<div dir="ltr"><div><div class="gmail_chip gmail_drive_chip" style="width:386px;height:20px;max-height:20px;background-color:rgb(245,245,245);margin:6px 0px;padding:10px;font-variant-numeric:normal;font-variant-east-asian:normal;font-variant-alternates:normal;font-size-adjust:none;font-kerning:auto;font-feature-settings:normal;font-stretch:normal;font-size:14px;line-height:20px;font-family:"Google Sans",sans-serif;border:1px solid rgb(221,221,221)"><a href="https://drive.google.com/file/d/1SxdOjBHWzdcm7n3TKQUqx37bdRHs_6Xk/view?usp=drive_web" target="_blank" style="color:rgb(32,33,36);display:inline-block;max-width:356px;overflow:hidden;text-overflow:ellipsis;text-decoration-line:none;border:none" aria-label="Cu2Cl6_input-structure_and_PP-structure.jpg"><img style="vertical-align: text-bottom; border: none; padding-right: 10px; height: 20px;" alt="" src="https://ssl.gstatic.com/docs/doclist/images/icon_10_generic_list.png"> <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="gmail_chip_remove" aria-label="Remove attachment" style="padding-left: 10px; cursor: pointer; width: 20px; height: 20px; float: right; display: none;"></div><div class="gmail_chip gmail_drive_chip" style="width:386px;height:20px;max-height:20px;background-color:rgb(245,245,245);margin:6px 0px;padding:10px;font-variant-numeric:normal;font-variant-east-asian:normal;font-variant-alternates:normal;font-size-adjust:none;font-kerning:auto;font-feature-settings:normal;font-stretch:normal;font-size:14px;line-height:20px;font-family:"Google Sans",sans-serif;border:1px solid rgb(221,221,221)"><a href="https://drive.google.com/file/d/1OL-vnhaYfl1aOveYEFxDpHp5UpmGCpDk/view?usp=drive_web" target="_blank" style="color:rgb(32,33,36);display:inline-block;max-width:356px;overflow:hidden;text-overflow:ellipsis;text-decoration-line:none;border:none" aria-label="NSCF_Cu2Cl6-AF_CC.inp"><img style="vertical-align: text-bottom; border: none; padding-right: 10px; height: 20px;" alt="" src="https://ssl.gstatic.com/docs/doclist/images/icon_10_generic_list.png"> <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="gmail_chip_remove" aria-label="Remove attachment" style="padding-left: 10px; cursor: pointer; width: 20px; height: 20px; float: right; display: none;"></div><div class="gmail_chip gmail_drive_chip" style="width:386px;height:20px;max-height:20px;background-color:rgb(245,245,245);margin:6px 0px;padding:10px;font-variant-numeric:normal;font-variant-east-asian:normal;font-variant-alternates:normal;font-size-adjust:none;font-kerning:auto;font-feature-settings:normal;font-stretch:normal;font-size:14px;line-height:20px;font-family:"Google Sans",sans-serif;border:1px solid rgb(221,221,221)"><a href="https://drive.google.com/file/d/1JFZHicoe0j4uX9Jvwn55aeBz_4gnE0tS/view?usp=drive_web" target="_blank" style="color:rgb(32,33,36);display:inline-block;max-width:356px;overflow:hidden;text-overflow:ellipsis;text-decoration-line:none;border:none" aria-label="pp_33_up_1.inp"><img style="vertical-align: text-bottom; border: none; padding-right: 10px; height: 20px;" alt="" src="https://ssl.gstatic.com/docs/doclist/images/icon_10_generic_list.png"> <span dir="ltr" style="vertical-align:bottom;text-decoration:none">pp_33_up_1.inp</span></a><img src="//ssl.gstatic.com/ui/v1/icons/mail/gm3/1x/close_baseline_nv700_20dp.png" class="gmail_chip_remove" aria-label="Remove attachment" style="padding-left: 10px; cursor: pointer; width: 20px; height: 20px; float: right; display: none;"></div><div class="gmail_chip gmail_drive_chip" style="width:386px;height:20px;max-height:20px;background-color:rgb(245,245,245);margin:6px 0px;padding:10px;font-variant-numeric:normal;font-variant-east-asian:normal;font-variant-alternates:normal;font-size-adjust:none;font-kerning:auto;font-feature-settings:normal;font-stretch:normal;font-size:14px;line-height:20px;font-family:"Google Sans",sans-serif;border:1px solid rgb(221,221,221)"><a href="https://drive.google.com/file/d/1uXn3-HzbI6LH-lpn8bKZVZ65Ay6KGu6n/view?usp=drive_web" target="_blank" style="color:rgb(32,33,36);display:inline-block;max-width:356px;overflow:hidden;text-overflow:ellipsis;text-decoration-line:none;border:none" aria-label="SCF_Cu2Cl6-AF_CC.inp"><img style="vertical-align: text-bottom; border: none; padding-right: 10px; height: 20px;" alt="" src="https://ssl.gstatic.com/docs/doclist/images/icon_10_generic_list.png"> <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="gmail_chip_remove" aria-label="Remove attachment" style="padding-left: 10px; cursor: pointer; width: 20px; height: 20px; float: right; display: none;"></div>Dear Quantum ESPRESSO Community,  </div><div><br></div>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.<div>  <br>To test this, I started with a well-known Cu2Cl6 molecule. I performed:  </div><div><br>(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><br>I am unsure why this is happening and would appreciate any insights on:  </div><div><br>(i) Why the atomic replacements occur in the output?  </div><div><br>(ii) How to correctly preserve the identity of the two Cu atoms while ensuring they remain distinguishable with different starting magnetizations?  <br><br>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><br>Any guidance on resolving this issue would be greatly appreciated.  <br><br>Best regards,<br>Prem <br><div><div dir="ltr" class="gmail_signature" data-smartmail="gmail_signature"><div dir="ltr"><div><font color="#0000ff">------------------------------------------------------------------------------------------------------</font></div><div><font color="#0000ff">Prem Prakash Sahu (He/Him)</font></div><div><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></font></div><div><span style="color:rgb(0,0,255)">------------------------------------------------------------------------------------------------------</span><br></div></div></div></div></div></div></div>