pymatgen.io.cp2k package
Module for CP2K input/output parsing as well as sets for standard calculations.
Submodules
pymatgen.io.cp2k.inputs module
This module defines the building blocks of a CP2K input file. The CP2K input structure is essentially a collection of “sections” which are similar to dictionary objects that activate modules of the CP2K executable, and then “keywords” which adjust variables inside of those modules. For example, FORCE_EVAL section will activate CP2K’s ability to calculate forces, and inside FORCE_EVAL, the Keyword “METHOD can be set to “QS” to set the method of force evaluation to be the quickstep (DFT) module.
A quick overview of the module:
- – Section class defines the basis of CP2K input and contains methods for manipulating these
objects similarly to Dicts.
- – Keyword class defines the keywords used inside of Section objects that changes variables in
CP2K programs.
- – SectionList and KeywordList classes are lists of Section and Keyword objects that have
the same dictionary key. This deals with repeated sections and keywords.
- – Cp2kInput class is special instantiation of Section that is used to represent the full CP2K
calculation input.
- – The rest of the classes are children of Section intended to make initialization of common
sections easier.
- class AtomicMetadata(info: BasisInfo | PotentialInfo | None = None, element: Element | None = None, potential: Literal['All Electron', 'Pseudopotential'] | None = None, name: str | None = None, alias_names: list = <factory>, filename: str | None = None, version: str | None = None)[source]
Bases:
MSONableMetadata for basis sets and potentials in CP2K.
- info[source]
Info about this object
- Type:
BasisInfo | PotentialInfo | None
- potential[source]
The potential for this object
- Type:
Literal[‘All Electron’, ‘Pseudopotential’] | None
- info: BasisInfo | PotentialInfo | None = None[source]
- class BandStructure(kpoint_sets: Sequence[KpointSet], filename: str = 'BAND.bs', added_mos: int = -1, keywords: dict | None = None, subsections: dict | None = None)[source]
Bases:
SectionSpecify high symmetry paths for outputting the band structure in CP2K.
- Parameters:
kpoint_sets – Sequence of KpointSet objects for the band structure calculation.
filename – Filename for the band structure output
added_mos – Added (unoccupied) molecular orbitals for the calculation.
keywords – additional keywords
subsections – additional subsections.
- classmethod from_kpoints(kpoints: VaspKpoints, kpoints_line_density: int = 20) Self[source]
Initialize band structure section from a line-mode Kpoint object.
- Parameters:
kpoints – a kpoint object from the vasp module, which was constructed in line mode
kpoints_line_density – Number of kpoints along each path
TODO: kpoints objects are defined in the vasp module instead of a code agnostic module if this changes in the future as other codes are added, then this will need to change
- class Band_Structure(kpoint_sets: Sequence[KpointSet], filename: str = 'BAND.bs', added_mos: int = -1, keywords: dict | None = None, subsections: dict | None = None)[source]
Bases:
BandStructure- Parameters:
kpoint_sets – Sequence of KpointSet objects for the band structure calculation.
filename – Filename for the band structure output
added_mos – Added (unoccupied) molecular orbitals for the calculation.
keywords – additional keywords
subsections – additional subsections.
- class BasisFile(objects: Sequence | None = None)[source]
Bases:
DataFileData file for basis sets only.
- class BasisInfo(electrons: int | None = None, core: int | None = None, valence: int | None = None, polarization: int | None = None, diffuse: int | None = None, cc: bool | None = False, pc: bool | None = False, sr: bool | None = False, molopt: bool | None = False, admm: bool | None = False, lri: bool | None = False, contracted: bool | None = None, xc: str | None = None)[source]
Bases:
MSONableSummary info about a basis set.
- valence[source]
Number of basis functions per valence electron OR number of exp if it is a FIT formatted admm basis
- Type:
int | None
- class BrokenSymmetry(l_alpha: Sequence = (-1,), n_alpha: Sequence = (0,), nel_alpha: Sequence = (-1,), l_beta: Sequence = (-1,), n_beta: Sequence = (0,), nel_beta: Sequence = (-1,))[source]
Bases:
SectionDefine the required atomic orbital occupation assigned in initialization of the density matrix, by adding or subtracting electrons from specific angular momentum channels. It works only with GUESS ATOMIC.
Initialize the broken symmetry section.
- Parameters:
l_alpha – Angular momentum quantum number of the orbitals whose occupation is changed
n_alpha – Principal quantum number of the orbitals whose occupation is changed. Default is the first not occupied
nel_alpha – Orbital occupation change per angular momentum quantum number. In unrestricted calculations applied to spin alpha
l_beta – Same as L_alpha for beta channel
n_beta – Same as N_alpha for beta channel
nel_beta – Same as NEL_alpha for beta channel
- class Cell(lattice: Lattice, keywords: dict | None = None, **kwargs)[source]
Bases:
SectionControls the cell/lattice parameters for the simulation.
Initialize the cell section.
- Parameters:
lattice – pymatgen lattice object
keywords – additional keywords
- class Coord(structure: Structure | Molecule, aliases: dict | None = None, keywords: dict | None = None, subsections: dict | None = None, **kwargs)[source]
Bases:
SectionSpecify the coordinates of the atoms using a pymatgen structure object.
- Parameters:
structure – Pymatgen structure object
alias (bool) – whether or not to identify the sites by Element + number so you can do things like assign unique magnetization do different elements.
keywords – additional keywords
subsections – additional subsections.
- class Cp2kInput(name: str = 'CP2K_INPUT', subsections: dict | None = None, **kwargs)[source]
Bases:
SectionSpecial instance of ‘Section’ class that is meant to represent the overall CP2K input. Distinguishes itself from Section by overriding get_str() to not print this section’s title and by implementing the file i/o.
Initialize Cp2kInput by calling the super.
- write_file(input_filename: str = 'cp2k.inp', output_dir: str = '.', make_dir_if_not_present: bool = True)[source]
Write input to a file.
- Parameters:
input_filename (str, optional) – Defaults to “cp2k.inp”.
output_dir (str, optional) – Defaults to “.”.
make_dir_if_not_present (bool, optional) – Defaults to True.
- class DOS(ndigits: int = 6, keywords: dict | None = None, subsections: dict | None = None, **kwargs)[source]
Bases:
SectionControls printing of the density of states.
Initialize the DOS section.
- Parameters:
ndigits – how many digits of precision to print. As of 2022.1, this is necessary to not lose information.
keywords – additional keywords
subsections – additional subsections
- class DataFile(objects: Sequence | None = None)[source]
Bases:
MSONableA data file for a CP2K calc.
- class Davidson(new_prec_each: int = 20, preconditioner: str = 'FULL_SINGLE_INVERSE', keywords: dict | None = None, subsections: dict | None = None, **kwargs)[source]
Bases:
SectionParameters for davidson diagonalization.
- Parameters:
new_prec_each (int) – How often to recalculate the preconditioner.
preconditioner (str) –
Preconditioner to use. “FULL_ALL”: Most effective state selective preconditioner based on diagonalization,
requires the ENERGY_GAP parameter to be an underestimate of the HOMO-LUMO gap. This preconditioner is recommended for almost all systems, except very large systems where make_preconditioner would dominate the total computational cost.
- ”FULL_KINETIC”: Cholesky inversion of S and T, fast construction, robust, use for
very large systems.
- ”FULL_SINGLE”: Based on H-eS diagonalization, not as good as FULL_ALL, but
somewhat cheaper to apply.
- ”FULL_SINGLE_INVERSE”: Based on H-eS cholesky inversion, similar to FULL_SINGLE
in preconditioning efficiency but cheaper to construct, might be somewhat less robust. Recommended for large systems.
- ”FULL_S_INVERSE”: Cholesky inversion of S, not as good as FULL_KINETIC,
yet equally expensive.
”NONE”: skip preconditioning
keywords – additional keywords
subsections – additional subsections.
- class Dft(basis_set_filenames: Sequence[str] = ('BASIS_MOLOPT',), potential_filename: str = 'GTH_POTENTIALS', uks: bool = True, wfn_restart_file_name: str | None = None, keywords: dict | None = None, subsections: dict | None = None, **kwargs)[source]
Bases:
SectionControls the DFT parameters in CP2K.
Initialize the DFT section.
- Parameters:
basis_set_filenames – Name of the file that contains the basis set information. Defaults to “BASIS_MOLOPT”.
potential_filename – Name of the file that contains the pseudopotential information. Defaults to “GTH_POTENTIALS”.
uks – Whether to run unrestricted Kohn Sham (spin polarized). Defaults to True.
wfn_restart_file_name – Defaults to None.
keywords – additional keywords to add.
subsections – Any subsections to initialize with. Defaults to None.
- class DftPlusU(eps_u_ramping=1e-05, init_u_ramping_each_scf=False, l=-1, u_minus_j=0, u_ramping=0, keywords: dict | None = None, subsections: dict | None = None, **kwargs)[source]
Bases:
SectionControls DFT+U for an atom kind.
Initialize the DftPlusU section.
- Parameters:
eps_u_ramping – (float) SCF convergence threshold at which to start ramping the U value
init_u_ramping_each_scf – (bool) Whether or not to do u_ramping each scf cycle
l – (int) angular moment of the orbital to apply the +U correction
u_minus_j – (float) the effective U parameter, Ueff = U-J
u_ramping – (float) stepwise amount to increase during ramping until u_minus_j is reached
keywords – additional keywords
subsections – additional subsections
- class Diagonalization(eps_adapt: float = 0, eps_iter: float = 1e-08, eps_jacobi: float = 0, jacobi_threshold: float = 1e-07, keywords: dict | None = None, subsections: dict | None = None, **kwargs)[source]
Bases:
SectionControls diagonalization settings (if using traditional diagonalization).
Initialize the diagonalization section.
- class EDensityCube(keywords: dict | None = None, subsections: dict | None = None, **kwargs)[source]
Bases:
SectionControls printing of the electron density cube file.
Basic object representing a CP2K Section. Sections activate different parts of the calculation. For example, FORCE_EVAL section will activate CP2K’s ability to calculate forces.
- Parameters:
name – The name of the section (must match name in CP2K)
subsections – A dictionary of subsections that are nested in this section. Format is {‘NAME’: Section(args, **kwargs). The name you chose for ‘NAME’ to index that subsection does not *have to be the same as the section’s true name, but we recommend matching them. You can specify a blank dictionary if there are no subsections, or if you want to insert the subsections later.
repeats – Whether or not this section can be repeated. Most sections cannot. Default=False.
description – Description of this section for easier readability
keywords – the keywords to be set for this section. Each element should be a Keyword object. This can be more cumbersome than simply using kwargs for building a class in a script, but is more convenient for the class instantiations of CP2K sections (see below).
section_parameters – the section parameters for this section. Section parameters are specialized keywords that modify the behavior of the section overall. Most sections do not have section parameters, but some do. Unlike normal Keywords, these are specified as strings and not as Keyword objects.
location – the path to the section in the form ‘SECTION/SUBSECTION1/SUBSECTION3’, example for QS module: ‘FORCE_EVAL/DFT/QS’. This location is used to automatically determine if a subsection requires a supersection to be activated.
verbose – Controls how much is printed to CP2K input files (Also see Keyword). If True, then a description of the section will be printed with it as a comment (if description is set). Default=True.
alias – An alias for this class to use in place of the name.
keyword (kwargs are interpreted as)
as (value pairs and added to the keywords array)
objects (Keyword)
- class E_Density_Cube(keywords: dict | None = None, subsections: dict | None = None, **kwargs)[source]
Bases:
EDensityCubeBasic object representing a CP2K Section. Sections activate different parts of the calculation. For example, FORCE_EVAL section will activate CP2K’s ability to calculate forces.
