diff --git a/doc/html/user/MUSR/BmwLibs.html b/doc/html/user/MUSR/BmwLibs.html index b9d6f6f2..795d441e 100644 --- a/doc/html/user/MUSR/BmwLibs.html +++ b/doc/html/user/MUSR/BmwLibs.html @@ -1,7 +1,7 @@ - + @@ -21,7 +21,7 @@ - + @@ -63,8 +63,6 @@ - +
@@ -121,6 +119,8 @@ pre {
+

+

To be written...

BMWlibs for musrfit

    @@ -138,7 +138,7 @@ pre {
 
-
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+
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@@ -169,17 +169,15 @@ pre {
-
+

- +

-

-

\ No newline at end of file diff --git a/doc/html/user/MUSR/LibFitPofB.html b/doc/html/user/MUSR/LibFitPofB.html index 2b1b32ce..d8707b07 100644 --- a/doc/html/user/MUSR/LibFitPofB.html +++ b/doc/html/user/MUSR/LibFitPofB.html @@ -1,7 +1,7 @@ - + @@ -21,7 +21,7 @@ - + @@ -63,8 +63,6 @@ - +
@@ -121,6 +119,8 @@ pre {
+

+

libFitPofB

@@ -169,7 +169,7 @@ Assuming an array of N \frac{\partial^2}{\partial z^2}B_i(z) = \frac{1}{\lambda_i^2}B_i(z)

-for each layer i taking into account the boundary conditions(1) +for each layer i taking into account the boundary conditions(1)

B_1(0) = B_N(d) = \mu_0H

@@ -275,11 +275,11 @@ When investigating superconductors in the mixed state by means of conventional & B(\mathbf{r}) = \langle B \rangle \sum\limits_{\mathbf{K}}B_{\mathbf{K}}\exp(-\imath\mathbf{K}\mathbf{r}),

where \mathbf{r}=(x,y), \mathbf{K} are the reciprocal lattice vectors of a two-dimensional vortex lattice and the B_{\mathbf{K}} are the Fourier coefficients depending on the magnetic penetration depth \lambda and the superconducting coherence length \xi. The B_{\mathbf{K}} for some specific models are as follows:
-
London model with Gaussian cutoff(2)

B_{\mathbf{K}} = \frac{\exp\left({-K^2\xi^2/2}\right)}{1 + K^2\lambda^2}

-
Modified London model(3)

B_{\mathbf{K}} = \frac{\exp\left({-K^2\xi^2/2(1-b)}\right)}{1 + K^2\lambda^2/(1-b)},

where b = \langle B \rangle/\mu_0H_{\mathrm{c}2}. -
Analytical Ginzburg-Landau model(4)

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}},

where 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)} and K_1 is a modified Bessel function. +
London model with Gaussian cutoffJ. Low Temp. Phys. 73, 355 (1988).">(2)

B_{\mathbf{K}} = \frac{\exp\left({-K^2\xi^2/2}\right)}{1 + K^2\lambda^2}

+
Modified London modelPhys. Rev. B 52, 10569 (1995).">(3)

B_{\mathbf{K}} = \frac{\exp\left({-K^2\xi^2/2(1-b)}\right)}{1 + K^2\lambda^2/(1-b)},

where b = \langle B \rangle/\mu_0H_{\mathrm{c}2}. +
Analytical Ginzburg-Landau modelPhys. Rev. B 55, 11107 (1997).">(4)

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}},

where 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)} and K_1 is a modified Bessel function.
-Apart from the mentioned analytical models the numerical Ginzburg-Landau model (5) is available. In this case B(\mathbf{r}) is obtained by an iterative minimization of the free energy of the vortex lattice. +Apart from the mentioned analytical models the numerical Ginzburg-Landau model Phys. Rev. B 68, 054506 (2003).">(5) is available. In this case B(\mathbf{r}) is obtained by an iterative minimization of the free energy of the vortex lattice.

Concerning the applicability (e.g. field regions) of each of the mentioned models please refer to the original publications!

