aiida_vasp.parsers.vasp

Parser module for composing output of a VASP calculation.

The simplified parser outputs the following nodes:

1. A misc node that stores simple summary information such as total energies,

   total run times, any warnings issues during the calculation and if the calculation was finished.

2. A arrays node that for storing miscellaneous quantities that are arrays by nature and typically

   have a large size.

3. A trajectory node for storing the trajectory of geometry optimisation and AIMD.

4. A bands node for storing the band structure.

5. A dos node for storing the density of states.

6. Other nodes for storing other relevant quantities such as the born effective charges.

Main difference from the previous version

1. pydantic is used to validate the parser settings at submission time.

2. When parsing retrieved data, we take a ‘parse as much as possible’ approach - the quantities are always parsed if available, and only excluded during the stage of composing the output nodes. This is simpler from the previous ‘parse only when needed’ approach, where multiple checks have be done to work out which parser to call and which quantities to include.

3. All parser logic is contained in a single class and can be extended by updating content parsers and modify the default settings and update/add the _compose_xx methods.

Module Contents

Classes

ParserSettingsConfig	Settings for the VASP parser.
VaspParser	Class for parsing VASP output files and storing the results in AiiDA.
NotificationComposer	Compose errors codes based on the notifications

Functions

gather_quantities	Gather quantities and put them into the target dictionary
get_structure_node	Compose a structure node from the dictionary output by the parser
is_all_empty	Check if all elements of a dictionary or list are empty
get_kpoints_node	Get a KpointData node from parsed kpoints data and cell matrix

Data

DEFAULT_EXCLUDED_QUANTITIES
DEFAULT_EXCLUDED_NODE
DEFAULT_REQUIRED_QUANTITIES
DEFAULT_FILE_MAPPING
MISC_QUANTITIES
ALLOW_EMPTY
STANDALONE_ARRAY_QUANTITIES

API

exception aiida_vasp.parsers.vasp.ParserError

Bases: RuntimeError

exception aiida_vasp.parsers.vasp.QuantityMissingError

Bases: aiida_vasp.parsers.vasp.ParserError

exception aiida_vasp.parsers.vasp.RequiredQuantityMissingError

Bases: aiida_vasp.parsers.vasp.ParserError

exception aiida_vasp.parsers.vasp.MissingFileError

Bases: aiida_vasp.parsers.vasp.ParserError

aiida_vasp.parsers.vasp.DEFAULT_EXCLUDED_QUANTITIES = ('elastic_moduli', 'symmetries', 'parameters')

aiida_vasp.parsers.vasp.DEFAULT_EXCLUDED_NODE = ('bands', 'dos', 'kpoints', 'trajectory', 'energies', 'wavecar', 'chgcar', 'projectors')

aiida_vasp.parsers.vasp.DEFAULT_REQUIRED_QUANTITIES = ('run_status', 'run_stats')

aiida_vasp.parsers.vasp.DEFAULT_FILE_MAPPING = None

aiida_vasp.parsers.vasp.MISC_QUANTITIES = ('total_energies', 'notifications', 'run_status', 'run_stats', 'version', 'forces', 'stress', 'site_...

aiida_vasp.parsers.vasp.ALLOW_EMPTY = ('notifications',)

aiida_vasp.parsers.vasp.STANDALONE_ARRAY_QUANTITIES = None

class aiida_vasp.parsers.vasp.ParserSettingsConfig(/, **data: typing.Any)

Bases: aiida_vasp.utils.opthold.OptionContainer

Settings for the VASP parser.

Initialization

Create a new model by parsing and validating input data from keyword arguments.

Raises [ValidationError][pydantic_core.ValidationError] if the input data cannot be validated to form a valid model.

self is explicitly positional-only to allow self as a field name.

include_quantity: List[str] = 'Field(...)'

exclude_quantity: List[str] = 'Field(...)'

required_quantity: List[str] = 'Field(...)'

include_node: List[str] = 'Field(...)'

exclude_node: List[str] = 'Field(...)'

file_mapping: Dict[str, str] = 'Field(...)'

kpoints_from_ibzkpt: bool = False

check_completeness: bool = True

electronic_step_energies: bool = False

energy_type: List[str] = 'Field(...)'

keep_stream_history: bool = 'Field(...)'

ignore_notification_errors: bool = 'Field(...)'

critical_notification_errors: List[str] = 'Field(...)'

critical_objects: List[str] = 'Field(...)'

check_errors: bool = 'Field(...)'

check_ionic_convergence: bool = 'Field(...)'

omit_structure: bool = 'Field(...)'

class aiida_vasp.parsers.vasp.VaspParser(node: aiida.orm.CalcJobNode)

Bases: aiida.parsers.parser.Parser

Class for parsing VASP output files and storing the results in AiiDA.