- Parameters:
name – The name of the section (must match name in CP2K)
subsections – A dictionary of subsections that are nested in this section. Format is {‘NAME’: Section(args, **kwargs). The name you chose for ‘NAME’ to index that subsection does not *have to be the same as the section’s true name, but we recommend matching them. You can specify a blank dictionary if there are no subsections, or if you want to insert the subsections later.
repeats – Whether or not this section can be repeated. Most sections cannot. Default=False.
description – Description of this section for easier readability
keywords – the keywords to be set for this section. Each element should be a Keyword object. This can be more cumbersome than simply using kwargs for building a class in a script, but is more convenient for the class instantiations of CP2K sections (see below).
section_parameters – the section parameters for this section. Section parameters are specialized keywords that modify the behavior of the section overall. Most sections do not have section parameters, but some do. Unlike normal Keywords, these are specified as strings and not as Keyword objects.
location – the path to the section in the form ‘SECTION/SUBSECTION1/SUBSECTION3’, example for QS module: ‘FORCE_EVAL/DFT/QS’. This location is used to automatically determine if a subsection requires a supersection to be activated.
verbose – Controls how much is printed to CP2K input files (Also see Keyword). If True, then a description of the section will be printed with it as a comment (if description is set). Default=True.
alias – An alias for this class to use in place of the name.
keyword (kwargs are interpreted as)
as (value pairs and added to the keywords array)
objects (Keyword)
- class ForceEval(keywords: dict | None = None, subsections: dict | None = None, **kwargs)[source]
Bases:
SectionControls the calculation of energy and forces in CP2K.
Initialize the ForceEval section.
- class GaussianTypeOrbitalBasisSet(info: BasisInfo | None = None, element: Element | None = None, potential: Literal['All Electron', 'Pseudopotential'] | None = None, name: str | None = None, alias_names: list = <factory>, filename: str | None = None, version: str | None = None, nset: int | None = None, n: list[int] | None = None, lmax: list[int] | None = None, lmin: list[int] | None = None, nshell: list[dict[int, int]] | None = None, exponents: list[list[float]] | None = None, coefficients: list[dict[int, dict[int, dict[int, float]]]] | None = None)[source]
Bases:
AtomicMetadataModel definition of a GTO basis set.
- nshell[source]
Number of shells for angular momentum l for each set
- Type:
list[dict[int, int]] | None
- class Global(project_name: str = 'CP2K', run_type: str = 'ENERGY_FORCE', keywords: dict | None = None, **kwargs)[source]
Bases:
SectionControls ‘global’ settings for CP2K execution such as RUN_TYPE and PROJECT_NAME.
Initialize the global section.
- Parameters:
project_name – Defaults to “CP2K”.
run_type – what type of calculation to run
keywords – Additional keywords to add
- class GthPotential(info: PotentialInfo = None, element: Element | None = None, potential: Literal['All Electron', 'Pseudopotential'] | None = None, name: str | None = None, alias_names: list = <factory>, filename: str | None = None, version: str | None = None, n_elecs: dict[int, int] | None = None, r_loc: float | None = None, nexp_ppl: int | None = None, c_exp_ppl: Sequence | None = None, radii: dict[int, float] | None = None, nprj: int | None = None, nprj_ppnl: dict[int, int] | None = None, hprj_ppnl: dict[int, dict[int, dict[int, float]]] | None = None)[source]
Bases:
AtomicMetadataRepresentation of GTH-type (pseudo)potential.
- c_exp_ppl[source]
Sequence = field(None, description=”Coefficients of the local pseudopotential functions
- Type:
Sequence | None
- radii[source]
Radius of the nonlocal part for angular momentum quantum number l defined by the Gaussian function exponents alpha_prj_ppnl
- Type:
dict[int, float] | None
- nprj_ppnl[source]
Number of the non-local projectors for the angular momentum quantum number
- Type:
dict[int, int] | None
- hprj_ppnl[source]
Coefficients of the non-local projector functions. Coeff ij for ang momentum l
- Type:
dict[int, dict[int, dict[int, float]]] | None
- )
- class Keyword(name: str, *values, description: str | None = None, units: str | None = None, verbose: bool | None = False, repeats: bool | None = False)[source]
Bases:
MSONableA keyword argument in CP2K. Within CP2K Sections, which activate features of the CP2K code, the keywords are arguments that control the functionality of that feature. For example, the section “FORCE_EVAL” activates the evaluation of forces/energies, but within “FORCE_EVAL” the keyword “METHOD” controls whether or not this will be done with, say, “Quickstep” (DFT) or “EIP” (empirical interatomic potential).
Initialize a keyword. These Keywords and the value passed to them are sometimes as simple as KEYWORD VALUE, but can also be more elaborate such as KEYWORD [UNITS] VALUE1 VALUE2, which is why this class exists: to handle many values and control easy printing to an input file.
- Parameters:
name – The name of this keyword. Must match an acceptable keyword from CP2K
values – All non-keyword arguments after ‘name’ are interpreted as the values to set for this keyword. i.e: KEYWORD ARG1 ARG2 would provide two values to the keyword.
description – The description for this keyword. This can make readability of input files easier for some. Default=None.
units – The units for this keyword. If not specified, CP2K default units will be used. Consult manual for default units. Default=None.
verbose – Whether the description should be printed with the string of this keyword
repeats – Whether or not this keyword may be repeated. Default=False.
- class KeywordList(keywords: Sequence[Keyword])[source]
Bases:
MSONableSome keywords can be repeated, which makes accessing them via the normal dictionary methods a little unnatural. This class deals with this by defining a collection of same-named keywords that are accessed by one name.
Initialize a keyword list given a sequence of keywords.
- Parameters:
keywords – A list of keywords. Must all have the same name (case-insensitive)
- class Kind(specie: str, alias: str | None = None, magnetization: float = 0.0, basis_set: GaussianTypeOrbitalBasisSet | str | None = 'GTH_BASIS', potential: GthPotential | str | None = 'GTH_POTENTIALS', ghost: bool = False, aux_basis: GaussianTypeOrbitalBasisSet | str | None = None, keywords: dict | None = None, subsections: dict | None = None, **kwargs)[source]
Bases:
SectionSpecify the information for the different atom types being simulated.
Initialize a KIND section.
- Parameters:
specie – Object representing the atom.
alias – Alias for the atom, can be used for specifying modifications to certain atoms but not all, e.g. Mg_1 and Mg_2 to force difference oxidation states on the two atoms.
magnetization – From the CP2K Manual: The magnetization used in the atomic initial guess. Adds magnetization/2 spin-alpha electrons and removes magnetization/2 spin-beta electrons.
basis_set – Basis set for this atom, accessible from the basis set file specified
potential – Pseudopotential for this atom, accessible from the potential file
ghost – Turn this into ghost atom (disable the potential)
aux_basis – Auxiliary basis to use with ADMM
keywords – additional keywords
subsections – additional subsections
kwargs – Additional kwargs to pass to Section()
- class KpointSet(npoints: int, kpoints: Iterable, units: str = 'B_VECTOR')[source]
Bases:
SectionSpecify a kpoint line to be calculated between special points.
- Parameters:
npoints (int) – Number of kpoints along the line.
kpoints – A dictionary of {label: kpoint} kpoints defining the path
units (str) –
Units for the kpoint coordinates. Options: “B_VECTOR” (reciprocal coordinates)
”CART_ANGSTROM” (units of 2*Pi/Angstrom) “CART_BOHR” (units of 2*Pi/Bohr).
- class Kpoint_Set(npoints: int, kpoints: Iterable, units: str = 'B_VECTOR')[source]
Bases:
KpointSet- Parameters:
npoints (int) – Number of kpoints along the line.
kpoints – A dictionary of {label: kpoint} kpoints defining the path
units (str) –
Units for the kpoint coordinates. Options: “B_VECTOR” (reciprocal coordinates)
”CART_ANGSTROM” (units of 2*Pi/Angstrom) “CART_BOHR” (units of 2*Pi/Bohr).
- class Kpoints(kpts: Sequence | Sequence[Sequence[int]], weights: Sequence | None = None, eps_geo: float = 1e-06, full_grid: bool = False, parallel_group_size: int = -1, scheme: str = 'MONKHORST-PACK', symmetry: bool = False, units: str = 'B_VECTOR', verbose: bool = False, wavefunctions: str = 'COMPLEX')[source]
Bases:
SectionDescription of the k-points to use for the calculation.
- Parameters:
kpts (list, tuple) – a 2D array for the kpoints of the form [(1,1,1),]. If len(kpts) == 1. Then it is taken as subdivisions for automatic kpoint scheme. If it has more entries, it is taken as manual entries for kpoints.
weights (list, tuple) – a weight for each kpoint. Default is to weigh each by 1
eps_geo (float) – tolerance for symmetry. Default=1e-6
full_grid (bool) – use full (not reduced) kpoint grid. Default=False.
parallel_group_size (int) – from CP2K manual: Number of processors to be used for a single kpoint. This number must divide the total number of processes. The number of groups must divide the total number of kpoints. Value=-1 (smallest possible number of processes per group, satisfying the constraints). Value=0 (all processes). Value=n (exactly n processes). Default=-1.
scheme (str) – kpoint generation scheme. Default=’Monkhorst-Pack’
symmetry (bool) – Use symmetry to reduce the number of kpoints. Default=False.
units (str) – Units for the kpoint coordinates (reciprocal coordinates or cartesian). Default=’B_VECTOR’ (reciprocal)
verbose (bool) – verbose output for kpoints. Default=False
wavefunctions (str) – Whether to use complex or real valued wavefunctions (if available). Default=’complex’.
- classmethod from_kpoints(kpoints: VaspKpoints, structure: Structure | None = None) Self[source]
Initialize the section from a Kpoints object (pymatgen.io.vasp.inputs). CP2K does not have an automatic gamma-point constructor, so this is generally used to get the number of divisions from a kpoint static constructor and then build a Monkhorst-Pack grid, which is sufficient for gamma-recommended systems so long as the grid is fine enough.
- Parameters:
- class LDOS(index: int = 1, alias: str | None = None, keywords: dict | None = None, subsections: dict | None = None, **kwargs)[source]
Bases:
SectionControls printing of the LDOS (List-Density of states). i.e. projects onto specific atoms.
Initialize the LDOS section.
- Parameters:
index – Index of the atom to project onto
alias – section alias
keywords – additional keywords
subsections – additional subsections
- class MOCubes(write_cube: bool = False, nhomo: int = 1, nlumo: int = 1, keywords: dict | None = None, subsections: dict | None = None, **kwargs)[source]
Bases:
SectionControls printing of the molecular orbital eigenvalues.
Initialize the MO_CUBES section.
- class MO_Cubes(write_cube: bool = False, nhomo: int = 1, nlumo: int = 1, keywords: dict | None = None, subsections: dict | None = None, **kwargs)[source]
Bases:
MOCubesInitialize the MO_CUBES section.
- class Mgrid(cutoff: float = 1200, rel_cutoff: float = 80, ngrids: int = 5, progression_factor: int = 3, keywords: dict | None = None, subsections: dict | None = None, **kwargs)[source]
Bases:
SectionControls the multigrid for numerical integration.
Initialize the MGRID section.
- Parameters:
cutoff – Cutoff energy (in Rydbergs for historical reasons) defining how find of Gaussians will be used
rel_cutoff – The relative cutoff energy, which defines how to map the Gaussians onto the multigrid. If the value is too low then, even if you have a high cutoff with sharp Gaussians, they will be mapped to the course part of the multigrid
ngrids – number of grids to use
progression_factor – divisor that decides how to map Gaussians the multigrid after the highest mapping is decided by rel_cutoff
keywords – additional keywords
subsections – additional subsections
- class OrbitalTransformation(minimizer: str = 'CG', preconditioner: str = 'FULL_ALL', algorithm: str = 'STRICT', rotation: bool = False, occupation_preconditioner: bool = False, energy_gap: float = -1, linesearch: str = '2PNT', keywords: dict | None = None, subsections: dict | None = None, **kwargs)[source]
Bases:
SectionTurns on the Orbital Transformation scheme for diagonalizing the Hamiltonian. Often faster and with guaranteed convergence compared to normal diagonalization, but requires the system to have a band gap.
