A collection of one or more AtomGraph objects, with similar components arranged in contiguous arrays (often padded by the GPU warp size to prevent one system from flowing into another). Work units covering all systems are laid out in additional, contiguous arrays. While individual topologies (AtomGraphs) have Hybrid POINTER-kind objects for details such as charges and atom type indices and all of the POINTER-kind objects targeted a single ARRAY-kind object of the correct memory type, the synthesis, which may have many topologies and a great deal more overall information, stores most of its data in a series of ARRAY-kind objects, one for each member variable. More...

#include <atomgraph_synthesis.h>

Public Member Functions
int	getUniqueTopologyCount () const
	Get the number of unique topologies described by the synthesis.

const std::vector< AtomGraph * > &	getUniqueTopologies () const
	Get a const reference to the list of all pointers for unique topologies making up this synthesis.

std::vector< int >	getTopologyIndices () const
	Get a const reference to the list of all topology indices, indicating the topologies describing each systems contained within this synthesis.

RestraintApparatus *	getSystemRestraintPointer (int system_index) const
	Get a restraint apparatus pointer for a sepcific system contained within the synthesis.

int	getSystemCount () const
	Get the number of systems that this synthesis describes.

int	getPaddedAtomCount () const
	Get the entire padded number of atoms covering all systems.

int	getAtomOffset (int system_index) const
	Get the starting point for atoms of a specific system in the lineup of all topologies.

int	getVirtualSiteCount () const
	Get the total number of virtual sites across all systems, including replicas.

int	getBondTermCount () const
	Get the total number of bond terms across all systems, including replicas.

int	getAngleTermCount () const
	Get the total number of bond angle terms across all systems, including replicas.

int	getDihedralTermCount () const
	Get the total number of cosine-based dihedral terms across all systems and replicas.

int	getUreyBradleyTermCount () const
	Get the total number of Urey-Bradley terms across all systems and replicas.

int	getCharmmImproperTermCount () const
	Get the total number of CHARMM improper terms across all systems and replicas.

int	getCmapTermCount () const
	Get the total number of CMAP terms across all systems and replicas.

int	getLJTypeCount () const
	Get the number of unique atom types (a parameter, not an extensive quantity dependent on the number of systems).

int	getChargeTypeCount () const
	Get the number of unique charge parameters.

int	getBondParameterCount () const
	Get the number of unique harmonic bond parameter sets.

int	getAngleParameterCount () const
	Get the number of unique harmonic bond angle parameter sets.

int	getDihedralParameterCount () const
	Get the number of unique cosine-based dihedral parameter sets.

int	getUreyBradleyParameterCount () const
	Get the number of unique Urey-Bradley harmonic angle parameter sets.

int	getCharmmImproperParameterCount () const
	Get the number of unique CHARMM improper parameter sets.

int	getCmapSurfaceCount () const
	Get the number of unique CMAP surfaces.

const Hybrid< int > &	getSystemAtomCounts () const
	Get the sizes of all individual systems as a const reference to the Hybrid array member variable.

const Hybrid< int > &	getSystemAtomOffsets () const
	Get the starting locations of all individual systems as a const reference to the Hybrid array member variable.

const Hybrid< int > &	getDegreesOfFreedom () const
	Get the numbers of unconstrained degrees of freedom for all individual systems in the.

const Hybrid< int > &	getConstrainedDegreesOfFreedom () const
	Get the numbers of constrained degrees of freedom for all individual systems in the.

UnitCellType	getUnitCellType () const
	Get the unit cell type that will be taken for all systems (TRICLINIC subsumes ORTHORHOMBIC in a sort of type promotion).

ImplicitSolventModel	getImplicitSolventModel () const
	Get the implicit solvent model in use across all systems.

double	getDielectricConstant () const
	Get the dielectric constant (supporting the implicit solvent model) for all systems.

double	getSaltConcentration () const
	Get the salt concentration (supporting the implicit solvent model) for all systems.

double	getCoulombConstant () const
	Get the fundamental Coulomb constant defining the electrostatics of all systems.

int	getValenceWorkUnitCount () const
	Get the overall number of valence work units needed to account for interactions in all systems.

int2	getValenceWorkUnitSize () const
	Get the maximum size of valence work units, whether for organic molecules or solvent (rigid water) residues. This will have been either set by the user or tailored by the automated heuristics to produce the best saturation.

