pymatgen.io.vasp package
This package implements modules for input and output to and from VASP. It imports the key classes form both vasp_input and vasp_output to allow most classes to be simply called as pymatgen.io.vasp.Incar for example, to retain backwards compatibility.
Submodules
pymatgen.io.vasp.help module
Get help with VASP parameters from VASP wiki.
- class VaspDoc[source]
Bases:
objectA VASP documentation helper.
Init for VaspDoc.
- classmethod get_help(tag: str, fmt: str = 'text') str[source]
Get help on a VASP tag.
- Parameters:
tag (str) – VASP tag, e.g. ISYM.
- Returns:
Help text.
pymatgen.io.vasp.inputs module
Classes for reading/manipulating/writing VASP input files. All major VASP input files.
- class Incar(params: dict[str, Any] | None = None)[source]
Bases:
dict,MSONableINCAR object for reading and writing INCAR files. Essentially a dictionary with some helper functions.
Create an Incar object.
- Parameters:
params (dict) – Input parameters as a dictionary.
- check_params() None[source]
Check INCAR for invalid tags or values. If a tag doesn’t exist, calculation will still run, however VASP will ignore the tag and set it as default without letting you know.
- diff(other: Self) dict[str, dict[str, Any]][source]
Diff function for Incar. Compare two Incars and indicate which parameters are the same and which are not. Useful for checking whether two runs were done using the same parameters.
- Parameters:
other (Incar) – The other Incar object to compare to.
- Returns:
- of the following format:
{“Same” : parameters_that_are_the_same, “Different”: parameters_that_are_different} Note that the parameters are return as full dictionaries of values. E.g. {“ISIF”:3}
- Return type:
dict[str, dict]
- classmethod from_dict(dct: dict[str, Any]) Self[source]
- Parameters:
dct (dict) – Serialized Incar
- Returns:
Incar
- classmethod from_file(filename: PathLike) Self[source]
Read an Incar object from a file.
- Parameters:
filename (str) – Filename for file
- Returns:
Incar object
- classmethod from_str(string: str) Self[source]
Read an Incar object from a string.
- Parameters:
string (str) – Incar string
- Returns:
Incar object
- get_str(sort_keys: bool = False, pretty: bool = False) str[source]
Get a string representation of the INCAR. Differ from the __str__ method to provide options for pretty printing.
- Parameters:
sort_keys (bool) – Whether to sort the INCAR parameters alphabetically. Defaults to False.
pretty (bool) – Whether to pretty align output. Defaults to False.
- class Kpoints(comment: str = 'Default gamma', num_kpts: int = 0, style: KpointsSupportedModes = KpointsSupportedModes.Gamma, kpts: Sequence[Kpoint] = ((1, 1, 1),), kpts_shift: Vector3D = (0, 0, 0), kpts_weights: list[float] | None = None, coord_type: Literal['Reciprocal', 'Cartesian'] | None = None, labels: list[str] | None = None, tet_number: int = 0, tet_weight: float = 0, tet_connections: list[tuple] | None = None)[source]
Bases:
MSONableKPOINTS reader/writer.
Highly flexible constructor for Kpoints object. The flexibility comes at the cost of usability and in general, it is recommended that you use the default constructor only if you know exactly what you are doing and requires the flexibility. For most usage cases, the three automatic schemes can be constructed far more easily using the convenience static constructors (automatic, gamma_automatic, monkhorst_automatic) and it is recommended that you use those.
- Parameters:
comment (str) – String comment for Kpoints. Defaults to “Default gamma”.
num_kpts – Following VASP method of defining the KPOINTS file, this parameter is the number of kpoints specified. If set to 0 (or negative), VASP automatically generates the KPOINTS.
style – Style for generating KPOINTS. Use one of the Kpoints.supported_modes enum types.
kpts (2D array) – Array of kpoints. Even when only a single specification is required, e.g. in the automatic scheme, the kpts should still be specified as a 2D array. e.g. [(20,),] or [(2, 2, 2),].
kpts_shift (3x1 array) – Shift for kpoints.
kpts_weights (list[float]) – Optional weights for explicit kpoints.
coord_type – In line-mode, this variable specifies whether the Kpoints were given in Cartesian or Reciprocal coordinates.
labels – In line-mode, this should provide a list of labels for each kpt. It is optional in explicit kpoint mode as comments for k-points.
tet_number – For explicit kpoints, specifies the number of tetrahedrons for the tetrahedron method.
tet_weight – For explicit kpoints, specifies the weight for each tetrahedron for the tetrahedron method.
tet_connections – For explicit kpoints, specifies the connections of the tetrahedrons for the tetrahedron method. Format is a list of tuples, [ (sym_weight, [tet_vertices]), …]
The default behavior of the constructor is for a Gamma centered, 1x1x1 KPOINTS with no shift.
- classmethod automatic(subdivisions: int) Self[source]
Constructor for a fully automatic Kpoint grid, with gamma centered Monkhorst-Pack grids and the number of subdivisions along each reciprocal lattice vector determined by the scheme in the VASP manual.
- Parameters:
subdivisions (int) – Number of subdivisions along each reciprocal lattice vector.
- Returns:
Kpoints object
- classmethod automatic_density(structure: Structure, kppa: float, force_gamma: bool = False) Self[source]
Get an automatic Kpoint object based on a structure and a kpoint density. Uses Gamma centered meshes for hexagonal cells and face-centered cells, Monkhorst-Pack grids otherwise.
- Algorithm:
Uses a simple approach scaling the number of divisions along each reciprocal lattice vector proportional to its length.
- Parameters:
structure (Structure) – Input structure
kppa (float) – Grid density
force_gamma (bool) – Force a gamma centered mesh (default is to use gamma only for hexagonal cells or odd meshes)
- Returns:
Kpoints
- classmethod automatic_density_by_lengths(structure: Structure, length_densities: Sequence[float], force_gamma: bool = False) Self[source]
Get an automatic Kpoint object based on a structure and a k-point density normalized by lattice constants.
- Algorithm:
For a given dimension, the # of k-points is chosen as length_density = # of kpoints * lattice constant, e.g. [50.0, 50.0, 1.0] would have k-points of 50/a x 50/b x 1/c.
- Parameters:
structure (Structure) – Input structure
length_densities (list[float]) – Defines the density of k-points in each
dimension
[50.0 (e.g.)
50.0
1.0].
force_gamma (bool) – Force a gamma centered mesh
- Returns:
Kpoints
- classmethod automatic_density_by_vol(structure: Structure, kppvol: int, force_gamma: bool = False) Self[source]
Get an automatic Kpoint object based on a structure and a kpoint density per inverse Angstrom^3 of reciprocal cell.
- Algorithm:
Same as automatic_density()
- Parameters:
structure (Structure) – Input structure
kppvol (int) – Grid density per Angstrom^(-3) of reciprocal cell
force_gamma (bool) – Force a gamma centered mesh
- Returns:
Kpoints
- classmethod automatic_gamma_density(structure: Structure, kppa: float) Self[source]
Get an automatic Kpoint object based on a structure and a kpoint density. Uses Gamma centered meshes always. For GW.
- Algorithm:
Uses a simple approach scaling the number of divisions along each reciprocal lattice vector proportional to its length.
- Parameters:
structure – Input structure
kppa – Grid density
- classmethod automatic_linemode(divisions: int, ibz: HighSymmKpath) Self[source]
Convenient static constructor for a KPOINTS in mode line_mode. gamma centered Monkhorst-Pack grids and the number of subdivisions along each reciprocal lattice vector determined by the scheme in the VASP manual.
- Parameters:
divisions – Parameter determining the number of k-points along each high symmetry line.
ibz – HighSymmKpath object (pymatgen.symmetry.bandstructure)
- Returns:
Kpoints object
- classmethod from_dict(dct: dict) Self[source]
- Parameters:
dct (dict) – Dict representation.
- Returns:
Kpoints
- classmethod from_file(filename: PathLike) Self[source]
Reads a Kpoints object from a KPOINTS file.
- Parameters:
filename (PathLike) – filename to read from.
- Returns:
Kpoints object
- classmethod from_str(string: str) Self[source]
Reads a Kpoints object from a KPOINTS string.
- Parameters:
string (str) – KPOINTS string.
- Returns:
Kpoints object
- classmethod gamma_automatic(kpts: Kpoint = (1, 1, 1), shift: Vector3D = (0, 0, 0)) Self[source]
Constructor for an automatic Gamma centered Kpoint grid.
- Parameters:
kpts – Subdivisions N_1, N_2 and N_3 along reciprocal lattice vectors. Defaults to (1, 1, 1)
shift – Shift to be applied to the kpoints. Defaults to (0, 0, 0).
- Returns:
Kpoints object
- property kpts: Sequence[tuple[float, float, float] | tuple[int]][source]
A sequence of Kpoints, where each Kpoint is a tuple of 3 or 1.
- classmethod monkhorst_automatic(kpts: Kpoint = (2, 2, 2), shift: Vector3D = (0, 0, 0)) Self[source]
Convenient static constructor for an automatic Monkhorst pack Kpoint grid.
- Parameters:
kpts – Subdivisions N_1, N_2, N_3 along reciprocal lattice vectors. Defaults to (2, 2, 2)
shift – Shift to be applied to the kpoints. Defaults to (0, 0, 0).
- Returns:
Kpoints object
- property style: KpointsSupportedModes[source]
Style for kpoint generation. One of Kpoints_supported_modes enum.
- supported_modes[source]
alias of
KpointsSupportedModes
- class KpointsSupportedModes(value, names=None, *, module=None, qualname=None, type=None, start=1, boundary=None)[source]
Bases:
EnumEnum type of all supported modes for Kpoint generation.
- class Orbital(n, l, j, E, occ)[source]
Bases:
NamedTupleCreate new instance of Orbital(n, l, j, E, occ)
- class OrbitalDescription(l, E, Type, Rcut, Type2, Rcut2)[source]
Bases:
NamedTupleCreate new instance of OrbitalDescription(l, E, Type, Rcut, Type2, Rcut2)
- class Poscar(structure: Structure, comment: str | None = None, selective_dynamics: ArrayLike | None = None, true_names: bool = True, velocities: ArrayLike | None = None, predictor_corrector: ArrayLike | None = None, predictor_corrector_preamble: str | None = None, lattice_velocities: ArrayLike | None = None, sort_structure: bool = False)[source]
Bases:
MSONableObject for representing the data in a POSCAR or CONTCAR file.
- true_names[source]
Boolean indication whether Poscar contains actual real names parsed from either a POTCAR or the POSCAR itself.
- selective_dynamics[source]
Selective dynamics attribute for each site if available. A Nx3 array of booleans.
- velocities[source]
Velocities for each site (typically read in from a CONTCAR). A Nx3 array of floats.
- predictor_corrector[source]
Predictor corrector coordinates and derivatives for each site; i.e. a list of three 1x3 arrays for each site (typically read in from an MD CONTCAR).
- predictor_corrector_preamble[source]
Predictor corrector preamble contains the predictor-corrector key, POTIM, and thermostat parameters that precede the site-specific predictor corrector data in MD CONTCAR.
- lattice_velocities[source]
Lattice velocities and current lattice (typically read in from an MD CONTCAR). A 6x3 array of floats.
- temperature[source]
Temperature of velocity Maxwell-Boltzmann initialization. Initialized to -1 (MB hasn’t been performed).
- Parameters:
structure (Structure) – Structure object.
comment (str | None, optional) – Optional comment line for POSCAR. Defaults to unit cell formula of structure. Defaults to None.
selective_dynamics (ArrayLike | None, optional) – Bool values for selective dynamics, where N is the number of sites. Defaults to None.
true_names (bool, optional) – Set to False if the names in the POSCAR are not well-defined and ambiguous. This situation arises commonly in VASP < 5 where the POSCAR sometimes does not contain element symbols. Defaults to True.
velocities (ArrayLike | None, optional) – Velocities for the POSCAR. Typically parsed in MD runs or can be used to initialize velocities. Defaults to None.
predictor_corrector (ArrayLike | None, optional) – Predictor corrector for the POSCAR. Typically parsed in MD runs. Defaults to None.
predictor_corrector_preamble (str | None, optional) – Preamble to the predictor corrector. Defaults to None.
lattice_velocities (ArrayLike | None, optional) – Lattice velocities and current lattice for the POSCAR. Available in MD runs with variable cell. Defaults to None.
sort_structure (bool, optional) – Whether to sort the structure. Useful if species are not grouped properly together. Defaults to False.
- classmethod from_dict(dct: dict) Self[source]
- Parameters:
dct (dict) – Dict representation.
- Returns:
Poscar
- classmethod from_file(filename: PathLike, check_for_potcar: bool = True, read_velocities: bool = True, **kwargs: dict[str, Any]) Self[source]
Read POSCAR from a file.
The code will try its best to determine the elements in the POSCAR in the following order:
1. If check_for_potcar is True, the code will try to check if a POTCAR is in the same directory as the POSCAR and use elements from that by default. (This is the VASP default sequence of priority). 2. If the input file is VASP5-like and contains element symbols in the 6th line, the code will use that if check_for_potcar is False or there is no POTCAR found. 3. Failing (2), the code will check if a symbol is provided at the end of each coordinate.
If all else fails, the code will just assign the first n elements in increasing atomic number, where n is the number of species, to the Poscar, where a warning would be issued. For example, H, He, Li, …. This will ensure at least a unique element is assigned to each site and any analysis that does not require specific elemental properties should work.
- Parameters:
filename (str) – File name containing Poscar data.
check_for_potcar (bool) – Whether to check if a POTCAR is present in the same directory as the POSCAR. Defaults to True.
read_velocities (bool) – Whether to read or not velocities if they are present in the POSCAR. Default is True.
- Returns:
Poscar object.
- classmethod from_str(data: str, default_names: list[str] | None = None, read_velocities: bool = True) Self[source]
Read POSCAR from a string.
The code will try its best to determine the elements in the POSCAR in the following order:
1. If default_names are supplied and valid, it will use those. Usually, default names comes from an external source, such as a POTCAR in the same directory.
2. If there are no valid default names but the input file is VASP5-like and contains element symbols in the 6th line, the code will use that.
3. Failing (2), the code will check if a symbol is provided at the end of each coordinate.
If all else fails, the code will just assign the first n elements in increasing atomic number, where n is the number of species, to the Poscar. For example, H, He, Li, …. This will ensure at least a unique element is assigned to each site and any analysis that does not require specific elemental properties should work fine.
- Parameters:
data (str) – String containing Poscar data.
default_names ([str]) – Default symbols for the POSCAR file, usually coming from a POTCAR in the same directory.
read_velocities (bool) – Whether to read or not velocities if they are present in the POSCAR. Default is True.
- Returns:
Poscar object.
- get_str(direct: bool = True, vasp4_compatible: bool = False, significant_figures: int = 16) str[source]
Return a string to be written as a POSCAR file. By default, site symbols are written, which is compatible for vasp >= 5.
- Parameters:
direct (bool) – Whether coordinates are output in direct or Cartesian. Defaults to True.
vasp4_compatible (bool) – Set to True to omit site symbols on 6th line to maintain backward vasp 4.x compatibility. Defaults to False.
significant_figures (int) – Number of significant digits to output all quantities. Defaults to 16. Note that positions are output in fixed point, while velocities are output in scientific format.
- Returns:
representation of POSCAR.
- Return type:
str
- get_string(direct: bool = True, vasp4_compatible: bool = False, significant_figures: int = 16) str[source]
Return a string to be written as a POSCAR file. By default, site symbols are written, which is compatible for vasp >= 5.
- Parameters:
direct (bool) – Whether coordinates are output in direct or Cartesian. Defaults to True.
vasp4_compatible (bool) – Set to True to omit site symbols on 6th line to maintain backward vasp 4.x compatibility. Defaults to False.
significant_figures (int) – Number of significant digits to output all quantities. Defaults to 16. Note that positions are output in fixed point, while velocities are output in scientific format.
- Returns:
representation of POSCAR.
- Return type:
str
- property lattice_velocities: ArrayLike | None[source]
Lattice velocities in Poscar (including the current lattice vectors).
- property natoms: list[int][source]
Sequence of number of sites of each type associated with the Poscar. Similar to 7th line in vasp 5+ POSCAR or the 6th line in vasp 4 POSCAR.
- set_temperature(temperature: float) None[source]
Initialize the velocities based on Maxwell-Boltzmann distribution. Removes linear, but not angular drift (same as VASP).
Scale the energies to the exact temperature (microcanonical ensemble) Velocities are given in A/fs. This is the VASP default when direct/cartesian is not specified (even when positions are given in direct coordinates).
Overwrite imported velocities, if any.
- Parameters:
temperature (float) – Temperature in Kelvin.
- class Potcar(symbols: Sequence[str] | None = None, functional: str | None = None, sym_potcar_map: dict[str, str] | None = None)[source]
Bases:
list,MSONableRead and write POTCAR files for calculations. Consists of a list of PotcarSingle.
- Parameters:
symbols (list[str]) – Element symbols for POTCAR. This should correspond to the symbols used by VASP. e.g. “Mg”, “Fe_pv”, etc.
functional (str) – Functional used. To know what functional options there are, use Potcar.FUNCTIONAL_CHOICES. Note that VASP has different versions of the same functional. By default, the old PBE functional is used. If you want the newer ones, use PBE_52 or PBE_54. Note that if you intend to compare your results with the Materials Project, you should use the default setting. You can also override the default by setting PMG_DEFAULT_FUNCTIONAL in your .pmgrc.yaml.
sym_potcar_map (dict) – Allows a user to specify a specific element symbol to raw POTCAR mapping.
- FUNCTIONAL_CHOICES = ('PBE', 'PBE_52', 'PBE_52_W_HASH', 'PBE_54', 'PBE_54_W_HASH', 'PBE_64', 'LDA', 'LDA_52', 'LDA_52_W_HASH', 'LDA_54', 'LDA_54_W_HASH', 'LDA_64', 'PW91', 'LDA_US', 'PW91_US', 'Perdew_Zunger81')[source]
- classmethod from_dict(dct: dict) Self[source]
- Parameters:
dct (dict) – Dict representation.
- Returns:
Potcar
- classmethod from_file(filename: PathLike) Self[source]
Reads Potcar from file.
- Parameters:
filename – Filename
- Returns:
Potcar
- set_symbols(symbols: Sequence[str], functional: str | None = None, sym_potcar_map: dict[str, str] | None = None) None[source]
Initialize the POTCAR from a set of symbols. Currently, the POTCARs can be fetched from a location specified in .pmgrc.yaml. Use pmg config to add this setting.
- Parameters:
symbols (list[str]) – A list of element symbols
functional (str) – The functional to use. If None, the setting PMG_DEFAULT_FUNCTIONAL in .pmgrc.yaml is used, or if this is not set, it will default to PBE.
sym_potcar_map (dict) – A map of symbol:raw POTCAR string. If sym_potcar_map is specified, POTCARs will be generated from the given map data rather than the config file location.
- class PotcarSingle(data: str, symbol: str | None = None)[source]
Bases:
objectObject for a single POTCAR. The builder assumes the POTCAR contains the complete untouched string “data” and a dict of keywords.
- keywords[source]
Keywords parsed from the POTCAR as a dict. All keywords are also accessible as attributes in themselves. e.g. potcar.enmax, potcar.encut, etc.
- Type:
dict
MD5 hashes of the entire POTCAR file and the actual data are validated against a database of known good hashes. Appropriate warnings or errors are raised if validation fails.
- Parameters:
data (str) – Complete, single and raw POTCAR file as a string.
symbol (str) – POTCAR symbol corresponding to the filename suffix e.g. “Tm_3” for POTCAR.TM_3”. If not given, pymatgen will attempt to extract the symbol from the file itself, but is not always reliable!
- property electron_configuration: list[tuple[int, str, int]] | None[source]
Electronic configuration of the PotcarSingle.
- classmethod from_file(filename: PathLike) Self[source]
Read PotcarSingle from file.
- Parameters:
filename – Filename.
- Returns:
PotcarSingle
- classmethod from_symbol_and_functional(symbol: str, functional: str | None = None) Self[source]
Make a PotcarSingle from a symbol and functional.
- Parameters:
symbol (str) – Symbol, e.g. Li_sv
functional (str) – Functional, e.g. PBE
- Returns:
PotcarSingle
- functional_dir: ClassVar[dict[str, str]] = {'LDA': 'POT_LDA_PAW', 'LDA_52': 'POT_LDA_PAW_52', 'LDA_52_W_HASH': 'POTPAW_LDA_52', 'LDA_54': 'POT_LDA_PAW_54', 'LDA_54_W_HASH': 'POTPAW_LDA_54', 'LDA_64': 'POT_LDA_PAW_64', 'LDA_US': 'POT_LDA_US', 'PBE': 'POT_GGA_PAW_PBE', 'PBE_52': 'POT_GGA_PAW_PBE_52', 'PBE_52_W_HASH': 'POTPAW_PBE_52', 'PBE_54': 'POT_GGA_PAW_PBE_54', 'PBE_54_W_HASH': 'POTPAW_PBE_54', 'PBE_64': 'POT_PAW_PBE_64', 'PW91': 'POT_GGA_PAW_PW91', 'PW91_US': 'POT_GGA_US_PW91', 'Perdew_Zunger81': 'POT_LDA_PAW'}[source]
- functional_tags: ClassVar[dict[str, dict[Literal['name', 'class'], str]]] = {'91': {'class': 'GGA', 'name': 'PW91'}, 'am': {'class': 'GGA', 'name': 'AM05'}, 'ca': {'class': 'LDA', 'name': 'Perdew-Zunger81'}, 'hl': {'class': 'LDA', 'name': 'Hedin-Lundquist'}, 'lm': {'class': 'GGA', 'name': 'Langreth-Mehl-Hu'}, 'pb': {'class': 'GGA', 'name': 'Perdew-Becke'}, 'pe': {'class': 'GGA', 'name': 'PBE'}, 'ps': {'class': 'GGA', 'name': 'PBEsol'}, 'pw': {'class': 'GGA', 'name': 'PW86'}, 'rp': {'class': 'GGA', 'name': 'revPBE'}, 'wi': {'class': 'LDA', 'name': 'Wigner Interpolation'}}[source]
- property hash_sha256_from_file: str | None[source]
SHA256 hash of the POTCAR file as read from the file. None if no SHA256 hash is found.
- identify_potcar(mode: Literal['data', 'file'] = 'data', data_tol: float = 1e-06) tuple[list[str], list[str]][source]
Identify the symbol and compatible functionals associated with this PotcarSingle.
This method checks the summary statistics of either the POTCAR metadadata (PotcarSingle._summary_stats[key][“header”] for key in (“keywords”, “stats”) ) or the entire POTCAR file (PotcarSingle._summary_stats) against a database of hashes for POTCARs distributed with VASP 5.4.4.
- Parameters:
mode ("data" or "file") – “data” mode checks the POTCAR header keywords and stats only while “file” mode checks the entire summary stats.
data_tol (float) – Tolerance for comparing the summary statistics of the POTCAR with the reference statistics.
- Returns:
List of symbols associated with the PotcarSingle potcar_functionals (list): List of potcar functionals associated with
the PotcarSingle
- Return type:
symbol (list)
- identify_potcar_hash_based(mode: Literal['data', 'file'] = 'data') tuple[list[str], list[str]][source]
Identify the symbol and compatible functionals associated with this PotcarSingle.
This method checks the MD5 hash of either the POTCAR metadadata (PotcarSingle.md5_header_hash) or the entire POTCAR file (PotcarSingle.md5_computed_file_hash) against a database of hashes for POTCARs distributed with VASP 5.4.4.
- Parameters:
mode ("data" | "file") – “data” mode checks the hash of the POTCAR metadata in self.keywords, while “file” mode checks the hash of the entire POTCAR file.
- Returns:
List of symbols associated with the PotcarSingle potcar_functionals (list): List of potcar functionals associated with
the PotcarSingle
- Return type:
symbol (list)
- property is_valid: bool[source]
Check that POTCAR matches reference metadata. Parsed metadata is stored in self._summary_stats as a human-readable dict,
- self._summary_stats = {
- “keywords”: {
“header”: list[str], “data”: list[str],
}, “stats”: {
“header”: dict[float], “data”: dict[float],
},
}
- Rationale:
- Each POTCAR is structured as
Header (self.keywords) Data (actual pseudopotential values in data blocks)
For the Data block of POTCAR, there are unformatted data blocks of unknown length and contents/data type, e.g. you might see
<float> <bool> <Data Keyword> <int> <int> <float> <float> … <float> <Data Keyword> <float> … <float>
but this is impossible to process algorithmically without a full POTCAR schema. Note also that POTCARs can contain different data keywords
All keywords found in the header, essentially self.keywords, and the data block (<Data Keyword> above) are stored in self._summary_stats[“keywords”]
To avoid issues of copyright, statistics (mean, mean of abs vals, variance, max, min) for the numeric values in the header and data sections of POTCAR are stored in self._summary_stats[“stats”]
tol is then used to match statistical values within a tolerance
- parse_functions: ClassVar[dict[str, Any]] = {'COPYR': <method 'strip' of 'str' objects>, 'DEXC': <function _parse_float>, 'EATOM': <function _parse_float>, 'EAUG': <function _parse_float>, 'EMMIN': <function _parse_float>, 'ENMAX': <function _parse_float>, 'ENMIN': <function _parse_float>, 'GGA': <function _parse_list>, 'ICORE': <function _parse_int>, 'IUNSCR': <function _parse_int>, 'LCOR': <function _parse_bool>, 'LEXCH': <method 'strip' of 'str' objects>, 'LPAW': <function _parse_bool>, 'LULTRA': <function _parse_bool>, 'LUNSCR': <function _parse_bool>, 'NDATA': <function _parse_int>, 'POMASS': <function _parse_float>, 'QCUT': <function _parse_float>, 'QGAM': <function _parse_float>, 'RAUG': <function _parse_float>, 'RCLOC': <function _parse_float>, 'RCORE': <function _parse_float>, 'RDEP': <function _parse_float>, 'RDEPT': <function _parse_float>, 'RMAX': <function _parse_float>, 'RPACOR': <function _parse_float>, 'RRKJ': <function _parse_list>, 'RWIGS': <function _parse_float>, 'SHA256': <method 'strip' of 'str' objects>, 'STEP': <function _parse_list>, 'TITEL': <method 'strip' of 'str' objects>, 'VRHFIN': <method 'strip' of 'str' objects>, 'ZVAL': <function _parse_float>}[source]
- property potential_type: Literal['NC', 'PAW', 'US'][source]
NC (Norm-conserving), US (Ultra-soft), PAW (Projector augmented wave).
- Type:
Type of PSP
- property sha256_computed_file_hash: str[source]
Compute a SHA256 hash of the PotcarSingle EXCLUDING lines starting with ‘SHA256’ and ‘COPYR’.
- verify_potcar() tuple[bool, bool][source]
Attempt to verify the integrity of the POTCAR data.
This method checks the whole file (removing only the SHA256 metadata) against the SHA256 hash in the header if this is found. If no SHA256 hash is found in the file, the file hash (md5 hash of the whole file) is checked against all POTCAR file hashes known to pymatgen.
- Returns:
has_sha256 and passed_hash_check.
- Return type:
tuple[bool, bool]
- exception UnknownPotcarWarning[source]
Bases:
UserWarningWarning raised when POTCAR hashes do not pass validation.
- class VaspInput(incar: dict | Incar, kpoints: Kpoints | None, poscar: Poscar, potcar: Potcar | str | None, potcar_spec: bool = False, optional_files: dict[PathLike, object] | None = None, **kwargs)[source]
Bases:
dict,MSONableContain a set of vasp input objects corresponding to a run.
Initialize a VaspInput object with the given input files.
- Parameters:
incar (Incar) – The Incar object.
kpoints (Kpoints) – The Kpoints object.
poscar (Poscar) – The Poscar object.
potcar (Potcar or str) – The Potcar object.
potcar_spec (bool = False) – used to share POTCAR info without license issues. True –> POTCAR is a list of symbols, write POTCAR.spec False –> POTCAR is a VASP POTCAR, write POTCAR
optional_files (dict) – Other input files supplied as a dict of {filename: object}. The object should follow standard pymatgen conventions in implementing a as_dict() and from_dict method.
**kwargs – Additional keyword arguments to be stored in the VaspInput object.
- classmethod from_dict(dct: dict) Self[source]
- Parameters:
dct (dict) – Dict representation.
- Returns:
VaspInput
- classmethod from_directory(input_dir: PathLike, optional_files: dict | None = None) Self[source]
Read in a set of VASP inputs from a directory. Note that only the standard INCAR, POSCAR, POTCAR and KPOINTS files are read unless optional_filenames is specified.
- Parameters:
input_dir (PathLike) – Directory to read VASP input from.
optional_files (dict) – Optional files to read in as a dict of {filename: Object type}. Objects must have from_file method.
- run_vasp(run_dir: PathLike = '.', vasp_cmd: list | None = None, output_file: PathLike = 'vasp.out', err_file: PathLike = 'vasp.err') None[source]
Write input files and run VASP.
- Parameters:
run_dir – Where to write input files and do the run.
vasp_cmd – Args to be supplied to run VASP. Otherwise, the PMG_VASP_EXE in .pmgrc.yaml is used.
output_file – File to write output.
err_file – File to write err.
- write_input(output_dir: PathLike = '.', make_dir_if_not_present: bool = True, cif_name: str | None = None, zip_name: str | None = None, files_to_transfer: dict | None = None) None[source]
Write VASP inputs to a directory.
- Parameters:
output_dir (PathLike) – Directory to write to. Defaults to current directory (“.”).
make_dir_if_not_present (bool) – Create the directory if not present. Defaults to True.
cif_name (str or None) – If a str, the name of the CIF file to write the POSCAR to (the POSCAR will also be written).
zip_name (str or None) – If a str, the name of the zip to archive the VASP input set to.
files_to_transfer (dict) –
- A dictionary of
{ < input filename >: < output filepath >}.
This allows the transfer of < input filename > files from a previous calculation to < output filepath >.
pymatgen.io.vasp.optics module
Classes for parsing and manipulating VASP optical properties calculations.
- class DielectricFunctionCalculator(cder_real: NDArray, cder_imag: NDArray, eigs: NDArray, kweights: NDArray, nedos: int, deltae: float, ismear: int, sigma: float, efermi: float, cshift: float, ispin: int, volume: float)[source]
Bases:
MSONablePost-process VASP optical properties calculations.
This objects helps load the different parameters from the vasprun.xml file but allows users to override them as needed.
The standard vasprun.xml from an
LOPTICS=.True.calculation already contains the complex frequency dependent dielectric functions. However you have no way to decompose the different contributions. Since theWAVEDERfile is also written during an optical calculation, you can reconstruct the dielectric functions purely in Python and have full control over contribution from different bands and k-points.- VASP’s linear optics follow these steps:
Calculate the imaginary part
Perform symmetry operations (this is not implemented here)
Calculate the real part
Currently, this Calculator only works for
ISYM=0calculations since we cannot guarantee that our externally defined symmetry operations are the same as VASP’s. This can be fixed by printing the symmetry operators into the vasprun.xml file. If this happens in future versions of VASP, we can dramatically speed up the calculations here by considering only the irreducible kpoints.- classmethod from_directory(directory: PathLike) Self[source]
Construct a DielectricFunction from a directory containing vasprun.xml and WAVEDER files.
- classmethod from_vasp_objects(vrun: Vasprun, waveder: Waveder) Self[source]
Construct a DielectricFunction from Vasprun, Kpoint, and Waveder.
- Parameters:
vrun – Vasprun object
kpoint – Kpoint object
waveder – Waveder object
- get_epsilon(idir: int, jdir: int, efermi: float | None = None, nedos: int | None = None, deltae: float | None = None, ismear: int | None = None, sigma: float | None = None, cshift: float | None = None, mask: NDArray | None = None) tuple[NDArray, NDArray][source]
Compute the frequency dependent dielectric function.
- Parameters:
idir – First direction of the dielectric tensor
jdir – Second direction of the dielectric tensor
efermi – Fermi energy
nedos – Number of points in the DOS
deltae – Energy step in the DOS
ismear – Smearing method (only has 0:gaussian, >0:Methfessel-Paxton)
sigma – Smearing width
cshift – Complex shift used for Kramer-Kronig transformation
mask – Mask for the bands/kpoint/spin index to include in the calculation
- plot_weighted_transition_data(idir: int, jdir: int, mask: NDArray | None = None, min_val: float = 0.0)[source]
Data for plotting the weight matrix elements as a scatter plot.
Since the computation of the final spectrum (especially the smearing part) is still fairly expensive. This function can be used to check the values of some portion of the spectrum (defined by the mask). In a sense, we are looking at the imaginary part of the dielectric function before the smearing is applied.
- Parameters:
idir – First direction of the dielectric tensor.
jdir – Second direction of the dielectric tensor.
mask – Mask to apply to the CDER for the bands/kpoint/spin index to include in the calculation
min_val – Minimum value below this value the matrix element will not be shown.
- delta_methfessel_paxton(x: NDArray, n: int) NDArray[source]
D_n (x) = exp -x^2 * sum_i=0^n A_i H_2i(x) where H is a Hermite polynomial and A_i = (-1)^i / ( i! 4^i sqrt(pi) ).
- epsilon_imag(cder: NDArray, eigs: NDArray, kweights: ArrayLike, efermi: float, nedos: int, deltae: float, ismear: int, sigma: float, idir: int, jdir: int, mask: NDArray | None = None) tuple[NDArray, NDArray][source]
Replicate the EPSILON_IMAG function of VASP.
- Parameters:
cder – The data written to the WAVEDER (nbands, nbands, nkpoints, nspin, diri, dirj)
eigs – The eigenvalues (nbands, nkpoints, nspin)
kweights – The kpoint weights (nkpoints)
efermi – The fermi energy
nedos – The sampling of the energy values
deltae – The energy grid spacing
ismear – The smearing parameter used by the
step_func.sigma – The width of the smearing
idir – The first direction of the dielectric tensor
jdir – The second direction of the dielectric tensor
mask – Mask for the bands/kpoint/spin index to include in the calculation
- Returns:
Array of size nedos with the imaginary part of the dielectric function.
- Return type:
np.array
- get_delta(x0: float, sigma: float, nx: int, dx: float, ismear: int = 3) NDArray[source]
Get the smeared delta function to be added to form the spectrum.
This replaces the SLOT function from VASP. Uses finite differences instead of evaluating the delta function since the step function is more likely to have analytic form.
- Parameters:
x0 – The center of the dielectric function.
sigma – The width of the smearing
nx – The number of grid points in the output grid.
dx – The gridspacing of the output grid.
ismear – The smearing parameter used by the
step_func.
- Returns:
Array of size nx with delta function on the desired outputgrid.
- Return type:
np.array
- get_step(x0: float, sigma: float, nx: int, dx: float, ismear: int) float[source]
Get the smeared step function to be added to form the spectrum.
This replaces the SLOT function from VASP.
- Parameters:
x0 – The center of the dielectric function.
sigma – The width of the smearing
nx – The number of grid points in the output grid.
dx – The gridspacing of the output grid.
ismear – The smearing parameter used by the
step_func.
- Returns:
Array of size nx with step function on the desired outputgrid.
- Return type:
np.array
- kramers_kronig(eps: NDArray, nedos: int, deltae: float, cshift: float = 0.1) NDArray[source]
Perform the Kramers-Kronig transformation.
Perform the Kramers-Kronig transformation exactly as VASP does it. The input eps should be complex and the imaginary part of the dielectric function should be stored as the real part of the complex input array. The output should be the complex dielectric function.
- Parameters:
eps – The dielectric function with the imaginary part stored as the real part and nothing in the imaginary part.
nedos – The sampling of the energy values
deltae – The energy grid spacing
cshift – The shift of the imaginary part of the dielectric function.
- Returns:
Array of size nedos with the complex dielectric function.
- Return type:
np.array
pymatgen.io.vasp.outputs module
Classes for reading/manipulating/writing VASP output files.
