Topics

31

General Questions and Answers / why the transimission peak corresponding to a localized state

« on: July 13, 2011, 10:05 »

Dear everyone:
 
I have now encountered a result which I can not understand well. Please help me to explain it.
 
I have put the result in the attachment. The solid line is the transmission spectrum of the molecular junction (Au/molecule/Au system), the dash line is the projected density of state to the bare molecule and the down-triangle is the MPSH for bare molecule+6Au (which are the nearest neighboring Au atoms to acount for the interaction between molecule and the surface electrodes.)
 
As seen, there are two sharp PDOS  peaks locating at 0.3 and 1.0 eV and two broad PDOS peaks at 0.2 and 1.4 eV. The MPSH for the two sharp PDOS peaks are very localized and the two broad PDOS peaks are delocalized which can be understood. But the transmission at 0.3 and 1.0 eV are 0.74 and 0.73 respectively, which are noticeable. To my knowledge, a localized PDOS should has a very small transmission. Do I have a wrong understand? Or is there something else I misunderstand? And In what case, the localized PDOS can have a noticeable transmission?
 
Please help. Any explanation is appreciated.
 
Best regards.
 
Yours,
 
Guangping

32

General Questions and Answers / Again for the MPSH implemented in 2008.10

« on: April 3, 2011, 06:11 »

Dear all,

I wonder at what k point does the MPSH in 2008.10 is calculated.

Is it calculated at Gamma point or an average over all the K points used in the calculation.

I think it is calculated at the Gamma point, if it is average over the K points, it has non sense or how to average?

Any advice is welcome.

Best.

33

General Questions and Answers / Question about the convergence

« on: December 22, 2010, 06:09 »

I have encountered a convergence problem,for my system,for other bias there is no problem in convergence.Even I have got the convergence for V=1.0, 1.5 ,2.0V, but for V=1.2Vand 1.4V,the convergence is hard to achived,I calculate V=1.4V using a initio guess from V=1.5.Even if I choose diagonal_mixing_parameter = 0.00001,my tolerance=0.0001.

The convergence process is as the following,the q varies slightly, but the Ebs and dRho....             
Who can tell me the underling reason?
                                                                                                                                               
in addition there is nothing strange for the spectrum at V=1.0V and 1.5V.
                                                                                             
Thanks in advance.
                                                                                                                                                                                                                                                                                                               
......
                     
# sc 204 : q =  585.99929 e  Ebs = -536.20515 Ry  dRho =  1.1830E-03
# sc 205 : q =  585.99917 e  Ebs = -536.76316 Ry  dRho =  8.6365E-04
# sc 206 : q =  585.99915 e  Ebs = -536.81562 Ry  dRho =  1.0491E-03
# sc 207 : q =  585.99923 e  Ebs = -536.82648 Ry  dRho =  1.0925E-03
# sc 208 : q =  585.99924 e  Ebs = -536.77731 Ry  dRho =  9.0449E-04
# sc 209 : q =  585.99924 e  Ebs = -536.78277 Ry  dRho =  9.4113E-04
# sc 210 : q =  585.99971 e  Ebs = -536.76664 Ry  dRho =  8.7112E-04
# sc 211 : q =  585.99926 e  Ebs = -536.20515 Ry  dRho =  1.1830E-03
# sc 212 : q =  585.99914 e  Ebs = -536.77953 Ry  dRho =  9.2239E-04
# sc 213 : q =  585.99914 e  Ebs = -536.82901 Ry  dRho =  1.0987E-03
# sc 214 : q =  585.99923 e  Ebs = -536.82727 Ry  dRho =  1.0910E-03
# sc 215 : q =  585.99926 e  Ebs = -536.77637 Ry  dRho =  8.9766E-04
# sc 216 : q =  585.99926 e  Ebs = -536.77149 Ry  dRho =  8.9816E-04
# sc 217 : q =  585.99971 e  Ebs = -536.76023 Ry  dRho =  8.4768E-04
# sc 218 : q =  585.99926 e  Ebs = -536.20514 Ry  dRho =  1.1829E-03
# sc 219 : q =  585.99921 e  Ebs = -536.77788 Ry  dRho =  9.1608E-04
# sc 220 : q =  585.99944 e  Ebs = -536.78886 Ry  dRho =  9.4414E-04
# sc 221 : q =  585.99913 e  Ebs = -536.34500 Ry  dRho =  6.5681E-04
# sc 222 : q =  585.99912 e  Ebs = -536.83700 Ry  dRho =  1.1288E-03
# sc 223 : q =  585.99913 e  Ebs = -536.83785 Ry  dRho =  1.1306E-03
# sc 224 : q =  585.99925 e  Ebs = -536.83654 Ry  dRho =  1.1317E-03
# sc 225 : q =  585.99919 e  Ebs = -536.76811 Ry  dRho =  8.6867E-04
# sc 226 : q =  585.99919 e  Ebs = -536.80860 Ry  dRho =  1.0286E-03
# sc 227 : q =  585.99971 e  Ebs = -536.80245 Ry  dRho =  9.9508E-04
# sc 228 : q =  585.99914 e  Ebs = -536.20515 Ry  dRho =  1.1829E-03
# sc 229 : q =  585.99916 e  Ebs = -536.82852 Ry  dRho =  1.0964E-03

