From 955db30b326873367f36ec53dcfaee131ec3882e Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Wed, 17 Jul 2024 19:14:04 -0400 Subject: [PATCH] use LAMMPS-GUI consistently --- doc/src/Howto_lammps_gui.rst | 60 ++++++++++++++++++------------------ doc/src/Tools.rst | 26 ++++++++-------- 2 files changed, 43 insertions(+), 43 deletions(-) diff --git a/doc/src/Howto_lammps_gui.rst b/doc/src/Howto_lammps_gui.rst index dd85df5498..e8872d423c 100644 --- a/doc/src/Howto_lammps_gui.rst +++ b/doc/src/Howto_lammps_gui.rst @@ -1,11 +1,11 @@ -Using the LAMMPS GUI +Using the LAMMPS-GUI ==================== -This document describes **LAMMPS GUI version 1.6**. +This document describes **LAMMPS-GUI version 1.6**. ----- -LAMMPS GUI is a graphical text editor customized for editing LAMMPS +LAMMPS-GUI is a graphical text editor customized for editing LAMMPS input files that is linked to the :ref:`LAMMPS library ` and thus can run LAMMPS directly using the contents of the editor's text buffer as input. It can retrieve and display information from LAMMPS @@ -16,17 +16,17 @@ to the online LAMMPS documentation for known LAMMPS commands and styles. .. note:: - Pre-compiled, ready-to-use LAMMPS GUI executables for Linux (Ubuntu + Pre-compiled, ready-to-use LAMMPS-GUI executables for Linux (Ubuntu 20.04LTS or later and compatible), macOS (version 11 aka Big Sur or later), and Windows (version 10 or later) :ref:`are available ` for download. None-MPI LAMMPS executables of the same LAMMPS version are included in these packages as well. The - source code for the LAMMPS GUI is included in the LAMMPS source code + source code for the LAMMPS-GUI is included in the LAMMPS source code distribution and can be found in the ``tools/lammps-gui`` folder. It can be compiled alongside LAMMPS when :doc:`compiling with CMake `. -LAMMPS GUI tries to provide an experience similar to what people +LAMMPS-GUI tries to provide an experience similar to what people traditionally would do to run LAMMPS using a command line window but just rolled into a single executable: @@ -42,13 +42,13 @@ that they are most comfortable with. It is often *required* to adopt this workflow when running LAMMPS simulations on high-performance computing facilities. -The main benefit of using the LAMMPS GUI application instead is that +The main benefit of using the LAMMPS-GUI application instead is that many basic tasks can be done directly from the GUI without switching to a text console window or using external programs, let alone writing scripts to extract data from the generated output. It also integrates well with graphical desktop environments. -LAMMPS GUI thus makes it easier for beginners to get started running +LAMMPS-GUI thus makes it easier for beginners to get started running simple LAMMPS simulations. It is very suitable for tutorials on LAMMPS since you only need to learn how to use a single program for most tasks and thus time can be saved and people can focus on learning LAMMPS. It @@ -58,7 +58,7 @@ visualization and analysis tools, and run LAMMPS from the command line or a batch script. The following text provides a detailed tour of the features and -functionality of the LAMMPS GUI. Suggestions for new features and +functionality of the LAMMPS-GUI. Suggestions for new features and reports of bugs are always welcome. You can use the :doc:`the same channels as for LAMMPS itself ` for that purpose. @@ -67,7 +67,7 @@ channels as for LAMMPS itself ` for that purpose. Main window ----------- -When LAMMPS GUI starts, it will show a main window, the editor, with +When LAMMPS-GUI starts, it will show a main window, the editor, with either an empty buffer or the contents of a loaded file. In the latter case it may look like the following: @@ -88,9 +88,9 @@ window will be stored when exiting and restored when starting again. Opening Files ^^^^^^^^^^^^^ -The LAMMPS GUI application will try to open the first command line +The LAMMPS-GUI application will try to open the first command line argument as a LAMMPS input script, further arguments are ignored. -When no argument is given, LAMMPS GUI will start with an empty buffer. +When no argument is given, LAMMPS-GUI will start with an empty buffer. Files can also be opened via the ``File`` menu or by drag-and-drop of a file from a graphical file manager into the editor window. Only one file can be edited at a time, so opening a new file with a filled buffer @@ -103,7 +103,7 @@ or by clicking on the "Save" button at the very left in the status bar. Running LAMMPS ^^^^^^^^^^^^^^ -From within the LAMMPS GUI main window LAMMPS can be started either from +From within the LAMMPS-GUI main window LAMMPS can be started either from the ``Run`` menu using the ``Run LAMMPS from Editor Buffer`` entry, by the keyboard shortcut `Ctrl-Enter` (`Command-Enter` on macOS), or by clicking on the green "Run" button in the status bar. All of these @@ -182,7 +182,7 @@ would normally be seen in the command line window, as shown below. :align: center :scale: 50% -LAMMPS GUI captures the screen output from LAMMPS as it is generated and +LAMMPS-GUI