Object to encapsulate molecular dynamics control information. Like other namelist encapsualtors, this object can take input file data as part of its construction, or by a series of setters. Validation of each piece of data is handled as it appears either in the contructor or via setters. Getter functions dispense the internal information to any application using STORMM libraries. More...

#include <nml_dynamics.h>

Public Member Functions
int	getStepCount () const
	Get the total number of dynamics steps.

int	getDiagnosticPrintFrequency () const
	Get the printing frequency for energies and other state variables of the system or collection of systems.

int	getTrajectoryPrintFrequency () const
	Get the printing frequency for trajectory snapshots.

int	getCenterOfMassMotionPurgeFrequency () const
	Get the frequency for purging motion of the system's center of mass.

double	getTimeStep () const
	Get the simulation time step.

double	getElectrostaticCutoff () const
	Get the electrostatic pairwise cutoff in periodic simulations.

double	getVanDerWaalsCutoff () const
	Get the van-der Waals pairwise cutoff in periodic simulations.

VdwSumMethod	getVdwSummation () const
	Get the method for computing van-der Waals interactions between particles.

double	getCoulombConstant () const
	Get the value of Coulomb's constant.

double	getElec14Screening () const
	Get the electrostatic 1:4 screening value.

double	getVdw14Screening () const
	Get the van-der Waals 1:4 screening value.

bool	coulombSetByUser () const
	Report whether the value of Coulomb's constant was set explicitly or left at the default value.

bool	elec14SetByUser () const
	Report whether the electrostatic 1:4 scaling was set explicitly or left at its default value.

bool	vdw14SetByUser () const
	Report whether the van-der Waals 1:4 scaling was set explicitly or left at its default value.

ApplyConstraints	constrainGeometry () const
	Indicate whether general geometric constraints (RATTLE for hub-and-spoke bonded groups, SETTLE for rigid water molecules) are to be implemented.

ApplyConstraints	useShake () const
	Indicate whether SHAKE (and, by extension, RATTLE in the velocity-Verlet integrator) should be implemented.

ApplyConstraints	useSettle () const
	Indicate whether SHAKE (and, by extension, RATTLE in the velocity-Verlet integrator) should be implemented.

double	getRattleTolerance () const
	Get the RATTLE tolerance.

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

RattleMethod	getCpuRattleMethod () const
	Get the CPU-based method of implementing RATTLE for multiple constrained bonds connected to one central atom. This determines the order in which the position of the central atom is updated with each iteration.

ThermostatKind	getThermostatKind () const
	Get the thermostat kind.

int	getThermostatEvolutionStart () const
	Get the starting step for temperature evolution from the initial temperature profile to the final temperature profile across all atoms and all systems.

int	getThermostatEvolutionEnd () const
	Get the final step for temperature evolution from the initial temperature profile to the final temperature profile across all atoms and all systems.

int	getThermostatCacheDepth () const
	Get the depth of the thermostat's random number cache.

int	getThermostatSeed () const
	Get the random seed to be used in the thermostat's random number generators.

int	getThermostatLayerCount () const
	Get the number of distinct layers to the thermostat, the number of different temperature and system groups that must be parsed (in order) that the temperature profiles at which to maintain all systems of the synthesis are to be maintained. This function also serves as a check on the consistency of array sizes: for each initial temeprature specification, there must be a final temperature specification, a label, a label index, and an atom mask (even if the latter three are "all", -1 (integer code for all), and "@=" (all atoms).

int	getAndersenFrequency () const
	Get the frequncy of velocity reassignments for a "massive" Andersen thermostat, one in which all velocities are reassigned after a particular number of steps.

double	getLangevinFrequency () const
	Get the Langevin collison frequency, in units of inverse femtoseconds.

