Burst¶

class hoomd.write.Burst(trigger, filename, filter=hoomd.filter.All(), mode='ab', dynamic=None, logger=None, max_burst_size=-1, write_at_start=False)¶

Bases: GSD

Write the last $N$ stored frames in the GSD format.

When triggered, Burst adds a frame (up the last $N$ frames) in a buffer. Call dump to write the frames to the file. When the the next frame would result in $N + 1$ frames being stored, the oldest frame is removed and the new frame is added.

Parameters:

trigger (hoomd.trigger.trigger_like) – Select the timesteps to store in the buffer.
filename (str) – File name to write.
filter (hoomd.filter.filter_like) – Select the particles to write. Defaults to hoomd.filter.All.
mode (str) – The file open mode. Defaults to 'ab'.
dynamic (list[str]) – Field names and/or field categores to save in all frames. Defaults to ['property'].
logger (hoomd.logging.Logger) – Provide log quantities to write. Defaults to None.
max_burst_size (int) – The maximum number of frames to store before between writes. -1 represents no limit. Defaults to -1.
write_at_start (bool) – When True and the file does not exist or has 0 frames: write one frame with the current state of the system when hoomd.Simulation.run is called. Defaults to False.
clear_whole_buffer_after_dump (bool) – When True the buffer is emptied after calling dump each time. When False, dump removes frames from the buffer until the end index. Defaults to True.
precision (str) – Write precision for floating-point data. One of 'single' or 'double'. Defaults to 'single'.

Warning

Burst errors when attempting to create a file or writing to one with zero frames when write_at_start is False.

Note

When analyzing files created by Burst, generally the first frame is not associated with the call to Burst.dump.

Example:

burst = hoomd.write.Burst(
    trigger=hoomd.trigger.Periodic(1_000),
    filename=burst_filename,
    max_burst_size=100,
    write_at_start=True,
)
simulation.operations.writers.append(burst)

See also

The base class hoomd.write.GSD

Members inherited from AutotunedObject:

property kernel_parameters¶: Kernel parameters. Read more...

property is_tuning_complete¶: Check if kernel parameter tuning is complete. Read more...

tune_kernel_parameters()¶: Start tuning kernel parameters. Read more...

Members inherited from TriggeredOperation:

trigger¶: The trigger to activate this operation. Read more...

Members inherited from GSD:

filename¶: File name to write (read-only). Read more...

filter¶: Select the particles to write (read-only). Read more...

mode¶: The file open mode (read-only). Read more...

dynamic¶: Field names and/or field categores to save in all frames. Read more...

write_diameter¶: When False, do not write particles/diameter. Set to True to write non-default particle diameters. Read more...

maximum_write_buffer_size¶: Size (in bytes) to buffer in memory before writing to the file. Read more...

auto_flush_period¶: Time (in seconds) to wait between automatic calls to flush(). Read more...

property logger¶: Provide log quantities to write. Read more...

flush()¶: Flush the write buffer to the file. Read more...

Members defined in Burst:

max_burst_size¶

The maximum number of frames to store before between writes. -1 represents no limit.

Example:

burst.max_burst_size = 200

Type:: int

write_at_start¶

When True and the file does not exist or has 0 frames: write one frame with the current state of the system when hoomd.Simulation.run is called (read only).

Example:

write_at_start = burst.write_at_start

Type:: bool

clear_whole_buffer_after_dump¶

When True the buffer is emptied after calling dump each time. When False, dump removes frames from the buffer until the end index.

Example:

burst.clear_buffer_after_dump = False

Type:: bool

__len__()¶

Get the current length of the internal frame buffer.

Example:

buffered_frames = len(burst)

dump(start=0, end=-1)¶

Write stored frames in range to the file and empties the buffer.

This method alllows for custom writing of frames at user specified conditions.

Parameters:

start (int) – The first frame to write. Defaults to 0.
end (int) – The last frame to write. Defaults to -1 (last frame).

Example:

burst.dump()