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"Thanks for the suggestion! I’ll take a look at the XCRYSDEN installation to make sure everything is set up correctly. </div>
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<div dir="ltr" id="x_divRplyFwdMsg"><span style="font-family: Calibri, sans-serif; font-size: 11pt; color: rgb(0, 0, 0);"><b>From:</b> Vahid Askarpour <vh261281@dal.ca><br>
<b>Sent:</b> Friday, March 14, 2025 5:20 PM<br>
<b>To:</b> Ms. Chandrika K. <BL.EN.R4ECE21001@bl.students.amrita.edu>; Quantum ESPRESSO users Forum <users@lists.quantum-espresso.org><br>
<b>Subject:</b> Re: [QE-users] Xcryden :Warning message "Huge number of bonds "</span>
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<div style="direction: ltr;">I just visualized the scf.in with XCRYSDEN. I get the following output with ~ 42 bonds and no warning message:</div>
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<div style="direction: ltr;">reading PRIMCOORD</div>
<div style="direction: ltr;">reading CONVCOORD</div>
<div style="direction: ltr;">Number of Atoms: 10</div>
<div style="direction: ltr;">Number of Frames: 12</div>
<div style="direction: ltr;">natoms: 10 , ndel: 0</div>
<div style="direction: ltr;">Filtered number of atoms: 10</div>
<div style="direction: ltr;">Estimated number of bonds = 42</div>
<div style="direction: ltr;">sInfo(dim) = 3; periodic(dim) = 3</div>
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<div style="direction: ltr;">Maybe your XCRYSDEN installation is the issue.</div>
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<div style="direction: ltr;">Cheers,</div>
<div style="direction: ltr;">Vahid</div>
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<div style="direction: ltr;">Department of Physics and Atmospheric Science</div>
<div style="direction: ltr;">Dalhousie University, Halifax, NS</div>
<div style="direction: ltr;">CANADA</div>
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<blockquote>
<div style="direction: ltr;">On Mar 14, 2025, at 8:16 AM, Ms. Chandrika K. via users <users@lists.quantum-espresso.org> wrote:</div>
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<b>CAUTION:</b> The Sender of this email is not from within Dalhousie.</div>
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Thanks for reply and please find the vc-relax and scf input files given below for reference.</div>
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&CONTROL</div>
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calculation = 'vc-relax'</div>
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prefix = 'BaTiO3'</div>
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outdir='/home/p_surekha/BT-ICSD/Outdir'</div>
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pseudo_dir='.'</div>
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nstep=300</div>
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/</div>
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&SYSTEM</div>
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ibrav=0</div>
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nat=5, </div>
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ntyp=3,</div>
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ecutwfc=37</div>
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ecutrho=575</div>
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vdw_corr="Grimme-D2"</div>
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occupations="smearing"</div>
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degauss=0.005</div>
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smearing="gaussian"</div>
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/</div>
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&ELECTRONS</div>
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conv_thr=1e-6</div>
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electron_maxstep = 100</div>
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&IONS </div>
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&CELL</div>
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ATOMIC_SPECIES</div>
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Ba 137.360 Ba.pbe-spn-rrkjus_psl.1.0.0.UPF</div>
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Ti 47.900 Ti.pbe-spn-rrkjus_psl.1.0.0.UPF</div>
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O 15.999 O.pbe-n-rrkjus_psl.1.0.0.UPF</div>
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ATOMIC_POSITIONS (Angstrom)</div>
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Ba 0.0000 0.0000 0.0077</div>
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Ti 1.9979 1.9979 2.0849</div>
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O 1.9979 1.9979 3.9763</div>
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O 0.0000 1.9979 1.9852</div>
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O 1.9979 0.0000 1.9852</div>
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K_POINTS AUTOMATIC</div>
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10 10 10 0 0 0 </div>
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CELL_PARAMETERS (angstrom)</div>
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3.9957780000 0.0000000000 0.0000000000</div>
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0.0000000000 3.9957780000 0.0000000000</div>
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0.0000000000 0.0000000000 4.0383120000</div>
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<u>Please find the scf input file attached </u></div>
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&CONTROL</div>
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calculation = 'scf'</div>
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prefix = 'BaTiO3'</div>
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outdir='/home/p_surekha/BT-ICSD/Outdir'</div>
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pseudo_dir='.'</div>
