HDF5Writer

class narupatools.frame.hdf5.writer.HDF5Writer(filename: str, *, title: Optional[str] = None, author: Optional[str] = None, overwrite_existing: bool = False)

Writer for HDF5 trajectory containing interactive forces.

Inheritance

Methods

__init__	Initialize self.
close	Close the file being written to.
create_interaction	Save an IMD interaction to the trajectory.
end_interaction	Mark an interaction as having finished.
reopen	Reopen a writer for a different file, discarding the old state.
save_frame	Save a trajectory frame.
save_interaction	Save an IMD interaction to the trajectory.
save_topology	Save the topology of the given frame to the file.

__init__(filename: str, *, title: Optional[str] = None, author: Optional[str] = None, overwrite_existing: bool = False)

Initialize self. See help(type(self)) for accurate signature.

close() → None

Close the file being written to.

create_interaction(*, key: str, interaction: narupa.imd.particle_interaction.ParticleInteraction, frame_index: int, potential_energy: Optional[float] = None, forces: Optional[numpy.ndarray] = None) → None

Save an IMD interaction to the trajectory.

Parameters

• frame_index – Index of the frame in the main trajectory this interaction corresponds to.

• key – Unique key of interaction.

• interaction – Interaction to save.

• potential_energy – Potential energy of interaction in kilojoules per mole.

• forces – Forces on affected atoms in kilojoules per mole per nanometer.

end_interaction(*, key: str, frame_index: int) → None

Mark an interaction as having finished.

Parameters

• key – Key of the interaction.

• frame_index – Current frame of the simulation.

reopen(filename: str, *, title: Optional[str] = None, author: Optional[str] = None) → None

Reopen a writer for a different file, discarding the old state.

This closes the previous file.

Parameters

• filename – Name of the file to write to.

• title – Title to add to the trajectory.

• author – Name of the author.

save_frame(*, coordinates: numpy.ndarray, time: float, potential_energy: float, kinetic_energy: float, velocities: Optional[numpy.ndarray] = None, forces: Optional[numpy.ndarray] = None) → None

Save a trajectory frame.

Parameters

• coordinates – Atomic coordinates in nanometers.

• velocities – Atomic velocities in nanometers per picoseconds.

• time – Time in picoseconds.

• potential_energy – Potential energy in kilojoules per mole.

• kinetic_energy – Kinetic energy in kilojoules per mole.

• forces – Atomic forces in kilojoules per mole per nanometer.

save_interaction(*, key: str, interaction: narupa.imd.particle_interaction.ParticleInteraction, frame_index: int, potential_energy: Optional[float] = None, forces: Optional[numpy.ndarray] = None) → None

Save an IMD interaction to the trajectory.

Parameters

• frame_index – Index of the frame in the main trajectory this interaction corresponds to.

• key – Unique key of interaction.

• interaction – Interaction to save.

• potential_energy – Potential energy of interaction in kilojoules per mole.

• forces – Forces on affected atoms in kilojoules per mole per nanometer.

save_topology(frame: narupa.trajectory.frame_data.FrameData) → None

Save the topology of the given frame to the file.

Parameters

frame – Frame to get topology from.

Attributes

coordinates	Array of atom coordinates in nanometers.
forces	Array of forces in kilojoules per mole per nanometer.
interactions	Group containing interactions.
kinetic_energy	Array of kinetic energies in kilojoules per mole.
potential_energy	Array of potential energies in kilojoules per mole.
realtime	Array of real times in seconds since the first frame.
time	Array of frame times in picoseconds.
velocities	Array of atom velocities in nanometers per picoseconds.

coordinates

Array of atom coordinates in nanometers.

forces

Array of forces in kilojoules per mole per nanometer.

interactions

Group containing interactions.

kinetic_energy

Array of kinetic energies in kilojoules per mole.

potential_energy

Array of potential energies in kilojoules per mole.

realtime

Array of real times in seconds since the first frame.

time

Array of frame times in picoseconds.

velocities

Array of atom velocities in nanometers per picoseconds.