From 72c29c6250154e543aef06fbc1680e8b4a165031 Mon Sep 17 00:00:00 2001 From: Andreas Suter Date: Tue, 8 May 2012 05:28:03 +0000 Subject: [PATCH] updating docu --- ChangeLog | 1 + doc/html/user/MUSR/BmwLibs.html | 35 +--- doc/html/user/MUSR/LibFitPofB.html | 49 ++---- doc/html/user/MUSR/LibZFRelaxation.html | 35 +--- doc/html/user/MUSR/Msr2Data.html | 79 +++------ doc/html/user/MUSR/MusrFit.html | 158 ++++++++---------- .../user/MUSR/MusrFitAcknowledgements.html | 35 +--- doc/html/user/MUSR/MusrFitSetup.html | 91 ++++------ doc/html/user/MUSR/MusrGui.html | 39 +---- doc/html/user/MUSR/QuickStart.html | 37 +--- doc/html/user/MUSR/TutorialSingleHisto.html | 37 +--- doc/html/user/MUSR/WebHome.html | 37 +--- .../pub/System/DocumentGraphics/external.gif | Bin 79 -> 63 bytes .../user/pub/System/PatternSkin/print.css | 2 +- .../pub/System/PatternSkinTheme2009/style.css | 18 +- .../user/pub/System/SkinTemplates/base.css | 2 +- doc/musrfit_dox.cfg | 2 +- src/classes/PRunMuMinus.cpp | 8 +- 18 files changed, 193 insertions(+), 472 deletions(-) diff --git a/ChangeLog b/ChangeLog index b193df36..8ff48b37 100644 --- a/ChangeLog +++ b/ChangeLog @@ -9,6 +9,7 @@ changes since 0.11.0 NEW 2012-04-24 added a first version for negative muon fitting. At the same time substaintial bug fixing has been carried out (mainly the logx/logy handling). +CHANGED 2012-05-08 updating docu changes since 0.10.0 =================================== diff --git a/doc/html/user/MUSR/BmwLibs.html b/doc/html/user/MUSR/BmwLibs.html index 795d441e..ddd61b2f 100644 --- a/doc/html/user/MUSR/BmwLibs.html +++ b/doc/html/user/MUSR/BmwLibs.html @@ -1,7 +1,7 @@ - + @@ -21,7 +21,7 @@ - + @@ -109,7 +109,7 @@ pre { - +
@@ -144,39 +144,12 @@ pre {

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Oscar Fridolin
Telefon:1234512345
E-Mail:oscarfridolin@psi.ch
Büro:WHGA/019
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diff --git a/doc/html/user/MUSR/LibFitPofB.html b/doc/html/user/MUSR/LibFitPofB.html index d8707b07..63b784ae 100644 --- a/doc/html/user/MUSR/LibFitPofB.html +++ b/doc/html/user/MUSR/LibFitPofB.html @@ -1,7 +1,7 @@ - + @@ -21,7 +21,7 @@ - + @@ -109,7 +109,7 @@ pre { - +
@@ -147,13 +147,13 @@ where \gamma_{\mu} = 2\pi\times 135.54~\mathrm{MHz/T}low-energy μSR in the Meissner state or by conventional μSR in the mixed state. In the following the basic usage of the library in musrfit 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.

-Remark 1: In order to supply certain information needed for the calculations but not suited to be stored in the musrfit msr files an XML configuration file in the working directory is used. For details, see below. +Remark 1: In order to supply certain information needed for the calculations but not suited to be stored in the musrfit msr files an XML configuration file in the working directory is used. For details, see below.

-Remark 2: The implementations in this library heavily rely on FFTW3. 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 ("wisdom handling"). In case this feature shall be used, a valid wisdom file has to be specified in the XML file. +Remark 2: The implementations in this library heavily rely on FFTW3. 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 ("wisdom handling"). In case this feature shall be used, a valid wisdom file has to be specified in the XML file.

-Remark 3: The model functions described in the following do generally not behave nicely in conjunction with MINUIT function minimizations (or maximizations). The analysis process at the moment in most cases involves some tedious trial-and-error procedure, where the displayed MINUIT 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 msr2data cannot be advised. +Remark 3: The model functions described in the following do generally not behave nicely in conjunction with MINUIT function minimizations (or maximizations). The analysis process at the moment in most cases involves some tedious trial-and-error procedure, where the displayed MINUIT 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 msr2data cannot be advised.

-Remark 4: If these classes still prove useful and results obtained through them are part of scientific publications, +Remark 4: 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.

2 LE-μSR

@@ -281,7 +281,7 @@ where \mathbf{r}=(x,y)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! +Concerning the applicability (e.g. field regions) of each of the mentioned models please refer to the original publications!

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 XML file.
The muon-spin depolarization functions finally are calculated using the following lines in the THEORY block of a musrfit msr file:
2D triangular vortex lattice, London model with Gaussian cutoff 
@@ -328,7 +328,7 @@ The parameters are: 
    
  
  1.  Ginzburg-Landau coherence length (nm)
 
 
 

-Remark: In order to improve the convergence of MIGRAD it has proven useful to use the log-likelihood maximization instead of the χ2 minimization routines and to choose sufficiently large initial steps for the parameters. Calling MINOS in conjunction with these functions is futile.
Therefore, the COMMANDS block of the msr file could look like:
+Remark: In order to improve the convergence of MIGRAD it has proven useful to use the log-likelihood maximization instead of the χ2 minimization routines and to choose sufficiently large initial steps for the parameters. Calling MINOS in conjunction with these functions is futile.
Therefore, the COMMANDS block of the msr file could look like:
 
 COMMANDS
 STRATEGY 0
@@ -368,7 +368,7 @@ Notes
 
 <data_path>DATA_PATH_PREFIX</data_path> 
 specify the DATA_PATH_PREFIX to the TRIM.SP implantation profiles (inside a <LEM> environment)
 
 
 <N_theory>N_THEORY</N_theory> 
 specify the number of points N_THEORY for which B(z) is calculated (inside a <LEM> environment)
The specification of this number is not needed if the calculation of the inverse of B(z) is implemented!
 
 
 <energy_list></energy_list> 
 set the energies for which TRIM.SP implantation profiles are available (inside a <LEM> environment) 

-
 <energy_label>LABEL</energy_label> 
 specify the LABEL within the file name of a available TRIM.SP RGE file (inside a <energy_list> environment)
The expected name of the RGE file will be: DATA_PATH_PREFIX + LABEL + .rge
+
 <energy_label>LABEL</energy_label> 
 specify the LABEL within the file name of a available TRIM.SP RGE file (inside a <energy_list> environment)
The expected name of the RGE file will be: DATA_PATH_PREFIX + LABEL + .rge
 
 
 <energy>E</energy> 
 specify the muon energy E (in keV) belonging to the TRIM.SP RGE file given above (inside a <energy_list> environment)
@@ -420,39 +420,12 @@ An example XML file looks as follows:

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Oscar Fridolin
Telefon:1234512345
E-Mail:oscarfridolin@psi.ch
Büro:WHGA/019
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- +

diff --git a/doc/html/user/MUSR/LibZFRelaxation.html b/doc/html/user/MUSR/LibZFRelaxation.html index fd157a64..929249c3 100644 --- a/doc/html/user/MUSR/LibZFRelaxation.html +++ b/doc/html/user/MUSR/LibZFRelaxation.html @@ -1,7 +1,7 @@ - + @@ -21,7 +21,7 @@ - + @@ -109,7 +109,7 @@ pre { - +
@@ -225,39 +225,12 @@ The parameters are:

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Oscar Fridolin
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E-Mail:oscarfridolin@psi.ch
Büro:WHGA/019
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diff --git a/doc/html/user/MUSR/Msr2Data.html b/doc/html/user/MUSR/Msr2Data.html index 2200443d..c253c405 100644 --- a/doc/html/user/MUSR/Msr2Data.html +++ b/doc/html/user/MUSR/Msr2Data.html @@ -1,7 +1,7 @@ - + @@ -21,7 +21,7 @@ - + @@ -109,7 +109,7 @@ pre { - +
@@ -147,7 +147,7 @@ pre {

Before the usage of msr2data will be explained in greater detail first be aware of the following:

-If using msr2data always bear in mind its limitations! +If using msr2data always bear in mind its limitations!

