576 lines
44 KiB
HTML
576 lines
44 KiB
HTML
|
||
|
||
<!DOCTYPE html>
|
||
<!--[if IE 8]><html class="no-js lt-ie9" lang="en" > <![endif]-->
|
||
<!--[if gt IE 8]><!--> <html class="no-js" lang="en" > <!--<![endif]-->
|
||
<head>
|
||
<meta charset="utf-8">
|
||
|
||
<meta name="viewport" content="width=device-width, initial-scale=1.0">
|
||
|
||
<title>Tutorial for musrfit — musrfit 1.9.0 documentation</title>
|
||
|
||
|
||
|
||
|
||
|
||
|
||
|
||
|
||
|
||
|
||
|
||
|
||
|
||
|
||
|
||
|
||
<link rel="stylesheet" href="_static/css/theme.css" type="text/css" />
|
||
<link rel="stylesheet" href="_static/pygments.css" type="text/css" />
|
||
<link rel="index" title="Index" href="genindex.html" />
|
||
<link rel="search" title="Search" href="search.html" />
|
||
<link rel="next" title="User manual" href="user-manual.html" />
|
||
<link rel="prev" title="How to Cite musrfit?" href="cite.html" />
|
||
|
||
|
||
<script src="_static/js/modernizr.min.js"></script>
|
||
|
||
</head>
|
||
|
||
<body class="wy-body-for-nav">
|
||
|
||
|
||
<div class="wy-grid-for-nav">
|
||
|
||
|
||
<nav data-toggle="wy-nav-shift" class="wy-nav-side">
|
||
<div class="wy-side-scroll">
|
||
<div class="wy-side-nav-search">
|
||
|
||
|
||
|
||
<a href="index.html" class="icon icon-home"> musrfit
|
||
|
||
|
||
|
||
</a>
|
||
|
||
|
||
|
||
|
||
<div class="version">
|
||
1.9
|
||
</div>
|
||
|
||
|
||
|
||
|
||
<div role="search">
|
||
<form id="rtd-search-form" class="wy-form" action="search.html" method="get">
|
||
<input type="text" name="q" placeholder="Search docs" />
|
||
<input type="hidden" name="check_keywords" value="yes" />
|
||
<input type="hidden" name="area" value="default" />
|
||
</form>
|
||
</div>
|
||
|
||
|
||
</div>
|
||
|
||
<div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="main navigation">
|
||
|
||
|
||
|
||
|
||
|
||
|
||
<ul class="current">
|
||
<li class="toctree-l1"><a class="reference internal" href="cite.html">How to Cite <code class="docutils literal notranslate"><span class="pre">musrfit</span></code>?</a></li>
|
||
<li class="toctree-l1 current"><a class="current reference internal" href="#">Tutorial for <code class="docutils literal notranslate"><span class="pre">musrfit</span></code></a><ul>
|
||
<li class="toctree-l2"><a class="reference internal" href="#single-histogram-fit-tutorial">Single-histogram-fit tutorial</a><ul>
|
||
<li class="toctree-l3"><a class="reference internal" href="#the-msr-file">The msr file</a></li>
|
||
<li class="toctree-l3"><a class="reference internal" href="#determine-t0-and-the-data-range-using-musrt0">Determine t0 and the data range using musrt0</a></li>
|
||
<li class="toctree-l3"><a class="reference internal" href="#fit-the-model-to-the-data-using-musrfit">Fit the model to the data using <code class="docutils literal notranslate"><span class="pre">musrfit</span></code></a></li>
|
||
<li class="toctree-l3"><a class="reference internal" href="#view-the-data-and-the-fit-using-musrview">View the data and the fit using <code class="docutils literal notranslate"><span class="pre">musrview</span></code></a></li>
|
||
<li class="toctree-l3"><a class="reference internal" href="#process-multiple-msr-files-using-msr2data">Process multiple msr files using <code class="docutils literal notranslate"><span class="pre">msr2data</span></code></a></li>
|
||
<li class="toctree-l3"><a class="reference internal" href="#further-reading">Further reading</a></li>
|
||
</ul>
|
||
</li>
|
||
<li class="toctree-l2"><a class="reference internal" href="#asymmtery-fit-tutorial">Asymmtery-fit tutorial</a></li>
|
||
</ul>
|
||
</li>
|
||
<li class="toctree-l1"><a class="reference internal" href="user-manual.html">User manual</a></li>
|
||
<li class="toctree-l1"><a class="reference internal" href="user-libs.html">Documentation of user libs (user functions)</a></li>
|
||
<li class="toctree-l1"><a class="reference internal" href="setup-standard.html">Setting up <code class="docutils literal notranslate"><span class="pre">musrfit</span></code> on Different Platforms</a></li>
|
||
<li class="toctree-l1"><a class="reference internal" href="setup-dks.html">Setting up <code class="docutils literal notranslate"><span class="pre">musrfit</span></code> / <code class="docutils literal notranslate"><span class="pre">DKS</span></code>: High Speed Fitting with GPU’s</a></li>
|
||
<li class="toctree-l1"><a class="reference internal" href="musredit.html"><code class="docutils literal notranslate"><span class="pre">musredit</span></code>: the GUI Based Interface to <code class="docutils literal notranslate"><span class="pre">musrfit</span></code></a></li>
|
||
<li class="toctree-l1"><a class="reference internal" href="mupp.html">mupp - μSR Parameter Plotter</a></li>
|
||
