update of the docu.
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<head>
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<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
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<title>User manual — musrfit 1.7.6 documentation</title>
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<title>User manual — musrfit 1.8.0 documentation</title>
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<link rel="stylesheet" href="_static/haiku.css" type="text/css" />
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<script type="text/javascript">
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var DOCUMENTATION_OPTIONS = {
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URL_ROOT: './',
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VERSION: '1.7.6',
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VERSION: '1.8.0',
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COLLAPSE_INDEX: false,
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FILE_SUFFIX: '.html',
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HAS_SOURCE: true
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<script type="text/javascript" src="_static/underscore.js"></script>
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<link rel="top" title="musrfit 1.7.6 documentation" href="index.html" />
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<link rel="top" title="musrfit 1.8.0 documentation" href="index.html" />
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<link rel="prev" title="Tutorial for musrfit" href="tutorial.html" />
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</head>
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<body>
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<div class="header"><h1 class="heading"><a href="index.html">
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<span>musrfit 1.7.6 documentation</span></a></h1>
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<span>musrfit 1.8.0 documentation</span></a></h1>
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<h2 class="heading"><span>User manual</span></h2>
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</div>
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<div class="topnav">
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@ -443,12 +443,77 @@ Supported values for <tt class="docutils literal"><span class="pre"><graphic_
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</div>
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<p>Will dump the LEM header information of run 3456 including the content of the run summary file.</p>
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</div>
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<div class="section" id="addrun">
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<span id="index-10"></span><h3>addRun<a class="headerlink" href="#addrun" title="Permalink to this headline">¶</a></h3>
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<p><tt class="docutils literal"><span class="pre">addRun</span></tt> allows to add the histograms of various runs and save the result in a file.
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This can be done either by a list of runs (option1), or by a run file (option2).</p>
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<div class="highlight-bash"><div class="highlight"><pre><span></span>usage0: addRun [--help | -h] | [--version | -v]
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usage1: addRun <options1> -rl <runList>
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usage2: addRun <options2> -in <inputFile>
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<option1>:
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-t0 <ival>: <ival> is a comma separted list of global t0-bin`s, or
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<ival> is a comma separted list of '-1', then it is assumed that there is a prompt peak.
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Under this condition the t0-bin will be determined automatically by
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the position of the max-value of the corresponing histograms.
|
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If t0's are not provided, t0-bin will be taken from the file.
|
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-f <format>: <format> is the output file format to be used.
|
||||
For supported formats see below.
|
||||
-y <year> : the year at which runs were measured. Format yyyy.
|
||||
If not provided, the current year is used.
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||||
-i <instrument> : <instrument> is one of gps, ltf, flame, gpd, hifi, dolly, lem
|
||||
-m <dev> : <dev> is pta or tdc (only needed for bulk). Default: tdc
|
||||
-o <fln> : output file name.
|
||||
-rl <runList> can be:
|
||||
(i) <run0> <run1> <run2> ... <runN> : run numbers, e.g. 123 124
|
||||
(ii) <run0>-<runN> : a range, e.g. 123-125 -> 123 124 125
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||||
(iii) <run0>:<runN>:<step> : a sequence, e.g. 123:127:2 -> 123 125 127
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||||
<step> will give the step width and has to be a positive number!
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a <runList> can also combine (i)-(iii), e.g. 123 128-130 133, etc.
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||||
|
||||
<option2>:
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-f <format>: <format> is file format of the output-file to be used.
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||||
-o <fln> : output file name.
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||||
-in <inputFile>: the file name of the file containing the necessary run information
|
||||
to add runs with various t0's, fgb's, lgb's, different years, etc.
|
||||
The structure of the <inputFile> is:
|
||||
Lines starting with a '%' and empty lines are ignored.
|
||||
A single run needs to provide the following information:
|
||||
file <path-name>: needs to be a full path name
|
||||
t0 <t0-bin> : needs to be the t0 bin or
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||||
0 to take the t0 bin from the file, or
|
||||
-1 for automatic determination via prompt peak (see above).
|
||||
Example:
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||||
% file 1. 6 histos present, hence 6 t0-bins
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||||
file /home/test/data/deltat_tdc_gps_4324.bin
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||||
t0 401, 400, 399, 400, 358, 400
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||||
% file 2, take t0-bins from the file
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||||
file /home/test/data/deltat_tdc_gps_4325.bin
|
||||
% file 3, deduce to t0-bin's from the prompt peak
|
||||
file /home/test/data/deltat_tdc_gps_4325.bin
|
||||
t0 -1, -1, -1, -1, -1, -1
|
||||
|
||||
Supported uSR file formats:
|
||||
MusrRoot, PSI-BIN, PSI-MDU, MUD, NeXus
|
||||
</pre></div>
|
||||
</div>
|
||||
</div>
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||||
<div class="section" id="musrfit-startup-xml">
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||||
<span id="musrfit-startup"></span><span id="index-10"></span><h3>musrfit_startup.xml<a class="headerlink" href="#musrfit-startup-xml" title="Permalink to this headline">¶</a></h3>
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||||
<span id="musrfit-startup"></span><span id="index-11"></span><h3>musrfit_startup.xml<a class="headerlink" href="#musrfit-startup-xml" title="Permalink to this headline">¶</a></h3>
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||||
<p><tt class="docutils literal"><span class="pre">musrfit_startup.xml</span></tt> is a configuration file located at <tt class="docutils literal"><span class="pre">$HOME\.musrfit</span></tt>. In this file the following XML tags are allowed to define settings:</p>
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<dl class="docutils">
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<dt><strong><data_path>PATH_TO_DATA</data_path></strong></dt>
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||||
<dd>add the new path <tt class="docutils literal"><span class="pre">PATH_TO_DATA</span></tt> where <tt class="docutils literal"><span class="pre">musrfit</span></tt> and <tt class="docutils literal"><span class="pre">musrview</span></tt> will search for data files.</dd>
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<dt><strong><run_name_template inst=”instrument_name”>template</run_name_template></strong></dt>
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<dd><p class="first"><tt class="docutils literal"><span class="pre">instrument_name</span></tt> is the name of the instrument, e.g. gps. <tt class="docutils literal"><span class="pre">template</span></tt> allows to generate the potential path fragment where to search for files.
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||||
These path fragments are added to all present <tt class="docutils literal"><span class="pre">data_path</span></tt>. This is used e.g. by addRun in order to find runs. To illustrate this here an example:</p>
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<p><tt class="docutils literal"><span class="pre">d%yyyy%/tdc/lem%yy%_his_%rrrr%.root</span></tt>.</p>
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<p><tt class="docutils literal"><span class="pre">%yyyy%</span></tt> will be replaced by the provided year (4 digits, e.g. 2020). <tt class="docutils literal"><span class="pre">%yy%</span></tt> will be replaced by the provided year (2 digits, e.g. 18).
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||||
<tt class="docutils literal"><span class="pre">%rrrr%</span></tt> will be replaced by the run number. Here 4 <tt class="docutils literal"><span class="pre">r</span></tt> are given, hence the run 123 will be replaced to <tt class="docutils literal"><span class="pre">0123</span></tt>, i.e. leading zero’s will be added.
