def get_cif_node(self, store=False, parse_policy='lazy'):
"""
Creates a CIF node, that can be used in AiiDA workflow.
:return: :py:class:`aiida.orm.nodes.data.cif.CifData` object
"""
from aiida.orm.nodes.data.cif import CifData
import tempfile
cifnode = None
with tempfile.NamedTemporaryFile(mode='w+') as f:
f.write(self.cif)
f.flush()
cifnode = CifData(file=f.name,
source=self.source,
parse_policy=parse_policy)
# Maintaining backwards-compatibility. Parameter 'store' should
# be removed in the future, as the new node can be stored later.
if store:
cifnode.store()
return cifnode
def create_cif_data(cls):
"""Create CifData object."""
with tempfile.NamedTemporaryFile(mode='w+') as fhandle:
filename = fhandle.name
fhandle.write(cls.valid_sample_cif_str)
fhandle.flush()
a_cif = CifData(file=filename,
source={
'version': '1234',
'db_name': 'COD',
'id': '0000001'
})
a_cif.store()
g_ne = Group(label='non_empty_group')
g_ne.store()
g_ne.add_nodes(a_cif)
g_e = Group(label='empty_group')
g_e.store()
cls.cif = a_cif
return {
DummyVerdiDataListable.NODE_ID_STR: a_cif.id,
DummyVerdiDataListable.NON_EMPTY_GROUP_ID_STR: g_ne.id,
DummyVerdiDataListable.EMPTY_GROUP_ID_STR: g_e.id
}
def refine_inline(node):
"""
Refine (reduce) the cell of :py:class:`aiida.orm.nodes.data.cif.CifData`,
find and remove symmetrically equivalent atoms.
:param node: a :py:class:`aiida.orm.nodes.data.cif.CifData` instance.
:return: dict with :py:class:`aiida.orm.nodes.data.cif.CifData`
.. note:: can be used as inline calculation.
"""
from aiida.orm.nodes.data.structure import StructureData, ase_refine_cell
if len(node.values.keys()) > 1:
raise ValueError('CifData seems to contain more than one data '
'block -- multiblock CIF files are not '
'supported yet')
name = list(node.values.keys())[0]
original_atoms = node.get_ase(index=None)
if len(original_atoms) > 1:
raise ValueError('CifData seems to contain more than one crystal '
'structure -- such refinement is not supported '
'yet')
original_atoms = original_atoms[0]
refined_atoms, symmetry = ase_refine_cell(original_atoms)
cif = CifData(ase=refined_atoms)
if name != str(0):
cif.values.rename(str(0), name)
# Remove all existing symmetry tags before overwriting:
for tag in symmetry_tags:
cif.values[name].RemoveCifItem(tag)
cif.values[name]['_symmetry_space_group_name_H-M'] = symmetry['hm']
cif.values[name]['_symmetry_space_group_name_Hall'] = symmetry['hall']
cif.values[name]['_symmetry_Int_Tables_number'] = symmetry['tables']
cif.values[name]['_symmetry_equiv_pos_as_xyz'] = \
[symop_string_from_symop_matrix_tr(symmetry['rotations'][i],
symmetry['translations'][i])
for i in range(len(symmetry['rotations']))]
# Summary formula has to be calculated from non-reduced set of atoms.
cif.values[name]['_chemical_formula_sum'] = \
StructureData(ase=original_atoms).get_formula(mode='hill',
separator=' ')
# If the number of reduced atoms multiplies the number of non-reduced
# atoms, the new Z value can be calculated.
if '_cell_formula_units_Z' in node.values[name].keys():
old_Z = node.values[name]['_cell_formula_units_Z']
if len(original_atoms) % len(refined_atoms):
new_Z = old_Z * len(original_atoms) // len(refined_atoms)
cif.values[name]['_cell_formula_units_Z'] = new_Z
return {'cif': cif}
def mg_mof74_cifdata():
"""CifData for Mg MOF74 CIF."""
from aiida.orm import CifData # pylint: disable=import-outside-toplevel
with open(os.path.join(DATA_DIR, 'Mg_MOF_74.cif'), 'rb') as handle:
cif = CifData(file=handle)
return cif
def _get_cif(name):
from aiida.orm import CifData
if name == "pyrite":
with open_resource_binary("cif", "pyrite.cif") as handle:
return CifData(file=handle)
raise ValueError(name)
def parse_stdout(self, filelike):
"""Parse the content written by the script to standard out.
