[QE-users] Issue with Molecular Orbital Plot in Quantum ESPRESSO (Cu₂Cl₆ System)

[Jonathan Konyi Kakulu]

Use just SCF and PP files

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From: users <users-bounces at lists.quantum-espresso.org> on behalf of Prem Prakash Sahu <premprakash.sahu at unifi.it>
Sent: Monday, March 24, 2025 5:44:54 PM
To: users at lists.quantum-espresso.org <users at lists.quantum-espresso.org>
Subject: [QE-users] Issue with Molecular Orbital Plot in Quantum ESPRESSO (Cu₂Cl₆ System)

[https://ssl.gstatic.com/docs/doclist/images/icon_10_generic_list.png] Cu2Cl6_input-structure_and_PP-structure.jpg<https://drive.google.com/file/d/1SxdOjBHWzdcm7n3TKQUqx37bdRHs_6Xk/view?usp=drive_web>[X]
[https://ssl.gstatic.com/docs/doclist/images/icon_10_generic_list.png] NSCF_Cu2Cl6-AF_CC.inp<https://drive.google.com/file/d/1OL-vnhaYfl1aOveYEFxDpHp5UpmGCpDk/view?usp=drive_web>[X]
[https://ssl.gstatic.com/docs/doclist/images/icon_10_generic_list.png] pp_33_up_1.inp<https://drive.google.com/file/d/1JFZHicoe0j4uX9Jvwn55aeBz_4gnE0tS/view?usp=drive_web>[X]
[https://ssl.gstatic.com/docs/doclist/images/icon_10_generic_list.png] SCF_Cu2Cl6-AF_CC.inp<https://drive.google.com/file/d/1uXn3-HzbI6LH-lpn8bKZVZ65Ay6KGu6n/view?usp=drive_web>[X]
Dear Quantum ESPRESSO Community,

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.

To test this, I started with a well-known Cu2Cl6 molecule. I performed:

(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.
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.

I am unsure why this is happening and would appreciate any insights on:

(i) Why the atomic replacements occur in the output?

(ii) How to correctly preserve the identity of the two Cu atoms while ensuring they remain distinguishable with different starting magnetizations?

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.

Any guidance on resolving this issue would be greatly appreciated.

Best regards,
Prem
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Prem Prakash Sahu (He/Him)
PhD Scholar
Dipartimento di Chimica "Ugo Schiff" (DICUS)
University of Florence, 50019 Sesto Fiorentino, Italy
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