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Messages - zh

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The k-mesh size is too coarse. You need to increase it for the geometry optimization and DOS calculations.

"bands_above_fermi_level=None," in the DOS calculations should not be "None".

The difference may be not related to the ATK version.

Please don't misuse DFT+U. Even some U value (in most case they may be very large) would give the band gap close to the experimental data, the physics meaning of this U may lose. To get a better prediction on the band gap, the DFT+U is not the best solution.

My suggest is to first try the use of linear response method in Quantum espresso or ABINT codes to estimate the U value for MoS2. The obtained U value would be more physics meaningful even such U values couldn't give the band gap to match the experimental results.

Please refer to the details of LDA+U (or GGA+U) methodology. The implementation of counting (calculating) occupation of local orbitals would also the affect the calculation results even if the same U is applied on the same orbital in the two different codes.

The ATK-DFT or VASP can generate the spin-up and spin-down charge densities. You need to store these charge densities separately into two different files.  And then use the same reference (ELF or all-electron charge density) to get the local volumes (basin) of every atom by using critic2 . In this way, you may be able to the local charge of spin-up and spin-down components for every atom. 

It cannot be done.

I recommend the use of critic2 to perform the Bader charge analysis even if the all-electron density is provided by the ATK-DFT code.
The critic2 ( provides the superposition all-electron charge of atoms.  One can also use the ELF(electron localization function) as reference to determine the basin, local maximum and so on.

General Questions and Answers / Re: Optimization
« on: March 21, 2017, 09:54 »
Yes, you are right.

General Questions and Answers / Re: Optimization
« on: March 19, 2017, 06:39 »
1. Look at the manual :

With the default values for
"target_stress" , "constraints", and "optimizer_method" in OptimizeGeometry().
2. No.
3.  No.

The center region or scatter region contains the conductor (i.e., the molecule in your case) and the buffer layers. The latter ones have the same components with those of electrodes. The spin setup for buffer layers should be same as those in the electrodes. The spin setup of molecule could be different to the spin setup of electrodes.

"what's more, should we set initial-spin again when calculating transport under finite bias?"
Sure, you should set the initial spin again in the calculation of finite bias.

The code one is preferable.

These three ways mentioned in your post mean just the different starting points (in particular, the charge density) for the anti-parallel spin configurations at finite bias. The different starting points may affect the convergence speed (e.g., the computation time).  In principles, all of them should give a nearly same result for a given finite bias, the little difference may appear because of the numerical noise. The most safe way for the convergence problem is the third one. 

Please show the band structure of your calculated system. From the band dispersion in such plot, one may judge whether your result is reasonable or not.

General Questions and Answers / Re: electron density
« on: March 13, 2017, 02:09 »
how to calculate the electron density of any 2d material (example: MoS2) at the edge of conduction band?
Thanks in advance....
Please look at:

The wavefunction at a given k-point and eigenvalue  can be accessed.

I just check the atk2014 version. This version doesn't support the constraints on atoms for dynamic matrix calculations. Please use the latest version of ATK.

Yes, you are right.   
For example, the following papers estimated the quantum  capacitance from density of states:
J. Phys. Chem. C 2015, 119, 6464−6470
J. Phys. Chem. C 2014, 118, 4 − 15

When you do the calculations of  force constants and dynamic matrix, you can fix the atoms of substrate. In such case, only the atoms of adsorbate molecule will be made by small displacement to calculate the vibration frequencies.

The list of constrained atoms.

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