Messages

1

General Questions and Answers / Re: HybridSOGGA.HSE06 for device calculation showing error at central region

« on: August 21, 2023, 11:28 »

Yes, I agree that the calculations are fast, but what I'm concerned about is the results it is providing.

I have sent the input files through email. Please have a look.

Thank you,

Sumit

2

General Questions and Answers / Re: HybridSOGGA.HSE06 for device calculation showing error at central region

« on: August 18, 2023, 14:57 »

Dear Anders,

Thank you for your reply. I have tried to do the calculation in the 2022 version and the calculation ran without an error but the off-diagonal parts in the transmission matrix i.e. T(real-up-down) and T(imag-up-down) are zero. And weirdly it's printing the same values for T(up) and T(down). But the same system with LDA shows polarization in transmission: https://pubs.acs.org/doi/full/10.1021/acs.jpclett.2c03747, which reverses while we change the handedness of the helix. Could you please help me find out the problem?

Thank you,

Sumit

3

General Questions and Answers / HybridSOGGA.HSE06 for device calculation showing error at central region

« on: July 18, 2023, 15:40 »

Hi,

I was trying to test whether the noncolinear SOC along with hybrid functional is implemented in version 2021.06-SP2 using HybridSOGGA.HSE06 in the place of SOLDA.PZ (which ran perfectly). The calculation stopped while calculating the density matrices of the central region showing the error:

atkpython: /slowfs/qatkdev2/bamboo/de02vlbamboo10/bamboo-agent-home/xml-data/build-dir/QL-Q2-BLD/c++/src/physics/blocksparseatompairmatrix.cpp:361: BlockSparseAtomPairMatrix& BlockSparseAtomPairMatrix::operator+=(const BlockSparseAtomPairMatrix&): Assertion `spin_type_ == source.spinType()' failed.

My question would be if it's not implemented why it's only showing problems while doing the calculation of the central region why not the electrodes (attached the log file for your reference)?

P.S: Previously I have asked about the availability of the noncolinear SOC with hybrid functional for device calculation within the NEGF framework is available or not and got the reply from Ulrik that it would be implemented in the newer release. Could you please confirm if the error I'm getting is due to the non-implementation?

Waiting for your quick response!

Thank you,

Sumit

4

General Questions and Answers / Re: Use of Hybrid functional in device calculation with spin-orbit interaction

« on: July 17, 2023, 14:22 »

Dear Ulrik,

Is the hybrid functional with spin-orbit coupling implemented for device calculation in the new release? I'm using quantumatk/2021.06-SP2 where it is not implemented. Did you implement it in the newer version?

Please let me know.

Regards,

Sumit

5

General Questions and Answers / Spin flip components of transmission function

« on: April 29, 2022, 13:16 »

Hi,

I was wondering if it is possible to print the 'DownUp' component of the transmission function while doing the non-collinear spin-orbit calculation of a molecular junction?

As from the output, only the 'Up,' 'Down,' 'Re(UpDown),' and 'Im(UpDown)' components are returned by the program, whereas the 'UpDown' components are spin-flip components, but there should be 'DownUp' component as well. My question: is it possible to print 'Re(DownUp)' and 'Im(DownUp)' components in the same spirit as the previous spin-flip components returned by the program?

Any help/comment will be highly appreciated.

Thanks

Sumit

6

General Questions and Answers / Re: How can I print Hamiltonian and overlap matrix for a molecular junction device?

« on: April 8, 2022, 16:56 »

Hi,

I wanted to plot the Im(H), which will sufficiently modify with spin-orbit calculations ( I mean, there will be more non-trivial terms at the off-diagonal, including spin-orbit interactions)...

I needed the whole matrix, but the format is not so straightforward; I want the matrix in square form. Is there some way to do that? Any help is very much appreciated.

Thank you

Sumit

7

General Questions and Answers / Re: How can I print Hamiltonian and overlap matrix for a molecular junction device?

« on: April 6, 2022, 13:12 »

Hi Anders,

Adding:

print('Hamiltonian : ', hamiltonian)
print('Overlap : ', overlap)
print('')

I'm able to print the Hamiltonian and Overlap for each SCF cycle. I have added the output below.