<li class="toctree-l1"><a class="reference internal" href="msr2data.html">msr2data - A Program for Automatically Processing Multiple <code class="docutils literal notranslate"><span class="pre">musrfit</span></code> msr Files</a></li>
|
||
<li class="toctree-l1"><a class="reference internal" href="any2many.html">any2many - a Universal μSR-file-format converter</a></li>
|
||
<li class="toctree-l1"><a class="reference internal" href="musr-root.html">MusrRoot - an Extensible Open File Format for μSR</a></li>
|
||
<li class="toctree-l1"><a class="reference internal" href="acknowledgement.html">Acknowledgements</a></li>
|
||
<li class="toctree-l1"><a class="reference internal" href="bugtracking.html">Bugtracking</a></li>
|
||
</ul>
|
||
|
||
|
||
|
||
</div>
|
||
</div>
|
||
</nav>
|
||
|
||
<section data-toggle="wy-nav-shift" class="wy-nav-content-wrap">
|
||
|
||
|
||
<nav class="wy-nav-top" aria-label="top navigation">
|
||
|
||
<i data-toggle="wy-nav-top" class="fa fa-bars"></i>
|
||
<a href="index.html">musrfit</a>
|
||
|
||
</nav>
|
||
|
||
|
||
<div class="wy-nav-content">
|
||
|
||
<div class="rst-content">
|
||
|
||
|
||
|
||
|
||
|
||
|
||
|
||
|
||
|
||
|
||
|
||
|
||
|
||
|
||
|
||
|
||
|
||
<div role="navigation" aria-label="breadcrumbs navigation">
|
||
|
||
<ul class="wy-breadcrumbs">
|
||
|
||
<li><a href="index.html">Docs</a> »</li>
|
||
|
||
<li>Tutorial for <code class="docutils literal notranslate"><span class="pre">musrfit</span></code></li>
|
||
|
||
|
||
<li class="wy-breadcrumbs-aside">
|
||
|
||
|
||
<a href="_sources/tutorial.rst.txt" rel="nofollow"> View page source</a>
|
||
|
||
|
||
</li>
|
||
|
||
</ul>
|
||
|
||
|
||
<hr/>
|
||
</div>
|
||
<div role="main" class="document" itemscope="itemscope" itemtype="http://schema.org/Article">
|
||
<div itemprop="articleBody">
|
||
|
||
<div class="section" id="tutorial-for-musrfit">
|
||
<span id="index-0"></span><h1>Tutorial for <code class="docutils literal notranslate"><span class="pre">musrfit</span></code><a class="headerlink" href="#tutorial-for-musrfit" title="Permalink to this headline">¶</a></h1>
|
||
<div class="section" id="single-histogram-fit-tutorial">
|
||
<h2>Single-histogram-fit tutorial<a class="headerlink" href="#single-histogram-fit-tutorial" title="Permalink to this headline">¶</a></h2>
|
||
<p>The μSR-data-analysis process using musrfit is based on so-called msr files. These files contain all
|
||
information needed for the analysis such as names of the data files, a theory function, fit and plot parameters,
|
||
and so on. It is the idea of this page to explain the basic use of an msr file and the different programs
|
||
of the <code class="docutils literal notranslate"><span class="pre">musrfit</span></code> suite using the example of a single-histogram fit to time-differential transverse-field
|
||
μSR data. For a complete description of all options please refer to the <a class="reference internal" href="user-manual.html#user-manual"><span class="std std-ref">manual</span></a>.</p>
|
||
<p>The example deals with a diamagnetic sample that has been measured in an applied field of approximately 150 G in
|
||
the <a class="reference external" href="https://www.psi.ch/smus/gps">GPS spectrometer</a> at <a class="reference external" href="https://www.psi.ch">PSI</a> using the “transverse geometry”.
|
||
In this geometry the muon spin is rotated about 50° up and the field is applied parallel to the muon momentum.
|
||
Hence, the relevant positron counters (to detect the spin precession) are placed above (histogram 3), below (histogram 4) and right of (histogram 5) the sample. The run numbers start from 3110.</p>
|
||
<p>To analyze these data (in a simple way) one starts out from the msr file <code class="docutils literal notranslate"><span class="pre">3110_tutorial.msr</span></code> provided together
|
||
with the source-code distribution in the sub-directory <code class="docutils literal notranslate"><span class="pre">doc/examples/</span></code>. This ASCII file can be edited using any
|
||
text editor. For convenience the editor <code class="docutils literal notranslate"><span class="pre">musredit</span></code> is provided which offer some msr-file-specific functionalities
|
||
and additionally serve as front ends to the underlying programs. In the following it is assumed that the file is
|
||
open within <code class="docutils literal notranslate"><span class="pre">musredit</span></code>.</p>
|
||
<div class="section" id="the-msr-file">
|
||
<h3>The msr file<a class="headerlink" href="#the-msr-file" title="Permalink to this headline">¶</a></h3>
|
||
<p>The msr file itself is divided into different blocks; a full description of the format can be found <a class="reference internal" href="user-manual.html#msr-file-format"><span class="std std-ref">here</span></a>.
