Pore example

[rmatsum836]

Graphene slit pore example using the porebuilder recipe in mBuild. This working example plots the number density profile of water within the slit pore.

[rmatsum836]

If I recall correctly, this is ready to be tested by another user.

[ahy3nz]

I like this example - it's a pretty sophisticated workflow and utilizes other packages like pore-builder and mtools.

• Personally, I'm proud of myself for being able to get the plugin system to work in mbuild's setup.py to work with the pore-builder, but there might be some hand-holding needed to get the mb recipe plugins to work super easily
• The reference num density folder is incorrect np.loadtxt('ref_data/numden.txt') not reference-data in the notebook
• Lastly, I only ran for 43000 steps and looked at only 2 frames:

But the notebook itself is complete and functional (I got it to run)

[rmatsum836]

Thanks for running this and catching my dumb mistakes. Definitely weird about the results you're getting though, I'll check this.

[rmatsum836]

So for some reason the dimensions used for the number density calculation were all wrong but it should be fixed now.

[mattwthompson]

soft requirement on https://github.com/rmatsum836/Pore-Builder/pull/18

My GROMACS build is borked on my macbook but I can try running the simulation tomorrow. But initial structure looks good.

[rmatsum836]

Could someone retest this when they have a chance?

[ahy3nz]

Okay I ran the simulation in its entirety this time: I'm not really worried about the simulation/analysis, but we should try to figure out something with these dependencies (mtools and porebuilder) #2

[rmatsum836]

Thanks @uppittu11 for testing this out! I added some markdown cells and cleaned up the number density profile at the end of the notebook. If there are no other comments, I think this is ready to go.

[mattwthompson]

Looks nice to me, thanks for the contribution!