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<div class="section" id="fix-ave-spatial-command">
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<span id="index-0"></span><h1>fix ave/spatial command</h1>
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<div class="section" id="syntax">
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<h2>Syntax</h2>
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<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">ave</span><span class="o">/</span><span class="n">spatial</span> <span class="n">Nevery</span> <span class="n">Nrepeat</span> <span class="n">Nfreq</span> <span class="n">dim</span> <span class="n">origin</span> <span class="n">delta</span> <span class="o">...</span> <span class="n">value1</span> <span class="n">value2</span> <span class="o">...</span> <span class="n">keyword</span> <span class="n">args</span> <span class="o">...</span>
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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"><span class="doc">fix</span></a> command</li>
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<li>ave/spatial = style name of this fix command</li>
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<li>Nevery = use input values every this many timesteps</li>
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<li>Nrepeat = # of times to use input values for calculating averages</li>
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<li>Nfreq = calculate averages every this many timesteps</li>
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<li>dim, origin, delta can be repeated 1, 2, or 3 times for 1d, 2d, or 3d bins</li>
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</ul>
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<pre class="literal-block">
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dim = <em>x</em> or <em>y</em> or <em>z</em>
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origin = <em>lower</em> or <em>center</em> or <em>upper</em> or coordinate value (distance units)
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delta = thickness of spatial bins in dim (distance units)
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</pre>
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<ul class="simple">
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<li>one or more input values can be listed</li>
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<li>value = vx, vy, vz, fx, fy, fz, density/mass, density/number, c_ID, c_ID[I], f_ID, f_ID[I], v_name</li>
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</ul>
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<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">vx</span><span class="p">,</span><span class="n">vy</span><span class="p">,</span><span class="n">vz</span><span class="p">,</span><span class="n">fx</span><span class="p">,</span><span class="n">fy</span><span class="p">,</span><span class="n">fz</span> <span class="o">=</span> <span class="n">atom</span> <span class="n">attribute</span> <span class="p">(</span><span class="n">velocity</span><span class="p">,</span> <span class="n">force</span> <span class="n">component</span><span class="p">)</span>
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<span class="n">density</span><span class="o">/</span><span class="n">number</span><span class="p">,</span> <span class="n">density</span><span class="o">/</span><span class="n">mass</span> <span class="o">=</span> <span class="n">number</span> <span class="ow">or</span> <span class="n">mass</span> <span class="n">density</span>
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<span class="n">c_ID</span> <span class="o">=</span> <span class="n">per</span><span class="o">-</span><span class="n">atom</span> <span class="n">vector</span> <span class="n">calculated</span> <span class="n">by</span> <span class="n">a</span> <span class="n">compute</span> <span class="k">with</span> <span class="n">ID</span>
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<span class="n">c_ID</span><span class="p">[</span><span class="n">I</span><span class="p">]</span> <span class="o">=</span> <span class="n">Ith</span> <span class="n">column</span> <span class="n">of</span> <span class="n">per</span><span class="o">-</span><span class="n">atom</span> <span class="n">array</span> <span class="n">calculated</span> <span class="n">by</span> <span class="n">a</span> <span class="n">compute</span> <span class="k">with</span> <span class="n">ID</span>
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<span class="n">f_ID</span> <span class="o">=</span> <span class="n">per</span><span class="o">-</span><span class="n">atom</span> <span class="n">vector</span> <span class="n">calculated</span> <span class="n">by</span> <span class="n">a</span> <span class="n">fix</span> <span class="k">with</span> <span class="n">ID</span>
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<span class="n">f_ID</span><span class="p">[</span><span class="n">I</span><span class="p">]</span> <span class="o">=</span> <span class="n">Ith</span> <span class="n">column</span> <span class="n">of</span> <span class="n">per</span><span class="o">-</span><span class="n">atom</span> <span class="n">array</span> <span class="n">calculated</span> <span class="n">by</span> <span class="n">a</span> <span class="n">fix</span> <span class="k">with</span> <span class="n">ID</span>
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<span class="n">v_name</span> <span class="o">=</span> <span class="n">per</span><span class="o">-</span><span class="n">atom</span> <span class="n">vector</span> <span class="n">calculated</span> <span class="n">by</span> <span class="n">an</span> <span class="n">atom</span><span class="o">-</span><span class="n">style</span> <span class="n">variable</span> <span class="k">with</span> <span class="n">name</span>
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</pre></div>
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</div>
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<ul class="simple">
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<li>zero or more keyword/arg pairs may be appended</li>
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<li>keyword = <em>region</em> or <em>bound</em> or <em>discard</em> or <em>norm</em> or <em>ave</em> or <em>units</em> or <em>file</em> or <em>overwrite</em> or <em>title1</em> or <em>title2</em> or <em>title3</em></li>
