Provide the means to read a series of topology and coordinate files, then organize them into corresponding lists of AtomGraph and PhaseSpace objects. The object can also export coordinates in other formats. Error checking is provided to abort the (test) program or issue a warning, and the object can signal whether dependent tests should be run or aborted. More...

#include <test_system_manager.h>

Public Member Functions
std::string	getTopologyBasePath () const
	Return the base path for topologies.

std::string	getCoordinateBasePath () const
	Return the base path for coordinates.

std::string	getTopologyExtension () const
	Return the extension for topologies.

std::string	getCoordinateExtension () const
	Return the extension for coordinates.

std::string	getTopologyFile (int index) const
	Return the full name of a topology file according to some index in the list.

std::string	getCoordinateFile (int index) const
	Return the full name of a coordinate file according to some index in the list.

CoordinateFrame	exportCoordinateFrame (int index) const
	Get a copy of the coordinates for one system as a CoordinateFrame object.

PhaseSpace	exportPhaseSpace (int index) const
	Get a copy of the coordinates for one system as a PhaseSpace object.

AtomGraph	exportAtomGraph (int index) const
	Export the topology for one system.

template<typename T>
CoordinateSeries< T >	exportCoordinateSeries (const int base_system, int frame_count, double perturbation_sigma=0.0, int xrs_seed=915083, int scale_bits=0) const
	Get a coordinate series out of the object, based on one system from its repository.


	TestSystemManager ()
	The constructor takes lists of topologies, then lists of coordinates, with a one-to-one correspondence of files in each list.

	TestSystemManager (const std::string &topology_base_in, const std::string &topology_extn_in, const std::vector< std::string > &topology_names_in, const std::string &coordinate_base_in, const std::string &coordinate_extn_in, const std::vector< std::string > &coordinate_names_in, ExceptionResponse policy=ExceptionResponse::WARN, TestPriority fault_response_in=TestPriority::ABORT, TestPriority all_go_response_in=TestPriority::CRITICAL, const DynamicsControls &dyncon=DynamicsControls())

	TestSystemManager (const std::string &topology_base_in, const std::string &topology_extn_in, const std::vector< std::string > &topology_names_in, const std::string &coordinate_base_in, const std::string &coordinate_extn_in, const std::vector< std::string > &coordinate_names_in, const DynamicsControls &dyncon, ExceptionResponse policy=ExceptionResponse::WARN)

	TestSystemManager (const std::string &topology_base_in, const std::vector< std::string > &topology_names_in, const std::string &coordinate_base_in, const std::vector< std::string > &coordinate_names_in, ExceptionResponse policy=ExceptionResponse::WARN, TestPriority fault_response_in=TestPriority::ABORT, TestPriority all_go_response_in=TestPriority::CRITICAL, const DynamicsControls &dyncon=DynamicsControls())

	TestSystemManager (const std::string &topology_base_in, const std::vector< std::string > &topology_names_in, const std::string &coordinate_base_in, const std::vector< std::string > &coordinate_names_in, const DynamicsControls &dyncon, ExceptionResponse policy=ExceptionResponse::WARN)

	TestSystemManager (const std::vector< std::string > &topology_names_in, const std::vector< std::string > &coordinate_names_in, ExceptionResponse policy=ExceptionResponse::WARN, TestPriority fault_response_in=TestPriority::ABORT, TestPriority all_go_response_in=TestPriority::CRITICAL, const DynamicsControls &dyncon=DynamicsControls())

	TestSystemManager (const std::vector< std::string > &topology_names_in, const std::vector< std::string > &coordinate_names_in, const DynamicsControls &dyncon, ExceptionResponse policy=ExceptionResponse::WARN)


int	getSystemCount () const
	Get the number of systems in the object.

int	getSystemCount (UnitCellType query_bc) const

int	getSystemCount (const std::vector< UnitCellType > &query_bc) const


std::vector< int >	getQualifyingSystems (UnitCellType uc_choice) const
	Get a list of all topologies meeting a specific unit cell type.

std::vector< int >	getQualifyingSystems (const std::vector< UnitCellType > &uc_choice) const

std::vector< int >	getQualifyingSystems (int critical_atom_count, RelationalOperator rel) const


TestPriority	getTestingStatus () const
	Get the planned course of action for subsequent tests in the event that a file is non-existent, or for any reason unreadable.

TestPriority	getTestingStatus (int index) const

TestPriority	getTestingStatus (const std::vector< int > &indices) const


const PhaseSpace &	viewCoordinates (int index)
	Get a const reference to the coordinates for one or more systems.

const std::vector< PhaseSpace > &	viewCoordinates ()


const AtomGraph &	getTopologyReference (int index) const
	Get a const reference to the topology for one or more systems.

const std::vector< AtomGraph > &	getTopologyReference () const


AtomGraph *	getTopologyPointer (int index)
	Get a pointer to one or more topologies.

const AtomGraph *	getTopologyPointer (int index) const

std::vector< AtomGraph * >	getTopologyPointer ()

const std::vector< AtomGraph * >	getTopologyPointer () const


PhaseSpaceSynthesis	exportPhaseSpaceSynthesis (const std::vector< int > &index_key, double perturbation_sigma=0.0, int xrs_seed=7108262, int scale_bits=40, int vel_bits=default_velocity_scale_bits, int frc_bits=default_force_scale_bits) const
	Get a synthesis of coordinates with fixed-precision storage ready for positions, velocities, and forces.

