Translator for data node
aiida.restapi.translator.nodes.data.
DataTranslator
Bases: aiida.restapi.translator.nodes.node.NodeTranslator
aiida.restapi.translator.nodes.node.NodeTranslator
Translator relative to resource ‘data’ and aiida class ~aiida.orm.nodes.data.data.Data
Data
Bases: aiida.orm.nodes.node.Node
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__
__copy__
Copying a Data node is not supported, use copy.deepcopy or call Data.clone().
__deepcopy__
Create a clone of the Data node by pipiong through to the clone method and return the result.
an unstored clone of this Data node
__module__
_abc_impl
_export_format_replacements
_exportcontent
Converts a Data node to one (or multiple) files.
Note: Export plugins should return utf8-encoded bytes, which can be directly dumped to file.
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
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.
(bytes, dict)
_get_converters
Get all implemented converter formats. The convention is to find all _get_object_… methods. Returns a list of strings.
_get_exporters
Get all implemented export formats. The convention is to find all _prepare_… methods. Returns a dictionary of method_name: method_function
_get_importers
Get all implemented import formats. The convention is to find all _parse_… methods. Returns a list of strings.
_logger
_plugin_type_string
_query_type_string
_source_attributes
_storable
_unstorable_message
_validate
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.
clone
Create a clone of the Data node.
convert
Convert the AiiDA StructureData into another python object
object_format – Specify the output format
creator
Return the creator of this node or None if it does not exist.
the creating node or None
export
Save a Data object to a file.
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
the list of files created
get_export_formats
Get the list of valid export format strings
a list of valid formats
importfile
Populate a Data object from a file.
importstring
Converts a Data object to other text format.
fileformat – a string (the extension) to describe the file format.
a string with the structure description.
set_source
Sets the dictionary describing the source of Data object.
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.
some limitations for setting the data source exist, see _validate method.
dictionary describing the source of Data object.
__label__
_aiida_class
alias of aiida.orm.nodes.data.data.Data
aiida.orm.nodes.data.data.Data
_aiida_type
_result_type
get_downloadable_data
Return content in the specified format for download
node – node representing cif file to be downloaded
download_format – export format
content of the node in the specified format for download
Translator for CifData
aiida.restapi.translator.nodes.data.cif.
CifDataTranslator
Bases: aiida.restapi.translator.nodes.data.DataTranslator
aiida.restapi.translator.nodes.data.DataTranslator
Translator relative to resource ‘structures’ and aiida class CifData
CifData
Bases: aiida.orm.nodes.data.singlefile.SinglefileData
aiida.orm.nodes.data.singlefile.SinglefileData
Wrapper for Crystallographic Interchange File (CIF)
the file (physical) is held as the authoritative source of information, so all conversions are done through the physical file: when setting ase or values, a physical CIF file is generated first, the values are updated from the physical CIF file.
ase
values
_PARSE_POLICIES
_PARSE_POLICY_DEFAULT
_SCAN_TYPES
_SCAN_TYPE_DEFAULT
_SET_INCOMPATIBILITIES
__init__
Construct a new instance and set the contents to that of the file.
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)
_ase
_get_object_ase
Converts CifData to ase.Atoms
an ase.Atoms object
_get_object_pycifrw
Converts CifData to PyCIFRW.CifFile
a PyCIFRW.CifFile object
_prepare_cif
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.
Validates MD5 hash of CIF file.
_values
ASE object, representing the CIF.
requires ASE module.
from_md5
Return a list of all CIF files that match a given MD5 hash.
the hash has to be stored in a _md5 attribute, otherwise the CIF file will not be found.
_md5
generate_md5
Computes and returns MD5 hash of the CIF file.
get_ase
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().
get_formulae
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.
get_or_create
Pass the same parameter of the init; if a file with the same md5 is found, that CifData is returned.
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.
