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2
doc/Eqs/pair_yukawa.tex
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@ -6,4 +6,4 @@ $$
E = A \frac{e^{- \kappa r}}{r} \qquad r < r_c
$$
\end{document}
\end{document}

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doc/Eqs/pair_yukawa_colloid.tex Normal file
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@ -0,0 +1,9 @@
\documentclass[12pt]{article}
\begin{document}
$$
E = \frac{A}{\kappa} e^{- \kappa (r - (r_i + r_j))} \qquad r < r_c
$$
\end{document}

6
doc/Section_commands.html
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@ -327,8 +327,8 @@ of each style or click on the style itself for a full description:
<TR ALIGN="center"><TD ><A HREF = "fix_nve_asphere.html">nve/asphere</A></TD><TD ><A HREF = "fix_nve_limit.html">nve/limit</A></TD><TD ><A HREF = "fix_nve_noforce.html">nve/noforce</A></TD><TD ><A HREF = "fix_nve_sphere.html">nve/sphere</A></TD><TD ><A HREF = "fix_nvt.html">nvt</A></TD><TD ><A HREF = "fix_nvt_asphere.html">nvt/asphere</A></TD><TD ><A HREF = "fix_nvt_sllod.html">nvt/sllod</A></TD><TD ><A HREF = "fix_nvt_sphere.html">nvt/sphere</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_orient_fcc.html">orient/fcc</A></TD><TD ><A HREF = "fix_planeforce.html">planeforce</A></TD><TD ><A HREF = "fix_poems.html">poems</A></TD><TD ><A HREF = "fix_pour.html">pour</A></TD><TD ><A HREF = "fix_press_berendsen.html">press/berendsen</A></TD><TD ><A HREF = "fix_print.html">print</A></TD><TD ><A HREF = "fix_rdf.html">rdf</A></TD><TD ><A HREF = "fix_reax_bonds.html">reax/bonds</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_recenter.html">recenter</A></TD><TD ><A HREF = "fix_rigid.html">rigid</A></TD><TD ><A HREF = "fix_setforce.html">setforce</A></TD><TD ><A HREF = "fix_shake.html">shake</A></TD><TD ><A HREF = "fix_spring.html">spring</A></TD><TD ><A HREF = "fix_spring_rg.html">spring/rg</A></TD><TD ><A HREF = "fix_spring_self.html">spring/self</A></TD><TD ><A HREF = "fix_temp_berendsen.html">temp/berendsen</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_temp_rescale.html">temp/rescale</A></TD><TD ><A HREF = "fix_thermal_conductivity.html">thermal/conductivity</A></TD><TD ><A HREF = "fix_tmd.html">tmd</A></TD><TD ><A HREF = "fix_ttm.html">ttm</A></TD><TD ><A HREF = "fix_viscosity.html">viscosity</A></TD><TD ><A HREF = "fix_viscous.html">viscous</A></TD><TD ><A HREF = "fix_wall_gran.html">wall/gran</A></TD><TD ><A HREF = "fix_wall_lj126.html">wall/lj126</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_wall_lj93.html">wall/lj93</A></TD><TD ><A HREF = "fix_wall_reflect.html">wall/reflect</A></TD><TD ><A HREF = "fix_wiggle.html">wiggle</A>
<TR ALIGN="center"><TD ><A HREF = "fix_temp_rescale.html">temp/rescale</A></TD><TD ><A HREF = "fix_thermal_conductivity.html">thermal/conductivity</A></TD><TD ><A HREF = "fix_tmd.html">tmd</A></TD><TD ><A HREF = "fix_ttm.html">ttm</A></TD><TD ><A HREF = "fix_viscosity.html">viscosity</A></TD><TD ><A HREF = "fix_viscous.html">viscous</A></TD><TD ><A HREF = "fix_wall_colloid.html">wall/colloid</A></TD><TD ><A HREF = "fix_wall_gran.html">wall/gran</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_wall_lj126.html">wall/lj126</A></TD><TD ><A HREF = "fix_wall_lj93.html">wall/lj93</A></TD><TD ><A HREF = "fix_wall_reflect.html">wall/reflect</A></TD><TD ><A HREF = "fix_wiggle.html">wiggle</A>
</TD></TR></TABLE></DIV>
<P>These are fix styles contributed by users, which can be used if
@ -382,7 +382,7 @@ potentials. Click on the style itself for a full description:
<TR ALIGN="center"><TD ><A HREF = "pair_lj96_cut.html">lj96/cut</A></TD><TD ><A HREF = "pair_lubricate.html">lubricate</A></TD><TD ><A HREF = "pair_meam.html">meam</A></TD><TD ><A HREF = "pair_morse.html">morse</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_morse.html">morse/opt</A></TD><TD ><A HREF = "pair_peri_pmb.html">peri/pmb</A></TD><TD ><A HREF = "pair_reax.html">reax</A></TD><TD ><A HREF = "pair_resquared.html">resquared</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_soft.html">soft</A></TD><TD ><A HREF = "pair_sw.html">sw</A></TD><TD ><A HREF = "pair_table.html">table</A></TD><TD ><A HREF = "pair_tersoff.html">tersoff</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_tersoff_zbl.html">tersoff/zbl</A></TD><TD ><A HREF = "pair_yukawa.html">yukawa</A>
<TR ALIGN="center"><TD ><A HREF = "pair_tersoff_zbl.html">tersoff/zbl</A></TD><TD ><A HREF = "pair_yukawa.html">yukawa</A><A HREF = "pair_yukawa_colloid.html">yukawa/colloid</A>
</TD></TR></TABLE></DIV>
<P>These are pair styles contributed by users, which can be used if

