libMesh::PolymerChain Class Reference

#include <polymer_chain.h>

Inheritance diagram for libMesh::PolymerChain:

Collaboration diagram for libMesh::PolymerChain:

Public Member Functions
	PolymerChain (const std::size_t chain_id)
	PolymerChain (const std::size_t chain_id, PMPeriodicBoundary &pm_pb)
	~PolymerChain ()
void	read_data (const std::string &filename)
void	read_data_pizza (const std::string &filename)
void	read_data_vtk (const std::string &filename)
void	read_data_csv (const std::string &filename)
void	read_pbc_count ()
void	add_bead (const Point &pt, const PointType point_type, const int parent_id, const std::vector< Real > &rot_vec)
void	generate_polymer_chains (const unsigned int n_beads, const unsigned int n_chains, const Real init_bondLength, const Point init_bbox_min, const Point init_bbox_max, const std::string &filename, unsigned int comm_in_rank)
void	generate_polymer_chain (const Point pt0, const std::size_t Nb, const Real Ls, const Point &bbox_min, const Point &bbox_max, const std::string &filename)
void	print_info () const
void	write_polymer_chain (const unsigned int &step_id, const unsigned int &o_step, const Real &real_time, const std::vector< Point > &center0, const std::vector< Real > &lvec, std::vector< std::string > &output_file, unsigned int comm_in_rank) const
void	write_polymer_trajectory (const unsigned int &o_step, unsigned int comm_in_rank) const
void	write_polymer_com (const unsigned int &step_id, const unsigned int &o_step, const std::vector< Real > &lvec, unsigned int comm_in_rank) const
void	write_polymer_stretch (const unsigned int &step_id, const unsigned int &o_step, const std::vector< Real > &lvec, unsigned int comm_in_rank) const
void	write_polymer_rog (const unsigned int &step_id, const unsigned int &o_step, const std::vector< Real > &lvec, unsigned int comm_in_rank) const
void	write_polymer_msd (const unsigned int &step_id, const unsigned int &o_step, const std::vector< Point > &center0, const std::vector< Real > &lvec, unsigned int comm_in_rank) const
void	write_bead (const unsigned int &step_id, const unsigned int &o_step, const Real &real_time, const std::vector< Point > &center0, const std::vector< Real > &lvec, const std::vector< std::string > &output_file, unsigned int comm_in_rank) const
void	write_bead_trajectory (const unsigned int &o_step, unsigned int comm_in_rank) const
void	write_bead_com (const unsigned int &step_id, const unsigned int &o_step, const std::vector< Real > &lvec, unsigned int comm_in_rank) const
void	write_bead_msd (const unsigned int &step_id, const unsigned int &o_step, const std::vector< Point > &center0, const std::vector< Real > &lvec, unsigned int comm_in_rank) const
void	write_time (const unsigned int &step_id, const unsigned int &o_step, const Real &real_time, unsigned int comm_in_rank) const
void	write_unfolded_polymer_chain (const std::string &filename) const
void	write_unfolded_com (const std::string &filename) const
std::size_t	chain_id () const
std::size_t	n_chains () const
std::size_t	n_beads () const
std::size_t	n_bonds () const
std::size_t	n_springs () const
const std::vector< PointParticle * > &	beads ()
const std::vector< std::vector< std::size_t > > &	bonds ()
Point	spring_vector (const unsigned int i) const
Point	end_to_end_vector () const
Point	end_to_end_vector_square () const
Real	compute_chain_length ()
void	compute_center_of_mass (const std::vector< Real > &lvec, std::vector< Point > &center) const
void	initial_bead_center_of_mass (std::vector< Point > &center0) const
void	initial_chain_center_of_mass (std::vector< Point > &center0) const
void	compute_chain_stretch (const std::vector< Real > &lvec, std::vector< Point > &stretch) const
void	compute_radius_of_gyration (const std::vector< Real > &lvec, const std::vector< Point > &center, std::vector< Real > &RgSqrt) const
void	compute_mean_square_displacement (const std::vector< Point > &R0, const std::vector< Point > &Rt, Point &msd) const
bool	check_chain (const Real &Ls)
Point	bead_vector (const Point &bead0, const Point &bead1) const

Constructor & Destructor Documentation

libMesh::PolymerChain::PolymerChain

(

const std::size_t

chain_id

)

libMesh::PolymerChain::PolymerChain	(	const std::size_t	chain_id,
		PMPeriodicBoundary &	pm_pb
	)

libMesh::PolymerChain::~PolymerChain

(

)

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Member Function Documentation

void libMesh::PolymerChain::add_bead	(	const Point &	pt,
		const PointType	point_type,
		const int	parent_id,
		const std::vector< Real > &	rot_vec
	)

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Point libMesh::PolymerChain::bead_vector	(	const Point &	bead0,
		const Point &	bead1
	)		const

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const std::vector<PointParticle*>& libMesh::PolymerChain::beads ( )

inline

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const std::vector<std::vector<std::size_t> >& libMesh::PolymerChain::bonds ( )

inline

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std::size_t libMesh::PolymerChain::chain_id ( ) const

inline

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bool libMesh::PolymerChain::check_chain

(

const Real &

Ls

)

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void libMesh::PolymerChain::compute_center_of_mass	(	const std::vector< Real > &	lvec,
		std::vector< Point > &	center
	)		const

