Hi Ajit, answers in line:

Jeremy,

Thanks for referring to those examples. Things are more clear to me now. But i still have some concerns about the implementation. I am actually trying to use two temp model in my work.

Here's the ttm reference as well then:

Jones, Templeton, Wagner, Olmsted, & Modine, "Electron transport enhanced molecular dynamics for metals and semi-metals," IJNME 83 (8-9) 2010.

1. Can't we use normal fix/NVT or NVE or NPT in these type of problems?

No, you cannot use any other fix that performs time integration with ATC (except for Hardy). The reason is that ATC provides it's own thermostatting based on the user-specified coupling. If other thermostats are used, the two will conflict.

2. I didn't observe the advantage of using fix/atc thermal coupling clearly. Like in the examples on Argon, it was mentioned that temp's on left and right ends are maintained at 40 &20 k respectively. It can be implemented directly with out using any coupling to observe a steady state temp profile. So, what's the point in using this method.

There are three main (intended) applications of the AtC dynamics packages (again distinct from Hardy): 1) multiscale coupling with a larger finite element model, 2) multiphysics coupling, e.g., MD with an electron temperature model, and 3) prescription of NEMD conditions including boundary conditions, initial conditions, and sources corresponding to those typically encountered in finite elements. In mode 3, standard Lammps commands of creating regions and then applying heat fluxes and thermostats to atoms in those regions is equivalent to using AtC with piecewise constant elements and no time filtering (the Templeton et al. paper describes this in more detail). AtC would make setting up these problems much easier, but more importantly significantly generalizes the method to use other type of shape functions and basing the thermostat effort on time filtered values. Empirically this has been shown to have advantages as can be seen in the Si conductivity example in Templeton et al. The decay of the piecewise linear shape function results in a smoother transition from the thermostatted to non-thermostatted regions and so we were able to calculate the conductivity of a Si sheet that was much thinner than had been done in the past using other methods, to the best of our knowledge.

3. How much will the computation time vary with using fix/atc-thermal or ttm compared to the simulation with out using them?

It depends on how big your finite element mesh is and how much/what type of thermostatting you do. Also, our finite element calculations are not parallelized (the interactions with the atoms is parallelized using the same scheme as Lammps). Our code up until now has been primarily for research, so it is far from optimized. We will be looking at improving performance over the next year, although unless you need a very large grid or are running on a very large number of processors, if your Lammps simulation cost is acceptable I would think adding AtC would not make it unacceptable.

Jeremy