NOTE: OT has poor convergence for metallic systems and cannot use SCF mixing or smearing. Therefore, you should not use it for metals or systems with ‘small’ band gaps. In that case, use normal diagonalization
Initialize the OT section.
- Parameters:
minimizer – The minimizer to use with the OT method. Default is conjugate gradient method, which is more robust, but more well-behaved systems should use DIIS, which can be as much as 50% faster.
preconditioner – Preconditioner to use for OT, FULL_ALL tends to be most robust, but is not always most efficient. For difficult systems, FULL_SINGLE_INVERSE can be more robust, and is reasonably efficient with large systems. For huge, but well behaved, systems, where construction of the preconditioner can take a very long time, FULL_KINETIC can be a good choice.
algorithm – What algorithm to use for OT. ‘Strict’: Taylor or diagonalization based algorithm. IRAC: Orbital Transformation based Iterative Refinement of the Approximate Congruence transformation (OT/IR).
rotation – Introduce additional variables to allow subspace rotations (i.e fractional occupations)
occupation_preconditioner – include the fractional occupation in the preconditioning
energy_gap – Guess for the band gap. For FULL_ALL, should be smaller than the actual band gap, so simply using 0.01 is a robust value. Choosing a larger value will help if you start with a bad initial guess though. For FULL_SINGLE_INVERSE, energy_gap is treated as a lower bound. Values lower than 0.05 in this case can lead to stability issues.
linesearch (str) – From the manual: 1D line search algorithm to be used with the OT minimizer, in increasing order of robustness and cost. MINIMIZER CG combined with LINESEARCH GOLD should always find an electronic minimum. Whereas the 2PNT minimizer is almost always OK, 3PNT might be needed for systems in which successive OT CG steps do not decrease the total energy.
keywords – additional keywords
subsections – additional subsections
- class PBE(parameterization: str = 'ORIG', scale_c: float = 1, scale_x: float = 1, keywords: dict | None = None, subsections: dict | None = None)[source]
Bases:
SectionInfo about the PBE functional.
- Parameters:
parameterization (str) – ORIG: original PBE PBESOL: PBE for solids/surfaces REVPBE: revised PBE
scale_c (float) – scales the correlation part of the functional.
scale_x (float) – scales the exchange part of the functional.
keywords – additional keywords
subsections – additional subsections.
- class PDOS(nlumo: int = -1, keywords: dict | None = None, subsections: dict | None = None, **kwargs)[source]
Bases:
SectionControls printing of projected density of states onto the different atom KINDS (elemental decomposed DOS).
Initialize the PDOS section.
- Parameters:
nlumo – how many unoccupied orbitals to include (-1==ALL)
keywords – additional keywords
subsections – additional subsections
- class PotentialFile(objects: Sequence | None = None)[source]
Bases:
DataFileData file for potentials only.
- class PotentialInfo(electrons: int | None = None, potential_type: str | None = None, nlcc: bool | None = None, xc: str | None = None)[source]
Bases:
MSONableMetadata for this potential.
- class QS(method: str = 'GPW', eps_default: float = 1e-10, eps_pgf_orb: float | None = None, extrapolation: str = 'ASPC', keywords: dict | None = None, subsections: dict | None = None, **kwargs)[source]
Bases:
SectionControls the quickstep settings (DFT driver).
Initialize the QS Section.
- Parameters:
method ("GPW" | "GAPW") – What DFT methodology to use. GPW (Gaussian Plane Waves) for DFT with pseudopotentials or GAPW (Gaussian Augmented Plane Waves) for all electron calculations.
eps_default (float) – The default level of convergence accuracy. NOTE: This is a global value for all the numerical value of all EPS_* values in QS module. It is not the same as EPS_SCF, which sets convergence accuracy of the SCF cycle alone.
eps_pgf_orb – Precision for the overlap matrix. Default is to use sqrt(eps_default)
extrapolation ("PS" | "ASPC") – Method use for extrapolation. If using gamma-point-only calculation, then one should either PS or ASPC (ASPC especially for MD runs). See the manual for other options.
keywords – Additional keywords to add
subsections – Subsections to initialize with.
- class Scf(max_scf: int = 50, eps_scf: float = 1e-06, scf_guess: str = 'RESTART', keywords: dict | None = None, subsections: dict | None = None, **kwargs)[source]
Bases:
SectionControls the self consistent field loop.
Initialize the Scf section.
- Parameters:
max_scf (int) – Maximum number of SCF loops before terminating. Defaults to 50.
eps_scf (float) – Convergence criteria for SCF loop. Defaults to 1e-6.
scf_guess –
Initial guess for SCF loop. “ATOMIC”: Generate an atomic density using the atomic code “CORE”: Diagonalize the core Hamiltonian for an initial guess. “HISTORY_RESTART”: Extrapolated from previous RESTART files. “MOPAC”: Use same guess as MOPAC for semi-empirical methods or a simple
diagonal density matrix for other methods.
”NONE”: Skip initial guess (only for NON-SCC DFTB). “RANDOM”: Use random wavefunction coefficients. “RESTART”: Use the RESTART file as an initial guess (and ATOMIC if not present). “SPARSE”: Generate a sparse wavefunction using the atomic code (for OT based
methods).
keywords – Additional keywords
subsections – Additional subsections
- class Section(name: str, subsections: dict | None = None, repeats: bool = False, description: str | None = None, keywords: dict | None = None, section_parameters: Sequence[str] = (), location: str | None = None, verbose: bool | None = False, alias: str | None = None, **kwargs)[source]
Bases:
MSONableBasic input representation of input to CP2K. Activates functionality inside of the CP2K executable.
Basic object representing a CP2K Section. Sections activate different parts of the calculation. For example, FORCE_EVAL section will activate CP2K’s ability to calculate forces.
- Parameters:
name – The name of the section (must match name in CP2K)
subsections – A dictionary of subsections that are nested in this section. Format is {‘NAME’: Section(args, **kwargs). The name you chose for ‘NAME’ to index that subsection does not *have to be the same as the section’s true name, but we recommend matching them. You can specify a blank dictionary if there are no subsections, or if you want to insert the subsections later.
repeats – Whether or not this section can be repeated. Most sections cannot. Default=False.
description – Description of this section for easier readability
keywords – the keywords to be set for this section. Each element should be a Keyword object. This can be more cumbersome than simply using kwargs for building a class in a script, but is more convenient for the class instantiations of CP2K sections (see below).
section_parameters – the section parameters for this section. Section parameters are specialized keywords that modify the behavior of the section overall. Most sections do not have section parameters, but some do. Unlike normal Keywords, these are specified as strings and not as Keyword objects.
location – the path to the section in the form ‘SECTION/SUBSECTION1/SUBSECTION3’, example for QS module: ‘FORCE_EVAL/DFT/QS’. This location is used to automatically determine if a subsection requires a supersection to be activated.
verbose – Controls how much is printed to CP2K input files (Also see Keyword). If True, then a description of the section will be printed with it as a comment (if description is set). Default=True.
alias – An alias for this class to use in place of the name.
keyword (kwargs are interpreted as)
as (value pairs and added to the keywords array)
objects (Keyword)
- by_path(path: str)[source]
Access a sub-section using a path. Used by the file parser.
- Parameters:
path (str) – Path to section of form ‘SUBSECTION1/SUBSECTION2/SUBSECTION_OF_INTEREST’
- check(path: str)[source]
Check if section exists within the current using a path. Can be useful for cross-checking whether or not required dependencies have been satisfied, which CP2K does not enforce.
- Parameters:
path (str) – Path to section of form ‘SUBSECTION1/SUBSECTION2/SUBSECTION_OF_INTEREST’
- get(d, default=None)[source]
Similar to get for dictionaries. This will attempt to retrieve the section or keyword matching d. Will not raise an error if d does not exist.
- Parameters:
d – the key to retrieve, if present
default – what to return if d is not found
- get_keyword(d, default=None)[source]
Get function, only for subsections.
- Parameters:
d – Name of keyword to get
default – return if d is not found in keyword list
- get_section(d, default=None)[source]
Get function, only for subsections.
- Parameters:
d – Name of section to get
default – return if d is not found in subsections
- insert(d: Section | SectionList) None[source]
Insert a new section as a subsection of the current one.
- setitem(key, value, strict=False)[source]
Helper function for setting items. Kept separate from the double-underscore function so that “strict” option can be made possible.
strict will only set values for items that already have a key entry (no insertion).
- update(dct: dict, strict=False) Section[source]
Update the Section according to a dictionary argument. This is most useful for providing user-override settings to default parameters. As you pass a dictionary the class variables like “description”, “location”, or “repeats” are not included. Therefore, it is recommended that this be used to modify existing Section objects to a user’s needs, but not used for the creation of new Section child-classes.
- Parameters:
dct (dict) –
A dictionary containing the update information. Should use nested dictionaries to specify the full path of the update. If a section or keyword does not exist, it will be created, but only with the values that are provided in “d”, not using default values from a Section object. Example: {
- ’SUBSECTION1’: {
‘SUBSEC2’: {‘NEW_KEYWORD’: ‘NEW_VAL’}, ‘NEW_SUBSEC’: {‘NEW_KWD’: ‘NEW_VAL’} }
}
strict (bool) – If true, only update existing sections and keywords. If false, allow new sections and keywords. Default: False
- class SectionList(sections: Sequence[Section])[source]
Bases:
MSONableSection list.
Initialize a SectionList object using a sequence of sections.
- Parameters:
sections – A list of keywords. Must all have the same name (case-insensitive)
- class Smear(elec_temp: float = 300, method: str = 'FERMI_DIRAC', fixed_magnetic_moment: float = -100.0, keywords: dict | None = None, subsections: dict | None = None, **kwargs)[source]
Bases:
SectionControl electron smearing.
Basic object representing a CP2K Section. Sections activate different parts of the calculation. For example, FORCE_EVAL section will activate CP2K’s ability to calculate forces.
- Parameters:
name – The name of the section (must match name in CP2K)
subsections – A dictionary of subsections that are nested in this section. Format is {‘NAME’: Section(args, **kwargs). The name you chose for ‘NAME’ to index that subsection does not *have to be the same as the section’s true name, but we recommend matching them. You can specify a blank dictionary if there are no subsections, or if you want to insert the subsections later.
repeats – Whether or not this section can be repeated. Most sections cannot. Default=False.
description – Description of this section for easier readability
keywords – the keywords to be set for this section. Each element should be a Keyword object. This can be more cumbersome than simply using kwargs for building a class in a script, but is more convenient for the class instantiations of CP2K sections (see below).
section_parameters – the section parameters for this section. Section parameters are specialized keywords that modify the behavior of the section overall. Most sections do not have section parameters, but some do. Unlike normal Keywords, these are specified as strings and not as Keyword objects.
location – the path to the section in the form ‘SECTION/SUBSECTION1/SUBSECTION3’, example for QS module: ‘FORCE_EVAL/DFT/QS’. This location is used to automatically determine if a subsection requires a supersection to be activated.
verbose – Controls how much is printed to CP2K input files (Also see Keyword). If True, then a description of the section will be printed with it as a comment (if description is set). Default=True.
alias – An alias for this class to use in place of the name.
keyword (kwargs are interpreted as)
as (value pairs and added to the keywords array)
objects (Keyword)
- class Subsys(keywords: dict | None = None, subsections: dict | None = None, **kwargs)[source]
Bases:
SectionControls the definition of the system to be simulated.