- class BSVasprun(filename: PathLike, parse_projected_eigen: bool | str = False, parse_potcar_file: bool | str = False, occu_tol: float = 1e-08, separate_spins: bool = False)[source]
Bases:
VasprunA highly optimized version of Vasprun that parses only eigenvalues for bandstructures. All other properties like structures, parameters, etc. are ignored.
- Parameters:
filename – Filename to parse
parse_projected_eigen – Whether to parse the projected eigenvalues. Defaults to False. Set to True to obtain projected eigenvalues. Note that this can take an extreme amount of time and memory. So use this wisely.
parse_potcar_file – Whether to parse the potcar file to read the potcar hashes for the potcar_spec attribute. Defaults to True, where no hashes will be determined and the potcar_spec dictionaries will read {“symbol”: ElSymbol, “hash”: None}. By Default, looks in the same directory as the vasprun.xml, with same extensions as Vasprun.xml. If a string is provided, looks at that filepath.
occu_tol – Sets the minimum tol for the determination of the vbm and cbm. Usually the default of 1e-8 works well enough, but there may be pathological cases.
separate_spins (bool) – Whether the band gap, CBM, and VBM should be reported for each individual spin channel. Defaults to False, which computes the eigenvalue band properties independent of the spin orientation. If True, the calculation must be spin-polarized.
- class Chgcar(poscar: Poscar | Structure, data: dict[str, NDArray], data_aug: NDArray | None = None)[source]
Bases:
VolumetricDataCHGCAR file reader.
- Parameters:
- class Dynmat(filename: PathLike)[source]
Bases:
objectDYNMAT file reader.
- data[source]
A nested dict containing the DYNMAT data of the form: [atom <int>][disp <int>][‘dispvec’] =
displacement vector (part of first line in dynmat block, e.g. “0.01 0 0”)
- [atom <int>][disp <int>][‘dynmat’] =
<list> list of dynmat lines for this atom and this displacement
- Type:
dict
Authors: Patrick Huck
- Parameters:
filename – Name of file containing DYNMAT.
- class Eigenval(filename: PathLike, occu_tol: float = 1e-08, separate_spins: bool = False)[source]
Bases:
objectEIGENVAL file reader.
- eigenvalues[source]
Eigenvalues as a dict of {(spin): np.ndarray(shape=(nkpt, nbands, 2))}. This representation is based on actual ordering in VASP and is meant as an intermediate representation to be converted into proper objects. The kpoint index is 0-based (unlike the 1-based indexing in VASP).
- Type:
dict
Read input from filename to construct Eigenval object.
- Parameters:
filename (PathLike) – filename of EIGENVAL to read.
occu_tol (float) – tolerance for determining band gap.
separate_spins (bool) – whether the band gap, CBM, and VBM should be reported for each individual spin channel. Defaults to False, which computes the eigenvalue band properties independent of the spin orientation. If True, the calculation must be spin-polarized.
- property eigenvalue_band_properties: tuple[float, float, float, bool] | tuple[tuple[float, float], tuple[float, float], tuple[float, float], tuple[bool, bool]][source]
Band properties from the eigenvalues as a tuple of (band gap, cbm, vbm, is_band_gap_direct). In the case of separate_spins=True, the band gap, cbm, vbm, and is_band_gap_direct are each tuples of 2, with index 0 representing the spin-up channel and index 1 representing the spin-down channel.
- class Elfcar(poscar: Poscar | Structure, data: dict[str, NDArray])[source]
Bases:
VolumetricDataRead an ELFCAR file which contains the Electron Localization Function (ELF).
For ELF, “total” key refers to Spin.up, and “diff” refers to Spin.down.
This also contains information on the kinetic energy density.
- classmethod from_file(filename: str) Self[source]
Read a ELFCAR file.
- Parameters:
filename – Filename
- Returns:
Elfcar
- get_alpha() VolumetricData[source]
Get the parameter alpha where ELF = 1/(1 + alpha^2).
- class KpointOptProps(tdos: Dos | None = None, idos: Dos | None = None, pdos: list | None = None, efermi: float | None = None, eigenvalues: dict | None = None, projected_eigenvalues: dict | None = None, projected_magnetisation: ndarray | None = None, kpoints: Kpoints | None = None, actual_kpoints: list | None = None, actual_kpoints_weights: list | None = None, dos_has_errors: bool | None = None)[source]
Bases:
objectSimple container class to store KPOINTS_OPT data in a separate namespace. Used by Vasprun.
- class Locpot(poscar: Poscar, data: ndarray, **kwargs)[source]
Bases:
VolumetricDataLOCPOT file reader.
- Parameters:
poscar (Poscar) – Poscar object containing structure.
data (np.ndarray) – Actual data.
- class Oszicar(filename: PathLike)[source]
Bases:
objectOSZICAR parser for VASP.
In general, while OSZICAR is useful for a quick look at the output from a VASP run, we recommend using the Vasprun parser instead, which gives far richer information.
- electronic_steps[source]
All electronic steps as a list of list of dict. e.g. [[{“rms”: 160.0, “E”: 4507.24605593, “dE”: 4507.2, “N”: 1, “deps”: -17777.0, “ncg”: 16576}, …], [….] where electronic_steps[index] refers the list of electronic steps in one ionic_step, electronic_steps[index][subindex] refers to a particular electronic step at subindex in ionic step at index. The dict of properties depends on the type of VASP run, but in general, “E”, “dE” and “rms” should be present in almost all runs.
- Type:
list
- ionic_steps[source]
All ionic_steps as a list of dict, e.g. [{“dE”: -526.36, “E0”: -526.36024, “mag”: 0.0, “F”: -526.36024}, …] This is the typical output from VASP at the end of each ionic step. The stored dict might be different depending on the type of VASP run.
- Type:
list
- Parameters:
filename (PathLike) – The file to parse.
- class Outcar(filename: PathLike)[source]
Bases:
objectParser for data in OUTCAR that is not available in Vasprun.xml.
Note, this class works a bit differently than most of the other VASP objects, since OUTCAR can be very different depending on which “type of run” performed.
Create the OUTCAR class with a filename reads “regular parameters” that are always present.
- magnetization[source]
Magnetization on each ion as a tuple of dict, e.g. ({“d”: 0.0, “p”: 0.003, “s”: 0.002, “tot”: 0.005}, … )
- Type:
tuple
- chemical_shielding[source]
Chemical shielding on each ion as a dictionary with core and valence contributions.
- Type:
dict
- unsym_cs_tensor[source]
Unsymmetrized chemical shielding tensor matrixes on each ion as a list. e.g. [[[sigma11, sigma12, sigma13], [sigma21, sigma22, sigma23], [sigma31, sigma32, sigma33]], …]
- Type:
list
- cs_g0_contribution[source]
G=0 contribution to chemical shielding. 2D rank 3 matrix.
- Type:
np.array
- cs_core_contribution[source]
Core contribution to chemical shielding. dict. e.g. {‘Mg’: -412.8, ‘C’: -200.5, ‘O’: -271.1}
- Type:
dict
- efg[source]
Electric Field Gradient (EFG) tensor on each ion as a tuple of dict, e.g. ({“cq”: 0.1, “eta”, 0.2, “nuclear_quadrupole_moment”: 0.3}, {“cq”: 0.7, “eta”, 0.8, “nuclear_quadrupole_moment”: 0.9}, …)
- Type:
tuple
- charge[source]
Charge on each ion as a tuple of dict, e.g. ({“p”: 0.154, “s”: 0.078, “d”: 0.0, “tot”: 0.232}, …)
- Type:
tuple
- is_stopped[source]
True if OUTCAR is from a stopped run (using STOPCAR, see VASP Manual).
- Type:
bool
- run_stats[source]
Various useful run stats as a dict including “System time (sec)”, “Total CPU time used (sec)”, “Elapsed time (sec)”, “Maximum memory used (kb)”, “Average memory used (kb)”, “User time (sec)”, “cores”.
- Type:
dict
- sampling_radii[source]
Size of the sampling radii in VASP for the test charges for the electrostatic potential at each atom. Total array size is the number of elements present in the calculation.
- Type:
np.array
- electrostatic_potential[source]
Average electrostatic potential at each atomic position in order of the atoms in POSCAR.
- Type:
np.array
- final_energy_contribs[source]
Individual contributions to the total final energy as a dictionary. Include contributions from keys, e.g.: {‘DENC’: -505778.5184347, ‘EATOM’: 15561.06492564, ‘EBANDS’: -804.53201231, ‘EENTRO’: -0.08932659, ‘EXHF’: 0.0, ‘Ediel_sol’: 0.0, ‘PAW double counting’: 664.6726974100002, ‘PSCENC’: 742.48691646, ‘TEWEN’: 489742.86847338, ‘XCENC’: -169.64189814}
- Type:
dict
- final_energy[source]
Final energy after extrapolation of sigma back to 0, i.e. energy(sigma->0).
- Type:
float
- final_energy_wo_entrp[source]
Final energy before extrapolation of sigma, i.e. energy without entropy.
- Type:
float
- has_onsite_density_matrices[source]
Boolean for if onsite density matrices have been set.
- Type:
bool
One can then call a specific reader depending on the type of run being performed. These are currently: read_igpar(), read_lepsilon() and read_lcalcpol(), read_core_state_eign(), read_avg_core_pot().
See the documentation of those methods for more documentation.
Authors: Rickard Armiento, Shyue Ping Ong
- Parameters:
filename (PathLike) – OUTCAR file to parse.
- read_avg_core_poten() list[list][source]
Read the core potential at each ionic step.
- Returns:
A list for each ionic step containing a list of the average core potentials for each atom: [[avg core pot]].
Example
The average core potential of the 2nd atom of the structure at the last ionic step is: [-1][1]
- read_chemical_shielding() None[source]
Parse the NMR chemical shieldings data. Only the second part “absolute, valence and core” will be parsed. And only the three right most field (ISO_SHIELDING, SPAN, SKEW) will be retrieved.
- Set self.data[“chemical_shielding”] as:
List of chemical shieldings in the order of atoms from the OUTCAR. Maryland notation is adopted.
- read_core_state_eigen() list[dict][source]
Read the core state eigenenergies at each ionic step.
- Returns:
[core state eig]}]. The core state eigenenergie list for each AO is over all ionic step.
- Return type:
A list of dict over the atom such as [{“AO”
Example
The core state eigenenergie of the 2s AO of the 6th atom of the structure at the last ionic step is [5][“2s”][-1].
- read_corrections(reverse: bool = True, terminate_on_match: bool = True) None[source]
Read the dipol qudropol corrections into self.data[“dipol_quadrupol_correction”].
- Parameters:
reverse (bool) – Whether to start from end of OUTCAR. Defaults to True.
terminate_on_match (bool) – Whether to terminate once match is found. Defaults to True.
- read_cs_core_contribution() None[source]
Parse the core contribution of NMR chemical shielding.
- Set self.data[“cs_core_contribution”] as:
list[list]: G0 contribution matrix.
- read_cs_g0_contribution() None[source]
Parse the G0 contribution of NMR chemical shielding.
- Set self.data[“cs_g0_contribution”] as:
list[list]: G0 contribution matrix.
- read_cs_raw_symmetrized_tensors() None[source]
Parse the matrix form of NMR tensor before corrected to table.
- Returns:
nsymmetrized tensors list in the order of atoms.
- read_elastic_tensor() None[source]
Parse the elastic tensor data.
- Set self.data[“elastic_tensor”] as:
6x6 array corresponding to the elastic tensor from the OUTCAR.
- read_electrostatic_potential() None[source]
Parse the eletrostatic potential for the last ionic step.
- read_fermi_contact_shift() None[source]
Read Fermi contact (isotropic) hyperfine coupling parameter.
Output example: Fermi contact (isotropic) hyperfine coupling parameter (MHz) ————————————————————- ion A_pw A_1PS A_1AE A_1c A_tot ————————————————————-
1 -0.002 -0.002 -0.051 0.000 -0.052 2 -0.002 -0.002 -0.051 0.000 -0.052 3 0.056 0.056 0.321 -0.048 0.321
[-0.002, -0.002, -0.051, 0.0, -0.052], [0.056, 0.056, 0.321, -0.048, 0.321]] from ‘fch’ data.
- read_freq_dielectric() None[source]
Parse the frequency dependent dielectric function (obtained with LOPTICS). Frequencies (in eV) are in self.frequencies, and dielectric tensor function is given as self.dielectric_tensor_function.
- read_igpar() None[source]
Read IGPAR.
See VASP sections “LBERRY, IGPAR, NPPSTR, DIPOL” for info on what these are.
- Renders accessible:
er_ev = e<r>_ev (dictionary with Spin.up/Spin.down as keys) er_bp = e<r>_bp (dictionary with Spin.up/Spin.down as keys) er_ev_tot = spin up + spin down summed er_bp_tot = spin up + spin down summed p_elc = spin up + spin down summed p_ion = spin up + spin down summed.
- read_internal_strain_tensor()[source]
Read the internal strain tensor and populates self.internal_strain_tensor with an array of voigt notation tensors for each site.
- read_lepsilon_ionic() None[source]
Read the ionic component of a LEPSILON run.
TODO: Document the actual variables.
- read_neb(reverse: bool = True, terminate_on_match: bool = True) None[source]
Read NEB data. This only works with OUTCARs from both normal VASP NEB calculations or from the CI NEB method implemented by Henkelman et al.
- Parameters:
reverse (bool) – Read files in reverse. Defaults to false. Useful for large files, esp OUTCARs, especially when used with terminate_on_match. Defaults to True here since we usually want only the final value.
terminate_on_match (bool) – Whether to terminate when there is at least one match in each key in pattern. Defaults to True here since we usually want only the final value.
- Renders accessible:
tangent_force - Final tangent force. energy - Final energy. These can be accessed under Outcar.data[key]
- read_nmr_efg() None[source]
Parse the NMR Electric Field Gradient interpreted values.
- Set self.data[“efg”] as:
Electric Field Gradient tensors as a list of dict in the order of atoms from OUTCAR. Each dict key/value pair corresponds to a component of the tensors.
- read_nmr_efg_tensor() list[NDArray][source]
Parses the NMR Electric Field Gradient Raw Tensors.
- Returns:
A list of Electric Field Gradient Tensors in the order of Atoms from OUTCAR.
- read_onsite_density_matrices() None[source]
Parse the onsite density matrices.
- Set self.data[“onsite_density_matrices”] as:
List with index corresponding to atom index in Structure.
- read_pattern(patterns: dict[str, str], reverse: bool = False, terminate_on_match: bool = False, postprocess: Callable = <class 'str'>) None[source]
General pattern reading. Use monty’s regrep method and take the same arguments.
- Parameters:
patterns (dict) – A dict of patterns, e.g. {“energy”: r”energy\(sigma->0\)\s+=\s+([\d\-.]+)”}.
reverse (bool) – Read files in reverse. Defaults to false. Useful for large files, esp OUTCARs, especially when used with terminate_on_match.
terminate_on_match (bool) – Whether to terminate when there is at least one match in each key in pattern.
postprocess (Callable) – A post processing function to convert all matches. Defaults to str, i.e., no change.
- Renders accessible:
Any attribute in patterns. For example, {“energy”: r”energy\(sigma->0\)\s+=\s+([\d\-.]+)”} will set the value of self.data[“energy”] = [[-1234], [-3453], …], to the results from regex and postprocess. Note that the returned values are lists of lists, because you can grep multiple items on one line.
- read_table_pattern(header_pattern: str, row_pattern: str, footer_pattern: str, postprocess: Callable = <class 'str'>, attribute_name: str | None = None, last_one_only: bool = True, first_one_only: bool = False) list[source]
- Parse table-like data. A table composes of three parts: header,
main body, footer. All the data matches “row pattern” in the main body will be returned.
- Args:
- header_pattern (str): The regular expression pattern matches the
table header. This pattern should match all the text immediately before the main body of the table. For multiple sections table match the text until the section of interest. MULTILINE and DOTALL options are enforced, as a result, the “.” meta-character will also match “
- ” in this
section.
- row_pattern (str): The regular expression matches a single line in
the table. Capture interested field using regular expression groups.
- footer_pattern (str): The regular expression matches the end of the
table. E.g. a long dash line.
- postprocess (Callable): A post processing function to convert all
matches. Defaults to str, i.e., no change.
- attribute_name (str): Name of this table. If present the parsed data
will be attached to “data. e.g. self.data[“efg”] = […]
- last_one_only (bool): All the tables will be parsed, if this option
is set to True, only the last table will be returned. The enclosing list will be removed. i.e. Only a single table will be returned. Default to be True. Incompatible with first_one_only.
- first_one_only (bool): Only the first occurrence of the table will be
parsed and the parsing procedure will stop. The enclosing list will be removed. i.e. Only a single table will be returned. Incompatible with last_one_only.
- Returns:
List of tables. 1) A table is a list of rows. 2) A row if either a list of attribute values in case the capturing group is defined without name in row_pattern, or a dict in case that named capturing groups are defined by row_pattern.
- class Procar(filename: PathLike)[source]
Bases:
objectPROCAR file reader.
- data[source]
The PROCAR data of the form below. It should VASP uses 1-based indexing, but all indices are converted to 0-based here. { spin: nd.array accessed with (k-point index, band index, ion index, orbital index) }
- Type:
dict
- weights[source]
The weights associated with each k-point as an nd.array of length nkpoints.
- Type:
np.array
- phase_factors[source]
Phase factors, where present (e.g. LORBIT = 12). A dict of the form: { spin: complex nd.array accessed with (k-point index, band index, ion index, orbital index) }
- Type:
dict
- Parameters:
filename – The PROCAR to read.
- get_occupation(atom_index: int, orbital: str) dict[source]
Get the occupation for a particular orbital of a particular atom.
- Parameters:
atom_num (int) – Index of atom in the PROCAR. It should be noted that VASP uses 1-based indexing for atoms, but this is converted to 0-based indexing in this parser to be consistent with representation of structures in pymatgen.
orbital (str) – An orbital. If it is a single character, e.g. s, p, d or f, the sum of all s-type, p-type, d-type or f-type orbitals occupations are returned respectively. If it is a specific orbital, e.g. px, dxy, etc., only the occupation of that orbital is returned.
- Returns:
Sum occupation of orbital of atom.
- exception VaspParseError[source]
Bases:
ParseErrorException class for VASP parsing.
- class Vasprun(filename: PathLike, ionic_step_skip: int | None = None, ionic_step_offset: int = 0, parse_dos: bool = True, parse_eigen: bool = True, parse_projected_eigen: bool = False, parse_potcar_file: PathLike | bool = True, occu_tol: float = 1e-08, separate_spins: bool = False, exception_on_bad_xml: bool = True)[source]
Bases:
MSONableVastly improved cElementTree-based parser for vasprun.xml files. Uses iterparse to support incremental parsing of large files. Speedup over Dom is at least 2x for smallish files (~1 Mb) to orders of magnitude for larger files (~10 Mb).
VASP results
- ionic_steps[source]
All ionic steps in the run as a list of {“structure”: structure at end of run, “electronic_steps”: {All electronic step data in vasprun file}, “stresses”: stress matrix}.
- Type:
list
- eigenvalues[source]
Final eigenvalues as a dict of {(spin, kpoint index):[[eigenvalue, occu]]}. The kpoint index is 0-based (unlike the 1-based indexing in VASP).
- Type:
dict
- projected_eigenvalues[source]
Final projected eigenvalues as a dict of {spin: nd-array}. To access a particular value, you need to do Vasprun.projected_eigenvalues[spin][kpoint index][band index][atom index][orbital_index]. The kpoint, band and atom indices are 0-based (unlike the 1-based indexing in VASP).
- Type:
dict
- projected_magnetisation[source]
Final projected magnetization as a numpy array with the shape (nkpoints, nbands, natoms, norbitals, 3). Where the last axis is the contribution in the 3 Cartesian directions. This attribute is only set if spin-orbit coupling (LSORBIT = True) or non-collinear magnetism (LNONCOLLINEAR = True) is turned on in the INCAR.
- Type:
np.array
- other_dielectric[source]
Dictionary, with the tag comment as key, containing other variants of the real and imaginary part of the dielectric constant (e.g., computed by RPA) in function of the energy (frequency). Optical properties (e.g. absorption coefficient) can be obtained through this. The data is given as a tuple of 3 values containing each of them the energy, the real part tensor, and the imaginary part tensor ([energies],[[real_partxx,real_partyy,real_partzz,real_partxy, real_partyz,real_partxz]],[[imag_partxx,imag_partyy,imag_partzz,imag_partxy, imag_partyz, imag_partxz]]).
- Type:
dict
- nionic_steps[source]
The total number of ionic steps. This number is always equal to the total number of steps in the actual run even if ionic_step_skip is used.
- Type:
int
- force_constants[source]
Force constants computed in phonon DFPT run(IBRION = 8). The data is a 4D numpy array of shape (natoms, natoms, 3, 3).
- Type:
np.array
- normalmode_eigenvals[source]
Normal mode frequencies. 1D numpy array of size 3*natoms.
- Type:
np.array
- normalmode_eigenvecs[source]
Normal mode eigen vectors. 3D numpy array of shape (3*natoms, natoms, 3).
- Type:
np.array
- md_data[source]
Available only for ML MD runs, i.e., INCAR with ML_LMLFF = .TRUE. md_data is a list of dict with the following format: [{‘energy’: {‘e_0_energy’: -525.07195568, ‘e_fr_energy’: -525.07195568, ‘e_wo_entrp’: -525.07195568, ‘kinetic’: 3.17809233, ‘lattice kinetic’: 0.0, ‘nosekinetic’: 1.323e-5, ‘nosepot’: 0.0, ‘total’: -521.89385012}, ‘forces’: [[0.17677989, 0.48309874, 1.85806696], …], ‘structure’: Structure object}].
- Type:
list
- parameters[source]
Incar object with parameters that VASP actually used, including all defaults.
- Type:
- actual_kpoints[source]
List of actual kpoints, e.g. [[0.25, 0.125, 0.08333333], [-0.25, 0.125, 0.08333333], [0.25, 0.375, 0.08333333], ….].
- Type:
list
- actual_kpoints_weights[source]
List of kpoint weights, e.g. [0.04166667, 0.04166667, 0.04166667, 0.04166667, 0.04166667, ….].
- Type:
list
- potcar_symbols[source]
List of POTCAR symbols. e.g. [“PAW_PBE Li 17Jan2003”, “PAW_PBE Fe 06Sep2000”, ..].
- Type:
list
- kpoints_opt_props[source]
Object whose attributes are the data from KPOINTS_OPT (if present, else None). Attributes of the same name have the same format and meaning as Vasprun (or they are None if absent). Attributes are: tdos, idos, pdos, efermi, eigenvalues, projected_eigenvalues, projected magnetisation, kpoints, actual_kpoints, actual_kpoints_weights, dos_has_errors.
- Type:
object
Author: Shyue Ping Ong
- Parameters:
filename (str) – Filename to parse
ionic_step_skip (int) – If ionic_step_skip is a number > 1, only every ionic_step_skip ionic steps will be read for structure and energies. This is very useful if you are parsing very large vasprun.xml files and you are not interested in every single ionic step. Note that the final energies may not be the actual final energy in the vasprun.
ionic_step_offset (int) – Used together with ionic_step_skip. If set, the first ionic step read will be offset by the amount of ionic_step_offset. For example, if you want to start reading every 10th structure but only from the 3rd structure onwards, set ionic_step_skip to 10 and ionic_step_offset to 3. Main use case is when doing statistical structure analysis with extremely long time scale multiple VASP calculations of varying numbers of steps.
parse_dos (bool) – Whether to parse the dos. Defaults to True. Set to False to shave off significant time from the parsing if you are not interested in getting those data.
parse_eigen (bool) – Whether to parse the eigenvalues. Defaults to True. Set to False to shave off significant time from the parsing if you are not interested in getting those data.
parse_projected_eigen (bool) – Whether to parse the projected eigenvalues and magnetization. Defaults to False. Set to True to obtain projected eigenvalues and magnetization. Note that this can take an extreme amount of time and memory. So use this wisely.
parse_potcar_file (PathLike/bool) – Whether to parse the potcar file to read the potcar hashes for the potcar_spec attribute. Defaults to True, where no hashes will be determined and the potcar_spec dictionaries will read {“symbol”: ElSymbol, “hash”: None}. By Default, looks in the same directory as the vasprun.xml, with same extensions as Vasprun.xml. If a path is provided, look at that path.
occu_tol (float) – Sets the minimum tol for the determination of the vbm and cbm. Usually the default of 1e-8 works well enough, but there may be pathological cases.
separate_spins (bool) – Whether the band gap, CBM, and VBM should be reported for each individual spin channel. Defaults to False, which computes the eigenvalue band properties independent of the spin orientation. If True, the calculation must be spin-polarized.
exception_on_bad_xml (bool) – Whether to throw a ParseException if a malformed XML is detected. Default to True, which ensures only proper vasprun.xml are parsed. You can set to False if you want partial results (e.g., if you are monitoring a calculation during a run), but use the results with care. A warning is issued.
- calculate_efermi(tol: float = 0.001) float[source]
Calculate the Fermi level using a robust algorithm.
Sometimes VASP can set the Fermi level inside a band due to issues in the way band occupancies are handled. This method tries to detect and correct this.
More details: https://www.vasp.at/forum/viewtopic.php?f=4&t=17981.
- property complete_dos: CompleteDos[source]
A CompleteDos object which incorporates the total DOS and all projected DOS.
- property complete_dos_normalized: CompleteDos[source]
A CompleteDos object which incorporates the total DOS and all projected DOS. Normalized by the volume of the unit cell with units of states/eV/unit cell volume.
- property converged: bool[source]
Whether a relaxation run has both ionically and electronically converged.
- property converged_electronic: bool[source]
Whether electronic step converged in the final ionic step.
- property converged_ionic: bool[source]
Whether ionic step convergence has been reached, i.e. VASP exited before reaching the max ionic steps for a relaxation run. In case IBRION=0 (MD) or EDIFFG=0, returns True if the max ionic steps are reached.
- property dielectric: tuple[list, list, list][source]
The real and imaginary part of the dielectric constant (e.g., computed by RPA) in function of the energy (frequency). Optical properties (e.g. absorption coefficient) can be obtained through this.
- Returns:
The data is given as a tuple of 3 for the energy, the real part tensor, and the imaginary part tensor: ([energies], [[real_partxx, real_partyy, real_partzz, real_partxy, real_partyz, real_partxz]], [[imag_partxx, imag_partyy, imag_partzz, imag_partxy, imag_partyz, imag_partxz]]).
- property eigenvalue_band_properties: tuple[float, float, float, bool] | tuple[tuple[float, float], tuple[float, float], tuple[float, float], tuple[bool, bool]][source]
Band properties from the eigenvalues as a tuple, (band gap, cbm, vbm, is_band_gap_direct). In the case of separate_spins=True, the band gap, cbm, vbm, and is_band_gap_direct are each lists of length 2, with index 0 representing the spin-up channel and index 1 representing the spin-down channel.
- property epsilon_ionic: list[float][source]
The ionic part of the static dielectric constant. Present when it’s a DFPT run (LEPSILON=TRUE) and IBRION=5, 6, 7 or 8.
- property epsilonassets: list[float][source]
The static part of the dielectric constant. Present only when it’s a DFPT run (LEPSILON=TRUE).
- property epsilonassets_wolfe: list[float][source]
The static part of the dielectric constant without any local field effects. Present only when it’s a DFPT run (LEPSILON=TRUE).
- get_band_structure(kpoints_filename: str | None = None, efermi: float | Literal['smart'] | None = None, line_mode: bool = False, force_hybrid_mode: bool = False, ignore_kpoints_opt: bool = False) BandStructureSymmLine | BandStructure[source]
Get the band structure.
- Parameters:
kpoints_filename – Full path of the KPOINTS file from which the band structure is generated. If None is provided, the code will try to intelligently determine the appropriate KPOINTS file by substituting the filename of the vasprun.xml with KPOINTS (or KPOINTS_OPT). The latter is the default behavior.
efermi – The Fermi energy associated with the bandstructure, in eV. By default (None), uses the value reported by VASP in vasprun.xml. To manually set the Fermi energy, pass a float. Pass ‘smart’ to use the calculate_efermi() method, which calculates the Fermi level by first checking whether it lies within a small tolerance (by default 0.001 eV) of a band edge) If it does, the Fermi level is placed in the center of the bandgap. Otherwise, the value is identical to the value reported by VASP.
line_mode – Force the band structure to be considered as a run along symmetry lines. (Default: False)
force_hybrid_mode – Makes it possible to read in self-consistent band structure calculations for every type of functional. (Default: False)
ignore_kpoints_opt – Normally, if KPOINTS_OPT data exists, it has the band structure data. Set this flag to ignore it. (Default: False)
- Returns:
a BandStructure object (or more specifically a BandStructureSymmLine object if the run is detected to be a run along symmetry lines)
Two types of runs along symmetry lines are accepted: non-sc with Line-Mode in the KPOINT file or hybrid, self-consistent with a uniform grid+a few kpoints along symmetry lines (explicit KPOINTS file) (it’s not possible to run a non-sc band structure with hybrid functionals). The explicit KPOINTS file needs to have data on the kpoint label as commentary.
If VASP was run with KPOINTS_OPT, it reads the data from that file unless told otherwise. This overrides hybrid mode.
- get_computed_entry(inc_structure: bool = True, parameters: list[str] | None = None, data: dict | None = None, entry_id: str | None = None) ComputedStructureEntry | ComputedEntry[source]
Get a ComputedEntry or ComputedStructureEntry from the Vasprun.
- Parameters:
inc_structure (bool) – Whether to return ComputedStructureEntries instead of ComputedEntries.
parameters (list) – Input parameters to include. It has to be one of the properties supported by the Vasprun object. If is None, a default set of parameters that are necessary for typical post-processing will be set.
data (dict) – Output data to include. Have to be the properties supported by the Vasprun object.
entry_id (str) – An entry id for the ComputedEntry. Defaults to “vasprun-{current datetime}”
- Returns:
ComputedStructureEntry/ComputedEntry
- get_potcars(path: PathLike | bool) Potcar | None[source]
Get the POTCAR from the specified path.
- Parameters:
path (PathLike | bool) – If a str or Path, the path to search for POTCARs. If a bool, whether to take the search path from the specified vasprun.xml
- Returns:
The POTCAR from the specified path or None if not found/no path specified.
- Return type:
Potcar | None
- get_trajectory() Trajectory[source]
Get a Trajectory, an alternative representation of self.structures as a single object. Forces are added as site properties.
- Returns:
Trajectory
- property hubbards: dict[str, float][source]
Hubbard U values used for a GGA+U run, otherwise an empty dict.
- property md_n_steps: int[source]
Number of steps for MD runs.
Count all the actual MD steps if ML enabled.
- property optical_absorption_coeff: list[float] | None[source]
The optical absorption coefficient from the dielectric constants. Note that this method is only implemented for optical properties calculated with GGA and BSE.
- property run_type: str[source]
The run type. Currently detects GGA, metaGGA, HF, HSE, B3LYP, and hybrid functionals based on relevant INCAR tags. LDA is assigned if PAW POTCARs are used and no other functional is detected.
Hubbard U terms and vdW corrections are detected automatically as well.
- class VolumetricData(structure: Structure, data: dict[str, ndarray], distance_matrix: ndarray | None = None, data_aug: ndarray | None = None)[source]
Bases:
VolumetricDataContainer for volumetric data that allows for reading/writing with Poscar-type data.
Typically, this constructor is not used directly and the static from_file constructor is used. This constructor is designed to allow summation and other operations between VolumetricData objects.
- Parameters:
structure (Structure) – associated with the volumetric data
data (dict[str, np.array]) – Actual volumetric data.
distance_matrix (np.array) – A pre-computed distance matrix if available. Useful so pass distance_matrices between sums, short-circuiting an otherwise expensive operation.
data_aug (np.array) – Any extra information associated with volumetric data (typically augmentation charges)
- static parse_file(filename: PathLike) tuple[Poscar, dict, dict][source]
Parse a generic volumetric data file in the VASP like format. Used by subclasses for parsing files.
- Parameters:
filename (PathLike) – Path of file to parse.
- Returns:
Poscar object, data dict, data_aug dict
- Return type:
tuple[Poscar, dict, dict]
- class WSWQ(nspin: int, nkpoints: int, nbands: int, me_real: ndarray, me_imag: ndarray)[source]
Bases:
MSONableRead a WSWQ file. The WSWQ file is used to calculation the wave function overlaps between:
W: Wavefunctions in the current directory’s WAVECAR file.
WQ: Wavefunctions stored in the WAVECAR.qqq file.
The overlap is computed using the overlap operator S which make the PAW wavefunctions orthogonormal:
<W_k,m| S | W_k,n> = delta_{mn}
The WSWQ file contains matrix elements of the overlap operator S evaluated between the planewave wavefunctions W and WQ:
COVL_k,mn = < W_s,k,m | S | WQ_s,k,n >
- The indices of WSWQ.data are:
[spin][kpoint][band_i][band_j]
- class Wavecar(filename: PathLike = 'WAVECAR', verbose: bool = False, precision: Literal['normal', 'accurate'] = 'normal', vasp_type: Literal['std', 'gam', 'ncl'] | None = None)[source]
Bases:
objectContainer for the (pseudo-) wavefunctions from VASP.
Coefficients are read from the given WAVECAR file and the corresponding G-vectors are generated using the algorithm developed in WaveTrans (see acknowledgments below). To understand how the wavefunctions are evaluated, please see the evaluate_wavefunc docstring.
It should be noted that the pseudopotential augmentation is not included in the WAVECAR file. As a result, some caution should be exercised when deriving value from this information.
The usefulness of this class is to allow the user to do projections or band unfolding style manipulations of the wavefunction. An example of this can be seen in the work of Shen et al. 2017 (https://doi.org/10.1103/PhysRevMaterials.1.065001).
- vasp_type[source]
String that determines VASP type the WAVECAR was generated with. One of ‘std’, ‘gam’, ‘ncl’.
- Type:
str
- band_energy[source]
The list of band eigenenergies (and corresponding occupancies) for each kpoint, where the first index corresponds to the index of the k-point (e.g. self.band_energy[kp]).
- Type:
list
- Gpoints[source]
The list of generated G-points for each k-point (a double list), which are used with the coefficients for each k-point and band to recreate the wavefunction (e.g. self.Gpoints[kp] is the list of G-points for k-point kp). The G-points depend on the k-point and reciprocal lattice and therefore are identical for each band at the same k-point. Each G-point is represented by integer multipliers (e.g. assuming Gpoints[kp][n] == [n_1, n_2, n_3], then G_n = n_1*b_1 + n_2*b_2 + n_3*b_3)
- Type:
list
- coeffs[source]
The list of coefficients for each k-point and band for reconstructing the wavefunction. For non-spin-polarized, the first index corresponds to the kpoint and the second corresponds to the band (e.g. self.coeffs[kp][b] corresponds to k-point kp and band b). For spin-polarized calculations, the first index is for the spin. If the calculation was non-collinear, then self.coeffs[kp][b] will have two columns (one for each component of the spinor).
- Type:
list
- Acknowledgments:
This code is based upon the Fortran program, WaveTrans, written by R. M. Feenstra and M. Widom from the Dept. of Physics at Carnegie Mellon University. To see the original work, please visit: https://www.andrew.cmu.edu/user/feenstra/wavetrans/
Author: Mark Turiansky
Extract information from the given WAVECAR.
- Parameters:
filename (PathLike) – input file. Defaults to WAVECAR.
verbose (bool) – determines whether processing information is shown
precision (str) – determines how fine the fft mesh is (normal or accurate), only the first letter matters.
vasp_type (str) – determines the VASP type that is used, allowed values are {‘std’, ‘gam’, ‘ncl’} (only first letter is required).
- evaluate_wavefunc(kpoint: int, band: int, r: ndarray, spin: int = 0, spinor: int = 0) complex64[source]
Evaluate the wavefunction for a given position, r.
