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Messages - AsifShah

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1
General Questions and Answers / M3GNet energies
« on: March 16, 2024, 08:08 »
Dear Admin,
When using M3GNet to calculate the total energy of a system the output shows nothing. Is it due to some bug?

Thanks
Here is the code:
# %% MoSe2

# Set up lattice
lattice = Hexagonal(3.288*Angstrom, 40.0*Angstrom)

# Define elements
elements = [Molybdenum, Selenium, Selenium]

# Define coordinates
fractional_coordinates = [[ 0.333333333333,  0.666666666667,  0.5           ],
                          [ 0.666666666667,  0.333333333333,  0.4583975     ],
                          [ 0.666666666667,  0.333333333333,  0.5416025     ]]

# Set up configuration
mose2 = BulkConfiguration(
    bravais_lattice=lattice,
    elements=elements,
    fractional_coordinates=fractional_coordinates
    )
mose2_name = "mose2"


# %% Set LCAOCalculator

from tremolox.neighborlistcalculator.M3GNetCalculator import TremoloXM3GNetDirectPESCalculator
calculator = TremoloXM3GNetDirectPESCalculator(device='cpu')


# %% Set Calculator

mose2.setCalculator(calculator)

mose2.update()

nlsave('TE.hdf5', mose2)


# %% TotalEnergy

total_energy = TotalEnergy(
    configuration=mose2
)
nlsave('TE.hdf5', total_energy)


2
General Questions and Answers / Re: Zero bias transmission
« on: March 13, 2024, 14:36 »
Thanks

3
Dear Ander Bloms,

Thanks for your response. I still have a doubt, when you say QATK includes the effects of all atoms, "Does that mean it takes account of an electron scattering from energy E1 to E2? In other words, if an electron is traveling with energy E1 from the electrode and encounters a scatterer in the central region taking it to energy E2, will such an event be included in the transmission calculated from QATK?"

4
General Questions and Answers / Zero bias transmission
« on: March 5, 2024, 17:26 »
Dear Admin,
Does zero bias transmission include scattering across an interface with defect or it is ballistic?

If ballistic, why am I observing an increase of transmission in conduction and valence bands with defect at interface with respect to pristine interface?

5
General Questions and Answers / Re: M3GNET
« on: February 20, 2024, 05:40 »
Dear Julian,

Can you kindly help in this regard?

Thanks

6
Hi,
In LCAO calculator u can choose hybrid under exchange-correlation as shown below in attached pic.

Thanks

7
General Questions and Answers / Re: M3GNET
« on: February 16, 2024, 10:29 »
Dear Julian,

I was trying to run M3GNet on windows 11, core i5 with 4 cores and 8 logical threads with GTX 1650 NVidia Graphics card having 1024 CUDA cores and 8 GB memory, Graphics boost clock 1560 MHz.

When running as atkpython input.py > output.log in CMD, I observed a 50% (from 1 hour to 30 mins) speed up in a certain MD simulation with 600 atoms (for 3 ps) on GPU using 'device=cuda'.
However, the output file shows following before starting MD run:
Enabled: False                                                               |
| Number of Domains: 1                                                         |
| Decomposition Pattern: 1x1x1                                                 |
| CPU Information:                                                             |
|  Process ID 0 at ASH (4 threads)


Is it possible to increase the number of threads (beyond 4) or how to properly utilize Cuda cores to see more speed up as my final system has 5K atoms?
Also, I have this doubt that if I am running on Cuda cores, shouldn't the number of threads be equal to the number of Cuda cores = 1024, instead log file shows only 4 threads = CPU cores? Furthermore,  I observed that GPU utilization was showing 0% when the simulation was running, though there was a 2x speedup.

Thanks

8
General Questions and Answers / Re: Query regarding GPU
« on: February 16, 2024, 03:06 »
Thanks for your response.


9
General Questions and Answers / Query regarding GPU
« on: February 15, 2024, 09:35 »
Dear Admin,
We plan to perform QATK calculations on GPU.
Are there any particular GPU specifications we should consider for running QATK before buying one?

