From 211099b7caef05a523e90de89d4b6ad25d65a05f Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Fri, 27 Dec 2024 22:57:51 -0500 Subject: [PATCH] small updates and corrections to the LAMMPS-GUI howto --- doc/src/Howto_lammps_gui.rst | 31 ++++++++++++++++++++++--------- 1 file changed, 22 insertions(+), 9 deletions(-) diff --git a/doc/src/Howto_lammps_gui.rst b/doc/src/Howto_lammps_gui.rst index 58d42c0bde..67260519ea 100644 --- a/doc/src/Howto_lammps_gui.rst +++ b/doc/src/Howto_lammps_gui.rst @@ -100,10 +100,11 @@ MacOS 11 and later ^^^^^^^^^^^^^^^^^^ After downloading the ``LAMMPS-macOS-multiarch-GUI-.dmg`` -installer package, you need to double-click it and then, in the window -that opens, drag the app bundle as indicated into the "Applications" -folder. The follow the instructions in the "README.txt" file to -get access to the other included executables. +application bundle disk image, you need to double-click it and then, in +the window that opens, drag the app bundle as indicated into the +"Applications" folder. Afterwards, the disk image can be unmounted. +Then follow the instructions in the "README.txt" file to get access to +the other included command-line executables. Linux on x86\_64 ^^^^^^^^^^^^^^^^ @@ -117,15 +118,25 @@ into the "LAMMPS_GUI" folder and execute "./lammps-gui" directly. The second variant uses `flatpak `_ and requires the flatpak management and runtime software to be installed. -After downloading the ``LAMMPS-GUI-Linux-x86_64-GUI-.tar.gz`` +After downloading the ``LAMMPS-GUI-Linux-x86_64-GUI-.flatpak`` flatpak bundle, you can install it with ``flatpak install --user -LAMMPS-GUI-Linux-x86_64-GUI-.tar.gz``. After installation, +LAMMPS-GUI-Linux-x86_64-GUI-.flatpak``. After installation, LAMMPS-GUI should be integrated into your desktop environment under "Applications > Science" but also can be launched from the console with ``flatpak run org.lammps.lammps-gui``. The flatpak bundle also includes the console LAMMPS executable ``lmp`` which can be launched to run -simulations with, for example: ``flatpak run --command=lmp -org.lammps.lammps-gui -in in.melt``. +simulations with, for example with: + +.. code-block:: sh + + flatpak run --command=lmp org.lammps.lammps-gui -in in.melt + +Other bundled command-line executables are run the same way and can be +listed with: + +.. code-block:: sh + + ls $(flatpak info --show-location org.lammps.lammps-gui )/files/bin Compiling from Source @@ -268,7 +279,9 @@ This text would normally be seen in the command-line window. :scale: 50% LAMMPS-GUI captures the screen output from LAMMPS as it is generated and -updates the *Output* window regularly during a run. +updates the *Output* window regularly during a run. If there are any +warnings or errors in the LAMMPS output, they are highlighted by using +bold text colored in red. By default, the *Output* window is replaced each time a run is started. The runs are counted and the run number for the current run is displayed