The standard output will contain a list of relative filepaths where the generated CIF files have been written.
:param filelike: filelike object of stdout
:returns: an exit code in case of an error, None otherwise
"""
from aiida.orm import CifData
content = filelike.read().strip()
if not content:
return self.exit_codes.ERROR_EMPTY_OUTPUT_FILE
# The filelike should be in binary mode, so we should decode the bytes, assuming the content is in `utf-8`
content = content.decode('utf-8')
try:
cifs = {}
for line in content.split('\n'):
filename = line.strip()
output_name = os.path.splitext(os.path.basename(filename))[0]
with self.retrieved.open(filename, 'rb') as handle:
cifs[output_name] = CifData(file=handle)
except Exception: # pylint: disable=broad-except
self.logger.exception(
'Failed to open a generated from the stdout file\n%s',
traceback.format_exc())
return self.exit_codes.ERROR_PARSING_OUTPUT_DATA
self.out('cifs', cifs)
return
def get_ase_structure(self):
"""
:return: ASE structure corresponding to the cif file.
"""
from aiida.orm import CifData
cif = correct_cif(self.cif)
return CifData.read_cif(io.StringIO(cif))
def aiida_cif_merge(aiida_cif_a, aiida_cif_b):
"""Merge the coordinates of two CifData into a sigle one. Note: the two unit cells must be the same."""
ase_a = aiida_cif_a.get_ase()
ase_b = aiida_cif_b.get_ase()
if not ase_cells_are_similar(ase_a, ase_b.cell):
raise ValueError('Attempting to merge two CifData (<{}> and <{}>) with different unit cells.'.format(
aiida_cif_a.pk, aiida_cif_b.pk))
ase_ab = ase.Atoms( #Maybe there is a more direct way...
symbols=list(ase_a.symbols) + list(ase_b.symbols),
cell=ase_a.cell,
positions=list(ase_a.positions) + list(ase_b.positions),
pbc=True)
cif_ab = CifData(ase=ase_ab, filename='fragments_a_b.cif') #TODO: check why the filename is not assigned. # pylint: disable=fixme
cif_ab.label = 'Loaded structure'
cif_ab.description = 'Fragment A: {} atoms, fragment B: {} atoms.'.format(len(ase_a), len(ase_b))
return cif_ab
def cif_import(filename):
"""Import .cif file into CifData object."""
from aiida.orm import CifData
try:
node, _ = CifData.get_or_create(filename)
echo.echo_success('imported {}'.format(str(node)))
except ValueError as err:
echo.echo_critical(err)
def get_ase_structure(self):
"""
Returns ASE representation of the CIF.
.. note:: To be removed, as it is duplicated in
:py:class:`aiida.orm.nodes.data.cif.CifData`.
"""
from aiida.orm import CifData
return CifData.read_cif(StringIO(self.cif))
def _generate_cif_data(element):
"""Return `UpfData` node."""
from aiida.orm import CifData
filename = os.path.join('tests', 'fixtures', 'cif', '{}.cif'.format(element))
filepath = os.path.abspath(filename)
with io.open(filepath, 'r') as handle:
cif = CifData(file=handle.name)
return cif
def _on_file_upload(self, change=None):
"""When file upload button is pressed."""
for fname, item in change['new'].items():
frmt = fname.split('.')[-1]
if frmt == 'cif':
self.structure = CifData(file=io.BytesIO(item['content']))
else:
self.structure = get_ase_from_file(io.StringIO(
item['content'].decode()),
format=frmt)
self.file_upload.value.clear()
break
def _get_cif_ase_inline(struct, parameters):
"""
Creates :py:class:`aiida.orm.nodes.data.cif.CifData` using ASE.
.. note:: requires ASE module.
"""
from aiida.orm import CifData
kwargs = {}
if parameters is not None:
kwargs = parameters.get_dict()
cif = CifData(ase=struct.get_ase(**kwargs))
formula = struct.get_formula(mode='hill', separator=' ')
for i in cif.values.keys():
cif.values[i]['_symmetry_space_group_name_H-M'] = 'P 1'
cif.values[i]['_symmetry_space_group_name_Hall'] = 'P 1'
cif.values[i]['_symmetry_Int_Tables_number'] = 1
cif.values[i]['_cell_formula_units_Z'] = 1
cif.values[i]['_chemical_formula_sum'] = formula
return {'cif': cif}
def example_base_workchain_widom_2(raspa_code):
"""Run base workchain for widom insertion calculation (1 component)."""
