Store the parameters for a simulation thermostat. Includes Berendsen, Andersen, and Langevin methods. This class can be assembled like many of the control objects, i.e. MinimizationControls, based on namelists. More...

#include <thermostat.h>

Public Member Functions
ThermostatKind	getKind () const
	Get the kind of thermostat.

ThermostatPartition	getBathPartitions () const
	Indicate whether this thermostat applies a common target temperature to all atoms, to individual systems, or to some finer compartmentalization based on individual atoms.

PrecisionModel	getCacheConfiguration () const
	Get the random number caching precision.

int	getAtomCount () const
	Get the total number of atoms that this thermostat can serve.

int	getStepNumber () const
	Get the step number according to this thermostat. The thermostat will serve as an official reference for the official simulation step number.

int	getRandomSeed () const
	Get the random seed used to initialize Xoshiro256++ state vectors.

int	getRandomCacheDepth () const
	Get the random number cache depth. The quantity of random numbers that will be produced and cached for each atom is three times this setting, as it implies values for random perturbations in the Cartesian X, Y, and Z directions.

int	getInitialEvolutionStep () const
	Get the step at which to begin changing the temperature from its initial value T(init) to its final value T(final). This is the last step that the thermostat will pull the system towards a value of T(init). Afterwards, the target will begin to change.

int	getFinalEvolutionStep () const
	Get the step at which the temperature evolution is expected to be complete. This is the step when the thermostat will begin pulling the system towards T(final), although the system itself may or may not be there by this time.

ullint4	getGeneratorState (int atom_index, HybridTargetLevel tier=HybridTargetLevel::HOST) const
	Get the generator state for a particular atom. For retrieving large numbers of states, one should used the abstract.

double	getCachedRandomResult (int atom_index, int cache_row, HybridTargetLevel tier=HybridTargetLevel::HOST) const
	Get one of the cached random numbers. This function returns the result as a double-precision real, but if a single-precision result is queried it will be converted to double and can then be put back in a float without changing its value. For retrieving large numbers of results, one should used the abstract.

double	getInitialTemperature (int atom_index=0) const
	Get the initial target temperature for this thermostat, in units of Kelvin.

double	getFinalTemperature (int atom_index=0) const
	Get the end-point target temperature for this thermostat, in units of Kelvin.

template<typename T>
std::vector< T >	getTemperatureSpread (int step_number=0) const
	Get the spread of temperature targets for all segments of the thermostat at a specific time step.

std::vector< int4 >	getPartitionMap () const
	Get the partition boundaries between different segments of the thermostat as a vector of integer tuples, with the partition lower and upper boundaries in the "x" and "y" members, the number of constrained degrees of freedom in the "z" member, and the number of unconstrained degrees of freedom in the "w" member of each tuple.

template<typename Tcalc>
Tcalc	getAtomTarget (int atom_index=0) const
	Get the current target temperature for this thermostat, in units of Kelvin, for a specific atom.

template<typename Tcalc>
Tcalc	getPartitionTarget (int index=0) const
	Get the current target temperature for a specific partition within this thermostat, in units of Kelvin.

int	getPartitionConstrainedDoF (int index=0) const
	Get the number of constrained degrees of freedom for a particular partition of this thermostat.

int	getPartitionFreeDoF (int index=0) const
	Get the number of degrees of freedom for a particular partition of this thermostat, in absence of any constraints.

int	getAndersenResetFrequency () const
	Get the Andersen reset frequency.

double	getLangevinCollisionFrequency () const
	Get the collision frequency for the Langevin thermostat (in units of femtoseconds).

double	getLangevinImplicitFactor () const
	Get the "implicit" Langevin factor, the portion of the velocity update to apply immediately after forces have been computed.

double	getLangevinExplicitFactor () const
	Get the "explicit" Langevin factor, the portion of the velocity update to apply on the second half of the update, as new particle positions are being computed.

double	getTimeStep () const
	Get the time step, in units of femtoseconds.

