forked from lijiext/lammps
191 lines
7.3 KiB
Plaintext
191 lines
7.3 KiB
Plaintext
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
|
|
|
|
:link(lws,http://lammps.sandia.gov)
|
|
:link(ld,Manual.html)
|
|
:link(lc,Section_commands.html#comm)
|
|
|
|
:line
|
|
|
|
fix saed/vtk command :h3
|
|
|
|
[Syntax:]
|
|
|
|
fix ID group-ID saed/vtk Nevery Nrepeat Nfreak c_ID attribute args ... keyword args ... :pre
|
|
|
|
ID, group-ID are documented in "fix"_fix.html command :ulb,l
|
|
saed/vtk = style name of this fix command :l
|
|
Nevery = use input values every this many timesteps :l
|
|
Nrepeat = # of times to use input values for calculating averages :l
|
|
Nfreq = calculate averages every this many timesteps :l
|
|
c_ID = saed compute ID :l
|
|
|
|
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 :pre
|
|
|
|
:ule
|
|
|
|
[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 :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
|
|
|
|
[Description:]
|
|
|
|
Time average computed intensities from "compute_saed"_compute_saed.txt 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"_compute_saed.txt
|
|
values, e.g.
|
|
|
|
compute 3 top saed 0.0251 Al O
|
|
fix saed/vtk 1 1 1 c_3 file Al2O3_001.saed :pre
|
|
|
|
:line
|
|
|
|
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. Nrepeat*Nevery can not exceed Nfreq.
|
|
|
|
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.
|
|
|
|
:line
|
|
|
|
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 :pre
|
|
|
|
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.
|
|
|
|
:line
|
|
|
|
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"_unfix.html
|
|
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"_restart.html. None of the "fix_modify"_fix_modify.html options
|
|
are relevant to this fix.
|
|
|
|
No parameter of this fix can be used with the {start/stop} keywords of
|
|
the "run"_run.html command. This fix is not invoked during "energy
|
|
minimization"_minimize.html.
|
|
|
|
[Restrictions:]
|
|
|
|
The attributes for fix_saed_vtk must match the values assigned in the
|
|
associated "compute_saed"_compute_saed.html command.
|
|
|
|
[Related commands:]
|
|
|
|
"compute_saed"_compute_saed.html
|
|
|
|
[Default:]
|
|
|
|
The option defaults are ave = one, start = 0, no file output.
|
|
|
|
:line
|
|
|
|
:link(Coleman)
|
|
[(Coleman)] Coleman, Spearot, Capolungo, MSMSE, 21, 055020
|
|
(2013).
|
|
|