#include <cstdint>
#include <numeric>
#include <cstdlib>
#include <iostream>
#include <iomanip>
#include <cmath>
#include <stdexcept>
#include <vector>
#include <sstream>
#include <ctime>
#include <array>
#include <sys/types.h>
#include <sys/stat.h>
#include <span>
#include <unordered_map>
#include <unordered_set>
#include "definitions.h"
#include "mpi.h"
#include "spatial_cells/spatial_cell_wrapper.hpp"
#include "vdf_compression/compression.h"
#include "common.h"
#include "ioread.h"
#include "phiprof.hpp"
#include "parameters.h"
#include "logger.h"
#include "vdf_compression/compression_tools.h"
#include "vlsv_reader_parallel.h"
#include "vlasovsolver/vlasovmover.h"
#include "object_wrapper.h"
#include "velocity_mesh_parameters.h"
#include "grid.h"

Include dependency graph for ioread.cpp:

Functions
void	checkExternalCommands ()
	Checks for command files written to the local directory. If a file STOP was written and is readable, then a bailout with restart writing is initiated. If a file KILL was written and is readable, then a bailout without a restart is initiated. If a file SAVE was written and is readable, then restart writing without a bailout is initiated. If a file DOLB was written and is readable, then a new load balancing is initiated. To avoid bailing out upfront on a new run the files are renamed with the date to keep a trace. The function should only be called by MASTER_RANK. This ensures that resetting P::bailout_write_restart works.
bool	exitOnError (bool success, const string &message, MPI_Comm comm)
	Collective exit on error functions.
bool	readCellIds (vlsv::ParallelReader &file, vector< CellID > &fileCells, const int masterRank, MPI_Comm comm)
	Read cell ID's Read in cell ID's from file. Note: Uses the newer version of vlsv parallel reader.
bool	readNBlocks (vlsv::ParallelReader &file, const std::string &meshName, std::vector< size_t > &nBlocks, int masterRank, MPI_Comm comm)
template<typename T>
bool	readScalarParameter (vlsv::ParallelReader &file, string name, T &value, int masterRank, MPI_Comm comm)
template<typename T>
bool	checkScalarParameter (vlsv::ParallelReader &file, const string &name, T correctValue, int masterRank, MPI_Comm comm)
template<typename fileReal>
bool	_readBlockDataCompressionNone (vlsv::ParallelReader &file, const std::string &spatMeshName, const std::vector< uint64_t > &fileCells, const uint64_t localCellStartOffset, const uint64_t localCells, const vmesh::LocalID *blocksPerCell, const std::vector< uint64_t > &blockSumOffsets, const uint64_t localBlockStartOffset, const uint64_t localBlocks, dccrg::Dccrg< SpatialCell, dccrg::Cartesian_Geometry > &mpiGrid, std::function< vmesh::GlobalID(vmesh::GlobalID)> blockIDremapper, const uint popID)
template<typename fileReal>
bool	_readBlockData (vlsv::ParallelReader &file, const std::string &spatMeshName, const std::vector< uint64_t > &fileCells, const uint64_t localCellStartOffset, const uint64_t localCells, const vmesh::LocalID *blocksPerCell, const std::vector< uint64_t > &blockSumOffsets, const uint64_t localBlockStartOffset, const uint64_t localBlocks, dccrg::Dccrg< SpatialCell, dccrg::Cartesian_Geometry > &mpiGrid, std::function< vmesh::GlobalID(vmesh::GlobalID)> blockIDremapper, const uint popID)
bool	readBlockData (vlsv::ParallelReader &file, const string &meshName, const vector< CellID > &fileCells, const uint64_t localCellStartOffset, const uint64_t localCells, dccrg::Dccrg< SpatialCell, dccrg::Cartesian_Geometry > &mpiGrid)
template<typename fileReal>
static bool	_readCellParamsVariable (vlsv::ParallelReader &file, const vector< uint64_t > &fileCells, const uint64_t localCellStartOffset, const uint64_t localCells, const string &variableName, const size_t cellParamsIndex, const size_t expectedVectorSize, dccrg::Dccrg< SpatialCell, dccrg::Cartesian_Geometry > &mpiGrid)
bool	readCellParamsVariable (vlsv::ParallelReader &file, const vector< CellID > &fileCells, const uint64_t localCellStartOffset, const uint64_t localCells, const string &variableName, const size_t cellParamsIndex, const size_t expectedVectorSize, dccrg::Dccrg< SpatialCell, dccrg::Cartesian_Geometry > &mpiGrid)
template<unsigned long int N>
bool	readFsGridVariable (vlsv::ParallelReader &file, const string &variableName, int numWritingRanks, fsgrids::technicalspan technical, FieldSolverGrid &fsgrid, std::span< std::array< Real, N > > targetData)
bool	readIonosphereNodeVariable (vlsv::ParallelReader &file, const string &variableName, SBC::SphericalTriGrid &grid, ionosphereParameters index)
bool	exec_readGrid (dccrg::Dccrg< SpatialCell, dccrg::Cartesian_Geometry > &mpiGrid, fsgrids::perbspan perb, fsgrids::efieldspan e, fsgrids::technicalspan technical, FieldSolverGrid &fsgrid, const std::string &name)
	Read in state from a vlsv file in order to restart simulations.
bool	readGrid (dccrg::Dccrg< SpatialCell, dccrg::Cartesian_Geometry > &mpiGrid, fsgrids::perbspan perb, fsgrids::efieldspan e, fsgrids::technicalspan technical, FieldSolverGrid &fsgrid, const std::string &name)
	Read in state from a vlsv file in order to restart simulations.
bool	readFileCells (dccrg::Dccrg< SpatialCell, dccrg::Cartesian_Geometry > &mpiGrid, const std::string &name)
	Refine the grid to be identical to the file's.
bool	readFsgridDecomposition (vlsv::ParallelReader &file, std::array< fsgrid::Task_t, 3 > &decomposition)

