2008-05-15 05:40:02 +08:00
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<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>
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<HR>
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<H3>fix thermal/conductivity command
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</H3>
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<P><B>Syntax:</B>
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</P>
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<PRE>fix ID group-ID thermal/conductivity N edim Nbin keyword value ...
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</PRE>
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<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
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<LI>thermal/conductivity = style name of this fix command
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<LI>N = perform kinetic energy exchange every N steps
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<LI>edim = <I>x</I> or <I>y</I> or <I>z</I> = direction of kinetic energy transfer
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2008-06-25 07:22:45 +08:00
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<LI>Nbin = # of layers in edim direction (must be even number)
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2008-05-15 05:40:02 +08:00
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<LI>zero or more keyword/value pairs may be appended
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<LI>keyword = <I>swap</I>
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<PRE> <I>swap</I> value = Nswap = number of swaps to perform every N steps
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</PRE>
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</UL>
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<P><B>Examples:</B>
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</P>
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<PRE>fix 1 all thermal/conductivity 100 z 20
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fix 1 all thermal/conductivity 50 z 20 swap 2
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</PRE>
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<P><B>Description:</B>
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</P>
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<P>Use the Muller-Plathe algorithm described in <A HREF = "#Muller-Plathe">this
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paper</A> to exchange kinetic energy between two particles
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in different regions of the simulation box every N steps. This
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induces a temperature gradient in the system. As described below this
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enables a thermal conductivity of the fluid to be calculated. This
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algorithm is sometimes called a reverse non-equilibrium MD (reverse
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NEMD) approach to computing thermal conductivity. This is because the
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usual NEMD approach is to impose a temperature gradient on the system
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and measure the response as the resulting heat flux. In the
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Muller-Plathe method, the heat flux is imposed, and the temperature
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gradient is the system's response.
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</P>
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2009-07-03 00:40:58 +08:00
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<P>See the <A HREF = "compute_heat_flux.html">compute heat/flux</A> command for details
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on how to compute thermal conductivity in an alternate way, via the
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Green-Kubo formalism.
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</P>
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2008-05-15 05:40:02 +08:00
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<P>The simulation box is divided into <I>Nbin</I> layers in the <I>edim</I>
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2008-06-25 07:22:45 +08:00
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direction, where the layer 1 is at the low end of that dimension and
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the layer <I>Nbin</I> is at the high end. Every N steps, Nswap pairs of
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atoms are chosen in the following manner. Only atoms in the fix group
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are considered. The hottest Nswap atoms in layer 1 are selected.
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Similarly, the coldest Nswap atoms in the "middle" layer (see below)
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are selected. The two sets of Nswap atoms are paired up and their
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velocities are exchanged. This effectively swaps their kinetic
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energies, assuming their masses are the same. Over time, this induces
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a temperature gradient in the system which can be measured using
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commands such as the following, which writes the temperature profile
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(assuming z = edim) to the file tmp.profile:
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2008-05-15 05:40:02 +08:00
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</P>
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<PRE>compute ke all ke/atom
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2010-05-24 22:45:47 +08:00
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variable temp atom c_ke/1.5
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2008-05-15 05:40:02 +08:00
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fix 3 all ave/spatial 10 100 1000 z lower 0.05 v_temp &
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file tmp.profile units reduced
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</PRE>
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<P>Note that by default, Nswap = 1, though this can be changed by the
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optional <I>swap</I> keyword. Setting this parameter appropriately, in
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conjunction with the swap rate N, allows the heat flux to be adjusted
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across a wide range of values, and the kinetic energy to be exchanged
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in large chunks or more smoothly.
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</P>
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2008-06-25 07:22:45 +08:00
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<P>The "middle" layer for velocity swapping is defined as the <I>Nbin</I>/2 +
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1 layer. Thus if <I>Nbin</I> = 20, the two swapping layers are 1 and 11.
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This should lead to a symmetric temperature profile since the two
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layers are separated by the same distance in both directions in a
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periodic sense. This is why <I>Nbin</I> is restricted to being an even
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number.
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</P>
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2008-05-15 05:40:02 +08:00
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<P>As described below, the total kinetic energy transferred by these
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swaps is computed by the fix and can be output. Dividing this
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quantity by time and the cross-sectional area of the simulation box
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yields a heat flux. The ratio of heat flux to the slope of the
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2012-11-15 00:08:42 +08:00
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temperature profile is proportional to the thermal conductivity of the
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fluid, in appropriate units. See the <A HREF = "#Muller-Plathe">Muller-Plathe
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paper</A> for details.
