MilupHPC class. More...

#include "miluphpc.h"

Inheritance diagram for Miluphpc:

Collaboration diagram for Miluphpc:

Public Member Functions
real	removeParticles ()
	Remove particles in dependence of some criterion. More...

void	fixedLoadBalancing ()
	Load balancing via equidistant ranges. More...

void	dynamicLoadBalancing (int bins=5000)
	Pre-calculations for `updateRangeApproximately`. More...

void	updateRangeApproximately (int aimedParticlesPerProcess, int bins=5000)
	Update the ranges (approximately and dynamically). More...

void	updateRange (int aimedParticlesPerProcess)
	Update the range in dependence on number of (MPI) processes and aimed particles per process. More...

	Miluphpc (SimulationParameters simulationParameters)
	Constructor to set up simulation. More...

	~Miluphpc ()
	Destructor freeing class instances. More...

void	prepareSimulation ()
	Prepare the simulation, including. More...

void	numParticlesFromFile (const std::string &filename)
	Determine amount of particles (`numParticles` and `numParticlesLocal`) from initial file/particle distribution file. More...

void	distributionFromFile (const std::string &filename)
	Read initial/particle distribution file (in parallel) More...

real	tree ()
	Wrapper function for building the tree (and domain tree). More...

real	pseudoParticles ()
	Wrapper function for calculating pseudo-particles. More...

real	gravity ()
	Wrapper function for Gravity-related stuff. More...

real	sph ()

real	rhs (int step, bool selfGravity=true, bool assignParticlesToProcess=true)

virtual void	integrate (int step=0)=0

void	afterIntegrationStep ()

real	particles2file (int step)

real	particles2file (const std::string &filename, int *particleIndices, int length)

real	configParameters2file (HighFive::File &h5file)

void	getMemoryInfo ()

Public Attributes
int	subStep
	current sub-step (there are possibly more sub-steps within a step!) More...

real	h_searchRadius
	search radius for SPH (MPI-process overarching) neighbor search More...

real	totalEnergy
	total energy More...

real	totalAngularMomentum
	total angular momentum More...

H5Profiler &	profiler = H5Profiler::getInstance("log/performance.h5")
	H5 profiler instance. More...

Curve::Type	curveType
	Space-filling curve type to be used (Lebesgue or Hilbert) More...

SPH::KernelHandler	kernelHandler
	Instance to handle the SPH `Kernel` instance on device and host. More...

SimulationTimeHandler *	simulationTimeHandler
	Instance to handle the `SimulationTime` instances on device and host. More...

integer	numParticles
	number of particles (to be allocated) More...

integer	sumParticles
	(real) number of particles on all processes More...

integer	numParticlesLocal

integer	numNodes
	number of nodes (to be allocated) More...

IntegratedParticleHandler *	integratedParticles

integer *	d_mutex

ParticleHandler *	particleHandler
	Instance to handle the `Particles` instance on device and host. More...

SubDomainKeyTreeHandler *	subDomainKeyTreeHandler
	Instance to handle the `SubDomainKeyTree` instance on device and host. More...

TreeHandler *	treeHandler
	Instance to handle the `Tree` instance on device and host. More...

DomainListHandler *	domainListHandler
	Instance to handle the `DomainList` instance on device and host. More...

DomainListHandler *	lowestDomainListHandler
	Instance to handle the (lowest) `DomainList` instance on device and host. More...

MaterialHandler *	materialHandler
	Instance to handle `Materials` instances on device and host. More...

HelperHandler *	buffer
	buffer instance More...

SimulationParameters	simulationParameters
	buffer (need for revising) More...

