#include <cstddef>
#include <cstdlib>
#include <iostream>
#include <iomanip>
#include <cmath>
#include <sstream>
#include <ctime>
#include <cstring>
#include <array>
#include <algorithm>
#include <limits>
#include <initializer_list>
#include "object_wrapper.h"
#include "datareduction/datareductionoperator.h"
#include "iowrite.h"
#include "vdf_compression/compression.h"
#include "math.h"
#include "grid.h"
#include "phiprof.hpp"
#include "parameters.h"
#include "logger.h"
#include "vlasovsolver/vlasovmover.h"
#include "velocity_mesh_parameters.h"
#include "sysboundary/ionosphere.h"
#include "fieldtracing/fieldtracing.h"

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Functions
bool	writeVelocityDistributionData (const uint popID, Writer &vlsvWriter, const dccrg::Dccrg< SpatialCell, dccrg::Cartesian_Geometry > &mpiGrid, const std::vector< CellID > &cells, MPI_Comm comm)
bool	writeVelocityDistributionDataAsterix (const uint popID, Writer &vlsvWriter, dccrg::Dccrg< SpatialCell, dccrg::Cartesian_Geometry > &mpiGrid, const std::vector< CellID > &cells, std::vector< std::vector< char > > &mpl_bytes, MPI_Comm comm)
bool	updateLocalIds (dccrg::Dccrg< SpatialCell, dccrg::Cartesian_Geometry > &mpiGrid, const std::vector< CellID > &local_cells, MPI_Comm comm)
bool	globalSuccess (bool success, const string &errorMessage, MPI_Comm comm)
bool	writeVelocityDistributionData (Writer &vlsvWriter, const dccrg::Dccrg< SpatialCell, dccrg::Cartesian_Geometry > &mpiGrid, const vector< CellID > &cells, MPI_Comm comm)
bool	writeVelocityDistributionDataAsterix (Writer &vlsvWriter, dccrg::Dccrg< SpatialCell, dccrg::Cartesian_Geometry > &mpiGrid, const vector< CellID > &cells, std::vector< std::vector< char > > &mlp_bytes, MPI_Comm comm)
bool	writeVspaceDataCompressionNone (const uint popID, Writer &vlsvWriter, dccrg::Dccrg< SpatialCell, dccrg::Cartesian_Geometry > &mpiGrid, const std::vector< CellID > &cells, std::size_t totalBlocks, MPI_Comm comm)
bool	writeDataReducer (const dccrg::Dccrg< SpatialCell, dccrg::Cartesian_Geometry > &mpiGrid, const std::vector< CellID > &cells, const FieldSolverData &fieldSolverData, const bool writeAsFloat, const bool writeFsGrid, DataReducer &dataReducer, cint dataReducerIndex, Writer &vlsvWriter)
bool	writeCommonGridData (Writer &vlsvWriter, const dccrg::Dccrg< SpatialCell, dccrg::Cartesian_Geometry > &mpiGrid, const vector< uint64_t > &local_cells, const uint &fileIndex, MPI_Comm comm)
bool	writeGhostZoneDomainAndLocalIdNumbers (const dccrg::Dccrg< SpatialCell, dccrg::Cartesian_Geometry > &mpiGrid, Writer &vlsvWriter, const string &meshName, const vector< uint64_t > &ghost_cells)
bool	writeDomainSizes (Writer &vlsvWriter, const string &meshName, const unsigned int &numberOfLocalZones, const unsigned int &numberOfGhostZones)
bool	writeDomainExtents (Writer &vlsvWriter, const string &meshName, const std::vector< CellID > &local_cells, const dccrg::Dccrg< SpatialCell, dccrg::Cartesian_Geometry > &mpiGrid)
bool	writeZoneGlobalIdNumbers (const dccrg::Dccrg< SpatialCell, dccrg::Cartesian_Geometry > &mpiGrid, Writer &vlsvWriter, const string &meshName, const vector< uint64_t > &local_cells, const vector< uint64_t > &ghost_cells)
bool	writeBoundingBoxNodeCoordinates (Writer &vlsvWriter, const string &meshName, const int masterRank, MPI_Comm comm)
bool	writeMeshBoundingBox (Writer &vlsvWriter, const string &meshName, const int masterRank, MPI_Comm comm)
bool	writeVersionInfo (const std::string &version, vlsv::Writer &vlsvWriter, MPI_Comm comm)
bool	writeConfigInfo (const std::string &config, vlsv::Writer &vlsvWriter, MPI_Comm comm)
bool	writeFsGridMetadata (FieldSolverGrid &fsgrid, fsgrids::consttechnicalspan technical, vlsv::Writer &vlsvWriter, bool writeIDs=false)
bool	writeIonosphereGridMetadata (vlsv::Writer &vlsvWriter)
bool	writeVelocitySpace (dccrg::Dccrg< SpatialCell, dccrg::Cartesian_Geometry > &mpiGrid, Writer &vlsvWriter, int index, const vector< uint64_t > &cells)
bool	checkForSameMembers (const vector< uint64_t > &local_cells, const vector< uint64_t > &ghost_cells)
bool	writeGrid (dccrg::Dccrg< SpatialCell, dccrg::Cartesian_Geometry > &mpiGrid, const FieldSolverData &fieldSolverData, fsgrids::consttechnicalspan technical, const std::string &versionInfo, const std::string &configInfo, DataReducer *dataReducer, const uint &outputFileTypeIndex, const int &stripe, const bool writeGhosts, bool compress_vdfs)
	Write out system into a vlsv file.
bool	writeRestart (dccrg::Dccrg< SpatialCell, dccrg::Cartesian_Geometry > &mpiGrid, const FieldSolverData &fieldSolverData, fsgrids::consttechnicalspan technical, const std::string &versionInfo, const std::string &configInfo, DataReducer &dataReducer, const string &name, const uint &fileIndex, const bool dateInFileName, const int &stripe, bool compress_vdfs)
	Write out a restart of the simulation into a vlsv file. All block data in remote cells will be reset.
bool	writeDiagnostic (const dccrg::Dccrg< SpatialCell, dccrg::Cartesian_Geometry > &mpiGrid, DataReducer &dataReducer)
	Write out simulation diagnostics into diagnostic.txt.

