diff --git a/doc/html/.buildinfo b/doc/html/.buildinfo
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--- a/doc/html/.buildinfo
+++ /dev/null
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-# Sphinx build info version 1
-# This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
-config: eec60d1156b3ecdeb8b69fcbd6a0b13b
-tags: 645f666f9bcd5a90fca523b33c5a78b7
diff --git a/doc/html/_sources/acknowledgement.txt b/doc/html/_sources/acknowledgement.txt
deleted file mode 100644
index 7e8c47fa..00000000
--- a/doc/html/_sources/acknowledgement.txt
+++ /dev/null
@@ -1,22 +0,0 @@
-.. include:: <isogrk1.txt>
-.. index:: acknowledgment
-
-.. _acknowledgment:
-
-Acknowledgements
-================
-
-
-**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! 
-
-**Uldis Locans**
-  I am very much indebted to Uldis work on :ref:`DKS <setup-dks>` enabling the GPU support for ``musrfit``. His kind, calm, and 
-  extremely competent way to deal with his projects as well as to deal with the chaos of physicists way to think is admirable. Many thanks Uldis!
-
-**Zaher Salman**
-  Thanks for his beta-NMR and web-interface contributions to ``musrfit``!
-
-**Robert Scheuermann**
-  Thanks for his constant contructive input on ``musrfit``! 
diff --git a/doc/html/_sources/any2many.txt b/doc/html/_sources/any2many.txt
deleted file mode 100644
index 6b5fd201..00000000
--- a/doc/html/_sources/any2many.txt
+++ /dev/null
@@ -1,8 +0,0 @@
-.. include:: <isogrk1.txt>
-.. index:: any2many
-
-any2many - a Universal |mgr|\SR-file-format converter
-=====================================================
-
-``any2many`` allows to convert most |mgr|\SR-file-formats from one to the other.
-For a detailed description see :ref:`here <any2many>`.
\ No newline at end of file
diff --git a/doc/html/_sources/bugtracking.txt b/doc/html/_sources/bugtracking.txt
deleted file mode 100644
index 55a5ff54..00000000
--- a/doc/html/_sources/bugtracking.txt
+++ /dev/null
@@ -1,9 +0,0 @@
-.. index:: bugtracking
-.. _bugtracking:
-
-Bugtracking
-===========
-
-For reporting bugs or requesting new features and improvements please use 
-the `bitbucket-repo <https://bitbucket.org/muonspin/musrfit/issues>`_ (preferred) 
-or send an e-mail to A. Suter at PSI.
diff --git a/doc/html/_sources/cite.txt b/doc/html/_sources/cite.txt
deleted file mode 100644
index 5a71e6f1..00000000
--- a/doc/html/_sources/cite.txt
+++ /dev/null
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-.. include:: <isogrk1.txt>
-.. index:: cite
-.. _cite:
-
-How to Cite ``musrfit``?
-========================
-
-Since quite some effort is going into the development and maintenance of the ``musrfit`` package, you should at least acknowledge it in your publication if you have used it to analyze your data. Even better of course is to cite it properly by the reference given beneath 
-
- * A.\  Suter, B.M. Wojek, "Musrfit: A Free Platform-Independent Framework for |mgr|\SR Data Analysis", Physics Procedia **30**, 69 (2012). `<http://dx.doi.org/10.1016/j.phpro.2012.04.042>`_
-
-The GPU high speed ``musrfit`` version is utilizing ``DKS``. In case you are using this version, please also add the following citations
-
- * A.\  Adelmann, U. Locans, A. Suter, "The Dynamic Kernel Scheduler—Part 1", Computer Physics Communications **207**, 83 (2016). `<https://doi.org/10.1016/j.cpc.2016.05.013>`_
- * U.\  Locans, *et al.*, "Real-time computation of parameter fitting and image reconstruction using graphical processing units", Computer Physics Communications **215**, 71 (2017). `<https://doi.org/10.1016/j.cpc.2017.02.007>`_
- * U.\ Locans and A.\ Suter, "Musrfit – Real Time Parameter Fitting Using GPUs", JPS Conf. Proc. *21*, 011051 (2018). `<http://dx.doi.org/10.7566/JPSCP.21.011051>`_
-
-
diff --git a/doc/html/_sources/index.txt b/doc/html/_sources/index.txt
deleted file mode 100644
index b4ed7d2f..00000000
--- a/doc/html/_sources/index.txt
+++ /dev/null
@@ -1,31 +0,0 @@
-.. musrfit docu documentation master file, created by
-   sphinx-quickstart on Sun Jun 17 11:00:32 2018.
-   You can adapt this file completely to your liking, but it should at least
-   contain the root `toctree` directive.
-
-Welcome to the musrfit documentation!
-=====================================
-
-.. toctree::
-   :maxdepth: 2
-   
-   cite
-   tutorial
-   user-manual
-   user-libs
-   setup-standard  
-   setup-dks
-   musredit
-   mupp
-   msr2data
-   any2many
-   musr-root
-   acknowledgement
-   bugtracking
-   
-
-Indices and tables
-==================
-
-* :ref:`genindex`
-* :ref:`search`
diff --git a/doc/html/_sources/msr2data.txt b/doc/html/_sources/msr2data.txt
deleted file mode 100644
index 8e77bbca..00000000
--- a/doc/html/_sources/msr2data.txt
+++ /dev/null
@@ -1,374 +0,0 @@
-.. include:: <isogrk1.txt>
-.. index:: msr2data
-
-.. _msr2data:
-
-msr2data - A Program for Automatically Processing Multiple ``musrfit`` msr Files
-================================================================================
-
-``msr2data`` (originally written by B. M. Wojek) is a program implemented in ``C++``. Its purpose is 
-to process multiple msr files (input files for ``musrfit``) with the same parameters and summarize the fitting 
-results either in a *TRIUMF DB* [#f1]_ or a *column ASCII* file. This allows essentially to
-
-#. Collect the fit parameters.
-#. Generate *new* input msr files based on old ones.
-
-.. [#f1] For an abridged description of this format see `here <http://musr.org/xyfit/dbformat.html>`_. The DB files 
-         produced by ``msr2data`` can be viewed for instance with :ref:`mupp <mupp>` or |mgr|\View `see here <http://musr.org/muview/>`_, 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!
-
-.. _msr2data-basic-usage:         
-
-Basic Types of Usage
---------------------
-
-Apart from numerous :ref:`optional parameters <msr2data-opt-param>` that might be set, in principle there are four different ways of calling ``msr2data``. 
-These differ in how the list of runs which should be processed is supplied: 
-
-**msr2data <run> <extension> [optional parameters]**
-  A single run number. 
-**msr2data <firstRunNo> <lastRunNo> <extension> [optional parameters]**
-  An interval of run numbers is specified through the first and the last run number. The condition ``<firstRunNo>`` < ``<lastRunNo>`` is not necessary. 
-**msr2data \[ <runList> \] <extension> [optional parameters]**
-  Where ``<runList>`` is one or a combination of the following:
-  
-  #. ``<run0>, <run1>, <run2>, ... <runN>`` : run numbers, *e.g.* 123 124, 
-  #. ``<run0>-<runN>`` : a range, *e.g.* 123-125 -> 123 124 125, 
-  #. ``<run0>:<runN>:<step>`` : a sequence, *e.g.* 123:127:2 -> 123 125 127. ``<step>`` has to be a positive integer. 
-  #. A ``<runList>`` can also combine (1)-(3), *e.g.* 123 128-130 133, etc. 
-    
-**msr2data <runListFileName> <extension> [optional parameters]**
-  An ASCII file containing a list of run numbers and optional external parameters is passed to ``msr2data``. For the structure of the ASCII file 
-  see :ref:`below <run-list-file_structure>`. 
-  
-All four basic types of calling ``msr2data`` contain the *mandatory* file-name ``<extension>`` passed right after the list of runs. The meaning of 
-this ``<extension>`` should become clear after giving examples for all four cases:
-
-.. code-block:: bash
-
-  $ msr2data 8472 _tf_h13
-  
-generates the DB file ``out.db`` (can be changed by using the -o option) from ``8472_tf_h13.msr``.   
-
-.. code-block:: bash
-
-  $ msr2data 8472 8474 _tf_h13
-  
-generates the DB file ``out.db`` (can be changed by using the -o option) from ``8472_tf_h13.msr``, ``8473_tf_h13.msr``, and ``8474_tf_h13.msr``.   
-
-.. code-block:: bash
-
-  $ msr2data [8472 8470] _tf_h13
-  
-generates the DB file ``out.db`` (can be changed by using the -o option) from ``8472_tf_h13.msr`` and ``8470_tf_h13.msr``. 
-
-.. code-block:: bash
-
-  $ msr2data [8470:8474:2] _tf_h13
-  
-generates the DB file ``out.db`` (can be changed by using the -o option) from ``8470_tf_h13.msr``, ``8472_tf_h13.msr``, and ``8474_tf_h13.msr``.   
-  
-.. _run-list-file_structure:
-
-Run List File Structure
-+++++++++++++++++++++++
-
-.. code-block:: bash
-
-  $ msr2data run.list _tf_h13
-
-generates the DB file ``out.db`` (can be changed by using the -o option) from all runs listed in the ASCII file ``run.list`` in the working directory. 
-In this file it is also possible to include *external* parameters which should be put in the resulting DB file. The structure of the ``run.list`` is the following:  
-
-::
-
-  RUN VAR1 VAR2 VAR3 ...
-  8460 200 27.1 46.2 ...
-  8472 205 27.1 46.3 ...
-  8453 210 27.2 45.9 ...
-  ·     ·    ·    ·
-  ·     ·    ·    ·
-  ·     ·    ·    ·
-
-*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: 
-
-* The output files in the examples above are only newly created if they did *not* exist before invoking ``msr2data``. 
-  If the files were already present the msr file data would be appended! 
-* 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:  
-
-  .. code-block:: bash
-  
-    $ msr2data 8472 8460 "" 
-  
-.. _msr2data-opt-param:
-
-Optional Parameters
--------------------
-
-As mentioned already above there are some optional parameters which change the behavior of ``msr2data`` and can be passed in any order. Here is a complete list: 
-
-**data**
-  The output file format is changed to a simple column ASCII file (default output file name: out.dat). 
-**new**
-  An existing output file is deleted before new information is written to it. 
-**header**
-  Force the output of the file header even if the output file was present before. 
-**noheader**
-  The output of the file header is suppressed—also if the output file is newly created.
-  If either both or none of the header options are given, ``msr2data`` writes the file header only to new files 
-  and it solely appends the data blocks to an existing output file assuming that the header is present already. 
-**nosummary**
-  There will be no attempt to read additional information like the temperature or the applied magnetic field from 
-  the data files even if these information were present there. 
-**paramList <param>**
-  option used to select the parameters which shall be exported. ``<param>`` is a list of parameter numbers to be exported. 
-  Allowed lists are: ``<startNo>-<endNo>``, *e.g.* ``1-16`` will export parameters 1 to 16. Space separated numbers, *e.g.:* ``1 3 5``. 
-  A combination of both is possible, *e.g.* ``1-16 19 31 62``, and so on. 
-**-o<outputFileName>, -o <outputFileName>**
-  The processed data will be written to the file ``<outputFileName>`` instead of the default ``out.db`` or ``out.dat``. 
-  If ``<outputFileName>`` is equal to none (case-insensitive) the parameter data are not appended to any output file. 
-**fit**
-  Additionally to the final data collection ``msr2data`` will invoke ``musrfit`` to fit the specified runs. 
-  All msr files are assumed to be present, none is newly generated! 
-**fit-<template>[!]**
-  Additionally to the final data collection ``msr2data`` will generate msr files for the runs specified in the list 
-  of runs and invoke :ref:`musrfit <musrfit>` for performing fits of the data. As template for the first run the file 
-  ``<template><extension>.msr`` (or if not available: ``<template><extension>.mlog``) is used; the subsequent input 
-  files will be created using the msr output of the last processed runs ("chain fit"). However, if for all runs only 
-  the given template should be used one has to append an exclamation mark (**!**) to the ``<template>``. 
-**msr-<template>**
-  The same as ``fit-<template>[!]``, *without* calling ``musrfit`` and the final data collection, *i.e.* only the msr files for the given runs are generated. 
-**-k**
-  If specified together with the ``fit-<template>`` option, the :ref:`- -keep-mn2-output <musrfit>` option is passed to ``musrfit``. 
-  In the case no fits should be done, this option is ignored. 
-**-t**
-  In case this option is given additionally to the ``fit-<template> option``, ``musrfit`` is called with 
-  the :ref:`- -title-from-data-file <musrfit>` option. If no fitting is done, this option is ignored. 
-
-**Examples:**
-
-In order to illustrate the usage of these parameters a few examples with explanations are given below: 
-
-.. code-block:: bash
-
-  $ msr2data 8400 8460 _tf_h13 -oABC.db fit-8472 
-  
-Using ``8472_tf_h13.msr`` as first template, ``msr2data`` generates subsequent msr input files ``8400_tf_h13.msr`` through ``8460_tf_h13.msr``, 
-calls ``musrfit`` to perform a fit of these files and collects the results of the fits together with the DB header in the new file ``ABC.db``. 
-Additionally, some information about external parameters like the temperature will be passed to ``ABC.db`` if it is present in the data files.   
-
-.. code-block:: bash
-
-  $ msr2data [8500 8502-8504 8507] _zf fit-8472 noheader nosummary -o DEF.db 
-  
-Using ``8472_zf.msr`` as first template, ``msr2data`` generates subsequent msr input files ``8500_zf.msr``, ``8502_zf.msr``, ``8503_zf.msr``, 
-``8504_zf.msr``, and ``8507_zf.msr``, calls ``musrfit`` to perform a fit of these files and collects the results of the fits in the file ``DEF.db`` 
-*without* writing the DB file header or attempting to read additional information from the data files.
-
-.. code-block:: bash
-
-  $ msr2data 8595 8585 "" noheader fit-8472! -oGHI.dat data nosummary -k 
-  
-Using ``8472.msr`` as template for all runs, ``msr2data`` generates the msr input files ``8595.msr`` through ``8585.msr``, calls ``musrfit`` with 
-the option ``--keep-mn2-ouput`` to perform a fit of these files and collects the results of the fits in the column-structured ASCII file ``GHI.dat`` 
-*without* writing any file header or attempting to read additional information from the data files.   
-
-.. code-block:: bash
-
-  $ msr2data 8472 8475 "" fit -o none
-  
-Take the *given* msr files ``8472.msr`` through ``8475.msr`` and call ``musrfit`` *without* finally summarizing the results.
-
-.. code-block:: bash
-
-  $ 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!*
-
-.. code-block:: bash
-
-  $ msr2data [8472 8475-8479] _tf_h13 paramList 1-16 data -o bestData.dat 
-  
-Will collect the parameters 1 to 16 from the msr-files ``8472_tf_h13.msr``, ``8475_tf_h13.msr``, ``8476_tf_h13.msr``, ``8477_tf_h13.msr``, ``8478_tf_h13.msr``, 
-and ``8479_tf_h13.msr`` and write these parameters into a column like output file ``bestData.dat``.  
-  
-.. index:: msr2-data-global-mode
-  
-The Global Mode  
----------------
-  
-Apart from all the options described :ref:`above <msr2data-opt-param>` there is another program option: **global**. 
-This option changes the general behavior of ``msr2data`` in that way that instead of processing one msr file for each 
-run it combines all specified runs in *one single msr file* with the possibility to define common parameters for all 
-runs as well as run-specific parameters. When writing the obtained parameters to a DB file or a column-structured 
-ASCII file that single msr file is read and the parameters valid for each run are extracted. The global option can be 
-used in conjunction with any of the described invocations of ``msr2data`` and together with all options stated :ref:`above <msr2data-opt-param>`.   
-
-File Generation
-+++++++++++++++
-
-The general idea of this mode is to generate a global msr file on the basis of a working single-run msr file. For this 
-purpose a single-run template containing information about common and run-specific parameters should be created. These 
-parameters are identified through their parameter names: 
-
-**run-specific parameters**
-  these parameters are tagged with the current run number in the format ``%0Xu``, *i.e.* ``X`` digits with leading zeros, 
-  at the end of the parameter name, *e.g.* for a 4-digit-formatted run number ``alpha0123`` if the run number was 123 or 
-  for a 8-digit-formatted run number ``alpha00123456`` if the run number was 123456. ``X`` has to be at least 4. 
-**common parameters**
-  all parameters that are not run specific 
-  
-The :ref:`FITPARAMETER block <msr-fitparameter-block>` of an exemplary template file ``8472_example.msr`` could therefore look like:  
-
-::
-
-  FITPARAMETER
-  #       No   Name      Value     Step        Pos_Error    Boundaries
-          1    Phase     35.8359   -3.94496    3.93749
-          2    Asy8472   0.04501   -0.00208    0.00211      0       0.33
-          3    Field     143.212   -0.27960    0.27885      100     200
-          4    Rate8472  0.14245   -0.02501    0.02279      0       1
-            
-Here the parameters **2** and **4** would be treated as *run-specific* whereas the parameters **1** and **3** would be *common* to the original and all newly added runs.
-
-Normally, within the template file there should *not* appear explicitly any run-specific parameters in the :ref:`THEORY <msr-theory-block>` and 
-:ref:`FUNCTIONS <msr-functions-block>` blocks. If however, those parameters are met, ``msr2data`` will try to substitute them by mapped parameters 
-and add them accordingly to the map contained in each :ref:`RUN block <msr-run-block>`.
-
-When ``msr2data`` is called to generate a global msr file, *e.g.*
-
-.. code-block:: bash
-
-  $ msr2data 8471 8470 _example msr-8472 global 
-  
-a new msr file ``8471+global_example.msr`` is created. As can be seen in the example, the name of the global msr file always starts with the 
-first specified run number followed by the ``+global`` identifier and the template ``<extension>``. The example's global FITPARAMETER block would be:
-
-:: 
-
-  FITPARAMETER
-  #       No   Name      Value     Step        Pos_Error    Boundaries
-
-  # Common parameters for all runs
-
-          1    Phase     35.8359   -3.94496    3.93749
-          2    Field     143.212   -0.27960    0.27885      100     200
-
-  # Specific parameters for run 8471
-            
-          3    Asy8471   0.04501   -0.00208    0.00211      0       0.33
-          4    Rate8471  0.14245   -0.02501    0.02279      0       1
-
-  # Specific parameters for run 8470
-
-          5    Asy8470   0.04501   -0.00208    0.00211      0       0.33
-          6    Rate8470  0.14245   -0.02501    0.02279      0       1
-
-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! 
