Added the online documentation of musrfit to the repository.
This commit is contained in:
Bastian M. Wojek
parent
c78c9cc3dd
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09c810b461
@ -6,6 +6,7 @@
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changes since 0.9.0
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===================================
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NEW Added the online documentation to the repository. It can be found under "doc/html".
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NEW added chisq per run block information (all fit types). The same output rules as for the expected chisq are in place.
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NEW calculate expected chisq (Pearson's chisq) for single histogram fits. It always will send this information to the stdout
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but only writes it to the msr-file if a corresponding flag in the musrfit_startup.xml is enabling it. The following
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158
doc/html/MUSR/BmwLibs.html
Normal file
158
doc/html/MUSR/BmwLibs.html
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<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
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<html lang="en_US">
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<title> MUSR :: BmwLibs</title>
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<div class="patternContent"><div class="foswikiTopic">To be written...
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<p></p>
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<h1><a name="BMWlibs_for_61musrfit_61"></a> BMWlibs for <code>musrfit</code> </h1> <ul>
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<li> <a href="LibFitPofB.html"> <code>libFitPofB</code>: routines for calculating transverse-field muon-spin depolarization functions from various static field distributions in superconductors</a>
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</li> <li> <a href="LibZFRelaxation.html"> <code>libZFRelaxation</code>: routines for calculating zero-field muon-spin depolarization functions from various static field distributions</a>
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</li></ul>
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<p></p>
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-- <a href="http://www.fsf.org/register_form?referrer=8369" target="_top">BMW</a> & <a href="http://lmu.web.psi.ch/lem/group.html" target="_top">AS</a></div><!-- /foswikiTopic-->
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This topic: MUSR<span class='foswikiSeparator'> > </span><a href="WebHome.html" class="foswikiCurrentWebHomeLink">WebHome</a> > <a href="MusrFit.html">MusrFit</a><span class='foswikiSeparator'> > </span>BmwLibs <br />
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Topic revision: r5 - 10 Jul 2011 - 17:49:32 - <a href="https://intranet.psi.ch/Main/BastianWojek">BastianWojek</a>
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434
doc/html/MUSR/LibFitPofB.html
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434
doc/html/MUSR/LibFitPofB.html
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<script src="https://intranet.psi.ch/pub/System/ChecklistPlugin/itemstatechange.js" language="javascript" type="text/javascript"></script><script src="https://intranet.psi.ch/pub/System/TimeTablePlugin/timetabletooltips.js" language="javascript" type="text/javascript"></script></head>
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<a name="TopIc"></a>
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<h1><a name="libFitPofB"></a> libFitPofB </h1>
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<a name="foswikiTOC"></a><div class="foswikiToc"> <ul>
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<li> <a href="LibFitPofB.html#libFitPofB"> libFitPofB </a>
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</li> <li> <a href="LibFitPofB.html#A_1_Introduction"> 1 Introduction </a>
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</li> <li> <a href="LibFitPofB.html#A_2_LE_45SR"> 2 LE-μSR </a> <ul>
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<li> <a href="LibFitPofB.html#A_2.1_One_45dimensional_London_model_for_the_Meissner_state_of_isotropic_superconductors"> 2.1 One-dimensional London model for the Meissner state of isotropic superconductors </a>
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</li></ul>
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</li> <li> <a href="LibFitPofB.html#A_3_Conventional_40bulk_41_SR"> 3 Conventional (bulk) μSR </a> <ul>
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<li> <a href="LibFitPofB.html#A_3.1_Field_distributions_in_the_mixed_state_of_isotropic_superconductors"> 3.1 Field distributions in the mixed state of isotropic superconductors </a>
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</li></ul>
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</li> <li> <a href="LibFitPofB.html#A_4_The_XML_startup_file"> 4 The XML startup file </a>
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</li></ul>
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</div>
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<a name="IntroDuction"></a>
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<h1><a name="A_1_Introduction"></a> 1 Introduction </h1>
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<p></p>
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<code>libFitPofB</code> is a collection of <code>C++</code> classes using the <code><a href="MusrFit.html">musrfit</a></code> <code><a href="MusrFit.html#UserFunctions1">user-function interface</a></code> in order to facilitate the usage in conjunction with <code>musrfit</code>. The classes contained in this library generally implement calculations of one-dimensional static magnetic field distributions <img alt="P(B)" class="mmpImage" src="../pub/MUSR/LibFitPofB/_MathModePlugin_9cc0fd47eedada7247b14775bd308deb.png" title="PofB" /> which lead to muon-spin depolarization functions
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<p style="text-align:center">
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<img alt="\mathcal{P}(t) = \int P(B)\cos\left(\gamma_{\mu} B t + \varphi\right) \mathrm{d}B," class="mmpImage" src="../pub/MUSR/LibFitPofB/_MathModePlugin_70e57aa1afa7d337fa46f427b34feb54.png" title="PofT" />
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</p>
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where <img alt="\gamma_{\mu} = 2\pi\times 135.54~\mathrm{MHz/T}" class="mmpImage" src="../pub/MUSR/LibFitPofB/_MathModePlugin_9bb7e08c8e276a92650d89d6918b3769.png" title="gamma_mu" /> is the gyromagnetic ratio of the muon and <img alt="\varphi" class="mmpImage" src="../pub/MUSR/LibFitPofB/_MathModePlugin_2339fd9b358ebe241da05c665668d48b.png" title="phi" /> is the initial phase of the muon spins with respect to the positron detector.<br>
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At the moment the only available implementations deal with field distributions measured in local isotropic superconductors, either by means of <a href="http://lmu.web.psi.ch/lem/" target="_top">low-energy μSR</a> in the Meissner state or by conventional μSR in the mixed state. In the following the basic usage of the library in <code>musrfit</code> is explained—the calculations by themselves are only outlined. For further information please refer to the original literature and/or the source code of the implementation.
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<p></p>
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<hr />
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<strong><font color="#000000">Remark 1:</font></strong> In order to supply certain information needed for the calculations but not suited to be stored in the <code>musrfit</code> msr files an XML configuration file in the working directory is used. For details, see <a href="#XmlFile" class="foswikiCurrentTopicLink">below</a>.
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<p></p>
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<strong><font color="#000000">Remark 2:</font></strong> The implementations in this library heavily rely on <code><a href="http://www.fftw.org/" target="_top">FFTW3</a></code>. In principle, it always checks what is the best way to do efficient Fourier transforms for a given machine before the transforms are actually done. If repeatedly Fourier transforms of the same (sizable) length should be done, it might be worth storing the once obtained information in an external file and just load it the next time this information is needed (<a href="http://fftw.org/fftw3_doc/Wisdom.html" target="_top">"wisdom handling"</a>). In case this feature shall be used, a valid wisdom file has to be specified in the <a href="#XmlFile" class="foswikiCurrentTopicLink">XML file</a>.
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<p></p>
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<strong><font color="#000000">Remark 3:</font></strong> The model functions described in the following do generally not behave nicely in conjunction with <code>MINUIT</code> function minimizations (or maximizations). The analysis process at the moment in most cases involves some tedious <em>trial-and-error</em> procedure, where the displayed <code>MINUIT</code> information as always deserves attention. This is especially true if small effects should be analyzed (e.g. small diamagnetic shifts in superconductors). The parameter uncertainty in many cases has to be estimated independently. Due to these limitations, also the use of the fit option of <code><a href="Msr2Data.html">msr2data</a></code> cannot be advised.
|
||||
<p></p>
|
||||
<strong><font color="#000000">Remark 4:</font></strong> If these classes still prove useful and results obtained through them are part of scientific publications,
|
||||
an acknowledgement of the use of the library is appreciated.
|
||||
<p></p>
|
||||
<h1><a name="A_2_LE_45SR"></a> 2 LE-μSR </h1>
|
||||
<h2><a name="A_2.1_One_45dimensional_London_model_for_the_Meissner_state_of_isotropic_superconductors"></a> 2.1 One-dimensional London model for the Meissner state of isotropic superconductors </h2>
|
||||
<p></p>
|
||||
The models for analyzing LE-μSR data assume the magnetic induction <img alt="B(z)" class="mmpImage" src="../pub/MUSR/LibFitPofB/_MathModePlugin_532f98969690650ac4d127919a0eda38.png" title="BofZ" /> to vary only in the dimension parallel to the momentum of the incident muons. In such a case the magnetic field distribution is given by
|
||||
<p style="text-align:center">
|
||||
<img alt="P(B) = n(z) \left\vert \frac{\mathrm{d}B(z)}{\mathrm{d}z}\right\vert^{-1}," class="mmpImage" src="../pub/MUSR/LibFitPofB/_MathModePlugin_d5a20ca7e3a33f6badc441163d1efe34.png" title="PofB-from-NofZ" />
|
||||
</p>
|
||||
where <img alt="n(z)" class="mmpImage" src="../pub/MUSR/LibFitPofB/_MathModePlugin_86f4cdca957f08c4d0ad3107b42d5502.png" title="NofZ" /> is the muon implantation profile simulated by <code>TRIM.SP</code>.
|
||||
<p></p>
|
||||
Assuming an array of <img alt="N" class="mmpImage" src="../pub/MUSR/LibFitPofB/_MathModePlugin_ae6486e95514c0c6f88837cbc62a522c.png" title="N" /> isotropic local superconductors with a total thickness <img alt="d" class="mmpImage" src="../pub/MUSR/LibFitPofB/_MathModePlugin_7d1f8851f7efae8cd5d65842fb528f66.png" title="d" /> in the Meissner state the magnetic induction is given by solving the 1D London equation
|
||||
<p style="text-align:center">
|
||||
<img alt="\frac{\partial^2}{\partial z^2}B_i(z) = \frac{1}{\lambda_i^2}B_i(z)" class="mmpImage" src="../pub/MUSR/LibFitPofB/_MathModePlugin_dfd02951094e1cb98f48e3f6d4562f38.png" title="London-eq" />
|
||||
</p>
|
||||
for each layer <img alt="i" class="mmpImage" src="../pub/MUSR/LibFitPofB/_MathModePlugin_c465118a8d86d5f25bba37cc1dcb38a0.png" title="i" /> taking into account the boundary conditions<a name="FootNote1text"></a><span class="FootNoteTextLink" title="F. London, Superfluids: Macroscopic Theory of Superconductivity, Dover (1961), p. 34"><a href="#FootNote1note" class="foswikiCurrentTopicLink">(1)</a></span>
|
||||
<p style="text-align:center">
|
||||
<img alt="B_1(0) = B_N(d) = \mu_0H" class="mmpImage" src="../pub/MUSR/LibFitPofB/_MathModePlugin_432d7664e0756ded77e7423dd256c122.png" title="cond1" />
|
||||
</p>
|
||||
<p style="text-align:center">
|
||||
<img alt="B_i(d_i) = B_{i+1}(d_i)" class="mmpImage" src="../pub/MUSR/LibFitPofB/_MathModePlugin_1c744b7e1104ae8c4a6bf4f8391df10b.png" title="cond2" />
|
||||
</p>
|
||||
<p style="text-align:center">
|
||||
<img alt="\lambda_i^2B_i'(z)\Big\vert_{z=d_i} = \lambda_{i+1}^2B_{i+1}'(z)\Big\vert_{z=d_i}," class="mmpImage" src="../pub/MUSR/LibFitPofB/_MathModePlugin_a5feddf35c572c4579cbef865caf8863.png" title="cond3" />
|
||||
</p>
|
||||
where the <img alt="d_i" class="mmpImage" src="../pub/MUSR/LibFitPofB/_MathModePlugin_6997ecca9587ccd09cc532d4476ae3a8.png" title="d_i" /> specify the interfaces between two adjacent layers and <img alt="\lambda_i" class="mmpImage" src="../pub/MUSR/LibFitPofB/_MathModePlugin_88f576f1799d16c1df9f3205ab2946f2.png" title="lambda_i" /> is the magnetic field penetration depth in the constituent <img alt="i" class="mmpImage" src="../pub/MUSR/LibFitPofB/_MathModePlugin_c465118a8d86d5f25bba37cc1dcb38a0.png" title="i" />.
|
||||
<p></p>
|
||||
The calculation of the field distribution has been set up for a superconducting half-space as well as superconducting thin films with up to three superconducting layers with different penetration depths. The muon-spin depolarization functions are calculated using the following lines in the THEORY block of a <code>musrfit</code> msr file: <dl>
|
||||
<dt> Superconducting half-space </dt><dd> <pre>
|
||||
userFcn libFitPofB TLondon1DHS 1 2 3 4 5
|
||||
</pre>
|
||||
</dd></dl>
|
||||
The parameters are: <ol>
|
||||
<li> phase (deg)
|
||||
</li> <li> muon implantation energy as specified in the <a href="#XmlFile" class="foswikiCurrentTopicLink">XML startup file</a> (keV)
|
||||
</li> <li> applied field (G)
|
||||
</li> <li> thickness of the dead layer (nm)
|
||||
</li> <li> magnetic field penetration depth (nm)
|
||||
</li></ol>
|
||||
<p></p> <dl>
|
||||
<dt> Superconducting thin film (one layer) </dt><dd> <pre>
|
||||
userFcn libFitPofB TLondon1D1L 1 2 3 4 5 6 [a b]
|
||||
</pre>
|
||||
</dd></dl>
|
||||
The mandatory parameters are: <ol>
|
||||
<li> phase (deg)
|
||||
</li> <li> muon implantation energy as specified in the <a href="#XmlFile" class="foswikiCurrentTopicLink">XML startup file</a> (keV)
|
||||
</li> <li> applied field (G)
|
||||
</li> <li> thickness of the dead layer (nm)
|
||||
</li> <li> thickness of the actually superconducting layer (nm)
|
||||
</li> <li> magnetic field penetration depth (nm)
|
||||
</li></ol>
|
||||
<p></p>
|
||||
The optional parameters are: <ol>
|
||||
<li type="a"> fraction <i>f</i><sub>1</sub> of muons in the thin film contributing to the signal (0 ≤ <i>f</i><sub>1</sub> ≤ 1)
|
||||
</li> <li type="a"> fraction <i>f</i><sub>s</sub> of muons in the substrate contributing to the signal (0 ≤ <i>f</i><sub>s</sub> ≤ 1)
|
||||
</li></ol>
|
||||
<p></p> <dl>
|
||||
<dt> Superconducting thin-film bilayer heterostructure </dt><dd> <pre>
|
||||
userFcn libFitPofB TLondon1D2L 1 2 3 4 5 6 7 8 [a b c]
|
||||
</pre>
|
||||
</dd></dl>
|
||||
The mandatory parameters are: <ol>
|
||||
<li> phase (deg)
|
||||
</li> <li> muon implantation energy as specified in the <a href="#XmlFile" class="foswikiCurrentTopicLink">XML startup file</a> (keV)
|
||||
</li> <li> applied field (G)
|
||||
</li> <li> thickness of the dead layer (nm)
|
||||
</li> <li> thickness of the actually superconducting first layer (nm)
|
||||
</li> <li> thickness of the actually superconducting second layer (nm)
|
||||
</li> <li> magnetic field penetration depth of the first layer (nm)
|
||||
</li> <li> magnetic field penetration depth of the second layer (nm)
|
||||
</li></ol>
|
||||
<p></p>
|
||||
The optional parameters are: <ol>
|
||||
<li type="a"> fraction <i>f</i><sub>1</sub> of muons in the dead and first layer contributing to the signal (0 ≤ <i>f</i><sub>1</sub> ≤ 1)
|
||||
</li> <li type="a"> fraction <i>f</i><sub>2</sub> of muons in the second layer contributing to the signal (0 ≤ <i>f</i><sub>2</sub> ≤ 1)
|
||||
</li> <li type="a"> fraction <i>f</i><sub>s</sub> of muons in the substrate contributing to the signal (0 ≤ <i>f</i><sub>s</sub> ≤ 1)
|
||||
</li></ol>
|
||||
<p></p> <dl>
|
||||
<dt> Superconducting thin-film trilayer heterostructure </dt><dd> <pre>
|
||||
userFcn libFitPofB TLondon1D3L 1 2 3 4 5 6 7 8 9 10 [a b c d]
|
||||
</pre>
|
||||
</dd></dl>
|
||||
The mandatory parameters are: <ol>
|
||||
<li> phase (deg)
|
||||
</li> <li> muon implantation energy as specified in the <a href="#XmlFile" class="foswikiCurrentTopicLink">XML startup file</a> (keV)
|
||||
</li> <li> applied field (G)
|
||||
</li> <li> thickness of the dead layer (nm)
|
||||
</li> <li> thickness of the actually superconducting first layer (nm)
|
||||
</li> <li> thickness of the actually superconducting second layer (nm)
|
||||
</li> <li> thickness of the actually superconducting third layer (nm)
|
||||
</li> <li> magnetic field penetration depth of the first layer (nm)
|
||||
</li> <li> magnetic field penetration depth of the second layer (nm)
|
||||
</li> <li> magnetic field penetration depth of the third layer (nm)
|
||||
</li></ol>
|
||||
<p></p>
|
||||
The optional parameters are: <ol>
|
||||
<li type="a"> fraction <i>f</i><sub>1</sub> of muons in the dead and first layer contributing to the signal (0 ≤ <i>f</i><sub>1</sub> ≤ 1)
|
||||
</li> <li type="a"> fraction <i>f</i><sub>2</sub> of muons in the second layer contributing to the signal (0 ≤ <i>f</i><sub>2</sub> ≤ 1)
|
||||
</li> <li type="a"> fraction <i>f</i><sub>3</sub> of muons in the third layer contributing to the signal (0 ≤ <i>f</i><sub>3</sub> ≤ 1)
|
||||
</li> <li type="a"> fraction <i>f</i><sub>s</sub> of muons in the substrate contributing to the signal (0 ≤ <i>f</i><sub>s</sub> ≤ 1)
|
||||
</li></ol>
|
||||
<p></p>
|
||||
<p></p>
|
||||
<p></p>
|
||||
Notes
|
||||
<p></p>
|
||||
<a name="FootNote1note"></a><span class="FootNoteLabel"><a href="LibFitPofB.html#FootNote1text" class="foswikiCurrentWebHomeLink"> <strong>1</strong> </a></span>: <span class="FootNote">F. London, Superfluids: Macroscopic Theory of Superconductivity, Dover (1961), p. 34</span>
|
||||
<p></p>
|
||||
<p></p>
|
||||
<p></p>
|
||||
<hr />
|
||||
<p></p>
|
||||
<h1><a name="A_3_Conventional_40bulk_41_SR"></a> 3 Conventional (bulk) μSR </h1>
|
||||
<h2><a name="A_3.1_Field_distributions_in_the_mixed_state_of_isotropic_superconductors"></a> 3.1 Field distributions in the mixed state of isotropic superconductors </h2>
|
||||
<p></p>
|
||||
When investigating superconductors in the mixed state by means of conventional μSR a two-dimensional flux-line lattice is probed randomly by the muons. The spatial field distributions within such an ordered lattice are modeled using the Fourier series
|
||||
<p style="text-align:center">
|
||||
<img alt="B(\mathbf{r}) = \langle B \rangle \sum\limits_{\mathbf{K}}B_{\mathbf{K}}\exp(-\imath\mathbf{K}\mathbf{r})," class="mmpImage" src="../pub/MUSR/LibFitPofB/_MathModePlugin_c25933e91d56089992506f463d71de8f.png" title="spatialB" />
|
||||
</p>
|
||||
where <img alt="\mathbf{r}=(x,y)" class="mmpImage" src="../pub/MUSR/LibFitPofB/_MathModePlugin_e47f33589d28eaa3f9baccb7a80fdbaa.png" title="r" />, <img alt="\mathbf{K}" class="mmpImage" src="../pub/MUSR/LibFitPofB/_MathModePlugin_e6688a12ee4e821abc31b4c1dd511539.png" title="K" /> are the reciprocal lattice vectors of a two-dimensional vortex lattice and the <img alt="B_{\mathbf{K}}" class="mmpImage" src="../pub/MUSR/LibFitPofB/_MathModePlugin_8fa3ac8f18b7bc49eb89163d6528684c.png" title="Bk" /> are the Fourier coefficients depending on the magnetic penetration depth <img alt="\lambda" class="mmpImage" src="../pub/MUSR/LibFitPofB/_MathModePlugin_28f3ed750a4819b4256c2f9be649f594.png" title="lambda" /> and the superconducting coherence length <img alt="\xi" class="mmpImage" src="../pub/MUSR/LibFitPofB/_MathModePlugin_e8414d477977d226317c020980b7d34f.png" title="xi" />. The <img alt="B_{\mathbf{K}}" class="mmpImage" src="../pub/MUSR/LibFitPofB/_MathModePlugin_8fa3ac8f18b7bc49eb89163d6528684c.png" title="Bk" /> for some specific models are as follows: <dl>
|
||||
<dt> London model with Gaussian cutoff<a name="FootNote2text"></a><span class="FootNoteTextLink" title="E.H. Brandt, [[http://dx.doi.org/10.1007/BF00683568][J. Low Temp. Phys. *73*, 355 (1988)]]."><a href="#FootNote2note" class="foswikiCurrentTopicLink">(2)</a></span> </dt><dd> <p style="text-align:center"><img alt="B_{\mathbf{K}} = \frac{\exp\left({-K^2\xi^2/2}\right)}{1 + K^2\lambda^2}" class="mmpImage" src="../pub/MUSR/LibFitPofB/_MathModePlugin_469d5d1b83125e4915e2f073d8150b12.png" title="BkLondon" /></p>
|
||||
</dd> <dt> Modified London model<a name="FootNote3text"></a><span class="FootNoteTextLink" title="T.M. Riseman _et al._, [[http://dx.doi.org/10.1103/PhysRevB.52.10569][Phys. Rev. B *52*, 10569 (1995)]]."><a href="#FootNote3note" class="foswikiCurrentTopicLink">(3)</a></span> </dt><dd> <p style="text-align:center"><img alt="B_{\mathbf{K}} = \frac{\exp\left({-K^2\xi^2/2(1-b)}\right)}{1 + K^2\lambda^2/(1-b)}," class="mmpImage" src="../pub/MUSR/LibFitPofB/_MathModePlugin_b6719fad8e30208538b34bc94040b7a5.png" title="BkML" /></p> where <img alt="b = \langle B \rangle/\mu_0H_{\mathrm{c}2}." class="mmpImage" src="../pub/MUSR/LibFitPofB/_MathModePlugin_039b3b38df7c6f284089c14f1efdf643.png" title="b" />
|
||||
</dd> <dt> Analytical Ginzburg-Landau model<a name="FootNote4text"></a><span class="FootNoteTextLink" title="A. Yaouanc, P. Dalmas de R&eacute;otier and E.H. Brandt, [[http://dx.doi.org/10.1103/PhysRevB.55.11107][Phys. Rev. B *55*, 11107 (1997)]]."><a href="#FootNote4note" class="foswikiCurrentTopicLink">(4)</a></span> </dt><dd> <p style="text-align:center"><img alt="B_{\mathbf{K}} = \frac{f_{\infty}K_1\left(\frac{\xi_v}{\lambda}\sqrt{f_{\infty}^2+\lambda^2K^2}\right)}{K_1\left(\frac{\xi_v}{\lambda}f_{\infty}\right)\sqrt{f_{\infty}^2+\lambda^2K^2}}," class="mmpImage" src="../pub/MUSR/LibFitPofB/_MathModePlugin_3146cb17887e3a20cc2078f103605af5.png" title="BkAGL" /></p> where <img alt="f_{\infty} = 1 - b^4,~\xi_v = \xi\left(\sqrt{2}-{3\xi}/\left({4\lambda}\right)\right)\sqrt{(1+b^4)(1-2b(1-b)^2)}" class="mmpImage" src="../pub/MUSR/LibFitPofB/_MathModePlugin_e0b0e98f9a3974249b42b6910523c8a4.png" title="f_inf_and_xi_v" /> and <img alt="K_1" class="mmpImage" src="../pub/MUSR/LibFitPofB/_MathModePlugin_3cee3cc69dbe918398ec39a72a465014.png" title="K1" /> is a modified Bessel function.
|
||||
</dd></dl>
|
||||
Apart from the mentioned analytical models the <strong>numerical Ginzburg-Landau model</strong> <a name="FootNote5text"></a><span class="FootNoteTextLink" title="E.H. Brandt, [[http://dx.doi.org/10.1103/PhysRevB.68.054506][Phys. Rev. B *68*, 054506 (2003)]]."><a href="#FootNote5note" class="foswikiCurrentTopicLink">(5)</a></span> is available. In this case <img alt="B(\mathbf{r})" class="mmpImage" src="../pub/MUSR/LibFitPofB/_MathModePlugin_373e9bf1fc97e2c6aacf93bcc090402c.png" title="BofR" /> is obtained by an iterative minimization of the free energy of the vortex lattice.
|
||||
<p></p>
|
||||
<font color="#ff0000">Concerning the applicability (e.g. field regions) of each of the mentioned models please refer to the original publications!</font>
|
||||
<p></p>
|
||||
At the moment, the calculation of the field distribution has been implemented for triangular flux-line lattices. The number of grid lines in which the inter-vortex distance is divided for the calculations to be specified through the <a href="#XmlFile" class="foswikiCurrentTopicLink">XML file</a>.<br>The muon-spin depolarization functions finally are calculated using the following lines in the THEORY block of a <code>musrfit</code> msr file: <dl>
|
||||
<dt> 2D triangular vortex lattice, London model with Gaussian cutoff </dt><dd> <pre>
|
||||
userFcn libFitPofB TBulkTriVortexLondon 1 2 3 4
|
||||
</pre>
|
||||
</dd></dl>
|
||||
The parameters are: <ol>
|
||||
<li> phase (deg)
|
||||
</li> <li> mean magnetic induction (G)
|
||||
</li> <li> magnetic penetration depth (nm)
|
||||
</li> <li> Ginzburg-Landau coherence length (nm)
|
||||
</li></ol>
|
||||
<p></p> <dl>
|
||||
<dt> 2D triangular vortex lattice, modified London model </dt><dd> <pre>
|
||||
userFcn libFitPofB TBulkTriVortexML 1 2 3 4
|
||||
</pre>
|
||||
</dd></dl>
|
||||
The parameters are: <ol>
|
||||
<li> phase (deg)
|
||||
</li> <li> mean magnetic induction (G)
|
||||
</li> <li> magnetic penetration depth (nm)
|
||||
</li> <li> Ginzburg-Landau coherence length (nm)
|
||||
</li></ol>
|
||||
<p></p> <dl>
|
||||
<dt> 2D triangular vortex lattice, analytical Ginzburg-Landau model </dt><dd> <pre>
|
||||
userFcn libFitPofB TBulkTriVortexAGL 1 2 3 4
|
||||
</pre>
|
||||
</dd></dl>
|
||||
The parameters are: <ol>
|
||||
<li> phase (deg)
|
||||
</li> <li> mean magnetic induction (G)
|
||||
</li> <li> magnetic penetration depth (nm)
|
||||
</li> <li> Ginzburg-Landau coherence length (nm)
|
||||
</li></ol>
|
||||
<p></p> <dl>
|
||||
<dt> 2D triangular vortex lattice, numerical Ginzburg-Landau model </dt><dd> <pre>
|
||||
userFcn libFitPofB TBulkTriVortexNGL 1 2 3 4
|
||||
</pre>
|
||||
</dd></dl>
|
||||
The parameters are: <ol>
|
||||
<li> phase (deg)
|
||||
</li> <li> mean magnetic induction (G)
|
||||
</li> <li> magnetic penetration depth (nm)
|
||||
</li> <li> Ginzburg-Landau coherence length (nm)
|
||||
</li></ol>
|
||||
<p></p>
|
||||
<strong><font color="#000000">Remark:</font></strong> In order to improve the convergence of <code>MIGRAD</code> it has proven useful to use the log-likelihood maximization instead of the χ<sup>2</sup> minimization routines and to choose sufficiently large initial steps for the parameters. Calling <code>MINOS</code> in conjunction with these functions is futile.<br>Therefore, the <a href="MusrFit.html#TheCommandsBlock">COMMANDS block</a> of the msr file could look like:
|
||||
<pre>
|
||||
COMMANDS
|
||||
STRATEGY 0
|
||||
MAX_LIKELIHOOD
|
||||
MIGRAD
|
||||
HESSE
|
||||
SAVE
|
||||
</pre>
|
||||
<p></p>
|
||||
<p></p>
|
||||
<p></p>
|
||||
Notes
|
||||
<p></p>
|
||||
<a name="FootNote2note"></a><span class="FootNoteLabel"><a href="LibFitPofB.html#FootNote2text" class="foswikiCurrentWebHomeLink"> <strong>2</strong> </a></span>: <span class="FootNote">E.H. Brandt, <a href="http://dx.doi.org/10.1007/BF00683568" target="_top">J. Low Temp. Phys. <strong>73</strong>, 355 (1988)</a>.</span>
|
||||
<p></p>
|
||||
<a name="FootNote3note"></a><span class="FootNoteLabel"><a href="LibFitPofB.html#FootNote3text" class="foswikiCurrentWebHomeLink"> <strong>3</strong> </a></span>: <span class="FootNote">T.M. Riseman <em>et al.</em>, <a href="http://dx.doi.org/10.1103/PhysRevB.52.10569" target="_top">Phys. Rev. B <strong>52</strong>, 10569 (1995)</a>.</span>
|
||||
<p></p>
|
||||
<a name="FootNote4note"></a><span class="FootNoteLabel"><a href="LibFitPofB.html#FootNote4text" class="foswikiCurrentWebHomeLink"> <strong>4</strong> </a></span>: <span class="FootNote">A. Yaouanc, P. Dalmas de Réotier and E.H. Brandt, <a href="http://dx.doi.org/10.1103/PhysRevB.55.11107" target="_top">Phys. Rev. B <strong>55</strong>, 11107 (1997)</a>.</span>
|
||||
<p></p>
|
||||
<a name="FootNote5note"></a><span class="FootNoteLabel"><a href="LibFitPofB.html#FootNote5text" class="foswikiCurrentWebHomeLink"> <strong>5</strong> </a></span>: <span class="FootNote">E.H. Brandt, <a href="http://dx.doi.org/10.1103/PhysRevB.68.054506" target="_top">Phys. Rev. B <strong>68</strong>, 054506 (2003)</a>.</span>
|
||||
<p></p>
|
||||
<p></p>
|
||||
<p></p>
|
||||
<hr />
|
||||
<p></p>
|
||||
<a name="XmlFile"></a>
|
||||
<h1><a name="A_4_The_XML_startup_file"></a> 4 The XML startup file </h1>
|
||||
<code><b>BMW_startup.xml</b></code> is a configuration file located in the working directory. In this file some settings like the time and field resolution of the calculations as well as the present muon implantation profiles for a LE-μSR analysis have to be defined. The following XML tags are allowed to define settings: <dl>
|
||||
<dt> <debug>ONE_OR_ZERO</debug> </dt><dd> activate the debugging output of the settings read from the XML file by setting <strong>1</strong>, deactivate it with <strong>0</strong>
|
||||
</dd> <dt> <wisdom>PATH_TO_FILE</wisdom> </dt><dd> specify the <strong>PATH_TO_FILE</strong> to an <a href="http://fftw.org/fftw3_doc/Wisdom.html#Wisdom" target="_top">FFTW3 wisdom file</a> that should be used; if the <strong>PATH_TO_FILE</strong> is invalid, no FFTW3 wisdom will be used
|
||||
</dd> <dt> <delta_t>ResT</delta_t> </dt><dd> set the time resolution <strong>ResT</strong> for the calculated depolarization function in <strong>microseconds</strong>
|
||||
</dd> <dt> <delta_B>ResB</delta_B> </dt><dd> set the field resolution <strong>ResB</strong> for the calculated field distribution in <strong>Gauss</strong>
|
||||
</dd> <dt> <VortexLattice></VortexLattice> </dt><dd> set the parameters used for the calculation of the spatial field distribution of a vortex lattice <dl>
|
||||
<dt> <N_VortexGrid>N</N_VortexGrid> </dt><dd> specify the number of points <strong>N</strong> (in each of the two dimensions) for which the fields within the vortex lattice are calculated (inside a <VortexLattice> environment)
|
||||
</dd></dl>
|
||||
</dd> <dt> <LEM></LEM> </dt><dd> set the parameters used for the calculation of LE-μSR field distributions <dl>
|
||||
<dt> <data_path>DATA_PATH_PREFIX</data_path> </dt><dd> specify the <strong>DATA_PATH_PREFIX</strong> to the <code>TRIM.SP</code> implantation profiles (inside a <LEM> environment)
|
||||
</dd> <dt> <N_theory>N_THEORY</N_theory> </dt><dd> specify the number of points <strong>N_THEORY</strong> for which <i>B</i>(<i>z</i>) is calculated (inside a <LEM> environment)<br>The specification of this number is not needed if the calculation of the inverse of <i>B</i>(<i>z</i>) is implemented!
