Messages

31

General Questions and Answers / Error in Molecular Dynamic Simulation: Particle leaving simulation territory!

« on: March 27, 2023, 18:14 »

Dear ATK staffs and users,
I am trying to implement self-defined CLAY force field in molecular dynamic simulation (ATK2022), but keep getting the error "Particle leaving simulation territory!". If I replace the Si and O force field with Pedone_2006Fe2, then the simulation can run smoothly without problem. A similar problem had been posted earlier (https://forum.quantumatk.com/index.php?topic=6641.msg27814#msg27814), does the errors occur because bond potential is not suitable for molecular dynamic simulation?

32

General Questions and Answers / Re: Is it possible to extract the fitted MTP parameter set?

« on: February 21, 2023, 10:25 »

Thank you for your reply. Please correct me if am wrong, the mentioned paper used Green-Kubo approach to calculate, and the method required the kinetic energy, potential energy and potential derivative of individual atoms, we can use funtcion ConfigurationVelocities to calculate kinetic energy part and function Forces to calculate the potential derivative. However, I can't find a way to extract potential or total energy of individual atom.


 

Nevermind, built in features of quantumatk can use this method (https://aip.scitation.org/doi/10.1063/5.0089247) to calculate thermal conductivity, the results are pretty good.

33

General Questions and Answers / Re: Why some built-in classical potentials seem to have incorrect atomic info?

« on: February 19, 2023, 15:02 »

Thanks!

34

General Questions and Answers / Why some built-in classical potentials seem to have incorrect atomic info?

« on: February 16, 2023, 10:43 »

Good day to staffs and users,
I noticed some of the prebuilt classical force fields have incorrect particle mass stated. One of the example is StillingerWeber_MoS_2013(), I wonder why the atomic mass of Mo and S are stated as 1.0 a.u.? Nevertheless, the results based on this potential still give accurate results, hopefully someone can explain to me.
Thank you.

35

General Questions and Answers / Re: Is it possible to extract the fitted MTP parameter set?

« on: February 13, 2023, 05:26 »

Thank you for your reply. Please correct me if am wrong, the mentioned paper used Green-Kubo approach to calculate, and the method required the kinetic energy, potential energy and potential derivative of individual atoms, we can use funtcion ConfigurationVelocities to calculate kinetic energy part and function Forces to calculate the potential derivative. However, I can't find a way to extract potential or total energy of individual atom.


 

36

General Questions and Answers / Is it possible to extract the fitted MTP parameter set?

« on: January 6, 2023, 11:33 »

Dear developers and users,
Happy new year to all!
I am doing some calculation with the MomentTensorPotentialTraining module and couldn't find a way to extract the fitted parameters. The reason why I am interested in these fitted parameters is to calculate the local potential/forces as mentioned in this paper (https://doi.org/10.1103/PhysRevB.105.115202). Can someone clarify if the extraction is possible within quantumatk?

best regards
sukhito teh

37

General Questions and Answers / Re: Heisenberg Exchange of NiO with GGA+U

« on: September 13, 2022, 06:32 »

I had also calculated the heisenberg exchange of CrI3 and Ni3TeO6, and both of them predicted ferromagnetic ground state (which is qualitatively correct for cri3 but incorrect for Ni3TeO6), hopefully the developers can check and fix this issue. Thank you for your attention,

38

General Questions and Answers / Heisenberg Exchange of NiO with GGA+U

« on: September 12, 2022, 19:32 »

Dear developers and users,
I tried to calculate Heisenberg exchange of NiO, and the results show Ni1 and Ni2 have ferromagnetic coupling of about 15.4 meV, which is contradict to experiment or dft results.
I have attached my input files, any comments and suggestions are very much appreciated.

39

General Questions and Answers / Re: Does BlochState supports non-collinear calculation?

« on: May 25, 2022, 05:42 »

Thank you for spending time to explain this simple concept to me. Actually I'm just playing around with different analysis tools of ATK, and your explanation clear up a lot of things for me.

40

General Questions and Answers / Re: Does BlochState supports non-collinear calculation?

« on: May 24, 2022, 06:59 »

Yes BlochState does support non-collinear spin. However the documentation is a bit confusing on this point: A BlochState is a kind of GridValues object, and GridValues was really mostly designed for representing spin-densities, which really is a combination of a scalar density n(r) and a vector magnetization m(r). A wave function can't be split into such two fields: it is a two component complex spinor field. You can directly access the complex spinor values by using the index operator:

Code

bloch_state = BlochState(...)

spinor_value = bloch_state[i, j, k] # spinor_value will be PhysicalQuantity array of length 2: [up, down]

You can get the dimensions of the grid with:

Code

dimensions = bloch_state.shape

.

Also if you are going to do a lot of bloch state analysis I suggest you to first do the DFT SCF ground state and save that to a file, then do the analysis in a separate script like so:

Code

configuration = nlread('my_groundstate_calc.hdf5', BulkConfiguration)[-1]

bloch_state = BlochState(configuration, ...)

Then if there are errors or you need to do multiple bloch state calculations you don't need to redo the expensive SCF calculation.

Thank you for your reply and explanation! Please correct me if I am wrong, do you mean that both the collinear and non collinear spin polarized wavefunctions are represented in  two component complex spinor field (up and down spin respectively)? Is there a way to 'project' the wavefunction to x, y or z components for non-collinear case?

41

General Questions and Answers / Does BlochState supports non-collinear calculation?

« on: May 20, 2022, 16:19 »

Dear developers and users,
I tried to calculate the blochstate of a Bulkconfiguration with spin orbit coupling exchange correlation, yet the result of bloch state is represented in spin up and spin down values. Though I am able to return a result by projecting to Spin.Z axis, when I tried to perform projection to Spin.Y or Spin.X axis, the following error occurs:

Traceback (most recent call last):
  File "test.py", line 7, in <module>
    arrayx=bloch_state.spinProjection(spin=Spin.X).toArray()
  File "zipdir/NL/Analysis/GridValues.py", line 1145, in spinProjection
NL.ComputerScienceUtilities.Exceptions.NLValueError: Spin not supported: Spin.X

I had attached the input of calculation.

Thank you for your attention.