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doc/Section_commands.html
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@ -323,7 +323,7 @@ of each style or click on the style itself for a full description:
<TR ALIGN="center"><TD ><A HREF = "fix_npt_asphere.html">npt/asphere</A></TD><TD ><A HREF = "fix_nve.html">nve</A></TD><TD ><A HREF = "fix_nve_asphere.html">nve/asphere</A></TD><TD ><A HREF = "fix_nve_dipole.html">nve/dipole</A></TD><TD ><A HREF = "fix_nve_gran.html">nve/gran</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_nvt.html">nvt</A></TD></TR>
<TR ALIGN="center"><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_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_print.html">print</A></TD><TD ><A HREF = "fix_rdf.html">rdf</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_rescale.html">temp/rescale</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_tmd.html">tmd</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><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_tmd.html">tmd</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><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>
<HR>

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doc/Section_commands.txt
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@ -424,6 +424,7 @@ of each style or click on the style itself for a full description:
"spring/self"_fix_spring_self.html,
"temp/rescale"_fix_temp_rescale.html,
"tmd"_fix_tmd.html,
"viscosity"_fix_viscosity.html,
"viscous"_fix_viscous.html,
"wall/gran"_fix_wall_gran.html,
"wall/lj126"_fix_wall_lj126.html,

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doc/Section_howto.html
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@ -751,6 +751,9 @@ deform</A> should be set to "remap v", since that is what
<A HREF = "fix_nvt_sllod.html">fix nvt/sllod</A> assumes to generate a velocity
profile consistent with the applied shear strain rate.
</P>
<P>An alternative method for calculating viscosities is provided via the
<A HREF = "fix_viscosity.html">fix viscosity</A> command.
</P>
<HR>
<A NAME = "4_14"></A><H4>4.14 Aspherical particles

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doc/Section_howto.txt
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@ -744,6 +744,9 @@ deform"_fix_deform.html should be set to "remap v", since that is what
"fix nvt/sllod"_fix_nvt_sllod.html assumes to generate a velocity
profile consistent with the applied shear strain rate.
An alternative method for calculating viscosities is provided via the
"fix viscosity"_fix_viscosity.html command.
:line
4.14 Aspherical particles :link(4_14),h4

1
doc/fix.html
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@ -130,6 +130,7 @@ for individual fixes for info on which ones can be restarted.
<LI><A HREF = "fix_spring_self.html">spring/self</A> - spring from each atom to its origin
<LI><A HREF = "fix_temp_rescale.html">temp/rescale</A> - temperature control by velocity rescaling
<LI><A HREF = "fix_tmd.html">tmd</A> - guide a group of atoms to a new configuration
<LI><A HREF = "fix_viscosity.html">viscosity</A> - Muller-Plathe momentum exchange for viscosity calculation
<LI><A HREF = "fix_viscous.html">viscous</A> - viscous damping for granular simulations
<LI><A HREF = "fix_wall_gran.html">wall/gran</A> - frictional wall(s) for granular simulations
<LI><A HREF = "fix_wall_lj126.html">wall/lj126</A> - Lennard-Jones 12-6 wall

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doc/fix.txt
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@ -134,6 +134,8 @@ Here is an alphabetic list of fix styles available in LAMMPS:
"temp/rescale"_fix_temp_rescale.html - temperature control by \
velocity rescaling
"tmd"_fix_tmd.html - guide a group of atoms to a new configuration
"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

