7. Menus¶
The menu bar has entries File, Edit, Run, View, Tutorials, and About. Instead of using the mouse to click on them, the individual menus can also be activated by hitting the Alt key together with the corresponding underlined letter, that is Alt-F activates the File menu. For the corresponding activated sub-menus, the key corresponding to the underlined letters can be used to select entries instead of using the mouse.
LAMMPS-GUI Combined Window Mode
In joined window mode there can be only one menu bar, so the displayed menu bar is that of the section / tab that has currently the focus. If access to the menu bar of a specific window is needed, e.g. to open a new LAMMPS input file, it may be needed to either first click into the corresponding area or use the F6 or Shift-F6 keyboard shortcuts to switch focus.
7.1. File¶
In addition, up to 5 recent file names will be listed after the Open Input File entry that allows re-opening recently opened files. This list is stored when quitting and recovered when starting again.
Files that are not what they are opened as. Each of these entries
expects a certain kind of file, and the file dialogs offer All files
as well, so a file can be picked that does not fit: a binary file for the
editor or the text viewer, something that is not a picture for the slide
show, an image for the plotter. Rather than refuse it or fill a window
with unreadable content, LAMMPS-GUI asks – “… does not look like a
text file. Do you want to open it anyway?” – and the answer defaults
to No, since the usual reason to see the question is a name that was
mistyped or a file that was picked by mistake. Answering Yes opens it
regardless, which is occasionally what is wanted: an input file with a
stray null byte in it can still be edited. A file that looks right is
never asked about. The same check applies to the edit, open and
plot commands of the command window.
Plotting external data files. The Plot Data File… entry
(Ctrl-Shift-P) opens a dialog to select a file with column-oriented
numeric data and plots it in a standalone Charts window
without running a simulation. Supported formats are whitespace-separated
columns (.dat), comma-separated values (.csv), YAML (including the segmented thermo output that LAMMPS
itself writes), and JSON; the format is
recognized from the file name extension or, failing that, from the
content. After the file is read, a dialog lets you pick which column
provides the x axis and which columns to plot; column names can also be
edited at this point. The block-structured output of the fix ave/*
styles is recognized as such, and that dialog then also offers to average
the blocks with error bars or to show a single one (see importing
fix ave/* output). Because there is no associated simulation, the
Units and Norm controls are hidden in such a standalone chart window.
All the post-processing and export features described for the
Charts window are available here as well.
7.2. Edit¶
The Edit menu offers the usual editor functions like Undo, Redo, Cut, Copy, Paste, and a Find and Replace dialog (keyboard shortcut Ctrl-F).
Changed in version 3.1: The Preferences dialog and the option to reset all settings to their defaults have moved to the View menu, which is where the window layout they configure is controlled.
7.3. Run¶
The Run menu has options to start and stop a LAMMPS process. Rather than calling the LAMMPS executable as a separate executable, the LAMMPS-GUI is linked to the LAMMPS library and thus can run LAMMPS internally through the LAMMPS C-library interface in a separate thread.
Specifically, a LAMMPS instance will be created by calling
lammps_open_no_mpi
(through the LammpsWrapper C++ adapter). The buffer contents are
then executed by calling lammps_commands_string.
Certain commands and features are only available after a LAMMPS instance
is created. Its presence is indicated by a small LAMMPS L logo in
the status bar at the bottom left of the main window. As an
alternative, it is also possible to run LAMMPS using the contents of the
edited file by reading the file. This is mainly provided as a fallback
option in case the input uses some feature that is not available when
running from a string buffer.
The LAMMPS calculations are run in a concurrent thread so that the GUI can stay responsive and be updated during the run. The GUI can retrieve data from the running LAMMPS instance and tell it to stop at the next timestep. The Stop LAMMPS entry will do this by calling the lammps_force_timeout library function, which is equivalent to a timer timeout 0 command.