PhaseSpaceSynthesis	exportPhaseSpaceSynthesis (UnitCellType uc_choice) const

PhaseSpaceSynthesis	exportPhaseSpaceSynthesis (const std::vector< UnitCellType > &uc_choice) const


AtomGraphSynthesis	exportAtomGraphSynthesis (const std::vector< int > &index_key, ExceptionResponse policy=ExceptionResponse::SILENT, const GpuDetails &gpu=null_gpu) const
	Get a synthesis of topologies based on a series of system indices from the manager.

AtomGraphSynthesis	exportAtomGraphSynthesis (UnitCellType uc_choice, ExceptionResponse policy=ExceptionResponse::SILENT, const GpuDetails &gpu=null_gpu) const

AtomGraphSynthesis	exportAtomGraphSynthesis (const std::vector< UnitCellType > &uc_choice, ExceptionResponse policy=ExceptionResponse::SILENT, const GpuDetails &gpu=null_gpu) const


SystemCache	exportSystemCache (const std::vector< int > &index_key, const TestEnvironment &oe, const std::vector< std::string > &x_name_list={}, const std::vector< CoordinateFileKind > &x_type_list={}, const std::vector< std::string > &r_name_list={}, const std::vector< CoordinateFileKind > &r_type_list={}, const std::vector< std::string > &label_list={})
	Produce a SystemCache based on a compilation of the systems read into the manager.

SystemCache	exportSystemCache (const std::string &fnml)

Detailed Description

Provide the means to read a series of topology and coordinate files, then organize them into corresponding lists of AtomGraph and PhaseSpace objects. The object can also export coordinates in other formats. Error checking is provided to abort the (test) program or issue a warning, and the object can signal whether dependent tests should be run or aborted.

Constructor & Destructor Documentation

◆ TestSystemManager()

stormm::testing::TestSystemManager::TestSystemManager ( )

The constructor takes lists of topologies, then lists of coordinates, with a one-to-one correspondence of files in each list.

Overloaded:

Create a blank object (so that this object can be easily containerized)
Accept straight lists of file names for both topologies and the coordinates
Accept a common base name and extension for the topologies and the coordinates
Accept a common base name for the topologies and the coordinates

Member Function Documentation

◆ exportAtomGraph()

AtomGraph stormm::testing::TestSystemManager::exportAtomGraph ( int index ) const

Export the topology for one system.

Parameters

index The system of interest.

◆ exportAtomGraphSynthesis()

AtomGraphSynthesis stormm::testing::TestSystemManager::exportAtomGraphSynthesis	(	const std::vector< int > &	index_key,
		ExceptionResponse	policy = ExceptionResponse::SILENT,
		const GpuDetails &	gpu = null_gpu ) const

Get a synthesis of topologies based on a series of system indices from the manager.

Overloaded:

Select a list of systems based on their indices within the manager
Select all systems conforming to one or more specific types of unit cell (a critical factor in building a synthesis is that all systems use similar boundary conditions)

Descriptions of parameters follow from getPhaseSpaceSynthesis() above, with the addition of:

Parameters

policy	Specify whether to report abnormal input. In most cases, the AtomGraphSynthesis will report being given a longer list of topologies than was required (unused topologies). For most testing purposes, this is benign, and should not be raised to the end user's attention.
gpu	Details of the GPU that will handle the workload (this helps in laying out valence work units)

◆ exportCoordinateFrame()

CoordinateFrame stormm::testing::TestSystemManager::exportCoordinateFrame ( int index ) const

Get a copy of the coordinates for one system as a CoordinateFrame object.

Parameters

index The system of interest

◆ exportCoordinateSeries()

template<typename T>

CoordinateSeries< T > stormm::testing::TestSystemManager::exportCoordinateSeries	(	const int	base_system,
		int	frame_count,
		double	perturbation_sigma = 0.0,
		int	xrs_seed = 915083,
		int	scale_bits = 0 ) const

Get a coordinate series out of the object, based on one system from its repository.

Parameters

base_system
frame_count	The number of frames in the series, each a copy of the original coordinate set
perturbation_sigma	The Gaussian width by which to perturb coordinates
xrs_seed	Random number generator seed
scale_bits	The number of bits after the decimal to include, if the data type of the coordinate series is integral (fixed precision)

◆ exportPhaseSpace()

PhaseSpace stormm::testing::TestSystemManager::exportPhaseSpace ( int index ) const

Get a copy of the coordinates for one system as a PhaseSpace object.

