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2012-05-23 17:47:58 +00:00
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16
doc/pair_brownian.html
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@ -19,7 +19,7 @@
</H3> </H3>
<P><B>Syntax:</B> <P><B>Syntax:</B>
</P> </P>
<PRE>pair_style style mu flaglog flagfld cutinner cutoff t_target seed <PRE>pair_style style mu flaglog flagfld cutinner cutoff t_target seed flagHI flagVF
</PRE> </PRE>
<UL><LI>style = <I>brownian</I> or <I>brownian/poly</I> <UL><LI>style = <I>brownian</I> or <I>brownian/poly</I>
<LI>mu = dynamic viscosity (dynamic viscosity units) <LI>mu = dynamic viscosity (dynamic viscosity units)
@ -29,10 +29,12 @@
<LI>cutoff = outer cutoff for interactions (distance units) <LI>cutoff = outer cutoff for interactions (distance units)
<LI>t_target = target temp of the system (temperature units) <LI>t_target = target temp of the system (temperature units)
<LI>seed = seed for the random number generator (positive integer) <LI>seed = seed for the random number generator (positive integer)
<LI>flagHI (optional) = 0/1 to include/exclude 1/r hydrodynamic interactions
<LI>flagVF (optional) = 0/1 to include/exclude volume fraction corrections in the long-range isotropic terms
</UL> </UL>
<P><B>Examples:</B> <P><B>Examples:</B>
</P> </P>
<PRE>pair_style brownian 1.5 1 1 2.01 2.5 2.0 5878567 (assuming radius=1) <PRE>pair_style brownian 1.5 1 1 2.01 2.5 2.0 5878567 (assuming radius = 1)
pair_coeff 1 1 2.05 2.8 pair_coeff 1 1 2.05 2.8
pair_coeff * * pair_coeff * *
</PRE> </PRE>
@ -55,6 +57,11 @@ For details, refer to either of the lubrication pair styles.
the system. The random number <I>seed</I> is used to generate random the system. The random number <I>seed</I> is used to generate random
numbers for the thermostatting procedure. numbers for the thermostatting procedure.
</P> </P>
<P>The <I>flagHI</I> and <I>flagVF</I> settings are optional. Neither should be
used, or both must be defined.
</P>
<HR>
<P>The following coefficients must be defined for each pair of atoms <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 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 above, or in the data file or restart files read by the
@ -135,6 +142,9 @@ brownian.
lubricate</A>, <A HREF = "pair_lubricateU.html">pair_style lubricate</A>, <A HREF = "pair_lubricateU.html">pair_style
lubricateU</A> lubricateU</A>
</P> </P>
<P><B>Default:</B> none <P><B>Default:</B>
</P>
<P>The default settings for the optional args are flagHI = 1 and flagVF =
1.
</P> </P>
</HTML> </HTML>

19
doc/pair_brownian.txt
View File

@ -13,7 +13,7 @@ pair_style brownian/poly/omp command :h3
[Syntax:] [Syntax:]
pair_style style mu flaglog flagfld cutinner cutoff t_target seed :pre pair_style style mu flaglog flagfld cutinner cutoff t_target seed flagHI flagVF :pre
style = {brownian} or {brownian/poly} style = {brownian} or {brownian/poly}
mu = dynamic viscosity (dynamic viscosity units) mu = dynamic viscosity (dynamic viscosity units)
@ -22,11 +22,13 @@ flagfld = 0/1 to include/exclude Fast Lubrication Dynamics effects
cutinner = inner cutoff distance (distance units) cutinner = inner cutoff distance (distance units)
cutoff = outer cutoff for interactions (distance units) cutoff = outer cutoff for interactions (distance units)
t_target = target temp of the system (temperature units) t_target = target temp of the system (temperature units)
seed = seed for the random number generator (positive integer) :ul seed = seed for the random number generator (positive integer)
flagHI (optional) = 0/1 to include/exclude 1/r hydrodynamic interactions
flagVF (optional) = 0/1 to include/exclude volume fraction corrections in the long-range isotropic terms :ul
[Examples:] [Examples:]
pair_style brownian 1.5 1 1 2.01 2.5 2.0 5878567 (assuming radius=1) pair_style brownian 1.5 1 1 2.01 2.5 2.0 5878567 (assuming radius = 1)
pair_coeff 1 1 2.05 2.8 pair_coeff 1 1 2.05 2.8
pair_coeff * * :pre pair_coeff * * :pre
@ -49,6 +51,11 @@ The {t_target} setting is used to specify the target temperature of
the system. The random number {seed} is used to generate random the system. The random number {seed} is used to generate random
numbers for the thermostatting procedure. numbers for the thermostatting procedure.
