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test_structure_environments.py
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test_structure_environments.py
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#!/usr/bin/env python
__author__ = "waroquiers"
import json
import os
import shutil
import unittest
import numpy as np
from monty.tempfile import ScratchDir
from pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies import (
MultiWeightsChemenvStrategy,
SimplestChemenvStrategy,
)
from pymatgen.analysis.chemenv.coordination_environments.structure_environments import (
LightStructureEnvironments,
StructureEnvironments,
)
from pymatgen.core.periodic_table import Species
from pymatgen.util.testing import PymatgenTest
se_files_dir = os.path.join(
PymatgenTest.TEST_FILES_DIR,
"chemenv",
"structure_environments_files",
)
class StructureEnvironmentsTest(PymatgenTest):
def test_structure_environments(self):
with ScratchDir("."):
f = open("{}/{}".format(se_files_dir, "se_mp-7000.json"), "r")
dd = json.load(f)
f.close()
se = StructureEnvironments.from_dict(dd)
isite = 6
csm_and_maps_fig, csm_and_maps_subplot = se.get_csm_and_maps(isite=isite)
np.testing.assert_array_almost_equal(
csm_and_maps_subplot.lines[0].get_xydata().flatten(), [0.0, 0.53499332]
)
np.testing.assert_array_almost_equal(
csm_and_maps_subplot.lines[1].get_xydata().flatten(), [1.0, 0.47026441]
)
np.testing.assert_array_almost_equal(
csm_and_maps_subplot.lines[2].get_xydata().flatten(), [2.0, 0.00988778]
)
environments_figure, environments_subplot = se.get_environments_figure(isite=isite)
np.testing.assert_array_almost_equal(
np.array(environments_subplot.patches[0].get_xy()),
[
[1.0, 1.0],
[1.0, 0.99301365],
[1.00179228, 0.99301365],
[1.00179228, 1.0],
[1.0, 1.0],
],
)
np.testing.assert_array_almost_equal(
np.array(environments_subplot.patches[1].get_xy()),
[
[1.0, 0.99301365],
[1.0, 0.0],
[1.00179228, 0.0],
[1.00179228, 0.99301365],
[1.0, 0.99301365],
],
)
np.testing.assert_array_almost_equal(
np.array(environments_subplot.patches[2].get_xy()),
[
[1.00179228, 1.0],
[1.00179228, 0.99301365],
[2.25, 0.99301365],
[2.25, 1.0],
[1.00179228, 1.0],
],
)
np.testing.assert_array_almost_equal(
np.array(environments_subplot.patches[3].get_xy()),
[
[1.00179228, 0.99301365],
[1.00179228, 0.0],
[2.22376156, 0.0],
[2.22376156, 0.0060837],
[2.25, 0.0060837],
[2.25, 0.99301365],
[1.00179228, 0.99301365],
],
)
np.testing.assert_array_almost_equal(
np.array(environments_subplot.patches[4].get_xy()),
[
[2.22376156, 0.0060837],
[2.22376156, 0.0],
[2.25, 0.0],
[2.25, 0.0060837],
[2.22376156, 0.0060837],
],
)
se.save_environments_figure(isite=isite, imagename="image.png")
self.assertTrue(os.path.exists("image.png"))
self.assertEqual(len(se.differences_wrt(se)), 0)
self.assertFalse(se.__ne__(se))
ce = se.ce_list[isite][4][0]
self.assertTrue(ce.__len__(), 4)
symbol, mingeom = ce.minimum_geometry(symmetry_measure_type="csm_wocs_ctwocc")
self.assertEqual(symbol, "T:4")
self.assertAlmostEqual(mingeom["symmetry_measure"], 0.00988778424054)
np.testing.assert_array_almost_equal(
mingeom["other_symmetry_measures"]["rotation_matrix_wcs_csc"],