4
doc/Section_commands.txt
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@ -441,6 +441,7 @@ of each style or click on the style itself for a full description:
"ttm"_fix_ttm.html,
"viscosity"_fix_viscosity.html,
"viscous"_fix_viscous.html,
"wall/colloid"_fix_wall_colloid.html,
"wall/gran"_fix_wall_gran.html,
"wall/lj126"_fix_wall_lj126.html,
"wall/lj93"_fix_wall_lj93.html,
@ -558,7 +559,8 @@ potentials. Click on the style itself for a full description:
"table"_pair_table.html,
"tersoff"_pair_tersoff.html,
"tersoff/zbl"_pair_tersoff_zbl.html,
"yukawa"_pair_yukawa.html :tb(c=4,ea=c)
"yukawa"_pair_yukawa.html
"yukawa/colloid"_pair_yukawa_colloid.html :tb(c=4,ea=c)
These are pair styles contributed by users, which can be used if
"LAMMPS is built with the appropriate package"_Section_start.html#2_3.

54
doc/atom_style.html
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@ -15,7 +15,7 @@
</P>
<PRE>atom_style style args
</PRE>
<UL><LI>style = <I>angle</I> or <I>atomic</I> or <I>bond</I> or <I>charge</I> or <I>dipole</I> or <I>dpd</I> or <I>ellipsoid</I> or <I>full</I> or <I>granular</I> or <I>molecular</I> or <I>peri</I> or <I>hybrid</I>
<UL><LI>style = <I>angle</I> or <I>atomic</I> or <I>bond</I> or <I>charge</I> or <I>colloid</I> or <I>dipole</I> or <I>dpd</I> or <I>ellipsoid</I> or <I>full</I> or <I>granular</I> or <I>molecular</I> or <I>peri</I> or <I>hybrid</I>
</UL>
<PRE> args = none for any style except <I>hybrid</I>
<I>hybrid</I> args = list of one or more sub-styles
@ -57,33 +57,40 @@ quantities.
<TR><TD ><I>atomic</I> </TD><TD > only the default values </TD><TD > coarse-grain liquids, solids, metals </TD></TR>
<TR><TD ><I>bond</I> </TD><TD > bonds </TD><TD > bead-spring polymers </TD></TR>
<TR><TD ><I>charge</I> </TD><TD > charge </TD><TD > atomic system with charges </TD></TR>
<TR><TD ><I>colloid</I> </TD><TD > angular velocity </TD><TD > extended spherical particles </TD></TR>
<TR><TD ><I>dipole</I> </TD><TD > charge and dipole moment </TD><TD > atomic system with dipoles </TD></TR>
<TR><TD ><I>dpd</I> </TD><TD > default values, also communicates velocities </TD><TD > DPD models </TD></TR>
<TR><TD ><I>ellipsoid</I> </TD><TD > quaternion for particle orientation, angular momentum </TD><TD > aspherical particles </TD></TR>
<TR><TD ><I>ellipsoid</I> </TD><TD > quaternion for particle orientation, angular momentum </TD><TD > extended aspherical particles </TD></TR>
<TR><TD ><I>full</I> </TD><TD > molecular + charge </TD><TD > bio-molecules </TD></TR>
<TR><TD ><I>granular</I> </TD><TD > diameter, density, angular velocity </TD><TD > granular models </TD></TR>
<TR><TD ><I>molecular</I> </TD><TD > bonds, angles, dihedrals, impropers </TD><TD > uncharged molecules </TD></TR>
<TR><TD ><I>peri</I> </TD><TD > density, volume </TD><TD > mesocopic Peridynamic models
</TD></TR></TABLE></DIV>
<P>All of the styles define point particles, except the <I>ellipsoid</I> and
<I>granular</I> and <I>peri</I> styles. These define finite-size particles.
For <I>ellipsoidal</I> systems, the <A HREF = "shape.html">shape</A> command is used to
specify the size and shape of particles, which can be spherical or
aspherical. For <I>granular</I> systems, the particles are spherical and
