Messages

181

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?

182

General Questions and Answers / Re: two "0" values in the calculation result of MPSH energy spectrum. Why?

« on: October 3, 2010, 02:02 »

See http://quantumwise.com/forum/index.php?topic=103.0

Thank you so much.

183

General Questions and Answers / Re: two "0" values in the calculation result of MPSH energy spectrum. Why?

« on: October 2, 2010, 15:30 »

I see nothing wrong here. You happen to have two molecular levels that coincide with the average Fermi level, but if there were more decimals I'm sure you would not have 0.000000000 eV but perhaps 0.0043 eV or so. They might not even be degenerate, but only so to within 2 decimals.

To print the spectrum with more decimals (nlPrint doesn't do a supergood job there...), replace the line

Code

if processIsMaster(): nlPrint(projected_hamiltonian_energy_spectrum)

by

Code

if processIsMaster(): 
    print "# MPSH Spectrum (eV)"
    print "# -----------------------------------------------------------------------------"
    for E in projected_hamiltonian_energy_spectrum.energies():
        print E.inUnitsOf(eV)

Dear Anders Blom ,
If I want to output the transmission_spectrum to the output file,and have some more decimals.How should I change the following command,except using the script in the forum to extract from the VNL file.
if processIsMaster(): nlPrint(transmission_spectrum)
if processIsMaster(): file.addToSample(transmission_spectrum, 'twoprobe_configuration', 'Transmission Spectrum')

Thank you in advance.I am not familiar with python.

184

General Questions and Answers / Re: Pseudopotential transfer between ATK and SIESTA

« on: October 2, 2010, 09:41 »

I just tried your pp with ATK 10.8, it works fine.

I use ATK-2008.10,and it does not work.Maybe there is difference as zh suggested between the upf I generated and AKT use.Is there different in format for the pps used in 2008.10 and 2010.8
But when I tried to make the format the same ,2008 yet does not work
Thank you and zh again.

185

General Questions and Answers / Re: Pseudopotential transfer between ATK and SIESTA

« on: October 1, 2010, 11:02 »

APE can generate all the kinds of PP for a input files?

Sorry, I can not understand your questions. Please state your question more clear.  Anyway, about the detailed usage of APE, please refer to its manual.

I followed your instruction，and download the APE，and learn how to use,but when give the generated psf format pp to sieta,siesta always complains it.Oh....and the upf can not be used by atk.The attachment is the pps generate by APE.

186

General Questions and Answers / Re: Pseudopotential transfer between ATK and SIESTA

« on: September 29, 2010, 05:57 »

see  here to find out how to download it:

http://www.tddft.org/programs/APE/

Dear zh,
Thanks for your help.APE can generate all the kinds of PP for a input files?

187

General Questions and Answers / Re: Pseudopotential transfer between ATK and SIESTA

« on: September 28, 2010, 10:50 »

There are some software tools out there which can convert different pseudopotential formats between each other. Google something like "upf psf convert pseudopotential".

Dear Anders Blom,
Can you give some hints on the  software tools which can convert different pseudopotential formats between each other.I need one software to convert the psf format which siesta can use to upf format which ATK uses.

I have found a tool called "pspconvert",but I can not download it.http://www.tddft.org/trac/APE/browser/pspconvert?desc=1

Can you suggest another one!


Thanks in advance.