def launch_calculation(code, calculation, max_num_machines,
max_wallclock_seconds, with_mpi, daemon):
"""Run a Q2rCalculation."""
from aiida.plugins import CalculationFactory
from aiida_quantumespresso.utils.resources import get_default_options
# Check that the parent calculation node comes from quantumespresso.ph.
# I cannot move this check into the option declaration, because CalcJobNode is not subclassed by the specific
# calculation plugins (only Process is), and there is no feature yet to filter by the associated process_type.
expected_process_type = 'aiida.calculations:quantumespresso.ph'
if calculation.process_type != expected_process_type:
raise click.BadParameter(
'The input calculation node has a process_type: {}; should be {}'.
format(calculation.process_type, expected_process_type))
inputs = {
'code': code,
'parent_folder': calculation.outputs.remote_folder,
'metadata': {
'options':
get_default_options(max_num_machines, max_wallclock_seconds,
with_mpi),
}
}
launch.launch_process(CalculationFactory('quantumespresso.q2r'), daemon,
**inputs)
def test_ph_qpoint_list(
aiida_profile, fixture_localhost, fixture_sandbox, generate_calc_job, fixture_code, generate_structure,
generate_kpoints_mesh, generate_remote_data, file_regression
):
"""Test a `PhCalculation` with a qpoint list instead of a mesh."""
entry_point_name = 'quantumespresso.ph'
parent_entry_point = 'quantumespresso.pw'
remote_path = fixture_sandbox.abspath
structure = generate_structure()
kpoints = generate_kpoints_mesh(2).get_kpoints_mesh(print_list=True)
qpoints = orm.KpointsData()
qpoints.set_cell(structure.cell)
qpoints.set_kpoints(kpoints)
inputs = {
'code': fixture_code(entry_point_name),
'parent_folder': generate_remote_data(fixture_localhost, remote_path, parent_entry_point),
'qpoints': qpoints,
'parameters': orm.Dict(dict={'INPUTPH': {}}),
'metadata': {
'options': get_default_options()
}
}
generate_calc_job(fixture_sandbox, entry_point_name, inputs)
with fixture_sandbox.open('aiida.in') as handle:
input_written = handle.read()
file_regression.check(input_written, encoding='utf-8', extension='.in')
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 launch_calculation(code, parent_folder, single_file, max_num_machines, max_wallclock_seconds, with_mpi, daemon):
"""Run a Pw2wannier90Calculation with some sample parameters and the provided inputs."""
from aiida.orm import Dict
from aiida.plugins import CalculationFactory
from aiida_quantumespresso.utils.resources import get_default_options
parameters = {
'inputpp': {
'write_amn': True,
'write_mmn': True,
'write_unk': False,
'scdm_proj': True,
'scdm_entanglement': 'isolated',
}
}
settings = {'ADDITIONAL_RETRIEVE_LIST': ['*.amn', '*.mmn', '*.eig']}
inputs = {
'code': code,
'parent_folder': parent_folder,
'nnkp_file': single_file,
'parameters': Dict(dict=parameters),
'settings': Dict(dict=settings),
'metadata': {
'options': get_default_options(max_num_machines, max_wallclock_seconds, with_mpi),
}
}
launch.launch_process(CalculationFactory('quantumespresso.pw2wannier90'), daemon, **inputs)
def validate_inputs(self):
"""
Validate inputs that depend might depend on each other and cannot be validated by the spec. Also define
dictionary `inputs` in the context, that will contain the inputs for the calculation that will be launched
in the `run_calculation` step.
"""
self.ctx.inputs = AttributeDict({
'code':
self.inputs.code,
'qpoints':
self.inputs.qpoints,
'parent_folder':
self.inputs.parent_folder,
})
if 'parameters' in self.inputs:
self.ctx.inputs.parameters = self.inputs.parameters.get_dict()
else:
self.ctx.inputs.parameters = {}
if 'INPUTPH' not in self.ctx.inputs.parameters:
self.ctx.inputs.parameters['INPUTPH'] = {}
if 'settings' in self.inputs:
self.ctx.inputs.settings = self.inputs.settings.get_dict()
else:
self.ctx.inputs.settings = {}
if 'options' in self.inputs:
self.ctx.inputs._options = self.inputs.options.get_dict()
else:
self.ctx.inputs._options = get_default_options()
if self.inputs.only_initialization.value:
self.ctx.inputs.settings['ONLY_INITIALIZATION'] = True
def launch_workflow(code, datum, kpoints_mesh, clean_workdir, max_num_machines,
max_wallclock_seconds, with_mpi, daemon):
"""Run the `MatdynBaseWorkChain` for a previously completed `Q2rCalculation`."""
