NoseHooverIntegrator¶

class OpenMM::NoseHooverIntegrator¶

This is an Integrator which simulates a System using one or more Nose Hoover chain thermostats, using the “middle” leapfrog propagation algorithm described in J. Phys. Chem. A 2019, 123, 6056-6079.

Methods

`NoseHooverIntegrator`	Create a `NoseHooverIntegrator`.
`NoseHooverIntegrator`	Create a `NoseHooverIntegrator`.
`~NoseHooverIntegrator`
`step`	Advance a simulation through time by taking a series of time steps.
`addThermostat`	Add a simple Nose-Hoover Chain thermostat to control the temperature of the full system
`addSubsystemThermostat`	Add a Nose-Hoover Chain thermostat to control the temperature of a collection of atoms and/or pairs of connected atoms within the full system.
`getTemperature`	Get the temperature of the i-th chain for controling absolute particle motion (in Kelvin).
`setTemperature`	set the (absolute motion) temperature of the i-th chain.
`getRelativeTemperature`	Get the temperature of the i-th chain for controling pairs’ relative particle motion (in Kelvin).
`setRelativeTemperature`	set the (relative pair motion) temperature of the i-th chain.
`getCollisionFrequency`	Get the collision frequency for absolute motion of the i-th chain (in 1/picosecond).
`setCollisionFrequency`	Set the collision frequency for absolute motion of the i-th chain.
`getRelativeCollisionFrequency`	Get the collision frequency for pairs’ relative motion of the i-th chain (in 1/picosecond).
`setRelativeCollisionFrequency`	Set the collision frequency for pairs’ relative motion of the i-th chain.
`computeHeatBathEnergy`	Compute the total (potential + kinetic) heat bath energy for all heat baths associated with this integrator, at the current time.
`getNumThermostats`	Get the number of Nose-Hoover chains registered with this integrator.
`getThermostat`	Get the `NoseHooverChain` thermostat
`hasSubsystemThermostats`	Return false, if this integrator was set up with the ‘default constructor’ that thermostats the whole system, true otherwise.
`getMaximumPairDistance`	Gets the maximum distance (in nm) that a connected pair may stray from each other.
`setMaximumPairDistance`	Sets the maximum distance (in nm) that a connected pair may stray from each other, implemented using a hard wall.
`getAllThermostatedIndividualParticles`	Get a list of all individual atoms (i.e.
`getAllThermostatedPairs`	Get a list of all connected Drude-like pairs, and their target relative temperature, in the system.

NoseHooverIntegrator(double stepSize)¶

Create a NoseHooverIntegrator(). This version creates a bare leapfrog integrator with no thermostats; any thermostats should be added by calling addThermostat.

Parameters

stepSize – the step size with which to integrate the system (in picoseconds)

NoseHooverIntegrator(double temperature, double collisionFrequency, double stepSize, int chainLength = 3, int numMTS = 3, int numYoshidaSuzuki = 7)¶

Create a NoseHooverIntegrator().

Parameters

temperature – the target temperature for the system (in Kelvin).
collisionFrequency – the frequency of the interaction with the heat bath (in inverse picoseconds).
stepSize – the step size with which to integrate the system (in picoseconds)
chainLength – the number of beads in the Nose-Hoover chain.
numMTS – the number of step in the multiple time step chain propagation algorithm.
numYoshidaSuzuki – the number of terms in the Yoshida-Suzuki multi time step decomposition used in the chain propagation algorithm (must be 1, 3, 5, or 7).

~NoseHooverIntegrator()¶

void step(int steps)¶

Advance a simulation through time by taking a series of time steps.

Parameters

steps – the number of time steps to take

int addThermostat(double temperature, double collisionFrequency, int chainLength, int numMTS, int numYoshidaSuzuki)¶

Add a simple Nose-Hoover Chain thermostat to control the temperature of the full system

Parameters

temperature – the target temperature for the system.
collisionFrequency – the frequency of the interaction with the heat bath (in 1/ps).
chainLength – the number of beads in the Nose-Hoover chain
numMTS – the number of step in the multiple time step chain propagation algorithm.
numYoshidaSuzuki – the number of terms in the Yoshida-Suzuki multi time step decomposition used in the chain propagation algorithm (must be 1, 3, 5, or 7).

int addSubsystemThermostat(const std::vector<int> &thermostatedParticles, const std::vector<std::pair<int, int>> &thermostatedPairs, double temperature, double collisionFrequency, double relativeTemperature, double relativeCollisionFrequency, int chainLength = 3, int numMTS = 3, int numYoshidaSuzuki = 7)¶

Add a Nose-Hoover Chain thermostat to control the temperature of a collection of atoms and/or pairs of connected atoms within the full system. A list of atoms defining the atoms to be thermostated is provided and the thermostat will only control members of that list. Additionally a list of pairs of connected atoms may be provided; in this case both the center of mass absolute motion of each pair is controlled as well as their motion relative to each other, which is independently thermostated. If both the list of thermostated particles and thermostated pairs are empty all particles will be thermostated.

