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1

Questions and Answers / error when we save input and output / setNativelocks failed

« Last post by gloria.cardenas on Today at 02:06 »

Hello,
We are having an error when we want to save the file as *.py and also as *.hdf5 using the graphical interface. We get the following message in the console: "setNativelocks failed: function not implemented". We don´t have a problem running the ATK in the console. We have used ATK for much time and suddenly this error was obtained.
Could you suggest to me which would be the problem?
Thank you in advance.
Dr. Gloria Cardenas-Jiron

2

Questions and Answers / Re: zero point energy

« Last post by SMA on Yesterday at 12:22 »

I have followed the tutorial. But the effect of changed mass is not reflected in the vibrational mode. It is showing the mode of H2 molecule only.
Please help to resolve the issue.
# Molecule Configuration
# -------------------------------------------------------------

# Define elements
elements = [Hydrogen, Hydrogen]

# Define coordinates
cartesian_coordinates = [[ 0.  ,  0.  ,  0.  ],
                         [ 0.  ,  0.  ,  0.75]]*Angstrom

# Set up configuration
molecule_configuration = MoleculeConfiguration(
    elements=elements,
    cartesian_coordinates=cartesian_coordinates
    )
# Define a new class where the H atom has mass 2.00
class H2(Hydrogen):
    @staticmethod
    def atomicMass():
        return 2.00*Units.atomic_mass_unit

PeriodicTable.ALL_ELEMENTS.append(H2)

# Replace all atoms tagged "H2" with hydrogen-2
for index in molecule_configuration.indicesFromTags("H2"):
    molecule_configuration.elements()[index] = H2

# Add tags
molecule_configuration.addTags('H2', [0,1])

# -------------------------------------------------------------
# Calculator
# -------------------------------------------------------------
numerical_accuracy_parameters = NumericalAccuracyParameters(
    density_mesh_cutoff=80.0*Hartree,
    )

calculator = LCAOCalculator(
    numerical_accuracy_parameters=numerical_accuracy_parameters,
    )

molecule_configuration.setCalculator(calculator)
nlprint(molecule_configuration)
molecule_configuration.update()
nlsave('D2-vib.hdf5', molecule_configuration)

# -------------------------------------------------------------
# Optimize Geometry
# -------------------------------------------------------------
molecule_configuration = OptimizeGeometry(
    molecule_configuration,
    max_forces=0.05*eV/Ang,
    max_steps=200,
    max_step_length=0.2*Ang,
    trajectory_filename='D2-dos-vib.hdf',
    disable_stress=True,
    optimizer_method=LBFGS(),
)
nlsave('D2.nc.dos-vib.hdf5', molecule_configuration)
nlprint(molecule_configuration)

# -------------------------------------------------------------
# Dynamical Matrix
# -------------------------------------------------------------
dynamical_matrix = DynamicalMatrix(
    molecule_configuration,
    filename='D2-vib.hdf5',
    object_id='dynamical_matrix',
    repetitions=Automatic,
    atomic_displacement=0.01*Angstrom,
    acoustic_sum_rule=True,
    finite_difference_method=Central,
    force_tolerance=1e-08*Hartree/Bohr**2,
    processes_per_displacement=1,
    log_filename_prefix='forces_displacement_',
    use_wigner_seitz_scheme=False,
    )
dynamical_matrix.update()

# -------------------------------------------------------------
# Phonon Density Of States
# -------------------------------------------------------------
qpoint_grid = MonkhorstPackGrid()

phonon_density_of_states = PhononDensityOfStates(
    configuration=molecule_configuration,
    dynamical_matrix=dynamical_matrix,
    qpoints=qpoint_grid,
    number_of_bands=None,
    )
nlsave('D2.nc.dos-vib.hdf5', phonon_density_of_states)
nlprint(phonon_density_of_states)

# -------------------------------------------------------------
# Vibrational Mode
# -------------------------------------------------------------
vibrational_mode = VibrationalMode(
    configuration=molecule_configuration,
    dynamical_matrix=dynamical_matrix,
    kpoint_fractional=[0, 0, 0],
    mode_indices=None,
    )
nlsave('D2-vib.hdf5', vibrational_mode)

3

Questions and Answers / Problem with Grimme D3 correction in bulk MoS2

« Last post by donetti on Yesterday at 11:37 »

As a preliminary step of my calculations I tried to optimize the geometry of bulk MoS2 starting from the cell in the database.

