6. Editor Window

The Editor window of LAMMPS-GUI has most of the usual functionality that similar programs have: text selection via mouse or with cursor moves while holding the Shift key, Cut (Ctrl-X), Copy (Ctrl-C), Paste (Ctrl-V), Undo (Ctrl-Z), Redo (Ctrl-Shift-Z), Select All (Ctrl-A). When trying to exit the editor with a modified buffer, a dialog will pop up asking whether to cancel the exit operation, or to save or not save the buffer contents to a file.

The editor has an auto-save mode that can be enabled or disabled in the Preferences dialog. In auto-save mode, the editor buffer is automatically saved before running LAMMPS or before exiting LAMMPS-GUI.

6.1. Context Specific Word Completion

By default, LAMMPS-GUI displays a small pop-up frame with possible choices for LAMMPS input script commands or styles after 2 characters of a word have been typed.

The word can then be completed through selecting an entry by scrolling up and down with the cursor keys and selecting with the ‘Enter’ key or by clicking on the entry with the mouse. The automatic completion pop-up can be disabled in the Preferences dialog, but the completion can still be requested manually by either hitting the Shift+TAB key or by right-clicking with the mouse and selecting the option from the context menu. Most of the completion information is retrieved from the active LAMMPS instance and thus it shows only available options that have been enabled when compiling LAMMPS. That list, however, excludes accelerated styles and commands; for improved clarity, only the non-suffix versions of styles are shown.

Like the syntax highlighting, the completion and the context-specific help are aware of & line continuations: on a continuation line, completions and help are offered for the command that is being continued.

6.2. Syntax Highlighting

The editor highlights LAMMPS input scripts following the same parsing rules as LAMMPS itself: comments, single, double, and triple quoted strings, $ variable substitutions, and numbers are recognized, and command names are colored by category. Arguments are colored by their role in the command, for example the ID, group-ID, and style name of a fix command. IDs use the same color whether they are being defined (fix, compute, dump) or referenced (fix_modify, unfix, and so on). A few commands embed a second command in their argument list; the keyword that starts the embedded part is shown in the color of the command it stands for, that is the modify keyword of the write_dump command is colored like dump_modify and the dump keyword of the rerun command like read_dump. The arguments following such a keyword are colored as arguments of the embedded command, also when the command is spread over multiple lines with & line continuations. Lines joined with the & line continuation character are highlighted in the context of the command they continue, including style names or quoted strings that are split across lines.

Sub-styles of hybrid styles are recognized the same way LAMMPS parses them – by checking against the known styles of the loaded library – and are shown in their own color, both in the arguments of the *_style command and in the sub-style position of the corresponding *_coeff commands, where they also auto-complete. Words in those positions that are not a known style are treated as arguments of the sub-styles and are never marked as unknown. On dump image lines the dump image keywords are marked, and on both dump image and dump_modify lines color names are displayed in their actual color; keywords and color names auto-complete in the positions where they are expected. Color names with too little contrast against the editor background (for example yellow on a light theme) are placed on a small dark or light chip so they remain readable.

Command and style names that are not known to the LAMMPS library that LAMMPS-GUI has loaded – for example due to a typo or because the corresponding package was not included when the library was compiled – are marked with a wavy underline. The marker is not shown for the word at the cursor position, so partially typed names are not flagged while typing, and it is suppressed for names constructed with $ substitutions. When LAMMPS-GUI is running without a usable LAMMPS library (for example in plugin mode before a library has been selected), the known-name information is unavailable and no words are marked.

6.3. Line Reformatting

The editor supports reformatting lines according to the syntax in order to have consistently aligned lines. This primarily means adding whitespace padding to commands, type specifiers, IDs and names. This reformatting is performed manually by hitting the ‘Tab’ key. It is also possible to have this done automatically when hitting the ‘Enter’ key to start a new line. This feature can be turned on or off in the Preferences dialog for Editor Settings with the “Reformat with ‘Enter’” checkbox. The amount of padding for multiple categories can be adjusted in the same dialog.

Internally this functionality is achieved by splitting the line into “words” and then putting it back together with padding added where the context can be detected; otherwise a single space is used between words.

6.4. Context Specific Help

A unique feature of LAMMPS-GUI is the option to look up the LAMMPS documentation for the command in the current line. This can be done by either clicking the right mouse button or by using the Ctrl-? keyboard shortcut. When using the mouse, there are additional entries in the context menu that open the corresponding documentation page in the online LAMMPS documentation in a web browser window. When using the keyboard, the first of those entries is chosen.

If the current line defines an index style variable, the context menu also has a Set Variables… entry that opens the corresponding dialog from the Edit menu.

If the word under the cursor is a file, then additionally the context menu has an entry to open the file in a read-only text viewer window. If the file is a LAMMPS restart file, instead the menu entry offers to inspect the restart.

The text viewer is a convenient way to view the contents of files that are referenced in the input. The file viewer also supports on-the-fly decompression based on the file name suffix in a similar fashion as available with LAMMPS. If the necessary decompression program is missing or the file cannot be decompressed, the viewer window will contain a corresponding message.

6.5. Inspecting a Restart file

When LAMMPS-GUI is asked to “Inspect a Restart”, it will read the restart file into a LAMMPS instance and then open three different windows. The first window is a text viewer with the output of an info command with system information stored in the restart. The second window is a text viewer containing a data file generated with a write_data command. The third window is a Snapshot Image Viewer containing a visualization of the system in the restart.

Large Restart Files

If the restart file is larger than 250 MBytes, a dialog will ask for confirmation before continuing, since large restart files may require large amounts of RAM: the entire system must be read into memory. Thus restart files for large simulations that have been run on an HPC cluster may overload a laptop or local workstation. The Show Details… button will display a rough estimate of the additional memory required.