The {flagHI} and {flagVF} settings are optional. Neither should be
used, or both must be defined.
:line
The following coefficients must be defined for each pair of atoms The following coefficients must be defined for each pair of atoms
types via the "pair_coeff"_pair_coeff.html command as in the examples 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 above, or in the data file or restart files read by the
@ -129,4 +136,8 @@ Only spherical particles are allowed for pair_style brownian/poly.
lubricate"_pair_lubricate.html, "pair_style lubricate"_pair_lubricate.html, "pair_style
lubricateU"_pair_lubricateU.html lubricateU"_pair_lubricateU.html
[Default:] none [Default:]
The default settings for the optional args are flagHI = 1 and flagVF =
1.

57
doc/pair_lubricate.html
View File

@ -19,7 +19,7 @@
</H3> </H3>
<P><B>Syntax:</B> <P><B>Syntax:</B>
</P> </P>
<PRE>pair_style style mu flaglog flagfld cutinner cutoff <PRE>pair_style style mu flaglog flagfld cutinner cutoff flagHI flagVF
</PRE> </PRE>
<UL><LI>style = <I>lubricate</I> or <I>lubricate/poly</I> <UL><LI>style = <I>lubricate</I> or <I>lubricate/poly</I>
<LI>mu = dynamic viscosity (dynamic viscosity units) <LI>mu = dynamic viscosity (dynamic viscosity units)
@ -27,6 +27,8 @@
<LI>flagfld = 0/1 to include/exclude Fast Lubrication Dynamics effects <LI>flagfld = 0/1 to include/exclude Fast Lubrication Dynamics effects
<LI>cutinner = inner cutoff distance (distance units) <LI>cutinner = inner cutoff distance (distance units)
<LI>cutoff = outer cutoff for interactions (distance units) <LI>cutoff = outer cutoff for interactions (distance units)
<LI>flagHI (optional) = 0/1 to include/exclude 1/r hydrodynamic interactions
<LI>flagVF (optional) = 0/1 to include/exclude volume fraction corrections in the long-range isotropic terms
</UL> </UL>
<P><B>Examples:</B> (all assume radius = 1) <P><B>Examples:</B> (all assume radius = 1)
</P> </P>
@ -51,17 +53,22 @@ Melrose)</A>
</CENTER> </CENTER>
<P>which represents the dissipation W between two nearby particles due to <P>which represents the dissipation W between two nearby particles due to
their relative velocities in the presence of a background solvent with their relative velocities in the presence of a background solvent with
viscosity mu. Note that this is dynamic viscosity which has units of viscosity <I>mu</I>. Note that this is dynamic viscosity which has units of
mass/distance/time, not kinematic viscosity. mass/distance/time, not kinematic viscosity.
</P> </P>
<P>The Asq (squeeze) term is the strongest and is always included. It <P>The Asq (squeeze) term is the strongest and is included if <I>flagHI</I> is
scales as 1/gap where gap is the separation between the surfaces of set to 1 (default). It scales as 1/gap where gap is the separation
the 2 particles. The Ash (shear) and Apu (pump) terms are only between the surfaces of the 2 particles. The Ash (shear) and Apu
include if <I>flaglog</I> is set to 1. Thy are the next strongest (pump) terms are only included if <I>flaglog</I> is set to 1. They are the
interactions, and the only other singular interaction, and scale as next strongest interactions, and the only other singular interaction,
log(gap). The Atw (twist) term is currently not included. It is and scale as log(gap). Note that <I>flaglog</I> = 1 and <I>flagHI</I> = 0 is
invalid, and will result in a warning message, after which <I>flagHI</I> will
be set to 1. The Atw (twist) term is currently not included. It is
typically a very small contribution to the lubrication forces. typically a very small contribution to the lubrication forces.
</P> </P>
<P>The <I>flagHI</I> and <I>flagVF</I> settings are optional. Neither should be
used, or both must be defined.
