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updated the docu and adopted the ChangLog

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ChangeLog
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@ -12,6 +12,11 @@ or
https://bitbucket.org/muonspin/musrfit/commits/all https://bitbucket.org/muonspin/musrfit/commits/all
Release of V1.6.1, 2020/05/25
=============================
For asymmetry fits: allow alpha, beta in the RUN block to be functions.
Release of V1.6.0, 2020/05/16 Release of V1.6.0, 2020/05/16
============================= =============================

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# Sphinx build info version 1 # Sphinx build info version 1
# This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done. # This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
config: 90c2680fff90669033f1bce5f6912272 config: 2fd2e79340d6214c8fde0515f4f3fbe3
tags: 645f666f9bcd5a90fca523b33c5a78b7 tags: 645f666f9bcd5a90fca523b33c5a78b7

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doc/html/_sources/user-manual.rst.txt
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@ -775,7 +775,7 @@ The FUNCTIONS Block
+++++++++++++++++++ +++++++++++++++++++
Here some auxiliary functions can be defined. These functions can currently *only* operate on the defined parameters. They can be used in the Here some auxiliary functions can be defined. These functions can currently *only* operate on the defined parameters. They can be used in the
:ref:`THEORY block <msr-theory-block>` and for one specific case in the :ref:`RUN block <msr-run-block>`. Supported is the use of basic arithmetic: :ref:`THEORY block <msr-theory-block>` and for three specific cases in the :ref:`RUN block <msr-run-block>` (`norm`, `alpha`, and `beta`). Supported is the use of basic arithmetic:
:math:`+` :math:`+`
Addition Addition
@ -1064,18 +1064,24 @@ In order to describe the operations needed for fitting and plotting, quite some
.. _msr-alpha-beta: .. _msr-alpha-beta:
**alpha, beta** (fit type 2, 3, 5) **alpha, beta** (fit type 2, 3, 5)
These parameters are used to correct the asymmetry for different detector efficiencies, solid angles and initial asymmetries. They are defined as :math:`\alpha = N_{0,b}/N_{0,f}` and :math:`\beta = A_{0,b}/A_{0,f}`. If the parameters are not specified in the :ref:`RUN block <msr-run-block>`, for each one the value of 1 is assumed (for fittype 5, alpha is estimated from the ratio of :math:`\sum_i \left( N_{\mathrm{bp}}(i)+N_{\mathrm{bm}}(i) \right)` and :math:`\sum_i \left( N_{\mathrm{fp}}(i)+N_{\mathrm{fm}}(i) \right)`). Example for alpha with fit parameter number 1: These parameters are used to correct the asymmetry for different detector efficiencies, solid angles and initial asymmetries. They are defined as :math:`\alpha = N_{0,b}/N_{0,f}` and :math:`\beta = A_{0,b}/A_{0,f}`. If the parameters are not specified in the :ref:`RUN block <msr-run-block>`, for each one the value of 1 is assumed (for fittype 5, alpha is estimated from the ratio of :math:`\sum_i \left( N_{\mathrm{bp}}(i)+N_{\mathrm{bm}}(i) \right)` and :math:`\sum_i \left( N_{\mathrm{fp}}(i)+N_{\mathrm{fm}}(i) \right)`). Both, `alpha` as well as `beta` can be expressed through a function. Example for alpha with fit parameter number 1:
:: ::
alpha 1 alpha 1
Example for an ``alpha`` defined via function number 1:
::
alpha fun1
.. index:: norm .. index:: norm
.. _msr-norm: .. _msr-norm:
**norm** (fit type 0) **norm** (fit type 0)
Number of the fit parameter that represents the normalization constant :math:`N_0` of the histogram; the value of this parameter is given either per nanosecond or per bin (see :ref:`below <msr-commands-block>`). Number of the fit parameter that represents the normalization constant :math:`N_0` of the histogram; the value of this parameter is given either per nanosecond or per bin (see :ref:`below <msr-commands-block>`).
