aiida.cmdline.commands package

aiida.cmdline.commands.click_subcmd_complete(cmd_group)

Create a subcommand completion function for a click command group.

Submodules

class aiida.cmdline.commands.calculation.Calculation

Bases: aiida.cmdline.baseclass.VerdiCommandWithSubcommands

Query and interact with calculations

Different subcommands allow to list the running calculations, show the content of the input/output files, see the logs, etc.

__init__()

A dictionary with valid commands and functions to be called: list.

__module__ = 'aiida.cmdline.commands.calculation'

_abstract = False

calculation_cleanworkdir(*args)

Clean the working directory of calculations by removing all the content of the associated RemoteFolder node. Calculations can be identified by pk with the -k flag or by specifying limits on the modification times with -p/-o flags

calculation_gotocomputer(*args)

Open a shell to the calc folder on the cluster

This command opens a ssh connection to the scratch folder on the remote computer on which the calculation is being/has been executed.

calculation_inputcat(*args)

Show an input file of a calculation node.

It shows the files in the raw_input subdirectory. Use the -h option for more help on the command line options.

calculation_inputls(*args)

Show the list of input files of a calculation node.

It shows the files in the raw_input subdirectory. Use the -h option for more help on the command line options.

calculation_kill(*args)

Kill a calculation.

Pass a list of calculation PKs to kill them. If you also pass the -f option, no confirmation will be asked.

calculation_list(*args)

Return a list of calculations on screen.

calculation_logshow(*args)

calculation_outputcat(*args)

Show an output file of a calculation node.

It shows the files in the ‘path’ subdirectory of the output node of files retrieved by the parser. Therefore, this will not work before files are retrieved by the daemon. Use the -h option for more help on the command line options.

calculation_outputls(*args)

Show the list of output files of a calculation node.

It lists the files in the ‘path’ subdirectory of the output node of files retrieved by the parser. Therefore, this will not work before files are retrieved by the daemon. Use the -h option for more help on the command line options.

calculation_plugins(*args)

calculation_res(*args)

Print all or somoe data from the “res” output node.

calculation_show(*args)

complete_plugins(subargs_idx, subargs)

Return the list of plugins of the JobCalculation subclass of Calculation

This allows to setup and configure a code from command line.

TODO: think if we want to allow to change path and prepend/append text.

class aiida.cmdline.commands.code.Code

Bases: aiida.cmdline.baseclass.VerdiCommandWithSubcommands

Setup and manage codes to be used

This command allows to list, add, modify, configure codes.

__init__()

x.__init__(…) initializes x; see help(type(x)) for signature

__module__ = 'aiida.cmdline.commands.code'

_abstract = False

code_delete(*args)

Delete a code

Does not delete the code if there are calculations that are using it (i.e., if there are output links)

code_hide(*args)

Hide one or more codes from the verdi show command

code_list(*args)

List available codes

code_rename(*args)

code_reveal(*args)

Reveal (if it was hidden before) one or more codes from the verdi show command

code_setup(*args)

code_show(*args)

Show information on a given code

code_update(*args)

complete_code_names(subargs_idx, subargs)

complete_code_names_and_pks(subargs_idx, subargs)

complete_code_pks(subargs_idx, subargs)

get_code(code_id)

Get a Computer object with given identifier, that can either be the numeric ID (pk), or the label (if unique).

Note

Since all command line arguments get converted to string types, we cannot assess the intended type (an integer pk or a string label) from the type of the variable code_id. If the code_id can be converted into an integer we will assume the value corresponds to a pk. This means, however, that if there would be another code, with a label directly equivalent to the string value of that pk, that this code can not be referenced by its label, as the other code, corresponding to the integer pk, will get matched first.

get_code_data(django_filter=None)

Retrieve the list of codes in the DB. Return a tuple with (pk, label, computername, owneremail).

Parameters:django_filter – a django query object (e.g. obtained with Q()) to filter the results on the AiidaOrmCode class.

static print_list_res(show_owner)

class aiida.cmdline.commands.code.CodeInputValidationClass

Bases: object

A class with information for the validation of input text of Codes

__dict__ = dict_proxy({'_computer_validator': <function _computer_validator>, '__module__': 'aiida.cmdline.commands.code', '_conf_attributes_local': [('folder_with_code', 'Folder with the code', 'The folder on your local computer in which there are the files to be stored in the AiiDA repository and then copied over for every submitted calculation', False), ('local_rel_path', 'Relative path of the executable', 'The relative path of the executable file inside the folder entered in the previous step', False)], 'remote_abs_path': '', '_get_remote_abs_path_string': <function _get_remote_abs_path_string>, '_set_folder_with_code_string': <function _set_folder_with_code_string>, '_set_is_local_string': <function _set_is_local_string>, '_conf_attributes_start': [('label', 'Label', 'A label to refer to this code', False), ('description', 'Description', 'A human-readable description of this code', False), ('is_local', 'Local', 'True or False; if True, then you have to provide a folder with files that will be stored in AiiDA and copied to the remote computers for every calculation submission. If True, the code is just a link to a remote computer and an absolute path there', False), ('input_plugin', 'Default input plugin', "A string of the default input plugin to be used with this code that is recognized by the CalculationFactory. Use the 'verdi calculation plugins' command to get the list of existingplugins", False)], '_get_label_string': <function _get_label_string>, '_folder_with_code_validator': <function _folder_with_code_validator>, '_set_local_rel_path_string': <function _set_local_rel_path_string>, '__dict__': <attribute '__dict__' of 'CodeInputValidationClass' objects>, '__weakref__': <attribute '__weakref__' of 'CodeInputValidationClass' objects>, 'description': '', '_local_rel_path_validator': <function _local_rel_path_validator>, '_description_validator': <function _description_validator>, '_conf_attributes_end': [('prepend_text', 'Text to prepend to each command execution\nFOR INSTANCE, MODULES TO BE LOADED FOR THIS CODE', 'This is a multiline string, whose content will be prepended inside\nthe submission script before the real execution of the job. It is\nyour responsibility to write proper bash code!', True), ('append_text', 'Text to append to each command execution', 'This is a multiline string, whose content will be appended inside\nthe submission script after the real execution of the job. It is\nyour responsibility to write proper bash code!', True)], '_get_is_local_string': <function _get_is_local_string>, '_get_input_plugin_string': <function _get_input_plugin_string>, 'label': '', 'append_text': '', '_set_remote_abs_path_string': <function _set_remote_abs_path_string>, '_get_computer_string': <function _get_computer_string>, '_set_description_string': <function _set_description_string>, '_set_input_plugin_string': <function _set_input_plugin_string>, '_conf_attributes_relabel': [('label', 'Label', 'A label to refer to this code', False), ('description', 'Description', 'A human-readable description of this code', False)], 'create_code': <function create_code>, '_input_plugin_validator': <function _input_plugin_validator>, '_set_prepend_text_string': <function _set_prepend_text_string>, '_set_append_text_string': <function _set_append_text_string>, '_remote_abs_path_validator': <function _remote_abs_path_validator>, '_get_local_rel_path_string': <function _get_local_rel_path_string>, '_set_computer_string': <function _set_computer_string>, 'ask': <function ask>, '_get_description_string': <function _get_description_string>, '_get_prepend_text_string': <function _get_prepend_text_string>, 'input_plugin': None, '_conf_attributes_remote': [('computer', 'Remote computer name', 'The computer name as on which the code resides, as stored in the AiiDA database', False), ('remote_abs_path', 'Remote absolute path', 'The (full) absolute path on the remote machine', False)], 'is_local': False, 'folder_with_code': '', '_get_append_text_string': <function _get_append_text_string>, 'prepend_text': '', '_label_validator': <function _label_validator>, '__doc__': '\n A class with information for the validation of input text of Codes\n ', '_get_folder_with_code_string': <function _get_folder_with_code_string>, 'computer': None, '_append_text_validator': <function _append_text_validator>, '_is_local_validator': <function _is_local_validator>, 'set_and_validate_from_code': <function set_and_validate_from_code>, 'local_rel_path': '', '_prepend_text_validator': <function _prepend_text_validator>, '_set_label_string': <function _set_label_string>})

