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<li>compute reduce command</li>
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<div itemprop="articleBody">
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<div class="section" id="compute-reduce-command">
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<span id="index-0"></span><h1>compute reduce command<a class="headerlink" href="#compute-reduce-command" title="Permalink to this headline">¶</a></h1>
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</div>
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<div class="section" id="compute-reduce-region-command">
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<h1>compute reduce/region command<a class="headerlink" href="#compute-reduce-region-command" title="Permalink to this headline">¶</a></h1>
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<div class="section" id="syntax">
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<h2>Syntax<a class="headerlink" href="#syntax" title="Permalink to this headline">¶</a></h2>
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<div class="highlight-python"><div class="highlight"><pre>compute ID group-ID style arg mode input1 input2 ... keyword args ...
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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="compute.html"><em>compute</em></a> command</li>
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<li>style = <em>reduce</em> or <em>reduce/region</em></li>
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</ul>
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<pre class="literal-block">
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<em>reduce</em> arg = none
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<em>reduce/region</em> arg = region-ID
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region-ID = ID of region to use for choosing atoms
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</pre>
|
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<ul class="simple">
|
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<li>mode = <em>sum</em> or <em>min</em> or <em>max</em> or <em>ave</em> or <em>sumsq</em> or <em>avesq</em></li>
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<li>one or more inputs can be listed</li>
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<li>input = x, y, z, vx, vy, vz, fx, fy, fz, c_ID, c_ID[N], f_ID, f_ID[N], v_name</li>
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</ul>
|
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<div class="highlight-python"><div class="highlight"><pre>x,y,z,vx,vy,vz,fx,fy,fz = atom attribute (position, velocity, force component)
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<HR>
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|
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<H3>compute reduce command
|
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</H3>
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<H3>compute reduce/region command
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</H3>
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<P><B>Syntax:</B>
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</P>
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<PRE>compute ID group-ID style arg mode input1 input2 ... keyword args ...
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</PRE>
|
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<UL><LI>ID, group-ID are documented in <A HREF = "compute.html">compute</A> command
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|
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<LI>style = <I>reduce</I> or <I>reduce/region</I>
|
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|
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<PRE> <I>reduce</I> arg = none
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<I>reduce/region</I> arg = region-ID
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region-ID = ID of region to use for choosing atoms
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</PRE>
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<LI>mode = <I>sum</I> or <I>min</I> or <I>max</I> or <I>ave</I> or <I>sumsq</I> or <I>avesq</I>
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|
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<LI>one or more inputs can be listed
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|
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<LI>input = x, y, z, vx, vy, vz, fx, fy, fz, c_ID, c_ID[N], f_ID, f_ID[N], v_name
|
||||
|
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<PRE> x,y,z,vx,vy,vz,fx,fy,fz = atom attribute (position, velocity, force component)
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c_ID = per-atom or local vector calculated by a compute with ID
|
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c_ID[I] = Ith column of per-atom or local array calculated by a compute with ID
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f_ID = per-atom or local vector calculated by a fix with ID
|
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f_ID[I] = Ith column of per-atom or local array calculated by a fix with ID
|
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v_name = per-atom vector calculated by an atom-style variable with name
|
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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/args pairs may be appended</li>
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<li>keyword = <em>replace</em></li>
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</ul>
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<pre class="literal-block">
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<em>replace</em> args = vec1 vec2
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v_name = per-atom vector calculated by an atom-style variable with name
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</PRE>
|
