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4
doc/Section_commands.html
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@ -323,8 +323,8 @@ 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_npt_sphere.html">npt/sphere</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_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></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_nvt_sphere.html">nvt/sphere</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_press_berendsen.html">press/berendsen</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_print.html">print</A></TD><TD ><A HREF = "fix_rdf.html">rdf</A></TD><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></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_spring_self.html">spring/self</A></TD><TD ><A HREF = "fix_temp_berendsen.html">temp/berendsen</A></TD><TD ><A HREF = "fix_temp_rescale.html">temp/rescale</A></TD><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></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_spring_self.html">spring/self</A></TD><TD ><A HREF = "fix_temp_berendsen.html">temp/berendsen</A></TD><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_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></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_wall_lj126.html">wall/lj126</A></TD><TD ><A HREF = "fix_wall_lj93.html">wall/lj93</A></TD><TD ><A HREF = "fix_wall_reflect.html">wall/reflect</A></TD><TD ><A HREF = "fix_wiggle.html">wiggle</A>
</TD></TR></TABLE></DIV>
<HR>

1
doc/Section_commands.txt
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@ -426,6 +426,7 @@ of each style or click on the style itself for a full description:
"spring/self"_fix_spring_self.html,
"temp/berendsen"_fix_temp_berendsen.html,
"temp/rescale"_fix_temp_rescale.html,
"thermal/conductivity"_fix_thermal_conductivity.html,
"tmd"_fix_tmd.html,
"viscosity"_fix_viscosity.html,
"viscous"_fix_viscous.html,

1
doc/fix.html
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@ -154,6 +154,7 @@ list of fix styles available in LAMMPS:
<LI><A HREF = "fix_spring_self.html">spring/self</A> - spring from each atom to its origin
<LI><A HREF = "fix_temp_berendsen.html">temp/berendsen</A> - temperature control by Berendsen thermostat
<LI><A HREF = "fix_temp_rescale.html">temp/rescale</A> - temperature control by velocity rescaling
<LI><A HREF = "fix_thermal_conductivity.html">thermal/conductivity</A> - Muller-Plathe kinetic energy exchange for thermal conductivity calculation
<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

2
doc/fix.txt
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@ -160,6 +160,8 @@ list of fix styles available in LAMMPS:
Berendsen thermostat
"temp/rescale"_fix_temp_rescale.html - temperature control by \
velocity rescaling
"thermal/conductivity"_fix_thermal_conductivity.html - Muller-Plathe kinetic energy exchange for \
thermal conductivity calculation
"tmd"_fix_tmd.html - guide a group of atoms to a new configuration
"viscosity"_fix_viscosity.html - Muller-Plathe momentum exchange for \
viscosity calculation