Variables
Logger	logFile
Logger	diagnostic

Function Documentation

◆ _readBlockData()

template<typename fileReal>

bool _readBlockData	(	vlsv::ParallelReader &	file,
		const std::string &	spatMeshName,
		const std::vector< uint64_t > &	fileCells,
		const uint64_t	localCellStartOffset,
		const uint64_t	localCells,
		const vmesh::LocalID *	blocksPerCell,
		const std::vector< uint64_t > &	blockSumOffsets,
		const uint64_t	localBlockStartOffset,
		const uint64_t	localBlocks,
		dccrg::Dccrg< SpatialCell, dccrg::Cartesian_Geometry > &	mpiGrid,
		std::function< vmesh::GlobalID(vmesh::GlobalID)>	blockIDremapper,
		const uint	popID )

Read velocity block mesh data and distribution function data belonging to this process for the given particle species. This function must be called simultaneously by all processes.

Parameters

file	VLSV reader with input file open.
spatMeshName	Name of the spatial mesh.
fileCells	List of all spatial cell IDs.
localCellStartOffset	The offset from which to start reading cells.
localCells	How many spatial cells after the offset to read.
blocksPerCell	Number of velocity blocks for this particle species in each spatial cell belonging to this process.
localBlockStartOffset	Offset into velocity block data arrays from which to start reading data.
localBlocks	Number of velocity blocks for this species assigned to this process.
mpiGrid	Parallel grid library.
popID	ID of the particle species who's data is to be read.

Returns: If true, velocity block data was read successfully.

Definition at line 954 of file ioread.cpp.

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◆ _readBlockDataCompressionNone()

template<typename fileReal>

bool _readBlockDataCompressionNone	(	vlsv::ParallelReader &	file,
		const std::string &	spatMeshName,
		const std::vector< uint64_t > &	fileCells,
		const uint64_t	localCellStartOffset,
		const uint64_t	localCells,
		const vmesh::LocalID *	blocksPerCell,
		const std::vector< uint64_t > &	blockSumOffsets,
		const uint64_t	localBlockStartOffset,
		const uint64_t	localBlocks,
		dccrg::Dccrg< SpatialCell, dccrg::Cartesian_Geometry > &	mpiGrid,
		std::function< vmesh::GlobalID(vmesh::GlobalID)>	blockIDremapper,
		const uint	popID )

Definition at line 371 of file ioread.cpp.

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◆ _readCellParamsVariable()

template<typename fileReal>

bool _readCellParamsVariable	(	vlsv::ParallelReader &	file,
		const vector< uint64_t > &	fileCells,
		const uint64_t	localCellStartOffset,
		const uint64_t	localCells,
		const string &	variableName,
		const size_t	cellParamsIndex,
		const size_t	expectedVectorSize,
		dccrg::Dccrg< SpatialCell, dccrg::Cartesian_Geometry > &	mpiGrid )

static

Reads cell parameters from the file and saves them in the right place in mpiGrid

Parameters

file	Some parallel vlsv reader with a file open
fileCells	List of all cell ids
localCellStartOffset	Offset in the fileCells list for this process ( calculated so that the amount of blocks is distributed somewhat evenly between processes)
localCells	The amount of cells to read in this process after localCellStartOffset
cellParamsIndex	The parameter of the cell index e.g. CellParams::RHOM
expectedVectorSize	The amount of elements in the parameter (parameter can be a scalar or a vector of size N)
mpiGrid	Vlasiator's grid (the parameters are saved here)

Returns: Returns true if the operation is successful

Definition at line 1239 of file ioread.cpp.

