Messages

1

General Questions and Answers / non-adiabatic molecular dynamics

« on: August 16, 2016, 17:43 »

Hi,

I would like to know the possibility of performing non-adiabatic molecular dynamics calculations.

Thanks for your reply,

2

General Questions and Answers / Re: Capacitance-Bias Variation

« on: April 2, 2015, 19:10 »

Hi,

Thanks for your reply. Yes, it is a sign error. But I have directly followed your script where -e is used. Thus I must get a positive variation but I have obtained a negative one.

3

General Questions and Answers / Re: Capacitance-Bias Variation

« on: March 24, 2015, 21:09 »

Hi,

Sorry, is there anybody who can solve the problem that I have encountered?

Thanks,

4

General Questions and Answers / Capacitance-Bias Variation

« on: March 17, 2015, 20:50 »

Hi,
I have followed http://quantumwise.com/publications/tutorials/item/511-calculation-of-atomic-scale-capacitance
to reveal the Capacitance -Bias variation of a device structure. Using the mulliken-analysis, for my device, I have obtained the capacitance as +1.54625e-20 Farad. But when I have plotted Capacitance-Bias variation it gives a negative capacitance varying from approximately -2.0e-20 to -1.54625e-20. So it is almost bias independent and converged to the capacitance that I have obtained. But the variation is negative but should be positive, what is the mistake here? Thanks for your help.

5

General Questions and Answers / Re: DFTB, halorg and mio problem

« on: November 11, 2014, 06:41 »

Hi Anders,

Thanks for your quick reply. Then, I think the common SK files in halorg and mio folders will not be matter during the merging.

6

General Questions and Answers / DFTB, halorg and mio problem

« on: November 10, 2014, 13:37 »

Hi,

I am trying to perform a calculation using dftb through the corresponding parameter halorg obtained in dftb.org website. It says halorg requires mio. Thus I have downloaded both halorg and mio folders and copied them under the ...\atkpython\share\tightbinding\dftb\  but in script generator I was not able to get the halorg under the Predefined Slater-Koster basis set.
Could you please write the possible reason of that?

Thanks,

7

General Questions and Answers / Re: Objects in the nc file disappear

« on: October 1, 2013, 13:36 »

Hi Anders,

In order to test the problem I need to send the nc file but it is too large. Actually I have already re-run the py file and got a new nc file and added the spectrum without any problem. But here the problem is related to the vanishing or disappearing of objects in the nc file after trying to add optical spectrum. The interesting point is that the emerging nc file is sufficiently large without involving any object. Actually I have applied to the following script, keeping the default parameters in the optical spectrum:

nc_file="C:/Users/file.nc"
bulk_configuration = nlread(nc_file,BulkConfiguration,object_id='gID000')[0]

optical_spectrum = OpticalSpectrum(
    configuration=bulk_configuration,
    kpoints=MonkhorstPackGrid(11,11,11),
    energies=numpy.linspace(0,5,101)*eV,
    broadening=0.1*eV,
    bands_below_fermi_level=4,
    bands_above_fermi_level=4,
    )
nlsave(nc_file, optical_spectrum)

8

General Questions and Answers / Re: Objects in the nc file disappear

« on: September 30, 2013, 22:22 »

Hi,

This is the first time that I have encountered with such a problem. Calculation time is short. I can save the spectrum to a different file but in the original nc file all the objects (including BulkConfiguration) become disappearing. So I need to re-run the py file to get a new nc file and to add the spectrum. The size of the nc file is not zero but sufficiently large without objects. I am using the 12.8.

Thanks for your interest,
 

 

9

General Questions and Answers / Objects in the nc file disappear

« on: September 29, 2013, 10:24 »

Hi,

It is very strange that when I try to add the optical spectrum to a converged nc file all the the objects in the nc file disappear and nc file shows nothing. 
Could you please explain the reason?
Thanks,

10

General Questions and Answers / Re: can we start simulation from middle??

« on: May 16, 2013, 16:05 »

Thanks for your reply.  However when I do what you have written, even if I have already tem. checkpointfile, I have enecountered with the following in the first statement of the output file:

"Warning:
  The provided initial state parameter has no pre-calculated data.
  Proceeding without setting an initial state."

That is, it starts from the left electrode calculation.

Is there anything wrong?

Thanks,

11

General Questions and Answers / Re: can we start simulation from middle??

« on: May 15, 2013, 23:36 »

Hi,

In atk 12.8, to restart a stopped calculation, we can use:

configuration = nlread("checkpointfile.nc")[0]
configuration.update(force_restart=True)
nlsave("file.nc",configuration)

given in the mini-tutorials.

In atk 11.2.3 "force_restart" is not recognized. How can we employ this script in atk 11.2.3?

Thanks,

12

General Questions and Answers / Re: "No voltage drop data in file"

« on: May 15, 2013, 23:31 »

Thanks,

13

General Questions and Answers / "No voltage drop data in file"

« on: May 14, 2013, 23:45 »

Hi,

I have constructed a NetCDF file which contains Device configuration and 10 voltage drops for biases from 0.1 V to 1.0 V. For each voltage drop the object ID was named as "Grid Values" using the script given in the mini-tutorials. When I drop the this NetCDF file to the "Analyzer" through the "voltage_drop_analyzer.py" file, I have encountered with the error "No voltage drop data in file".

How can I resolve this problem?

Thanks,

14

General Questions and Answers / AttributeError: electrodeDensityMatrixCalculator

« on: March 14, 2013, 15:16 »

Hi,

During a Device calculation using atk 11.2.3, I have encountered the following error:

Traceback (most recent call last):
  File "./zipdir/NL/Calculators/BulkCalculatorInterface.py", line 183, in _update
  File "./zipdir/NL/Calculators/LCAOCalculator/LCAOCalculator.py", line 1019, in scfLoop
  File "./zipdir/NL/Calculators/LCAOCalculator/LCAOCalculator.py", line 733, in scfLoopHamiltonian
  File "./zipdir/NL/Calculators/GenericParameters/CheckpointHandler.py", line 127, in _storeIfNecessary
  File "./zipdir/NL/CommonConcepts/Configurations/DeviceConfiguration.py", line 570, in _nlsave
  File "./zipdir/NL/Calculators/HuckelCalculator/ExtractState.py", line 48, in extractElectrodeState
  File "./zipdir/NLEngine.py", line 851, in <lambda>
  File "./zipdir/NLEngine.py", line 64, in _swig_getattr
AttributeError: electrodeDensityMatrixCalculator
/home/QuantumWise/atk-11.2.3/atkpython/bin/atkpython: line 3: 10516 Segmentation fault      PSEUDOPOTENTIALS_PATH=$EXEC_DIR/../share/pseudopotentials GPAW_SETUP_PATH=$EXEC_DIR/../share/gpaw-setups/ PYTHONHOME=$EXEC_DIR/.. PYTHONPATH= LD_LIBRARY_PATH=$EXEC_DIR/../lib $EXEC_DIR/atkpython_exec $*

Could you please explain the reason of this error?

15

General Questions and Answers / Re: Custom Analyzer

« on: December 18, 2012, 13:30 »

Many thanks for the script you have sent