def bandpath(self, path=None, npoints=None, special_points=None,
density=None, transformation=None):
"""Return a :class:`~ase.dft.kpoints.BandPath` for this lattice.
See :meth:`ase.cell.Cell.bandpath` for description of parameters.
>>> BCT(3, 5).bandpath()
BandPath(path='GXYSGZS1NPY1Z,XP', cell=[3x3], special_points={GNPSS1XYY1Z}, kpts=[51x3])
.. note:: This produces the standard band path following AFlow
conventions. If your cell does not follow this convention,
you will need :meth:`ase.cell.Cell.bandpath` instead or
the kpoints may not correspond to your particular cell.
"""
if special_points is None:
special_points = self.get_special_points()
if path is None:
path = self._variant.special_path
elif not isinstance(path, str):
from ase.dft.kpoints import resolve_custom_points
special_points = dict(special_points)
path = resolve_custom_points(path, special_points, self._eps)
cell = self.tocell()
if transformation is not None:
cell = transformation.dot(cell)
bandpath = BandPath(cell=cell, path=path,
special_points=special_points)
return bandpath.interpolate(npoints=npoints, density=density)
def bandpath(self,
path=None,
npoints=None,
special_points=None,
density=None,
transformation=None):
"""Return a :class:`~ase.dft.kpoints.BandPath` for this lattice.
See :meth:`ase.cell.Cell.bandpath` for description of parameters.
>>> BCT(3, 5).bandpath()
BandPath(path='GXYSGZS1NPY1Z,XP', cell=[3x3], special_points={GNPSS1XYY1Z}, kpts=[51x3])
"""
if special_points is None:
special_points = self.get_special_points()
if path is None:
path = self._variant.special_path
elif not isinstance(path, str):
from ase.dft.kpoints import resolve_custom_points
special_points = dict(special_points)
path = resolve_custom_points(path, special_points, self._eps)
cell = self.tocell()
if transformation is not None:
cell = transformation.dot(cell)
bandpath = BandPath(cell=cell,
path=path,
special_points=special_points)
return bandpath.interpolate(npoints=npoints, density=density)
def bandpath(
self,
path: str = None,
npoints: int = None,
*,
density: float = None,
special_points: Mapping[str, Sequence[float]] = None,
eps: float = 2e-4,
pbc: Union[bool,
Sequence[bool]] = True) -> "ase.dft.kpoints.BandPath":
"""Build a :class:`~ase.dft.kpoints.BandPath` for this cell.
If special points are None, determine the Bravais lattice of
this cell and return a suitable Brillouin zone path with
standard special points.
If special special points are given, interpolate the path
directly from the available data.
Parameters:
path: string
String of special point names defining the path, e.g. 'GXL'.
npoints: int
Number of points in total. Note that at least one point
is added for each special point in the path.
density: float
density of kpoints along the path in Å⁻¹.
special_points: dict
Dictionary mapping special points to scaled kpoint coordinates.
For example ``{'G': [0, 0, 0], 'X': [1, 0, 0]}``.
eps: float
Tolerance for determining Bravais lattice.
pbc: three bools
Whether cell is periodic in each direction. Normally not
necessary. If cell has three nonzero cell vectors, use
e.g. pbc=[1, 1, 0] to request a 2D bandpath nevertheless.