each has a specified diameter. For <I>peri</I> systems, the particles are
spherical and each has a specified volume.
<P>All of the styles define point particles, except the <I>colloid</I>,
<I>dipole</I>, <I>ellipsoid</I>, <I>granular</I>, and <I>peri</I> styles. These define
finite-size particles. For <I>colloid</I>, <I>dipole</I>, and <I>ellipsoid</I>
systems, the <A HREF = "shape.html">shape</A> command is used to specify the size
and shape of particles on a per-type basis, which is spherical for
<I>colloid</I> and <I>dipole</I> particles and spherical or aspherical for
<I>ellipsoid</I> particles. For <I>granular</I> systems, the particles are
spherical and each has a per-particle specified diameter. For <I>peri</I>
systems, the particles are spherical and each has a per-particle
specified volume.
</P>
<P>All of the styles assign mass to particles on a per-type basis, using
the <A HREF = "mass.html">mass</A> command, except the <I>granular</I> and <I>peri</I> styles.
For <I>granular</I> systems, the specified diameter and density are used to
calculate each particle's mass. For <I>peri</I> systems, the speficied
volume and density are used to calculate each particle's mass.
the <A HREF = "mass.html">mass</A> command, except the <I>granular</I> and <I>peri</I> styles
which assign mass on a per-particle basis. For <I>granular</I> systems,
the specified diameter and density are used to calculate each
particle's mass. For <I>peri</I> systems, the speficied volume and density
are used to calculate each particle's mass.
</P>
<P>Only the <I>dpd</I> and <I>granular</I> styles communicate velocities with ghost
atoms; the others do not. This is because the pairwise interactions
calculated by the <A HREF = "pair_dpd.html">pair_style dpd</A> and <A HREF = "pair_gran.html">pair_style
granular</A> commands require velocities.
<P>Only the <I>colloid</I>, <I>dpd</I>, and <I>granular</I> styles communicate
velocities and angular velocities (if defined) with ghost atoms; the
others do not. This is because the pairwise interactions calculated
by the pair styles that typically use these atom styles
(e.g. <A HREF = "pair_dpd.html">pair_style dpd</A> and <A HREF = "pair_gran.html">pair_style
granular</A>) require velocities of both particles.
</P>
<HR>
@ -111,12 +118,13 @@ section</A>.
</P>
<P>The <I>angle</I>, <I>bond</I>, <I>full</I>, and <I>molecular</I> styles are part of the
"molecular" package. The <I>granular</I> style is part of the "granular"
package. The <I>dpd</I> style is part of the "dpd" package. The <I>dipole</I>
style is part of the "dipole" package. The <I>ellipsoid</I> style is part
of the "asphere" package. The <I>peri</I> style is part of the "peri"
package for Peridynamics. They are 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.
package. The <I>dpd</I> style is part of the "dpd" package. The <I>colloid</I>
style is part of the "colloid" package. The <I>dipole</I> style is part of
the "dipole" package. The <I>ellipsoid</I> style is part of the "asphere"
package. The <I>peri</I> style is part of the "peri" package for
Peridynamics. They are 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.
</P>
<P><B>Related commands:</B>
</P>