captures the screen output from LAMMPS as it is generated and updates the *Output* window regularly during a run. By default, the *Output* window will be replaced each time a run is started. @@ -205,7 +205,7 @@ right mouse button into the *Output* window text area. :scale: 50% .. versionadded:: 1.6 - + Should the *Output* window contain embedded YAML format text (see above for a demonstration), for example from using :doc:`thermo_style yaml ` or :doc:`thermo_modify line yaml `, the @@ -213,7 +213,7 @@ keyboard shortcut `Ctrl-Y` (`Command-Y` on macOS) is available to save only the YAML parts to a file. This option is also available from a context menu by clicking with the right mouse button into the *Output* window text area. - + Charts Window ------------- @@ -282,7 +282,7 @@ below. :align: center :scale: 75% -Like the *Output* and *Charts* windows, its content is continuously +Like for the *Output* and *Charts* windows, its content is continuously updated during a run. It will show "(none)" if there are no variables defined. Note that it is also possible to *set* :doc:`index style variables `, that would normally be set via command line @@ -396,7 +396,7 @@ Context Specific Help :align: center :scale: 50% -A unique feature of the LAMMPS GUI is the option to look up the +A unique feature of the LAMMPS-GUI is the option to look up the 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 clicking the mouse there are additional entries in the @@ -426,7 +426,7 @@ The ``File`` menu offers the usual options: a dialog will open to select a new file name - ``Save As`` will open a dialog to select and new file name and save the buffer to it -- ``Quit`` will exit LAMMPS GUI. If there are unsaved changes, a dialog +- ``Quit`` will exit LAMMPS-GUI. If there are unsaved changes, a dialog will appear to either cancel the operation, or to save or not save the edited file. @@ -447,7 +447,7 @@ 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 +the LAMMPS-GUI is linked to the LAMMPS library and thus can run LAMMPS internally through the :ref:`LAMMPS C-library interface `. @@ -491,12 +491,12 @@ in an ``Image Viewer`` window. The ``View in OVITO`` entry will launch `OVITO `_ with a :doc:`data file ` containing the current state of -the system. This option is only available if the LAMMPS GUI can find +the system. This option is only available if the LAMMPS-GUI can find the OVITO executable in the system path. The ``View in VMD`` entry will launch VMD with a :doc:`data file ` containing the current state of the system. This option -is only available if the LAMMPS GUI can find the VMD executable in the +is only available if the LAMMPS-GUI can find the VMD executable in the system path. View @@ -514,8 +514,8 @@ 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`` 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 Howto`` +number of LAMMPS-GUI itself. The ``Quick Help`` displays a dialog +with a minimal description of LAMMPS-GUI. The ``LAMMPS-GUI Howto`` entry will open this documentation page from the online documentation in a web browser window. The ``LAMMPS Manual`` entry will open the main page of the LAMMPS documentation in the web browser. @@ -526,7 +526,7 @@ Preferences ----------- The ``Preferences`` dialog allows customization of the behavior and -look of the LAMMPS GUI application. The settings are grouped and each +look of the LAMMPS-GUI application. The settings are grouped and each group is displayed within a tab. .. |guiprefs1| image:: JPG/lammps-gui-prefs-general.png @@ -547,9 +547,9 @@ General Settings: ^^^^^^^^^^^^^^^^^ - *Echo input to log:* when checked, all input commands, including - variable expansions, will be echoed to the log window. This is + variable expansions, will be echoed to the *Output* window. This is equivalent to using `-echo screen` at the command line. There is no - log *file* produced by default, since LAMMPS GUI uses `-log none`. + log *file* produced by default, since LAMMPS-GUI uses `-log none`. - *Include citation details:* when checked full citation info will be included to the log window. This is equivalent to using `-cite screen` on the command line. @@ -571,12 +571,12 @@ General Settings: chart window will be replaced when a new snapshot image is requested, otherwise each command will create a new image window. - *Path to LAMMPS Shared Library File:* this option is only visible - when LAMMPS GUI was compiled to load the LAMMPS library at run time + when LAMMPS-GUI was compiled to load the LAMMPS library at run time instead of being linked to it directly. With 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. After this setting was changed, - LAMMPS GUI needs to be re-launched. + LAMMPS-GUI needs to be re-launched. - *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. @@ -691,7 +691,7 @@ available (On macOS use the Command key instead of Ctrl/Control). - Ctrl+Shift+H - Quick Help - Ctrl+Shift+G - - LAMMPS GUI Howto + - LAMMPS-GUI Howto * - Ctrl+Shift+M - LAMMPS Manual - Ctrl+? diff --git a/doc/src/Tools.rst b/doc/src/Tools.rst index 48af3eba98..102d240f57 