Initialize the subsys section.
- class VHartreeCube(keywords: dict | None = None, subsections: dict | None = None, **kwargs)[source]
Bases:
SectionControls printing of the hartree potential as a cube file.
Basic object representing a CP2K Section. Sections activate different parts of the calculation. For example, FORCE_EVAL section will activate CP2K’s ability to calculate forces.
- Parameters:
name – The name of the section (must match name in CP2K)
subsections – A dictionary of subsections that are nested in this section. Format is {‘NAME’: Section(args, **kwargs). The name you chose for ‘NAME’ to index that subsection does not *have to be the same as the section’s true name, but we recommend matching them. You can specify a blank dictionary if there are no subsections, or if you want to insert the subsections later.
repeats – Whether or not this section can be repeated. Most sections cannot. Default=False.
description – Description of this section for easier readability
keywords – the keywords to be set for this section. Each element should be a Keyword object. This can be more cumbersome than simply using kwargs for building a class in a script, but is more convenient for the class instantiations of CP2K sections (see below).
section_parameters – the section parameters for this section. Section parameters are specialized keywords that modify the behavior of the section overall. Most sections do not have section parameters, but some do. Unlike normal Keywords, these are specified as strings and not as Keyword objects.
location – the path to the section in the form ‘SECTION/SUBSECTION1/SUBSECTION3’, example for QS module: ‘FORCE_EVAL/DFT/QS’. This location is used to automatically determine if a subsection requires a supersection to be activated.
verbose – Controls how much is printed to CP2K input files (Also see Keyword). If True, then a description of the section will be printed with it as a comment (if description is set). Default=True.
alias – An alias for this class to use in place of the name.
keyword (kwargs are interpreted as)
as (value pairs and added to the keywords array)
objects (Keyword)
- class V_Hartree_Cube(keywords: dict | None = None, subsections: dict | None = None, **kwargs)[source]
Bases:
VHartreeCubeBasic object representing a CP2K Section. Sections activate different parts of the calculation. For example, FORCE_EVAL section will activate CP2K’s ability to calculate forces.
- Parameters:
name – The name of the section (must match name in CP2K)
subsections – A dictionary of subsections that are nested in this section. Format is {‘NAME’: Section(args, **kwargs). The name you chose for ‘NAME’ to index that subsection does not *have to be the same as the section’s true name, but we recommend matching them. You can specify a blank dictionary if there are no subsections, or if you want to insert the subsections later.
repeats – Whether or not this section can be repeated. Most sections cannot. Default=False.
description – Description of this section for easier readability
keywords – the keywords to be set for this section. Each element should be a Keyword object. This can be more cumbersome than simply using kwargs for building a class in a script, but is more convenient for the class instantiations of CP2K sections (see below).
section_parameters – the section parameters for this section. Section parameters are specialized keywords that modify the behavior of the section overall. Most sections do not have section parameters, but some do. Unlike normal Keywords, these are specified as strings and not as Keyword objects.
location – the path to the section in the form ‘SECTION/SUBSECTION1/SUBSECTION3’, example for QS module: ‘FORCE_EVAL/DFT/QS’. This location is used to automatically determine if a subsection requires a supersection to be activated.
verbose – Controls how much is printed to CP2K input files (Also see Keyword). If True, then a description of the section will be printed with it as a comment (if description is set). Default=True.
alias – An alias for this class to use in place of the name.
keyword (kwargs are interpreted as)
as (value pairs and added to the keywords array)
objects (Keyword)
- class XCFunctional(functionals: Sequence[str] = (), keywords: dict | None = None, subsections: dict | None = None, **kwargs)[source]
Bases:
SectionInfo about which XC functional to use.
Basic object representing a CP2K Section. Sections activate different parts of the calculation. For example, FORCE_EVAL section will activate CP2K’s ability to calculate forces.
- Parameters:
name – The name of the section (must match name in CP2K)
subsections – A dictionary of subsections that are nested in this section. Format is {‘NAME’: Section(args, **kwargs). The name you chose for ‘NAME’ to index that subsection does not *have to be the same as the section’s true name, but we recommend matching them. You can specify a blank dictionary if there are no subsections, or if you want to insert the subsections later.
repeats – Whether or not this section can be repeated. Most sections cannot. Default=False.
description – Description of this section for easier readability
keywords – the keywords to be set for this section. Each element should be a Keyword object. This can be more cumbersome than simply using kwargs for building a class in a script, but is more convenient for the class instantiations of CP2K sections (see below).
section_parameters – the section parameters for this section. Section parameters are specialized keywords that modify the behavior of the section overall. Most sections do not have section parameters, but some do. Unlike normal Keywords, these are specified as strings and not as Keyword objects.
location – the path to the section in the form ‘SECTION/SUBSECTION1/SUBSECTION3’, example for QS module: ‘FORCE_EVAL/DFT/QS’. This location is used to automatically determine if a subsection requires a supersection to be activated.
verbose – Controls how much is printed to CP2K input files (Also see Keyword). If True, then a description of the section will be printed with it as a comment (if description is set). Default=True.
alias – An alias for this class to use in place of the name.
keyword (kwargs are interpreted as)
as (value pairs and added to the keywords array)
objects (Keyword)
- class Xc_Functional(functionals: Sequence[str] = (), keywords: dict | None = None, subsections: dict | None = None, **kwargs)[source]
Bases:
XCFunctionalBasic object representing a CP2K Section. Sections activate different parts of the calculation. For example, FORCE_EVAL section will activate CP2K’s ability to calculate forces.
- Parameters:
name – The name of the section (must match name in CP2K)
subsections – A dictionary of subsections that are nested in this section. Format is {‘NAME’: Section(args, **kwargs). The name you chose for ‘NAME’ to index that subsection does not *have to be the same as the section’s true name, but we recommend matching them. You can specify a blank dictionary if there are no subsections, or if you want to insert the subsections later.
repeats – Whether or not this section can be repeated. Most sections cannot. Default=False.
description – Description of this section for easier readability
keywords – the keywords to be set for this section. Each element should be a Keyword object. This can be more cumbersome than simply using kwargs for building a class in a script, but is more convenient for the class instantiations of CP2K sections (see below).
section_parameters – the section parameters for this section. Section parameters are specialized keywords that modify the behavior of the section overall. Most sections do not have section parameters, but some do. Unlike normal Keywords, these are specified as strings and not as Keyword objects.
location – the path to the section in the form ‘SECTION/SUBSECTION1/SUBSECTION3’, example for QS module: ‘FORCE_EVAL/DFT/QS’. This location is used to automatically determine if a subsection requires a supersection to be activated.
verbose – Controls how much is printed to CP2K input files (Also see Keyword). If True, then a description of the section will be printed with it as a comment (if description is set). Default=True.
alias – An alias for this class to use in place of the name.
keyword (kwargs are interpreted as)
as (value pairs and added to the keywords array)
objects (Keyword)
pymatgen.io.cp2k.outputs module
This module defines the CP2K output parser along with a few other functions for parsing CP2K-related outputs.
- class Cp2kOutput(filename, verbose=False, auto_load=False)[source]
Bases:
objectParse output file from CP2K. The CP2K output file is very flexible in the way that it is returned. This class will automatically parse parameters that should always be present, but other parsing features may be called depending on the run type.
Initialize the Cp2kOutput object.
- Parameters:
filename – (str) Name of the CP2K output file to parse
verbose – (bool) Whether or not to parse with verbosity (will parse lots of data that may not be useful)
auto_load (bool) – Whether or not to automatically load basic info like energies and structures.
- property band_structure: BandStructure | None[source]
Band structure object if it has been parsed.
- property complete_dos: CompleteDos | None[source]
Complete dos object if it has been parsed.
- property is_molecule: bool[source]
True if the CP2K output was generated for a molecule (i.e. no periodicity in the cell).
- parse_atomic_kind_info()[source]
Parse info on what atomic kinds are present and what basis/pseudopotential is describing each of them.
- parse_bandstructure(bandstructure_filename=None) None[source]
Parse a CP2K bandstructure file.
- Parameters:
bandstructure_filename – Filename containing bandstructure info. If
provided (not)
by (then the pmg name of "BAND.bs" will be assumed)
parser. (the filename)
- parse_cp2k_params()[source]
Parse the CP2K general parameters from CP2K output file into a dictionary.
- parse_dos(dos_file=None, pdos_files=None, ldos_files=None)[source]
Parse the dos files produced by CP2K calculation. CP2K produces different files based on the input file rather than assimilating them all into one file.
One file type is the overall DOS file, which is used for k-point calculations. For non-kpoint calculation, the overall DOS is generally not calculated, but the element-projected pDOS is. Separate files are created for each spin channel and each atom kind. If requested, CP2K can also do site/local projected dos (ldos). Each site requested will have a separate file for each spin channel (if spin polarized calculation is performed).
If possible, this function will assimilate the ldos files into a CompleteDos object. Either provide a list of PDOS file paths, or use glob to find the .pdos_ALPHA extension in the calculation directory.
- Parameters:
dos_file (str) – Name of the dos file, otherwise will be inferred
pdos_files (list) – list of pdos file paths, otherwise they will be inferred
ldos_files (list) – list of ldos file paths, otherwise they will be inferred
- parse_energies()[source]
Get the total energy from a CP2K calculation. Presently, the energy reported in the trajectory (pos.xyz) file takes precedence over the energy reported in the main output file. This is because the trajectory file keeps track of energies in between restarts, while the main output file may or may not depending on whether a particular machine overwrites or appends it.
- parse_files()[source]
Identify files present in the directory with the CP2K output file. Looks for trajectories, dos, and cubes.
- parse_global_params()[source]
Parse the GLOBAL section parameters from CP2K output file into a dictionary.
- parse_homo_lumo()[source]
Find the HOMO - LUMO gap in [eV]. Returns the last value. For gaps/eigenvalues decomposed by spin up/spin down channel and over many ionic steps, see parse_mo_eigenvalues().
- parse_hyperfine(hyperfine_filename=None)[source]
Parse a file containing hyperfine coupling tensors for each atomic site.
- parse_ionic_steps()[source]
Parse the ionic step info. If already parsed, this will just assimilate.
- parse_mo_eigenvalues()[source]
Parse the MO eigenvalues from the CP2K output file. Will get the eigenvalues (and band gap) at each ionic step (if more than one exist).
Everything is decomposed by spin channel. If calculation was performed without spin polarization, then only Spin.up will be present, which represents the average of up and down.
- parse_scf_params()[source]
Retrieve the most import SCF parameters: the max number of scf cycles (max_scf), the convergence cutoff for scf (eps_scf),.
- parse_structures(trajectory_file=None, lattice_file=None)[source]
Parse the structures from a CP2K calculation. Static calculations simply use the initial structure. For calculations with ionic motion, the function will look for the appropriate trajectory and lattice files based on naming convention. If no file is given, and no file is found, it is assumed that the lattice/structure remained constant, and the initial lattice/structure is used. CP2K does not output the trajectory in the main output file by default, so non static calculations have to reference the trajectory file.
- ran_successfully()[source]
Sanity checks that the program ran successfully. Looks at the bottom of the CP2K output file for the “PROGRAM ENDED” line, which is printed when successfully ran. Also grabs the number of warnings issued.
- read_pattern(patterns, reverse=False, terminate_on_match=False, postprocess=<class 'str'>)[source]
Originally from pymatgen.io.vasp.outputs.Outcar.
General pattern reading. Uses monty’s regrep method. Takes 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, row_pattern, footer_pattern, postprocess=<class 'str'>, attribute_name=None, last_one_only=True, strip=None)[source]
This function originated in pymatgen.io.vasp.outputs.Outcar.
