#include <MolecularDynamics.h>

Inheritance diagram for MolecularDynamics< DIM, ROTATION >:

Collaboration diagram for MolecularDynamics< DIM, ROTATION >:

Public Member Functions
	MolecularDynamics (const unsigned T, uvec &&IT)

int	initialize (const shared_ptr< DomainBase > &D) override

int	process (const shared_ptr< DomainBase > &D) override
	Process and update both stiffness and resistance.

int	process_resistance (const shared_ptr< DomainBase > &D) override
	Process and update resistance.

Public Member Functions inherited from Constraint
	Constraint (unsigned, unsigned, std::vector< Node::DOF > &&, std::vector< Node::DOF > &&, unsigned)

const sp_vec &	get_resistance () const

const sp_mat &	get_stiffness () const

const vec &	get_auxiliary_resistance () const

const vec &	get_auxiliary_load () const

const sp_mat &	get_auxiliary_stiffness () const

void	set_multiplier_size (unsigned)

unsigned	get_multiplier_size () const

Public Member Functions inherited from ConditionalModifier
	ConditionalModifier (unsigned, unsigned, std::vector< Node::DOF > &&, std::vector< Node::DOF > &&)

virtual void	stage (const shared_ptr< DomainBase > &)
	Some algorithms need to manually modify some variables after solving.

std::set< uword >	get_involving_nodes (const shared_ptr< DomainBase > &) const
	Return a set of all nodes involved.

const uvec &	get_node_dof () const

void	deinitialize ()

bool	is_initialized () const

void	set_start_step (unsigned)

unsigned	get_start_step () const

void	set_end_step (unsigned)

unsigned	get_end_step () const

virtual bool	is_connected () const
	Indicate if this modifier can be deemed as an element that needs to account for connectivity.

bool	validate_step (const shared_ptr< DomainBase > &) const
	Validate itself against the current active step to see if itself needs to be applied.

virtual void	update_status (const vec &)

virtual void	clear_status ()

virtual void	commit_status ()

virtual void	reset_status ()

Public Member Functions inherited from UniqueTag
	UniqueTag (const UniqueTag &)=delete

	UniqueTag (UniqueTag &&)=delete

UniqueTag &	operator= (const UniqueTag &)=delete

UniqueTag &	operator= (UniqueTag &&)=delete

	~UniqueTag () override=default

	Tag (unsigned=0)

	Tag (const Tag &)=default

	Tag (Tag &&) noexcept=default

Public Member Functions inherited from Tag
	Tag (unsigned=0)

	Tag (const Tag &)=default

	Tag (Tag &&) noexcept=default

Tag &	operator= (const Tag &)=delete

Tag &	operator= (Tag &&)=delete

virtual	~Tag ()=default

void	set_tag (unsigned) const

unsigned	get_tag () const

void	enable ()

void	disable ()

void	guard ()

void	unguard ()

bool	is_active () const

bool	is_guarded () const

virtual void	print ()

Protected Member Functions
void	apply_interaction (const bool full, const shared_ptr< Element > &element) const

void	apply_interaction (const bool full, const shared_ptr< InteractionPair > &pair) const

virtual int	process_impl (const shared_ptr< DomainBase > &, bool)=0

int	process_entrypoint (const shared_ptr< DomainBase > &D, const bool full)

Protected Member Functions inherited from ConditionalModifier
double	get_amplitude (const shared_ptr< DomainBase > &) const

const std::vector< Node::DOF > &	get_dof_component () const
	Return the DoF components, falls back to the DoF order.

bool	validate_node (const shared_ptr< DomainBase > &) const

bool	validate_element (const shared_ptr< DomainBase > &) const

uvec	collect_node_dof (const shared_ptr< DomainBase > &) const

Protected Attributes
std::vector< shared_ptr< Element > >	elements

double	space = 0.

