Topics

1

General Questions and Answers / License limit

« on: August 12, 2025, 19:55 »

Hello,
how exactly license consumption is counted for QuantumATK jobs. From user experience, the license usage does not scale linearly with -n in the MPI command.
For instance, I’ve submitted jobs using --nodes=1 to --nodes=4 (sometimes 6 too) and corresponding values like -n 40, -n 80, and even -n 160, and they’ve often run without any license-related errors.
This makes it difficult to determine in advance how many licenses a job will actually consume. But sometimes I got the instructions from the IT admin that I used more than 100 Licenses (with the same setting of submission script). Below is the submission script we use for submitting jobs in our local cluster.
#!/bin/bash
# Job name
#SBATCH --job-name hse_sc

#SBATCH --nodes=1                       # Number of nodes
#SBATCH --ntasks-per-node=40              # How many tasks on each node
##SBATCH --cpus-per-task=20
#SBATCH --time=72:00:00
#SBATCH --exclusive
#Export all environment variables
#SBATCH --export=ALL


# Load the QuantumATK module

# Load the QuantumATK module
module use /n/work00/software/modulefiles
module load puck_quantumatk/2023.12-sp1


# Set the executables
export ATK_EXE=/n/work00/software/quantumatk/V-2023.12-SP1/bin/atkpython
export MPI_EXE=/n/work00/software/quantumatk/V-2023.12-SP1/mpi/bin/mpiexec.hydra
export SNPSLMD_LICENSE_FILE=27027@acme

#export MKL_DYNAMIC=TRUE


# Threading
#export OMP_NUM_THREADS=2             
export MKL_DYNAMIC=TRUE



${MPI_EXE} -n 12 ${ATK_EXE} optical_spectrum.py > optical_doped.log

2

General Questions and Answers / Phonon dispersion is senstitive to "processes_per_displacement" paramter of DM?

« on: March 18, 2024, 14:55 »

Hi,
I calculated the graphene phonon dispersion spectrum using the following script:

Code

# -------------------------------------------------------------
# Bulk Configuration
# -------------------------------------------------------------

# Set up lattice
lattice = Hexagonal(2.4612*Angstrom, 30.0*Angstrom)

# Define elements
elements = [Carbon, Carbon]

# Define coordinates
fractional_coordinates = [[ 0.333333333333,  0.6666666666     ,  0.5           ],
                          [ 0.666666666666,  0.3333333333  ,  0.5           ]]

# Set up configuration
bulk_configuration = BulkConfiguration(
    bravais_lattice=lattice,
    elements=elements,
    fractional_coordinates=fractional_coordinates
    )


# -------------------------------------------------------------
# Calculator
# -------------------------------------------------------------
#----------------------------------------
# Basis Set
#----------------------------------------
basis_set = [
    GGABasis.Carbon_DoubleZetaPolarized,
    ]
#----------------------------------------
# Exchange-Correlation
#----------------------------------------
exchange_correlation = SGGA.PBE

k_point_sampling = MonkhorstPackGrid(
    na=51,
    nb=51,
    )
numerical_accuracy_parameters = NumericalAccuracyParameters(
    density_mesh_cutoff=110.0*Hartree,
    k_point_sampling=k_point_sampling,
    occupation_method=FermiDirac(0.05*eV),

    )
poisson_solver = FastFourier2DSolver(
    boundary_conditions=[[PeriodicBoundaryCondition(),PeriodicBoundaryCondition()],
                         [PeriodicBoundaryCondition(),PeriodicBoundaryCondition()],
                         [DirichletBoundaryCondition(),DirichletBoundaryCondition()]]
    )
iteration_control_parameters = IterationControlParameters(
 tolerance=1e-08,
 max_steps=10000,
 )
  

calculator = LCAOCalculator(
    exchange_correlation=exchange_correlation,
    numerical_accuracy_parameters=numerical_accuracy_parameters,
    poisson_solver=poisson_solver,
    iteration_control_parameters=iteration_control_parameters,
    )

bulk_configuration.setCalculator(calculator)
nlprint(bulk_configuration)
bulk_configuration.update()
nlsave('gr_mp_fhi_dzp.hdf5', bulk_configuration)