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<LI>zero or more keyword/args pairs may be appended
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|
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<LI>keyword = <I>replace</I>
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<PRE> <I>replace</I> args = vec1 vec2
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vec1 = reduced value from this input vector will be replaced
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vec2 = replace it with vec1[N] where N is index of max/min value from vec2
|
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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<a class="headerlink" href="#examples" title="Permalink to this headline">¶</a></h2>
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<div class="highlight-python"><div class="highlight"><pre>compute 1 all reduce sum c_force
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vec2 = replace it with vec1[N] where N is index of max/min value from vec2
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</PRE>
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</UL>
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<P><B>Examples:</B>
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||||
</P>
|
||||
<PRE>compute 1 all reduce sum c_force
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||||
compute 1 all reduce/region subbox sum c_force
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compute 2 all reduce min c_press[2] f_ave v_myKE
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compute 3 fluid reduce max c_index[1] c_index[2] c_dist replace 1 3 replace 2 3
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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<a class="headerlink" href="#description" title="Permalink to this headline">¶</a></h2>
|
||||
<p>Define a calculation that “reduces” one or more vector inputs into
|
||||
compute 3 fluid reduce max c_index[1] c_index[2] c_dist replace 1 3 replace 2 3
|
||||
</PRE>
|
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<P><B>Description:</B>
|
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</P>
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<P>Define a calculation that "reduces" one or more vector inputs into
|
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scalar values, one per listed input. The inputs can be per-atom or
|
||||
local quantities; they cannot be global quantities. Atom attributes
|
||||
are per-atom quantities, <a class="reference internal" href="compute.html"><em>computes</em></a> and <a class="reference internal" href="fix.html"><em>fixes</em></a>
|
||||
may generate any of the three kinds of quantities, and <a class="reference internal" href="variable.html"><em>atom-style variables</em></a> generate per-atom quantities. See the
|
||||
<a class="reference external" href="variable">variable</a> command and its special functions which can
|
||||
are per-atom quantities, <A HREF = "compute.html">computes</A> and <A HREF = "fix.html">fixes</A>
|
||||
may generate any of the three kinds of quantities, and <A HREF = "variable.html">atom-style
|
||||
variables</A> generate per-atom quantities. See the
|
||||
<A HREF = "variable">variable</A> command and its special functions which can
|
||||
perform the same operations as the compute reduce command on global
|
||||
vectors.</p>
|
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<p>The reduction operation is specified by the <em>mode</em> setting. The <em>sum</em>
|
||||
option adds the values in the vector into a global total. The <em>min</em>
|
||||
or <em>max</em> options find the minimum or maximum value across all vector
|
||||
values. The <em>ave</em> setting adds the vector values into a global total,
|
||||
then divides by the number of values in the vector. The <em>sumsq</em>
|
||||
vectors.
|
||||
</P>
|
||||
<P>The reduction operation is specified by the <I>mode</I> setting. The <I>sum</I>
|
||||
option adds the values in the vector into a global total. The <I>min</I>
|
||||
or <I>max</I> options find the minimum or maximum value across all vector
|
||||
values. The <I>ave</I> setting adds the vector values into a global total,
|
||||
then divides by the number of values in the vector. The <I>sumsq</I>
|
||||
option sums the square of the values in the vector into a global
|
||||
total. The <em>avesq</em> setting does the same as <em>sumsq</em>, then divdes the
|
||||
total. The <I>avesq</I> setting does the same as <I>sumsq</I>, then divdes the
|
||||
sum of squares by the number of values. The last two options can be
|
||||
useful for calculating the variance of some quantity, e.g. variance =
|
||||
sumsq - ave^2.</p>
|
||||
<p>Each listed input is operated on independently. For per-atom inputs,
|
||||
sumsq - ave^2.
|
||||
</P>
|
||||
<P>Each listed input is operated on independently. For per-atom inputs,
|
||||
the group specified with this command means only atoms within the
|
||||
group contribute to the result. For per-atom inputs, if the compute
|
||||
reduce/region command is used, the atoms must also currently be within
|
||||
@ -203,159 +86,115 @@ the region. Note that an input that produces per-atom quantities may
|
||||
define its own group which affects the quantities it returns. For
|
||||
example, if a compute is used as an input which generates a per-atom
|
||||
vector, it will generate values of 0.0 for atoms that are not in the
|
||||
group specified for that compute.</p>
|
||||
<p>Each listed input can be an atom attribute (position, velocity, force
|
||||
component) or can be the result of a <a class="reference internal" href="compute.html"><em>compute</em></a> or
|
||||
<a class="reference internal" href="fix.html"><em>fix</em></a> or the evaluation of an atom-style
|
||||
<a class="reference internal" href="variable.html"><em>variable</em></a>.</p>
|
||||
<p>The atom attribute values (x,y,z,vx,vy,vz,fx,fy,fz) are
|
||||
group specified for that compute.