54
doc/atom_style.txt
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@ -12,7 +12,7 @@ atom_style command :h3
atom_style style args :pre
style = {angle} or {atomic} or {bond} or {charge} or {dipole} or \
style = {angle} or {atomic} or {bond} or {charge} or {colloid} or {dipole} or \
{dpd} or {ellipsoid} or {full} or {granular} or {molecular} or \
{peri} or {hybrid} :ul
args = none for any style except {hybrid}
@ -54,32 +54,39 @@ quantities.
{atomic} | only the default values | coarse-grain liquids, solids, metals |
{bond} | bonds | bead-spring polymers |
{charge} | charge | atomic system with charges |
{colloid} | angular velocity | extended spherical particles |
{dipole} | charge and dipole moment | atomic system with dipoles |
{dpd} | default values, also communicates velocities | DPD models |
{ellipsoid} | quaternion for particle orientation, angular momentum | aspherical particles |
{ellipsoid} | quaternion for particle orientation, angular momentum | extended aspherical particles |
{full} | molecular + charge | bio-molecules |
{granular} | diameter, density, angular velocity | granular models |
{molecular} | bonds, angles, dihedrals, impropers | uncharged molecules |
{peri} | density, volume | mesocopic Peridynamic models :tb(c=3,s=|)
All of the styles define point particles, except the {ellipsoid} and
{granular} and {peri} styles. These define finite-size particles.
For {ellipsoidal} systems, the "shape"_shape.html command is used to
specify the size and shape of particles, which can be spherical or
aspherical. For {granular} systems, the particles are spherical and
each has a specified diameter. For {peri} systems, the particles are
spherical and each has a specified volume.
All of the styles define point particles, except the {colloid},
{dipole}, {ellipsoid}, {granular}, and {peri} styles. These define
finite-size particles. For {colloid}, {dipole}, and {ellipsoid}
systems, the "shape"_shape.html command is used to specify the size
and shape of particles on a per-type basis, which is spherical for
{colloid} and {dipole} particles and spherical or aspherical for
{ellipsoid} particles. For {granular} systems, the particles are
spherical and each has a per-particle specified diameter. For {peri}
systems, the particles are spherical and each has a per-particle
specified volume.
All of the styles assign mass to particles on a per-type basis, using
the "mass"_mass.html command, except the {granular} and {peri} styles.
For {granular} systems, the specified diameter and density are used to
calculate each particle's mass. For {peri} systems, the speficied
volume and density are used to calculate each particle's mass.
the "mass"_mass.html command, except the {granular} and {peri} styles
which assign mass on a per-particle basis. For {granular} systems,
the specified diameter and density are used to calculate each
particle's mass. For {peri} systems, the speficied volume and density
are used to calculate each particle's mass.
Only the {dpd} and {granular} styles communicate velocities with ghost
atoms; the others do not. This is because the pairwise interactions
calculated by the "pair_style dpd"_pair_dpd.html and "pair_style
granular"_pair_gran.html commands require velocities.
Only the {colloid}, {dpd}, and {granular} styles communicate
velocities and angular velocities (if defined) with ghost atoms; the
others do not. This is because the pairwise interactions calculated
by the pair styles that typically use these atom styles
(e.g. "pair_style dpd"_pair_dpd.html and "pair_style
granular"_pair_gran.html) require velocities of both particles.
:line
@ -107,12 +114,13 @@ This command cannot be used after the simulation box is defined by a
The {angle}, {bond}, {full}, and {molecular} styles are part of the
"molecular" package. The {granular} style is part of the "granular"
package. The {dpd} style is part of the "dpd" package. The {dipole}
style is part of the "dipole" package. The {ellipsoid} style is part
of the "asphere" package. The {peri} style is part of the "peri"
package for Peridynamics. They are only enabled if LAMMPS was built
with that package. See the "Making LAMMPS"_Section_start.html#2_3
section for more info.
package. The {dpd} style is part of the "dpd" package. The {colloid}
style is part of the "colloid" package. The {dipole} style is part of
the "dipole" package. The {ellipsoid} style is part of the "asphere"
package. The {peri} style is part of the "peri" package for
Peridynamics. They are only enabled if LAMMPS was built with that
package. See the "Making LAMMPS"_Section_start.html#2_3 section for
more info.
[Related commands:]

3
doc/fix.html
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@ -164,7 +164,8 @@ list of fix styles available in LAMMPS:
<LI><A HREF = "fix_ttm.html">ttm</A> - two-temperature model for electronic/atomic coupling
<LI><A HREF = "fix_viscosity.html">viscosity</A> - Muller-Plathe momentum exchange for viscosity calculation
<LI><A HREF = "fix_viscous.html">viscous</A> - viscous damping for granular simulations
<LI><A HREF = "fix_wall_gran.html">wall/gran</A> - frictional wall(s) for granular simulations
<LI><A HREF = "fix_wall_colloid.html">wall/colloid</A> - Lennard-Jones wall interacting with finite-size particles
<LI><A HREF = "fix_wall_gran.html">wall/gran</A> - frictional wall(s) for granular simulations
<LI><A HREF = "fix_wall_lj126.html">wall/lj126</A> - Lennard-Jones 12-6 wall
<LI><A HREF = "fix_wall_lj93.html">wall/lj93</A> - Lennard-Jones 9-3 wall
<LI><A HREF = "fix_wall_reflect.html">wall/reflect</A> - reflecting wall(s)

