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<h1>LAMMPS Documentation</h1>

<div class="section" id="aug-2016-version">

<h2>23 Aug 2016 version</h2>

<h2>27 Aug 2016 version</h2>

</div>

<div class="section" id="version-info">

<h2>Version info:</h2>

</div>

<div class="section" id="description">

<h2>Description</h2>

<p>This fix implements the Gaussian dynamics (GD) method to simulate a system at

constant mass flux <a class="reference internal" href="#strong"><span class="std std-ref">(Strong)</span></a>. GD is a nonequilibrium molecular

dynamics simulation method that can be used to study fluid flows through

pores, pipes, and channels. In its original implementation GD was used to

compute the pressure required to achieve a fixed mass flux through an opening.

The flux can be conserved in any combination of the directions, x, y, or z,

using xflag,yflag,zflag. This fix does not initialize a net flux through

a system, it only conserves the center-of-mass momentum that is present

when the fix is declared in the input script. Use the <a class="reference internal" href="velocity.html"><span class="doc">velocity</span></a>

command to generate an initial center-of-mass momentum.</p>

<p>GD applies an external fluctuating gravitational field that acts as a driving

force to keep the system away from equilibrium. To maintain steady state, a

profile-unbiased thermostat must be implemented to dissipate the heat that is

added by the driving force. <a class="reference internal" href="compute_temp_profile.html"><span class="doc">Compute temp/profile</span></a>

can be used to implement a profile-unbiased thermostat.</p>

<p>A common use of this fix is to compute a pressure drop across a pipe, pore, or

membrane. The pressure profile can be computed in LAMMPS with <a class="reference internal" href="compute_stress_atom.html"><span class="doc">compute  stress/atom</span></a> and <a class="reference internal" href="fix_ave_chunk.html"><span class="doc">fix ave/chunk</span></a>,

or with the hardy method in <a class="reference internal" href="fix_atc.html"><span class="doc">fix atc</span></a>. Note that the simple

<a class="reference internal" href="compute_stress_atom.html"><span class="doc">compute stress/atom</span></a> method is only accurate away

from inhomogeneities in the fluid, such as fixed wall atoms. Further, the

computed pressure profile must be corrected for the acceleration applied by

GD before computing a pressure drop or comparing it to other methods, such as

the pump method <a class="reference internal" href="#zhu"><span class="std std-ref">(Zhu)</span></a>. The pressure correction is discussed and

described in <a class="reference internal" href="#strong"><span class="std std-ref">(Strong)</span></a>.</p>

<p>This fix implements the Gaussian dynamics (GD) method to simulate a

system at constant mass flux <a class="reference internal" href="#strong"><span class="std std-ref">(Strong)</span></a>. GD is a

nonequilibrium molecular dynamics simulation method that can be used

to study fluid flows through pores, pipes, and channels. In its

original implementation GD was used to compute the pressure required

to achieve a fixed mass flux through an opening.  The flux can be

conserved in any combination of the directions, x, y, or z, using

xflag,yflag,zflag. This fix does not initialize a net flux through a

system, it only conserves the center-of-mass momentum that is present

when the fix is declared in the input script. Use the

<a class="reference internal" href="velocity.html"><span class="doc">velocity</span></a> command to generate an initial center-of-mass

momentum.</p>

<p>GD applies an external fluctuating gravitational field that acts as a

driving force to keep the system away from equilibrium. To maintain

steady state, a profile-unbiased thermostat must be implemented to

dissipate the heat that is added by the driving force. <a class="reference internal" href="compute_temp_profile.html"><span class="doc">Compute temp/profile</span></a> can be used to implement a

profile-unbiased thermostat.</p>

<p>A common use of this fix is to compute a pressure drop across a pipe,

pore, or membrane. The pressure profile can be computed in LAMMPS with

<a class="reference internal" href="compute_stress_atom.html"><span class="doc">compute stress/atom</span></a> and <a class="reference internal" href="fix_ave_chunk.html"><span class="doc">fix ave/chunk</span></a>, or with the hardy method in <a class="reference internal" href="fix_atc.html"><span class="doc">fix atc</span></a>. Note that the simple <a class="reference internal" href="compute_stress_atom.html"><span class="doc">compute stress/atom</span></a> method is only accurate away

from inhomogeneities in the fluid, such as fixed wall atoms. Further,

the computed pressure profile must be corrected for the acceleration

applied by GD before computing a pressure drop or comparing it to

other methods, such as the pump method <a class="reference internal" href="#zhu"><span class="std std-ref">(Zhu)</span></a>. The pressure

correction is discussed and described in <a class="reference internal" href="#strong"><span class="std std-ref">(Strong)</span></a>.</p>

