AmoebaVdwForce Class Reference
This class implements an interaction between pairs of particles that varies harmonically with the distance between them. More...
Public Member Functions | |
| def | getNumParticles |
| getNumParticles(self) -> int | |
| def | setParticleParameters |
| setParticleParameters(self, int particleIndex, int ivIndex, int classIndex, double sigma, double epsilon, double reductionFactor) | |
| def | getParticleParameters |
| getParticleParameters(self, int particleIndex) | |
| def | addParticle |
| addParticle(self, int ivIndex, int classIndex, double sigma, double epsilon, double reductionFactor) -> int | |
| def | setSigmaCombiningRule |
| setSigmaCombiningRule(self, string sigmaCombiningRule) | |
| def | getSigmaCombiningRule |
| getSigmaCombiningRule(self) -> string | |
| def | setEpsilonCombiningRule |
| setEpsilonCombiningRule(self, string epsilonCombiningRule) | |
| def | getEpsilonCombiningRule |
| getEpsilonCombiningRule(self) -> string | |
| def | setParticleExclusions |
| setParticleExclusions(self, int particleIndex, vectori exclusions) | |
| def | getParticleExclusions |
| getParticleExclusions(self, int particleIndex) | |
| def | setCutoff |
| setCutoff(self, double cutoff) | |
| def | getCutoff |
| getCutoff(self) -> double | |
| def | setUseNeighborList |
| setUseNeighborList(self, int neighborListFlag) | |
| def | getUseNeighborList |
| getUseNeighborList(self) -> int | |
| def | setPBC |
| setPBC(self, int pbcFlag) | |
| def | getPBC |
| getPBC(self) -> int | |
| def | __init__ |
| __init__(self) -> AmoebaVdwForce __init__(self, AmoebaVdwForce other) -> AmoebaVdwForce | |
| def | __del__ |
| __del__(self) | |
Public Attributes | |
| this | |
Detailed Description
This class implements an interaction between pairs of particles that varies harmonically with the distance between them.
To use it, create a VdwForce object then call addAngle() once for each angle. After a angle has been added, you can modify its force field parameters by calling setAngleParameters().
Member Function Documentation
| def __del__ | ( | self | ) |
__del__(self)
Reimplemented from Force.
| def __init__ | ( | self, | ||
| args | ||||
| ) |
__init__(self) -> AmoebaVdwForce __init__(self, AmoebaVdwForce other) -> AmoebaVdwForce
Create a Amoeba VdwForce.
| def addParticle | ( | self, | ||
| args | ||||
| ) |
addParticle(self, int ivIndex, int classIndex, double sigma, double epsilon, double reductionFactor) -> int
Set the force field parameters for a vdw particle.
- Parameters:
-
particleIndex the particle index ivIndex the iv index classIndex the class index into the sig-eps table sigma vdw sigma epsilon vdw epsilon reductionFactor the reduction factor
| def getCutoff | ( | self | ) |
getCutoff(self) -> double
Get cutoff
| def getEpsilonCombiningRule | ( | self | ) |
getEpsilonCombiningRule(self) -> string
Get epsilon combining rule
| def getNumParticles | ( | self | ) |
getNumParticles(self) -> int
Get the number of particles
| def getParticleExclusions | ( | self, | ||
| args | ||||
| ) |
getParticleExclusions(self, int particleIndex)
Get exclusions for specified particle
- Parameters:
-
particleIndex particle index exclusions output vector of exclusions
| def getParticleParameters | ( | self, | ||
| args | ||||
| ) |
getParticleParameters(self, int particleIndex)
Get the force field parameters for a vdw particle.
- Parameters:
-
particleIndex the particle index ivIndex the iv index classIndex the class index into the sig-eps table sigma vdw sigma epsilon vdw epsilon reductionFactor the reduction factor
| def getPBC | ( | self | ) |
getPBC(self) -> int
Get periodic boundary conditions flag
| def getSigmaCombiningRule | ( | self | ) |
getSigmaCombiningRule(self) -> string
Get sigma combining rule
| def getUseNeighborList | ( | self | ) |
getUseNeighborList(self) -> int
Get neighbor list flag for vdw ixn
| def setCutoff | ( | self, | ||
| args | ||||
| ) |
setCutoff(self, double cutoff)
Set cutoff
- Parameters:
-
cutoff cutoff
| def setEpsilonCombiningRule | ( | self, | ||
| args | ||||
| ) |
setEpsilonCombiningRule(self, string epsilonCombiningRule)
Set epsilon combining rule
- Parameters:
-
epsilonCombiningRule epsilon combining rule: 'ARITHMETIC', 'GEOMETRIC'. 'HARMONIC', 'HHG'
| def setParticleExclusions | ( | self, | ||
| args | ||||
| ) |
setParticleExclusions(self, int particleIndex, vectori exclusions)
Set exclusions for specified particle
- Parameters:
-
particleIndex particle index exclusions output vector of exclusions
| def setParticleParameters | ( | self, | ||
| args | ||||
| ) |
setParticleParameters(self, int particleIndex, int ivIndex, int classIndex, double sigma, double epsilon, double reductionFactor)
Set the force field parameters for a vdw particle.
- Parameters:
-
particleIndex the particle index ivIndex the iv index classIndex the class index into the sig-eps table sigma vdw sigma epsilon vdw epsilon reductionFactor the reduction factor
| def setPBC | ( | self, | ||
| args | ||||
| ) |
setPBC(self, int pbcFlag)
Set flag for employing periodic boundary conditions
- Parameters:
-
pbcFlag if nonozero, use periodic boundary conditions
| def setSigmaCombiningRule | ( | self, | ||
| args | ||||
| ) |
setSigmaCombiningRule(self, string sigmaCombiningRule)
Set sigma combining rule
- Parameters:
-
sigmaCombiningRule sigma combining rule: 'ARITHMETIC', 'GEOMETRIC'. 'CUBIC-MEAN'
| def setUseNeighborList | ( | self, | ||
| args | ||||
| ) |
setUseNeighborList(self, int neighborListFlag)
Set flag for using neighbor list for vdw ixn
- Parameters:
-
neighboristFlag neighbor list flag
Member Data Documentation
The documentation for this class was generated from the following file:
- openmm.py