4
doc/fix.txt
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@ -173,8 +173,8 @@ list of fix styles available in LAMMPS:
"viscosity"_fix_viscosity.html - Muller-Plathe momentum exchange for \
viscosity calculation
"viscous"_fix_viscous.html - viscous damping for granular simulations
"wall/gran"_fix_wall_gran.html - frictional wall(s) for \
granular simulations
"wall/colloid"_fix_wall_colloid.html - Lennard-Jones wall interacting with finite-size particles
"wall/gran"_fix_wall_gran.html - frictional wall(s) for granular simulations
"wall/lj126"_fix_wall_lj126.html - Lennard-Jones 12-6 wall
"wall/lj93"_fix_wall_lj93.html - Lennard-Jones 9-3 wall
"wall/reflect"_fix_wall_reflect.html - reflecting wall(s)

3
doc/pair_coeff.html
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@ -141,7 +141,8 @@ the pair_style command, and coefficients specified by the associated
<LI><A HREF = "pair_table.html">pair_style table</A> - tabulated pair potential
<LI><A HREF = "pair_tersoff.html">pair_style tersoff</A> - Tersoff 3-body potential
<LI><A HREF = "pair_tersoff.html">pair_style tersoff/zbl</A> - Tersoff/ZBL 3-body potential
<LI><A HREF = "pair_yukawa.html">pair_style yukawa</A> - Yukawa potential
<LI><A HREF = "pair_yukawa.html">pair_style yukawa</A> - Yukawa potential
<LI><A HREF = "pair_yukawa_colloid.html">pair_style yukawa/colloid</A> - screened Yukawa potential for finite-size particles
</UL>
<P>There are also additional pair styles submitted by users which are
included in the LAMMPS distribution. The list of these with links to

3
doc/pair_coeff.txt
View File

@ -138,7 +138,8 @@ the pair_style command, and coefficients specified by the associated
"pair_style table"_pair_table.html - tabulated pair potential
"pair_style tersoff"_pair_tersoff.html - Tersoff 3-body potential
"pair_style tersoff/zbl"_pair_tersoff.html - Tersoff/ZBL 3-body potential
"pair_style yukawa"_pair_yukawa.html - Yukawa potential :ul
"pair_style yukawa"_pair_yukawa.html - Yukawa potential
"pair_style yukawa/colloid"_pair_yukawa_colloid.html - screened Yukawa potential for finite-size particles :ul
There are also additional pair styles submitted by users which are
included in the LAMMPS distribution. The list of these with links to

5
doc/pair_colloid.html
View File

@ -59,6 +59,11 @@ Lennard-Jones formula
<P>with A_ss set appropriately, which results from letting both particle
sizes go to zero.
</P>
<P>When used in combination with <A HREF = "pair_colloid.html">pair_style
yukawa/colloid</A>, the two terms become the so-called
DLVO potential, which combines electrostatic repulsion and van der
Waals attraction.
</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

5
doc/pair_colloid.txt
View File

@ -56,6 +56,11 @@ Lennard-Jones formula
with A_ss set appropriately, which results from letting both particle
sizes go to zero.
When used in combination with "pair_style
yukawa/colloid"_pair_colloid.html, the two terms become the so-called
DLVO potential, which combines electrostatic repulsion and van der
Waals attraction.
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

3
doc/pair_style.html
View File

@ -143,7 +143,8 @@ the pair_style command, and coefficients specified by the associated
<LI><A HREF = "pair_table.html">pair_style table</A> - tabulated pair potential
<LI><A HREF = "pair_tersoff.html">pair_style tersoff</A> - Tersoff 3-body potential
<LI><A HREF = "pair_tersoff.html">pair_style tersoff/zbl</A> - Tersoff/ZBL 3-body potential
<LI><A HREF = "pair_yukawa.html">pair_style yukawa</A> - Yukawa potential
<LI><A HREF = "pair_yukawa.html">pair_style yukawa</A> - Yukawa potential
<LI><A HREF = "pair_yukawa_colloid.html">pair_style yukawa/colloid</A> - screened Yukawa potential for finite-size particles
</UL>
<P>There are also additional pair styles submitted by users which are
included in the LAMMPS distribution. The list of these with links to

