forked from lijiext/lammps
486 lines
26 KiB
HTML
486 lines
26 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 ave/histo 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 ave/histo 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-ave-histo-command">
|
|
<span id="index-0"></span><h1>fix ave/histo command<a class="headerlink" href="#fix-ave-histo-command" title="Permalink to this headline">¶</a></h1>
|
|
</div>
|
|
<div class="section" id="fix-ave-histo-weight-command">
|
|
<h1>fix ave/histo/weight command<a class="headerlink" href="#fix-ave-histo-weight-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 style Nevery Nrepeat Nfreq lo hi Nbin value1 value2 ... keyword args ...
|
|
</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>style = <em>ave/histo</em> or <em>ave/histo/weight</em> = style name of this fix command</li>
|
|
<li>Nevery = use input values every this many timesteps</li>
|
|
<li>Nrepeat = # of times to use input values for calculating histogram</li>
|
|
<li>Nfreq = calculate histogram every this many timesteps</li>
|
|
<li>lo,hi = lo/hi bounds within which to histogram</li>
|
|
<li>Nbin = # of histogram bins</li>
|
|
<li>one or more input values can be listed</li>
|
|
<li>value = x, y, z, vx, vy, vz, fx, fy, fz, c_ID, c_ID[N], f_ID, f_ID[N], v_name</li>
|
|
</ul>
|
|
<div class="highlight-python"><div class="highlight"><pre>x,y,z,vx,vy,vz,fx,fy,fz = atom attribute (position, velocity, force component)
|
|
c_ID = scalar or vector calculated by a compute with ID
|
|
c_ID[I] = Ith component of vector or Ith column of array calculated by a compute with ID
|
|
f_ID = scalar or vector calculated by a fix with ID
|
|
f_ID[I] = Ith component of vector or Ith column of array calculated by a fix with ID
|
|
v_name = value(s) calculated by an equal-style or atom-style variable with name
|
|
</pre></div>
|
|
</div>
|
|
<ul class="simple">
|
|
<li>zero or more keyword/arg pairs may be appended</li>
|
|
<li>keyword = <em>mode</em> or <em>file</em> or <em>ave</em> or <em>start</em> or <em>beyond</em> or <em>overwrite</em> or <em>title1</em> or <em>title2</em> or <em>title3</em></li>
|
|
</ul>
|
|
<pre class="literal-block">
|
|
<em>mode</em> arg = <em>scalar</em> or <em>vector</em>
|
|
scalar = all input values are scalars
|
|
vector = all input values are vectors
|
|
<em>file</em> arg = filename
|
|
filename = name of file to output histogram(s) to
|
|
<em>ave</em> args = <em>one</em> or <em>running</em> or <em>window</em>
|
|
one = output a new average value every Nfreq steps
|
|
running = output cumulative average of all previous Nfreq steps
|
|
window M = output average of M most recent Nfreq steps
|
|
<em>start</em> args = Nstart
|
|
Nstart = start averaging on this timestep
|
|
<em>beyond</em> arg = <em>ignore</em> or <em>end</em> or <em>extra</em>
|
|
ignore = ignore values outside histogram lo/hi bounds
|
|
end = count values outside histogram lo/hi bounds in end bins
|
|
extra = create 2 extra bins for value outside histogram lo/hi bounds
|
|
<em>overwrite</em> arg = none = overwrite output file with only latest output
|
|
<em>title1</em> arg = string
|
|
string = text to print as 1st line of output file
|
|
<em>title2</em> arg = string
|
|
string = text to print as 2nd line of output file
|
|
<em>title3</em> arg = string
|
|
string = text to print as 3rd line of output file, only for vector mode
|
|
</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 all ave/histo 100 5 1000 0.5 1.5 50 c_myTemp file temp.histo ave running
|
|
fix 1 all ave/histo 100 5 1000 -5 5 100 c_thermo_press[2] c_thermo_press[3] title1 "My output values"
|
|
fix 1 all ave/histo 1 100 1000 -2.0 2.0 18 vx vy vz mode vector ave running beyond extra
|
|
fix 1 all ave/histo/weight 1 1 1 10 100 2000 c_XRD[1] c_XRD[2]
|
|
</pre></div>
|
|
</div>
|
|
</div>
|
|
<div class="section" id="description">
|
|
<h2>Description<a class="headerlink" href="#description" title="Permalink to this headline">¶</a></h2>
|
|
<p>Use one or more values as inputs every few timesteps, histogram them,
|
|
and average the histogram over longer timescales. The resulting
|
|
histogram can be used by other <a class="reference internal" href="Section_howto.html#howto-15"><span>output commands</span></a>, and can also be written to a
|
|
file. The fix ave/histo/weight command has identical syntax to fix
|
|
ave/histo, except that exactly two values must be specified. See
|
|
details below.</p>
|
|
