`jarvis.io.vasp.outputs`¶

Modulet for analzing VASP outputs.

Module Contents¶

Classes¶

`Chgcar`	Class handling VASP CHGCAR file data.
`Locpot`	Read LOCPOT files.
`Oszicar`	Construct Oszicar object.
`Outcar`	Construct OUTCAR object.
`Waveder`	Class for reading a WAVEDER file.
`Wavecar`	Class for VASP Pseudowavefunction stored in WAVECAR.
`Vasprun`	Construct vasprun.xml handling object.

Functions¶

parse_raman_dat([vasp_raman_path])

Parse vasp_raman.dat .

Attributes¶

`RYTOEV`
`AUTOA`
`TPI`
`HSQDTM`

jarvis.io.vasp.outputs.RYTOEV = 13.605826¶

jarvis.io.vasp.outputs.AUTOA = 0.529177249¶

jarvis.io.vasp.outputs.TPI¶

jarvis.io.vasp.outputs.HSQDTM¶

class jarvis.io.vasp.outputs.Chgcar(filename='', atoms=None, chg=[], chgdif=None, aug=None, augdiff=None, dim=None, nsets=1, lines='')[source]¶

Bases: object

Class handling VASP CHGCAR file data.

to_dict()[source]¶: Convert to a dictionary.

classmethod from_dict(d={})[source]¶: Construct class from a dictionary.

is_spin_polarized()[source]¶: Check if the calculations is spin-polarized, ISPIN=2.

is_spin_orbit()[source]¶: Check if the calculations is spin-orbit, LSORBIT=T.

modify_grid(chg_set=0, multiply_volume=True, final_grid=[50, 50, 50], write_file=True, filename='New_CHGCAR')[source]¶: Modify grid and Write a charge set to a file for visualization.

read_file(lines='')[source]¶: Read CHGCAR.

chg_set(text, start, end, volume, ng)[source]¶: Return CHGCAR sets.

class jarvis.io.vasp.outputs.Locpot(filename='', atoms=None, chg=[], chgdif=None, aug=None, augdiff=None, dim=None, nsets=1, lines='')[source]¶

Bases: Chgcar

Read LOCPOT files.

vac_potential(direction='X', Ef=0, filename='Avg.png', plot=True)[source]¶: Calculate vacuum potential used in work-function calculation.

class jarvis.io.vasp.outputs.Oszicar(filename, data={})[source]¶

Bases: object

Construct Oszicar object.

property magnetic_moment¶: Get magnetic moment.

property ionic_steps¶: Get all ionic steps realted data.

property electronic_steps¶: Get all electronic steps realted data.

classmethod from_dict(d={})[source]¶: Construct class from a dictionary.

to_dict()[source]¶: Convert class to a dictionary.

class jarvis.io.vasp.outputs.Outcar(filename, data={})[source]¶

Bases: object

Construct OUTCAR object.

property nions¶: Get number of ions.

property nbands¶: Get number of bands.

property nedos¶: Get number of dos points.

property efermi¶: Get Fermi energy.

property all_band_energies¶: Get all band energies.

property bandgap¶: Get bandgap.

property nelect¶: Get number of electrons.

property phonon_eigenvalues¶: Get phonon eigenvalues.

property converged¶: Check if calculation is converged.

property efg_raw_tensor¶: Get raw electric field gradient tensor.

property quad_mom¶: Get quadrupole momemnt.

property piezoelectric_tensor¶: Get piezoelectric tensor.

classmethod from_dict(d={})[source]¶: Construct class from a dictionary.

to_dict()[source]¶: Convert class to a dictionary.

magnetization(dir='x', elements=[])[source]¶: Get magnetization in x,y,z.

total_charge(elements=[])[source]¶: Get total charge.

efg_tensor_diag(std_conv=True, prec=3)[source]¶: Get diagonalized electric field gradient tensor.

freq_dielectric_tensor()[source]¶: Parse dielectric function.

elastic_props(atoms=None, vacuum=False)[source]¶

Obtain elastic tensor and calculate related properties.

For 3D and 2D cases.

Args:

outcar: OUTCAR file path

vacuum: whether the structure has vaccum such as 2D materials for vacuum structures bulk and shear mod. Needs extra attention and elastic tensor are in Nm^-1 rather than GPa

Returns:

info: data for elastic tensor (in string and object representation), bulk, shear modulus, and phonon modes

class jarvis.io.vasp.outputs.Waveder(filename, gamma_only=False)[source]¶

Bases: object

Class for reading a WAVEDER file.

The LOPTICS tag produces a WAVEDER file. The WAVEDER contains the derivative of the orbitals with respect to k.

property cder_data¶: Return the orbital derivative between states.

property nbands¶: Return the number of bands in the calculation.

property nkpoints¶: Return the number of k-points in the calculation.

property nelect¶: Return the number of electrons in the calculation.

get_orbital_derivative_between_states(band_i, band_j, kpoint, spin, cart_dir)[source]¶

Return a valuebetween bands band_i and band_j.

For k-point index, spin-channel and cartesian direction.

Args:

band_i (Integer): Index of band i

band_j (Integer): Index of band j

kpoint (Integer): Index of k-point

spin (Integer): Index of spin-channel (0 or 1)

cart_dir (Integer): Index of cartesian direction (0,1,2)

Returns:: a float value

class jarvis.io.vasp.outputs.Wavecar(filename='WAVECAR', lsorbit=False, lgamma=False, recl=None, nspin=None, rtag=None, nkpts=None, nbands=None, encut=None, lattice_mat=None, nplws=None, wfc=None, efermi=None, kvecs=None, energies=None, occs=None, gvec=None)[source]¶

Bases: object

Class for VASP Pseudowavefunction stored in WAVECAR.