# pylint: disable=no-member
print("Testing RASPA Xenon and Krypton widom insertion through RaspaBaseWorkChain ...")
parameters = Dict(
dict={
"GeneralSettings": {
"SimulationType": "MonteCarlo",
"NumberOfCycles": 50,
"PrintEvery": 10,
"Forcefield": "GenericMOFs",
"EwaldPrecision": 1e-6,
"CutOff": 12.0,
},
"System": {
"tcc1rs": {
"type": "Framework",
"ExternalTemperature": 300.0,
}
},
"Component": {
"krypton": {
"MoleculeDefinition": "TraPPE",
"WidomProbability": 1.0,
"CreateNumberOfMolecules": 0,
"BlockPocketsFileName": "block_tcc1rs_methane",
},
"xenon": {
"MoleculeDefinition": "TraPPE",
"WidomProbability": 1.0,
"CreateNumberOfMolecules": 0,
"BlockPocketsFileName": "block_tcc1rs_xenon",
},
},
})
# framework
pwd = os.path.dirname(os.path.realpath(__file__))
structure = CifData(file=os.path.join(pwd, '..', 'files', 'TCC1RS.cif'))
structure_label = structure.filename[:-4].lower()
block_pocket_node1 = SinglefileData(file=os.path.join(pwd, '..', 'files', 'block_pocket.block')).store()
block_pocket_node2 = SinglefileData(file=os.path.join(pwd, '..', 'files', 'block_pocket.block')).store()
# Constructing builder
builder = RaspaBaseWorkChain.get_builder()
# Specifying the code
builder.raspa.code = raspa_code
# Specifying the framework
builder.raspa.framework = {
structure_label: structure,
}
# Specifying the input parameters
builder.raspa.parameters = parameters
# Specifying the block pockets
builder.raspa.block_pocket = {
"block_tcc1rs_methane": block_pocket_node1,
"block_tcc1rs_xenon": block_pocket_node2,
}
# Add fixers that could handle physics-related problems.
builder.fixers = {
'fixer_001': ('aiida_raspa.utils', 'check_widom_convergence', 0.1, 2000),
}
# Specifying the scheduler options
builder.raspa.metadata.options = {
"resources": {
"num_machines": 1,
"num_mpiprocs_per_machine": 1,
},
"max_wallclock_seconds": 1 * 30 * 60, # 30 min
"withmpi": False,
}
run(builder)
def example_ff_files(raspa_code, submit=True):
"""Prepare and submit RASPA calculation with components mixture."""
# parameters
parameters = Dict(
dict={
"GeneralSettings": {
"SimulationType": "MonteCarlo",
"NumberOfInitializationCycles": 200,
"NumberOfCycles": 300,
"PrintEvery": 100,
"Forcefield": "Local",
"ChargeMethod": "Ewald",
"EwaldPrecision": 1e-6,
"CutOff": 12.0,
},
"System": {
"irmof_1": {
"type": "Framework",
"UnitCells": "1 1 1",
"HeliumVoidFraction": 0.149,
"ExternalTemperature": 300.0,
"ExternalPressure": 1e5,
}
},
"Component": {
"CO2": {
"MoleculeDefinition": "Local",
"MolFraction": 0.30,
"TranslationProbability": 1.0,
"RotationProbability": 1.0,
"ReinsertionProbability": 1.0,
"SwapProbability": 1.0,
"CreateNumberOfMolecules": 0,
},
"N2": {
"MoleculeDefinition": "Local",
"MolFraction": 0.70,
"TranslationProbability": 1.0,
"RotationProbability": 1.0,
"ReinsertionProbability": 1.0,
"SwapProbability": 1.0,
"CreateNumberOfMolecules": 0,
},
},
})
# Contructing builder
pwd = os.path.dirname(os.path.realpath(__file__))
builder = raspa_code.get_builder()
builder.framework = {
"irmof_1":
