I have a cube with periodic boundary conditions in two dimensions and shrink
wrap conditions in the third (call it z). I am using the NVT ensemble.
correction: you are *not* using the NVT ensemble, you are using the
"fix nvt" integrator.
I am wondering about the volume part of the computation. What is the volume
piece of the shrink wrap dimension? Is it whatever the instantaneous
there is no "volume part" of the computation. fix nvt disregards the
volume completely. please see below.
envelope of the z dimension is? Or is there something else going on? That
is, V is value of the three bounding dimensions are. Whether the dimension
is fixed or not.
your logic is inverted from the one that is employed in LAMMPS. none
of those n?? fixes *enforce* any kind of statistical mechanical
ensemble. it is the other way around, they are a prerequisite for
obtaining the desired ensemble.
fix nve does plain velocity-verlet style time integration AND NOTHING
ELSE. if you have a well equilibrated system, with fully periodic
boundaries and *NO OTHER* manipulations of the system, you will sample
the NVE statistical mechanical ensemble, but only then.
fix nvt adds to this manipulation of the kinetic energy through
coupling it to nose-hoover chains which, under the same conditions as
above, will result in an NVT ensemble, i.e. the same as if you had an
infinitely large NVE system equilibrated to the desired temperature.
fix nph adds manipulation of the volume in response to pressure.
fix nph adds both, manipulation of the kinetic energy and the volume.
similar manipulations can also be obtained through other means (fix
langevin, fix press/berendsen, fix temp/berendsen, fix temp/csvr and
so on) and people argue whether those truly sample the corresponding
statistical mechanical ensembles. some (e.g. langevin and berendsen)
have known and sometimes significant deficiencies, yet how much impact
those have, depends on the particular scenario.
regardless of that, a system with non-periodic boundaries always
represents an *infinite* volume, whether lammps uses fixed or
shrinkwrap (or m) boundaries is merely a question of practicality (no
point in doing bookkeeping on empty space). it has no impact on the
statistical mechanical situation and none of the conventional
statistical mechanical ensembles apply to such simulations.