)
def test_substitute(self):
structure = Structure.from_file(os.path.join(os.path.dirname(__file__),
"..", "..", "..",
"test_files", "Li2O.cif"))
molecule = FunctionalGroups["methyl"]
structure_copy = copy.deepcopy(structure)
structure_copy_graph = copy.deepcopy(structure)
sg = StructureGraph.with_local_env_strategy(structure, MinimumDistanceNN())
sg_copy = copy.deepcopy(sg)
# Ensure that strings and molecules lead to equivalent substitutions
sg.substitute_group(1, molecule, MinimumDistanceNN)
sg_copy.substitute_group(1, "methyl", MinimumDistanceNN)
self.assertEqual(sg, sg_copy)
# Ensure that the underlying structure has been modified as expected
structure_copy.substitute(1, "methyl")
self.assertEqual(structure_copy, sg.structure)
# Test inclusion of graph dictionary
graph_dict = {(0, 1): {"weight": 0.5},
(0, 2): {"weight": 0.5},
(0, 3): {"weight": 0.5},
}
sg_with_graph = StructureGraph.with_local_env_strategy(structure_copy_graph,
MinimumDistanceNN())
sg_with_graph.substitute_group(1, "methyl", MinimumDistanceNN,
graph_dict=graph_dict)
edge = sg_with_graph.graph.get_edge_data(11, 13)[0]
self.assertEqual(edge["weight"], 0.5)
def shifted_sites_after_prismatic_disto(struct, metal_index, angle):
mini = MinimumDistanceNN(tol=0.3)
print("rotating around index : ", metal_index)
neighbor_O = mini.get_nn_info(struct, metal_index)
[X, Y, Z] = struct[metal_index].coords
print("metal coords : ", [X, Y, Z])
trueSites = [] # list of dict with index and shifted coordinates
O_above = [O['site_index'] for O in neighbor_O if O['site'].z - Z > 0]
O_below = [O['site_index'] for O in neighbor_O if O['site'].z - Z < 0]
symOperation = find_symmop(struct,
angle,
translation=(0, 0, 0),
center=[X, Y, Z])
trueSites += find_translated_sites(struct, O_above, symOperation)
symOperation = find_symmop(struct,
-angle,
translation=(0, 0, 0),
center=[X, Y, Z])
trueSites += find_translated_sites(struct, O_below, symOperation)
return (trueSites)
def test_mul(self):
square_sg_mul = self.square_sg * (2, 1, 1)
square_sg_mul_ref_str = """Structure Graph
Structure:
Full Formula (H2)
Reduced Formula: H2
abc : 10.000000 5.000000 50.000000
angles: 90.000000 90.000000 90.000000
Sites (2)
# SP a b c
--- ---- --- --- ---
0 H 0 0 0
1 H 0.5 0 -0
Graph: bonds
from to to_image
---- ---- ------------
0 0 (0, 1, 0)
0 0 (0, -1, 0)
0 1 (0, 0, 0)
0 1 (-1, 0, 0)
1 1 (0, 1, 0)
1 1 (0, -1, 0)
"""
square_sg_mul_actual_str = str(square_sg_mul)
# only testing bonds portion,
# the c frac_coord of the second H can vary from
# 0 to -0 depending on machine precision
square_sg_mul_ref_str = "\n".join(
square_sg_mul_ref_str.splitlines()[11:])
square_sg_mul_actual_str = "\n".join(
square_sg_mul_actual_str.splitlines()[11:])
self.assertEqual(square_sg_mul_actual_str, square_sg_mul_ref_str)
# test sequential multiplication
sq_sg_1 = self.square_sg * (2, 2, 1)
sq_sg_1 = sq_sg_1 * (2, 2, 1)
sq_sg_2 = self.square_sg * (4, 4, 1)
self.assertEqual(sq_sg_1.graph.number_of_edges(),
sq_sg_2.graph.number_of_edges())
mos2_sg_mul = self.mos2_sg * (3, 3, 1)
for idx in mos2_sg_mul.structure.indices_from_symbol("Mo"):
self.assertEqual(mos2_sg_mul.get_coordination_of_site(idx), 6)
mos2_sg_premul = StructureGraph.with_local_env_strategy(
self.structure * (3, 3, 1), MinimumDistanceNN())
self.assertTrue(mos2_sg_mul == mos2_sg_premul)
# test 3D Structure
nio_sg = StructureGraph.with_local_env_strategy(
self.NiO, MinimumDistanceNN())
nio_sg = nio_sg * 3
for n in range(len(nio_sg)):
self.assertEqual(nio_sg.get_coordination_of_site(n), 6)
def test_get_local_order_params(self):
nn = MinimumDistanceNN()
ops = nn.get_local_order_parameters(self.diamond, 0)
self.assertAlmostEqual(ops['tetrahedral'], 0.9999934389036574)
ops = nn.get_local_order_parameters(self.nacl, 0)
