def convert(self, value, param, ctx):
"""Attempt to interpret the value as a file first and if that fails try to load as a node."""
from aiida.orm import StructureData, QueryBuilder
try:
filepath = pathlib.Path(
__file__
).parent.parent / 'common' / 'data' / DEFAULT_STRUCTURES_MAPPING[
value]
except KeyError:
try:
return types.DataParamType(
sub_classes=('aiida.data:structure', )).convert(
value, param, ctx)
except click.BadParameter:
filepath = value
try:
import ase.io
except ImportError as exception:
raise click.BadParameter(
f'failed to load a structure with identifier `{value}`.\n'
'Cannot parse from file because `ase` is not installed.'
) from exception
try:
filepath = click.Path(exists=True,
dir_okay=False,
resolve_path=True).convert(
filepath, param, ctx)
except click.BadParameter as exception:
raise click.BadParameter(
f'failed to load a structure with identifier `{value}` and it can also not be resolved as a file.'
) from exception
try:
structure = StructureData(ase=ase.io.read(filepath))
except Exception as exception: # pylint: disable=broad-except
raise click.BadParameter(
f'file `{value}` could not be parsed into a `StructureData`: {exception}'
) from exception
duplicate = QueryBuilder().append(StructureData,
filters={
'extras._aiida_hash':
structure._get_hash()
}).first() # pylint: disable=protected-access
if duplicate:
return duplicate[0]
return structure
def convert(self, value, param, ctx):
is_path = False
# Alternative one could check if int or uuid
# aiida allows also for shorten uuids
from aiida.orm import StructureData, QueryBuilder
try:
structure = types.DataParamType(
sub_classes=('aiida.data:structure', )).convert(
value, param, ctx)
except (NotExistent, click.exceptions.BadParameter) as er:
echo.echo(f'Tried to load node, could not fine one for {value}. '
'I will further check if it is a filepath.')
is_path = True
if is_path:
# If it is a path to a file try to convert the structure
pathtype = click.Path(exists=True,
dir_okay=False,
resolve_path=True)
filename = pathtype.convert(value, param, ctx)
try:
import ase.io
except ImportError:
echo.echo_critical(
'You have not installed the package ase. \nYou can install it with: pip install ase'
)
try:
asecell = ase.io.read(filename)
structure = StructureData(ase=asecell)
except ValueError as err:
echo.echo_critical(str(err))
# do not store structure, since this option is for calculation and workflow
# input, which will store the structure anyway.
# do not store again if structure is already there.
duplicate = QueryBuilder().append(StructureData,
filters={
'extras._aiida_hash':
structure._get_hash()
}).first() # pylint: disable=protected-access
if duplicate:
return duplicate[0]
return structure
from aiida.cmdline.params import types
from aiida.cmdline.params.arguments.overridable import OverridableArgument
CALCULATION = OverridableArgument('calculation', type=types.CalculationParamType())
CALCULATIONS = OverridableArgument('calculations', nargs=-1, type=types.CalculationParamType())
CODE = OverridableArgument('code', type=types.CodeParamType())
CODES = OverridableArgument('codes', nargs=-1, type=types.CodeParamType())
COMPUTER = OverridableArgument('computer', type=types.ComputerParamType())
COMPUTERS = OverridableArgument('computers', nargs=-1, type=types.ComputerParamType())
DATUM = OverridableArgument('datum', type=types.DataParamType())
DATA = OverridableArgument('data', nargs=-1, type=types.DataParamType())
GROUP = OverridableArgument('group', type=types.GroupParamType())
GROUPS = OverridableArgument('groups', nargs=-1, type=types.GroupParamType())
NODE = OverridableArgument('node', type=types.NodeParamType())
NODES = OverridableArgument('nodes', nargs=-1, type=types.NodeParamType())
PROCESS = OverridableArgument('process', type=types.CalculationParamType())
PROCESSES = OverridableArgument('processes', nargs=-1, type=types.CalculationParamType())
"""Command line scripts to launch a `MatdynCalculation` for testing and demonstration purposes."""
