def test_get_number_electrons(self):
from aiida_alloy.utils import get_numelectrons_structure_upffamily
from aiida_alloy.utils import randomize_asestructure_elements
from aiida.orm.nodes.data.upf import get_pseudos_from_structure
test_seed = 42
test_largerandom_ase = randomize_asestructure_elements(
self.basic_ase_supercell, self.randomcell_elements,
self.randomcell_concentrations, test_seed)
expected_electron_dict = {
'Al': 3,
'Mg': 2,
'Cu': 11,
}
expected_E = 0
for i in range(len(test_largerandom_ase)):
element = test_largerandom_ase[i].symbol
expected_E += expected_electron_dict[element]
test_largerandom_structure = StructureData(ase=test_largerandom_ase)
pseudos = get_pseudos_from_structure(test_largerandom_structure,
TEST_UPF_FAMILY)
computed_E = get_numelectrons_structure_upffamily(
test_largerandom_structure, pseudos)
assert expected_E == computed_E
def get_common_inputs():
"""Return the dictionary of inputs to be used as the basis for each `PwBaseWorkChain`."""
protocol, protocol_modifiers = self._get_protocol()
checked_pseudos = protocol.check_pseudos(
modifier_name=protocol_modifiers.get('pseudo', None),
pseudo_data=protocol_modifiers.get('pseudo_data', None))
known_pseudos = checked_pseudos['found']
inputs = AttributeDict({
'pw': {
'code': self.inputs.code,
'parameters': self.ctx.parameters,
'metadata': {},
}
})
if 'pseudo_family' in self.inputs:
inputs.pw['pseudos'] = get_pseudos_from_structure(
self.inputs.structure, self.inputs.pseudo_family.value)
else:
inputs.pw['pseudos'] = get_pseudos_from_dict(
self.inputs.structure, known_pseudos)
if 'set_2d_mesh' in self.inputs:
inputs['set_2d_mesh'] = self.inputs.set_2d_mesh
if 'options' in self.inputs:
inputs.pw.metadata.options = self.inputs.options.get_dict()
else:
inputs.pw.metadata.options = get_default_options(with_mpi=True)
return inputs
def wf_setupparams(base_parameter, structure,
pseudo_familyname, nume2bnd_ratio,
cellpress_parameter):
from aiida.orm.nodes.data.upf import get_pseudos_from_structure
import collections
def update(d, u):
for k, v in u.items():
if isinstance(v, collections.Mapping):
d[k] = update(d.get(k, {}), v)
else:
d[k] = v
return d
pseudos = get_pseudos_from_structure(structure, pseudo_familyname.value)
nelec = get_numelectrons_structure_upffamily(structure, pseudos)
nbnd = nelec * nume2bnd_ratio.value
nbnd = max(nbnd, 20) # minimum of 20 bands to avoid certain crashes
parameter_dict = base_parameter.get_dict()
parameter_dict['SYSTEM']['nbnd'] = nbnd
cellpress_dict = cellpress_parameter.get_dict()
parameter_dict.update(cellpress_dict)
parameters = Dict(dict=parameter_dict)
return parameters
def run_pw_nscf(self):
"""Run the NSCF step with pw.x"""
self.out('scf_output', self.ctx.pw_scf.outputs.output_parameters)
try:
# Check if it's an explicit list of kpoints; this raises AttributeError if it's a mesh
self.inputs.kpoints_nscf.get_kpoints()
# If I am here, this an explicit grid, I stop
raise ValueError(
"You should pass an MP grid; we'll take care of converting to an explicit one"
)
except AttributeError:
# Check that the one provided is an unshifted mesh
assert self.inputs.kpoints_nscf.get_kpoints_mesh()[1] == [
0, 0, 0
], "You should pass an unshifted mesh"
self.ctx.kpoints_nscf_explicit = get_explicit_kpoints(
self.inputs.kpoints_nscf
)
nscf_parameters = self.ctx.scf_parameters.copy()
nscf_parameters['CONTROL']['calculation'] = 'nscf'
inputs = {
'code':
self.inputs.pw_code,
'structure':
self.inputs.structure,
'pseudos':
get_pseudos_from_structure(
self.inputs.structure, self.inputs.pseudo_family.value
),
'parameters':
orm.Dict(dict=nscf_parameters),
'kpoints':
self.ctx.kpoints_nscf_explicit,
'parent_folder':
self.ctx.pw_scf.outputs.remote_folder,
'metadata': {
'options': {
'resources': {
'num_machines': int(self.inputs.num_machines)
},
'max_wallclock_seconds':
int(self.inputs.max_wallclock_seconds),
'withmpi': True,
}
}
}
running = self.submit(
CalculationFactory('quantumespresso.pw'), **inputs
)
self.report(
'launching PwCalculation<{}> (NSCF step)'.format(running.pk)
)
return ToContext(pw_nscf=running)
def get_nummachines_forcalc(structure, pseudo_familyname):
# NOTE: used very adhoc guess for nodes, assuming quadratic scaling
pseudos = get_pseudos_from_structure(structure, pseudo_familyname)
num_electrons = get_numelectrons_structure_upffamily(structure, pseudos)
a2 = 1.5 * 10**-6
a1 = 5.7 * 10**-3
a0 = 2
numnodes = a2 * num_electrons**2 + a1 * num_electrons + a0
numnodes = max(round(numnodes / 2) * 2, 2) # force even # of nodes
return numnodes
def validate_and_prepare_pseudos_inputs(structure,
pseudos=None,
pseudo_family=None): # pylint: disable=invalid-name
"""Validate the given pseudos mapping or pseudo potential family with respect to the given structure.
