aiida.orm.nodes.data package¶
Module with Node sub classes for data structures.
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class
aiida.orm.nodes.data.
Data
(backend=None, user=None, computer=None, **kwargs)[source]¶ Bases:
aiida.orm.nodes.node.Node
The base class for all Data nodes.
AiiDA Data classes are subclasses of Node and must support multiple inheritance.
Architecture note: Calculation plugins are responsible for converting raw output data from simulation codes to Data nodes. Data nodes are responsible for validating their content (see _validate method).
-
__abstractmethods__
= frozenset({})¶
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__deepcopy__
(memo)[source]¶ Create a clone of the Data node by pipiong through to the clone method and return the result.
- Returns
an unstored clone of this Data node
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__module__
= 'aiida.orm.nodes.data.data'¶
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_abc_impl
= <_abc_data object>¶
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_export_format_replacements
= {}¶
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_exportcontent
(fileformat, main_file_name='', **kwargs)[source]¶ Converts a Data node to one (or multiple) files.
Note: Export plugins should return utf8-encoded bytes, which can be directly dumped to file.
- Parameters
fileformat (str) – the extension, uniquely specifying the file format.
main_file_name (str) – (empty by default) Can be used by plugin to infer sensible names for additional files, if necessary. E.g. if the main file is ‘../myplot.gnu’, the plugin may decide to store the dat file under ‘../myplot_data.dat’.
kwargs – other parameters are passed down to the plugin
- Returns
a tuple of length 2. The first element is the content of the otuput file. The second is a dictionary (possibly empty) in the format {filename: filecontent} for any additional file that should be produced.
- Return type
(bytes, dict)
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_get_converters
()[source]¶ Get all implemented converter formats. The convention is to find all _get_object_… methods. Returns a list of strings.
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_get_exporters
()[source]¶ Get all implemented export formats. The convention is to find all _prepare_… methods. Returns a dictionary of method_name: method_function
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_get_importers
()[source]¶ Get all implemented import formats. The convention is to find all _parse_… methods. Returns a list of strings.
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_logger
= <Logger aiida.orm.nodes.data.data.Data (REPORT)>¶
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_plugin_type_string
= 'data.data.Data.'¶
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_query_type_string
= 'data.data.'¶
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_source_attributes
= ['db_name', 'db_uri', 'uri', 'id', 'version', 'extras', 'source_md5', 'description', 'license']¶
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_storable
= True¶
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_unstorable_message
= 'storing for this node has been disabled'¶
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_validate
()[source]¶ Perform validation of the Data object.
Note
validation of data source checks license and requires attribution to be provided in field ‘description’ of source in the case of any CC-BY* license. If such requirement is too strict, one can remove/comment it out.
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convert
(object_format=None, *args)[source]¶ Convert the AiiDA StructureData into another python object
- Parameters
object_format – Specify the output format
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property
creator
¶ Return the creator of this node or None if it does not exist.
- Returns
the creating node or None
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export
(path, fileformat=None, overwrite=False, **kwargs)[source]¶ Save a Data object to a file.
- Parameters
fname – string with file name. Can be an absolute or relative path.
fileformat – kind of format to use for the export. If not present, it will try to use the extension of the file name.
overwrite – if set to True, overwrites file found at path. Default=False
kwargs – additional parameters to be passed to the _exportcontent method
- Returns
the list of files created
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classmethod
get_export_formats
()[source]¶ Get the list of valid export format strings
- Returns
a list of valid formats
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importfile
(fname, fileformat=None)[source]¶ Populate a Data object from a file.
- Parameters
fname – string with file name. Can be an absolute or relative path.
fileformat – kind of format to use for the export. If not present, it will try to use the extension of the file name.
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importstring
(inputstring, fileformat, **kwargs)[source]¶ Converts a Data object to other text format.
- Parameters
fileformat – a string (the extension) to describe the file format.
- Returns
a string with the structure description.
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property
source
¶ Gets the dictionary describing the source of Data object. Possible fields:
db_name: name of the source database.
db_uri: URI of the source database.
uri: URI of the object’s source. Should be a permanent link.
id: object’s source identifier in the source database.
version: version of the object’s source.
extras: a dictionary with other fields for source description.
source_md5: MD5 checksum of object’s source.
description: human-readable free form description of the object’s source.
license: a string with a type of license.
Note
some limitations for setting the data source exist, see
_validate
method.- Returns
dictionary describing the source of Data object.
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class
aiida.orm.nodes.data.
BaseType
(*args, **kwargs)[source]¶ Bases:
aiida.orm.nodes.data.data.Data
Data sub class to be used as a base for data containers that represent base python data types.
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__abstractmethods__
= frozenset({})¶
-
__hash__
= None¶
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__init__
(*args, **kwargs)[source]¶ - Parameters
backend_entity (
aiida.orm.implementation.BackendEntity
) – the backend model supporting this entity
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__module__
= 'aiida.orm.nodes.data.base'¶
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_abc_impl
= <_abc_data object>¶
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_logger
= <Logger aiida.orm.nodes.data.base.BaseType (REPORT)>¶
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_plugin_type_string
= 'data.base.BaseType.'¶
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_query_type_string
= 'data.base.'¶
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property
value
¶
-
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class
aiida.orm.nodes.data.
ArrayData
(backend=None, user=None, computer=None, **kwargs)[source]¶ Bases:
aiida.orm.nodes.data.data.Data
Store a set of arrays on disk (rather than on the database) in an efficient way using numpy.save() (therefore, this class requires numpy to be installed).
Each array is stored within the Node folder as a different .npy file.
- Note
Before storing, no caching is done: if you perform a
get_array()
call, the array will be re-read from disk. If instead the ArrayData node has already been stored, the array is cached in memory after the first read, and the cached array is used thereafter. If too much RAM memory is used, you can clear the cache with theclear_internal_cache()
method.
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__abstractmethods__
= frozenset({})¶
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__module__
= 'aiida.orm.nodes.data.array.array'¶
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_abc_impl
= <_abc_data object>¶
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_arraynames_from_files
()[source]¶ Return a list of all arrays stored in the node, listing the files (and not relying on the properties).
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_arraynames_from_properties
()[source]¶ Return a list of all arrays stored in the node, listing the attributes starting with the correct prefix.
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_cached_arrays
= None¶
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_logger
= <Logger aiida.orm.nodes.data.array.array.ArrayData (REPORT)>¶
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_plugin_type_string
= 'data.array.array.ArrayData.'¶
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_query_type_string
= 'data.array.array.'¶
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_validate
()[source]¶ Check if the list of .npy files stored inside the node and the list of properties match. Just a name check, no check on the size since this would require to reload all arrays and this may take time and memory.
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array_prefix
= 'array|'¶
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clear_internal_cache
()[source]¶ Clear the internal memory cache where the arrays are stored after being read from disk (used in order to reduce at minimum the readings from disk). This function is useful if you want to keep the node in memory, but you do not want to waste memory to cache the arrays in RAM.
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delete_array
(name)[source]¶ Delete an array from the node. Can only be called before storing.
- Parameters
name – The name of the array to delete from the node.
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get_array
(name)[source]¶ Return an array stored in the node
- Parameters
name – The name of the array to return.
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get_arraynames
()[source]¶ Return a list of all arrays stored in the node, listing the files (and not relying on the properties).
New in version 0.7: Renamed from arraynames
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get_iterarrays
()[source]¶ Iterator that returns tuples (name, array) for each array stored in the node.
New in version 1.0: Renamed from iterarrays
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get_shape
(name)[source]¶ Return the shape of an array (read from the value cached in the properties for efficiency reasons).
- Parameters
name – The name of the array.
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class
aiida.orm.nodes.data.
BandsData
(backend=None, user=None, computer=None, **kwargs)[source]¶ Bases:
aiida.orm.nodes.data.array.kpoints.KpointsData
Class to handle bands data
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__abstractmethods__
= frozenset({})¶
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__module__
= 'aiida.orm.nodes.data.array.bands'¶
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_abc_impl
= <_abc_data object>¶
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_custom_export_format_replacements
= {'dat': 'dat_multicolumn', 'gnu': 'gnuplot', 'pdf': 'mpl_pdf', 'png': 'mpl_png', 'py': 'mpl_singlefile'}¶
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_get_bandplot_data
(cartesian, prettify_format=None, join_symbol=None, get_segments=False, y_origin=0.0)[source]¶ Get data to plot a band structure
- Parameters
cartesian – if True, distances (for the x-axis) are computed in cartesian coordinates, otherwise they are computed in reciprocal coordinates. cartesian=True will fail if no cell has been set.
prettify_format – by default, strings are not prettified. If you want to prettify them, pass a valid prettify_format string (see valid options in the docstring of :py:func:prettify_labels).
join_symbols – by default, strings are not joined. If you pass a string, this is used to join strings that are much closer than a given threshold. The most typical string is the pipe symbol:
|
.get_segments – if True, also computes the band split into segments
y_origin – if present, shift bands so to set the value specified at
y=0
- Returns
a plot_info dictiorary, whose keys are
x
(array of distances for the x axis of the plot);y
(array of bands),labels
(list of tuples in the format (float x value of the label, label string),band_type_idx
(array containing an index for each band: if there is only one spin, then it’s an array of zeros, of length equal to the number of bands at each point; if there are two spins, then it’s an array of zeros or ones depending on the type of spin; the length is always equalt to the total number of bands per kpoint).
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_logger
= <Logger aiida.orm.nodes.data.array.bands.BandsData (REPORT)>¶
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_matplotlib_get_dict
(main_file_name='', comments=True, title='', legend=None, legend2=None, y_max_lim=None, y_min_lim=None, y_origin=0.0, prettify_format=None, **kwargs)[source]¶ Prepare the data to send to the python-matplotlib plotting script.
- Parameters
comments – if True, print comments (if it makes sense for the given format)
plot_info – a dictionary
setnumber_offset – an offset to be applied to all set numbers (i.e. s0 is replaced by s[offset], s1 by s[offset+1], etc.)
color_number – the color number for lines, symbols, error bars and filling (should be less than the parameter max_num_agr_colors defined below)
title – the title
legend – the legend (applied only to the first of the set)
legend2 – the legend for second-type spins (applied only to the first of the set)
y_max_lim – the maximum on the y axis (if None, put the maximum of the bands)
y_min_lim – the minimum on the y axis (if None, put the minimum of the bands)
y_origin – the new origin of the y axis -> all bands are replaced by bands-y_origin
prettify_format – if None, use the default prettify format. Otherwise specify a string with the prettifier to use.
kwargs – additional customization variables; only a subset is accepted, see internal variable ‘valid_additional_keywords
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_plugin_type_string
= 'data.array.bands.BandsData.'¶
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_prepare_agr
(main_file_name='', comments=True, setnumber_offset=0, color_number=1, color_number2=2, legend='', title='', y_max_lim=None, y_min_lim=None, y_origin=0.0, prettify_format=None)[source]¶ Prepare an xmgrace agr file.
- Parameters
comments – if True, print comments (if it makes sense for the given format)
plot_info – a dictionary
setnumber_offset – an offset to be applied to all set numbers (i.e. s0 is replaced by s[offset], s1 by s[offset+1], etc.)
color_number – the color number for lines, symbols, error bars and filling (should be less than the parameter max_num_agr_colors defined below)
color_number2 – the color number for lines, symbols, error bars and filling for the second-type spins (should be less than the parameter max_num_agr_colors defined below)
legend – the legend (applied only to the first set)
title – the title
y_max_lim – the maximum on the y axis (if None, put the maximum of the bands); applied after shifting the origin by
y_origin
y_min_lim – the minimum on the y axis (if None, put the minimum of the bands); applied after shifting the origin by
y_origin
y_origin – the new origin of the y axis -> all bands are replaced by bands-y_origin
prettify_format – if None, use the default prettify format. Otherwise specify a string with the prettifier to use.
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_prepare_agr_batch
(main_file_name='', comments=True, prettify_format=None)[source]¶ Prepare two files, data and batch, to be plot with xmgrace as: xmgrace -batch file.dat
- Parameters
main_file_name – if the user asks to write the main content on a file, this contains the filename. This should be used to infer a good filename for the additional files. In this case, we remove the extension, and add ‘_data.dat’
comments – if True, print comments (if it makes sense for the given format)
prettify_format – if None, use the default prettify format. Otherwise specify a string with the prettifier to use.
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_prepare_dat_blocks
(main_file_name='', comments=True)[source]¶ Format suitable for gnuplot using blocks. Columns with x and y (path and band energy). Several blocks, separated by two empty lines, one per energy band.
- Parameters
comments – if True, print comments (if it makes sense for the given format)
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_prepare_dat_multicolumn
(main_file_name='', comments=True)[source]¶ Write an N x M matrix. First column is the distance between kpoints, The other columns are the bands. Header contains number of kpoints and the number of bands (commented).
- Parameters
comments – if True, print comments (if it makes sense for the given format)
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_prepare_gnuplot
(main_file_name='', title='', comments=True, prettify_format=None, y_max_lim=None, y_min_lim=None, y_origin=0.0)[source]¶ Prepare an gnuplot script to plot the bands, with the .dat file returned as an independent file.
- Parameters
main_file_name – if the user asks to write the main content on a file, this contains the filename. This should be used to infer a good filename for the additional files. In this case, we remove the extension, and add ‘_data.dat’
title – if specified, add a title to the plot
comments – if True, print comments (if it makes sense for the given format)
prettify_format – if None, use the default prettify format. Otherwise specify a string with the prettifier to use.
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_prepare_json
(main_file_name='', comments=True)[source]¶ Prepare a json file in a format compatible with the AiiDA band visualizer
- Parameters
comments – if True, print comments (if it makes sense for the given format)
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_prepare_mpl_pdf
(main_file_name='', *args, **kwargs)[source]¶ Prepare a python script using matplotlib to plot the bands, with the JSON returned as an independent file.
For the possible parameters, see documentation of
_matplotlib_get_dict()
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_prepare_mpl_png
(main_file_name='', *args, **kwargs)[source]¶ Prepare a python script using matplotlib to plot the bands, with the JSON returned as an independent file.
For the possible parameters, see documentation of
_matplotlib_get_dict()
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_prepare_mpl_singlefile
(*args, **kwargs)[source]¶ Prepare a python script using matplotlib to plot the bands
For the possible parameters, see documentation of
_matplotlib_get_dict()
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_prepare_mpl_withjson
(main_file_name='', *args, **kwargs)[source]¶ Prepare a python script using matplotlib to plot the bands, with the JSON returned as an independent file.
For the possible parameters, see documentation of
_matplotlib_get_dict()
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_query_type_string
= 'data.array.bands.'¶
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_validate_bands_occupations
(bands, occupations=None, labels=None)[source]¶ Validate the list of bands and of occupations before storage. Kpoints must be set in advance. Bands and occupations must be convertible into arrays of Nkpoints x Nbands floats or Nspins x Nkpoints x Nbands; Nkpoints must correspond to the number of kpoints.
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property
array_labels
¶ Get the labels associated with the band arrays
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get_bands
(also_occupations=False, also_labels=False)[source]¶ Returns an array (nkpoints x num_bands or nspins x nkpoints x num_bands) of energies. :param also_occupations: if True, returns also the occupations array. Default = False
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set_bands
(bands, units=None, occupations=None, labels=None)[source]¶ Set an array of band energies of dimension (nkpoints x nbands). Kpoints must be set in advance. Can contain floats or None. :param bands: a list of nkpoints lists of nbands bands, or a 2D array of shape (nkpoints x nbands), with band energies for each kpoint :param units: optional, energy units :param occupations: optional, a 2D list or array of floats of same shape as bands, with the occupation associated to each band
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set_kpointsdata
(kpointsdata)[source]¶ Load the kpoints from a kpoint object. :param kpointsdata: an instance of KpointsData class
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show_mpl
(**kwargs)[source]¶ Call a show() command for the band structure using matplotlib. This uses internally the ‘mpl_singlefile’ format, with empty main_file_name.
Other kwargs are passed to self._exportcontent.
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property
units
¶ Units in which the data in bands were stored. A string
-
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class
aiida.orm.nodes.data.
KpointsData
(backend=None, user=None, computer=None, **kwargs)[source]¶ Bases:
aiida.orm.nodes.data.array.array.ArrayData
Class to handle array of kpoints in the Brillouin zone. Provide methods to generate either user-defined k-points or path of k-points along symmetry lines. Internally, all k-points are defined in terms of crystal (fractional) coordinates. Cell and lattice vector coordinates are in Angstroms, reciprocal lattice vectors in Angstrom^-1 . :note: The methods setting and using the Bravais lattice info assume the PRIMITIVE unit cell is provided in input to the set_cell or set_cell_from_structure methods.
