Add mini ToC for HowTo only and reorganize the introduction
This commit is contained in:
Axel Kohlmeyer
@ -498,3 +498,7 @@ systems. Some unit and regression testing is applied as well.
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A detailed discussion of the LAMMPS developer GitHub workflow can be
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found in the file `doc/github-development-workflow.md
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<https://github.com/lammps/lammps/blob/develop/doc/github-development-workflow.md>`_
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.. raw:: latex
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\clearpage
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@ -1,36 +1,25 @@
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Using LAMMPS-GUI
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================
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LAMMPS-GUI is a graphical text editor programmed using the `Qt Framework
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<https://www.qt.io/>`_ and customized for editing LAMMPS input files. It
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is linked to the :ref:`LAMMPS library <lammps_c_api>` and thus can run
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LAMMPS directly using the contents of the editor's text buffer as input.
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It *differs* from other known interfaces to LAMMPS in that it can
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retrieve and display information from LAMMPS *while it is running*,
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display visualizations created with the :doc:`dump image command
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<dump_image>`, can launch the online LAMMPS documentation for known
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LAMMPS commands and styles, and directly integrates with a collection
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of LAMMPS tutorials (:ref:`Gravelle1 <Gravelle1>`).
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This document describes **LAMMPS-GUI version 1.6**.
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-----
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LAMMPS-GUI is a graphical text editor customized for editing LAMMPS
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input files that is linked to the :ref:`LAMMPS library <lammps_c_api>`
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and thus can run LAMMPS directly using the contents of the editor's text
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buffer as input. It can retrieve and display information from LAMMPS
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while it is running, display visualizations created with the :doc:`dump
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image command <dump_image>`, and is adapted specifically for editing
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LAMMPS input files through text completion and reformatting, and linking
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to the online LAMMPS documentation for known LAMMPS commands and styles.
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.. contents::
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.. note::
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Pre-compiled, ready-to-use LAMMPS-GUI executables for Linux x86\_64
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(Ubuntu 20.04LTS or later and compatible), macOS (version 11 aka Big
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Sur or later), and Windows (version 10 or later) :ref:`are available
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<lammps_gui_install>` for download. Non-MPI LAMMPS executables (as
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``lmp``) for running LAMMPS from the command-line and :doc:`some
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LAMMPS tools <Tools>` compiled executables are also included. Also,
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the pre-compiled LAMMPS-GUI packages include the WHAM executables
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from http://membrane.urmc.rochester.edu/content/wham/ for use with
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LAMMPS tutorials documented in this paper (:ref:`Gravelle1
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<Gravelle1>`).
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The source code for LAMMPS-GUI is included in the LAMMPS source code
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distribution and can be found in the ``tools/lammps-gui`` folder. It
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can be compiled alongside LAMMPS when :doc:`compiling with CMake
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<Build_cmake>`.
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----
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LAMMPS-GUI tries to provide an experience similar to what people
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traditionally would have running LAMMPS using a command-line window and
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@ -65,8 +54,8 @@ simple LAMMPS simulations. It is very suitable for tutorials on LAMMPS
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since you only need to learn how to use a single program for most tasks
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and thus time can be saved and people can focus on learning LAMMPS.
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The tutorials at https://lammpstutorials.github.io/ are specifically
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updated for use with LAMMPS-GUI and can their tutorial materials can
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be downloaded and loaded directly from the GUI.
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updated for use with LAMMPS-GUI and their tutorial materials can
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be downloaded and edited directly from the GUI.
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Another design goal is to keep the barrier low when replacing part of
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the functionality of LAMMPS-GUI with external tools. That said, LAMMPS-GUI
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@ -79,10 +68,31 @@ has some unique functionality that is not found elsewhere:
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- monitoring of simulation progress
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- interactive visualization using the :doc:`dump image <dump_image>`
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command with the option to copy-paste the resulting settings
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- automatic slide show generation from dump image out at runtime
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- automatic plotting of thermodynamics data at runtime
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- automatic slide show generation from dump image output at runtime
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- automatic plotting of thermodynamic data at runtime
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- inspection of binary restart files
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.. admonition:: Download LAMMPS-GUI for your platform
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:class: Hint
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Pre-compiled, ready-to-use LAMMPS-GUI executables for Linux x86\_64
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(Ubuntu 20.04LTS or later and compatible), macOS (version 11 aka Big
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Sur or later), and Windows (version 10 or later) :ref:`are available
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<lammps_gui_install>` for download. Non-MPI LAMMPS executables (as
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``lmp``) for running LAMMPS from the command-line and :doc:`some
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LAMMPS tools <Tools>` compiled executables are also included. Also,
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the pre-compiled LAMMPS-GUI packages include the WHAM executables
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from http://membrane.urmc.rochester.edu/content/wham/ for use with
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LAMMPS tutorials documented in this paper (:ref:`Gravelle1
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<Gravelle1>`).
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The source code for LAMMPS-GUI is included in the LAMMPS source code
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distribution and can be found in the ``tools/lammps-gui`` folder. It
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can be compiled alongside LAMMPS when :doc:`compiling with CMake
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<Build_cmake>`.
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-----
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The following text provides a detailed tour of the features and
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functionality of LAMMPS-GUI. Suggestions for new features and
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reports of bugs are always welcome. You can use the :doc:`the same
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@ -93,9 +103,11 @@ channels as for LAMMPS itself <Errors_bugs>` for that purpose.
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Installing Pre-compiled LAMMPS-GUI Packages
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-------------------------------------------
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LAMMPS-GUI is available as pre-compiled binary packages for Linux
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x86\_64, macOS 11 and later, and Windows 10 and later. Alternately, it
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can be compiled from source.
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LAMMPS-GUI is available for download as pre-compiled binary packages for
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Linux x86\_64, macOS 11 and later, and Windows 10 and later from the
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`LAMMPS release pages on GitHub <https://github.com/lammps/lammps/releases/>`_.
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A backup download location is at https://download.lammps.org/static/
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Alternately, LAMMPS-GUI can be compiled from source when building LAMMPS.
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Windows 10 and later
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^^^^^^^^^^^^^^^^^^^^
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@ -467,11 +479,11 @@ correspond to (via their mass) and then colorize them in the image and
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set their atom diameters accordingly. If this is not possible, for
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instance when using reduced (= 'lj') :doc:`units <units>`, then
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LAMMPS-GUI will check the current pair style and if it is a
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Lennard-Jones type potential, it will extract the *sigma* parameter
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for each atom type and assign atom diameters from those numbers.
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For cases where atom diameters are not auto-detected, the *Atom size* field
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can be edited and a suitable value set manually. The default value
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is inferred from the x-direction lattice spacing.
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Lennard-Jones type potential, it will extract the *sigma* parameter for
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each atom type and assign atom diameters from those numbers. For cases
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where atom diameters are not auto-detected, the *Atom size* field can be
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edited and a suitable value set manually. The default value is inferred
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from the x-direction lattice spacing.
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If elements cannot be detected the default sequence of colors of the
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:doc:`dump image <dump_image>` command is assigned to the different atom
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@ -1027,3 +1039,7 @@ Window), and `Ctrl-Q` (Quit Application) are supported.
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.. _Gravelle2:
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**(Gravelle2)** Gravelle https://lammpstutorials.github.io/
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.. raw:: latex
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\clearpage
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