def sssp(aiida_profile, generate_upf_data):
"""Create an SSSP pseudo potential family from scratch."""
from aiida.common.constants import elements
from aiida.plugins import GroupFactory
aiida_profile.reset_db()
SsspFamily = GroupFactory('pseudo.family.sssp')
cutoffs = {}
stringency = 'standard'
with tempfile.TemporaryDirectory() as dirpath:
for values in elements.values():
element = values['symbol']
upf = generate_upf_data(element)
filename = os.path.join(dirpath, f'{element}.upf')
with open(filename, 'w+b') as handle:
with upf.open(mode='rb') as source:
handle.write(source.read())
handle.flush()
cutoffs[element] = {
'cutoff_wfc': 30.0,
'cutoff_rho': 240.0,
}
label = 'SSSP/1.1/PBE/efficiency'
family = SsspFamily.create_from_folder(dirpath, label)
family.set_cutoffs(cutoffs, stringency, unit='Ry')
return family
def test_pseudopotential_group_get_structure():
"""Test get_pseudos from structure"""
Pseudo = DataFactory("gaussian.pseudo")
PseudopotentialGroup = GroupFactory("gaussian.pseudo")
pseudogroup, created = PseudopotentialGroup.objects.get_or_create("test")
assert created
pseudogroup.store()
with open(TEST_DIR.joinpath("GTH_POTENTIALS.LiH"), "r") as fhandle:
pseudos = Pseudo.from_cp2k(fhandle)
pseudogroup.add_nodes([pseudo.store() for pseudo in pseudos])
StructureData = DataFactory("structure")
structure = StructureData(cell=[[4.796302, 0, 0], [0, 4.796302, 0],
[0, 0, 4.796302]],
pbc=True)
structure.append_atom(position=(0.000, 0.000, 0.000), symbols="Li")
structure.append_atom(position=(0.500, 0.500, 0.000), symbols="Li")
structure.append_atom(position=(0.500, 0.000, 0.500), symbols="Li")
structure.append_atom(position=(0.000, 0.500, 0.500), symbols="Li")
structure.append_atom(position=(0.000, 0.500, 0.000), symbols="H")
structure.append_atom(position=(0.000, 0.000, 0.500), symbols="H")
structure.append_atom(position=(0.500, 0.000, 0.000), symbols="H")
structure.append_atom(position=(0.500, 0.500, 0.500), symbols="H")
retrieved_pseudos = pseudogroup.get_pseudos(structure=structure)
assert retrieved_pseudos == {
"Li": [p for p in pseudos if p.element == "Li"],
"H": [p for p in pseudos if p.element == "H"],
}
def convert(self, value, _, __):
"""Convert the entry point name to the corresponding class.
:param value: entry point name that should correspond to subclass of `PseudoPotentialFamily` group plugin
:return: the `PseudoPotentialFamily` subclass
:raises: `click.BadParameter` if the entry point cannot be loaded or is not subclass of `PseudoPotentialFamily`
"""
from aiida.common import exceptions
from aiida.plugins import GroupFactory
from aiida_pseudo.groups.family import PseudoPotentialFamily
try:
family_type = GroupFactory(value)
except exceptions.EntryPointError as exception:
raise click.BadParameter(
f'`{value}` is not an existing group plugin.') from exception
if not issubclass(family_type, PseudoPotentialFamily):
raise click.BadParameter(
f'`{value}` entry point is not a subclass of `PseudoPotentialFamily`.'
)
PseudoPotentialFamily.entry_point = value
return family_type
def sssp(generate_upf_data):
"""Create an SSSP pseudo potential family from scratch."""
from aiida.plugins import GroupFactory
SsspFamily = GroupFactory('pseudo.family.sssp') # pylint: disable=invalid-name
label = 'SSSP/1.1/PBE/efficiency'
try:
family = SsspFamily.objects.get(label=label)
except exceptions.NotExistent:
pass
else:
return family
cutoffs_dict = {'normal': {}}
with tempfile.TemporaryDirectory() as dirpath:
for values in elements.values():
element = values['symbol']
upf = generate_upf_data(element)
filename = os.path.join(dirpath, f'{element}.upf')
with open(filename, 'w+b') as handle:
with upf.open(mode='rb') as source:
handle.write(source.read())
handle.flush()
cutoffs_dict['normal'][element] = {'cutoff_wfc': 30., 'cutoff_rho': 240.}
family = SsspFamily.create_from_folder(dirpath, label)
for stringency, cutoffs in cutoffs_dict.items():
family.set_cutoffs(cutoffs, stringency, unit='Ry')
return family
def pseudo_dojo(aiida_profile, generate_psp8_data):
"""Create an PseudoDojo pseudo potential family from scratch."""
