Adding the linked cells in the cudaCoordination

[Iximiel]

Description

I think that now the cudaCoordination has the correct shape:
Each kernel is one of the cells setup with the linkcells and runs on all the atoms in the cells and in the surrounding cells.

Now it is possible adding a new switching function without getting too crazy, with a some template shenanigans.

A next step could be set up a way to use non orthogonal pbc also in the kernels.

I wanted to post some benchmark but I encountered this problem:

I asked for a cutoff of 4 with atoms evenly distributed in a simple cubic arrangement with a cell size of 1, and I am getting cells of 125 atoms instead of 64 (with some cells that have less atoms).

I think this is a problem in linkcells in the way in which it is assigning atoms to their cells.

Target release

I would like my code to appear in release V2.10

Type of contribution

• changes to code or doc authored by PLUMED developers, or additions of code in the core or within the default modules
• changes to a module not authored by you
• new module contribution or edit of a module authored by you

Copyright

• I agree to transfer the copyright of the code I have written to the PLUMED developers or to the author of the code I am modifying.

• the module I added or modified contains a COPYRIGHT file with the correct license information. Code should be released under an open source license. I also used the command cd src && ./header.sh mymodulename in order to make sure the headers of the module are correct.

Tests

• I added a new regtest or modified an existing regtest to validate my changes.
• I verified that all regtests are passed successfully on GitHub Actions.