|
||
In the file <code class="docutils literal notranslate"><span class="pre">3110_tutorial.msr</span></code> these blocks are successively:</p>
|
||
<p><a class="reference internal" href="user-manual.html#msr-title-block"><span class="std std-ref">The title</span></a></p>
|
||
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">sample</span> <span class="n">XYZ</span>
|
||
</pre></div>
|
||
</div>
|
||
<p>A descriptive title of the file.</p>
|
||
<p><a class="reference internal" href="user-manual.html#msr-fitparameter-block"><span class="std std-ref">The FITPARAMETER block</span></a></p>
|
||
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">FITPARAMETER</span>
|
||
<span class="c1"># No Name Value Step Pos_Error Boundaries</span>
|
||
<span class="mi">1</span> <span class="n">NormUp</span> <span class="mi">4500</span> <span class="mi">5</span> <span class="n">none</span> <span class="mi">0</span> <span class="n">none</span>
|
||
<span class="mi">2</span> <span class="n">BgUp</span> <span class="mi">200</span> <span class="mi">1</span> <span class="n">none</span> <span class="mi">0</span> <span class="n">none</span>
|
||
<span class="mi">3</span> <span class="n">PhaseUp</span> <span class="mi">15</span> <span class="mi">1</span> <span class="n">none</span>
|
||
|
||
<span class="mi">4</span> <span class="n">NormDown</span> <span class="mi">4500</span> <span class="mi">5</span> <span class="n">none</span> <span class="mi">0</span> <span class="n">none</span>
|
||
<span class="mi">5</span> <span class="n">BgDown</span> <span class="mi">200</span> <span class="mi">1</span> <span class="n">none</span> <span class="mi">0</span> <span class="n">none</span>
|
||
<span class="mi">6</span> <span class="n">PhaseDown</span> <span class="mi">195</span> <span class="mi">1</span> <span class="n">none</span>
|
||
|
||
<span class="mi">7</span> <span class="n">NormRight</span> <span class="mi">600</span> <span class="mi">5</span> <span class="n">none</span> <span class="mi">0</span> <span class="n">none</span>
|
||
<span class="mi">8</span> <span class="n">BgRight</span> <span class="mi">40</span> <span class="mi">1</span> <span class="n">none</span> <span class="mi">0</span> <span class="n">none</span>
|
||
<span class="mi">9</span> <span class="n">PhaseRight</span> <span class="mi">285</span> <span class="mi">1</span> <span class="n">none</span>
|
||
|
||
<span class="mi">10</span> <span class="n">AsymSig1</span> <span class="mf">0.17</span> <span class="mf">0.01</span> <span class="n">none</span> <span class="mi">0</span> <span class="mf">0.33</span>
|
||
<span class="mi">11</span> <span class="n">RateSig1</span> <span class="mf">2.5</span> <span class="mf">0.1</span> <span class="n">none</span> <span class="mi">0</span> <span class="n">none</span>
|
||
<span class="mi">12</span> <span class="n">FieldSig1</span> <span class="mi">100</span> <span class="mi">1</span> <span class="n">none</span>
|
||
|
||
<span class="mi">13</span> <span class="n">AsymSig2</span> <span class="mf">0.02</span> <span class="mf">0.01</span> <span class="n">none</span> <span class="mi">0</span> <span class="mf">0.33</span>
|
||
<span class="mi">14</span> <span class="n">RateSig2</span> <span class="mf">0.5</span> <span class="mf">0.1</span> <span class="n">none</span>
|
||
<span class="mi">15</span> <span class="n">FieldSig2</span> <span class="mi">150</span> <span class="mi">1</span> <span class="n">none</span>
|
||
</pre></div>
|
||
</div>
|
||
<p>The list of parameters used in the theory function to describe the set of data.
|
||
Each parameter has a number, a name, an initial value and an initial step (for
|
||
the fitting process). If a parameter should be fixed, the initial step is set
|
||
to 0. After a fit (see below), this block contains the determined parameter values
|
||
and uncertainties (in the <code class="docutils literal notranslate"><span class="pre">Step</span></code> column). If asymmetric errors are determined, these
|
||
will be listed in the <code class="docutils literal notranslate"><span class="pre">Step</span></code> column (negative) and the <code class="docutils literal notranslate"><span class="pre">Pos_Error</span></code> column (positive).
|
||
Optionally, lower and upper boundaries for the parameters can be specified as
|
||
shown above.</p>
|
||
<p>The meaning of the parameters above is explained in the following:</p>
|
||
<p>Since a <a class="reference internal" href="user-manual.html#single-histogram-fit"><span class="std std-ref">single-histogram fit</span></a> should be done, some
|
||
histogram-specific parameters are needed. These are a normalization constant (parameter 1),
|
||
a parameter describing the background of uncorrelated events (parameter 2) and the initial
|
||
phase of the spin precession with respect to the detector (parameter 3). As stated above,
|
||
there are three histograms containing useful information (“Up”, “Down”, “Right”); hence,
|
||
this set of parameters has to be present for each of them (parameters 1–9).