Private Member Functions
real	reset ()
	Reset arrays, values, ... More...

real	boundingBox ()
	Calculate bounding boxes/simulation domain. More...

real	parallel_tree ()
	Parallel version regarding tree-stuff. More...

real	parallel_pseudoParticles ()
	Parallel version regarding computation of pseudo-particles. More...

real	parallel_gravity ()
	Parallel version regarding computation of gravitational stuff. More...

real	parallel_sph ()
	Parallel version regarding computation of SPH-stuff. More...

template<typename T >
integer	sendParticlesEntry (integer sendLengths, integer receiveLengths, T entry, T entryBuffer, T *copyBuffer)
	Send particles/Exchange particles among MPI processes. More...

template<typename T >
integer	sendParticles (T sendBuffer, T receiveBuffer, integer sendLengths, integer receiveLengths)
	Send particles/Exchange particles among MPI processes. More...

template<typename U , typename T >
real	arrangeParticleEntries (U sortArray, U sortedArray, T entry, T temp)
	Function to sort an array `entry` in dependence of another array `sortArray` More...

real	assignParticles ()
	Assign particles to correct process in dependence of particle key and ranges. More...

real	angularMomentum ()
	Calculate the angular momentum for all particles. More...

real	energy ()
	Calculate the total amount of energy. More...

Detailed Description

MilupHPC class.

Abstract base class for integrator classes implementing the right-hand-side via modular functions for different parts of the simulation.

Definition at line 74 of file miluphpc.h.

Constructor & Destructor Documentation

◆ Miluphpc()

Miluphpc::Miluphpc ( SimulationParameters simulationParameters )

Constructor to set up simulation.

Parameters

simulationParameters all the information required to set up simulation

Definition at line 3 of file miluphpc.cpp.

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◆ ~Miluphpc()

Miluphpc::~Miluphpc ( )

Destructor freeing class instances.

Definition at line 97 of file miluphpc.cpp.

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Member Function Documentation

◆ afterIntegrationStep()

void Miluphpc::afterIntegrationStep ( )

Function to be called after successful integration (step)

Definition at line 471 of file miluphpc.cpp.

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◆ angularMomentum()

real Miluphpc::angularMomentum ( )

private

Calculate the angular momentum for all particles.

Returns: accumulated time of functions within

Definition at line 484 of file miluphpc.cpp.

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◆ arrangeParticleEntries()

template<typename U , typename T >

real Miluphpc::arrangeParticleEntries	(	U *	sortArray,
		U *	sortedArray,
		T *	entry,
		T *	temp
	)

private

Function to sort an array entry in dependence of another array sortArray

Template Parameters

U	type of the arrays determining the sorting
T	type of the arrays to be sorted

Parameters

sortArray	array to be sorted (rather sorting behaviour should be determined)
sortedArray	sorted array (result of sorting)
entry	(relevant) array to be sorted
temp	buffer needed for sorting process

Returns: accumulated time of functions within

Definition at line 944 of file miluphpc.cpp.

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◆ assignParticles()

real Miluphpc::assignParticles ( )

private

Assign particles to correct process in dependence of particle key and ranges.

First an extra array is used to save the information of process assignment for each particle, this extra array is used as key for sorting all of the attributes of the Particle class and finally the sub-array determined by the process assignment are sent to the corresponding process via MPI.

Returns: accumulated time of functions within

Definition at line 700 of file miluphpc.cpp.

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◆ boundingBox()

real Miluphpc::boundingBox ( )

private

Calculate bounding boxes/simulation domain.

To derive the bounding boxes of the simulation domain the maximum and minimum value for each coordinate axis is determined locally on each process and afterwards reduced to all processes to get the global maximum and minimum via MPI_Allreduce().

Returns: accumulated time of functions within

Definition at line 643 of file miluphpc.cpp.

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◆ configParameters2file()

real Miluphpc::configParameters2file ( HighFive::File & h5file )

Definition at line 3736 of file miluphpc.cpp.

◆ distributionFromFile()

void Miluphpc::distributionFromFile ( const std::string & filename )

Read initial/particle distribution file (in parallel)

Parameters

filename initial conditions file to be read

Definition at line 161 of file miluphpc.cpp.