__module__ = 'aiida.cmdline.commands.code'

__weakref__

list of weak references to the object (if defined)

_append_text_validator(append_text)

Validates the append_text.

_computer_validator(computer)

Validates the computer.

_conf_attributes_end = [('prepend_text', 'Text to prepend to each command execution\nFOR INSTANCE, MODULES TO BE LOADED FOR THIS CODE', 'This is a multiline string, whose content will be prepended inside\nthe submission script before the real execution of the job. It is\nyour responsibility to write proper bash code!', True), ('append_text', 'Text to append to each command execution', 'This is a multiline string, whose content will be appended inside\nthe submission script after the real execution of the job. It is\nyour responsibility to write proper bash code!', True)]

_conf_attributes_local = [('folder_with_code', 'Folder with the code', 'The folder on your local computer in which there are the files to be stored in the AiiDA repository and then copied over for every submitted calculation', False), ('local_rel_path', 'Relative path of the executable', 'The relative path of the executable file inside the folder entered in the previous step', False)]

_conf_attributes_relabel = [('label', 'Label', 'A label to refer to this code', False), ('description', 'Description', 'A human-readable description of this code', False)]

_conf_attributes_remote = [('computer', 'Remote computer name', 'The computer name as on which the code resides, as stored in the AiiDA database', False), ('remote_abs_path', 'Remote absolute path', 'The (full) absolute path on the remote machine', False)]

_conf_attributes_start = [('label', 'Label', 'A label to refer to this code', False), ('description', 'Description', 'A human-readable description of this code', False), ('is_local', 'Local', 'True or False; if True, then you have to provide a folder with files that will be stored in AiiDA and copied to the remote computers for every calculation submission. If True, the code is just a link to a remote computer and an absolute path there', False), ('input_plugin', 'Default input plugin', "A string of the default input plugin to be used with this code that is recognized by the CalculationFactory. Use the 'verdi calculation plugins' command to get the list of existingplugins", False)]

_description_validator(folder_with_code)

Validates the folder_with_code.

_folder_with_code_validator(folder_with_code)

Validates the folder_with_code.

_get_append_text_string()

_get_computer_string()

_get_description_string()

_get_folder_with_code_string()

_get_input_plugin_string()

Return the input plugin string

_get_is_local_string()

_get_label_string()

_get_local_rel_path_string()

_get_prepend_text_string()

_get_remote_abs_path_string()

_input_plugin_validator(input_plugin)

Validates the input_plugin, checking it is in the list of existing plugins.

_is_local_validator(is_local)

Validates the is_local.

_label_validator(label)

Validates the label.

_local_rel_path_validator(local_rel_path)

Validates the local_rel_path.

_prepend_text_validator(prepend_text)

Validates the prepend_text.

_remote_abs_path_validator(remote_abs_path)

Validates the remote_abs_path.

_set_append_text_string(string)

Set the append_text starting from a string.

_set_computer_string(string)

Set the computer starting from a string.

_set_description_string(string)

Set the description starting from a string.

_set_folder_with_code_string(string)

Set the folder_with_code starting from a string.

_set_input_plugin_string(string)

Set the input_plugin starting from a string.

_set_is_local_string(string)

Set the is_local starting from a string.

_set_label_string(string)

Set the label starting from a string.

_set_local_rel_path_string(string)

Set the local_rel_path starting from a string.

_set_prepend_text_string(string)

Set the prepend_text starting from a string.

_set_remote_abs_path_string(string)

Set the remote_abs_path starting from a string.

append_text = ''

ask()

computer = None

create_code()

Create a code with the information contained in this class, BUT DOES NOT STORE IT.

description = ''

folder_with_code = ''

input_plugin = None

is_local = False

label = ''

local_rel_path = ''

prepend_text = ''

remote_abs_path = ''

set_and_validate_from_code(kwargs)

This method is used by the Code Orm, for the utility to setup a new code from the verdi shell

aiida.cmdline.commands.code.cmdline_fill(attributes, store, print_header=True)

This allows to manage comments from command line.

class aiida.cmdline.commands.comment.Comment

Bases: aiida.cmdline.baseclass.VerdiCommandWithSubcommands

Manage general properties of nodes in the database

__init__()

A dictionary with valid commands and functions to be called.

