Changeset 3209 for Tutorials/PythonScript/Scripting.htm

Timestamp:

Dec 28, 2017 12:50:40 PM (5 years ago)

Author:

toby

Message:

Add simulation to scriptable & add to tutorial; add sphinx index to ctrlsGUI; remove path from RunGSASII.bat

File:

• Tutorials/PythonScript/Scripting.htm (modified) (8 diffs)

Tutorials/PythonScript/Scripting.htm

@@ -8 +8 @@
 To demonstrate the use of the 
 <A href="http://gsas-ii.readthedocs.io/en/latest/GSASIIscripts.html" target="_blank">
-GSASIIscriptable module</A>, we create a Python script to duplicate the
-refinement in the
-<A
-href="https://subversion.xray.aps.anl.gov/pyGSAS/Tutorials/CWCombined/Combined%20refinement.htm"
-target="_blank">GSAS-II CW Combined Refinement</A>
-tutorial. This uses a Python script
-to perform the same refinements steps as in that tutorial, but without use of the GSAS-II
+GSASIIscriptable module</A>. This uses a Python script
+to perform a refinement or computation, but without use of the GSAS-II
 graphical user interface. Note that the
 <A href="http://gsas-ii.readthedocs.io/en/latest/GSASIIscripts.html" target="_blank">
@@ -22 +17 @@
 by Jackson O'Donnell, as a summer undergraduate visitor under
 supervisor Dr. Maria Chan. Other programming contributions are welcome. 
+<P>
+This tutorial has three sections:
+<OL type="A">
+<LI><a href="#multistep"> Create a Multi-step Script</A></LI>
+<LI><a href="#SingleStep">Single-Step Refinement</a></LI>
+<LI><a href="#Simulate">Powder Pattern Simulation</a></LI>
+</OL>
+The first section duplicates the refinement in the
+<A
+href="https://subversion.xray.aps.anl.gov/pyGSAS/Tutorials/CWCombined/Combined%20refinement.htm"
+target="_blank">GSAS-II CW Combined Refinement</A>
+tutorial as a multi-step process. The second section repeats the previous
+refinement, but demonstrates how a complex process can be entered into
+a single Python dict and the refinement executed with a single
+function call. The third section shows how a pattern simulation,
+rather than refinement can be executed from a script. 
+
 
 <h2>Prerequisites</h2>
@@ -45 +57 @@
 <P>
 The exercise can be performed by placing all of the Python commands
-into a script, (which is supplied for 
-<A href="https://subversion.xray.aps.anl.gov/trac/pyGSAS/browser/Tutorials/PythonScript/data/example.py?format=txt">
-download here</A>),
+into a script, 
 but a more pedagogical approach will be to enter the
 commands into a Python interpreter. Use of IPython or Jupyter to run
 Python will make this a more pleasant experience. 
 
-<h2>Multi-step Script Approach</h2>
+<a name="multistep">
+<h2>A. Create a Multi-step Script</h2></a>
+
+Note that the script in this section is supplied for 
+<A href="https://subversion.xray.aps.anl.gov/trac/pyGSAS/browser/Tutorials/PythonScript/data/example.py?format=txt">
+download here</A>, but some editing will be needed to match where files
+are found on your computer.
 
 <h4>0: Load the GSASIIscriptable module</H4>
@@ -450 +466 @@
 
 </blockquote>
-<a name="SingleStep"><h2>Single Step Approach</h2></a>
+<a name="SingleStep">
+<h2>B. Single-Step Refinement</h2></a>
 <blockquote>
 
@@ -457 +474 @@
 GSASIIscriptable module documentation</A>,
 the <I>project</i><tt>.do_refinements()</tt> method can be used to
-perform multiple refinement steps. To duplicate the above steps into a
+perform multiple refinement steps.
+Note that this version of the exercise can be 
+<A href="https://subversion.xray.aps.anl.gov/trac/pyGSAS/browser/Tutorials/PythonScript/data/SingleStep.py?format=txt">
+downloaded here</A>.
+To duplicate the above steps into a
 single call, a more complex set of dicts must be created, as shown
 below: 
 