ValenceKernelSize	getValenceThreadBlockSize () const
	Get the necessary thread block size for evaluating the valence work units.

const Hybrid< int2 > &	getValenceWorkUnitAbstracts () const
	Get the abstracts (condensed lists of import and instruction set limits) for the valence work units spanning all systems in this synthesis.

NbwuKind	getNonbondedWorkType () const
	Get the type of non-bonded work required by systems in this synthesis.

int	getNonbondedWorkUnitCount () const
	Get the number of non-bonded work units serving systems in this synthesis.

int	getRandomCacheDepth () const
	Get the depth of the random numbers cache that the non-bonded work units of this topology synthesis will try to fill. This will raise a warning and return zero if no cache depth has yet been set.

int	getReductionWorkUnitCount () const
	Get the number of reduction work units spanning all systems.

RdwuPerSystem	getRdwuPerSystem () const
	Get a qualitative assessment of the number of reduction work units assigned to any one system.

const Hybrid< int > &	getReductionWorkUnitAbstracts () const
	Get the reduction work unit abstracts (this is not required for valence or non-bonded work units as the abstracts needed for implementing these work units are produced by member functions of this class (see below). The reduction work, however, is managed by an abstract splicing together elements of this class, PhaseSpaceSynthesis, and a small class allocating temporary storage space.

SyValenceKit< double >	getDoublePrecisionValenceKit (HybridTargetLevel tier=HybridTargetLevel::HOST) const
	Get a minimal kit with double-precision parameter detail for computing valence interactions for all systems based on the work units stored in this object.

SyValenceKit< float >	getSinglePrecisionValenceKit (HybridTargetLevel tier=HybridTargetLevel::HOST) const
	Get a minimal kit with single-precision parameter detail for computing valence interactions for all systems based on the work units stored in this object.

SyRestraintKit< double, double2, double4 >	getDoublePrecisionRestraintKit (HybridTargetLevel tier=HybridTargetLevel::HOST) const
	Get a minimal kit with double-precision parameter detail for computing valence interactions for all systems based on the work units stored in this object.

SyRestraintKit< float, float2, float4 >	getSinglePrecisionRestraintKit (HybridTargetLevel tier=HybridTargetLevel::HOST) const
	Get a minimal kit with single-precision parameter detail for computing valence interactions for all systems based on the work units stored in this object.

SyNonbondedKit< double, double2 >	getDoublePrecisionNonbondedKit (HybridTargetLevel tier=HybridTargetLevel::HOST) const
	Get a minimal kit with double-precision real numbers for computing non-bonded interactions for all systems based on work units stored in this object.

SyNonbondedKit< float, float2 >	getSinglePrecisionNonbondedKit (HybridTargetLevel tier=HybridTargetLevel::HOST) const
	Get a minimal kit with single-precision real numbers for computing non-bonded interactions for all systems based on work units stored in this object.

SyAtomUpdateKit< double, double2, double4 >	getDoublePrecisionAtomUpdateKit (HybridTargetLevel tier=HybridTargetLevel::HOST) const
	Get a minimal kit with double-precision real numbers for updating atom and virtual site positions based on work units stored in this object.

SyAtomUpdateKit< float, float2, float4 >	getSinglePrecisionAtomUpdateKit (HybridTargetLevel tier=HybridTargetLevel::HOST) const
	Get a minimal kit with single-precision real numbers for updating atom and virtual site positions based on work units stored in this object.

const AtomGraphSynthesis *	getSelfPointer () const
	Get a const pointer to the object itself, useful for retrieving a valid pointer when the object is available as a const reference.

void	loadNonbondedWorkUnits (const StaticExclusionMaskSynthesis &poly_se, InitializationTask init_request=InitializationTask::NONE, int random_cache_depth=0, const GpuDetails &gpu=null_gpu)
	Construct non-bonded work units for all unique topologies (there are no restraints for non-bonded interactions that might distinguish systems with the same topology, as was a consideration when developing the valence work units). Load the instructions into the topology synthesis for availability on the GPU.


