print(
"Pseudo or pseudo family not found. You may want to load the "
"pseudo family, or set auto_pseudos to False.")
raise
else:
raw_pseudos = [
("Ba.pbesol-spn-rrkjus_psl.0.2.3-tot-pslib030.UPF", 'Ba', 'pbesol'),
("Ti.pbesol-spn-rrkjus_psl.0.2.3-tot-pslib030.UPF", 'Ti', 'pbesol'),
("O.pbesol-n-rrkjus_psl.0.1-tested-pslib030.UPF", 'O', 'pbesol')
]
pseudos_to_use = {}
for fname, elem, pot_type in raw_pseudos:
absname = os.path.realpath(
os.path.join(os.path.dirname(__file__), "data", fname))
pseudo, created = UpfData.get_or_create(absname, use_first=True)
if created:
print "Created the pseudo for {}".format(elem)
else:
print "Using the pseudo for {} from DB: {}".format(elem, pseudo.pk)
pseudos_to_use[elem] = pseudo
for k, v in pseudos_to_use.iteritems():
calc.use_pseudo(v, kind=k)
calc.use_kpoints(kpoints)
if settings is not None:
calc.use_settings(settings)
#from aiida.orm.data.remote import RemoteData
#calc.set_outdir(remotedata)
def create_inputs(inpath, outpath):
""" create ``crystal17.main`` input nodes from an existing run
NB: none of the nodes are stored, also
existing basis will be retrieved if availiable
:param inpath: path to .d12 file
:param outpath: path to .out file
:return: dictionary of inputs, with keys 'structure', 'parameters', 'settings', 'structure', 'basis'
"""
from aiida.orm import DataFactory, CalculationFactory
calc_cls = CalculationFactory('crystal17.main')
basis_cls = DataFactory('crystal17.basisset')
struct_cls = DataFactory('structure')
structsettings_cls = DataFactory('crystal17.structsettings')
inputs = {}
with open(inpath) as f:
d12content = f.read()
output_dict, basis_sets, atom_props = extract_data(d12content)
cryparse = CrystalOutputPlugin()
if not os.path.exists(outpath):
raise OutputParsingError(
"The raw data file does not exist: {}".format(outpath))
with open(outpath) as f:
try:
data = cryparse.read_file(f, log_warnings=False)
except IOError as err:
raise OutputParsingError(
"Error in CRYSTAL 17 run output: {}".format(err))
# we retrieve the initial primitive geometry and symmetry
atoms = _create_atoms(data)
# convert fragment (i.e. unfixed) to fixed
if "fragment" in atom_props:
frag = atom_props.pop("fragment")
atom_props["fixed"] = [
i + 1 for i in range(atoms.get_number_of_atoms())
if i + 1 not in frag
]
atoms.set_tags(_create_tags(atom_props, atoms))
structure = struct_cls(ase=atoms)
inputs['structure'] = structure
settings_dict = {"kinds": {}}
for key, vals in atom_props.items():
settings_dict["kinds"][key] = [
structure.sites[i - 1].kind_name for i in vals
]
settings_dict["operations"] = data["initial"]["primitive_symmops"]
# TODO retrieve centering code, crystal system and spacegroup
settings_dict["space_group"] = 1
settings_dict["crystal_type"] = 1
settings_dict["centring_code"] = 1
settings = structsettings_cls(data=settings_dict)
parameters = calc_cls.prepare_and_validate(output_dict, structure,
settings)
inputs['parameters'] = parameters
inputs['settings'] = settings
inputs["basis"] = {}
for bset in basis_sets:
bfile = tempfile.NamedTemporaryFile(delete=False)
try:
with open(bfile.name, "w") as f:
f.write(bset)
bdata, _ = basis_cls.get_or_create(
