git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@3341 f3b2605a-c512-4ea7-a41b-209d697bcdaa

doc/Eqs/pair_yukawa_colloid.tex

@@ -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}

doc/Section_commands.html

@@ -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_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_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_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

doc/Section_commands.txt

@@ -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.

doc/atom_style.html

@@ -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
+<P>All of the styles define point particles, except the <I>colloid</I>,
-<I>granular</I> and <I>peri</I> styles.  These define finite-size particles.
+<I>dipole</I>, <I>ellipsoid</I>, <I>granular</I>, and <I>peri</I> styles.  These define
-For <I>ellipsoidal</I> systems, the <A HREF = "shape.html">shape</A> command is used to
+finite-size particles.  For <I>colloid</I>, <I>dipole</I>, and <I>ellipsoid</I>
-specify the size and shape of particles, which can be spherical or
+systems, the <A HREF = "shape.html">shape</A> command is used to specify the size
-aspherical.  For <I>granular</I> systems, the particles are spherical and
+and shape of particles on a per-type basis, which is spherical for
-each has a specified diameter.  For <I>peri</I> systems, the particles are
+<I>colloid</I> and <I>dipole</I> particles and spherical or aspherical for
-spherical and each has a specified volume.
+<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.
+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
+which assign mass on a per-particle basis.  For <I>granular</I> systems,
-calculate each particle's mass.  For <I>peri</I> systems, the speficied
+the specified diameter and density are used to calculate each
-volume and density are used to calculate each particle's mass.
+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
+<P>Only the <I>colloid</I>, <I>dpd</I>, and <I>granular</I> styles communicate
-atoms; the others do not.  This is because the pairwise interactions
+velocities and angular velocities (if defined) with ghost atoms; the
-calculated by the <A HREF = "pair_dpd.html">pair_style dpd</A> and <A HREF = "pair_gran.html">pair_style
+others do not.  This is because the pairwise interactions calculated
-granular</A> commands require velocities.
+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>
+package.  The <I>dpd</I> style is part of the "dpd" package.  The <I>colloid</I>
-style is part of the "dipole" package.  The <I>ellipsoid</I> style is part
+style is part of the "colloid" package.  The <I>dipole</I> style is part of
-of the "asphere" package.  The <I>peri</I> style is part of the "peri"
+the "dipole" package.  The <I>ellipsoid</I> style is part of the "asphere"
-package for Peridynamics.  They are only enabled if LAMMPS was built
+package.  The <I>peri</I> style is part of the "peri" package for
-with that package.  See the <A HREF = "Section_start.html#2_3">Making LAMMPS</A>
+Peridynamics.  They are only enabled if LAMMPS was built with that
-section for more info.
+package.  See the <A HREF = "Section_start.html#2_3">Making LAMMPS</A> section for
+more info.
 </P>
 <P><B>Related commands:</B>
 </P>

doc/atom_style.txt

@@ -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
+All of the styles define point particles, except the {colloid},
-{granular} and {peri} styles.  These define finite-size particles.
+{dipole}, {ellipsoid}, {granular}, and {peri} styles.  These define
-For {ellipsoidal} systems, the "shape"_shape.html command is used to
+finite-size particles.  For {colloid}, {dipole}, and {ellipsoid}
-specify the size and shape of particles, which can be spherical or
+systems, the "shape"_shape.html command is used to specify the size
-aspherical.  For {granular} systems, the particles are spherical and
+and shape of particles on a per-type basis, which is spherical for
-each has a specified diameter.  For {peri} systems, the particles are
+{colloid} and {dipole} particles and spherical or aspherical for
-spherical and each has a specified volume.
+{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.
+the "mass"_mass.html command, except the {granular} and {peri} styles
-For {granular} systems, the specified diameter and density are used to
+which assign mass on a per-particle basis.  For {granular} systems,
-calculate each particle's mass.  For {peri} systems, the speficied
+the specified diameter and density are used to calculate each
-volume and density are used to calculate each particle's mass.
+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
+Only the {colloid}, {dpd}, and {granular} styles communicate
-atoms; the others do not.  This is because the pairwise interactions
+velocities and angular velocities (if defined) with ghost atoms; the
-calculated by the "pair_style dpd"_pair_dpd.html and "pair_style
+others do not.  This is because the pairwise interactions calculated
-granular"_pair_gran.html commands require velocities.
+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}
+package.  The {dpd} style is part of the "dpd" package.  The {colloid}
-style is part of the "dipole" package.  The {ellipsoid} style is part
+style is part of the "colloid" package.  The {dipole} style is part of
-of the "asphere" package.  The {peri} style is part of the "peri"
+the "dipole" package.  The {ellipsoid} style is part of the "asphere"
-package for Peridynamics.  They are only enabled if LAMMPS was built
+package.  The {peri} style is part of the "peri" package for
-with that package.  See the "Making LAMMPS"_Section_start.html#2_3
+Peridynamics.  They are only enabled if LAMMPS was built with that
-section for more info.
+package.  See the "Making LAMMPS"_Section_start.html#2_3 section for
+more info.
 
