forked from lijiext/lammps
218 lines
7.5 KiB
Plaintext
218 lines
7.5 KiB
Plaintext
.. index:: fix saed/vtk
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fix saed/vtk command
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====================
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Syntax
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""""""
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.. parsed-literal::
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fix ID group-ID saed/vtk Nevery Nrepeat Nfreak c_ID attribute args ... keyword args ...
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* ID, group-ID are documented in :doc:`fix <fix>` command
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* saed/vtk = style name of this fix command
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* Nevery = use input values every this many timesteps
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* Nrepeat = # of times to use input values for calculating averages
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* Nfreq = calculate averages every this many timesteps
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* c_ID = saed compute ID
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.. parsed-literal::
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keyword = *file* or *ave* or *start* or *file* or *overwrite*\ :l
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*ave* args = *one* or *running* or *window M*
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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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*start* args = Nstart
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Nstart = start averaging on this timestep
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*file* arg = filename
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filename = name of file to output time averages to
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*overwrite* arg = none = overwrite output file with only latest output
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Examples
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""""""""
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.. parsed-literal::
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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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.. parsed-literal::
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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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Description
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"""""""""""
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Time average computed intensities from :doc:`compute saed <compute_saed>` 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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To produce output in the image data vtk format ghost data is added
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outside the *Kmax* 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*[h k l]/norm([h k l]), where R_Ewald=1/lambda.
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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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Fix saed/vtk is designed to work only with :doc:`compute saed <compute_saed>`
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values, e.g.
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.. parsed-literal::
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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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----------
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The *Nevery*\ , *Nrepeat*\ , and *Nfreq* 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 *Nfreq*\ . The average is over *Nrepeat*
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quantities, computed in the preceding portion of the simulation every
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*Nevery* timesteps. *Nfreq* must be a multiple of *Nevery* and
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*Nevery* must be non-zero even if *Nrepeat* is 1.
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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.
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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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----------
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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 *file* 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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By default the header contains the following information (with example data):
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.. parsed-literal::
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# 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
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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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In this example, kspace is sampled across a 337 x 219 x 209 point mesh
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where the mesh spacing is approximately 0.005, 0.007, and 0.008
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inv(length) units in the k1, k2, and k3 directions, respectively.
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The data is shifted by -0.85, -0.85, -0.85 inv(length) units so that
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the origin will lie at 0, 0, 0. Here, 15,424,827 kspace points are
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sampled in total.
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----------
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Additional optional keywords also affect the operation of this fix.
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The *ave* keyword determines how the values produced every *Nfreq*
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steps are averaged with values produced on previous steps that were
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multiples of *Nfreq*\ , before they are accessed by another output
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command or written to a file.
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If the *ave* setting is *one*\ , then the values produced on timesteps
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that are multiples of *Nfreq* are independent of each other; they are
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output as-is without further averaging.
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If the *ave* setting is *running*\ , then the values produced on
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timesteps that are multiples of *Nfreq* 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 :doc:`unfix <unfix>`
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command, or by re-defining the fix by re-specifying it.
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If the *ave* setting is *window*\ , then the values produced on
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timesteps that are multiples of *Nfreq* 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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The *start* 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 *start* to a larger value can avoid including a 0.0 in a
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running or windowed average.
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The *file* keyword allows a filename to be specified. Every *Nfreq*
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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 *file* 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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The *overwrite* 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 *ave running* setting.
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Restart, fix_modify, output, run start/stop, minimize info
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""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
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No information about this fix is written to :doc:`binary restart files <restart>`. None of the :doc:`fix_modify <fix_modify>` options
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are relevant to this fix.
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No parameter of this fix can be used with the *start/stop* keywords of
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the :doc:`run <run>` command. This fix is not invoked during :doc:`energy minimization <minimize>`.
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Restrictions
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""""""""""""
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The attributes for fix_saed_vtk must match the values assigned in the
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associated :doc:`compute_saed <compute_saed>` command.
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Related commands
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""""""""""""""""
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:doc:`compute_saed <compute_saed>`
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Default
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"""""""
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The option defaults are ave = one, start = 0, no file output.
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----------
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.. _Coleman:
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**(Coleman)** Coleman, Spearot, Capolungo, MSMSE, 21, 055020
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(2013).
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.. _lws: http://lammps.sandia.gov
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.. _ld: Manual.html
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.. _lc: Section_commands.html#comm
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