def populate_restapi_database(clear_database_before_test):
"""Populates the database with a considerable set of nodes to test the restAPI"""
# pylint: disable=unused-argument
from aiida import orm
struct_forcif = orm.StructureData().store()
orm.StructureData().store()
orm.StructureData().store()
orm.Dict().store()
orm.Dict().store()
orm.CifData(ase=struct_forcif.get_ase()).store()
orm.KpointsData().store()
orm.FolderData().store()
orm.CalcFunctionNode().store()
orm.CalcJobNode().store()
orm.CalcJobNode().store()
orm.WorkFunctionNode().store()
orm.WorkFunctionNode().store()
orm.WorkChainNode().store()
def test_check_for_export_format_version(self):
"""Test the check for the export format version."""
# Creating a folder for the import/export files
export_file_tmp_folder = tempfile.mkdtemp()
unpack_tmp_folder = tempfile.mkdtemp()
try:
struct = orm.StructureData()
struct.store()
filename = os.path.join(export_file_tmp_folder, 'export.tar.gz')
export([struct], outfile=filename, silent=True)
with tarfile.open(filename, 'r:gz', format=tarfile.PAX_FORMAT) as tar:
tar.extractall(unpack_tmp_folder)
with open(os.path.join(unpack_tmp_folder, 'metadata.json'), 'r', encoding='utf8') as fhandle:
metadata = json.load(fhandle)
metadata['export_version'] = 0.0
with open(os.path.join(unpack_tmp_folder, 'metadata.json'), 'wb') as fhandle:
json.dump(metadata, fhandle)
with tarfile.open(filename, 'w:gz', format=tarfile.PAX_FORMAT) as tar:
tar.add(unpack_tmp_folder, arcname='')
self.tearDownClass()
self.setUpClass()
with self.assertRaises(exceptions.IncompatibleArchiveVersionError):
import_data(filename, silent=True)
finally:
# Deleting the created temporary folders
shutil.rmtree(export_file_tmp_folder, ignore_errors=True)
shutil.rmtree(unpack_tmp_folder, ignore_errors=True)
def test_group_import_existing(self, temp_dir):
"""
Testing what happens when I try to import a group that already exists in the
database. This should raise an appropriate exception
"""
grouplabel = 'node_group_existing'
# Create another user
new_email = '[email protected]'
user = orm.User(email=new_email)
user.store()
# Create a structure data node
sd1 = orm.StructureData()
sd1.user = user
sd1.label = 'sd'
sd1.store()
# Create a group and add the data inside
group = orm.Group(label=grouplabel)
group.store()
group.add_nodes([sd1])
# At this point we export the generated data
filename = os.path.join(temp_dir, 'export1.tar.gz')
export([group], outfile=filename, silent=True)
self.clean_db()
self.insert_data()
# Creating a group of the same name
group = orm.Group(label='node_group_existing')
group.store()
import_data(filename, silent=True)
# The import should have created a new group with a suffix
# I check for this:
builder = orm.QueryBuilder().append(
orm.Group, filters={'label': {
'like': grouplabel + '%'
}})
self.assertEqual(builder.count(), 2)
# Now I check for the group having one member, and whether the name is different:
builder = orm.QueryBuilder()
builder.append(orm.Group,
filters={'label': {
'like': grouplabel + '%'
}},
tag='g',
project='label')
builder.append(orm.StructureData, with_group='g')
self.assertEqual(builder.count(), 1)
# I check that the group name was changed:
self.assertTrue(builder.all()[0][0] != grouplabel)
# I import another name, the group should not be imported again
import_data(filename, silent=True)
builder = orm.QueryBuilder()
builder.append(orm.Group,
filters={'label': {
'like': grouplabel + '%'
}})
self.assertEqual(builder.count(), 2)
def test_check_for_export_format_version(aiida_profile, tmp_path):
"""Test the check for the export format version."""