153
doc/fix_thermal_conductivity.html Normal file
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@ -0,0 +1,153 @@
<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 thermal/conductivity command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>fix ID group-ID thermal/conductivity N edim Nbin keyword value ...
</PRE>
<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
<LI>thermal/conductivity = style name of this fix command
<LI>N = perform kinetic energy exchange every N steps
<LI>edim = <I>x</I> or <I>y</I> or <I>z</I> = direction of kinetic energy transfer
<LI>Nbin = # of layers in edim direction
<LI>zero or more keyword/value pairs may be appended
<LI>keyword = <I>swap</I>
<PRE> <I>swap</I> value = Nswap = number of swaps to perform every N steps
</PRE>
</UL>
<P><B>Examples:</B>
</P>
<PRE>fix 1 all thermal/conductivity 100 z 20
fix 1 all thermal/conductivity 50 z 20 swap 2
</PRE>
<P><B>Description:</B>
</P>
<P>Use the Muller-Plathe algorithm described in <A HREF = "#Muller-Plathe">this
paper</A> to exchange kinetic energy between two particles
in different regions of the simulation box every N steps. This
induces a temperature gradient in the system. As described below this
enables a thermal conductivity of the fluid to be calculated. This
algorithm is sometimes called a reverse non-equilibrium MD (reverse
NEMD) approach to computing thermal conductivity. This is because the
usual NEMD approach is to impose a temperature gradient on the system
and measure the response as the resulting heat flux. In the
Muller-Plathe method, the heat flux is imposed, and the temperature
gradient is the system's response.
</P>
<P>The simulation box is divided into <I>Nbin</I> layers in the <I>edim</I>
direction. Every N steps, Nswap pairs of atoms are chosen in the
following manner. Only atoms in the fix group are considered. The
hottest Nswap atoms in the bottom layer are selected. Similarly, the
coldest Nswap atoms in the middle later are selected. The two sets of
Nswap atoms are paired up and their velocities are exchanged. This
effectively swaps their kinetic energies, assuming their masses are
the same. Over time, this induces a temperature gradient in the
system which can be measured using commands such as the following,
which writes the temperature profile (assuming z = edim) to the file
tmp.profile:
</P>
<PRE>compute ke all ke/atom
variable temp atom c_ke<B></B>/1.5
fix 3 all ave/spatial 10 100 1000 z lower 0.05 v_temp &
file tmp.profile units reduced
</PRE>
<P>Note that by default, Nswap = 1, though this can be changed by the
optional <I>swap</I> keyword. Setting this parameter appropriately, in
conjunction with the swap rate N, allows the heat flux to be adjusted
across a wide range of values, and the kinetic energy to be exchanged
in large chunks or more smoothly.
</P>
<P>As described below, the total kinetic energy transferred by these
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 heat flux. The ratio of heat flux to the slope of the
temperature profile is the thermal conductivity of the fluid,
in appopriate units. See the <A HREF = "#Muller-Plathe">Muller-Plathe paper</A> for
details.
</P>
<P>IMPORTANT NOTE: After equilibration, if the temperature gradient you
observe is not linear, then you are likely swapping energy too
frequently and are not in a regime of linear response. In this case
you cannot accurately infer a thermal conductivity and should try
increasing the Nevery parameter.
</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 kinetic energy transferred between the bottom and
middle of the simulation box (in the <I>edim</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 energy; see the <A HREF = "units.html">units</A> command for
details. 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>. The scalar value calculated by this fix is
"intensive", meaning it is independent of the number of atoms in the
simulation.
</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>LAMMPS does not check, but the masses of all exchanged atom pairs
should be the same to use this fix in a way that conserves 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>LAMMPS does not check, but you should not use this fix to swap the
kinetic energy 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>. This is
because application of the constraints will alter the amount of
transferred momentum. You should, however, be able to use flexible
molecules. See the <A HREF = "#Zhang">Zhang paper</A> for a discussion and results
of this idea.
</P>
<P>When running a simulation with large, massive particles or molecules
in a background solvent, you may want to only exchange kinetic energy
bewteen solvent particles.
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "fix_ave_spatial.html">fix ave/spatial</A>
</P>
<P><B>Default:</B>
</P>
<P>The option defaults are swap = 1.
</P>
<HR>
<A NAME = "Muller-Plathe"></A>
<P><B>(Muller-Plathe)</B> Muller-Plathe and Reith, Computational and
Theoretical Polymer Science, 9, 203-209 (1999).
</P>
<A NAME = "Zhang"></A>
<P><B>(Zhang)</B> Zhang, Lussetti, de Souza, Muller-Plathe, J Phys Chem B,
109, 15060-15067 (2005).
</P>
</HTML>