@@ -183,7 +183,7 @@ RUN VAR1 VAR2 VAR3 ... · · · · · · · · -The first not commented and not empty line determines the parameter names and labels and has to be present!
+The first not commented and not empty line determines the parameter names and labels and has to be present!
It is allowed to add comments (with a preceding #) or empty lines to the run-list file.

The following should be mentioned together with the above examples:
    @@ -191,7 +191,7 @@ The following should be mentioned together with the above examples:
    • If the files have been newly created, also the DB 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 header and noheader options as shall be seen later.
      -
    • If the musrfit output files do not have an <extension> as specified above like 8472.msr one has to call msr2data like in the following example: 
      +
    •  If the musrfit output files do not have an <extension> as specified above like 8472.msr one has to call msr2data like in the following example: 
       msr2data 8472 8460 ""
    @@ -232,7 +232,7 @@ Take the given msr files 8472.msr through < 
     msr2data 8472 8475 _tf_h13 msr-8471!
    -Using 8471_tf_h13.msr as template for all runs, msr2data generates the msr input files 8472_tf_h13.msr through 8475_tf_h13.msr. No fitting will be performed and no DB or ASCII output will be generated! +Using 8471_tf_h13.msr as template for all runs, msr2data generates the msr input files 8472_tf_h13.msr through 8475_tf_h13.msr. No fitting will be performed and no DB or ASCII output will be generated!

    4 The Global Mode

    @@ -282,7 +282,7 @@ The example's global FITPARAMETER block would be:
     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.
    
 During this reorganization all the affected parameter occurrences are changed accordingly!
 
    
-Please be aware of the fact that comments in the template msr file are not propagated to the newly generated global msr file!
+Please be aware of the fact that comments in the template msr file are not propagated to the newly generated global msr file!
 
    
 
     4.2  Parameter Extraction 
    
 After fitting some model to the specified data the fit parameters can be extracted from the global msr file to a DB or column-structured ASCII file—as usual this includes also parameters stored in the run data files or externally specified parameters given in a run-list file.
@@ -306,13 +306,13 @@ The single run msr files are not deleted at the moment. The information containe
 msr2data 8471 8470 -OneRunFit_example -o OneRunFits.db

    -Please be aware that the program in this mode always generates new single-run msr files and always calls musrfit 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. +Please be aware that the program in this mode always generates new single-run msr files and always calls musrfit 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.

    5 Known Limitations

    • The indexing run number of the msr file has to be at the begin of every filename.
    • Within the data file name the RUN# has the format %0Xu, i.e. X digits with leading zeros, and has to be the rightmost number given in this format in the file name. X has to be at least 4. The highest treatable run number is 232-1 = 4294967295. -
    • In order to keep msr2data working properly the msr files should only contain one STATISTIC block at the end of the file and one FITPARAMETER block right after the TITLE—musrfit itself allows to have more creative msr files... +
    • In order to keep msr2data working properly the msr files should only contain one STATISTIC block at the end of the file and one FITPARAMETER block right after the TITLE—musrfit itself allows to have more creative msr files...
    • The msr-file generation from a template takes only care of runs given on the first line of a RUN block. ADDRUN statements are simply copied! Since this is most probably not what one likes to do, it is suggested not to use the fit-<template> and msr-<template> options if ADDRUN statements were present in the template file.
    • msr2data will write only up to two successive empty lines in newly generated msr files. In case more subsequent empty lines are encountered in a template file, these are not copied! Actually, this measure is not a limitation but has been introduced to keep the msr files in a reasonable shape.
    @@ -321,21 +321,21 @@ msr2data 8471 8470 -OneRunFit_example -o OneRunFits.db

    6 The Graphical User Interface Provided by musrgui / musredit

    musrgui/musredit, editors designed especially for the manipulation of musrfit msr files and graphical front ends to musrfit, offer an almost self-explanatory graphical user interface to msr2data depicted below:
    msr2data-input-tabs.png
    -
    1–3
    Choose one of the ways to specify your list of runs. -
    4
    Give the file extension here, e.g. _zf for files like 8472_zf.msr. If the files do not have an extension this field stays empty. musrgui / musredit take care of passing the "" to msr2data as mentioned above. -
    5
    Activates the fit-<template> option if <template> is entered. In case the option "Chain Fit" is not set the given template will be used for the input-file generation for all 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! -
    6
    Activates the -o<outputFileName> option if <outputFileName> is entered. If nothing is entered the default output file out.db or out.dat is used. -
    7
    If not set, the noheader option is passed to msr2data. -
    8
    If set, the nosummary option is passed to msr2data. -
    9
    If set, the -k option is passed to msr2data. -
    10
    If set, the data option is passed to msr2data. -
    11
    If set, the output file is deleted before msr2data is called. Otherwise the data is appended to the file if it existed before msr2data has been called. -
    12
    If set, after processing by msr2data all specified msr files are opened in tabs in musrgui / musredit. -
    13
    If set, the -t option is passed to msr2data. -
    14
    If set, msr2data is called with the option msr-<template> (instead of fit-<template>) and hence is only producing the msr input files without any fitting. -
    15
    If set, msr2data is called with the option fit, i.e. no template will be used to generate new msr input files; only existing files are fed to musrfit. -
    16
    If set, msr2data is operating in the global mode. -
    17
    If set, msr2data is operating in the extended global mode. +
    1–3
    Choose one of the ways to specify your list of runs. +
    4
    Give the file extension here, e.g. _zf for files like 8472_zf.msr. If the files do not have an extension this field stays empty. musrgui / musredit take care of passing the "" to msr2data as mentioned above. +
    5
    Activates the fit-<template> option if <template> is entered. In case the option "Chain Fit" is not set the given template will be used for the input-file generation for all 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! +
    6
    Activates the -o<outputFileName> option if <outputFileName> is entered. If nothing is entered the default output file out.db or out.dat is used. +
    7
    If not set, the noheader option is passed to msr2data. +
    8
    If set, the nosummary option is passed to msr2data. +
    9
    If set, the -k option is passed to msr2data. +
    10
    If set, the data option is passed to msr2data. +
    11
    If set, the output file is deleted before msr2data is called. Otherwise the data is appended to the file if it existed before msr2data has been called. +
    12
    If set, after processing by msr2data all specified msr files are opened in tabs in musrgui / musredit. +
    13
    If set, the -t option is passed to msr2data. +
    14
    If set, msr2data is called with the option msr-<template> (instead of fit-<template>) and hence is only producing the msr input files without any fitting. +
    15
    If set, msr2data is called with the option fit, i.e. no template will be used to generate new msr input files; only existing files are fed to musrfit. +
    16
    If set, msr2data is operating in the global mode. +
    17
    If set, msr2data is operating in the extended global mode.

    @@ -385,39 +385,12 @@ For reporting bugs or requesting new features and improvements please use the

