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

Fri Mar 14 16:09:04 CET 2025

hello
If you do 'cat  -A'  of your input,  that's what you probably will get for the positions

ATOMIC_POSITIONS (Angstrom)$
BaM-bM-^@M-^BM-bM-^@M-^BM-bM-^@M-^BM-bM-^@M-^B0.0000 0.0000 0.0077$
TiM-bM-^@M-^BM-bM-^@M-^BM-bM-^@M-^BM-bM-^@M-^B1.9979 1.9979 2.0849$
OM-bM-^@M-^BM-bM-^@M-^BM-bM-^@M-^BM-bM-^@M-^BM-bM-^@M-^B1.9979 1.9979 3.9763$
OM-bM-^@M-^BM-bM-^@M-^BM-bM-^@M-^BM-bM-^@M-^BM-bM-^@M-^B0.0000 1.9979 1.9852$
OM-bM-^@M-^BM-bM-^@M-^BM-bM-^@M-^BM-bM-^@M-^BM-bM-^@M-^B1.9979 0.0000 1.9852$

To clean it up do

awk '{print$0}' prova  > prova_clean
and retry

hope this helps
Pietro
________________________________
From: users <users-bounces at lists.quantum-espresso.org> on behalf of Ms. Chandrika K. via users <users at lists.quantum-espresso.org>
Sent: Friday, March 14, 2025 12:16
To: Giovanni Cantele <giovanni.cantele at spin.cnr.it>; Quantum ESPRESSO users Forum <users at lists.quantum-espresso.org>
Subject: Re: [QE-users] Xcryden :Warning message "Huge number of bonds "

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<mailto: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<mailto: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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