QuantumATK Forum

QuantumATK => General Questions and Answers => Topic started by: juwon on November 26, 2023, 11:50

Title: How can I set a specific atom to an anion or a cation?
Post by: juwon on November 26, 2023, 11:50

Using the bulk configuration, I want to add an anion or a cation with the builder.

Is setting the partial charge by selecting the wanted atom correct for transforming the atom to ion?

For example, I add Fluorine in my structure and want to transform it into -1 charged Fluorine ion.
Can I do that by selecting the Fluorine atom and change the 'Set Partial Charges' to minus 1, in the "Coordinate Tools > Partial Charges"?

Title: Re: How can I set a specific atom to an anion or a cation?
Post by: Anders Blom on December 1, 2023, 21:44

If you are planning to do forcefield calculations, you can use partial charges, yes.

It in DFT, it's both easier and a bit trickier... Depending on exactly how the F atom binds to the other atoms, there will be some amount of charge transfer, so it will never be exactly -1 unless isolated in vacuum. DFT doesn't care about partial charges, but you can charge the entire simulation cell ("charge" keyword) in which case the electronegativity of the F will probably lead it to having the correct charge (or 0.9 or whatever it adjusts to). If the F atom is not bound, and you want the extra electron in the system to go onto it, you could use a compensation charge. I haven't tried exactly that...

Title: Re: How can I set a specific atom to an anion or a cation?
Post by: juwon on December 3, 2023, 10:16

Thank you for your reply.

I am trying to do DFT calculation, but I think in my system the slight charge difference induced by charge transfer is not that important.

Now I am using 2022.12 version of quantumATK, and in Builder > Coordinate Tools > Partial Charges section, I can find that there are three parts that I can define.

1. Set Partial Charges (e)
2. Total Charge (e)
3. Scale Charges

I was thinking of setting the partial charge (which is 1. above), but I am not sure about the scale charges (which is 3. above).
Is it okay if I just set the scale charge by the reference ionic scale (ionic radius)?

Thank you again in advance.

Title: Re: How can I set a specific atom to an anion or a cation?
Post by: dprai on December 28, 2023, 13:57

Is this feature available in Quantum Atk 2019 version?

Title: Re: How can I set a specific atom to an anion or a cation?
Post by: Anders Blom on January 5, 2024, 20:04

I think 2019 has all the same features in this respect.

Note that partial charges has no influence on DFT calculations, only forcefields that support it.