◆ dynamicLoadBalancing()

void Miluphpc::dynamicLoadBalancing ( int bins = 5000 )

Pre-calculations for updateRangeApproximately.

Potential wrapper functions if more range determination functions come into exist.

Parameters

bins	amount of bins the range will be subdivided

Definition at line 2885 of file miluphpc.cpp.

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◆ energy()

real Miluphpc::energy ( )

private

Calculate the total amount of energy.

Returns: accumulated time of functions within

Definition at line 538 of file miluphpc.cpp.

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◆ fixedLoadBalancing()

void Miluphpc::fixedLoadBalancing ( )

Load balancing via equidistant ranges.

Definition at line 2839 of file miluphpc.cpp.

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◆ getMemoryInfo()

void Miluphpc::getMemoryInfo ( )

Definition at line 3760 of file miluphpc.cpp.

◆ gravity()

real Miluphpc::gravity ( )

Wrapper function for Gravity-related stuff.

The gravitational force computation corresponds to the Barnes-Hut method. First all relevant lowest domain list nodes belonging to another process are determined. Then the pseudo-particles and particles to be sent can be determined by checking the extended $\theta$-criterion for all nodes and all relevant lowest domain list nodes. This is done in an approach where particles are either marked to be sent or not in an extra array and afterwards copied to contiguous memory in order to send them via MPI. After receiving, the particles are inserted into the local tree, whereas first the pseudo-particles and then the particles are inserted. Since complete sub-trees are inserted, no new pseudo-particles are generated during this process. Afterwards, the actual force computation can be accomplished locally. Finally the inserted (pseudo-)particles are removed.

Returns: accumulated time for functions within

Definition at line 1241 of file miluphpc.cpp.

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◆ integrate()

virtual void Miluphpc::integrate ( int step = 0 )

pure virtual

Abstract method for integration. Implemented by integration classes, calling rhs() different times

Parameters

step

Implemented in ExplicitEuler, Leapfrog, and PredictorCorrectorEuler.

◆ numParticlesFromFile()

void Miluphpc::numParticlesFromFile ( const std::string & filename )

Determine amount of particles (numParticles and numParticlesLocal) from initial file/particle distribution file.

Since the information of how many particles to be simulated is needed to allocate (the right amount of) memory, this function need to be called before distributionFromFile()

Parameters

filename initial conditions file to be read

Definition at line 123 of file miluphpc.cpp.

◆ parallel_gravity()

real Miluphpc::parallel_gravity ( )

private

Parallel version regarding computation of gravitational stuff.

Returns: accumulated time of functions within

Definition at line 1248 of file miluphpc.cpp.

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◆ parallel_pseudoParticles()

real Miluphpc::parallel_pseudoParticles ( )

private

Parallel version regarding computation of pseudo-particles.

Returns: accumulated time of functions within

Definition at line 1061 of file miluphpc.cpp.

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◆ parallel_sph()

real Miluphpc::parallel_sph ( )

private

Parallel version regarding computation of SPH-stuff.

Returns: accumulated time of functions within

Definition at line 2216 of file miluphpc.cpp.

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◆ parallel_tree()

real Miluphpc::parallel_tree ( )

private

Parallel version regarding tree-stuff.

Returns: accumulated time of functions within

Definition at line 958 of file miluphpc.cpp.

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◆ particles2file() [1/2]

real Miluphpc::particles2file	(	const std::string &	filename,
		int *	particleIndices,
		int	length
	)

Write particles or rather particle's information/attributes to file. Particles to be outputted determined by particleIndices

Parameters

filename	file name of output H5 file
particleIndices	particle's indices to be outputted
length	amount of particles to be outputted

Returns: accumulated time for functions within

Definition at line 3620 of file miluphpc.cpp.