CifData(file=os.path.join(pwd, '..', 'files', 'IRMOF-1_eqeq.cif')),
}
# Note: Here the SinglefileData in the dict are stored otherwise the dry_run crashes.
# However, this is not needed for real calculations (e.g., using --submit), since the work chains stores them.
builder.file = {
"file_1":
SinglefileData(file=os.path.join(
pwd, '..', 'files', 'force_field_mixing_rules.def')).store(),
"file_2":
SinglefileData(
file=os.path.join(pwd, '..', 'files', 'pseudo_atoms.def')).store(),
"file_3":
SinglefileData(
file=os.path.join(pwd, '..', 'files', 'CO2.def')).store(),
"file_4":
SinglefileData(
file=os.path.join(pwd, '..', 'files', 'N2.def')).store(),
}
builder.parameters = parameters
builder.metadata.options = {
"resources": {
"num_machines": 1,
"num_mpiprocs_per_machine": 1,
},
"max_wallclock_seconds": 1 * 30 * 60, # 30 min
"withmpi": False,
}
builder.metadata.dry_run = False
builder.metadata.store_provenance = True
if submit:
print(
"Testing RASPA CO2/N2 adsorption in IRMOF-1, using Local force field ..."
)
res, pk = run_get_pk(builder)
print("calculation pk: ", pk)
print("CO2/N2 uptake ({:s}): {:.2f}/{:.2f} ".format(
res['output_parameters']["irmof_1"]["components"]['N2']
["loading_absolute_unit"],
res['output_parameters']["irmof_1"]["components"]['CO2']
["loading_absolute_average"],
res['output_parameters']["irmof_1"]["components"]['N2']
["loading_absolute_average"],
))
print("OK, calculation has completed successfully")
else:
print("Generating test input ...")
builder.metadata.dry_run = True
builder.metadata.store_provenance = False
run(builder)
print("Submission test successful")
print("In order to actually submit, add '--submit'")
print("-----")
def _generate_structure_cif(cif_filepath):
"""Return a `StructureData` from a cif file."""
from aiida.orm import CifData
structure = CifData.get_or_create(cif_filepath)[0].get_structure()
return structure
def test_extract_structure_info(clear_database_aiida_fleur, generate_structure,
generate_work_chain_node, fixture_localhost):
"""
I do not test 'extras' here due to some kind of bug
"""
from aiida_fleur.tools.data_handling import extract_structure_info
from aiida_fleur.tools.common_aiida import create_group
from aiida_fleur.tools.read_cif_folder import wf_struc_from_cif
from aiida.orm import CalcFunctionNode, load_node, CifData
from aiida.common import LinkType
pks = []
uuids = []
for i in range(3):
structure_bulk = generate_structure()
structure_bulk.append_atom(position=(i, 0., -1.99285), symbols='Se')
structure_bulk.store()
pks.append(structure_bulk.pk)
uuids.append(structure_bulk.uuid)
cif_data = CifData(file=TEST_CIF)
cif_data.store()
cif_structure = wf_struc_from_cif(cif_data)
print(cif_structure.get_incoming().all())
# create CalcFunction having StructureData input
calc_function = CalcFunctionNode()
calc_function.set_attribute('process_label', 'test_label')
calc_function.add_incoming(structure_bulk,
link_type=LinkType.INPUT_CALC,
link_label='test_calcfundtion')
calc_function.store()
# create WorkChainNode scf having StructureData input
scf_wc = generate_work_chain_node(computer=fixture_localhost,
