Commit c80dad00 authored by Steve Plimpton's avatar Steve Plimpton
Browse files

new fix flow/gauss command

parent a0592d1b

doc/.gitignore

+1 −1
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/html

doc/html/Section_commands.html

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@@ -778,12 +778,12 @@ USER-INTEL, k = KOKKOS, o = USER-OMP, t = OPT.</p> 
<a class="reference internal" href="Section_start.html#start-3"><span class="std std-ref">LAMMPS is built with the appropriate package</span></a>.</p>

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<colgroup>

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<col width="15%" />

<col width="15%" />

<col width="15%" />

<col width="20%" />

<col width="13%" />

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<tr class="row-odd"><td><a class="reference internal" href="fix_adapt_fep.html"><span class="doc">adapt/fep</span></a></td>
@@ -798,56 +798,63 @@ USER-INTEL, k = KOKKOS, o = USER-OMP, t = OPT.</p> 
<td><a class="reference internal" href="fix_eos_cv.html"><span class="doc">eos/cv</span></a></td>

<td><a class="reference internal" href="fix_eos_table.html"><span class="doc">eos/table</span></a></td>

<td><a class="reference internal" href="fix_eos_table_rx.html"><span class="doc">eos/table/rx</span></a></td>

<td><a class="reference internal" href="fix_gle.html"><span class="doc">gle</span></a></td>

<td><a class="reference internal" href="fix_flow_gauss.html"><span class="doc">flow/gauss</span></a></td>

</tr>

<tr class="row-odd"><td><a class="reference internal" href="fix_imd.html"><span class="doc">imd</span></a></td>

<tr class="row-odd"><td><a class="reference internal" href="fix_gle.html"><span class="doc">gle</span></a></td>

<td><a class="reference internal" href="fix_imd.html"><span class="doc">imd</span></a></td>

<td><a class="reference internal" href="fix_ipi.html"><span class="doc">ipi</span></a></td>

<td><a class="reference internal" href="fix_langevin_drude.html"><span class="doc">langevin/drude</span></a></td>

<td><a class="reference internal" href="fix_langevin_eff.html"><span class="doc">langevin/eff</span></a></td>

<td><a class="reference internal" href="fix_lb_fluid.html"><span class="doc">lb/fluid</span></a></td>

<td><a class="reference internal" href="fix_lb_momentum.html"><span class="doc">lb/momentum</span></a></td>

</tr>

<tr class="row-even"><td><a class="reference internal" href="fix_lb_pc.html"><span class="doc">lb/pc</span></a></td>

<tr class="row-even"><td><a class="reference internal" href="fix_lb_momentum.html"><span class="doc">lb/momentum</span></a></td>

<td><a class="reference internal" href="fix_lb_pc.html"><span class="doc">lb/pc</span></a></td>

<td><a class="reference internal" href="fix_lb_rigid_pc_sphere.html"><span class="doc">lb/rigid/pc/sphere</span></a></td>

<td><a class="reference internal" href="fix_lb_viscous.html"><span class="doc">lb/viscous</span></a></td>

<td><a class="reference internal" href="fix_meso.html"><span class="doc">meso</span></a></td>

<td><a class="reference internal" href="fix_manifoldforce.html"><span class="doc">manifoldforce</span></a></td>

<td><a class="reference internal" href="fix_meso_stationary.html"><span class="doc">meso/stationary</span></a></td>

</tr>

<tr class="row-odd"><td><a class="reference internal" href="fix_nve_manifold_rattle.html"><span class="doc">nve/manifold/rattle</span></a></td>

<tr class="row-odd"><td><a class="reference internal" href="fix_meso_stationary.html"><span class="doc">meso/stationary</span></a></td>

<td><a class="reference internal" href="fix_nve_manifold_rattle.html"><span class="doc">nve/manifold/rattle</span></a></td>

<td><a class="reference internal" href="fix_nvt_manifold_rattle.html"><span class="doc">nvt/manifold/rattle</span></a></td>

<td><a class="reference internal" href="fix_nh_eff.html"><span class="doc">nph/eff</span></a></td>

<td><a class="reference internal" href="fix_nh_eff.html"><span class="doc">npt/eff</span></a></td>

<td><a class="reference internal" href="fix_nve_eff.html"><span class="doc">nve/eff</span></a></td>

<td><a class="reference internal" href="fix_nh_eff.html"><span class="doc">nvt/eff</span></a></td>

</tr>

<tr class="row-even"><td><a class="reference internal" href="fix_nvt_sllod_eff.html"><span class="doc">nvt/sllod/eff</span></a></td>

