frame_vtk.cpp File Reference

#include "frame_vtk.h"
#include "vec3.h"
#include <vector>
#include <string>
#include <fstream>
#include <algorithm>
#include <iterator>
#include <map>
#include <utility>
#include <sstream>
#include <boost/filesystem.hpp>

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Classes
struct	nr_part
struct	r_part
struct	bond

Functions
template<typename T >
void	write_bonds (ostream &vtkfile, map< int, T > &data_map, vector< bond > &bonds, map< int, int > &id2idx)
template<typename T >
void	write_bonds_with_mesh (ostream &vtkfile, map< int, T > &data_map, vector< bond > &bonds, vector< bond > &mesh_bonds, map< int, int > &id2idx)
void	write_vtu_header (ofstream &vtkfile, int np, int nb)
void	write_vtu_footer (ofstream &vtkfile)
void	write_vtu_particle_data_end (ofstream &vtkfile)
void	write_vtu_rot_base_data (ofstream &vtkfile, map< int, r_part > &datamap, bool unwrap)
void	write_vtu_nr_base_data (ofstream &vtkfile, map< int, nr_part > &datamap, bool unwrap)
int	get_version (const string &infilename)
vector< string >	get_filenames (const string &infilename, int version, bool relpath=false)
void	do_single_frame_vtk (const string &infilename, const string &outfilename, int iframe, bool with_list, const string &listfilename, bool remove_xbonds, double bond_remove_dist)
void	do_single_frame_vtk_r (const string &infilename, const string &outfilename, int iframe, bool with_list, const string &listfilename, bool remove_xbonds, double bond_remove_dist, bool with_brklist, const string &brklistname, bool unwrap, bool relpath)
void	do_single_frame_vtk_single_r (const string &infilename, const string &outfilename, int iframe, int ptag, bool unwrap, bool remove_xbonds, double bond_remove_dist)
void	do_single_frame_sliced_vtk (const string &, const string &, int, bool, const string &, double, double)
void	do_single_frame_sliced_vtk_r (const string &infilename, const string &outfilename, int iframe, bool with_list, const string &listfilename, double slz_min, double slz_max)
void	writeMeshFile (const string &infilename, const string &outfilename, int snapNum)

Function Documentation

do_single_frame_sliced_vtk()

void do_single_frame_sliced_vtk	(	const string &	,
		const string &	,
		int	,
		bool	,
		const string &	,
		double	,
		double
	)

do_single_frame_sliced_vtk_r()

void do_single_frame_sliced_vtk_r	(	const string &	infilename,
		const string &	outfilename,
		int	iframe,
		bool	with_list,
		const string &	listfilename,
		double	slz_min,
		double	slz_max
	)

write a slice , doesn't write bonds

References r_part::angvel, r_part::force, get_filenames(), get_version(), esys::lsm::bpu::iter(), r_part::mass, r_part::pos, r_part::q1, r_part::q2, r_part::q3, r_part::q4, r_part::rad, r_part::tag, r_part::vel, and Vec3::Z().

Referenced by main().

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do_single_frame_vtk()

void do_single_frame_vtk	(	const string &	infilename,
		const string &	outfilename,
		int	iframe,
		bool	with_list,
		const string &	listfilename,
		bool	remove_xbonds,
		double	bond_remove_dist
	)

Read snapshot with non-rotational particles and write it to vtk unstructured grid (.vtu) file

Parameters

infilename	the name of the header file
outfilename	the "base" name of the output file
iframe	the frame number
with_list
listfilename

References nr_part::circ_shift, nr_part::force, get_filenames(), get_version(), nr_part::init_pos, esys::lsm::bpu::iter(), nr_part::mass, nr_part::pos, nr_part::proc_id, nr_part::rad, nr_part::tag, nr_part::vel, write_bonds(), write_vtu_footer(), write_vtu_header(), write_vtu_nr_base_data(), and write_vtu_particle_data_end().

Referenced by main().

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do_single_frame_vtk_r()

void do_single_frame_vtk_r	(	const string &	infilename,
		const string &	outfilename,
		int	iframe,
		bool	with_list,
		const string &	listfilename,
		bool	remove_xbonds,
		double	bond_remove_dist,
		bool	with_brklist,
		const string &	brklistname,
		bool	unwrap,
		bool	relpath
	)

Read snapshot with rotational particles and write it to vtk unstructured grid (.vtu) file

Parameters

infilename	the name of the header file
outfilename	the "base" name of the output file
iframe	the frame number
with_list
listfilename
remove_xbonds	if "true", bonds crossing a circular boundary are not written to the file
bond_remove_dist	distance threshold to detect if a bond is crossing a circular boundary
with_brklist
brklistname
unwrap	if "true", the model is unwrapped, i.e. movements across a circular boundary are taken into account
relpath	if "true" the filenames in the header file are taken to be relative to the path of the header

References r_part::angvel, r_part::circ_shift, r_part::force, get_filenames(), get_version(), r_part::init_pos, esys::lsm::bpu::iter(), r_part::mass, r_part::pos, r_part::proc_id, r_part::q1, r_part::q2, r_part::q3, r_part::q4, r_part::rad, r_part::tag, r_part::vel, write_bonds(), write_bonds_with_mesh(), write_vtu_footer(), write_vtu_header(), write_vtu_particle_data_end(), and write_vtu_rot_base_data().

