Messages

1

Installation and License Questions / Re: Installing QuantumATK-U-2022.12-Linux64.bin

« on: June 8, 2023, 17:43 »

Removing the line 'module load PE-intel' from the script settled the issue.
Thanks so much,

Frank

2

Installation and License Questions / Re: Installing QuantumATK-U-2022.12-Linux64.bin

« on: June 7, 2023, 17:17 »

Thanks for your instructions - I deinstalled the earlier version of  QuantumATK-U-2022.12  and followed your description when installing QuantumATK-U-2022.12-SP1.

Here is my test script:

#!/bin/bash
#SBATCH --nodes 1
#SBATCH --ntasks-per-node 8
#SBATCH --cpus-per-task 1
#SBATCH --exclusive
#SBATCH --mem=50g
#SBATCH -p batch
#SBATCH -A cnms
#SBATCH -t 4:00:00

module load PE-intel
export SNPSLMD_LICENSE_FILE="27020@151.141.244.36"

/home/fhagelberg/QuantumATK/QuantumATK-U-2022.12-SP1/mpi/bin/mpiexec.hydra -n 1 /home/fhagelberg/QuantumATK/QuantumATK-U-2022.12-SP1/atkpython/bin/atkpython Fgraphene-half-spinit-lower-edge.py > Fgraphene-half-spinit-lower-edge.log
#END

Once more, the job fails with an error message:

Traceback (most recent call last):
  File "/home/fhagelberg/QuantumATK/QuantumATK-U-2022.12-SP1/atkpython/bin/atkpython", line 8, in <module>
    sys.exit(__run_atkpython())
  File "zipdir/ATKExecutables/atkwrappers/__init__.py", line 837, in __run_atkpython
  File "<frozen zipimport>", line 281, in load_module
  File "zipdir/NL/__init__.py", line 13, in <module>
  File "zipdir/NL/ATKLicenseHelpers.py", line 193, in atkpythonLicenseCheck
  File "zipdir/NL/ATKLicenseHelpers.py", line 167, in atkpythonLicenseCheck
  File "<frozen zipimport>", line 281, in load_module
  File "zipdir/NLEngine.py", line 21, in <module>
ImportError: /software/tools/compilers/intel/compilers_and_libraries_2016.1.150/linux/mpi/intel64/lib/libmpifort.so.12: undefined symbol: MPI_UNWEIGHTED

I submitted the installbuilder file in a separate post. Please let me know about any other relevant information I could supply.
 
Frank

3

Installation and License Questions / Re: Installing QuantumATK-U-2022.12-Linux64.bin

« on: June 7, 2023, 17:08 »

It seems that the installbuilder file was not attached to my previous post. According to the response, there was a size problem. This is strange since the file was within the specified size limits (and had one of the allowed extensions (log)). Anyway, I try again - this time, I submit the file in three portions.

4

Installation and License Questions / Installing QuantumATK-U-2022.12-Linux64.bin

« on: June 2, 2023, 23:34 »

I'm reaching out with a question related to QuantumATK-U-2022.12-Linux64.bin.  I installed this version on the CADES-Machines at Oak Ridge National Laboratories (ORNL), but I fail when trying to run batch jobs with it.

At the same time, I am successful running the earlier version, QuantumATK-T-2022.03-Linux64.bin, on CADES. Here is an example for a working  QuantumATK-T-2022.03-Linux64.bin submission script:

#!/bin/bash
#SBATCH --nodes 3
#SBATCH --ntasks-per-node 16
#SBATCH --cpus-per-task 1
#SBATCH --exclusive
#SBATCH --mem=50g
#SBATCH -p batch
#SBATCH -A cnms
#SBATCH -t 48:00:00

module load PE-intel
export SNPSLMD_LICENSE_FILE="27020@151.141.244.36"

/home/fhagelberg/QuantumATK/QuantumATK-T-2022.03/libexec/mpiexec.hydra -n 3 /home/fhagelberg/QuantumATK/QuantumATK-T-2022.03//bin/atkpython bias_run_AFM_0.4_gate_polarized-b.py > bias_run_AFM_0.4_gate_polarized-b.log
#END