@@ -414,7 +414,7 @@ An example XML file looks as follows:
 
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+
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@@ -445,17 +445,15 @@ An example XML file looks as follows:
-
+

- +

-

-

\ No newline at end of file diff --git a/doc/html/user/MUSR/LibZFRelaxation.html b/doc/html/user/MUSR/LibZFRelaxation.html index 736f1071..fd157a64 100644 --- a/doc/html/user/MUSR/LibZFRelaxation.html +++ b/doc/html/user/MUSR/LibZFRelaxation.html @@ -1,7 +1,7 @@ - + @@ -21,7 +21,7 @@ - + @@ -63,8 +63,6 @@ - +
@@ -121,6 +119,8 @@ pre {
+

+

libZFRelaxation

@@ -219,7 +219,7 @@ The parameters are:
 
-
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+
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@@ -250,17 +250,15 @@ The parameters are:
-
+

- +

-

-

\ No newline at end of file diff --git a/doc/html/user/MUSR/Msr2Data.html b/doc/html/user/MUSR/Msr2Data.html index dd97a9ab..2200443d 100644 --- a/doc/html/user/MUSR/Msr2Data.html +++ b/doc/html/user/MUSR/Msr2Data.html @@ -1,7 +1,7 @@ - + @@ -21,7 +21,7 @@ - + @@ -63,8 +63,6 @@ - +
@@ -121,6 +119,8 @@ pre {
+

+

msr2data

@@ -142,7 +142,7 @@ pre {

1 Introduction

-msr2data (originally written by B. M. Wojek) is a program implemented in C++. Its purpose is to process multiple musrfit msr files with the same parameters and summarize the fitting results either in a TRIUMF DB (1) or a column ASCII file. It evolved from a script called mlog2db which has been written only for collecting fit results of LEM data stored in mlog files generated by musrfit and putting them together in a file with the DB format for further analysis. Therefore, any peculiarities, e.g. in supplying options to msr2data are owed its original purpose. +msr2data (originally written by B. M. Wojek) is a program implemented in C++. Its purpose is to process multiple musrfit msr files with the same parameters and summarize the fitting results either in a TRIUMF DB here. The DB files produced by msr2data can be viewed for instance with μView, however, they are not completely 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!">(1) or a column ASCII file. It evolved from a script called mlog2db which has been written only for collecting fit results of LEM data stored in mlog files generated by musrfit and putting them together in a file with the DB format for further analysis. Therefore, any peculiarities, e.g. in supplying options to msr2data are owed its original purpose. msr2data is free software and licensed under the GNU GPL version 2 or any later version (at your option).

Before the usage of msr2data will be explained in greater detail first be aware of the following: @@ -379,7 +379,7 @@ For reporting bugs or requesting new features and improvements please use the
 
-
+
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@@ -410,17 +410,15 @@ For reporting bugs or requesting new features and improvements please use the
-
+

- +

-

-

\ No newline at end of file diff --git a/doc/html/user/MUSR/MusrFit.html b/doc/html/user/MUSR/MusrFit.html index f767f3ed..f6d715a1 100644 --- a/doc/html/user/MUSR/MusrFit.html +++ b/doc/html/user/MUSR/MusrFit.html @@ -1,7 +1,7 @@ - + @@ -21,7 +21,7 @@ - + @@ -63,8 +63,6 @@ - +
@@ -121,6 +119,8 @@ pre {
+

+

musrfit User Manual

@@ -131,11 +131,11 @@ pre {
  • 2.1 musrfit
  • 2.2 musrview
  • 2.3 musrt0 -
  • 2.4 musrparam -
  • 2.5 musrfit_startup.xml -
  • 2.6 msr2msr -
  • 2.7 any2many -
  • 2.8 nexus_dump +
  • 2.4 musrfit_startup.xml +
  • 2.5 msr2msr +
  • 2.6 any2many +
  • 2.7 nexus_dump +
  • 2.8 read_musrRoot_runHeader
  • 3 Auxiliary Programs
  • 4 Description of the msr File Format
      @@ -253,36 +253,8 @@ When all channels have been set correctly for the first histogram, pressing of t Using the key Q, musrt0 can be interrupted. No changes to the msr file are applied in this case.
      Closing a window by clicking the X button is equivalent to pressing Q, i.e. musrt0 is simply terminated.

