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