Commands and keyboard shortcuts

Keyboard shortcuts

Keys	Action
F5	Integrate (run)
Ctrl+Enter	Apply the edited model
Ctrl+O, Ctrl+S, Ctrl+N	Open, save, new model
Ctrl+Q	Quit (⌘ instead of Ctrl on a Mac)
F1	Help

XPPAUT's two-key commands

XPPAUT users drive it with two-letter commands, and those keep working here whenever the cursor is not in a text field. They can be switched off under View > XPPAUT keyboard commands.

Keys	XPPAUT menu	Action
I G	Initial conds > Go	Integrate
I L	Initial conds > Last	Start from the end of the last run
I S	Initial conds > Shift	The same, and the time goes on
N N	Nullcline > New	Draw nullclines
N E	Nullcline > Erase	Hide nullclines
N F	Nullcline > Freeze	Keep the nullclines drawn
K C, K A, K R	Kinescope > Capture, Autoplay, Reset	Capture a figure, play the frames, empty the Kinescope
D D	Dir.field > Direct field	Toggle the direction field
S G	Sing pts > Go	Find an equilibrium
E	Erase	Clear kept curves
W F	Window > Fit	Fit the plots (or double-click a plot)
F Q	File > Quit	Quit

The command window

Type a command and press Enter. Use the Up and Down arrows to recall earlier commands. help lists them all.

Command	Action
run	Integrate.
set I=0.5 total=200	Set parameters, initial values or options.
get I	Show a value.
whos	List variables and parameters with their values.
ic last	Start the next run where the last one ended.
ic shift	The same, and the start time T0 becomes the time the run ended (XPPAUT's Shift).
ic read ics.dat, ic write ics.dat	Read the initial values from a text file, one number per variable in order; or write them, one per line.
ic u[1..20] = sin([j]/3)	Initial values from a formula: one variable (ic V = vk + 0.1) or a numbered range, [j] the index (XPPAUT's formUla).
click -0.3 0, click keep	Start a run at that point of the phase plane, as a click does; click keep keeps each such run (click keep off stops).
kinescope capture phase, kinescope play 200, kinescope save film.gif	XPPAUT's Kinescope: a picture of a figure (time, phase, auto, auto2) as it is shown; play the frames (200 ms each); write them as an animated GIF (kinescope frames NAME: PNG files). kinescope show 3, kinescope stop, kinescope clear.
range iapp 0 0.3 10 film	Film the Range: each run drawn alone and captured by the Kinescope (XPPAUT's Range with Movie).
eq	Find an equilibrium and report its stability.
eq all 200	Every equilibrium Newton's method finds from 200 random points (100 if left out) in the phase plane's window: XPPAUT's Sing pts > Monte Carlo.
nullclines, nullclines off	Show or hide nullclines.
nullclines freeze, nullclines freeze iapp 0 0.4 6	Keep the nullclines drawn, or those for 6 values of iapp from 0 to 0.4 (XPPAUT's Freeze, Freeze > Range). nullclines show 3 shows the third set alone (0: all), nullclines play steps through them, nullclines unfreeze deletes them.
dirfield	Toggle the direction field.
erase	Remove kept curves.
use hopf	Apply a named parameter set.
auto steady iapp	Follow steady states as iapp varies.
auto from 2 periodic	Continue from labelled point 2. Actions: periodic, two, extend, switch, doubling, fixed.
auto set ds=0.01 nmax=300	AUTO numerics.
auto reset	Clear the diagram.
auto save d.auto, auto load d.auto	Save the diagram, with AUTO's settings and restart data, as XPPAUT's .auto file; load one back to continue from its points.
auto orbit 6	Make the periodic orbit at point 6 the current run (one period).
range I 0 1.6 50 V	Run 50 times with I from 0 to 1.6 and plot the max and min of V (XPPAUT's Range). Leave out V to keep each trajectory, write lyap for the Liapunov exponent, add continue to start each run where the last ended, or eq to follow the equilibrium instead of running (XPPAUT's Sing pts > Range). The name can also be a variable (its initial value). After the first range a second one, range I 0 1.6 50 gk 1 3 20 V, runs a 50 by 20 grid (XPPAUT's 2par range); without its count, range I 0 1.6 50 gk 1 3 V, both move together along a line. sweep does the same.
bvp	Solve the boundary-value problem given by the model's bndry statements.
view3d X Y Z	Show three columns in the 3D view. view3d spin turns it slowly (view3d spin 60 at 60 degrees a second, view3d spin off stops it); view3d angles 30 60 sets theta and phi.
ani pend.ani, ani play, ani row 100	Open an XPPAUT animation, play it, or show one frame.
spectrum V 1024	Power spectral density of V in windows of 1024 points. spectrum V W coherence compares two columns (psd, cross, coherence).
fourier V, power V	Fourier series of V over the run: cos and sin, or amplitude and phase.
hist V 50 -1 1	Histogram of V in 50 bins from -1 to 1 (leave out the range to take it from the data).
hist2d V W 20	Two-dimensional histogram of V and W.
xcorr V W 100	Cross-correlation of V and W over about 100 lags; xcorr V is the autocorrelation.
mean V	Mean and standard deviation of V, and the run's largest Liapunov exponent.
prc	Phase response curves of the limit cycle (prc 500 settles for 500 time units first).
hfun V'-V; 0	H function for weak coupling, one formula per variable; primed names are the other cell.
fitdata v.dat V 2 gca,gk	Fit gca and gk so that V matches column 2 of v.dat.
open file.ode, new, save	Model files.
export run.csv	Save the last run as CSV. Every number is written exactly.
export d.csv auto	Save the points of the bifurcation diagram as CSV (range: the last Range that measures or follows equilibria; analysis: the Analysis result; equilibria: the last eq all; nullclines: those shown and frozen).
export fig.svg phase	Save a figure (time, phase, auto, auto2) as SVG; .png saves it as shown.
script session.py	Save the session as a Python script that repeats it (see below).
echo off, echo on	Hide or show each action as Python in the command window.
continue 50	Integrate 50 more time units from the end of the last run (C C).
clc	Clear the command window.
show phase, hide help	Bring a window forward, or close it: time, phase, auto, editor, data, analysis, 3d, animator, help, console, workspace, models.
layout side, layout tabs	Put the phase plane beside the time series (also in View), or all plots back in tabs.
help auto	Open a manual page.

