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<title>fix viscosity command — LAMMPS 15 May 2015 version documentation</title>
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<div class="section" id="fix-viscosity-command">
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<span id="index-0"></span><h1>fix viscosity command<a class="headerlink" href="#fix-viscosity-command" title="Permalink to this headline">¶</a></h1>
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<div class="section" id="syntax">
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<h2>Syntax<a class="headerlink" href="#syntax" title="Permalink to this headline">¶</a></h2>
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<div class="highlight-python"><div class="highlight"><pre>fix ID group-ID viscosity N vdim pdim Nbin keyword value ...
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</pre></div>
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</div>
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<ul class="simple">
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<li>ID, group-ID are documented in <a class="reference internal" href="fix.html"><em>fix</em></a> command</li>
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<li>viscosity = style name of this fix command</li>
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<li>N = perform momentum exchange every N steps</li>
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<li>vdim = <em>x</em> or <em>y</em> or <em>z</em> = which momentum component to exchange</li>
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<li>pdim = <em>x</em> or <em>y</em> or <em>z</em> = direction of momentum transfer</li>
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<li>Nbin = # of layers in pdim direction (must be even number)</li>
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<li>zero or more keyword/value pairs may be appended</li>
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<li>keyword = <em>swap</em> or <em>target</em></li>
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</ul>
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<pre class="literal-block">
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<em>swap</em> value = Nswap = number of swaps to perform every N steps
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<em>vtarget</em> value = V or INF = target velocity of swap partners (velocity units)
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</pre>
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</div>
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<div class="section" id="examples">
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<h2>Examples<a class="headerlink" href="#examples" title="Permalink to this headline">¶</a></h2>
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<div class="highlight-python"><div class="highlight"><pre>fix 1 all viscosity 100 x z 20
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fix 1 all viscosity 50 x z 20 swap 2 vtarget 1.5
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</pre></div>
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</div>
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</div>
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<div class="section" id="description">
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<h2>Description<a class="headerlink" href="#description" title="Permalink to this headline">¶</a></h2>
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<p>Use the Muller-Plathe algorithm described in <a class="reference internal" href="#muller-plathe"><span>this paper</span></a> to exchange momenta between two particles in
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different regions of the simulation box every N steps. This induces a
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shear velocity profile in the system. As described below this enables
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a viscosity of the fluid to be calculated. This algorithm is
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sometimes called a reverse non-equilibrium MD (reverse NEMD) approach
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to computing viscosity. This is because the usual NEMD approach is to
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impose a shear velocity profile on the system and measure the response
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via an off-diagonal component of the stress tensor, which is
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proportional to the momentum flux. In the Muller-Plathe method, the
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momentum flux is imposed, and the shear velocity profile is the
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system’s response.</p>
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<p>The simulation box is divided into <em>Nbin</em> layers in the <em>pdim</em>
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direction, where the layer 1 is at the low end of that dimension and
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the layer <em>Nbin</em> 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. Nswap atoms in layer 1 with positive velocity
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components in the <em>vdim</em> direction closest to the target value <em>V</em> are
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selected. Similarly, Nswap atoms in the “middle” layer (see below) with
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negative velocity components in the <em>vdim</em> direction closest to the
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negative of the target value <em>V</em> are selected. The two sets of Nswap
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atoms are paired up and their <em>vdim</em> momenta components are swapped
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within each pair. This resets their velocities, typically in opposite
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directions. Over time, this induces a shear velocity profile in the
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system which can be measured using commands such as the following,
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which writes the profile to the file tmp.profile:</p>
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<div class="highlight-python"><div class="highlight"><pre>fix f1 all ave/spatial 100 10 1000 z lower 0.05 vx &
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file tmp.profile units reduced
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</pre></div>
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</div>
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<p>Note that by default, Nswap = 1 and vtarget = INF, though this can be
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changed by the optional <em>swap</em> and <em>vtarget</em> keywords. When vtarget =
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INF, one or more atoms with the most positive and negative velocity
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components are selected. Setting these parameters appropriately, in
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conjunction with the swap rate N, allows the momentum flux rate to be
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adjusted across a wide range of values, and the momenta to be
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exchanged in large chunks or more smoothly.</p>
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<p>The “middle” layer for momenta swapping is defined as the <em>Nbin</em>/2 + 1
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layer. Thus if <em>Nbin</em> = 20, the two swapping layers are 1 and 11.