|
||
The remaining parameters are used to model the decay asymmetry which is assumed to be equal
|
||
for all histograms. In this example one has two signals (<em>e.g.</em> from the sample and the
|
||
sample holder), each with an amplitude (parameters 10 and 13), a depolarization rate
|
||
(parameters 11 and 14) and a mean field (here given in Gauss, parameters 12 and 15).</p>
|
||
<p><a class="reference internal" href="user-manual.html#msr-theory-block"><span class="std std-ref">The THEORY block</span></a></p>
|
||
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">THEORY</span>
|
||
<span class="n">asymmetry</span> <span class="mi">10</span>
|
||
<span class="n">simplExpo</span> <span class="mi">11</span> <span class="p">(</span><span class="n">rate</span><span class="p">)</span>
|
||
<span class="n">TFieldCos</span> <span class="n">map1</span> <span class="n">fun1</span> <span class="p">(</span><span class="n">phase</span> <span class="n">frequency</span><span class="p">)</span>
|
||
<span class="o">+</span>
|
||
<span class="n">asymmetry</span> <span class="mi">13</span>
|
||
<span class="n">simpleGss</span> <span class="mi">14</span> <span class="p">(</span><span class="n">rate</span><span class="p">)</span>
|
||
<span class="n">TFieldCos</span> <span class="n">map1</span> <span class="n">fun2</span> <span class="p">(</span><span class="n">phase</span> <span class="n">frequency</span><span class="p">)</span>
|
||
</pre></div>
|
||
</div>
|
||
<p>The THEORY block is used to define a fit-parameter-dependent theory function used to model
|
||
the decay asymmetry. Different <a class="reference internal" href="user-manual.html#msr-theory-block"><span class="std std-ref">predefined</span></a> and <a class="reference internal" href="user-manual.html#id38"><span class="std std-ref">user-defined</span></a>
|
||
functions can be combined here. Theory lines following each other are <em>multiplied</em> and the <strong>+</strong> sign
|
||
is used to add different (here: two) signal contributions. The numbers are the parameter numbers
|
||
according to the <code class="docutils literal notranslate"><span class="pre">FITPARAMETER</span> <span class="pre">block</span></code>. <code class="docutils literal notranslate"><span class="pre">map</span></code> and <code class="docutils literal notranslate"><span class="pre">fun</span></code> are used to refer to
|
||
histogram-dependent parameters and to interrelate fit parameters, respectively (see below).</p>
|
||
<p><a class="reference internal" href="user-manual.html#msr-functions-block"><span class="std std-ref">The FUNCTIONS block</span></a></p>
|
||
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">FUNCTIONS</span>
|
||
<span class="n">fun1</span> <span class="o">=</span> <span class="n">gamma_mu</span> <span class="o">*</span> <span class="n">par12</span>
|
||
<span class="n">fun2</span> <span class="o">=</span> <span class="n">gamma_mu</span> <span class="o">*</span> <span class="n">par15</span>
|
||
</pre></div>
|
||
</div>
|
||
<p>Here functions interrelating different fit parameters and predefined constants can be defined for
|
||
the use in the <code class="docutils literal notranslate"><span class="pre">THEORY</span> <span class="pre">block</span></code>. In the example, the functions are used to calculate the
|
||
muon-spin-precession frequencies for the given fields [<span class="math notranslate nohighlight">\(\nu = \gamma_\mu B / (2\pi)\)</span>]. One
|
||
function is used for each signal. Altogether, the theory function defined above is
|
||
<span class="math notranslate nohighlight">\(A(t) = p_{10} e^{-p_{11} t} \cos(\varphi_i \pi/180 + \gamma_\mu p_{12} t) + p_{13} e^{-(p_{14} t)^2/2} \cos(\varphi_i \pi/180 + \gamma_\mu p_{15} t)\)</span>, where the <em>p</em> are the parameters in the <code class="docutils literal notranslate"><span class="pre">FITPARAMETER</span> <span class="pre">block</span></code> and <span class="math notranslate nohighlight">\(\varphi_i = p_3, p_6, p_9\)</span>
|
||
depending on the histogram as shall be seen later.</p>
|
||
<p><a class="reference internal" href="user-manual.html#msr-run-block"><span class="std std-ref">The RUN block</span></a></p>
|
||
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">RUN</span> <span class="n">data</span><span class="o">/</span><span class="n">deltat_pta_gps_3110</span> <span class="n">PIM3</span> <span class="n">PSI</span> <span class="n">PSI</span><span class="o">-</span><span class="n">BIN</span> <span class="p">(</span><span class="n">name</span> <span class="n">beamline</span> <span class="n">institute</span> <span class="n">data</span><span class="o">-</span><span class="n">file</span><span class="o">-</span><span class="nb">format</span><span class="p">)</span>
|
||
<span class="n">fittype</span> <span class="mi">0</span> <span class="p">(</span><span class="n">single</span> <span class="n">histogram</span> <span class="n">fit</span><span class="p">)</span>
|
||
<span class="n">norm</span> <span class="mi">1</span>
|
||
<span class="n">backgr</span><span class="o">.</span><span class="n">fit</span> <span class="mi">2</span>
|
||
<span class="nb">map</span> <span class="mi">3</span> <span class="mi">0</span> <span class="mi">0</span> <span class="mi">0</span> <span class="mi">0</span> <span class="mi">0</span> <span class="mi">0</span> <span class="mi">0</span> <span class="mi">0</span> <span class="mi">0</span>
|
||
<span class="n">forward</span> <span class="mi">3</span>
|
||
<span class="n">data</span> <span class="mi">1</span> <span class="mi">8000</span>
|
||
<span class="n">t0</span> <span class="mi">1</span>
|
||
<span class="n">fit</span> <span class="mi">0</span> <span class="mf">4.9</span>
|
||
<span class="n">packing</span> <span class="mi">20</span>
|
||
</pre></div>
|
||
</div>
|
||
<p>The RUN blocks are used to collect information on the data to be analyzed. Specifically, these are:</p>
|
||
<blockquote>
|
||
<div><div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">RUN</span> <span class="n">data</span><span class="o">/</span><span class="n">deltat_pta_gps_3110</span> <span class="n">PIM3</span> <span class="n">PSI</span> <span class="n">PSI</span><span class="o">-</span><span class="n">BIN</span> <span class="p">(</span><span class="n">name</span> <span class="n">beamline</span> <span class="n">institute</span> <span class="n">data</span><span class="o">-</span><span class="n">file</span><span class="o">-</span><span class="nb">format</span><span class="p">)</span>