The wavefunction is given by the k-point and band. It is evaluated at the given position by summing over the components. Formally,
psi_n^k (r) = sum_{i=1}^N c_i^{n,k} exp (i (k + G_i^{n,k}) cdot r)
where psi_n^k is the wavefunction for the nth band at k-point k, N is the number of plane waves, c_i^{n,k} is the ith coefficient that corresponds to the nth band and k-point k, and G_i^{n,k} is the ith G-point corresponding to k-point k.
NOTE: This function is very slow; a discrete fourier transform is the preferred method of evaluation (see Wavecar.fft_mesh).
- Parameters:
kpoint (int) – the index of the kpoint where the wavefunction will be evaluated.
band (int) – the index of the band where the wavefunction will be evaluated.
r (np.array) – the position where the wavefunction will be evaluated.
spin (int) – spin index for the desired wavefunction (only for ISPIN = 2, default = 0).
spinor (int) – component of the spinor that is evaluated (only used if vasp_type == ‘ncl’).
- Returns:
A complex value corresponding to the evaluation of the wavefunction.
- fft_mesh(kpoint: int, band: int, spin: int = 0, spinor: int = 0, shift: bool = True) ndarray[source]
Place the coefficients of a wavefunction onto an fft mesh.
Once the mesh has been obtained, a discrete fourier transform can be used to obtain real-space evaluation of the wavefunction. The output of this function can be passed directly to numpy’s fft function. For .. rubric:: Example
mesh = Wavecar(‘WAVECAR’).fft_mesh(kpoint, band) evals = np.fft.ifftn(mesh)
- Parameters:
kpoint (int) – the index of the kpoint where the wavefunction will be evaluated
band (int) – the index of the band where the wavefunction will be evaluated
spin (int) – the spin of the wavefunction for the desired wavefunction (only for ISPIN = 2, default = 0)
spinor (int) – component of the spinor that is evaluated (only used if vasp_type == ‘ncl’)
shift (bool) – determines if the zero frequency coefficient is placed at index (0, 0, 0) or centered
- Returns:
a numpy ndarray representing the 3D mesh of coefficients
- get_parchg(poscar: Poscar, kpoint: int, band: int, spin: int | None = None, spinor: int | None = None, phase: bool = False, scale: int = 2) Chgcar[source]
Generate a Chgcar object, which is the charge density of the specified wavefunction.
This function generates a Chgcar object with the charge density of the wavefunction specified by band and kpoint (and spin, if the WAVECAR corresponds to a spin-polarized calculation). The phase tag is a feature that is not present in VASP. For a real wavefunction, the phase tag being turned on means that the charge density is multiplied by the sign of the wavefunction at that point in space. A warning is generated if the phase tag is on and the chosen kpoint is not Gamma.
Note: Augmentation from the PAWs is NOT included in this function. The maximal charge density will differ from the PARCHG from VASP, but the qualitative shape of the charge density will match.
- Parameters:
poscar (pymatgen.io.vasp.inputs.Poscar) – Poscar object that has the structure associated with the WAVECAR file
kpoint (int) – the index of the kpoint for the wavefunction
band (int) – the index of the band for the wavefunction
spin (int) – optional argument to specify the spin. If the Wavecar has ISPIN = 2, spin is None generates a Chgcar with total spin and magnetization, and spin == {0, 1} specifies just the spin up or down component.
spinor (int) – optional argument to specify the spinor component for noncollinear data wavefunctions (allowed values of None, 0, or 1)
phase (bool) – flag to determine if the charge density is multiplied by the sign of the wavefunction. Only valid for real wavefunctions.
scale (int) – scaling for the FFT grid. The default value of 2 is at least as fine as the VASP default.
- Returns:
A Chgcar object.
- write_unks(directory: PathLike) None[source]
Write the UNK files to the given directory.
Write the cell-periodic part of the Bloch wavefunctions from the WAVECAR file to each of the UNK files. There will be one UNK file for each of the kpoints in the WAVECAR file.
Note
Wannier90 expects the full kpoint grid instead of the symmetry- reduced one that VASP stores the wavefunctions on. You should run a nscf calculation with ISYM=0 to obtain the correct grid.
- Parameters:
directory (PathLike) – directory to write the UNK files.
- class Waveder(cder_real: ndarray, cder_imag: ndarray)[source]
Bases:
MSONableRepresentation of the WAVEDER file.
The LOPTICS tag produces a WAVEDER file which contains the derivative of the orbitals with respect to k. Since the data is complex, we need to split it into the real and imaginary parts for JSON serialization.
Note
The way that VASP writes the WAVEDER and WAVEDERF has slightly different logic when indexing the bands. This results in the formatted WAVDERF only indexing between filled bands. (i.e. all the matrix elements are between the states i=1:8 and j=1:8 in a two atom Si calculation, which is likely a VASP bug). As such, it is recommended to used the hidden
LVEL=.True.flag in VASP which will force indexing over all bands.- The order of the indices of the data are:
- [
band index1, band index2, kpoint index, spin index, cartesian direction,
]
- cder_real[source]
Real part of the derivative of the orbitals with respect to k.
- Type:
numpy.ndarray
- cder_imag[source]
Imaginary part of the derivative of the orbitals with respect to k.
- Type:
numpy.ndarray
Author: Miguel Dias Costa, Kamal Choudhary, Jimmy-Xuan Shen
- classmethod from_binary(filename: PathLike, data_type: Literal['complex64', 'float64', 'float32'] = 'complex64') Self[source]
Read the WAVEDER file.
- Parameters:
filename – Name of file containing WAVEDER.
data_type – Data type of the WAVEDER file. Default is complex64. If the file was generated with the “gamma” version of VASP, the data type can be either “float64” or “float32”.
- Returns:
Waveder object.
- classmethod from_formatted(filename: PathLike) Self[source]
Read the WAVEDERF file.
Note: This file is only produced when LOPTICS is true and VASP has been recompiled after uncommenting the line that calls WRT_CDER_BETWEEN_STATES_FORMATTED in linear_optics.F.
It is recommended to use from_binary instead since the binary file is much smaller and contains the same information.
- Parameters:
filename (PathLike) – The name of the WAVEDER file.
- Returns:
A Waveder object.
- get_orbital_derivative_between_states(band_i: int, band_j: int, kpoint: int, spin: Literal[0, 1], cart_dir: Literal[0, 1, 2]) float[source]
Get a float between bands band_i and band_j for k-point index, spin-channel and Cartesian direction.
- Parameters:
band_i (int) – Index of band i
band_j (int) – Index of band j
kpoint (int) – Index of k-point
spin (int) – Spin-channel (0 or 1)
cart_dir (int) – Index of Cartesian direction (0, 1, 2)
- Returns:
a float value
- class Xdatcar(filename: PathLike, ionicstep_start: int = 1, ionicstep_end: int | None = None, comment: str | None = None)[source]
Bases:
objectXDATCAR parser. Only tested with VASP 5.x files.
Authors: Ram Balachandran
Init a Xdatcar.
- Parameters:
filename (PathLike) – The XDATCAR file.
ionicstep_start (int) – Starting number of ionic step.
ionicstep_end (int) – Ending number of ionic step.
comment (str) – Optional comment attached to this set of structures.
- concatenate(filename: PathLike, ionicstep_start: int = 1, ionicstep_end: int | None = None) None[source]
Concatenate structures in file to Xdatcar.
- Parameters:
filename (PathLike) – The XDATCAR file to be concatenated.
ionicstep_start (int) – Starting number of ionic step.
ionicstep_end (int) – Ending number of ionic step.
- TODO (rambalachandran): Check to ensure the new concatenating file
has the same lattice structure and atoms as the Xdatcar class.
- get_str(ionicstep_start: int = 1, ionicstep_end: int | None = None, significant_figures: int = 8) str[source]
Write Xdatcar to a string.
- Parameters:
ionicstep_start (int) – Starting number of ionic step.
ionicstep_end (int) – Ending number of ionic step.
significant_figures (int) – Number of significant digits.
- property natoms: list[int][source]
Sequence of number of sites of each type associated with the Poscar. Similar to 7th line in VASP 5+ Xdatcar.
- get_adjusted_fermi_level(efermi: float, cbm: float, band_structure: BandStructureSymmLine, energy_step: float = 0.01) float[source]
When running a band structure computation, the Fermi level needs to be taken from the static run that gave the charge density used for the non-self consistent band structure run. Sometimes this Fermi level is too low because of the mismatch between the uniform grid used in the static run and the band structure k-points (e.g., the VBM is on Gamma and the Gamma point is not in the uniform mesh).
Here we use a procedure looking for energy levels higher than the static Fermi level and lower than the LUMO. If any of these levels make the band structure appears insulating (not metallic anymore), we keep this adjusted fermi level.
This procedure has shown to detect most insulators correctly.
- Parameters:
efermi (float) – The Fermi energy of the static run.
cbm (float) – The conduction band minimum of the static run.
band_structure (BandStructureSymmLine) – A band structure object.
energy_step (float) – The step length for increasing energy during search.
- Returns:
A new adjusted Fermi level.
- Return type:
float
- get_band_structure_from_vasp_multiple_branches(dir_name: str, efermi: float | None = None, projections: bool = False) BandStructureSymmLine | BandStructure | None[source]
Get band structure info from a VASP directory.
It takes into account that a run can be divided in several branches named “branch_x”. If the run has not been divided in branches the method will turn to parsing vasprun.xml directly.
- Parameters:
dir_name – Directory containing all bandstructure runs.
efermi – Efermi for bandstructure.
projections – True if you want to get the data on site projections if any. Note that this is sometimes very large
- Returns:
A BandStructure Object. None is there’s a parsing error.
pymatgen.io.vasp.sets module
This module defines the VaspInputSet abstract base class and a concrete implementation for the parameters developed and tested by the core team of pymatgen, including the Materials Virtual Lab, Materials Project and the MIT high throughput project. The basic concept behind an input set is to specify a scheme to generate a consistent set of VASP inputs from a structure without further user intervention. This ensures comparability across runs.
Read the following carefully before implementing new input sets:
99% of what needs to be done can be done by specifying user_incar_settings to override some of the defaults of various input sets. Unless there is an extremely good reason to add a new set, do not add one. e.g. if you want to turn the Hubbard U off, just set “LDAU”: False as a user_incar_setting.
All derivative input sets should inherit appropriate configurations (e.g., from MPRelaxSet), and more often than not, VaspInputSet should be the superclass. Superclass delegation should be used where possible. In particular, you are not supposed to implement your own as_dict or from_dict for derivative sets unless you know what you are doing. Improper overriding the as_dict and from_dict protocols is the major cause of implementation headaches. If you need an example, look at how the MPStaticSet is initialized.
The above are recommendations. The following are UNBREAKABLE rules:
All input sets must take in a structure, list of structures or None as the first argument. If None, the input set should perform a stateless initialization and before any output can be written, a structure must be set.
user_incar_settings, user_kpoints_settings and user_<whatever>_settings are ABSOLUTE. Any new sets you implement must obey this. If a user wants to override your settings, you assume he knows what he is doing. Do not magically override user supplied settings. You can issue a warning if you think the user is wrong.
All input sets must save all supplied args and kwargs as instance variables. e.g. self.arg = arg and self.kwargs = kwargs in the __init__. This ensures the as_dict and from_dict work correctly.
- exception BadInputSetWarning[source]
Bases:
UserWarningWarning class for bad but legal VASP inputs.
- class DictSet(*args, **kwargs)[source]
Bases:
VaspInputSetAlias for VaspInputSet.
- class LobsterSet(structure: Structure | None = <property object>, config_dict: dict = <factory>, files_to_transfer: dict = <factory>, user_incar_settings: dict = <factory>, user_kpoints_settings: dict = <factory>, user_potcar_settings: dict = <factory>, constrain_total_magmom: bool = False, sort_structure: bool = True, user_potcar_functional: UserPotcarFunctional = 'PBE_54', force_gamma: bool = False, reduce_structure: Literal['niggli', 'LLL'] | None = None, vdw: str | None = None, use_structure_charge: bool = False, standardize: bool = False, sym_prec: float = 0.1, international_monoclinic: bool = True, validate_magmom: bool = True, inherit_incar: bool | list[str] = False, auto_kspacing: bool = False, auto_ismear: bool = False, auto_ispin: bool = False, auto_lreal: bool = False, auto_metal_kpoints: bool = False, bandgap_tol: float = 0.0001, bandgap: float | None = None, prev_incar: str | dict | None = None, prev_kpoints: str | Kpoints | None = None, _valid_potcars: Sequence[str] | None = ('PBE_52', 'PBE_54'), isym: int = 0, ismear: int = -5, reciprocal_density: int | None = None, address_basis_file: str | None = None, user_supplied_basis: dict | None = None)[source]
Bases:
VaspInputSetInput set to prepare VASP runs that can be digested by Lobster (See cohp.de).
- Parameters:
structure (Structure) – input structure.
isym (int) – ISYM entry for INCAR, only isym=-1 and isym=0 are allowed
ismear (int) – ISMEAR entry for INCAR, only ismear=-5 and ismear=0 are allowed
reciprocal_density (int) – density of k-mesh by reciprocal volume
user_supplied_basis (dict) – dict including basis functions for all elements in structure, e.g. {“Fe”: “3d 3p 4s”, “O”: “2s 2p”}; if not supplied, a standard basis is used
address_basis_file (str) – address to a file similar to “BASIS_PBE_54_standard.yaml” in pymatgen.io.lobster.lobster_basis
user_potcar_settings (dict) – dict including potcar settings for all elements in structure, e.g. {“Fe”: “Fe_pv”, “O”: “O”}; if not supplied, a standard basis is used.
**kwargs – Other kwargs supported by VaspInputSet.
- CONFIG = {'INCAR': {'ALGO': 'FAST', 'EDIFF_PER_ATOM': 5e-05, 'ENCUT': 520, 'IBRION': 2, 'ISIF': 3, 'ISMEAR': -5, 'ISPIN': 2, 'LASPH': True, 'LDAU': True, 'LDAUJ': {'F': {'Co': 0, 'Cr': 0, 'Fe': 0, 'Mn': 0, 'Mo': 0, 'Ni': 0, 'V': 0, 'W': 0}, 'O': {'Co': 0, 'Cr': 0, 'Fe': 0, 'Mn': 0, 'Mo': 0, 'Ni': 0, 'V': 0, 'W': 0}}, 'LDAUL': {'F': {'Co': 2, 'Cr': 2, 'Fe': 2, 'Mn': 2, 'Mo': 2, 'Ni': 2, 'V': 2, 'W': 2}, 'O': {'Co': 2, 'Cr': 2, 'Fe': 2, 'Mn': 2, 'Mo': 2, 'Ni': 2, 'V': 2, 'W': 2}}, 'LDAUPRINT': 1, 'LDAUTYPE': 2, 'LDAUU': {'F': {'Co': 3.32, 'Cr': 3.7, 'Fe': 5.3, 'Mn': 3.9, 'Mo': 4.38, 'Ni': 6.2, 'V': 3.25, 'W': 6.2}, 'O': {'Co': 3.32, 'Cr': 3.7, 'Fe': 5.3, 'Mn': 3.9, 'Mo': 4.38, 'Ni': 6.2, 'V': 3.25, 'W': 6.2}}, 'LORBIT': 11, 'LREAL': 'AUTO', 'LWAVE': False, 'MAGMOM': {'Ce': 5, 'Ce3+': 1, 'Co': 0.6, 'Co3+': 0.6, 'Co4+': 1, 'Cr': 5, 'Dy3+': 5, 'Er3+': 3, 'Eu': 10, 'Eu2+': 7, 'Eu3+': 6, 'Fe': 5, 'Gd3+': 7, 'Ho3+': 4, 'La3+': 0.6, 'Lu3+': 0.6, 'Mn': 5, 'Mn3+': 4, 'Mn4+': 3, 'Mo': 5, 'Nd3+': 3, 'Ni': 5, 'Pm3+': 4, 'Pr3+': 2, 'Sm3+': 5, 'Tb3+': 6, 'Tm3+': 2, 'V': 5, 'W': 5, 'Yb3+': 1}, 'NELM': 100, 'NSW': 99, 'PREC': 'Accurate', 'SIGMA': 0.05}, 'KPOINTS': {'reciprocal_density': 64}, 'PARENT': 'VASPIncarBase', 'POTCAR': {'Ac': 'Ac', 'Ag': 'Ag', 'Al': 'Al', 'Ar': 'Ar', 'As': 'As', 'Au': 'Au', 'B': 'B', 'Ba': 'Ba_sv', 'Be': 'Be_sv', 'Bi': 'Bi', 'Br': 'Br', 'C': 'C', 'Ca': 'Ca_sv', 'Cd': 'Cd', 'Ce': 'Ce', 'Cl': 'Cl', 'Co': 'Co', 'Cr': 'Cr_pv', 'Cs': 'Cs_sv', 'Cu': 'Cu_pv', 'Dy': 'Dy_3', 'Er': 'Er_3', 'Eu': 'Eu', 'F': 'F', 'Fe': 'Fe_pv', 'Ga': 'Ga_d', 'Gd': 'Gd', 'Ge': 'Ge_d', 'H': 'H', 'He': 'He', 'Hf': 'Hf_pv', 'Hg': 'Hg', 'Ho': 'Ho_3', 'I': 'I', 'In': 'In_d', 'Ir': 'Ir', 'K': 'K_sv', 'Kr': 'Kr', 'La': 'La', 'Li': 'Li_sv', 'Lu': 'Lu_3', 'Mg': 'Mg_pv', 'Mn': 'Mn_pv', 'Mo': 'Mo_pv', 'N': 'N', 'Na': 'Na_pv', 'Nb': 'Nb_pv', 'Nd': 'Nd_3', 'Ne': 'Ne', 'Ni': 'Ni_pv', 'Np': 'Np', 'O': 'O', 'Os': 'Os_pv', 'P': 'P', 'Pa': 'Pa', 'Pb': 'Pb_d', 'Pd': 'Pd', 'Pm': 'Pm_3', 'Pr': 'Pr_3', 'Pt': 'Pt', 'Pu': 'Pu', 'Rb': 'Rb_sv', 'Re': 'Re_pv', 'Rh': 'Rh_pv', 'Ru': 'Ru_pv', 'S': 'S', 'Sb': 'Sb', 'Sc': 'Sc_sv', 'Se': 'Se', 'Si': 'Si', 'Sm': 'Sm_3', 'Sn': 'Sn_d', 'Sr': 'Sr_sv', 'Ta': 'Ta_pv', 'Tb': 'Tb_3', 'Tc': 'Tc_pv', 'Te': 'Te', 'Th': 'Th', 'Ti': 'Ti_pv', 'Tl': 'Tl_d', 'Tm': 'Tm_3', 'U': 'U', 'V': 'V_pv', 'W': 'W_pv', 'Xe': 'Xe', 'Y': 'Y_sv', 'Yb': 'Yb_2', 'Zn': 'Zn', 'Zr': 'Zr_sv'}, 'POTCAR_FUNCTIONAL': 'PBE'}[source]
- property incar_updates: dict[str, Any][source]
Updates to the INCAR config for this calculation type.
- class MITMDSet(structure: Structure | None = None, config_dict: dict = <factory>, files_to_transfer: dict = <factory>, user_incar_settings: dict = <factory>, user_kpoints_settings: dict = <factory>, user_potcar_settings: dict = <factory>, constrain_total_magmom: bool = False, sort_structure: bool = True, user_potcar_functional: UserPotcarFunctional = None, force_gamma: bool = False, reduce_structure: Literal['niggli', 'LLL'] | None = None, vdw: str | None = None, use_structure_charge: bool = False, standardize: bool = False, sym_prec: float = 0.1, international_monoclinic: bool = True, validate_magmom: bool = True, inherit_incar: bool | list[str] = False, auto_kspacing: bool = False, auto_ismear: bool = False, auto_ispin: bool = False, auto_lreal: bool = False, auto_metal_kpoints: bool = False, bandgap_tol: float = 0.0001, bandgap: float | None = None, prev_incar: str | dict | None = None, prev_kpoints: str | Kpoints | None = None, _valid_potcars: Sequence[str] | None = None, start_temp: float = 0.0, end_temp: float = 300.0, nsteps: int = 1000, time_step: float = 2, spin_polarized: bool = False)[source]
Bases:
VaspInputSetWrite a VASP MD run. This DOES NOT do multiple stage runs.
- Parameters:
structure (Structure) – Input structure.
start_temp (float) – Starting temperature.
end_temp (float) – Final temperature.
nsteps (int) – Number of time steps for simulations. NSW parameter.
time_step (float) – The time step for the simulation. The POTIM parameter. Defaults to 2fs.
spin_polarized (bool) – Whether to do spin polarized calculations. The ISPIN parameter. Defaults to False.
**kwargs – Other kwargs supported by VaspInputSet.
- CONFIG = {'INCAR': {'ALGO': 'FAST', 'EDIFF': 1e-05, 'ENCUT': 520, 'IBRION': 2, 'ICHARG': 1, 'ISIF': 3, 'ISMEAR': -5, 'ISPIN': 2, 'ISYM': 0, 'LDAU': True, 'LDAUJ': {'F': {'Ag': 0, 'Co': 0, 'Cr': 0, 'Cu': 0, 'Fe': 0, 'Mn': 0, 'Mo': 0, 'Nb': 0, 'Ni': 0, 'Re': 0, 'Ta': 0, 'V': 0, 'W': 0}, 'O': {'Ag': 0, 'Co': 0, 'Cr': 0, 'Cu': 0, 'Fe': 0, 'Mn': 0, 'Mo': 0, 'Nb': 0, 'Ni': 0, 'Re': 0, 'Ta': 0, 'V': 0, 'W': 0}, 'S': {'Fe': 0, 'Mn': 0}}, 'LDAUL': {'F': {'Ag': 2, 'Co': 2, 'Cr': 2, 'Cu': 2, 'Fe': 2, 'Mn': 2, 'Mo': 2, 'Nb': 2, 'Ni': 2, 'Re': 2, 'Ta': 2, 'V': 2, 'W': 2}, 'O': {'Ag': 2, 'Co': 2, 'Cr': 2, 'Cu': 2, 'Fe': 2, 'Mn': 2, 'Mo': 2, 'Nb': 2, 'Ni': 2, 'Re': 2, 'Ta': 2, 'V': 2, 'W': 2}, 'S': {'Fe': 2, 'Mn': 2.5}}, 'LDAUPRINT': 1, 'LDAUTYPE': 2, 'LDAUU': {'F': {'Ag': 1.5, 'Co': 3.4, 'Cr': 3.5, 'Cu': 4, 'Fe': 4.0, 'Mn': 3.9, 'Mo': 4.38, 'Nb': 1.5, 'Ni': 6, 'Re': 2, 'Ta': 2, 'V': 3.1, 'W': 4.0}, 'O': {'Ag': 1.5, 'Co': 3.4, 'Cr': 3.5, 'Cu': 4, 'Fe': 4.0, 'Mn': 3.9, 'Mo': 4.38, 'Nb': 1.5, 'Ni': 6, 'Re': 2, 'Ta': 2, 'V': 3.1, 'W': 4.0}, 'S': {'Fe': 1.9, 'Mn': 2.5}}, 'LORBIT': '11', 'LREAL': 'AUTO', 'LWAVE': False, 'MAGMOM': {'Ce': 5, 'Ce3+': 1, 'Co': 0.6, 'Co3+': 0.6, 'Co4+': 1, 'Cr': 5, 'Dy3+': 5, 'Er3+': 3, 'Eu': 10, 'Eu2+': 7, 'Eu3+': 6, 'Fe': 5, 'Gd3+': 7, 'Ho3+': 4, 'La3+': 0.6, 'Lu3+': 0.6, 'Mn': 5, 'Mn3+': 4, 'Mn4+': 3, 'Mo': 5, 'Nd3+': 3, 'Ni': 5, 'Pm3+': 4, 'Pr3+': 2, 'Sm3+': 5, 'Tb3+': 6, 'Tm3+': 2, 'V': 5, 'W': 5, 'Yb3+': 1}, 'NELM': 200, 'NELMIN': 6, 'NSW': 99, 'PREC': 'Accurate', 'SIGMA': 0.05}, 'KPOINTS': {'length': 25}, 'PARENT': 'VASPIncarBase', 'POTCAR': {'Ac': {'hash': 'd6854224d20e3de6e6fd7399503791d1', 'symbol': 'Ac'}, 'Ag': {'hash': 'e8ffa02fe3f3a51338ac1ac91ae968b9', 'symbol': 'Ag'}, 'Al': {'hash': 'a6fd9a46aec185f4ad2acd0cbe4ae2fa', 'symbol': 'Al'}, 'Ar': {'hash': 'e782fc6292623b396091bf8b871c272f', 'symbol': 'Ar'}, 'As': {'hash': '8005364db225a254e52cba350bedd032', 'symbol': 'As'}, 'Au': {'hash': 'a9182d436a13194b744640ac940ab9b0', 'symbol': 'Au'}, 'B': {'hash': '18ed2875dfa6305324cec3d7d59273ae', 'symbol': 'B'}, 'Ba': {'hash': 'c0477913afb63dfae3439f3534fbf0ed', 'symbol': 'Ba_sv'}, 'Be': {'hash': 'fb974e44d56a8c62c6bbd1a1eb70c3a7', 'symbol': 'Be'}, 'Bi': {'hash': 'e29661c79d59abae3b3ba69eae24b1a5', 'symbol': 'Bi'}, 'Br': {'hash': '40f9594b4506684a69158c8975cfb9d6', 'symbol': 'Br'}, 'C': {'hash': 'c0a8167dbb174fe492a3db7f5006c0f8', 'symbol': 'C'}, 'Ca': {'hash': 'eb006721e214c04b3c13146e81b3a27d', 'symbol': 'Ca_sv'}, 'Cd': {'hash': '0506b2d0ac28d5fe2b5ced77a701aa86', 'symbol': 'Cd'}, 'Ce': {'hash': 'ff3a09f2ff91798e58eb4b9854e9be4a', 'symbol': 'Ce'}, 'Cl': {'hash': '779b9901046c78fe51c5d80224642aeb', 'symbol': 'Cl'}, 'Co': {'hash': 'b169bca4e137294d2ab3df8cbdd09083', 'symbol': 'Co'}, 'Cr': {'hash': '82c14307937c7509fda4e9bc023d243d', 'symbol': 'Cr'}, 'Cs': {'hash': '096b53a7d80cc0086976bcda50d536e5', 'symbol': 'Cs_sv'}, 'Cu': {'hash': '8ca4e43a30de0c397e51f16bbb20d678', 'symbol': 'Cu'}, 'Dy': {'hash': 'd4a05220ab0a2d4c03a76872ea724a1e', 'symbol': 'Dy_3'}, 'Er': {'hash': 'daa65a04877317f8c3c593ddeaa8a132', 'symbol': 'Er_3'}, 'Eu': {'hash': 'd466d046adf21f6146ee9644049ea268', 'symbol': 'Eu'}, 'F': {'hash': '180141c33d032bfbfff30b3bea9d23dd', 'symbol': 'F'}, 'Fe': {'hash': '9530da8244e4dac17580869b4adab115', 'symbol': 'Fe'}, 'Ga': {'hash': '6e0b9d58412b1bfcd7252aff13d476c2', 'symbol': 'Ga'}, 'Gd': {'hash': '1f0d42b1e5f6769d319d3f247992aeb9', 'symbol': 'Gd'}, 'Ge': {'hash': '79e788788c31e196a460553010512d3f', 'symbol': 'Ge'}, 'H': {'hash': 'bb43c666e3d36577264afe07669e9582', 'symbol': 'H'}, 'He': {'hash': '47f9434aa3db96c85d7c4b3e4c2df09b', 'symbol': 'He'}, 'Hf': {'hash': 'b113f150cbf9c736f8244a6c25b0482e', 'symbol': 'Hf'}, 'Hg': {'hash': 'c2f15dfb5fd53396c5427635e5019160', 'symbol': 'Hg'}, 'Ho': {'hash': '661891464a27e87cf7e1324dd1893b77', 'symbol': 'Ho_3'}, 'I': {'hash': 'f4ff16a495dd361ff5824ee61b418bb0', 'symbol': 'I'}, 'In': {'hash': '7df38c0cdb4e6d9a9b93f09d690bb3ae', 'symbol': 'In'}, 'Ir': {'hash': 'dbcf7dcc6f4fb40df7b3d26904f60a66', 'symbol': 'Ir'}, 'K': {'hash': '3e84f86d37f203a4fb01de36af57e430', 'symbol': 'K_sv'}, 'Kr': {'hash': '39b9b85ae3982e6c012fb549b2840ce5', 'symbol': 'Kr'}, 'La': {'hash': '9b3ce03d18f7c0b40471a817ff91b287', 'symbol': 'La'}, 'Li': {'hash': '65e83282d1707ec078c1012afbd05be8', 'symbol': 'Li'}, 'Lu': {'hash': 'd40a90babf1224b88ffb4c3273ac3848', 'symbol': 'Lu_3'}, 'Mg': {'hash': '1771eb72adbbfa6310d66e7517e49930', 'symbol': 'Mg'}, 'Mn': {'hash': 'd082dba29b57ab59b3165e605dbf71b8', 'symbol': 'Mn'}, 'Mo': {'hash': '84e18fd84a98e3d7fa8f055952410df0', 'symbol': 'Mo_pv'}, 'N': {'hash': 'b98fd027ddebc67da4063ff2cabbc04b', 'symbol': 'N'}, 'Na': {'hash': '1a89e79f7e21d99e8cf5788979f6a987', 'symbol': 'Na'}, 'Nb': {'hash': '7bcee99a4dc3094be0f9fd7961c02966', 'symbol': 'Nb_pv'}, 'Nd': {'hash': '0c64e63070cee837c967283fffa001df', 'symbol': 'Nd'}, 'Ne': {'hash': '52064eee378b9e37a295a674f1c278f0', 'symbol': 'Ne'}, 'Ni': {'hash': '653f5772e68b2c7fd87ffd1086c0d710', 'symbol': 'Ni'}, 'Np': {'hash': '20cb30b714200c4db870550b288ac4cd', 'symbol': 'Np'}, 'O': {'hash': '7a25bc5b9a5393f46600a4939d357982', 'symbol': 'O'}, 'Os': {'hash': '35c2cb48d48a9c38c40fb82bbe70626d', 'symbol': 'Os'}, 'P': {'hash': '7dc3393307131ae67785a0cdacb61d5f', 'symbol': 'P'}, 'Pa': {'hash': 'a1fdb1089d0727f415416ec8082246ba', 'symbol': 'Pa'}, 'Pb': {'hash': '704c2c967247d7f84090d2536c91877d', 'symbol': 'Pb'}, 'Pd': {'hash': 'a395eb3aaf2fcab12fac3030a1146f61', 'symbol': 'Pd'}, 'Pm': {'hash': 'a2c9485ea86b2a7cf175077e6e5c7b3e', 'symbol': 'Pm'}, 'Pr': {'hash': '92f191499bf5346ea652bb806350ad87', 'symbol': 'Pr'}, 'Pt': {'hash': 'a604ea3c6a9cc23c739b762f625cf449', 'symbol': 'Pt'}, 'Pu': {'hash': 'f1d01e845dccc52d448679911f301a73', 'symbol': 'Pu'}, 'Rb': {'hash': 'e447c648d870b066b3514e6b800727ab', 'symbol': 'Rb_pv'}, 'Re': {'hash': '72385e193c92a8acfe17ea49004c2be1', 'symbol': 'Re'}, 'Rh': {'hash': '2c3dba3fcc6058ca1b1cfa75e45084bc', 'symbol': 'Rh'}, 'Ru': {'hash': '7925f4d4b68076d70af7cd86eef9ba8d', 'symbol': 'Ru_pv'}, 'S': {'hash': 'd368db6899d8839859bbee4811a42a88', 'symbol': 'S'}, 'Sb': {'hash': 'd82c022b02fc5344e85bd1909f9ee3e7', 'symbol': 'Sb'}, 'Sc': {'hash': 'dc386f505ad0c43385a7715b4111cb75', 'symbol': 'Sc_sv'}, 'Se': {'hash': '67a8804ede9f1112726e3d136978ef19', 'symbol': 'Se'}, 'Si': {'hash': 'b2b0ea6feb62e7cde209616683b8f7f5', 'symbol': 'Si'}, 'Sm': {'hash': 'e5e274e7cd99602ca81d146155abdf88', 'symbol': 'Sm_3'}, 'Sn': {'hash': '849b0795e148f93113a06be8fd5f5001', 'symbol': 'Sn_d'}, 'Sr': {'hash': 'ca6a5429c120a0ab705824386a76fe5b', 'symbol': 'Sr_sv'}, 'Ta': {'hash': 'd4e2cfe9338ef80da592d5bb9dc782c7', 'symbol': 'Ta'}, 'Tb': {'hash': '0790955c547003956c0fd4f080f7f508', 'symbol': 'Tb_3'}, 'Tc': {'hash': '9592642886319309a39d55c5717c6f48', 'symbol': 'Tc'}, 'Te': {'hash': '72719856e22fb1d3032df6f96d98a0f2', 'symbol': 'Te'}, 'Th': {'hash': 'aea79f322180fa6f0bfa74cb2a156dcf', 'symbol': 'Th'}, 'Ti': {'hash': 'c617e8b539c3f44a0ab6e8da2a92d318', 'symbol': 'Ti'}, 'Tl': {'hash': '2aa0d5406aaab7ebfbc761da382f1352', 'symbol': 'Tl'}, 'Tm': {'hash': '94a07cb7949b01305cb161da0cbfb492', 'symbol': 'Tm_3'}, 'U': {'hash': '72702eabbb1bc02b4167590dc848ed5d', 'symbol': 'U'}, 'V': {'hash': '7f1297a2e1d963e2a4d81b61f85e4ded', 'symbol': 'V_pv'}, 'W': {'hash': '2a33e0d5c700640535f60ac0a12177ab', 'symbol': 'W_pv'}, 'Xe': {'hash': '338472e581f58b41d37c002a5e22353b', 'symbol': 'Xe'}, 'Y': {'hash': '4ed187e77cd54f198bb88020278b143d', 'symbol': 'Y_sv'}, 'Yb': {'hash': '9f472bd422f640710f7d93e2d9ce89f4', 'symbol': 'Yb'}, 'Zn': {'hash': 'e35ee27f8483a63bb68dbc236a343af3', 'symbol': 'Zn'}, 'Zr': {'hash': 'd221d2c0bac4f8e81af2f5c42a314274', 'symbol': 'Zr'}}, 'POTCAR_FUNCTIONAL': 'PBE'}[source]
- property incar_updates: dict[str, Any][source]
Updates to the INCAR config for this calculation type.
- class MITNEBSet(structures: list[Structure], unset_encut: bool = False, **kwargs)[source]
Bases:
VaspInputSetWrite NEB inputs.
Note that EDIFF is not on a per atom basis for this input set.
- Parameters:
structures – List of Structure objects.
unset_encut (bool) – Whether to unset ENCUT.
**kwargs – Other kwargs supported by VaspInputSet.
- write_input(output_dir: PathLike, make_dir_if_not_present: bool = True, write_cif: bool = False, write_path_cif: bool = False, write_endpoint_inputs: bool = False) None[source]
NEB inputs has a special directory structure where inputs are in 00, 01, 02, ….
- Parameters:
output_dir (PathLike) – Directory to output the VASP input files
make_dir_if_not_present (bool) – Set to True if you want the directory (and the whole path) to be created if it is not present.
write_cif (bool) – If true, writes a CIF along with each POSCAR.
write_path_cif (bool) – If true, writes a CIF for each image.
write_endpoint_inputs (bool) – If true, writes input files for running endpoint calculations.
