Messages

1

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

« on: April 9, 2024, 09:34 »

These are the dynamical matrix files for both cases.
I think this is complete information!

Now, the question can be addressed: why phonon dispersion is senstitive to "processes_per_displacement" paramter?

2

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

« on: April 9, 2024, 09:29 »

Hi,
These are relevant data of both cases ( with processes = 28 and 4).

3

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

« on: April 2, 2024, 11:09 »

Here are the log files for forces and scf.

4

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

« on: March 31, 2024, 00:28 »

Here are the output (in zip files) and script for the case in which I used a large value (28) for processes_per_displacement.
The attached image is for the case when I used the value of processes_per_displacement =4.

The only question is why the energies are that much off!

5

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

« on: March 27, 2024, 10:39 »

Thank you for your input!

I understand that I may have overgeneralized regarding geometry optimization and script parameters.

My primary focus is on the unexpected behaviour of phonon energies when changing the "processes_per_displacement" parameter within my script.

Using a large value for "processes_per_displacement" (e.g., 26) results in unusually high phonon energies (~12000 meV), while a smaller value (e.g., 4) produces the expected range for graphene (~200 meV).

This discrepancy is puzzling and leads me to question the impact of this parameter.

I am using QuantumATK Version U-2022.12. 
I used the Wigner-Seitz scheme in both cases. I changed only "processes_per_displacement".

6

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?

7

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

8

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

9

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

                                 
 

10

General Questions and Answers / Re: Moment Tensor Potential Attribute

« on: March 14, 2023, 17:22 »

Hi,
Yes, it worked with the capital "S".

Thanks for the help.

11

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.

12

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

« on: January 13, 2023, 09:09 »

Hi,
I also want to add one more thing.
Using 'use_wigner_seitz_scheme=True', and invoking supercell sizes 3, and 5 for testing convergence.
What I got the supercell size of 3 is giving positive energies and with a larger supercell size the imaginary modes appeared. This is something unusual?
I have shared the script.

13

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

« on: January 12, 2023, 19:36 »

Thanks a lot for your nice input. I will keep these things for further calculations.
I encountered numerical artifacts during optimization, for example:

Consider 2D square lattice with two atoms (A&B) basis (side of square lattice = a*sqrt(2)) where 'a' is the bond length, the atomic position in fractional coordinates A(0,0,0.5) & B(0.5,0.5,0.5). Now upon geometry optimization, the fractional coordinates remain the same but the cartesian coordinates show some non-zero values in of x and y plane for atom A, of the order of 10^-10 or even smaller time. Like atom A being at ( -10^-12, -10^9, 0.5).

Is this numerical noise could be the cause of imaginary modes?

14

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

« on: January 12, 2023, 16:00 »

Hi,
Thanks for working on the script.
Indeed the results are reproduced.
By tuning the max_interaction_range we need to set 'use_wigner_seitz_scheme=False'. QATK allows setting use_wigner_seitz_scheme=True only when we consider the max_interaction_range (Default) which includes all atoms. And with this (True) setting when one checks repetitions = checkNumberOfRepetitions(bulk_configuration) the automatic algorithm of ATK suggest a larger supercell.
So, one can limit the max_intr_range and use a smaller supercell as ATK suggests with
repetitions = checkNumberOfRepetitions(bulk_configuration,    max_interaction_range=4.0*Angstrom).
The parameters used in the dynamical matrix calculations affect too much on phonon calculations.
One thing I also noticed is that during optimization the symmetry gets broken for some 2D structures, which leads to the imaginary phonon frequencies also.
At the same time when we enforce the symmetry using constraints, the next issue came up with force and stress convergence. Which also affects the phonon energy relations.

Is the tuning of parameters the only way to check or there is a robust rule of thumb on which one can rely and move on to study the next structure if imaginary frequencies showed up?

 

15

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

« on: January 12, 2023, 14:34 »

Hi Tue,
Thanks for the comment!
I used the DFT-PW method, and I have also shared the .py file already.
First I optimized the structure and then use repetitions=(7, 7, 1).
You may consider a look at the script.


Best Regards,
krabidix