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test_pdf.py
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#!/usr/bin/env python
import unittest
from matador.fingerprints.pdf import PDF, PDFOverlap, PDFFactory
from matador.scrapers.castep_scrapers import res2dict
from matador.utils.cell_utils import abc2cart, cart2volume
import numpy as np
from os.path import realpath
REAL_PATH = "/".join(realpath(__file__).split("/")[:-1]) + "/"
DEBUG = True
class PDFCalculatorTest(unittest.TestCase):
"""Test PDF calculator."""
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_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_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)
@unittest.skip
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_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)
@unittest.skip("Not sure this test is worthwhile anymore...")
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 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)
class PDFFactoryCalculatorTest(unittest.TestCase):
"""Test PDFFactory."""
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 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_concurrent_projected_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": True,
}
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
)
for key in doc["pdf"].elem_gr:
np.testing.assert_array_almost_equal(
doc["pdf"].elem_gr[key], cursor[ind]["pdf"].elem_gr[key], decimal=6
)
if __name__ == "__main__":
unittest.main()