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remove vars from constraints (see G2obj.removeNonRefined); new tutorial

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2<h2>List of GSAS-II tutorials</H2><UL>
4    <p> A list of available tutorials appears below. Each tutorial is a
5    web page that can be opened using the link below, but most tutorials also need
6    to have example data files downloaded. This can also be done with links included below,
7    but it can be easier to access tutorials using
8    <b>Help/Tutorials</b> menu item.
9    When this menu entry is used from inside GSAS-II (unless "browse tutorial on web" is selected),
10    the data files are downloaded to a local directory and GSAS-II will start from that directory
11    for most file open commands. Most tutorials have also been recorded as videos of the computer screen
12    along with naration. Links are provided below where videos are available.
13    </p>
14</UL><h4>Getting started</H4><UL>
15<LI><A href=" GSAS.htm">Starting GSAS-II</A>
16 [link: <A href="">video</A>, no example data].
17<blockquote><I>An introduction to GSAS-II with starting instructions and a brief description of the displays.</I></blockquote>
18</UL><h4>Rietveld refinement</H4><UL>
19<LI><A href=" CW Powder Data.htm">CW Neutron Powder fit for Yttrium-Iron Garnet</A>
20 [links: <A href="">video</A>, <A href="">Exercise files</A>].
21<blockquote><I>This shows a simple Rietveld refinement with constraints from CW neutron powder diffraction data.</I></blockquote>
22<LI><A href=" X.htm">Fitting laboratory X-ray powder data for fluoroapatite</A>
23 [links: <A href="">video</A>, <A href="">Exercise files</A>].
24<blockquote><I>This shows a simple Rietveld refinement with CuKa lab Bragg-Brentano powder data.</I></blockquote>
25<LI><A href=" refinement.htm">Combined X-ray/CW-neutron refinement of PbSO4</A>
26 [links: <A href="">video</A>, <A href="">Exercise files</A>].
27<blockquote><I>This shows Rietveld refinement of a structure with room temperature lab CuKa data and low temperature CW neutron data;
28     use is made of the lattice parameter offsets to account for thermal expansion.</I></blockquote>
29<LI><A href=" Joint Refinement/TOF combined XN Rietveld refinement in GSAS.htm">Combined X-ray/TOF-neutron Rietveld refinement</A>
30 [links: <A href="">video</A>, <A href=" Joint Refinement/data">Exercise files</A>].
31<blockquote><I>This shows Rietveld refinement with high resolution synchrotron powder data and neutron TOF data</I></blockquote>
32<LI><A href="">Simple Magnetic Structure Analysis</A>
33 [links: <A href="">video</A>, <A href="">Exercise files</A>].
34<blockquote><I>Analysis of a simple antiferromagnet and a simple ferromagnet from CW neutron powder data</I></blockquote>
35<LI><A href="">Simulating Powder Diffraction with GSAS-II</A>
36 [links: <A href="">video</A>, <A href="">Exercise files</A>].
37<blockquote><I>This show how to create a simulated powder pattern from a lab diffractometer.</I></blockquote>
38<LI><A href="">Fitting the Starting Background using Fixed Points</A>
39 [links: <A href="">video</A>, <A href="">Exercise files</A>].
40<blockquote><I>This shows how to get an initial estimate of background parameters from a suite of fixed points
41     before beginning Rietveld refinement.</I></blockquote>
42<LI><A href="">Create a Publication-Ready Rietveld Plot</A>
43 [link: <A href="">Exercise files</A>].
44<blockquote><I>Shows how to create a customized version of a plot from a fit,
45     with enlarged letters, different colors or symbols which can be written
46     as a bitmap file, a pdf file or be exported to the Grace or Igor Pro
47     plotting programs.</I></blockquote>
48</UL><h4>Parametric sequential fitting</H4><UL>
49<LI><A href="">Sequential refinement of multiple datasets</A>
50 [links: <A href="">video</A>, <A href="">Exercise files</A>].
51<blockquote><I>This shows the fitting of a structural model to multiple data sets collected as a function of temperature (7-300K).
52     This tutorial is the prerequisite for the next one.</I></blockquote>
53<UL><LI><A href="">Parametric Fitting and Pseudo Variables for Sequential Fits</A> <A href="#prereq">*</A>
54 [link: <A href="">video</A>, no example data].