-
__abstractmethods__
= frozenset({})¶
-
__module__
= 'aiida.orm.nodes.data.array.kpoints'¶
-
_abc_impl
= <_abc_data object>¶
-
_change_reference
(kpoints, to_cartesian=True)[source]¶ Change reference system, from cartesian to crystal coordinates (units of b1,b2,b3) or viceversa. :param kpoints: a list of (3) point coordinates :return kpoints: a list of (3) point coordinates in the new reference
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property
_dimension
¶ Dimensionality of the structure, found from its pbc (i.e. 1 if it’s a 1D structure, 2 if its 2D, 3 if it’s 3D …). :return dimensionality: 0, 1, 2 or 3 :note: will return 3 if pbc has not been set beforehand
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_logger
= <Logger aiida.orm.nodes.data.array.kpoints.KpointsData (REPORT)>¶
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_plugin_type_string
= 'data.array.kpoints.KpointsData.'¶
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_query_type_string
= 'data.array.kpoints.'¶
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_set_cell
(value)[source]¶ Validate if ‘value’ is a allowed crystal unit cell :param value: something compatible with a 3x3 tuple of floats
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_set_labels
(value)[source]¶ set label names. Must pass in input a list like:
[[0,'X'],[34,'L'],... ]
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_validate_kpoints_weights
(kpoints, weights)[source]¶ Validate the list of kpoints and of weights before storage. Kpoints and weights must be convertible respectively to an array of N x dimension and N floats
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property
cell
¶ The crystal unit cell. Rows are the crystal vectors in Angstroms. :return: a 3x3 numpy.array
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get_description
()[source]¶ Returns a string with infos retrieved from kpoints node’s properties. :param node: :return: retstr
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get_kpoints
(also_weights=False, cartesian=False)[source]¶ Return the list of kpoints
- Parameters
also_weights – if True, returns also the list of weights. Default = False
cartesian – if True, returns points in cartesian coordinates, otherwise, returns in crystal coordinates. Default = False.
-
get_kpoints_mesh
(print_list=False)[source]¶ Get the mesh of kpoints.
- Parameters
print_list – default=False. If True, prints the mesh of kpoints as a list
- Raises
AttributeError – if no mesh has been set
- Return mesh,offset
(if print_list=False) a list of 3 integers and a list of three floats 0<x<1, representing the mesh and the offset of kpoints
- Return kpoints
(if print_list = True) an explicit list of kpoints coordinates, similar to what returned by get_kpoints()
-
property
labels
¶ Labels associated with the list of kpoints. List of tuples with kpoint index and kpoint name:
[(0,'G'),(13,'M'),...]
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property
pbc
¶ The periodic boundary conditions along the vectors a1,a2,a3.
- Returns
a tuple of three booleans, each one tells if there are periodic boundary conditions for the i-th real-space direction (i=1,2,3)
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property
reciprocal_cell
¶ Return the reciprocal cell in units of 1/Angstrom from the internally set cell
-
set_cell
(cell, pbc=None)[source]¶ Set a cell to be used for symmetry analysis. To set a cell from an AiiDA structure, use “set_cell_from_structure”.
- Parameters
cell – 3x3 matrix of cell vectors. Orientation: each row represent a lattice vector. Units are Angstroms.
pbc – list of 3 booleans, True if in the nth crystal direction the structure is periodic. Default = [True,True,True]
-
set_cell_from_structure
(structuredata)[source]¶ Set a cell to be used for symmetry analysis from an AiiDA structure. Inherits both the cell and the pbc’s. To set manually a cell, use “set_cell”
- Parameters
structuredata – an instance of StructureData
-
set_kpoints
(kpoints, cartesian=False, labels=None, weights=None, fill_values=0)[source]¶ Set the list of kpoints. If a mesh has already been stored, raise a ModificationNotAllowed
- Parameters
kpoints –
a list of kpoints, each kpoint being a list of one, two or three coordinates, depending on self.pbc: if structure is 1D (only one True in self.pbc) one allows singletons or scalars for each k-point, if it’s 2D it can be a length-2 list, and in all cases it can be a length-3 list. Examples:
[[0.,0.,0.],[0.1,0.1,0.1],…] for 1D, 2D or 3D
[[0.,0.],[0.1,0.1,],…] for 1D or 2D
[[0.],[0.1],…] for 1D
[0., 0.1, …] for 1D (list of scalars)
For 0D (all pbc are False), the list can be any of the above or empty - then only Gamma point is set. The value of k for the non-periodic dimension(s) is set by fill_values
cartesian – if True, the coordinates given in input are treated as in cartesian units. If False, the coordinates are crystal, i.e. in units of b1,b2,b3. Default = False
labels – optional, the list of labels to be set for some of the kpoints. See labels for more info
weights – optional, a list of floats with the weight associated to the kpoint list
fill_values – scalar to be set to all non-periodic dimensions (indicated by False in self.pbc), or list of values for each of the non-periodic dimensions.
-
set_kpoints_mesh
(mesh, offset=None)[source]¶ Set KpointsData to represent a uniformily spaced mesh of kpoints in the Brillouin zone. This excludes the possibility of set/get kpoints
- Parameters
mesh – a list of three integers, representing the size of the kpoint mesh along b1,b2,b3.
offset – (optional) a list of three floats between 0 and 1. [0.,0.,0.] is Gamma centered mesh [0.5,0.5,0.5] is half shifted [1.,1.,1.] by periodicity should be equivalent to [0.,0.,0.] Default = [0.,0.,0.].
-
set_kpoints_mesh_from_density
(distance, offset=None, force_parity=False)[source]¶ Set a kpoints mesh using a kpoints density, expressed as the maximum distance between adjacent points along a reciprocal axis
- Parameters
distance – distance (in 1/Angstrom) between adjacent kpoints, i.e. the number of kpoints along each reciprocal axis i is where is the norm of the reciprocal cell vector.
offset – (optional) a list of three floats between 0 and 1. [0.,0.,0.] is Gamma centered mesh [0.5,0.5,0.5] is half shifted Default = [0.,0.,0.].
force_parity – (optional) if True, force each integer in the mesh to be even (except for the non-periodic directions).
- Note
a cell should be defined first.
- Note
the number of kpoints along non-periodic axes is always 1.
-
-
class
aiida.orm.nodes.data.
ProjectionData
(backend=None, user=None, computer=None, **kwargs)[source]¶ Bases:
aiida.orm.nodes.data.orbital.OrbitalData
,aiida.orm.nodes.data.array.array.ArrayData
A class to handle arrays of projected wavefunction data. That is projections of a orbitals, usually an atomic-hydrogen orbital, onto a given bloch wavefunction, the bloch wavefunction being indexed by s, n, and k. E.g. the elements are the projections described as < orbital | Bloch wavefunction (s,n,k) >
-
__abstractmethods__
= frozenset({})¶
-
__module__
= 'aiida.orm.nodes.data.array.projection'¶
-
_abc_impl
= <_abc_data object>¶
-
_check_projections_bands
(projection_array)[source]¶ Checks to make sure that a reference bandsdata is already set, and that projection_array is of the same shape of the bands data
- Parameters
projwfc_arrays – nk x nb x nwfc array, to be checked against bands
- Raise
AttributeError if energy is not already set
- Raise
AttributeError if input_array is not of same shape as dos_energy
-
_find_orbitals_and_indices
(**kwargs)[source]¶ Finds all the orbitals and their indicies associated with kwargs essential for retrieving the other indexed array parameters
- Parameters
kwargs – kwargs that can call orbitals as in get_orbitals()
- Returns
retrieve_indexes, list of indicicies of orbitals corresponding to the kwargs
- Returns
all_orbitals, list of orbitals to which the indexes correspond
-
_logger
= <Logger aiida.orm.nodes.data.array.projection.ProjectionData (REPORT)>¶
-
_plugin_type_string
= 'data.array.projection.ProjectionData.'¶
-
_query_type_string
= 'data.array.projection.'¶
-
get_pdos
(**kwargs)[source]¶ Retrieves all the pdos arrays corresponding to the input kwargs
- Parameters
kwargs – inputs describing the orbitals associated with the pdos arrays
- Returns
a list of tuples containing the orbital, energy array and pdos array associated with all orbitals that correspond to kwargs
-
get_projections
(**kwargs)[source]¶ Retrieves all the pdos arrays corresponding to the input kwargs
- Parameters
kwargs – inputs describing the orbitals associated with the pdos arrays
- Returns
a list of tuples containing the orbital, and projection arrays associated with all orbitals that correspond to kwargs
-
get_reference_bandsdata
()[source]¶ Returns the reference BandsData, using the set uuid via set_reference_bandsdata
- Returns
a BandsData instance
- Raises
AttributeError – if the bandsdata has not been set yet
exceptions.NotExistent – if the bandsdata uuid did not retrieve bandsdata
-
set_orbitals
(**kwargs)[source]¶ This method is inherited from OrbitalData, but is blocked here. If used will raise a NotImplementedError
-
set_projectiondata
(list_of_orbitals, list_of_projections=None, list_of_energy=None, list_of_pdos=None, tags=None, bands_check=True)[source]¶ Stores the projwfc_array using the projwfc_label, after validating both.
- Parameters
list_of_orbitals – list of orbitals, of class orbital data. They should be the ones up on which the projection array corresponds with.
list_of_projections – list of arrays of projections of a atomic wavefunctions onto bloch wavefunctions. Since the projection is for every bloch wavefunction which can be specified by its spin (if used), band, and kpoint the dimensions must be nspin x nbands x nkpoints for the projwfc array. Or nbands x nkpoints if spin is not used.
energy_axis – list of energy axis for the list_of_pdos
list_of_pdos – a list of projected density of states for the atomic wavefunctions, units in states/eV
tags – A list of tags, not supported currently.
bands_check – if false, skips checks of whether the bands has been already set, and whether the sizes match. For use in parsers, where the BandsData has not yet been stored and therefore get_reference_bandsdata cannot be called
-
set_reference_bandsdata
(value)[source]¶ Sets a reference bandsdata, creates a uuid link between this data object and a bandsdata object, must be set before any projection arrays
- Parameters
value – a BandsData instance, a uuid or a pk
- Raise
exceptions.NotExistent if there was no BandsData associated with uuid or pk
-
-
class
aiida.orm.nodes.data.
TrajectoryData
(structurelist=None, **kwargs)[source]¶ Bases:
aiida.orm.nodes.data.array.array.ArrayData
Stores a trajectory (a sequence of crystal structures with timestamps, and possibly with velocities).
-
__abstractmethods__
= frozenset({})¶
-
__init__
(structurelist=None, **kwargs)[source]¶ - Parameters
backend_entity (
aiida.orm.implementation.BackendEntity
) – the backend model supporting this entity
-
__module__
= 'aiida.orm.nodes.data.array.trajectory'¶
-
_abc_impl
= <_abc_data object>¶
-
_internal_validate
(stepids, cells, symbols, positions, times, velocities)[source]¶ Internal function to validate the type and shape of the arrays. See the documentation of py:meth:.set_trajectory for a description of the valid shape and type of the parameters.
-
_logger
= <Logger aiida.orm.nodes.data.array.trajectory.TrajectoryData (REPORT)>¶
-
_parse_xyz_pos
(inputstring)[source]¶ Load positions from a XYZ file.
Note
The steps and symbols must be set manually before calling this import function as a consistency measure. Even though the symbols and steps could be extracted from the XYZ file, the data present in the XYZ file may or may not be correct and the same logic would have to be present in the XYZ-velocities function. It was therefore decided not to implement it at all but require it to be set explicitly.
Usage:
from aiida.orm.nodes.data.array.trajectory import TrajectoryData t = TrajectoryData() # get sites and number of timesteps t.set_array('steps', arange(ntimesteps)) t.set_array('symbols', array([site.kind for site in s.sites])) t.importfile('some-calc/AIIDA-PROJECT-pos-1.xyz', 'xyz_pos')
-
_parse_xyz_vel
(inputstring)[source]¶ Load velocities from a XYZ file.
Note
The steps and symbols must be set manually before calling this import function as a consistency measure. See also comment for
_parse_xyz_pos()
-
_plugin_type_string
= 'data.array.trajectory.TrajectoryData.'¶
-
_prepare_cif
(trajectory_index=None, main_file_name='')[source]¶ Write the given trajectory to a string of format CIF.
-
_prepare_xsf
(index=None, main_file_name='')[source]¶ Write the given trajectory to a string of format XSF (for XCrySDen).
-
_query_type_string
= 'data.array.trajectory.'¶
-
_validate
()[source]¶ Verify that the required arrays are present and that their type and dimension are correct.
-
get_cells
()[source]¶ Return the array of cells, if it has already been set.
- Raises
KeyError – if the trajectory has not been set yet.
-
get_cif
(index=None, **kwargs)[source]¶ Creates
aiida.orm.nodes.data.cif.CifData
New in version 1.0: Renamed from _get_cif
-
get_index_from_stepid
(stepid)[source]¶ Given a value for the stepid (i.e., a value among those of the
steps
array), return the array index of that stepid, that can be used in other methods such asget_step_data()
orget_step_structure()
.New in version 0.7: Renamed from get_step_index
Note
Note that this function returns the first index found (i.e. if multiple steps are present with the same value, only the index of the first one is returned).
- Raises
ValueError – if no step with the given value is found.
-
get_positions
()[source]¶ Return the array of positions, if it has already been set.
- Raises
KeyError – if the trajectory has not been set yet.
-
get_step_data
(index)[source]¶ Return a tuple with all information concerning the stepid with given index (0 is the first step, 1 the second step and so on). If you know only the step value, use the
get_index_from_stepid()
method to get the corresponding index.If no velocities were specified, None is returned as the last element.
- Returns
A tuple in the format
(stepid, time, cell, symbols, positions, velocities)
, wherestepid
is an integer,time
is a float,cell
is a matrix,symbols
is an array of lengthn
, positions is a array, and velocities is eitherNone
or a array- Parameters
index – The index of the step that you want to retrieve, from 0 to
self.numsteps - 1
.- Raises
IndexError – if you require an index beyond the limits.
KeyError – if you did not store the trajectory yet.
-
get_step_structure
(index, custom_kinds=None)[source]¶ Return an AiiDA
aiida.orm.nodes.data.structure.StructureData
node (not stored yet!) with the coordinates of the given step, identified by its index. If you know only the step value, use theget_index_from_stepid()
method to get the corresponding index.Note
The periodic boundary conditions are always set to True.
New in version 0.7: Renamed from step_to_structure
- Parameters
index – The index of the step that you want to retrieve, from 0 to
self.numsteps- 1
.custom_kinds – (Optional) If passed must be a list of
aiida.orm.nodes.data.structure.Kind
objects. There must be one kind object for each different string in thesymbols
array, withkind.name
set to this string. If this parameter is omitted, the automatic kind generation of AiiDAaiida.orm.nodes.data.structure.StructureData
nodes is used, meaning that the strings in thesymbols
array must be valid chemical symbols.
-
get_stepids
()[source]¶ Return the array of steps, if it has already been set.
New in version 0.7: Renamed from get_steps
- Raises
KeyError – if the trajectory has not been set yet.
-
get_structure
(store=False, **kwargs)[source]¶ Creates
aiida.orm.nodes.data.structure.StructureData
.New in version 1.0: Renamed from _get_aiida_structure
- Parameters
converter – specify the converter. Default ‘ase’.
store – If True, intermediate calculation gets stored in the AiiDA database for record. Default False.
- Returns
-
get_times
()[source]¶ Return the array of times (in ps), if it has already been set.
- Raises
KeyError – if the trajectory has not been set yet.
-
get_velocities
()[source]¶ Return the array of velocities, if it has already been set.
Note
This function (differently from all other
get_*
functions, will not raise an exception if the velocities are not set, but rather returnNone
(both if no trajectory was not set yet, and if it the trajectory was set but no velocities were specified).
-
property
numsites
¶ Return the number of stored sites, or zero if nothing has been stored yet.
-
property
numsteps
¶ Return the number of stored steps, or zero if nothing has been stored yet.
-
set_structurelist
(structurelist)[source]¶ Create trajectory from the list of
aiida.orm.nodes.data.structure.StructureData
instances.- Parameters
structurelist – a list of
aiida.orm.nodes.data.structure.StructureData
instances.- Raises
ValueError – if symbol lists of supplied structures are different
-
set_trajectory
(symbols, positions, stepids=None, cells=None, times=None, velocities=None)[source]¶ Store the whole trajectory, after checking that types and dimensions are correct.
Parameters
stepids
,cells
andvelocities
are optional variables. If nothing is passed forcells
orvelocities
nothing will be stored. However, if no input is given forstepids
a consecutive sequence [0,1,2,…,len(positions)-1] will be assumed.- Parameters
symbols – string list with dimension
n
, wheren
is the number of atoms (i.e., sites) in the structure. The same list is used for each step. Normally, the string should be a valid chemical symbol, but actually any unique string works and can be used as the name of the atomic kind (see also theget_step_structure()
method).positions – float array with dimension , where
s
is the length of thestepids
array andn
is the length of thesymbols
array. Units are angstrom. In particular,positions[i,j,k]
is thek
-th component of thej
-th atom (or site) in the structure at the time step with indexi
(identified by step numberstep[i]
and with timestamptimes[i]
).stepids – integer array with dimension
s
, wheres
is the number of steps. Typically represents an internal counter within the code. For instance, if you want to store a trajectory with one step every 10, starting from step 65, the array will be[65,75,85,...]