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||||
For the given example <tt class="docutils literal"><span class="pre">%rrrrr%</span></tt> would be replaced to <tt class="docutils literal"><span class="pre">00123</span></tt> etc.</p>
|
||||
<p>If the year is 2019 and the run 123, the above template would be expanded to</p>
|
||||
<p class="last"><tt class="docutils literal"><span class="pre">d2019/tdc/lem19_his_0123.root</span></tt>.</p>
|
||||
</dd>
|
||||
<dt><strong><write_per_run_block_chisq>y/n</write_per_run_block_chisq></strong></dt>
|
||||
<dd>if enabled <span class="math">\(\chi^2\)</span> for each <a class="reference internal" href="#msr-run-block"><em>RUN block</em></a> will be written to the <a class="reference internal" href="#msr-statistic-block"><em>STATISTIC block</em></a> of the resulting msr file. Additionally,
|
||||
in case a <span class="math">\(\chi^2\)</span> single-histogram fit is done, also <a class="reference external" href="http://en.wikipedia.org/wiki/Pearson's_chi-square_test">Pearson’s</a> <span class="math">\(\chi^2\)</span> will be added.</dd>
|
||||
@ -524,14 +589,14 @@ in case a <span class="math">\(\chi^2\)</span> single-histogram fit is done, als
|
||||
</div>
|
||||
</div>
|
||||
<div class="section" id="description-of-the-msr-file-format">
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||||
<span id="msr-file-format"></span><span id="index-11"></span><h2>Description of the msr File Format<a class="headerlink" href="#description-of-the-msr-file-format" title="Permalink to this headline">¶</a></h2>
|
||||
<span id="msr-file-format"></span><span id="index-12"></span><h2>Description of the msr File Format<a class="headerlink" href="#description-of-the-msr-file-format" title="Permalink to this headline">¶</a></h2>
|
||||
<p>The programs are using an input file to control their action. This input file has the extension <tt class="docutils literal"><span class="pre">.msr</span></tt> (msr file). The msr file is built up from different blocks. Each block starts with a keyword and is, with the exception of the title, terminated by an empty line. Comments start with the character <tt class="docutils literal"><span class="pre">#</span></tt>. The various input blocks are described below.</p>
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||||
<div class="section" id="the-title">
|
||||
<span id="msr-title-block"></span><span id="index-12"></span><h3>The Title<a class="headerlink" href="#the-title" title="Permalink to this headline">¶</a></h3>
|
||||
<span id="msr-title-block"></span><span id="index-13"></span><h3>The Title<a class="headerlink" href="#the-title" title="Permalink to this headline">¶</a></h3>
|
||||
<p>The first line of the msr file is the title line. Unlike all the other input blocks, it does not start with a block keyword. It is just a simple text line, in which any information can be placed. The title text will be used in the graphical representation of the data as a headline.</p>
|
||||
</div>
|
||||
<div class="section" id="the-fitparameter-block">
|
||||
<span id="msr-fitparameter-block"></span><span id="index-13"></span><h3>The FITPARAMETER Block<a class="headerlink" href="#the-fitparameter-block" title="Permalink to this headline">¶</a></h3>
|
||||
<span id="msr-fitparameter-block"></span><span id="index-14"></span><h3>The FITPARAMETER Block<a class="headerlink" href="#the-fitparameter-block" title="Permalink to this headline">¶</a></h3>
|
||||
<p>The FITPARAMETER block is used to define the fit parameters in a MINUIT typical style. There are various possible parameter definitions which are listed here:</p>
|
||||
<div class="highlight-python"><div class="highlight"><pre><span></span>1. <no> <name> <value> <step>
|
||||
2. <no> <name> <value> <step> <lower_boundary> <upper_boundary>
|
||||
@ -582,7 +647,7 @@ in case a <span class="math">\(\chi^2\)</span> single-histogram fit is done, als
|
||||
</table>
|
||||
</div>
|
||||
<div class="section" id="the-theory-block">
|
||||
<span id="msr-theory-block"></span><span id="index-14"></span><h3>The THEORY Block<a class="headerlink" href="#the-theory-block" title="Permalink to this headline">¶</a></h3>
|
||||
<span id="msr-theory-block"></span><span id="index-15"></span><h3>The THEORY Block<a class="headerlink" href="#the-theory-block" title="Permalink to this headline">¶</a></h3>
|
||||
<p>The THEORY block is used to define the fit function. There is a set of predefined functions available. It is also possible to use externally defined functions. How to use them will be explained afterwards, here only the predefined functions are described.</p>
|
||||
<table border="1" class="docutils">
|
||||
<colgroup>
|
||||
@ -956,7 +1021,7 @@ userFcn libMyLibrary.so TMyFunction 2 3 4 map1 fun1
|
||||
</div>
|
||||
</div>
|
||||
<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-16"></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, and some meta information from the data files.
|
||||
They can be used in the <a class="reference internal" href="#msr-theory-block"><em>THEORY block</em></a> and for three specific cases in the <a class="reference internal" href="#msr-run-block"><em>RUN block</em></a> (<cite>norm</cite>, <cite>alpha</cite>, and <cite>beta</cite>).
|
||||
Supported is the use of basic arithmetic:</p>
|
||||
@ -981,7 +1046,7 @@ acosh(), asinh(), atanh(), exp(), log(), ln(), sqrt(), pow(base, exponent)</stro
|
||||
</ul>
|
||||
<p>The fit parameters are accessed either directly through parX, where ‘X’ is the number of the parameter in the <a class="reference internal" href="#msr-fitparameter-block"><em>FITPARAMETER block</em></a>,
|
||||
<em>e.g.</em> <em>par5</em> or through a mapping with mapY, where ‘Y’ specifies the mapping number in the <a class="reference internal" href="#msr-run-block"><em>RUN block</em></a> as explained below.</p>
|
||||
<p id="index-16">The available meta information form the data files are:</p>
|
||||
<p id="index-17">The available meta information form the data files are:</p>
|
||||
<table border="1" class="docutils">
|
||||
<colgroup>
|
||||
<col width="29%" />
|
||||
@ -1041,7 +1106,7 @@ fun2 = par3 * ( 1.0 - par5 )
|
||||
</div>
|
||||
</div>
|
||||
<div class="section" id="the-global-block">
|
||||
<span id="msr-global-block"></span><span id="index-17"></span><h3>The GLOBAL Block<a class="headerlink" href="#the-global-block" title="Permalink to this headline">¶</a></h3>
|
||||
<span id="msr-global-block"></span><span id="index-18"></span><h3>The GLOBAL Block<a class="headerlink" href="#the-global-block" title="Permalink to this headline">¶</a></h3>
|
||||
<p>The GLOBAL block is used to collect data which otherwise need to be specified in every single run entry of the <a class="reference internal" href="#msr-run-block"><em>RUN block</em></a>.
|
||||
Therefore, this block is only present to potentially shorten the msr file and to ease the handling for the user. The logic will by like that:</p>
|
||||
<ol class="arabic simple">
|
||||
@ -1148,7 +1213,7 @@ fittype 0 (single histogram fit)
|
||||
</div>
|
||||
</div>
|
||||
<div class="section" id="the-run-block">
|
||||
<span id="msr-run-block"></span><span id="index-18"></span><h3>The RUN Block<a class="headerlink" href="#the-run-block" title="Permalink to this headline">¶</a></h3>
|
||||
<span id="msr-run-block"></span><span id="index-19"></span><h3>The RUN Block<a class="headerlink" href="#the-run-block" title="Permalink to this headline">¶</a></h3>
|
||||
<p>The RUN block is used to collect the data needed for a particular run to be fitted. This includes the run name, fit type, data format, etc.
|
||||
The RUN block is slightly differently organized than the other blocks. The information is collected via labels followed by the information.
|
||||
Each run to be fitted has its <em>own</em> RUN block. A RUN block starts with a run-file line which has the structure</p>
|
||||
@ -1222,7 +1287,7 @@ RUN beautiful-data MUE4 PSI DB
|
||||
</div>
|
||||
<p>After this short digression back to the RUN-block description.</p>
|
||||
<p>In order to describe the operations needed for fitting and plotting, quite some information are needed. These information are following the RUN statement and are listed below. Depending on the fit type these information vary and hence it is indicated for which fit/plot type the information is applicable</p>
|
||||
<span id="index-19"></span><dl class="docutils" id="msr-addrun">
|
||||
<span id="index-20"></span><dl class="docutils" id="msr-addrun">
|
||||
<dt><strong>ADDRUN <run_file_name> <beamline> <facility> <file_format></strong> (optional)</dt>
|
||||
<dd><p class="first">If an ADDRUN is just following after a RUN statement, these runs will be added. More than one ADDRUN statements are possible, <em>i.e.</em> adding up as many runs as wished. It is also possible to add runs with different file formats. If the t0’s are given in the data files, the ADDRUN statement is all what is needed, otherwise just add the t0’s with the addt0 statement.</p>
|
||||
<p>For a <a class="reference internal" href="#single-histogram-fit"><em>Single Histogram Fit</em></a> or a <a class="reference internal" href="#negative-muon-musr-fit"><em>MuMinus Fit</em></a> it will be</p>
|
||||
@ -1241,7 +1306,7 @@ etc.