<div class="admonition note">

<p class="first admonition-title">Note</p>

<p class="last">For a complete example including the considerations discussed above, see

the examples/USER/flow_gauss directory.</p>

<p class="last">For a complete example including the considerations discussed

above, see the examples/USER/flow_gauss directory.</p>

</div>

<div class="admonition note">

<p class="first admonition-title">Note</p>

<p class="last">Only the flux of the atoms in group-ID will be conserved. If the

velocities of the group-ID atoms are coupled to the velocities of other atoms

in the simulation, the flux will not be conserved. For example, in a

simulation with fluid atoms and harmonically constrained wall atoms, if a

single thermostat is applied to group <em>all</em>, the fluid atom velocities will be

coupled to the wall atom velocities, and the flux will not be conserved. This

issue can be avoided by thermostatting the fluid and wall groups separately.</p>

velocities of the group-ID atoms are coupled to the velocities of

other atoms in the simulation, the flux will not be conserved. For

example, in a simulation with fluid atoms and harmonically constrained

wall atoms, if a single thermostat is applied to group <em>all</em>, the

fluid atom velocities will be coupled to the wall atom velocities, and

the flux will not be conserved. This issue can be avoided by

thermostatting the fluid and wall groups separately.</p>

</div>

<dl class="docutils">

<dt>Adding an acceleration to atoms does work on the system. This added energy</dt>

<dd>can be optionally subtracted from the potential energy for the thermodynamic</dd>

</dl>

<p>output (see below) to check that the timestep is small enough to conserve

energy. Since the applied acceleration is fluctuating in time, the work cannot

be computed from a potential. As a result, computing the work is slightly more

computationally expensive than usual, so it is not performed by default. To

invoke the work calculation, use the <em>energy</em> keyword. The

<p>Adding an acceleration to atoms does work on the system. This added

energy can be optionally subtracted from the potential energy for the

thermodynamic output (see below) to check that the timestep is small

enough to conserve energy. Since the applied acceleration is

fluctuating in time, the work cannot be computed from a potential. As

a result, computing the work is slightly more computationally

expensive than usual, so it is not performed by default. To invoke the

work calculation, use the <em>energy</em> keyword. The

<a class="reference internal" href="fix_modify.html"><span class="doc">fix_modify</span></a> <em>energy</em> option also invokes the work

calculation, and overrides an <em>energy no</em> setting here. If neither <em>energy yes</em>

or <em>fix_modify energy yes</em> are set, the global scalar computed by the fix

will return zero.</p>

calculation, and overrides an <em>energy no</em> setting here. If neither

<em>energy yes</em> or <em>fix_modify energy yes</em> are set, the global scalar

computed by the fix will return zero.</p>

<div class="admonition note">

<p class="first admonition-title">Note</p>

<p class="last">In order to check energy conservation, any other fixes that do work on

the system must have <em>fix_modify energy yes</em> set as well. This includes

thermostat fixes and any constraints that hold the positions of wall atoms

fixed, such as <a class="reference internal" href="fix_spring_self.html"><span class="doc">fix spring/self</span></a>.</p>

<p class="last">In order to check energy conservation, any other fixes that do

work on the system must have <em>fix_modify energy yes</em> set as well. This

includes thermostat fixes and any constraints that hold the positions

of wall atoms fixed, such as <a class="reference internal" href="fix_spring_self.html"><span class="doc">fix spring/self</span></a>.</p>

</div>

</div>

<hr class="docutils" />

<p id="strong"><strong>(Strong)</strong> Strong and Eaves, J. Phys. Chem. Lett. 7, 1907 (2016).</p>

<p id="evans"><strong>(Evans)</strong> Evans and Morriss, Phys. Rev. Lett. 56, 2172 (1986).</p>

<p id="zhu"><strong>(Zhu)</strong> Zhu, Tajkhorshid, and Schulten, Biophys. J. 83, 154 (2002).</p>

<hr class="docutils" />

</div>

</div>

  </dt>

  <dt><a href="fix_flow_gauss.html#index-0">fix flow/gauss</a>

  </dt>

  <dt><a href="fix_freeze.html#index-0">fix freeze</a>

  </dt>

  <dt><a href="fix_nve_eff.html#index-0">fix nve/eff</a>

  </dt>

  </dl></td>

  <td style="width: 33%" valign="top"><dl>

  <dt><a href="fix_nve_limit.html#index-0">fix nve/limit</a>

  </dt>

  </dl></td>

  <td style="width: 33%" valign="top"><dl>

  <dt><a href="fix_nve_line.html#index-0">fix nve/line</a>

  </dt>

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LAMMPS Documentation :c,h3

23 Aug 2016 version :c,h4

27 Aug 2016 version :c,h4

Version info: :h4