from aiida.orm import Bool
from aiida.plugins import WorkflowFactory
from aiida_quantumespresso.utils.resources import get_default_options
inputs = {
'matdyn': {
'code': code,
'kpoints': kpoints_mesh,
'force_constants': datum,
'metadata': {
'options':
get_default_options(max_num_machines, max_wallclock_seconds,
with_mpi),
}
}
}
if clean_workdir:
inputs['clean_workdir'] = Bool(True)
launch.launch_process(WorkflowFactory('quantumespresso.matdyn.base'),
daemon, **inputs)
def launch(code, calculation, kpoints, max_num_machines, max_wallclock_seconds,
daemon, clean_workdir):
"""
Run the PhBaseWorkChain for a previously completed PwCalculation
"""
from aiida.orm.data.base import Bool
from aiida.orm.data.parameter import ParameterData
from aiida.orm.utils import WorkflowFactory
from aiida.work.launch import run, submit
from aiida_quantumespresso.utils.resources import get_default_options
PhBaseWorkChain = WorkflowFactory('quantumespresso.ph.base')
parameters = {'INPUTPH': {}}
options = get_default_options(max_num_machines, max_wallclock_seconds)
inputs = {
'code': code,
'qpoints': kpoints,
'parent_folder': calculation.out.remote_folder,
'parameters': ParameterData(dict=parameters),
'options': ParameterData(dict=options),
}
if clean_workdir:
inputs['clean_workdir'] = Bool(True)
if daemon:
workchain = submit(PhBaseWorkChain, **inputs)
click.echo('Submitted {}<{}> to the daemon'.format(
PhBaseWorkChain.__name__, workchain.pk))
else:
run(PhBaseWorkChain, **inputs)
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 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 launch(
code, parent_calc, kpoints, max_num_machines, max_wallclock_seconds, daemon):
"""
Run the MatdynBaseWorkChain for a previously completed Q2rCalculation
"""
from aiida.orm.data.parameter import ParameterData
from aiida.orm.utils import CalculationFactory, WorkflowFactory
from aiida.work.run import run, submit
from aiida_quantumespresso.utils.resources import get_default_options
MatdynBaseWorkChain = WorkflowFactory('quantumespresso.matdyn.base')
options = get_default_options(max_num_machines, max_wallclock_seconds)
inputs = {
'code': code,
'kpoints': kpoints,
'parent_folder': parent_calc.out.force_constants,
'options': ParameterData(dict=options),
}
if daemon:
workchain = submit(MatdynBaseWorkChain, **inputs)
click.echo('Submitted {}<{}> to the daemon'.format(MatdynBaseWorkChain.__name__, workchain.pid))
else:
run(MatdynBaseWorkChain, **inputs)
def _generate_inputs_pw():
"""Generate default inputs for a `PwCalculation."""
from aiida.orm import Dict
from aiida_quantumespresso.utils.resources import get_default_options
inputs = {
'code': fixture_code('quantumespresso.pw'),
'structure': generate_structure(),
'kpoints': generate_kpoints_mesh(2),
'parameters': Dict(dict={
'CONTROL': {
'calculation': 'scf'
},
'SYSTEM': {
'ecutrho': 240.0,
'ecutwfc': 30.0
}
}),
'pseudos': {
'Si': generate_upf_data('Si')
},
'metadata': {
'options': get_default_options()
}
}
return inputs
def launch_workflow(code, calculation, kpoints_mesh, clean_workdir,
max_num_machines, max_wallclock_seconds, with_mpi, daemon):
"""Run the `PhBaseWorkChain` for a previously completed `PwCalculation`."""