bfile.name, use_first=False, store_basis=False)
# TODO report if bases created or retrieved
finally:
os.remove(bfile.name)
inputs["basis"][bdata.element] = bdata
return inputs
def test_submit_mgo(new_database, new_workdir):
"""Test submitting a calculation"""
from aiida.orm import DataFactory
ParameterData = DataFactory('parameter')
StructureData = DataFactory('structure')
BasisSetData = DataFactory('crystal17.basisset')
from aiida.common.folders import SandboxFolder
# get code
code = get_main_code(new_workdir)
# Prepare input parameters
inparams = ParameterData(dict={
"title": "MgO Bulk",
"scf": {
"k_points": (8, 8)
}
})
# MgO
atoms = crystal(symbols=[12, 8],
basis=[[0, 0, 0], [0.5, 0.5, 0.5]],
spacegroup=225,
cellpar=[4.21, 4.21, 4.21, 90, 90, 90])
instruct = StructureData(ase=atoms)
from aiida_crystal17.workflows.symmetrise_3d_struct import (
run_symmetrise_3d_structure)
instruct, settings = run_symmetrise_3d_structure(instruct)
mg_basis, _ = BasisSetData.get_or_create(
os.path.join(TEST_DIR, "input_files", "sto3g", 'sto3g_Mg.basis'))
o_basis, _ = BasisSetData.get_or_create(
os.path.join(TEST_DIR, "input_files", "sto3g", 'sto3g_O.basis'))
# set up calculation
calc = code.new_calc()
# calc.label = "aiida_crystal17 test"
# calc.description = "Test job submission with the aiida_crystal17 plugin"
# calc.set_max_wallclock_seconds(30)
calc.set_withmpi(False)
calc.set_resources({"num_machines": 1, "num_mpiprocs_per_machine": 1})
calc.use_parameters(inparams)
calc.use_structure(instruct)
calc.use_settings(settings)
calc.use_basisset(mg_basis, "Mg")
calc.use_basisset(o_basis, "O")
calc.store_all()
# output input files and scripts to temporary folder
with SandboxFolder() as folder:
subfolder, script_filename = calc.submit_test(folder=folder)
print("inputs created successfully at {}".format(subfolder.abspath))
print([
os.path.basename(p)
for p in glob.glob(os.path.join(subfolder.abspath, "*"))
])
with open(os.path.join(subfolder.abspath,
calc._DEFAULT_INPUT_FILE)) as f:
input_content = f.read()
with open(os.path.join(subfolder.abspath,
calc._DEFAULT_EXTERNAL_FILE)) as f:
gui_content = f.read()
expected_input = """MgO Bulk
EXTERNAL
END
12 3
1 0 3 2. 0.
1 1 3 8. 0.
1 1 3 2. 0.
8 2
1 0 3 2. 0.
1 1 3 6. 0.
99 0
END
SHRINK
8 8
END
"""
assert input_content == expected_input
expected_gui = [
'3 5 6', ' 0.000000000E+00 -2.105000000E+00 -2.105000000E+00',
' -2.105000000E+00 -2.105000000E+00 0.000000000E+00',
' -2.105000000E+00 0.000000000E+00 -2.105000000E+00', '48',
' 1.000000000E+00 0.000000000E+00 0.000000000E+00',
' 0.000000000E+00 1.000000000E+00 0.000000000E+00',
' 0.000000000E+00 0.000000000E+00 1.000000000E+00',
' 0.000000000E+00 0.000000000E+00 0.000000000E+00',
' -1.000000000E+00 0.000000000E+00 0.000000000E+00',
' 0.000000000E+00 -1.000000000E+00 0.000000000E+00',
' 0.000000000E+00 0.000000000E+00 -1.000000000E+00',
' 0.000000000E+00 -2.105000000E+00 -2.105000000E+00',
' 0.000000000E+00 1.000000000E+00 0.000000000E+00',
' -1.000000000E+00 0.000000000E+00 0.000000000E+00',
' 0.000000000E+00 0.000000000E+00 1.000000000E+00',
' -2.105000000E+00 0.000000000E+00 -2.105000000E+00',