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◆ particles2file() [2/2]

real Miluphpc::particles2file ( int step )

Write all of the information/particle distribution to H5 file

Parameters

step	simulation step, used to name file

Returns: accumulated time for functions within

Definition at line 3409 of file miluphpc.cpp.

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◆ prepareSimulation()

void Miluphpc::prepareSimulation ( )

Prepare the simulation, including.

loading the initial conditions
copying to device
computing the bounding boxes
initial ranges (load balancing)

Definition at line 235 of file miluphpc.cpp.

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◆ pseudoParticles()

real Miluphpc::pseudoParticles ( )

Wrapper function for calculating pseudo-particles.

The pseudo-particle computation starts with determining the lowest domain list, this information is stored in a separate instance of the DomainList class continues with the local COM computation, the resetting of the domain list nodes that are not lowest domain list nodes, the preparation for the exchange by copying the information into contiguous memory, subsequent communication via MPI, the updating of the lowest domain list nodes and finally ends with the computation of the remaining domain list node pseudo-particles.

Returns: accumulated time for functions within

Definition at line 1054 of file miluphpc.cpp.

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◆ removeParticles()

real Miluphpc::removeParticles ( )

Remove particles in dependence of some criterion.

Criterion can be specified in the config file. Removing particles can be accomplished by marking the particles to be removed via an extra array and using this one as key for sorting all the (pseudo-)particle arrays and finally deleting them by overwriting those entries with default values.

Returns: accumulated time of functions within

Definition at line 3040 of file miluphpc.cpp.

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◆ reset()

real Miluphpc::reset ( )

private

Reset arrays, values, ...

This function embraces resetting the

pseudo-particles
child array
the boundaries
the domain list nodes
the neighbor list
and so forth ...

ensuring correct starting conditions.

Returns: accumulated time of functions within

Definition at line 586 of file miluphpc.cpp.

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◆ rhs()

real Miluphpc::rhs	(	int	step,
		bool	selfGravity = `true`,
		bool	assignParticlesToProcess = `true`
	)

Right Hand Side - all of the simulation without integration itself.

This method is used/called by the different integrators in order to integrate or execute the simulation. The force or acceleration computation and necessary steps to calculate them are encapsulated in this function whose individual components and interoperation are depicted in the following. This right-hand-side is called once or several times within a (sub-)integration step in dependence of the integration scheme. In addition, the function depends on whether the simulation runs single-node or multi-node, gravity and/or SPH are included into the simulation and some other conditions.

Parameters

step	simulation step, regarding output
selfGravity	apply self-gravity y/n (needed since gravity is decoupled)
assignParticlesToProcess	assign particles to correct process y/n

Returns: accumulated time for functions within

Definition at line 294 of file miluphpc.cpp.

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◆ sendParticles()

template<typename T >

integer Miluphpc::sendParticles	(	T *	sendBuffer,
		T *	receiveBuffer,
		integer *	sendLengths,
		integer *	receiveLengths
	)

private

Send particles/Exchange particles among MPI processes.

Template Parameters

T

Parameters

sendBuffer
receiveBuffer
sendLengths
receiveLengths

Returns

Definition at line 3174 of file miluphpc.cpp.

◆ sendParticlesEntry()

template<typename T >

integer Miluphpc::sendParticlesEntry	(	integer *	sendLengths,
		integer *	receiveLengths,
		T *	entry,
		T *	entryBuffer,
		T *	copyBuffer
	)

private

Send particles/Exchange particles among MPI processes.

Template Parameters

T

Parameters

sendLengths
receiveLengths
entry
entryBuffer
copyBuffer

Returns

Definition at line 3327 of file miluphpc.cpp.

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◆ sph()

real Miluphpc::sph ( )

Wrapper function for SPH-related stuff

Similar to the gravitational force computation is the SPH part. The relevant lowest domain list nodes are determined in order to decide which particles need to be sent, which is also done in an analogous approach in the gravitational part. However, in this case only particles are sent and after exchanging those particles, the insertion includes generation of new pseudo-particles similar to building or rather extending the local tree. With inserted particles from the other processes the FRNN search can be done and subsequent computation of the density, speed of sound and pressure realized. The corresponding particle properties are sent again, so that the actual force computation can be performed. Finally, the inserted and generated (pseudo-)particles are removed.