Use the explicitly passed pseudos dictionary or use the pseudo_family in combination with the structure to obtain
that dictionary.
The pseudos dictionary should now be a dictionary of UPF nodes with the kind as linkname
As such, if there are multiple kinds with the same element, there will be duplicate UPF nodes
but multiple links for the same input node are not allowed. Moreover, to couple the UPF nodes
to the Calculation instance, we have to go through the use_pseudo method, which takes the kind
name as an additional parameter. When creating a Calculation through a Process instance, one
cannot call the use methods directly but rather should pass them as keyword arguments. However,
we can pass the additional parameters by using them as the keys of a dictionary
:param structure: StructureData node
:param pseudos: a dictionary where keys are the kind names and value are UpfData nodes
:param pseudo_family: pseudopotential family name to use, should be Str node
:raises: ValueError if neither pseudos or pseudo_family is specified or if no UpfData is found for
every element in the structure
:returns: a dictionary of UpfData nodes where the key is the kind name
.. deprecated:: 4.0.0
This functionality is now implemented in ``aiida-pseudo``.
"""
from aiida.orm import Str
warnings.warn(
'this function is deprecated and will be removed in `v4.0.0`.',
AiidaDeprecationWarning)
if pseudos and pseudo_family:
raise ValueError(
'you cannot specify both "pseudos" and "pseudo_family"')
elif pseudos is None and pseudo_family is None:
raise ValueError(
'neither an explicit pseudos dictionary nor a pseudo_family was specified'
)
elif pseudo_family:
# This will already raise some exceptions, potentially, like the ones below
pseudos = get_pseudos_from_structure(structure, pseudo_family.value)
elif isinstance(pseudos, (str, Str)):
raise TypeError(
'you passed "pseudos" as a string - maybe you wanted to pass it as "pseudo_family" instead?'
)
for kind in structure.get_kind_names():
if kind not in pseudos:
raise ValueError(f'no pseudo available for element {kind}')
elif not isinstance(pseudos[kind], (LegacyUpfData, UpfData)):
raise ValueError(
f'pseudo for element {kind} is not of type UpfData')
return pseudos
def wf_setupparams(base_parameter, structure, pseudo_familyname,
nume2bnd_ratio):
pseudos = get_pseudos_from_structure(structure, pseudo_familyname.value)
nelec = get_numelectrons_structure_upffamily(structure, pseudos)
nbnd = nelec * nume2bnd_ratio.value
nbnd = max(nbnd, 20) # minimum of 20 bands to avoid certain crashes
parameter_dict = base_parameter.get_dict()
parameter_dict['SYSTEM']['nbnd'] = nbnd
parameters = Dict(dict=parameter_dict)
return parameters
def launch_calculation(code, structure, pseudo_family, max_num_machines,
max_wallclock_seconds, with_mpi, daemon):
"""Run a CpCalculation."""
from aiida.orm import Dict
from aiida.orm.nodes.data.upf import get_pseudos_from_structure
from aiida.plugins import CalculationFactory
from aiida_quantumespresso.utils.resources import get_default_options
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'
},
}
inputs = {
'code': code,
'structure': structure,
'pseudos': get_pseudos_from_structure(structure, pseudo_family),
'parameters': Dict(dict=parameters),
'metadata': {
'options':
get_default_options(max_num_machines, max_wallclock_seconds,
with_mpi),
}
}
launch.launch_process(CalculationFactory('quantumespresso.cp'), daemon,
**inputs)
def run_pw_scf(self):
"""Run the SCF with pw.x."""
# A fixed value, for testing
ecutwfc = 30.
