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General Questions and Answers / Re: Charge transfer
« Last post by Petr Khomyakov on November 25, 2021, 15:42 »
You might consider using the Bader analysis instead of Mulliken population, see https://docs.quantumatk.com/manual/Types/BaderCharges/BaderCharges.html and reference therein.

Another way is based on the electron density analysis, as described, e.g., in this paper First-principles study of the dipole layer formation at metal-organic interfaces, Paul C. Rusu, Gianluca Giovannetti, Christ Weijtens, Reinder Coehoorn, and Geert Brocks
Phys. Rev. B 81, 125403 – Published 3 March 2010.
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General Questions and Answers / Computing surface energies
« Last post by Weckman on November 24, 2021, 22:20 »
I would like to study the stability of different surface orientations of wurtzite/zinc blende materials which exhibit asymmetric surfaces for certain lattice orientations and therefore would like to use the periodic surface model (electrode) to compute the relative stabilities of these surfaces.

I do not yet have the full licence in my disposal, so I ran some test calculations on my desktop for Au(111) surface. However, when I compute the total energy of surfaces with varying thickness, in some instances I get negative surface energies.

For example, when using surfaces with 6 and 8 layers of gold, medium basis set and SG15 pseudo, I get energies
6   -22519.98379
7   -26273.25555
8   -30026.51107
Making a linear fit gives a slope of -3751.264 eV, close to that of a bulk calculation (-3753.231 eV). However, the intercept is negative and so is the surface energy.

If I use a HGH pseudo, I get a positive surface energies that vary depending on the basis set used.

What I would like to know:
Is this a correct approach to take and are the results some kind of an artifact resulting from a thin surface model or am I making a fundamental error somewhere or how should I approach the issue? In the original paper ("First-principles Green’s-function method for surface calculations: A pseudopotential localized basis set approach") the authors discuss developing the procedure for SG15 pseudos. However, QuantumATK allows me to set from a variety of different pseudos. Is the Green's function method suitable for all the available pseudos and basis sets?

- Weckman

3
General Questions and Answers / Charge transfer
« Last post by khariyahA on November 24, 2021, 20:21 »
Hi Sir,

Im currently studying about GNR for gas sensor. I have difficulty in interpreting and calculate charge transfer from mulliken population result.

I really need help and i appreciate any advice regarding this. Thankyou :)
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General Questions and Answers / How to build a hollow nanoshell?
« Last post by sajadkhajoei on November 23, 2021, 18:43 »
Hi,
Does anyone know how to simulate a hollow nanoshell of different structures such as titanium dioxide or magnetite? Thanks.
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General Questions and Answers / Re: Job termination problem during HSE calculation
« Last post by filipr on November 23, 2021, 08:18 »
Exit Code 9 from an MPI program means that the program was killed by the host system.

It could be that the job scheduling system on your cluster killed the job because it used too much memory or was taking longer than the requested wall time allocation. See if you got a mail from the queuing system or ask you system administrator.
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General Questions and Answers / Job termination problem during HSE calculation
« Last post by dua.harkishan@yahoo.com on November 22, 2021, 12:52 »
I am trying to optimize one nanotube having 182 atoms using HSE functional with the help of LCAO calculator. Initially, I have submitted the job using m_file with two nodes (8 proc each. One node having 128 GB RAM and other node having 96 GB RAM). However, the job terminated with the following message "=   BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES=   PID 244987 RUNNING AT compute-0-1 =   EXIT CODE: 9 =   CLEANING UP REMAINING PROCESSES=   YOU CAN IGNORE THE BELOW CLEANUP MESSAGES". After that we have submitted the Job using four nodes with four processor each and RAMs are 128 GB, 96 GB, 64 GB and 64 GB and this time also the job terminated with the same error. Next, I have submitted the using three nodes except compute-0-1 and this time the job stopped without showing any error. I am attaching all the log files for your reference. Kindly help me in this regard.
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General Questions and Answers / Re: Adsorption energy
« Last post by dprai on November 18, 2021, 09:58 »
You can follow this tutorial.
https://docs.quantumatk.com/tutorials/geometry_optimization/geometry_optimization.html
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General Questions and Answers / Re: Adsorption energy
« Last post by dprai on November 18, 2021, 09:20 »
Yes. You have to calculate the total energy of the host material and total energy of the molecules separately. Please check your inbox. I have asked you some query.
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General Questions and Answers / Re: Adsorption energy
« Last post by khariyahA on November 18, 2021, 08:52 »
Thankyou dprai for the reply  :)

Is that mean i need to do manual calculation using the formula ? Im still not clear, do i need to do another separate simulation to get ( the total energy of host + total energy of the the gas ) ?
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General Questions and Answers / Re: Adsorption energy
« Last post by dprai on November 18, 2021, 08:31 »
There is a formula for adsorption energy calculation. The one you obtained is the CP corrected total energy of the complex.
For adsorption energy do,  total energy of the complex - (total energy of the host + total energy of the gas)
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