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lammps/examples/USER/diffraction/README
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This is a simple example of showing the computation of virutal x-ray
and electron diffraction patterns for Ni.
In addition to the LAMMPS output, a simple visualizaiton of the electron
diffraction data is included. The visualization was created using the VisIt
Open Source visualiztion software develeoped at Larrence Livermore National
Laboraatory (https://wci.llnl.gov/simulation/computer-codes/visit/).
Below is a step by step guide to produce similar images:
a) Open the diffraction .vtk files in VisIt
b) Click add->pseudocolor->intensity;
*Note, green name means its ready to be drawn
c) Click Draw;
*Note, you will see the full rectangular mesh grid which is what we
are wanting.
We need to remove ghost data (those values set to -1).
d) Select intensity plot;
Click Operators->Selection->Isovolume;
Double click isovolume (under intensity plot);
Change lower bound to 0;
Click Apply;
Click Dismiss;
Click Draw;
 
*Note, now you will see only where there was valid intensity data (if you
don't use Zone it will be a sphere).  But most intensity are low so color
the intensity by log scale.
e) Select intensity plot
Double click Pseudocolor;
Change Scale to Log;
Check Mimimum Limit;
Input non-zero minimum limit (i.e. 1);
Click Apply;
Click Dismiss;
Note, clicking apply will change the scale automatically.  But unless
you have used Zone and a thin dR_Ewald you likely have lots of extra
data visualized that does not intersect the Ewald sphere.  Next, we
want to take a spherical slice to mimic the intersection of Ewald's
sphere with reciprocal space.
f) Select intensity plot;
Click Operators->Slicing>Spherical Slice;
Double click Spherical Slice;
Change the origin/radius to represent the center of your Ewald sphere;
**(i.e. 39.84063 0 0) and radius (i.e. 39.84063) for lambda = 0.251 **
Click Apply;
Click Dismiss;
Click Draw;
This is the saed pattern, but we are not guaranteed to be aligned correctly
with the zone axis.
g) On the menu bar... select Controls -> View;
Change View Normal to the zone axis of choice (i.e. -1 0 0);
Adjust Up Vector if desired (i.e. 0 1 0);
Turn off Perspective view;
Click Apply;
Click Dismiss;
*Note that for the primary x, y, and z zone axis you can use the drop
own Align to axis.  However, it is likely that there is a bunch of extra
annotations on the image that don't look appealing.
h) On the menu bar... select Control-> Annotation;
*Here you can change what is visualized along side the data and how
you display axis information.  I typically turn most all the display
information off.
i) Save the image
Click File-> Set save options
Click Save
** Note, further fine tuning can be achieved by adjusing the color table and
max/min values **
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