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<div class="section" id="fix-saed-vtk-command">
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<span id="index-0"></span><h1>fix saed/vtk command<a class="headerlink" href="#fix-saed-vtk-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>fix ID group-ID saed/vtk Nevery Nrepeat Nfreak c_ID attribute args ... 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="fix.html"><em>fix</em></a> command</li>
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<li>saed/vtk = 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>c_ID = saed compute ID</li>
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</ul>
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<pre class="literal-block">
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keyword = <em>file</em> or <em>ave</em> or <em>start</em> or <em>file</em> or <em>overwrite</em>:l
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<em>ave</em> args = <em>one</em> or <em>running</em> or <em>window M</em>
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<HR>
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<H3>fix saed/vtk command
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</H3>
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<P><B>Syntax:</B>
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</P>
|
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<PRE>fix ID group-ID saed/vtk Nevery Nrepeat Nfreak c_ID attribute args ... keyword args ...
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</PRE>
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<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
|
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|
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<LI>saed/vtk = style name of this fix command
|
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|
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<LI>Nevery = use input values every this many timesteps
|
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|
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<LI>Nrepeat = # of times to use input values for calculating averages
|
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|
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<LI>Nfreq = calculate averages every this many timesteps
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<LI>c_ID = saed compute ID
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|
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<PRE>keyword = <I>file</I> or <I>ave</I> or <I>start</I> or <I>file</I> or <I>overwrite</I>:l
|
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<I>ave</I> args = <I>one</I> or <I>running</I> or <I>window M</I>
|
||||
one = output a 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>start</em> args = Nstart
|
||||
<I>start</I> args = Nstart
|
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Nstart = start averaging on this timestep
|
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<em>file</em> arg = filename
|
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filename = name of file to output time averages to
|
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<em>overwrite</em> arg = none = overwrite output file with only latest output
|
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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 saed 0.0251 Al O Kmax 1.70 Zone 0 0 1 dR_Ewald 0.01 c 0.5 0.5 0.5
|
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compute 2 all saed 0.0251 Ni Kmax 1.70 Zone 0 0 0 c 0.05 0.05 0.05 manual echo
|
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</pre></div>
|
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</div>
|
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<div class="highlight-python"><div class="highlight"><pre>fix saed/vtk 1 1 1 c_1 file Al2O3_001.saed
|
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fix saed/vtk 1 1 1 c_2 file Ni_000.saed
|
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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">
|
||||
<h2>Description<a class="headerlink" href="#description" title="Permalink to this headline">¶</a></h2>
|
||||
<p>Time average computed intensities from <a class="reference external" href="compute_saed.txt">compute_saed</a> and
|
||||
write output to a file in the 3rd generation vtk image data format for
|
||||
visualization directly in parallelized visualization software packages
|
||||
like ParaView and VisIt. Note that if no time averaging is done, this
|
||||
command can be used as a convenient way to simply output diffraction
|
||||
intensities at a single snapshot.</p>
|
||||
<p>To produce output in the image data vtk format ghost data is added
|
||||
outside the <em>Kmax</em> range assigned in the compute saed. The ghost data is
|
||||
assigned a value of -1 and can be removed setting a minimum isovolume
|
||||
of 0 within the vizualiziton software. SAED images can be created by
|
||||
visualizing a spherical slice of the data that is centered at
|
||||
R_Ewald*[h k l]/norm([h k l]), where R_Ewald=1/lambda.</p>
|
||||
<p>The group specified within this command is ignored. However, note that
|
||||
<I>file</I> arg = filename
|
||||
filename = name of file to output time averages to
|
||||
<I>overwrite</I> arg = none = overwrite output file with only latest output
|
||||
</PRE>
|
||||
|
||||
</UL>
|
||||
<P><B>Examples:</B>
|
||||
</P>
|
||||
<PRE>compute 1 all saed 0.0251 Al O Kmax 1.70 Zone 0 0 1 dR_Ewald 0.01 c 0.5 0.5 0.5
|
||||
compute 2 all saed 0.0251 Ni Kmax 1.70 Zone 0 0 0 c 0.05 0.05 0.05 manual echo
|
||||
</PRE>
|
||||
<PRE>fix saed/vtk 1 1 1 c_1 file Al2O3_001.saed
|
||||
fix saed/vtk 1 1 1 c_2 file Ni_000.saed
|
||||
</PRE>
|
||||
<P><B>Description:</B>
|
||||
</P>
|
||||
<P>Time average computed intensities from <A HREF = "compute_saed.txt">compute_saed</A> and
|
||||
write output to a file in the 3rd generation vtk image data format for
|
||||
visualization directly in parallelized visualization software packages
|
||||
like ParaView and VisIt. Note that if no time averaging is done, this
|
||||
command can be used as a convenient way to simply output diffraction
|
||||
intensities at a single snapshot.