|
||||
</dd> <dt> <energy_list></energy_list> </dt><dd> set the energies for which <code>TRIM.SP</code> implantation profiles are available (inside a <LEM> environment) <dl>
|
||||
<dt> <energy_label>LABEL</energy_label> </dt><dd> specify the <strong>LABEL</strong> within the file name of a available <code>TRIM.SP</code> RGE file (inside a <energy_list> environment)<br><font color="#0000ff">The expected name of the RGE file will be: <strong>DATA_PATH_PREFIX</strong> + <strong>LABEL</strong> + .rge</font>
|
||||
</dd> <dt> <energy>E</energy> </dt><dd> specify the muon energy <strong>E</strong> (in <strong>keV</strong>) belonging to the <code>TRIM.SP</code> RGE file given above (inside a <energy_list> environment)
|
||||
</dd></dl>
|
||||
</dd></dl>
|
||||
</dd></dl>
|
||||
<p></p>
|
||||
An example XML file looks as follows:
|
||||
<pre class="html">
|
||||
<?xml version="1.0" encoding="UTF-8"?>
|
||||
<BMW>
|
||||
<debug>0</debug>
|
||||
<wisdom>/home/user/WordsOfWisdom.dat</wisdom>
|
||||
<delta_t>0.01</delta_t>
|
||||
<delta_B>0.5</delta_B>
|
||||
<VortexLattice>
|
||||
<N_VortexGrid>1024</N_VortexGrid>
|
||||
</VortexLattice>
|
||||
<LEM>
|
||||
<data_path>/home/user/TrimSP/some-sample-</data_path>
|
||||
<N_theory>5000</N_theory>
|
||||
<energy_list>
|
||||
<energy_label>02_0</energy_label>
|
||||
<energy>2.0</energy>
|
||||
<energy_label>03_0</energy_label>
|
||||
<energy>3.0</energy>
|
||||
<energy_label>03_6</energy_label>
|
||||
<energy>3.6</energy>
|
||||
<energy_label>05_0</energy_label>
|
||||
<energy>5.0</energy>
|
||||
<energy_label>05_3</energy_label>
|
||||
<energy>5.3</energy>
|
||||
</energy_list>
|
||||
</LEM>
|
||||
</BMW>
|
||||
</pre>
|
||||
<p></p>
|
||||
-- <a href="http://www.fsf.org/register_form?referrer=8369" target="_top">BMW</a> & <a href="http://lmu.web.psi.ch/lem/group.html" target="_top">AS</a></div><!-- /foswikiTopic-->
|
||||
<p></p>
|
||||
</div><!-- /patternContent-->
|
||||
<hr />
|
||||
This topic: MUSR<span class='foswikiSeparator'> > </span><a href="WebHome.html" class="foswikiCurrentWebHomeLink">WebHome</a> > <a href="MusrFit.html">MusrFit</a> > <a href="BmwLibs.html">BmwLibs</a><span class='foswikiSeparator'> > </span>LibFitPofB <br />
|
||||
Topic revision: r16 - 10 Jul 2011 - 17:49:49 - <a href="https://intranet.psi.ch/Main/BastianWojek">BastianWojek</a>
|
||||
</div>
|
||||
</div>
|
||||
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|
||||
<div class="clear"> </div>
|
||||
</div><div id="patternBottomBar"><div id="patternBottomBarContents"><div id="patternWebBottomBar">Ideas, requests, problems regarding <a href="https://intranet.psi.ch/Main/WebHome">PSI Wiki</a>? <a href="mailto:psi.intranet@psi.ch?subject=Foswiki%20Feedback%20on%20MUSR.LibFitPofB">Send feedback</a></div></div></div>
|
||||
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|
||||
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|
||||
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|
||||
</div></div><!-- /endWrap -->
|
||||
<p></p>
|
||||
<p></p>
|
||||
<p></p>
|
||||
<p></p>
|
||||
</body>
|
||||
|
||||
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|
||||
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|
||||
<p></p>
|
||||
<p></p>
|
||||
<p></p>
|
||||
239
doc/html/MUSR/LibZFRelaxation.html
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239
doc/html/MUSR/LibZFRelaxation.html
Normal file
@ -0,0 +1,239 @@
|
||||
<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
|
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|
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|
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|
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|
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<div class="patternContent"><div class="foswikiTopic">
|
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<a name="TopIc"></a>
|
||||
<h1><a name="libZFRelaxation"></a> libZFRelaxation </h1>
|
||||
<a name="foswikiTOC"></a><div class="foswikiToc"> <ul>
|
||||
<li> <a href="LibZFRelaxation.html#libZFRelaxation"> libZFRelaxation </a>
|
||||
</li> <li> <a href="LibZFRelaxation.html#A_1_Introduction"> 1 Introduction </a>
|
||||
</li> <li> <a href="LibZFRelaxation.html#A_2_Isotropic_static_Gaussian_broadened_randomly_oriented_internal_fields"> 2 Isotropic static Gaussian broadened randomly oriented internal fields </a>
|
||||
</li> <li> <a href="LibZFRelaxation.html#A_3_Isotropic_static_Lorentzian_broadened_randomly_oriented_internal_fields"> 3 Isotropic static Lorentzian broadened randomly oriented internal fields </a>
|
||||
</li> <li> <a href="LibZFRelaxation.html#A_4_Static_Gaussian_distributed_fields_with_uniaxial_anisotropy"> 4 Static Gaussian distributed fields with uniaxial anisotropy </a>
|
||||
</li></ul>
|
||||
</div>
|
||||
<a name="IntroDuction"></a>
|
||||
<h1><a name="A_1_Introduction"></a> 1 Introduction </h1>
|
||||
<p></p>
|
||||
<code>libZFRelaxation</code> is a collection of <code>C++</code> classes using the <code><a href="MusrFit.html">musrfit</a></code> <code><a href="MusrFit.html#UserFunctions1">user-function interface</a></code> in order to facilitate the usage in conjunction with <code>musrfit</code>. The classes contained in this library implement the calculation of some additional zero-field μSR relaxation functions which are not built-in into <code>musrfit</code>.
|
||||
<p></p>
|
||||
In the following the use of the implemented functions is shortly introduced—for details on the applicability and derivation of these functions please refer to the original publications.
|
||||
<p></p>
|
||||
If these classes prove useful and results obtained through them are part of scientific publications,
|
||||
an acknowledgement of the use of the library is appreciated.
|
||||
<p></p>
|
||||
<h1><a name="A_2_Isotropic_static_Gaussian_broadened_randomly_oriented_internal_fields"></a> 2 Isotropic static Gaussian broadened randomly oriented internal fields </h1>
|
||||
<p></p>
|
||||
E. I. Kornilov and V. Yu. Pomjakushin, Phys. Lett. A <b>153</b>, 364–367 (1991), doi: <a href="http://dx.doi.org/10.1016/0375-9601(91)90959-C" target="_top">10.1016/0375-9601(91)90959-C</a>
|
||||
<p></p>
|
||||
<p style="text-align:center">
|
||||
<img alt="\mathcal{P}(t) = \left(1-\alpha\right)\exp\left(-\frac{\sigma_{\mathrm{L}}^2t^2}{2}\right)+\alpha\left(\cos\left(2\pi\nu t\right)-\frac{\sigma_{\mathrm{T}}^2t}{2\pi\nu}\sin\left(2\pi\nu t\right)\right)\exp\left(-\frac{\sigma_{\mathrm{T}}^2t^2}{2}\right)" class="mmpImage" src="../pub/MUSR/LibZFRelaxation/_MathModePlugin_fca91646b118061038b53ada5563c17c.png" title="ZFMagGss" />
|
||||
</p>
|
||||
<p></p>
|
||||
<code>musrfit</code> THEORY-block line: <pre>
|
||||
userFcn libZFRelaxation ZFMagGss 1 2 3 4
|
||||
</pre>
|
||||
The parameters are: <ol>
|
||||
<li> the precessing fraction α (= 2/3 in the article),
|
||||
</li> <li> the "internal frequency" ν (MHz),
|
||||
</li> <li> the "transverse depolarization rate" σ<sub>T</sub> (μs<sup>-1</sup>),
|
||||
</li> <li> the "longitudinal depolarization rate" σ<sub>L</sub> (μs<sup>-1</sup>) (= 0 in the article).
|
||||
</li></ol>
|
||||
<p></p>
|
||||
<h1><a name="A_3_Isotropic_static_Lorentzian_broadened_randomly_oriented_internal_fields"></a> 3 Isotropic static Lorentzian broadened randomly oriented internal fields </h1>
|
||||
<p></p>
|
||||
M. I. Larkin, Y. Fudamoto, I. M. Gat, A. Kinkhabwala, K. M. Kojima, G. M. Luke, J. Merrin, B. Nachumi, Y. J. Uemura, M. Azuma, T. Saito, and M. Takano, Physica B <b>289–290</b>, 153–156 (2000), doi: <a href="http://dx.doi.org/10.1016/S0921-4526(00)00337-9"" target="_top">10.1016/S0921-4526(00)00337-9</a>
|
||||
<p></p>
|
||||
<p style="text-align:center">
|
||||
<img alt="\mathcal{P}(t) = \left(1-\alpha\right)\exp\left(-a_{\mathrm{L}}t\right) + \alpha\left(\cos\left(2\pi\nu t\right)-\frac{a_{\mathrm{T}}}{2\pi\nu}\sin\left(2\pi\nu t\right)\right)\exp\left(-a_{\mathrm{T}}t\right)" class="mmpImage" src="../pub/MUSR/LibZFRelaxation/_MathModePlugin_975f948b57199037b2b8bfb5e986b6a9.png" title="ZFMagExp" />
|
||||
</p>
|
||||
<p></p>
|
||||
<code>musrfit</code> THEORY-block line: <pre>
|
||||
userFcn libZFRelaxation ZFMagExp 1 2 3 4
|
||||
</pre>
|
||||
The parameters are: <ol>
|
||||
<li> the precessing fraction α (= 2/3 in the article),
|
||||
</li> <li> the "internal frequency" ν (MHz),
|
||||
</li> <li> the "transverse depolarization rate" a<sub>T</sub> (μs<sup>-1</sup>),
|
||||
</li> <li> the "longitudinal depolarization rate" a<sub>L</sub> (μs<sup>-1</sup>) (= 0 in the article).
|
||||
</li></ol>
|
||||
<p></p>
|
||||
<h1><a name="A_4_Static_Gaussian_distributed_fields_with_uniaxial_anisotropy"></a> 4 Static Gaussian distributed fields with uniaxial anisotropy </h1>
|
||||
<p></p>
|
||||
G. Solt, Hyperfine Interactions <b>96</b>, 167–175 (1995), doi: <a href="http://dx.doi.org/10.1007/BF02066280" target="_top">10.1007/BF02066280</a>
|
||||
<p></p>
|
||||
<p style="text-align:center">
|
||||
<img alt="\mathcal{P}(t) = \frac{1}{2}\sin^2\Theta + \left(\frac{3}{2}\cos^2\Theta-\frac{1}{2}\right)f_1\left(\epsilon\right) + \sin^2\Theta f_2(\epsilon, \sigma_1, t) + \left(\frac{3}{2}\cos^2\Theta-\frac{1}{2}\right)f_3\left(\epsilon, \sigma_1, t\right)," class="mmpImage" src="../pub/MUSR/LibZFRelaxation/_MathModePlugin_4611c56f1556464dd8a6eaabbe070c05.png" title="UniaxialStatGssKT" />
|
||||
</p>
|
||||
where
|
||||
<p style="text-align:center">
|
||||
<img alt="\epsilon = \left(\frac{\sigma_1}{\sigma_3}\right)^2-1,\quad p(x) = 1+\epsilon x^2," class="mmpImage" src="../pub/MUSR/LibZFRelaxation/_MathModePlugin_2b4a75902dcb0b8de5a662656d3b9066.png" title="epsilon_p(x)" />
|
||||
</p>
|
||||
<p style="text-align:center">
|
||||
<img alt="f_1\left(\epsilon\right) = 1 - \frac{\sqrt{1+\epsilon}}{\epsilon}\left(\sqrt{1+\epsilon}-\left\lbrace \begin{matrix} \left(\mathrm{asinh}\sqrt{\epsilon}\right)/\sqrt{\epsilon} \\ \left(\arcsin\sqrt{-\epsilon}\right)/\sqrt{-\epsilon} \end{matrix} \right\rbrace\right),\:\mathrm{for}\,\bigg\lbrace\begin{matrix}\epsilon > 0 \\ \epsilon < 0\end{matrix}\,," class="mmpImage" src="../pub/MUSR/LibZFRelaxation/_MathModePlugin_5100b245762fc5c6dee8db3b05032a18.png" title="f1" />
|
||||
</p>
|
||||
<p style="text-align:center">
|
||||
<img alt="f_2\left(\epsilon, \sigma_1, t\right) = \sqrt{1+\epsilon}\int_0^1\mathrm{d}x\left(\frac{1}{p(x)^{3/2}}-\frac{\gamma_{\mu}^2\sigma_1^2t^2}{p(x)^{5/2}}\right)\exp\left(-\frac{\gamma_{\mu}^2\sigma_1^2t^2}{2\,p(x)}\right)," class="mmpImage" src="../pub/MUSR/LibZFRelaxation/_MathModePlugin_0a70ac778f3ffbf2c93d46b23559d371.png" title="f2" />
|
||||
</p>
|
||||
and
|
||||
<p style="text-align:center">
|
||||
<img alt="f_3\left(\epsilon, \sigma_1, t\right) = \sqrt{1+\epsilon}\int_0^1\mathrm{d}x\left(1-x^2\right)\left(\frac{1}{p(x)^{3/2}}-\frac{\gamma_{\mu}^2\sigma_1^2t^2}{p(x)^{5/2}}\right)\exp\left(-\frac{\gamma_{\mu}^2\sigma_1^2t^2}{2\,p(x)}\right)." class="mmpImage" src="../pub/MUSR/LibZFRelaxation/_MathModePlugin_52c5f826fb399ae721887c5fb4e31de0.png" title="f3" />
|
||||
</p>
|
||||
<p></p>
|
||||
<code>musrfit</code> THEORY-block line: <pre>
|
||||
userFcn libZFRelaxation UniaxialStatGssKT 1 2 3
|
||||
</pre>
|
||||
The parameters are: <ol>
|
||||
<li> σ<sub>1</sub> (μs<sup>-1</sup>),
|
||||
</li> <li> σ<sub>3</sub> (μs<sup>-1</sup>),
|
||||
</li> <li> Θ (°).
|
||||
</li></ol>
|
||||
<p></p>
|
||||
-- <a href="http://www.fsf.org/register_form?referrer=8369" target="_top">BMW</a> & <a href="http://lmu.web.psi.ch/lem/group.html" target="_top">AS</a></div><!-- /foswikiTopic-->
|
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|
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|
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|
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This topic: MUSR<span class='foswikiSeparator'> > </span><a href="WebHome.html" class="foswikiCurrentWebHomeLink">WebHome</a> > <a href="MusrFit.html">MusrFit</a> > <a href="BmwLibs.html">BmwLibs</a><span class='foswikiSeparator'> > </span>LibZFRelaxation <br />
|
||||
Topic revision: r2 - 10 Jul 2011 - 17:50:10 - <a href="https://intranet.psi.ch/Main/BastianWojek">BastianWojek</a>
|
||||
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|
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|
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|
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|
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373
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<h1><a name="A_61_61msr2data_61_61"></a> <code><b>msr2data</b></code> </h1>
|
||||
<p></p>
|
||||
<a name="foswikiTOC"></a><div class="foswikiToc"> <ul>
|
||||
<li> <a href="Msr2Data.html#A_61_61msr2data_61_61"> msr2data </a>
|
||||
</li> <li> <a href="Msr2Data.html#A_1_Introduction"> 1 Introduction </a>
|
||||
</li> <li> <a href="Msr2Data.html#A_2_Basic_Types_of_Usage"> 2 Basic Types of Usage </a>
|
||||
</li> <li> <a href="Msr2Data.html#A_3_Optional_Parameters"> 3 Optional Parameters </a>
|
||||
</li> <li> <a href="Msr2Data.html#A_4_The_Global_Mode"> 4 The Global Mode </a> <ul>
|
||||
<li> <a href="Msr2Data.html#A_4.1_File_Generation"> 4.1 File Generation </a>
|
||||
</li> <li> <a href="Msr2Data.html#A_4.2_Parameter_Extraction"> 4.2 Parameter Extraction </a>
|
||||
</li> <li> <a href="Msr2Data.html#A_4.3_The_Extended_Global_Mode"> 4.3 The Extended Global Mode </a>
|
||||
</li></ul>
|
||||
</li> <li> <a href="Msr2Data.html#A_5_Known_Limitations"> 5 Known Limitations </a>
|
||||
</li> <li> <a href="Msr2Data.html#A_6_The_Graphical_User_Interface_Provided_by_61_61musrgui_61_61_47_61_61musredit_61_61"> 6 The Graphical User Interface Provided by musrgui / musredit </a>
|
||||
</li> <li> <a href="Msr2Data.html#A_7_Bugtracking"> 7 Bugtracking </a>
|
||||
</li></ul>
|
||||
</div>
|
||||
<p></p>
|
||||
<a name="IntroDuction"></a>
|
||||
<h1><a name="A_1_Introduction"></a> 1 Introduction </h1>
|
||||
<code>msr2data</code> (originally written by B. M. Wojek) is a program implemented in <code>C++</code>. Its purpose is to process multiple <code><a href="MusrFit.html">musrfit</a></code> msr files with the same parameters and summarize the fitting results either in a TRIUMF <strong>DB</strong> <a name="FootNote1text"></a><span class="FootNoteTextLink" title=" For an abridged description of this format see [[http://musr.org/xyfit/dbformat.html][here]]. The *DB* files produced by =msr2data= can be viewed for instance with [[http://musr.org/muview/][&mu;View]], however, they are <em>not completely</em> backward-compatible to the original "db language" since the parameter names can be longer than five or six characters! In order to establish this backward compatibility (if needed) the user has to ensure the correct length of the parameter names in the msr files!"><a href="#FootNote1note" class="foswikiCurrentTopicLink">(1)</a></span> or a <strong>column ASCII</strong> file. It evolved from a script called <code>mlog2db</code> which has been written only for collecting fit results of <a href="http://lmu.web.psi.ch/lem/" target="_top">LEM</a> data stored in mlog files generated by <code>musrfit</code> and putting them together in a file with the <strong>DB</strong> format for further analysis. Therefore, any peculiarities, e.g. in supplying options to <code>msr2data</code> are owed its original purpose.
|
||||
<code>msr2data</code> is <a href="http://www.gnu.org/philosophy/free-sw.html" target="_top">free software</a> and licensed under the <a href="http://www.gnu.org/licenses/old-licenses/gpl-2.0.html" target="_top">GNU GPL version 2</a> or any later version (at your option).
|
||||
<p></p>
|
||||
Before the usage of msr2data will be explained in greater detail first be aware of the following:
|
||||
<p></p>
|
||||
<strong><font color="#ff0000">If using msr2data always bear in mind <a href="#KnownLimitations" class="foswikiCurrentTopicLink">its limitations</a>!</font></strong>
|
||||
<p></p>
|
||||
<p></p>
|
||||
<p></p>
|
||||
Notes
|
||||
<p></p>
|
||||
<a name="FootNote1note"></a><span class="FootNoteLabel"><a href="Msr2Data.html#FootNote1text" class="foswikiCurrentWebHomeLink"> <strong>1</strong> </a></span>: <span class="FootNote"> For an abridged description of this format see <a href="http://musr.org/xyfit/dbformat.html" target="_top">here</a>. The <strong>DB</strong> files produced by <code>msr2data</code> can be viewed for instance with <a href="http://musr.org/muview/" target="_top">μView</a>, however, they are <em>not completely</em> backward-compatible to the original "db language" since the parameter names can be longer than five or six characters! In order to establish this backward compatibility (if needed) the user has to ensure the correct length of the parameter names in the msr files!</span>
|
||||
<p></p>
|
||||
<p></p>
|
||||
<p></p>
|
||||
<hr />
|
||||
<p></p>
|
||||
<a name="BasicTypesOfUsage"></a>
|
||||
<h1><a name="A_2_Basic_Types_of_Usage"></a> 2 Basic Types of Usage </h1>
|
||||
Apart from numerous <a href="#OptionalParameters" class="foswikiCurrentTopicLink">optional parameters</a> that might be set or not, in principle there are four different ways of calling <code>msr2data</code>. These differ in how the list of runs which should be processed is supplied: <dl>
|
||||
<dt> msr2data <run> <extension> [optional parameters] </dt><dd> A single run number.
|
||||
</dd> <dt> msr2data <firstRunNo> <lastRunNo> <extension> [optional parameters] </dt><dd> An interval of run numbers is specified through the first and the last run number. The condition <strong><firstRunNo> < <lastRunNo></strong> is <em>not</em> necessary.
|
||||
</dd> <dt> msr2data \[<run1> <run2> ... <runN> \] <extension> [optional parameters] </dt><dd> A space separated list of run numbers can be enclosed in <strong>[</strong> and <strong>]</strong>. Every run that should be processed has to be specified explicitly by its run number.
|
||||
</dd> <dt> msr2data <runListFileName> <extension> [optional parameters] </dt><dd> An ASCII file containing a list of run numbers and optional external parameters is passed to <code>msr2data</code>. For the structure of the ASCII file see <a href="#RunListStructure" class="foswikiCurrentTopicLink">below</a>.
|
||||
</dd></dl>
|
||||
<p></p>
|
||||
All four basic types of calling <code>msr2data</code> contain the <em>mandatory</em> file-name <strong><extension></strong> passed right after the list of runs. The meaning of this <strong><extension></strong> should become clear after giving examples for all four cases:
|
||||
<pre class="bash">msr2data 8472 _tf_h13</pre> generates the <strong>DB</strong> file <code><b>out.db</b></code> (can be changed by using <a href="#OptionalParameters" class="foswikiCurrentTopicLink">the -o option</a>) from <code><b>8472_tf_h13.msr</b></code>.
|
||||
<pre class="bash">msr2data 8472 8474 _tf_h13</pre> generates the <strong>DB</strong> file <code><b>out.db</b></code> (can be changed by using <a href="#OptionalParameters" class="foswikiCurrentTopicLink">the -o option</a>) from <code><b>8472_tf_h13.msr</b></code>, <code><b>8473_tf_h13.msr</b></code>, and <code><b>8474_tf_h13.msr</b></code>.
|
||||
<pre class="bash">msr2data [8472 8470] _tf_h13</pre> generates the <strong>DB</strong> file <code><b>out.db</b></code> (can be changed by using <a href="#OptionalParameters" class="foswikiCurrentTopicLink">the -o option</a>) from <code><b>8472_tf_h13.msr</b></code> and <code><b>8470_tf_h13.msr</b></code>.
|
||||
<pre class="bash">msr2data run.list _tf_h13</pre> generates the <strong>DB</strong> file <code><b>out.db</b></code> (can be changed by using <a href="#OptionalParameters" class="foswikiCurrentTopicLink">the -o option</a>) from all runs listed in the ASCII file <code><b>run.list</b></code> in the working directory. In this file it is also possible to include external parameters which should be put in the resulting <strong>DB</strong> file. The structure of the <code><b>run.list</b></code> is the following:
|
||||
<a name="RunListStructure"></a>
|
||||
<pre>
|
||||
RUN VAR1 VAR2 VAR3 ...
|
||||
8460 200 27.1 46.2 ...
|
||||
8472 205 27.1 46.3 ...
|
||||
8453 210 27.2 45.9 ...
|
||||
· · · ·
|
||||
· · · ·
|
||||
· · · ·
|
||||
</pre>
|
||||
<font color="#ff0000">The first not commented and not empty line determines the parameter names and labels and has to be present!</font><br/>
|
||||
It is allowed to add comments (with a preceding <strong>#</strong>) or empty lines to the run-list file.
|
||||
<p></p>
|
||||
The following should be mentioned together with the above examples: <ul>
|
||||
<li> The output files in the examples above are only newly created if they did not exist before invoking <strong>msr2data</strong>. If the files were already present the msr-file data would be appended!
|
||||
</li> <li> If the files have been newly created, also the <strong>DB</strong> file header is written. If the files were present before, only the data blocks are appended. The output of the header can either be forced or completely suppressed with the <a href="#OptionalParameters" class="foswikiCurrentTopicLink">header and noheader options</a> as shall be seen later.
|
||||
</li></ul>
|
||||
<a name="NoExtension"></a> <ul>
|
||||
<li> <font color="#ff0000">If the <code>musrfit</code> output files do not have an <extension> as specified above like <code><b>8472.msr</b></code> one has to call <code>msr2data</code> like in the following example:</font> <pre class="bash">
|
||||
msr2data 8472 8460 ""
|
||||
</pre>
|
||||
</li></ul>
|
||||
<p></p>
|
||||
<a name="OptionalParameters"></a>
|
||||
<h1><a name="A_3_Optional_Parameters"></a> 3 Optional Parameters </h1>
|
||||
As mentioned already above there are some optional parameters which change the behavior of <code>msr2data</code> and can be passed in any order. Here is a complete list: <dl>
|
||||
<dt> data </dt><dd> The output file format is changed to a simple column ASCII file (default output file name: <code><b>out.dat</b></code>).
|
||||
</dd> <dt> new </dt><dd> An existing output file is deleted before new information is written to it.
|
||||
</dd> <dt> header </dt><dd> Force the output of the file header—even if the output file was present before.
|
||||
</dd> <dt> noheader </dt><dd> The output of the file header is suppressed—also if the output file is newly created.<br>If either both or none of the header options are given, <code>msr2data</code> writes the file header only to new files and it solely appends the data blocks to an existing output file assuming that the header is present already.
|
||||
</dd> <dt> nosummary </dt><dd> There will be no attempt to read additional information like the temperature or the applied magnetic field from the data files even if these information were present there.
|
||||
</dd> <dt> -o<outputFileName>, -o <outputFileName> </dt><dd> The processed data will be written to the file <strong><outputFileName></strong> instead of the default <code><b>out.db</b></code> or <code><b>out.dat</b></code>. If <strong><outputFileName></strong> is equal to <strong>none</strong> (case-insensitive) the parameter data are <em>not appended</em> to any output file.
