1
General Questions and Answers / Re: Implementing a new Reactive Forcefield
« on: April 21, 2024, 03:11 »
Dear Admin,
Sure. Looking forward to your response.
Sure. Looking forward to your response.
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2
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.
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.
3
General Questions and Answers / Re: Implementing a new Reactive Forcefield
« on: April 10, 2024, 05:59 »
Dear Admin,
Kindly help in this regard.
Kindly help in this regard.
4
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
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
5
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)
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)
7
General Questions and Answers / Re: Zero bias transmission
« on: March 9, 2024, 10:55 »
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?"
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?"
8
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?
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?
9
General Questions and Answers / Re: M3GNET
« on: February 20, 2024, 05:40 »
Dear Julian,
Can you kindly help in this regard?
Thanks
Can you kindly help in this regard?
Thanks
10
General Questions and Answers / Re: Spin-polarized calculation with Hybrid Functional
« on: February 20, 2024, 05:38 »
Hi,
In LCAO calculator u can choose hybrid under exchange-correlation as shown below in attached pic.
Thanks
In LCAO calculator u can choose hybrid under exchange-correlation as shown below in attached pic.
Thanks
11
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
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
12
General Questions and Answers / Re: Query regarding GPU
« on: February 16, 2024, 03:06 »
Thanks for your response.
13
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?
We plan to perform QATK calculations on GPU.
Are there any particular GPU specifications we should consider for running QATK before buying one?
14
General Questions and Answers / Re: Bug/Error in using MoS2 StillingerWeber2017
« on: February 10, 2024, 18:47 »
Thanks it worked.
15
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
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