__module__ = 'aiida.cmdline.commands.comment'

_abstract = False

comment_add(*args)

Add comment to a node

comment_remove(*args)

Remove comments. The user can only remove its own comments

comment_show(*args)

Show the comments of a node

comment_update(*args)

Update a comment

class aiida.cmdline.commands.computer.Computer

Bases: aiida.cmdline.baseclass.VerdiCommandWithSubcommands

Setup and manage computers to be used

This command allows to list, add, modify and configure computers.

__init__()

A dictionary with valid commands and functions to be called.

__module__ = 'aiida.cmdline.commands.computer'

_abstract = False

_computer_create_temp_file(transport, scheduler, dbauthinfo)

Internal test to check if it is possible to create a temporary file and then delete it in the work directory

Note:

exceptions could be raised

Parameters:

• transport – an open transport
• scheduler – the corresponding scheduler class
• dbauthinfo – the dbauthinfo object (from which one can get computer and aiidauser)

Returns:

True if the test succeeds, False if it fails.

_computer_test_get_jobs(transport, scheduler, dbauthinfo)

Internal test to check if it is possible to check the queue state.

Note:

exceptions could be raised

Parameters:

• transport – an open transport
• scheduler – the corresponding scheduler class
• dbauthinfo – the dbauthinfo object (from which one can get computer and aiidauser)

Returns:

True if the test succeeds, False if it fails.

complete_computers(subargs_idx, subargs)

computer_configure(*args)

Configure the authentication information for a given computer

computer_delete(*args)

Configure the authentication information for a given computer

Does not delete the computer if there are calculations that are using it.

computer_disable(*args)

Disable a computer.

If a computer is disabled, AiiDA does not try to connect to it to submit new calculations or check for the state of existing calculations. Useful, for instance, if you know that a computer is under maintenance.

computer_enable(*args)

Enable a computer.

computer_list(*args)

List available computers

computer_rename(*args)

Rename a computer

computer_setup(*args)

Setup a new or existing computer

computer_show(*args)

Show information on a given computer

computer_test(*args)

Test the connection to a computer.

It tries to connect, to get the list of calculations on the queue and to perform other tests.

computer_update(*args)

Update an existing computer

get_computer(name)

Get a Computer object with given name, or raise NotExistent

get_computer_names()

Retrieve the list of computers in the DB.

ToDo: use an API or cache the results, sometime it is quite slow!

aiida.cmdline.commands.computer.prompt_for_computer_configuration(computer)

class aiida.cmdline.commands.daemon.Daemon

Bases: aiida.cmdline.baseclass.VerdiCommandWithSubcommands

Manage the AiiDA daemon

This command allows to interact with the AiiDA daemon. Valid subcommands are:

• start: start the daemon
• stop: restart the daemon
• restart: restart the aiida daemon, waiting for it to cleanly exit before restarting it.
• status: inquire the status of the Daemon.
• logshow: show the log in a continuous fashion, similar to the ‘tail -f’ command. Press CTRL+C to exit.

__init__()

A dictionary with valid commands and functions to be called: start, stop, status and restart.

__module__ = 'aiida.cmdline.commands.daemon'

_abstract = False

_clean_pid_files()

Tries to remove the celery.pid files from the .aiida/daemon subfolder. This is typically needed when the computer is restarted with the daemon still on.

_get_pid_full_path()

Return the full path of the celery.pid file.

configure_user(*args)

Configure the user that can run the daemon.

daemon_logshow(*args)

Show the log of the daemon, press CTRL+C to quit.

daemon_restart(*args)

Restart the daemon. Before restarting, wait for the daemon to really shut down.

daemon_start(*args)

Start the daemon

daemon_status(*args)

Print the status of the daemon

daemon_stop(*args, **kwargs)

Stop the daemon.

Parameters:wait_for_death – If True, also verifies that the process was already killed. It attempts at most max_retries times, with sleep_between_retries seconds between one attempt and the following one (both variables are for the time being hardcoded in the function). Returns:None if wait_for_death is False. True/False if the process was actually dead or after all the retries it was still alive.

get_daemon_pid()

Return the daemon pid, as read from the celery.pid file. Return None if no pid is found (or the pid is not valid).

kill_daemon()

This is the actual call that kills the daemon.

There are some print statements inside, but no sys.exit, so it is safe to be called from other parts of the code.

aiida.cmdline.commands.daemon._get_env_with_venv_bin()

aiida.cmdline.commands.daemon.is_daemon_user()

Return True if the user is the current daemon user, False otherwise.

class aiida.cmdline.commands.data.Data

Bases: aiida.cmdline.baseclass.VerdiCommandRouter

Setup and manage data specific types

There is a list of subcommands for managing specific types of data. For instance, ‘data upf’ manages pseudopotentials in the UPF format.

__init__()

A dictionary with valid commands and functions to be called.

__module__ = 'aiida.cmdline.commands.data'

_abstract = False

class aiida.cmdline.commands.data.Depositable

Bases: object

Provides shell completion for depositable data nodes.

Note

classes, inheriting Depositable, MUST NOT contain attributes, starting with _deposit_, which are not plugins for depositing.

__dict__ = dict_proxy({'deposit_parameters_postfix': '_parameters', '__module__': 'aiida.cmdline.commands.data', 'get_deposit_plugins': <function get_deposit_plugins>, '__dict__': <attribute '__dict__' of 'Depositable' objects>, 'deposit_prefix': '_deposit_', '__weakref__': <attribute '__weakref__' of 'Depositable' objects>, '__doc__': '\n Provides shell completion for depositable data nodes.\n\n .. note:: classes, inheriting Depositable, MUST NOT contain\n attributes, starting with ``_deposit_``, which are not plugins for\n depositing.\n ', 'deposit': <function deposit>})

__module__ = 'aiida.cmdline.commands.data'

__weakref__

list of weak references to the object (if defined)

deposit(*args)

Deposit the data node to a given database.

Parameters:args – a namespace with parsed command line parameters.

deposit_parameters_postfix = '_parameters'

deposit_prefix = '_deposit_'

get_deposit_plugins()

Get the list of all implemented deposition methods for data class.

class aiida.cmdline.commands.data.Exportable

Bases: object

Provides shell completion for exportable data nodes.

Note

classes, inheriting Exportable, MUST NOT contain attributes, starting with _export_, which are not plugins for exporting.