# Creating a folder for the archive files
export_file_tmp_folder = tmp_path / 'export_tmp'
export_file_tmp_folder.mkdir()
unpack_tmp_folder = tmp_path / 'unpack_tmp'
unpack_tmp_folder.mkdir()
aiida_profile.reset_db()
struct = orm.StructureData()
struct.store()
filename = str(export_file_tmp_folder / 'export.aiida')
export([struct], filename=filename, file_format='tar.gz')
with tarfile.open(filename, 'r:gz', format=tarfile.PAX_FORMAT) as tar:
tar.extractall(unpack_tmp_folder)
with (unpack_tmp_folder / 'metadata.json').open(
'r', encoding='utf8') as fhandle:
metadata = json.load(fhandle)
metadata['export_version'] = 0.0
with (unpack_tmp_folder / 'metadata.json').open('wb') as fhandle:
json.dump(metadata, fhandle)
with tarfile.open(filename, 'w:gz', format=tarfile.PAX_FORMAT) as tar:
tar.add(unpack_tmp_folder, arcname='')
aiida_profile.reset_db()
with pytest.raises(exceptions.IncompatibleArchiveVersionError):
import_data(filename)
def generate_structure() -> orm.StructureData:
"""
Generates the structure for the calculation.
It will create a bcc structure in a square lattice.
:return: structure to be used in the calculation
:rtype: orm.StructureData
"""
cell = [
[2.848116, 0.000000, 0.000000],
[0.000000, 2.848116, 0.000000],
[0.000000, 0.000000, 2.848116],
]
positions = [
(0.0000000, 0.0000000, 0.0000000),
(0.5000000, 0.5000000, 0.5000000),
]
fractional = True
symbols = ['Fe', 'Fe']
names = ['Fe1', 'Fe2']
structure = orm.StructureData(cell=cell)
for position, symbol, name in zip(positions, symbols, names):
if fractional:
position = np.dot(position, cell).tolist()
structure.append_atom(position=position, symbols=symbol, name=name)
return structure
def test_pw_wrong_ibrav(fixture_sandbox, generate_calc_job, fixture_code, generate_kpoints_mesh, generate_upf_data):
"""Test that a `PwCalculation` with an incorrect `ibrav` raises."""
entry_point_name = 'quantumespresso.pw'
parameters = {'CONTROL': {'calculation': 'scf'}, 'SYSTEM': {'ecutrho': 240.0, 'ecutwfc': 30.0, 'ibrav': 2}}
# Here we use the wrong order of unit cell vectors on purpose.
param = 5.43
cell = [[0, param / 2., param / 2.], [-param / 2., 0, param / 2.], [-param / 2., param / 2., 0]]
structure = orm.StructureData(cell=cell)
structure.append_atom(position=(0., 0., 0.), symbols='Si', name='Si')
structure.append_atom(position=(param / 4., param / 4., param / 4.), symbols='Si', name='Si')
upf = generate_upf_data('Si')
inputs = {
'code': fixture_code(entry_point_name),
'structure': structure,
'kpoints': generate_kpoints_mesh(2),
'parameters': orm.Dict(dict=parameters),
'pseudos': {
'Si': upf
},
'metadata': {
'options': get_default_options()
}
}
with pytest.raises(QEInputValidationError):
generate_calc_job(fixture_sandbox, entry_point_name, inputs)
def scale_structure(structure: orm.StructureData,
scale_factor: orm.Float) -> orm.StructureData:
"""Scale the structure with the given scaling factor."""
ase = structure.get_ase().copy()
ase.set_cell(ase.get_cell() * float(scale_factor)**(1 / 3),
scale_atoms=True)
return orm.StructureData(ase=ase)
def create_diamond_fcc(element):
"""Calculation function to create the crystal structure of a given element.
For simplicity, only Si and Ge are valid elements.
:param element: The element to create the structure with.
:return: The structure.