</P>
<P><I>Cutinner</I> sets the minimum center-to-center separation that will be <P><I>Cutinner</I> sets the minimum center-to-center separation that will be
used in calculations irrespective of the actual separation. <I>Cutoff</I> used in calculations irrespective of the actual separation. <I>Cutoff</I>
is the maximum center-to-center separation at which an interaction is is the maximum center-to-center separation at which an interaction is
@ -77,9 +84,10 @@ represented by the following equation
<P>where U represents the velocities and angular velocities of the <P>where U represents the velocities and angular velocities of the
particles, U^<I>infty</I> represents the velocity and the angular velocity particles, U^<I>infty</I> represents the velocity and the angular velocity
of the undisturbed fluid, and E^<I>infty</I> represents the rate of strain of the undisturbed fluid, and E^<I>infty</I> represents the rate of strain
tensor of the undisturbed fluid with viscosity mu. Again, note that tensor of the undisturbed fluid with viscosity <I>mu</I>. Again, note that
this is dynamic viscosity which has units of mass/distance/time, not this is dynamic viscosity which has units of mass/distance/time, not
kinematic viscosity. kinematic viscosity. Volume fraction corrections to R_FU are included
as long as <I>flagVF</I> is set to 1 (default).
</P> </P>
<P>IMPORTANT NOTE: When using the FLD terms, these pair styles are <P>IMPORTANT NOTE: When using the FLD terms, these pair styles are
designed to be used with explicit time integration and a designed to be used with explicit time integration and a
@ -92,21 +100,35 @@ lubricateU</A> command.
<P>Style <I>lubricate</I> requires monodisperse spherical particles; style <P>Style <I>lubricate</I> requires monodisperse spherical particles; style
<I>lubricate/poly</I> allows for polydisperse spherical particles. <I>lubricate/poly</I> allows for polydisperse spherical particles.
</P> </P>
<P>The viscosity mu can be varied in a time-dependent manner over the <P>The viscosity <I>mu</I> can be varied in a time-dependent manner over the
course of a simluation, in which case in which case the pair_style course of a simluation, in which case in which case the pair_style
setting for mu will be overridden. See the <A HREF = "fix_adapt.html">fix adapt</A> setting for <I>mu</I> will be overridden. See the <A HREF = "fix_adapt.html">fix adapt</A>
command for details. command for details.
</P> </P>
<P>If the suspension is sheared via the <A HREF = "fix_deform.html">fix deform</A> <P>If the suspension is sheared via the <A HREF = "fix_deform.html">fix deform</A>
command then the pair style uses the shear rate to adjust the command then the pair style uses the shear rate to adjust the
hydrodynamic interactions accordingly. hydrodynamic interactions accordingly. Volume changes due to fix
deform are accounted for when computing the volume fraction
corrections to R_FU.
</P>
<P>When computing the volume fraction corrections to R_FU, the presence
of walls (whether moving or stationary) will affect the volume
fraction available to colloidal particles. This is currently accounted
for with the following types of walls: <A HREF = "fix_wall.html">wall/lj93</A>,
<A HREF = "fix_wall.html">wall/lj126</A>, <A HREF = "fix_wall.html">wall/colloid</A>, and
<A HREF = "fix_wall.html">wall/harmonic</A>. For these wall styles, the correct
volume fraction will be used when walls do not coincide with the box
boundary, as well as when walls move and thereby cause a change in the
volume fraction. Other wall styles will still work, but they will
result in the volume fraction being computed based on the box
boundaries.
</P> </P>
<P>Since lubrication forces are dissipative, it is usually desirable to <P>Since lubrication forces are dissipative, it is usually desirable to
thermostat the system at a constant temperature. If Brownian motion thermostat the system at a constant temperature. If Brownian motion
(at a constant temperature) is desired, it can be set using the (at a constant temperature) is desired, it can be set using the
<A HREF = "pair_brownian.html">pair_style brownian</A> command. These pair styles <A HREF = "pair_brownian.html">pair_style brownian</A> command. These pair styles
and the <I>brownian</I> style should use consistent parameters for <I>mu</I>, and the brownian style should use consistent parameters for <I>mu</I>,
<I>flaglog</I>, <I>flagfld</I>, <I>cutinner</I>, and <I>cutoff</I>. <I>flaglog</I>, <I>flagfld</I>, <I>cutinner</I>, <I>cutoff</I>, <I>flagHI</I> and <I>flagVF</I>.
</P> </P>
<HR> <HR>
@ -189,7 +211,10 @@ lubricate.
<P><A HREF = "pair_coeff.html">pair_coeff</A>, <A HREF = "pair_lubricateU.html">pair_style <P><A HREF = "pair_coeff.html">pair_coeff</A>, <A HREF = "pair_lubricateU.html">pair_style
lubricateU</A> lubricateU</A>
</P> </P>
<P><B>Default:</B> none <P><B>Default:</B>
</P>
<P>The default settings for the optional args are flagHI = 1 and flagVF =
1.
