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  <H1></H1><div class="section" id="lammps-documentation">

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<h1>LAMMPS Documentation</h1>

<h1>LAMMPS Documentation</h1>

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

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

<h2>23 Aug 2016 version</h2>

<h2>27 Aug 2016 version</h2>

</div>

</div>

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

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

<h2>Version info:</h2>

<h2>Version info:</h2>

</div>

</div>

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

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

<h2>Description</h2>

<h2>Description</h2>

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

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

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

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

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

nonequilibrium molecular dynamics simulation method that can be used

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

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

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

original implementation GD was used to compute the pressure required

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

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

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

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

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

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

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

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

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

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

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

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

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

momentum.</p>

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

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

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

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

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

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

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

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

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>,

profile-unbiased thermostat.</p>

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

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

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

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

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

<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

computed pressure profile must be corrected for the acceleration applied by

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

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

the computed pressure profile must be corrected for the acceleration

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

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

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

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">

<div class="admonition note">

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

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

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

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

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

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

</div>

</div>

<div class="admonition note">

<div class="admonition note">

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

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

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

<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

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

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

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

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

example, in a simulation with fluid atoms and harmonically constrained

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

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

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

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

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

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

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

</div>

</div>

<dl class="docutils">

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

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

energy can be optionally subtracted from the potential energy for the

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

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

</dl>

enough to conserve energy. Since the applied acceleration is

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

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

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

a result, computing the work is slightly more computationally

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

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

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

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

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

<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>

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

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

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

will return zero.</p>

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

<div class="admonition note">

<div class="admonition note">

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

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

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

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

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

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

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

includes thermostat fixes and any constraints that hold the positions

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

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>

</div>

</div>

<hr class="docutils" />

<hr class="docutils" />

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

<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="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>

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

<hr class="docutils" />

</div>

</div>

</div>

</div>

  </dt>

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

  </dt>

  </dt>

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

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

  </dt>

  </dt>

  </dl></td>

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

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

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

  </dt>

  </dt>

  </dl></td>

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

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

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

  </dt>

  </dt>

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<TITLE>LAMMPS Users Manual</TITLE>

<TITLE>LAMMPS Users Manual</TITLE>

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<META NAME="docnumber" CONTENT="27 Aug 2016 version">

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LAMMPS Documentation :c,h3

LAMMPS Documentation :c,h3

23 Aug 2016 version :c,h4

27 Aug 2016 version :c,h4

Version info: :h4

Version info: :h4