"""
from aiida import orm
import numpy as np
elem_alat = {
'Si': 5.431, # Angstrom
'Ge': 5.658, # Angstrom
}
# Validate input element
symbol = element.value
if symbol not in elem_alat:
raise ValueError('Valid elements are only Si and Ge')
# Create cell starting having lattice parameter alat corresponding to the element
alat = elem_alat[symbol]
cell = np.array([[0., 0.5, 0.5], [0.5, 0., 0.5], [0.5, 0.5, 0.]]) * alat
# Create a structure data object
structure = orm.StructureData(cell=cell)
structure.append_atom(position=(0., 0., 0.), symbols=symbol)
structure.append_atom(position=(0.25 * alat, 0.25 * alat, 0.25 * alat),
symbols=symbol)
return structure
def _make_supercell(structure, supercell):
from itertools import product
mag_atoms = supercell.get_array('mag_atoms')
sc = tuple(supercell.get_array('data'))
x, y, z = sc
grid = np.array(list(product(range(x), range(y), range(z))))
cell = structure.cell
new = orm.StructureData()
new.set_cell((np.array(cell).T * sc).T)
kinds = structure.kinds
sites = structure.sites
counter = {k.name: 0 for k in kinds}
for R_cryst in grid:
for n, site in enumerate(sites):
pos = np.array(site.position) + np.dot(R_cryst, cell)
name = site.kind_name
counter[name] += 1
new.append_atom(
position=pos,
symbols=name,
name=f'{name}{counter[name] if name in mag_atoms else ""}',
)
return new
def launch():
"""Launch the relax work chain for a basic silicon crystal structure at a range of scaling factors."""
print(f'Running {STRUCTURE} with {CODE}')
pymatgen_structure = Structure.from_file(
f'../../../common/data/{STRUCTURE}.cif')
structure = orm.StructureData(pymatgen=pymatgen_structure)
parameters_dict = {
'structure': structure,
'sub_process_class': 'common_workflows.relax.abinit',
'generator_inputs': {
'protocol': 'precise',
'relax_type': RelaxType.ATOMS,
'threshold_forces': 0.001,
'calc_engines': {
'relax': {
'code': CODE,
'options': {
'withmpi': True,
'max_wallclock_seconds': 24 * 60**2,
'resources': {
'num_machines': 1,
'num_mpiprocs_per_machine': 4
}
}
}
},
**KWARGS
}
}
run(EquationOfStateWorkChain, **parameters_dict)
def test_pw_ibrav_tol(fixture_sandbox, generate_calc_job, fixture_code, generate_kpoints_mesh, generate_upf_data):
"""Test that `IBRAV_TOLERANCE` controls the tolerance when checking cell consistency."""
entry_point_name = 'quantumespresso.pw'
parameters = {'CONTROL': {'calculation': 'scf'}, 'SYSTEM': {'ecutrho': 240.0, 'ecutwfc': 30.0, 'ibrav': 2}}
# The structure needs to be rotated in the same way QE does it for ibrav=2.
param = 5.43
eps = 0.1
cell = [[-param / 2., eps, param / 2.], [-eps, param / 2. + eps, param / 2.], [-param / 2., param / 2., 0]]
structure = orm.StructureData(cell=cell)
structure.append_atom(position=(0., 0., 0.), symbols='Si', name='Si')
structure.append_atom(position=(param / 4., param / 4., param / 4.), symbols='Si', name='Si')
upf = generate_upf_data('Si')
inputs = {
'code': fixture_code(entry_point_name),
'structure': structure,
'kpoints': generate_kpoints_mesh(2),
'parameters': orm.Dict(dict=parameters),
'pseudos': {
'Si': upf
},
'metadata': {
'options': get_default_options()
},
}
# Without adjusting the tolerance, the check fails.
with pytest.raises(QEInputValidationError):
generate_calc_job(fixture_sandbox, entry_point_name, inputs)
# After adjusting the tolerance, the input validation no longer fails.
inputs['settings'] = orm.Dict(dict={'ibrav_cell_tolerance': eps})
generate_calc_job(fixture_sandbox, entry_point_name, inputs)
def generate_inputs_default():
"""Return only those inputs that the parser will expect to be there."""
a = 5.43
structure = orm.StructureData(
cell=[[a / 2., a / 2., 0], [a / 2., 0, a / 2.], [0, a / 2., a / 2.]])