' 0.000000000E+00 -1.000000000E+00 0.000000000E+00',
' 1.000000000E+00 0.000000000E+00 0.000000000E+00',
' 0.000000000E+00 0.000000000E+00 -1.000000000E+00',
' 0.000000000E+00 -2.105000000E+00 -2.105000000E+00',
' -1.000000000E+00 0.000000000E+00 0.000000000E+00',
' 0.000000000E+00 -1.000000000E+00 0.000000000E+00',
' 0.000000000E+00 0.000000000E+00 1.000000000E+00',
' 0.000000000E+00 -2.105000000E+00 -2.105000000E+00',
' 1.000000000E+00 0.000000000E+00 0.000000000E+00',
' 0.000000000E+00 1.000000000E+00 0.000000000E+00',
' 0.000000000E+00 0.000000000E+00 -1.000000000E+00',
' 0.000000000E+00 -2.105000000E+00 -2.105000000E+00',
' 0.000000000E+00 -1.000000000E+00 0.000000000E+00',
' 1.000000000E+00 0.000000000E+00 0.000000000E+00',
' 0.000000000E+00 0.000000000E+00 1.000000000E+00',
' 0.000000000E+00 -2.105000000E+00 -2.105000000E+00',
' 0.000000000E+00 1.000000000E+00 0.000000000E+00',
' -1.000000000E+00 0.000000000E+00 0.000000000E+00',
' 0.000000000E+00 0.000000000E+00 -1.000000000E+00',
' 0.000000000E+00 0.000000000E+00 0.000000000E+00',
' 1.000000000E+00 0.000000000E+00 0.000000000E+00',
' 0.000000000E+00 -1.000000000E+00 0.000000000E+00',
' 0.000000000E+00 0.000000000E+00 -1.000000000E+00',
' 0.000000000E+00 -2.105000000E+00 -2.105000000E+00',
' -1.000000000E+00 0.000000000E+00 0.000000000E+00',
' 0.000000000E+00 1.000000000E+00 0.000000000E+00',
' 0.000000000E+00 0.000000000E+00 1.000000000E+00',
' 0.000000000E+00 -2.105000000E+00 -2.105000000E+00',
' 0.000000000E+00 1.000000000E+00 0.000000000E+00',
' 1.000000000E+00 0.000000000E+00 0.000000000E+00',
' 0.000000000E+00 0.000000000E+00 -1.000000000E+00',
' -2.105000000E+00 -4.210000000E+00 -2.105000000E+00',
' 0.000000000E+00 -1.000000000E+00 0.000000000E+00',
' -1.000000000E+00 0.000000000E+00 0.000000000E+00',
' 0.000000000E+00 0.000000000E+00 1.000000000E+00',
' -2.105000000E+00 0.000000000E+00 -2.105000000E+00',
' -1.000000000E+00 0.000000000E+00 0.000000000E+00',
' 0.000000000E+00 1.000000000E+00 0.000000000E+00',
' 0.000000000E+00 0.000000000E+00 -1.000000000E+00',
' 0.000000000E+00 -2.105000000E+00 -2.105000000E+00',
' 1.000000000E+00 0.000000000E+00 0.000000000E+00',
' 0.000000000E+00 -1.000000000E+00 0.000000000E+00',
' 0.000000000E+00 0.000000000E+00 1.000000000E+00',
' 0.000000000E+00 -2.105000000E+00 -2.105000000E+00',
' 0.000000000E+00 -1.000000000E+00 0.000000000E+00',
' -1.000000000E+00 0.000000000E+00 0.000000000E+00',
' 0.000000000E+00 0.000000000E+00 -1.000000000E+00',
' 0.000000000E+00 0.000000000E+00 0.000000000E+00',
' 0.000000000E+00 1.000000000E+00 0.000000000E+00',
' 1.000000000E+00 0.000000000E+00 0.000000000E+00',
' 0.000000000E+00 0.000000000E+00 1.000000000E+00',
' -2.105000000E+00 -4.210000000E+00 -2.105000000E+00',
' 0.000000000E+00 0.000000000E+00 1.000000000E+00',
' -1.000000000E+00 0.000000000E+00 0.000000000E+00',
' 0.000000000E+00 -1.000000000E+00 0.000000000E+00',
' -2.105000000E+00 0.000000000E+00 -2.105000000E+00',
' 0.000000000E+00 0.000000000E+00 -1.000000000E+00',
' 1.000000000E+00 0.000000000E+00 0.000000000E+00',
' 0.000000000E+00 1.000000000E+00 0.000000000E+00',
' -2.105000000E+00 -4.210000000E+00 -2.105000000E+00',