<tr class="row-even"><td><a class="reference internal" href="fix_nh_eff.html"><span class="doc">nvt/eff</span></a></td>

<td><a class="reference internal" href="fix_nvt_sllod_eff.html"><span class="doc">nvt/sllod/eff</span></a></td>

<td><a class="reference internal" href="fix_phonon.html"><span class="doc">phonon</span></a></td>

<td><a class="reference internal" href="fix_pimd.html"><span class="doc">pimd</span></a></td>

<td><a class="reference internal" href="fix_qbmsst.html"><span class="doc">qbmsst</span></a></td>

<td><a class="reference internal" href="fix_qeq_reax.html"><span class="doc">qeq/reax</span></a></td>

<td><a class="reference internal" href="fix_qmmm.html"><span class="doc">qmmm</span></a></td>

</tr>

<tr class="row-odd"><td><a class="reference internal" href="fix_qtb.html"><span class="doc">qtb</span></a></td>

<tr class="row-odd"><td><a class="reference internal" href="fix_qmmm.html"><span class="doc">qmmm</span></a></td>

<td><a class="reference internal" href="fix_qtb.html"><span class="doc">qtb</span></a></td>

<td><a class="reference internal" href="fix_reax_bonds.html"><span class="doc">reax/c/bonds</span></a></td>

<td><a class="reference internal" href="fix_reaxc_species.html"><span class="doc">reax/c/species</span></a></td>

<td><a class="reference internal" href="fix_rx.html"><span class="doc">rx</span></a></td>

<td><a class="reference internal" href="fix_saed_vtk.html"><span class="doc">saed/vtk</span></a></td>

<td><a class="reference internal" href="fix_shardlow.html"><span class="doc">shardlow</span></a></td>

</tr>

<tr class="row-even"><td><a class="reference internal" href="fix_smd.html"><span class="doc">smd</span></a></td>

<tr class="row-even"><td><a class="reference internal" href="fix_shardlow.html"><span class="doc">shardlow</span></a></td>

<td><a class="reference internal" href="fix_smd.html"><span class="doc">smd</span></a></td>

<td><a class="reference internal" href="fix_smd_adjust_dt.html"><span class="doc">smd/adjust/dt</span></a></td>

<td><a class="reference internal" href="fix_smd_integrate_tlsph.html"><span class="doc">smd/integrate/tlsph</span></a></td>

<td><a class="reference internal" href="fix_smd_integrate_ulsph.html"><span class="doc">smd/integrate/ulsph</span></a></td>

<td><a class="reference internal" href="fix_smd_move_triangulated_surface.html"><span class="doc">smd/move/triangulated/surface</span></a></td>

<td><a class="reference internal" href="fix_smd_setvel.html"><span class="doc">smd/setvel</span></a></td>

</tr>

<tr class="row-odd"><td><a class="reference internal" href="fix_smd_tlsph_reference_configuration.html"><span class="doc">smd/tlsph/reference/configuration</span></a></td>

<tr class="row-odd"><td><a class="reference internal" href="fix_smd_setvel.html"><span class="doc">smd/setvel</span></a></td>

<td><a class="reference internal" href="fix_smd_tlsph_reference_configuration.html"><span class="doc">smd/tlsph/reference/configuration</span></a></td>

<td><a class="reference internal" href="fix_smd_wall_surface.html"><span class="doc">smd/wall/surface</span></a></td>

<td><a class="reference internal" href="fix_temp_rescale_eff.html"><span class="doc">temp/rescale/eff</span></a></td>

<td><a class="reference internal" href="fix_ti_rs.html"><span class="doc">ti/rs</span></a></td>

<td><a class="reference internal" href="fix_ti_spring.html"><span class="doc">ti/spring</span></a></td>

<td><a class="reference internal" href="fix_ttm.html"><span class="doc">ttm/mod</span></a></td>

</tr>

<tr class="row-even"><td><a class="reference internal" href="fix_ttm.html"><span class="doc">ttm/mod</span></a></td>

<td>&nbsp;</td>

<td>&nbsp;</td>

<td>&nbsp;</td>

<td>&nbsp;</td>

<td>&nbsp;</td>

</tr>

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</table>

doc/html/fix_flow_gauss.html

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  <div class="section" id="fix-flow-gauss-command">

