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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@2819 f3b2605a-c512-4ea7-a41b-209d697bcdaa

This commit is contained in:
sjplimp 2009-05-19 14:43:06 +00:00
parent a12fe07b28
commit 65317f1486
6 changed files with 70 additions and 26 deletions
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2
doc/fix_rigid.html
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@ -211,7 +211,7 @@ exclude
</P>
<P><B>Default:</B>
</P>
<P>The option defaults are force * 1 1 1 and torque * 1 1 1, meaning
<P>The option defaults are force * on on on and torque * on on on meaning
all rigid bodies are acted on by center-of-mass force and torque.
</P>
</HTML>

2
doc/fix_rigid.txt
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@ -202,6 +202,6 @@ exclude
[Default:]
The option defaults are force * 1 1 1 and torque * 1 1 1, meaning
The option defaults are force * on on on and torque * on on on meaning
all rigid bodies are acted on by center-of-mass force and torque.

25
doc/pair_gayberne.html
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@ -51,17 +51,20 @@ curvatures <A HREF = "#Everaers">(Everaers)</A>:
<P>The variable names utilized as potential parameters are for the most
part taken from <A HREF = "#Everaers">(Everaers)</A> in order to be consistent with
its RE-squared potential fix. Details on the upsilon and mu
parameters are given <A HREF = "gbdoc">here</A>. Use of this pair style requires
the NVE, NVT, or NPT fixes with the <I>asphere</I> extension (e.g. <A HREF = "fix_nve_asphere.html">fix
nve/asphere</A>) in order to integrate particle
rotation. Additionally, <A HREF = "atom_style.html">atom_style ellipsoid</A> should
be used since it defines the rotational state of the ellipsoidal
particles.
parameters are given <A HREF = "gbdoc">here</A>.
</P>
<P>More details of the Gay-Berne formulation are given in the references
listed below and in <A HREF = "PDF/pair_gayberne_extra.pdf">this supplementary
document</A>.
</P>
<P>Use of this pair style requires the NVE, NVT, or NPT fixes with the
<I>asphere</I> extension (e.g. <A HREF = "fix_nve_asphere.html">fix nve/asphere</A>) in
order to integrate particle rotation. Additionally, <A HREF = "atom_style.html">atom_style
ellipsoid</A> should be used since it defines the
rotational state of the ellipsoidal particles. The size and shape of
the ellipsoidal particles are defined by the <A HREF = "shape.html">shape</A>
command.
</P>
<P>The following coefficients must be defined for each pair of atoms
types via the <A HREF = "pair_coeff.html">pair_coeff</A> command as in the examples
above, or in the data file or restart files read by the
@ -81,6 +84,11 @@ commands, or by mixing as described below:
<P>The last coefficient is optional. If not specified, the global
cutoff specified in the pair_style command is used.
</P>
<P>It is typical for the Gay-Berne potential to define <I>sigma</I> as the
minimum of the 3 "shape" diameters for a I,I interaction, though this
is not required. Note that this is a different meaning for <I>sigma</I>
than the <A HREF = "pair_resquared.html">pair_style resquared</A> potential uses.
</P>
<P>The epsilon_i and epsilon_j coefficients are actually defined for atom
types, not for pairs of atom types. Thus, in a series of pair_coeff
commands, they only need to be specified once for each atom type.
@ -149,7 +157,10 @@ to be specified in an input script that reads a restart file.
</P>
<P>This style is part of the "asphere" package. It is only enabled if
LAMMPS was built with that package. See the <A HREF = "Section_start.html#2_3">Making
LAMMPS</A> section for more info.
LAMMPS</A> section for more info. You must also
define a size and shape for each particle type via the
<A HREF = "shape.html">shape</A> command which requires <A HREF = "atom_style.html">atom_style
ellipsoid</A>.
</P>
<P>The Gay-Berne potential does not become isotropic as r increases
<A HREF = "#Everaers">(Everaers)</A>. The distance-of-closest-approach

