Link cells without PBC

[gtribello]

Description

I have modified the link cells class to ensure it works even if you are not running a simulation with PBC.

Please note that to use the link cell class, you need to use the functions below:

#include "tools/LinkCells.h"

// Declare a link cells object
LinkCells linkcells;

// Create a link cells object
linkcells(comm)

// Set the link cell cutoff
linkcells.setCutoff( nl_cut );

// Allocate each atom in a list to its appropriate cell
std::vector<Vector> ltmp_pos;     // Vector of atomic positions
std::vector<unsigned> indices;    // index to use for each of the atoms -- index in colvar NOT index in MD code. 
linkcells.buildCellLists( ltmp_pos, indices, getPbc() );

// Retrieve the atoms in the cells that are needed
unsigned ncells_required;
std::vector<unsigned> indices( 1+ablocks.size() )
std::vector<unsigned> cells_required( linkcells.getNumberOfCells() );
linkcells.addRequiredCells( linkcells.findMyCell( pos ), ncells_required, cells_required );
// Now get the indices of the atoms in the link cells positions
unsigned natoms=1; indices[0]=pTaskList[i];
linkcells.retrieveAtomsInCells( ncells_required, cells_required, natoms, indices );

I've copy and pasted these commands from the class where I use stuff. It dawns on me that how you use the interface in that second bunch of calls is less clear than it could be. It perhaps be worth writing a wrapper around all that stuff.

Target release

I would like my code to appear in release 2.10

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.

[gtribello]

@GiovanniBussi there are regtests for this specific class in adjmat/rt-link and adjmat/rt-link-nopbc :-)

[gtribello]

Hello @GiovanniBussi and @carlocamilloni

I have merged the master into this. If it passes the tests I think we can merge it safely. I don't think it needs to be backported onto v2.9. This is an improvement on what I did in the previous fix so I think it makes sense to do it on master only.

[gtribello]

Yay! I fixed it, and the problem was a stupid typo that I made! I don't know why this was working on my machine and not on GitHub but I think you can go ahead and merge this into master. @GiovanniBussi or @carlocamilloni