User Guide#

The Set Cell step changes the periodic cell of the current structure and moves its contents with it.

How the cell is changed#

“Adjust cell by” chooses how:

density or volume: scale the cell uniformly to a density or a volume. Either may be a variable, e.g. a density saved from an earlier step.
the mean volume of the last NPT run: scale the cell uniformly to the mean volume of the last NPT run earlier in the flowchart, over its equilibrated part (the mean volume, not the cube of the mean length). This is the usual way to prepare constant-volume production runs of a liquid at its equilibrium density:
```
Model Chemistry, Packmol, minimization
LAMMPS: velocities, NPT equilibration
Set Cell: the mean volume of the last NPT run
LAMMPS: NVT equilibration, then the production runs
```
cell parameters: set a, b, c and the angles.
uniform contraction/expansion: change the volume by a fraction, e.g. “1%” or “-2%”.

“Move the contents by” chooses how the atoms follow the cell:

molecule centers: each molecule is made whole and moved rigidly with its center of mass, so its bonds and angles are unchanged. This is what a liquid of molecules needs: scaling the atoms instead would stretch every bond, which a rigid water model’s constraints (SHAKE) cannot recover from in the first step.
atoms: every atom is scaled with the cell (an affine transformation, keeping the fractional coordinates), as for a crystal or an extended network.
automatic (the default): molecule centers when the system is made of separate molecules, none of them spanning the cell; the atoms otherwise. The output says which was used and why.

The velocities are not changed.

The new volume, density and cell parameters, which can be stored in variables or tables.