Bulk -devicecal-reg

[GJK]

Most papers say we calculated the BSE (band structure energy ) ,adsorbtion energy using ATK-how to calculate it-kindly provide any tutorials with formulas if possible.

Thanks in advance

[zh]

The band structure calculation is already implemented, and one can access it by calling Bandstructure(). Please refer to the manual: http://quantumwise.com/documents/manuals/latest/ReferenceManual/index.html/ref.bandstructure.html
If you didn't understand the concept of band structure, please refer to wiki here: http://en.wikipedia.org/wiki/Electronic_band_structure

For the calculations of adsorption energy, one has to do three separated  calculations: 1) the geometry optimization and total energy calculation of substrate system, 2) the geometry optimization and total energy calculation of isolated adsorbate molecule; 3) the the geometry optimization and total energy calculation of the molecule adsorbed on the substrate.   The adsorption energy is estimated by the formula:  total energy of  molecule adsorbed on substrate   -  total energy of isolated adsorbate molecule  -  total energy of substrate

[GJK]

Thank you so much Mr.Zh

[GJK]

Hi,

Kindly suggest me how to calculate formation energy and polarisability

Thanks in advance

[GJK]

The band structure calculation is already implemented, and one can access it by calling Bandstructure(). Please refer to the manual: http://quantumwise.com/documents/manuals/latest/ReferenceManual/index.html/ref.bandstructure.html
If you didn't understand the concept of band structure, please refer to wiki here: http://en.wikipedia.org/wiki/Electronic_band_structure

For the calculations of adsorption energy, one has to do three separated  calculations: 1) the geometry optimization and total energy calculation of substrate system, 2) the geometry optimization and total energy calculation of isolated adsorbate molecule; 3) the the geometry optimization and total energy calculation of the molecule adsorbed on the substrate.   The adsorption energy is estimated by the formula:  total energy of  molecule adsorbed on substrate   -  total energy of isolated adsorbate molecule  -  total energy of substrate

Hi Mr.Zh

I have a big doubt--kindly clarify
there are three geometry optimization format ---device,bulk and molecule
suppose assume my system is graphene with cytosine(DNA base) adsorbed on it.Then for calculating the adsorption energy what tool should I use for the substrate(graphene),adsorption molecule(cytosine) and the complex system(graphene+cytosine)..

My question is should optimize them in
bulk configuration
    (or)
substrate(graphene) and the complex system(graphene+cytosine) optimized in bulk configuration
adsorption molecule(cytosine) --optimized in molecule configuration

Thanks in advance

[zh]

"bulk configuration
    (or)
substrate(graphene) and the complex system(graphene+cytosine) optimized in bulk configuration
adsorption molecule(cytosine) --optimized in molecule configuration
"
Yes, it is better to do in the above way.

[GJK]

"bulk configuration
    (or)
substrate(graphene) and the complex system(graphene+cytosine) optimized in bulk configuration
adsorption molecule(cytosine) --optimized in molecule configuration
"
Yes, it is better to do in the above way.

Hi Mr.Zh,

Sorry I am not getting at you.Kindly clarify me either
1.Bulk optmization
(or)
2.Bulk and device optmization

[zh]

It is quite clear.  Choose (1). 

[GJK]

Hi,

Kindly suggest me how to calculate formation energy and polarisability

Thanks in advance

Hi Dr.Zh

Kindly help me how to obtain polarisability from the results obtained in the polarisation for a bulk and device configuration of GNR.

[zh]

Your question is not clear.  The electron and spin both can polarized. The former one may correspond to electron dipole and dielectric properties. The latter one may correspond to spin density and magnetic moment.
Please read the manual:
http://quantumwise.com/documents/manuals/latest/ReferenceManual/index.html/ref.polarization.html
http://quantumwise.com/documents/manuals/latest/ReferenceManual/index.html/ref.spin.html

[GJK]

Dear Mr.Zh,

These values I took from the manual which you suggested me ---| Polarization                                                                 |
    +------------------------------------------------------------------------------+
    | Electronic fractional polarization.                                          |
    | Values wrapped to the interval [-0.5,0.5]                                    |
    |       [  4.94399555e-14 ]                                                    |
    |  Pe=  [ -4.10079517e-13 ]                                                    |
    |       [ -4.62727745e-01 ]                                                    |
    +------------------------------------------------------------------------------+
    | Ionic fractional polarization.                                               |
    | Values wrapped to the interval [-0.5,0.5]                                    |
    |       [  0.00000000e+00 ]                                                    |
    |  Pi=  [  0.00000000e+00 ]                                                    |
    |       [ -2.44642000e-01 ]                                                    |
    +------------------------------------------------------------------------------+
    | Total fractional polarization. Pt = Pe + Pi.                                 |
    | Values wrapped to the interval [-0.5,0.5]                                    |
    |       [  4.94399555e-14 ]                                                    |
    |  Pt=  [ -4.10079517e-13 ]                                                    |
    |       [  2.92630255e-01 ]                                                    |
    +------------------------------------------------------------------------------+
    | Total cartesian polarization.                                                |
    |       [  4.91636310e-14 ]                                                    |
    |  Pt=  [ -4.07787544e-13 ] C/Meter**2                                         |
    |       [  2.93835822e-01 ]                                                    |
    +------------------------------------------------------------------------------+
    | Polarizarion quantum.                                                        |
    |       [  9.94410906e-01 ]                                                    |
    |  Pq=  [  9.94410906e-01 ] C/Meter**2                                         |
    |       [  1.00411976e+00 ]                                                    |
    +--------------------------------------------------------

In my system(BULk-GNR) Iam getting the values for polarisation like this.My question is how to calculate the factor polarisability(alpha) from these values becaues P=alpha*E???

[Anders Blom]

To calculate alpha you need to apply a (small but finite) electric field and compute P. At the moment this is not possible in ATK for a bulk system.