stormm::stmath::CoordinateSeries< T > Class Template Reference

Store the coordinates and box information for a series of frames, in one of several levels of precision. Individual frames can be extracted into CoordinateFrame, and PhaseSpace, and PhaseSpaceSynthesis objects, or new frames can be added from CoordinateFrame objects. This object is not the CoordinateFrame equivalent of a PhaseSpaceSynthesis object, however: its purpose is to collect only the coordinates of many frames of a single system at the appropriate level of precision. More...

#include <coordinate_series.h>

Public Member Functions
	CoordinateSeries (const CoordinateSeries &original, HybridFormat format_in)
	A special copy constructor can create an object with an altered memory format.
HybridFormat	getFormat () const
	Get the memory format.
int	getAtomCount () const
	Get the number of atoms in each frame of the series.
int	getFrameCount () const
	Get the number of frames in the series.
int	getFrameCapacity () const
	Get the maximum number of frames that the object can hold.
UnitCellType	getUnitCellType () const
	Get the unit cell type of the coordinate system.
int	getFixedPrecisionBits () const
	Get the fixed precision bits after the decimal (if applicable, warn if the data type is non-integer).
std::vector< double >	getBoxSpaceTransform (int frame_index, HybridTargetLevel tier=HybridTargetLevel::HOST) const
	Get the transformation matrix to take coordinates into box (fractional) space. The result should be interpreted as a 3x3 matrix in column-major format.
std::vector< double >	getInverseTransform (int frame_index, HybridTargetLevel tier=HybridTargetLevel::HOST) const
	Get the transformation matrix to take coordinates from fractional space back into real space. The result should be interpreted as a 3x3 matrix in column-major format.
CoordinateFrame	exportFrame (size_t frame_index, HybridTargetLevel tier=HybridTargetLevel::HOST) const
	Prepare a CoordinateFrame object based on one frame of the series, accomplishing any necessary data conversions to put the coordinates back into the familiar double-precision format.
PhaseSpace	exportPhaseSpace (size_t frame_index, HybridTargetLevel tier=HybridTargetLevel::HOST) const
	Prepare a PhaseSpace object based on one frame of the series, accomplishing any data conversions needed to put the coordinates back into the familiar double-precision format.
void	exportToFile (const std::string &file_name, CoordinateFileKind output_kind=CoordinateFileKind::AMBER_CRD, PrintSituation expectation=PrintSituation::UNKNOWN, int low_index=0, int high_index=0, HybridTargetLevel tier=HybridTargetLevel::HOST) const
	Export the contents of this coordinate series to a trajectory file.
const Hybrid< T > &	getCoordinateReference (CartesianDimension dim) const
	Get a const reference to the one of the Cartesian coordinate arrays.
const Hybrid< T > *	getCoordinatePointer (CartesianDimension dim) const
	Get a const pointer to one of the Cartesian coordinate arrays.
const Hybrid< double > &	getBoxTransforms () const
	Get a const reference to the box space transformation matrices.
const Hybrid< double > *	getBoxTransformPointer () const
	Get a const pointer to the box space transformation matrices.
const Hybrid< double > &	getInverseTransforms () const
	Get a const reference to the box space transformation matrices.
const Hybrid< double > *	getInverseTransformPointer () const
	Get a const pointer to the box space transformation matrices.
const Hybrid< double > *	getBoxDimensionPointer () const
	Get a const pointer to the list of box dimensions for all frames.
const CoordinateSeries< T > *	getSelfPointer () const
	Get a const pointer to the object iself, so that it may be passed to functions by const reference and still emit a const poiner.
void	importFromFile (const std::string &file_name, CoordinateFileKind file_kind=CoordinateFileKind::UNKNOWN, const std::vector< int > &frame_numbers={}, int replica_count=1, int frame_index_start=-1)
	Import coordinates from a file. This function accepts directives to read a subset of the coordinates and integrate them into the series at a specified point.
void	reserve (const int new_frame_capacity)
	Reserve capacity in this series. The new frames will be uninitialized.
void	shrinkToFit ()
