forked from lijiext/lammps
162 lines
6.7 KiB
Plaintext
162 lines
6.7 KiB
Plaintext
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
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:link(lws,http://lammps.sandia.gov)
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:link(ld,Manual.html)
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:link(lc,Section_commands.html#comm)
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:line
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fix thermal/conductivity command :h3
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[Syntax:]
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fix ID group-ID thermal/conductivity N edim Nbin keyword value ... :pre
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ID, group-ID are documented in "fix"_fix.html command :ulb,l
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thermal/conductivity = style name of this fix command :l
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N = perform kinetic energy exchange every N steps :l
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edim = {x} or {y} or {z} = direction of kinetic energy transfer :l
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Nbin = # of layers in edim direction (must be even number) :l
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zero or more keyword/value pairs may be appended :l
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keyword = {swap} :l
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{swap} value = Nswap = number of swaps to perform every N steps :pre
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:ule
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[Examples:]
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fix 1 all thermal/conductivity 100 z 20
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fix 1 all thermal/conductivity 50 z 20 swap 2 :pre
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[Description:]
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Use the Muller-Plathe algorithm described in "this
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paper"_#Muller-Plathe 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 the thermal conductivity of a material 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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See the "compute heat/flux"_compute_heat_flux.html 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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The simulation box is divided into {Nbin} layers in the {edim}
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direction, where the layer 1 is at the low end of that dimension and
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the layer {Nbin} 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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compute ke all ke/atom
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variable temp atom c_ke/1.5
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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 :pre
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Note that by default, Nswap = 1, though this can be changed by the
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optional {swap} 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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The "middle" layer for velocity swapping is defined as the {Nbin}/2 +
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1 layer. Thus if {Nbin} = 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 {Nbin} is restricted to being an even
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number.
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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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temperature profile is proportional to the thermal conductivity of the
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fluid, in appropriate units. See the "Muller-Plathe
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paper"_#Muller-Plathe for details.
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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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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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[Restart, fix_modify, output, run start/stop, minimize info:]
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No information about this fix is written to "binary restart
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files"_restart.html. None of the "fix_modify"_fix_modify.html options
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are relevant to this fix.
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This fix computes a global scalar which can be accessed by various
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"output commands"_Section_howto.html#howto_15. The scalar is the
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cummulative kinetic energy transferred between the bottom and middle
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of the simulation box (in the {edim} 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 "units"_units.html command for details.
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The scalar value calculated by this fix is "intensive".
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No parameter of this fix can be used with the {start/stop} keywords of
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the "run"_run.html command. This fix is not invoked during "energy
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minimization"_minimize.html.
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[Restrictions:]
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This fix is part of the MISC package. It is only enabled if LAMMPS
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was built with that package. See the "Making
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LAMMPS"_Section_start.html#start_3 section for more info.
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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 {vdim}).
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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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"fix shake"_fix_shake.html or "fix rigid"_fix_rigid.html. 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 "Zhang paper"_#Zhang for a discussion and results
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of this idea.
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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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[Related commands:]
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"fix ave/spatial"_fix_ave_spatial.html, "fix
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viscosity"_fix_viscosity.html, "compute
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heat/flux"_compute_heat_flux.html
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[Default:]
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The option defaults are swap = 1.
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:line
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:link(Muller-Plathe)
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[(Muller-Plathe)] Muller-Plathe, J Chem Phys, 106, 6082 (1997).
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:link(Zhang)
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[(Zhang)] Zhang, Lussetti, de Souza, Muller-Plathe, J Phys Chem B,
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109, 15060-15067 (2005).
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