Changeset 3218

Timestamp:

Jan 11, 2018 9:44:24 AM (6 years ago)

Author:

toby

Message:

add new stuff to simulate tutorial

Location:

Tutorials/PythonScript

Files:

• PbSO4.png (added)
• Scripting.htm (modified) (4 diffs)
• data/sim.py (modified) (1 diff)

Tutorials/PythonScript/Scripting.htm

@@ -584 +584 @@
 <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
+# step 1, setup: add a phase to the project
 phase0 = gpx.add_phase(os.path.join(datadir,"PbSO4-Wyckoff.cif"),
                       phasename="PbSO4",fmthint='CIF') </textarea></blockquote>
@@ -595 +595 @@
 ``[phase0]``.
 
-<blockquote><textarea rows="6" cols="70" readonly>
-# setup step 2: add a simulated histogram and link it to the previous phase(s)
+<blockquote><textarea rows="6" cols="80" readonly>
+# step 2, setup: 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"),
@@ -602 +602 @@
                           phases=gpx.phases())</textarea></blockquote>
 
-Finally, to perform the simulation computation, a refinement is
+Note that the computed pattern cannot be seen above "simulated noise"
+unless the intensities are large enough. We can change the pattern
+scale factor using the Scale factor (parameter
+<tt>hist1.data['Sample Parameters']['Scale'][0]</tt>), as shown below.
+
+<blockquote><textarea rows="3" cols="70" readonly>
+# Step 3: Set the scale factor to adjust the y scale
+hist1.SampleParameters['Scale'][0] = 1000000.
+</textarea></blockquote>
+
+Next, to perform the simulation computation, a refinement is
 needed:
 
-<blockquote><textarea rows="3" cols="70" readonly>
+<blockquote><textarea rows="4" cols="80" readonly>
+# step 4, compute: turn off parameter optimization and calculate pattern
 gpx.data['Controls']['data']['max cyc'] = 0 # refinement not needed
 gpx.do_refinements([{}])
@@ -612 +623 @@
 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
+initiated then with <I>proj</i>.<tt>do_refinements</tt>. To keep the
+results in a .gpx file, the
 project is saved. 
 
-</blockquote>
+<P>
+Finally, we want to do something with the results. The histogram could
+be written to a file with the <A href=
+"http://gsas-ii.readthedocs.io/en/latest/GSASIIscriptable.html#GSASIIscriptable.G2PwdrData.Export">
+<i>histogram.</i><tt>Export()</tt></A> command. Note that the first time
+a refinement computation is done with a dummy histogram the "observed"
+pattern is set from the calculated intensities. Here an alternate option is
+used, where the values are retrieved and plotted.
+
+<blockquote><textarea rows="6" cols="70" readonly>
+# step 5, retrieve results & plot
+x = gpx.histogram(0).getdata('x')
+y = gpx.histogram(0).getdata('ycalc')
+import matplotlib.pyplot as plt
+plt.plot(x,y)
+plt.savefig('PbSO4.png') # to show on screen use: plt.show()</textarea></blockquote>
+
+Note that in the above, <tt>gpx.histogram(0)</tt> is used to show how
+to reference <tt>hist1</tt> when the histogram object is not
+known. The generated two-theta values and computed intensity values
+are retrieved and the remaining lines generate a very simple plot
+which is saved to a file, as shown below.
+</blockquote>
+
+<img src="PbSO4.png">
 
 <hr>
 <address></address>
-<!-- hhmts start -->Last modified: Thu Dec 28 12:18:27 CST 2017 <!-- hhmts end -->
+<!-- hhmts start -->Last modified: Thu Jan 11 09:41:57 CST 2018 <!-- hhmts end -->
 </body> </html>

Tutorials/PythonScript/data/sim.py

@@ -14 +14 @@
 gpx = G2sc.G2Project(filename='PbSO4sim.gpx') # create a project
 
-# setup step 1: add a phase to the project
+# step 1, setup: add a phase to the project
 phase0 = gpx.add_phase(os.path.join(datadir,"PbSO4-Wyckoff.cif"),
                       phasename="PbSO4",fmthint='CIF')
 
-# setup step 2: add a simulated histogram and link it to the previous phase(s)
+# step 2, setup: 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())
+
+# Step 3: Set the scale factor to adjust the y scale
+hist1.SampleParameters['Scale'][0] = 1000000.
+
+# step 4, compute: turn off parameter optimization and calculate pattern
 gpx.data['Controls']['data']['max cyc'] = 0 # refinement not needed
 gpx.do_refinements([{}])
 gpx.save()
 
+# step 5, retrieve results & plot
+x = gpx.histogram(0).getdata('x')
+y = gpx.histogram(0).getdata('ycalc')
+import matplotlib.pyplot as plt
+plt.plot(x,y)
+plt.savefig('PbSO4.png') # to show on screen use: plt.show()
 
 
+