docs: shorten the line length

Author: ycexiao

doc/source/quickstart.rst

@@ -4,7 +4,9 @@ PDFmorph Tutorial
 #################
 
 Welcome! This will be a quick tutorial to accquaint users with PDFmorph
-and some of what it can do.
+and some of what it can do. To see more details and definitions about
+the morphs
+please see the publication describing ``diffpy.pdfmorph``.
 
 As we described in the README and installation instructions, please make
 sure that you are familiar with working with your command line terminal
@@ -13,7 +15,10 @@ before using this application.
 Before you've started this tutorial, please ensure that you've installed
 all necessary software and dependencies.
 
-In this tutorial, we will demonstrate how to use PDFmorph to compare two PDFs measured from the same material at different temperatures. The morphs showcased include "stretch", "scale", and "smear".
+In this tutorial, we will demonstrate how to use PDFmorph to compare
+two
+PDFs measured from the same material at different temperatures.
+The morphs showcased include "stretch", "scale", and "smear".
 
 Basic PDFmorph Workflow
 =======================
@@ -52,7 +57,8 @@ Basic PDFmorph Workflow
        * Note that these files have the ``.gr`` extension, which
          indicates that they are measured PDFs. The ``.cgr`` file
          extension indicates that a file is a calculated PDF, such as
-         those generated by the `PDFgui <https://www.diffpy.org/products/pdfgui.html>`_
+         those generated by the
+	 `PDFgui <https://www.diffpy.org/products/pdfgui.html>`_
          program.
 
     4. First, we will run the PDFmorph application without any morphing
@@ -216,17 +222,22 @@ at various temperatures to determine whether a phase change has occurred.
 PDFmorph currently allows users to morph a PDF against all files in a
 selected directory and plot resulting :math:`R_w` values from each morph.
 
-1. Within the ``additionalData`` directory, ``cd`` into the ``morphsequence`` directory.
-   Inside, you will find multiple PDFs of :math:`SrFe_2As_2` measured at various temperatures.
-   These PDFs are from `"Atomic Pair Distribution Function Analysis: A primer" <https://github.com/Billingegroup/pdfttp_data/>`_.
-2. Let us start by getting the Rw of ``SrFe2As2_150K.gr`` compared to all other files in the
-   directory. Run ::
+1. Within the ``additionalData`` directory, ``cd`` into the
+   ``morphsequence`` directory. Inside, you will find multiple PDFs of
+   :math:`SrFe_2As_2` measured at various temperatures. These PDFs are
+   from `"Atomic Pair Distribution Function Analysis: A primer"
+   <https://global.oup.com/academic/product/
+   atomic-pair-distribution-function-analysis-9780198885801>`_.
+
+2. Let us start by getting the Rw of ``SrFe2As2_150K.gr`` compared to
+   all other files in the directory. Run ::
 
        pdfmorph SrFe2As2_150K.gr . --multiple-targets
 
-   The multiple tag indicates we are comparing PDF file (first input) against all PDFs in
-   a directory (second input). Our choice of file was ``SeFe2As2_150K.gr``
-   and directory was the cwd, which should be ``morphsequence``.
+   The multiple tag indicates we are comparing PDF file (first input)
+   against all PDFs in a directory (second input). Our choice of file
+   was ``SeFe2As2_150K.gr`` and directory was the cwd, which should be
+   ``morphsequence``.
 
 .. figure:: images/ex_tutorial_bar.png
    :align: center
@@ -235,14 +246,16 @@ selected directory and plot resulting :math:`R_w` values from each morph.
    Bar chart of :math:`R_W` values for each target file. Target files are
    listed in ASCII sort order.
 
-3. After running this, we get chart of Rw values for each target file. However, this chart can
-   be a bit confusing to interpret. To get a more understandable plot, run ::
+3. After running this, we get chart of Rw values for each target file.
+   However, this chart can be a bit confusing to interpret. To get a
+   more understandable plot, run ::
 
        pdfmorph SrFe2As2_150K.gr . --multiple-targets --sort-by=temperature
 
-   This plots the Rw against the temperature parameter value provided at the top of each file.
-   Parameters are entries of the form ``<parameter_name> = <parameter_value>`` and are located
-   above the ``r`` versus ``gr`` table in each PDF file.::
+   This plots the Rw against the temperature parameter value provided
+   at the top of each file. Parameters are entries of the form
+   ``<parameter_name> = <parameter_value>`` and are located above
+   the ``r`` versus ``gr`` table in each PDF file.::
 
      # SrFe2As2_150K.gr
      [PDF Parameters]
@@ -254,94 +267,127 @@ selected directory and plot resulting :math:`R_w` values from each morph.
    :align: center
    :figwidth: 100%
 
-   The :math:`R_W` plotted against the temperature the target PDF was measured at.
+   The :math:`R_W` plotted against the temperature the target PDF was
+   measured at.
 