Example
-------
>>> cell = Cell.fromcellpar([4, 4, 4, 60, 60, 60])
>>> cell.bandpath('GXW', npoints=20)
BandPath(path='GXW', cell=[3x3], special_points={GKLUWX}, kpts=[20x3])
"""
# TODO: Combine with the rotation transformation from bandpath()
cell = self.uncomplete(pbc)
if special_points is None:
from ase.lattice import identify_lattice
lat, op = identify_lattice(cell, eps=eps)
bandpath = lat.bandpath(path, npoints=npoints, density=density)
return bandpath.transform(op)
else:
from ase.dft.kpoints import BandPath, resolve_custom_points
path = resolve_custom_points(path, special_points, eps=eps)
bandpath = BandPath(cell, path=path, special_points=special_points)
return bandpath.interpolate(npoints=npoints, density=density)
def bandpath(self, path=None, npoints=50, special_points=None):
# npoints should depend on the length of the path
if special_points is None:
special_points = self.get_special_points()
if path is None:
path = self.variant.special_path
bandpath = BandPath(cell=self.tocell(),
labelseq=path,
special_points=special_points)
return bandpath.interpolate(npoints=npoints)
def bandpath(self,
path=None,
npoints=None,
density=None,
special_points=None,
eps=2e-4):
"""Build a :class:`~ase.dft.kpoints.BandPath` for this cell.
If special points are None, determine the Bravais lattice of
this cell and return a suitable Brillouin zone path with
standard special points.
If special special points are given, interpolate the path
directly from the available data.
Parameters:
path: string
String of special point names defining the path, e.g. 'GXL'.
npoints: int
Number of points in total. Note that at least one point
is added for each special point in the path.
density: float
density of kpoints along the path in Å⁻¹.
special_points: dict
Dictionary mapping special points to scaled kpoint coordinates.
For example ``{'G': [0, 0, 0], 'X': [1, 0, 0]}``.
eps: float
Tolerance for determining Bravais lattice.
Example
-------
>>> cell = Cell.fromcellpar([4, 4, 4, 60, 60, 60])
>>> cell.bandpath('GXW', npoints=20)
BandPath(path='GXW', cell=[3x3], special_points={GKLUWX}, kpts=[20x3])
"""
# TODO: Combine with the rotation transformation from bandpath()
if special_points is None:
from ase.lattice import identify_lattice
lat, op = identify_lattice(self, eps=eps)
path = lat.bandpath(path, npoints=npoints, density=density)
return path.transform(op)
else:
from ase.dft.kpoints import BandPath, resolve_custom_points
path = resolve_custom_points(path, special_points, eps=eps)
path = BandPath(self, path=path, special_points=special_points)
return path.interpolate(npoints=npoints, density=density)
def test_band_structure_setup(testing_calculator):
c = testing_calculator
from ase.dft.kpoints import BandPath
atoms = ase.build.bulk('Ag')
bp = BandPath(cell=atoms.cell,
path='GX',
special_points={
'G': [0, 0, 0],
'X': [0.5, 0, 0.5]
})
bp = bp.interpolate(npoints=10)
c.set_bandpath(bp)
kpt_list = c.cell.bs_kpoint_list.value.split('\n')
assert len(kpt_list) == 10
assert list(map(float, kpt_list[0].split())) == [0., 0., 0.]
assert list(map(float, kpt_list[-1].split())) == [0.5, 0.0, 0.5]
def test_castep_interface():
"""Simple shallow test of the CASTEP interface"""
import os
import re
import tempfile
import warnings
import numpy as np
import ase
import ase.lattice.cubic
from ase.calculators.castep import (Castep, CastepOption, CastepParam,
CastepCell, make_cell_dict,
make_param_dict, CastepKeywords,
create_castep_keywords,
import_castep_keywords,
CastepVersionError)
