stormm::synthesis::PhaseSpaceSynthesis Class Reference

A fixed-precision representation of coordinates, velocities, and forces to manage a set of simulations. The time steps are stored in units of femtoseconds. Coordinates are stored as long long integers to utilize the 32-bit int pipeline for difference computations, bypassing fp64 computations wherever possible to get the best throughput on many visualization, AI-oriented, and gaming cards. More...

#include <phasespace_synthesis.h>

Public Member Functions
HybridFormat	getFormat () const
	Get the memory format of the object.
int	getSystemCount () const
	Get the number of systems in the object.
int	getUniqueTopologyCount () const
	Get the number of unique topologies in the object.
UnitCellType	getUnitCellType () const
	Get the unit cell type.
CoordinateCycle	getCyclePosition () const
	Get the current position in the coordinate cycle.
int	getGlobalPositionBits () const
	Get the global position scaling bit count.
int	getLocalPositionBits () const
	Get the local position scaling bit count.
int	getVelocityBits () const
	Get the velocity scaling bit count.
int	getForceAccumulationBits () const
	Get the force accumulation bit count.
float	getForceScalingFactor () const
	Get the force scaling factor used in fixed-precision accumulation.
float	getInverseForceScalingFactor () const
	Get the inverse of the force scaling factor used in fixed-precision accumulation.
const std::vector< AtomGraph * > &	getUniqueTopologies () const
	Get a list of unique topology pointers from this coordinate synthesis, const-casted for accessibility to other functions.
int	getAtomOffset (int system_index) const
	Get the starting index of atoms for one of the systems, using its index.
int	getAtomCount (int system_index) const
	Get the number of atoms in one of the systems, using its index.
int	getPaddedAtomCount () const
	Get the total number of atoms across all systems in the synthesis, including padding between systems and after the end of the final system.
int	getUniqueTopologyIndex (int system_index) const
	Get the index of the unique topology used by a particular system in the synthesis.
std::vector< int >	getUniqueTopologyIndices () const
	Get the unique topology index of all systems in the synthesis.
std::vector< int >	getUniqueTopologyExampleIndices () const
	Get a list of system indices from within this coordinate synthesis, providing examples of each unique topology as presented in the order the topology pointers appear in the output of getUniqueTopologies() above.
int	getTopologyInstanceCount (int topology_index) const
	Get the number of systems that make use of a particular topology.
std::vector< int >	getSystemIndicesByTopology (int topology_index) const
	Get a list of system indices which all reference the same unique topology (the unique topology index is determined by the order in which each unique topology appears in the overall list of systems in the object).
const PhaseSpaceSynthesis *	getSelfPointer () const
	Get a const pointer to the object itself.
PhaseSpace	exportSystem (int index, HybridTargetLevel tier=HybridTargetLevel::HOST) const
	Export a system's coordinates, velocities, and forces to a PhaseSpace object.
void	primeConjugateGradientCalculation ()
	Set the alternate positions to the current forces, and initialize velocities to zero, as part of the first step of conjugate gradient optimization. This primes the system so that the alternate coordinates and velocities arrays can hold the prior forces and temporary conjugate gradient memory.
void	printTrajectory (const std::vector< int > &system_indices, const std::string &file_name, double current_time, CoordinateFileKind output_kind, PrintSituation expectation) const
	Print a list of structures to a trajectory file. Download will be performed when calling this function, over the subset of relevant frames and data.
