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use LAMMPS-GUI consistently

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Axel Kohlmeyer
2024-07-17 19:14:04 -04:00
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doc/src/Howto_lammps_gui.rst
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@ -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 <lammps_c_api>`
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
<lammps_gui_install>` 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
<Build_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 <Errors_bugs>` for that purpose.
@ -67,7 +67,7 @@ channels as for LAMMPS itself <Errors_bugs>` 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
<thermo_style>` or :doc:`thermo_modify line yaml <thermo_modify>`, 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 <variable>`, 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
<lammps_c_api>`.
@ -491,12 +491,12 @@ in an ``Image Viewer`` window.
The ``View in OVITO`` entry will launch `OVITO <https://ovito.org>`_
with a :doc:`data file <write_data>` 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
<write_data>` 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+?

26
doc/src/Tools.rst
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@ -93,7 +93,7 @@ Miscellaneous tools
* :ref:`i-PI <ipi>`
* :ref:`kate <kate>`
* :ref:`LAMMPS shell <lammps_shell>`
* :ref:`LAMMPS GUI <lammps_gui>`
* :ref:`LAMMPS-GUI <lammps_gui>`
* :ref:`LAMMPS magic patterns for file(1) <magic>`
* :ref:`Offline build tool <offline>`
* :ref:`singularity/apptainer <singularity_tool>`
@ -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 <lammps_c_api>`
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 <https://www.qt.io/product/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
<Howto_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**