Referenced by main().

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do_single_frame_vtk_single_r()

void do_single_frame_vtk_single_r	(	const string &	infilename,
		const string &	outfilename,
		int	iframe,
		int	ptag,
		bool	unwrap,
		bool	remove_xbonds,
		double	bond_remove_dist
	)

write particles of single tag from frame

Parameters

infilename	the input file name
outfilename	the output file name base
iframe	frame nr.
ptag	particle tag to write out
unwrap	unwrap x-circular boundaries

References r_part::angvel, r_part::force, get_filenames(), get_version(), esys::lsm::bpu::iter(), r_part::mass, r_part::pos, r_part::q1, r_part::q2, r_part::q3, r_part::q4, r_part::rad, r_part::tag, r_part::vel, write_bonds(), write_vtu_footer(), write_vtu_header(), write_vtu_particle_data_end(), and write_vtu_rot_base_data().

Referenced by main().

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get_filenames()

vector<string> get_filenames	(	const string &	infilename,
		int	version,
		bool	relpath = false
	)

Get data file names from the header file

Parameters

infilename	the file name of the header file (incl. the _0.txt part)
the	snapshot version
relpath

References esys::lsm::bpu::iter().

Referenced by do_single_frame_sliced_vtk_r(), do_single_frame_vtk(), do_single_frame_vtk_r(), and do_single_frame_vtk_single_r().

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get_version()

int get_version

(

const string &

infilename

)

Get snapshot version.

Parameters

infilename

the file name of the header file (incl. the _0.txt part)

Referenced by do_single_frame_sliced_vtk_r(), do_single_frame_vtk(), do_single_frame_vtk_r(), and do_single_frame_vtk_single_r().

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write_bonds()

template<typename T >

void write_bonds	(	ostream &	vtkfile,
		map< int, T > &	data_map,
		vector< bond > &	bonds,
		map< int, int > &	id2idx
	)

Write bonds to vtk file.

Parameters

vtkfile	the output file stream
data_map	STL map containing particle data, particle ID as key. Used for bond strains.
bonds	bond data: particle ids and bond tag
id2idx	mapping between particle ID and index

References esys::lsm::bpu::iter().

Referenced by do_single_frame_vtk(), do_single_frame_vtk_r(), and do_single_frame_vtk_single_r().

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write_bonds_with_mesh()

template<typename T >

void write_bonds_with_mesh	(	ostream &	vtkfile,
		map< int, T > &	data_map,
		vector< bond > &	bonds,
		vector< bond > &	mesh_bonds,
		map< int, int > &	id2idx
	)

Write bonds to vtk file. Version with bonded mesh IG.

Parameters

vtkfile	the output file stream
data_map	STL map containing particle data, particle ID as key. Used for bond strains.
bonds	bond data: particle ids and bond tag
mesh_bonds	mesh bond data: particle ids and triangle id -> bond tag
id2idx	mapping between particle ID and index

References esys::lsm::bpu::iter().

Referenced by do_single_frame_vtk_r().

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write_vtu_footer()

void write_vtu_footer

(

ofstream &

vtkfile

)

write base vtu file footer

Parameters

vtkfile

the ofstream connected to the output file

Referenced by do_single_frame_vtk(), do_single_frame_vtk_r(), and do_single_frame_vtk_single_r().

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write_vtu_header()

void write_vtu_header	(	ofstream &	vtkfile,
		int	np,
		int	nb
	)

write vtu file header

Parameters

vtkfile	the ofstream connected to the output file
np	nr. of particles
nb	nr. of bonds

Referenced by do_single_frame_vtk(), do_single_frame_vtk_r(), and do_single_frame_vtk_single_r().

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write_vtu_nr_base_data()

void write_vtu_nr_base_data	(	ofstream &	vtkfile,
		map< int, nr_part > &	datamap,
		bool	unwrap
	)

write base particle data to vtu file

Parameters

vtkfile	the ofstream connected to the output file
datamap
unwrap

References esys::lsm::bpu::iter().

Referenced by do_single_frame_vtk().

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write_vtu_particle_data_end()

void write_vtu_particle_data_end

(

ofstream &

vtkfile

)

finalize particle data section in vtu file

Parameters

vtkfile

the ofstream connected to the output file

Referenced by do_single_frame_vtk(), do_single_frame_vtk_r(), and do_single_frame_vtk_single_r().

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write_vtu_rot_base_data()

void write_vtu_rot_base_data	(	ofstream &	vtkfile,
		map< int, r_part > &	datamap,
		bool	unwrap
	)

write base particle data to vtu file

Parameters

vtkfile	the ofstream connected to the output file
datamap
unwrap

References esys::lsm::bpu::iter().

Referenced by do_single_frame_vtk_r(), and do_single_frame_vtk_single_r().

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writeMeshFile()

void writeMeshFile	(	const string &	infilename,
		const string &	outfilename,
		int	snapNum
	)

Referenced by main().

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