from __future__ import absolute_import
from aiida.cmdline.params import options, types
from aiida.cmdline.utils import decorators
from ..utils import launch
from ..utils import options as options_qe
from . import cmd_launch
@cmd_launch.command('matdyn')
@options.CODE(required=True, type=types.CodeParamType(entry_point='quantumespresso.matdyn'))
@options.DATUM(
required=True,
type=types.DataParamType(sub_classes=('aiida.data:quantumespresso.force_constants',)),
help='A ForceConstantsData node produced by a `Q2rCalculation`'
)
@options_qe.KPOINTS_MESH(default=[1, 1, 1])
@options_qe.MAX_NUM_MACHINES()
@options_qe.MAX_WALLCLOCK_SECONDS()
@options_qe.WITH_MPI()
@options_qe.DAEMON()
@decorators.with_dbenv()
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,
if isinstance(value, list):
entry[i] = ','.join(value)
for i in range(len(entry), len(LIST_PROJECT_HEADERS)):
entry.append(None)
counter += 1
struct_list_data.extend(entry_list)
if raw:
echo.echo(tabulate(struct_list_data, tablefmt='plain'))
else:
echo.echo(tabulate(struct_list_data, headers='firstrow'))
echo.echo('\nTotal results: {}\n'.format(counter))
@structure.command('show')
@arguments.DATA(
type=types.DataParamType(sub_classes=('aiida.data:structure', )))
@options.VISUALIZATION_FORMAT(type=click.Choice(VISUALIZATION_FORMATS),
default='ase')
@decorators.with_dbenv()
def structure_show(data, fmt):
"""Visualize StructureData objects."""
try:
show_function = getattr(cmd_show, '_show_{}'.format(fmt))
except AttributeError:
echo.echo_critical(
'visualization format {} is not supported'.format(fmt))
show_function(fmt, data)
@structure.command('export')
from click_spinner import spinner as cli_spinner
from jsonextended import edict
import tabulate
from aiida_crystal17.cmndline import options
@verdi.group("crystal17.basis")
def basisset():
"""Commandline interface for working with Crystal Basis Set Data."""
@basisset.command()
@click.argument(
"node",
type=types.DataParamType(sub_classes=("aiida.data:crystal17.basisset", )))
@click.option("--content",
"-c",
is_flag=True,
help="include full basis content")
@decorators.with_dbenv()
def show(node, content):
"""Show the contents of a basis set node."""
edict.pprint(node.metadata, depth=None, print_func=click.echo)
if content:
click.echo("---")
click.echo(node.content)
def try_grab_description(ctx, param, value):
"""
# Copyright (c), The AiiDA team. All rights reserved. #
# This file is part of the AiiDA code. #
# #
# The code is hosted on GitHub at https://github.com/aiidateam/aiida-core #
# For further information on the license, see the LICENSE.txt file #
# For further information please visit http://www.aiida.net #
###########################################################################
"""`verdi data array` command."""
from aiida.cmdline.commands.cmd_data import verdi_data
from aiida.cmdline.params import arguments, options, types
@verdi_data.group('array')
def array():
"""Manipulate ArrayData objects (numpy arrays)."""
