pdos-CORh.pwtk

35c-pdos-CORh
35c-pdos-CORh

DESCRIPTION
This example shows how to calculate and plot PDOSes and LDOSes. The structure considered is a two-layer slab of CO/Rh(100)-c(2x2).
The meaning of LDOS & PDOS is taken from projwfc.x, i.e.:
PDOS = DOS projected to a given atomic orbital
LDOS = \sum_i PDOS_i, where PDOS_i are orbital-projected DOSes in the pdos_atm file, e.g., LDOS(p) = PDOS(px) + PDOS(py) + PDOS(pz)
EXAMPLE SOURCE FILE
pdos-CORh.pwtk
SOURCE
# the pw.x input data are imported from CORh.pwtk with ::pwtk::import
import CORh.pwtk

# the rootname used for the I/O files
set name CO-Rh100-c2x2-2L

# let's use the ::pwtk::relax_fromXSF workflow to load the structure
# from the XSF file and perform structural relaxation
#
# let's fix the bottom-layer atoms of Rh(100)-c2x2, i.e., the two last atoms (-fix_last 2)

relax_fromXSF pw.x -cell -fix_last 2 $name.xsf


# basic input data for projwfc.x

PROJWFC {
    ngauss  = 0
    degauss = 0.01
    DeltaE  = 0.05
}

## this makes the Gnuplot plotting window alive for 3 seconds
#::pwtk::gp::pause 3

# the -nscf {8 8 1} option requests the NSCF pw.x calculation with a
# denser non-shifted 8x8x1 k-mesh;
# let's PDOSes into a default window terminal (-t win)

pdos_run -nscf {8 8 1} -t win $name


# let's also plot all LDOSes and PDOSes into PDF (-t pdf) using
# ::pwtk::ldos_fullplot & ::pwtk::pdos_fullplot
#
# the Fermi energy is taken from the pw.$name.nscf.out file (i.e. -e pw.$name.nscf.out)
# created by the above ::pwtk::pdos_run workflow


ldos_fullplot -e pw.$name.nscf.out -t pdf $name
pdos_fullplot -e pw.$name.nscf.out -t pdf $name


# ------------------------
# plotting specific LDOSes
# ------------------------

# let's plot the LDOSes of CO and the Rh atom to which CO binds are;
# the respective atom numbers are 1, 2, 4 for O, C, Rh, respectively (see
# CO-Rh100-c2x2-2L.xsf)
#
# for the explanation of ::pwtk::sumldos options, see ::pwtk::pdos_atm_files
#
# -f ... pattern for the filenames (aka 'filpdos')
# -s ... list of atom symbols
# -n ... list of atom numbers

sumldos -f $name -s {C O} CO;  # the CO-projectd DOS was saved to the 'CO' file
sumldos -f $name -n 4    Rh4;  # the DOS projected to Rh atom No.4 was saved to the 'Rh4' file


# ::pwtk::ldos_plot displays LDOSes with a "single plot";
# let's plot into a default window terminal (-t win)

ldos_plot -e pw.$name.nscf.out -t win {CO Rh4} CO-Rh

# let's also plot into a PDF file (-t pdf)

ldos_plot -e pw.$name.nscf.out -t pdf {CO Rh4} CO-Rh

# let's also plot each LDOS into a separate plot as well as together with ::pwtk::ldos_multiplot

ldos_multiplot -e pw.$name.nscf.out -t win {CO Rh4 {CO Rh4}} CO-Rh_multi
ldos_multiplot -e pw.$name.nscf.out -t pdf {CO Rh4 {CO Rh4}} CO-Rh_multi


# ------------------------
# plotting specific PDOSes
# ------------------------

# we can define custom orbital combinations with ::pwtk::orbitalGroup

orbitalGroup p��� {px + py}; # p orbitals perpendicular to the surface normal and CO axis
orbitalGroup p��� pz;         # p orbital along the surface normal and CO axis

orbitalGroup d��� {dx2-y2 + dxy}; # d orbitals perpendicular to the surface normal and CO axis
orbitalGroup d��� dz2;             # d orbital along the surface normal and CO axis

# CO and the Rh atoms to which CO binds are atoms 1, 2, 4 for
# O, C, Rh, respectively (see CO-Rh100-c2x2-2L.xsf)
#
# we do not really need ::pwtk::sumpdos here; it is used to have
# simpler and more readable filenames; for full explanation of
# ::pwtk::sumpdos options, see ::pwtk::pdos_atm_files
#
# -f ... pattern for the filenames (aka 'filpdos')
# -n ... list of atom numbers
# -l ... list of orbital angular momentum s, p, d

sumpdos -f $name -n 1 -l s O-2s
sumpdos -f $name -n 1 -l p O-2p

sumpdos -f $name -n 2 -l s C-2s
sumpdos -f $name -n 2 -l p C-2p

sumpdos -f $name -n 4 -l s Rh-5s
sumpdos -f $name -n 4 -l d Rh-4d


# Let's plot PDOSes twice: into a default window terminal (-t win) and
# in a PDF file (-t pdf). Hence, we save specs into a variable.
#
# Note that in the PDOS specs, we can specify 'ldos' (for LDOS),
# individual orbitals (s, p, d), group-orbitals defined with
# ::pwtk::orbitalGroup, and also orbital expressions (or
# combinations), e.g. {dxz + dyz}
#
# 'ldos' stands for the sum of all orbitals of a given type, e.g., for p
# orbitals, ldos = px + py + pz

set pdos_specs {
    {
        O-2p ldos
        C-2p ldos
        Rh-5s ldos
        Rh-4d ldos
    }
    {
        O-2s s
        O-2p p���
        O-2p p���
    } {
        C-2s s
        C-2p p���
        C-2p p���
    } {
        Rh-5s s
        Rh-4d d���
        Rh-4d d���
        Rh-4d {dxz + dyz}        
    }
}
# the above specs define four PDOS plots:
# * plot #1: O 2p, C 2p, Rh 5s, and Rh 4d
# * plot #2: O 2s, 2p∥ and 2p⟂
# * plot #3: C 2s, 2p∥ and 2p⟂
# * plot #4: Rh 5s, d∥, 4d⟂, 4dxz + 4dyz


# ::pwtk::pdos_multiplot plots the PDOSes into a multi plot;
# let's plot multiplot into a window and a PDF file

pdos_multiplot -e pw.$name.nscf.out -t win $pdos_specs O-C-Rh-pdos
pdos_multiplot -e pw.$name.nscf.out -t pdf $pdos_specs O-C-Rh-pdos
TABLE OF CONTENTS

35c-pdos-CORh
