def is_dupe(self, doc, sim_tol=5e-2, extra_pdfs=None):
""" Compare doc with all other structures at same stoichiometry via PDF overlap.
Parameters:
doc (dict): structure to compare.
Keyword Arguments:
sim_tol (float): similarity tolerance to compare to
extra_pdfs (list(dict)): list of structures with extra pdfs
to compare against
"""
new_pdf = PDF(doc, projected=True)
for ind, pdf in enumerate(self.pdfs):
if sorted(doc["stoichiometry"]) == self._stoichs[ind]:
dist = new_pdf.get_sim_distance(pdf, projected=True)
if dist < sim_tol:
return True
if extra_pdfs is not None:
for ind, _doc in enumerate(extra_pdfs):
pdf = _doc["pdf"]
if sorted(doc["stoichiometry"]) == sorted(
_doc["stoichiometry"]):
dist = new_pdf.get_sim_distance(pdf,
projected=pdf.projected)
if dist < sim_tol:
return True
return False
def test_pdf_primitive_vs_supercell(self):
test_doc, success = res2dict(REAL_PATH + "data/KP_primitive.res",
db=False)
test_doc["text_id"] = ["primitive", "cell"]
test_doc["lattice_cart"] = abc2cart(test_doc["lattice_abc"])
test_doc["cell_volume"] = cart2volume(test_doc["lattice_cart"])
supercell_doc, success = res2dict(REAL_PATH + "data/KP_supercell.res",
db=False)
supercell_doc["text_id"] = ["supercell", "cell"]
supercell_doc["lattice_cart"] = abc2cart(supercell_doc["lattice_abc"])
supercell_doc["cell_volume"] = cart2volume(
supercell_doc["lattice_cart"])
test_doc["pdf"] = PDF(test_doc,
dr=0.01,
low_mem=True,
rmax=10,
num_images="auto",
debug=DEBUG)
supercell_doc["pdf"] = PDF(
supercell_doc,
dr=0.01,
low_mem=True,
rmax=10,
num_images="auto",
debug=DEBUG,
)
overlap = PDFOverlap(test_doc["pdf"], supercell_doc["pdf"])
self.assertLessEqual(overlap.similarity_distance, 1e-3)
self.assertGreaterEqual(overlap.similarity_distance, 0.0)
def pdf_sim_dist(doc_test, doc_supercell):
doc_test["text_id"] = ["test", "cell"]
doc_supercell["text_id"] = ["super", "cell"]
pdf_test = PDF(doc_test, low_mem=True)
pdf_supercell = PDF(doc_supercell, low_mem=True)
overlap = PDFOverlap(pdf_test, pdf_supercell)
return overlap.similarity_distance
def test_pdf_from_projected(self):
doc, success = res2dict(REAL_PATH + "data/LiPZn-r57des.res")
doc["lattice_cart"] = abc2cart(doc["lattice_abc"])
doc["text_id"] = ["unprojected", "test"]
doc["pdf_unprojected"] = PDF(doc, dr=0.01, **{"debug": False})
doc["text_id"] = ["projected", "test"]
doc["pdf_projected"] = PDF(doc, dr=0.01, **{"debug": False})
np.testing.assert_array_almost_equal(doc["pdf_unprojected"].gr,
doc["pdf_projected"].gr)
def test_single_atom_pdf(self):
from math import ceil
doc = dict()
box_size = 20
rmax = 41
dr = 0.1
num_images = "auto"
doc["positions_frac"] = [[0.5, 0.5, 0.5]]
doc["atom_types"] = ["C"]
doc["lattice_cart"] = np.asarray([[box_size, 0, 0], [0, box_size, 0],
[0, 0, box_size]])
doc["cell_volume"] = box_size**3
doc["text_id"] = ["hist", "ogram"]
doc["pdf"] = PDF(
doc,
num_images=num_images,
dr=dr,
rmax=rmax,
lazy=True,
style="histogram",
debug=True,
)
doc["pdf"].calc_pdf()
doc["text_id"] = ["smear"]
doc["pdf_smear"] = PDF(
doc,
num_images=num_images,
gaussian_width=0.01,
dr=0.1,
rmax=rmax,
lazy=True,