Variables
Logger	logFile
Logger	diagnostic
char *	IObuffer = 0

Function Documentation

◆ checkForSameMembers()

bool checkForSameMembers	(	const vector< uint64_t > &	local_cells,
		const vector< uint64_t > &	ghost_cells )

This function makes sure that local cells and ghost cells do not have any identical members (used for error checking)

Parameters

local_cells	List of local cells within this process
ghost_cells	List of ghost cells within this process (cells on the process boundary)

Definition at line 1800 of file iowrite.cpp.

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◆ globalSuccess()

bool globalSuccess	(	bool	success,
		const string &	errorMessage,
		MPI_Comm	comm )

Checks the success of write IO

Parameters

success	Parameter for determining whether the IO has been successful
errorMessage	The message to be shown if global success is false
comm	The MPI comm

Returns: Returns true if all of the processes running this function had success value of true, false otherwise

Definition at line 110 of file iowrite.cpp.

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◆ updateLocalIds()

bool updateLocalIds	(	dccrg::Dccrg< SpatialCell, dccrg::Cartesian_Geometry > &	mpiGrid,
		const std::vector< CellID > &	local_cells,
		MPI_Comm	comm )

Updates local ids across MPI to let other processes know in which order this process saves the local cell ids

Parameters

mpiGrid	Vlasiator's MPI grid
local_cells	local cells on in the current process (no ghost cells included)
comm	The MPi comm

Returns: Returns true if operation was successful

Definition at line 79 of file iowrite.cpp.

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◆ writeBoundingBoxNodeCoordinates()

bool writeBoundingBoxNodeCoordinates	(	Writer &	vlsvWriter,
		const string &	meshName,
		const int	masterRank,
		MPI_Comm	comm )

Writes the node coordinates. This means basically every cell's node (Corner of each cell). Note: The grid is a structured one, so writing the nodes means starting from the corner of the grid and writing coordinates per every cell length until reaching the other corner of the grid

Parameters

vlsvWriter	Some vlsv writer with a file open
meshName	Name of the mesh (SpatialGrid used in writeGrid and should be the default)
masterRank	The master rank (Vlasiator uses 0)
comm	The MPI comm

Returns: Returns true if the operation was successful

Definition at line 1225 of file iowrite.cpp.

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◆ writeCommonGridData()

bool writeCommonGridData	(	Writer &	vlsvWriter,
		const dccrg::Dccrg< SpatialCell, dccrg::Cartesian_Geometry > &	mpiGrid,
		const vector< uint64_t > &	local_cells,
		const uint &	fileIndex,
		MPI_Comm	comm )

Writes common grid data such as parameters (time steps, x_min, ..) as well as local cell ids as variables

Parameters

vlsvWriter	Some vlsv writer with a file open
mpiGrid	Vlasiator's grid
local_cells	The local cell ids in this process
fileIndex	File index, file will be called "name.index.vlsv"
comm	The MPI comm

Returns: Returns true if operation was successful

Definition at line 926 of file iowrite.cpp.

