def test_castep_cell_null_init(self):
null_cell = CastepCell()
self.assertEqual(null_cell.blocks, {})
self.assertEqual(null_cell.tags, {})
with self.assertRaises(ValueError):
structure = null_cell.structure
def test_castep_cell_from_structure(self):
cell = CastepCell.from_structure(self.si_structure)
self.assertEqual(cell.blocks['lattice_cart'].values,
[['ang'], ['5.43', '0.0', '0.0'],
['0.0', '5.43', '0.0'], ['0.0', '0.0', '5.43']])
self.assertEqual(cell.blocks['positions_frac'].values[0],
['Si', '0.0', '0.0', '0.0'])
self.assertEqual(cell.blocks['positions_frac'].values[7],
['Si', '0.75', '0.75', '0.25'])
def test_castep_cell_from_structure(self):
cell = CastepCell.from_structure(self.si_structure)
self.assertEqual(
cell.blocks["lattice_cart"].values,
[
["ang"],
["5.43", "0.0", "0.0"],
["0.0", "5.43", "0.0"],
["0.0", "0.0", "5.43"],
],
)
self.assertEqual(cell.blocks["positions_frac"].values[0],
["Si", "0.0", "0.0", "0.0"])
self.assertEqual(cell.blocks["positions_frac"].values[7],
["Si", "0.75", "0.75", "0.25"])
def test_castep_cell_from_singlepoint_file(self):
cc = CastepCell.from_file(self.zns_singlepoint_cell)
self.assertEqual(set(cc.blocks.keys()),
set(('lattice_cart', 'positions_abs', 'species_pot')))
self.assertEqual({k: v.value
for k, v in cc.tags.items()}, {
'fix_all_cell': ['true'],
'fix_all_ions': ['true'],
'symmetry_generate': ['true'],
'kpoint_mp_grid': ['4', '4', '4'],
'snap_to_symmetry': ['true']
})
self.assertEqual(cc.blocks['species_pot'].values[1], ['S', 'NCP'])
self.assertEqual(cc.blocks['species_pot'].comments, ['', ''])
structure = cc.structure
self.assertIsInstance(structure, Structure)
assert_array_almost_equal(
structure.lattice.matrix,
[[0., 2.71, 2.71], [2.71, 0., 2.71], [2.71, 2.71, 0.]])
def test_castep_cell_from_singlepoint_file(self):
cc = CastepCell.from_file(self.zns_singlepoint_cell)
self.assertEqual(set(cc.blocks.keys()),
{"lattice_cart", "positions_abs", "species_pot"})
self.assertEqual(
{k: v.value
for k, v in cc.tags.items()},
{
"fix_all_cell": ["true"],
"fix_all_ions": ["true"],
"symmetry_generate": ["true"],
"kpoint_mp_grid": ["4", "4", "4"],
"snap_to_symmetry": ["true"],
},
)
self.assertEqual(cc.blocks["species_pot"].values[1], ["S", "NCP"])
self.assertEqual(cc.blocks["species_pot"].comments, ["", ""])
structure = cc.structure
self.assertIsInstance(structure, Structure)
assert_array_almost_equal(
structure.lattice.matrix,
[[0.0, 2.71, 2.71], [2.71, 0.0, 2.71], [2.71, 2.71, 0.0]],
)
def kgen(
filename="POSCAR",
code="vasp",
directory=None,
make_folders=False,
symprec=0.01,
kpts_per_split=None,
ibzkpt=None,
spg=None,
density=60,
phonon=False,
mode="bradcrack",
cart_coords=False,
kpt_list=None,
labels=None,
):
"""Generate KPOINTS files for VASP band structure calculations.
This script provides a wrapper around several frameworks used to generate
k-points along a high-symmetry path. The paths found in Bradley and
Cracknell, SeeK-path, and pymatgen are all supported.
It is important to note that the standard primitive cell symmetry is
different between SeeK-path and pymatgen. If the correct the structure
is not used, the high-symmetry points (and band path) may be invalid.
Args:
filename (:obj:`str`, optional): Path to VASP structure file. Default
is ``POSCAR``.
code (:obj:`str`, optional): Calculation type. Default is 'vasp';
'questaal' also supported.
directory (:obj:`str`, optional): The output file directory.
make_folders (:obj:`bool`, optional): Generate folders and copy in
required files (INCAR, POTCAR, POSCAR, and possibly CHGCAR) from
the current directory.
symprec (:obj:`float`, optional): The precision used for determining
the cell symmetry.
kpts_per_split (:obj:`int`, optional): If set, the k-points are split
into separate k-point files (or folders) each containing the number
of k-points specified. This is useful for hybrid band structure
calculations where it is often intractable to calculate all
k-points in the same calculation.
ibzkpt (:obj:`str`, optional): Path to IBZKPT file. If set, the
generated k-points will be appended to the k-points in this file
and given a weight of 0. This is necessary for hybrid band
structure calculations.
spg (:obj:`str` or :obj:`int`, optional): The space group international
number or symbol to override the symmetry determined by spglib.
This is not recommended and only provided for testing purposes.
