diff --git a/doc/Section_howto.html b/doc/Section_howto.html index 7deb92ce1b..6144efe2ff 100644 --- a/doc/Section_howto.html +++ b/doc/Section_howto.html @@ -2106,6 +2106,29 @@ print "average viscosity: $v [Pa.s/ @ $T K, ${ndens} /A^3"
+

6.22 Calculating diffusion +

+

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 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 command, and a line fit to the vector to +compute its slope via the variable slope function, and +thus extract D. +

+

The second method is to measure the velocity auto-correlation function +(VACF) of the system, via the compute vacf +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 command, +and time integrated via the variable trap function, +and thus extract D. +

@@ -2153,29 +2176,4 @@ Phys, 79, 926 (1983).

(Shinoda) Shinoda, Shiga, and Mikami, Phys Rev B, 69, 134103 (2004).

-
- -

6.22 Calculating diffusion -

-

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 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 command, and a line fit to the vector to -compute its slope via the variable slope function, and -thus extract D. -

-

The second method is to measure the velocity auto-correlation function -(VACF) of the system, via the compute vacf -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 command, -and time integrated via the variable trap function, -and thus extract D. -

diff --git a/doc/Section_howto.txt b/doc/Section_howto.txt index b093e31491..31fb9da87f 100644 --- a/doc/Section_howto.txt +++ b/doc/Section_howto.txt @@ -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.