3
doc/pair_style.txt
View File

@ -140,7 +140,8 @@ the pair_style command, and coefficients specified by the associated
"pair_style table"_pair_table.html - tabulated pair potential
"pair_style tersoff"_pair_tersoff.html - Tersoff 3-body potential
"pair_style tersoff/zbl"_pair_tersoff.html - Tersoff/ZBL 3-body potential
"pair_style yukawa"_pair_yukawa.html - Yukawa potential :ul
"pair_style yukawa"_pair_yukawa.html - Yukawa potential
"pair_style yukawa/colloid"_pair_yukawa_colloid.html - screened Yukawa potential for finite-size particles :ul
There are also additional pair styles submitted by users which are
included in the LAMMPS distribution. The list of these with links to

126
doc/pair_yukawa_colloid.html Normal file
View File

@ -0,0 +1,126 @@
<HTML>
<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
</CENTER>
<HR>
<H3>pair_style yukawa/colloid command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>pair_style yukawa/colloid kappa cutoff
</PRE>
<UL><LI>kappa = screening length (inverse distance units)
<LI>cutoff = global cutoff for colloidal Yukawa interactions (distance units)
</UL>
<P><B>Examples:</B>
</P>
<PRE>pair_style yukawa/colloid 2.0 2.5
pair_coeff 1 1 100.0 2.3
pair_coeff * * 100.0
</PRE>
<P><B>Description:</B>
</P>
<P>Style <I>yukawa/colloid</I> computes pairwise interactions with the formula
</P>
<CENTER><IMG SRC = "Eqs/pair_yukawa_colloid.jpg">
</CENTER>
<P>where Ri and Rj are the radii of the two particles and Rc is the
cutoff.
</P>
<P>In contrast to <A HREF = "pair_yukawa.html">pair_style yukawa</A>, this functional
form arises from the Coulombic interaction between two colloid
particles, screened due to the presence of an electrolyte.
<A HREF = "pair_yukawa.html">Pair_style yukawa</A> is a screened Coulombic potential
between two point-charges and uses no such approximation.
</P>
<P>This potential applies to nearby particle pairs for which the Derjagin
approximation holds, meaning h << Ri + Rj, where h is the
surface-to-surface separation of the two particles.
</P>
<P>When used in combination with <A HREF = "pair_colloid.html">pair_style colloid</A>,
the two terms become the so-called DLVO potential, which combines
electrostatic repulsion and van der Waals attraction.
</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
<A HREF = "read_data.html">read_data</A> or <A HREF = "read_restart.html">read_restart</A>
commands, or by mixing as described below:
</P>
<UL><LI>A (energy/distance units)
<LI>cutoff (distance units)
</UL>
<P>The prefactor A is determined from the relationship between surface
charge and surface potential due to the presence of electrolyte. Note
that the A for this potential style has different units than the A
used in <A HREF = "pair_yukawa.html">pair_style yukawa</A>. For low surface
potentials, i.e. less than about 25 mV, A can be written as:
</P>
<PRE>A = 2 * PI * R*eps*eps0 * kappa * psi^2
</PRE>
<P>where
</P>
<UL><LI>R = colloid radius (distance units)
<LI>eps0 = permittivity of free space (charge^2/energy/distance units)
<LI>eps = relative permittivity of fluid medium (dimensionless)
<LI>kappa = inverse screening length (1/distance units)
<LI>psi = surface potential (energy/charge units)
</UL>
<P>The last coefficient is optional. If not specified, the global
yukawa/colloid cutoff is used.
</P>
<HR>
<P><B>Mixing, shift, table, tail correction, restart, rRESPA info</B>:
</P>
<P>For atom type pairs I,J and I != J, the A coefficient and cutoff
distance for this pair style can be mixed. A is an energy value mixed
like a LJ epsilon. The default mix value is <I>geometric</I>. See the
"pair_modify" command for details.
</P>
<P>This pair style supports the <A HREF = "pair_modify.html">pair_modify</A> shift
option for the energy of the pair interaction.
</P>
<P>The <A HREF = "pair_modify.html">pair_modify</A> table option is not relevant
for this pair style.
</P>
<P>This pair style does not support the <A HREF = "pair_modify.html">pair_modify</A>
tail option for adding long-range tail corrections to energy and
pressure.
</P>
<P>This pair style writes its information to <A HREF = "restart.html">binary restart
files</A>, so pair_style and pair_coeff commands do not need
to be specified in an input script that reads a restart file.
</P>
<P>This pair style can only be used via the <I>pair</I> keyword of the
<A HREF = "run_style.html">run_style respa</A> command. It does not support the
<I>inner</I>, <I>middle</I>, <I>outer</I> keywords.
</P>
<HR>
<P><B>Restrictions:</B>
</P>
<P>This style is part of the "colloid" 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.
</P>
<P>Because this potential uses the radii of the particles, the atom style
must support particles whose size is set via the <A HREF = "shape.html">shape</A>
command. For example <A HREF = "atom_style.html">atom_style</A> colloid or
ellipsoid. Only spherical mono-disperse particles are currently
allowed for pair_style yukawa/colloid, which means the 3 shape
diameters for all particle types must be the same.
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "pair_coeff.html">pair_coeff</A>
</P>
<P><B>Default:</B> none
</P>
</HTML>