Thank You

Sumit



| Calculation Converged in 13 steps                                            |
|                                                                              |
| Fermi Level  = -3.889050 eV                                                  |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
|                                                                              |
| DFT Calculation  [Finished Wed Apr  6 12:59:52 2022]                         |
|                                                                              |
+------------------------------------------------------------------------------+


Hamiltonian :  [[-3.59032220e-01-1.29056719e-20j  3.46412440e-12-1.21667632e-12j
   8.17982219e-02+1.44061808e-20j ... -7.19852035e-08-4.70211730e-09j
   8.39974836e-02-1.84622872e-09j  9.38259570e-08+3.90192286e-09j]
 [ 3.46412440e-12+1.21667632e-12j -3.59029030e-01+1.29056719e-20j
   4.45180078e-12+1.09713035e-12j ... -7.54532144e-02-4.43759714e-09j
  -9.37885388e-08+3.89844158e-09j  8.39971402e-02+1.84622872e-09j]
 [ 8.17982219e-02-1.44061808e-20j  4.45180078e-12-1.09713035e-12j
   4.59094866e-01-6.82920960e-21j ...  1.76589278e-07+1.09730678e-08j
  -9.22280117e-03-9.46961721e-09j -6.39674337e-08-1.41767968e-09j]
 ...
 [-7.19852035e-08+4.70211730e-09j -7.54532144e-02+4.43759714e-09j
   1.76589278e-07-1.09730678e-08j ... -4.35606266e-02-2.56545139e-24j
  -6.43143228e-07-6.79178074e-10j -1.48253265e-03-3.49468552e-08j]
 [ 8.39974836e-02+1.84622872e-09j -9.37885388e-08-3.89844158e-09j
  -9.22280117e-03+9.46961721e-09j ... -6.43143228e-07+6.79178074e-10j
   1.46149708e-01-3.67281117e-22j -1.01890544e-12-6.57268857e-13j]
 [ 9.38259570e-08-3.90192286e-09j  8.39971402e-02-1.84622872e-09j
  -6.39674337e-08+1.41767968e-09j ... -1.48253265e-03+3.49468552e-08j
  -1.01890544e-12+6.57268857e-13j  1.46155125e-01+3.67281117e-22j]] Hartree
Overlap :  [[ 9.99999999e-01+0.j  0.00000000e+00+0.j -8.47863236e-10+0.j ...
   0.00000000e+00+0.j -1.51349581e-01+0.j  0.00000000e+00+0.j]
 [ 0.00000000e+00+0.j  9.99999999e-01+0.j  0.00000000e+00+0.j ...
   8.94296345e-02+0.j  0.00000000e+00+0.j -1.51349581e-01+0.j]
 [-8.47863236e-10+0.j  0.00000000e+00+0.j  1.00000000e+00+0.j ...
   0.00000000e+00+0.j  1.89803809e-01+0.j  0.00000000e+00+0.j]
 ...
 [ 0.00000000e+00+0.j  8.94296345e-02+0.j  0.00000000e+00+0.j ...
   9.99999997e-01+0.j  0.00000000e+00+0.j  0.00000000e+00+0.j]
 [-1.51349581e-01+0.j  0.00000000e+00+0.j  1.89803809e-01+0.j ...
   0.00000000e+00+0.j  9.99999997e-01+0.j  0.00000000e+00+0.j]
 [ 0.00000000e+00+0.j -1.51349581e-01+0.j  0.00000000e+00+0.j ...
   0.00000000e+00+0.j  0.00000000e+00+0.j  9.99999997e-01+0.j]]

......................................

