TABLE OF CONTENTS

15-vib-mol-spectra

DESCRIPTION

This example shows how to calculate molecular vibrational spectra using the pw.x, ph.x, and dynmat.x calculations.

REMARK

In PWTK, calculations subsequent to pw.x (in the current case ph.x & dynmat.x) inherit the value of the "outdir" and "prefix" variables from the CONTROL namelist. Hence, there is no need to set them in the INPUTPH and DYNMAT namelists.

BEWARE

This example requires the OpenBabel program (http://openbabel.org).

EXAMPLE SOURCE FILE

vib-mol-spectra.pwtk

SOURCE

# generate the coordinates of ethane molecule (C2H6) from the SMILES specs,
# https://en.wikipedia.org/wiki/Simplified_molecular-input_line-entry_system

set coor [::pwtk::smilesToCoor CC]

# get the number of atoms

set nat [::pwtk::getNAtoms $coor]

# calculate orthorhombic box size that encapsulates the molecule with a 6 Å of vacuum

lassign [::pwtk::boxify $coor 6] A B C


# the pw.x input data
#
# (N.B. see the 32-calcmol example (file: calcmol.pwtk), where a
# molecule is calculated with the convenient ::pwtk::calcmol workflow)

CONTROL {
    calculation = 'relax'
    prefix = 'C2H6'  outdir = '.'  pseudo_dir = '.'
}
SYSTEM "
   ibrav = 8  A = $A  B = $B  C = $C
   nat = $nat  ntyp = 2
   ecutwfc = 50
"
ELECTRONS { conv_thr = 1e-9 }
IONS {}
ATOMIC_SPECIES {
    H  1.0079  H.pz-vbc.UPF
    C  12.011  C.pz-vbc.UPF
}
ATOMIC_POSITIONS (angstrom) $coor
K_POINTS (automatic) { 1 1 1  0 0 0 }

# ph.x input data
#
# REMARK: calculations automatically inherit the value of the "outdir"
# and "prefix" variables from the CONTROL namelist. Hence, there is no
# need to set them here.

INPUTPH {
    tr2_ph = 1d-17
    lraman = .true.
    asr    = .true.
    zue    = .true.
    epsil  = .true.
    trans  = .true.
    fildyn = 'C2H6.dyn'
} {
    0.0 0.0 0.0
}

# dynmat.x input data
#
# REMARK: the value of "fildyn" is inherited from the INPUTPH
# namelist. Hence, there is no need to set it here.

DYNMAT {
    asr = 'zero-dim'
}

# run calculations

runPW relax.C2H6
runPH ph.C2H6
set dmo [runDYNMAT dynmat.C2H6]; # we need the name of the dynmat.x
                                 # output file (dmo) for subsequent
                                 # vibrational spectra plotting


# plot the vibrational spectra from the dynmat.x output file with
# ::pwtk::dmo_vibSpectrum (by default, it plots to EPS image)

dmo_vibSpectrum $dmo

# this is how to plot in window

dmo_vibSpectrum -t win $dmo

# this is how to plot to PNG image

dmo_vibSpectrum -t png $dmo