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_spacegroup_numbers
Get the spacegroup international number.
get_structure
Creates aiida.orm.nodes.data.structure.StructureData.
aiida.orm.nodes.data.structure.StructureData
New in version 1.0: Renamed from _get_aiida_structure
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)
aiida.orm.nodes.data.structure.StructureData node.
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
False when at least one atomic site fractional coordinate is not equal to ? and True otherwise
has_attached_hydrogens
Check if there are hydrogens without coordinates, specified as attached to the atoms of the structure.
True if there are attached hydrogens, False otherwise.
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
True if there are partial occupancies, False otherwise
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.
boolean, True if no atomic sites are defined or if any of the defined sites contain undefined positions and False otherwise
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
True when there are unknown species in any of the formulae, False if not, None if no formula found
parse
Parses CIF file and sets attributes.
scan_type – See set_scan_type
read_cif
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
Set the contents of the CifData starting from an ASE atoms object
aseatoms – the ASE atoms object
set_file
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.
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.
set_parse_policy
Set the parse policy.
parse_policy – Either ‘eager’ (parse CIF file on set_file) or ‘lazy’ (defer parsing until needed)
set_scan_type
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
scan_type – Either ‘standard’ or ‘flex’ (see _scan_types)
set_values
Set internal representation to values.
Warning: This also writes a new CIF file.
values – PyCifRW CifFile object
requires PyCifRW module.
store
Store the node.
PyCifRW structure, representing the CIF datablocks.
alias of aiida.orm.nodes.data.cif.CifData
aiida.orm.nodes.data.cif.CifData
get_derived_properties
Generic function extended for cif. Currently it is not implemented.
node – node object
empty dict
Translator for code
aiida.restapi.translator.nodes.data.code.
CodeTranslator
Translator relative to resource ‘codes’ and aiida class Code
Code
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
backend_entity (aiida.orm.implementation.entities.BackendEntity) – the backend model supporting this entity
aiida.orm.implementation.entities.BackendEntity
__str__
Return str(self).
_set_local
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
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).
can_run_on
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.
full_label
Get full label of this code.
Returns label of the form <code-label>@<computer-name>.
get
Get a Computer object with given identifier string, that can either be the numeric ID (pk), or the label (and computername) (if unique).
pk – the numeric ID (pk) for code
label – the code label identifying the code to load
machinename – the machine name where code is setup
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
Return the postexec_code, or an empty string if no post-exec code was defined.
get_builder
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.
it also sets the builder.code value.
builder.code
a ProcessBuilder instance with the code input already populated with ourselves
aiida.common.EntryPointError – if the specified plugin does not exist.
ValueError – if no default plugin was specified.
get_code_helper
get_computer_label
Get label of this code’s computer.
get_computer_name
Deprecated since version 1.4.0: Will be removed in v2.0.0, use the self.get_computer_label() method instead.
get_description
Return a string description of this Code instance.
string description of this Code instance
get_execname
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.
get_from_string
Get a Computer object with given identifier string in the format label@machinename. See the note below for details on the string detection algorithm.
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).
code_string – the code string identifying the code to load
aiida.common.InputValidationError – if code_string is not of string type
get_full_text_info
Return a list of lists with a human-readable detailed information on this code.
Deprecated since version 1.4.0: Will be removed in v2.0.0.
list of lists where each entry consists of two elements: a key and a value
get_input_plugin_name
Return the name of the default input plugin (or None if no input plugin was set.
get_local_executable
get_prepend_text
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.
get_remote_computer
get_remote_exec_path
hidden
Determines whether the Code is hidden or not
hide
Hide the code (prevents from showing it in the verdi code list)
is_local
Return True if the code is ‘local’, False if it is ‘remote’ (see also documentation of the set_local and set_remote functions).
label
Return the node label.
the label
list_for_plugin
Return a list of valid code strings for a given plugin.
plugin – The string of the plugin.
labels – if True, return a list of code names, otherwise return the code PKs (integers).
a list of string, with the code names if labels is True, otherwise a list of integers with the code PKs.
relabel
Relabel this code.
new_label – new code label
raise_error – Set to False in order to return a list of errors instead of raising them.
