Commands¶
MicroBenthos provides a command line interface for its operations under microbenthos
.
Usage: microbenthos [OPTIONS] COMMAND [ARGS]...
Console entry point for microbenthos
Options:
-v, --verbosity Set verbosity of console logging
--logger <TEXT INTEGER RANGE>...
Set specified logger to loglevel (example:
microbenthos.model 20)
--version Show the version and exit.
--help Show this message and exit.
Commands:
export Export options
setup Setup configuration
simulate Run simulation from definition file
To view the log messages on the console, use the -v
flag. For increased verbosity of console
log messages, use it multiple times, e.g. -vv
, -vvv
, etc.
The various subcommands available are:
Command: simulate¶
$ microbenthos simulate --help
Usage: microbenthos simulate [OPTIONS] MODEL_FILE
Run simulation from definition file
Options:
-o, --output-dir DIRECTORY Output directory for simulation
--output-same Output to same location as definition file
-x, --exporter TEXT Add an exporter to run. Form: -x <name>
<export_type>
["<option1>=val,<option2>=val2"]
-sTime, --simtime-total TEXT Total simulation time. Example: "10h"
-sLims, --simtime-lims TEXT Simulation time step limits. Example: "0.1
500"
-sSweeps, --max-sweeps INTEGER RANGE
Max number of sweeps of equation in each
timestep
-sRes, --max-residual FLOAT The max residual allowed for the time steps
-sSolver, --fipy-solver TEXT Solver type to use from fipy
-sSnapshot, --snapshot-interval INTEGER RANGE
Interval in seconds between simulation
snapshots
-O, --overwrite Overwrite file, if exists
-c, --compression INTEGER RANGE
Compression level for data (default: 9)
--confirm / -Y, --no-confirm Confirm before running simulation
--progress INTEGER RANGE Show progress bar (0 to disable)
--progress-tag TEXT Tag for progress bar
--plot / --no-plot Show graphical plot of model data
--video / --no-video Save video of simulation plot. This can slow
things down.
--frames / --no-frames Save frames of simulation plot. This can
slow things down.
--budget Track variable budget over time and show in
plot
--resume INTEGER Resume simulation by restoring from stored
data at time index
-eqns, --show-eqns Show equations that will be solved
--help Show this message and exit.
Note
By default, a progress bar exporter and model data exporter are added if not specified. The
progress bar can be turned off using the --no-progress
switch.
Command: export video¶
$ microbenthos export video --help
Usage: microbenthos export video [OPTIONS] DATAFILE
Export video from model data
Options:
-o, --outfile FILE Name of the output file
-O, --overwrite Overwrite file, if exists
--from-time TEXT Clock time to start video ("5 h" or "0.25 d" or
"0.45 day")
--till-time TEXT Clock time to end video ("5 h" or "0.25 d" or
"0.45 day")
--style TEXT Plot style name from matplotlib
--writer TEXT Animation writer class to use
--figsize TEXT Figure size in inches (example: "9.6x5.4")
--dpi INTEGER RANGE Dots per inch for figure export
--show Show figure on screen during export
--budget Show temporal budget error of variables
--fps INTEGER RANGE Frames per second for export (default: 10)
--bitrate INTEGER RANGE Bitrate for video encoding (default: 1400)
--artist-tag TEXT Artist tag in metadata
--progress INTEGER RANGE Position of progress bar
--help Show this message and exit.
Note
The graphical exporter in MicroBenthos uses matplotlib
to render the plots and
animations. For video export, ffmpeg
or one of the other animation backends for
matplotlib.animation
should be available.
Command: export model¶
$ microbenthos export model --help
Usage: microbenthos export model [OPTIONS] MODEL_FILE
Load a model from a file and export it after validation.
Options:
--key TEXT Load this key from the input file
-v, --verbose Set this to see verbose output
--help Show this message and exit.
Command: setup completion¶
$ microbenthos setup completion --help
Usage: microbenthos setup completion [OPTIONS]
Setup CLI completion for shell
Options:
--shell TEXT The shell to install completion [required]
--show-code Show the installed code
--help Show this message and exit.