-            
-.. note::     
-
-  Please be aware of the fact that comments in the template msr file are *not* propagated to the newly generated global msr file!
-  
-.. index:: msr2data-global-param-extraction  
-  
-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 :ref:`run-list file <run-list-file_structure>`. 
-In order to reach this goal the global msr file has to obey certain rules: 
-
-* The order of the parameters has to match the one described above, meaning the common parameters are listed first followed by 
-  the same number of parameters specific to each run tagged by the according run numbers at the end of the parameter names and 
-  having the same order as the specified list of runs.
-* The RUN blocks have to be ordered according to the list of runs to be processed. 
-
-Following these rules -- which is achieved most easily by generating the global msr file using ``msr2data`` as shown above -- the parameters can be extracted *e.g.* like
-
-.. code-block:: bash
-
-  $ msr2data 8471 8470 _example global data -o globalFit.dat 
-  
-This will read in the file ``8471+global_example.msr``, extract for each run all relevant parameters from the msr file as well as 
-from the according data files (if available) and append all of them in columns to the ASCII file ``globalFit.dat``.   
-
-.. index:: msr2data-global-extended
-
-The Extended Global Mode
-++++++++++++++++++++++++
-
-If a new global input file is generated, it is also possible to do an automatic pre-analysis for each single run using the specified template first; 
-afterwards the run-specific parameters of these single-run msr files are collected into the global msr file. In special cases this might be useful 
-to obtain a better set of starting values for the parameters, however, in most cases it will not replace the "manual review" of the generated global 
-input file. The option is activated by choosing the keyword **global+**. For example 
-
-.. code-block:: bash
-
-  $ msr2data 8471 8470 _example global+ msr-8472 
-  
-Here, ``8472_example.msr`` is first used as template to generate the file ``8471-OneRunFit_example.msr``, then ``musrfit`` is called for it, the result 
-is used to generate ``8470-OneRunFit_example.msr`` and ``musrfit`` is called for that file. Finally, the global fit file ``8471+global_example.msr`` is 
-produced — including the fit results of the ``OneRunFit`` files for the run-specific parameters.  
-
-By appending an exclamation mark **!** to the **global+** option, the given template will be used for every new file generation (similar to the fit option 
-explained before). The **+[!]** extension will be ignored, if no new global input file is generated.
-The single run msr files are *not* deleted at the moment. The information contained in them might be useful for some people. Of course the data can also 
-be collected by ``msr2data``. *E.g.* in order to produce a DB file ``OneRunFits.db`` one could call 
-
-.. code-block:: bash
-
-  $ msr2data 8471 8470 -OneRunFit_example -o OneRunFits.db 
-
-.. note::  
-
-  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.
-  
-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 :math:`2^{32}-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...  
-* The msr-file generation from a template takes only care of runs given on the *first* line of a ``RUN block``. :ref:`ADDRUN <msr-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.   
-  
-The Graphical User Interface for msr2data Provided by musredit  
---------------------------------------------------------------
-
-:ref:`musredit <musredit-sec>`, 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:
-
-.. image:: ../images/msr2data-GUI.*
-
-1. and 2. Choose one of the ways to specify your list of runs as described under :ref:`basic usage <msr2data-basic-usage>`.
-
-3. 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. ``musredit`` takes care of passing the "" to ``msr2data`` as mentioned above. 
-4. 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! 
-5. Activates the ``-o <outputFileName>`` option if ``<outputFileName>`` is entered. If nothing is entered the default output file ``out.db`` or ``out.dat`` is used.  
-
-The options tags correspond essentially to the description in :ref:`optional parameters <msr2data-opt-param>`.
\ No newline at end of file
diff --git a/doc/html/_sources/mupp.txt b/doc/html/_sources/mupp.txt
deleted file mode 100644
index c8156723..00000000
--- a/doc/html/_sources/mupp.txt
+++ /dev/null
@@ -1,238 +0,0 @@
-.. include:: <isogrk1.txt>
-.. index:: mupp
-.. _mupp:
-
-mupp - |mgr|\SR Parameter Plotter
-=================================
-
-``mupp`` is a little helper program which allows to quickly plot a collection of msr-file parameters,
-as for instance generated by :ref:`msr2data <msr2data>`. It can handle ``db``- and ``dat``-files.
-Also a collection of ``msr``-files can be invoked. ``mupp`` is heavily inspired by |mgr|\View (see
-`here <http://musr.org/muview/>`_).
-
-``mupp`` can be operated from within as graphical user interface or via a command line scripting interface.
-The ``mupp`` GUI can be invoked either directly from the command line or from within :ref:`musredit <musredit-sec>`.
-
-Each collection bundles a number of runs, where a run is a single |mgr|\SR measurement.
-A run is analyzed by a number of parameters (defined in the msr-files), and complemented by
-additional physical parameters as the temperature, magnetic field, implantation energy, etc.
-Hence parameters can be seen as vectors and can be plot against each other. 
-
-.. index:: mupp-gui
-
-The Graphical User Interface
-----------------------------
-
-A typical setting could look like this
-
-.. image:: ../images/mupp-gui-0.*
-
-1. shows the list of loaded collections. A collection is defined as ``db``- or ``dat``-file (typically the 
-   output from :ref:`msr2data <msr2data>`). If you call the open-dialog and select a collection of
-   ``msr``-files, ``mupp`` will call ``msr2data`` and tries to generate a collection on-the-fly.
-2. in this list, the data-tags of the currently selected collection is presented. The data-tags can be
-   directly dragged over to the ``x``- and ``y``-axis list. Another way is to select the data-tag
-   wished and click ``add X`` to add the selected data-tag to the ``x``-axis list. Analogous it is done
-   for the ``y``-axis.
-3. ``x``-axis list. The labels are followed by ``(-X-)`` where the number ``X`` corresponds to the
-   selection it corresponds to. The numbering of the collection is as given in the collection list.
-4. ``y``-axis list. The labels are followed by ``(-X-)`` where the number ``X`` corresponds to the
-   selection it corresponds to. The numbering of the collection is as given in the collection list.
-5. ``add X`` allows to add the currently selected data-tag to the ``x``-axis list.   
-6. ``add Y`` allows to add the currently selected data-tag to the ``y``-axis list. 
-7. ``remove X`` will remove the selected ``x``-axis tag.
-8. ``remove Y`` will remove the selected ``y``-axis tag.
-9. Often one would like to compare trends of different settings. In the above example each collections
-   holds an energy scans for a given temperature. Each collection is measured at a different temperature.
-   Now, instead of adding ``x``- and ``y``-axis tags for each collection, you can do the following:
-   you add ``x``- and ``y``-axis data-tags for the first collection. Afterwards you select all the other
-   collections of interest and click on ``Add Ditto``. ``mupp`` will then add the corresponding
-   ``x``- and ``y``-axis data-tags accordingly. This is less error prone and quicker!
-10. Clicking the ``Plot`` button will invoke ``mupp_plot`` (a ``ROOT`` based application) which will
-    present the data, as shown here
-    
-    .. image:: ../images/mupp-plot-0.*
-      :height: 600px
-      
-11. ``Remove Collection``: will remove the selected collection
-12. ``Refresh Collection``: will reload the collection (``db``- or ``dat``-file). This is often useful
-    during beamtime where the collection is growing run-by-run.
-13. Command history window.
-14. This is the script command line. Currently it allows to perform the tasks without mouse gambling.
-    In the future much more commands are planed. See the ``Help / Cmd's`` for the currently available
-    commands.
-
-Define Variable Dialog
-++++++++++++++++++++++    
-
-.. image:: ../images/mupp-add-var.*
-
-1. Variable text edit window.
-2. Collection link window.
-3. Shows the parameters of the selected collection.
-4. Check if the variable/error variable from the edit window is valid.
-5. Add the variable to the selected collection(s) if the parsing is successful.
-
-A variable defined here is a mathematical expression defined by parameters of loaded collections.
-Since a parameter also has an associated error, also newly defined variables **always** need
-to be defined together with a corresponding error variable. If the name of a variable is defined
-as ``SigmaSC_10`` (see the above snapshot), the error variable need to be named as ``SigmaSC_10Err``.
-
-Currently the following mathematical functions are defined: ``max``, ``min``, ``abs``, ``sin``, ``cos``,
-``tan``, ``exp``, ``log``, ``ln``, ``pow``.
-
-.. index:: mupp-scripting
-    
-The Scripting Interface
------------------------
-
-``mupp`` can also be operated in a scripting like manner. The use cases are plot updates during run time, 
-or web-based interaction which requests figures. A script is invoked by the command line option ``-s`` (see
-:ref:`mupp command line summary <mupp-usage>`. Currently the following scripting commands are available:
-
-**loadPath <dir>** 
-  set the load path to ``<dir>``. Bash variables like $HOME are accepted. This is the path where to look for collection files (``db``- and ``dat``-files).
-
-**load <coll>** 
-  will load the collection ``<coll>``.
-
-**selectAll** 
-  will select all loaded collections. This means every plot of variable x/y will be carried out to *ALL* collections.
-  
-**select <nn>** 
-  selects collection ``<nn>``, where ``<nn>`` is either the *number* of the collections, or its *name*, *e.g.* 
-  select YBCO-40nm-T5K-FC150mT-Escan.db.
-  
-**x <label>**   
-  add ``<label>`` as a *x*-variable. Only *one* is allowed.
-  
-**y <label(s)>**
-  add ``<label(s)>`` as *y*-variable. *Multiple* labels are possible. 
-  
-**norm**
-  this will normalize all the *y*-variables by their maximum.   
-  
-**savePath <dir>**
-  set the save path to ``<dir>``. The place where the macros, and/or the plot output will be saved.  
-  
-**plot <fln>**
-  where ``<fln>`` is the file name with extension under which the plot should be saved.
-  
-**macro <fln>**
-  where ``<fln>`` is the file name under which the root macro should be saved.
-  
-**var <var_name> = <expr>**
-  defines a variable.
-  <expr> is a mathematical expression where collection variables are addressed 
-  via the '$', e.g. ``dataT`` is addressed by ``$dataT``, etc. An example:
-  
-  ``var invT = 1000.0 / $dataT``
-  
-  Each variable has to be accompanied by its error variable. An error variable
-  is defined by the ``<var_name>`` followed by ``Err``
-  For the above example the error variable is
-  
-  ``var invTErr = $invT * $dataTErr / $dataT``
-  
-**col <nn> : <var_name>**
-   links <var_name> to the collection <nn>, where <nn> is the number of the 
-   collection as defined by the order of load, starting with 0.   
-  
-An example script file ``sigmaSC-vs-temp.txt`` might look like this:
-
-::
-
-  # This is a comment
-  # Script: sigmaSC-vs-temp.txt
-
-  loadPath ./
-
-  load YBCO-40nm-FC-E3p8keV-B10mT-Tscan.db  # collection 0
-  load YBCO-40nm-FC-E3p8keV-B150mT-Tscan.db # collection 1
-
-  # define variables: for each variable an associated error variable is needed.
-  # B=10mT
-  var SigmaSC_10 = pow(abs(pow($Sigma,2.0)-pow(0.11,2.0)), 0.5) # 0.11 (1/us) is the nuclear contribution (T>Tc)
-  var SigmaSC_10Err = pow(pow($Sigma*$SigmaErr,2.0)+pow(0.11*0.0025,2.0), 0.5)/$SigmaSC_10
-  # B=150mT
-  var SigmaSC_150 = pow(abs(pow($Sigma,2.0)-pow(0.075,2.0)), 0.5) # 0.075 (1/us) is the nuclear contribution (T>Tc)
-  var SigmaSC_150Err = pow(pow($Sigma*$SigmaErr,2.0)+pow(0.075*0.0025,2.0), 0.5)/$SigmaSC_150
-
-  # link variables to collections
-  col 0 : SigmaSC_10    # error variable SigmaSC_10Err doesn't need to be given, it is automatically linked to SigmaSC_10
-  col 1 : SigmaSC_150
-
-  norm # normalize the plot to the maximum of each y-data-set
-
-  # the next 3 cmds means the following: use collection 0, add dataT to the x-axis,
-  # and SigmaSC_10 to the y-axis
-  select 0 
-  x dataT
-  y SigmaSC_10
-
-  select 1
-  x dataT
-  y SigmaSC_150
-
-  # where to save the output
-  savePath ./
-  
-  # create a pdf output file of the above defined xy-data sets. Currently also
-  # other file formats are supported, like png, jpg, etc.
-  plot SigmaSCVsTemp.pdf
-
-  # creates a ROOT macro which can be used for further refinement
-  macro SigmaSCVsTemp.C
-
-  # end
-
-.. index:: mupp-usage
-.. _mupp-usage:
-
-The Usage Summary
------------------
-
-::
- 
-  usage: mupp [OPTIONS] [[--path <fit-param-path>] <fit-param-file-names>]
-
-  OPTIONS:
-    -h, --help: this help
-    -v, --version: current mupp version
-    -s <fln>, --script <fln>: <fln> being a mupp script.
-    --path <fit-param-path>: path where to look for the <fit-param-file-names>
-    <fit-param-file-names>: list of file name(s) to be loaded.
-       allowed formats are: db, dat, msr
-
-
-  SCRIPT COMMANDS:
-     Lines starting with '#', '%', or '//' are comments and will be ignored.
-     The same is true for empty lines. Comments are also allowed at the end
-     for a command, i.e. loadPath ./ # the best place ever.
-
-     load <coll>     : load a collection. <coll> is the filename of the
-                       collection (*.db, *.dat)
-     loadPath <path> : set the load path to <path>; accepting bash variables
-                       like $HOME, etc.
-     x <var-name>    : set a x-axis variable. <var-name> is a data tag of
-                       the db/dat-file.
-     y <var-name>    : set a y-axis variable. <var-name> is a data tag of
-                       the db/dat-file.
-     select <nn>     : select collection <nn>, where <nn> is the row-number
-                       or the name of the collection to be selected.
-     selectAll       : i.e. already set 'x', 'y' will apply to ALL collections
-                       present.
-     savePath <path> : sets the save path to <path>; accepting bash variables
-                       like $HOME, etc.
-     plot <fln>      : where <fln> is the file name with extension under which
-                       the plot should be saved.
-     macro <fln>     : where <fln> is the file name under which the root macro
-                       should be saved.
-     var <var_name> = <expr> : defines a variable.
-                               <expr> is a mathematical expression where
-                               collection variables are addressed via the '$',
-                               e.g. dataT is addressed by $dataT, etc.
-     col <nn> : <var_name>   : links <var_name> to the collection <nn>, where
-                               <nn> is the number of the collection as defined
-                               by the order of load, starting with 0.
-              
diff --git a/doc/html/_sources/musr-root.txt b/doc/html/_sources/musr-root.txt
deleted file mode 100644
index 29c6963a..00000000
--- a/doc/html/_sources/musr-root.txt
+++ /dev/null
@@ -1,681 +0,0 @@
-.. include:: <isogrk1.txt>
-.. index:: MusrRoot
-
-.. _MusrRoot:
-
-MusrRoot - an Extensible Open File Format for |mgr|\SR
-======================================================
-
-Until 2011 different |mgr|\SR file formats were used within PSI. The bulk-|mgr|\SR instruments were 
-writing their data in the ``PSI-BIN`` file format, which is a fixed binary format with rather stringent 
-limitations. The LE-|mgr|\SR (LEM) instrument was using a ROOT (CERN) based file format which was tightly 
-tailored to the special needs of the LEM instrument. This situation was unsatisfactorily and hence it 
-was decided to move forward to a open file format called ``MusrRoot`` to be described in the following.
-
-Some Basics Concerning ROOT Files
----------------------------------
-
-The |mgr|\SR data acquisition systems at PSI are utilizing MIDAS (see `Midas Home Page <https://midas.triumf.ca/MidasWiki/index.php/Main_Page>`_). 
-The MIDAS analyzer, which is responsible to build histograms, especially the |mgr|\SR decay histograms, makes 
-it very easy to build ROOT (see `ROOT/CERN home page <https://root.cern.ch>`_ ) histogram objects (these 
-are ``TH1F`` objects for |mgr|\SR decay histograms). ROOT is a ``C++`` object-oriented data mining and 
-analysis frame work. These histograms can be collected and saved in ROOT files (``TFile``). In order to ease 
-the understanding of the upcoming definitions, a few ROOT related things shall be summaries here. For details 
-concerning the ROOT frame work documentation please check `ROOT/CERN Users Guide(s) <https://root.cern.ch/root-user-guides-and-manuals>`_ 
-and `ROOT/CERN Reference Guide <https://root.cern.ch/guides/reference-guide>`_. 
-
-ROOT files (``TFile``) are binary files which can hold any kind of objects. A ``TFile`` is organized similarly 
-to a directory structure of an operating system. Within the ROOT framework, there is a ``TFile`` browser available 
-which allows to inspect these files. This browser (``TBrowser``) will show all object saved in the ``TFile`` directly, 
-if they derive from ``TObject``. 
-
-The ``MusrRoot`` file format to be described below is only using a small subset of possible ROOT objects, namely:
-
-* ``TFolder``: this are the top level objects in the ``MusrRoot`` file.
-* ``TH1F``: Hold the |mgr|-decay-histograms.
-* ``TObjArray``: Holding collection of header information.
-* ``TObjString``: Holding the content of any header information. 
-
-Since all these objects are deriving form ``TObject``, they will be directly accessible via the ``TBrowser``-object. 
-For instance, the |mgr|-decay-histograms can be directly plotted, are even fitted, out of the box. 
-
-MusrRoot an Extensible Open File Format for |mgr|\SR 
-----------------------------------------------------
-
-As mentioned before, ROOT files are open-file-format files meaning that they can contain more entries (and most probably will) than the ones specified in the following. The specified ones will be the mandatory ones for all instruments. Before defining all mandatory entries, the MusrRoot file structure shall be sketched.
-
-The MusrRoot file structure looks like: 
-
-::
-
-  histos ---|
-            |- DecayAnaModule ---|
-            |                    |- hDecay001
-            |                    |- hDecay002
-            |                    ...