</P> </P>
<HR> <HR>

59
doc/pair_lubricate.txt
View File

@ -13,14 +13,16 @@ pair_style lubricate/poly/omp command :h3
[Syntax:] [Syntax:]
pair_style style mu flaglog flagfld cutinner cutoff :pre pair_style style mu flaglog flagfld cutinner cutoff flagHI flagVF :pre
style = {lubricate} or {lubricate/poly} style = {lubricate} or {lubricate/poly}
mu = dynamic viscosity (dynamic viscosity units) mu = dynamic viscosity (dynamic viscosity units)
flaglog = 0/1 log terms in the lubrication approximation off/on flaglog = 0/1 log terms in the lubrication approximation off/on
flagfld = 0/1 to include/exclude Fast Lubrication Dynamics effects flagfld = 0/1 to include/exclude Fast Lubrication Dynamics effects
cutinner = inner cutoff distance (distance units) cutinner = inner cutoff distance (distance units)
cutoff = outer cutoff for interactions (distance units) :ul cutoff = outer cutoff for interactions (distance units)
flagHI (optional) = 0/1 to include/exclude 1/r hydrodynamic interactions
flagVF (optional) = 0/1 to include/exclude volume fraction corrections in the long-range isotropic terms :ul
[Examples:] (all assume radius = 1) [Examples:] (all assume radius = 1)
@ -45,17 +47,22 @@ Melrose)"_#Ball
which represents the dissipation W between two nearby particles due to which represents the dissipation W between two nearby particles due to
their relative velocities in the presence of a background solvent with their relative velocities in the presence of a background solvent with
viscosity mu. Note that this is dynamic viscosity which has units of viscosity {mu}. Note that this is dynamic viscosity which has units of
mass/distance/time, not kinematic viscosity. mass/distance/time, not kinematic viscosity.
The Asq (squeeze) term is the strongest and is always included. It The Asq (squeeze) term is the strongest and is included if {flagHI} is
scales as 1/gap where gap is the separation between the surfaces of set to 1 (default). It scales as 1/gap where gap is the separation
the 2 particles. The Ash (shear) and Apu (pump) terms are only between the surfaces of the 2 particles. The Ash (shear) and Apu
include if {flaglog} is set to 1. Thy are the next strongest (pump) terms are only included if {flaglog} is set to 1. They are the
interactions, and the only other singular interaction, and scale as next strongest interactions, and the only other singular interaction,
log(gap). The Atw (twist) term is currently not included. It is and scale as log(gap). Note that {flaglog} = 1 and {flagHI} = 0 is
invalid, and will result in a warning message, after which {flagHI} will
be set to 1. The Atw (twist) term is currently not included. It is
typically a very small contribution to the lubrication forces. typically a very small contribution to the lubrication forces.
The {flagHI} and {flagVF} settings are optional. Neither should be
used, or both must be defined.
{Cutinner} sets the minimum center-to-center separation that will be {Cutinner} sets the minimum center-to-center separation that will be
used in calculations irrespective of the actual separation. {Cutoff} used in calculations irrespective of the actual separation. {Cutoff}
is the maximum center-to-center separation at which an interaction is is the maximum center-to-center separation at which an interaction is
@ -71,9 +78,10 @@ represented by the following equation
where U represents the velocities and angular velocities of the where U represents the velocities and angular velocities of the
particles, U^{infty} represents the velocity and the angular velocity particles, U^{infty} represents the velocity and the angular velocity
of the undisturbed fluid, and E^{infty} represents the rate of strain of the undisturbed fluid, and E^{infty} represents the rate of strain
tensor of the undisturbed fluid with viscosity mu. Again, note that tensor of the undisturbed fluid with viscosity {mu}. Again, note that
this is dynamic viscosity which has units of mass/distance/time, not this is dynamic viscosity which has units of mass/distance/time, not
kinematic viscosity. kinematic viscosity. Volume fraction corrections to R_FU are included
as long as {flagVF} is set to 1 (default).
IMPORTANT NOTE: When using the FLD terms, these pair styles are IMPORTANT NOTE: When using the FLD terms, these pair styles are
designed to be used with explicit time integration and a designed to be used with explicit time integration and a
@ -86,21 +94,35 @@ lubricateU"_pair_lubricateU.html command.
Style {lubricate} requires monodisperse spherical particles; style Style {lubricate} requires monodisperse spherical particles; style
{lubricate/poly} allows for polydisperse spherical particles. {lubricate/poly} allows for polydisperse spherical particles.
The viscosity mu can be varied in a time-dependent manner over the The viscosity {mu} can be varied in a time-dependent manner over the
course of a simluation, in which case in which case the pair_style course of a simluation, in which case in which case the pair_style
setting for mu will be overridden. See the "fix adapt"_fix_adapt.html setting for {mu} will be overridden. See the "fix adapt"_fix_adapt.html
command for details. command for details.