from aiida.common.constants import elements
from aiida.plugins import GroupFactory, DataFactory
aiida_profile.reset_db()
PseudoDojo = GroupFactory('pseudo.family.pseudo_dojo') # pylint: disable=invalid-name
Psp8Data = DataFactory('pseudo.psp8')
cutoffs = {}
stringency = 'standard'
with tempfile.TemporaryDirectory() as dirpath:
for values in elements.values():
element = values['symbol']
psp8 = generate_psp8_data(element)
filename = os.path.join(dirpath, f'{element}.psp8')
with open(filename, 'w+b') as handle:
with psp8.open(mode='rb') as source:
handle.write(source.read())
handle.flush()
cutoffs[element] = {
'cutoff_wfc': 36.0,
'cutoff_rho': 144.0,
}
label = 'PseudoDojo/0.4/PBE/SR/standard/psp8'
family = PseudoDojo.create_from_folder(dirpath, label, pseudo_type=Psp8Data)
family.set_cutoffs(cutoffs, stringency, unit='Ry')
return family
def group_path_ls(path, type_string, recursive, as_table, no_virtual,
with_description, no_warn):
# pylint: disable=too-many-arguments,too-many-branches
"""Show a list of existing group paths."""
from aiida.plugins import GroupFactory
from aiida.tools.groups.paths import GroupPath, InvalidPath
try:
path = GroupPath(path or '',
cls=GroupFactory(type_string),
warn_invalid_child=not no_warn)
except InvalidPath as err:
echo.echo_critical(str(err))
if recursive:
children = path.walk()
else:
children = path.children
if as_table or with_description:
from tabulate import tabulate
headers = ['Path', 'Sub-Groups']
if with_description:
headers.append('Description')
rows = []
for child in sorted(children):
if no_virtual and child.is_virtual:
continue
row = [
child.path if child.is_virtual else click.style(child.path,
bold=True),
len([c for c in child.walk() if not c.is_virtual])
]
if with_description:
row.append(
'-' if child.is_virtual else child.get_group().description)
rows.append(row)
echo.echo(tabulate(rows, headers=headers))
else:
for child in sorted(children):
if no_virtual and child.is_virtual:
continue
echo.echo(child.path, bold=not child.is_virtual)
def test_pseudopotential_group_get():
Pseudo = DataFactory("gaussian.pseudo")
PseudopotentialGroup = GroupFactory("gaussian.pseudo")
pseudogroup, created = PseudopotentialGroup.objects.get_or_create("test")
assert created
pseudogroup.store()
with open(TEST_DIR.joinpath("GTH_POTENTIALS.LiH"), "r") as fhandle:
pseudos = Pseudo.from_cp2k(fhandle)
pseudogroup.add_nodes([pseudo.store() for pseudo in pseudos])
retrieved_pseudos = pseudogroup.get_pseudos(elements=["Li", "H"])
assert retrieved_pseudos == {
"Li": [p for p in pseudos if p.element == "Li"],
"H": [p for p in pseudos if p.element == "H"],
}
def convert(self, value, _, __):
"""Convert the entry point name to the corresponding class.
:param value: entry point name that should correspond to subclass of `BasisSet` group plugin
:return: the `BasisSet` subclass
:raises: `click.BadParameter` if the entry point cannot be loaded or is not subclass of `BasisSet`
"""
from aiida.common import exceptions
from aiida.plugins import GroupFactory
from aiida_basis.groups.set import BasisSet
try:
basis_set_type = GroupFactory(value)
except exceptions.EntryPointError as exception:
raise click.BadParameter(f'`{value}` is not an existing group plugin.') from exception
if not issubclass(basis_set_type, BasisSet):
raise click.BadParameter(f'`{value}` entry point is not a subclass of `BasisSet`.')
BasisSet.entry_point = value
return basis_set_type
# -*- coding: utf-8 -*-
"""Utilities to manipulate the workflow input protocols."""
import pathlib
from typing import Optional, Union
import yaml
from aiida.plugins import DataFactory, GroupFactory
StructureData = DataFactory('structure')
PseudoPotentialFamily = GroupFactory('pseudo.family')
class ProtocolMixin:
"""Utility class for processes to build input mappings for a given protocol based on a YAML configuration file."""