      - -

      2.4 musrparam

      -musrparam is used in order to extract the fit parameters of multiple msr output files and to summarize them in a multi-column ASCII file which then can be imported by other programs like gnuplot, qtiplot or Origin® to name just a few. -As mandatory parameters it accepts two file names in the following order:
      -
      <input_file_name>
      file name of the control file to extract the parameters. -
      -The input file itself has the following structure: -
      -   msr-file-name-1, independent-var1-1, independent-var2-1
-   msr-file-name-2, independent-var1-2, independent-var2-2
-   etc.
-
      -It is allowed to add comment lines starting with %. -

      -
      <output_file_name>
      file name of the generated output file. -
      -The output will have the structure: -
      -   msr-file-name-1, independent-var1-1, ..., par1, err_par1, par2, err_par2, par3, err_par3, ...
-   msr-file-name-2, independent-var1-2, ..., par1, err_par1, par2, err_par2, par3, err_par3, ...
-   etc.
-
      -If positive and negative errors are present, it will be -
      -   msr-file-name-1, independent-var1-1, ..., par1, err_par1-, err_par1+, par2, err_par2-, err_par2+, ...
-   etc.
-
      -

      -

      2.5 musrfit_startup.xml

      +

      2.4 musrfit_startup.xml

      musrfit_startup.xml is a configuration file located at the musrfit binary path. In this file the following XML tags are allowed to define settings:
      <data_path>PATH_TO_DATA</data_path>
      add the new path PATH_TO_DATA where musrfit and musrview will search for data files
      <write_per_run_block_chisq>y/n</write_per_run_block_chisq>
      if enabled χ2 for each RUN block will be written to the STATISTIC block of the resulting msr file. Additionally, in case a χ2 single-histogram fit is done, also Pearson's χ2 will be added. @@ -338,7 +310,7 @@ An example would look like:

      -

      2.6 msr2msr

      +

      2.5 msr2msr

      msr2msr is a small utility for converting existing WKM msr files into musrfit msr files. It accepts the following parameters:
      <msr_file_in>
      input WKM msr file (mandatory first parameter)
      <msr_file_out>
      converted output musrfit msr file (mandatory second parameter) @@ -350,12 +322,12 @@ A typical example then looks like: If the input file has already the musrfit msr file structure, the output file will be just a copy of the input file.

      -

      2.7 any2many

      +

      2.6 any2many

      any2many is a muSR data file converter. Currently different facilities (PSI, TRIUMF, ISIS, J-PARC) are saving their muSR data files in different formats, or even worse some instruments are using other muSR data formats than others. The aim of any2many is that these files can be converted into each other. Of course only a subset of header information can be converted.

      Currently any2many can convert the following muSR data file formats:
        -
      • input formats: PSI-BIN (PSI bulk), ROOT (PSI LEM), MUD (TRIUMF), NeXus IDF1 and NeXus IDF2 (ISIS), PSI-MDU (PSI bulk internal only), WKM (outdated ascii file format). -
      • output formats: PSI-BIN, ROOT, MUD, NeXus1-HDF4, NeXus1-HDF5, NeXus1-XML, NeXus2-HDF4, NeXus2-HDF5, NeXus2-XML, WKM, ASCII +
      • input formats: MusrRoot, PSI-BIN (PSI bulk), ROOT (PSI LEM), MUD (TRIUMF), NeXus IDF1 and NeXus IDF2 (ISIS), PSI-MDU (PSI bulk internal only), WKM (outdated ascii file format). +
      • output formats: MusrRoot, PSI-BIN, ROOT, MUD, NeXus1-HDF4, NeXus1-HDF5, NeXus1-XML, NeXus2-HDF4, NeXus2-HDF5, NeXus2-XML, WKM, ASCII

      Since the goal was to create a very flexible converter tool, it has ample of options which will listed below, followed by many examples showing how to use it. The options:
      @@ -396,9 +368,13 @@ Will take the runs 100 through 117 and convert the NeXus input file Will read the two files '2010/lem10_his_0123.root' and '2010/lem10_his_0012.root', rebin them with 25 and export them as LEM ROOT files with adding rebin25 to the name, e.g. 2010/lem10_his_0123_rebin25.root.

      -

      2.8 nexus_dump

      +

      2.7 nexus_dump

      nexus_dump is a little program which tries to read a NeXus file and send the relevant information (required header info, start of the histos, etc.) to the standard output.

