I want to impose reflecting BCs at the non-periodic direction of my simulation box. To this end I need to use fix wall/reflect
Is there any way for direct inclusion of this command in PyIron?
Best regards
wall/reflect is currently not natively supported by pyiron, but if you know the LAMMPS command, you can include it for example via:
job.input.control['fix___fixname'] = 'all wall/reflect xlo EDGE xhi EDGE'
(I took the first example on the LAMMPS page you shared). If your LAMMPS input is not too complicated, this pyiron should be able to place this command in the appropriate position.
Sams's solution is definitely the easiest way if you just want to insert one fix. But you can even load full LAMMPS scripts inside pyiron, here is an example:
https://github.com/jan-janssen/pyiron-free-energy/blob/master/free_energy.ipynb
The important part is to keep the read_data structure.inp and the include potential.inp to use the structure and interatomic potential defined by pyiron. Finally if you also copy the dump, dump_modify and thermo part you can use the pyiron parsers, otherwise you can always parse the output yourself, like I demonstrated in the above example.
Related
I'm using windows 10 and python 3.3. I tried to download fasttext_model300 to calculate soft cosine similarity between documents, but when I run my python file, it stops after arriving at this statement:
fasttext_model300 = api.load('fasttext-wiki-news-subwords-300')
There are no errors or not responding, It just stops without any reaction.
Does anybody know why it happens?
Thanks
I'd recommend against using the gensim api.load() functionality. It dynamically runs new, unversioned source code from remote servers – which is opaque in its operations & suboptimal for maintaining a secure local configuration, or debugging any issues which occur.
Instead, find the actual exact data files you trust and download them as plain data. Then, use specific library operations, like the KeyedVectors.load_word2vec_format() method, so instantiate exactly the model you need, using precise local-file paths you understand.
Following those steps may make it clearer what, if anything, is going wrong. If it doesn't, try also enabling logging at the INFO level to gather more information about what progress is made before failure (and add any new details as a comment or to your question).
python3 -m gensim.downloader --download fasttext-wiki-news-subwords-300
Try using this. Source : https://awesomeopensource.com/project/RaRe-Technologies/gensim-data
autoscan produced a series of function checks (AC_FUNC_* and AC_CHECK_FUNCS), and AC_CHECK_HEADERS. Now I need to pull in gnulib code. Do I just try to import every function and header that autoscan identified? Half of them don't show up in the gnulib-tool --list output. Or do I wait until ./configure fails on some platform?
My suggestion would be to ignore autoscan entirely and instead try to figure out which platform you're targeting.
In particular autoscan will try to add tests for functions that are available in every single platform since 1990, but might be missing on a non-SysV OS for instance.
Start with a base platform target (such as C99 and the latest POSIX), and then figure out which other OSes you want to target and what they are missing.
Don't try to cover bases for OSes you have no access to, it's likely you won't actually know what is needed for them to build, let alone run.
Full disclosure: I have changed my opinion on gnulib over the years and not suggest it to be used anymore, if at all possible.
There are two ways to determine which list of gnulib modules you might need:
You can scan your source code or your object files (with nm) by hand.
You can import all the POSIX header file modules via gnulib-tool, then add -DGNULIB_POSIXCHECK to the CFLAGS, compile your package, and analyze the resulting warnings.
Also, some gnulib overrides exist for the sake of old platforms only. You can read the list of what each override fixes, and apply your own judgement.
For my personal use, several times I have modified the matplotlib gtk backend (also the tk and wx) , replacing the window with a notebook. This is because I use too many plots at the same time.
This time around I feel I can take the challenge to do a pull-request for my changes. But I want to do it as clean as possible. That is where I need advice (clean is the key).
I would like to place my class TabbedFigureManagerGTK3 inside
backend_gtk3.py
The problem is that using
matplotlib.use('gtk3cairo')
or
matplotlib.use('gtk3agg')
Directs the specified backend (gtk3cairo or gtk3agg) to use backend_gtk3.FigureManagerGTK3
I do not want to replicate backend_gtk3agg.py and backend_gtk3cairo.py just to change the call to backend_gtk3.FigureManagerGTK3
I would like to implement a solution that allows the user to pass an option to the backend, and from there it choses the traditional FigureManagerGTK3 or my TabbedFigureManagerGTK3
I am looking for a recomendation on how to do it that has more chances to be accepted upstream (after pull-request and the whole shebang).