# XXX on porting this test to pytest it wasn't skipped as it should be.
# At any rate it failed then. Maybe someone should look into that ...
#
# Hence, call the constructor to trigger our test skipping hack:
Castep()
tmp_dir = tempfile.mkdtemp()
# We have fundamentally two sets of tests: one if CASTEP is present, the other
# if it isn't
has_castep = False
# Try creating and importing the castep keywords first
try:
create_castep_keywords(castep_command=os.environ['CASTEP_COMMAND'],
path=tmp_dir,
fetch_only=20)
has_castep = True # If it worked, it must be present
except KeyError:
print('Could not find the CASTEP_COMMAND environment variable - please'
' set it to run the full set of Castep tests')
except CastepVersionError:
print(
'Invalid CASTEP_COMMAND provided - please set the correct one to '
'run the full set of Castep tests')
try:
castep_keywords = import_castep_keywords(
castep_command=os.environ.get('CASTEP_COMMAND', ''))
except CastepVersionError:
castep_keywords = None
# Start by testing the fundamental parts of a CastepCell/CastepParam object
boolOpt = CastepOption('test_bool', 'basic', 'defined')
boolOpt.value = 'TRUE'
assert boolOpt.raw_value is True
float3Opt = CastepOption('test_float3', 'basic', 'real vector')
float3Opt.value = '1.0 2.0 3.0'
assert np.isclose(float3Opt.raw_value, [1, 2, 3]).all()
# Generate a mock keywords object
mock_castep_keywords = CastepKeywords(make_param_dict(), make_cell_dict(),
[], [], 0)
mock_cparam = CastepParam(mock_castep_keywords, keyword_tolerance=2)
mock_ccell = CastepCell(mock_castep_keywords, keyword_tolerance=2)
# Test special parsers
mock_cparam.continuation = 'default'
mock_cparam.reuse = 'default'
assert mock_cparam.reuse.value is None
mock_ccell.species_pot = ('Si', 'Si.usp')
mock_ccell.species_pot = ('C', 'C.usp')
assert 'Si Si.usp' in mock_ccell.species_pot.value
assert 'C C.usp' in mock_ccell.species_pot.value
symops = (np.eye(3)[None], np.zeros(3)[None])
mock_ccell.symmetry_ops = symops
assert """1.0 0.0 0.0
0.0 1.0 0.0
0.0 0.0 1.0
0.0 0.0 0.0""" in mock_ccell.symmetry_ops.value
# check if the CastepOpt, CastepCell comparison mechanism works
if castep_keywords:
p1 = CastepParam(castep_keywords)
p2 = CastepParam(castep_keywords)
assert p1._options == p2._options
p1._options['xc_functional'].value = 'PBE'
p1.xc_functional = 'PBE'
assert p1._options != p2._options
c = Castep(directory=tmp_dir, label='test_label', keyword_tolerance=2)
if castep_keywords:
c.xc_functional = 'PBE'
else:
c.param.xc_functional = 'PBE' # In "forgiving" mode, we need to specify
lattice = ase.lattice.cubic.BodyCenteredCubic('Li')
print('For the sake of evaluating this test, warnings')
print('about auto-generating pseudo-potentials are')
print('normal behavior and can be safely ignored')
lattice.calc = c
param_fn = os.path.join(tmp_dir, 'myParam.param')
with open(param_fn, 'w') as param:
param.write('XC_FUNCTIONAL : PBE #comment\n')
param.write('XC_FUNCTIONAL : PBE #comment\n')
param.write('#comment\n')
param.write('CUT_OFF_ENERGY : 450.\n')
c.merge_param(param_fn)
assert c.calculation_required(lattice)
if has_castep:
assert c.dryrun_ok()
c.prepare_input_files(lattice)
# detecting pseudopotentials tests
# typical filenames
files = [
'Ag_00PBE.usp', 'Ag_00.recpot', 'Ag_C18_PBE_OTF.usp',
'ag-optgga1.recpot', 'Ag_OTF.usp', 'ag_pbe_v1.4.uspp.F.UPF',
'Ni_OTF.usp', 'fe_pbe_v1.5.uspp.F.UPF', 'Cu_01.recpot'
]
pp_path = os.path.join(tmp_dir, 'test_pp')
os.makedirs(pp_path)
for f in files:
with open(os.path.join(pp_path, f), 'w') as _f:
_f.write('DUMMY PP')
c = Castep(directory=tmp_dir,
label='test_label_pspots',
castep_pp_path=pp_path)
c._pedantic = True
atoms = ase.build.bulk('Ag')
atoms.calc = c
# I know, unittest would be nicer... maybe at a later point
# disabled, but may be useful still
# try:
# # this should yield no files
# atoms.calc.find_pspots(suffix='uspp')
# raise AssertionError
# # this should yield no files
# atoms.calc.find_pspots(suffix='uspp')
# raise AssertionError
# except RuntimeError as e:
# #print(e)
# pass
# # print(e)
# pass
try:
# this should yield non-unique files
atoms.calc.find_pspots(suffix='recpot')
raise AssertionError
except RuntimeError:
pass
# now let's see if we find all...
atoms.calc.find_pspots(pspot='00PBE', suffix='usp')
assert atoms.calc.cell.species_pot.value.split()[-1] == 'Ag_00PBE.usp'
atoms.calc.find_pspots(pspot='00', suffix='recpot')
assert atoms.calc.cell.species_pot.value.split()[-1] == 'Ag_00.recpot'
atoms.calc.find_pspots(pspot='C18_PBE_OTF', suffix='usp')
assert atoms.calc.cell.species_pot.value.split(
)[-1] == 'Ag_C18_PBE_OTF.usp'
atoms.calc.find_pspots(pspot='optgga1', suffix='recpot')
assert atoms.calc.cell.species_pot.value.split()[-1] == 'ag-optgga1.recpot'
atoms.calc.find_pspots(pspot='OTF', suffix='usp')
assert atoms.calc.cell.species_pot.value.split()[-1] == 'Ag_OTF.usp'
atoms.calc.find_pspots(suffix='UPF')
assert (atoms.calc.cell.species_pot.value.split()[-1] ==
'ag_pbe_v1.4.uspp.F.UPF')
# testing regular workflow
c = Castep(directory=tmp_dir,
label='test_label_pspots',
castep_pp_path=pp_path,
find_pspots=True,
keyword_tolerance=2)
c._build_missing_pspots = False
atoms = ase.build.bulk('Ag')
atoms.calc = c
# this should raise an error due to ambuiguity
try:
c._fetch_pspots()
raise AssertionError
except RuntimeError:
pass
for e in ['Ni', 'Fe', 'Cu']:
atoms = ase.build.bulk(e)
atoms.calc = c
c._fetch_pspots()
# test writing to file
tmp_dir = os.path.join(tmp_dir, 'input_files')
c = Castep(directory=tmp_dir,
find_pspots=True,
castep_pp_path=pp_path,
keyword_tolerance=2)
c._label = 'test'
atoms = ase.build.bulk('Cu')
atoms.calc = c
c.prepare_input_files()
with open(os.path.join(tmp_dir, 'test.cell'), 'r') as f:
assert re.search(r'Cu Cu_01\.recpot',
''.join(f.readlines())) is not None
# test keyword conflict management
c = Castep(cut_off_energy=300.)
assert float(c.param.cut_off_energy.value) == 300.0
with warnings.catch_warnings(record=True) as w:
warnings.simplefilter("always")
c.basis_precision = 'MEDIUM'
assert issubclass(w[-1].category, UserWarning)
assert "conflicts" in str(w[-1].message)
assert c.param.cut_off_energy.value is None
assert c.param.basis_precision.value.strip() == 'MEDIUM'
with warnings.catch_warnings(record=True) as w:
warnings.simplefilter("always")
c.cut_off_energy = 200.0
assert c.param.basis_precision.value is None
assert issubclass(w[-1].category, UserWarning)
assert 'option "cut_off_energy" conflicts' in str(w[-1].message)
# test kpoint setup options
with warnings.catch_warnings():
warnings.simplefilter("ignore")
