forked from lijiext/lammps
577 lines
30 KiB
HTML
577 lines
30 KiB
HTML
|
|
|
|
<!DOCTYPE html>
|
|
<!--[if IE 8]><html class="no-js lt-ie9" lang="en" > <![endif]-->
|
|
<!--[if gt IE 8]><!--> <html class="no-js" lang="en" > <!--<![endif]-->
|
|
<head>
|
|
<meta charset="utf-8">
|
|
|
|
<meta name="viewport" content="width=device-width, initial-scale=1.0">
|
|
|
|
<title>fix srd command — LAMMPS 15 May 2015 version documentation</title>
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
<link rel="stylesheet" href="_static/css/theme.css" type="text/css" />
|
|
|
|
|
|
|
|
<link rel="stylesheet" href="_static/sphinxcontrib-images/LightBox2/lightbox2/css/lightbox.css" type="text/css" />
|
|
|
|
|
|
|
|
<link rel="top" title="LAMMPS 15 May 2015 version documentation" href="index.html"/>
|
|
|
|
|
|
<script src="_static/js/modernizr.min.js"></script>
|
|
|
|
</head>
|
|
|
|
<body class="wy-body-for-nav" role="document">
|
|
|
|
<div class="wy-grid-for-nav">
|
|
|
|
|
|
<nav data-toggle="wy-nav-shift" class="wy-nav-side">
|
|
<div class="wy-side-nav-search">
|
|
|
|
|
|
|
|
<a href="Manual.html" class="icon icon-home"> LAMMPS
|
|
|
|
|
|
|
|
</a>
|
|
|
|
|
|
<div role="search">
|
|
<form id="rtd-search-form" class="wy-form" action="search.html" method="get">
|
|
<input type="text" name="q" placeholder="Search docs" />
|
|
<input type="hidden" name="check_keywords" value="yes" />
|
|
<input type="hidden" name="area" value="default" />
|
|
</form>
|
|
</div>
|
|
|
|
|
|
</div>
|
|
|
|
<div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="main navigation">
|
|
|
|
|
|
|
|
<ul>
|
|
<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
|
|
<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
|
|
<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
|
|
<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
|
|
<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
|
|
<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
|
|
<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
|
|
<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
|
|
<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
|
|
<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
|
|
<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
|
|
<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
|
|
<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
|
|
</ul>
|
|
|
|
|
|
|
|
</div>
|
|
|
|
</nav>
|
|
|
|
<section data-toggle="wy-nav-shift" class="wy-nav-content-wrap">
|
|
|
|
|
|
<nav class="wy-nav-top" role="navigation" aria-label="top navigation">
|
|
<i data-toggle="wy-nav-top" class="fa fa-bars"></i>
|
|
<a href="Manual.html">LAMMPS</a>
|
|
</nav>
|
|
|
|
|
|
|
|
<div class="wy-nav-content">
|
|
<div class="rst-content">
|
|
<div role="navigation" aria-label="breadcrumbs navigation">
|
|
<ul class="wy-breadcrumbs">
|
|
<li><a href="Manual.html">Docs</a> »</li>
|
|
|
|
<li>fix srd command</li>
|
|
<li class="wy-breadcrumbs-aside">
|
|
|
|
|
|
<a href="http://lammps.sandia.gov">Website</a>
|
|
<a href="Section_commands.html#comm">Commands</a>
|
|
|
|
</li>
|
|
</ul>
|
|
<hr/>
|
|
|
|
</div>
|
|
<div role="main" class="document" itemscope="itemscope" itemtype="http://schema.org/Article">
|
|
<div itemprop="articleBody">
|
|
|
|
<div class="section" id="fix-srd-command">
|
|
<span id="index-0"></span><h1>fix srd command<a class="headerlink" href="#fix-srd-command" title="Permalink to this headline">¶</a></h1>
|
|
<div class="section" id="syntax">
|
|
<h2>Syntax<a class="headerlink" href="#syntax" title="Permalink to this headline">¶</a></h2>
|
|
<div class="highlight-python"><div class="highlight"><pre>fix ID group-ID srd N groupbig-ID Tsrd hgrid seed keyword value ...