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.
- Parameters:
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 “n” 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.
strip (list) – Whether or not to strip contents out of the file before reading for a table pattern. This is mainly used by parse_scf_opt(), to strip HFX info out of the SCF loop start or DFT+U warnings out of the SCF loop iterations.
- 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 the capturing group is defined without name in row_pattern, or a dict in case that named capturing groups are defined by row_pattern.
- parse_energy_file(energy_file)[source]
Parse energy file for calculations with multiple ionic steps.
- parse_pdos(dos_file=None, spin_channel=None, total=False)[source]
Parse a single DOS file created by CP2K. Must contain one PDOS snapshot. i.e. you cannot use this cannot deal with multiple concatenated dos files.
- Parameters:
dos_file (list) – list of pdos_ALPHA file paths
spin_channel (int) – Which spin channel the file corresponds to. By default, CP2K will write the file with ALPHA or BETA in the filename (for spin up or down), but you can specify this here, in case you have a manual file name. spin_channel == 1 –> spin up, spin_channel == -1 –> spin down.
total (bool) – Whether to grab the total occupations, or the orbital decomposed ones.
sigma (float) – width for gaussian smearing, if desired
- Returns:
orbital decomposed DOS dict: i.e. pdoss = {specie: {orbital.s: {Spin.up: … }, orbital.px: {Spin.up: … } …}}
energy levels of this dos file
fermi energy (in eV).
DOS object is not created here
- Return type:
Everything necessary to create a dos object, in dict format
pymatgen.io.cp2k.sets module
This module defines input sets for CP2K and is a work in progress. The structure/philosophy of this module is based on the Vasp input sets in Pymatgen. These sets are meant to contain tested parameters that will result in successful, reproducible, consistent calculations without need for intervention 99% of the time. 99% of the time, you only need to provide a pymatgen structure object and let the defaults take over from there.
The sets are intended to be very general, e.g. a set for geometry relaxation, and so most of the time, if you have specific needs, you can simply specify them via the keyword argument override_default_params (see Section.update() method). If you have the need to create a new input set (say for a standardized high throughput calculation) then you can create a new child of the Cp2kInputSet class.
- In order to implement a new Set within the current code structure, follow this 3 step flow:
Inherit from Cp2kInputSet or one of its children and call the super() constructor
Create the new sections and insert them into self and its subsections as needed
Call self.update(override_default_params) in order to allow user settings.
- class CellOptSet(**kwargs)[source]
Bases:
DftSetQuick Constructor for cell optimization relaxation.
- Parameters:
structure – Pymatgen structure or molecule object
basis_and_potential (dict) – Basis set and pseudo-potential to use for each element. See DftSet.get_basis_and_potential for allowed formats.
element_defaults (dict) – Default settings such as initial magnetization for each element. See DftSet.create_subsys for allowed formats.
ot (bool) – Whether or not to use orbital transformation method for matrix diagonalization. OT is the flagship scf solver of CP2K, and will provide speed-ups for this part of the calculation, but the system must have a band gap for OT to be used (higher band-gap –> faster convergence).
energy_gap (float) – Estimate of energy gap for pre-conditioner. Default is -1, leaving it up to CP2K.
eps_default (float) – Replaces all EPS_XX Keywords in the DFT section value, ensuring an overall accuracy of at least this much.
eps_scf (float) –
The convergence criteria for leaving the SCF loop. Default is 1e-6. Should ensure reasonable results, but is not applicable to all situations.
Note: eps_scf is not in units of energy, as in most DFT codes. For OT method, it is the largest gradient of the energy with respect to changing any of the molecular orbital coefficients. For diagonalization, it is the largest change in the density matrix from the last step.
max_scf (int) – The max number of SCF cycles before terminating the solver. NOTE: With the OT solver, this corresponds to the max number of INNER scf loops, and then the outer loops are set with outer_max_scf, while with diagonalization it corresponds to the overall (INNER*OUTER) number of SCF steps, with the inner loop limit set by
minimizer (str) – The minimization scheme. DIIS can be as much as 50% faster than the more robust conjugate gradient method, and so it is chosen as default. Switch to CG if dealing with a difficult system.
preconditioner (str) – Pre-conditioner for the OT method. FULL_SINGLE_INVERSE is very robust and compatible with non-integer occupations from IRAC+rotation. FULL_ALL is considered “best” but needs algorithm to be set to STRICT. Only change from these two when simulation cell gets to be VERY large, in which case FULL_KINETIC might be preferred.
algorithm (str) – Algorithm for the OT method. STRICT assumes that the orbitals are strictly orthogonal to each other, which works well for wide gap ionic systems, but can diverge for systems with small gaps, fractional occupations, and some other cases. IRAC (iterative refinement of the approximate congruency) transformation is not analytically correct and uses a truncated polynomial expansion, but is robust to the problems with STRICT, and so is the default.
linesearch (str) – Linesearch method for CG. 2PNT is the default, and is the fastest, but is not as robust as 3PNT. 2PNT is required as of CP2K v9.1 for compatibility with irac+rotation. This may be upgraded in the future. 3PNT can be good for wide gapped transition metal systems as an alternative.
rotation (bool) – Whether or not to allow for rotation of the orbitals in the OT method. This equates to allowing for fractional occupations in the calculation.
occupation_preconditioner (bool) – Whether or not to account for fractional occupations in the preconditioner. This method is not fully integrated as of CP2K v9.1 and is set to false by default.
cutoff (int) – Cutoff energy (in Ry) for the finest level of the multigrid. A high cutoff will allow you to have very accurate calculations PROVIDED that REL_CUTOFF is appropriate. By default cutoff is set to 0, leaving it up to the set.
rel_cutoff (int) – This cutoff decides how the Gaussians are mapped onto the different levels of the multigrid. If REL_CUTOFF is too low, then even if you have a high CUTOFF, all Gaussians will be mapped onto the coarsest level of the multi-grid, and thus the effective integration grid for the calculation may still be too coarse. By default 50Ry is chosen, which should be sufficient given the cutoff is large enough.
ngrids (int) – number of multi-grids to use. CP2K default is 4, but the molopt basis files recommend 5.
progression_factor (int) – Divisor of CUTOFF to get the cutoff for the next level of the multigrid.
wfn_restart_file_name (str) – RESTART file for the initial wavefunction guess.
kpoints (Kpoints) – kpoints object from pymatgen.io.vasp.inputs.Kpoints. By default, CP2K runs with gamma point only.
smearing (bool) – whether or not to activate smearing (should be done for systems containing no (or a very small) band gap.
cell (dict[str, Any]) – Keywords to add to the CELL section such as SYMMETRY. See https://manual.cp2k.org/trunk/CP2K_INPUT/FORCE_EVAL/SUBSYS/CELL.html#CP2K_INPUT.FORCE_EVAL.SUBSYS.CELL
- exception Cp2kValidationError(message)[source]
Bases:
ExceptionCP2K validation exception. Not exhausted. May raise validation errors for features which actually do work if using a newer version of CP2K.
- class DftSet(structure: Structure | Molecule, project_name: str = 'CP2K', basis_and_potential: dict | None = None, element_defaults: dict[str, dict[str, Any]] | None = None, xc_functionals: list | str | None = None, multiplicity: int = 0, ot: bool = True, energy_gap: float = -1, qs_method: str = 'GPW', eps_default: float = 1e-12, eps_scf: float = 1e-06, max_scf: int | None = None, minimizer: str = 'DIIS', preconditioner: str = 'FULL_SINGLE_INVERSE', algorithm: str = 'IRAC', linesearch: str = '2PNT', rotation: bool = True, occupation_preconditioner: bool = False, cutoff: float | None = None, rel_cutoff: int = 50, ngrids: int = 5, progression_factor: int = 3, override_default_params: dict | None = None, wfn_restart_file_name: str | None = None, kpoints: Kpoints | None = None, smearing: bool = False, cell: dict[str, Any] | None = None, **kwargs)[source]
Bases:
Cp2kInputBase for an input set using the Quickstep module (i.e. a DFT calculation). The DFT section is pretty vast in CP2K, so this set hopes to make the DFT setup fairly simple. The provided parameters are pretty conservative, and so they should not need to be changed very often.
- Parameters:
structure – Pymatgen structure or molecule object
basis_and_potential (dict) – Basis set and pseudo-potential to use for each element. See DftSet.get_basis_and_potential for allowed formats.
element_defaults (dict) – Default settings such as initial magnetization for each element. See DftSet.create_subsys for allowed formats.
ot (bool) – Whether or not to use orbital transformation method for matrix diagonalization. OT is the flagship scf solver of CP2K, and will provide speed-ups for this part of the calculation, but the system must have a band gap for OT to be used (higher band-gap –> faster convergence).
energy_gap (float) – Estimate of energy gap for pre-conditioner. Default is -1, leaving it up to CP2K.
eps_default (float) – Replaces all EPS_XX Keywords in the DFT section value, ensuring an overall accuracy of at least this much.
eps_scf (float) –
The convergence criteria for leaving the SCF loop. Default is 1e-6. Should ensure reasonable results, but is not applicable to all situations.
Note: eps_scf is not in units of energy, as in most DFT codes. For OT method, it is the largest gradient of the energy with respect to changing any of the molecular orbital coefficients. For diagonalization, it is the largest change in the density matrix from the last step.
max_scf (int) – The max number of SCF cycles before terminating the solver. NOTE: With the OT solver, this corresponds to the max number of INNER scf loops, and then the outer loops are set with outer_max_scf, while with diagonalization it corresponds to the overall (INNER*OUTER) number of SCF steps, with the inner loop limit set by
minimizer (str) – The minimization scheme. DIIS can be as much as 50% faster than the more robust conjugate gradient method, and so it is chosen as default. Switch to CG if dealing with a difficult system.
preconditioner (str) – Pre-conditioner for the OT method. FULL_SINGLE_INVERSE is very robust and compatible with non-integer occupations from IRAC+rotation. FULL_ALL is considered “best” but needs algorithm to be set to STRICT. Only change from these two when simulation cell gets to be VERY large, in which case FULL_KINETIC might be preferred.
algorithm (str) – Algorithm for the OT method. STRICT assumes that the orbitals are strictly orthogonal to each other, which works well for wide gap ionic systems, but can diverge for systems with small gaps, fractional occupations, and some other cases. IRAC (iterative refinement of the approximate congruency) transformation is not analytically correct and uses a truncated polynomial expansion, but is robust to the problems with STRICT, and so is the default.
linesearch (str) – Linesearch method for CG. 2PNT is the default, and is the fastest, but is not as robust as 3PNT. 2PNT is required as of CP2K v9.1 for compatibility with irac+rotation. This may be upgraded in the future. 3PNT can be good for wide gapped transition metal systems as an alternative.
rotation (bool) – Whether or not to allow for rotation of the orbitals in the OT method. This equates to allowing for fractional occupations in the calculation.
occupation_preconditioner (bool) – Whether or not to account for fractional occupations in the preconditioner. This method is not fully integrated as of CP2K v9.1 and is set to false by default.
cutoff (int) – Cutoff energy (in Ry) for the finest level of the multigrid. A high cutoff will allow you to have very accurate calculations PROVIDED that REL_CUTOFF is appropriate. By default cutoff is set to 0, leaving it up to the set.
rel_cutoff (int) – This cutoff decides how the Gaussians are mapped onto the different levels of the multigrid. If REL_CUTOFF is too low, then even if you have a high CUTOFF, all Gaussians will be mapped onto the coarsest level of the multi-grid, and thus the effective integration grid for the calculation may still be too coarse. By default 50Ry is chosen, which should be sufficient given the cutoff is large enough.
ngrids (int) – number of multi-grids to use. CP2K default is 4, but the molopt basis files recommend 5.
progression_factor (int) – Divisor of CUTOFF to get the cutoff for the next level of the multigrid.
wfn_restart_file_name (str) – RESTART file for the initial wavefunction guess.
kpoints (Kpoints) – kpoints object from pymatgen.io.vasp.inputs.Kpoints. By default, CP2K runs with gamma point only.
smearing (bool) – whether or not to activate smearing (should be done for systems containing no (or a very small) band gap.
cell (dict[str, Any]) – Keywords to add to the CELL section such as SYMMETRY. See https://manual.cp2k.org/trunk/CP2K_INPUT/FORCE_EVAL/SUBSYS/CELL.html#CP2K_INPUT.FORCE_EVAL.SUBSYS.CELL
- activate_hybrid(hybrid_functional: str = 'PBE0', hf_fraction: float = 0.25, gga_x_fraction: float = 0.75, gga_c_fraction: float = 1, max_memory: int = 2000, cutoff_radius: float = 8.0, potential_type: str | None = None, omega: float = 0.11, scale_coulomb: float = 1, scale_gaussian: float = 1, scale_longrange: float = 1, admm: bool = True, admm_method: str = 'BASIS_PROJECTION', admm_purification_method: str = 'NONE', admm_exch_correction_func: str = 'DEFAULT', eps_schwarz: float = 1e-07, eps_schwarz_forces: float = 1e-06, screen_on_initial_p: bool = True, screen_p_forces: bool = True) None[source]
Basic set for activating hybrid DFT calculation using Auxiliary Density Matrix Method.