<p>The group specified with this command is ignored for global and local
|
|
input values. For per-atom input values, only atoms in the group
|
|
contribute to the histogram. Note that regardless of the specified
|
|
group, specified values may represent calculations performed by
|
|
computes and fixes which store their own “group” definition.</p>
|
|
<p>A histogram is simply a count of the number of values that fall within
|
|
a histogram bin. <em>Nbins</em> are defined, with even spacing between <em>lo</em>
|
|
and <em>hi</em>. Values that fall outside the lo/hi bounds can be treated in
|
|
different ways; see the discussion of the <em>beyond</em> keyword below.</p>
|
|
<p>Each input value 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 equal-style or atom-style
|
|
<a class="reference internal" href="variable.html"><em>variable</em></a>. The set of input values can be either all
|
|
global, all per-atom, or all local quantities. Inputs of different
|
|
kinds (e.g. global and per-atom) cannot be mixed. Atom attributes are
|
|
per-atom vector values. See the doc page for individual “compute” and
|
|
“fix” commands to see what kinds of quantities they generate.</p>
|
|
<p>The input values must either be all scalars or all vectors (or
|
|
arrays), depending on the setting of the <em>mode</em> keyword.</p>
|
|
<p>Note that the output of this command is a single histogram for all
|
|
input values combined together, not one histogram per input value.
|
|
See below for details on the format of the output of this fix.</p>
|
|
<p>If <em>mode</em> = vector, then the input values may either be vectors or
|
|
arrays. If a global array is listed, then it is the same as if the
|
|
individual columns of the array had been listed one by one.
|
|
E.g. these 2 fix ave/histo commands are equivalent, since the <a class="reference internal" href="compute_com_chunk.html"><em>compute com/chunk</em></a> command creates a global array
|
|
with 3 columns:</p>
|
|
<div class="highlight-python"><div class="highlight"><pre>compute myCOM all com/chunk
|
|
fix 1 all ave/histo 100 1 100 c_myCOM file tmp1.com mode vector
|
|
fix 2 all ave/histo 100 1 100 c_myCOM[1] c_myCOM[2] c_myCOM[3] file tmp2.com mode vector
|
|
</pre></div>
|
|
</div>
|
|
<p>If the fix ave/histo/weight command is used, exactly two values must
|
|
be specified. If the values are vectors, they must be the same
|
|
length. The first value (a scalar or vector) is what is histogrammed
|
|
into bins, in the same manner the fix ave/histo command operates. The
|
|
second value (a scalar or vector) is used as a “weight”. This means
|
|
that instead of each value tallying a “1” to its bin, the
|
|
corresponding weight is tallied. E.g. the Nth entry in the first
|
|
vector tallies the Nth entry (weight) in the second vector.</p>
|
|
<hr class="docutils" />
|
|
<p>The <em>Nevery</em>, <em>Nrepeat</em>, and <em>Nfreq</em> arguments specify on what
|
|
timesteps the input values will be used in order to contribute to the
|
|
histogram. The final histogram is generated on timesteps that are
|
|
multiple of <em>Nfreq</em>. It is averaged over <em>Nrepeat</em> histograms,
|
|
computed in the preceding portion of the simulation every <em>Nevery</em>
|
|
timesteps. <em>Nfreq</em> must be a multiple of <em>Nevery</em> and <em>Nevery</em> must
|
|
be non-zero even if <em>Nrepeat</em> is 1. Also, the timesteps contributing
|
|
to the histogram cannot overlap, i.e. Nfreq > (Nrepeat-1)*Nevery is
|
|
required.</p>
|
|
<p>For example, if Nevery=2, Nrepeat=6, and Nfreq=100, then input values
|
|
on timesteps 90,92,94,96,98,100 will be used to compute the final
|
|
histogram 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 of the histogram is done; a histogram is
|
|
simply generated on timesteps 100,200,etc.</p>
|
|
<hr class="docutils" />
|
|
<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
|
|
previously defined in the input script. If <em>mode</em> = scalar, then if
|
|
no bracketed term is appended, the global scalar calculated by the
|
|
compute is used. If a bracketed term is appended, the Ith element of
|
|
the global vector calculated by the compute is used. If <em>mode</em> =
|
|
vector, then if no bracketed term is appended, the global or per-atom
|
|
or local vector calculated by the compute is used. Or if the compute
|
|
calculates an array, all of the columns of the array are used as if
|
|
they had been specified as individual vectors (see description above).
