[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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