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Real libMesh::PolymerChain::compute_chain_length

(

)

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void libMesh::PolymerChain::compute_chain_stretch	(	const std::vector< Real > &	lvec,
		std::vector< Point > &	stretch
	)		const

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void libMesh::PolymerChain::compute_mean_square_displacement	(	const std::vector< Point > &	R0,
		const std::vector< Point > &	Rt,
		Point &	msd
	)		const

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void libMesh::PolymerChain::compute_radius_of_gyration	(	const std::vector< Real > &	lvec,
		const std::vector< Point > &	center,
		std::vector< Real > &	RgSqrt
	)		const

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Point libMesh::PolymerChain::end_to_end_vector

(

)

const

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Point libMesh::PolymerChain::end_to_end_vector_square

(

)

const

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void libMesh::PolymerChain::generate_polymer_chain	(	const Point	pt0,
		const std::size_t	Nb,
		const Real	Ls,
		const Point &	bbox_min,
		const Point &	bbox_max,
		const std::string &	filename
	)

void libMesh::PolymerChain::generate_polymer_chains	(	const unsigned int	n_beads,
		const unsigned int	n_chains,
		const Real	init_bondLength,
		const Point	init_bbox_min,
		const Point	init_bbox_max,
		const std::string &	filename,
		unsigned int	comm_in_rank
	)

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void libMesh::PolymerChain::initial_bead_center_of_mass

(

std::vector< Point > &

center0

)

const

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void libMesh::PolymerChain::initial_chain_center_of_mass

(

std::vector< Point > &

center0

)

const

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std::size_t libMesh::PolymerChain::n_beads ( ) const

inline

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std::size_t libMesh::PolymerChain::n_bonds ( ) const

inline

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std::size_t libMesh::PolymerChain::n_chains ( ) const

inline

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std::size_t libMesh::PolymerChain::n_springs ( ) const

inline

void libMesh::PolymerChain::print_info

(

)

const

void libMesh::PolymerChain::read_data

(

const std::string &

filename

)

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void libMesh::PolymerChain::read_data_csv

(

const std::string &

filename

)

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void libMesh::PolymerChain::read_data_pizza

(

const std::string &

filename

)

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void libMesh::PolymerChain::read_data_vtk

(

const std::string &

filename

)

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void libMesh::PolymerChain::read_pbc_count

(

)

Point libMesh::PolymerChain::spring_vector

(

const unsigned int

i

)

const

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void libMesh::PolymerChain::write_bead	(	const unsigned int &	step_id,
		const unsigned int &	o_step,
		const Real &	real_time,
		const std::vector< Point > &	center0,
		const std::vector< Real > &	lvec,
		const std::vector< std::string > &	output_file,
		unsigned int	comm_in_rank
	)		const

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void libMesh::PolymerChain::write_bead_com	(	const unsigned int &	step_id,
		const unsigned int &	o_step,
		const std::vector< Real > &	lvec,
		unsigned int	comm_in_rank
	)		const

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void libMesh::PolymerChain::write_bead_msd	(	const unsigned int &	step_id,
		const unsigned int &	o_step,
		const std::vector< Point > &	center0,
		const std::vector< Real > &	lvec,
		unsigned int	comm_in_rank
	)		const

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void libMesh::PolymerChain::write_bead_trajectory	(	const unsigned int &	o_step,
		unsigned int	comm_in_rank
	)		const

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void libMesh::PolymerChain::write_polymer_chain	(	const unsigned int &	step_id,
		const unsigned int &	o_step,
		const Real &	real_time,
		const std::vector< Point > &	center0,
		const std::vector< Real > &	lvec,
		std::vector< std::string > &	output_file,
		unsigned int	comm_in_rank
	)		const

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void libMesh::PolymerChain::write_polymer_com	(	const unsigned int &	step_id,
		const unsigned int &	o_step,
		const std::vector< Real > &	lvec,
		unsigned int	comm_in_rank
	)		const

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void libMesh::PolymerChain::write_polymer_msd	(	const unsigned int &	step_id,
		const unsigned int &	o_step,
		const std::vector< Point > &	center0,
		const std::vector< Real > &	lvec,
		unsigned int	comm_in_rank
	)		const

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void libMesh::PolymerChain::write_polymer_rog	(	const unsigned int &	step_id,
		const unsigned int &	o_step,
		const std::vector< Real > &	lvec,
		unsigned int	comm_in_rank
	)		const

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void libMesh::PolymerChain::write_polymer_stretch	(	const unsigned int &	step_id,
		const unsigned int &	o_step,
		const std::vector< Real > &	lvec,
		unsigned int	comm_in_rank
	)		const

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void libMesh::PolymerChain::write_polymer_trajectory	(	const unsigned int &	o_step,
		unsigned int	comm_in_rank
	)		const

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void libMesh::PolymerChain::write_time	(	const unsigned int &	step_id,
		const unsigned int &	o_step,
		const Real &	real_time,
		unsigned int	comm_in_rank
	)		const

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void libMesh::PolymerChain::write_unfolded_com

(

const std::string &

filename

)

const

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void libMesh::PolymerChain::write_unfolded_polymer_chain

(

const std::string &

filename

)

const

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---

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

• /home/cody/copss-hydrodynamics-public/src/polymer_chain.h
• /home/cody/copss-hydrodynamics-public/src/polymer_chain.C