pymatgen.transformations package
The transformations package defines various transformations that can be applied on structures, i.e., converting one structure to another.
Submodules
pymatgen.transformations.advanced_transformations module
This module implements more advanced transformations.
- class AddAdsorbateTransformation(adsorbate, selective_dynamics=False, height=0.9, mi_vec=None, repeat=None, min_lw=5.0, translate=True, reorient=True, find_args=None)[source]
Bases:
AbstractTransformationCreate absorbate structures.
Use AdsorbateSiteFinder to add an absorbate to a slab.
- Parameters:
adsorbate (Molecule) – molecule to add as adsorbate
selective_dynamics (bool) – flag for whether to assign non-surface sites as fixed for selective dynamics
height (float) – height criteria for selection of surface sites
mi_vec – vector corresponding to the vector concurrent with the miller index, this enables use with slabs that have been reoriented, but the miller vector must be supplied manually
repeat (3-tuple or list) – repeat argument for supercell generation
min_lw (float) – minimum length and width of the slab, only used if repeat is None
translate (bool) – flag on whether to translate the molecule so that its CoM is at the origin prior to adding it to the surface
reorient (bool) – flag on whether or not to reorient adsorbate along the miller index
find_args (dict) – dictionary of arguments to be passed to the call to self.find_adsorption_sites, e.g. {“distance”:2.0}
- apply_transformation(structure: Structure, return_ranked_list: bool | int = False)[source]
- Parameters:
structure – Must be a Slab structure
return_ranked_list (bool | int, optional) –
If return_ranked_list is int, that number of structures.
is returned. If False, only the single lowest energy structure is returned. Defaults to False.
Returns: Slab with adsorbate
- class ChargeBalanceTransformation(charge_balance_sp)[source]
Bases:
AbstractTransformationThis is a transformation that disorders a structure to make it charge balanced, given an oxidation state-decorated structure.
- Parameters:
charge_balance_sp – specie to add or remove. Currently only removal is supported.
- class CubicSupercellTransformation(min_atoms: int | None = None, max_atoms: int | None = None, min_length: float = 15.0, force_diagonal: bool = False, force_90_degrees: bool = False, angle_tolerance: float = 0.001)[source]
Bases:
AbstractTransformationA transformation that aims to generate a nearly cubic supercell structure from a structure.
The algorithm solves for a transformation matrix that makes the supercell cubic. The matrix must have integer entries, so entries are rounded (in such a way that forces the matrix to be non-singular). From the supercell resulting from this transformation matrix, vector projections are used to determine the side length of the largest cube that can fit inside the supercell. The algorithm will iteratively increase the size of the supercell until the largest inscribed cube’s side length is at least ‘min_length’ and the number of atoms in the supercell falls in the range
min_atoms < n < max_atoms.- Parameters:
max_atoms – Maximum number of atoms allowed in the supercell.
min_atoms – Minimum number of atoms allowed in the supercell.
min_length – Minimum length of the smallest supercell lattice vector.
force_diagonal – If True, return a transformation with a diagonal transformation matrix.
force_90_degrees – If True, return a transformation for a supercell with 90 degree angles (if possible). To avoid long run times, please use max_atoms
angle_tolerance – tolerance to determine the 90 degree angles.
- apply_transformation(structure: Structure) Structure[source]
The algorithm solves for a transformation matrix that makes the supercell cubic. The matrix must have integer entries, so entries are rounded (in such a way that forces the matrix to be non-singular). From the supercell resulting from this transformation matrix, vector projections are used to determine the side length of the largest cube that can fit inside the supercell. The algorithm will iteratively increase the size of the supercell until the largest inscribed cube’s side length is at least ‘num_nn_dists’ times the nearest neighbor distance and the number of atoms in the supercell falls in the range defined by min_atoms and max_atoms.
- Returns:
Transformed supercell.
- Return type:
supercell
- class DisorderOrderedTransformation(max_sites_to_merge=2)[source]
Bases:
AbstractTransformationNot to be confused with OrderDisorderedTransformation, this transformation attempts to obtain a disordered structure from an input ordered structure. This may or may not be physically plausible, further inspection of the returned structures is advised. The main purpose for this transformation is for structure matching to crystal prototypes for structures that have been derived from a parent prototype structure by substitutions or alloying additions.
- Parameters:
max_sites_to_merge – only merge this number of sites together.
- static _get_disorder_mappings(composition, partitions)[source]
Private method to obtain the mapping to create a disordered structure from a given partition.
- static _partition_species(composition, max_components=2)[source]
Private method to split a list of species into various partitions.
- apply_transformation(structure: Structure, return_ranked_list: bool | int = False)[source]
- Parameters:
structure – ordered structure
return_ranked_list (bool | int, optional) –
If return_ranked_list is int, that number of structures.
is returned. If False, only the single lowest energy structure is returned. Defaults to False.
- Returns:
Transformed disordered structure(s)
- class DopingTransformation(dopant, ionic_radius_tol=inf, min_length=10, alio_tol=0, codopant=False, max_structures_per_enum=100, allowed_doping_species=None, **kwargs)[source]
Bases:
AbstractTransformationA transformation that performs doping of a structure.
- Parameters:
dopant (Species-like) – E.g., Al3+. Must have oxidation state.
ionic_radius_tol (float) – E.g., Fractional allowable ionic radii mismatch for dopant to fit into a site. Default of inf means that any dopant with the right oxidation state is allowed.
min_length (float) – Min. lattice parameter between periodic images of dopant. Defaults to 10A for now.
alio_tol (int) – If this is not 0, attempt will be made to dope sites with oxidation_states +- alio_tol of the dopant. E.g., 1 means that the ions like Ca2+ and Ti4+ are considered as potential doping sites for Al3+.
codopant (bool) – If True, doping will be carried out with a codopant to maintain charge neutrality. Otherwise, vacancies will be used.
max_structures_per_enum (float) – Maximum number of structures to return per enumeration. Note that there can be more than one candidate doping site, and each site enumeration will return at max max_structures_per_enum structures. Defaults to 100.
allowed_doping_species (list) – Species that are allowed to be doping sites. This is an inclusionary list. If specified, any sites which are not
**kwargs – Same keyword args as
EnumerateStructureTransformation, i.e., min_cell_size, etc.
