Messages

1

General Questions and Answers / Re: Nanowires transport properties

« on: October 16, 2010, 16:29 »

This is a good starting point
Enjoy !!!

http://quantumwise.com/documents/tutorials/ATKTutorialDevice/XHTML/

2

General Questions and Answers / Re: How to create MPSH in new version

« on: August 11, 2010, 11:57 »

Ok, don't worry. Thank you very much for your help.

Have a nice day.

3

General Questions and Answers / Re: How to create MPSH in new version

« on: August 11, 2010, 11:47 »

Hi Anders,
I made this input script  in the way that you suggested:
#################################################
configuration = nlread("name.nc", object_id="gID000")[0]

projection_list = ProjectionList([80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124])
eigenstate = Eigenstate(
    configuration=configuration,
    quantum_number=82,
    projection_list=projection_list,
    spin=Spin.Up,
    )
nlsave('name-MPSH.nc', eigenstate, labels=['82Up'])
#################################################################################

And the program gives this error :

+------------------------------------------------------------------------------+
| NanoLanguageScript execution started                                         |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
|                                                                              |
| Atomistix ToolKit 10.8.0                                                     |
|                                                                              |
+------------------------------------------------------------------------------+
Traceback (most recent call last):
  File "/tmp/5734084645051856.py", line 10, in <module>
    spin=Spin.Up,
  File "./zipdir/NL/Analysis/Eigenstate.py", line 47, in __init__
  File "./zipdir/NL/Analysis/AnalysisUtilities.py", line 17, in checkConfiguration
NL.ComputerScienceUtilities.Exceptions.NLTypeError: The parameter, configuration, must be an instance of the MoleculeConfiguration.

NanoLanguageScript execution failure
+------------------------------------------------------------------------------+
| NanoLanguageScript execution finished                                        |
+------------------------------------------------------------------------------+

Do you have an idea what the problem is?

4

General Questions and Answers / Re: How to create MPSH in new version

« on: August 11, 2010, 11:26 »

Thank you very much. Now it is clear.

5

General Questions and Answers / Re: How to create MPSH in new version

« on: August 11, 2010, 11:16 »

Hi Anders,
thank you very much for the fast answer. I already have Molecule energy spectra and I know  how to project over the atoms that I need.
The problem that I have is that I want to used this function: calculateProjectedHamiltonianEigenstates

calculateProjectedHamiltonianEigenstates(
    self_consistent_calculation = scf,
    projection_atoms = (32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76),
   quantum_numbers = [(72,73,74,75),Spin.Up]
)

I need the eigenstates in order to able them to relate with the shape of the 'molecule orbitals'. MoleculeEnergySpectrum is giving me only the energies.

In the MoleculeEnergySpectrum class we have only 3 list of argument:
http://quantumwise.com/documents/manuals/latest/ReferenceManual/XHTML/ref.molecularenergyspectrum.html


 MolecularEnergySpectrum(
configuration,
energy_zero_parameter,
projection_list
)

We don have list of argument such as Spin and Quantum Number to be able to specify which number molecule orbitals I need. Is it correct?
Sorry that I am bothering you again with this.

 

6

General Questions and Answers / How to create MPSH in new version

« on: August 11, 2010, 10:37 »

Dear all,
I am a little bit confuse with the new version. My aim is to project Hamiltonian in the scattering region.
In the old version I used this script:
######################################
from ATK.TwoProbe import *

# Restore initial density from old calculation
scf = restoreSelfConsistentCalculation("name.nc")

vnl_file = VNLFile('name.vnl')
atomic_configuration = vnl_file.readAtomicConfigurations()['name']

projected_hamiltonian_eigenstates = calculateProjectedHamiltonianEigenstates(
    self_consistent_calculation = scf,
    projection_atoms = (32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76),
   quantum_numbers = [(72,73,74,75),Spin.Up]
)


vnl_file = VNLFile("name-MPSH.vnl")
vnl_file.addToSample(atomic_configuration,'name-MPSH')
for projected_hamiltonian_eigenstates_index,state in enumerate(projected_hamiltonian_eigenstates):
    label = 'Projected Hamiltonian Eigenstates-0V'+' '+str(projected_hamiltonian_eigenstates_index)
    vnl_file.addToSample(state, 'name-MPSH', label)
#############################################################################

So now in the new Nanolenguage :
instead to used readAtomicConfiguration I should use nlread ('name-file', object_id="gID000")[0]

That is Ok.

Now, how I should replace restartSelfConsistentCoalculations?

How to save my output file because the new version is not using .vnl files anymore?

Or with one word can you just write a small script from the beginning to the end, please?

Few more points that I noticed :
When I have Transmission spectra  in old version was possible to place the mouse at some point of the screen and I will have X and Y coordinates. The same was valid for the Molecule Energy spectra. It was possible to see the number of Molecule orbital and the energy from the window. In the new version it is not possible. I believe that will be very useful and convenient to have these features back in the new version. 

7

General Questions and Answers / Re: Error: 'function' object has no attribute 'isabs'

« on: August 2, 2010, 10:25 »

Hi Anders,
I have this error when I drop it to everything.
It is not a huge problem, because I am saving my geometry  before to start making the input file. So in the case when i have only coordinates in the file it is working but at the moment when the script contains the ATK_DFT parameters such as basis set and so I have this error.
I just decided to let you know.

8

General Questions and Answers / Error: 'function' object has no attribute 'isabs'

« on: July 30, 2010, 11:04 »

Hi all,
I am playing now with the new version. I am having small problem. After making my geometry and input file with VNL/ATK I saved my file such as "input.py". The file after this is executable-running without a problem but when I wanted to open the same file with VNL again I am having this error:

The following error message was generated when running the script:
'function' object has no attribute 'isabs'
Typically this is caused by a syntax error or a spelling mistake; the message above should be helpful in correcting the issue in such cases.

