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<div dir="auto">Use just SCF and PP files</div>
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<div id="divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" style="font-size:11pt" color="#000000"><b>From:</b> users <users-bounces@lists.quantum-espresso.org> on behalf of Prem Prakash Sahu <premprakash.sahu@unifi.it><br>
<b>Sent:</b> Monday, March 24, 2025 5:44:54 PM<br>
<b>To:</b> users@lists.quantum-espresso.org <users@lists.quantum-espresso.org><br>
<b>Subject:</b> [QE-users] Issue with Molecular Orbital Plot in Quantum ESPRESSO (Cu₂Cl₆ System)</font>
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<a href="https://drive.google.com/file/d/1SxdOjBHWzdcm7n3TKQUqx37bdRHs_6Xk/view?usp=drive_web" target="_blank" aria-label="Cu2Cl6_input-structure_and_PP-structure.jpg" style="color:rgb(32,33,36); display:inline-block; max-width:356px; overflow:hidden; text-overflow:ellipsis; text-decoration-line:none; border:none"><img alt="" src="https://ssl.gstatic.com/docs/doclist/images/icon_10_generic_list.png" style="vertical-align:text-bottom; border:none; padding-right:10px; height:20px"> <span dir="ltr" style="vertical-align:bottom; text-decoration:none">Cu2Cl6_input-structure_and_PP-structure.jpg</span></a><img src="//ssl.gstatic.com/ui/v1/icons/mail/gm3/1x/close_baseline_nv700_20dp.png" class="x_gmail_chip_remove" aria-label="Remove attachment" style="padding-left:10px; width:20px; height:20px; float:right; display:none"></div>
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<a href="https://drive.google.com/file/d/1OL-vnhaYfl1aOveYEFxDpHp5UpmGCpDk/view?usp=drive_web" target="_blank" aria-label="NSCF_Cu2Cl6-AF_CC.inp" style="color:rgb(32,33,36); display:inline-block; max-width:356px; overflow:hidden; text-overflow:ellipsis; text-decoration-line:none; border:none"><img alt="" src="https://ssl.gstatic.com/docs/doclist/images/icon_10_generic_list.png" style="vertical-align:text-bottom; border:none; padding-right:10px; height:20px"> <span dir="ltr" style="vertical-align:bottom; text-decoration:none">NSCF_Cu2Cl6-AF_CC.inp</span></a><img src="//ssl.gstatic.com/ui/v1/icons/mail/gm3/1x/close_baseline_nv700_20dp.png" class="x_gmail_chip_remove" aria-label="Remove attachment" style="padding-left:10px; width:20px; height:20px; float:right; display:none"></div>
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<a href="https://drive.google.com/file/d/1uXn3-HzbI6LH-lpn8bKZVZ65Ay6KGu6n/view?usp=drive_web" target="_blank" aria-label="SCF_Cu2Cl6-AF_CC.inp" style="color:rgb(32,33,36); display:inline-block; max-width:356px; overflow:hidden; text-overflow:ellipsis; text-decoration-line:none; border:none"><img alt="" src="https://ssl.gstatic.com/docs/doclist/images/icon_10_generic_list.png" style="vertical-align:text-bottom; border:none; padding-right:10px; height:20px"> <span dir="ltr" style="vertical-align:bottom; text-decoration:none">SCF_Cu2Cl6-AF_CC.inp</span></a><img src="//ssl.gstatic.com/ui/v1/icons/mail/gm3/1x/close_baseline_nv700_20dp.png" class="x_gmail_chip_remove" aria-label="Remove attachment" style="padding-left:10px; width:20px; height:20px; float:right; display:none"></div>
Dear Quantum ESPRESSO Community, </div>
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I am currently working on understanding molecular orbital (MO) plots for two-center and poly-center molecular complexes, particularly in the context of computing magnetic exchange coupling.
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To test this, I started with a well-known Cu2Cl6 molecule. I performed: </div>
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(i) SCF calculation in the antiferromagnetic state (with starting magnetizations of Cu1 = +0.5 and Cu2 = -0.5); (ii) NSCF calculation; and (iii) For post-processing, I used pp.x to visualize molecular orbitals.</div>
<div>However, I encountered an unexpected issue, in the PP output file and its cube file: all Cl atoms are being replaced by Cu atoms when visualizing the geometry. <br>
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I am unsure why this is happening and would appreciate any insights on: </div>
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(i) Why the atomic replacements occur in the output? </div>
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(ii) How to correctly preserve the identity of the two Cu atoms while ensuring they remain distinguishable with different starting magnetizations? <br>
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I am attaching SCF, NSCF, and pp.x input files, along with the cube file for the particular band and the input and output geometry images for reference. <br>
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Any guidance on resolving this issue would be greatly appreciated. <br>
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Best regards,<br>
Prem <br>
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<div><font color="#0000ff">------------------------------------------------------------------------------------------------------</font></div>
<div><font color="#0000ff">Prem Prakash Sahu (He/Him)</font></div>
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<div><font color="#0000ff">PhD Scholar</font></div>
<div><font color="#0000ff">Dipartimento di Chimica "Ugo Schiff" </font><span style="color:rgb(0,0,255)">(DICUS)</span></div>
<div dir="auto"><font color="#0000ff">University of Florence, 50019 Sesto Fiorentino, Italy<br>
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