' 0.000000000E+00 0.000000000E+00 1.000000000E+00',
' 0.000000000E+00 -1.000000000E+00 0.000000000E+00',
' 1.000000000E+00 0.000000000E+00 0.000000000E+00',
' -2.105000000E+00 -2.105000000E+00 -4.210000000E+00',
' 0.000000000E+00 0.000000000E+00 -1.000000000E+00',
' 0.000000000E+00 1.000000000E+00 0.000000000E+00',
' -1.000000000E+00 0.000000000E+00 0.000000000E+00',
' 0.000000000E+00 0.000000000E+00 0.000000000E+00',
' 0.000000000E+00 0.000000000E+00 1.000000000E+00',
' 1.000000000E+00 0.000000000E+00 0.000000000E+00',
' 0.000000000E+00 1.000000000E+00 0.000000000E+00',
' 0.000000000E+00 -2.105000000E+00 -2.105000000E+00',
' 0.000000000E+00 0.000000000E+00 -1.000000000E+00',
' -1.000000000E+00 0.000000000E+00 0.000000000E+00',
' 0.000000000E+00 -1.000000000E+00 0.000000000E+00',
' -2.105000000E+00 0.000000000E+00 -2.105000000E+00',
' 0.000000000E+00 0.000000000E+00 1.000000000E+00',
' 0.000000000E+00 1.000000000E+00 0.000000000E+00',
' -1.000000000E+00 0.000000000E+00 0.000000000E+00',
' 0.000000000E+00 0.000000000E+00 0.000000000E+00',
' 0.000000000E+00 0.000000000E+00 -1.000000000E+00',
' 0.000000000E+00 -1.000000000E+00 0.000000000E+00',
' 1.000000000E+00 0.000000000E+00 0.000000000E+00',
' 0.000000000E+00 -2.105000000E+00 -2.105000000E+00',
' 0.000000000E+00 0.000000000E+00 -1.000000000E+00',
' -1.000000000E+00 0.000000000E+00 0.000000000E+00',
' 0.000000000E+00 1.000000000E+00 0.000000000E+00',
' 0.000000000E+00 0.000000000E+00 0.000000000E+00',
' 0.000000000E+00 0.000000000E+00 1.000000000E+00',
' 1.000000000E+00 0.000000000E+00 0.000000000E+00',
' 0.000000000E+00 -1.000000000E+00 0.000000000E+00',
' 0.000000000E+00 -2.105000000E+00 -2.105000000E+00',
' 0.000000000E+00 0.000000000E+00 -1.000000000E+00',
' 0.000000000E+00 -1.000000000E+00 0.000000000E+00',
' -1.000000000E+00 0.000000000E+00 0.000000000E+00',
' 0.000000000E+00 -2.105000000E+00 -2.105000000E+00',
' 0.000000000E+00 0.000000000E+00 1.000000000E+00',
' 0.000000000E+00 1.000000000E+00 0.000000000E+00',
' 1.000000000E+00 0.000000000E+00 0.000000000E+00',
' -2.105000000E+00 -2.105000000E+00 -4.210000000E+00',
' 0.000000000E+00 0.000000000E+00 -1.000000000E+00',
' 1.000000000E+00 0.000000000E+00 0.000000000E+00',
' 0.000000000E+00 -1.000000000E+00 0.000000000E+00',
' -2.105000000E+00 -4.210000000E+00 -2.105000000E+00',
' 0.000000000E+00 0.000000000E+00 1.000000000E+00',
' -1.000000000E+00 0.000000000E+00 0.000000000E+00',
' 0.000000000E+00 1.000000000E+00 0.000000000E+00',
' 0.000000000E+00 0.000000000E+00 0.000000000E+00',
' 0.000000000E+00 0.000000000E+00 -1.000000000E+00',
' 0.000000000E+00 1.000000000E+00 0.000000000E+00',
' 1.000000000E+00 0.000000000E+00 0.000000000E+00',
' -2.105000000E+00 -2.105000000E+00 -4.210000000E+00',
' 0.000000000E+00 0.000000000E+00 1.000000000E+00',
' 0.000000000E+00 -1.000000000E+00 0.000000000E+00',
' -1.000000000E+00 0.000000000E+00 0.000000000E+00',
' -2.105000000E+00 -2.105000000E+00 0.000000000E+00',
' 0.000000000E+00 -1.000000000E+00 0.000000000E+00',
' 0.000000000E+00 0.000000000E+00 -1.000000000E+00',
' 1.000000000E+00 0.000000000E+00 0.000000000E+00',