ApplyConstraints	constrainGeometry () const
	Get the order whether to apply geometric constraints.

double	getRattleTolerance () const
	Get the convergence criterion for RATTLE bond length constraints.

int	getRattleIterations () const
	Get the number of RATTLE iterations to attempt.

bool	loadSynthesisForces () const
	Get an indication of whether extra forces should be loaded from the synthesis in periodic systems.

const Thermostat *	getSelfPointer () const
	Get a pointer to the object itself, useful if it has been passed to a function by.

void	setAtomCount (int atom_count_in, int new_seed=-1, const GpuDetails &gpu=null_gpu)
	Set the number of atoms for which the thermostat is responsible.

void	checkCompartments (const AtomGraphSynthesis *poly_ag)
	Check the compartmentalization if the thermostat regulates a synthesis of systems.

void	setEvolutionWindow (int init_step_in, int final_step_in)
	Set the step at which temperature evolution, away from T(init), shall begin.

void	setCacheConfiguration (PrecisionModel cache_config_in, const GpuDetails &gpu=null_gpu)
	Set the random number cache configuration.

void	setRandomCacheDepth (int depth_in, const GpuDetails &gpu=null_gpu)
	Set the random number cache depth. This value is kept on a tight leash, as it can easily lead to allocating too much memory. A hundred-thousand atom system with cache depth 8 leads to over 13.7MB of memory allocation.

void	setLangevinCollisionFrequency (double langevin_frequency_in)
	Set the collision frequency for the Langevin thermostat. This will also set the scaled form of the value.

void	setAndersenResetFrequency (int andersen_frequency_in)
	Set the Andersen velocity reassignment frequency. This will be taken from user input.

void	setTimeStep (double time_step_in)
	Set the time step. This will also set the scaled form of the value.

void	incrementStep ()
	Increase the step count by one. This will advance the simulation's official step counter.

void	decrementStep ()
	Decrease the step count by one. This will cause the simulation's official step counter to backtrack.

void	setGeometryConstraints (ApplyConstraints cnst_geometry_in)
	Set the instruction for carrying out geometric constraints during dynamics.

void	setRattleTolerance (double rattle_tolerance_in)
	Set the convergence criterion for RATTLE.

void	setRattleIterations (int rattle_iterations_in)
	Set the maximum number of iterations to take when attempting to converge RATTLE bond length constraints.

void	setSynthesisForceLoading (bool load_synthesis_forces_in=true)
	Set the integrator to take prior force computations residing in the PhaseSpaceSynthesis into account. This will have an effect in the dynamics of periodic systems when particle movement is fused to valence interaction computations. In this situation, by default all prior force computations would be expected to reside in the neighbor list grid (non-bonded forces). For non-periodic calculations, all prior force computations will be expected to accumulate in the PhaseSpaceSynthesis, meaning that this setting will have no effect.

void	validateTemperature (double temperature_in)
	Validate the initial or final target temperature.

void	validateEvolutionWindow ()
	Validate the initial and final steps for applying the temperature evolution.

void	validateRandomCacheDepth ()
	Validate the random number cache depth. A maxmimum cache depth of 15 (45 total random numbers per atom) is enforced, and tightened in cases of exceptionally large systems.

void	initializeRandomStates (int new_seed=default_thermostat_random_seed, int scrub_cycles=25, HybridTargetLevel tier=HybridTargetLevel::HOST, const GpuDetails &gpu=null_gpu)
	Initialize the random state vectors of a thermostat, whether for Langevin or Andersen thermostating. This passes a call on to a general-purpose function for seeding the generators and will recruit the GPU if available to expedite the process.

void	refresh (size_t index_start, size_t index_end, int refresh_depth=0)
	Fill or refill the random number cache for a subset of the atoms, advancing the thermostat's random number generators in the process. This CPU-based function is intended to mimic GPU functionality, but the GPU operations are expected to be fused with other kernels.


	Thermostat (ThermostatKind kind_in=ThermostatKind::NONE, PrecisionModel cache_config_in=PrecisionModel::SINGLE, int random_seed_in=default_thermostat_random_seed, const GpuDetails &gpu=null_gpu)
	Constructors for the Thermostat object. Any information can be added via setter functions after constructing the object.