structure.append_atom(position=(0., 0., 0.), symbols='Si', name='Si1')
structure.append_atom(position=(a / 4., a / 4., a / 4.),
symbols='Si',
name='Si2')
structure.store()
parameters = {
'CONTROL': {
'calculation': 'scf'
},
'SYSTEM': {
'ecutrho': 240.0,
'ecutwfc': 30.0
}
}
kpoints = orm.KpointsData()
kpoints.set_cell_from_structure(structure)
kpoints.set_kpoints_mesh_from_density(0.15)
return AttributeDict({
'structure': structure,
'kpoints': kpoints,
'parameters': orm.Dict(dict=parameters),
'settings': orm.Dict()
})
def test_dangling_link_to_existing_db_node(self, temp_dir):
"""A dangling link that references a Node that is not included in the archive should `not` be importable"""
struct = orm.StructureData()
struct.store()
struct_uuid = struct.uuid
calc = orm.CalculationNode()
calc.add_incoming(struct, LinkType.INPUT_CALC, 'input')
calc.store()
calc.seal()
calc_uuid = calc.uuid
filename = os.path.join(temp_dir, 'export.aiida')
export([struct], filename=filename, file_format='tar.gz')
unpack = SandboxFolder()
with tarfile.open(filename, 'r:gz', format=tarfile.PAX_FORMAT) as tar:
tar.extractall(unpack.abspath)
with open(unpack.get_abs_path('data.json'), 'r',
encoding='utf8') as fhandle:
data = json.load(fhandle)
data['links_uuid'].append({
'output': calc.uuid,
'input': struct.uuid,
'label': 'input',
'type': LinkType.INPUT_CALC.value
})
with open(unpack.get_abs_path('data.json'), 'wb') as fhandle:
json.dump(data, fhandle)
with tarfile.open(filename, 'w:gz', format=tarfile.PAX_FORMAT) as tar:
tar.add(unpack.abspath, arcname='')
# Make sure the CalculationNode is still in the database
builder = orm.QueryBuilder().append(orm.CalculationNode,
project='uuid')
self.assertEqual(
builder.count(),
1,
msg=
f'There should be a single CalculationNode, instead {builder.count()} has been found'
)
self.assertEqual(builder.all()[0][0], calc_uuid)
with self.assertRaises(DanglingLinkError):
import_data(filename)
# Using the flag `ignore_unknown_nodes` should import it without problems
import_data(filename, ignore_unknown_nodes=True)
builder = orm.QueryBuilder().append(orm.StructureData, project='uuid')
self.assertEqual(
builder.count(),
1,
msg=
f'There should be a single StructureData, instead {builder.count()} has been found'
)
self.assertEqual(builder.all()[0][0], struct_uuid)
def read_structure(structure_file):
structure = orm.StructureData(ase=aseread(structure_file))
structure.store()
print(
'Structure {} read and stored with pk {}.'.format(
structure.get_formula(), structure.pk
)
)
return structure
def silicon_builder(db_test_app):
"""Prepare a mock - ready calculation for silicon"""
silicon = orm.StructureData()
r_unit = 2.6954645
silicon.set_cell(np.array([[1, 1, 0], [1, 0, 1], [0, 1, 1]]) * r_unit)
silicon.append_atom(symbols=["Si"], position=[0, 0, 0])
silicon.append_atom(symbols=["Si"], position=[r_unit * 0.5] * 3)
silicon.label = "Si"
silicon.description = "A silicon structure"
param_dict = {
# Notice that the keywords are group into two sub-dictionaries
# just like you would do when preparing the inputs by hand
"CELL": {
"symmetry_generate": True,
"snap_to_symmetry": True,
# Pass a list of string to set a BLOCK inputs
#"cell_constraints":
#["0 0 0", "0 0 0"]
},
"PARAM": {
"task": "singlepoint",
"basis_precision": "medium",
"fix_occupancy":
True, # Use bool type to make it easy for querying
"opt_strategy": "memory",
"num_dump_cycles": 0,
"write_formatted_density": True
}
}
# We need to create a Dict node that holds the dictionary
param = orm.Dict(dict=param_dict)