from aiida.orm import Bool, Dict
from aiida.plugins import WorkflowFactory
from aiida_quantumespresso.utils.resources import get_default_options
inputs = {
'ph': {
'code': code,
'qpoints': kpoints_mesh,
'parent_folder': calculation.outputs.remote_folder,
'parameters': Dict(dict={'INPUTPH': {}}),
'metadata': {
'options':
get_default_options(max_num_machines, max_wallclock_seconds,
with_mpi),
}
}
}
if clean_workdir:
inputs['clean_workdir'] = Bool(True)
launch.launch_process(WorkflowFactory('quantumespresso.ph.base'), daemon,
**inputs)
def launch_calculation(code, kpoints_mesh, calculation, max_num_machines,
max_wallclock_seconds, with_mpi, daemon):
"""Run a PhCalculation."""
from aiida import orm
from aiida.plugins import CalculationFactory
from aiida_quantumespresso.utils.resources import get_default_options
# Check that the parent calculation node comes from quantumespresso.pw.
# I cannot move this check into the option declaration, because CalcJobNode is not subclassed by the specific
# calculation plugins (only Process is), and there is no feature yet to filter by the associated process_type.
expected_process_type = 'aiida.calculations:quantumespresso.pw'
if calculation.process_type != expected_process_type:
raise click.BadParameter(
'The input calculation node has a process_type: {}; should be {}'.
format(calculation.process_type, expected_process_type))
parent_folder = calculation.get_outgoing(
node_class=orm.RemoteData,
link_label_filter='remote_folder').one().node
inputs = {
'code': code,
'qpoints': kpoints_mesh,
'parameters': orm.Dict(dict={'INPUTPH': {}}),
'parent_folder': parent_folder,
'metadata': {
'options':
get_default_options(max_num_machines, max_wallclock_seconds,
with_mpi),
}
}
launch.launch_process(CalculationFactory('quantumespresso.ph'), daemon,
**inputs)
def validate_inputs(self):
"""
Validate inputs that depend might depend on each other and cannot be validated by the spec. Also define
dictionary `inputs` in the context, that will contain the inputs for the calculation that will be launched
in the `run_calculation` step.
"""
self.ctx.inputs = AttributeDict({
'code':
self.inputs.code,
'parent_folder':
self.inputs.parent_folder,
})
if 'parameters' in self.inputs:
self.ctx.inputs.parameters = self.inputs.parameters.get_dict()
else:
self.ctx.inputs.parameters = {'INPUT': {}}
if 'settings' in self.inputs:
self.ctx.inputs.settings = self.inputs.settings.get_dict()
else:
self.ctx.inputs.settings = {}
if 'options' in self.inputs:
self.ctx.inputs._options = self.inputs.options.get_dict()
else:
self.ctx.inputs._options = get_default_options()
def launch_workflow(code, calculation, clean_workdir, max_num_machines,
max_wallclock_seconds, with_mpi, daemon):
"""Run the `Q2rBaseWorkChain` for a previously completed `PhCalculation`."""
from aiida.orm import Bool
from aiida.plugins import WorkflowFactory
from aiida_quantumespresso.utils.resources import get_default_options
expected_process_type = 'aiida.calculations:quantumespresso.ph'
if calculation.process_type != expected_process_type:
raise click.BadParameter(
'The input calculation node has a process_type: {}; should be {}'.
format(calculation.process_type, expected_process_type))
inputs = {
'q2r': {
'code': code,
'parent_folder': calculation.outputs.remote_folder,
'metadata': {
'options':
get_default_options(max_num_machines, max_wallclock_seconds,
with_mpi),
}
}
}
if clean_workdir:
inputs['clean_workdir'] = Bool(True)
launch.launch_process(WorkflowFactory('quantumespresso.q2r.base'), daemon,
**inputs)
def launch_workflow(code, structure, pseudo_family, kpoints_distance, ecutwfc,
ecutrho, hubbard_u, hubbard_v, hubbard_file_pk,
starting_magnetization, smearing,
automatic_parallelization, clean_workdir, max_num_machines,
max_wallclock_seconds, with_mpi, daemon):
"""Run a `PwBaseWorkChain`."""
