[QE-users] phonon calculation : Vibrational frequency with no-intensity
Stefano Baroni
baroni at sissa.it
Sat May 9 10:53:41 CEST 2020
Aluminum oxide is an insulator, even if aluminum is a “metal”. SB
--
Stefano Baroni, Trieste -- swift message written and sent on the go
> On 9 May 2020, at 10:24, Abdulla Bin Afif <abdulla.binafif at ntnu.no> wrote:
>
>
> Dear Paolo and QE friends,
>
> Thanks for the reply.
>
> In my organometallic molecule /compound , TMA (trimethylealuminum ), as there is metal Al at the centre, I cannot put epsil=true, the code stops (as its defined only for insulators).
>
> Effective charges are calculated only when both trans and epsil are true.
>
> I am not sure, how to move forward.
>
> I am a beginner, if someone can share the input files for vibration calculations on a compound with a metal that would be great.
>
> Thanks and Regards,
> Abdulla Bin Afif
>
>
> From: users <users-bounces at lists.quantum-espresso.org> On Behalf Of Paolo Giannozzi
> Sent: Tuesday, May 5, 2020 9:45 PM
> To: Quantum ESPRESSO users Forum <users at lists.quantum-espresso.org>
> Subject: Re: [QE-users] phonon calculation : Vibrational frequency with no intensity
>
> On Tue, May 5, 2020 at 9:32 PM Abdulla Bin Afif <abdulla.binafif at ntnu.no> wrote:
>
> Reading Dynamical Matrix from file dmat.TMA
> ...Force constants read
> ...epsilon and Z* not read (not found on file)
>
> here is the answer: no effective charges (epsil=.true. in the phonon input, ONLY FOR INSULATORS), no IR activity
>
> Paolo
> --
> Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche,
> Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
> Phone +39-0432-558216, fax +39-0432-558222
>
>
>
> Hi QE community ,
>
> I am trying to calculate IR vibration frequency modes of TMA (trimethylaluminum ) organometallic, I am getting the frequency values but not the intensity. The procedure works well for CO2 molecule, where I can see both vibrational frequency and intensity. I am not sure why it doesn’t work for TMA, I tried changing the, 1. Occupations, from Gaussian to fixed in scf , 2. Epsil to true in ph.x , 3. Changed the k points, but it doesn’t work.
>
> The steps I am doing are, 1. Scf, 2. Ph.x 3. dynmat.x
>
> Pw. In
> &CONTROL
> calculation = 'scf',
> outdir = '.',
> prefix = 'calc',
> pseudo_dir = '.',
> tprnfor = .true.,
> tstress = .true.,
> /
> &SYSTEM
> degauss = 0.00734986475817d0,
> ecutrho = 367.493237909d0,
> ecutwfc = 36.7493237909d0,
> ibrav=0,
> nat = 13,
> ntyp = 3,
> occupations = 'fixed',
> smearing = 'cold',
> input_dft='PBE',
> /
> &ELECTRONS
> diagonalization='david',
> conv_thr=7.34986475817e-07,
> mixing_mode='plain',
> electron_maxstep=100,
> mixing_beta=0.7d0,
> /
> CELL_PARAMETERS angstrom
> 15.000000000 0.0000000000 0.0000000000
> 0.0000000000 15.000000000 0.0000000000
> 0.0000000000 0.0000000000 15.000000000
>
> ATOMIC_SPECIES
> Al 26.98154 Al.UPF,
> C 12.011 C.UPF,
> H 1.00794 H.UPF,
> ATOMIC_POSITIONS {crystal}
> Al 0.5344800000 0.5466800000 0.5342700000
> C 0.4242100000 0.6103500000 0.5344500000
> C 0.6447600000 0.6103500000 0.5344500000
> C 0.5344800000 0.4193500000 0.5344500000
> H 0.4032300000 0.6226500000 0.4659700000
> H 0.3735600000 0.5709800000 0.5685900000
> H 0.4329000000 0.6737500000 0.5688800000
> H 0.6657400000 0.6222700000 0.6029900000
> H 0.6954000000 0.5711800000 0.5000900000
> H 0.6360700000 0.6739400000 0.5003700000