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</ul>
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<pre class="literal-block">
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<em>region</em> arg = region-ID
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<em>bound</em> args = x/y/z lo hi
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x/y/z = <em>x</em> or <em>y</em> or <em>z</em> to bound bins in this dimension
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lo = <em>lower</em> or coordinate value (distance units)
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hi = <em>upper</em> or coordinate value (distance units)
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<em>discard</em> arg = <em>mixed</em> or <em>no</em> or <em>yes</em>
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mixed = discard atoms outside bins only if bin bounds are explicitly set
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no = always keep out-of-bounds atoms
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yes = always discard out-of-bounds atoms
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<em>norm</em> arg = <em>all</em> or <em>sample</em>
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region-ID = ID of region atoms must be in to contribute to spatial averaging
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<em>ave</em> args = <em>one</em> or <em>running</em> or <em>window M</em>
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one = output new average value every Nfreq steps
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running = output cumulative average of all previous Nfreq steps
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window M = output average of M most recent Nfreq steps
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<em>units</em> arg = <em>box</em> or <em>lattice</em> or <em>reduced</em>
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<em>file</em> arg = filename
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filename = file to write results to
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<em>overwrite</em> arg = none = overwrite output file with only latest output
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<em>title1</em> arg = string
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string = text to print as 1st line of output file
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<em>title2</em> arg = string
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string = text to print as 2nd line of output file
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<em>title3</em> arg = string
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string = text to print as 3rd line of output file
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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</h2>
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<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">fix</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">ave</span><span class="o">/</span><span class="n">spatial</span> <span class="mi">10000</span> <span class="mi">1</span> <span class="mi">10000</span> <span class="n">z</span> <span class="n">lower</span> <span class="mf">0.02</span> <span class="n">c_myCentro</span> <span class="n">units</span> <span class="n">reduced</span> <span class="o">&</span>
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<span class="n">title1</span> <span class="s2">"My output values"</span>
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<span class="n">fix</span> <span class="mi">1</span> <span class="n">flow</span> <span class="n">ave</span><span class="o">/</span><span class="n">spatial</span> <span class="mi">100</span> <span class="mi">10</span> <span class="mi">1000</span> <span class="n">y</span> <span class="mf">0.0</span> <span class="mf">1.0</span> <span class="n">vx</span> <span class="n">vz</span> <span class="n">norm</span> <span class="n">sample</span> <span class="n">file</span> <span class="n">vel</span><span class="o">.</span><span class="n">profile</span>
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<span class="n">fix</span> <span class="mi">1</span> <span class="n">flow</span> <span class="n">ave</span><span class="o">/</span><span class="n">spatial</span> <span class="mi">100</span> <span class="mi">5</span> <span class="mi">1000</span> <span class="n">z</span> <span class="n">lower</span> <span class="mf">1.0</span> <span class="n">y</span> <span class="mf">0.0</span> <span class="mf">2.5</span> <span class="n">density</span><span class="o">/</span><span class="n">mass</span> <span class="n">ave</span> <span class="n">running</span>
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<span class="n">fix</span> <span class="mi">1</span> <span class="n">flow</span> <span class="n">ave</span><span class="o">/</span><span class="n">spatial</span> <span class="mi">100</span> <span class="mi">5</span> <span class="mi">1000</span> <span class="n">z</span> <span class="n">lower</span> <span class="mf">1.0</span> <span class="n">y</span> <span class="mf">0.0</span> <span class="mf">2.5</span> <span class="n">density</span><span class="o">/</span><span class="n">mass</span> <span class="n">bound</span> <span class="n">y</span> <span class="mf">5.0</span> <span class="mf">20.0</span> <span class="n">discard</span> <span class="n">yes</span> <span class="n">ave</span> <span class="n">running</span>
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</pre></div>
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</div>
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<p><strong>NOTE:</strong></p>
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<p>The fix ave/spatial command has been replaced by the more flexible
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<a class="reference internal" href="fix_ave_chunk.html"><span class="doc">fix ave/chunk</span></a> and <a class="reference internal" href="compute_chunk_atom.html"><span class="doc">compute chunk/atom</span></a> commands. The fix ave/spatial
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command will be removed from LAMMPS sometime in the summer of 2015.</p>
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<p>Any fix ave/spatial command can be replaced by the two new commands.
