"Hole" in liquid after switching from fix NPT to fix NVT

LAMMPS LAMMPS General Discussion
1

Hello,

I am currently trying to simulate nanoporous structures using a polarizable forcefield. In the equilibration I want to do an NPT run first to adjust the box size and then continue the equilibration in the NVT ensemble. My Problem is that currently as soon as I switch from fix NPT to fix NVT a hole appears in my liquid.
Here is a cutout of my box at the last frame of the NPT run (there is no hole anywhere):

image

and here at the end of the NVT run:

image

My input/data:
data.nvt2.lmp (4.4 MB)

The structure is periodic in x-y direction. It is basically a nanotube connecting two graphene walls. The transition between tube and wall basically has 1 90° angle as making any “normal” transition with reasonable angles would make the structure unfeasably large. The unphysical angle is also why I have to freeze the wall part, as well as some of the atoms of the tube.

The output of the simulation:
lmp.out (121.9 KB)

I probably did something really stupid in my input. Has anyone ever had a similar problem and can Help me? Any clue is greatly appreciated.

Cheers,
Nicolas

2

It’s a bubble, plain and simple.

Your liquid has too much available volume to fill. It minimises its free energy by forming a void. Because its vapour pressure is likely incredibly low at your chosen temperature, the void has zero ions or molecules in it on average.

Simply gradually decrease your simulation volume, for example with fix deform. Be careful that you do not distort the bonds in your nanoporous structure as you proceed.

You can’t completely trust an NPT simulation to “impose the correct pressure” on a highly inhomogeneous simulation box such as yours. You should run with an NVT integrator such that the density of a suitable “bulk” region of your liquid is, on average, what it would be in an equivalent NPT bulk simulation.

1 Like
3

Thank you very much!