Messages

1

General Questions and Answers / Calculate overlap between Bloch states

« on: November 22, 2017, 13:45 »

Hi all,

I'd like to compute the overlap between Bloch states. For a given computed wavefunction \psi_k I have tried getting its overlap with itself as a first test as:

Code

wfc = nlread('file.hdf5', BlochState)[-1] 

wfc_array = wfc.toArray() 

wfc_s0 = wfc_array[:,:,:,0] 

psi_2 = numpy.conj(wfc_s0) * wfc_s0

delta_x = wfc.gridCoordinate(1,1,1).inUnitsOf(Bohr)[0]

integrated_x = numpy.trapz(psi_2, axis=0, dx=delta_x)

integrated_y = numpy.trapz(integrated_x, axis=0, dx=delta_x)

overlap = numpy.trapz(integrated_y, axis=0, dx=delta_x)

(Note: cell is simple cubic so dx=dy=dz)

And that final 'overlap' would be the final result. Does this seem correct? The overlap doesn't integrate to 1 , or to a number of electrons as far as I can see. Although that's to be expected perhaps? Any feedback would be greatly appreciated.

Thanks for your help,
A

2

General Questions and Answers / Re: EffectiveBandstructure with Spin-Orbit?

« on: August 31, 2017, 18:13 »

Great! Thanks

3

General Questions and Answers / EffectiveBandstructure with Spin-Orbit?

« on: August 31, 2017, 13:02 »

Hi all,

I've tried calculating an EffectiveBandstructure using a Noncollinear Spin-Orbit calculator and I get the following error:

"ValueError: shapes (200,200) and (400,) not aligned: 200 (dim 1) != 400 (dim 0)"

Was it never intended to work with NC-SO? or is it just broken?

Thanks for your help!

4

General Questions and Answers / Error when reading .nc files in VNL 2016.0

« on: August 3, 2016, 19:25 »

Hi,

I've found that I can't read back .nc files of completed calculations. Not sure what are the circumstances in which this happens but here's an example:

- Run a DFT calculation of a simple system (alpha-tin)
- Try to read back the resulting .nc file

I can't seem to read the .nc file with either the GUI or atkpython. Here's the error I get from the GUI if I try to drop the output file back into the builder:

Code

Traceback (most recent call last):
  File "./zipdir/NL/GUI/MainWindow/MainWindow.py", line 1073, in toolBarDropEvent
  File "./zipdir/NL/GUI/Tools/Tool.py", line 804, in dropEvent
  File "./zipdir/NL/GUI/DnD/DropExtractor.py", line 200, in extract
  File "./zipdir/NL/GUI/DnD/MimeData.py", line 443, in instances
  File "./zipdir/NL/IO/NLSaveUtilities.py", line 422, in nlread
  File "./zipdir/NL/ComputerScienceUtilities/Timer.py", line 45, in __call__
  File "./zipdir/NL/IO/NLSaveUtilities.py", line 422, in <lambda>
  File "./zipdir/NL/CommonConcepts/Configurations/ReadConfigurations.py", line 121, in nlreadBulkConfiguration
  File "./zipdir/NL/NanoLanguage/ScopeExecuter.py", line 214, in scope_execute
NLScopeExecutionError: unexpected indent (<string>, line 6)

The error from atkpython when trying to read using nlread is longer, but ends in the same last line anyway.

I've attached the input file from my example. The output is too large to attach. Hopefully this provides enough information to debug this.

Best,
Alfonso

5

General Questions and Answers / Re: "IndentationError: unexpected indent" with ATK 2016

« on: August 3, 2016, 18:03 »

I believe there is a bug.

To reproduce this you need to select the OpenMX basis set and then set "Script detail" to "Show defaults". The resulting script generated by VNL2016 will have that mistake.

It seems to only happen with OpenMX basis sets and only when you select "show defaults" - which introduces the comment "# Basis set for X". There doesn't seem to be a line break after the comment.

6

General Questions and Answers / AdaptiveGrid error

« on: February 2, 2016, 19:45 »

Hi all,

I'm trying to compute the TransmissionSpectrum of a BulkConfiguration with the following script:

Code

bulk_configuration = nlread('scc.nc', BulkConfiguration)[-1]


# Adaptive grid

adaptive_grid = AdaptiveGrid(
        kA_range = [-0.5, 0.5],
        kB_range = [-0.5, 0.5],
        tolerance=1e-2,
        error_measure=Absolute,
        number_of_initial_levels=2,
        maximum_number_of_levels=7)

# -------------------------------------------------------------
# Transmission Spectrum
# -------------------------------------------------------------
transmission_spectrum = TransmissionSpectrum(
    configuration=bulk_configuration,
    energies=numpy.linspace(-0.05,0.05,7)*eV,
    kpoints=adaptive_grid,
    energy_zero_parameter=AverageFermiLevel,
    infinitesimal=1e-06*eV,
    self_energy_calculator=RecursionSelfEnergy(),
    )

