pymatgen-io-validation

v0.0.4

A comprehensive I/O validator for electronic structure calculations For more information about how to use this package see README

Latest version published 6 months ago

License: modified BSD

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Release Date: May 14, 2024
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License

modified BSD

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Last Release: 6 months ago
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Package

Python Versions Compatibility: >=3.8

Age: 8 months
Latest Release: 6 months ago
Dependencies: 3 Direct
Versions: 4
Maintainers: 5
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Readme

pymatgen-io-validation

This package is an extension to pymatgen for performing I/O validation. Specifically, this package checks for discrepancies between a specific calculation and a provided input set; it also checks for known bugs when certain input parameters are used in combination, alongside several other small checks. The motivation for creating this package was to ensure VASP calculations performed by groups outside of the Materials Project (MP) are compliant with MP data, thus enabling their raw data to be included in the MP Database.

Installation

You can install this package by simply running

pip install pymatgen-io-validation

Usage

For validating calculations from the raw files, run:

from pymatgen.io.validation import ValidationDoc
validation_doc = ValidationDoc.from_directory(dir_name = path_to_vasp_calculation_directory)

In the above case, whether a calculation passes the validator can be accessed via validation_doc.valid. Moreover, reasons for an invalidated calculation can be accessed via validation_doc.reasons (this will be empty for valid calculations). Last but not least, warnings for potential issues (sometimes minor, sometimes major) can be accessed via validation_doc.warnings.

For validating calculations from TaskDoc objects from the Emmet package, run:

from pymatgen.io.validation import ValidationDoc
validation_doc = ValidationDoc.from_task_doc(task_doc = my_task_doc)

Contributors

Matthew Kuner (lead), email: matthewkuner@gmail.com
Aaron Kaplan
Janosh Riebesell
Jason Munro