self.ctx.scf_parameters = {
'CONTROL': {
'calculation': 'scf',
},
'SYSTEM': {
'ecutwfc': ecutwfc,
'ecutrho': ecutwfc * 8.,
}
}
inputs = {
'code':
self.inputs.pw_code,
'structure':
self.inputs.structure,
'pseudos':
get_pseudos_from_structure(
self.inputs.structure, self.inputs.pseudo_family.value
),
'parameters':
orm.Dict(dict=self.ctx.scf_parameters),
'kpoints':
self.inputs.kpoints_scf,
'metadata': {
'options': {
# int is used to convert from AiiDA nodes to python ints
'resources': {
'num_machines': int(self.inputs.num_machines)
},
'max_wallclock_seconds':
int(self.inputs.max_wallclock_seconds),
'withmpi': True,
}
}
}
running = self.submit(
CalculationFactory('quantumespresso.pw'), **inputs
)
self.report(
'launching PwCalculation<{}> (SCF step)'.format(running.pk)
)
return ToContext(pw_scf=running)
####################
SiriusParameters = DataFactory('sirius.scf')
StructureData = DataFactory('structure')
KpointsData = DataFactory('array.kpoints')
Dict = DataFactory('dict')
SinglefileData = DataFactory('singlefile')
NLCGParameters = DataFactory('sirius.py.nlcg')
parameters = SiriusParameters(sirius_json)
nlcgconfig = yaml.load(open('nlcg.yaml', 'r'))
nlcgconfig = {'System': nlcgconfig['System'], 'CG': nlcgconfig['CG']}
nlcgparams = NLCGParameters(nlcgconfig)
structure, magnetization, kpoints = from_sirius_json(sirius_json)
pseudos = get_pseudos_from_structure(structure, args.pseudos)
print('tasks_per_core', args.ntasks_per_core)
# 'num_cores_per_machine': 1,
comp_resources = {
'num_mpiprocs_per_machine': args.ntasks_per_node,
'num_machines': args.nodes,
'num_cores_per_mpiproc': args.ntasks_per_core
}
# set up calculation
inputs = {
'code': code,
'sirius_config': parameters,
'structure': structure,
'kpoints': kpoints,
s = StructureData(cell=cell)
s.append_atom(position=(0., 0., 0.), symbols='Ba')
s.append_atom(position=(alat / 2., alat / 2., alat / 2.), symbols='Ti')
s.append_atom(position=(alat / 2., alat / 2., 0.), symbols='O')
s.append_atom(position=(alat / 2., 0., alat / 2.), symbols='O')
s.append_atom(position=(0., alat / 2., alat / 2.), symbols='O')
kpoints = KpointsData()
kpoints.set_kpoints_mesh([2, 2, 2])
# set up calculation
inputs = {
'code': code,
'sirius_config': parameters,
'structure': s,
'kpoints': kpoints,
'metadata': {
'description': "Test job submission with the aiida_sirius plugin",
},
'pseudos': get_pseudos_from_structure(s, 'sssp_efficiency')
}
# Note: in order to submit your calculation to the aiida daemon, do:
# from aiida.engine import submit
# future = submit(CalculationFactory('sirius'), **inputs)
calc = CalculationFactory('sirius.scf')
result = run(calc, **inputs)
res = result['sirius'].get_content()
print("Result: \n{}".format(res))
structure = load_node(<STRUCTURE PK>) # REPLACE <STRUCTURE PK>
builder.structure = structure
# Define calculation
parameters = {
'CONTROL': {
'calculation': 'scf', # self-consistent field
},
'SYSTEM': {
'ecutwfc': 30., # wave function cutoff in Ry
'ecutrho': 240., # density cutoff in Ry
},
}
builder.parameters = Dict(dict=parameters)
# Select pseudopotentials
builder.pseudos = get_pseudos_from_structure(structure, '<PP FAMILY>') # REPLACE <PP FAMILY>
# Define K-point mesh in reciprocal space
KpointsData = DataFactory('array.kpoints')
kpoints = KpointsData()
kpoints.set_kpoints_mesh([4,4,4])
builder.kpoints = kpoints
# Set resources
builder.metadata.options.resources = {'num_machines': 1}
# Submit the job
calcjob = submit(builder)
print('Submitted CalcJob with PK=' + str(calcjob.pk))
"precond": precond,
"tol": 1e-09,
},
"System": {
"T": 300.0,
"smearing": "gaussian-spline"
},
}
nlcgparams = NLCGParameters(nlcgconfig)
structure, magnetization, kpoints = from_sirius_json(sirius_json)
####################################################
# # Warning pseudopotentials are taken from aiida! #
####################################################
pseudos = get_pseudos_from_structure(structure, 'normcons')
# 'num_cores_per_machine': 1,
comp_resources = {
'num_mpiprocs_per_machine': args.ntasks_per_node,
'num_machines': args.nodes,
'num_cores_per_mpiproc': args.ntasks_per_core
}
# set up calculation
inputs = {
'code': code,
'sirius_config': parameters,
'structure': structure,
'kpoints': kpoints,
'nlcgparams': nlcgparams,
# load SIRIUS parameters from json
sirius_json = json.load(open('sirius.json', 'r'))
# extract structure, magnetization, kppoints (for the sake of AiiDA provenance)
structure, magnetization, kpoints = helpers.from_sirius_json(sirius_json)
# set up calculation
inputs = {
'code': code,
'sirius_config': SiriusParameters(sirius_json),
'sirius_md_params': md_parameters,
'structure': structure,
'kpoints': kpoints,
'metadata': {
'options': {
'withmpi': True,
'prepend_text': '#SBATCH --nodelist=ault02',
'max_wallclock_seconds': 3600
},
},
'pseudos': get_pseudos_from_structure(structure, 'sg15_pz')
}
calc = CalculationFactory('sirius.md')
# result = submit(calc, **inputs)
submit(calc, **inputs)
# res = result['sirius'].get_content()
# print("Result: \n{}".format(res))
'restart_mode': 'from_scratch',
'wf_collect': True,
},
'SYSTEM': {
'ecutwfc': 30.,
'ecutrho': 240.,
},
'ELECTRONS': {
'conv_thr': 1.e-6,
}
})
kpoints = KpointsData()
kpoints.set_kpoints_mesh([4, 4, 4])
builder.pseudos = get_pseudos_from_structure(s, pseudo_family)
builder.metadata.options.resources = {'num_machines': 1}
builder.metadata.options.max_wallclock_seconds = 1800
builder.metadata.label = 'My generic title'
builder.metadata.description = 'My generic description'
builder.structure = s
builder.parameters = parameters
builder.kpoints = kpoints
calc = submit(builder)
print(f'created calculation with PK={calc.pk}')
def run_calculation(
name,
struct,
group,
codename,
pseudo_family,
k_distance=0.20,
scale_element_init_moment={},
input_namelists={},
code_runtime_options=None
):
"""
This function converts a given initial structure into an AiiDA readable format
to perform a static SCF calculation.