|
||||
<p class="last">ADDRUN is <em>not</em> available for the fit type <a class="reference internal" href="#non-musr-fit"><em>Non-muSR Fit</em></a>.</p>
|
||||
</dd>
|
||||
</dl>
|
||||
<span id="index-20"></span><dl class="docutils" id="msr-fittype">
|
||||
<span id="index-21"></span><dl class="docutils" id="msr-fittype">
|
||||
<dt><strong>fittype</strong> (required if not already defined in the GLOBAL block)</dt>
|
||||
<dd><p class="first">This tag is used to indicate which type of fit is wished. The supported fit types are:</p>
|
||||
<dl class="docutils">
|
||||
@ -1266,7 +1331,7 @@ etc.
|
||||
</div>
|
||||
</dd>
|
||||
</dl>
|
||||
<span id="index-21"></span><dl class="docutils" id="msr-alpha-beta">
|
||||
<span id="index-22"></span><dl class="docutils" id="msr-alpha-beta">
|
||||
<dt><strong>alpha, beta</strong> (fit type 2, 3, 5)</dt>
|
||||
<dd><p class="first">These parameters are used to correct the asymmetry for different detector efficiencies, solid angles and initial asymmetries. They are defined as <span class="math">\(\alpha = N_{0,b}/N_{0,f}\)</span> and <span class="math">\(\beta = A_{0,b}/A_{0,f}\)</span>. If the parameters are not specified in the <a class="reference internal" href="#msr-run-block"><em>RUN block</em></a>, for each one the value of 1 is assumed (for fittype 5, alpha is estimated from the ratio of <span class="math">\(\sum_i \left( N_{\mathrm{bp}}(i)+N_{\mathrm{bm}}(i) \right)\)</span> and <span class="math">\(\sum_i \left( N_{\mathrm{fp}}(i)+N_{\mathrm{fm}}(i) \right)\)</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-python"><div class="highlight"><pre><span></span>alpha 1
|
||||
@ -1278,7 +1343,7 @@ etc.
|
||||
</div>
|
||||
</dd>
|
||||
</dl>
|
||||
<span id="index-22"></span><dl class="docutils" id="msr-norm">
|
||||
<span id="index-23"></span><dl class="docutils" id="msr-norm">
|
||||
<dt><strong>norm</strong> (fit type 0)</dt>
|
||||
<dd><p class="first">Number of the fit parameter that represents the normalization constant <span class="math">\(N_0\)</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"><em>below</em></a>).
|
||||
It is possible to substitute the parameter number by a function, for instance to relate <span class="math">\(N_0\)</span>‘s of different histograms through an <span class="math">\(\alpha\)</span>
|
||||
@ -1292,25 +1357,25 @@ parameter. Example for a <tt class="docutils literal"><span class="pre">norm</sp
|
||||
</div>
|
||||
</dd>
|
||||
</dl>
|
||||
<span id="index-23"></span><dl class="docutils" id="msr-backgr-fit">
|
||||
<span id="index-24"></span><dl class="docutils" id="msr-backgr-fit">
|
||||
<dt><strong>backgr.fit</strong> (fit type 0)</dt>
|
||||
<dd>Parameter number specifying the constant background in a histogram. Its value is given either per nanosecond or per bin (see <a class="reference internal" href="#msr-commands-block"><em>below</em></a>). If this keyword is present,
|
||||
any information on a background line are ignored.</dd>
|
||||
</dl>
|
||||
<span id="index-24"></span><dl class="docutils" id="msr-lifetime">
|
||||
<span id="index-25"></span><dl class="docutils" id="msr-lifetime">
|
||||
<dt><strong>lifetime</strong> (fit type 0)</dt>
|
||||
<dd>Fit parameter representing the lifetime of the muon. If it is not specified the value <span class="math">\(\tau_\mu=2.197019~ \mu\mathrm{s}\)</span> is used in the calculations.</dd>
|
||||
<dt><strong>lifetimecorrection</strong> (fit type 0) <em>obsolete</em></dt>
|
||||
<dd>Does not accept any arguments. If present, the output in <tt class="docutils literal"><span class="pre">musrview</span></tt> is corrected for the exponential decay of the muon. This item is <em>obsolete</em> in the RUN block
|
||||
and will be transferred to the <a class="reference internal" href="#msr-plot-block"><em>PLOT block</em></a>, which allows switching between histogram view and asymmetry view much quicker.</dd>
|
||||
</dl>
|
||||
<span id="index-25"></span><dl class="docutils" id="msr-map">
|
||||
<span id="index-26"></span><dl class="docutils" id="msr-map">
|
||||
<dt><strong>map</strong></dt>
|
||||
<dd>On this line the mapping of run-dependent parameters is done. Parameter numbers given here may be accessed through map1, map2, etc. in the
|
||||
<a class="reference internal" href="#msr-theory-block"><em>THEORY</em></a> and <a class="reference internal" href="#msr-functions-block"><em>FUNCTIONS</em></a> blocks (see also <a class="reference internal" href="#msr-map-intro"><em>maps</em></a>). The first ten maps
|
||||
are always present and have the value 0 if not used; however, the total number of maps is not restricted!</dd>
|
||||
</dl>
|
||||
<span id="index-26"></span><dl class="docutils" id="msr-forward">
|
||||
<span id="index-27"></span><dl class="docutils" id="msr-forward">
|
||||
<dt><strong>forward</strong> (fit type 0, 1, 4)</dt>
|
||||
<dd><p class="first">Number of the histogram in the data file to be processed. If histograms shall be grouped, all the numbers which shall be grouped. Examples:</p>
|
||||
<div class="last highlight-python"><div class="highlight"><pre><span></span>forward 3 # no grouping, take histogram number 3
|
||||
@ -1320,7 +1385,7 @@ forward 1-10 12 # group histograms with numbers from 1 to 10 and additionally hi
|
||||
</div>
|
||||
</dd>
|
||||
</dl>
|
||||
<span id="index-27"></span><dl class="docutils" id="msr-forward-backward">
|
||||
<span id="index-28"></span><dl class="docutils" id="msr-forward-backward">
|
||||
<dt><strong>forward, backward</strong> (fit types 2, 3)</dt>
|
||||
<dd><p class="first">Numbers of the histograms in the data file that should be taken to calculate the asymmetry. If histograms shall be grouped, all the numbers which shall be grouped. Examples:</p>
|
||||
<div class="last highlight-python"><div class="highlight"><pre><span></span># build forward/backward asymmetry with histogram 1 and 3
|
||||
@ -1344,12 +1409,12 @@ backward 3 4
|
||||
</div>
|
||||
</dd>
|
||||
</dl>
|
||||
<span id="index-28"></span><dl class="docutils" id="msr-backgr-fix">
|
||||
<span id="index-29"></span><dl class="docutils" id="msr-backgr-fix">
|
||||
<dt><strong>backgr.fix</strong> (fit types 0, 1, 2, 3, 5)</dt>
|
||||
<dd>A fixed constant background in counts per nanosecond or per bin (see <a class="reference internal" href="#msr-commands-block"><em>below</em></a>) may be given at this point.
|
||||
The background is specified for all histograms in the order <span class="math">\(B_f B_b [B_r B_l]\)</span>. If this keyword is present, <em>any</em> information on a <tt class="docutils literal"><span class="pre">background</span></tt> line is ignored.</dd>
|
||||
</dl>
|
||||
<span id="index-29"></span><dl class="docutils" id="msr-background-single-histo">
|
||||
<span id="index-30"></span><dl class="docutils" id="msr-background-single-histo">
|
||||
<dt><strong>background</strong> (fit type 0, 1)</dt>
|
||||
<dd><p class="first">The numbers of the first and the last channel of an interval from which the constant background should be calculated are specified here.
|
||||
In case histograms are being grouped, the specified channels are interpreted with respect to the first histogram. Example:</p>
|
||||
@ -1358,7 +1423,7 @@ In case histograms are being grouped, the specified channels are interpreted wit
|
||||
</div>
|
||||
</dd>
|
||||
</dl>
|
||||
<span id="index-30"></span><dl class="docutils" id="msr-background-asymmetry">
|
||||
<span id="index-31"></span><dl class="docutils" id="msr-background-asymmetry">
|
||||
<dt><strong>background</strong> (fit types 2, 3, 5)</dt>
|
||||
<dd><p class="first">The numbers of the first and the last channel of an interval from which the constant background should be calculated are specified here.
|
||||
For all the histograms this is done together in the following order: <span class="math">\(k_{f,\rm first} k_{f,\rm last} k_{b,\rm first} k_{b, \rm last} [k_{r,\rm first} k_{r,\rm last} k_{l,\rm first} k_{l,\rm last}]\)</span>.