25
doc/pair_gayberne.txt
View File

@ -48,17 +48,20 @@ curvatures "(Everaers)"_#Everaers:
The variable names utilized as potential parameters are for the most
part taken from "(Everaers)"_#Everaers in order to be consistent with
its RE-squared potential fix. Details on the upsilon and mu
parameters are given "here"_gbdoc. Use of this pair style requires
the NVE, NVT, or NPT fixes with the {asphere} extension (e.g. "fix
nve/asphere"_fix_nve_asphere.html) in order to integrate particle
rotation. Additionally, "atom_style ellipsoid"_atom_style.html should
be used since it defines the rotational state of the ellipsoidal
particles.
parameters are given "here"_gbdoc.
More details of the Gay-Berne formulation are given in the references
listed below and in "this supplementary
document"_PDF/pair_gayberne_extra.pdf.
Use of this pair style requires the NVE, NVT, or NPT fixes with the
{asphere} extension (e.g. "fix nve/asphere"_fix_nve_asphere.html) in
order to integrate particle rotation. Additionally, "atom_style
ellipsoid"_atom_style.html should be used since it defines the
rotational state of the ellipsoidal particles. The size and shape of
the ellipsoidal particles are defined by the "shape"_shape.html
command.
The following coefficients must be defined for each pair of atoms
types via the "pair_coeff"_pair_coeff.html command as in the examples
above, or in the data file or restart files read by the
@ -78,6 +81,11 @@ cutoff (distance units) :ul
The last coefficient is optional. If not specified, the global
cutoff specified in the pair_style command is used.
It is typical for the Gay-Berne potential to define {sigma} as the
minimum of the 3 "shape" diameters for a I,I interaction, though this
is not required. Note that this is a different meaning for {sigma}
than the "pair_style resquared"_pair_resquared.html potential uses.
The epsilon_i and epsilon_j coefficients are actually defined for atom
types, not for pairs of atom types. Thus, in a series of pair_coeff
commands, they only need to be specified once for each atom type.
@ -146,7 +154,10 @@ This pair style can only be used via the {pair} keyword of the
This style is part of the "asphere" package. It is only enabled if
LAMMPS was built with that package. See the "Making
LAMMPS"_Section_start.html#2_3 section for more info.
LAMMPS"_Section_start.html#2_3 section for more info. You must also
define a size and shape for each particle type via the
"shape"_shape.html command which requires "atom_style
ellipsoid"_atom_style.html.
The Gay-Berne potential does not become isotropic as r increases
"(Everaers)"_#Everaers. The distance-of-closest-approach