The Extend Run… entry (keyboard shortcut Ctrl-E) opens a dialog
asking for a number of steps and then continues the previous run for
that many more steps without clearing the system. This requires a
system state, e.g. from a previous run or an inspected restart file.
The continuation executes a timer timeout off command, which resets the
expired timer in case the previous run was interrupted with Stop
LAMMPS, followed by run <steps> pre yes post no. The captured
output and thermodynamic data are appended to the existing Output
and Charts windows after a message noting the extension. Typical
use cases are continuing a run that was stopped (e.g. after writing a
restart file first), or extending a run that did not produce enough
frames for a smooth animation or enough data for a plot.
The Relaunch LAMMPS Instance will destroy the current LAMMPS thread and free its data and then create a new thread with a new LAMMPS instance. This is usually not needed, since LAMMPS-GUI tries to detect when this is needed and does it automatically. This is available in case it missed something and LAMMPS behaves in unexpected ways.
The Check Input via Heuristics entry (keyboard shortcut Ctrl-K)
runs a fast static check of the editor buffer and reports its findings
in a dialog: unknown commands and style names (validated against the
loaded LAMMPS library), unbalanced quotes, dangling line continuations,
variables used before they are defined, references to undefined groups,
references to computes, fixes, or variables that are defined nowhere in
the buffer, missing input files, missing required arguments, and
non-numeric arguments where strictly numeric values are required. When
no problems are found, a corresponding message is shown; otherwise the
cursor moves to the first finding. The same check runs automatically
before every run (this can be disabled in the Editor Settings of the
Preferences dialog); in that case only error-level findings trigger a
dialog asking whether to run anyway, while warnings are only noted in
the status bar. The checker is designed to avoid false alarms: any
word containing a $ substitution is exempt from checking, and
script features that make static analysis unreliable (include files,
jump loops, if/then commands, python scripting, shell commands, restart
files, runtime plugins) disable the affected groups of checks.
The Check Input via Dry Run entry (keyboard shortcut Ctrl-Shift-K) validates the buffer by actually executing it: the equivalent of the -skiprun command-line flag is applied, so LAMMPS parses every command and executes the setup phase of every run and minimize command without computing any timesteps. This is a much deeper check than the static one, but it takes as long as the setup of a real run and has the same side effects: output files may be created or overwritten and shell commands are executed, which is why the action first asks for confirmation. The captured output is shown in an Output window; errors are reported with the usual error dialog and the offending line is highlighted in the editor. On success, a dialog confirms that the input passed and points to the Output window for any LAMMPS warnings.
The Set Variables… entry opens a dialog box where index style variables can be set. Those variables are passed to the LAMMPS instance when it is created and are thus set before a run is started.
The Set Variables dialog will be pre-populated with entries that are set as index variables in the input and any variables that are used but not defined, if the built-in parser can detect them. New rows for additional variables can be added through the Add Row button and existing rows can be deleted by clicking on the X icons on the right.
The dialog follows edits to the input script: when a variable ...
index command in the editor is changed, the dialog picks up the
new value the next time it is opened or a run is started, even if
the value had been changed in the dialog before. A value edited in
the dialog so that it differs from the input script is shown in
bold with a tooltip listing the script value, and the overridden
value in the editor is surrounded by a thin frame as a reminder
that the input script line is not what LAMMPS will use. Values
from the dialog are passed to LAMMPS before the input script runs,
so they take precedence over variable ... index commands in the
input, exactly like the -var command line flag to LAMMPS.
The Create Image entry will send a dump image command to the LAMMPS instance, read the resulting file, and show it in an Image Viewer window.
The Open Command Window entry opens the Command window, a shell prompt for the ordinary work that surrounds a
run: post-processing a dump file with a script, looking at what a run
just wrote, calling a plotting tool. It is not a terminal emulator
and cannot run full-screen programs such as vim or top.