|
||||
@ -1368,7 +1433,7 @@ In case histograms are being grouped, the specified channels are interpreted wit
|
||||
</div>
|
||||
</dd>
|
||||
</dl>
|
||||
<span id="index-31"></span><dl class="docutils" id="msr-data-single-histo">
|
||||
<span id="index-32"></span><dl class="docutils" id="msr-data-single-histo">
|
||||
<dt><strong>data</strong> (fit type 0, 1, 4)</dt>
|
||||
<dd><p class="first">The numbers of the first and the last channel of an interval from which the data is taken are specified here.
|
||||
In case histograms are being grouped, the specified channels are interpreted with respect to the first histogram.
|
||||
@ -1378,7 +1443,7 @@ Typically these channels are referred to as <tt class="docutils literal"><span c
|
||||
</div>
|
||||
</dd>
|
||||
</dl>
|
||||
<span id="index-32"></span><dl class="docutils" id="msr-data-asymmetry">
|
||||
<span id="index-33"></span><dl class="docutils" id="msr-data-asymmetry">
|
||||
<dt><strong>data</strong> (fit type 2, 3, 5)</dt>
|
||||
<dd><p class="first">The numbers of the first and the last channel of an interval from which the data is taken are specified here.
|
||||
Typically these channels are referred to as first good bin / last good bin (fgb/lgb). For all the histograms this is
|
||||
@ -1389,7 +1454,7 @@ In case histograms are being grouped, the specified channels are interpreted wit
|
||||
</div>
|
||||
</dd>
|
||||
</dl>
|
||||
<span id="index-33"></span><dl class="docutils" id="msr-t0-single-histo">
|
||||
<span id="index-34"></span><dl class="docutils" id="msr-t0-single-histo">
|
||||
<dt><strong>t0</strong> (fit type 0, 1, 4)</dt>
|
||||
<dd><p class="first">The number of the time-zero channel of the histogram. Example:</p>
|
||||
<div class="last highlight-python"><div class="highlight"><pre><span></span>t0 3419 # t0 channel = 3419
|
||||
@ -1398,7 +1463,7 @@ t0 3419 3434 # t0 channels for groupings: forward f1 f2. 3419 t0 for f1, 3434
|
||||
</div>
|
||||
</dd>
|
||||
</dl>
|
||||
<span id="index-34"></span><dl class="docutils" id="msr-t0-asymmetry">
|
||||
<span id="index-35"></span><dl class="docutils" id="msr-t0-asymmetry">
|
||||
<dt><strong>t0</strong> (fit type 2, 3, 5)</dt>
|
||||
<dd><p class="first">The numbers of time-zero channels of the histograms in the order <span class="math">\(t_{0,f} t_{0,b}\)</span>. For fit type 5, the time-zero is the channel of the start of beam pulse. Example:</p>
|
||||
<div class="last highlight-python"><div class="highlight"><pre><span></span>t0 3419 3418 # t0 channels: forward (3419), backward (3418)
|
||||
@ -1407,25 +1472,25 @@ t0 3419 3418 3417 3416 # t0 channels (assuming forward f1 f2, backward b1 b2): f
|
||||
</div>
|
||||
</dd>
|
||||
</dl>
|
||||
<span id="index-35"></span><dl class="docutils" id="msr-addt0-single-histo">
|
||||
<span id="index-36"></span><dl class="docutils" id="msr-addt0-single-histo">
|
||||
<dt><strong>addt0</strong> (fit type 0, 1, 4)</dt>
|
||||
<dd>The number of the time-zero channel of the histogram. If grouping of histograms is present (see <a class="reference internal" href="#msr-forward"><em>forward</em></a>) the
|
||||
same syntax as for <a class="reference internal" href="#msr-t0-single-histo"><em>t0</em></a> applies. If one addt0 is given, the total number of addt0’s needs to be equal to
|
||||
the total number of <a class="reference internal" href="#msr-addrun"><em>ADDRUN</em></a>‘s!</dd>
|
||||
</dl>
|
||||
<span id="index-36"></span><dl class="docutils" id="msr-addt0-asymmetry">
|
||||
<span id="index-37"></span><dl class="docutils" id="msr-addt0-asymmetry">
|
||||
<dt><strong>addt0</strong> (fit type 2, 3, 5)</dt>
|
||||
<dd>The numbers of time-zero channels of the histograms in the order <span class="math">\(t_{0,f} t_{0,b} [t_{0,r} t_{0,l}]\)</span>.
|
||||
If grouping of histograms is present (see <a class="reference internal" href="#msr-forward-backward"><em>forward</em></a>) the same syntax as for <a class="reference internal" href="#msr-t0-asymmetry"><em>t0</em></a> applies.
|
||||
If one addt0 is given, the total number of addt0’s needs to be equal to the total number of <a class="reference internal" href="#msr-addrun"><em>ADDRUN</em></a>‘s!</dd>
|
||||
</dl>
|
||||
<span id="index-37"></span><dl class="docutils" id="msr-xy-data">
|
||||
<span id="index-38"></span><dl class="docutils" id="msr-xy-data">
|
||||
<dt><strong>xy-data</strong> (fit type 8)</dt>
|
||||
<dd>Specification of the data from an ASCII or DB file which should be used as <em>x</em> and <em>y</em> data (in this order).
|
||||
For a simple ASCII file the column numbers are used, in the case of a DB file one can either specify the variable
|
||||
numbers or the name of the variables as given in the DB header.</dd>
|
||||
</dl>
|
||||
<span id="index-38"></span><dl class="docutils" id="msr-fit">
|
||||
<span id="index-39"></span><dl class="docutils" id="msr-fit">
|
||||
<dt><strong>fit</strong></dt>
|
||||
<dd><p class="first">The range of data that should be considered when the fitting is done. For the μSR fit types 0, 1, 2, 3, and 4 the
|
||||
starting and end times are given in micro-seconds. For the non-μSR fit type 8 the starting and end points of the
|
||||
@ -1449,19 +1514,19 @@ An example:</p>
|
||||
</div>
|
||||
</dd>
|
||||
</dl>
|
||||
<span id="index-39"></span><dl class="docutils" id="msr-packing">
|
||||
<span id="index-40"></span><dl class="docutils" id="msr-packing">
|
||||
<dt><strong>packing</strong></dt>
|
||||
<dd>Number of data channels to be binned together. For the non-μSR fit type 8 the binning is supposed to be 1.