__dict__ = dict_proxy({'export_parameters_postfix': '_parameters', 'append_export_cmdline_arguments': <function append_export_cmdline_arguments>, 'export_prefix': '_export_', 'print_or_store': <function print_or_store>, '__module__': 'aiida.cmdline.commands.data', 'get_export_plugins': <function get_export_plugins>, 'export': <function export>, '__dict__': <attribute '__dict__' of 'Exportable' objects>, '__weakref__': <attribute '__weakref__' of 'Exportable' objects>, '__doc__': '\n Provides shell completion for exportable data nodes.\n\n .. note:: classes, inheriting Exportable, MUST NOT contain attributes,\n starting with ``_export_``, which are not plugins for exporting.\n '})

__module__ = 'aiida.cmdline.commands.data'

__weakref__

list of weak references to the object (if defined)

append_export_cmdline_arguments(parser)

Function (to be overloaded in a subclass) to add custom export command line arguments.

Parameters:parser – a ArgParse parser object Returns:change the parser in place

export(*args)

Export the data node to a given format.

export_parameters_postfix = '_parameters'

export_prefix = '_export_'

get_export_plugins()

Get the list of all implemented exporters for data class.

print_or_store(node, output_fname, fileformat, other_args={}, overwrite=False)

Depending on the parameters, either print the (single) output file on screen, or stores the file(s) on disk.

Parameters:

• node – the Data node to print or store on disk
• output_fname – The filename to store the main file. If empty or None, print instead
• fileformat – a string to pass to the _exportstring method
• other_args – a dictionary with additional kwargs to pass to _exportstring
• overwrite – if False, stops if any file already exists (when output_fname is not empty

Note:

this function calls directly sys.exit(1) when an error occurs (or e.g. if check_overwrite is True and a file already exists).

class aiida.cmdline.commands.data.Importable

Bases: object

Provides shell completion for importable data nodes.

Note

classes, inheriting Importable, MUST NOT contain attributes, starting with _import_, which are not plugins for importing.

__dict__ = dict_proxy({'import_prefix': '_import_', '__module__': 'aiida.cmdline.commands.data', 'importfile': <function importfile>, '__dict__': <attribute '__dict__' of 'Importable' objects>, 'import_parameters_postfix': '_parameters', '__weakref__': <attribute '__weakref__' of 'Importable' objects>, '__doc__': '\n Provides shell completion for importable data nodes.\n\n .. note:: classes, inheriting Importable, MUST NOT contain attributes,\n starting with ``_import_``, which are not plugins for importing.\n ', 'get_import_plugins': <function get_import_plugins>})

__module__ = 'aiida.cmdline.commands.data'

__weakref__

list of weak references to the object (if defined)

get_import_plugins()

Get the list of all implemented importers for data class.

import_parameters_postfix = '_parameters'

import_prefix = '_import_'

importfile(*args)

class aiida.cmdline.commands.data.Listable

Bases: object

Provides shell completion for listable data nodes.

Note

classes, inheriting Listable, MUST define value for property dataclass (preferably in __init__), which has to point to correct *Data class.

__dict__ = dict_proxy({'append_list_cmdline_arguments': <function append_list_cmdline_arguments>, '__module__': 'aiida.cmdline.commands.data', 'list': <function list>, 'get_column_names': <function get_column_names>, 'query_group': <function query_group>, 'query_past_days': <function query_past_days>, '__dict__': <attribute '__dict__' of 'Listable' objects>, 'query': <function query>, '__weakref__': <attribute '__weakref__' of 'Listable' objects>, '__doc__': '\n Provides shell completion for listable data nodes.\n\n .. note:: classes, inheriting Listable, MUST define value for property\n ``dataclass`` (preferably in ``__init__``), which\n has to point to correct \\*Data class.\n '})

__module__ = 'aiida.cmdline.commands.data'

__weakref__

list of weak references to the object (if defined)

append_list_cmdline_arguments(parser)

Append additional command line parameters, that are later parsed and used in the query construction.

Parameters:parser – instance of argparse.ArgumentParser

get_column_names()

Return the list with column names.

Note

neither the number nor correspondence of column names and actual columns in the output from the query() are checked.

list(*args)

List all instances of given data class.

Parameters:args – a list of command line arguments.

query(args)

Perform the query

query_group(filters, args)

Subselect to filter data nodes by their group.

Parameters:

• q_object – a query object
• args – a namespace with parsed command line parameters.

query_past_days(filters, args)

Subselect to filter data nodes by their age.

Parameters:

• filters – the filters to be enriched.
• args – a namespace with parsed command line parameters.

class aiida.cmdline.commands.data.Visualizable

Bases: object

Provides shell completion for visualizable data nodes.

Note

classes, inheriting Visualizable, MUST NOT contain attributes, starting with _show_, which are not plugins for visualization.

In order to specify a default visualization format, one has to override _default_show_format property (preferably in __init__), setting it to the name of default visualization tool.

__dict__ = dict_proxy({'get_show_plugins': <function get_show_plugins>, '__module__': 'aiida.cmdline.commands.data', 'show_parameters_postfix': '_parameters', 'show': <function show>, '__dict__': <attribute '__dict__' of 'Visualizable' objects>, 'show_prefix': '_show_', '__weakref__': <attribute '__weakref__' of 'Visualizable' objects>, '__doc__': '\n Provides shell completion for visualizable data nodes.\n\n .. note:: classes, inheriting Visualizable, MUST NOT contain\n attributes, starting with ``_show_``, which are not plugins for\n visualization.\n\n In order to specify a default visualization format, one has to override\n ``_default_show_format`` property (preferably in\n ``__init__``), setting it to the name of default visualization tool.\n '})

__module__ = 'aiida.cmdline.commands.data'

__weakref__

list of weak references to the object (if defined)

get_show_plugins()

Get the list of all implemented plugins for visualizing the structure.

show(*args)

Show the data node with a visualization program.

show_parameters_postfix = '_parameters'

show_prefix = '_show_'

class aiida.cmdline.commands.data._Array

Bases: aiida.cmdline.baseclass.VerdiCommandWithSubcommands, aiida.cmdline.commands.data.Visualizable

View and manipulate Array data classes.

__init__()

A dictionary with valid commands and functions to be called.