	PhaseSpaceSynthesis (const std::vector< PhaseSpace > &ps_list, const std::vector< AtomGraph * > &ag_list, int globalpos_scale_bits_in=default_globalpos_scale_bits, int localpos_scale_bits_in=default_localpos_scale_bits, int velocity_scale_bits_in=default_velocity_scale_bits, int force_scale_bits_in=default_force_scale_bits, HybridFormat format_in=default_hpc_format, const GpuDetails &gpu=null_gpu)
	The constructor works from a series PhaseSpace object, importing The LabFrame is not a POINTER-kind object of any sort.
	PhaseSpaceSynthesis (const std::vector< PhaseSpace > &ps_list, const std::vector< AtomGraph * > &ag_list, const std::vector< int > &index_key, int globalpos_scale_bits_in=default_globalpos_scale_bits, int localpos_scale_bits_in=default_localpos_scale_bits, int velocity_scale_bits_in=default_velocity_scale_bits, int force_scale_bits_in=default_force_scale_bits, HybridFormat format_in=default_hpc_format, const GpuDetails &gpu=null_gpu)
	PhaseSpaceSynthesis (const std::vector< PhaseSpace > &ps_list, const std::vector< int > &ps_index_key, const std::vector< AtomGraph * > &ag_list, const std::vector< int > &ag_index_key, int globalpos_scale_bits_in=default_globalpos_scale_bits, int localpos_scale_bits_in=default_localpos_scale_bits, int velocity_scale_bits_in=default_velocity_scale_bits, int force_scale_bits_in=default_force_scale_bits, HybridFormat format_in=default_hpc_format, const GpuDetails &gpu=null_gpu)
	PhaseSpaceSynthesis (const PhaseSpaceSynthesis &original)
	Copy and move constructors work much like their counterparts in the smaller PhaseSpace object.
	PhaseSpaceSynthesis (const PhaseSpaceSynthesis &original, HybridFormat format_in)
	PhaseSpaceSynthesis (PhaseSpaceSynthesis &&original)
PhaseSpaceSynthesis &	operator= (const PhaseSpaceSynthesis &other)
	Copy and move assignment operators must also be explicitly written out.
PhaseSpaceSynthesis &	operator= (PhaseSpaceSynthesis &&other)
const AtomGraph *	getSystemTopologyPointer (int system_index) const
	Get the topology pointer for a particular system within the synthesis.
const std::vector< AtomGraph * > &	getSystemTopologyPointer () const
const Hybrid< llint > *	getCoordinateHandle (CartesianDimension dim, TrajectoryKind kind, CoordinateCycle orientation) const
	Get a pointer to one of the Hybrid objects holding system coordinates. If the synthesis uses extended precision data, the result of this function must be supplemented with the equivalent call to getCoordinateOverflowHandle().
const Hybrid< llint > *	getCoordinateHandle (CartesianDimension dim, TrajectoryKind kind=TrajectoryKind::POSITIONS) const
Hybrid< llint > *	getCoordinateHandle (CartesianDimension dim, TrajectoryKind kind, CoordinateCycle orientation)
Hybrid< llint > *	getCoordinateHandle (CartesianDimension dim, TrajectoryKind kind=TrajectoryKind::POSITIONS)
const Hybrid< int > *	getCoordinateOverflowHandle (CartesianDimension dim, TrajectoryKind kind, CoordinateCycle orientation) const
	Get a pointer to one of the Hybrid objects holding system coordinates. Overloading and descriptions of input parameters follow from getCoordinateHandle(), above.
const Hybrid< int > *	getCoordinateOverflowHandle (CartesianDimension dim, TrajectoryKind kind=TrajectoryKind::POSITIONS) const
Hybrid< int > *	getCoordinateOverflowHandle (CartesianDimension dim, TrajectoryKind kind, CoordinateCycle orientation)
Hybrid< int > *	getCoordinateOverflowHandle (CartesianDimension dim, TrajectoryKind kind=TrajectoryKind::POSITIONS)
const Hybrid< double > *	getBoxTransformsHandle (CoordinateCycle orientation) const
	Get a pointer to the box space transforms. Overloading and description of the optional input parameter follows from getCoordinateHandle(), above.
const Hybrid< double > *	getBoxTransformsHandle () const
Hybrid< double > *	getBoxTransformsHandle (CoordinateCycle orientation)
Hybrid< double > *	getBoxTransformsHandle ()
const Hybrid< double > *	getInverseTransformsHandle (CoordinateCycle orientation) const
	Get a pointer to the inverse transform that takes coordinates back into real space. Overloading and description of the optional input parameter follows from getCoordinateHandle(), above.
const Hybrid< double > *	getInverseTransformsHandle () const
Hybrid< double > *	getInverseTransformsHandle (CoordinateCycle orientation)
