An object to collect the components of a valence work unit (which will also track frozen atoms to implement coordinate updates, velocity updates, and constraints). While the work unit is encoded in the AtomGraphSynthesis object, the assembly is best done by a dedicated object with plenty of its own methods operating on a single topology (AtomGraph). All systems in the AtomGraphSynthesis are designed to function independently of one another–the only difference is that they have consensus tables of most parameters and differen atom indexing. Translating a valence work unit into a list of instructions within an AtomGraphSynthesis is therefore a critical member function of this class. More...

#include <valence_workunit.h>

Public Member Functions
	ValenceWorkUnit (ValenceDelegator vdel_in, std::vector< int > tvwu_coverage, int list_index_in, int seed_atom_in, int max_atoms_in=maximum_valence_work_unit_atoms)
	The constructor takes a specific input topology (multiple systems using the same topology in an AtomGraphSynthesis can thereby take the same valence work unit and translate the atom indices as appropriate rather than regenerating the work unit for many equivalent systems). Mapping starts from a specific atom and proceeds until a maximum number of atoms has been accumulated in order to process as many related valence terms as possible.

int	getImportedAtomCount () const
	Get the number of atoms currently imported into this work unit.

int	getMovedAtomCount () const
	Get the number of atoms currently set to be moved by this work unit.

int	getUpdatedAtomCount () const
	Get the number of atoms currently set to be updated by this work unit.

int	getListIndex () const
	Get the list index of this work unit.

int	getMinAtomIndex () const
	Get the minimum topological atom index of any used by this work unit.

int	getMaxAtomIndex () const
	Get the maximum topological atom index of any used by this work unit.

int	getMaxAtoms () const
	Get the maximum atom count that this work unit can hold.

std::vector< int >	getAtomImportList (int atom_offset=0) const
	Get the list of imported atoms.

int	getImportedAtomIndex (int slot, int atom_offset=0) const
	Get a specific imported atom.

std::vector< uint2 >	getAtomManipulationMasks () const
	Get bitmasks of moving atoms and atoms that this work unit is assigned to update. Bits signify 1 for an atom being moving or an update assignment. The masks are encoded in a tuple with the x members making a mask for each segment of moving atoms and the y members making a mask for each segment of assigned update atoms.

int	getPaddedConstraintInstructionCount () const
	Get the padded size of the largest constraint group. The padding extends the size of each constraint group in the work unit to the minimum factor of two, with a maximum allowed size of 16.

std::vector< int >	getTaskCounts () const
	Get a vector describing the number of each type of item this work unit can be tasked to perform.

void	storeCompositeBondInstructions (const std::vector< int > &bond_param_map={}, const std::vector< int > &ubrd_param_map={})
	Compute and store a vector of the bond instructions. This function accepts parameter interpretation tables in order to produce instructions for a collated topology handling many systems (AtomGraphSynthesis).

void	storeAngleInstructions (const std::vector< int > &parameter_map={})
	Store a vector of the harmonic angle instructions. This function accepts a parameter interpretation table in order to produce instructions for a collated topology handling many systems (AtomGraphSynthesis).

void	storeCompositeDihedralInstructions (const std::vector< int > &dihe_param_map={}, const std::vector< int > &dihe14_param_map={}, const std::vector< int > &cimp_param_map={})
	Store a vector of the composite (cosine-based) dihedral, associated 1:4 interactions, as well as CHARMM improper dihedral instructions. This function accepts parameter interpretation tables in order to produce instructions for a collated topology handling many systems (AtomGraphSynthesis).

void	storeCmapInstructions (const std::vector< int > &parameter_map={})
	Store a vector of the CMAP instructions. This function accepts a parameter interpretation table in order to produce instructions for a collated topology handling many systems (AtomGraphSynthesis).

void	storeInferred14Instructions (const std::vector< int > &parameter_map={})
	Store a vector of the inferred 1:4 attenuated pair interaction instructions. This function accepts a parameter interpretation table in order to produce instructions for a collated topology handling many systems (AtomGraphSynthesis).