100644 --- a/doc/src/Tools.rst +++ b/doc/src/Tools.rst @@ -93,7 +93,7 @@ Miscellaneous tools * :ref:`i-PI ` * :ref:`kate ` * :ref:`LAMMPS shell ` - * :ref:`LAMMPS GUI ` + * :ref:`LAMMPS-GUI ` * :ref:`LAMMPS magic patterns for file(1) ` * :ref:`Offline build tool ` * :ref:`singularity/apptainer ` @@ -656,7 +656,7 @@ you first need to use the :doc:`clear` command. .. _lammps_gui: -LAMMPS GUI +LAMMPS-GUI ---------- .. versionadded:: 2Aug2023 @@ -664,7 +664,7 @@ LAMMPS GUI Overview ^^^^^^^^ -LAMMPS GUI is a graphical text editor customized for editing LAMMPS +LAMMPS-GUI is a graphical text editor customized for editing LAMMPS input files that is linked to the :ref:`LAMMPS C-library ` and thus can run LAMMPS directly using the contents of the editor's text buffer as input. It can retrieve and display information from LAMMPS @@ -693,7 +693,7 @@ Features A detailed discussion and explanation of all features and functionality are in the :doc:`Howto_lammps_gui` tutorial Howto page. -Here are a few highlights of LAMMPS GUI +Here are a few highlights of LAMMPS-GUI - Text editor with syntax highlighting customized for LAMMPS - Text editor features command completion for known commands and styles @@ -717,19 +717,19 @@ Parallelization ^^^^^^^^^^^^^^^ Due to its nature as a graphical application, it is not possible to use -the LAMMPS GUI in parallel with MPI, but OpenMP multi-threading and GPU +the LAMMPS-GUI in parallel with MPI, but OpenMP multi-threading and GPU acceleration is available and enabled by default. Prerequisites and portability ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ -LAMMPS GUI is programmed in C++ based on the C++11 standard and using +LAMMPS-GUI is programmed in C++ based on the C++11 standard and using the `Qt GUI framework `_. Currently, Qt version 5.12 or later is required; Qt 5.15LTS is recommended; support for Qt version 6.x is available. Building LAMMPS with CMake is required. -The LAMMPS GUI has been successfully compiled and tested on: +The LAMMPS-GUI has been successfully compiled and tested on: - Ubuntu Linux 20.04LTS x86_64 using GCC 9, Qt version 5.12 - Fedora Linux 40 x86\_64 using GCC 14 and Clang 17, Qt version 5.15LTS @@ -749,20 +749,20 @@ available from https://download.lammps.org/static or https://github.com/lammps/lammps/releases. You can unpack the archives (or mount the macOS disk image) and run the GUI directly in place. The folder may also be moved around and added to the ``PATH`` environment -variable so the executables will be found automatically. The LAMMPS GUI +variable so the executables will be found automatically. The LAMMPS-GUI executable is called ``lammps-gui`` and either takes no arguments or attempts to load the first argument as LAMMPS input file. Compilation ^^^^^^^^^^^ -The source for the LAMMPS GUI is included with the LAMMPS source code +The source for the LAMMPS-GUI is included with the LAMMPS source code distribution in the folder ``tools/lammps-gui`` and thus it can be can be built as part of a regular LAMMPS compilation. :doc:`Using CMake ` is required. To enable its compilation, the CMake variable ``-D BUILD_LAMMPS_GUI=on`` must be set when creating the CMake configuration. All other settings (compiler, flags, compile type) for -LAMMPS GUI are then inherited from the regular LAMMPS build. If the Qt +LAMMPS-GUI are then inherited from the regular LAMMPS build. If the Qt library is packaged for Linux distributions, then its location is typically auto-detected since the required CMake configuration files are stored in a location where CMake can find them without additional help. @@ -775,7 +775,7 @@ Qt6_DIR=/path/to/qt6/lib/cmake/Qt6``, if necessary. When both, Qt5 and Qt6 are available, Qt6 will be preferred unless ``-D LAMMPS_GUI_USE_QT5=yes`` is set. -It is possible to build the LAMMPS GUI as a standalone compilation +It is possible to build the LAMMPS-GUI as a standalone compilation (e.g. when LAMMPS has been compiled with traditional make). Then the CMake configuration needs to be told where to find the LAMMPS headers and the LAMMPS library, via ``-D LAMMPS_SOURCE_DIR=/path/to/lammps/src``. @@ -831,13 +831,13 @@ There is a custom `x64-GUI-MSVC` build configuration provided in the compilation settings for project. Choosing this configuration will activate building the `lammps-gui.exe` executable in addition to LAMMPS through importing package selection from the ``windows.cmake`` preset -file and enabling building the LAMMPS GUI and disabling building with MPI. +file and enabling building the LAMMPS-GUI and disabling building with MPI. When requesting an installation from the `Build` menu in Visual Studio, it will create a compressed ``LAMMPS-Win10-amd64.zip`` zip file with the executables and required dependent .dll files. This zip file can be uncompressed and ``lammps-gui.exe`` run directly from there. The uncompressed folder can be added to the ``PATH`` environment and LAMMPS -and LAMMPS GUI can be launched from anywhere from the command line. +and LAMMPS-GUI can be launched from anywhere from the command line. **MinGW64 Cross-compiler**