The View in OVITO entry will launch OVITO with a data file containing the current state of the system. This option is only available if LAMMPS-GUI can find the OVITO executable in the system path.
The View in VMD entry will launch VMD with a data file containing the current state of the system. This option is only available if LAMMPS-GUI can find the VMD executable in the system path.
7.4. View¶
The View menu offers to show or hide additional windows with log output, charts, slide show, variables, snapshot images, or the Command window. With the Combined Main Window layout these are panels docked into the main window instead of windows of their own, and the same entries show and hide the panels. The default settings for their visibility can be changed in the Preferences dialog.
With that layout the menu also has the Next Panel (F6) and Previous Panel (Shift-F6) entries, which move the keyboard focus between the editor and the panels around it; see the keyboard shortcuts for what they walk through. They are not shown with individual windows, where switching windows is the window manager’s job.
The View menu is also where the Preferences dialog is opened (keyboard shortcut Ctrl-P), and where all stored preferences and settings can be deleted, so they are reset to their default values. Resetting the preferences also deletes a LAMMPS shared library that was previously downloaded into the configuration folder; the library files for all supported platforms are removed in case the configuration folder is shared between multiple computers.
7.5. Tutorials¶
The Tutorials menu supports several collections of LAMMPS tutorials for beginners and intermediate LAMMPS users. The menu has one submenu per collection, for example Soft Matter (the molecular tutorials documented in Gravelle1), Materials Science, and Granular / DEM. Each submenu lists its individual tutorial sessions; selecting one begins that session.
Collections are released incrementally. A collection that is not yet fully published is labeled in the menu with its status, e.g. (coming soon) or (planned). Within such a collection only the tutorials that are already available can be launched; the remaining entries are shown (so you can preview what is coming) but are disabled. A collection with no tutorials available yet appears as a single disabled submenu.
Selecting an available tutorial opens a ‘wizard’ dialog where you can
choose in which folder you want to work, whether you want that folder to
be wiped from any files, whether you want to download the solution
files (which can be large) to a solution sub-folder, and whether you
want the corresponding tutorial’s online version opened in your web
browser. The dialog will then start downloading the files requested
(download progress is reported in the status line) and load the first
input file for the selected session into LAMMPS-GUI.
Should individual tutorial files fail to download, the remaining files are still fetched, and a dialog afterwards lists the files that are missing. That dialog offers a Report Issue button that opens the issue tracker of the tutorial’s file repository in a web browser, so the missing files can be reported; alternatively they can be reported by email to akohlmey@gmail.com.
7.6. About¶
The About menu finally offers a couple of dialog windows and an option to launch the LAMMPS online documentation in a web browser. The About LAMMPS-GUI entry displays a dialog with a summary of the configuration settings of the LAMMPS library in use and the version number of LAMMPS-GUI itself. The Quick Help displays a dialog with a minimal description of LAMMPS-GUI. The LAMMPS-GUI Documentation entry will open the LAMMPS-GUI online documentation website https://lammps-gui.lammps.org in a web browser window. The LAMMPS Manual entry will open the main page of the LAMMPS online documentation in a web browser window. The LAMMPS Tutorial entry will open the main page of the set of LAMMPS tutorials authored and maintained by Simon Gravelle at https://lammpstutorials.github.io/ in a web browser window. The Check for LAMMPS update entry – available only in the plugin version of LAMMPS-GUI – compares the downloaded LAMMPS shared library with the latest version available online and offers to download and install an update when a newer version is found; LAMMPS-GUI is then relaunched to activate it. The checksum of the downloaded file is verified before it replaces the current library, which is renamed to a backup name first; leftover backup files and partial downloads in the configuration folder are cleaned up on the next launch of LAMMPS-GUI.
(Gravelle1) Gravelle, Alvares, Gissinger, Kohlmeyer, Living Journal of Computational Molecular Science, 6(1), 3037. https://doi.org/10.33011/livecoms.6.1.3037 (2025)
