New binary LAMMPS-GUI packages (v1.6.2) with the latest bugfixes and improvements have been posted to LAMMPS Testing Repository: .
This is to add some improvements for an upcoming publication of revised LAMMPS tutorials and in anticipation of the upcoming stable release of LAMMPS.
Thus, if you have a little time, please download this new version and give it a try and report any problems or suggestions for further improvements. Either here (by preference) or via email to me personally. The manual has been updated and a PDF of that updated version is available for download as well.
Thanks in advance for any feedback.
Here are the most important changes:
the name LAMMPS-GUI is used consistently
more consistent and compact window titles
the main window (Editor) has a new shortcut button (bottom left) to save the buffer
in the snapshot image viewer it is now possible to copy the dump and dump modify command lines with all settings use to the clipboard, so that they can be inserted into the LAMMPS input in the Editor window (from the File menu or with keyboard shortcut CTRL-D)
the snapshot image viewer can assign atom diameters based on “sigma” value from Lennard-Jones potentials (for as long as they can be retrieved through Pair::extract()). This is useful when using reduced units (= lj) since the default method based on atomic masses will fail.
from the slideshow viewer it is now possible to delete all image files that it knows about
when using “thermo_style yaml” or “thermo_modify line yaml” it is now possible to export only the YAML data from the output/log window to a file (from the context menu or with CTRL-Y) for easy post-processing
many forms of crashes have been avoided warnings printed by Qt reduced
the default setting for polling LAMMPS for thermo data has been reduced from 100ms to 10ms to better accommodate small/fast tutorial examples
New binary LAMMPS-GUI packages (v1.6.3) with the latest bugfixes and improvements have been posted to LAMMPS Testing Repository: . .
This version adds a text file viewer which can be opened from either the menu, CTRL-SHIFT-F, or from the context menu when right clicking on a file name in a LAMMPS input in the editor window.
As usually, any feedback (also to other parts of the LAMMPS-GUI) are welcome.
There is another update with LAMMPS-GUI version 1.6.4.
This now adds YAML file support for the export from the Charts window
and allows to open the website of the LAMMPS tutorial from the About menu.
My TODO list for 1.6 series is now empty. If you have any suggestion for an additional feature or modification or have a bug to report, this is the last chance.
Here is another upload of the LAMMPS-GUI 1.6 series, version 1.6.5
This version has two new features:
the file viewer can now read compressed text files, if a suitable compression/decompression program is available (e.g. gzip, bzip2, xz, etc.). It works similar to how it is done in LAMMPS, so if you can use the compressed file with LAMMPS, then you can also read it with LAMMPS-GUI.
the snapshot image viewer has another button which will recenter the atoms on the screen. This is particularly useful for partially filled boxes or when using a LAMMPS group to show only a subsystem.
there are also a bunch of low-level changes to LAMMPS included that make parsing of numbers more portable and more robust.
As a reminder, the complete (and rather long) dump and dump_modify commands to reproduce exactly this image with dump image or dump movie can be copied to the clipboard with CTRL-D or from the File menu. This can be pasted into your input and then adjusted.
As usual, any kind of feedback, ideas, bug reports, praise, insults are welcome.
This has a few bugs fixes, updated documentation, and the following changes:
there is now an auto-save mode (can be enabled in the Editor preferences) where the editor buffer is saved automatically before starting a run or exiting LAMMPS-GUI
the snapshot image viewer has a new button where you can toggle between “shiny” (default) and “matted” surfaces of the rendered objects.
also the menu bar layout was revised and all buttons moved to a second line and thus allowing to make the image window smaller. The Height and Width entries are resized based on the selected font (i.e. the numbers are no longer obscured with larger fonts).
the URLs to the documentation are adjusted depending on whether a stable, release, or development version was compiled, since we have these three versions of the online manual available.
the table that is mapping commands to the documentation was updated for recently added new commands and styles
The “re-indent on ‘Return’” feature is no longer turned on by default.
The maximum number of threads is curbed to 16 by default. If you want more, you need to explicitly change this in the Preferences. This is to avoid very slow runs with many threads on small systems.
For Linux there is now a flatpak bundle available
As usual, any kind of feedback, ideas, bug reports, praise, insults are welcome.
Creating an image should be doable. You can already create one by having an input file that has only “read_restart somesystem.restart” and then do a run (to read it) and then launch the snapshot image viewer.
You can add “info system group region compute fix” to that input and you get available introspection info. Please check it out.
So it would be mostly a matter of automating this process.
Please see attached a screenshot for what I have just committed to a pending pull request branch.
