The RNMED method is implemented as described in these papers:
F. Mueller-Plathe. A simple nonequilibrium molecular dynamics method for calculating the thermal conductivity. J. Chem. Phys., 106(14):6082–6085, 1997
https://doi.org/10.1063/1.473271.
C. Nieto-Draghi and J. B. Avalos. Non-equilibrium momentum exchange algorithm for molecular dynamics simulation of heat flow in multicomponent systems. Mol. Phys., 101(14):2303–2307,
2003.https://doi.org/10.1080/0026897031000154338In short, the energy is exchanged by swapping the momenta of the hottest atom in the heat sink region and the coldest atom in the heat source region. This way an external heat flow between sink and source region is established which is counterbalanced by a heat flux in the configuration from source to sink. When steady-state is reached the external heat flux (which can be measured from the exchanged energy) is equal to the internal heat flux. The thermal conductivity can then be calculated from this heat flux and the temperature gradient using Fourier's law, as described in the tutorial.
We normally recommend a slab-like setup where the top and bottom layers of the surfaces are frozen (after equilibration) and thin heat sink and source regions are assigned adjacent to these frozen caps, e.g. as shown in the attached picture.
These regions can be specified as tags. The thickness should be between 5 and 10 Ang.
The exchange interval should be chosen as big as possible to avoid a too large temperature gradient, and but not too big so that one still gets a measurable gradient. Recommended values are 100 -200. If the temperature gradient becomes too large, then one should increase the value. I have attached an example script of a thermal conductivity simulation.
The heat flux can be extracted when opening the MD-Trajectory in the MD-Analyzer. The measurement "average_heat_current" can be enabled which show the time evolution of the average energy exchanged per time. This can be used to monitor if one has reached a steady-state. The heat flux is obtained by dividing the heat current by the cross-sectional area of the configuration, i.e. the A-B-surface area if the current is along C. The temperature gradient can be obtained from the MD-Analyzer, by plotting the temperature profile and fitting the slope in a selected region as shown in the third attached picture. The tutorial
https://docs.quantumatk.com/tutorials/interfacial_thermal_conductance/interfacial_thermal_conductance.html#investigating-the-grain-size-dependence-of-the-thermal-conductivity outlines this, but the functionality displayed there is a bit outdated.
Since this gives you full control over all details, but can be a bit cumbersome to do, we have implemented a convenience function that does combines all these steps and prints the thermal conductivity to the log:
https://docs.quantumatk.com/manual/Types/ThermalConductivity/ThermalConductivity.html#thermalconductivity
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