|
|
If a bracketed term is appended, the Ith column of the global or
|
|
per-atom or local array calculated by the compute is used.</p>
|
|
<p>Note that there is a <a class="reference internal" href="compute_reduce.html"><em>compute reduce</em></a> command
|
|
which can sum per-atom quantities into a global scalar or vector which
|
|
can thus be accessed by fix ave/histo. Or it can be a compute defined
|
|
not in your input script, but by <a class="reference internal" href="thermo_style.html"><em>thermodynamic output</em></a> or other fixes such as <a class="reference internal" href="fix_nh.html"><em>fix nvt</em></a> or <a class="reference internal" href="fix_temp_rescale.html"><em>fix temp/rescale</em></a>. See
|
|
the doc pages for these commands which give the IDs of these computes.
|
|
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
|
|
previously defined in the input script. If <em>mode</em> = scalar, then if
|
|
no bracketed term is appended, the global scalar calculated by the fix
|
|
is used. If a bracketed term is appended, the Ith element of the
|
|
global vector calculated by the fix is used. If <em>mode</em> = vector, then
|
|
if no bracketed term is appended, the global or per-atom or local
|
|
vector calculated by the fix is used. Or if the fix calculates an
|
|
array, all of the columns of the array are used as if they had been
|
|
specified as individual vectors (see description above). If a
|
|
bracketed term is appended, the Ith column of the global or per-atom
|
|
or local array calculated by the fix is used.</p>
|
|
<p>Note that some fixes only produce their values on certain timesteps,
|
|
which must be compatible with <em>Nevery</em>, else an error will result.
|
|
Users can also write code for their own fix 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="#id5"><span class="problematic" id="id6">v_</span></a>”, a variable name must follow which has
|
|
been previously defined in the input script. If <em>mode</em> = scalar, then
|
|
only equal-style variables can be used, which produce a global value.
|
|
If <em>mode</em> = vector, then only atom-style variables can be used, which
|
|
produce a per-atom vector. See the <a class="reference internal" href="variable.html"><em>variable</em></a> command
|
|
for details. Note that variables of style <em>equal</em> and <em>atom</em> define a
|
|
formula which can reference individual atom properties or
|
|
thermodynamic keywords, or they can invoke other computes, fixes, or
|
|
variables when they are evaluated, so this is a very general means of
|
|
specifying quantities to histogram.</p>
|
|
<hr class="docutils" />
|
|
<p>Additional optional keywords also affect the operation of this fix.</p>
|
|
<p>If the <em>mode</em> keyword is set to <em>scalar</em>, then all input values must
|
|
be global scalars, or elements of global vectors. If the <em>mode</em>
|
|
keyword is set to <em>vector</em>, then all input values must be global or
|
|
per-atom or local vectors, or columns of global or per-atom or local
|
|
arrays.</p>
|
|
<p>The <em>beyond</em> keyword determines how input values that fall outside the
|
|
<em>lo</em> to <em>hi</em> bounds are treated. Values such that <em>lo</em> <= value <=
|
|
<em>hi</em> are assigned to one bin. Values on a bin boundary are assigned
|
|
to the lower of the 2 bins. If <em>beyond</em> is set to <em>ignore</em> then
|
|
values < <em>lo</em> and values > <em>hi</em> are ignored, i.e. they are not binned.