self.assertAlmostEqual(ops['octahedral'], 0.9999995266669)
def get_MO_pairs(struct, metal_str="Mn"):
print("getting {} - O pairs".format(metal_str))
atom_pair_list = []
mini = MinimumDistanceNN(tol=0.3)
for center_index in struct.indices_from_symbol(metal_str):
neighbor_O = mini.get_nn_info(struct, center_index)
atom_pair_list += [[center_index, O['site_index']] for O in neighbor_O
if O['site'].species_string in ["O", "S"]]
return (atom_pair_list)
def test_all_nn_classes(self):
self.assertAlmostEqual(MinimumDistanceNN().get_cn(self.diamond, 0), 4)
self.assertAlmostEqual(MinimumDistanceNN().get_cn(self.nacl, 0), 6)
self.assertAlmostEqual(
MinimumDistanceNN(tol=0.01).get_cn(self.cscl, 0), 8)
self.assertAlmostEqual(
MinimumDistanceNN(tol=0.1).get_cn(self.mos2, 0), 6)
for image in MinimumDistanceNN(tol=0.1).get_nn_images(self.mos2, 0):
self.assertTrue(image in [(0, 0, 0), (0, 1,
0), (-1, 0,
0), (0, 0,
0), (0, 1,
0), (-1, 0,
0)])
self.assertAlmostEqual(
MinimumOKeeffeNN(tol=0.01).get_cn(self.diamond, 0), 4)
self.assertAlmostEqual(
MinimumOKeeffeNN(tol=0.01).get_cn(self.nacl, 0), 6)
self.assertAlmostEqual(
MinimumOKeeffeNN(tol=0.01).get_cn(self.cscl, 0), 8)
self.assertAlmostEqual(
MinimumVIRENN(tol=0.01).get_cn(self.diamond, 0), 4)
self.assertAlmostEqual(MinimumVIRENN(tol=0.01).get_cn(self.nacl, 0), 6)
self.assertAlmostEqual(MinimumVIRENN(tol=0.01).get_cn(self.cscl, 0), 8)
self.assertAlmostEqual(
BrunnerNN_reciprocal(tol=0.01).get_cn(self.diamond, 0), 4)
self.assertAlmostEqual(
BrunnerNN_reciprocal(tol=0.01).get_cn(self.nacl, 0), 6)
self.assertAlmostEqual(
BrunnerNN_reciprocal(tol=0.01).get_cn(self.cscl, 0), 14)
self.assertAlmostEqual(
BrunnerNN_relative(tol=0.01).get_cn(self.diamond, 0), 16)
self.assertAlmostEqual(
BrunnerNN_relative(tol=0.01).get_cn(self.nacl, 0), 18)
self.assertAlmostEqual(
BrunnerNN_relative(tol=0.01).get_cn(self.cscl, 0), 8)
self.assertAlmostEqual(
BrunnerNN_real(tol=0.01).get_cn(self.diamond, 0), 16)
self.assertAlmostEqual(
BrunnerNN_real(tol=0.01).get_cn(self.nacl, 0), 18)
self.assertAlmostEqual(
BrunnerNN_real(tol=0.01).get_cn(self.cscl, 0), 8)
self.assertAlmostEqual(EconNN(tol=0.01).get_cn(self.diamond, 0), 4)
self.assertAlmostEqual(EconNN(tol=0.01).get_cn(self.nacl, 0), 6)
self.assertAlmostEqual(EconNN(tol=0.01).get_cn(self.cscl, 0), 14)
self.assertAlmostEqual(VoronoiNN(tol=0.5).get_cn(self.diamond, 0), 4)
self.assertAlmostEqual(VoronoiNN(tol=0.5).get_cn(self.nacl, 0), 6)
self.assertAlmostEqual(VoronoiNN(tol=0.5).get_cn(self.cscl, 0), 8)
def metal_envt(struc):
# Counts the Me environment in a structure
# argument : pymatgen.core.structure
# return : 2elt list of (7 element list) : the i th element is the
# propotion of A with i A neighbors
A = "Mg"
B = "Mn"
C = "Na"
# neighborA = [0 for i in range(0, 7, 1)]
# neighborB = [0 for i in range(0, 7, 1)]
# A_indices = struc.indices_from_symbol(A)
nbC = len(struc.indices_from_symbol(C))
neighborC = np.zeros(6)
#print("{0} {1}".format(nbC,C))
sCopy = RemoveSpeciesTransformation(["O"]).apply_transformation(struc)
# print(sCopy)
mini = MinimumDistanceNN(tol=0.3)
for i, site in enumerate(sCopy):
# print(str(i))
# print(site)
siteName = site.species_string
if siteName == C:
neigList = mini.get_nn_info(sCopy, i)
#print("{0} closest neighboors \n".format(len(neigList)))
coordA = 0
coordB = 0
for neighbor in neigList:
# index = neighbor['site_index']
neighborName = neighbor['site'].species_string
#print(" ( {0} at {1} ) ".format(neighborName,index))
if neighborName == A:
coordA += 1
if neighborName == B:
coordB += 1
neighborC[coordA] += 1
#print("neighborC list :" , neighborC)
if nbC == 0:
normalizedNeighborC = [0 for i in neighborC]
else:
normalizedNeighborC = [i / nbC for i in neighborC]
print("coordination {0} : {1} \nnormalized by {2} : {3} \n".format(