|
||||
</dd> <dt> fit </dt><dd> Additionally to the final data collection <code>msr2data</code> will invoke musrfit to fit the specified runs. All msr files are assumed to be present, none is newly generated!
|
||||
</dd> <dt> fit-<template>[!] </dt><dd> Additionally to the final data collection <code>msr2data</code> will generate msr files for the runs specified in the list of runs and invoke <code>musrfit</code> for performing fits of the data. As template for the first run the file <code><b><template><extension>.msr</b></code> (or if not available: <code><b><template><extension>.mlog</b></code>) is used; the subsequent input files will be created using the msr output of the last processed runs ("chain fit"). However, if for <em>all</em> runs only the given template should be used one has to append an exclamation mark (<strong>!</strong>) to the <strong><template></strong>.
|
||||
</dd> <dt> msr-<template> </dt><dd> The same as <strong>fit-<template>[!]</strong>, <em>without</em> calling <code>musrfit</code> and the final data collection, i.e. only the msr files for the given runs are generated.
|
||||
</dd> <dt> -k </dt><dd> If specified together with the <strong>fit-<template></strong> option, the <strong>--keep-mn2-output</strong> <a href="MusrFit.html#MusrFit">option</a> is passed to <code>musrfit</code>. In the case no fits should be done, this option is ignored.
|
||||
</dd> <dt> -t </dt><dd> In case this option is given additionally to the <strong>fit-<template></strong> option, <code>musrfit</code> is called with the <strong>--title-from-data-file</strong> <a href="MusrFit.html#MusrFit">option</a>. If no fitting is done, this option is ignored.
|
||||
</dd></dl>
|
||||
<p></p>
|
||||
In order to illustrate the usage of these parameters a few examples with explanations are given below:
|
||||
<pre class="bash">
|
||||
msr2data 8400 8460 _tf_h13 -oABC.db fit-8472
|
||||
</pre>
|
||||
Using <code><b>8472_tf_h13.msr</b></code> as first template, <code>msr2data</code> generates subsequent msr input files <code><b>8400_tf_h13.msr</b></code> through <code><b>8460_tf_h13.msr</b></code>, calls <code>musrfit</code> to perform a fit of these files and collects the results of the fits together with the <strong>DB</strong> header in the new file <code><b>ABC.db</b></code>. Additionally, some information about external parameters like the temperature will be passed to <code><b>ABC.db</b></code> if it is present in the data files.
|
||||
<pre class="bash">
|
||||
msr2data [8500 8505] _zf fit-8472 noheader nosummary -o DEF.db
|
||||
</pre>
|
||||
Using <code><b>8472_zf.msr</b></code> as first template, <code>msr2data</code> generates subsequent msr input files <code><b>8500_zf.msr</b></code> and <code><b>8505_zf.msr</b></code>, calls <code>musrfit</code> to perform a fit of these files and collects the results of the fits in the file <code><b>DEF.db</b></code> without writing the <strong>DB</strong> file header or attempting to read additional information from the data files.
|
||||
<pre class="bash">
|
||||
msr2data 8595 8585 "" noheader fit-8472! -oGHI.dat data nosummary -k
|
||||
</pre>
|
||||
Using <code><b>8472.msr</b></code> as template for <em>all</em> runs, <code>msr2data</code> generates the msr input files <code><b>8595.msr</b></code> through <code><b>8585.msr</b></code>, calls <code>musrfit</code> with the option <strong>--keep-mn2-ouput</strong> to perform a fit of these files and collects the results of the fits in the column-structured ASCII file <code><b>GHI.dat</b></code> without writing any file header or attempting to read additional information from the data files.
|
||||
<pre class="bash">
|
||||
msr2data 8472 8475 "" fit -o none
|
||||
</pre>
|
||||
Take the <strong>given</strong> msr files <code><b>8472.msr</b></code> through <code><b>8475.msr</b></code> and call <code>musrfit</code> <em>without</em> finally summarizing the results.
|
||||
<pre class="bash">
|
||||
msr2data 8472 8475 _tf_h13 msr-8471!
|
||||
</pre>
|
||||
Using <code><b>8471_tf_h13.msr</b></code> as template for <em>all</em> runs, <code>msr2data</code> generates the msr input files <code><b>8472_tf_h13.msr</b></code> through <code><b>8475_tf_h13.msr</b></code>. <font color="#ff0000">No fitting will be performed and no DB or ASCII output will be generated!</font>
|
||||
<p></p>
|
||||
<a name="TheGlobalMode"></a>
|
||||
<h1><a name="A_4_The_Global_Mode"></a> 4 The Global Mode </h1>
|
||||
Apart from all the options described <a href="#OptionalParameters" class="foswikiCurrentTopicLink">above</a> there is another program option: <strong>global</strong>. This option changes the general behavior of <code>msr2data</code> in that way that instead of processing one msr file for each run it combines all specified runs in one single msr file with the possibility to define common parameters for all runs as well as run-specific parameters. When writing the obtained parameters to a DB file or a column-structured ASCII file that single msr file is read and the parameters valid for each run are extracted. The <strong>global</strong> option can be used in conjunction with any of the described <a href="#BasicTypesOfUsage" class="foswikiCurrentTopicLink">invocations</a> of <code>msr2data</code> and together with all options stated <a href="#OptionalParameters" class="foswikiCurrentTopicLink">above</a>.
|
||||
<p></p>
|
||||
<a name="GlobalFileGeneration"></a>
|
||||
<h2><a name="A_4.1_File_Generation"></a> 4.1 File Generation </h2>
|
||||
The general idea of this mode is to generate a global msr file on the basis of a working single-run msr file. For this purpose a single-run template containing information about common and run-specific parameters should be created. These parameters are identified through their parameter names: <dl>
|
||||
<dt> run-specific parameters </dt><dd> these parameters are tagged with the current run number in the format <strong>%0Xu</strong>, i.e. <strong>X</strong> digits with leading zeros, at the end of the parameter name, e.g. for a 4-digit-formatted run number <strong>alpha0123</strong> if the run number was <strong>123</strong> or for a 8-digit-formatted run number <strong>alpha00123456</strong> if the run number was <strong>123456</strong>. <strong>X</strong> has to be at least 4.
|
||||
</dd> <dt> common parameters </dt><dd> all parameters that are not run specific
|
||||
</dd></dl>
|
||||
The FITPARAMETER block of an exemplary template file <code><b>8472_example.msr</b></code> could therefore look like:<pre>
|
||||
FITPARAMETER
|
||||
# No Name Value Step Pos_Error Boundaries
|
||||
1 Phase 35.8359 -3.94496 3.93749
|
||||
2 Asy8472 0.04501 -0.00208 0.00211 0 0.33
|
||||
3 Field 143.212 -0.27960 0.27885 100 200
|
||||
4 Rate8472 0.14245 -0.02501 0.02279 0 1
|
||||
</pre>
|
||||
Here the parameters <strong>2</strong> and <strong>4</strong> would be treated as run-specific whereas the parameters <strong>1</strong> and <strong>3</strong> would be common to the original and all newly added runs.
|
||||
<p></p>
|
||||
Normally, within the template file there should <em>not</em> appear explicitly any run-specific parameters in the THEORY and FUNCTIONS blocks. If however, those parameters are met, <code>msr2data</code> will try to substitute them by mapped parameters and add them accordingly to the map contained in each RUN block.
|
||||
<p></p>
|
||||
When <code>msr2data</code> is called to generate a global msr file, e.g.<pre class="bash">
|
||||
msr2data 8471 8470 _example msr-8472 global
|
||||
</pre>
|
||||
a new msr file <code><b>8471+global_example.msr</b></code> is created. As can be seen in the example, the name of the global msr file always starts with the first specified run number followed by the <strong>+global</strong> identifier and the template <strong><extension></strong>.
|
||||
The example's global FITPARAMETER block would be:<pre>
|
||||
FITPARAMETER
|
||||
# No Name Value Step Pos_Error Boundaries
|
||||
|
||||
# Common parameters for all runs
|
||||
|
||||
1 Phase 35.8359 -3.94496 3.93749
|
||||
2 Field 143.212 -0.27960 0.27885 100 200
|
||||
|
||||
# Specific parameters for run 8471
|
||||
|
||||
3 Asy8471 0.04501 -0.00208 0.00211 0 0.33
|
||||
4 Rate8471 0.14245 -0.02501 0.02279 0 1
|
||||
|
||||
# Specific parameters for run 8470
|
||||
|
||||
5 Asy8470 0.04501 -0.00208 0.00211 0 0.33
|
||||
6 Rate8470 0.14245 -0.02501 0.02279 0 1
|
||||
</pre>
|
||||
This shows that the fit parameters are reorganized in a way that the common parameters appear at the beginning of the parameter list and they are followed by copies of the parameters specific to each run (in the specified order!). Additionally, for each specified run new RUN blocks are created—for each run as many as found for the template run.<br>
|
||||
During this reorganization all the affected parameter occurrences are changed accordingly!
|
||||
<p></p>
|
||||
<font color="#ff0000">Please be aware of the fact that comments in the template msr file are <em>not</em> propagated to the newly generated global msr file!</font>
|
||||
<p></p>
|
||||
<h2><a name="A_4.2_Parameter_Extraction"></a> 4.2 Parameter Extraction </h2>
|
||||
After fitting some model to the specified data the fit parameters can be extracted from the global msr file to a <strong>DB</strong> or column-structured ASCII file—as usual this includes also parameters stored in the run data files or externally specified parameters given in a <a href="#RunListStructure" class="foswikiCurrentTopicLink">run-list file</a>.
|
||||
In order to reach this goal the global msr file has to obey certain rules: <ul>
|
||||
<li> The order of the parameters has to match the one described <a href="#GlobalFileGeneration" class="foswikiCurrentTopicLink">above</a>, meaning the common parameters are listed first followed by the same number of parameters specific to each run tagged by the according run numbers at the end of the parameter names and having the same order as the specified list of runs.
|
||||
</li> <li> The RUN blocks have to be ordered according to the list of runs to be processed.
|
||||
</li></ul>
|
||||
Following these rules—which is achieved most easily by generating the global msr file using <code>msr2data</code> as shown <a href="#GlobalFileGeneration" class="foswikiCurrentTopicLink">above</a>—the parameters can be extracted e.g. like <pre class="bash">
|
||||
msr2data 8471 8470 _example global data -o globalFit.dat
|
||||
</pre>
|
||||
This will read in the file <code><b>8471+global_example.msr</b></code>, extract for each run all relevant parameters from the msr file as well as from the according data files (if available) and append all of them in columns to the ASCII file <code><b>globalFit.dat</b></code>.
|
||||
<p></p>
|
||||
<a name="GlobalPlus"></a>
|
||||
<h2><a name="A_4.3_The_Extended_Global_Mode"></a> 4.3 The Extended Global Mode </h2>
|
||||
If a new global input file is generated, it is also possible to do an automatic pre-analysis for each single run using the specified template first; afterwards the run-specific parameters of these single-run msr files are collected in the global msr file. In special cases this might be useful to obtain a better set of starting values for the parameters, however, in most cases it will not replace the "manual review" of the generated global input file. The option is activated by choosing the keyword <strong>global+</strong>. For example <pre class="bash">
|
||||
msr2data 8471 8470 _example global+ msr-8472
|
||||
</pre>
|
||||
Here, <code><b>8472_example.msr</b></code> is first used as template to generate the file <code><b>8471-OneRunFit_example.msr</b></code>, then <code>musrfit</code> is called for it, the result is used to generate <code><b>8470-OneRunFit_example.msr</b></code> and <code>musrfit</code> is called for that file. Finally, the global fit file <code><b>8471+global_example.msr</b></code> is produced—including the fit results of the OneRunFit files for the run-specific parameters.<br>
|
||||
By appending an exclamation mark <strong>!</strong> to the <strong>global+</strong> option, the given template will be used for every new file generation (similar to the <strong>fit</strong> option explained <a href="#OptionalParameters" class="foswikiCurrentTopicLink">before</a>). The <strong>+[!]</strong> extension will be ignored, if no new global input file is generated.<br>
|
||||
The single run msr files are not deleted at the moment. The information contained in them might be useful for some people. Of course the data can also be collected by <code>msr2data</code>. E.g. in order to produce a <strong>DB</strong> file <code><b>OneRunFits.db</b></code> one could call <pre class="bash">
|
||||
msr2data 8471 8470 -OneRunFit_example -o OneRunFits.db
|
||||
</pre>
|
||||
<p></p>
|
||||
<font color="#ff0000">Please be aware that the program in this mode always generates new single-run msr files and always calls <code>musrfit</code> for them. In case there are already single-run fits present, these cannot be used in conjunction with this option. The program on purpose behaves in this way in order to ensure the file integrity and correct parameter order within these files.</font>
|
||||
<p></p>
|
||||
<a name="KnownLimitations"></a>
|
||||
<h1><a name="A_5_Known_Limitations"></a> 5 Known Limitations </h1> <ul>
|
||||
<li> The indexing run number of the msr file has to be at the begin of every filename.
|
||||
</li> <li> Within the data file name the <strong>RUN#</strong> has the format <strong>%0Xu</strong>, i.e. <strong>X</strong> digits with leading zeros, and has to be the rightmost number given in this format in the file name. <strong>X</strong> has to be at least 4. The highest treatable run number is 2<sup>32</sup>-1 = 4294967295.
|
||||
</li> <li> In order to keep <code>msr2data</code> working properly the msr files should only contain <em><font color="#ff0000">one</font> STATISTIC block at the end of the file</em> and <i><font color="#ff0000">one</font> FITPARAMETER block right after the TITLE</i>—<code>musrfit</code> itself allows to have more creative msr files...
|
||||
</li> <li> The msr-file generation from a template takes only care of runs given on the first line of a RUN block. <a href="MusrFit.html#AddRun">ADDRUN statements</a> are simply copied! Since this is most probably not what one likes to do, it is suggested not to use the <strong>fit-<template></strong> and <strong>msr-<template></strong> options if ADDRUN statements were present in the template file.
|
||||
</li> <li> <code>msr2data</code> will write only up to <em>two successive</em> empty lines in newly generated msr files. In case more subsequent empty lines are encountered in a template file, these are <em>not</em> copied! Actually, this measure is not a limitation but has been introduced to keep the msr files in a reasonable shape.
|
||||
</li></ul>
|
||||
<p></p>
|
||||
<a name="MusrGuiInterface"></a>
|
||||
<h1><a name="A_6_The_Graphical_User_Interface_Provided_by_61_61musrgui_61_61_47_61_61musredit_61_61"></a> 6 The Graphical User Interface Provided by <code><b>musrgui</b></code> / <code><b>musredit</b></code> </h1>
|
||||
<code><a href="MusrGui.html">musrgui/musredit</a></code>, editors designed especially for the manipulation of <code>musrfit</code> msr files and graphical front ends to <code><a href="MusrFit.html">musrfit</a></code>, offer an almost self-explanatory graphical user interface to <code>msr2data</code> depicted below:<br>
|
||||
<img src="../pub/MUSR/Msr2Data/msr2data-input-tabs.png" alt="msr2data-input-tabs.png" width='612' height='605' align="right" /> <dl>
|
||||
<dt> <font color="#ff0000">1–3</font> </dt><dd> Choose one of the <a href="#BasicTypesOfUsage" class="foswikiCurrentTopicLink">ways</a> to specify your list of runs.
|
||||
</dd> <dt> <font color="#ff0000">4</font> </dt><dd> Give the file extension here, e.g. <strong>_zf</strong> for files like <code><b>8472_zf.msr</b></code>. If the files do not have an extension this field stays empty. <code>musrgui</code> / <code>musredit</code> take care of passing the <strong>""</strong> to <code>msr2data</code> as mentioned <a href="#NoExtension" class="foswikiCurrentTopicLink">above</a>.
|
||||
</dd> <dt> <font color="#ff0000">5</font> </dt><dd> Activates the <strong>fit-<template></strong> option if <strong><template></strong> is entered. In case the option "Chain Fit" is <em>not</em> set the given template will be used for the input-file generation for <em>all</em> runs to be fitted—otherwise the output of the first fit serves as template for the second and so on. The template field stays empty if no fits should be performed!
|
||||
</dd> <dt> <font color="#ff0000">6</font> </dt><dd> Activates the <strong>-o<outputFileName></strong> option if <strong><outputFileName></strong> is entered. If nothing is entered the default output file <code><b>out.db</b></code> or <code><b>out.dat</b></code> is used.
|
||||
</dd> <dt> <font color="#ff0000">7</font> </dt><dd> If <em>not</em> set, the <strong>noheader</strong> option is passed to <code>msr2data</code>.
|
||||
</dd> <dt> <font color="#ff0000">8</font> </dt><dd> If set, the <strong>nosummary</strong> option is passed to <code>msr2data</code>.
|
||||
</dd> <dt> <font color="#ff0000">9</font> </dt><dd> If set, the <strong>-k</strong> option is passed to <code>msr2data</code>.
|
||||
</dd> <dt> <font color="#ff0000">10</font> </dt><dd> If set, the <strong>data</strong> option is passed to <code>msr2data</code>.
|
||||
</dd> <dt> <font color="#ff0000">11</font> </dt><dd> If set, the output file is deleted before <code>msr2data</code> is called. Otherwise the data is appended to the file if it existed before <code>msr2data</code> has been called.
|
||||
</dd> <dt> <font color="#ff0000">12</font> </dt><dd> If set, after processing by <code>msr2data</code> all specified msr files are opened in tabs in <code>musrgui</code> / <code>musredit</code>.
|
||||
</dd> <dt> <font color="#ff0000">13</font> </dt><dd> If set, the <strong>-t</strong> option is passed to <code>msr2data</code>.
|
||||
</dd> <dt> <font color="#ff0000">14</font> </dt><dd> If set, <code>msr2data</code> is called with the option <strong>msr-<template></strong> (instead of <strong>fit-<template></strong>) and hence is only producing the msr input files without any fitting.
|
||||
</dd> <dt> <font color="#ff0000">15</font> </dt><dd> If set, <code>msr2data</code> is called with the option <strong>fit</strong>, i.e. no template will be used to generate new msr input files; only existing files are fed to <code>musrfit</code>.
|
||||
</dd> <dt> <font color="#ff0000">16</font> </dt><dd> If set, <code>msr2data</code> is operating in the <a href="#TheGlobalMode" class="foswikiCurrentTopicLink">global mode</a>.
|
||||
</dd> <dt> <font color="#ff0000">17</font> </dt><dd> If set, <code>msr2data</code> is operating in the <a href="#GlobalPlus" class="foswikiCurrentTopicLink">extended global mode</a>.
|
||||
</dd></dl>
|
||||
<p></p>
|
||||
<a name="BugTracking"></a>
|
||||
<h1><a name="A_7_Bugtracking"></a> 7 Bugtracking </h1>
|
||||
<p></p>
|
||||
For reporting bugs or requesting new features and improvements please use the <a href="https://tracker.intranet.psi.ch/jira/browse/MUSR" target="_top">PSI Tracker</a> or send an e-mail to A. Suter.
|
||||
<p></p>
|
||||
-- <a href="http://www.fsf.org/register_form?referrer=8369" target="_top">BMW</a> & <a href="http://lmu.web.psi.ch/lem/group.html" target="_top">AS</a></div><!-- /foswikiTopic-->
|
||||
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|
||||
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|
||||
<hr />
|
||||
This topic: MUSR<span class='foswikiSeparator'> > </span><a href="WebHome.html" class="foswikiCurrentWebHomeLink">WebHome</a> > <a href="MusrFit.html">MusrFit</a><span class='foswikiSeparator'> > </span>Msr2Data <br />
|
||||
Topic revision: r38 - 20 Jul 2011 - 12:13:59 - <a href="https://intranet.psi.ch/Main/BastianWojek">BastianWojek</a>
|
||||
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|
||||
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||||
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||||
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|
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</div><div id="patternBottomBar"><div id="patternBottomBarContents"><div id="patternWebBottomBar">Ideas, requests, problems regarding <a href="https://intranet.psi.ch/Main/WebHome">PSI Wiki</a>? <a href="mailto:psi.intranet@psi.ch?subject=Foswiki%20Feedback%20on%20MUSR.Msr2Data">Send feedback</a></div></div></div>
|
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<div class="patternContent"><div class="foswikiTopic"><h1><a name="Acknowledgements_45_61_61musrfit_61_61"></a> Acknowledgements - <code><b>musrfit</b></code> </h1>
|
||||
<p></p> <dl>
|
||||
<dt> Bastian M. Wojek </dt><dd> I am very much indebted to <a href="http://www.fsf.org/register_form?referrer=8369" target="_top">BMW</a> for his rigorous testing of <code><a href="MusrFit.html">musrfit</a></code>, his many useful suggestions, contributions, and for the largest part of the <a href="WebHome.html" class="foswikiCurrentWebHomeLink">user manual of <code>musrfit</code></a> which makes it accessible to a broader audience! Many thanks Bastian!
|
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|
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|
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-- <a href="http://www.fsf.org/register_form?referrer=8369" target="_top">BMW</a> & <a href="http://lmu.web.psi.ch/lem/group.html" target="_top">AS</a></div><!-- /foswikiTopic-->
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This topic: MUSR<span class='foswikiSeparator'> > </span><a href="WebHome.html" class="foswikiCurrentWebHomeLink">WebHome</a> > <a href="MusrFit.html">MusrFit</a><span class='foswikiSeparator'> > </span>MusrFitAcknowledgements <br />
|
||||
Topic revision: r4 - 10 Jul 2011 - 17:50:36 - <a href="https://intranet.psi.ch/Main/BastianWojek">BastianWojek</a>
|
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</div><div id="patternBottomBar"><div id="patternBottomBarContents"><div id="patternWebBottomBar">Ideas, requests, problems regarding <a href="https://intranet.psi.ch/Main/WebHome">PSI Wiki</a>? <a href="mailto:psi.intranet@psi.ch?subject=Foswiki%20Feedback%20on%20MUSR.MusrFitAcknowledgements">Send feedback</a></div></div></div>
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820
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<div class="patternContent"><div class="foswikiTopic"><h1><a name="Setting_up_61_61musrfit_61_61_on_Different_Platforms"></a> Setting up <code><b>musrfit</b></code> on Different Platforms </h1>
|
||||
<p></p>
|
||||
<a name="foswikiTOC"></a><div class="foswikiToc"> <ul>
|
||||
<li> <a href="MusrFitSetup.html#Setting_up_61_61musrfit_61_61_on_Different_Platforms"> Setting up musrfit on Different Platforms </a>
|
||||
</li> <li> <a href="MusrFitSetup.html#A_1_Supported_Operating_Systems_and_Software_Requirements"> 1 Supported Operating Systems and Software Requirements </a>
|
||||
</li> <li> <a href="MusrFitSetup.html#A_2_OS_Restrictions"> 2 OS Restrictions </a>
|
||||
</li> <li> <a href="MusrFitSetup.html#A_3_GNU_47Linux"> 3 GNU/Linux </a> <ul>
|
||||
<li> <a href="MusrFitSetup.html#A_3.1_Requirements"> 3.1 Requirements </a> <ul>
|
||||
<li> <a href="MusrFitSetup.html#A_3.1.1_Everything_but_61_61ROOT_61_61_and_61_61NeXus_61_61"> 3.1.1 Everything but ROOT and NeXus </a>
|
||||
</li> <li> <a href="MusrFitSetup.html#A_3.1.2_Installation_of_61_61NeXus_61_61_requirements_40optional_41"> 3.1.2 Installation of NeXus requirements (optional) </a>
|
||||
</li> <li> <a href="MusrFitSetup.html#A_3.1.3_61_61ROOT_61_61"> 3.1.3 ROOT </a>
|
||||
</li></ul>
|
||||
</li> <li> <a href="MusrFitSetup.html#A_3.2_61_61musrfit_61_61"> 3.2 musrfit </a>
|
||||
</li> <li> <a href="MusrFitSetup.html#A_3.3_61_61musredit_61_61"> 3.3 musredit </a>
|
||||
</li> <li> <a href="MusrFitSetup.html#A_3.4_61_61musrgui_61_61"> 3.4 musrgui </a>
|
||||
</li> <li> <a href="MusrFitSetup.html#A_3.5_Check_of_the_installation"> 3.5 Check of the installation </a>
|
||||
</li></ul>
|
||||
</li> <li> <a href="MusrFitSetup.html#A_4_MS_Windows"> 4 MS Windows </a> <ul>
|
||||
<li> <a href="MusrFitSetup.html#A_4.1_Requirements"> 4.1 Requirements </a> <ul>
|
||||
<li> <a href="MusrFitSetup.html#A_4.1.1_Setting_up_Cygwin"> 4.1.1 Setting up Cygwin </a>
|
||||
</li> <li> <a href="MusrFitSetup.html#A_4.1.2_Installation_of_61_61NeXus_61_61_requirements_40optional_41"> 4.1.2 Installation of NeXus requirements (optional) </a>
|
||||
</li> <li> <a href="MusrFitSetup.html#A_4.1.3_61_61ROOT_61_61"> 4.1.3 ROOT </a>
|
||||
</li></ul>
|
||||
</li> <li> <a href="MusrFitSetup.html#A_4.2_61_61musrfit_61_61"> 4.2 musrfit </a>
|
||||
</li> <li> <a href="MusrFitSetup.html#A_4.3_61_61musredit_61_61"> 4.3 musredit </a>
|
||||
</li> <li> <a href="MusrFitSetup.html#A_4.4_61_61musrgui_61_61"> 4.4 musrgui </a>
|
||||
</li> <li> <a href="MusrFitSetup.html#A_4.5_Check_of_the_installation"> 4.5 Check of the installation </a>
|
||||
</li> <li> <a href="MusrFitSetup.html#A_4.6_Possible_problems"> 4.6 Possible problems </a>
|
||||
</li></ul>
|
||||
</li> <li> <a href="MusrFitSetup.html#A_5_Mac_OS_X"> 5 Mac OS X </a> <ul>
|
||||
<li> <a href="MusrFitSetup.html#A_5.1_Requirements_40_61_61MacPorts_61_61_41"> 5.1 Requirements (MacPorts) </a> <ul>
|
||||
<li> <a href="MusrFitSetup.html#A_5.1.1_Everything_but_61_61ROOT_61_61_and_61_61NeXus_61_61"> 5.1.1 Everything but ROOT and NeXus </a>
|
||||
</li> <li> <a href="MusrFitSetup.html#A_5.1.2_Installation_of_61_61NeXus_61_61_requirements_40optional_41"> 5.1.2 Installation of NeXus requirements (optional) </a>
|
||||
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|
||||
</li></ul>
|
||||
</li> <li> <a href="MusrFitSetup.html#A_5.2_Requirements_40_61_61Fink_61_61_41"> 5.2 Requirements (Fink) </a> <ul>
|
||||
<li> <a href="MusrFitSetup.html#A_5.2.1_Everything_but_61_61ROOT_61_61_and_61_61NeXus_61_61"> 5.2.1 Everything but ROOT and NeXus </a>
|
||||
</li> <li> <a href="MusrFitSetup.html#A_5.2.2_Installation_of_61_61NeXus_61_61_requirements_40optional_41"> 5.2.2 Installation of NeXus requirements (optional) </a>
|
||||
</li> <li> <a href="MusrFitSetup.html#A_5.2.3_61_61ROOT_61_61"> 5.2.3 ROOT </a>
|
||||
</li></ul>
|
||||
</li> <li> <a href="MusrFitSetup.html#A_5.3_61_61musrfit_61_61"> 5.3 musrfit </a>
|
||||
</li> <li> <a href="MusrFitSetup.html#A_5.4_61_61musredit_61_61"> 5.4 musredit </a>
|
||||
</li> <li> <a href="MusrFitSetup.html#A_5.5_61_61musrgui_61_61"> 5.5 musrgui </a>
|
||||
</li> <li> <a href="MusrFitSetup.html#A_5.6_Check_of_the_installation"> 5.6 Check of the installation </a>
|
||||
</li></ul>
|
||||
</li></ul>
|
||||
</div>
|
||||
<p></p>
|
||||
<h1><a name="A_1_Supported_Operating_Systems_and_Software_Requirements"></a> 1 Supported Operating Systems and Software Requirements </h1>
|
||||
<p></p>
|
||||
This page is intended to demonstrate for the interested user which steps are necessary to set up the <a href="http://www.gnu.org/philosophy/free-sw.html" target="_top">free software</a> μSR data analysis framework <code><a href="MusrFit.html">musrfit</a></code>. While the preferred way is to run the software on <strong>GNU/Linux</strong>, with some restrictions it can also be set up under <strong>MS Windows</strong> and <strong>MacOS X</strong>. <font color="#ff0000">In case <code>musrfit</code> should be installed according to the description found on this page, the user is strongly encouraged to <em>read completely</em> each section dealing with the present installation step <em>before</em> starting the installation process!</font>
|
||||
<p></p>
|
||||
<a name="ReqSw"></a>
|
||||
Apart from <a href="http://gcc.gnu.org/" target="_top">GCC, the GNU Compiler Collection</a>, the GNU build tools <a href="http://www.gnu.org/software/autoconf/" target="_top">autoconf</a>, <a href="http://www.gnu.org/software/automake/" target="_top">automake</a> and <a href="http://www.gnu.org/software/libtool/" target="_top">libtool</a> as well as the helper tool <a href="http://pkg-config.freedesktop.org/wiki/" target="_top">pkg-config</a> <code>musrfit</code> requires the installation of a few open-source libraries and programs: <dl>
|
||||
<dt> <a href="http://www.boost.org/" target="_top">boost C++ libraries</a> </dt><dd> The powerful <code>Spirit</code> parser framework used by <code>musrfit</code> is included in that collection of libraries. <em>Required version ≥ 1.33</em>
|
||||
</dd> <dt> <a href="http://www.gnu.org/software/gsl/" target="_top">GNU Scientific Library</a> </dt><dd> A numerical <code>C</code> and <code>C++</code> library which provides efficient implementations of various mathematical routines. <em>Required version ≥ 1.9</em>
|
||||
</dd> <dt> <a href="http://www.fftw.org/" target="_top">FFTW</a> </dt><dd> A <code>C</code> implementation for the fast computation of discrete Fourier transforms. <em>Required version ≥ 3.1</em>
|
||||
</dd> <dt> <a href="http://root.cern.ch/" target="_top">ROOT</a> </dt><dd> A <code>C++</code> data analysis framework developed at <a href="http://www.cern.ch/" target="_top">CERN</a>. <em>Required version ≥ 5.22</em>
|
||||
</dd> <dt> <a href="http://xmlsoft.org/" target="_top">libxml2</a> </dt><dd> The <code>XML</code> <code>C</code> parser and toolkit of <a href="http://www.gnome.org/" target="_top">Gnome</a>. <em>Required version ≥ 2.0</em>
|
||||
</dd></dl>
|
||||
<p></p>
|
||||
<a name="ReqSwNeXus"></a>
|
||||
Additionally, <font color="#ff0000">only if</font> <code>musrfit</code> should support reading of data files in the <code>NeXus</code> format the following libraries are needed: <dl>
|
||||
<dt> <a href="http://www.hdfgroup.org/products/hdf4/" target="_top">HDF4</a> </dt><dd> A library and multi-object file format for storing and managing data.
