VariableLangevinIntegrator Class Reference
This is an error contolled, variable time step Integrator that simulates a System using Langevin dynamics. More...
Public Member Functions | |
| def | getTemperature |
| getTemperature(self) -> double | |
| def | setTemperature |
| setTemperature(self, double temp) | |
| def | getFriction |
| getFriction(self) -> double | |
| def | setFriction |
| setFriction(self, double coeff) | |
| def | getErrorTolerance |
| getErrorTolerance(self) -> double | |
| def | setErrorTolerance |
| setErrorTolerance(self, double tol) | |
| def | getRandomNumberSeed |
| getRandomNumberSeed(self) -> int | |
| def | setRandomNumberSeed |
| setRandomNumberSeed(self, int seed) | |
| def | step |
| step(self, int steps) | |
| def | stepTo |
| stepTo(self, double time) | |
| def | __init__ |
| __init__(self, double temperature, double frictionCoeff, double errorTol) -> VariableLangevinIntegrator __init__(self, VariableLangevinIntegrator other) -> VariableLangevinIntegrator | |
| def | __del__ |
| __del__(self) | |
Public Attributes | |
| this | |
Detailed Description
This is an error contolled, variable time step Integrator that simulates a System using Langevin dynamics.
It compares the result of the Langevin integrator to that of an explicit Euler integrator, takes the difference between the two as a measure of the integration error in each time step, and continuously adjusts the step size to keep the error below a specified tolerance. This both improves the stability of the integrator and allows it to take larger steps on average, while still maintaining comparable accuracy to a fixed step size integrator.
It is best not to think of the error tolerance as having any absolute meaning. It is just an adjustable parameter that affects the step size and integration accuracy. You should try different values to find the largest one that produces a trajectory sufficiently accurate for your purposes. 0.001 is often a good starting point.
Member Function Documentation
| def __del__ | ( | self | ) |
__del__(self)
Reimplemented from Integrator.
| def __init__ | ( | self, | ||
| args | ||||
| ) |
__init__(self, double temperature, double frictionCoeff, double errorTol) -> VariableLangevinIntegrator __init__(self, VariableLangevinIntegrator other) -> VariableLangevinIntegrator
Create a VariableLangevinIntegrator.
- Parameters:
-
temperature the temperature of the heat bath (in Kelvin) frictionCoeff the friction coefficient which couples the system to the heat bath (in inverse picoseconds) errorTol the error tolerance
| def getErrorTolerance | ( | self | ) |
getErrorTolerance(self) -> double
Get the error tolerance.
| def getFriction | ( | self | ) |
getFriction(self) -> double
Get the friction coefficient which determines how strongly the system is coupled to the heat bath (in inverse ps).
| def getRandomNumberSeed | ( | self | ) |
getRandomNumberSeed(self) -> int
Get the random number seed. See setRandomNumberSeed() for details.
| def getTemperature | ( | self | ) |
getTemperature(self) -> double
Get the temperature of the heat bath (in Kelvin).
| def setErrorTolerance | ( | self, | ||
| args | ||||
| ) |
setErrorTolerance(self, double tol)
Set the error tolerance.
| def setFriction | ( | self, | ||
| args | ||||
| ) |
setFriction(self, double coeff)
Set the friction coefficient which determines how strongly the system is coupled to the heat bath (in inverse ps).
- Parameters:
-
coeff the friction coefficient, measured in 1/ps
| def setRandomNumberSeed | ( | self, | ||
| args | ||||
| ) |
setRandomNumberSeed(self, int seed)
Set the random number seed. The precise meaning of this parameter is undefined, and is left up to each Platform to interpret in an appropriate way. It is guaranteed that if two simulations are run with different random number seeds, the sequence of random forces will be different. On the other hand, no guarantees are made about the behavior of simulations that use the same seed. In particular, Platforms are permitted to use non-deterministic algorithms which produce different results on successive runs, even if those runs were initialized identically.
| def setTemperature | ( | self, | ||
| args | ||||
| ) |
setTemperature(self, double temp)
Set the temperature of the heat bath (in Kelvin).
- Parameters:
-
temp the temperature of the heat bath, measured in Kelvin
| def step | ( | self, | ||
| args | ||||
| ) |
step(self, int steps)
Advance a simulation through time by taking a series of time steps.
- Parameters:
-
steps the number of time steps to take
Reimplemented from Integrator.
| def stepTo | ( | self, | ||
| args | ||||
| ) |
stepTo(self, double time)
Advance a simulation through time by taking a series of steps until a specified time is reached. When this method returns, the simulation time will exactly equal the time which was specified. If you call this method and specify a time that is earlier than the current time, it will return without doing anything.
- Parameters:
-
time the time to which the simulation should be advanced
Member Data Documentation
The documentation for this class was generated from the following file:
- openmm.py