	Shrink the object's various arrays to accommodate only the current frame and atom counts. Mimics the Standard Template Library vector shrink_to_fit() member function.
	CoordinateSeries (int natom_in=0, int nframe_in=0, UnitCellType unit_cell_in=UnitCellType::NONE, int globalpos_scale_bits_in=0, HybridFormat format_in=default_hpc_format)
	There are several options for constructing this collection of coordinate frames.
	CoordinateSeries (const std::string &file_name, int atom_count_in=0, CoordinateFileKind file_kind=CoordinateFileKind::UNKNOWN, const std::vector< int > &frame_numbers={}, int replica_count=1, UnitCellType unit_cell_in=UnitCellType::NONE, int globalpos_scale_bits_in=0, HybridFormat format_in=default_hpc_format)
	CoordinateSeries (PhaseSpace *ps, int nframe_in, int globalpos_scale_bits_in=0, HybridFormat format_in=default_hpc_format)
	CoordinateSeries (const PhaseSpace &ps, int nframe_in, int globalpos_scale_bits_in=0, HybridFormat format_in=default_hpc_format)
	CoordinateSeries (CoordinateFrame *cf, int nframe_in, int globalpos_scale_bits_in=0, HybridFormat format_in=default_hpc_format)
	CoordinateSeries (const CoordinateFrame &cf, int nframe_in, int globalpos_scale_bits_in=0, HybridFormat format_in=default_hpc_format)
	CoordinateSeries (const CoordinateSeries &original)=default
	Use the default copy and move constructors, copy and move assignment operators. This object has no const members to trigger implicit deletions and no POINTER-kind Hybrid objects to repair.
	CoordinateSeries (CoordinateSeries &&original)=default
CoordinateSeries &	operator= (const CoordinateSeries &other)=default
CoordinateSeries &	operator= (CoordinateSeries &&other)=default
template<typename Toriginal>
	CoordinateSeries (const CoordinateSeries< Toriginal > &original, int globalpos_scale_bits_in=0, HybridFormat format_in=default_hpc_format)
	Special copy constructor to take a CoordinateSeries of one data type into another. The implementation requires a special declaration (template <typename T> template <typename Toriginal>...) with two uses of the template keyword because of the nested nature of these templates. In other contexts template <typename T, typename Toriginal> would suffice.
template<typename Treport>
std::vector< Treport >	getInterlacedCoordinates (int frame_index, int globalpos_bits_out=-1, HybridTargetLevel tier=HybridTargetLevel::HOST) const
	Get the interlaced coordinates of one frame.
template<typename Treport>
std::vector< Treport >	getInterlacedCoordinates (int frame_index, int low_index, int high_index, int globalpos_bits_out=-1, HybridTargetLevel tier=HybridTargetLevel::HOST) const
std::vector< double >	getBoxDimensions (int frame_index, HybridTargetLevel tier=HybridTargetLevel::HOST) const
	Get the box dimensions in their pure form for a particular frame.
const Hybrid< double > &	getBoxDimensions () const
void	extractFrame (CoordinateFrame *cf, size_t frame_index, const GpuDetails &gpu) const
	Extract coordinates to a pre-existing object.
void	extractFrame (PhaseSpace *ps, size_t frame_index, TrajectoryKind kind, CoordinateCycle time_point, const GpuDetails &gpu) const
void	extractFrame (PhaseSpace *ps, size_t frame_index, TrajectoryKind kind, const GpuDetails &gpu) const
void	extractFrame (PhaseSpace *ps, size_t frame_index, const GpuDetails &gpu) const
void	extractFrame (CoordinateFrame *cf, size_t frame_index, HybridTargetLevel tier) const
void	extractFrame (PhaseSpace *ps, size_t frame_index, TrajectoryKind kind, CoordinateCycle time_point, HybridTargetLevel tier) const
void	extractFrame (PhaseSpace *ps, size_t frame_index, TrajectoryKind kind, HybridTargetLevel tier) const
void	extractFrame (PhaseSpace *ps, size_t frame_index, HybridTargetLevel tier) const
const Hybrid< T > *	getFramesHandle (CartesianDimension dim) const
	Get a pointer to one of the coordinate arrays.
Hybrid< T > *	getFramesHandle (CartesianDimension dim)
const Hybrid< double > *	getBoxTransformsHandle () const
	Get a pointer to the box space transform. Overloading follows from getCoordinateHandle(), above.
Hybrid< double > *	getBoxTransformsHandle ()
const Hybrid< double > *	getInverseTransformsHandle () const
	Get a pointer to the inverse transform that takes coordinates back into real space. Overloading follows from getCoordinateHandle(), above.
Hybrid< double > *	getInverseTransformsHandle ()
const Hybrid< double > *	getBoxDimensionsHandle () const
