Keep atoms inside main box

[Marc Riera]

Hello! I was wondering if there is any way that we can keep the atoms inside the main box in a PBC simulation. I am running some PBC MB-nrg simulations, and seems like i-pi is putting atoms in boxes adjacent to the main box.

To clarify, let's say that my box is 10x10x10. Althoug I start will all my coordinates (x,y,z) between -5 and +5, at some point of the simulation, i-pi is giving me values larger than +5 or lower than -5. Is there any keyword I need to add to the xml file in order to avoid this, and have all the coordinates always between -5 and 5?

thanks!

[Michele Ceriotti]

So, if you need to "wrap" coordinates before sending them to the driver code you can use pbc="True" in the <ffsocket> tag. 

If you need to wrap for visualization or analysis, you can do that with a post-processing step, many tools are available (and actually on 

a separate branch we've implemented that in i-pi-mux-coordinates, we'll merge soon). 

Note however it's better *not to wrap*, as wrapped coordinates do not allow you to evaluate diffusion coefficients.

M

[Marc Riera]

Thanks for the heads up, Michelle. 

It was mainly for visualization purposes, so I will wait til you guys merge the feature and then use it.

I think we are done with the implementation of MB-nrg in PBC, then. Now it is time to have fun with simulations! 

Thanks a lot,

Marc