From 21b5ea51a70c16ec9c81f0bef2a06d2d2b06e742 Mon Sep 17 00:00:00 2001 From: sjplimp Date: Fri, 6 Nov 2009 21:01:28 +0000 Subject: [PATCH] git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@3341 f3b2605a-c512-4ea7-a41b-209d697bcdaa --- doc/Eqs/pair_yukawa.tex | 2 +- doc/Eqs/pair_yukawa_colloid.jpg | Bin 0 -> 1942 bytes doc/Eqs/pair_yukawa_colloid.tex | 9 +++ doc/Section_commands.html | 6 +- doc/Section_commands.txt | 4 +- doc/atom_style.html | 54 ++++++++------ doc/atom_style.txt | 54 ++++++++------ doc/fix.html | 3 +- doc/fix.txt | 4 +- doc/pair_coeff.html | 3 +- doc/pair_coeff.txt | 3 +- doc/pair_colloid.html | 5 ++ doc/pair_colloid.txt | 5 ++ doc/pair_style.html | 3 +- doc/pair_style.txt | 3 +- doc/pair_yukawa_colloid.html | 126 ++++++++++++++++++++++++++++++++ doc/pair_yukawa_colloid.txt | 121 ++++++++++++++++++++++++++++++ doc/read_data.html | 1 + doc/read_data.txt | 1 + doc/shape.html | 19 +++-- doc/shape.txt | 19 +++-- 21 files changed, 367 insertions(+), 78 deletions(-) create mode 100644 doc/Eqs/pair_yukawa_colloid.jpg create mode 100644 doc/Eqs/pair_yukawa_colloid.tex create mode 100644 doc/pair_yukawa_colloid.html create mode 100644 doc/pair_yukawa_colloid.txt diff --git a/doc/Eqs/pair_yukawa.tex b/doc/Eqs/pair_yukawa.tex index 01347ec201..382cf249a8 100644 --- a/doc/Eqs/pair_yukawa.tex +++ b/doc/Eqs/pair_yukawa.tex @@ -6,4 +6,4 @@ $$ E = A \frac{e^{- \kappa r}}{r} \qquad r < r_c $$ -\end{document} \ No newline at end of file +\end{document} diff --git a/doc/Eqs/pair_yukawa_colloid.jpg b/doc/Eqs/pair_yukawa_colloid.jpg new file mode 100644 index 0000000000000000000000000000000000000000..db6e2ea81a37ea10df7bbfebd92a7f45baf4cf19 GIT binary patch literal 1942 zcmZ9Nc~sJg7RP@GhQ8bo#|>}+&B~<*<+$g*R+_dmY9MMFxG&`rX1;O@R9Z~SY{ndO z(u|0(a4SSM6h=EGRSx z0D(Y2$XWsFaljwY1VbPYu;yCR)YM!D)zN~kp}&5;whm0+&=95%gTalFCU7J3?_e-f zYg2O+%F@yjZi2Q!Ti75iEG^W1z>Q{i)w{_mY z>cz5u!oFPnldNemg`?diKoAwY!5fk*(<5CRL9$~yREnooCcyrmqqA~ekh6vFPGcWFP+yieI4f+;V#KWrC2 z2S77JtpE>(59)=Way>ja7Ao4x!_b;V8NUyCo>LwijDtR#Gqc}GBjlxiS@alQ|xP6SkwU;jYr6z|)q}OwO~c z5#X^$5qS|<4=11+St~#Ggw%KpIF(MK9hU!`MY~uazg5?d!_DKrei^^Yp4!7 zkB2V2`k&x@hTl*?ijwhAT_T)&8Kc#aHwE6dq!2+iX_68K2)g!@L#%DDN&#a2KJE zH-8I;9M=H8EX};Udn8wQ+O5EHS)l zW$7?BQZ`d~vul;w#=bJJyQ!W*OSV76c=_N(lOw6#Tr%DYUge8Ri+iR`PGq+)-Y>f) zUFuZc3!+A&DW?}ty1BZ&X%NWA`#<=c^py+9#dC+BxKS;f&+4L2t9<0+bY(uKSHzC+ z`eOM&u`OV4R8Hxx!Q8OS1XBE>q=F@px*9CoP%^%Dxyi}qa&dIF-plzGL5{_C_8{p) z{+L5$ctiNP0LIpbDx!qqA50KPOP0oDZL$bdeh149JBV06$-D!6(YI6XJ5FuwOIYCT zK{4og(leoN3FP7|Ocuhf+Jh+`Ku$V30Vi)oBD2LlHpNqgqgS&Bwr)A>I8s+Qxhtk& zxvgZUL7;P%%Fq;3v4QgIwrQ#0k2~vTmYtrrr~xe1Y17iMmXqk~7=dzS9JC#yhpK{I z3z3D`Ng4c0xGp}mgyiIjpO44@&uA-xM3cS|p|y3Qx0L;t^M9M`n^PzzCKkT-R5Z4_ z`@tRwz{rL$KY)jJ4YzHPMMA&nM-3+q`V;#=XS2Pb@$4~rVdE1Efcwm!pcw} zp~uL#CnsY#UrrePVxKd`iBZV<$Ks0S$)#yGR9rdx{9>TzmNQ9X4pH0KvI1XneNdUz zvgV13?*rlJa#}nkiHsk`~k-&WMe*ETpcitB71{QI^pRhuyn(TckqtU!~ zd&rLz$W9p_WC-I3^+D{abFuH7xzpM!df`?@g4M7Zn8~K$7;i6R$Da7iefG>{hbBw> z_sLJ`cMbSPfIhe@_1t0fAIeexOFypLV?shDD9v=sgcfslg*bp(Mbv{T?Hl=|EHC>o zch^@hagt7Yolyoq>Iq?aD2akYHD1RfKE9Qz0mnrsJVCKJIB^_}J8&ur9Ah86L8DMV z9i@srU{^wSIyvWbo+sM-=5a=QWpX0Nwj989i$>YaPYdbZseKKaBh!>atcaH!-Q$Ud zf=2>7#U*g8v_x20Pz}Pwlw*4C-K&AYcB{~dE$=^`d75|>dndX*Ja{jS7q2-#J!c43M+*>ngTJOr=;0s>oW2O@=gjFz115nve/aspherenve/limitnve/noforcenve/spherenvtnvt/aspherenvt/sllodnvt/sphere orient/fccplaneforcepoemspourpress/berendsenprintrdfreax/bonds recenterrigidsetforceshakespringspring/rgspring/selftemp/berendsen -temp/rescalethermal/conductivitytmdttmviscosityviscouswall/granwall/lj126 -wall/lj93wall/reflectwiggle +temp/rescalethermal/conductivitytmdttmviscosityviscouswall/colloidwall/gran +wall/lj126wall/lj93wall/reflectwiggle