Note 1: When running ADMM with CP2K, memory is very important. If the memory requirements exceed what is available (see max_memory), then CP2K will have to calculate the 4-electron integrals for HFX during each step of the SCF cycle. ADMM provides a huge speed up by making the memory requirements feasible to fit into RAM, which means you only need to calculate the integrals once each SCF cycle. But, this only works if it fits into memory. When setting up ADMM calculations, we recommend doing whatever is possible to fit all the 4EI into memory.
Note 2: This set is designed for reliable high-throughput calculations, NOT for extreme accuracy. Please review the in-line comments in this method if you want more control.
- Parameters:
hybrid_functional (str) – Type of hybrid functional. This set supports HSE (screened) and PBE0 (truncated). Default is PBE0, which converges easier in the GPW basis used by CP2K.
hf_fraction (float) – fraction of exact HF exchange energy to mix. Default: 0.25
gga_x_fraction (float) – fraction of gga exchange energy to retain. Default: 0.75
gga_c_fraction (float) – fraction of gga correlation energy to retain. Default: 1.0
max_memory (int) – Maximum memory available to each MPI process (in Mb) in the calculation. Most modern computing nodes will have ~2Gb per core, or 2048 Mb, but check for your specific system. This value should be as large as possible while still leaving some memory for the other parts of CP2K. Important: If this value is set larger than the memory limits, CP2K will likely seg-fault. Default: 2000
cutoff_radius (float) – for truncated hybrid functional (i.e. PBE0), this is the cutoff radius. The default is selected as that which generally gives convergence, but maybe too low (if you want very high accuracy) or too high (if you want a quick screening). Default: 8 angstroms
potential_type (str) – what interaction potential to use for HFX. Available in CP2K are COULOMB, GAUSSIAN, IDENTITY, LOGRANGE, MIX_CL, MIX_CL_TRUNC, MIX_LG, SHORTRANGE, and TRUNCATED. Default is None, and it will be set automatically depending on the named hybrid_functional that you use, but setting it to one of the acceptable values will constitute a user-override.
omega (float) – For HSE, this specifies the screening parameter. HSE06 sets this as 0.2, which is the default.
scale_coulomb – Scale for the coulomb operator if using a range separated functional
scale_gaussian – Scale for the gaussian operator (if applicable)
scale_longrange – Scale for the coulomb operator if using a range separated functional
admm – Whether or not to use the auxiliary density matrix method for the exact HF exchange contribution. Highly recommended. Speed ups between 10x and 1000x are possible when compared to non ADMM hybrid calculations.
admm_method – Method for constructing the auxiliary basis
admm_purification_method – Method for purifying the auxiliary density matrix so as to preserve properties, such as idempotency. May lead to shifts in the eigenvalues.
admm_exch_correction_func – Which functional to use to calculate the exchange correction E_x(primary) - E_x(aux)
eps_schwarz – Screening threshold for HFX, in Ha. Contributions smaller than this will be screened. The smaller the value, the more accurate, but also the more costly. Default value is 1e-7. 1e-6 works in a large number of cases, but is quite aggressive, which can lead to convergence issues.
eps_schwarz_forces – Same as for eps_schwarz, but for screening contributions to forces. Convergence is not as sensitive with respect to eps_schwarz forces as compared to eps_schwarz, and so 1e-6 should be good default.
screen_on_initial_p – If an initial density matrix is provided, in the form of a CP2K wfn restart file, then this initial density will be used for screening. This is generally very computationally efficient, but, as with eps_schwarz, can lead to instabilities if the initial density matrix is poor.
screen_p_forces – Same as screen_on_initial_p, but for screening of forces.
- activate_localize(states='OCCUPIED', preconditioner='FULL_ALL', restart=False) None[source]
Activate calculation of the maximally localized wannier functions.
- Parameters:
states – Which states to calculate. occupied, unoccupied, mixed states, or all states. At present, unoccupied orbitals are only implemented for GPW.
preconditioner – Preconditioner to use for optimize
restart – Initialize from the localization restart file
- activate_motion(max_drift: float = 0.003, rms_drift: float = 0.0015, max_force: float = 0.00045, rms_force: float = 0.0003, max_iter: int = 200, optimizer: str = 'BFGS', trust_radius: float = 0.25, line_search: str = '2PNT', ensemble: str = 'NVE', temperature: float = 300, timestep: float = 0.5, nsteps: int = 3, thermostat: str = 'NOSE', nproc_rep: int = 1) None[source]
Turns on the motion section for GEO_OPT, CELL_OPT, etc. calculations. Will turn on the printing subsections and also bind any constraints to their respective atoms.
- activate_nonperiodic(solver='ANALYTIC') None[source]
Activates a calculation with non-periodic calculations by turning of PBC and changing the poisson solver. Still requires a CELL to put the atoms.
- activate_robust_minimization() None[source]
Modify the set to use more robust SCF minimization technique.
- activate_tddfpt(**kwargs) None[source]
Activate TDDFPT for calculating excited states. Only works with GPW. Supports hfx.
- activate_vdw_potential(dispersion_functional: str, potential_type: str) None[source]
Activate van der Waals dispersion corrections.
- Parameters:
dispersion_functional – Type of dispersion functional. Options: pair_potential or non_local
potential_type – What type of potential to use, given a dispersion functional type Options: DFTD2, DFTD3, DFTD3(BJ), DRSLL, LMKLL, RVV10
- activate_very_strict_minimization() None[source]
Method to modify the set to use very strict SCF minimization scheme.
- static get_basis_and_potential(structure: Structure | IStructure, basis_and_potential: dict[str, dict[str, Any]], cp2k_data_dir: str | None = None) dict[str, dict[str, Any]][source]
Get a dictionary of basis and potential info for constructing the input file.
data in basis_and_potential argument can be specified in several ways:
Strategy 1: Element-specific info (takes precedence)
Provide a basis and potential object:
el: {‘basis’: obj, ‘potential’: obj}
Provide a hash of the object that matches the keys in the pmg configured CP2K data files.
el: {‘basis’: hash, ‘potential’: hash}
3. Provide the name of the basis and potential AND the basis_filenames and potential_filename keywords specifying where to find these objects
- el: {
‘basis’: name, ‘potential’: name, ‘basis_filenames’: [filenames], ‘potential_filename’: filename
}
Strategy 2: global descriptors
In this case, any elements not present in the argument will be dealt with by searching the pmg configured CP2K data files to find a objects matching your requirements.
- functional: Find potential and basis that have been optimized for a specific functional like PBE.
Can be None if you do not require them to match.
basis_type: type of basis to search for (e.g. DZVP-MOLOPT).
- aux_basis_type: type of basis to search for (e.g. pFIT). Some elements do not have all aux types
available. Use aux_basis_type that is universal to avoid issues, or avoid using this strategy.
potential_type: “Pseudopotential” or “All Electron”
*BE WARNED* CP2K data objects can have the same name, this will sort those and choose the first one that matches.
Will raise an error if no basis/potential info can be found according to the input.
- static get_cutoff_from_basis(basis_sets, rel_cutoff) float[source]
Given a basis and a relative cutoff. Determine the ideal cutoff variable.
- static get_xc_functionals(xc_functionals: list | str | None = None) list[source]
Get XC functionals. If simplified names are provided in kwargs, they will be expanded into their corresponding X and C names.
- modify_dft_print_iters(iters, add_last: Literal['no', 'numeric', 'symbolic'] = 'no')[source]
Modify all DFT print iterations at once. Common use is to set iters to the max number of iterations + 1 and then set add_last to numeric. This would have the effect of printing only the first and last iteration, which might be useful for speeding up/saving space on GEO_OPT or MD runs where you don’t need the intermediate values.
- Parameters:
iters (int) – print each “iters” iterations.
add_last (str) – Whether to explicitly include the last iteration, and how to mark it. numeric: mark last iteration with the iteration number symbolic: mark last iteration with the letter “l” no: do not explicitly include the last iteration
- print_bandstructure(kpoints_line_density: int = 20) None[source]
Attaches a non-scf band structure calc the end of an SCF loop.
This requires a kpoint calculation, which is not always default in CP2K.
- Parameters:
kpoints_line_density – number of kpoints along each branch in line-mode calc.
- print_dos(ndigits=6) None[source]
Activate printing of the overall DOS file.
Note: As of 2022.1, ndigits needs to be set to a sufficient value to ensure data is not lost. Note: As of 2022.1, can only be used with a k-point calculation.
- print_e_density(stride=(2, 2, 2)) None[source]
Controls the printing of cube files with electronic density and, for UKS, the spin density.
- print_ldos(nlumo: int = -1) None[source]
Activate the printing of LDOS files, printing one for each atom kind by default.
- Parameters:
nlumo (int) – Number of virtual orbitals to be added to the MO set (-1=all). CAUTION: Setting this value to be higher than the number of states present may cause a Cholesky error.
- print_mo_cubes(write_cube: bool = False, nlumo: int = -1, nhomo: int = -1) None[source]
Activate printing of molecular orbitals.
- Parameters:
write_cube (bool) – whether to write cube file for the MOs instead of out file
nlumo (int) – Controls the number of lumos printed and dumped as a cube (-1=all)
nhomo (int) – Controls the number of homos printed and dumped as a cube (-1=all)
- print_pdos(nlumo: int = -1) None[source]
Activate creation of the PDOS file.
- Parameters:
nlumo (int) – Number of virtual orbitals to be added to the MO set (-1=all). CAUTION: Setting this value to be higher than the number of states present may cause a Cholesky error.
- class HybridCellOptSet(**kwargs)[source]
Bases:
DftSetQuick Constructor for hybrid cell optimization relaxation.
- Parameters:
structure – Pymatgen structure or molecule object
basis_and_potential (dict) – Basis set and pseudo-potential to use for each element. See DftSet.get_basis_and_potential for allowed formats.
element_defaults (dict) – Default settings such as initial magnetization for each element. See DftSet.create_subsys for allowed formats.
ot (bool) – Whether or not to use orbital transformation method for matrix diagonalization. OT is the flagship scf solver of CP2K, and will provide speed-ups for this part of the calculation, but the system must have a band gap for OT to be used (higher band-gap –> faster convergence).
energy_gap (float) – Estimate of energy gap for pre-conditioner. Default is -1, leaving it up to CP2K.
eps_default (float) – Replaces all EPS_XX Keywords in the DFT section value, ensuring an overall accuracy of at least this much.
eps_scf (float) –
The convergence criteria for leaving the SCF loop. Default is 1e-6. Should ensure reasonable results, but is not applicable to all situations.
