Index: /trunk/help/gsasII.html
===================================================================
 /trunk/help/gsasII.html (revision 4667)
+++ /trunk/help/gsasII.html (revision 4668)
@@ 3677,13 +3677,19 @@
This window provides the main controls and a few
global parameters for GSASII.


What can I do here?
On this page, there are three or four sets of
controls. The first is for how refinements operate.

+"Times New Roman"'>This window provides access to the controls that
+determine how GSASII performs minimizations as well as few
+global parameters for GSASII. Note that many other customization
+settings are set as configuration variables
+in the Preferences menu. (See the
+
+Programmer's documentation for a description of those.)
+
+
+Refinement Controls: These
+controls determine how refinements are performed. The first determines
+the computational engine used to minimize the structure.
+
+
@@ 3693,22 +3699,23 @@
 analytic Hessian: This is the default option and is usually
 the most useful. It uses as customdeveloped leastsquares
+ the most useful. It uses a customdeveloped leastsquares
minimizer that uses singularvalue decomposition (SVD) to reduce the
errors caused by correlated variables and the
 LevenbergMarquardt algorithm to downweight the offdiagonal
+ LevenbergMarquardt algorithm to upweight diagonal
Hessian terms when refinements fail to lower χ^{2}.
 analytic Jacobian: This uses a numpyprovided leastsq
 minimizer, which not applicable for larger
 problems as it requires
+ minimizer, which not applicable for
+ problem with a large number of histograms as it requires
much more memory than the Hessian routines. This because it
 creates a Jacobian matrix is shaped N x M (N parameters x M
 observations) and uses that to create the N x N Hessian. The
 "Hessian" minimizers create the Hessian matrix directly.
+ creates a Jacobian matrix that is shaped N x M (N parameters x M
+ observations) while the Hessian methods create a Jacobian matrix
+ only each histogram.
 numeric: This also uses the numpy leastsq
minimizer, and is also not applicable for larger
 problems. Unlike, the "analytic Jacobian", numerical derivates
 are computed for derivatives rather than analytical derivatives
+ problems. Unlike, the "analytic Jacobian", numerical derivatives
+ are computed rather than use the analytical derivatives
that are coded directly into GSASII. This will be slower than
 the analytical derivatives and will converge more slowly. It is
+ the analytical derivatives and will is often less accurate which
+ results in slower convergence. It is
typically used for code development to check the accuracy of the
analytical derivative formulations.
@@ 3716,5 +3723,6 @@
Hessian but does not include the LevenbergMarquardt
algorithm. It can be faster, but is more prone to
 diverge when severe correlation is present.
+ diverge when severe correlation is present. It is possible that
+ it might be better for singlecrystal refinements.
@@ 3735,20 +3743,19 @@
 Min deltaM/M
  This determines when convergence is recognized;
 the refinement will stop when the change in the minimization
 function is less than this value. Set Min deltaM/M = 1.0 to force just a
single cycle to be performed. The default is 0.001. A value less than
 10^{4} causes the refinement to cycle with no meaningful
 improvement since shifts become a small fraction of the
 parameter's uncertainties. Set Min deltaM/M = 1.0 to force
 refinement to stop after a single refinement.
 The allowed range is 10^{9} to 1.0.

+  A refinement will stop when the change in the minimization function
+ (M=Σ[w(IoIc)^{2}])
+ is less than this value. The allowed range is 10^{9} to
+ 1.0, with a default of 0.001. A value of
+ 1.0 stops the refinement after a single cycle. Values less than
+ 10^{4} cause refinements to continue even if there is
+ no meaningful improvement.
+
 Max cycles
 This determines the maximum number of refinement cycles that
 will be performed. This is only available with the "Hessian" minimizers.
+ will be performed. This is only available with the "Hessian" minimizers.
 Initial lambda
  Note that here λ is the Marquardt coefficient, which when large
 downweights the significance of the offdiagonal terms in the
+
 Note that here λ is the Marquardt coefficient, where a weight of
+ 1+λ is applied to the diagonal elements of the Hessian. When λ is
+ large, this downweights the significance of the offdiagonal terms in the
Hessian. Thus, when λ is large, the refinement is effectively one of
steepestdescents, where correlation between variables is
@@ 3756,18 +3763,22 @@
slow and may not always find the local minimum.
This is only available with the "analytical Hessian" minimizer.

+
 SVD zero tolerance
 This determines the level where SVD considers values to be the
same. Default is 10^{6}. Make larger to where problems occur due to correlation. This is only available with the "Hessian" minimizers.

+
 Initial shift factor
  ?

+  A “damping multiplier” applied during the first refinement
+ cycle, for Jacobean/numeric refinements only.
+ Should be in interval (0.1, 100). See the
+ SciPy leastsq docs
+ for more information.
+
A set of controls is provided for
+
Single Crystal: A set of controls is provided for
control of singlecrystal refinements.
These only appear when single crystal (HKLF) histograms are present
in the project.
+in the project.
@@ 3775,31 +3786,38 @@
 When checked, refinements are against F^{2} rather than
F.

+
 Min obs/sig
  ?

+  Conventional cutoff for single crystal refinements as to what reflections
+ should be considered observed, typical values are 2.0 (2σ) or 3.0 (3σ).
+
 Min extinct.
  ?

+  (needs further work)
+
 Max deltF/sig
  ?

+  Removes reflections that are very poorly fit. Should be used
+ only with extreme care, since poorlyfit reflections could be an
+ indication that the structure is wrong.
+
 Max dspacing
 Reflections with dspace values larger than this value are ignored.

+
 Min dspacing
 Reflections with dspace values smaller than this value are ignored.

+
A set of controls is for
sequential refinement. Settings here determine if "normal" or "sequential"
refinement is performed. If no datasets are selected, then all "used"
histograms are included in one combined refinement. However, if any
number histogram are selected used here, then a
sequential refinement is performed, where a fit is made to each
histogram in turn. Only the first item below is shown in "normal" mode.
+
Sequential Settings:
+A set of controls is for
+sequential refinement. Settings here determine if a "normal" or "sequential"
+refinement is performed. If no datasets are selected here, then all
+histograms linked to phases in the project and that are flagged as
+"used" are included in one potentially large (combined)
+refinement. However, if any
+number of histograms are selected here, then a
+sequential refinement is performed, where a fit is made to the
+structural model(s) fitting each selected
+histogram in turn. Only the first item below is shown in "normal" mode.
@@ 3811,5 +3829,5 @@
set as "normal". The button is labeled "Select" when in normal refinement
mode and "Reselect" in sequential refinement mode.

+
 Reverse order?
 Normally, in a sequential histograms are fit in the order they
@@ 3818,5 +3836,5 @@
but when this option is selected, the sequential fit is performed
with the last tree entry first.

+
 Copy results to next histogram?
 When this option is selected, the fitted parameters from each
@@ 3830,11 +3848,29 @@
refinement is completed. For subsequent refinements, it is usually
better to start with the results from the previous fit.

+
 Clear previous seq. results
 When this button is pressed, the "Sequential Results" entry
with the results from the last sequential fit is deleted from the
tree.

+
+Global Settings:
+This is a location for parameters that apply to an entire project.
+At present there is only one.
+
+
+  CIF Author
+  The value provided here is used when creating a CIF of an
+ entire project.
+
+
+
+
+What can I do here?
+This offers a place to change how
+GSASII performs refinements, but has no specific menu commands or
+graphics.
+