mirror of https://gitlab.com/QEF/q-e.git
157 lines
6.2 KiB
Plaintext
157 lines
6.2 KiB
Plaintext
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Copyright (C) 2013-2016 Guido Fratesi
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MOLECULARNEXAFS
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This code combines the output of different codes (pw.x, projwfc.x,
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and mainly xspectra.x) to evaluate the NEXAFS spectrum of a molecule
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containing inequivalent atoms belonging to the same species.
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The theoretical framework adopted is explained in the following
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publication, which should be cited in papers using this tool
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(additionally to relevant papers for the NEXAFS calculation):
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* Azimuthal Dichroism in Near-Edge X-ray Absorption Fine Structure
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Spectra of Planar Molecules
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Guido Fratesi, Valeria Lanzilotto, Luca Floreano, and Gian Paolo Brivio
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J. Phys. Chem. C 2013, 117, 6632−6638
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http://dx.doi.org/10.1021/jp312569q
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Further examples are also described in:
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Phys. Chem. Chem. Phys., 2014, 16, 14834
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http://dx.doi.org/10.1039/c4cp01625d
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The spectrum for each inequivalent atom of the same species sums up
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into a total spectrum, where the contributions from each atom (as
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evaluated by xspectra.x) have to be properly aligned before the
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summation. For example, a molecule like pyridine contains C atoms in
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three different sites, C1, C2, and C3. This example is adopted below.
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For each inequivalent atom in the molecule, the code requires:
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1) A full-core-hole (FCH) calculation of the total energy by pw.x
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(by a FCH pseudopotential at C_i). The code will return the
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core-level shifts (CLS) as a by-product.
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2) Half-core-hole (HCH) calculations of the NEXAFS spectrum by
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xspectra.x for the three directions X-Y-Z. Those will be read as
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prefix(iat)//suffix(idir)
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3) Since xspectra.x energy scales may not refer to the vacuum level
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(more commonly the Fermi level or the middle of the HOMO-LUMO gap
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may have been used), one also need to input the reference energy
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level of the HCH xspectra.x calculation, and the corresponding
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vacuum level.
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The vacuum level might be estimated by the Makov-Payne correction
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directly in the HCH pw.x SCF calculation if the unit cell is
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cubic, or by running additional calculations accessing the vacuum
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level, then by evaluating the vacuum-to-HOMO energy difference in
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this case, summed to the HOMO of the original calculation.
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For adsorbed molecules, one should refer to the Fermi level both
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for NEXAFS and the XPS, as is generally done in the experiments.
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So we should set both evacuum=0 and efermi=0, and the new zero
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will be the average core level binding energy with respect to the
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Fermi level.
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4) Eventually, energies from xspectra.x output files will be shifted
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(E->E+eshift) so that the new zero of energy is the weighted
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average of core-level binding energies:
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eshift(iat)= -(evacuum(iat)-efermi(iat)) + dcorebe(iat)
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where the first term sets the vacuum level at zero and the second
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one adds to the transition energy the core level shift.
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Recall that by the pseudopotential approach binding energies are
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defined only up to a constant.
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5) Optionally, the PDOS of p symmetry can be taken as an approximation
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to the spectrum for a K edge: the comparison is useful for checking
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the results.
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=======================================================================
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NAMELIST / CONTROL /
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-----------------------------------------------------------------------
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syslabel character(len=80) DEFAULT='MOLECULE'
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System label for output files
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doxps logical DEFAULT=.TRUE.
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Plot XPS spectrum
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donexafs logical DEFAULT=.TRUE.
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Compute and plot NEXAFS spectrum
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nat integer DEFAULT=0
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The number of inequivalent atoms in the molecule
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atweight(1:nat) real(DP) DEFAULT=1, 1, . . .
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The multiplicities of the inequivalent atoms in the molecule
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-----------------------------------------------------------------------
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NAMELIST / XPS /
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-----------------------------------------------------------------------
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erangexps(1:2) real(DP) DEFAULT=(-5:5)
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Energy range for plotting
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nptxps integer DEFAULT=501
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Number of points for plotting
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delorentz, degauss, lorentzratio real(DP) DEFAULT=0.2, 0.2, 0.5
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Pseudovoigt parameters.
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The spectrum is plotted as:
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lorentzratio * lorentzian + (1-lorentzratio)*gaussian
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delorentz=HWHM of the Lorentzian
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degauss=STDDEV of the Gaussian
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etotfch(1:nat) real(DP) DEFAULT=0
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Total energy (Ry) with a FCH in that given atom
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-----------------------------------------------------------------------
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NAMELIST / NEXAFS /
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-----------------------------------------------------------------------
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dosingleatoms logical DEFAULT=.TRUE.
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Set to true to also output the results of each atom in a separate file
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dopdosp logical DEFAULT=.FALSE.
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Set to true to also read and sum the PDOS (p) of each atom, with
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analogous procedure as for the NEXAFS spectrum.
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erangenexafs(1:2) real(DP) DEFAULT=(-10:20)
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Energy range for plotting
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nptnexafs integer DEFAULT=3001
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Number of points for plotting
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efermi(1:nat) real(DP) DEFAULT=0
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Reference energy level of the HCH xspectra.x calculation. Should
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be left to zero in case of molecules adsorbed on metals (assuming
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the Fermi level was taken as a reference for xspectra.x).
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evacuum(1:nat) real(DP) DEFAULT=0
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Vacuum level of the HCH calculation. Should be left to zero in
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case of molecules adsorbed on metals.
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prefix(1:nat) character(len=80) DEFAULT='xanes.dat.001', 'xanes.dat.002', . . .
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The files containing the spectrum computed by xspectra.x should
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follow this naming convention:
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prefix(iat)//suffix(nu), where
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Iat=1,nat identifies the inequivalent atom
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nu=1,2,3 the three directions x,y,z
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suffix(1:3) character(len=80) DEFAULT='.xspectraX.dat', '.xspectraY.dat', '.xspectraZ.dat'
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Direction-dependent suffix of xspectra.x spectrum file
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atlabel(0:nat) character(len=80) DEFAULT='SUM', '001', '002', . . .
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Atomic labels (the 0-th element is for the summed spectrum).
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pdospfile(1:nat) character(len=80) DEFAULT='pdosp.dat.001', 'pdosp.dat.002', . . .
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The files containing the p-pdos from projwfc.x.
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=======================================================================
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