55<blockquote><I>This explores the results of the sequential refinement obtained in the previous tutorial; includes
56     plotting of variables and fitting the changes with simple equations.</I></blockquote>
58<LI><A href=" Sequential Single Peak Fit/TOF Sequential Single Peak Fit.htm">Sequential fitting of single peaks and strain analysis of result</A>
59 [links: <A href="">video</A>, <A href=" Sequential Single Peak Fit/data">Exercise files</A>].
60<blockquote><I>This shows the fitting of single peaks in a sequence of TOF powder patterns from a sample under load; includes
61      fitting of the result to get Hookes Law coefficients for elastic deformations.</I></blockquote>
62</UL><h4>Structure solution</H4><UL>
63<LI><A href=" Peaks.htm">Fitting individual peaks & autoindexing</A>
64 [links: <A href="">video</A>, <A href="">Exercise files</A>].
65<blockquote><I>This covers two examples of selecting individual powder diffraction peaks, fitting them and then
66     indexing to determine the crystal lattice and possible space group. This is the prerequisite for the next two tutorials.</I></blockquote>
67<UL><LI><A href=" Flipping in GSAS.htm">Charge Flipping structure solution for jadarite</A> <A href="#prereq">*</A>
68 [no example data or video].
69<blockquote><I>Solving the structure of jadarite (HLiNaSiB3O8) by charge flipping from Pawley extracted intensities
70     from a high resolution synchrotron powder pattern.</I></blockquote>
72<UL><LI><A href=" Flipping - sucrose.htm">Charge Flipping structure solution for sucrose</A> <A href="#prereq">*</A>
73 [no example data or video].
74<blockquote><I>Solving the structure of sucrose (C12H22O11) by charge flipping from Pawley extracted intensities
75     from a high resolution synchrotron powder pattern.</I></blockquote>
77<LI><A href="">Charge Flipping structure solution with Xray single crystal data</A>
78 [link: <A href="">Exercise files</A>].
79<blockquote><I>Solving the structure of dipyridyl disulfate by charge flipping and then refine the structure by least-squares.</I></blockquote>
80<LI><A href=" Charge Flipping/Charge Flipping with TOF single crystal data in GSASII.htm">Charge flipping with neutron TOF single crystal data</A>
81 [link: <A href=" Charge Flipping/data">Exercise files</A>].
82<blockquote><I>Solving the crystal structure or rubrene (C42H28) from single crystal neutron data via charge flipping and then refine the structure by least squares.</I></blockquote>
83<LI><A href=" in GSAS.htm">Monte-Carlo simulated annealing structure determination</A>
84 [link: <A href="">Exercise files</A>].
85<blockquote><I>Solving the structures of 3-aminoquinoline and α-d-lactose monohydrate from powder diffraction data via Monte Carlo/Simulated Annealing (MC/SA).</I></blockquote>
86</UL><h4>Stacking Fault Modeling</H4><UL>
87<LI><A href=" Faults-I.htm">Stacking fault simulations for diamond</A>
88 [link: <A href="">video</A>, no example data].
89<blockquote><I>This shows how to simulate the diffraction patterns from faulted diamond.</I></blockquote>
90<LI><A href=" Faults II.htm">Stacking fault simulations for Keokuk kaolinite</A>
91 [link: <A href="">Exercise files</A>].
92<blockquote><I>This shows how to simulate some diffraction patterns from well ordered Keokuk kaolinite (Al2Si2O5(OH)4) clay.</I></blockquote>
93<LI><A href=" Faults-III.htm">Stacking fault simulations for Georgia kaolinite</A>
94 [link: <A href="">Exercise files</A>].
95<blockquote><I>This shows how to simulate some diffraction patterns from poorly ordered Georgia kaolinite (Al2Si2O5(OH)4) clay.</I></blockquote>
96</UL><h4>Powder diffractometer calibration</H4><UL>
97<LI><A href="">Determining Starting Profile Parameters from a Standard</A>
98 [links: <A href="">video</A>, <A href="">Exercise files</A>].