|
||||
</dd> <dt> <a href="http://www.hdfgroup.org/HDF5/" target="_top">HDF5</a> </dt><dd> A data model, library, and file format for storing and managing data.
|
||||
</dd> <dt> <a href="http://www.minixml.org/" target="_top">minixml</a> </dt><dd> A small <code>XML</code> library that can be used to read and write <code>XML</code> and <code>XML</code> -like data files. <em>Required version ≥ 2.2</em>
|
||||
</dd> <dt> <a href="http://www.nexusformat.org/" target="_top">NeXus</a> </dt><dd> A common data format for neutron, x-ray, and muon science.
|
||||
</dd></dl>
|
||||
<p></p>
|
||||
If optionally the editor and graphical user interface <code><a href="MusrGui.html">musrgui</a></code> / <code><a href="MusrGui.html">musredit</a></code> is going to be installed there is one further requirement: <dl>
|
||||
<dt> <a href="http://www.qtsoftware.com/" target="_top">Qt</a> </dt><dd> A cross-platform application and user interface framework. <em>Required version ≥ 3.3 & ≪ 4.0 (<code>musrgui</code>) <strong>OR</strong> ≥ 4.6 (<code>musredit</code>)</em>
|
||||
</dd></dl>
|
||||
<p></p>
|
||||
Each of the following sections focusing on the installation of <code>musrfit</code> on the different operating systems will also give a brief introduction on the installation of the requirements before the actual <code>musrfit</code> installation is described.
|
||||
<p></p>
|
||||
<h1><a name="A_2_OS_Restrictions"></a> 2 OS Restrictions </h1>
|
||||
Before the further installation will be described, please note the following restrictions: <dl>
|
||||
<dt> GNU/Linux </dt><dd> No serious problems are known at the moment.
|
||||
</dd> <dt> MS Windows </dt><dd> The setup of <code>musrfit</code> (including the requirements) using <code>Visual C++</code> has not been tested. If anybody likes to do this: Just go ahead and have fun! However, not very much assistance can be expected, although it would be an interesting experiment.
|
||||
</dd> <dt> Mac OS X </dt><dd> On <code>10.6 Snow Leopard</code> <code>Qt3</code> for Mac is not supported any more since this was based on a 32-bit only API. <code>Snow Leopard</code> -users are advised to use the <code>Qt4</code> based <code>musredit</code> or to rely on the standard <code>Qt3</code> version for <code>X11</code> in order to run <code>musrgui</code>.
|
||||
</dd></dl>
|
||||
<p></p>
|
||||
<h1><a name="A_3_GNU_47Linux"></a> 3 GNU/Linux </h1>
|
||||
<h2><a name="A_3.1_Requirements"></a> 3.1 Requirements </h2>
|
||||
<h3><a name="A_3.1.1_Everything_but_61_61ROOT_61_61_and_61_61NeXus_61_61"></a> 3.1.1 Everything but <code><b>ROOT</b></code> and <code><b>NeXus</b></code> </h3>
|
||||
Depending on the GNU/Linux distribution chosen, the above mentioned software—except the <code>ROOT</code> system and the <code>NeXus</code> library—should be available from the distributor and could be easily installed in the form of binary packages. If done in this way there should be taken care of installing <strong>both</strong>, the libraries and the header (dev, devel) files.<br>
|
||||
On a <a href="https://www.scientificlinux.org/" target="_top">Scientific Linux</a> (<a href="http://www.redhat.com/" target="_top">Red Hat</a>) system the following command executed as superuser from the shell will do the trick:
|
||||
<pre class="bash">
|
||||
yum install boost boost-devel gsl gsl-devel fftw3 fftw3-devel libxml2 libxml2-devel qt qt-devel
|
||||
</pre>
|
||||
When dealing with a distribution that uses the dpkg/apt package manager like <a href="http://www.debian.org/" target="_top">Debian</a> or <a href="http://www.ubuntu.com/" target="_top">Ubuntu</a> the installation would look like:
|
||||
<pre class="bash">
|
||||
apt-get install libboost-dev gsl-bin libgsl0-dev fftw3 fftw3-dev libxml2 libxml2-dev libqt3-mt libqt3-mt-dev qt3-dev-tools
|
||||
</pre>
|
||||
Everyone should know best himself which is the way to install distribution software on the chosen distribution <img src="../pub/Main/SmiliesPluginPSI/wink.gif" alt="wink" title="wink" border="0" />
|
||||
<p></p>
|
||||
In case the distribution does not include the required software it has to be compiled from the source files which normally means to download the source code from the corresponding website, to unpack the source tree and call the following from the shell:
|
||||
<pre class="bash">
|
||||
./configure
|
||||
make
|
||||
make install
|
||||
</pre>
|
||||
In order to obtain some information about the possible options for the installation, calling <code>./configure --help</code> might give some useful hints. <br>
|
||||
For any further information on the standard installation of software, please refer to the web search engine of choice and ask for "install software on linux"...
|
||||
<p></p>
|
||||
<h3><a name="A_3.1.2_Installation_of_61_61NeXus_61_61_requirements_40optional_41"></a> 3.1.2 Installation of <code><b>NeXus</b></code> requirements (optional) </h3>
|
||||
<font color="#ff0000">Only if</font> <code>musrfit</code> should support reading data files in the <code>NeXus</code> format the further <a href="#ReqSwNeXus" class="foswikiCurrentTopicLink">required</a> software has to be set up. The required libraries and header files could either be available through the user's GNU/Linux distribution or if this is not the case, the packages can be installed from the source code. E.g. on Red Hat-like systems binary packages for <code>MXML</code>, <code>HDF4</code>, and <code>HDF5</code> might be called <code><b>mxml, mxml-devel, hdf, hdf-devel, hdf5, hdf5-devel</b></code>, on Debian-like systems <code><b>libmxml1, libmxml-dev, libhdf4-0, libhdf4-dev, libhdf5-serial-1.8.4, libhdf5-serial-dev</b></code>.
|
||||
<p></p>
|
||||
Even though there might exist binary packages for the <code>NeXus</code> library, it is best to build and install it directly from the source code which can be found <a href="http://download.nexusformat.org/kits/" target="_top">here</a>.
|
||||
<p></p>
|
||||
<h3><a name="A_3.1.3_61_61ROOT_61_61"></a> 3.1.3 <code><b>ROOT</b></code> </h3>
|
||||
The <code>ROOT</code> system may or may not be part of the GNU/Linux distribution. If it is, it should be checked that the provided binaries are of a recent version and then these in principle can be installed using a package manager as described above. <br>
|
||||
In case the distribution provides no or only outdated binary packages there are the following possibilities: <ul>
|
||||
<li> Visit the <code>ROOT</code> <a href="http://root.cern.ch/drupal/content/downloading-root" target="_top">web page</a> and download the packed precompiled binary version matching best the GNU/Linux distribution. Then unpack the bundle to its final destination.
|
||||
</li> <li> If there is no precompiled binary version of <code>ROOT</code> available for your system or e.g. <code>ROOT</code> should be compiled with another version of <code>GCC</code> visit the <a href="http://root.cern.ch/drupal/content/downloading-root" target="_top">web page</a> and download the 'complete source tree for all systems'. Then unpack this source tree to its destination (e.g. /opt/root-system)<a name="FootNote1text"></a><span class="FootNoteTextLink" title="In case only a single user is working at the machine it might be considerable to change the ownership of the =ROOT= folder so that the user has easy write access to this directory: <!--�verbatim1672�-->"><a href="#FootNote1note" class="foswikiCurrentTopicLink">(1)</a></span>, configure<a name="FootNote2text"></a><span class="FootNoteTextLink" title=" When using =GCC= &#8805; 4.2 please make sure that the environment variables *USE_PARALLEL_MINUIT2* and *USE_OPENMP* are <em>not</em> set! Otherwise =MINUIT2= will be compiled with parallelization support and cannot be used together with =musrfit= afterwards since the =musrfit= code is <em>not</em> fully thread-safe! When compiled with =GCC= &#8805; 4.2 =musrfit= itself will parallelize the &chi;<sup>2</sup> calculation."><a href="#FootNote2note" class="foswikiCurrentTopicLink">(2)</a></span> it (here using the minimal set of options) and compile it as follows right below: <pre class="bash">
|
||||
cd /opt/root-system
|
||||
./configure linux --gminimal --enable-asimage --enable-mathmore --enable-minuit2 --enable-xml
|
||||
(or in case of a 64 bit installation: ./configure linuxx8664gcc --gminimal --enable-asimage --enable-mathmore --enable-minuit2 --enable-xml)
|
||||
make
|
||||
(or in case there are multiple processors available, e.g.: make -j4)
|
||||
</pre>
|
||||
</li></ul>
|
||||
After one of the two setup variants has been executed the system should be told where to find the <code>ROOT</code> installation, therefore the following is suggested: <ul>
|
||||
<li> As superuser create a file <strong>/etc/ld.so.conf.d/root-system.conf</strong> where the path to the <code>lib</code> directory of <code>ROOT</code> is added and call <strong>/sbin/ldconfig</strong> afterwards. In the example mentioned above one way of doing this is: <pre class="bash">
|
||||
echo "/opt/root-system/lib" >> /etc/ld.so.conf.d/root-system.conf
|
||||
/sbin/ldconfig
|
||||
</pre>
|
||||
</li> <li> <font color="#ff0000">Additionally</font>, as normal user one should append the following lines to the <strong>~/.bashrc</strong> and/or <strong>~/.bash_profile</strong> (and then either restart the shell or call the same commands once more from the shell) in order to change some path-setting environment variables: <pre class="bash">
|
||||
export ROOTSYS=/opt/root-system/
|
||||
export PATH=$ROOTSYS/bin:$PATH
|
||||
</pre>
|
||||
</li></ul>
|
||||
<p></p>
|
||||
<a name="MusrFitInstallation"></a>
|
||||
<h2><a name="A_3.2_61_61musrfit_61_61"></a> 3.2 <code><b>musrfit</b></code> </h2>
|
||||
When all required software has been set up it can be proceeded with the <code>musrfit</code> installation. First, the most recent source code should be downloaded. The preferred way of doing so is to check out directly the subversion repository (if clients of subversion and ssh are installed). Assuming the code should be located in ~/musrfit this is achieved most easily calling from the terminal
|
||||
<pre class="bash">
|
||||
cd
|
||||
svn co svn+ssh://svn@savannah.psi.ch/repos/nemu/lem/trunk/analysis/musrfit musrfit
|
||||
</pre>
|
||||
When asked (twice) for a password, type "svn".
|
||||
If the repository had been checked out already before, one can update the local copy using:
|
||||
<pre class="bash">
|
||||
cd
|
||||
svn up musrfit
|
||||
</pre>
|
||||
<p></p>
|
||||
<font color="#ff0000">As an alternative (if subversion is not available)</font>, the source code can also be downloaded and extracted from a tarball.
|
||||
<pre class="bash">
|
||||
cd
|
||||
curl http://savannah.psi.ch/viewcvs/trunk/analysis/musrfit.tar.gz -G --data-binary root=nemu%2Flem | tar xz
|
||||
</pre>
|
||||
<p></p>
|
||||
After the source-code extraction the <strong>autogen.sh</strong> script is called to prepare the build environment. If it has been executed successfully the <strong>configure</strong> script should be ready to collect all the information needed to create the Makefiles. <font color="#ff0000">If <code>musrfit</code> should support <code>NeXus</code> data files this has to be enabled by specifying the <strong>--enable-NeXus</strong> switch when calling <strong>configure</strong>.</font> For an overview of all available options just call <code>./configure --help</code>. Besides the standard options there are a few special options which should be mentioned here:
|
||||
<p></p> <dl>
|
||||
<dt> --prefix </dt><dd> Specify the installation prefix, e.g. /opt/root-system (<em>by default: /usr/local</em>)
|
||||
</dd> <dt> --with-rootsys </dt><dd> Specify the top of the <code>ROOT</code> installation directory, e.g. /opt/root-system
|
||||
</dd> <dt> --with-fftw3 </dt><dd> Specify the prefix of the <code>FFTW3</code> installation. e.g. /usr/local or /usr
|
||||
</dd> <dt> --with-gsl </dt><dd> Set the prefix of the <code>GSL</code> installation, e.g. /usr/local or /usr
|
||||
</dd> <dt> --with-boostinc </dt><dd> Set the path to the header files of the <code>Boost</code> installation, e.g. /usr/local/include or /usr/include
|
||||
</dd> <dt> --with-hdf4 </dt><dd> Set the prefix of the <code>HDF4</code> installation, e.g. /usr/local (<em>only useful in conjunction with the <code>NeXus</code> support</em>)
|
||||
</dd> <dt> --with-hdf5 </dt><dd> Set the prefix of the <code>HDF5</code> installation, e.g. /usr (<em>only useful in conjunction with the <code>NeXus</code> support</em>)
|
||||
</dd> <dt> --with-nexus </dt><dd> Set the prefix of the <code>NeXus</code> installation, e.g. /usr/local (<em>only useful in conjunction with the <code>NeXus</code> support</em>)
|
||||
</dd> <dt> --disable-omp </dt><dd> Switches off the <a href="http://en.wikipedia.org/wiki/OpenMP" target="_top">OpenMP</a> features of <code>musrfit</code> (parallelization of the χ<sup>2</sup> calculation when compiled with GCC ≥ 4.2)
|
||||
</dd></dl>
|
||||
<p></p>
|
||||
Normally it should not be necessary to make use of any of the options except for specifying the installation path with <strong>--prefix</strong>. The other paths should be detected automatically. If this does not work for some reason the <strong>configure</strong> script will terminate and ask for the information.
|
||||
When the <strong>configure</strong> script has been called successfully everything is ready for building the <code>musrfit</code> libraries and executables. A standard installation sequence (without <code>NeXus</code> support) might then look like<a name="FootNote3text"></a><span class="FootNoteTextLink" title="In case the normal user has no write permissions to the &#36;ROOTSYS and the installation path the "make install" commands have to be executed as superuser."><a href="#FootNote3note" class="foswikiCurrentTopicLink">(3)</a></span>:
|
||||
<pre class="bash">
|
||||
cd musrfit
|
||||
sh autogen.sh
|
||||
./configure --prefix=$ROOTSYS
|
||||
make
|
||||
make install
|
||||
/sbin/ldconfig (as superuser)
|
||||
</pre>
|
||||
In order to finish the installation of <code>musrfit</code> two more things should be done: <ul>
|
||||
<li> Define the <strong>MUSRFITPATH</strong> environment variable containing the path to the <code>musrfit</code> executables and XML files. E.g. if the location of the example above is used append the following line to the <strong>~/.bashrc</strong> and <strong>~/.bash_profile</strong> (and then either restart the shell or call the same commands once more from the shell): <pre class="bash">
|
||||
export MUSRFITPATH=/opt/root-system/bin
|
||||
</pre>
|
||||
</li> <li> Adjust the paths where <code>musrfit</code> will search for data files in the installed <strong>musrfit_startup.xml</strong>. For detailed information on this XML file refer to the <a href="MusrFit.html#MusrfitStartupXml">manual</a>.
|
||||
</li></ul>
|
||||
<p></p>
|
||||
<a name="MusrGuiInstallLinux"></a>
|
||||
<h2><a name="A_3.3_61_61musredit_61_61"></a> 3.3 <code><b>musredit</b></code> </h2>
|
||||
If <code>Qt4.6</code> or higher is set up on the machine the installation of the <code>musrfit</code> editor is also straight forward:
|
||||
<pre class="bash">
|
||||
cd src/musredit
|
||||
qmake musredit.pro
|
||||
</pre>
|
||||
If everything went fine <code>musredit</code> can be compiled and installed:
|
||||
<pre class="bash">
|
||||
make
|
||||
make install
|
||||
</pre>
|
||||
In case one does not like the executable <strong>musredit</strong> to be copied to the default installation directory $ROOTSYS/bin the last "make install" can be skipped and the executable can be copied somewhere else instead. However, the <strong>musredit_startup.xml</strong> should go to the installation directory <strong>MUSRFITPATH</strong> of the <code>musrfit</code> executables.
|
||||
Eventually, in the installed <strong>musredit_startup.xml</strong> the path specifications should be adjusted to match the local <code>musrfit</code> installation. For detailed information on this XML file refer to the <a href="MusrGui.html#MusrguiStartupXml">manual</a>.
|
||||
<p></p>
|
||||
<h2><a name="A_3.4_61_61musrgui_61_61"></a> 3.4 <code><b>musrgui</b></code> </h2>
|
||||
If <code>Qt4.6</code> or higher is not available but <code>Qt3</code> is set up <code>musrgui</code> can be installed. For this please follow the instructions for the <a href="#MusrGuiInstallLinux" class="foswikiCurrentTopicLink">musredit installation</a> where simply every <code>musredit</code> occurrence has to be replaced by <code>musrgui</code>.<br>
|
||||
If there are problems during the <code>qmake</code> step, e.g. "uic: File generated with too old version of Qt Designer", this most probably means the <code>Qt4</code> version of qmake is being used. In order to use the <code>Qt3</code> version it should be enough to specify the full path to its location when calling it. Within the most GNU/Linux distributions this location will be something like /usr/lib/qt-3.3/bin/qmake.
|
||||
<p></p>
|
||||
<h2><a name="A_3.5_Check_of_the_installation"></a> 3.5 Check of the installation </h2>
|
||||
In order to perform a quick test for finding out if the installation has been completed successfully, a few msr files together with the corresponding data files can be found in the <code>musrfit</code> source tree at <strong>src/tests/CheckMusrfitInstall/</strong>.<br>
|
||||
If <code>musrgui</code> has been installed, just open one of the <strong>test-*.msr</strong> files in the editor and test the <code>musrfit</code> functionalities. Otherwise, if only the terminal should be used, as an initial test for instance the following could be done:
|
||||
<pre class="bash">
|
||||
cd src/tests/CheckMusrfitInstall
|
||||
musrview test-histo-ROOT-NPP.msr
|
||||
</pre>
|
||||
<p></p>
|
||||
<p></p>
|
||||
<p></p>
|
||||
Notes
|
||||
<p></p>
|
||||
<a name="FootNote1note"></a><span class="FootNoteLabel"><a href="MusrFitSetup.html#FootNote1text" class="foswikiCurrentWebHomeLink"> <strong>1</strong> </a></span>: <span class="FootNote">In case only a single user is working at the machine it might be considerable to change the ownership of the <code>ROOT</code> folder so that the user has easy write access to this directory: <pre class="bash">chown username:username /opt/root-system/ -R</pre></span>
|
||||
<p></p>
|
||||
<a name="FootNote2note"></a><span class="FootNoteLabel"><a href="MusrFitSetup.html#FootNote2text" class="foswikiCurrentWebHomeLink"> <strong>2</strong> </a></span>: <span class="FootNote"> When using <code>GCC</code> ≥ 4.2 please make sure that the environment variables <strong>USE_PARALLEL_MINUIT2</strong> and <strong>USE_OPENMP</strong> are <em>not</em> set! Otherwise <code>MINUIT2</code> will be compiled with parallelization support and cannot be used together with <code>musrfit</code> afterwards since the <code>musrfit</code> code is <em>not</em> fully thread-safe! When compiled with <code>GCC</code> ≥ 4.2 <code>musrfit</code> itself will parallelize the χ<sup>2</sup> calculation.</span>
|
||||
<p></p>
|
||||
<a name="FootNote3note"></a><span class="FootNoteLabel"><a href="MusrFitSetup.html#FootNote3text" class="foswikiCurrentWebHomeLink"> <strong>3</strong> </a></span>: <span class="FootNote">In case the normal user has no write permissions to the $ROOTSYS and the installation path the "make install" commands have to be executed as superuser.</span>
|
||||
<p></p>
|
||||
<p></p>
|
||||
<p></p>
|
||||
<hr />
|
||||
<p></p>
|
||||
<h1><a name="A_4_MS_Windows"></a> 4 MS Windows </h1>
|
||||
Under Windows a native installation is not supported but there is the possibility to run <code>musrfit</code> through <a href="http://www.cygwin.com/" target="_top">Cygwin</a> which has the great advantage that one gains additionally various nice <code>UNIX</code> tools also for other purposes <img src="../pub/Main/SmiliesPluginPSI/wink.gif" alt="wink" title="wink" border="0" /> <br>
|
||||
<font color="#ff0000">Please also be aware of the fact that the X server which is going to be installed with Cygwin has to be started (e.g. by selecting it from the "Programs" folder) before any graphical application (<code>musrview</code>, <code>musrgui</code>, etc.) is run</font>.
|
||||
<p></p>
|
||||
<font color="#ff00ff">One more advice: Please never try to install either <code>ROOT</code> or <code>musrfit</code> from or to a directory containing spaces in the absolute path or in case you do, do not wonder if some errors occur!<br>
|
||||
msr files, however, might be saved in such directories like ...\My Documents\...</font>
|
||||
<p></p>
|
||||
<h2><a name="A_4.1_Requirements"></a> 4.1 Requirements </h2>
|
||||
<h3><a name="A_4.1.1_Setting_up_Cygwin"></a> 4.1.1 Setting up Cygwin </h3>
|
||||
For the start go to the Cygwin website, download the <a href="http://cygwin.com/setup.exe" target="_top">setup file</a> and use it to install <strong>Cygwin 1.7</strong>. During the installation process you will be asked where you want to install Cygwin and normally the default choice should just be fine.
|
||||
At some point you will be asked which packages should be installed—make sure that you choose at least the following (or packages with revisions close to the following) in order to fulfill the <code>musrfit</code> requirements and be able to work with this base system:
|
||||
<p></p>
|
||||
<code><b>a2ps, alternatives, autoconf, automake, base-cygwin, base-files, base-passwd bash, bash-completion, bc, binutils, bison, boost, boost-devel, bzip2, cmake, colorgcc, coreutils, curl, cygutils, cygwin, editrights, fftw3, findutils, flex, font-adobe-dpi100, font-adobe-dpi75, font-alias, font-bitstream-dpi100, font-bitstream-dpi75, font-encodings, font-ibm-type1, font-sun-misc, font-util, font-xfree86-type1, fontconfig, freeglut, gawk, gcc-tools-autoconf, gcc-tools-automake, gcc4, gcc4-core, gcc4-fortran, gcc4-g++, gccmakedep, gd, gettext, ghostscript, ghostscript-fonts-std, giflib, gmp, grep, groff, gsl, gsl-apps, gsl-devel, gv, gzip, inputproto, jasper, jpeg, lapack, less, libboost, libbz2_1, libcharset1, libcurl4, libfftw3-devel, libfftw3_3, libgcc1, libgd-devel, libgif-devel, libGL-devel, libGL1, libGLU-devel, libGLU1, libglut-devel, libglut3, libgmp-devel libgmp3, libgomp1, libICE-devel, libICE6, libjpeg-devel, libjpeg62, liblapack-devel, libmpfr-devel, libmpfr1, libncurses-devel, libncurses9, libOSMesa-devel, libOSMesa7, libpng, libpng14, libpng14-devel, libreadline6, libSM-devel, libSM6, libssh2_1, libstdc++6, libstdc++6-devel, libtiff-devel, libtiff5, libtool, libX11-devel, libX11_6, libXau-devel, libXau6, libXaw7, libxcb-devel, libxcb-xlib-devel libXcursor-devel, libXcursor1, libXdmcp-devel, libXdmcp6, libXext-devel, libXext6, libXfixes-devel, libXfixes3, libXfont-devel, libXfont1, libXft-devel, libXft2, libXi-devel, libXi6, libxkbfile1, libxml2, libxml2-devel, libXmu-devel, libXmu6, libXpm-devel, libXpm4, libXrender-devel, libXrender1, libXt-devel, libXt6, login, m4, make, makedepend, man, mpfr, nano, opengl, openssh, openssl, pdftk, perl, ping, pkg-config, psutils, python, qt3, qt3-bin, qt3-devel, readline, rebase, rgb, rsync, run, screen, sed, subversion, tar, tcltk, terminfo, unzip, util-linux, vim, w32api, which, X-start-menu-icons, xauth, xextproto, xfontsel, xinit, xkbcomp, xkeyboard-config, xkill, xlogo, xlsfonts, xorg-cf-files, xorg-scripts, xorg-server, xproto, xrdb, xrefresh, xset, xterm, zip, zlib, zlib-devel, zlib0, libQt3Support4-devel, libQtAssistantClient4-devel, libQtCore4-devel, libQtDBus4-devel, libQtDesigner4-devel, libQtGui4-devel, libQtHelp4-devel, libQtNetwork4-devel, libQtOpenGL4-devel, libQtScript4-devel, libQtScriptTools4-devel, libQtSql4-devel, libQtSvg4-devel, libQtTest4-devel, libQtWebKit4-devel, libQtXml4-devel, libQtXmlPatterns4-devel</b></code>
|
||||
<p></p>
|
||||
After these installations already most of the required software is present and the Cygwin shell can be started now for the further steps! Inside the shell the <code>POSIX</code> naming convention applies, therefore, paths will be given with separating <strong>/</strong> instead of <strong>\</strong> in <code>DOS</code>. The file structure accessible through this shell can also be accessed through the Windows Explorer—just go to the directory which you specified as "cygwin root" during the installation: this is the equivalent to <strong>/</strong> in the shell. By default, the different hard drives or network shares like <strong>C:\</strong> can be found at <strong>/cygdrive/c/</strong> in the shell—the cygdrive prefix can in principle also be changed but for now we stick to the default.
|
||||
<p></p>
|
||||
Since later on the <code>boost</code> header files should be used and in the standard Cygwin installation these are found at a version specific location, the later handling will be easier if a symbolic link to these files is created now in the terminal (in case it had not been present before):
|
||||
<pre class="bash">
|
||||
ln -sf /usr/include/boost-x_yy_z/boost /usr/include/boost
|
||||
</pre>
|
||||
where <strong>x_yy_z</strong> has to be substituted by the correct version number, e.g. <strong>1_33_1</strong>.
|
||||
<p></p>
|
||||
<h3><a name="A_4.1.2_Installation_of_61_61NeXus_61_61_requirements_40optional_41"></a> 4.1.2 Installation of <code><b>NeXus</b></code> requirements (optional) </h3>
|
||||
<font color="#ff0000">Only if</font> <code>musrfit</code> should support reading data files in the <code>NeXus</code> format the further <a href="#ReqSwNeXus" class="foswikiCurrentTopicLink">required</a> software has to be set up. Under Cygwin of all the required libraries only <code>HDF5</code> is available. The packages <code><b>hdf5</b></code> and <code><b>libhdf5-devel</b></code> can be installed through the Cygwin setup. One should also make sure that <code><b>bison</b></code>, <code><b>flex</b></code> and a package containing <nobr><b>/usr/lib/librpc.a</b></nobr> (e.g. <code><b>sunrpc</b></code> = <strong>4.0-3</strong>, <font color="#ff0000">but not</font> <code><b>sunrpc</b></code> = <strong>4.0-4</strong>) are installed.
|
||||
<p></p>
|
||||
All other libraries have to be built from the sources. The following lines will track the installation of <code>JPEG</code> <strong>6b</strong>, <code>MXML</code> <strong>2.5</strong>, <code>HDF</code> <strong>4.2.5</strong>, and <code>NeXus</code> <strong>4.2.1</strong>. The version numbers and source-code locations might of course change with time but should be easily adjustable.
|
||||
<pre class="bash">
|
||||
cd
|
||||
mkdir nexus
|
||||
cd nexus
|
||||
curl http://www.hdfgroup.org/ftp/lib-external/jpeg/src/jpegsrc.v6b.tar.gz -G | tar xz
|
||||
cd jpeg-6b
|
||||
./configure --prefix=/usr/local --enable-static
|
||||
make
|
||||
make install
|
||||
cd ..
|
||||
curl http://ftp.easysw.com/pub/mxml/2.5/mxml-2.5.tar.gz -G | tar xz
|
||||
cd mxml-2.5
|
||||
./configure --prefix=/usr/local --enable-static
|
||||
make
|
||||
make install
|
||||
cd ..
