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Writing Tutorials #81

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4a5acea
Initial reformatting
Jun 22, 2023
0e77508
Code block and equation formatting
Jun 26, 2023
78d6ad6
Merge branch 'main' of https://github.com/diffpy/diffpy.pdfmorph into…
Jun 27, 2023
a16d57c
Add new tutorial files
Jul 3, 2023
051f368
Add morph shape tutorial, new tutorial files
Jul 3, 2023
7663bfa
Some rewording
Jul 3, 2023
597df51
Add ability to perform multiple morphs, testfiles
Jul 4, 2023
91fc072
Add test, temp sort option, fix depreciation
Jul 5, 2023
69c1544
Revert version.py, add tests
Jul 5, 2023
72f735e
Add plotting, saving options
Jul 6, 2023
72fcb24
Merge remote-tracking branch 'origin/morph_sequence' into reformat_do…
Jul 6, 2023
6068c0a
Added tutorial for morph sequence
Jul 6, 2023
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Some rewording
  • Loading branch information
Andrew Yang
Andrew Yang committed Jul 3, 2023
commit 7663bfa0f83ce3f0e8a7769b7fbd15cdf4ad0d78
2 changes: 1 addition & 1 deletion doc/source/mod_pdfmorph_api.rst
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diffpy.pdfmorph.pdfmorph_api
#####################
############################

.. automodule:: diffpy.pdfmorph.pdfmorph_api
:members:
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9 changes: 6 additions & 3 deletions doc/source/quickstart.rst
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Expand Up @@ -194,9 +194,12 @@ We can use PDFmorph to morph a bulk material PDF to simulate these shape effects
Currently, the supported nanoparticle shapes include: spheres and spheroids.

* Within the ``additionalData`` directory, ``cd`` into the ``morphshape`` subdirectory.
* Inside, you will find a sample Ni bulk material PDF ``Ni_bulk.gr``.
Inside, you will find a sample Ni bulk material PDF ``Ni_bulk.gr``.
This PDF is from `"Atomic Pair Distribution Function Analysis: A primer" <https://github.com/Billingegroup/pdfttp_data/>`_.
* There are also multiple ``.cgr`` files with calculated Ni nanoparticles of various shapes..
There are also multiple ``.cgr`` files with calculated Ni nanoparticle PDFs.

* Let us apply various shape effect morphs on the bulk material to reproduce these calculated PDFs.

* Spherical Shape
1. The ``Ni_nano_sphere.cgr`` file contains a generated spherical nanoparticle with unknown radius.
First, let us plot ``Ni_blk.gr`` against ``Ni_nano_sphere.cgr`` ::
Expand All @@ -219,7 +222,7 @@ Currently, the supported nanoparticle shapes include: spheres and spheroids.

pdfmorph Ni_bulk.gr Ni_nano_sphere.cgr --radius=11.2 -a

5. We can see that the Rw value has decreased from before. Run without the ``-a`` tag to refine ::
5. We can see that the Rw value has significantly decreased from before. Run without the ``-a`` tag to refine ::

pdfmorph Ni_bulk.gr Ni_nano_sphere.cgr --radius=11.2

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