fix thermal/conductivity command
fix ID group-ID thermal/conductivity N edim Nbin keyword value ...
ID, group-ID are documented in fix command
thermal/conductivity = style name of this fix command
N = perform kinetic energy exchange every N steps
edim = x or y or z = direction of kinetic energy transfer
Nbin = # of layers in edim direction (must be even number)
zero or more keyword/value pairs may be appended
keyword = swap
swap value = Nswap = number of swaps to perform every N steps
fix 1 all thermal/conductivity 100 z 20 fix 1 all thermal/conductivity 50 z 20 swap 2
Use the Muller-Plathe algorithm described in this paper to exchange kinetic energy between two particles in different regions of the simulation box every N steps. This induces a temperature gradient in the system. As described below this enables the thermal conductivity of a material to be calculated. This algorithm is sometimes called a reverse non-equilibrium MD (reverse NEMD) approach to computing thermal conductivity. This is because the usual NEMD approach is to impose a temperature gradient on the system and measure the response as the resulting heat flux. In the Muller-Plathe method, the heat flux is imposed, and the temperature gradient is the system’s response.
See the compute heat/flux command for details on how to compute thermal conductivity in an alternate way, via the Green-Kubo formalism.
The simulation box is divided into Nbin layers in the edim direction, where the layer 1 is at the low end of that dimension and the layer Nbin is at the high end. Every N steps, Nswap pairs of atoms are chosen in the following manner. Only atoms in the fix group are considered. The hottest Nswap atoms in layer 1 are selected. Similarly, the coldest Nswap atoms in the “middle” layer (see below) are selected. The two sets of Nswap atoms are paired up and their velocities are exchanged. This effectively swaps their kinetic energies, assuming their masses are the same. If the masses are different, an exchange of velocities relative to center of mass motion of the 2 atoms is performed, to conserve kinetic energy. Over time, this induces a temperature gradient in the system which can be measured using commands such as the following, which writes the temperature profile (assuming z = edim) to the file tmp.profile:
compute ke all ke/atom variable temp atom c_ke/1.5 compute layers all chunk/atom bin/1d z lower 0.05 units reduced fix 3 all ave/chunk 10 100 1000 layers v_temp file tmp.profile
Note that by default, Nswap = 1, though this can be changed by the optional swap keyword. Setting this parameter appropriately, in conjunction with the swap rate N, allows the heat flux to be adjusted across a wide range of values, and the kinetic energy to be exchanged in large chunks or more smoothly.
The “middle” layer for velocity swapping is defined as the Nbin/2 + 1 layer. Thus if Nbin = 20, the two swapping layers are 1 and 11. This should lead to a symmetric temperature profile since the two layers are separated by the same distance in both directions in a periodic sense. This is why Nbin is restricted to being an even number.
As described below, the total kinetic energy transferred by these swaps is computed by the fix and can be output. Dividing this quantity by time and the cross-sectional area of the simulation box yields a heat flux. The ratio of heat flux to the slope of the temperature profile is proportional to the thermal conductivity of the fluid, in appropriate units. See the Muller-Plathe paper for details.
If your system is periodic in the direction of the heat flux, then the flux is going in 2 directions. This means the effective heat flux in one direction is reduced by a factor of 2. You will see this in the equations for thermal conductivity (kappa) in the Muller-Plathe paper. LAMMPS is simply tallying kinetic energy which does not account for whether or not your system is periodic; you must use the value appropriately to yield a kappa for your system.
After equilibration, if the temperature gradient you observe is not linear, then you are likely swapping energy too frequently and are not in a regime of linear response. In this case you cannot accurately infer a thermal conductivity and should try increasing the Nevery parameter.
Restart, fix_modify, output, run start/stop, minimize info
This fix computes a global scalar which can be accessed by various output commands. The scalar is the cumulative kinetic energy transferred between the bottom and middle of the simulation box (in the edim direction) is stored as a scalar quantity by this fix. This quantity is zeroed when the fix is defined and accumulates thereafter, once every N steps. The units of the quantity are energy; see the units command for details. The scalar value calculated by this fix is “intensive”.
Swaps conserve both momentum and kinetic energy, even if the masses of the swapped atoms are not equal. Thus you should not need to thermostat the system. If you do use a thermostat, you may want to apply it only to the non-swapped dimensions (other than vdim).
LAMMPS does not check, but you should not use this fix to swap the kinetic energy of atoms that are in constrained molecules, e.g. via fix shake or fix rigid. This is because application of the constraints will alter the amount of transferred momentum. You should, however, be able to use flexible molecules. See the Zhang paper for a discussion and results of this idea.
When running a simulation with large, massive particles or molecules in a background solvent, you may want to only exchange kinetic energy between solvent particles.
The option defaults are swap = 1.
(Muller-Plathe) Muller-Plathe, J Chem Phys, 106, 6082 (1997).
(Zhang) Zhang, Lussetti, de Souza, Muller-Plathe, J Phys Chem B, 109, 15060-15067 (2005).