Instances of the extraction classes are returned by calls to the vasp and affiliated methods. They simply grep the OUTCAR for values of interest, e.g. eigenvalues or vasp parameters. Indeed, these should contain an Extract attribute which refers to a class capable of handling the output of the method or vasp object. They can be instanciated as follows:
>>> a = vasp.Extract('outdir')
>>> a = vasp.epitaxial.Extract('outdir')
Where outdir is the location of the relevant calculation. The results from the calculations can then be accessed as attributes:
>>> a.total_energy
array(-666.667) * eV
It is possible to extract calculations from a complete folder tree:
>>> from pylada.vasp import MassExtract
>>> a = MassExtract('outdir')
>>> a.total_energy
{
'/some/path': array(-666.667) * eV,
'/some/otherpath': array(-999.996) * eV,
}
The extraction classes are separated into I/O (IOMixin) and actual methods to grep the OUTCAR for results (ExtractBase). This setup makes it convenient to change the kind of object that can be grepped, from the standard file on a hard-disk, to a file in a database.
Extract derives from the following classes.
Bases: pylada.tools.extract.AbstractExtractBase, pylada.vasp.extract.mixin.IOMixin, pylada.vasp.extract.base.ExtractBase
Extracts DFT data from an OUTCAR.
Hubbard U/NLEP parameters.
Type of LDA+U performed.
Returns the kind of algorithms.
Greps total energies for all electronic steps from OUTCAR.
Greps alpha+bet from OUTCAR
Returns Condunction Band Minimum.
Returns a shallow copy of this object.
| Parameters: | kwargs – Any keyword argument is set as an attribute of this object. The attribute must exist. |
|---|
Greps execution date and time.
Computes density of the material.
Dielectric constant of the material.
Directory where output should be found.
Greps EDIFF from OUTCAR.
Greps EDIFFG from OUTCAR.
Greps eigenvalues from OUTCAR.
In spin-polarized cases, the leading dimension of the numpy array are spins, followed by kpoints, and finally with bands. In spin-unpolarized cases, the leading dimension are the kpoints, followed by the bands.
Electronic contribution to the dielectric constant.
Greps average atomic electrostatic potentials from OUTCAR.
Energy cutoff.
Greps total energy extrapolated to $sigma=0$ from OUTCAR.
Greps total energy from OUTCAR.
Greps total energy extrapolated to $sigma=0$ from OUTCAR.
List of errors.
Errors that are encountered more than once are not repeated.
Returns charge state of the system.
Fermi energy at zero kelvin.
This procedure recomputes the fermi energy using a step-function. It avoids negative occupation numbers. As such, it may be different from the fermi energy given by vasp, depeneding on the smearing and the smearing function.
Greps fermi energy from OUTCAR.
Greps recommended or actual fft setting from OUTCAR.
Forces on each atom.
Returns vasp functional used for calculation.
Requires the functional to be pasted at the end of the calculations.
True if the material is half-metallic.
Returns the kind of algorithms.
Greps IBRION from OUTCAR.
Greps ICHARG from OUTCAR.
Structure at start of calculations.
Greps ionic_charges from OUTCAR.
Ionic contribution to the dielectric constant.
Alias for stoichiometry.
True if this is a DFT calculation, as opposed to GW.
True if this is a GW calculation, as opposed to DFT.
True if program is running on this functional.
A file ‘.pylada_is_running’ is created in the output folder when it is set-up to run CRYSTAL. The same file is removed when CRYSTAL returns (more specifically, when the pylada.process.ProgramProcess is polled). Hence, this file serves as a marker of those jobs which are currently running.
Greps ISIF from OUTCAR.
Greps smearing function from OUTCAR.
Greps ISPIN from OUTCAR.
Greps ISTART from OUTCAR.
Greps ISYM from OUTCAR.
iterates over input/output files.
| Parameters: |
|
|---|
Greps k-points from OUTCAR.
Numpy array where each row is a k-vector in cartesian units.
Greps LASPH from OUTCAR.
Greps LWAVE from OUTCAR.
Greps LCOMPAT from OUTCAR.
Greps LCORR from OUTCAR.
Greps LDIAG from OUTCAR.
Greps LDIPOL from OUTCAR.
Greps LELF from OUTCAR.
Greps LGGA_COMPAT from OUTCAR.
Greps LMAXMIX from OUTCAR.
Greps LNONCOLLINEAR from OUTCAR.
Greps LORBIT from OUTCAR.
Greps LREAL from OUTCAR.
Greps LREAL_COMPAT from OUTCAR.
Greps LSECVAR from OUTCAR.
Greps LSORBIT from OUTCAR.
Greps LVTOT from OUTCAR.
Greps LWAVE from OUTCAR.
Greps partial charges from OUTCAR.
This is a numpy array where the first dimension is the ion (eg one row per ion), and the second the partial charges for each angular momentum. The total is not included.
Greps METAGGA from OUTCAR.
Returns magnetic moment from OUTCAR.
Greps multiplicity of each k-point from OUTCAR.
Greps POSCAR title from OUTCAR.
Number of bands in calculation.
Number of bands in calculation.
Greps nelect from OUTCAR.
Greps NELM from OUTCAR.
Greps NELMDL from OUTCAR.
Greps NELMIN from OUTCAR.
True if non-selfconsistent calculation.
Greps NSW from OUTCAR.
Greps NUPDOWN from OUTCAR.
Greps occupations from OUTCAR.
In spin-polarized cases, the leading dimension of the numpy array are spins, followed by kpoints, and finally with bands. In spin-unpolarized cases, the leading dimension are the kpoints, followed by the bands.
Greps partial charges from OUTCAR.
This is a numpy array where the first dimension is the ion (eg one row per ion), and the second the partial charges for each angular momentum. The total is not included.
Greps POTIM from OUTCAR.
Greps PREC from OUTCAR.
Greps last pressure from OUTCAR
Greps all pressures from OUTCAR
Title of the first POTCAR.
Greps pressure from OUTCAR
Greps quasi-particle eigenvalues from OUTCAR.
In spin-polarized cases, the leading dimension of the numpy array are spins, followed by kpoints, and finally with bands. In spin-unpolarized cases, the leading dimension are the kpoints, followed by the bands.
Reciprocal space volume (including 2pi).
Greps recommended or actual fft setting from OUTCAR.
Returns the kind of relaxation performed in this calculation.
Greps self-energies of each eigenvalue from OUTCAR.
In spin-polarized cases, the leading dimension of the numpy array are spins, followed by kpoints, and finally with bands. In spin-unpolarized cases, the leading dimension are the kpoints, followed by the bands.
Greps smearing function from OUTCAR.
Greps species from OUTCAR.
Stoichiometry of the compound.
Returns final total stress.
Returns total stress at each relaxation step.
Greps structure and total energy from OUTCAR.
Greps system title from OUTCAR.
Greps total energies for all ionic steps from OUTCAR.
Greps total energy from OUTCAR.
Uncache values.
Greps number of valence bands from OUTCAR.
Returns Valence Band Maximum.
Unit-cell volume.
List of warnings.
Warnings that are encountered more than once are not repeated.
Greps XC(G=0) from OUTCAR
Bases: pylada.jobfolder.extract.AbstractMassExtract
Extracts all Vasp calculations in directory and sub-directories.
Trolls through all subdirectories for vasp calculations, and organises results as a dictionary where keys are the name of the diretories.
Usage is simply:
>>> from pylada.vasp import MassExtract
>>> a = MassExtract('path') # or nothing if path is current directory.
>>> a.success
{
'/some/path/': True,
'/some/other/path': True
}
>>> a.eigenvalues