121
doc/pair_yukawa_colloid.txt Normal file
View File

@ -0,0 +1,121 @@
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
:line
pair_style yukawa/colloid command :h3
[Syntax:]
pair_style yukawa/colloid kappa cutoff :pre
kappa = screening length (inverse distance units)
cutoff = global cutoff for colloidal Yukawa interactions (distance units) :ul
[Examples:]
pair_style yukawa/colloid 2.0 2.5
pair_coeff 1 1 100.0 2.3
pair_coeff * * 100.0 :pre
[Description:]
Style {yukawa/colloid} computes pairwise interactions with the formula
:c,image(Eqs/pair_yukawa_colloid.jpg)
where Ri and Rj are the radii of the two particles and Rc is the
cutoff.
In contrast to "pair_style yukawa"_pair_yukawa.html, this functional
form arises from the Coulombic interaction between two colloid
particles, screened due to the presence of an electrolyte.
"Pair_style yukawa"_pair_yukawa.html is a screened Coulombic potential
between two point-charges and uses no such approximation.
This potential applies to nearby particle pairs for which the Derjagin
approximation holds, meaning h << Ri + Rj, where h is the
surface-to-surface separation of the two particles.
When used in combination with "pair_style colloid"_pair_colloid.html,
the two terms become the so-called DLVO potential, which combines
electrostatic repulsion and van der Waals attraction.
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
"read_data"_read_data.html or "read_restart"_read_restart.html
commands, or by mixing as described below:
A (energy/distance units)
cutoff (distance units) :ul
The prefactor A is determined from the relationship between surface
charge and surface potential due to the presence of electrolyte. Note
that the A for this potential style has different units than the A
used in "pair_style yukawa"_pair_yukawa.html. For low surface
potentials, i.e. less than about 25 mV, A can be written as:
A = 2 * PI * R*eps*eps0 * kappa * psi^2 :pre
where
R = colloid radius (distance units)
eps0 = permittivity of free space (charge^2/energy/distance units)
eps = relative permittivity of fluid medium (dimensionless)
kappa = inverse screening length (1/distance units)
psi = surface potential (energy/charge units) :ul
The last coefficient is optional. If not specified, the global
yukawa/colloid cutoff is used.
:line
[Mixing, shift, table, tail correction, restart, rRESPA info]:
For atom type pairs I,J and I != J, the A coefficient and cutoff
distance for this pair style can be mixed. A is an energy value mixed
like a LJ epsilon. The default mix value is {geometric}. See the
"pair_modify" command for details.
This pair style supports the "pair_modify"_pair_modify.html shift
option for the energy of the pair interaction.
The "pair_modify"_pair_modify.html table option is not relevant
for this pair style.
This pair style does not support the "pair_modify"_pair_modify.html
tail option for adding long-range tail corrections to energy and
pressure.
This pair style writes its information to "binary restart
files"_restart.html, so pair_style and pair_coeff commands do not need
to be specified in an input script that reads a restart file.
This pair style can only be used via the {pair} keyword of the
"run_style respa"_run_style.html command. It does not support the
{inner}, {middle}, {outer} keywords.
:line
[Restrictions:]
This style is part of the "colloid" 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.
Because this potential uses the radii of the particles, the atom style
must support particles whose size is set via the "shape"_shape.html
command. For example "atom_style"_atom_style.html colloid or
ellipsoid. Only spherical mono-disperse particles are currently
allowed for pair_style yukawa/colloid, which means the 3 shape
diameters for all particle types must be the same.
[Related commands:]
"pair_coeff"_pair_coeff.html
[Default:] none

1
doc/read_data.html
View File

@ -270,6 +270,7 @@ of analysis.
<TR><TD >atomic</TD><TD > atom-ID atom-type x y z</TD></TR>
<TR><TD >bond</TD><TD > atom-ID molecule-ID atom-type x y z</TD></TR>
<TR><TD >charge</TD><TD > atom-ID atom-type q x y z</TD></TR>
<TR><TD >colloid</TD><TD > atom-ID atom-type x y z</TD></TR>
<TR><TD >dipole</TD><TD > atom-ID atom-type q x y z mux muy muz</TD></TR>
<TR><TD >dpd</TD><TD > atom-ID atom-type x y z</TD></TR>
<TR><TD >ellipsoid</TD><TD > atom-ID atom-type x y z quatw quati quatj quatk</TD></TR>