void	storePositionalRestraintInstructions (const std::vector< int > &kr_param_map={}, const std::vector< int > &xyz_param_map={})
	Store a vector of the positional restraint instructions for this work unit. This function accepts parameter interpretation tables showing how the raw list of restraint settings (k(2,3), r(1,2,3,4), and x / y / z targets) can be condensed by an AtomGraphSynthesis.

void	storeDistanceRestraintInstructions (const std::vector< int > &kr_param_map={})
	Store a vector of the distance restraint instructions for this work unit. This function accepts a parameter interpretation table showing how the raw list of restraint settings (k(2,3) and r(1,2,3,4)) can be condensed by an AtomGraphSynthesis.

void	storeAngleRestraintInstructions (const std::vector< int > &kr_param_map={})
	Store a vector of the three-point angle restraint instructions for this work unit. This function accepts a parameter interpretation table showing how the raw list of restraint settings (k(2,3) and r(1,2,3,4)) can be condensed by an AtomGraphSynthesis.

void	storeDihedralRestraintInstructions (const std::vector< int > &kr_param_map={})
	Store a vector of the four-point dihedral restraint instructions for this work unit. This function accepts a parameter interpretation table showing how the raw list of restraint settings (k(2,3) and r(1,2,3,4)) can be condensed by an AtomGraphSynthesis.

void	storeVirtualSiteInstructions (const std::vector< int > &parameter_map={})
	Store a vector of the virtual site instructions for this work unit. This function accepts a parameter interpretation table showing how the raw list of unique virtual site frames from one topology maps into a larger selection kept by an AtomGraphSynthesis.

void	storeSettleGroupInstructions (const std::vector< int > &parameter_map={})
	Store a vector of the SETTLE constraint group instructions for this work unit. This function accepts a parameter interpretation table showing how the raw list of unique SETTLE geometries in one topology maps into a possibly more diverse list curated by an AtomGraphSynthesis.

void	storeConstraintGroupInstructions (const std::vector< int > &parameter_map={}, const std::vector< int > &group_param_bounds={})
	Store a vector of the hub-and-spoke constraint group instructions for this work unit. This function accepts a parameter interpretation table showing how the raw list of unique constraint groups in one topology maps into a possibly more diverse list curated by an AtomGraphSynthesis.

const std::vector< uint2 > &	getCompositeBondInstructions () const
	Get the stored vector of composite bond instructions.

const std::vector< uint2 > &	getAngleInstructions () const
	Get the stored vector of angle instructions.

const std::vector< uint3 > &	getCompositeDihedralInstructions () const
	Get the stored vector of composite dihedral instructions.

const std::vector< uint2 > &	getCmapInstructions () const
	Get the stored vector of CMAP instructions.

const std::vector< uint > &	getInferred14Instructions () const
	Get the stored vector of CMAP instructions.

const std::vector< uint2 > &	getPositionalRestraintInstructions () const
	Get the stored vector of positional restraint instructions.

const std::vector< uint2 > &	getDistanceRestraintInstructions () const
	Get the stored vector of distance restraint instructions.

const std::vector< uint2 > &	getAngleRestraintInstructions () const
	Get the stored vector of three-point angle restraint instructions.

const std::vector< uint2 > &	getDihedralRestraintInstructions () const
	Get the stored vector of four-point dihedral restraint instructions.

const std::vector< uint2 > &	getVirtualSiteInstructions () const
	Get the stored vector of virtual site placement instructions.

const std::vector< uint2 > &	getSettleGroupInstructions () const
	Get the stored vector of SETTLE constraint group instructions.

const std::vector< uint2 > &	getConstraintGroupInstructions () const
	Get the stored vector of hub-and-spoke constraint group instructions.

uint2	getCompositeBondInstruction (int index) const
	Get a specific composite bond instruction.