Hybrid< double > *	getInverseTransformsHandle ()
const Hybrid< double > *	getBoxDimensionsHandle (CoordinateCycle orientation) const
	Get a pointer to the transform that takes coordinates back into real space. Overloading and description of the optional input parameter follows from getCoordinateHandle(), above.
const Hybrid< double > *	getBoxDimensionsHandle () const
Hybrid< double > *	getBoxDimensionsHandle (CoordinateCycle orientation)
Hybrid< double > *	getBoxDimensionsHandle ()
const Hybrid< llint > *	getBoxVectorsHandle (CoordinateCycle orientation) const
	Get a pointer to the box space transforms. Overloading and description of the optional input parameter follows from getCoordinateHandle(), above.
const Hybrid< llint > *	getBoxVectorsHandle () const
Hybrid< llint > *	getBoxVectorsHandle (CoordinateCycle orientation)
Hybrid< llint > *	getBoxVectorsHandle ()
const Hybrid< int > *	getBoxVectorsOverflowHandle (CoordinateCycle orientation) const
	Get a pointer to the box space transforms. Overloading and description of the optional input parameter follows from getCoordinateHandle(), above.
const Hybrid< int > *	getBoxVectorsOverflowHandle () const
Hybrid< int > *	getBoxVectorsOverflowHandle (CoordinateCycle orientation)
Hybrid< int > *	getBoxVectorsOverflowHandle ()
const PsSynthesisReader	data (HybridTargetLevel tier=HybridTargetLevel::HOST) const
	Get the reader or writer, as appropriate based on the const-ness of this object.
const PsSynthesisReader	data (CoordinateCycle orientation, HybridTargetLevel tier=HybridTargetLevel::HOST) const
PsSynthesisWriter	data (HybridTargetLevel tier=HybridTargetLevel::HOST)
PsSynthesisWriter	data (CoordinateCycle orientation, HybridTargetLevel tier=HybridTargetLevel::HOST)
const PsSynthesisBorders	borders (CoordinateCycle orientation, HybridTargetLevel tier=HybridTargetLevel::HOST) const
	Get the read-only summary of the system sizes. The data is never needed in as a collection of device viewable pointers to host-side data, as this information is constant as of the creation of the object and therefore consistent on both the CPU host and GPU device.
const PsSynthesisBorders	borders (HybridTargetLevel tier=HybridTargetLevel::HOST) const
void	extractSystem (PhaseSpace *ps, int index, HybridTargetLevel origin=HybridTargetLevel::HOST, HybridTargetLevel destination=HybridTargetLevel::HOST, const GpuDetails &gpu=null_gpu) const
	Extract the phase space (plus forces) of a specific system within the synthesis.
CoordinateFrame	exportCoordinates (int index, CoordinateCycle orientation, HybridFormat format_out, TrajectoryKind trajkind=TrajectoryKind::POSITIONS, HybridTargetLevel tier=HybridTargetLevel::HOST) const
	Export a system's coordinates, velocities, or forces to a compact CoordinateFrame object.
CoordinateFrame	exportCoordinates (int index, CoordinateCycle orientation, TrajectoryKind trajkind=TrajectoryKind::POSITIONS, HybridTargetLevel tier=HybridTargetLevel::HOST) const
CoordinateFrame	exportCoordinates (int index, HybridFormat format_out, TrajectoryKind trajkind=TrajectoryKind::POSITIONS, HybridTargetLevel tier=HybridTargetLevel::HOST) const
CoordinateFrame	exportCoordinates (int index, TrajectoryKind trajkind=TrajectoryKind::POSITIONS, HybridTargetLevel tier=HybridTargetLevel::HOST) const
std::vector< double >	getInterlacedCoordinates (int index, CoordinateCycle orientation, TrajectoryKind trajkind=TrajectoryKind::POSITIONS, HybridTargetLevel tier=HybridTargetLevel::HOST) const
	Get the interlaced X, Y, and Z coordinates of one system in particular. The result is comparable to the getInterlacedCoordinates() functions held by CoordinateFrame and PhaseSpace objects. The result will be provided in internal units of Angstroms (for positions), Angstroms per femtosecond (for velocities), or kcal/mol-A (for forces).
std::vector< double >	getInterlacedCoordinates (int index, TrajectoryKind trajkind=TrajectoryKind::POSITIONS, HybridTargetLevel tier=HybridTargetLevel::HOST) const
void	updateCyclePosition ()