|
||||
curl http://www.hdfgroup.org/ftp/HDF/HDF_Current/src/hdf-4.2.5.tar.gz -G | tar xz
|
||||
cd hdf-4.2.5
|
||||
./configure --prefix=/usr/local --enable-static --disable-fortran --with-jpeg=/usr/local
|
||||
make
|
||||
make install
|
||||
cd ..
|
||||
curl http://download.nexusformat.org/kits/nexus-4.2.1.tar.gz -G | tar xz
|
||||
cd nexus-4.2.1
|
||||
./configure --prefix=/usr/local --with-hdf4=/usr/local --with-hdf5=/usr --with-xml=/usr/local
|
||||
make
|
||||
make install
|
||||
</pre>
|
||||
<p></p>
|
||||
<h3><a name="A_4.1.3_61_61ROOT_61_61"></a> 4.1.3 <code><b>ROOT</b></code> </h3>
|
||||
In order to install the <code>ROOT</code> system, there are two possibilities: <ul>
|
||||
<li> Download the precompiled <strong>Cygwin GCC 4.3</strong> package of the most recent <code>ROOT</code> version from the <a href="http://root.cern.ch/drupal/content/downloading-root" target="_top">web page</a> and unpack it <font color="#ff0000">in a Cygwin shell</font> (in order to get the line endings correctly) at the final location. Suppose the package has been downloaded to <strong>C:\</strong> and the <code>ROOT</code> tree should be in <strong>C:\root</strong>, this is achieved by:<pre class="bash">
|
||||
cd /cygdrive/c
|
||||
tar xzf root_v5.xx.yy.win32gcc-gcc-4.3.tar.gz
|
||||
</pre>
|
||||
</li> <li> If due to some reason there was no precompiled <strong>Cygwin GCC 4.3</strong> package available or <code>ROOT</code> should be built from source, one has to visit the <a href="http://root.cern.ch/drupal/content/downloading-root" target="_top">web page</a>, download the 'complete source tree for all systems' and save it for instance in <strong>C:\</strong>.<br>Then go to the Cygwin shell and unpack this source tree, configure<a name="FootNote4text"></a><span class="FootNoteTextLink" title=" When using =GCC= &#8805; 4.2 please make sure that the environment variables *USE_PARALLEL_MINUIT2* and *USE_OPENMP* are <em>not</em> set! Otherwise =MINUIT2= will be compiled with parallelization support and cannot be used together with =musrfit= afterwards since the =musrfit= code is <em>not</em> fully thread-safe! When compiled with =GCC= &#8805; 4.2 =musrfit= itself will parallelize the &chi;<sup>2</sup> calculation."><a href="#FootNote4note" class="foswikiCurrentTopicLink">(2)</a></span> it (here using the minimal set of options) and compile it as follows right below:<pre class="bash">
|
||||
cd /cygdrive/c
|
||||
tar xzf root_v5.xx.yy.source.tar.gz
|
||||
cd root
|
||||
./configure win32gcc --gminimal --enable-asimage --enable-mathmore --enable-minuit2 --enable-xml
|
||||
make
|
||||
</pre>
|
||||
</li></ul>
|
||||
<p></p>
|
||||
In order to finalize the <code>ROOT</code> installation and to prepare already the installation of <code>musrfit</code> and <code>musredit</code> this is a good time for setting necessary environment variables for the use in Cygwin. For accomplishing that put the following lines at the end of the <strong>/home/Username/.bashrc</strong> (<strong>C:\cygwin\home\Username\.bashrc</strong> for the user "Username" and the "cygwin root" at "C:\cygwin"):
|
||||
<pre class="bash">
|
||||
export DISPLAY=:0.0
|
||||
export QTDIR=/usr/lib/qt4
|
||||
export ROOTSYS=/cygdrive/c/root
|
||||
export PATH=$ROOTSYS/bin:$QTDIR/bin:/usr/i686-pc-cygwin/bin:$PATH
|
||||
export MUSRFITPATH=$ROOTSYS/bin
|
||||
</pre>
|
||||
<p></p>
|
||||
Afterwards close the Cygwin shell and reopen it again for the installation of <code>musrfit</code>.
|
||||
<p></p>
|
||||
<h2><a name="A_4.2_61_61musrfit_61_61"></a> 4.2 <code><b>musrfit</b></code> </h2>
|
||||
First, the most recent source code should be downloaded. The preferred way of doing so is to check out directly the subversion repository (if clients of subversion and ssh are installed). Assuming the code should be located in ~/musrfit this is achieved most easily calling from the terminal
|
||||
<pre class="bash">
|
||||
cd
|
||||
svn co svn+ssh://svn@savannah.psi.ch/repos/nemu/lem/trunk/analysis/musrfit musrfit
|
||||
</pre>
|
||||
When asked (twice) for a password, type "svn".
|
||||
If the repository had been checked out already before, one can update the local copy using:
|
||||
<pre class="bash">
|
||||
cd
|
||||
svn up musrfit
|
||||
</pre>
|
||||
<p></p>
|
||||
<font color="#ff0000">As an alternative (if subversion is not available)</font>, the source code can also be downloaded and extracted from a tarball.
|
||||
<pre class="bash">
|
||||
cd
|
||||
curl http://savannah.psi.ch/viewcvs/trunk/analysis/musrfit.tar.gz -G --data-binary root=nemu%2Flem | tar xz
|
||||
</pre>
|
||||
<p></p>
|
||||
After the source-code extraction the <strong>autogen.sh</strong> script is called to prepare the build environment. If it has been executed successfully the <strong>configure</strong> script should be ready to collect all the information needed to create the Makefiles. <font color="#ff0000">If <code>musrfit</code> should support <code>NeXus</code> data files this has to be enabled by specifying the <nobr><b>--enable-static</b></nobr> <nobr><b>--enable-NeXus</b></nobr> switches when calling <strong>configure</strong>.</font> For an overview of all available options just call <code>./configure --help</code>. Besides the standard options there are a few special options which should be mentioned here:
|
||||
<p></p> <dl>
|
||||
<dt> --prefix </dt><dd> Specify the installation prefix, e.g. /opt/root-system (<em>by default: /usr/local</em>)
|
||||
</dd> <dt> --with-rootsys </dt><dd> Specify the top of the <code>ROOT</code> installation directory, e.g. /opt/root-system
|
||||
</dd> <dt> --with-fftw3 </dt><dd> Specify the prefix of the <code>FFTW3</code> installation. e.g. /usr/local or /usr
|
||||
</dd> <dt> --with-gsl </dt><dd> Set the prefix of the <code>GSL</code> installation, e.g. /usr/local or /usr
|
||||
</dd> <dt> --with-boostinc </dt><dd> Set the path to the header files of the <code>Boost</code> installation, e.g. /usr/local/include or /usr/include
|
||||
</dd> <dt> --with-hdf4 </dt><dd> Set the prefix of the <code>HDF4</code> installation, e.g. /usr/local (<em>only useful in conjunction with the <code>NeXus</code> support</em>)
|
||||
</dd> <dt> --with-hdf5 </dt><dd> Set the prefix of the <code>HDF5</code> installation, e.g. /usr (<em>only useful in conjunction with the <code>NeXus</code> support</em>)
|
||||
</dd> <dt> --with-nexus </dt><dd> Set the prefix of the <code>NeXus</code> installation, e.g. /usr/local (<em>only useful in conjunction with the <code>NeXus</code> support</em>)
|
||||
</dd> <dt> --disable-omp </dt><dd> Switches off the <a href="http://en.wikipedia.org/wiki/OpenMP" target="_top">OpenMP</a> features of <code>musrfit</code> (parallelization of the χ<sup>2</sup> calculation when compiled with GCC ≥ 4.2)
|
||||
</dd></dl>
|
||||
<p></p>
|
||||
Normally it should not be necessary to make use of any of the options except for specifying the installation path with <strong>--prefix</strong>. The other paths should be detected automatically. If this does not work for some reason the <strong>configure</strong> script will terminate and ask for the information.
|
||||
When the <strong>configure</strong> script has been called successfully everything is ready for building the <code>musrfit</code> libraries and executables. A standard installation sequence (without <code>NeXus</code> support) might then look like:
|
||||
<pre class="bash">
|
||||
cd musrfit
|
||||
sh autogen.sh
|
||||
./configure --prefix=$ROOTSYS
|
||||
make
|
||||
make install
|
||||
</pre>
|
||||
In order to finish the installation of <code>musrfit</code> the paths where <code>musrfit</code> searches for data files should be adjusted in the installed <strong>musrfit_startup.xml</strong> (/cygdrive/c/root/bin/musrfit_startup.xml or C:\root\bin\musrfit_startup.xml). The paths have to obey the <code>POSIX</code> naming convention. For detailed information on this XML file refer to the <a href="MusrFit.html#MusrfitStartupXml">manual</a>.
|
||||
<p></p>
|
||||
<a name="MusrEditInstallCygwin"></a>
|
||||
<h2><a name="A_4.3_61_61musredit_61_61"></a> 4.3 <code><b>musredit</b></code> </h2>
|
||||
If <code>Qt4.5</code> is set up on the machine the installation of the <code>musrfit</code> editor is also straight forward:
|
||||
<pre class="bash">
|
||||
cd src/musredit
|
||||
qmake-qt4 musredit.pro
|
||||
</pre>
|
||||
If everything went fine <code>musredit</code> can be compiled and installed:
|
||||
<pre class="bash">
|
||||
make
|
||||
make install
|
||||
</pre>
|
||||
Eventually, in the installed <strong>musredit_startup.xml</strong> (<strong>/cygdrive/c/root/bin/musredit_startup.xml</strong> or <strong>C:\root\bin\musredit_startup.xml</strong>) the path specifications should be adjusted to match the local <code>musrfit</code> installation. For detailed information on this XML file refer to the <a href="MusrGui.html#MusrguiStartupXml">manual</a>.
|
||||
<p></p>
|
||||
<hr />
|
||||
In case one likes to get the editor started just with starting the X server from the Windows start menu the file <strong>~/.startxwinrc</strong> with the following contents can be created:<pre class="bash">
|
||||
#!/bin/sh
|
||||
|
||||
export DISPLAY=:0.0
|
||||
export QTDIR=/usr/lib/qt4
|
||||
export ROOTSYS=/cygdrive/c/root
|
||||
export PATH=$ROOTSYS/bin:$QTDIR/bin:/usr/i686-pc-cygwin/bin:$PATH
|
||||
export MUSRFITPATH=$ROOTSYS/bin
|
||||
|
||||
musredit &
|
||||
</pre>
|
||||
<hr />
|
||||
<p></p>
|
||||
<h2><a name="A_4.4_61_61musrgui_61_61"></a> 4.4 <code><b>musrgui</b></code> </h2>
|
||||
If <code>Qt4.5</code> is not available but <code>Qt3</code> is set up <code>musrgui</code> can be installed. For this please follow the instructions for the <a href="#MusrGuiInstallLinux" class="foswikiCurrentTopicLink">musredit installation</a> where simply every <code>musredit</code> occurrence has to be replaced by <code>musrgui</code>, and <code>qt4</code> is replaced by <code>qt3</code>.
|
||||
<p></p>
|
||||
<h2><a name="A_4.5_Check_of_the_installation"></a> 4.5 Check of the installation </h2>
|
||||
In order to perform a quick test for finding out if the installation has been completed successfully, a few msr files together with the corresponding data files can be found in the <code>musrfit</code> source tree at <strong>src/tests/CheckMusrfitInstall/</strong>.<br>
|
||||
If <code>musrgui</code> has been installed, just open one of the <strong>test-*.msr</strong> files in the editor and test the <code>musrfit</code> functionalities. Otherwise, if only the terminal should be used, as an initial test for instance the following could be done:
|
||||
<pre class="bash">
|
||||
cd src/tests/CheckMusrfitInstall
|
||||
musrview test-histo-ROOT-NPP.msr
|
||||
</pre>
|
||||
<p></p>
|
||||
<h2><a name="A_4.6_Possible_problems"></a> 4.6 Possible problems </h2>
|
||||
It might be that especially when running on Windows 7 <code>musredit</code> and <code>musrgui</code> produce errors like a "STATUS_ACCESS_VIOLATION".
|
||||
In this case, try to do the following: Close all Cygwin programs (including the terminals and X server) and run from a Windows command prompt (cmd)<pre class="bash">
|
||||
C:\cygwin\bin\ash.exe /bin/rebaseall
|
||||
</pre>
|
||||
If this does not resolve the problem, try to change the compatibility settings of <strong>C:\cygwin\bin\sh.exe</strong> and <strong>C:\cygwin\bin\bash.exe</strong> so that they are executed with administrator privileges.
|
||||
<p></p>
|
||||
<h1><a name="A_5_Mac_OS_X"></a> 5 Mac OS X </h1>
|
||||
With Mac OS X the situation is up to some extent similar like on MS Windows but still different since Mac OS X is a UNIX system. The similarity is that also on OS X a helping framework—<i>either</i> <code><a href="http://www.macports.org/" target="_top">MacPorts</a></code> <em>or</em> <code><a href="http://www.finkproject.org/" target="_top">Fink</a></code>—which provides open-source software is employed to fulfill the basic software requirements of <code>musrfit</code>. <font color="#ff0000">In the following, both possibilities (using <code>MacPorts</code> or <code>Fink</code>) are described but it is emphasized here that it should be followed <em>only one of the possible routes</em>.</font>
|
||||
<p></p>
|
||||
<h2><a name="A_5.1_Requirements_40_61_61MacPorts_61_61_41"></a> 5.1 Requirements (<code><b>MacPorts</b></code>) </h2>
|
||||
<h3><a name="A_5.1.1_Everything_but_61_61ROOT_61_61_and_61_61NeXus_61_61"></a> 5.1.1 Everything but <code><b>ROOT</b></code> and <code><b>NeXus</b></code> </h3>
|
||||
Before proceeding with the usage of the <code><a href="http://www.macports.org/" target="_top">MacPorts</a></code> system first a few useful tools provided by Apple together with OS X (on the installation DVD/CDs) should be installed: <dl>
|
||||
<dt> <a href="http://developer.apple.com/technology/tools.html" target="_top">Xcode tools</a> </dt><dd> Useful developer tools including for instance the GNU compiler collection
|
||||
</dd> <dt> X11 </dt><dd> The X-window system (automatically installed on 10.5 Leopard and 10.6 Snow Leopard)
|
||||
</dd></dl>
|
||||
<p></p>
|
||||
After installing the Xcode tools go to the <a href="http://www.macports.org/install.php" target="_top">MacPorts install page</a>, download the installer for your system and follow the installation instructions on the page. By default the <code>MacPorts</code> system will be installed in <strong>/opt/local</strong>.<br>
|
||||
To be sure that the newest version of the software is used a <code>MacPorts</code> upgrade should be performed by typing in a terminal:
|
||||
<pre class="bash">
|
||||
sudo port -v selfupdate
|
||||
</pre>
|
||||
<hr />
|
||||
<strong>Remark</strong>: <code>MacPorts</code> uses <a href="http://rsync.samba.org/" target="_top">rsync</a> in order to synchronize the list of available packages. It frequently happens that this service is blocked by firewalls. In this case it should be possible to download a local version of the package repository and do the synchronization.
|
||||
If this step becomes necessary (<strong>and only then</strong>) it can be done in the following way: <ol>
|
||||
<li> Get a local version of the repository:<pre class="bash">
|
||||
svn co http://svn.macports.org/repository/macports/trunk/dports ~/dports
|
||||
</pre>
|
||||
</li> <li> Edit the file <strong>/opt/local/etc/macports/sources.conf</strong>: At the end of the file, comment the line beginning with "rsync://" and add a new line pointing to your local copy, e.g.<pre class="bash">
|
||||
file:///Users/username/dports
|
||||
</pre>
|
||||
</li> <li> Synchronize the packages:<pre class="bash">
|
||||
sudo port -v -d sync
|
||||
</pre>
|
||||
</li></ol>
|
||||
<hr />
|
||||
Then the <code>MacPorts</code> system should be set up and can be used to install additional software.<br>
|
||||
The installation of the software mentioned <a href="#ReqSw" class="foswikiCurrentTopicLink">above</a> is then done in the terminal:
|
||||
<pre class="bash">
|
||||
sudo port -v install pkgconfig autoconf automake libtool fftw-3 fftw-3-single gsl boost libxml2 qt3-mac
|
||||
</pre>
|
||||
Under OS X 10.6 Snow Leopard it will not be possible to install <code><b>qt3-mac</b></code> since the system is by default a 64-bit system and the old <code><b>qt3-mac</b></code> depends on software which is only available for 32-bit systems. It is suggested to install <code><b>qt4-mac</b></code> instead and use <code>musredit</code>. (It would also be possible to install the <code><b>qt3</b></code> port instead; the disadvantage is that the <code><b>qt3</b></code> version does not support Apple's aqua style and a great deal of additional software has to be installed to meet its dependencies. At the moment this seems to be the only possibility to get <code>musrgui</code> running on OS X 10.6.)
|
||||
<p></p>
|
||||
<h3><a name="A_5.1.2_Installation_of_61_61NeXus_61_61_requirements_40optional_41"></a> 5.1.2 Installation of <code><b>NeXus</b></code> requirements (optional) </h3>
|
||||
<p></p>
|
||||
<font color="#ff0000">Only if</font> <code>musrfit</code> should support reading data files in the <code>NeXus</code> format the further <a href="#ReqSwNeXus" class="foswikiCurrentTopicLink">required</a> packages are set up:
|
||||
<pre class="bash">
|
||||
sudo port -v install jpeg6b hdf4 hdf5-18
|
||||
</pre>
|
||||
Unfortunately, the <code>minixml</code> and <code>NeXus</code> libraries have to be compiled and installed directly from the source code. Given the respective version numbers of <strong>2.5</strong> and <strong>4.2.1</strong> (which are subject to change with time) this can be achieved for example by:
|
||||
<pre class="bash">
|
||||
cd
|
||||
curl http://ftp.easysw.com/pub/mxml/2.5/mxml-2.5.tar.gz -G | tar xz
|
||||
cd mxml-2.5
|
||||
./configure --prefix=/usr/local
|
||||
make
|
||||
sudo make install
|
||||
cd ..
|
||||
curl http://download.nexusformat.org/kits/nexus-4.2.1.tar.gz -G | tar xz
|
||||
cd nexus-4.2.1
|
||||
./configure --prefix=/usr/local
|
||||
make
|
||||
sudo make install
|
||||
</pre>
|
||||
<p></p>
|
||||
<h3><a name="A_5.1.3_61_61ROOT_61_61"></a> 5.1.3 <code><b>ROOT</b></code> </h3>
|
||||
For installing the <code>ROOT</code> system there are two <strong>independent</strong> possibilities: <ul>
|
||||
<li> Visit the <code>ROOT</code> <a href="http://root.cern.ch/drupal/content/downloading-root" target="_top">web page</a> and download the packed precompiled binary version matching the OS X version. Then unpack the bundle to its final destination (e.g. /opt/root-system).
|
||||
</li> <li> If there is no precompiled binary version of <code>ROOT</code> available for your system or e.g. <code>ROOT</code> should be compiled with another version of <code>GCC</code> visit the <a href="http://root.cern.ch/drupal/content/downloading-root" target="_top">web page</a> and download the 'complete source tree for all systems'. Then unpack this source tree to its destination (e.g. /opt/root-system). In case only a single user is working at the machine it might be considerable to change the ownership of the <code>ROOT</code> folder so that the user ("username" in the example) has easy write access to this directory: <pre class="bash">sudo chown -R username:staff /opt/root-system/ </pre> Finally, <code>ROOT</code> can be configured (here using the minimal set of options) and compiled as stated right below: <pre class="bash">
|
||||
cd /opt/root-system
|
||||
./configure --gminimal --enable-asimage --enable-mathmore --enable-minuit2 --enable-xml
|
||||
make
|
||||
</pre>
|
||||
</li></ul>
|
||||
<p></p>
|
||||
In order to finalize the <code>ROOT</code> installation and to prepare already the installation of <code>musrfit</code> and <code>musrgui</code> / <code>musredit</code> this is a good time for setting necessary environment variables for the use in Mac OS X. Put the following lines (without the comments in parentheses and with the paths adjusted to your local installation) into the file <strong>~/.MacOSX/environment.plist</strong> and <font color="#ff0000">re-login</font>:<br>
|
||||
<pre class="html">
|
||||
<?xml version="1.0" encoding="UTF-8"?>
|
||||
<!DOCTYPE plist PUBLIC "-//Apple//DTD PLIST 1.0//EN" "http://www.apple.com/DTDs/PropertyList-1.0.dtd">
|
||||
<plist version="1.0">
|
||||
<dict>
|
||||
<key>MUSRFITPATH</key>
|
||||
<string>/opt/root-system/bin</string> (where to find the musrfit executables)
|
||||
<key>QTDIR</key>
|
||||
<string>/opt/local/lib/qt3mac</string> (where to find Qt3 (for musrgui) or Qt4 (for musredit))
|
||||
<key>ROOTSYS</key>
|
||||
<string>/opt/root-system</string> (where to find the ROOT system)
|
||||
</dict>
|
||||
</plist>
|
||||
</pre>
|
||||
<p></p>
|
||||
Additionally, one might want to put a line in <strong>~/.profile</strong> (or <strong>~/.bash_profile</strong>) to look for executables also in the <code>ROOT</code> and <code>Qt</code> binary directories:
|
||||
<pre class="bash">
|
||||
export PATH=$ROOTSYS/bin:$QTDIR/bin:$PATH
|
||||
</pre>
|
||||
<p></p>
|
||||
<h2><a name="A_5.2_Requirements_40_61_61Fink_61_61_41"></a> 5.2 Requirements (<code><b>Fink</b></code>) </h2>
|
||||
<h3><a name="A_5.2.1_Everything_but_61_61ROOT_61_61_and_61_61NeXus_61_61"></a> 5.2.1 Everything but <code><b>ROOT</b></code> and <code><b>NeXus</b></code> </h3>
|
||||
Before proceeding with the usage of the <code><a href="http://www.finkproject.org/" target="_top">Fink</a></code> system first a few useful tools provided by Apple together with OS X (on the installation DVD/CDs) should be installed: <dl>
|
||||
<dt> <a href="http://developer.apple.com/technology/tools.html" target="_top">Xcode tools</a> </dt><dd> Useful developer tools including for instance the GNU compiler collection
|
||||
</dd> <dt> X11 </dt><dd> The X-window-system (automatically installed on 10.5 Leopard and 10.6 Snow Leopard)
|
||||
</dd></dl>
|
||||
<p></p>
|
||||
After installing the Xcode tools go to the <a href="http://www.finkproject.org/download/index.php?phpLang=en" target="_top">Fink download page</a>, download the installer for your system and follow the installation instructions on the page.
|
||||
By default the <code>Fink</code> system is installed in <strong>/sw</strong>. After the basic setup make sure that in <strong>/sw/etc/fink.conf</strong> the line starting with <strong>Trees:</strong> reads like:
|
||||
<pre>
|
||||
Trees: local/main stable/main stable/crypto unstable/main
|
||||
</pre>
|
||||
After applying the changes above to the configuration file, the <code>Fink</code> core system should be upgraded to its newest version by typing in a terminal:
|
||||
<pre class="bash">
|
||||
sudo fink selfupdate
|
||||
</pre>
|
||||
Then the <code>Fink</code> system should be set up and can be used to install additional software.<br>
|
||||
The <code>Fink</code> installer package also contains a graphical user interface called <code>FinkCommander</code> and it is suggested to use that for installing the following packages (or packages with revisions close to the following)—it is necessary to compile a few packages from source since no binary packages are available, however, this is done automatically by the <code>FinkCommander</code> after you have chosen the software packages for installation:
|
||||
<p></p>
|
||||
<code><b>autoconf automake boost1.41.nopython boost1.41.nopython-shlibs fftw3 fftw3-shlibs gsl gsl-shlibs libtool2 libtool2-shlibs libxml2 libxml2-bin libxml2-shlibs pkgconfig qt3mac qt3mac-shlibs</b></code>
|
||||
<p></p>
|
||||
Under OS X 10.6 Snow Leopard it will not be possible to install <code><b>qt3mac</b></code> since the system is by default a 64-bit system and the old <code><b>qt3-mac</b></code> depends on software which is only available for 32-bit systems. It is suggested to install <code><b>qt4mac</b></code> instead and use <code>musredit</code>.
|
||||
<p></p>
|
||||
Also, due to some not fulfilled dependencies, it might not be possible to install FFTW3 through Fink. In this case (<font color="#ff0000">and ONLY in THIS case</font>) simply download the FFTW3 source code from <a href="http://www.fftw.org/download.html" target="_top">its download page</a> and install it from a terminal using the following commands (for the FFTW version 3.x.y):
|
||||
<pre class="bash">
|
||||
tar xz fftw-3.x.y
|
||||
cd fftw-3.x.y
|
||||
./configure --enable-single --enable-shared --enable-threads --prefix=/usr/local
|
||||
make
|
||||
sudo make install
|
||||
</pre>
|
||||
<p></p>
|
||||
Since later on the <code>boost</code> header files should be used and in the standard <code>Fink</code> installation these are found at a version specific location, the later handling will be easier if a symbolic link to this files is created now in the terminal (if it did not exist earlier), e.g.:
|
||||
<pre class="bash">
|
||||
ln -sf /sw/include/boost-x_yy_z/boost /sw/include/boost
|
||||
</pre>
|
||||
where <strong>x_yy_z</strong> has to be substituted by the correct version number, e.g. <strong>1_41_0</strong>.
|
||||
<p></p>
|
||||
<h3><a name="A_5.2.2_Installation_of_61_61NeXus_61_61_requirements_40optional_41"></a> 5.2.2 Installation of <code><b>NeXus</b></code> requirements (optional) </h3>
|
||||
<p></p>
|
||||
<font color="#ff0000">Only if</font> <code>musrfit</code> should support reading data files in the <code>NeXus</code> format the further <a href="#ReqSwNeXus" class="foswikiCurrentTopicLink">required</a> packages can be installed through <code>Fink</code>:
|
||||
<p></p>
|
||||
<code><b>libjpeg hdf hdf5-18 hdf5-18-shlibs</b></code>
|
||||
<p></p>
|
||||
Unfortunately, the <code>minixml</code> and <code>NeXus</code> libraries have to be compiled and installed directly from the source code. Given the respective version numbers of <strong>2.5</strong> and <strong>4.2.1</strong> (which are subject to change with time) this can be achieved for example by:
|
||||
<pre class="bash">
|
||||
cd
|
||||
curl http://ftp.easysw.com/pub/mxml/2.5/mxml-2.5.tar.gz -G | tar xz
|
||||
cd mxml-2.5
|
||||
./configure --prefix=/usr/local
|
||||
make
|
||||
sudo make install
|
||||
cd ..
|
||||
curl http://download.nexusformat.org/kits/nexus-4.2.1.tar.gz -G | tar xz
|
||||
cd nexus-4.2.1
|
||||
./configure --prefix=/usr/local
|
||||
make
|
||||
sudo make install
|
||||
</pre>
|
||||
<p></p>
|
||||
<h3><a name="A_5.2.3_61_61ROOT_61_61"></a> 5.2.3 <code><b>ROOT</b></code> </h3>
|
||||
For installing the <code>ROOT</code> system there are some <strong>independent</strong> possibilities: <ul>
|
||||
<li> Visit the <code>ROOT</code> <a href="http://root.cern.ch/drupal/content/downloading-root" target="_top">web page</a> and download the packed precompiled binary version matching the OS X version. Then unpack the bundle to its final destination (e.g. /opt/root-system).
|
||||
</li> <li> If there is no precompiled binary version of <code>ROOT</code> available for your system or e.g. <code>ROOT</code> should be compiled with another version of <code>GCC</code> visit the <a href="http://root.cern.ch/drupal/content/downloading-root" target="_top">web page</a> and download the 'complete source tree for all systems'. Then unpack this source tree to its destination (e.g. /opt/root-system). In case only a single user is working at the machine it might be considerable to change the ownership of the <code>ROOT</code> folder so that the user ("username" in the example) has easy write access to this directory: <pre class="bash">sudo chown -R username:staff /opt/root-system/ </pre> Finally, <code>ROOT</code> can be configured (here using the minimal set of options) and compiled as stated right below: <pre class="bash">
|
||||
cd /opt/root-system
|
||||
./configure --gminimal --enable-asimage --enable-mathmore --enable-minuit2 --enable-xml
|
||||
make
|
||||
</pre>
|
||||
</li> <li> <code>ROOT</code> is also available through the <code>FinkCommander</code>! Install <strong>root5</strong> or <strong>root5-devel</strong>. However, this versions also have to be compiled locally since there are no binary packages. The manual installation mentioned right above should be preferred in this case.