## -------------------------------------------------------------
## Optimize Geometry
## -------------------------------------------------------------  
 
   
bulk_configuration = OptimizeGeometry(
bulk_configuration,
max_forces=0.0001*eV/Ang,
max_stress=1.0e-04*eV/Angstrom**3,
max_steps=20000,
max_step_length=0.4*Ang,
optimize_cell=True,
trajectory_filename=None,
optimizer_method=LBFGS(),
enable_optimization_stop_file=False,
)
bulk_configuration.update()
nlsave('gr_mp_fhi_dzp.hdf5', bulk_configuration)
nlprint(bulk_configuration)



bulk_configuration = nlread('gr_mp_fhi_dzp.hdf5', BulkConfiguration)[1]
# -------------------------------------------------------------
# Dynamical Matrix
# -------------------------------------------------------------
dynamical_matrix = DynamicalMatrix(
    bulk_configuration,
    filename= 'gr_mp_fhi.hdf5',
    object_id='dynamical_matrix',
    repetitions=(11, 11, 1),
    atomic_displacement=0.01*Angstrom,
    acoustic_sum_rule=True,
    finite_difference_method=Central,
    #max_interaction_range=3.5*Angstrom,
    force_tolerance=1e-08*Hartree/Bohr**2,
    processes_per_displacement=28,
    log_filename_prefix='forces_fhi_mp_',
    use_wigner_seitz_scheme=True,
    )
dynamical_matrix.update()
  
# -------------------------------------------------------------
# Phonon Bandstructure
# -------------------------------------------------------------
phonon_bandstructure = PhononBandstructure(
    configuration=bulk_configuration,
    dynamical_matrix=dynamical_matrix,
    route=['G', 'K', 'M', 'G'],
    points_per_segment=100,
    number_of_bands=All
    )

nlsave('gr_mp_fhi_dzp.hdf5', phonon_bandstructure)

filename = 'gr_mp_fhi_ph_band.dat'#.format(band_index)
with open(filename, 'w') as f:
    phonon_bandstructure.nlprint(f)

In  processes_per_displacement, the parameter of the dynamical matrix is set to just '4' using a single node, and then the results obtained match the literature.
But when I use larger supercell repetitions=(11, 11, 1), I need to set  processes_per_displacement for more processes, so I set it to '28'. Then, the phonon energies are ~ 12000 meV (with negative energies, too), quite off from the simple graphene phonon dispersion. This processes_per_displacement  is a sensitive parameter.
Why is it so? What am I missing here?

3

General Questions and Answers / Error: Using pre-calculated data for TrainingSet for MTP training

« on: December 7, 2023, 11:29 »

Hi,
I am using my pre-calculated data (BulkConfigurations) as the TrainingSet following: https://docs.quantumatk.com/manual/Types/TrainingSet/TrainingSet.html#trainingset-c
The pre-calculated data was obtained using LCAO and saved in '.hdf5', files, there are a number of BulkConfigurations.
When I am using following script:
 

Code

import glob
import os
directory = ''

filenames= glob.glob(os.path.join(directory, 'data_*.hdf5'))


bulk_configurations = []


for filename in filenames:
    bulk_configurations.append(nlread(filename, BulkConfiguration)[0])
    
calculator = bulk_configurations[0].calculator()
training_set= TrainingSet(bulk_configurations, recalculate_training_data=False, calculator = calculator )
scan_over_non_linear_coefficients = scanOverNonLinearCoefficients(
    perform_optimization=False

# Moment Tensor Potential Training
moment_tensor_potential_training = MomentTensorPotentialTraining(
    filename='MTP.hdf5',
    object_id='mtp',
    training_sets= training_set, 
    calculator=calculator,  
    fitting_parameters_list=scan_over_non_linear_coefficients
)
moment_tensor_potential_training.update()

It gives the error: "training_sets miss data. Check that all required energy, forces, or stress data is provided.".
The Bulkconfigurations are converged. What could be the possible solution to this error?

Best,
krabidix

4

General Questions and Answers / NanoTube Wrapper

« on: July 31, 2023, 10:37 »

Hi,
Can we use the script for Builder plugin tools for e.g for TubeWrapper ?
I didn't find any attributes in BulkConfiguration class for most of the plugins.