34

General Questions and Answers / The numerical implement about MPSH

« on: November 30, 2010, 13:02 »

As I konw the MPSH is the diagonalization of th Hamiltonian of the subsystem which is from the converged Hamiltonian of the whole tranport system.Now I wonder how to do it in practical?
If I konwn the converged Rho(charge density) for the space grids.Then I abstract the part belong to the subsystem, and the use it to construct the Hamiltonian of the subsystem the diagonalize it.Can this make sense? Or there are better way to do this in atk?
By this, I mean how to do in numerical practice to do MPSH in atk.
Thanks.

35

General Questions and Answers / How to understand the real convergence

« on: November 15, 2010, 13:43 »

Hi all,
As we know if the convergence is below the criterion,we say the convergence is achived.However if you use the converged *.nc file as an initial guess for the same task,and perform it again,you may find the convergence is above the former criterion,i.e. it needs some scf for the new task.However this is the same task as before,and the initial guess is a converged one.
How to understand it?
And the so called converged *.nc file is reliable? Or we need to get it converged once again?
Even if it converged once again,if we repeat the steps used above,we will probably find the second converged *.nc file not converge to the criterion yet. I know if we repeat it time by time and at last we can find the converged *nc file will really converge for the next rerun.
But problem is :How can we do with the firt so called converged *nc file and the results calculted from it?

Any advice is welcome!

36

General Questions and Answers / Can we specify the basis for a species

« on: November 9, 2010, 06:55 »

Hi all,
Is there a way to specify the basis for certain species instead of using SZP ,DZP and so on.
I want to different the same species for their different locations.
Say,for Au atoms,some at the surface and some in the bulk.I want to different them in the same calculation.
I know this can be done by siesta.
We can specify Au_bulk and Au_surface in the input file, and give Au_bulk.psf and Au_surface.psf,this is enough,in addition,you can specify the basis for them by setting the rc's instead of using DZP,SZP and so on.

I wonder how to do it in ATK-2008.10.

Thanks.

37

General Questions and Answers / Why the MPSH spectrum does not aggree with the transmission spectrum

« on: October 8, 2010, 14:15 »

Hi,all:
I have calculate a molecule sandwiched between two Au electrodes.And I found the MPSH spectrum of the bare molecular do not aggree with the transmission spectrum at some place(as shown in FIG1) though some aggree.There is a transmission peak at -1eV,while no MPSH.MPSH of FIG1 is for the bare molecular without any Au atoms.As I know the transmission spectrum is for the whole system including the bulk electrode and surface atoms.So I guess the transmission peak at -1eV maybe from the surface.So I recalculate the MPSH for bare molecule and the neighouring 3 Au atoms at each side (so 6 Au atoms in all)which connect the molecule to the surface.And the MPSH is in FIG2.But this time the aggreement is yet not good.
I think if there is a peak in the transmission spectrum, there should a corresponding MPSH state for the bare molecule,for the molecule connect the left and right electrodes.(Am I right?)
So who can tell me the reasion?

38

General Questions and Answers / Some doubt about MPSH result

« on: October 7, 2010, 09:21 »

Hi,as I kown,the MPSH can be regarded as the value of the selected atoms under the bias and inlcuded the effect of the surroundings.Am I right?
But how to explain the following phenomenon:

The selected atoms have 124 electrons,and should have 62 occupied orbitals if treated as isolated.And the MPSH HOMO orbital of the selected atoms should at 62 or so,and LUMO at 61 or so.

After the convergency,there are 124.096 (Mulliken) electrons on the selected atoms.So I expected the 61th (for the quntum number is started with zero) MPSH orbital is HOMO,and 62th MPSH orbital is LUMO.
And as I kown,the smallest positive number is LUMO and the biggest negative number is HOMO,as atk put the fermi energy to zero.

But the MPSH result shows:
58       -2.51662803866
59       -2.10063289295
60       -2.02243292869
61       -1.78048389083
62       -1.44400824774
63        0.936283743779
64        1.46552142409
65        1.87921738475
66        1.89000122501
67        2.33287791883
68        2.59222292105
69        2.79361757147

Since there are 63 occupied orbitals in the MPSH ,there should be 126 electrons on the selected atoms.
But in fact there are only 124.096.

I expcted the 61th (ie.62) MPSH is the HOMO,for there is 124 electrons.But now the extra 0.096 electron makes the 62th (ie.63) MPSH HOMO.
Is this so?
or
What is wrong?