Changeset 4668


Ignore:
Timestamp:
Dec 2, 2020 11:39:06 AM (11 months ago)
Author:
toby
Message:

updates to refinement options

File:
1 edited

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  • trunk/help/gsasII.html

    r4664 r4668  
    36773677
    36783678<p class=MsoNormal style='margin-left:.5in'><span style='mso-fareast-font-family:
    3679 "Times New Roman"'>This window provides the main controls and a few
    3680 global parameters for GSAS-II.
    3681 
    3682 <h5 style='margin-left:.5in'><span
    3683 style='mso-fareast-font-family:"Times New Roman"'>
    3684 What can I do here?</span></h5>
    3685 <p style='margin-left:0.75in'>On this page, there are three or four sets of
    3686 controls. The first is for how refinements operate.
    3687 </p>
     3679"Times New Roman"'>This window provides access to the controls that
     3680determine how GSAS-II performs minimizations as well as few
     3681global parameters for GSAS-II. Note that many other customization
     3682settings are set as <A Href=#Preferences>configuration variables</a>
     3683in the Preferences menu. (See the
     3684<a
     3685href="https://gsas-ii.readthedocs.io/en/latest/GSASIIutil.html#module-config_example">
     3686Programmer's documentation</a> for a description of those.)
     3687</P>
     3688
     3689<p style='margin-left:0.75in'><U>Refinement Controls:</u><i> These
     3690controls determine how refinements are performed. The first determines
     3691the computational engine used to minimize the structure.
     3692</i></p>
     3693
    36883694<A name="RefineType"></A>
    36893695<DL style='margin-left:1.0in'>
     
    36933699    <UL style='margin-left:0.25in'>
    36943700      <LI><U>analytic Hessian</U>: This is the default option and is usually
    3695       the most useful. It uses as custom-developed least-squares
     3701      the most useful. It uses a custom-developed least-squares
    36963702      minimizer that uses singular-value decomposition (SVD) to reduce the
    36973703      errors caused by correlated variables and the
    3698       Levenberg-Marquardt algorithm to down-weight the off-diagonal
     3704      Levenberg-Marquardt algorithm to up-weight diagonal
    36993705      Hessian terms when refinements fail to lower χ<sup>2</sup>.
    37003706      <LI><u>analytic Jacobian</u>: This uses a numpy-provided <I>leastsq</I>
    3701       minimizer, which not applicable for larger
    3702       problems as it requires
     3707      minimizer, which not applicable for
     3708      problem with a large number of histograms as it requires
    37033709      much more memory than the Hessian routines. This because it
    3704       creates a Jacobian matrix is shaped N x M (N parameters x M
    3705       observations) and uses that to create the N x N Hessian. The
    3706       "Hessian" minimizers create the Hessian matrix directly.
     3710      creates a Jacobian matrix that is shaped N x M (N parameters x M
     3711      observations) while the Hessian methods create a Jacobian matrix
     3712      only each histogram.
    37073713      <LI><u>numeric</u>: This also uses the numpy <I>leastsq</I>
    37083714      minimizer, and is also not applicable for larger
    3709       problems. Unlike, the "analytic Jacobian", numerical derivates
    3710       are computed for derivatives rather than analytical derivatives
     3715      problems. Unlike, the "analytic Jacobian", numerical derivatives
     3716      are computed rather than use the analytical derivatives
    37113717      that are coded directly into GSAS-II. This will be slower than
    3712       the analytical derivatives and will converge more slowly. It is
     3718      the analytical derivatives and will is often less accurate which
     3719      results in slower convergence. It is
    37133720      typically used for code development to check the accuracy of the
    37143721      analytical derivative formulations.
     
