Topics

1

General Questions and Answers / AIMD simulation of KPF6 (LCAO)

« on: January 12, 2023, 11:51 »

 Phase diagram of KPF6 (potassium hexafluorophosphate)
KPF6 crystal
  The script
 
The trajectory of KPF6

Simulation conditions:

1000 atoms(5x5x5);
    time_step=1*femtoSecond,
    reservoir_temperature=350*Kelvin,
    reservoir_pressure=[1000, 1000, 1000, 1000, 1000, 1000]*bar,
    thermostat_timescale=100*femtoSecond,
    barostat_timescale=1000*femtoSecond,
    initial_velocity=initial_velocity,
    heating_rate=0*Kelvin/picoSecond,
    compression_rate=0*bar/femtoSecond,
    coupling_mask=[[True, True, True], [True, True, True], [True, True, True]],
    chain_length=3,

1. Why does the simulation box eventually become so distorted? According to the phase diagram, KPF6 crystal may undergo phase transformation. Is it necessary to define the simulation box as a triclinic system?
2. The chemical bond of PF6 has broken, but it is obvious that the chemical bond of PF6 will not break at this temperature.
3. Are these results due to the inaccuracy of LCAO? However, the AIMD based on LCAO should predict the physical laws, even though the value may have some deviation.

I have been troubled by this problem for a long time and can't solve it with all kinds of methods. If someone can help me solve it, I will thank him very much.

2

General Questions and Answers / CrystalPropertyValidation

« on: January 12, 2023, 04:05 »

Dear QuantumATK Staff：
         I run the example in the ATK manual to learn the CrystalPropertyValidation module.

         The example:
        
setVerbosity(MinimalLog)

# Set up lattice
lattice = FaceCenteredCubic(5.4306*Angstrom)

# Define elements
elements = [Silicon, Silicon]

# Define coordinates
fractional_coordinates = [[ 0.  ,  0.  ,  0.  ],
                          [ 0.25,  0.25,  0.25]]

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

# Setting up the reference calculator
# -------------------------------------------------------------
# MTP Calculator
# -------------------------------------------------------------

potentialSet = Tersoff_Si_1988()
calculator = TremoloXCalculator(parameters=potentialSet)
bulk_configuration.setCalculator(calculator)


# Setting up the test calculator
# -------------------------------------------------------------
# MTP Calculator
# -------------------------------------------------------------

potentialSet = MTP_Si_2019b()
relative_calculator = TremoloXCalculator(parameters=potentialSet)


crystal_property_validation = CrystalPropertyValidation(
        bulk_configuration,
        relative_calculator,
        relative_calculator,
        calculate_reference_data=True,
        calculate_volume_energy_plot=True,
        calculate_elastic_constants=True,
        calculate_phonon_bandstructure=True,
        calculate_delta_test=True,
        optimize_geometry_parameters=None,
        log_filename_prefix=None,
        dynamical_matrix_filename='dynamical_matrix.hdf5',
        dynamical_matrix_repetitions=(5, 5, 5),
    )
nlsave(f'crystal_property_validation.hdf5', crystal_property_validation)
nlprint(crystal_property_validation)
crystal_property_validation.plotEnergyvsVolume()

I encountered the following problems:

Traceback (most recent call last):
  File "/home/ATK/QuantumATK/QuantumATK-U-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 "si_crystal_property_validation.py", line 40, in <module>
    crystal_property_validation = CrystalPropertyValidation(
TypeError: __init__() got multiple values for argument 'calculate_reference_data'
application called MPI_Abort(MPI_COMM_WORLD, 1) - process 42


I have tried many ways but can't solve it, so I hope I can get your help.

3

General Questions and Answers / AIMD trajectory to MTP training data

« on: June 22, 2022, 04:28 »

Dear ATK-Staff/developer:
when I loaded the AIMD trajectory object which was precalculated：

# Load another Trajectory object with precalculated data.
trajectory_training_data_input = nlread('KPF6_MD_trajectory_300K_0.1GPa.hdf5', Trajectory)[0]
training_sets.append(
   TrainingSet(trajectory_training_data_input,
                       # sample_size=100,
                        calculator=calculator,
                        recalculate_training_data=False)

I encountered the following problem:

Traceback (most recent call last):
  File "test3.py", line 58, in <module>
trajectory_training_data_input=nlread('KPF6_MD_trajectory_300K_0.1GPa.hdf5', Trajectory)[0]
IndexError: list index out of range
application called MPI_Abort(MPI_COMM_WORLD, 1) - process 31

The  measurements of MD_trajectory are shown as follow: kinetic_energy, potential_energy, volume, temperature, pressure and stress.
And that are differs from the “energy”, “force” and “stress”required for the training set. Moreover,  there is no option for “force” in the measurements  in AIMD simulation.

So how do I solve this problem so that I can make use of the AIMD data that has been calculated before.

4

General Questions and Answers / MTP——“No new candidates found in active learning MD”

« on: June 18, 2022, 09:08 »

Dear ATK-Staff/developer,

I used the AIMD  trajectory as the initial training set to generate the MTP potential, although I lowered the basis set of the MTP many times, the same problem still occurs--"  No new candidates found in active learning MD", is there any way to solve such a problem, or my initial training set has question?

part of the code:

trajectory=nlread('800K_0GPa_2ps.hdf5',MDTrajectory)[-1]
training_set = TrainingSet(trajectory,
                        sample_size=1000,
                        calculator=calculator)

fitting_parameters = MomentTensorPotentialFittingParameters(
    basis_size=200,
    inner_cutoff_radii=0.9 * Angstrom,
    tapering_cutoff_radii=1.1 * Angstrom,
    outer_cutoff_radii= 6.0 * Angstrom,
    constant_terms=constant_terms,
    mtp_filename='mtp_potential.mtp',
    forces_cap= 100.0 * eV / Angstrom,
    non_linear_coefficients_parameters=non_linear_coefficients_parameters,
)

 WARNING: The condition number of the optimized training matrix is            |
|          5.09e+13.This could lead to accuracy problems when calculating the  |
|          extrapolation grade.Consider reducing the number of MTP basis       |
|          functions or adding more diverse training configurations until the  |
|          condition number is lower.                                          |