C, neighborC, nbC, normalizedNeighborC))
return normalizedNeighborC
def get_layer_indices(struct, separator_specie, refIndex=-1):
# fonction to gather the indexes of all the atoms in layers separated by Na atoms
# input : the layered structure, the index of one non-Na reference atom
# returns : an ordered list of indexes of all the atoms in the layer of
# the reference atom
A = "Mn"
B = "Mg"
C = "O"
# if no reference is given, takes the first atom of A as a reference
if refIndex == -1:
layerIndices = [struct.indices_from_symbol(C)[0]]
else:
layerIndices = [refIndex]
mini = MinimumDistanceNN(tol=0.5)
# algorithm : 2 buffer list (prev and new atomList) and a definitive list
# adds all neighbor of the old buffer atoms to a new buffer list
# if they are non-Na and non-already counted in the definitive List
# Stops when the new buffer is empty (all non-Na atoms next to the layer
# have been counted)
prevAtomList = layerIndices
finish = False
while not finish:
newAtomList = []
for prevAtomIndex in prevAtomList:
neigList = mini.get_nn_info(struct, prevAtomIndex)
for neighbor in neigList:
index = neighbor['site_index']
name = neighbor['site'].species_string
# print(name)
if not (name in separator_specie +
[struct[prevAtomIndex].species_string]) and not (
index in layerIndices):
layerIndices.append(index)
if len(newAtomList) > 0:
previousAtomList = newAtomList
layerIndices = layerIndices + newAtomList
else:
finish = True
layerIndices.sort()
return layerIndices
def test_all_nn_classes(self):
self.assertAlmostEqual(MinimumDistanceNN().get_cn(self.diamond, 0), 4)
self.assertAlmostEqual(MinimumDistanceNN().get_cn(self.nacl, 0), 6)
self.assertAlmostEqual(
MinimumDistanceNN(tol=0.01).get_cn(self.cscl, 0), 8)
self.assertAlmostEqual(
MinimumDistanceNN(tol=0.1).get_cn(self.mos2, 0), 6)
for image in MinimumDistanceNN(tol=0.1).get_nn_images(self.mos2, 0):
self.assertTrue(image in [[0, 0, 0], [0, 1, 0], [-1, 0, 0], \
[0, 0, 0], [0, 1, 0], [-1, 0, 0]])
self.assertAlmostEqual(
MinimumOKeeffeNN(tol=0.01).get_cn(self.diamond, 0), 4)
self.assertAlmostEqual(
MinimumOKeeffeNN(tol=0.01).get_cn(self.nacl, 0), 6)
self.assertAlmostEqual(
MinimumOKeeffeNN(tol=0.01).get_cn(self.cscl, 0), 8)
self.assertAlmostEqual(
MinimumVIRENN(tol=0.01).get_cn(self.diamond, 0), 4)
self.assertAlmostEqual(MinimumVIRENN(tol=0.01).get_cn(self.nacl, 0), 6)
self.assertAlmostEqual(MinimumVIRENN(tol=0.01).get_cn(self.cscl, 0), 8)
self.assertAlmostEqual(BrunnerNN(tol=0.01).get_cn(self.diamond, 0), 4)
self.assertAlmostEqual(BrunnerNN(tol=0.01).get_cn(self.nacl, 0), 6)
self.assertAlmostEqual(BrunnerNN(tol=0.01).get_cn(self.cscl, 0), 14)
self.assertAlmostEqual(
BrunnerNN(mode="real", tol=0.01).get_cn(self.diamond, 0), 16)
self.assertAlmostEqual(
BrunnerNN(mode="real", tol=0.01).get_cn(self.nacl, 0), 18)
self.assertAlmostEqual(
BrunnerNN(mode="real", tol=0.01).get_cn(self.cscl, 0), 8)
self.assertAlmostEqual(
BrunnerNN(mode="relative", tol=0.01).get_cn(self.diamond, 0), 16)
self.assertAlmostEqual(
BrunnerNN(mode="relative", tol=0.01).get_cn(self.nacl, 0), 18)
self.assertAlmostEqual(
BrunnerNN(mode="relative", tol=0.01).get_cn(self.cscl, 0), 8)
self.assertAlmostEqual(EconNN(tol=0.01).get_cn(self.diamond, 0), 4)
self.assertAlmostEqual(EconNN(tol=0.01).get_cn(self.nacl, 0), 6)
self.assertAlmostEqual(EconNN(tol=0.01).get_cn(self.cscl, 0), 14)
self.assertAlmostEqual(VoronoiNN_modified().get_cn(self.diamond, 0), 4)
self.assertAlmostEqual(VoronoiNN_modified().get_cn(self.nacl, 0), 6)
self.assertAlmostEqual(VoronoiNN_modified().get_cn(self.cscl, 0), 8)
def get_local_env_method(method): # pylint:disable=too-many-return-statements
"""get a local environment method based on its name"""
method = method.lower()
if method.lower() == "crystalnn":