	AtomGraphSynthesis (const std::vector< AtomGraph * > &topologies_in, const std::vector< RestraintApparatus * > &restraints_in, const std::vector< int > &topology_indices_in, const std::vector< int > &restraint_indices_in, ExceptionResponse policy_in=ExceptionResponse::WARN, const GpuDetails &gpu=null_gpu, StopWatch *timer_in=nullptr)
	The constructor takes a series of topologies and NMR restraints. The NMR restraints point to specific topologies and thereby apply to any coordinate sets that also point to those topologies.

	AtomGraphSynthesis (const std::vector< AtomGraph * > &topologies_in, const std::vector< RestraintApparatus * > &restraints_in, ExceptionResponse policy_in=ExceptionResponse::WARN, const GpuDetails &gpu=null_gpu, StopWatch *timer_in=nullptr)

	AtomGraphSynthesis (const std::vector< AtomGraph * > &topologies_in, const std::vector< int > &topology_indices_in, ExceptionResponse policy_in=ExceptionResponse::WARN, const GpuDetails &gpu=null_gpu, StopWatch *timer_in=nullptr)

	AtomGraphSynthesis (const std::vector< AtomGraph * > &topologies_in, ExceptionResponse policy_in=ExceptionResponse::WARN, const GpuDetails &gpu=null_gpu, StopWatch *timer_in=nullptr)


	AtomGraphSynthesis (const AtomGraphSynthesis &original)
	The presence of POINTER-kind Hybrid objects necessitates manually written copy and move constructors as well as copy and move assignment operators, but all are valid.

	AtomGraphSynthesis (AtomGraphSynthesis &&original)

AtomGraphSynthesis &	operator= (const AtomGraphSynthesis &original)

AtomGraphSynthesis &	operator= (AtomGraphSynthesis &&original)


const AtomGraph *	getSystemTopologyPointer (int system_index) const
	Get a topology pointer for a specific system contained within the synthesis.

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


int	getAtomCount () const
	Get the number of atoms in one or more systems.

int	getAtomCount (int system_index) const


std::vector< AtomicRadiusSet >	getPBRadiiSet () const
	Get the name of the PB radii set for one or more systems.

std::vector< AtomicRadiusSet >	getPBRadiiSet (int low_limit, int high_limit) const

AtomicRadiusSet	getPBRadiiSet (int index) const


template<typename T>
std::vector< T >	getPartialCharges (HybridTargetLevel tier=HybridTargetLevel::HOST) const
	Get partial charges stored within the synthesis.

template<typename T>
std::vector< T >	getPartialCharges (int system_index, HybridTargetLevel tier=HybridTargetLevel::HOST) const

template<typename T>
std::vector< T >	getPartialCharges (int system_index, int low_index, int high_index, HybridTargetLevel tier=HybridTargetLevel::HOST) const


template<typename T>
std::vector< T >	getAtomicMasses (HybridTargetLevel tier) const
	Get the masses (or inverse masses) of atoms in the synthesis.

template<typename T>
std::vector< T >	getAtomicMasses (HybridTargetLevel tier, int system_index) const

template<typename T>
std::vector< T >	getAtomicMasses (HybridTargetLevel tier, int system_index, int low_index, int high_index) const


void	setImplicitSolventModel ()
	Apply an implicit solvent model to the synthesis. Any mode of operation other than taking the original topologies' parameters as is (calling this member function with no arguments) will cause changes ot the underlying topologies.

void	setImplicitSolventModel (ImplicitSolventModel igb_in, const NeckGeneralizedBornKit< double > &ngbk, const std::vector< AtomicRadiusSet > &radii_sets_in, double dielectric_in=80.0, double saltcon_in=0.0, ExceptionResponse policy=ExceptionResponse::WARN)

void	setImplicitSolventModel (ImplicitSolventModel igb_in, const NeckGeneralizedBornKit< double > &ngbk, AtomicRadiusSet radii_set=AtomicRadiusSet::NONE, double dielectric_in=80.0, double saltcon_in=0.0, ExceptionResponse policy=ExceptionResponse::WARN)