kpoints = orm.KpointsData()
# Use gamma and 0.25, 0.25, 0.25
kpoints.set_kpoints_mesh((4, 4, 4), offset=(0, 0, 0))
c9 = OTFGData(otfg_entry="C9")
CastepCalculation = CalculationFactory('castep.castep')
code_path = check_output(['which', 'castep.mock'],
universal_newlines=True).strip()
castep_mock = orm.Code((db_test_app.localhost, code_path),
input_plugin_name='castep.castep')
builder = CastepCalculation.get_builder()
builder.structure = silicon
builder.parameters = param
builder.kpoints = kpoints
builder.code = castep_mock
builder.pseudos = {'Si': c9}
builder.metadata.options.withmpi = False
builder.metadata.options.resources = {
'num_machines': 1,
'tot_num_mpiprocs': 2
}
builder.metadata.options.max_wallclock_seconds = 600
builder.metadata.label = "Si SINGLEPOINT"
builder.metadata.description = 'A Example CASTEP calculation for silicon'
return builder
def strain_inputs(configure, strain_kind, strain_parameters, sample):
import pymatgen
from aiida import orm
structure = orm.StructureData()
structure.set_pymatgen(pymatgen.Structure.from_file(sample('POSCAR')))
return dict(structure=structure,
strain_kind=orm.Str(strain_kind),
strain_parameters=orm.Str(strain_parameters),
strain_strengths=orm.List(list=[-0.2, -0.1, 0., 0.1, 0.2]))
def test_nodes_in_group(self, temp_dir):
"""
This test checks that nodes that belong to a specific group are
correctly imported and exported.
"""
from aiida.common.links import LinkType
# Create another user
new_email = '[email protected]'
user = orm.User(email=new_email)
user.store()
# Create a structure data node that has a calculation as output
sd1 = orm.StructureData()
sd1.user = user
sd1.label = 'sd1'
sd1.store()
jc1 = orm.CalcJobNode()
jc1.computer = self.computer
jc1.set_option('resources', {
'num_machines': 1,
'num_mpiprocs_per_machine': 1
})
jc1.user = user
jc1.label = 'jc1'
jc1.add_incoming(sd1, link_type=LinkType.INPUT_CALC, link_label='link')
jc1.store()
jc1.seal()
# Create a group and add the data inside
gr1 = orm.Group(label='node_group')
gr1.store()
gr1.add_nodes([sd1, jc1])
gr1_uuid = gr1.uuid
# At this point we export the generated data
filename1 = os.path.join(temp_dir, 'export1.tar.gz')
export([sd1, jc1, gr1], outfile=filename1, silent=True)
n_uuids = [sd1.uuid, jc1.uuid]
self.clean_db()
self.insert_data()
import_data(filename1, silent=True)
# Check that the imported nodes are correctly imported and that
# the user assigned to the nodes is the right one
for uuid in n_uuids:
self.assertEqual(orm.load_node(uuid).user.email, new_email)
# Check that the exported group is imported correctly
builder = orm.QueryBuilder()
builder.append(orm.Group, filters={'uuid': {'==': gr1_uuid}})
self.assertEqual(builder.count(), 1, 'The group was not found.')
def _generate_structure():
"""Return a `StructureData` representing bulk GaAs."""
from aiida import orm
param = 2.84
structure = orm.StructureData(
cell=[[-param, 0, param], [0, param, param], [-param, param, 0]])
structure.append_atom(symbols='Ga', position=[0, 0, 0])
structure.append_atom(
symbols='As', position=[-0.5 * param, 0.5 * param, 0.5 * param])
return structure
def rescale(structure, scale):
"""Calculation function to rescale a structure
:param structure: An AiiDA structure to rescale
:param scale: The scale factor (for the lattice constant)
:return: The rescaled structure
"""
from aiida import orm
ase = structure.get_ase()
ase.set_cell(ase.get_cell() * float(scale), scale_atoms=True)
return orm.StructureData(ase=ase)
def test_control_of_licenses(self):
"""Test control of licenses."""