|
||||
</P>
|
||||
<P>Each listed input can be an atom attribute (position, velocity, force
|
||||
component) or can be the result of a <A HREF = "compute.html">compute</A> or
|
||||
<A HREF = "fix.html">fix</A> or the evaluation of an atom-style
|
||||
<A HREF = "variable.html">variable</A>.
|
||||
</P>
|
||||
<P>The atom attribute values (x,y,z,vx,vy,vz,fx,fy,fz) are
|
||||
self-explanatory. Note that other atom attributes can be used as
|
||||
inputs to this fix by using the <a class="reference internal" href="compute_property_atom.html"><em>compute property/atom</em></a> command and then specifying
|
||||
an input value from that compute.</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
|
||||
inputs to this fix by using the <A HREF = "compute_property_atom.html">compute
|
||||
property/atom</A> command and then specifying
|
||||
an input value from that compute.
|
||||
</P>
|
||||
<P>If a value begins with "c_", a compute ID must follow which has been
|
||||
previously defined in the input script. Computes can generate
|
||||
per-atom or local quantities. See the individual
|
||||
<a class="reference internal" href="compute.html"><em>compute</em></a> doc page for details. If no bracketed integer
|
||||
<A HREF = "compute.html">compute</A> doc page for details. If no bracketed integer
|
||||
is appended, the vector calculated by the compute is used. If a
|
||||
bracketed integer is appended, the Ith column of the 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"><em>add them to LAMMPS</em></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
|
||||
compute styles and <A HREF = "Section_modify.html">add them to LAMMPS</A>.
|
||||
</P>
|
||||
<P>If a value begins with "f_", a fix ID must follow which has been
|
||||
previously defined in the input script. Fixes can generate per-atom
|
||||
or local quantities. See the individual <a class="reference internal" href="fix.html"><em>fix</em></a> doc page for
|
||||
or local quantities. See the individual <A HREF = "fix.html">fix</A> doc page for
|
||||
details. Note that some fixes only produce their values on certain
|
||||
timesteps, which must be compatible with when compute reduce
|
||||
references the values, else an error results. If no bracketed integer
|
||||
is appended, the vector calculated by the fix is used. If a bracketed
|
||||
integer is appended, the Ith column of the array calculated by the fix
|
||||
is used. Users can also write code for their own fix style and <a class="reference internal" href="Section_modify.html"><em>add them to LAMMPS</em></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
|
||||
is used. Users can also write code for their own fix style and <A HREF = "Section_modify.html">add
|
||||
them to LAMMPS</A>.
|
||||
</P>
|
||||
<P>If a value begins with "v_", a variable name must follow which has
|
||||
been previously defined in the input script. It must be an
|
||||
<a class="reference internal" href="variable.html"><em>atom-style variable</em></a>. Atom-style variables can
|
||||
<A HREF = "variable.html">atom-style variable</A>. Atom-style variables 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
|
||||
reduce.</p>
|
||||
<hr class="docutils" />
|
||||
<p>If the <em>replace</em> keyword is used, two indices <em>vec1</em> and <em>vec2</em> are
|
||||
reduce.
|
||||
</P>
|
||||
<HR>
|
||||
|
||||
<P>If the <I>replace</I> keyword is used, two indices <I>vec1</I> and <I>vec2</I> are
|
||||
specified, where each index ranges from 1 to the # of input values.
|
||||
The replace keyword can only be used if the <em>mode</em> is <em>min</em> or <em>max</em>.