	Modify the object's cycle position, as in the course of propagating dynamics.
void	updateCyclePosition (CoordinateCycle time_point)
void	initializeForces (CoordinateCycle orientation, int index=-1)
	Initialize the forces within a PhaseSpaceSynthesis object. This is the analog of the eponymous function in the PhaseSpace object.
void	initializeForces (int index=-1)
void	importSystem (const PhaseSpaceReader &psr, int system_index, CoordinateCycle orientation, HybridTargetLevel tier=HybridTargetLevel::HOST)
	Import a system from one of the other coordinate objects, or from a series of C-style arrays with trusted lengths. The imported system's size must correspond to that expected by the atom count of the system it will replace.
void	importSystem (const PhaseSpaceReader &psr, int system_index, HybridTargetLevel tier=HybridTargetLevel::HOST)
void	importSystem (const PhaseSpaceWriter &psw, int system_index, CoordinateCycle orientation, HybridTargetLevel tier=HybridTargetLevel::HOST)
void	importSystem (const PhaseSpaceWriter &psw, int system_index, HybridTargetLevel tier=HybridTargetLevel::HOST)
void	importSystem (const PhaseSpace &ps, int system_index, CoordinateCycle orientation, HybridTargetLevel tier=HybridTargetLevel::HOST)
void	importSystem (const PhaseSpace &ps, int system_index, HybridTargetLevel tier=HybridTargetLevel::HOST)
void	importSystem (const CoordinateFrameReader &cfr, int system_index, CoordinateCycle orientation, TrajectoryKind kind=TrajectoryKind::POSITIONS, HybridTargetLevel tier=HybridTargetLevel::HOST)
void	importSystem (const CoordinateFrameReader &cfr, int system_index, TrajectoryKind kind=TrajectoryKind::POSITIONS, HybridTargetLevel tier=HybridTargetLevel::HOST)
void	importSystem (const CoordinateFrameWriter &cfw, int system_index, CoordinateCycle orientation, TrajectoryKind kind=TrajectoryKind::POSITIONS, HybridTargetLevel tier=HybridTargetLevel::HOST)
void	importSystem (const CoordinateFrameWriter &cfw, int system_index, TrajectoryKind kind=TrajectoryKind::POSITIONS, HybridTargetLevel tier=HybridTargetLevel::HOST)
void	importSystem (const CoordinateFrame &cf, int system_index, CoordinateCycle orientation, TrajectoryKind kind=TrajectoryKind::POSITIONS, HybridTargetLevel tier=HybridTargetLevel::HOST)
void	importSystem (const CoordinateFrame &cf, int system_index, TrajectoryKind kind=TrajectoryKind::POSITIONS, HybridTargetLevel tier=HybridTargetLevel::HOST)
template<typename T>
void	importSystem (const T *x_import, const T *y_import, const T *z_import, const double *box_xform_in, const double *inverse_xform_in, const double *box_dimensions_in, int system_index, CoordinateCycle orientation, double inverse_scaling_factor=1.0, TrajectoryKind kind=TrajectoryKind::POSITIONS, HybridTargetLevel tier=HybridTargetLevel::HOST)
template<typename T>
void	importSystem (const CoordinateSeriesReader< T > &csr, int frame_index, int system_index, CoordinateCycle orientation, TrajectoryKind kind=TrajectoryKind::POSITIONS, HybridTargetLevel tier=HybridTargetLevel::HOST)
template<typename T>
void	importSystem (const CoordinateSeriesReader< T > &csr, int frame_index, int system_index, TrajectoryKind kind=TrajectoryKind::POSITIONS, HybridTargetLevel tier=HybridTargetLevel::HOST)
template<typename T>
void	importSystem (const CoordinateSeriesWriter< T > &csw, int frame_index, int system_index, CoordinateCycle orientation, TrajectoryKind kind=TrajectoryKind::POSITIONS, HybridTargetLevel tier=HybridTargetLevel::HOST)
template<typename T>
void	importSystem (const CoordinateSeriesWriter< T > &csw, int frame_index, int system_index, TrajectoryKind kind=TrajectoryKind::POSITIONS, HybridTargetLevel tier=HybridTargetLevel::HOST)
template<typename T>
void	importSystem (const CoordinateSeries< T > &cs, int frame_index, int system_index, CoordinateCycle orientation, TrajectoryKind kind=TrajectoryKind::POSITIONS, HybridTargetLevel tier=HybridTargetLevel::HOST)
template<typename T>
void	importSystem (const CoordinateSeries< T > &cs, int frame_index, int system_index, TrajectoryKind kind=TrajectoryKind::POSITIONS, HybridTargetLevel tier=HybridTargetLevel::HOST)