	Thermostat (int atom_count_in, ThermostatKind kind_in, double temperature_in, PrecisionModel cache_config_in=PrecisionModel::SINGLE, int random_seed_in=default_thermostat_random_seed, const GpuDetails &gpu=null_gpu)

	Thermostat (int atom_count_in, ThermostatKind kind_in, double init_temperature_in, double final_temperature_in, int initial_evolution_step_in, int final_evolution_step_in, PrecisionModel cache_config_in=PrecisionModel::SINGLE, int random_seed_in=default_thermostat_random_seed, const GpuDetails &gpu=null_gpu)

	Thermostat (int atom_count_in, ThermostatKind kind_in, const std::vector< double > &initial_temperatures_in, const std::vector< double > &final_temperatures_in, const std::vector< int2 > &paritions_in, int initial_evolution_step_in=default_tstat_evo_window_start, int final_evolution_step_in=default_tstat_evo_window_end, PrecisionModel cache_config_in=PrecisionModel::SINGLE, int random_seed_in=default_thermostat_random_seed, const GpuDetails &gpu=null_gpu)

	Thermostat (const AtomGraph *ag, ThermostatKind kind_in, double initial_temperature_in, double final_temperature_in, int initial_evolution_step_in, int final_evolution_step_in, PrecisionModel cache_config_in=PrecisionModel::SINGLE, int random_seed_in=default_thermostat_random_seed, const GpuDetails &gpu=null_gpu)

	Thermostat (const AtomGraph &ag, ThermostatKind kind_in, double initial_temperature_in, double final_temperature_in, int initial_evolution_step_in, int final_evolution_step_in, PrecisionModel cache_config_in=PrecisionModel::SINGLE, int random_seed_in=default_thermostat_random_seed, const GpuDetails &gpu=null_gpu)

	Thermostat (const AtomGraph *ag, ThermostatKind kind_in, double temperature_in=default_simulation_temperature, PrecisionModel cache_config_in=PrecisionModel::SINGLE, int random_seed_in=default_thermostat_random_seed, const GpuDetails &gpu=null_gpu)

	Thermostat (const AtomGraph &ag, ThermostatKind kind_in, double temperature_in=default_simulation_temperature, PrecisionModel cache_config_in=PrecisionModel::SINGLE, int random_seed_in=default_thermostat_random_seed, const GpuDetails &gpu=null_gpu)

	Thermostat (const AtomGraph *ag, ThermostatKind kind_in, const std::vector< double > &initial_temperatures_in, const std::vector< double > &final_temperatures_in, const std::vector< int2 > &paritions_in, int initial_evolution_step_in=default_tstat_evo_window_start, int final_evolution_step_in=default_tstat_evo_window_end, PrecisionModel cache_config_in=PrecisionModel::SINGLE, int random_seed_in=default_thermostat_random_seed, const GpuDetails &gpu=null_gpu)

	Thermostat (const AtomGraph &ag, ThermostatKind kind_in, const std::vector< double > &initial_temperatures_in, const std::vector< double > &final_temperatures_in, const std::vector< int2 > &paritions_in, int initial_evolution_step_in=default_tstat_evo_window_start, int final_evolution_step_in=default_tstat_evo_window_end, PrecisionModel cache_config_in=PrecisionModel::SINGLE, int random_seed_in=default_thermostat_random_seed, const GpuDetails &gpu=null_gpu)

	Thermostat (const AtomGraphSynthesis *poly_ag, ThermostatKind kind_in, double initial_temperature_in, double final_temperature_in, int initial_evolution_step_in, int final_evolution_step_in, PrecisionModel cache_config_in=PrecisionModel::SINGLE, int random_seed_in=default_thermostat_random_seed, const GpuDetails &gpu=null_gpu)