139
doc/fix_thermal_conductivity.txt Normal file
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@ -0,0 +1,139 @@
"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 thermal/conductivity command :h3
[Syntax:]
fix ID group-ID thermal/conductivity N edim Nbin keyword value ... :pre
ID, group-ID are documented in "fix"_fix.html command :ulb,l
thermal/conductivity = style name of this fix command :l
N = perform kinetic energy exchange every N steps :l
edim = {x} or {y} or {z} = direction of kinetic energy transfer :l
Nbin = # of layers in edim direction :l
zero or more keyword/value pairs may be appended :l
keyword = {swap} :l
{swap} value = Nswap = number of swaps to perform every N steps :pre
:ule
[Examples:]
fix 1 all thermal/conductivity 100 z 20
fix 1 all thermal/conductivity 50 z 20 swap 2 :pre
[Description:]
Use the Muller-Plathe algorithm described in "this
paper"_#Muller-Plathe to exchange kinetic energy between two particles
in different regions of the simulation box every N steps. This
induces a temperature gradient in the system. As described below this
enables a thermal conductivity of the fluid to be calculated. This
algorithm is sometimes called a reverse non-equilibrium MD (reverse
NEMD) approach to computing thermal conductivity. This is because the
usual NEMD approach is to impose a temperature gradient on the system
and measure the response as the resulting heat flux. In the
Muller-Plathe method, the heat flux is imposed, and the temperature
gradient is the system's response.
The simulation box is divided into {Nbin} layers in the {edim}
direction. Every N steps, Nswap pairs of atoms are chosen in the
following manner. Only atoms in the fix group are considered. The
hottest Nswap atoms in the bottom layer are selected. Similarly, the
coldest Nswap atoms in the middle later are selected. The two sets of
Nswap atoms are paired up and their velocities are exchanged. This
effectively swaps their kinetic energies, assuming their masses are
the same. Over time, this induces a temperature gradient in the
system which can be measured using commands such as the following,
which writes the temperature profile (assuming z = edim) to the file
tmp.profile:
compute ke all ke/atom
variable temp atom c_ke[]/1.5
fix 3 all ave/spatial 10 100 1000 z lower 0.05 v_temp &
file tmp.profile units reduced :pre
Note that by default, Nswap = 1, though this can be changed by the
optional {swap} keyword. Setting this parameter appropriately, in
conjunction with the swap rate N, allows the heat flux to be adjusted
across a wide range of values, and the kinetic energy to be exchanged
in large chunks or more smoothly.
As described below, the total kinetic energy transferred by these
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 heat flux. The ratio of heat flux to the slope of the
temperature profile is the thermal conductivity of the fluid,
in appopriate units. See the "Muller-Plathe paper"_#Muller-Plathe for
details.
IMPORTANT NOTE: After equilibration, if the temperature gradient you
observe is not linear, then you are likely swapping energy too
frequently and are not in a regime of linear response. In this case
you cannot accurately infer a thermal conductivity and should try
increasing the Nevery parameter.
[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 kinetic energy transferred between the bottom and
middle of the simulation box (in the {edim} 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 energy; see the "units"_units.html command for
details. This quantity can be accessed by various "output
commands"_Section_howto.html#4_15, such as "thermo_style
custom"_thermo_style.html. The scalar value calculated by this fix is
"intensive", meaning it is independent of the number of atoms in the
simulation.
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:]
LAMMPS does not check, but the masses of all exchanged atom pairs
should be the same to use this fix in a way that conserves 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}).
LAMMPS does not check, but you should not use this fix to swap the
kinetic energy of atoms that are in constrained molecules, e.g. via
"fix shake"_fix_shake.html or "fix rigid"_fix_rigid.html. This is
because application of the constraints will alter the amount of
transferred momentum. You should, however, be able to use flexible
molecules. See the "Zhang paper"_#Zhang for a discussion and results
of this idea.
When running a simulation with large, massive particles or molecules
in a background solvent, you may want to only exchange kinetic energy
bewteen solvent particles.
[Related commands:]
"fix ave/spatial"_fix_ave_spatial.html
[Default:]
The option defaults are swap = 1.
:line
:link(Muller-Plathe)
[(Muller-Plathe)] Muller-Plathe and Reith, Computational and
Theoretical Polymer Science, 9, 203-209 (1999).
:link(Zhang)
[(Zhang)] Zhang, Lussetti, de Souza, Muller-Plathe, J Phys Chem B,
109, 15060-15067 (2005).

3
doc/fix_viscosity.html
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@ -144,8 +144,7 @@ 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><A HREF = "fix_ave_spatial.html">fix ave/spatial</A>
</P>
<P><B>Default:</B>
</P>

3
doc/fix_viscosity.txt
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@ -133,8 +133,7 @@ solvent particles.
[Related commands:]
"fix ave/spatial"_fix_ave_spatial.html, "fix
nvt/sllod"_fix_nvt_sllod.html
"fix ave/spatial"_fix_ave_spatial.html
[Default:]