-            |
-            |- SCAnaModule ---|
-            ...               |- hSampleTemperature
-                              |- hSampleMagneticField
-                              ...
-  RunHeader ---|
-               |- RunInfo
-               |- DetectorInfo ---|
-               |                  |- Detector001
-               |                  |- Detector002
-               |                  ...
-               |
-               |- SampleEnvironmentInfo
-               |- MagneticFieldEnvironmentInfo
-               |- BeamlineInfo
-               ...
-               
-where ``hDecay001``, etc. are ROOT histograms (to be more specific: ``TH1F``), containing the |mgr|\SR decay histograms. There can be as many as needed, especially there is no limitation about their length. The histogram object names will be ``hDecayXXX``, where ``XXX`` (leading zero int, *i.e.* ``%03d`` 
-in ``C/C++`` notation, starting with '1') is the histogram number. The title and name of the histogram (see description of the ``TH1F`` ROOT class) contains the label of the histogram, like 'top', 'forward', etc. How many of these histograms are present is accessible through the ``RunInfo`` folder in which the necessary header information are found (details see next sections). The folder ``SCAnaModule`` contains histograms of some of the slow-control parameters, as for instance the sample temperature versus time, the applied field versus time, etc. Again the label of the histogram will give more specific information about its content. 
-
-Run Information Contained in ``RunHeader``
-++++++++++++++++++++++++++++++++++++++++++
-
-The ``RunHeader`` contains all needed meta-information to describe a |mgr|\SR-run. The list of the minimal number of required "folders" of the ``RunHeader`` is given in the following structure:
-
-::
-
-  RunHeader (TFolder) ---|
-                         |- RunInfo (TObjArray)
-                         |- DetectorInfo (TObjArray)
-                         |- SampleEnvironmentInfo (TObjArray)
-                         |- MagneticFieldEnvironmentInfo (TObjArray)
-                         |- BeamlineInfo (TObjArray)
-
-In brackets the object type is given. ``RunInfo`` contains most information relevant for the user and will be itemized in :ref:`RunInfo Overview <musr-root-overview>` and :ref:`RunInfo Required <run-info-required>`. ``DetectorInfo`` contains detector specific information, like detector name, time zero bin, etc. (details is found under :ref:`DetectorInfo Required <detector-info-required>`). ``SampleEnvironmentInfo`` (details under :ref:`SampleEnvironmentInfo Required <sample-environment-info-required>`), and ``MagneticFieldEnvironmentInfo`` (details under :ref:`MagneticFieldEnvironmentInfo Required <magnetic-field-environment-info-required>`) store additional, more detailed information concerning the sample environment. ``BeamlineInfo`` stores beamline relevant information (details under :ref:`BeamlineInfo Required <beamline-info-required>`).
-
-Before elaborating more on the required items within this structure, a few words on the ROOT types used here: ``RunHeader`` is a ``TFolder`` object. All the "sub-directory" entries are of type ``TObjArray`` and collect items of type ``TObjString`` or other ``TObjArray`` (*i.e.* sub-directories and sub-sub-directories, etc.).
-
-.. index:: MusrRoot-Overview
-.. _musr-root-overview:
-
-``RunInfo`` Overview
-^^^^^^^^^^^^^^^^^^^^
-
-======================== ============================ =====================================================
-Name                     Internal Type                Comment
-======================== ============================ =====================================================
-Version                  ``TString``                  GIT version of ``TMusrRunHeader``
-Generic Validator URL    ``TString``                  URL of the generic ``MusrRoot`` validation xsd-file.
-Specific Validator URL   ``TString``                  URL of the instrument specific validation xsd-file.
-Generator                ``TString``                  Program which wrote the ``MusrRoot`` file, *e.g.* ``nemu_analyzer``
-File Name                ``TString``                  File name of the ``MusrRoot`` file, *e.g.* ``deltat_tdc_gps_4295.root``
-Run Title                ``TString`` 
-Run Number               ``Int_t`` 
-Run Start Time           ``TString``                  ISO 8601 date time
-Run Stop Time            ``TString``                  ISO 8601 date time
-Run Duration             ``TMusrRunPhysicalQuantity`` run duration in sec
-Laboratory               ``TString``                  *e.g.* PSI
-Instrument               ``TString``                  *e.g.* GPS
-Muon Beam Momentum       ``TMusrRunPhysicalQuantity`` *e.g.* 28.1 MeV/c
-Muon Species             ``TString``                  positive, or negative muon
-Muon Source              ``TString``                  *e.g.* Target E - Low Energy Muons or "Target M" ... 
-Setup                    ``TString``  
-Comment                  ``TString`` 
-Sample Name              ``TString`` 
-Sample Temperature       ``TMusrRunPhysicalQuantity`` *e.g.* 3.21 +- 0.05 K; SP: 3.2; CF1
-Sample Magnetic Field    ``TMusrRunPhysicalQuantity`` *e.g.* 350.002 +- 0.005 G; SP: 350; WXY
-No of Histos             ``Int_t``
-Time Resolution          ``TMusrRunPhysicalQuantity`` *e.g.* 0.1953125 ns
-RedGreen Offsets         ``TIntVector``               *e.g.* 0; 20
-======================== ============================ =====================================================
-
-These entries should be clear except for the ``RedGreen Offsets`` and the column "Internal Type" which shortly will be discussed before specifying the content of the other required folders.
-
-#. ``RedGreen Offsets``: in case experiments are performed with external stimuli, there will be a collection of related histograms. 
-   For instance for electrical field experiments, there will be histograms for field on/off, doubling the number of needed histograms. 
-   In order to distinguish them easier in the data file, the ``RedGreen Offsets`` were introduced. One selection of histograms 
-   (assuming for the moment 8 detectors) will be numbered from 1 to 8 (lets say the field off ones). The other set of histograms 
-   (field on in this example) will then start with 21 through 28 (see table above). The same will be true for the detector information 
-   (see :ref:`DetectorInfo Required <detector-info-required>`). The entry ``No of Histos`` will only give 8 for the given example, 
-   meaning that red/green multiplication is defined rather via ``RedGreen Offsets`` than the number of histograms. 
-#. Internal Types: in order to ease the handling of the ``MusrRoot`` run header, a class ``TMusrRunHeader`` is available which deals 
-   with it. The "Internal Type" specified, corresponds to the internal representation in within this class. In the ``MusrRoot`` file 
-   these entries are all saved as browsable ROOT strings (``TObjStringv). The only special type is ``TMusrRunPhysicalQuantity`` which 
-   is introduced to deal with physical quantities. They always can be represented in the following way:
-   
-   ::
-   
-     <property name> <value> +- <estimated error> <unit>; SP: <demand>; <description>
-     
-Not all of these values are needed to be given and depending on which are given, the representation in the ``MusrRootv file will be different (handled by ``TMusrRunHeader``). Examples are given in the comment column of the table above. For details see  :ref:`TMusrRunPhysicalQuantity - Possible Representations <musr-run-physical-quantity>`. 
-
-A mock-up ``TBrowser`` print-out would look like the one shown in the following figure. You might notice, that at the end of each entry you find a ``-@X``, where ``X`` is a number. This is an encoding of the internal type of the entry and is the price to be payed not using derived types. The next section will explain this in much more detail. 
-
-.. image:: ../images/MusrRoot-RunInfo.*
-
-``TMusrRunHeader`` mock up. The red shaded entries are of type ``TMusrRunPhysicalQuantity``
-
-.. _musr-run-header-concept:
-
-TMusrRunHeader Concept
-----------------------
-
-The different |mgr|\SR instruments need different information to be written into the data file (next to the most important ones: the histograms). The above defined properties are the *minimal number of required* ones. There are different possible approaches to deal with it on the implementation level. 
-
-* A base class dealing with *minimal* required standard is defined. Afterwards for each instrument a class 
-  is derived which is extending the base class to the needs of the instrument.
-* The base class is defined in a more abstract way, and some external, text-based description is given which defines the details of the instrument. 
-
-Even though the first approach is very clean, it would mean a lot of maintenance work. The 2nd approach is slightly more demanding for the handling class (``TMusrRunHeader`` and helper classes), but having the advantage of easy maintainability and expandability. The idea is that all header information can be classified into 7 groups (see previous and following section(s))
-
-#. Strings, represented by ``TString``
-#. Integers, represented by ``Int_t``
-#. Floating point numbers, represented by ``Double_t``
-#. Physical quantities, represented by :ref:`TMusrRunPhysicalQuantity - Possible Representations <musr-run-physical-quantity>`
-#. Collection of strings, represented by ``TStringVector``
-#. Collection of integers, represented by ``TIntVector``
-#. Collection of floating point numbers, represented by ``TDoubleVector`` 
-
-These properties can be collected by themselves in form of vectors. This way any needed information can be written into the ROOT file. The class ``TMusrRunHeader`` is implementing this run header concept. In following section code snippets will be discussed, showing how this is used on level of the ``MIDAS`` analyzer, ``musrfit`` reader routine, and ``any2many`` conversion routines. The section :ref:`Validation <musr-root-validation>` will discuss how to validate ``MusrRoot`` files. 
-
-    
-User Interface for MusrRoot Run Header
-++++++++++++++++++++++++++++++++++++++
-
-There are two things needed to deal with the ``MusrRoot`` run header, namely writing it and reading it. I will start with the writing as will be done in the ``MIDAS`` analyzer. 
-
-Writing a MusrRoot Run Header
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-
-An example program ``write_musrRoot_runHeader`` which is writing a full run header is part of the ``musrfit`` package. Here I will concentrate just on the most essential parts. First one needs an instance of ``TMusrRunHeader``
-
-.. code-block:: c++
-
-  TMusrRunHeader *header = new TMusrRunHeader();
-  TMusrRunPhysicalQuantity prop;
-  
-``header`` is the instance of ``TMusrRunHeader``. ``prop`` is an instance of ``TMusrRunPhysicalQuantity`` which will be needed further down in the description. In the next step some run header entries will be added 
-
-.. code-block:: c++
-
-  header->Set("RunInfo/File Name", "deltat_tdc_gps_2871.root");
-  header->Set("RunInfo/Run Title", "here comes the run title");
-  header->Set("RunInfo/Run Number", 2871);
-  
-Adding information is done via the multiple overloaded ``Set(<pathName>,<value>)`` method. Here ``<pathName>`` is a string representing the "path" like representation in the ``MusrRoot`` file structure, followed by the "value" to be set, *e.g.* "=File Name=". ``<value>`` can be any of the types listed at the beginning of :ref:`Sec. TMusrRunHeader Concept <musr-run-header-concept>`. Here a few examples how to set ``TMusrRunPhysicalQuantity``. 
-
-.. code-block:: c++
-
-  prop.Set("Sample Temperature", 3.2, 3.21, 0.05, "K", "CF1");
-  header->Set("RunInfo/Sample Temperature", prop);
-
-  prop.Set("Time Resolution", 0.1953125, "ns", "TDC 9999");
-  header->Set("RunInfo/Time Resolution", prop);
-
-  prop.Set("CF3", MRH_UNDEFINED, 3.27, 0.09, "K", "strange temperature");
-  header->Set("SampleEnvironmentInfo/CF3", prop);
-  
-Here ``TMusrRunPhysicalQuantity`` objects are fed via the use of the overloaded set-method. For details see :ref:`TMusrRunPhysicalQuantity - Possible Representations <musr-run-physical-quantity>`.   
-
-To set some property within "sub-sub-directories" it would like this: 
-
-.. code-block:: c++
-
-  header->Set("DetectorInfo/Detector001/Time Zero Bin", 3419.0);
-  
-To write the whole run header into a file would look something like this: 
-
-.. code-block:: c++
-
-  TFile *f = new TFile(fileName, "RECREATE", "write_musrRoot_runHeader");
-  if (f->IsZombie()) {
-    delete f;
-    return -1;
-  }
-
-  // create the needed TFolder object
-  TFolder *runHeader = new TFolder("RunHeader", "MusrRoot Run Header Info");
-
-  // create the "directory" structure
-  if (header->FillFolder(runHeader)) {
-    runHeader->Write(); // write run header to file
-  }
-
-  f->Close();
-
-Reading a MusrRoot Run Header 
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-
-The following code snippet shows how the extract the full run header from the ``MusrRoot`` file. 
-
-.. code-block:: c++
-
-  TFile *f = new TFile(fileName, "READ", "read_musrRoot_runHeader");
-  if (f->IsZombie()) {
-    delete f;
-    return -1;
-  }
-
-  TFolder *runHeader = 0;
-  f->GetObject("RunHeader", runHeader);
-  if (runHeader == 0) {
-    cerr << endl << ">> **ERROR** Couldn't get top folder RunHeader";
-    closeFile(f);
-    return -1;
-  }
-
-  TMusrRunHeader *header = new TMusrRunHeader(fileName);
-
-  if (!header->ExtractAll(runHeader)) {
-    cerr << endl << ">> **ERROR** couldn't extract all RunHeader information";
-    closeFile(f);
-    return -1;
-  }
-
-  f->Close();
-  delete f;
-
-
-The routine ``ExtractAll(TFolder *runHeader)`` decodes all the ``TObjString`` objects and fills internal data structures. This means when reading a MusrRoot -file the above handling is always needed. After the ``ExtractAll`` call, parameters can be extracted via the getter routines available. For instance to read the Run Number, the code would look like   
-
-.. code-block:: c++
-
-  Bool_t ok;
-  Int_t ival;  
-  header->Get("RunInfo/Run Number", ival, ok);
-  if (ok)
-    cout << endl << "Run Number: " << ival;
-  else
-    cout << endl << "**ERROR** Couldn't obtain the 'Run Number'.";
-    
-Reading a ``TMusrRunPhysicalQuantity`` object, *e.g.* the sample temperature looks like this 
-
-.. code-block:: c++
-
-  TMusrRunPhysicalQuantity prop;
-
-  header->Get("RunInfo/Sample Temperature", prop, ok);
-  if (ok) {
-    cout << endl << "Sample Temperature: " << prop.GetValue() << " +- ";
-    cout << prop.GetError() << " " << prop.GetUnit().Data();
-    cout << "; SP: " << prop.GetDemand() << "; " << prop.GetDescription().Data();
-  } else {
-    cout << endl << "**ERROR** Couldn't obtain the 'Sample Temperature'.";
-  }
-
-.. index:: MusrRoot-Validation
-.. _musr-root-validation:
-
-Validation of a MusrRoot File 
-+++++++++++++++++++++++++++++
-
-Since ``MusrRoot`` is an open and extensible file format a mechanism is needed to validate that a given file is indeed holding the minimum of required entries. To check this the following scheme is implemented in the program ``musrRootValidation``:
-
-.. image:: ../images/MusrRootValidationScheme.*
-
-``MusrRoot`` validation scheme
-
-In the following this validation scheme will be discussed as it is implemented in ``musrRootValidation``: 
-
-#. It is checked if the given file name is a ``TFile``
-#. The file structure is recursively parsed and mapped into an temporary XML file. XML is used 
-   since there are ample of parser and validation frameworks at hand. For details check any decent 
-   book about XML. Here the ``libxml2`` is used, because also ROOT is requiring it.
-#. In a next step the XML file (holding the structure of the supposed ``MusrRoot`` file is validated 
-   against a XML schema. The minimum of required entries is described by ``MusrRoot.xsd`` which is 
-   part of ``musrfit`` but also available from the PSI/LMU web-page.
-#. If the schema validation is successful additional semantic checks (like is the number of decay 
-   histograms the same as the number of detector entries, etc.) will be preformed. 
-
-This validation scheme is useful for people which define instrument specific extensions of the base ``MusrRoot``, as for instance the LEM instrument at PSI. It is also useful for people writing file converters in order to cross check if the generated file is valid.    
-   
-.. _run-info-required:
-
-RunInfo (Required)
-------------------
-
-========================== ============================= =====================================================
-Name                       Internal Type                 Comment
-========================== ============================= =====================================================
-Version                    ``TString``                   GIT version of ``TMusrRunHeader``
-Generic Validator URL      ``TString``                   URL of the generic ``MusrRoot`` validation xsd-file. 
-                                                         *e.g.* `<http://lmu.web.psi.ch/facilities/software/MusrRoot/Validation/MusrRoot.xsd>`_
-Specific Validator URL     ``TString``                   URL of the instrument specific validation xsd-file.
-                                                         *e.g.* for LEM: `<http://lmu.web.psi.ch/facilities/software/MusrRoot/Validation/MusrRootLEM.xsd>`_
-Generator                  ``TString``                   Program which wrote the ``MusrRoot`` file, *e.g.* ``nemu_analyzer``
-File Name                  ``TString``                   File name of the ``MusrRoot`` file, *e.g.* ``deltat_tdc_gps_4295.root``
-Run Title                  ``TString``
-Run Number                 ``Int_t``
-Run Start Time             ``TString``                   ISO 8601 date time
-Run Stop Time              ``TString``                   ISO 8601 date time
-Run Duration               ``TMusrRunPhysicalQuantity``  run duration in sec 
-Laboratory                 ``TString``                   *e.g.* PSI
-Instrument                 ``TString``                   *e.g.* GPS
-Muon Beam Momentum         ``TMusrRunPhysicalQuantity``  *e.g.* 28.1 MeV/c
-Muon Species               ``TString``                   poitive or negative muon
-Muon Source                ``TString``                   *e.g.* "Target E - Low Energy Muons" or "Target M" ...
-Setup                      ``TString``                  
-Comment                    ``TString``
-Sample Name                ``TString``
-Sample Temperature         ``TMusrRunPhysicalQuantity``  *e.g.* 3.21 +- 0.05 K; SP: 3.2; CF1 
-Sample Magnetic Field      ``TMusrRunPhysicalQuantity``  *e.g.* 350.002 +- 0.005 G; SP: 350; WEW 
-No of Histos               ``Int_t``
-Time Resolution            ``TMusrRunPhysicalQuantity``  *e.g.* 0.1953125 ns
-RedGreen Offsets           ``TIntVector``                *e.g.* 0; 20 
-========================== ============================= =====================================================
-
-.. _detector-info-required:
-
-DetectorInfo (Required)
------------------------
-
-The ``DetectorInfo`` is organized in a sub-tree like
-
-::
-
-  DetectorInfo ---|
-                  |- Detector001
-                  |- Detector002
-                  ...