from aiida.orm import Bool, Float, Str, Dict
from aiida.plugins import WorkflowFactory
from aiida_quantumespresso.utils.resources import get_default_options, get_automatic_parallelization_options
builder = WorkflowFactory('quantumespresso.pw.base').get_builder()
parameters = {
'SYSTEM': {
'ecutwfc': ecutwfc,
'ecutrho': ecutrho,
},
}
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))
builder.pw.code = code
builder.pw.structure = structure
builder.pw.parameters = Dict(dict=parameters)
builder.pseudo_family = Str(pseudo_family)
builder.kpoints_distance = Float(kpoints_distance)
if hubbard_file:
builder.hubbard_file = hubbard_file
if automatic_parallelization:
automatic_parallelization = get_automatic_parallelization_options(
max_num_machines, max_wallclock_seconds)
builder.automatic_parallelization = Dict(
dict=automatic_parallelization)
else:
builder.pw.metadata.options = get_default_options(
max_num_machines, max_wallclock_seconds, with_mpi)
if clean_workdir:
builder.clean_workdir = Bool(True)
launch.launch_process(builder, daemon)
def launch(code, structure, pseudo_family, kpoints, max_num_machines,
max_wallclock_seconds, daemon, automatic_parallelization,
clean_workdir, final_scf, group):
"""
Run the PwRelaxWorkChain for a given input structure
"""
from aiida.orm.data.base import Bool, Str
from aiida.orm.data.parameter import ParameterData
from aiida.orm.utils import WorkflowFactory
from aiida.work.run import run, submit
from aiida_quantumespresso.utils.resources import get_default_options
PwRelaxWorkChain = WorkflowFactory('quantumespresso.pw.relax')
parameters = {
'SYSTEM': {
'ecutwfc': 30.,
'ecutrho': 240.,
},
}
inputs = {
'code': code,
'structure': structure,
'pseudo_family': Str(pseudo_family),
'kpoints': kpoints,
'parameters': ParameterData(dict=parameters),
}
if automatic_parallelization:
parallelization = {
'max_num_machines': max_num_machines,
'target_time_seconds': 0.5 * max_wallclock_seconds,
'max_wallclock_seconds': max_wallclock_seconds
}
inputs['automatic_parallelization'] = ParameterData(
dict=parallelization)
else:
options = get_default_options(max_num_machines, max_wallclock_seconds)
inputs['options'] = ParameterData(dict=options)
if clean_workdir:
inputs['clean_workdir'] = Bool(True)
if final_scf:
inputs['final_scf'] = Bool(True)
if group:
inputs['group'] = Str(group)
if daemon:
workchain = submit(PwRelaxWorkChain, **inputs)
click.echo('Submitted {}<{}> to the daemon'.format(
PwRelaxWorkChain.__name__, workchain.pid))
else:
run(PwRelaxWorkChain, **inputs)
def launch(code, structure, pseudo_family, kpoints, max_num_machines,
max_wallclock_seconds, daemon, mode):
"""
Run a PwCalculation for a given input structure
"""
from aiida.orm import load_node
from aiida.orm.data.parameter import ParameterData
from aiida.orm.data.upf import get_pseudos_from_structure
from aiida.orm.utils import CalculationFactory
from aiida.work.run import run, submit
from aiida_quantumespresso.utils.resources import get_default_options
PwCalculation = CalculationFactory('quantumespresso.pw')
parameters = {
'CONTROL': {
'calculation': mode,
},
'SYSTEM': {
'ecutwfc': 30.,
'ecutrho': 240.,
},
}
inputs = {
'code': code,
'structure': structure,
'pseudo': get_pseudos_from_structure(structure, pseudo_family),
'kpoints': kpoints,
'parameters': ParameterData(dict=parameters),
'settings': ParameterData(dict={}),
'_options': get_default_options(max_num_machines,
max_wallclock_seconds),
}
process = PwCalculation.process()
if daemon:
calculation = submit(process, **inputs)
click.echo('Submitted {}<{}> to the daemon'.format(
PwCalculation.__name__, calculation.pid))
else:
click.echo('Running a PwCalculation in the {} mode... '.format(mode))
results, pk = run(process, _return_pid=True, **inputs)
calculation = load_node(pk)
click.echo('PwCalculation<{}> terminated with state: {}'.format(