Returns: accumulated time for functions within

Definition at line 2207 of file miluphpc.cpp.

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◆ tree()

real Miluphpc::tree ( )

Wrapper function for building the tree (and domain tree).

To build the parallel tree it is necessary to determine the domain list or common coarse tree nodes which are derived from the ranges. After that, the tree is built locally and finally all the domain list nodes or rather those attributes as indices are either saved to an instance of the omainList class or if they do not exist after building the tree created and afterwards assigned.

Returns: accumulated time for functions within

Definition at line 951 of file miluphpc.cpp.

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◆ updateRange()

void Miluphpc::updateRange ( int aimedParticlesPerProcess )

Update the range in dependence on number of (MPI) processes and aimed particles per process.

Counting the particles per process, calculating the aimed particles per process as quotient of total number of particles and number of processes, determining the particle keys, sorting them and determining the new ranges as the indices of the multiplies of the aimed number of particles per process.

Parameters

aimedParticlesPerProcess optimal number of particles per process

Definition at line 2912 of file miluphpc.cpp.

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◆ updateRangeApproximately()

void Miluphpc::updateRangeApproximately	(	int	aimedParticlesPerProcess,
		int	bins = `5000`
	)

Update the ranges (approximately and dynamically).

A histogram is generated with the amount of bins given by bins. The possible range is distributed accordingly and particles are sorted in dependence of their key into, in order to extract the ranges.

Parameters

aimedParticlesPerProcess	aimed amount particles per process
bins	amount of bins the range will be subdivided

Definition at line 2988 of file miluphpc.cpp.

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Member Data Documentation

◆ buffer

HelperHandler* Miluphpc::buffer

buffer instance

Todo:: revise buffer handling buffer instance

Definition at line 325 of file miluphpc.h.

◆ curveType

Curve::Type Miluphpc::curveType

Space-filling curve type to be used (Lebesgue or Hilbert)

Definition at line 277 of file miluphpc.h.

◆ d_mutex

integer* Miluphpc::d_mutex

Definition at line 307 of file miluphpc.h.

◆ domainListHandler

DomainListHandler* Miluphpc::domainListHandler

Instance to handle the DomainList instance on device and host.

Definition at line 315 of file miluphpc.h.

◆ h_searchRadius

real Miluphpc::h_searchRadius

search radius for SPH (MPI-process overarching) neighbor search

Definition at line 215 of file miluphpc.h.

◆ integratedParticles

IntegratedParticleHandler* Miluphpc::integratedParticles

Instance(s) to handle the IntegratedParticles instance(s) on device and host

Memory for this may or may not be allocated within child classes. This depends on whether instances are needed for cache particle information e.g. for predictor-corrector integrators.

Definition at line 305 of file miluphpc.h.

◆ kernelHandler

SPH::KernelHandler Miluphpc::kernelHandler

Instance to handle the SPH Kernel instance on device and host.

Definition at line 280 of file miluphpc.h.

◆ lowestDomainListHandler

DomainListHandler* Miluphpc::lowestDomainListHandler

Instance to handle the (lowest) DomainList instance on device and host.

Definition at line 317 of file miluphpc.h.

◆ materialHandler

MaterialHandler* Miluphpc::materialHandler

Instance to handle Materials instances on device and host.

Definition at line 319 of file miluphpc.h.

◆ numNodes

integer Miluphpc::numNodes

number of nodes (to be allocated)

Definition at line 296 of file miluphpc.h.

◆ numParticles

integer Miluphpc::numParticles

number of particles (to be allocated)

Definition at line 285 of file miluphpc.h.