- apply_transformation(structure: Structure, return_ranked_list: bool | int = False)[source]
- Parameters:
structure (Structure) – Input structure to dope
return_ranked_list (bool | int, optional) –
If return_ranked_list is int, that number of structures.
is returned. If False, only the single lowest energy structure is returned. Defaults to False.
- Returns:
Structure, “energy”: float}]
- Return type:
[{“structure”
- class EnumerateStructureTransformation(min_cell_size: int = 1, max_cell_size: int = 1, symm_prec: float = 0.1, refine_structure: bool = False, enum_precision_parameter: float = 0.001, check_ordered_symmetry: bool = True, max_disordered_sites: int | None = None, sort_criteria: str | Callable = 'ewald', timeout: float | None = None, n_jobs: int = -1)[source]
Bases:
AbstractTransformationOrder a disordered structure using enumlib. For complete orderings, this generally produces fewer structures that the OrderDisorderedStructure transformation, and at a much faster speed.
- Parameters:
min_cell_size – The minimum cell size wanted. Must be an int. Defaults to 1.
max_cell_size – The maximum cell size wanted. Must be an int. Defaults to 1.
symm_prec – Tolerance to use for symmetry.
refine_structure – This parameter has the same meaning as in enumlib_caller. If you are starting from a structure that has been relaxed via some electronic structure code, it is usually much better to start with symmetry determination and then obtain a refined structure. The refined structure have cell parameters and atomic positions shifted to the expected symmetry positions, which makes it much less sensitive precision issues in enumlib. If you are already starting from an experimental cif, refinement should have already been done and it is not necessary. Defaults to False.
enum_precision_parameter (float) – Finite precision parameter for enumlib. Default of 0.001 is usually ok, but you might need to tweak it for certain cells.
check_ordered_symmetry (bool) – Whether to check the symmetry of the ordered sites. If the symmetry of the ordered sites is lower, the lowest symmetry ordered sites is included in the enumeration. This is important if the ordered sites break symmetry in a way that is important getting possible structures. But sometimes including ordered sites slows down enumeration to the point that it cannot be completed. Switch to False in those cases. Defaults to True.
max_disordered_sites (int) – An alternate parameter to max_cell size. Will sequentially try larger and larger cell sizes until (i) getting a result or (ii) the number of disordered sites in the cell exceeds max_disordered_sites. Must set max_cell_size to None when using this parameter.
sort_criteria (str or callable) – Sort by Ewald energy (“ewald”, must have oxidation states and slow) or M3GNet relaxed energy (“m3gnet_relax”, which is the most accurate but most expensive and provides pre-relaxed structures - needs m3gnet package installed) or by M3GNet static energy (“m3gnetassets”) or by number of sites (“nsites”, the fastest, the default). The expense of m3gnet_relax or m3gnetassets can be worth it if it significantly reduces the number of structures to be considered. m3gnet_relax speeds up the subsequent DFT calculations. Alternatively, a callable can be supplied that returns a (Structure, energy) tuple.
timeout (float) – timeout in minutes to pass to EnumlibAdaptor.
n_jobs (int) – Number of parallel jobs used to compute energy criteria. This is used only when the Ewald or m3gnet or callable sort_criteria is used. Default is -1, which uses all available CPUs.
- apply_transformation(structure: Structure, return_ranked_list: bool | int = False)[source]
Returns either a single ordered structure or a sequence of all ordered structures.
- Parameters:
structure – Structure to order.
return_ranked_list (bool | int, optional) –
If return_ranked_list is int, that number of structures
is returned. If False, only the single lowest energy structure is returned. Defaults to False.
- Returns:
Depending on returned_ranked list, either a transformed structure or a list of dictionaries, where each dictionary is of the form {“structure” = …. , “other_arguments”}
The list of ordered structures is ranked by Ewald energy / atom, if the input structure is an oxidation state decorated structure. Otherwise, it is ranked by number of sites, with smallest number of sites first.
- class GrainBoundaryTransformation(rotation_axis, rotation_angle, expand_times=4, vacuum_thickness=0.0, ab_shift=None, normal=False, ratio=True, plane=None, max_search=20, tol_coi=1e-08, rm_ratio=0.7, quick_gen=False)[source]
Bases:
AbstractTransformationA transformation that creates a gb from a bulk structure.
- Parameters:
rotation_axis (list) – Rotation axis of GB in the form of a list of integer e.g.: [1, 1, 0]
rotation_angle (float, in unit of degree) – rotation angle used to generate GB. Make sure the angle is accurate enough. You can use the enum* functions in this class to extract the accurate angle. e.g.: The rotation angle of sigma 3 twist GB with the rotation axis [1, 1, 1] and GB plane (1, 1, 1) can be 60.000000000 degree. If you do not know the rotation angle, but know the sigma value, we have provide the function get_rotation_angle_from_sigma which is able to return all the rotation angles of sigma value you provided.
expand_times (int) – The multiple times used to expand one unit grain to larger grain. This is used to tune the grain length of GB to warrant that the two GBs in one cell do not interact with each other. Default set to 4.
vacuum_thickness (float) – The thickness of vacuum that you want to insert between two grains of the GB. Default to 0.
ab_shift (list of float, in unit of a, b vectors of Gb) – in plane shift of two grains
normal (logic) – determine if need to require the c axis of top grain (first transformation matrix) perpendicular to the surface or not. default to false.
ratio (list of integers) –
lattice axial ratio. If True, will try to determine automatically from structure. For cubic system, ratio is not needed and can be set to None. For tetragonal system, ratio = [mu, mv], list of two integers, that is, mu/mv = c2/a2. If it is irrational, set it to None. For orthorhombic system, ratio = [mu, lam, mv], list of three integers,
that is, mu:lam:mv = c2:b2:a2. If irrational for one axis, set it to None.
e.g. mu:lam:mv = c2,None,a2, means b2 is irrational. For rhombohedral system, ratio = [mu, mv], list of two integers, that is, mu/mv is the ratio of (1+2*cos(alpha))/cos(alpha). If irrational, set it to None. For hexagonal system, ratio = [mu, mv], list of two integers, that is, mu/mv = c2/a2. If it is irrational, set it to none.