Rationale

Parameter	Reason
ADDGRID	ADDGRID must be set to False. MP uses ADDGRID = False, as the VASP manual states "please do not use this tag [ADDGRID] as default in all your calculations!". ADDGRID can affect the outputted forces, hence all calculations are thus required to have ADDGRID = False for compatibility.
AEXX / AMGGAX / AMGGAC / AGGAX / ALDAC / ALDAX	These parameters should be the VASP defaults unless otherwise specified in a given MP input set, as changing them is effectively a change to the level of theory.
ALGO / IALGO	ALGO must be one of: "Normal", "Conjugate", "All", "Fast", "Exact". (This corresponds to an IALGO of 38, 58, 58, 68, 90, respectively).
DEPER / EBREAK / WEIMIN	DEPER, EBREAK, and WEIMIN should not be changed according to the VASP wiki, hence MP requires them to remain as their default values.
EDIFF	EDIFF must be equal to or greater than the value in the relevant MP input set. This will ensure compatibility between results with those in the MP Database.
EDIFFG	Should be the same or better than in the relevant MP input set. For MP input sets with an energy-based cutoff, the calculation must have an energy change between the last two steps be less in magnitude than the specified EDIFFG (so even if your calculation uses force-based convergence, the energy must converge within the MP input set’s specification). The same logic applies to MP input sets with force-based EDIFFG settings.
EFERMI	EFERMI must be one of: "LEGACY", "MIDGAP"
EFIELD	Current MP input sets used to construct the main MP database do not set EFIELD, and hence we require this to be unset or set to 0.
ENAUG	If ENAUG is present in the relevant MP input set, then a calculation’s ENAUG must be equal to or better than that value.
ENCUT	ENCUT must be equal to or greater than the value in the relevant MP input set, as otherwise results will likely be incompatible with MP.
ENINI	ENINI must not be adjusted for high-throughput calculations, and hence should be left equal to the value used for ENCUT in the relevant MP input set. Values greater than the ENCUT in the relevant MP input set will also be accepted, though we expect this to be uncommon and do not recommend it.
EPSILON	EPSILON must be set to the VASP default of 1. Changing the dielectric constant of the medium will cause results to be incompatible with MP.
GGA / METAGGA	The level of theory used must match the relevant MP input set. Moreover, GGA and METAGGA should never be set simultaneously, as this has been shown to result in seriously erroneous results. See https://github.com/materialsproject/atomate2/issues/453#issuecomment-1699605867 for more details.
GGA_COMPAT	GGA_COMPAT must be set to the VASP default of True. The VASP manual only recommends setting this to False for noncollinear magnetic calculations, which are not currently included in the MP database.
IBRION	IBRION values must be one of: -1, 1, 2. Other IBRION values correspond to non-standard forms of DFT calculations that are not included in the MP database. (Note that, while phonon data is included in the MP database, such values are not calculated using, say, IBRION = 5. Such logic applies to all other IBRION values not allowed).
ICHARG	ICHARG must be set to be compatible with the calculation type. For example, if the relevant MP input set is for a SCF calculation, ICHARG $\leq 9$ must be used. For NSCF calculations, the value for ICHARG must exactly match the value contained in the relevant MP input set.
ICORELEVEL	ICORELEVEL must be set to 0. MP does not explicitly calculate core energies.
IDIPOL	IDIPOL must be set to 0 (the VASP default).
IMAGES	IMAGES must be set to 0 to match MP calculations.
INIWAV	INIWAV must be set as the VASP default of 1 to be consistent with MP calculations.
ISPIN	All values of ISPIN are allowed, though it should be noted that virtually all MP calculations permit spin symmetry breaking, and have ferromagnetic, antiferrogmanetic, or nonmagnetic ordering.
ISMEAR	The appropriate ISMEAR depends on the bandgap of the material (which cannot be known a priori). As per the VASP manual: for metals (bandgap = 0), any ISMEAR value in [0, 1, 2] is acceptable. For nonmetals (bandgap > 0), any ISMEAR value in [-5, 0] is acceptable. Hence, for those who are performing normal relaxations/static calculations and want to ensure their calculations are MP-compatible, we recommend setting ISMEAR to 0.
ISIF	MP allows any ISIF $\geq 2$. This value is restricted as such simply because all ISIF values $\geq 2$ output the complete stress tensor.
ISYM	ISYM must be one of -1, 0, 1, 2, except for when the relevant MP input set uses a hybrid functional, in which case ISYM=3 is also allowed.
ISTART	ISTART must be one of: 0, 1, 2.
IVDW	IVDW must be set to 0. MP currently does not apply any vdW dispersion corrections.
IWAVPR	IWAVPR must be set to 0 (the default). VASP discourages users from setting this tag.
KGAMMA	KGAMMA must be set to True (the VASP default). This is only relevant when no KPOINTS file is used.
KSPACING / KPOINTS	The KSPACING parameter or KPOINTS file must correspond with at least 0.9 times the number of KPOINTS in the non-symmetry-reduced Brillouin zone specified by the relevant MP input set (i.e., not the number of points in the irreducible wedge of the first Brillouin zone). Hence, either method of specifying the KPOINTS can be chosen. This ensures that a calculation uses a comparable number of kpoints to MP.
Kpoint mesh type (for KPOINTS)	The type of Kpoint mesh must be valid for the symmetry of the crystal structure in the calculation. For example, for a hexagonal closed packed structure, one must use a $\Gamma$-centered mesh. All Kpoints generated using Pymatgen should be valid.
LASPH	LASPH must be set to True (this is *not* the VASP default).
LCALCEPS	LCALCEPS must be set to False (the VASP default).
LBERRY	LBERRY must be set to False (the VASP default).
LCALCPOL	LCALCPOL must be set to False (the VASP default).
LCHIMAG	LCHIMAG must be set to False (the VASP default).
LCORR	LCORR must be set to True (the VASP default) for calculations with IALGO = 58.
LDAU / LDAUU / LDAUJ / LDAUL / LDAUTYPE	For DFT$`+U`$ calculations, all parameters corresponding to $+U$ or $+J$ corrections must exactly match those specified in the relevant MP input set. Alternatively, LDAU = False (DFT) is always acceptable.
LDIPOL	LDIPOL must be set to False (the VASP default).
LMONO	LMONO must be set to False (the VASP default).