from aiida.common.folders import SandboxFolder
from aiida.tools.importexport.dbexport import export_tree
struct = orm.StructureData()
struct.source = {'license': 'GPL'}
struct.store()
folder = SandboxFolder()
export_tree([struct], folder=folder, silent=True, allowed_licenses=['GPL'])
# Folder should contain two files of metadata + nodes/
self.assertEqual(len(folder.get_content_list()), 3)
folder = SandboxFolder()
export_tree([struct], folder=folder, silent=True, forbidden_licenses=['Academic'])
# Folder should contain two files of metadata + nodes/
self.assertEqual(len(folder.get_content_list()), 3)
folder = SandboxFolder()
with self.assertRaises(LicensingException):
export_tree([struct], folder=folder, silent=True, allowed_licenses=['CC0'])
folder = SandboxFolder()
with self.assertRaises(LicensingException):
export_tree([struct], folder=folder, silent=True, forbidden_licenses=['GPL'])
def cc_filter(license_):
return license_.startswith('CC')
def gpl_filter(license_):
return license_ == 'GPL'
def crashing_filter():
raise NotImplementedError('not implemented yet')
folder = SandboxFolder()
with self.assertRaises(LicensingException):
export_tree([struct], folder=folder, silent=True, allowed_licenses=cc_filter)
folder = SandboxFolder()
with self.assertRaises(LicensingException):
export_tree([struct], folder=folder, silent=True, forbidden_licenses=gpl_filter)
folder = SandboxFolder()
with self.assertRaises(LicensingException):
export_tree([struct], folder=folder, silent=True, allowed_licenses=crashing_filter)
folder = SandboxFolder()
with self.assertRaises(LicensingException):
export_tree([struct], folder=folder, silent=True, forbidden_licenses=crashing_filter)
def test_control_of_licenses():
"""Test control of licenses."""
struct = orm.StructureData()
struct.source = {'license': 'GPL'}
struct.store()
folder = SandboxFolder()
export([struct],
file_format='folder',
writer_init={'folder': folder},
allowed_licenses=['GPL'])
# Folder should contain two files of metadata + nodes/
assert len(folder.get_content_list()) == 3
folder.erase(create_empty_folder=True)
assert len(folder.get_content_list()) == 0
export([struct],
file_format='folder',
writer_init={'folder': folder},
forbidden_licenses=['Academic'])
# Folder should contain two files of metadata + nodes/
assert len(folder.get_content_list()) == 3
with pytest.raises(LicensingException):
export([struct], file_format='null', allowed_licenses=['CC0'])
with pytest.raises(LicensingException):
export([struct], file_format='null', forbidden_licenses=['GPL'])
def cc_filter(license_):
return license_.startswith('CC')
def gpl_filter(license_):
return license_ == 'GPL'
def crashing_filter():
raise NotImplementedError('not implemented yet')
with pytest.raises(LicensingException):
export([struct], file_format='null', allowed_licenses=cc_filter)
with pytest.raises(LicensingException):
export([struct], file_format='null', forbidden_licenses=gpl_filter)
with pytest.raises(LicensingException):
export([struct], file_format='null', allowed_licenses=crashing_filter)
with pytest.raises(LicensingException):
export([struct],
file_format='null',
forbidden_licenses=crashing_filter)
def test_pw_ibrav(
fixture_sandbox, generate_calc_job, fixture_code, generate_kpoints_mesh, generate_upf_data, file_regression
):
"""Test a `PwCalculation` where `ibrav` is explicitly specified."""
entry_point_name = 'quantumespresso.pw'
parameters = {'CONTROL': {'calculation': 'scf'}, 'SYSTEM': {'ecutrho': 240.0, 'ecutwfc': 30.0, 'ibrav': 2}}