This option will only take effect when ``mode = 'bradcrack'``.
line_density (:obj:`int`, optional): Density of k-points along the
path.
phonon (:obj:`bool`, optional): Write phonon q-point path instead of
k-points. (Not appropriate for most codes.)
mode (:obj:`str`, optional): Method used for calculating the
high-symmetry path. The options are:
bradcrack
Use the paths from Bradley and Cracknell. See [brad]_.
pymatgen
Use the paths from pymatgen. See [curt]_.
latimer-munro
Use the paths from Latimer & Munro. See [lm]_.
seekpath
Use the paths from SeeK-path. See [seek]_.
cart_coords (:obj:`bool`, optional): Whether the k-points are returned
in cartesian or reciprocal coordinates. Defaults to ``False``
(fractional coordinates).
kpt_list (:obj:`list`, optional): List of k-points to use, formatted as
a list of subpaths, each containing a list of fractional k-points.
For example::
[ [[0., 0., 0.], [0., 0., 0.5]],
[[0.5, 0., 0.], [0.5, 0.5, 0.]] ]
Will return points along ``0 0 0 -> 0 0 1/2 | 1/2 0 0
-> 1/2 1/2 0``
path_labels (:obj:`list`, optional): The k-point labels. These should
be provided as a :obj:`list` of :obj:`str` for each subpath of the
overall path. For example::
[ ['Gamma', 'Z'], ['X', 'M'] ]
combined with the above example for ``kpt_list`` would indicate the
path: Gamma -> Z | X -> M. If no labels are provided, letters from
A -> Z will be used instead. If a label begins with '@' it will be
concealed when plotting with sumo-bandplot.
"""
if code.lower() == "vasp":
structure = Poscar.from_file(filename).structure
elif code.lower() == "questaal":
if filename.split(".")[0] == "site":
site = QuestaalSite.from_file(filename)
structure = site.structure
alat = site.alat
else:
structure = QuestaalInit.from_file(filename).structure
alat = None
elif code.lower() == "castep":
if cart_coords:
logging.warning("Ignoring request for Cartesian coordinates: "
"not applicable to CASTEP band structure format.")
cart_coords = False
if ibzkpt:
logging.warning('Ignoring request to use IBZKPT ("hybrid mode"), '
"for CASTEP workflow the SCF mesh should already "
"be set in input .cell file.")
structure = CastepCell.from_file(filename).structure
else:
raise ValueError(f'Code "{code}" not recognized.')
if phonon and (code.lower() not in phonon_supported_codes):
logging.error("Cannot write phonon path for {code}. "
"Supported codes: {supported}".format(
code=code,
supported=", ".join(phonon_supported_codes)))
sys.exit()
kpath, kpoints, labels = get_path_data(
structure,
mode=mode,
symprec=symprec,
kpt_list=kpt_list,
labels=labels,
spg=spg,
line_density=density,
cart_coords=cart_coords,
)
logging.info("\nk-point label indices:")
for i, label in enumerate(labels):
if label:
logging.info(f"\t{label}: {i + 1}")
if not kpt_list and not np.allclose(structure.lattice.matrix,
kpath.prim.lattice.matrix):
prim_filename = f"{os.path.basename(filename)}_prim"
if code.lower() == "questaal":
QuestaalInit.from_structure(kpath.prim).to_file(prim_filename)
elif code.lower() == "castep":
CastepCell.from_structure(kpath.prim).to_file(prim_filename)
else:
kpath.prim.to(filename=prim_filename)
logging.error(
"\nWARNING: The input structure does not match the "
"expected standard\nprimitive symmetry, the path may be "
"incorrect! Use at your own risk.\n\nThe correct "
"symmetry primitive structure has been saved as {}.".format(
prim_filename))
ibz = _parse_ibzkpt(ibzkpt)
if ibz and kpts_per_split is None:
logging.info("\nFound {} total kpoints in path, do you want to "
"split them up? (y/n)".format(len(kpoints)))
if input()[0].lower() == "y":
logging.info("How many kpoints per file?")
kpts_per_split = int(input())
if code.lower() == "vasp":
sumo.io.vasp.write_kpoint_files(
filename,
kpoints,
labels,
make_folders=make_folders,
ibzkpt=ibz,
kpts_per_split=kpts_per_split,
directory=directory,
cart_coords=cart_coords,
)
elif code.lower() == "castep":
sumo.io.castep.write_kpoint_files(
filename,
kpoints,
labels,
make_folders=make_folders,
kpts_per_split=kpts_per_split,
phonon=phonon,
directory=directory,
)
elif code.lower() == "questaal":
if cart_coords:
kpoints = [kpoint / (2 * np.pi) for kpoint in kpoints]
if alat is not None:
logging.info(
f"Multiplying kpoint values by ALAT = {alat} Bohr")
_bohr_to_angstrom = 0.5291772
kpoints = [
kpoint * alat * _bohr_to_angstrom for kpoint in kpoints
]
sumo.io.questaal.write_kpoint_files(
filename,
kpoints,
labels,
make_folders=make_folders,
directory=directory,
cart_coords=cart_coords,
)