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Oscar Fridolin
Telefon:1234512345
E-Mail:oscarfridolin@psi.ch
Büro:WHGA/019
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diff --git a/doc/html/user/MUSR/MusrFit.html b/doc/html/user/MUSR/MusrFit.html index f6d715a1..2e015a1e 100644 --- a/doc/html/user/MUSR/MusrFit.html +++ b/doc/html/user/MUSR/MusrFit.html @@ -1,7 +1,7 @@ - + @@ -21,7 +21,7 @@ - + @@ -109,7 +109,7 @@ pre { - +
@@ -156,7 +156,7 @@ pre {
  • 5 The Fit Types
  • 6 User Functions
      @@ -183,6 +183,7 @@ If called from within a shell it accepts several parameters:
      -c, --chisq-only
      Instead of fitting the model, musrfit calculates χ2 only once and sends the result to the standard output if called with this option. This might be useful for the adjustment of the initial values of the fit parameters.
      -t, --title-from-data-file
      If this option is given musrfit will replace the title in the <msr_file> by the run title in the data file of the first run appearing in a RUN block. In case there is no run title in the data file no substitution is done.
      --dump <type>
      is writing a data file with the fit data and the theory; <type> can be ascii (data in columns) or root (data in ROOT histograms) +
      --timeout <timeout_tag>
      overwrites the predefined timeout tag 'none'. <timeout_tag>='none' means the timeout facility is not enabled. <timeout_tag> = nn will set the timeout to nn (sec). If during a fit this timeout is reached, musrfit will terminate. This is used to prevent orphan musrfit process to jam the system.
      --help
      displays a small help notice in the shell explaining the basic usage of the program
      --version
      prints the version number of musrfit
      @@ -196,6 +197,7 @@ the fit described in the input file will be executed and the results will be wri musrview is an interactive graphical user interface for the presentation of the analyzed data and the corresponding fits. If called from within a shell it accepts the following parameters:
      <msr_file>
      name of the msr input or output file to be displayed—this parameter is mandatory
      --<graphic_format_extension>
      will produce a graphics output file without starting a ROOT session. The filename is based on the name of the <msr_file>, e.g. 8472.msr → 8472_0.png
      Supported values for <graphic_format_extension> are eps, pdf, gif, jpg, png, svg, xpm, root +
      --timeout <timeout>
      <timeout> given in seconds after which musrview terminates. If <timeout> <= 0, no timeout will take place. Default for <timeout> is 0.
      --help
      displays a small help notice in the shell explaining the basic usage of the program
      --version
      prints the version number of musrview
      @@ -228,6 +230,7 @@ Additionally, some functions can be accessed using key-shortcuts:
      musrt0 is a user interface for the determination of t0 and the time windows of data and background needed to be specified in the RUN blocks of the msr file. It can be operated either as an interactive program or in a non-interactive mode. In the non-interactive mode it accepts the following parameters:
      <msr_file>
      name of an msr file
      -g, --getT0FromPromptPeak [<firstGoodBinOffset>]
      tries to estimate t0 from the prompt peak (maximum entry) in each histogram and writes the corresponding values to the t0 lines in the RUN blocks of the msr file. If an optional number <firstGoodBinOffset> is given, the lower limit of the data range will be set to t0 + <firstGoodBinOffset>. +
      --timeout <timeout>
      <timeout> given in seconds after which musrview terminates. If <timeout> <= 0, no timeout will take place. Default for <timeout> is 0.
      --help
      displays a small help notice in the shell explaining the basic usage of the program
      --version
      prints the version number of musrt0
      @@ -236,7 +239,7 @@ The interactive mode of musrt0 is started if the program is called 
      musrt0 8472.msr
      Then a ROOT canvas depicting the histogram of the data set mentioned first in the RUN block is drawn in different colors:
      musrt0
      -The colors of the data points represent the choice of the time windows of data (blue) and background (red), as well as t0 (green line). In order to change these ranges the mouse cross-hair is moved to a channel of choice and one of the following keys is pressed:
      +The colors of the data points represent the choice of the time windows of data (blue) and background (red), as well as t0 (green line). In order to change these ranges the mouse cross-hair is moved to a channel of choice and one of the following keys is pressed:
      q
      close the currently open histogram and opens the next (see also below)
      Q
      quit musrt0 without writing into the msr file
      z
      zoom into the region about the t0 @@ -271,7 +274,7 @@ Closing a window by clicking the X button is equivalent to pres
      <marker>X</marker>
      use the ROOT marker number X (inside a <marker_list> environment)
      <color_list></color_list>
      specify the order in which musrview should use colors when plotting data (inside a <root_settings> environment)
      -
      <color>R,G,B</color>
      use the RGB coded color (inside a <color_list> environment) +
      <color>R,G,B</color>
      use the RGB coded color (inside a <color_list> environment)
      @@ -379,7 +382,7 @@ Will read the two files '2010/lem10_his_0123.root' and '2010/

      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.

      -Before going to use musrgui / musredit it is strongly recommended to read this manual first! +Before going to use musrgui / musredit it is strongly recommended to read this manual first!

      4 Description of the msr File Format

      @@ -455,140 +458,146 @@ The THEORY block is used to define the fit function. There is a set of predefine abbreviation parameters mathematical expression - reference + reference + const + c + \mathrm{const}\,(1) + \mathrm{const} + + asymmetry a A\,(1) A - + simplExpo se \lambda\,(\mu\text{s}^{-1}) \exp\left(-\lambda t\right) - + generExpo ge \lambda\,(\mu\text{s}^{-1}), \beta\,(1) \exp\left[-\left(\lambda t\right)^{\beta}\right] - + simpleGss sg \sigma\,(\mu\text{s}^{-1}) \exp\left[-\frac{1}{2}\left(\sigma t\right)^2\right] - + statGssKT stg \sigma\,(\mu\text{s}^{-1}) \frac{1}{3} + \frac{2}{3} \left[1-(\sigma t)^2\right] \exp\left[-\frac{1}{2}\left(\sigma t\right)^2\right] dead! - + statGssKTLF 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 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 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) 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) 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 Phys. Rev. B 20 (1979) 850; P. Dalmas de Réotier and A. Yaouanc, J. Phys.: Condens. Matter 4 (1992) 4533 ">(8) - + combiLGKT lgkt \lambda\,(\mu\text{s}^{-1}), \sigma\,(\mu\text{s}^{-1}) \frac{1}{3}+\frac{2}{3}\left(1-\sigma^2 t^2-\lambda t\right)\exp\left(-\frac{\sigma^2t^2}{2}-\lambda t\right) dead! - + spinGlass spg \lambda\,(\mu\text{s}^{-1}), \gamma\,(\mu\text{s}^{-1}), q\,(1) \frac{1}{3}\exp\left(-\sqrt{\frac{4\lambda^2(1-q)t}{\gamma}}\right)+\frac{2}{3}\left(1-\frac{q\lambda^2t^2}{\sqrt{\frac{4\lambda^2(1-q)t}{\gamma}+q\lambda^2t^2}}\right)\exp\left(-\sqrt{\frac{4\lambda^2(1-q)t}{\gamma}+q\lambda^2t^2}\right) dead! - + rdAnisoHf 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) Phys. Rev. B 34 (1986) 4467 ">(9) - + TFieldCos tf \varphi\,(^{\circ}), \nu\,(\mathrm{MHz}) \cos\left(2\pi\nu t+\frac{\pi\varphi}{180}\right) dead! - + internFld if \alpha\,(1), \varphi\,(^{\circ}), \nu\,(\mathrm{MHz}), \lambda_{\mathrm{T}}\,(\mu\text{s}^{-1}), \lambda_{\mathrm{L}}\,(\mu\text{s}^{-1}) \alpha\,\cos\left(2\pi\nu t+\frac{\pi\varphi}{180}\right)\exp\left(-\lambda_{\mathrm{T}}t\right)+(1-\alpha)\,\exp\left(-\lambda_{\mathrm{L}}t\right) dead! - + Bessel b \varphi\,(^{\circ}), \nu\,(\mathrm{MHz}) j_0\left(2\pi\nu t+\frac{\pi\varphi}{180}\right) dead! - + internBsl ib \alpha\,(1), \varphi\,(^{\circ}), \nu\,(\mathrm{MHz}), \lambda_{\mathrm{T}}\,(\mu\text{s}^{-1}), \lambda_{\mathrm{L}}\,(\mu\text{s}^{-1}) \alpha\,j_0\left(2\pi\nu t+\frac{\pi\varphi}{180}\right)\exp\left(-\lambda_{\mathrm{T}}t\right)+(1-\alpha)\,\exp\left(-\lambda_{\mathrm{L}}t\right) dead! - + abragam ab \sigma\,(\mu\text{s}^{-1}), \gamma\,(\mathrm{MHz}) \exp\left[-\frac{\sigma^2}{\gamma^2}\left(e^{-\gamma t}-1+\gamma t\right)\right] - dead! + dead! - + skewedGss skg \varphi\,(^{\circ}), \nu\,(\mathrm{MHz}), \sigma_{-}\,(\mu\text{s}^{-1}), \sigma_{+}\,(\mu\text{s}^{-1}) \frac{\sigma_{-}}{\sigma_{+}+\sigma_{-}}\exp\left[-\frac{\sigma_{-}^2t^2}{2}\right]\left\lbrace\cos\left(2\pi\nu t+\frac{\pi\varphi}{180}\right)+\sin\left(2\pi\nu t+\frac{\pi\varphi}{180}\right)\mathrm{Erfi}\left(\frac{\sigma_{-}t}{\sqrt{2}}\right)\right\rbrace+ \frac{\sigma_{+}}{\sigma_{+}+\sigma_{-}}\exp\left[-\frac{\sigma_{+}^2t^2}{2}\right]\left\lbrace\cos\left(2\pi\nu t+\frac{\pi\varphi}{180}\right)-\sin\left(2\pi\nu t+\frac{\pi\varphi}{180}\right)\mathrm{Erfi}\left(\frac{\sigma_{+}t}{\sqrt{2}}\right)\right\rbrace - memo pdf + memo pdf - + polynom p t_0\,([t]), a_0\,(1),\,a_1\,(1),\,\dots,\,a_{n}\,(1) @@ -743,7 +752,7 @@ The RUN block is used to collect the data needed for a particular run to be fitt <file_format> - file format: NEXUS, ROOT-NPP, ROOT-PPC, PSI-BIN, PSI-MDU, WKM, MUD, MDU-ASCII, ASCII, DB + file format: MUSR-ROOT, NEXUS, ROOT-NPP, ROOT-PPC, PSI-BIN, PSI-MDU, WKM, MUD, MDU-ASCII, ASCII, DB