Initialization

Initialize the Parser instance

_init_user_settings() → aiida_vasp.parsers.vasp.ParserSettingsConfig

Initialize the settings from the inputs.

_get_quantities_to_parse() → aiida.engine.ExitCode | None

Return the list of quantities to parse.

_post_process_quantities() → aiida.engine.ExitCode | None

Post-process the parsed quantities.

parse(**kwargs: Any) → aiida.engine.ExitCode | None

Parse outputs, store results in database.

_create_outputs() → aiida.engine.ExitCode | None

Create the output nodes

_compose_misc(quantities_each: dict[str, Any]) → aiida.orm.Dict

Compose the misc output node

_compose_structure(quantities_each: dict[str, Any]) → aiida.orm.StructureData | None

Compose the structure output node

_compose_wavecar(quantities_each: dict[str, Any]) → None

Compose the wavecar output node

_compose_chgcar(quantities_each: dict[str, Any]) → None

Compose the chgcar output node

_compose_arrays(quantities_each: dict[str, Any]) → dict[str, aiida.orm.ArrayData]

Generate the generic arrays output node

_make_standalone_array(quantities_each: dict[str, Any], name: str, file_name: str = 'vasprun.xml') → aiida.orm.ArrayData | None

Compose the dielectrics output node

_compose_kpoints(quantities_each: dict[str, Any]) → aiida.orm.KpointsData

Compose the kpoints output node

_compose_trajectory(quantities_each: dict[str, Any]) → aiida.orm.TrajectoryData | None

Compose the trajectory output

_compose_bands(quantities_each: dict[str, Any]) → aiida.orm.BandsData

Compose the band node

_compose_dos(quantities_each: dict[str, Any]) → aiida.orm.ArrayData | None

Compose the dos node

_check_vasp_errors(parser_notifications: dict[str, Any]) → aiida.engine.ExitCode | None

Detect simple vasp execution problems and returns the exit_codes to be set

aiida_vasp.parsers.vasp.gather_quantities(quantities_each: dict[str, Any], namespace: str, dst: dict[str, Any], fields: list[str], flatten_dict: bool = False) → None

Gather quantities and put them into the target dictionary

class aiida_vasp.parsers.vasp.NotificationComposer(notifications: list[dict[str, Any]], run_status: dict[str, Any], inputs: dict[str, Any], exit_codes: Any, critical_notifications: list[str])

Compose errors codes based on the notifications

Initialization

Composed error codes based on the notifications

Some of the errors need to have additional properties inspected before they can be emitted, as they might be trigged in a harmless way.

To add new checkers, one needs to implement a property with the name of the error for this class and contains the code for checking. This property should return the exit_code or return None. The property is inspected if its name is in the list critical notifications.

compose() → aiida.engine.ExitCode | None

Compose the exit codes

Returns None if no exit code should be emitted, otherwise emit the error code.

property brmix: aiida.engine.ExitCode | None

Check if BRMIX should be emitted

property edddav_zhegv: aiida.engine.ExitCode | None

Check if EDDDAV call to ZHEGV should be emitted. Sometimes it has converged.

property eddrmm_zhegv: aiida.engine.ExitCode | None

Check if EDDRMM call to ZHEGV should be emitted. Sometimes it has converged.

aiida_vasp.parsers.vasp.get_structure_node(structure_dict: dict[str, Any]) → aiida.orm.StructureData

Compose a structure node from the dictionary output by the parser

aiida_vasp.parsers.vasp.is_all_empty(obj: dict | list) → bool

Check if all elements of a dictionary or list are empty

aiida_vasp.parsers.vasp.get_kpoints_node(kpoints_data: dict[str, Any], cell: list[list] | numpy.ndarray)

Get a KpointData node from parsed kpoints data and cell matrix