Hamiltonian :  [[-3.59032220e-01-1.29056719e-20j  3.46412440e-12-1.21667632e-12j
   8.17982219e-02+1.44061808e-20j ... -7.19852035e-08-4.70211730e-09j
   8.39974836e-02-1.84622872e-09j  9.38259570e-08+3.90192286e-09j]
 [ 3.46412440e-12+1.21667632e-12j -3.59029030e-01+1.29056719e-20j
   4.45180078e-12+1.09713035e-12j ... -7.54532144e-02-4.43759714e-09j
  -9.37885388e-08+3.89844158e-09j  8.39971402e-02+1.84622872e-09j]
 [ 8.17982219e-02-1.44061808e-20j  4.45180078e-12-1.09713035e-12j
   4.59094866e-01-6.82920960e-21j ...  1.76589278e-07+1.09730678e-08j
  -9.22280117e-03-9.46961721e-09j -6.39674337e-08-1.41767968e-09j]
 ...
 [-7.19852035e-08+4.70211730e-09j -7.54532144e-02+4.43759714e-09j
   1.76589278e-07-1.09730678e-08j ... -4.35606266e-02-2.56545139e-24j
  -6.43143228e-07-6.79178074e-10j -1.48253265e-03-3.49468552e-08j]
 [ 8.39974836e-02+1.84622872e-09j -9.37885388e-08-3.89844158e-09j
  -9.22280117e-03+9.46961721e-09j ... -6.43143228e-07+6.79178074e-10j
   1.46149708e-01-3.67281117e-22j -1.01890544e-12-6.57268857e-13j]
 [ 9.38259570e-08-3.90192286e-09j  8.39971402e-02-1.84622872e-09j
  -6.39674337e-08+1.41767968e-09j ... -1.48253265e-03+3.49468552e-08j
  -1.01890544e-12+6.57268857e-13j  1.46155125e-01+3.67281117e-22j]] Hartree
Overlap :  [[ 9.99999999e-01+0.j  0.00000000e+00+0.j -8.47863236e-10+0.j ...
   0.00000000e+00+0.j -1.51349581e-01+0.j  0.00000000e+00+0.j]
 [ 0.00000000e+00+0.j  9.99999999e-01+0.j  0.00000000e+00+0.j ...
   8.94296345e-02+0.j  0.00000000e+00+0.j -1.51349581e-01+0.j]
 [-8.47863236e-10+0.j  0.00000000e+00+0.j  1.00000000e+00+0.j ...
   0.00000000e+00+0.j  1.89803809e-01+0.j  0.00000000e+00+0.j]
 ...
 [ 0.00000000e+00+0.j  8.94296345e-02+0.j  0.00000000e+00+0.j ...
   9.99999997e-01+0.j  0.00000000e+00+0.j  0.00000000e+00+0.j]
 [-1.51349581e-01+0.j  0.00000000e+00+0.j  1.89803809e-01+0.j ...
   0.00000000e+00+0.j  9.99999997e-01+0.j  0.00000000e+00+0.j]
 [ 0.00000000e+00+0.j -1.51349581e-01+0.j  0.00000000e+00+0.j ...
   0.00000000e+00+0.j  0.00000000e+00+0.j  9.99999997e-01+0.j]]