. No checks are done on duplicate elements or on the ordering, but anyway this array should be sorted in ascending order, without duplicate elements. (If not specified, stepids will be set tonumpy.arange(s)
by default) It is internally stored as an array named ‘steps’.cells – if specified float array with dimension , where
s
is the length of thestepids
array. Units are angstrom. In particular,cells[i,j,k]
is thek
-th component of thej
-th cell vector at the time step with indexi
(identified by step numberstepid[i]
and with timestamptimes[i]
).times – if specified, float array with dimension
s
, wheres
is the length of thestepids
array. Contains the timestamp of each step in picoseconds (ps).velocities – if specified, must be a float array with the same dimensions of the
positions
array. The array contains the velocities in the atoms.
Todo
Choose suitable units for velocities
-
show_mpl_pos
(**kwargs)[source]¶ Shows the positions as a function of time, separate for XYZ coordinates
- Parameters
stepsize (int) – The stepsize for the trajectory, set higher than 1 to reduce number of points
mintime (int) – Time to start from
maxtime (int) – Maximum time
elements (list) – A list of atomic symbols that should be displayed. If not specified, all atoms are displayed.
indices (list) – A list of indices of that atoms that can be displayed. If not specified, all atoms of the correct species are displayed.
dont_block (bool) – If True, interpreter is not blocked when figure is displayed.
-
property
symbols
¶ Return the array of symbols, if it has already been set.
- Raises
KeyError – if the trajectory has not been set yet.
-
-
class
aiida.orm.nodes.data.
XyData
(backend=None, user=None, computer=None, **kwargs)[source]¶ Bases:
aiida.orm.nodes.data.array.array.ArrayData
A subclass designed to handle arrays that have an “XY” relationship to each other. That is there is one array, the X array, and there are several Y arrays, which can be considered functions of X.
-
__abstractmethods__
= frozenset({})¶
-
__module__
= 'aiida.orm.nodes.data.array.xy'¶
-
_abc_impl
= <_abc_data object>¶
-
_arrayandname_validator
(array, name, units)[source]¶ Validates that the array is an numpy.ndarray and that the name is of type basestring. Raises InputValidationError if this not the case.
-
_logger
= <Logger aiida.orm.nodes.data.array.xy.XyData (REPORT)>¶
-
_plugin_type_string
= 'data.array.xy.XyData.'¶
-
_query_type_string
= 'data.array.xy.'¶
-
get_x
()[source]¶ Tries to retrieve the x array and x name raises a NotExistent exception if no x array has been set yet. :return x_name: the name set for the x_array :return x_array: the x array set earlier :return x_units: the x units set earlier
-
get_y
()[source]¶ Tries to retrieve the y arrays and the y names, raises a NotExistent exception if they have not been set yet, or cannot be retrieved :return y_names: list of strings naming the y_arrays :return y_arrays: list of y_arrays :return y_units: list of strings giving the units for the y_arrays
-
set_x
(x_array, x_name, x_units)[source]¶ Sets the array and the name for the x values.
- Parameters
x_array – A numpy.ndarray, containing only floats
x_name – a string for the x array name
x_units – the units of x
-
set_y
(y_arrays, y_names, y_units)[source]¶ Set array(s) for the y part of the dataset. Also checks if the x_array has already been set, and that, the shape of the y_arrays agree with the x_array. :param y_arrays: A list of y_arrays, numpy.ndarray :param y_names: A list of strings giving the names of the y_arrays :param y_units: A list of strings giving the units of the y_arrays
-
-
class
aiida.orm.nodes.data.
Bool
(*args, **kwargs)[source]¶ Bases:
aiida.orm.nodes.data.base.BaseType
Data sub class to represent a boolean value.
-
__abstractmethods__
= frozenset({})¶
-
__module__
= 'aiida.orm.nodes.data.bool'¶
-
_abc_impl
= <_abc_data object>¶
-
_logger
= <Logger aiida.orm.nodes.data.bool.Bool (REPORT)>¶
-
_plugin_type_string
= 'data.bool.Bool.'¶
-
_query_type_string
= 'data.bool.'¶
-
_type
¶ alias of
builtins.bool
-
-
class
aiida.orm.nodes.data.
CifData
(ase=None, file=None, filename=None, values=None, source=None, scan_type=None, parse_policy=None, **kwargs)[source]¶ Bases:
aiida.orm.nodes.data.singlefile.SinglefileData
Wrapper for Crystallographic Interchange File (CIF)
Note
the file (physical) is held as the authoritative source of information, so all conversions are done through the physical file: when setting
ase
orvalues
, a physical CIF file is generated first, the values are updated from the physical CIF file.-
_PARSE_POLICIES
= ('eager', 'lazy')¶
-
_PARSE_POLICY_DEFAULT
= 'eager'¶
-
_SCAN_TYPES
= ('standard', 'flex')¶
-
_SCAN_TYPE_DEFAULT
= 'standard'¶
-
_SET_INCOMPATIBILITIES
= [('ase', 'file'), ('ase', 'values'), ('file', 'values')]¶
-
__abstractmethods__
= frozenset({})¶
-
__init__
(ase=None, file=None, filename=None, values=None, source=None, scan_type=None, parse_policy=None, **kwargs)[source]¶ Construct a new instance and set the contents to that of the file.
- Parameters
file – an absolute filepath or filelike object for CIF. Hint: Pass io.BytesIO(b”my string”) to construct the SinglefileData directly from a string.
filename – specify filename to use (defaults to name of provided file).
ase – ASE Atoms object to construct the CifData instance from.
values – PyCifRW CifFile object to construct the CifData instance from.
source –
scan_type – scan type string for parsing with PyCIFRW (‘standard’ or ‘flex’). See CifFile.ReadCif
parse_policy – ‘eager’ (parse CIF file on set_file) or ‘lazy’ (defer parsing until needed)
-
__module__
= 'aiida.orm.nodes.data.cif'¶
-
_abc_impl
= <_abc_data object>¶
-
_ase
= None¶
-
_logger
= <Logger aiida.orm.nodes.data.cif.CifData (REPORT)>¶
-
_plugin_type_string
= 'data.cif.CifData.'¶
-
_prepare_cif
(**kwargs)[source]¶ Return CIF string of CifData object.
If parsed values are present, a CIF string is created and written to file. If no parsed values are present, the CIF string is read from file.
-
_query_type_string
= 'data.cif.'¶
-
_values
= None¶
-
property
ase
¶ ASE object, representing the CIF.
Note
requires ASE module.
-
classmethod
from_md5
(md5)[source]¶ Return a list of all CIF files that match a given MD5 hash.
Note
the hash has to be stored in a
_md5
attribute, otherwise the CIF file will not be found.
-
get_ase
(**kwargs)[source]¶ Returns ASE object, representing the CIF. This function differs from the property
ase
by the possibility to pass the keyworded arguments (kwargs) to ase.io.cif.read_cif().Note
requires ASE module.
-
get_formulae
(mode='sum')[source]¶ Return chemical formulae specified in CIF file.
Note: This does not compute the formula, it only reads it from the appropriate tag. Use refine_inline to compute formulae.
-
classmethod
get_or_create
(filename, use_first=False, store_cif=True)[source]¶ Pass the same parameter of the init; if a file with the same md5 is found, that CifData is returned.
- Parameters
filename – an absolute filename on disk
use_first – if False (default), raise an exception if more than one CIF file is found. If it is True, instead, use the first available CIF file.
store_cif (bool) – If false, the CifData objects are not stored in the database. default=True.
- Return (cif, created)
where cif is the CifData object, and create is either True if the object was created, or False if the object was retrieved from the DB.
-
get_structure
(converter='pymatgen', store=False, **kwargs)[source]¶ Creates
aiida.orm.nodes.data.structure.StructureData
.New in version 1.0: Renamed from _get_aiida_structure
- Parameters
converter – specify the converter. Default ‘pymatgen’.
store – if True, intermediate calculation gets stored in the AiiDA database for record. Default False.
primitive_cell – if True, primitive cell is returned, conventional cell if False. Default False.
occupancy_tolerance – If total occupancy of a site is between 1 and occupancy_tolerance, the occupancies will be scaled down to 1. (pymatgen only)
site_tolerance – This tolerance is used to determine if two sites are sitting in the same position, in which case they will be combined to a single disordered site. Defaults to 1e-4. (pymatgen only)
- Returns
-
property
has_atomic_sites
¶ Returns whether there are any atomic sites defined in the cif data. That is to say, it will check all the values for the _atom_site_fract_* tags and if they are all equal to ? that means there are no relevant atomic sites defined and the function will return False. In all other cases the function will return True
- Returns
False when at least one atomic site fractional coordinate is not equal to ? and True otherwise
-
property
has_attached_hydrogens
¶ Check if there are hydrogens without coordinates, specified as attached to the atoms of the structure.
- Returns
True if there are attached hydrogens, False otherwise.
-
property
has_partial_occupancies
¶ Return if the cif data contains partial occupancies
A partial occupancy is defined as site with an occupancy that differs from unity, within a precision of 1E-6
- Returns
True if there are partial occupancies, False otherwise
-
property
has_undefined_atomic_sites
¶ Return whether the cif data contains any undefined atomic sites.
An undefined atomic site is defined as a site where at least one of the fractional coordinates specified in the _atom_site_fract_* tags, cannot be successfully interpreted as a float. If the cif data contains any site that matches this description, or it does not contain any atomic site tags at all, the cif data is said to have undefined atomic sites.
- Returns
boolean, True if no atomic sites are defined or if any of the defined sites contain undefined positions and False otherwise
-
property
has_unknown_species
¶ Returns whether the cif contains atomic species that are not recognized by AiiDA.
The known species are taken from the elements dictionary in aiida.common.constants, with the exception of the “unknown” placeholder element with symbol ‘X’, as this could not be used to construct a real structure. If any of the formula of the cif data contain species that are not in that elements dictionary, the function will return True and False in all other cases. If there is no formulae to be found, it will return None
- Returns
True when there are unknown species in any of the formulae, False if not, None if no formula found
-
parse
(scan_type=None)[source]¶ Parses CIF file and sets attributes.
- Parameters
scan_type – See set_scan_type
-
static
read_cif
(fileobj, index=-1, **kwargs)[source]¶ A wrapper method that simulates the behavior of the old function ase.io.cif.read_cif by using the new generic ase.io.read function.
Somewhere from 3.12 to 3.17 the tag concept was bundled with each Atom object. When reading a CIF file, this is incremented and signifies the atomic species, even though the CIF file do not have specific tags embedded. On reading CIF files we thus force the ASE tag to zero for all Atom elements.
-
set_ase
(aseatoms)[source]¶ Set the contents of the CifData starting from an ASE atoms object
- Parameters
aseatoms – the ASE atoms object
-
set_file
(file, filename=None)[source]¶ Set the file.
If the source is set and the MD5 checksum of new file is different from the source, the source has to be deleted.
- Parameters
file – filepath or filelike object of the CIF file to store. Hint: Pass io.BytesIO(b”my string”) to construct the file directly from a string.
filename – specify filename to use (defaults to name of provided file).
-
set_parse_policy
(parse_policy)[source]¶ Set the parse policy.
- Parameters
parse_policy – Either ‘eager’ (parse CIF file on set_file) or ‘lazy’ (defer parsing until needed)
-
set_scan_type
(scan_type)[source]¶ Set the scan_type for PyCifRW.
The ‘flex’ scan_type of PyCifRW is faster for large CIF files but does not yet support the CIF2 format as of 02/2018. See the CifFile.ReadCif function
- Parameters
scan_type – Either ‘standard’ or ‘flex’ (see _scan_types)
-
set_values
(values)[source]¶ Set internal representation to values.
Warning: This also writes a new CIF file.
- Parameters
values – PyCifRW CifFile object
Note
requires PyCifRW module.
-
property
values
¶ PyCifRW structure, representing the CIF datablocks.
Note
requires PyCifRW module.
-
-
class
aiida.orm.nodes.data.
Code
(remote_computer_exec=None, local_executable=None, input_plugin_name=None, files=None, **kwargs)[source]¶ Bases:
aiida.orm.nodes.data.data.Data
A code entity. It can either be ‘local’, or ‘remote’.
Local code: it is a collection of files/dirs (added using the add_path() method), where one file is flagged as executable (using the set_local_executable() method).
Remote code: it is a pair (remotecomputer, remotepath_of_executable) set using the set_remote_computer_exec() method.
For both codes, one can set some code to be executed right before or right after the execution of the code, using the set_preexec_code() and set_postexec_code() methods (e.g., the set_preexec_code() can be used to load specific modules required for the code to be run).
-
HIDDEN_KEY
= 'hidden'¶
-
__abstractmethods__
= frozenset({})¶
-
__init__
(remote_computer_exec=None, local_executable=None, input_plugin_name=None, files=None, **kwargs)[source]¶ - Parameters
backend_entity (
aiida.orm.implementation.BackendEntity
) – the backend model supporting this entity
-
__module__
= 'aiida.orm.nodes.data.code'¶
-
_abc_impl
= <_abc_data object>¶
-
_logger
= <Logger aiida.orm.nodes.data.code.Code (REPORT)>¶
-
_plugin_type_string
= 'data.code.Code.'¶
-
_query_type_string
= 'data.code.'¶
-
_set_local
()[source]¶ Set the code as a ‘local’ code, meaning that all the files belonging to the code will be copied to the cluster, and the file set with set_exec_filename will be run.
It also deletes the flags related to the local case (if any)
-
_set_remote
()[source]¶ Set the code as a ‘remote’ code, meaning that the code itself has no files attached, but only a location on a remote computer (with an absolute path of the executable on the remote computer).
It also deletes the flags related to the local case (if any)
-
_validate
()[source]¶ Perform validation of the Data object.
Note
validation of data source checks license and requires attribution to be provided in field ‘description’ of source in the case of any CC-BY* license. If such requirement is too strict, one can remove/comment it out.
-
can_run_on
(computer)[source]¶ Return True if this code can run on the given computer, False otherwise.
Local codes can run on any machine; remote codes can run only on the machine on which they reside.
TODO: add filters to mask the remote machines on which a local code can run.
-
property
full_label
¶ Get full label of this code.
Returns label of the form <code-label>@<computer-name>.
-
classmethod
get
(pk=None, label=None, machinename=None)[source]¶ Get a Computer object with given identifier string, that can either be the numeric ID (pk), or the label (and computername) (if unique).
- Parameters
pk – the numeric ID (pk) for code
label – the code label identifying the code to load
machinename – the machine name where code is setup
- Raises
aiida.common.NotExistent – if no code identified by the given string is found
aiida.common.MultipleObjectsError – if the string cannot identify uniquely a code
aiida.common.InputValidationError – if neither a pk nor a label was passed in
-
get_append_text
()[source]¶ Return the postexec_code, or an empty string if no post-exec code was defined.
-
get_builder
()[source]¶ Create and return a new ProcessBuilder for the CalcJob class of the plugin configured for this code.
The configured calculation plugin class is defined by the get_input_plugin_name method.
Note
it also sets the
builder.code
value.- Returns
a ProcessBuilder instance with the code input already populated with ourselves
- Raises
aiida.common.EntryPointError – if the specified plugin does not exist.
ValueError – if no default plugin was specified.
-
classmethod
get_code_helper
(label, machinename=None)[source]¶ - Parameters
label – the code label identifying the code to load
machinename – the machine name where code is setup
- Raises
aiida.common.NotExistent – if no code identified by the given string is found
aiida.common.MultipleObjectsError – if the string cannot identify uniquely a code
-
get_description
()[source]¶ Return a string description of this Code instance.
- Returns
string description of this Code instance
-
get_execname
()[source]¶ Return the executable string to be put in the script. For local codes, it is ./LOCAL_EXECUTABLE_NAME For remote codes, it is the absolute path to the executable.
-
classmethod
get_from_string
(code_string)[source]¶ Get a Computer object with given identifier string in the format label@machinename. See the note below for details on the string detection algorithm.
Note
the (leftmost) ‘@’ symbol is always used to split code and computername. Therefore do not use ‘@’ in the code name if you want to use this function (‘@’ in the computer name are instead valid).
- Parameters
code_string – the code string identifying the code to load
- Raises
aiida.common.NotExistent – if no code identified by the given string is found
aiida.common.MultipleObjectsError – if the string cannot identify uniquely a code
aiida.common.InputValidationError – if code_string is not of string type
-
get_full_text_info
(verbose=False)[source]¶ Return a (multiline) string with a human-readable detailed information on this computer
-
get_input_plugin_name
()[source]¶ Return the name of the default input plugin (or None if no input plugin was set.
-
get_prepend_text
()[source]¶ Return the code that will be put in the scheduler script before the execution, or an empty string if no pre-exec code was defined.
Determines whether the Code is hidden or not
-
is_local
()[source]¶ Return True if the code is ‘local’, False if it is ‘remote’ (see also documentation of the set_local and set_remote functions).
-
classmethod
list_for_plugin
(plugin, labels=True)[source]¶ Return a list of valid code strings for a given plugin.
- Parameters
plugin – The string of the plugin.
labels – if True, return a list of code names, otherwise return the code PKs (integers).