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You simply need to split the fix ave/spatial arguments across the two
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new commands. For example, this command:</p>
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<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">fix</span> <span class="mi">1</span> <span class="n">flow</span> <span class="n">ave</span><span class="o">/</span><span class="n">spatial</span> <span class="mi">100</span> <span class="mi">10</span> <span class="mi">1000</span> <span class="n">y</span> <span class="mf">0.0</span> <span class="mf">1.0</span> <span class="n">vx</span> <span class="n">vz</span> <span class="n">norm</span> <span class="n">sample</span> <span class="n">file</span> <span class="n">vel</span><span class="o">.</span><span class="n">profile</span>
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</pre></div>
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</div>
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<p>could be replaced by:</p>
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<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="n">cc1</span> <span class="n">flow</span> <span class="n">chunk</span><span class="o">/</span><span class="n">atom</span> <span class="nb">bin</span><span class="o">/</span><span class="mi">1</span><span class="n">d</span> <span class="n">y</span> <span class="mf">0.0</span> <span class="mf">1.0</span>
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<span class="n">fix</span> <span class="mi">1</span> <span class="n">flow</span> <span class="n">ave</span><span class="o">/</span><span class="n">chunk</span> <span class="mi">100</span> <span class="mi">10</span> <span class="mi">1000</span> <span class="n">cc1</span> <span class="n">vx</span> <span class="n">vz</span> <span class="n">norm</span> <span class="n">sample</span> <span class="n">file</span> <span class="n">vel</span><span class="o">.</span><span class="n">profile</span>
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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</h2>
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<p>Use one or more per-atom vectors as inputs every few timesteps, bin
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their values spatially into 1d, 2d, or 3d bins based on current atom
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coordinates, and average the bin values over longer timescales. The
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resulting bin averages can be used by other <a class="reference internal" href="Section_howto.html#howto-15"><span class="std std-ref">output commands</span></a> such as <a class="reference internal" href="thermo_style.html"><span class="doc">thermo_style custom</span></a>, and can also be written to a file.</p>
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<p>The group specified with the command means only atoms within the group
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contribute to bin averages. If the <em>region</em> keyword is used, the atom
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must be in both the specified group and the specified geometric
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<a class="reference internal" href="region.html"><span class="doc">region</span></a> in order to contribute to bin averages.</p>
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<p>Each listed value can be an atom attribute (position, velocity, force
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component), a mass or number density, or the result of a
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<a class="reference internal" href="compute.html"><span class="doc">compute</span></a> or <a class="reference internal" href="fix.html"><span class="doc">fix</span></a> or the evaluation of an
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atom-style <a class="reference internal" href="variable.html"><span class="doc">variable</span></a>. In the latter cases, the
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compute, fix, or variable must produce a per-atom quantity, not a
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global quantity. If you wish to time-average global quantities from a
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compute, fix, or variable, then see the <a class="reference internal" href="fix_ave_time.html"><span class="doc">fix ave/time</span></a> command.</p>
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<p><a class="reference internal" href="compute.html"><span class="doc">Computes</span></a> that produce per-atom quantities are those
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which have the word <em>atom</em> in their style name. See the doc pages for
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individual <a class="reference internal" href="fix.html"><span class="doc">fixes</span></a> to determine which ones produce per-atom
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quantities. <a class="reference internal" href="variable.html"><span class="doc">Variables</span></a> of style <em>atom</em> are the only
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ones that can be used with this fix since all other styles of variable
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produce global quantities.</p>
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<p>The per-atom values of each input vector are binned and averaged
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independently of the per-atom values in other input vectors.</p>
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<p>The size and dimensionality of the bins (1d = layers or slabs, 2d =
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pencils, 3d = boxes) are determined by the <em>dim</em>, <em>origin</em>, and
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<em>delta</em> settings and how many times they are specified (1, 2, or 3).