      @@ -779,7 +788,7 @@ In order to describe the operations needed for fitting and plotting, quite some
      ADDRUN <run_file_name> <beamline> <facility> <file_format> (optional)
      If an ADDRUN is just following after a RUN statement, these runs will be added. More than one ADDRUN statements are possible, i.e. adding up as many runs as wished. It is also possible to add runs with different file formats. If the t0's are given in the data files, the ADDRUN statement is all what is needed, otherwise just add the t0's with the addt0 statement.
      -For a 'Single Histogram Fit' it will be 
      +For a 'Single Histogram Fit' or a 'MuMinus Fit' it will be 
       addt0 t0AddRun1
 addt0 t0AddRun2
 etc.
@@ -793,17 +802,14 @@ etc.
 
       fittype (required) 
       This tag is used to indicate which type of fit is wished. The supported fit types are: 
      
 
       0 
       Single Histogram Fit
 
       
       2 
       Asymmetry Fit
-
       
       4 
       Asymmetry Fit in a Rotating Reference Frame (Fitting is actually never going to be supported; eventually, it will be possible to plot data in a rotating reference frame)
+
       
       4 
       MuMinus Fit. This is a single histogram fit especially for negative muon μSR
 
       
       8 
       Non-μSR Fit
 
       
 
       
 
      
       The description of these fit types can be found in the corresponding section.
 
       
      
-
       alpha, beta (fit types 2, 4) 
       These parameters are used to correct the asymmetry for different detector efficiencies, solid angles and initial asymmetries. They are defined as α≡N0,b/N0,f and β≡|A0,b/A0,f|. If the parameters are not specified in the RUN block, for each one the value of 1 is assumed.
-
       
-
       
      
-
       alpha2, beta2 (fit type 4) 
       α and β parameters for the calculation of the asymmetry of the second pair of detectors for a plot in a rotating reference frame.
+
       alpha, beta (fit types 2) 
       These parameters are used to correct the asymmetry for different detector efficiencies, solid angles and initial asymmetries. They are defined as α≡N0,b/N0,f and β≡|A0,b/A0,f|. If the parameters are not specified in the RUN block, for each one the value of 1 is assumed.
 
       
 
      
  
      
@@ -824,14 +830,14 @@ etc.
 
       
 
      
  
      
-
       forward (fit type 0) 
       Number of the histogram in the data file to be processed. If histograms shall be grouped, all the numbers which shall be grouped. Examples: 
      +
       forward (fit type 0, 4) 
       Number of the histogram in the data file to be processed. If histograms shall be grouped, all the numbers which shall be grouped. Examples: 
         forward 3       # no grouping, take histogram number 3
   forward 1 2     # group histogram number 1 and 2
   forward 1-10 12 # group histograms with numbers from 1 to 10 and additionally histogram 12 
 
      
 
       
 
       
      
-
       forward, backward (fit types 2, 4) 
       Numbers of the histograms in the data file that should be taken to calculate the asymmetry. If histograms shall be grouped, all the numbers which shall be grouped. Examples: 
      +
       forward, backward (fit types 2) 
       Numbers of the histograms in the data file that should be taken to calculate the asymmetry. If histograms shall be grouped, all the numbers which shall be grouped. Examples: 
         # build forward/backward asymmetry with histogram 1 and 3
   forward  1
   backward 3
@@ -844,45 +850,45 @@ etc.
 
      
 
       
 
       
      
-
       backgr.fix (fit types 0, 2, 4) 
       A fixed constant background in counts per nanosecond or per bin (see below) may be given at this point. The background is specified for all histograms in the order Bf Bb [Br Bl]. If this keyword is present, any information on a background line is ignored.
+
       backgr.fix (fit types 0, 2) 
       A fixed constant background in counts per nanosecond or per bin (see below) may be given at this point. The background is specified for all histograms in the order Bf Bb [Br Bl]. If this keyword is present, any information on a background line is ignored.
 
       
 
       
      
 
       background (fit type 0) 
       The numbers of the first and the last channel of an interval from which the constant background should be calculated are specified here. In case histograms are being grouped, the specified channels are interpreted with respect to the first histogram.
 
       
 
       
      
-
       background (fit types 2, 4) 
       The numbers of the first and the last channel of an interval from which the constant background should be calculated are specified here. For all the histograms this is done together in the following order: kf,first kf,last kb,first kb,last [kr,first kr,last kl,first kl,last]. In case histograms are being grouped, the specified channels are interpreted with respect to the first histograms.
+
       background (fit types 2) 
       The numbers of the first and the last channel of an interval from which the constant background should be calculated are specified here. For all the histograms this is done together in the following order: kf,first kf,last kb,first kb,last [kr,first kr,last kl,first kl,last]. In case histograms are being grouped, the specified channels are interpreted with respect to the first histograms.
 
       
 
      
  
      
-
       data (fit type 0) 
       The numbers of the first and the last channel of an interval from which the data is taken are specified here. In case histograms are being grouped, the specified channels are interpreted with respect to the first histogram.
+
       data (fit type 0, 4) 
       The numbers of the first and the last channel of an interval from which the data is taken are specified here. In case histograms are being grouped, the specified channels are interpreted with respect to the first histogram.
 
       
 
       
      
-
       data (fit types 2, 4) 
       The numbers of the first and the last channel of an interval from which the data is taken are specified here. For all the histograms this is done together in the following order: kf,first kf,last kb,first kb,last [kr,first kr,last kl,first kl,last]. In case histograms are being grouped, the specified channels are interpreted with respect to the first histograms.
+
       data (fit types 2) 
       The numbers of the first and the last channel of an interval from which the data is taken are specified here. For all the histograms this is done together in the following order: kf,first kf,last kb,first kb,last [kr,first kr,last kl,first kl,last]. In case histograms are being grouped, the specified channels are interpreted with respect to the first histograms.
 
       
  
      
-
       t0 (fit type 0) 
       The number of the time-zero channel of the histogram. Example: 
      +
       t0 (fit type 0, 4) 
       The number of the time-zero channel of the histogram. Example: 
         t0 3419        # t0 channel = 3419
   t0 3419 3434   # t0 channels for groupings: forward f1 f2. 3419 t0 for f1, 3434 t0 for f2. 
 
      
 
       
 
       
      
-
       t0 (fit types 2, 4) 
       The numbers of time-zero channels of the histograms in the order t0,f t0,b. Example: 
      +
       t0 (fit types 2) 
       The numbers of time-zero channels of the histograms in the order t0,f t0,b. Example: 
         t0 3419 3418           # t0 channels: forward (3419), backward (3418)
   t0 3419 3418 3417 3416 # t0 channels (assuming forward f1 f2, backward b1 b2): forward (3419, f1), backward (3418, b1); forward (3417, f2), backward (3416, b2)
 
      
 
       
 
      
  
      
-
       addt0 (fit type 0) 
       The number of the time-zero channel of the histogram. If grouping of histograms is present (see forward) the same syntax as for t0 applies. If one addt0 is given, the total number of addt0's needs to be equal to the total number of ADDRUN's!
+
       addt0 (fit type 0, 4) 
       The number of the time-zero channel of the histogram. If grouping of histograms is present (see forward) the same syntax as for t0 applies. If one addt0 is given, the total number of addt0's needs to be equal to the total number of ADDRUN's!
 