If the suspension is sheared via the "fix deform"_fix_deform.html If the suspension is sheared via the "fix deform"_fix_deform.html
command then the pair style uses the shear rate to adjust the command then the pair style uses the shear rate to adjust the
hydrodynamic interactions accordingly. hydrodynamic interactions accordingly. Volume changes due to fix
deform are accounted for when computing the volume fraction
corrections to R_FU.
When computing the volume fraction corrections to R_FU, the presence
of walls (whether moving or stationary) will affect the volume
fraction available to colloidal particles. This is currently accounted
for with the following types of walls: "wall/lj93"_fix_wall.html,
"wall/lj126"_fix_wall.html, "wall/colloid"_fix_wall.html, and
"wall/harmonic"_fix_wall.html. For these wall styles, the correct
volume fraction will be used when walls do not coincide with the box
boundary, as well as when walls move and thereby cause a change in the
volume fraction. Other wall styles will still work, but they will
result in the volume fraction being computed based on the box
boundaries.
Since lubrication forces are dissipative, it is usually desirable to Since lubrication forces are dissipative, it is usually desirable to
thermostat the system at a constant temperature. If Brownian motion thermostat the system at a constant temperature. If Brownian motion
(at a constant temperature) is desired, it can be set using the (at a constant temperature) is desired, it can be set using the
"pair_style brownian"_pair_brownian.html command. These pair styles "pair_style brownian"_pair_brownian.html command. These pair styles
and the {brownian} style should use consistent parameters for {mu}, and the brownian style should use consistent parameters for {mu},
{flaglog}, {flagfld}, {cutinner}, and {cutoff}. {flaglog}, {flagfld}, {cutinner}, {cutoff}, {flagHI} and {flagVF}.
:line :line
@ -183,7 +205,10 @@ Only spherical particles are allowed for pair_style lubricate/poly.
"pair_coeff"_pair_coeff.html, "pair_style "pair_coeff"_pair_coeff.html, "pair_style
lubricateU"_pair_lubricateU.html lubricateU"_pair_lubricateU.html
[Default:] none [Default:]
The default settings for the optional args are flagHI = 1 and flagVF =
1.
:line :line

68
doc/pair_lubricateU.html
View File

@ -15,7 +15,7 @@
</H3> </H3>
<P><B>Syntax:</B> <P><B>Syntax:</B>
</P> </P>
<PRE>pair_style style mu flaglog cutinner cutoff gdot <PRE>pair_style style mu flaglog cutinner cutoff gdot flagHI flagVF
</PRE> </PRE>
<UL><LI>style = <I>lubricateU</I> or <I>lubricateU/poly</I> <UL><LI>style = <I>lubricateU</I> or <I>lubricateU/poly</I>
<LI>mu = dynamic viscosity (dynamic viscosity units) <LI>mu = dynamic viscosity (dynamic viscosity units)
@ -23,10 +23,12 @@
<LI>cutinner = inner cut off distance (distance units) <LI>cutinner = inner cut off distance (distance units)
<LI>cutoff = outer cutoff for interactions (distance units) <LI>cutoff = outer cutoff for interactions (distance units)
<LI>gdot = shear rate (1/time units) <LI>gdot = shear rate (1/time units)
<LI>flagHI (optional) = 0/1 to include/exclude 1/r hydrodynamic interactions
<LI>flagVF (optional) = 0/1 to include/exclude volume fraction corrections in the long-range isotropic terms
</UL> </UL>
<P><B>Examples:</B> (all assume radius = 1) <P><B>Examples:</B> (all assume radius = 1)
</P> </P>
<PRE>pair_style lubricateU 1.5 1 2.01 2.5 0.01 <PRE>pair_style lubricateU 1.5 1 2.01 2.5 0.01 1 1
pair_coeff 1 1 2.05 2.8 pair_coeff 1 1 2.05 2.8
pair_coeff * * pair_coeff * *
</PRE> </PRE>
@ -44,16 +46,22 @@ Melrose)</A>
</CENTER> </CENTER>
<P>which represents the dissipation W between two nearby particles due to <P>which represents the dissipation W between two nearby particles due to
their relative velocities in the presence of a background solvent with their relative velocities in the presence of a background solvent with
viscosity mu. Note that this is dynamic viscosity which has units of viscosity <I>mu</I>. Note that this is dynamic viscosity which has units of
mass/distance/time, not kinematic viscosity. mass/distance/time, not kinematic viscosity.
