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Topics - AsifShah

Pages: [1] 2 3
1
General Questions and Answers / M3GNet error
« on: April 20, 2024, 21:21 »
Dear Admin,

When running M3GNet based molecular dynamics alongwith DZ3 correction as:

from tremolox.neighborlistcalculator.M3GNetCalculator import TremoloXM3GNetDirectPESCalculator
calculator_m3gnet = TremoloXM3GNetDirectPESCalculator(device='cpu')
calculator_d3 = TremoloXCalculator(parameters=DispersionD3Z(xc='PBE'))
calculator = CombinedCalculator([calculator_m3gnet,calculator_d3])

The simulations runs for sometime (few picoseconds) and then I get the following error:

TremoloXCalculator: Cart_create with procs 1 1 1 and periods 1 1 1 failed
Traceback (most recent call last):
  File "/home/Asif/QATK_V2023_12/quantumatk/V-2023.12/atkpython/bin/atkpython", line 8, in <module>
    sys.exit(__run_atkpython())
             ^^^^^^^^^^^^^^^^^
  File "zipdir/ATKExecutables/atkwrappers/__init__.py", line 780, in __run_atkpython
  File "VF_Multilayer_MoS2.py", line 406, in <module>
    md_trajectory = MolecularDynamics(
                    ^^^^^^^^^^^^^^^^^^
  File "zipdir/NL/Dynamics/MolecularDynamics/MolecularDynamics.py", line 1073, in MolecularDynamics
  File "zipdir/NL/Dynamics/MolecularDynamics/DynamicsEnergyForcesStress.py", line 30, in wrapped_analysis
  File "zipdir/NL/Calculators/DensityFunctionalTheory/LCAOCalculator/Analysis/FastEnergyForcesStress.py", line 46, in forcesFunction
  File "zipdir/NL/Calculators/DensityFunctionalTheory/LCAOCalculator/Analysis/FastEnergyForcesStress.py", line 72, in _checkAndUpdate
  File "zipdir/NL/Calculators/DensityFunctionalTheory/LCAOCalculator/Analysis/FastEnergyForcesStress.py", line 100, in _update
  File "zipdir/NL/CommonConcepts/Configurations/AtomicConfiguration.py", line 3080, in update
  File "zipdir/NL/Calculators/CombinedCalculator.py", line 373, in _update
  File "zipdir/NL/CommonConcepts/Configurations/AtomicConfiguration.py", line 3080, in update
  File "build/atkpython/lib/python3.11/site-packages/tremolox/neighborlistcalculator/neighborlistcalculator.py", line 467, in _update
  File "build/atkpython/lib/python3.11/site-packages/tremolox/TremoloBaseCalculator.py", line 501, in _update
  File "build/atkpython/lib/python3.11/site-packages/tremolox/calculation/calculation.py", line 311, in __init__
  File "build/atkpython/lib/python3.11/site-packages/tremolox/calculation/calculation.py", line 251, in wrapper
  File "build/atkpython/lib/python3.11/site-packages/tremolox/calculation/calculation.py", line 540, in _setSystem
  File "build/atkpython/lib/python3.11/site-packages/tremolox/pymolo_avx.py", line 813, in conf_data_domain
tremolox.RuntimeError: SomeError: Error in file /slowfs/qatkdev2/users/qatktest/de02vlbamboo06/exlibs/.conan/data/tremolox/2023.08/quantumatk/stable/build/0bd0f4ede5a9e99cf053738a382952d716d95ea1/src/comm.cpp, line 234 (0): SomeError: StartParallel: Cart_create failed

Kindly help in this regard.

2
General Questions and Answers / Implementing a new Reactive Forcefield
« on: March 30, 2024, 03:40 »
Dear Admin,
I am trying to implement a new MoS2 reactive forcefield file into my simulation. The method I use is as follows:

1. I send the configuration to workflow and then choose the forcefield calculator. Then, I choose some inbuilt forcefield and add an optimization block.
2. Then send it to editor with all details present.
3. Then change reactive forcefield parameters with new parameters.

But it shows error. I have attached the python file and as well as the reactive forcefield parameter file. Kindly look into the matter why simulations shows error "Segmentation fault- core dumped"

Thanks
Regards

3
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)

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 / 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?

6
General Questions and Answers / Bug/Error in using MoS2 StillingerWeber2017
« on: February 9, 2024, 06:52 »
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

7
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)
===================================================================================

8
General Questions and Answers / Settings LJ for Tags
« on: January 9, 2024, 02:54 »
Dear Admin,

I have an LJ potential curve for an interface with two materials (Tagged as 'L' and 'R'). I want to implement it in QuantumATK but it requires atom by atom interaction.

Is there a way to implement LJ potential for tags?

9
General Questions and Answers / M3GNET
« on: December 19, 2023, 13:35 »
Dear Admin,

How to access M3GNET in new QATK release V2023.12
I tried using forcefield block but it does not show M3GNET there?

10
General Questions and Answers / Error while designing Spatial Regions
« on: December 4, 2023, 04:43 »
Dear Admin,

I am trying to make a FET with multiple spatial regions, however, the QATK keeps shutting down while I am making spatial regions on an atomistic structure. Please see the attached image for errors and kindly provide a possible solution.

Thanks

11
General Questions and Answers / Is it possible to combine two forcefields?
« on: October 27, 2023, 04:50 »
Dear Admin,

Can I combine two reactive forcefields for two materials while using LJ potential between them?
Or can I combine reactive forcefield with any other forcefield such as tersoff, MTP etc for two materials while using LJ between them?


12
General Questions and Answers / Atoms going out of simulation box
« on: October 24, 2023, 05:55 »
Dear Admin/All,
I was running some heating simulations on gold. After it becomes amorphous at melting point the atoms move outside simulation box. how to avoid this? Though the atoms in MD trajectory dont go out of simulation box but when I send last trajectory to builder or viewer it goes outside box.
Please see attached images.

13
General Questions and Answers / Unusual computational issue with geometry optimization cycle
« on: October 20, 2023, 05:30 »
Dear Admin/All,
I am performing spin calculation on a system however, I observed something unusual. There have so far been 7 converged electronic cycles but only 5 geometry optimization steps have been performed. If I am not wrong, shouldn't each converged electronic cycle update atomic positions and hence both should be equal. Why is there this issue, please clarify. I have attached screenshot below as well.
1. grep OPT is used to see completed geometry steps = 5
2. fermi level is used to see completed electronic cycles = 7


Thanks
Regards

14
General Questions and Answers / Transmission with Different electrodes
« on: June 5, 2023, 11:15 »
Dear Admin,
I want to calculate zero-bias transmission with different electrodes. I am not an expert at Quantum Transport but will the transmission spectrum depend on the direction of transmission i.e from left to right electrode or right to left electrode?

And how does ATK calculate zero bias transmission?
And how to calculate transmission from left to right and right to left?

15
General Questions and Answers / DFT calcualtions using LCAO
« on: April 10, 2023, 14:07 »
Dear admin,

Are DFT calculations using ATK LCAO calculator reliable for interfaces between 2D materials such as WS2 and Gold?
I have seen some discrepancies between interfacial distances calculated from VASP using plane-wave and ATK using LCAO.


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