Parameters
----------
name : str
The name of the structure or calculations eg. name='Fe'
struct : Structure object
The defect structure
group : str
The name of the group to store AiiDA nodes on AiiDA database. Its advisable to keep track
of this name to make sure you organize your data
codename : str
The name of the code configured on AiiDA database to perform this type of calculations
pseudo_family : str
A pseudopotential family configured on AiiDA database
k_distance : float
The density of k-point mesh use for k-point integration in DFT. For more see this
material cloud page for its usage: https://www.materialscloud.org/work/tools/qeinputgenerator
Default=0.2.
scale_element_init_moment : dict
A user define dictionary type of magnetic ions to scale its magnetic moment.
Default={}.
input_namelists : dict
A user define Quantum ESPRESSO (QE) input namelists. Default={}
mu_plus : bool
If True, to specify a total charge of the system and initialise a
starting charge of muon. Defualt=False
code_runtime_options : None
The HPC requirements of number of nodes and k-points. Depends on the code
configure in `codename`.
Returns
-------
Submit calculation to AiiDA daemon
"""
from aiida_quantumespresso.utils.resources import get_default_options, get_automatic_parallelization_options
from aiida.orm import Group
g, just_created = Group.objects.get_or_create(group)
code = Code.get_from_string(codename)
builder = code.get_builder()
builder.metadata.label = "{} - Unitcell".format(name)
builder.metadata.description = "Magnetic test for - {}".format(name)
StructureData = DataFactory("structure")
labeled_structure, nspin, magnetic_elements_kinds = analyze_pymatgen_structure(struct, mark_muon=False)
builder.structure = StructureData(pymatgen=labeled_structure)
structure_copy = StructureData(pymatgen=labeled_structure)
if nspin == 2:
# Set all polarizations to 0.4
for k in magnetic_elements_kinds.keys():
for idx in magnetic_elements_kinds[k].keys():
magnetic_elements_kinds[k][idx] = magnetic_elements_kinds[k][idx] * scale_element_init_moment.get(k, 1.)
elif nspin == 4:
raise NotImplemented("Non collinear case not implemented.")
Dict = DataFactory('dict')
parameters_dict = {
'CONTROL': {
'calculation': 'scf',
'restart_mode': 'from_scratch',
},
'SYSTEM': {
'ecutwfc': 60.,
'ecutrho': 600.,
'occupations':'smearing',
'smearing': 'm-v',
'degauss' : 0.02,
'nspin': nspin, #
},
'ELECTRONS': {
'conv_thr' : 1.e-7,
'mixing_beta' : 0.30,
'mixing_mode' : 'local-TF'
}
}
#print('Old Dictionary\n', parameters_dict)
#override
parameters_dict=merge(input_namelists, parameters_dict)
#print('New Dictionary\n', parameters_dict)
parameters = Dict(dict=parameters_dict)
builder.parameters = parameters
if nspin == 2:
parameters_dict['SYSTEM']['starting_magnetization'] = merge_dict_of_dicts(magnetic_elements_kinds)
KpointsData = DataFactory('array.kpoints')
#kpoints = KpointsData()
#kpoints.set_kpoints_mesh([2,2,2],offset=(0,0,0))
kpoints = KpointsData()
kpoints.set_cell_from_structure(builder.structure)
kpoints.set_kpoints_mesh_from_density(k_distance, force_parity=False)
kpoints.store()
settings_dict={}
num_k_points = np.prod(kpoints.get_kpoints_mesh()[0])
if num_k_points==1:
settings_dict={'gamma_only': True}
else:
settings_dict={'gamma_only': False}
builder.pseudos = get_pseudos_from_structure(structure_copy, pseudo_family)
#builder.metadata.options.resources = resources
#builder.metadata.options.max_wallclock_seconds = 259200 #86400
builder.parameters = parameters
builder.kpoints = kpoints
# AAAA: automatic_parallelization does not work!!!
automatic_parallelization = False
if automatic_parallelization:
automatic_parallelization = get_automatic_parallelization_options(1, 24*60*60-60*5)
builder.automatic_parallelization = Dict(dict=automatic_parallelization)
else:
if code_runtime_options is None or code_runtime_options == '':
# num machines, time, mpi
default_options = get_default_options(1, 24*60*60-60*5, True)
builder.metadata.options = default_options
else:
exec_options = code_runtime_options.split('|')[0].split()
default_options = get_default_options(int(exec_options[0]), int(exec_options[1]), True)
builder.metadata.options = default_options
if code_runtime_options is None or code_runtime_options == '':
npool = np.min([4, num_k_points])
settings_dict['cmdline'] = ['-nk', str(npool), '-ndiag', '1']
else:
parallel_options = code_runtime_options.split('|')[1]
settings_dict['cmdline'] = parallel_options.strip().split()
clean_workdir = False
final_scf = False
if clean_workdir:
builder.clean_workdir = Bool(True)
if final_scf:
builder.final_scf = Bool(True)
calc = submit(builder)
if not (g is None):
g.add_nodes(calc)
print(name +' magnetic test calculation created with PK = {}'.format(calc.pk))
return calc
def launch_calculation(
code, structures, num_images, num_steps, pseudo_family, kpoints_mesh, ecutwfc, ecutrho, smearing, max_num_machines,
max_wallclock_seconds, with_mpi, daemon, parent_folder, dry_run
):
"""
Run a NebCalculation.