|
|
</pre></div>
|
|
</div>
|
|
<ul class="simple">
|
|
<li>ID, group-ID are documented in <a class="reference internal" href="fix.html"><em>fix</em></a> command</li>
|
|
<li>srd = style name of this fix command</li>
|
|
<li>N = reset SRD particle velocities every this many timesteps</li>
|
|
<li>groupbig-ID = ID of group of large particles that SRDs interact with</li>
|
|
<li>Tsrd = temperature of SRD particles (temperature units)</li>
|
|
<li>hgrid = grid spacing for SRD grouping (distance units)</li>
|
|
<li>seed = random # seed (positive integer)</li>
|
|
<li>zero or more keyword/value pairs may be appended</li>
|
|
<li>keyword = <em>lamda</em> or <em>collision</em> or <em>overlap</em> or <em>inside</em> or <em>exact</em> or <em>radius</em> or <em>bounce</em> or <em>search</em> or <em>cubic</em> or <em>shift</em> or <em>tstat</em> or <em>rescale</em></li>
|
|
</ul>
|
|
<pre class="literal-block">
|
|
<em>lamda</em> value = mean free path of SRD particles (distance units)
|
|
<em>collision</em> value = <em>noslip</em> or <em>slip</em> = collision model
|
|
<em>overlap</em> value = <em>yes</em> or <em>no</em> = whether big particles may overlap
|
|
<em>inside</em> value = <em>error</em> or <em>warn</em> or <em>ignore</em> = how SRD particles which end up inside a big particle are treated
|
|
<em>exact</em> value = <em>yes</em> or <em>no</em>
|
|
<em>radius</em> value = rfactor = scale collision radius by this factor
|
|
<em>bounce</em> value = Nbounce = max # of collisions an SRD particle can undergo in one timestep
|
|
<em>search</em> value = sgrid = grid spacing for collision partner searching (distance units)
|
|
<em>cubic</em> values = style tolerance
|
|
style = <em>error</em> or <em>warn</em>
|
|
tolerance = fractional difference allowed (0 <= tol <= 1)
|
|
<em>shift</em> values = flag shiftseed
|
|
flag = <em>yes</em> or <em>no</em> or <em>possible</em> = SRD bin shifting for better statistics
|
|
<em>yes</em> = perform bin shifting each time SRD velocities are rescaled
|
|
<em>no</em> = no shifting
|
|
<em>possible</em> = shift depending on mean free path and bin size
|
|
shiftseed = random # seed (positive integer)
|
|
<em>tstat</em> value = <em>yes</em> or <em>no</em> = thermostat SRD particles or not
|
|
<em>rescale</em> value = <em>yes</em> or <em>no</em> or <em>rotate</em> or <em>collide</em> = rescaling of SRD velocities
|
|
<em>yes</em> = rescale during velocity rotation and collisions
|
|
<em>no</em> = no rescaling
|
|
<em>rotate</em> = rescale during velocity rotation, but not collisions
|
|
<em>collide</em> = rescale during collisions, but not velocity rotation
|
|
</pre>
|
|
</div>
|
|
<div class="section" id="examples">
|
|
<h2>Examples<a class="headerlink" href="#examples" title="Permalink to this headline">¶</a></h2>
|
|
<div class="highlight-python"><div class="highlight"><pre>fix 1 srd srd 10 big 1.0 0.25 482984
|
|
fix 1 srd srd 10 big 0.5 0.25 482984 collision slip search 0.5
|
|
</pre></div>
|
|
</div>
|
|
</div>
|
|
<div class="section" id="description">
|
|
<h2>Description<a class="headerlink" href="#description" title="Permalink to this headline">¶</a></h2>
|
|
<p>Treat a group of partilces as stochastic rotation dynamics (SRD)
|
|
particles that serve as a background solvent when interacting with big
|
|
(colloidal) particles in groupbig-ID. The SRD formalism is described
|
|
in <a class="reference internal" href="#hecht"><span>(Hecht)</span></a>. The key idea behind using SRD particles as a
|
|
cheap coarse-grained solvent is that SRD particles do not interact
|
|
with each other, but only with the solute particles, which in LAMMPS