	Thermostat (const AtomGraphSynthesis &poly_ag, ThermostatKind kind_in, double initial_temperature_in, double final_temperature_in, int initial_evolution_step_in, int final_evolution_step_in, PrecisionModel cache_config_in=PrecisionModel::SINGLE, int random_seed_in=default_thermostat_random_seed, const GpuDetails &gpu=null_gpu)

	Thermostat (const AtomGraphSynthesis *poly_ag, ThermostatKind kind_in, double temperature_in=default_simulation_temperature, PrecisionModel cache_config_in=PrecisionModel::SINGLE, int random_seed_in=default_thermostat_random_seed, const GpuDetails &gpu=null_gpu)

	Thermostat (const AtomGraphSynthesis &poly_ag, ThermostatKind kind_in, double temperature_in=default_simulation_temperature, PrecisionModel cache_config_in=PrecisionModel::SINGLE, int random_seed_in=default_thermostat_random_seed, const GpuDetails &gpu=null_gpu)

	Thermostat (const AtomGraphSynthesis *poly_ag, ThermostatKind kind_in, const std::vector< double > &initial_temperatures_in, const std::vector< double > &final_temperatures_in, const std::vector< int2 > &paritions_in, int initial_evolution_step_in=default_tstat_evo_window_start, int final_evolution_step_in=default_tstat_evo_window_end, PrecisionModel cache_config_in=PrecisionModel::SINGLE, int random_seed_in=default_thermostat_random_seed, const GpuDetails &gpu=null_gpu)

	Thermostat (const AtomGraphSynthesis &poly_ag, ThermostatKind kind_in, const std::vector< double > &initial_temperatures_in, const std::vector< double > &final_temperatures_in, const std::vector< int2 > &paritions_in, int initial_evolution_step_in=default_tstat_evo_window_start, int final_evolution_step_in=default_tstat_evo_window_end, PrecisionModel cache_config_in=PrecisionModel::SINGLE, int random_seed_in=default_thermostat_random_seed, const GpuDetails &gpu=null_gpu)

	Thermostat (const AtomGraphSynthesis *poly_ag, const DynamicsControls &dyncon, const SystemCache &sc, const std::vector< int > &sc_origins, const GpuDetails &gpu=null_gpu)

	Thermostat (const AtomGraphSynthesis &poly_ag, const DynamicsControls &dyncon, const SystemCache &sc, const std::vector< int > &sc_origins, const GpuDetails &gpu=null_gpu)


	Thermostat (const Thermostat &original)=default
	The default copy and move constructors and assignment operators are best for this object with no POINTER-kind Hybrid objects.

	Thermostat (Thermostat &&original)=default

Thermostat &	operator= (const Thermostat &original)=default

Thermostat &	operator= (Thermostat &&original)=default


const ThermostatReader< double >	dpData (HybridTargetLevel tier=HybridTargetLevel::HOST) const
	Get the abstract.

ThermostatWriter< double >	dpData (HybridTargetLevel tier=HybridTargetLevel::HOST)

const ThermostatReader< float >	spData (HybridTargetLevel tier=HybridTargetLevel::HOST) const

ThermostatWriter< float >	spData (HybridTargetLevel tier=HybridTargetLevel::HOST)


void	setTemperature (double initial_temperature_in, double final_temperature_in=-1.0)
	Set the initial target temperature.

void	setTemperature (const std::vector< double > &initial_temperatures_in, const std::vector< double > &final_temperatures_in, const std::vector< int2 > &partitions_in)

Detailed Description

Store the parameters for a simulation thermostat. Includes Berendsen, Andersen, and Langevin methods. This class can be assembled like many of the control objects, i.e. MinimizationControls, based on namelists.

Constructor & Destructor Documentation

◆ Thermostat() [1/2]

stormm::trajectory::Thermostat::Thermostat	(	ThermostatKind	kind_in = ThermostatKind::NONE,
		PrecisionModel	cache_config_in = PrecisionModel::SINGLE,
		int	random_seed_in = default_thermostat_random_seed,
		const GpuDetails &	gpu = null_gpu )

Constructors for the Thermostat object. Any information can be added via setter functions after constructing the object.