-
-
-
-For each histogram in the ``histos/DecayAnaModule`` corresponds detector entry here.
-
-The numbering of the detectors has to correspond the its histogram, *e.g.* ``hDecay023 <=> Detector023``, *i.e.* potentially discontinuous to show red / green breaks.
-
-``Detector<XXX>`` has the elements 
-
-========================== ============================= =====================================================
-Name                       Internal Type                 Comment
-========================== ============================= =====================================================
-Name                       ``TString``                   detector name, *e.g.* Left-NPP
-Histo Number               ``Int_t``                     histogram number. This number corresponds to the histogram 
-                                                         number in the ``histos/DecayAnaModule`` sub-tree.
-Histo Length               ``Int_t``                     length of the histogram (in bins)
-Time Zero Bin              ``Double_t``                  The type is ``Double_t`` since for the high-field spectrometer 
-                                                         at PSI an ``Int_t`` representation would be not good enough.  
-First Good Bin             ``Int_t``
-Last Good Bin              ``Int_t``
-========================== ============================= =====================================================
-
-.. _sample-environment-info-required:
-
-SampleEnvironmentInfo (Required)
---------------------------------
-
-Here only a single entry is required, namely 
-
-========================== ============================= =====================================================
-Name                       Internal Type                 Comment
-========================== ============================= =====================================================
-Cryo                       ``TString``                   name of the used cryostat/oven, *e.g.* ``Konti-2`` 
-========================== ============================= =====================================================
-
-.. _magnetic-field-environment-info-required:
-
-MagneticFieldEnvironmentInfo (Required)
----------------------------------------
-
-Here only a single entry is required, namely 
-
-========================== ============================= =====================================================
-Name                       Internal Type                 Comment
-========================== ============================= =====================================================
-Magnet Name                ``TString``                   name of the used magnet, *e.g.* ``WEW``. 
-                                                         In case of ZF measurements, there might be an entry like ZF. 
-========================== ============================= =====================================================
-
-.. _beamline-info-required:
-
-BeamlineInfo (Required)
------------------------
-
-Here only a single entry is required, namely 
-
-========================== ============================= =====================================================
-Name                       Internal Type                 Comment
-========================== ============================= =====================================================
-Name                       ``TString``                   name of the beamline, *e.g.* ``piM3.2``
-========================== ============================= =====================================================
-
-Exhaustive MusrRoot Tree Including Everything Required
-------------------------------------------------------
-
-Here it is assumed that there are hypothetical *red / green data* with electric field on/off and light on/off, 
-and hence 4 data sets per detector, and 8 detectors of the instrument: ``left/forward``, ``top/forward``, ``right/forward``, 
-``bottom/forward``, ``left/backward``, ``top/backward``, ``right/backward``, ``bottom/backward``. To show the whole 
-tree structure, it will be split in the representation afterwards, but keep in mind: this will be all part of a 
-single ``MusrRoot`` file. I will add comments in the tree structure by the symbol ``#``. Lets start with the |mgr|\SR data histograms: 
-
-::
-
-  histos -|
-          |- DecayAnaModule -|
-                             |- hDecay001 # left/forward, electric field off, light off
-                             |- hDecay002 # top/forward, electric field off, light off
-                             |- hDecay003 # right/forward, electric field off, light off
-                             |- hDecay004 # bottom/forward, electric field off, light off
-                             ...
-                             |- hDecay007 # right/backward, electric field off, light off
-                             |- hDecay008 # bottom/backward, electric field off, light off
-                             |- hDecay011 # left/forward, electric field on, light off
-                             |- hDecay012 # top/forward, electric field on, light off
-                             |- hDecay013 # right/forward, electric field on, light off
-                             |- hDecay014 # bottom/forward, electric field on, light off
-                             ...
-                             |- hDecay017 # right/backward, electric field on, light off
-                             |- hDecay018 # bottom/backward, electric field on, light off
-                             |- hDecay021 # left/forward, electric field off, light on
-                             |- hDecay022 # top/forward, electric field off, light on
-                             |- hDecay023 # right/forward, electric field off, light on
-                             |- hDecay024 # bottom/forward, electric field off, light on
-                             ...
-                             |- hDecay027 # right/backward, electric field off, light on
-                             |- hDecay028 # bottom/backward, electric field off, light on
-                             |- hDecay031 # left/forward, electric field on, light on
-                             |- hDecay032 # top/forward, electric field on, light on
-                             |- hDecay033 # right/forward, electric field on, light on
-                             |- hDecay034 # bottom/forward, electric field on, light on
-                             ...
-                             |- hDecay037 # right/backward, electric field on, light on
-                             |- hDecay038 # bottom/backward, electric field on, light on
-                             ...
-
-*Comments*: as can be seen the histograms are continuous numbered until there is a red / green mode switch where 
-the histogram number "jumps" (*e.g.* from ``008`` to ``011``). In order to fill in the different red / green 
-histograms an offset is added (here 10, 20, and 30).                              
-
-Next the whole ``RunHeader``. Here the information will be grouped in different folders collecting related information, 
-like general run info, detector info, sample and magnetic field environment info, beamline info, etc.
-
-::
-
-  RunInfo:
-    000 - Version: $Id: TMusrRunHeader.cpp 5092 2012-03-13 07:47:00Z nemu $ -@0
-    001 - Generic Validator URL: http://lmu.web.psi.ch/facilities/software/MusrRoot/Validation/MusrRoot.xsd -@0
-    002 - Specific Validator URL: http://lmu.web.psi.ch/facilities/software/MusrRoot/Validation/MusrRootLEM.xsd -@0
-    003 - Generator: nemu_analyzer -@0
-    004 - File Name: lem12_his_0234.root -@0
-    005 - Run Title: here comes the run title -@0
-    006 - Run Number: 234 -@1
-    007 - Run Start Time: 2012-04-19 14:25:22 -@0
-    008 - Run Stop Time: 2012-04-19 19:13:47 -@0
-    009 - Run Duration: 17305 sec -@3
-    010 - Laboratory: PSI -@0
-    011 - Instrument: LEM -@0
-    012 - Muon Beam Momentum: 28.1 MeV/c -@3
-    013 - Muon Species: positive muon -@0
-    014 - Muon Source: target E -@0
-    015 - Setup: a very special setup -@0
-    016 - Comment: nothing more to be said -@0
-    017 - Sample Name: the best ever -@0
-    018 - Sample Temperature: 3.21 +- 0.05 K; SP: 3.2 -@3
-    019 - Sample Magnetic Field: 350.002 +- 0.005 G; SP: 350 -@3
-    020 - No of Histos: 8 -@1
-    021 - Time Resolution: 0.1953125 ns;  TDC 9999 -@3
-    022 - RedGreen Offsets: 0; 10; 20; 30
-  DetectorInfo:
-    Detector001:
-      023 - Name: Left/Forward - electric field off, light off -@0
-      024 - Histo Number: 1 -@1
-      025 - Histo Length: 66661 -@1
-      026 - Time Zero Bin: 3419.000000 -@2
-      027 - First Good Bin: 3419 -@1
-      028 - Last Good Bin: 66661 -@1
-    Detector002:
-      029 - Name: Top/Forward - electric field off, light off -@0
-      030 - Histo Number: 2 -@1
-      031 - Histo Length: 66661 -@1
-      032 - Time Zero Bin: 3419.000000 -@2
-      033 - First Good Bin: 3419 -@1
-      034 - Last Good Bin: 66661 -@1
-
-    ...
-
-    Detector038:
-      213 - Name: Bottom/Backward - electric field on, light on -@0
-      214 - Histo Number: 38 -@1
-      215 - Histo Length: 66661 -@1
-      216 - Time Zero Bin: 3419.000000 -@2
-      217 - First Good Bin: 3419 -@1
-      218 - Last Good Bin: 66661 -@1
-
-  SampleEnvironmentInfo:
-    219 - Cryo: Konti-1 -@0
-    220 - Insert: X123 -@0
-    221 - Orientation: c-axis perp spin, perp field. spin perp field -@0
-  MagneticFieldEnvironmentInfo:
-    222 - Magnet Name: WEW -@0
-    223 - Current: 17.34 A -@3
-  BeamlineInfo:
-    224 - Name: muE4 -@0
-  ScalerInfo:
-    225 - Ip: 12332123 -@1
-  RunSummary:
-    0000 - Wed Oct  5 01:30:37 2011 Run 2856 started.
-    0001 - Wed Oct  5 02:02:51 2011 Run 2856 stopped.
-    0002 - 
-    0003 - LCO, T=170.02(K), wTF ~30(G)/5.18(A), Tr/Sa=15.02/8.50(kV), E=5.63(keV), LEDb off, BP off
-    0004 - =========================================================================================
-    0005 - 
-    0006 - #BUC---- B e g i n of User Comment ------ Do not edit this line
-    0007 - #EUC----   E n d   of User Comment ------ Do not edit this line
-    0008 - 
-    0009 - ======================   E v e n t  definition   =========================
-    0010 -
-    0011 - Events: 
-    0012 - Event_0: (BC)-MCP1-(e+); Event_1:( BC)-TD-MCP2-(e+); Event_2: LEmuSR, (BC)-TD-e 
-    ...
-
-
-
-*Comment*: the last sub-tree ``RunSummary`` is not following ``TMusrRunHeader`` rule ``<number> - <label>: <value> -@<type>``. 
-It is added in the instrument analyzer directly by other means than the ``TMusrRunHeader::Set``-method. This is no problem! 
-Since ``RunSummary`` is not part of the required ``MusrRoot``-file. One is quite free in adding any ROOT based information here. 
-                             
-.. index:: MusrRoot-TMusrRunPhysicalQuantity
-.. _musr-run-physical-quantity:
-
-TMusrRunPhysicalQuantity - Possible Representations 
----------------------------------------------------
-
-A physical property can be described as 
-
-::
-
-  <property name>: <value> +- <estimated error> <unit>; SP: <demand>; <description>
-  
-where ``<property name>`` is the name of the quantity, *e.g.* Sample Temperature, ``<value>`` the value 
-of the quantity, ``<estimated error>`` the error estimate, *e.g.* the standard deviation, ``<unit>`` the unit, 
-*e.g.* K, ``<demand>`` a demand value, *e.g.* the set point of the temperature. ``<description>`` is a 
-possible additional comment for this quantity.
-
-.. note:: 
-
-  Not *all* of these quantities are always needed. The list of handled combination are given 
-  hereafter together with the ``C++`` code snipped how to set it. It is assumed that ``TMusrRunPhysicalQuantity prop;`` 
-  is somewhere defined.
-  
-**Possibility 1**
-
-:: 
-
-  <property name>: <value> <unit> [; <description>]
-  
-Code snippet: 
-
-.. code-block:: c++
-
-  prop.Set("Muon Beam Momentum", 28.1, "MeV/c");
-  header->Set("RunInfo/Muon Beam Momentum", prop);
-
-  prop.Set("Time Resolution", 0.1953125, "ns", "TDC 9999");
-  header->Set("RunInfo/Time Resolution", prop);
-  
-Result in the ``RunHeader/RunInfo``:   
-
-::
-
-  011 - Muon Beam Momentum: 28.1 MeV/c -@3
-  013 - Time Resolution: 0.1953125 ns; TDC 9999 -@3
-  
-The number on front of the token (*e.g.* ``011`` in front of Muon Beam Momentum) will depend on the position where 
-the entry has been added. The last token, ``-@3``, is the encoding of the type: here ``TMusrRunPhysicalQuantity``.   
-
-**Possibility 2**
-
-::
-
-  <property name>: <val> +- <err> <unit>[; <description>]
-  
-Code snippet:   
-  
-.. code-block:: c++
-  
-  prop.Set("CF3", MRH_UNDEFINED, 3.27, 0.09, "K", "strange temperature");
-  header->Set("SampleEnvironmentInfo/CF3", prop);
-  
-Result in the ``RunHeader/SampleEnvironmentInfo``:   
-
-::
- 
-  033 - CF3: 3.27 +- 0.09 K; strange temperature -@3 
-  
-**Possibility 3**
-
-::
-
-  <property name>: <val> <unit>; SP: <demand>[; <description>]
-    
-Code snippet:
-
-.. code-block:: c++
-
-  prop.Set("CF4", 3.25, 3.28, "K");
-  header->Set("SampleEnvironmentInfo/CF4", prop);
-
-  prop.Set("CF5", 3.26, 3.29, "K", "another strange temperature");
-  header->Set("SampleEnvironmentInfo/CF5", prop);
-  
-Result in the ``RunHeader/SampleEnvironmentInfo``:   
-
-::
-
-  034 - CF4: 3.28 K; SP: 3.25 -@3
-  035 - CF5: 3.29 K; SP: 3.26; another strange temperature -@3
-  
-**Possibility 4**
-
-::
-
-  <property name>: <value> +- <estimated error> <unit>; SP: <demand>; <description>
-    
-Code snippet:
-
-.. code-block:: c++
-  
-  prop.Set("Sample Magnetic Field", 350.0, 350.002, 0.005, "G", "WXY");
-  header->Set("RunInfo/Sample Magnetic Field", prop);
-  
-Result in the ``RunHeader/SampleEnvironmentInfo``:  
-
-::
-
-  017 - Sample Magnetic Field: 350.002 +- 0.005 G; SP: 350.0; WXY -@3
diff --git a/doc/html/_sources/musredit.txt b/doc/html/_sources/musredit.txt
deleted file mode 100644
index 087c5315..00000000
--- a/doc/html/_sources/musredit.txt
+++ /dev/null
@@ -1,515 +0,0 @@
-.. include:: <isogrk1.txt>
-.. index:: musredit
-
-.. _musredit-sec:
-
-``musredit``: the GUI Based Interface to ``musrfit``
-====================================================
-
-Introduction
-------------
-
-.. _Qt: https://qt.io
-
-``musredit`` is an editor 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. It is implemented in ``C++`` and use the `Qt`_ framework. ``musredit`` is based on Qt 4.6, Qt 5.6 (or above), or Qt6.x. 
-The Qt 5.6 and Qt 6.x version of ``musredit`` will be actively developed, whereas the Qt 4.x version will only get bug fixing and eventually will be dropped.
-On this documentation page only the features related to ``musrfit`` are described — the basic editor functions which should be self-explanatory are *not*.
-``musrgui`` is an outdated early version of ``musredit`` and will not described anymore. If still in use, the user is urged to switch to ``musredit``.
-
-.. note::
-
-  Before going on using ``musredit`` it is strongly recommended to read the :ref:`manual of musrfit <user-manual>` first!
-  
-Available Executable, Configuration Files and their Basic Usage
-----------------------------------------------------------------
-
-musredit (musrgui)
-++++++++++++++++++
-
-``musredit`` (``musrgui``) is the editor executable. If called from within a shell it accepts a few optional parameters: 
-
-**<msr-files>**
-  File names of the msr files that should be opened in separate editor tabs on startup of ``musredit``. 
-**- -help**
-  Displays a small help notice in the shell explaining the basic usage of the program. 
-**- -version**
-  Prints the version number of ``musredit``. 
-
-If called without any parameters an empty editor window opens.
-
-.. index:: musredit_startup
-
-musredit_startup.xml
-++++++++++++++++++++
-
-``musredit_startup.xml`` is the configuration file located under ``$HOME\.musrfit\musredit``. It is also possible to have another version 
-of this file in the working directory which then will be used!
-
-In this file the following ``XML`` tags are allowed to define settings and might proof useful for all users of ``musredit``: 
-
-**<general></general>**
-  set the default paths to executable and files in this environment 
-  
-  **<exec_path>PATH_TO_EXEC</exec_path>**
-    set the path ``PATH_TO_EXEC`` where the executable ``musrfit``, ``musrview``, ``musrt0``, etc. can be found (inside the ``<general>`` environment) 
-  **<default_save_path>SAVE_PATH</default_save_path>**
-    specify the path ``SAVE_PATH`` where ``musredit`` point by default when opening and saving msr files (inside the ``<general>`` environment). Default is the current directory. 
-  **<msr_default_file_path>MSR_DEF_PATH</msr_default_file_path>**
-    set the path ``MSR_DEF_PATH`` where the default msr files provided by ``musredit`` are stored (inside the ``<general>`` environment) 
-  **<timeout>3600</timeout>**
-    timeout in seconds after which :ref:`musrview <musrview>` canvas will automatically quit. A value of 0 or 
-    a negative number will keep the ``musrview`` canvas open without self-determination.
-  **<keep_minuit2_output>y/n</keep_minuit2_output>**
-    flag indicating if the ``MINUIT2`` output shall be kept per msr-file ('y') or only for the current msr-file ('n'). 
-  **<dump_ascii>y/n</dump_ascii>**
-    flag indicating if ``musrfit`` shall dump fit data into ascii format. See help of :ref:`musrfit <musrfit>`.
-  **<dump_root>y/n</dump_root>**
-    flag indicating if ``musrfit`` shall dump fit data into root format. See help of :ref:`musrfit <musrfit>`.
-  **<title_from_data_file>y/n</title_from_data_file>**
-    specify if ``musrfit`` should be called with the ``-t`` option by default (inside the ``<general>`` environment) 
-  **<chisq_pre_run_block>y/n</chisq_pre_run_block>**
-    flag indicating if per-run chisq shall be written into the msr-output-file. 
-  **<estimate_n0>y/n</estimate_n0>** 
-    flag indicating if for a single histogram fit :math:`N_0` shall be estimated before the fit procedure starts. 
-  **<musrview_show_fourier>y/n</musrview_show_fourier>**
-    flag indicating if ``musrview`` will directly present the Fourier transform rather than the time domain data. 
-  **<musrview_show_avg>y/n</musrview_show_avg>**
-    flag indicating if ``musrview`` will directly present averaged data, typically used for Fourier power spectra. 