|
||
</pre></div>
|
||
</div>
|
||
<p>The path to the data file and the file format (NEXUS, ROOT-NPP, ROOT-PPC, PSI-BIN, PSI-MDU, WKM, MUD, MDU-ASCII).</p>
|
||
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">fittype</span> <span class="mi">0</span> <span class="p">(</span><span class="n">single</span> <span class="n">histogram</span> <span class="n">fit</span><span class="p">)</span>
|
||
</pre></div>
|
||
</div>
|
||
<p>the fit type (0 = single-histogram fit)</p>
|
||
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">norm</span> <span class="mi">1</span>
|
||
</pre></div>
|
||
</div>
|
||
<p>the number of the fit parameter representing the normalization constant</p>
|
||
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">backgr</span><span class="o">.</span><span class="n">fit</span> <span class="mi">2</span>
|
||
</pre></div>
|
||
</div>
|
||
<p>the number of the fit parameter representing the background</p>
|
||
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="nb">map</span> <span class="mi">3</span> <span class="mi">0</span> <span class="mi">0</span> <span class="mi">0</span> <span class="mi">0</span> <span class="mi">0</span> <span class="mi">0</span> <span class="mi">0</span> <span class="mi">0</span> <span class="mi">0</span>
|
||
</pre></div>
|
||
</div>
|
||
<p>the definition of the <strong>maps</strong> used in the <code class="docutils literal notranslate"><span class="pre">THEORY</span> <span class="pre">block</span></code> — RUN-block-specific
|
||
parameters are given here; in this example, <strong>map1</strong> is substituted by <strong>parameter 3</strong>
|
||
in the <code class="docutils literal notranslate"><span class="pre">THEORY</span> <span class="pre">block</span></code> for this RUN block and <strong>map2</strong>, <strong>map3</strong>, and so on are undefined.</p>
|
||
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">forward</span> <span class="mi">3</span>
|
||
</pre></div>
|
||
</div>
|
||
<p>the histogram number; in this example 3 corresponds to the histogram of the “Up” positron counter</p>
|
||
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">data</span> <span class="mi">1</span> <span class="mi">8000</span>
|
||
</pre></div>
|
||
</div>
|
||
<p>start and end bins of the range containing useful data in the histogram (to be adjusted, <em>e.g.</em> by using <code class="docutils literal notranslate"><span class="pre">musrt0</span></code>, see below)</p>
|
||
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">t0</span> <span class="mi">1</span>
|
||
</pre></div>
|
||
</div>
|
||
<p>histogram bin corresponding to the time zero (muon implantation time) (to be adjusted, <em>e.g.</em> by <code class="docutils literal notranslate"><span class="pre">musrt0</span></code>, see below)</p>
|
||
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">fit</span> <span class="mi">0</span> <span class="mf">4.9</span>
|
||
</pre></div>
|
||
</div>
|
||
<p>start and end times (in μs) defining the fit range. <em>In case the fit range
|
||
exceeds the range of useful data (specified above using the data tag), eventually
|
||
this data range is used as fit range.</em></p>
|
||
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">packing</span> <span class="mi">20</span>
|
||
</pre></div>
|
||
</div>
|
||
<p>the packing of the histograms (in histogram bins)</p>
|
||
<p>Since the data of three histograms is to be analyzed, the file contains not only one but
|
||
three RUN blocks — each defining the histogram-specific information following the example given above.</p>
|
||
</div></blockquote>
|
||
<p><a class="reference internal" href="user-manual.html#msr-commands-block"><span class="std std-ref">The COMMAND block</span></a></p>
|
||
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">COMMANDS</span>
|
||
<span class="n">MINIMIZE</span>
|
||
<span class="n">MINOS</span>
|
||
<span class="n">SAVE</span>
|
||
</pre></div>
|
||
</div>
|
||
<p>In the <code class="docutils literal notranslate"><span class="pre">COMMANDS</span> <span class="pre">block</span></code>, a sequence of operations that should be performed is defined.
|
||
Here, the requested operations are the minimization of <span class="math notranslate nohighlight">\(\chi^2\)</span> (MINIMIZE), the
|
||
calculation of <em>asymmetric errors</em> (MINOS) as well as saving the found parameter values
|
||
and uncertainties to the msr file (SAVE). A full description of the possible commands can
|
||
be found <a class="reference internal" href="user-manual.html#msr-commands-block"><span class="std std-ref">here</span></a>.</p>
|
||
<p><a class="reference internal" href="user-manual.html#msr-fourier-block"><span class="std std-ref">The FOURIER block</span></a></p>
|
||
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">FOURIER</span>
|
||
<span class="n">units</span> <span class="n">Gauss</span> <span class="c1"># units either 'Gauss', 'MHz', or 'Mc/s'</span>
|
||
<span class="n">fourier_power</span> <span class="mi">10</span>
|
||
<span class="n">apodization</span> <span class="n">WEAK</span> <span class="c1"># NONE, WEAK, MEDIUM, STRONG</span>
|
||
<span class="n">plot</span> <span class="n">POWER</span> <span class="c1"># REAL, IMAG, REAL_AND_IMAG, POWER, PHASE</span>
|
||
<span class="n">phase</span> <span class="n">par3</span>
|
||
<span class="nb">range</span> <span class="mf">0.0</span> <span class="mf">600.0</span>
|
||
</pre></div>
|
||
</div>
|
||
<p>The <code class="docutils literal notranslate"><span class="pre">FOURIER</span> <span class="pre">block</span></code> is used to define basic settings for the Fourier transform available
|
||
in <a class="reference internal" href="user-manual.html#musrview"><span class="std std-ref">musrview</span></a>. These are:</p>
|
||
<blockquote>
|
||
<div><div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">units</span> <span class="n">Gauss</span> <span class="c1"># units either 'Gauss', 'MHz', or 'Mc/s'</span>