# see eq. 15 and 16 in
# https://pubs.acs.org/doi/full/10.1021/acs.inorgchem.0c02996
# for the x_diff_weight parameter.
# in the paper it is called δen and it is set to 3
# we found better results by lowering this weight
return CrystalNN(porous_adjustment=True,
x_diff_weight=1.5,
search_cutoff=4.5)
if method.lower() == "econnn":
return EconNN()
if method.lower() == "brunnernn":
return BrunnerNN_relative()
if method.lower() == "minimumdistance":
return MinimumDistanceNN()
if method.lower() == "vesta":
return VESTA_NN
if method.lower() == "voronoinn":
return VoronoiNN()
if method.lower() == "atr":
return ATR_NN
if method.lower() == "li":
return LI_NN
return JmolNN()
def scene_dicts():
structure = Structure.from_file(str(Path(__file__).parent / "mgo_defects" / "Va_O1_0" / "CONTCAR-finish"))
graph = MinimumDistanceNN().get_bonded_structure(structure=structure)
return SceneDicts(
{"125_up": {"vertices": np.array([[0] * 3, [0.1] * 3, [0.2] * 3]),
"faces": np.array([[0, 1, 2]])}},
structure_graph=graph)
def test_no_duplicate_hops(self):
test_structure_dict = {
"@module":
"pymatgen.core.structure",
"@class":
"Structure",
"charge":
None,
"lattice": {
"matrix": [[2.990355, -5.149042, 0.0],
[2.990355, 5.149042, 0.0], [0.0, 0.0, 24.51998]]
},
"sites": [
{
"species": [{
"element": "Ba",
"occu": 1
}],
"abc": [0.005572, 0.994428, 0.151095],
"properties": {}
},
],
}
test_structure = Structure.from_dict(test_structure_dict)
nn = MinimumDistanceNN(cutoff=6, get_all_sites=True)
sg = StructureGraph.with_local_env_strategy(test_structure, nn)
self.assertEqual(sg.graph.number_of_edges(), 3)
def __init__(self,
structure,
migrating_specie,
max_path_length=10,
symprec=0.1,
vac_mode=False):
"""
Args:
structure: Input structure that contains all sites.
migrating_specie (Specie-like): The specie that migrates. E.g.,
"Li".
max_path_length (float): Maximum length of NEB path in the unit
of Angstrom. Defaults to None, which means you are setting the
value to the min cutoff until finding 1D or >1D percolating paths.
symprec (float): Symmetry precision to determine equivalence.
"""
self.structure = structure
self.migrating_specie = get_el_sp(migrating_specie)
self.symprec = symprec
self.a = SpacegroupAnalyzer(self.structure, symprec=self.symprec)
self.symm_structure = self.a.get_symmetrized_structure()
self.only_sites = self.get_only_sites()
self.unique_hops = None
# Generate the graph edges between these all the sites
self.s_graph = StructureGraph.with_local_env_strategy(
self.only_sites,
MinimumDistanceNN(
cutoff=max_path_length,
get_all_sites=True)) # weights in this graph are the distances
self.s_graph.set_node_attributes()
def test_all_nn_classes(self):
self.assertEqual(MinimumDistanceNN(cutoff=5, get_all_sites=True).get_cn(
self.cscl, 0), 14)
self.assertEqual(MinimumDistanceNN().get_cn(self.diamond, 0), 4)
self.assertEqual(MinimumDistanceNN().get_cn(self.nacl, 0), 6)
self.assertEqual(MinimumDistanceNN().get_cn(self.lifepo4, 0), 6)
self.assertEqual(MinimumDistanceNN(tol=0.01).get_cn(self.cscl, 0), 8)
self.assertEqual(MinimumDistanceNN(tol=0.1).get_cn(self.mos2, 0), 6)
for image in MinimumDistanceNN(tol=0.1).get_nn_images(self.mos2, 0):
self.assertTrue(image in [(0, 0, 0), (0, 1, 0), (-1, 0, 0),
(0, 0, 0), (0, 1, 0), (-1, 0, 0)])
okeeffe = MinimumOKeeffeNN(tol=0.01)
self.assertEqual(okeeffe.get_cn(self.diamond, 0), 4)
self.assertEqual(okeeffe.get_cn(self.nacl, 0), 6)
self.assertEqual(okeeffe.get_cn(self.cscl, 0), 8)
self.assertEqual(okeeffe.get_cn(self.lifepo4, 0), 2)
virenn = MinimumVIRENN(tol=0.01)
self.assertEqual(virenn.get_cn(self.diamond, 0), 4)
self.assertEqual(virenn.get_cn(self.nacl, 0), 6)
self.assertEqual(virenn.get_cn(self.cscl, 0), 8)
self.assertEqual(virenn.get_cn(self.lifepo4, 0), 2)
brunner_recip = BrunnerNN_reciprocal(tol=0.01)
self.assertEqual(brunner_recip.get_cn(self.diamond, 0), 4)
self.assertEqual(brunner_recip.get_cn(self.nacl, 0), 6)
self.assertEqual(brunner_recip.get_cn(self.cscl, 0), 14)
self.assertEqual(brunner_recip.get_cn(self.lifepo4, 0), 6)
brunner_rel = BrunnerNN_relative(tol=0.01)
self.assertEqual(brunner_rel.get_cn(self.diamond, 0), 4)
self.assertEqual(brunner_rel.get_cn(self.nacl, 0), 6)
self.assertEqual(brunner_rel.get_cn(self.cscl, 0), 14)
self.assertEqual(brunner_rel.get_cn(self.lifepo4, 0), 6)
