#include <iostream>
#include <limits>
#include <stdint.h>
#include <cmath>
#include <list>
#include <sstream>
#include <dirent.h>
#include <stdio.h>
#include <unordered_set>
#include <vlsv_reader.h>
#include <vlsv_writer.h>
#include <vlsv_amr.h>
#include <boost/program_options.hpp>
#include <Eigen/Dense>
#include <phiprof.hpp>
#include "vlsv_util.h"
#include "vlsvreaderinterface.h"
#include "vlsvextract.h"

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Functions
uint64_t	convUInt (const char *ptr, const datatype::type &dataType, const uint64_t &dataSize)
bool	convertSlicedVelocityMesh (vlsvinterface::Reader &vlsvReader, const string &fname, const string &meshName, CellStructure &cellStruct, const std::string &popName)
void	applyTranslation (const Real V_bulk, Real transform)
void	applyRotation (const Real B, Real transform)
void	getBulkVelocity (Real *V_bulk, vlsvinterface::Reader &vlsvReader, const string &meshName, const string &popName, const uint64_t &cellID)
void	getB (Real *B, vlsvinterface::Reader &vlsvReader, const string &meshName, const uint64_t &cellID)
bool	convertVelocityBlocks2 (vlsvinterface::Reader &vlsvReader, const string &fname, const string &meshName, CellStructure &cellStruct, const uint64_t &cellID, const bool rotate, const bool plasmaFrame, vlsv::Writer &out, const std::string &popName)
template<class T>
bool	createCellIdList (T &vlsvReader, unordered_set< uint64_t > &cellIdList)
bool	convertVelocityBlocks2 (vlsvinterface::Reader &vlsvReader, const string &fname, const string &meshName, CellStructure &cellStruct, const uint64_t &cellID, const bool rotate, const bool plasmaFrame)
void	getCellCoordinates (const CellStructure &cellStruct, const uint64_t cellId, Real *coordinates)
uint64_t	searchForBestCellId (const CellStructure &cellStruct, const uint64_t cellIdList, const Real coordinates, const uint64_t sizeOfCellIdList)
uint64_t	searchForBestCellId (const CellStructure &cellStruct, const unordered_set< uint64_t > &cellIdList, const std::array< Real, 3 > coordinates)
bool	setVelocityMeshVariables (vlsv::Reader &vlsvReader, CellStructure &cellStruct)
bool	setVelocityMeshVariables (vlsv::Reader &vlsvReader, CellStructure &cellStruct, const std::string &popName)
bool	setSpatialCellVariables (Reader &vlsvReader, CellStructure &cellStruct)
uint64_t	getCellIdFromCoords (const CellStructure &cellStruct, const unordered_set< uint64_t > cellIdList, const std::array< Real, 3 > coords)
void	printUsageMessage ()
bool	retrieveOptions (const int argn, char *args[], UserOptions &mainOptions)
void	setCoordinatesAlongALine (const CellStructure &cellStruct, const std::array< Real, 3 > &start, const std::array< Real, 3 > &end, uint32_t numberOfCoordinates, std::vector< std::array< Real, 3 > > &outputCoordinates)
template<class T>
void	extractDistribution (const string &fileName, const UserOptions &mainOptions)
int	main (int argn, char *args[])

Variables
static bool	runDebug = false

Function Documentation

◆ applyRotation()

void applyRotation	(	const Real *	B,
		Real *	transform )

Definition at line 372 of file vlsvextract.cpp.

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◆ applyTranslation()

void applyTranslation	(	const Real *	V_bulk,
		Real *	transform )

Definition at line 347 of file vlsvextract.cpp.

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◆ convertSlicedVelocityMesh()

bool convertSlicedVelocityMesh	(	vlsvinterface::Reader &	vlsvReader,
		const string &	fname,
		const string &	meshName,
		CellStructure &	cellStruct,
		const std::string &	popName )

Definition at line 107 of file vlsvextract.cpp.

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◆ convertVelocityBlocks2() [1/2]

bool convertVelocityBlocks2	(	vlsvinterface::Reader &	vlsvReader,
		const string &	fname,
		const string &	meshName,
		CellStructure &	cellStruct,
		const uint64_t &	cellID,
		const bool	rotate,
		const bool	plasmaFrame )

Driver function for convertVelocityBlocks. Reads the names of existing particle species and calls convertVelocityBlocks2 for each of them.

Parameters

vlsvReader	VLSV file reader that has input file open.
fname	Name of the input file.
meshName	Name of the spatial mesh.
cellStruct	Struct containing mesh metadata.
cellID	ID of the spatial cell whose distribution function(s) are to be extracted.
rotate	If true, distribution function(s) are rotated so that the magnetic field points along +vz axis.
plasmaFrame	If true, distribution function(s) are translated to local plasma rest frame.

Returns: If true, all distributions were extracted successfully.

Definition at line 1058 of file vlsvextract.cpp.

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◆ convertVelocityBlocks2() [2/2]

bool convertVelocityBlocks2	(	vlsvinterface::Reader &	vlsvReader,
		const string &	fname,
		const string &	meshName,
		CellStructure &	cellStruct,
		const uint64_t &	cellID,
		const bool	rotate,
		const bool	plasmaFrame,
		vlsv::Writer &	out,
		const std::string &	popName )

Definition at line 727 of file vlsvextract.cpp.