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◆ writeConfigInfo()

bool writeConfigInfo	(	const std::string &	config,
		vlsv::Writer &	vlsvWriter,
		MPI_Comm	comm )

Definition at line 1378 of file iowrite.cpp.

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◆ writeDataReducer()

bool writeDataReducer	(	const dccrg::Dccrg< SpatialCell, dccrg::Cartesian_Geometry > &	mpiGrid,
		const std::vector< CellID > &	cells,
		const FieldSolverData &	fieldSolverData,
		const bool	writeAsFloat,
		const bool	writeFsGrid,
		DataReducer &	dataReducer,
		cint	dataReducerIndex,
		Writer &	vlsvWriter )

Writes info received from data reducer. This function writes out the variable arrays into the file

Parameters

mpiGrid	The Vlasiator's grid
cells	List of local cells (no ghost cells included)
writeAsFloat	If true, the data reducer writes variable arrays as float instead of double
dataReducer	The data reducer which contains the necessary functions for calculating variables
dataReducerIndex	Index in the data reducer (determines which variable to read) Note: size of the data reducer can be retrieved with dataReducer.size()
vlsvWriter	Some vlsv writer with a file open

Returns: Returns true if operation was successful

Definition at line 790 of file iowrite.cpp.

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◆ writeDiagnostic()

bool writeDiagnostic	(	const dccrg::Dccrg< SpatialCell, dccrg::Cartesian_Geometry > &	mpiGrid,
		DataReducer &	dataReducer )

Write out simulation diagnostics into diagnostic.txt.

Parameters

mpiGrid	The DCCRG grid with spatial cells
dataReducer	Contains datareductionoperators that are used to compute diagnostic data

Definition at line 2422 of file iowrite.cpp.

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◆ writeDomainExtents()

bool writeDomainExtents	(	Writer &	vlsvWriter,
		const string &	meshName,
		const std::vector< CellID > &	local_cells,
		const dccrg::Dccrg< SpatialCell, dccrg::Cartesian_Geometry > &	mpiGrid )

Writes domain extents into the vlsv file, so a box that contains all the cells in this process

Parameters

vlsvWriter	Some vlsv writer with a file open
meshName	Name of the mesh (SpatialGrid used in the writeGrid function)
local_cells	Cells that are local to current process
mpiGrid	Vlaisator's MPI grid

Returns: Returns true if operation was successful

Definition at line 1080 of file iowrite.cpp.

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◆ writeDomainSizes()

bool writeDomainSizes	(	Writer &	vlsvWriter,
		const string &	meshName,
		const unsigned int &	numberOfLocalZones,
		const unsigned int &	numberOfGhostZones )

Writes domain sizes into the vlsv file, so the number of ghost and local cell ids in this process

Parameters

vlsvWriter	Some vlsv writer with a file open
meshName	Name of the mesh (SpatialGrid used in the writeGrid function)
numberOfLocalZones	Number of local cells in this process
numberOfGhostZones	Number of ghost cells in this process ( Cells on the process boundary )

Returns: Returns true if operation was successful

Definition at line 1050 of file iowrite.cpp.

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◆ writeFsGridMetadata()

bool writeFsGridMetadata	(	FieldSolverGrid &	fsgrid,
		fsgrids::consttechnicalspan	technical,
		vlsv::Writer &	vlsvWriter,
		bool	writeIDs = false )

Writes the mesh metadata for Visit to read FSGrid variable data.

Parameters

fsgrid	An fsgrid instance used to extract metadata info.
vlsvWriter	file object to write into.

Definition at line 1400 of file iowrite.cpp.

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◆ writeGhostZoneDomainAndLocalIdNumbers()

bool writeGhostZoneDomainAndLocalIdNumbers	(	const dccrg::Dccrg< SpatialCell, dccrg::Cartesian_Geometry > &	mpiGrid,
		Writer &	vlsvWriter,
		const string &	meshName,
		const vector< uint64_t > &	ghost_cells )

Writes ghost cell ids into the file

Parameters

mpiGrid	Vlasiator's grid
vlsvWriter	Some vlsv writer with a file open
meshName	Name of the mesh (If unsure, put SpatialGrid)
ghost_cells	List of cell ids on the process boundary (Ghost cells)

Returns: Returns true if operation was successful

See also: updateLocalIds

Definition at line 986 of file iowrite.cpp.