style="smear",
debug=True,
)
doc["pdf_smear"].calc_pdf()
doc["text_id"] = ["low"]
doc["pdf_low"] = PDF(
doc,
low_mem=True,
num_images=num_images,
gaussian_width=0.01,
dr=0.1,
rmax=rmax,
lazy=True,
style="smear",
debug=True,
)
doc["pdf_low"].calc_pdf()
peaks = [20, np.sqrt(2) * 20, np.sqrt(3) * 20, 40]
indices = [ceil(peak / dr) for peak in peaks]
self.assertListEqual(
np.where(doc["pdf_low"].gr > 1e-8)[0].tolist(), indices)
self.assertListEqual(
np.where(doc["pdf"].gr > 1e-8)[0].tolist(), indices)
self.assertListEqual(
np.where(doc["pdf_smear"].gr > 1e-8)[0].tolist(), indices)
def calc_pdfs(self):
""" Compute PDFs for each structure in the generation. """
self._pdfs = []
self._stoichs = []
for structure in self.populace:
self._pdfs.append(PDF(structure, projected=True))
self._stoichs.append(sorted(structure["stoichiometry"]))
def test_concurrent_pdf(self):
import glob
import numpy as np
import time
from copy import deepcopy
files = glob.glob(REAL_PATH + "data/hull-KPSn-KP/*.res")[0:24]
cursor = [res2dict(file, db=False)[0] for file in files]
serial_cursor = deepcopy(cursor)
pdf_args = {
"dr": 0.1,
"num_images": "auto",
"gaussian_width": 0.1,
"lazy": False,
"projected": False,
}
start = time.time()
pdf_factory = PDFFactory(cursor, **pdf_args)
factory_elapsed = time.time() - start
start = time.time()
for doc in serial_cursor:
doc["pdf"] = PDF(doc, **pdf_args, timing=False)
serial_elapsed = time.time() - start
print("{:.2f} s over {} processes vs {:.2f} s in serial".format(
factory_elapsed, pdf_factory.nprocs, serial_elapsed))
print("Corresponding to a speedup of {:.1f} vs ideal {:.1f}".format(
serial_elapsed / factory_elapsed, pdf_factory.nprocs))
for ind, doc in enumerate(serial_cursor):
np.testing.assert_array_almost_equal(doc["pdf"].gr,
cursor[ind]["pdf"].gr,
decimal=6)
def calculate_pdf(self, **kwargs):
""" Calculate and set the PDF with the passed parameters. """
from matador.fingerprints.pdf import PDF
if 'pdf' not in self._data:
self._data['pdf'] = PDF(self._data,
label=self.formula_tex,
**kwargs)
return self._data['pdf']
def pdf(self):
""" Returns a PDF object (pair distribution function) for the
structure, calculated with default PDF settings.
"""
from matador.fingerprints.pdf import PDF
if 'pdf' not in self._data:
self._data['pdf'] = PDF(self._data, label=self.formula_tex)
return self._data['pdf']
def test_overlap_smear_vs_hist(self):
doc, success = res2dict(REAL_PATH + "data/LiPZn-r57des.res")
doc["lattice_cart"] = abc2cart(doc["lattice_abc"])
doc["text_id"] = ["smear", "test"]
doc["pdf_smear"] = PDF(
doc,
num_images=3,
dr=0.01,
gaussian_width=0.1,
projected=False,
style="smear",
low_mem=True,
)
doc["text_id"] = ["hist", "test"]
doc["pdf_hist"] = PDF(doc,
num_images=3,
dr=0.1,
projected=False,
style="histogram")
overlap = PDFOverlap(doc["pdf_smear"], doc["pdf_hist"])
self.assertLessEqual(overlap.similarity_distance, 0.02)
self.assertGreater(overlap.similarity_distance, 0.0)
def test_identity_overlap(self):
doc, success = res2dict(REAL_PATH + "data/LiPZn-r57des.res")
doc["lattice_cart"] = abc2cart(doc["lattice_abc"])
