D3Potential

class D3Potential(file=None, S6=None, a1=None, S8=None, a2=None, S6r=None, r_cut=None, bond_rcut=None, triple_rcut=None, k3=None, taper_factor=None, ATM=None)

Constructor of the potential.

Parameters:

• file (str) – The name of the file that contains the D3 parameters.

• S6 (float) – The dimensionless BJ/Z parameter S6

• a1 (float) – The dimensionless BJ parameter a1 By setting S6r = 0 and a1!=0 or a2!=0 one chooses BJ damping

• S8 (float) – The dimensionless BJ/Z parameter S8

• a2 (PhysicalQuantity of type length) – The BJ parameter a2 By setting S6r = 0 and a1!=0 or a2!=0 one chooses BJ damping

• S6r (float) – The dimensionless Z parameter S6r By setting S6r != 0 and a1=a2=0 one chooses Z damping

• r_cut (PhysicalQuantity of type length) – The cutoff radius for the interactions

• bond_rcut (PhysicalQuantity of type length) – The cutoff radius for the coordination numbers

• triple_rcut (PhysicalQuantity of type length) – The cutoff radius for the ATM interaction

• k3 (float) – The dimensionless k3 smoothing parameter

• taper_factor (float) – The dimensionless taper_factor for bond_rcut and r_cut

• ATM (bool) – The parameter to switch on the Axilrod-Teller-Muto three-body terms

classmethod getAllParameterNames()

Return the names of all used parameters as a list.

getAllParameters()

Return all parameters of this potential and their current values as a <parameterName / parameterValue> dictionary.

static getDefaults()

Get the default parameters of this potential and return them in form of a dictionary of <parameter name, default value> key-value pairs.

getParameter(parameterName)

Get the current value of the parameter parameterName.

setParameter(parameterName, value)

Set the parameter parameterName to the given value.

Parameters:

• parameterName (str) – The name of the parameter that will be modified.

• value – The new value that will be assigned to the parameter parameterName.

Usage Examples

Define a D3 potential for a SiC/SiO₂ interface to be used with an MTPPotential by adding particle types and interaction functions to the TremoloXPotentialSet.

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

# Set up lattice
vector_a = [9.228, 0.0, 0.0]*Angstrom
vector_b = [4.613999999999999, -2.663894142040934, 0.0]*Angstrom
vector_c = [0.0, 0.0, 9.185292029012857]*Angstrom
lattice = UnitCell(vector_a, vector_b, vector_c)

# Define elements
elements = [Silicon, Silicon, Silicon, Carbon, Carbon, Carbon, Silicon, Silicon,
            Silicon, Carbon, Carbon, Carbon, Oxygen, Oxygen, Oxygen, Silicon,
            Oxygen, Silicon]

# Define coordinates
fractional_coordinates = [[-0.            ,  0.666666666667,  0.            ],
                          [ 0.333333333333,  0.666666666667,  0.            ],
                          [ 0.666666666667,  0.666666666667,  0.            ],
                          [-0.            ,  0.666666666667,  0.211586087177],
                          [ 0.333333333333,  0.666666666667,  0.211586087177],
                          [ 0.666666666667,  0.666666666667,  0.211586087177],
                          [ 0.            ,  0.333333333333,  0.274787126204],
                          [ 0.333333333333,  0.333333333333,  0.274787126204],
                          [ 0.666666666667,  0.333333333333,  0.274787126204],
                          [ 0.            ,  0.333333333333,  0.486373213382],
                          [ 0.333333333333,  0.333333333333,  0.486373213382],
                          [ 0.666666666667,  0.333333333333,  0.486373213382],
                          [ 0.833330938737,  0.333338122527,  0.676754885757],
                          [ 0.833330938737,  0.833338122527,  0.676754885757],
                          [ 0.333330938737,  0.833338122527,  0.676754885757],
                          [-0.000002394597,  0.333338122527,  0.733058104206],
                          [-0.000002394597,  0.333338122527,  0.901967759553],
                          [-0.000002394597,  0.333338122527,  1.0708774149  ]]

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

# -------------------------------------------------------------
# Calculator
# -------------------------------------------------------------

# Create a new MTP potential set
mtp_potential_set = TremoloXPotentialSet('MTP')
mtp_potential_set.addParticleType(ParticleType('Si'))
mtp_potential_set.addParticleType(ParticleType('O'))
mtp_potential_set.addParticleType(ParticleType('C'))

mtp_potential_set.addPotential(MTPPotential(
    file = 'mtp-file.mtp',
    suppress_intercept = False,
))