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◆ writeGrid()

bool writeGrid	(	dccrg::Dccrg< SpatialCell, dccrg::Cartesian_Geometry > &	mpiGrid,
		const FieldSolverData &	fieldSolverData,
		fsgrids::consttechnicalspan	technical,
		const std::string &	versionInfo,
		const std::string &	configInfo,
		DataReducer *	dataReducer,
		const uint &	outputFileTypeIndex,
		const int &	stripe,
		const bool	writeGhosts,
		bool	compress_vdfs )

Write out system into a vlsv file.

Parameters

mpiGrid	The DCCRG grid with spatial cells
dataReducer	Contains datareductionoperators that are used to compute data that is added into file
index	Index to call the correct member of the various parameter vectors
writeGhosts	If true, writes out ghost cells (cells that exist on the process boundary so other process' cells)

Definition at line 1829 of file iowrite.cpp.

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◆ writeIonosphereGridMetadata()

bool writeIonosphereGridMetadata ( vlsv::Writer & vlsvWriter )

Writes the mesh metadata for Visit to read the Ionosphere grid and its variables.

Definition at line 1496 of file iowrite.cpp.

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◆ writeMeshBoundingBox()

bool writeMeshBoundingBox	(	Writer &	vlsvWriter,
		const string &	meshName,
		const int	masterRank,
		MPI_Comm	comm )

Function for writing the bounding box. This writes only if the process running it is the master rank. This array contains info on the boundaries of the grid so for example the number of cells in x, y, z direction. Note that this is not the physical coordinate bounding box, but the computational domain bounding box, measured in blocks and cells.

Parameters

vlsvWriter	Some vlsv writer with a file open
meshName	Name of the mesh to write ("SpatialGrid" is used in writeGrid and it should be the default)
masterRank	The master process' id. Vlasiator uses 0 as the master process id, so by default should be 0
comm	MPI comm

Returns: Returns true if operation was successful

Definition at line 1311 of file iowrite.cpp.

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◆ writeRestart()

bool writeRestart	(	dccrg::Dccrg< SpatialCell, dccrg::Cartesian_Geometry > &	mpiGrid,
		const FieldSolverData &	fieldSolverData,
		fsgrids::consttechnicalspan	technical,
		const std::string &	versionInfo,
		const std::string &	configInfo,
		DataReducer &	dataReducer,
		const string &	name,
		const uint &	fileIndex,
		const bool	dateInFileName,
		const int &	stripe,
		bool	compress_vdfs )

Write out a restart of the simulation into a vlsv file. All block data in remote cells will be reset.

Parameters

mpiGrid	The DCCRG grid with spatial cells
dataReducer	Contains datareductionoperators that are used to compute data that is added into file
name	File name prefix, file will be called "name.index.vlsv"
fileIndex	File index, file will be called "name.index.vlsv"

Definition at line 2048 of file iowrite.cpp.

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◆ writeVelocityDistributionData() [1/2]

bool writeVelocityDistributionData	(	const uint	popID,
		Writer &	vlsvWriter,
		const dccrg::Dccrg< SpatialCell, dccrg::Cartesian_Geometry > &	mpiGrid,
		const std::vector< CellID > &	cells,
		MPI_Comm	comm )

Writes the velocity distribution of specified population into the file.

Parameters

vlsvWriter	Some vlsv writer with a file open.
mpiGrid	Vlasiator's grid.
cells	Vector of local cells within this process (no ghost cells).
comm	The MPI communicator.

Returns: Returns true if operation was successful.

Definition at line 161 of file iowrite.cpp.

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◆ writeVelocityDistributionData() [2/2]

bool writeVelocityDistributionData	(	Writer &	vlsvWriter,
		const dccrg::Dccrg< SpatialCell, dccrg::Cartesian_Geometry > &	mpiGrid,
		const vector< CellID > &	cells,
		MPI_Comm	comm )

Writes the velocity distribution into the file.

Parameters

vlsvWriter	Some vlsv writer with a file open.
mpiGrid	Vlasiator's grid.
cells	Vector of local cells within this process (no ghost cells).
comm	The MPI communicator.

Returns: Returns true if operation was successful.

Definition at line 135 of file iowrite.cpp.