plane (list) – Grain boundary plane in the form of a list of integers e.g.: [1, 2, 3]. If none, we set it as twist GB. The plane will be perpendicular to the rotation axis.
max_search (int) – max search for the GB lattice vectors that give the smallest GB lattice. If normal is true, also max search the GB c vector that perpendicular to the plane. For complex GB, if you want to speed up, you can reduce this value. But too small of this value may lead to error.
tol_coi (float) – tolerance to find the coincidence sites. When making approximations to the ratio needed to generate the GB, you probably need to increase this tolerance to obtain the correct number of coincidence sites. To check the number of coincidence sites are correct or not, you can compare the generated Gb object’s sigma with enum* sigma values (what user expected by input).
rm_ratio (float) – the criteria to remove the atoms which are too close with each other. rm_ratio * bond_length of bulk system is the criteria of bond length, below which the atom will be removed. Default to 0.7.
quick_gen (bool) – whether to quickly generate a supercell, if set to true, no need to find the smallest cell.
- Returns:
Grain boundary structure (gb (Structure) object).
- apply_transformation(structure: Structure)[source]
Applies the transformation.
- Parameters:
structure – Input Structure
return_ranked_list (bool | int, optional) –
If return_ranked_list is int, that number of structures
is returned. If False, only the single lowest energy structure is returned. Defaults to False.
- Returns:
Grain boundary Structures.
- class MagOrderParameterConstraint(order_parameter, species_constraints=None, site_constraint_name=None, site_constraints=None)[source]
Bases:
MSONableThis class can be used to supply MagOrderingTransformation to just a specific subset of species or sites that satisfy the provided constraints. This can be useful for setting an order parameters for, for example, ferrimagnetic structures which might order on certain motifs, with the global order parameter dependent on how many sites satisfy that motif.
- Parameters:
(float) (order_parameter) – any number from 0.0 to 1.0, typically 0.5 (antiferromagnetic) or 1.0 (ferromagnetic)
(list) (site_constraints) – str or list of strings of Species symbols that the constraint should apply to
(str) (site_constraint_name) – name of the site property that the constraint should apply to, e.g. “coordination_no”
(list) – list of values of the site property that the constraints should apply to
- class MagOrderingTransformation(mag_species_spin, order_parameter=0.5, energy_model=None, **kwargs)[source]
Bases:
AbstractTransformationThis transformation takes a structure and returns a list of collinear magnetic orderings. For disordered structures, make an ordered approximation first.
- Parameters:
mag_species_spin – A mapping of elements/species to their spin magnitudes, e.g. {“Fe3+”: 5, “Mn3+”: 4}
list) (order_parameter (float or) – if float, a specifies a global order parameter and can take values from 0.0 to 1.0 (e.g. 0.5 for antiferromagnetic or 1.0 for ferromagnetic), if list has to be a list of
pymatgen.transformations.advanced_transformations.MagOrderParameterConstraintto specify more complicated orderings, see documentation for MagOrderParameterConstraint more details on usageenergy_model – Energy model to rank the returned structures, see :mod: pymatgen.analysis.energy_models for more information (note that this is not necessarily a physical energy). By default, returned structures use SymmetryModel() which ranks structures from most symmetric to least.
kwargs – Additional kwargs that are passed to
EnumerateStructureTransformationsuch as min_cell_size etc.- static _add_dummy_species(structure, order_parameters)[source]
- Parameters:
structure – ordered Structure
order_parameters – list of MagOrderParameterConstraints
- Returns:
A structure decorated with disordered DummySpecies on which to perform the enumeration. Note that the DummySpecies are super-imposed on to the original sites, to make it easier to retrieve the original site after enumeration is performed (this approach is preferred over a simple mapping since multiple species may have the same DummySpecies, depending on the constraints specified). This approach can also preserve site properties even after enumeration.
- _add_spin_magnitudes(structure: Structure)[source]
Replaces Spin.up/Spin.down with spin magnitudes specified by mag_species_spin.
- static _remove_dummy_species(structure)[source]
- Returns:
Structure with dummy species removed, but
their corresponding spin properties merged with the original sites. Used after performing enumeration.
- apply_transformation(structure: Structure, return_ranked_list: bool | int = False) Structure | list[Structure][source]
Apply MagOrderTransformation to an input structure.
- Parameters:
structure (Structure) – Any ordered structure.
return_ranked_list (bool | int, optional) – If return_ranked_list is int, that number of structures is returned. If False, only the single lowest energy structure is returned. Defaults to False.
- Raises:
ValueError – On disordered structures.
- Returns:
Structure(s) after MagOrderTransformation.
- Return type:
- class MonteCarloRattleTransformation(rattle_std: float, min_distance: float, seed: int | None = None, **kwargs)[source]
Bases:
AbstractTransformationUses a Monte Carlo rattle procedure to randomly perturb the sites in a structure.
This class requires the hiPhive package to be installed.
Rattling atom i is carried out as a Monte Carlo move that is accepted with a probability determined from the minimum interatomic distance \(d_{ij}\). If \(\\min(d_{ij})\) is smaller than \(d_{min}\) the move is only accepted with a low probability.
This process is repeated for each atom a number of times meaning the magnitude of the final displacements is not directly connected to rattle_std.
- Parameters:
rattle_std – Rattle amplitude (standard deviation in normal distribution). Note: this value is not directly connected to the final average displacement for the structures
min_distance – Interatomic distance used for computing the probability for each rattle move.
seed – Seed for setting up NumPy random state from which random numbers are generated. If
None, a random seed will be generated (default). This option allows the output of this transformation to be deterministic.**kwargs – Additional keyword arguments to be passed to the hiPhive mc_rattle function.
- class MultipleSubstitutionTransformation(sp_to_replace, r_fraction, substitution_dict, charge_balance_species=None, order=True)[source]
Bases:
objectPerforms multiple substitutions on a structure. For example, can do a fractional replacement of Ge in LiGePS with a list of species, creating one structure for each substitution. Ordering is done using a dummy element so only one ordering must be done per substitution oxidation state. Charge balancing of the structure is optionally performed.