' -2.105000000E+00 -2.105000000E+00 -4.210000000E+00',
' 0.000000000E+00 1.000000000E+00 0.000000000E+00',
' 0.000000000E+00 0.000000000E+00 1.000000000E+00',
' -1.000000000E+00 0.000000000E+00 0.000000000E+00',
' 0.000000000E+00 -2.105000000E+00 -2.105000000E+00',
' 1.000000000E+00 0.000000000E+00 0.000000000E+00',
' 0.000000000E+00 0.000000000E+00 -1.000000000E+00',
' 0.000000000E+00 1.000000000E+00 0.000000000E+00',
' 0.000000000E+00 -2.105000000E+00 -2.105000000E+00',
' -1.000000000E+00 0.000000000E+00 0.000000000E+00',
' 0.000000000E+00 0.000000000E+00 1.000000000E+00',
' 0.000000000E+00 -1.000000000E+00 0.000000000E+00',
' 0.000000000E+00 -2.105000000E+00 -2.105000000E+00',
' 0.000000000E+00 1.000000000E+00 0.000000000E+00',
' 0.000000000E+00 0.000000000E+00 -1.000000000E+00',
' -1.000000000E+00 0.000000000E+00 0.000000000E+00',
' 0.000000000E+00 0.000000000E+00 0.000000000E+00',
' 0.000000000E+00 -1.000000000E+00 0.000000000E+00',
' 0.000000000E+00 0.000000000E+00 1.000000000E+00',
' 1.000000000E+00 0.000000000E+00 0.000000000E+00',
' -2.105000000E+00 -2.105000000E+00 -4.210000000E+00',
' -1.000000000E+00 0.000000000E+00 0.000000000E+00',
' 0.000000000E+00 0.000000000E+00 -1.000000000E+00',
' 0.000000000E+00 -1.000000000E+00 0.000000000E+00',
' 0.000000000E+00 -2.105000000E+00 -2.105000000E+00',
' 1.000000000E+00 0.000000000E+00 0.000000000E+00',
' 0.000000000E+00 0.000000000E+00 1.000000000E+00',
' 0.000000000E+00 1.000000000E+00 0.000000000E+00',
' 0.000000000E+00 -2.105000000E+00 -2.105000000E+00',
' 0.000000000E+00 1.000000000E+00 0.000000000E+00',
' 0.000000000E+00 0.000000000E+00 1.000000000E+00',
' 1.000000000E+00 0.000000000E+00 0.000000000E+00',
' 0.000000000E+00 -2.105000000E+00 -2.105000000E+00',
' 0.000000000E+00 -1.000000000E+00 0.000000000E+00',
' 0.000000000E+00 0.000000000E+00 -1.000000000E+00',
' -1.000000000E+00 0.000000000E+00 0.000000000E+00',
' 0.000000000E+00 0.000000000E+00 0.000000000E+00',
' -1.000000000E+00 0.000000000E+00 0.000000000E+00',
' 0.000000000E+00 0.000000000E+00 1.000000000E+00',
' 0.000000000E+00 1.000000000E+00 0.000000000E+00',
' 0.000000000E+00 -2.105000000E+00 -2.105000000E+00',
' 1.000000000E+00 0.000000000E+00 0.000000000E+00',
' 0.000000000E+00 0.000000000E+00 -1.000000000E+00',
' 0.000000000E+00 -1.000000000E+00 0.000000000E+00',
' 0.000000000E+00 0.000000000E+00 0.000000000E+00',
' 0.000000000E+00 -1.000000000E+00 0.000000000E+00',
' 0.000000000E+00 0.000000000E+00 1.000000000E+00',
' -1.000000000E+00 0.000000000E+00 0.000000000E+00',
' -2.105000000E+00 -2.105000000E+00 0.000000000E+00',
' 0.000000000E+00 1.000000000E+00 0.000000000E+00',
' 0.000000000E+00 0.000000000E+00 -1.000000000E+00',
' 1.000000000E+00 0.000000000E+00 0.000000000E+00',
' -2.105000000E+00 -2.105000000E+00 -4.210000000E+00',
' 1.000000000E+00 0.000000000E+00 0.000000000E+00',
' 0.000000000E+00 0.000000000E+00 1.000000000E+00',
' 0.000000000E+00 -1.000000000E+00 0.000000000E+00',
' 0.000000000E+00 -2.105000000E+00 -2.105000000E+00',
' -1.000000000E+00 0.000000000E+00 0.000000000E+00',
' 0.000000000E+00 0.000000000E+00 -1.000000000E+00',
' 0.000000000E+00 1.000000000E+00 0.000000000E+00',