__module__ = 'aiida.cmdline.commands.data'

_abstract = False

_show_json_date(exec_name, node_list)

Show contents of ArrayData nodes.

class aiida.cmdline.commands.data._Bands

Bases: aiida.cmdline.baseclass.VerdiCommandWithSubcommands, aiida.cmdline.commands.data.Listable, aiida.cmdline.commands.data.Visualizable, aiida.cmdline.commands.data.Exportable

Manipulation on the bands

__init__()

A dictionary with valid commands and functions to be called.

__module__ = 'aiida.cmdline.commands.data'

_abstract = False

_export_agr(node, output_fname, overwrite, **kwargs)

Export a .agr file, to be visualized with the XMGrace plotting software.

_export_agr_batch(node, output_fname, overwrite, **kwargs)

Export a .agr batch file, to be visualized with the XMGrace plotting software.

_export_dat_blocks(node, output_fname, overwrite, **kwargs)

Export a .dat file with one line per datapoint (kpt, energy), with multiple bands separated in stanzas (i.e. having at least an empty newline inbetween).

_export_dat_multicolumn(node, output_fname, overwrite, **kwargs)

Export a .dat file with one line per kpoint, with multiple energy values on the same line separated by spaces.

_export_gnuplot(node, output_fname, overwrite, **kwargs)

Export a Gnuplot file, together with the corresponding .dat file, to be visualized with the Gnuplot plotting software.

Run with ‘gnuplot -p filename’ to see the plot (and keep the window with the plot open).

_export_json(node, output_fname, overwrite, **kwargs)

Export a .dat file with one line per datapoint (kpt, energy), with multiple bands separated in stanzas (i.e. having at least an empty newline inbetween).

_export_mpl_pdf(node, output_fname, overwrite, **kwargs)

Export a .pdf file generated using matplotlib

_export_mpl_png(node, output_fname, overwrite, **kwargs)

Export a .png file generated using matplotlib

_export_mpl_singlefile(node, output_fname, overwrite, **kwargs)

Export a .py file that would produce the plot using matplotlib when run with python (with data dumped within the same python file)

_export_mpl_withjson(node, output_fname, overwrite, **kwargs)

Export a .py file that would produce the plot using matplotlib when run with python (with data dumped in an external json filee)

_show_xmgrace(exec_name, list_bands)

Plugin for show the bands with the XMGrace plotting software.

append_export_cmdline_arguments(parser)

Additional command line arguments for the ‘export’ command

Parameters:parser – instance of argparse.ArgumentParser

append_list_cmdline_arguments(parser)

Append additional command line parameters, that are later parsed and used in the query construction.

Parameters:parser – instance of argparse.ArgumentParser

get_column_names()

Return the list with column names.

Note:neither the number nor correspondence of column names and actual columns in the output from the query() are checked.

query(args)

Perform the query and return information for the list.

Parameters:args – a namespace with parsed command line parameters. Returns:table (list of lists) with information, describing nodes. Each row describes a single hit.

class aiida.cmdline.commands.data._Cif

Bases: aiida.cmdline.baseclass.VerdiCommandWithSubcommands, aiida.cmdline.commands.data.Listable, aiida.cmdline.commands.data.Visualizable, aiida.cmdline.commands.data.Exportable, aiida.cmdline.commands.data.Importable, aiida.cmdline.commands.data.Depositable

Visualize CIF structures

__init__()

A dictionary with valid commands and functions to be called.

__module__ = 'aiida.cmdline.commands.data'

_abstract = False

_deposit_tcod(node, parameter_data=None, **kwargs)

Deposition plugin for TCOD.

_deposit_tcod_parameters(parser, **kwargs)

Command line parameters deposition plugin for TCOD.

_export_cif(node, output_fname, overwrite, **kwargs)

Exporter to CIF.

_export_tcod(node, output_fname, overwrite, parameter_data=None, **kwargs)

Plugin for TCOD

_export_tcod_parameters(parser, **kwargs)

Command line parameters for TCOD

_import_cif(filename, **kwargs)

Importer from CIF.

_show_jmol(exec_name, structure_list)

Plugin for jmol

_show_vesta(exec_name, structure_list)

Plugin for VESTA, added by Yue-Wen FANG and Abel Carreras at Kyoto University in the group of Prof. Isao Tanaka’s lab

get_column_names()

Return the list with column names.

Note:neither the number nor correspondence of column names and actual columns in the output from the query() are checked.

query(args)

Perform the query and return information for the list.

Parameters:args – a namespace with parsed command line parameters. Returns:table (list of lists) with information, describing nodes. Each row describes a single hit.

class aiida.cmdline.commands.data._Parameter

Bases: aiida.cmdline.baseclass.VerdiCommandWithSubcommands, aiida.cmdline.commands.data.Visualizable

View and manipulate Parameter data classes.

__init__()

A dictionary with valid commands and functions to be called.

__module__ = 'aiida.cmdline.commands.data'

_abstract = False

_show_json_date(exec_name, node_list)

Show contents of ParameterData nodes.

class aiida.cmdline.commands.data._Remote

Bases: aiida.cmdline.baseclass.VerdiCommandWithSubcommands

Manage RemoteData objects

__init__()

x.__init__(…) initializes x; see help(type(x)) for signature

__module__ = 'aiida.cmdline.commands.data'

_abstract = False

do_cat(*args)

Show the content of remote files in RemoteData objects.

do_listdir(*args)

List directory content on remote RemoteData objects.

do_show(*args)

Show information on a RemoteData object.

class aiida.cmdline.commands.data._Structure

Bases: aiida.cmdline.baseclass.VerdiCommandWithSubcommands, aiida.cmdline.commands.data.Listable, aiida.cmdline.commands.data.Visualizable, aiida.cmdline.commands.data.Exportable, aiida.cmdline.commands.data.Importable, aiida.cmdline.commands.data.Depositable

Visualize AiIDA structures

__init__()

A dictionary with valid commands and functions to be called.

__module__ = 'aiida.cmdline.commands.data'

_abstract = False

_deposit_tcod(node, parameter_data=None, **kwargs)

Deposition plugin for TCOD.

_deposit_tcod_parameters(parser, **kwargs)

Command line parameters deposition plugin for TCOD.

_export_cif(node, output_fname, overwrite, **kwargs)

Exporter to CIF.

_export_tcod(node, output_fname, overwrite, parameter_data=None, **kwargs)

Plugin for TCOD

_export_tcod_parameters(parser, **kwargs)

Command line parameters for TCOD

_export_xsf(node, output_fname, overwrite, **kwargs)

Exporter to XSF.

