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View Code? Open in Web Editor NEWFinite-volume Vlasov-Maxwell code for Plasma Physics simulations
License: GNU General Public License v3.0
Finite-volume Vlasov-Maxwell code for Plasma Physics simulations
License: GNU General Public License v3.0
Referencing: openjournals/joss-reviews#3618
JOSS wants: "References: Is the list of references complete, and is everything cited appropriately that should be cited (e.g., papers, datasets, software)? Do references in the text use the proper citation syntax?"
test
Referencing: openjournals/joss-reviews#3618
JOSS wants: "Community guidelines: Are there clear guidelines for third parties wishing to 1) Contribute to the software 2) Report issues or problems with the software 3) Seek support" presumably in something like contrib.md
. I think if you poke around at other projects you'll find some suitable boiler plate language for this.
I got the following traceback with the latest version of the code. Apologies if this is due to an additional package that I need to install since my last attempt several weeks ago.
bash-3.2$ make extract
python3 sources/extract.py
Energy plot
Traceback (most recent call last):
File "/Users/tclune/swdev/tmp/ESVM/sources/extract.py", line 77, in <module>
fig.savefig('figures/energy_log.png',bbox_inches='tight')
File "/Users/tclune/installed/Core/homebrew/lib/python3.9/site-packages/matplotlib/figure.py", line 3015, in savefig
self.canvas.print_figure(fname, **kwargs)
File "/Users/tclune/installed/Core/homebrew/lib/python3.9/site-packages/matplotlib/backend_bases.py", line 2230, in print_figure
self.figure.draw(renderer)
File "/Users/tclune/installed/Core/homebrew/lib/python3.9/site-packages/matplotlib/artist.py", line 74, in draw_wrapper
result = draw(artist, renderer, *args, **kwargs)
File "/Users/tclune/installed/Core/homebrew/lib/python3.9/site-packages/matplotlib/artist.py", line 51, in draw_wrapper
return draw(artist, renderer, *args, **kwargs)
File "/Users/tclune/installed/Core/homebrew/lib/python3.9/site-packages/matplotlib/figure.py", line 2790, in draw
mimage._draw_list_compositing_images(
File "/Users/tclune/installed/Core/homebrew/lib/python3.9/site-packages/matplotlib/image.py", line 132, in _draw_list_compositing_images
a.draw(renderer)
File "/Users/tclune/installed/Core/homebrew/lib/python3.9/site-packages/matplotlib/artist.py", line 51, in draw_wrapper
return draw(artist, renderer, *args, **kwargs)
File "/Users/tclune/installed/Core/homebrew/lib/python3.9/site-packages/matplotlib/_api/deprecation.py", line 431, in wrapper
return func(*inner_args, **inner_kwargs)
File "/Users/tclune/installed/Core/homebrew/lib/python3.9/site-packages/matplotlib/axes/_base.py", line 2921, in draw
mimage._draw_list_compositing_images(renderer, self, artists)
File "/Users/tclune/installed/Core/homebrew/lib/python3.9/site-packages/matplotlib/image.py", line 132, in _draw_list_compositing_images
a.draw(renderer)
File "/Users/tclune/installed/Core/homebrew/lib/python3.9/site-packages/matplotlib/artist.py", line 51, in draw_wrapper
return draw(artist, renderer, *args, **kwargs)
File "/Users/tclune/installed/Core/homebrew/lib/python3.9/site-packages/matplotlib/axis.py", line 1142, in draw
ticklabelBoxes, ticklabelBoxes2 = self._get_tick_bboxes(ticks_to_draw,
File "/Users/tclune/installed/Core/homebrew/lib/python3.9/site-packages/matplotlib/axis.py", line 1068, in _get_tick_bboxes
return ([tick.label1.get_window_extent(renderer)
File "/Users/tclune/installed/Core/homebrew/lib/python3.9/site-packages/matplotlib/axis.py", line 1068, in <listcomp>
return ([tick.label1.get_window_extent(renderer)
File "/Users/tclune/installed/Core/homebrew/lib/python3.9/site-packages/matplotlib/text.py", line 903, in get_window_extent
bbox, info, descent = self._get_layout(self._renderer)