|
||||
</li></ul>
|
||||
<p></p>
|
||||
In order to finalize the <code>ROOT</code> installation and to prepare already the installation of <code>musrfit</code> and <code>musrgui</code> / <code>musredit</code> this is a good time for setting necessary environment variables for the use in Mac OS X. Put the following lines (without the comments in parentheses and with the paths adjusted to your local installation) into the file <strong>~/.MacOSX/environment.plist</strong> and <font color="#ff0000">re-login</font>:<br>
|
||||
<pre class="html">
|
||||
<?xml version="1.0" encoding="UTF-8"?>
|
||||
<!DOCTYPE plist PUBLIC "-//Apple//DTD PLIST 1.0//EN" "http://www.apple.com/DTDs/PropertyList-1.0.dtd">
|
||||
<plist version="1.0">
|
||||
<dict>
|
||||
<key>MUSRFITPATH</key>
|
||||
<string>/opt/root-system/bin</string> (where to find the musrfit executables)
|
||||
<key>QTDIR</key>
|
||||
<string>/sw/lib/qt3mac</string> (where to find Qt3 (for musrgui) or Qt4 (for musredit))
|
||||
<key>ROOTSYS</key>
|
||||
<string>/opt/root-system</string> (where to find the ROOT system)
|
||||
</dict>
|
||||
</plist>
|
||||
</pre>
|
||||
<p></p>
|
||||
Additionally, one might want to put a line in <strong>~/.profile</strong> (or <strong>~/.bash_profile</strong>) to look for executables also in the <code>ROOT</code> and <code>Qt</code> binary directories:
|
||||
<pre class="bash">
|
||||
export PATH=$ROOTSYS/bin:$QTDIR/bin:$PATH
|
||||
</pre>
|
||||
<p></p>
|
||||
<p></p>
|
||||
<h2><a name="A_5.3_61_61musrfit_61_61"></a> 5.3 <code><b>musrfit</b></code> </h2>
|
||||
First, the most recent source code should be downloaded. The preferred way of doing so is to check out directly the subversion repository (if clients of subversion and ssh are installed). Assuming the code should be located in ~/musrfit this is achieved most easily calling from the terminal
|
||||
<pre class="bash">
|
||||
cd
|
||||
svn co svn+ssh://svn@savannah.psi.ch/repos/nemu/lem/trunk/analysis/musrfit musrfit
|
||||
</pre>
|
||||
When asked (twice) for a password, type "svn".
|
||||
If the repository had been checked out already before, one can update the local copy using:
|
||||
<pre class="bash">
|
||||
cd
|
||||
svn up musrfit
|
||||
</pre>
|
||||
<p></p>
|
||||
<font color="#ff0000">As an alternative (if subversion is not available)</font>, the source code can also be downloaded and extracted from a tarball.
|
||||
<pre class="bash">
|
||||
cd
|
||||
curl http://savannah.psi.ch/viewcvs/trunk/analysis/musrfit.tar.gz -G --data-binary root=nemu%2Flem | tar xz
|
||||
</pre>
|
||||
<p></p>
|
||||
After the source-code extraction the <strong>autogen.sh</strong> script is called to prepare the build environment. If it has been executed successfully the <strong>configure</strong> script should be ready to collect all the information needed to create the Makefiles. <font color="#ff0000">If <code>musrfit</code> should support <code>NeXus</code> data files this has to be enabled by specifying the <strong>--enable-NeXus</strong> switch when calling <strong>configure</strong>.</font> For an overview of all available options just call <code>./configure --help</code>. Besides the standard options there are a few special options which should be mentioned here:
|
||||
<p></p> <dl>
|
||||
<dt> --prefix </dt><dd> Specify the installation prefix, e.g. /opt/root-system (<em>by default: /usr/local</em>)
|
||||
</dd> <dt> --with-rootsys </dt><dd> Specify the top of the <code>ROOT</code> installation directory, e.g. /opt/root-system
|
||||
</dd> <dt> --with-fftw3 </dt><dd> Specify the prefix of the <code>FFTW3</code> installation. e.g. /sw
|
||||
</dd> <dt> --with-gsl </dt><dd> Set the prefix of the <code>GSL</code> installation, e.g. /sw
|
||||
</dd> <dt> --with-boostinc </dt><dd> Set the path to the header files of the <code>Boost</code> installation, e.g. /sw/include
|
||||
</dd> <dt> --with-hdf4 </dt><dd> Set the prefix of the <code>HDF4</code> installation, e.g. /sw (<em>only useful in conjunction with the <code>NeXus</code> support</em>)
|
||||
</dd> <dt> --with-hdf5 </dt><dd> Set the prefix of the <code>HDF5</code> installation, e.g. /sw (<em>only useful in conjunction with the <code>NeXus</code> support</em>)
|
||||
</dd> <dt> --with-nexus </dt><dd> Set the prefix of the <code>NeXus</code> installation, e.g. /usr/local (<em>only useful in conjunction with the <code>NeXus</code> support</em>)
|
||||
</dd> <dt> --disable-omp </dt><dd> Switches off the <a href="http://en.wikipedia.org/wiki/OpenMP" target="_top">OpenMP</a> features of <code>musrfit</code> (parallelization of the χ<sup>2</sup> calculation when compiled with GCC ≥ 4.2)
|
||||
</dd></dl>
|
||||
<p></p>
|
||||
Normally it should not be necessary to make use of any of the options except for specifying the installation path with <strong>--prefix</strong>. The other paths should be detected automatically. If this does not work for some reason the <strong>configure</strong> script will terminate and ask for the information.
|
||||
When the <strong>configure</strong> script has been called successfully everything is ready for building the <code>musrfit</code> libraries and executables. A standard installation sequence (without <code>NeXus</code> support) might then look like:
|
||||
<pre class="bash">
|
||||
cd musrfit
|
||||
sh autogen.sh
|
||||
./configure --prefix=$ROOTSYS
|
||||
make
|
||||
make install
|
||||
</pre>
|
||||
In order to finish the installation of <code>musrfit</code> the paths where <code>musrfit</code> searches for data files should be adjusted in the installed <strong>musrfit_startup.xml</strong> ($ROOTSYS/bin/musrfit_startup.xml). For detailed information on this XML file refer to the <a href="MusrFit.html#MusrfitStartupXml">manual</a>.
|
||||
<p></p>
|
||||
<a name="MusrGuiInstall"></a>
|
||||
<h2><a name="A_5.4_61_61musredit_61_61"></a> 5.4 <code><b>musredit</b></code> </h2>
|
||||
If <code>Qt4.6</code> or higher is set up on the machine the installation of the <code>musrfit</code> editor is also straight forward:
|
||||
<pre class="bash">
|
||||
cd src/musredit
|
||||
qmake musredit.pro
|
||||
</pre>
|
||||
If everything went fine <code>musredit</code> can be compiled and installed:
|
||||
<pre class="bash">
|
||||
make
|
||||
make install
|
||||
</pre>
|
||||
The last command copies <strong>musredit.app</strong> to the standard program directory <strong>/Applications</strong> and the <strong>musredit_startup.xml</strong> to <strong>$ROOTSYS/bin/musredit_startup.xml</strong>. Eventually, in the installed <strong>musredit_startup.xml</strong> the path specifications have to be adjusted to match the local <code>musrfit</code> installation. For detailed information on this XML file refer to the <a href="MusrGui.html#MusrguiStartupXml">manual</a>.
|
||||
<p></p>
|
||||
<h2><a name="A_5.5_61_61musrgui_61_61"></a> 5.5 <code><b>musrgui</b></code> </h2>
|
||||
If <code>Qt3</code> is set up the installation of the <code>musrfit</code> editor can be done as follows from within the shell:
|
||||
<pre class="bash">
|
||||
cd src/musrgui
|
||||
qmake musrgui.pro
|
||||
make
|
||||
make install
|
||||
</pre>
|
||||
The last command copies <strong>musrgui.app</strong> to the standard program directory <strong>/Applications</strong> <a name="FootNote5text"></a><span class="FootNoteTextLink" title="In the case ==qt3-mac== has not been installed, there will be no *musrgui.app* but only the executable *musrgui* which will be placed in the directory *$ROOTSYS/bin* and has to be called from the terminal."><a href="#FootNote5note" class="foswikiCurrentTopicLink">(4)</a></span> and the <strong>musrgui_startup.xml</strong> to <strong>$ROOTSYS/bin/musrgui_startup.xml</strong>. Eventually, in the installed <strong>musrgui_startup.xml</strong> the path-specifications have to be adjusted to match the local <code>musrfit</code> installation. For detailed information on this XML file refer to the <a href="MusrGui.html#MusrguiStartupXml">manual</a>.
|
||||
<p></p>
|
||||
Under some circumstances it might happen, that if <code>musrgui</code> was called from <code>Finder</code> the necessary libraries for executing <code>musrfit</code> could not be found.
|
||||
In that case, the only workaround for the moment is to export the environment variable <strong>DYLD_LIBRARY_PATH</strong> in the shell and call <code>musrgui</code> from a terminal!
|
||||
In order to accomplish that, add the following lines to <strong>~/.profile</strong> and call <code>musrgui</code> with the specified command (e.g. mgui):
|
||||
<pre class="bash">
|
||||
export DYLD_LIBRARY_PATH=/opt/root-system/lib:/sw/lib:$DYLD_LIBRARY_PATH
|
||||
alias mgui='/Applications/musrgui.app/Contents/MacOS/musrgui'
|
||||
</pre>
|
||||
<p></p>
|
||||
<p></p>
|
||||
<p></p>
|
||||
Notes
|
||||
<p></p>
|
||||
<a name="FootNote5note"></a><span class="FootNoteLabel"><a href="MusrFitSetup.html#FootNote5text" class="foswikiCurrentWebHomeLink"> <strong>4</strong> </a></span>: <span class="FootNote">In the case <code><b>qt3-mac</b></code> has not been installed, there will be no <strong>musrgui.app</strong> but only the executable <strong>musrgui</strong> which will be placed in the directory <strong>$ROOTSYS/bin</strong> and has to be called from the terminal.</span>
|
||||
<p></p>
|
||||
<p></p>
|
||||
<p></p>
|
||||
<hr />
|
||||
<p></p>
|
||||
<h2><a name="A_5.6_Check_of_the_installation"></a> 5.6 Check of the installation </h2>
|
||||
In order to perform a quick test for finding out if the installation has been completed successfully, a few msr files together with the corresponding data files can be found in the <code>musrfit</code> source tree at <strong>src/tests/CheckMusrfitInstall/</strong>.<br>
|
||||
If <code>musrgui</code> has been installed, just open one of the <strong>test-*.msr</strong> files in the editor and test the <code>musrfit</code> functionalities. Otherwise, if only the terminal should be used, as an initial test for instance the following could be done:
|
||||
<pre class="bash">
|
||||
cd src/tests/CheckMusrfitInstall
|
||||
musrview test-histo-ROOT-NPP.msr
|
||||
</pre>
|
||||
<p></p>
|
||||
-- <a href="http://www.fsf.org/register_form?referrer=8369" target="_top">BMW</a> & <a href="http://lmu.web.psi.ch/lem/group.html" target="_top">AS</a></div><!-- /foswikiTopic-->
|
||||
<p></p>
|
||||
</div><!-- /patternContent-->
|
||||
<hr />
|
||||
This topic: MUSR<span class='foswikiSeparator'> > </span><a href="WebHome.html" class="foswikiCurrentWebHomeLink">WebHome</a> > <a href="MusrFit.html">MusrFit</a><span class='foswikiSeparator'> > </span>MusrFitSetup <br />
|
||||
Topic revision: r46 - 11 Jul 2011 - 20:24:58 - <a href="https://intranet.psi.ch/Main/BastianWojek">BastianWojek</a>
|
||||
</div>
|
||||
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|
||||
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|
||||
<div class="clear"> </div>
|
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</div><div id="patternBottomBar"><div id="patternBottomBarContents"><div id="patternWebBottomBar">Ideas, requests, problems regarding <a href="https://intranet.psi.ch/Main/WebHome">PSI Wiki</a>? <a href="mailto:psi.intranet@psi.ch?subject=Foswiki%20Feedback%20on%20MUSR.MusrFitSetup">Send feedback</a></div></div></div>
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|
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|
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|
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|
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|
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|
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|
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|
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|
||||
<p></p>
|
||||
<p></p>
|
||||
<p></p>
|
||||
345
doc/html/MUSR/MusrGui.html
Normal file
345
doc/html/MUSR/MusrGui.html
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<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
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<html lang="en_US">
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<link rel="stylesheet" href="../pub/System/HeadlinesPlugin/style.css" type="text/css" media="all" />
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<link rel="alternate" href="https://intranet.psi.ch/wiki/bin/edit/MUSR/MusrGui?t=1312204524" type="application/x-wiki" title="edit MusrGui" />
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<style type="text/css" media="all">
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@import url('../pub/System/SkinTemplates/base.css');
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</style>
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<style type="text/css" media="all">
|
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@import url('../pub/System/PatternSkinTheme2009/layout.css');
|
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@import url('../pub/System/PatternSkinTheme2009/style.css');
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@import url('../pub/System/PatternSkinTheme2009/colors.css');
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</style>
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<style type="text/css" media="all">
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@import url('../pub/System/PatternSkinTheme2009/column_left.css');
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</style><style type="text/css" media="all">
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.patternBookView .foswikiTopRow,
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.patternWebIndicator a img,
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.patternWebIndicator a:hover img {
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background-color:#D0D0D0;
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}
|
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#patternTopBarContents { background-image:url(../pub/System/PatternSkin/header5.gif); background-repeat:repeat-x;}
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#patternTopBarContents { background-color:#ffffff;}
|
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.patternBookView {
|
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border-color:#D0D0D0;
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}
|
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.patternPreviewPage #patternMain {
|
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/* uncomment to set the preview image */
|
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/*background-image:url("/pub/System/PreviewBackground/preview2bg.gif");*/
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</style>
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<style type="text/css" media="all">
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@import url("../pub/System/PsiSkin/psicolors.css");
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@import url("../pub/System/PsiSkin/psistyle.css");
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#patternSideBarContents h2,
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#patternSideBarContents li,
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#patternTopBarButtons ul {
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height:1%;
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width:100%;
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box-shadow: 0 0 10px #ccc;
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<script src="https://intranet.psi.ch/pub/System/ChecklistPlugin/itemstatechange.js" language="javascript" type="text/javascript"></script><script src="https://intranet.psi.ch/pub/System/TimeTablePlugin/timetabletooltips.js" language="javascript" type="text/javascript"></script></head>
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<div id="patternMainContents">
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<div class="patternContent"><div class="foswikiTopic">
|
||||
<h1><a name="A_61_61musrgui_47_musredit_61_61"></a> <code><b>musrgui / musredit</b></code> </h1>
|
||||
<p></p>
|
||||
<a name="foswikiTOC"></a><div class="foswikiToc"> <ul>
|
||||
<li> <a href="MusrGui.html#A_61_61musrgui_47_musredit_61_61"> musrgui / musredit </a>
|
||||
</li> <li> <a href="MusrGui.html#A_1_Introduction"> 1 Introduction </a>
|
||||
</li> <li> <a href="MusrGui.html#A_2_Available_Executables_44_Configuration_Files_and_their_Basic_Usage"> 2 Available Executables, Configuration Files and their Basic Usage </a> <ul>
|
||||
<li> <a href="MusrGui.html#A_2.1_musrgui_47_musredit"> 2.1 musrgui / musredit </a>
|
||||
</li> <li> <a href="MusrGui.html#A_2.2_musrgui_startup.xml_47_musredit_startup.xml"> 2.2 musrgui_startup.xml / musredit_startup.xml </a>
|
||||
</li></ul>
|
||||
</li> <li> <a href="MusrGui.html#A_3_61_61musrfit_61_61_Features"> 3 musrfit Features </a>
|
||||
</li> <li> <a href="MusrGui.html#A_4_Editor_Features"> 4 Editor Features </a>
|
||||
</li> <li> <a href="MusrGui.html#A_5_Bugtracking"> 5 Bugtracking </a>
|
||||
</li></ul>
|
||||
</div>
|
||||
<p></p>
|
||||
<h1><a name="A_1_Introduction"></a> 1 Introduction </h1>
|
||||
<code>musrgui</code> and <code>musredit</code> are editors which also provide a graphical user interface to the programs contained in the <code><a href="MusrFit.html">musrfit</a></code> suite and are intended to help the user handle <code>musrfit</code> msr files. They are implemented in <code>C++</code> and use the <a href="http://qt.nokia.com/" target="_top">Qt</a> framework. Principally, <code>musrgui</code> and <code>musredit</code> are doing the same, but are based on different Qt versions. <code>musrgui</code> is based on Qt 3.x and will only be maintained on bug-fixing level since the Qt 3.x licensing is less straight forward than the Qt 4.x one. <code>musredit</code> is based on Qt 4.6 (or above) and this is the program which will be developed further.<br>
|
||||
On this documentation page only the features related to <code>musrfit</code> are described—the basic editor functions which should be self-explanatory are not.
|
||||
<strong><font color="#ff0000">Before going on using <code>musrgui</code> / <code>musredit</code> it is strongly recommended to read the <a href="MusrFit.html">manual</a> of <code>musrfit</code> first!</font></strong>
|
||||
<p></p>
|
||||
<h1><a name="A_2_Available_Executables_44_Configuration_Files_and_their_Basic_Usage"></a> 2 Available Executables, Configuration Files and their Basic Usage </h1>
|
||||
<a name="MusrEdit"></a>
|
||||
<h2><a name="A_2.1_musrgui_47_musredit"></a> 2.1 musrgui / musredit </h2>
|
||||
<code>musrgui</code> / <code>musredit</code> are the editor executables. If called from within a shell they accept a few optional parameters: <dl>
|
||||
<dt> <msr_files> </dt><dd> file names of the msr files that should be opened in separate editor tabs on startup of <code>musrgui</code> / <code>musredit</code>.
|
||||
</dd> <dt> --help </dt><dd> displays a small help notice in the shell explaining the basic usage of the program
|
||||
</dd> <dt> --version </dt><dd> prints the version number of <code>musrgui</code> / <code>musredit</code>
|
||||
</dd></dl>
|
||||
<p></p>
|
||||
If called without any parameters an empty editor window opens.
|
||||
<p></p>
|
||||
<a name="MusreditStartupXml"></a>
|
||||
<h2><a name="A_2.2_musrgui_startup.xml_47_musredit_startup.xml"></a> 2.2 musrgui_startup.xml / musredit_startup.xml </h2>
|
||||
<code><b>musrgui_startup.xml</b></code> / <code><b>musredit_startup.xml</b></code> are configuration files located at the <code>musrgui</code> / <code>musredit</code> binary path. It is also possible to have another version of this file in the working directory which then will be used!
|
||||
<p></p>
|
||||
In this file the following XML tags are allowed to define settings and might proof useful for all users of <code>musrgui</code> / <code>musredit</code>: <dl>
|
||||
<dt> <general></general> </dt><dd> set the default paths to executables and files in this environment <dl>
|
||||
<dt> <exec_path>PATH_TO_EXEC</exec_path> </dt><dd> set the path <strong>PATH_TO_EXEC</strong> where the executables <code>musrfit</code>, <code>musrview</code>, <code>musrt0</code>, etc. can be found (inside the <general> environment)
|
||||
</dd> <dt> <default_save_path>SAV_PATH</default_save_path> </dt><dd> specify the path <strong>SAV_PATH</strong> where <code>musrgui</code> / <code>musredit</code> point by default when opening and saving msr files (inside the <general> environment)
|
||||
</dd> <dt> <msr_default_file_path>MSR_DEF_PATH</msr_default_file_path> </dt><dd> set the path <strong>MSR_DEF_PATH</strong> where the <a href="#MusrfitFeatures" class="foswikiCurrentTopicLink">default msr files provided by</a> <code>musrgui</code> are stored (inside the <general> environment)
|
||||
</dd> <dt> <title_from_data_file>y/n</title_from_data_file> </dt><dd> specify if <code>musrfit</code> should be called with the <a href="MusrFit.html#MusrFit">-t option</a> by default (inside the <general> environment)
|
||||
</dd> <dt> <enable_musrt0>y/n</enable_musrt0> </dt><dd> specify if <code><a href="MusrFit.html#MusrT0">musrt0</a></code> can be called from within <code>musrgui</code> / <code>musredit</code> (inside the <general> environment)
|
||||
</dd></dl>
|
||||
</dd> <dt> <font_settings></font_settings> </dt><dd> set the default font in this environment <dl>
|
||||
<dt> <font_name>FONT</font_name> </dt><dd> specify the name of the font <strong>FONT</strong> to be used by default in <code>musrgui</code> / <code>musredit</code> (inside the <font_settings> environment)
|
||||
</dd> <dt> <font_size>N</font_size> </dt><dd> specify the size <strong>N</strong> of the font to be used by default in <code>musrgui</code> / <code>musredit</code> (inside the <font_settings> environment)
|
||||
</dd></dl>
|
||||
</dd> <dt> <msr_file_defaults></msr_file_defaults> </dt><dd> put the default settings for newly created msr files in this environment <dl>
|
||||
<dt> <beamline>BL</beamline> </dt><dd> set the name of the muon beamline <strong>BL</strong> here (inside a <msr_file_defaults>-environment)
|
||||
</dd> <dt> <institute>INST</institute> </dt><dd> set the name of the facility <strong>INST</strong> where the beamline <strong>BL</strong> is located. Valid settings are <strong>PSI</strong>, <strong>RAL</strong>, <strong>JPARC</strong>, and <strong>TRIUMF</strong> (inside a <msr_file_defaults> environment)
|
||||
</dd> <dt> <file_format>FF</file_format> </dt><dd> specify the default data file format <strong>FF</strong> here. Valid formats are <strong>NEXUS</strong>, <strong>ROOT-NPP</strong>, <strong>ROOT-PPC</strong>, <strong>PSI-BIN</strong>, <strong>PSI-MDU</strong>, <strong>MDU-ASCII</strong>, <strong>WKM</strong>, <strong>MUD</strong>, <strong>ASCII</strong>, and <strong>DB</strong> (inside a <msr_file_defaults> environment)
|
||||
</dd> <dt> <lifetime_correction>y/n</lifetime_correction> </dt><dd> choose if by default the <strong>lifetimecorrection</strong> <a href="MusrFit.html#LifeTimeCorrection">option</a> should be set (inside a <msr_file_defaults> environment)
|
||||
</dd></dl>
|
||||
</dd> <dt> <msr2data_defaults></msr2data_defaults> </dt><dd> define the default <a href="Msr2Data.html#OptionalParameters">options</a> for calling <code><a href="Msr2Data.html">msr2data</a></code> in this environment; the options set here are ticked by default in the <a href="Msr2Data.html#MusrGuiInterface">graphical interface</a> of <code>musrgui</code> / <code>musredit</code>. <dl>
|
||||
<dt> <chain_fit>y/n</chain_fit> </dt><dd> (un)set the chain fit (<strong>!</strong>) option (inside a <msr2data_defaults> environment)
|
||||
</dd> <dt> <write_data_header>y/n</write_data_header> </dt><dd> (un)set the <strong>noheader</strong> option (inside a <msr2data_defaults> environment)
|
||||
</dd> <dt> <ignore_data_header_info>y/n</ignore_data_header_info> </dt><dd> (un)set the <strong>nosummary</strong> option (inside a <msr2data_defaults> environment)
|
||||
</dd> <dt> <keep_minuit2_output>y/n</keep_minuit2_output> </dt><dd> (un)set the <strong>-k</strong> option (inside a <msr2data_defaults> environment)
|
||||
</dd> <dt> <write_column_data>y/n</write_column_data> </dt><dd> (un)set the <strong>data</strong> option (inside a <msr2data_defaults> environment)
|
||||
</dd> <dt> <create_msr_file_only>y/n</create_msr_file_only> </dt><dd> (un)set the <strong>msr</strong> option in case a template run is specified (inside a <msr2data_defaults> environment)
|
||||
</dd> <dt> <fit_only>y/n</fit_only> </dt><dd> (un)set the <strong>fit</strong> option in case no template run is specified (inside a <msr2data_defaults> environment)
|
||||
</dd> <dt> <global>y/n</global> </dt><dd> (un)set the <strong>global</strong> option (inside a <msr2data_defaults> environment)
|
||||
</dd> <dt> <global_plus>y/n</global_plus> </dt><dd> (un)set the <strong>global+</strong> option (inside a <msr2data_defaults> environment)
|
||||
</dd> <dt> <recreate_data_file>y/n</recreate_data_file> </dt><dd> (un)set the <code>musrgui</code> / <code>musredit</code> option for recreating the output file (inside a <msr2data_defaults> environment)
|
||||
</dd> <dt> <open_file_after_fitting>y/n</open_file_after_fitting> </dt><dd> (un)set the <code>musrgui</code> / <code>musredit</code> option for opening msr files after fitting (inside a <msr2data_defaults> environment)
|
||||
</dd></dl>
|
||||
</dd></dl>
|
||||
<p></p>
|
||||
Additionally, there are some settings defined in this XML file which should be only changed by experienced users who like to add new features to <code>musrgui</code> / <code>musredit</code>: <dl>
|
||||
<dt> <help_section></help_section> </dt><dd> define various help messages in this environment <dl>
|
||||
<dt> <help_main>HELP TEXT</help_main> </dt><dd> set the main help message <strong>HELP TEXT</strong> here (inside a <help_section> environment)
|
||||
</dd></dl>
|
||||
</dd> <dt> <func_pixmap_path>PIX_PATH</func_pixmap_path> </dt><dd> set the path <strong>PIX_PATH</strong> to <img alt="LaTeX_logo.png" src="../pub/MUSR/MusrGui/LaTeX_logo.png" /> pixmaps visualizing the various supported theory functions
|
||||
</dd> <dt> <theory_functions></theory_functions> </dt><dd> define the functions for a msr file's THEORY block <a href="MusrFit.html#TheoryTable">according to the correct syntax</a> in this environment <dl>
|
||||
<dt> <func></func> </dt><dd> specify a function here (inside a <theory_functions> environment) <dl>
|
||||
<dt> <name>NAME</name> </dt><dd> the <strong>NAME</strong> of the function in the msr file (inside a <func> environment)
|
||||
</dd> <dt> <comment>COMMENT</comment> </dt><dd> description of the used parameters (inside a <func> environment)
|
||||
</dd> <dt> <label>LABEL</label> </dt><dd> <strong>LABEL</strong> of the function in the <code>musrgui</code> / <code>musredit</code> menu (inside a <func> environment)
|
||||
</dd> <dt> <pixmap>PIXMAP</pixmap> </dt><dd> <img alt="LaTeX_logo.png" src="../pub/MUSR/MusrGui/LaTeX_logo.png" /> picture used to describe the function and stored in the <strong>PIX_PATH</strong> (inside a <func> environment)
|
||||
</dd> <dt> <params>N</params> </dt><dd> number of parameters <strong>N</strong> used by the function (inside a <func> environment)
|
||||
</dd></dl>
|
||||
</dd></dl>
|
||||
</dd></dl>
|
||||
<p></p>
|
||||
An example of the <code><b>musrgui_startup.xml</b></code> looks like:
|
||||
<pre class="html">
|
||||
<?xml version="1.0" encoding="UTF-8"?>
|
||||
<musrgui_startup xmlns="https://intranet.psi.ch/MUSR/MusrGui">
|
||||
<general>
|
||||
<exec_path>/usr/local/bin</exec_path>
|
||||
<default_save_path>./</default_save_path>
|
||||
<msr_default_file_path>/home/user/analysis/musrfit/src/musrgui</msr_default_file_path>
|
||||
</general>
|
||||
<font_settings>
|
||||
<font_name>Courier New</font_name>
|
||||
<font_size>10</font_size>
|
||||
</font_settings>
|
||||
<msr_file_defaults>
|
||||
<beamline>mue4</beamline>
|
||||
<institute>psi</institute>
|
||||
<file_format>root-npp</file_format>
|
||||
<lifetime_correction>y</lifetime_correction>
|
||||
</msr_file_defaults>
|
||||
<msr2data_defaults>
|
||||
<chain_fit>y</chain_fit>
|
||||
<write_data_header>y</write_data_header>
|
||||
<ignore_data_header_info>n</ignore_data_header_info>
|
||||
<keep_minuit2_output>n</keep_minuit2_output>
|
||||
<write_column_data>n</write_column_data>
|
||||
<recreate_data_file>n</recreate_data_file>
|
||||
<open_file_after_fitting>y</open_file_after_fitting>
|
||||
<create_msr_file_only>n</create_msr_file_only>
|
||||
<fit_only>n</fit_only>
|
||||
<global>n</global>
|
||||
<global_plus>n</global_plus>
|
||||
</msr2data_defaults>
|
||||
<help_section>
|
||||
<help_main>
|
||||
For a detailed description of the aim and structure of a msr file see http://lmu.web.psi.ch/facilities/software/musrfit/user/MUSR/MusrFit.html
|
||||
</help_main>
|
||||
</help_section>
|
||||
<func_pixmap_path>/home/user/analysis/musrfit/src/musrgui/latex_images</func_pixmap_path>
|
||||
<theory_functions>
|
||||
<func>
|
||||
<name>asymmetry</name>
|
||||
<comment></comment>
|
||||
<label>Asymmetry</label>
|
||||
<pixmap>asymmetry.png</pixmap>
|
||||
<params>1</params>
|
||||
</func>
|
||||
<func>
|
||||
<name>simplExpo</name>
|
||||
<comment>(rate)</comment>
|
||||
<label>simple Exp</label>
|
||||
<pixmap>simpleExp.png</pixmap>
|
||||
<params>1</params>
|
||||
</func>
|
||||
<func>
|
||||
<name>simplGss</name>
|
||||
<comment>(rate)</comment>
|
||||
<label>simple Gauss</label>
|
||||
<pixmap>simpleGauss.png</pixmap>
|
||||
<params>1</params>
|
||||
</func>
|
||||
</theory_function>
|
||||
</musrgui_startup>
|
||||
</pre>
|
||||
<p></p>
|
||||
<a name="MusrfitFeatures"></a>
|
||||
<h1><a name="A_3_61_61musrfit_61_61_Features"></a> 3 <code><b>musrfit</b></code> Features </h1>
|
||||
The features of <code>musrfit</code> which can be accessed by the graphical front ends <code>musrgui</code> / <code>musredit</code> are described in the following. All functions can either be called by choosing them from the MusrFit menu, by clicking the respective button in the MusrFit bar, or by using a keyboard shortcut.