Note: eps_scf is not in units of energy, as in most DFT codes. For OT method, it is the largest gradient of the energy with respect to changing any of the molecular orbital coefficients. For diagonalization, it is the largest change in the density matrix from the last step.
max_scf (int) – The max number of SCF cycles before terminating the solver. NOTE: With the OT solver, this corresponds to the max number of INNER scf loops, and then the outer loops are set with outer_max_scf, while with diagonalization it corresponds to the overall (INNER*OUTER) number of SCF steps, with the inner loop limit set by
minimizer (str) – The minimization scheme. DIIS can be as much as 50% faster than the more robust conjugate gradient method, and so it is chosen as default. Switch to CG if dealing with a difficult system.
preconditioner (str) – Pre-conditioner for the OT method. FULL_SINGLE_INVERSE is very robust and compatible with non-integer occupations from IRAC+rotation. FULL_ALL is considered “best” but needs algorithm to be set to STRICT. Only change from these two when simulation cell gets to be VERY large, in which case FULL_KINETIC might be preferred.
algorithm (str) – Algorithm for the OT method. STRICT assumes that the orbitals are strictly orthogonal to each other, which works well for wide gap ionic systems, but can diverge for systems with small gaps, fractional occupations, and some other cases. IRAC (iterative refinement of the approximate congruency) transformation is not analytically correct and uses a truncated polynomial expansion, but is robust to the problems with STRICT, and so is the default.
linesearch (str) – Linesearch method for CG. 2PNT is the default, and is the fastest, but is not as robust as 3PNT. 2PNT is required as of CP2K v9.1 for compatibility with irac+rotation. This may be upgraded in the future. 3PNT can be good for wide gapped transition metal systems as an alternative.
rotation (bool) – Whether or not to allow for rotation of the orbitals in the OT method. This equates to allowing for fractional occupations in the calculation.
occupation_preconditioner (bool) – Whether or not to account for fractional occupations in the preconditioner. This method is not fully integrated as of CP2K v9.1 and is set to false by default.
cutoff (int) – Cutoff energy (in Ry) for the finest level of the multigrid. A high cutoff will allow you to have very accurate calculations PROVIDED that REL_CUTOFF is appropriate. By default cutoff is set to 0, leaving it up to the set.
rel_cutoff (int) – This cutoff decides how the Gaussians are mapped onto the different levels of the multigrid. If REL_CUTOFF is too low, then even if you have a high CUTOFF, all Gaussians will be mapped onto the coarsest level of the multi-grid, and thus the effective integration grid for the calculation may still be too coarse. By default 50Ry is chosen, which should be sufficient given the cutoff is large enough.
ngrids (int) – number of multi-grids to use. CP2K default is 4, but the molopt basis files recommend 5.
progression_factor (int) – Divisor of CUTOFF to get the cutoff for the next level of the multigrid.
wfn_restart_file_name (str) – RESTART file for the initial wavefunction guess.
kpoints (Kpoints) – kpoints object from pymatgen.io.vasp.inputs.Kpoints. By default, CP2K runs with gamma point only.
smearing (bool) – whether or not to activate smearing (should be done for systems containing no (or a very small) band gap.
cell (dict[str, Any]) – Keywords to add to the CELL section such as SYMMETRY. See https://manual.cp2k.org/trunk/CP2K_INPUT/FORCE_EVAL/SUBSYS/CELL.html#CP2K_INPUT.FORCE_EVAL.SUBSYS.CELL
- class HybridRelaxSet(**kwargs)[source]
Bases:
DftSetQuick Constructor for hybrid geometry relaxation.
- Parameters:
structure – Pymatgen structure or molecule object
basis_and_potential (dict) – Basis set and pseudo-potential to use for each element. See DftSet.get_basis_and_potential for allowed formats.
element_defaults (dict) – Default settings such as initial magnetization for each element. See DftSet.create_subsys for allowed formats.
ot (bool) – Whether or not to use orbital transformation method for matrix diagonalization. OT is the flagship scf solver of CP2K, and will provide speed-ups for this part of the calculation, but the system must have a band gap for OT to be used (higher band-gap –> faster convergence).
energy_gap (float) – Estimate of energy gap for pre-conditioner. Default is -1, leaving it up to CP2K.
eps_default (float) – Replaces all EPS_XX Keywords in the DFT section value, ensuring an overall accuracy of at least this much.
eps_scf (float) –
The convergence criteria for leaving the SCF loop. Default is 1e-6. Should ensure reasonable results, but is not applicable to all situations.
Note: eps_scf is not in units of energy, as in most DFT codes. For OT method, it is the largest gradient of the energy with respect to changing any of the molecular orbital coefficients. For diagonalization, it is the largest change in the density matrix from the last step.
max_scf (int) – The max number of SCF cycles before terminating the solver. NOTE: With the OT solver, this corresponds to the max number of INNER scf loops, and then the outer loops are set with outer_max_scf, while with diagonalization it corresponds to the overall (INNER*OUTER) number of SCF steps, with the inner loop limit set by
minimizer (str) – The minimization scheme. DIIS can be as much as 50% faster than the more robust conjugate gradient method, and so it is chosen as default. Switch to CG if dealing with a difficult system.
preconditioner (str) – Pre-conditioner for the OT method. FULL_SINGLE_INVERSE is very robust and compatible with non-integer occupations from IRAC+rotation. FULL_ALL is considered “best” but needs algorithm to be set to STRICT. Only change from these two when simulation cell gets to be VERY large, in which case FULL_KINETIC might be preferred.
algorithm (str) – Algorithm for the OT method. STRICT assumes that the orbitals are strictly orthogonal to each other, which works well for wide gap ionic systems, but can diverge for systems with small gaps, fractional occupations, and some other cases. IRAC (iterative refinement of the approximate congruency) transformation is not analytically correct and uses a truncated polynomial expansion, but is robust to the problems with STRICT, and so is the default.
linesearch (str) – Linesearch method for CG. 2PNT is the default, and is the fastest, but is not as robust as 3PNT. 2PNT is required as of CP2K v9.1 for compatibility with irac+rotation. This may be upgraded in the future. 3PNT can be good for wide gapped transition metal systems as an alternative.
rotation (bool) – Whether or not to allow for rotation of the orbitals in the OT method. This equates to allowing for fractional occupations in the calculation.
occupation_preconditioner (bool) – Whether or not to account for fractional occupations in the preconditioner. This method is not fully integrated as of CP2K v9.1 and is set to false by default.
cutoff (int) – Cutoff energy (in Ry) for the finest level of the multigrid. A high cutoff will allow you to have very accurate calculations PROVIDED that REL_CUTOFF is appropriate. By default cutoff is set to 0, leaving it up to the set.
rel_cutoff (int) – This cutoff decides how the Gaussians are mapped onto the different levels of the multigrid. If REL_CUTOFF is too low, then even if you have a high CUTOFF, all Gaussians will be mapped onto the coarsest level of the multi-grid, and thus the effective integration grid for the calculation may still be too coarse. By default 50Ry is chosen, which should be sufficient given the cutoff is large enough.
ngrids (int) – number of multi-grids to use. CP2K default is 4, but the molopt basis files recommend 5.
progression_factor (int) – Divisor of CUTOFF to get the cutoff for the next level of the multigrid.
wfn_restart_file_name (str) – RESTART file for the initial wavefunction guess.
kpoints (Kpoints) – kpoints object from pymatgen.io.vasp.inputs.Kpoints. By default, CP2K runs with gamma point only.
smearing (bool) – whether or not to activate smearing (should be done for systems containing no (or a very small) band gap.
cell (dict[str, Any]) – Keywords to add to the CELL section such as SYMMETRY. See https://manual.cp2k.org/trunk/CP2K_INPUT/FORCE_EVAL/SUBSYS/CELL.html#CP2K_INPUT.FORCE_EVAL.SUBSYS.CELL
- class HybridStaticSet(**kwargs)[source]
Bases:
DftSetQuick Constructor for static calculations.
- Parameters:
structure – Pymatgen structure or molecule object
basis_and_potential (dict) – Basis set and pseudo-potential to use for each element. See DftSet.get_basis_and_potential for allowed formats.
element_defaults (dict) – Default settings such as initial magnetization for each element. See DftSet.create_subsys for allowed formats.
ot (bool) – Whether or not to use orbital transformation method for matrix diagonalization. OT is the flagship scf solver of CP2K, and will provide speed-ups for this part of the calculation, but the system must have a band gap for OT to be used (higher band-gap –> faster convergence).
energy_gap (float) – Estimate of energy gap for pre-conditioner. Default is -1, leaving it up to CP2K.
eps_default (float) – Replaces all EPS_XX Keywords in the DFT section value, ensuring an overall accuracy of at least this much.
eps_scf (float) –
The convergence criteria for leaving the SCF loop. Default is 1e-6. Should ensure reasonable results, but is not applicable to all situations.
Note: eps_scf is not in units of energy, as in most DFT codes. For OT method, it is the largest gradient of the energy with respect to changing any of the molecular orbital coefficients. For diagonalization, it is the largest change in the density matrix from the last step.
max_scf (int) – The max number of SCF cycles before terminating the solver. NOTE: With the OT solver, this corresponds to the max number of INNER scf loops, and then the outer loops are set with outer_max_scf, while with diagonalization it corresponds to the overall (INNER*OUTER) number of SCF steps, with the inner loop limit set by
minimizer (str) – The minimization scheme. DIIS can be as much as 50% faster than the more robust conjugate gradient method, and so it is chosen as default. Switch to CG if dealing with a difficult system.
preconditioner (str) – Pre-conditioner for the OT method. FULL_SINGLE_INVERSE is very robust and compatible with non-integer occupations from IRAC+rotation. FULL_ALL is considered “best” but needs algorithm to be set to STRICT. Only change from these two when simulation cell gets to be VERY large, in which case FULL_KINETIC might be preferred.
algorithm (str) – Algorithm for the OT method. STRICT assumes that the orbitals are strictly orthogonal to each other, which works well for wide gap ionic systems, but can diverge for systems with small gaps, fractional occupations, and some other cases. IRAC (iterative refinement of the approximate congruency) transformation is not analytically correct and uses a truncated polynomial expansion, but is robust to the problems with STRICT, and so is the default.
linesearch (str) – Linesearch method for CG. 2PNT is the default, and is the fastest, but is not as robust as 3PNT. 2PNT is required as of CP2K v9.1 for compatibility with irac+rotation. This may be upgraded in the future. 3PNT can be good for wide gapped transition metal systems as an alternative.
rotation (bool) – Whether or not to allow for rotation of the orbitals in the OT method. This equates to allowing for fractional occupations in the calculation.
occupation_preconditioner (bool) – Whether or not to account for fractional occupations in the preconditioner. This method is not fully integrated as of CP2K v9.1 and is set to false by default.
cutoff (int) – Cutoff energy (in Ry) for the finest level of the multigrid. A high cutoff will allow you to have very accurate calculations PROVIDED that REL_CUTOFF is appropriate. By default cutoff is set to 0, leaving it up to the set.
rel_cutoff (int) – This cutoff decides how the Gaussians are mapped onto the different levels of the multigrid. If REL_CUTOFF is too low, then even if you have a high CUTOFF, all Gaussians will be mapped onto the coarsest level of the multi-grid, and thus the effective integration grid for the calculation may still be too coarse. By default 50Ry is chosen, which should be sufficient given the cutoff is large enough.
ngrids (int) – number of multi-grids to use. CP2K default is 4, but the molopt basis files recommend 5.
progression_factor (int) – Divisor of CUTOFF to get the cutoff for the next level of the multigrid.
wfn_restart_file_name (str) – RESTART file for the initial wavefunction guess.
kpoints (Kpoints) – kpoints object from pymatgen.io.vasp.inputs.Kpoints. By default, CP2K runs with gamma point only.
smearing (bool) – whether or not to activate smearing (should be done for systems containing no (or a very small) band gap.
cell (dict[str, Any]) – Keywords to add to the CELL section such as SYMMETRY. See https://manual.cp2k.org/trunk/CP2K_INPUT/FORCE_EVAL/SUBSYS/CELL.html#CP2K_INPUT.FORCE_EVAL.SUBSYS.CELL
- class RelaxSet(**kwargs)[source]
Bases:
DftSetQuick Constructor for geometry relaxation.