[
[-0.8433079817973094, -0.19705747216466898, 0.5000000005010193],
[0.4868840909509757, 0.11377118475194581, 0.8660254034951744],
[-0.22754236927612112, 0.9737681809261427, 1.3979531202869064e-13],
],
)
self.assertEqual(mingeom["detailed_voronoi_index"], {"index": 0, "cn": 4})
self.assertAlmostEqual(
mingeom["other_symmetry_measures"]["scaling_factor_wocs_ctwocc"],
1.6270605877934026,
)
ce_string = ce.__str__()
self.assertTrue("csm1 (with central site) : 0.00988" in ce_string)
self.assertTrue("csm2 (without central site) : 0.00981" in ce_string)
self.assertTrue("csm1 (with central site) : 12.987" in ce_string)
self.assertTrue("csm2 (without central site) : 11.827" in ce_string)
self.assertTrue("csm1 (with central site) : 32.466" in ce_string)
self.assertTrue("csm2 (without central site) : 32.466" in ce_string)
self.assertTrue("csm1 (with central site) : 34.644" in ce_string)
self.assertTrue("csm2 (without central site) : 32.466" in ce_string)
mingeoms = ce.minimum_geometries(symmetry_measure_type="csm_wocs_ctwocc", max_csm=12.0)
self.assertEqual(len(mingeoms), 2)
mingeoms = ce.minimum_geometries(symmetry_measure_type="csm_wocs_ctwcc", max_csm=12.0)
self.assertEqual(len(mingeoms), 1)
mingeoms = ce.minimum_geometries(n=3)
self.assertEqual(len(mingeoms), 3)
ce2 = se.ce_list[7][4][0]
self.assertTrue(ce.is_close_to(ce2, rtol=0.01, atol=1e-4))
self.assertFalse(ce.is_close_to(ce2, rtol=0.0, atol=1e-8))
self.assertFalse(ce.__eq__(ce2))
self.assertTrue(ce.__ne__(ce2))
def test_light_structure_environments(self):
with ScratchDir("."):
f = open("{}/{}".format(se_files_dir, "se_mp-7000.json"), "r")
dd = json.load(f)
f.close()
se = StructureEnvironments.from_dict(dd)
strategy = SimplestChemenvStrategy()
lse = LightStructureEnvironments.from_structure_environments(
structure_environments=se, strategy=strategy, valences="undefined"
)
isite = 6
nb_set = lse.neighbors_sets[isite][0]
neighb_coords = [
np.array([0.2443798, 1.80409653, -1.13218359]),
np.array([1.44020353, 1.11368738, 1.13218359]),
np.array([2.75513098, 2.54465207, -0.70467298]),
np.array([0.82616785, 3.65833945, 0.70467298]),
]
neighb_indices = [0, 3, 5, 1]
neighb_images = [[0, 0, -1], [0, 0, 0], [0, 0, -1], [0, 0, 0]]
np.testing.assert_array_almost_equal(neighb_coords, nb_set.neighb_coords)
np.testing.assert_array_almost_equal(neighb_coords, [s.coords for s in nb_set.neighb_sites])
nb_sai = nb_set.neighb_sites_and_indices
np.testing.assert_array_almost_equal(neighb_coords, [sai["site"].coords for sai in nb_sai])
np.testing.assert_array_almost_equal(neighb_indices, [sai["index"] for sai in nb_sai])
nb_iai = nb_set.neighb_indices_and_images
np.testing.assert_array_almost_equal(neighb_indices, [iai["index"] for iai in nb_iai])
np.testing.assert_array_equal(neighb_images, [iai["image_cell"] for iai in nb_iai])
self.assertEqual(nb_set.__len__(), 4)
self.assertEqual(nb_set.__hash__(), 4)
self.assertFalse(nb_set.__ne__(nb_set))
self.assertEqual(
nb_set.__str__(),
"Neighbors Set for site #6 :\n"
" - Coordination number : 4\n"
" - Neighbors sites indices : 0, 1, 2, 3\n",
)
stats = lse.get_statistics()