10
Thanks it worked.

11
Dear Admin,

Please fix the bug/error when using StillingerWeber 2017:

Traceback (most recent call last):
  File "/home/user/QV/quantumatk/V-2023.09/bin/../atkpython/bin/atkpython", line 8, in <module>
    sys.exit(__run_atkpython())
             ^^^^^^^^^^^^^^^^^
  File "zipdir/ATKExecutables/atkwrappers/__init__.py", line 900, in __run_atkpython
  File "StillWeber2017.py", line 588, in <module>
    optimized_configuration = OptimizeGeometry(
                              ^^^^^^^^^^^^^^^^^
  File "zipdir/NL/Dynamics/Optimization/OptimizeGeometry.py", line 611, in OptimizeGeometry
  File "zipdir/NL/CommonConcepts/Configurations/AtomicConfiguration.py", line 3069, in update
  File "build/atkpython/lib/python3.11/site-packages/tremolox/TremoloBaseCalculator.py", line 499, in _update
  File "build/atkpython/lib/python3.11/site-packages/tremolox/calculation/calculation.py", line 303, in __init__
  File "build/atkpython/lib/python3.11/site-packages/tremolox/calculation/calculation.py", line 246, in wrapper
  File "build/atkpython/lib/python3.11/site-packages/tremolox/calculation/calculation.py", line 421, in _setPotentials
  File "build/atkpython/lib/python3.11/site-packages/tremolox/potentialsets/potentialsetbase.py", line 424, in _register
  File "build/atkpython/lib/python3.11/site-packages/tremolox/potentials/potentials.py", line 1880, in _register
  File "build/atkpython/lib/python3.11/site-packages/tremolox/potentials/potentials.py", line 1870, in _convertValues
  File "build/atkpython/lib/python3.11/site-packages/tremolox/potentials/checks.py", line 144, in apply
TypeError: The parameter B = 84.0315436536 Ang**4 must have a unit that can be converted to Ang**5.0.



Paper: M. Wen, S. N. Shirodkar, P. Plechá?, E. Kaxiras, R. S. Elliott, and E. B. Tadmor, A force-matching Stillinger-Weber potential for MoS2: Parameterization and Fisher information theory based sensitivity analysis, Journal of Applied Physics, 122, p. 244301, 2017.

Thanks

12
General Questions and Answers / Re: Error on Cluster
« on: February 9, 2024, 04:51 »
Dear Filipr,
Thanks for responding.

GPU Response:
1. When I run on single GPU core, it runs very well and gives output nicely. (See attached Au_MoS2.py file)
2. When I run on multiple GPU cores, it shows an error (See attached file Error.txt).
3. Also see the attached Au_MoS2.log file.
4. Also see attached cpuinfoo.txt

CPU Response:
1. When I run on single or  multiple CPU cores, the output file shows this:
[0] MPI startup(): Intel(R) MPI Library, Version 2021.8  Build 20221129 (id: 339ec755a1)
  • MPI startup(): Copyright (C) 2003-2022 Intel Corporation.  All rights reserved.
  • [0] MPI startup(): library kind: release
  • MPI startup(): libfabric version: 1.13.2rc1-impi


===================================================================================
=   BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES
=   RANK 0 PID 805 RUNNING AT ssdnode2
=   KILLED BY SIGNAL: 4 (Illegal instruction)
===================================================================================

===================================================================================
=   BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES
=   RANK 1 PID 806 RUNNING AT ssdnode2
=   KILLED BY SIGNAL: 4 (Illegal instruction)
===================================================================================

===================================================================================
=   BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES
=   RANK 2 PID 807 RUNNING AT ssdnode2
=   KILLED BY SIGNAL: 4 (Illegal instruction)
===================================================================================


13
Hi,
One approach is to test and verify it for your application as:
1. Optimize your material using this MTP and DFT and compare bond lengths, angles etc.
2. Run a small one atom movement NEB using MTP and DFT and compare results.

After verification, if you are using it for molecular dynamics make sure you verify/optimize all states of interest with DFT to check consistency.

14
Thanks for your response.

I am facing a convergence issue in non-zero bias transmission. I tried reducing pulay mixing, history steps but nothng is helping.
Can I have your email ID so that I can share my file?

15
General Questions and Answers / Error on Cluster
« on: February 2, 2024, 13:51 »
Dear Admin,

Any idea what is causing this error? QuantumATK version is latest one released in december 2023.V12.

I do not face any issue on previous version of QATK on same cluster.

===================================================================================
=   BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES
=   RANK 0 PID 181758 RUNNING AT node10
=   KILLED BY SIGNAL: 4 (Illegal instruction)
===================================================================================

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