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Messages - Daniele Stradi

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76
General Questions and Answers / Re: Can not understand the results by using ghost atom
« on: November 28, 2017, 08:56 »
Dear Guang-Ping Zhang

in graphene-M(111), with M being a noble metal, the interaction between the graphene and the metal is mediated mainly by charge transfer to/from the metal surface state.
It is very likely that, by including the ghost atom, you (i) improve the description of the Cu(111) surface state, and (ii) reduce somehow the effect of the basis set superimposition error at typical binding distances.

For relevant literature, see:
Phys. Rev. B 79, 075441
Phys. Rev. B 94, 155431   

Regards,
Daniele.

77
General Questions and Answers / Re: optimize geometry
« on: November 20, 2017, 08:54 »
Hi,
you should increase the density_mesh_cutoff until the error disappears.
Regards,
Daniele.

78
General Questions and Answers / Re: Stress at gate of MOSFET
« on: November 2, 2017, 17:17 »
The reason for the appearance of a 3x3 matrix is that the stress is actually a tensorial quantity, see e.g.:
https://en.wikipedia.org/wiki/Cauchy_stress_tensor

What you probably want is the hydrostatic stress:
https://en.wikipedia.org/wiki/Hydrostatic_stress

If you want the hydrostatic component of the stress, you can calculate it from the trace of the 3x3 matrix.

Regards,
Daniele

79
General Questions and Answers / Re: Stress at gate of MOSFET
« on: November 1, 2017, 10:32 »
Could you please define better what you mean by "put stress on the gate"? It would be also of great help if you could attach a script with your calculation.

Thanks!
Daniele

80
Installation and License Questions / Re: VNL crashses when showing bandstructure calculation
« on: November 1, 2017, 10:31 »
The right place to find answer to your questions is the QE forum:
http://www.quantum-espresso.org/forum/

81
General Questions and Answers / Re: Bader charge analysis
« on: October 26, 2017, 16:22 »
Dear Wang,

How to know the result is resonable?
The reliability of the result is based on chemical intuition. If there is an error, you would normally see an unphysically large charge on some atoms, which is not the case in your calculation.

Besides, how to get the Bader charges transferred from the Al atom to N atom with below txt scprit
To get the charge transferred to a certain atom, you should compare the charge calculated using Bader analysis with the atomic number of the corresponding isolated atom. In your case, for example, you can see that 9.4122 - 7 = 2.4122 electrons have been donated to N. However notice the two WARNING messages at the beginning of the log file. I would suggest you to increase the fineness of the grid to obtain more converged results.

Daniele

82
General Questions and Answers / Re: DFT+U Anisotropic or SphericalSymmetric
« on: October 16, 2017, 17:22 »
Hi Cyrille,

I will check it in detail, but it might be related to how the shells are filled in the Anysotropic method, check the description in the manual:
https://docs.quantumwise.com/manuals/ATKDFT.html#sect2-atkdft-hubbardu

Daniele

83
General Questions and Answers / Re: Is this EDP curve correct?
« on: October 10, 2017, 09:14 »
Could you please have a look at the density matrix of the last SCF loop in your output file? In particular, the two columns DM (density matrix) and DD (density difference).

+------------------------------------------------------------------------------+
| Density Matrix Report                       DM        DD                     |
+------------------------------------------------------------------------------+
|   0  In   [ -0.000 ,  0.000 ,  0.000 ]    3.52719   0.52719                  |
|   1  As   [  1.520 ,  1.520 ,  1.520 ]    4.47281  -0.52719                  |
+------------------------------------------------------------------------------+
|   3 E = -2.67569 dE =  2.502366e-04 dH =  9.448242e-05                       |
+------------------------------------------------------------------------------+

My first guess is that the charge density has been drained away from the central region due to inappropriate simulation parameters. In this case, the column DM should be 0.0.
Regards,
Daniele

84
General Questions and Answers / Re: device
« on: October 9, 2017, 09:33 »
Unfortunately, there is no easy trick. You should make the device larger, so that the electrode repetitions are without gas molecules.
May I ask you why you can't increase the length of your device?