-  **<enable_musrt0>y/n</enable_musrt0>**
-    specify if :ref:`musrt0 <musrt0>` can be called from within ``musredit`` (inside the ``<general>`` environment) 
-    
-**<font_settings></font_settings>**
-  set the default font in this environment 
-    
-  **<font_name>FONT</font_name>**
-    specify the name of the font ``FONT`` to be used by default in ``musredit`` (inside the ``<font_settings>`` environment) 
-  **<font_size>N</font_size>**
-    specify the size ``N`` of the font to be used by default in ``musredit`` (inside the ``<font_settings>`` environment)
-    
-**<msr_file_defaults></msr_file_defaults>**
-  put the default settings for newly created msr files in this environment
-
-  **<beamline>BL</beamline>**
-    set the name of the muon beamline ``BL`` here (inside a ``<msr_file_defaults>`` environment) 
-  **<institute>INST</institute>**
-    set the name of the facility ``INST`` where the beamline ``BL`` is located. Valid settings are ``PSI``, ``RAL``, ``JPARC``, and ``TRIUMF`` (inside a ``<msr_file_defaults>`` environment) 
-  **<file_format>FF</file_format>**
-    specify the default data file format ``FF`` here. Valid formats are ``NEXUS``, ``MUSR-ROOT``, ``ROOT-NPP``, ``ROOT-PPC``, ``PSI-BIN``, ``PSI-MDU``, ``MDU-ASCII``, ``WKM``, ``MUD``, ``ASCII``, and ``DB`` (inside a ``<msr_file_defaults>`` environment) 
-  **<lifetime_correction>y/n</lifetime_correction>**
-    choose if by default the ``lifetimecorrection`` option should be set (inside a ``<msr_file_defaults>`` environment) 
-
-**<msr2data_defaults></msr2data_defaults>**
-  define the default options for calling :ref:`msr2data <msr2data>` in this environment; the options set here are ticked by default in the graphical interface of ``musredit``.     
-  
-  **<chain_fit>y/n</chain_fit>**
-    (un)set the chain fit (!) option (inside a ``<msr2data_defaults>`` environment) 
-  **<write_data_header>y/n</write_data_header>**
-    (un)set the noheader option (inside a ``<msr2data_defaults>`` environment) 
-  **<ignore_data_header_info>y/n</ignore_data_header_info>**
-    (un)set the nosummary option (inside a ``<msr2data_defaults>`` environment) 
-  **<keep_minuit2_output>y/n</keep_minuit2_output>**
-    (un)set the ``-k`` option (inside a ``<msr2data_defaults>`` environment) 
-  **<write_column_data>y/n</write_column_data>**
-    (un)set the ``data`` option (inside a ``<msr2data_defaults>`` environment) 
-  **<create_msr_file_only>y/n</create_msr_file_only>**
-    (un)set the ``msr`` option in case a template run is specified (inside a ``<msr2data_defaults>`` environment) 
-  **<fit_only>y/n</fit_only>**
-    (un)set the ``fit`` option in case no template run is specified (inside a ``<msr2data_defaults>`` environment) 
-  **<global>y/n</global>**
-    (un)set the ``global`` option (inside a ``<msr2data_defaults>`` environment) 
-  **<global_plus>y/n</global_plus>**
-    (un)set the ``global+`` option (inside a ``<msr2data_defaults>`` environment) 
-  **<recreate_data_file>y/n</recreate_data_file>**
-    (un)set the ``musredit`` option for recreating the output file (inside a ``<msr2data_defaults>`` environment) 
-  **<open_file_after_fitting>y/n</open_file_after_fitting>**
-    (un)set the ``musredit`` option for opening msr files after fitting (inside a ``<msr2data_defaults>`` environment)
-    
-Additionally, there are some settings defined in this XML file which should be only changed by experienced users who like to add new features to ``musredit``:     
-
-**<help_section></help_section>**
-  define various help messages in this environment
-
-  **<musr_web_X>LINK</musr_web_X>**
-    define the ``LINK`` to the help page ``musr_web_X``, where ``X`` is ``main``, ``title``, ``parameters``, ``theory``, ``functions``, ``run``, 
-    ``command``, ``fourier``, ``plot``, ``statistics``, ``msr2data``, or ``musrFT`` (inside a ``<help_section>`` environment) 
-
-**<func_pixmap_path>PIX_PATH</func_pixmap_path>**
-  set the path ``PIX_PATH`` to LaTeX pixmaps visualizing the various supported theory functions 
-  
-**<theory_functions></theory_functions>**
-  define the functions for a msr file's :ref:`THEORY block <msr-theory-block>` according to the correct syntax in this environment   
-  
-  **<func></func>** 
-    specify a function here (inside a ``<theory_functions>`` environment) 
-    
-    **<name>NAME</name>**
-      the ``NAME`` of the function in the msr file (inside a ``<func>`` environment) 
-    **<comment>COMMENT</comment>**
-      description of the used parameters (inside a ``<func>`` environment) 
-    **<label>LABEL</label>**
-      ``LABEL`` of the function in the ``musredit`` menu (inside a ``<func>`` environment) 
-    **<pixmap>PIXMAP</pixmap>**
-      LaTeX picture used to describe the function and stored in the ``PIX_PATH`` (inside a ``<func>`` environment) 
-    **<params>N</params>**
-      number of parameters ``N`` used by the function (inside a ``<func>`` environment) 
-      
-An example of the ``musredit_startup.xml`` looks like:    
-
-.. code-block:: xml
-
-  <?xml version="1.0" encoding="UTF-8"?>
-  <musredit_startup xmlns="http://lmu.web.psi.ch/musrfit/user/MUSR/MusrGui.html">
-    <comment>
-      This is handling default setting parameters for the musredit.
-    </comment>
-    <general>
-      <exec_path>/usr/local/root/bin</exec_path>
-      <default_save_path>./</default_save_path>
-      <msr_default_file_path>/usr/local/root/share/doc/musrfit/templates</msr_default_file_path>
-      <timeout>3600</timeout>
-      <keep_minuit2_output>n</keep_minuit2_output>
-      <dump_ascii>n</dump_ascii>
-      <dump_root>n</dump_root>
-      <title_from_data_file>y</title_from_data_file>
-      <chisq_per_run_block>n</chisq_per_run_block>
-      <estimate_n0>y</estimate_n0>
-      <musrview_show_fourier>n</musrview_show_fourier>
-      <musrview_show_avg>n</musrview_show_avg>
-      <enable_musrt0>y</enable_musrt0>
-    </general>
-    <recent_files>
-      <path_file_name>/usr/local/root/share/doc/musrfit/examples/test-histo-PSI-BIN.msr</path_file_name>
-    </recent_files>
-    <help_section>
-      <musr_web_main>file:///usr/local/root/share/doc/musrfit/html/user/MUSR/MusrFit.html</musr_web_main>
-      <musr_web_title>file:///usr/local/root/share/doc/musrfit/html/user/MUSR/MusrFit.html#TheTitle</musr_web_title>
-      <musr_web_parameters>file:///usr/local/root/share/doc/musrfit/html/user/MUSR/MusrFit.html#TheFitparameterBlock</musr_web_parameters>
-      <musr_web_theory>file:///usr/local/root/share/doc/musrfit/html/user/MUSR/MusrFit.html#TheTheoryBlock</musr_web_theory>
-      <musr_web_functions>file:///usr/local/root/share/doc/musrfit/html/user/MUSR/MusrFit.html#TheFunctionsBlock</musr_web_functions>
-      <musr_web_run>file:///usr/local/root/share/doc/musrfit/html/user/MUSR/MusrFit.html#TheRunBlock</musr_web_run>
-      <musr_web_command>file:///usr/local/root/share/doc/musrfit/html/user/MUSR/MusrFit.html#TheCommandsBlock</musr_web_command>
-      <musr_web_fourier>file:///usr/local/root/share/doc/musrfit/html/user/MUSR/MusrFit.html#TheFourierBlock</musr_web_fourier>
-      <musr_web_plot>file:///usr/local/root/share/doc/musrfit/html/user/MUSR/MusrFit.html#ThePlotBlock</musr_web_plot>
-      <musr_web_statistic>file:///usr/local/root/share/doc/musrfit/html/user/MUSR/MusrFit.html#TheStatisticBlock</musr_web_statistic>
-      <musr_web_msr2data>file:///usr/local/root/share/doc/musrfit/html/user/MUSR/Msr2Data.html</musr_web_msr2data>
-      <musr_web_musrFT>file:///usr/local/root/share/doc/musrfit/html/user/MUSR/MusrFit.html#A_2.3_musrFT</musr_web_musrFT>
-    </help_section>
-    <font_settings>
-      <font_name>Monospace</font_name>
-      <font_size>12</font_size>
-    </font_settings>
-    <msr_file_defaults>
-      <beamline>mue4</beamline>
-      <institute>psi</institute>
-      <file_format>musr-root</file_format>
-      <lifetime_correction>y</lifetime_correction>
-    </msr_file_defaults>
-    <msr2data_defaults>
-      <chain_fit>y</chain_fit>
-      <write_data_header>y</write_data_header>
-      <ignore_data_header_info>n</ignore_data_header_info>
-      <keep_minuit2_output>n</keep_minuit2_output>
-      <write_column_data>n</write_column_data>
-      <recreate_data_file>n</recreate_data_file>
-      <open_file_after_fitting>y</open_file_after_fitting>
-      <create_msr_file_only>n</create_msr_file_only>
-      <fit_only>n</fit_only>
-      <global>n</global>
-      <global_plus>n</global_plus>
-    </msr2data_defaults>
-    <func_pixmap_path>/usr/local/root/share/doc/musrfit/latex_images</func_pixmap_path>
-    <theory_functions>
-      <func>
-        <name>asymmetry</name>
-        <comment></comment>
-        <label>Asymmetry</label>
-        <pixmap>asymmetry.png</pixmap>
-        <params>1</params>
-      </func>
-      <func>
-        <name>statGssKT</name>
-        <comment>(rate)</comment>
-        <label>static Gauss KT</label>
-        <pixmap>statGssKT.png</pixmap>
-        <params>1</params>
-      </func>
-    </theory_functions>
-  </musredit_startup>
-  
-.. index:: musredit-features
-
-musredit Features
------------------
-
-The features of ``musrfit`` which can be accessed by the graphical front ends ``musredit`` will be described in the following. All functions 
-can either be called by choosing them from the *MusrFit menu*, by clicking the respective button in the *MusrFit bar*, or by using a *keyboard shortcut*. 
-
-**musrWiz**
-
-  .. image:: ../images/musrWiz.* 
-
-  ``musrWiz`` is a helper programs which allows to create a msr-file from scratch without too much a priori knowledge. For details see :ref:`musrWiz <musrWiz>`. 
-
-.. index:: musrWiz
-.. _musrWiz:
-
-**Calculate Chisq**
-
-  .. image:: ../images/musrchisq.*
-
-  Calls ``musrfit`` with the option ``-c``, *i.e.* calculates the :math:`\chi^2` or log max-likelihood for the active msr file tab. Shortcut-key: ``Alt+C``.
-  The equivalent call on the command line would be
-
-  .. code-block:: bash
-
-    $ musrfit -c <msr-file>
-
-**Fit**    
-  
-  .. image:: ../images/musrfit.*
-  
-  Calls ``musrfit`` for fitting of the active msr file in the currently active tab. Shortcut-key: ``Alt+F``.
-  The equivalent call on the command line could look like
-  
-  .. code-block:: bash
-  
-    $ musrfit <msr-file> [optional parameters]
-    
-  The optional parameters may be chosen under :ref:`Preferences <musredit-prefs>`. For further information refer to the manual of :ref:`musrfit <user-manual>`. 
-
-**Swap Msr <-> Mlog**
-
-  .. image:: ../images/musrswap.*
-  
-  Swap the msr and mlog files. *E.g.*, for a file called ``8472_zf.msr``, this is copied to ``8472_zf.mlog`` and vice versa. Shortcut-key: ``Alt+S``.
-  
-**Set Steps**
-
-  .. image:: ../images/musrStep.*
-  
-  ``musrStep`` allows to adjust the step size, *i.e.* the initial steps for the fitter. Shortcut-key: ``Alt+P``.
-  
-**Msr2Data**
-
-  .. image:: ../images/msr2data.*
-  
-  Opens a graphical interface to the ``msr2data`` program described in detail in its :ref:`own manual <msr2data>`. Shortcut-key: ``Alt+2``.
-  
-**mupp**
-
-  .. image:: ../images/mupp.*
-  
-  Application which allows to plot ``*.db`` and ``*.dat`` parameter files. Shortcut-key: ``Alt+U``.
-  For a detailed description see the :ref:`mupp docu <mupp>`.
-  
-**View**
-
-  .. image:: ../images/musrview.*
-  
-  Calls ``musrview`` from the active tab of ``musredit``. For more details see the :ref:`musrview <musrview>` docu. Shortcut-key: ``Alt+V``.
-  The equivalent call on the command line could look like
-  
-  .. code-block:: bash
-  
-    $ musrview <msr-file> [optional parameters]
-    
-**T0**
-
-  .. image:: ../images/musrt0-icon.*
-  
-  Calls ``musrt0`` which allows to set the ``T0`` values for all the runs. For more details see the :ref:`musrt0 <musrt0>` docu.
-  The equivalent call on the command line could look like
-  
-  .. code-block:: bash
-  
-    $ musrt0 <msr-file> [optional parameters]
-    
-**Raw Fourier**
-
-  .. image:: ../images/musrFT.*
-  
-  Calls ``musrFT`` which allows to perform a Fourier transform of the raw data. For more details see the :ref:`musrFT <musrFT>` docu. 
-  The equivalent call on the command line could look like
-  
-  .. code-block:: bash
-
-    $ musrFT <msr-file> [optional parameters]
-
-.. _musredit-prefs:  
-  
-**Preferences**
-
-  .. image:: ../images/musrprefs.*
-
-  Opens a window in which the optional parameters that should be passed to musrfit can be chosen.
-  For further information refer to the manual of :ref:`musrfit <musrfit>`. 
-  
-**Dump Header**
-
-  .. image:: ../images/musrdump.*
-  
-  Opens a file dialog which allows to select a |mgr|\SR data file. When this file can be read, the run header info is dumped into a dialog window. 
-  Essentially this calls ``dump_header`` internally. 
-  
-musrWiz
--------
-
-``musrWiz`` is a helper program which allows to easily create the necessary msr-file needed as an input for ``musrfit``. 
-``musrWiz`` is still in it's early stage; not all options are already implemented and here and there you will likely find some bugs. 
-From ``musredit`` it can be accessed via the MusrFit menu or the wand 
-
-.. image:: ../images/musredit-musrWiz.*
-
-The ``musrWiz`` GUI is organized in a couple of different dialogues which some information needs to be provided by the user. 
-In the following these different dialogues will be discussed briefly. 
-
-.. index:: musrWiz-Introduction
-
-musrWiz-Introduction
-++++++++++++++++++++
-
-The introduction dialogue 
-
-.. image:: ../images/musrWiz-Intro.*
-
-#. an explicit msr-file name can be provided here. More often the msr-file name is generated out of the run number.
-#. year of the run data.
-#. run number. If no explicit msr-file is provided, the run number together with fit type and type of measurement will be used to generate the msr-file name.
-#. from the pull down menu the institute (for which a necessary ``xml``-file is provided) has to be choosen.
-#. from the pull down menu the the instrument can be chosen.
-#. the fit type has to be chosen. Possible fit types are: ``Single Histo`` / ``Single Histo RRF`` / ``Asymmetry`` / ``Asymmetry RRF`` / ``Mu Minus`` / ``None muSR``
-#. type of measurement is essentially needed for the grouping of the detectors. Possible are: ``ZF`` for zero field measurements / ``TF`` for transverse field measurements / ``LF`` for longitudinal field measurements. 
-   Depending on the choice and instrument some additional question might be asked, *e.g.* which magnet has been used.
-#. ``T0``'s: this last menu defines from where to get the t0's. The options are: ``from data file``, *i.e.* the t0 are assumed to be correctly set 
-   in the provided data file ``call musrT0``, *i.e.* after the msr-file is generated, ``musrt0`` will be called which allows the user to find the 
-   proper t0 from the prompt peak ``enter here`` will provide a pop-up menu where the t0 parameter can be given explicitly. 
-   
-If all this information have been provided ``Next>`` will lead you the the theory dialogue.   
-
-.. index:: musrWiz-Theory
-
-musrWiz - Theory
-++++++++++++++++
-
-The theory dialogue is used to define the fitting function. There are two ways of using it:
-
-#. choose a template theory function. This option has the advantage that the next steps will be very easy because 
-   within the template almost everything is already pre-defined. The disadvantage is that you are not free in setting 
-   up your theory function as you would like to have.
-#. freely write your theory function. The advantage here is that you can customize your theory function at your needs. 
-   This will come at the cost that you also will need to define ``maps``, ``functions``, etc. yourself. The good thing    
-   though is that at the very end you can save this as a template for future re-use. 
-
-First the template path will be described. The theory dialogue looks like this
-
-.. image:: ../images/musrWiz-Theory.*
-
-#. This is a text edit field were you can enter the theory fit function as you would like to have it. In the example 
-   given the theory reads :math:`p1 \exp(-p2\, t) \cos(2 \pi\, f1 + m1)`, where ``pX`` stands for parameter, ``fX`` for function, 
-   ``mX`` for map, and ``X`` for the corresponding number.
-#. The ``Clear All`` button will clear whatever you entered in the text field above.
-#. This pull-down menu allows to select a theory function which will be added to the text field above by pressing 
-   the ``Add`` button. Pre defined theory function starting with a ``T`` are templates rather than only theory function strings.
-#. The ``Add`` button is used to add the chosen theory function / template from the pull-down menu to its left.
-#. The ``Check`` button is used to make a syntactical check of whatever is written in the text edit field. 
-
-.. index:: musrWiz-Functions
-
-musrWiz - Functions
-+++++++++++++++++++
-
-In the Functions dialogue all the necessary functions can be entered. A function operates *only* on fitting parameters. 
-This is different to the theory function which operates on the fitting parameters and the time. The dialogue looks like this 
-
-.. image:: ../images/musrWiz-Functions.*
-
-
-#. a text edit field in which the various needed functions can be entered. In case a template theory is used, the appropriate function should be shown here and *no* editing will be needed here.
-#. pressing ``Show Theory`` button will pop-up a little window showing the previously entered theory function. This is handy when defining its own theory, *i.e.* not working with a template. 
-
-.. image:: ../images/musrWiz-Functions-and-Theory.*
-
-.. index:: musrWiz-Maps
-
-musrWiz - Maps
-++++++++++++++
-
-.. image:: ../images/musrWiz-Maps.*
-
-The map dialogue will list the maps previously used in the theory and functions blocks/dialogues before. Again, if a template is used, nothing needs to be entered here.