Hamiltonian :  [[-3.59032220e-01-1.29056719e-20j  3.46412440e-12-1.21667632e-12j
   8.17982219e-02+1.44061808e-20j ... -7.19852035e-08-4.70211730e-09j
   8.39974836e-02-1.84622872e-09j  9.38259570e-08+3.90192286e-09j]
 [ 3.46412440e-12+1.21667632e-12j -3.59029030e-01+1.29056719e-20j
   4.45180078e-12+1.09713035e-12j ... -7.54532144e-02-4.43759714e-09j
  -9.37885388e-08+3.89844158e-09j  8.39971402e-02+1.84622872e-09j]
 [ 8.17982219e-02-1.44061808e-20j  4.45180078e-12-1.09713035e-12j
   4.59094866e-01-6.82920960e-21j ...  1.76589278e-07+1.09730678e-08j
  -9.22280117e-03-9.46961721e-09j -6.39674337e-08-1.41767968e-09j]
 ...
 [-7.19852035e-08+4.70211730e-09j -7.54532144e-02+4.43759714e-09j
   1.76589278e-07-1.09730678e-08j ... -4.35606266e-02-2.56545139e-24j
  -6.43143228e-07-6.79178074e-10j -1.48253265e-03-3.49468552e-08j]
 [ 8.39974836e-02+1.84622872e-09j -9.37885388e-08-3.89844158e-09j
  -9.22280117e-03+9.46961721e-09j ... -6.43143228e-07+6.79178074e-10j
   1.46149708e-01-3.67281117e-22j -1.01890544e-12-6.57268857e-13j]
 [ 9.38259570e-08-3.90192286e-09j  8.39971402e-02-1.84622872e-09j
  -6.39674337e-08+1.41767968e-09j ... -1.48253265e-03+3.49468552e-08j
  -1.01890544e-12+6.57268857e-13j  1.46155125e-01+3.67281117e-22j]] Hartree
Overlap :  [[ 9.99999999e-01+0.j  0.00000000e+00+0.j -8.47863236e-10+0.j ...
   0.00000000e+00+0.j -1.51349581e-01+0.j  0.00000000e+00+0.j]
 [ 0.00000000e+00+0.j  9.99999999e-01+0.j  0.00000000e+00+0.j ...
   8.94296345e-02+0.j  0.00000000e+00+0.j -1.51349581e-01+0.j]
 [-8.47863236e-10+0.j  0.00000000e+00+0.j  1.00000000e+00+0.j ...
   0.00000000e+00+0.j  1.89803809e-01+0.j  0.00000000e+00+0.j]
 ...
 [ 0.00000000e+00+0.j  8.94296345e-02+0.j  0.00000000e+00+0.j ...
   9.99999997e-01+0.j  0.00000000e+00+0.j  0.00000000e+00+0.j]
 [-1.51349581e-01+0.j  0.00000000e+00+0.j  1.89803809e-01+0.j ...
   0.00000000e+00+0.j  9.99999997e-01+0.j  0.00000000e+00+0.j]
 [ 0.00000000e+00+0.j -1.51349581e-01+0.j  0.00000000e+00+0.j ...
   0.00000000e+00+0.j  0.00000000e+00+0.j  9.99999997e-01+0.j]]

Hamiltonian :  [[-3.59032220e-01-1.29056719e-20j  3.46412440e-12-1.21667632e-12j
   8.17982219e-02+1.44061808e-20j ... -7.19852035e-08-4.70211730e-09j
   8.39974836e-02-1.84622872e-09j  9.38259570e-08+3.90192286e-09j]
 [ 3.46412440e-12+1.21667632e-12j -3.59029030e-01+1.29056719e-20j
   4.45180078e-12+1.09713035e-12j ... -7.54532144e-02-4.43759714e-09j
  -9.37885388e-08+3.89844158e-09j  8.39971402e-02+1.84622872e-09j]
 [ 8.17982219e-02-1.44061808e-20j  4.45180078e-12-1.09713035e-12j
   4.59094866e-01-6.82920960e-21j ...  1.76589278e-07+1.09730678e-08j
  -9.22280117e-03-9.46961721e-09j -6.39674337e-08-1.41767968e-09j]
 ...
 [-7.19852035e-08+4.70211730e-09j -7.54532144e-02+4.43759714e-09j
   1.76589278e-07-1.09730678e-08j ... -4.35606266e-02-2.56545139e-24j
  -6.43143228e-07-6.79178074e-10j -1.48253265e-03-3.49468552e-08j]
 [ 8.39974836e-02+1.84622872e-09j -9.37885388e-08-3.89844158e-09j
  -9.22280117e-03+9.46961721e-09j ... -6.43143228e-07+6.79178074e-10j
   1.46149708e-01-3.67281117e-22j -1.01890544e-12-6.57268857e-13j]
 [ 9.38259570e-08-3.90192286e-09j  8.39971402e-02-1.84622872e-09j
  -6.39674337e-08+1.41767968e-09j ... -1.48253265e-03+3.49468552e-08j
  -1.01890544e-12+6.57268857e-13j  1.46155125e-01+3.67281117e-22j]] Hartree
Overlap :  [[ 9.99999999e-01+0.j  0.00000000e+00+0.j -8.47863236e-10+0.j ...
   0.00000000e+00+0.j -1.51349581e-01+0.j  0.00000000e+00+0.j]
 [ 0.00000000e+00+0.j  9.99999999e-01+0.j  0.00000000e+00+0.j ...
   8.94296345e-02+0.j  0.00000000e+00+0.j -1.51349581e-01+0.j]
 [-8.47863236e-10+0.j  0.00000000e+00+0.j  1.00000000e+00+0.j ...
   0.00000000e+00+0.j  1.89803809e-01+0.j  0.00000000e+00+0.j]
 ...
 [ 0.00000000e+00+0.j  8.94296345e-02+0.j  0.00000000e+00+0.j ...
   9.99999997e-01+0.j  0.00000000e+00+0.j  0.00000000e+00+0.j]
 [-1.51349581e-01+0.j  0.00000000e+00+0.j  1.89803809e-01+0.j ...
   0.00000000e+00+0.j  9.99999997e-01+0.j  0.00000000e+00+0.j]
 [ 0.00000000e+00+0.j -1.51349581e-01+0.j  0.00000000e+00+0.j ...
   0.00000000e+00+0.j  0.00000000e+00+0.j  9.99999997e-01+0.j]]