Best regards,
Krabidix

5

General Questions and Answers / Setting max_interaction_range for phonon dispersion

« on: March 18, 2023, 15:17 »

Hi,
What general guidelines should be followed when setting "max_interaction_range" for phonon dispersion calculations to achieve reliable results, taking into account its effects on supercell size and the occurrence of imaginary frequencies? Specifically, when using the default interaction range, larger supercells are suggested 

Code

repetitions = checkNumberOfRepetitions(bulk_configuration),

while specifying a smaller max_interaction_range leads to smaller supercells 

Code

repetitions = checkNumberOfRepetitions(bulk_configuration, max_interaction_range=5.0*Angstrom).

Furthermore, the choice of interaction range can influence the presence or absence of imaginary frequencies in different cases.
For some systems, the lower interaction range manages to eliminate imaginary frequencies, while the default value of the interaction range shows imaginary frequencies, and there are some cases in which situations got reversed i.e default interaction range eliminates imaginary frequency and the lower interaction range does not.
So, is there any general rule which needs to be followed while calculating reliable phonon dispersion?

Best regard,
krabidix

                                 
 

6

General Questions and Answers / Moment Tensor Potential Attribute

« on: March 12, 2023, 18:33 »

Hi,
I was trying to run the tutorial on MTP  https://docs.quantumatk.com/tutorials/mtp_basic/mtp_basic.html.
The tutorial works fine, although to plot the results the below commands:

Code

moment_tensor_potential_training=nlread('MTP_basics_results.hdf5',MomentTensorPotentialTraining)[0]
moment_tensor_potential_training._nlplotscatter(fit_index=1)

are not working.
When using 2022.12 version following error showed up:
Traceback (most recent call last):
  File "/n/work00/software/quantumatk/2022.12/bin/../atkpython/bin/atkpython", line 8, in <module>
    sys.exit(__run_atkpython())
  File "zipdir/ATKExecutables/atkwrappers/__init__.py", line 879, in __run_atkpython
  File "plot.py", line 2, in <module>
    moment_tensor_potential_training._nlplotscatter(fit_index=1)
AttributeError: 'MomentTensorPotentialTraining' object has no attribute '_nlplotscatter'

When version 2022.03-sp1 used following error occurred:
  File "zipdir/NL/IO/NLSaveUtilities.py", line 669, in nlread
  File "zipdir/NL/IO/HDF5.py", line 568, in readHDF5
  File "zipdir/NL/IO/HDF5.py", line 699, in readHDF5Group
  File "zipdir/NL/IO/HDF5.py", line 638, in readHDF5GroupToSerializable
  File "zipdir/NL/IO/HDF5.py", line 614, in readHDF5Dict
  File "zipdir/NL/IO/HDF5.py", line 699, in readHDF5Group
  File "zipdir/NL/IO/HDF5.py", line 659, in readHDF5GroupToSerializable
  File "zipdir/NL/IO/Serializable.py", line 331, in _fromVersionedData
  File "zipdir/NL/CommonConcepts/Calculator.py", line 67, in _createObject
  File "zipdir/NL/QuantumATK/ScopeExecuter.py", line 244, in scope_execute
NL.ComputerScienceUtilities.Exceptions.NLScopeExecutionError: __init__() got an unexpected keyword argument 'paw_grid_tolerance'

Kindly, help me in resolving the problem.

7

General Questions and Answers / Data preview is not visible!

« on: January 3, 2023, 12:24 »

Hi,

In QuantumATK 2022.12 version how can we enable data preview? The data preview is not visible.

https://docs.quantumatk.com/guides/data_view/data_view.html

Thanks

8

General Questions and Answers / Unable to reproduce phonon dispersion in QuantumATK

« on: December 20, 2022, 14:44 »

Dear QuantumATK experts,

I tried to replicate the phonon band structure of a simple system (hexagonal monolayer of Cu) as done in https://doi.org/10.1155/2016/8429510 (see Fig 3 or attached image Phonon_bs_ref.PNG)
The results from QuantumATK have imaginary frequencies and even after tuning parameters (e.g: max_interaction_range, atomic_displacement) that control the force constants, I am not able to vanish the imaginary frequencies (see attached Phonon_bs_qatk.PNG).

Please, comment on how can I rid of these imaginary frequencies.


The input file is also attached.


Thanks!
krabidix