jianmu
/
lammps
forked from lijiext/lammps
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@11553 f3b2605a-c512-4ea7-a41b-209d697bcdaa

This commit is contained in:
sjplimp 2014-02-12 23:18:18 +00:00
parent 0bd0e95bad
commit 553baf3f4d
2 changed files with 46 additions and 50 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

48
doc/Section_howto.html
View File

@ -2106,6 +2106,29 @@ print "average viscosity: $v [Pa.s/</B> @ $T K, ${ndens} /A^3"
</PRE>
<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>
<HR>
<HR>
@ -2153,29 +2176,4 @@ 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>

48
doc/Section_howto.txt
View File

@ -2093,6 +2093,29 @@ print "average viscosity: $v \[Pa.s/] @ $T K, $\{ndens\} /A^3" :pre
: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.
:line
:line
@ -2129,28 +2152,3 @@ 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.