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◆ convUInt()

uint64_t convUInt	(	const char *	ptr,
		const datatype::type &	dataType,
		const uint64_t &	dataSize )

Definition at line 84 of file vlsvextract.cpp.

◆ createCellIdList()

template<class T>

bool createCellIdList	(	T &	vlsvReader,
		unordered_set< uint64_t > &	cellIdList )

Definition at line 992 of file vlsvextract.cpp.

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◆ extractDistribution()

template<class T>

void extractDistribution	(	const string &	fileName,
		const UserOptions &	mainOptions )

Definition at line 1805 of file vlsvextract.cpp.

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◆ getB()

void getB	(	Real *	B,
		vlsvinterface::Reader &	vlsvReader,
		const string &	meshName,
		const uint64_t &	cellID )

Definition at line 563 of file vlsvextract.cpp.

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◆ getBulkVelocity()

void getBulkVelocity	(	Real *	V_bulk,
		vlsvinterface::Reader &	vlsvReader,
		const string &	meshName,
		const string &	popName,
		const uint64_t &	cellID )

Definition at line 450 of file vlsvextract.cpp.

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◆ getCellCoordinates()

void getCellCoordinates	(	const CellStructure &	cellStruct,
		const uint64_t	cellId,
		Real *	coordinates )

Definition at line 1109 of file vlsvextract.cpp.

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◆ getCellIdFromCoords()

uint64_t getCellIdFromCoords	(	const CellStructure &	cellStruct,
		const unordered_set< uint64_t >	cellIdList,
		const std::array< Real, 3 >	coords )

Definition at line 1465 of file vlsvextract.cpp.

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◆ main()

int main	(	int	argn,
		char *	args[] )

Definition at line 1988 of file vlsvextract.cpp.

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◆ printUsageMessage()

void printUsageMessage ( )

Definition at line 1499 of file vlsvextract.cpp.

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◆ retrieveOptions()

bool retrieveOptions	(	const int	argn,
		char *	args[],
		UserOptions &	mainOptions )

Definition at line 1513 of file vlsvextract.cpp.

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◆ searchForBestCellId() [1/2]

uint64_t searchForBestCellId	(	const CellStructure &	cellStruct,
		const uint64_t *	cellIdList,
		const Real *	coordinates,
		const uint64_t	sizeOfCellIdList )

Definition at line 1142 of file vlsvextract.cpp.

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◆ searchForBestCellId() [2/2]

uint64_t searchForBestCellId	(	const CellStructure &	cellStruct,
		const unordered_set< uint64_t > &	cellIdList,
		const std::array< Real, 3 >	coordinates )

Definition at line 1189 of file vlsvextract.cpp.

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◆ setCoordinatesAlongALine()

void setCoordinatesAlongALine	(	const CellStructure &	cellStruct,
		const std::array< Real, 3 > &	start,
		const std::array< Real, 3 > &	end,
		uint32_t	numberOfCoordinates,
		std::vector< std::array< Real, 3 > > &	outputCoordinates )

Definition at line 1734 of file vlsvextract.cpp.

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◆ setSpatialCellVariables()

bool setSpatialCellVariables	(	Reader &	vlsvReader,
		CellStructure &	cellStruct )

Set correct spatial mesh variables to cellStruct. This function leaves the velocity mesh-related variables untouched.

Parameters

vlsvReader	VLSV file reader with input file open.
cellStruct	Struct where spatial mesh variables are written.

Returns: If true, spatial mesh variables were read successfully.

Definition at line 1396 of file vlsvextract.cpp.

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◆ setVelocityMeshVariables() [1/2]

bool setVelocityMeshVariables	(	vlsv::Reader &	vlsvReader,
		CellStructure &	cellStruct )

Read velocity mesh metadata from older Vlasiator VLSV files.

Parameters

vlsvReader	VLSV reader that has input file open.
cellStruct	Struct where read metadata is written.

Returns: If true, metadata was read successfully.

Definition at line 1228 of file vlsvextract.cpp.

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◆ setVelocityMeshVariables() [2/2]

bool setVelocityMeshVariables	(	vlsv::Reader &	vlsvReader,
		CellStructure &	cellStruct,
		const std::string &	popName )

Read velocity mesh metadata for the given particle species.

Parameters

vlsvReader	VLSV reader that has input file open.
cellStruct	Struct where read metadata is written.
popName	Name of the particle species.

Returns: If true, metadata was read successfully.

Definition at line 1304 of file vlsvextract.cpp.

Variable Documentation

◆ runDebug

bool runDebug = false

static

Definition at line 52 of file vlsvextract.cpp.

Functions

Variables

Function Documentation

◆ applyRotation()

◆ applyTranslation()

◆ convertSlicedVelocityMesh()

◆ convertVelocityBlocks2() [1/2]

◆ convertVelocityBlocks2() [2/2]

◆ convUInt()

◆ createCellIdList()

◆ extractDistribution()

◆ getB()

◆ getBulkVelocity()

◆ getCellCoordinates()

◆ getCellIdFromCoords()

◆ main()

◆ printUsageMessage()

◆ retrieveOptions()

◆ searchForBestCellId() [1/2]

◆ searchForBestCellId() [2/2]

◆ setCoordinatesAlongALine()

◆ setSpatialCellVariables()

◆ setVelocityMeshVariables() [1/2]

◆ setVelocityMeshVariables() [2/2]

Variable Documentation

◆ runDebug