Note
There are no checks to make sure that removal fractions are possible and rounding may occur. Currently charge balancing only works for removal of species.
Performs multiple fractional substitutions on a transmuter.
- Parameters:
sp_to_replace – species to be replaced
r_fraction – fraction of that specie to replace
substitution_dict – dictionary of the format {2: [“Mg”, “Ti”, “V”, “As”, “Cr”, “Ta”, “N”, “Nb”], 3: [“Ru”, “Fe”, “Co”, “Ce”, “As”, “Cr”, “Ta”, “N”, “Nb”], 4: [“Ru”, “V”, “Cr”, “Ta”, “N”, “Nb”], 5: [“Ru”, “W”, “Mn”] } The number is the charge used for each of the list of elements (an element can be present in multiple lists)
charge_balance_species – If specified, will balance the charge on the structure using that specie.
order – Whether to order the structures.
- apply_transformation(structure: Structure, return_ranked_list: bool | int = False)[source]
Applies the transformation.
- Parameters:
structure – Input Structure
return_ranked_list (bool | int, optional) –
If return_ranked_list is int, that number of structures
is returned. If False, only the single lowest energy structure is returned. Defaults to False.
- Returns:
Structures with all substitutions applied.
- class SQSTransformation(scaling, cluster_size_and_shell=None, search_time=60, directory=None, instances=None, temperature=1, wr=1, wn=1, wd=0.5, tol=0.001, best_only=True, remove_duplicate_structures=True, reduction_algo='LLL')[source]
Bases:
AbstractTransformationA transformation that creates a special quasirandom structure (SQS) from a structure with partial occupancies.
- Parameters:
scaling (int or list) –
Scaling factor to determine supercell. Two options are possible: a. (preferred) Scales number of atoms, e.g., for a structure with 8 atoms,
scaling=4 would lead to a 32 atom supercell
A sequence of three scaling factors, e.g., [2, 1, 1], which specifies that the supercell should have dimensions 2a x b x c
cluster_size_and_shell (Optional[Dict[int, int]]) – Dictionary of cluster interactions with entries in the form number of atoms: nearest neighbor shell
- Keyword Arguments:
search_time (float) – Time spent looking for the ideal SQS in minutes (default: 60)
directory (str) – Directory to run mcsqs calculation and store files (default: None runs calculations in a temp directory)
instances (int) – Specifies the number of parallel instances of mcsqs to run (default: number of cpu cores detected by Python)
temperature (int or float) – Monte Carlo temperature (default: 1), “T” in atat code
wr (int or float) – Weight assigned to range of perfect correlation match in objective function (default = 1)
wn (int or float) – Multiplicative decrease in weight per additional point in cluster (default: 1)
wd (int or float) – Exponent of decay in weight as function of cluster diameter (default: 0)
tol (int or float) – Tolerance for matching correlations (default: 1e-3)
best_only (bool) – only return structures with lowest objective function
remove_duplicate_structures (bool) – only return unique structures
reduction_algo (str) – The lattice reduction algorithm to use. Currently supported options are “niggli” or “LLL”. “False” does not reduce structure.
- static _get_disordered_substructure(struc_disordered)[source]
Converts disordered structure into a substructure consisting of only disordered sites :param struc_disordered: pymatgen disordered Structure object
- Returns:
pymatgen Structure object representing a substructure of disordered sites.
- static _get_max_neighbor_distance(struct, shell)[source]
Calculate maximum nearest neighbor distance :param struct: pymatgen Structure object :param shell: nearest neighbor shell, such that shell=1 is the first nearest
neighbor, etc.
- Returns:
maximum nearest neighbor distance, in angstroms
- static _get_unique_bestsqs_strucs(sqs, best_only, return_ranked_list, remove_duplicate_structures, reduction_algo)[source]
- Gets unique sqs structures with lowest objective function. Requires an mcsqs output that has been run
in parallel, otherwise returns Sqs.bestsqs
- Parameters:
sqs (Sqs) – Sqs class object.
best_only (bool) – only return structures with lowest objective function.
return_ranked_list (bool | int, optional) –
If return_ranked_list is int, that number of structures.
is returned. If False, only the single lowest energy structure is returned. Defaults to False.
remove_duplicate_structures (bool) – only return unique structures.
reduction_algo (str) – The lattice reduction algorithm to use. Currently supported options are “niggli” or “LLL”. “False” does not reduce structure.
- Returns:
- Structure, ‘objective_function’: …}, unless run in serial
(returns a single structure Sqs.bestsqs)
- Return type:
list of dicts of the form {‘structure’
- static _sqs_cluster_estimate(struc_disordered, cluster_size_and_shell: dict[int, int] | None = None)[source]
Set up an ATAT cluster.out file for a given structure and set of constraints :param struc_disordered: disordered pymatgen Structure object :param cluster_size_and_shell: dict of integers {cluster: shell}.
- Returns:
distance in angstroms} for mcsqs calculation
- Return type:
dict of {cluster size
- apply_transformation(structure: Structure, return_ranked_list: bool | int = False)[source]
Applies SQS transformation.
- Parameters:
structure (pymatgen Structure) – pymatgen Structure with partial occupancies
return_ranked_list (bool | int, optional) –
If return_ranked_list is int, that number of structures
is returned. If False, only the single lowest energy structure is returned. Defaults to False.
- Returns:
pymatgen Structure which is an SQS of the input structure
- class SlabTransformation(miller_index, min_slab_size, min_vacuum_size, lll_reduce=False, center_slab=False, in_unit_planes=False, primitive=True, max_normal_search=None, shift=0, tol=0.1)[source]
Bases:
AbstractTransformationA transformation that creates a slab from a structure.
- Parameters:
miller_index (3-tuple or list) – miller index of slab
min_slab_size (float) – minimum slab size in angstroms
min_vacuum_size (float) – minimum size of vacuum
lll_reduce (bool) – whether to apply LLL reduction
center_slab (bool) – whether to center the slab
primitive (bool) – whether to reduce slabs to most primitive cell
in_unit_planes (bool) – Whether to set min_slab_size and min_vac_size in units of hkl planes (True) or Angstrom (False, the default). Setting in units of planes is useful for ensuring some slabs have a certain n_layer of atoms. e.g. for Cs (100), a 10 Ang slab will result in a slab with only 2 layer of atoms, whereas Fe (100) will have more layer of atoms. By using units of hkl planes instead, we ensure both slabs have the same number of atoms. The slab thickness will be in min_slab_size/math.ceil(self._proj_height/dhkl) multiples of oriented unit cells.
max_normal_search (int) – maximum index to include in linear combinations of indices to find c lattice vector orthogonal to slab surface
shift (float) – shift to get termination
tol (float) – tolerance for primitive cell finding.
