[Pw_forum] Omit Atoms from Vibrational Energy Calculation

[William Joseph Ivan DeBenedetti]

Dear QE users,

I am attempting a vibrational energy calculation of an adsorbate on a TiO2 slab, I am interested in calculating the vibrational frequencies of the adsorbate (an organic molecule) but not the slab itself. Does anyone know how one might go about implementing this in .phx?

I have checked the documentation for the phonon package on the QE website and searched the forums with no luck.

I have included my input file below.

Thanks,

Will DeBenedetti
Doctoral Candidate
Cornell University

cat > $INFILE << EOF
&CONTROL
 calculation = 'scf',
 restart_mode = 'from_scratch',
 prefix='$PREFIX',
 pseudo_dir='$PSEUDO_DIR',
 tstress=.true.,
 tprnfor=.true.,
/
&SYSTEM
 ibrav=0,
 nat=52,
 ntyp=4,
 ecutwfc=60,
 ecutrho=500,
 occupations='smearing',
 smearing='gaussian',
 degauss=0.01
/
&ELECTRONS
 conv_thr = 1.0D-6,
 mixing_mode = 'local-TF',
 mixing_beta = 0.3d0,
 diagonalization = 'david',
/
&IONS
 ion_dynamics='bfgs',
/
&CELL
 cell_dynamics = 'bfgs',
 press=0.1d0,
/
ATOMIC_SPECIES
 Ti 47.88d0 Ti_PBE.UPF
 O  16.00d0 O_PBE.UPF
 C  12.01d0 C_PBE.UPF
 H   1.0d0   H_PBE.UPF

CELL_PARAMETERS Bohr
14.36733988d0     0.0d0      0.0d0
0.0d0   7.18366994d0      0.0d0
0.0d0   0.0d0     62.0d0

ATOMIC_POSITIONS angstrom
Ti     0.000000000         0.000000000         5.484694341
Ti     1.900716424         1.900716424        10.331637610
Ti     0.000000000         1.900716424         7.908165704
Ti     1.900716424         0.000000000        12.755108429
Ti     3.801432848         0.000000000         5.484694341
Ti     5.702149272         1.900716424        10.331637610
Ti     3.801432848         1.900716424         7.908165704
Ti     5.702149272         0.000000000        12.755108429
O     0.000000000         0.000000000         7.423471214
O     1.900716424         1.900716424        12.270415570
O     0.000000000         1.900716424         9.846942577
O     1.900716424         0.000000000         4.999999852
O     1.900716424         0.000000000        10.816331557
O     0.000000000         1.900716424         5.969388288
O     5.702149272         1.900716424        12.270415570
O     3.801432848         1.900716424         9.846942577
O     5.702149272         0.000000000         4.999999852
O     5.702149272         0.000000000        10.816331557
O     3.801432848         1.900716424         5.969388288
O     5.702149272         1.900716424         8.392860194
O     3.801432848         0.000000000        13.239803463
O     3.91954       -0.90338        3.71425
O     3.64158        1.28524        3.89859
O     5.58403       -1.01922   14.47657
O     5.77636        1.14600   14.33321
C     3.66908        0.26398        2.95220
C     4.68681        0.64677        1.91622
C     5.88245       -0.05604        1.69530
C     6.78648        0.40256        0.72400
C     6.50157        1.54908   -0.02435
C     5.31137        2.24576        0.18945
C     4.41100        1.79490        1.15522
C     5.87148        0.11358   15.25171
C     5.00636        0.40232   16.44596
C     3.61041        0.55832   16.37536
C     2.88508        0.92364   17.51528
C     3.54382        1.14132   18.72818
C     4.92900        0.98552   18.80663
C     5.65627        0.61590   17.67184
H     6.12131       -0.93836        2.27069
H     7.71305       -0.12957        0.55411
H     7.20099        1.90429   -0.77089
H     5.08606        3.13466   -0.38544
H     3.49321        2.35191        1.31441
H     5.44203        1.16504   19.74289
H     6.73357        0.52300   17.74347
H     1.81222        1.05293   17.45492
H     2.98275        1.43849   19.60480
H     3.07422        0.42139   15.45283

K_POINTS automatic
  2 2 1 0 0 0

EOF

module load espresso/5.4.0

ibrun pw.x < $INFILE > $OUTFILE # Run the executable named pw.x

$INFILE = "$PREFIX.ph.in"
$OUTFILE = "$PREFIX.ph.out"

cat > $INFILE << EOF
title_line
&INPUTPH

tr2_ph=1.0d-12,
amass(1)=47.88,
amass(2)=12.010,
amass(3)=16.00,
amass(4)=1.0,
epsil=.false.,
!lraman=.true.,
asr=.true.,
prefix='$PREFIX',
fildyn='ANA.dyn',
 /
 2 2 1
EOF


module load espresso/5.4.0
ibrun ph.x < $INFILE > $OUTFILE

rm *.igk *.wfc*
rm -r *.save



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