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: lj96/cutlubricatemeammorse morse/optperi/pmbreaxresquared softswtabletersoff -tersoff/zblyukawa +tersoff/zblyukawayukawa/colloid

These are pair styles contributed by users, which can be used if diff --git a/doc/Section_commands.txt b/doc/Section_commands.txt index a64ab18452..7a81bfffe3 100644 --- a/doc/Section_commands.txt +++ b/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. diff --git a/doc/atom_style.html b/doc/atom_style.html index 60e5fef1e2..92e0c00163 100644 --- a/doc/atom_style.html +++ b/doc/atom_style.html @@ -15,7 +15,7 @@ 

atom_style style args
-
  • style = angle or atomic or bond or charge or dipole or dpd or ellipsoid or full or granular or molecular or peri or hybrid +
    • 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 
      args = none for any style except hybrid
   hybrid args = list of one or more sub-styles 
@@ -57,33 +57,40 @@ 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 
 
 
-
    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 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 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 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 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 and pair_style
-granular 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 and pair_style
+granular) require velocities of both particles.
 
    
 
    
 
@@ -111,12 +118,13 @@ section.
 
    
 
    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 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 for
+more info.
 
    
 
    Related commands:
 
    
diff --git a/doc/atom_style.txt b/doc/atom_style.txt
index 497f790b1d..b172896f51 100644
--- a/doc/atom_style.txt
+++ b/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
-{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:]
 
diff --git a/doc/fix.html b/doc/fix.html
index 5772869ebd..ed409c6e71 100644
--- a/doc/fix.html
+++ b/doc/fix.html
@@ -164,7 +164,8 @@ list of fix styles available in LAMMPS:
 
  • ttm - two-temperature model for electronic/atomic coupling
 
  • viscosity - Muller-Plathe momentum exchange for      viscosity calculation
 
  • viscous - viscous damping for granular simulations
-
  • wall/gran - frictional wall(s) for      granular simulations
+
  • wall/colloid - Lennard-Jones wall interacting with finite-size particles
+
  • wall/gran - frictional wall(s) for granular simulations
 
  • wall/lj126 - Lennard-Jones 12-6 wall
 
  • wall/lj93 - Lennard-Jones 9-3 wall
 
  • wall/reflect - reflecting wall(s)
diff --git a/doc/fix.txt b/doc/fix.txt
index 8edef30c98..89540b1286 100644
--- a/doc/fix.txt
+++ b/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 \
-     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)
diff --git a/doc/pair_coeff.html b/doc/pair_coeff.html
index c7c7e0932c..7fe9e166b5 100644
--- a/doc/pair_coeff.html
+++ b/doc/pair_coeff.html
@@ -141,7 +141,8 @@ the pair_style command, and coefficients specified by the associated
 
  • pair_style table - tabulated pair potential
 
  • pair_style tersoff - Tersoff 3-body potential
 
  • pair_style tersoff/zbl - Tersoff/ZBL 3-body potential
-
  • pair_style yukawa - Yukawa potential 
+
  • pair_style yukawa - Yukawa potential
+
  • pair_style yukawa/colloid - screened Yukawa potential for finite-size particles