_export_xyz(node, output_fname, overwrite, **kwargs)

Exporter to XYZ.

_import_ase(filename, **kwargs)

Imports a structure in a number of formats using the ASE routines.

_import_pwi(filename, **kwargs)

Imports a structure from a quantumespresso input file.

_import_xyz(filename, **kwargs)

Imports an XYZ-file.

_import_xyz_parameters(parser)

Adding some functionality to the parser to deal with importing files

_show_ase(exec_name, structure_list)

Plugin to show the structure with the ASE visualizer

_show_jmol(exec_name, structure_list)

Plugin for jmol

_show_vesta(exec_name, structure_list)

Plugin for VESTA This VESTA plugin was added by Yue-Wen FANG and Abel Carreras at Kyoto University in the group of Prof. Isao Tanaka’s lab

_show_vmd(exec_name, structure_list)

Plugin for vmd

_show_xcrysden(exec_name, structure_list)

Plugin for xcrysden

append_list_cmdline_arguments(parser)

Append additional command line parameters, that are later parsed and used in the query construction.

Parameters:parser – instance of argparse.ArgumentParser

get_column_names()

Return the list with column names.

Note

neither the number nor correspondence of column names and actual columns in the output from the query() are checked.

query(args)

Perform the query

class aiida.cmdline.commands.data._Trajectory

Bases: aiida.cmdline.baseclass.VerdiCommandWithSubcommands, aiida.cmdline.commands.data.Listable, aiida.cmdline.commands.data.Visualizable, aiida.cmdline.commands.data.Exportable, aiida.cmdline.commands.data.Depositable

View and manipulate TrajectoryData instances.

__init__()

A dictionary with valid commands and functions to be called.

__module__ = 'aiida.cmdline.commands.data'

_abstract = False

_deposit_tcod(node, parameter_data=None, **kwargs)

Deposition plugin for TCOD.

_deposit_tcod_parameters(parser, **kwargs)

Command line parameters deposition plugin for TCOD.

_export_cif(node, output_fname, overwrite, **kwargs)

Exporter to CIF.

_export_cif_parameters(parser, **kwargs)

Describe command line parameters.

_export_tcod(node, output_fname, overwrite, parameter_data=None, **kwargs)

Plugin for TCOD

_export_tcod_parameters(parser, **kwargs)

Command line parameters for TCOD

_export_xsf(node, output_fname, overwrite, **kwargs)

Exporter to XSF.

_show_jmol(exec_name, trajectory_list, **kwargs)

Plugin for jmol

_show_jmol_parameters(parser)

Describe command line parameters.

_show_mpl_heatmap(exec_name, trajectory_list, **kwargs)

Produces a matplotlib plot of the trajectory

_show_mpl_heatmap_parameters(parser)

Describe command line parameters for _show_mpl_heatmap

_show_mpl_pos(exec_name, trajectory_list, **kwargs)

Produces a matplotlib plot of the trajectory

_show_mpl_pos_parameters(parser)

Describe command line parameters for _show_pos

_show_xcrysden(exec_name, trajectory_list, **kwargs)

Plugin for xcrysden

class aiida.cmdline.commands.data._Upf

Bases: aiida.cmdline.baseclass.VerdiCommandWithSubcommands, aiida.cmdline.commands.data.Importable

Setup and manage upf to be used

This command allows to list and configure upf.

__init__()

A dictionary with valid commands and functions to be called.

__module__ = 'aiida.cmdline.commands.data'

_abstract = False

_import_upf(filename, **kwargs)

Importer from UPF.

exportfamily(*args)

Export a pseudopotential family into a folder. Call without parameters to get some help.

listfamilies(*args)

Print on screen the list of upf families installed

uploadfamily(*args)

Upload a new pseudopotential family.

Returns the numbers of files found and the number of nodes uploaded.

Call without parameters to get some help.

class aiida.cmdline.commands.devel.Devel(*args, **kwargs)

Bases: aiida.cmdline.baseclass.VerdiCommandWithSubcommands

AiiDA commands for developers

Provides a set of tools for developers. For instance, it allows to run the django tests for the db application and the unittests of the AiiDA modules.

If you want to limit the tests to a specific subset of modules, pass them as parameters.

An invalid parameter will make the code print the list of all valid parameters.

Note: the test called ‘db’ will run all db.* tests.

__init__(*args, **kwargs)

x.__init__(…) initializes x; see help(type(x)) for signature

__module__ = 'aiida.cmdline.commands.devel'

_abstract = False

_dbprefix = 'db.'

_dbrawprefix = 'db'

base_allowed_test_folders = ['aiida.scheduler', 'aiida.transport', 'aiida.common', 'aiida.tests.work', 'aiida.utils', 'aiida.control', 'aiida.cmdline.tests']

calculation_getresults(*args)

Routine to get a list of results of a set of calculations, still under development.

complete_properties(subargs_idx, subargs)

I complete with subargs that were not used yet.

complete_tests(subargs_idx, subargs)

I complete with subargs that were not used yet.

get_querydict_from_keyvalue(key, separator_filter, value)

parse_arg(arg)

run_delproperty(*args)

Delete a global AiiDA property from the config file in .aiida.

run_describeproperties(*args)

List all valid properties that can be stored in the AiiDA config file.

Only properties listed in the _property_table of aida.common.setup can be used.

run_getproperty(*args)

Get a global AiiDA property from the config file in .aiida.

run_listislands(*args)

List all AiiDA nodes, that have no parents and children.

run_listproperties(*args)

List all found global AiiDA properties.

run_play(*args)

Open a browser and play the Aida triumphal march by Giuseppe Verdi

run_query(*args)

run_setproperty(*args)

Define a global AiiDA property in the config file in .aiida.