Here is a submission script I used to test QuantumATK-U-2022.12-Linux64.bin:

#!/bin/bash
#SBATCH --nodes 1
#SBATCH --ntasks-per-node 2
#SBATCH --cpus-per-task 1
#SBATCH --exclusive
#SBATCH --mem=50g
#SBATCH -p batch
#SBATCH -A cnms
#SBATCH -t 4:00:00

module load PE-intel
export SNPSLMD_LICENSE_FILE="27020@151.141.244.36"

/home/fhagelberg/QuantumATK-U/QuantumATK-U-2022.12/mpi/bin/mpiexec.hydra -n 1 /home/fhagelberg/QuantumATK-U/QuantumATK-U-2022.12/atkpython/bin/atkpython MoSe2_H_AFM.py > MoSe2_H_AFM-b.log
#END

This script fails, with the following error message:

/home/fhagelberg/QuantumATK-U/QuantumATK-U-2022.12/atkpython/bin/atkpython: line 2: /slowfs/qatkdev2/bamboo/de02vlbamboo20/bamboo-agent-home/xml-data/build-dir/quantumsource/application/build/atkpython/bin/python: No such file or directory

I also want to mention that, installing  QuantumATK-U-2022.12-Linux64.bin on CADES, I received a success message, but also a note that said "Cannot install wrappers".

Would you have some advice on what to change in my QuantumATK-U-2022.12-Linux64.bin script?

I add that the technical staff of CADES could not help me with this. I sent this question two times to Synopsys Support  - for which I qualify - but did not receive any answer -  I'm hoping for better luck with the QuantumATK forum.

5

General Questions and Answers / Eliminating spatial regions when viewing results?

« on: April 6, 2023, 21:37 »

Some of my QuantumATK calculations involve gate fields. These require defining spatial regions, as shown in the attached picture. When analyzing the result files in the Viewer, I often find that important details of the structure are blocked from sight by the white sheets that mark the spatial regions. Is there a way to get rid of these sheets in the Viewer?

Thanks,
Frank

6

General Questions and Answers / HartreeDifferencePotential - spin projection

« on: December 22, 2021, 18:06 »

I'd like to compute spin projections of the Hartree Difference Potential, specifically projections on spin-up/spin-down populations, and the difference between both. Could you suggest a script that would achieve this? I have access to QuantumATK S-2021.06. Thanks!

7

General Questions and Answers / Re: Rashba effect

« on: September 23, 2020, 00:44 »

Thank you, Troels - I haven't been on the Quantum-ATK forum in a while and found your response only today. It seems plausible that the spins see the screened electric field. I'll continue using the non-collinear approach to explore Rashba interactions.

Regards,
Frank

8

General Questions and Answers / Rashba effect

« on: July 16, 2020, 18:55 »

Hello - I have a question  about the extent to which the Rashba effect can be included in transport computations with ATK (version 2018.6 or higher).  While there are various versions of the Rashba effect, I want to understand this effect broadly as the interaction of an electron spin with an electric field applied in a direction perpendicular to the electron momentum. To a degree, such an interaction is certainly represented in ATK.  If we  expose a device to a perpendicular electric field and allow for non-collinear spins, we'll calculate the impact of the electrically modified device on the spins of the electrons traversing the device.  I'd like to find out if ATK includes, in addition, the interaction between the electron spins and the screened perpendicular electric field (which one might describe by a Hamiltonian of the form H_R ~ -\sigma . (p X E/2 m), with sigma as the array of spin matrices, p as the electron momentum, and E as the electric field).

Thanks,
Frank

9

General Questions and Answers / Re: Back engine exception - memory

« on: May 14, 2020, 19:00 »

Thank you, Anders - it looks like the answer to my second question was right in front of my eyes. I'm now experimenting with the memory-usage estimator which indeed seems to be a very direct way to get an initial memory guess.
As to my attempted spin-orbit calculation: if I understand correctly, the PseudoDojo potential is not available for spin-orbit jobs in the ATK/VNL 2018.6 release, the version that I'm using right now.  Comparing the available options (SG15 versus OMX) in terms of memory, I find that OMX makes substantially lower demands than SG15.

