[QE-users] Xcryden :Warning message "Huge number of bonds "

[Tone Kokalj]

Dear Chandrika,

Your structure looks fine to me. To reduce the number of displayed
bonds for Ti, reduce the chemical-connectivity factor or respective
radii.

Best regards,
Tone
-- 
Jožef Stefan Institute, Ljubljana, Slovenia


On Fri, 2025-03-14 at 11:16 +0000, Ms. Chandrika K. via users wrote:
> Thanks for reply and please find the vc-relax and scf input files
> given below for reference.
> &CONTROL
>     calculation = 'vc-relax'
>     prefix = 'BaTiO3'
>     outdir='/home/p_surekha/BT-ICSD/Outdir'
>     pseudo_dir='.'
>     nstep=300
>  /
>  
> &SYSTEM
>     ibrav=0
>     nat=5, 
>     ntyp=3,
>     ecutwfc=37
>     ecutrho=575
>     vdw_corr="Grimme-D2"
>     occupations="smearing"
>     degauss=0.005
>     smearing="gaussian"
>      /
> 
> &ELECTRONS
>      conv_thr=1e-6
> electron_maxstep = 100
>  /
> &IONS     
>  /
> &CELL
>     /
> ATOMIC_SPECIES
>   Ba 137.360 Ba.pbe-spn-rrkjus_psl.1.0.0.UPF
>   Ti 47.900  Ti.pbe-spn-rrkjus_psl.1.0.0.UPF
>   O  15.999  O.pbe-n-rrkjus_psl.1.0.0.UPF
> 
> ATOMIC_POSITIONS (Angstrom)
> Ba    0.0000 0.0000 0.0077
> Ti    1.9979 1.9979 2.0849
> O     1.9979 1.9979 3.9763
> O     0.0000 1.9979 1.9852
> O     1.9979 0.0000 1.9852
>  
> K_POINTS AUTOMATIC
>  10  10  10  0  0  0  
> 
> CELL_PARAMETERS (angstrom)
>  3.9957780000 0.0000000000 0.0000000000
>  0.0000000000 3.9957780000 0.0000000000
>  0.0000000000 0.0000000000 4.0383120000
> 
> Please find the scf input file attached 
> 
> &CONTROL
>     calculation = 'scf'
>     prefix = 'BaTiO3'
>     outdir='/home/p_surekha/BT-ICSD/Outdir'
>     pseudo_dir='.'
>  /
>  &SYSTEM
>     ibrav=6    
>     celldm(1)=7.41
>     celldm(3)=1.01
>     nat=5,
>     ntyp=3,
>     ecutwfc=37
>     ecutrho=575
>     vdw_corr="Grimme-D2"
>     occupations="smearing"
>     degauss=0.005
>     smearing="gaussian"
>      /
> 
> &ELECTRONS
>      conv_thr=1e-6
> electron_maxstep = 100
>  /
> 
> ATOMIC_SPECIES
>   Ba 137.360 Ba.pbe-spn-rrkjus_psl.1.0.0.UPF
>   Ti 47.900  Ti.pbe-spn-rrkjus_psl.1.0.0.UPF
>   O  15.999  O.pbe-n-rrkjus_psl.1.0.0.UPF
> 
> ATOMIC_POSITIONS (angstrom)
> Ba            0.0000000000        0.0000000000        0.0199890087
> Ti            1.9605044037        1.9605044037        2.0158280987
> O             1.9605044037        1.9605044037        3.9015088218
> O             0.0000000000        1.9605044037        1.9381529944
> O             1.9605044037        0.0000000000        1.9381529944
> 
> K_POINTS AUTOMATIC
>  10  10  10  0  0  0  
> From: Giovanni Cantele <giovanni.cantele at spin.cnr.it>
> Sent: Friday, March 14, 2025 2:19 PM
> To: Ms. Chandrika K. <BL.EN.R4ECE21001 at bl.students.amrita.edu>;
> Quantum ESPRESSO users Forum <users at lists.quantum-espresso.org>
> Subject: Re: [QE-users] Xcryden :Warning message "Huge number of
> bonds "
>  
> Hi,
> can you share the file you're trying to visualize with XCrysDen. It
> is likely a problem of your input geometry,
> but I'm not sure about that.
> Giovanni
> -- 
> 
> Giovanni Cantele, PhD
> CNR-SPIN
> c/o Dipartimento di Fisica
> Universita' di Napoli "Federico II"
> Complesso Universitario M. S. Angelo - Ed. 6
> Via Cintia, I-80126, Napoli, Italy
> e-mail: giovanni.cantele at spin.cnr.it
> Phone: +39 081 676910
> Skype contact: giocan74
> 
> ResearcherID: http://www.researcherid.com/rid/A-1951-2009
> Web page: https://sites.google.com/view/giovanni-cantele/home
> 
> 
> Il giorno ven 14 mar 2025 alle ore 09:25 Ms. Chandrika K. via users
> <users at lists.quantum-espresso.org> ha scritto:
> > Hi all,
> > When visualising the supercell of tetragonal BaTiO₃ using Xcrysden,
> > I am receiving a warning message stating "Huge number of bonds." I
> > have cross-verified the lattice parameters, performed vc-relax, and
> > used the optimised cell parameters and atomic coordinates, but the
> > warning persists.
> > Any guidance on this issue would be of great help.
> > Regards 
> > Chandrika 
> > Research Scholar 
> > 
> > 
> > 
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