void	setImplicitSolventModel (ImplicitSolventModel igb_in, const NeckGeneralizedBornTable &ngb_tab, const std::vector< AtomicRadiusSet > &radii_sets_in, double dielectric_in=80.0, double saltcon_in=0.0, ExceptionResponse policy=ExceptionResponse::WARN)

void	setImplicitSolventModel (ImplicitSolventModel igb_in, const NeckGeneralizedBornTable &ngb_tab, AtomicRadiusSet radii_set=AtomicRadiusSet::NONE, double dielectric_in=80.0, double saltcon_in=0.0, ExceptionResponse policy=ExceptionResponse::WARN)

Detailed Description

A collection of one or more AtomGraph objects, with similar components arranged in contiguous arrays (often padded by the GPU warp size to prevent one system from flowing into another). Work units covering all systems are laid out in additional, contiguous arrays. While individual topologies (AtomGraphs) have Hybrid POINTER-kind objects for details such as charges and atom type indices and all of the POINTER-kind objects targeted a single ARRAY-kind object of the correct memory type, the synthesis, which may have many topologies and a great deal more overall information, stores most of its data in a series of ARRAY-kind objects, one for each member variable.

Constructor & Destructor Documentation

◆ AtomGraphSynthesis() [1/2]

stormm::synthesis::AtomGraphSynthesis::AtomGraphSynthesis	(	const std::vector< AtomGraph * > &	topologies_in,
		const std::vector< RestraintApparatus * > &	restraints_in,
		const std::vector< int > &	topology_indices_in,
		const std::vector< int > &	restraint_indices_in,
		ExceptionResponse	policy_in = ExceptionResponse::WARN,
		const GpuDetails &	gpu = null_gpu,
		StopWatch *	timer_in = nullptr )

The constructor takes a series of topologies and NMR restraints. The NMR restraints point to specific topologies and thereby apply to any coordinate sets that also point to those topologies.

Overloaded:

Prepare the energy surface with or without restraints
Accept lists of unique topologies and restraints with auxiliary lists of indices for replicating them, or accept explicit lists of topologies and restraints with one index for each system.

Parameters

topologies_in	List of input topology pointers
restraints_in	List of input restraint collections
topology_indices_in	Indicators of which topologies describe each system in this synthesis. This allows a synthesis to describe many copies of each system in its work units while storing relatively small amounts of data.
restraint_indices_in	Indicators of which collections of restraints supplement the energy surfaces of each system within this synthesis. Different sets of restraints allow many systems referencing the same topology to evolve on different energy surfaces.
policy	Instruction on what to do if questionable input is encountered
vwu_atom_limit	Maximum number of atoms to include in each valence work unit, taken from user input or a pre-computed value based on known launch bounds of the kernel that will evaluate the work units
timer_in	Timer to track the wall time of this setup

◆ AtomGraphSynthesis() [2/2]

stormm::synthesis::AtomGraphSynthesis::AtomGraphSynthesis ( const AtomGraphSynthesis & original )

The presence of POINTER-kind Hybrid objects necessitates manually written copy and move constructors as well as copy and move assignment operators, but all are valid.

Parameters

original	The original object to copy or move
other	Another object placed on the right hand side of the assignment statement

Member Function Documentation

◆ getAtomCount()

int stormm::synthesis::AtomGraphSynthesis::getAtomCount ( ) const

Get the number of atoms in one or more systems.

Overloaded:

Get the total number of atoms, summed over all systems, including replicas. This does not include padding.
Get the total number of atoms in a specific sytem, without padding.

Parameters

system_index index of the system of interest

◆ getAtomicMasses()

template<typename T>

std::vector< T > stormm::synthesis::AtomGraphSynthesis::getAtomicMasses ( HybridTargetLevel tier ) const

Get the masses (or inverse masses) of atoms in the synthesis.

Overloaded:

Get masses for all systems, padded by the warp size between systems
Get masses for a single system
Get masses for a specific range of atoms in a single system

Parameters

tier	Obtain the data from arrays on the host or the device
system_index	Index of the specific system to query
low_index	Lower limit of atoms in the system to query (will be validated)
high_index	Upper limit of atoms in the system to query (will be validated)

◆ getAtomOffset()

int stormm::synthesis::AtomGraphSynthesis::getAtomOffset ( int system_index ) const

Get the starting point for atoms of a specific system in the lineup of all topologies.

