ICODE-ADC/lammps
4
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases Wiki Activity

document new features

Browse Source
This commit is contained in:
Axel Kohlmeyer
2024-07-17 19:14:22 -04:00
parent 955db30b32
commit 2e2dc2abe5
1 changed files with 48 additions and 29 deletions
Download Patch File Download Diff File Expand all files Collapse all files

77
doc/src/Howto_lammps_gui.rst
View File

@ -264,9 +264,17 @@ displays the images created by LAMMPS as they are written.
The various buttons at the bottom right of the window allow single
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 <https://ffmpeg.org/>`_ is
installed.
zoom in or zoom out of the displayed images. The button on the very
left triggers an export of the slide show animation to a movie file,
provided the `FFmpeg program <https://ffmpeg.org/>`_ is installed.
.. versionadded:: 1.6
When clicking on the "garbage can" icon, all image files used for the
slide show will be deleted. Since their number can be large for long
simulations, this allows to safely clean up clutter in the working
directory.
Variable Info
-------------
@ -298,26 +306,37 @@ record a log for each run attempt by using the command
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
-----------------------
Snapshot Image Viewer
---------------------
By selecting the ``Create Image`` entry in the ``Run`` menu, or by
hitting the `Ctrl-I` (`Command-I` on macOS) keyboard shortcut, or by
clicking on the "palette" button in the status bar, LAMMPS GUI will send
a custom :doc:`write_dump image <dump_image>` command to LAMMPS and read
the resulting snapshot image with the current state of the system into
an image viewer window. This functionality is not available *during* an
ongoing run. When LAMMPS is not yet initialized, LAMMPS GUI will try to
identify the line with the first run or minimize command and execute all
command up to that line from the input buffer and then add a "run 0"
command. This will initialize the system so an image of the initial
state of the system can be rendered. If there was an error, the
snapshot image viewer will not appear.
clicking on the "palette" button in the status bar of the *Editor*
window, LAMMPS-GUI will send a custom :doc:`write_dump image
<dump_image>` command to LAMMPS and read the resulting snapshot image
with the current state of the system into an image viewer window. This
functionality is *not* available *during* an ongoing run since it is
sending commands to LAMMPS. When LAMMPS is not yet initialized,
LAMMPS-GUI will try to identify the line with the first run or minimize
command and execute all commands up to that line from the input buffer
and then add a "run 0" command. This will initialize the system so an
image of the initial state of the system can be rendered. If there was
an error, the snapshot image viewer will not appear.
When possible, LAMMPS GUI will try to detect which elements the atoms
correspond to (via their mass) and then colorize them in the image
accordingly. Otherwise the default predefined sequence of colors is
assigned to the different atom types.
.. versionadded: 1.6
Assignment of atom diameters from Lennard-Jones *sigma* values
When possible, LAMMPS-GUI will try to detect which elements the atoms
correspond to (via their mass) and then colorize them in the image and
set their atom diameters accordingly. If this is not possible, for
instance when using reduced (= 'lj') :doc:`units <units>`, then
LAMMPS-GUI will check the current pair style and if it is a
Lennard-Jones potential from which it will extract the *sigma* parameter
for each atom type and assign atom diamaters from those numbers.
Otherwise the default predefined sequence of colors is assigned to the
different atom types and the diameters are all the same.
.. image:: JPG/lammps-gui-image.png
:align: center
@ -339,21 +358,21 @@ may take several seconds. From the ``File`` menu of the image window,
the current image can be saved to a file or copied into the
cut-n-paste buffer for pasting into another application.
Editor Functions
----------------
Editor Window
-------------
The editor has most of the usual functionality that similar programs
have: text selection via mouse or with cursor moves while holding the
Shift key, Cut (`Ctrl-X`), Copy (`Ctrl-C`), Paste (`Ctrl-V`), Undo
(`Ctrl-Z`), Redo (`Ctrl-Shift-Z`), Select All (`Ctrl-A`). When trying
to exit the editor with a modified buffer, a dialog will pop up asking
whether to cancel the exit operation, or to save or not save the buffer
contents to a file.
The *Editor* window of LAMMPS-GUI has most of the usual functionality
that similar programs have: text selection via mouse or with cursor
moves while holding the Shift key, Cut (`Ctrl-X`), Copy (`Ctrl-C`),
Paste (`Ctrl-V`), Undo (`Ctrl-Z`), Redo (`Ctrl-Shift-Z`), Select All
(`Ctrl-A`). When trying to exit the editor with a modified buffer, a
dialog will pop up asking whether to cancel the exit operation, or to
save or not save the buffer contents to a file.
Context Specific Word Completion
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
By default, LAMMPS GUI will display a small pop-up frame with possible
By default, LAMMPS-GUI will display a small pop-up frame with possible
choices for LAMMPS input script commands or styles after 2 characters of
a word have been typed.