[Pw_forum] Omit Atoms from Vibrational Energy Calculation
Giuseppe Mattioli
giuseppe.mattioli at ism.cnr.it
Thu Apr 27 14:09:11 CEST 2017
Dear Will
+--------------------------------------------------------------------
Variable: nat_todo
Type: INTEGER
Default: 0, i.e. displace all atoms
Description: Choose the subset of atoms to be used in the linear response
calculation: "nat_todo" atoms, specified in input (see below)
are displaced. Can be used to estimate modes for a molecule
adsorbed over a surface without performing a full fledged
calculation. Use with care, at your own risk, and be aware
that this is an approximation and may not work.
IMPORTANT:
* "nat_todo" <= nat
* if linear-response is calculated for a given atom, it
should also be done for all symmetry-equivalent atoms,
or else you will get incorrect results
+--------------------------------------------------------------------
This is written into the Doc/INPUT_PH.txt file.
HTH
Giuseppe
On Wednesday, April 26, 2017 09:11:28 PM William Joseph Ivan DeBenedetti wrote:
> 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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Giuseppe Mattioli
CNR - ISTITUTO DI STRUTTURA DELLA MATERIA
v. Salaria Km 29,300 - C.P. 10
I 00015 - Monterotondo Stazione (RM), Italy
Tel + 39 06 90672342 - Fax +39 06 90672316
E-mail: <giuseppe.mattioli at ism.cnr.it>
http://www.ism.cnr.it/en/staff/giuseppe-mattioli/
ResearcherID: F-6308-2012
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