|
|
can be spheroids, ellipsoids, or line segments, or triangles, or rigid
|
|
bodies containing multiple spherioids or ellipsoids or line segments
|
|
or triangles. The collision and rotation properties of the model
|
|
imbue the SRD particles with fluid-like properties, including an
|
|
effective viscosity. Thus simulations with large solute particles can
|
|
be run more quickly, to measure solute propoerties like diffusivity
|
|
and viscosity in a background fluid. The usual LAMMPS fixes for such
|
|
simulations, such as <a class="reference internal" href="fix_deform.html"><em>fix deform</em></a>, <a class="reference internal" href="fix_viscosity.html"><em>fix viscosity</em></a>, and <a class="reference internal" href="fix_nvt_sllod.html"><em>fix nvt/sllod</em></a>,
|
|
can be used in conjunction with the SRD model.</p>
|
|
<p>For more details on how the SRD model is implemented in LAMMPS, <a class="reference internal" href="kspace_style.html#petersen"><span>this paper</span></a> describes the implementation and usage of pure SRD
|
|
fluids. <a class="reference internal" href="#lechman"><span>This paper</span></a>, which is nearly complete, describes
|
|
the implementation and usage of mixture systems (solute particles in
|
|
an SRD fluid). See the examples/srd directory for sample input
|
|
scripts using SRD particles in both settings.</p>
|
|
<p>This fix does 2 things:</p>
|
|
<p>(1) It advects the SRD particles, performing collisions between SRD
|
|
and big particles or walls every timestep, imparting force and torque
|
|
to the big particles. Collisions also change the position and
|
|
velocity of SRD particles.</p>
|
|
<p>(2) It resets the velocity distribution of SRD particles via random
|
|
rotations every N timesteps.</p>
|
|
<p>SRD particles have a mass, temperature, characteristic timestep
|
|
dt_SRD, and mean free path between collisions (lamda). The
|
|
fundamental equation relating these 4 quantities is</p>
|
|
<div class="highlight-python"><div class="highlight"><pre><span class="n">lamda</span> <span class="o">=</span> <span class="n">dt_SRD</span> <span class="o">*</span> <span class="n">sqrt</span><span class="p">(</span><span class="n">Kboltz</span> <span class="o">*</span> <span class="n">Tsrd</span> <span class="o">/</span> <span class="n">mass</span><span class="p">)</span>
|
|
</pre></div>
|
|
</div>
|
|
<p>The mass of SRD particles is set by the <a class="reference internal" href="mass.html"><em>mass</em></a> command
|
|
elsewhere in the input script. The SRD timestep dt_SRD is N times the
|
|
step dt defined by the <a class="reference internal" href="timestep.html"><em>timestep</em></a> command. Big
|
|
particles move in the normal way via a time integration <a class="reference internal" href="fix.html"><em>fix</em></a>
|
|
with a short timestep dt. SRD particles advect with a large timestep
|
|
dt_SRD >= dt.</p>
|
|
<p>If the <em>lamda</em> keyword is not specified, the the SRD temperature
|
|
<em>Tsrd</em> is used in the above formula to compute lamda. If the <em>lamda</em>
|
|
keyword is specified, then the <em>Tsrd</em> setting is ignored and the above
|
|
equation is used to compute the SRD temperature.</p>
|
|
<p>The characteristic length scale for the SRD fluid is set by <em>hgrid</em>
|
|
which is used to bin SRD particles for purposes of resetting their
|
|
velocities. Normally hgrid is set to be 1/4 of the big particle
|
|
diameter or smaller, to adequately resolve fluid properties around the
|
|
big particles.</p>
|
|
<p>Lamda cannot be smaller than 0.6 * hgrid, else an error is generated
|