- class SubstituteSurfaceSiteTransformation(atom, selective_dynamics=False, height=0.9, mi_vec=None, target_species=None, sub_both_sides=False, range_tol=0.01, dist_from_surf=0)[source]
Bases:
AbstractTransformationUse AdsorptionSiteFinder to perform substitution-type doping on the surface and returns all possible configurations where one dopant is substituted per surface. Can substitute one surface or both.
- Parameters:
atom (str) – atom corresponding to substitutional dopant
selective_dynamics (bool) – flag for whether to assign non-surface sites as fixed for selective dynamics
height (float) – height criteria for selection of surface sites
mi_vec – vector corresponding to the vector concurrent with the miller index, this enables use with slabs that have been reoriented, but the miller vector must be supplied manually
target_species – List of specific species to substitute
sub_both_sides (bool) – If true, substitute an equivalent site on the other surface
range_tol (float) – Find viable substitution sites at a specific distance from the surface +- this tolerance
dist_from_surf (float) – Distance from the surface to find viable substitution sites, defaults to 0 to substitute at the surface.
- apply_transformation(structure: Structure, return_ranked_list: bool | int = False)[source]
- Parameters:
structure – Must be a Slab structure
return_ranked_list (bool | int, optional) –
If return_ranked_list is int, that number of structures.
is returned. If False, only the single lowest energy structure is returned. Defaults to False.
Returns: Slab with sites substituted
- class SubstitutionPredictorTransformation(threshold=0.01, scale_volumes=True, **kwargs)[source]
Bases:
AbstractTransformationThis transformation takes a structure and uses the structure prediction module to find likely site substitutions.
- Parameters:
threshold – Threshold for substitution.
scale_volumes – Whether to scale volumes after substitution.
**kwargs – Args for SubstitutionProbability class lambda_table, alpha.
- apply_transformation(structure: Structure, return_ranked_list: bool | int = False)[source]
Applies the transformation.
- Parameters:
structure – Input Structure
return_ranked_list (bool | int, optional) –
If return_ranked_list is int, that number of structures
is returned. If False, only the single lowest energy structure is returned. Defaults to False.
- Returns:
Predicted Structures.
- class SuperTransformation(transformations, nstructures_per_trans=1)[source]
Bases:
AbstractTransformationThis is a transformation that is inherently one-to-many. It is constructed from a list of transformations and returns one structure for each transformation. The primary use for this class is extending a transmuter object.
- Parameters:
transformations ([transformations]) – List of transformations to apply to a structure. One transformation is applied to each output structure.
nstructures_per_trans (int) – If the transformations are one-to-many and, nstructures_per_trans structures from each transformation are added to the full list. Defaults to 1, i.e., only best structure.
- apply_transformation(structure: Structure, return_ranked_list: bool | int = False)[source]
Applies the transformation.
- Parameters:
structure – Input Structure
return_ranked_list (bool | int, optional) –
If return_ranked_list is int, that number of structures
is returned. If False, only the single lowest energy structure is returned. Defaults to False.
- Returns:
Structures with all transformations applied.
- _find_codopant(target, oxidation_state, allowed_elements=None)[source]
Finds the element from “allowed elements” that (i) possesses the desired “oxidation state” and (ii) is closest in ionic radius to the target specie.
- Parameters:
target – (Species) provides target ionic radius.
oxidation_state – (float) codopant oxidation state.
allowed_elements – ([str]) List of allowed elements. If None, all elements are tried.
- Returns:
(Species) with oxidation_state that has ionic radius closest to target.
- _proj(b, a)[source]
Returns vector projection (np.ndarray) of vector b (np.ndarray) onto vector a (np.ndarray).
- _round_and_make_arr_singular(arr: ndarray) ndarray[source]
This function rounds all elements of a matrix to the nearest integer, unless the rounding scheme causes the matrix to be singular, in which case elements of zero rows or columns in the rounded matrix with the largest absolute valued magnitude in the unrounded matrix will be rounded to the next integer away from zero rather than to the nearest integer.
The transformation is as follows. First, all entries in ‘arr’ will be rounded to the nearest integer to yield ‘arr_rounded’. If ‘arr_rounded’ has any zero rows, then one element in each zero row of ‘arr_rounded’ corresponding to the element in ‘arr’ of that row with the largest absolute valued magnitude will be rounded to the next integer away from zero (see the ‘_round_away_from_zero(x)’ function) rather than the nearest integer. This process is then repeated for zero columns. Also note that if ‘arr’ already has zero rows or columns, then this function will not change those rows/columns.
- Parameters:
arr – Input matrix
- Returns:
Transformed matrix.
pymatgen.transformations.site_transformations module
This module defines site transformations which transforms a structure into another structure. Site transformations differ from standard transformations in that they operate in a site-specific manner. All transformations should inherit the AbstractTransformation ABC.
- class AddSitePropertyTransformation(site_properties)[source]
Bases:
AbstractTransformationSimple transformation to add site properties to a given structure.
- Parameters:
site_properties (dict) – site properties to be added to a structure.
- class InsertSitesTransformation(species, coords, coords_are_cartesian=False, validate_proximity=True)[source]
Bases:
AbstractTransformationThis transformation substitutes certain sites with certain species.
- Parameters:
species – A list of species. e.g., [“Li”, “Fe”]
coords – A list of coords corresponding to those species. e.g., [[0,0,0],[0.5,0.5,0.5]].
coords_are_cartesian (bool) – Set to True if coords are given in Cartesian coords. Defaults to False.
validate_proximity (bool) – Set to False if you do not wish to ensure that added sites are not too close to other sites. Defaults to True.