-4. Between 192K and 198K, the Rw has a sharp increase, indicating that we may have a phase change.
-   To confirm, let us now apply morphs onto ``SrFe2As2_150K.gr`` with all other files in ``morphsequence``
-   as targets ::
+4. Between 192K and 198K, the Rw has a sharp increase, indicating that
+   we may have a phase change. To confirm, let us now apply morphs
+   onto `` SrFe2As2_150K.gr`` with all other files in
+   ``morphsequence`` as targets ::
 
        pdfmorph --scale=1 --stretch=0 SrFe2As2_150K.gr . --multiple-targets --sort-by=temperature
 
-   Note that we are not applying a smear since it takes a long time to apply and does not significantly
-   change the Rw values in this example.
+   Note that we are not applying a smear since it takes a long time to
+   apply and does not significantly change the Rw values in this example.
+
 5. We should now see a sharper increase in Rw between 192K and 198K.
+
 6. Go back to the terminal to see optimized morphing parameters from each morph.
-7. On the morph with ``SrFe2As2_192K.gr`` as target, ``scale = 0.972085`` and ``stretch = 0.000508``
-   and with ``SrFe2As2_198K.gr`` as target, ``scale = 0.970276`` and ``stretch = 0.000510``.
-   These are very similar, meaning that thermal lattice expansion (accounted for by ``stretch``)
-   is not occurring. This, coupled with the fact that the Rw significantly increases suggests
-   a phase change in this temperature regime. (In fact, :math:`SrFe_2As_2` does transition from
-   orthorhombic at lower temperature to tetragonal at higher temperature!). More sophisticated analysis
-   can be done with `PDFgui <https://www.diffpy.org/products/pdfgui.html>`_.
-8. Finally, let us save all the morphed PDFs into a directory named ``savedMorphs``. ::
+
+7. On the morph with ``SrFe2As2_192K.gr`` as target, ``scale =
+   0.972085`` and ``stretch = 0.000508`` and with ``SrFe2As2_198K.gr``
+   as target, ``scale = 0.970276`` and ``stretch = 0.000510``. These
+   are very similar, meaning that thermal lattice expansion (accounted
+   for by ``stretch``) is not occurring. This, coupled with the fact
+   that the Rw significantly increases suggests a phase change in this
+   temperature regime. (In fact, :math:`SrFe_2As_2` does transition
+   from orthorhombic at lower temperature to tetragonal at higher
+   temperature!). More sophisticated analysis can be done with
+   `PDFgui <https://www.diffpy.org/products/pdfgui.html>`_.
+
+8. Finally, let us save all the morphed PDFs into a directory
+   named ``savedMorphs``. ::
 
      pdfmorph SrFe2As2_150K.gr . --scale=1 --stretch=0 --multiple-targets \
     --sort-by=temperature --plot-parameter=stretch \
     --save=savedMorphs
 
-   Entering the directory with ``cd`` and viewing its contents with ``ls``, we see a file named
-   ``Morph_Reference_Table.txt`` with data about the input morph parameters and re-
-   fined output parameters and a directory named ``Morphs`` containing all the morphed
-   PDFs. See the ``--save-names-file`` option to see how you can set the names for these
-   saved morphs!
+   Entering the directory with ``cd`` and viewing its contents with
+   ``ls``, we see a file named ``Morph_Reference_Table.txt`` with data
+   about the input morph parameters and re- fined output parameters
+   and a directory named ``Morphs`` containing all the morphed
+   PDFs. See the ``--save-names-file`` option to see how you can set
+   the names for these saved morphs!
 