Detailed Description

A fixed-precision representation of coordinates, velocities, and forces to manage a set of simulations. The time steps are stored in units of femtoseconds. Coordinates are stored as long long integers to utilize the 32-bit int pipeline for difference computations, bypassing fp64 computations wherever possible to get the best throughput on many visualization, AI-oriented, and gaming cards.

Constructor & Destructor Documentation

PhaseSpaceSynthesis() [1/2]

stormm::synthesis::PhaseSpaceSynthesis::PhaseSpaceSynthesis	(	const std::vector< PhaseSpace > &	ps_list,
		const std::vector< AtomGraph * > &	ag_list,
		int	globalpos_scale_bits_in = default_globalpos_scale_bits,
		int	localpos_scale_bits_in = default_localpos_scale_bits,
		int	velocity_scale_bits_in = default_velocity_scale_bits,
		int	force_scale_bits_in = default_force_scale_bits,
		HybridFormat	format_in = default_hpc_format,
		const GpuDetails &	gpu = null_gpu )

The constructor works from a series PhaseSpace object, importing The LabFrame is not a POINTER-kind object of any sort.

Overloaded:

• Take arrays of PhaseSpace objects and AtomGraph pointers
• Take a SystemCache object and unpack it
• Skip the specification of thermostats, barostats, and the time step (just use defaults), but explicitly specify at least the global position scaling bit count and possibly other bit counts

Parameters

ps_list	Array of input coordinates, velocities, and forces objects
ag_list	Array of pointers to input topologies
index_key	Indices of the given topology and coordinate objects to assemble into a larger list of systems to be held within the resulting PhaseSpaceSynthesis object.
ps_index_key	Indices of the given coordinate objects to assemble into a larger list of systems to be held within the resulting PhaseSpaceSynthesis object.
ag_index_key	Indices of the given topology objects to assemble into a larger list of systems to be held within the resulting PhaseSpaceSynthesis object.

PhaseSpaceSynthesis() [2/2]

stormm::synthesis::PhaseSpaceSynthesis::PhaseSpaceSynthesis

(

const PhaseSpaceSynthesis &

original

)

Copy and move constructors work much like their counterparts in the smaller PhaseSpace object.

Parameters

original	The original PhaseSpaceSynthesis object
format_in	Make the copy with an arbitrary memory layout, copying data based on the priority rules set forth in the deepCopy() function for Hybrid objects.

Member Function Documentation

borders()

const PsSynthesisBorders stormm::synthesis::PhaseSpaceSynthesis::borders	(	CoordinateCycle	orientation,
		HybridTargetLevel	tier = HybridTargetLevel::HOST ) const

Get the read-only summary of the system sizes. The data is never needed in as a collection of device viewable pointers to host-side data, as this information is constant as of the creation of the object and therefore consistent on both the CPU host and GPU device.