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◆ writeVelocityDistributionDataAsterix() [1/2]

bool writeVelocityDistributionDataAsterix	(	const uint	popID,
		Writer &	vlsvWriter,
		dccrg::Dccrg< SpatialCell, dccrg::Cartesian_Geometry > &	mpiGrid,
		const std::vector< CellID > &	cells,
		std::vector< std::vector< char > > &	mpl_bytes,
		MPI_Comm	comm )

Definition at line 634 of file iowrite.cpp.

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◆ writeVelocityDistributionDataAsterix() [2/2]

bool writeVelocityDistributionDataAsterix	(	Writer &	vlsvWriter,
		dccrg::Dccrg< SpatialCell, dccrg::Cartesian_Geometry > &	mpiGrid,
		const vector< CellID > &	cells,
		std::vector< std::vector< char > > &	mlp_bytes,
		MPI_Comm	comm )

Definition at line 145 of file iowrite.cpp.

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◆ writeVelocitySpace()

bool writeVelocitySpace	(	dccrg::Dccrg< SpatialCell, dccrg::Cartesian_Geometry > &	mpiGrid,
		Writer &	vlsvWriter,
		int	index,
		const vector< uint64_t > &	cells )

This function writes the velocity space.

Parameters

mpiGrid	Vlasiator's grid.
vlsvWriter	some vlsv writer with a file open.
index	Index to call the correct member of the various parameter vectors.
cells	Vector containing local cells of this process.

Returns: Returns true if the operation was successful.

See also: writeVelocityDistributionData.

Definition at line 1603 of file iowrite.cpp.

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◆ writeVersionInfo()

bool writeVersionInfo	(	const std::string &	version,
		vlsv::Writer &	vlsvWriter,
		MPI_Comm	comm )

Definition at line 1355 of file iowrite.cpp.

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◆ writeVspaceDataCompressionNone()

bool writeVspaceDataCompressionNone	(	const uint	popID,
		Writer &	vlsvWriter,
		dccrg::Dccrg< SpatialCell, dccrg::Cartesian_Geometry > &	mpiGrid,
		const std::vector< CellID > &	cells,
		std::size_t	totalBlocks,
		MPI_Comm	comm )

Definition at line 342 of file iowrite.cpp.

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◆ writeZoneGlobalIdNumbers()

bool writeZoneGlobalIdNumbers	(	const dccrg::Dccrg< SpatialCell, dccrg::Cartesian_Geometry > &	mpiGrid,
		Writer &	vlsvWriter,
		const string &	meshName,
		const vector< uint64_t > &	local_cells,
		const vector< uint64_t > &	ghost_cells )

Writes the zone global id numbers into the file. The vlsv file needs to know in which order the local cells + ghost cells are written. Local cells are first appended to a vector called global ids, after which the ghost cells are appended. The global ids vector will then be saved into a vlsv file

Parameters

mpiGrid	Vlasiator's MPI grid
vlsvWriter	Some vlsv writer with a file open
meshName	Name of the mesh ("SpatialGrid" used in the writeGrid function and it should be the default)
local_cells	Vector containing the local cells of this process
ghost_cells	Vector containing the ghost cells of this process ( The cells on process boundary )

Returns: Returns true if the operation was successful

Definition at line 1141 of file iowrite.cpp.

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Variable Documentation

◆ diagnostic

Logger diagnostic

Definition at line 59 of file iowrite.cpp.

◆ IObuffer

char* IObuffer = 0

Definition at line 61 of file iowrite.cpp.

◆ logFile

Logger logFile

extern

Definition at line 25 of file main.cpp.

Functions

Variables

Function Documentation

◆ checkForSameMembers()

◆ globalSuccess()

◆ updateLocalIds()

◆ writeBoundingBoxNodeCoordinates()

◆ writeCommonGridData()

◆ writeConfigInfo()

◆ writeDataReducer()

◆ writeDiagnostic()

◆ writeDomainExtents()

◆ writeDomainSizes()

◆ writeFsGridMetadata()

◆ writeGhostZoneDomainAndLocalIdNumbers()

◆ writeGrid()

◆ writeIonosphereGridMetadata()

◆ writeMeshBoundingBox()

◆ writeRestart()

◆ writeVelocityDistributionData() [1/2]

◆ writeVelocityDistributionData() [2/2]

◆ writeVelocityDistributionDataAsterix() [1/2]

◆ writeVelocityDistributionDataAsterix() [2/2]

◆ writeVelocitySpace()

◆ writeVersionInfo()

◆ writeVspaceDataCompressionNone()

◆ writeZoneGlobalIdNumbers()

Variable Documentation

◆ diagnostic

◆ IObuffer

◆ logFile