Comments (4)
Ideas of how to robustly find atoms in a molecule that are the 'enhancements' or functional groups:
- Define an interface radius or side length
- 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.
- 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).
- 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.
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The pairings would be between the interface atoms and the atoms marked as 'enhancement'.
from kappa.
The code at its core is now added but there are still problems with it so I will not close the issue quite yet.
from kappa.
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.
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Related Issues (20)
- Missing simple repeated molecule combination function
- Calculations using kappa HOT 5
- Program crashes on CNT generation for tubes with length != 3 and radius != 1 HOT 1
- Consider a different recursive algorithm to accumulate the desired number of valence states in bond type assignment
- Redundant build code in molecule.py
- Should be able to remove zero modes more easily
- Major rework of forcefields needed
- Redundant functions in atom type parsing
- Forcefield object is not needed in Molecule instantiation HOT 1
- Missing forcefield parameter file implementation from AmberTools HOT 1
- Missing analytical Hessian calculation HOT 1
- Inconsistent kappa values calculated HOT 4
- Missing consideration of improper torsionals in energy calculations
- Consider hydrogenating every carbon base structure HOT 1
- Memory problem storing parameters from parsing, particular dihedral parameters. HOT 1
- Consider performing green's function coefficient calculation in separate package HOT 2
- Missing special consideration of special chemical groups in parameter assignment HOT 3
- Need to store 'grid' values based on parameterization, allow for plotting. HOT 1
- CNTs (armchair) have one section deformed initially
- Dihedral ff parameters do not get assigned as intended in some molecules
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