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from __future__ import annotations
from pytest import approx
from pymatgen.core.structure import Molecule
from pymatgen.io.adf import AdfInput, AdfKey, AdfOutput, AdfTask
from pymatgen.util.testing import TEST_FILES_DIR, MatSciTest
__author__ = "Xin Chen, chenxin13@mails.tsinghua.edu.cn"
TEST_DIR = f"{TEST_FILES_DIR}/io/adf"
geometry_string = """GEOMETRY
smooth conservepoints
optim all cartesian
iterations 250
step rad=0.15 angle=10.0
hessupd BFGS
converge e=0.001 grad=0.0003 rad=0.01 angle=0.5
END
"""
zlm_fit_string = """ZLMFIT
AtomDepQuality
10 good
12 normal
subend
END
"""
atoms_string = """ATOMS
O -0.90293455 0.66591421 0.00000000
H 0.05706545 0.66591421 0.00000000
H -1.22338913 1.57085004 0.00000000
END
"""
h2o_xyz = """3
0.0
O -0.90293455 0.66591421 0.0
H 0.05706545 0.66591421 0.0
H -1.22338913 1.57085004 0.0
"""
rhb18_xyz = """19
0.0
Rh -0.453396 -0.375115 0.000000
B 0.168139 3.232791 0.000000
B -0.270938 1.639058 0.000000
B 0.206283 2.604044 1.459430
B 0.404410 1.880136 2.866764
B -0.103309 0.887485 1.655272
B 0.436856 0.371367 3.299887
B 0.016593 -0.854959 1.930982
B 0.563233 -1.229713 3.453066
B 0.445855 -2.382027 2.415013
B 0.206283 2.604044 -1.459430
B 0.404410 1.880136 -2.866764
B -0.103309 0.887485 -1.655272
B 0.436856 0.371367 -3.299887
B 0.563233 -1.229713 -3.453066
B 0.016593 -0.854959 -1.930982
B 0.200456 -2.309538 -0.836316
B 0.200456 -2.309538 0.836316
B 0.445855 -2.382027 -2.415013
"""
def readfile(file_object):
"""`
Return the content of the file as a string.
Args:
file_object (file or str): The file to read. This can be either a File object or a file path.
Returns:
content (str): The content of the file.
"""
if hasattr(file_object, "read"):
return file_object.read()
with open(file_object, encoding="utf-8") as file:
return file.read()
class TestAdfKey:
def test_simple(self):
unrestricted = AdfKey("unrestricted")
assert str(unrestricted).strip() == "UNRESTRICTED"
def test_options(self):
charge = AdfKey("charge", [-1, 0])
charge_string = "CHARGE -1 0\n"
assert str(charge) == "CHARGE -1 0\n"
assert str(AdfKey.from_dict(charge.as_dict())) == charge_string
def test_subkeys(self):
smooth = AdfKey("smooth", ["conservepoints"])
optim = AdfKey("optim", ["all", "cartesian"])
iterations = AdfKey("iterations", [250])
step = AdfKey("step", [("rad", 0.15), ("angle", 10.0)])
hessupd = AdfKey("hessupd", ["BFGS"])
converge = AdfKey(
"converge",
[("e", 1.0e-3), ("grad", 3.0e-4), ("rad", 1.0e-2), ("angle", 0.5)],
)
geo = AdfKey("geometry", subkeys=[smooth, optim, iterations, step, hessupd, converge])
assert str(geo) == geometry_string
assert str(AdfKey.from_dict(geo.as_dict())) == geometry_string
assert geo.has_subkey("optim")
def test_end(self):
geo = AdfKey("Geometry")
assert str(geo) == "GEOMETRY\nEND\n"
def test_subkeys_subkeys(self):
atom_dep_quality = AdfKey("AtomDepQuality", subkeys=[AdfKey("10", ["good"]), AdfKey("12", ["normal"])])
zlmfit = AdfKey("zlmfit", subkeys=[atom_dep_quality])
assert str(zlmfit) == zlm_fit_string
assert str(AdfKey.from_dict(zlmfit.as_dict())) == zlm_fit_string
def test_from_str(self):
k1 = AdfKey.from_str("CHARGE -1 0")
assert k1.key == "CHARGE"
assert k1.options == [-1, 0]
k2 = AdfKey.from_str("step rad=0.15 angle=10.0")
assert k2.key == "step"
assert k2.options[0] == ["rad", approx(0.15)]
assert k2.options[1] == ["angle", approx(10.0)]
k3 = AdfKey.from_str("GEOMETRY\noptim all\niterations 100\nEND\n")
assert k3.key == "GEOMETRY"
assert k3.subkeys[0].options[0] == "all"
assert k3.subkeys[1].options[0] == 100
k4 = AdfKey.from_str(
"""SCF
iterations 300
converge 1.0e-7 1.0e-7
mixing 0.2
diis n=100 ok=0.0001 cyc=100 cx=5.0 cxx=10.0
END"""
)
assert k4.key == "SCF"
assert k4.subkeys[0].key == "iterations"
