stormm::namelist::MinimizeControls Class Reference

Object to encapsulate energy minimization 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_minimize.h>

Public Member Functions
int	getTotalCycles () const
	Get the total number of minimization cycles.
int	getSteepestDescentCycles () const
	Get the number of steepest descent cycles.
int	getClashDampingCycles () const
	Get the number of clash-relaxation cycles.
int	getDiagnosticPrintFrequency () const
	Get the diagnostic output printing frequency, akin to the major contribution to pmemd and sander mdout files.
bool	getCheckpointProduction () const
	Get the directive on whether to produce a checkpoint file for the final state of each energy minimization run.
double	getElectrostaticCutoff () const
	Get the electrostatic cutoff.
double	getLennardJonesCutoff () const
	Get the Lennard-Jones cutoff.
VdwSumMethod	getVdwSummation () const
	Get the manner in which the van-der Waals (Lennard-Jones) function vanishes.
double	getInitialStep () const
	Get the initial step length.
double	getConvergenceTarget () const
	Get the convergence criterion.
double	getAbsoluteClashDistance () const
	Get the absolute clash distance, below which two particles will be deemed colliding.
double	getVdwClashRatio () const
	Get the minimum ratio of inter-particle distance to the pairwise van-der Waals sigma parameter, below which two particles will be deemed colliding.
const NamelistEmulator &	getTranscript () const
	Get the original namelist emulator object as a transcript of the user input.
void	setTotalCycles (int cycles_in)
	Set the total number of minimization cycles.
void	setSteepestDescentCycles (int cycles_in)
	Set the number of steepest descent cycles.
void	setClashDampingCycles (int cycles_in)
	Set the number of clash damping cycles.
void	setAbsoluteClashDistance (double clash_minimum_distance_in)
	Set the minimum inter-particle separation defining an electrostatic clash.
void	setVdwClashRatio (double clash_vdw_ratio_in)
	Set the minimum ratio of inter-particle separation to Lennard-Jones sigma defining a van-der Waals clash.
void	setDiagnosticPrintFrequency (int frequency_in)
	Set the diagnostic printing frequency.
void	setCheckpointProduction (bool produce_in)
	Set the checkpoint production flag.
void	setElectrostaticCutoff (double cutoff_in)
	Set the electrostatic cutoff.
void	setLennardJonesCutoff (double cutoff_in)
	Set the Lennard-Jones cutoff.
void	setInitialStep (double step_size_in)
	Set the initial step length.
void	setConvergenceTarget (double target_in)
	Set the convergence criterion, the target for the root mean squared value of all gradients obtained after the minimization, in kcal/mol.
	MinimizeControls (ExceptionResponse policy_in=ExceptionResponse::DIE, WrapTextSearch wrap=WrapTextSearch::NO)
	The constructor can prepare an object with default settings or read the corresponding namelist to accept user input.
	MinimizeControls (const TextFile &tf, int *start_line, bool *found_nml, ExceptionResponse policy_in=ExceptionResponse::DIE, WrapTextSearch wrap=WrapTextSearch::NO)
	MinimizeControls (const MinimizeControls &original)=default
	As with other control objects, copy and move constructors, plus copy and move assignment operators, can all take their default forms.
	MinimizeControls (MinimizeControls &&original)=default
MinimizeControls &	operator= (const MinimizeControls &original)=default
MinimizeControls &	operator= (MinimizeControls &&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)

Detailed Description

Object to encapsulate energy minimization 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

MinimizeControls()

stormm::namelist::MinimizeControls::MinimizeControls	(	ExceptionResponse	policy_in = ExceptionResponse::DIE,
		WrapTextSearch	wrap = WrapTextSearch::NO )

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 &minimize namelist
found_nml	Indicator of whether namelist input was found
policy_in	Requested error handling behavior
wrap	Indicate that the search for a &minimize 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

setAbsoluteClashDistance()

void stormm::namelist::MinimizeControls::setAbsoluteClashDistance

(

double

clash_minimum_distance_in

)

Set the minimum inter-particle separation defining an electrostatic clash.

Parameters

clash_minimum_distance_in

setCheckpointProduction()

void stormm::namelist::MinimizeControls::setCheckpointProduction

(

bool

produce_in

)

Set the checkpoint production flag.

Parameters

produce_in

Whether to produce a checkpoint at the end of the run

setClashDampingCycles()

void stormm::namelist::MinimizeControls::setClashDampingCycles

(

int

cycles_in

)

Set the number of clash damping cycles.

Parameters

cycles_in

The requested number of clash damping cycles

setConvergenceTarget()

void stormm::namelist::MinimizeControls::setConvergenceTarget

(

double

target_in

)

Set the convergence criterion, the target for the root mean squared value of all gradients obtained after the minimization, in kcal/mol.

Parameters

target_in

The requested convergence target

setDiagnosticPrintFrequency()

void stormm::namelist::MinimizeControls::setDiagnosticPrintFrequency

(

int

frequency_in

)

Set the diagnostic printing frequency.

Parameters

frequency_in

The chosen printing interval

setInitialStep()

void stormm::namelist::MinimizeControls::setInitialStep

(

double

step_size_in

)

Set the initial step length.

Parameters

step_size_in

The requested initial step length

setSteepestDescentCycles()

void stormm::namelist::MinimizeControls::setSteepestDescentCycles

(

int

cycles_in

)

Set the number of steepest descent cycles.

Parameters

cycles_in

The requested number of steepest descent cycles

setTotalCycles()

void stormm::namelist::MinimizeControls::setTotalCycles

(

int

cycles_in

)

Set the total number of minimization cycles.

Parameters

cycles_in

The requested number of minimization cycles

setVdwClashRatio()

void stormm::namelist::MinimizeControls::setVdwClashRatio

(

double

clash_vdw_ratio_in

)

Set the minimum ratio of inter-particle separation to Lennard-Jones sigma defining a van-der Waals clash.

Parameters

clash_vdw_ratio_in

The ratio to apply

setVdwSummation()

void stormm::namelist::MinimizeControls::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

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

• src/Namelists/nml_minimize.h
• src/Namelists/nml_minimize.cpp