RPMDIntegrator Class Reference
This is an Integrator which simulates a System using ring polymer molecular dynamics (RPMD). More...
Public Member Functions | |
| def | getNumCopies |
| getNumCopies(self) -> int | |
| def | getTemperature |
| getTemperature(self) -> double | |
| def | setTemperature |
| setTemperature(self, double temp) | |
| def | getFriction |
| getFriction(self) -> double | |
| def | setFriction |
| setFriction(self, double coeff) | |
| def | getRandomNumberSeed |
| getRandomNumberSeed(self) -> int | |
| def | setRandomNumberSeed |
| setRandomNumberSeed(self, int seed) | |
| def | setPositions |
| setPositions(self, int copy, std.vector<(Vec3,std.allocator<(Vec3)>)> positions) | |
| def | setVelocities |
| setVelocities(self, int copy, std.vector<(Vec3,std.allocator<(Vec3)>)> velocities) | |
| def | step |
| step(self, int steps) | |
| def | getState |
| getState(self, copy, getPositions = False, getVelocities = False, getForces = False, getEnergy = False, getParameters = False, enforcePeriodicBox = False, groups = -1) -> State Get a State object recording the current state information about one copy of the system. | |
| def | __init__ |
| __init__(self, int numCopies, double temperature, double frictionCoeff, double stepSize) -> RPMDIntegrator __init__(self, RPMDIntegrator other) -> RPMDIntegrator | |
| def | __del__ |
| __del__(self) | |
Public Attributes | |
| this | |
Detailed Description
This is an Integrator which simulates a System using ring polymer molecular dynamics (RPMD).
It simulates many copies of the System, with successive copies connected by harmonic springs to form a ring. This allows certain quantum mechanical effects to be efficiently simulated.
Because this Integrator simulates many copies of the System at once, it must be used differently from other Integrators. Instead of setting positions and velocities by calling methods of the Context, you should use the corresponding methods of the Integrator to set them for specific copies of the System. Similarly, you should retrieve state information for particular copies by calling getState() on the Integrator. Do not query the Context for state information.
Member Function Documentation
| def __del__ | ( | self | ) |
__del__(self)
Reimplemented from Integrator.
| def __init__ | ( | self, | ||
| args | ||||
| ) |
__init__(self, int numCopies, double temperature, double frictionCoeff, double stepSize) -> RPMDIntegrator __init__(self, RPMDIntegrator other) -> RPMDIntegrator
Create a RPMDIntegrator.
- Parameters:
-
numCopies the number of copies of the system that should be simulated temperature the temperature of the heat bath (in Kelvin) frictionCoeff the friction coefficient which couples the system to the heat bath (in inverse picoseconds) stepSize the step size with which to integrator the system (in picoseconds)
| 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 getNumCopies | ( | self | ) |
getNumCopies(self) -> int
Get the number of copies of the system being simulated.
| def getRandomNumberSeed | ( | self | ) |
getRandomNumberSeed(self) -> int
Get the random number seed. See setRandomNumberSeed() for details.
| def getState | ( | self, | ||
| copy, | ||||
getPositions = False, |
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getVelocities = False, |
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getForces = False, |
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getEnergy = False, |
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getParameters = False, |
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enforcePeriodicBox = False, |
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groups = -1 | ||||
| ) |
getState(self, copy, getPositions = False, getVelocities = False, getForces = False, getEnergy = False, getParameters = False, enforcePeriodicBox = False, groups = -1) -> State Get a State object recording the current state information about one copy of the system.
copy -- the index of the copy for which to retrieve state information getPositions -- whether to store particle positions in the State getVelocities -- whether to store particle velocities in the State getForces -- whether to store the forces acting on particles in the State getEnergy -- whether to store potential and kinetic energy in the State getParameter -- whether to store context parameters in the State enforcePeriodicBox -- if false, the position of each particle will be whatever position is stored in the Context, regardless of periodic boundary conditions. If true, particle positions will be translated so the center of every molecule lies in the same periodic box. groups -- a set of bit flags for which force groups to include when computing forces and energies. Group i will be included if (groups&(1<<i)) != 0. The default value includes all groups.
| def getTemperature | ( | self | ) |
getTemperature(self) -> double
Get the temperature of the heat bath (in Kelvin).
| 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 setPositions | ( | self, | ||
| args | ||||
| ) |
setPositions(self, int copy, std.vector<(Vec3,std.allocator<(Vec3)>)> positions)
Set the positions of all particles in one copy of the system.
- Parameters:
-
copy the index of the copy for which to set positions positions the positions of all particles in the system
| 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 setVelocities | ( | self, | ||
| args | ||||
| ) |
setVelocities(self, int copy, std.vector<(Vec3,std.allocator<(Vec3)>)> velocities)
Get the velocities of all particles in one copy of the system.
- Parameters:
-
copy the index of the copy for which to set velocities velocities the velocities of all particles in the system
| 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.
Member Data Documentation
The documentation for this class was generated from the following file:
- openmm.py