-
-#. The ``Show Theory`` button allows to show the currently defined theory and the functions. 
-
-.. index:: musrWiz-FitParam
-
-musrWiz - Fit Parameters
-++++++++++++++++++++++++
-
-.. image:: ../images/musrWiz-FitParam.*
-
-In the fit parameter dialogue all parameter names can be defined. Furthermore the starting values for the parameters, the step 
-(initial step size for the parameter fit), and any boundaries can be defined here. 
-
-#. The ``Show Theory`` button allows to show the currently defined theory and the functions.
-
-.. index:: musrWiz-FitInfo
-
-musrWiz - Fit Info
-++++++++++++++++++
-
-Collects all the ``musrfit`` and ``MINUIT2`` specific fit commands.
-
-.. image:: ../images/musrWiz-FitInfo.*
-
-
-#. allows to define the time fit range (start time, end time).
-#. packing defines how many bins of the original data shall be combined (added, also called re-binning).
-#. in this text field to fitting commands are given (see the ``MINUIT`` and :ref:`musrfit <msr-commands-block>` manual for details). 
-
-.. index:: musrWiz-Create
-
-musrWiz - Create
-++++++++++++++++
-
-Collects the last necessary information before creating the msr-file.
-
-.. image:: ../images/musrWiz-Create.*
-
-
-#. shows the path where the msr-file will be saved. If you would like to save it somewhere else press the ``Save As (msr-file path)`` button.
-#. pressing this button will allow you to find the path where to save the msr-file.
-#. pressing this button will save to current configuration as a template for future re-use. 
-
-.. index:: musrStep
-
-musrStep
---------
-
-``musrStep`` is a little helper program which allows to reset the initial step size. This sometimes comes very handy if working on an instrument 
-with many detectors after a fit slightly went wrong leaving you with a far too small initial step size for further iterations. To edit all the steps 
-individually is tedious and error prone. Here ``musrStep`` can help. 
-
-.. image:: ../images/musrStep-GUI.*
-
-When invoking ``musrStep`` the above dialogue will popup
-
-#. shows the relevant parts of the FITPARAMETER block. The only editable column is step.
-#. ``Check Specific`` will popup a dialogue where a template string can be entered, *e.g.* ``Asym``. As a result all fit parameters containing the template string will be selected.
-#. ``Check All`` will select all fit parameters.
-#. ``Uncheck All`` will unselect all fit parameters.
-#. ``Modify Automatic`` will change all the step values automatically. It basically sets all the step sizes to 1% of 
-   the corresponding fit parameter value, except the phases where the step will be set to a value of 5 degrees.
-#. ``Modify Selected`` will start the dialogue shown beneath. Follow the description there.
-#. ``Save&Quit`` will save the current step values, close the dialogue and reload the modified msr-file.
-#. ``Cancel`` will cancel the ``musrStep`` dialogue without modifying anything. 
-
-.. image:: ../images/musrStep-Modify-Selected.*
-
-When clicking on ``Modify Selected`` the above dialogue will be presented. It allows to manipulate all selected fit parameter step values according to the following rules 
-
-#. ``Scale by Factor`` will scale the step value by the factor given in the field (2). If the ``Absolute Value`` check box is selected, rather than scaling the factor value will be used to modify the step value.
-#. scaling factor or absolute value to modify the step values of the selected fit parameters.
-#. checking the ``Absolute Value`` check box will change the meaning from *Scale by Factor* to *Copy Factor Value*.
-#. ``Scale Automatically`` will modify the step values of the selected fit parameters according to the rules described before.
-#. ``Cancel`` will cancel the dialogue. 
diff --git a/doc/html/_sources/setup-dks.txt b/doc/html/_sources/setup-dks.txt
deleted file mode 100644
index 0ea9328b..00000000
--- a/doc/html/_sources/setup-dks.txt
+++ /dev/null
@@ -1,275 +0,0 @@
-:tocdepth: 3
-
-.. include:: <isogrk1.txt>
-.. index:: dks
-
-.. _setup-dks:
-
-Setting up ``musrfit`` / ``DKS``: High Speed Fitting with GPU's 
-===============================================================
-
-In the years 2016/2017 we explored ways to speed up current fitting frameworks, especially ``musrfit.`` 
-This allows now to analyze histogram sets of high field spectrometers like ``HAL-9500`` at PSI without 
-the *error-prone* RRF fitting (see U. Locans and A. Suter, 
-`musrfit - Real Time Parameter Fitting Using GPU <http://dx.doi.org/10.7566/JPSCP.21.011051>`_, and the 
-Memo from A. Suter, "Rotating Reference Frame Fits", in the ``musrfit`` source code). At the same time 
-it can help to speed-up elaborate global fits tremendously, and dealing properly with muonium. It also 
-allows Apple macOS users to speed up their fitting code on the CPU. Currently it is not straight forward 
-to get ``musrfit`` multi-threaded under macOS since Apple doesn't be default support ``OpenMP``. ``DKS`` 
-enables ``musrfit`` to utilize ``OpenCL`` instead which is present on macOS by default. 
-
-.. warning:: 
-
-  Before you run into the shop to buy a gamer graphic card or a Tesla card, make sure that you have an 
-  appropriate server with a sufficiently strong power supply! 
-  
-.. note::
-
-  However, the current ``musrfit/DKS`` version doesn't yet support all theory functions on the GPU. 
-  In case the theory function is not yet available for the GPU, ``musrfit`` will fall back to the CPU implementation. 
-  
-Conceptually the setup of ``musrfit/DKS`` is as following:
-
-#. install the latest hardware driver for your graphic card.
-#. install the GPU SDK which enables number crunching (``CUDA`` for NVIDIA, ``OpenCL`` for AMD)
-#. install ``DKS``
-#. install the ``musrfit`` version which is ``DKS`` ready   
-
-In the following the description for the installation of ``musrfit/DKS`` for the following systems will be discussed in some more detail:
-
-* NVIDIA Tesla K40c
-* AMD Graphic Card (Radeon R9 390X)
-* macOS in order to get ``OpenCL`` support 
-
-The usage of ``musrfit`` with GPU acceleration and ``OpenCL`` support is described in the 
-:ref:`User manual of the μSR data analysis software musrfit <user-manual>`. The additional 
-``musrfit/DKS`` are found :ref:`here <msr-commands-block-dks>`.
-
-.. index:: dks-setup-tesla
-
-Setting up ``musrfit/DKS`` for a Tesla K40c (NVIDIA) 
-----------------------------------------------------
-
-It is assumed that the Tesla K40c is already physically installed on your system. For now I only 
-will discuss to set it up for a Linux based system. In order to check that your operating systems 
-see the card, enter the following command in the terminal: 
-
-.. code-block:: bash
-
-  $ lspci | grep NVIDIA
-
-The response should look something like 
-
-::
-
-  05:00.0 3D controller: NVIDIA Corporation GK110BGL [Tesla K40c] (rev a1)
-  
-which means that the OS physically recognizes your card. 
-
-Driver Installation for the Tesla K40c 
-++++++++++++++++++++++++++++++++++++++
-
-Next, you will need to download and install the driver for your card. Select the proper operating system, 
-card, etc. from the `NVIDIA download center <http://www.nvidia.com/Download/index.aspx?lang=en-us>`_. At PSI 
-we are running currently Red Hat Enterprise Linux 7.x (RHEL) for which we will get a ``rpm`` (something like 
-``nvidia-diag-driver-local-repo-rhel7-375.66-1.x86_64.rpm``). Install it and make sure there is no conflict 
-with the nouveau driver of the system. 
-
-.. index:: cuda-install
-
-Installation of CUDA
-++++++++++++++++++++
-
-Download the `CUDA SDK <https://developer.nvidia.com/cuda-downloads>`_ form NVIDIA for your system. Again, 
-for the RHEL 7.x this is an ``rpm``. After the installation of the rpm you should reboot your machine. 
-Afterwards you are ready for the installation of ``DKS``. 
-
-.. index:: dks-install
-
-Installation of DKS
-+++++++++++++++++++
-
-For the following list of commands the ``'$'`` will be given as the command prompt. *Do not enter it!* 
-Also some comments will be added starting with a ``'#'`` which can be omitted. They are only there to 
-explain what is going on. ``DKS`` stands for Dynamical Kernel Scheduler and provides a thin interface 
-allowing host applications to incorporate GPU's and other hardware accelerators.
-
-Details can be found in the papers listed :ref:`here <cite>`, or on the `DKS wiki page <https://gitlab.psi.ch/uldis_l/DKS/wikis/home>`_.
-
-In brief the installation should be something like this:
-
-.. code-block:: bash
-
-  # go to whatever directory you would like to clone/install DKS
-  # For macOS DKS will likely to got to $HOME/Applications to be consistent with the musrfit docu for macOS
-  $ cd $HOME/Apps
-  $ git clone https://gitlab.psi.ch/uldis_l/DKS.git
-  $ cd DKS
-  $ mkdir build
-  $ cd build
-  $ cmake ../ -DENABLE_MUSR=1 -DCMAKE_INSTALL_PREFIX=../exec
-  $ cmake --build ./ --clean-first
-  $ make install
-  
-Since ``DKS`` is installed in a non-standard path, a couple of additional small steps are required. 
-This will be different for Linux compared to macOS.
-
-For **Linux:**
-
-add the ``DKS`` library path to ``/etc/ld.so.conf.d/musrfit-x86_64.conf`` and execute as super user
-
-.. code-block:: bash
-
-  $ /sbin/ldconfig
-  
-For **macOS:**  
-
-add the ``DKS`` path to ``$HOME/.profile``:
-
-.. code-block:: bash
-
-  export DKS=$HOME/Applications/DKS/exec
-  export LD_LIBRARY_PATH=$DKS/lib:$LD_LIBRARY_PATH
-
-  launchctl setenv DKS $DKS
-  launchctl setenv LD_LIBRARY_PATH $LD_LIBRARY_PATH
-  
-  
-.. _musrfit-dks-install:  
-  
-Installation of musrfit for DKS 
-+++++++++++++++++++++++++++++++
- 
-Most of the installation steps are the same as described for ``musrfit`` without GPU support. 
-Here only the differences are explained. First checkout ``musrfit``, then you will need to 
-switch the working branch which is done by
- 
-.. code-block:: bash
- 
- $ cd $HOME/Apps/musrfit
- $ git checkout dks6
- 
-Install via cmake
-^^^^^^^^^^^^^^^^^
-
-There is on more configuration switch 
-
-**-Ddks=<value>**
-  it allows to enable/disable ``DKS`` support. The default is ``<value>=1``, *i.e.* enabled. To disable use ``<value>=0``. 
-  
-For a typical setup on a RHEL or macOS system it could look like this   
-
-.. code-block:: bash
-
-  $ cmake ../ -DCMAKE_INSTALL_PREFIX=$ROOTSYS -DASlibs=1 -DBMWlibs=1 -Dnexus=1 -Ddks=1
-
-After
-
-.. code-block:: bash
-
-  $ cmake --build ./ --clean-first -- -j8
-  $ make install
-  
-and updating the shared library lookup table (*only* needed for Linux)   
-
-.. code-block:: bash
-
-  $ /sbin/ldconfig # as superuser / root
-  
-you are done with the setup. 
-
-.. index:: dks-setup-amd-graphic-card
-
-Setting up ``musrfit/DKS`` for a AMD Graphic Card (Radeon R9 390X)
-------------------------------------------------------------------
-
-Driver Installation for an AMD Graphic Card, *e.g.* Radeon R9 390X 
-++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
-
-This will depend slightly on the AMD Card and operating system. Here I will summaries how it was done 
-on a RHEL (Linux) system using a Radeon R9 390X.
-
-It is assumed that the Radeon R9 390X is already physically installed on your system. For now I only 
-will discuss to set it up for a Linux based system. In order to check that your operating systems see 
-the card, enter the following command in the terminal:
-
-.. code-block:: bash
-
-  $ lspci | grep AMD
-  
-The response should look something like   
-
-::
-
-  84:00.0 VGA compatible controller: Advanced Micro Devices, Inc. [AMD/ATI] Hawaii XT / Grenada XT [Radeon R9 290X/390X] (rev 80)
-  
-which means that the OS physically recognizes your card.   
-
-For RHEL7.x the AMDGPU-PRO driver should be used. It can be downloaded from `AMD <http://support.amd.com/en-us/kb-articles/Pages/AMDGPU-PRO-RedHat-Install.aspx>`_. Unpack the driver 
-
-.. code-block:: bash
-
-  $ tar -Jxvf amdgpu-pro-17.10-414273.tar.xz
-  $ cd amdgpu-pro-17.10-414273
-
-Install the driver as root
-
-.. code-block:: bash
-
-  $ ./amdgpu-pro-install --compute -y
-  
-Here I assume that the AMD graphic card is only used for computation. You need to add the following command 
-in order that the user **blabla** (change this to the appropriate user name) can access the GPU (otherwise 
-only root works):   
-
-.. code-block:: bash
-
-  $ /sbin/usermod -a -G video blabla
-  
-Reboot the machine. 
-
-AMD APP Software Development Kit (SDK) to enable ``OpenCL`` support
-+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
-
-The AMD APP Software Development Kit (SDK) is a complete development platform created by AMD to allow you to 
-quickly and easily develop applications accelerated by AMD APP technology. The SDK provides samples, documentation, 
-and other materials to quickly get you started leveraging accelerated compute using ``OpenCL`` or ``C++ AMP`` in your 
-``C/C++`` applications. 
-
-Download the AMD APP SDK 3.0 from `AMD-SDK <http://developer.amd.com/tools-and-sdks/opencl-zone/amd-accelerated-parallel-processing-app-sdk/>`_.
-
-Extract the installer
-
-.. code-block:: bash
-
-  $ tar -xvjf AMD-APP-SDKInstaller-v3.0.130.136-GA-linux64.tar.bz2
-
-Run the installer
-
-.. code-block:: bash
-
-  $ ./AMD-APP-SDK-v3.0.130.136-GA-linux64.sh
-
-This will install the AMD APP SDK to ``/opt/AMDAPPSDK-3.0/`` where you can find the ``OpenCL`` include 
-and library files, as well as documentation and sample code. The install guide for AMD OpenCL SDK can 
-be found at `AMD SDK Installation Notes <http://developer.amd.com/wordpress/media/2012/10/AMD_APP_SDK_InstallationNotes.pdf>`_.
-
-Installation of DKS and musrfit
-+++++++++++++++++++++++++++++++
- 
-To install ``DKS`` and ``musrfit`` follow the instructions :ref:`above <musrfit-dks-install>`.
-
-.. index:: dks-opencl-macOS
-
-Setting up ``musrfit/DKS`` for macOS for OpenCL support 
--------------------------------------------------------
-
-Since Apple is not providing an out-of-the-box ``OpenMP`` support on their macOS compiler framework (Xcode), 
-typically ``musrfit`` is just running *single threaded*. Here ``DKS`` can help since it delivers ``OpenCL`` 
-support which is present on macOS. Hence, if you would like to run ``musrfit`` multi-threaded the easiest 
-way is to use ``DKS``. 
-
-Since there is no graphic card involved, you do not need any graphic card driver of additional SDK. 
-The only thing you need ``DKS`` and the proper ``musrfit`` version.
-
-The installation instruction for ``DKS/musrfit`` can be found :ref:`here <musrfit-dks-install>`. 
diff --git a/doc/html/_sources/setup-standard.txt b/doc/html/_sources/setup-standard.txt
deleted file mode 100644
index 6c37b6bf..00000000
--- a/doc/html/_sources/setup-standard.txt
+++ /dev/null
@@ -1,1379 +0,0 @@
-:tocdepth: 4
-
-.. include:: <isogrk1.txt>
-.. index:: setup
-
-.. _musrfit-setup:
-
-Setting up ``musrfit`` on Different Platforms
-=============================================
-
-.. index:: supported-operating-systems
-.. _supported-operating-systems:
-
-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 <http://www.gnu.org/philosophy/free-sw.html>`_ 
-|mgr|\SR data analysis framework :ref:`musrfit <user-manual>`. While the preferred way is to run the software on **GNU/Linux** or **MacOS X/macOS**, with some restrictions 
-it can also be set up under **MS Windows** (cygwin, only for the *very brave*, probably it is easier for most MS Windows users to install a Virtual Machine running Linux). 
-
-.. note::
-
-  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 <http://gcc.gnu.org/>`_ (``gcc``, ``g++``), the build tool `cmake <https://cmake.org/>`_ is needed. Furthermore the helper 
-tool `pkg-config <http://pkg-config.freedesktop.org/wiki/>`_ needs to be in place, and musrfit requires the installation of a few open-source libraries and programs including 
-their header packages:  
-
-.. index:: boost-c++
-
-**boost C++ libraries**
-  The powerful Spirit parser framework used by musrfit is included in that collection of libraries. *Required version ≥ 1.33* (see `boost C++ libraries <http://www.boost.org/>`_).
-
-.. index:: gnu-gsl  
-
-**GNU Scientific Library**
-  A numerical ``C`` and ``C++`` library which provides efficient implementations of various mathematical routines. *Required version ≥ 1.9* (see `GNU Scientific Library <http://www.gnu.org/software/gsl/>`_). 
-
-.. index:: fftw
-
-**FFTW**
-  A ``C`` implementation for the fast computation of discrete Fourier transforms. *Required version ≥ 3.1* (see `FFTW <http://www.fftw.org/>`_). 
-
-.. index:: root-cern
-
-**ROOT**
-  A C++ data analysis framework developed at `CERN <http://www.cern.ch/>`_. *Required version ≥ 5.22* (see `ROOT <http://root.cern.ch/>`_).
-
-.. index:: libxml2   
-
-**libxml2**  
-  The ``XML C`` parser and toolkit of `gnome <http://www.gnome.org/>`_. *Required version ≥ 2.0* (see `libxml2 <http://xmlsoft.org/>`_). 
-  
-Additionally, *only* if ``musrfit`` should support reading of data files in the `NeXus` format the following libraries are needed:   
-  
-.. index:: hdf4    
-
-**HDF4**
-  A library and multi-object file format for storing and managing data (see `HDF4 <http://www.hdfgroup.org/products/hdf4/>`_). ``HDF4`` is "outdated" and its support will soon be dropped. The single only reason why it is still required is that ISIS is not able to cope to implement HDF5 V2 of the NeXus muon instrument specification which has been agreed in 2012!   