- Returns
a list of string, with the code names if labels is True, otherwise a list of integers with the code PKs.
-
relabel
(new_label, raise_error=True)[source]¶ Relabel this code.
- Parameters
new_label – new code label
raise_error – Set to False in order to return a list of errors instead of raising them.
-
reveal
()[source]¶ Reveal the code (allows to show it in the verdi code list) By default, it is revealed
-
set_append_text
(code)[source]¶ Pass a string of code that will be put in the scheduler script after the execution of the code.
-
set_files
(files)[source]¶ Given a list of filenames (or a single filename string), add it to the path (all at level zero, i.e. without folders). Therefore, be careful for files with the same name!
- Todo
decide whether to check if the Code must be a local executable to be able to call this function.
-
set_input_plugin_name
(input_plugin)[source]¶ Set the name of the default input plugin, to be used for the automatic generation of a new calculation.
-
set_local_executable
(exec_name)[source]¶ Set the filename of the local executable. Implicitly set the code as local.
-
set_prepend_text
(code)[source]¶ Pass a string of code that will be put in the scheduler script before the execution of the code.
-
set_remote_computer_exec
(remote_computer_exec)[source]¶ Set the code as remote, and pass the computer on which it resides and the absolute path on that computer.
- Parameters
remote_computer_exec – a tuple (computer, remote_exec_path), where computer is a aiida.orm.Computer and remote_exec_path is the absolute path of the main executable on remote computer.
-
class
aiida.orm.nodes.data.
Float
(*args, **kwargs)[source]¶ Bases:
aiida.orm.nodes.data.numeric.NumericType
Data sub class to represent a float value.
-
__abstractmethods__
= frozenset({})¶
-
__module__
= 'aiida.orm.nodes.data.float'¶
-
_abc_impl
= <_abc_data object>¶
-
_logger
= <Logger aiida.orm.nodes.data.float.Float (REPORT)>¶
-
_plugin_type_string
= 'data.float.Float.'¶
-
_query_type_string
= 'data.float.'¶
-
_type
¶ alias of
builtins.float
-
-
class
aiida.orm.nodes.data.
FolderData
(**kwargs)[source]¶ Bases:
aiida.orm.nodes.data.data.Data
Data sub class to represent a folder on a file system.
-
__abstractmethods__
= frozenset({})¶
-
__init__
(**kwargs)[source]¶ Construct a new FolderData to which any files and folders can be added.
Use the tree keyword to simply wrap a directory:
folder = FolderData(tree=’/absolute/path/to/directory’)
Alternatively, one can construct the node first and then use the various repository methods to add objects:
folder = FolderData() folder.put_object_from_tree(‘/absolute/path/to/directory’) folder.put_object_from_filepath(‘/absolute/path/to/file.txt’) folder.put_object_from_filelike(filelike_object)
- Parameters
tree (str) – absolute path to a folder to wrap
-
__module__
= 'aiida.orm.nodes.data.folder'¶
-
_abc_impl
= <_abc_data object>¶
-
_logger
= <Logger aiida.orm.nodes.data.folder.FolderData (REPORT)>¶
-
_plugin_type_string
= 'data.folder.FolderData.'¶
-
_query_type_string
= 'data.folder.'¶
-
-
class
aiida.orm.nodes.data.
Int
(*args, **kwargs)[source]¶ Bases:
aiida.orm.nodes.data.numeric.NumericType
Data sub class to represent an integer value.
-
__abstractmethods__
= frozenset({})¶
-
__module__
= 'aiida.orm.nodes.data.int'¶
-
_abc_impl
= <_abc_data object>¶
-
_logger
= <Logger aiida.orm.nodes.data.int.Int (REPORT)>¶
-
_plugin_type_string
= 'data.int.Int.'¶
-
_query_type_string
= 'data.int.'¶
-
_type
¶ alias of
builtins.int
-
-
class
aiida.orm.nodes.data.
List
(**kwargs)[source]¶ Bases:
aiida.orm.nodes.data.data.Data
,collections.abc.MutableSequence
Data sub class to represent a list.
-
_LIST_KEY
= 'list'¶
-
__abstractmethods__
= frozenset({})¶
-
__hash__
= None¶
-
__init__
(**kwargs)[source]¶ - Parameters
backend_entity (
aiida.orm.implementation.BackendEntity
) – the backend model supporting this entity
-
__module__
= 'aiida.orm.nodes.data.list'¶
-
_abc_impl
= <_abc_data object>¶
-
_logger
= <Logger aiida.orm.nodes.data.list.List (REPORT)>¶
-
_plugin_type_string
= 'data.list.List.'¶
-
_query_type_string
= 'data.list.'¶
-
_using_list_reference
()[source]¶ This function tells the class if we are using a list reference. This means that calls to self.get_list return a reference rather than a copy of the underlying list and therefore self.set_list need not be called. This knwoledge is essential to make sure this class is performant.
Currently the implementation assumes that if the node needs to be stored then it is using the attributes cache which is a reference.
- Returns
True if using self.get_list returns a reference to the underlying sequence. False otherwise.
- Return type
bool
-
index
(value[, start[, stop]]) → integer -- return first index of value.[source]¶ Raises ValueError if the value is not present.
Supporting start and stop arguments is optional, but recommended.
-
pop
([index]) → item -- remove and return item at index (default last).[source]¶ Raise IndexError if list is empty or index is out of range.
-
-
class
aiida.orm.nodes.data.
OrbitalData
(backend=None, user=None, computer=None, **kwargs)[source]¶ Bases:
aiida.orm.nodes.data.data.Data
Used for storing collections of orbitals, as well as providing methods for accessing them internally.
-
__abstractmethods__
= frozenset({})¶
-
__module__
= 'aiida.orm.nodes.data.orbital'¶
-
_abc_impl
= <_abc_data object>¶
-
_logger
= <Logger aiida.orm.nodes.data.orbital.OrbitalData (REPORT)>¶
-
_plugin_type_string
= 'data.orbital.OrbitalData.'¶
-
_query_type_string
= 'data.orbital.'¶
-
clear_orbitals
()[source]¶ Remove all orbitals that were added to the class Cannot work if OrbitalData has been already stored
-
get_orbitals
(**kwargs)[source]¶ Returns all orbitals by default. If a site is provided, returns all orbitals cooresponding to the location of that site, additional arguments may be provided, which act as filters on the retrieved orbitals.
- Parameters
site – if provided, returns all orbitals with position of site
- Kwargs
attributes than can filter the set of returned orbitals
- Return list_of_outputs
a list of orbitals
-
-
class
aiida.orm.nodes.data.
Dict
(**kwargs)[source]¶ Bases:
aiida.orm.nodes.data.data.Data
Data sub class to represent a dictionary.
-
__abstractmethods__
= frozenset({})¶
-
__init__
(**kwargs)[source]¶ Store a dictionary as a Node instance.
Usual rules for attribute names apply, in particular, keys cannot start with an underscore, or a ValueError will be raised.
Initial attributes can be changed, deleted or added as long as the node is not stored.
- Parameters
dict – the dictionary to set
-
__module__
= 'aiida.orm.nodes.data.dict'¶
-
_abc_impl
= <_abc_data object>¶
-
_logger
= <Logger aiida.orm.nodes.data.dict.Dict (REPORT)>¶
-
_plugin_type_string
= 'data.dict.Dict.'¶
-
_query_type_string
= 'data.dict.'¶
-
property
dict
¶ Return an instance of AttributeManager that transforms the dictionary into an attribute dict.
Note
this will allow one to do node.dict.key as well as node.dict[key].
- Returns
an instance of the AttributeResultManager.
-
keys
()[source]¶ Iterator of valid keys stored in the Dict object.
- Returns
iterator over the keys of the current dictionary
-
-
class
aiida.orm.nodes.data.
RemoteData
(remote_path=None, **kwargs)[source]¶ Bases:
aiida.orm.nodes.data.data.Data
Store a link to a file or folder on a remote machine.
Remember to pass a computer!
-
__abstractmethods__
= frozenset({})¶
-
__init__
(remote_path=None, **kwargs)[source]¶ - Parameters
backend_entity (
aiida.orm.implementation.BackendEntity
) – the backend model supporting this entity
-
__module__
= 'aiida.orm.nodes.data.remote'¶
-
_abc_impl
= <_abc_data object>¶
-
_logger
= <Logger aiida.orm.nodes.data.remote.RemoteData (REPORT)>¶
-
_plugin_type_string
= 'data.remote.RemoteData.'¶
-
_query_type_string
= 'data.remote.'¶
-
_validate
()[source]¶ Perform validation of the Data object.
Note
validation of data source checks license and requires attribution to be provided in field ‘description’ of source in the case of any CC-BY* license. If such requirement is too strict, one can remove/comment it out.
-
getfile
(relpath, destpath)[source]¶ Connects to the remote folder and gets a string with the (full) content of the file.
- Parameters
relpath – The relative path of the file to show.
destpath – A path on the local computer to get the file
- Returns
a string with the file content
-
property
is_empty
¶ Check if remote folder is empty
-
listdir
(relpath='.')[source]¶ Connects to the remote folder and lists the directory content.
- Parameters
relpath – If ‘relpath’ is specified, lists the content of the given subfolder.
- Returns
a flat list of file/directory names (as strings).
-
listdir_withattributes
(path='.')[source]¶ Connects to the remote folder and lists the directory content.
- Parameters
relpath – If ‘relpath’ is specified, lists the content of the given subfolder.
- Returns
a list of dictionaries, where the documentation is in :py:class:Transport.listdir_withattributes.
-
-
class
aiida.orm.nodes.data.
SinglefileData
(file, filename=None, **kwargs)[source]¶ Bases:
aiida.orm.nodes.data.data.Data
Data class that can be used to store a single file in its repository.
-
DEFAULT_FILENAME
= 'file.txt'¶
-
__abstractmethods__
= frozenset({})¶
-
__init__
(file, filename=None, **kwargs)[source]¶ Construct a new instance and set the contents to that of the file.
- Parameters
file – an absolute filepath or filelike object whose contents to copy. Hint: Pass io.BytesIO(b”my string”) to construct the SinglefileData directly from a string.
filename – specify filename to use (defaults to name of provided file).
-
__module__
= 'aiida.orm.nodes.data.singlefile'¶
-
_abc_impl
= <_abc_data object>¶
-
_logger
= <Logger aiida.orm.nodes.data.singlefile.SinglefileData (REPORT)>¶
-
_plugin_type_string
= 'data.singlefile.SinglefileData.'¶
-
_query_type_string
= 'data.singlefile.'¶
-
_validate
()[source]¶ Ensure that there is one object stored in the repository, whose key matches value set for filename attr.
-
property
filename
¶ Return the name of the file stored.
- Returns
the filename under which the file is stored in the repository
-
get_content
()[source]¶ Return the content of the single file stored for this data node.
- Returns
the content of the file as a string
-
open
(key=None, mode='r')[source]¶ Return an open file handle to the content of this data node.
- Parameters
key – optional key within the repository, by default is the filename set in the attributes
mode – the mode with which to open the file handle (default: read mode)
- Returns
a file handle
-
set_file
(file, filename=None)[source]¶ Store the content of the file in the node’s repository, deleting any other existing objects.
- Parameters
file – an absolute filepath or filelike object whose contents to copy Hint: Pass io.BytesIO(b”my string”) to construct the file directly from a string.
filename – specify filename to use (defaults to name of provided file).
-
-
class
aiida.orm.nodes.data.
Str
(*args, **kwargs)[source]¶ Bases:
aiida.orm.nodes.data.base.BaseType
Data sub class to represent a string value.
-
__abstractmethods__
= frozenset({})¶
-
__module__
= 'aiida.orm.nodes.data.str'¶
-
_abc_impl
= <_abc_data object>¶
-
_logger
= <Logger aiida.orm.nodes.data.str.Str (REPORT)>¶
-
_plugin_type_string
= 'data.str.Str.'¶
-
_query_type_string
= 'data.str.'¶
-
_type
¶ alias of
builtins.str
-
-
class
aiida.orm.nodes.data.
StructureData
(cell=None, pbc=None, ase=None, pymatgen=None, pymatgen_structure=None, pymatgen_molecule=None, **kwargs)[source]¶ Bases:
aiida.orm.nodes.data.data.Data
This class contains the information about a given structure, i.e. a collection of sites together with a cell, the boundary conditions (whether they are periodic or not) and other related useful information.
-
__abstractmethods__
= frozenset({})¶
-
__init__
(cell=None, pbc=None, ase=None, pymatgen=None, pymatgen_structure=None, pymatgen_molecule=None, **kwargs)[source]¶ - Parameters
backend_entity (
aiida.orm.implementation.BackendEntity
) – the backend model supporting this entity
-
__module__
= 'aiida.orm.nodes.data.structure'¶
-
_abc_impl
= <_abc_data object>¶
-
_adjust_default_cell
(vacuum_factor=1.0, vacuum_addition=10.0, pbc=(False, False, False))[source]¶ If the structure was imported from an xyz file, it lacks a defined cell, and the default cell is taken ([[1,0,0], [0,1,0], [0,0,1]]), leading to an unphysical definition of the structure. This method will adjust the cell
-
_dimensionality_label
= {0: '', 1: 'length', 2: 'surface', 3: 'volume'}¶
-
_get_object_ase
()[source]¶ Converts
StructureData
to ase.Atoms- Returns
an ase.Atoms object
-
_get_object_phonopyatoms
()[source]¶ Converts StructureData to PhonopyAtoms
- Returns
a PhonopyAtoms object
-
_get_object_pymatgen
(**kwargs)[source]¶ Converts
StructureData
to pymatgen object- Returns
a pymatgen Structure for structures with periodic boundary conditions (in three dimensions) and Molecule otherwise
Note
Requires the pymatgen module (version >= 3.0.13, usage of earlier versions may cause errors).
-
_get_object_pymatgen_molecule
(**kwargs)[source]¶ Converts
StructureData
to pymatgen Molecule object- Returns
a pymatgen Molecule object corresponding to this
StructureData
object.
Note
Requires the pymatgen module (version >= 3.0.13, usage of earlier versions may cause errors)
-
_get_object_pymatgen_structure
(**kwargs)[source]¶ Converts
StructureData
to pymatgen Structure object :param add_spin: True to add the spins to the pymatgen structure. Default is False (no spin added).Note
The spins are set according to the following rule:
if the kind name ends with 1 -> spin=+1
if the kind name ends with 2 -> spin=-1
- Returns
a pymatgen Structure object corresponding to this
StructureData
object- Raises
ValueError – if periodic boundary conditions does not hold in at least one dimension of real space; if there are partial occupancies together with spins (defined by kind names ending with ‘1’ or ‘2’).
Note
Requires the pymatgen module (version >= 3.0.13, usage of earlier versions may cause errors)
-
_logger
= <Logger aiida.orm.nodes.data.structure.StructureData (REPORT)>¶
-
_plugin_type_string
= 'data.structure.StructureData.'¶
-
_prepare_chemdoodle
(main_file_name='')[source]¶ Write the given structure to a string of format required by ChemDoodle.
-
_prepare_xsf
(main_file_name='')[source]¶ Write the given structure to a string of format XSF (for XCrySDen).
-
_query_type_string
= 'data.structure.'¶
-
_set_incompatibilities
= [('ase', 'cell'), ('ase', 'pbc'), ('ase', 'pymatgen'), ('ase', 'pymatgen_molecule'), ('ase', 'pymatgen_structure'), ('cell', 'pymatgen'), ('cell', 'pymatgen_molecule'), ('cell', 'pymatgen_structure'), ('pbc', 'pymatgen'), ('pbc', 'pymatgen_molecule'), ('pbc', 'pymatgen_structure'), ('pymatgen', 'pymatgen_molecule'), ('pymatgen', 'pymatgen_structure'), ('pymatgen_molecule', 'pymatgen_structure')]¶
-
append_atom
(**kwargs)[source]¶ Append an atom to the Structure, taking care of creating the corresponding kind.
- Parameters
ase – the ase Atom object from which we want to create a new atom (if present, this must be the only parameter)
position – the position of the atom (three numbers in angstrom)
symbols – passed to the constructor of the Kind object.
weights – passed to the constructor of the Kind object.
name – passed to the constructor of the Kind object. See also the note below.
Note
Note on the ‘name’ parameter (that is, the name of the kind):
if specified, no checks are done on existing species. Simply, a new kind with that name is created. If there is a name clash, a check is done: if the kinds are identical, no error is issued; otherwise, an error is issued because you are trying to store two different kinds with the same name.
if not specified, the name is automatically generated. Before adding the kind, a check is done. If other species with the same properties already exist, no new kinds are created, but the site is added to the existing (identical) kind. (Actually, the first kind that is encountered). Otherwise, the name is made unique first, by adding to the string containing the list of chemical symbols a number starting from 1, until an unique name is found
Note
checks of equality of species are done using the
compare_with()
method.
-
append_kind
(kind)[source]¶ Append a kind to the
StructureData
. It makes a copy of the kind.- Parameters
kind – the site to append, must be a Kind object.
-
append_site
(site)[source]¶ Append a site to the
StructureData
. It makes a copy of the site.- Parameters
site – the site to append. It must be a Site object.