It is possible to substitute the parameter number by a function here (and only here in a RUN block), for instance to relate :math:`N_0`\'s of different histograms through an :math:`\alpha` It is possible to substitute the parameter number by a function, for instance to relate :math:`N_0`\'s of different histograms through an :math:`\alpha`
parameter. Example for a ``norm`` defined by fit parameter number 12: parameter. Example for a ``norm`` defined by fit parameter number 12:
:: ::

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@ -1,6 +1,6 @@
var DOCUMENTATION_OPTIONS = { var DOCUMENTATION_OPTIONS = {
URL_ROOT: document.getElementById("documentation_options").getAttribute('data-url_root'), URL_ROOT: document.getElementById("documentation_options").getAttribute('data-url_root'),
VERSION: '1.6.0', VERSION: '1.6.1',
LANGUAGE: 'None', LANGUAGE: 'None',
COLLAPSE_INDEX: false, COLLAPSE_INDEX: false,
FILE_SUFFIX: '.html', FILE_SUFFIX: '.html',

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doc/html/acknowledgement.html
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@ -4,7 +4,7 @@
<html xmlns="http://www.w3.org/1999/xhtml"> <html xmlns="http://www.w3.org/1999/xhtml">
<head> <head>
<meta charset="utf-8" /> <meta charset="utf-8" />
<title>Acknowledgements &#8212; musrfit 1.6.0 documentation</title> <title>Acknowledgements &#8212; musrfit 1.6.1 documentation</title>
<link rel="stylesheet" href="_static/nature.css" type="text/css" /> <link rel="stylesheet" href="_static/nature.css" type="text/css" />
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@ -30,7 +30,7 @@
<li class="right" > <li class="right" >
<a href="musr-root.html" title="MusrRoot - an Extensible Open File Format for μSR" <a href="musr-root.html" title="MusrRoot - an Extensible Open File Format for μSR"
accesskey="P">previous</a> |</li> accesskey="P">previous</a> |</li>
<li class="nav-item nav-item-0"><a href="index.html">musrfit 1.6.0 documentation</a> &#187;</li> <li class="nav-item nav-item-0"><a href="index.html">musrfit 1.6.1 documentation</a> &#187;</li>
</ul> </ul>
</div> </div>
@ -100,12 +100,12 @@ extremely competent way to deal with his projects as well as to deal with the ch
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<a href="musr-root.html" title="MusrRoot - an Extensible Open File Format for μSR" <a href="musr-root.html" title="MusrRoot - an Extensible Open File Format for μSR"
>previous</a> |</li> >previous</a> |</li>
<li class="nav-item nav-item-0"><a href="index.html">musrfit 1.6.0 documentation</a> &#187;</li> <li class="nav-item nav-item-0"><a href="index.html">musrfit 1.6.1 documentation</a> &#187;</li>
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@ -4,7 +4,7 @@
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<head> <head>
<meta charset="utf-8" /> <meta charset="utf-8" />
<title>any2many - a Universal μSR-file-format converter &#8212; musrfit 1.6.0 documentation</title> <title>any2many - a Universal μSR-file-format converter &#8212; musrfit 1.6.1 documentation</title>
<link rel="stylesheet" href="_static/nature.css" type="text/css" /> <link rel="stylesheet" href="_static/nature.css" type="text/css" />
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@ -30,7 +30,7 @@
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@ -90,12 +90,12 @@ For a detailed description see <a class="reference internal" href="user-manual.h
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@ -26,7 +26,7 @@
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@ -81,12 +81,12 @@ or send an e-mail to A. Suter at PSI.</p>
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@ -23,7 +23,7 @@
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@ -611,12 +611,12 @@
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<a href="#" title="General Index" <a href="#" title="General Index"
>index</a></li> >index</a></li>
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@ -4,7 +4,7 @@
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<title>msr2data - A Program for Automatically Processing Multiple musrfit msr Files &#8212; musrfit 1.6.0 documentation</title> <title>msr2data - A Program for Automatically Processing Multiple musrfit msr Files &#8212; musrfit 1.6.1 documentation</title>
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@ -30,7 +30,7 @@
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@ -418,12 +418,12 @@ fit serves as template for the second and so on. The template field stays empty
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@ -4,7 +4,7 @@
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@ -30,7 +30,7 @@
