espressomd.io package

Subpackages

• espressomd.io.writer package
  • Submodules
  • espressomd.io.writer.h5md module
    • H5md
    • UnitSystem
  • espressomd.io.writer.vtf module
    • vtf_pid_map()
    • writevcf()
    • writevsf()
  • Module contents

Submodules

espressomd.io.mpiio module

class espressomd.io.mpiio.Mpiio(**kwargs)

Bases: ScriptInterfaceHelper

MPI-IO object.

Used to output particle data using MPI-IO to binary files.

read(prefix=None, positions=False, velocities=False, types=False, bonds=False)

MPI-IO read.

This function reads data dumped by write(). See the write() documentation for details.

Note

The files must be read on the same number of processes that wrote the data. The data must be read on a machine with the same architecture (otherwise, this might silently fail).

write(prefix=None, positions=False, velocities=False, types=False, bonds=False)

MPI-IO write.

Outputs binary data using MPI-IO to several files starting with prefix. Suffixes are:

• head: Information about fields that are dumped,

• pref: Information about processes: 1 int per process,

• id: Particle ids: 1 int per particle,

• pos: Position information (if dumped): 3 doubles per particle,

• vel: Velocity information (if dumped): 3 doubles per particle,

• typ: Type information (if dumped): 1 int per particle,

• bond: Bond information (if dumped): variable amount of data,

• boff: Bond offset information (if bonds are dumped): 1 int per particle.

Note

Do not read the files on a machine with a different architecture!

Parameters:

• prefix (str or pathlib.Path) – Common prefix for the filenames.

• positions (bool, optional) – Indicates if positions should be dumped.

• velocities (bool, optional) – Indicates if velocities should be dumped.

• types (bool, optional) – Indicates if types should be dumped.

• bonds (bool, optional) – Indicates if bonds should be dumped.

Raises:

ValueError – If no prefix was given or none of the output fields are chosen.

espressomd.io.vtk module

class espressomd.io.vtk.VTKReader

Bases: object

Reader for VTK multi-piece uniform grids written in XML format.

error_tolerance = 1e-05

static get_array_names(reader, type_name)

classmethod get_file_format(filepath)

classmethod get_piece_topology(piece, array, bounding_box_lower, bounding_box_upper)

parse(filepath)

classmethod reconstruct_array(reader, array_name)

type_map = {'ImageData': vtk.vtkXMLImageDataReader, 'UnstructuredGrid': vtk.vtkXMLUnstructuredGridReader}

Module contents