LennardJonesSpline2Potential¶
- class LennardJonesSpline2Potential(particleType1=None, particleType2=None, r_b=None, r_e=None, r_m=None, r_s=None, sigma=None, epsilon=None, sigmaSpecial=None, epsilonSpecial=None, bonded_mode=None)¶
Constructor of the potential.
- Parameters:
particleType1 (ParticleType or ParticleIdentifier) – Identifier of the first particle type.
particleType2 (ParticleType or ParticleIdentifier) – Identifier of the second particle type.
r_b (PhysicalQuantity of type length) – The outer cutoff radius. Must be larger than r_e.
r_e (PhysicalQuantity of type length) – The third cutoff radius. Must be larger than r_m.
r_m (PhysicalQuantity of type length) – The second cutoff radius. Must be larger than r_s.
r_s (PhysicalQuantity of type length) – The first cutoff radius.
sigma (PhysicalQuantity of type length) – Potential parameter.
epsilon (PhysicalQuantity of type energy) – Potential parameter.
sigmaSpecial (PhysicalQuantity of type length) – Potential parameter. This parameter is only used when bonded_mode is set to evaluate34.
epsilonSpecial (PhysicalQuantity of type energy) – Potential parameter. This parameter is only used when bonded_mode is set to evaluate34.
bonded_mode –
Either LennardJonesSpline2Potential.evaluateAll or LennardJonesSpline2Potential.evaluate34.
If evaluateAll is chosen, interactions between all particles - even those that are connected by fixed bonds - are evaluated, using the sigma and epsilon parameters.
If evaluate34 is chosen, interactions between particles that are connected by bonds with a path length of at most two (i.e. are connected by a bond or are bonded to a common atom) are omitted. Interactions between particles that are connected by a bonded path of length three use the sigmaSpecial and epsilonSpecial parameters, while all other interactions use the normal sigma and epsilon parameters.
- 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.
Notes¶
In contrast to the LennardJonesSplinePotential, the LennardJonesSpline2Potential is zero outside an interval \([r_s, r_b]\), and yields the original Lennard-Jones energy
only within an interval \([r_m, r_e]\). Cubic splines are use to ensure a smooth transition to zero over the intervals \([r_s, r_m]\), as well as \([r_e, r_b]\).
If not specified explicitly in the potential, the Lennard-Jones parameters \(\sigma\) and \(\epsilon\) are taken from the ParticleType the potential acts on. The parameters between different types are calculated based on the Lorentz-Berthelot mixing rules
and
When using bonded force fields the
bonded_mode
parameter can be used to modify how this potential acts between
atoms that are connected via less than 4 bonds. If
LennardJonesPotential.evaluateAll
(or “mode_bondless”) is chosen, the
potential acts between all selected atoms independent of the bonds between
them. If LennardJonesPotential.evaluate34
(or “mode_14”) is chosen, the
potential is switched off for all atoms that are connected via one or two consecutive
bonds. For atoms separated by exactly three bonds (i.e. atoms 1 and 4 in a bonded sequence),
the special Lennard-Jones parameters (respectively the combined epsilon14
and sigma14
of the ParticleType) are used instead.