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reading_procedures

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At this moment there are three procedures that can read input files:

Fireball

read_FIREBALL_all(name = 'phi_' , geom='answer.bas', fermi=None, orbs = 'sp', pbc=(1,1), imaginary = False, cut_min=-15.0, cut_max=5.0, cut_at=-1, lvs = None, lower_atoms=[], lower_coefs=[])

This procedure reads geometry from geom – 'answer.bas'.

It reads the The Fermi Level, eigen-energies and the LCAO coefficients from name+'s.dat',+'px.dat',+'py.dat',+'pz.dat'; in case of 'spd' orbitals also name+'dxy.dat',+'dxz.dat',+'dyz.dat',+'dz2.dat',+'dx2y2.dat'

GPAW

read_GPAW_all(name = 'OUTPUT.gpw', fermi = None, orbs = 'sp', pbc=(1,1), imaginary = False, cut_min=-15.0, cut_max=5.0, cut_at=-1, lower_atoms=[], lower_coefs=[] )

This procedure reads all needed informations (eigen-energies, LCAO coefficients, geometry, the Fermi Level) from the name (GPAW output) file.

FHI-AIMS

read_AIMS_all(name = 'KS_eigenvectors.band_1.kpt_1.out', geom='geometry.in', fermi=None, orbs = 'sp', pbc=(1,1), imaginary = False, cut_min=-15.0, cut_max=5.0, cut_at=-1, lower_atoms=[], lower_coefs=[])

This procedure reads geometry from geom – 'geometry.in'. BEWARE if the PP-AFM pre-calculations are done from a Hartree potential from FHI-AIMS and when the cube file DOESN'T have an origin at (0.0,0.0,0.0), then the atomic geometry written in geometry.in differs by the AFM calculations by a shift that is written the cube origin (!!! the cube is in atomic units !!!).

The eigen-energies (relative to the Fermi level) and the LCAO coefficient are read from the name file.

FHI-AIMS is the only DFT code, which can serve as an input for PP-STM calculations for spin-polarized systems. An example how to take into account tunneling from orbitals from both spins:

eigEn1, coefs1, Ratin = RS.read_AIMS_all(name = 'KS_eigenvectors_up.band_1.kpt_1.out', geom='geometry.in',fermi=fermi, orbs = 'spd', pbc=(0,0),
					imaginary = False, cut_min=-15., cut_max=5., cut_at=-1,
					lower_atoms=[], lower_coefs=[])
eigEn2, coefs2, Ratin = RS.read_AIMS_all(name = 'KS_eigenvectors_dn.band_1.kpt_1.out', geom='geometry.in',fermi=fermi, orbs = 'spd', pbc=(0,0),
					imaginary = False, cut_min=-15., cut_max=5., cut_at=-1,
					lower_atoms=[], lower_coefs=[])

eigEn = np.concatenate((eigEn1, eigEn2), axis=0)
coefs = np.concatenate((coefs1, coefs2), axis=0)
Outputs:

These procedures has three outputs: eigen-energies (one dimensional numpy array); LCAO coefficients (two dimensional numpy array); Atomic geometry coordinates (two dimensional numpy array).

reading_procedures.1493997348.txt.gz · Last modified: 2017/05/05 17:15 (external edit)