|
(unless the <em>shift</em> keyword is used, see below). The velocities of
|
|
SRD particles are bounded by Vmax, which is set so that an SRD
|
|
particle will not advect further than Dmax = 4*lamda in dt_SRD. This
|
|
means that roughly speaking, Dmax should not be larger than a big
|
|
particle diameter, else SRDs may pass thru big particles without
|
|
colliding. A warning is generated if this is the case.</p>
|
|
<p>Collisions between SRD particles and big particles or walls are
|
|
modeled as a lightweight SRD point particle hitting a heavy big
|
|
particle of given diameter or a wall at a point on its surface and
|
|
bouncing off with a new velocity. The collision changes the momentum
|
|
of the SRD particle. It imparts a force and torque to the big
|
|
particle. It imparts a force to a wall. Static or moving SRD walls
|
|
are setup via the <a class="reference internal" href="fix_wall_srd.html"><em>fix wall/srd</em></a> command. For the
|
|
remainder of this doc page, a collision of an SRD particle with a wall
|
|
can be viewed as a collision with a big particle of infinite radius
|
|
and mass.</p>
|
|
<p>The <em>collision</em> keyword sets the style of collisions. The <em>slip</em>
|
|
style means that the tangential component of the SRD particle momentum
|
|
is preserved. Thus a force is imparted to a big particle, but no
|
|
torque. The normal component of the new SRD velocity is sampled from
|
|
a Gaussian distribution at temperature <em>Tsrd</em>.</p>
|
|
<p>For the <em>noslip</em> style, both the normal and tangential components of
|
|
the new SRD velocity are sampled from a Gaussian distribution at
|
|
temperature <em>Tsrd</em>. Additionally, a new tangential direction for the
|
|
SRD velocity is chosen randomly. This collision style imparts torque
|
|
to a big particle. Thus a time integrator <a class="reference internal" href="fix.html"><em>fix</em></a> that rotates
|
|
the big particles appropriately should be used.</p>
|
|
<hr class="docutils" />
|
|
<p>The <em>overlap</em> keyword should be set to <em>yes</em> if two (or more) big
|
|
particles can ever overlap. This depends on the pair potential
|
|
interaction used for big-big interactions, or could be the case if
|
|
multiple big particles are held together as rigid bodies via the <a class="reference internal" href="fix_rigid.html"><em>fix rigid</em></a> command. If the <em>overlap</em> keyword is <em>no</em> and
|
|
big particles do in fact overlap, then SRD/big collisions can generate
|
|
an error if an SRD ends up inside two (or more) big particles at once.
|
|
How this error is treated is determined by the <em>inside</em> keyword.
|
|
Running with <em>overlap</em> set to <em>no</em> allows for faster collision
|
|
checking, so it should only be set to <em>yes</em> if needed.</p>
|
|
<p>The <em>inside</em> keyword determines how a collision is treated if the
|
|
computation determines that the timestep started with the SRD particle
|
|
already inside a big particle. If the setting is <em>error</em> then this
|
|
generates an error message and LAMMPS stops. If the setting is <em>warn</em>
|
|
then this generates a warning message and the code continues. If the
|
|
setting is <em>ignore</em> then no message is generated. One of the output
|
|
quantities logged by the fix (see below) tallies the number of such
|
|
events, so it can be monitored. Note that once an SRD particle is
|
|
inside a big particle, it may remain there for several steps until it
|
|
drifts outside the big particle.</p>
|
|
<p>The <em>exact</em> keyword determines how accurately collisions are computed.
