HOOMD-blue stores and computes all values in a system of generic, fully self-consistent set of units. No conversion factors need to be applied to values at every step. For example, a value with units of force comes from dividing energy by distance.
The three fundamental units are:
- distance - 𝒟
- energy - ℰ
- mass - ℳ
All other units that appear in HOOMD-blue are derived from these. Values can be converted into any other system of units by assigning the desired units to 𝒟, ℰ, and ℳ and then multiplying by the appropriate conversion factors.
The standard Lennard-Jones symbols σ and ϵ are intentionally not referred to here. When you assign a value to ϵ in hoomd, for example, you are assigning it in units of energy: ϵ = 5ℰ. ϵ is NOT the unit of energy - it is a value with units of energy.
HOOMD-blue accepts all temperature inputs and provides all temperature output values in units of energy: kT, where k is Boltzmann's constant. When using physical units, the value kB is determined by the choices for distance, energy, and mass. In reduced units, one usually reports the value
Most of the argument inputs in HOOMD take the argument name kT
to make it explicit. A few areas of the code may still refer to this as temperature
.
The unit of charge used in HOOMD-blue is also reduced, but is not represented using just the 3 fundamental units -the permittivity of free space ε0 is also present. The units of charge are: (4πε0𝒟ℰ)1/2. Divide a given charge by this quantity to convert it into an input value for HOOMD-blue.
Here are some commonly used derived units:
- time -
$\tau = \sqrt{\frac{\mathcal{M} \mathcal{D}^2}{\mathcal{E}}}$ - volume - 𝒟3
- velocity -
$\frac{\mathcal{D}}{\tau}$ - momentum -
$\mathcal{M} \frac{\mathcal{D}}{\tau}$ - acceleration -
$\frac{\mathcal{D}}{\tau^2}$ - force -
$\frac{\mathcal{E}}{\mathcal{D}}$ - pressure -
$\frac{\mathcal{E}}{\mathcal{D}^3}$
There are many possible choices of physical units that one can assign. One common choice is:
- distance - 𝒟 = nm
- energy - ℰ = kJ/mol
- mass - ℳ = amu
Derived units / values in this system:
- time - picoseconds
- velocity - nm/picosecond
- k = 0.00831445986144858 kJ/mol/Kelvin