Parameters

system_index index of the system of interest

◆ getDoublePrecisionAtomUpdateKit()

SyAtomUpdateKit< double, double2, double4 > stormm::synthesis::AtomGraphSynthesis::getDoublePrecisionAtomUpdateKit ( HybridTargetLevel tier = HybridTargetLevel::HOST ) const

Get a minimal kit with double-precision real numbers for updating atom and virtual site positions based on work units stored in this object.

Parameters

tier	Level at which to obtain pointers for the abstract

◆ getDoublePrecisionNonbondedKit()

SyNonbondedKit< double, double2 > stormm::synthesis::AtomGraphSynthesis::getDoublePrecisionNonbondedKit ( HybridTargetLevel tier = HybridTargetLevel::HOST ) const

Get a minimal kit with double-precision real numbers for computing non-bonded interactions for all systems based on work units stored in this object.

Parameters

tier	Level at which to obtain pointers for the abstract

◆ getDoublePrecisionRestraintKit()

SyRestraintKit< double, double2, double4 > stormm::synthesis::AtomGraphSynthesis::getDoublePrecisionRestraintKit ( HybridTargetLevel tier = HybridTargetLevel::HOST ) const

Get a minimal kit with double-precision parameter detail for computing valence interactions for all systems based on the work units stored in this object.

Parameters

tier	Level at which to obtain pointers for the abstract

◆ getDoublePrecisionValenceKit()

SyValenceKit< double > stormm::synthesis::AtomGraphSynthesis::getDoublePrecisionValenceKit ( HybridTargetLevel tier = HybridTargetLevel::HOST ) const

Get a minimal kit with double-precision parameter detail for computing valence interactions for all systems based on the work units stored in this object.

Parameters

tier	Level at which to obtain pointers for the abstract

◆ getPartialCharges()

template<typename T>

std::vector< T > stormm::synthesis::AtomGraphSynthesis::getPartialCharges ( HybridTargetLevel tier = HybridTargetLevel::HOST ) const

Get partial charges stored within the synthesis.

Overloaded:

Get partial charges for all systems, padded by the warp size between systems
Get partial charges for a single system
Get partial charges for a specific range of atoms in a single system

Parameters

tier	Obtain the data from arrays on the host or the device
system_index	Index of the specific system to query
low_index	Lower limit of atoms in the system to query (will be validated)
high_index	Upper limit of atoms in the system to query (will be validated)

◆ getPBRadiiSet()

std::vector< AtomicRadiusSet > stormm::synthesis::AtomGraphSynthesis::getPBRadiiSet ( ) const

Get the name of the PB radii set for one or more systems.

Overloaded:

Get the PB radii set for all systems
Get the PB radii set for a series of systems between low and high limits
Get the PB radii set for a specific system

◆ getSinglePrecisionAtomUpdateKit()

SyAtomUpdateKit< float, float2, float4 > stormm::synthesis::AtomGraphSynthesis::getSinglePrecisionAtomUpdateKit ( HybridTargetLevel tier = HybridTargetLevel::HOST ) const

Get a minimal kit with single-precision real numbers for updating atom and virtual site positions based on work units stored in this object.

Parameters

tier	Level at which to obtain pointers for the abstract

◆ getSinglePrecisionNonbondedKit()

SyNonbondedKit< float, float2 > stormm::synthesis::AtomGraphSynthesis::getSinglePrecisionNonbondedKit ( HybridTargetLevel tier = HybridTargetLevel::HOST ) const

Get a minimal kit with single-precision real numbers for computing non-bonded interactions for all systems based on work units stored in this object.

Parameters

tier	Level at which to obtain pointers for the abstract

◆ getSinglePrecisionRestraintKit()

SyRestraintKit< float, float2, float4 > stormm::synthesis::AtomGraphSynthesis::getSinglePrecisionRestraintKit ( HybridTargetLevel tier = HybridTargetLevel::HOST ) const

Get a minimal kit with single-precision parameter detail for computing valence interactions for all systems based on the work units stored in this object.