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◆ checkExternalCommands()

void checkExternalCommands ( )

Checks for command files written to the local directory. If a file STOP was written and is readable, then a bailout with restart writing is initiated. If a file KILL was written and is readable, then a bailout without a restart is initiated. If a file SAVE was written and is readable, then restart writing without a bailout is initiated. If a file DOLB was written and is readable, then a new load balancing is initiated. To avoid bailing out upfront on a new run the files are renamed with the date to keep a trace. The function should only be called by MASTER_RANK. This ensures that resetting P::bailout_write_restart works.

Check in local directory for external commands passed to the simulation. Only executed by MASTER_RANK.

Definition at line 72 of file ioread.cpp.

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◆ checkScalarParameter()

template<typename T>

bool checkScalarParameter	(	vlsv::ParallelReader &	file,
		const string &	name,
		T	correctValue,
		int	masterRank,
		MPI_Comm	comm )

A function for checking the scalar parameter

Parameters

file	Some parallel vlsv reader with a file open
name	Name of the parameter
correctValue	The correct value of the parameter to compare to
masterRank	The master process' id (Vlasiator uses 0 so this should be 0 by default)
comm	MPI comm (Default should be MPI_COMM_WORLD)

Returns: Returns true if the operation is successful

Definition at line 350 of file ioread.cpp.

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◆ exec_readGrid()

bool exec_readGrid	(	dccrg::Dccrg< SpatialCell, dccrg::Cartesian_Geometry > &	mpiGrid,
		fsgrids::perbspan	perb,
		fsgrids::efieldspan	e,
		fsgrids::technicalspan	technical,
		FieldSolverGrid &	fsgrid,
		const std::string &	name )

Read in state from a vlsv file in order to restart simulations.

Parameters

mpiGrid	Vlasiator's grid
name	Name of the restart file e.g. "restart.00052.vlsv"

Returns: Returns true if the operation was successful

See also: readGrid

Definition at line 1628 of file ioread.cpp.

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◆ exitOnError()

bool exitOnError	(	bool	success,
		const string &	message,
		MPI_Comm	comm )

Collective exit on error functions.

If any process(es) have a false success values then the program will abort and write out the message to the logfile

Parameters

success	This process' value for successful execution
message	Error message to be shown upon failure
comm	MPI comm

Returns: Returns true if the operation was successful

Definition at line 152 of file ioread.cpp.

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◆ readBlockData()

bool readBlockData	(	vlsv::ParallelReader &	file,
		const string &	meshName,
		const vector< CellID > &	fileCells,
		const uint64_t	localCellStartOffset,
		const uint64_t	localCells,
		dccrg::Dccrg< SpatialCell, dccrg::Cartesian_Geometry > &	mpiGrid )

Read velocity block data of all existing particle species.

Parameters

file	VLSV reader.
meshName	Name of the spatial mesh.
fileCells	Vector containing spatial cell IDs.
localCellStartOffset	Offset into fileCells, determines where the cells belonging to this process start.
localCells	Number of spatial cells assigned to this process.
mpiGrid	Parallel grid library.

Returns: If true, velocity block data was read successfully.

Definition at line 1015 of file ioread.cpp.

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◆ readCellIds()

bool readCellIds	(	vlsv::ParallelReader &	file,
		vector< CellID > &	fileCells,
		const int	masterRank,
		MPI_Comm	comm )

Read cell ID's Read in cell ID's from file. Note: Uses the newer version of vlsv parallel reader.

Parameters

file	Some vlsv reader with a file open
fileCells	Vector in whic to store the cell ids
masterRank	The simulation's master rank id (Vlasiator uses 0, which should be the default)
comm	MPI comm (MPI_COMM_WORLD should be the default)

Definition at line 178 of file ioread.cpp.

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◆ readCellParamsVariable()

bool readCellParamsVariable	(	vlsv::ParallelReader &	file,
		const vector< CellID > &	fileCells,
		const uint64_t	localCellStartOffset,
		const uint64_t	localCells,
		const string &	variableName,
		const size_t	cellParamsIndex,
		const size_t	expectedVectorSize,
		dccrg::Dccrg< SpatialCell, dccrg::Cartesian_Geometry > &	mpiGrid )

Reads cell parameters from the file and saves them in the right place in mpiGrid

Parameters

file	Some parallel vlsv reader with a file open
fileCells	List of all cell ids
localCellStartOffset	Offset in the fileCells list for this process ( calculated so that the amount of blocks is distributed somewhat evenly between processes)
localCells	The amount of cells to read in this process after localCellStartOffset
cellParamsIndex	The parameter of the cell index e.g. CellParams::RHOM
expectedVectorSize	The amount of elements in the parameter (parameter can be a scalar or a vector of size N)
mpiGrid	Vlasiator's grid (the parameters are saved here)

Returns: Returns true if the operation is successful

Definition at line 1291 of file ioread.cpp.