uint2	getAngleInstruction (int index) const
	Get a specific angle instruction.

uint3	getCompositeDihedralInstruction (int index) const
	Get a specific composite dihedral instruction.

uint2	getCmapInstruction (int index) const
	Get a specific CMAP instruction.

uint	getInferred14Instruction (int index) const
	Get a specific CMAP instruction.

uint2	getPositionalRestraintInstruction (int index) const
	Get a specific positional restraint instruction.

uint2	getDistanceRestraintInstruction (int index) const
	Get a specific distance restraint instruction.

uint2	getAngleRestraintInstruction (int index) const
	Get a specific three-point angle restraint instruction.

uint2	getDihedralRestraintInstruction (int index) const
	Get a specific four-point dihedral restraint instruction.

uint2	getVirtualSiteInstruction (int index) const
	Get a specific virtual site placement instruction.

uint2	getSettleGroupInstruction (int index) const
	Get a specific SETTLE constraint group instruction.

uint2	getConstraintGroupInstruction (int index) const
	Get a specific hub-and-spoke constraint group instruction.

const std::vector< uint > &	getAccumulationFlags (VwuTask vtask) const
	Get the bitstrings indicating which energetic interactions each work unit is responsible for accumulating into the official energy outputs.

const std::vector< uint > &	getAtomUpdateFlags () const
	Get the bitstrings indicating which of the imported (cached) atoms this work unit is responsible for updating in the global postion and velocity arrays.

const std::vector< int > &	getSimpleTaskList (VwuTask vtask) const
	Get the topological indices of each task assigned to this work unit. Assignment of an energy / force-producing term or constraint group does not imply that a work unit is responsible for updating the final positions of all atoms involved. Composite task lists must be accessed with the special-purpose functions below.

const std::vector< int > &	getCompositeBondTaskList () const
	Get the composite bond tasks assigned to this work unit. This will return a vector of concatenated bond and Urey-Bradley term indices into the original topology. Interpreting which is which requires the corresponding vector of composite bond term instructions.

const std::vector< int2 > &	getCompositeDihedralTaskList () const
	Get the composite dihedral tasks assigned to this work unit. This will return a vector of tuples containing the topological indices of dihedrals or CHARMM impropers that the work unit evaluates. Interpretation of the tuples will depend on knowing whether each term index pertains to a standard cosine-based dihedral or a CHARMM improper dihedral, for which the corresponding instructions list must be accessed.

ValenceDelegator *	getDelegatorPointer ()
	Get the pointer to the ValenceDelegator managing the creation of this object.

const AtomGraph *	getTopologyPointer () const
	Get a pointer to the topology for which this work unit applies.

const RestraintApparatus *	getRestraintApparatusPointer () const
	Get a pointer to the restraint collection for which this work unit applies.

void	setListIndex (int list_index_in)
	Set the list index of this work unit, in the event that the list of work units for a particular topology needs to be re-ordered.

void	setAtomLimit (int new_limit)
	Set the atom limit for a valence work unit. This can be useful in situations where it is desirable to form several work units out of a single molecule, despite there being enough room in just one to hold all atoms of the molecule.

void	addNewAtomImport (int atom_index)
	Add a new atom to a work unit. This will update the associated ValenceDelegator and all assignments therein.

void	addNewAtomUpdate (const int atom_index)
	Add a new atom to the list of updates that a work unit shall perform. The atom must already be part of the atom import list.

void	makeAtomMoveList ()
	Create the move list for atoms in the work unit. Any atom that the work unit is responsible for updating must be moved by the work unit, but also any atom sharing a constraint group with one of the atoms which is on the official update list.

void	sortAtomSets ()
	Sort the atom lists (import, movement, and update) of this work unit into ascending order. This will optimize memory access when reading the atoms and set the stage for mapping valence terms / atom groups to the local list.

void	makeAtomUpdateMask ()
	Create a bit mask spanning the atom imports, marking all of those that the work unit is responsible for updating in the global position and velocity arrays.

void	logActivities ()
	Log all activities of this work unit: valence terms, restraints, virtual sites, and constraints. This will translate the topological indices of atoms into indices of the local import list.

