Need thermal conductivity calculation for full molecules

[ajkerr0]

Need to make available the thermal conductivity code but applied to the Molecule objects.

Things to note:

• Need to have masses go in the diagonal and be applied to each x,y,z position correctly
• Might start with default drag coefficients
• Need to signify which atoms are outside of the main interfaces, which atoms 'are' the interface
  • Need to keep track of power that is driven through the interface(s) as this will be related to the conductivity of the entire molecule
  • This could relate to Issue #26 and how you define interfaces to be plotted
• Have to choose which atoms are going to be driven which will almost certainly be the ones outside of the interfaces.

[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.