def setUpClass(cls, *args, **kwargs):
super(TestUpfParser, cls).setUpClass(*args, **kwargs)
filepath_base = os.path.abspath(os.path.join(__file__, os.pardir, os.pardir, os.pardir, 'fixtures', 'pseudos'))
filepath_barium = os.path.join(filepath_base, 'Ba.pbesol-spn-rrkjus_psl.0.2.3-tot-pslib030.UPF')
filepath_oxygen = os.path.join(filepath_base, 'O.pbesol-n-rrkjus_psl.0.1-tested-pslib030.UPF')
filepath_carbon = os.path.join(filepath_base, 'C_pbe_v1.2.uspp.F.UPF')
cls.pseudo_barium = orm.UpfData(file=filepath_barium).store()
cls.pseudo_oxygen = orm.UpfData(file=filepath_oxygen).store()
cls.pseudo_carbon = orm.UpfData(file=filepath_carbon).store()
def setUpClass(cls, *args, **kwargs):
super().setUpClass(*args, **kwargs)
filepath_base = os.path.abspath(os.path.join(STATIC_DIR, 'pseudos'))
cls.filepath_barium = os.path.join(
filepath_base, 'Ba.pbesol-spn-rrkjus_psl.0.2.3-tot-pslib030.UPF')
cls.filepath_oxygen = os.path.join(
filepath_base, 'O.pbesol-n-rrkjus_psl.0.1-tested-pslib030.UPF')
cls.filepath_carbon = os.path.join(filepath_base,
'C_pbe_v1.2.uspp.F.UPF')
cls.pseudo_barium = orm.UpfData(file=cls.filepath_barium).store()
cls.pseudo_oxygen = orm.UpfData(file=cls.filepath_oxygen).store()
cls.pseudo_carbon = orm.UpfData(file=cls.filepath_carbon).store()
def test_constructor(self):
"""Tests for the constructor of `UpfData`."""
filename = 'C.some_custom_filename.upf'
upf = orm.UpfData(file=self.filepath_carbon, filename=filename)
self.assertEqual(upf.filename, filename)
# Store and check that the filename is unchanged
upf.store()
self.assertEqual(upf.filename, filename)
def test_cif_structure_roundtrip(self):
from aiida.tools.dbexporters.tcod import export_cif, export_values
from aiida.common.folders import SandboxFolder
import tempfile
with tempfile.NamedTemporaryFile(mode='w+') as tmpf:
tmpf.write('''
data_test
_cell_length_a 10
_cell_length_b 10
_cell_length_c 10
_cell_angle_alpha 90
_cell_angle_beta 90
_cell_angle_gamma 90
loop_
_atom_site_label
_atom_site_fract_x
_atom_site_fract_y
_atom_site_fract_z
C 0 0 0
O 0.5 0.5 0.5
''')
tmpf.flush()
a = orm.CifData(filepath=tmpf.name)
c = a.get_structure()
c.store()
pd = orm.Dict()
code = orm.Code(local_executable='test.sh')
with tempfile.NamedTemporaryFile(mode='w+') as tmpf:
tmpf.write("#/bin/bash\n\necho test run\n")
tmpf.flush()
code.put_object_from_filelike(tmpf, 'test.sh')
code.store()
calc = orm.CalcJobNode(computer=self.computer)
calc.set_option('resources', {
'num_machines': 1,
'num_mpiprocs_per_machine': 1
})
calc.add_incoming(code, LinkType.INPUT_CALC, "code")
calc.set_option('environment_variables', {
'PATH': '/dev/null',
'USER': '******'
})
with tempfile.NamedTemporaryFile(mode='w+', prefix="Fe") as tmpf:
tmpf.write("<UPF version=\"2.0.1\">\nelement=\"Fe\"\n")
tmpf.flush()
upf = orm.UpfData(filepath=tmpf.name)
upf.store()
calc.add_incoming(upf, LinkType.INPUT_CALC, "upf")
with tempfile.NamedTemporaryFile(mode='w+') as tmpf:
tmpf.write("data_test")
tmpf.flush()
cif = orm.CifData(filepath=tmpf.name)
cif.store()
calc.add_incoming(cif, LinkType.INPUT_CALC, "cif")
with SandboxFolder() as fhandle:
calc.put_object_from_tree(fhandle.abspath)
calc.store()
fd = orm.FolderData()
with fd.open('_scheduler-stdout.txt', 'w') as fhandle:
fhandle.write(u"standard output")
with fd.open('_scheduler-stderr.txt', 'w') as fhandle:
fhandle.write(u"standard error")
fd.store()
fd.add_incoming(calc, LinkType.CREATE, calc.link_label_retrieved)
pd.add_incoming(calc, LinkType.CREATE, "create1")
pd.store()
with self.assertRaises(ValueError):
export_cif(c, parameters=pd)
c.add_incoming(calc, LinkType.CREATE, "create2")
export_cif(c, parameters=pd)
values = export_values(c, parameters=pd)
values = values['0']
self.assertEquals(values['_tcod_computation_environment'],