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@ -298,12 +298,12 @@ SCRIPT COMMANDS:
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@ -4,7 +4,7 @@
<html xmlns="http://www.w3.org/1999/xhtml"> <html xmlns="http://www.w3.org/1999/xhtml">
<head> <head>
<meta charset="utf-8" /> <meta charset="utf-8" />
<title>MusrRoot - an Extensible Open File Format for μSR &#8212; musrfit 1.6.0 documentation</title> <title>MusrRoot - an Extensible Open File Format for μSR &#8212; musrfit 1.6.1 documentation</title>
<link rel="stylesheet" href="_static/nature.css" type="text/css" /> <link rel="stylesheet" href="_static/nature.css" type="text/css" />
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@ -30,7 +30,7 @@
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<a href="any2many.html" title="any2many - a Universal μSR-file-format converter" <a href="any2many.html" title="any2many - a Universal μSR-file-format converter"
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@ -910,12 +910,12 @@ the entry has been added. The last token, <code class="docutils literal notransl
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&#169; Copyright 2020, Andreas Suter. &#169; Copyright 2020, Andreas Suter.
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@ -4,7 +4,7 @@
<html xmlns="http://www.w3.org/1999/xhtml"> <html xmlns="http://www.w3.org/1999/xhtml">
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<meta charset="utf-8" /> <meta charset="utf-8" />
<title>musredit: the GUI Based Interface to musrfit &#8212; musrfit 1.6.0 documentation</title> <title>musredit: the GUI Based Interface to musrfit &#8212; musrfit 1.6.1 documentation</title>
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@ -30,7 +30,7 @@
<li class="right" > <li class="right" >
<a href="setup-dks.html" title="Setting up musrfit / DKS: High Speed Fitting with GPU’s" <a href="setup-dks.html" title="Setting up musrfit / DKS: High Speed Fitting with GPU’s"
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@ -531,12 +531,12 @@ the corresponding fit parameter value, except the phases where the step will be
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<a href="setup-dks.html" title="Setting up musrfit / DKS: High Speed Fitting with GPU’s" <a href="setup-dks.html" title="Setting up musrfit / DKS: High Speed Fitting with GPU’s"
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&#169; Copyright 2020, Andreas Suter. &#169; Copyright 2020, Andreas Suter.
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@ -4,7 +4,7 @@
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@ -27,7 +27,7 @@
<li class="right" style="margin-right: 10px"> <li class="right" style="margin-right: 10px">
<a href="genindex.html" title="General Index" <a href="genindex.html" title="General Index"
accesskey="I">index</a></li> accesskey="I">index</a></li>
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@ -75,12 +75,12 @@
<li class="right" style="margin-right: 10px"> <li class="right" style="margin-right: 10px">
<a href="genindex.html" title="General Index" <a href="genindex.html" title="General Index"
>index</a></li> >index</a></li>
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@ -4,7 +4,7 @@ i
<html xmlns="http://www.w3.org/1999/xhtml"> <html xmlns="http://www.w3.org/1999/xhtml">
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@ -30,7 +30,7 @@ i
<li class="right" > <li class="right" >
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@ -309,12 +309,12 @@ The only thing you need <code class="docutils literal notranslate"><span class="
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doc/html/setup-standard.html
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@ -4,7 +4,7 @@
<html xmlns="http://www.w3.org/1999/xhtml"> <html xmlns="http://www.w3.org/1999/xhtml">
<head> <head>
<meta charset="utf-8" /> <meta charset="utf-8" />
<title>Setting up musrfit on Different Platforms &#8212; musrfit 1.6.0 documentation</title> <title>Setting up musrfit on Different Platforms &#8212; musrfit 1.6.1 documentation</title>
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@ -30,7 +30,7 @@
<li class="right" > <li class="right" >
<a href="user-libs.html" title="Documentation of user libs (user functions)" <a href="user-libs.html" title="Documentation of user libs (user functions)"
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@ -1293,12 +1293,12 @@ $ musrview test-histo-ROOT-NPP.msr
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@ -4,7 +4,7 @@
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@ -30,7 +30,7 @@
<li class="right" > <li class="right" >
<a href="cite.html" title="How to Cite musrfit?" <a href="cite.html" title="How to Cite musrfit?"
