Update morph instructions

Author: Sparks29032

doc/manual/pdfmorph.texinfo

@@ -110,7 +110,7 @@ model-independent way. It was originally designed to help a researcher
 answer a question: "Has my material undergone a phase transition between
 these two measurements?"
 
-A common approach to compare two PDFs is to plot the difference curve below
+A common approach to compare two PDFs is to plot the fdifference curve below
 the two PDFs. However, a significant signal can be seen in the difference curve
 due to benign effects such as thermal expansion (peak shifts), increased thermal
 motion (peak broadening), or a change in scale due to differences in the incident
@@ -125,7 +125,8 @@ a list of morphs to apply, which includes "stretching" (scaling the @math{r}-axi
 the abscissa, to simulate isotropic expansion/compression), "smearing" (peak broadening
 by convlution with a Gaussian), and "scaling" (scaling the ordinate axis). By default,
 @code{PDFmorph} will refine the intensity of the morphs to best match the morphed to
-the target PDF.
+the target PDF. All morphed PDFs generated by @code{PDFmorph} can easily be saved and
+exported (see the @code{--save} option in @ref{PDFmorph options}).
 
 @code{PDFmorph} includes other morphs including those that factor in nanoparticle
 shape effects. For a full list of available morphs, see @ref{Available morphs}.
@@ -404,6 +405,13 @@ We have reached the optimal fit for our PDF!
 @ScreenShot{images/qs_tutorial_morphed,png}
 @caption{The optimal fit after applying the scale, smear, and stretch morphs.}
 @end float
+@item To save your new morphed PDF as a file named @code{morph.gr}, use the save command
+@example
+pdfmorph darkSub_rh20_C_01.gr darkSub_rh20_C_44.gr --scale=0.8 \
+--smear=-0.84 --stretch=0.005 --rmin=1.5 --rmax=30 \
+--save=morph.gr
+@end example
+Type @code{ls} to confirm a new file named @code{morph.gr} has been saved.
 @item Now, try it on your own!
 If you have personally collected or otherwise readily available PDF data,
 try this process to see if you can morph your PDFs to one another.
@@ -523,6 +531,17 @@ can be done with @url{https://www.diffpy.org/products/pdfgui, PDFgui}.
 @caption{The refined stretch factor for each target PDF. There is very little change between @math{192K} and
 @math{198K}.}
 @end float
+@item Finally, let us save all the morphed PDFs into a directory named @code{savedMorphs}.
+@example
+pdfmorph SrFe2As2_150K.gr . --scale=1 --stretch=0 --multiple \
+--sort-by=temperature --plot-parameter=stretch \
+--save=savedMorphs
+@end example
+Entering the directory with @code{cd} and viewing its contents with @code{ls},
+we see a file named @code{Morph_Reference_Table.txt} with data about the input morph
+parameters and refined output parameters and a directory named @code{Morphs} containing
+all the morphed PDFs. See the @code{--save-names-file} option to see how you can
+set the names for these saved morphs!
 @end enumerate
 
 @node    Nanoparticle shape effect, , Performing multiple morphs, Extra tutorials
@@ -626,12 +645,20 @@ pdfmorph Ni_bulk.gr Ni_nano_spheroid.cgr --radius=12 --pradius=6 -a
 * Shape-related morphs::
 @end menu
 
-In this section, we detail a few use-cases for morphs.
+In this section, we detail the available morphs and the theory behind when they can
+(and should) be applied.
 
 @node    Temperature-related morphs, Shape-related morphs, Available morphs, Available morphs
 @section Temperature-related morphs
 @cindex  temperature-related morphs
 
+In this section, we describe the following morphs:
+@itemize
+@item @code{--stretch=STRETCH} -
+@item @code{--scale=SCALE} - scale the ordinate by
+@item @code{--smear=SMEAR} - convolute the
+@end itemize
+
 @node    Shape-related morphs, , Temperature-related morphs, Available morphs
 @section Shape-related morphs
 @cindex  shape-related morphs
@@ -642,7 +669,7 @@ In this section, we detail a few use-cases for morphs.
 @chapter PDFmorph options
 @cindex  pdfmorph options
 
-Explaination of options
+
 
 @c End TexInfo file
 @node Index, Top