I have a question about the energy balance in the case of NVT simulation.
I am simulating fracture of graphene using the REBO potential on a sheet of about 70 000 atoms under periodic boundary conditions in the two in-plane directions and fixed in the third direction. time step is 1fs, temperature 0.1K. units are metal.
The simulation consist in successively increasing the x size of the simulation box by 0.01% and running an NVT simulation for 20 000 time steps. (Doing so, I simulate an monoaxial strain tensile test at a strain rate of 5e^-9 fs^-1.
My question concern the energy balance under NVT conditions.
I customized the thermo style with f_NVT so that the column “etotal” (total energy) includes the energy given to the thermostat. Moreover I know that by computing the difference “etotal-f_NVT” I get the total energy (internal energy) of the system regardless of what have been given to the thermostat.
— Interesting lines
variable TimeStep equal 0.001 #timestep 1fs
variable Temp equal 0.1 #temperature
variable Tdamp equal 0.1 #Tdamp de Nose-Hoover 100fs
NVT
fix NVT all nvt temp {Temp} {Temp} ${Tdamp}
fix_modify NVT energy yes
#Define thermo parameters in log file
thermo ${ThermalFreq}
thermo_style custom step time lx ly temp pe ke etotal pxx pyy pxy pzz f_NVT