|
||||
<p></p> <dl>
|
||||
<dt> <img alt="musrasym.png" src="../pub/MUSR/MusrGui/musrasym.png" /> Asymmetry Default (Alt+a) </dt><dd> Generate a full msr file suitable for the <a href="MusrFit.html#FitTypes">fit type</a> <strong>2</strong> of <code>musrfit</code> from defaults. Calling this function opens a window where the relative path and file name to a data file as well as the file format that should be used have to be specified. For instance if the data file <code><b>/path-to-datadir/2007/lem07_his_8472.root</b></code> should be used and <code><b>/path-to-datadir</b></code> is on the path where <code>musrfit</code> <a href="MusrFit.html#PathToDataFiles">looks for data files</a> then the file name would be <code><b>2007/lem07_his_8472</b></code> and the file format either <strong>ROOT-NPP</strong> or <strong>ROOT-PPC</strong>.
|
||||
</dd></dl>
|
||||
<p></p> <dl>
|
||||
<dt> <img alt="musrsinglehisto.png" src="../pub/MUSR/MusrGui/musrsinglehisto.png" /> Single-Histogram Default (Alt+h) </dt><dd> Generate a full msr file suitable for the <a href="MusrFit.html#FitTypes">fit type</a> <strong>0</strong> of <code>musrfit</code> from defaults. Calling this function opens a window where the relative path and file name to a data file as well as the file format that should be used have to be specified. For instance if the data file <code><b>/path-to-datadir/d2007/deltat_pta_gps_8472.bin</b></code> should be used and <code><b>/path-to-datadir</b></code> is on the path where <code>musrfit</code> <a href="MusrFit.html#PathToDataFiles">looks for data files</a> then the file name would be <code><b>d2007/deltat_pta_gps_8472</b></code> and the file format <strong>PSI-BIN</strong>.
|
||||
</dd></dl>
|
||||
<p></p> <dl>
|
||||
<dt> <img alt="musrcalcchisq.png" src="../pub/MUSR/MusrGui/musrcalcchisq.png" /> Calculate Chisq (Alt+c) </dt><dd> <pre class="bash">musrfit <msr_file> --chisq-only</pre> is called for the <strong><msr_file></strong> selected in the editor. For further information refer to the <a href="MusrFit.html#MusrFit">manual</a> of <code>musrfit</code>.
|
||||
</dd></dl>
|
||||
<p></p> <dl>
|
||||
<dt> <img alt="musrfit.png" src="../pub/MUSR/MusrGui/musrfit.png" /> Fit (Alt+f) </dt><dd> <pre class="bash">musrfit <msr_file> [optional parameters]</pre> is called for the <strong><msr_file></strong> selected in the editor. The optional parameters may be chosen under <a href="#MusrPrefs" class="foswikiCurrentTopicLink">Preferences</a>. For further information refer to the <a href="MusrFit.html#MusrFit">manual</a> of <code>musrfit</code>.
|
||||
</dd></dl>
|
||||
<p></p> <dl>
|
||||
<dt> <img alt="musrswap.png" src="../pub/MUSR/MusrGui/musrswap.png" /> Swap Msr ↔ Mlog (Alt+s) </dt><dd> Swap the msr and mlog files. E.g., for a file called <code><b>8472_zf.msr</b></code>, this is copied to <code><b>8472_zf.mlog</b></code> and vice versa.
|
||||
</dd></dl>
|
||||
<p></p> <dl>
|
||||
<dt> <img alt="musrmsr2data.png" src="../pub/MUSR/MusrGui/musrmsr2data.png" /> Msr2data (Alt+m) </dt><dd> Opens a graphical interface to the <code>msr2data</code> program described in detail in its own <a href="Msr2Data.html#MusrGuiInterface">manual</a>.
|
||||
</dd></dl>
|
||||
<p></p> <dl>
|
||||
<dt> <img alt="musrview.png" src="../pub/MUSR/MusrGui/musrview.png" /> View (Alt+v) </dt><dd> <pre class="bash">musrview <msr_file></pre> is called for the <strong><msr_file></strong> selected in the editor. For further information refer to the <a href="MusrFit.html#MusrView">manual</a> of <code>musrfit</code>.
|
||||
</dd></dl>
|
||||
<p></p> <dl>
|
||||
<dt> <img alt="musrt0.png" src="../pub/MUSR/MusrGui/musrt0.png" /> T0 (Alt+t) </dt><dd> <pre class="bash">musrt0 <msr_file></pre> is called for the <strong><msr_file></strong> selected in the editor. For further information refer to the <a href="MusrFit.html#MusrT0">manual</a> of <code>musrfit</code>.
|
||||
</dd></dl>
|
||||
<p></p>
|
||||
<a name="MusrPrefs"></a> <dl>
|
||||
<dt> <img alt="musrprefs.png" src="../pub/MUSR/MusrGui/musrprefs.png" /> Preferences (Alt+p) </dt><dd> Opens a window in which the optional parameters that should be passed to <code>musrfit</code> can be chosen. These options are <code><b>--keep-mn2-output</b></code>, <code><b>--dump ascii</b></code>, <code><b>--dump root</b></code>, and <code><b>--title-from-data-file</b></code>. For further information refer to the <a href="MusrFit.html#MusrFit">manual</a> of <code>musrfit</code>. Additionally, the access to <code>musrt0</code> can be enabled temporarily.
|
||||
</dd></dl>
|
||||
<p></p>
|
||||
<a name="EditorFeatures"></a>
|
||||
<h1><a name="A_4_Editor_Features"></a> 4 Editor Features </h1>
|
||||
Besides the functions described above and which are mostly interfacing <code>musrfit/msr2data</code> the editors of <code>musrgui</code> / <code>musredit</code> offer various functions for manipulating especially <code>musrfit</code> msr files:
|
||||
<img src="../pub/MUSR/MusrGui/musrgui-editor-v0.png" alt="musrgui editor features" width='415' height='566' align="right" /> <ul>
|
||||
<li> Upon right-clicking an open msr file a menu as shown to the right is displayed which offers the addition of any valid msr file block or theory function. In case a simple theory function is chosen, the function will be inserted into the THEORY block using the <a href="MusrFit.html#TheoryTable">correct syntax</a>. If one chooses to add a whole block to the file a dialog opens in which the necessary information for each block as described in the <a href="MusrFit.html#DescriptionOfTheMsrFileFormat">manual</a> of <code>musrfit</code> can be supplied. <font color="#0000ff">This feature is available only in <code>musrgui</code>. In <code>musredit</code> the respective functions can be accessed through the <em>Edit</em> menu.</font>
|
||||
</li> <li> In order to comment or uncomment lines in a msr file select the according lines and apply <strong>Edit → (Un)Comment</strong> or use the keyboard shortcut <strong>Ctrl+(Shift)+m</strong>.
|
||||
</li></ul>
|
||||
<p></p>
|
||||
<a name="BugTracking"></a>
|
||||
<h1><a name="A_5_Bugtracking"></a> 5 Bugtracking </h1>
|
||||
<p></p>
|
||||
For reporting bugs or requesting new features and improvements please use the <a href="https://tracker.intranet.psi.ch/jira/browse/MUSR" target="_top">PSI Tracker</a> or send an e-mail to A. Suter.
|
||||
<p></p>
|
||||
-- <a href="http://www.fsf.org/register_form?referrer=8369" target="_top">BMW</a> & <a href="http://lmu.web.psi.ch/lem/group.html" target="_top">AS</a></div><!-- /foswikiTopic-->
|
||||
<p></p>
|
||||
</div><!-- /patternContent-->
|
||||
<hr />
|
||||
This topic: MUSR<span class='foswikiSeparator'> > </span><a href="WebHome.html" class="foswikiCurrentWebHomeLink">WebHome</a> > <a href="MusrFit.html">MusrFit</a><span class='foswikiSeparator'> > </span>MusrGui <br />
|
||||
Topic revision: r18 - 20 Jul 2011 - 12:22:56 - <a href="https://intranet.psi.ch/Main/BastianWojek">BastianWojek</a>
|
||||
</div>
|
||||
</div>
|
||||
</div>
|
||||
<div class="clear"> </div>
|
||||
</div><div id="patternBottomBar"><div id="patternBottomBarContents"><div id="patternWebBottomBar">Ideas, requests, problems regarding <a href="https://intranet.psi.ch/Main/WebHome">PSI Wiki</a>? <a href="mailto:psi.intranet@psi.ch?subject=Foswiki%20Feedback%20on%20MUSR.MusrGui">Send feedback</a></div></div></div>
|
||||
</div>
|
||||
</div>
|
||||
</div>
|
||||
</div></div><!-- /endWrap -->
|
||||
<p></p>
|
||||
<p></p>
|
||||
<p></p>
|
||||
<p></p>
|
||||
</body>
|
||||
|
||||
<!-- Mirrored from intranet.psi.ch/MUSR/MusrGui?cover=print by HTTrack Website Copier/3.x [XR&CO'2010], Mon, 01 Aug 2011 13:15:38 GMT -->
|
||||
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||||
</html>
|
||||
<p></p>
|
||||
<p></p>
|
||||
<p></p>
|
||||
<p></p>
|
||||
<p></p>
|
||||
294
doc/html/MUSR/QuickStart.html
Normal file
294
doc/html/MUSR/QuickStart.html
Normal file
@ -0,0 +1,294 @@
|
||||
<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
|
||||
<html lang="en_US">
|
||||
|
||||
<!-- Mirrored from intranet.psi.ch/MUSR/QuickStart?cover=print by HTTrack Website Copier/3.x [XR&CO'2010], Mon, 01 Aug 2011 13:15:36 GMT -->
|
||||
<!-- Added by HTTrack --><meta http-equiv="content-type" content="text/html;charset=iso-8859-1"><!-- /Added by HTTrack -->
|
||||
<head>
|
||||
<link rel="stylesheet" href="../pub/System/HeadlinesPlugin/style.css" type="text/css" media="all" />
|
||||
<title> MUSR :: QuickStart</title>
|
||||
|
||||
<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1" /> <meta name="robots" content="noindex" /> <link rel="alternate" type="application/rss+xml" title="RSS Feed" href="WebRsshtml.html" />
|
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<meta name="scripturl" content="https://intranet.psi.ch/wiki/bin" />
|
||||
<meta name="scriptsuffix" content="" />
|
||||
|
||||
<meta name="WEBTOPIC" content="QuickStart" />
|
||||
<meta name="WEB" content="MUSR" />
|
||||
<meta name="SCRIPTURLPATH" content="/wiki/bin" />
|
||||
<meta name="SCRIPTSUFFIX" content="" />
|
||||
<meta name="TEXT_JUMP" content="Jump" />
|
||||
<meta name="TEXT_SEARCH" content="Search" />
|
||||
<meta name="TEXT_NUM_TOPICS" content="Number of topics:" />
|
||||
<meta name="TEXT_MODIFY_SEARCH" content="Modify search" />
|
||||
|
||||
<link rel="icon" href="../pub/Main/WebPreferences/favicon.ico" type="image/x-icon" /> <link rel="shortcut icon" href="../pub/Main/WebPreferences/favicon.ico" type="image/x-icon" />
|
||||
<link rel="alternate" href="https://intranet.psi.ch/wiki/bin/edit/MUSR/QuickStart?t=1312204523" type="application/x-wiki" title="edit QuickStart" />
|
||||
<meta name="description" content="QuickStart" />
|
||||
<base /><!--[if IE]></base><![endif]-->
|
||||
|
||||
<style type="text/css" media="all">
|
||||
@import url('../pub/System/SkinTemplates/base.css');
|
||||
</style>
|
||||
<style type="text/css" media="all">
|
||||
@import url('../pub/System/PatternSkinTheme2009/layout.css');
|
||||
@import url('../pub/System/PatternSkinTheme2009/style.css');
|
||||
@import url('../pub/System/PatternSkinTheme2009/colors.css');
|
||||
</style>
|
||||
<style type="text/css" media="all">
|
||||
@import url('../pub/System/PatternSkinTheme2009/column_left.css');
|
||||
@import url('../pub/System/PatternSkinTheme2009/variant_twiki.css');
|
||||
</style><style type="text/css" media="all">
|
||||
/* Styles that are set using variables */
|
||||
.patternBookView .foswikiTopRow,
|
||||
.patternWebIndicator a img,
|
||||
.patternWebIndicator a:hover img {
|
||||
background-color:#D0D0D0;
|
||||
}
|
||||
#patternTopBarContents { background-image:url(../pub/System/PatternSkin/header5.gif); background-repeat:repeat-x;}
|
||||
#patternTopBarContents { background-color:#ffffff;}
|
||||
.patternBookView {
|
||||
border-color:#D0D0D0;
|
||||
}
|
||||
.patternPreviewPage #patternMain {
|
||||
/* uncomment to set the preview image */
|
||||
/*background-image:url("/pub/System/PreviewBackground/preview2bg.gif");*/
|
||||
}
|
||||
</style>
|
||||
<style type="text/css" media="all">
|
||||
@import url("../pub/System/PsiSkin/psicolors.css");
|
||||
@import url("../pub/System/PsiSkin/psistyle.css");
|
||||
.foswikiTopic {overflow: hidden;}
|
||||
</style>
|
||||
|
||||
|
||||
|
||||
<style type="text/css" media="all">
|
||||
@import url("../pub/System/PatternSkin/print.css");
|
||||
.foswikiAttachments, #patternInfo, #patternBottomBar {display: none;}
|
||||
.patternContent {overflow: visible}
|
||||
</style>
|
||||
<!--[if IE]><style type="text/css" media="screen">
|
||||
pre {
|
||||
height:1%;
|
||||
overflow-x:auto;
|
||||
}
|
||||
.foswikiAttachments,
|
||||
.foswikiForm,
|
||||
.foswikiHelp,
|
||||
.foswikiPreviewArea,
|
||||
.patternPreviewPage .foswikiForm,
|
||||
.patternSigLine,
|
||||
.patternToolBar,
|
||||
.patternTop,
|
||||
.patternTopicAction,
|
||||
#patternSideBarContents .patternLeftBarPersonal,
|
||||
#patternSideBarContents h2,
|
||||
#patternSideBarContents li,
|
||||
#patternTopBarButtons ul {
|
||||
height:1%;
|
||||
}
|
||||
#patternSideBarContents .patternLeftBarPersonal {
|
||||
width:100%;
|
||||
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|
||||
.foswikiFormStep {
|
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height:100%;
|
||||
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|
||||
#foswikiLogin,
|
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.patternShadow {
|
||||
border:10px solid #fff;
|
||||
margin-top:10px;
|
||||
margin-bottom:10px;
|
||||
border:2px solid #ccc;
|
||||
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|
||||
</style><![endif]-->
|
||||
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|
||||
#foswikiLogin,
|
||||
.patternShadow {
|
||||
border:10px solid #fff;
|
||||
margin-top:10px;
|
||||
margin-bottom:10px;
|
||||
box-shadow: 0 0 10px #ccc;
|
||||
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|
||||
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|
||||
|
||||
|
||||
<script src="https://intranet.psi.ch/pub/System/ChecklistPlugin/itemstatechange.js" language="javascript" type="text/javascript"></script><script src="https://intranet.psi.ch/pub/System/TimeTablePlugin/timetabletooltips.js" language="javascript" type="text/javascript"></script></head>
|
||||
<body class="patternViewPage patternPrintPage" id="BodyTop">
|
||||
<a name="PageTop"></a><div class="foswikiPage"><div id="patternScreen">
|
||||
<div id="patternPageShadow">
|
||||
<div id="patternPage">
|
||||
<div id="patternOuter">
|
||||
<div id="patternFloatWrap">
|
||||
<div id="patternMain">
|
||||
<div id="patternMainContents">
|
||||
<div class="patternContent"><div class="foswikiTopic"><h1><a name="Quickstart_for_61_61WKM_61_61_users"></a> Quickstart for <code><b>WKM</b></code> users </h1>
|
||||
<a name="foswikiTOC"></a><div class="foswikiToc"> <ul>
|
||||
<li> <a href="QuickStart.html#Quickstart_for_61_61WKM_61_61_users"> Quickstart for WKM users </a> <ul>
|
||||
<li> <a href="QuickStart.html#Introduction"> Introduction </a>
|
||||
</li> <li> <a href="QuickStart.html#Differences_between_61WKM_61_and_61musrfit_61_msr_files"> Differences between WKM and musrfit msr files </a>
|
||||
</li> <li> <a href="QuickStart.html#Selected_new_features_in_61musrfit_61"> Selected new features in musrfit </a>
|
||||
</li></ul>
|
||||
</li></ul>
|
||||
</div>
|
||||
<h2><a name="Introduction"></a> Introduction </h2>
|
||||
<p></p>
|
||||
<code>musrfit</code> is a program suite for analyzing μSR data. It is implemented in <code>C++/<a href="http://root.cern.ch/" target="_top">ROOT</a></code> and uses the <a href="http://www.cern.ch/minuit/" target="_top">MINUIT2</a> libraries developed at <a href="http://www.cern.ch/" target="_top">CERN</a> for fitting data.
|
||||
Installation instructions for Linux, MS Windows, and Mac OS X can be found <a href="MusrFitSetup.html">here</a>. The full user manual is available <a href="MusrFit.html">here</a>.<br>
|
||||
In principle the programs can be used in the same fashion as <code>WKM</code> (<code>wkmfit, wkmview</code>).
|
||||
E.g., for fitting data as defined in the input file <code><b>8472.msr</b></code> one types:<pre>musrfit 8472.msr</pre> for plotting data and the corresponding
|
||||
fit one calls:<pre>musrview 8472.msr</pre>
|
||||
Additionally, there are editors called <code><a href="MusrGui.html">musrgui/musredit</a></code> available which can do everything the <code>emacs</code> plug-in for <code>WKM</code> is capable of and even more. <strong><font color="#ff0000">However, before going to use only <code>musrgui</code> / <code>musredit</code> it is strongly recommended to read at least this "Quickstart" since there are a few differences between the programs as well as new features which are partially described in the following.</font></strong>
|
||||
<p></p>
|
||||
<h2><a name="Differences_between_61WKM_61_and_61musrfit_61_msr_files"></a> Differences between <code>WKM</code> and <code>musrfit</code> msr files </h2>
|
||||
<p></p>
|
||||
The msr file format of <code>WKM</code> has some weaknesses and has therefore been extended for the use with <code>musrfit</code>. Existing <code>WKM</code> files can be converted using the <a href="MusrFit.html#Msr2Msr">small utility</a> <code>msr2msr</code>. The changes are: <ul>
|
||||
<li> The <code>musrfit</code> msr and mlog files contain an additional column in the FITPARAMETER block for the representation of positive uncertainties if <code>MINOS</code> was called during fitting. In that case the <strong>Step</strong> column holds the negative uncertainties. If there has not been performed an error analysis using <code>MINOS</code>, the symmetric error can be found in the <strong>Step</strong> column, whereas the <strong>Pos_Error</strong> column contains only <strong>none</strong> entries. The beginning of the FITPARAMETER block then might look like this <pre>
|
||||
FITPARAMETER
|
||||
# No Name Value Step Pos_Error Boundaries
|
||||
1 Phase 35.8359 -3.94496 3.93749
|
||||
2 Asy 0.04501 -0.00208 0.00211 0 0.33
|
||||
3 Field 143.212 -0.27960 0.27885 100 200
|
||||
4 Rate 0.14245 -0.02501 0.02279 0 1
|
||||
</pre> or that <pre>
|
||||
FITPARAMETER
|
||||
# No Name Value Step Pos_Error Boundaries
|
||||
1 Phase 35.8359 3.94496 none
|
||||
2 Asy 0.04501 0.00208 none 0 0.33
|
||||
3 Field 143.212 0.27960 none 100 200
|
||||
4 Rate 0.14245 0.02501 none 0 1
|
||||
</pre>
|
||||
</li> <li> Blank lines and lines beginning with <strong>#</strong> are handled as comments. Therefore this works: <pre>
|
||||
# Signal 1, first field, ...
|
||||
|
||||
2 Asy1 0.04501 -0.00208 0.00211 0 0.33
|
||||
3 Field1 143.212 -0.27960 0.27885 100 200
|
||||
4 Rate1 0.14245 -0.02501 0.02279 0 1
|
||||
|
||||
# Signal 2, second field, ...
|
||||
|
||||
5 Asy2 0.14501 -0.00208 0.00211 0 0.33
|
||||
6 Field2 343.212 -2.27960 2.27885 0 1000
|
||||
7 Rate2 0.42045 -0.02501 0.02279 0 1
|
||||
</pre>
|
||||
</li> <li> In the RUN block, the first line of each run has the format: <pre>
|
||||
RUN 2008/lem08_his_8472 MUE4 PSI ROOT-NPP (name beamline institute data-file-format)
|
||||
</pre> where the supported μSR-data file formats are: <strong>ROOT-NPP</strong>, <strong>ROOT-PPC</strong>, <strong>WKM</strong>, <strong>PSI-BIN</strong>, <strong>PSI-MDU</strong>, <strong>MDU-ASCII</strong>, <strong>MUD</strong>, and <strong>NEXUS</strong>
|
||||
</li> <li> The commands <strong>SET BATCH</strong> and <strong>END RETURN</strong> may be omitted in the COMMANDS block.
|
||||
</li></ul>
|
||||
<p></p>
|
||||
<h2><a name="Selected_new_features_in_61musrfit_61"></a> Selected new features in <code>musrfit</code> </h2> <ul>
|
||||
<li> If single-histogram fits are done, the normalization and background constants are given either "per nanosecond" or "per rebinned bin". The nanosecond normalization allows to change the binning without the need of re-doing the fit to the data.
|
||||
</li> <li> The use of functions in the RUN block is now possible for the normalization parameter, e.g. for the definition of an α parameter in simultaneous single-histogram fits of two histograms.
|
||||
</li> <li> Apart from the default χ<sup>2</sup> minimization, when doing single-histogram fits (fit type <strong>0</strong>) in <code>musrfit</code> there is also the possibility to do a log-likelihood maximization instead. For switching, just put <strong>MAX_LIKELIHOOD</strong> in the COMMANDS block.
|
||||
</li> <li> Since <code>musrfit</code> invokes <code>MINUIT2</code> instead of <code>MINUIT</code> there are the following advantages compared to <code>WKM</code>: <ul>
|
||||
<li> No ten character restriction on parameter names
|
||||
</li> <li> No restriction on the number of parameters used for a fit (apart from the computer memory)
|
||||
</li> <li> Possibility to constrain the parameters to semi-defined intervals (like par > a or par < b). The FITPARAMETER-block syntax in the msr input file is: <pre>
|
||||
FITPARAMETER
|
||||
# No Name Value Step Pos_Error Boundaries
|
||||
# Specify only a lower boundary for the parameter
|
||||
1 Asy1 0.04501 -0.00208 0.00211 0 none
|
||||
|
||||
# Specify only an upper boundary for the parameter
|
||||
2 Rate1 0.14245 -0.02501 0.02279 none 10
|
||||
|
||||
# Specify lower and upper boundaries for the parameter
|
||||
3 Asy2 0.14501 -0.00208 0.00211 0 0.33
|
||||
|
||||
# Do not specify boundaries at all
|
||||
4 Field2 343.212 -2.27960 2.27885
|
||||
5 Rate2 0.42045 -0.02501 0.02279 none none
|
||||
</pre>
|
||||
</li></ul>
|
||||
</li> <li> The restriction of only ten mapped parameters is lifted!
|
||||
</li> <li> The supported table functions in <code>WKM</code> have been replaced by direct integrations in <code>musrfit</code>.
|
||||
</li> <li> Some constants for use in the FUNCTIONS block are predefined: <ul>
|
||||
<li> <strong>gamma_mu</strong> = γ<sub>μ</sub>/2π = 0.0135538817 MHz/G
|
||||
</li> <li> <strong>pi</strong> = π = 3.14159265358979323846
|
||||
</li></ul>
|
||||
</li> <li> As theory function also the so called skewed Gaussian can be chosen. The properties of this function are summarized in <a href="http://nemu.web.psi.ch/doc/LEM_Memo/skewedGaussian/skewedGaussian.pdf" target="_top">a memo</a> <span class="foswikiIcon"><img src="../pub/System/DocumentGraphics/pdf.png" width="16" height="16" alt="pdf" /></span>. The function is called in the THEORY block as follows: <pre>
|
||||
skewedGss 1 2 3 4 (phase frequency rate_m rate_p)
|
||||
</pre>
|
||||
</li> <li> After fitting it is possible to keep the <code>MINUIT2</code> output including the correlation matrix of the parameters. Calling <code>musrfit</code> with the <strong>--keep-mn2-ouput</strong> or <strong>-k</strong> option will provide you an ASCII and a ROOT file with the complete output, e.g. <pre>musrfit 8472.msr --keep-mn2-ouput</pre> generates <code><b>8472-mn2.output</b></code> and <code><b>8472-mn2.root</b></code> (and of course <code><b>8472.mlog</b></code>).
|
||||
</li> <li> The PLOT block has been extended. Additionally to the old range options for instance it is possible to specify individual plot ranges for each run, change the binning used for the data presentation with a global packing parameter for all runs or present the data on (semi-)logarithmic scales. For details on this options refer to the <a href="MusrFit.html#ThePlotBlock">manual</a>.
|
||||
</li> <li> It is possible to have multiple PLOT blocks within a single msr file. Each PLOT block generates an individual <code>ROOT</code> canvas.
|
||||
</li> <li> For passing options to the Fourier transformation a new FOURIER block has been created. Here it is possible to specify parameters like the number of points used for the discrete transform or the apodization that should be used. For details on the FOURIER block refer to the <a href="MusrFit.html#TheFourierBlock">manual</a>.
|
||||
</li> <li> For checking the initial values of the given fit parameters one might use the <strong>--chisq-only</strong> or <strong>-c</strong> option of <code>musrfit</code>. Instead of fitting the data <code>musrfit</code> calculates χ<sup>2</sup> only once and sends the result to the standard output if called with this option.
|
||||
</li> <li> There is the possibility to define a few external parameters in the XML file <code><b>musrfit_startup.xml</b></code> located in the binary directory. At the moment one can set various paths to the data files or the colors and markers as well as the default settings for the built-in Fourier transform which should be used in <code>musrview</code>. For details refer to the <a href="MusrFit.html#MusrfitStartupXml">manual</a>.
|
||||
</li> <li> Through the ROOT-dictionary mechanism <code>musrfit</code> supports the definition of external fit functions. For details, refer to the <a href="MusrFit.html#UserFunctions">manual</a>.
|
||||
</li> <li> Yet another useful feature implemented in <code>musrfit</code> is the addition of several μSR runs into one "combined run" with increased statistics. In order to do so an ADDRUN line has to be added to the RUN block after the line containing the RUN statement, e.g.: <pre>
|
||||
RUN 2007/lem07_his_2018 MUE4 PSI ROOT-NPP
|
||||
ADDRUN 2007/lem07_2019_rb1_npp MUE4 PSI WKM
|
||||
ADDRUN 2007/lem07_2020 MUE4 PSI PSI-BIN
|
||||
</pre> It is possible to add more than one ADDRUN line which might even be stored in files with different formats. The remaining RUN-block statements (with the exception of t0) then refer to the "combined run". For further details refer to the <a href="MusrFit.html#TheRunBlock">manual</a>.
|
||||
</li> <li> <code>musrfit</code> also supports one-dimensional fitting of non-μSR data stored in ASCII files or in the <strong>DB</strong> format. For this purpose the new fit and plot type <strong>8 (non-muSR fit/plot)</strong> has been introduced. Theory functions like <strong>simplExpo</strong> or <strong>simpleGss</strong> accept a second argument, the so called "time shift <i>t</i><sub>1</sub>": e<sup>-λ<i>t</i></sup> → e<sup>-λ(<i>t</i>-<i>t</i><sub>1</sub>)</sup><br> <br> The further syntax of the msr input file can be seen in the following full example for fitting the exponential decay of a magnetic field into a local superconductor: <img alt="B(z)=B_0 \mathrm{e}^{-\left(z-z_0\right)/\lambda_{\mathrm{L}}}" class="mmpImage" src="../pub/MUSR/QuickStart/_MathModePlugin_616b0638293d1e0ff42a44f8ea7895ff.png" /> <pre>
|
||||
superconductor.msr
|
||||
###############################################################
|
||||
FITPARAMETER
|
||||
# Nr. Name Value Step Pos_Error Boundaries
|
||||
1 B0 50.056 0 none
|
||||
2 z0 10.9405 -2.68635 2.37574
|
||||
3 lambdaL 206.121 -6.21524 7.02819
|
||||
|
||||
###############################################################
|
||||
THEORY
|
||||
asymmetry 1
|
||||
simplExpo fun1 2 (rate tshift)
|
||||
|
||||
###############################################################
|
||||
FUNCTIONS
|
||||
fun1 = 1.0 / par3
|
||||
|
||||
###############################################################
|
||||
RUN superconductor-data MUE4 PSI DB (name beamline institute data-file-format)
|
||||
fittype 8 (non muSR fit)
|
||||
map 0 0 0 0 0 0 0 0 0 0
|
||||
xy-data range field
|
||||
fit 0.00 150.00
|
||||
packing 1
|
||||
|
||||
###############################################################
|
||||
COMMANDS
|
||||
MINIMIZE
|
||||
MINOS
|
||||
SAVE
|
||||
|
||||
###############################################################
|
||||
PLOT 8 (non muSR plot)
|
||||
runs 1
|
||||
range 0.00 140.00
|
||||
|
||||
###############################################################
|
||||
STATISTIC --- 2008-10-10 14:02:32
|
||||
chisq = 10.0, NDF = 10, chisq/NDF = 1.0
|
||||
</pre> In the above example <code>musrfit</code> reads the data from the file <code><b>superconductor-data.db</b></code>; the <i>x</i> and <i>y</i> data are specified by the <strong>DB</strong> parameter names <code><b>range</b></code> and <code><b>field</b></code>. An alternative specification of the <i>x</i> and <i>y</i> data by the parameter number in the <strong>DB</strong> file is also possible!
