CoulombDebye¶
- class CoulombDebye(r_cut=None, kappa=None, bonded_mode=None, doEEM=None)¶
Constructor of the Coulomb solver.
- Parameters:
r_cut (PhysicalQuantity of type length) – The cutoff radius of this Coulomb solver.
kappa (PhysicalQuantity of type length**-1) – Damping parameter in the Debye method. It determines how fast the Coulomb interactions decay with the particle distance.
bonded_mode –
Either CoulombDebye.evaluateAll or CoulombDebye.evaluate4.
If evaluateAll is chosen, interactions between all particles - even those that are connected by bonds - are evaluated, using the sigma and epsilon parameters.
If evaluate4 is chosen, interactions between particles that are connected by a path of bonds of length less than four are omitted.
doEEM (bool) – Whether or not electronegativity equalization method (EEM) is used to determine the charges. It is switched off by default.
- 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 potential for Quartz by adding particle types and interaction functions to the TremoloXPotentialSet.
# -------------------------------------------------------------
# Set up a SiO2 Quartz crystal
# -------------------------------------------------------------
# Set up lattice
lattice = Hexagonal(4.916*Angstrom, 5.4054*Angstrom)
# Define elements
elements = [Silicon, Silicon, Silicon, Oxygen, Oxygen, Oxygen, Oxygen, Oxygen,
Oxygen]
# Define coordinates
fractional_coordinates = [[ 0.4697, 0.0000, 0.0000 ],
[ 0.0000, 0.4697, 0.66666667],
[ 0.5303, 0.5303, 0.33333333],
[ 0.4135, 0.2669, 0.1191 ],
[ 0.2669, 0.4135, 0.547567 ],
[ 0.7331, 0.1466, 0.785767 ],
[ 0.5865, 0.8534, 0.214233 ],
[ 0.8534, 0.5865, 0.452433 ],
[ 0.1466, 0.7331, 0.8809 ]]
# Set up configuration
bulk_configuration = BulkConfiguration(
bravais_lattice=lattice,
elements=elements,
fractional_coordinates=fractional_coordinates
)
# -------------------------------------------------------------
# Calculator
# -------------------------------------------------------------
# Create the Pedone_2006Fe2 potential by hand, by adding the individual components
potentialSet = TremoloXPotentialSet(name='Pedone_2006Fe2')
# Add the particle types to the potential set
potentialSet.addParticleType(ParticleType(symbol='Si', mass=28.0855*atomic_mass_unit, charge=2.4))
potentialSet.addParticleType(ParticleType(symbol='O', mass=15.9994*atomic_mass_unit, charge=-1.2))
# Add the pair potentials to the potential set
potentialSet.addPotential(MorsePotential('Si', 'O', r_0=2.1*Angstrom, k=2.0067*1/Ang, E_0=0.340554*eV, r_i=6.0*Angstrom, r_cut=7.5*Angstrom))
potentialSet.addPotential(Repulsive12Potential('Si', 'O', r_cut=7.5*Angstrom, c=1.0*Ang**12*eV))
potentialSet.addPotential(MorsePotential('O', 'O', r_0=3.618701*Angstrom, k=1.379316*1/Ang, E_0=0.042395*eV, r_i=6.0*Angstrom, r_cut=7.5*Angstrom))
potentialSet.addPotential(Repulsive12Potential('O', 'O', r_cut=7.5*Angstrom, c=22.0*Ang**12*eV))
# Add the coulomb solver to the potential set
potentialSet.setCoulombSolver(CoulombDebye(r_cut=9.0*Angstrom, kappa=0.5))
# Create the calculator from the potential set
calculator = TremoloXCalculator(parameters=potentialSet)
bulk_configuration.setCalculator(calculator)
bulk_configuration.update()
Notes¶
The CoulombDebye solver calculates the electrostatic interactions between particles with partial charges, as defined in ParticleType.
The electrostatic interactions between two particles \(i\) and \(j\) are calculated as a screened Coulomb sum:
When using bonded force fields the
bonded_mode
parameter can be used to modify how this potential acts between
atoms that are connected by less than 4 bonds. If CoulombSolver.evaluateAll
(or “mode_bondless”) is chosen, the potential acts between all selected atoms
independent of the bonds between them. If CoulombSolver.evaluate4
(or
“mode_14”) is chosen, the potential is switched off for all atoms that are
connected via one, two, or three consecutive bonds.