Note that some parameters are hardcoded.
"""
from aiida.orm import Dict
from aiida.orm.nodes.data.upf import get_pseudos_from_structure
from aiida.plugins import CalculationFactory
from aiida_quantumespresso.utils.resources import get_default_options
pw_parameters = {
'CONTROL': {
'calculation': 'relax',
},
'SYSTEM': {
'ecutwfc': ecutwfc,
'ecutrho': ecutrho,
}
}
neb_parameters = {
'PATH': {
'restart_mode': ('restart' if parent_folder else 'from_scratch'),
'opt_scheme': 'broyden',
'num_of_images': num_images,
'nstep_path': num_steps,
},
}
try:
validate.validate_smearing(pw_parameters, smearing)
except ValueError as exception:
raise click.BadParameter(str(exception))
inputs = {
'code': code,
'first_structure': structures[0],
'last_structure': structures[1],
'pw': {
'pseudos': get_pseudos_from_structure(structures[0], pseudo_family),
'kpoints': kpoints_mesh,
'parameters': Dict(dict=pw_parameters),
},
'parameters': Dict(dict=neb_parameters),
'metadata': {
'options': get_default_options(max_num_machines, max_wallclock_seconds, with_mpi),
}
}
if parent_folder:
inputs['parent_folder'] = parent_folder
if dry_run:
if daemon:
# .submit() would forward to .run(), but it's better to stop here,
# since it's a bit unexpected and the log messages output to screen
# would be confusing ("Submitted NebCalculation<None> to the daemon")
raise click.BadParameter('cannot send to the daemon if in dry_run mode', param_hint='--daemon')
inputs['metadata']['store_provenance'] = False
inputs['metadata']['dry_run'] = True
launch.launch_process(CalculationFactory('quantumespresso.neb'), daemon, **inputs)
kpoints.set_kpoints_mesh([2, 2, 2])
# 'num_cores_per_machine': 1,
comp_resources = {'num_mpiprocs_per_machine': 2,
'num_machines': 1,
'num_cores_per_mpiproc': 6}
# set up calculation
inputs = {
'code': code,
'sirius_config': parameters,
'structure': s,
'kpoints': kpoints,
'nlcgparams': nlcgparams,
'metadata': {
'description': "Test job submission with the aiida_sirius plugin",
'options': {
'resources': comp_resources,
'withmpi': True,
'max_wallclock_seconds': 200
}
},
'pseudos': get_pseudos_from_structure(s, 'normcons')
}
# Note: in order to submit your calculation to the aiida daemon, do:
# from aiida.engine import submit
# future = submit(CalculationFactory('sirius'), **inputs)
calc = CalculationFactory('sirius.py.nlcg')
result = submit(calc, **inputs)
def launch_calculation(code, structure, pseudo_family, kpoints_mesh, ecutwfc,
ecutrho, hubbard_u, hubbard_v, hubbard_file_pk,
starting_magnetization, smearing, max_num_machines,
max_wallclock_seconds, with_mpi, daemon, parent_folder,
dry_run, mode, unfolded_kpoints):
"""Run a PwCalculation."""
from aiida.orm import Dict
from aiida.orm.nodes.data.upf import get_pseudos_from_structure
from aiida.plugins import CalculationFactory
from aiida_quantumespresso.utils.resources import get_default_options
parameters = {
'CONTROL': {
'calculation': mode,
},
'SYSTEM': {
'ecutwfc': ecutwfc,
'ecutrho': ecutrho,
}
}
if mode in CALCS_REQUIRING_PARENT and not parent_folder:
raise click.BadParameter(
"calculation '{}' requires a parent folder".format(mode),
param_hint='--parent-folder')
try:
hubbard_file = validate.validate_hubbard_parameters(
structure, parameters, hubbard_u, hubbard_v, hubbard_file_pk)
except ValueError as exception:
raise click.BadParameter(str(exception))
try:
validate.validate_starting_magnetization(structure, parameters,
starting_magnetization)
except ValueError as exception:
raise click.BadParameter(str(exception))
try:
validate.validate_smearing(parameters, smearing)
except ValueError as exception:
raise click.BadParameter(str(exception))
if unfolded_kpoints:
from aiida.orm import KpointsData
unfolded_list = kpoints_mesh.get_kpoints_mesh(print_list=True)
kpoints_mesh = KpointsData()
kpoints_mesh.set_kpoints(unfolded_list)
inputs = {
'code': code,
'structure': structure,
'pseudos': get_pseudos_from_structure(structure, pseudo_family),
'kpoints': kpoints_mesh,
'parameters': Dict(dict=parameters),
'metadata': {
'options':
get_default_options(max_num_machines, max_wallclock_seconds,
with_mpi),
}
}
if parent_folder:
inputs['parent_folder'] = parent_folder
if hubbard_file:
inputs['hubbard_file'] = hubbard_file
if dry_run:
if daemon:
# .submit() would forward to .run(), but it's better to stop here,
# since it's a bit unexpected and the log messages output to screen
# would be confusing ("Submitted PwCalculation<None> to the daemon")
raise click.BadParameter(
'cannot send to the daemon if in dry_run mode',
param_hint='--daemon')
inputs['metadata']['store_provenance'] = False
inputs['metadata']['dry_run'] = True
launch.launch_process(CalculationFactory('quantumespresso.pw'), daemon,
**inputs)
def qePwOriginalSubmit(codename,
structure,
kpoints,
pseudo_family,
metadata,
pseudo_dict={},
add_parameters={},
del_parameters={},
cluster_options={},
settings_dict={}):
"""
:code:`qePwOriginalSubmit` will submit an original computational task to the desired computer by using certain code.