|
||||
For the single histogram RRF fit (fittype 1) and asymmetry RRF fit (fittype 3) this parameter is meaningless.</dd>
|
||||
</dl>
|
||||
</div>
|
||||
<div class="section" id="the-commands-block">
|
||||
<span id="msr-commands-block"></span><span id="index-40"></span><h3>The COMMANDS Block<a class="headerlink" href="#the-commands-block" title="Permalink to this headline">¶</a></h3>
|
||||
<span id="msr-commands-block"></span><span id="index-41"></span><h3>The COMMANDS Block<a class="headerlink" href="#the-commands-block" title="Permalink to this headline">¶</a></h3>
|
||||
<p>The COMMANDS block is used to specify the commands which are passed from <tt class="docutils literal"><span class="pre">musrfit</span></tt> to <tt class="docutils literal"><span class="pre">MINUIT2</span></tt>. The supported commands
|
||||
after the <tt class="docutils literal"><span class="pre">COMMANDS</span></tt> keyword are listed in the two tables below (<a class="reference internal" href="#minuit2-command-overview"><em>Minuit2 Command Overview</em></a> and <a class="reference internal" href="#dks-command-overview"><em>DKS Command Overview</em></a>)
|
||||
and further described in <a class="reference internal" href="#musrfit-command-block-details"><em>musrfit Command Block Details</em></a>.</p>
|
||||
<div class="section" id="minuit2-command-overview">
|
||||
<span id="index-41"></span><span id="id21"></span><h4>Minuit2 Command Overview<a class="headerlink" href="#minuit2-command-overview" title="Permalink to this headline">¶</a></h4>
|
||||
<span id="index-42"></span><span id="id21"></span><h4>Minuit2 Command Overview<a class="headerlink" href="#minuit2-command-overview" title="Permalink to this headline">¶</a></h4>
|
||||
<table border="1" class="docutils">
|
||||
<colgroup>
|
||||
<col width="20%" />
|
||||
@ -1610,7 +1675,7 @@ Used for statistical analysis only.</td>
|
||||
</table>
|
||||
</div>
|
||||
<div class="section" id="dks-command-overview">
|
||||
<span id="index-42"></span><span id="id31"></span><h4>DKS Command Overview<a class="headerlink" href="#dks-command-overview" title="Permalink to this headline">¶</a></h4>
|
||||
<span id="index-43"></span><span id="id31"></span><h4>DKS Command Overview<a class="headerlink" href="#dks-command-overview" title="Permalink to this headline">¶</a></h4>
|
||||
<table border="1" class="docutils">
|
||||
<colgroup>
|
||||
<col width="28%" />
|
||||
@ -1678,7 +1743,7 @@ It allows to use all your threads of your CPU(s) during the minimization.</td></
|
||||
</table>
|
||||
</div>
|
||||
<div class="section" id="musrfit-command-block-details">
|
||||
<span id="index-43"></span><span id="id36"></span><h4><tt class="docutils literal"><span class="pre">musrfit</span></tt> Command Block Details<a class="headerlink" href="#musrfit-command-block-details" title="Permalink to this headline">¶</a></h4>
|
||||
<span id="index-44"></span><span id="id36"></span><h4><tt class="docutils literal"><span class="pre">musrfit</span></tt> Command Block Details<a class="headerlink" href="#musrfit-command-block-details" title="Permalink to this headline">¶</a></h4>
|
||||
<p>A standard COMMANDS block then looks like this:</p>
|
||||
<div class="highlight-python"><div class="highlight"><pre><span></span><span class="n">COMMANDS</span>
|
||||
<span class="n">MINIMIZE</span>
|
||||
@ -1775,7 +1840,7 @@ SAVE
|
||||
<p><em>Note:</em> If a fit is invoked, the sector command results will only be written to file, if the fit <em>has converged</em>!</p>
|
||||
</div>
|
||||
<div class="section" id="dks-extensions-of-the-commands-block-enabling-gpu-and-general-opencl-support">
|
||||
<span id="msr-commands-block-dks"></span><span id="index-44"></span><h4>DKS extensions of the COMMANDS block enabling GPU and general OpenCL support<a class="headerlink" href="#dks-extensions-of-the-commands-block-enabling-gpu-and-general-opencl-support" title="Permalink to this headline">¶</a></h4>
|
||||
<span id="msr-commands-block-dks"></span><span id="index-45"></span><h4>DKS extensions of the COMMANDS block enabling GPU and general OpenCL support<a class="headerlink" href="#dks-extensions-of-the-commands-block-enabling-gpu-and-general-opencl-support" title="Permalink to this headline">¶</a></h4>
|
||||
<p>In case you are running the musrfit / DKS version, there are a couple commands which allow you to control the way how the fit shall be performed. These commands are:</p>
|
||||
<table border="1" class="docutils">
|
||||
<colgroup>
|
||||
@ -1808,27 +1873,27 @@ In the <a class="reference internal" href="#msr-theory-block"><em>THEORY table</
|
||||
</div>
|
||||
</div>
|
||||
<div class="section" id="the-fourier-block">
|
||||
<span id="msr-fourier-block"></span><span id="index-45"></span><h3>The FOURIER Block<a class="headerlink" href="#the-fourier-block" title="Permalink to this headline">¶</a></h3>
|
||||
<span id="msr-fourier-block"></span><span id="index-46"></span><h3>The FOURIER Block<a class="headerlink" href="#the-fourier-block" title="Permalink to this headline">¶</a></h3>
|
||||
<p>If a Fourier transform is carried out the results are plotted within <tt class="docutils literal"><span class="pre">musrview</span></tt>. As input data the actual data <em>shown</em> in <tt class="docutils literal"><span class="pre">musrview</span></tt> is used,
|
||||
<em>i.e.</em> the currently time range shown in <tt class="docutils literal"><span class="pre">musrview</span></tt>! In the FOURIER block of the msr file all necessary parameters for calculating and presenting
|
||||
the Fourier transform of the data specified in the <a class="reference internal" href="#msr-plot-block"><em>PLOT block</em></a> is given. If the FOURIER block is not present in the msr file,
|
||||
either the parameters set in the <a class="reference internal" href="#musrfit-startup"><em>XML startup</em></a> file or the system defaults are taken when the Fourier transform is performed.
|
||||
The block starts with the <em>FOURIER</em> keyword and may contain the following entries on the successive lines:</p>
|
||||
<span id="index-46"></span><dl class="docutils" id="msr-fourier-block-units">
|
||||
<span id="index-47"></span><dl class="docutils" id="msr-fourier-block-units">
|
||||
<dt><strong>units</strong></dt>
|
||||
<dd>Here is specified in which domain the Fourier-transformed data is presented. One may choose between the fields (<em>Gauss</em>) or (<em>Tesla</em>), the frequency (<em>MHz</em>), and the angular-frequency domain (<em>Mc/s</em>).</dd>
|
||||
</dl>
|
||||
<span id="index-47"></span><dl class="docutils" id="msr-fourier-block-fourier-power">
|
||||
<span id="index-48"></span><dl class="docutils" id="msr-fourier-block-fourier-power">
|
||||
<dt><strong>fourier_power</strong></dt>
|
||||
<dd>It is possible (but not necessary) to set the number of data points used for the Fourier transform here. As argument the exponent <em>n<21</em> of a power of 2 is accepted.
|
||||
The number of data points is then 2<sup>n</sup>. <strong>Attention:</strong> If the number of points given here is bigger than the actual number of available data points,
|
||||
the input data vector is filled with zeros until the number of requested points is reached (<em>zero padding</em>)!</dd>
|
||||
</dl>
|
||||
<span id="index-48"></span><dl class="docutils" id="msr-fourier-block-dc-corrected">
|
||||
<span id="index-49"></span><dl class="docutils" id="msr-fourier-block-dc-corrected">
|
||||
<dt><strong>dc-corrected</strong></dt>
|
||||
<dd>a flag to remove a potential DC-offset of the signal. Allowed entries are <tt class="docutils literal"><span class="pre">dc-corrected</span> <span class="pre">true</span> <span class="pre">|</span> <span class="pre">1</span> <span class="pre">|</span> <span class="pre">false</span> <span class="pre">|</span> <span class="pre">0</span></tt>.</dd>
|
||||
</dl>
|
||||
<span id="index-49"></span><dl class="docutils" id="msr-fourier-block-apodization">
|
||||
<span id="index-50"></span><dl class="docutils" id="msr-fourier-block-apodization">
|
||||
<dt><strong>apodization</strong></dt>
|
||||
<dd><p class="first">Here is decided if the data should be apodized before the Fourier transform is performed and if yes, which apodization should be used (for further details about apodization of
|
||||
μSR data refer to the <a class="reference external" href="https://open.library.ubc.ca/cIRcle/collections/ubctheses/831/items/1.0085550">PhD thesis of T.M. Riseman (UBC)</a>). The argument to be put after the
|
||||
@ -1846,7 +1911,7 @@ keyword is therefore one of the following: <strong>NONE, WEAK, MEDIUM</strong> o
|
||||
</dl>
|
||||
</dd>
|
||||
</dl>
|
||||
<span id="index-50"></span><dl class="docutils" id="msr-fourier-block-plot">
|
||||
<span id="index-51"></span><dl class="docutils" id="msr-fourier-block-plot">
|
||||
<dt><strong>plot</strong></dt>
|
||||
<dd><p class="first">At this point it is possible to set the part of the Fourier-transformed data which should be plotted by default if the Fourier transform is done by pressing the <em>f</em>-key in <tt class="docutils literal"><span class="pre">musrview</span></tt>.