<span id="index-0"></span><h1>fix flow/gauss command</h1>

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

<h2>Syntax</h2>

<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">fix</span> <span class="n">ID</span> <span class="n">group</span><span class="o">-</span><span class="n">ID</span> <span class="n">flow</span><span class="o">/</span><span class="n">gauss</span> <span class="n">xflag</span> <span class="n">yflag</span> <span class="n">zflag</span> <span class="n">keyword</span>

</pre></div>

</div>

<ul class="simple">

<li>ID, group-ID are documented in <a class="reference internal" href="fix.html"><span class="doc">fix</span></a> command</li>

<li>flow/gauss = style name of this fix command</li>

<li>xflag,yflag,zflag = 0 or 1</li>

</ul>

<div class="highlight-default"><div class="highlight"><pre><span></span><span class="mi">0</span> <span class="o">=</span> <span class="n">do</span> <span class="ow">not</span> <span class="n">conserve</span> <span class="n">current</span> <span class="ow">in</span> <span class="n">this</span> <span class="n">dimension</span>

<span class="mi">1</span> <span class="o">=</span> <span class="n">conserve</span> <span class="n">current</span> <span class="ow">in</span> <span class="n">this</span> <span class="n">dimension</span>

</pre></div>

</div>

<ul class="simple">

<li>zero or more keyword/value pairs may be appended</li>

<li>keyword = <em>energy</em></li>

</ul>

<pre class="literal-block">

<em>energy</em> value = no or yes

  no = do not compute work done by this fix

  yes = compute work done by this fix

</pre>

</div>

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

<h2>Examples</h2>

<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">fix</span> <span class="n">GD</span> <span class="n">fluid</span> <span class="n">flow</span><span class="o">/</span><span class="n">gauss</span> <span class="mi">1</span> <span class="mi">0</span> <span class="mi">0</span>

<span class="n">fix</span> <span class="n">GD</span> <span class="n">fluid</span> <span class="n">flow</span><span class="o">/</span><span class="n">gauss</span> <span class="mi">1</span> <span class="mi">1</span> <span class="mi">1</span> <span class="n">energy</span> <span class="n">yes</span>

</pre></div>

</div>

</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>

<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>

</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>

</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

<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>

<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>

</div>

</div>

<hr class="docutils" />

<div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info">

<h2>Restart, fix_modify, output, run start/stop, minimize info</h2>

<p>This fix is part of the USER-MISC package.  It is only enabled if

LAMMPS was built with that package.  See the <a class="reference internal" href="Section_start.html#start-3"><span class="std std-ref">Making LAMMPS</span></a> section for more info.</p>

<p>No information about this fix is written to <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>.</p>

<p>The <a class="reference internal" href="fix_modify.html"><span class="doc">fix_modify</span></a> <em>energy</em> option is supported by this

fix to subtract the work done from the

system&#8217;s potential energy as part of <a class="reference internal" href="thermo_style.html"><span class="doc">thermodynamic output</span></a>.</p>

<p>This fix computes a global scalar and a global 3-vector of forces,

which can be accessed by various <a class="reference internal" href="Section_howto.html#howto-15"><span class="std std-ref">output commands</span></a>.  The scalar is the negative of the

work done on the system, see above discussion.  The vector is the total force

that this fix applied to the group of atoms on the current timestep.

The scalar and vector values calculated by this fix are &#8220;extensive&#8221;.</p>

<p>No parameter of this fix can be used with the <em>start/stop</em> keywords of

the <a class="reference internal" href="run.html"><span class="doc">run</span></a> command.</p>

</div>

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

<h2>Restrictions</h2>

<blockquote>

<div>none</div></blockquote>

</div>

<div class="section" id="related-commands">

<h2>Related commands</h2>

<p><a class="reference internal" href="fix_addforce.html"><span class="doc">fix addforce</span></a>, <a class="reference internal" href="compute_temp_profile.html"><span class="doc">compute temp/profile</span></a>, <a class="reference internal" href="velocity.html"><span class="doc">velocity</span></a></p>

</div>

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

<h2>Default</h2>

<p>The option default for the <em>energy</em> keyword is energy = no.</p>

<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>

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doc/src/Section_commands.txt

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@@ -622,6 +622,7 @@ package"_Section_start.html#start_3. 
"eos/cv"_fix_eos_cv.html,

"eos/table"_fix_eos_table.html,

"eos/table/rx"_fix_eos_table_rx.html,

"flow/gauss"_fix_flow_gauss.html,

"gle"_fix_gle.html,

"imd"_fix_imd.html,

"ipi"_fix_ipi.html,

doc/src/fix_flow_gauss.txt

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