Thanks again,
Frank

10

General Questions and Answers / Back engine exception - memory

« on: May 12, 2020, 17:57 »

Hello,

I struggle with memory restrictions when running device jobs. Two questions in this context:

(1) When trying to run a spin-orbit calculation involving a device (SOGGA, OMX - please see attached .py file), I came in conflict with machine memory caps. I consulted online advice on how to reduce the memory demands of my job (e.g.  https://docs.quantumatk.com/technicalnotes/advanced_performance/advanced_performance.html) and implemented what I found (see the Device Algorithm Settings block in the attached .py file). In this case, I received an error message that I couldn't decipher:

"Calculating Density Matrix :
** Back Engine Exception : info is nonzero
** Location of Exception : greensfunctioncalculator.cpp:843"
(see the attached output file)

This probably has to do with some erroneous algorithm settings. Could you give me some advice on this?

(2) Is there some way to determine the overall memory required by an ATK job? This would be extremely helpful. It happens very often that I start a job successfully, just to find it terminated with a memory error after many hours of running time.

Thanks,
Frank Hagelberg

11

General Questions and Answers / Re: VNL crashes - problems with Builder

« on: September 9, 2019, 16:29 »

Thanks, I will do this.

12

General Questions and Answers / Re: VNL crashes - problems with Builder

« on: September 9, 2019, 14:39 »

Any arbitrary file I try to load into the Builder.
I 've been using the Builder for files with extension *.py and *.hdf5. Any .py or .hdf5 file gives rise to a crash of the Builder.

Thanks,
Frank

13

General Questions and Answers / VNL crashes - problems with Builder

« on: September 8, 2019, 21:51 »

Dear Sir/Madam

Here's my problem: whenever I load any file into Builder, VNL crashes.
This does not happen when I use the Builder Plugin option. In this case, the chosen structure appears in the Builder window, and I can manipulate it using the Builder tools. However, when I try to load a second structure from the Plugin menu into the Builder, I get an error message (attached: Error1).
Also, trying to close Builder yields an error message (attached: Error2).

I'm using QuantumATK 2018.06. The operating system of my computer is Windows 7 Enterprise.
I installed QuantumATK 2018.06 one year ago and until now did not encounter any problems related to Builder. I checked if some destructive interference with recent computer updates could be at the root of the sudden trouble. This does not seem to be the case.

I realize that there is some material on VNL crashes due to Builder on this forum, but I did not find anything that obviously speaks to the problem at hand.

Thanks,
Frank

14

General Questions and Answers / Re: QuantumATK-2018,convergence problems

« on: November 21, 2018, 17:11 »

Hi Ulrik,

Thanks for the quick response. I ran a first test, and the outcome suggests that indeed, making FHI-DZP the pseudopotential-basis set choice in ATK-2018 takes care of the unphysical states.

Frank

15

General Questions and Answers / QuantumATK-2018,convergence problems

« on: November 19, 2018, 17:59 »

Hello,
I have a question related to QuantumATK-2018. Enclosed is an input file (aGNR-2Fe….) for a device calculation involving an armchair graphene nanoribbon (aGNR) with substitutional Fe atoms. This is part of a follow-up project of an earlier study on the spin-filtering efficiency of aGNRs with embedded transition metal impurities (F. Hagelberg, A.Kaiser, I.Sukuba, M. Probst, Mol. Phys. 115, 2231 (2017)). The earlier work was done with ATK-2015. Trying to reproduce some of the previous results with QuantumATK-2018, I fail completely. The atomic populations seem to oscillate between a physically reasonable state and an unphysical state that includes extremely high atomic populations at the ends of the central region. I enclose the output file corresponding (atkjob-aGNR-2Fe…I reduced the size a bit) for illustration (see, for instance, the last population block in that file). I tried to attain convergence by varying the DFT methd (i.e. GGA versus LDA, DFT+U) as well as the exchange-correlation functional, but this didn’t improve the erroneous output. Are there some critical DFT-related features in QuantumATK-2018 that were not present in ATK-2015, and that I possibly mishandle?

Thanks,
Frank Hagelberg