['PATH=/dev/null\nUSER=unknown'])
self.assertEquals(values['_tcod_computation_command'],
['cd 1; ./_aiidasubmit.sh'])
def create_builder():
builder = OptimizeFirstPrinciplesTightBinding.get_builder()
# Add the input structure
builder.structure = orm.StructureData()
builder.structure.set_ase(read_vasp('inputs/POSCAR'))
# Specify that QuantumEspressoFirstPrinciplesRun should be used to run the first-principles calculations
builder.fp_run_workflow = QuantumEspressoFirstPrinciplesRun
# Set the inputs for the QuantumEspressoFirstPrinciplesRun workflow
common_qe_parameters = orm.Dict(
dict=dict(
CONTROL=dict(etot_conv_thr=1e-3),
SYSTEM=dict(noncolin=True, lspinorb=True, nbnd=36, ecutwfc=30),
)
)
pseudo_dir = pathlib.Path(__file__
).parent.absolute() / 'inputs' / 'pseudos'
pseudos = {
'In':
orm.UpfData(
file=str(pseudo_dir / 'In.rel-pbe-dn-kjpaw_psl.1.0.0.UPF')
),
'Sb':
orm.UpfData(file=str(pseudo_dir / 'Sb.rel-pbe-n-kjpaw_psl.1.0.0.UPF'))
}
# We use the same general Quantum ESPRESSO parameters for the
# scf, nscf, and bands calculations. The calculation type and
# k-points will be set by the workflow.
repeated_pw_inputs = {
'pseudos': pseudos,
'parameters': common_qe_parameters,
'metadata': METADATA_PW,
'code': CODE_PW
}
builder.fp_run = {
'scf': repeated_pw_inputs,
'bands': {
'pw': repeated_pw_inputs
},
'to_wannier': {
'nscf': repeated_pw_inputs,
'pw2wannier': {
'code': CODE_PW2WANNIER,
'metadata': METADATA_PW2WANNIER
},
'wannier': {
'code': CODE_WANNIER,
'metadata': METADATA_WANNIER
}
}
}
# Setting the k-points for the reference bandstructure
kpoints_list = []
kvals = np.linspace(0, 0.5, 20, endpoint=False)
kvals_rev = np.linspace(0.5, 0, 20, endpoint=False)
for k in kvals_rev:
kpoints_list.append((k, k, 0)) # Z to Gamma
for k in kvals:
kpoints_list.append((0, k, k)) # Gamma to X
for k in kvals:
kpoints_list.append((k, 0.5, 0.5)) # X to L
for k in kvals_rev:
kpoints_list.append((k, k, k)) # L to Gamma
for k in np.linspace(0, 0.375, 21, endpoint=True):
kpoints_list.append((k, k, 2 * k)) # Gamma to K
builder.kpoints = orm.KpointsData()
builder.kpoints.set_kpoints(
kpoints_list,
labels=[(i * 20, label)
for i, label in enumerate(['Z', 'G', 'X', 'L', 'G', 'K'])]
)
# Setting the k-points mesh used to run the SCF and Wannier calculations
builder.kpoints_mesh = orm.KpointsData()
builder.kpoints_mesh.set_kpoints_mesh([6, 6, 6])
builder.wannier.code = CODE_WANNIER
builder.code_tbmodels = orm.Code.get_from_string('tbmodels')
# Setting the workflow to evaluate the tight-binding models
builder.model_evaluation_workflow = BandDifferenceModelEvaluation
# Setting the additional inputs for the model evaluation workflow
builder.model_evaluation = dict(
code_bands_inspect=orm.Code.get_from_string('bands_inspect')
)
# Set the initial energy window value
builder.initial_window = orm.List(list=[-1, 3, 10, 18])
# Tolerance for the energy window.
builder.window_tol = orm.Float(1.5)
# Tolerance for the 'cost_value'.
builder.cost_tol = orm.Float(0.3)
# The tolerances are set higher than might be appropriate for a 'production'
# run to make the example run more quickly.
# Setting the parameters for Wannier90
builder.wannier_parameters = orm.Dict(
dict=dict(
num_wann=14,
num_bands=36,
dis_num_iter=100,
num_iter=0,
spinors=True,
# exclude_bands=range(1, )
)
)
# Choose the Wannier90 trial orbitals
builder.wannier_projections = orm.List(
list=['In : s; pz; px; py', 'Sb : pz; px; py']
)
# Set the resource requirements for the Wannier90 run
builder.wannier.metadata = METADATA_WANNIER
# Set the symmetry file
builder.symmetries = orm.SinglefileData(
file=os.path.abspath('inputs/symmetries.hdf5')
)
# Pick the relevant bands from the reference calculation
builder.slice_reference_bands = orm.List(list=list(range(12, 26)))
return builder