> H 0.5343200000 0.3950300000 0.4659700000
> H 0.5939000000 0.3951800000 0.5685900000
> H 0.4752400000 0.3951800000 0.5688800000
> K_POINTS (automatic)
> 1 1 1 0 0 0
>
> Ph.in
> Normal modes for TMA
> &inputph
> tr2_ph=1.0d-12,
> prefix='calc',
> amass(1)=26.98,
> amass(2)=12.011,
> amass(3)=1.00794,
> outdir='./'
> trans=.true.,
> asr=.true.,
> fildyn='dmat.TMA'
> /
> 0.0 0.0 0.0
>
> dm.in
> & input fildyn='dmat.TMA', asr='zero-dim' /
>
> dm.out
> Program DYNMAT v.6.4.1 starts on 5May2020 at 12:27:40
>
> This program is part of the open-source Quantum ESPRESSO suite
> for quantum simulation of materials; please cite
> "P. Giannozzi et al., J. Phys.:Condens. Matter 21 395502 (2009);
> "P. Giannozzi et al., J. Phys.:Condens. Matter 29 465901 (2017);
> URL http://www.quantum-espresso.org",
> in publications or presentations arising from this work. More details at
> http://www.quantum-espresso.org/quote
>
> Parallel version (MPI & OpenMP), running on 24 processor cores
> Number of MPI processes: 24
> Threads/MPI process: 1
>
> MPI processes distributed on 1 nodes
> R & G space division: proc/nbgrp/npool/nimage = 24
>
> Reading Dynamical Matrix from file dmat.TMA
> ...Force constants read
> ...epsilon and Z* not read (not found on file)
> Acoustic Sum Rule: || Z*(ASR) - Z*(orig)|| = 0.000000E+00
> Acoustic Sum Rule: ||dyn(ASR) - dyn(orig)||= 3.710913E-01
> A direction for q was not specified:TO-LO splitting will be absent
>
> Polarizability (A^3 units)
> multiply by 1.000000 for Clausius-Mossotti correction
> 0.000000 0.000000 0.000000
> 0.000000 0.000000 0.000000
> 0.000000 0.000000 0.000000
>
> IR activities are in (D/A)^2/amu units
>
> # mode [cm-1] [THz] IR
> 1 -498.14 -14.9339 0.0000
> 2 -439.13 -13.1647 0.0000
> 3 -414.02 -12.4119 0.0000
> 4 -343.48 -10.2972 0.0000
> 5 -273.35 -8.1950 0.0000
> 6 -226.68 -6.7958 0.0000
> 7 -120.77 -3.6206 0.0000
> 8 -4.54 -0.1361 0.0000
> 9 -1.61 -0.0482 0.0000
> 10 -1.02 -0.0307 0.0000
> 11 1.26 0.0377 0.0000
> 12 7.19 0.2154 0.0000
> 13 74.46 2.2324 0.0000
> 14 220.15 6.5999 0.0000
> 15 411.75 12.3439 0.0000
> 16 529.26 15.8669 0.0000
> 17 611.01 18.3177 0.0000
> 18 646.47 19.3806 0.0000
> 19 673.65 20.1955 0.0000
> 20 751.68 22.5349 0.0000
> 21 792.17 23.7485 0.0000
> 22 1061.21 31.8144 0.0000
> 23 1077.23 32.2945 0.0000
> 24 1091.77 32.7305 0.0000
> 25 1337.17 40.0873 0.0000
> 26 1338.69 40.1330 0.0000
> 27 1345.59 40.3398 0.0000
> 28 1346.59 40.3699 0.0000
> 29 1358.78 40.7352 0.0000
> 30 1366.21 40.9581 0.0000
> 31 2858.21 85.6871 0.0000
> 32 2944.10 88.2618 0.0000
> 33 3077.75 92.2687 0.0000
> 34 3170.75 95.0567 0.0000
> 35 3178.78 95.2974 0.0000
> 36 3181.27 95.3721 0.0000
> 37 3186.56 95.5307 0.0000
> 38 3190.00 95.6339 0.0000
> 39 3195.97 95.8129 0.0000
>
> DYNMAT : 0.15s CPU 0.54s WALL
>
>
> This run was terminated on: 12:27:40 5May2020
>
> =------------------------------------------------------------------------------=
> JOB DONE.
> =------------------------------------------------------------------------------=
>
>
>
> Thanks and Regards,
>
> Abdulla Bin Afif
> Ph.D. Candidate
> Norwegian University of Science and Technology (NTNU)
> MTP - Department of Mechanical and Industrial Engineering
> Richard Birkelandsvei 2b
> NO-7491 Trondheim. Norway
>
> Email: abdulla.binafif at ntnu.no
> Mobil: +47 41348358
>
>
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