Parameters

index The system of interest

◆ exportPhaseSpaceSynthesis()

PhaseSpaceSynthesis stormm::testing::TestSystemManager::exportPhaseSpaceSynthesis	(	const std::vector< int > &	index_key,
		double	perturbation_sigma = 0.0,
		int	xrs_seed = 7108262,
		int	scale_bits = 40,
		int	vel_bits = default_velocity_scale_bits,
		int	frc_bits = default_force_scale_bits ) const

Get a synthesis of coordinates with fixed-precision storage ready for positions, velocities, and forces.

Overloaded:

Select a list of systems based on their indices within the manager
Select all systems conforming to one or more specific types of unit cell (a critical factor in building a synthesis is that all systems use similar boundary conditions)

Parameter descriptions follow from getCoordinateSeries() above, with the addition of:

Parameters

index_key	A series of system indices from within the TestSystemManager with which to compose the synthesis. Topologies and coordinates will be drawn upon.
uc_choice	The choice or choices of unit cell to select (one instance of each matching system will be included in the result)
vel_bits	The number of bits in the fraction for the velocity representation
frc_bits	The number of bits in the fraction for the force representation

◆ exportSystemCache()

SystemCache stormm::testing::TestSystemManager::exportSystemCache	(	const std::vector< int > &	index_key,
		const TestEnvironment &	oe,
		const std::vector< std::string > &	x_name_list = {},
		const std::vector< CoordinateFileKind > &	x_type_list = {},
		const std::vector< std::string > &	r_name_list = {},
		const std::vector< CoordinateFileKind > &	r_type_list = {},
		const std::vector< std::string > &	label_list = {} )

Produce a SystemCache based on a compilation of the systems read into the manager.

Overloaded:

Accept a list of system indices, and optionally labels to apply
Accept a string input for a &files namelist

Parameters

index_key	A series of system indices from within the TestSystemManager with which to compose the cache. Topologies and coordinates will be drawn upon.
x_name_list	A list of trajectory file names for each cache item
x_type_list	A list of file types for each trajectory file to write
r_name_list	A list of restart file names for each cache item
r_type_list	A list of file types for each restart file to write
label_list	A list of labels to apply to each cache item. If provided, this array have the same length as index_key.
fnml	A string containing the contents of a &files namelist

◆ getQualifyingSystems()

std::vector< int > stormm::testing::TestSystemManager::getQualifyingSystems ( UnitCellType uc_choice ) const

Get a list of all topologies meeting a specific unit cell type.

Overloaded:

Return a list of topologies matching one selected unit cell type.
Return a list of topologies matching any of a list of unit cell types.

Parameters

uc_choice The unit cell type of interest

◆ getSystemCount()

int stormm::testing::TestSystemManager::getSystemCount ( ) const

Get the number of systems in the object.

Overloaded:

Obtain the total number of systems
Obtain the number of systems adhering to selected boundary conditions

Parameters

query_bc The boundary conditions of interest

◆ getTestingStatus()

TestPriority stormm::testing::TestSystemManager::getTestingStatus ( ) const

Get the planned course of action for subsequent tests in the event that a file is non-existent, or for any reason unreadable.

Overloaded:

Return a general status for any and all systems covered by the manager
Return a specific status for an individual system by index
Return the overall status for a collections of systems, specified by index

Parameters

index	Index of the system of interest
indices	Indices of the systems of interest

◆ getTopologyPointer()

AtomGraph * stormm::testing::TestSystemManager::getTopologyPointer ( int index )

Get a pointer to one or more topologies.

Overloaded:

Get a pointer to a single topology
Get a vector of pointers to all topologies in order
Return const results for a const object or non-const results for a non-const object

Parameters

index Identifier of a specific topology of interest

◆ getTopologyReference()

const AtomGraph & stormm::testing::TestSystemManager::getTopologyReference ( int index ) const

Get a const reference to the topology for one or more systems.

Overloaded:

Get a reference to a single topology
Get a reference to the vector of all topologies in order

Parameters

index The system of interest

◆ viewCoordinates()

const PhaseSpace & stormm::testing::TestSystemManager::viewCoordinates ( int index )

Get a const reference to the coordinates for one or more systems.

Overloaded:

Get a reference to a single coordinate set
Get a const reference to the vector of all coordinate sets

Parameters

index The system of interest

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

src/UnitTesting/test_system_manager.h
src/UnitTesting/test_system_manager.cpp

Public Member Functions

Detailed Description

Constructor & Destructor Documentation

◆ TestSystemManager()

Member Function Documentation

◆ exportAtomGraph()

◆ exportAtomGraphSynthesis()

◆ exportCoordinateFrame()

◆ exportCoordinateSeries()

◆ exportPhaseSpace()

◆ exportPhaseSpaceSynthesis()

◆ exportSystemCache()

◆ getQualifyingSystems()

◆ getSystemCount()

◆ getTestingStatus()

◆ getTopologyPointer()

◆ getTopologyReference()

◆ viewCoordinates()