      + +

      2.8 read_musrRoot_runHeader

      +read_musrRoot_runHeader is a little program which tries to read a MusrRoot file and send the relevant header information to the standard output. +

      3 Auxiliary Programs

      Additionally to the programs mentioned above editor front ends called musrgui/musredit and another tool named msr2data are available. The purpose of msr2data is to process multiple msr files with the same parameters and to summarize the fitting results either in a DB or a column ASCII file. Also, new msr files can be generated from a template. For details refer to its manual. @@ -422,7 +398,7 @@ are various possible parameter definitions which are listed here: 2. <no> <name> <value> <step> <lower_boundary> <upper_boundary> 3. <no> <name> <value> <step> <pos_error> <lower_boundary> <upper_boundary> -where <no> is the parameter number, <name> is the parameter name (1), <value> is the initial guess of the parameter, <step> the inital step width, <lower/upper_boundary> is the lower/upper boundary for the parameter (2). +where <no> is the parameter number, <name> is the parameter name (1), <value> is the initial guess of the parameter, <step> the inital step width, <lower/upper_boundary> is the lower/upper boundary for the parameter (2).

      In the output file, <value> will be the MINUIT fit value, <step> will contain the error estimate (or the negative error estimate if MINOS was successfully used), <pos_error> will have the value none if MINOS has not been used, otherwise it will show the positive error estimate.

      @@ -519,35 +495,35 @@ The THEORY block is used to define the fit function. There is a set of predefine sgktlf \nu\,(\mathrm{MHz}), \sigma\,(\mu\text{s}^{-1}) G_{\mathrm{G,LF}}(t) \equiv 1-\frac{2\sigma^2}{(2\pi\nu)^2}\left[1-\exp\left(-\frac{1}{2}\sigma^2t^2\right)\cos(2\pi\nu t)\right]+\frac{2\sigma^4}{(2\pi\nu)^3}\int^t_0 \exp\left(-\frac{1}{2}\sigma^2\tau^2\right)\sin(2\pi\nu\tau)\mathrm{d}\tau - (4) + Phys. Rev. B 20 (1979) 850 ">(4) dynGssKTLF dgktlf \nu\,(\mathrm{MHz}), \sigma\,(\mu\text{s}^{-1}), \Gamma\,(\mathrm{MHz}) \frac{1}{2\pi \imath}\int_{\gamma-\imath\infty}^{\gamma+\imath\infty} \frac{f_{\mathrm{G}}(s+\Gamma)}{1-\Gamma f_{\mathrm{G}}(s+\Gamma)} \exp(s t) \mathrm{d}s,\mathrm{where}\,f_{\mathrm{G}}(s)\equiv \int_0^{\infty}G_{\mathrm{G,LF}}(t)\exp(-s t) \mathrm{d}t - (5) + Phys. Rev. B 20 (1979) 850; P. Dalmas de Réotier and A. Yaouanc, J. Phys.: Condens. Matter 4 (1992) 4533; A. Keren, Phys. Rev. B 50 (1994) 10039 ">(5) statExpKT sekt \lambda\,(\mu\text{s}^{-1}) \frac{1}{3} + \frac{2}{3} \left[1-\lambda t\right] \exp\left(-\lambda t\right) - (6) + Phys. Rev. B 31 (1985) 546 ">(6) statExpKTLF sektlf \nu\,(\mathrm{MHz}), a\,(\mu\text{s}^{-1}) 1-\frac{a}{2\pi\nu}j_1(2\pi\nu t)\exp\left(-at\right)-\left(\frac{a}{2\pi\nu}\right)^2 \left[j_0(2\pi\nu t)\exp\left(-at\right)-1\right]-a\left[1+\left(\frac{a}{2\pi\nu}\right)^2\right]\int^t_0 \exp\left(-a\tau\right)j_0(2\pi\nu\tau)\mathrm{d}\tau \equiv G_{\mathrm{L,LF}}(t) - (7) + Phys. Rev. B 31 (1985) 546 ">(7) dynExpKTLF dektlf \nu\,(\mathrm{MHz}), a\,(\mu\text{s}^{-1}), \Gamma\,(\mathrm{MHz}) \frac{1}{2\pi \imath}\int_{\gamma-\imath\infty}^{\gamma+\imath\infty} \frac{f_{\mathrm{L}}(s+\Gamma)}{1-\Gamma f_{\mathrm{L}}(s+\Gamma)} \exp(s t) \mathrm{d}s,\mathrm{where}\,f_{\mathrm{L}}(s)\equiv \int_0^{\infty}G_{\mathrm{L,LF}}(t)\exp(-s t) \mathrm{d}t - (8) + Phys. Rev. B 20 (1979) 850; P. Dalmas de Réotier and A. Yaouanc, J. Phys.: Condens. Matter 4 (1992) 4533 ">(8) combiLGKT @@ -568,7 +544,7 @@ The THEORY block is used to define the fit function. There is a set of predefine rahf \nu\,(\mathrm{MHz}), \lambda\,(\mu\text{s}^{-1}) \frac{1}{6}\left(1-\frac{\nu t}{2}\right)\exp\left(-\frac{\nu t}{2}\right)+\frac{1}{3}\left(1-\frac{\nu t}{4}\right)\exp\left(-\frac{\nu t + 2.44949\lambda t}{4}\right) - (9) + Phys. Rev. B 34 (1986) 4467 ">(9) TFieldCos @@ -972,7 +948,7 @@ The last accepted command in the COMMAND block is SCALE_N0_BKG TRUE | FA The Fourier transform is done and the results are plotted within musrview —as input data the actual data shown in musrview is used. In the FOURIER block of the msr file all necessary parameters for calculating and presenting the Fourier transform of the data specified in the PLOT block is given. If the FOURIER block is not present in the msr file, either the parameters set in the XML startup file or the system defaults are taken when the Fourier transform is performed. The block starts with the FOURIER keyword and may contain the following entries on the successive lines:
      units
      Here is specified in which domain the Fourier-transformed data is presented. One may choose between the field (Gauss), the frequency (MHz), and the angular-frequency domain (Mc/s).
      fourier_power
      It is possible (but not necessary) to set the number of data points used for the Fourier transform here. As argument the exponent n<21 of a power of 2 is accepted. The number of data points is then 2n. Attention: If the number of points given here is bigger than the actual number of available data points, the input data vector is filled with zeros until the number of requested points is reached (zero padding)! -
      apodization
      Here is decided if the data should be apodized before the Fourier transform is done and if yes, which apodization should be used(10). The argument to be put after the keyword is therefore one of the following: NONE, WEAK, MEDIUM or STRONG. If the data should be apodized, they are manipulated as follows: each data value is multiplied by the function \sum_{j=0}^4 c_j \left(\frac{i}{n}\right)^{2j}, where i is the data-point index and n is the total number of data points. The coefficients c_j for the different apodizations are given by:
      +
      apodization
      Here is decided if the data should be apodized before the Fourier transform is done and if yes, which apodization should be usedthe PhD thesis of T.M. Riseman <span class="foswikiIcon">pdf">(10). The argument to be put after the keyword is therefore one of the following: NONE, WEAK, MEDIUM or STRONG. If the data should be apodized, they are manipulated as follows: each data value is multiplied by the function \sum_{j=0}^4 c_j \left(\frac{i}{n}\right)^{2j}, where i is the data-point index and n is the total number of data points. The coefficients c_j for the different apodizations are given by:
      WEAK
      c_0 = 1,\, c_1 = -1.319391,\, c_2 = 0.703484,\, c_3=c_4=0
      MEDIUM
      c_0 = 1,\, c_1 = -1.831292,\, c_2 = 0.983734,\, c_3=c_4=0
      STRONG
      c_0 = 1,\, c_1 = -2.708894,\, c_2 = 2.953575,\, c_3=-1.599128,\, c_4=0.399782 @@ -1448,7 +1424,7 @@ For reporting bugs or requesting new features and improvements please use the
    •  
    -
    +
    Ideas, requests, problems regarding PSI Wiki? Send feedback
    @@ -1479,17 +1455,15 @@ For reporting bugs or requesting new features and improvements please use the
    -
    +