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This should lead to a symmetric velocity profile since the two layers
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are separated by the same distance in both directions in a periodic
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sense. This is why <em>Nbin</em> is restricted to being an even number.</p>
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<p>As described below, the total momentum transferred by these velocity
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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 momentum flux. The ratio of momentum flux to the slope of
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the shear velocity profile is proportional to the viscosity of the
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fluid, in appropriate units. See the <a class="reference internal" href="#muller-plathe"><span>Muller-Plathe paper</span></a> for details.</p>
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<div class="admonition warning">
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<p class="first admonition-title">Warning</p>
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<p class="last">If your system is periodic in the direction of the
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momentum flux, then the flux is going in 2 directions. This means the
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effective momentum flux in one direction is reduced by a factor of 2.
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You will see this in the equations for viscosity in the Muller-Plathe
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paper. LAMMPS is simply tallying momentum which does not account for
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whether or not your system is periodic; you must use the value
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appropriately to yield a viscosity for your system.</p>
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</div>
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<div class="admonition warning">
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<p class="first admonition-title">Warning</p>
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<p class="last">After equilibration, if the velocity profile you
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observe is not linear, then you are likely swapping momentum 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 viscosity and should try increasing
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the Nevery parameter.</p>
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</div>
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<p>An alternative method for calculating a viscosity is to run a NEMD
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simulation, as described in <a class="reference internal" href="Section_howto.html#howto-13"><span>Section_howto 13</span></a> of the manual. NEMD simulations
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deform the simmulation box via the <a class="reference internal" href="fix_deform.html"><em>fix deform</em></a>
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command. Thus they cannot be run on a charged system using a <a class="reference internal" href="kspace_style.html"><em>PPPM solver</em></a> since PPPM does not currently support
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non-orthogonal boxes. Using fix viscosity keeps the box orthogonal;
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thus it does not suffer from this limitation.</p>
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</div>
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<div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info">
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<h2>Restart, fix_modify, output, run start/stop, minimize info<a class="headerlink" href="#restart-fix-modify-output-run-start-stop-minimize-info" title="Permalink to this headline">¶</a></h2>
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<p>No information about this fix is written to <a class="reference internal" href="restart.html"><em>binary restart files</em></a>. None of the <a class="reference internal" href="fix_modify.html"><em>fix_modify</em></a> options
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are relevant to this fix.</p>
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<p>This fix computes a global scalar which can be accessed by various
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<a class="reference internal" href="Section_howto.html#howto-15"><span>output commands</span></a>. The scalar is the
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cummulative momentum transferred between the bottom and middle of the
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simulation box (in the <em>pdim</em> 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 momentum = mass*velocity. The scalar value calculated by
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this fix is “intensive”.</p>
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<p>No parameter of this fix can be used with the <em>start/stop</em> keywords of
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the <a class="reference internal" href="run.html"><em>run</em></a> command. This fix is not invoked during <a class="reference internal" href="minimize.html"><em>energy minimization</em></a>.</p>
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</div>
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<div class="section" id="restrictions">
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<h2>Restrictions<a class="headerlink" href="#restrictions" title="Permalink to this headline">¶</a></h2>
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<p>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 <a class="reference internal" href="Section_start.html#start-3"><span>Making LAMMPS</span></a> section for more info.</p>
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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 <em>vdim</em>).</p>
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<p>LAMMPS does not check, but you should not use this fix to swap
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velocities of atoms that are in constrained molecules, e.g. via <a class="reference internal" href="fix_shake.html"><em>fix shake</em></a> or <a class="reference internal" href="fix_rigid.html"><em>fix rigid</em></a>. This is because
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application of the constraints will alter the amount of transferred
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momentum. You should, however, be able to use flexible molecules.
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See the <a class="reference internal" href="#maginn"><span>Maginn paper</span></a> for an example of using this algorithm
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in a computation of alcohol molecule properties.</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 momenta bewteen
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solvent particles.</p>
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</div>
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<div class="section" id="related-commands">
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<h2>Related commands<a class="headerlink" href="#related-commands" title="Permalink to this headline">¶</a></h2>
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<p><a class="reference internal" href="fix_ave_spatial.html"><em>fix ave/spatial</em></a>, <a class="reference internal" href="fix_thermal_conductivity.html"><em>fix thermal/conductivity</em></a></p>
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</div>
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<div class="section" id="default">
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<h2>Default<a class="headerlink" href="#default" title="Permalink to this headline">¶</a></h2>
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<p>The option defaults are swap = 1 and vtarget = INF.</p>
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<hr class="docutils" />
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<p id="muller-plathe"><strong>(Muller-Plathe)</strong> Muller-Plathe, Phys Rev E, 59, 4894-4898 (1999).</p>
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<p id="maginn"><strong>(Maginn)</strong> Kelkar, Rafferty, Maginn, Siepmann, Fluid Phase Equilibria,
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260, 218-231 (2007).</p>
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