	Get a pointer to the transform that takes coordinates back into real space. Overloading follows from getCoordinateHandle(), above.
Hybrid< double > *	getBoxDimensionsHandle ()
const CoordinateSeriesReader< T >	data (HybridTargetLevel tier=HybridTargetLevel::HOST) const
	Get the abstract for this object, containing C-style pointers for the most rapid access to any of its member variables.
CoordinateSeriesWriter< T >	data (HybridTargetLevel tier=HybridTargetLevel::HOST)
const CoordinateSeriesReader< void >	templateFreeData (HybridTargetLevel tier=HybridTargetLevel::HOST) const
	Get the object's abstract, with all templated type pointers cast to void pointers. The true data type can be encoded in a separate 64-bit unsigned integer code (use std::type_index() as seen in DataTypes/common_types.h). Parameter descriptions and overloading match those in data() above.
CoordinateSeriesWriter< void >	templateFreeData (HybridTargetLevel tier=HybridTargetLevel::HOST)
void	importFrame (const CoordinateFrameReader &cfr, int atom_start, int atom_end, int frame_index=-1)
	Import coordinates from a CoordinateFrame or PhaseSpace object. The original object must have the same number of atoms as the CoordinateSeries itself, or else a range of atoms within the original coordinate object must be specified that fits the CoordinateSeries. The default behavior is to push the new coordinates to the back of the list, but any frame index within the bounds of the current list may also be specified.
void	importFrame (const CoordinateFrameReader &cfr, int frame_index=-1)
void	importFrame (const CoordinateFrameWriter &cfw, int atom_start, int atom_end, int frame_index=-1)
void	importFrame (const CoordinateFrameWriter &cfw, int frame_index=-1)
void	importFrame (const CoordinateFrame &cf, int atom_start, int atom_end, int frame_index=-1)
void	importFrame (const CoordinateFrame &cf, int frame_index=-1)
void	importFrame (const CoordinateFrame *cf, int atom_start, int atom_end, int frame_index=-1)
void	importFrame (const CoordinateFrame *cf, int frame_index=-1)
void	importFrame (const PhaseSpace &ps, int atom_start, int atom_end, int frame_index=-1, TrajectoryKind kind=TrajectoryKind::POSITIONS, CoordinateCycle orientation=CoordinateCycle::WHITE)
void	importFrame (const PhaseSpace &ps, int frame_index=-1, TrajectoryKind kind=TrajectoryKind::POSITIONS, CoordinateCycle orientation=CoordinateCycle::WHITE)
void	importFrame (const PhaseSpace *ps, int atom_start, int atom_end, int frame_index=-1, TrajectoryKind kind=TrajectoryKind::POSITIONS, CoordinateCycle orientation=CoordinateCycle::WHITE)
void	importFrame (const PhaseSpace *ps, int frame_index=-1, TrajectoryKind kind=TrajectoryKind::POSITIONS, CoordinateCycle orientation=CoordinateCycle::WHITE)
void	resize (int new_frame_count)
	Resize the series, allocating new capacity if needed, initializing new frames with the provided coordinate set. ("New" frames are defined as any frames with indices greater than the original maximum index, regardless of whether new capacity was allocated to hold them or if the size simply increased within the existing space available.)
void	resize (int new_frame_count, const CoordinateFrameReader &cfr, int atom_start=0, int atom_end=0)
void	resize (int new_frame_count, const CoordinateFrameWriter &cfw, int atom_start=0, int atom_end=0)
void	resize (int new_frame_count, const CoordinateFrame &cf, int atom_start=0, int atom_end=0)
void	resize (int new_frame_count, CoordinateFrame *cf, int atom_start=0, int atom_end=0)
void	resize (int new_frame_count, const PhaseSpace &ps, int atom_start=0, int atom_end=0)
void	resize (int new_frame_count, PhaseSpace *ps, int atom_start=0, int atom_end=0)
void	pushBack (const CoordinateFrameReader &cfr, int atom_start=0, int atom_end=0)
	Push a coordinate set to the back of the list. This invokes the import member function after reallocating the frame series with 25% spare capacity if the original capacity is insufficient.
void	pushBack (const CoordinateFrameWriter &cfw, int atom_start=0, int atom_end=0)
void	pushBack (const CoordinateFrame &cf, int atom_start=0, int atom_end=0)
void	pushBack (CoordinateFrame *cf, int atom_start=0, int atom_end=0)
void	pushBack (const PhaseSpace &ps, int atom_start=0, int atom_end=0)
void	pushBack (PhaseSpace *ps, int atom_start=0, int atom_end=0)