:param codename: (mandatory) A string represents the code for pw.x that you want to use.
:type codename: python string object
:param structure: (mandatory) The structure of your system.
:type structure: aiida.orm.StructureData object
:param add_parameters: (optional, default = {}) The desired parameters that you want to state, it can be
incomplete, because inside the function there is a default setting for parameters which can
be used in most cases, but if you have specific need, you can put that in parameters,
the format is similar as pw.x input file.
If you want to assign DFT+U and spin-polarization, you need to specify it on your own.
In Aiida, there is a very efficient way to specify the :code:`hubbard_u`,
:code:`starting_magnetization` and :code:`starting_ns_eigenvalue`. I give some examples
in below:
.. code-block:: python
# hubbard_u
'SYSTEM': {
'hubbard_u': {
'Fe': 5.0,
'Fe3': 5.0 # if you have different spins of same atom, then you should use
newStructure function to create the structure
},
'starting_magnetization': {
'Fe': 0.1,
'Fe3': 0.1,
},
'starting_ns_eigenvalue': [
[1, 1, 'Fe', 1.0] # represent: starting_ns_eigenvalue(1, 1, 1)=1.0
# others are the same, if you want to assign to Fe3, just replace Fe with Fe3.
]
}
:type add_parameters: python dictionary
:param del_parameters: (optional, default = {}) The tags that we would like to delete, for example if we do not
want to use spin-polarized simulation, then 'nspin' needs to be deleted. Same structure
as add_parameters.
e.g. :code:`{'CONTROL': [key1, key2, key3], 'SYSTEM': [key1, key2, key3]}`
:type del_parameters: python dictionary object
:param kpoints: (mandatory) The kpoints that you want to use, if the kpoints has only 1 list, then it is the kpoint
mesh, but if two lists are detected, then the first will be k-point mesh, the second one will be the
origin of k-point mesh.e.g. [[3, 3, 1]] or [[3, 3, 1],[0.5, 0.5, 0.5]]
:type kpoints: python list object
:param pseudo_family: (mandatory) The pseudopotential family that you want to use. Make sure that you already have
that configured, otherwise an error will occur.
:type pseudo_family: python string object.
:param pseudo_dict: (optional, default = {}) which contains the pseudopotential files that we want to use in the
simulation. In here it is very important to note that the path of the pseudopotential file
has to be in the absolute path.
e.g.
.. code-block:: python
pseudo_dict = {
'Fe': UpfData(absolute_path),
'Fe3': UpfData(absolute_path)
}
:type pseudo_dict: python dictionary object.
:param cluster_options: (optional, default = {}) The detailed option for the cluster. Different cluster may have
different settings. Only the following 3 keys can have effects: (1) resources (2) account
(3) queue_name
:type cluster_options: python dictionary object
:param metadata: (mandatory) The dictionary that contains information about metadata. For example: label and
description. label and description are mendatory.
e.g. :code:`{'label':{}, 'description':{}}`
:type metadata: python dictionary object
:param settings_dict: (optional, default = {}) which contains the additional information for the pw.x
calculation. e.g. Fixed atom, retrieving more files, parser options, etc. And the
command-line options.
:type settings_dict: python dictionary object
:returns: uuid of the new CalcJobNode
"""
code = Code.get_from_string(codename)
computer = codename.split('@')[1] # get the name of the cluster
pw_builder = code.get_builder()
# pseudopotential
# check whether pseudo_family and pseudo_dict are set at the same time, if true, then break
if len(pseudo_family) > 0 and len(pseudo_dict) > 0:
return ValueError(
"You cannot set pseudo_family and pseudo_dict at the same time")
if len(pseudo_family) == 0 and len(pseudo_dict) == 0:
return ValueError(
"You need to specify at least one in pseudo_family or pseudo_dict."
