CoulombEwald¶
- class CoulombEwald(alpha=None, epsilon=None, bonded_mode=None)¶
Constructor of the Coulomb solver.
- Parameters:
alpha (PhysicalQuantity of type length**-1) – Splitting parameter of the Ewald summation.
epsilon (float) – The accuracy of the Ewald-summation. It is used to determine the cutoff radius for the short-range interactions such that erfc(alpha * r_cut) <= epsilon.
bonded_mode –
Either CoulombEwald.evaluateAll or CoulombEwald.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.
- 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(CoulombEwald(alpha=0.1*Angstrom**-1, epsilon=1.0e-10))
# Create the calculator from the potential set
calculator = TremoloXCalculator(parameters=potentialSet)
bulk_configuration.setCalculator(calculator)
bulk_configuration.update()
Notes¶
This Coulomb solver provides an efficient method to calculate the long-range electrostatic interactions between particles with partial charges, as defined in ParticleType.
The CoulombEwald solver works only for periodic systems, i.e. BulkConfiguration.
Similar to CoulombSPME, the method evaluates a screened, short-range part of the electrostatic interactions as a pair-wise sum in real space, whereas the remaining long-range contributions are calculated in reciprocal space [1].
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.