# The structure needs to be rotated in the same way QE does it for ibrav=2.
param = 5.43
cell = [[-param / 2., 0, param / 2.], [0, param / 2., param / 2.], [-param / 2., param / 2., 0]]
structure = orm.StructureData(cell=cell)
structure.append_atom(position=(0., 0., 0.), symbols='Si', name='Si')
structure.append_atom(position=(param / 4., param / 4., param / 4.), symbols='Si', name='Si')
upf = generate_upf_data('Si')
inputs = {
'code': fixture_code(entry_point_name),
'structure': structure,
'kpoints': generate_kpoints_mesh(2),
'parameters': orm.Dict(dict=parameters),
'pseudos': {
'Si': upf
},
'metadata': {
'options': get_default_options()
}
}
calc_info = generate_calc_job(fixture_sandbox, entry_point_name, inputs)
cmdline_params = ['-in', 'aiida.in']
local_copy_list = [(upf.uuid, upf.filename, u'./pseudo/Si.upf')]
retrieve_list = ['aiida.out', './out/aiida.save/data-file-schema.xml', './out/aiida.save/data-file.xml']
retrieve_temporary_list = [['./out/aiida.save/K*[0-9]/eigenval*.xml', '.', 2]]
# Check the attributes of the returned `CalcInfo`
assert isinstance(calc_info, datastructures.CalcInfo)
assert sorted(calc_info.cmdline_params) == sorted(cmdline_params)
assert sorted(calc_info.local_copy_list) == sorted(local_copy_list)
assert sorted(calc_info.retrieve_list) == sorted(retrieve_list)
assert sorted(calc_info.retrieve_temporary_list) == sorted(retrieve_temporary_list)
assert sorted(calc_info.remote_symlink_list) == sorted([])
with fixture_sandbox.open('aiida.in') as handle:
input_written = handle.read()
# Checks on the files written to the sandbox folder as raw input
assert sorted(fixture_sandbox.get_content_list()) == sorted(['aiida.in', 'pseudo', 'out'])
file_regression.check(input_written, encoding='utf-8', extension='.in')
def _generate_structure():
"""Return a `StructureData` representing bulk O2Sr."""
from aiida import orm
structure = orm.StructureData(
cell=[[-1.7828864010, 1.7828864010, 3.3905324933],
[1.7828864010, -1.7828864010, 3.3905324933],
[1.7828864010, 1.7828864010, -3.3905324933]])
structure.append_atom(symbols='Sr', position=[0, 0, 0])
structure.append_atom(
symbols='O', position=[1.7828864010, 1.7828864010, 0.7518485043])
structure.append_atom(symbols='O', position=[0, 0, 2.6386839890])
return structure
def rescale(structure, scale):
"""
Calcfunction to rescale a structure by a scaling factor.
Uses ase.
:param structure: An AiiDA structure to rescale
:param scale: The scale factor
:return: The rescaled structure
"""
the_ase = structure.get_ase()
new_ase = the_ase.copy()
new_ase.set_cell(the_ase.get_cell() * float(scale), scale_atoms=True)
new_structure = orm.StructureData(ase=new_ase)
return new_structure
def test_calc_of_structuredata(aiida_profile, tmp_path, file_format):
"""Simple ex-/import of CalcJobNode with input StructureData"""
aiida_profile.reset_db()
struct = orm.StructureData()
struct.store()
computer = orm.Computer(
label='localhost-test',
description='localhost computer set up by test manager',
hostname='localhost-test',
workdir=str(tmp_path / 'workdir'),
transport_type='local',
scheduler_type='direct')
computer.store()
computer.configure()
calc = orm.CalcJobNode()
calc.computer = computer
calc.set_option('resources', {
'num_machines': 1,
'num_mpiprocs_per_machine': 1
})
calc.add_incoming(struct, link_type=LinkType.INPUT_CALC, link_label='link')
calc.store()
calc.seal()
pks = [struct.pk, calc.pk]
attrs = {}
for pk in pks:
node = orm.load_node(pk)
attrs[node.uuid] = dict()
for k in node.attributes.keys():
attrs[node.uuid][k] = node.get_attribute(k)
filename = str(tmp_path / 'export.aiida')
export([calc], filename=filename, file_format=file_format)
aiida_profile.reset_db()
import_data(filename)
for uuid in attrs:
node = orm.load_node(uuid)
for k in attrs[uuid].keys():
assert attrs[uuid][k] == node.get_attribute(k)
def structure_init():
"""
Workfunction to create structure of a given element taking it from a reference
list of scructures and a reference volume.
:param element: The element to create the structure with.
:return: The structure and the kpoint mesh (from file, releted to the structure!).
