[QE-users] Errors of phonon calcualtions with Grimme's DFT-D3
Thomas Brumme
tbrumme at msx.tu-dresden.de
Wed Aug 9 11:30:38 CEST 2023
Dear Jibiao Li,
I think D3 is not implemented in the phonon code - at least if I look at
the beginning of
the phonon.f90 which summarized what is possible:
https://gitlab.com/QEF/q-e/-/blob/develop/PHonon/PH/phonon.f90?ref_type=heads
There I can read:
!! Not implemented in \(\texttt{ph.x}\):
!! [6] [5] + constraints on the magnetization
!! [7] Tkatchenko-Scheffler, DFT-D3
Sorry, but for D3 you probably need to use another code which is
interfaced with QE.
Phonopy is working with QE.
Kind regards
Thomas
On 8/6/23 04:12, Jibiao Li via users wrote:
> Dear All,
>
> I try to perform phonon calculations in the develop version of QE, but
> I got an error message below
>
> ... ...
> Alpha used in Ewald sum = 2.8000
>
> Reading Grimme-D3 Hessian from file: ./atop.hess
> forrtl: severe (24): end-of-file during read, unit 1, file
> /home/jibiaoli/calc/monomers/first/./atop.hess
> Image PC Routine Line Source
> ph.x 00000000010A6DD8 Unknown Unknown Unknown
> ph.x 00000000010E1F7A Unknown Unknown Unknown
> ph.x 00000000005ECAFD d2ionq_dispd3_ 51
> d2ionq_disp.f90
> ph.x 00000000005762F6 dynmat0_new_ 61
> dynmat0.f90
> ph.x 00000000004A7277 phq_init_ 407
> phq_init.f90
> ph.x 000000000047684F initialize_ph_ 96
> initialize_ph.f90
> ph.x 000000000040C947 do_phonon_ 100
> do_phonon.f90
> ph.x 00000000004071C2 MAIN__ 78
> phonon.f90
> ph.x 0000000000407122 Unknown Unknown Unknown
> libc-2.31.so 00007FA1520FC0B3 __libc_start_main Unknown Unknown
> ph.x 000000000040702E Unknown Unknown Unknown
>
> ===================================================================================
> = BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES
> = RANK 1 PID 145409 RUNNING AT ubuntue
> = KILLED BY SIGNAL: 9 (Killed)
>
>
> Any suggestion to resolve this problem?
>
> I look forward to receiving your reply.
>
> Sincerely
>
> Jibiao Li
>
> phonons at Gamma
> &inputph
> tr2_ph=1.0d-14,
> prefix='atop',
> alpha_mix=0.15,
> fildyn='phG.dyn',
> amass(1)=15.999
> amass(2)=1.0079
> amass(3)=106.4
> outdir='./'
> nat_todo=3,
> /
> 0.0 0.0 0.0
> 1 2 3
>
>
> &CONTROL
> calculation = 'scf' ,
> restart_mode = 'from_scratch' ,
> outdir = './' ,
> pseudo_dir = '/home/jibiaoli/pseudo/PAW' ,
> prefix = 'atop' ,
> tstress = .true. ,
> tprnfor = .true. ,
> /
> &SYSTEM
> ibrav = 4,
> celldm(1) = 15.6677255,
> celldm(3) = 3.4,
> nat = 48,
> ntyp = 3,
> ecutwfc = 49 ,
> ecutrho = 411 ,
> occupations = 'smearing' ,
> degauss = 0.02D0 ,
> smearing = 'marzari-vanderbilt' ,
> vdw_corr = 'DFT-D3',
> /
> &ELECTRONS
> electron_maxstep = 299,
> mixing_beta = 0.2D0 ,
> diagonalization = 'david' ,
> /
> ATOMIC_SPECIES
> O 15.999 O.pbe-n-kjpaw_psl.1.0.0.UPF
> H 1.0079 H.pbe-kjpaw_psl.1.0.0.UPF
> Pd 106.40 Pd.pbe-n-kjpaw_psl.1.0.0.UPF
> ATOMIC_POSITIONS angstrom
> H 2.1703819667 3.1677699191 11.4894189267
> O 1.5740335760 2.3936195417 11.4400536939
