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Diffusion: diffus.f

This procedure computes time dependence of the mean square displacement (MSD) and evaluates the self-diffusion coefficient.

Compilation:

f77 -O3 -o diffus diffus.f tranal_base.f

Input parameters for this utility follow after the trajectory parameters in the NAMELIST block DIFF:

 $DIFF
 parameter=value(s),
 ...
 $END

The following parameters are used:

Futher comments

For each time $t$ the MSD is computed as:


\begin{displaymath}
\langle \Delta r^2(t)\rangle = \langle (\vec{r}(t_0+t)-\vec{r}(t_0))^2\rangle
\end{displaymath} (14)

where averaging is taken over all molecules of type IDF and all acceptable initial times $t_0$: $t_{beg} \le t_0 \le t_{end}-t$, where $t_{beg}$ and $t_{end}$ are the initial and final time of a continuous part of the whole trajectory respectively. A trajectory is regarded as continuous if each next configuration differ from the previous no more than parameter BREAKM defined in the trajectory part (TRAJ) of the input file.

The output file consists of the following columns:

The first column- time $t$.

The second: for each $t$, evaluation of the diffusion coefficient as:


\begin{displaymath}D_{av} = \frac{\langle \Delta r^2(t)\rangle}{6t}\end{displaymath}

The third column: for each $t$, evaluation of the diffusion coefficient as:


\begin{displaymath}D_{dif} = \frac{1}{6}\frac{\partial\langle \Delta r^2(t)\rangle}{\partial t}\end{displaymath}

The 4-th column: root square of the MSD (average particle displacement)

5-th - 7-th columns: Evaluation of diffusion coefficient in X-, Y-, and Z-directions as:


\begin{displaymath}D_{X} = \frac{\langle \Delta x^2(t)\rangle}{2t}\end{displaymath}

In all cases, diffusion is given in $10^{-5}cm^2/s$.


next up previous contents
Next: Dryrun: dryrun.f Up: Tranal utility Previous: Dielectric constant: diel.f   Contents
Alexander Lyubartsev 2015-02-06