-
-.. index:: hdf5  
-
-**HDF5**
-  A data model, library, and file format for storing and managing data (see `HDF5 <https://portal.hdfgroup.org/display/support>`_). 
-
-.. index:: minixml
-
-**minixml**
-  A small ``XML`` library that can be used to read and write ``XML`` and ``XML``-like data files. *Required version ≥ 2.2* (see `minixml <http://www.minixml.org/>`_).
-  Currently the ``MXML`` support in ``NeXus`` is broken and hence you will **not** need to install ``minixml`` for the time being. 
-
-.. index:: nexus
-
-**NeXus**
-  A common data format for neutron, x-ray, and muon science. *Required version ≥ 4.4* (see `NeXus <http://www.nexusformat.org/>`_). 
-  
-If *optionally* the editor and graphical user interface ``musrgui`` / ``musredit`` is going to be installed there is one further requirement: 
-
-.. index:: qt
-
-**Qt**
-  A cross-platform application and user interface framework. *Required version ≥ 4.6* (musredit) (see `Qt <http://qt.io/>`_). Currently the **Qt5** is the main development part. Qt6 just kicked in, but is not widely available yet.
-
-Each of the following sections focusing on the installation of ``musrfit`` on the different operating systems will also give a brief introduction on the installation of the requirements before the actual musrfit installation is described.   
-  
-.. index:: os-restrictions
-
-OS Restrictions 
----------------
-
-Before the installation procedure will be described, please note the following restrictions:
-
-**GNU/Linux**
-  No serious problems are currently known. Tested distributions: `RHEL <https://www.redhat.com/de/technologies/linux-platforms/enterprise-linux>`_, `Fedora <https://getfedora.org/>`_,
-  `Debian <https://www.debian.org/>`_, `Ubuntu <https://www.ubuntu.com/>`_, `Mint <https://linuxmint.com/>`_, `openSUSE <https://en.opensuse.org/Main_Page>`_, 
-  `manjaro <https://de.manjaro.org/>`_, and `antergos <https://antergos.com/>`_.
-**Mac OS X/macOS**
-  No serious problems are currently known for macOS ≥ 10.6.
-**MS Windows**
-  Native *MS Windows* support is currently not available. Potential ways to get ``musrfit`` running are:
-  
-  * via installation of Linux via the Microsoft App store for Windows 10.
-  * via installation of the virtual machine on which you install Linux (probably the easiest for most Windows users).
-  * via `cygwin`_. 
-  
-.. _cygwin: https://www.cygwin.com/  
-  
-.. index:: gnu-linux
-.. _gnu-linux:
-
-GNU/Linux
----------
-
-.. index:: gnu-linux-requirements
-.. _gnu-linux-requirements:
-
-Requirements
-++++++++++++
-
-Everything but ROOT and NeXus
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-
-Depending on the GNU/Linux distribution chosen, the above mentioned software -- except ``ROOT/CERN`` and ``NeXus`` -- should be available from 
-the distributor and could be easily installed in the form of binary packages. If done in this way there should be taken care of installing *both*, 
-the libraries and the header (dev, devel) files.
-
-On a `Red Hat Linux <https://www.redhat.com/en>`_ (or other RPM-package base Linux distributions) system the following command executed as *superuser* 
-from the shell will do the trick (never type the '$' it is the shell prompt of your system): 
-
-For **Qt4**:
-
-  .. code-block:: bash
-
-    $ yum install git cmake boost-devel gsl-devel fftw-devel libxml2-devel qt-devel qtwebkit-devel
-
-For **Qt5**:
-
-  .. code-block:: bash
-
-    $ yum install epel-release
-    $ yum install git cmake boost-devel gsl-devel fftw-devel libxml2-devel qt5-qtbase-devel qt5-qtsvg-devel
-
-Depending on your distribution **Qt4** is still the default but is likely to be replaced by **Qt5** in the very near future.   
-  
-When dealing with a distribution that uses the dpkg/apt package manager like `Debian <https://www.debian.org/>`_ or `Ubuntu <https://www.ubuntu.com/>`_ 
-the installation would look like: 
-
-For **Qt4**:
-
-  .. code-block:: bash
-  
-    $ apt-get install git cmake libboost-dev libgsl-dev libfftw3-dev libxml2-dev libqt4-dev libqtwebkit-dev
-
-For **Qt5**:
-    
-  .. code-block:: bash
-
-    $ apt-get install git cmake libboost-dev libgsl-dev libfftw3-dev libxml2-dev qt5-default qtbase5-dev libqt5svg5-dev
-    
-    
-Everyone should know best himself which is the way to install distribution software on the chosen distribution.
-
-In case the distribution does not include the required software it has to be compiled from the source files. This means either to download 
-the source code from the corresponding website, or to clone the git repo. If you need to follow this line, please check the install details of the corresponding package.
-
-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"...
-
-.. index:: nexus-build-linux    
-
-Installation of NeXus requirements (optional)
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-
-*Only* if ``musrfit`` should support reading/writing 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. In principle
-NeXus should support ``MXML``, ``HDF4``, and ``HDF5``. At the time of this writing, the ``MXML`` support in the
-NeXus project is broken, and ``HDF4`` is outdated on most platforms, yet since ISIS/RAL is still **not** up-to-date ``HDF4`` still
-needs to be dragged on (comment: if you are a ISIS user, please complain about ``HDF4``). Hence, the necessary packages to build ``NeXus`` are ``HDF4`` and ``HDF5``. This means, for a rpm-package based distro try something like:
-
-  .. code-block:: bash
-  
-    $ yum install hdf-devel hdf5-devel
-    
-and on a deb-package based distro try something like:
-
-  .. code-block:: bash
-  
-    $ apt-get install libhdf4-dev libhdf5-dev
-
-**Only NeXus Version ≥ 4.4 is support!**  
-
-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 <https://github.com/nexusformat/code>`_. 
-
-A brief instruction how to get ``NeXus`` compiled from source (lines starting with '#' are comments *only*): 
-
-.. code-block:: bash
-
-  $ cd Downloads
-  $ # create a directory for the NeXus source code
-  $ mkdir nexus
-  $ cd nexus
-  $ # get the source code from the master repository
-  $ git clone https://github.com/nexusformat/code.git
-  $ # next we will build NeXus out-of-source
-  $ mkdir build
-  $ cd build
-  $ cmake -DENABLE_HDF5=1 -DENABLE_HDF4=1 -DENABLE_MXML=0 ../code
-  $ cmake --build ./ --clean-first
-  $ # make install needs either to be carried out as root or sudo depending on your linux flavour.
-  $ sudo make install
-
-.. index:: root-build-linux    
-
-ROOT
-^^^^
-
-The ROOT framework may or may not be part of the GNU/Linux distribution. Some distributions are packing ROOT in a 
-manner incompatible with the way it is needed by ``musrfit``, though the situation is improving. If you are 
-experienced enough you can try the packed ROOT version. Often ROOT is split in many sub-packages. Install the 
-necessary ones (guess from the description below). **One Warning:** if the ROOT packages are upgraded after a 
-yum update (apt-get update; apt-get upgrade) you might need to recompile ``musrfit``. *If you are not sure about 
-all this: install ROOT from source*. Before installing ROOT from source you will need to install some additional header packages. 
-
-For RPM based systems (RedHat, Fedora, *etc*) this will likely to be ``libX11-devel``, ``libXft-devel``, ``libXpm-devel``, and ``libXext-devel``: 
-
-.. code-block:: bash
-
-  $ yum install libX11-devel libXft-devel libXpm-devel libXext-devel
-  
-For a dpkg/apt based system (Debian, Ubuntu, *etc*) this will likely to be ``libx11-dev``, ``libxft-dev``, ``libxpm-dev``, and ``libxext-dev``:   
-
-.. code-block:: bash
-
-  $ apt-get install libx11-dev libxft-dev libxpm-dev libxext-dev
-
-Also make sure that you have installed all required packages listed under :ref:`Required Software <gnu-linux-requirements>` (*e.g.* fftw, gsl, *etc*).   
-  
-In the following it is assumed that ``ROOT`` shall be installed under ``$HOME/Apps``. If you want to install 
-it somewhere else, just systematically replace the related terms of the following description. For the 
-following list of commands the '$' will be given, the command prompt. Do not enter it! Also some comments will 
-be added starting with a '#' which can be omitted. They are only there to explain what is going on.
-
-.. code-block:: bash
-
-  $ cd $HOME
-  $ # creat the Apps directory if not already present
-  $ mkdir Apps
-  $ cd Apps
-  $ git clone http://github.com/root-project/root.git
-  $ cd root
-  $ git tag -l
-  $ # git tag -l will list all available tags. In the next command choose the tag v6-16-00 
-  $ # or the latest official release number
-  $ git checkout -b v6-16-00 v6-16-00
-  $ # now ROOT is ready to be configured. Below you will find the minimal ROOT configuration needed.
-  $ # since we are using cmake build now, first we will need to create the build directory.
-  $ mkdir root_build
-  $ cd root_build
-  $ cmake ../ -Dgminimal=ON -Dasimage=ON -Dmathmore=On -Dminuit2=ON -Dxml=ON -DCMAKE_INSTALL_PREFIX=../root_exec
-  $ # next will be the make called via cmake. If running on a multicore CPU you can speed up tremendously by 
-  $ # calling it with the option -j <number>, where <number> is the number of threads which you want to give,
-  $ # e.g. cmake --build ./ --clean-first -- -j8
-  $ cmake --build ./ --clean-first
-  $ # as a last step of the ROOT build process we need to install it
-  $ make install
-
-What is still missing is that the system should be told where to find the ``ROOT`` installation, therefore the following is suggested:   
-
-* As superuser create a file ``/etc/ld.so.conf.d/cern-root.conf`` where the path to the lib directory of ``ROOT`` is 
-  added and call ``/sbin/ldconfig`` afterwards. In the example mentioned above one way of doing this is 
-  (``<home>`` has to be the path to your home, *e.g.* ``/home/luke_skywalker``): 
-
-  .. code-block:: bash
-  
-    $ echo "<home>/Apps/root/root_exec/lib" >> /etc/ld.so.conf.d/cern-root.conf
-    $ /sbin/ldconfig
-
-* Additionally, as normal user one should append the following lines to the ``~/.bashrc`` and/or ``~/.bash_profile``
-  (``~./profile`` on Debian like systems, 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:    
-  
-  .. code-block:: bash
-  
-    $ export ROOTSYS=$HOME/Apps/root/root_exec
-    $ export PATH=$ROOTSYS/bin:$PATH
-    
-If an update of ROOT is needed, simple do the following:
-
-.. code-block:: bash
-
-  $ cd $HOME/Apps/root
-  $ git pull
-  $ cd root_build
-  $ cmake --build ./ --clean-first
-    
-.. index:: musrfit-build-linux    
-
-musrfit
-+++++++
-
-When all required software has been set up you can proceed with the ``musrfit`` installatio. First, the most 
-recent source code should be downloaded. The preferred way of doing so is to clone the ``musrfit`` repository via git. 
-Assuming the code should be located in ``$HOME/Apps`` this is achieved most easily calling from the terminal 
-
-.. code-block:: bash
-
-  $ cd $HOME/Apps
-  $ git clone https://bitbucket.org/muonspin/musrfit.git
-  $ cd musrfit
-
-or  
-  
-.. code-block:: bash
-
-  $ cd $HOME/Apps
-  $ git clone git://gitlab.psi.ch/nemu/musrfit.git
-  $ cd musrfit
-
-.. note::  
-  
-  after cloning the ``musrfit`` repo you will automatically be on the 
-  ``root6`` branch. If you want to get legacy ROOT 5.34.xx support, you 
-  will needed to switch branches first. 
-  
-**Update:** If a local repository clone is already present (it needs to be newer than Dec. 2016), one can update it using:   
-
-.. code-block:: bash
-
-  $ cd $HOME/Apps/musrfit
-  $ git pull
-  $ cd build
-  $ xargs rm < install_manifest.txt
-  $ cmake --build ./ --clean-first
-  $ make install
-
-.. _musrfit at bitbucket: https://bitbucket.org/muonspin/musrfit/downloads 
-  
-As an alternative (if git is not available), the source code can also be downloaded from the following web-page: `musrfit at bitbucket`_
-  
-.. index:: musrfit-build-cmake-linux    
-
-musrfit build with cmake 
-^^^^^^^^^^^^^^^^^^^^^^^^
-
-Currently the following configuration switches for ``musrfit`` are available: 
-
-
-**-DCMAKE_INSTALL_PREFIX=<prefix-path>**
-  Specify the installation prefix, *i.e.* the place where ``musrfit`` shall be installed, *e.g.* ``$ROOTSYS`` if already defined (by default: ``/usr/local``). 
-**-Dnexus=<value>**
-  enable/disable the support of ``NeXus`` data files (requires the ``HDF4``, ``HDF5`` and ``NeXus`` libraries to be installed). 
-  <value>=1 enables ``NeXus``, <value>=0 disables ``NeXus``. The default setting, *i.e.* the switch is not provided is ``NeXus`` support is disabled. 
-**-DASlibs=<value>**
-  enable/disable the ``ASlibs``. <value>=1 enables the ``ASlibs``, <value>=0 disables the ``ASlibs``. The default setting, *i.e.* the 
-  switch is not provided is ``ASlibs`` support is disabled. For details see Documentation of :ref:`user libs <user-libs>`. 
-**-DBMWlibs=<value>**
-  enable/disable the ``BMWlibs``. <value>=1 enables the ``BMWlibs``, <value>=0 disables the ``BMWlibs``. The default setting, *i.e.* the 
-  switch is not provided is ``BMWlibs`` support is disabled. For details see Documentation of :ref:`user libs <user-libs>`.  
-**-DBNMRlibs=<value>**
-  enable/disable the ``BNMRlibs``. <value>=1 enables the ``BNMRlibs``, <value>=0 disables the ``BNMRlibs``. The default setting, 
-  *i.e.* the switch is not provided is ``BNMRlibs`` support is disabled. 
-**-Dqt_based_tools=<value>**
-  Will try to get ``musredit``, ``musrWiz``, ``musrStep``, and ``mupp`` installed, if ``Qt`` is found. 
-  By default this is enabled. Again <value>=0 means disabled, <value>=1 enabled. 
-**-Dqt_version=<value>**
-  Allows to specify which ``Qt`` version shall be tried. <value> can take the values: ``AUTO, 3, 4, 5, 6``. 
-  If the value is set to ``AUTO``, this highest installed version is chosen, otherwise the specified version is used. 
-**-Dtry_OpenMP=<value>**
-  Will check if ``OpenMP`` support is possible, and if yes use it. The default is enabled 
-
-Normally it should not be necessary to make use of any of the options except for specifying the installation path with ``-DCMAKE_INSTALL_PREFIX``. 
-``musrfit`` build with ``cmake`` takes the ``out-of-source`` approach. Therefore a typical configuration / make / install process including 
-``NeXus`` support would look like 
-
-.. code-block:: bash
-
-  $ cd $HOME/Apps/musrfit
-  $ mkdir build
-  $ cd build
-  $ cmake ../ -DCMAKE_INSTALL_PREFIX=$ROOTSYS -Dnexus=1
-  # below it is assumed that multiple cores are present, hence the -j8 option
-  $ cmake --build ./ --clean-first -- -j8
-  $ make install
-  $ /sbin/ldconfig                                  # (as superuser)
-
-.. index:: musrfit-post-install-linux  
-  
-musrfit last step of the installation 
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-
-In order to finish the installation of musrfit two more things should be done: 
-
-  * Define the *MUSRFITPATH* environment variable containing the path to the ``musrfit`` executables and ``XML`` files. 
-    *E.g.* if the location of the example above is used append the following line to the ``~/.bashrc`` and 
-    ``~/.bash_profile`` (and then either restart the shell, source the file, or call the same commands once more from the shell): 
-
-    .. code-block:: bash
-    
-      export MUSRFITPATH=$ROOTSYS/bin
-      
-  * Adjust the paths where ``musrfit`` will search for data files in the installed ``musrfit_startup.xml``. For 
-    detailed information on this XML file refer to the :ref:`manual <musrfit-startup>`. 
-
-
-.. index:: musredit-install-linux    
-    
-musredit
-++++++++
-
-In the latest version of ``musrfit`` the configure script tries to determine automatically the highest available ``Qt`` version. 
-In case this is found, the editor ``musredit`` is built already together with ``musrfit``.
-
-musrgui (depreciated)
-+++++++++++++++++++++
-
-If ``Qt4.6`` or higher is not available but ``Qt3`` is set up ``musrgui`` can be installed. For this please 
-follow the instructions for the ``musredit`` installation where simply every ``musredit`` occurrence has to 
-be replaced by ``musrgui``. If there are problems during the ``qmake`` step, *e.g.* 
-"uic: File generated with too old version of Qt Designer", this most probably means the ``Qt4`` version of ``qmake`` 
-is being used. In order to use the ``Qt3`` version it should be enough to specify the full path to its location 
-when calling it. Within the most GNU/Linux distributions this location will be something like ``/usr/lib/qt-3.3/bin/qmake``. 
-
-Check the installation
-++++++++++++++++++++++
-
-In order to perform a quick test for finding out if the installation has been completed successfully, a few msr files 
-together with the corresponding data files can be found in the ``musrfit`` source tree at ``doc/examples/``.
-If ``musrgui`` has been installed, just open one of the ``test-*.msr`` files in the editor and test the ``musrfit`` 
-functionalities. Otherwise, if only the terminal should be used, as an initial test for instance the following could be done: 
-
-.. code-block:: bash
-
-  $ cd $HOME/Apps/musrfit/doc/examples
-  $ musrview test-histo-ROOT-NPP.msr
-
-MS Windows
-----------
-
-.. note::
-
-  The description here is only for the very brave ones. It hasn't been tested for quite a while and therefore gives you 
-  rather a flavour of what needs to be done rather than a real instruction how to setup ``musrfit``. If you just need 
-  ``musrfit`` to work on a MS Windows platform, it is recommended to install it via a linux virtual machine!
-
-.. note::
-
-  For adventurous guys using Windows 10, there is the possibility to activate the built in Ubuntu bash-shell. It allows 
-  to install ``musrfit`` as described in the Linux section. 