LEFG	LEFG must be set to False (the VASP default), unless explicitly specified to be True by the relevant MP input set.
LEPSILON	LEPSILON must be set to False (the VASP default), unless explicitly specified to be True by the relevant MP input set.
LHFCALC	The value of LHFCALC should match that of the relevant MP input set, as it will otherwise result in a change in the level of theory applied in the calculation.
LHYPERFINE	LHYPERFINE must be set to False (the VASP default).
LKPROJ	LKPROJ must be set to False (the VASP default).
LKPOINTS_OPT	LKPOINTS_OPT must be set to False.
LMAXPAW	LMAXPAW must remain unspecified, as the VASP wiki states that "Energies should be evaluated with the default setting for LMAXPAW".
LMAXMIX	LMAXMIX must be set to 6. This is based on tests from Aaron Kaplan (@esoteric-ephemera) — see the "bench_vasp_pars.docx" document in https://github.com/materialsproject/pymatgen/issues/3322.
LMAXTAU	LMAXTAU must be set to 6 (the VASP default when using LASPH = True).
LMP2LT / LSMP2LT	Both must be set to False (VASP defaults)
LNONCOLLINEAR / LSORBIT	Both must be set to False (VASP defaults)
LOCPROJ	LOCPROJ must be set to None (the VASP default).
LOPTICS	LOPTICS must be set to False (the VASP default), unless explicitly specified by the relevant MP input set.
LORBIT	LORBIT must *not* be None if the user also sets ISPIN=2, otherwise all values of LORBIT are acceptable. This is due to magnetization values not being output when ISPIN=2 and LORBIT = None are set together.
LREAL	If the LREAL in the relevant MP input set is "Auto", then the user must be one of: "Auto", False. Otherwise, if the LREAL in the relevant MP input set is False, then the user must use False.
LRPA	LRPA must be set to False (the VASP default). MP does not currently support random phase approximation (RPA) calculations.
LSPECTRAL	LSPECTRAL must be set to False (the VASP default for most calculations).
LSUBROT	LSUBROT must be set to False (the VASP default).
MAGMOM	While any initial magnetic moments are allowed, the final total magnetic moment for any given atom must be less than 5 $\mu_B$ (Bohr magnetons) (except for elements Gd and Eu, which must be less than 10 $\mu_B$). This simply serves as a filter for erroneous data.
ML_LMFF	ML_LMFF must be set to False (the VASP default).
NGX / NGY / NGZ	The values for NGX/NGY/NGZ must be at least 0.9 times the default value for the respective parameter generated by VASP. If the user simply does not specify these parameters, the calculation should be compatible with MP data.
NGFX / NGFY / NGFZ	The values for NGFX/NGFY/NGFZ must be at least 0.9 times the default value for the respective parameter generated by VASP. If the user simply does not specify these parameters, the calculation should be compatible with MP data.
NLSPLINE	NLSPLINE should be set to False (the VASP default), unless explicitly specified by the relevant MP input set.
NBANDS	NBANDS must be greater than the value $\mathrm{ceil}(\mathrm{NELECT}/2) + 1 $(minimum allowable number of bands to avoid degeneracy) and less than 4 times (minimum allowable number of bands to avoid degeneracy). For high-throughput calculations, it is generally recommended to not set this parameter directly. See https://github.com/materialsproject/custodian/issues/224 for more information.
NELECT	NELECT must not be changed from the default value VASP would use for the particular structure and pseudopotentials calculated. The easiest way to ensure that NELECT is compliant with MP data is to simply not specify NELECT in the INCAR file.
NWRITE	NWRITE must be set to be $\geq 2$ (the VASP default is 2).
POTIM	POTIM $\leq 5$. We suggest not setting POTIM in the INCAR file, and rather allowing VASP to set it to the default value of 0.5.
PSTRESS	PSTRESS must be set to exactly 0.0 (the VASP default).
PREC	PREC must be one of: "High", "Accurate".
ROPT	ROPT should be set to be less than or equal to the default ROPT value (which is set based on the PREC tag). Hence, it is recommended to not set the ROPT tag in the INCAR file.
RWIGS	RWIGS should not be set in the INCAR file.
SCALEE	SCALEE should not be set in the INCAR file.
SYMPREC	SYMPREC must be less than or equal to 1e-3 (as this is the maximum value that the Custodian package will set SYMPREC as of March 2024). For general use, we recommend leaving SYMPREC as the default generated by your desired MP input set.
SIGMA	There are several rules for setting SIGMA: SIGMA must be $\leq 0.05$ for non-metals (bandgap $> 0$). SIGMA must be $\leq 0.2$ for a metal (bandgap = 0). For metals, the SIGMA value must be small enough that the entropy term in the energy is $\leq$ 1 meV/atom (as suggested by the VASP manual).
VCA	MP data does not include Virtual Crystal Approximation (VCA) calculations from VASP. As such, this parameter should not be set.
VASP version	The following versions of VASP are allowed: 5.4.4 or $>$ 6.0.0. For example, versions $<=$ 5.4.3 are not allowed, whereas version 6.3.1 is allowed.

pymatgen-io-validation dependencies

numpy pymatgen requests

FAQs

What is pymatgen-io-validation?

A comprehensive I/O validator for electronic structure calculations. Visit Snyk Advisor to see a full health score report for pymatgen-io-validation, including popularity, security, maintenance & community analysis.

Is pymatgen-io-validation popular?

The python package pymatgen-io-validation receives a total of 266 weekly downloads. As such, pymatgen-io-validation popularity was classified as limited. Visit the popularity section on Snyk Advisor to see the full health analysis.

Is pymatgen-io-validation well maintained?

We found indications that pymatgen-io-validation maintenance is sustainable demonstrating some project activity. We saw a total of 3 open source contributors collaborating on the project. See the full package health analysis to learn more about the package maintenance status.

Is pymatgen-io-validation safe to use?

The python package pymatgen-io-validation was scanned for known vulnerabilities and missing license, and no issues were found. Thus the package was deemed as safe to use. See the full health analysis review.

Last updated on 27 October-2024, at 15:27 (UTC).

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Readme

pymatgen-io-validation

Installation

Usage

Contributors

Rationale

pymatgen-io-validation dependencies

FAQs

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