Detailed Description

template<typename T>
class stormm::stmath::CoordinateSeries< T >

Store the coordinates and box information for a series of frames, in one of several levels of precision. Individual frames can be extracted into CoordinateFrame, and PhaseSpace, and PhaseSpaceSynthesis objects, or new frames can be added from CoordinateFrame objects. This object is not the CoordinateFrame equivalent of a PhaseSpaceSynthesis object, however: its purpose is to collect only the coordinates of many frames of a single system at the appropriate level of precision.

Constructor & Destructor Documentation

CoordinateSeries() [1/4]

template<typename T>

stormm::trajectory::CoordinateSeries< T >::CoordinateSeries ( int natom_in = 0, int nframe_in = 0, UnitCellType unit_cell_in = UnitCellType::NONE, int globalpos_scale_bits_in = 0, HybridFormat format_in = default_hpc_format )

explicit

There are several options for constructing this collection of coordinate frames.

Overloaded:

• Allocate to hold a given number of atoms and frames
• Create from any of the coordinate file formats (restart and input coordinate formats will create only one frame, but this limit can be increased later)
• From an existing PhaseSpace or CoordinateFrame object (as a pointer or a copy, with the option to make many copies immediately)

Parameters

natom_in	The number of atoms expected
nframe_in	Initial number of frames to allocate for
unit_cell_in	The type of unit cell to prepare for (this can be modified after creating the object)
file_name	File to read from
frame_numbers_in	Frame numbers of the file to read (default all frames)
replica_count_in	The number of times to replicate a series of one of more frames read from a file (this is useful for immediately making many copies of a restrart or input coordinates file, which has only one frame)
atom_count_in	The number of atoms to expect (critical if the input file is an Amber .crd format trajectory, otherwise can be left at zero to be filled in when the file is read)
ps	Pre-existing object with a complete coordinate set to use as a template. When constructing from a pre-existing PhaseSpace object, nframe_in indicates a number of copies to allocate for and create.
cf	Pre-existing object with a complete coordinate set to use as a template. When constructing from a pre-existing CoordinateFrame, nframe_in indicates a number of copies to allocate for and create.

CoordinateSeries() [2/4]

template<typename T>

stormm::trajectory::CoordinateSeries< T >::CoordinateSeries ( const CoordinateSeries< T > & original )

default

Use the default copy and move constructors, copy and move assignment operators. This object has no const members to trigger implicit deletions and no POINTER-kind Hybrid objects to repair.

Parameters

original	The original object, being copied or moved
other	The other object, being copied or moved by assignment

CoordinateSeries() [3/4]

template<typename T>

stormm::trajectory::CoordinateSeries< T >::CoordinateSeries ( const CoordinateSeries< T > & original, HybridFormat format_in )

explicit

A special copy constructor can create an object with an altered memory format.

