Differences

This shows you the differences between two versions of the page.

--- reading_procedures [2017/05/05 17:22]
+++ reading_procedures [2017/05/05 17:22]
krejcio
@@ Line 1: / Line 1: @@
+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).
+== Density of States ==
+There is also a procedure, how to plot a pseudo projected density of state, pseudo means that the density is not normalized, off-site terms are not take into account and normalizations to the overlap matrix is also missing:
+**pPDOS(eig, coeffs, energies, eta=0.1, atoms=[], orbs='sp' ,spherical='all')**
+eig - eigen-energies obtained from reading procedures.
+coeffs - the LCAO coefficients obtained from the reading procedures.
+energies - array of energies on which you want to calculate DOS - e.g energies = np.arange(-2.,2.,0.01).
+eta - width of the Lorentzian for smearing of the eigenstates.
+atoms = [] ... all atoms; [0] 1st atom only; [1,5] 2nd & 6th atom ....
+orbs = 'sp' or 'spd'.
+spherical = 'all' or 's' or 'p' or 'd' or 'px', 'py', 'pz', 'dxy', 'dxz', 'dyz', 'dz2', 'dx2y2'- projection to only some of the spherical harmonics of the atomic orbitals.

Nanosurf Lab

User Tools

Site Tools

Differences

Page Tools