entry_point_name='aiida_fleur.scf',
inputs={'structure': load_node(pks[1])})
scf_wc.store()
scf_wc.set_attribute('process_label', 'fleur_scf_wc')
# create a group
group = create_group(name='test_group',
nodes=pks[:2],
description='test_description')
result = extract_structure_info(keys=[
'uuid', 'formula', 'pk', 'symmetry', 'pbc', 'volume', 'total_energy',
'child_nodes', 'natoms', 'group', 'label', 'description', 'cif_file',
'cif_number', 'cif_uuid', 'cif_ref', 'calcfunctions', 'band', 'dos',
'eos', 'init_cls', 'corehole', 'primitive', 'cell', 'scf'
])
# print(result)
# assert 0
correct_result = [
sorted({
'formula': 'AlB2',
'pk': cif_structure.pk,
'uuid': cif_structure.uuid,
'natoms': 3,
'cell':
'[[3.009, 0.0, 0.0], [-1.5045, 2.6058704399874, 0.0], [0.0, 0.0, 3.262]]',
'pbc': '(True, True, True)',
'label': '',
'description': '',
# 'extras': "{{'_aiida_hash': {0}}}".format(cif_structure.get_hash()),
'symmetry': 'Amm2 (38)',
'volume': 25.57755127009385,
'child_nodes': 0,
'primitive': False,
'cif_file': ['AlB.cif', cif_data.uuid],
'group': [],
'scf': [],
'band': [],
'dos': [],
'eos': [],
'init_cls': [],
'corehole': [],
'calcfunctions': [[], []],
}),
sorted({
'formula': 'SeSi2',
'pk': pks[2],
'uuid': uuids[2],
'natoms': 3,
'cell':
'[[2.715, 2.715, 0.0], [2.715, 0.0, 2.715], [0.0, 2.715, 2.715]]',
'pbc': '(True, True, True)',
'label': '',
'description': '',
# 'extras': "{{'_aiida_hash': {0}}}".format(load_node(pks[2]).get_hash()),
'symmetry': 'P1 (1)',
'volume': 40.02575174999999,
'child_nodes': 1,
'primitive': False,
'cif_file': ['', ''],
'group': [],
'scf': [],
'band': [],
'dos': [],
'eos': [],
'init_cls': [],
'corehole': [],
'calcfunctions': [[calc_function.uuid], ['test_label']],
}),
sorted({
'formula': 'SeSi2',
'pk': pks[1],
'uuid': uuids[1],
'natoms': 3,
'cell':
'[[2.715, 2.715, 0.0], [2.715, 0.0, 2.715], [0.0, 2.715, 2.715]]',
'pbc': '(True, True, True)',
'label': '',
'description': '',
# 'extras': "{{'_aiida_hash': {0}}}".format(load_node(pks[1]).get_hash()),
'symmetry': 'P1 (1)',
'volume': 40.02575174999999,
'child_nodes': 1,
'primitive': False,
'cif_file': ['', ''],
'group': ['test_group'],
'scf': [scf_wc.uuid],
'band': [],
'dos': [],
'eos': [],
'init_cls': [],
'corehole': [],
'calcfunctions': [[], []],
}),
sorted({
'formula': 'SeSi2',
'pk': pks[0],
'uuid': uuids[0],
'natoms': 3,
'cell':
'[[2.715, 2.715, 0.0], [2.715, 0.0, 2.715], [0.0, 2.715, 2.715]]',
'pbc': '(True, True, True)',
'label': '',
'description': '',
# 'extras': "{{'_aiida_hash': {0}}}".format(load_node(pks[0]).get_hash),
'symmetry': 'Imm2 (44)',
'volume': 40.02575174999999,
'child_nodes': 0,
'primitive': False,
'cif_file': ['', ''],
'group': ['test_group'],
'scf': [],
'band': [],
'dos': [],
'eos': [],
'init_cls': [],
'corehole': [],
'calcfunctions': [[], []],
})
]
for i in result:
assert sorted(i) in correct_result
def example_base_restart_timeout(raspa_code):
"""Run base workchain for GCMC with restart after timeout."""
# pylint: disable=no-member
print("Testing RaspaBaseWorkChain restart after timeout...")
print(
"This long simulation will require ca. 3 iterations (i.e., 2 restarts)."