85
General Questions and Answers / Re: "unrealistic" relaxation of H2O molecules
« on: October 4, 2017, 11:15 »
Hi Cyrille,

I think that the two H2O molecules (i.e. the axial ligands) should stay oriented along the C axis only if the complex formed with the Co atom is octahedral. As far as I can see, the ligand field (i.e. the spatial distribution of coordinating ligands around the Co atom) in your system is not perfectly octahedral. This might drive your system away from an equilibrium geometry in which the two H2O molecules are axially oriented. Another possibility, is that the U that you are using is inappropriate and does not favor octahedral coordination of the ligands.

There could be two things that could be done to improve the situation:

1) I would first try to see if the U parameter that you are using is suitable to describe an octahedral complex. I would construct a Co(H2O)6 molecular complex, in which the 6 H2O molecules are coordinated in octahedral geometry (C-Co-C angles should be 120 degrees). If the U parameter that you are using is appropriate to describe an octahedral complex, then this octahedral complex should be stable upon geometry optimization. I would also try to distort this complex in the equatorial position, so that the angles resemble those that the Co atom has with the organic ligands in the 2D MOF, and relax it to see if it recovers an octahedral geometry.

2) I would try to start the optimization of the 2D MOF from a geometry where the coordination sphere around the ligand is perfectly octahedral. This means that the angles between four equatorial C-Co-C ligands should be perfectly 120 degrees.

Regards,
Daniele.

86
General Questions and Answers / Re: Underestimation of bandgap
« on: September 28, 2017, 09:16 »
Because of the so-called self-interaction error due to the use of approximate exchange-correlation functionals. See e.g.:

J. P. Perdew and Alex Zunger
Self-interaction correction to density-functional approximations for many-electron systems
Phys. Rev. B 23, 5048
https://journals.aps.org/prb/abstract/10.1103/PhysRevB.23.5048

87
General Questions and Answers / Re: Optical properties
« on: September 27, 2017, 13:43 »
For semiconductors, a correct description of the band gap is important to evaluate the optical properties. Therefore, MGGA should be preferred, since this exchange-correlation functional gives much better band gaps for semiconductors, compared to GGA.
Check more in the following tutorial:
https://docs.quantumwise.com/tutorials/optical/optical.html

88
General Questions and Answers / Re: d-band center from VASP DOSCAR
« on: September 27, 2017, 10:42 »
Dear mmg016,

this option is not directly available. However, you can still extract do it with scripting! You can extract the DOS projected on the d-shell, and with some python scripting you can determine the center of the d-band according to the definition of Hammer and Norskov.

Regards,
Daniele.

89
Scripts, Tutorials and Applications / Re: For DFT+U in ATK, is the U is the Ueff, i.e., Ueff = U-J?
« on: September 22, 2017, 11:03 »
Yes, that is correct. It is U-J. Check:
https://docs.quantumwise.com/manuals/ATKDFT.html#sect2-atkdft-hubbardu

Regards,
Daniele.

90
General Questions and Answers / Re: crystal field splitting
« on: September 13, 2017, 17:09 »
The way they calculate the crystal field splitting is by projecting the local density of states onto the d-orbitals with the relevant symmetry:

t2g = d_{xy}, d_{xz}, d_{yz}
eg = d_{z2}, d_{x2-y2}

Therefore, to calculate the projection on the t2g manifold, you simply have to sum up the projections on the d_{xy}, d_{xz}, d_{yz} orbitals. However, this cannot be done in VNL, only by scripting by querying the ProjectedDensityOfStates object using evaluate():

https://docs.quantumwise.com/manuals/Types/ProjectedDensityOfStates/ProjectedDensityOfStates.html

Regards,
Daniele.

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