Protected Attributes inherited from Constraint
unsigned	lagrangian_size

vec	trial_lambda {lagrangian_size, fill::zeros}

vec	current_lambda {lagrangian_size, fill::zeros}

sp_vec	resistance

sp_mat	stiffness

vec	auxiliary_resistance

vec	auxiliary_load

sp_mat	auxiliary_stiffness

Protected Attributes inherited from ConditionalModifier
unsigned	start_step {1u}

unsigned	end_step {static_cast<unsigned>(-1)}

const std::vector< Node::DOF >	dof_order

uvec	target_node

uvec	target_element

uvec	target_dof

Detailed Description

template<unsigned DIM, bool ROTATION>
class MolecularDynamics< DIM, ROTATION >

A MolecularDynamics class.

Author: tlc

Date: 02/12/2025

Version: 0.1.0

Constructor & Destructor Documentation

◆ MolecularDynamics()

template<unsigned DIM, bool ROTATION>

MolecularDynamics< DIM, ROTATION >::MolecularDynamics	(	const unsigned	T,
		uvec &&	IT
	)

inline

Member Function Documentation

◆ apply_interaction() [1/2]

template<unsigned DIM, bool ROTATION>

void MolecularDynamics< DIM, ROTATION >::apply_interaction	(	const bool	full,
		const shared_ptr< Element > &	element
	)		const

inlineprotected

◆ apply_interaction() [2/2]

template<unsigned DIM, bool ROTATION>

void MolecularDynamics< DIM, ROTATION >::apply_interaction	(	const bool	full,
		const shared_ptr< InteractionPair > &	pair
	)		const

inlineprotected

◆ initialize()

template<unsigned DIM, bool ROTATION>

int MolecularDynamics< DIM, ROTATION >::initialize ( const shared_ptr< DomainBase > & D )

inlineoverridevirtual

Reimplemented from ConditionalModifier.

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◆ process()

template<unsigned DIM, bool ROTATION>

int MolecularDynamics< DIM, ROTATION >::process ( const shared_ptr< DomainBase > & )

inlineoverridevirtual

Process and update both stiffness and resistance.

This method provides all necessary pieces of typical constraints/loads required, including additional blocks in original global stiffness, border matrix resistance of multiplier, external loads.

Implements ConditionalModifier.

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◆ process_entrypoint()

template<unsigned DIM, bool ROTATION>

int MolecularDynamics< DIM, ROTATION >::process_entrypoint	(	const shared_ptr< DomainBase > &	D,
		const bool	full
	)

inlineprotected

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◆ process_impl()

template<unsigned DIM, bool ROTATION>

virtual int MolecularDynamics< DIM, ROTATION >::process_impl	(	const shared_ptr< DomainBase > &	,
		bool
	)

protectedpure virtual

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◆ process_resistance()

template<unsigned DIM, bool ROTATION>

int MolecularDynamics< DIM, ROTATION >::process_resistance ( const shared_ptr< DomainBase > & D )

inlineoverridevirtual

Process and update resistance.

For some algorithms, the global stiffness is formed only once in each substep. After calling solver, the storage may contain factorization. It is not correct to modify it in those algorithms. This method should provide updated constraint/load resistance but must not touch global stiffness.

Reimplemented from ConditionalModifier.

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Member Data Documentation

◆ elements

template<unsigned DIM, bool ROTATION>

std::vector<shared_ptr<Element> > MolecularDynamics< DIM, ROTATION >::elements

protected

◆ space

template<unsigned DIM, bool ROTATION>

double MolecularDynamics< DIM, ROTATION >::space = 0.

protected

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

Constraint/MolecularDynamics.h

Public Member Functions

Protected Member Functions

Protected Attributes

Detailed Description

Constructor & Destructor Documentation

◆ MolecularDynamics()

Member Function Documentation

◆ apply_interaction() [1/2]

◆ apply_interaction() [2/2]

◆ initialize()

◆ process()

◆ process_entrypoint()

◆ process_impl()

◆ process_resistance()

Member Data Documentation

◆ elements

◆ space