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 GSAS-II. - -

##### -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 GSAS-II performs minimizations as well as few +global parameters for GSAS-II. 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 custom-developed least-squares + the most useful. It uses a custom-developed least-squares minimizer that uses singular-value decomposition (SVD) to reduce the errors caused by correlated variables and the - Levenberg-Marquardt algorithm to down-weight the off-diagonal + Levenberg-Marquardt algorithm to up-weight diagonal Hessian terms when refinements fail to lower χ2.
• analytic Jacobian: This uses a numpy-provided 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 GSAS-II. 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 Levenberg-Marquardt 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 single-crystal refinements.

@@ -3735,20 +3743,19 @@

Min delta-M/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 delta-M/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 delta-M/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(Io-Ic)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 - down-weights the significance of the off-diagonal 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 down-weights the significance of the off-diagonal terms in the Hessian. Thus, when λ is large, the refinement is effectively one of steepest-descents, 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 single-crystal 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 F2 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 delt-F/sig
-
? -
+
Removes reflections that are very poorly fit. Should be used + only with extreme care, since poorly-fit reflections could be an + indication that the structure is wrong. +

Max d-spacing
Reflections with d-space values larger than this value are ignored. -
+

Min d-spacing
Reflections with d-space 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 +GSAS-II performs refinements, but has no specific menu commands or +graphics. +