def test_calcjob_submit_mgo(db_test_app, input_symmetry, get_structure,
data_regression, file_regression):
"""Test submitting a calculation."""
code = db_test_app.get_or_create_code("crystal17.main")
# Prepare input parameters
inparams = CryInputParamsData(data={
"title": "MgO Bulk",
"scf": {
"k_points": (8, 8)
}
})
instruct = get_structure("MgO")
sym_calc = run_get_node(
WorkflowFactory("crystal17.sym3d"),
structure=instruct,
settings=orm.Dict(dict={
"symprec": 0.01,
"compute_primitive": True
}),
).node
instruct = sym_calc.get_outgoing().get_node_by_label("structure")
symmetry = sym_calc.get_outgoing().get_node_by_label("symmetry")
with open_resource_text("basis_sets", "sto3g", "sto3g_Mg.basis") as handle:
mg_basis, _ = BasisSetData.get_or_create(handle)
with open_resource_text("basis_sets", "sto3g", "sto3g_O.basis") as handle:
o_basis, _ = BasisSetData.get_or_create(handle)
# set up calculation
builder = code.get_builder()
builder.metadata = db_test_app.get_default_metadata(dry_run=True)
builder.parameters = inparams
builder.structure = instruct
builder.basissets = {"Mg": mg_basis, "O": o_basis}
if input_symmetry:
builder.symmetry = symmetry
process_options = builder.process_class(inputs=builder).metadata.options
with db_test_app.sandbox_folder() as folder:
calc_info = db_test_app.generate_calcinfo("crystal17.main", folder,
builder)
with folder.open(process_options.input_file_name) as f:
input_content = f.read()
with folder.open("fort.34") as f:
gui_content = f.read() # noqa: F841
# TODO test fort.34 (but rounded)
file_regression.check(input_content)
data_regression.check(sanitize_calc_info(calc_info))
def test_basis_show(db_test_app):
with open_resource_text("basis_sets", "sto3g", "sto3g_O.basis") as handle:
node, created = BasisSetData.get_or_create(handle)
runner = CliRunner()
result = runner.invoke(basisset, ["show", str(node.pk)])
assert result.exit_code == 0
expected = """\
atomic_number: 8
author: John Smith
basis_type: all-electron
class: sto3g
element: O
filename: sto3g_O.basis
md5: 1ca6e23f7f1b1f5517117bec1d581ca2
num_shells: 2
orbital_types: [S, SP]
year: 1999
"""
assert dedent(expected) == str(result.output)
result2 = runner.invoke(basisset, ["show", "-c", str(node.pk)])
assert result2.exit_code == 0
def test_read_crystal_fort25(data_regression):
with open_resource_text(
"doss", "cubic_rocksalt_orbitals", "cubic-rocksalt_2x1_pdos.doss.f25"
) as handle:
data, arrays = parse_crystal_fort25_aiida(handle)
data_regression.check(
{"results": recursive_round(data, 9), "arrays": recursive_round(arrays, 9)}
)
def test_create_builder(db_test_app, get_structure):
"""Test preparation of inputs."""
db_test_app.get_or_create_code("crystal17.main")
inparams = {"scf.k_points": (8, 8)}
instruct = get_structure("MgO")
with open_resource_text("basis_sets", "sto3g", "sto3g_Mg.basis") as handle:
mg_basis, _ = BasisSetData.get_or_create(handle)
with open_resource_text("basis_sets", "sto3g", "sto3g_O.basis") as handle:
o_basis, _ = BasisSetData.get_or_create(handle)
sym_calc = run_get_node(
WorkflowFactory("crystal17.sym3d"),
structure=instruct,
settings=DataFactory("dict")(dict={
"symprec": 0.01,
"compute_primitive": True
}),
).node
instruct = sym_calc.get_outgoing().get_node_by_label("structure")
symmetry = sym_calc.get_outgoing().get_node_by_label("symmetry")
calc_cls = CalculationFactory("crystal17.main")
builder = calc_cls.create_builder(
inparams,
instruct,
{
"O": o_basis,
"Mg": mg_basis
},
symmetry=symmetry,
unflatten=True,
)
assert isinstance(builder.structure, orm.StructureData)
builder.parameters
def test_create_single_from_file(db_test_app):
db_test_app.get_or_create_computer()
with open_resource_text("basis_sets", "sto3g", "sto3g_Mg.basis") as handle:
basis = BasisSetData(filepath=handle)
print(basis.filename)
expected_meta = {
"num_shells": 3,
"author": "John Smith",
"atomic_number": 12,
"filename": "sto3g_Mg.basis",
"element": "Mg",
"year": 1999,
"basis_type": "all-electron",
"class": "sto3g",
"md5": "0731ecc3339d2b8736e61add113d0c6f",
"orbital_types": ["S", "SP", "SP"],
}
assert basis.metadata == expected_meta
expected_content = """\
12 3
1 0 3 2. 0.
1 1 3 8. 0.
1 1 3 2. 0."""
assert basis.content == expected_content
basis.store()
# try retrieving a pre-existing (stored) basis
with open_resource_text("basis_sets", "sto3g", "sto3g_Mg.basis") as handle:
basis, created = BasisSetData.get_or_create(basis_file=handle)
assert not created
def test_create_vesta_input(file_regression):
with open_resource_text("ech3", "mgo_sto3g_scf", "DENS_CUBE.DAT") as handle:
cube_data = read_gaussian_cube(handle, return_density=False)
atoms = ase.Atoms(
cell=cube_data.cell,
positions=cube_data.atoms_positions,
numbers=cube_data.atoms_atomic_number,
pbc=True,
)
content = create_vesta_input(
atoms,
"input.cube",
settings={
"show_compass": False,
"bonds": {"compute": [["Mg", "O", 0, 3, 0, 0, True, False]]},
},
)
file_regression.check(content, extension=".vesta")
def test_read_density_cube(data_regression):
with open_resource_text("ech3", "mgo_sto3g_scf", "DENS_CUBE.DAT") as handle:
data = read_gaussian_cube(handle, return_density=True)._asdict()
data.pop("density")
data_regression.check(recursive_round(data, 2))