- class MITRelaxSet(structure: Structure | None = <property object>, config_dict: dict = <factory>, files_to_transfer: dict = <factory>, user_incar_settings: dict = <factory>, user_kpoints_settings: dict = <factory>, user_potcar_settings: dict = <factory>, constrain_total_magmom: bool = False, sort_structure: bool = True, user_potcar_functional: UserPotcarFunctional = None, force_gamma: bool = False, reduce_structure: Literal['niggli', 'LLL'] | None = None, vdw: str | None = None, use_structure_charge: bool = False, standardize: bool = False, sym_prec: float = 0.1, international_monoclinic: bool = True, validate_magmom: bool = True, inherit_incar: bool | list[str] = False, auto_kspacing: bool = False, auto_ismear: bool = False, auto_ispin: bool = False, auto_lreal: bool = False, auto_metal_kpoints: bool = False, bandgap_tol: float = 0.0001, bandgap: float | None = None, prev_incar: str | dict | None = None, prev_kpoints: str | Kpoints | None = None, _valid_potcars: Sequence[str] | None = None)[source]
Bases:
VaspInputSetStandard implementation of VaspInputSet utilizing parameters in the MIT High-throughput project. The parameters are chosen specifically for a high-throughput project, which means in general pseudopotentials with fewer electrons were chosen.
- Parameters:
structure (Structure) – The Structure to create inputs for. If None, the input set is initialized without a Structure but one must be set separately before the inputs are generated.
**kwargs – Keywords supported by VaspInputSet.
- Please refer:
A Jain, G. Hautier, C. Moore, S. P. Ong, C. Fischer, T. Mueller, K. A. Persson, G. Ceder. A high-throughput infrastructure for density functional theory calculations. Computational Materials Science, 2011, 50(8), 2295-2310. doi:10.1016/j.commatsci.2011.02.023
- CONFIG = {'INCAR': {'ALGO': 'FAST', 'EDIFF': 1e-05, 'ENCUT': 520, 'IBRION': 2, 'ICHARG': 1, 'ISIF': 3, 'ISMEAR': -5, 'ISPIN': 2, 'ISYM': 0, 'LDAU': True, 'LDAUJ': {'F': {'Ag': 0, 'Co': 0, 'Cr': 0, 'Cu': 0, 'Fe': 0, 'Mn': 0, 'Mo': 0, 'Nb': 0, 'Ni': 0, 'Re': 0, 'Ta': 0, 'V': 0, 'W': 0}, 'O': {'Ag': 0, 'Co': 0, 'Cr': 0, 'Cu': 0, 'Fe': 0, 'Mn': 0, 'Mo': 0, 'Nb': 0, 'Ni': 0, 'Re': 0, 'Ta': 0, 'V': 0, 'W': 0}, 'S': {'Fe': 0, 'Mn': 0}}, 'LDAUL': {'F': {'Ag': 2, 'Co': 2, 'Cr': 2, 'Cu': 2, 'Fe': 2, 'Mn': 2, 'Mo': 2, 'Nb': 2, 'Ni': 2, 'Re': 2, 'Ta': 2, 'V': 2, 'W': 2}, 'O': {'Ag': 2, 'Co': 2, 'Cr': 2, 'Cu': 2, 'Fe': 2, 'Mn': 2, 'Mo': 2, 'Nb': 2, 'Ni': 2, 'Re': 2, 'Ta': 2, 'V': 2, 'W': 2}, 'S': {'Fe': 2, 'Mn': 2.5}}, 'LDAUPRINT': 1, 'LDAUTYPE': 2, 'LDAUU': {'F': {'Ag': 1.5, 'Co': 3.4, 'Cr': 3.5, 'Cu': 4, 'Fe': 4.0, 'Mn': 3.9, 'Mo': 4.38, 'Nb': 1.5, 'Ni': 6, 'Re': 2, 'Ta': 2, 'V': 3.1, 'W': 4.0}, 'O': {'Ag': 1.5, 'Co': 3.4, 'Cr': 3.5, 'Cu': 4, 'Fe': 4.0, 'Mn': 3.9, 'Mo': 4.38, 'Nb': 1.5, 'Ni': 6, 'Re': 2, 'Ta': 2, 'V': 3.1, 'W': 4.0}, 'S': {'Fe': 1.9, 'Mn': 2.5}}, 'LORBIT': '11', 'LREAL': 'AUTO', 'LWAVE': False, 'MAGMOM': {'Ce': 5, 'Ce3+': 1, 'Co': 0.6, 'Co3+': 0.6, 'Co4+': 1, 'Cr': 5, 'Dy3+': 5, 'Er3+': 3, 'Eu': 10, 'Eu2+': 7, 'Eu3+': 6, 'Fe': 5, 'Gd3+': 7, 'Ho3+': 4, 'La3+': 0.6, 'Lu3+': 0.6, 'Mn': 5, 'Mn3+': 4, 'Mn4+': 3, 'Mo': 5, 'Nd3+': 3, 'Ni': 5, 'Pm3+': 4, 'Pr3+': 2, 'Sm3+': 5, 'Tb3+': 6, 'Tm3+': 2, 'V': 5, 'W': 5, 'Yb3+': 1}, 'NELM': 200, 'NELMIN': 6, 'NSW': 99, 'PREC': 'Accurate', 'SIGMA': 0.05}, 'KPOINTS': {'length': 25}, 'PARENT': 'VASPIncarBase', 'POTCAR': {'Ac': {'hash': 'd6854224d20e3de6e6fd7399503791d1', 'symbol': 'Ac'}, 'Ag': {'hash': 'e8ffa02fe3f3a51338ac1ac91ae968b9', 'symbol': 'Ag'}, 'Al': {'hash': 'a6fd9a46aec185f4ad2acd0cbe4ae2fa', 'symbol': 'Al'}, 'Ar': {'hash': 'e782fc6292623b396091bf8b871c272f', 'symbol': 'Ar'}, 'As': {'hash': '8005364db225a254e52cba350bedd032', 'symbol': 'As'}, 'Au': {'hash': 'a9182d436a13194b744640ac940ab9b0', 'symbol': 'Au'}, 'B': {'hash': '18ed2875dfa6305324cec3d7d59273ae', 'symbol': 'B'}, 'Ba': {'hash': 'c0477913afb63dfae3439f3534fbf0ed', 'symbol': 'Ba_sv'}, 'Be': {'hash': 'fb974e44d56a8c62c6bbd1a1eb70c3a7', 'symbol': 'Be'}, 'Bi': {'hash': 'e29661c79d59abae3b3ba69eae24b1a5', 'symbol': 'Bi'}, 'Br': {'hash': '40f9594b4506684a69158c8975cfb9d6', 'symbol': 'Br'}, 'C': {'hash': 'c0a8167dbb174fe492a3db7f5006c0f8', 'symbol': 'C'}, 'Ca': {'hash': 'eb006721e214c04b3c13146e81b3a27d', 'symbol': 'Ca_sv'}, 'Cd': {'hash': '0506b2d0ac28d5fe2b5ced77a701aa86', 'symbol': 'Cd'}, 'Ce': {'hash': 'ff3a09f2ff91798e58eb4b9854e9be4a', 'symbol': 'Ce'}, 'Cl': {'hash': '779b9901046c78fe51c5d80224642aeb', 'symbol': 'Cl'}, 'Co': {'hash': 'b169bca4e137294d2ab3df8cbdd09083', 'symbol': 'Co'}, 'Cr': {'hash': '82c14307937c7509fda4e9bc023d243d', 'symbol': 'Cr'}, 'Cs': {'hash': '096b53a7d80cc0086976bcda50d536e5', 'symbol': 'Cs_sv'}, 'Cu': {'hash': '8ca4e43a30de0c397e51f16bbb20d678', 'symbol': 'Cu'}, 'Dy': {'hash': 'd4a05220ab0a2d4c03a76872ea724a1e', 'symbol': 'Dy_3'}, 'Er': {'hash': 'daa65a04877317f8c3c593ddeaa8a132', 'symbol': 'Er_3'}, 'Eu': {'hash': 'd466d046adf21f6146ee9644049ea268', 'symbol': 'Eu'}, 'F': {'hash': '180141c33d032bfbfff30b3bea9d23dd', 'symbol': 'F'}, 'Fe': {'hash': '9530da8244e4dac17580869b4adab115', 'symbol': 'Fe'}, 'Ga': {'hash': '6e0b9d58412b1bfcd7252aff13d476c2', 'symbol': 'Ga'}, 'Gd': {'hash': '1f0d42b1e5f6769d319d3f247992aeb9', 'symbol': 'Gd'}, 'Ge': {'hash': '79e788788c31e196a460553010512d3f', 'symbol': 'Ge'}, 'H': {'hash': 'bb43c666e3d36577264afe07669e9582', 'symbol': 'H'}, 'He': {'hash': '47f9434aa3db96c85d7c4b3e4c2df09b', 'symbol': 'He'}, 'Hf': {'hash': 'b113f150cbf9c736f8244a6c25b0482e', 'symbol': 'Hf'}, 'Hg': {'hash': 'c2f15dfb5fd53396c5427635e5019160', 'symbol': 'Hg'}, 'Ho': {'hash': '661891464a27e87cf7e1324dd1893b77', 'symbol': 'Ho_3'}, 'I': {'hash': 'f4ff16a495dd361ff5824ee61b418bb0', 'symbol': 'I'}, 'In': {'hash': '7df38c0cdb4e6d9a9b93f09d690bb3ae', 'symbol': 'In'}, 'Ir': {'hash': 'dbcf7dcc6f4fb40df7b3d26904f60a66', 'symbol': 'Ir'}, 'K': {'hash': '3e84f86d37f203a4fb01de36af57e430', 'symbol': 'K_sv'}, 'Kr': {'hash': '39b9b85ae3982e6c012fb549b2840ce5', 'symbol': 'Kr'}, 'La': {'hash': '9b3ce03d18f7c0b40471a817ff91b287', 'symbol': 'La'}, 'Li': {'hash': '65e83282d1707ec078c1012afbd05be8', 'symbol': 'Li'}, 'Lu': {'hash': 'd40a90babf1224b88ffb4c3273ac3848', 'symbol': 'Lu_3'}, 'Mg': {'hash': '1771eb72adbbfa6310d66e7517e49930', 'symbol': 'Mg'}, 'Mn': {'hash': 'd082dba29b57ab59b3165e605dbf71b8', 'symbol': 'Mn'}, 'Mo': {'hash': '84e18fd84a98e3d7fa8f055952410df0', 'symbol': 'Mo_pv'}, 'N': {'hash': 'b98fd027ddebc67da4063ff2cabbc04b', 'symbol': 'N'}, 'Na': {'hash': '1a89e79f7e21d99e8cf5788979f6a987', 'symbol': 'Na'}, 'Nb': {'hash': '7bcee99a4dc3094be0f9fd7961c02966', 'symbol': 'Nb_pv'}, 'Nd': {'hash': '0c64e63070cee837c967283fffa001df', 'symbol': 'Nd'}, 'Ne': {'hash': '52064eee378b9e37a295a674f1c278f0', 'symbol': 'Ne'}, 'Ni': {'hash': '653f5772e68b2c7fd87ffd1086c0d710', 'symbol': 'Ni'}, 'Np': {'hash': '20cb30b714200c4db870550b288ac4cd', 'symbol': 'Np'}, 'O': {'hash': '7a25bc5b9a5393f46600a4939d357982', 'symbol': 'O'}, 'Os': {'hash': '35c2cb48d48a9c38c40fb82bbe70626d', 'symbol': 'Os'}, 'P': {'hash': '7dc3393307131ae67785a0cdacb61d5f', 'symbol': 'P'}, 'Pa': {'hash': 'a1fdb1089d0727f415416ec8082246ba', 'symbol': 'Pa'}, 'Pb': {'hash': '704c2c967247d7f84090d2536c91877d', 'symbol': 'Pb'}, 'Pd': {'hash': 'a395eb3aaf2fcab12fac3030a1146f61', 'symbol': 'Pd'}, 'Pm': {'hash': 'a2c9485ea86b2a7cf175077e6e5c7b3e', 'symbol': 'Pm'}, 'Pr': {'hash': '92f191499bf5346ea652bb806350ad87', 'symbol': 'Pr'}, 'Pt': {'hash': 'a604ea3c6a9cc23c739b762f625cf449', 'symbol': 'Pt'}, 'Pu': {'hash': 'f1d01e845dccc52d448679911f301a73', 'symbol': 'Pu'}, 'Rb': {'hash': 'e447c648d870b066b3514e6b800727ab', 'symbol': 'Rb_pv'}, 'Re': {'hash': '72385e193c92a8acfe17ea49004c2be1', 'symbol': 'Re'}, 'Rh': {'hash': '2c3dba3fcc6058ca1b1cfa75e45084bc', 'symbol': 'Rh'}, 'Ru': {'hash': '7925f4d4b68076d70af7cd86eef9ba8d', 'symbol': 'Ru_pv'}, 'S': {'hash': 'd368db6899d8839859bbee4811a42a88', 'symbol': 'S'}, 'Sb': {'hash': 'd82c022b02fc5344e85bd1909f9ee3e7', 'symbol': 'Sb'}, 'Sc': {'hash': 'dc386f505ad0c43385a7715b4111cb75', 'symbol': 'Sc_sv'}, 'Se': {'hash': '67a8804ede9f1112726e3d136978ef19', 'symbol': 'Se'}, 'Si': {'hash': 'b2b0ea6feb62e7cde209616683b8f7f5', 'symbol': 'Si'}, 'Sm': {'hash': 'e5e274e7cd99602ca81d146155abdf88', 'symbol': 'Sm_3'}, 'Sn': {'hash': '849b0795e148f93113a06be8fd5f5001', 'symbol': 'Sn_d'}, 'Sr': {'hash': 'ca6a5429c120a0ab705824386a76fe5b', 'symbol': 'Sr_sv'}, 'Ta': {'hash': 'd4e2cfe9338ef80da592d5bb9dc782c7', 'symbol': 'Ta'}, 'Tb': {'hash': '0790955c547003956c0fd4f080f7f508', 'symbol': 'Tb_3'}, 'Tc': {'hash': '9592642886319309a39d55c5717c6f48', 'symbol': 'Tc'}, 'Te': {'hash': '72719856e22fb1d3032df6f96d98a0f2', 'symbol': 'Te'}, 'Th': {'hash': 'aea79f322180fa6f0bfa74cb2a156dcf', 'symbol': 'Th'}, 'Ti': {'hash': 'c617e8b539c3f44a0ab6e8da2a92d318', 'symbol': 'Ti'}, 'Tl': {'hash': '2aa0d5406aaab7ebfbc761da382f1352', 'symbol': 'Tl'}, 'Tm': {'hash': '94a07cb7949b01305cb161da0cbfb492', 'symbol': 'Tm_3'}, 'U': {'hash': '72702eabbb1bc02b4167590dc848ed5d', 'symbol': 'U'}, 'V': {'hash': '7f1297a2e1d963e2a4d81b61f85e4ded', 'symbol': 'V_pv'}, 'W': {'hash': '2a33e0d5c700640535f60ac0a12177ab', 'symbol': 'W_pv'}, 'Xe': {'hash': '338472e581f58b41d37c002a5e22353b', 'symbol': 'Xe'}, 'Y': {'hash': '4ed187e77cd54f198bb88020278b143d', 'symbol': 'Y_sv'}, 'Yb': {'hash': '9f472bd422f640710f7d93e2d9ce89f4', 'symbol': 'Yb'}, 'Zn': {'hash': 'e35ee27f8483a63bb68dbc236a343af3', 'symbol': 'Zn'}, 'Zr': {'hash': 'd221d2c0bac4f8e81af2f5c42a314274', 'symbol': 'Zr'}}, 'POTCAR_FUNCTIONAL': 'PBE'}[source]
- class MPAbsorptionSet(structure: Structure | None = <property object>, config_dict: dict = <factory>, files_to_transfer: dict = <factory>, user_incar_settings: dict = <factory>, user_kpoints_settings: dict = <factory>, user_potcar_settings: dict = <factory>, constrain_total_magmom: bool = False, sort_structure: bool = True, user_potcar_functional: UserPotcarFunctional = None, force_gamma: bool = True, reduce_structure: Literal['niggli', 'LLL'] | None = None, vdw: str | None = None, use_structure_charge: bool = False, standardize: bool = False, sym_prec: float = 0.1, international_monoclinic: bool = True, validate_magmom: bool = True, inherit_incar: bool = True, auto_kspacing: bool = False, auto_ismear: bool = False, auto_ispin: bool = False, auto_lreal: bool = False, auto_metal_kpoints: bool = False, bandgap_tol: float = 0.0001, bandgap: float | None = None, prev_incar: str | dict | None = None, prev_kpoints: str | Kpoints | None = None, _valid_potcars: Sequence[str] | None = None, mode: str = 'IPA', copy_wavecar: bool = True, nbands_factor: float = 2, reciprocal_density: float = 400, nkred: Tuple3Ints | None = None, nedos: int = 2001, nbands: int | None = None)[source]
Bases:
VaspInputSetMP input set for generating frequency dependent dielectrics.
Two modes are supported: “IPA” or “RPA”. A typical sequence is mode=”STATIC” -> mode=”IPA” -> mode=”RPA”(optional) For all steps other than the first one (static), the recommendation is to use from_prev_calculation on the preceding run in the series. It is important to ensure Gamma centred kpoints for the RPA step.
- Parameters:
structure (Structure) – Input structure.
mode (str) – Supported modes are “IPA”, “RPA”
copy_wavecar (bool) – Whether to copy the WAVECAR from a previous run. Defaults to True.
nbands (int) – For subsequent calculations, it is generally recommended to perform NBANDS convergence starting from the NBANDS of the previous run for DIAG, and to use the exact same NBANDS for RPA. This parameter is used by from_previous_calculation to set nband.
nbands_factor (int) – Multiplicative factor for NBANDS when starting from a previous calculation. Only applies if mode==”IPA”. Need to be tested for convergence.
reciprocal_density – the k-points density
nkred – the reduced number of kpoints to calculate, equal to the k-mesh. Only applies in “RPA” mode because of the q->0 limit.
nedos – the density of DOS, default: 2001.
**kwargs – All kwargs supported by VaspInputSet. Typically, user_incar_settings is a commonly used option.
- CONFIG = {'INCAR': {'ALGO': 'FAST', 'EDIFF_PER_ATOM': 5e-05, 'ENCUT': 520, 'IBRION': 2, 'ISIF': 3, 'ISMEAR': -5, 'ISPIN': 2, 'LASPH': True, 'LDAU': True, 'LDAUJ': {'F': {'Co': 0, 'Cr': 0, 'Fe': 0, 'Mn': 0, 'Mo': 0, 'Ni': 0, 'V': 0, 'W': 0}, 'O': {'Co': 0, 'Cr': 0, 'Fe': 0, 'Mn': 0, 'Mo': 0, 'Ni': 0, 'V': 0, 'W': 0}}, 'LDAUL': {'F': {'Co': 2, 'Cr': 2, 'Fe': 2, 'Mn': 2, 'Mo': 2, 'Ni': 2, 'V': 2, 'W': 2}, 'O': {'Co': 2, 'Cr': 2, 'Fe': 2, 'Mn': 2, 'Mo': 2, 'Ni': 2, 'V': 2, 'W': 2}}, 'LDAUPRINT': 1, 'LDAUTYPE': 2, 'LDAUU': {'F': {'Co': 3.32, 'Cr': 3.7, 'Fe': 5.3, 'Mn': 3.9, 'Mo': 4.38, 'Ni': 6.2, 'V': 3.25, 'W': 6.2}, 'O': {'Co': 3.32, 'Cr': 3.7, 'Fe': 5.3, 'Mn': 3.9, 'Mo': 4.38, 'Ni': 6.2, 'V': 3.25, 'W': 6.2}}, 'LORBIT': 11, 'LREAL': 'AUTO', 'LWAVE': False, 'MAGMOM': {'Ce': 5, 'Ce3+': 1, 'Co': 0.6, 'Co3+': 0.6, 'Co4+': 1, 'Cr': 5, 'Dy3+': 5, 'Er3+': 3, 'Eu': 10, 'Eu2+': 7, 'Eu3+': 6, 'Fe': 5, 'Gd3+': 7, 'Ho3+': 4, 'La3+': 0.6, 'Lu3+': 0.6, 'Mn': 5, 'Mn3+': 4, 'Mn4+': 3, 'Mo': 5, 'Nd3+': 3, 'Ni': 5, 'Pm3+': 4, 'Pr3+': 2, 'Sm3+': 5, 'Tb3+': 6, 'Tm3+': 2, 'V': 5, 'W': 5, 'Yb3+': 1}, 'NELM': 100, 'NSW': 99, 'PREC': 'Accurate', 'SIGMA': 0.05}, 'KPOINTS': {'reciprocal_density': 64}, 'PARENT': 'VASPIncarBase', 'POTCAR': {'Ac': 'Ac', 'Ag': 'Ag', 'Al': 'Al', 'Ar': 'Ar', 'As': 'As', 'Au': 'Au', 'B': 'B', 'Ba': 'Ba_sv', 'Be': 'Be_sv', 'Bi': 'Bi', 'Br': 'Br', 'C': 'C', 'Ca': 'Ca_sv', 'Cd': 'Cd', 'Ce': 'Ce', 'Cl': 'Cl', 'Co': 'Co', 'Cr': 'Cr_pv', 'Cs': 'Cs_sv', 'Cu': 'Cu_pv', 'Dy': 'Dy_3', 'Er': 'Er_3', 'Eu': 'Eu', 'F': 'F', 'Fe': 'Fe_pv', 'Ga': 'Ga_d', 'Gd': 'Gd', 'Ge': 'Ge_d', 'H': 'H', 'He': 'He', 'Hf': 'Hf_pv', 'Hg': 'Hg', 'Ho': 'Ho_3', 'I': 'I', 'In': 'In_d', 'Ir': 'Ir', 'K': 'K_sv', 'Kr': 'Kr', 'La': 'La', 'Li': 'Li_sv', 'Lu': 'Lu_3', 'Mg': 'Mg_pv', 'Mn': 'Mn_pv', 'Mo': 'Mo_pv', 'N': 'N', 'Na': 'Na_pv', 'Nb': 'Nb_pv', 'Nd': 'Nd_3', 'Ne': 'Ne', 'Ni': 'Ni_pv', 'Np': 'Np', 'O': 'O', 'Os': 'Os_pv', 'P': 'P', 'Pa': 'Pa', 'Pb': 'Pb_d', 'Pd': 'Pd', 'Pm': 'Pm_3', 'Pr': 'Pr_3', 'Pt': 'Pt', 'Pu': 'Pu', 'Rb': 'Rb_sv', 'Re': 'Re_pv', 'Rh': 'Rh_pv', 'Ru': 'Ru_pv', 'S': 'S', 'Sb': 'Sb', 'Sc': 'Sc_sv', 'Se': 'Se', 'Si': 'Si', 'Sm': 'Sm_3', 'Sn': 'Sn_d', 'Sr': 'Sr_sv', 'Ta': 'Ta_pv', 'Tb': 'Tb_3', 'Tc': 'Tc_pv', 'Te': 'Te', 'Th': 'Th', 'Ti': 'Ti_pv', 'Tl': 'Tl_d', 'Tm': 'Tm_3', 'U': 'U', 'V': 'V_pv', 'W': 'W_pv', 'Xe': 'Xe', 'Y': 'Y_sv', 'Yb': 'Yb_2', 'Zn': 'Zn', 'Zr': 'Zr_sv'}, 'POTCAR_FUNCTIONAL': 'PBE'}[source]
- property incar_updates: dict[str, Any][source]
Updates to the INCAR config for this calculation type.
- class MPHSEBSSet(structure: Structure | None = <property object>, config_dict: dict = <factory>, files_to_transfer: dict = <factory>, user_incar_settings: dict = <factory>, user_kpoints_settings: dict = <factory>, user_potcar_settings: dict = <factory>, constrain_total_magmom: bool = False, sort_structure: bool = True, user_potcar_functional: UserPotcarFunctional = None, force_gamma: bool = False, reduce_structure: Literal['niggli', 'LLL'] | None = None, vdw: str | None = None, use_structure_charge: bool = False, standardize: bool = False, sym_prec: float = 0.1, international_monoclinic: bool = True, validate_magmom: bool = True, inherit_incar: bool | list[str] = False, auto_kspacing: bool = False, auto_ismear: bool = False, auto_ispin: bool = False, auto_lreal: bool = False, auto_metal_kpoints: bool = False, bandgap_tol: float = 0.0001, bandgap: float | None = None, prev_incar: str | dict | None = None, prev_kpoints: str | Kpoints | None = None, _valid_potcars: Sequence[str] | None = None, added_kpoints: list[Vector3D] = <factory>, mode: str = 'gap', reciprocal_density: float = 50, copy_chgcar: bool = True, kpoints_line_density: float = 20, nbands_factor: float = 1.2, zero_weighted_reciprocal_density: float = 100, dedos: float = 0.02, optics: bool = False)[source]
Bases:
VaspInputSetImplementation of a VaspInputSet for HSE band structure computations.
Remember that HSE band structures must be self-consistent in VASP. A band structure along symmetry lines for instance needs BOTH a uniform grid with appropriate weights AND a path along the lines with weight 0.
Thus, the “uniform” mode is just like regular static SCF but allows adding custom kpoints (e.g., corresponding to known VBM/CBM) to the uniform grid that have zero weight (e.g., for better gap estimate).
The “gap” mode behaves just like the “uniform” mode, however, if starting from a previous calculation, the VBM and CBM k-points will automatically be added to
added_kpoints.The “line” mode is just like “uniform” mode, but additionally adds k-points along symmetry lines with zero weight.
The “uniform_dense” mode is like “uniform” mode but additionally adds a denser uniform mesh with zero weight. This can be useful when calculating Fermi surfaces or BoltzTraP/AMSET electronic transport using hybrid DFT.
- Parameters:
structure (Structure) – Structure to compute
added_kpoints (list) – a list of kpoints (list of 3 number list) added to the run. The k-points are in fractional coordinates
mode (str) – “Line” - generate k-points along symmetry lines for bandstructure. “Uniform” - generate uniform k-points grid.
reciprocal_density (int) – k-point density to use for uniform mesh.
copy_chgcar (bool) – Whether to copy the CHGCAR of a previous run.
kpoints_line_density (int) – k-point density for high symmetry lines
dedos (float) – Energy difference used to set NEDOS, based on the total energy range.
optics (bool) – Whether to add LOPTICS (used for calculating optical response).
nbands_factor (float) – Multiplicative factor for NBANDS when starting from a previous calculation. Choose a higher number if you are doing an LOPTICS calculation.
**kwargs – Keywords supported by VaspInputSet.
- CONFIG = {'INCAR': {'ALGO': 'All', 'EDIFF_PER_ATOM': 5e-05, 'ENCUT': 520, 'HFSCREEN': 0.2, 'IBRION': 2, 'ICHARG': 1, 'ISIF': 3, 'ISMEAR': 0, 'ISPIN': 2, 'LHFCALC': True, 'LORBIT': 11, 'LREAL': 'AUTO', 'LWAVE': False, 'MAGMOM': {'Ce': 5, 'Ce3+': 1, 'Co': 0.6, 'Co3+': 0.6, 'Co4+': 1, 'Cr': 5, 'Dy3+': 5, 'Er3+': 3, 'Eu': 10, 'Eu2+': 7, 'Eu3+': 6, 'Fe': 5, 'Gd3+': 7, 'Ho3+': 4, 'La3+': 0.6, 'Lu3+': 0.6, 'Mn': 5, 'Mn3+': 4, 'Mn4+': 3, 'Mo': 5, 'Nd3+': 3, 'Ni': 5, 'Pm3+': 4, 'Pr3+': 2, 'Sm3+': 5, 'Tb3+': 6, 'Tm3+': 2, 'V': 5, 'W': 5, 'Yb3+': 1}, 'NELM': 100, 'NSW': 99, 'PREC': 'Accurate', 'PRECFOCK': 'Fast', 'SIGMA': 0.05}, 'KPOINTS': {'reciprocal_density': 50}, 'PARENT': 'VASPIncarBase', 'POTCAR': {'Ac': 'Ac', 'Ag': 'Ag', 'Al': 'Al', 'Ar': 'Ar', 'As': 'As', 'Au': 'Au', 'B': 'B', 'Ba': 'Ba_sv', 'Be': 'Be_sv', 'Bi': 'Bi', 'Br': 'Br', 'C': 'C', 'Ca': 'Ca_sv', 'Cd': 'Cd', 'Ce': 'Ce', 'Cl': 'Cl', 'Co': 'Co', 'Cr': 'Cr_pv', 'Cs': 'Cs_sv', 'Cu': 'Cu_pv', 'Dy': 'Dy_3', 'Er': 'Er_3', 'Eu': 'Eu', 'F': 'F', 'Fe': 'Fe_pv', 'Ga': 'Ga_d', 'Gd': 'Gd', 'Ge': 'Ge_d', 'H': 'H', 'He': 'He', 'Hf': 'Hf_pv', 'Hg': 'Hg', 'Ho': 'Ho_3', 'I': 'I', 'In': 'In_d', 'Ir': 'Ir', 'K': 'K_sv', 'Kr': 'Kr', 'La': 'La', 'Li': 'Li_sv', 'Lu': 'Lu_3', 'Mg': 'Mg_pv', 'Mn': 'Mn_pv', 'Mo': 'Mo_pv', 'N': 'N', 'Na': 'Na_pv', 'Nb': 'Nb_pv', 'Nd': 'Nd_3', 'Ne': 'Ne', 'Ni': 'Ni_pv', 'Np': 'Np', 'O': 'O', 'Os': 'Os_pv', 'P': 'P', 'Pa': 'Pa', 'Pb': 'Pb_d', 'Pd': 'Pd', 'Pm': 'Pm_3', 'Pr': 'Pr_3', 'Pt': 'Pt', 'Pu': 'Pu', 'Rb': 'Rb_sv', 'Re': 'Re_pv', 'Rh': 'Rh_pv', 'Ru': 'Ru_pv', 'S': 'S', 'Sb': 'Sb', 'Sc': 'Sc_sv', 'Se': 'Se', 'Si': 'Si', 'Sm': 'Sm_3', 'Sn': 'Sn_d', 'Sr': 'Sr_sv', 'Ta': 'Ta_pv', 'Tb': 'Tb_3', 'Tc': 'Tc_pv', 'Te': 'Te', 'Th': 'Th', 'Ti': 'Ti_pv', 'Tl': 'Tl_d', 'Tm': 'Tm_3', 'U': 'U', 'V': 'V_pv', 'W': 'W_pv', 'Xe': 'Xe', 'Y': 'Y_sv', 'Yb': 'Yb_2', 'Zn': 'Zn', 'Zr': 'Zr_sv'}, 'POTCAR_FUNCTIONAL': 'PBE_52'}[source]
- property incar_updates: dict[str, Any][source]
Updates to the INCAR config for this calculation type.
- class MPHSERelaxSet(structure: Structure | None = <property object>, config_dict: dict = <factory>, files_to_transfer: dict = <factory>, user_incar_settings: dict = <factory>, user_kpoints_settings: dict = <factory>, user_potcar_settings: dict = <factory>, constrain_total_magmom: bool = False, sort_structure: bool = True, user_potcar_functional: UserPotcarFunctional = None, force_gamma: bool = False, reduce_structure: Literal['niggli', 'LLL'] | None = None, vdw: str | None = None, use_structure_charge: bool = False, standardize: bool = False, sym_prec: float = 0.1, international_monoclinic: bool = True, validate_magmom: bool = True, inherit_incar: bool | list[str] = False, auto_kspacing: bool = False, auto_ismear: bool = False, auto_ispin: bool = False, auto_lreal: bool = False, auto_metal_kpoints: bool = False, bandgap_tol: float = 0.0001, bandgap: float | None = None, prev_incar: str | dict | None = None, prev_kpoints: str | Kpoints | None = None, _valid_potcars: Sequence[str] | None = None)[source]
Bases:
VaspInputSetSame as the MPRelaxSet, but with HSE parameters.
- CONFIG = {'INCAR': {'ALGO': 'All', 'EDIFF_PER_ATOM': 5e-05, 'ENCUT': 520, 'HFSCREEN': 0.2, 'IBRION': 2, 'ICHARG': 1, 'ISIF': 3, 'ISMEAR': 0, 'ISPIN': 2, 'LHFCALC': True, 'LORBIT': 11, 'LREAL': 'AUTO', 'LWAVE': False, 'MAGMOM': {'Ce': 5, 'Ce3+': 1, 'Co': 0.6, 'Co3+': 0.6, 'Co4+': 1, 'Cr': 5, 'Dy3+': 5, 'Er3+': 3, 'Eu': 10, 'Eu2+': 7, 'Eu3+': 6, 'Fe': 5, 'Gd3+': 7, 'Ho3+': 4, 'La3+': 0.6, 'Lu3+': 0.6, 'Mn': 5, 'Mn3+': 4, 'Mn4+': 3, 'Mo': 5, 'Nd3+': 3, 'Ni': 5, 'Pm3+': 4, 'Pr3+': 2, 'Sm3+': 5, 'Tb3+': 6, 'Tm3+': 2, 'V': 5, 'W': 5, 'Yb3+': 1}, 'NELM': 100, 'NSW': 99, 'PREC': 'Accurate', 'PRECFOCK': 'Fast', 'SIGMA': 0.05}, 'KPOINTS': {'reciprocal_density': 50}, 'PARENT': 'VASPIncarBase', 'POTCAR': {'Ac': 'Ac', 'Ag': 'Ag', 'Al': 'Al', 'Ar': 'Ar', 'As': 'As', 'Au': 'Au', 'B': 'B', 'Ba': 'Ba_sv', 'Be': 'Be_sv', 'Bi': 'Bi', 'Br': 'Br', 'C': 'C', 'Ca': 'Ca_sv', 'Cd': 'Cd', 'Ce': 'Ce', 'Cl': 'Cl', 'Co': 'Co', 'Cr': 'Cr_pv', 'Cs': 'Cs_sv', 'Cu': 'Cu_pv', 'Dy': 'Dy_3', 'Er': 'Er_3', 'Eu': 'Eu', 'F': 'F', 'Fe': 'Fe_pv', 'Ga': 'Ga_d', 'Gd': 'Gd', 'Ge': 'Ge_d', 'H': 'H', 'He': 'He', 'Hf': 'Hf_pv', 'Hg': 'Hg', 'Ho': 'Ho_3', 'I': 'I', 'In': 'In_d', 'Ir': 'Ir', 'K': 'K_sv', 'Kr': 'Kr', 'La': 'La', 'Li': 'Li_sv', 'Lu': 'Lu_3', 'Mg': 'Mg_pv', 'Mn': 'Mn_pv', 'Mo': 'Mo_pv', 'N': 'N', 'Na': 'Na_pv', 'Nb': 'Nb_pv', 'Nd': 'Nd_3', 'Ne': 'Ne', 'Ni': 'Ni_pv', 'Np': 'Np', 'O': 'O', 'Os': 'Os_pv', 'P': 'P', 'Pa': 'Pa', 'Pb': 'Pb_d', 'Pd': 'Pd', 'Pm': 'Pm_3', 'Pr': 'Pr_3', 'Pt': 'Pt', 'Pu': 'Pu', 'Rb': 'Rb_sv', 'Re': 'Re_pv', 'Rh': 'Rh_pv', 'Ru': 'Ru_pv', 'S': 'S', 'Sb': 'Sb', 'Sc': 'Sc_sv', 'Se': 'Se', 'Si': 'Si', 'Sm': 'Sm_3', 'Sn': 'Sn_d', 'Sr': 'Sr_sv', 'Ta': 'Ta_pv', 'Tb': 'Tb_3', 'Tc': 'Tc_pv', 'Te': 'Te', 'Th': 'Th', 'Ti': 'Ti_pv', 'Tl': 'Tl_d', 'Tm': 'Tm_3', 'U': 'U', 'V': 'V_pv', 'W': 'W_pv', 'Xe': 'Xe', 'Y': 'Y_sv', 'Yb': 'Yb_2', 'Zn': 'Zn', 'Zr': 'Zr_sv'}, 'POTCAR_FUNCTIONAL': 'PBE_52'}[source]
- class MPMDSet(structure: Structure | None = <property object>, config_dict: dict = <factory>, files_to_transfer: dict = <factory>, user_incar_settings: dict = <factory>, user_kpoints_settings: dict = <factory>, user_potcar_settings: dict = <factory>, constrain_total_magmom: bool = False, sort_structure: bool = True, user_potcar_functional: UserPotcarFunctional = None, force_gamma: bool = False, reduce_structure: Literal['niggli', 'LLL'] | None = None, vdw: str | None = None, use_structure_charge: bool = False, standardize: bool = False, sym_prec: float = 0.1, international_monoclinic: bool = True, validate_magmom: bool = True, inherit_incar: bool | list[str] = False, auto_kspacing: bool = False, auto_ismear: bool = False, auto_ispin: bool = False, auto_lreal: bool = False, auto_metal_kpoints: bool = False, bandgap_tol: float = 0.0001, bandgap: float | None = None, prev_incar: str | dict | None = None, prev_kpoints: str | Kpoints | None = None, _valid_potcars: Sequence[str] | None = None, start_temp: float = 0.0, end_temp: float = 300.0, nsteps: int = 1000, time_step: float | None = None, spin_polarized: bool = False)[source]
Bases:
VaspInputSetThis a modified version of the old MITMDSet pre 2018/03/12.