|
||
</pre></div>
|
||
</div>
|
||
<p>the units of the Fourier domain</p>
|
||
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">fourier_power</span> <span class="mi">10</span>
|
||
</pre></div>
|
||
</div>
|
||
<p>the number of data points used for the discrete transform, here <span class="math notranslate nohighlight">\(2^{10}=1024\)</span>.</p>
|
||
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">apodization</span> <span class="n">WEAK</span> <span class="c1"># NONE, WEAK, MEDIUM, STRONG</span>
|
||
</pre></div>
|
||
</div>
|
||
<p>the <a class="reference internal" href="user-manual.html#msr-fourier-block-apodization"><span class="std std-ref">apodization</span></a> to be used</p>
|
||
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">plot</span> <span class="n">POWER</span> <span class="c1"># REAL, IMAG, REAL_AND_IMAG, POWER, PHASE</span>
|
||
</pre></div>
|
||
</div>
|
||
<p>what should be plotted (real part, imaginary part, and so on)</p>
|
||
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">phase</span> <span class="n">par3</span>
|
||
</pre></div>
|
||
</div>
|
||
<p>the initial phase of the input data is given here in degrees. Optionally, a phase parameter
|
||
from the <code class="docutils literal notranslate"><span class="pre">FITPARAMETER</span> <span class="pre">block</span></code> can be given, here <strong>par3</strong> takes the value of <strong>parameter 3</strong>.</p>
|
||
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="nb">range</span> <span class="mf">0.0</span> <span class="mf">600.0</span>
|
||
</pre></div>
|
||
</div>
|
||
<p>the start and end points of the range of the Fourier transform in the units specified above</p>
|
||
</div></blockquote>
|
||
<p><a class="reference internal" href="user-manual.html#msr-plot-block"><span class="std std-ref">The PLOT block</span></a></p>
|
||
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">PLOT</span> <span class="mi">0</span> <span class="p">(</span><span class="n">single</span> <span class="n">histo</span> <span class="n">plot</span><span class="p">)</span>
|
||
<span class="n">runs</span> <span class="mi">1</span> <span class="mi">2</span>
|
||
<span class="nb">range</span> <span class="mi">0</span> <span class="mi">4</span> <span class="o">-</span><span class="mf">0.2</span> <span class="mf">0.2</span>
|
||
</pre></div>
|
||
</div>
|
||
<p>The <code class="docutils literal notranslate"><span class="pre">PLOT</span> <span class="pre">block</span></code> defines which data (corresponding to the given RUN blocks) is plotted when
|
||
<a class="reference internal" href="user-manual.html#musrview"><span class="std std-ref">musrview</span></a> is called. In the given example, a canvas would be drawn containing
|
||
the (life-time-corrected) data of the first two <code class="docutils literal notranslate"><span class="pre">RUN</span> <span class="pre">blocks</span></code> (“Up” and “Down” positron counters).
|
||
The abscissa would range from 0 to 4 μs, the axis of ordinates from -0.2 to 0.2.
|
||
It is possible to define more than one <code class="docutils literal notranslate"><span class="pre">PLOT</span> <span class="pre">block</span></code>. Each <code class="docutils literal notranslate"><span class="pre">PLOT</span> <span class="pre">block</span></code> corresponds to a
|
||
separate canvas. Therefore, the second <code class="docutils literal notranslate"><span class="pre">PLOT</span> <span class="pre">block</span></code> in the file</p>
|
||
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">PLOT</span> <span class="mi">0</span> <span class="p">(</span><span class="n">single</span> <span class="n">histo</span> <span class="n">plot</span><span class="p">)</span>
|
||
<span class="n">runs</span> <span class="mi">3</span>
|
||
<span class="n">use_fit_ranges</span>
|
||
</pre></div>
|
||
</div>
|
||
<p>produces an additional window containing the (not life-time-corrected) data of the third <code class="docutils literal notranslate"><span class="pre">RUN</span> <span class="pre">block</span></code>
|
||
(“Right” positron counter). The abscissa ranges from 0 to 4.9 μs (according to the fit range given
|
||
in the <code class="docutils literal notranslate"><span class="pre">RUN</span> <span class="pre">block</span></code>).</p>
|
||
<p><a class="reference internal" href="user-manual.html#msr-statistic-block"><span class="std std-ref">The STATISTIC block</span></a></p>
|
||
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">STATISTIC</span> <span class="o">---</span> <span class="mi">2011</span><span class="o">-</span><span class="mi">07</span><span class="o">-</span><span class="mi">09</span> <span class="mi">10</span><span class="p">:</span><span class="mi">58</span><span class="p">:</span><span class="mi">44</span>
|
||
<span class="n">chisq</span> <span class="o">=</span> <span class="mf">1348.1764</span><span class="p">,</span> <span class="n">NDF</span> <span class="o">=</span> <span class="mi">1146</span><span class="p">,</span> <span class="n">chisq</span><span class="o">/</span><span class="n">NDF</span> <span class="o">=</span> <span class="mf">1.176419</span>
|
||
</pre></div>
|
||
</div>
|
||
<p>This block is the last block of a msr file. It contains some information on the fit: the
|
||
date and time as well as the absolute and normalized values of <span class="math notranslate nohighlight">\(\chi^2\)</span> and the
|
||
number of degrees of freedom in the fit.
|
||
These information only have a meaning if the fitting procedure has been executed at
|
||
least once and the fit has converged!</p>
|
||
</div>
|
||
<div class="section" id="determine-t0-and-the-data-range-using-musrt0">
|
||
<h3>Determine t0 and the data range using musrt0<a class="headerlink" href="#determine-t0-and-the-data-range-using-musrt0" title="Permalink to this headline">¶</a></h3>
|
||
<p>Before the given model can be fitted to the data, the data ranges and time zeros of the different
|
||
<code class="docutils literal notranslate"><span class="pre">RUN</span> <span class="pre">blocks</span></code> have to be set correctly. This can be achieved using <a class="reference internal" href="user-manual.html#musrt0"><span class="std std-ref">musrt0</span></a>.