@classmethod
def get_protocol_filepath(cls) -> pathlib.Path:
"""Return the ``pathlib.Path`` to the ``.yaml`` file that defines the protocols."""
raise NotImplementedError
@classmethod
def get_default_protocol(cls) -> str:
"""Return the default protocol for a given workflow class.
:param cls: the workflow class.
:return: the default protocol.
"""
return cls._load_protocol_file()['default_protocol']
@classmethod
def get_available_protocols(cls) -> dict:
"""Return the available protocols for a given workflow class.
from aiida.common.lang import type_check
from aiida.engine import ToContext, if_, while_, BaseRestartWorkChain, process_handler, ProcessHandlerReport, ExitCode
from aiida.plugins import CalculationFactory, GroupFactory
from aiida_quantumespresso.calculations.functions.create_kpoints_from_distance import create_kpoints_from_distance
from aiida_quantumespresso.common.types import ElectronicType, SpinType
from aiida_quantumespresso.utils.defaults.calculation import pw as qe_defaults
from aiida_quantumespresso.utils.mapping import update_mapping, prepare_process_inputs
from aiida_quantumespresso.utils.pseudopotential import validate_and_prepare_pseudos_inputs
from aiida_quantumespresso.utils.resources import get_default_options, get_pw_parallelization_parameters
from aiida_quantumespresso.utils.resources import cmdline_remove_npools, create_scheduler_resources
from ..protocols.utils import ProtocolMixin
PwCalculation = CalculationFactory('quantumespresso.pw')
SsspFamily = GroupFactory('pseudo.family.sssp')
PseudoDojoFamily = GroupFactory('pseudo.family.pseudo_dojo')
CutoffsPseudoPotentialFamily = GroupFactory('pseudo.family.cutoffs')
def validate_pseudo_family(value, _):
"""Validate the `pseudo_family` input."""
if value:
import warnings
from aiida.common.warnings import AiidaDeprecationWarning
warnings.warn(
'`pseudo_family` is deprecated, use `pw.pseudos` instead.',
AiidaDeprecationWarning)
class PwBaseWorkChain(ProtocolMixin, BaseRestartWorkChain):
from aiida.common.lang import type_check
from aiida.engine import ToContext, if_, while_, BaseRestartWorkChain, process_handler, ProcessHandlerReport, ExitCode
from aiida.plugins import CalculationFactory, GroupFactory
from aiida_quantumespresso.calculations.functions.create_kpoints_from_distance import create_kpoints_from_distance
from aiida_quantumespresso.common.types import ElectronicType, SpinType
from aiida_quantumespresso.utils.defaults.calculation import pw as qe_defaults
from aiida_quantumespresso.utils.mapping import update_mapping, prepare_process_inputs
from aiida_quantumespresso.utils.pseudopotential import validate_and_prepare_pseudos_inputs
from aiida_quantumespresso.utils.resources import get_default_options, get_pw_parallelization_parameters
from aiida_quantumespresso.utils.resources import cmdline_remove_npools, create_scheduler_resources
from ..protocols.utils import ProtocolMixin
PwCalculation = CalculationFactory('quantumespresso.pw')
SsspFamily = GroupFactory('pseudo.family.sssp')
PseudoDojoFamily = GroupFactory('pseudo.family.pseudo_dojo')
def validate_pseudo_family(value, _):
"""Validate the `pseudo_family` input."""
if value:
import warnings
from aiida.common.warnings import AiidaDeprecationWarning
warnings.warn(
'`pseudo_family` is deprecated, use `pw.pseudos` instead.',
AiidaDeprecationWarning)
class PwBaseWorkChain(ProtocolMixin, BaseRestartWorkChain):
"""Workchain to run a Quantum ESPRESSO pw.x calculation with automated error handling and restarts."""
def test_create_basisset_group():
BasisSetGroup = GroupFactory("gaussian.basisset")
basisgroup, created = BasisSetGroup.objects.get_or_create("test")
assert created
basisgroup.store()
def test_create_pseudopotential_group():
PseudopotentialGroup = GroupFactory("gaussian.pseudo")
pseudogroup, created = PseudopotentialGroup.objects.get_or_create("test")
assert created
pseudogroup.store()