This set serves as the basis for the amorphous skyline paper.
Aykol, M.; Dwaraknath, S. S.; Sun, W.; Persson, K. A. Thermodynamic Limit for Synthesis of Metastable Inorganic Materials. Sci. Adv. 2018, 4 (4).
Class for writing a VASP MD run. This DOES NOT do multiple stage runs. Precision remains normal, to increase accuracy of stress tensor.
- Parameters:
structure (Structure) – Input structure.
start_temp (int) – Starting temperature.
end_temp (int) – Final temperature.
nsteps (int) – Number of time steps for simulations. NSW parameter.
time_step (float) – The time step for the simulation. The POTIM parameter. Defaults to None, which will set it automatically to 2.0 fs for non-hydrogen containing structures and 0.5 fs for hydrogen containing structures.
spin_polarized (bool) – Whether to do spin polarized calculations. The ISPIN parameter. Defaults to False.
**kwargs – Other kwargs supported by VaspInputSet.
- CONFIG = {'INCAR': {'ALGO': 'FAST', 'EDIFF_PER_ATOM': 5e-05, 'ENCUT': 520, 'IBRION': 2, 'ISIF': 3, 'ISMEAR': -5, 'ISPIN': 2, 'LASPH': True, 'LDAU': True, 'LDAUJ': {'F': {'Co': 0, 'Cr': 0, 'Fe': 0, 'Mn': 0, 'Mo': 0, 'Ni': 0, 'V': 0, 'W': 0}, 'O': {'Co': 0, 'Cr': 0, 'Fe': 0, 'Mn': 0, 'Mo': 0, 'Ni': 0, 'V': 0, 'W': 0}}, 'LDAUL': {'F': {'Co': 2, 'Cr': 2, 'Fe': 2, 'Mn': 2, 'Mo': 2, 'Ni': 2, 'V': 2, 'W': 2}, 'O': {'Co': 2, 'Cr': 2, 'Fe': 2, 'Mn': 2, 'Mo': 2, 'Ni': 2, 'V': 2, 'W': 2}}, 'LDAUPRINT': 1, 'LDAUTYPE': 2, 'LDAUU': {'F': {'Co': 3.32, 'Cr': 3.7, 'Fe': 5.3, 'Mn': 3.9, 'Mo': 4.38, 'Ni': 6.2, 'V': 3.25, 'W': 6.2}, 'O': {'Co': 3.32, 'Cr': 3.7, 'Fe': 5.3, 'Mn': 3.9, 'Mo': 4.38, 'Ni': 6.2, 'V': 3.25, 'W': 6.2}}, 'LORBIT': 11, 'LREAL': 'AUTO', 'LWAVE': False, 'MAGMOM': {'Ce': 5, 'Ce3+': 1, 'Co': 0.6, 'Co3+': 0.6, 'Co4+': 1, 'Cr': 5, 'Dy3+': 5, 'Er3+': 3, 'Eu': 10, 'Eu2+': 7, 'Eu3+': 6, 'Fe': 5, 'Gd3+': 7, 'Ho3+': 4, 'La3+': 0.6, 'Lu3+': 0.6, 'Mn': 5, 'Mn3+': 4, 'Mn4+': 3, 'Mo': 5, 'Nd3+': 3, 'Ni': 5, 'Pm3+': 4, 'Pr3+': 2, 'Sm3+': 5, 'Tb3+': 6, 'Tm3+': 2, 'V': 5, 'W': 5, 'Yb3+': 1}, 'NELM': 100, 'NSW': 99, 'PREC': 'Accurate', 'SIGMA': 0.05}, 'KPOINTS': {'reciprocal_density': 64}, 'PARENT': 'VASPIncarBase', 'POTCAR': {'Ac': 'Ac', 'Ag': 'Ag', 'Al': 'Al', 'Ar': 'Ar', 'As': 'As', 'Au': 'Au', 'B': 'B', 'Ba': 'Ba_sv', 'Be': 'Be_sv', 'Bi': 'Bi', 'Br': 'Br', 'C': 'C', 'Ca': 'Ca_sv', 'Cd': 'Cd', 'Ce': 'Ce', 'Cl': 'Cl', 'Co': 'Co', 'Cr': 'Cr_pv', 'Cs': 'Cs_sv', 'Cu': 'Cu_pv', 'Dy': 'Dy_3', 'Er': 'Er_3', 'Eu': 'Eu', 'F': 'F', 'Fe': 'Fe_pv', 'Ga': 'Ga_d', 'Gd': 'Gd', 'Ge': 'Ge_d', 'H': 'H', 'He': 'He', 'Hf': 'Hf_pv', 'Hg': 'Hg', 'Ho': 'Ho_3', 'I': 'I', 'In': 'In_d', 'Ir': 'Ir', 'K': 'K_sv', 'Kr': 'Kr', 'La': 'La', 'Li': 'Li_sv', 'Lu': 'Lu_3', 'Mg': 'Mg_pv', 'Mn': 'Mn_pv', 'Mo': 'Mo_pv', 'N': 'N', 'Na': 'Na_pv', 'Nb': 'Nb_pv', 'Nd': 'Nd_3', 'Ne': 'Ne', 'Ni': 'Ni_pv', 'Np': 'Np', 'O': 'O', 'Os': 'Os_pv', 'P': 'P', 'Pa': 'Pa', 'Pb': 'Pb_d', 'Pd': 'Pd', 'Pm': 'Pm_3', 'Pr': 'Pr_3', 'Pt': 'Pt', 'Pu': 'Pu', 'Rb': 'Rb_sv', 'Re': 'Re_pv', 'Rh': 'Rh_pv', 'Ru': 'Ru_pv', 'S': 'S', 'Sb': 'Sb', 'Sc': 'Sc_sv', 'Se': 'Se', 'Si': 'Si', 'Sm': 'Sm_3', 'Sn': 'Sn_d', 'Sr': 'Sr_sv', 'Ta': 'Ta_pv', 'Tb': 'Tb_3', 'Tc': 'Tc_pv', 'Te': 'Te', 'Th': 'Th', 'Ti': 'Ti_pv', 'Tl': 'Tl_d', 'Tm': 'Tm_3', 'U': 'U', 'V': 'V_pv', 'W': 'W_pv', 'Xe': 'Xe', 'Y': 'Y_sv', 'Yb': 'Yb_2', 'Zn': 'Zn', 'Zr': 'Zr_sv'}, 'POTCAR_FUNCTIONAL': 'PBE'}[source]
- property incar_updates: dict[str, Any][source]
Updates to the INCAR config for this calculation type.
- class MPMetalRelaxSet(structure: Structure | None = <property object>, config_dict: dict = <factory>, files_to_transfer: dict = <factory>, user_incar_settings: dict = <factory>, user_kpoints_settings: dict = <factory>, user_potcar_settings: dict = <factory>, constrain_total_magmom: bool = False, sort_structure: bool = True, user_potcar_functional: UserPotcarFunctional = None, force_gamma: bool = False, reduce_structure: Literal['niggli', 'LLL'] | None = None, vdw: str | None = None, use_structure_charge: bool = False, standardize: bool = False, sym_prec: float = 0.1, international_monoclinic: bool = True, validate_magmom: bool = True, inherit_incar: bool | list[str] = False, auto_kspacing: bool = False, auto_ismear: bool = False, auto_ispin: bool = False, auto_lreal: bool = False, auto_metal_kpoints: bool = False, bandgap_tol: float = 0.0001, bandgap: float | None = None, prev_incar: str | dict | None = None, prev_kpoints: str | Kpoints | None = None, _valid_potcars: Sequence[str] | None = None)[source]
Bases:
VaspInputSetImplementation of VaspInputSet utilizing parameters in the public Materials Project, but with tuning for metals. Key things are a denser k point density, and a.
- CONFIG = {'INCAR': {'ALGO': 'FAST', 'EDIFF_PER_ATOM': 5e-05, 'ENCUT': 520, 'IBRION': 2, 'ISIF': 3, 'ISMEAR': -5, 'ISPIN': 2, 'LASPH': True, 'LDAU': True, 'LDAUJ': {'F': {'Co': 0, 'Cr': 0, 'Fe': 0, 'Mn': 0, 'Mo': 0, 'Ni': 0, 'V': 0, 'W': 0}, 'O': {'Co': 0, 'Cr': 0, 'Fe': 0, 'Mn': 0, 'Mo': 0, 'Ni': 0, 'V': 0, 'W': 0}}, 'LDAUL': {'F': {'Co': 2, 'Cr': 2, 'Fe': 2, 'Mn': 2, 'Mo': 2, 'Ni': 2, 'V': 2, 'W': 2}, 'O': {'Co': 2, 'Cr': 2, 'Fe': 2, 'Mn': 2, 'Mo': 2, 'Ni': 2, 'V': 2, 'W': 2}}, 'LDAUPRINT': 1, 'LDAUTYPE': 2, 'LDAUU': {'F': {'Co': 3.32, 'Cr': 3.7, 'Fe': 5.3, 'Mn': 3.9, 'Mo': 4.38, 'Ni': 6.2, 'V': 3.25, 'W': 6.2}, 'O': {'Co': 3.32, 'Cr': 3.7, 'Fe': 5.3, 'Mn': 3.9, 'Mo': 4.38, 'Ni': 6.2, 'V': 3.25, 'W': 6.2}}, 'LORBIT': 11, 'LREAL': 'AUTO', 'LWAVE': False, 'MAGMOM': {'Ce': 5, 'Ce3+': 1, 'Co': 0.6, 'Co3+': 0.6, 'Co4+': 1, 'Cr': 5, 'Dy3+': 5, 'Er3+': 3, 'Eu': 10, 'Eu2+': 7, 'Eu3+': 6, 'Fe': 5, 'Gd3+': 7, 'Ho3+': 4, 'La3+': 0.6, 'Lu3+': 0.6, 'Mn': 5, 'Mn3+': 4, 'Mn4+': 3, 'Mo': 5, 'Nd3+': 3, 'Ni': 5, 'Pm3+': 4, 'Pr3+': 2, 'Sm3+': 5, 'Tb3+': 6, 'Tm3+': 2, 'V': 5, 'W': 5, 'Yb3+': 1}, 'NELM': 100, 'NSW': 99, 'PREC': 'Accurate', 'SIGMA': 0.05}, 'KPOINTS': {'reciprocal_density': 64}, 'PARENT': 'VASPIncarBase', 'POTCAR': {'Ac': 'Ac', 'Ag': 'Ag', 'Al': 'Al', 'Ar': 'Ar', 'As': 'As', 'Au': 'Au', 'B': 'B', 'Ba': 'Ba_sv', 'Be': 'Be_sv', 'Bi': 'Bi', 'Br': 'Br', 'C': 'C', 'Ca': 'Ca_sv', 'Cd': 'Cd', 'Ce': 'Ce', 'Cl': 'Cl', 'Co': 'Co', 'Cr': 'Cr_pv', 'Cs': 'Cs_sv', 'Cu': 'Cu_pv', 'Dy': 'Dy_3', 'Er': 'Er_3', 'Eu': 'Eu', 'F': 'F', 'Fe': 'Fe_pv', 'Ga': 'Ga_d', 'Gd': 'Gd', 'Ge': 'Ge_d', 'H': 'H', 'He': 'He', 'Hf': 'Hf_pv', 'Hg': 'Hg', 'Ho': 'Ho_3', 'I': 'I', 'In': 'In_d', 'Ir': 'Ir', 'K': 'K_sv', 'Kr': 'Kr', 'La': 'La', 'Li': 'Li_sv', 'Lu': 'Lu_3', 'Mg': 'Mg_pv', 'Mn': 'Mn_pv', 'Mo': 'Mo_pv', 'N': 'N', 'Na': 'Na_pv', 'Nb': 'Nb_pv', 'Nd': 'Nd_3', 'Ne': 'Ne', 'Ni': 'Ni_pv', 'Np': 'Np', 'O': 'O', 'Os': 'Os_pv', 'P': 'P', 'Pa': 'Pa', 'Pb': 'Pb_d', 'Pd': 'Pd', 'Pm': 'Pm_3', 'Pr': 'Pr_3', 'Pt': 'Pt', 'Pu': 'Pu', 'Rb': 'Rb_sv', 'Re': 'Re_pv', 'Rh': 'Rh_pv', 'Ru': 'Ru_pv', 'S': 'S', 'Sb': 'Sb', 'Sc': 'Sc_sv', 'Se': 'Se', 'Si': 'Si', 'Sm': 'Sm_3', 'Sn': 'Sn_d', 'Sr': 'Sr_sv', 'Ta': 'Ta_pv', 'Tb': 'Tb_3', 'Tc': 'Tc_pv', 'Te': 'Te', 'Th': 'Th', 'Ti': 'Ti_pv', 'Tl': 'Tl_d', 'Tm': 'Tm_3', 'U': 'U', 'V': 'V_pv', 'W': 'W_pv', 'Xe': 'Xe', 'Y': 'Y_sv', 'Yb': 'Yb_2', 'Zn': 'Zn', 'Zr': 'Zr_sv'}, 'POTCAR_FUNCTIONAL': 'PBE'}[source]
- class MPNMRSet(structure: Structure | None = <property object>, config_dict: dict = <factory>, files_to_transfer: dict = <factory>, user_incar_settings: dict = <factory>, user_kpoints_settings: dict = <factory>, user_potcar_settings: dict = <factory>, constrain_total_magmom: bool = False, sort_structure: bool = True, user_potcar_functional: UserPotcarFunctional = None, force_gamma: bool = False, reduce_structure: Literal['niggli', 'LLL'] | None = None, vdw: str | None = None, use_structure_charge: bool = False, standardize: bool = False, sym_prec: float = 0.1, international_monoclinic: bool = True, validate_magmom: bool = True, inherit_incar: bool = True, auto_kspacing: bool = False, auto_ismear: bool = False, auto_ispin: bool = False, auto_lreal: bool = False, auto_metal_kpoints: bool = False, bandgap_tol: float = 0.0001, bandgap: float | None = None, prev_incar: str | dict | None = None, prev_kpoints: str | Kpoints | None = None, _valid_potcars: Sequence[str] | None = None, mode: Literal['cs', 'efg'] = 'cs', isotopes: list = <factory>, reciprocal_density: int = 100, small_gap_multiply: tuple[float, float] | None = None)[source]
Bases:
VaspInputSetInit a MPNMRSet.
- Parameters:
structure (Structure) – Structure from previous run.
mode (str) – The NMR calculation to run “cs”: for Chemical Shift “efg” for Electric Field Gradient
isotopes (list) – list of Isotopes for quadrupole moments
reciprocal_density (int) – density of k-mesh by reciprocal volume.
lepsilon (bool) – Whether to add static dielectric calculation
lcalcpol (bool) – Whether to turn on evaluation of the Berry phase approximations for electronic polarization
reciprocal_density – For static calculations, we usually set the reciprocal density by volume. This is a convenience arg to change that, rather than using user_kpoints_settings. Defaults to 100, which is ~50% more than that of standard relaxation calculations.
small_gap_multiply ([float, float]) – If the gap is less than 1st index, multiply the default reciprocal_density by the 2nd index.
**kwargs – Keywords supported by MPRelaxSet.
- CONFIG = {'INCAR': {'ALGO': 'FAST', 'EDIFF_PER_ATOM': 5e-05, 'ENCUT': 520, 'IBRION': 2, 'ISIF': 3, 'ISMEAR': -5, 'ISPIN': 2, 'LASPH': True, 'LDAU': True, 'LDAUJ': {'F': {'Co': 0, 'Cr': 0, 'Fe': 0, 'Mn': 0, 'Mo': 0, 'Ni': 0, 'V': 0, 'W': 0}, 'O': {'Co': 0, 'Cr': 0, 'Fe': 0, 'Mn': 0, 'Mo': 0, 'Ni': 0, 'V': 0, 'W': 0}}, 'LDAUL': {'F': {'Co': 2, 'Cr': 2, 'Fe': 2, 'Mn': 2, 'Mo': 2, 'Ni': 2, 'V': 2, 'W': 2}, 'O': {'Co': 2, 'Cr': 2, 'Fe': 2, 'Mn': 2, 'Mo': 2, 'Ni': 2, 'V': 2, 'W': 2}}, 'LDAUPRINT': 1, 'LDAUTYPE': 2, 'LDAUU': {'F': {'Co': 3.32, 'Cr': 3.7, 'Fe': 5.3, 'Mn': 3.9, 'Mo': 4.38, 'Ni': 6.2, 'V': 3.25, 'W': 6.2}, 'O': {'Co': 3.32, 'Cr': 3.7, 'Fe': 5.3, 'Mn': 3.9, 'Mo': 4.38, 'Ni': 6.2, 'V': 3.25, 'W': 6.2}}, 'LORBIT': 11, 'LREAL': 'AUTO', 'LWAVE': False, 'MAGMOM': {'Ce': 5, 'Ce3+': 1, 'Co': 0.6, 'Co3+': 0.6, 'Co4+': 1, 'Cr': 5, 'Dy3+': 5, 'Er3+': 3, 'Eu': 10, 'Eu2+': 7, 'Eu3+': 6, 'Fe': 5, 'Gd3+': 7, 'Ho3+': 4, 'La3+': 0.6, 'Lu3+': 0.6, 'Mn': 5, 'Mn3+': 4, 'Mn4+': 3, 'Mo': 5, 'Nd3+': 3, 'Ni': 5, 'Pm3+': 4, 'Pr3+': 2, 'Sm3+': 5, 'Tb3+': 6, 'Tm3+': 2, 'V': 5, 'W': 5, 'Yb3+': 1}, 'NELM': 100, 'NSW': 99, 'PREC': 'Accurate', 'SIGMA': 0.05}, 'KPOINTS': {'reciprocal_density': 64}, 'PARENT': 'VASPIncarBase', 'POTCAR': {'Ac': 'Ac', 'Ag': 'Ag', 'Al': 'Al', 'Ar': 'Ar', 'As': 'As', 'Au': 'Au', 'B': 'B', 'Ba': 'Ba_sv', 'Be': 'Be_sv', 'Bi': 'Bi', 'Br': 'Br', 'C': 'C', 'Ca': 'Ca_sv', 'Cd': 'Cd', 'Ce': 'Ce', 'Cl': 'Cl', 'Co': 'Co', 'Cr': 'Cr_pv', 'Cs': 'Cs_sv', 'Cu': 'Cu_pv', 'Dy': 'Dy_3', 'Er': 'Er_3', 'Eu': 'Eu', 'F': 'F', 'Fe': 'Fe_pv', 'Ga': 'Ga_d', 'Gd': 'Gd', 'Ge': 'Ge_d', 'H': 'H', 'He': 'He', 'Hf': 'Hf_pv', 'Hg': 'Hg', 'Ho': 'Ho_3', 'I': 'I', 'In': 'In_d', 'Ir': 'Ir', 'K': 'K_sv', 'Kr': 'Kr', 'La': 'La', 'Li': 'Li_sv', 'Lu': 'Lu_3', 'Mg': 'Mg_pv', 'Mn': 'Mn_pv', 'Mo': 'Mo_pv', 'N': 'N', 'Na': 'Na_pv', 'Nb': 'Nb_pv', 'Nd': 'Nd_3', 'Ne': 'Ne', 'Ni': 'Ni_pv', 'Np': 'Np', 'O': 'O', 'Os': 'Os_pv', 'P': 'P', 'Pa': 'Pa', 'Pb': 'Pb_d', 'Pd': 'Pd', 'Pm': 'Pm_3', 'Pr': 'Pr_3', 'Pt': 'Pt', 'Pu': 'Pu', 'Rb': 'Rb_sv', 'Re': 'Re_pv', 'Rh': 'Rh_pv', 'Ru': 'Ru_pv', 'S': 'S', 'Sb': 'Sb', 'Sc': 'Sc_sv', 'Se': 'Se', 'Si': 'Si', 'Sm': 'Sm_3', 'Sn': 'Sn_d', 'Sr': 'Sr_sv', 'Ta': 'Ta_pv', 'Tb': 'Tb_3', 'Tc': 'Tc_pv', 'Te': 'Te', 'Th': 'Th', 'Ti': 'Ti_pv', 'Tl': 'Tl_d', 'Tm': 'Tm_3', 'U': 'U', 'V': 'V_pv', 'W': 'W_pv', 'Xe': 'Xe', 'Y': 'Y_sv', 'Yb': 'Yb_2', 'Zn': 'Zn', 'Zr': 'Zr_sv'}, 'POTCAR_FUNCTIONAL': 'PBE'}[source]
- property incar_updates: dict[str, Any][source]
Updates to the INCAR config for this calculation type.
- class MPNonSCFSet(structure: Structure | None = <property object>, config_dict: dict = <factory>, files_to_transfer: dict = <factory>, user_incar_settings: dict = <factory>, user_kpoints_settings: dict = <factory>, user_potcar_settings: dict = <factory>, constrain_total_magmom: bool = False, sort_structure: bool = True, user_potcar_functional: UserPotcarFunctional = None, force_gamma: bool = False, reduce_structure: Literal['niggli', 'LLL'] | None = None, vdw: str | None = None, use_structure_charge: bool = False, standardize: bool = False, sym_prec: float = 0.1, international_monoclinic: bool = True, validate_magmom: bool = True, inherit_incar: bool = True, auto_kspacing: bool = False, auto_ismear: bool = False, auto_ispin: bool = False, auto_lreal: bool = False, auto_metal_kpoints: bool = False, bandgap_tol: float = 0.0001, bandgap: float | None = None, prev_incar: str | dict | None = None, prev_kpoints: str | Kpoints | None = None, _valid_potcars: Sequence[str] | None = None, mode: str = 'line', nedos: int = 2001, dedos: float = 0.005, reciprocal_density: float = 100, kpoints_line_density: float = 20, optics: bool = False, copy_chgcar: bool = True, nbands_factor: float = 1.2, small_gap_multiply: tuple[float, float] | None = None)[source]
Bases:
VaspInputSetInit a MPNonSCFSet. Typically, you would use the classmethod from_prev_calc to initialize from a previous SCF run.
- Parameters:
structure (Structure) – Structure to compute
mode (str) – Line, Uniform or Boltztrap mode supported.
nedos (int) – nedos parameter. Default to 2001.
dedos (float) – setting nedos=0 and uniform mode in from_prev_calc, an automatic nedos will be calculated using the total energy range divided by the energy step dedos
reciprocal_density (int) – density of k-mesh by reciprocal volume (defaults to 100)
kpoints_line_density (int) – Line density for Line mode.
optics (bool) – whether to add dielectric function
copy_chgcar – Whether to copy the old CHGCAR when starting from a previous calculation.
nbands_factor (float) – Multiplicative factor for NBANDS when starting from a previous calculation. Choose a higher number if you are doing an LOPTICS calculation.
small_gap_multiply ([float, float]) – When starting from a previous calculation, if the gap is less than 1st index, multiply the default reciprocal_density by the 2nd index.
**kwargs – Keywords supported by MPRelaxSet.
- CONFIG = {'INCAR': {'ALGO': 'FAST', 'EDIFF_PER_ATOM': 5e-05, 'ENCUT': 520, 'IBRION': 2, 'ISIF': 3, 'ISMEAR': -5, 'ISPIN': 2, 'LASPH': True, 'LDAU': True, 'LDAUJ': {'F': {'Co': 0, 'Cr': 0, 'Fe': 0, 'Mn': 0, 'Mo': 0, 'Ni': 0, 'V': 0, 'W': 0}, 'O': {'Co': 0, 'Cr': 0, 'Fe': 0, 'Mn': 0, 'Mo': 0, 'Ni': 0, 'V': 0, 'W': 0}}, 'LDAUL': {'F': {'Co': 2, 'Cr': 2, 'Fe': 2, 'Mn': 2, 'Mo': 2, 'Ni': 2, 'V': 2, 'W': 2}, 'O': {'Co': 2, 'Cr': 2, 'Fe': 2, 'Mn': 2, 'Mo': 2, 'Ni': 2, 'V': 2, 'W': 2}}, 'LDAUPRINT': 1, 'LDAUTYPE': 2, 'LDAUU': {'F': {'Co': 3.32, 'Cr': 3.7, 'Fe': 5.3, 'Mn': 3.9, 'Mo': 4.38, 'Ni': 6.2, 'V': 3.25, 'W': 6.2}, 'O': {'Co': 3.32, 'Cr': 3.7, 'Fe': 5.3, 'Mn': 3.9, 'Mo': 4.38, 'Ni': 6.2, 'V': 3.25, 'W': 6.2}}, 'LORBIT': 11, 'LREAL': 'AUTO', 'LWAVE': False, 'MAGMOM': {'Ce': 5, 'Ce3+': 1, 'Co': 0.6, 'Co3+': 0.6, 'Co4+': 1, 'Cr': 5, 'Dy3+': 5, 'Er3+': 3, 'Eu': 10, 'Eu2+': 7, 'Eu3+': 6, 'Fe': 5, 'Gd3+': 7, 'Ho3+': 4, 'La3+': 0.6, 'Lu3+': 0.6, 'Mn': 5, 'Mn3+': 4, 'Mn4+': 3, 'Mo': 5, 'Nd3+': 3, 'Ni': 5, 'Pm3+': 4, 'Pr3+': 2, 'Sm3+': 5, 'Tb3+': 6, 'Tm3+': 2, 'V': 5, 'W': 5, 'Yb3+': 1}, 'NELM': 100, 'NSW': 99, 'PREC': 'Accurate', 'SIGMA': 0.05}, 'KPOINTS': {'reciprocal_density': 64}, 'PARENT': 'VASPIncarBase', 'POTCAR': {'Ac': 'Ac', 'Ag': 'Ag', 'Al': 'Al', 'Ar': 'Ar', 'As': 'As', 'Au': 'Au', 'B': 'B', 'Ba': 'Ba_sv', 'Be': 'Be_sv', 'Bi': 'Bi', 'Br': 'Br', 'C': 'C', 'Ca': 'Ca_sv', 'Cd': 'Cd', 'Ce': 'Ce', 'Cl': 'Cl', 'Co': 'Co', 'Cr': 'Cr_pv', 'Cs': 'Cs_sv', 'Cu': 'Cu_pv', 'Dy': 'Dy_3', 'Er': 'Er_3', 'Eu': 'Eu', 'F': 'F', 'Fe': 'Fe_pv', 'Ga': 'Ga_d', 'Gd': 'Gd', 'Ge': 'Ge_d', 'H': 'H', 'He': 'He', 'Hf': 'Hf_pv', 'Hg': 'Hg', 'Ho': 'Ho_3', 'I': 'I', 'In': 'In_d', 'Ir': 'Ir', 'K': 'K_sv', 'Kr': 'Kr', 'La': 'La', 'Li': 'Li_sv', 'Lu': 'Lu_3', 'Mg': 'Mg_pv', 'Mn': 'Mn_pv', 'Mo': 'Mo_pv', 'N': 'N', 'Na': 'Na_pv', 'Nb': 'Nb_pv', 'Nd': 'Nd_3', 'Ne': 'Ne', 'Ni': 'Ni_pv', 'Np': 'Np', 'O': 'O', 'Os': 'Os_pv', 'P': 'P', 'Pa': 'Pa', 'Pb': 'Pb_d', 'Pd': 'Pd', 'Pm': 'Pm_3', 'Pr': 'Pr_3', 'Pt': 'Pt', 'Pu': 'Pu', 'Rb': 'Rb_sv', 'Re': 'Re_pv', 'Rh': 'Rh_pv', 'Ru': 'Ru_pv', 'S': 'S', 'Sb': 'Sb', 'Sc': 'Sc_sv', 'Se': 'Se', 'Si': 'Si', 'Sm': 'Sm_3', 'Sn': 'Sn_d', 'Sr': 'Sr_sv', 'Ta': 'Ta_pv', 'Tb': 'Tb_3', 'Tc': 'Tc_pv', 'Te': 'Te', 'Th': 'Th', 'Ti': 'Ti_pv', 'Tl': 'Tl_d', 'Tm': 'Tm_3', 'U': 'U', 'V': 'V_pv', 'W': 'W_pv', 'Xe': 'Xe', 'Y': 'Y_sv', 'Yb': 'Yb_2', 'Zn': 'Zn', 'Zr': 'Zr_sv'}, 'POTCAR_FUNCTIONAL': 'PBE'}[source]
- property incar_updates: dict[str, Any][source]
Updates to the INCAR config for this calculation type.
- class MPRelaxSet(structure: Structure | None = <property object>, config_dict: dict = <factory>, files_to_transfer: dict = <factory>, user_incar_settings: dict = <factory>, user_kpoints_settings: dict = <factory>, user_potcar_settings: dict = <factory>, constrain_total_magmom: bool = False, sort_structure: bool = True, user_potcar_functional: UserPotcarFunctional = None, force_gamma: bool = False, reduce_structure: Literal['niggli', 'LLL'] | None = None, vdw: str | None = None, use_structure_charge: bool = False, standardize: bool = False, sym_prec: float = 0.1, international_monoclinic: bool = True, validate_magmom: bool = True, inherit_incar: bool | list[str] = False, auto_kspacing: bool = False, auto_ismear: bool = False, auto_ispin: bool = False, auto_lreal: bool = False, auto_metal_kpoints: bool = False, bandgap_tol: float = 0.0001, bandgap: float | None = None, prev_incar: str | dict | None = None, prev_kpoints: str | Kpoints | None = None, _valid_potcars: Sequence[str] | None = None)[source]
Bases:
VaspInputSetImplementation of VaspInputSet utilizing parameters in the public Materials Project. Typically, the pseudopotentials chosen contain more electrons than the MIT parameters, and the k-point grid is ~50% more dense. The LDAUU parameters are also different due to the different PSPs used, which result in different fitted values.
- Parameters:
structure (Structure) – The Structure to create inputs for. If None, the input set is initialized without a Structure but one must be set separately before the inputs are generated.
**kwargs – Keywords supported by VaspInputSet.
- CONFIG = {'INCAR': {'ALGO': 'FAST', 'EDIFF_PER_ATOM': 5e-05, 'ENCUT': 520, 'IBRION': 2, 'ISIF': 3, 'ISMEAR': -5, 'ISPIN': 2, 'LASPH': True, 'LDAU': True, 'LDAUJ': {'F': {'Co': 0, 'Cr': 0, 'Fe': 0, 'Mn': 0, 'Mo': 0, 'Ni': 0, 'V': 0, 'W': 0}, 'O': {'Co': 0, 'Cr': 0, 'Fe': 0, 'Mn': 0, 'Mo': 0, 'Ni': 0, 'V': 0, 'W': 0}}, 'LDAUL': {'F': {'Co': 2, 'Cr': 2, 'Fe': 2, 'Mn': 2, 'Mo': 2, 'Ni': 2, 'V': 2, 'W': 2}, 'O': {'Co': 2, 'Cr': 2, 'Fe': 2, 'Mn': 2, 'Mo': 2, 'Ni': 2, 'V': 2, 'W': 2}}, 'LDAUPRINT': 1, 'LDAUTYPE': 2, 'LDAUU': {'F': {'Co': 3.32, 'Cr': 3.7, 'Fe': 5.3, 'Mn': 3.9, 'Mo': 4.38, 'Ni': 6.2, 'V': 3.25, 'W': 6.2}, 'O': {'Co': 3.32, 'Cr': 3.7, 'Fe': 5.3, 'Mn': 3.9, 'Mo': 4.38, 'Ni': 6.2, 'V': 3.25, 'W': 6.2}}, 'LORBIT': 11, 'LREAL': 'AUTO', 'LWAVE': False, 'MAGMOM': {'Ce': 5, 'Ce3+': 1, 'Co': 0.6, 'Co3+': 0.6, 'Co4+': 1, 'Cr': 5, 'Dy3+': 5, 'Er3+': 3, 'Eu': 10, 'Eu2+': 7, 'Eu3+': 6, 'Fe': 5, 'Gd3+': 7, 'Ho3+': 4, 'La3+': 0.6, 'Lu3+': 0.6, 'Mn': 5, 'Mn3+': 4, 'Mn4+': 3, 'Mo': 5, 'Nd3+': 3, 'Ni': 5, 'Pm3+': 4, 'Pr3+': 2, 'Sm3+': 5, 'Tb3+': 6, 'Tm3+': 2, 'V': 5, 'W': 5, 'Yb3+': 1}, 'NELM': 100, 'NSW': 99, 'PREC': 'Accurate', 'SIGMA': 0.05}, 'KPOINTS': {'reciprocal_density': 64}, 'PARENT': 'VASPIncarBase', 'POTCAR': {'Ac': 'Ac', 'Ag': 'Ag', 'Al': 'Al', 'Ar': 'Ar', 'As': 'As', 'Au': 'Au', 'B': 'B', 'Ba': 'Ba_sv', 'Be': 'Be_sv', 'Bi': 'Bi', 'Br': 'Br', 'C': 'C', 'Ca': 'Ca_sv', 'Cd': 'Cd', 'Ce': 'Ce', 'Cl': 'Cl', 'Co': 'Co', 'Cr': 'Cr_pv', 'Cs': 'Cs_sv', 'Cu': 'Cu_pv', 'Dy': 'Dy_3', 'Er': 'Er_3', 'Eu': 'Eu', 'F': 'F', 'Fe': 'Fe_pv', 'Ga': 'Ga_d', 'Gd': 'Gd', 'Ge': 'Ge_d', 'H': 'H', 'He': 'He', 'Hf': 'Hf_pv', 'Hg': 'Hg', 'Ho': 'Ho_3', 'I': 'I', 'In': 'In_d', 'Ir': 'Ir', 'K': 'K_sv', 'Kr': 'Kr', 'La': 'La', 'Li': 'Li_sv', 'Lu': 'Lu_3', 'Mg': 'Mg_pv', 'Mn': 'Mn_pv', 'Mo': 'Mo_pv', 'N': 'N', 'Na': 'Na_pv', 'Nb': 'Nb_pv', 'Nd': 'Nd_3', 'Ne': 'Ne', 'Ni': 'Ni_pv', 'Np': 'Np', 'O': 'O', 'Os': 'Os_pv', 'P': 'P', 'Pa': 'Pa', 'Pb': 'Pb_d', 'Pd': 'Pd', 'Pm': 'Pm_3', 'Pr': 'Pr_3', 'Pt': 'Pt', 'Pu': 'Pu', 'Rb': 'Rb_sv', 'Re': 'Re_pv', 'Rh': 'Rh_pv', 'Ru': 'Ru_pv', 'S': 'S', 'Sb': 'Sb', 'Sc': 'Sc_sv', 'Se': 'Se', 'Si': 'Si', 'Sm': 'Sm_3', 'Sn': 'Sn_d', 'Sr': 'Sr_sv', 'Ta': 'Ta_pv', 'Tb': 'Tb_3', 'Tc': 'Tc_pv', 'Te': 'Te', 'Th': 'Th', 'Ti': 'Ti_pv', 'Tl': 'Tl_d', 'Tm': 'Tm_3', 'U': 'U', 'V': 'V_pv', 'W': 'W_pv', 'Xe': 'Xe', 'Y': 'Y_sv', 'Yb': 'Yb_2', 'Zn': 'Zn', 'Zr': 'Zr_sv'}, 'POTCAR_FUNCTIONAL': 'PBE'}[source]
- class MPSOCSet(structure: Structure | None = <property object>, config_dict: dict = <factory>, files_to_transfer: dict = <factory>, user_incar_settings: dict = <factory>, user_kpoints_settings: dict = <factory>, user_potcar_settings: dict = <factory>, constrain_total_magmom: bool = False, sort_structure: bool = True, user_potcar_functional: UserPotcarFunctional = None, force_gamma: bool = False, reduce_structure: Literal['niggli', 'LLL'] | None = None, vdw: str | None = None, use_structure_charge: bool = False, standardize: bool = False, sym_prec: float = 0.1, international_monoclinic: bool = True, validate_magmom: bool = True, inherit_incar: bool = True, auto_kspacing: bool = False, auto_ismear: bool = False, auto_ispin: bool = False, auto_lreal: bool = False, auto_metal_kpoints: bool = False, bandgap_tol: float = 0.0001, bandgap: float | None = None, prev_incar: str | dict | None = None, prev_kpoints: str | Kpoints | None = None, _valid_potcars: Sequence[str] | None = None, saxis: Tuple3Ints = (0, 0, 1), nbands_factor: float = 1.2, lepsilon: bool = False, lcalcpol: bool = False, reciprocal_density: float = 100, small_gap_multiply: tuple[float, float] | None = None, magmom: list[Vector3D] | None = None, copy_chgcar: bool = True)[source]
Bases:
VaspInputSetAn input set for running spin-orbit coupling (SOC) calculations.