-
property
cell
¶ Returns the cell shape.
- Returns
a 3x3 list of lists.
-
property
cell_angles
¶ Get the angles between the cell lattice vectors in degrees.
-
property
cell_lengths
¶ Get the lengths of cell lattice vectors in angstroms.
-
get_ase
()[source]¶ Get the ASE object. Requires to be able to import ase.
- Returns
an ASE object corresponding to this
StructureData
object.
Note
If any site is an alloy or has vacancies, a ValueError is raised (from the site.get_ase() routine).
-
get_cif
(converter='ase', store=False, **kwargs)[source]¶ Creates
aiida.orm.nodes.data.cif.CifData
.New in version 1.0: Renamed from _get_cif
- Parameters
converter – specify the converter. Default ‘ase’.
store – If True, intermediate calculation gets stored in the AiiDA database for record. Default False.
- Returns
-
get_composition
()[source]¶ Returns the chemical composition of this structure as a dictionary, where each key is the kind symbol (e.g. H, Li, Ba), and each value is the number of occurences of that element in this structure. For BaZrO3 it would return {‘Ba’:1, ‘Zr’:1, ‘O’:3}. No reduction with smallest common divisor!
- Returns
a dictionary with the composition
-
get_description
()[source]¶ Returns a string with infos retrieved from StructureData node’s properties
- Parameters
self – the StructureData node
- Returns
retsrt: the description string
-
get_dimensionality
()[source]¶ This function checks the dimensionality of the structure and calculates its length/surface/volume :return: returns the dimensionality and length/surface/volume
-
get_formula
(mode='hill', separator='')[source]¶ Return a string with the chemical formula.
- Parameters
mode –
a string to specify how to generate the formula, can assume one of the following values:
’hill’ (default): count the number of atoms of each species, then use Hill notation, i.e. alphabetical order with C and H first if one or several C atom(s) is (are) present, e.g.
['C','H','H','H','O','C','H','H','H']
will return'C2H6O'
['S','O','O','H','O','H','O']
will return'H2O4S'
From E. A. Hill, J. Am. Chem. Soc., 22 (8), pp 478–494 (1900)’hill_compact’: same as hill but the number of atoms for each species is divided by the greatest common divisor of all of them, e.g.
['C','H','H','H','O','C','H','H','H','O','O','O']
will return'CH3O2'
’reduce’: group repeated symbols e.g.
['Ba', 'Ti', 'O', 'O', 'O', 'Ba', 'Ti', 'O', 'O', 'O', 'Ba', 'Ti', 'Ti', 'O', 'O', 'O']
will return'BaTiO3BaTiO3BaTi2O3'
’group’: will try to group as much as possible parts of the formula e.g.
['Ba', 'Ti', 'O', 'O', 'O', 'Ba', 'Ti', 'O', 'O', 'O', 'Ba', 'Ti', 'Ti', 'O', 'O', 'O']
will return'(BaTiO3)2BaTi2O3'
’count’: same as hill (i.e. one just counts the number of atoms of each species) without the re-ordering (take the order of the atomic sites), e.g.
['Ba', 'Ti', 'O', 'O', 'O','Ba', 'Ti', 'O', 'O', 'O']
will return'Ba2Ti2O6'
’count_compact’: same as count but the number of atoms for each species is divided by the greatest common divisor of all of them, e.g.
['Ba', 'Ti', 'O', 'O', 'O','Ba', 'Ti', 'O', 'O', 'O']
will return'BaTiO3'
separator – a string used to concatenate symbols. Default empty.
- Returns
a string with the formula
Note
in modes reduce, group, count and count_compact, the initial order in which the atoms were appended by the user is used to group and/or order the symbols in the formula
-
get_kind
(kind_name)[source]¶ Return the kind object associated with the given kind name.
- Parameters
kind_name – String, the name of the kind you want to get
- Returns
The Kind object associated with the given kind_name, if a Kind with the given name is present in the structure.
- Raise
ValueError if the kind_name is not present.
-
get_kind_names
()[source]¶ Return a list of kind names (in the same order of the
self.kinds
property, but return the names rather than Kind objects)Note
This is NOT necessarily a list of chemical symbols! Use get_symbols_set for chemical symbols
- Returns
a list of strings.
-
get_pymatgen
(**kwargs)[source]¶ Get pymatgen object. Returns Structure for structures with periodic boundary conditions (in three dimensions) and Molecule otherwise. :param add_spin: True to add the spins to the pymatgen structure. Default is False (no spin added).
Note
The spins are set according to the following rule:
if the kind name ends with 1 -> spin=+1
if the kind name ends with 2 -> spin=-1
Note
Requires the pymatgen module (version >= 3.0.13, usage of earlier versions may cause errors).
-
get_pymatgen_molecule
()[source]¶ Get the pymatgen Molecule object.
Note
Requires the pymatgen module (version >= 3.0.13, usage of earlier versions may cause errors).
- Returns
a pymatgen Molecule object corresponding to this
StructureData
object.
-
get_pymatgen_structure
(**kwargs)[source]¶ Get the pymatgen Structure object. :param add_spin: True to add the spins to the pymatgen structure. Default is False (no spin added).
Note
The spins are set according to the following rule:
if the kind name ends with 1 -> spin=+1
if the kind name ends with 2 -> spin=-1
Note
Requires the pymatgen module (version >= 3.0.13, usage of earlier versions may cause errors).
- Returns
a pymatgen Structure object corresponding to this
StructureData
object.- Raises
ValueError – if periodic boundary conditions do not hold in at least one dimension of real space.
-
get_site_kindnames
()[source]¶ Return a list with length equal to the number of sites of this structure, where each element of the list is the kind name of the corresponding site.
Note
This is NOT necessarily a list of chemical symbols! Use
[ self.get_kind(s.kind_name).get_symbols_string() for s in self.sites]
for chemical symbols- Returns
a list of strings
-
get_symbols_set
()[source]¶ Return a set containing the names of all elements involved in this structure (i.e., for it joins the list of symbols for each kind k in the structure).
- Returns
a set of strings of element names.
-
property
has_vacancies
¶ Return whether the structure has vacancies in the structure.
- Returns
a boolean, True if at least one kind has a vacancy
-
property
is_alloy
¶ Return whether the structure contains any alloy kinds.
- Returns
a boolean, True if at least one kind is an alloy
-
property
kinds
¶ Returns a list of kinds.
-
property
pbc
¶ Get the periodic boundary conditions.
- Returns
a tuple of three booleans, each one tells if there are periodic boundary conditions for the i-th real-space direction (i=1,2,3)
-
reset_cell
(new_cell)[source]¶ Reset the cell of a structure not yet stored to a new value.
- Parameters
new_cell – list specifying the cell vectors
- Raises
ModificationNotAllowed: if object is already stored
-
reset_sites_positions
(new_positions, conserve_particle=True)[source]¶ Replace all the Site positions attached to the Structure
- Parameters
new_positions – list of (3D) positions for every sites.
conserve_particle – if True, allows the possibility of removing a site. currently not implemented.
- Raises
aiida.common.ModificationNotAllowed – if object is stored already
ValueError – if positions are invalid
Note
it is assumed that the order of the new_positions is given in the same order of the one it’s substituting, i.e. the kind of the site will not be checked.
-
set_pymatgen
(obj, **kwargs)[source]¶ Load the structure from a pymatgen object.
Note
Requires the pymatgen module (version >= 3.0.13, usage of earlier versions may cause errors).
-
set_pymatgen_molecule
(mol, margin=5)[source]¶ Load the structure from a pymatgen Molecule object.
- Parameters
margin – the margin to be added in all directions of the bounding box of the molecule.
Note
Requires the pymatgen module (version >= 3.0.13, usage of earlier versions may cause errors).
-
set_pymatgen_structure
(struct)[source]¶ Load the structure from a pymatgen Structure object.
Note
periodic boundary conditions are set to True in all three directions.
Note
Requires the pymatgen module (version >= 3.3.5, usage of earlier versions may cause errors).
- Raises
ValueError – if there are partial occupancies together with spins.
-
property
sites
¶ Returns a list of sites.
-
-
class
aiida.orm.nodes.data.
UpfData
(file=None, filename=None, source=None, **kwargs)[source]¶ Bases:
aiida.orm.nodes.data.singlefile.SinglefileData
Data sub class to represent a pseudopotential single file in UPF format.
-
__abstractmethods__
= frozenset({})¶
-
__init__
(file=None, filename=None, source=None, **kwargs)[source]¶ Create UpfData instance from pseudopotential file.
- Parameters
file – filepath or filelike object of the UPF potential file to store. Hint: Pass io.BytesIO(b”my string”) to construct directly from a string.
filename – specify filename to use (defaults to name of provided file).
source – Dictionary with information on source of the potential (see “.source” property).
-
__module__
= 'aiida.orm.nodes.data.upf'¶
-
_abc_impl
= <_abc_data object>¶
-
_logger
= <Logger aiida.orm.nodes.data.upf.UpfData (REPORT)>¶
-
_plugin_type_string
= 'data.upf.UpfData.'¶
-
_query_type_string
= 'data.upf.'¶
-
property
element
¶ Return the element of the UPF pseudopotential.
- Returns
the element
-
classmethod
from_md5
(md5)[source]¶ Return a list of all UpfData that match the given md5 hash.
Note
assumes hash of stored UpfData nodes is stored in the md5 attribute
- Parameters
md5 – the file hash
- Returns
list of existing UpfData nodes that have the same md5 hash
-
classmethod
get_or_create
(filepath, use_first=False, store_upf=True)[source]¶ Get the UpfData with the same md5 of the given file, or create it if it does not yet exist.
- Parameters
filepath – an absolute filepath on disk
use_first – if False (default), raise an exception if more than one potential is found. If it is True, instead, use the first available pseudopotential.
store_upf – boolean, if false, the UpfData if created will not be stored.
- Returns
tuple of UpfData and boolean indicating whether it was created.
-
classmethod
get_upf_group
(group_label)[source]¶ Return the UPF family group with the given label.
- Parameters
group_label – the family group label
- Returns
the Group with the given label, if it exists
-
classmethod
get_upf_groups
(filter_elements=None, user=None)[source]¶ Return all names of groups of type UpfFamily, possibly with some filters.
- Parameters
filter_elements – A string or a list of strings. If present, returns only the groups that contains one UPF for every element present in the list. The default is None, meaning that all families are returned.
user – if None (default), return the groups for all users. If defined, it should be either a User instance or the user email.
- Returns
list of Group entities of type UPF.
-
property
md5sum
¶ Return the md5 checksum of the UPF pseudopotential file.
- Returns
the md5 checksum
-
set_file
(file, filename=None)[source]¶ Store the file in the repository and parse it to set the element and md5 attributes.
- Parameters
file – filepath or filelike object of the UPF potential file to store. Hint: Pass io.BytesIO(b”my string”) to construct the file directly from a string.
filename – specify filename to use (defaults to name of provided file).
-
store
(*args, **kwargs)[source]¶ Store the node, reparsing the file so that the md5 and the element are correctly reset.
-
upffamily_type_string
= 'data.upf'¶
-
-
class
aiida.orm.nodes.data.
NumericType
(*args, **kwargs)[source]¶ Bases:
aiida.orm.nodes.data.base.BaseType
Sub class of Data to store numbers, overloading common operators (
+
,*
, …).-
__abstractmethods__
= frozenset({})¶
-
__module__
= 'aiida.orm.nodes.data.numeric'¶
-
_abc_impl
= <_abc_data object>¶
-
_logger
= <Logger aiida.orm.nodes.data.numeric.NumericType (REPORT)>¶
-
_plugin_type_string
= 'data.numeric.NumericType.'¶
-
_query_type_string
= 'data.numeric.'¶
-
Subpackages¶
Submodules¶
Data sub class to be used as a base for data containers that represent base python data types.
-
class
aiida.orm.nodes.data.base.
BaseType
(*args, **kwargs)[source]¶ Bases:
aiida.orm.nodes.data.data.Data
Data sub class to be used as a base for data containers that represent base python data types.
-
__abstractmethods__
= frozenset({})¶
-
__hash__
= None¶
-
__init__
(*args, **kwargs)[source]¶ - Parameters
backend_entity (
aiida.orm.implementation.BackendEntity
) – the backend model supporting this entity
-
__module__
= 'aiida.orm.nodes.data.base'¶
-
_abc_impl
= <_abc_data object>¶
-
_logger
= <Logger aiida.orm.nodes.data.base.BaseType (REPORT)>¶
-
_plugin_type_string
= 'data.base.BaseType.'¶
-
_query_type_string
= 'data.base.'¶
-
property
value
¶
-
-
aiida.orm.nodes.data.base.
to_aiida_type
(value)[source]¶ Turns basic Python types (str, int, float, bool) into the corresponding AiiDA types.
Data sub class to represent a boolean value.
-
class
aiida.orm.nodes.data.bool.
Bool
(*args, **kwargs)[source]¶ Bases:
aiida.orm.nodes.data.base.BaseType
Data sub class to represent a boolean value.
-
__abstractmethods__
= frozenset({})¶
-
__module__
= 'aiida.orm.nodes.data.bool'¶
-
_abc_impl
= <_abc_data object>¶
-
_logger
= <Logger aiida.orm.nodes.data.bool.Bool (REPORT)>¶
-
_plugin_type_string
= 'data.bool.Bool.'¶
-
_query_type_string
= 'data.bool.'¶
-
_type
¶ alias of
builtins.bool
-
Tools for handling Crystallographic Information Files (CIF)
-
class
aiida.orm.nodes.data.cif.
CifData
(ase=None, file=None, filename=None, values=None, source=None, scan_type=None, parse_policy=None, **kwargs)[source]¶ Bases:
aiida.orm.nodes.data.singlefile.SinglefileData
Wrapper for Crystallographic Interchange File (CIF)
Note
the file (physical) is held as the authoritative source of information, so all conversions are done through the physical file: when setting
ase
orvalues
, a physical CIF file is generated first, the values are updated from the physical CIF file.-
_PARSE_POLICIES
= ('eager', 'lazy')¶
-
_PARSE_POLICY_DEFAULT
= 'eager'¶
-
_SCAN_TYPES
= ('standard', 'flex')¶
-
_SCAN_TYPE_DEFAULT
= 'standard'¶
-
_SET_INCOMPATIBILITIES
= [('ase', 'file'), ('ase', 'values'), ('file', 'values')]¶
-
__abstractmethods__
= frozenset({})¶
-
__init__
(ase=None, file=None, filename=None, values=None, source=None, scan_type=None, parse_policy=None, **kwargs)[source]¶ Construct a new instance and set the contents to that of the file.
- Parameters
file – an absolute filepath or filelike object for CIF. Hint: Pass io.BytesIO(b”my string”) to construct the SinglefileData directly from a string.
filename – specify filename to use (defaults to name of provided file).
ase – ASE Atoms object to construct the CifData instance from.
values – PyCifRW CifFile object to construct the CifData instance from.
source –
scan_type – scan type string for parsing with PyCIFRW (‘standard’ or ‘flex’). See CifFile.ReadCif
parse_policy – ‘eager’ (parse CIF file on set_file) or ‘lazy’ (defer parsing until needed)
-
__module__
= 'aiida.orm.nodes.data.cif'¶
-
_abc_impl
= <_abc_data object>¶
-
_ase
= None¶
-
_logger
= <Logger aiida.orm.nodes.data.cif.CifData (REPORT)>¶
-
_plugin_type_string
= 'data.cif.CifData.'¶
-
_prepare_cif
(**kwargs)[source]¶ Return CIF string of CifData object.
If parsed values are present, a CIF string is created and written to file. If no parsed values are present, the CIF string is read from file.
-
_query_type_string
= 'data.cif.'¶
-
_values
= None¶
-
property
ase
¶ ASE object, representing the CIF.
Note
requires ASE module.
-
classmethod
from_md5
(md5)[source]¶ Return a list of all CIF files that match a given MD5 hash.
Note
the hash has to be stored in a
_md5
attribute, otherwise the CIF file will not be found.
-
get_ase
(**kwargs)[source]¶ Returns ASE object, representing the CIF. This function differs from the property
ase
by the possibility to pass the keyworded arguments (kwargs) to ase.io.cif.read_cif().Note
requires ASE module.
-
get_formulae
(mode='sum')[source]¶ Return chemical formulae specified in CIF file.
Note: This does not compute the formula, it only reads it from the appropriate tag. Use refine_inline to compute formulae.
-
classmethod
get_or_create
(filename, use_first=False, store_cif=True)[source]¶ Pass the same parameter of the init; if a file with the same md5 is found, that CifData is returned.
- Parameters
filename – an absolute filename on disk
use_first – if False (default), raise an exception if more than one CIF file is found. If it is True, instead, use the first available CIF file.
store_cif (bool) – If false, the CifData objects are not stored in the database. default=True.
- Return (cif, created)
where cif is the CifData object, and create is either True if the object was created, or False if the object was retrieved from the DB.