       
 
       
      
-
       addt0 (fit types 2, 4) 
       The numbers of time-zero channels of the histograms in the order t0,f t0,b [t0,r t0,l]. If grouping of histograms is present (see forward) the same syntax as for t0 applies. If one addt0 is given, the total number of addt0's needs to be equal to the total number of ADDRUN's!
+
       addt0 (fit types 2) 
       The numbers of time-zero channels of the histograms in the order t0,f t0,b [t0,r t0,l]. If grouping of histograms is present (see forward) the same syntax as for t0 applies. If one addt0 is given, the total number of addt0's needs to be equal to the total number of ADDRUN's!
 
       
 
       
      
 
       xy-data (fit type 8) 
       Specification of the data from an ASCII or DB file which should be used as x and y data (in this order). For a simple ASCII file the column numbers are used, in the case of a DB file one can either specify the variable numbers or the name of the variables as given in the DB header.  
 
       
 
       
      
-
       fit 
       The range of data that should be considered when the fitting is done. For the μSR fit types 0, 2, and 4 here the starting and end times are given in microseconds. For the non-μSR fit type 8 the starting and end points of the fitting range are given in the units of the x data.
      In case the fit range specified here is larger than the data range (in any direction), eventually the data range will be used as fit range.
+
       fit 
       The range of data that should be considered when the fitting is done. For the μSR fit types 0, 2, and 4 here the starting and end times are given in microseconds. For the non-μSR fit type 8 the starting and end points of the fitting range are given in the units of the x data.
      In case the fit range specified here is larger than the data range (in any direction), eventually the data range will be used as fit range.
 
       
 
       
      
 
       packing 
       Number of data channels to be binned together. For the non-μSR fit type 8 the binning is supposed to be 1.
@@ -991,14 +997,14 @@ Notes
 
       4.8  The PLOT Block 
      
 The PLOT block is intended to collect all the information needed for the graphical presentation of the data and fits using musrview. The PLOT keyword at the beginning of the block is followed by a number which indicates the plot type. The plot types match the fit types. Additionally, it is possible to provide information using the following keywords: 
      
 
       runs 
       The numbers of the runs to be plotted have to be put here. The runs are numbered according to their appearance in the RUN block.
-
       
       range 
       Here it is possible to define the plotting range explicitly. Depending on the plot type the following settings are allowed where the times are given in microseconds and the N in counts: 
      
-
       0 without lifetimecorrection 
       tmin tmax [ Nmin Nmax ]
-
       
       0 with lifetimecorrection, 2, 4 
       tmin tmax [ Amin Amax ]
+
       
       range 
       Here it is possible to define the plotting range explicitly. Depending on the plot type the following settings are allowed where the times are given in microseconds and the N in counts (type 0, 4) or in counts/nsec (type 0): 
      
+
       0 without lifetimecorrection, 4 
       tmin tmax [ Nmin Nmax ]
+
       
       0 with lifetimecorrection, 2 
       tmin tmax [ Amin Amax ]
 
       
       8 
       xmin xmax [ ymin ymax ]
 
       
 
       
       sub_ranges 
       Here it is possible to define the plotting range for each run individually. For the different plot types the command has the structure 
      
-
       0 without lifetimecorrection 
       tmin1 tmax1 tmin2 tmax2 ... tminn tmaxn [ Nmin Nmax ] (n = the number of runs to be plotted)
-
       
       0 with lifetimecorrection, 2, 4 
       tmin1 tmax1 tmin2 tmax2 ... tminn tmaxn [ Amin Amax ] (n = the number of runs to be plotted)
+
       0 without lifetimecorrection, 4 
       tmin1 tmax1 tmin2 tmax2 ... tminn tmaxn [ Nmin Nmax ] (n = the number of runs to be plotted)
+
       
       0 with lifetimecorrection, 2 
       tmin1 tmax1 tmin2 tmax2 ... tminn tmaxn [ Amin Amax ] (n = the number of runs to be plotted)
 
       
       8 
        not yet implemented.
 
       
 
       
       use_fit_ranges [ ymin ymax] 
       The fit ranges of the individual runs are used to present the data. Optionally, an ordinate range can be provided.
@@ -1076,9 +1082,20 @@ For the graphical representation in plot type 2 the equation ab
    • and plotted together with the function given in the THEORY block.

    - -

    5.3 Rotating-Reference-Frame Asymmetry Fit

    -(Is going to be implemented as pure plotting option...) + +

    5.3 Negative Muon μSR Fit

    +The negative muon μSR fit (fit type 4) is used for single histogram fits of MuMinus, i.e. +
    +N(t) = \sum_i N_i\,\mathrm{e}^{-t/\tau_i} \left[ 1 + A_i(t)\right] + B(t) +
    +where i runs over the different lifetime channels of \mu^{-}, and
    +
    N_i
    counts of lifetime channel i +
    \tau_i
    lifetime of lifetime channel i +
    A_i(t)
    depolarization function of lifetime channel i +
    B(t)
    B(t)= B_0 + \sum_j B_j \cos(j \omega_{\rm cyclotron} t) the background +
    +

    +Since MuMinus is quite generic, the full functional depends has to be written in the THEORY Block.

    5.4 Non-μSR Fit

    @@ -1354,7 +1371,7 @@ This way the efficiency of the user function can be increased by almost a factor

    -Important remark: If musrfit has been built with parallelization support (default for GCC ≥ 4.2) it should be taken care of the thread safety of the user-function operator(). During the function optimization of musrfit the operator() is called once for any given set of parameters in order to allow the safe execution of any calculation. Within the single-histogram and asymmetry fits the calculation of χ2 or the log-likelihood is parallelized and the operator() is expected to evaluate to reasonable values for a fixed set of parameters (but changing t) beginning with the second function call. +Important remark: If musrfit has been built with parallelization support (default for GCC ≥ 4.2) it should be taken care of the thread safety of the user-function operator(). During the function optimization of musrfit the operator() is called once for any given set of parameters in order to allow the safe execution of any calculation. Within the single-histogram and asymmetry fits the calculation of χ2 or the log-likelihood is parallelized and the operator() is expected to evaluate to reasonable values for a fixed set of parameters (but changing t) beginning with the second function call. In case this cannot be ensured, the parallelization can be disabled by --disable-omp on the configure level of the program installation.

    @@ -1430,39 +1447,12 @@ For reporting bugs or requesting new features and improvements please use the

    - -
    - -
    -
    -
    - - - - - - - - - - - - - - - - - -
    Oscar Fridolin
    Telefon:1234512345
    E-Mail:oscarfridolin@psi.ch
    Büro:WHGA/019
    -
    -
    -

    - +

    diff --git a/doc/html/user/MUSR/MusrFitAcknowledgements.html b/doc/html/user/MUSR/MusrFitAcknowledgements.html index 77d2199b..44cedbe6 100644 --- a/doc/html/user/MUSR/MusrFitAcknowledgements.html +++ b/doc/html/user/MUSR/MusrFitAcknowledgements.html @@ -1,7 +1,7 @@ - + @@ -21,7 +21,7 @@ - + @@ -109,7 +109,7 @@ pre { - +
    @@ -142,39 +142,12 @@ pre {

    - -
    - -
    -
    -
    - - - - - - - - - - - - - - - - - -
    Oscar Fridolin
    Telefon:1234512345
    E-Mail:oscarfridolin@psi.ch
    Büro:WHGA/019
    -
    -
    -

    - +

    diff --git a/doc/html/user/MUSR/MusrFitSetup.html b/doc/html/user/MUSR/MusrFitSetup.html index 4aed7b08..8e2bfd62 100644 --- a/doc/html/user/MUSR/MusrFitSetup.html +++ b/doc/html/user/MUSR/MusrFitSetup.html @@ -1,7 +1,7 @@ - + @@ -21,7 +21,7 @@ - + @@ -109,7 +109,7 @@ pre { - +
    @@ -171,7 +171,7 @@ pre {

    1 Supported Operating Systems and Software Requirements

    -This page is intended to demonstrate for the interested user which steps are necessary to set up the free software μSR data analysis framework musrfit. While the preferred way is to run the software on GNU/Linux, with some restrictions it can also be set up under MS Windows and MacOS X. In case musrfit should be installed according to the description found on this page, the user is strongly encouraged to read completely each section dealing with the present installation step before starting the installation process! +This page is intended to demonstrate for the interested user which steps are necessary to set up the free software μSR data analysis framework musrfit. While the preferred way is to run the software on GNU/Linux, with some restrictions it can also be set up under MS Windows and MacOS X. In case musrfit should be installed according to the description found on this page, the user is strongly encouraged to read completely each section dealing with the present installation step before starting the installation process!