 [Related commands:]
 

doc/fix.html

@@ -164,6 +164,7 @@ 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_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

doc/fix.txt

@@ -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 \
+"wall/colloid"_fix_wall_colloid.html - Lennard-Jones wall interacting with finite-size particles
-     granular simulations
+"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)

doc/pair_coeff.html

@@ -142,6 +142,7 @@ the pair_style command, and coefficients specified by the associated
 <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_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

doc/pair_coeff.txt

@@ -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

doc/pair_colloid.html

@@ -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

doc/pair_colloid.txt

@@ -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

doc/pair_style.html

@@ -144,6 +144,7 @@ the pair_style command, and coefficients specified by the associated
 <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_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

doc/pair_style.txt

@@ -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

doc/pair_yukawa_colloid.html

@@ -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>

doc/pair_yukawa_colloid.txt

@@ -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

doc/read_data.html

@@ -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>

doc/read_data.txt

@@ -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

doc/shape.html

@@ -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
+Currently, only the <I>colloid</I>, <I>dipole</I>, and <I>ellipsoid</I> styles do.
-<I>granular</I> and <I>peri</I> styles require the shape to be set for indivual
+The <I>granular</I> and <I>peri</I> styles also define finite-size spherical
-particles, not types.  For these styles, the only option currently
+particles, but their size is set on a per-particle basis.  These are
-allowed is for spherical particles, so a single diameter value
+are defined in the data file read by the <A HREF = "read_data.html">read_data</A>
-suffices to determine the shape.  Per-atom diameters are defined in
+command, or set to default values by the
-the data file read by the <A HREF = "read_data.html">read_data</A> command, or set
+<A HREF = "create_atoms.html">create_atoms</A> command, or set to new values by the
-to default values by the <A HREF = "create_atoms.html">create_atoms</A> command, or
+<A HREF = "set.html">set diameter</A> command.
-set to new values by the <A HREF = "set.html">set diamter</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
+Ellipsoids which are in fact spherical can be defined by setting all 3
-all 3 shape components the same.
+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)

doc/shape.txt

@@ -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
+Currently, only the {colloid}, {dipole}, and {ellipsoid} styles do.
-{granular} and {peri} styles require the shape to be set for indivual
+The {granular} and {peri} styles also define finite-size spherical
-particles, not types.  For these styles, the only option currently
+particles, but their size is set on a per-particle basis.  These are
-allowed is for spherical particles, so a single diameter value
+are defined in the data file read by the "read_data"_read_data.html
-suffices to determine the shape.  Per-atom diameters are defined in
+command, or set to default values by the
-the data file read by the "read_data"_read_data.html command, or set
+"create_atoms"_create_atoms.html command, or set to new values by the
-to default values by the "create_atoms"_create_atoms.html command, or
+"set diameter"_set.html command.
-set to new values by the "set diamter"_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
+Ellipsoids which are in fact spherical can be defined by setting all 3
-all 3 shape components the same.
+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)