Detailed Description

An object to collect the components of a valence work unit (which will also track frozen atoms to implement coordinate updates, velocity updates, and constraints). While the work unit is encoded in the AtomGraphSynthesis object, the assembly is best done by a dedicated object with plenty of its own methods operating on a single topology (AtomGraph). All systems in the AtomGraphSynthesis are designed to function independently of one another–the only difference is that they have consensus tables of most parameters and differen atom indexing. Translating a valence work unit into a list of instructions within an AtomGraphSynthesis is therefore a critical member function of this class.

Constructor & Destructor Documentation

◆ ValenceWorkUnit()

stormm::synthesis::ValenceWorkUnit::ValenceWorkUnit	(	ValenceDelegator *	vdel_in,
		std::vector< int > *	tvwu_coverage,
		int	list_index_in,
		int	seed_atom_in,
		int	max_atoms_in = maximum_valence_work_unit_atoms )

The constructor takes a specific input topology (multiple systems using the same topology in an AtomGraphSynthesis can thereby take the same valence work unit and translate the atom indices as appropriate rather than regenerating the work unit for many equivalent systems). Mapping starts from a specific atom and proceeds until a maximum number of atoms has been accumulated in order to process as many related valence terms as possible.

Parameters

vdel_in	Valence delegator managing the creation of this valence work unit
tvwu_coverage	Array spanning all atoms in the system to mark whether any one of them has been included in the valence work unit currently under construction. This is distinct from arrays with similar functionality held by the ValenceDelegator object, which track whether an atom has been included as an update priority in any valence work unit. Having this work-unit specific resource ensures that atoms are not included multiple times in the import array. It is cleared after each work unit's construction so as to not require re-allocation.
list_index_in	Index of this unit in a larger list (the unit should remember its own index number, for the purposes of coordinating with other work units)
seed_atom_in	The first atom to incorporate into the work unit. Subsequent atoms will be either bonded in some chain to the seed, retracing previous topological indices whereby previous work units left some atoms behind, or jumping forward to the next new molecule.
max_atoms_in	The maximum number of atoms to accumulate in the work unit

Member Function Documentation

◆ addNewAtomImport()

void stormm::synthesis::ValenceWorkUnit::addNewAtomImport ( int atom_index )

Add a new atom to a work unit. This will update the associated ValenceDelegator and all assignments therein.

Parameters

atom_index Index of the atom of interest

◆ getAccumulationFlags()

const std::vector< uint > & stormm::synthesis::ValenceWorkUnit::getAccumulationFlags ( VwuTask vtask ) const

Get the bitstrings indicating which energetic interactions each work unit is responsible for accumulating into the official energy outputs.

Parameters

vtask The type of task accumulator

◆ getAngleInstruction()

uint2 stormm::synthesis::ValenceWorkUnit::getAngleInstruction ( int index ) const

Get a specific angle instruction.

Parameters

index Index of the instruction to retrieve

◆ getAngleRestraintInstruction()

uint2 stormm::synthesis::ValenceWorkUnit::getAngleRestraintInstruction ( int index ) const

Get a specific three-point angle restraint instruction.

Parameters

index Index of the instruction to retrieve

◆ getAtomImportList()

std::vector< int > stormm::synthesis::ValenceWorkUnit::getAtomImportList ( int atom_offset = 0 ) const

Get the list of imported atoms.

Parameters

atom_offset Offset of the atoms to add to the topological indices, if importing from a synthesis of many systems

◆ getCmapInstruction()

uint2 stormm::synthesis::ValenceWorkUnit::getCmapInstruction ( int index ) const

Get a specific CMAP instruction.

