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doc/manual/source/quickstart.rst

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@@ -188,26 +188,26 @@ Tutorials for these additional functionalities are included below. Additional
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files for these tutorials can be downloaded
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:download:`here <../../../tutorial/additionalData.zip>`.
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Performing a Sequence of Morphs
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-------------------------------
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Performing Multiple Morphs
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--------------------------
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It may be useful to morph a PDF against multiple targets:
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for example, you may want to morph a PDF against a sequence of PDFs measured
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for example, you may want to morph a PDF against multiple PDFs measured
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at various temepratures to determine whether a phase change has occured.
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PDFmorph currently allows users to morph a PDF against all files in a
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selected directory and plot resulting :math:`R_w` values from each morph.
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1. Within the ``additionalData`` directory, ``cd`` into the ``morphsequence`` directory.
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1. Within the ``additionalData`` directory, ``cd`` into the ``morphMultiple`` directory.
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Inside, you will find multiple PDFs of :math:`SrFe_2As_2` measured at various temperatures.
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These PDFs are from `"Atomic Pair Distribution Function Analysis: A primer" <https://github.com/Billingegroup/pdfttp_data/>`_.
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2. Let us start by getting the Rw of ``SrFe2As2_150K.gr`` compared to all other files in the
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directory. Run ::
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pdfmorph SrFe2As2_150K.gr . --multiple
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The sequence tag indicates we are comparing PDF file (first input) against all PDFs in
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The multiple tag indicates we are comparing PDF file (first input) against all PDFs in
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a directory (second input). Our choice of file was ``SeFe2As2_150K.gr``
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and directory was the cwd, which should be ``morphsequence``.
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and directory was the cwd, which should be ``morphMultiple``.
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3. After running this, we get chart of Rw values for each target file. However, this chart can
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be a bit confusing to interpret. To get a more understandable plot, run ::
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The temperature option can be used when our files end in ``_#K.gr`` or ``_#K.cgr`` where ``#``
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is a temperature (float value). When enabled, PDFmorph will plot Rw values against the temperatures.
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4. Between 192K and 198K, the Rw has a sharp increase, indicating that we may have a phase change.
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To confirm, let us now apply morphs onto ``SrFe2As2_150K.gr`` with all other files in ``morphsequence``
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To confirm, let us now apply morphs onto ``SrFe2As2_150K.gr`` with all other files in ``morphMultiple``
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as targets ::
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pdfmorph --scale=1 --stretch=0 SrFe2As2_150K.gr . --multiple --temperature
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We can use PDFmorph to morph a bulk material PDF to simulate these shape effects.
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Currently, the supported nanoparticle shapes include: spheres and spheroids.
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* Within the ``additionalData`` directory, ``cd`` into the ``morphshape`` subdirectory.
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* Within the ``additionalData`` directory, ``cd`` into the ``morphShape`` subdirectory.
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Inside, you will find a sample Ni bulk material PDF ``Ni_bulk.gr``.
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This PDF is from `"Atomic Pair Distribution Function Analysis: A primer" <https://github.com/Billingegroup/pdfttp_data/>`_.
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There are also multiple ``.cgr`` files with calculated Ni nanoparticle PDFs.

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