8

General Questions and Answers / Re: How can I print Hamiltonian and overlap matrix for a molecular junction device?

« on: April 6, 2022, 12:41 »

Hi Anders,

Thank you for your response.

I tried to print those matrices for simple molecule_configuration (Benzene), but I didn't find anything. I have attached the input file; please suggest where I'm making a mistake.

Thanks

Sumit

9

General Questions and Answers / How can I print Hamiltonian and overlap matrix for a molecular junction device?

« on: April 4, 2022, 17:18 »

Hi,

While doing device NEGF-DFT calculation, is it possible to print the Hamiltonian and Overlap matrices?

Please suggest how to print/extract them from a converged NEGF-DFT calculation.

I really appreciate any help you can provide.

Sumit

10

General Questions and Answers / Re: Use of Hybrid functional in device calculation with spin-orbit interaction

« on: September 17, 2021, 10:43 »

Hi Ulrik,

Thanks for your information.

Waiting for the next release soon!

Thanks again

Sumit

11

General Questions and Answers / Use of Hybrid functional in device calculation with spin-orbit interaction

« on: September 16, 2021, 14:03 »

Hi,

I was trying to calculate IV characteristics for molecular junction in LCAO calculator, the spin-orbit coupling (non-collinear) is implemented in the LCAO calculator for pure functional. My question is it possible to do transport calculation with spin-orbit coupling in molecular junction with hybrid functional like HSE06? Because when I'm selecting hybrid functional calculation the calculator is automatically changed itself to the Unpolarized configuration. Is there any way out or I'm making something conceptually very wrong?

Waiting for your quick response!

Thank You

Sumit

12

General Questions and Answers / Zero Bias Transmission

« on: June 9, 2021, 13:49 »

While calculating transmission at zero bias in a molecular junction device, is it required to consider the whole DFT-NEGF cycle? As per my knowledge, the non-equilibria is the consequence of bias voltage (non-linear regime). At 0 bias (equilibrium), the transmission coefficient can be calculated from the equilibrium part of the density matrices; the non-equilibrium part of the density matrices will be zero. Is it possible to consider only the DFT cycle without NEGF formalism to calculate transmission at 0 bias? However, the DFT-NEGF considers integration over both equilibrium and non-equilibrium density matrices.

Looking forward to your response/comments...

Thanks

Sumit

13

General Questions and Answers / Re: Optimization of device central region

« on: June 4, 2021, 15:20 »

But the extended molecules already consider the slabs from the electrodes... Is it possible to consider only the molecule as the central region and not the extended molecule (molecule+slabs of electrodes)?

14

General Questions and Answers / Re: Optimization of device central region

« on: June 4, 2021, 09:26 »

Dear All,

I was trying to make a molecular junction in which the central region only consists of organic molecules, not the layers of metallic electrodes. However, as in ATK, the central region has to be the same or greater than the total size (left+right) of the electrodes; the central region always considers some layers of the electrodes. Is it possible to consider the only molecule as the central region to see the effects coming only from the molecule? However, electrodes may induce some effects on the molecule, but considering some metallic layers inside will definitely affect the results, what is your take on this?

Thanks
Sumit