Only properties in the _property_table of aiida.common.setup can be modified.

run_tests(*args)

separators = [('~=', 'iexact'), ('>=', 'gte'), ('<=', 'lte'), ('>', 'gt'), ('<', 'lt'), ('=', '')]

tick_daemon(*args)

Call all the functions that the daemon would call if running once and return.

aiida.cmdline.commands.devel.apply_function(function, value)

The function must be defined in this file and be in the format applyfunct_FUNCNAME where FUNCNAME is the string passed as the parameter ‘function’; applyfunct_FUNCNAME will accept only one parameter (‘value’) and return an appropriate value.

aiida.cmdline.commands.devel.applyfunct_keys(value)

Return the keys of a dictionary.

aiida.cmdline.commands.devel.applyfunct_len(value)

Return the length of an object.

exception aiida.cmdline.commands.exportfile.DanglingLinkError

Bases: exceptions.Exception

__module__ = 'aiida.cmdline.commands.exportfile'

__weakref__

list of weak references to the object (if defined)

class aiida.cmdline.commands.exportfile.Export

Bases: aiida.cmdline.baseclass.VerdiCommandWithSubcommands

Create and manage AiiDA export archives

__init__()

x.__init__(…) initializes x; see help(type(x)) for signature

__module__ = 'aiida.cmdline.commands.exportfile'

_abstract = False

cli(*args)

aiida.cmdline.commands.exportfile.migrate_v1_to_v2(metadata, data)

Migration of export files from v0.1 to v0.2, which means generalizing the field names with respect to the database backend

Parameters:

• data – the content of an export archive data.json file
• metadata – the content of an export archive metadata.json file

aiida.cmdline.commands.exportfile.migrate_v2_to_v3(metadata, data)

Migration of export files from v0.2 to v0.3, which means adding the link types to the link entries and making the entity key names backend agnostic by effectively removing the prefix ‘aiida.backends.djsite.db.models’

Parameters:

• data – the content of an export archive data.json file
• metadata – the content of an export archive metadata.json file

aiida.cmdline.commands.exportfile.update_metadata(metadata, version)

Update the metadata with a new version number and a notification of the conversion that was executed

Parameters:

• metadata – the content of an export archive metadata.json file
• version – string version number that the updated metadata should get

aiida.cmdline.commands.exportfile.verify_metadata_version(metadata, version=None)

Utility function to verify that the metadata has the correct version number. If no version number is passed, it will just extract the version number and return it.

Parameters:

• metadata – the content of an export archive metadata.json file
• version – string version number that the metadata is expected to have

class aiida.cmdline.commands.graph.Graph

Bases: aiida.cmdline.baseclass.VerdiCommandWithSubcommands

Utility to explore the nodes in the database graph More specifically it allow the user to:

- Generate and render graph
- (TODO) Find if two nodes of a graph are connected
- (TODO) Extend functionalities

A list dictionary with available subcommands can be found in __init__ function

__init__()

A dictionary with valid subcommands as keys and corresponding functions as values

__module__ = 'aiida.cmdline.commands.graph'

_abstract = False

graph_generate(*args)

Function to generate a graph given a root node user-specified by its pk. :param args: root_pk :return: Generate a .dot file that can be rendered by graphviz utility dot

class aiida.cmdline.commands.group.Group

Bases: aiida.cmdline.baseclass.VerdiCommandWithSubcommands

Setup and manage groups

There is a list of subcommands to perform specific operation on groups.

__init__()

A dictionary with valid commands and functions to be called: list.

__module__ = 'aiida.cmdline.commands.group'

_abstract = False

group_addnodes(*args)

Add nodes to a given group.

group_create(*args)

Create a new empty group.

group_delete(*args)

Delete an existing group.

group_description(*args)

Edit the group description.

group_list(*args)

Print a list of groups in the DB.

group_removenodes(*args)

Remove nodes from a given group.

group_show(*args)

Show information on a given group. Pass the PK as a parameter.

class aiida.cmdline.commands.importfile.Import

Bases: aiida.cmdline.baseclass.VerdiCommand

Import nodes and group of nodes

This command allows to import nodes from file, for backup purposes or to share data with collaborators.

__module__ = 'aiida.cmdline.commands.importfile'

_abstract = False

complete(subargs_idx, subargs)

Method called when the user asks for the bash completion. Print a list of valid keywords. Returning without printing will use standard bash completion.

Parameters:

• subargs_idx – the index of the subargs where the TAB key was pressed (0 is the first element of subargs)
• subargs – a list of subarguments to this command

run(*args)

Method executed when the command is called from the command line.

class aiida.cmdline.commands.node.Node

Bases: aiida.cmdline.baseclass.VerdiCommandRouter

Manage operations on AiiDA nodes

There is a list of subcommands for managing specific types of data. For instance, ‘node repo’ manages the files in the local repository.

__init__()

A dictionary with valid commands and functions to be called.

__module__ = 'aiida.cmdline.commands.node'

_abstract = False

class aiida.cmdline.commands.node._Delete

Bases: aiida.cmdline.baseclass.VerdiCommand

__module__ = 'aiida.cmdline.commands.node'

_abstract = False

run(*args)

Deletes a node and it’s inferred data provenance :raise ValueError: if no valid pk or uuid is given.

class aiida.cmdline.commands.node._Description(node_subclass='data')

Bases: aiida.cmdline.baseclass.VerdiCommandWithSubcommands

See or modify the label of one or more set of nodes

__init__(node_subclass='data')

x.__init__(…) initializes x; see help(type(x)) for signature

__module__ = 'aiida.cmdline.commands.node'

_abstract = False

_node_class_ok(n)

run(*args)

Method executed when the command is called from the command line.

class aiida.cmdline.commands.node._Label(node_subclass='data')

Bases: aiida.cmdline.baseclass.VerdiCommandWithSubcommands

See or modify the label of one or more set of nodes

__init__(node_subclass='data')

x.__init__(…) initializes x; see help(type(x)) for signature

__module__ = 'aiida.cmdline.commands.node'

_abstract = False

_node_class_ok(n)

run(*args)

Method executed when the command is called from the command line.

class aiida.cmdline.commands.node._Repo

Bases: aiida.cmdline.baseclass.VerdiCommandWithSubcommands

Show files and their contents in the local repository

__init__()

A dictionary with valid commands and functions to be called.

__module__ = 'aiida.cmdline.commands.node'

_abstract = False

cat(*args)

Output the content of a file in the repository folder.

ls(*args)

List the files in the repository folder.

class aiida.cmdline.commands.node._Show

Bases: aiida.cmdline.baseclass.VerdiCommandWithSubcommands

__module__ = 'aiida.cmdline.commands.node'

_abstract = False

run(*args)

Method executed when the command is called from the command line.

class aiida.cmdline.commands.node._Tree

Bases: aiida.cmdline.baseclass.VerdiCommand

Show a tree of the nodes.

