Author Topic: how to view electron density with isosurface option  (Read 9111 times)

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Offline premkumar85

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how to view electron density with isosurface option
« on: August 5, 2009, 08:57 »
i am calculating the electron density of gold two probe system . when i drag this vnl file to Nanoscope I couldn't able to view the electron density with isosurface option. i have exported that picture for your attention.

Offline zh

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Re: how to view electron density with isosurface option
« Reply #1 on: August 5, 2009, 09:03 »
Did you place the returned object of "calculateElectronDensity()" into your vnl file?  Please take a look at the example shown in the manual:
http://www.quantumwise.com/documents/manuals/ATK-2008.10/ref.calculateelectrondensity.html
.
If yes, do the following things. When your calculation of electron density is normally finished, you can load the saved ".vnl" file by the "Result Browser" and then some information in the panel of "Result Browser" will show the electron density is available. To visualize it, you need to drop the "Sample" on the "Nanoscope".  Then, right click the panel of "Nanoscope" and choose ""Insert Plot"----> "Isosurface" in the pop-out menu.
« Last Edit: August 5, 2009, 09:21 by zh »

Offline Nordland

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Re: how to view electron density with isosurface option
« Reply #2 on: August 5, 2009, 09:15 »
Two things:

1) First of all I think that your system has converged to zero charge, and hence you are looking at the density from zero electrons. If this is the case,
then you need to make sure that the system converge to a physical stable state.

2) Alternative the isovalue for the electron density is set to a value where there is no density. Try using the slider in the properties window to see if there is any density at all in the system

Offline Anders Blom

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Re: how to view electron density with isosurface option
« Reply #3 on: August 5, 2009, 10:24 »
I don't think it has converged to zero density since the colorbar indicates finite charge. Most likely you have just chosen a very high, or very low, isovalue.

You can use a contour plane plot to get an idea of the magnitude of the charge. Use plane normal [001] and make sure to place the plane in the middle of the cell in XY to catch the central region atoms.
« Last Edit: August 5, 2009, 10:26 by Anders Blom »

Offline premkumar85

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Re: how to view electron density with isosurface option
« Reply #4 on: August 5, 2009, 10:52 »
i used contour plot for electron density calculation. it shows the election density around the atoms but why doesn't it get reflected in isosurface plot?

Offline Anders Blom

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Re: how to view electron density with isosurface option
« Reply #5 on: August 5, 2009, 11:00 »
Ok, I take back my previous comment. Most likely you have indeed converged to zero charge, although there is some finite charge in the electrodes, hence the colorbar limits.

So, your calculation seems to have converged to an unphysical state, which you can confirm by having a look at the output log. Thus you need to go back and tune the parameters.

Offline premkumar85

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Re: how to view electron density with isosurface option
« Reply #6 on: August 5, 2009, 12:29 »
this is the log for my scf calculation.


# sc 236 : q =  692.96685 e  Etot = -12616.42988 Ry  dRho =  9.8658E-03  dEtot = -2.2788E-05 Ry


 after this i run a separate script for electron density calculation. that log show q = 692.96685 e. then how can you say system converged to zero charge?

Offline Anders Blom

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Re: how to view electron density with isosurface option
« Reply #7 on: August 5, 2009, 12:36 »
I can't :) But then I didn't see the output until now. It doesn't seem to converge very well (many steps, and the final dRho is suspiciously large), but it does converge.

So, let's back up a bit.

Maybe you just need to adjust the isovalue a bit. The default isovalue is chosen automatically based on the min/max of the data set. In this case, it seems perhaps there is an unphysically large max value, and so the default isovalue is very large. Try lowering it to 1 or so and let's see.


Offline Nayab Shiraz

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Re: how to view electron density with isosurface option
« Reply #8 on: March 24, 2020, 15:36 »
Hello

Can you please explain what changing isovalue does? I can see that changing isovalue shows different electron densities but how do I know which isovalue to use?

Offline Petr Khomyakov

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Re: how to view electron density with isosurface option
« Reply #9 on: March 24, 2020, 19:50 »
Changing isovalue means changing isovalue surface where a particular quantity is constant, which is given by isovalue.