|
|
A setting of <em>yes</em> computes the time and position of each collision as
|
|
SRD and big particles move together. A setting of <em>no</em> estimates the
|
|
position of each collision based on the end-of-timestep positions of
|
|
the SRD and big particle. If <em>overlap</em> is set to yes, the setting of
|
|
the <em>exact</em> keyword is ignored since time-accurate collisions are
|
|
needed.</p>
|
|
<p>The <em>radius</em> keyword scales the effective size of big particles. If
|
|
big particles will overlap as they undergo dynamics, then this keyword
|
|
can be used to scale down their effective collision radius by an
|
|
amount <em>rfactor</em>, so that SRD particle will only collide with one big
|
|
particle at a time. For example, in a Lennard-Jones system at a
|
|
temperature of 1.0 (in reduced LJ units), the minimum separation
|
|
bewteen two big particles is as small as about 0.88 sigma. Thus an
|
|
<em>rfactor</em> value of 0.85 should prevent dual collisions.</p>
|
|
<p>The <em>bounce</em> keyword can be used to limit the maximum number of
|
|
collisions an SRD particle undergoes in a single timestep as it
|
|
bounces between nearby big particles. Note that if the limit is
|
|
reached, the SRD can be left inside a big particle. A setting of 0 is
|
|
the same as no limit.</p>
|
|
<hr class="docutils" />
|
|
<p>There are 2 kinds of bins created and maintained when running an SRD
|
|
simulation. The first are “SRD bins” which are used to bin SRD
|
|
particles and reset their velocities, as discussed above. The second
|
|
are “search bins” which are used to identify SRD/big particle
|
|
collisions.</p>
|
|
<p>The <em>search</em> keyword can be used to choose a search bin size for
|
|
identifying SRD/big particle collisions. The default is to use the
|
|
<em>hgrid</em> parameter for SRD bins as the search bin size. Choosing a
|
|
smaller or large value may be more efficient, depending on the
|
|
problem. But, in a statistical sense, it should not change the
|
|
simulation results.</p>
|
|
<p>The <em>cubic</em> keyword can be used to generate an error or warning when
|
|
the bin size chosen by LAMMPS creates SRD bins that are non-cubic or
|
|
different than the requested value of <em>hgrid</em> by a specified
|
|
<em>tolerance</em>. Note that using non-cubic SRD bins can lead to
|
|
undetermined behavior when rotating the velocities of SRD particles,
|
|
hence LAMMPS tries to protect you from this problem.</p>
|
|
<p>LAMMPS attempts to set the SRD bin size to exactly <em>hgrid</em>. However,
|
|
there must be an integer number of bins in each dimension of the
|
|
simulation box. Thus the actual bin size will depend on the size and
|
|
shape of the overall simulation box. The actual bin size is printed
|
|
as part of the SRD output when a simulation begins.</p>
|
|
<p>If the actual bin size in non-cubic by an amount exceeding the
|
|
tolerance, an error or warning is printed, depending on the style of
|
|
the <em>cubic</em> keyword. Likewise, if the actual bin size differs from
|
|
the requested <em>hgrid</em> value by an amount exceeding the tolerance, then
|
|
an error or warning is printed. The <em>tolerance</em> is a fractional
|
|
difference. E.g. a tolerance setting of 0.01 on the shape means that
|
|
if the ratio of any 2 bin dimensions exceeds (1 +/- tolerance) then an
|
|
error or warning is generated. Similarly, if the ratio of any bin
|
|
dimension with <em>hgrid</em> exceeds (1 +/- tolerance), then an error or
|
|
warning is generated.</p>
|
|
<div class="admonition warning">
|
|
<p class="first admonition-title">Warning</p>
|
|
<p class="last">The fix srd command can be used with simluations the
|
|
size and/or shape of the simulation box changes. This can be due to
|
|
non-periodic boundary conditions or the use of fixes such as the <a class="reference internal" href="fix_deform.html"><em>fix deform</em></a> or <a class="reference internal" href="fix_wall_srd.html"><em>fix wall/srd</em></a> commands
|
|
to impose a shear on an SRD fluid or an interaction with an external
|
|
wall. If the box size changes then the size of SRD bins must be
|
|
recalculated every reneighboring. This is not necessary if only the
|
|
box shape changes. This re-binning is always done so as to fit an
|
|
integer number of bins in the current box dimension, whether it be a
|
|
fixed, shrink-wrapped, or periodic boundary, as set by the
|
|
<a class="reference internal" href="boundary.html"><em>boundary</em></a> command. If the box size or shape changes,
|
|
then the size of the search bins must be recalculated avery
|
|
reneighboring. Note that changing the SRD bin size may alter the
|
|
properties of the SRD fluid, such as its viscosity.</p>
|
|
</div>
|
|
<p>The <em>shift</em> keyword determines whether the coordinates of SRD
|
|
particles are randomly shifted when binned for purposes of rotating
|
|
their velocities. When no shifting is performed, SRD particles are
|
|
binned and the velocity distribution of the set of SRD particles in
|
|
each bin is adjusted via a rotation operator. This is a statistically
|
|
valid operation if SRD particles move sufficiently far between
|
|
successive rotations. This is determined by their mean-free path
|
|
lamda. If lamda is less than 0.6 of the SRD bin size, then shifting
|
|
is required. A shift means that all of the SRD particles are shifted
|
|
by a vector whose coordinates are chosen randomly in the range [-1/2
|
|
bin size, 1/2 bin size]. Note that all particles are shifted by the
|
|
same vector. The specified random number <em>shiftseed</em> is used to
|
|
generate these vectors. This operation sufficiently randomizes which
|
|
SRD particles are in the same bin, even if lamda is small.</p>
|
|
<p>If the <em>shift</em> flag is set to <em>no</em>, then no shifting is performed, but
|
|
bin data will be communicated if bins overlap processor boundaries.