-
get_structure
(converter='pymatgen', store=False, **kwargs)[source]¶ Creates
aiida.orm.nodes.data.structure.StructureData
.New in version 1.0: Renamed from _get_aiida_structure
- Parameters
converter – specify the converter. Default ‘pymatgen’.
store – if True, intermediate calculation gets stored in the AiiDA database for record. Default False.
primitive_cell – if True, primitive cell is returned, conventional cell if False. Default False.
occupancy_tolerance – If total occupancy of a site is between 1 and occupancy_tolerance, the occupancies will be scaled down to 1. (pymatgen only)
site_tolerance – This tolerance is used to determine if two sites are sitting in the same position, in which case they will be combined to a single disordered site. Defaults to 1e-4. (pymatgen only)
- Returns
-
property
has_atomic_sites
¶ Returns whether there are any atomic sites defined in the cif data. That is to say, it will check all the values for the _atom_site_fract_* tags and if they are all equal to ? that means there are no relevant atomic sites defined and the function will return False. In all other cases the function will return True
- Returns
False when at least one atomic site fractional coordinate is not equal to ? and True otherwise
-
property
has_attached_hydrogens
¶ Check if there are hydrogens without coordinates, specified as attached to the atoms of the structure.
- Returns
True if there are attached hydrogens, False otherwise.
-
property
has_partial_occupancies
¶ Return if the cif data contains partial occupancies
A partial occupancy is defined as site with an occupancy that differs from unity, within a precision of 1E-6
- Returns
True if there are partial occupancies, False otherwise
-
property
has_undefined_atomic_sites
¶ Return whether the cif data contains any undefined atomic sites.
An undefined atomic site is defined as a site where at least one of the fractional coordinates specified in the _atom_site_fract_* tags, cannot be successfully interpreted as a float. If the cif data contains any site that matches this description, or it does not contain any atomic site tags at all, the cif data is said to have undefined atomic sites.
- Returns
boolean, True if no atomic sites are defined or if any of the defined sites contain undefined positions and False otherwise
-
property
has_unknown_species
¶ Returns whether the cif contains atomic species that are not recognized by AiiDA.
The known species are taken from the elements dictionary in aiida.common.constants, with the exception of the “unknown” placeholder element with symbol ‘X’, as this could not be used to construct a real structure. If any of the formula of the cif data contain species that are not in that elements dictionary, the function will return True and False in all other cases. If there is no formulae to be found, it will return None
- Returns
True when there are unknown species in any of the formulae, False if not, None if no formula found
-
parse
(scan_type=None)[source]¶ Parses CIF file and sets attributes.
- Parameters
scan_type – See set_scan_type
-
static
read_cif
(fileobj, index=-1, **kwargs)[source]¶ A wrapper method that simulates the behavior of the old function ase.io.cif.read_cif by using the new generic ase.io.read function.
Somewhere from 3.12 to 3.17 the tag concept was bundled with each Atom object. When reading a CIF file, this is incremented and signifies the atomic species, even though the CIF file do not have specific tags embedded. On reading CIF files we thus force the ASE tag to zero for all Atom elements.
-
set_ase
(aseatoms)[source]¶ Set the contents of the CifData starting from an ASE atoms object
- Parameters
aseatoms – the ASE atoms object
-
set_file
(file, filename=None)[source]¶ Set the file.
If the source is set and the MD5 checksum of new file is different from the source, the source has to be deleted.
- Parameters
file – filepath or filelike object of the CIF file to store. Hint: Pass io.BytesIO(b”my string”) to construct the file directly from a string.
filename – specify filename to use (defaults to name of provided file).
-
set_parse_policy
(parse_policy)[source]¶ Set the parse policy.
- Parameters
parse_policy – Either ‘eager’ (parse CIF file on set_file) or ‘lazy’ (defer parsing until needed)
-
set_scan_type
(scan_type)[source]¶ Set the scan_type for PyCifRW.
The ‘flex’ scan_type of PyCifRW is faster for large CIF files but does not yet support the CIF2 format as of 02/2018. See the CifFile.ReadCif function
- Parameters
scan_type – Either ‘standard’ or ‘flex’ (see _scan_types)
-
set_values
(values)[source]¶ Set internal representation to values.
Warning: This also writes a new CIF file.
- Parameters
values – PyCifRW CifFile object
Note
requires PyCifRW module.
-
property
values
¶ PyCifRW structure, representing the CIF datablocks.
Note
requires PyCifRW module.
-
-
aiida.orm.nodes.data.cif.
cif_from_ase
(ase, full_occupancies=False, add_fake_biso=False)[source]¶ Construct a CIF datablock from the ASE structure. The code is taken from https://wiki.fysik.dtu.dk/ase/epydoc/ase.io.cif-pysrc.html#write_cif, as the original ASE code contains a bug in printing the Hermann-Mauguin symmetry space group symbol.
- Parameters
ase – ASE “images”
- Returns
array of CIF datablocks
-
aiida.orm.nodes.data.cif.
has_pycifrw
()[source]¶ - Returns
True if the PyCifRW module can be imported, False otherwise.
-
aiida.orm.nodes.data.cif.
parse_formula
(formula)[source]¶ Parses the Hill formulae, written with spaces for separators.
-
aiida.orm.nodes.data.cif.
pycifrw_from_cif
(datablocks, loops=None, names=None)[source]¶ Constructs PyCifRW’s CifFile from an array of CIF datablocks.
- Parameters
datablocks – an array of CIF datablocks
loops – optional dict of lists of CIF tag loops.
names – optional list of datablock names
- Returns
CifFile
-
class
aiida.orm.nodes.data.code.
Code
(remote_computer_exec=None, local_executable=None, input_plugin_name=None, files=None, **kwargs)[source]¶ Bases:
aiida.orm.nodes.data.data.Data
A code entity. It can either be ‘local’, or ‘remote’.
Local code: it is a collection of files/dirs (added using the add_path() method), where one file is flagged as executable (using the set_local_executable() method).
Remote code: it is a pair (remotecomputer, remotepath_of_executable) set using the set_remote_computer_exec() method.
For both codes, one can set some code to be executed right before or right after the execution of the code, using the set_preexec_code() and set_postexec_code() methods (e.g., the set_preexec_code() can be used to load specific modules required for the code to be run).
-
HIDDEN_KEY
= 'hidden'¶
-
__abstractmethods__
= frozenset({})¶
-
__init__
(remote_computer_exec=None, local_executable=None, input_plugin_name=None, files=None, **kwargs)[source]¶ - Parameters
backend_entity (
aiida.orm.implementation.BackendEntity
) – the backend model supporting this entity
-
__module__
= 'aiida.orm.nodes.data.code'¶
-
_abc_impl
= <_abc_data object>¶
-
_logger
= <Logger aiida.orm.nodes.data.code.Code (REPORT)>¶
-
_plugin_type_string
= 'data.code.Code.'¶
-
_query_type_string
= 'data.code.'¶
-
_set_local
()[source]¶ Set the code as a ‘local’ code, meaning that all the files belonging to the code will be copied to the cluster, and the file set with set_exec_filename will be run.
It also deletes the flags related to the local case (if any)
-
_set_remote
()[source]¶ Set the code as a ‘remote’ code, meaning that the code itself has no files attached, but only a location on a remote computer (with an absolute path of the executable on the remote computer).
It also deletes the flags related to the local case (if any)
-
_validate
()[source]¶ Perform validation of the Data object.
Note
validation of data source checks license and requires attribution to be provided in field ‘description’ of source in the case of any CC-BY* license. If such requirement is too strict, one can remove/comment it out.
-
can_run_on
(computer)[source]¶ Return True if this code can run on the given computer, False otherwise.
Local codes can run on any machine; remote codes can run only on the machine on which they reside.
TODO: add filters to mask the remote machines on which a local code can run.
-
property
full_label
¶ Get full label of this code.
Returns label of the form <code-label>@<computer-name>.
-
classmethod
get
(pk=None, label=None, machinename=None)[source]¶ Get a Computer object with given identifier string, that can either be the numeric ID (pk), or the label (and computername) (if unique).
- Parameters
pk – the numeric ID (pk) for code
label – the code label identifying the code to load
machinename – the machine name where code is setup
- Raises
aiida.common.NotExistent – if no code identified by the given string is found
aiida.common.MultipleObjectsError – if the string cannot identify uniquely a code
aiida.common.InputValidationError – if neither a pk nor a label was passed in
-
get_append_text
()[source]¶ Return the postexec_code, or an empty string if no post-exec code was defined.
-
get_builder
()[source]¶ Create and return a new ProcessBuilder for the CalcJob class of the plugin configured for this code.
The configured calculation plugin class is defined by the get_input_plugin_name method.
Note
it also sets the
builder.code
value.- Returns
a ProcessBuilder instance with the code input already populated with ourselves
- Raises
aiida.common.EntryPointError – if the specified plugin does not exist.
ValueError – if no default plugin was specified.
-
classmethod
get_code_helper
(label, machinename=None)[source]¶ - Parameters
label – the code label identifying the code to load
machinename – the machine name where code is setup
- Raises
aiida.common.NotExistent – if no code identified by the given string is found
aiida.common.MultipleObjectsError – if the string cannot identify uniquely a code
-
get_description
()[source]¶ Return a string description of this Code instance.
- Returns
string description of this Code instance
-
get_execname
()[source]¶ Return the executable string to be put in the script. For local codes, it is ./LOCAL_EXECUTABLE_NAME For remote codes, it is the absolute path to the executable.
-
classmethod
get_from_string
(code_string)[source]¶ Get a Computer object with given identifier string in the format label@machinename. See the note below for details on the string detection algorithm.
Note
the (leftmost) ‘@’ symbol is always used to split code and computername. Therefore do not use ‘@’ in the code name if you want to use this function (‘@’ in the computer name are instead valid).
- Parameters
code_string – the code string identifying the code to load
- Raises
aiida.common.NotExistent – if no code identified by the given string is found
aiida.common.MultipleObjectsError – if the string cannot identify uniquely a code
aiida.common.InputValidationError – if code_string is not of string type
-
get_full_text_info
(verbose=False)[source]¶ Return a (multiline) string with a human-readable detailed information on this computer
-
get_input_plugin_name
()[source]¶ Return the name of the default input plugin (or None if no input plugin was set.
-
get_prepend_text
()[source]¶ Return the code that will be put in the scheduler script before the execution, or an empty string if no pre-exec code was defined.
Determines whether the Code is hidden or not
-
is_local
()[source]¶ Return True if the code is ‘local’, False if it is ‘remote’ (see also documentation of the set_local and set_remote functions).
-
classmethod
list_for_plugin
(plugin, labels=True)[source]¶ Return a list of valid code strings for a given plugin.
- Parameters
plugin – The string of the plugin.
labels – if True, return a list of code names, otherwise return the code PKs (integers).
- Returns
a list of string, with the code names if labels is True, otherwise a list of integers with the code PKs.
-
relabel
(new_label, raise_error=True)[source]¶ Relabel this code.
- Parameters
new_label – new code label
raise_error – Set to False in order to return a list of errors instead of raising them.
-
reveal
()[source]¶ Reveal the code (allows to show it in the verdi code list) By default, it is revealed
-
set_append_text
(code)[source]¶ Pass a string of code that will be put in the scheduler script after the execution of the code.
-
set_files
(files)[source]¶ Given a list of filenames (or a single filename string), add it to the path (all at level zero, i.e. without folders). Therefore, be careful for files with the same name!
- Todo
decide whether to check if the Code must be a local executable to be able to call this function.
-
set_input_plugin_name
(input_plugin)[source]¶ Set the name of the default input plugin, to be used for the automatic generation of a new calculation.
-
set_local_executable
(exec_name)[source]¶ Set the filename of the local executable. Implicitly set the code as local.
-
set_prepend_text
(code)[source]¶ Pass a string of code that will be put in the scheduler script before the execution of the code.
-
set_remote_computer_exec
(remote_computer_exec)[source]¶ Set the code as remote, and pass the computer on which it resides and the absolute path on that computer.
- Parameters
remote_computer_exec – a tuple (computer, remote_exec_path), where computer is a aiida.orm.Computer and remote_exec_path is the absolute path of the main executable on remote computer.
Module with Node sub class Data to be used as a base class for data structures.
-
class
aiida.orm.nodes.data.data.
Data
(backend=None, user=None, computer=None, **kwargs)[source]¶ Bases:
aiida.orm.nodes.node.Node
The base class for all Data nodes.
AiiDA Data classes are subclasses of Node and must support multiple inheritance.
Architecture note: Calculation plugins are responsible for converting raw output data from simulation codes to Data nodes. Data nodes are responsible for validating their content (see _validate method).
-
__abstractmethods__
= frozenset({})¶
-
__deepcopy__
(memo)[source]¶ Create a clone of the Data node by pipiong through to the clone method and return the result.
- Returns
an unstored clone of this Data node
-
__module__
= 'aiida.orm.nodes.data.data'¶
-
_abc_impl
= <_abc_data object>¶
-
_export_format_replacements
= {}¶
-
_exportcontent
(fileformat, main_file_name='', **kwargs)[source]¶ Converts a Data node to one (or multiple) files.
Note: Export plugins should return utf8-encoded bytes, which can be directly dumped to file.
- Parameters
fileformat (str) – the extension, uniquely specifying the file format.
main_file_name (str) – (empty by default) Can be used by plugin to infer sensible names for additional files, if necessary. E.g. if the main file is ‘../myplot.gnu’, the plugin may decide to store the dat file under ‘../myplot_data.dat’.
kwargs – other parameters are passed down to the plugin
- Returns
a tuple of length 2. The first element is the content of the otuput file. The second is a dictionary (possibly empty) in the format {filename: filecontent} for any additional file that should be produced.
- Return type
(bytes, dict)
-
_get_converters
()[source]¶ Get all implemented converter formats. The convention is to find all _get_object_… methods. Returns a list of strings.
-
_get_exporters
()[source]¶ Get all implemented export formats. The convention is to find all _prepare_… methods. Returns a dictionary of method_name: method_function
-
_get_importers
()[source]¶ Get all implemented import formats. The convention is to find all _parse_… methods. Returns a list of strings.
-
_logger
= <Logger aiida.orm.nodes.data.data.Data (REPORT)>¶
-
_plugin_type_string
= 'data.data.Data.'¶
-
_query_type_string
= 'data.data.'¶
-
_source_attributes
= ['db_name', 'db_uri', 'uri', 'id', 'version', 'extras', 'source_md5', 'description', 'license']¶
-
_storable
= True¶
-
_unstorable_message
= 'storing for this node has been disabled'¶
-
_validate
()[source]¶ Perform validation of the Data object.
Note
validation of data source checks license and requires attribution to be provided in field ‘description’ of source in the case of any CC-BY* license. If such requirement is too strict, one can remove/comment it out.
-
convert
(object_format=None, *args)[source]¶ Convert the AiiDA StructureData into another python object
- Parameters
object_format – Specify the output format
-
property
creator
¶ Return the creator of this node or None if it does not exist.
- Returns
the creating node or None
-
export
(path, fileformat=None, overwrite=False, **kwargs)[source]¶ Save a Data object to a file.
- Parameters
fname – string with file name. Can be an absolute or relative path.
fileformat – kind of format to use for the export. If not present, it will try to use the extension of the file name.
overwrite – if set to True, overwrites file found at path. Default=False
kwargs – additional parameters to be passed to the _exportcontent method
- Returns
the list of files created
-
classmethod
get_export_formats
()[source]¶ Get the list of valid export format strings
- Returns
a list of valid formats
-
importfile
(fname, fileformat=None)[source]¶ Populate a Data object from a file.
- Parameters
fname – string with file name. Can be an absolute or relative path.
fileformat – kind of format to use for the export. If not present, it will try to use the extension of the file name.
-
importstring
(inputstring, fileformat, **kwargs)[source]¶ Converts a Data object to other text format.
- Parameters
fileformat – a string (the extension) to describe the file format.
- Returns
a string with the structure description.
-
property
source
¶ Gets the dictionary describing the source of Data object. Possible fields:
db_name: name of the source database.
db_uri: URI of the source database.
uri: URI of the object’s source. Should be a permanent link.
id: object’s source identifier in the source database.
version: version of the object’s source.
extras: a dictionary with other fields for source description.
source_md5: MD5 checksum of object’s source.
description: human-readable free form description of the object’s source.
license: a string with a type of license.
Note
some limitations for setting the data source exist, see
_validate
method.- Returns
dictionary describing the source of Data object.
-
Data sub class to represent a dictionary.
-
class
aiida.orm.nodes.data.dict.
Dict
(**kwargs)[source]¶ Bases:
aiida.orm.nodes.data.data.Data
Data sub class to represent a dictionary.
-
__abstractmethods__
= frozenset({})¶
-
__init__
(**kwargs)[source]¶ Store a dictionary as a Node instance.
Usual rules for attribute names apply, in particular, keys cannot start with an underscore, or a ValueError will be raised.
Initial attributes can be changed, deleted or added as long as the node is not stored.
