Collect output directives relating to the diagnostics file. While the output frequency is controlled by another namelist such as &minimize or &dynamics, STORMM is designed to handle many trajectories and thus the user is faced with a choice of what information to present and in what format. More...

#include <nml_report.h>

Public Member Functions
OutputSyntax	getOutputSyntax () const
	Get the output format–what program will be able to read the results?

OutputScope	getOutputScope () const
	Get the scope of results: will all systems' results be displayed, or some statistical reduction?

EnergySample	getEnergySamplingMethod () const
	Get the type of energy or state variable sampling (mean, time series, final value).

const std::string &	getUsername () const
	Get the method for grouping systems.

const std::string &	getReportVariable () const
	Get the (base) name of the matrix variable under which to store results.

timeval	getStartDate () const
	Get the date on which the program began to run, taken as the time that this ReportControls object was constructed.

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

bool	printWallTimeData () const
	Indicate whether to print timings data from the calculations.

int	getReportFileWidth () const
	Get the requested width for the output file.

int	getReportedQuantityCount () const
	Get the number of reported quantities.

const std::vector< StateVariable > &	getReportedQuantities () const
	Get a list of the energy components to display. The actual results will depend on whether each energy term is applicable, i.e. kinetic energy will not be displayed in a conjugate gradient energy minimization run and the pressure will not be displayed for a system run in isolated boundary conditions.

int	getSDFileDataRequestCount () const
	Get the number of data item requests for printing to an SD file.

const std::vector< MdlMolDataRequest > &	getSDFileDataRequests () const
	Get a list of data items to be displayed in an SD file. Reported quantities can include topological parameters, components of the molecular mechanics energy for the structure, the username, and notes about external factors affecting the final conformation.

MdlMolDataRequest	getSDFileDataRequest (int index) const
	Get a specific data request to be displayed in an SD file.

int	getCommonPathLimit () const
	Get the maximum number of common paths to be permitted in system output.

int	getCommonPathThreshold () const
	Get the required number of times a root path must be repeated in order to become one of the common paths used to condense output tables.

int	getEnergyDecimalPlaces () const
	Get the number of decimal places with which to express energetic quantities in output tables. This precision will be consistent across all energy quantities.

double	getOutlierSigmaFactor () const
	Get the multiplier for the number of standard deviations from the mean that defines an outlier among the energetics of a group of systems.

int	getOutlierCount () const
	Get the maximum number of outliers to report (per group, or per the whole synthesis if there is no grouping) in terms of systems deviating from the expected (mean) energy.

void	setUsername (const std::string &username_in)
	Set the username.

void	setReportVariable (const std::string &report_variable_in)
	Set the name of the matrix variable for reporting state quantities (volume, temperature, energy components).

void	setReportFileWidth (int report_file_width_in)
	Set the report file width.

void	addDataItem (const MdlMolDataRequest &ask)
	Add a request for a data item in an output SD file.

void	setCommonPathLimit (int common_path_limit_in)
	Set the upper limit on the number of common paths used to condense output files.

void	setCommonPathThreshold (int common_path_threshold)
	Set the number of instances that a common root path must appear in order for it to be declared a common path with a token variable to condense output tables.

void	setEnergyDecimalPlaces (int energy_decimal_places_in)
	Set the number of digits after the decimal with which to express energetic quantities.


	ReportControls (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.

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


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

	ReportControls (ReportControls &&original)=default

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

ReportControls &	operator= (ReportControls &&original)=default


void	setOutputSyntax (OutputSyntax report_layout_in)
	Set the output format.

void	setOutputSyntax (const std::string &report_layout_in)


void	setOutputScope (OutputScope report_scope_in)
	Set the scope of the output.

void	setOutputScope (const std::string &report_scope_in)


void	setStateSampling (EnergySample state_sampling_in)
	Set the method for reporting samples of system state variables.

void	setStateSampling (const std::string &state_sampling_in)


void	setWallTimeData (bool preference)
	Set the preference for printing wall clock timings.

void	setWallTimeData (const std::string &preference)


void	setReportedQuantities (const std::string &quantity_in)
	Set the reported quantities that will be reported. Some quantities are obligatory: Total, total potential, and total kinetic energy; thermodynamic integration energy derivatives (if applicable); pressure and volume (if applicable); and overall system temperature. By default, all components of the molecular mechanics energy are also recorded, but requesting specific components through this function will disable all molecular mechanics energy components not specifically requested.

void	setReportedQuantities (StateVariable quantities_in)

void	setReportedQuantities (const std::vector< StateVariable > &quantities_in)

Detailed Description

Collect output directives relating to the diagnostics file. While the output frequency is controlled by another namelist such as &minimize or &dynamics, STORMM is designed to handle many trajectories and thus the user is faced with a choice of what information to present and in what format.

