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General Questions and Answers / Re: Significance of 'Other neighboring bond breakings after geometry optimization'!

« on: January 6, 2021, 17:11 »

I am not sure what I can suggest. It is hard to say in the multiple interactions. But if you have the point case to see the physisorption, I would like to recommend a few more sampling.

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General Questions and Answers / Re: HOMO-LUMO of a slab+molecule system

« on: January 6, 2021, 17:02 »

MullikenPolulation in analysis will be one of options to see the charge transfer between the absorbed molecule and surface.

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General Questions and Answers / Re: Multilayer simulation of any material

« on: December 17, 2020, 19:58 »

To avoid the artificial effect by periodic boundary condition, QuantumATK provides open boundary condition such as Dirichlet or Neumann boundary condition.
You can setup in the Poisson Solver.
The below manual explains different Poisson solvers.
https://docs.quantumatk.com/manual/includes/PoissonSolvers.html

Or you can build it with a long enough vacuum length using the periodic boundary condition. Honestly, it is hard to say what will be approximately vacuum region, because it depends on the configuration and surface dipole effect.

If you would like to confirm the vacuum state, HartreeDifferencePotential or ElectrostaticDifferencePotential analysis will be useful.

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General Questions and Answers / Re: HOMO-LUMO of a slab+molecule system

« on: December 17, 2020, 19:37 »

You can analyze the MolecularEnergySpectrum.
It shows the energy levels and homo-lumo gap.
The below manuel will be useful.
https://docs.quantumatk.com/manual/Types/MolecularEnergySpectrum/MolecularEnergySpectrum.html

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General Questions and Answers / Re: HOMO-LUMO of a slab+molecule system

« on: December 17, 2020, 06:42 »

I recommend to search papers. You can easily find cluster model, periodic model for adsorption energy and charge transfer.
(For instance, J. Phys. Chem. B 2005, 109, 38, 17943–17950, International Journal of Molecular Sciences 10(10):4310-29 ...)

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General Questions and Answers / Re: HOMO-LUMO of a slab+molecule system

« on: December 16, 2020, 16:25 »

I am not sure what is your purpose to simulate it finally.

In the slab model, you can analyze the BandStructure, DensityOfStates, or MolecularEnergySpectrum related to homo and lumo energy.
In the molecular model, cluster model is commonly used to analyze the homo-lumo energy or adsorption energy. You need to assume the cluster as a surface.

If you would like to obtain the adsorption energy between molecule and surface, one probe device model (using surface NEGF) or slab model will be good starting because it will be more realistic than cluster as a surface.

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General Questions and Answers / Re: Result deviation between with or without geometrical optimization

« on: December 15, 2020, 11:21 »

If it is different configuration before and after relaxation, it will give different energy.

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General Questions and Answers / Re: miscellaneous: spatial regions

« on: December 15, 2020, 11:08 »

Do you confirm the exact calculation settings between configuration with spatial regions and configuration without spatial regions?
If you use default condition for above two configurations, default setting will be different in two cases. (For instance, poisson_solver)

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Scripts, Tutorials and Applications / Re: Problem in geometry optimization

« on: December 11, 2020, 14:12 »

Can you check your Iteration settings such as Tolerance or Force tolerance or stress error tolerance in Optimize Geometry?

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General Questions and Answers / Re: miscellaneous: spatial regions

« on: December 11, 2020, 13:50 »

Can you provide the input script?

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General Questions and Answers / Re: Query regatding MD Simulation

« on: December 2, 2020, 21:51 »

Can you describe in detail? Which MD do you want? If you would like to run MD using Force field parameter, do you know the force field parameter? If you cannot find it in Nanolab GUI, you need to customize it.

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General Questions and Answers / Re: QM/MM simulations

« on: November 24, 2020, 12:50 »

As I known, this is not working at the same time as you mentioned.
You can use DFT-MD as well as force field MD.
Or during the force field MD simulation, you can add the DFT step in a certain step.
See an example, 14.3 section in the QuantumATK reference paper. https://iopscience.iop.org/article/10.1088/1361-648X/ab4007/meta

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