|
|
An error will be generated if lamda < 0.6 of the SRD bin size. If the
|
|
<em>shift</em> flag is set to <em>possible</em>, then shifting is performed only if
|
|
lamda < 0.6 of the SRD bin size. A warning is generated to let you
|
|
know this is occurring. If the <em>shift</em> flag is set to <em>yes</em> then
|
|
shifting is performed regardless of the magnitude of lamda. Note that
|
|
the <em>shiftseed</em> is not used if the <em>shift</em> flag is set to <em>no</em>, but
|
|
must still be specified.</p>
|
|
<p>Note that shifting of SRD coordinates requires extra communication,
|
|
hence it should not normally be enabled unless required.</p>
|
|
<p>The <em>tstat</em> keyword will thermostat the SRD particles to the specified
|
|
<em>Tsrd</em>. This is done every N timesteps, during the velocity rotation
|
|
operation, by rescaling the thermal velocity of particles in each SRD
|
|
bin to the desired temperature. If there is a streaming velocity
|
|
associated with the system, e.g. due to use of the <a class="reference internal" href="fix_deform.html"><em>fix deform</em></a> command to perform a simulation undergoing
|
|
shear, then that is also accounted for. The mean velocity of each bin
|
|
of SRD particles is set to the position-dependent streaming velocity,
|
|
based on the coordinates of the center of the SRD bin. Note that
|
|
collisions of SRD particles with big particles or walls has a
|
|
thermostatting effect on the colliding particles, so it may not be
|
|
necessary to thermostat the SRD particles on a bin by bin basis in
|
|
that case. Also note that for streaming simulations, if no
|
|
thermostatting is performed (the default), then it may take a long
|
|
time for the SRD fluid to come to equilibrium with a velocity profile
|
|
that matches the simulation box deformation.</p>
|
|
<p>The <em>rescale</em> keyword enables rescaling of an SRD particle’s velocity
|
|
if it would travel more than 4 mean-free paths in an SRD timestep. If
|
|
an SRD particle exceeds this velocity it is possible it will be lost
|
|
when migrating to other processors or that collisions with big
|
|
particles will be missed, either of which will generate errors. Thus
|
|
the safest mode is to run with rescaling enabled. However rescaling
|
|
removes kinetic energy from the system (the particle’s velocity is
|
|
reduced). The latter will not typically be a problem if
|
|
thermostatting is enabled via the <em>tstat</em> keyword or if SRD collisions
|
|
with big particles or walls effectively thermostat the system. If you
|
|
wish to turn off rescaling (on is the default), e.g. for a pure SRD
|
|
system with no thermostatting so that the temperature does not decline
|
|
over time, the <em>rescale</em> keyword can be used. The <em>no</em> value turns
|
|
rescaling off during collisions and the per-bin velocity rotation
|
|
operation. The <em>collide</em> and <em>rotate</em> values turn it on for
|
|
one of the operations and off for the other.</p>
|
|
<hr class="docutils" />
|
|
<div class="admonition warning">
|
|
<p class="first admonition-title">Warning</p>
|
|
<p class="last">This fix is normally used for simulations with a huge
|
|
number of SRD particles relative to the number of big particles,
|
|
e.g. 100 to 1. In this scenario, computations that involve only big
|
|
particles (neighbor list creation, communication, time integration)
|
|
can slow down dramatically due to the large number of background SRD
