Need thermal conductivity calculation for full molecules about kappa

[ajkerr0]

Ideas of how to robustly find atoms in a molecule that are the 'enhancements' or functional groups:

1. Define an interface radius or side length
2. Rotate and translate molecules (or copies or virtual molecules) so that their interface positions are at the origin pointed towards the x-direction. Find all atomic positions that are inside a certain zone, say: x > 0, -radius < y < radius, -radius < z < radius that are NOT interface atoms.
3. Find all atomic pairings that contribute to the thermal conductivity of the molecule. At the very least find all pairings that are within the cutoff distance of non-bonded interactions (if nonbonded interactions are turned on). Also consider finding all pairings that are at most 3 bonds away (dihedral interactions), 2 bonds away (angle), 1 bond (stretching).
4. From this list of pairings we should be able to use the same thermal conductivity code, put calculate the power by iterating over the pairs in all 3 directions.

[ajkerr0]

The pairings would be between the interface atoms and the atoms marked as 'enhancement'.

[ajkerr0]

The code at its core is now added but there are still problems with it so I will not close the issue quite yet.

[ajkerr0]

In its essence, the calculation is there so we will close the issue. We should add specific issues for the kinks that need to be worked out.