@array.command('show')
@arguments.DATA(type=types.DataParamType(sub_classes=('aiida.data:array', )))
@options.DICT_FORMAT()
def array_show(data, fmt):
"""Visualize ArrayData objects."""
from aiida.cmdline.utils.echo import echo_dictionary
for node in data:
the_dict = {}
for arrayname in node.get_arraynames():
the_dict[arrayname] = node.get_array(arrayname).tolist()
echo_dictionary(the_dict, fmt)
if isinstance(value, list):
entry[i] = ','.join(value)
for i in range(len(entry), len(LIST_PROJECT_HEADERS)):
entry.append(None)
counter += 1
bands_list_data.extend(entry_list)
if raw:
echo.echo(tabulate(bands_list_data, tablefmt='plain'))
else:
echo.echo(tabulate(bands_list_data, headers='firstrow'))
echo.echo(f'\nTotal results: {counter}\n')
@bands.command('show')
@arguments.DATA(
type=types.DataParamType(sub_classes=('aiida.data:array.bands', )))
@options.VISUALIZATION_FORMAT(type=click.Choice(VISUALIZATION_FORMATS),
default='xmgrace')
@decorators.with_dbenv()
def bands_show(data, fmt):
"""Visualize BandsData objects."""
try:
show_function = getattr(cmd_show, f'_show_{fmt}')
except AttributeError:
echo.echo_critical(f'visualization format {fmt} is not supported')
show_function(fmt, data)
@bands.command('export')
@arguments.DATUM(
type=types.CodeParamType(), cls=MultipleValueOption,
help='One or multiple codes identified by their ID, UUID or label.')
COMPUTER = OverridableOption(
'-Y', '--computer', 'computer',
type=types.ComputerParamType(),
help='A single computer identified by its ID, UUID or label.')
COMPUTERS = OverridableOption(
'-Y', '--computers', 'computers',
type=types.ComputerParamType(), cls=MultipleValueOption,
help='One or multiple computers identified by their ID, UUID or label.')
DATUM = OverridableOption(
'-D', '--datum', 'datum',
type=types.DataParamType(),
help='A single datum identified by its ID, UUID or label.')
DATA = OverridableOption(
'-D', '--data', 'data',
type=types.DataParamType(), cls=MultipleValueOption,
help='One or multiple data identified by their ID, UUID or label.')
GROUP = OverridableOption(
'-G', '--group', 'group',
type=types.GroupParamType(),
help='A single group identified by its ID, UUID or name.')
GROUPS = OverridableOption(
'-G', '--groups', 'groups',
type=types.GroupParamType(), cls=MultipleValueOption,
# This file is part of the AiiDA code. #
# #
# The code is hosted on GitHub at https://github.com/aiidateam/aiida-core #
# For further information on the license, see the LICENSE.txt file #
# For further information please visit http://www.aiida.net #
###########################################################################
"""`verdi data singlefile` command."""
from aiida.cmdline.commands.cmd_data import verdi_data
from aiida.cmdline.params import arguments, types
from aiida.cmdline.utils import decorators, echo
@verdi_data.group('singlefile')
def singlefile():
"""Work with SinglefileData nodes."""
@singlefile.command('content')
@arguments.DATUM(
type=types.DataParamType(sub_classes=('aiida.data:singlefile', )))
@decorators.with_dbenv()
def singlefile_content(datum):
"""Show the content of the file."""
try:
echo.echo(datum.get_content())
except (IOError, OSError) as exception:
echo.echo_critical(
'could not read the content for SinglefileData<{}>: {}'.format(
datum.pk, str(exception)))
# -*- coding: utf-8 -*-
"""Pre-defined overridable options for commonly used command line interface parameters."""
import click
from aiida.cmdline.params import types
from aiida.cmdline.params.options import OverridableOption
from . import validate
STRUCTURE = OverridableOption(
'-s',
'--structure',
type=types.DataParamType(sub_classes=('aiida.data:structure', )),
help='StructureData node.')
PSEUDO_FAMILY = OverridableOption('-p',
'--pseudo-family',
'pseudo_family',
type=click.STRING,
help='Pseudo potential family name.')
KPOINTS_DISTANCE = OverridableOption(
'-K',
'--kpoints-distance',
type=click.FLOAT,
default=0.5,
show_default=True,
help=
'The minimal distance between k-points in reciprocal space in inverse Ångström.'