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doc/fix_viscosity.html Normal file
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@ -0,0 +1,125 @@
<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>fix viscosity command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>fix ID group-ID viscosity N vdim pdim Nbin
</PRE>
<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
<LI>viscosity = style name of this fix command
<LI>N = perform momentum exchange every N steps
<LI>vdim = <I>x</I> or <I>y</I> or <I>z</I> = which momentum component to exchange
<LI>pdim = <I>x</I> or <I>y</I> or <I>z</I> = direction of momentum transfer
<LI>Nbin = # of layers in pdim direction
</UL>
<P><B>Examples:</B>
</P>
<PRE>fix 1 all viscosity 100 x z 20
</PRE>
<P><B>Description:</B>
</P>
<P>Use the Muller-Plathe algorithm described in <A HREF = "#Muller-Plathe">this
paper</A> to exchange momenta between two particles in
different regions of the simulation box every N steps. This induces a
shear velocity profile in the system. As described below this enables
a viscosity of the fluid to be calculated. This algorithm is
sometimes called a reverse non-equilibrium MD (reverse NEMD) approach
to computing viscosity. This is because the usual NEMD approach is to
impose a shear velocity profile on the system and measure the response
via an off-diagonal component of the stress tensor, which is
proportional to the momentum flux. In the Muller-Plathe method, the
momentum flux is imposed, and the shear velocity profile is the
system's response.
</P>
<P>The simulation box is divided into <I>Nbin</I> layers in the <I>pdim</I>
direction. Every N steps, two atoms are chosen in the following
manner. Only atoms in the fix group are considered. The atom in the
bottom layer with the most positive momentum component in the <I>vdim</I>
direction is the first atom. The atom in the middle later with the
most negative momentum component in the <I>vdim</I> direction is the second
atom. The <I>vdim</I> momenta components of these two atoms are swapped,
which resets their velocities, typically in opposite directions. Over
time, this induces a shear velocity profile in the system which can be
measured using commands such as the following, which writes the
profile to the file tmp.profile:
</P>
<PRE>compute c1 all attribute/atom vx
fix f1 all ave/spatial 100 10 1000 z lower 0.05 tmp.profile &
compute c1 units reduced
</PRE>
<P>As described below, the total momentum transferred by these velocity
swaps is computed by the fix and can be output. Dividing this
quantity by time and the cross-sectional area of the simulation box
yields a momentum flux. The ratio of momentum flux to the slope of
the shear velocity profile is the viscosity of the fluid, in
appopriate units. See the <A HREF = "#Muller-Plathe">Muller-Plathe paper</A> for
details.
</P>
<P>An alternative method for calculating a viscosity is to run a NEMD
simulation, as described in <A HREF = "Section_howto.html#4_13">this section</A> of
the manual. NEMD simulations deform the simmulation box via the <A HREF = "fix_deform.html">fix
deform</A> command. Thus they cannot be run on a charged
system using a <A HREF = "kspace_style.html">PPPM solver</A> since PPPM does not
currently support non-orthogonal boxes. Using fix viscosity keeps the
box orthogonal; thus it does not suffer from this limitation.
</P>
<P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
</P>
<P>No information about this fix is written to <A HREF = "restart.html">binary restart
files</A>. None of the <A HREF = "fix_modify.html">fix_modify</A> options
are relevant to this fix.
</P>
<P>The cummulative momentum transferred between the bottom and middle of
the simulatoin box (in the <I>pdim</I> direction) is stored as a scalar
quantity by this fix. This quantity is zeroed when the fix is defined
and accumlates thereafter, once every N steps. The units of the
quantity are momentum = mass*velocity. This quantity can be
accessed by various <A HREF = "Section_howto.html#4_15">output commands</A>, such as
<A HREF = "thermo_style.html">thermo_style custom</A>.
</P>
<P>No parameter of this fix can be used with the <I>start/stop</I> keywords of
the <A HREF = "run.html">run</A> command. This fix is not invoked during <A HREF = "minimize.html">energy
minimization</A>.
</P>
<P><B>Restrictions:</B>
</P>
<P>If the masses of the atom pairs are the same, the swaps conserve both
momentum and kinetic energy. Thus you should not need to thermostat
the system. If you do use a thermostat, you may want to apply it only
to the non-swapped dimensions (other than <I>vdim</I>).
</P>
<P>You should not swap velocities of atoms that are in constrained
molecules, e.g. via <A HREF = "fix_shake.html">fix shake</A> or <A HREF = "fix_rigid.html">fix
rigid</A>, since application of the constraints will alter
the amount of transferred momentum. You should, however, be able to
use flexible molecules with this approach. LAMMPS does not check that
this advice is followed.
</P>
<P>When running a simulation with large, massive particles or molecules
in a background solvent, you may want to only exchange momenta bewteen
solvent particles.
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "fix_ave_spatial.html">fix ave/spatial</A>, <A HREF = "fix_nvt_sllod.html">fix
nvt/sllod</A>
</P>
<P><B>Default:</B> none
</P>
<HR>
<A NAME = "Muller-Plathe"></A>
<P><B>(Muller-Plathe)</B> Muller-Plathe, Phys Rev E, 59, 4894-4898 (1999).
</P>
</HTML>