|
||||
It works as follows. A min/max is computed as usual on the <em>vec2</em>
|
||||
input vector. The index N of that value within <em>vec2</em> is also stored.
|
||||
Then, instead of performing a min/max on the <em>vec1</em> input vector, the
|
||||
stored index is used to select the Nth element of the <em>vec1</em> vector.</p>
|
||||
<p>Thus, for example, if you wish to use this compute to find the bond
|
||||
with maximum stretch, you can do it as follows:</p>
|
||||
<div class="highlight-python"><div class="highlight"><pre>compute 1 all property/local batom1 batom2
|
||||
compute 2 all bond/local dist
|
||||
compute 3 all reduce max c_1[1] c_1[2] c_2 replace 1 3 replace 2 3
|
||||
thermo_style custom step temp c_3[1] c_3[2] c_3[3]
|
||||
</pre></div>
|
||||
</div>
|
||||
<p>The first two input values in the compute reduce command are vectors
|
||||
with the IDs of the 2 atoms in each bond, using the <a class="reference internal" href="compute_property_local.html"><em>compute property/local</em></a> command. The last input
|
||||
value is bond distance, using the <a class="reference internal" href="compute_bond_local.html"><em>compute bond/local</em></a> command. Instead of taking the
|
||||
The replace keyword can only be used if the <I>mode</I> is <I>min</I> or <I>max</I>.
|
||||
It works as follows. A min/max is computed as usual on the <I>vec2</I>
|
||||
input vector. The index N of that value within <I>vec2</I> is also stored.
|
||||
Then, instead of performing a min/max on the <I>vec1</I> input vector, the
|
||||
stored index is used to select the Nth element of the <I>vec1</I> vector.
|
||||
</P>
|
||||
<P>Thus, for example, if you wish to use this compute to find the bond
|
||||
with maximum stretch, you can do it as follows:
|
||||
</P>
|
||||
<PRE>compute 1 all property/local batom1 batom2
|
||||
compute 2 all bond/local dist
|
||||
compute 3 all reduce max c_1[1] c_1[2] c_2 replace 1 3 replace 2 3
|
||||
thermo_style custom step temp c_3[1] c_3[2] c_3[3]
|
||||
</PRE>
|
||||
<P>The first two input values in the compute reduce command are vectors
|
||||
with the IDs of the 2 atoms in each bond, using the <A HREF = "compute_property_local.html">compute
|
||||
property/local</A> command. The last input
|
||||
value is bond distance, using the <A HREF = "compute_bond_local.html">compute
|
||||
bond/local</A> command. Instead of taking the
|
||||
max of the two atom ID vectors, which does not yield useful
|
||||
information in this context, the <em>replace</em> keywords will extract the
|
||||
information in this context, the <I>replace</I> keywords will extract the
|
||||
atom IDs for the two atoms in the bond of maximum stretch. These atom
|
||||
IDs and the bond stretch will be printed with thermodynamic output.</p>
|
||||
<hr class="docutils" />
|
||||
<p>If a single input is specified this compute produces a global scalar
|
||||
IDs and the bond stretch will be printed with thermodynamic output.
|
||||
</P>
|
||||
<HR>
|
||||
|
||||
<P>If a single input is specified this compute produces a global scalar
|
||||
value. If multiple inputs are specified, this compute produces a
|
||||
global vector of values, the length of which is equal to the number of
|
||||
inputs specified.</p>
|
||||
<p>As discussed below, for the <em>sum</em> and <em>sumsq</em> modes, the value(s)
|
||||
produced by this compute are all “extensive”, meaning their value
|
||||
inputs specified.