-<blockquote><textarea rows="39" cols="75" readonly>
+<blockquote><textarea rows="38" cols="75" readonly>
 # tutorial step 4: turn on background refinement (Hist)
 refdict0 = {"set": {"Background": { "no. coeffs": 3, "refine": True }},
@@ -515 +536 @@
 dictList = [refdict0,refdict1,refdict2,refdict3,
             refdict4a,refdict4b,
-            refdict5a,refdict5b,refdict5c]
-</textarea></blockquote>
+            refdict5a,refdict5b,refdict5c]</textarea></blockquote>
+
 Steps 4 through 10, above then can be performed with these few commands:
 <blockquote><textarea rows="4" cols="75" readonly>
@@ -522 +543 @@
 gpx.data['Controls']['data']['max cyc'] = 8 # not in API
 hist2.data['Sample Parameters']['Gonio. radius'] = 650. # not in API
-gpx.do_refinements(dictList)
-</textarea></blockquote>
-Note that this version of the exercise can be 
-<A href="https://subversion.xray.aps.anl.gov/trac/pyGSAS/browser/Tutorials/PythonScript/data/SingleStep.py?format=txt">
-downloaded here</A>).
+gpx.do_refinements(dictList)</textarea></blockquote>
+
+</blockquote>
+<a name="Simulate">
+<h2>C. Powder Pattern Simulation</h2></a>
+<blockquote>
+Use of the 
+<A href="http://gsas-ii.readthedocs.io/en/latest/GSASIIscripts.html" target="_blank">
+GSASIIscriptable module</A> makes it very simple to simulate a powder
+diffraction pattern using GSAS-II. This is demonstrated in this
+section. 
+
+Note that the Python commands can be 
+<A
+href="https://subversion.xray.aps.anl.gov/trac/pyGSAS/browser/Tutorials/PythonScript/data/sim.py?format=txt">downloaded here</A>.
+<P>
+As before, the location of the GSASIIscripts Python module must be
+defined and the module must be loaded:
+
+<blockquote><textarea rows="3" cols="60" readonly>
+import os,sys
+sys.path.insert(0,os.path.expanduser("~/g2conda/GSASII/"))
+import GSASIIscriptable as G2sc</textarea></blockquote>
+
+To simplify this example, as before we will define the location where files will
+be read from and written (as <tt>datadir</tt> and
+<tt>workdir</tt>). Note that files "inst_d1a.prm" and
+"PbSO4-Wyckoff.cif" from <A
+href="https://subversion.xray.aps.anl.gov/pyGSAS/Tutorials/PythonScript/data/">here</A>
+are needed. 
+
+<blockquote><textarea rows="2" cols="70" readonly>
+workdir = "/Users/toby/Scratch/PythonScript"
+datadir = "/Users/toby/software/G2/Tutorials/PythonScript/data"</textarea></blockquote>
+
+We then need to create a project and for this example we choose to
+define the phase first. (It would work equally well to create the
+histogram first and then define the phase.)
+
+<blockquote><textarea rows="4" cols="70" readonly>
+gpx = G2sc.G2Project(filename='PbSO4sim.gpx') # create a project
+# setup step 1: add a phase to the project
+phase0 = gpx.add_phase(os.path.join(datadir,"PbSO4-Wyckoff.cif"),
+                      phasename="PbSO4",fmthint='CIF') </textarea></blockquote>
+
+We then add a "dummy" histogram to the project. Note that an
+instrument parameter file is specified, but not a data file. The range
+of data to be used and the step size must be specified. The phases
+parameter is specified as ``gpx.phases()`` which creates a list of all
+the previously read phases, which in this case is equivalent to
+``[phase0]``.
+
+<blockquote><textarea rows="6" cols="70" readonly>
+# setup step 2: add a simulated histogram and link it to the previous phase(s)
+hist1 = gpx.add_simulated_powder_histogram("PbSO4 simulation",
+                          os.path.join(datadir,"inst_d1a.prm"),
+                          5.,120.,0.01,
+                          phases=gpx.phases())</textarea></blockquote>
+
+Finally, to perform the simulation computation, a refinement is
+needed:
+
+<blockquote><textarea rows="3" cols="70" readonly>
+gpx.data['Controls']['data']['max cyc'] = 0 # refinement not needed
+gpx.do_refinements([{}])
+gpx.save()</textarea></blockquote>
+
+However, there is no need to actually optimize any variables,
+so the number of refinement cycles is set to zero. Refinement is
+initiated then with <I>proj</i>.<tt>do_refinements</tt>. Finally, the
+project is saved. 
 
 </blockquote>
@@ -532 +619 @@
 <hr>
 <address></address>
-<!-- hhmts start -->Last modified: Tue Dec 26 17:03:22 CST 2017 <!-- hhmts end -->
+<!-- hhmts start -->Last modified: Thu Dec 28 12:18:27 CST 2017 <!-- hhmts end -->
 </body> </html>