"""
import pymatgen as mg
structure_file = op.realpath(op.join(op.dirname(__file__), 'data/Si.cif'))
in_structure = mg.Structure.from_file(structure_file, primitive=False)
newreduced = in_structure.copy()
newreduced.scale_lattice(float(20.4530) * in_structure.num_sites)
structure = orm.StructureData(pymatgen_structure=newreduced)
return structure
def test_calc_of_structuredata(self, temp_dir):
"""Simple ex-/import of CalcJobNode with input StructureData"""
from aiida.common.links import LinkType
struct = orm.StructureData()
struct.store()
calc = orm.CalcJobNode()
calc.computer = self.computer
calc.set_option('resources', {
'num_machines': 1,
'num_mpiprocs_per_machine': 1
})
calc.add_incoming(struct,
link_type=LinkType.INPUT_CALC,
link_label='link')
calc.store()
calc.seal()
pks = [struct.pk, calc.pk]
attrs = {}
for pk in pks:
node = orm.load_node(pk)
attrs[node.uuid] = dict()
for k in node.attributes.keys():
attrs[node.uuid][k] = node.get_attribute(k)
filename = os.path.join(temp_dir, 'export.aiida')
export([calc], filename=filename, silent=True)
self.clean_db()
self.create_user()
# NOTE: it is better to load new nodes by uuid, rather than assuming
# that they will have the first 3 pks. In fact, a recommended policy in
# databases is that pk always increment, even if you've deleted elements
import_data(filename, silent=True)
for uuid in attrs:
node = orm.load_node(uuid)
for k in attrs[uuid].keys():
self.assertEqual(attrs[uuid][k], node.get_attribute(k))
def generate_inputs():
"""Return only those inputs that the parser will expect to be there."""
alat = 5.4
ase = crystal(
'Si',
[(0, 0, 0)],
spacegroup=227,
cellpar=[alat, alat, alat, 90, 90, 90],
primitive_cell=True,
)
structure = orm.StructureData(ase=ase)
parameters = {
'CONTROL': {
'calculation': 'cp',
'restart_mode': 'from_scratch',
'wf_collect': False,
'iprint': 1,
'isave': 100,
'dt': 3.0,
'max_seconds': 25 * 60,
'nstep': 10,
},
'SYSTEM': {
'ecutwfc': 30.0,
'ecutrho': 240.0,
'nr1b': 24,
'nr2b': 24,
'nr3b': 24,
},
'ELECTRONS': {
'electron_damping': 1.0e-1,
'electron_dynamics': 'damp',
'emass': 400.0,
'emass_cutoff': 3.0,
},
'IONS': {
'ion_dynamics': 'none'
},
}
return AttributeDict({
'structure': structure,
'parameters': orm.Dict(dict=parameters),
})
def test_symmetry_reduction(self):
from aiida.tools.dbexporters.tcod import export_values
from ase import Atoms
a = Atoms('BaTiO3', cell=(4., 4., 4.))
a.set_scaled_positions((
(0.0, 0.0, 0.0),
(0.5, 0.5, 0.5),
(0.5, 0.5, 0.0),
(0.5, 0.0, 0.5),
(0.0, 0.5, 0.5),
))
a.set_chemical_symbols(['Ba', 'Ti', 'O', 'O', 'O'])
val = export_values(orm.StructureData(ase=a),
reduce_symmetry=True,
store=True)['0']
self.assertEqual(val['_atom_site_label'], ['Ba1', 'Ti1', 'O1'])
self.assertEqual(val['_symmetry_space_group_name_H-M'], 'Pm-3m')
self.assertEqual(val['_symmetry_space_group_name_Hall'], '-P 4 2 3')
def _apply_single_strain(structure: orm.StructureData, strain_kind: orm.Str,
strain_parameters: orm.Str,
strength_value: orm.Float) -> orm.StructureData:
"""
Applies a specific strain (kind, parameters, and value) to the given
structure, and returns the strained structure.
"""
strain_classname = 'strain.structure.' + strain_kind.value
strain_class = get_object_from_string(strain_classname)
strain_parametername = 'strain.parameter.' + strain_parameters.value
strain_parameters = get_object_from_string(strain_parametername)
strain_instance = strain_class(**strain_parameters)
pmg_structure = structure.get_pymatgen_structure()
new_pmg_structure = strain_instance.apply(pmg_structure,
strength_value.value)
new_structure_data = orm.StructureData()
new_structure_data.set_pymatgen(new_pmg_structure)
return new_structure_data