    37163723      Hessian</U> but does not include the Levenberg-Marquardt
    37173724      algorithm. It can be faster, but is more prone to
    3718       diverge when severe correlation is present.
     3725      diverge when severe correlation is present. It is possible that
     3726      it might be better for single-crystal refinements.
    37193727    </UL>
    37203728<p style='margin-left:0.25in'>
     
    37353743</p>
    37363744  <DT><B>Min delta-M/M</B></DT>
    3737   <DD>This determines when convergence is recognized;
    3738     the refinement will stop when the change in the minimization
    3739     function is less than this value. Set Min delta-M/M = 1.0 to force just a
    3740 single cycle to be performed. The default is 0.001. A value less than
    3741     10<sup>-4</sup> causes the refinement to cycle with no meaningful
    3742     improvement since shifts become a small fraction of the
    3743     parameter's uncertainties. Set Min delta-M/M = 1.0 to force
    3744     refinement to stop after a single refinement.
    3745     The allowed range is 10<sup>-9</sup> to 1.0.
    3746   </DD>
     3745  <DD>A refinement will stop when the change in the minimization function
     3746    (M=Σ[w(Io-Ic)<sup>2</sup>])
     3747    is less than this value.  The allowed range is 10<sup>-9</sup> to
     3748    1.0, with a default of 0.001. A value of
     3749    1.0 stops the refinement after a single cycle. Values less than
     3750    10<sup>-4</sup> cause refinements to continue even if there is
     3751    no meaningful improvement.
     3752  </DD><P></P>
    37473753  <DT><B>Max cycles</B></DT>
    37483754  <DD>This determines the maximum number of refinement cycles that
    3749     will be performed. This is only available with the "Hessian" minimizers.</DD>
     3755    will be performed. This is only available with the "Hessian" minimizers.</DD><P></P>
    37503756  <DT><B>Initial lambda</B></DT>
    3751   <DD>Note that here λ is the Marquardt coefficient, which when large
    3752     down-weights the significance of the off-diagonal terms in the
     3757  <DD>Note that here λ is the Marquardt coefficient, where a weight of
     3758    1+λ is applied to the diagonal elements of the Hessian. When λ is
     3759    large, this down-weights the significance of the off-diagonal terms in the
    37533760    Hessian. Thus, when λ is large, the refinement is effectively one of
    37543761    steepest-descents, where correlation between variables is
     
    37563763    slow and may not always find the local minimum.
    37573764    This is only available with the "analytical Hessian" minimizer.
    3758   </DD>
     3765  </DD><P></P>
    37593766  <DT><B>SVD zero tolerance</B></DT>
    37603767  <DD>This determines the level where SVD considers values to be the
    37613768    same. Default is 10<sup>-6</sup>. Make larger to where problems occur due to correlation. This is only available with the "Hessian" minimizers.
    3762   </DD>
     3769  </DD><P></P>
    37633770  <DT><B>Initial shift factor</B></DT>
    3764   <DD>?
    3765   </DD>
     3771  <DD>A “damping multiplier” applied during the first refinement
     3772    cycle, for Jacobean/numeric refinements only.
     3773    Should be in interval (0.1, 100). See the
     3774    <A href="https://docs.scipy.org/doc/scipy/reference/generated/scipy.optimize.leastsq.html">SciPy leastsq docs</A>
     3775    for more information.
     3776  </DD><P></P>
    37663777</DL>
    37673778  <A name="SingleXtlSettings"></A>
    3768 <p style='margin-left:0.75in'>A set of controls is provided for
     3779<p style='margin-left:0.75in'><U>Single Crystal:</u><i> A set of controls is provided for
    37693780control of single-crystal refinements.
    37703781These only appear when single crystal (HKLF) histograms are present
    3771 in the project.
     3782in the project. </i>
    37723783</p>
    37733784<DL style='margin-left:1.0in'>
     