- Parameters:
structure (Structure) – the structure must have the ‘magmom’ site property and each magnetic moment value must have 3 components. eg:
magmom = [[0,0,2], ...]saxis (tuple) – magnetic moment orientation
copy_chgcar – Whether to copy the old CHGCAR. Defaults to True.
nbands_factor (float) – Multiplicative factor for NBANDS. Choose a higher number if you are doing an LOPTICS calculation.
reciprocal_density (int) – density of k-mesh by reciprocal volume.
small_gap_multiply ([float, float]) – If the gap is less than 1st index, multiply the default reciprocal_density by the 2nd index.
lepsilon (bool) – Whether to add static dielectric calculation
lcalcpol (bool) – Whether to turn on evaluation of the Berry phase approximations for electronic polarization
magmom (list[list[float]]) – Override for the structure magmoms.
**kwargs – Keywords supported by VaspInputSet.
- CONFIG = {'INCAR': {'ALGO': 'FAST', 'EDIFF_PER_ATOM': 5e-05, 'ENCUT': 520, 'IBRION': 2, 'ISIF': 3, 'ISMEAR': -5, 'ISPIN': 2, 'LASPH': True, 'LDAU': True, 'LDAUJ': {'F': {'Co': 0, 'Cr': 0, 'Fe': 0, 'Mn': 0, 'Mo': 0, 'Ni': 0, 'V': 0, 'W': 0}, 'O': {'Co': 0, 'Cr': 0, 'Fe': 0, 'Mn': 0, 'Mo': 0, 'Ni': 0, 'V': 0, 'W': 0}}, 'LDAUL': {'F': {'Co': 2, 'Cr': 2, 'Fe': 2, 'Mn': 2, 'Mo': 2, 'Ni': 2, 'V': 2, 'W': 2}, 'O': {'Co': 2, 'Cr': 2, 'Fe': 2, 'Mn': 2, 'Mo': 2, 'Ni': 2, 'V': 2, 'W': 2}}, 'LDAUPRINT': 1, 'LDAUTYPE': 2, 'LDAUU': {'F': {'Co': 3.32, 'Cr': 3.7, 'Fe': 5.3, 'Mn': 3.9, 'Mo': 4.38, 'Ni': 6.2, 'V': 3.25, 'W': 6.2}, 'O': {'Co': 3.32, 'Cr': 3.7, 'Fe': 5.3, 'Mn': 3.9, 'Mo': 4.38, 'Ni': 6.2, 'V': 3.25, 'W': 6.2}}, 'LORBIT': 11, 'LREAL': 'AUTO', 'LWAVE': False, 'MAGMOM': {'Ce': 5, 'Ce3+': 1, 'Co': 0.6, 'Co3+': 0.6, 'Co4+': 1, 'Cr': 5, 'Dy3+': 5, 'Er3+': 3, 'Eu': 10, 'Eu2+': 7, 'Eu3+': 6, 'Fe': 5, 'Gd3+': 7, 'Ho3+': 4, 'La3+': 0.6, 'Lu3+': 0.6, 'Mn': 5, 'Mn3+': 4, 'Mn4+': 3, 'Mo': 5, 'Nd3+': 3, 'Ni': 5, 'Pm3+': 4, 'Pr3+': 2, 'Sm3+': 5, 'Tb3+': 6, 'Tm3+': 2, 'V': 5, 'W': 5, 'Yb3+': 1}, 'NELM': 100, 'NSW': 99, 'PREC': 'Accurate', 'SIGMA': 0.05}, 'KPOINTS': {'reciprocal_density': 64}, 'PARENT': 'VASPIncarBase', 'POTCAR': {'Ac': 'Ac', 'Ag': 'Ag', 'Al': 'Al', 'Ar': 'Ar', 'As': 'As', 'Au': 'Au', 'B': 'B', 'Ba': 'Ba_sv', 'Be': 'Be_sv', 'Bi': 'Bi', 'Br': 'Br', 'C': 'C', 'Ca': 'Ca_sv', 'Cd': 'Cd', 'Ce': 'Ce', 'Cl': 'Cl', 'Co': 'Co', 'Cr': 'Cr_pv', 'Cs': 'Cs_sv', 'Cu': 'Cu_pv', 'Dy': 'Dy_3', 'Er': 'Er_3', 'Eu': 'Eu', 'F': 'F', 'Fe': 'Fe_pv', 'Ga': 'Ga_d', 'Gd': 'Gd', 'Ge': 'Ge_d', 'H': 'H', 'He': 'He', 'Hf': 'Hf_pv', 'Hg': 'Hg', 'Ho': 'Ho_3', 'I': 'I', 'In': 'In_d', 'Ir': 'Ir', 'K': 'K_sv', 'Kr': 'Kr', 'La': 'La', 'Li': 'Li_sv', 'Lu': 'Lu_3', 'Mg': 'Mg_pv', 'Mn': 'Mn_pv', 'Mo': 'Mo_pv', 'N': 'N', 'Na': 'Na_pv', 'Nb': 'Nb_pv', 'Nd': 'Nd_3', 'Ne': 'Ne', 'Ni': 'Ni_pv', 'Np': 'Np', 'O': 'O', 'Os': 'Os_pv', 'P': 'P', 'Pa': 'Pa', 'Pb': 'Pb_d', 'Pd': 'Pd', 'Pm': 'Pm_3', 'Pr': 'Pr_3', 'Pt': 'Pt', 'Pu': 'Pu', 'Rb': 'Rb_sv', 'Re': 'Re_pv', 'Rh': 'Rh_pv', 'Ru': 'Ru_pv', 'S': 'S', 'Sb': 'Sb', 'Sc': 'Sc_sv', 'Se': 'Se', 'Si': 'Si', 'Sm': 'Sm_3', 'Sn': 'Sn_d', 'Sr': 'Sr_sv', 'Ta': 'Ta_pv', 'Tb': 'Tb_3', 'Tc': 'Tc_pv', 'Te': 'Te', 'Th': 'Th', 'Ti': 'Ti_pv', 'Tl': 'Tl_d', 'Tm': 'Tm_3', 'U': 'U', 'V': 'V_pv', 'W': 'W_pv', 'Xe': 'Xe', 'Y': 'Y_sv', 'Yb': 'Yb_2', 'Zn': 'Zn', 'Zr': 'Zr_sv'}, 'POTCAR_FUNCTIONAL': 'PBE'}[source]
- property incar_updates: dict[str, Any][source]
Updates to the INCAR config for this calculation type.
- class MPScanRelaxSet(structure: Structure | None = <property object>, config_dict: dict = <factory>, files_to_transfer: dict = <factory>, user_incar_settings: dict = <factory>, user_kpoints_settings: dict = <factory>, user_potcar_settings: dict = <factory>, constrain_total_magmom: bool = False, sort_structure: bool = True, user_potcar_functional: UserPotcarFunctional = 'PBE_54', force_gamma: bool = False, reduce_structure: Literal['niggli', 'LLL'] | None = None, vdw: str | None = None, use_structure_charge: bool = False, standardize: bool = False, sym_prec: float = 0.1, international_monoclinic: bool = True, validate_magmom: bool = True, inherit_incar: bool | list[str] = False, auto_kspacing: bool = True, auto_ismear: bool = True, auto_ispin: bool = False, auto_lreal: bool = False, auto_metal_kpoints: bool = False, bandgap_tol: float = 0.0001, bandgap: float | None = None, prev_incar: str | dict | None = None, prev_kpoints: str | Kpoints | None = None, _valid_potcars: Sequence[str] | None = ('PBE_52', 'PBE_54'))[source]
Bases:
VaspInputSetWrite a relaxation input set using the accurate and numerically efficient r2SCAN variant of the Strongly Constrained and Appropriately Normed (SCAN) metaGGA density functional.
Notes
1. This functional is officially supported in VASP 6.0.0 and above. On older version, source code may be obtained by contacting the authors of the referenced manuscript. The original SCAN functional, available from VASP 5.4.3 onwards, maybe used instead by passing user_incar_settings={“METAGGA”: “SCAN”} when instantiating this InputSet. r2SCAN and SCAN are expected to yield very similar results.
2. Meta-GGA calculations require POTCAR files that include information on the kinetic energy density of the core-electrons, i.e. “PBE_52” or “PBE_54”. Make sure the POTCARs include the following lines (see VASP wiki for more details):
$ grep kinetic POTCAR kinetic energy-density mkinetic energy-density pseudized kinetic energy density (partial)
- Parameters:
bandgap (float) – Bandgap of the structure in eV. The bandgap is used to compute the appropriate k-point density and determine the smearing settings. Metallic systems (default, bandgap = 0) use a KSPACING value of 0.22 and Methfessel-Paxton order 2 smearing (ISMEAR=2, SIGMA=0.2). Non-metallic systems (bandgap > 0) use the tetrahedron smearing method (ISMEAR=-5, SIGMA=0.05). The KSPACING value is calculated from the bandgap via Eqs. 25 and 29 of Wisesa, McGill, and Mueller [1] (see References). Note that if ‘user_incar_settings’ or ‘user_kpoints_settings’ override KSPACING, the calculation from bandgap is not performed.
vdw (str) – set “rVV10” to enable SCAN+rVV10, which is a versatile van der Waals density functional by combing the SCAN functional with the rVV10 non-local correlation functional. rvv10 is the only dispersion correction available for SCAN at this time.
**kwargs – Keywords supported by VaspInputSet.
References
P. Wisesa, K.A. McGill, T. Mueller, Efficient generation of generalized Monkhorst-Pack grids through the use of informatics, Phys. Rev. B. 93 (2016) 1-10. doi:10.1103/PhysRevB.93.155109.
James W. Furness, Aaron D. Kaplan, Jinliang Ning, John P. Perdew, and Jianwei Sun. Accurate and Numerically Efficient r2SCAN Meta-Generalized Gradient Approximation. The Journal of Physical Chemistry Letters 0, 11 DOI: 10.1021/acs.jpclett.0c02405
- CONFIG = {'INCAR': {'ALGO': 'ALL', 'EDIFF': 1e-05, 'EDIFFG': -0.02, 'ENAUG': 1360, 'ENCUT': 680, 'IBRION': 2, 'ISIF': 3, 'ISMEAR': 0, 'ISPIN': 2, 'KSPACING': 0.22, 'LAECHG': True, 'LASPH': True, 'LCHARG': True, 'LELF': False, 'LMIXTAU': True, 'LORBIT': 11, 'LREAL': 'Auto', 'LVTOT': True, 'LWAVE': False, 'MAGMOM': {'Ce': 5, 'Ce3+': 1, 'Co': 0.6, 'Co3+': 0.6, 'Co4+': 1, 'Cr': 5, 'Dy3+': 5, 'Er3+': 3, 'Eu': 10, 'Eu2+': 7, 'Eu3+': 6, 'Fe': 5, 'Gd3+': 7, 'Ho3+': 4, 'La3+': 0.6, 'Lu3+': 0.6, 'Mn': 5, 'Mn3+': 4, 'Mn4+': 3, 'Mo': 5, 'Nd3+': 3, 'Ni': 5, 'Pm3+': 4, 'Pr3+': 2, 'Sm3+': 5, 'Tb3+': 6, 'Tm3+': 2, 'V': 5, 'W': 5, 'Yb3+': 1}, 'METAGGA': 'R2SCAN', 'NELM': 200, 'NSW': 99, 'PREC': 'Accurate', 'SIGMA': 0.05}, 'PARENT': 'VASPIncarBase', 'POTCAR': {'Ac': 'Ac', 'Ag': 'Ag', 'Al': 'Al', 'Am': 'Am', 'Ar': 'Ar', 'As': 'As', 'At': 'At', 'Au': 'Au', 'B': 'B', 'Ba': 'Ba_sv', 'Be': 'Be_sv', 'Bi': 'Bi', 'Br': 'Br', 'C': 'C', 'Ca': 'Ca_sv', 'Cd': 'Cd', 'Ce': 'Ce', 'Cf': 'Cf', 'Cl': 'Cl', 'Cm': 'Cm', 'Co': 'Co', 'Cr': 'Cr_pv', 'Cs': 'Cs_sv', 'Cu': 'Cu_pv', 'Dy': 'Dy_3', 'Er': 'Er_3', 'Eu': 'Eu', 'F': 'F', 'Fe': 'Fe_pv', 'Fr': 'Fr_sv', 'Ga': 'Ga_d', 'Gd': 'Gd', 'Ge': 'Ge_d', 'H': 'H', 'He': 'He', 'Hf': 'Hf_pv', 'Hg': 'Hg', 'Ho': 'Ho_3', 'I': 'I', 'In': 'In_d', 'Ir': 'Ir', 'K': 'K_sv', 'Kr': 'Kr', 'La': 'La', 'Li': 'Li_sv', 'Lu': 'Lu_3', 'Mg': 'Mg_pv', 'Mn': 'Mn_pv', 'Mo': 'Mo_pv', 'N': 'N', 'Na': 'Na_pv', 'Nb': 'Nb_pv', 'Nd': 'Nd_3', 'Ne': 'Ne', 'Ni': 'Ni_pv', 'Np': 'Np', 'O': 'O', 'Os': 'Os_pv', 'P': 'P', 'Pa': 'Pa', 'Pb': 'Pb_d', 'Pd': 'Pd', 'Pm': 'Pm_3', 'Po': 'Po_d', 'Pr': 'Pr_3', 'Pt': 'Pt', 'Pu': 'Pu', 'Ra': 'Ra_sv', 'Rb': 'Rb_sv', 'Re': 'Re_pv', 'Rh': 'Rh_pv', 'Rn': 'Rn', 'Ru': 'Ru_pv', 'S': 'S', 'Sb': 'Sb', 'Sc': 'Sc_sv', 'Se': 'Se', 'Si': 'Si', 'Sm': 'Sm_3', 'Sn': 'Sn_d', 'Sr': 'Sr_sv', 'Ta': 'Ta_pv', 'Tb': 'Tb_3', 'Tc': 'Tc_pv', 'Te': 'Te', 'Th': 'Th', 'Ti': 'Ti_pv', 'Tl': 'Tl_d', 'Tm': 'Tm_3', 'U': 'U', 'V': 'V_pv', 'W': 'W_sv', 'Xe': 'Xe', 'Y': 'Y_sv', 'Yb': 'Yb_3', 'Zn': 'Zn', 'Zr': 'Zr_sv'}, 'POTCAR_FUNCTIONAL': 'PBE_54'}[source]
- class MPScanStaticSet(structure: Structure | None = <property object>, config_dict: dict = <factory>, files_to_transfer: dict = <factory>, user_incar_settings: dict = <factory>, user_kpoints_settings: dict = <factory>, user_potcar_settings: dict = <factory>, constrain_total_magmom: bool = False, sort_structure: bool = True, user_potcar_functional: UserPotcarFunctional = 'PBE_54', force_gamma: bool = False, reduce_structure: Literal['niggli', 'LLL'] | None = None, vdw: str | None = None, use_structure_charge: bool = False, standardize: bool = False, sym_prec: float = 0.1, international_monoclinic: bool = True, validate_magmom: bool = True, inherit_incar: bool = True, auto_kspacing: bool = True, auto_ismear: bool = True, auto_ispin: bool = False, auto_lreal: bool = False, auto_metal_kpoints: bool = False, bandgap_tol: float = 0.0001, bandgap: float | None = None, prev_incar: str | dict | None = None, prev_kpoints: str | Kpoints | None = None, _valid_potcars: Sequence[str] | None = ('PBE_52', 'PBE_54'), lepsilon: bool = False, lcalcpol: bool = False)[source]
Bases:
MPScanRelaxSetCreate input files for a static calculation using the accurate and numerically efficient r2SCAN variant of the Strongly Constrained and Appropriately Normed (SCAN) metaGGA functional.
- Parameters:
structure (Structure) – Structure from previous run.
bandgap (float) – Bandgap of the structure in eV. The bandgap is used to compute the appropriate k-point density and determine the smearing settings.
lepsilon (bool) – Whether to add static dielectric calculation
lcalcpol (bool) – Whether to turn on evaluation of the Berry phase approximations for electronic polarization.
**kwargs – Keywords supported by MPScanRelaxSet.
- class MPStaticSet(structure: Structure | None = <property object>, config_dict: dict = <factory>, files_to_transfer: dict = <factory>, user_incar_settings: dict = <factory>, user_kpoints_settings: dict = <factory>, user_potcar_settings: dict = <factory>, constrain_total_magmom: bool = False, sort_structure: bool = True, user_potcar_functional: UserPotcarFunctional = None, force_gamma: bool = False, reduce_structure: Literal['niggli', 'LLL'] | None = None, vdw: str | None = None, use_structure_charge: bool = False, standardize: bool = False, sym_prec: float = 0.1, international_monoclinic: bool = True, validate_magmom: bool = True, inherit_incar: bool = True, auto_kspacing: bool = False, auto_ismear: bool = False, auto_ispin: bool = False, auto_lreal: bool = False, auto_metal_kpoints: bool = False, bandgap_tol: float = 0.0001, bandgap: float | None = None, prev_incar: str | dict | None = None, prev_kpoints: str | Kpoints | None = None, _valid_potcars: Sequence[str] | None = None, lepsilon: bool = False, lcalcpol: bool = False, reciprocal_density: int = 100, small_gap_multiply: tuple[float, float] | None = None)[source]
Bases:
VaspInputSetCreate input files for a static calculation.
- Parameters:
structure (Structure) – Structure from previous run.
lepsilon (bool) – Whether to add static dielectric calculation
lcalcpol (bool) – Whether to turn on evaluation of the Berry phase approximations for electronic polarization
reciprocal_density (int) – For static calculations, we usually set the reciprocal density by volume. This is a convenience arg to change that, rather than using user_kpoints_settings. Defaults to 100, which is ~50% more than that of standard relaxation calculations.
small_gap_multiply ([float, float]) – If the gap is less than 1st index, multiply the default reciprocal_density by the 2nd index.
**kwargs – Keywords supported by MPRelaxSet.
- CONFIG = {'INCAR': {'ALGO': 'FAST', 'EDIFF_PER_ATOM': 5e-05, 'ENCUT': 520, 'IBRION': 2, 'ISIF': 3, 'ISMEAR': -5, 'ISPIN': 2, 'LASPH': True, 'LDAU': True, 'LDAUJ': {'F': {'Co': 0, 'Cr': 0, 'Fe': 0, 'Mn': 0, 'Mo': 0, 'Ni': 0, 'V': 0, 'W': 0}, 'O': {'Co': 0, 'Cr': 0, 'Fe': 0, 'Mn': 0, 'Mo': 0, 'Ni': 0, 'V': 0, 'W': 0}}, 'LDAUL': {'F': {'Co': 2, 'Cr': 2, 'Fe': 2, 'Mn': 2, 'Mo': 2, 'Ni': 2, 'V': 2, 'W': 2}, 'O': {'Co': 2, 'Cr': 2, 'Fe': 2, 'Mn': 2, 'Mo': 2, 'Ni': 2, 'V': 2, 'W': 2}}, 'LDAUPRINT': 1, 'LDAUTYPE': 2, 'LDAUU': {'F': {'Co': 3.32, 'Cr': 3.7, 'Fe': 5.3, 'Mn': 3.9, 'Mo': 4.38, 'Ni': 6.2, 'V': 3.25, 'W': 6.2}, 'O': {'Co': 3.32, 'Cr': 3.7, 'Fe': 5.3, 'Mn': 3.9, 'Mo': 4.38, 'Ni': 6.2, 'V': 3.25, 'W': 6.2}}, 'LORBIT': 11, 'LREAL': 'AUTO', 'LWAVE': False, 'MAGMOM': {'Ce': 5, 'Ce3+': 1, 'Co': 0.6, 'Co3+': 0.6, 'Co4+': 1, 'Cr': 5, 'Dy3+': 5, 'Er3+': 3, 'Eu': 10, 'Eu2+': 7, 'Eu3+': 6, 'Fe': 5, 'Gd3+': 7, 'Ho3+': 4, 'La3+': 0.6, 'Lu3+': 0.6, 'Mn': 5, 'Mn3+': 4, 'Mn4+': 3, 'Mo': 5, 'Nd3+': 3, 'Ni': 5, 'Pm3+': 4, 'Pr3+': 2, 'Sm3+': 5, 'Tb3+': 6, 'Tm3+': 2, 'V': 5, 'W': 5, 'Yb3+': 1}, 'NELM': 100, 'NSW': 99, 'PREC': 'Accurate', 'SIGMA': 0.05}, 'KPOINTS': {'reciprocal_density': 64}, 'PARENT': 'VASPIncarBase', 'POTCAR': {'Ac': 'Ac', 'Ag': 'Ag', 'Al': 'Al', 'Ar': 'Ar', 'As': 'As', 'Au': 'Au', 'B': 'B', 'Ba': 'Ba_sv', 'Be': 'Be_sv', 'Bi': 'Bi', 'Br': 'Br', 'C': 'C', 'Ca': 'Ca_sv', 'Cd': 'Cd', 'Ce': 'Ce', 'Cl': 'Cl', 'Co': 'Co', 'Cr': 'Cr_pv', 'Cs': 'Cs_sv', 'Cu': 'Cu_pv', 'Dy': 'Dy_3', 'Er': 'Er_3', 'Eu': 'Eu', 'F': 'F', 'Fe': 'Fe_pv', 'Ga': 'Ga_d', 'Gd': 'Gd', 'Ge': 'Ge_d', 'H': 'H', 'He': 'He', 'Hf': 'Hf_pv', 'Hg': 'Hg', 'Ho': 'Ho_3', 'I': 'I', 'In': 'In_d', 'Ir': 'Ir', 'K': 'K_sv', 'Kr': 'Kr', 'La': 'La', 'Li': 'Li_sv', 'Lu': 'Lu_3', 'Mg': 'Mg_pv', 'Mn': 'Mn_pv', 'Mo': 'Mo_pv', 'N': 'N', 'Na': 'Na_pv', 'Nb': 'Nb_pv', 'Nd': 'Nd_3', 'Ne': 'Ne', 'Ni': 'Ni_pv', 'Np': 'Np', 'O': 'O', 'Os': 'Os_pv', 'P': 'P', 'Pa': 'Pa', 'Pb': 'Pb_d', 'Pd': 'Pd', 'Pm': 'Pm_3', 'Pr': 'Pr_3', 'Pt': 'Pt', 'Pu': 'Pu', 'Rb': 'Rb_sv', 'Re': 'Re_pv', 'Rh': 'Rh_pv', 'Ru': 'Ru_pv', 'S': 'S', 'Sb': 'Sb', 'Sc': 'Sc_sv', 'Se': 'Se', 'Si': 'Si', 'Sm': 'Sm_3', 'Sn': 'Sn_d', 'Sr': 'Sr_sv', 'Ta': 'Ta_pv', 'Tb': 'Tb_3', 'Tc': 'Tc_pv', 'Te': 'Te', 'Th': 'Th', 'Ti': 'Ti_pv', 'Tl': 'Tl_d', 'Tm': 'Tm_3', 'U': 'U', 'V': 'V_pv', 'W': 'W_pv', 'Xe': 'Xe', 'Y': 'Y_sv', 'Yb': 'Yb_2', 'Zn': 'Zn', 'Zr': 'Zr_sv'}, 'POTCAR_FUNCTIONAL': 'PBE'}[source]
- class MVLElasticSet(structure: Structure | None = <property object>, config_dict: dict = <factory>, files_to_transfer: dict = <factory>, user_incar_settings: dict = <factory>, user_kpoints_settings: dict = <factory>, user_potcar_settings: dict = <factory>, constrain_total_magmom: bool = False, sort_structure: bool = True, user_potcar_functional: UserPotcarFunctional = None, force_gamma: bool = False, reduce_structure: Literal['niggli', 'LLL'] | None = None, vdw: str | None = None, use_structure_charge: bool = False, standardize: bool = False, sym_prec: float = 0.1, international_monoclinic: bool = True, validate_magmom: bool = True, inherit_incar: bool | list[str] = False, auto_kspacing: bool = False, auto_ismear: bool = False, auto_ispin: bool = False, auto_lreal: bool = False, auto_metal_kpoints: bool = False, bandgap_tol: float = 0.0001, bandgap: float | None = None, prev_incar: str | dict | None = None, prev_kpoints: str | Kpoints | None = None, _valid_potcars: Sequence[str] | None = None)[source]
Bases:
VaspInputSetMVL denotes VASP input sets that are implemented by the Materials Virtual Lab (http://materialsvirtuallab.org) for various research.
This input set is used to calculate elastic constants in VASP. It is used in the following work:
Z. Deng, Z. Wang, I.-H. Chu, J. Luo, S. P. Ong. “Elastic Properties of Alkali Superionic Conductor Electrolytes from First Principles Calculations”, J. Electrochem. Soc. 2016, 163(2), A67-A74. doi: 10.1149/2.0061602jes
To read the elastic constants, you may use the Outcar class which parses the elastic constants.
- Parameters:
structure (pymatgen.Structure) – Input structure.
potim (float) – POTIM parameter. The default of 0.015 is usually fine, but some structures may require a smaller step.
**kwargs – Parameters supported by MPRelaxSet.
- CONFIG = {'INCAR': {'ALGO': 'FAST', 'EDIFF_PER_ATOM': 5e-05, 'ENCUT': 520, 'IBRION': 2, 'ISIF': 3, 'ISMEAR': -5, 'ISPIN': 2, 'LASPH': True, 'LDAU': True, 'LDAUJ': {'F': {'Co': 0, 'Cr': 0, 'Fe': 0, 'Mn': 0, 'Mo': 0, 'Ni': 0, 'V': 0, 'W': 0}, 'O': {'Co': 0, 'Cr': 0, 'Fe': 0, 'Mn': 0, 'Mo': 0, 'Ni': 0, 'V': 0, 'W': 0}}, 'LDAUL': {'F': {'Co': 2, 'Cr': 2, 'Fe': 2, 'Mn': 2, 'Mo': 2, 'Ni': 2, 'V': 2, 'W': 2}, 'O': {'Co': 2, 'Cr': 2, 'Fe': 2, 'Mn': 2, 'Mo': 2, 'Ni': 2, 'V': 2, 'W': 2}}, 'LDAUPRINT': 1, 'LDAUTYPE': 2, 'LDAUU': {'F': {'Co': 3.32, 'Cr': 3.7, 'Fe': 5.3, 'Mn': 3.9, 'Mo': 4.38, 'Ni': 6.2, 'V': 3.25, 'W': 6.2}, 'O': {'Co': 3.32, 'Cr': 3.7, 'Fe': 5.3, 'Mn': 3.9, 'Mo': 4.38, 'Ni': 6.2, 'V': 3.25, 'W': 6.2}}, 'LORBIT': 11, 'LREAL': 'AUTO', 'LWAVE': False, 'MAGMOM': {'Ce': 5, 'Ce3+': 1, 'Co': 0.6, 'Co3+': 0.6, 'Co4+': 1, 'Cr': 5, 'Dy3+': 5, 'Er3+': 3, 'Eu': 10, 'Eu2+': 7, 'Eu3+': 6, 'Fe': 5, 'Gd3+': 7, 'Ho3+': 4, 'La3+': 0.6, 'Lu3+': 0.6, 'Mn': 5, 'Mn3+': 4, 'Mn4+': 3, 'Mo': 5, 'Nd3+': 3, 'Ni': 5, 'Pm3+': 4, 'Pr3+': 2, 'Sm3+': 5, 'Tb3+': 6, 'Tm3+': 2, 'V': 5, 'W': 5, 'Yb3+': 1}, 'NELM': 100, 'NSW': 99, 'PREC': 'Accurate', 'SIGMA': 0.05}, 'KPOINTS': {'reciprocal_density': 64}, 'PARENT': 'VASPIncarBase', 'POTCAR': {'Ac': 'Ac', 'Ag': 'Ag', 'Al': 'Al', 'Ar': 'Ar', 'As': 'As', 'Au': 'Au', 'B': 'B', 'Ba': 'Ba_sv', 'Be': 'Be_sv', 'Bi': 'Bi', 'Br': 'Br', 'C': 'C', 'Ca': 'Ca_sv', 'Cd': 'Cd', 'Ce': 'Ce', 'Cl': 'Cl', 'Co': 'Co', 'Cr': 'Cr_pv', 'Cs': 'Cs_sv', 'Cu': 'Cu_pv', 'Dy': 'Dy_3', 'Er': 'Er_3', 'Eu': 'Eu', 'F': 'F', 'Fe': 'Fe_pv', 'Ga': 'Ga_d', 'Gd': 'Gd', 'Ge': 'Ge_d', 'H': 'H', 'He': 'He', 'Hf': 'Hf_pv', 'Hg': 'Hg', 'Ho': 'Ho_3', 'I': 'I', 'In': 'In_d', 'Ir': 'Ir', 'K': 'K_sv', 'Kr': 'Kr', 'La': 'La', 'Li': 'Li_sv', 'Lu': 'Lu_3', 'Mg': 'Mg_pv', 'Mn': 'Mn_pv', 'Mo': 'Mo_pv', 'N': 'N', 'Na': 'Na_pv', 'Nb': 'Nb_pv', 'Nd': 'Nd_3', 'Ne': 'Ne', 'Ni': 'Ni_pv', 'Np': 'Np', 'O': 'O', 'Os': 'Os_pv', 'P': 'P', 'Pa': 'Pa', 'Pb': 'Pb_d', 'Pd': 'Pd', 'Pm': 'Pm_3', 'Pr': 'Pr_3', 'Pt': 'Pt', 'Pu': 'Pu', 'Rb': 'Rb_sv', 'Re': 'Re_pv', 'Rh': 'Rh_pv', 'Ru': 'Ru_pv', 'S': 'S', 'Sb': 'Sb', 'Sc': 'Sc_sv', 'Se': 'Se', 'Si': 'Si', 'Sm': 'Sm_3', 'Sn': 'Sn_d', 'Sr': 'Sr_sv', 'Ta': 'Ta_pv', 'Tb': 'Tb_3', 'Tc': 'Tc_pv', 'Te': 'Te', 'Th': 'Th', 'Ti': 'Ti_pv', 'Tl': 'Tl_d', 'Tm': 'Tm_3', 'U': 'U', 'V': 'V_pv', 'W': 'W_pv', 'Xe': 'Xe', 'Y': 'Y_sv', 'Yb': 'Yb_2', 'Zn': 'Zn', 'Zr': 'Zr_sv'}, 'POTCAR_FUNCTIONAL': 'PBE'}[source]
- class MVLGBSet(structure: Structure | None = <property object>, config_dict: dict = <factory>, files_to_transfer: dict = <factory>, user_incar_settings: dict = <factory>, user_kpoints_settings: dict = <factory>, user_potcar_settings: dict = <factory>, constrain_total_magmom: bool = False, sort_structure: bool = True, user_potcar_functional: UserPotcarFunctional = None, force_gamma: bool = False, reduce_structure: Literal['niggli', 'LLL'] | None = None, vdw: str | None = None, use_structure_charge: bool = False, standardize: bool = False, sym_prec: float = 0.1, international_monoclinic: bool = True, validate_magmom: bool = True, inherit_incar: bool | list[str] = False, auto_kspacing: bool = False, auto_ismear: bool = False, auto_ispin: bool = False, auto_lreal: bool = False, auto_metal_kpoints: bool = False, bandgap_tol: float = 0.0001, bandgap: float | None = None, prev_incar: str | dict | None = None, prev_kpoints: str | Kpoints | None = None, _valid_potcars: Sequence[str] | None = None, k_product: int = 40, slab_mode: bool = False, is_metal: bool = True)[source]
Bases:
VaspInputSetWrite a VASP input files for grain boundary calculations, slab or bulk.
- Parameters:
structure (Structure) – provide the structure
k_product – Kpoint number * length for a & b directions, also for c direction in bulk calculations. Default to 40.
slab_mode (bool) – Defaults to False. Use default (False) for a bulk supercell. Use True if you are performing calculations on a slab-like (i.e., surface) of the GB, for example, when you are calculating the work of separation.
is_metal (bool) – Defaults to True. This determines whether an ISMEAR of 1 is used (for metals) or not (for insulators and semiconductors) by default. Note that it does not override user_incar_settings, which can be set by the user to be anything desired.