Parameters

orientation	Indicate whether to retrieve box information at the WHITE or BLACK stage of the coordinate cycle. If unspecified, the object's internal coordinate cycle stage will guide the selection.
tier	The level (host or device) at which to get the set of pointers

data()

const PsSynthesisReader stormm::synthesis::PhaseSpaceSynthesis::data

(

HybridTargetLevel

tier = HybridTargetLevel::HOST

)

const

Get the reader or writer, as appropriate based on the const-ness of this object.

Overloaded:

• Get a read-only abstract for a const object
• Get a writeable abstract for a mutable object
• Choose the stage in the time cycle that shall be deemed the relevant coordinates

Parameters

tier	The level (host or device) at which to get the set of pointers
orientation	Stage in the object's time cycle to take as the current coordinates

exportCoordinates()

CoordinateFrame stormm::synthesis::PhaseSpaceSynthesis::exportCoordinates	(	int	index,
		CoordinateCycle	orientation,
		HybridFormat	format_out,
		TrajectoryKind	trajkind = TrajectoryKind::POSITIONS,
		HybridTargetLevel	tier = HybridTargetLevel::HOST ) const

Export a system's coordinates, velocities, or forces to a compact CoordinateFrame object.

Overloaded:

• Provide the stage of the coordinate cycle from which to obtain coordinates, or make the current point in the time cycle the basis of the new frame, or specify the point in the time cycle to draw from
• Build the new frame based on the current format of the PhaseSpaceSynthesis, or specify a format

Parameters

index	Index of the system of interest within the synthesis
trajkind	Type of coordinates to copy
orientation	Stage of the coordinate cycle from which to obtain coordinates
format_out	The format of the new frame
tier	The level (host or device) at which to get the data

exportSystem()

PhaseSpace stormm::synthesis::PhaseSpaceSynthesis::exportSystem	(	int	index,
		HybridTargetLevel	tier = HybridTargetLevel::HOST ) const

Export a system's coordinates, velocities, and forces to a PhaseSpace object.

Parameters

index	Index of the system of interest within the synthesis
tier	The level (host or device) at which to get the data

extractSystem()

void stormm::synthesis::PhaseSpaceSynthesis::extractSystem	(	PhaseSpace *	ps,
		int	index,
		HybridTargetLevel	origin = HybridTargetLevel::HOST,
		HybridTargetLevel	destination = HybridTargetLevel::HOST,
		const GpuDetails &	gpu = null_gpu ) const

Extract the phase space (plus forces) of a specific system within the synthesis.

Parameters

ps	Pointer to an allocated PhaseSpace object (i.e. the original) ready to accept data from the synthesis (which may have evolved since it was first loaded)
trajkind	Type of coordinates to copy
index	Index of the system of interest within the synthesis
origin	The level (host or device) at which to get the data
destination	The level (host or device) at which to get the data
gpu	Details of the GPU in use

getAtomCount()

int stormm::synthesis::PhaseSpaceSynthesis::getAtomCount

(

int

system_index

)

const

Get the number of atoms in one of the systems, using its index.

Parameters

system_index

Index of the system of interest

getAtomOffset()

int stormm::synthesis::PhaseSpaceSynthesis::getAtomOffset

(

int

system_index

)

const

Get the starting index of atoms for one of the systems, using its index.

Parameters

system_index

Index of the system of interest

getCoordinateHandle()

const Hybrid< llint > * stormm::synthesis::PhaseSpaceSynthesis::getCoordinateHandle	(	CartesianDimension	dim,
		TrajectoryKind	kind,
		CoordinateCycle	orientation ) const

Get a pointer to one of the Hybrid objects holding system coordinates. If the synthesis uses extended precision data, the result of this function must be supplemented with the equivalent call to getCoordinateOverflowHandle().