Parameters

index Index of the instruction to retrieve

◆ getCompositeBondInstruction()

uint2 stormm::synthesis::ValenceWorkUnit::getCompositeBondInstruction ( int index ) const

Get a specific composite bond instruction.

Parameters

index Index of the instruction to retrieve

◆ getCompositeDihedralInstruction()

uint3 stormm::synthesis::ValenceWorkUnit::getCompositeDihedralInstruction ( int index ) const

Get a specific composite dihedral instruction.

Parameters

index Index of the instruction to retrieve

◆ getConstraintGroupInstruction()

uint2 stormm::synthesis::ValenceWorkUnit::getConstraintGroupInstruction ( int index ) const

Get a specific hub-and-spoke constraint group instruction.

Parameters

index Index of the instruction to retrieve

◆ getDihedralRestraintInstruction()

uint2 stormm::synthesis::ValenceWorkUnit::getDihedralRestraintInstruction ( int index ) const

Get a specific four-point dihedral restraint instruction.

Parameters

index Index of the instruction to retrieve

◆ getDistanceRestraintInstruction()

uint2 stormm::synthesis::ValenceWorkUnit::getDistanceRestraintInstruction ( int index ) const

Get a specific distance restraint instruction.

Parameters

index Index of the instruction to retrieve

◆ getImportedAtomIndex()

int stormm::synthesis::ValenceWorkUnit::getImportedAtomIndex	(	int	slot,
		int	atom_offset = 0 ) const

Get a specific imported atom.

Parameters

slot	Index of the atom of interest from within the work unit's array (this will return a topological index found in position atom_idx of the local import list)
atom_offset	Offset of the atoms to add to the topological indices, if importing from a larger synthesis of topologies / systems

◆ getInferred14Instruction()

uint stormm::synthesis::ValenceWorkUnit::getInferred14Instruction ( int index ) const

Get a specific CMAP instruction.

Parameters

index Index of the instruction to retrieve

◆ getPositionalRestraintInstruction()

uint2 stormm::synthesis::ValenceWorkUnit::getPositionalRestraintInstruction ( int index ) const

Get a specific positional restraint instruction.

Parameters

index Index of the instruction to retrieve

◆ getSettleGroupInstruction()

uint2 stormm::synthesis::ValenceWorkUnit::getSettleGroupInstruction ( int index ) const

Get a specific SETTLE constraint group instruction.

Parameters

index Index of the instruction to retrieve

◆ getSimpleTaskList()

const std::vector< int > & stormm::synthesis::ValenceWorkUnit::getSimpleTaskList ( VwuTask vtask ) const

Get the topological indices of each task assigned to this work unit. Assignment of an energy / force-producing term or constraint group does not imply that a work unit is responsible for updating the final positions of all atoms involved. Composite task lists must be accessed with the special-purpose functions below.

Parameters

vtask The type of task, i.e. bonded interactions, or SETTLE constraint groups

◆ getVirtualSiteInstruction()

uint2 stormm::synthesis::ValenceWorkUnit::getVirtualSiteInstruction ( int index ) const

Get a specific virtual site placement instruction.

Parameters

index Index of the instruction to retrieve

◆ setAtomLimit()

void stormm::synthesis::ValenceWorkUnit::setAtomLimit ( int new_limit )

Set the atom limit for a valence work unit. This can be useful in situations where it is desirable to form several work units out of a single molecule, despite there being enough room in just one to hold all atoms of the molecule.

Parameters

new_limit The new limit on the number of atoms. This cannot be lower than the number of atoms already in the work unit.

◆ setListIndex()

void stormm::synthesis::ValenceWorkUnit::setListIndex ( int list_index_in )

Set the list index of this work unit, in the event that the list of work units for a particular topology needs to be re-ordered.

Parameters

list_index_in The new list index for the work unit

◆ storeAngleInstructions()

void stormm::synthesis::ValenceWorkUnit::storeAngleInstructions ( const std::vector< int > & parameter_map = {} )

Store a vector of the harmonic angle instructions. This function accepts a parameter interpretation table in order to produce instructions for a collated topology handling many systems (AtomGraphSynthesis).