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See details below.</p>
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<div class="admonition note">
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<p class="first admonition-title">Note</p>
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<p class="last">This fix works by creating an array of size Nbins by Nvalues on
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each processor. Nbins is the total number of bins; Nvalues is the
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number of input values specified. Each processor loops over its
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atoms, tallying its values to the appropriate bin. Then the entire
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array is summed across all processors. This means that using a large
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number of bins (easy to do for 2d or 3d bins) will incur an overhead
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in memory and computational cost (summing across processors), so be
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careful to use reasonable numbers of bins.</p>
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</div>
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<hr class="docutils" />
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<p>The <em>Nevery</em>, <em>Nrepeat</em>, and <em>Nfreq</em> arguments specify on what
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timesteps the input values will be used to bin them and contribute to
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the average. The final averaged quantities are generated on timesteps
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that are a multiples of <em>Nfreq</em>. The average is over <em>Nrepeat</em>
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quantities, computed in the preceding portion of the simulation every
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<em>Nevery</em> timesteps. <em>Nfreq</em> must be a multiple of <em>Nevery</em> and
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<em>Nevery</em> must be non-zero even if <em>Nrepeat</em> is 1. Also, the timesteps
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contributing to the average value cannot overlap,
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i.e. Nrepeat*Nevery can not exceed Nfreq.</p>
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<p>For example, if Nevery=2, Nrepeat=6, and Nfreq=100, then values on
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timesteps 90,92,94,96,98,100 will be used to compute the final average
|
|
on timestep 100. Similarly for timesteps 190,192,194,196,198,200 on
|
|
timestep 200, etc. If Nrepeat=1 and Nfreq = 100, then no time
|
|
averaging is done; values are simply generated on timesteps
|
|
100,200,etc.</p>
|
|
<hr class="docutils" />
|
|
<p>Each per-atom property is also averaged over atoms in each bin. The
|
|
way the averaging is one across the <em>Nrepeat</em> timesteps to produce
|
|
output on the <em>Nfreq</em> timesteps, and across multiple <em>Nfreq</em> outputs,
|
|
is determined by the <em>norm</em> and <em>av</em> keyword settings, as discussed
|
|
below.</p>
|
|
<p>Bins can be 1d layers or slabs, 2d pencils, or 3d boxes. This depends
|
|
on how many times (1, 2, or 3) the <em>dim</em>, <em>origin</em>, and <em>delta</em>
|
|
settings are specified in the fix ave/spatial command. For 2d or 3d
|
|
bins, there is no restriction on specifying dim = x before dim = y, or
|
|
dim = y before dim = z. Bins in a particular <em>dim</em> have a bin size in
|
|
that dimension given by <em>delta</em>. Every Nfreq steps, when averaging is
|
|
being performed and the per-atom property is calculated for the first
|
|
time, the number of bins and the bin sizes and boundaries are
|
|
computed. Thus if the simulation box changes size during a
|
|
simulation, the number of bins and their boundaries may also change.