- Parameters
dict – the dictionary to set
-
__module__
= 'aiida.orm.nodes.data.dict'¶
-
_abc_impl
= <_abc_data object>¶
-
_logger
= <Logger aiida.orm.nodes.data.dict.Dict (REPORT)>¶
-
_plugin_type_string
= 'data.dict.Dict.'¶
-
_query_type_string
= 'data.dict.'¶
-
property
dict
¶ Return an instance of AttributeManager that transforms the dictionary into an attribute dict.
Note
this will allow one to do node.dict.key as well as node.dict[key].
- Returns
an instance of the AttributeResultManager.
-
keys
()[source]¶ Iterator of valid keys stored in the Dict object.
- Returns
iterator over the keys of the current dictionary
-
Data sub class to represent a float value.
-
class
aiida.orm.nodes.data.float.
Float
(*args, **kwargs)[source]¶ Bases:
aiida.orm.nodes.data.numeric.NumericType
Data sub class to represent a float value.
-
__abstractmethods__
= frozenset({})¶
-
__module__
= 'aiida.orm.nodes.data.float'¶
-
_abc_impl
= <_abc_data object>¶
-
_logger
= <Logger aiida.orm.nodes.data.float.Float (REPORT)>¶
-
_plugin_type_string
= 'data.float.Float.'¶
-
_query_type_string
= 'data.float.'¶
-
_type
¶ alias of
builtins.float
-
Data sub class to represent a folder on a file system.
-
class
aiida.orm.nodes.data.folder.
FolderData
(**kwargs)[source]¶ Bases:
aiida.orm.nodes.data.data.Data
Data sub class to represent a folder on a file system.
-
__abstractmethods__
= frozenset({})¶
-
__init__
(**kwargs)[source]¶ Construct a new FolderData to which any files and folders can be added.
Use the tree keyword to simply wrap a directory:
folder = FolderData(tree=’/absolute/path/to/directory’)
Alternatively, one can construct the node first and then use the various repository methods to add objects:
folder = FolderData() folder.put_object_from_tree(‘/absolute/path/to/directory’) folder.put_object_from_filepath(‘/absolute/path/to/file.txt’) folder.put_object_from_filelike(filelike_object)
- Parameters
tree (str) – absolute path to a folder to wrap
-
__module__
= 'aiida.orm.nodes.data.folder'¶
-
_abc_impl
= <_abc_data object>¶
-
_logger
= <Logger aiida.orm.nodes.data.folder.FolderData (REPORT)>¶
-
_plugin_type_string
= 'data.folder.FolderData.'¶
-
_query_type_string
= 'data.folder.'¶
-
Data sub class to represent an integer value.
-
class
aiida.orm.nodes.data.int.
Int
(*args, **kwargs)[source]¶ Bases:
aiida.orm.nodes.data.numeric.NumericType
Data sub class to represent an integer value.
-
__abstractmethods__
= frozenset({})¶
-
__module__
= 'aiida.orm.nodes.data.int'¶
-
_abc_impl
= <_abc_data object>¶
-
_logger
= <Logger aiida.orm.nodes.data.int.Int (REPORT)>¶
-
_plugin_type_string
= 'data.int.Int.'¶
-
_query_type_string
= 'data.int.'¶
-
_type
¶ alias of
builtins.int
-
Data sub class to represent a list.
-
class
aiida.orm.nodes.data.list.
List
(**kwargs)[source]¶ Bases:
aiida.orm.nodes.data.data.Data
,collections.abc.MutableSequence
Data sub class to represent a list.
-
_LIST_KEY
= 'list'¶
-
__abstractmethods__
= frozenset({})¶
-
__hash__
= None¶
-
__init__
(**kwargs)[source]¶ - Parameters
backend_entity (
aiida.orm.implementation.BackendEntity
) – the backend model supporting this entity
-
__module__
= 'aiida.orm.nodes.data.list'¶
-
_abc_impl
= <_abc_data object>¶
-
_logger
= <Logger aiida.orm.nodes.data.list.List (REPORT)>¶
-
_plugin_type_string
= 'data.list.List.'¶
-
_query_type_string
= 'data.list.'¶
-
_using_list_reference
()[source]¶ This function tells the class if we are using a list reference. This means that calls to self.get_list return a reference rather than a copy of the underlying list and therefore self.set_list need not be called. This knwoledge is essential to make sure this class is performant.
Currently the implementation assumes that if the node needs to be stored then it is using the attributes cache which is a reference.
- Returns
True if using self.get_list returns a reference to the underlying sequence. False otherwise.
- Return type
bool
-
index
(value[, start[, stop]]) → integer -- return first index of value.[source]¶ Raises ValueError if the value is not present.
Supporting start and stop arguments is optional, but recommended.
-
pop
([index]) → item -- remove and return item at index (default last).[source]¶ Raise IndexError if list is empty or index is out of range.
-
Module for defintion of base Data sub class for numeric based data types.
-
class
aiida.orm.nodes.data.numeric.
NumericType
(*args, **kwargs)[source]¶ Bases:
aiida.orm.nodes.data.base.BaseType
Sub class of Data to store numbers, overloading common operators (
+
,*
, …).-
__abstractmethods__
= frozenset({})¶
-
__module__
= 'aiida.orm.nodes.data.numeric'¶
-
_abc_impl
= <_abc_data object>¶
-
_logger
= <Logger aiida.orm.nodes.data.numeric.NumericType (REPORT)>¶
-
_plugin_type_string
= 'data.numeric.NumericType.'¶
-
_query_type_string
= 'data.numeric.'¶
-
-
class
aiida.orm.nodes.data.orbital.
OrbitalData
(backend=None, user=None, computer=None, **kwargs)[source]¶ Bases:
aiida.orm.nodes.data.data.Data
Used for storing collections of orbitals, as well as providing methods for accessing them internally.
-
__abstractmethods__
= frozenset({})¶
-
__module__
= 'aiida.orm.nodes.data.orbital'¶
-
_abc_impl
= <_abc_data object>¶
-
_logger
= <Logger aiida.orm.nodes.data.orbital.OrbitalData (REPORT)>¶
-
_plugin_type_string
= 'data.orbital.OrbitalData.'¶
-
_query_type_string
= 'data.orbital.'¶
-
clear_orbitals
()[source]¶ Remove all orbitals that were added to the class Cannot work if OrbitalData has been already stored
-
get_orbitals
(**kwargs)[source]¶ Returns all orbitals by default. If a site is provided, returns all orbitals cooresponding to the location of that site, additional arguments may be provided, which act as filters on the retrieved orbitals.
- Parameters
site – if provided, returns all orbitals with position of site
- Kwargs
attributes than can filter the set of returned orbitals
- Return list_of_outputs
a list of orbitals
-
-
class
aiida.orm.nodes.data.remote.
RemoteData
(remote_path=None, **kwargs)[source]¶ Bases:
aiida.orm.nodes.data.data.Data
Store a link to a file or folder on a remote machine.
Remember to pass a computer!
-
__abstractmethods__
= frozenset({})¶
-
__init__
(remote_path=None, **kwargs)[source]¶ - Parameters
backend_entity (
aiida.orm.implementation.BackendEntity
) – the backend model supporting this entity
-
__module__
= 'aiida.orm.nodes.data.remote'¶
-
_abc_impl
= <_abc_data object>¶
-
_logger
= <Logger aiida.orm.nodes.data.remote.RemoteData (REPORT)>¶
-
_plugin_type_string
= 'data.remote.RemoteData.'¶
-
_query_type_string
= 'data.remote.'¶
-
_validate
()[source]¶ Perform validation of the Data object.
Note
validation of data source checks license and requires attribution to be provided in field ‘description’ of source in the case of any CC-BY* license. If such requirement is too strict, one can remove/comment it out.
-
getfile
(relpath, destpath)[source]¶ Connects to the remote folder and gets a string with the (full) content of the file.
- Parameters
relpath – The relative path of the file to show.
destpath – A path on the local computer to get the file
- Returns
a string with the file content
-
property
is_empty
¶ Check if remote folder is empty
-
listdir
(relpath='.')[source]¶ Connects to the remote folder and lists the directory content.
- Parameters
relpath – If ‘relpath’ is specified, lists the content of the given subfolder.
- Returns
a flat list of file/directory names (as strings).
-
listdir_withattributes
(path='.')[source]¶ Connects to the remote folder and lists the directory content.
- Parameters
relpath – If ‘relpath’ is specified, lists the content of the given subfolder.
- Returns
a list of dictionaries, where the documentation is in :py:class:Transport.listdir_withattributes.
-
Data class that can be used to store a single file in its repository.
-
class
aiida.orm.nodes.data.singlefile.
SinglefileData
(file, filename=None, **kwargs)[source]¶ Bases:
aiida.orm.nodes.data.data.Data
Data class that can be used to store a single file in its repository.
-
DEFAULT_FILENAME
= 'file.txt'¶
-
__abstractmethods__
= frozenset({})¶
-
__init__
(file, filename=None, **kwargs)[source]¶ Construct a new instance and set the contents to that of the file.
- Parameters
file – an absolute filepath or filelike object whose contents to copy. Hint: Pass io.BytesIO(b”my string”) to construct the SinglefileData directly from a string.
filename – specify filename to use (defaults to name of provided file).
-
__module__
= 'aiida.orm.nodes.data.singlefile'¶
-
_abc_impl
= <_abc_data object>¶
-
_logger
= <Logger aiida.orm.nodes.data.singlefile.SinglefileData (REPORT)>¶
-
_plugin_type_string
= 'data.singlefile.SinglefileData.'¶
-
_query_type_string
= 'data.singlefile.'¶
-
_validate
()[source]¶ Ensure that there is one object stored in the repository, whose key matches value set for filename attr.
-
property
filename
¶ Return the name of the file stored.
- Returns
the filename under which the file is stored in the repository
-
get_content
()[source]¶ Return the content of the single file stored for this data node.
- Returns
the content of the file as a string
-
open
(key=None, mode='r')[source]¶ Return an open file handle to the content of this data node.
- Parameters
key – optional key within the repository, by default is the filename set in the attributes
mode – the mode with which to open the file handle (default: read mode)
- Returns
a file handle
-
set_file
(file, filename=None)[source]¶ Store the content of the file in the node’s repository, deleting any other existing objects.
- Parameters
file – an absolute filepath or filelike object whose contents to copy Hint: Pass io.BytesIO(b”my string”) to construct the file directly from a string.
filename – specify filename to use (defaults to name of provided file).
-
Data sub class to represent a string value.
-
class
aiida.orm.nodes.data.str.
Str
(*args, **kwargs)[source]¶ Bases:
aiida.orm.nodes.data.base.BaseType
Data sub class to represent a string value.
-
__abstractmethods__
= frozenset({})¶
-
__module__
= 'aiida.orm.nodes.data.str'¶
-
_abc_impl
= <_abc_data object>¶
-
_logger
= <Logger aiida.orm.nodes.data.str.Str (REPORT)>¶
-
_plugin_type_string
= 'data.str.Str.'¶
-
_query_type_string
= 'data.str.'¶
-
_type
¶ alias of
builtins.str
-
This module defines the classes for structures and all related functions to operate on them.
-
class
aiida.orm.nodes.data.structure.
StructureData
(cell=None, pbc=None, ase=None, pymatgen=None, pymatgen_structure=None, pymatgen_molecule=None, **kwargs)[source]¶ Bases:
aiida.orm.nodes.data.data.Data
This class contains the information about a given structure, i.e. a collection of sites together with a cell, the boundary conditions (whether they are periodic or not) and other related useful information.
-
__abstractmethods__
= frozenset({})¶
-
__init__
(cell=None, pbc=None, ase=None, pymatgen=None, pymatgen_structure=None, pymatgen_molecule=None, **kwargs)[source]¶ - Parameters
backend_entity (
aiida.orm.implementation.BackendEntity
) – the backend model supporting this entity
-
__module__
= 'aiida.orm.nodes.data.structure'¶
-
_abc_impl
= <_abc_data object>¶
-
_adjust_default_cell
(vacuum_factor=1.0, vacuum_addition=10.0, pbc=(False, False, False))[source]¶ If the structure was imported from an xyz file, it lacks a defined cell, and the default cell is taken ([[1,0,0], [0,1,0], [0,0,1]]), leading to an unphysical definition of the structure. This method will adjust the cell
-
_dimensionality_label
= {0: '', 1: 'length', 2: 'surface', 3: 'volume'}¶
-
_get_object_ase
()[source]¶ Converts
StructureData
to ase.Atoms- Returns
an ase.Atoms object
-
_get_object_phonopyatoms
()[source]¶ Converts StructureData to PhonopyAtoms
- Returns
a PhonopyAtoms object
-
_get_object_pymatgen
(**kwargs)[source]¶ Converts
StructureData
to pymatgen object- Returns
a pymatgen Structure for structures with periodic boundary conditions (in three dimensions) and Molecule otherwise
Note
Requires the pymatgen module (version >= 3.0.13, usage of earlier versions may cause errors).
-
_get_object_pymatgen_molecule
(**kwargs)[source]¶ Converts
StructureData
to pymatgen Molecule object- Returns
a pymatgen Molecule object corresponding to this
StructureData
object.
Note
Requires the pymatgen module (version >= 3.0.13, usage of earlier versions may cause errors)
-
_get_object_pymatgen_structure
(**kwargs)[source]¶ Converts
StructureData
to pymatgen Structure object :param add_spin: True to add the spins to the pymatgen structure. Default is False (no spin added).Note
The spins are set according to the following rule:
if the kind name ends with 1 -> spin=+1
if the kind name ends with 2 -> spin=-1
- Returns
a pymatgen Structure object corresponding to this
StructureData
object- Raises
ValueError – if periodic boundary conditions does not hold in at least one dimension of real space; if there are partial occupancies together with spins (defined by kind names ending with ‘1’ or ‘2’).
Note
Requires the pymatgen module (version >= 3.0.13, usage of earlier versions may cause errors)
-
_logger
= <Logger aiida.orm.nodes.data.structure.StructureData (REPORT)>¶
-
_plugin_type_string
= 'data.structure.StructureData.'¶
-
_prepare_chemdoodle
(main_file_name='')[source]¶ Write the given structure to a string of format required by ChemDoodle.
-
_prepare_xsf
(main_file_name='')[source]¶ Write the given structure to a string of format XSF (for XCrySDen).
-
_query_type_string
= 'data.structure.'¶
-
_set_incompatibilities
= [('ase', 'cell'), ('ase', 'pbc'), ('ase', 'pymatgen'), ('ase', 'pymatgen_molecule'), ('ase', 'pymatgen_structure'), ('cell', 'pymatgen'), ('cell', 'pymatgen_molecule'), ('cell', 'pymatgen_structure'), ('pbc', 'pymatgen'), ('pbc', 'pymatgen_molecule'), ('pbc', 'pymatgen_structure'), ('pymatgen', 'pymatgen_molecule'), ('pymatgen', 'pymatgen_structure'), ('pymatgen_molecule', 'pymatgen_structure')]¶
-
append_atom
(**kwargs)[source]¶ Append an atom to the Structure, taking care of creating the corresponding kind.
- Parameters
ase – the ase Atom object from which we want to create a new atom (if present, this must be the only parameter)
position – the position of the atom (three numbers in angstrom)
symbols – passed to the constructor of the Kind object.
weights – passed to the constructor of the Kind object.
name – passed to the constructor of the Kind object. See also the note below.
Note
Note on the ‘name’ parameter (that is, the name of the kind):
if specified, no checks are done on existing species. Simply, a new kind with that name is created. If there is a name clash, a check is done: if the kinds are identical, no error is issued; otherwise, an error is issued because you are trying to store two different kinds with the same name.
if not specified, the name is automatically generated. Before adding the kind, a check is done. If other species with the same properties already exist, no new kinds are created, but the site is added to the existing (identical) kind. (Actually, the first kind that is encountered). Otherwise, the name is made unique first, by adding to the string containing the list of chemical symbols a number starting from 1, until an unique name is found
Note
checks of equality of species are done using the
compare_with()
method.
-
append_kind
(kind)[source]¶ Append a kind to the
StructureData
. It makes a copy of the kind.- Parameters
kind – the site to append, must be a Kind object.
-
append_site
(site)[source]¶ Append a site to the
StructureData
. It makes a copy of the site.- Parameters
site – the site to append. It must be a Site object.
-
property
cell
¶ Returns the cell shape.
- Returns
a 3x3 list of lists.
-
property
cell_angles
¶ Get the angles between the cell lattice vectors in degrees.
-
property
cell_lengths
¶ Get the lengths of cell lattice vectors in angstroms.
-
get_ase
()[source]¶ Get the ASE object. Requires to be able to import ase.
- Returns
an ASE object corresponding to this
StructureData
object.
Note
If any site is an alloy or has vacancies, a ValueError is raised (from the site.get_ase() routine).
-
get_cif
(converter='ase', store=False, **kwargs)[source]¶ Creates
aiida.orm.nodes.data.cif.CifData
.New in version 1.0: Renamed from _get_cif
- Parameters
converter – specify the converter. Default ‘ase’.
store – If True, intermediate calculation gets stored in the AiiDA database for record. Default False.
- Returns
-
get_composition
()[source]¶ Returns the chemical composition of this structure as a dictionary, where each key is the kind symbol (e.g. H, Li, Ba), and each value is the number of occurences of that element in this structure. For BaZrO3 it would return {‘Ba’:1, ‘Zr’:1, ‘O’:3}. No reduction with smallest common divisor!