brunner_real = BrunnerNN_real(tol=0.01)
self.assertEqual(brunner_real.get_cn(self.diamond, 0), 4)
self.assertEqual(brunner_real.get_cn(self.nacl, 0), 6)
self.assertEqual(brunner_real.get_cn(self.cscl, 0), 14)
self.assertEqual(brunner_real.get_cn(self.lifepo4, 0), 30)
econn = EconNN()
self.assertEqual(econn.get_cn(self.diamond, 0), 4)
self.assertEqual(econn.get_cn(self.nacl, 0), 6)
self.assertEqual(econn.get_cn(self.cscl, 0), 14)
self.assertEqual(econn.get_cn(self.lifepo4, 0), 6)
voroinn = VoronoiNN(tol=0.5)
self.assertEqual(voroinn.get_cn(self.diamond, 0), 4)
self.assertEqual(voroinn.get_cn(self.nacl, 0), 6)
self.assertEqual(voroinn.get_cn(self.cscl, 0), 8)
self.assertEqual(voroinn.get_cn(self.lifepo4, 0), 6)
crystalnn = CrystalNN()
self.assertEqual(crystalnn.get_cn(self.diamond, 0), 4)
self.assertEqual(crystalnn.get_cn(self.nacl, 0), 6)
self.assertEqual(crystalnn.get_cn(self.cscl, 0), 8)
self.assertEqual(crystalnn.get_cn(self.lifepo4, 0), 6)
def get_metal_next_neighbor(struct, center_index):
next_metal_neighbors = []
# gather the indices of all metal next neighbors
# metals around neighbor of neighbor Os
mini = MinimumDistanceNN(tol=0.3)
neighbor_O = mini.get_nn_info(struct, center_index)
for O_index in [O['site_index'] for O in neighbor_O]:
next_metal_neighbors += [
M['site_index'] for M in mini.get_nn_info(struct, O_index)
if (M['site'].specie.symbol not in ["Na", "Li", "O"])
]
# remove the doubles and the metal center
next_metal_neighbors = set(next_metal_neighbors)
next_metal_neighbors.discard(center_index)
return (next_metal_neighbors)
def test_draw(self):
# draw MoS2 graph
self.mos2_sg.draw_graph_to_file('MoS2_single.pdf',
image_labels=True,
hide_image_edges=False)
mos2_sg = self.mos2_sg * (9, 9, 1)
mos2_sg.draw_graph_to_file('MoS2.pdf', algo='neato')
# draw MoS2 graph that's been successively multiplied
mos2_sg_2 = self.mos2_sg * (3, 3, 1)
mos2_sg_2 = mos2_sg_2 * (3, 3, 1)
mos2_sg_2.draw_graph_to_file('MoS2_twice_mul.pdf',
algo='neato',
hide_image_edges=True)
# draw MoS2 graph that's generated from a pre-multiplied Structure
mos2_sg_premul = StructureGraph.with_local_env_strategy(
self.structure * (3, 3, 1), MinimumDistanceNN())
mos2_sg_premul.draw_graph_to_file('MoS2_premul.pdf',
algo='neato',
hide_image_edges=True)
# draw graph for a square lattice
self.square_sg.draw_graph_to_file('square_single.pdf',
hide_image_edges=False)
square_sg = self.square_sg * (5, 5, 1)
square_sg.draw_graph_to_file('square.pdf',
algo='neato',
image_labels=True,
node_labels=False)
# draw graph for a body-centered square lattice
self.bc_square_sg.draw_graph_to_file('bc_square_single.pdf',
hide_image_edges=False)
bc_square_sg = self.bc_square_sg * (9, 9, 1)
bc_square_sg.draw_graph_to_file('bc_square.pdf',
algo='neato',
image_labels=False)
# draw graph for a body-centered square lattice defined in an alternative way
self.bc_square_sg_r.draw_graph_to_file('bc_square_r_single.pdf',
hide_image_edges=False)
bc_square_sg_r = self.bc_square_sg_r * (9, 9, 1)
bc_square_sg_r.draw_graph_to_file('bc_square_r.pdf',
algo='neato',
image_labels=False)
# delete generated test files
test_files = ('bc_square_r_single.pdf', 'bc_square_r.pdf',
'bc_square_single.pdf', 'bc_square.pdf',
'MoS2_premul.pdf', 'MOS2_single.pdf',
'MoS2_twice_mul.pdf', 'MoS2.pdf', 'square_single.pdf',
'square.pdf')
for test_file in test_files:
os.remove(test_file)
def test_all_nn_classes(self):
self.assertAlmostEqual(MinimumDistanceNN().get_cn(self.diamond, 0), 4)
self.assertAlmostEqual(MinimumDistanceNN().get_cn(self.nacl, 0), 6)
self.assertAlmostEqual(
MinimumDistanceNN(tol=0.01).get_cn(self.cscl, 0), 8)
self.assertAlmostEqual(
MinimumDistanceNN(tol=0.1).get_cn(self.mos2, 0), 6)
for image in MinimumDistanceNN(tol=0.1).get_nn_images(self.mos2, 0):
self.assertTrue(image in [[0, 0, 0], [0, 1, 0], [-1, 0, 0], \
[0, 0, 0], [0, 1, 0], [-1, 0, 0]])
self.assertAlmostEqual(
MinimumOKeeffeNN(tol=0.01).get_cn(self.diamond, 0), 4)
self.assertAlmostEqual(
MinimumOKeeffeNN(tol=0.01).get_cn(self.nacl, 0), 6)
self.assertAlmostEqual(
MinimumOKeeffeNN(tol=0.01).get_cn(self.cscl, 0), 8)
self.assertAlmostEqual(
MinimumVIRENN(tol=0.01).get_cn(self.diamond, 0), 4)
self.assertAlmostEqual(MinimumVIRENN(tol=0.01).get_cn(self.nacl, 0), 6)
