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Topics - GJK

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General Questions and Answers / Total dipole moment
« on: August 4, 2014, 18:28 »

Dipole moment calculation as said by the script gives dipole moment for three axes.

How to calculate the total dipole moment???

General Questions and Answers / Dipole Matrix-reg
« on: August 4, 2014, 18:25 »
Dear Dr.Anders,

In using the script provided in this link, I am getting the dipole moment along with quadrupoles for my bulk system of GNR.

But the dipole moment is resulted as a negative value in the Z direction.My question is whether it is the modulus value (or) the real value.Because the dipole moment has to be always positive right???

General Questions and Answers / Charge Carriers
« on: July 25, 2014, 15:32 »
How to calculate the number of charge carriers in a bulk system as well as device system ( I mean electron and hole carriers separately)

General Questions and Answers / ZGNR binding energy
« on: July 25, 2014, 15:31 »

How to calculate the binding energy in the case of adsorption followed by doping for graphene?

Scrolled through various posts an links I came across only with either adsorption or doping...

General Questions and Answers / Band Index of GNR
« on: July 19, 2014, 11:42 »

After going through the tutorial its crisp and clear to find the band index of valence and conduction band.But the band index is calculated for unit cell with even number of electrons.

So I am doubted with the following queries???

1.How to find the band index of valence and conduction band for a  GNR system containing odd number of electrons.(where special cases arise due to doping or adsorption).

2.From the various discussion  in  the forum its clear that band index and band structures are calculated for unit cell.But with special cases like adsorption (or) doping of GNR with various molecules (big or small) we can find the band structure for unit cell repeated(say 10 times along z direction).In that case (GNR with dopant or adsorbant)we get more number of electrons say for example 200,203 depending on cases.How to find the band index in these cases ???

If you say same procedure like as you have did for unit cell of ZGNR the band index for 200 electrons comes to be 100 for conduction band and 99 for valence band.Am I correct???But for the case of 203 electrons how to find the band index???

Waiting for the favorable suggestions after scrolling through the journals and forum???

General Questions and Answers / Script Please
« on: July 15, 2014, 19:46 »

Kindly provide the script for calculating the formation energy of GNR either doped or adsorbed with a biomolecule???


I have scrolled through the posts regarding Band Gap in the forum.
Thanks for the scripts for calculating the direct and indirect band gap.
It will be highly grateful if you could provide the scripts for calculating the,
1. overall band gap value(from spin up and spin down states)
2. Spin up band gap value
3.Spin down band gap value for the spin polarised ZGNR.


Both Ionisation potential and electron affinity calculations are very well explained for benzene molecule by removing charge(E+1) and adding charge (E-1)

Can we use the same procedure for graphene related studies where a biomolecule is adsorbed on graphene. Thus in this complex system by adding and removing charge can we use the same procedure provided for benzene to evaluate the electron affinity and ionisation potential

Your assistance will be highly grateful

General Questions and Answers / Polarisation -reg
« on: June 22, 2014, 10:18 »

It is very well understood from tutorial that ATK calculates electronic Pe and ionic Pi polarisation.

My questions are???
1. Why you use the interval [-0.5,0.5] and can we use some other interval values by changing in the code.If then how and what values should we use???

2. How to calculate Total cartesian polarization(formula)
(In the tutorial we have the formula for Pq=e* R/omega but no formula for Total cartesian polarization)

3.Is Total cartesian polarization same as total fractional polarisation???

4.What polarisation value should we consider for the result is it Total cartesian polarization (or) Polarisation quantum??? which is correct

Dear all,

Here with I have attached the Mulliken population file of
1. Hydrogen Passivated ZGNR
2.Isolated Biomolecule
3.Combined system of ZGNR and biomolecule

Question No 1:
Kindly help me in finding the total charge transfer between the molecule and ZGNR.

Question No 2:
As I have attached the biomolecule to ZGNR carbon atom via Nitrogen atom,I need to find the charge transfer between the carbon and nitrogen atom whose positions  in the Mulliken population report for the three sytems mentioned above are as follows;
1. Hydrogen Passivated ZGNR (Carbon Number:54)
2.Isolated Biomolecule(Nitrogen Number:0)
3.Combined system of ZGNR and biomolecule(Carbon Number:54 and Nitrogen Number:79)

Note; Already I have verified the links provided by you for the charge transfer.

Question 3:

Your kind assistance will be helpful.: From these links I understood that we should calculate the electron density and take the difference for overall charge transfer between the two systems.How to get the electron density value from the colour mapping.It is showing a range of values.Already I know that isovalue=electron density.(Most molecular modeling software packages allow the user to choose a value for the electron density, often called the IsoValue. How to get the electron density value for my system so that I can easily calculate the charge transfer from the formula given by you???


For GNR the Brillouine zone route is (gamma and Z).
Points per segment-200

For DNA and amino acids what should we specify for Brillouine zone route and Points per segment(resolution)

General Questions and Answers / Molecule in Bulk
« on: May 27, 2014, 10:15 »

I optimized my molecule in bulk and then turn out to estimate the band structure,DOS and transmission spectrum etc..All the results were analysed expect transmission spectrum??? why???

Dear Dr.Anders,

I have attached my files which I got for Band gap analysis of ZGNR with and without molecule attachement.

1.With perfect ZGNR(file BSori) I am geeting band crossing at Fermi level so noband gap.Am I right??

2.For the molecule adsorbed ZGNR I am getting a band structure(as attached(file BS).Does it have a band gap or not???

3.The electron density and iso surface of perfect ZGNR(hydrogen passivated) is attached.The electron density runs from 0(blue)-1(green)-2(red) and the iso surface is showing as -1(blue)-0(green)-1(red).From isosurface value I predict that my electron density is 1(Angstrom cube).Am I correct??

4.What actually the isosurface says about electron density (or) electron difference density etc???

Thanks in advance

Dear all,

I wonder why we need less k points for bulk and more for device calculations are used during optimization of  ZGNR.

Your assistance is required???

General Questions and Answers / ZGNR-DOS
« on: May 21, 2014, 17:53 »

I used ZGNR with k points(nA,nB,nC--1,1,150) .By default we have kA,kB,kC values in DOS block as (1,1,1).

My First question is ???
 ::) :o :-[
1. What k points should I fix in the DOS where we have kA,kB,kC (1,1,1). Should I fix the default values (1,1,1) or the values which I mentioned in the calculator (nA,nB,nC--1,1,150).

2.My next question is for calculating Transmission path ways,Transmission eigen states and eigen values,I found Energy parameter in the blocks along with quantum number.By default energy value is 0 and quantum number empty.What values should I fix because my transmission spectrum is calculated in energy range 2 eV- -2 eV.

Waiting for your assistance.


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