**kwargs – Other kwargs supported by MPRelaxSet.
- CONFIG = {'INCAR': {'ALGO': 'FAST', 'EDIFF_PER_ATOM': 5e-05, 'ENCUT': 520, 'IBRION': 2, 'ISIF': 3, 'ISMEAR': -5, 'ISPIN': 2, 'LASPH': True, 'LDAU': True, 'LDAUJ': {'F': {'Co': 0, 'Cr': 0, 'Fe': 0, 'Mn': 0, 'Mo': 0, 'Ni': 0, 'V': 0, 'W': 0}, 'O': {'Co': 0, 'Cr': 0, 'Fe': 0, 'Mn': 0, 'Mo': 0, 'Ni': 0, 'V': 0, 'W': 0}}, 'LDAUL': {'F': {'Co': 2, 'Cr': 2, 'Fe': 2, 'Mn': 2, 'Mo': 2, 'Ni': 2, 'V': 2, 'W': 2}, 'O': {'Co': 2, 'Cr': 2, 'Fe': 2, 'Mn': 2, 'Mo': 2, 'Ni': 2, 'V': 2, 'W': 2}}, 'LDAUPRINT': 1, 'LDAUTYPE': 2, 'LDAUU': {'F': {'Co': 3.32, 'Cr': 3.7, 'Fe': 5.3, 'Mn': 3.9, 'Mo': 4.38, 'Ni': 6.2, 'V': 3.25, 'W': 6.2}, 'O': {'Co': 3.32, 'Cr': 3.7, 'Fe': 5.3, 'Mn': 3.9, 'Mo': 4.38, 'Ni': 6.2, 'V': 3.25, 'W': 6.2}}, 'LORBIT': 11, 'LREAL': 'AUTO', 'LWAVE': False, 'MAGMOM': {'Ce': 5, 'Ce3+': 1, 'Co': 0.6, 'Co3+': 0.6, 'Co4+': 1, 'Cr': 5, 'Dy3+': 5, 'Er3+': 3, 'Eu': 10, 'Eu2+': 7, 'Eu3+': 6, 'Fe': 5, 'Gd3+': 7, 'Ho3+': 4, 'La3+': 0.6, 'Lu3+': 0.6, 'Mn': 5, 'Mn3+': 4, 'Mn4+': 3, 'Mo': 5, 'Nd3+': 3, 'Ni': 5, 'Pm3+': 4, 'Pr3+': 2, 'Sm3+': 5, 'Tb3+': 6, 'Tm3+': 2, 'V': 5, 'W': 5, 'Yb3+': 1}, 'NELM': 100, 'NSW': 99, 'PREC': 'Accurate', 'SIGMA': 0.05}, 'KPOINTS': {'reciprocal_density': 64}, 'PARENT': 'VASPIncarBase', 'POTCAR': {'Ac': 'Ac', 'Ag': 'Ag', 'Al': 'Al', 'Ar': 'Ar', 'As': 'As', 'Au': 'Au', 'B': 'B', 'Ba': 'Ba_sv', 'Be': 'Be_sv', 'Bi': 'Bi', 'Br': 'Br', 'C': 'C', 'Ca': 'Ca_sv', 'Cd': 'Cd', 'Ce': 'Ce', 'Cl': 'Cl', 'Co': 'Co', 'Cr': 'Cr_pv', 'Cs': 'Cs_sv', 'Cu': 'Cu_pv', 'Dy': 'Dy_3', 'Er': 'Er_3', 'Eu': 'Eu', 'F': 'F', 'Fe': 'Fe_pv', 'Ga': 'Ga_d', 'Gd': 'Gd', 'Ge': 'Ge_d', 'H': 'H', 'He': 'He', 'Hf': 'Hf_pv', 'Hg': 'Hg', 'Ho': 'Ho_3', 'I': 'I', 'In': 'In_d', 'Ir': 'Ir', 'K': 'K_sv', 'Kr': 'Kr', 'La': 'La', 'Li': 'Li_sv', 'Lu': 'Lu_3', 'Mg': 'Mg_pv', 'Mn': 'Mn_pv', 'Mo': 'Mo_pv', 'N': 'N', 'Na': 'Na_pv', 'Nb': 'Nb_pv', 'Nd': 'Nd_3', 'Ne': 'Ne', 'Ni': 'Ni_pv', 'Np': 'Np', 'O': 'O', 'Os': 'Os_pv', 'P': 'P', 'Pa': 'Pa', 'Pb': 'Pb_d', 'Pd': 'Pd', 'Pm': 'Pm_3', 'Pr': 'Pr_3', 'Pt': 'Pt', 'Pu': 'Pu', 'Rb': 'Rb_sv', 'Re': 'Re_pv', 'Rh': 'Rh_pv', 'Ru': 'Ru_pv', 'S': 'S', 'Sb': 'Sb', 'Sc': 'Sc_sv', 'Se': 'Se', 'Si': 'Si', 'Sm': 'Sm_3', 'Sn': 'Sn_d', 'Sr': 'Sr_sv', 'Ta': 'Ta_pv', 'Tb': 'Tb_3', 'Tc': 'Tc_pv', 'Te': 'Te', 'Th': 'Th', 'Ti': 'Ti_pv', 'Tl': 'Tl_d', 'Tm': 'Tm_3', 'U': 'U', 'V': 'V_pv', 'W': 'W_pv', 'Xe': 'Xe', 'Y': 'Y_sv', 'Yb': 'Yb_2', 'Zn': 'Zn', 'Zr': 'Zr_sv'}, 'POTCAR_FUNCTIONAL': 'PBE'}[source]
- property incar_updates: dict[str, Any][source]
Updates to the INCAR config for this calculation type.
- class MVLGWSet(structure: Structure | None = <property object>, config_dict: dict = <factory>, files_to_transfer: dict = <factory>, user_incar_settings: dict = <factory>, user_kpoints_settings: dict = <factory>, user_potcar_settings: dict = <factory>, constrain_total_magmom: bool = False, sort_structure: bool = True, user_potcar_functional: UserPotcarFunctional = None, force_gamma: bool = True, reduce_structure: Literal['niggli', 'LLL'] | None = None, vdw: str | None = None, use_structure_charge: bool = False, standardize: bool = False, sym_prec: float = 0.1, international_monoclinic: bool = True, validate_magmom: bool = True, inherit_incar: bool = True, auto_kspacing: bool = False, auto_ismear: bool = False, auto_ispin: bool = False, auto_lreal: bool = False, auto_metal_kpoints: bool = False, bandgap_tol: float = 0.0001, bandgap: float | None = None, prev_incar: str | dict | None = None, prev_kpoints: str | Kpoints | None = None, _valid_potcars: Sequence[str] | None = None, reciprocal_density: float = 100, mode: str = 'STATIC', copy_wavecar: bool = True, nbands_factor: int = 5, ncores: int = 16, nbands: int | None = None)[source]
Bases:
VaspInputSetMVL denotes VASP input sets that are implemented by the Materials Virtual Lab (http://materialsvirtuallab.org) for various research. This is a flexible input set for GW calculations.
Note that unlike all other input sets in this module, the PBE_54 series of functional is set as the default. These have much improved performance for GW calculations.
A typical sequence is mode=”STATIC” -> mode=”DIAG” -> mode=”GW” -> mode=”BSE”. For all steps other than the first one (static), the recommendation is to use from_prev_calculation on the preceding run in the series.
- Parameters:
structure (Structure) – Input structure.
mode (str) – Supported modes are “STATIC” (default), “DIAG”, “GW”, and “BSE”.
nbands (int) – For subsequent calculations, it is generally recommended to perform NBANDS convergence starting from the NBANDS of the previous run for DIAG, and to use the exact same NBANDS for GW and BSE. This parameter is used by from_previous_calculation to set nband.
copy_wavecar – Whether to copy the old WAVECAR, WAVEDER and associated files when starting from a previous calculation.
nbands_factor (int) – Multiplicative factor for NBANDS when starting from a previous calculation. Only applies if mode==”DIAG”. Need to be tested for convergence.
reciprocal_density (int) – Density of k-mesh by reciprocal atom. Only applies if mode==”STATIC”. Defaults to 100.
ncores (int) – Numbers of cores used for the calculation. VASP will alter NBANDS if it was not dividable by ncores. Only applies if mode==”DIAG”.
**kwargs – All kwargs supported by VaspInputSet. Typically, user_incar_settings is a commonly used option.
- CONFIG = {'INCAR': {'ALGO': 'Normal', 'EDIFF': 1e-08, 'IBRION': -1, 'ICHARG': 1, 'ISMEAR': 0, 'ISPIN': 2, 'LORBIT': 11, 'LREAL': 'AUTO', 'LWAVE': True, 'MAGMOM': {'Ce': 5, 'Ce3+': 1, 'Co': 0.6, 'Co3+': 0.6, 'Co4+': 1, 'Cr': 5, 'Dy3+': 5, 'Er3+': 3, 'Eu': 10, 'Eu2+': 7, 'Eu3+': 6, 'Fe': 5, 'Gd3+': 7, 'Ho3+': 4, 'La3+': 0.6, 'Lu3+': 0.6, 'Mn': 5, 'Mn3+': 4, 'Mn4+': 3, 'Mo': 5, 'Nd3+': 3, 'Ni': 5, 'Pm3+': 4, 'Pr3+': 2, 'Sm3+': 5, 'Tb3+': 6, 'Tm3+': 2, 'V': 5, 'W': 5, 'Yb3+': 1}, 'NELM': 100, 'PREC': 'Accurate', 'SIGMA': 0.01}, 'KPOINTS': {'reciprocal_density': 100}, 'PARENT': 'VASPIncarBase', 'POTCAR': {'Ac': 'Ac', 'Ag': 'Ag_sv_GW', 'Al': 'Al_GW', 'Ar': 'Ar_GW', 'As': 'As_GW', 'At': 'At_d_GW', 'Au': 'Au_sv_GW', 'B': 'B_GW', 'Ba': 'Ba_sv_GW', 'Be': 'Be_sv_GW', 'Bi': 'Bi_d_GW', 'Br': 'Br_GW', 'C': 'C_GW', 'Ca': 'Ca_sv_GW', 'Cd': 'Cd_sv_GW', 'Ce': 'Ce_GW', 'Cl': 'Cl_GW', 'Co': 'Co_sv_GW', 'Cr': 'Cr_sv_GW', 'Cs': 'Cs_sv_GW', 'Cu': 'Cu_sv_GW', 'Dy': 'Dy_3', 'Er': 'Er_3', 'Eu': 'Eu', 'F': 'F_GW', 'Fe': 'Fe_sv_GW', 'Ga': 'Ga_d_GW', 'Gd': 'Gd', 'Ge': 'Ge_d_GW', 'H': 'H_GW', 'He': 'He_GW', 'Hf': 'Hf_sv_GW', 'Hg': 'Hg_sv_GW', 'Ho': 'Ho_3', 'I': 'I_GW', 'In': 'In_d_GW', 'Ir': 'Ir_sv_GW', 'K': 'K_sv_GW', 'Kr': 'Kr_GW', 'La': 'La_GW', 'Li': 'Li_sv_GW', 'Lu': 'Lu_3', 'Mg': 'Mg_sv_GW', 'Mn': 'Mn_sv_GW', 'Mo': 'Mo_sv_GW', 'N': 'N_GW', 'Na': 'Na_sv_GW', 'Nb': 'Nb_sv_GW', 'Nd': 'Nd_3', 'Ne': 'Ne_GW', 'Ni': 'Ni_sv_GW', 'Np': 'Np', 'O': 'O_GW', 'Os': 'Os_sv_GW', 'P': 'P_GW', 'Pa': 'Pa', 'Pb': 'Pb_d_GW', 'Pd': 'Pd_sv_GW', 'Pm': 'Pm_3', 'Po': 'Po_d_GW', 'Pr': 'Pr_3', 'Pt': 'Pt_sv_GW', 'Pu': 'Pu', 'Rb': 'Rb_sv_GW', 'Re': 'Re_sv_GW', 'Rh': 'Rh_sv_GW', 'Rn': 'Rn_d_GW', 'Ru': 'Ru_sv_GW', 'S': 'S_GW', 'Sb': 'Sb_d_GW', 'Sc': 'Sc_sv_GW', 'Se': 'Se_GW', 'Si': 'Si_GW', 'Sm': 'Sm_3', 'Sn': 'Sn_d_GW', 'Sr': 'Sr_sv_GW', 'Ta': 'Ta_sv_GW', 'Tb': 'Tb_3', 'Tc': 'Tc_sv_GW', 'Te': 'Te_GW', 'Th': 'Th', 'Ti': 'Ti_sv_GW', 'Tl': 'Tl_d_GW', 'Tm': 'Tm_3', 'U': 'U', 'V': 'V_sv_GW', 'W': 'W_sv_GW', 'Xe': 'Xe_GW', 'Y': 'Y_sv_GW', 'Yb': 'Yb_3', 'Zn': 'Zn_sv_GW', 'Zr': 'Zr_sv_GW'}, 'POTCAR_FUNCTIONAL': 'PBE_54'}[source]
- classmethod from_prev_calc(prev_calc_dir: PathLike, mode: str = 'DIAG', **kwargs) Self[source]
Generate a set of VASP input files for GW or BSE calculations from a directory of previous Exact Diag VASP run.
- Parameters:
prev_calc_dir (PathLike) – The directory contains the outputs( vasprun.xml of previous VASP run.
mode (str) – Supported modes are “STATIC”, “DIAG” (default), “GW”, and “BSE”.
**kwargs – All kwargs supported by MVLGWSet, other than structure, prev_incar and mode, which are determined from the prev_calc_dir.
- property incar_updates: dict[str, Any][source]
Updates to the INCAR config for this calculation type.
- class MVLNPTMDSet(structure: Structure | None = <property object>, config_dict: dict = <factory>, files_to_transfer: dict = <factory>, user_incar_settings: dict = <factory>, user_kpoints_settings: dict = <factory>, user_potcar_settings: dict = <factory>, constrain_total_magmom: bool = False, sort_structure: bool = True, user_potcar_functional: UserPotcarFunctional = None, force_gamma: bool = False, reduce_structure: Literal['niggli', 'LLL'] | None = None, vdw: str | None = None, use_structure_charge: bool = False, standardize: bool = False, sym_prec: float = 0.1, international_monoclinic: bool = True, validate_magmom: bool = True, inherit_incar: bool | list[str] = False, auto_kspacing: bool = False, auto_ismear: bool = False, auto_ispin: bool = False, auto_lreal: bool = False, auto_metal_kpoints: bool = False, bandgap_tol: float = 0.0001, bandgap: float | None = None, prev_incar: str | dict | None = None, prev_kpoints: str | Kpoints | None = None, _valid_potcars: Sequence[str] | None = None, start_temp: float = 0.0, end_temp: float = 300.0, nsteps: int = 1000, time_step: float = 2, spin_polarized: bool = False)[source]
Bases:
VaspInputSetWrite a VASP MD run in NPT ensemble.
Notes
To eliminate Pulay stress, the default ENCUT is set to a rather large value of ENCUT, which is 1.5 * ENMAX.
- CONFIG = {'INCAR': {'ALGO': 'FAST', 'EDIFF': 1e-05, 'ENCUT': 520, 'IBRION': 2, 'ICHARG': 1, 'ISIF': 3, 'ISMEAR': -5, 'ISPIN': 2, 'ISYM': 0, 'LDAU': True, 'LDAUJ': {'F': {'Ag': 0, 'Co': 0, 'Cr': 0, 'Cu': 0, 'Fe': 0, 'Mn': 0, 'Mo': 0, 'Nb': 0, 'Ni': 0, 'Re': 0, 'Ta': 0, 'V': 0, 'W': 0}, 'O': {'Ag': 0, 'Co': 0, 'Cr': 0, 'Cu': 0, 'Fe': 0, 'Mn': 0, 'Mo': 0, 'Nb': 0, 'Ni': 0, 'Re': 0, 'Ta': 0, 'V': 0, 'W': 0}, 'S': {'Fe': 0, 'Mn': 0}}, 'LDAUL': {'F': {'Ag': 2, 'Co': 2, 'Cr': 2, 'Cu': 2, 'Fe': 2, 'Mn': 2, 'Mo': 2, 'Nb': 2, 'Ni': 2, 'Re': 2, 'Ta': 2, 'V': 2, 'W': 2}, 'O': {'Ag': 2, 'Co': 2, 'Cr': 2, 'Cu': 2, 'Fe': 2, 'Mn': 2, 'Mo': 2, 'Nb': 2, 'Ni': 2, 'Re': 2, 'Ta': 2, 'V': 2, 'W': 2}, 'S': {'Fe': 2, 'Mn': 2.5}}, 'LDAUPRINT': 1, 'LDAUTYPE': 2, 'LDAUU': {'F': {'Ag': 1.5, 'Co': 3.4, 'Cr': 3.5, 'Cu': 4, 'Fe': 4.0, 'Mn': 3.9, 'Mo': 4.38, 'Nb': 1.5, 'Ni': 6, 'Re': 2, 'Ta': 2, 'V': 3.1, 'W': 4.0}, 'O': {'Ag': 1.5, 'Co': 3.4, 'Cr': 3.5, 'Cu': 4, 'Fe': 4.0, 'Mn': 3.9, 'Mo': 4.38, 'Nb': 1.5, 'Ni': 6, 'Re': 2, 'Ta': 2, 'V': 3.1, 'W': 4.0}, 'S': {'Fe': 1.9, 'Mn': 2.5}}, 'LORBIT': '11', 'LREAL': 'AUTO', 'LWAVE': False, 'MAGMOM': {'Ce': 5, 'Ce3+': 1, 'Co': 0.6, 'Co3+': 0.6, 'Co4+': 1, 'Cr': 5, 'Dy3+': 5, 'Er3+': 3, 'Eu': 10, 'Eu2+': 7, 'Eu3+': 6, 'Fe': 5, 'Gd3+': 7, 'Ho3+': 4, 'La3+': 0.6, 'Lu3+': 0.6, 'Mn': 5, 'Mn3+': 4, 'Mn4+': 3, 'Mo': 5, 'Nd3+': 3, 'Ni': 5, 'Pm3+': 4, 'Pr3+': 2, 'Sm3+': 5, 'Tb3+': 6, 'Tm3+': 2, 'V': 5, 'W': 5, 'Yb3+': 1}, 'NELM': 200, 'NELMIN': 6, 'NSW': 99, 'PREC': 'Accurate', 'SIGMA': 0.05}, 'KPOINTS': {'length': 25}, 'PARENT': 'VASPIncarBase', 'POTCAR': {'Ac': {'hash': 'd6854224d20e3de6e6fd7399503791d1', 'symbol': 'Ac'}, 'Ag': {'hash': 'e8ffa02fe3f3a51338ac1ac91ae968b9', 'symbol': 'Ag'}, 'Al': {'hash': 'a6fd9a46aec185f4ad2acd0cbe4ae2fa', 'symbol': 'Al'}, 'Ar': {'hash': 'e782fc6292623b396091bf8b871c272f', 'symbol': 'Ar'}, 'As': {'hash': '8005364db225a254e52cba350bedd032', 'symbol': 'As'}, 'Au': {'hash': 'a9182d436a13194b744640ac940ab9b0', 'symbol': 'Au'}, 'B': {'hash': '18ed2875dfa6305324cec3d7d59273ae', 'symbol': 'B'}, 'Ba': {'hash': 'c0477913afb63dfae3439f3534fbf0ed', 'symbol': 'Ba_sv'}, 'Be': {'hash': 'fb974e44d56a8c62c6bbd1a1eb70c3a7', 'symbol': 'Be'}, 'Bi': {'hash': 'e29661c79d59abae3b3ba69eae24b1a5', 'symbol': 'Bi'}, 'Br': {'hash': '40f9594b4506684a69158c8975cfb9d6', 'symbol': 'Br'}, 'C': {'hash': 'c0a8167dbb174fe492a3db7f5006c0f8', 'symbol': 'C'}, 'Ca': {'hash': 'eb006721e214c04b3c13146e81b3a27d', 'symbol': 'Ca_sv'}, 'Cd': {'hash': '0506b2d0ac28d5fe2b5ced77a701aa86', 'symbol': 'Cd'}, 'Ce': {'hash': 'ff3a09f2ff91798e58eb4b9854e9be4a', 'symbol': 'Ce'}, 'Cl': {'hash': '779b9901046c78fe51c5d80224642aeb', 'symbol': 'Cl'}, 'Co': {'hash': 'b169bca4e137294d2ab3df8cbdd09083', 'symbol': 'Co'}, 'Cr': {'hash': '82c14307937c7509fda4e9bc023d243d', 'symbol': 'Cr'}, 'Cs': {'hash': '096b53a7d80cc0086976bcda50d536e5', 'symbol': 'Cs_sv'}, 'Cu': {'hash': '8ca4e43a30de0c397e51f16bbb20d678', 'symbol': 'Cu'}, 'Dy': {'hash': 'd4a05220ab0a2d4c03a76872ea724a1e', 'symbol': 'Dy_3'}, 'Er': {'hash': 'daa65a04877317f8c3c593ddeaa8a132', 'symbol': 'Er_3'}, 'Eu': {'hash': 'd466d046adf21f6146ee9644049ea268', 'symbol': 'Eu'}, 'F': {'hash': '180141c33d032bfbfff30b3bea9d23dd', 'symbol': 'F'}, 'Fe': {'hash': '9530da8244e4dac17580869b4adab115', 'symbol': 'Fe'}, 'Ga': {'hash': '6e0b9d58412b1bfcd7252aff13d476c2', 'symbol': 'Ga'}, 'Gd': {'hash': '1f0d42b1e5f6769d319d3f247992aeb9', 'symbol': 'Gd'}, 'Ge': {'hash': '79e788788c31e196a460553010512d3f', 'symbol': 'Ge'}, 'H': {'hash': 'bb43c666e3d36577264afe07669e9582', 'symbol': 'H'}, 'He': {'hash': '47f9434aa3db96c85d7c4b3e4c2df09b', 'symbol': 'He'}, 'Hf': {'hash': 'b113f150cbf9c736f8244a6c25b0482e', 'symbol': 'Hf'}, 'Hg': {'hash': 'c2f15dfb5fd53396c5427635e5019160', 'symbol': 'Hg'}, 'Ho': {'hash': '661891464a27e87cf7e1324dd1893b77', 'symbol': 'Ho_3'}, 'I': {'hash': 'f4ff16a495dd361ff5824ee61b418bb0', 'symbol': 'I'}, 'In': {'hash': '7df38c0cdb4e6d9a9b93f09d690bb3ae', 'symbol': 'In'}, 'Ir': {'hash': 'dbcf7dcc6f4fb40df7b3d26904f60a66', 'symbol': 'Ir'}, 'K': {'hash': '3e84f86d37f203a4fb01de36af57e430', 'symbol': 'K_sv'}, 'Kr': {'hash': '39b9b85ae3982e6c012fb549b2840ce5', 'symbol': 'Kr'}, 'La': {'hash': '9b3ce03d18f7c0b40471a817ff91b287', 'symbol': 'La'}, 'Li': {'hash': '65e83282d1707ec078c1012afbd05be8', 'symbol': 'Li'}, 'Lu': {'hash': 'd40a90babf1224b88ffb4c3273ac3848', 'symbol': 'Lu_3'}, 'Mg': {'hash': '1771eb72adbbfa6310d66e7517e49930', 'symbol': 'Mg'}, 'Mn': {'hash': 'd082dba29b57ab59b3165e605dbf71b8', 'symbol': 'Mn'}, 'Mo': {'hash': '84e18fd84a98e3d7fa8f055952410df0', 'symbol': 'Mo_pv'}, 'N': {'hash': 'b98fd027ddebc67da4063ff2cabbc04b', 'symbol': 'N'}, 'Na': {'hash': '1a89e79f7e21d99e8cf5788979f6a987', 'symbol': 'Na'}, 'Nb': {'hash': '7bcee99a4dc3094be0f9fd7961c02966', 'symbol': 'Nb_pv'}, 'Nd': {'hash': '0c64e63070cee837c967283fffa001df', 'symbol': 'Nd'}, 'Ne': {'hash': '52064eee378b9e37a295a674f1c278f0', 'symbol': 'Ne'}, 'Ni': {'hash': '653f5772e68b2c7fd87ffd1086c0d710', 'symbol': 'Ni'}, 'Np': {'hash': '20cb30b714200c4db870550b288ac4cd', 'symbol': 'Np'}, 'O': {'hash': '7a25bc5b9a5393f46600a4939d357982', 'symbol': 'O'}, 'Os': {'hash': '35c2cb48d48a9c38c40fb82bbe70626d', 'symbol': 'Os'}, 'P': {'hash': '7dc3393307131ae67785a0cdacb61d5f', 'symbol': 'P'}, 'Pa': {'hash': 'a1fdb1089d0727f415416ec8082246ba', 'symbol': 'Pa'}, 'Pb': {'hash': '704c2c967247d7f84090d2536c91877d', 'symbol': 'Pb'}, 'Pd': {'hash': 'a395eb3aaf2fcab12fac3030a1146f61', 'symbol': 'Pd'}, 'Pm': {'hash': 'a2c9485ea86b2a7cf175077e6e5c7b3e', 'symbol': 'Pm'}, 'Pr': {'hash': '92f191499bf5346ea652bb806350ad87', 'symbol': 'Pr'}, 'Pt': {'hash': 'a604ea3c6a9cc23c739b762f625cf449', 'symbol': 'Pt'}, 'Pu': {'hash': 'f1d01e845dccc52d448679911f301a73', 'symbol': 'Pu'}, 'Rb': {'hash': 'e447c648d870b066b3514e6b800727ab', 'symbol': 'Rb_pv'}, 'Re': {'hash': '72385e193c92a8acfe17ea49004c2be1', 'symbol': 'Re'}, 'Rh': {'hash': '2c3dba3fcc6058ca1b1cfa75e45084bc', 'symbol': 'Rh'}, 'Ru': {'hash': '7925f4d4b68076d70af7cd86eef9ba8d', 'symbol': 'Ru_pv'}, 'S': {'hash': 'd368db6899d8839859bbee4811a42a88', 'symbol': 'S'}, 'Sb': {'hash': 'd82c022b02fc5344e85bd1909f9ee3e7', 'symbol': 'Sb'}, 'Sc': {'hash': 'dc386f505ad0c43385a7715b4111cb75', 'symbol': 'Sc_sv'}, 'Se': {'hash': '67a8804ede9f1112726e3d136978ef19', 'symbol': 'Se'}, 'Si': {'hash': 'b2b0ea6feb62e7cde209616683b8f7f5', 'symbol': 'Si'}, 'Sm': {'hash': 'e5e274e7cd99602ca81d146155abdf88', 'symbol': 'Sm_3'}, 'Sn': {'hash': '849b0795e148f93113a06be8fd5f5001', 'symbol': 'Sn_d'}, 'Sr': {'hash': 'ca6a5429c120a0ab705824386a76fe5b', 'symbol': 'Sr_sv'}, 'Ta': {'hash': 'd4e2cfe9338ef80da592d5bb9dc782c7', 'symbol': 'Ta'}, 'Tb': {'hash': '0790955c547003956c0fd4f080f7f508', 'symbol': 'Tb_3'}, 'Tc': {'hash': '9592642886319309a39d55c5717c6f48', 'symbol': 'Tc'}, 'Te': {'hash': '72719856e22fb1d3032df6f96d98a0f2', 'symbol': 'Te'}, 'Th': {'hash': 'aea79f322180fa6f0bfa74cb2a156dcf', 'symbol': 'Th'}, 'Ti': {'hash': 'c617e8b539c3f44a0ab6e8da2a92d318', 'symbol': 'Ti'}, 'Tl': {'hash': '2aa0d5406aaab7ebfbc761da382f1352', 'symbol': 'Tl'}, 'Tm': {'hash': '94a07cb7949b01305cb161da0cbfb492', 'symbol': 'Tm_3'}, 'U': {'hash': '72702eabbb1bc02b4167590dc848ed5d', 'symbol': 'U'}, 'V': {'hash': '7f1297a2e1d963e2a4d81b61f85e4ded', 'symbol': 'V_pv'}, 'W': {'hash': '2a33e0d5c700640535f60ac0a12177ab', 'symbol': 'W_pv'}, 'Xe': {'hash': '338472e581f58b41d37c002a5e22353b', 'symbol': 'Xe'}, 'Y': {'hash': '4ed187e77cd54f198bb88020278b143d', 'symbol': 'Y_sv'}, 'Yb': {'hash': '9f472bd422f640710f7d93e2d9ce89f4', 'symbol': 'Yb'}, 'Zn': {'hash': 'e35ee27f8483a63bb68dbc236a343af3', 'symbol': 'Zn'}, 'Zr': {'hash': 'd221d2c0bac4f8e81af2f5c42a314274', 'symbol': 'Zr'}}, 'POTCAR_FUNCTIONAL': 'PBE'}[source]
- property incar_updates: dict[str, Any][source]
Updates to the INCAR config for this calculation type.
- class MVLRelax52Set(structure: Structure | None = <property object>, config_dict: dict = <factory>, files_to_transfer: dict = <factory>, user_incar_settings: dict = <factory>, user_kpoints_settings: dict = <factory>, user_potcar_settings: dict = <factory>, constrain_total_magmom: bool = False, sort_structure: bool = True, user_potcar_functional: UserPotcarFunctional = 'PBE_52', force_gamma: bool = False, reduce_structure: Literal['niggli', 'LLL'] | None = None, vdw: str | None = None, use_structure_charge: bool = False, standardize: bool = False, sym_prec: float = 0.1, international_monoclinic: bool = True, validate_magmom: bool = True, inherit_incar: bool | list[str] = False, auto_kspacing: bool = False, auto_ismear: bool = False, auto_ispin: bool = False, auto_lreal: bool = False, auto_metal_kpoints: bool = False, bandgap_tol: float = 0.0001, bandgap: float | None = None, prev_incar: str | dict | None = None, prev_kpoints: str | Kpoints | None = None, _valid_potcars: Sequence[str] | None = ('PBE_52', 'PBE_54'))[source]
Bases:
VaspInputSetImplementation of VaspInputSet utilizing the public Materials Project parameters for INCAR & KPOINTS and VASP’s recommended PAW potentials for POTCAR.
- Keynotes from VASP manual:
Recommended potentials for calculations using VASP.5.2+
- If dimers with short bonds are present in the compound (O2, CO,
N2, F2, P2, S2, Cl2), it is recommended to use the h potentials. Specifically, C_h, O_h, N_h, F_h, P_h, S_h, Cl_h
- Released on Oct 28, 2018 by VASP. Please refer to VASP
Manual 1.2, 1.3 & 10.2.1 for more details.
- Parameters:
structure (Structure) – input structure.
user_potcar_functional (str) – choose from “PBE_52” and “PBE_54”.
**kwargs – Other kwargs supported by VaspInputSet.
- CONFIG = {'INCAR': {'ALGO': 'FAST', 'EDIFF_PER_ATOM': 5e-05, 'ENCUT': 520, 'IBRION': 2, 'ICHARG': 1, 'ISIF': 3, 'ISMEAR': -5, 'ISPIN': 2, 'LDAU': True, 'LDAUJ': {'F': {'Co': 0, 'Cr': 0, 'Fe': 0, 'Mn': 0, 'Mo': 0, 'Ni': 0, 'V': 0, 'W': 0}, 'O': {'Co': 0, 'Cr': 0, 'Fe': 0, 'Mn': 0, 'Mo': 0, 'Ni': 0, 'V': 0, 'W': 0}}, 'LDAUL': {'F': {'Co': 2, 'Cr': 2, 'Fe': 2, 'Mn': 2, 'Mo': 2, 'Ni': 2, 'V': 2, 'W': 2}, 'O': {'Co': 2, 'Cr': 2, 'Fe': 2, 'Mn': 2, 'Mo': 2, 'Ni': 2, 'V': 2, 'W': 2}}, 'LDAUPRINT': 1, 'LDAUTYPE': 2, 'LDAUU': {'F': {'Co': 3.32, 'Cr': 3.7, 'Fe': 5.3, 'Mn': 3.9, 'Mo': 4.38, 'Ni': 6.2, 'V': 3.25, 'W': 6.2}, 'O': {'Co': 3.32, 'Cr': 3.7, 'Fe': 5.3, 'Mn': 3.9, 'Mo': 4.38, 'Ni': 6.2, 'V': 3.25, 'W': 6.2}}, 'LORBIT': 11, 'LREAL': 'AUTO', 'LWAVE': False, 'NELM': 100, 'NSW': 99, 'PREC': 'Accurate', 'SIGMA': 0.05}, 'KPOINTS': {'reciprocal_density': 64}, 'POTCAR': {'Ac': 'Ac', 'Ag': 'Ag', 'Al': 'Al', 'Am': 'Am', 'Ar': 'Ar', 'As': 'As', 'At': 'At_d', 'Au': 'Au', 'B': 'B', 'Ba': 'Ba_sv', 'Be': 'Be', 'Bi': 'Bi_d', 'Br': 'Br', 'C': 'C', 'Ca': 'Ca_sv', 'Cd': 'Cd', 'Ce': 'Ce', 'Cl': 'Cl', 'Cm': 'Cm', 'Co': 'Co', 'Cr': 'Cr_pv', 'Cs': 'Cs_sv', 'Cu': 'Cu', 'Dy': 'Dy_3', 'Er': 'Er_3', 'Eu': 'Eu_2', 'F': 'F', 'Fe': 'Fe', 'Fr': 'Fr_sv', 'Ga': 'Ga_d', 'Gd': 'Gd_3', 'Ge': 'Ge_d', 'H': 'H', 'He': 'He', 'Hf': 'Hf_pv', 'Hg': 'Hg', 'Ho': 'Ho_3', 'I': 'I', 'In': 'In_d', 'Ir': 'Ir', 'K': 'K_sv', 'Kr': 'Kr', 'La': 'La', 'Li': 'Li_sv', 'Lu': 'Lu_3', 'Mg': 'Mg', 'Mn': 'Mn_pv', 'Mo': 'Mo_sv', 'N': 'N', 'Na': 'Na_pv', 'Nb': 'Nb_sv', 'Nd': 'Nd_3', 'Ne': 'Ne', 'Ni': 'Ni', 'Np': 'Np', 'O': 'O', 'Os': 'Os', 'P': 'P', 'Pa': 'Pa', 'Pb': 'Pb_d', 'Pd': 'Pd', 'Pm': 'Pm_3', 'Po': 'Po_d', 'Pr': 'Pr_3', 'Pt': 'Pt', 'Pu': 'Pu', 'Ra': 'Ra_sv', 'Rb': 'Rb_sv', 'Re': 'Re', 'Rh': 'Rh_pv', 'Rn': 'Rn', 'Ru': 'Ru_pv', 'S': 'S', 'Sb': 'Sb', 'Sc': 'Sc_sv', 'Se': 'Se', 'Si': 'Si', 'Sm': 'Sm_3', 'Sn': 'Sn_d', 'Sr': 'Sr_sv', 'Ta': 'Ta_pv', 'Tb': 'Tb_3', 'Tc': 'Tc_pv', 'Te': 'Te', 'Th': 'Th', 'Ti': 'Ti_sv', 'Tl': 'Tl_d', 'Tm': 'Tm_3', 'U': 'U', 'V': 'V_sv', 'W': 'W_pv', 'Xe': 'Xe', 'Y': 'Y_sv', 'Yb': 'Yb_2', 'Zn': 'Zn', 'Zr': 'Zr_sv'}, 'POTCAR_FUNCTIONAL': 'PBE_52'}[source]
- class MVLScanRelaxSet(structure: Structure | None = <property object>, config_dict: dict = <factory>, files_to_transfer: dict = <factory>, user_incar_settings: dict = <factory>, user_kpoints_settings: dict = <factory>, user_potcar_settings: dict = <factory>, constrain_total_magmom: bool = False, sort_structure: bool = True, user_potcar_functional: UserPotcarFunctional = 'PBE_52', force_gamma: bool = False, reduce_structure: Literal['niggli', 'LLL'] | None = None, vdw: str | None = None, use_structure_charge: bool = False, standardize: bool = False, sym_prec: float = 0.1, international_monoclinic: bool = True, validate_magmom: bool = True, inherit_incar: bool | list[str] = False, auto_kspacing: bool = False, auto_ismear: bool = False, auto_ispin: bool = False, auto_lreal: bool = False, auto_metal_kpoints: bool = False, bandgap_tol: float = 0.0001, bandgap: float | None = None, prev_incar: str | dict | None = None, prev_kpoints: str | Kpoints | None = None, _valid_potcars: Sequence[str] | None = ('PBE_52', 'PBE_54'))[source]
Bases:
VaspInputSetWrite a relax input set using Strongly Constrained and Appropriately Normed (SCAN) semilocal density functional.
Notes
This functional is only available from VASP.5.4.3 upwards.
2. Meta-GGA calculations require POTCAR files that include information on the kinetic energy density of the core-electrons, i.e. “PBE_52” or “PBE_54”. Make sure the POTCAR including the following lines (see VASP wiki for more details):
$ grep kinetic POTCAR kinetic energy-density mkinetic energy-density pseudized kinetic energy density (partial)
- Parameters:
structure (Structure) – input structure.
vdw (str) – set “rVV10” to enable SCAN+rVV10, which is a versatile van der Waals density functional by combing the SCAN functional with the rVV10 non-local correlation functional.