|
||||
</P>
|
||||
<P>To produce output in the image data vtk format ghost data is added
|
||||
outside the <I>Kmax</I> range assigned in the compute saed. The ghost data is
|
||||
assigned a value of -1 and can be removed setting a minimum isovolume
|
||||
of 0 within the vizualiziton software. SAED images can be created by
|
||||
visualizing a spherical slice of the data that is centered at
|
||||
R_Ewald*[h k l]/norm([h k l]), where R_Ewald=1/lambda.
|
||||
</P>
|
||||
<P>The group specified within this command is ignored. However, note that
|
||||
specified values may represent calculations performed by saed computes
|
||||
which store their own “group” definitions.</p>
|
||||
<p>Fix saed/vtk is designed to work only with <a class="reference external" href="compute_saed.txt">compute_saed</a>
|
||||
values, e.g.</p>
|
||||
<div class="highlight-python"><div class="highlight"><pre>compute 3 top saed 0.0251 Al O
|
||||
fix saed/vtk 1 1 1 c_3 file Al2O3_001.saed
|
||||
</pre></div>
|
||||
</div>
|
||||
<hr class="docutils" />
|
||||
<p>The <em>Nevery</em>, <em>Nrepeat</em>, and <em>Nfreq</em> arguments specify on what
|
||||
which store their own "group" definitions.
|
||||
</P>
|
||||
<P>Fix saed/vtk is designed to work only with <A HREF = "compute_saed.txt">compute_saed</A>
|
||||
values, e.g.
|
||||
</P>
|
||||
<PRE>compute 3 top saed 0.0251 Al O
|
||||
fix saed/vtk 1 1 1 c_3 file Al2O3_001.saed
|
||||
</PRE>
|
||||
<HR>
|
||||
|
||||
<P>The <I>Nevery</I>, <I>Nrepeat</I>, and <I>Nfreq</I> arguments specify on what
|
||||
timesteps the input values will be used in order to contribute to the
|
||||
average. The final averaged quantities are generated on timesteps
|
||||
that are a multiple of <em>Nfreq</em>. The average is over <em>Nrepeat</em>
|
||||
that are a multiple of <I>Nfreq</I>. The average is over <I>Nrepeat</I>
|
||||
quantities, 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 average value cannot overlap, i.e. Nfreq >
|
||||
(Nrepeat-1)*Nevery is required.</p>
|
||||
<p>For example, if Nevery=2, Nrepeat=6, and Nfreq=100, then values on
|
||||
<I>Nevery</I> timesteps. <I>Nfreq</I> must be a multiple of <I>Nevery</I> and
|
||||
<I>Nevery</I> must be non-zero even if <I>Nrepeat</I> is 1. Also, the timesteps
|
||||
contributing to the average value cannot overlap, i.e. Nfreq >
|
||||
(Nrepeat-1)*Nevery is required.
|
||||
</P>
|
||||
<P>For example, if Nevery=2, Nrepeat=6, and Nfreq=100, then values on
|
||||
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>The output for fix ave/time/saed is a file writen with the 3rd generation
|
||||
vtk image data formatting. The filename assigned by the <em>file</em> keyword is
|
||||
appended with _N.vtk where N is an index (0,1,2...) to account for multiple
|
||||
diffraction intensity outputs.</p>
|
||||
<p>By default the header contains the following information (with example data):</p>
|
||||
<div class="highlight-python"><div class="highlight"><pre># vtk DataFile Version 3.0 c_SAED
|
||||
100,200,etc.
