8. Dialogs

8.1. Find and Replace

_images/lammps-gui-find.png

The Find and Replace dialog allows searching for and replacing text in the Editor window.

The dialog can be opened either from the Edit menu or with the keyboard shortcut Ctrl-F. You can enter the text to search for.

Through three checkboxes the search behavior can be adjusted:

  • If checked, “Match case” does a case-sensitive search; otherwise the search is case-insensitive.

  • If checked, “Wrap around” starts searching from the start of the document, if there is no match found from the current cursor position until the end of the document; otherwise the search will stop.

  • If checked, the “Whole word” setting only finds full word matches (white space and special characters are word boundaries).

Clicking on the Next button will search for the next occurrence of the search text and select / highlight it. Clicking on the Replace button will replace an already highlighted search text and find the next one. If no text is selected, or the selected text does not match the selection string, then the first click on the Replace button will only search and highlight the next occurrence of the search string. Clicking on the Replace All button will replace all occurrences from the cursor position to the end of the file; if the Wrap around box is checked, then it will replace all occurrences in the entire document. Clicking on the Done button will dismiss the dialog.

8.2. Preferences

The Preferences dialog allows customization of the behavior and look of LAMMPS-GUI. The settings are grouped and each group is displayed within a tab.

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8.2.1. General Settings

The following settings are available in this tab:

  • Echo input to output buffer: when checked, all input commands, including variable expansions, are echoed to the Output window. This is equivalent to using -echo screen on the command-line. There is no log file produced by default, since LAMMPS-GUI uses -log none.

  • Individual Windows / Combined Main Window: selects how the Output, Charts, Image, Slide Show, Variables, and Command window views are presented. With Individual Windows each of them is a window of its own, placed and stacked freely. With Combined Main Window they become panels docked around the editor: the editor keeps the center, the Charts, Image, and Slide Show views share a tabbed group on the right, and the Output, Variables, and Command window views share a group across the full width at the bottom. The panels have fixed places and are not dragged around; they are shown and hidden from the View menu, and the splitters between them can be moved to change their proportions. The windows opened on demand join them rather than floating above: a text viewer, an inspected data file or image, a slide show of image or movie files opened with View Image or Movie File(s)…, and a plot made with Plot Data File… all become further tabs of the group on the right, and are closed from their own File menu. A panel that shares its area with another is named by its tab, one that is alone by a title bar. The proportions are kept when the main window is resized and restored in the next session, and the main window remembers a size of its own for each of the two layouts. Changing this setting relaunches LAMMPS-GUI. A single session can be started in either layout without changing this setting, with the -j or -w command-line flag. In the combined window the views do not remember individual window sizes, and a keyboard shortcut that a view shares with the main window (for example Ctrl+S) is left to the main window, so only its menu entry remains for the view.

  • Include citation details: when checked, full citation info will be included in the Output window. This is equivalent to using -cite screen on the command-line.

  • Show Output window by default: when checked, the screen output of a LAMMPS run will be collected in an Output window during the run.

  • Show Charts window by default: when checked, the thermodynamic output of a LAMMPS run will be collected and displayed in a Charts window as line graphs.

  • Show Slide Show window by default: when checked, a Slide Show window will be shown with images from a dump image command, if present, in the LAMMPS input.

  • Open main window maximized: when checked, LAMMPS-GUI starts with its main window filling the screen instead of restoring the size it had when it was last closed. This applies to the combined main window only and is disabled for individual windows, where a maximized main window would cover the very windows it is meant to sit beside.

  • Download tutorial solutions enabled: this controls whether the “Download solutions” option is enabled by default when setting up a tutorial.

  • Open tutorial webpage enabled: this controls whether the “Open tutorial webpage in web browser” option is enabled by default when setting up a tutorial.

  • Select Default Font: Opens a font selection dialog where the type and size for the default font (used for everything but the editor and log) of the application can be set.

  • Select Text Font: Opens a font selection dialog where the type and size for the text editor and log font of the application can be set.

  • Data update interval: Allows the user to set, in milliseconds, the time interval between data updates during a LAMMPS run. The default is to update the data (for the Charts and Output windows) every 10 milliseconds. This is good for many cases. Set this to 100 milliseconds or more if LAMMPS-GUI consumes too many resources during a run. For LAMMPS runs that run very fast (for example in tutorial examples), however, data may be missed; this can be corrected by lowering this interval. However, this will make the GUI use more resources. This setting may be changed to a value between 1 and 1000 milliseconds.

  • Charts update interval: Allows the user to set, in milliseconds, the time interval between redrawing the plots in the Charts window. The default is to redraw the plots every 500 milliseconds. This is just for the drawing; data collection is managed with the previous setting.

  • HTTPS proxy setting: Allows the user to enter a URL for an HTTPS proxy. This may be needed when the LAMMPS input contains geturl commands or for downloading tutorial files from the Tutorials menu. If the https_proxy environment variable was set externally, its value is displayed but cannot be changed.

  • Download timeout: Sets the time, in seconds, after which a download (of tutorial files or the LAMMPS shared library) is aborted with an error message when no data has arrived. The default is 10 seconds. Users with a slow internet connection may want to increase this value so that the download of larger files, for example the LAMMPS shared library, is not canceled prematurely.