- class PartialRemoveSitesTransformation(indices, fractions, algo=1)[source]
Bases:
AbstractTransformationRemove fraction of specie from a structure. Requires an oxidation state decorated structure for Ewald sum to be computed.
Given that the solution to selecting the right removals is NP-hard, there are several algorithms provided with varying degrees of accuracy and speed. The options are as follows:
- ALGO_FAST:
This is a highly optimized algorithm to quickly go through the search tree. It is guaranteed to find the optimal solution, but will return only a single lowest energy structure. Typically, you will want to use this.
- ALGO_COMPLETE:
The complete algo ensures that you get all symmetrically distinct orderings, ranked by the estimated Ewald energy. But this can be an extremely time-consuming process if the number of possible orderings is very large. Use this if you really want all possible orderings. If you want just the lowest energy ordering, ALGO_FAST is accurate and faster.
- ALGO_BEST_FIRST:
This algorithm is for ordering the really large cells that defeats even ALGO_FAST. For example, if you have 48 sites of which you want to remove 16 of them, the number of possible orderings is around 2 x 10^12. ALGO_BEST_FIRST shortcircuits the entire search tree by removing the highest energy site first, then followed by the next highest energy site, and so on. It is guaranteed to find a solution in a reasonable time, but it is also likely to be highly inaccurate.
- ALGO_ENUMERATE:
This algorithm uses the EnumerateStructureTransformation to perform ordering. This algo returns complete orderings up to a single unit cell size. It is more robust than the ALGO_COMPLETE, but requires Gus Hart’s enumlib to be installed.
- Parameters:
indices – A list of list of indices. e.g. [[0, 1], [2, 3, 4, 5]]
fractions – The corresponding fractions to remove. Must be same length as indices. e.g., [0.5, 0.25]
algo – This parameter allows you to choose the algorithm to perform ordering. Use one of PartialRemoveSpecieTransformation.ALGO_* variables to set the algo.
- _fast_ordering(structure: Structure, num_remove_dict, num_to_return=1)[source]
This method uses the matrix form of ewaldsum to calculate the ewald sums of the potential structures. This is on the order of 4 orders of magnitude faster when there are large numbers of permutations to consider. There are further optimizations possible (doing a smarter search of permutations for example), but this won’t make a difference until the number of permutations is on the order of 30,000.
- apply_transformation(structure: Structure, return_ranked_list: bool | int = False)[source]
Apply the transformation.
- Parameters:
structure – input structure
return_ranked_list (bool | int) – Whether or not multiple structures are returned. If return_ranked_list is int, that number of structures is returned.
- Returns:
Depending on returned_ranked list, either a transformed structure or a list of dictionaries, where each dictionary is of the form {“structure” = …. , “other_arguments”} the key “transformation” is reserved for the transformation that was actually applied to the structure. This transformation is parsed by the alchemy classes for generating a more specific transformation history. Any other information will be stored in the transformation_parameters dictionary in the transmuted structure class.
- class RadialSiteDistortionTransformation(site_index, displacement=0.1, nn_only=False)[source]
Bases:
AbstractTransformationRadially perturbs atoms around a site. Can be used to create spherical distortion due to a point defect.
- Parameters:
site_index (int) – index of the site in structure to place at the center of the distortion (will not be distorted). This index must be provided before the structure is provided in apply_transformation in order to keep in line with the base class.
displacement (float) – distance to perturb the atoms around the objective site
nn_only (bool) – Whether or not to perturb beyond the nearest neighbors. If True, then only the nearest neighbors will be perturbed, leaving the other sites undisturbed. If False, then the nearest neighbors will receive the full displacement, and then subsequent sites will receive a displacement=0.1 / r, where r is the distance each site to the origin site. For small displacements, atoms beyond the NN environment will receive very small displacements, and these are almost equal. For large displacements, this difference is noticeable.
- apply_transformation(structure: Structure)[source]
Apply the transformation.
- Parameters:
structure – Structure or Molecule to apply the transformation to
- Returns:
the transformed structure
- property inverse[source]
Returns the inverse transformation if available. Otherwise, should return None.
- property is_one_to_many: bool[source]
Determines if a Transformation is a one-to-many transformation. If a Transformation is a one-to-many transformation, the apply_transformation method should have a keyword arg “return_ranked_list” which allows for the transformed structures to be returned as a ranked list.
- class RemoveSitesTransformation(indices_to_remove)[source]
Bases:
AbstractTransformationRemove certain sites in a structure.
- Parameters:
indices_to_remove – List of indices to remove. E.g., [0, 1, 2].
- class ReplaceSiteSpeciesTransformation(indices_species_map)[source]
Bases:
AbstractTransformationThis transformation substitutes certain sites with certain species.
- Parameters:
indices_species_map – A dict containing the species mapping in int-string pairs. E.g., { 1:”Na”} or {2:”Mn2+”}. Multiple substitutions can be done. Overloaded to accept sp_and_occu dictionary. E.g. {1: {“Ge”:0.75, “C”:0.25} }, which substitutes a single species with multiple species to generate a disordered structure.
- class TranslateSitesTransformation(indices_to_move, translation_vector, vector_in_frac_coords=True)[source]
Bases:
AbstractTransformationThis class translates a set of sites by a certain vector.
- Parameters:
indices_to_move – The indices of the sites to move
translation_vector – Vector to move the sites. If a list of list or numpy array of shape, (len(indices_to_move), 3), is provided then each translation vector is applied to the corresponding site in the indices_to_move.
vector_in_frac_coords – Set to True if the translation vector is in fractional coordinates, and False if it is in cartesian coordinations. Defaults to True.
pymatgen.transformations.standard_transformations module
This module defines standard transformations which transforms a structure into another structure. Standard transformations operate in a structure-wide manner, rather than site-specific manner. All transformations should inherit the AbstractTransformation ABC.
- class AutoOxiStateDecorationTransformation(symm_tol=0.1, max_radius=4, max_permutations=100000, distance_scale_factor=1.015)[source]
Bases:
AbstractTransformationThis transformation automatically decorates a structure with oxidation states using a bond valence approach.