1
doc/read_data.txt
View File

@ -250,6 +250,7 @@ angle: atom-ID molecule-ID atom-type x y z
atomic: atom-ID atom-type x y z
bond: atom-ID molecule-ID atom-type x y z
charge: atom-ID atom-type q x y z
colloid: atom-ID atom-type x y z
dipole: atom-ID atom-type q x y z mux muy muz
dpd: atom-ID atom-type x y z
ellipsoid: atom-ID atom-type x y z quatw quati quatj quatk

19
doc/shape.html
View File

@ -62,14 +62,13 @@ pages of individual commands for details.
</P>
<P>Note that the shape command can only be used if the <A HREF = "atom_style.html">atom
style</A> requires per-type atom shape to be set.
Currently, only the <I>dipole</I> and <I>ellipsoid</I> styles do. The
<I>granular</I> and <I>peri</I> styles require the shape to be set for indivual
particles, not types. For these styles, the only option currently
allowed is for spherical particles, so a single diameter value
suffices to determine the shape. Per-atom diameters are defined in
the data file read by the <A HREF = "read_data.html">read_data</A> command, or set
to default values by the <A HREF = "create_atoms.html">create_atoms</A> command, or
set to new values by the <A HREF = "set.html">set diamter</A> command.
Currently, only the <I>colloid</I>, <I>dipole</I>, and <I>ellipsoid</I> styles do.
The <I>granular</I> and <I>peri</I> styles also define finite-size spherical
particles, but their size is set on a per-particle basis. These are
are defined in the data file read by the <A HREF = "read_data.html">read_data</A>
command, or set to default values by the
<A HREF = "create_atoms.html">create_atoms</A> command, or set to new values by the
<A HREF = "set.html">set diameter</A> command.
</P>
<P>Dipoles use the atom shape to compute a moment of inertia for
rotational energy. See the <A HREF = "pair_dipole.html">pair_style dipole</A>
@ -79,8 +78,8 @@ particles are assumed to be spherical.
<P>Ellipsoids use the atom shape to compute a generalized inertia tensor.
For example, a shape setting of 3.0 1.0 1.0 defines a particle 3x
longer in x than in y or z and with a circular cross-section in yz.
Degenerate ellipsoids which are spherical can be defined by setting
all 3 shape components the same.
Ellipsoids which are in fact spherical can be defined by setting all 3
shape components the same.
</P>
<P>If you define a <A HREF = "atom_style.html">hybrid atom style</A> which includes one
(or more) sub-styles which require per-type shape and one (or more)

19
doc/shape.txt
View File

@ -59,14 +59,13 @@ pages of individual commands for details.
Note that the shape command can only be used if the "atom
style"_atom_style.html requires per-type atom shape to be set.
Currently, only the {dipole} and {ellipsoid} styles do. The
{granular} and {peri} styles require the shape to be set for indivual
particles, not types. For these styles, the only option currently
allowed is for spherical particles, so a single diameter value
suffices to determine the shape. Per-atom diameters are defined in
the data file read by the "read_data"_read_data.html command, or set
to default values by the "create_atoms"_create_atoms.html command, or
set to new values by the "set diamter"_set.html command.
Currently, only the {colloid}, {dipole}, and {ellipsoid} styles do.
The {granular} and {peri} styles also define finite-size spherical
particles, but their size is set on a per-particle basis. These are
are defined in the data file read by the "read_data"_read_data.html
command, or set to default values by the
"create_atoms"_create_atoms.html command, or set to new values by the
"set diameter"_set.html command.
Dipoles use the atom shape to compute a moment of inertia for
rotational energy. See the "pair_style dipole"_pair_dipole.html
@ -76,8 +75,8 @@ particles are assumed to be spherical.
Ellipsoids use the atom shape to compute a generalized inertia tensor.
For example, a shape setting of 3.0 1.0 1.0 defines a particle 3x
longer in x than in y or z and with a circular cross-section in yz.
Degenerate ellipsoids which are spherical can be defined by setting
all 3 shape components the same.
Ellipsoids which are in fact spherical can be defined by setting all 3
shape components the same.
If you define a "hybrid atom style"_atom_style.html which includes one
(or more) sub-styles which require per-type shape and one (or more)