Do I modify matplotlib.use to add something like **kwargs?
Do I just recreate the whole backend_gtk3agg.py and backend_gtk3cairo.py (subclassing of course)
Do I forget about trying to get this accepted and do it breaking the Coding guide
Thanks
Federico
This does sound like a nifty feature.
I would do it by modifying the existing manager and following how the PySide vs PyQt issue is handled (by using a secondary rcParams which controls which one the backend imports). In your case, I would add backend.gtk3.tabbed, or something similarly named, which controls how the manager behaves.
Write your modifications so that changes as little of the existing api as possible (breaking backwards compatibility is a no-go) and make it so a user that doesn't explicitly enable your changes won't even know they are there.
Also email the dev list, they are all pretty friendly. Or just open a PR, that is the most effective way to get feed back.
When using the magic function %edit from QtConsole with IPython, the call does not block, and does not execute the saved code. It does however save a temporary file...
I think this is intended behavior due to GUI editors and uncertainty, and whatever that reason is for not being able to communicate with subprocess (pyZMQ?).
What do you suggest as the best way to mix %edit/%run magics?
I would not mind calling two different commands (one to edit, and one after I have saved and execution is safe). But those commands need a way to synchronize this target file location, or someone to persist storage, and probably need some crude form of predicatably generating filenames such that you can edit more than one file at a time, and execute in arbitrarily. Session persistence is not a must.
Would writing my own magic do any good? Hope we can %edit macros soon, that would do well enough to make it work.
you shoudl be able to do %edit filename.py and %run filename.py. The non blocking behavior is expected, and IIRC due to technical reason. Not unsurmountable but difficult.
You could define your own magic if you wish, improvement are welcomed.
Hope we can %edit macros soon, that would do well enough to make it work.
For that too, PR are welcomed. I guess as a workaround/option you can %load macro which would put macro on input n+1 , edit it and redefine it, that might be a good extension for a cell magic %%macro macroname
If you have some executable code on your input (from QtConsole), you can type
%edit 1-5
This fires the editor, creates a temporarily file (automatically managed), and loads your input lines. This is nearly enough, now how to retrieve the name of that temp file pragmatically?
I see the print statement on Stdout, but its not visible to QtConsole AFAIK. Could maybe redirect stdout to catch that line, but that may not be an option anyway if your doing something else with stdout.
If I could retrieve the full pathname that was just created, this would be cake. Store it where some magics will know how to find it. Then issue a followup command when ready,pops the name off the stack, loads it into a macro, and run. All this with 2 input commands and no names to remember (unless you want to find and use that macro again, but for 1 shot stuff...)
How do I catch or retrieve the path of that temporary file?
The idea is that given a specific input to the program, somehow I want to automatically step-in through the complete program and dump its control flow along with all the data being used like classes and their variables. Is their a straightforward way to do this? Or can this be done by some scripting over gdb or does it require modification in gdb?
Ok the reason for this question is because of an idea regarding a debugging tool. What it does is this. Given two different inputs to a program, one causing an incorrect output and the other a correct one, it will tell what part of the control flow differ for them.
So What I think will be needed is a complete dump of these 2 control flows going into a diff engine. And if the two inputs are following similar control flows then their diff would (in many cases) give a good idea about why the bug exist.
This can be made into a very engaging tool with many features build on top of this.
Tell us a little more about the environment. dtrace, for example, will do a marvelous job of this in Solaris or Leopard. gprof is another possibility.
A bumpo version of this could be done with yes(1), or expect(1).
If you want to get fancy, GDB can be scripted with Python in some versions.
What you are describing sounds a bit like gdb's "tracepoint debugging".
See gdb's internal help "help tracepoint". You can also see a whitepaper
here: http://sourceware.org/gdb/talks/esc-west-1999/
Unfortunately, this functionality is not currently implemented for
native debugging, but I believe that CodeSourcery is doing some work
on it.
Check this out, unlike Coverity, Fenris is free and widly used..
How to print the next N executed lines automatically in GDB?