With LCAO and PBE (see attached script) I obtain an interlayer spacing larger than the experimental one (lattice constant c=12.86 A), as expected, since Van der Waals interactions are not correctly reproduced.  Thus, I tried to add either Grimme D2 or D3 corrections with default parameter values (the scripts are also attached). While the inclusion of D2 correction actually slightly reduces the interlayer spacing (c=12.26 A), the D3 correction seems to induce a repulsive force. The trajectory file from the optimization shows a steady increase of the interlayer spacing: I stopped the geometry optimization after several hours and 50 optimization steps with c=14.6 A. I tried to change the numerical accuracy parameters and the basis, but without luck: any attempt with D3 correction gives rise to an always-expanding optimization.

Am I doing anything wrong or the D3 correction is not supposed to work in this case?

Thank you in advance for any suggestion.
Luca Donetti

4

Questions and Answers / Re: zero point energy

« Last post by mlee on Yesterday at 09:53 »

You are right. It works from R-2020.09 version.
Before R-2020.09, the isotope can define a new element type (class) with modified mass and use that in the element list.
The below tutorial includes the C14 isotope with a new element type.
https://docs.quantumatk.com/tutorials/thermoelectrics_cnt_isotope/thermoelectrics_cnt_isotope.html

5

Questions and Answers / Re: BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES

« Last post by asma on October 19, 2020, 20:20 »

Thanks for your reply.

I'm trying to reduce the memory usage based on the below tutorial:
https://docs.quantumatk.com/technicalnotes/advanced_performance/advanced_performance.html

6

Questions and Answers / Re: SlaterKoster Parameters for Tungsten

« Last post by Petr Khomyakov on October 19, 2020, 11:28 »

In general, I would say that one should do SCF. To really validate Non-SCF, one would have to benchmark it against SCF-obtained results I think.

7

Questions and Answers / Re: BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES

« Last post by Petr Khomyakov on October 19, 2020, 11:13 »

It looks like not enough memory. It would be instructive to see your script and entire log file of the calculation.

8

Questions and Answers / Re: GGA-PAW Memory error

« Last post by filipr on October 19, 2020, 09:29 »

Dear Sadegh

I've looked through your input script and your calculation output and as you also have observed it should have enough memory to run a DFT calculation. Tt is also able to do a few optimization steps before it crashes. This does sound a bit weird, as if something is leaking memory or uses more memory than we would think. We will try to run you script and see if we can pinpoint the issue. Unfortunately, this may take a while as we have a lot of other things to do, so be patient.

Until then I have some suggestions for reducing the memory footprint:

I looked up the CPU you are running on, and it has 20 physical cores, and you have two of those, so a total of 40 available cores. Let's put them all to use

I see you are using the newest version (2020.09) which is quite well parallelized using threads. So I suggest that you run using 4 threads, this means that you should run with 40/4 = 10 processes (you can select 4 threads and 10 processes in the job manager). You have 13 k-points and ~70.000 plane waves to parallelize over. In order to reduce the number of wave functions to store in memory, you can distribute them over processes by choosing processes per k-point = 5. This should give a reasonable load balance with minimal memory consumption. So to summarize:

number of threads: 4
number of processes: 10
processes per k-point: 5 (this one you set in the calculator settings in the script generator)

I hope this makes the calculation run through.

9

Questions and Answers / Re: how to calculate dynamics of magnetizations

« Last post by Troels-Markussen on October 19, 2020, 09:01 »

Hi,

While QuantumATK can be used to calculate parameters entering the LLG equation (spin transfer torque, Gilbert damping, magnetic moments, etc.) we currently do not have any modules for calculating the magnetization dynamics by solving the LLG equation. This part was implemented by the authors them-self in the cited paper. Notice also that the calculation of spin-orbit torque was implemented by the authors them-self.

Regards,
Troels
 

10

Questions and Answers / Re: zero point energy

« Last post by SMA on October 19, 2020, 08:46 »

The version I am using is QuantumATK P-2019.03-SP1.
As per ypur suggestions I used the following input .
#setup H-H geometry
elements = [ Hydrogen2, Hydrogen2]
cartesian_coordinates = [[ 0.0,0.0,0.0],
                         [ 0.0,0.0,0.75]]*Angstrom
molecule_configuration = MoleculeConfiguration(
    elements=elements,
    cartesian_coordinates=cartesian_coordinates
    )

But It is displaying error as given below.

  File "h2-vib.py", line 2, in <module>
    elements = [ Hydrogen2, Hydrogen2]
NameError: name 'Hydrogen2' is not defined
application called MPI_Abort(MPI_COMM_WORLD, 1) - process 9