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@ -431,12 +431,12 @@ For a complete description please refer to the manuals of <a class="reference in
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@ -4,7 +4,7 @@
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<title>Documentation of user libs (user functions) &#8212; musrfit 1.6.0 documentation</title> <title>Documentation of user libs (user functions) &#8212; musrfit 1.6.1 documentation</title>
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@ -30,7 +30,7 @@
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<a href="user-manual.html" title="User manual" <a href="user-manual.html" title="User manual"
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</ul> </ul>
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@ -647,12 +647,12 @@ K(m)&amp;=\int_0^{\pi/2}\frac{\mathrm d\varphi}{\sqrt{1-m^2\sin^2{\varphi}}},\en
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@ -4,7 +4,7 @@
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<meta charset="utf-8" /> <meta charset="utf-8" />
<title>User manual &#8212; musrfit 1.6.0 documentation</title> <title>User manual &#8212; musrfit 1.6.1 documentation</title>
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@ -30,7 +30,7 @@
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<a href="tutorial.html" title="Tutorial for musrfit" <a href="tutorial.html" title="Tutorial for musrfit"
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@ -897,7 +897,7 @@ instead of specifying the parameters directly.</p>
<div class="section" id="the-functions-block"> <div class="section" id="the-functions-block">
<span id="msr-functions-block"></span><span id="index-15"></span><h3>The FUNCTIONS Block<a class="headerlink" href="#the-functions-block" title="Permalink to this headline"></a></h3> <span id="msr-functions-block"></span><span id="index-15"></span><h3>The FUNCTIONS Block<a class="headerlink" href="#the-functions-block" title="Permalink to this headline"></a></h3>
<p>Here some auxiliary functions can be defined. These functions can currently <em>only</em> operate on the defined parameters. They can be used in the <p>Here some auxiliary functions can be defined. These functions can currently <em>only</em> operate on the defined parameters. They can be used in the
<a class="reference internal" href="#msr-theory-block"><span class="std std-ref">THEORY block</span></a> and for one specific case in the <a class="reference internal" href="#msr-run-block"><span class="std std-ref">RUN block</span></a>. Supported is the use of basic arithmetic:</p> <a class="reference internal" href="#msr-theory-block"><span class="std std-ref">THEORY block</span></a> and for three specific cases in the <a class="reference internal" href="#msr-run-block"><span class="std std-ref">RUN block</span></a> (<cite>norm</cite>, <cite>alpha</cite>, and <cite>beta</cite>). Supported is the use of basic arithmetic:</p>
<dl class="simple"> <dl class="simple">
<dt><span class="math notranslate nohighlight">\(+\)</span></dt><dd><p>Addition</p> <dt><span class="math notranslate nohighlight">\(+\)</span></dt><dd><p>Addition</p>
</dd> </dd>
@ -1169,15 +1169,19 @@ a short digression is needed.</p>
</dd> </dd>
</dl> </dl>
<span id="index-20"></span><dl id="msr-alpha-beta"> <span id="index-20"></span><dl id="msr-alpha-beta">