Traceback (most recent call last):
  File "./zipdir/NL/GUI/Tools/ScriptGenerator/ScriptGenerator.py", line 474, in dropReceiver
  File "./zipdir/NL/NanoLanguage/ScopeExecuter.py", line 58, in execute
NLScopeExecutionError: 'function' object has no attribute 'isabs'

I didn't change a single letter in the file. It is created only with VNL.

Thank you very much in advance.

9

General Questions and Answers / Re: How to apply charge of the system in ATK 2008.10.0 ???

« on: May 24, 2010, 14:31 »

Nordland,
thank you for the fast answer.

10

General Questions and Answers / How to apply charge of the system in ATK 2008.10.0 ???

« on: May 24, 2010, 11:04 »

Dear All,
I would like to apply additional charge to my molecule in ATK version 2008.10.0.
Molecule -> Molecule 1-?
Can you tell me if it possible to do this at all in 2008.10.0 version?

From the information posted here in this forum, I found that this is possible in the new version ATK 2010.02 with the object LCAOCalculator. I found the tutorial as well : Properties of an isolated benzene molecule.

11

Scripts, Tutorials and Applications / Re: Function for charge density difference

« on: December 14, 2009, 11:46 »

Hi Anders, it is me again.
I printed the shapes of the two files

"print n1.shape, n2.shape"
(2, 113, 113, 468)
(2, 113, 113, 468)


for me they look the same. But it doesn't work again. 
Is it possible to send you the two *.py input files and have a fast look at them when you have time?
Thank you very much in advance.

12

Scripts, Tutorials and Applications / Re: Function for charge density difference

« on: December 14, 2009, 10:29 »

Thank you very much Anders for the fast replay.
I will try to understand what is going on.

13

Scripts, Tutorials and Applications / Function for charge density difference

« on: December 13, 2009, 13:57 »

Dear all,
I just want to ask you if it is possible to be create a script for charge redistrubution.


What I mean:
The transfered charged and the induced change in the electrostatic potential are obtained  by taking the difference between the self-consistent charge/potential  distribution in the equilibrium metal-molecule-metal junction and the charge/potential distribution in the isolated molecule plus the bare bimetallic junction.(Phys.Rev. B 69,085403 (2004))

I know that here we have a function written by ipsecog which calculated density difference.  I successfully used this function to calculated the density difference in different bias.
I trued to make the same for the charged redistribution for the : (metal-molecule-metal) - (molecule) and the error is :

File "elec_density-diffrence.py", line 22, in ?
    diff_density = calculateDensityDifference(density1,density2)
  File "elec_density-diffrence.py", line 15, in calculateDensityDifference
    density._ElectronDensity__electron_density_data = (n1-n2)
ValueError: shape mismatch: objects cannot be broadcast to a single shape


I know that is something wrong with the formats of the input files and I suspect that the reason is that for the metal-molecule-metal file I used Atk.TwoProbe method to calculate while for the molecule I used  ATK.KohnSham and according to me the size of the two files doesn't match. After this I made them text files but they are massive and impossible to handle.

I will really appreciate your help and ideas how to get the charge density difference.


----------------------------- This is my script-----------------------------------

from ATK.TwoProbe import *


def calculateDensityDifference (d1,d2):

    import copy

    n1 = d1.toArray()
    n2 = d2.toArray()
    density = copy.copy(d1)
    density._ElectronDensity__electron_density_data = (n1-n2)
    return density

scf1 = restoreSelfConsistentCalculation ('metal-molecule-metal.nc')
scf2 = restoreSelfConsistentCalculation ('molecule-scf.nc')
density1 = calculateElectronDensity(scf1)   # Two-probe
density2 = calculateElectronDensity(scf2)   # molecule 0.0 V bias
diff_density = calculateDensityDifference(density1,density2)

f = VNLFile('elec_density-difference.vnl')
f.addToSample(atomic_configuration,'elec_density-difference')
f.addToSample(density1,'elec_density-difference','Two-probe')
f.addToSample(density2,'elec_density-difference','Molecule')
f.addToSample(diff_density,'elec_density-difference','Difference density')

14

Installation and License Questions / Re: Error[88]: Operating in stand-alone mode using terminal client.

« on: September 10, 2009, 11:54 »

Hi Anders,
Yes I tried to tune with SSH and X terminal.
So that explain everything. 

Thank you very much for your help and fast answer.

15

Installation and License Questions / Re: Error[88]: Operating in stand-alone mode using terminal client.

« on: September 10, 2009, 11:34 »

Hi Anders ,
I am running the atk and the license file at the same machine.
I am not making client. I am following  the  license manual :

Stand-alone Licensing

To run ATK or VNL using a stand-alone license, the machine they are installed on must be configured using a one-time-only operation. Doing this requires administrative privileges, and is done by running configure_for_standalone_license as root:

sudo install_dir/nlpython/bin/configure_for_standalone_license

This should produce the following output:

Setting up machine for stand-alone license system:
 Success[0] -  System initialization successfully done.

Note, that this operation needs only to be performed once. Once this has been done, the following environment variables need to be set:

export LSHOST=no-net
export LSERVRC=pathto/license_file

where pathto is the full path to the directory in which the license file is located and license_file is the name of the license file.

You should now be ready to run ATK or VNL (no administrative privileges required).


Do you know how I can restart the license configuration?

Thank you very much for the fats reply .