fix saed/vtk command — LAMMPS 15 May 2015 version documentation

# fix saed/vtk command

## Syntax

    fix ID group-ID saed/vtk Nevery Nrepeat Nfreak c_ID attribute args ... keyword args ...

- ID, group-ID are documented in fix command
- saed/vtk = style name of this fix command
- Nevery = use input values every this many timesteps
- Nrepeat = # of times to use input values for calculating averages
- Nfreq = calculate averages every this many timesteps
- c_ID = saed compute ID

    keyword = file or ave or start or file or overwrite:l
      ave args = one or running or window M
        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
      start args = Nstart
        Nstart = start averaging on this timestep
      file arg = filename
        filename = name of file to output time averages to
      overwrite arg = none = overwrite output file with only latest output

## Examples

    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

    fix saed/vtk 1 1 1 c_1 file Al2O3_001.saed
    fix saed/vtk 1 1 1 c_2 file Ni_000.saed

## Description

Time average computed intensities from compute_saed 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.

To produce output in the image data vtk format ghost data is added outside the Kmax 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.

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.

Fix saed/vtk is designed to work only with compute_saed values, e.g.

    compute 3 top saed 0.0251 Al O
    fix saed/vtk 1 1 1 c_3 file Al2O3_001.saed

The Nevery, Nrepeat, and Nfreq 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 Nfreq. The average is over Nrepeat quantities, computed in the preceding portion of the simulation every Nevery timesteps. Nfreq must be a multiple of Nevery and Nevery must be non-zero even if Nrepeat is 1. Also, the timesteps contributing to the average value cannot overlap, i.e. Nfreq > (Nrepeat-1)*Nevery is required.

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.

The output for fix ave/time/saed is a file writen with the 3rd generation vtk image data formatting. The filename assigned by the file keyword is appended with _N.vtk where N is an index (0,1,2...) to account for multiple diffraction intensity outputs.

By default the header contains the following information (with example data):

    # 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
    POINT_DATA 15424827
    SCALARS intensity float
    LOOKUP_TABLE default
    ...data

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.

Additional optional keywords also affect the operation of this fix.

The ave keyword determines how the values produced every Nfreq steps are averaged with values produced on previous steps that were multiples of Nfreq, before they are accessed by another output command or written to a file.

If the ave setting is one, then the values produced on timesteps that are multiples of Nfreq are independent of each other; they are output as-is without further averaging.

If the ave setting is running, then the values produced on timesteps that are multiples of Nfreq 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 unfix command, or by re-defining the fix by re-specifying it.

If the ave setting is window, then the values produced on timesteps that are multiples of Nfreq 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.

The start 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 start to a larger value can avoid including a 0.0 in a running or windowed average.

The file keyword allows a filename to be specified. Every Nfreq 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 file 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.

The overwrite 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 ave running setting.

## Restart, fix_modify, output, run start/stop, minimize info

No information about this fix is written to binary restart files. None of the fix_modify options are relevant to this fix.

No parameter of this fix can be used with the start/stop keywords of the run command. This fix is not invoked during energy minimization.

## Restrictions

The attributes for fix_saed_vtk must match the values assigned in the associated compute_saed command.

## Related commands

compute_saed

## Default

The option defaults are ave = one, start = 0, no file output.

(Coleman) Coleman, Spearot, Capolungo, MSMSE, 21, 055020 (2013).