    - +

    -

    -

    \ No newline at end of file diff --git a/doc/html/user/MUSR/MusrFitAcknowledgements.html b/doc/html/user/MUSR/MusrFitAcknowledgements.html index 6a95340d..77d2199b 100644 --- a/doc/html/user/MUSR/MusrFitAcknowledgements.html +++ b/doc/html/user/MUSR/MusrFitAcknowledgements.html @@ -1,7 +1,7 @@ - + @@ -21,7 +21,7 @@ - + @@ -63,8 +63,6 @@ - +
    @@ -121,6 +119,8 @@ pre {
    +

    +

    Acknowledgements - musrfit

    Bastian M. Wojek
    I am very much indebted to BMW for his rigorous testing of musrfit, his many useful suggestions, contributions, and for the largest part of the user manual of musrfit which makes it accessible to a broader audience! Many thanks Bastian! @@ -136,7 +136,7 @@ pre {
     
    -
    Ideas, requests, problems regarding PSI Wiki? Send feedback
    +
    Ideas, requests, problems regarding PSI Wiki? Send feedback
    @@ -167,17 +167,15 @@ pre {
    -
    +

    - +

    -

    -

    \ No newline at end of file diff --git a/doc/html/user/MUSR/MusrFitSetup.html b/doc/html/user/MUSR/MusrFitSetup.html index 1c2d5d14..4aed7b08 100644 --- a/doc/html/user/MUSR/MusrFitSetup.html +++ b/doc/html/user/MUSR/MusrFitSetup.html @@ -1,7 +1,7 @@ - + @@ -21,7 +21,7 @@ - + @@ -63,8 +63,6 @@ - +
    @@ -121,6 +119,8 @@ pre {
    +

    +

    Setting up musrfit on Different Platforms

      @@ -235,7 +235,7 @@ Even though there might exist binary packages for the NeXus library The ROOT 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.
      In case the distribution provides no or only outdated binary packages there are the following possibilities:
      • Visit the ROOT web page and download the packed precompiled binary version matching best the GNU/Linux distribution. Then unpack the bundle to its final destination. -
      • If there is no precompiled binary version of ROOT available for your system or e.g. ROOT should be compiled with another version of GCC visit the web page and download the 'complete source tree for all systems'. Then unpack this source tree to its destination (e.g. /opt/root-system)(1), configure(2) it (here using the minimal set of options) and compile it as follows right below: 
        +
      • If there is no precompiled binary version of ROOT available for your system or e.g. ROOT should be compiled with another version of GCC visit the web page and download the 'complete source tree for all systems'. Then unpack this source tree to its destination (e.g. /opt/root-system)chown username:username /opt/root-system/ -R">(1), configure(2) it (here using the minimal set of options) and compile it as follows right below: 
         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)
@@ -292,7 +292,7 @@ After the source-code extraction the autogen.sh script is calle
  
 
        
 Normally it should not be necessary to make use of any of the options except for specifying the installation path with --prefix. The other paths should be detected automatically. If this does not work for some reason the configure script will terminate and ask for the information.
-When the configure script has been called successfully everything is ready for building the musrfit libraries and executables. A standard installation sequence (without NeXus support) might then look like(3):
+When the configure script has been called successfully everything is ready for building the musrfit libraries and executables. A standard installation sequence (without NeXus support) might then look like(3):
 
         cd musrfit
 sh autogen.sh
@@ -339,7 +339,7 @@ musrview test-histo-ROOT-NPP.msr
 
        
 Notes
 
        
- 1 : 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: 
        chown username:username /opt/root-system/ -R
         
+ 1 : 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:  
 
        
  2 :  When using GCC ≥ 4.2 please make sure that the environment variables USE_PARALLEL_MINUIT2 and USE_OPENMP are not set! Otherwise MINUIT2 will be compiled with parallelization support and cannot be used together with musrfit afterwards since the musrfit code is not fully thread-safe! When compiled with GCC ≥ 4.2 musrfit itself will parallelize the χ2 calculation. 
 
        
@@ -410,7 +410,7 @@ In order to install the ROOT system, there are two possibilities: <
 cd /cygdrive/c
 tar xzf root_v5.xx.yy.win32gcc-gcc-4.3.tar.gz
 
        
-
      • If due to some reason there was no precompiled Cygwin GCC 4.3 package available or ROOT should be built from source, one has to visit the web page, download the 'complete source tree for all systems' and save it for instance in C:\.
        Then go to the Cygwin shell and unpack this source tree, configure(2) it (here using the minimal set of options) and compile it as follows right below:
        +
      • If due to some reason there was no precompiled Cygwin GCC 4.3 package available or ROOT should be built from source, one has to visit the web page, download the 'complete source tree for all systems' and save it for instance in C:\.
        Then go to the Cygwin shell and unpack this source tree, configure(2) it (here using the minimal set of options) and compile it as follows right below:
         cd /cygdrive/c
 tar xzf root_v5.xx.yy.source.tar.gz
 cd root
@@ -774,7 +774,7 @@ qmake musrgui.pro
 make
 make install
        -The last command copies musrgui.app to the standard program directory /Applications (4) and the musrgui_startup.xml to $ROOTSYS/bin/musrgui_startup.xml. Eventually, in the installed musrgui_startup.xml the path-specifications have to be adjusted to match the local musrfit installation. For detailed information on this XML file refer to the manual. +The last command copies musrgui.app to the standard program directory /Applications (4) and the musrgui_startup.xml to $ROOTSYS/bin/musrgui_startup.xml. Eventually, in the installed musrgui_startup.xml the path-specifications have to be adjusted to match the local musrfit installation. For detailed information on this XML file refer to the manual.