PrecisionModel	getThermostatCacheConfig () const
	Get the thermostat cache configuration.

const std::vector< double > &	getInitialTemperatureTargets () const
	Get the vector of initial temperature targets for all groups of atoms and systems.

const std::vector< double > &	getFinalTemperatureTargets () const
	Get the vector of final temperature targets for all groups of atoms and systems.

const std::vector< std::string > &	getThermostatLabels () const
	Get the list of label groups within the systems cache to which each thermostated group of atoms belongs.

const std::vector< int > &	getThermostatLabelIndices () const
	Get the indices of systems within the label groups to which each thermostated group of atoms belongs.

const std::vector< std::string > &	getThermostatMasks () const
	Get the atom mask strings for each thermostated group of atoms.

int	getNTWarpMultiplicity () const
	Get the warp multiplicity for non-bonded pairwise calculations.

const NamelistEmulator &	getTranscript () const
	Get the original namelist emulator object as a transcript of the user input.

void	setStepCount (int total_step_count_in)
	Set the total number of dynamics steps.

void	setDiagnosticPrintFrequency (int diagnostic_frequency_in)
	Set the diagnostic printing frequency.

void	setTrajectoryPrintFrequency (int trajectory_frequency_in)
	Set the trajectory snapshot printing frequency.

void	setCenterOfMassMotionPurgeFrequency (int com_motion_purge_ferquency_in)
	Set the center of mass motion purge frequency.

void	setTimeStep (double time_step_in)
	Set the simulation time step.

void	setElectrostaticCutoff (double cutoff_in)
	Set the short-ranged electrostatic cutoff for the simulation.

void	setVanDerWaalsCutoff (double cutoff_in)
	Set the short-ranged van-der Waals cutoff for the simulation.

void	setCutoff (double cutoff_in)
	Set the cutoffs for short-ranged van-der Waals as well as electrostatic interactions in a periodic simulation.

void	setCoulombConstant (double coulomb_in)
	Set the value of Coulomb's constant.

void	setElec14Screening (double screening_in)
	Set the screening factor for 1:4 electrostatic interactions.

void	setVdw14Screening (double screening_in)
	Set the screening factor for 1:4 van-der Waals interactions.

void	setThermostatEvolutionStart (int thermo_evolution_start_in)
	Set the starting step for temperature evolution from the initial temperature profile to the final temperature profile across all atoms and all systems.

void	setThermostatEvolutionEnd (int step_number)
	Set the final step for temperature evolution from the initial temperature profile to the final temperature profile across all atoms and all systems.

void	setThermostatCacheDepth (int depth_in)
	Set the depth of the thermostat's random number cache.

void	setThermostatSeed (int igseed)
	Set the random seed to be used in the thermostat's random number generators.

void	setAndersenFrequency (int frequency_in)
	Set the velocity restart frequency for a "massive" Andersen thermostat.

void	setLangevinFrequency (double frequency_in)
	Set the stochastic collision frequency for a Langevin thermostat.

void	setThermostatGroup (double initial_target=default_simulation_temperature, double final_target=default_simulation_temperature, const std::string &label=std::string("all"), int label_index=-1, const std::string &mask=std::string("@="))
	Get the vector of initial temperature targets for all groups of atoms and systems.

void	setNTWarpMultiplicity (int mult_in)
	Get the warp multiplicity for non-bonded pairwise calculations. This applies only to periodic dynamics.


	DynamicsControls (ExceptionResponse policy_in=ExceptionResponse::DIE)
	The constructor can prepare an object with default settings or read the corresponding namelist to accept user input.

	DynamicsControls (const TextFile &tf, int start_line, bool found_nml, ExceptionResponse policy_in=ExceptionResponse::DIE, WrapTextSearch wrap=WrapTextSearch::NO)


	DynamicsControls (const DynamicsControls &original)=default
	As with other control objects, copy and move constructors, plus copy and move assignment operators, can all take their default forms.