99<blockquote><I>This shows how to determine profile parameters by fitting individual peaks
100        with data collected on a standard using a lab diffractometer.</I></blockquote>
101<LI><A href=" Calibration/Calibration of a TOF powder diffractometer.htm">Calibration of a Neutron TOF diffractometer</A>
102 [links: <A href="">video</A>, <A href=" Calibration/data">Exercise files</A>].
103<blockquote><I>This uses the fitted positions of all visible peaks in a pattern of NIST SRM 660b La11B6
104     (a=4.15689Å) obtained in a multiple single peak fit. The positions are compared to those expected from the
105     known lattice parameters to establish the diffractometer constants (difC, difA, difB and Zero) used for
106     calculating TOF peak positions from d-spacings. In addition, the peak fitting includes the various profile
107     coefficients thus fully describing the instrument contribution to the peak profiles.</I></blockquote>
108</UL><h4>2D Image Processing</H4><UL>
109<LI><A href=" of an area detector in GSAS.htm">Calibration of an area detector</A>
110 [links: <A href="">video</A>, <A href="">Exercise files</A>].
111<blockquote><I>A demonstration of calibrating a Perkin-Elmer area detector,  where the detector was intentionally tilted at 45 degrees.
112     This exercise is the prerequisite for the next one.</I></blockquote>
113<UL><LI><A href=" of area detector data in GSAS.htm">Integration of area detector data</A> <A href="#prereq">*</A>
114 [link: <A href="">video</A>, no example data].
115<blockquote><I>Integration of the image from a Perkin-Elmer area detector, where the detector was intentionally tilted at 45 degrees.</I></blockquote>
117<LI><A href=" fitting of 2D data in GSAS-II.htm">Strain fitting of 2D data</A>
118 [links: <A href="">video</A>, <A href="">Exercise files</A>].
119<blockquote><I>This show how to determine 3 strain tensor values using the method of He & Smith (Adv. in X-ray Anal. 41, 501, 1997)
120     directly froom a sequence of 2D imges from a loaded sample.</I></blockquote>
121<LI><A href=" analysis of 2D data in GSAS-II.htm">Texture analysis of 2D data</A>
122 [links: <A href="">video</A>, <A href="">Exercise files</A>].
123<blockquote><I>This shows 3 different methods for determining texture via spherical harmonics from 2D x-ray diffraction images. </I></blockquote>
124<LI><A href="">Area Detector Calibration with Multiple Distances: Determine Wavelength</A>
125 [links: <A href="">video</A>, <A href="">Exercise files</A>].
126<blockquote><I>To get an accurate wavelength, without knowing the sample-to-detector distance accurately, images recorded with
127     several different distances can be used. This exercise shows how to determine the wavelength from such a series.
128     This exercise is the prerequisite for the next one.</I></blockquote>
129<UL><LI><A href="">Area Detector Calibration with Multiple Distances: Calibrate Detector Distances</A> <A href="#prereq">*</A>
130 [link: <A href="">video</A>, no example data].
131<blockquote><I>To get an accurate wavelength, without knowing the sample-to-detector distance accurately, images recorded with
132     several different distances can be used. After using the previous exercise to determine the wavelength,
133     this exercise calibrates the detector distances and shows examples of how to mask, integrate, and save those parameters
134     for future reuse.</I></blockquote>
136</UL><h4>Small-Angle Scattering</H4><UL>
137<LI><A href=" Angle Size Distribution.htm">Small angle x-ray data size distribution (alumina powder)</A>
138 [links: <A href="">video</A>, <A href="">Exercise files</A>].
139<blockquote><I>This shows how to determine the size distribution of particles using data from a constant
140     wavelength synchrotron X-ray USAXS instrument. This is the prerequisite for the next tutorial</I></blockquote>
141<UL><LI><A href=" Small Angle Scattering Data.htm">Fitting small angle x-ray data (alumina powder)</A> <A href="#prereq">*</A>
142 [links: <A href="">video</A>, <A href="">Exercise files</A>].
143<blockquote><I>This shows how to fit small angle scattering data using data from a constant wavelength synchrotron X-ray USAXS instrument. </I></blockquote>
145<LI><A href=" Angle Image Processing.htm">Image Processing of small angle x-ray data</A>
146 [links: <A href="">video</A>, <A href="">Exercise files</A>].