' 0.000000000E+00 -2.105000000E+00 -2.105000000E+00', '2',
' 12 -2.105000000E+00 -2.105000000E+00 -4.210000000E+00',
' 8 -2.105000000E+00 -2.105000000E+00 -2.105000000E+00', '225 48'
]
gui_content_lines = gui_content.splitlines()
# print(gui_content_lines)
# difflib is too slow if there are a lot of differences
assert len(gui_content_lines) == len(expected_gui)
assert gui_content_lines[0:10] == expected_gui[0:10]
assert gui_content_lines[-1] == expected_gui[-1]
def test_bands(siesta_develop):
"""Test workfunction runs and outputs results in serial mode."""
from aiida.orm import Code, DataFactory, CalculationFactory
from aiida.orm.data.base import Float, Str
SiestaCalculation = CalculationFactory('siesta.siesta')
PsfData = DataFactory('siesta.psf')
StructureData = DataFactory('structure')
ParameterData = DataFactory('parameter')
KpointsData = DataFactory('array.kpoints')
codename = 'siesta@develop'
code = Code.get_from_string(codename)
inputs = SiestaCalculation.process().get_inputs_template()
inputs.code = code
inputs._options.resources = {
"num_machines": 1,
"num_mpiprocs_per_machine": 1,
}
inputs._options.max_wallclock_seconds = 30 * 60
# Define MgO structure
alat = 4.117 # MgO lattice constant, Angstroms
cell = create_FCC_structure(alat) # Creating MgO FCC-cell
structure = StructureData(cell=cell) # Creating structure from cell
# Placing basis atoms
structure.append_atom(position=(0.000 * alat, 0.000 * alat, 0.000 * alat),
symbols=['Mg'])
structure.append_atom(position=(0.500 * alat, 0.500 * alat, 0.500 * alat),
symbols=['O'])
inputs.structure = structure
# Pseudopotentials
# from aiida_siesta.data.psf import get_pseudos_from_structure
# inputs.pseudo = get_pseudos_from_structure(structure, "test_psf_family")
raw_pseudos = [
("Mg.psf", 'Mg'),
("O.psf", 'O'),
]
pseudo_dict = {}
for fname, kind in raw_pseudos:
absname = os.path.realpath(
os.path.join(os.path.dirname(__file__), '..', 'pseudos', fname))
pseudo, created = PsfData.get_or_create(absname, use_first=True)
if created:
print "Created the pseudo for {}".format(kind)
else:
print "Using the pseudo for {} from DB: {}".format(kind, pseudo.pk)
# Attach pseudo node to the calculation
pseudo_dict[kind] = pseudo
inputs.pseudo = pseudo_dict
# K-points mesh
kpoints_mesh = KpointsData()
kpoints_mesh.set_kpoints_mesh([6, 6, 6], [0.5, 0.5, 0.5])
inputs.kpoints = kpoints_mesh
# Bands' k-points
bandskpoints = KpointsData()
bandskpoints.set_cell(structure.cell, structure.pbc)
bandskpoints.set_kpoints_path([
('K', 'G', 39),
('G', 'X', 37),
('X', 'W', 19),
('W', 'L', 27),
('L', 'G', 32),
])
inputs.bandskpoints = bandskpoints
# Calculation parameters
parameters = ParameterData(
dict={
'xc-functional': 'LDA',
'xc-authors': 'CA',
'spin-polarized': False,
'meshcutoff': '200 Ry',
'max-scfiterations': 50,
'xml-write': True,
})
inputs.parameters = parameters
# Create and run Siesta calculation process
from aiida.work.run import run
JobCalc = SiestaCalculation.process()
result = run(JobCalc, **inputs)
assert result['bands_array'] is not None
def test_simple_submission(siesta_develop):
"""Test that single calculation is submitted."""