        Under some circumstances it might happen, that if musrgui was called from Finder the necessary libraries for executing musrfit could not be found. In that case, the only workaround for the moment is to export the environment variable DYLD_LIBRARY_PATH in the shell and call musrgui from a terminal! @@ -812,7 +812,7 @@ musrview test-histo-ROOT-NPP.msr
     
    -
    Ideas, requests, problems regarding PSI Wiki? Send feedback
    +
    Ideas, requests, problems regarding PSI Wiki? Send feedback
    @@ -843,17 +843,15 @@ musrview test-histo-ROOT-NPP.msr
    -
    +

    - +

    -

    -

    \ No newline at end of file diff --git a/doc/html/user/MUSR/MusrGui.html b/doc/html/user/MUSR/MusrGui.html index 916bb4b3..2afc3428 100644 --- a/doc/html/user/MUSR/MusrGui.html +++ b/doc/html/user/MUSR/MusrGui.html @@ -1,7 +1,7 @@ - + @@ -21,7 +21,7 @@ - + @@ -63,8 +63,6 @@ - +
    @@ -121,6 +119,8 @@ pre {
    +

    +

    musrgui / musredit

    @@ -451,7 +451,7 @@ For reporting bugs or requesting new features and improvements please use the
     
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    @@ -482,17 +482,15 @@ For reporting bugs or requesting new features and improvements please use the
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    \ No newline at end of file diff --git a/doc/html/user/MUSR/QuickStart.html b/doc/html/user/MUSR/QuickStart.html index 7b8b045b..239942cb 100644 --- a/doc/html/user/MUSR/QuickStart.html +++ b/doc/html/user/MUSR/QuickStart.html @@ -1,7 +1,7 @@ - + @@ -21,7 +21,7 @@ - + @@ -63,8 +63,6 @@ - +
    @@ -121,6 +119,8 @@ pre {
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    +

    Quickstart for WKM users

     
    -
    Ideas, requests, problems regarding PSI Wiki? Send feedback
    +
    Ideas, requests, problems regarding PSI Wiki? Send feedback
    @@ -305,17 +305,15 @@ RUN 2008/lem08_his_8472 MUE4 PSI ROOT-NPP (name beamline institute dat
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    \ No newline at end of file diff --git a/doc/html/user/MUSR/TutorialSingleHisto.html b/doc/html/user/MUSR/TutorialSingleHisto.html index c2566199..4b9d2bf1 100644 --- a/doc/html/user/MUSR/TutorialSingleHisto.html +++ b/doc/html/user/MUSR/TutorialSingleHisto.html @@ -1,7 +1,7 @@ - + @@ -21,7 +21,7 @@ - + @@ -63,8 +63,6 @@ - +
    @@ -121,6 +119,8 @@ pre {
    +

    +

    musrfit Single-Histogram-Fit Tutorial

    The μSR-data-analysis process using musrfit is based on so-called msr files. These files contain all information needed for the analysis such as names of the data files, a theory function, fit and plot parameters, and so on. It is the idea of this page to explain the basic use of an msr file and the different programs of the musrfit 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 manual. @@ -361,7 +361,7 @@ This page only summarizes the very basic features and options of the programs co
     
    -
    Ideas, requests, problems regarding PSI Wiki? Send feedback
    +
    Ideas, requests, problems regarding PSI Wiki? Send feedback
    @@ -392,17 +392,15 @@ This page only summarizes the very basic features and options of the programs co
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    - +

    -

    -

    \ No newline at end of file diff --git a/doc/html/user/MUSR/WebHome.html b/doc/html/user/MUSR/WebHome.html index df8494cc..933a0be5 100644 --- a/doc/html/user/MUSR/WebHome.html +++ b/doc/html/user/MUSR/WebHome.html @@ -1,7 +1,7 @@ - + @@ -21,7 +21,7 @@ - + @@ -63,8 +63,6 @@ - +
    @@ -121,6 +119,8 @@ pre {
    +