	DynamicsControls (DynamicsControls &&original)=default

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

DynamicsControls &	operator= (DynamicsControls &&original)=default


void	setVdwSummation (const std::string &vdw_method_in)
	Set the strategy for evaluating the tails of van-der Waals (Lennard-Jones) interactions.

void	setVdwSummation (const VdwSumMethod vdw_method_in)


void	setGeometricConstraints (const std::string &constrain_geometry_in)
	Stipulate whether geometric constraints will be implemented.

void	setGeometricConstraints (ApplyConstraints constrain_geometry_in=ApplyConstraints::YES)


void	setUseShake (const std::string &use_shake_in)
	Stipulate whether bonds to hydrogen atoms will be held rigid at their equilibrium length. Overloading follows from setGeometricConstraints(), above.

void	setUseShake (ApplyConstraints use_shake_in=ApplyConstraints::YES)


void	setUseSettle (const std::string &use_settle_in)
	Stipulate whether three-atom isosceles arrangements with two light atoms (e.g. water) will be held rigid at their equilibrium geometries. Overloading follows from setGeometricConstraints(), above.

void	setUseSettle (ApplyConstraints use_settle_in=ApplyConstraints::YES)


void	setCpuRattleMethod (const std::string &rattle_protocol_in)
	Set the RATTLE protocol to be used in CPU operations (the GPU will always use the "CENTER_SUM" approach).

void	setRattleTolerance (double rattle_tolerance_in)
	Set the simulation RATTLE tolerance.

void	setThermostatKind (const std::string &thermostat_kind_in)
	Get the thermostat kind.

void	setThermostatKind (ThermostatKind thermostat_kind_in)


void	setThermostatCacheConfig (const std::string &cache_config_in)
	Set the thermostat cache configuration.

void	setThermostatCacheConfig (PrecisionModel cache_config_in)

Detailed Description

Object to encapsulate molecular dynamics control information. Like other namelist encapsualtors, this object can take input file data as part of its construction, or by a series of setters. Validation of each piece of data is handled as it appears either in the contructor or via setters. Getter functions dispense the internal information to any application using STORMM libraries.

Constructor & Destructor Documentation

◆ DynamicsControls()

stormm::namelist::DynamicsControls::DynamicsControls ( ExceptionResponse policy_in = ExceptionResponse::DIE )

The constructor can prepare an object with default settings or read the corresponding namelist to accept user input.

Parameters

tf	Input file translated into RAM
start_line	Line of the input file to begin searching for the &solvent namelist
found_nml	Indicator that the namelist was found in the input file
policy_in	Requested error handling behavior
wrap	Indicate that the search for a &dynamics namelist should carry on from the beginning of an input file if no such namelist is found starting from the original starting point

Member Function Documentation

◆ setAndersenFrequency()

void stormm::namelist::DynamicsControls::setAndersenFrequency ( int frequency_in )

Set the velocity restart frequency for a "massive" Andersen thermostat.

Parameters

frequency_in The step frequency to set

◆ setCenterOfMassMotionPurgeFrequency()

void stormm::namelist::DynamicsControls::setCenterOfMassMotionPurgeFrequency ( int com_motion_purge_ferquency_in )

Set the center of mass motion purge frequency.

Parameters

com_motion_purge_ferquency_in The frequency with which to purge center of mass motion

◆ setCoulombConstant()

void stormm::namelist::DynamicsControls::setCoulombConstant ( double coulomb_in )

Set the value of Coulomb's constant.

Parameters

coulomb_in Define Coulomb's constant for the simulation

◆ setCpuRattleMethod()

void stormm::namelist::DynamicsControls::setCpuRattleMethod ( const std::string & rattle_protocol_in )

Set the RATTLE protocol to be used in CPU operations (the GPU will always use the "CENTER_SUM" approach).

Overloaded:

Provide a string to be translated into the protocol enumeration
Provide the enumeration itself

Parameters

rattle_protocol_in The RATTLE protocol to set

◆ setCutoff()

void stormm::namelist::DynamicsControls::setCutoff ( double cutoff_in )

Set the cutoffs for short-ranged van-der Waals as well as electrostatic interactions in a periodic simulation.