You can right click on filenames in the input file editor, select Inspect restart file, and you get three new windows: 1) the output of the info command after reading the restart, 2) a data file created with write_data, and 3) a snapshot image (that you can rotate, zoom and so on). If you already have an input file loaded, this will be unaffected.
There also is a menu entry in the “File” menu to inspect a restart file where then a file dialog opens to select a file.
New LAMMPS-GUI binary packages for testing are available.
New in version 1.6.7:
restart file inspector
bug fixes with storing and restoring font settings in preferences
a new menu entry for setting up LAMMPS tutorials by @simongravelle. You can pick a folder and the initial files (and optionally the solutions) will be downloaded and the first input loaded into the editor. This is work-in progress and the tutorials are currently being revised for use with LAMMPS-GUI.
New LAMMPS-GUI binary packages for testing are available.
We are only a few days away from releasing the next stable version of LAMMPS (and LAMMPS-GUI), so this is the last chance to try out the new version, try different things and make it crash or misbehave and report it.
New in version 1.6.8:
Charts are now plotted in raw and smoothed versions
Charts will ignore outlier data that can mess up plots and sometimes happens in error for yet undetermined reasons
The interval for redrawing charts can be set independent from the data update interval to avoid nasty flicker for fast jobs.
The manual has been updated with new screenshots and describing new features
I have uploaded one more test version of LAMMPS-GUI while we are close to the finishing line of the next stable release. As usual, any kind of feedback and bug report is highly appreciated.
New in version 1.6.9:
Find and replace function (I cannot believe that this was missing for over a year and nobody complained). It is a bit crude and simple, but since this went unnoticed for so long, I will consider looking into some polishing of the code only after specific requests are made.
For cases where the atom diameter cannot be deduced for dump image, there is an Atom size: field that allows to set a custom diameter (e.g. for SPH simulations). It is initialized to the x-direction lattice spacing.
Documentation updates.
Improved “Dark mode” support. When Qt switches to “dark mode” some colors are set differently. You may have to restart LAMMPS-GUI when changing from light to dark mode or vice versa for this to work.
LAMMPS-GUI is written in C++ and is using the C-library interface. So your python script would first have to be rewritten in C++ to add it to LAMMPS-GUI. But then there is the question of how to handle the various command line arguments in the context of the GUI, e.g. build a dialog offering all possible options as dropdown lists or text fields or radio buttons or?? Or use the “Wizard style” interface where you have multiple dialogs asking questions and then finally execute the command with the corrected settings.
It would probably be easier to contribute your script in the tools folder combined with a README file.
There are new test binaries with some maintenance updates and one more new feature: if there are URLs in the output window pointing to a webpage with additional explanations for an error or warning, that URL is now highlighted and double clicking it will open that URL (also available via context menu, i.e. left click).
This will be the base of the version of LAMMPS-GUI that we want to use for the tutorial at the upcoming LAMMPS workshop in Albuquerque in Summer. So bug reports, feature requests, or suggestions for improvements are - as usual - welcome. Just open one of the 8 tutorials available from the Tutorials menu, check out the instructions for the tutorial and let me know your thoughts.
Every time I post one of these test versions I keep thinking there is nothing more that can be added and that all bugs have been fixed, but then some new idea comes along or somebody finds an issues that has not been reported and we get another test version…
I finally gave it some tests and I find the work done since the launch of this project quite impressive. That’s nice!
Is there some place were we can report bugs for the LAMMPS-GUI? I think I’ve found some odd behavior in the way the plotting tool is reading the data. Some pointer must do weird stuff.
I’ve only played around with the smooth curve plotter.
There is a built-in limitation in how thermodynamic data is retrieved from the running simulation.
Since the data is cached and then retrieved from the cache, it needs to be polled fast enough, if the output is produced very fast. This increases the amount of CPU time used by LAMMPS-GUI. The default settings are so that it assumes the output to be done rather infrequent. You can change this by editing the “Data update interval” in the “Preferences” dialog in the General Settings tab. If you reduce the interval (to 10ms or even 1ms), the CPU usage increases but the chances for a race condition and skipping on data are lowered. As an alternative, you can increase the “thermo” argument and/or turn off support for multi-threading to slow down the calculation and with it the rate of creating output. For the same reason, there can be a difference between the collected data (e.g. some lines missing at the beginning or for the entire run and what is logged in the output file. For example, when I run your input on my machine, I have no problem.
This kind of data corruption used to happen more often, but I’ve added a mutex for accessing and updating the cached thermo data. It is not clear to me at the moment, where the remaining
race condition is and thus causing data corruption.
Some pointer must do weird stuff.