- Parameters:
symm_tol (float) – Symmetry tolerance used to determine which sites are symmetrically equivalent. Set to 0 to turn off symmetry.
max_radius (float) – Maximum radius in Angstrom used to find nearest neighbors.
max_permutations (int) – Maximum number of permutations of oxidation states to test.
distance_scale_factor (float) – A scale factor to be applied. This is useful for scaling distances, esp in the case of calculation-relaxed structures, which may tend to under (GGA) or over bind (LDA). The default of 1.015 works for GGA. For experimental structure, set this to 1.
- class ChargedCellTransformation(charge=0)[source]
Bases:
AbstractTransformationThe ChargedCellTransformation applies a charge to a structure (or defect object).
- Parameters:
charge – A integer charge to apply to the structure. Defaults to zero. Has to be a single integer. e.g. 2.
- class ConventionalCellTransformation(symprec: float = 0.01, angle_tolerance=5, international_monoclinic=True)[source]
Bases:
AbstractTransformationThis class finds the conventional cell of the input structure.
- Parameters:
symprec (float) – tolerance as in SpacegroupAnalyzer
angle_tolerance (float) – angle tolerance as in SpacegroupAnalyzer
international_monoclinic (bool) – whether to use beta (True) or alpha (False)
as the non-right-angle in the unit cell.
- class DeformStructureTransformation(deformation=((1, 0, 0), (0, 1, 0), (0, 0, 1)))[source]
Bases:
AbstractTransformationThis transformation deforms a structure by a deformation gradient matrix.
- Parameters:
deformation (array) – deformation gradient for the transformation.
- class DiscretizeOccupanciesTransformation(max_denominator=5, tol: float | None = None, fix_denominator=False)[source]
Bases:
AbstractTransformationDiscretizes the site occupancies in a disordered structure; useful for grouping similar structures or as a pre-processing step for order-disorder transformations.
- Parameters:
max_denominator – An integer maximum denominator for discretization. A higher denominator allows for finer resolution in the site occupancies.
tol – A float that sets the maximum difference between the original and discretized occupancies before throwing an error. If None, it is set to 1 / (4 * max_denominator).
fix_denominator (bool) – If True, will enforce a common denominator for all species. This prevents a mix of denominators (for example, 1/3, 1/4) that might require large cell sizes to perform an enumeration. ‘tol’ needs to be > 1.0 in some cases.
- class OrderDisorderedStructureTransformation(algo=0, symmetrized_structures=False, no_oxi_states=False)[source]
Bases:
AbstractTransformationOrder a disordered structure. The disordered structure must be oxidation state decorated for Ewald sum to be computed. No attempt is made to perform symmetry determination to reduce the number of combinations.
Hence, attempting to performing ordering on a large number of disordered sites may be extremely expensive. The time scales approximately with the number of possible combinations. The algorithm can currently compute approximately 5,000,000 permutations per minute.
Also, simple rounding of the occupancies are performed, with no attempt made to achieve a target composition. This is usually not a problem for most ordering problems, but there can be times where rounding errors may result in structures that do not have the desired composition. This second step will be implemented in the next iteration of the code.
If multiple fractions for a single species are found for different sites, these will be treated separately if the difference is above a threshold tolerance. currently this is .1
For example, if a fraction of .25 Li is on sites 0,1,2,3 and .5 on sites 4, 5, 6, 7 then 1 site from [0,1,2,3] will be filled and 2 sites from [4,5,6,7] will be filled, even though a lower energy combination might be found by putting all lithium in sites [4,5,6,7].
USE WITH CARE.
- Parameters:
algo (int) – Algorithm to use.
symmetrized_structures (bool) – Whether the input structures are instances of SymmetrizedStructure, and that their symmetry should be used for the grouping of sites.
no_oxi_states (bool) – Whether to remove oxidation states prior to ordering.
- apply_transformation(structure: Structure, return_ranked_list: bool | int = False)[source]
For this transformation, the apply_transformation method will return only the ordered structure with the lowest Ewald energy, to be consistent with the method signature of the other transformations. However, all structures are stored in the all_structures attribute in the transformation object for easy access.
- Parameters:
structure – Oxidation state decorated disordered structure to order
return_ranked_list (bool | int, optional) –
If return_ranked_list is int, that number of structures
is returned. If False, only the single lowest energy structure is returned. Defaults to False.
- Returns:
Depending on returned_ranked list, either a transformed structure or a list of dictionaries, where each dictionary is of the form {“structure” = …. , “other_arguments”} the key “transformation” is reserved for the transformation that was actually applied to the structure. This transformation is parsed by the alchemy classes for generating a more specific transformation history. Any other information will be stored in the transformation_parameters dictionary in the transmuted structure class.
- class OxidationStateDecorationTransformation(oxidation_states)[source]
Bases:
AbstractTransformationThis transformation decorates a structure with oxidation states.
- Parameters:
oxidation_states (dict) – Oxidation states supplied as a dict,
e.g. – 1, “O”:-2}.
{"Li" – 1, “O”:-2}.
- class OxidationStateRemovalTransformation[source]
Bases:
AbstractTransformationThis transformation removes oxidation states from a structure.
No arg needed.
- class PartialRemoveSpecieTransformation(specie_to_remove, fraction_to_remove, algo=0)[source]
Bases:
AbstractTransformationRemove fraction of specie from a structure.
Requires an oxidation state decorated structure for Ewald sum to be computed.
Given that the solution to selecting the right removals is NP-hard, there are several algorithms provided with varying degrees of accuracy and speed. Please see
pymatgen.transformations.site_transformations.PartialRemoveSitesTransformation.- Parameters:
specie_to_remove – Species to remove. Must have oxidation state E.g., “Li+”
fraction_to_remove – Fraction of specie to remove. E.g., 0.5
algo – This parameter allows you to choose the algorithm to perform ordering. Use one of PartialRemoveSpecieTransformation.ALGO_* variables to set the algo.
- apply_transformation(structure: Structure, return_ranked_list: bool | int = False)[source]
Apply the transformation.
- Parameters:
structure – input structure
return_ranked_list (bool | int, optional) –
If return_ranked_list is int, that number of structures
is returned. If False, only the single lowest energy structure is returned. Defaults to False.