Parameters

thermostatedParticles – list of particle ids to be thermostated.
thermostatedPairs – a list of pairs of connected atoms whose absolute center of mass motion and motion relative to one another will be independently thermostated.
temperature – the target temperature for each pair’s absolute of center of mass motion.
collisionFrequency – the frequency of the interaction with the heat bath for the pairs’ center of mass motion (in 1/ps).
relativeTemperature – the target temperature for each pair’s relative motion.
relativeCollisionFrequency – the frequency of the interaction with the heat bath for the pairs’ relative motion (in 1/ps).
chainLength – the number of beads in the Nose-Hoover chain.
numMTS – the number of step in the multiple time step chain propagation algorithm.
numYoshidaSuzuki – the number of terms in the Yoshida-Suzuki multi time step decomposition used in the chain propagation algorithm (must be 1, 3, 5, or 7).

double getTemperature(int chainID = 0) const¶

Get the temperature of the i-th chain for controling absolute particle motion (in Kelvin).

Parameters

chainID – the index of the Nose-Hoover chain thermostat (default=0).

Returns: the temperature.

void setTemperature(double temperature, int chainID = 0)¶

set the (absolute motion) temperature of the i-th chain.

Parameters

temperature – the temperature for the Nose-Hoover chain thermostat (in Kelvin).
chainID – The id of the Nose-Hoover chain thermostat for which the temperature is set (default=0).

double getRelativeTemperature(int chainID = 0) const¶

Get the temperature of the i-th chain for controling pairs’ relative particle motion (in Kelvin).

Parameters

chainID – the index of the Nose-Hoover chain thermostat (default=0).

Returns: the temperature.

void setRelativeTemperature(double temperature, int chainID = 0)¶

set the (relative pair motion) temperature of the i-th chain.

Parameters

temperature – the temperature for the Nose-Hoover chain thermostat (in Kelvin).
chainID – The id of the Nose-Hoover chain thermostat for which the temperature is set (default=0).

double getCollisionFrequency(int chainID = 0) const¶

Get the collision frequency for absolute motion of the i-th chain (in 1/picosecond).

Parameters

chainID – the index of the Nose-Hoover chain thermostat (default=0).

Returns: the collision frequency.

void setCollisionFrequency(double frequency, int chainID = 0)¶

Set the collision frequency for absolute motion of the i-th chain.

Parameters

frequency – the collision frequency in picosecond.
chainID – the index of the Nose-Hoover chain thermostat (default=0).

double getRelativeCollisionFrequency(int chainID = 0) const¶

Get the collision frequency for pairs’ relative motion of the i-th chain (in 1/picosecond).

Parameters

chainID – the index of the Nose-Hoover chain thermostat (default=0).

Returns: the collision frequency.

void setRelativeCollisionFrequency(double frequency, int chainID = 0)¶

Set the collision frequency for pairs’ relative motion of the i-th chain.

Parameters

frequency – the collision frequency in picosecond.
chainID – the index of the Nose-Hoover chain thermostat (default=0).

double computeHeatBathEnergy()¶: Compute the total (potential + kinetic) heat bath energy for all heat baths associated with this integrator, at the current time.

int getNumThermostats() const¶: Get the number of Nose-Hoover chains registered with this integrator.

const NoseHooverChain &getThermostat(int chainID = 0) const¶

Get the NoseHooverChain thermostat

Parameters

chainID – the index of the Nose-Hoover chain thermostat (default=0).

bool hasSubsystemThermostats() const¶: Return false, if this integrator was set up with the ‘default constructor’ that thermostats the whole system, true otherwise. Required for serialization.

double getMaximumPairDistance() const¶: Gets the maximum distance (in nm) that a connected pair may stray from each other. If zero, there are no constraints on the intra-pair separation.

void setMaximumPairDistance(double distance)¶: Sets the maximum distance (in nm) that a connected pair may stray from each other, implemented using a hard wall. If set to zero, the hard wall constraint is omited and the pairs are free to be separated by any distance.

const std::vector<int> &getAllThermostatedIndividualParticles() const¶: Get a list of all individual atoms (i.e. not involved in a connected Drude-like pair) in the system.

const std::vector<std::tuple<int, int, double>> &getAllThermostatedPairs() const¶: Get a list of all connected Drude-like pairs, and their target relative temperature, in the system.