Parameters

original	The original object, being copied or moved
format_in	The format to apply to the new object. Content is subject to the priority of the deepCopy() function for Hybrid objects, as it is with the PhaseSpace and CoordinateFrame objects.

CoordinateSeries() [4/4]

template<typename T>

template<typename Toriginal>

stormm::trajectory::CoordinateSeries< T >::CoordinateSeries	(	const CoordinateSeries< Toriginal > &	original,
		int	globalpos_scale_bits_in = 0,
		HybridFormat	format_in = default_hpc_format )

Special copy constructor to take a CoordinateSeries of one data type into another. The implementation requires a special declaration (template <typename T> template <typename Toriginal>...) with two uses of the template keyword because of the nested nature of these templates. In other contexts template <typename T, typename Toriginal> would suffice.

Parameters

original

The original object, being copied or moved

Member Function Documentation

data()

template<typename T>

const CoordinateSeriesReader< T > stormm::trajectory::CoordinateSeries< T >::data

(

HybridTargetLevel

tier = HybridTargetLevel::HOST

)

const

Get the abstract for this object, containing C-style pointers for the most rapid access to any of its member variables.

Overloaded:

• Get a read-only abstract from a const coordinate series
• Get a writeable abstract from a non-const coordinate series

Parameters

tier	Get pointers to data at the level of the CPU host or GPU device

exportFrame()

template<typename T>

CoordinateFrame stormm::trajectory::CoordinateSeries< T >::exportFrame	(	size_t	frame_index,
		HybridTargetLevel	tier = HybridTargetLevel::HOST ) const

Prepare a CoordinateFrame object based on one frame of the series, accomplishing any necessary data conversions to put the coordinates back into the familiar double-precision format.

Parameters

frame_index	The frame to extract
tier	Level at which to retrieve data (if STORMM is compiled to run on a GPU)

exportPhaseSpace()

template<typename T>

PhaseSpace stormm::trajectory::CoordinateSeries< T >::exportPhaseSpace	(	size_t	frame_index,
		HybridTargetLevel	tier = HybridTargetLevel::HOST ) const

Prepare a PhaseSpace object based on one frame of the series, accomplishing any data conversions needed to put the coordinates back into the familiar double-precision format.

Parameters

frame_index	The frame to extract
tier	Level at which to retrieve data (if STORMM is compiled to run on a GPU)

exportToFile()

template<typename T>

void stormm::trajectory::CoordinateSeries< T >::exportToFile	(	const std::string &	file_name,
		CoordinateFileKind	output_kind = CoordinateFileKind::AMBER_CRD,
		PrintSituation	expectation = PrintSituation::UNKNOWN,
		int	low_index = 0,
		int	high_index = 0,
		HybridTargetLevel	tier = HybridTargetLevel::HOST ) const

Export the contents of this coordinate series to a trajectory file.

Parameters

file_name	Name of the file to write
output_kind	The format of the file to write (checkpoint files print position and velocity data by obligation, but trajectory files can contain either of these as well as forces)
expectation	The condition in which the output file is expected to be found
low_index	The first frame index to export
high_index	The upper limit of frame indices to export
tier	Level at which to retrieve data (if STORMM is compiled to run on a GPU)

extractFrame()

template<typename T>

void stormm::trajectory::CoordinateSeries< T >::extractFrame	(	CoordinateFrame *	cf,
		size_t	frame_index,
		const GpuDetails &	gpu ) const

Extract coordinates to a pre-existing object.

Overloaded:

• Load coordinates into a CoordinateFrame object
• Load coordinates into a PhaseSpace object using the stated point in the time cycle or taking the object's current orientation

Parameters

cf	Coordinate frame into which coordinates shall be placed
ps	Phase space object into which coordinates shall be placed
frame_index	Frame to use in coordinate extraction

getBoxDimensions()

template<typename T>

std::vector< double > stormm::trajectory::CoordinateSeries< T >::getBoxDimensions	(	int	frame_index,
		HybridTargetLevel	tier = HybridTargetLevel::HOST ) const

Get the box dimensions in their pure form for a particular frame.

