Structure flip at the beginning of NPT equilibration

LAMMPS LAMMPS General Discussion
1

Hello, everyone. I hope you are doing well. I’m trying to equilibrate a system consisting of clay, which includes different components like water and silicate layers, etc. After performing several steps of equilibration using the NVT ensemble, I ran the final equilibration using NPT. I should also mention that my system has a relatively large tilt factor. I noticed that the system flips as soon as I run the NPT. However, the results seem okay. Here is the output between the initial and timestep 1000:

Step          Temp          Press            Lx             Ly             Lz             Xy             Xz             Yz          Density         Volume         TotEng         PotEng         KinEng    
     0   297.36351     -7692.1368      26.525123      24.479838      13.785691     -17.01407       0.76472811    -6.2272094      2.4243479      8951.4723     -108825.92     -109510.21      684.28856    
  1000   316.44015     -346.29438      26.350577      24.215107      13.847519      9.7041279      0.63722181    -6.4078182      2.4560712      8835.8526     -108817.56     -109545.74      728.18744

My question is, is it normal for LAMMPS to flip the structure, or is something wrong, and should I check my parameters and my system? Thank you all for your help :slight_smile: .

2

When having a triclinic box, LAMMPS tries to keep the tilt angle larger than 45 degrees. The “flatter” the box gets, the more the performance (LAMMPS is most efficient with near cube shaped subdomains) suffers and for very high tilt angles the neighbor list will be missing atoms.

1 Like
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Thank you very much for your reply. So if I understand correctly, unless I encounter issues with missing atoms (which means that the simulation will stop) , there should be no problems, as the flip is just Lammps trying to enhance the performance ?

4

Correct, see fix nvt command — LAMMPS documentation.

The flip keyword allows the tilt factors for a triclinic box to exceed half the distance of the parallel box length, as discussed below. If the flip value is set to yes , the bound is enforced by flipping the box when it is exceeded. If the flip value is set to no , the tilt will continue to change without flipping. Note that if applied stress induces large deformations (e.g. in a liquid), this means the box shape can tilt dramatically and LAMMPS will run less efficiently, due to the large volume of communication needed to acquire ghost atoms around a processor’s irregular-shaped subdomain. For extreme values of tilt, LAMMPS may also lose atoms and generate an error.