Deprecated since version 1.2.0: Will remove raise_error in v2.0.0. Use try/except instead.
reveal
Reveal the code (allows to show it in the verdi code list) By default, it is revealed
set_append_text
Pass a string of code that will be put in the scheduler script after the execution of the code.
set_files
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!
decide whether to check if the Code must be a local executable to be able to call this function.
set_input_plugin_name
Set the name of the default input plugin, to be used for the automatic generation of a new calculation.
set_local_executable
Set the filename of the local executable. Implicitly set the code as local.
set_prepend_text
Pass a string of code that will be put in the scheduler script before the execution of the code.
set_remote_computer_exec
Set the code as remote, and pass the computer on which it resides and the absolute path on that computer.
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.
alias of aiida.orm.nodes.data.code.Code
aiida.orm.nodes.data.code.Code
Generic function extended for codes data. Currently it is not implemented.
Translator for kpoints data
aiida.restapi.translator.nodes.data.kpoints.
KpointsDataTranslator
Translator relative to resource ‘kpoints’ and aiida class KpointsData
KpointsData
Bases: aiida.orm.nodes.data.array.array.ArrayData
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.
_change_reference
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
_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
_set_cell
Validate if ‘value’ is a allowed crystal unit cell :param value: something compatible with a 3x3 tuple of floats
_set_labels
set label names. Must pass in input a list like: [[0,'X'],[34,'L'],... ]
[[0,'X'],[34,'L'],... ]
_set_pbc
validate the pbc, then store them
_validate_kpoints_weights
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
cell
The crystal unit cell. Rows are the crystal vectors in Angstroms. :return: a 3x3 numpy.array
Returns a string with infos retrieved from kpoints node’s properties. :param node: :return: retstr
get_kpoints
Return the list of kpoints
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
Get the mesh of kpoints.
print_list – default=False. If True, prints the mesh of kpoints as a list
AttributeError – if no mesh has been set
(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
(if print_list = True) an explicit list of kpoints coordinates, similar to what returned by get_kpoints()
labels
Labels associated with the list of kpoints. List of tuples with kpoint index and kpoint name: [(0,'G'),(13,'M'),...]
[(0,'G'),(13,'M'),...]
pbc
The periodic boundary conditions along the vectors a1,a2,a3.
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)
reciprocal_cell
Compute reciprocal cell from the internally set cell.
reciprocal cell in units of 1/Angstrom with cell vectors stored as rows. Use e.g. reciprocal_cell[0] to access the first reciprocal cell vector.
set_cell
Set a cell to be used for symmetry analysis. To set a cell from an AiiDA structure, use “set_cell_from_structure”.
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
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”
structuredata – an instance of StructureData
set_kpoints
Set the list of kpoints. If a mesh has already been stored, raise a ModificationNotAllowed
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)
[[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
Set KpointsData to represent a uniformily spaced mesh of kpoints in the Brillouin zone. This excludes the possibility of set/get kpoints
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
Set a kpoints mesh using a kpoints density, expressed as the maximum distance between adjacent points along a reciprocal axis
distance – distance (in 1/Angstrom) between adjacent kpoints, i.e. the number of kpoints along each reciprocal axis i is \(|b_i|/distance\) where \(|b_i|\) 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).
a cell should be defined first.
the number of kpoints along non-periodic axes is always 1.
alias of aiida.orm.nodes.data.array.kpoints.KpointsData
aiida.orm.nodes.data.array.kpoints.KpointsData
Returns: data in a format required by dr.js to visualize a 2D plot with multiple data series.
Strategy: For the time being rely on the function implemented in seekpath to calculate brillouin zone faces, and triangulate them. The other fields of the response are retrieved by ordinary kpointsdata methods, except the logic to create a list of explicit keypoints from the mesh and the cell vectors.