|
||||
The argument may be one of the following:</p>
|
||||
@ -1864,7 +1929,7 @@ The argument may be one of the following:</p>
|
||||
</dl>
|
||||
</dd>
|
||||
</dl>
|
||||
<span id="index-51"></span><dl class="docutils" id="msr-fourier-block-phase">
|
||||
<span id="index-52"></span><dl class="docutils" id="msr-fourier-block-phase">
|
||||
<dt><strong>phase</strong></dt>
|
||||
<dd><p class="first">If a real Fourier shall be plotted, it is necessary to adopt the phases of the different detectors. The number of potentially provided phases can be either <strong>one</strong>, which means that this phase will be applied to <em>all</em> Fourier spectra,
|
||||
or the number of phases have to correspond to the number of runs in the plot block.</p>
|
||||
@ -1917,12 +1982,12 @@ list example, the first parameter number will be the reference phase. The compac
|
||||
</ol>
|
||||
</dd>
|
||||
</dl>
|
||||
<span id="index-52"></span><dl class="docutils" id="msr-fourier-block-range-for-phase-correction">
|
||||
<span id="index-53"></span><dl class="docutils" id="msr-fourier-block-range-for-phase-correction">
|
||||
<dt><strong>range_for_phase_correction</strong></dt>
|
||||
<dd>An interval in Fourier space given in units as define with the ‘units’ tag, or the tag ‘all’ in which case the range given under ‘range’ will be used.
|
||||
The given interval will be used for an automatic phasing of the real Fourier transform. This will allow to add real Fourier spectra coherently.</dd>
|
||||
</dl>
|
||||
<span id="index-53"></span><dl class="docutils" id="msr-fourier-block-range">
|
||||
<span id="index-54"></span><dl class="docutils" id="msr-fourier-block-range">
|
||||
<dt><strong>range</strong></dt>
|
||||
<dd>The plotting range is set here. The interval is specified through its start and end points given in the <em>units</em> set after the <strong>units</strong> tag.</dd>
|
||||
</dl>
|
||||
@ -1938,20 +2003,20 @@ range 0.0 17.03
|
||||
</div>
|
||||
</div>
|
||||
<div class="section" id="the-plot-block">
|
||||
<span id="msr-plot-block"></span><span id="index-54"></span><h3>The PLOT Block<a class="headerlink" href="#the-plot-block" title="Permalink to this headline">¶</a></h3>
|
||||
<span id="msr-plot-block"></span><span id="index-55"></span><h3>The PLOT Block<a class="headerlink" href="#the-plot-block" title="Permalink to this headline">¶</a></h3>
|
||||
<p>The PLOT block is intended to collect all the information needed for the graphical presentation of the data and fits using <tt class="docutils literal"><span class="pre">musrview</span></tt>.
|
||||
The PLOT keyword at the beginning of the block is followed by a number which indicates the plot type. The plot types have to match the <a class="reference internal" href="#fit-types"><em>fit types</em></a>.
|
||||
Additionally, it is possible to provide information using the following keywords:</p>
|
||||
<span id="index-55"></span><dl class="docutils" id="msr-plot-block-lifetimecorrection">
|
||||
<span id="index-56"></span><dl class="docutils" id="msr-plot-block-lifetimecorrection">
|
||||
<dt><strong>lifetimecorrection</strong></dt>
|
||||
<dd>Does not accept any arguments. If present, the output in <tt class="docutils literal"><span class="pre">musrview</span></tt> is corrected for the exponential decay of the muon. Only relevant for (type 0).</dd>
|
||||
</dl>
|
||||
<span id="index-56"></span><dl class="docutils" id="msr-plot-block-runs">
|
||||
<span id="index-57"></span><dl class="docutils" id="msr-plot-block-runs">
|
||||
<dt><strong>runs</strong></dt>
|
||||
<dd>The numbers of the runs to be plotted have to be put here. The runs are numbered according to their appearance in the <a class="reference internal" href="#msr-run-block"><em>RUN block</em></a>.
|
||||
The numbers is either a space separated list of numbers, an interval <em>e.g.</em> 1-16, or a combination of both.</dd>
|
||||
</dl>
|
||||
<span id="index-57"></span><dl class="docutils" id="msr-plot-block-range">
|
||||
<span id="index-58"></span><dl class="docutils" id="msr-plot-block-range">
|
||||
<dt><strong>range</strong></dt>
|
||||
<dd><p class="first">Here it is possible to define the plotting range explicitly. Depending on the plot type the following settings are allowed where the times are given in
|
||||
micro-seconds and the <em>N</em> in counts (types 0-4) or in counts/nsec (type 0, 1):</p>
|
||||
@ -1965,7 +2030,7 @@ micro-seconds and the <em>N</em> in counts (types 0-4) or in counts/nsec (type 0
|
||||
</dl>
|
||||
</dd>
|
||||
</dl>
|
||||
<span id="index-58"></span><dl class="docutils" id="msr-plot-block-sub-ranges">
|
||||
<span id="index-59"></span><dl class="docutils" id="msr-plot-block-sub-ranges">
|
||||
<dt><strong>sub_ranges</strong></dt>
|
||||
<dd><p class="first">Here it is possible to define the plotting range for each run individually. For the different plot types the command has the structure:</p>
|
||||
<dl class="last docutils">
|
||||
@ -1978,31 +2043,31 @@ micro-seconds and the <em>N</em> in counts (types 0-4) or in counts/nsec (type 0
|
||||
</dl>
|
||||
</dd>
|
||||
</dl>
|
||||
<span id="index-59"></span><dl class="docutils" id="msr-plot-block-use-fit-ranges">
|
||||
<span id="index-60"></span><dl class="docutils" id="msr-plot-block-use-fit-ranges">
|
||||
<dt><strong>use_fit_ranges</strong> [ <em>y</em><sub>min</sub> <em>y</em><sub>max</sub> ]</dt>
|
||||
<dd>The fit ranges of the individual runs are used to present the data. Optionally, an ordinate range can be provided.</dd>
|
||||
</dl>
|
||||
<span id="index-60"></span><dl class="docutils" id="msr-plot-block-view-packing">
|
||||
<span id="index-61"></span><dl class="docutils" id="msr-plot-block-view-packing">
|
||||
<dt><strong>view_packing</strong></dt>
|
||||
<dd>The data are presented in the packing given here rather than the binning used for the fit. <strong>WARNING:</strong> This is a global option and applies to all PLOT-blocks.</dd>
|
||||
</dl>
|
||||
<span id="index-61"></span><dl class="docutils" id="msr-plot-block-logx">
|
||||
<span id="index-62"></span><dl class="docutils" id="msr-plot-block-logx">
|
||||
<dt><strong>logx</strong></dt>
|
||||
<dd>Will present the time axis in a logarithmic scale. <em>So far no checking of negative and zero-valued data is performed, hence expect interesting output!</em></dd>
|
||||
</dl>
|
||||
<span id="index-62"></span><dl class="docutils" id="msr-plot-block-logy">
|
||||
<span id="index-63"></span><dl class="docutils" id="msr-plot-block-logy">
|
||||
<dt><strong>logy</strong></dt>
|
||||
<dd>Will present the axis of ordinates in a logarithmic scale. <em>So far no checking of negative and zero-valued data is performed, hence expect interesting output!</em></dd>
|
||||
</dl>
|
||||
<span id="index-63"></span><dl class="docutils" id="msr-plot-block-rrf-packing">
|
||||
<span id="index-64"></span><dl class="docutils" id="msr-plot-block-rrf-packing">
|
||||
<dt><strong>rrf_packing</strong> value</dt>
|
||||
<dd>In the rotating-reference-frame (RRF) representation, this will be the value for the packing. <strong>WARNING:</strong> For the time being, this is a global option and applies to all PLOT blocks.</dd>
|
||||
</dl>
|
||||
<span id="index-64"></span><dl class="docutils" id="msr-plot-block-rrf-freq">
|
||||
<span id="index-65"></span><dl class="docutils" id="msr-plot-block-rrf-freq">
|
||||
<dt><strong>rrf_freq</strong> value unit</dt>
|
||||
<dd>This entry provides the RRF “frequency” given by the value and the unit which can be: <em>kHz</em>, <em>MHz</em>, <em>Mc/s</em>, <em>G</em>, or <em>T</em>.</dd>
|
||||
</dl>
|
||||
<span id="index-65"></span><dl class="docutils" id="msr-plot-block-rrf-phase">
|
||||
<span id="index-66"></span><dl class="docutils" id="msr-plot-block-rrf-phase">
|
||||
<dt><strong>rrf_phase</strong> value</dt>
|
||||
<dd>A phase of the RRF can be provided, either as a value in degrees, or as a parX, <em>e.g.</em> par4, where ‘X’ is supposed to be the phase parameter number in the <a class="reference internal" href="#msr-fitparameter-block"><em>FITPARAMETER block</em></a>.</dd>
|
||||
<dt><strong>Notes:</strong></dt>
|
||||
@ -2037,7 +2102,7 @@ rrf_packing 75
|
||||
</div>
|
||||
</div>
|
||||
<div class="section" id="the-statistic-block">
|
||||
<span id="msr-statistic-block"></span><span id="index-66"></span><h3>The STATISTIC Block<a class="headerlink" href="#the-statistic-block" title="Permalink to this headline">¶</a></h3>
|
||||
<span id="msr-statistic-block"></span><span id="index-67"></span><h3>The STATISTIC Block<a class="headerlink" href="#the-statistic-block" title="Permalink to this headline">¶</a></h3>
|
||||
<p>The STATISTIC 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">\(\chi^2\)</span> and the number of degrees of freedom in the fit.
