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

[Paolo Giannozzi]

If you used an old QE version, this could be the reason:
https://gitlab.com/QEF/q-e/-/issues/645

Paolo
On 24/03/2025 16:44, Prem Prakash Sahu wrote:
> 	
> Non ricevi spesso messaggi di posta elettronica da 
> premprakash.sahu at unifi.it. Scopri perché è importante <https://aka.ms/ 
> LearnAboutSenderIdentification>
> 	
> 
> Cu2Cl6_input-structure_and_PP-structure.jpg <https://drive.google.com/ 
> file/d/1SxdOjBHWzdcm7n3TKQUqx37bdRHs_6Xk/view?usp=drive_web>
> NSCF_Cu2Cl6-AF_CC.inp <https://drive.google.com/file/d/1OL- 
> vnhaYfl1aOveYEFxDpHp5UpmGCpDk/view?usp=drive_web>
> pp_33_up_1.inp <https://drive.google.com/file/ 
> d/1JFZHicoe0j4uX9Jvwn55aeBz_4gnE0tS/view?usp=drive_web>
> SCF_Cu2Cl6-AF_CC.inp <https://drive.google.com/file/d/1uXn3-HzbI6LH- 
> lpn8bKZVZ65Ay6KGu6n/view?usp=drive_web>
> 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
> ------------------------------------------------------------------------------------------------------
> Prem Prakash Sahu (He/Him)
> PhD Scholar
> Dipartimento di Chimica "Ugo Schiff" (DICUS)
> University of Florence, 50019 Sesto Fiorentino, Italy
> ------------------------------------------------------------------------------------------------------
> 
> _______________________________________________________________________________
> 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)
> users mailing list users at lists.quantum-espresso.org
> https://lists.quantum-espresso.org/mailman/listinfo/users

-- 
Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche,
Univ. Udine, via delle Scienze 206, 33100 Udine Italy, +39-0432-558216