# This block of tests is going to generate a lot of conflict warnings.
# We already tested that those work, so just hide them from the output.
c = Castep(kpts=[
(0.0, 0.0, 0.0, 1.0),
])
assert c.cell.kpoint_list.value == '0.0 0.0 0.0 1.0'
c.set_kpts(((0.0, 0.0, 0.0, 0.25), (0.25, 0.25, 0.3, 0.75)))
assert c.cell.kpoint_list.value == '0.0 0.0 0.0 0.25\n0.25 0.25 0.3 0.75'
c.set_kpts(c.cell.kpoint_list.value.split('\n'))
assert c.cell.kpoint_list.value == '0.0 0.0 0.0 0.25\n0.25 0.25 0.3 0.75'
c.set_kpts([3, 3, 2])
assert c.cell.kpoint_mp_grid.value == '3 3 2'
c.set_kpts(None)
assert c.cell.kpoints_list.value is None
assert c.cell.kpoint_list.value is None
assert c.cell.kpoint_mp_grid.value is None
c.set_kpts('2 2 3')
assert c.cell.kpoint_mp_grid.value == '2 2 3'
c.set_kpts({'even': True, 'gamma': True})
assert c.cell.kpoint_mp_grid.value == '2 2 2'
assert c.cell.kpoint_mp_offset.value == '0.25 0.25 0.25'
c.set_kpts({'size': (2, 2, 4), 'even': False})
assert c.cell.kpoint_mp_grid.value == '3 3 5'
assert c.cell.kpoint_mp_offset.value == '0.0 0.0 0.0'
atoms = ase.build.bulk('Ag')
atoms.calc = c
c.set_kpts({'density': 10, 'gamma': False, 'even': None})
assert c.cell.kpoint_mp_grid.value == '27 27 27'
assert c.cell.kpoint_mp_offset.value == '0.018519 0.018519 0.018519'
c.set_kpts({
'spacing': (1 / (np.pi * 10)),
'gamma': False,
'even': True
})
assert c.cell.kpoint_mp_grid.value == '28 28 28'
assert c.cell.kpoint_mp_offset.value == '0.0 0.0 0.0'
# test band structure setup
from ase.dft.kpoints import BandPath
atoms = ase.build.bulk('Ag')
bp = BandPath(cell=atoms.cell,
path='GX',
special_points={
'G': [0, 0, 0],
'X': [0.5, 0, 0.5]
})
bp = bp.interpolate(npoints=10)
c = Castep(bandpath=bp)
kpt_list = c.cell.bs_kpoint_list.value.split('\n')
assert len(kpt_list) == 10
assert list(map(float, kpt_list[0].split())) == [0., 0., 0.]
assert list(map(float, kpt_list[-1].split())) == [0.5, 0.0, 0.5]
assert c.cell.kpoint_mp_grid.value == '2 2 2'
assert c.cell.kpoint_mp_offset.value == '0.25 0.25 0.25'
c.set_kpts({'size': (2, 2, 4), 'even': False})
assert c.cell.kpoint_mp_grid.value == '3 3 5'
assert c.cell.kpoint_mp_offset.value == '0.0 0.0 0.0'
atoms = ase.build.bulk('Ag')
atoms.set_calculator(c)
c.set_kpts({'density': 10, 'gamma': False, 'even': None})
assert c.cell.kpoint_mp_grid.value == '27 27 27'
assert c.cell.kpoint_mp_offset.value == '0.018519 0.018519 0.018519'
c.set_kpts({'spacing': (1 / (np.pi *10)), 'gamma': False, 'even': True})
assert c.cell.kpoint_mp_grid.value == '28 28 28'
assert c.cell.kpoint_mp_offset.value == '0.0 0.0 0.0'
# test band structure setup
from ase.dft.kpoints import BandPath
atoms = ase.build.bulk('Ag')
bp = BandPath(cell=atoms.cell,
path='GX',
special_points={'G': [0, 0, 0], 'X': [0.5, 0, 0.5]})
bp = bp.interpolate(npoints=10)
c = Castep(bandpath=bp)
kpt_list = c.cell.bs_kpoint_list.value.split('\n')
assert len(kpt_list) == 10
assert list(map(float, kpt_list[0].split())) == [0., 0., 0.]
assert list(map(float, kpt_list[-1].split())) == [0.5, 0.0, 0.5]
# cleanup
os.chdir(cwd)
shutil.rmtree(tmp_dir)