pk, calculation.get_state()))
click.echo('\n{link:25s} {node}'.format(link='Output link',
node='Node pk and type'))
click.echo('{s}'.format(s='-' * 60))
for link, node in sorted(calculation.get_outputs(also_labels=True)):
click.echo('{:25s} <{}> {}'.format(link, node.pk,
node.__class__.__name__))
def launch(code, calculation, kpoints, max_num_machines, max_wallclock_seconds,
daemon):
"""
Run a HpCalculation for a previously completed PwCalculation
"""
from aiida.orm import load_node
from aiida.orm.data.parameter import ParameterData
from aiida.orm.data.upf import get_pseudos_from_structure
from aiida.orm.utils import CalculationFactory
from aiida.work.launch import run_get_pid, submit
from aiida_quantumespresso.utils.resources import get_default_options
from aiida_quantumespresso_hp.utils.validation import validate_parent_calculation
HpCalculation = CalculationFactory('quantumespresso.hp')
try:
validate_parent_calculation(calculation)
except ValueError as exception:
raise click.BadParameter(
'invalid parent calculation: {}'.format(exception))
parameters = {'INPUTHP': {}}
inputs = {
'code': code,
'qpoints': kpoints,
'parameters': ParameterData(dict=parameters),
'parent_folder': calculation.out.remote_folder,
'options': get_default_options(max_num_machines,
max_wallclock_seconds),
}
click.echo('Running a hp.x calculation ... ')
process = HpCalculation.process()
if daemon:
calculation = submit(process, **inputs)
pk = calculation.pk
click.echo('Submitted {}<{}> to the daemon'.format(
HpCalculation.__name__, calculation.pk))
else:
results, pk = run_get_pid(process, **inputs)
calculation = load_node(pk)
click.echo('HpCalculation<{}> terminated with state: {}'.format(
pk, calculation.get_state()))
click.echo('\n{link:25s} {node}'.format(link='Output link',
node='Node pk and type'))
click.echo('{s}'.format(s='-' * 60))
for link, node in sorted(calculation.get_outputs(also_labels=True)):
click.echo('{:25s} <{}> {}'.format(link, node.pk,
node.__class__.__name__))
def inputs(fixture_code):
"""Fixture: inputs for Z2packBaseWorkChain."""
inputs = {
'code': fixture_code('z2pack.z2pack'),
'pw_code': fixture_code('quantumespresso.pw'),
'overlap_code': fixture_code('quantumespresso.pw2wannier90'),
'wannier90_code': fixture_code('wannier90.wannier90'),
'metadata': {
'options': get_default_options()
}
}
return inputs
def _generate_inputs_q2r():
"""Generate default inputs for a `Q2rCalculation."""
from aiida_quantumespresso.utils.resources import get_default_options
inputs = {
'code': fixture_code('quantumespresso.q2r'),
'parent_folder': generate_remote_data(fixture_localhost, fixture_sandbox.abspath, 'quantumespresso.ph'),
'metadata': {
'options': get_default_options()
}
}
return inputs
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 _generate_inputs_matdyn():
"""Generate default inputs for a `MatdynCalculation."""
from aiida_quantumespresso.utils.resources import get_default_options
inputs = {
'code': fixture_code('quantumespresso.matdyn'),
'force_constants': generate_force_constants_data,
'kpoints': generate_kpoints_mesh(2),
'metadata': {
'options': get_default_options()
}
}
return inputs
def inputs(fixture_code, remote, parameters, settings):
"""Fixture: inputs for Z2packBaseWorkChain."""
from aiida_quantumespresso.utils.resources import get_default_options
inputs = {
'code': fixture_code('quantumespresso.pw2gw'),
'parent_folder': remote,
'parameters': orm.Dict(dict=parameters),
'settings': orm.Dict(dict=settings),
'metadata': {
'options': get_default_options()
}
}
return inputs
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 test_ph_default(fixture_database, fixture_computer_localhost,
fixture_sandbox_folder, generate_calc_job,
generate_code_localhost, generate_structure,
generate_kpoints_mesh, generate_remote_data,
file_regression):
"""Test a default `PhCalculation`."""
