Module: File IO

File Writers

File writer classes are used to export data to persistent files.

Primary Simulation Result Data File Writer

FileIO::TrajectoryHDF5Writer writes trajectory HDF5 files, which is the current primary trajectory data export format of IDSimF.

class TrajectoryHDF5Writer

Public Functions

TrajectoryHDF5Writer(const std::string &hdf5Filename, bool compression = true)

Constructs a new HDF5 trajectory filewriter

Parameters:

  • hdf5Filename – A filename / path of a HDF5 file to write

  • compression – If true: the HDF5 file is written with data compression

void setParticleAttributes(const std::vector<std::string> &attributeNames, partAttribTransformFctType attributesTransformFct)

FIXME

Parameters:

  • attributeNames –

  • attributesTransformFct –

void setParticleAttributes(const std::vector<std::string> &attributeNames, partAttribTransformFctTypeInteger attributesTransformFct)
Parameters:

  • attributeNames –

  • attributesTransformFct –

void writeTimestep(std::vector<Core::Particle*> &particles, double time)

Writes a single time step to the HDF5 trajectory file

Note that an empty timestep, without any particles, is silently ignored.

Parameters:

  • particles – The particle ensemble in the simulation to write to the trajectory file

  • time – The current simulated time

template<typename DT>
void writeNumericListDataset(std::string dsName, const std::vector<DT> &values, H5::Group *group = nullptr)

Write a numeric vector to a dataset in the trajectory file

Parameters:

  • dsName – Name of the dataset in the HDF5 file to write the vector into

  • values – Numeric vector with values to write to the dataset

  • group – FIXME

void write3DVectorListDataset(std::string dsName, const std::vector<Core::Vector> &values, H5::Group *group = nullptr)
template<typename DT, std::size_t DIMS>
void writeArrayDataSet(std::string dsName, const std::vector<std::array<DT, DIMS>> &values, H5::Group *group = nullptr)
void writeTrajectoryAttribute(std::string attrName, int value)

Writes an integer attribute to the trajectory file

Parameters:

  • attrName – Name of the attribute to write

  • value – The value to write into the attribute in the trajectory file

void writeTrajectoryAttribute(std::string attrName, const std::vector<double> &values)

Writes an numeric vector attribute to the trajectory file

Parameters:

  • attrName – Name of the attribute to write

  • value – The values to write into the attribute in the trajectory file

void writeTrajectoryAttribute(std::string attrName, const std::vector<std::string> &values)

Writes an string vector attribute to the trajectory file

Parameters:

  • attrName – Name of the attribute to write

  • value – The values to write into the attribute in the trajectory file

void finalizeTrajectory()

Finalizes the trajectory, usually after the simulation has finished

void writeSplatTimes(std::vector<Core::Particle*> &particles)

Writes the splat (termination) times of the simulated particle ensemble to the HDF5 trajectory file

Parameters:

particles – The simulated particle ensemble

void writeStartSplatData(ParticleSimulation::ParticleStartSplatTracker tracker)
template<typename DT, std::size_t NCOLUMNS>
void writeArrayDataSet(std::string dsName, const std::vector<std::array<DT, NCOLUMNS>> &values, H5::Group *group)

FIXME

Template Parameters:

  • DT –

  • NCOLUMNS –

Parameters:

  • dsName –

  • values –

  • group –

FileIO::Scalar_writer writes tables of scalar values from simulations:

class Scalar_writer

File writer to write scalar values to a result file

Public Functions

explicit Scalar_writer(std::string transientFilename)

Constructor: Creates a file writer for a given result file

Parameters:

transientFilename – the name of the file to write to

~Scalar_writer()

Destructor

void writeTimestep(int intValue, double time)

Writes a scalar value to the result file

Parameters:

  • intValue – the scalar value to write

  • time – the time of the current time step

void writeTimestep(std::size_t sizeValue, double time)

Writes a scalar value to the result file

Parameters:

  • sizeValue – the scalar value to write

  • time – the time of the current time step

void writeTimestep(unsigned int unsignedIntValue, double time)

Writes a unsigned integer scalar value to the result file

Parameters:

  • unsignedIntValue – the scalar value to write

  • time – the time of the current time step

void writeTimestep(double doubleValue, double time)

Writes a scalar value to the result file

Parameters:

  • doubleValue – the scalar value to write

  • time – the time of the current time step

void writeTimestep(std::vector<double> doubleValues, double time)

Writes multiple values simultaneously to the result file

Parameters:

  • doubleValues – vector of values to write

  • time – the time of the current time step

Additional Result File Writer

Additional file writer provide additional export file formats.

Note

The additional file writer are currently not well maintained.

class SimpleVTKwriter

File writer to write particle cloud and Core data to legacy VTK files

Public Functions

SimpleVTKwriter(std::string basefilename)

Constructor: Creates a VTK filewriter to write to result files.