 Nanoparticle Shape Effects
 --------------------------
 
-A nanoparticle's finite size and shape can affect the shape of its PDF.
-We can use PDFmorph to morph a bulk material PDF to simulate these shape effects.
-Currently, the supported nanoparticle shapes include: spheres and spheroids.
+A nanoparticle's finite size and shape can affect the shape of its
+PDF. 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``.
-  This PDF is from `"Atomic Pair Distribution Function Analysis: A primer" <https://github.com/Billingegroup/pdfttp_data/>`_.
+* Within the ``additionalData`` directory, ``cd`` into the
+  ``morphShape`` subdirectory. 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 nanoparticle PDFs.
 
-* Let us apply various shape effect morphs on the bulk material to reproduce these calculated 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`` ::
+        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`` ::
 
                pdfmorph Ni_bulk.gr Ni_nano_sphere.cgr
 
            Despite the two being the same material, the Rw is quite large.
            To reduce the Rw, we will apply spherical shape effects onto the PDF.
-           However, in order to do so, we first need the radius of the spherical nanoparticle.
-        2. To get the radius, we can first observe a plot of ``Ni_nano_sphere.cgr`` ::
+           However, in order to do so, we first need the radius of the
+	   spherical nanoparticle.
+
+        2. To get the radius, we can first observe a plot of
+	   ``Ni_nano_sphere.cgr`` ::
 
                pdfmorph Ni_nano_sphere.cgr Ni_nano_sphere.cgr
 
-        3. Nanoparticles tend to have broader peaks at r-values larger than the particle size,
-           corresponding to the much weaker correlations between molecules.
-           On our plot, beyond r=22.5, peaks are too broad to be visible,
-           indicating our particle size to be about 22.4.
-           The approximate radius of a sphere would be half of that, or 11.2.
-        4. Now, we are ready to perform a morph applying spherical effects. To do so, we use the ``--radius`` parameter ::
+        3. Nanoparticles tend to have broader peaks at r-values larger
+	   than the particle size, corresponding to the much weaker
+	   correlations between molecules. On our plot, beyond r=22.5,
+	   peaks are too broad to be visible, indicating our particle
+	   size to be about 22.4. The approximate radius of a sphere
+	   would be half of that, or 11.2.
+
+
+        4. Now, we are ready to perform a morph applying spherical
+	   effects. To do so, we use the ``--radius`` parameter ::
 
                pdfmorph Ni_bulk.gr Ni_nano_sphere.cgr --radius=11.2 -a
 
-        5. We can see that the Rw value has significantly 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
 
-        6. After refining, we see the actual radius of the nanoparticle was closer to 12.
+        6. After refining, we see the actual radius of the
+	   nanoparticle was closer to 12.
+
     * Spheroidal Shape
-        1. The ``Ni_nano_spheroid.cgr`` file contains a calculated spheroidal Ni nanoparticle.
-           Again, we can begin by plotting the bulk material against our nanoparticle ::
+
+        1. The ``Ni_nano_spheroid.cgr`` file contains a calculated
+	   spheroidal Ni nanoparticle. Again, we can begin by plotting
+	   the bulk material against our nanoparticle ::
 
                pdfmorph Ni_bulk.gr Ni_nano_spheroid.cgr
 
-        2. Inside the ``Ni_nano_spheroid.cgr`` file, we are given that the equatorial radius is 12 and polar radius is 6.
-           This is enough information to define our spheroid. To apply spheroid shape effects onto our bulk, run ::
+        2. Inside the ``Ni_nano_spheroid.cgr`` file, we are given that
+	   the equatorial radius is 12 and polar radius is 6. This is
+	   enough information to define our spheroid. To apply
+	   spheroid shape effects onto our bulk, run ::
 
                pdfmorph Ni_bulk.gr Ni_nano_spheroid.cgr --radius=12 --pradius=6 -a
 
-           Note that the equatorial radius corresponds to the ``--radius`` parameter and polar radius to ``--pradius``.
+           Note that the equatorial radius corresponds to the
+	   ``--radius`` parameter and polar radius to ``--pradius``.
+
         3. Remove the ``-a`` tag to refine.
 
-There is also support for morphing from a nanoparticle to a bulk. When applying the inverse morphs,
-it is recommended to set ``--rmax=psize`` where ``psize`` is the longest diameter of the nanoparticle.
+There is also support for morphing from a nanoparticle to a bulk. When
+applying the inverse morphs, it is recommended to set ``--rmax=psize``
+where ``psize`` is the longest diameter of the nanoparticle.
 
 Bug Reports
 ===========