doc["text_id"] = ["pdf", "test"]
doc["pdf_smear"] = PDF(
doc,
num_images=3,
dr=0.001,
gaussian_width=0.1,
style="smear",
debug=False,
low_mem=True,
)
overlap = PDFOverlap(doc["pdf_smear"], doc["pdf_smear"])
self.assertEqual(overlap.similarity_distance, 0.0)
def test_auto_images_vs_large(self):
doc, success = res2dict(REAL_PATH + "data/LiPZn-r57des.res")
doc["lattice_cart"] = abc2cart(doc["lattice_abc"])
doc["text_id"] = ["pdf", "test"]
doc["pdf_num_images"] = PDF(doc,
low_mem=True,
num_images=5,
rmax=15,
dr=0.1,
**{
"debug": True,
"projected": False
})
doc["pdf_auto_images"] = PDF(doc,
low_mem=True,
num_images="auto",
rmax=15,
dr=0.1,
**{
"debug": True,
"projected": False
})
np.testing.assert_array_almost_equal(doc["pdf_num_images"].gr,
doc["pdf_auto_images"].gr)
def test_concurrent_pdf_stoichs(self):
import glob
import numpy as np
import time
from copy import deepcopy
from matador.hull import QueryConvexHull
files = glob.glob(REAL_PATH + "data/hull-KPSn-KP/*.res")
cursor = [res2dict(file, db=True)[0] for file in files]
hull = QueryConvexHull(
cursor=cursor,
no_plot=True,
hull_cutoff=0.5,
summary=True,
elements=["K", "Sn", "P"],
quiet=True,
)
serial_cursor = deepcopy(hull.cursor)
pdf_args = {
"dr": 0.1,
"num_images": "auto",
"gaussian_width": 0.1,
"lazy": False,
"projected": False,
}
start = time.time()
pdf_factory = PDFFactory(hull.cursor, **pdf_args)
factory_elapsed = time.time() - start
start = time.time()
for doc in serial_cursor:
doc["pdf"] = PDF(doc, **pdf_args, timing=False)
serial_elapsed = time.time() - start
print("{:.2f} s over {} processes vs {:.2f} s in serial".format(
factory_elapsed, pdf_factory.nprocs, serial_elapsed))
print("Corresponding to a speedup of {:.1f} vs ideal {:.1f}".format(
serial_elapsed / factory_elapsed, pdf_factory.nprocs))
for ind, doc in enumerate(serial_cursor):
np.testing.assert_array_almost_equal(doc["pdf"].gr,
hull.cursor[ind]["pdf"].gr,
decimal=6)
def test_ideal_gas_pdf(self, retry=0):
""" DEPRECATED.
Slow, and not very useful.
"""
# create fake matador doc
doc = dict()
max_retries = 1
self.assertLess(
retry,
max_retries,
msg="After {} attempts, PDF still failed.".format(retry))
num_atoms = 100
box_size = 10
num_samples = 1
rmax = 15
dr = 0.01
num_images = "auto"
i = 0
doc["atom_types"] = num_atoms * ["C"]
doc["lattice_cart"] = np.asarray([[box_size, 0, 0], [0, box_size, 0],
[0, 0, box_size]])
doc["cell_volume"] = box_size**3
doc["text_id"] = ["ideal", "gas"]
while i < num_samples:
doc["positions_frac"] = np.random.rand(num_atoms, 3)
doc["text_id"] = "hist"
doc["pdf"] = PDF(
doc,
num_images=num_images,
dr=dr,
rmax=rmax,
lazy=True,
style="histogram",
debug=True,
)
doc["pdf"].calc_pdf()
self.assertAlmostEqual(np.mean(doc["pdf"].gr[50:]), 1.0, places=1)
def _cif_set_unreduced_sites(doc):
""" Expands sites by symmetry operations found under the key
`symemtry_equiv_pos_as_xyz` in the cif_dict.
Parameters:
doc (dict): matador document to modify. Must contain symops
under doc['_cif']['_symmetry_equiv_pos_as_xyz']. This doc
is updated with new `positions_frac`, `num_atoms`, `atom_types`
and `site_occupancy`.