Two files are created: basefilename_particles.vtk - which the particle trajectory data is written to and basefilename_tree.vtk - which the tree / tree node data is written to

Parameters:

basefilename – basename for the result files to create

~SimpleVTKwriter()

Destructor

void write(BTree::Tree &tree, bool writeTree)

Writes the current state of a Core to the result files

Parameters:

  • tree – the Core to write to the file

  • writeTree – if true: also tree node information is written to the tree file, otherwise only particle information is written

Special Simulation File Writer

There are some file writers for special simulation requirements:

class InductionCurrentWriter

Public Functions

InductionCurrentWriter(std::vector<Core::Particle*> particles, std::string transientFilename, const std::vector<ParticleSimulation::SimionPotentialArray*> &weightFields, std::vector<double> weightFactors, double scale_mm_per_gu)

Constructor: Creates a induction current writer

Parameters:

  • particles – vector with links to the partilces in a particle cloud to write to a file

  • transientFilename – the filename of the file to write to

  • weightFields – a vector of the weight potential arrays for the individual detection electrodes. A weight field of a detection electrode is a potential array in which the detection electrode has 1 V potential while all other electrodes are on ground

  • weightFactors – scaling factors for the individual weight fields

  • scale_mm_per_gu – scaling factor between mm and grid units of the given weight potential arrays

~InductionCurrentWriter()

Destructor

void writeTimestep(double time)

Writes a time step to the file

Parameters:

time – the time of the current time step

class IdealizedQitFFTWriter

Simulation result file writer which writes the displacement current induced by a simulated ion cloud on the cap electrodes in an QIT simulation to a file.

The displacement current is approximated as the average displacement of the individual charged particles.

Public Functions

IdealizedQitFFTWriter(std::vector<Core::Particle*> particles, std::string transientFilename)

Constructor: Creates a filewriter with a given particle cloud and a file to write to

Parameters:

  • particles – vector with links to the partilces in a particle cloud to write to a file

  • transientFilename – the filename of the file to write to

~IdealizedQitFFTWriter()

Destructor

void writeTimestep(double time)

Writes a time step to the file: The current state of the particles in the particle cloud is used to determine the average velocity in z direction for all particles and the result is written to the result file.

Parameters:

time – the time of the current time step

void writeTimestepMassResolved(double time)

Writes a time step to the file in a mass resolved way: The current state of the particles in the particle cloud is used to determine the average velocity in z direction individually for groups containing particles with the same mass. The result is written to the result file.

Parameters:

time – the time of the current time step

void writeTimestepAverageIonCloudPosition(double time)

Writes a time step to the file in a mass resolved way: The current state of the particles in the particle cloud is used to determine the average velocity in z direction individually for groups containing particles with the same mass. The result is written to the result file.

Parameters:

time – the time of the current time step

class AverageChargePositionWriter

Filewriter to write the average position of the net charge in a Core to a file

Public Functions

explicit AverageChargePositionWriter(std::string transientFilename)

Constructor

Parameters:

transientFilename – a filename to write to

~AverageChargePositionWriter()

Destructor

void writeTimestep(const BTree::Tree &tree, double time)

Writes a timestep to the file

Parameters:

  • tree – a valid Core which contains the charged particles

  • time – the time of the current time step

File Readers

File readers import data from persistent files

FileIO::HDF5Reader is a general reader for HDF5 files.

class HDF5Reader

Public Functions

explicit HDF5Reader(const std::string &hdf5Filename)
template<hsize_t NDIMS>
DataField<NDIMS, double> readDataset(std::string datasetName) const
template<typename DTYPE>
std::vector<DTYPE> readAttributeVector(std::string groupName, std::string attributeName) const
hsize_t numberOfObjectsInGroup(std::string groupName) const
std::vector<std::string> namesOfObjectsInGroup(std::string groupName) const
std::vector<std::string> namesOfDatasetsInGroup(std::string groupName) const
int datasetNDims(std::string datasetName) const
template<hsize_t NDIMS, typename DTYPE>
struct DataField

Public Functions

DTYPE get(std::array<hsize_t, NDIMS> indices)

Public Members

hsize_t rank = 0
std::array<hsize_t, NDIMS> dims
std::vector<DTYPE> data
class IonCloudReader

File reader for importing structured simple ion clouds / ion initialization data from files

Public Functions

std::vector<std::unique_ptr<Core::Particle>> readIonCloud(std::string filename)

Reads particles from an ion cloud definition file

Parameters:

filename – a filename to read from

Throws:

IonCloudFileException – if the ion cloud file is incorrect

Returns:

Vector with unique pointers to the read and newly created particles

class MolecularStructureReader

Public Functions

std::unordered_map<std::string, std::shared_ptr<CollisionModel::MolecularStructure>> readMolecularStructure(std::string filename)