◆ numParticlesLocal

integer Miluphpc::numParticlesLocal

number of particles currently living on the (MPI) process

Temporarily are more particles on the process, e.g. for gravitational and SPH (force) calculations.

Definition at line 294 of file miluphpc.h.

◆ particleHandler

ParticleHandler* Miluphpc::particleHandler

Instance to handle the Particles instance on device and host.

Definition at line 309 of file miluphpc.h.

◆ profiler

H5Profiler& Miluphpc::profiler = H5Profiler::getInstance("log/performance.h5")

H5 profiler instance.

Definition at line 274 of file miluphpc.h.

◆ simulationParameters

SimulationParameters Miluphpc::simulationParameters

buffer (need for revising)

buffer (need for revising) buffer (need for revising) buffer (need for revising) buffer (need for revising) buffer (need for revising) buffer (need for revising) buffer (need for revising) buffer (need for revising) buffer (need for revising) collected information required to set up the simulation

Definition at line 351 of file miluphpc.h.

◆ simulationTimeHandler

SimulationTimeHandler* Miluphpc::simulationTimeHandler

Instance to handle the SimulationTime instances on device and host.

Definition at line 282 of file miluphpc.h.

◆ subDomainKeyTreeHandler

SubDomainKeyTreeHandler* Miluphpc::subDomainKeyTreeHandler

Instance to handle the SubDomainKeyTree instance on device and host.

Definition at line 311 of file miluphpc.h.

◆ subStep

int Miluphpc::subStep

current sub-step (there are possibly more sub-steps within a step!)

Definition at line 212 of file miluphpc.h.

◆ sumParticles

integer Miluphpc::sumParticles

(real) number of particles on all processes

Definition at line 287 of file miluphpc.h.

◆ totalAngularMomentum

real Miluphpc::totalAngularMomentum

total angular momentum

Definition at line 221 of file miluphpc.h.

◆ totalEnergy

real Miluphpc::totalEnergy

total energy

Definition at line 218 of file miluphpc.h.

◆ treeHandler

TreeHandler* Miluphpc::treeHandler

Instance to handle the Tree instance on device and host.

Definition at line 313 of file miluphpc.h.

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

include/miluphpc.h
src/miluphpc.cpp

Public Member Functions

Public Attributes

Private Member Functions

Detailed Description

Constructor & Destructor Documentation

◆ Miluphpc()

◆ ~Miluphpc()

Member Function Documentation

◆ afterIntegrationStep()

◆ angularMomentum()

◆ arrangeParticleEntries()

◆ assignParticles()

◆ boundingBox()

◆ configParameters2file()

◆ distributionFromFile()

◆ dynamicLoadBalancing()

◆ energy()

◆ fixedLoadBalancing()

◆ getMemoryInfo()

◆ gravity()

◆ integrate()

◆ numParticlesFromFile()

◆ parallel_gravity()

◆ parallel_pseudoParticles()

◆ parallel_sph()

◆ parallel_tree()

◆ particles2file() [1/2]

◆ particles2file() [2/2]

◆ prepareSimulation()

◆ pseudoParticles()

◆ removeParticles()

◆ reset()

◆ rhs()

◆ sendParticles()

◆ sendParticlesEntry()

◆ sph()

◆ tree()

◆ updateRange()

◆ updateRangeApproximately()

Member Data Documentation

◆ buffer

◆ curveType

◆ d_mutex

◆ domainListHandler

◆ h_searchRadius

◆ integratedParticles

◆ kernelHandler

◆ lowestDomainListHandler

◆ materialHandler

◆ numNodes

◆ numParticles

◆ numParticlesLocal

◆ particleHandler

◆ profiler

◆ simulationParameters

◆ simulationTimeHandler

◆ subDomainKeyTreeHandler

◆ subStep

◆ sumParticles

◆ totalAngularMomentum

◆ totalEnergy

◆ treeHandler