File "/Users/tclune/installed/Core/homebrew/lib/python3.9/site-packages/matplotlib/text.py", line 306, in _get_layout
_, lp_h, lp_d = renderer.get_text_width_height_descent(
File "/Users/tclune/installed/Core/homebrew/lib/python3.9/site-packages/matplotlib/backends/backend_agg.py", line 229, in get_text_width_height_descent
w, h, d = texmanager.get_text_width_height_descent(
File "/Users/tclune/installed/Core/homebrew/lib/python3.9/site-packages/matplotlib/texmanager.py", line 401, in get_text_width_height_descent
page, = dvi
File "/Users/tclune/installed/Core/homebrew/lib/python3.9/site-packages/matplotlib/dviread.py", line 251, in __iter__
while self._read():
File "/Users/tclune/installed/Core/homebrew/lib/python3.9/site-packages/matplotlib/dviread.py", line 331, in _read
self._dtable[byte](self, byte)
File "/Users/tclune/installed/Core/homebrew/lib/python3.9/site-packages/matplotlib/dviread.py", line 174, in wrapper
return method(self, *[f(self, byte-min) for f in get_args])
File "/Users/tclune/installed/Core/homebrew/lib/python3.9/site-packages/matplotlib/dviread.py", line 476, in _fnt_def
self._fnt_def_real(k, c, s, d, a, l)
File "/Users/tclune/installed/Core/homebrew/lib/python3.9/site-packages/matplotlib/dviread.py", line 483, in _fnt_def_real
raise FileNotFoundError("missing font metrics file: %s" % fontname)
FileNotFoundError: missing font metrics file: cmss12
make: *** [extract] Error 1
Part of openjournals/joss-reviews#3618
I'd like to suggest a few minor improvements to the paper:
The openjournals joss-reviews requires that there be a set of community guidelines.
Having modified the Makefile to compile with debug flags:
$ git diff makefile
diff --git a/makefile b/makefile
index 2ee2fed..db00548 100755
--- a/makefile
+++ b/makefile
@@ -30,13 +30,13 @@ F90 = gfortran
# openMP #
##########
-OPTS = -fopenmp -O3 -ffixed-line-length-none -fdefault-real-8
+#OPTS = -fopenmp -O3 -ffixed-line-length-none -fdefault-real-8
#########
# debug #
#########
-#OPTS = -g -fopenmp -fbacktrace -ffpe-trap=zero,overflow,underflow
+OPTS = -g -fopenmp -fbacktrace -ffpe-trap=zero,overflow,underflow
#####################################
#####################################
and running with the input-deck as provided I see floating-point errors:
...
-----------------------------------------
* Deduced parameters :
N_x = 205
N_vx = 801
n0 = 1.0000000000000000E+019
Te = 11604258.709350331
-----------------------------------------
Program received signal SIGFPE: Floating-point exception - erroneous arithmetic operation.
Backtrace for this error:
#0 0x7f7becf1c2ed in ???
#1 0x7f7becf1b503 in ???
#2 0x7f7bec58203f in ???
#3 0x7f7becbe9ea4 in ???
#4 0x7f7becb721fe in ???
#5 0x55c2128020e5 in __library_MOD_init_simu
at sources/library.f90:115
#6 0x55c212804e78 in esvm
at sources/esvm.f90:47
#7 0x55c212805c8a in main
at sources/esvm.f90:11
Floating point exception (core dumped)
This issue is part of the openjournal review.
Ideally there should be a step like make tests
that checks that correct values are returned for some test case that covers a reasonable fraction of the software.
Referencing: openjournals/joss-reviews#3618
The statement of need does not explicitly state who the target audience is? All plasma researchers? Students? Researchers in a specific subdomain?
This issue is part of the openjournal review.
make extract
generates lots of output like:
/Users/tclune/swdev/tmp/ESVM/sources/extract.py:291: MatplotlibDeprecationWarning: shading='flat' when X and Y have the same dimensions as C is deprecated since 3.3. Either specify the corners of the quadrilaterals with X and Y, or pass shading='auto', 'nearest' or 'gouraud', or set rcParams['pcolor.shading']. This will become an error two minor releases later.
plt.pcolormesh(X,VX,P,cmap=cmap,norm=norm,vmax=Maxval,vmin=Minval)
Not a deal breaker - just reporting to be thorough.
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