Overloaded:

• Get a const pointer to a const coordinate synthesis
• Get a non-const pointer to a mutable coordinate synthesis
• Indicate the specific stage in the time cycle, or accept the object's current stage

Parameters

dim	Indicate Cartesian X, Y, or Z values
kind	Indicate positions, velocities, or forces
orientation	The point in the time cycle (WHITE or BLACK) at which to set the pointer

getInterlacedCoordinates()

std::vector< double > stormm::synthesis::PhaseSpaceSynthesis::getInterlacedCoordinates	(	int	index,
		CoordinateCycle	orientation,
		TrajectoryKind	trajkind = TrajectoryKind::POSITIONS,
		HybridTargetLevel	tier = HybridTargetLevel::HOST ) const

Get the interlaced X, Y, and Z coordinates of one system in particular. The result is comparable to the getInterlacedCoordinates() functions held by CoordinateFrame and PhaseSpace objects. The result will be provided in internal units of Angstroms (for positions), Angstroms per femtosecond (for velocities), or kcal/mol-A (for forces).

Overloaded:

• Provide the stage of the coordinate cycle from which to obtain coordinates
• Assume that the WHITE stage of the coordinate cycle is desired

Parameters

index	Index of the system of interest within the synthesis
trajkind	Type of coordinates to copy
orientation	Stage of the coordinate cycle from which to obtain coordinates
tier	The level (host or device) at which to get the data

getSystemIndicesByTopology()

std::vector< int > stormm::synthesis::PhaseSpaceSynthesis::getSystemIndicesByTopology

(

int

topology_index

)

const

Get a list of system indices which all reference the same unique topology (the unique topology index is determined by the order in which each unique topology appears in the overall list of systems in the object).

Parameters

topology_index

Index of the unique topology of interest

getSystemTopologyPointer()

const AtomGraph * stormm::synthesis::PhaseSpaceSynthesis::getSystemTopologyPointer

(

int

system_index

)

const

Get the topology pointer for a particular system within the synthesis.

Overloaded:

• Get the topology pointer for a specific system
• Get topology pointers for all systems

Parameters

system_index

Index of the system of interest within the synthesis

getTopologyInstanceCount()

int stormm::synthesis::PhaseSpaceSynthesis::getTopologyInstanceCount

(

int

topology_index

)

const

Get the number of systems that make use of a particular topology.

Parameters

topology_index

Index of the unique topology of interest

getUniqueTopologyIndex()

int stormm::synthesis::PhaseSpaceSynthesis::getUniqueTopologyIndex

(

int

system_index

)

const

Get the index of the unique topology used by a particular system in the synthesis.

Parameters

system_index

Index of the system of interest

importSystem()

void stormm::synthesis::PhaseSpaceSynthesis::importSystem	(	const PhaseSpaceReader &	psr,
		int	system_index,
		CoordinateCycle	orientation,
		HybridTargetLevel	tier = HybridTargetLevel::HOST )

Import a system from one of the other coordinate objects, or from a series of C-style arrays with trusted lengths. The imported system's size must correspond to that expected by the atom count of the system it will replace.

Overloaded:

• Provide a PhaseSpace object (all coordinates, velocities, and forces of the input object will be transferred from the WHITE stage of the time cycle in the PhaseSpace object, into the specified stage of the time cycle in this synthesis, and other stages of the time cycle will be transferred accordingly).
• Provide three arrays of Cartesian X, Y, and Z coordinates, a scaling factor if the data type is fixed-precision integral, plus indications of whether the data is for positions, velocities, or forces, and at what stage of the time cycle the data is to enter the PhaseSpace object.
• Provide a CoordinateFrame or CoordinateSeries object with a frame number, plus indications of whether the object truly contains positions, velocities, or forces, and what stage of the time cycle the data is to enter the PhaseSpaceSynthesis.
• Provide an abstract of any of the major coordinate objects, plus the other information to target the import to the correct system, HPC tier, and place in the time cycle.

