quantum-espresso

History

Paolo Giannozzi 6148f5e5c5 Obscure line present in all examples replaced with a much simpler one. See https://stackoverflow.com/questions/50148175/what-does-cd-echo-0-sed-s-1-do-in-bash-script Note: some trailing blanks have been removed as well by the script I used. Use "git diff -b" to see only the true changes.		2022-09-03 11:53:33 +02:00
..
reference	Miscellaneous updates	2020-07-22 04:22:35 +09:00
README	Changes to calculation of molecular PDOS, by Guido Fratesi	2016-04-20 17:07:58 +00:00
run_example	Obscure line present in all examples replaced with a much simpler one.	2022-09-03 11:53:33 +02:00

README

This example shows how to calculate the Density of States (DOS)
projected onto molecular orbitals. A typical application is that
of a molecule adsorbed on a surface, where one would like to identify
contributions from HOMO/LUMO states to the electronic structure (DOS
and bands). Here we take a chain of H atoms as a model surface, with
a H2 molecule adsorbed, and we analyze the DOS and bands in terms of
the H2 orbitals (sigma, sigma*).

The calculation proceeds as follows (for the meaning of the cited input
variables see the appropriate INPUT_* file)

1) make a self-consistent calculation for the full system, which here
   is made of a chain of H atoms and a H2 molecule. In this example,
   coordinates have been set to adjust energy levels to convenient values
   input=chainH2.scf.in, output=chainH2.scf.out).

2) make a self-consistent calculation for the molecular part, with the
   same cell / k-point parameters as for the full system.
   (input=H2.scf.in, output=H2.scf.out).

3) use projfwc.x to project the crystal wavefunctions on an
   orthogonalized basis set of atomic orbitals for the full system and
   the molecular part (input=chainH2.projwfc.in,H2.projwfc.in,
   output=chainH2.projwfc.out,H2.projwfc.out). The projections are saved
   in files atomic_proj.xml files to be copied from $TMP_DIR/.

4) identify which wavefunctions of the orthogonalized basis set ot
   atomic orbitals of the full system correspond to the same set as in
   the molecular part (i.e., identify the proper range which will be
   denoted as i_atmwfc_beg_full to i_atmwfc_end_full, see outputs of
   step 3).

5) run molecularpdos.x providing in input the location of the
   atomic_proj.xml files for the full system and of the molecular
   part, and the ranges of atomic orbitals to be used
   (input=chainH2_onto_H2.in, output=chainH2_onto_H2.out).

6) do k-resolved analysis. Perform bands calculation with pw.x for
   both the interacting system and the molecule.
   Then repeat steps 3-4 with projwfc.x option kresolveddos=.true.
   and step 5 with the same kresolveddos=.true. in molecularpdos.x

7) if gnuplot is available, results are plotted to file
   project_chainH2_onto_H2.ps which shows projection of the DOS of the
   combined system on sigma and sigma* orbitals of the H2 molecule.