Purpose

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Purpose

A DynamicalSystem object contains an Atoms object, which holds infomation about velocities and accelerations of each atom, scalar quantities such as thermostat settings, and logical masks so that thermostatting can be applied to selected atoms etc.

Initialise a DynamicalSystem object like this:

$\begin{boxedminipage}{\textwidth} \begin{verbatim}call initialise(MyDS, MyAtoms)\end{verbatim} \end{boxedminipage}$

which copies MyAtoms into the internal atoms structure (and so MyAtoms is not required by MyDS after this call).

DynamicalSystem has an integrator,

$\begin{boxedminipage}{\textwidth} \begin{verbatim}call advance_verlet(MyDS,dt,forces)\end{verbatim} \end{boxedminipage}$

which takes a set of forces and integrates the equations of motion forward for a time dt.

gabor 2009-06-30