Parameters

ps	Complete phase space and time cycle data intended to replace one of the systems in the synthesis
system_index	Index of the system within this synthesis that the imported coordinates shall replace
orientation	Stage of the time cycle at which the WHITE stage of an input PhaseSpace object is to enter the synthesis, or at which the data in raw arrays, a CoordinateFrame, or a CoordinateSeries object is to enter the synthesis
tier	The level (host or device) at which to perform the transfer
x_import	Input Cartesian X coordinates (these could be positions, velocities, or forces)
y_import	Input Cartesian Y coordinates
z_import	Input Cartesian Z coordinates
box_xform_in	Transformation matrix to take coordinates into fractional space (for positions only–provide nullptr for velocities or forces)
inverse_xform_in	Transformation matrix to take coordinates back to real space. The units of elements in this matrix are Angstroms.
box_dimensions_in	Dimensions of the box (redundant with the information stored in either of the transformation matrices, but convenient and perhaps best able to preserve bitwise information to pass it directly). The units of this array are Angstroms.
kind	Specifies whether the Cartesian X, Y, and Z data are positions, velocities, or forces
scaling_factor	Scaling factor to take the input X, Y, and Z data into internal units of Angstroms, Angstroms per femtosecond, or kcal/mol-A^2
cf	Input coordinate frame object containing X, Y, and Z data as double-precision objects
cs	Input coordinate series object with X, Y, and Z data for many frames, one of which will be copied over. This object contains its own scaling factor.
frame_index	Index of a CoordinateSeries object to be transferred

initializeForces()

void stormm::synthesis::PhaseSpaceSynthesis::initializeForces	(	CoordinateCycle	orientation,
		int	index = -1 )

Initialize the forces within a PhaseSpaceSynthesis object. This is the analog of the eponymous function in the PhaseSpace object.

Overloaded:

• Initialize one or more systems' forces on the host if STORMM is compiled for CPU only
• Initialize one or more systems' forces on either the host or the device if STORMM is compiled for HPC
• Initialize forces for a specific point in the time cycle, or the current point

Parameters

orientation	Point in the time cycle at which to clear / initialize the forces
gpu	Details of the GPU in use
tier	The level (host or device) at which to initialize forces
index	Index of the system of interest within the synthesis–if negative, all systems will have their forces initialized

operator=()

PhaseSpaceSynthesis & stormm::synthesis::PhaseSpaceSynthesis::operator=

(

const PhaseSpaceSynthesis &

other

)

Copy and move assignment operators must also be explicitly written out.

Parameters

other

The other PhaseSpaceSynthesis object

primeConjugateGradientCalculation()

void stormm::synthesis::PhaseSpaceSynthesis::primeConjugateGradientCalculation

(

)

Set the alternate positions to the current forces, and initialize velocities to zero, as part of the first step of conjugate gradient optimization. This primes the system so that the alternate coordinates and velocities arrays can hold the prior forces and temporary conjugate gradient memory.

Parameters

gpu	Details of the GPU in use
tier	The level (host or device) at which to initialize vectors

printTrajectory()

void stormm::synthesis::PhaseSpaceSynthesis::printTrajectory	(	const std::vector< int > &	system_indices,
		const std::string &	file_name,
		double	current_time,
		CoordinateFileKind	output_kind,
		PrintSituation	expectation ) const

Print a list of structures to a trajectory file. Download will be performed when calling this function, over the subset of relevant frames and data.

Parameters

system_indices	List of system coordinates / velocities / forces to print
file_name	Name of the file to write, or base name of a set of files to write
current_time	Current time progress of the group of simulations
output_kind	The type of trajectory file to write
expectation	The state that the output trajectory file is expected to be found in

updateCyclePosition()

void stormm::synthesis::PhaseSpaceSynthesis::updateCyclePosition

(

)

Modify the object's cycle position, as in the course of propagating dynamics.

Overloaded:

• Increment the cycle position one step forward (this toggles between the WHITE and BLACK states, and is the same as decrementing the cycle position unless the time cycles takes on a third possible stage)
• Set the time cycle to a specific point

Parameters

time_point

The point in the time cycle which the object is to take as "current"

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

• src/Synthesis/phasespace_synthesis.h
• src/Synthesis/phasespace_synthesis.cpp