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◆ readFileCells()

bool readFileCells	(	dccrg::Dccrg< SpatialCell, dccrg::Cartesian_Geometry > &	mpiGrid,
		const std::string &	name )

Refine the grid to be identical to the file's.

Parameters

mpiGrid	Vlasiator's grid
name	Name of the restart file e.g. "restart.00052.vlsv"

Definition at line 1964 of file ioread.cpp.

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◆ readFsgridDecomposition()

bool readFsgridDecomposition	(	vlsv::ParallelReader &	file,
		std::array< fsgrid::Task_t, 3 > &	decomposition )

Definition at line 1986 of file ioread.cpp.

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◆ readFsGridVariable()

template<unsigned long int N>

bool readFsGridVariable	(	vlsv::ParallelReader &	file,
		const string &	variableName,
		int	numWritingRanks,
		fsgrids::technicalspan	technical,
		FieldSolverGrid &	fsgrid,
		std::span< std::array< Real, N > >	targetData )

Read a fsgrid variable (consinting of N real values) from the given vlsv file.

Parameters

file	VLSV parallel reader with a file open.
variableName	Name of the variable in the file
numWritingRanks	Number of mpi ranks that were used to write this file (used for reconstruction of the spatial order)
targetGrid	target location where the data will be stored.

Definition at line 1352 of file ioread.cpp.

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◆ readGrid()

bool readGrid	(	dccrg::Dccrg< SpatialCell, dccrg::Cartesian_Geometry > &	mpiGrid,
		fsgrids::perbspan	perb,
		fsgrids::efieldspan	e,
		fsgrids::technicalspan	technical,
		FieldSolverGrid &	fsgrid,
		const std::string &	name )

Read in state from a vlsv file in order to restart simulations.

Parameters

mpiGrid	Vlasiator's grid
name	Name of the restart file e.g. "restart.00052.vlsv"

Definition at line 1951 of file ioread.cpp.

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◆ readIonosphereNodeVariable()

bool readIonosphereNodeVariable	(	vlsv::ParallelReader &	file,
		const string &	variableName,
		SBC::SphericalTriGrid &	grid,
		ionosphereParameters	index )

Read an ionosphere variable from the given vlsv file. Note that only singular floating point values (no vectors) can be read at this time.

Parameters

file	VLSV parallel reader with a file open.
variableName	Name of the variable in the file
grid	the ionosphere grid that data will be deposited into
index	index into the nodes' parameters array, where the data will end up.

Definition at line 1570 of file ioread.cpp.

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◆ readNBlocks()

bool readNBlocks	(	vlsv::ParallelReader &	file,
		const std::string &	meshName,
		std::vector< size_t > &	nBlocks,
		int	masterRank,
		MPI_Comm	comm )

Definition at line 252 of file ioread.cpp.

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◆ readScalarParameter()

template<typename T>

bool readScalarParameter	(	vlsv::ParallelReader &	file,
		string	name,
		T &	value,
		int	masterRank,
		MPI_Comm	comm )

A function for reading parameters, e.g., 'timestep'.

Parameters

file	VLSV parallel reader with a file open.
name	Name of the parameter.
value	Variable in which to store the scalar variable (double, float, int .. ).
masterRank	The master process' id (Vlasiator uses 0 so this should equal 0 by default).
comm	MPI comm (MPI_COMM_WORLD should be the default).

Returns: Returns true if the operation is successful.

Definition at line 331 of file ioread.cpp.

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Variable Documentation

◆ diagnostic

Logger diagnostic

Definition at line 59 of file ioread.cpp.

◆ logFile

Logger logFile

extern

Definition at line 25 of file main.cpp.

Functions

Variables

Function Documentation

◆ _readBlockData()

◆ _readBlockDataCompressionNone()

◆ _readCellParamsVariable()

◆ checkExternalCommands()

◆ checkScalarParameter()

◆ exec_readGrid()

◆ exitOnError()

◆ readBlockData()

◆ readCellIds()

◆ readCellParamsVariable()

◆ readFileCells()

◆ readFsgridDecomposition()

◆ readFsGridVariable()

◆ readGrid()

◆ readIonosphereNodeVariable()

◆ readNBlocks()

◆ readScalarParameter()

Variable Documentation

◆ diagnostic

◆ logFile