- Returns
a dictionary with the composition
-
get_description
()[source]¶ Returns a string with infos retrieved from StructureData node’s properties
- Parameters
self – the StructureData node
- Returns
retsrt: the description string
-
get_dimensionality
()[source]¶ This function checks the dimensionality of the structure and calculates its length/surface/volume :return: returns the dimensionality and length/surface/volume
-
get_formula
(mode='hill', separator='')[source]¶ Return a string with the chemical formula.
- Parameters
mode –
a string to specify how to generate the formula, can assume one of the following values:
’hill’ (default): count the number of atoms of each species, then use Hill notation, i.e. alphabetical order with C and H first if one or several C atom(s) is (are) present, e.g.
['C','H','H','H','O','C','H','H','H']
will return'C2H6O'
['S','O','O','H','O','H','O']
will return'H2O4S'
From E. A. Hill, J. Am. Chem. Soc., 22 (8), pp 478–494 (1900)’hill_compact’: same as hill but the number of atoms for each species is divided by the greatest common divisor of all of them, e.g.
['C','H','H','H','O','C','H','H','H','O','O','O']
will return'CH3O2'
’reduce’: group repeated symbols e.g.
['Ba', 'Ti', 'O', 'O', 'O', 'Ba', 'Ti', 'O', 'O', 'O', 'Ba', 'Ti', 'Ti', 'O', 'O', 'O']
will return'BaTiO3BaTiO3BaTi2O3'
’group’: will try to group as much as possible parts of the formula e.g.
['Ba', 'Ti', 'O', 'O', 'O', 'Ba', 'Ti', 'O', 'O', 'O', 'Ba', 'Ti', 'Ti', 'O', 'O', 'O']
will return'(BaTiO3)2BaTi2O3'
’count’: same as hill (i.e. one just counts the number of atoms of each species) without the re-ordering (take the order of the atomic sites), e.g.
['Ba', 'Ti', 'O', 'O', 'O','Ba', 'Ti', 'O', 'O', 'O']
will return'Ba2Ti2O6'
’count_compact’: same as count but the number of atoms for each species is divided by the greatest common divisor of all of them, e.g.
['Ba', 'Ti', 'O', 'O', 'O','Ba', 'Ti', 'O', 'O', 'O']
will return'BaTiO3'
separator – a string used to concatenate symbols. Default empty.
- Returns
a string with the formula
Note
in modes reduce, group, count and count_compact, the initial order in which the atoms were appended by the user is used to group and/or order the symbols in the formula
-
get_kind
(kind_name)[source]¶ Return the kind object associated with the given kind name.
- Parameters
kind_name – String, the name of the kind you want to get
- Returns
The Kind object associated with the given kind_name, if a Kind with the given name is present in the structure.
- Raise
ValueError if the kind_name is not present.
-
get_kind_names
()[source]¶ Return a list of kind names (in the same order of the
self.kinds
property, but return the names rather than Kind objects)Note
This is NOT necessarily a list of chemical symbols! Use get_symbols_set for chemical symbols
- Returns
a list of strings.
-
get_pymatgen
(**kwargs)[source]¶ Get pymatgen object. Returns Structure for structures with periodic boundary conditions (in three dimensions) and Molecule otherwise. :param add_spin: True to add the spins to the pymatgen structure. Default is False (no spin added).
Note
The spins are set according to the following rule:
if the kind name ends with 1 -> spin=+1
if the kind name ends with 2 -> spin=-1
Note
Requires the pymatgen module (version >= 3.0.13, usage of earlier versions may cause errors).
-
get_pymatgen_molecule
()[source]¶ Get the pymatgen Molecule object.
Note
Requires the pymatgen module (version >= 3.0.13, usage of earlier versions may cause errors).
- Returns
a pymatgen Molecule object corresponding to this
StructureData
object.
-
get_pymatgen_structure
(**kwargs)[source]¶ Get the pymatgen Structure object. :param add_spin: True to add the spins to the pymatgen structure. Default is False (no spin added).
Note
The spins are set according to the following rule:
if the kind name ends with 1 -> spin=+1
if the kind name ends with 2 -> spin=-1
Note
Requires the pymatgen module (version >= 3.0.13, usage of earlier versions may cause errors).
- Returns
a pymatgen Structure object corresponding to this
StructureData
object.- Raises
ValueError – if periodic boundary conditions do not hold in at least one dimension of real space.
-
get_site_kindnames
()[source]¶ Return a list with length equal to the number of sites of this structure, where each element of the list is the kind name of the corresponding site.
Note
This is NOT necessarily a list of chemical symbols! Use
[ self.get_kind(s.kind_name).get_symbols_string() for s in self.sites]
for chemical symbols- Returns
a list of strings
-
get_symbols_set
()[source]¶ Return a set containing the names of all elements involved in this structure (i.e., for it joins the list of symbols for each kind k in the structure).
- Returns
a set of strings of element names.
-
property
has_vacancies
¶ Return whether the structure has vacancies in the structure.
- Returns
a boolean, True if at least one kind has a vacancy
-
property
is_alloy
¶ Return whether the structure contains any alloy kinds.
- Returns
a boolean, True if at least one kind is an alloy
-
property
kinds
¶ Returns a list of kinds.
-
property
pbc
¶ Get the periodic boundary conditions.
- Returns
a tuple of three booleans, each one tells if there are periodic boundary conditions for the i-th real-space direction (i=1,2,3)
-
reset_cell
(new_cell)[source]¶ Reset the cell of a structure not yet stored to a new value.
- Parameters
new_cell – list specifying the cell vectors
- Raises
ModificationNotAllowed: if object is already stored
-
reset_sites_positions
(new_positions, conserve_particle=True)[source]¶ Replace all the Site positions attached to the Structure
- Parameters
new_positions – list of (3D) positions for every sites.
conserve_particle – if True, allows the possibility of removing a site. currently not implemented.
- Raises
aiida.common.ModificationNotAllowed – if object is stored already
ValueError – if positions are invalid
Note
it is assumed that the order of the new_positions is given in the same order of the one it’s substituting, i.e. the kind of the site will not be checked.
-
set_pymatgen
(obj, **kwargs)[source]¶ Load the structure from a pymatgen object.
Note
Requires the pymatgen module (version >= 3.0.13, usage of earlier versions may cause errors).
-
set_pymatgen_molecule
(mol, margin=5)[source]¶ Load the structure from a pymatgen Molecule object.
- Parameters
margin – the margin to be added in all directions of the bounding box of the molecule.
Note
Requires the pymatgen module (version >= 3.0.13, usage of earlier versions may cause errors).
-
set_pymatgen_structure
(struct)[source]¶ Load the structure from a pymatgen Structure object.
Note
periodic boundary conditions are set to True in all three directions.
Note
Requires the pymatgen module (version >= 3.3.5, usage of earlier versions may cause errors).
- Raises
ValueError – if there are partial occupancies together with spins.
-
property
sites
¶ Returns a list of sites.
-
-
class
aiida.orm.nodes.data.structure.
Kind
(**kwargs)[source]¶ Bases:
object
This class contains the information about the species (kinds) of the system.
It can be a single atom, or an alloy, or even contain vacancies.
-
__dict__
= mappingproxy({'__module__': 'aiida.orm.nodes.data.structure', '__doc__': '\n This class contains the information about the species (kinds) of the system.\n\n It can be a single atom, or an alloy, or even contain vacancies.\n ', '__init__': <function Kind.__init__>, 'get_raw': <function Kind.get_raw>, 'reset_mass': <function Kind.reset_mass>, 'name': <property object>, 'set_automatic_kind_name': <function Kind.set_automatic_kind_name>, 'compare_with': <function Kind.compare_with>, 'mass': <property object>, 'weights': <property object>, 'get_symbols_string': <function Kind.get_symbols_string>, 'symbol': <property object>, 'symbols': <property object>, 'set_symbols_and_weights': <function Kind.set_symbols_and_weights>, 'is_alloy': <property object>, 'has_vacancies': <property object>, '__repr__': <function Kind.__repr__>, '__str__': <function Kind.__str__>, '__dict__': <attribute '__dict__' of 'Kind' objects>, '__weakref__': <attribute '__weakref__' of 'Kind' objects>})¶
-
__init__
(**kwargs)[source]¶ Create a site. One can either pass:
- Parameters
raw – the raw python dictionary that will be converted to a Kind object.
ase – an ase Atom object
kind – a Kind object (to get a copy)
Or alternatively the following parameters:
- Parameters
symbols – a single string for the symbol of this site, or a list of symbol strings
weights – (optional) the weights for each atomic species of this site. If only a single symbol is provided, then this value is optional and the weight is set to 1.
mass – (optional) the mass for this site in atomic mass units. If not provided, the mass is set by the self.reset_mass() function.
name – a string that uniquely identifies the kind, and that is used to identify the sites.
-
__module__
= 'aiida.orm.nodes.data.structure'¶
-
__weakref__
¶ list of weak references to the object (if defined)
-
compare_with
(other_kind)[source]¶ Compare with another Kind object to check if they are different.
Note
This does NOT check the ‘type’ attribute. Instead, it compares (with reasonable thresholds, where applicable): the mass, and the list of symbols and of weights. Moreover, it compares the
_internal_tag
, if defined (at the moment, defined automatically only when importing the Kind from ASE, if the atom has a non-zero tag). Note that the _internal_tag is only used while the class is loaded, but is not persisted on the database.- Returns
A tuple with two elements. The first one is True if the two sites are ‘equivalent’ (same mass, symbols and weights), False otherwise. The second element of the tuple is a string, which is either None (if the first element was True), or contains a ‘human-readable’ description of the first difference encountered between the two sites.
-
get_raw
()[source]¶ Return the raw version of the site, mapped to a suitable dictionary. This is the format that is actually used to store each kind of the structure in the DB.
- Returns
a python dictionary with the kind.
-
get_symbols_string
()[source]¶ Return a string that tries to match as good as possible the symbols of this kind. If there is only one symbol (no alloy) with 100% occupancy, just returns the symbol name. Otherwise, groups the full string in curly brackets, and try to write also the composition (with 2 precision only).
Note
If there is a vacancy (sum of weights<1), we indicate it with the X symbol followed by 1-sum(weights) (still with 2 digits precision, so it can be 0.00)
Note
Note the difference with respect to the symbols and the symbol properties!
-
property
has_vacancies
¶ Return whether the Kind contains vacancies, i.e. when the sum of the weights is less than one.
Note
the property uses the internal variable _sum_threshold as a threshold.
- Returns
boolean, True if the sum of the weights is less than one, False otherwise
-
property
is_alloy
¶ Return whether the Kind is an alloy, i.e. contains more than one element
- Returns
boolean, True if the kind has more than one element, False otherwise.
-
property
mass
¶ The mass of this species kind.
- Returns
a float
-
property
name
¶ Return the name of this kind. The name of a kind is used to identify the species of a site.
- Returns
a string
-
reset_mass
()[source]¶ Reset the mass to the automatic calculated value.
The mass can be set manually; by default, if not provided, it is the mass of the constituent atoms, weighted with their weight (after the weight has been normalized to one to take correctly into account vacancies).
This function uses the internal _symbols and _weights values and thus assumes that the values are validated.
It sets the mass to None if the sum of weights is zero.
-
set_automatic_kind_name
(tag=None)[source]¶ Set the type to a string obtained with the symbols appended one after the other, without spaces, in alphabetical order; if the site has a vacancy, a X is appended at the end too.
-
set_symbols_and_weights
(symbols, weights)[source]¶ Set the chemical symbols and the weights for the site.
Note
Note that the kind name remains unchanged.
-
property
symbol
¶ If the kind has only one symbol, return it; otherwise, raise a ValueError.
-
property
symbols
¶ List of symbols for this site. If the site is a single atom, pass a list of one element only, or simply the string for that atom. For alloys, a list of elements.
Note
Note that if you change the list of symbols, the kind name remains unchanged.
-
property
weights
¶ Weights for this species kind. Refer also to :func:validate_symbols_tuple for the validation rules on the weights.
-
-
class
aiida.orm.nodes.data.structure.
Site
(**kwargs)[source]¶ Bases:
object
This class contains the information about a given site of the system.
It can be a single atom, or an alloy, or even contain vacancies.
-
__dict__
= mappingproxy({'__module__': 'aiida.orm.nodes.data.structure', '__doc__': '\n This class contains the information about a given site of the system.\n\n It can be a single atom, or an alloy, or even contain vacancies.\n ', '__init__': <function Site.__init__>, 'get_raw': <function Site.get_raw>, 'get_ase': <function Site.get_ase>, 'kind_name': <property object>, 'position': <property object>, '__repr__': <function Site.__repr__>, '__str__': <function Site.__str__>, '__dict__': <attribute '__dict__' of 'Site' objects>, '__weakref__': <attribute '__weakref__' of 'Site' objects>})¶
-
__init__
(**kwargs)[source]¶ Create a site.
- Parameters
kind_name – a string that identifies the kind (species) of this site. This has to be found in the list of kinds of the StructureData object. Validation will be done at the StructureData level.
position – the absolute position (three floats) in angstrom
-
__module__
= 'aiida.orm.nodes.data.structure'¶
-
__weakref__
¶ list of weak references to the object (if defined)
-
get_ase
(kinds)[source]¶ Return a ase.Atom object for this site.
- Parameters
kinds – the list of kinds from the StructureData object.
Note
If any site is an alloy or has vacancies, a ValueError is raised (from the site.get_ase() routine).
-
get_raw
()[source]¶ Return the raw version of the site, mapped to a suitable dictionary. This is the format that is actually used to store each site of the structure in the DB.
- Returns
a python dictionary with the site.
-
property
kind_name
¶ Return the kind name of this site (a string).
The type of a site is used to decide whether two sites are identical (same mass, symbols, weights, …) or not.
-
property
position
¶ Return the position of this site in absolute coordinates, in angstrom.
-
Module of Data sub class to represent a pseudopotential single file in UPF format and related utilities.
-
class
aiida.orm.nodes.data.upf.
UpfData
(file=None, filename=None, source=None, **kwargs)[source]¶ Bases:
aiida.orm.nodes.data.singlefile.SinglefileData
Data sub class to represent a pseudopotential single file in UPF format.
-
__abstractmethods__
= frozenset({})¶
-
__init__
(file=None, filename=None, source=None, **kwargs)[source]¶ Create UpfData instance from pseudopotential file.
- Parameters
file – filepath or filelike object of the UPF potential file to store. Hint: Pass io.BytesIO(b”my string”) to construct directly from a string.
filename – specify filename to use (defaults to name of provided file).
source – Dictionary with information on source of the potential (see “.source” property).
-
__module__
= 'aiida.orm.nodes.data.upf'¶
-
_abc_impl
= <_abc_data object>¶
-
_logger
= <Logger aiida.orm.nodes.data.upf.UpfData (REPORT)>¶
-
_plugin_type_string
= 'data.upf.UpfData.'¶
-
_query_type_string
= 'data.upf.'¶
-
property
element
¶ Return the element of the UPF pseudopotential.
- Returns
the element
-
classmethod
from_md5
(md5)[source]¶ Return a list of all UpfData that match the given md5 hash.
Note
assumes hash of stored UpfData nodes is stored in the md5 attribute
- Parameters
md5 – the file hash
- Returns
list of existing UpfData nodes that have the same md5 hash
-
classmethod
get_or_create
(filepath, use_first=False, store_upf=True)[source]¶ Get the UpfData with the same md5 of the given file, or create it if it does not yet exist.
- Parameters
filepath – an absolute filepath on disk
use_first – if False (default), raise an exception if more than one potential is found. If it is True, instead, use the first available pseudopotential.
store_upf – boolean, if false, the UpfData if created will not be stored.
- Returns
tuple of UpfData and boolean indicating whether it was created.
-
classmethod
get_upf_group
(group_label)[source]¶ Return the UPF family group with the given label.
- Parameters
group_label – the family group label
- Returns
the Group with the given label, if it exists
-
classmethod
get_upf_groups
(filter_elements=None, user=None)[source]¶ Return all names of groups of type UpfFamily, possibly with some filters.
- Parameters
filter_elements – A string or a list of strings. If present, returns only the groups that contains one UPF for every element present in the list. The default is None, meaning that all families are returned.
user – if None (default), return the groups for all users. If defined, it should be either a User instance or the user email.
- Returns
list of Group entities of type UPF.
-
property
md5sum
¶ Return the md5 checksum of the UPF pseudopotential file.
- Returns
the md5 checksum
-
set_file
(file, filename=None)[source]¶ Store the file in the repository and parse it to set the element and md5 attributes.
- Parameters
file – filepath or filelike object of the UPF potential file to store. Hint: Pass io.BytesIO(b”my string”) to construct the file directly from a string.
filename – specify filename to use (defaults to name of provided file).
-
store
(*args, **kwargs)[source]¶ Store the node, reparsing the file so that the md5 and the element are correctly reset.
-
upffamily_type_string
= 'data.upf'¶
-