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doc/fix_viscosity.txt Normal file
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@ -0,0 +1,119 @@
"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
fix viscosity command :h3
[Syntax:]
fix ID group-ID viscosity N vdim pdim Nbin :pre
ID, group-ID are documented in "fix"_fix.html command
viscosity = style name of this fix command
N = perform momentum exchange every N steps
vdim = {x} or {y} or {z} = which momentum component to exchange
pdim = {x} or {y} or {z} = direction of momentum transfer
Nbin = # of layers in pdim direction :ul
[Examples:]
fix 1 all viscosity 100 x z 20 :pre
[Description:]
Use the Muller-Plathe algorithm described in "this
paper"_#Muller-Plathe to exchange momenta between two particles in
different regions of the simulation box every N steps. This induces a
shear velocity profile in the system. As described below this enables
a viscosity of the fluid to be calculated. This algorithm is
sometimes called a reverse non-equilibrium MD (reverse NEMD) approach
to computing viscosity. This is because the usual NEMD approach is to
impose a shear velocity profile on the system and measure the response
via an off-diagonal component of the stress tensor, which is
proportional to the momentum flux. In the Muller-Plathe method, the
momentum flux is imposed, and the shear velocity profile is the
system's response.
The simulation box is divided into {Nbin} layers in the {pdim}
direction. Every N steps, two atoms are chosen in the following
manner. Only atoms in the fix group are considered. The atom in the
bottom layer with the most positive momentum component in the {vdim}
direction is the first atom. The atom in the middle later with the
most negative momentum component in the {vdim} direction is the second
atom. The {vdim} momenta components of these two atoms are swapped,
which resets their velocities, typically in opposite directions. Over
time, this induces a shear velocity profile in the system which can be
measured using commands such as the following, which writes the
profile to the file tmp.profile:
compute c1 all attribute/atom vx
fix f1 all ave/spatial 100 10 1000 z lower 0.05 tmp.profile &
compute c1 units reduced :pre
As described below, the total momentum transferred by these velocity
swaps is computed by the fix and can be output. Dividing this
quantity by time and the cross-sectional area of the simulation box
yields a momentum flux. The ratio of momentum flux to the slope of
the shear velocity profile is the viscosity of the fluid, in
appopriate units. See the "Muller-Plathe paper"_#Muller-Plathe for
details.
An alternative method for calculating a viscosity is to run a NEMD
simulation, as described in "this section"_Section_howto.html#4_13 of
the manual. NEMD simulations deform the simmulation box via the "fix
deform"_fix_deform.html command. Thus they cannot be run on a charged
system using a "PPPM solver"_kspace_style.html since PPPM does not
currently support non-orthogonal boxes. Using fix viscosity keeps the
box orthogonal; thus it does not suffer from this limitation.
[Restart, fix_modify, output, run start/stop, minimize info:]
No information about this fix is written to "binary restart
files"_restart.html. None of the "fix_modify"_fix_modify.html options
are relevant to this fix.
The cummulative momentum transferred between the bottom and middle of
the simulatoin box (in the {pdim} direction) is stored as a scalar
quantity by this fix. This quantity is zeroed when the fix is defined
and accumlates thereafter, once every N steps. The units of the
quantity are momentum = mass*velocity. This quantity can be
accessed by various "output commands"_Section_howto.html#4_15, such as
"thermo_style custom"_thermo_style.html.
No parameter of this fix can be used with the {start/stop} keywords of
the "run"_run.html command. This fix is not invoked during "energy
minimization"_minimize.html.
[Restrictions:]
If the masses of the atom pairs are the same, the swaps conserve both
momentum and kinetic energy. Thus you should not need to thermostat
the system. If you do use a thermostat, you may want to apply it only
to the non-swapped dimensions (other than {vdim}).
You should not swap velocities of atoms that are in constrained
molecules, e.g. via "fix shake"_fix_shake.html or "fix
rigid"_fix_rigid.html, since application of the constraints will alter
the amount of transferred momentum. You should, however, be able to
use flexible molecules with this approach. LAMMPS does not check that
this advice is followed.
When running a simulation with large, massive particles or molecules
in a background solvent, you may want to only exchange momenta bewteen
solvent particles.
[Related commands:]
"fix ave/spatial"_fix_ave_spatial.html, "fix
nvt/sllod"_fix_nvt_sllod.html
[Default:] none
:line
:link(Muller-Plathe)
[(Muller-Plathe)] Muller-Plathe, Phys Rev E, 59, 4894-4898 (1999).