Translator for structure data
aiida.restapi.translator.nodes.data.structure.
StructureDataTranslator
Translator relative to resource ‘structures’ and aiida class StructureData
StructureData
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.
_adjust_default_cell
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
Converts StructureData to ase.Atoms
_get_object_phonopyatoms
Converts StructureData to PhonopyAtoms
a PhonopyAtoms object
_get_object_pymatgen
Converts StructureData to pymatgen object
a pymatgen Structure for structures with periodic boundary conditions (in three dimensions) and Molecule otherwise
Requires the pymatgen module (version >= 3.0.13, usage of earlier versions may cause errors).
_get_object_pymatgen_molecule
Converts StructureData to pymatgen Molecule object
a pymatgen Molecule object corresponding to this StructureData object.
Requires the pymatgen module (version >= 3.0.13, usage of earlier versions may cause errors)
_get_object_pymatgen_structure
Converts StructureData to pymatgen Structure object :param add_spin: True to add the spins to the pymatgen structure. Default is False (no spin added).
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
a pymatgen Structure object corresponding to this StructureData object
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’).
_internal_kind_tags
_parse_xyz
Read the structure from a string of format XYZ.
_prepare_chemdoodle
Write the given structure to a string of format required by ChemDoodle.
Write the given structure to a string of format CIF.
_prepare_xsf
Write the given structure to a string of format XSF (for XCrySDen).
_prepare_xyz
Write the given structure to a string of format XYZ.
_set_incompatibilities
Performs some standard validation tests.
append_atom
Append an atom to the Structure, taking care of creating the corresponding kind.
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 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
checks of equality of species are done using the compare_with() method.
compare_with()
append_kind
Append a kind to the StructureData. It makes a copy of the kind.
kind – the site to append, must be a Kind object.
append_site
Append a site to the StructureData. It makes a copy of the site.
site – the site to append. It must be a Site object.
Returns the cell shape.
a 3x3 list of lists.
cell_angles
Get the angles between the cell lattice vectors in degrees.
cell_lengths
Get the lengths of cell lattice vectors in angstroms.
clear_kinds
Removes all kinds for the StructureData object.
Also clear all sites!
clear_sites
Removes all sites for the StructureData object.
Get the ASE object. Requires to be able to import ase.
an ASE object corresponding to this StructureData object.
If any site is an alloy or has vacancies, a ValueError is raised (from the site.get_ase() routine).
get_cell_volume
Returns the cell volume in Angstrom^3.
a float.
get_cif
Creates aiida.orm.nodes.data.cif.CifData.
New in version 1.0: Renamed from _get_cif
converter – specify the converter. Default ‘ase’.
store – If True, intermediate calculation gets stored in the AiiDA database for record. Default False.
aiida.orm.nodes.data.cif.CifData node.
get_composition
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!
a dictionary with the composition
Returns a string with infos retrieved from StructureData node’s properties
self – the StructureData node
retsrt: the description string
get_dimensionality
This function checks the dimensionality of the structure and calculates its length/surface/volume :return: returns the dimensionality and length/surface/volume
get_formula
Return a string with the chemical formula.
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)
['C','H','H','H','O','C','H','H','H']
'C2H6O'
['S','O','O','H','O','H','O']
'H2O4S'
’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'
['C','H','H','H','O','C','H','H','H','O','O','O']
'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'
['Ba', 'Ti', 'O', 'O', 'O', 'Ba', 'Ti', 'O', 'O', 'O', 'Ba', 'Ti', 'Ti', 'O', 'O', 'O']
'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'
'(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'
['Ba', 'Ti', 'O', 'O', 'O','Ba', 'Ti', 'O', 'O', 'O']
'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'
'BaTiO3'
separator – a string used to concatenate symbols. Default empty.
a string with the formula
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
Return the kind object associated with the given kind name.
kind_name – String, the name of the kind you want to get
The Kind object associated with the given kind_name, if a Kind with the given name is present in the structure.