|
||||
</li></ul>
|
||||
<p></p>
|
||||
-- <a href="http://www.fsf.org/register_form?referrer=8369" target="_top">BMW</a> & <a href="http://lmu.web.psi.ch/lem/group.html" target="_top">AS</a></div><!-- /foswikiTopic-->
|
||||
<p></p>
|
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<hr />
|
||||
This topic: MUSR<span class='foswikiSeparator'> > </span><a href="WebHome.html" class="foswikiCurrentWebHomeLink">WebHome</a> > <a href="MusrFit.html">MusrFit</a><span class='foswikiSeparator'> > </span>QuickStart <br />
|
||||
Topic revision: r7 - 10 Jul 2011 - 17:48:19 - <a href="https://intranet.psi.ch/Main/BastianWojek">BastianWojek</a>
|
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305
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<div class="patternContent"><div class="foswikiTopic"><h1><a name="A_61_61musrfit_61_61_Single_45Histogram_45Fit_Tutorial"></a> <code><b>musrfit</b></code> Single-Histogram-Fit Tutorial </h1>
|
||||
<p></p>
|
||||
The μSR-data-analysis process using <code>musrfit</code> is based on so-called <code>msr</code> 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 <code>msr</code> file and the different programs of the <code>musrfit</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 href="MusrFit.html">manual</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 href="http://lmu.web.psi.ch/facilities/gps/gps.html" target="_top">GPS spectrometer</a> at <a href="http://www.psi.ch/" target="_top">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 <code>msr</code> file <strong>3110_tutorial.msr</strong> provided together with the source-code distribution in the sub-directory <strong>src/tests/CheckMusrfitInstall/</strong>. This ASCII file can be edited using any text editor. For convenience the editors <code>musredit</code>/<code>musrgui</code> are provided which offer some <code>msr</code>-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>musredit</code>.
|
||||
<p></p>
|
||||
<h1><a name="A_1_The_61msr_61_file"></a> 1 The <code>msr</code> file </h1>
|
||||
<p></p>
|
||||
The <code>msr</code> file itself is divided into different blocks—a full description of the format can be found <a href="MusrFit.html#DescriptionOfTheMsrFileFormat">here</a>.
|
||||
In the file <strong>3110_tutorial.msr</strong> these blocks are successively: <ul>
|
||||
<li> <a href="MusrFit.html#TheTitle">the title</a>:<pre>
|
||||
sample XYZ
|
||||
</pre> A descriptive title of the file.
|
||||
</li> <li> <a href="MusrFit.html#TheFitparameterBlock">the FITPARAMETER block</a>:<pre>
|
||||
FITPARAMETER
|
||||
# No Name Value Step Pos_Error Boundaries
|
||||
1 NormUp 4500 5 none 0 none
|
||||
2 BgUp 200 1 none 0 none
|
||||
3 PhaseUp 15 1 none
|
||||
|
||||
4 NormDown 4500 5 none 0 none
|
||||
5 BgDown 200 1 none 0 none
|
||||
6 PhaseDown 195 1 none
|
||||
|
||||
7 NormRight 600 5 none 0 none
|
||||
8 BgRight 40 1 none 0 none
|
||||
9 PhaseRight 285 1 none
|
||||
|
||||
10 AsymSig1 0.17 0.01 none 0 0.33
|
||||
11 RateSig1 2.5 0.1 none 0 none
|
||||
12 FieldSig1 100 1 none
|
||||
|
||||
13 AsymSig2 0.02 0.01 none 0 0.33
|
||||
14 RateSig2 0.5 0.1 none
|
||||
15 FieldSig2 150 1 none
|
||||
</pre> 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 <strong>Step</strong> column). If asymmetric errors are determined, these will be listed in the <strong>Step</strong> column (negative) and the <strong>Pos_Error</strong> column (positive). Optionally, lower and upper boundaries for the parameters can be specified as shown above.<br> The meaning of the parameters above is explained in the following:<br> Since a <a href="MusrFit.html#SingleHistogramFit">single-histogram fit</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).<br> 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 (e.g. 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).
|
||||
</li> <li> <a href="MusrFit.html#TheTheoryBlock">the THEORY block</a>:<pre>
|
||||
THEORY
|
||||
asymmetry 10
|
||||
simplExpo 11 (rate)
|
||||
TFieldCos map1 fun1 (phase frequency)
|
||||
+
|
||||
asymmetry 13
|
||||
simpleGss 14 (rate)
|
||||
TFieldCos map1 fun2 (phase frequency)
|
||||
</pre> The THEORY block is used to define a fit-parameter-dependent theory function used to model the decay asymmetry. Different <a href="MusrFit.html#TheoryTable">predefined</a> and <a href="MusrFit.html#UserFunctions">user-defined</a> functions can be combined here. Theory lines following each other are multiplied and the <strong>+</strong> sign is used to add different (here: two) signal contributions. The numbers are the parameter numbers according to the FITPARAMETER block. <strong>map</strong> and <strong>fun</strong> are used to refer to histogram-dependent parameters and to interrelate fit parameters, respectively (see below).
|
||||
</li> <li> <a href="MusrFit.html#TheFunctionsBlock">the FUNCTIONS block</a>:<pre>
|
||||
FUNCTIONS
|
||||
fun1 = gamma_mu * par12
|
||||
fun2 = gamma_mu * par15
|
||||
</pre> <a href="MusrFit.html#TheFunctionsBlock">Here</a> functions interrelating different fit parameters and predefined constants can be defined for the use in the THEORY block. In the example, the functions are used to calculate the muon-spin-precession frequencies for the given fields (ν = γ<sub>μ</sub><i>B</i>/2π). One function is used for each signal. Altogether, the theory function defined above is <i>A</i>(<i>t</i>) = <i>p</i><sub>10</sub> e<sup>-<i>p</i><sub>11</sub>t</sup> cos(φ<sub><i>i</i></sub>π/180 + γ<sub>μ</sub> <i>p</i><sub>12</sub> <i>t</i>) + <i>p</i><sub>13</sub> e<sup>-(<i>p</i><sub>14</sub><i>t</i>)<sup>2</sup>/2</sup> cos(φ<sub><i>i</i></sub>π/180 + γ<sub>μ</sub> <i>p</i><sub>15</sub><i>t</i>), where the <i>p</i> are the parameters in the FITPARAMETER block and φ<sub><i>i</i></sub> = <i>p</i><sub>3</sub>, <i>p</i><sub>6</sub>, <i>p</i><sub>9</sub> depending on the histogram as shall be seen later.
|
||||
</li> <li> <a href="MusrFit.html#TheRunBlock">the RUN block</a>:<pre>
|
||||
RUN data/deltat_pta_gps_3110 PIM3 PSI PSI-BIN (name beamline institute data-file-format)
|
||||
fittype 0 (single histogram fit)
|
||||
norm 1
|
||||
backgr.fit 2
|
||||
lifetimecorrection
|
||||
map 3 0 0 0 0 0 0 0 0 0
|
||||
forward 3
|
||||
data 1 8000
|
||||
t0 1
|
||||
fit 0 4.9
|
||||
packing 20
|
||||
</pre> The RUN blocks are used to collect information on the data to be analyzed. Specifically, these are: <ul>
|
||||
<li> <pre>RUN data/deltat_pta_gps_3110 PIM3 PSI PSI-BIN (name beamline institute data-file-format)</pre> <a href="MusrFit.html#PathToDataFiles">the path to the data file</a> and the file format (NEXUS, ROOT-NPP, ROOT-PPC, PSI-BIN, PSI-MDU, WKM, MUD, MDU-ASCII)
|
||||
</li> <li> <pre>fittype 0 (single histogram fit)</pre> the fit type (0 = single-histogram fit)
|
||||
</li> <li> <pre>norm 1</pre> the number of the fit parameter representing the normalization constant
|
||||
</li> <li> <pre>backgr.fit 2</pre> the number of the fit parameter representing the background
|
||||
</li> <li> <pre>lifetimecorrection</pre> a <a href="MusrFit.html#LifeTimeCorrection">tag</a> that specifies whether the histogram is plotted (line is not present) or the asymmetry (line is present)
|
||||
</li> <li> <pre>map 3 0 0 0 0 0 0 0 0 0</pre> the definition of the <strong>maps</strong> used in the THEORY block—RUN-block-specific parameters are given here; in this example, <strong>map1</strong> is substituted by parameter <strong>3</strong> in the THEORY block for this RUN block and <strong>map2</strong>, <strong>map3</strong>, and so on are undefined.
|
||||
</li> <li> <pre>forward 3</pre> the histogram number; in this example 3 corresponds to the histogram of the "Up" positron counter
|
||||
</li> <li> <pre>data 1 8000</pre> start and end bins of the range containing useful data in the histogram (to be adjusted, e.g. by using <code>musrt0</code>, see below)
|
||||
</li> <li> <pre>t0 1</pre> histogram bin corresponding to the time zero (muon implantation time) (to be adjusted, e.g. by <code>musrt0</code>, see below)
|
||||
</li> <li> <pre>fit 0 4.9</pre> start and end times (in μs) defining the fit range
|
||||
</li> <li> <pre>packing 20</pre> the packing of the histograms (in histogram bins)<br><br>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.
|
||||
</li></ul>
|
||||
</li> <li> <a href="MusrFit.html#TheCommandsBlock">the COMMANDS block</a>:<pre>
|
||||
COMMANDS
|
||||
MINIMIZE
|
||||
MINOS
|
||||
SAVE
|
||||
</pre> In the COMMANDS block, a sequence of operations that should be performed is defined. Here, the requested operations are the minimization of χ<sup>2</sup> (MINIMIZE), the calculation of asymmetric errors (MINOS) as well as saving the found parameter values and uncertainties to the <code>msr</code> file (SAVE). A full description of the possible commands can be found <a href="MusrFit.html#TheCommandsBlock">here</a>.
|
||||
</li> <li> <a href="MusrFit.html#TheFourierBlock">the FOURIER block</a>:<pre>
|
||||
FOURIER
|
||||
units Gauss # units either 'Gauss', 'MHz', or 'Mc/s'
|
||||
fourier_power 10
|
||||
apodization WEAK # NONE, WEAK, MEDIUM, STRONG
|
||||
plot POWER # REAL, IMAG, REAL_AND_IMAG, POWER, PHASE
|
||||
phase par3
|
||||
range 0.0 600.0
|
||||
</pre> The FOURIER block is used to define basic settings for the Fourier transform available in <code>musrview</code>. These are: <ul>
|
||||
<li> <pre>units Gauss # units either 'Gauss', 'MHz', or 'Mc/s'</pre> the units of the Fourier domain
|
||||
</li> <li> <pre>fourier_power 10</pre> the number of data points used for the discrete transform, here 2<sup><b>10</b></sup>=1024
|
||||
</li> <li> <pre>apodization WEAK # NONE, WEAK, MEDIUM, STRONG</pre> the <a href="MusrFit.html#TheFourierBlock">apodization</a> to be used
|
||||
</li> <li> <pre>plot POWER # REAL, IMAG, REAL_AND_IMAG, POWER, PHASE</pre> what should be plotted (real part, imaginary part, and so on)
|
||||
</li> <li> <pre>phase par3</pre> the initial phase of the input data is given here in degrees. Optionally, a phase parameter from the FITPARAMETER block can be given, here <strong>par3</strong> takes the value of parameter <strong>3</strong>.
|
||||
</li> <li> <pre>range 0.0 600.0</pre> the start and end points of the range of the Fourier transform in the units specified above
|
||||
</li></ul>
|
||||
</li> <li> <a href="MusrFit.html#ThePlotBlock">the PLOT block</a>:<pre>
|
||||
PLOT 0 (single histo plot)
|
||||
runs 1 2
|
||||
range 0 4 -0.2 0.2
|
||||
</pre> The PLOT block defines which data (corresponding to the given RUN blocks) is plotted when <code>musrview</code> is called. In the given example, a canvas would be drawn containing the (life-time-corrected) data of the first two RUN blocks ("Up" and "Down" positron counters). The abscissa would range from 0 to 4 μs, the axis of ordinates from -0.2 to 0.2.<br> It is possible to define more than one PLOT block. Each PLOT block corresponds to a separate canvas. Therefore, the second PLOT block in the file<pre>
|
||||
PLOT 0 (single histo plot)
|
||||
runs 3
|
||||
use_fit_ranges
|
||||
</pre> produces an additional window containing the (<i>not</i> life-time-corrected) data of the third RUN block ("Right" positron counter). The abscissa ranges from 0 to 4.9 μs (according to the fit range given in the RUN block).
|
||||
</li> <li> <a href="MusrFit.html#TheStatisticBlock">the STATISTIC block</a>:<pre>
|
||||
STATISTIC --- 2011-07-09 10:58:44
|
||||
chisq = 1348.1764586409397, NDF = 1146, chisq/NDF = 1.1764192483777833
|
||||
</pre> This block is the last block of a <code>msr</code> file. It contains some information on the fit: the date and time as well as the absolute and normalized values of χ<sup>2</sup> and the number of degrees of freedom in the fit.<br> These information only have a meaning if the fitting procedure has been executed at least once and the fit has converged!
|
||||
</li></ul>
|
||||
<p></p>
|
||||
<h1><a name="A_2_Determine_t0_and_the_data_range_using_61musrt0_61"></a> 2 Determine <i>t</i><sub>0</sub> and the data range using <code>musrt0</code> </h1>
|
||||
Before the given model can be fitted to the data, the data ranges and time zeros of the different RUN blocks have to be set correctly. This can be achieved using <code><a href="MusrFit.html#MusrT0">musrt0</a></code>. Starting this program by selecting the <img alt="musrt0.png" src="../pub/MUSR/MusrGui/musrt0.png" /> button in <code>musredit</code> or calling from a terminal <pre>musrt0 3110_tutorial.msr</pre> opens an interactive window plotting the data of the first RUN block:<br />
|
||||
<img src="../pub/MUSR/TutorialSingleHisto/musrt0-1.png" alt="musrt0-1" align="center" /><br />
|
||||
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:<br />
|
||||
<img src="../pub/MUSR/TutorialSingleHisto/musrt0-2.png" alt="musrt0-2" width='708' height='529' align="center" /><br />
|
||||
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 <i>t</i><sub>0</sub> and data-range values will be written to the <code>msr</code> file.
|
||||
A full description of <code>musrt0</code> can be found <a href="MusrFit.html#MusrT0">here</a>.
|
||||
<p></p>
|
||||
<h1><a name="A_3_Fit_the_model_to_the_data_using_61musrfit_61"></a> 3 Fit the model to the data using <code>musrfit</code> </h1>
|
||||
Now that the basics of the <code>msr</code> 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 <img alt="musrfit.png" src="../pub/MUSR/MusrGui/musrfit.png" /> button in <code>musredit</code> or calling from a terminal <pre>musrfit 3110_tutorial.msr</pre>
|
||||
<p></p>
|
||||
After the fitting procedure has finished the <code>msr</code> file is updated and contains the newly determined values of the fit parameters.
|
||||
<p></p>
|
||||
<h1><a name="A_4_View_the_data_and_the_fit_using_61musrview_61"></a> 4 View the data and the fit using <code>musrview</code> </h1>
|
||||
The data and the corresponding fit can be visualized by choosing <img alt="musrview.png" src="../pub/MUSR/MusrGui/musrview.png" /> in <code>musredit</code> or calling from a terminal <pre>musrview 3110_tutorial.msr</pre> This creates the windows according to the given PLOT blocks in the <code>msr</code> file:<br />
|
||||
<img src="../pub/MUSR/TutorialSingleHisto/musrview-1.png" alt="musrview-1" align="center" /><br />
|
||||
<img src="../pub/MUSR/TutorialSingleHisto/musrview-2.png" alt="musrview-2" align="center" /><br />
|
||||
The basic features of <code>musrview</code> can be found in the Musrfit menu. They include: <ul>
|
||||
<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>), e.g. for the asymmetry of the "Up" and "Down" detectors:<br /> <img src="../pub/MUSR/TutorialSingleHisto/musrview-3.png" alt="musrview-3" align="center" /><br />
|
||||
</li></ul>
|
||||
<p></p>
|
||||
<h1><a name="A_5_Process_multiple_61msr_61_files_using_61msr2data_61"></a> 5 Process multiple <code>msr</code> files using <code>msr2data</code> </h1>
|
||||
This short introduction is concluded by calling attention to the program <code><a href="Msr2Data.html">msr2data</a></code>. As the name indicates the main purpose of this program is to extract the FITPARAMETER-block information from multiple <code>msr</code> files with the same structure and to summarize them in a single ASCII file (either in TRIUMF DB format or simple columns). However, as described in detail in the <code><a href="Msr2Data.html">manual</a></code>, it is not only possible to collect data from <code>msr</code> files but also to create new <code>msr</code> files from a template and to process these files using <code>musrfit</code> on the fly.<br>
|
||||
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> (e.g. in the case one has done measurements at different temperatures) one can use the file <strong>3110_tutorial.msr</strong> as template, generate the files <strong>3111_tutorial.msr</strong> through <strong>3114_tutorial.msr</strong> with the corresponding updates in the RUN blocks, call for each one <code>musrfit</code> and finally summarize the FITPARAMETER-block information of all processed files in an ASCII output file <strong>tutorial-T-dependence.dat</strong> (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.<br>
|
||||
From the terminal this would be done as follows:<pre>
|
||||
msr2data 3110 3114 _tutorial fit-3110 -o tutorial-T-dependence.dat data
|
||||
</pre>
|
||||
To achieve the same in <code>musredit</code> one selects <img alt="musrmsr2data.png" src="../pub/MUSR/MusrGui/musrmsr2data.png" /> and fills the form accordingly:<br />
|
||||
<img src="../pub/MUSR/TutorialSingleHisto/msr2data.png" alt="msr2data" align="center" />
|
||||
<p></p>
|
||||
<h1><a name="A_6_Further_reading"></a> 6 Further reading </h1>
|
||||
This page only summarizes the very basic features and options of the programs contained in the <code>musrfit</code> suite. For a complete description please refer to the manuals of <ul>
|
||||
<li> <code><a href="MusrFit.html">musrfit</a></code> (including <code><a href="MusrFit.html#MusrFit">musrfit</a></code>, <code><a href="MusrFit.html#MusrView">musrview</a></code>, <code><a href="MusrFit.html#MusrT0">musrt0</a></code> and the full description of the <a href="MusrFit.html#DescriptionOfTheMsrFileFormat"><code>msr</code>-file format</a>)
|
||||
</li> <li> <code><a href="MusrGui.html">musredit</a></code>
|
||||
</li> <li> <code><a href="Msr2Data.html">msr2data</a></code>.
|
||||
</li></ul>
|
||||
<p></p>
|
||||
-- <a href="http://www.fsf.org/register_form?referrer=8369" target="_top">BMW</a> & <a href="http://lmu.web.psi.ch/lem/group.html" target="_top">AS</a> </div><!-- /foswikiTopic-->
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<hr />
|
||||
This topic: MUSR<span class='foswikiSeparator'> > </span>TutorialSingleHisto <br />
|
||||
Topic revision: r7 - 27 Jul 2011 - 19:45:59 - <a href="https://intranet.psi.ch/Main/BastianWojek">BastianWojek</a>
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168
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.foswikiTopic {overflow: hidden;}
|
||||
</style>
|
||||
|
||||
|
||||
|
||||
<style type="text/css" media="all">
|
||||
@import url("../pub/System/PatternSkin/print.css");
|
||||
.foswikiAttachments, #patternInfo, #patternBottomBar {display: none;}
|
||||
.patternContent {overflow: visible}
|
||||
</style>
|
||||
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|
||||
pre {
|
||||
height:1%;
|
||||
overflow-x:auto;
|
||||
}
|
||||
.foswikiAttachments,
|
||||
.foswikiForm,
|
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.foswikiHelp,
|
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.foswikiPreviewArea,
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.patternPreviewPage .foswikiForm,
|
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.patternSigLine,
|
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.patternToolBar,
|
||||
.patternTop,
|
||||
.patternTopicAction,
|
||||
#patternSideBarContents .patternLeftBarPersonal,
|
||||
#patternSideBarContents h2,
|
||||
#patternSideBarContents li,
|
||||
#patternTopBarButtons ul {
|
||||
height:1%;
|
||||
}
|
||||
#patternSideBarContents .patternLeftBarPersonal {
|
||||
width:100%;
|
||||
}
|
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.foswikiFormStep {
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height:100%;
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}
|
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#foswikiLogin,
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.patternShadow {
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border:10px solid #fff;
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margin-top:10px;
|
||||
margin-bottom:10px;
|
||||
border:2px solid #ccc;
|
||||
}
|
||||
</style><![endif]-->
|
||||
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#foswikiLogin,
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.patternShadow {
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border:10px solid #fff;
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margin-bottom:10px;
|
||||
box-shadow: 0 0 10px #ccc;
|
||||
}
|
||||
</style><![endif]-->
|
||||
|
||||
|
||||
<script src="https://intranet.psi.ch/pub/System/ChecklistPlugin/itemstatechange.js" language="javascript" type="text/javascript"></script><script src="https://intranet.psi.ch/pub/System/TimeTablePlugin/timetabletooltips.js" language="javascript" type="text/javascript"></script></head>
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<body class="patternViewPage patternPrintPage" id="BodyTop">
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<div id="patternFloatWrap">
|
||||
<div id="patternMain">
|
||||
<div id="patternMainContents">
|
||||
<div class="patternContent"><div class="foswikiTopic"><h1><a name="Welcome_to_the_MUSR_web"></a> Welcome to the MUSR web </h1>
|
||||
<p></p>
|
||||
<h2><a name="Documentation_of_the_SR_data_analysis_suite_61musrfit_61"></a> Documentation of the μSR data analysis suite <code>musrfit</code> </h2> <ul>
|
||||
<li> <a href="TutorialSingleHisto.html">Single-histogram-fit tutorial for <code>musrfit</code> introducing the basic features of the programs and <code>msr</code> files</a> <img src="../pub/System/DocumentGraphics/new.png" width="30" height="16" alt="New" border="0" />
|
||||
</li> <li> <a href="MusrFit.html">User manual of the μSR data analysis software <code>musrfit</code> </a>
|
||||
</li> <li> <a href="MusrFitSetup.html">Setting up <code>musrfit</code> on Different Platforms</a>
|
||||
</li> <li> <a href="QuickStart.html">Quick start page for <code>WKM</code> users</a>
|
||||
</li> <li> <a href="MusrGui.html">Documentation of <code>musrgui</code>/<code>musredit</code>—editors interfacing <code>musrfit</code> </a>
|
||||
</li> <li> <a href="Msr2Data.html">Documentation of <code>msr2data</code>—a program for automatically processing multiple musrfit <code>msr</code> files</a>
|
||||
</li> <li> <code>any2many</code>—a universal μSR-file-format converter <img src="../pub/System/DocumentGraphics/todo.png" width="37" height="16" alt="TODO" border="0" />
|
||||
</li> <li> Documentation of user libs (user functions) <ul>
|
||||
<li> <a href="BmwLibs.html">Meissner-Profiles / Vortex-Lattice related functions (BMW libs)</a>
|
||||
</li> <li> Nonlocal superconductivity related Meissner screening functions (AS libs)
|
||||
</li></ul>
|
||||
</li> <li> <a href="MusrFitAcknowledgements.html">Acknowledgements</a>
|
||||
</li></ul>
|
||||
<p></p>
|
||||
-- <a href="http://www.fsf.org/register_form?referrer=8369" target="_top">BMW</a> & <a href="http://lmu.web.psi.ch/lem/group.html" target="_top">AS</a></div><!-- /foswikiTopic-->
|
||||
<p></p>
|
||||
</div><!-- /patternContent-->
|
||||
<hr />
|
||||
This topic: MUSR<span class='foswikiSeparator'> > </span>WebHome <br />
|
||||
Topic revision: r22 - 30 Jul 2011 - 13:41:15 - <a href="https://intranet.psi.ch/Main/BastianWojek">BastianWojek</a>
|
||||
</div>
|
||||
</div>
|
||||
</div>
|
||||
<div class="clear"> </div>
|
||||
</div><div id="patternBottomBar"><div id="patternBottomBarContents"><div id="patternWebBottomBar">Ideas, requests, problems regarding <a href="https://intranet.psi.ch/Main/WebHome">PSI Wiki</a>? <a href="mailto:psi.intranet@psi.ch?subject=Foswiki%20Feedback%20on%20MUSR.WebHome">Send feedback</a></div></div></div>
|
||||
</div>
|
||||
</div>
|
||||
</div>
|
||||
</div></div><!-- /endWrap -->
|
||||
<p></p>
|
||||
<p></p>
|
||||
<p></p>
|
||||
<p></p>
|
||||
</body>
|
||||
|
||||
<!-- Mirrored from intranet.psi.ch/MUSR/WebHome?cover=print by HTTrack Website Copier/3.x [XR&CO'2010], Mon, 01 Aug 2011 13:16:03 GMT -->
|
||||
<!-- Added by HTTrack --><meta http-equiv="content-type" content="text/html;charset=iso-8859-1"><!-- /Added by HTTrack -->
|
||||
</html>
|
||||
<p></p>
|
||||
<p></p>
|
||||
<p></p>
|
||||
<p></p>
|
||||
<p></p>
|
||||
9
doc/html/index.html
Normal file
9
doc/html/index.html
Normal file
@ -0,0 +1,9 @@
|
||||
<html>
|
||||
<head>
|
||||
<meta http-equiv="Refresh" content="0;url=MUSR/WebHome.html" />
|
||||
</head>
|
||||
<body>
|
||||
<p>You should be automatically redirected to the documentation of <code>musrfit</code>.</p>
|
||||
<p>If this does not work, please click on <a href="MUSR/WebHome.html">this link</a>!</p>
|
||||
</body>
|
||||
</html>
|
||||
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doc/html/pub/MUSR/Msr2Data/msr2data-input-tabs.png
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60
doc/html/pub/MUSR/MusrFit/Makefile.TMyLibrary
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doc/html/pub/MUSR/MusrFit/Makefile.TMyLibrary
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|
||||
#---------------------------------------------------
|
||||
# get compilation flags from root-config
|
||||
|
||||
ROOTCFLAGS = $(shell $(ROOTSYS)/bin/root-config --cflags)
|
||||
|
||||
#---------------------------------------------------
|
||||
|
||||
OS = LINUX
|
||||
CXX = g++
|
||||
CXXFLAGS = -O3 -Wall -Wno-trigraphs -fPIC
|
||||
LOCALINCLUDE = .
|
||||
ROOTINCLUDE = $(ROOTSYS)/include
|
||||
INCLUDES = -I$(LOCALINCLUDE) -I$(ROOTINCLUDE)
|
||||
LD = g++
|
||||
LDFLAGS =
|
||||
SOFLAGS = -O -shared
|
||||
|
||||
# the output from the root-config script:
|
||||
CXXFLAGS += $(ROOTCFLAGS)
|
||||
LDFLAGS +=
|
||||
|
||||
# some definitions: headers (used to generate *Dict* stuff), sources, objects,...
|
||||
OBJS =
|
||||
OBJS += TMyFunction.o TMyLibraryDict.o
|
||||
|
||||
SHLIB = libTMyLibrary.so
|
||||
|
||||
# make the shared lib:
|
||||
#
|
||||
all: $(SHLIB)
|
||||
|
||||
$(SHLIB): $(OBJS)
|
||||
@echo "---> Building shared library $(SHLIB) ..."
|
||||
/bin/rm -f $(SHLIB)
|
||||
$(LD) $(OBJS) $(SOFLAGS) -o $(SHLIB)
|
||||
@echo "done"
|
||||
|
||||
# clean up: remove all object file (and core files)
|
||||
# semicolon needed to tell make there is no source
|
||||
# for this target!
|
||||
#
|
||||
clean:; @rm -f $(OBJS) *Dict* core*
|
||||
@echo "---> removing $(OBJS)"
|
||||
|
||||
#
|
||||
$(OBJS): %.o: %.cpp
|
||||
$(CXX) $(INCLUDES) $(CXXFLAGS) -c $<
|
||||
|
||||
# Generate the ROOT CINT dictionary
|
||||
|
||||
TMyLibraryDict.cpp: TMyFunction.h TMyLibraryLinkDef.h
|
||||
@echo "Generating dictionary $@..."
|
||||
rootcint -f $@ -c -p -I$(ROOTINCLUDE) $^
|
||||
|
||||
install: all
|
||||
@echo "Installing shared lib: libTApproximation.so"
|
||||
ifeq ($(OS),LINUX)
|
||||
cp -pv $(SHLIB) $(ROOTSYS)/lib
|
||||
cp -pv $(LOCALINCLUDE)/*.h $(ROOTSYS)/include
|
||||
endif
|
||||
BIN
doc/html/pub/MUSR/MusrFit/Theory-Tree-with-UserFcn.png
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