# Create a new D3 potential set
d3_potential_set = TremoloXPotentialSet('D3')
d3_potential_set.addParticleType(ParticleType('Si'))
d3_potential_set.addParticleType(ParticleType('O'))
d3_potential_set.addParticleType(ParticleType('C'))
# D3BJ parameters for PBE
d3_potential_set.addPotential(D3Potential(
    S6=+1.0000000000e+00,
    S8=+7.8750000000e-01,
    a1=+4.2890000000e-01,
    a2=+4.4407000000e+00*Bohr,
))

calculator = TremoloXCalculator(
    parameters=[mtp_potential_set, d3_potential_set]
)

bulk_configuration.setCalculator(calculator)

Define a D3 potential for a SiC/SiO₂ interface to be used in an LCAO-DFT CombinedCalculator by adding particle types and interaction functions to the TremoloXPotentialSet.

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

# Set up lattice
vector_a = [9.228, 0.0, 0.0]*Angstrom
vector_b = [4.613999999999999, -2.663894142040934, 0.0]*Angstrom
vector_c = [0.0, 0.0, 9.185292029012857]*Angstrom
lattice = UnitCell(vector_a, vector_b, vector_c)

# Define elements
elements = [Silicon, Silicon, Silicon, Carbon, Carbon, Carbon, Silicon, Silicon,
            Silicon, Carbon, Carbon, Carbon, Oxygen, Oxygen, Oxygen, Silicon,
            Oxygen, Silicon]

# Define coordinates
fractional_coordinates = [[-0.            ,  0.666666666667,  0.            ],
                          [ 0.333333333333,  0.666666666667,  0.            ],
                          [ 0.666666666667,  0.666666666667,  0.            ],
                          [-0.            ,  0.666666666667,  0.211586087177],
                          [ 0.333333333333,  0.666666666667,  0.211586087177],
                          [ 0.666666666667,  0.666666666667,  0.211586087177],
                          [ 0.            ,  0.333333333333,  0.274787126204],
                          [ 0.333333333333,  0.333333333333,  0.274787126204],
                          [ 0.666666666667,  0.333333333333,  0.274787126204],
                          [ 0.            ,  0.333333333333,  0.486373213382],
                          [ 0.333333333333,  0.333333333333,  0.486373213382],
                          [ 0.666666666667,  0.333333333333,  0.486373213382],
                          [ 0.833330938737,  0.333338122527,  0.676754885757],
                          [ 0.833330938737,  0.833338122527,  0.676754885757],
                          [ 0.333330938737,  0.833338122527,  0.676754885757],
                          [-0.000002394597,  0.333338122527,  0.733058104206],
                          [-0.000002394597,  0.333338122527,  0.901967759553],
                          [-0.000002394597,  0.333338122527,  1.0708774149  ]]

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

# -------------------------------------------------------------
# Calculator
# -------------------------------------------------------------

# Create a new D3 potential set
d3_potential_set = TremoloXPotentialSet('D3')
d3_potential_set.addParticleType(ParticleType('Si'))
d3_potential_set.addParticleType(ParticleType('O'))
d3_potential_set.addParticleType(ParticleType('C'))
# D3BJ parameters for PBE
d3_potential_set.addPotential(D3Potential(
    S6=+1.0000000000e+00,
    S8=+7.8750000000e-01,
    a1=+4.2890000000e-01,
    a2=+4.4407000000e+00*Bohr,
))

calculators = [
    TremoloXCalculator(parameters=d3_potential_set),
    LCAOCalculator()
]
calculator = CombinedCalculator(calculators)

bulk_configuration.setCalculator(calculator)

Notes

For most use cases it is more convenient to replace the the definition of the D3 potential through the TremoloXPotentialSet with a DispersionD3Z (zero damping) [1] or DispersionD3BJ (Becke-Johnson damping) [2] object which automatically supply the correct parameters for the chosen exchange-correlation functional.

[1]

S. Grimme, J. Antony, S. Ehrlich, and H. Krieg. A consistent and accurate ab initio parametrization of density functional dispersion correction (DFT-D) for the 94 elements H-Pu. J. Chem. Phys., 2010. doi:10.1063/1.3382344.

[2]

Stefan Grimme, Stephan Ehrlich, and Lars Goerigk. Effect of the damping function in dispersion corrected density functional theory. Journal of Computational Chemistry, 32(7):1456–1465, 2011.