|
|
In each dimension, bins are defined relative to a specified <em>origin</em>,
|
|
which may be the lower/upper edge of the simulation box in that
|
|
dimension, or its center point, or a specified coordinate value.
|
|
Starting at the origin, sufficient bins are created in both directions
|
|
to completely span the bin extent in that dimension. By default the
|
|
bin extent is the entire simulation box.</p>
|
|
<p>The <em>bound</em> keyword can be used one or more times to limit the extent
|
|
of bin coverage in specified dimensions, i.e. to only bin a portion of
|
|
the box. If the <em>lo</em> setting is <em>lower</em> or the <em>hi</em> setting is
|
|
<em>upper</em>, the bin extent in that direction extends to the box boundary.
|
|
If a numeric value is used for <em>lo</em> and/or <em>hi</em>, then the bin extent
|
|
in the <em>lo</em> or <em>hi</em> direction extends only to that value, which is
|
|
assumed to be inside (or at least near) the simulation box boundaries,
|
|
though LAMMPS does not check for this.</p>
|
|
<p>On each sampling timestep, each atom is mapped to the bin it currently
|
|
belongs to, based on its current position. Note that the group-ID and
|
|
region keyword can exclude specific atoms from this operation, as
|
|
discussed above. Note that between reneighboring timesteps, atoms can
|
|
move outside the current simulation box. If the box is periodic (in
|
|
that dimension) the atom is remapping into the periodic box for
|
|
purposes of binning. If the box in not periodic, the atom may have
|
|
moved outside the bounds of any bin.</p>
|
|
<p>The <em>discard</em> keyword determines what is done with any atom which is
|
|
outside the bounds of any bin. If <em>discard</em> is set to <em>yes</em>, the atom
|
|
will be ignored and not contribute to any bin averages. If <em>discard</em>
|
|
is set to <em>no</em>, the atom will be counted as if it were in the first or
|
|
last bin in that dimension. If (discard* is set to <em>mixed</em>, which is
|
|
the default, it will only be counted in the first or last bin if bins
|
|
extend to the box boundary in that dimension. This is the case if the
|
|
<em>bound</em> keyword settings are <em>lower</em> and <em>upper</em>, which is the
|
|
default. If the <em>bound</em> keyword settings are numeric values, then the
|
|
atom will be ignored if it is outside the bounds of any bin. Note
|
|
that in this case, it is possible that the first or last bin extends
|
|
beyond the numeric <em>bounds</em> settings, depending on the specified
|
|
<em>origin</em>. If this is the case, the atom is only ignored if it is
|
|
outside the first or last bin, not if it is simply outside the numeric
|
|
<em>bounds</em> setting.</p>
|
|
<p>For orthogonal simulation boxes, the bins are also layers, pencils, or
|
|
boxes aligned with the xyz coordinate axes. For triclinic
|
|
(non-orthogonal) simulation boxes, the bins are so that they are
|
|
parallel to the tilted faces of the simulation box. See <a class="reference internal" href="Section_howto.html#howto-12"><span class="std std-ref">this section</span></a> of the manual for a discussion of
|
|
the geometry of triclinic boxes in LAMMPS. As described there, a
|
|
tilted simulation box has edge vectors a,b,c. In that nomenclature,
|
|
bins in the x dimension have faces with normals in the “b” cross “c”
|
|
direction. Bins in y have faces normal to the “a” cross “c”
|
|
direction. And bins in z have faces normal to the “a” cross “b”
|
|
direction. Note that in order to define the size and position of
|
|
these bins in an unambiguous fashion, the <em>units</em> option must be set
|
|
to <em>reduced</em> when using a triclinic simulation box, as noted below.</p>
|
|
<hr class="docutils" />
|
|
<p>The atom attribute values (vx,vy,vz,fx,fy,fz) are self-explanatory.