Overloaded:

Construct a blank thermostat that applies no regulation
Construct a specific type of thermostat with default settings
Accept a type of thermostat and a temperature to maintain
Accept a temperature evolution profile
Accept a total number of atoms and a compartmentalization plan

Parameters

temperature_in A flat temperature to apply at all times

◆ Thermostat() [2/2]

stormm::trajectory::Thermostat::Thermostat ( const Thermostat & original )

default

The default copy and move constructors and assignment operators are best for this object with no POINTER-kind Hybrid objects.

Parameters

original	The object to copy or move
other	An object to clone or replace the present object with

Member Function Documentation

◆ checkCompartments()

void stormm::trajectory::Thermostat::checkCompartments ( const AtomGraphSynthesis * poly_ag )

Check the compartmentalization if the thermostat regulates a synthesis of systems.

Parameters

poly_ag The topology synthesis describing systems to regulate

◆ dpData()

const ThermostatReader< double > stormm::trajectory::Thermostat::dpData ( HybridTargetLevel tier = HybridTargetLevel::HOST ) const

Get the abstract.

Overloaded:

Get a reader for a const object
Get a (partially) writeable abstract for a non-const object

Parameters

tier	Indicate whether to take pointers to memory on the CPU host or on the GPU device

◆ getAtomTarget()

template<typename Tcalc>

Tcalc stormm::trajectory::Thermostat::getAtomTarget ( int atom_index = 0 ) const

Get the current target temperature for this thermostat, in units of Kelvin, for a specific atom.

Parameters

atom_index Index of the atom of interest

◆ getCachedRandomResult()

double stormm::trajectory::Thermostat::getCachedRandomResult	(	int	atom_index,
		int	cache_row,
		HybridTargetLevel	tier = HybridTargetLevel::HOST ) const

Get one of the cached random numbers. This function returns the result as a double-precision real, but if a single-precision result is queried it will be converted to double and can then be put back in a float without changing its value. For retrieving large numbers of results, one should used the abstract.

Parameters

atom_index	Index of the atom for which to get a result
cache_row	Row of the cache to query (the 0th row offers a result for Cartesian X influence on the atom, the 4th row offers a result for the Carteisan Y influence on the atom one cycle in the future)
tier	Indicate whether to take information from the CPU host or GPU device

◆ getFinalTemperature()

double stormm::trajectory::Thermostat::getFinalTemperature ( int atom_index = 0 ) const

Get the end-point target temperature for this thermostat, in units of Kelvin.

Parameters

atom_index Index of the atom of interest

◆ getInitialTemperature()

double stormm::trajectory::Thermostat::getInitialTemperature ( int atom_index = 0 ) const

Get the initial target temperature for this thermostat, in units of Kelvin.

Parameters

atom_index Index of the atom of interest (only provided if there are different regulated temperatures for unique subsets of atoms)

◆ getPartitionConstrainedDoF()

int stormm::trajectory::Thermostat::getPartitionConstrainedDoF ( int index = 0 ) const

Get the number of constrained degrees of freedom for a particular partition of this thermostat.

Parameters

index Index of the partition of interest

◆ getPartitionFreeDoF()

int stormm::trajectory::Thermostat::getPartitionFreeDoF ( int index = 0 ) const

Get the number of degrees of freedom for a particular partition of this thermostat, in absence of any constraints.

Parameters

index Index of the partition of interest

◆ getPartitionTarget()

template<typename Tcalc>

Tcalc stormm::trajectory::Thermostat::getPartitionTarget ( int index = 0 ) const

Get the current target temperature for a specific partition within this thermostat, in units of Kelvin.

Parameters

index Index of the partition of interest

◆ getTemperatureSpread()

template<typename T>

std::vector< T > stormm::trajectory::Thermostat::getTemperatureSpread ( int step_number = 0 ) const

Get the spread of temperature targets for all segments of the thermostat at a specific time step.