  • Path to LAMMPS Shared Library File: this option is only visible when LAMMPS-GUI was compiled to load the LAMMPS library at runtime instead of being linked to it directly. Using the Browse… button or by changing the text, a different shared library file with a different compilation of LAMMPS with different settings or from a different version can be loaded. The accompanying Download LAMMPS shared library… button retrieves a pre-built LAMMPS shared library from the LAMMPS web server. After changing this setting, LAMMPS-GUI needs to be re-launched. This setting is remembered separately for each compiler toolchain LAMMPS-GUI was built with, so for example an MSVC build and a MinGW build on the same machine each keep their own library: a library built against a different C runtime loads and runs, but its screen output would silently bypass the Output window.

  • Command window shell: selects the command interpreter that the Command window starts, from a list of the shells installed on the machine: on Unix-like systems the entries of /etc/shells that are actual shells (not nologin or a terminal multiplexer), on Windows cmd.exe, PowerShell, and a bash.exe from an installation such as Git for Windows, when present. A shell listed under more than one path (for example under both /bin and /usr/bin) is offered only once. The default is the user’s default shell (SHELL on Unix-like systems, COMSPEC on Windows). A change takes effect when the next shell starts: when the Command window is first opened, or on its File > Restart Shell.

8.2.2. Accelerators

This tab enables selection of an accelerator package and modification of some of its settings for use when running LAMMPS. This is equivalent to using the -sf and -pk flags on the command-line. Only settings supported by the LAMMPS library and local hardware are available. The Number of threads field allows setting the number of threads for the accelerator packages that support using threads (OPENMP, INTEL, KOKKOS, and GPU). Furthermore, the precision mode (double, mixed, or single) for the INTEL package can be selected, and for the GPU package, whether the neighbor lists are built on the GPU or the host (required for pair style hybrid) and whether only pair styles should be accelerated (i.e., run PPPM entirely on the CPU, which sometimes leads to better overall performance). Whether settings can be changed depends on which accelerator package is chosen (or “None”).

8.2.3. Snapshot Image

This tab allows setting defaults for the snapshot images displayed in the Image Viewer window, such as its dimensions, the zoom factor, and view angles. The Antialias switch will render images with double the number of pixels for width and height and then smoothly scale the image back to the requested size. This produces higher quality images with smoother edges at the expense of requiring more CPU time to render an initial image four times the size. The HQ Image mode option turns on “Screen Space Ambient Occlusion (SSAO)” mode when rendering images. This is also more time consuming, but produces a more ‘spatial’ representation of the system with shading of atoms by their depth. The Shiny Image mode option will render objects with a shiny surface when enabled. Otherwise, the surfaces will be matte. The Show Box option selects whether the system box is drawn as a colored set of sticks. Furthermore, the diameter of the sticks and their color can be set. Similarly, the Show Axes option selects whether a representation of the three system axes will be drawn or not (as colored and labeled arrows). In addition, the axes length and diameter can be set in fractions of the image size. The VDW Style checkbox selects whether atoms are represented by space filling spheres when checked or by smaller spheres and sticks. The Dynamic Bonds checkbox selects whether bonds between atoms shall be automatically determined from the atom distances (for instance to visualize simulations using force fields with implicit bonds), and the corresponding “Bond Cutoff” text field allows the user to set the cutoff used for that feature. Finally, there are a couple of text fields to select the two Background Colors. If the two colors differ, there will be a vertical background gradient starting with the “Background” color at the bottom and ending with the “Background2” color at the top.

These settings correspond to the available settings for the LAMMPS dump image and corresponding dump_modify commands.

8.2.4. Editor Settings

This tab allows adjusting settings of the editor window. Specifically, the amount of padding to be added to LAMMPS commands, types or type ranges, IDs (e.g., for fixes), and names (e.g., for groups). The value set is the minimum width for the text element and it can be chosen in the range between 1 and 32.

The three settings which follow enable or disable the automatic reformatting when hitting the ‘Enter’ key, the automatic display of the completion pop-up window, and whether auto-save mode is enabled. In auto-save mode, the editor buffer is saved before a run or before exiting LAMMPS-GUI.

The last setting enables or disables (default: enabled) the static input check (see the Check Input via Heuristics entry of the Run menu) that runs automatically before every run. Only error-level findings, which would make LAMMPS reject the input, open a dialog asking whether to run anyway; warnings are only noted in the status bar.

8.2.5. Charts Settings

This tab allows adjusting settings of the Charts window. Specifically, one can set the default chart title (if the title contains ‘%f’ it will be replaced with the name of the current input file), one can select whether by default the raw data, the smoothed data, or both will be plotted, the default smoothing parameters, the default size of the chart graph in pixels, and whether you want to display major and minor grid lines.

The Raw data, Processed data, and Error bars groups hold the defaults of the per-chart Chart Style… dialog (see Adjust chart style): the display style (Lines, Points, or Lines + Points), the color, the line width, and the point size of the two data series, plus the color and line width of the error bars that imported data can carry. Changing a color here also applies to charts that are already open, since a chart only stores a color of its own once one is picked in its Chart Style… dialog; the widths and display styles are picked up by charts created afterwards.