There are also additional pair styles submitted by users which are included in the LAMMPS distribution. The list of these with links to diff --git a/doc/pair_coeff.txt b/doc/pair_coeff.txt index 60cff766ad..20d73410c1 100644 --- a/doc/pair_coeff.txt +++ b/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 diff --git a/doc/pair_colloid.html b/doc/pair_colloid.html index 302ad45871..3413231db6 100644 --- a/doc/pair_colloid.html +++ b/doc/pair_colloid.html @@ -59,6 +59,11 @@ 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, 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 command as in the examples above, or in the data file or restart files read by the diff --git a/doc/pair_colloid.txt b/doc/pair_colloid.txt index 15583ac3dd..8d27f59177 100644 --- a/doc/pair_colloid.txt +++ b/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 diff --git a/doc/pair_style.html b/doc/pair_style.html index bb5f819402..7862a6a5ae 100644 --- a/doc/pair_style.html +++ b/doc/pair_style.html @@ -143,7 +143,8 @@ the pair_style command, and coefficients specified by the associated

  • pair_style table - tabulated pair potential
  • pair_style tersoff - Tersoff 3-body potential
  • pair_style tersoff/zbl - Tersoff/ZBL 3-body potential -
  • pair_style yukawa - Yukawa potential +
  • pair_style yukawa - Yukawa potential +
  • pair_style yukawa/colloid - screened Yukawa potential for finite-size particles

    There are also additional pair styles submitted by users which are included in the LAMMPS distribution. The list of these with links to diff --git a/doc/pair_style.txt b/doc/pair_style.txt index 0267793ac3..dea9579f58 100644 --- a/doc/pair_style.txt +++ b/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 diff --git a/doc/pair_yukawa_colloid.html b/doc/pair_yukawa_colloid.html new file mode 100644 index 0000000000..50e4d838c1 --- /dev/null +++ b/doc/pair_yukawa_colloid.html @@ -0,0 +1,126 @@ + +

    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands +
    + + + + + + +
    + +

    pair_style yukawa/colloid command +

    +

    Syntax: +

    +
    pair_style yukawa/colloid kappa cutoff 
+
    +
    • kappa = screening length (inverse distance units) +
    • cutoff = global cutoff for colloidal Yukawa interactions (distance units) +
    +

    Examples: +

    +
    pair_style yukawa/colloid 2.0 2.5
+pair_coeff 1 1 100.0 2.3
+pair_coeff * * 100.0 
+
    +

    Description: +

    +

    Style yukawa/colloid computes pairwise interactions with the formula +

    +
    +
    +

    where Ri and Rj are the radii of the two particles and Rc is the +cutoff. +

    +

    In contrast to pair_style yukawa, this functional +form arises from the Coulombic interaction between two colloid +particles, screened due to the presence of an electrolyte. +Pair_style yukawa 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, +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 command as in the examples +above, or in the data file or restart files read by the +read_data or read_restart +commands, or by mixing as described below: +

    +
    • A (energy/distance units) +
    • cutoff (distance units) +
    +

    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. 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 
+
    +

    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) +
    +

    The last coefficient is optional. If not specified, the global +yukawa/colloid cutoff is used. +

    +
    + +

    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 shift +option for the energy of the pair interaction. +

    +

    The pair_modify table option is not relevant +for this pair style. +

    +

    This pair style does not support the pair_modify +tail option for adding long-range tail corrections to energy and +pressure. +

    +

    This pair style writes its information to binary restart +files, 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 command. It does not support the +inner, middle, outer keywords. +

    +
    + +

    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 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 +command. For example atom_style 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 +

    +

    Default: none +

    + diff --git a/doc/pair_yukawa_colloid.txt b/doc/pair_yukawa_colloid.txt new file mode 100644 index 0000000000..05b81fb44f --- /dev/null +++ b/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 diff --git a/doc/read_data.html b/doc/read_data.html index 89e8cba3b6..e5859f2769 100644 --- a/doc/read_data.html +++ b/doc/read_data.html @@ -270,6 +270,7 @@ of analysis. 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 diff --git a/doc/read_data.txt b/doc/read_data.txt index f13a45eac7..f7fd07ea6d 100644 --- a/doc/read_data.txt +++ b/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 diff --git a/doc/shape.html b/doc/shape.html index 400ad2825b..397fd4fe4d 100644 --- a/doc/shape.html +++ b/doc/shape.html @@ -62,14 +62,13 @@ pages of individual commands for details.

    Note that the shape command can only be used if the atom style 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 command, or set -to default values by the create_atoms command, or -set to new values by the set diamter 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 +command, or set to default values by the +create_atoms command, or set to new values by the +set diameter command.

    Dipoles use the atom shape to compute a moment of inertia for rotational energy. See the pair_style dipole @@ -79,8 +78,8 @@ 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 which includes one (or more) sub-styles which require per-type shape and one (or more) diff --git a/doc/shape.txt b/doc/shape.txt index 176df444ae..baaca8fece 100644 --- a/doc/shape.txt +++ b/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 -{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)