espressomd.io.writer package

Submodules

espressomd.io.writer.h5md module

Interface module for the H5md core implementation.

class espressomd.io.writer.h5md.H5md(write_ordered=True, **kwargs)[source]

Bases: object

H5md file object.

Used for accessing the H5MD core implementation via the PScriptInterface.

Note

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

Parameters:
  • filename (str) – Name of the trajectory file.
  • write_pos (bool, optional) – If positions should be written.
  • write_vel (bool, optional) – If velocities should be written.
  • write_force (bool, optional) – If forces should be written.
  • write_species (bool, optional) – If types (called ‘species’ in the H5MD specification) should be written.
  • write_mass (bool, optional) – If masses should be written.
  • write_charge (bool, opional) – If charges should be written.
  • write_ordered (bool, optional) – If particle properties should be ordered according to ids.
close()[source]

Close the H5md file.

flush()[source]

Call the H5md flush method.

get_params()[source]

Get the parameters from the scriptinterface.

write()[source]

Call the H5md write method.

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