<dt><strong>alpha, beta</strong> (fit type 2, 3, 5)</dt><dd><p>These parameters are used to correct the asymmetry for different detector efficiencies, solid angles and initial asymmetries. They are defined as <span class="math notranslate nohighlight">\(\alpha = N_{0,b}/N_{0,f}\)</span> and <span class="math notranslate nohighlight">\(\beta = A_{0,b}/A_{0,f}\)</span>. If the parameters are not specified in the <a class="reference internal" href="#msr-run-block"><span class="std std-ref">RUN block</span></a>, for each one the value of 1 is assumed (for fittype 5, alpha is estimated from the ratio of <span class="math notranslate nohighlight">\(\sum_i \left( N_{\mathrm{bp}}(i)+N_{\mathrm{bm}}(i) \right)\)</span> and <span class="math notranslate nohighlight">\(\sum_i \left( N_{\mathrm{fp}}(i)+N_{\mathrm{fm}}(i) \right)\)</span>). Example for alpha with fit parameter number 1:</p> <dt><strong>alpha, beta</strong> (fit type 2, 3, 5)</dt><dd><p>These parameters are used to correct the asymmetry for different detector efficiencies, solid angles and initial asymmetries. They are defined as <span class="math notranslate nohighlight">\(\alpha = N_{0,b}/N_{0,f}\)</span> and <span class="math notranslate nohighlight">\(\beta = A_{0,b}/A_{0,f}\)</span>. If the parameters are not specified in the <a class="reference internal" href="#msr-run-block"><span class="std std-ref">RUN block</span></a>, for each one the value of 1 is assumed (for fittype 5, alpha is estimated from the ratio of <span class="math notranslate nohighlight">\(\sum_i \left( N_{\mathrm{bp}}(i)+N_{\mathrm{bm}}(i) \right)\)</span> and <span class="math notranslate nohighlight">\(\sum_i \left( N_{\mathrm{fp}}(i)+N_{\mathrm{fm}}(i) \right)\)</span>). Both, <cite>alpha</cite> as well as <cite>beta</cite> can be expressed through a function. Example for alpha with fit parameter number 1:</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">alpha</span> <span class="mi">1</span> <div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">alpha</span> <span class="mi">1</span>
</pre></div> </pre></div>
</div> </div>
<p>Example for an <code class="docutils literal notranslate"><span class="pre">alpha</span></code> defined via function number 1:</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">alpha</span> <span class="n">fun1</span>
</pre></div>
</div>
</dd> </dd>
</dl> </dl>
<span id="index-21"></span><dl id="msr-norm"> <span id="index-21"></span><dl id="msr-norm">
<dt><strong>norm</strong> (fit type 0)</dt><dd><p>Number of the fit parameter that represents the normalization constant <span class="math notranslate nohighlight">\(N_0\)</span> of the histogram; the value of this parameter is given either per nanosecond or per bin (see <a class="reference internal" href="#msr-commands-block"><span class="std std-ref">below</span></a>). <dt><strong>norm</strong> (fit type 0)</dt><dd><p>Number of the fit parameter that represents the normalization constant <span class="math notranslate nohighlight">\(N_0\)</span> of the histogram; the value of this parameter is given either per nanosecond or per bin (see <a class="reference internal" href="#msr-commands-block"><span class="std std-ref">below</span></a>).
It is possible to substitute the parameter number by a function here (and only here in a RUN block), for instance to relate <span class="math notranslate nohighlight">\(N_0\)</span>’s of different histograms through an <span class="math notranslate nohighlight">\(\alpha\)</span> It is possible to substitute the parameter number by a function, for instance to relate <span class="math notranslate nohighlight">\(N_0\)</span>’s of different histograms through an <span class="math notranslate nohighlight">\(\alpha\)</span>
parameter. Example for a <code class="docutils literal notranslate"><span class="pre">norm</span></code> defined by fit parameter number 12:</p> parameter. Example for a <code class="docutils literal notranslate"><span class="pre">norm</span></code> defined by fit parameter number 12:</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">norm</span> <span class="mi">12</span> <div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">norm</span> <span class="mi">12</span>
</pre></div> </pre></div>
@ -2429,12 +2433,12 @@ In case this cannot be ensured, the parallelization can be disabled by <em>–di
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