[QE-users] Fw: Xcryden :Warning message "Huge number of bonds "
Ms. Chandrika K.
BL.EN.R4ECE21001 at bl.students.amrita.edu
Fri Mar 14 13:21:18 CET 2025
"Thanks for the suggestion! I’ll take a look at the XCRYSDEN installation to make sure everything is set up correctly.
________________________________
From: Vahid Askarpour <vh261281 at dal.ca>
Sent: Friday, March 14, 2025 5:20 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 "
I just visualized the scf.in with XCRYSDEN. I get the following output with ~ 42 bonds and no warning message:
reading PRIMCOORD
reading CONVCOORD
Number of Atoms: 10
Number of Frames: 12
natoms: 10 , ndel: 0
Filtered number of atoms: 10
Estimated number of bonds = 42
sInfo(dim) = 3; periodic(dim) = 3
Maybe your XCRYSDEN installation is the issue.
Cheers,
Vahid
Department of Physics and Atmospheric Science
Dalhousie University, Halifax, NS
CANADA
[cell.png]
On Mar 14, 2025, at 8:16 AM, Ms. Chandrika K. via users <users at lists.quantum-espresso.org> wrote:
CAUTION: The Sender of this email is not from within Dalhousie.
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<mailto: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<mailto:BL.EN.R4ECE21001 at bl.students.amrita.edu>>; Quantum ESPRESSO users Forum <users at lists.quantum-espresso.org<mailto: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
_______________________________________________________________________________
The Quantum ESPRESSO Foundation stands in solidarity with all civilians worldwide who are victims of terrorism, military aggression, and indiscriminate warfare.
--------------------------------------------------------------------------------
Quantum ESPRESSO is supported by MaX (www.max-centre.eu<http://www.max-centre.eu/>)
users mailing list users at lists.quantum-espresso.org<mailto:users at lists.quantum-espresso.org>
https://lists.quantum-espresso.org/mailman/listinfo/users
_______________________________________________________________________________
The Quantum ESPRESSO Foundation stands in solidarity with all civilians worldwide who are victims of terrorism, military aggression, and indiscriminate warfare.
--------------------------------------------------------------------------------
Quantum ESPRESSO is supported by MaX (www.max-centre.eu<http://www.max-centre.eu/>)
users mailing list users at lists.quantum-espresso.org<mailto:users at lists.quantum-espresso.org>
https://lists.quantum-espresso.org/mailman/listinfo/users
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.quantum-espresso.org/pipermail/users/attachments/20250314/c2e40811/attachment.html>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: cell.png
Type: image/png
Size: 77016 bytes
Desc: cell.png
URL: <http://lists.quantum-espresso.org/pipermail/users/attachments/20250314/c2e40811/attachment.png>
More information about the users
mailing list