from aiida.orm import DataFactory
from aiida.common.example_helpers import test_and_get_code
PsfData = DataFactory('siesta.psf')
StructureData = DataFactory('structure')
ParameterData = DataFactory('parameter')
KpointsData = DataFactory('array.kpoints')
code = test_and_get_code('siesta', expected_code_type='siesta.siesta')
assert code is not None
# Si diamond structure
alat = 5.430 # angstrom
cell = [
[
0.5 * alat,
0.5 * alat,
0.,
],
[
0.,
0.5 * alat,
0.5 * alat,
],
[
0.5 * alat,
0.,
0.5 * alat,
],
]
# Si
# This was originally given in the "ScaledCartesian" format
#
s = StructureData(cell=cell)
s.append_atom(position=(0.000 * alat, 0.000 * alat, 0.000 * alat),
symbols=['Si'])
s.append_atom(position=(0.250 * alat, 0.250 * alat, 0.250 * alat),
symbols=['Si'])
parameters = ParameterData(
dict={
'xc-functional': 'LDA',
'xc-authors': 'CA',
'max-scfiterations': 50,
'dm-numberpulay': 4,
'dm-mixingweight': 0.3,
'dm-tolerance': 1.e-3,
'Solution-method': 'diagon',
'electronic-temperature': '25 meV',
'md-typeofrun': 'cg',
'md-numcgsteps': 3,
'md-maxcgdispl': '0.1 Ang',
'md-maxforcetol': '0.04 eV/Ang',
'xml-write': True
})
basis = ParameterData(dict={
'pao-energy-shift': '300 meV',
'%block pao-basis-sizes': 'Si DZP',
})
kpoints = KpointsData()
kpoints.set_kpoints_mesh([4, 4, 4])
calc = code.new_calc(max_wallclock_seconds=3600,
resources={
"num_machines": 1,
"num_mpiprocs_per_machine": 1,
})
calc.label = "Si bulk"
calc.description = "Test calculation with the Siesta code. Si bulk"
# Use raw pseudos for this example:
raw_pseudos = [("Si.psf", 'Si')]
calc.use_structure(s)
calc.use_code(code)
calc.use_parameters(parameters)
calc.use_basis(basis)
calc.use_kpoints(kpoints)
# Pseudo business
#
# TODO: understand how to work with pseudo families
# calc.use_pseudos_from_family(pseudo_family)
#
for fname, kind in raw_pseudos:
absname = op.realpath(
op.join(op.dirname(__file__), "..", "pseudos", fname))
pseudo, created = PsfData.get_or_create(absname, use_first=True)
if created:
print "\nCreated the pseudo for {}".format(kind)
else:
print "\nUsing the pseudo for {} from DB: {}".format(
kind, pseudo.pk)
# Attach pseudo node to the calculation
calc.use_pseudo(pseudo, kind=kind)
calc.store_all()
print "created calculation with PK={}".format(calc.pk)
subfolder, script_filename = calc.submit_test()
print "Test_submit for calculation (uuid='{}')".format(calc.uuid)
assert op.isfile(op.join(op.relpath(subfolder.abspath), script_filename))
print "Submit file in {}".format(
op.join(op.relpath(subfolder.abspath), script_filename))
assert op.isfile(op.join(op.relpath(subfolder.abspath), 'aiida.fdf'))
assert op.isfile(op.join(op.relpath(subfolder.abspath), 'Si.psf'))