|
|
Note that other atom attributes (including atom postitions x,y,z) can
|
|
be used as inputs to this fix by using the <a class="reference internal" href="compute_property_atom.html"><span class="doc">compute property/atom</span></a> command and then specifying
|
|
an input value from that compute.</p>
|
|
<p>The <em>density/number</em> value means the number density is computed in
|
|
each bin, i.e. a weighting of 1 for each atom. The <em>density/mass</em>
|
|
value means the mass density is computed in each bind, i.e. each atom
|
|
is weighted by its mass. The resulting density is normalized by the
|
|
volume of the bin so that units of number/volume or density are
|
|
output. See the <a class="reference internal" href="units.html"><span class="doc">units</span></a> command doc page for the
|
|
definition of density for each choice of units, e.g. gram/cm^3.</p>
|
|
<p>If a value begins with “<a href="#id1"><span class="problematic" id="id2">c_</span></a>”, a compute ID must follow which has been
|
|
previously defined in the input script. If no bracketed integer is
|
|
appended, the per-atom vector calculated by the compute is used. If a
|
|
bracketed integer is appended, the Ith column of the per-atom array
|
|
calculated by the compute is used. Users can also write code for
|
|
their own compute styles and <a class="reference internal" href="Section_modify.html"><span class="doc">add them to LAMMPS</span></a>.</p>
|
|
<p>If a value begins with “<a href="#id3"><span class="problematic" id="id4">f_</span></a>”, a fix ID must follow which has been
|
|
previously defined in the input script. If no bracketed integer is
|
|
appended, the per-atom vector calculated by the fix is used. If a
|
|
bracketed integer is appended, the Ith column of the per-atom array
|
|
calculated by the fix is used. Note that some fixes only produce
|
|
their values on certain timesteps, which must be compatible with
|
|
<em>Nevery</em>, else an error results. Users can also write code for their
|
|
own fix styles and <a class="reference internal" href="Section_modify.html"><span class="doc">add them to LAMMPS</span></a>.</p>
|
|
<p>If a value begins with “<a href="#id5"><span class="problematic" id="id6">v_</span></a>”, a variable name must follow which has
|
|
been previously defined in the input script. Variables of style
|
|
<em>atom</em> can reference thermodynamic keywords and various per-atom
|
|
attributes, or invoke other computes, fixes, or variables when they
|
|
are evaluated, so this is a very general means of generating per-atom
|
|
quantities to spatially average.</p>
|
|
<hr class="docutils" />
|
|
<p>Additional optional keywords also affect the operation of this fix.
|
|
The <em>region</em>, <em>bound</em>, and <em>discard</em> keywords were discussed above.</p>
|
|
<p>The <em>norm</em> keyword affects how averaging is done for the output
|
|
produced every <em>Nfreq</em> timesteps. For an <em>all</em> setting, a bin
|
|
quantity is summed over all atoms in all <em>Nrepeat</em> samples, as is the
|
|
count of atoms in the bin. The printed value for the bin is
|
|
Total-quantity / Total-count. In other words it is an average over
|
|
the entire <em>Nfreq</em> timescale.</p>
|
|
<p>For a <em>sample</em> setting, the bin quantity is summed over atoms for only
|
|
a single sample, as is the count, and a “average sample value” is
|
|
computed, i.e. Sample-quantity / Sample-count. The printed value for
|
|
the bin is the average of the <em>Nrepeat</em> “average sample values”, In
|
|
other words it is an average of an average.</p>
|
|
<p>The <em>ave</em> keyword determines how the bin values produced every <em>Nfreq</em>
|
|
steps are averaged with bin values produced on previous steps that
|
|
were multiples of <em>Nfreq</em>, before they are accessed by another output
|
|
command or written to a file.</p>
|
|
<p>If the <em>ave</em> setting is <em>one</em>, then the bin values produced on
|
|
timesteps that are multiples of <em>Nfreq</em> are independent of each other;
|
|
they are output as-is without further averaging.</p>
|
|
<p>If the <em>ave</em> setting is <em>running</em>, then the bin values produced on
|
|
timesteps that are multiples of <em>Nfreq</em> are summed and averaged in a
|
|
cumulative sense before being output. Each output bin value is thus
|
|
the average of the bin value produced on that timestep with all
|
|
preceding values for the same bin. This running average begins when