- Returns:
Depending on returned_ranked list, either a transformed structure or a list of dictionaries, where each dictionary is of the form {“structure” = …. , “other_arguments”} the key “transformation” is reserved for the transformation that was actually applied to the structure. This transformation is parsed by the alchemy classes for generating a more specific transformation history. Any other information will be stored in the transformation_parameters dictionary in the transmuted structure class.
- class PerturbStructureTransformation(distance: float = 0.01, min_distance: int | float | None = None)[source]
Bases:
AbstractTransformationThis transformation perturbs a structure by a specified distance in random directions. Used for breaking symmetries.
- Parameters:
distance – Distance of perturbation in angstroms. All sites will be perturbed by exactly that distance in a random direction.
min_distance – if None, all displacements will be equidistant. If int or float, perturb each site a distance drawn from the uniform distribution between ‘min_distance’ and ‘distance’.
- class PrimitiveCellTransformation(tolerance=0.5)[source]
Bases:
AbstractTransformationThis class finds the primitive cell of the input structure. It returns a structure that is not necessarily orthogonalized Author: Will Richards.
- Parameters:
tolerance (float) – Tolerance for each coordinate of a particular site. For example, [0.5, 0, 0.5] in Cartesian coordinates will be considered to be on the same coordinates as [0, 0, 0] for a tolerance of 0.5. Defaults to 0.5.
- class RemoveSpeciesTransformation(species_to_remove)[source]
Bases:
AbstractTransformationRemove all occurrences of some species from a structure.
- Parameters:
species_to_remove – List of species to remove. E.g., [“Li”, “Mn”].
- class RotationTransformation(axis, angle, angle_in_radians=False)[source]
Bases:
AbstractTransformationThe RotationTransformation applies a rotation to a structure.
- Parameters:
axis (3x1 array) – Axis of rotation, e.g., [1, 0, 0]
angle (float) – Angle to rotate
angle_in_radians (bool) – Set to True if angle is supplied in radians. Else degrees are assumed.
- class ScaleToRelaxedTransformation(unrelaxed_structure, relaxed_structure, species_map=None)[source]
Bases:
AbstractTransformationTakes the unrelaxed and relaxed structure and applies its site and volume relaxation to a structurally similar structures (e.g. bulk: NaCl and PbTe (rock-salt), slab: Sc(10-10) and Mg(10-10) (hcp), GB: Mo(001) sigma 5 GB, Fe(001) sigma 5). Useful for finding an initial guess of a set of similar structures closer to its most relaxed state.
- Parameters:
unrelaxed_structure (Structure) – Initial, unrelaxed structure
relaxed_structure (Structure) – Relaxed structure
species_map (dict) – A dict or list of tuples containing the species mapping in string-string pairs. The first species corresponds to the relaxed structure while the second corresponds to the species in the structure to be scaled. E.g., {“Li”:”Na”} or [(“Fe2+”,”Mn2+”)]. Multiple substitutions can be done. Overloaded to accept sp_and_occu dictionary E.g. {“Si: {“Ge”:0.75, “C”:0.25}}, which substitutes a single species with multiple species to generate a disordered structure.
- class SubstitutionTransformation(species_map: dict[SpeciesLike, SpeciesLike | dict[SpeciesLike, float]] | list[tuple[SpeciesLike, SpeciesLike]])[source]
Bases:
AbstractTransformationThis transformation substitutes species for one another.
- Parameters:
species_map – A dict or list of tuples containing the species mapping in string-string pairs. E.g., {“Li”: “Na”} or [(“Fe2+”,”Mn2+”)]. Multiple substitutions can be done. Overloaded to accept sp_and_occu dictionary E.g. {“Si: {“Ge”:0.75, “C”:0.25}}, which substitutes a single species with multiple species to generate a disordered structure.
- class SupercellTransformation(scaling_matrix=((1, 0, 0), (0, 1, 0), (0, 0, 1)))[source]
Bases:
AbstractTransformationThe RotationTransformation applies a rotation to a structure.
- Parameters:
scaling_matrix – A matrix of transforming the lattice vectors. Defaults to the identity matrix. Has to be all integers. e.g., [[2,1,0],[0,3,0],[0,0,1]] generates a new structure with lattice vectors a” = 2a + b, b” = 3b, c” = c where a, b, and c are the lattice vectors of the original structure.
- apply_transformation(structure)[source]
Apply the transformation.
- Parameters:
structure (Structure) – Input Structure
- Returns:
Supercell Structure.
- static from_scaling_factors(scale_a=1, scale_b=1, scale_c=1)[source]
Convenience method to get a SupercellTransformation from a simple series of three numbers for scaling each lattice vector. Equivalent to calling the normal with [[scale_a, 0, 0], [0, scale_b, 0], [0, 0, scale_c]].
- Parameters:
scale_a – Scaling factor for lattice direction a. Defaults to 1.
scale_b – Scaling factor for lattice direction b. Defaults to 1.
scale_c – Scaling factor for lattice direction c. Defaults to 1.
- Returns:
SupercellTransformation.
pymatgen.transformations.transformation_abc module
Defines an abstract base class contract for Transformation object.
- class AbstractTransformation[source]
Bases:
MSONableAbstract transformation class.
- abstract apply_transformation(structure: Structure)[source]
Applies the transformation to a structure. Depending on whether a transformation is one-to-many, there may be an option to return a ranked list of structures.
- Parameters:
structure – input structure
return_ranked_list (bool | int, optional) –
If return_ranked_list is int, that number of structures
is returned. If False, only the single lowest energy structure is returned. Defaults to False.
- Returns:
depending on returned_ranked list, either a transformed structure or a list of dictionaries, where each dictionary is of the form {‘structure’ = …. , ‘other_arguments’} the key ‘transformation’ is reserved for the transformation that was actually applied to the structure. This transformation is parsed by the alchemy classes for generating a more specific transformation history. Any other information will be stored in the transformation_parameters dictionary in the transmuted structure class.
- abstract property inverse: AbstractTransformation | None[source]
Returns the inverse transformation if available. Otherwise, should return None.
- abstract property is_one_to_many: bool[source]
Determines if a Transformation is a one-to-many transformation. If a Transformation is a one-to-many transformation, the apply_transformation method should have a keyword arg “return_ranked_list” which allows for the transformed structures to be returned as a ranked list.