entry_point_name = 'quantumespresso.ph'
parent_entry_point = 'quantumespresso.pw'
remote_path = fixture_sandbox_folder.abspath
inputs = {
'code':
generate_code_localhost(entry_point_name, fixture_computer_localhost),
'parent_folder':
generate_remote_data(fixture_computer_localhost, remote_path,
parent_entry_point),
'qpoints':
generate_kpoints_mesh(2),
'parameters':
orm.Dict(dict={'INPUTPH': {}}),
'metadata': {
'options': get_default_options()
}
}
calc_info = generate_calc_job(fixture_sandbox_folder, entry_point_name,
inputs)
cmdline_params = ['-in', 'aiida.in']
retrieve_list = [
'./out/_ph0/aiida.phsave/tensors.xml', 'DYN_MAT', 'aiida.out'
]
local_copy_list = []
# Check the attributes of the returned `CalcInfo`
assert isinstance(calc_info, datastructures.CalcInfo)
assert sorted(
calc_info.codes_info[0].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.remote_symlink_list) == sorted([])
with fixture_sandbox_folder.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_folder.get_content_list()) == sorted(
['DYN_MAT', 'aiida.in'])
file_regression.check(input_written, encoding='utf-8', extension='.in')
def launch_calculation(code, datum, kpoints_mesh, max_num_machines, max_wallclock_seconds, with_mpi, daemon):
"""Run a MatdynCalculation."""
from aiida.plugins import CalculationFactory
from aiida_quantumespresso.utils.resources import get_default_options
inputs = {
'code': code,
'kpoints': kpoints_mesh,
'force_constants': datum,
'metadata': {
'options': get_default_options(max_num_machines, max_wallclock_seconds, with_mpi),
}
}
launch.launch_process(CalculationFactory('quantumespresso.matdyn'), daemon, **inputs)
def submit_workchain(structure):
print("running dft band structure calculation for {}".format(
structure.get_formula()))
from aiida_quantumespresso.utils.resources import get_default_options
# Submit the DFT bands workchain
dft_workchain = submit(
PwBandStructureWorkChain,
code=code,
structure=structure,
#protocol=orm.Dict(dict={'name': 'theos-ht-1.0'}),
protocol=orm.Dict(dict={'name': 'testing'}),
options=orm.Dict(dict=get_default_options(
max_wallclock_seconds=3600 * 5, with_mpi=True)))
return dft_workchain
def _generate_inputs_ph():
"""Generate default inputs for a `PhCalculation."""
from aiida.orm import Dict
from aiida_quantumespresso.utils.resources import get_default_options
inputs = {
'code': fixture_code('quantumespresso.matdyn'),
'parent_folder': generate_remote_data(fixture_localhost, fixture_sandbox.abspath, 'quantumespresso.pw'),
'qpoints': generate_kpoints_mesh(2),
'parameters': Dict(dict={'INPUTPH': {}}),
'metadata': {
'options': get_default_options()
}
}
return inputs
def test_pw_default(aiida_profile, fixture_localhost, fixture_sandbox,
fixture_code, generate_calc_job, generate_remote_data,
tmpdir, file_regression):
"""Test a default `Pw2gwCalculation`."""
entry_point_name = 'quantumespresso.pw2gw'
parameters = {
'INPUTPP': {
'qplda': False,
'vxcdiag': False,
'vkb': False,
'Emin': 0.0,
'Emax': 15.0,
'DeltaE': 0.001,
}
}
parent = generate_remote_data(
fixture_localhost,
str(tmpdir),
'quantumespresso.pw',
)
inputs = {
'code': fixture_code(entry_point_name),
'parameters': orm.Dict(dict=parameters),
'parent_folder': parent,
'metadata': {
'options': get_default_options()
}
}
calc_info = generate_calc_job(fixture_sandbox, entry_point_name, inputs)
retrieve_list = [
'aiida.out', 'epsX.dat', 'epsY.dat', 'epsZ.dat', 'epsTOT.dat'
]
assert isinstance(calc_info, datastructures.CalcInfo)
assert sorted(calc_info.retrieve_list) == sorted(retrieve_list)
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'])
file_regression.check(input_written, encoding='utf-8', extension='.in')