espressomd.io.writer package

Submodules

espressomd.io.writer.h5md module

class espressomd.io.writer.h5md.H5md(**kwargs)[source]

Bases: ScriptInterfaceHelper

H5md file object.

Note

Bonds will be written to the file if they exist. The pypresso script will be written in the metadata.

Parameters:

  • file_path (str or pathlib.Path) – Path to the trajectory file, or an existing file to append data to (it must have the same specifications).

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

  • fields (set or str, optional) – List of fields to write to the trajectory file. Defaults to 'all'. See valid_fields() for the list of valid fields. This list defines the H5MD specifications. If the file in file_path already exists but has different specifications, an exception is raised.

  • chunk_size (int) – The chunk size for hdf5 write operations. Must be greater than 0.

get_params()

Get the parameters from the script interface.

valid_fields()

Get the list of valid fields.

write()

Call the H5md write method.

flush()

Call the H5md flush method.

close()

Close the H5md file.

file_path

Path to the trajectory file.

Type:

str

script_path

Path to the pypresso script, or empty string for interactive sessions.

Type:

str

fields

List of fields to write to the trajectory file.

Type:

list

mass_unit
Type:

str

length_unit
Type:

str

time_unit
Type:

str

force_unit
Type:

str

velocity_unit
Type:

str

charge_unit
Type:

str

chunk_size
Type:

int

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

Bases: object

Data class for writing H5MD trajectories with physical units. There are four settable units: ‘mass’, ‘length’, ‘time’, ‘charge’. Units should be written as strings following the specifications defined here, 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:
Returns:

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

Return type:

dict

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.System)

  • 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.System)

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

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

Module contents