|
|
If <em>beyond</em> is set to <em>end</em> then values < <em>lo</em> are counted in the
|
|
first bin and values > <em>hi</em> are counted in the last bin. If <em>beyond</em>
|
|
is set to <em>extend</em> then two extra bins are created, so that there are
|
|
Nbins+2 total bins. Values < <em>lo</em> are counted in the first bin and
|
|
values > <em>hi</em> are counted in the last bin (Nbins+1). Values between
|
|
<em>lo</em> and <em>hi</em> (inclusive) are counted in bins 2 thru Nbins+1. The
|
|
“coordinate” stored and printed for these two extra bins is <em>lo</em> and
|
|
<em>hi</em>.</p>
|
|
<p>The <em>ave</em> keyword determines how the histogram produced every <em>Nfreq</em>
|
|
steps are averaged with histograms 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 histograms 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 histograms produced on
|
|
timesteps that are multiples of <em>Nfreq</em> are summed and averaged in a
|
|
cumulative sense before being output. Each bin value in the histogram
|
|
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"><em>unfix</em></a> command, or by re-defining the fix by
|
|
re-specifying it.</p>
|
|
<p>If the <em>ave</em> setting is <em>window</em>, then the histograms produced on
|
|
timesteps that are multiples of <em>Nfreq</em> are summed within a moving
|
|
“window” of time, so that the last M histograms are used to produce
|
|
the output. E.g. if M = 3 and Nfreq = 1000, then the output on step
|
|
10000 will be the combined histogram of the individual histograms on
|
|
steps 8000,9000,10000. Outputs on early steps will be sums over less
|
|
than M histograms if they are not available.</p>
|
|
<p>The <em>start</em> keyword specifies what timestep histogramming will begin
|
|
on. The default is step 0. Often input values can be 0.0 at time 0,
|
|
so setting <em>start</em> to a larger value can avoid including a 0.0 in
|
|
a running or windowed histogram.</p>
|
|
<p>The <em>file</em> keyword allows a filename to be specified. Every <em>Nfreq</em>
|
|
steps, one histogram is written to the file. This includes a leading
|
|
line that contains the timestep, number of bins, the total count of
|
|
values contributing to the histogram, the count of values that were
|
|
not histogrammed (see the <em>beyond</em> keyword), the minimum value
|
|
encountered, and the maximum value encountered. The min/max values
|
|
include values that were not histogrammed. Following the leading
|
|
line, one line per bin is written into the file. Each line contains
|
|
the bin #, the coordinate for the center of the bin (between <em>lo</em> and
|
|
<em>hi</em>), the count of values in the bin, and the normalized count. The
|
|
normalized count is the bin count divided by the total count (not
|
|
including values not histogrammed), so that the normalized values sum
|
|
to 1.0 across all bins.</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-python"><div class="highlight"><pre><span class="c"># Histogram for fix ID</span>
|
|
<span class="c"># TimeStep Number-of-bins Total-counts Missing-counts Min-value Max-value</span>
|
|
<span class="c"># Bin Coord Count Count/Total</span>
|
|
</pre></div>
|
|
</div>
|
|
<p>In the first line, ID is replaced with the fix-ID. The second line
|
|
describes the six values that are printed at the first of each section
|
|
of output. The third describes the 4 values printed for each bin in
|
|
the histogram.</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 produces a global vector and global array which can be
|
|
accessed by various <a class="reference internal" href="Section_howto.html#howto-15"><span>output commands</span></a>.
|
|
The values can only be accessed on timesteps that are multiples of
|
|
<em>Nfreq</em> since that is when a histogram is generated. The global
|
|
vector has 4 values:</p>
|
|
<ul class="simple">
|
|
<li>1 = total counts in the histogram</li>
|
|
<li>2 = values that were not histogrammed (see <em>beyond</em> keyword)</li>
|
|
<li>3 = min value of all input values, including ones not histogrammed</li>
|
|
<li>4 = max value of all input values, including ones not histogrammed</li>
|
|
</ul>
|
|
<p>The global array has # of rows = Nbins and # of columns = 3. The
|
|
first column has the bin coordinate, the 2nd column has the count of
|
|
values in that histogram bin, and the 3rd column has the bin count
|
|
divided by the total count (not including missing counts), so that the
|
|
values in the 3rd column sum to 1.0.</p>
|
|
<p>The vector and array values calculated by this fix are all treated as
|
|
“intensive”. If this is not the case, e.g. due to histogramming
|
|
per-atom input values, then you will need to account for that when
|
|
interpreting the values produced by this fix.</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"><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>
|
|
<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_ave_atom.html"><em>fix ave/atom</em></a>, <a class="reference internal" href="fix_ave_spatial.html"><em>fix ave/spatial</em></a>, <a class="reference internal" href="fix_ave_time.html"><em>fix ave/time</em></a>,
|
|
<a class="reference internal" href="variable.html"><em>variable</em></a>, <a class="reference internal" href="fix_ave_correlate.html"><em>fix ave/correlate</em></a>,</p>
|
|
<p><strong>Default:</strong> none</p>
|
|
<p>The option defaults are mode = scalar, ave = one, start = 0, no file
|
|
output, beyond = ignore, and title 1,2,3 = strings as described above.</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> |