Your session as Python

Each action that changes the model or computes something is also written in the command window, in green after >>>, as the line of Python that does the same with the xpplab package:

>>> m = xs.load("lecar.ode")
>>> sol = m.run()
>>> m.parameters["iapp"] = 0.1
>>> sol = m.run()
>>> m.auto.equilibria("iapp")
>>> m.auto.continue_from(2, "periodic")

A slider is written once, when you let it go, with the value it ended at. File > Save session as Python script (or script session.py) saves all the lines so far, with the import they need. Run the script with Python (pip install xpplab) and it repeats the session's computations number for number: the same runs, the same bifurcation diagram, the same spectra, to the last bit, because the package runs the same engine. Data exported as CSV during the session is written again by the script, so the two can be compared file by file.

Figures are drawn again with matplotlib: the same data, but not the same picture. Changes to the view (zoom, windows, colours) are not written. View > Show actions as Python (or echo off) hides the lines in the command window; the script keeps them either way.

Command-line options

The desktop app takes a model file and these options:

xpplab [model.ode] [options]

With no model, it opens lecar.ode from its examples the first time it starts.

Option	Action
--cmd "command"	Run a command-window command after start-up. Repeat it to run several (up to 32), in order.
--then "command"	Run a command a few frames later, once the windows have been drawn, for example to export a figure. Repeatable, up to 32.
--screenshot file.png	Draw a number of frames, save the window to the file and exit. A name ending in .png gives a PNG; any other name gives a BMP.
--frames N	How many frames --screenshot draws before it saves (default 12), or how many frames --record saves.
--size WxH	Window size in pixels (default 1500x920).
--reset-layout	Put the windows back in their default places instead of the saved layout.
--record DIR	Save --frames frames as DIR/frame_00000.png, DIR/frame_00001.png, ... and exit.
--fps N	Frames a second of a recording (default 20). Time in the app runs at this rate however long each frame takes to save, so animations stay smooth.
--script FILE	Run commands at given frames of a recording. Each line is FRAME command; lines starting with # are comments.
--at FRAME "command"	Run one command at a given frame of a recording. Repeatable.
--log FILE	Write the command window's text to the file when the app exits.

Frames for --at and --script count from the first saved frame, which is frame 0. A command written @command runs without being echoed in the command window. Screenshots and recordings always start from the default layout and do not save it. If one fails, the error is written to a file named after it with .err added, for example s.png.err or frames.err. The app then exits with status 1; a run that works exits with 0, so scripts and CI can tell the two apart. The folder for --record must already exist.

Take a screenshot of the phase plane after a run:

xpplab lecar.ode --cmd run --cmd "show phase" --screenshot s.png

Record five seconds at 20 frames a second. The script demo.txt:

# frame command
0 set iapp=0.1
10 run
40 show phase
60 @nullclines

and the command:

xpplab lecar.ode --record frames --fps 20 --frames 100 --script demo.txt

The frames in frames/ can be turned into a video or an animated GIF with any tool; tools/make_demo.py does this for the README.