    Apart from GCC, the GNU Compiler Collection, the GNU build tools autoconf, automake and libtool as well as the helper tool pkg-config musrfit requires the installation of a few open-source libraries and programs:
    @@ -183,7 +183,7 @@ Apart from GCC, the GNU Compiler Col

    -Additionally, only if musrfit should support reading of data files in the NeXus format the following libraries are needed:
    +Additionally, only if musrfit should support reading of data files in the NeXus format the following libraries are needed:
    HDF4
    A library and multi-object file format for storing and managing data.
    HDF5
    A data model, library, and file format for storing and managing data.
    minixml
    A small XML library that can be used to read and write XML and XML -like data files. Required version ≥ 2.2 @@ -227,7 +227,7 @@ In order to obtain some information about the possible options for the installat 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"...

    3.1.2 Installation of NeXus requirements (optional)

    -Only if musrfit should support reading data files in the NeXus format the further required 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 MXML, HDF4, and HDF5 might be called mxml, mxml-devel, hdf, hdf-devel, hdf5, hdf5-devel, on Debian-like systems libmxml1, libmxml-dev, libhdf4-0, libhdf4-dev, libhdf5-serial-1.8.4, libhdf5-serial-dev. +Only if musrfit should support reading data files in the NeXus format the further required 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 MXML, HDF4, and HDF5 might be called mxml, mxml-devel, hdf, hdf-devel, hdf5, hdf5-devel, on Debian-like systems libmxml1, libmxml-dev, libhdf4-0, libhdf4-dev, libhdf5-serial-1.8.4, libhdf5-serial-dev.

    Even though there might exist binary packages for the NeXus library, it is best to build and install it directly from the source code which can be found here.

    @@ -248,7 +248,7 @@ After one of the two setup variants has been executed the system should be told echo "/opt/root-system/lib" >> /etc/ld.so.conf.d/root-system.conf /sbin/ldconfig -
  • Additionally, as normal user one should append the following lines to the ~/.bashrc and/or ~/.bash_profile (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: 
    +
  • Additionally, as normal user one should append the following lines to the ~/.bashrc and/or ~/.bash_profile (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: 
     export ROOTSYS=/opt/root-system/
 export PATH=$ROOTSYS/bin:$PATH
    @@ -268,13 +268,13 @@ cd svn up musrfit

    -As an alternative (if subversion is not available), the source code can also be downloaded and extracted from a tarball. +As an alternative (if subversion is not available), the source code can also be downloaded and extracted from a tarball. 
     cd
 curl http://savannah.psi.ch/viewcvs/trunk/analysis/musrfit.tar.gz -G --data-binary root=nemu%2Flem | tar xz

    -After the source-code extraction the autogen.sh script is called to prepare the build environment. If it has been executed successfully the configure script should be ready to collect all the information needed to create the Makefiles. If musrfit should support NeXus data files this has to be enabled by specifying the --enable-NeXus switch when calling configure. For an overview of all available options just call ./configure --help. Besides the standard options there are a few special options which should be mentioned here: +After the source-code extraction the autogen.sh script is called to prepare the build environment. If it has been executed successfully the configure script should be ready to collect all the information needed to create the Makefiles. If musrfit should support NeXus data files this has to be enabled by specifying the --enable-NeXus switch when calling configure. For an overview of all available options just call ./configure --help. Besides the standard options there are a few special options which should be mentioned here:

    --prefix
    Specify the installation prefix, e.g. /opt/root-system (by default: /usr/local)
    --with-rootsys
    Specify the top of the ROOT installation directory, e.g. /opt/root-system @@ -310,7 +310,7 @@ export MUSRFITPATH=/opt/root-system/bin

    3.3 musredit

    -In the latest version of musrfit the configure script tries to determine automatically if Qt4.6 or higher is set up on the machine. In case this is found, the editor musredit is built already together with musrfit. If not, one can either try to call the configure script with the "--with-qt4" option or install this editor separately: +In the latest version of musrfit the configure script tries to determine automatically if Qt4.6 or higher is set up on the machine. In case this is found, the editor musredit is built already together with musrfit. If not, one can either try to call the configure script with the "--with-qt4" option or install this editor separately: 
     cd src/musredit
 qmake musredit.pro
@@ -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:  
+ 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. 
 
    
@@ -351,10 +351,10 @@ Notes
 
    
 
     4  MS Windows 
    
 Under Windows a native installation is not supported but there is the possibility to run musrfit through Cygwin which has the great advantage that one gains additionally various nice UNIX tools also for other purposes wink 
    
-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 (musrview, musrgui, etc.) is run.
+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 (musrview, musrgui, etc.) is run.
 
    
-One more advice: Please never try to install either ROOT or musrfit from or to a directory containing spaces in the absolute path or in case you do, do not wonder if some errors occur!
    
-msr files, however, might be saved in such directories like ...\My Documents\...    
+One more advice: Please never try to install either ROOT or musrfit from or to a directory containing spaces in the absolute path or in case you do, do not wonder if some errors occur!
    
+msr files, however, might be saved in such directories like ...\My Documents\...    
 
    
 
     4.1  Requirements 
    
 
     4.1.1  Setting up Cygwin 
    
@@ -372,9 +372,9 @@ ln -sf /usr/include/boost-x_yy_z/boost /usr/include/boost
 where x_yy_z has to be substituted by the correct version number, e.g. 1_33_1.
 
    
 
     4.1.2  Installation of NeXus requirements (optional) 
    
-Only if musrfit should support reading data files in the NeXus format the further required software has to be set up. Under Cygwin of all the required libraries only HDF5 is available. The packages hdf5 and libhdf5-devel can be installed through the Cygwin setup. One should also make sure that bison, flex and a package containing /usr/lib/librpc.a (e.g. sunrpc = 4.0-3, but not sunrpc = 4.0-4) are installed.
+Only if musrfit should support reading data files in the NeXus format the further required software has to be set up. Under Cygwin of all the required libraries only HDF5 is available. The packages hdf5 and libhdf5-devel can be installed through the Cygwin setup. One should also make sure that bison, flex and a package containing /usr/lib/librpc.a (e.g. sunrpc = 4.0-3, but not sunrpc = 4.0-4) are installed.
 
    
-All other libraries have to be built from the sources. The following lines will track the installation of JPEG 6b, MXML 2.5, HDF 4.2.5, and NeXus 4.2.1. The version numbers and source-code locations might of course change with time but should be easily adjustable.
+All other libraries have to be built from the sources. The following lines will track the installation of JPEG 6b, MXML 2.5, HDF 4.2.7-patch1, and NeXus 4.2.1. The version numbers and source-code locations might of course change with time but should be easily adjustable.
 
     cd
 mkdir nexus
@@ -391,8 +391,8 @@ cd mxml-2.5
 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
+curl http://www.hdfgroup.org/ftp/HDF/HDF_Current/src/hdf-4.2.7-patch1.tar.gz -G | tar xz
+cd hdf-4.2.7-patch1
 ./configure --prefix=/usr/local --enable-static --disable-fortran --with-jpeg=/usr/local
 make
 make install
@@ -406,7 +406,7 @@ make install
 
    
 
     4.1.3  ROOT 
    
 In order to install the ROOT system, there are two possibilities: 
      