</P> </P>
<P>The Asq (squeeze) term is the strongest and is always included. It <P>The Asq (squeeze) term is the strongest and is included as long as
scales as 1/gap where gap is the separation between the surfaces of <I>flagHI</I> is set to 1 (default). It scales as 1/gap where gap is the
the 2 particles. The Ash (shear) and Apu (pump) terms are only separation between the surfaces of the 2 particles. The Ash (shear)
include if <I>flaglog</I> is set to 1. Thy are the next strongest and Apu (pump) terms are only included if <I>flaglog</I> is set to 1. They
interactions, and the only other singular interaction, and scale as are the next strongest interactions, and the only other singular
log(gap). The Atw (twist) term is currently not included. It is interaction, and scale as log(gap). Note that <I>flaglog</I> = 1 and
typically a very small contribution to the lubrication forces. <I>flagHI</I> = 0 is invalid, and will result in a warning message, after
which <I>flagHI</I> will be set to 1. The Atw (twist) term is currently not
included. It is typically a very small contribution to the lubrication
forces.
</P>
<P>The <I>flagHI</I> and <I>flagVF</I> settings are optional. Neither should be
used, or both must be defined.
</P> </P>
<P><I>Cutinner</I> sets the minimum center-to-center separation that will be <P><I>Cutinner</I> sets the minimum center-to-center separation that will be
used in calculations irrespective of the actual separation. <I>Cutoff</I> used in calculations irrespective of the actual separation. <I>Cutoff</I>
@ -68,11 +76,12 @@ solved to balance the forces and torques is
<CENTER><IMG SRC = "Eqs/fld2.jpg"> <CENTER><IMG SRC = "Eqs/fld2.jpg">
</CENTER> </CENTER>
<P>where U represents the velocities and angular velocities of the <P>where U represents the velocities and angular velocities of the
particles, U<I>infty</I> represents the velocities and the angular particles, U^<I>infty</I> represents the velocities and the angular
velocities of the undisturbed fluid, and E<I>infty</I> represents the rate velocities of the undisturbed fluid, and E^<I>infty</I> represents the rate
of strain tensor of the undisturbed fluid flow with viscosity mu. of strain tensor of the undisturbed fluid flow with viscosity
Again, note that this is dynamic viscosity which has units of <I>mu</I>. Again, note that this is dynamic viscosity which has units of
mass/distance/time, not kinematic viscosity. mass/distance/time, not kinematic viscosity. Volume fraction
corrections to R_FU are included if <I>flagVF</I> is set to 1 (default).
</P> </P>
<P>F<I>rest</I> represents the forces and torques due to all other types of <P>F<I>rest</I> represents the forces and torques due to all other types of
interactions, e.g. Brownian, electrostatic etc. Note that this interactions, e.g. Brownian, electrostatic etc. Note that this
@ -104,14 +113,28 @@ reset by the time integration fix.
</P> </P>
<P>If the suspension is sheared via the <A HREF = "fix_deform.html">fix deform</A> <P>If the suspension is sheared via the <A HREF = "fix_deform.html">fix deform</A>
command then the pair style uses the shear rate to adjust the command then the pair style uses the shear rate to adjust the
hydrodynamic interactions accordingly. hydrodynamic interactions accordingly. Volume changes due to fix
deform are accounted for when computing the volume fraction
corrections to R_FU.
</P>
<P>When computing the volume fraction corrections to R_FU, the presence
of walls (whether moving or stationary) will affect the volume
fraction available to colloidal particles. This is currently accounted
for with the following types of walls: <A HREF = "fix_wall.html">wall/lj93</A>,
<A HREF = "fix_wall.html">wall/lj126</A>, <A HREF = "fix_wall.html">wall/colloid</A>, and
"wall/harmonic_fix_wall.html". For these wall styles, the correct
volume fraction will be used when walls do not coincide with the box
boundary, as well as when walls move and thereby cause a change in the
volume fraction. To use these wall styles with pair_style <I>lubricateU</I>
or <I>lubricateU/poly</I>, the <I>fld yes</I> option must be specified in the
fix wall command.
</P> </P>
<P>Since lubrication forces are dissipative, it is usually desirable to <P>Since lubrication forces are dissipative, it is usually desirable to
thermostat the system at a constant temperature. If Brownian motion thermostat the system at a constant temperature. If Brownian motion
(at a constant temperature) is desired, it can be set using the (at a constant temperature) is desired, it can be set using the
<A HREF = "pair_brownian.html">pair_style brownian</A> command. These pair styles <A HREF = "pair_brownian.html">pair_style brownian</A> command. These pair styles
and the <I>brownian</I> style should use consistent parameters for <I>mu</I>, and the brownian style should use consistent parameters for <I>mu</I>,
<I>flaglog</I>, <I>flagfld = 1</I>, <I>cutinner</I>, and <I>cutoff</I>. <I>flaglog</I>, <I>flagfld</I>, <I>cutinner</I>, <I>cutoff</I>, <I>flagHI</I> and <I>flagVF</I>.