|
||
Starting this program by selecting the <code class="docutils literal notranslate"><span class="pre">musrt0</span></code> button in <code class="docutils literal notranslate"><span class="pre">musredit</span></code> or calling from a terminal</p>
|
||
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>$ musrt0 3110_tutorial.msr
|
||
</pre></div>
|
||
</div>
|
||
<p>opens an interactive window plotting the data of the first RUN block:</p>
|
||
<img alt="_images/tutorial-musrt0-1.png" src="_images/tutorial-musrt0-1.png" />
|
||
<p>The green line (at bin 1) represents time zero, the blue lines the start (at bin 1) and end (at bin 8000)
|
||
of the data range and the optional red lines give the limits of the background range (if the background
|
||
shall not be determined by the fit). All lines can be either dragged to reasonable locations or set by
|
||
pressing the corresponding keyboard shortcuts. In the example the time zero can be set by pressing <strong>T</strong>
|
||
(which moves the green line to the bin containing the maximum number of counts), the start of the data
|
||
range should be set to about five bins later by zooming into the graph around bin 250 and pressing <strong>d</strong>
|
||
when the cursor is found at a suitable location:</p>
|
||
<img alt="_images/tutorial-musrt0-2.png" src="_images/tutorial-musrt0-2.png" />
|
||
<p>After all lines have been adjusted for the first histogram, one can go on to the second by pressing <strong>q</strong>.
|
||
This procedure is repeated until all ranges have been set correctly. When finished with the last histogram
|
||
the new t0 and data-range values will be written to the msr file. A full description of <code class="docutils literal notranslate"><span class="pre">musrt0</span></code> can be
|
||
found <a class="reference internal" href="user-manual.html#musrt0"><span class="std std-ref">here</span></a>.</p>
|
||
</div>
|
||
<div class="section" id="fit-the-model-to-the-data-using-musrfit">
|
||
<h3>Fit the model to the data using <code class="docutils literal notranslate"><span class="pre">musrfit</span></code><a class="headerlink" href="#fit-the-model-to-the-data-using-musrfit" title="Permalink to this headline">¶</a></h3>
|
||
<p>Now that the basics of the msr file have been introduced and the necessary adjustments have been done one
|
||
can proceed with fitting the specified model to the data. This is done by selecting the <code class="docutils literal notranslate"><span class="pre">musrfit</span></code> icon
|
||
in <code class="docutils literal notranslate"><span class="pre">musredit</span></code> or calling from a terminal</p>
|
||
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>$ musrfit 3110_tutorial.msr
|
||
</pre></div>
|
||
</div>
|
||
<p>After the fitting procedure has finished the msr file is updated and contains the newly determined values
|
||
of the fit parameters.</p>
|
||
</div>
|
||
<div class="section" id="view-the-data-and-the-fit-using-musrview">
|
||
<h3>View the data and the fit using <code class="docutils literal notranslate"><span class="pre">musrview</span></code><a class="headerlink" href="#view-the-data-and-the-fit-using-musrview" title="Permalink to this headline">¶</a></h3>
|
||
<p>The data and the corresponding fit can be visualized by choosing the <code class="docutils literal notranslate"><span class="pre">musrview</span></code> icon in <code class="docutils literal notranslate"><span class="pre">musredit</span></code> or
|
||
calling from a terminal</p>
|
||
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>$ musrview 3110_tutorial.msr
|
||
</pre></div>
|
||
</div>
|
||
<p>This creates the windows according to the given PLOT blocks in the msr file:</p>
|
||
<img alt="_images/tutorial-musrview-1.png" src="_images/tutorial-musrview-1.png" />
|
||
<p>The basic features of <code class="docutils literal notranslate"><span class="pre">musrview</span></code> can be found in the <code class="docutils literal notranslate"><span class="pre">Musrfit</span> <span class="pre">menu</span></code>. They include:</p>
|
||
<ul class="simple">
|
||
<li>export the shown data and the model to an ASCII file with comma-separated values</li>
|
||
<li>presenting the difference between the shown data and the model (keyboard shortcut: <strong>d</strong>)</li>
|
||
<li>calculate and show the Fourier transform of the shown data (keyboard shortcut: <strong>f</strong>), <em>e.g.</em> for
|
||
the asymmetry of the “Up” and “Down” detectors:</li>
|
||
</ul>
|
||
<img alt="_images/tutorial-musrview-FT.png" src="_images/tutorial-musrview-FT.png" />
|
||
</div>
|
||
<div class="section" id="process-multiple-msr-files-using-msr2data">
|
||
<h3>Process multiple msr files using <code class="docutils literal notranslate"><span class="pre">msr2data</span></code><a class="headerlink" href="#process-multiple-msr-files-using-msr2data" title="Permalink to this headline">¶</a></h3>
|
||
<p>This short introduction is concluded by calling attention to the program <a class="reference internal" href="msr2data.html#msr2data"><span class="std std-ref">msr2data</span></a>.