    +

    Welcome to the MUSR web

    Documentation of the μSR data analysis suite musrfit

    +-- AS & BMW - last update 28. March 2012

    @@ -148,7 +149,7 @@ pre {
     
    -
    Ideas, requests, problems regarding PSI Wiki? Send feedback
    +
    Ideas, requests, problems regarding PSI Wiki? Send feedback
    @@ -179,17 +180,15 @@ pre { - +

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    -

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none;border-width:1px;}.foswikiHorizontalList ul li.foswikiLast{border:none;} \ No newline at end of file diff --git a/doc/musrfit.dox b/doc/musrfit.dox index eced5d4c..34325042 100644 --- a/doc/musrfit.dox +++ b/doc/musrfit.dox @@ -51,6 +51,9 @@ How to setup musrfit on different platforms: \texttt{http://lmu.web.psi.ch/facil - \ref MuSRFit A graphical user interface based on PerlQt (written by Z. Salman) for an easy to use interface to the musrfit framework. Compared to the more general approach of writting msr-files, it has some limitations, though it might be easier for a first user of the musrfit framework. - \ref any2many Should be a "universal" muSR data-file-format converter. - \ref nexus_dump Is a small program to dump NeXus file information (mainly run header info) to the standard output. +- \ref musrRootValidation This is a program to validate MusrRoot files. +- \ref read_musrRoot_runHeader Is a small program to dump MusrRoot file information (mainly run header info) to the standard output. +- \ref write_musrRoot_runHeader Is a little example program showing how to write MusrRoot files. \section roadmap Road map and missing features @@ -142,4 +145,19 @@ PSI firewall required). \section nexus_dump nexus_dump

    This is a little help program which reads a NeXus file and dumps most of the relevant information to the standard output. +//**************************************************************************************************** +\page musrRootValidationPage +\section musrRootValidation musrRootValidation +

    This program allows to validate a given (or supposedly given) MusrRoot file if it is consistent with the minimal required entries via XML Schema schemes. +Please check \htmlonlyMusrRoot web-page\endhtmlonly \latexonly MusrRoot web-page: \texttt{http://lmu.web.psi.ch/facilities/software/musrfit/user/MUSR/MusrRoot.html}\endlatexonly + +//**************************************************************************************************** +\page read_musrRoot_runHeader_Page +\section read_musrRoot_runHeader read_musrRoot_runHeader +

    This is a little help program which reads a MusrRoot file and dumps the RunHeader information to the standard output. + +//**************************************************************************************************** +\page write_musrRoot_runHeader_Page +\section write_musrRoot_runHeader write_musrRoot_runHeader +

    This is a little help program shows how to write a MusrRoot file. */ diff --git a/doc/musrfit_dox.cfg b/doc/musrfit_dox.cfg index 47a2da9f..29f64c30 100644 --- a/doc/musrfit_dox.cfg +++ b/doc/musrfit_dox.cfg @@ -23,7 +23,7 @@ PROJECT_NAME = musrfit # This could be handy for archiving the generated documentation or # if some version control system is used. -PROJECT_NUMBER = 0.9.0 +PROJECT_NUMBER = 0.10.0 # The OUTPUT_DIRECTORY tag is used to specify the (relative or absolute) # base path where the generated documentation will be put. @@ -507,12 +507,17 @@ INPUT = musrfit.dox \ ../src/classes/PTheory.cpp \ ../src/classes/PUserFcnBase.cpp \ ../src/classes/PUserFcn.cpp \ + ../src/external/MusrRoot/TMusrRunHeader.h \ + ../src/external/MusrRoot/TMusrRunHeader.cpp \ ../src/msr2data.cpp \ ../src/msr2msr.cpp \ ../src/musrfit.cpp \ - ../src/musrparam.cpp \ ../src/musrt0.cpp \ - ../src/musrview.cpp + ../src/musrview.cpp \ + ../src/nexus_dump.cpp \ + ../src/musrRootValidation.cpp \ + ../src/read_musrRoot_runHeader.cpp \ + ../src/write_musrRoot_runHeader.cpp # If the value of the INPUT tag contains directories, you can use the # FILE_PATTERNS tag to specify one or more wildcard pattern (like *.cpp diff --git a/src/external/MusrRoot/MusrRootValidationScheme.odp b/src/external/MusrRoot/MusrRootValidationScheme.odp new file mode 100644 index 00000000..3b125661 Binary files /dev/null and b/src/external/MusrRoot/MusrRootValidationScheme.odp differ