|
|
the fix is defined; it can only be restarted by deleting the fix via
|
|
the <a class="reference internal" href="unfix.html"><span class="doc">unfix</span></a> command, or re-defining the fix by
|
|
re-specifying it.</p>
|
|
<p>If the <em>ave</em> setting is <em>window</em>, then the bin values produced on
|
|
timesteps that are multiples of <em>Nfreq</em> are summed and averaged within
|
|
a moving “window” of time, so that the last M values for the same bin
|
|
are used to produce the output. E.g. if M = 3 and Nfreq = 1000, then
|
|
the output on step 10000 will be the average of the individual bin
|
|
values on steps 8000,9000,10000. Outputs on early steps will average
|
|
over less than M values if they are not available.</p>
|
|
<p>The <em>units</em> keyword determines the meaning of the distance units used
|
|
for the bin size <em>delta</em> and for <em>origin</em> and <em>bounds</em> values if they
|
|
are coordinate value. For orthogonal simulation boxes, any of the 3
|
|
options may be used. For non-orthogonal (triclinic) simulation boxes,
|
|
only the <em>reduced</em> option may be used.</p>
|
|
<p>A <em>box</em> value selects standard distance units as defined by the
|
|
<a class="reference internal" href="units.html"><span class="doc">units</span></a> command, e.g. Angstroms for units = real or metal.
|
|
A <em>lattice</em> value means the distance units are in lattice spacings.
|
|
The <a class="reference internal" href="lattice.html"><span class="doc">lattice</span></a> command must have been previously used to
|
|
define the lattice spacing. A <em>reduced</em> value means normalized
|
|
unitless values between 0 and 1, which represent the lower and upper
|
|
faces of the simulation box respectively. Thus an <em>origin</em> value of
|
|
0.5 means the center of the box in any dimension. A <em>delta</em> value of
|
|
0.1 means 10 bins span the box in that dimension.</p>
|
|
<p>Consider a non-orthogonal box, with bins that are 1d layers or slabs
|
|
in the x dimension. No matter how the box is tilted, an <em>origin</em> of
|
|
0.0 means start layers at the lower “b” cross “c” plane of the
|
|
simulation box and an <em>origin</em> of 1.0 means to start layers at the
|
|
upper “b” cross “c” face of the box. A <em>delta</em> value of 0.1 means
|
|
there will be 10 layers from 0.0 to 1.0, regardless of the current
|
|
size or shape of the simulation box.</p>
|
|
<p>The <em>file</em> keyword allows a filename to be specified. Every <em>Nfreq</em>
|
|
timesteps, a section of bin info will be written to a text file in the
|
|
following format. A line with the timestep and number of bin is
|
|
written. Then one line per bin is written, containing the bin ID
|
|
(1-N), the coordinate of the center of the bin, the number of atoms
|
|
in the bin, and one or more calculated values. The number of values
|
|
in each line corresponds to the number of values specified in the fix
|
|
ave/spatial command. The number of atoms and the value(s) are average
|
|
quantities. If the value of the <em>units</em> keyword is <em>box</em> or
|
|
<em>lattice</em>, the “coord” is printed in box units. If the value of the
|
|
<em>units</em> keyword is <em>reduced</em>, the “coord” is printed in reduced units
|
|
(0-1).</p>
|
|
<p>The <em>overwrite</em> keyword will continuously overwrite the output file
|
|
with the latest output, so that it only contains one timestep worth of
|
|
output. This option can only be used with the <em>ave running</em> setting.</p>
|
|
<p>The <em>title1</em> and <em>title2</em> and <em>title3</em> keywords allow specification of
|
|
the strings that will be printed as the first 3 lines of the output
|
|
file, assuming the <em>file</em> keyword was used. LAMMPS uses default
|
|
values for each of these, so they do not need to be specified.</p>
|
|
<p>By default, these header lines are as follows:</p>
|
|
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="c1"># Spatial-averaged data for fix ID and group name</span>
|
|
<span class="c1"># Timestep Number-of-bins</span>
|
|
<span class="c1"># Bin Coord1 Coord2 Coord3 Count value1 value2 ...</span>
|
|
</pre></div>
|
|
</div>
|
|
<p>In the first line, ID and name are replaced with the fix-ID and group
|
|
name. The second line describes the two values that are printed at
|
|
the first of each section of output. In the third line the values are
|
|
replaced with the appropriate fields from the fix ave/spatial command.