"""
from matador.utils.cell_utils import wrap_frac_coords
from matador.utils.cell_utils import calc_pairwise_distances_pbc
from matador.fingerprints.pdf import PDF
species_sites = dict()
species_occ = dict()
symmetry_ops = []
symmetry_functions = []
def _apply_sym_op(x=None, y=None, z=None, symmetry=None):
""" Returns the site after the applied symmetry operation, in string representation. """
# cannot use a listcomp here due to interplay with functools
return [eval(symmetry[0]), eval(symmetry[1]), eval(symmetry[2])]
for symmetry in doc['_cif']['_symmetry_equiv_pos_as_xyz']:
symmetry = tuple(elem.strip() for elem in symmetry.strip('\'').split(','))
# check the element before doing an eval, as it is so unsafe
allowed_chars = ['x', 'y', 'z', '.', '/', '+', '-',
'0', '1', '2', '3', '4', '5', '6', '7', '8', '9']
for element in symmetry:
for character in element:
if character not in allowed_chars:
raise RuntimeError('You are trying to do something naughty with the symmetry element {}'
.format(element))
symmetry_ops.append(symmetry)
symmetry_functions.append(functools.partial(_apply_sym_op, symmetry=symmetry))
for ind, site in enumerate(doc['positions_frac']):
species = doc['atom_types'][ind]
occupancy = doc['site_occupancy'][ind]
if doc['atom_types'][ind] not in species_sites:
species_sites[species] = []
species_occ[species] = []
for symmetry in symmetry_functions:
x, y, z = site
new_site = symmetry(x=x, y=y, z=z)
new_site = wrap_frac_coords([new_site])[0]
species_sites[species].append(new_site)
species_occ[species].append(occupancy)
unreduced_sites = []
unreduced_occupancies = []
unreduced_species = []
# this loop assumes that no symmetry operation can map 2 unlike sites upon one another
for species in species_sites:
unreduced_sites.extend(species_sites[species])
unreduced_occupancies.extend(species_occ[species])
unreduced_species.extend(len(species_sites[species]) * [species])
# check that the symmetry procedure has not generated overlapping atoms
# this can happen for certain symmetries/cells if positions are not
# reported to sufficient precision
images = PDF._get_image_trans_vectors_auto(
doc['lattice_cart'],
0.1, 0.01, max_num_images=1,
)
poscarts = frac2cart(doc['lattice_cart'], unreduced_sites)
distances = calc_pairwise_distances_pbc(
poscarts,
images,
doc['lattice_cart'],
0.01,
compress=False,
filter_zero=False,
per_image=True
)
dupe_set = set()
for img in distances:
try:
i_s, j_s = np.where(~img.mask)
except ValueError:
# ValueError will be raised if there is only one atom as i_s, j_s cannot be unpacked
continue
for i, j in zip(i_s, j_s):
if i == j:
continue
else:
# sites can overlap if they have partial occupancy
if i not in dupe_set and unreduced_species[i] == unreduced_species[j]:
dupe_set.add(j)
doc['positions_frac'] = unreduced_sites
doc['site_occupancy'] = unreduced_occupancies
doc['atom_types'] = unreduced_species
doc['site_occupancy'] = [
atom for ind, atom in enumerate(unreduced_occupancies) if ind not in dupe_set
]
doc['atom_types'] = [
atom for ind, atom in enumerate(unreduced_species) if ind not in dupe_set
]
doc['positions_frac'] = [
atom for ind, atom in enumerate(unreduced_sites) if ind not in dupe_set
]
_num_atoms = np.sum(doc['site_occupancy'])
if abs(_num_atoms - round(_num_atoms, 0)) < EPS:
_num_atoms = int(round(_num_atoms, 0))
doc['num_atoms'] = _num_atoms
if len(doc['site_occupancy']) != len(doc['positions_frac']):
raise RuntimeError('Size mismatch between positions and occs, {} vs {}'
.format(len(doc['site_occupancy']), len(doc['positions_frac'])))
if len(doc['positions_frac']) != len(doc['atom_types']):
raise RuntimeError('Size mismatch between positions and types')