assert k4.subkeys[1].key == "converge"
assert k4.subkeys[1].options[0] == approx(1e-7)
assert k4.subkeys[2].options[0] == approx(0.2)
def test_option_operations(self):
k1 = AdfKey("Charge", [-1, 0])
k1.add_option(2)
assert k1.options == [-1, 0, 2]
k1.remove_option(0)
assert k1.options == [0, 2]
k2 = AdfKey.from_str("step rad=0.15 angle=10.0")
k2.add_option(["length", 0.1])
assert k2.options[2] == ["length", approx(0.1)]
k2.remove_option("rad")
assert k2.options[0] == ["angle", approx(10.0)]
def test_atom_block_key(self):
block = AdfKey("atoms")
mol = Molecule.from_str(h2o_xyz, "xyz")
for site in mol:
block.add_subkey(AdfKey(str(site.specie), list(site.coords)))
assert str(block) == atoms_string
energy_task = """TITLE ADF_RUN
UNITS
length angstrom
angle degree
END
XC
GGA PBE
END
BASIS
type DZ
core small
END
SCF
iterations 300
END
GEOMETRY SinglePoint
END
"""
class TestAdfTask:
def test_energy(self):
task = AdfTask()
assert str(task) == energy_task
def test_serialization(self):
task = AdfTask()
adf_task = AdfTask.from_dict(task.as_dict())
assert task.title == adf_task.title
assert task.basis_set == adf_task.basis_set
assert task.scf == adf_task.scf
assert task.geo == adf_task.geo
assert task.operation == adf_task.operation
assert task.units == adf_task.units
assert str(task) == str(adf_task)
rhb18 = {
"title": "RhB18",
"basis_set": AdfKey.from_str("BASIS\ntype TZP\ncore small\nEND"),
"xc": AdfKey.from_str("XC\nHybrid PBE0\nEND"),
"units": AdfKey.from_str("UNITS\nlength angstrom\nEND"),
"other_directives": [
AdfKey.from_str("SYMMETRY"),
AdfKey.from_str("RELATIVISTIC scalar zora"),
AdfKey.from_str("INTEGRATION 6.0 6.0 6.0"),
AdfKey.from_str("SAVE TAPE21"),
AdfKey.from_str("A1FIT 10.0"),
],
"geo_subkeys": [
AdfKey.from_str("optim all"),
AdfKey.from_str("iterations 300"),
AdfKey.from_str("step rad=0.15 angle=10.0"),
AdfKey.from_str("hessupd BFGS"),
],
"scf": AdfKey.from_str(
"""SCF
iterations 300
converge 1.0e-7 1.0e-7
mixing 0.2
lshift 0.0
diis n=100 ok=0.0001 cyc=100 cx=5.0 cxx=10.0
END"""
),
}
class TestAdfInput(MatSciTest):
def test_main(self):
tmp_file = f"{self.tmp_path}/adf.temp"
mol = Molecule.from_str(rhb18_xyz, "xyz")
mol.set_charge_and_spin(-1, 3)
task = AdfTask("optimize", **rhb18)
inp = AdfInput(task)
inp.write_file(mol, tmp_file)
expected = readfile(f"{TEST_DIR}/RhB18_adf.inp")
assert readfile(tmp_file) == expected
class TestAdfOutput:
def test_analytical_freq(self):
filename = f"{TEST_DIR}/analytical_freq/adf.out"
adf_out = AdfOutput(filename)
assert adf_out.final_energy == approx(-0.54340325)
assert len(adf_out.energies) == 4
assert len(adf_out.structures) == 4
assert adf_out.frequencies[0] == approx(1553.931)
assert adf_out.frequencies[2] == approx(3793.086)
assert adf_out.normal_modes[0][2] == approx(0.071)
assert adf_out.normal_modes[0][6] == approx(0.000)
assert adf_out.normal_modes[0][7] == approx(-0.426)
assert adf_out.normal_modes[0][8] == approx(-0.562)
def test_numerical_freq(self):
filename = f"{TEST_DIR}/numerical_freq/adf.out"
adf_out = AdfOutput(filename)
assert adf_out.freq_type == "Numerical"
assert len(adf_out.final_structure) == 4
assert len(adf_out.frequencies) == 6
assert len(adf_out.normal_modes) == 6
assert adf_out.frequencies[0] == approx(938.21)
assert adf_out.frequencies[3] == approx(3426.64)
assert adf_out.frequencies[4] == approx(3559.35)
assert adf_out.frequencies[5] == approx(3559.35)
assert adf_out.normal_modes[1][0] == approx(0.067)
assert adf_out.normal_modes[1][3] == approx(-0.536)
assert adf_out.normal_modes[1][7] == approx(0.000)
assert adf_out.normal_modes[1][9] == approx(-0.536)
def test_single_point(self):
filename = f"{TEST_DIR}/sp/adf.out"
adf_out = AdfOutput(filename)
assert adf_out.final_energy == approx(-0.74399276)
assert len(adf_out.final_structure) == 4
|