)
help="Title of the publication."),
click.option('--author-name',
type=click.STRING,
default=None,
help="Full name of the publication author."),
click.option('--author-email',
type=click.STRING,
default=None,
help="E-mail address of the publication author."),
click.option('--url',
type=click.STRING,
default=None,
help="URL of the deposition API."),
click.option(
'--parameters',
type=types.DataParamType(sub_classes=('aiida.data:dict', )),
help=
"Dict to be exported alongside the to be deposited Data node. By default, if "
"the node originates from a calculation with single Dict in the output, aforementioned "
"Dict is picked automatically. Instead, the option is used in the case the calculation produces "
"more than a single instance of Dict."),
click.option(
'--replace',
type=click.INT,
default=None,
help="ID of the structure to be redeposited (replaced), if any."),
click.option(
'-m',
'--message',
type=click.STRING,
default=None,
# yapf: disable
from __future__ import absolute_import
import click
from aiida.cmdline.params import options, types
from aiida.cmdline.utils import decorators
from ..utils import launch, validate
from . import cmd_launch
@cmd_launch.command('cod-tools')
@options.CODE(required=True, help='Code that references a supported cod-tools script.')
@click.option(
'-N', '--node', 'cif', type=types.DataParamType(sub_classes=('aiida.data:cif',)), required=True,
help='CifData node to use as input.')
@click.option('-p', '--parameters', type=click.STRING, help='Command line parameters.')
@click.option(
'-d', '--daemon', is_flag=True, default=False, show_default=True, callback=validate.validate_daemon_dry_run,
help='Submit the process to the daemon instead of running it locally.')
@options.DRY_RUN(callback=validate.validate_daemon_dry_run)
@decorators.with_dbenv()
def launch_calculation(code, cif, parameters, daemon, dry_run):
"""Run any cod-tools calculation for the given ``CifData`` node.
The ``-p/--parameters`` option takes a single string with any command line parameters that you want to be passed
to the calculation, and by extension the cod-tools script. Example::
aiida-codtools calculation launch cod-tools -X cif-filter -N 95 -p '--use-c-parser --authors "Jane Doe"'
'-S', '--cif-select', required=True, type=types.CodeParamType(entry_point='codtools.cif_select'),
help='Code that references the codtools cif_select script.')
@click.option(
'-r', '--group-cif-raw', required=False, type=types.GroupParamType(),
help='Group with the raw CifData nodes to be cleaned.')
@click.option(
'-c', '--group-cif-clean', required=False, type=types.GroupParamType(),
help='Group to which to add the cleaned CifData nodes.')
@click.option(
'-s', '--group-structure', required=False, type=types.GroupParamType(),
help='Group to which to add the final StructureData nodes.')
@click.option(
'-w', '--group-workchain', required=False, type=types.GroupParamType(),
help='Group to which to add the WorkChain nodes.')
@click.option(
'-N', '--node', type=types.DataParamType(sub_classes=('aiida.data:cif',)), default=None, required=False,
help='Specify the explicit CifData node for which to run the clean workchain.')
@click.option(
'-M', '--max-entries', type=click.INT, default=None, show_default=True, required=False,
help='Maximum number of CifData entries to clean.')
@click.option(
'-f', '--skip-check', is_flag=True, default=False,
help='Skip the check whether the CifData node is an input to an already submitted workchain.')
@click.option(
'-p', '--parse-engine', type=click.Choice(['ase', 'pymatgen']), default='pymatgen', show_default=True,
help='Select the parse engine for parsing the structure from the cleaned cif if requested.')
@click.option(
'-d', '--daemon', is_flag=True, default=False, show_default=True,
help='Submit the process to the daemon instead of running it locally.')