Constructor & Destructor Documentation

◆ ReportControls()

stormm::namelist::ReportControls::ReportControls	(	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

◆ addDataItem()

void stormm::namelist::ReportControls::addDataItem ( const MdlMolDataRequest & ask )

Add a request for a data item in an output SD file.

Parameters

ask	The requested data item

◆ getSDFileDataRequest()

MdlMolDataRequest stormm::namelist::ReportControls::getSDFileDataRequest ( int index ) const

Get a specific data request to be displayed in an SD file.

Parameters

index Index of the request to produce

◆ getUsername()

const std::string & stormm::namelist::ReportControls::getUsername ( ) const

Get the method for grouping systems.

Get the name of the user responsible for generating the results.

◆ setCommonPathLimit()

void stormm::namelist::ReportControls::setCommonPathLimit ( int common_path_limit_in )

Set the upper limit on the number of common paths used to condense output files.

Parameters

common_path_limit_in The maximum number of path shortcuts to create

◆ setCommonPathThreshold()

void stormm::namelist::ReportControls::setCommonPathThreshold ( int common_path_threshold )

Set the number of instances that a common root path must appear in order for it to be declared a common path with a token variable to condense output tables.

Parameters

common_path_threshold The number of path tree instances needed to create a shortcut

◆ setEnergyDecimalPlaces()

void stormm::namelist::ReportControls::setEnergyDecimalPlaces ( int energy_decimal_places_in )

Set the number of digits after the decimal with which to express energetic quantities.

Parameters

energy_decimal_places_in The number of digits after each energy quantity decimal

◆ setOutputScope()

void stormm::namelist::ReportControls::setOutputScope ( OutputScope report_scope_in )

Set the scope of the output.

Overloaded:

Supply the enumeration directly
Supply a string that can be translated into the enumeration

Parameters

report_scope_in The breadth of reporting for energies and the outcomes of other state variables across all systems in the calculation

◆ setOutputSyntax()

void stormm::namelist::ReportControls::setOutputSyntax ( OutputSyntax report_layout_in )

Set the output format.

Overloaded:

Supply the enumeration directly
Supply a string that can be translated into the enumeration

Parameters

report_layout_in The chosen layout for the output report, setting up for parsing by one of several plotting programs that can be used in analysis

◆ setReportedQuantities()

void stormm::namelist::ReportControls::setReportedQuantities ( const std::string & quantity_in )

Set the reported quantities that will be reported. Some quantities are obligatory: Total, total potential, and total kinetic energy; thermodynamic integration energy derivatives (if applicable); pressure and volume (if applicable); and overall system temperature. By default, all components of the molecular mechanics energy are also recorded, but requesting specific components through this function will disable all molecular mechanics energy components not specifically requested.

Overloaded:

Accept a string to translate into some state variable code
Accept a single state variable to report
Accept a vector of state variables to report

Parameters

quantity_in	String indicating some state variable
quantities_in	A state variable quantity, or list of quantities, to include in the diagnostics report file

◆ setReportFileWidth()

void stormm::namelist::ReportControls::setReportFileWidth ( int report_file_width_in )

Set the report file width.

Parameters

report_file_width_in The general width (in ASCII characters) of report output

◆ setReportVariable()

void stormm::namelist::ReportControls::setReportVariable ( const std::string & report_variable_in )

Set the name of the matrix variable for reporting state quantities (volume, temperature, energy components).

Parameters

report_variable_in The base name of the matrix variable to use

◆ setStateSampling()

void stormm::namelist::ReportControls::setStateSampling ( EnergySample state_sampling_in )

Set the method for reporting samples of system state variables.

Overloaded:

Supply the enumeration directly.
Supply a string that can be translate into the enumeration.

Parameters

state_sampling_in The sampling method to set

◆ setUsername()

void stormm::namelist::ReportControls::setUsername ( const std::string & username_in )

Set the username.

Parameters

username_in A username reported in the input file, not detected automatically from the environment (as is the default behavior)

◆ setWallTimeData()

void stormm::namelist::ReportControls::setWallTimeData ( bool preference )

Set the preference for printing wall clock timings.

Overloaded:

Accept a single state variable to report
Accept a vector of state variables to report

Parameters

preference Set to TRUE to activate printing of wall time results

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

src/Namelists/nml_report.h
src/Namelists/nml_report.cpp

Public Member Functions

Detailed Description

Constructor & Destructor Documentation

◆ ReportControls()

Member Function Documentation

◆ addDataItem()

◆ getSDFileDataRequest()

◆ getUsername()

◆ setCommonPathLimit()

◆ setCommonPathThreshold()

◆ setEnergyDecimalPlaces()

◆ setOutputScope()

◆ setOutputSyntax()

◆ setReportedQuantities()

◆ setReportFileWidth()

◆ setReportVariable()

◆ setStateSampling()

◆ setUsername()

◆ setWallTimeData()