|
|
particles.</p>
|
|
</div>
|
|
<p>Three other input script commands will largely overcome this effect,
|
|
speeding up an SRD simulation by a significant amount. These are the
|
|
<a class="reference internal" href="atom_modify.html"><em>atom_modify first</em></a>, <a class="reference internal" href="neigh_modify.html"><em>neigh_modify include</em></a>, and <a class="reference internal" href="comm_modify.html"><em>comm_modify group</em></a>
|
|
commands. Each takes a group-ID as an argument, which in this case
|
|
should be the group-ID of the big solute particles.</p>
|
|
<p>Additionally, when a <a class="reference internal" href="pair_style.html"><em>pair_style</em></a> for big/big particle
|
|
interactions is specified, the <a class="reference internal" href="pair_coeff.html"><em>pair_coeff</em></a> command
|
|
should be used to turn off big/SRD interactions, e.g. by setting their
|
|
epsilon or cutoff length to 0.0.</p>
|
|
<p>The “delete_atoms overlap” command may be useful in setting up an SRD
|
|
simulation to insure there are no initial overlaps between big and SRD
|
|
particles.</p>
|
|
</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<a class="headerlink" href="#restart-fix-modify-output-run-start-stop-minimize-info" title="Permalink to this headline">¶</a></h2>
|
|
<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
|
|
are relevant to this fix.</p>
|
|
<p>This fix tabulates several SRD statistics which are stored in a vector
|
|
of length 12, which can be accessed by various <a class="reference internal" href="Section_howto.html#howto-15"><span>output commands</span></a>. The vector values calculated
|
|
by this fix are “intensive”, meaning they do not scale with the size
|
|
of the simulation. Technically, the first 8 do scale with the size of
|
|
the simulation, but treating them as intensive means they are not
|
|
scaled when printed as part of thermodyanmic output.</p>
|
|
<p>These are the 12 quantities. All are values for the current timestep,
|
|
except for quantity 5 and the last three, each of which are
|
|
cummulative quantities since the beginning of the run.</p>
|
|
<ul class="simple">
|
|
<li><ol class="first arabic">
|
|
<li># of SRD/big collision checks performed</li>
|
|
</ol>
|
|
</li>
|
|
<li><ol class="first arabic" start="2">
|
|
<li># of SRDs which had a collision</li>
|
|
</ol>
|
|
</li>
|
|
<li><ol class="first arabic" start="3">
|
|
<li># of SRD/big colllisions (including multiple bounces)</li>
|
|
</ol>
|
|
</li>
|
|
<li><ol class="first arabic" start="4">
|
|
<li># of SRD particles inside a big particle</li>
|
|
</ol>
|
|
</li>
|
|
<li><ol class="first arabic" start="5">
|
|
<li># of SRD particles whose velocity was rescaled to be < Vmax</li>
|
|
</ol>
|
|
</li>
|
|
<li><ol class="first arabic" start="6">
|
|
<li># of bins for collision searching</li>
|
|
</ol>
|
|
</li>
|
|
<li><ol class="first arabic" start="7">
|
|
<li># of bins for SRD velocity rotation</li>
|
|
</ol>
|
|
</li>
|
|
<li><ol class="first arabic" start="8">
|
|
<li># of bins in which SRD temperature was computed</li>
|
|
</ol>
|
|
</li>
|
|
<li><ol class="first arabic" start="9">
|
|
<li>SRD temperature</li>
|
|
</ol>
|
|
</li>
|
|
<li><ol class="first arabic" start="10">
|
|
<li># of SRD particles which have undergone max # of bounces</li>
|
|
</ol>
|
|
</li>
|
|
<li><ol class="first arabic" start="11">
|
|
<li>max # of bounces any SRD particle has had in a single step</li>