Parameters

parameter_map Map of the angle parameter sets (optional)

◆ storeAngleRestraintInstructions()

void stormm::synthesis::ValenceWorkUnit::storeAngleRestraintInstructions ( const std::vector< int > & kr_param_map = {} )

Store a vector of the three-point angle restraint instructions for this work unit. This function accepts a parameter interpretation table showing how the raw list of restraint settings (k(2,3) and r(1,2,3,4)) can be condensed by an AtomGraphSynthesis.

Parameters

kr_param_map Mapping for k(2,3) and r(1,2,3,4) settings (optional)

◆ storeCmapInstructions()

void stormm::synthesis::ValenceWorkUnit::storeCmapInstructions ( const std::vector< int > & parameter_map = {} )

Store a vector of the CMAP instructions. This function accepts a parameter interpretation table in order to produce instructions for a collated topology handling many systems (AtomGraphSynthesis).

Parameters

parameter_map Map of the one topology's CMAP surface indices onto the synthesis (optional)

◆ storeCompositeBondInstructions()

void stormm::synthesis::ValenceWorkUnit::storeCompositeBondInstructions	(	const std::vector< int > &	bond_param_map = {},
		const std::vector< int > &	ubrd_param_map = {} )

Compute and store a vector of the bond instructions. This function accepts parameter interpretation tables in order to produce instructions for a collated topology handling many systems (AtomGraphSynthesis).

Parameters

bond_param_map	Map of the bond parameter sets (optional)
ubrd_param_map	Map of the Urey-Bradley parameter sets (optional)

◆ storeCompositeDihedralInstructions()

void stormm::synthesis::ValenceWorkUnit::storeCompositeDihedralInstructions	(	const std::vector< int > &	dihe_param_map = {},
		const std::vector< int > &	dihe14_param_map = {},
		const std::vector< int > &	cimp_param_map = {} )

Store a vector of the composite (cosine-based) dihedral, associated 1:4 interactions, as well as CHARMM improper dihedral instructions. This function accepts parameter interpretation tables in order to produce instructions for a collated topology handling many systems (AtomGraphSynthesis).

Parameters

dihe_param_map	Map of the dihedral parameter sets (optional)
dihe_param_map	Map of the 1:4 scaling factor parameter pairs (optional)
dihe_param_map	Map of the CHARMM harmonic improper parameter sets (optional)

◆ storeConstraintGroupInstructions()

void stormm::synthesis::ValenceWorkUnit::storeConstraintGroupInstructions	(	const std::vector< int > &	parameter_map = {},
		const std::vector< int > &	group_param_bounds = {} )

Store a vector of the hub-and-spoke constraint group instructions for this work unit. This function accepts a parameter interpretation table showing how the raw list of unique constraint groups in one topology maps into a possibly more diverse list curated by an AtomGraphSynthesis.

Parameters

parameter_map	Mapping for SETTLE group mass and geometry specifications (optional)
group_param_bounds	Bounds for constraint group parameter sets in an AtomGraphSynthesis (required if parameter_map is supplied, to properly align the parameter indices of each instruction

◆ storeDihedralRestraintInstructions()

void stormm::synthesis::ValenceWorkUnit::storeDihedralRestraintInstructions ( const std::vector< int > & kr_param_map = {} )

Store a vector of the four-point dihedral restraint instructions for this work unit. This function accepts a parameter interpretation table showing how the raw list of restraint settings (k(2,3) and r(1,2,3,4)) can be condensed by an AtomGraphSynthesis.

