Error message for NPT Si-Ge-Si heating

[DSarkar]

Hi,

I am trying to make a stabilized Si-Ge-Si interface at 1200K. I designed two simulations (one of them is attached because of size constraint in attachments): one where the bulk structure was initialized to 0K, and another where initial velocities were initialized to 1200K (Maxwell-Boltzmann). Both are placed in an NPT Berendsen with high thermal coupling constant 50000 fs for slow heating, and set to run for 1 nm at 1fs step size. Both simulations get prematurely terminated: the first one shows some movie for 60 fs, whereas the second one does not display any movie at all, with an error message. The error message from the log files for both are also attached. Could you please let me know where I am going wrong in my methods?

Regards,

Debarghya

[Julian Schneider]

I would not recommend the approach to start from 0K, and then use a large coupling constant to slowly increase the temperature, especially not for Nose-Hoover-based thermostats, such as NPT-Melchionna. The problem with these thermostats is that the temperature does not approach the target temperature exponentially, but instead oscillates around the target temperature with an amplitudes that is, at least in the beginning, proportional to the difference between actual temperature (i.e. 0K) and target temperature (i.e. 1200 K). That means the temperature might at some point overshoot the target temperature by a considerable amount, which can destabilize the system. Instead, I recommend to use the NVT-Nose-Hoover-Chain-thermostat where you can set an initial and a final temperature, which linearly changes the target temperature from one to the other value during the simulation (while keeping the thermostat_timescale reasonably low at ~100 fs). Unfortunately, this is currently only possible for NVT and not NPT (in ATK-2016 it will be possible for all thermostats and barostats).
The error message that you encounter, though, has nothing to do with this. This might be a problem that we sometimes encounter if the trajectory is saved too often. You can try increasing the log_interval parameter to, say 500 steps and check if the problem still persists.

[DSarkar]

 Hi Julian,

Thanks for the detailed explanation. This understanding would definitely help me a lot in designing future simulations. I had a question about the effect of changing the coupling constant of the thermostat and barostat. In an attempt to understand the machinery better, I made a few sweeps of the parameters and have attached a small snapshot here due to file size constraints.
My observations are (all of which may not be obvious from this slide):
1. Thermostat time constant has the dominant effect in determining the envelope of KE /temperature variation dynamics.
2. Barostat time constant has its effect on the detailed fluctuations.
3. At higher coupling constants like >25 fs, a time step of 1 fs is sufficient to resolve the dynamics (since 0.5 fs timestep gives the same temperature profile). 4. But at lower coupling constants like 5 fs, there is a significant difference between 1fs timestep and 0.5 fs timestep.
My queries are:
1. Does the discrepancy between observations 3 and 4 above appear because the external forces "dominate" over the natural dynamics of the system and/or the external coupling is so fast that we need higher sampling to resolve it?
2. Based on all observations above, what would be an optimum coupling constant and time step for the system? What would be a standard procedure to determine these parameters properly in general for any system?
3. How can we know quantitatively that the system is relaxed? In other words, what command would give us the force on each atom which can be minimized?

Thanks a lot for your help.

Regards,

Debarghya