Parameters

step_number The step at which to assess the temperature targets

◆ initializeRandomStates()

void stormm::trajectory::Thermostat::initializeRandomStates	(	int	new_seed = default_thermostat_random_seed,
		int	scrub_cycles = 25,
		HybridTargetLevel	tier = HybridTargetLevel::HOST,
		const GpuDetails &	gpu = null_gpu )

Initialize the random state vectors of a thermostat, whether for Langevin or Andersen thermostating. This passes a call on to a general-purpose function for seeding the generators and will recruit the GPU if available to expedite the process.

Parameters

new_seed	A new random number seed to apply, if different from the one used during construction of this Thermostat object
scrub_cycles	Number of cycles of Xoshiro256++ generation to run in order to ensure that the newly seeded generators produce high-quality results
tier	Indicate whether to seed random states and cached numbers on the CPU host alone, or on the GPU device. Random number state vectors will be mirrored at both levels of memory if the GPU device layer is initialized, but the generators will not be advanced on the host.
gpu	Specifications of the GPU in use (if applicable)

◆ refresh()

void stormm::trajectory::Thermostat::refresh	(	size_t	index_start,
		size_t	index_end,
		int	refresh_depth = 0 )

Fill or refill the random number cache for a subset of the atoms, advancing the thermostat's random number generators in the process. This CPU-based function is intended to mimic GPU functionality, but the GPU operations are expected to be fused with other kernels.

Parameters

index_start	Starting index in the list of all atoms
index_end	Upper bound of atoms for which to cache random numbers
refresh_depth	The depth to which the cache is to be refreshed (the default of 0 will refresh all layers of prepared random numbers)

◆ setAndersenResetFrequency()

void stormm::trajectory::Thermostat::setAndersenResetFrequency ( int andersen_frequency_in )

Set the Andersen velocity reassignment frequency. This will be taken from user input.

Parameters

andersen_frequency_in The number of time steps between Andersen velocity resets

◆ setAtomCount()

void stormm::trajectory::Thermostat::setAtomCount	(	int	atom_count_in,
		int	new_seed = -1,
		const GpuDetails &	gpu = null_gpu )

Set the number of atoms for which the thermostat is responsible.

Parameters

atom_count_in	The total number of atoms to assign to this thermostat, whether all part of one system or a padded number collected within a synthesis
new_seed	New random number generator seed for initializing the random cache (if applicable). If set to -1, the object's original seed will be taken. Otherwise, the object will later record having been initialized with new_seed.
gpu	Details of any available GPU. If a real GPU is available, the random state vectors and cache will be initialized on the CPU host as well as the GPU device.

◆ setCacheConfiguration()

void stormm::trajectory::Thermostat::setCacheConfiguration	(	PrecisionModel	cache_config_in,
		const GpuDetails &	gpu = null_gpu )

Set the random number cache configuration.

Parameters

cache_config_in	The manner in which the cache is to be configured, storing random numbers in single- or double-precision
gpu	Details of the GPU that will handle future calculations with this thermostat. This is critical for getting random state vectors initialized on the GPU.

◆ setEvolutionWindow()

void stormm::trajectory::Thermostat::setEvolutionWindow	(	int	init_step_in,
		int	final_step_in )

Set the step at which temperature evolution, away from T(init), shall begin.

Parameters

init_step_in	Step number at which temperature evolution begins. Prior to this step, each bath's target temperature is its initial temperature. Following this step, the target temperature of each bath becomes a linear mixture of the initial and final temperatures.
init_step_in	Step number at which temperature evolution ends. After this point, the final temperature of each bath is the target.

◆ setGeometryConstraints()

void stormm::trajectory::Thermostat::setGeometryConstraints ( ApplyConstraints cnst_geometry_in )

Set the instruction for carrying out geometric constraints during dynamics.

Parameters

cnst_geometry_in The order for constraints to be applied

◆ setLangevinCollisionFrequency()

void stormm::trajectory::Thermostat::setLangevinCollisionFrequency ( double langevin_frequency_in )

Set the collision frequency for the Langevin thermostat. This will also set the scaled form of the value.