    37753786  <DD>When checked, refinements are against F<sup>2</sup> rather than
    37763787    |F|.
    3777   </DD>
     3788  </DD><P></P>
    37783789  <DT><B>Min obs/sig</B></DT>
    3779   <DD>?
    3780   </DD>
     3790  <DD>Conventional cutoff for single crystal refinements as to what reflections
     3791    should be considered observed, typical values are 2.0 (2σ) or 3.0 (3σ).
     3792  </DD><P></P>
    37813793  <DT><B>Min extinct.</B></DT>
    3782   <DD>?
    3783   </DD>
     3794  <DD>(needs further work)
     3795  </DD><P></P>
    37843796  <DT><B>Max delt-F/sig</B></DT>
    3785   <DD>?
    3786   </DD>
     3797  <DD>Removes reflections that are very poorly fit. Should be used
     3798    only with extreme care, since poorly-fit reflections could be an
     3799    indication that the structure is wrong.
     3800  </DD><P></P>
    37873801  <DT><B>Max d-spacing</B></DT>
    37883802  <DD>Reflections with d-space values larger than this value are ignored.
    3789   </DD>
     3803  </DD><P></P>
    37903804  <DT><B>Min d-spacing</B></DT>
    37913805  <DD>Reflections with d-space values smaller than this value are ignored.
    3792   </DD>
     3806  </DD><P></P>
    37933807 
    37943808</DL>
    37953809
    37963810  <A name="SequentialSettings"></A>
    3797 <p style='margin-left:0.75in'>A set of controls is for
    3798 sequential refinement. Settings here determine if "normal" or "sequential"
    3799 refinement is performed. If no datasets are selected, then all "used"
    3800 histograms are included in one combined refinement. However, if any
    3801 number histogram are selected used here, then a
    3802 sequential refinement is performed, where a fit is made to each
    3803 histogram in turn. Only the first item below is shown in "normal" mode.
     3811<p style='margin-left:0.75in'><U>Sequential Settings:</u><i>
     3812A set of controls is for
     3813sequential refinement. Settings here determine if a "normal" or "sequential"
     3814refinement is performed. If no datasets are selected here, then all
     3815histograms linked to phases in the project and that are flagged as
     3816"used" are included in one potentially large (combined)
     3817refinement. However, if any
     3818number of histograms are selected here, then a
     3819sequential refinement is performed, where a fit is made to the
     3820structural model(s) fitting each selected
     3821histogram in turn. Only the first item below is shown in "normal" mode. </i>
    38043822</p>
    38053823<DL style='margin-left:1.0in'>
     
    38113829    set as "normal". The button is labeled "Select" when in normal refinement
    38123830    mode and "Reselect" in sequential refinement mode.
    3813     </DD>
     3831    </DD><P></P>
    38143832  <DT><B>Reverse order?</B></DT>
    38153833  <DD>Normally, in a sequential histograms are fit in the order they
     
    38183836    but when this option is selected, the sequential fit is performed
    38193837    with the last tree entry first.
    3820   </DD>
     3838  </DD><P></P>
    38213839  <DT><B>Copy results to next histogram?</B></DT>
    38223840  <DD>When this option is selected, the fitted parameters from each
     
    38303848    refinement is completed. For subsequent refinements, it is usually
    38313849    better to start with the results from the previous fit.
    3832   </DD>
     3850  </DD><P></P>
    38333851  <DT><B>Clear previous seq. results</B></DT>
    38343852  <DD>When this button is pressed, the "Sequential Results" entry
    38353853    with the results from the last sequential fit is deleted from the
    38363854    tree.
    3837   </DD>
     3855  </DD><P></P>
    38383856</DL>
     3857<p style='margin-left:0.75in'><U>Global Settings:</u><i>
     3858This is a location for parameters that apply to an entire project.
     3859At present there is only one. </i>
     3860</p>
     3861<DL style='margin-left:1.0in'>
     3862  <DT><B>CIF Author</B></DT>
     3863  <DD>The value provided here is used when creating a CIF of an
     3864    entire project.
     3865  </DD><P></P>
     3866</DL>
     3867
     3868<h5 style='margin-left:.5in'><span
     3869style='mso-fareast-font-family:"Times New Roman"'>
     3870What can I do here?</span></h5>
     3871<p style='margin-left:0.75in'>This offers a place to change how
     3872GSAS-II performs refinements, but has no specific menu commands or
     3873graphics.
     3874</p>
    38393875
    38403876<h4 style='margin-left:0.25in'><a
     
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     7570<!-- hhmts start -->Last modified: Wed Dec  2 11:04:42 CST 2020 <!-- hhmts end -->
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