neighbors = lse.strategy.get_site_neighbors(site=lse.structure[isite])
self.assertArrayAlmostEqual(neighbors[0].coords, np.array([0.2443798, 1.80409653, -1.13218359]))
self.assertArrayAlmostEqual(neighbors[1].coords, np.array([1.44020353, 1.11368738, 1.13218359]))
self.assertArrayAlmostEqual(neighbors[2].coords, np.array([2.75513098, 2.54465207, -0.70467298]))
self.assertArrayAlmostEqual(neighbors[3].coords, np.array([0.82616785, 3.65833945, 0.70467298]))
equiv_site_index_and_transform = lse.strategy.equivalent_site_index_and_transform(neighbors[0])
self.assertEqual(equiv_site_index_and_transform[0], 0)
self.assertArrayAlmostEqual(equiv_site_index_and_transform[1], [0.0, 0.0, 0.0])
self.assertArrayAlmostEqual(equiv_site_index_and_transform[2], [0.0, 0.0, -1.0])
equiv_site_index_and_transform = lse.strategy.equivalent_site_index_and_transform(neighbors[1])
self.assertEqual(equiv_site_index_and_transform[0], 3)
self.assertArrayAlmostEqual(equiv_site_index_and_transform[1], [0.0, 0.0, 0.0])
self.assertArrayAlmostEqual(equiv_site_index_and_transform[2], [0.0, 0.0, 0.0])
self.assertEqual(stats["atom_coordination_environments_present"], {"Si": {"T:4": 3.0}})
self.assertEqual(stats["coordination_environments_atom_present"], {"T:4": {"Si": 3.0}})
self.assertEqual(
stats["fraction_atom_coordination_environments_present"],
{"Si": {"T:4": 1.0}},
)
site_info_ce = lse.get_site_info_for_specie_ce(specie=Species("Si", 4), ce_symbol="T:4")
np.testing.assert_array_almost_equal(site_info_ce["fractions"], [1.0, 1.0, 1.0])
np.testing.assert_array_almost_equal(
site_info_ce["csms"],
[0.009887784240541068, 0.009887786546730826, 0.009887787384385317],
)
self.assertEqual(site_info_ce["isites"], [6, 7, 8])
site_info_allces = lse.get_site_info_for_specie_allces(specie=Species("Si", 4))
self.assertEqual(site_info_allces["T:4"], site_info_ce)
self.assertFalse(lse.contains_only_one_anion("I-"))
self.assertFalse(lse.contains_only_one_anion_atom("I"))
self.assertTrue(lse.site_contains_environment(isite=isite, ce_symbol="T:4"))
self.assertFalse(lse.site_contains_environment(isite=isite, ce_symbol="S:4"))
self.assertFalse(lse.structure_contains_atom_environment(atom_symbol="Si", ce_symbol="S:4"))
self.assertTrue(lse.structure_contains_atom_environment(atom_symbol="Si", ce_symbol="T:4"))
self.assertFalse(lse.structure_contains_atom_environment(atom_symbol="O", ce_symbol="T:4"))
self.assertTrue(lse.uniquely_determines_coordination_environments)
self.assertFalse(lse.__ne__(lse))
envs = lse.strategy.get_site_coordination_environments(lse.structure[6])
self.assertEqual(len(envs), 1)
self.assertEqual(envs[0][0], "T:4")
multi_strategy = MultiWeightsChemenvStrategy.stats_article_weights_parameters()
lse_multi = LightStructureEnvironments.from_structure_environments(
strategy=multi_strategy, structure_environments=se, valences="undefined"
)
self.assertAlmostEqual(
lse_multi.coordination_environments[isite][0]["csm"],
0.009887784240541068,
)
self.assertAlmostEqual(lse_multi.coordination_environments[isite][0]["ce_fraction"], 1.0)
self.assertEqual(lse_multi.coordination_environments[isite][0]["ce_symbol"], "T:4")
if __name__ == "__main__":
unittest.main()