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-boun...@lists.quantum-espresso.org> on behalf of Ms.
Chandrika K. via users <users@lists.quantum-espresso.org>
Sent: Friday, March 14, 2025 12:16
To: Giovanni Cantele <giovanni.cant...@spin.cnr.it>; Quantum ESPRESSO users
Forum <users@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.cant...@spin.cnr.it>
Sent: Friday, March 14, 2025 2:19 PM
To: Ms. Chandrika K. <bl.en.r4ece21...@bl.students.amrita.edu>; Quantum
ESPRESSO users Forum <users@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.cant...@spin.cnr.it<mailto:giovanni.cant...@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@lists.quantum-espresso.org<mailto:users@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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warfare.
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