Parameters

kr_param_map Mapping for k(2,3) and r(1,2,3,4) settings (optional)

◆ storeDistanceRestraintInstructions()

void stormm::synthesis::ValenceWorkUnit::storeDistanceRestraintInstructions ( const std::vector< int > & kr_param_map = {} )

Store a vector of the distance restraint instructions for this work unit. This function accepts a parameter interpretation table showing how the raw list of restraint settings (k(2,3) and r(1,2,3,4)) can be condensed by an AtomGraphSynthesis.

Parameters

kr_param_map Mapping for k(2,3) and r(1,2,3,4) settings (optional)

◆ storeInferred14Instructions()

void stormm::synthesis::ValenceWorkUnit::storeInferred14Instructions ( const std::vector< int > & parameter_map = {} )

Store a vector of the inferred 1:4 attenuated pair interaction instructions. This function accepts a parameter interpretation table in order to produce instructions for a collated topology handling many systems (AtomGraphSynthesis).

Parameters

parameter_map Map of the one topology's attenuated interaction scaling factors onto the synthesis (optional)

◆ storePositionalRestraintInstructions()

void stormm::synthesis::ValenceWorkUnit::storePositionalRestraintInstructions	(	const std::vector< int > &	kr_param_map = {},
		const std::vector< int > &	xyz_param_map = {} )

Store a vector of the positional restraint instructions for this work unit. This function accepts parameter interpretation tables showing how the raw list of restraint settings (k(2,3), r(1,2,3,4), and x / y / z targets) can be condensed by an AtomGraphSynthesis.

Parameters

kr_param_map	Mapping for k(2,3) and r(1,2,3,4) settings (optional)
xyz_param_map	Mapping for Cartesian coordinate targets (optional)

◆ storeSettleGroupInstructions()

void stormm::synthesis::ValenceWorkUnit::storeSettleGroupInstructions ( const std::vector< int > & parameter_map = {} )

Store a vector of the SETTLE constraint group instructions for this work unit. This function accepts a parameter interpretation table showing how the raw list of unique SETTLE geometries in one topology maps into a possibly more diverse list curated by an AtomGraphSynthesis.

Parameters

parameter_map Mapping for SETTLE group mass and geometry specifications (optional)

◆ storeVirtualSiteInstructions()

void stormm::synthesis::ValenceWorkUnit::storeVirtualSiteInstructions ( const std::vector< int > & parameter_map = {} )

Store a vector of the virtual site instructions for this work unit. This function accepts a parameter interpretation table showing how the raw list of unique virtual site frames from one topology maps into a larger selection kept by an AtomGraphSynthesis.

Parameters

parameter_map Mapping for virtual site frame specifications (optional)

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

src/Synthesis/valence_workunit.h
src/Synthesis/valence_workunit.cpp

Public Member Functions

Detailed Description

Constructor & Destructor Documentation

◆ ValenceWorkUnit()

Member Function Documentation

◆ addNewAtomImport()

◆ getAccumulationFlags()

◆ getAngleInstruction()

◆ getAngleRestraintInstruction()

◆ getAtomImportList()

◆ getCmapInstruction()

◆ getCompositeBondInstruction()

◆ getCompositeDihedralInstruction()

◆ getConstraintGroupInstruction()

◆ getDihedralRestraintInstruction()

◆ getDistanceRestraintInstruction()

◆ getImportedAtomIndex()

◆ getInferred14Instruction()

◆ getPositionalRestraintInstruction()

◆ getSettleGroupInstruction()

◆ getSimpleTaskList()

◆ getVirtualSiteInstruction()

◆ setAtomLimit()

◆ setListIndex()

◆ storeAngleInstructions()

◆ storeAngleRestraintInstructions()

◆ storeCmapInstructions()

◆ storeCompositeBondInstructions()

◆ storeCompositeDihedralInstructions()

◆ storeConstraintGroupInstructions()

◆ storeDihedralRestraintInstructions()

◆ storeDistanceRestraintInstructions()

◆ storeInferred14Instructions()

◆ storePositionalRestraintInstructions()

◆ storeSettleGroupInstructions()

◆ storeVirtualSiteInstructions()