TABLE OF CONTENTS

391-lobster-analysis-CORh

DESCRIPTION

This example shows how to perform bonding analysis with LOBSTER; it requires the "lobster" executable, http://www.cohp.de/.

The structure considered is a two-layer slab of CO/Rh(100)-c(2x2).

EXAMPLE SOURCE FILE

lobster-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

# load CELL_PARAMETERS and ATOMIC_POSITIONS from the XSF file

CELL_PARAMETERS_and_ATOMIC_POSITIONS_fromXSF CO-Rh100-c2x2-2L.xsf


# FOR LOBSTER, we need PAW potentials nbnd=48

SYSTEM {
    nbnd = 48
}
ATOMIC_SPECIES {
    C     1.0  C.pbe-n-kjpaw_psl.1.0.0.UPF
    O     1.0  O.pbe-n-kjpaw_psl.1.0.0.UPF
    Rh    1.0  Rh.pbe-spn-kjpaw_psl.1.0.0.UPF
}


# the ::pwtk::lobster_run command performs pw.x SCF (option -scf), pw.x NSCF
# (option -nscf) and lobster calculations and makes basic DOS, COOP, COHP, and COBI plots
#
# the input for lobster can be specified with the LOBSTER card or as a
# command-line argument to the ::pwtk::lobster_run command
#
# with the -dir option, we request to perform calculations in a subdirectory

lobster_run -scf -nscf {6 6 1} -xf '' -v -dir lobster.$name $name {
    COHPstartEnergy  -10
    COHPendEnergy     6
    usebasisset      pbeVaspFit2015
    includeOrbitals  s p d

    # define the CO molecule
    molecule atom 1 atom 2

    # calculate COHP for the C-Rh bond
    cohpbetween atom 2 atom 4

    # calculated COHP between the CO molecule and Rh atom to which CO binds
    cohpbetween frag 1 atom 4
}


# once the lobster calculation was performed, we can instruct PWTK to
# make various plots with the ::pwtk::lobster_plot and
# ::pwtk::lobster_multiplot commands
#
# let's create a multiplot containing the following plots:
#
# - DOS projected to CO and its molecular orbitals
# - DOS projected to the CO molecule and Rh atom to which CO binds
# - DOS projected to individual s & p orbitals of C and O atom
# - DOS projected to s and average of px+py+pz orbitals of C and O atom
#
# N.B. if the -dir option was used for ::pwtk::lobster_run, also here
# the -dir option must be specified with the same directory

lobster_multiplot -nx 5 -v  -xr 0:8 -dir lobster.$name {
    { DOS.LCFO.frag1 {i0 i1 i2 i3 i4 i5 i6 i7 i8} }
    { DOS.atom1-2 i0 DOS.atom4 i0 }
    { DOS.orbatom1 { i1 i2 i3 i4 } DOS.orbatom2 {i1 i2 i3 i4 } }
    { DOS.orbatom1 { i1 (i2+i3+i4)/3.0 } DOS.orbatom2 {i1 (i2+i3+i4)/3.0 } }
}