The menu bar

The file menu

Open file: Open a .jam file
Save: Save settings in a file. The filename from the windows title bar will be used (that is the file that was last opened). This will save the lenses/substrates, the initial beam, the plot settings, the list of available lenses/substrates, the list of lenses that are used for fitting and all the path names.
Save as ...: Same as the item above but provides a file chooser dialog.
Reset: Reloads the file that was last opened.
Clear plot: Removes all components from the plot.
Export ...: Export the plotting area to various formats. These contain eps, jpg, several formats for exporting the raw data (e.g. Octave/Matlab) as well as a file export for .kat files that can be read by Finesse.
Import JamDB: Import a .jamDB file in which only substrates and materials are defined. These are used as predefined substrates.
Import beam data: Opens a file chooser dialog. From the data in the file you import, the beam parameters are estimated using a Levenberg-Marquardt algorithm. You will see some information for the fit (number of iteration, chi2) and the estimated beam parameters are automatically used as initial beam. The file needs to have the following form:

# Comments start with '#', empty lines are ignored
# 1. column 2. column 3. column
# position [cm] waist size [μm] waist size (orthogonal direction) [μm]

Settings: Saves all settings (the same as the 'Write file' command does) to a special file in the users home directory '$HOME/.JamMt/config' which is loaded everytime JamMt is started. On UNIX-like systems this file is hidden.
Quit: Quit JamMt

The edit menu

Initial beam: Set the parameters of the initial beam (w0, z0, lambda). The wave length of the initial beam is also used by the autofit routine.
Add substrate: Adds a new substrate to the plot. In case you add a thin lens, you can choose the focal length, the position and the aperture of that lens. The focal length can be chosen from the list of available lenses (-> see options menu) or you can directly type in the desired focal length (NOTE: the latter is not automatically attached to the list of available lenses!). The aperture is needed to warn you if the beam is getting too large (-> see plotting area). You can also define a substrate in this dialog. A substrate may be a beam splitter, a mirror or a 'thick' lens.
You can either use a predefined substrate (-> see options menu), or edit the values by hand (NOTE: the latter procedure will not attach the substrate to the list of available substrates!). The definition of a substrate consists of its thickness, the index of refraction, the position, the aperture, as well as the radius of curvature for the two interfaces (the keyword 'Infinity' is allowed here to define a plane interface). A tilted substrate can also be defined in this dialog.
New material: In this dialog you can add materials to JamMt, i.e. define the dispersion properties. This is done by defining the six coefficients that are used in the Sellmeier equation, given by

n2 = 1 + B12/(λ2 - C1) + B22/(λ2 - C2) + B32/(λ2 - C3)

where λ is the vacuum wavelength in m.
Add beam analyzer: Add a beam analyzer with a user defined name and position
Text label: Add custom text labels to the plot. This can be useful to mark important positions in your setup.

The View menu

Mode: Toggle between movement and rotation mode
Verbose: Show verbose information for all components and the beam
Autoscale: Toggle autoscale on/off
Zoom in/out: Here you can zoom the specified axis in and out
Orthogonal plane: Show the beam additionally for the orthogonal plane.
Display settings: In this dialog you can define which graphs you want to see (waist size, gouy phase or radius of curvature depending on the propagation length z) for the y and y2 axis and you can also define the plot range for each axis. The keyword 'auto' computes an autorange.

The Component menu

Edit: This opens the editor for the current component
Delete: Delete the current component
Flip: Flip the component (works only for thick lenses)
Next: Make the next component the current one
Previous: Make the previous component the current one
Ungroup: Remove the current component from its group
Ungroup all: Resolve the group which the current component belongs to
Set group id: Specify a group id for the current component
Convert to: If the current component is a thick lens, it can be converted to a monolithic cavity or right/left cavity endmirror

The Window menu

Cavities: Gives you an overview of all cavities that are currently used, including information about their eigenmode.
Beam analyzer: Presents an overview of all defined beam analyzer

The tools menu

Modematching assistant: This dialog gives you the opportunity to automatically search for a certain mode matching. You have to define the initial beam parameters, the parameters of the target beam, a shifting range (i.e. the range in which the lenses are shifted), the minimal visibility that you'd like to reach and the number of lenses that should be used.
Hitting the fit button will start the routine. A status bar pops up and every time a solution is found, it is attached to the text field. After the routine has finished (or you canceled it) you can simply choose a solution with the mouse or the arrow keys. The solution will then be shown in the drawing area. The lenses that are used for the fit can be edited by clicking the 'Edit fitting lenses' button. The dialog is the same as the 'Available lens' dialog.

There are different filter rules that you can apply on the solutions (press the filter button) to get rid of most of them.
Calculator: This will open a simple calculator in which you can do some calculations. Currently, only the operators +,-,*,/, as well as round brackets are recognized. There is one function available, called vis(max,min) that will calculate the visibility. To use a function simply type e.g. vis(0.9, 0.01) into the text field.
Thermal lens estimator: This tool can be used for simulating a thermal lens (only singlepass!). The calculation is done by iteratively computing the focal length of the thermal lens using an approximation big focal length, then propagate the beam through this lens and calculate the next thermal lens.
Component overview: This tool gives an overview of the distance between any two components in the plot. These values are normalized to a user specified unit. This is useful to express the distances in units of the grid of the table.
Database manager: Create, import/export, edit and delete database files.

The help menu

Documentation: Show this document.