|
||||
If enabled in the <a class="reference internal" href="#musrfit-startup"><em>XML file</em></a> for <span class="math">\(\chi^2\)</span>-single-histogram fits also <a class="reference external" href="http://en.wikipedia.org/wiki/Pearson's_chi-square_test">Pearson’s</a>
|
||||
@ -2046,9 +2111,9 @@ If enabled in the <a class="reference internal" href="#musrfit-startup"><em>XML
|
||||
</div>
|
||||
</div>
|
||||
<div class="section" id="fit-types">
|
||||
<span id="index-67"></span><span id="id37"></span><h2>Fit Types<a class="headerlink" href="#fit-types" title="Permalink to this headline">¶</a></h2>
|
||||
<span id="index-68"></span><span id="id37"></span><h2>Fit Types<a class="headerlink" href="#fit-types" title="Permalink to this headline">¶</a></h2>
|
||||
<div class="section" id="single-histogram-fit-fit-type-0">
|
||||
<span id="single-histogram-fit"></span><span id="index-68"></span><h3>Single Histogram Fit (fit type 0)<a class="headerlink" href="#single-histogram-fit-fit-type-0" title="Permalink to this headline">¶</a></h3>
|
||||
<span id="single-histogram-fit"></span><span id="index-69"></span><h3>Single Histogram Fit (fit type 0)<a class="headerlink" href="#single-histogram-fit-fit-type-0" title="Permalink to this headline">¶</a></h3>
|
||||
<p>The single-histogram fit (fit type 0) is used to fit a function directly to the raw data using</p>
|
||||
<div class="math">
|
||||
\[N(t) = N_0 e^{-t/\tau_\mu} [ 1 + A(t) ] + N_{\rm bkg}\]</div>
|
||||
@ -2069,7 +2134,7 @@ If the option lifetimecorrection is <em>set</em> in the PLOT block the asymmetry
|
||||
\[A(t) = \frac{N(t) - N_{\rm bkg}}{N_0} e^{+t/\tau_\mu} - 1\]</div>
|
||||
</div>
|
||||
<div class="section" id="single-histogram-rrf-fit-fit-type-1">
|
||||
<span id="single-histogram-rrf-fit"></span><span id="index-69"></span><h3>Single Histogram RRF Fit (fit type 1)<a class="headerlink" href="#single-histogram-rrf-fit-fit-type-1" title="Permalink to this headline">¶</a></h3>
|
||||
<span id="single-histogram-rrf-fit"></span><span id="index-70"></span><h3>Single Histogram RRF Fit (fit type 1)<a class="headerlink" href="#single-histogram-rrf-fit-fit-type-1" title="Permalink to this headline">¶</a></h3>
|
||||
<p>The single-histogram RRF fit (fit type 1) is used to fit the rotating reference frame asymmetry <span class="math">\(A_{\rm rrf}(t)\)</span> extracted from the raw data.
|
||||
The currently implemented version will fail at low fields/frequencies (for about < 1 Tesla). The same is true, if multiple frequencies with large
|
||||
enough separation are present, <em>e.g.</em> when dealing with muonium. <span class="math">\(A_{\rm rrf}(t)\)</span> is estimated the following way (for more details see the
|
||||
@ -2093,7 +2158,7 @@ of the <span class="math">\(N_0\)</span> estimate, line shape distortion due to
|
||||
For more details see the rrf-memo found in the source code under <musrfit>/doc/memo/rrf/rrf-notes.pdf or <a class="reference external" href="http://dx.doi.org/10.7566/JPSCP.21.011051">Musrfit–Real Time Parameter Fitting Using GPUs</a></p>
|
||||
</div>
|
||||
<div class="section" id="asymmetry-fit-fit-type-2">
|
||||
<span id="asymmetry-fit"></span><span id="index-70"></span><h3>Asymmetry Fit (fit type 2)<a class="headerlink" href="#asymmetry-fit-fit-type-2" title="Permalink to this headline">¶</a></h3>
|
||||
<span id="asymmetry-fit"></span><span id="index-71"></span><h3>Asymmetry Fit (fit type 2)<a class="headerlink" href="#asymmetry-fit-fit-type-2" title="Permalink to this headline">¶</a></h3>
|
||||
<p>For an asymmetry fit (fit type 2) two histograms are needed. These are given by the <a class="reference internal" href="#msr-forward-backward"><em>forward</em></a> and <a class="reference internal" href="#msr-forward-backward"><em>backward</em></a> keywords
|
||||
in the <a class="reference internal" href="#msr-run-block"><em>RUN block</em></a>. Additionally, the parameters <a class="reference internal" href="#msr-alpha-beta"><em>alpha</em></a> and <a class="reference internal" href="#msr-alpha-beta"><em>beta</em></a> which relate the detector
|
||||
efficiencies, solid angles and initial asymmetries of the two detectors can be supplied. The constant background for the two histograms is either given by
|
||||
@ -2127,13 +2192,13 @@ efficiencies, solid angles and initial asymmetries of the two detectors can be s
|
||||
<p>and plotted together with the function given in the THEORY block.</p>
|
||||
</div>
|
||||
<div class="section" id="asymmetry-rrf-fit-fit-type-3">
|
||||
<span id="asymmetry-rrf-fit"></span><span id="index-71"></span><h3>Asymmetry RRF Fit (fit type 3)<a class="headerlink" href="#asymmetry-rrf-fit-fit-type-3" title="Permalink to this headline">¶</a></h3>
|
||||
<span id="asymmetry-rrf-fit"></span><span id="index-72"></span><h3>Asymmetry RRF Fit (fit type 3)<a class="headerlink" href="#asymmetry-rrf-fit-fit-type-3" title="Permalink to this headline">¶</a></h3>
|
||||
<p>For asymmetry RRF Fit (fit type 3) two histograms are needed. In a first step, the unbinned asymmetry is formed as described for the asymmetry fit.