The format of VASP WAVECAR, as shown in

http://www.andrew.cmu.edu/user/feenstra/wavetrans/

is:

Record-length #spin components RTAG(a value specifying the precision) #k-points #bands ENCUT(maximum energy for plane waves) LatVec-A LatVec-B LatVec-C Loop over spin

Loop over k-points
#plane waves, k vector Loop over bands

band energy, band occupation

End loop over bands Loop over bands

Loop over plane waves
Plane-wave coefficient

End loop over plane waves

End loop over bands

End loop over k-points

End loop over spin

isSocWfc()[source]¶: Check if the WAVECAR is from an SOC calculation.

readWFHeader()[source]¶

Read the system information from WAVECAR.

It is written in the first two record.

rec1: recl, nspin, rtag rec2: nkpts, nbands, encut, ((cell(i,j) i=1, 3), j=1, 3)

setWFPrec()[source]¶: Set wavefunction coefficients precision.

TAG = 45200: single precision complex, np.complex64, or complex(qs) TAG = 45210: double precision complex, np.complex128, or complex(q)

readWFBand(ispin=1, ikpt=1, iband=1)[source]¶: Extract KS energies and Fermi occupations from WAVECAR.

gvectors(ikpt=1)[source]¶

Generate the G-vectors.

satisfies the following relation
(G + k)**2 / 2 < ENCUT

readBandCoeff(ispin=1, ikpt=1, iband=1, norm=False)[source]¶: Read the planewave coefficients of specified KS states.

whereRec(ispin=1, ikpt=1, iband=1)[source]¶: Return the rec position for specified KS state.

checkIndex(ispin, ikpt, iband)[source]¶: Check if the index is valid.

class jarvis.io.vasp.outputs.Vasprun(filename='vasprun.xml', data={})[source]¶

Bases: object

Construct vasprun.xml handling object.

property final_energy¶: Get final energy.

property nbands¶: Get number of electronic bands.

property nkpoints¶: Get number of kpoints.

property nspins¶: Get total numnber of spins.

property efermi¶: Get Fermi-energy.

property num_atoms¶: Get number of simulation atoms.

property num_types¶: Get number of atom types.

property dielectric_loptics¶: Get real and imag. dielectric function data.

property avg_absorption_coefficient¶: Get average absoprtion coefficient. Used in solar-cell module.

property converged_electronic¶: Check whether electronically converged.

property converged_ionic¶: Check whether ionically converged.

property converged¶: Check whether both electronically and ionically converged.

property dfpt_data¶: Get DFPT IBRION=8 LEPSILON lated data.

property get_dir_gap¶: Get direct bandgap.

property get_indir_gap¶: Get indirect bandgap.

property fermi_velocities¶: Get fermi velocities in m/s.

property elements¶: Get atom elements.

property all_energies¶: Get all total energies.

property is_spin_polarized¶: Check if the calculation is spin polarized.

property is_spin_orbit¶: Check if the calculation is spin orbit.

property all_structures¶: Get all structures.

property eigenvalues¶: Get all eigenvalues.

property all_forces¶: Get all forces.

property all_stresses¶: Get all stresses.

property all_input_parameters¶: Get all explicit input parameters. Need to add a few more.

property kpoints¶: Get Kpoints.

property total_dos¶: Get total density of states.

property partial_dos_spdf¶: Get partial density of states.

property projected_spins_kpoints_bands¶: Use for spin, kpoint and band projected bandstructure plots.

property projected_atoms_spins_kpoints_bands¶: Use for atom,spin,kpoint and band projected bandstructures.

classmethod from_dict(d={})[source]¶: Construct class from a dictionary.

to_dict()[source]¶: Convert class to a dictionary.

xml_to_dict()[source]¶: Convert XML to dictionary.

phonon_data(fc_mass=True)[source]¶: Get phonon data.

bandgap_occupation_tol(occu_tol=0.1)[source]¶: Get bandgap based on occupation tolerance.

vrun_structure_to_atoms(s={})[source]¶: Convert structure to Atoms object.

get_bandstructure(E_low=-4, E_high=4, spin=0, zero_efermi=True, kpoints_file_path='KPOINTS', plot=False, filename=None)[source]¶: Get electronic bandstructure plot.

get_spdf_dos(plot=False)[source]¶: Get spdf resolved partial density of states.

get_atom_resolved_dos(plot=False)[source]¶: Get atom resolved density of states.

jarvis.io.vasp.outputs.parse_raman_dat(vasp_raman_path='RAMANDIR-bulk@JVASP-1002_mp-149/vasp_raman.dat')[source]¶

Parse vasp_raman.dat .

generated by https://github.com/raman-sc/VASP

Activities to Intensities: J. At. Mol. Sci. 3 (2012) 1-22 Intensity = const0 * (nu0-nu)**4/nu * 1/(1-exp(-h*c*nu/(kB*T))) * activity Data for computing intensities, as in Materials Project’s paper:

T=300K, nu0=18796.9925 cm-1

jarvis.io.vasp.outputs¶

Module Contents¶

Classes¶

Functions¶

Attributes¶

`jarvis.io.vasp.outputs`¶