Thermodynamic observables

Objective

This module defines a set of thermodynamic observables commonly output by molecular simulation programs.

Module name and version

The name of this module is thermodynamics. The module version is 1.0.0.

Observables

Thermodynamic observables are stored in the observables group for global properties or in observables/<group> for subsystems, similarly to the particles group. The groups have the following contents:

observables
 \-- <group>
      +-- dimension: Integer[]
      \-- particle_number
      \-- (pressure)
      \-- (temperature)
      \-- (density)
      \-- ...
dimension

A scalar attribute of Integer type that gives the dimension of the space embedding the subsystem.

particle_number

The number of particles in the subsystem stored as scalar H5MD element of Integer datatype.

The following H5MD elements are optional, of scalar character, and use the Float datatype.

pressure

The pressure of the subsystem.

temperature

The (instantaneous) temperature of the subsystem as inferred from the kinetic energy.

density

The number density of the subsystem stored as Float or Integer datatype.

potential_energy

The potential energy of the subsystem.

kinetic_energy

The kinetic energy of the subsystem.

internal_energy

The internal energy of the subsystem, typically the sum of potential and kinetic energy.

enthalpy

The enthalpy of the subsystem.

The latter 4 quantities are stored as per-particle averages. The corresponding extensive quantities (scaling linearly with the system size) are obtained by multiplication with the number of particles. Per-volume averages follow by multiplication with the number density if present.