- Parameters:
structure – Pymatgen structure or molecule object
basis_and_potential (dict) – Basis set and pseudo-potential to use for each element. See DftSet.get_basis_and_potential for allowed formats.
element_defaults (dict) – Default settings such as initial magnetization for each element. See DftSet.create_subsys for allowed formats.
ot (bool) – Whether or not to use orbital transformation method for matrix diagonalization. OT is the flagship scf solver of CP2K, and will provide speed-ups for this part of the calculation, but the system must have a band gap for OT to be used (higher band-gap –> faster convergence).
energy_gap (float) – Estimate of energy gap for pre-conditioner. Default is -1, leaving it up to CP2K.
eps_default (float) – Replaces all EPS_XX Keywords in the DFT section value, ensuring an overall accuracy of at least this much.
eps_scf (float) –
The convergence criteria for leaving the SCF loop. Default is 1e-6. Should ensure reasonable results, but is not applicable to all situations.
Note: eps_scf is not in units of energy, as in most DFT codes. For OT method, it is the largest gradient of the energy with respect to changing any of the molecular orbital coefficients. For diagonalization, it is the largest change in the density matrix from the last step.
max_scf (int) – The max number of SCF cycles before terminating the solver. NOTE: With the OT solver, this corresponds to the max number of INNER scf loops, and then the outer loops are set with outer_max_scf, while with diagonalization it corresponds to the overall (INNER*OUTER) number of SCF steps, with the inner loop limit set by
minimizer (str) – The minimization scheme. DIIS can be as much as 50% faster than the more robust conjugate gradient method, and so it is chosen as default. Switch to CG if dealing with a difficult system.
preconditioner (str) – Pre-conditioner for the OT method. FULL_SINGLE_INVERSE is very robust and compatible with non-integer occupations from IRAC+rotation. FULL_ALL is considered “best” but needs algorithm to be set to STRICT. Only change from these two when simulation cell gets to be VERY large, in which case FULL_KINETIC might be preferred.
algorithm (str) – Algorithm for the OT method. STRICT assumes that the orbitals are strictly orthogonal to each other, which works well for wide gap ionic systems, but can diverge for systems with small gaps, fractional occupations, and some other cases. IRAC (iterative refinement of the approximate congruency) transformation is not analytically correct and uses a truncated polynomial expansion, but is robust to the problems with STRICT, and so is the default.
linesearch (str) – Linesearch method for CG. 2PNT is the default, and is the fastest, but is not as robust as 3PNT. 2PNT is required as of CP2K v9.1 for compatibility with irac+rotation. This may be upgraded in the future. 3PNT can be good for wide gapped transition metal systems as an alternative.
rotation (bool) – Whether or not to allow for rotation of the orbitals in the OT method. This equates to allowing for fractional occupations in the calculation.
occupation_preconditioner (bool) – Whether or not to account for fractional occupations in the preconditioner. This method is not fully integrated as of CP2K v9.1 and is set to false by default.
cutoff (int) – Cutoff energy (in Ry) for the finest level of the multigrid. A high cutoff will allow you to have very accurate calculations PROVIDED that REL_CUTOFF is appropriate. By default cutoff is set to 0, leaving it up to the set.
rel_cutoff (int) – This cutoff decides how the Gaussians are mapped onto the different levels of the multigrid. If REL_CUTOFF is too low, then even if you have a high CUTOFF, all Gaussians will be mapped onto the coarsest level of the multi-grid, and thus the effective integration grid for the calculation may still be too coarse. By default 50Ry is chosen, which should be sufficient given the cutoff is large enough.
ngrids (int) – number of multi-grids to use. CP2K default is 4, but the molopt basis files recommend 5.
progression_factor (int) – Divisor of CUTOFF to get the cutoff for the next level of the multigrid.
wfn_restart_file_name (str) – RESTART file for the initial wavefunction guess.
kpoints (Kpoints) – kpoints object from pymatgen.io.vasp.inputs.Kpoints. By default, CP2K runs with gamma point only.
smearing (bool) – whether or not to activate smearing (should be done for systems containing no (or a very small) band gap.
cell (dict[str, Any]) – Keywords to add to the CELL section such as SYMMETRY. See https://manual.cp2k.org/trunk/CP2K_INPUT/FORCE_EVAL/SUBSYS/CELL.html#CP2K_INPUT.FORCE_EVAL.SUBSYS.CELL
- class StaticSet(**kwargs)[source]
Bases:
DftSetQuick Constructor for static calculations.
- Parameters:
structure – Pymatgen structure or molecule object
basis_and_potential (dict) – Basis set and pseudo-potential to use for each element. See DftSet.get_basis_and_potential for allowed formats.
element_defaults (dict) – Default settings such as initial magnetization for each element. See DftSet.create_subsys for allowed formats.
ot (bool) – Whether or not to use orbital transformation method for matrix diagonalization. OT is the flagship scf solver of CP2K, and will provide speed-ups for this part of the calculation, but the system must have a band gap for OT to be used (higher band-gap –> faster convergence).
energy_gap (float) – Estimate of energy gap for pre-conditioner. Default is -1, leaving it up to CP2K.
eps_default (float) – Replaces all EPS_XX Keywords in the DFT section value, ensuring an overall accuracy of at least this much.
eps_scf (float) –
The convergence criteria for leaving the SCF loop. Default is 1e-6. Should ensure reasonable results, but is not applicable to all situations.
Note: eps_scf is not in units of energy, as in most DFT codes. For OT method, it is the largest gradient of the energy with respect to changing any of the molecular orbital coefficients. For diagonalization, it is the largest change in the density matrix from the last step.
max_scf (int) – The max number of SCF cycles before terminating the solver. NOTE: With the OT solver, this corresponds to the max number of INNER scf loops, and then the outer loops are set with outer_max_scf, while with diagonalization it corresponds to the overall (INNER*OUTER) number of SCF steps, with the inner loop limit set by
minimizer (str) – The minimization scheme. DIIS can be as much as 50% faster than the more robust conjugate gradient method, and so it is chosen as default. Switch to CG if dealing with a difficult system.
preconditioner (str) – Pre-conditioner for the OT method. FULL_SINGLE_INVERSE is very robust and compatible with non-integer occupations from IRAC+rotation. FULL_ALL is considered “best” but needs algorithm to be set to STRICT. Only change from these two when simulation cell gets to be VERY large, in which case FULL_KINETIC might be preferred.
algorithm (str) – Algorithm for the OT method. STRICT assumes that the orbitals are strictly orthogonal to each other, which works well for wide gap ionic systems, but can diverge for systems with small gaps, fractional occupations, and some other cases. IRAC (iterative refinement of the approximate congruency) transformation is not analytically correct and uses a truncated polynomial expansion, but is robust to the problems with STRICT, and so is the default.
linesearch (str) – Linesearch method for CG. 2PNT is the default, and is the fastest, but is not as robust as 3PNT. 2PNT is required as of CP2K v9.1 for compatibility with irac+rotation. This may be upgraded in the future. 3PNT can be good for wide gapped transition metal systems as an alternative.
rotation (bool) – Whether or not to allow for rotation of the orbitals in the OT method. This equates to allowing for fractional occupations in the calculation.
occupation_preconditioner (bool) – Whether or not to account for fractional occupations in the preconditioner. This method is not fully integrated as of CP2K v9.1 and is set to false by default.
cutoff (int) – Cutoff energy (in Ry) for the finest level of the multigrid. A high cutoff will allow you to have very accurate calculations PROVIDED that REL_CUTOFF is appropriate. By default cutoff is set to 0, leaving it up to the set.
rel_cutoff (int) – This cutoff decides how the Gaussians are mapped onto the different levels of the multigrid. If REL_CUTOFF is too low, then even if you have a high CUTOFF, all Gaussians will be mapped onto the coarsest level of the multi-grid, and thus the effective integration grid for the calculation may still be too coarse. By default 50Ry is chosen, which should be sufficient given the cutoff is large enough.
ngrids (int) – number of multi-grids to use. CP2K default is 4, but the molopt basis files recommend 5.
progression_factor (int) – Divisor of CUTOFF to get the cutoff for the next level of the multigrid.
wfn_restart_file_name (str) – RESTART file for the initial wavefunction guess.
kpoints (Kpoints) – kpoints object from pymatgen.io.vasp.inputs.Kpoints. By default, CP2K runs with gamma point only.
smearing (bool) – whether or not to activate smearing (should be done for systems containing no (or a very small) band gap.
cell (dict[str, Any]) – Keywords to add to the CELL section such as SYMMETRY. See https://manual.cp2k.org/trunk/CP2K_INPUT/FORCE_EVAL/SUBSYS/CELL.html#CP2K_INPUT.FORCE_EVAL.SUBSYS.CELL
pymatgen.io.cp2k.utils module
Utility functions for assisting with CP2K IO.
- get_truncated_coulomb_cutoff(inp_struct: Structure)[source]
Get the truncated Coulomb cutoff for a given structure.
- get_unique_site_indices(struct: Structure | Molecule)[source]
Get unique site indices for a structure according to site properties. Whatever site-property has the most unique values is used for indexing.
For example, if you have magnetic CoO with half Co atoms having a positive moment, and the other half having a negative moment. Then this function will create a dict of sites for Co_1, Co_2, O. This function also deals with “Species” properties like oxi_state and spin by pushing them to site properties.
This creates unique sites, based on site properties, but does not have anything to do with turning those site properties into CP2K input parameters. This will only be done for properties which can be turned into CP2K input parameters, which are stored in parsable_site_properties.
- natural_keys(text: str)[source]
Sort text by numbers coming after an underscore with natural number convention, Ex: [file_1, file_12, file_2] becomes [file_1, file_2, file_12].
- postprocessor(data: str) str | float | bool | None[source]
Helper function to post process the results of the pattern matching functions in Cp2kOutput and turn them to Python types.
- Parameters:
data (str) – The data to be post processed.
- Raises:
ValueError – If the data cannot be parsed.
- Returns:
The post processed data.
- Return type:
str | float | bool | None
- preprocessor(data: str, dir: str = '.') str[source]
CP2K contains internal preprocessor flags that are evaluated before execution. This helper function recognizes those preprocessor flags and replaces them with an equivalent CP2K input (this way everything is contained neatly in the CP2K input structure, even if the user preferred to use the flags.
CP2K preprocessor flags (with arguments) are:
- @INCLUDE FILENAME: Insert the contents of FILENAME into the file at
this location.
@SET VAR VALUE: set a variable, VAR, to have the value, VALUE. $VAR or ${VAR}: replace these with the value of the variable, as set
by the @SET flag.
@IF/@ELIF: Not implemented yet.
- Parameters:
data (str) – CP2K input to preprocess
dir (str, optional) – Path for include files. Default is ‘.’ (current directory).
- Returns:
Preprocessed string