-
    •  Download the precompiled Cygwin GCC 4.3 package of the most recent ROOT version from the web page and unpack it in a Cygwin shell (in order to get the line endings correctly) at the final location. Suppose the package has been downloaded to C:\ and the ROOT tree should be in C:\root, this is achieved by:
      +
    •  Download the precompiled Cygwin GCC 4.3 package of the most recent ROOT version from the web page and unpack it in a Cygwin shell (in order to get the line endings correctly) at the final location. Suppose the package has been downloaded to C:\ and the ROOT tree should be in C:\root, this is achieved by:
       cd /cygdrive/c
 tar xzf root_v5.xx.yy.win32gcc-gcc-4.3.tar.gz
 
      
@@ -443,13 +443,13 @@ cd
 svn up musrfit
 
      • 
 
      
-As an alternative (if subversion is not available), the source code can also be downloaded and extracted from a tarball.
+As an alternative (if subversion is not available), the source code can also be downloaded and extracted from a tarball.
 
       cd
 curl http://savannah.psi.ch/viewcvs/trunk/analysis/musrfit.tar.gz -G --data-binary root=nemu%2Flem | tar xz
 
      
 
      
-After the source-code extraction the autogen.sh script is called to prepare the build environment. If it has been executed successfully the configure script should be ready to collect all the information needed to create the Makefiles. If musrfit should support NeXus data files this has to be enabled by specifying the --enable-static --enable-NeXus switches when calling configure. For an overview of all available options just call ./configure --help. Besides the standard options there are a few special options which should be mentioned here:
+After the source-code extraction the autogen.sh script is called to prepare the build environment. If it has been executed successfully the configure script should be ready to collect all the information needed to create the Makefiles. If musrfit should support NeXus data files this has to be enabled by specifying the --enable-static --enable-NeXus switches when calling configure. For an overview of all available options just call ./configure --help. Besides the standard options there are a few special options which should be mentioned here:
 
       
      
 
       --prefix 
       Specify the installation prefix, e.g. /opt/root-system (by default: /usr/local)
 
       
       --with-rootsys 
       Specify the top of the ROOT installation directory, e.g. /opt/root-system
@@ -479,7 +479,7 @@ In order to finish the installation of musrfit the paths where 
      
 
 
       4.3  musredit 
      
-In the latest version of musrfit the configure script tries to determine automatically if Qt4.5 or higher is set up on the machine. In case this is found, the editor musredit is built already together with musrfit. If not, one can either try to call the configure script with the "--with-qt4" option or install this editor separately:
+In the latest version of musrfit the configure script tries to determine automatically if Qt4.5 or higher is set up on the machine. In case this is found, the editor musredit is built already together with musrfit. If not, one can either try to call the configure script with the "--with-qt4" option or install this editor separately:
 
       cd src/musredit
 qmake-qt4 musredit.pro
@@ -524,7 +524,7 @@ C:\cygwin\bin\ash.exe /bin/rebaseall
 If this does not resolve the problem, try to change the compatibility settings of C:\cygwin\bin\sh.exe and C:\cygwin\bin\bash.exe so that they are executed with administrator privileges.
 
      
 
       5  Mac OS X 
      
-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—either MacPorts or Fink—which provides open-source software is employed to fulfill the basic software requirements of musrfit. In the following, both possibilities (using MacPorts or Fink) are described but it is emphasized here that it should be followed only one of the possible routes.
+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—either MacPorts or Fink—which provides open-source software is employed to fulfill the basic software requirements of musrfit. In the following, both possibilities (using MacPorts or Fink) are described but it is emphasized here that it should be followed only one of the possible routes.
 
      
 
       5.1  Requirements (MacPorts) 
      
 
       5.1.1  Everything but ROOT and NeXus 
      
@@ -561,7 +561,7 @@ Under OS X 10.6 Snow Leopard it will not be possible to install qt3-mac
 
      
 
       5.1.2  Installation of NeXus requirements (optional) 
      
 
      
-Only if musrfit should support reading data files in the NeXus format the further required packages are set up:
+Only if musrfit should support reading data files in the NeXus format the further required packages are set up:
 
       sudo port -v install jpeg6b hdf4 hdf5-18
 
      
@@ -591,7 +591,7 @@ make
 
      
 
     
 
    
-In order to finalize the ROOT installation and to prepare already the installation of musrfit and musrgui / musredit 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 ~/.MacOSX/environment.plist and re-login:
    
+In order to finalize the ROOT installation and to prepare already the installation of musrfit and musrgui / musredit 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 ~/.MacOSX/environment.plist and re-login:
    
 
     <?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">
@@ -635,7 +635,7 @@ The Fink installer package also contains a graphical user interface
 
    
 Under OS X 10.6 Snow Leopard it will not be possible to install qt3mac since the system is by default a 64-bit system and the old qt3-mac depends on software which is only available for 32-bit systems. It is suggested to install qt4mac instead and use musredit.
 
    
-Also, due to some not fulfilled dependencies, it might not be possible to install FFTW3 through Fink. In this case (and ONLY in THIS case) simply download the FFTW3 source code from its download page and install it from a terminal using the following commands (for the FFTW version 3.x.y):
+Also, due to some not fulfilled dependencies, it might not be possible to install FFTW3 through Fink. In this case (and ONLY in THIS case) simply download the FFTW3 source code from its download page and install it from a terminal using the following commands (for the FFTW version 3.x.y):
 
     tar xz fftw-3.x.y
 cd fftw-3.x.y
@@ -652,7 +652,7 @@ where x_yy_z has to be substituted by the correct version numbe
 
    
 
     5.2.2  Installation of NeXus requirements (optional) 
    
 
    
-Only if musrfit should support reading data files in the NeXus format the further required packages can be installed through Fink:
+Only if musrfit should support reading data files in the NeXus format the further required packages can be installed through Fink:
 
    
 libjpeg hdf hdf5-18 hdf5-18-shlibs
 
    
@@ -683,7 +683,7 @@ make
  • ROOT is also available through the FinkCommander! Install root5 or root5-devel. 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.

    • -In order to finalize the ROOT installation and to prepare already the installation of musrfit and musrgui / musredit 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 ~/.MacOSX/environment.plist and re-login:
    +In order to finalize the ROOT installation and to prepare already the installation of musrfit and musrgui / musredit 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 ~/.MacOSX/environment.plist and re-login:
     <?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">
@@ -718,13 +718,13 @@ cd
 svn up musrfit

    -As an alternative (if subversion is not available), the source code can also be downloaded and extracted from a tarball. +As an alternative (if subversion is not available), the source code can also be downloaded and extracted from a tarball. 
     cd
 curl http://savannah.psi.ch/viewcvs/trunk/analysis/musrfit.tar.gz -G --data-binary root=nemu%2Flem | tar xz

    -After the source-code extraction the autogen.sh script is called to prepare the build environment. If it has been executed successfully the configure script should be ready to collect all the information needed to create the Makefiles. If musrfit should support NeXus data files this has to be enabled by specifying the --enable-NeXus switch when calling configure. For an overview of all available options just call ./configure --help. Besides the standard options there are a few special options which should be mentioned here: +After the source-code extraction the autogen.sh script is called to prepare the build environment. If it has been executed successfully the configure script should be ready to collect all the information needed to create the Makefiles. If musrfit should support NeXus data files this has to be enabled by specifying the --enable-NeXus switch when calling configure. For an overview of all available options just call ./configure --help. Besides the standard options there are a few special options which should be mentioned here:

    --prefix
    Specify the installation prefix, e.g. /opt/root-system (by default: /usr/local)
    --with-rootsys
    Specify the top of the ROOT installation directory, e.g. /opt/root-system @@ -754,7 +754,7 @@ In order to finish the installation of musrfit the paths where

    5.4 musredit

    -In the latest version of musrfit the configure script tries to determine automatically if Qt4.5 or higher is set up on the machine. In case this is found, the editor musredit is built already together with musrfit. If not, one can either try to call the configure script with the "--with-qt4" option or install this editor separately: +In the latest version of musrfit the configure script tries to determine automatically if Qt4.5 or higher is set up on the machine. In case this is found, the editor musredit is built already together with musrfit. If not, one can either try to call the configure script with the "--with-qt4" option or install this editor separately: 
     cd src/musredit
 qmake musredit.pro
@@ -818,39 +818,12 @@ musrview test-histo-ROOT-NPP.msr