__module__ = 'aiida.cmdline.commands.node'

_abstract = False

_build_tree(node, label_type=None, show_pk=True, max_depth=None, follow_links=None, depth=0)

_ctime(nodelab)

print_node_tree(node, max_depth, follow_links=None)

run(*args)

Show node information.

aiida.cmdline.commands.node.cat_repo_files(node, path)

Given a Node and a relative path to a file in the Node repository directory, prints in output the content of the file.

Parameters:

• node – a Node instance
• path – a string with the relative path to list. Must be a file.

Raises:

ValueError – if the file is not found, or is a directory.

aiida.cmdline.commands.node.list_repo_files(node, path, color)

Given a Node and a relative path prints in output the list of files in the given path in the Node repository directory.

Parameters:

• node – a Node instance
• path – a string with the relative path to list. Can be a file.
• color – boolean, if True prints with the codes to show colors.

Raises:

ValueError – if the file or directory is not found.

aiida.cmdline.commands.node.print_node_info(node, print_groups=False)

This allows to manage profiles from command line.

class aiida.cmdline.commands.profile.Profile

Bases: aiida.cmdline.baseclass.VerdiCommandWithSubcommands

List AiiDA profiles, and set the default profile.

Allow to see the list of AiiDA profiles, and to set the default profile (the to be used by any verdi command when no ‘-p’ option is given).

__init__()

A dictionary with valid commands and functions to be called.

__module__ = 'aiida.cmdline.commands.profile'

_abstract = False

complete_processes_profiles(subargs_idx, subargs)

profile_delete(*args)

Deletes profile

Asks whether to delete associated database and associated database user.

Specify argument ‘–force’ to skip any questions warning about loss of data.

profile_list(*args)

profile_setdefault(*args)

class aiida.cmdline.commands.rehash.Rehash

Bases: aiida.cmdline.baseclass.VerdiCommand

Re-hash all nodes.

__module__ = 'aiida.cmdline.commands.rehash'

_abstract = False

complete(subargs_idx, subargs)

No completion after ‘verdi rehash’.

run(*args)

Method executed when the command is called from the command line.

This allows to hook-up the AiIDA built-in RESTful API. Main advantage of doing this by means of a verdi command is that different profiles can be selected at hook-up (-p flag).

class aiida.cmdline.commands.restapi.Restapi

Bases: aiida.cmdline.baseclass.VerdiCommand

verdi command used to hook up the AiIDA REST API. Example Usage:

verdi -p <profile_name> restapi –host 127.0.0.5 –port 6789 –config-dir <location of the onfig.py file>

__module__ = 'aiida.cmdline.commands.restapi'

_abstract = False

aiida = <module 'aiida' from '/home/docs/checkouts/readthedocs.org/user_builds/aiida-core/checkouts/v0.12.1/docs/source/../../aiida/__init__.py'>

complete(subargs_idx, subargs)

No particular completion features required

default_config_dir = '/home/docs/checkouts/readthedocs.org/user_builds/aiida-core/checkouts/v0.12.1/aiida/restapi/common'

default_host = '127.0.0.1'

default_port = '5000'

os = <module 'os' from '/home/docs/checkouts/readthedocs.org/user_builds/aiida-core/envs/v0.12.1/lib/python2.7/os.pyc'>

parse_aiida_profile = False

run(*args)

Hook up the default RESTful API of AiiDA. args include port, host, config_file

class aiida.cmdline.commands.shell.Shell

Bases: aiida.cmdline.baseclass.VerdiCommand

Run the interactive shell with the AiiDA environment loaded.

This command opens an ipython shell with the AiiDA environment loaded.

__module__ = 'aiida.cmdline.commands.shell'

_abstract = False

_ipython()

Start IPython >= 1.0

_ipython_pre_011()

Start IPython pre-0.11

_ipython_pre_100()

Start IPython pre-1.0.0

bpython()

complete(subargs_idx, subargs)

Method called when the user asks for the bash completion. Print a list of valid keywords. Returning without printing will use standard bash completion.

Parameters:

• subargs_idx – the index of the subargs where the TAB key was pressed (0 is the first element of subargs)
• subargs – a list of subarguments to this command

get_start_namespace()

Load all default and custom modules

handle_noargs(*args)

ipython()

Start any version of IPython

run(*args)

Method executed when the command is called from the command line.

run_shell(shell=None)

shells = ['ipython', 'bpython']

This allows to setup and configure a user from command line.

class aiida.cmdline.commands.user.User

Bases: aiida.cmdline.baseclass.VerdiCommandWithSubcommands

List and configure new AiiDA users.

Allow to see the list of AiiDA users, their permissions, and to configure old and new users.

__init__()

A dictionary with valid commands and functions to be called.

__module__ = 'aiida.cmdline.commands.user'

_abstract = False

cli(*args)

complete_emails(subargs_idx, subargs)

aiida.cmdline.commands.user.do_configure(email, first_name, last_name, institution, no_password, non_interactive=False, force=False, **kwargs)

class aiida.cmdline.commands.work.Work

Bases: aiida.cmdline.baseclass.VerdiCommandWithSubcommands

Manage the AiiDA worflow manager

__init__()

x.__init__(…) initializes x; see help(type(x)) for signature

__module__ = 'aiida.cmdline.commands.work'

_abstract = False

cli(*args)

complete_plugins(subargs_idx, subargs)

Return the list of plugins registered under the ‘workflows’ category

aiida.cmdline.commands.work._build_query(projections=None, order_by=None, limit=None, past_days=None)

class aiida.cmdline.commands.workflow.Workflow

Bases: aiida.cmdline.baseclass.VerdiCommandWithSubcommands

Manage the AiiDA legacy worflow manager

Valid subcommands are: * list: list the running workflows running and their state. Pass a -h | option for further help on valid options. * kill: kill a given workflow * report: show the report of a given workflow

__init__()

A dictionary with valid commands and functions to be called: list.

__module__ = 'aiida.cmdline.commands.workflow'

_abstract = False

print_logshow(*args)

print_report(*args)

Print the report of a workflow.

workflow_kill(*args)

Kill a workflow.

Pass a list of workflow PKs to kill them. If you also pass the -f option, no confirmation will be asked. If you pass the -q option, additional information will be suppressed

workflow_list(*args)

Return a list of workflows on screen