From e7b9bc2d4fbbac36a001e547c19a378eb07e0269 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Fri, 29 Sep 2023 18:53:18 -0400 Subject: [PATCH] update docs --- doc/src/Howto_lammps_gui.rst | 50 ++++++++++++++++++++++++------------ 1 file changed, 34 insertions(+), 16 deletions(-) diff --git a/doc/src/Howto_lammps_gui.rst b/doc/src/Howto_lammps_gui.rst index 4492a13915..0b5237d1f6 100644 --- a/doc/src/Howto_lammps_gui.rst +++ b/doc/src/Howto_lammps_gui.rst @@ -172,17 +172,19 @@ be seen in the command line window, as shown below. LAMMPS GUI captures the screen output as it is generated and updates the log window regularly during a run. -By default, there will be a new window for each run, so that it is -possible to visually compare outputs from different runs. It is also -possible to change the behavior of LAMMPS GUI in the preferences dialog -to *replace* an existing log window for a new run or to not show the log -window by default. It is also possible to show or hide the current log -window from the ``View`` menu. +By default, the log window will be replaced each time a run is started. +The runs are counted and the run number for the current run is displayed +in the window title. It is possible to change the behavior of LAMMPS +GUI in the preferences dialog to create a *new* log window for every run +or to not show the current log window. It is also possible to show or +hide the *current* log window from the ``View`` menu. The text in the log window is read-only and cannot be modified, but -editor commands to select and copy all or parts of the text can be used. -The "Select All" and "Copy" functions are also available via a context -menu by clicking with the right mouse button. +editor hotkeys to select and copy all or parts of the text can be used +to transfer text to another editor program. The "Select All" and "Copy" +functions, as well as a "Save Log to File" option are also available via +a context menu by clicking with the right mouse button into the log +window text area. Chart Window ------------ @@ -199,10 +201,16 @@ The drop down menu on the top right allows selection of different properties that are computed and written to thermo output. Only one property can be shown at a time. The plots will be updated with new data as the run progresses, so they can be used to visually monitor the -evolution of available properties. From the ``File`` menu on the top -left, it is possible to save an image of the currently displayed plot or -export the data in either plain text columns (for use by plotting tools -like `gnuplot `_ or `grace +evolution of available properties. The window title will show the +current run number that this chart window corresponds to. Same as +explained for the log window above, by default, the chart window will +be replaced on each new run, but the behavior can be changed in the +preferences dialog. + +From the ``File`` menu on the top left, it is possible to save an image +of the currently displayed plot or export the data in either plain text +columns (for use by plotting tools like `gnuplot +`_ or `grace `_), or as CSV data which can be imported for further processing with Microsoft Excel or `pandas `_ @@ -230,8 +238,7 @@ stepping through the sequence of images or playing an animation (as a continuous loop or once from first to last). It is also possible to zoom in or zoom out of the displayed images, and to export the slide show animation to a movie file, if `ffmpeg `_ is -installed. The slide show window will be closed when a new file is -loaded. +installed. Variable Info ------------- @@ -252,6 +259,17 @@ 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 flags, via the "Set Variables..." dialog from the ``Run`` menu. +LAMMPS GUI will automatically set the variable "gui_run" to the +current value of the run counter. That way it would be possible +to automatically record a log for each run attempt by using the +command + +.. code-block:: LAMMPS + + log logfile-${gui_run}.txt + +at the beginning of an input file. That would record logs to files +``logfile-1.txt``, ``logfile-2.txt``, and so on for successive runs. Viewing Snapshot Images ----------------------- @@ -518,7 +536,7 @@ General Settings: - *Replace image window on new render:* when checked, an existing 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 options is only available +- *Path to LAMMPS Shared Library File:* this option is only visible 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