Parameters

langevin_frequency_in The collision frequency to take, in events per femtosecond

◆ setRandomCacheDepth()

void stormm::trajectory::Thermostat::setRandomCacheDepth	(	int	depth_in,
		const GpuDetails &	gpu = null_gpu )

Set the random number cache depth. This value is kept on a tight leash, as it can easily lead to allocating too much memory. A hundred-thousand atom system with cache depth 8 leads to over 13.7MB of memory allocation.

Parameters

depth_in	The depth to take
gpu	Details of the GPU that will handle future calculations with this thermostat. This is critical for getting random state vectors initialized on the GPU.

◆ setRattleIterations()

void stormm::trajectory::Thermostat::setRattleIterations ( int rattle_iterations_in )

Set the maximum number of iterations to take when attempting to converge RATTLE bond length constraints.

Parameters

rattle_iterations_in The number of iterations to permit

◆ setRattleTolerance()

void stormm::trajectory::Thermostat::setRattleTolerance ( double rattle_tolerance_in )

Set the convergence criterion for RATTLE.

Parameters

rattle_tolerance_in The convergence criterion to set

◆ setSynthesisForceLoading()

void stormm::trajectory::Thermostat::setSynthesisForceLoading ( bool load_synthesis_forces_in = true )

Set the integrator to take prior force computations residing in the PhaseSpaceSynthesis into account. This will have an effect in the dynamics of periodic systems when particle movement is fused to valence interaction computations. In this situation, by default all prior force computations would be expected to reside in the neighbor list grid (non-bonded forces). For non-periodic calculations, all prior force computations will be expected to accumulate in the PhaseSpaceSynthesis, meaning that this setting will have no effect.

Parameters

load_synthesis_forces_in Indicate whether the synthesis forces shuld be loaded

◆ setTemperature()

void stormm::trajectory::Thermostat::setTemperature	(	double	initial_temperature_in,
		double	final_temperature_in = -1.0 )

Set the initial target temperature.

Overloaded:

Set the temperature to a single value (if the final temperatures are also consistent, this will set common_temperature to TRUE and de-allocate any existing Hybrid data related to unique temperature compartments).
Set the temperatures of unique subsets of the atoms to a series of values based on a compartmentalization

Parameters

init_temp_in	Temperature or temperatures that the thermostat shall start with, and continue to apply until the initial step in its evolution
partitions_in	A new compartmentalization scheme (the same interpretation described in setCompartments() above applies)

◆ setTimeStep()

void stormm::trajectory::Thermostat::setTimeStep ( double time_step_in )

Set the time step. This will also set the scaled form of the value.

Parameters

time_step_in The time step to take, in units of femtoseconds

◆ validateEvolutionWindow()

void stormm::trajectory::Thermostat::validateEvolutionWindow ( )

Validate the initial and final steps for applying the temperature evolution.

Parameters

step_in The step number to validate (it will be checked for a positive value)

The documentation for this class was generated from the following files:

src/Trajectory/thermostat.h
src/Trajectory/thermostat.cpp

Public Member Functions

Detailed Description

Constructor & Destructor Documentation

◆ Thermostat() [1/2]

◆ Thermostat() [2/2]

Member Function Documentation

◆ checkCompartments()

◆ dpData()

◆ getAtomTarget()

◆ getCachedRandomResult()

◆ getFinalTemperature()

◆ getInitialTemperature()

◆ getPartitionConstrainedDoF()

◆ getPartitionFreeDoF()

◆ getPartitionTarget()

◆ getTemperatureSpread()

◆ initializeRandomStates()

◆ refresh()

◆ setAndersenResetFrequency()

◆ setAtomCount()

◆ setCacheConfiguration()

◆ setEvolutionWindow()

◆ setGeometryConstraints()

◆ setLangevinCollisionFrequency()

◆ setRandomCacheDepth()

◆ setRattleIterations()

◆ setRattleTolerance()

◆ setSynthesisForceLoading()

◆ setTemperature()

◆ setTimeStep()

◆ validateEvolutionWindow()