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&SYSTEM</div>
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ibrav=6 </div>
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celldm(1)=7.41</div>
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celldm(3)=1.01</div>
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nat=5,</div>
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ntyp=3,</div>
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ecutwfc=37</div>
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ecutrho=575</div>
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vdw_corr="Grimme-D2"</div>
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occupations="smearing"</div>
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degauss=0.005</div>
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smearing="gaussian"</div>
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/</div>
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&ELECTRONS</div>
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conv_thr=1e-6</div>
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electron_maxstep = 100</div>
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ATOMIC_SPECIES</div>
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Ba 137.360 Ba.pbe-spn-rrkjus_psl.1.0.0.UPF</div>
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Ti 47.900 Ti.pbe-spn-rrkjus_psl.1.0.0.UPF</div>
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O 15.999 O.pbe-n-rrkjus_psl.1.0.0.UPF</div>
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ATOMIC_POSITIONS (angstrom)</div>
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Ba 0.0000000000 0.0000000000 0.0199890087</div>
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Ti 1.9605044037 1.9605044037 2.0158280987</div>
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O 1.9605044037 1.9605044037 3.9015088218</div>
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O 0.0000000000 1.9605044037 1.9381529944</div>
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O 1.9605044037 0.0000000000 1.9381529944</div>
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K_POINTS AUTOMATIC</div>
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10 10 10 0 0 0 </div>
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<div id="x_x_divRplyFwdMsg" dir="ltr" class="x_x_elementToProof"><span style="font-family: Calibri, sans-serif; font-size: 11pt;"><b>From:</b> Giovanni Cantele <<a href="mailto:giovanni.cantele@spin.cnr.it" id="OWAddf31089-7189-7b48-b8e7-737e40f8b486" class="OWAAutoLink">giovanni.cantele@spin.cnr.it</a>><br>
</span></div>
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<b>Sent:</b> Friday, March 14, 2025 2:19 PM</div>
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<b>To:</b> Ms. Chandrika K. <<a href="mailto:BL.EN.R4ECE21001@bl.students.amrita.edu" id="OWAe0957792-0c55-a689-9445-8bc6bcd2d13a" class="OWAAutoLink">BL.EN.R4ECE21001@bl.students.amrita.edu</a>>; Quantum ESPRESSO users Forum <<a href="mailto:users@lists.quantum-espresso.org" id="OWA1b5c4d7d-584e-658a-87e8-42735fb428c2" class="OWAAutoLink">users@lists.quantum-espresso.org</a>><br>
<b>Subject:</b> Re: [QE-users] Xcryden :Warning message "Huge number of bonds "</div>
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Hi,</div>
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can you share the file you're trying to visualize with XCrysDen. It is likely a problem of your input geometry,</div>
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but I'm not sure about that.</div>
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Giovanni</div>
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-- <br>
<br>
Giovanni Cantele, PhD<br>
CNR-SPIN<br>
c/o Dipartimento di Fisica<br>
Universita' di Napoli "Federico II"<br>
Complesso Universitario M. S. Angelo - Ed. 6<br>
Via Cintia, I-80126, Napoli, Italy</div>
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<a href="mailto:giovanni.cantele@spin.cnr.it" id="OWA39e624e0-0bfb-2a18-11a0-ed41ce3678df" class="x_x_OWAAutoLink" style="color: rgb(17, 85, 204);">e-mail: giovanni.cantele@spin.cnr.it</a></div>
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Phone: +39 081 676910<br>
Skype contact: giocan74<br>
<br>
ResearcherID: <span style="color: rgb(17, 85, 204);"><a href="http://www.researcherid.com/rid/A-1951-2009" id="OWA0348704f-6d0a-b82a-babe-fb193e8f68ee" class="x_x_OWAAutoLink" data-auth="NotApplicable" style="color: rgb(17, 85, 204);">http://www.researcherid.com/rid/A-1951-2009</a></span><br>
Web page: <span style="color: rgb(17, 85, 204);"><a href="https://sites.google.com/view/giovanni-cantele/home" id="OWA18668885-00a2-942f-0e48-a08d7d79b496" class="x_x_OWAAutoLink" data-auth="NotApplicable" style="color: rgb(17, 85, 204);">https://sites.google.com/view/giovanni-cantele/home</a></span></div>
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Il giorno ven 14 mar 2025 alle ore 09:25 Ms. Chandrika K. via users <<a href="mailto:users@lists.quantum-espresso.org" id="OWAf6a73834-7284-00d3-4210-3e90e8308361" class="x_x_OWAAutoLink">users@lists.quantum-espresso.org</a>> ha scritto:</div>
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Hi all,<br>
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.</div>
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Any guidance on this issue would be of great help.</div>
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Regards </div>
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Chandrika </div>
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Research Scholar </div>
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<span style="font-family: Helvetica; font-size: 14px;">Quantum ESPRESSO is supported by MaX (<a href="http://www.max-centre.eu/" id="OWAb9e3915e-14a5-b9fa-8483-e5873cc26ca8" class="OWAAutoLink" data-auth="NotApplicable" style="text-align: left;">www.max-centre.eu</a>)</span><br>
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