ValueError if the kind_name is not present.
get_kind_names
Return a list of kind names (in the same order of the self.kinds property, but return the names rather than Kind objects)
self.kinds
This is NOT necessarily a list of chemical symbols! Use get_symbols_set for chemical symbols
a list of strings.
get_pymatgen
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).
get_pymatgen_molecule
Get the pymatgen Molecule object.
get_pymatgen_structure
Get the pymatgen Structure object. :param add_spin: True to add the spins to the pymatgen structure. Default is False (no spin added).
a pymatgen Structure object corresponding to this StructureData object.
ValueError – if periodic boundary conditions do not hold in at least one dimension of real space.
get_site_kindnames
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.
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
[ self.get_kind(s.kind_name).get_symbols_string() for s in self.sites]
a list of strings
get_symbols_set
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).
a set of strings of element names.
has_vacancies
Return whether the structure has vacancies in the structure.
a boolean, True if at least one kind has a vacancy
is_alloy
Return whether the structure contains any alloy kinds.
a boolean, True if at least one kind is an alloy
kinds
Returns a list of kinds.
Get the periodic boundary conditions.
reset_cell
Reset the cell of a structure not yet stored to a new value.
new_cell – list specifying the cell vectors
ModificationNotAllowed: if object is already stored
reset_sites_positions
Replace all the Site positions attached to the Structure
new_positions – list of (3D) positions for every sites.
conserve_particle – if True, allows the possibility of removing a site. currently not implemented.
aiida.common.ModificationNotAllowed – if object is stored already
ValueError – if positions are invalid
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.
Load the structure from a ASE object
Set the cell.
set_cell_angles
set_cell_lengths
set_pbc
Set the periodic boundary conditions.
set_pymatgen
Load the structure from a pymatgen object.
set_pymatgen_molecule
Load the structure from a pymatgen Molecule object.
margin – the margin to be added in all directions of the bounding box of the molecule.
set_pymatgen_structure
Load the structure from a pymatgen Structure object.
periodic boundary conditions are set to True in all three directions.
Requires the pymatgen module (version >= 3.3.5, usage of earlier versions may cause errors).
ValueError – if there are partial occupancies together with spins.
sites
Returns a list of sites.
alias of aiida.orm.nodes.data.structure.StructureData
Returns: derived properties of the structure.
Translator for upf data
aiida.restapi.translator.nodes.data.upf.
UpfDataTranslator
Translator relative to resource ‘upfs’ and aiida class UpfData
UpfData
Data sub class to represent a pseudopotential single file in UPF format.
Create UpfData instance from pseudopotential file.
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.
source – Dictionary with information on source of the potential (see “.source” property).
_prepare_json
Returns UPF PP in json format.
_prepare_upf
Return UPF content.
Validate the UPF potential file stored for this node.
element
Return the element of the UPF pseudopotential.
the element
Return a list of all UpfData that match the given md5 hash.
assumes hash of stored UpfData nodes is stored in the md5 attribute
md5 – the file hash
list of existing UpfData nodes that have the same md5 hash
Get the UpfData with the same md5 of the given file, or create it if it does not yet exist.
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.
tuple of UpfData and boolean indicating whether it was created.
get_upf_family_names
Get the list of all upf family names to which the pseudo belongs.
get_upf_group
Return the UPF family group with the given label.
group_label – the family group label
the Group with the given label, if it exists
get_upf_groups
Return all names of groups of type UpfFamily, possibly with some filters.
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.
list of Group entities of type UPF.
md5sum
Return the md5 checksum of the UPF pseudopotential file.
the md5 checksum
Store the file in the repository and parse it to set the element and md5 attributes.
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.
Store the node, reparsing the file so that the md5 and the element are correctly reset.
alias of aiida.orm.nodes.data.upf.UpfData
aiida.orm.nodes.data.upf.UpfData