</P> </P>
<HR> <HR>
@ -166,8 +189,8 @@ LAMMPS</A> section for more info.
forces/torques on the particles have been already been computed when forces/torques on the particles have been already been computed when
it is invoked. This requires this style to be defined as the last of it is invoked. This requires this style to be defined as the last of
the pair styles, and that no fixes apply additional constraint forces. the pair styles, and that no fixes apply additional constraint forces.
One exception is the <A HREF = "fix_wall.html">fix wall/colloid</A> command, which One exception is the <A HREF = "fix_wall.html">fix wall/colloid</A> commands, which
has an "fld" option to apply its wall forces correctly. has an "fld" option to apply their wall forces correctly.
</P> </P>
<P>Only spherical monodisperse particles are allowed for pair_style <P>Only spherical monodisperse particles are allowed for pair_style
lubricateU. lubricateU.
@ -184,7 +207,10 @@ deform</A> with the same rate of shear (erate).
<P><A HREF = "pair_coeff.html">pair_coeff</A>, <A HREF = "pair_lubricate.html">pair_style <P><A HREF = "pair_coeff.html">pair_coeff</A>, <A HREF = "pair_lubricate.html">pair_style
lubricate</A> lubricate</A>
</P> </P>
<P><B>Default:</B> none <P><B>Default:</B>
</P>
<P>The default settings for the optional args are flagHI = 1 and flagVF =
1.
</P> </P>
<HR> <HR>

70
doc/pair_lubricateU.txt
View File

@ -11,18 +11,20 @@ pair_style lubricateU/poly command :h3
[Syntax:] [Syntax:]
pair_style style mu flaglog cutinner cutoff gdot :pre pair_style style mu flaglog cutinner cutoff gdot flagHI flagVF :pre
style = {lubricateU} or {lubricateU/poly} style = {lubricateU} or {lubricateU/poly}
mu = dynamic viscosity (dynamic viscosity units) mu = dynamic viscosity (dynamic viscosity units)
flaglog = 0/1 log terms in the lubrication approximation on/off flaglog = 0/1 log terms in the lubrication approximation on/off
cutinner = inner cut off distance (distance units) cutinner = inner cut off distance (distance units)
cutoff = outer cutoff for interactions (distance units) cutoff = outer cutoff for interactions (distance units)
gdot = shear rate (1/time units) :ul gdot = shear rate (1/time units)
flagHI (optional) = 0/1 to include/exclude 1/r hydrodynamic interactions
flagVF (optional) = 0/1 to include/exclude volume fraction corrections in the long-range isotropic terms :ul
[Examples:] (all assume radius = 1) [Examples:] (all assume radius = 1)
pair_style lubricateU 1.5 1 2.01 2.5 0.01 pair_style lubricateU 1.5 1 2.01 2.5 0.01 1 1
pair_coeff 1 1 2.05 2.8 pair_coeff 1 1 2.05 2.8
pair_coeff * * :pre pair_coeff * * :pre
@ -40,16 +42,22 @@ Melrose)"_#Ball
which represents the dissipation W between two nearby particles due to which represents the dissipation W between two nearby particles due to
their relative velocities in the presence of a background solvent with their relative velocities in the presence of a background solvent with
viscosity mu. Note that this is dynamic viscosity which has units of viscosity {mu}. Note that this is dynamic viscosity which has units of
mass/distance/time, not kinematic viscosity. mass/distance/time, not kinematic viscosity.
The Asq (squeeze) term is the strongest and is always included. It The Asq (squeeze) term is the strongest and is included as long as
scales as 1/gap where gap is the separation between the surfaces of {flagHI} is set to 1 (default). It scales as 1/gap where gap is the
the 2 particles. The Ash (shear) and Apu (pump) terms are only separation between the surfaces of the 2 particles. The Ash (shear)
include if {flaglog} is set to 1. Thy are the next strongest and Apu (pump) terms are only included if {flaglog} is set to 1. They
interactions, and the only other singular interaction, and scale as are the next strongest interactions, and the only other singular
log(gap). The Atw (twist) term is currently not included. It is interaction, and scale as log(gap). Note that {flaglog} = 1 and
typically a very small contribution to the lubrication forces. {flagHI} = 0 is invalid, and will result in a warning message, after
which {flagHI} will be set to 1. The Atw (twist) term is currently not
included. It is typically a very small contribution to the lubrication
forces.