    - -
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    -
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    - - - - - - - - - - - - - - - - - -
    Oscar Fridolin
    Telefon:1234512345
    E-Mail:oscarfridolin@psi.ch
    Büro:WHGA/019
    -
    -
    -

    - +

    diff --git a/doc/html/user/MUSR/MusrGui.html b/doc/html/user/MUSR/MusrGui.html index 2afc3428..62414641 100644 --- a/doc/html/user/MUSR/MusrGui.html +++ b/doc/html/user/MUSR/MusrGui.html @@ -1,7 +1,7 @@ - + @@ -21,7 +21,7 @@ - + @@ -109,7 +109,7 @@ pre { - +
    @@ -140,7 +140,7 @@ pre {

    1 Introduction

    musrgui and musredit are editors which also provide a graphical user interface to the programs contained in the musrfit suite and are intended to help the user handle musrfit msr files. They are implemented in C++ and use the Qt framework. Principally, musrgui and musredit are doing the same, but are based on different Qt versions. musrgui 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. musredit is based on Qt 4.6 (or above) and this is the program which will be developed further.
    On this documentation page only the features related to musrfit are described—the basic editor functions which should be self-explanatory are not. -Before going on using musrgui / musredit it is strongly recommended to read the manual of musrfit first! +Before going on using musrgui / musredit it is strongly recommended to read the manual of musrfit first!

    2 Available Executables, Configuration Files and their Basic Usage

    @@ -306,7 +306,7 @@ The features of musrfit which can be accessed by the graphical fron

    4 Editor Features

    Besides the functions described above and which are mostly interfacing musrfit/msr2data the editors of musrgui / musredit offer various functions for manipulating especially musrfit msr files: musrgui editor features
      -
    • 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 correct syntax. 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 manual of musrfit can be supplied. This feature is available only in musrgui. In musredit the respective functions can be accessed through the Edit menu. +
    • 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 correct syntax. 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 manual of musrfit can be supplied. This feature is available only in musrgui. In musredit the respective functions can be accessed through the Edit menu.
    • In order to comment or uncomment lines in a msr file select the according lines and apply Edit → (Un)Comment or use the keyboard shortcut Ctrl+(Shift)+m.

    @@ -457,39 +457,12 @@ For reporting bugs or requesting new features and improvements please use the

    - -
    - -
    -
    -
    - - - - - - - - - - - - - - - - - -
    Oscar Fridolin
    Telefon:1234512345
    E-Mail:oscarfridolin@psi.ch
    Büro:WHGA/019
    -
    -
    -

    - +

    diff --git a/doc/html/user/MUSR/QuickStart.html b/doc/html/user/MUSR/QuickStart.html index 239942cb..bdec7633 100644 --- a/doc/html/user/MUSR/QuickStart.html +++ b/doc/html/user/MUSR/QuickStart.html @@ -1,7 +1,7 @@ - + @@ -21,7 +21,7 @@ - + @@ -109,7 +109,7 @@ pre { - +
    @@ -137,7 +137,7 @@ Installation instructions for Linux, MS Windows, and Mac OS X can be found WKM (wkmfit, wkmview). E.g., for fitting data as defined in the input file 8472.msr one types:
    musrfit 8472.msr
    for plotting data and the corresponding fit one calls:
    musrview 8472.msr
    -Additionally, there are editors called     musrgui/musredit available which can do everything the emacs plug-in for WKM is capable of and even more. However, before going to use only musrgui / musredit 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. +Additionally, there are editors called musrgui/musredit available which can do everything the emacs plug-in for WKM is capable of and even more. However, before going to use only musrgui / musredit 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.

    Differences between WKM and musrfit msr files

    @@ -280,39 +280,12 @@ RUN 2008/lem08_his_8472 MUE4 PSI ROOT-NPP (name beamline institute dat

    - -
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    - - - - - - - - - - - - - - - - - -
    Oscar Fridolin
    Telefon:1234512345
    E-Mail:oscarfridolin@psi.ch
    Büro:WHGA/019
    -
    -
    -

    - +

    diff --git a/doc/html/user/MUSR/TutorialSingleHisto.html b/doc/html/user/MUSR/TutorialSingleHisto.html index 4b9d2bf1..b926cd3f 100644 --- a/doc/html/user/MUSR/TutorialSingleHisto.html +++ b/doc/html/user/MUSR/TutorialSingleHisto.html @@ -1,7 +1,7 @@ - + @@ -21,7 +21,7 @@ - + @@ -109,7 +109,7 @@ pre { - +
    @@ -196,7 +196,7 @@ packing 20 
  • forward         3
    the histogram number; in this example 3 corresponds to the histogram of the "Up" positron counter 
  • data            1        8000
    start and end bins of the range containing useful data in the histogram (to be adjusted, e.g. by using musrt0, see below) 
  • t0              1
    histogram bin corresponding to the time zero (muon implantation time) (to be adjusted, e.g. by musrt0, see below) -
  • fit             0       4.9
    start and end times (in μs) defining the fit range.
    In case the fit range exceeds the range of useful data (specified above using the data tag), eventually this data range is used as fit range. +
  • fit             0       4.9
    start and end times (in μs) defining the fit range.
    In case the fit range exceeds the range of useful data (specified above using the data tag), eventually this data range is used as fit range. 
  • packing         20
    the packing of the histograms (in histogram bins)

    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.
  • the COMMANDS block:
    @@ -367,39 +367,12 @@ This page only summarizes the very basic features and options of the programs co

    • - -
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    Oscar Fridolin
    Telefon:1234512345
    E-Mail:oscarfridolin@psi.ch
    Büro:WHGA/019
    -
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    - +

    diff --git a/doc/html/user/MUSR/WebHome.html b/doc/html/user/MUSR/WebHome.html index 933a0be5..ec0d6884 100644 --- a/doc/html/user/MUSR/WebHome.html +++ b/doc/html/user/MUSR/WebHome.html @@ -1,7 +1,7 @@ - + @@ -21,7 +21,7 @@ - + @@ -109,7 +109,7 @@ pre { - +
    @@ -139,7 +139,7 @@ pre {
  • Acknowledgements

    • --- AS & BMW - last update 28. March 2012
    +-- AS & BMW - last update May 8, 2012

    @@ -155,39 +155,12 @@ pre {

    - -
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    Oscar Fridolin
    Telefon:1234512345
    E-Mail:oscarfridolin@psi.ch
    Büro:WHGA/019
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    - +

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\ No newline at end of file diff --git a/doc/musrfit_dox.cfg b/doc/musrfit_dox.cfg index 29f64c30..30fbbfe5 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 = 0.10.0 +PROJECT_NUMBER = 0.11.0 # The OUTPUT_DIRECTORY tag is used to specify the (relative or absolute) # base path where the generated documentation will be put. diff --git a/src/classes/PRunMuMinus.cpp b/src/classes/PRunMuMinus.cpp index b19d4380..19d91db0 100644 --- a/src/classes/PRunMuMinus.cpp +++ b/src/classes/PRunMuMinus.cpp @@ -84,7 +84,7 @@ PRunMuMinus::~PRunMuMinus() // CalcChiSquare //-------------------------------------------------------------------------- /** - *

    Calculate chi-square. (Not yet implemented) + *

    Calculate chi-square. * * return: * - chisq value @@ -139,7 +139,7 @@ Double_t PRunMuMinus::CalcChiSquare(const std::vector& par) // CalcChiSquareExpected (public) //-------------------------------------------------------------------------- /** - *

    Calculate expected chi-square. Currently not implemented. + *

    Calculate expected chi-square. * * return: * - chisq value == 0.0 @@ -196,7 +196,7 @@ Double_t PRunMuMinus::CalcChiSquareExpected(const std::vector& par) // CalcMaxLikelihood //-------------------------------------------------------------------------- /** - *

    Calculate log max-likelihood. (Not yet implemented) + *

    Calculate log max-likelihood. * * return: * - log max-likelihood value @@ -296,7 +296,7 @@ void PRunMuMinus::CalcNoOfFitBins() // CalcTheory //-------------------------------------------------------------------------- /** - *

    Calculate theory for a given set of fit-parameters. (Not yet implemented) + *

    Calculate theory for a given set of fit-parameters. */ void PRunMuMinus::CalcTheory() {