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reading_procedures [2017/05/05 17:15] krejcio created |
reading_procedures [2017/05/05 17:22] |
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- | At this moment there are three procedures that can read input files: | ||
- | == Fireball == | ||
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- | **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=[])** | ||
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- | This procedure reads geometry from //geom// -- '__answer.bas__'. | ||
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- | 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__' | ||
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- | == GPAW == | ||
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- | **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=[] )** | ||
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- | This procedure reads all needed informations (eigen-energies, LCAO coefficients, geometry, the Fermi Level) from the //name// (//GPAW// output) file. | ||
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- | == FHI-AIMS == | ||
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- | **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=[])** | ||
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- | 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 !!!). | ||
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- | The eigen-energies (relative to the Fermi level) and the LCAO coefficient are read from the //name// file. | ||
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- | //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: | ||
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- | 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) | ||
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- | == Outputs: == | ||
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- | These procedures has three outputs: eigen-energies (one dimensional numpy array); LCAO coefficients (two dimensional numpy array); Atomic geometry coordinates (two dimensional numpy array). |