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28
doc/Section_howto.html
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@ -33,7 +33,8 @@
6.18 <A HREF = "#howto_18">Elastic constants</A><BR>
6.19 <A HREF = "#howto_19">Library interface to LAMMPS</A><BR>
6.20 <A HREF = "#howto_20">Calculating thermal conductivity</A><BR>
6.21 <A HREF = "#howto_21">Calculating viscosity</A> <BR>
6.21 <A HREF = "#howto_21">Calculating viscosity</A><BR>
6.22 <A HREF = "#howto_22">Calculating diffusion</A> <BR>
<P>The example input scripts included in the LAMMPS distribution and
highlighted in <A HREF = "Section_example.html">Section_example</A> also show how to
@ -2152,4 +2153,29 @@ Phys, 79, 926 (1983).
<P><B>(Shinoda)</B> Shinoda, Shiga, and Mikami, Phys Rev B, 69, 134103 (2004).
</P>
<HR>
<A NAME = "howto_22"></A><H4>6.22 Calculating diffusion
</H4>
<P>The diffusion coefficient D of a material can be measured in at least
2 ways using various options in LAMMPS. See the examples/DIFFUSE
directory for scripts that implement the 2 methods discussed here for
a simple Lennard-Jones fluid model.
</P>
<P>The first method is to measure the mean-squared displacement (MSD) of
the system, via the <A HREF = "compute_msd.html">compute msd</A> command. The slope
of the MSD versus time is proportional to the diffusion coefficient.
The instantaneous MSD values can be accumulated in a vector via the
<A HREF = "fix_vector.html">fix vector</A> command, and a line fit to the vector to
compute its slope via the <A HREF = "variable.html">variable slope</A> function, and
thus extract D.
</P>
<P>The second method is to measure the velocity auto-correlation function
(VACF) of the system, via the <A HREF = "compute_vacf.html">compute vacf</A>
command. The time-integral of the VACF is proportional to the
diffusion coefficient. The instantaneous VACF values can be
accumulated in a vector via the <A HREF = "fix_vector.html">fix vector</A> command,
and time integrated via the <A HREF = "variable.html">variable trap</A> function,
and thus extract D.
</P>
</HTML>

28
doc/Section_howto.txt
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@ -30,7 +30,8 @@ This section describes how to perform common tasks using LAMMPS.
6.18 "Elastic constants"_#howto_18
6.19 "Library interface to LAMMPS"_#howto_19
6.20 "Calculating thermal conductivity"_#howto_20
6.21 "Calculating viscosity"_#howto_21 :all(b)
6.21 "Calculating viscosity"_#howto_21
6.22 "Calculating diffusion"_#howto_22 :all(b)
The example input scripts included in the LAMMPS distribution and
highlighted in "Section_example"_Section_example.html also show how to
@ -2128,3 +2129,28 @@ Phys, 79, 926 (1983).
:link(Shinoda)
[(Shinoda)] Shinoda, Shiga, and Mikami, Phys Rev B, 69, 134103 (2004).
:line
6.22 Calculating diffusion :link(howto_22),h4
The diffusion coefficient D of a material can be measured in at least
2 ways using various options in LAMMPS. See the examples/DIFFUSE
directory for scripts that implement the 2 methods discussed here for
a simple Lennard-Jones fluid model.
The first method is to measure the mean-squared displacement (MSD) of
the system, via the "compute msd"_compute_msd.html command. The slope
of the MSD versus time is proportional to the diffusion coefficient.
The instantaneous MSD values can be accumulated in a vector via the
"fix vector"_fix_vector.html command, and a line fit to the vector to
compute its slope via the "variable slope"_variable.html function, and
thus extract D.
The second method is to measure the velocity auto-correlation function
(VACF) of the system, via the "compute vacf"_compute_vacf.html
command. The time-integral of the VACF is proportional to the
diffusion coefficient. The instantaneous VACF values can be
accumulated in a vector via the "fix vector"_fix_vector.html command,
and time integrated via the "variable trap"_variable.html function,
and thus extract D.