X-Git-Url: https://hackdaworld.org/gitweb/?a=blobdiff_plain;f=posic%2Fthesis%2Fbasics.tex;h=24bfc19832f0f9d0e14bdc24e1e8579202357693;hb=4774842a09e4f15ab187088ffce234f44a7a11c4;hp=bc9e8a9b9e1630bdc3b4a9669d0ea173a67df199;hpb=99f1fbedcebc576e310584134307b9c14724d930;p=lectures%2Flatex.git diff --git a/posic/thesis/basics.tex b/posic/thesis/basics.tex index bc9e8a9..24bfc19 100644 --- a/posic/thesis/basics.tex +++ b/posic/thesis/basics.tex @@ -2,8 +2,38 @@ \section{Molecular dynamics simulations} +\subsection{Introduction to molecular dynamics simulations} -\subsection{Potentials} +Basically, molecular dynamics (MD) simulation is a technique to compute a system of particles, referred to as molecules, evolving in time. +The MD method was introduced by Alder and Wainwright in 1957 \cite{alder1,alder2} to study the interactions of hard spheres. +The basis of the approach are Newton's equations of motion to describe classicaly the many-body system. +MD simulation is the numerical way of solving the $N$-body problem ($N > 3$) which cannot be solved analytically. +Quantum mechanical effects are taken into account by an analytical interaction potential between the nuclei. + +By MD simulation techniques a complete description of the system in the sense of classical mechanics on the microscopic level is obtained. +This microscopic information has to be translated to macroscopic observables by means of statistical mechanics. + +The basic idea is to integrate Newton's equations numerically. +A system of $N$ particles of masses $m_i$ ($i=1,\ldots,N$) at positions ${\bf r}_i$ and velocities $\dot{{\bf r}}_i$ is given by +\begin{equation} +m_i \frac{d^2}{dt^2} {\bf r}_i = {\bf F}_i \, \textrm{.} +\end{equation} +The forces ${\bf F}_i$ are obtained from the potential energy $U(\{{\bf r}\})$: +\begin{equation} +{\bf F}_i = - \nabla_{{\bf r}_i} U({\{\bf r}\}) \, \textrm{.} +\end{equation} +Given the initial conditions ${\bf r}_i(t_0)$ and $\dot{{\bf r}}_i(t_0)$ the equations can be integrated by a certain integration algorithm. +The solution of these equations provides the complete information of a system evolving in time. + +The following chapters cover the tools of the trade necessary for the MD simulation technique. +First a detailed overview of the available integration algorithms is given, including their advantages and disadvantages. +After that the interaction potentials and their accuracy for describing certain systems of elements are discussed. + + + +\subsection{Integration algorithms} + +\subsection{Interaction potentials} \subsubsection{The Lennard-Jones potential} @@ -30,7 +60,7 @@ Writing down the derivation of the Lennard-Jones potential in respect to $x_i$ ( \label{eq:lj-d} \end{equation} one can easily identify $\sigma$ by the equilibrium distance of the atoms $r_e=\sqrt[6]{2} \sigma$. -Applying the equilibrium distance into \eqref{eq:lj-p} $\epsilon$ turns out to be half the negative well depth. +Applying the equilibrium distance into \eqref{eq:lj-p} $\epsilon$ turns out to be the negative well depth. The $i$th component of the force $F^j$ on particle $j$ is obtained by \begin{equation} F_i^j = - \frac{\partial}{\partial x_i} U^{LJ}(r) \, \textrm{.}