@decorators.with_dbenv()
def launch_cif_clean(cif_filter, cif_select, group_cif_raw, group_cif_clean, group_structure, group_workchain, node,
else:
new_entry.append(elm)
entry[i] = ','.join(new_entry)
for i in range(len(entry), len(LIST_PROJECT_HEADERS)):
entry.append(None)
counter += 1
cif_list_data.extend(entry_list)
if raw:
echo.echo(tabulate(cif_list_data, tablefmt='plain'))
else:
echo.echo(tabulate(cif_list_data, headers='firstrow'))
echo.echo('\nTotal results: {}\n'.format(counter))
@cif.command('show')
@arguments.DATA(type=types.DataParamType(sub_classes=('aiida.data:cif', )))
@options.VISUALIZATION_FORMAT(type=click.Choice(VISUALIZATION_FORMATS),
default='jmol')
@decorators.with_dbenv()
def cif_show(data, fmt):
"""Visualize CifData objects."""
try:
show_function = getattr(cmd_show, '_show_{}'.format(fmt))
except AttributeError:
echo.echo_critical(
'visualization format {} is not supported'.format(fmt))
show_function(fmt, data)
@cif.command('content')
from aiida.cmdline.params.options import OverridableOption
from .defaults import get_inpgen, get_fleur, get_si_bulk_structure
from .types import StructureNodeOrFileParamType
STRUCTURE_OR_FILE = OverridableOption(
'-s',
'--structure',
type=StructureNodeOrFileParamType(),
help=
'StructureData node, given by pk or uuid or file in any for mat which will be converted.'
)
STRUCTURE = OverridableOption(
'-s',
'--structure',
type=types.DataParamType(sub_classes=('aiida.data:structure', )),
help='StructureData node, given by pk or uuid.')
FULL_PROVENANCE = OverridableOption(
'-fp',
'--full-provenance',
is_flag=True,
default=False,
show_default=True,
help=('Store the full or reduced provenance. Example with the "-as" '
'also the given file will be stored in the database together with a '
'calcfunction extracting the structure.'))
INPGEN = OverridableOption(
'-i',
'--inpgen',
if isinstance(value, list):
entry[i] = ','.join(value)
for i in range(len(entry), len(LIST_PROJECT_HEADERS)):
entry.append(None)
counter += 1
struct_list_data.extend(entry_list)
if raw:
echo.echo(tabulate(struct_list_data, tablefmt='plain'))
else:
echo.echo(tabulate(struct_list_data, headers='firstrow'))
echo.echo('\nTotal results: {}\n'.format(counter))
@trajectory.command('show')
@arguments.DATA(
type=types.DataParamType(sub_classes=('aiida.data:array.trajectory', )))
@options.VISUALIZATION_FORMAT(type=click.Choice(VISUALIZATION_FORMATS),
default='jmol')
@show_options
@decorators.with_dbenv()
def trajectory_show(data, fmt):
"""Visualize a trajectory."""
try:
show_function = getattr(cmd_show, '_show_{}'.format(fmt))
except AttributeError:
echo.echo_critical(
'visualization format {} is not supported'.format(fmt))
show_function(fmt, data)
# -*- coding: utf-8 -*-
###########################################################################
# Copyright (c), The AiiDA team. All rights reserved. #
# This file is part of the AiiDA code. #
# #
# The code is hosted on GitHub at https://github.com/aiidateam/aiida-core #
# For further information on the license, see the LICENSE.txt file #
# For further information please visit http://www.aiida.net #
###########################################################################
"""`verdi data dict` command."""
from aiida.cmdline.commands.cmd_data import verdi_data
from aiida.cmdline.params import arguments, options, types
@verdi_data.group('sirius')
def siriusscf():
"""Manipulate Dict objects (python dictionaries)."""
@siriusscf.command('show')
@arguments.DATA(
type=types.DataParamType(sub_classes=('aiida.data:sirius.scf', )))
@options.DICT_FORMAT()
def siriusscf_show(data, fmt):
"""Show contents of Dict nodes."""
from aiida.cmdline.utils.echo import echo_dictionary
for node in data:
echo_dictionary(node.get_dict(), fmt)