)
if len(pseudo_family) != 0:
pw_builder.pseudos = get_pseudos_from_structure(
structure, family_name=pseudo_family)
if len(pseudo_dict) != 0:
pw_builder.pseudos = pseudo_dict
# set kpoints
kpts = KpointsData()
if len(kpoints) == 1:
kpts.set_kpoints_mesh(mesh=kpoints[0])
else:
kpts.set_kpoints_mesh(mesh=kpoints[0], offset=kpoints[1])
# parameters
parameters_default = Dict(dict=pwParameter)
# add parameters in add_parameters
parameters_tmp = deepcopy(parameters_default)
for key, value in add_parameters.items():
for key2, value2 in value.items():
parameters_tmp[key][key2] = value2
# delete parameters in del_parameters
for key, value in del_parameters.items():
tmp = parameters_tmp[key]
for key2 in value:
if key2 in tmp.keys():
tmp.pop(key2)
else:
pass
parameters_default = parameters_tmp
# set labels and description
pw_builder.metadata.label = metadata['label']
pw_builder.metadata.description = metadata['description']
# set default options for slurm
pw_builder.metadata.options['resources'] = slurm_options[computer]['qe'][
'resources'] # in here machine = node
pw_builder.metadata.options['max_wallclock_seconds'] = slurm_options[
computer]['qe']['max_wallclock_seconds'] #in here machine = node
pw_builder.metadata.options['account'] = slurm_options[computer]['qe'][
'account'] # in here machine = node
pw_builder.metadata.options['scheduler_stderr'] = slurm_options[computer][
'qe']['scheduler_stderr']
pw_builder.metadata.options['scheduler_stderr'] = slurm_options[computer][
'qe']['scheduler_stderr']
pw_builder.metadata.options['queue_name'] = slurm_options[computer]['qe'][
'queue_name']
# revised by cluster_options
if len(cluster_options) > 0:
if 'resources' in cluster_options.keys():
pw_builder.metadata.options['resources'] = cluster_options[
'resources']
if 'account' in cluster_options.keys():
pw_builder.metadata.options['account'] = cluster_options['account']
if 'queue_name' in cluster_options.keys():
pw_builder.metadata.options['queue_name'] = cluster_options[
'queue_name']
# initialize the settings_dict
if len(settings_dict) == 0:
settings_dict['cmdline'] = ['-nk', '4']
else:
pass # do nothing
# get atomic occupations
if 'lda_plus_u' in parameters_default['SYSTEM']:
if parameters_default['SYSTEM']['lda_plus_u']:
settings_dict['parser_options'] = {
'parse_atomic_occupations': True
}
# launch the simulation
pw_builder.structure = structure
pw_builder.kpoints = kpts
pw_builder.parameters = parameters_default
pw_builder.settings = Dict(dict=settings_dict)
calc = submit(pw_builder)
return calc.uuid
def qePwContinueSubmit(uuid,
pseudo_family,
pseudo_dict={},
codename='',
parent_folder=True,
add_parameters={},
del_parameters={},
kpoints=[],
cluster_options={},
metadata={},
settings_dict={}):
"""
`qePwContinueSubmit` will continue a simulation with similar or modified input parameters. All the parameters are
listed in the kwargs.
:param uuid: (mandatory) The uuid of previous calculation. We will start our calculation from there. Because uuid
is the unique identification number for each CalcJobNode
**Notice**: The uuid must be in the results dictionary, if not the program will shout KeyError.
And if you are testing, you could use assignValue to quickly create a dictionary that contains
the uuid that you want to continue.
:type uuid: python string object
:param pseudo_family: (mandatory) The pseudopotential family that you want to use. Make sure that you already have
that configured, otherwise an error will occur. This is mendatory.
:type pseudo_family: python string object
:param pseudo_dict: (optional, default = {}) Which contains the pseudopotential files that we want to use in the
simulation.
:type pseudo_dict: python dictionary object
:param codename: (optional, default = '') Represent the code for pw.x that you want to use. If you want to use the
same as previous calculation, then you need to use Str('')
:type codename: python string object
:param parent_folder: (optional, default = True) If parent_folder is True, then the calculation will start with the
output files from previous calculations.
:type parent_folder: python boolean object
:param add_parameters: (optional, default = {}) The desired parameters that you want to state, it can be incomplete,
because inside the function there is a default setting for parameters which can be used in
most cases, but if you have specific need, you can put that in parameters, the format is
similar as pw.x input file.
If you want to assign DFT+U and spin-polarization, you need to specify it on your own.
e.g. :code:`{'CONTROL':{}, 'SYSTEM':{}}`
**Notice**: more options in qePwOriginalSubmit function. In qePwContinueSubmit,
we assume that the user wants to restart from previous converged wave functions and
charge density, so we set ['CONTROL']['restart_mode']='restart', ['ELECTRON'][
'startingwfc']='file and ['ELECTRON']['startingpot']='file'.
:type add_parameters: python dictionary object
:param del_parameters: (optional, default = {})The tags that we would like to delete, for example if we do not
want to use spin-polarized simulation, then 'nspin' needs to be deleted. Same structure as
add_parameters.
e.g. :code:`{'CONTROL': [key1, key2, key3], 'SYSTEM': [key1, key2, key3]}`
:type del_parameters: python dictionary object
:param kpoints: (optional, default = []), if you want to keep the k-points for previous calculation, just use an
empty list :code:`[]`. The kpoints that you want to use, if the kpoints has only 1 list,
then it is the kpoint mesh, but if two lists are detected, then the first will be k-point mesh,
the second one will be the origin of k-point mesh.e.g. [[3, 3, 1]] or [[3, 3, 1],[0.5, 0.5, 0.5]]
:type kpoints: python list object
:param cluster_options: (optional, default = {}) The detailed option for the cluster. Different cluster may have
different settings. Only the following 3 keys can have effects: (1) resources (2)
account (3) queue_name. If value is :code:`{}`, then it means we will use previous settings
:type cluster_options: python dictionary object
:param metadata: (optional, default = {}) The dictionary that contains information about metadata. For example:
label and description.label and description are mendatory. If value is :code:`{}`,
then it means we will use previous settings.