)
parameters = Dict(
dict={
"GeneralSettings": {
"SimulationType": "MonteCarlo",
"NumberOfInitializationCycles": 5000, # many, to pass timeout
"NumberOfCycles": 5000, # many, to pass timeout
"PrintEvery": 1000,
"Forcefield": "GenericMOFs",
"RemoveAtomNumberCodeFromLabel": True,
"ChargeMethod": "None",
"CutOff": 12.0,
# WriteBinaryRestartFileEvery not needed: if missing RaspaBaseWorkChain will assign a default of 1000
},
"System": {
"irmof_1": {
"type": "Framework",
"UnitCells": "1 1 1",
"ExternalTemperature": 300.0,
"ExternalPressure": 1e5,
}
},
"Component": {
"krypton": {
"MoleculeDefinition": "TraPPE",
"TranslationProbability": 0.5,
"ReinsertionProbability": 0.5,
"SwapProbability": 1.0,
"BlockPocketsFileName": {
"irmof_1": "irmof_1_krypton",
},
},
},
})
# framework
pwd = os.path.dirname(os.path.realpath(__file__))
structure = CifData(file=os.path.join(pwd, '..', 'files', 'IRMOF-1.cif'))
structure_label = "irmof_1"
block_pocket_node1 = SinglefileData(
file=os.path.join(pwd, '..', 'files', 'IRMOF-1_test.block')).store()
# Constructing builder
builder = RaspaBaseWorkChain.get_builder()
# Specifying the code
builder.raspa.code = raspa_code
# Specifying the framework
builder.raspa.framework = {
structure_label: structure,
}
# Specifying the input parameters
builder.raspa.parameters = parameters
# Specifying the block pockets
builder.raspa.block_pocket = {
"irmof_1_krypton": block_pocket_node1,
}
# Specifying the scheduler options
builder.raspa.metadata.options = {
"resources": {
"num_machines": 1,
"num_mpiprocs_per_machine": 1,
},
"max_wallclock_seconds": 1 * 30 * 60, # 30 min
"withmpi": True,
"mpirun_extra_params":
["timeout",
"5"], # kill the calculation after 5 seconds, to test restart
}
# Specify RaspaBaseWorkChain options
builder.max_iterations = Int(
8
) # number of maximum iterations: prevent for infinite restart (default: 5)
run(builder)
def example_base_workchain_gcmc(raspa_code):
"""Run base workchain for GCMC calculations with 2 components."""
# pylint: disable=no-member
print("Testing RASPA Xenon:Krypton GCMC through RaspaBaseWorkChain ...")
parameters = Dict(
dict={
"GeneralSettings": {
"SimulationType": "MonteCarlo",
"NumberOfCycles": 2000,
"NumberOfInitializationCycles": 2000,
"PrintEvery": 200,
"Forcefield": "GenericMOFs",
"RemoveAtomNumberCodeFromLabel": True,
"EwaldPrecision": 1e-6,
"CutOff": 12.0,
},
"System": {
"irmof_1": {
"type": "Framework",
"UnitCells": "1 1 1",
"HeliumVoidFraction": 0.149,
"ExternalTemperature": 300.0,
"ExternalPressure": 1e5,
}
},
"Component": {
"krypton": {
"MoleculeDefinition": "TraPPE",
"TranslationProbability": 0.5,
"ReinsertionProbability": 0.5,
"SwapProbability": 1.0,
"BlockPocketsFileName": {
"irmof_1": "irmof_1_krypton",
},
},
"xenon": {
"MoleculeDefinition": "TraPPE",
"TranslationProbability": 0.5,
"ReinsertionProbability": 0.5,
"SwapProbability": 1.0,
"BlockPocketsFileName": {
"irmof_1": "irmof_1_xenon",
},
},
},
})
# framework
pwd = os.path.dirname(os.path.realpath(__file__))
structure = CifData(file=os.path.join(pwd, '..', 'files', 'IRMOF-1.cif'))
structure_label = "irmof_1"
block_pocket_node1 = SinglefileData(
file=os.path.join(pwd, '..', 'files', 'IRMOF-1_test.block')).store()
block_pocket_node2 = SinglefileData(
file=os.path.join(pwd, '..', 'files', 'IRMOF-1_test.block')).store()
# Constructing builder
builder = RaspaBaseWorkChain.get_builder()
# Specifying the code
builder.raspa.code = raspa_code
# Specifying the framework
builder.raspa.framework = {
structure_label: structure,
}
# Specifying the input parameters
builder.raspa.parameters = parameters
# Specifying the block pockets
builder.raspa.block_pocket = {
"irmof_1_krypton": block_pocket_node1,
"irmof_1_xenon": block_pocket_node2,
}
# Add fixers that could handle physics-related problems.
builder.fixers = {
'fixer_001':
('aiida_raspa.utils', 'check_gcmc_convergence', 0.10, 2000, 2000),
}
# Specifying the scheduler options
builder.raspa.metadata.options = {
"resources": {
"num_machines": 1,
"num_mpiprocs_per_machine": 1,
},
"max_wallclock_seconds": 1 * 30 * 60, # 30 min
"withmpi": False,
}
run(builder)