Parameters

cutoff_in

◆ setDiagnosticPrintFrequency()

void stormm::namelist::DynamicsControls::setDiagnosticPrintFrequency ( int diagnostic_frequency_in )

Set the diagnostic printing frequency.

Parameters

diagnostic_frequency_in The frequency with which to store energy and state variables

◆ setElec14Screening()

void stormm::namelist::DynamicsControls::setElec14Screening ( double screening_in )

Set the screening factor for 1:4 electrostatic interactions.

Parameters

screening_in The screening factor to set

◆ setElectrostaticCutoff()

void stormm::namelist::DynamicsControls::setElectrostaticCutoff ( double cutoff_in )

Set the short-ranged electrostatic cutoff for the simulation.

Parameters

cutoff_in

◆ setGeometricConstraints()

void stormm::namelist::DynamicsControls::setGeometricConstraints ( const std::string & constrain_geometry_in )

Stipulate whether geometric constraints will be implemented.

Overloaded:

Provide a parseable string to indicate the constraint instruction
Provide the explicit enumeration

Parameters

constrain_geometry_in Indicate whether to activate RATTLE and SETTLE

◆ setLangevinFrequency()

void stormm::namelist::DynamicsControls::setLangevinFrequency ( double frequency_in )

Set the stochastic collision frequency for a Langevin thermostat.

Parameters

frequency_in The collision frequency to set, in units of inverse femtoseconds

◆ setNTWarpMultiplicity()

void stormm::namelist::DynamicsControls::setNTWarpMultiplicity ( int mult_in )

Get the warp multiplicity for non-bonded pairwise calculations. This applies only to periodic dynamics.

Parameters

mult_in The warp multiplicity to set

◆ setRattleTolerance()

void stormm::namelist::DynamicsControls::setRattleTolerance ( double rattle_tolerance_in )

Set the simulation RATTLE tolerance.

Parameters

tol_in The requested tolerance

◆ setStepCount()

void stormm::namelist::DynamicsControls::setStepCount ( int total_step_count_in )

Set the total number of dynamics steps.

Parameters

total_step_count_in The number of steps to take

◆ setThermostatCacheConfig()

void stormm::namelist::DynamicsControls::setThermostatCacheConfig ( const std::string & cache_config_in )

Set the thermostat cache configuration.

Overloaded:

Provide a parseable string to indicate the configuration
Provide the explicit enumeration

Parameters

cache_config_in The cache configuration to set

◆ setThermostatCacheDepth()

void stormm::namelist::DynamicsControls::setThermostatCacheDepth ( int depth_in )

Set the depth of the thermostat's random number cache.

Parameters

depth_in The depth that the cache shall take

◆ setThermostatEvolutionEnd()

void stormm::namelist::DynamicsControls::setThermostatEvolutionEnd ( int step_number )

Set the final step for temperature evolution from the initial temperature profile to the final temperature profile across all atoms and all systems.

Parameters

step_number The requested step number

◆ setThermostatEvolutionStart()

void stormm::namelist::DynamicsControls::setThermostatEvolutionStart ( int thermo_evolution_start_in )

Set the starting step for temperature evolution from the initial temperature profile to the final temperature profile across all atoms and all systems.

Parameters

step_number The requested step number

◆ setThermostatGroup()

void stormm::namelist::DynamicsControls::setThermostatGroup	(	double	initial_target = default_simulation_temperature,
		double	final_target = default_simulation_temperature,
		const std::string &	label = std::string("all"),
		int	label_index = -1,
		const std::string &	mask = std::string("@=") )

Get the vector of initial temperature targets for all groups of atoms and systems.