self.assertAlmostEqual(MinimumVIRENN(tol=0.01).get_cn(self.cscl, 0), 8)
def test_no_duplicate_hops(self):
test_structure = Structure(
lattice=[[2.990355, -5.149042, 0.0], [2.990355, 5.149042, 0.0], [0.0, 0.0, 24.51998]],
species=["Ba"],
coords=[[0.005572, 0.994428, 0.151095]],
)
nn = MinimumDistanceNN(cutoff=6, get_all_sites=True)
sg = StructureGraph.with_local_env_strategy(test_structure, nn)
self.assertEqual(sg.graph.number_of_edges(), 3)
def test_from_local_env_and_equality_and_diff(self):
nn = MinimumDistanceNN()
sg = StructureGraph.with_local_env_strategy(self.structure, nn)
self.assertEqual(sg.graph.number_of_edges(), 6)
nn2 = MinimumOKeeffeNN()
sg2 = StructureGraph.with_local_env_strategy(self.structure, nn2)
self.assertTrue(sg == sg2)
self.assertTrue(sg == self.mos2_sg)
# TODO: find better test case where graphs are different
diff = sg.diff(sg2)
self.assertEqual(diff['dist'], 0)
def test_extract_molecules(self):
structure_file = os.path.join(os.path.dirname(__file__), "..", "..", "..",
'test_files/H6PbCI3N_mp-977013_symmetrized.cif')
s = Structure.from_file(structure_file)
nn = MinimumDistanceNN()
sg = StructureGraph.with_local_env_strategy(s, nn)
molecules = sg.get_subgraphs_as_molecules()
self.assertEqual(molecules[0].composition.formula, "H3 C1")
self.assertEqual(len(molecules), 1)
molecules = self.mos2_sg.get_subgraphs_as_molecules()
self.assertEqual(len(molecules), 0)
def with_distance(cls, structure: Structure, migrating_specie: str,
max_distance: float, **kwargs) -> "MigrationGraph":
"""
Using a specific nn strategy to get the connectivity graph between all the migrating ion sites.
Args:
max_distance: Maximum length of NEB path in the unit
of Angstrom. Defaults to None, which means you are setting the
value to the min cutoff until finding 1D or >1D percolating paths.
Returns:
A constructed MigrationGraph object
"""
only_sites = get_only_sites_from_structure(structure, migrating_specie)
migration_graph = StructureGraph.with_local_env_strategy(
only_sites,
MinimumDistanceNN(cutoff=max_distance, get_all_sites=True),
)
return cls(structure=structure, m_graph=migration_graph, **kwargs)
def __init__(
self,
structure,
migrating_specie,
max_path_length=10,
symprec=0.1,
vac_mode=False,
name: str = None,
):
"""
Construct the FullPathMapper object using a structure will all mobile sites occupied.
A structure graph is generated by connecting all sites withing max_path_length distance of each other
The sites are decorated with Migration graph objects and then grouped together based on their equivalence.
Args:
structure: Input structure that contains all sites.
migrating_specie (Specie-like): The specie that migrates. E.g.,
"Li".
max_path_length (float): Maximum length of NEB path in the unit
of Angstrom. Defaults to None, which means you are setting the
value to the min cutoff until finding 1D or >1D percolating paths.
symprec (float): Symmetry precision to determine equivalence.
"""
self.structure = structure
self.migrating_specie = get_el_sp(migrating_specie)
self.max_path_length = max_path_length
self.symprec = symprec
self.name = name
self.a = SpacegroupAnalyzer(self.structure, symprec=self.symprec)
self.symm_structure = self.a.get_symmetrized_structure()
self.only_sites = self.get_only_sites()
if vac_mode:
raise NotImplementedError
self.vac_mode = vac_mode
self.unique_hops = None
# Generate the graph edges between these all the sites
self.s_graph = StructureGraph.with_local_env_strategy(
self.only_sites,
MinimumDistanceNN(cutoff=max_path_length, get_all_sites=True),
) # weights in this graph are the distances
self.s_graph.set_node_attributes()
self.populate_edges_with_migration_paths()
self.group_and_label_hops()
self._populate_unique_hops_dict()
def test_extract_molecules(self):
structure_file = os.path.join(
PymatgenTest.TEST_FILES_DIR,
"H6PbCI3N_mp-977013_symmetrized.cif",
)
s = Structure.from_file(structure_file)
nn = MinimumDistanceNN()
sg = StructureGraph.with_local_env_strategy(s, nn)
molecules = sg.get_subgraphs_as_molecules()
self.assertEqual(molecules[0].composition.formula, "H3 C1")
self.assertEqual(len(molecules), 1)
molecules = self.mos2_sg.get_subgraphs_as_molecules()
self.assertEqual(len(molecules), 0)
def apply_transformation(self, structure):
"""
Apply the transformation.
