QuantumATK Forum

QuantumATK => General Questions and Answers => Topic started by: lwh on December 8, 2016, 11:24

Title: partial charges calculation
Post by: lwh on December 8, 2016, 11:24

Hi all,
I am trying to calculate partial charges for a system that contains Bi, V and O atoms (24 atoms in total).
Since ATK-Classical package doesn't provide the potential parameters for this system, I added the parameters manually, using  Lennard-Jones potential function for all interactions.
I used TremoloXCalculator, run the script, but output partial charges were zero since I didn't have a way to include the electrostatics of the system. Do you have a suggestion on
how to solve this problem? Thanks a lot!

Title: Re: partial charges calculation
Post by: Julian Schneider on December 8, 2016, 11:40

Is your question that you want to include electrostatic interactions via partial charges in your system?

In that case you need to specify the charges of each particle type when you define the particle types, i.e. something like

Code

potential_set.addParticleType(ParticleType(symbol='O', mass=15.9994*atomic_mass_unit, sigma=3.17*Angstrom, epsilon=0.0067*eV, charge=0.5*elementary_charge))

(see http://www.docs.quantumwise.com/manuals/Types/ParticleType/ParticleType.html#particletype-c (http://www.docs.quantumwise.com/manuals/Types/ParticleType/ParticleType.html#particletype-c))

You need to add a coulomb solver to the potential set to add the resulting coulomb interactions (see e.g. http://www.docs.quantumwise.com/manuals/Types/CoulombSPME/CoulombSPME.html#coulombspme-c (http://www.docs.quantumwise.com/manuals/Types/CoulombSPME/CoulombSPME.html#coulombspme-c)), but I see you have already done that.

Title: Re: partial charges calculation
Post by: lwh on December 8, 2016, 12:23

Thanks for the reply!

the thing is that I don't have partial charges and I want to calculate them first.
Since I am not using the built-in potential for my system I am not sure what else
should be added to this script to be able to calculate partial charges.
From .log file:
| Partial Charges with TremoloX-Potential:                                     |
| Potential                                                                         |
+------------------------------------------------------------------------------+
  Index      Atom       Partial charge (e)
+------------------------------------------------------------------------------+
  0          O            0.00000
  1          O            0.00000
  2          O            0.00000
  3          O            0.00000
  4          V            0.00000
  5          V            0.00000
  6          V            0.00000
  7          V            0.00000
.
.
.

So instead of this, I would like to get some non-zero values for partial charges.
Can that be done in any way?
Thank you for your help.

Title: Re: partial charges calculation
Post by: Julian Schneider on December 8, 2016, 13:07

The partial charges analysis in ATK just gives you the partial charges that you have defined in the classical potential for the system. If no partial charges are defined then the output will be zero (see http://www.docs.quantumwise.com/manuals/Types/PartialCharges/PartialCharges.html#partialcharges-c (http://www.docs.quantumwise.com/manuals/Types/PartialCharges/PartialCharges.html#partialcharges-c).

The only exception is if you use a ReaxFF potential. In that case the charges are calculated self-consistently, based on the charge-equilibration method (see http://pubs.acs.org/doi/abs/10.1021/j100161a070?journalCode=jpchax (http://pubs.acs.org/doi/abs/10.1021/j100161a070?journalCode=jpchax)) and the output of partial charges will give you the calculated charges.

Generally, if you implement a potential from a paper, it should have partial charges defined with the definition of the potential, and you should use these.
If you want to develop your own potential, it is important that the non-Coulomb potential terms and parameters need to be chosen and adjusted to work with the chosen set of partial charges.
You normally cannot just use any arbitrary combination of partial charges and non-Coulomb potentials.
An initial guess for partial charges could be obtained e.g. from the Bader (http://www.docs.quantumwise.com/manuals/Types/Bader/Bader.html#bader-c (http://www.docs.quantumwise.com/manuals/Types/Bader/Bader.html#bader-c) or Mulliken  (http://www.docs.quantumwise.com/manuals/Types/MullikenPopulation/MullikenPopulation.html#mullikenpopulation-c (http://www.docs.quantumwise.com/manuals/Types/MullikenPopulation/MullikenPopulation.html#mullikenpopulation-c)) charges.