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from __future__ import annotations
import pytest
from pytest import approx
from pymatgen.core import Structure
from pymatgen.io.res import AirssProvider, ResParseError, ResWriter
from pymatgen.util.testing import TEST_FILES_DIR
TEST_DIR = f"{TEST_FILES_DIR}/io/res"
res_coc = f"{TEST_DIR}/coc-115925-9326-14.res"
@pytest.mark.parametrize("provider", [AirssProvider.from_file(res_coc, "strict")])
class TestAirssProvider:
def test_cggf(self, provider: AirssProvider):
entry = provider.get_cut_grid_gmax_fsbc()
assert entry is not None
cut, gs, gm, fsbc = entry
assert cut == approx(326.5366)
assert gs == approx(1.75)
assert gm == approx(16.201)
assert fsbc == "automatic"
def test_moks(self, provider: AirssProvider):
entry = provider.get_mpgrid_offset_nkpts_spacing()
assert entry is not None
grid, offset, nkpts, spacing = entry
assert grid == (6, 6, 8)
assert offset == (0, 0, 0)
assert nkpts == 144
assert spacing == approx(0.05)
def test_pspots(self, provider: AirssProvider):
ps_pots = provider.get_pspots()
assert ps_pots["Co"] == "3|2.2|2.0|1.0|8|9|10|40:41:32(qc=5)"
assert ps_pots["C"] == "2|1.4|8|9|10|20:21(qc=5)"
def test_titl(self, provider: AirssProvider):
assert provider.seed == "coc-115925-9326-14"
assert provider.energy == approx(-3.90427411e003)
assert provider.spacegroup_label == "R3"
assert provider.pressure == approx(15.0252)
assert provider.volume == approx(57.051984)
def test_lattice(self, provider: AirssProvider):
assert provider.lattice.lengths == approx((5.07144, 5.07144, 3.89024))
assert provider.lattice.angles == approx((49.32125, 49.32125, 60))
def test_misc(self, provider: AirssProvider):
rs_info = provider.get_run_start_info()
assert rs_info is not None
date, path = rs_info
assert path == "/path/to/airss/run"
assert date.day == 16
assert date.month == 7
assert date.year == 2021
castep_v = provider.get_castep_version()
assert castep_v == "19.11"
frd = provider.get_func_rel_disp()
assert frd is not None
functional, rel, disp = frd
assert functional == "Perdew Burke Ernzerhof"
assert rel == "Koelling-Harmon"
assert disp == "off"
airss_v = provider.get_airss_version()
assert airss_v is not None
assert airss_v[0] == "0.9.1"
assert airss_v[1].year == 2018
def test_end_of_file_newline(self, provider: AirssProvider):
"""https://github.com/materialsproject/pymatgen/issues/3636"""
string = ResWriter(provider.entry).string
assert string.endswith("\n")
def test_empty_rems_no_blank_line(self, provider: AirssProvider):
"""https://github.com/materialsproject/pymatgen/issues/3636"""
entry = provider.entry
del entry.data["rems"]
string = ResWriter(entry).string
assert all(string.splitlines())
def test_entry(self, provider: AirssProvider):
entry1 = provider.entry
assert entry1.energy == provider.energy
string1 = ResWriter(entry1).string
entry2 = AirssProvider.from_str(string1).entry
string2 = ResWriter(entry2).string
assert entry1 == entry2
assert string1 == string2
def test_raise(self, provider: AirssProvider):
entry = provider.entry
string = ResWriter(entry).string
string_strip = "\n".join(line for line in string.splitlines() if "REM" not in line)
prov = AirssProvider.from_str(string_strip, "strict")
assert entry.structure == prov.entry.structure
with pytest.raises(ResParseError, match="No CASTEP version found in REM"):
prov.get_castep_version()
def test_as_dict(self, provider: AirssProvider):
verbose_dict = provider.as_dict(verbose=True)
assert sorted(verbose_dict) == [
"@class",
"@module",
"@version",
"parse_rems",
"res",
]
# test round-trip serialization/deserialization gives same dict
assert AirssProvider.from_dict(verbose_dict).as_dict() == verbose_dict
# non-verbose case
dct = provider.as_dict(verbose=False)
assert sorted(dct) == [
"appearances",
"energy",
"integrated_absolute_spin_density",
"integrated_spin_density",
"pressure",
"rems",
"seed",
"spacegroup_label",
"structure",
"volume",
]
assert dct["seed"] == "coc-115925-9326-14"
assert dct["energy"] == approx(-3904.2741)
assert dct["spacegroup_label"] == "R3"
assert dct["pressure"] == approx(15.0252)
assert dct["volume"] == approx(57.051984)
def test_sfac_writer(self, provider: AirssProvider):
"""https://github.com/materialsproject/pymatgen/issues/3677"""
sfac = ResWriter._sfac_from_sites(provider.structure)
specie_nums = [ion.specie_num for ion in sfac.ions]
assert set(specie_nums) == {1, 2}
assert len(sfac.species) == max(specie_nums)
assert [str(sp) for sp in sfac.species] == ["C", "Co"]
class TestSpin:
def test_read_spin(self):
with open(res_coc, encoding="utf-8") as file:
lines = file.readlines()
# add spin to a line
lines[25] = f"{lines[25][:-1]} -1.4\n"
contents = "".join(lines)
provider = AirssProvider.from_str(contents)
for site in provider.structure:
if site.properties["magmom"] is not None:
assert site.properties.get("magmom") == approx(-1.4)
return
pytest.fail("valid 'magmom' not found in any site properties")
def test_gh_2938_example(self):
res_spin_file = f"{TEST_DIR}/spins-in-last-col.res"
with open(res_spin_file, encoding="utf-8") as res_file:
contents = res_file.read()
provider = AirssProvider.from_str(contents)
for site in provider.structure:
if site.properties["magmom"] is not None:
assert site.properties.get("magmom") in (
3.31,
4.12,
-0.01,
-0.04,
-0.17,
)
class TestStructureModule:
def test_structure_from_file(self):
structure: Structure = Structure.from_file(res_coc)
# just check that we read it
assert structure.lattice.angles == approx((49.32125, 49.32125, 60))
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