> H 2.1702795024 1.6192086817 11.4893627144
> Pd -0.0045915754 -0.0102383957 9.0266998715
> Pd -2.7651688140 4.7874278555 9.0360251883
> Pd 5.5259827527 -0.0001828639 9.0387617051
> Pd 2.7689931581 4.7956210226 9.0246308039
> Pd -1.3946621870 2.3938110685 9.0271708745
> Pd 4.1536116232 2.3931749457 9.0252316830
> Pd 1.3691550331 2.3939966336 9.0670107322
> Pd 2.7694105684 -0.0086872195 9.0249397450
> Pd -0.0054827549 4.7974751761 9.0269897862
> Pd 0.0066605988 3.1870668155 6.7670981200
> Pd 5.5283163914 3.1928013873 6.7495035331
> Pd 1.3818262753 0.8042230686 6.7653225775
> Pd -1.3828050324 5.5824639267 6.7487397927
> Pd 6.9077402952 0.7968151976 6.7553886260
> Pd 4.1480097045 5.5845055762 6.7479017041
> Pd 4.1467102526 0.7971898792 6.7545181138
> Pd 1.3813552626 5.5860818516 6.7546258538
> Pd 2.7589306780 3.1885119775 6.7642409667
> Pd 2.7636561440 1.5955976180 4.5130315840 0 0 0
> Pd 0.0000000000 6.3823904740 4.5130315840 0 0 0
> Pd 1.3818280720 3.9889940460 4.5130315840 0 0 0
> Pd -1.3818280720 3.9889940460 4.5130315840 0 0 0
> Pd 4.1454842150 3.9889940460 4.5130315840 0 0 0
> Pd 0.0000000000 1.5955976180 4.5130315840 0 0 0
> Pd -2.7636561440 6.3823904740 4.5130315840 0 0 0
> Pd 5.5273122870 1.5955976180 4.5130315840 0 0 0
> Pd 2.7636561440 6.3823904740 4.5130315840 0 0 0
> Pd -0.0000000000 4.7867928550 2.2565157920 0 0 0
> Pd 1.3818280720 2.3933964280 2.2565157920 0 0 0
> Pd 2.7636561400 0.0000000000 2.2565157920 0 0 0
> Pd -1.3818280720 2.3933964280 2.2565157920 0 0 0
> Pd 4.1454842150 2.3933964280 2.2565157920 0 0 0
> Pd 0.0000000000 0.0000000000 2.2565157920 0 0 0
> Pd -2.7636561440 4.7867928550 2.2565157920 0 0 0
> Pd 5.5273122870 0.0000000000 2.2565157920 0 0 0
> Pd 2.7636561440 4.7867928550 2.2565157920 0 0 0
> Pd -0.0000000000 3.1911952370 0.0000000000 0 0 0
> Pd 5.5273122870 3.1911952370 0.0000000000 0 0 0
> Pd 1.3818280720 0.7977988090 0.0000000000 0 0 0
> Pd -1.3818280720 5.5845916650 0.0000000000 0 0 0
> Pd 6.9091403590 0.7977988090 0.0000000000 0 0 0
> Pd 4.1454842150 5.5845916650 0.0000000000 0 0 0
> Pd 4.1454842150 0.7977988090 0.0000000000 0 0 0
> Pd 1.3818280720 5.5845916650 0.0000000000 0 0 0
> Pd 2.7636561440 3.1911952370 0.0000000000 0 0 0
> K_POINTS automatic
> 6 6 1 0 0 0
>
>
> ------------------------------------------------------------------------
>
> Jibiao Li
>
> Department of Materials Science and Engineering
>
> Yangtze Normal University
>
> Juxian Avenue 16, Fuling, Chongqing, China 408100
>
> Scopus Research ID: 54944118000
> <https://www.scopus.com/authid/detail.uri?authorId=54944118000>
>
> Web of Science Research ID:
> http://www.webofscience.com/wos/author/record/GLS-7259-2022
>
>
>
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--
Dr. rer. nat. Thomas Brumme
Theoretical chemistry
TU Dresden - KOE / 103
Bergstr. 66c
01069 Dresden
Tel: +49 (0)351 463 39449
email:thomas.brumme at tu-dresden.de
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