espressomd.io.writer package

Submodules

espressomd.io.writer.h5md module

Interface module for the H5md core implementation.

class espressomd.io.writer.h5md.H5md(file_path, unit_system=<espressomd.io.writer.h5md.UnitSystem object>)[source]

Bases: object

H5md file object.

Used for accessing the H5MD core implementation.

Note

Bonds will be written to the file automatically if they exist.

Parameters

  • file_path (str) – Path to the trajectory file.

  • unit_system (UnitSystem, optional) – Physical units for the data.

close()[source]

Close the H5md file.

flush()[source]

Call the H5md flush method.

get_params()[source]

Get the parameters from the script interface.

write()[source]

Call the H5md write method.

class espressomd.io.writer.h5md.UnitSystem(**kwargs)[source]

Bases: object

Data class for writing H5MD trajectories with physical units <https://nongnu.org/h5md/modules/units.html>. There are four settable units: ‘mass’, ‘length’, ‘time’, ‘charge’. Units should be written as strings following the specifications defined here <https://nongnu.org/h5md/modules/units.html#unit-string>, e.g. UnitSystem(time='ps', mass='u', length='nm', charge='e').

espressomd.io.writer.vtf module

espressomd.io.writer.vtf.vtf_pid_map(system, types='all')[source]

Generates a VTF particle index map to ESPResSo id. This fills the gap for particle ID’s as required by VMD

Parameters

  • system (espressomd.System() object)

  • types (str) – Specifies the particle types. The id mapping depends on which particles are going to be printed. This should be the same as the one used in writevsf() and writevsf().

Returns

dict

Return type

A dictionary where the values are the VTF indices and the keys are the ESPresSo particle id

espressomd.io.writer.vtf.writevcf(system, fp, types='all')[source]

writes a VCF (VTF Coordinate Format) to a file. This can be used to write a timestep to a VTF file.

Parameters

  • system (espressomd.System() object)

  • types (str) – Specifies the particle types. The string ‘all’ will write all particles

  • fp (file) – File pointer to write to.

espressomd.io.writer.vtf.writevsf(system, fp, types='all')[source]

writes a VST (VTF Structure Format) to a file. This can be used to write the header of a VTF file.

Parameters

  • system (espressomd.System() object)

  • types (str) – Specifies the particle types. The string ‘all’ will write all particles

  • fp (file) – File pointer to write to.

Module contents