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QuantumATK => General Questions and Answers => Topic started by: krabidix on March 18, 2024, 14:55

Title: Phonon dispersion is senstitive to "processes_per_displacement" paramter of DM?
Post by: krabidix 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?
Title: Re: Phonon dispersion is senstitive to "processes_per_displacement" paramter of DM?
Post by: Anders Blom on March 26, 2024, 23:23
It shouldn't matter, but there is a lot going on here. What is the repetition in the calculation that gives good results? Do you use the Wigner-Seitz scheme in both cases? Are there convergence issues indicated in any log file? Code version (we fixed some symmetry-related problems that gave negative energies recently)?

There is no real need to optimize the geometry since the structure is symmetric (fractional coordinates constrained to 1/3 and 2/3). Yes, you can optimize the lattice constant, but that would be a simple equation of state (vary the parameter a for 5-10 runs and fit a parabola), much more efficient.

Do you need spin-polarization? Not sure it makes a difference, just takes longer... I try without first, at least, while testing other parameters.
Title: Re: Phonon dispersion is senstitive to "processes_per_displacement" paramter of DM?
Post by: krabidix 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".
Title: Re: Phonon dispersion is senstitive to "processes_per_displacement" paramter of DM?
Post by: Anders Blom on March 27, 2024, 22:36
I think we need to look at the exact scripts and output. If you don't want to share them publicly, you can email then.
Title: Re: Phonon dispersion is senstitive to "processes_per_displacement" paramter of DM?
Post by: krabidix 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!
Title: Re: Phonon dispersion is senstitive to "processes_per_displacement" paramter of DM?
Post by: Anders Blom on April 1, 2024, 20:10
Could you zip the log files too, might help to look at them before rerunning, the HDF5 files don't tell us much how the problem arises
Title: Re: Phonon dispersion is senstitive to "processes_per_displacement" paramter of DM?
Post by: krabidix on April 2, 2024, 11:09
Here are the log files for forces and scf.
Title: Re: Phonon dispersion is senstitive to "processes_per_displacement" paramter of DM?
Post by: Anders Blom on April 6, 2024, 00:43
These are for 28 processes, right? The point will be to compare with the run using 4, so please upload those too.
Title: Re: Phonon dispersion is senstitive to "processes_per_displacement" paramter of DM?
Post by: krabidix on April 9, 2024, 09:29
Hi,
These are relevant data of both cases ( with processes = 28 and 4).
Title: Re: Phonon dispersion is senstitive to "processes_per_displacement" paramter of DM?
Post by: krabidix 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?
Title: Re: Phonon dispersion is senstitive to "processes_per_displacement" paramter of DM?
Post by: Anders Blom on April 12, 2024, 23:15
From these files it is at least clear that the self-consistent loops proceeds very differently in the two cases for some displacements (but not all), and in the end of course this makes a big difference for the dynamical matrix.

Now, when I submit this to our bug fixing team, the first thing they will ask is if it was tested in the latest version. I personally don't have a machine with 168 cores at hand to test on, but you do, so it would be really helpful if you could rerun this with V-2023.12-SP1 (which has many new features compared to U anyway), since in theory it could have been fixed since the version you used. This should only take you 7-8 hours :-)

Second, I find your choice of processes_per_displacement=28 odd when you run on 24-core machines. This gives at the very least odd load-balancing and unnecessary network communications.

So, please check using processes_per_displacement=24 instead. One can argue that any value should work numerically, so we might still look into it, but only if it appears in V-version also.

The nice news, once we resolve this, is that the speedup using a large processes_per_displacement is substantial, basically linear!
Title: Re: Phonon dispersion is senstitive to "processes_per_displacement" paramter of DM?
Post by: krabidix on April 24, 2024, 13:15
Hi,
The latest version does not make any difference.
The question remains why "process_per_displacement" parameter is so sensitive to phonon calculations ?
Title: Re: Phonon dispersion is senstitive to "processes_per_displacement" paramter of DM?
Post by: krabidix on April 24, 2024, 13:17
Here are the bulk_configuration and other script files if the QuantumATK team wants to investigate the issue.
Title: Re: Phonon dispersion is senstitive to "processes_per_displacement" paramter of DM?
Post by: Anders Blom on April 24, 2024, 19:29
Thanks for trying 2023, it is certainly concerning that you still see the problem. However, we have also run multiple versions of this calculation with the current version and cannot reproduce it. In theory there could be unusual connection to your hardware or MPI libraries etc, but would you also mind running it with 24 and not 28 processes?
Title: Re: Phonon dispersion is senstitive to "processes_per_displacement" paramter of DM?
Post by: krabidix on April 30, 2024, 07:59
With '24' and '4' cores, the results match.
Title: Re: Phonon dispersion is senstitive to "processes_per_displacement" paramter of DM?
Post by: Anders Blom on April 30, 2024, 20:19
Aha, interesting... I'll make sure to forward this to our developers, however at least now you have a workable way to run the calculations fast, and correctly!