Overloaded:

• Get the dimensions for a specific system on the CPU host or GPU device
• Get the dimensions for all systems at both levels

Parameters

frame_index	The frame for which to extract the transformation matrix
tier	Level at which to retrieve data (if STORMM is compiled to run on a GPU)

getBoxSpaceTransform()

template<typename T>

std::vector< double > stormm::trajectory::CoordinateSeries< T >::getBoxSpaceTransform	(	int	frame_index,
		HybridTargetLevel	tier = HybridTargetLevel::HOST ) const

Get the transformation matrix to take coordinates into box (fractional) space. The result should be interpreted as a 3x3 matrix in column-major format.

Parameters

frame_index	The frame for which to extract the transformation matrix
tier	Level at which to retrieve data (if STORMM is compiled to run on a GPU)

getCoordinatePointer()

template<typename T>

const Hybrid< T > * stormm::trajectory::CoordinateSeries< T >::getCoordinatePointer

(

CartesianDimension

dim

)

const

Get a const pointer to one of the Cartesian coordinate arrays.

Parameters

dim	The dimension of interest

getCoordinateReference()

template<typename T>

const Hybrid< T > & stormm::trajectory::CoordinateSeries< T >::getCoordinateReference

(

CartesianDimension

dim

)

const

Get a const reference to the one of the Cartesian coordinate arrays.

Parameters

dim	The dimension of interest

getFramesHandle()

template<typename T>

const Hybrid< T > * stormm::trajectory::CoordinateSeries< T >::getFramesHandle

(

CartesianDimension

dim

)

const

Get a pointer to one of the coordinate arrays.

Overloaded:

• Get a const pointer to the storage array of a const object.
• Get a non-const pointer to the storage space of a mutable object.

Parameters

dim	Specify coordinate data along one of the Cartesian axes

getInterlacedCoordinates()

template<typename T>

template<typename Treport>

std::vector< Treport > stormm::trajectory::CoordinateSeries< T >::getInterlacedCoordinates	(	int	frame_index,
		int	globalpos_bits_out = -1,
		HybridTargetLevel	tier = HybridTargetLevel::HOST ) const

Get the interlaced coordinates of one frame.

Overloaded:

• Get coordinates for all atoms in a frame
• Get coordinates for a selected range of atoms in a frame

Parameters

frame_index	Index of the frame to access
globalpos_bits_out	The number of bits after the point to apply if a fixed-precision output is required. Setting this to <= 0 indicates floating point output.
low_index	The lower atom index of a range
high_index	The upper atom index of a range
tier	The level at which to access coordinates

getInverseTransform()

template<typename T>

std::vector< double > stormm::trajectory::CoordinateSeries< T >::getInverseTransform	(	int	frame_index,
		HybridTargetLevel	tier = HybridTargetLevel::HOST ) const

Get the transformation matrix to take coordinates from fractional space back into real space. The result should be interpreted as a 3x3 matrix in column-major format.

Parameters

frame_index	The frame for which to extract the transformation matrix
tier	Level at which to retrieve data (if STORMM is compiled to run on a GPU)

importFrame()

template<typename T>

void stormm::trajectory::CoordinateSeries< T >::importFrame	(	const CoordinateFrameReader &	cfr,
		int	atom_start,
		int	atom_end,
		int	frame_index = -1 )

Import coordinates from a CoordinateFrame or PhaseSpace object. The original object must have the same number of atoms as the CoordinateSeries itself, or else a range of atoms within the original coordinate object must be specified that fits the CoordinateSeries. The default behavior is to push the new coordinates to the back of the list, but any frame index within the bounds of the current list may also be specified.