Parameters

initial_target	The initial target temperature
final_target	The equilibrium target temperature
label	The label group from within the cache to which the stated temperatures will be applied
label_index	Index of the system within the label group to which the stated temperatures apply, e.g. 4 would indicate the fifth system in the named label group. A value
mask	String encoding an atom mask for the atoms in the label group and index to which the stated temperatures apply

◆ setThermostatKind()

void stormm::namelist::DynamicsControls::setThermostatKind ( const std::string & thermostat_kind_in )

Get the thermostat kind.

Overloaded:

Provide the type by parseable string
Provide the explicit enumeration

Parameters

thermostat_kind_in The type of thermostat requested

◆ setThermostatSeed()

void stormm::namelist::DynamicsControls::setThermostatSeed ( int igseed )

Set the random seed to be used in the thermostat's random number generators.

Parameters

igseed The seed to set

◆ setTimeStep()

void stormm::namelist::DynamicsControls::setTimeStep ( double time_step_in )

Set the simulation time step.

Parameters

time_step_in The requested time step

◆ setTrajectoryPrintFrequency()

void stormm::namelist::DynamicsControls::setTrajectoryPrintFrequency ( int trajectory_frequency_in )

Set the trajectory snapshot printing frequency.

Parameters

trajectory_frequency_in The frequency with which to store energy and state variables

◆ setUseSettle()

void stormm::namelist::DynamicsControls::setUseSettle ( const std::string & use_settle_in )

Stipulate whether three-atom isosceles arrangements with two light atoms (e.g. water) will be held rigid at their equilibrium geometries. Overloading follows from setGeometricConstraints(), above.

Parameters

use_settle_in

◆ setUseShake()

void stormm::namelist::DynamicsControls::setUseShake ( const std::string & use_shake_in )

Stipulate whether bonds to hydrogen atoms will be held rigid at their equilibrium length. Overloading follows from setGeometricConstraints(), above.

Parameters

use_shake_in

◆ setVanDerWaalsCutoff()

void stormm::namelist::DynamicsControls::setVanDerWaalsCutoff ( double cutoff_in )

Set the short-ranged van-der Waals cutoff for the simulation.

Parameters

cutoff_in

◆ setVdw14Screening()

void stormm::namelist::DynamicsControls::setVdw14Screening ( double screening_in )

Set the screening factor for 1:4 van-der Waals interactions.

Parameters

screening_in The screening factor to set

◆ setVdwSummation()

void stormm::namelist::DynamicsControls::setVdwSummation ( const std::string & vdw_method_in )

Set the strategy for evaluating the tails of van-der Waals (Lennard-Jones) interactions.

Overloaded:

Provide a keyword that indicates some value of the enumerator
Provide a value of the enumerator itself

Parameters

vdw_method_in The input determining how van-der Waals interactions will vanish

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

src/Namelists/nml_dynamics.h
src/Namelists/nml_dynamics.cpp

Public Member Functions

Detailed Description

Constructor & Destructor Documentation

◆ DynamicsControls()

Member Function Documentation

◆ setAndersenFrequency()

◆ setCenterOfMassMotionPurgeFrequency()

◆ setCoulombConstant()

◆ setCpuRattleMethod()

◆ setCutoff()

◆ setDiagnosticPrintFrequency()

◆ setElec14Screening()

◆ setElectrostaticCutoff()

◆ setGeometricConstraints()

◆ setLangevinFrequency()

◆ setNTWarpMultiplicity()

◆ setRattleTolerance()

◆ setStepCount()

◆ setThermostatCacheConfig()

◆ setThermostatCacheDepth()

◆ setThermostatEvolutionEnd()

◆ setThermostatEvolutionStart()

◆ setThermostatGroup()

◆ setThermostatKind()

◆ setThermostatSeed()

◆ setTimeStep()

◆ setTrajectoryPrintFrequency()

◆ setUseSettle()

◆ setUseShake()

◆ setVanDerWaalsCutoff()

◆ setVdw14Screening()

◆ setVdwSummation()