|
||||
Afterwards the RRF transformation is carried out, <em>i.e.</em> point 4. and 5. as sketched in the single histogramm RRF fit. The same reservations as for
|
||||
the single histogram RRF fit apply: <strong>if you not urgently need it: do not use it! There are better ways to deal with the analysis of high frequency data!</strong></p>
|
||||
</div>
|
||||
<div class="section" id="negative-muon-mgrsr-fit-fit-type-4">
|
||||
<span id="negative-muon-musr-fit"></span><span id="index-72"></span><h3>Negative Muon μSR Fit (fit type 4)<a class="headerlink" href="#negative-muon-mgrsr-fit-fit-type-4" title="Permalink to this headline">¶</a></h3>
|
||||
<span id="negative-muon-musr-fit"></span><span id="index-73"></span><h3>Negative Muon μSR Fit (fit type 4)<a class="headerlink" href="#negative-muon-mgrsr-fit-fit-type-4" title="Permalink to this headline">¶</a></h3>
|
||||
<p>The negative muon μSR fit (fit type 4) is used for single histogram fits of MuMinus, <em>i.e.</em></p>
|
||||
<div class="math">
|
||||
\[N(t) = \sum_i N_i\,\mathrm{e}^{-t/\tau_i} \left[ 1 + A_i(t)\right] + N_{\rm bkg}(t)\]</div>
|
||||
@ -2149,7 +2214,7 @@ the single histogram RRF fit apply: <strong>if you not urgently need it: do not
|
||||
<p>Since MuMinus is quite generic, the full functional depends has to be written in the <a class="reference internal" href="#msr-theory-block"><em>THEORY Block</em></a>.</p>
|
||||
</div>
|
||||
<div class="section" id="beta-nmr-asymmetry-fit-fit-type-5">
|
||||
<span id="bnmr-asymmetry-fit"></span><span id="index-73"></span><h3>beta-NMR Asymmetry Fit (fit type 5)<a class="headerlink" href="#beta-nmr-asymmetry-fit-fit-type-5" title="Permalink to this headline">¶</a></h3>
|
||||
<span id="bnmr-asymmetry-fit"></span><span id="index-74"></span><h3>beta-NMR Asymmetry Fit (fit type 5)<a class="headerlink" href="#beta-nmr-asymmetry-fit-fit-type-5" title="Permalink to this headline">¶</a></h3>
|
||||
<p>Four histograms are needed for a beta-NMR asymmetry fit (fit type 5), two for positive helecity and two for negative. These are given by the <a class="reference internal" href="#msr-forward-backward"><em>forward</em></a> and <a class="reference internal" href="#msr-forward-backward"><em>backward</em></a> keywords
|
||||
in the <a class="reference internal" href="#msr-run-block"><em>RUN block</em></a>. Additionally, the parameters <a class="reference internal" href="#msr-alpha-beta"><em>alpha</em></a> and <a class="reference internal" href="#msr-alpha-beta"><em>beta</em></a> which relate the detector
|
||||
efficiencies, solid angles and initial asymmetries of the two detectors can be supplied. The constant background for the two histograms is either given by
|
||||
@ -2189,7 +2254,7 @@ efficiencies, solid angles and initial asymmetries of the two detectors can be s
|
||||
<p>and plotted together with the function given in the THEORY block.</p>
|
||||
</div>
|
||||
<div class="section" id="non-mgrsr-fit-fit-type-8">
|
||||
<span id="non-musr-fit"></span><span id="index-74"></span><h3>Non-μSR Fit (fit type 8)<a class="headerlink" href="#non-mgrsr-fit-fit-type-8" title="Permalink to this headline">¶</a></h3>
|
||||
<span id="non-musr-fit"></span><span id="index-75"></span><h3>Non-μSR Fit (fit type 8)<a class="headerlink" href="#non-mgrsr-fit-fit-type-8" title="Permalink to this headline">¶</a></h3>
|
||||
<p>In the case of a non-μSR fit (fit type 8) the fitting function is</p>
|
||||
<div class="math">
|
||||
\[y = f(x),\]</div>
|
||||
@ -2198,7 +2263,7 @@ efficiencies, solid angles and initial asymmetries of the two detectors can be s
|
||||
</div>
|
||||
</div>
|
||||
<div class="section" id="id38">
|
||||
<span id="index-75"></span><span id="id39"></span><h2>User Functions<a class="headerlink" href="#id38" title="Permalink to this headline">¶</a></h2>
|
||||
<span id="index-76"></span><span id="id39"></span><h2>User Functions<a class="headerlink" href="#id38" title="Permalink to this headline">¶</a></h2>
|
||||
<p><tt class="docutils literal"><span class="pre">musrfit</span></tt> offers the possibility to plug-in user-defined functions implemented in <tt class="docutils literal"><span class="pre">C++</span></tt> classes to the fitting and plotting routines.
|
||||
In order to do so, basically two things are needed:</p>
|
||||
<blockquote>
|
||||
@ -2216,7 +2281,7 @@ In order to do so, basically two things are needed:</p>
|
||||
</div></blockquote>
|
||||
<p>Since the first is simpler this will be explained using an explicit example, before it is discussed why the second option is needed and how it can be used.</p>
|
||||
<div class="section" id="user-function-without-global-user-function-object-access">
|
||||
<span id="user-functions-without-global-part"></span><span id="index-76"></span><h3>User Function without global user-function-object access<a class="headerlink" href="#user-function-without-global-user-function-object-access" title="Permalink to this headline">¶</a></h3>
|
||||
<span id="user-functions-without-global-part"></span><span id="index-77"></span><h3>User Function without global user-function-object access<a class="headerlink" href="#user-function-without-global-user-function-object-access" title="Permalink to this headline">¶</a></h3>
|
||||
<p>In the following it is explained in detail how the implementation of a user function is done using the simple example of <span class="math">\(f_a(x) = \sin(a x)/(a x)\)</span>,
|
||||
where the parameter <span class="math">\(a\)</span> should be determined by the fit. Although not necessary for this simple example, the source code is split into two parts,
|
||||
namely a header file <tt class="docutils literal"><span class="pre">TMyFunction.h</span></tt> containing the class declaration and a second file <tt class="docutils literal"><span class="pre">TMyFunction.cpp</span></tt> including the function implementation
|
||||
@ -2314,7 +2379,7 @@ refer to the <a class="reference external" href="https://root.cern.ch/interactin
|
||||
<p>Finally, please be aware of the <a class="reference internal" href="#user-function-important"><em>remark</em></a> at the end of this section.</p>
|
||||
</div>
|
||||
<div class="section" id="user-function-with-global-user-function-object-access">
|
||||
<span id="user-functions-with-global-part"></span><span id="index-77"></span><h3>User Function with global user-function-object access<a class="headerlink" href="#user-function-with-global-user-function-object-access" title="Permalink to this headline">¶</a></h3>
|
||||
<span id="user-functions-with-global-part"></span><span id="index-78"></span><h3>User Function with global user-function-object access<a class="headerlink" href="#user-function-with-global-user-function-object-access" title="Permalink to this headline">¶</a></h3>
|
||||
<p>Before explaining how to use global objects within user functions, it will be shortly explained where is the problem and why this might be a sensible approach.
|
||||
In <tt class="docutils literal"><span class="pre">musrfit</span></tt> each <a class="reference internal" href="#msr-run-block"><em>RUN block</em></a> (histogram, asymmetry, ...) is owning its own theory-function tree. An example is shown in the figure below.
|
||||
The bluish nodes are default musrfit functions, whereas the red nodes represent user functions (here labeled by <tt class="docutils literal"><span class="pre">uF1</span></tt> and <tt class="docutils literal"><span class="pre">uF2</span></tt>). Without global user-function
|
||||
@ -2453,7 +2518,7 @@ In case this cannot be ensured, the parallelization can be disabled by <em>̵
|
||||
</div>
|
||||
</div>
|
||||
<div class="section" id="rge-file-handler-for-low-energy-mgrsr">
|
||||
<span id="rge-handler"></span><span id="index-78"></span><h3>rge-file handler for Low-Energy μSR<a class="headerlink" href="#rge-file-handler-for-low-energy-mgrsr" title="Permalink to this headline">¶</a></h3>
|
||||
<span id="rge-handler"></span><span id="index-79"></span><h3>rge-file handler for Low-Energy μSR<a class="headerlink" href="#rge-file-handler-for-low-energy-mgrsr" title="Permalink to this headline">¶</a></h3>
|
||||
<p>In the case of LE-μSR, the muon stopping distribution might have a profound impact on the muon polarization function <span class="math">\(P(t)\)</span>. In case of transverse field μSR measurements it can be written as</p>
|
||||
<div class="math">
|
||||
\[P(t) = \int_0^\infty n(z) \cos(\gamma_\mu B(z) t + \varphi) \, dz\]</div>
|
||||
@ -2597,7 +2662,7 @@ here:</p>
|
||||
</div>
|
||||
</div>
|
||||
<div class="section" id="technical-description-of-the-musrfit-framework">
|
||||
<span id="technical-musrfit"></span><span id="index-79"></span><h2>Technical Description of the musrfit framework<a class="headerlink" href="#technical-description-of-the-musrfit-framework" title="Permalink to this headline">¶</a></h2>
|
||||
<span id="technical-musrfit"></span><span id="index-80"></span><h2>Technical Description of the musrfit framework<a class="headerlink" href="#technical-description-of-the-musrfit-framework" title="Permalink to this headline">¶</a></h2>
|
||||
<p>A technical description of the musrfit framework can be found on its own <a class="reference external" href="http://lmu.web.psi.ch/musrfit/technical/index.html">docu</a>.</p>
|
||||
</div>
|
||||
</div>
|
||||
@ -2617,8 +2682,8 @@ here:</p>
|
||||
</div>
|
||||
|
||||
<div class="footer">
|
||||
© Copyright 2021, Andreas Suter.
|
||||
Last updated on Oct 06, 2021.
|
||||
© Copyright 2022, Andreas Suter.
|
||||
Last updated on May 29, 2022.
|
||||
Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.2.3.
|
||||
</div>
|
||||
</body>
|
||||
|
||||
Reference in New Issue
Block a user