Parameters

tier	Level at which to obtain pointers for the abstract

◆ getSinglePrecisionValenceKit()

SyValenceKit< float > stormm::synthesis::AtomGraphSynthesis::getSinglePrecisionValenceKit ( HybridTargetLevel tier = HybridTargetLevel::HOST ) const

Get a minimal kit with single-precision parameter detail for computing valence interactions for all systems based on the work units stored in this object.

Parameters

tier	Level at which to obtain pointers for the abstract

◆ getSystemRestraintPointer()

RestraintApparatus * stormm::synthesis::AtomGraphSynthesis::getSystemRestraintPointer ( int system_index ) const

Get a restraint apparatus pointer for a sepcific system contained within the synthesis.

Parameters

system_index Index of the system of interest

◆ getSystemTopologyPointer()

const AtomGraph * stormm::synthesis::AtomGraphSynthesis::getSystemTopologyPointer ( int system_index ) const

Get a topology pointer for a specific system contained 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

◆ loadNonbondedWorkUnits()

void stormm::synthesis::AtomGraphSynthesis::loadNonbondedWorkUnits	(	const StaticExclusionMaskSynthesis &	poly_se,
		InitializationTask	init_request = InitializationTask::NONE,
		int	random_cache_depth = 0,
		const GpuDetails &	gpu = null_gpu )

Construct non-bonded work units for all unique topologies (there are no restraints for non-bonded interactions that might distinguish systems with the same topology, as was a consideration when developing the valence work units). Load the instructions into the topology synthesis for availability on the GPU.

Parameters

poly_se	Synthesis of static exclusion masks for a compilation of systems in isolated boundary conditions.
init_request	Indicate a pattern for the non-bonded work units to initialize accumulators for subsequent force and energy calculations.
random_cache_depth	Number of random values to store for each atom in the synthesis (the actual number of values stored is multiplied by three, for Cartesian X, Y, and Z contributions)
gpu	Details of the GPU in use (this may change the profile of the workload)

◆ setImplicitSolventModel()

void stormm::synthesis::AtomGraphSynthesis::setImplicitSolventModel ( )

Apply an implicit solvent model to the synthesis. Any mode of operation other than taking the original topologies' parameters as is (calling this member function with no arguments) will cause changes ot the underlying topologies.

Overloaded:

Take the implicit solvent models as described in the original topologies
Apply specific atomic radius sets to each system
Apply a common atomic radius set ot all systems
Accept a GB neck model, its double-precision abstract, or no such model

Parameters

igb_in	A specific, established implicit solvent model (from literature and hard-coded into STORMM) to apply
dielectric_in	The desired dielectric constant
saltcon_in	The intended salt concentration (affects the GB decay parameter Kappa)
radii_sets_in	Radii to impart to the topology (this is often coupled to the choice of implicit solvent model, but for purposes of experimentation or new model development might be flexible)
policy	Indicator of what to do if the topology's PB radii to not meet the implicit solvent model requirements, or there is some other problem

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

src/Synthesis/atomgraph_synthesis.h
src/Synthesis/ag_synthesis_constructors.cpp
src/Synthesis/ag_synthesis_mechanics.cpp

Public Member Functions

Detailed Description

Constructor & Destructor Documentation

◆ AtomGraphSynthesis() [1/2]

◆ AtomGraphSynthesis() [2/2]

Member Function Documentation

◆ getAtomCount()

◆ getAtomicMasses()

◆ getAtomOffset()

◆ getDoublePrecisionAtomUpdateKit()

◆ getDoublePrecisionNonbondedKit()

◆ getDoublePrecisionRestraintKit()

◆ getDoublePrecisionValenceKit()

◆ getPartialCharges()

◆ getPBRadiiSet()

◆ getSinglePrecisionAtomUpdateKit()

◆ getSinglePrecisionNonbondedKit()

◆ getSinglePrecisionRestraintKit()

◆ getSinglePrecisionValenceKit()

◆ getSystemRestraintPointer()

◆ getSystemTopologyPointer()

◆ loadNonbondedWorkUnits()

◆ setImplicitSolventModel()