Right now if rpa_local is 0, the reaction will not be considered (there is no direction for this case). However, this means that a reaction network might be possibly incomplete with these reactants/products missing.

For a lot of reactions with similar rates, if the cutoff rate is lowered below anyone. A lot of reactions are then considered in the species visualization. What is desired is a way of showing only the dominant 5-10 reactions.
Related to Ezgi's reaction network.

Add required scripts to Caviness to post process visualization .out file to .svg files.

Currently, the edge properties for non-equilibrated reactions shows the forward rate. However, it would be more useful if the net rate was shown.

Is there a way to run the visualization tool without having to rerun the MKM? Sometimes I would like to lower the visualization parameters in tube.inp, which shouldn't change the results in OUT.d.

Would it be as straightforward as copying these lines from the chemkin.sh bash script and putting it in its own script?

#generate the svg file for visualization
echo 'Generating Visualization Files now!'
cd OUT.d
cp rpa_visualizationBasis100.out ../Species.d/
cp rpa_visualizationNormalized.out ../Species.d/
cp rpa_visualizationMaxRateNormalized.out ../Species.d/
cd ..
cd Species.d
for i in *.out; do
    unflatten -c 10 $i | dot -Tsvg -o ${i%.*}.svg
    rm $i 2> /dev/null
done

Add ability to specify rank and node spacing to change overall compactness of Reaction Path Analysis diagram

The current version of graphviz included in the Ubuntu 20.04 distribution (graphviz 2.42.2-3build2) generates .svg files that partially crop the image. The issue is with the default monitor dpi (dots-per-inch) used in the new version. Ubuntu and Windows assume a monitor dpi of 96.

The fix/workaround is to code the dpi into the dot command by adding the option -Gdpi=96. So a conversion from a example.out file to a example.svg file now looks like:

dot -Tsvg -Gdpi=96 example.out -oexample.svg

These edits can be done in the chemkin.sh and refinevisualization.sh scripts.
While the current graphviz version on Caviness does not have this issue we may need to address this at some point if/when graphiz versions are updated.

This should be added to the documentation.

Hello,

I am trying to get your tool working with complex reactions mechanisms (e.g. Glarborg et al. [2018]), where different type of reactions are implemented. The following problems have occurred:

• Three body reactions with '+ M' and '(+M)' will lead to an error. I am trying to
• Irreversible reactions denoted by '=>' are not accepted, as you are splitting reactants and products by '<=>' in the reaction string
• Float stoichiometric coefficients are used in several gas phase mechanisms. However, you only accept integers.

All those bugs can be circumvent by the user, but they are very minor and can be fixed in minutes. If I find the time, I will try it myself and commit a pull request.

Anyways, thank you for your great work!

Currently, only reaction properties are displayed. It would be useful to have species properties (such as coverage, enthalpy, entropy, Gibbs energy) displayed as well.

Hi, I'm investigating renview to see if it can help in my research work. Unfortunately, it looks like it remains stuck somewhere after the creation of the result directory (see the message below obtained after a Crtl C). I tried several things without any success. Let me add that I tested graphiz with small examples from its manual and they worked fine.
So if if someone can help, I ll be grateful.

message (unbuntu 20.04): File "run.py", line 64, in
run(**default_kwargs)
File "run.py", line 20, in run
gg.generate_visualizations()
File "/home/hc/.local/lib/python3.8/site-packages/renview/GraphGenerator/init.py", line 662, in generate_visualizations
check_call(['dot', '-Tsvg', f.name, '-o', filename_svg], shell=True)
File "/usr/lib/python3.8/subprocess.py", line 359, in check_call
retcode = call(*popenargs, **kwargs)
File "/usr/lib/python3.8/subprocess.py", line 342, in call
return p.wait(timeout=timeout)
File "/usr/lib/python3.8/subprocess.py", line 1079, in wait
return self._wait(timeout=timeout)
File "/usr/lib/python3.8/subprocess.py", line 1804, in _wait
(pid, sts) = self._try_wait(0)
File "/usr/lib/python3.8/subprocess.py", line 1762, in _try_wait
(pid, sts) = os.waitpid(self.pid, wait_flags)
KeyboardInterrupt

Hello there,

This is a very good tool to analyse a reaction path, and it will help me a lot in my research. But I am having few doubts, I was trying to draw the reaction path for the Hydrogen combustion for my mechanism file, can you please tell me how to generate input files for a given mechanism? Also, I want to confirm one thing, this reaction path viewer generates the reaction path for an instant or for a whole reaction duration?

Thanks in advance
Akash Rodhiya

Specifying parenthesis in species name crashes the code.