But get the following error:

Code

Traceback (most recent call last):
  File "tran.py", line 23, in <module>
    self_energy_calculator=RecursionSelfEnergy(),
  File "./zipdir/NL/Analysis/TransmissionSpectrum.py", line 202, in __init__
  File "./zipdir/NL/ComputerScienceUtilities/Timer.py", line 45, in __call__
  File "./zipdir/NL/Analysis/TransmissionSpectrum.py", line 202, in <lambda>
  File "./zipdir/NL/Analysis/TransmissionSpectrum.py", line 1680, in calculateBulkTransmissionSpectrum
  File "./zipdir/NL/ComputerScienceUtilities/Functions.py", line 148, in numpyToStdVectorCartesian3D
AttributeError: AdaptiveGrid instance has no attribute 'shape'

What am I doing wrong? I did notice that the manual entry for AdaptiveGrid only references DeviceConfiguration objects (on the usage examples anyway) -- Does this only work for DeviceConfiguration? Thanks in advance

7

General Questions and Answers / Re: Problem when calculating InelasticTransmissionSpectrum

« on: January 26, 2016, 16:13 »

It's apparently something to do with the cluster I'm using. I tried your Au script and got the same error as before. Ran it on a different cluster and it ran fine. No idea why it's doing that. All other calculations I've attempted run fine.

Thanks for your help, Jess.

8

General Questions and Answers / Re: Problem when calculating InelasticTransmissionSpectrum

« on: January 26, 2016, 11:57 »

What about the DFT calculation? Can't reproduce it with that either? I suppose I could run it again with some freely available DFTB parameters and send you the NC file.

No idea why that 100*Ha is there. Will check how it got there.

9

General Questions and Answers / Re: Problem when calculating InelasticTransmissionSpectrum

« on: January 22, 2016, 14:03 »

I've sent the NC files to Jess. (posted email address didn't work, added a dot between name and surname and seemed to work. hopefully you received the email correctly)

10

General Questions and Answers / Re: Problem when calculating InelasticTransmissionSpectrum

« on: January 22, 2016, 13:01 »

I did not try more than 1 k/q-point as it's a NW structure (more like a chain, really). Should I?

I'll email you the NC files Jess, thanks you both for your help.

11

General Questions and Answers / Problem when calculating InelasticTransmissionSpectrum

« on: January 21, 2016, 19:22 »

I've been trying to calculate the InelasticTransmissionSpectrum but get an error just when it gets to that very point (i.e. DynamicalMatrix & HamiltonianDerivatives calculations finish without errors).

Just when the output gets to this point:

+------------------------------------------------------------------------------+
| Calculating inelastic transmission spectrum                                  |
+------------------------------------------------------------------------------+
InelasticTransmissionSpectrum: k-index (1 / 1), q-index (1 / 1)

Calculation stops with the following error written to stderr:

mypath/QuantumWise/VNL-ATK-2015.1/bin/atkpython: line 11:  2949 Illegal instruction     $EXEC_DIR/atkpython_exec "$@"

Attached is the input file I'm using. I've tried using LOE instead of XLOE and using a DFT calculator. Also tried with an applied bias of 25mV. Same error every time. Can provide nc files if needed (too large to attach here)

Would someone please take a look see why I'm getting this? thanks in advance

12

General Questions and Answers / Re: About the nanowire builder

« on: December 10, 2015, 18:02 »

I read 2015.1 brings changes to the Wulff & nanowire constructors. Has the validity of the nanowire builder been fully checked now?

13

General Questions and Answers / Re: Parallel TransmissionSpectrum?

« on: October 29, 2015, 01:52 »

Got it to parallelise via threading anyway (mkl presumably). Was probably doing something wrong before.

14

General Questions and Answers / Threading

« on: October 27, 2015, 17:38 »

I noticed that in the latest release letter you advise regarding MKL_NUM_THREADS.

I know how to combine OMP_NUM_THREADS with MPI processes but haven't much experience with MKL_NUM_THREADS (just recently started using intel compilers).

An example: 24 core machine. Due to memory constraints let's say I want to run only 6 MPI processes. I would usually do something like:

export OMP_NUM_THREADS=4
mpirun -n 6 .....

As to use 6 threaded (4x) MPI processes. How would that work with MKL_NUM_THREADS as well?  Should I set OMP to 1 and MKL to 4? Any guidance is highly appreciated.

Thanks in advance.

15

General Questions and Answers / Parallel TransmissionSpectrum?

« on: October 27, 2015, 17:25 »

I thought I'd read something about ATK 2015 being able to parallelise TransmissionSpectrum calculations beyond the number of k-points / energy points? Now I can't find it so maybe I'm wrong.

In a calculation with a kpoint grid of (1,1), can one parallelise across more than energy points? e.g. If I'm calculating just the fermi level, can I parallelise that?

Thanks in advance