147<blockquote><I>This shows how to  reduce 2D SAXS data to create 1D absolute scaled data. </I></blockquote>
148<LI><A href=" Refinement of Small Angle Scattering Data.htm">Sequential refinement with small angle scattering data</A>
149 [links: <A href="">video</A>, <A href="">Exercise files</A>].
150<blockquote><I>This shows how to fit USAXS small angle scattering data for a suite of samples to demonstrate the
151     sequential refinement technique in GSAS-II for SASD and demonstrates fitting with a hard sphere structure
152     factor for non-dilute systems. </I></blockquote>
154<LI><A href=" twin refinement in GSAS.htm">Merohedral twin refinements</A>
155 [links: <A href="">video</A>, <A href="">Exercise files</A>].
156<blockquote><I>This shows how to use GSAS-II to refine the structure of a few single crystal structures where there is merohedral twinning. </I></blockquote>
157<LI><A href=" Single Crystal Refinement/TOF single crystal refinement in GSAS.htm">Single crystal refinement from TOF data</A>
158 [link: <A href=" Single Crystal Refinement/data">Exercise files</A>].
159<blockquote><I>This shows how to refine the structure of sapphire (really corundum, Al2O3) from single crystal diffraction data
160     collected at the SNS on the TOPAZ instrument at room temperature.  </I></blockquote>
161<LI><A href="">Scripting a GSAS-II Refinement from Python</A>
162 [link: <A href="">Exercise files</A>].
163<blockquote><I>This demonstrates the use of the GSASIIscriptable module. This uses a Python script to perform a refinement or
164     computation, but without use of the GSAS-II graphical user interface. This is a prerequisite for the next tutorial.</I></blockquote>
165<UL><LI><A href="">Running a GSAS-II Refinement from the Command Line</A> <A href="#prereq">*</A>
166 [link: <A href="">Exercise files</A>].
167<blockquote><I>This shows a unix script that duplicates the previous Python Scripting GSAS-II tutorial. </I></blockquote>
170<A name=prereq>* Indented tutorials require the previous unindented tutorial as a prerequisite
171<h3>Tutorials with video-recorded examples</H3>
172<UL><LI><A href="">Starting GSAS-II</A></LI>
173<LI><A href="">CW Neutron Powder fit for Yttrium-Iron Garnet</A></LI>
174<LI><A href="">Fitting laboratory X-ray powder data for fluoroapatite</A></LI>
175<LI><A href="">Combined X-ray/CW-neutron refinement of PbSO4</A></LI>
176<LI><A href="">Combined X-ray/TOF-neutron Rietveld refinement</A></LI>
177<LI><A href="">Simple Magnetic Structure Analysis</A></LI>
178<LI><A href="">Simulating Powder Diffraction with GSAS-II</A></LI>
179<LI><A href="">Fitting the Starting Background using Fixed Points</A></LI>
180<LI><A href="">Sequential refinement of multiple datasets</A></LI>
181<LI><A href="">Parametric Fitting and Pseudo Variables for Sequential Fits</A></LI>
182<LI><A href="">Sequential fitting of single peaks and strain analysis of result</A></LI>
183<LI><A href="">Fitting individual peaks & autoindexing</A></LI>
184<LI><A href="">Stacking fault simulations for diamond</A></LI>
185<LI><A href="">Determining Starting Profile Parameters from a Standard</A></LI>
186<LI><A href="">Calibration of a Neutron TOF diffractometer</A></LI>
187<LI><A href="">Calibration of an area detector</A></LI>
188<LI><A href="">Integration of area detector data</A></LI>
189<LI><A href="">Strain fitting of 2D data</A></LI>
190<LI><A href="">Texture analysis of 2D data</A></LI>
191<LI><A href="">Area Detector Calibration with Multiple Distances: Determine Wavelength</A></LI>
192<LI><A href="">Area Detector Calibration with Multiple Distances: Calibrate Detector Distances</A></LI>
193<LI><A href="">Small angle x-ray data size distribution (alumina powder)</A></LI>
194<LI><A href="">Fitting small angle x-ray data (alumina powder)</A></LI>
195<LI><A href="">Image Processing of small angle x-ray data</A></LI>
196<LI><A href="">Sequential refinement with small angle scattering data</A></LI>
197<LI><A href="">Merohedral twin refinements</A></LI>
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