|
||
As the name indicates the main purpose of this program is to extract the <code class="docutils literal notranslate"><span class="pre">FITPARAMETER</span></code> block
|
||
information from multiple msr files with the same structure and to summarize them in a single
|
||
ASCII file (either in <code class="docutils literal notranslate"><span class="pre">TRIUMF</span> <span class="pre">DB</span></code> format or simple columns). However, as described in detail
|
||
in the manual, it is not only possible to collect data from msr files but also to create new
|
||
msr files from a template and to process these files using <code class="docutils literal notranslate"><span class="pre">musrfit</span></code> on the fly.</p>
|
||
<p>Assuming the successive runs <strong>3111</strong> through <strong>3114</strong> can be analyzed using the same model introduced
|
||
above for run <strong>3110</strong> (<em>e.g.</em> in the case one has done measurements at different temperatures) one can
|
||
use the file <code class="docutils literal notranslate"><span class="pre">3110_tutorial.msr</span></code> as template, generate the files <code class="docutils literal notranslate"><span class="pre">3111_tutorial.msr</span></code> through
|
||
<code class="docutils literal notranslate"><span class="pre">3114_tutorial.msr</span></code> with the corresponding updates in the RUN blocks, call for each one <code class="docutils literal notranslate"><span class="pre">musrfit</span></code>
|
||
and finally summarize the FITPARAMETER block information of all processed files in an ASCII output
|
||
file <code class="docutils literal notranslate"><span class="pre">tutorial-T-dependence.dat</span></code> (simple columns). If further information on the temperature or the
|
||
applied field is available in the data files these will be included as well in the resulting ASCII file.
|
||
From the terminal this would be done as follows:</p>
|
||
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>$ msr2data <span class="m">3110</span> <span class="m">3114</span> _tutorial fit-3110 -o tutorial-T-dependence.dat data
|
||
</pre></div>
|
||
</div>
|
||
<p>To achieve the same in <code class="docutils literal notranslate"><span class="pre">musredit</span></code> (in this snapshot in the <em>dark theme</em>) one selects the <code class="docutils literal notranslate"><span class="pre">msr2data</span></code> icon and fills the form accordingly:</p>
|
||
<img alt="_images/tutorial-musredit-msr2data.png" src="_images/tutorial-musredit-msr2data.png" />
|
||
</div>
|
||
<div class="section" id="further-reading">
|
||
<h3>Further reading<a class="headerlink" href="#further-reading" title="Permalink to this headline">¶</a></h3>
|
||
<p>This page only summarizes the very basic features and options of the programs contained in the <code class="docutils literal notranslate"><span class="pre">musrfit</span></code> suite.
|
||
For a complete description please refer to the manuals of <a class="reference internal" href="user-manual.html#musrfit"><span class="std std-ref">musrfit</span></a> (including <a class="reference internal" href="user-manual.html#musrview"><span class="std std-ref">musrview</span></a>,
|
||
<a class="reference internal" href="user-manual.html#musrt0"><span class="std std-ref">musrt0</span></a>, and <a class="reference internal" href="user-manual.html#musrft"><span class="std std-ref">musrFT</span></a>), <a class="reference internal" href="mupp.html#mupp"><span class="std std-ref">mupp</span></a>, <a class="reference internal" href="musredit.html#musredit-sec"><span class="std std-ref">musredit</span></a>, and <a class="reference internal" href="msr2data.html#msr2data"><span class="std std-ref">msr2data</span></a>.</p>
|
||
</div>
|
||
</div>
|
||
<div class="section" id="asymmtery-fit-tutorial">
|
||
<h2>Asymmtery-fit tutorial<a class="headerlink" href="#asymmtery-fit-tutorial" title="Permalink to this headline">¶</a></h2>
|
||
<p>to be written yet.</p>
|
||
</div>
|
||
</div>
|
||
|
||
|
||
</div>
|
||
|
||
</div>
|
||
<footer>
|
||
|
||
<div class="rst-footer-buttons" role="navigation" aria-label="footer navigation">
|
||
|
||
<a href="user-manual.html" class="btn btn-neutral float-right" title="User manual" accesskey="n" rel="next">Next <span class="fa fa-arrow-circle-right"></span></a>
|
||
|
||
|
||
<a href="cite.html" class="btn btn-neutral" title="How to Cite musrfit?" accesskey="p" rel="prev"><span class="fa fa-arrow-circle-left"></span> Previous</a>
|
||
|
||
</div>
|
||
|
||
|
||
<hr/>
|
||
|
||
<div role="contentinfo">
|
||
<p>
|
||
© Copyright 2023, Andreas Suter.
|
||
Last updated on Feb 17, 2023.
|
||
|
||
</p>
|
||
</div>
|
||
Built with <a href="http://sphinx-doc.org/">Sphinx</a> using a <a href="https://github.com/rtfd/sphinx_rtd_theme">theme</a> provided by <a href="https://readthedocs.org">Read the Docs</a>.
|
||
|
||
</footer>
|
||
|
||
</div>
|
||
</div>
|
||
|
||
</section>
|
||
|
||
</div>
|
||
|
||
|
||
|
||
|
||
|
||
<script type="text/javascript">
|
||
var DOCUMENTATION_OPTIONS = {
|
||
URL_ROOT:'./',
|
||
VERSION:'1.9.0',
|
||
LANGUAGE:'None',
|
||
COLLAPSE_INDEX:false,
|
||
FILE_SUFFIX:'.html',
|
||
HAS_SOURCE: true,
|
||
SOURCELINK_SUFFIX: '.txt'
|
||
};
|
||
</script>
|
||
<script type="text/javascript" src="_static/jquery.js"></script>
|
||
<script type="text/javascript" src="_static/underscore.js"></script>
|
||
<script type="text/javascript" src="_static/doctools.js"></script>
|
||
<script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.1/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
|
||
|
||
|
||
|
||
|
||
|
||
<script type="text/javascript" src="_static/js/theme.js"></script>
|
||
|
||
|
||
<script type="text/javascript">
|
||
jQuery(function () {
|
||
SphinxRtdTheme.Navigation.enable(true);
|
||
});
|
||
</script>
|
||
|
||
</body>
|
||
</html> |