|
||||
</P>
|
||||
<P>As discussed below, for the <I>sum</I> and <I>sumsq</I> modes, the value(s)
|
||||
produced by this compute are all "extensive", meaning their value
|
||||
scales linearly with the number of atoms involved. If normalized
|
||||
values are desired, this compute can be accessed by the <a class="reference internal" href="thermo_style.html"><em>thermo_style custom</em></a> command with <a class="reference internal" href="thermo_modify.html"><em>thermo_modify norm yes</em></a> set as an option. Or it can be accessed by a
|
||||
<a class="reference internal" href="variable.html"><em>variable</em></a> that divides by the appropriate atom count.</p>
|
||||
<hr class="docutils" />
|
||||
<p><strong>Output info:</strong></p>
|
||||
<p>This compute calculates a global scalar if a single input value is
|
||||
values are desired, this compute can be accessed by the <A HREF = "thermo_style.html">thermo_style
|
||||
custom</A> command with <A HREF = "thermo_modify.html">thermo_modify norm
|
||||
yes</A> set as an option. Or it can be accessed by a
|
||||
<A HREF = "variable.html">variable</A> that divides by the appropriate atom count.
|
||||
</P>
|
||||
<HR>
|
||||
|
||||
<P><B>Output info:</B>
|
||||
</P>
|
||||
<P>This compute calculates a global scalar if a single input value is
|
||||
specified or a global vector of length N where N is the number of
|
||||
inputs, and which can be accessed by indices 1 to N. These values can
|
||||
be used by any command that uses global scalar or vector values from a
|
||||
compute as input. See <a class="reference internal" href="Section_howto.html#howto-15"><span>Section_howto 15</span></a>
|
||||
for an overview of LAMMPS output options.</p>
|
||||
<p>All the scalar or vector values calculated by this compute are
|
||||
“intensive”, except when the <em>sum</em> or <em>sumsq</em> modes are used on
|
||||
compute as input. See <A HREF = "Section_howto.html#howto_15">Section_howto 15</A>
|
||||
for an overview of LAMMPS output options.
|
||||
</P>
|
||||
<P>All the scalar or vector values calculated by this compute are
|
||||
"intensive", except when the <I>sum</I> or <I>sumsq</I> modes are used on
|
||||
per-atom or local vectors, in which case the calculated values are
|
||||
“extensive”.</p>
|
||||
<p>The scalar or vector values will be in whatever <a class="reference internal" href="units.html"><em>units</em></a> the
|
||||
quantities being reduced are in.</p>
|
||||
</div>
|
||||
<div class="section" id="restrictions">
|
||||
<h2>Restrictions<a class="headerlink" href="#restrictions" title="Permalink to this headline">¶</a></h2>
|
||||
<blockquote>
|
||||
<div>none</div></blockquote>
|
||||
</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="compute.html"><em>compute</em></a>, <a class="reference internal" href="fix.html"><em>fix</em></a>, <a class="reference internal" href="variable.html"><em>variable</em></a></p>
|
||||
<p><strong>Default:</strong> none</p>
|
||||
</div>
|
||||
</div>
|
||||
|
||||
|
||||
</div>
|
||||
</div>
|
||||
<footer>
|
||||
|
||||
|
||||
<hr/>
|
||||
|
||||
<div role="contentinfo">
|
||||
<p>
|
||||
© Copyright .
|
||||
</p>
|
||||
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|
||||
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|
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|
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|
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|
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|
||||
</section>
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||||
|
||||
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|
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|
||||
|
||||
|
||||
|
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|
||||
<script type="text/javascript">
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|
||||
</body>
|
||||
</html>
|
||||
"extensive".
|
||||
</P>
|
||||
<P>The scalar or vector values will be in whatever <A HREF = "units.html">units</A> the
|
||||
quantities being reduced are in.
|
||||
</P>
|
||||
<P><B>Restrictions:</B> none
|
||||
</P>
|
||||
<P><B>Related commands:</B>
|
||||
</P>
|
||||
<P><A HREF = "compute.html">compute</A>, <A HREF = "fix.html">fix</A>, <A HREF = "variable.html">variable</A>
|
||||
</P>
|
||||
<P><B>Default:</B> none
|
||||
</P>
|
||||
</HTML>
|
||||
|
||||
Reference in New Issue
Block a user