Args:
structure: Structure or Molecule to apply the transformation to
Returns:
the transformed structure
"""
structure = structure.copy()
site = structure[self.site_index]
def f(x, r, r0):
return x * r0 / r
r0 = max([
site.distance(_["site"]) for _ in MinimumDistanceNN().get_nn_info(
structure, self.site_index)
])
if hasattr(structure, "lattice"):
m = structure.lattice.matrix
m = (abs(m) > 1e-5) * m
a, b, c = m[0], m[1], m[2]
x = abs(np.dot(a, np.cross(b, c)) / np.linalg.norm(np.cross(b, c)))
y = abs(np.dot(b, np.cross(a, c)) / np.linalg.norm(np.cross(a, c)))
z = abs(np.dot(c, np.cross(a, b)) / np.linalg.norm(np.cross(a, b)))
rmax = np.floor(min([x, y, z]) / 2)
else:
rmax = np.max(structure.distance_matrix)
for vals in structure.get_neighbors(site,
r=r0 if self.nn_only else rmax):
site2, distance, index = vals[:3]
v = site2.coords - site.coords
kwargs = {
"indices": [index],
"vector":
v * f(self.displacement, distance, r0) / np.linalg.norm(v)
}
if hasattr(structure, "lattice"):
kwargs["frac_coords"] = False
structure.translate_sites(**kwargs)
return structure
def get_neighbors_of_site_with_index_future(struct, n, approach="min_dist", \
delta=0.1, cutoff=10.0):
"""
Returns the neighbors of a given site using a specific neighbor-finding
method.
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.
Returns: neighbor sites.
"""
warnings.warn('This function will go into Pymatgen very soon.')
if approach == "min_dist":
return MinimumDistanceNN(tol=delta, cutoff=cutoff).get_nn(
struct, n)
elif approach == "voronoi":
return VoronoiNN(tol=delta, cutoff=cutoff).get_nn(
struct, n)
elif approach == "min_OKeeffe":
return MinimumOKeeffeNN(tol=delta, cutoff=cutoff).get_nn(
struct, n)
elif approach == "min_VIRE":
return MinimumVIRENN(tol=delta, cutoff=cutoff).get_nn(
struct, n)
else:
raise RuntimeError("unsupported neighbor-finding method ({}).".format(
approach))
def __init__(
self,
structure,
structure_graph=None,
larsen_dim=None,
cheon_dim=None,
gorai_dim=None,
):
"""
This class uses 3 algorithms implemented in pymatgen to automate recognition of low-dimensional materials.
Args:
structure (object): pmg Structure object.
structure_graph (object): pmg StructureGraph object.
larsen_dim (int): As defined in P. M. Larsen et al., Phys. Rev. Materials 3, 034003 (2019).
cheon_dim (int): As defined in Cheon, G. et al., Nano Lett. 2017.
gorai_dim (int): As defined in Gorai, P. et al., J. Mater. Chem. A 2, 4136 (2016).
"""
self.structure = structure
self.structure_graph = structure_graph
self.larsen_dim = larsen_dim
self.cheon_dim = cheon_dim
self.gorai_dim = gorai_dim
# Default to MinimumDistanceNN for generating structure graph.
sgraph = MinimumDistanceNN().get_bonded_structure(structure)
self.structure_graph = sgraph
# Get Larsen dimensionality
self.larsen_dim = get_dimensionality_larsen(self.structure_graph)
def get_MMOO_quadruplets(struct):
AB_list = get_Mn_Mn_pairs(struct)
print("nb of pairs to test : {}".format(len(AB_list)))
quadruplets = []
for A, B in AB_list:
mini = MinimumDistanceNN(tol=0.35)
O_A_indices = [O['site_index'] for O in mini.get_nn_info(struct, A)]
O_pair = [
O['site_index'] for O in mini.get_nn_info(struct, B)
if O["site_index"] in O_A_indices
]
# O_pair = O_A_indices & O_B_indices
nb_O = len(O_pair)
if nb_O == 2:
quadruplets.append({"metal_pair": [A, B], "oxygen_pair": O_pair})
elif nb_O > 2:
O_pair_dict = [
O for O in mini.get_nn_info(struct, B)
if O['site_index'] in O_pair
]
print("common O between atoms {} are not a pair : {}".format(
[A, B], O_pair))
for O in O_pair_dict:
dA, imgA = O["site"].distance_and_image(struct[B], jimage=None)
dB, imgB = O["site"].distance_and_image(struct[A], jimage=None)
# print(imgA,imgB)
O["hash"] = hash((tuple(imgA), tuple(imgB)))
#print("O site : {}, dist : {}".format(O["site_index"],dA+dB))
O_pair = [
O["site_index"] for O in sorted(O_pair, key=itemgetter('hash'))
]
print("sorted O list : {}".format(
[dictA["site_index"] for dictA in O_pair]))
while len(O_pair) > 0:
O1 = O_pair.pop()
O2 = O_pair.pop()
quadruplets.append({
"metal_pair": [A, B],
"oxygen_pair": [O1, O2]
})
else:
print("Not enough O in the pair !!")