21
doc/pair_resquared.html
View File

@ -28,7 +28,7 @@ pair_coeff * * 1.0 1.0 1.7 3.4 3.4 1.0 1.0 1.0
<A HREF = "#Everaers">(Everaers)</A>, <A HREF = "#Babadi">(Babadi)</A> between pairs of
ellipsoidal and/or spherical Lennard-Jones particles. For ellipsoidal
interactions, the potential considers the ellipsoid as being comprised
of small spheres of size sigma. LJ particles are a single sphere of
of small spheres of size sigma. LJ particles are a single sphere of
size sigma. The distinction is made to allow the pair style to make
efficient calculations of ellipsoid/solvent interactions.
</P>
@ -39,9 +39,9 @@ in <A HREF = "PDF/pair_resquared_extra.pdf">this supplementary document</A>.
<I>asphere</I> extension (e.g. <A HREF = "fix_nve_asphere.html">fix nve/asphere</A>) in
order to integrate particle rotation. Additionally, <A HREF = "atom_style.html">atom_style
ellipsoid</A> should be used since it defines the
rotational state of the ellipsoidal particles and the
<A HREF = "shape.html">shape</A> command should be used to specify ellipsoid
diameters.
rotational state of the ellipsoidal particles. The size and shape of
the ellipsoidal particles are defined by the <A HREF = "shape.html">shape</A>
command.
</P>
<P>The following coefficients must be defined for each pair of atoms
types via the <A HREF = "pair_coeff.html">pair_coeff</A> command as in the examples
@ -59,6 +59,14 @@ commands:
<LI>epsilon_j_c = relative well depth of type J for end-to-end interactions
<LI>cutoff (distance units)
</UL>
<P>The last coefficient is optional. If not specified, the global
cutoff specified in the pair_style command is used.
</P>
<P>As described above, <I>sigma</I> is the size of the small spheres which are
integrated over to create the potential. Note that this is a
different meaning for <I>sigma</I> than the <A HREF = "pair_gayberne.html">pair_style
gayberne</A> potential uses.
</P>
<P>The parameters used depend on the type of the interacting particles,
i.e. ellipsoid or LJ sphere. The type of particle is determined by
the diameters specified with the <A HREF = "shape.html">shape</A> command. LJ
@ -173,7 +181,10 @@ command</A>.
</P>
<P>This style is part of the "asphere" package. It is only enabled if
LAMMPS was built with that package. See the <A HREF = "Section_start.html#2_3">Making
LAMMPS</A> section for more info.
LAMMPS</A> section for more info. You must also
define a size and shape for each particle type via the
<A HREF = "shape.html">shape</A> command which requires <A HREF = "atom_style.html">atom_style
ellipsoid</A>.
</P>
<P>The distance-of-closest-approach approximation used by LAMMPS becomes
less accurate when high-aspect ratio ellipsoids are used.

21
doc/pair_resquared.txt
View File

@ -25,7 +25,7 @@ Style {resquared} computes the RE-squared anisotropic interaction
"(Everaers)"_#Everaers, "(Babadi)"_#Babadi between pairs of
ellipsoidal and/or spherical Lennard-Jones particles. For ellipsoidal
interactions, the potential considers the ellipsoid as being comprised
of small spheres of size sigma. LJ particles are a single sphere of
of small spheres of size sigma. LJ particles are a single sphere of
size sigma. The distinction is made to allow the pair style to make
efficient calculations of ellipsoid/solvent interactions.
@ -36,9 +36,9 @@ Use of this pair style requires the NVE, NVT, or NPT fixes with the
{asphere} extension (e.g. "fix nve/asphere"_fix_nve_asphere.html) in
order to integrate particle rotation. Additionally, "atom_style
ellipsoid"_atom_style.html should be used since it defines the
rotational state of the ellipsoidal particles and the
"shape"_shape.html command should be used to specify ellipsoid
diameters.
rotational state of the ellipsoidal particles. The size and shape of
the ellipsoidal particles are defined by the "shape"_shape.html
command.
The following coefficients must be defined for each pair of atoms
types via the "pair_coeff"_pair_coeff.html command as in the examples
@ -56,6 +56,14 @@ epsilon_j_b = relative well depth of type J for face-to-face interactions
epsilon_j_c = relative well depth of type J for end-to-end interactions
cutoff (distance units) :ul
The last coefficient is optional. If not specified, the global
cutoff specified in the pair_style command is used.
As described above, {sigma} is the size of the small spheres which are
integrated over to create the potential. Note that this is a
different meaning for {sigma} than the "pair_style
gayberne"_pair_gayberne.html potential uses.
The parameters used depend on the type of the interacting particles,
i.e. ellipsoid or LJ sphere. The type of particle is determined by
the diameters specified with the "shape"_shape.html command. LJ
@ -170,7 +178,10 @@ command"_run_style.html.
This style is part of the "asphere" package. It is only enabled if
LAMMPS was built with that package. See the "Making
LAMMPS"_Section_start.html#2_3 section for more info.
LAMMPS"_Section_start.html#2_3 section for more info. You must also
define a size and shape for each particle type via the
"shape"_shape.html command which requires "atom_style
ellipsoid"_atom_style.html.
The distance-of-closest-approach approximation used by LAMMPS becomes
less accurate when high-aspect ratio ellipsoids are used.