:type metadata: python dictionary object
:param settings_dict: (optional, default = {}) which contains the additional information for the pw.x calculation.
e.g. Fixed atom, retrieving more files, parser options, etc. And the command-line options.
If value is :code:`{}`, then it means we will use previous settings.
:type settings_dict: python dictionary object
:returns: uuid of the CalcJobNode of the newest calculation.
"""
node = load_node(uuid=uuid)
if len(codename) == 0: # not going to change cluster
computer = node.computer.label
restart_builder = node.get_builder_restart() # get the restart_builder
else:
computer = codename.split('@')[1]
code = Code.get_from_string(codename)
restart_builder = code.get_builder()
parameters_tmp = deepcopy(node.inputs.parameters)
parameters_dict = parameters_tmp.get_dict()
calc_type = parameters_dict['CONTROL']['calculation']
# change the parameters (since this is the continuation of the previous calculation)
parameters_tmp['CONTROL']['restart_mode'] = 'restart'
parameters_tmp['ELECTRONS'][
'startingwfc'] = 'file' # from wave function in aiida.save
parameters_tmp['ELECTRONS'][
'startingpot'] = 'file' # from charge density in aiida.save
if calc_type == 'relax' or calc_type == 'vc-relax':
structure = node.outputs.output_structure
elif calc_type == 'scf' or calc_type == 'nscf':
structure = node.inputs.structure
# assign parameters in add_parameters
for key, value in add_parameters.items():
for key2, value2 in value.items():
parameters_tmp[key][key2] = value2
# delete parameters in del_parameters
for key, value in del_parameters.items():
tmp = parameters_tmp[key]
for key2 in value:
if key2 in tmp.keys():
tmp.pop(key2)
parameters_default = parameters_tmp
# reset the kpoints
if len(kpoints) > 0:
kpts = KpointsData()
if len(kpoints) == 1:
kpts.set_kpoints_mesh(mesh=kpoints[0])
else:
kpts.set_kpoints_mesh(mesh=kpoints[0], offset=kpoints[1])
else:
kpts = node.inputs.kpoints
# pseudopotential
# check whether pseudo_family and pseudo_dict are set at the same time, if true, then break
if len(pseudo_family) > 0 and len(pseudo_dict) > 0:
return ValueError(
"You cannot set pseudo_family and pseudo_dict at the same time")
if len(pseudo_family) == 0 and len(pseudo_dict) == 0:
return ValueError(
"You need to specify at least one in pseudo_family or pseudo_dict."
)
if len(pseudo_family) != 0:
restart_builder.pseudos = get_pseudos_from_structure(
structure, family_name=pseudo_family)
if len(pseudo_dict) != 0:
restart_builder.pseudos = pseudo_dict
# set default options for slurm
restart_builder.metadata.options['resources'] = slurm_options[computer][
'qe']['resources'] # in here machine = node
restart_builder.metadata.options['max_wallclock_seconds'] = slurm_options[
computer]['qe']['max_wallclock_seconds'] # in here machine = node
restart_builder.metadata.options['account'] = slurm_options[computer][
'qe']['account'] # in here machine = node
restart_builder.metadata.options['scheduler_stderr'] = slurm_options[
computer]['qe']['scheduler_stderr']
restart_builder.metadata.options['scheduler_stderr'] = slurm_options[
computer]['qe']['scheduler_stderr']
restart_builder.metadata.options['queue_name'] = slurm_options[computer][
'qe']['queue_name']
# reset cluster_options:
if len(cluster_options) > 0:
if 'resources' in cluster_options.keys():
restart_builder.metadata.options['resources'] = cluster_options[
'resources']
if 'account' in cluster_options.keys():
restart_builder.metadata.options['account'] = cluster_options[
'account']
if 'queue_name' in cluster_options.keys():
restart_builder.metadata.options['queue_name'] = cluster_options[
'queue_name']
# reset metadata
if len(metadata) > 0:
if 'label' in metadata.keys():
restart_builder.metadata.label = metadata['label']
else:
restart_builder.metadata.label = node.label
if 'description' in metadata.keys():
restart_builder.metadata.description = metadata['description']
else:
restart_builder.metadata.description = node.description
else:
restart_builder.metadata.label = node.label
restart_builder.metadata.description = node.description
# assign the parent_folder
if parent_folder:
restart_builder.parent_folder = node.outputs.remote_folder
# set settings_dict
if len(settings_dict) > 0:
pass
else:
settings_dict = node.inputs.settings.get_dict()
# submit the calculation
restart_builder.structure = structure
restart_builder.kpoints = kpts
restart_builder.parameters = parameters_default
restart_builder.settings = Dict(dict=settings_dict)
calc = submit(restart_builder)
return calc.uuid