print("Valid MMOO quadruplets : {}".format(len(quadruplets)))
return (quadruplets)
def get_NNs_pm(atoms, site_idx, NN_method):
"""
Get coordinating atoms to the adsorption site
Args:
atoms (Atoms object): atoms object of MOF
site_idx (int): ASE index of adsorption site
NN_method (string): string representing the desired Pymatgen
nearest neighbor algorithm:
refer to http://pymatgen.org/_modules/pymatgen/analysis/local_env.html
Returns:
neighbors_idx (list of ints): ASE indices of coordinating atoms
"""
#Convert ASE Atoms object to Pymatgen Structure object
bridge = pm_ase.AseAtomsAdaptor()
struct = bridge.get_structure(atoms)
#Select Pymatgen NN algorithm
NN_method = NN_method.lower()
if NN_method == 'vire':
nn_object = MinimumVIRENN()
elif NN_method == 'voronoi':
nn_object = VoronoiNN()
elif NN_method == 'jmol':
nn_object = JmolNN()
elif NN_method == 'min_dist':
nn_object = MinimumDistanceNN()
elif NN_method == 'okeeffe':
nn_object = MinimumOKeeffeNN()
elif NN_method == 'brunner_real':
nn_object = BrunnerNN_real()
elif NN_method == 'brunner_recpirocal':
nn_object = BrunnerNN_reciprocal()
elif NN_method == 'brunner_relative':
nn_object = BrunnerNN_relative()
elif NN_method == 'econ':
nn_object = EconNN()
elif NN_method == 'dict':
#requires a cutoff dictionary located in the pwd
nn_object = CutOffDictNN(cut_off_dict='cut_off_dict.txt')
elif NN_method == 'critic2':
nn_object = Critic2NN()
elif NN_method == 'openbabel':
nn_object = OpenBabelNN()
elif NN_method == 'covalent':
nn_object = CovalentBondNN()
elif NN_method == 'crystal':
nn_object = CrystalNN(porous_adjustment=True)
elif NN_method == 'crystal_nonporous':
nn_object = CrystalNN(porous_adjustment=False)
else:
raise ValueError('Invalid NN algorithm specified')
#Find coordinating atoms
with warnings.catch_warnings():
warnings.simplefilter('ignore')
neighbors = nn_object.get_nn_info(struct, site_idx)
neighbors_idx = []
for neighbor in neighbors:
neighbors_idx.append(neighbor['site_index'])
return neighbors_idx
def metalBondCount(struc):
# Counts the metal metal bounds in a structure
# argument pymatgen.core.structure
# return [ normalizedBonds, normalizedAA, normalizedBB]
# normalizedBond = 3 elt list =[ nb AA bonds, nb BB bonds, nb AB bonds ] / nb of metal
# normalizedAA = 7 element list : the ith elt is the number of A with i A-neighbor
# (ie if there are 1/4 of the Mg surrounded by 3 Mg, normalizedAA[3] = 0.25)
# normalizedBB = idem for B
# Logically, if nbA = nbB, normalizedAA = normalizedBB
A = "Mg"
B = "Mn"
countAA = 0
countAB = 0
countBB = 0
neighborAA = [0 for i in range(7)]
neighborBB = [0 for i in range(7)]
A_indices = struc.indices_from_symbol(A)
B_indices = struc.indices_from_symbol(B)
nbA = len(A_indices)
nbB = len(B_indices)
nbTot = nbA + nbB
print("{0} {1}, {2} {3} : {4}".format(nbA, A, nbB, B, nbTot))
sCopy = RemoveSpeciesTransformation(["Na",
"O"]).apply_transformation(struc)
# struc.remove_species('O')
mini = MinimumDistanceNN(tol=0.3)
for i, site in enumerate(sCopy):
# print(str(i))
neigList = mini.get_nn_info(sCopy, i)
#print("{0} closest neighboors \n".format(len(neigList)))
coord = 0
for neighbor in neigList:
index = neighbor['site_index']
name = neighbor['site'].species_string
# print(" ( {0} at {1} ) ".format(name,index))
if site.species_string == A:
if name == A:
countAA += 1
coord += 1
if name == B:
countAB += 1
if site.species_string == B:
if name == A:
countAB += 1
if name == B:
countBB += 1
coord += 1
if site.species_string == A:
neighborAA[coord] += 1
elif site.species_string == B:
neighborBB[coord] += 1
bonds = [countAA // 2, countBB // 2, countAB // 2]
normalizedBonds = [i / nbTot for i in bonds]
print("[{3}{3}, {4}{4}, {3}{4}] = {0} normalized by {1} : {2} \n".format(
bonds, nbTot, normalizedBonds, A, B))
if nbA > 0:
normalizedAA = [i / nbA for i in neighborAA]
print(
"[Nombre de {0} avec [1-6] {0} autour] = {1} normalized by {2} : {3} \n"
.format(A, neighborAA, nbA, normalizedAA))
else:
normalizedAA = neighborAA
if nbB > 0:
normalizedBB = [i / nbB for i in neighborBB]
print(
"[Nombre de {0} avec [1-6] {0} autour] = {1} normalized by {2} : {3} \n"
.format(B, neighborBB, nbB, normalizedBB))
else:
normalizedBB = neighborBB
return [normalizedBonds, normalizedAA, normalizedBB]