|
|
</ol>
|
|
</li>
|
|
<li><ol class="first arabic" start="12">
|
|
<li># of reneighborings due to SRD particles moving too far</li>
|
|
</ol>
|
|
</li>
|
|
</ul>
|
|
<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"><em>run</em></a> command. This fix is not invoked during <a class="reference internal" href="minimize.html"><em>energy minimization</em></a>.</p>
|
|
</div>
|
|
<div class="section" id="restrictions">
|
|
<h2>Restrictions<a class="headerlink" href="#restrictions" title="Permalink to this headline">¶</a></h2>
|
|
<p>This command can only be used if LAMMPS was built with the SRD
|
|
package. See the <a class="reference internal" href="Section_start.html#start-3"><span>Making LAMMPS</span></a> section
|
|
for more info on packages.</p>
|
|
</div>
|
|
<div class="section" id="related-commands">
|
|
<h2>Related commands<a class="headerlink" href="#related-commands" title="Permalink to this headline">¶</a></h2>
|
|
<p><a class="reference internal" href="fix_wall_srd.html"><em>fix wall/srd</em></a></p>
|
|
</div>
|
|
<div class="section" id="default">
|
|
<h2>Default<a class="headerlink" href="#default" title="Permalink to this headline">¶</a></h2>
|
|
<p>The option defaults are lamda inferred from Tsrd, collision = noslip,
|
|
overlap = no, inside = error, exact = yes, radius = 1.0, bounce = 0,
|
|
search = hgrid, cubic = error 0.01, shift = no, tstat = no, and
|
|
rescale = yes.</p>
|
|
<hr class="docutils" />
|
|
<p id="hecht"><strong>(Hecht)</strong> Hecht, Harting, Ihle, Herrmann, Phys Rev E, 72, 011408 (2005).</p>
|
|
<p id="petersen"><strong>(Petersen)</strong> Petersen, Lechman, Plimpton, Grest, in’ t Veld, Schunk, J
|
|
Chem Phys, 132, 174106 (2010).</p>
|
|
<p id="lechman"><strong>(Lechman)</strong> Lechman, et al, in preparation (2010).</p>
|
|
</div>
|
|
</div>
|
|
|
|
|
|
</div>
|
|
</div>
|
|
<footer>
|
|
|
|
|
|
<hr/>
|
|
|
|
<div role="contentinfo">
|
|
<p>
|
|
© Copyright .
|
|
</p>
|
|
</div>
|
|
Built with <a href="http://sphinx-doc.org/">Sphinx</a> using a <a href="https://github.com/snide/sphinx_rtd_theme">theme</a> provided by <a href="https://readthedocs.org">Read the Docs</a>.
|
|
|
|
</footer>
|
|
|
|
</div>
|
|
</div>
|
|
|
|
</section>
|
|
|
|
</div>
|
|
|
|
|
|
|
|
|
|
|
|
<script type="text/javascript">
|
|
var DOCUMENTATION_OPTIONS = {
|
|
URL_ROOT:'./',
|
|
VERSION:'15 May 2015 version',
|
|
COLLAPSE_INDEX:false,
|
|
FILE_SUFFIX:'.html',
|
|
HAS_SOURCE: true
|
|
};
|
|
</script>
|
|
<script type="text/javascript" src="_static/jquery.js"></script>
|
|
<script type="text/javascript" src="_static/underscore.js"></script>
|
|
<script type="text/javascript" src="_static/doctools.js"></script>
|
|
<script type="text/javascript" src="https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
|
|
<script type="text/javascript" src="_static/sphinxcontrib-images/LightBox2/lightbox2/js/jquery-1.11.0.min.js"></script>
|
|
<script type="text/javascript" src="_static/sphinxcontrib-images/LightBox2/lightbox2/js/lightbox.min.js"></script>
|
|
<script type="text/javascript" src="_static/sphinxcontrib-images/LightBox2/lightbox2-customize/jquery-noconflict.js"></script>
|
|
|
|
|
|
|
|
|
|
|
|
<script type="text/javascript" src="_static/js/theme.js"></script>
|
|
|
|
|
|
|
|
|
|
<script type="text/javascript">
|
|
jQuery(function () {
|
|
SphinxRtdTheme.StickyNav.enable();
|
|
});
|
|
</script>
|
|
|
|
|
|
</body>
|
|
</html> |