**kwargs – Other kwargs supported by VaspInputSet.
- CONFIG = {'INCAR': {'ALGO': 'FAST', 'EDIFF_PER_ATOM': 5e-05, 'ENCUT': 520, 'IBRION': 2, 'ISIF': 3, 'ISMEAR': -5, 'ISPIN': 2, 'LASPH': True, 'LDAU': True, 'LDAUJ': {'F': {'Co': 0, 'Cr': 0, 'Fe': 0, 'Mn': 0, 'Mo': 0, 'Ni': 0, 'V': 0, 'W': 0}, 'O': {'Co': 0, 'Cr': 0, 'Fe': 0, 'Mn': 0, 'Mo': 0, 'Ni': 0, 'V': 0, 'W': 0}}, 'LDAUL': {'F': {'Co': 2, 'Cr': 2, 'Fe': 2, 'Mn': 2, 'Mo': 2, 'Ni': 2, 'V': 2, 'W': 2}, 'O': {'Co': 2, 'Cr': 2, 'Fe': 2, 'Mn': 2, 'Mo': 2, 'Ni': 2, 'V': 2, 'W': 2}}, 'LDAUPRINT': 1, 'LDAUTYPE': 2, 'LDAUU': {'F': {'Co': 3.32, 'Cr': 3.7, 'Fe': 5.3, 'Mn': 3.9, 'Mo': 4.38, 'Ni': 6.2, 'V': 3.25, 'W': 6.2}, 'O': {'Co': 3.32, 'Cr': 3.7, 'Fe': 5.3, 'Mn': 3.9, 'Mo': 4.38, 'Ni': 6.2, 'V': 3.25, 'W': 6.2}}, 'LORBIT': 11, 'LREAL': 'AUTO', 'LWAVE': False, 'MAGMOM': {'Ce': 5, 'Ce3+': 1, 'Co': 0.6, 'Co3+': 0.6, 'Co4+': 1, 'Cr': 5, 'Dy3+': 5, 'Er3+': 3, 'Eu': 10, 'Eu2+': 7, 'Eu3+': 6, 'Fe': 5, 'Gd3+': 7, 'Ho3+': 4, 'La3+': 0.6, 'Lu3+': 0.6, 'Mn': 5, 'Mn3+': 4, 'Mn4+': 3, 'Mo': 5, 'Nd3+': 3, 'Ni': 5, 'Pm3+': 4, 'Pr3+': 2, 'Sm3+': 5, 'Tb3+': 6, 'Tm3+': 2, 'V': 5, 'W': 5, 'Yb3+': 1}, 'NELM': 100, 'NSW': 99, 'PREC': 'Accurate', 'SIGMA': 0.05}, 'KPOINTS': {'reciprocal_density': 64}, 'PARENT': 'VASPIncarBase', 'POTCAR': {'Ac': 'Ac', 'Ag': 'Ag', 'Al': 'Al', 'Ar': 'Ar', 'As': 'As', 'Au': 'Au', 'B': 'B', 'Ba': 'Ba_sv', 'Be': 'Be_sv', 'Bi': 'Bi', 'Br': 'Br', 'C': 'C', 'Ca': 'Ca_sv', 'Cd': 'Cd', 'Ce': 'Ce', 'Cl': 'Cl', 'Co': 'Co', 'Cr': 'Cr_pv', 'Cs': 'Cs_sv', 'Cu': 'Cu_pv', 'Dy': 'Dy_3', 'Er': 'Er_3', 'Eu': 'Eu', 'F': 'F', 'Fe': 'Fe_pv', 'Ga': 'Ga_d', 'Gd': 'Gd', 'Ge': 'Ge_d', 'H': 'H', 'He': 'He', 'Hf': 'Hf_pv', 'Hg': 'Hg', 'Ho': 'Ho_3', 'I': 'I', 'In': 'In_d', 'Ir': 'Ir', 'K': 'K_sv', 'Kr': 'Kr', 'La': 'La', 'Li': 'Li_sv', 'Lu': 'Lu_3', 'Mg': 'Mg_pv', 'Mn': 'Mn_pv', 'Mo': 'Mo_pv', 'N': 'N', 'Na': 'Na_pv', 'Nb': 'Nb_pv', 'Nd': 'Nd_3', 'Ne': 'Ne', 'Ni': 'Ni_pv', 'Np': 'Np', 'O': 'O', 'Os': 'Os_pv', 'P': 'P', 'Pa': 'Pa', 'Pb': 'Pb_d', 'Pd': 'Pd', 'Pm': 'Pm_3', 'Pr': 'Pr_3', 'Pt': 'Pt', 'Pu': 'Pu', 'Rb': 'Rb_sv', 'Re': 'Re_pv', 'Rh': 'Rh_pv', 'Ru': 'Ru_pv', 'S': 'S', 'Sb': 'Sb', 'Sc': 'Sc_sv', 'Se': 'Se', 'Si': 'Si', 'Sm': 'Sm_3', 'Sn': 'Sn_d', 'Sr': 'Sr_sv', 'Ta': 'Ta_pv', 'Tb': 'Tb_3', 'Tc': 'Tc_pv', 'Te': 'Te', 'Th': 'Th', 'Ti': 'Ti_pv', 'Tl': 'Tl_d', 'Tm': 'Tm_3', 'U': 'U', 'V': 'V_pv', 'W': 'W_pv', 'Xe': 'Xe', 'Y': 'Y_sv', 'Yb': 'Yb_2', 'Zn': 'Zn', 'Zr': 'Zr_sv'}, 'POTCAR_FUNCTIONAL': 'PBE'}[source]
- class MVLSlabSet(structure: Structure | None = <property object>, config_dict: dict = <factory>, files_to_transfer: dict = <factory>, user_incar_settings: dict = <factory>, user_kpoints_settings: dict = <factory>, user_potcar_settings: dict = <factory>, constrain_total_magmom: bool = False, sort_structure: bool = True, user_potcar_functional: UserPotcarFunctional = None, force_gamma: bool = False, reduce_structure: Literal['niggli', 'LLL'] | None = None, vdw: str | None = None, use_structure_charge: bool = False, standardize: bool = False, sym_prec: float = 0.1, international_monoclinic: bool = True, validate_magmom: bool = True, inherit_incar: bool | list[str] = False, auto_kspacing: bool = False, auto_ismear: bool = False, auto_ispin: bool = False, auto_lreal: bool = False, auto_metal_kpoints: bool = False, bandgap_tol: float = 0.0001, bandgap: float | None = None, prev_incar: str | dict | None = None, prev_kpoints: str | Kpoints | None = None, _valid_potcars: Sequence[str] | None = None, k_product: int = 50, bulk: bool = False, auto_dipole: bool = False, set_mix: bool = True)[source]
Bases:
VaspInputSetWrite a set of slab VASP runs, including both slabs (along the c direction) and orient unit cells (bulk), to ensure the same KPOINTS, POTCAR and INCAR criterion.
- Parameters:
structure – Structure
k_product – default to 50, kpoint number * length for a & b directions, also for c direction in bulk calculations
bulk
auto_dipole
set_mix
sort_structure
**kwargs – Other kwargs supported by VaspInputSet.
- CONFIG = {'INCAR': {'ALGO': 'FAST', 'EDIFF_PER_ATOM': 5e-05, 'ENCUT': 520, 'IBRION': 2, 'ISIF': 3, 'ISMEAR': -5, 'ISPIN': 2, 'LASPH': True, 'LDAU': True, 'LDAUJ': {'F': {'Co': 0, 'Cr': 0, 'Fe': 0, 'Mn': 0, 'Mo': 0, 'Ni': 0, 'V': 0, 'W': 0}, 'O': {'Co': 0, 'Cr': 0, 'Fe': 0, 'Mn': 0, 'Mo': 0, 'Ni': 0, 'V': 0, 'W': 0}}, 'LDAUL': {'F': {'Co': 2, 'Cr': 2, 'Fe': 2, 'Mn': 2, 'Mo': 2, 'Ni': 2, 'V': 2, 'W': 2}, 'O': {'Co': 2, 'Cr': 2, 'Fe': 2, 'Mn': 2, 'Mo': 2, 'Ni': 2, 'V': 2, 'W': 2}}, 'LDAUPRINT': 1, 'LDAUTYPE': 2, 'LDAUU': {'F': {'Co': 3.32, 'Cr': 3.7, 'Fe': 5.3, 'Mn': 3.9, 'Mo': 4.38, 'Ni': 6.2, 'V': 3.25, 'W': 6.2}, 'O': {'Co': 3.32, 'Cr': 3.7, 'Fe': 5.3, 'Mn': 3.9, 'Mo': 4.38, 'Ni': 6.2, 'V': 3.25, 'W': 6.2}}, 'LORBIT': 11, 'LREAL': 'AUTO', 'LWAVE': False, 'MAGMOM': {'Ce': 5, 'Ce3+': 1, 'Co': 0.6, 'Co3+': 0.6, 'Co4+': 1, 'Cr': 5, 'Dy3+': 5, 'Er3+': 3, 'Eu': 10, 'Eu2+': 7, 'Eu3+': 6, 'Fe': 5, 'Gd3+': 7, 'Ho3+': 4, 'La3+': 0.6, 'Lu3+': 0.6, 'Mn': 5, 'Mn3+': 4, 'Mn4+': 3, 'Mo': 5, 'Nd3+': 3, 'Ni': 5, 'Pm3+': 4, 'Pr3+': 2, 'Sm3+': 5, 'Tb3+': 6, 'Tm3+': 2, 'V': 5, 'W': 5, 'Yb3+': 1}, 'NELM': 100, 'NSW': 99, 'PREC': 'Accurate', 'SIGMA': 0.05}, 'KPOINTS': {'reciprocal_density': 64}, 'PARENT': 'VASPIncarBase', 'POTCAR': {'Ac': 'Ac', 'Ag': 'Ag', 'Al': 'Al', 'Ar': 'Ar', 'As': 'As', 'Au': 'Au', 'B': 'B', 'Ba': 'Ba_sv', 'Be': 'Be_sv', 'Bi': 'Bi', 'Br': 'Br', 'C': 'C', 'Ca': 'Ca_sv', 'Cd': 'Cd', 'Ce': 'Ce', 'Cl': 'Cl', 'Co': 'Co', 'Cr': 'Cr_pv', 'Cs': 'Cs_sv', 'Cu': 'Cu_pv', 'Dy': 'Dy_3', 'Er': 'Er_3', 'Eu': 'Eu', 'F': 'F', 'Fe': 'Fe_pv', 'Ga': 'Ga_d', 'Gd': 'Gd', 'Ge': 'Ge_d', 'H': 'H', 'He': 'He', 'Hf': 'Hf_pv', 'Hg': 'Hg', 'Ho': 'Ho_3', 'I': 'I', 'In': 'In_d', 'Ir': 'Ir', 'K': 'K_sv', 'Kr': 'Kr', 'La': 'La', 'Li': 'Li_sv', 'Lu': 'Lu_3', 'Mg': 'Mg_pv', 'Mn': 'Mn_pv', 'Mo': 'Mo_pv', 'N': 'N', 'Na': 'Na_pv', 'Nb': 'Nb_pv', 'Nd': 'Nd_3', 'Ne': 'Ne', 'Ni': 'Ni_pv', 'Np': 'Np', 'O': 'O', 'Os': 'Os_pv', 'P': 'P', 'Pa': 'Pa', 'Pb': 'Pb_d', 'Pd': 'Pd', 'Pm': 'Pm_3', 'Pr': 'Pr_3', 'Pt': 'Pt', 'Pu': 'Pu', 'Rb': 'Rb_sv', 'Re': 'Re_pv', 'Rh': 'Rh_pv', 'Ru': 'Ru_pv', 'S': 'S', 'Sb': 'Sb', 'Sc': 'Sc_sv', 'Se': 'Se', 'Si': 'Si', 'Sm': 'Sm_3', 'Sn': 'Sn_d', 'Sr': 'Sr_sv', 'Ta': 'Ta_pv', 'Tb': 'Tb_3', 'Tc': 'Tc_pv', 'Te': 'Te', 'Th': 'Th', 'Ti': 'Ti_pv', 'Tl': 'Tl_d', 'Tm': 'Tm_3', 'U': 'U', 'V': 'V_pv', 'W': 'W_pv', 'Xe': 'Xe', 'Y': 'Y_sv', 'Yb': 'Yb_2', 'Zn': 'Zn', 'Zr': 'Zr_sv'}, 'POTCAR_FUNCTIONAL': 'PBE'}[source]
- as_dict(verbosity: int = 2) dict[str, Any][source]
- Parameters:
verbosity (int) – Verbosity of dict. e.g. whether to include Structure.
- Returns:
MSONable MVLGBSet representation.
- Return type:
dict
- property incar_updates: dict[str, Any][source]
Updates to the INCAR config for this calculation type.
- class MatPESStaticSet(structure: Structure | None = <property object>, config_dict: dict = <factory>, files_to_transfer: dict = <factory>, user_incar_settings: dict = <factory>, user_kpoints_settings: dict = <factory>, user_potcar_settings: dict = <factory>, constrain_total_magmom: bool = False, sort_structure: bool = True, user_potcar_functional: UserPotcarFunctional = None, force_gamma: bool = False, reduce_structure: Literal['niggli', 'LLL'] | None = None, vdw: str | None = None, use_structure_charge: bool = False, standardize: bool = False, sym_prec: float = 0.1, international_monoclinic: bool = True, validate_magmom: bool = True, inherit_incar: tuple[str, ...] | bool = ('LPEAD', 'NGX', 'NGY', 'NGZ', 'SYMPREC', 'IMIX', 'LMAXMIX', 'KGAMMA', 'ISYM', 'NCORE', 'NPAR', 'NELMIN', 'IOPT', 'NBANDS', 'KPAR', 'AMIN', 'NELMDL', 'BMIX', 'AMIX_MAG', 'BMIX_MAG'), auto_kspacing: bool = False, auto_ismear: bool = False, auto_ispin: bool = False, auto_lreal: bool = False, auto_metal_kpoints: bool = False, bandgap_tol: float = 0.0001, bandgap: float | None = None, prev_incar: dict | str | None = None, prev_kpoints: str | Kpoints | None = None, _valid_potcars: Sequence[str] | None = None, xc_functional: Literal['R2SCAN', 'PBE', 'PBE+U'] = 'PBE')[source]
Bases:
VaspInputSetCreate input files for a MatPES static calculation.
The goal of MatPES is to generate potential energy surface data. This is a distinctly different from the objectives of the MP static calculations, which aims to obtain primarily accurate energies and also electronic structure (DOS). For PES data, force accuracy (and to some extent, stress accuracy) is of paramount importance.
The default POTCAR versions have been updated to PBE_54 from the old PBE set used in the MPStaticSet. However, U values are still based on PBE. The implicit assumption here is that the PBE_54 and PBE POTCARs are sufficiently similar that the U values fitted to the old PBE functional still applies.
- Parameters:
structure (Structure) – The Structure to create inputs for. If None, the input set is initialized without a Structure but one must be set separately before the inputs are generated.
xc_functional ('R2SCAN'|'PBE') – Exchange-correlation functional to use. Defaults to ‘PBE’.
**kwargs – Keywords supported by VaspInputSet.
- CONFIG = {'INCAR': {'ALGO': 'Normal', 'EDIFF': 1e-05, 'ENAUG': 1360, 'ENCUT': 680, 'GGA': 'PE', 'ISMEAR': 0, 'ISPIN': 2, 'KSPACING': 0.22, 'LAECHG': True, 'LASPH': True, 'LCHARG': True, 'LDAU': False, 'LDAUJ': {'F': {'Co': 0, 'Cr': 0, 'Fe': 0, 'Mn': 0, 'Mo': 0, 'Ni': 0, 'V': 0, 'W': 0}, 'O': {'Co': 0, 'Cr': 0, 'Fe': 0, 'Mn': 0, 'Mo': 0, 'Ni': 0, 'V': 0, 'W': 0}}, 'LDAUL': {'F': {'Co': 2, 'Cr': 2, 'Fe': 2, 'Mn': 2, 'Mo': 2, 'Ni': 2, 'V': 2, 'W': 2}, 'O': {'Co': 2, 'Cr': 2, 'Fe': 2, 'Mn': 2, 'Mo': 2, 'Ni': 2, 'V': 2, 'W': 2}}, 'LDAUTYPE': 2, 'LDAUU': {'F': {'Co': 3.32, 'Cr': 3.7, 'Fe': 5.3, 'Mn': 3.9, 'Mo': 4.38, 'Ni': 6.2, 'V': 3.25, 'W': 6.2}, 'O': {'Co': 3.32, 'Cr': 3.7, 'Fe': 5.3, 'Mn': 3.9, 'Mo': 4.38, 'Ni': 6.2, 'V': 3.25, 'W': 6.2}}, 'LMAXMIX': 6, 'LMIXTAU': True, 'LORBIT': 11, 'LREAL': False, 'LWAVE': False, 'MAGMOM': {'Ce': 5, 'Ce3+': 1, 'Co': 0.6, 'Co3+': 0.6, 'Co4+': 1, 'Cr': 5, 'Dy3+': 5, 'Er3+': 3, 'Eu': 10, 'Eu2+': 7, 'Eu3+': 6, 'Fe': 5, 'Gd3+': 7, 'Ho3+': 4, 'La3+': 0.6, 'Lu3+': 0.6, 'Mn': 5, 'Mn3+': 4, 'Mn4+': 3, 'Mo': 5, 'Nd3+': 3, 'Ni': 5, 'Pm3+': 4, 'Pr3+': 2, 'Sm3+': 5, 'Tb3+': 6, 'Tm3+': 2, 'V': 5, 'W': 5, 'Yb3+': 1}, 'NELM': 200, 'NSW': 0, 'PREC': 'Accurate', 'SIGMA': 0.05}, 'PARENT': 'PBE64Base', 'POTCAR': {'Ac': 'Ac', 'Ag': 'Ag', 'Al': 'Al', 'Am': 'Am', 'Ar': 'Ar', 'As': 'As', 'At': 'At', 'Au': 'Au', 'B': 'B', 'Ba': 'Ba_sv', 'Be': 'Be_sv', 'Bi': 'Bi', 'Br': 'Br', 'C': 'C', 'Ca': 'Ca_sv', 'Cd': 'Cd', 'Ce': 'Ce', 'Cf': 'Cf', 'Cl': 'Cl', 'Cm': 'Cm', 'Co': 'Co', 'Cr': 'Cr_pv', 'Cs': 'Cs_sv', 'Cu': 'Cu_pv', 'Dy': 'Dy_3', 'Er': 'Er_3', 'Eu': 'Eu', 'F': 'F', 'Fe': 'Fe_pv', 'Fr': 'Fr_sv', 'Ga': 'Ga_d', 'Gd': 'Gd', 'Ge': 'Ge_d', 'H': 'H', 'He': 'He', 'Hf': 'Hf_pv', 'Hg': 'Hg', 'Ho': 'Ho_3', 'I': 'I', 'In': 'In_d', 'Ir': 'Ir', 'K': 'K_sv', 'Kr': 'Kr', 'La': 'La', 'Li': 'Li_sv', 'Lu': 'Lu_3', 'Mg': 'Mg_pv', 'Mn': 'Mn_pv', 'Mo': 'Mo_pv', 'N': 'N', 'Na': 'Na_pv', 'Nb': 'Nb_pv', 'Nd': 'Nd_3', 'Ne': 'Ne', 'Ni': 'Ni_pv', 'Np': 'Np', 'O': 'O', 'Os': 'Os_pv', 'P': 'P', 'Pa': 'Pa', 'Pb': 'Pb_d', 'Pd': 'Pd', 'Pm': 'Pm_3', 'Po': 'Po_d', 'Pr': 'Pr_3', 'Pt': 'Pt', 'Pu': 'Pu', 'Ra': 'Ra_sv', 'Rb': 'Rb_sv', 'Re': 'Re_pv', 'Rh': 'Rh_pv', 'Rn': 'Rn', 'Ru': 'Ru_pv', 'S': 'S', 'Sb': 'Sb', 'Sc': 'Sc_sv', 'Se': 'Se', 'Si': 'Si', 'Sm': 'Sm_3', 'Sn': 'Sn_d', 'Sr': 'Sr_sv', 'Ta': 'Ta_pv', 'Tb': 'Tb_3', 'Tc': 'Tc_pv', 'Te': 'Te', 'Th': 'Th', 'Ti': 'Ti_pv', 'Tl': 'Tl_d', 'Tm': 'Tm_3', 'U': 'U', 'V': 'V_pv', 'W': 'W_sv', 'Xe': 'Xe', 'Y': 'Y_sv', 'Yb': 'Yb_3', 'Zn': 'Zn', 'Zr': 'Zr_sv'}, 'POTCAR_FUNCTIONAL': 'PBE_64'}[source]
- VaspInputGenerator[source]
alias of
VaspInputSet
- class VaspInputSet(structure: Structure | None = <property object>, config_dict: dict = <factory>, files_to_transfer: dict = <factory>, user_incar_settings: dict = <factory>, user_kpoints_settings: dict = <factory>, user_potcar_settings: dict = <factory>, constrain_total_magmom: bool = False, sort_structure: bool = True, user_potcar_functional: UserPotcarFunctional = None, force_gamma: bool = False, reduce_structure: Literal['niggli', 'LLL'] | None = None, vdw: str | None = None, use_structure_charge: bool = False, standardize: bool = False, sym_prec: float = 0.1, international_monoclinic: bool = True, validate_magmom: bool = True, inherit_incar: bool | list[str] = False, auto_kspacing: bool = False, auto_ismear: bool = False, auto_ispin: bool = False, auto_lreal: bool = False, auto_metal_kpoints: bool = False, bandgap_tol: float = 0.0001, bandgap: float | None = None, prev_incar: str | dict | None = None, prev_kpoints: str | Kpoints | None = None, _valid_potcars: Sequence[str] | None = None)[source]
Bases:
InputGenerator,ABCBase class representing a set of VASP input parameters with a structure supplied as init parameters and initialized from a dict of settings. This allows arbitrary settings to be input. In general, this is rarely used directly unless there is a source of settings in yaml format (e.g., from a REST interface). It is typically used by other VaspInputSets for initialization.
Special consideration should be paid to the way the MAGMOM initialization for the INCAR is done. The initialization differs depending on the type of structure and the configuration settings. The order in which the magmom is determined is as follows:
If the site is specified in user_incar_settings, use that setting.
- If the site itself has a magmom setting (i.e. site.properties[“magmom”] = float),
that is used. This can be set with structure.add_site_property().
- If the species of the site has a spin setting, that is used. This can be set
with structure.add_spin_by_element().
If the species itself has a particular setting in the config file, that is used, e.g. Mn3+ may have a different magmom than Mn4+.
Lastly, the element symbol itself is checked in the config file. If there are no settings, a default value of 0.6 is used.
- Parameters:
structure (Structure) – The Structure to create inputs for. If None, the input set is initialized without a Structure but one must be set separately before the inputs are generated.
config_dict (dict) – The config dictionary to use.
files_to_transfer (dict) – A dictionary of {filename: filepath}. This allows the transfer of files from a previous calculation.
user_incar_settings (dict) – User INCAR settings. This allows a user to override INCAR settings, e.g. setting a different MAGMOM for various elements or species. Note that in the new scheme, ediff_per_atom and hubbard_u are no longer args. Instead, the CONFIG supports EDIFF_PER_ATOM and EDIFF keys. The former scales with # of atoms, the latter does not. If both are present, EDIFF is preferred. To force such settings, just supply user_incar_settings={“EDIFF”: 1e-5, “LDAU”: False} for example. The keys ‘LDAUU’, ‘LDAUJ’, ‘LDAUL’ are special cases since pymatgen defines different values depending on what anions are present in the structure, so these keys can be defined in one of two ways, e.g. either {“LDAUU”:{“O”:{“Fe”:5}}} to set LDAUU for Fe to 5 in an oxide, or {“LDAUU”:{“Fe”:5}} to set LDAUU to 5 regardless of the input structure. If a None value is given, that key is unset. For example, {“ENCUT”: None} will remove ENCUT from the incar settings. Finally, KSPACING is a special setting and can be set to “auto” in which the KSPACING is set automatically based on the band gap.
user_kpoints_settings (dict or Kpoints) – Allow user to override kpoints setting by supplying a dict. e.g. {“reciprocal_density”: 1000}. User can also supply Kpoints object.
user_potcar_settings (dict) – Allow user to override POTCARs. e.g. {“Gd”: “Gd_3”}. This is generally not recommended.
constrain_total_magmom (bool) – Whether to constrain the total magmom (NUPDOWN in INCAR) to be the sum of the expected MAGMOM for all species.
sort_structure (bool) – Whether to sort the structure (using the default sort order of electronegativity) before generating input files. Defaults to True, the behavior you would want most of the time. This ensures that similar atomic species are grouped together.
user_potcar_functional (str) – Functional to use. Default (None) is to use the functional in the config dictionary. Valid values: “PBE”, “PBE_52”, “PBE_54”, “LDA”, “LDA_52”, “LDA_54”, “PW91”, “LDA_US”, “PW91_US”.
force_gamma (bool) – Force gamma centered kpoint generation. Default (False) is to use the Automatic Density kpoint scheme, which will use the Gamma centered generation scheme for hexagonal cells, and Monkhorst-Pack otherwise.
reduce_structure (None/str) – Before generating the input files, generate the reduced structure. Default (None), does not alter the structure. Valid values: None, “niggli”, “LLL”.
vdw – Adds default parameters for van-der-Waals functionals supported by VASP to INCAR. Supported functionals are: DFT-D2, undamped DFT-D3, DFT-D3 with Becke-Jonson damping, Tkatchenko-Scheffler, Tkatchenko-Scheffler with iterative Hirshfeld partitioning, MBD@rSC, dDsC, Dion’s vdW-DF, DF2, optPBE, optB88, optB86b and rVV10.
use_structure_charge (bool) – If set to True, then the overall charge of the structure (structure.charge) is used to set the NELECT variable in the INCAR. Default is False.
standardize (float) – Whether to standardize to a primitive standard cell. Defaults to False.
sym_prec (float) – Tolerance for symmetry finding.
international_monoclinic (bool) – Whether to use international convention (vs Curtarolo) for monoclinic. Defaults True.
validate_magmom (bool) – Ensure that the missing magmom values are filled in with the VASP default value of 1.0.
inherit_incar (bool) – Whether to inherit INCAR settings from previous calculation. This might be useful to port Custodian fixes to child jobs but can also be dangerous e.g. when switching from GGA to meta-GGA or relax to static jobs. Defaults to True.
auto_kspacing (bool) – If true, determines the value of KSPACING from the bandgap of a previous calculation.
auto_ismear (bool) – If true, the values for ISMEAR and SIGMA will be set automatically depending on the bandgap of the system. If the bandgap is not known (e.g., there is no previous VASP directory) then ISMEAR=0 and SIGMA=0.2; if the bandgap is zero (a metallic system) then ISMEAR=2 and SIGMA=0.2; if the system is an insulator, then ISMEAR=-5 (tetrahedron smearing). Note, this only works when generating the input set from a previous VASP directory.
auto_ispin (bool) – If generating input set from a previous calculation, this controls whether to disable magnetisation (ISPIN = 1) if the absolute value of all magnetic moments are less than 0.02.
auto_lreal (bool) – If True, automatically use the VASP recommended LREAL based on cell size.
auto_metal_kpoints – If true and the system is metallic, try and use
reciprocal_density_metalinstead ofreciprocal_densityfor metallic systems. Note, this only works if the bandgap is not None.bandgap_tol (float) – Tolerance for determining if a system is metallic when KSPACING is set to “auto”. If the bandgap is less than this value, the system is considered metallic. Defaults to 1e-4 (eV).
bandgap (float) – Used for determining KSPACING if KSPACING == “auto” or ISMEAR if auto_ismear == True. Set automatically when using from_prev_calc.
prev_incar (str or dict) – Previous INCAR used for setting parent INCAR when inherit_incar == True. Set automatically when using from_prev_calc.
prev_kpoints (str or Kpoints) – Previous Kpoints. Set automatically when using from_prev_calc.
- as_dict(verbosity: int = 2) dict[source]
- Parameters:
verbosity – Verbosity for generated dict. If 1, structure is
excluded.
- Returns:
MSONable VaspInputSet representation.
- Return type:
dict
- calculate_ng(max_prime_factor: int = 7, must_inc_2: bool = True, custom_encut: float | None = None, custom_prec: str | None = None) tuple[source]
Calculate the NGX, NGY, and NGZ values using the information available in the INCAR and POTCAR This is meant to help with making initial guess for the FFT grid so we can interact with the Charge density API.
- Parameters:
max_prime_factor (int) – the valid prime factors of the grid size in each direction VASP has many different setting for this to handle many compiling options. For typical MPI options all prime factors up to 7 are allowed
must_inc_2 (bool) – Whether 2 must be a prime factor of the result. Defaults to True.
custom_encut (float | None) – Calculates the FFT grid parameters using a custom ENCUT that may be different from what is generated by the input set. Defaults to None. Do not use this unless you know what you are doing.
custom_prec (str | None) – Calculates the FFT grid parameters using a custom prec that may be different from what is generated by the input set. Defaults to None. Do not use this unless you know what you are doing.
- estimate_nbands() int[source]
Estimate the number of bands that VASP will initialize a calculation with by default. Note that in practice this can depend on # of cores (if not set explicitly).
Note that this formula is slightly different than the formula on the VASP wiki (as of July 2023). This is because the formula in the source code (main.F) is slightly different than what is on the wiki.
- static from_directory(directory: PathLike, optional_files: dict | None = None) VaspInput[source]
Load a set of VASP inputs from a directory.
Note that only the standard INCAR, POSCAR, POTCAR and KPOINTS files are read unless optional_filenames is specified.
- Parameters:
directory – Directory to read VASP inputs from.
optional_files – Optional files to read in as well as a dict of {filename: Object class}. Object class must have a static/class method from_file.
- classmethod from_prev_calc(prev_calc_dir: PathLike, **kwargs) Self[source]
Generate a set of VASP input files for static calculations from a directory of previous VASP run.
- Parameters:
prev_calc_dir (PathLike) – Directory containing the outputs( vasprun.xml and OUTCAR) of previous VASP run.
**kwargs – All kwargs supported by MPStaticSet, other than prev_incar and prev_structure and prev_kpoints which are determined from the prev_calc_dir.
- get_input_set(structure: Structure | None = None, prev_dir: PathLike | None = None, potcar_spec: bool = False) VaspInput[source]
Get a VASP input set.
Note, if both
structureandprev_dirare set, then the structure specified will be preferred over the final structure from the last VASP run.- Parameters:
structure (Structure) – A structure.
prev_dir (PathLike) – A previous directory to generate the input set from.
potcar_spec (bool) – Instead of generating a Potcar object, use a list of potcar symbols. This will be written as a “POTCAR.spec” file. This is intended to help sharing an input set with people who might not have a license to specific Potcar files. Given a “POTCAR.spec”, the specific POTCAR file can be re-generated using pymatgen with the “generate_potcar” function in the pymatgen CLI.
- Returns:
A VASP input object.
- Return type:
- property kpoints_updates: dict[source]
Updates to the kpoints configuration for this calculation type.
Note, these updates will be ignored if the user has set user_kpoint_settings.
- Returns:
- A dictionary of updates to apply to the KPOINTS config
or a Kpoints object.
- Return type:
dict or Kpoints
- override_from_prev_calc(prev_calc_dir: PathLike = '.') Self[source]
Update the input set to include settings from a previous calculation.
- Parameters:
prev_calc_dir (PathLike) – The path to the previous calculation directory.
- Returns:
- A new input set with settings (Structure, k-points, incar, etc)
updated using the previous VASP run.
- Return type:
- property potcar_functional: UserPotcarFunctional[source]
The functional used for POTCAR generation.
- write_input(output_dir: str, make_dir_if_not_present: bool = True, include_cif: bool | str = False, potcar_spec: bool = False, zip_output: bool | str = False) None[source]
Write a set of VASP input to a directory.
- Parameters:
output_dir (str) – Directory to output the VASP input files
make_dir_if_not_present (bool) – Set to True if you want the directory (and the whole path) to be created if it is not present.
include_cif (bool) – Whether to write a CIF file in the output directory for easier opening by VESTA.
potcar_spec (bool) – Instead of writing the POTCAR, write a “POTCAR.spec”. This is intended to help sharing an input set with people who might not have a license to specific Potcar files. Given a “POTCAR.spec”, the specific POTCAR file can be re-generated using pymatgen with the “generate_potcar” function in the pymatgen CLI.
zip_output (bool) – If True, output will be zipped into a file with the same name as the InputSet (e.g., MPStaticSet.zip).
- auto_kspacing(bandgap: float | None, bandgap_tol: float) float[source]
Set kspacing based on the bandgap
- batch_write_input(structures: Sequence[Structure], vasp_input_set=<class 'pymatgen.io.vasp.sets.MPRelaxSet'>, output_dir: PathLike = '.', make_dir_if_not_present: bool = True, subfolder: Callable | None = None, sanitize: bool = False, include_cif: bool = False, potcar_spec: bool = False, zip_output: bool = False, **kwargs)[source]
Batch write VASP input for a sequence of structures to output_dir, following the format output_dir/{group}/{formula}_{number}.
- Parameters:
structures ([Structure]) – Sequence of Structures.
vasp_input_set (VaspInputSet) – VaspInputSet class that creates VASP input files from structures. Note that a class should be supplied. Defaults to MPRelaxSet.
output_dir (str) – Directory to output files. Defaults to current directory “.”.
make_dir_if_not_present (bool) – Create the directory if not present. Defaults to True.
subfolder (callable) – Function to create subdirectory name from structure. Defaults to simply “formula_count”.
sanitize (bool) – Boolean indicating whether to sanitize the structure before writing the VASP input files. Sanitized output are generally easier for viewing and certain forms of analysis. Defaults to False.
include_cif (bool) – Whether to output a CIF as well. CIF files are generally better supported in visualization programs.
potcar_spec (bool) – Instead of writing the POTCAR, write a “POTCAR.spec”. This is intended to help sharing an input set with people who might not have a license to specific Potcar files. Given a “POTCAR.spec”, the specific POTCAR file can be re-generated using pymatgen with the “generate_potcar” function in the pymatgen CLI.
zip_output (bool) – If True, output will be zipped into a file with the same name as the InputSet (e.g., MPStaticSet.zip)
**kwargs – Additional kwargs are passed to the vasp_input_set class in addition to structure.
- get_structure_from_prev_run(vasprun: Vasprun, outcar: Outcar | None = None) Structure[source]
Process structure from previous run.
- get_valid_magmom_struct(structure: Structure, inplace: bool = True, spin_mode: str = 'auto') Structure[source]
Make sure that the structure has valid magmoms based on the kind of calculation.
Fill in missing Magmom values.
- Parameters:
structure – The input structure
inplace – True: edit magmoms of the input structure; False: return new structure
spin_mode –
“scalar”/”vector”/”none”/”auto” only first letter (s/v/n) is needed. dictates how the spin configuration will be determined.
auto: read the existing magmom values and decide
scalar: use a single scalar value (for spin up/down)
vector: use a vector value for spin-orbit systems
none: Remove all the magmom information
- Returns:
New structure if inplace is False
- get_vasprun_outcar(path: PathLike, parse_dos: bool = True, parse_eigen: bool = True) tuple[Vasprun, Outcar][source]
Get a Vasprun and Outcar from a directory.
- Parameters:
path – Path to get the vasprun.xml and OUTCAR.
parse_dos – Whether to parse dos. Defaults to True.
parse_eigen – Whether to parse eigenvalue. Defaults to True.
- Returns:
Vasprun and Outcar files.
- next_num_with_prime_factors(n: int, max_prime_factor: int, must_inc_2: bool = True) int[source]
Get the next number greater than or equal to n that only has the desired prime factors.
- Parameters:
n (int) – Initial guess at the grid density
max_prime_factor (int) – the maximum prime factor
must_inc_2 (bool) – 2 must be a prime factor of the result
- Returns:
first product of the prime_factors that is >= n
- Return type:
int
- primes_less_than(max_val: int) list[int][source]
Get the primes less than or equal to the max value.
- standardize_structure(structure: Structure, sym_prec: float = 0.1, international_monoclinic: bool = True) Structure[source]
Get the symmetrically standardized structure.
- Parameters:
structure (Structure) – The structure.
sym_prec (float) – Tolerance for symmetry finding for standardization.
international_monoclinic (bool) – Whether to use international convention (vs Curtarolo) for monoclinic. Defaults True.
- Returns:
The symmetrized structure.