|
||||
</P>
|
||||
<HR>
|
||||
|
||||
<P>The output for fix ave/time/saed is a file writen with the 3rd generation
|
||||
vtk image data formatting. The filename assigned by the <I>file</I> keyword is
|
||||
appended with _N.vtk where N is an index (0,1,2...) to account for multiple
|
||||
diffraction intensity outputs.
|
||||
</P>
|
||||
<P>By default the header contains the following information (with example data):
|
||||
</P>
|
||||
<PRE># vtk DataFile Version 3.0 c_SAED
|
||||
Image data set
|
||||
ASCII
|
||||
DATASET STRUCTURED_POINTS
|
||||
DIMENSIONS 337 219 209
|
||||
ASPECT_RATIO 0.00507953 0.00785161 0.00821458
|
||||
ORIGIN -0.853361 -0.855826 -0.854316
|
||||
ORIGIN -0.853361 -0.855826 -0.854316
|
||||
POINT_DATA 15424827
|
||||
SCALARS intensity float
|
||||
LOOKUP_TABLE default
|
||||
...data
|
||||
</pre></div>
|
||||
</div>
|
||||
<p>In this example, kspace is sampled across a 337 x 219 x 209 point mesh
|
||||
where the mesh spacing is approximately 0.005, 0.007, and 0.008
|
||||
inv(length) units in the k1, k2, and k3 directions, respectively.
|
||||
...data
|
||||
</PRE>
|
||||
<P>In this example, kspace is sampled across a 337 x 219 x 209 point mesh
|
||||
where the mesh spacing is approximately 0.005, 0.007, and 0.008
|
||||
inv(length) units in the k1, k2, and k3 directions, respectively.
|
||||
The data is shifted by -0.85, -0.85, -0.85 inv(length) units so that
|
||||
the origin will lie at 0, 0, 0. Here, 15,424,827 kspace points are
|
||||
sampled in total.</p>
|
||||
<hr class="docutils" />
|
||||
<p>Additional optional keywords also affect the operation of this fix.</p>
|
||||
<p>The <em>ave</em> keyword determines how the values produced every <em>Nfreq</em>
|
||||
sampled in total.
|
||||
</P>
|
||||
<HR>
|
||||
|
||||
<P>Additional optional keywords also affect the operation of this fix.
|
||||
</P>
|
||||
<P>The <I>ave</I> keyword determines how the values produced every <I>Nfreq</I>
|
||||
steps are averaged with 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 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 values produced on
|
||||
timesteps that are multiples of <em>Nfreq</em> are summed and averaged in a
|
||||
multiples of <I>Nfreq</I>, before they are accessed by another output
|
||||
command or written to a file.
|
||||
</P>
|
||||
<P>If the <I>ave</I> setting is <I>one</I>, then the values produced on timesteps
|
||||
that are multiples of <I>Nfreq</I> are independent of each other; they are
|
||||
output as-is without further averaging.
|
||||
</P>
|
||||
<P>If the <I>ave</I> setting is <I>running</I>, then the values produced on
|
||||
timesteps that are multiples of <I>Nfreq</I> are summed and averaged in a
|
||||
cumulative sense before being output. Each output value is thus the
|
||||
average of the value produced on that timestep with all preceding
|
||||
values. 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 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 are used to
|
||||
only be restarted by deleting the fix via the <A HREF = "unfix.html">unfix</A>
|
||||
command, or by re-defining the fix by re-specifying it.
|
||||
</P>
|
||||
<P>If the <I>ave</I> setting is <I>window</I>, then the values produced on
|
||||
timesteps that are multiples of <I>Nfreq</I> are summed and averaged within
|
||||
a moving "window" of time, so that the last M values 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 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>start</em> keyword specifies what timestep averaging will begin on.
|
||||
values if they are not available.
|
||||
</P>
|
||||
<P>The <I>start</I> keyword specifies what timestep averaging 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 average.</p>
|
||||
<p>The <em>file</em> keyword allows a filename to be specified. Every <em>Nfreq</em>
|
||||
steps, the vector of saed intensity data is written to a new file using
|
||||
the 3rd generation vtk format. The base of each file is assigned by
|
||||
the <em>file</em> keyword and this string is appended with _N.vtk where N is
|
||||
setting <I>start</I> to a larger value can avoid including a 0.0 in a
|
||||
running or windowed average.