The {flagHI} and {flagVF} settings are optional. Neither should be
used, or both must be defined.
{Cutinner} sets the minimum center-to-center separation that will be {Cutinner} sets the minimum center-to-center separation that will be
used in calculations irrespective of the actual separation. {Cutoff} used in calculations irrespective of the actual separation. {Cutoff}
@ -64,11 +72,12 @@ solved to balance the forces and torques is
:c,image(Eqs/fld2.jpg) :c,image(Eqs/fld2.jpg)
where U represents the velocities and angular velocities of the where U represents the velocities and angular velocities of the
particles, U{infty} represents the velocities and the angular particles, U^{infty} represents the velocities and the angular
velocities of the undisturbed fluid, and E{infty} represents the rate velocities of the undisturbed fluid, and E^{infty} represents the rate
of strain tensor of the undisturbed fluid flow with viscosity mu. of strain tensor of the undisturbed fluid flow with viscosity
Again, note that this is dynamic viscosity which has units of {mu}. Again, note that this is dynamic viscosity which has units of
mass/distance/time, not kinematic viscosity. mass/distance/time, not kinematic viscosity. Volume fraction
corrections to R_FU are included if {flagVF} is set to 1 (default).
F{rest} represents the forces and torques due to all other types of F{rest} represents the forces and torques due to all other types of
interactions, e.g. Brownian, electrostatic etc. Note that this interactions, e.g. Brownian, electrostatic etc. Note that this
@ -100,14 +109,28 @@ Style {lubricateU} requires monodisperse spherical particles; style
If the suspension is sheared via the "fix deform"_fix_deform.html If the suspension is sheared via the "fix deform"_fix_deform.html
command then the pair style uses the shear rate to adjust the command then the pair style uses the shear rate to adjust the
hydrodynamic interactions accordingly. hydrodynamic interactions accordingly. Volume changes due to fix
deform are accounted for when computing the volume fraction
corrections to R_FU.
When computing the volume fraction corrections to R_FU, the presence
of walls (whether moving or stationary) will affect the volume
fraction available to colloidal particles. This is currently accounted
for with the following types of walls: "wall/lj93"_fix_wall.html,
"wall/lj126"_fix_wall.html, "wall/colloid"_fix_wall.html, and
"wall/harmonic_fix_wall.html". For these wall styles, the correct
volume fraction will be used when walls do not coincide with the box
boundary, as well as when walls move and thereby cause a change in the
volume fraction. To use these wall styles with pair_style {lubricateU}
or {lubricateU/poly}, the {fld yes} option must be specified in the
fix wall command.
Since lubrication forces are dissipative, it is usually desirable to Since lubrication forces are dissipative, it is usually desirable to
thermostat the system at a constant temperature. If Brownian motion thermostat the system at a constant temperature. If Brownian motion
(at a constant temperature) is desired, it can be set using the (at a constant temperature) is desired, it can be set using the
"pair_style brownian"_pair_brownian.html command. These pair styles "pair_style brownian"_pair_brownian.html command. These pair styles
and the {brownian} style should use consistent parameters for {mu}, and the brownian style should use consistent parameters for {mu},
{flaglog}, {flagfld = 1}, {cutinner}, and {cutoff}. {flaglog}, {flagfld}, {cutinner}, {cutoff}, {flagHI} and {flagVF}.
:line :line
@ -162,8 +185,8 @@ Currently, these pair styles assume that all other types of
forces/torques on the particles have been already been computed when forces/torques on the particles have been already been computed when
it is invoked. This requires this style to be defined as the last of it is invoked. This requires this style to be defined as the last of
the pair styles, and that no fixes apply additional constraint forces. the pair styles, and that no fixes apply additional constraint forces.
One exception is the "fix wall/colloid"_fix_wall.html command, which One exception is the "fix wall/colloid"_fix_wall.html commands, which
has an "fld" option to apply its wall forces correctly. has an "fld" option to apply their wall forces correctly.
Only spherical monodisperse particles are allowed for pair_style Only spherical monodisperse particles are allowed for pair_style
lubricateU. lubricateU.
@ -180,7 +203,10 @@ deform"_fix_deform.html with the same rate of shear (erate).
"pair_coeff"_pair_coeff.html, "pair_style "pair_coeff"_pair_coeff.html, "pair_style
lubricate"_pair_lubricate.html lubricate"_pair_lubricate.html
[Default:] none [Default:]
The default settings for the optional args are flagHI = 1 and flagVF =
1.
:line :line