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  • Created 29 Jun 2010

Eigenfunction and electron density output files

  1. Sapan Agarwal


    What are the different columns in the psi_fxx.dat files? What are the units for each column? What are the units for the psi_fxx.vtk file?

    Similarly, what are the columns and units of the *_electron_density_vtk.dat file and the *_electron_density_vtk.dat.vtk file?

    Thank you for all your help, I really appreciate it.

    Regards, Sapan

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  2. Ross Maspero


    Just in case people still want to know, I think that the values in the psi_fxx.vtk file represent the atomic positions (in x,y,z) and their respective wave function probabilities (psi^2)

    Hope this helps


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  3. Ross Maspero

    I forgot to mention that I think it only does this for k = (0,0,0)

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  4. tonmoy kumar bhowmick

    How can I get only the wave functions (psi) including the complex part if any; not the probability(psi^2)

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  5. Tillmann Christoph Kubis

    @Ross Maspero: Sorry for the late reply. NEMO5/Schroedinger should dump out the eigenfunctions always for the last k-point that has been solved. That can differ from Gamma…

    @Tonmoy Kumar Bhowmick: You should add the option “complex_WF” in the output list of the Schroedinger, such as e.g. output=(eigenfunctions_VTK,orbital_resolved,complex_WF)

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  6. Jeremy Scher

    Hi Tillmann (or anyone else who may know),

    I know this thread is over a year old now, but I thought I would post here rather than start a separate one. Could you tell me what exactly 'orbital_resolved' and 'complex_WF' are supposed to output? I have checked the documentation and neither are listed for the Schroedinger solver. When I include them in my output list, they don't actually appear to output anything different than when I don't include them.

    Thanks for the help!

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  7. Tillmann Christoph Kubis

    When you have "orbital_resolved" in the output list, the output of |wave function|^2 will contain the information of the contribution of each orbital to the total |wave function|^2. When you add the "complex_WF" then you will get the actual complex wave function as extra output as well.

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  8. James Fonseca

    Hi Jeremy,

    Could you share your input file? 

    Does it work if you also add the following line to the Schroedinger solver?

    orbital_resolved = true

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  9. Jeremy Scher

    Here is my attached input deck. I just added orbital_resolved = true to the schroed solver, so I'm checking to see if that was the problem. Keep in mind you won't be able to run this yourself since I am using a modified material database.

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  10. Jeremy Scher

    An update: I was able to get output for the contribution of each orbital to psi^2. I do have a couple other questions, if anyone with the knowledge would be so kind as to answer:

    • What type of basis functions is NEMO5 using for the orbitals? STO? Gaussian?
    • I have psi^2, but is there anyway I can see at the actual eigenvectors themselves, or see what the coefficients of the orbital functions are? The intention is to be able to identify the form of the eigenvectors of particular states.
    • If I can't output the eigenvectors themselves, can I evaluate psi at points other than the atomic positions?

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  11. Mahesh R Neupane

    It is STO. Please review earlier papers by Prof. Klimeck’s group on NEMO3D for detail. I am not aware of any method or module that would help you on eigen vector prob. I think, Jim might be able to shed some lights on this issue. Thanks Mahesh

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  12. Jeremy Scher

    Thank you Mahesh,

    I have reviewed the various solvers listed in the manual, and it doesn't look like there exists one that outputs the STO coefficients. Does anyone know if there is one? Or if there might be an easy 'hack' to get at them, without modifying a ton of source code?

    - Jeremy

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  13. Mahesh R Neupane

    Jeremy, I have not looked at the NEMO5 code in detail, but well aware of the theory and method used based on my experience working with early version of NEMO. If I were you, I will look into the references in the source code, if any. If not, please wait for someone from the development group to respond to you. Hopefully, you will get your answer from someone from the group. Good luck, Mahesh

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  14. Dhruba Mandal

    Sir ,

                I am Dhruba Mandal a final year M tech student NIT Silchar Assam India. My project is Modelling and Simulation of Quantum Dot. I have seen this paper is " Moving Toward Nano -TCAD Quantum dot Simulations Matching Experimental Data" using NEMO 3-D and also watched NEMO5 workshop video available on Nano hub.I have download the tar.gz file but problem is that for installing the tar.gz file .

    I have extracted the file but during configure some problem is occuring . so can anyone tell me how to install NEMO5 software on Kubuntu 14.10 Plasma 4 system.


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  15. James Fonseca

    Hi Dhruba, It’s impossible to say without knowing exactly what you are doing and what error messages you see.

    It is probably best to try the suggested approach of running the precompiled NEMO5 on nanoHUB workspace. Jim

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