|
||||
</P>
|
||||
<P>The <I>file</I> keyword allows a filename to be specified. Every <I>Nfreq</I>
|
||||
steps, the vector of saed intensity data is written to a new file using
|
||||
the 3rd generation vtk format. The base of each file is assigned by
|
||||
the <I>file</I> keyword and this string is appended with _N.vtk where N is
|
||||
an index (0,1,2...) to account for situations with multiple diffraction
|
||||
intensity outputs.</p>
|
||||
<p>The <em>overwrite</em> keyword will continuously overwrite the output file
|
||||
intensity outputs.
|
||||
</P>
|
||||
<P>The <I>overwrite</I> 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>
|
||||
</div>
|
||||
<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>No parameter of this fix can be used with the <em>start/stop</em> keywords of
|
||||
the <a class="reference internal" href="run.html"><em>run</em></a> command. This fix is not invoked during <a class="reference internal" href="minimize.html"><em>energy minimization</em></a>.</p>
|
||||
</div>
|
||||
<div class="section" id="restrictions">
|
||||
<h2>Restrictions<a class="headerlink" href="#restrictions" title="Permalink to this headline">¶</a></h2>
|
||||
<p>The attributes for fix_saed_vtk must match the values assigned in the
|
||||
associated <a class="reference internal" href="compute_saed.html"><em>compute_saed</em></a> command.</p>
|
||||
</div>
|
||||
<div class="section" id="related-commands">
|
||||
<h2>Related commands<a class="headerlink" href="#related-commands" title="Permalink to this headline">¶</a></h2>
|
||||
<p><a class="reference internal" href="compute_saed.html"><em>compute_saed</em></a></p>
|
||||
</div>
|
||||
<div class="section" id="default">
|
||||
<h2>Default<a class="headerlink" href="#default" title="Permalink to this headline">¶</a></h2>
|
||||
<p>The option defaults are ave = one, start = 0, no file output.</p>
|
||||
<hr class="docutils" />
|
||||
<p id="coleman"><strong>(Coleman)</strong> Coleman, Spearot, Capolungo, MSMSE, 21, 055020
|
||||
(2013).</p>
|
||||
</div>
|
||||
</div>
|
||||
output. This option can only be used with the <I>ave running</I> setting.
|
||||
</P>
|
||||
<P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
|
||||
</P>
|
||||
<P>No information about this fix is written to <A HREF = "restart.html">binary restart
|
||||
files</A>. None of the <A HREF = "fix_modify.html">fix_modify</A> options
|
||||
are relevant to this fix.
|
||||
</P>
|
||||
<P>No parameter of this fix can be used with the <I>start/stop</I> keywords of
|
||||
the <A HREF = "run.html">run</A> command. This fix is not invoked during <A HREF = "minimize.html">energy
|
||||
minimization</A>.
|
||||
</P>
|
||||
<P><B>Restrictions:</B>
|
||||
</P>
|
||||
<P>The attributes for fix_saed_vtk must match the values assigned in the
|
||||
associated <A HREF = "compute_saed.html">compute_saed</A> command.
|
||||
</P>
|
||||
<P><B>Related commands:</B>
|
||||
</P>
|
||||
<P><A HREF = "compute_saed.html">compute_saed</A>
|
||||
</P>
|
||||
<P><B>Default:</B>
|
||||
</P>
|
||||
<P>The option defaults are ave = one, start = 0, no file output.
|
||||
</P>
|
||||
<HR>
|
||||
|
||||
<A NAME = "Coleman"></A>
|
||||
|
||||
</div>
|
||||
</div>
|
||||
<footer>
|
||||
|
||||
|
||||
<hr/>
|
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|
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|
||||
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|
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|
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||||
<P><B>(Coleman)</B> Coleman, Spearot, Capolungo, MSMSE, 21, 055020
|
||||
(2013).
|
||||
</P>
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</HTML>
|
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|
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Reference in New Issue
Block a user