|
|
The Coord2 and Coord3 entries in the third line only appear for 2d and
|
|
3d bins respectively. For 1d bins, the word Coord1 is replaced by
|
|
just Coord.</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</h2>
|
|
<p>No information about this fix is written to <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>. None of the <a class="reference internal" href="fix_modify.html"><span class="doc">fix_modify</span></a> options
|
|
are relevant to this fix.</p>
|
|
<p>This fix computes a global array of values 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 values can
|
|
only be accessed on timesteps that are multiples of <em>Nfreq</em> since that
|
|
is when averaging is performed. The global array has # of rows =
|
|
Nbins and # of columns = Ndim+1+Nvalues, where Ndim = 1,2,3 for
|
|
1d,2d,3d bins. The first 1 or 2 or 3 columns have the bin coordinates
|
|
(center of the bin) in the appropriate dimensions, the next column has
|
|
the count of atoms in that bin, and the remaining columns are the
|
|
Nvalue quantities. When the array is accessed with an I that exceeds
|
|
the current number of bins, than a 0.0 is returned by the fix instead
|
|
of an error, since the number of bins can vary as a simulation runs,
|
|
depending on the simulation box size. 2d or 3d bins are ordered so
|
|
that the last dimension(s) vary fastest. The array values calculated
|
|
by this fix are “intensive”, since they are already normalized by the
|
|
count of atoms in each bin.</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. This fix is not invoked during <a class="reference internal" href="minimize.html"><span class="doc">energy minimization</span></a>.</p>
|
|
</div>
|
|
<div class="section" id="restrictions">
|
|
<h2>Restrictions</h2>
|
|
<p>When the <em>ave</em> keyword is set to <em>running</em> or <em>window</em> then the number
|
|
of bins must remain the same during the simulation, so that the
|
|
appropriate averaging can be done. This will be the case if the
|
|
simulation box size doesn’t change or if the <em>units</em> keyword is set to
|
|
<em>reduced</em>.</p>
|
|
</div>
|
|
<div class="section" id="related-commands">
|
|
<h2>Related commands</h2>
|
|
<p><a class="reference internal" href="compute.html"><span class="doc">compute</span></a>, <a class="reference internal" href="fix_ave_atom.html"><span class="doc">fix ave/atom</span></a>, <a class="reference internal" href="fix_ave_histo.html"><span class="doc">fix ave/histo</span></a>, <a class="reference internal" href="fix_ave_time.html"><span class="doc">fix ave/time</span></a>,
|
|
<a class="reference internal" href="variable.html"><span class="doc">variable</span></a>, <a class="reference internal" href="fix_ave_correlate.html"><span class="doc">fix ave/correlate</span></a>,
|
|
<a class="reference internal" href="fix_ave_spatial_sphere.html"><span class="doc">fix ave/spatial/sphere</span></a></p>
|
|
</div>
|
|
<div class="section" id="default">
|
|
<h2>Default</h2>
|
|
<p>The option defaults are bound = lower and upper in all dimensions,
|
|
discard = mixed, norm = all, ave = one, units = lattice, no file
|
|
output, and title 1,2,3 = strings as described above.</p>
|
|
</div>
|
|
</div>
|
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</div>
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</div>
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<hr/>
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