Overloaded:

• Accept all types of single-frame coordinate objects
• Accept all atoms or a subset of the atoms that fits the current atom count of the CoordinateSeries

Parameters

cfr	Coordinates to import. The CoordinateFrameReader is the most basic object available for importation. Both CoordinateFrame and PhaseSpace objects can create CoordinateFrameReaders or writers, and the writers can be const-ified into readers.
cfw	Coordinates to import
cf	Coordinates to import
ps	Coordinates to import
atom_start	First atom from the coordinate set to add to a frame of the series
atom_end	Limit of atoms from the coordinate set to add to a frame of the series
frame_index	Index of the frame into which the coordinates should be imported. The default value of -1 adds the new coordinates to the end of the list.

importFromFile()

template<typename T>

void stormm::trajectory::CoordinateSeries< T >::importFromFile	(	const std::string &	file_name,
		CoordinateFileKind	file_kind = CoordinateFileKind::UNKNOWN,
		const std::vector< int > &	frame_numbers = {},
		int	replica_count = 1,
		int	frame_index_start = -1 )

Import coordinates from a file. This function accepts directives to read a subset of the coordinates and integrate them into the series at a specified point.

Parameters

file_name	Name of the file
file_kind	The kind of coordinate file being read, default UNKNOWN which will lead to automatic deduction of the file type
frame_numbers	List of frame indices (starting from zero) to import from the file (if the file is too small to hold one or more frames with the requested indices, this is an error)
replica_count_in	The number of replicas of the frames from this file (default 1). If additional replicas are requested, the whole series will be added in sequence, i.e. frames 3, 5, 8, 9, 3, 5, 8, 9, 3, ...
frame_index_start	The starting index of the series for incorporating frames found in the file. A negative value in this argument triggers addition to the end of any existing series.

pushBack()

template<typename T>

void stormm::trajectory::CoordinateSeries< T >::pushBack	(	const CoordinateFrameReader &	cfr,
		int	atom_start = 0,
		int	atom_end = 0 )

Push a coordinate set to the back of the list. This invokes the import member function after reallocating the frame series with 25% spare capacity if the original capacity is insufficient.

Overloaded:

• Accept all types of single-frame coordinate objects
• Accept all atoms or a subset of the atoms that fits the current atom count of the CoordinateSeries

Parameters

cfr	Coordinates to import. The CoordinateFrameReader is the most basic object available for importation. Both CoordinateFrame and PhaseSpace objects can create CoordinateFrameReaders or writers, and the writers can be const-ified into readers.
cfw	Coordinates to import
cf	Coordinates to import
ps	Coordinates to import
atom_start	First atom from the coordinate set to add to a frame of the series
atom_end	Limit of atoms from the coordinate set to add to a frame of the series

reserve()

template<typename T>

void stormm::trajectory::CoordinateSeries< T >::reserve

(

const int

new_frame_capacity

)

Reserve capacity in this series. The new frames will be uninitialized.

Parameters

new_frame_capacity

The new capacity to prepare for. If such capacity already exists, the function will do nothing.

resize()

template<typename T>

void stormm::trajectory::CoordinateSeries< T >::resize

(

int

new_frame_count

)

Resize the series, allocating new capacity if needed, initializing new frames with the provided coordinate set. ("New" frames are defined as any frames with indices greater than the original maximum index, regardless of whether new capacity was allocated to hold them or if the size simply increased within the existing space available.)

Overloaded:

• Accept all types of single-frame coordinate objects
• Accept all atoms or a subset of the atoms that fits the current atom count of the CoordinateSeries

Parameters

new_frame_count	The number of new frames that the list shall report holding. This is less than or equal to the capacity; if there is insufficient capacity when resize() is called, new capacity will be allocated to hold precisely new_frame_count frames.
cfr	Optional coordinate set to use in initializing new frames. If no coordinates are provided, the series will report holding frames but have undefined values in them.
cfw	Optional coordinate set to use in initializing new frames
cf	Optional coordinate set to use in initializing new frames
ps	Optional coordinate set to use in initializing new frames
atom_start	First atom from the coordinate set to add to a frame of the series (the default value is zero, to use all atoms)
atom_end	Limit of atoms from the coordinate set to add to a frame of the series (the default value of zero will trigger an access to atom count from the coordinate object to load all of its atoms)

---

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

• src/Trajectory/coordinate_series.h