Pressure Compute in Deposition Simulation

Hi all,

I have a more conceptual question about the reporting of pressure when the number of atoms in a simulation is changing. My simulation is periodic in x and y, with z being fixed. I apply the dynamic degrees of freedom change to the temperature as suggested in documentation, and I can see the clear difference here. I tried applying a similar modification to a pressure compute, both allowing dynamic DoF and using the new temperature compute, however, no change can be seen. My first thought is the either I didn’t implement it correctly, or the change is so small, it doesn’t appear in the output (difference is smaller than 1e-5). Is there another reason I’m not considering? I run in 08Feb2023 as my version.
The pressure compute commands I used are:
compute temp1 all temp
compute_modify temp1 dynamic/dof yes extra/dof 0
compute press1 all pressure temp1
compute_modify press1 dynamic/dof yes extra/dof 0

Thanks.

Please provide a simple, minimal, but complete example input deck, so that somebody can properly reproduce what you are talking about. Without a way to reproduce, it is next to impossible to provide meaningful advice.

KoLi.meam (216 Bytes)
Kolibrary.meam (965 Bytes)
quicktest.mod (1.2 KB)

Here are the potential files and the example input deck. Still running 08Feb2023, with the KOKKOS, KSPACE, MANYBODY, MEAM, MOLECULE, OPENMP, and RIGID packages installed. Using the command options -k on t 4 -sf kk when executing.
I’m mostly just curious about the lack of mention of pressure in the fix deposit documentation, since temperature is clearly pointed out.

Hi @jphilips,

I tried applying a similar modification to a pressure compute, both allowing dynamic DoF and using the new temperature compute, however, no change can be seen.
[…]
compute temp1 all temp
compute_modify temp1 dynamic/dof yes extra/dof 0
compute press1 all pressure temp1
compute_modify press1 dynamic/dof yes extra/dof 0

Please have a look at both the compute_modify and compute pressure manual pages.

As far as I can understand it, the extra/dof option only applies to compute that calculate a temperature. As stated in the compute pressure command, they only compute temperature through another compute. As such your last command seems pointless, it applies to the former and not to the latter.

What about making two pressure computes, one with and one without the modified temperature compute? That should make your point. You can also compare with virial term only and kinetic term only computes to see if there are noticeable differences in your systems.

I’m mostly just curious about the lack of mention of pressure in the fix deposit documentation, since temperature is clearly pointed out.

The physical meaning of the “pressure” computed at the molecular scale in non-periodic systems with non-homogeneous density such as surfaces can quickly become a tricky question. This becomes especially true in systems with void. The temperature, on the other hand, is clearly defined and correlated with the number of atoms.

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