2015-07-17 06:30:07 +08:00
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<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
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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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<LI>ave/time/saed = style name of this fix command
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<LI>Nevery = use input values every this many timesteps
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<LI>Nrepeat = # of times to use input values for calculating averages
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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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<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>
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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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<I>start</I> args = Nstart
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Nstart = start averaging on this timestep
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<I>file</I> arg = filename
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filename = name of file to output time averages to
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<I>overwrite</I> arg = none = overwrite output file with only latest output
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</PRE>
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</UL>
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<P><B>Examples:</B>
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</P>
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2015-07-22 07:11:53 +08:00
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<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>
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2015-07-17 06:30:07 +08:00
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<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>
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<P><B>Description:</B>
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</P>
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<P>Time average computed intensities from <A HREF = "compute_saed.txt">compute_saed</A> and
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write output to a file in the 3rd generation vtk image data format for
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visualization directly in parallelized visualization software packages
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like ParaView and VisIt. Note that if no time averaging is done, this
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command can be used as a convenient way to simply output diffraction
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intensities at a single snapshot.
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</P>
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<P>To produce output in the image data vtk format ghost data is added
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outside the <I>Kmax</I> range assigned in the compute saed. The ghost data is
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assigned a value of -1 and can be removed setting a minimum isovolume
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of 0 within the vizualiziton software. SAED images can be created by
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visualizing a spherical slice of the data that is centered at
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R_Ewald*<B>h k l</B>/norm(<B>h k l</B>), where R_Ewald=1/lambda.
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</P>
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<P>The group specified within this command is ignored. However, note that
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specified values may represent calculations performed by saed computes
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which store their own "group" definitions.
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</P>
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<P>Fix saed/vtk is designed to work only with <A HREF = "compute_saed.txt">compute_saed</A>
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2015-07-22 07:11:53 +08:00
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values, e.g.
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2015-07-17 06:30:07 +08:00
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</P>
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2015-07-22 07:11:53 +08:00
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<PRE>compute 3 top saed 0.0251 Al O
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fix saed/vtk 1 1 1 c_3 file Al2O3_001.saed
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</PRE>
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2015-07-17 06:30:07 +08:00
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<HR>
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<P>The <I>Nevery</I>, <I>Nrepeat</I>, and <I>Nfreq</I> arguments specify on what
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timesteps the input values will be used in order to contribute to the
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average. The final averaged quantities are generated on timesteps
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that are a multiple of <I>Nfreq</I>. The average is over <I>Nrepeat</I>
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quantities, computed in the preceding portion of the simulation every
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<I>Nevery</I> timesteps. <I>Nfreq</I> must be a multiple of <I>Nevery</I> and
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<I>Nevery</I> must be non-zero even if <I>Nrepeat</I> is 1. Also, the timesteps
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contributing to the average value cannot overlap, i.e. Nfreq >
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(Nrepeat-1)*Nevery is required.
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</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
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on timestep 100. Similarly for timesteps 190,192,194,196,198,200 on
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timestep 200, etc. If Nrepeat=1 and Nfreq = 100, then no time
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averaging is done; values are simply generated on timesteps
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100,200,etc.
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</P>
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<HR>
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<P>The output for fix ave/time/saed is a file writen with the 3rd generation
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vtk image data formatting. The filename assigned by the <I>file</I> keyword is
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appended with _N.vtk where N is an index (0,1,2...) to account for multiple
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diffraction intensity outputs.
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</P>
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<P>By default the header contains the following information (with example data):
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</P>
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<P># vtk DataFile Version 3.0 c_SAED
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Image data set
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ASCII
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DATASET STRUCTURED_POINTS
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DIMENSIONS 337 219 209
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ASPECT_RATIO 0.00507953 0.00785161 0.00821458
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ORIGIN -0.853361 -0.855826 -0.854316 \n POINT_DATA 15424827
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SCALARS intensity float
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LOOKUP_TABLE default
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...data
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</P>
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<HR>
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<P>Additional optional keywords also affect the operation of this fix.
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</P>
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<P>The <I>ave</I> keyword determines how the values produced every <I>Nfreq</I>
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steps are averaged with values produced on previous steps that were
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multiples of <I>Nfreq</I>, before they are accessed by another output
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command or written to a file.
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</P>
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<P>If the <I>ave</I> setting is <I>one</I>, then the values produced on timesteps
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that are multiples of <I>Nfreq</I> are independent of each other; they are
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output as-is without further averaging.
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</P>
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<P>If the <I>ave</I> setting is <I>running</I>, then the values produced on
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timesteps that are multiples of <I>Nfreq</I> are summed and averaged in a
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cumulative sense before being output. Each output value is thus the
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average of the value produced on that timestep with all preceding
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values. This running average begins when the fix is defined; it can
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only be restarted by deleting the fix via the <A HREF = "unfix.html">unfix</A>
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command, or by re-defining the fix by re-specifying it.
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</P>
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<P>If the <I>ave</I> setting is <I>window</I>, then the values produced on
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timesteps that are multiples of <I>Nfreq</I> are summed and averaged within
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a moving "window" of time, so that the last M values are used to
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produce the output. E.g. if M = 3 and Nfreq = 1000, then the output
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on step 10000 will be the average of the individual values on steps
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8000,9000,10000. Outputs on early steps will average over less than M
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values if they are not available.
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</P>
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<P>The <I>start</I> keyword specifies what timestep averaging will begin on.
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The default is step 0. Often input values can be 0.0 at time 0, so
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setting <I>start</I> to a larger value can avoid including a 0.0 in a
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running or windowed average.
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</P>
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<P>The <I>file</I> keyword allows a filename to be specified. Every <I>Nfreq</I>
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steps, the vector of saed intensity data is written to a new file using
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the 3rd generation vtk format. The base of each file is assigned by
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the <I>file</I> keyword and this string is appended with _N.vtk where N is
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an index (0,1,2...) to account for situations with multiple diffraction
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intensity outputs.
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</P>
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<P>The <I>overwrite</I> keyword will continuously overwrite the output file
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with the latest output, so that it only contains one timestep worth of
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output. This option can only be used with the <I>ave running</I> setting.
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</P>
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<P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
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</P>
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<P>No information about this fix is written to <A HREF = "restart.html">binary restart
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files</A>. None of the <A HREF = "fix_modify.html">fix_modify</A> options
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are relevant to this fix.
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</P>
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<P>No parameter of this fix can be used with the <I>start/stop</I> keywords of
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the <A HREF = "run.html">run</A> command. This fix is not invoked during <A HREF = "minimize.html">energy
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minimization</A>.
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</P>
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<P><B>Restrictions:</B>
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</P>
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<P>The attributes for fix_saed_vtk must match the values assigned in the
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associated <A HREF = "compute_saed.txt">compute_saed</A> command.
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</P>
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<P><B>Related commands:</B>
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</P>
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<P><A HREF = "compute_saed.html">compute_saed</A>
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</P>
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<P><B>Default:</B>
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</P>
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<P>The option defaults are ave = one, start = 0, no file output.
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</P>
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<HR>
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<A NAME = "Coleman"></A>
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<P><B>(Coleman)</B> Coleman, Spearot, Capolungo, MSMSE, 21, 055020
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(2013).
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</P>
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</HTML>
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