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</P>
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<P>IMPORTANT NOTE: If your system is periodic in the direction of the
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heat flux, then the flux is going in 2 directions. This means the
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effective heat flux in one direction is reduced by a factor of 2. You
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will see this in the equations for thermal conductivity (kappa) in the
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Muller-Plathe paper. LAMMPS is simply tallying kinetic energy which
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does not account for whether or not your system is periodic; you must
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use the value appropriately to yield a kappa for your system.
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2008-05-15 05:40:02 +08:00
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</P>
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<P>IMPORTANT NOTE: After equilibration, if the temperature gradient you
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observe is not linear, then you are likely swapping energy too
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frequently and are not in a regime of linear response. In this case
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you cannot accurately infer a thermal conductivity and should try
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increasing the Nevery parameter.
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</P>
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<P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
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</P>
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<P>No information about this fix is written to <A HREF = "restart.html">binary restart
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files</A>. None of the <A HREF = "fix_modify.html">fix_modify</A> options
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are relevant to this fix.
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</P>
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2010-04-03 00:51:06 +08:00
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<P>This fix computes a global scalar which can be accessed by various
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2011-08-26 01:01:01 +08:00
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<A HREF = "Section_howto.html#howto_15">output commands</A>. The scalar is the
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2010-04-03 00:51:06 +08:00
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cummulative kinetic energy transferred between the bottom and middle
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of the simulation box (in the <I>edim</I> direction) is stored as a scalar
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quantity by this fix. This quantity is zeroed when the fix is defined
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and accumlates thereafter, once every N steps. The units of the
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quantity are energy; see the <A HREF = "units.html">units</A> command for details.
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The scalar value calculated by this fix is "intensive".
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2008-05-15 05:40:02 +08:00
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</P>
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<P>No parameter of this fix can be used with the <I>start/stop</I> keywords of
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the <A HREF = "run.html">run</A> command. This fix is not invoked during <A HREF = "minimize.html">energy
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minimization</A>.
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</P>
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<P><B>Restrictions:</B>
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</P>
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2010-07-16 08:14:20 +08:00
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<P>Swaps conserve both momentum and kinetic energy, even if the masses of
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the swapped atoms are not equal. Thus you should not need to
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thermostat the system. If you do use a thermostat, you may want to
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apply it only to the non-swapped dimensions (other than <I>vdim</I>).
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2008-05-15 05:40:02 +08:00
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</P>
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<P>LAMMPS does not check, but you should not use this fix to swap the
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kinetic energy of atoms that are in constrained molecules, e.g. via
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<A HREF = "fix_shake.html">fix shake</A> or <A HREF = "fix_rigid.html">fix rigid</A>. This is
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because application of the constraints will alter the amount of
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transferred momentum. You should, however, be able to use flexible
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molecules. See the <A HREF = "#Zhang">Zhang paper</A> for a discussion and results
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of this idea.
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</P>
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<P>When running a simulation with large, massive particles or molecules
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in a background solvent, you may want to only exchange kinetic energy
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bewteen solvent particles.
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</P>
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<P><B>Related commands:</B>
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</P>
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2008-05-15 05:40:50 +08:00
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<P><A HREF = "fix_ave_spatial.html">fix ave/spatial</A>, <A HREF = "fix_viscosity.html">fix
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2009-07-03 00:40:58 +08:00
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viscosity</A>, <A HREF = "compute_heat_flux.html">compute
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heat/flux</A>
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2008-05-15 05:40:02 +08:00
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</P>
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<P><B>Default:</B>
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</P>
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<P>The option defaults are swap = 1.
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</P>
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<HR>
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<A NAME = "Muller-Plathe"></A>
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2010-12-24 02:44:17 +08:00
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<P><B>(Muller-Plathe)</B> Muller-Plathe, J Chem Phys, 106, 6082 (1997).
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</P>
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<A NAME = "Zhang"></A>
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<P><B>(Zhang)</B> Zhang, Lussetti, de Souza, Muller-Plathe, J Phys Chem B,
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109, 15060-15067 (2005).
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</P>
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</HTML>
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