-  
-.. note::
-  
-  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\...``
-  
-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.
-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 started.   
-  
-Requirements
-++++++++++++
-
-.. index:: cygwin
-
-Setting up Cygwin
-^^^^^^^^^^^^^^^^^
-For the start go to the Cygwin website, download the setup file and use it to install Cygwin 1.7 or newer. During the installation 
-process you will be asked where you want to install Cygwin and normally the default choice should just be fine. At some point you 
-will be asked which packages should be installed. Make sure that you choose at least the following (or packages with revisions close 
-to the following) in order to fulfill the ``musrfit`` requirements and be able to work with this base system: 
-
-::
-
-  a2ps, alternatives, autoconf, automake, base-cygwin, base-files, base-passwd bash, bash-completion, 
-  bc, binutils, bison, boost, boost-devel, bzip2, cmake, colorgcc, coreutils, curl, cygutils, cygwin, 
-  editrights, fftw3, findutils, flex, font-adobe-dpi100,   font-adobe-dpi75, font-alias, 
-  font-bitstream-dpi100, font-bitstream-dpi75, font-encodings, font-ibm-type1, font-sun-misc, font-util, 
-  font-xfree86-type1, fontconfig, freeglut, gawk, gcc-tools-autoconf, gcc-tools-automake, gcc4, 
-  gcc4-core, gcc4-fortran, gcc4-g++,   gccmakedep, gd, gettext, ghostscript, ghostscript-fonts-std, 
-  giflib, gmp, grep, groff, gsl, gsl-apps, gsl-devel, gv, gzip,   inputproto, jasper, jpeg, lapack, 
-  less, libboost, libbz2_1, libcharset1, libcurl4, libfftw3-devel, libfftw3_3, libgcc1, libgd-devel,
-  libgif-devel, libGL-devel, libGL1, libGLU-devel, libGLU1, libglut-devel, libglut3, libgmp-devel, 
-  libgmp3, libgomp1, libICE-devel,   libICE6, libjpeg-devel, libjpeg62, liblapack-devel, libmpfr-devel, 
-  libmpfr1, libncurses-devel, libncurses9, libOSMesa-devel,   libOSMesa7, libpng, libpng14, libpng14-devel, 
-  libreadline6, libSM-devel, libSM6, libssh2_1, libstdc++6, libstdc++6-devel,   libtiff-devel, libtiff5, 
-  libtool, libX11-devel, libX11_6, libXau-devel, libXau6, libXaw7, libxcb-devel, libxcb-xlib-devel,
-  libXcursor-devel, libXcursor1, libXdmcp-devel, libXdmcp6, libXext-devel, libXext6, libXfixes-devel, 
-  libXfixes3, libXfont-devel,   libXfont1, libXft-devel, libXft2, libXi-devel, libXi6, libxkbfile1, 
-  libxml2, libxml2-devel, libXmu-devel, libXmu6, libXpm-devel,   libXpm4, libXrender-devel, libXrender1, 
-  libXt-devel, libXt6, login, m4, make, makedepend, man, mpfr, nano, opengl, openssh, openssl, pdftk, 
-  perl, ping, pkg-config, psutils, python, qt3, qt3-bin, qt3-devel, readline, rebase, rgb, rsync, run, 
-  screen, sed, subversion,   tar, tcltk, terminfo, unzip, util-linux, vim, w32api, which, 
-  X-start-menu-icons, xauth, xextproto, xfontsel, xinit, xkbcomp,   xkeyboard-config, xkill, xlogo, 
-  xlsfonts, xorg-cf-files, xorg-scripts, xorg-server, xproto, xrdb, xrefresh, xset, xterm, zip, zlib, 
-  zlib-devel, zlib0, libQt3Support4-devel, libQtAssistantClient4-devel, libQtCore4-devel, 
-  libQtDBus4-devel, libQtDesigner4-devel,   libQtGui4-devel, libQtHelp4-devel, libQtNetwork4-devel, 
-  libQtOpenGL4-devel, libQtScript4-devel, libQtScriptTools4-devel,   libQtSql4-devel, libQtSvg4-devel, 
-  libQtTest4-devel, libQtWebKit4-devel, libQtXml4-devel, libQtXmlPatterns4-devel
-  
-After these installations already most of the required software is present and the Cygwin shell can be started now for the further steps! 
-Inside the shell the POSIX naming convention applies, therefore, paths will be given with separating "/" instead of "\" in DOS. The file 
-structure accessible through this shell can also be accessed through the Windows Explorer — just go to the directory which you specified 
-as "cygwin root" during the installation: this is the equivalent to "/" in the shell. By default, the different hard drives or network shares 
-like ``C:\`` can be found at ``/cygdrive/c/`` in the shell — the cygdrive prefix can in principle also be changed but for now we stick to the default.   
-
-Since later on the boost header files should be used and in the standard Cygwin installation these are found at a version specific location, 
-the later handling will be easier if a symbolic link to these files is created now in the terminal (in case it had not been present before): 
-
-.. code-block:: bash
-
-  $ 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``.   
-  
-Everything but ROOT and NeXus
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-
-.. index:: nexus-build-windows    
-
-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 NeXus Version ≥ 4.4 is support!**  
-
-.. code-block:: bash
-
-  $ cd
-  $ mkdir nexus
-  $ cd nexus
-  $ curl http://www.hdfgroup.org/ftp/lib-external/jpeg/src/jpegsrc.v6b.tar.gz -G | tar xz
-  $ cd jpeg-6b
-  $ ./configure --prefix=/usr/local --enable-static
-  $ make
-  $ make install
-  $ cd ..
-  $ # create a directory for the NeXus source code
-  $ mkdir nexus
-  $ cd nexus
-  $ # get the source code from the master repository
-  $ git clone https://github.com/nexusformat/code.git
-  $ # next we will build NeXus out-of-source
-  $ mkdir build
-  $ cd build
-  $ cmake -DENABLE_HDF5=1 -DENABLE_HDF4=1 -DENABLE_MXML=0 ../code
-  $ make
-  $ make install
-
-  
-.. index:: root-build-windows
-
-ROOT
-^^^^
-
-In order to install the ``ROOT`` system, there are two possibilities: 
-
-* Download the precompiled Cygwin GCC 4.3 (or newer) 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:
-  
-  .. _web page: https://root.cern.ch/downloading-root
-    
-  .. code-block:: bash
-    
-    $ 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 it (here using the minimal set of options) 
-  and compile it as follows right below:
-    
-  .. code-block:: bash
-    
-    $ cd /cygdrive/c
-    $ tar xzf root_v5.xx.yy.source.tar.gz
-    $ cd root
-    $ ./configure win32gcc --gminimal --enable-asimage --enable-mathmore --enable-minuit2 --enable-xml
-    $ make
-      
-* In order to finalize the ``ROOT`` installation and to prepare already the installation of ``musrfit`` and 
-  ``musredit`` this is a good time for setting necessary environment variables for the use in Cygwin. For 
-  accomplishing that put the following lines at the end of the ``/home/Username/.bashrc`` (``C:\cygwin\home\Username\.bashrc`` 
-  for the user ``Username`` and the ``cygwin root`` at ``C:\cygwin``):
-
-  .. code-block:: bash
-    
-    export DISPLAY=:0.0
-    export QTDIR=/usr/lib/qt4
-    export ROOTSYS=/cygdrive/c/root
-    export PATH=$ROOTSYS/bin:$QTDIR/bin:/usr/i686-pc-cygwin/bin:$PATH
-    export MUSRFITPATH=$ROOTSYS/bin
-      
-Afterwards close the Cygwin shell and reopen it again for the installation of ``musrfit``.       
-  
-.. index:: musrfit-build-windows  
-  
-musrfit
-+++++++
-
-First, the most recent source code should be downloaded. The preferred way of doing so is to clone the ``musrfit`` 
-repository via git. Assuming the code should be located in ``~/musrfit`` this is achieved most easily calling from the terminal 
-
-.. code-block:: bash
-
-  $ cd
-  $ git clone https://bitbucket.org/muonspin/musrfit.git 
-
-or  
-
-.. code-block:: bash
-
-  $ cd
-  $ git clone git://gitlab.psi.ch/nemu/musrfit.git
-  
-If the repository had been checked out already before, one can update the local copy using: 
-
-.. code-block:: bash
-
-  $ cd musrfit
-  $ git pull
-
-As an alternative (if git is not available), the source code can also be downloaded from the following 
-web-page: `musrfit at bitbucket`_.
-   
-.. index:: musrfit-build-cmake-windows  
-
-musrfit build with cmake 
-^^^^^^^^^^^^^^^^^^^^^^^^
-
-Currently the following configuration switches for ``musrfit`` are available:
-
-**-DCMAKE_INSTALL_PREFIX=<prefix-path>**
-  Specify the installation prefix, *i.e.* the place where ``musrfit`` shall be installed, *e.g.* ``$ROOTSYS`` if already defined (by default: ``/usr/local``) 
-**-Dnexus=<value>**
-  enable/disable the support of ``NeXus`` data files (requires the ``HDF4``, ``HDF5`` and ``NeXus`` libraries to be installed). 
-  <value>=1 enables ``NeXus``, <value>=0 disables ``NeXus``. The default setting, *i.e.* the switch is not provided is ``NeXus`` support is disabled. 
-**-DASlibs=<value>**
-  enable/disable the ``ASlibs``. <value>=1 enables the ``ASlibs``, <value>=0 disables the ``ASlibs``. 
-  The default setting, *i.e.* the switch is not provided is ``ASlibs`` support is *disabled*. For details see Documentation of :ref:`user libs <user-libs>`. 
-**-DBMWlibs=<value>**
-  enable/disable the ``BMWlibs``. <value>=1 enables the ``BMWlibs``, <value>=0 disables the ``BMWlibs``. 
-  The default setting, *i.e.* the switch is not provided is ``BMWlibs`` support is *disabled*. For details see Documentation of :ref:`user libs <user-libs>`. 
-**-DBNMRlibs=<value>**
-  enable/disable the ``BNMRlibs``. <value>=1 enables the ``BNMRlibs``, <value>=0 disables the ``BNMRlibs``. 
-  The default setting, *i.e.* the switch is not provided is ``BNMRlibs`` support is *disabled*. 
-**-Dqt_based_tools=<value>**
-  Will try to get ``musredit``, ``musrWiz``, ``musrStep``, and ``mupp`` installed, if ``Qt`` is found. 
-  By default this is *enabled*. Again <value>=0 means disabled, <value>=1 enabled. 
-**-Dqt_version=<value>**
-  Allows to specify which ``Qt`` version shall be tried. <value> can take the values: ``AUTO, 3, 4, 5, 6``. 
-  If the value is set to ``AUTO``, this highest installed version is chosen, otherwise the specified version is used. 
-**-Dtry_OpenMP=<value>**
-  Will check if ``OpenMP`` support is possible, and if yes use it. The default is *enabled*. 
-
-Normally it should not be necessary to make use of any of the options except for specifying the installation path with 
-``-DCMAKE_INSTALL_PREFIX``. ``musrfit`` build with ``cmake`` takes the out-of-source approach. Therefore a typical 
-configuration / make / install process including ``NeXus`` support would look like
-
-.. code-block:: bash
-
-  $ cd $HOME/Apps/musrfit
-  $ mkdir build
-  $ cd build
-  $ cmake ../ -DCMAKE_INSTALL_PREFIX=$ROOTSYS -Dnexus=1
-  # below it is assumed that multiple cores are present, hence the -j8 option
-  $ cmake --build ./ --clean-first -- -j8
-  $ make install
-  $ /sbin/ldconfig                                  # (as superuser)
-
-
-.. index:: musredit-install-windows
-
-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 
-readily with ``musrfit``. If not, try the following:
-
-.. code-block:: bash
-
-  $ cd src/musredit
-  $ qmake-qt4 musredit.pro
-  
-If everything went fine ``musredit`` can be compiled and installed:  
-
-.. code-block:: bash
-
-  $ make
-  $ make install
-
-In case one likes to get the editor started just with starting the X server from the Windows start 
-menu the file ``~/.startxwinrc`` with the following contents can be created:  
-  
-.. code-block:: bash
-
-  #!/bin/sh
-
-  export DISPLAY=:0.0
-  export QTDIR=/usr/lib/qt4
-  export ROOTSYS=/cygdrive/c/root
-  export PATH=$ROOTSYS/bin:$QTDIR/bin:/usr/i686-pc-cygwin/bin:$PATH
-  export MUSRFITPATH=$ROOTSYS/bin
-
-  musredit &
-  
-musrgui (depreciated)
-+++++++++++++++++++++
-
-If ``Qt4.5`` or higher is not available but ``Qt3`` is set up ``musrgui`` can be installed. For this 
-please follow the instructions for the ``musredit`` installation where simply every ``musredit`` occurrence 
-has to be replaced by ``musrgui``, and ``qt4`` is replaced by ``qt3``. 
-
-Check the installation
-++++++++++++++++++++++
-
-In order to perform a quick test for finding out if the installation has been completed successfully, 
-a few msr files together with the corresponding data files can be found in the ``musrfit`` source tree 
-at doc/examples/.
-If ``musrgui`` has been installed, just open one of the ``test-*.msr`` files in the editor and test 
-the ``musrfit`` functionalities. Otherwise, if only the terminal should be used, as an initial test 
-for instance the following could be done:
-
-.. code-block:: bash
-
-  $ cd doc/examples
-  $ musrview test-histo-ROOT-NPP.msr
-
-Potential Problems
-++++++++++++++++++
-
-It might be that especially when running on Windows 7 ``musredit`` and ``musrgui`` produce errors like a 
-"STATUS_ACCESS_VIOLATION". In this case, try to do the following: Close all Cygwin programs (including 
-the terminals and X server) and run from a Windows command prompt (cmd)
-
-.. code-block:: bash
-
-  $ 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.   
-
-Mac OS X / macOS
-----------------
-
-.. note::
-
-  macOS 11 alias **Big Sur**: ``musrfit`` is ready for **Big Sur** on Intel based macs. The ``DKS`` version of   
-  ``musrfit`` for macOS **Big Sur** is ready as well.
-
-.. note::
-
-  macOS Catalina is slightly different in some aspects, so if it happens that you have it installed, please
-  first check :ref:`note-on-catalina` before you proceed.
-
-.. _MacPorts: https://www.macports.org/
-.. _Fink: http://www.finkproject.org/
-
-With Mac OS X / macOS 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 . 
-
-.. warning::
-  
-  If you decide to upgrade your macOS, e.g. from ``High Sierra`` to ``Mojave``, you will typically need to 
-  unistall ``musrfit``, ``ROOT``, and `MacPorts`_ / `Fink`_ first, do the upgrade of the macOS and start the 
-  installation of `MacPorts`_ / `Fink`_ , ``ROOT``, and ``musrfit`` from scratch!
-
-.. index:: macports
-
-Requirements (MacPorts) 
-+++++++++++++++++++++++
-
-Before proceeding with the usage of the ``MacPorts`` system first a few useful tools provided by Apple together 
-with OS X (on the installation DVD/CDs) should be installed: 
-
- **Xcode**
-   Useful developer tools including for instance the GNU compiler collection. It can be installed via the Apple App store. 
-   Starting from ``XCode`` ≥ 4.3 the command line tools need to be installed manually. The necessary command line tools 
-   can be installed via the following commands entered in the terminal
-   
-   .. code-block:: bash
-   
-     $ xcode-select --install
-     $ sudo xcodebuild -license
-     
-**X11**
-  The X-window system is automatically installed on 10.5 Leopard and 10.6 Snow Leopard. For some other versions you also 
-  will need to install `XQuartz <http://xquartz.macosforge.org/trac>`_. If ``ROOT`` runs without ``XQuartz`` *do not*
-  install it.
-  
-After installing the ``Xcode`` tools go to the `MacPorts install page <http://www.macports.org/install.php>`_, download 
-the installer for your system and follow the installation instructions on the page. By default the MacPorts system will be 
-installed in ``/opt/local``. To be sure that the newest version of the software is used a MacPorts upgrade should be performed 
-by typing in a terminal:   
-
-.. code-block:: bash
-
-  $ sudo port -v selfupdate
-
-**Remark:** MacPorts uses `rsync <http://rsync.samba.org/>`_ in order to synchronize the list of available packages. It frequently 
-happens that this service is blocked by firewalls. In this case it should be possible to download a local version of the package 
-repository and do the synchronization. If this step becomes necessary (*and only then*) it can be done in the following way:   
-
-#. Get a local version of the repository:
-
-   .. code-block:: bash
-      
-      $ svn co http://svn.macports.org/repository/macports/trunk/dports ~/dports
-      
-#. Edit the file ``/opt/local/etc/macports/sources.conf``: At the end of the file, comment the line beginning with ``rsync://`` and 
-   add a new line pointing to your local copy, *e.g.*
-   
-   .. code-block:: bash
-   
-     file:///Users/username/dports
-     
-#. Synchronize the packages:     
-
-   .. code-block:: bash
-   
-      $ sudo port -v -d sync
-      
-Then the MacPorts system should be set up and can be used to install additional software.      
-
-The installation of the software mentioned above is then done in the terminal:
-
-.. code-block:: bash
-
-  $ sudo port -v install pkgconfig autoconf automake libtool cmake fftw-3 fftw-3-single gsl boost libxml2 qt5 qt5-qtsvg
-  
-With ``Qt5``, ``musredit`` will be installed. If it happens that you used ``musrgui`` in the past, 
-please change over to ``musredit`` since there will be no further development for ``musrgui`` anymore!   
-      
-
-.. index:: nexus-build-macports
-
-Installation of NeXus requirements (optional) 
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-
-*Only* if ``musrfit`` should support reading data files in the ``NeXus`` format the further required packages are set up: 
-
-.. code-block:: bash
-
-  $ sudo port -v install hdf4 hdf5
-
-**Only NeXus Version ≥ 4.4 is support!**  
-
-To get things compiled do:
-
-.. code-block:: bash
-
-  $ # get and install NeXus
-  $ cd $HOME/Applications
-  $ # get the source code from the master repository
-  $ git clone https://github.com/nexusformat/code.git nexus/code
-  $ # next we will build NeXus out-of-source
-  $ cd nexus
-  $ mkdir build
-  $ cd build
-  $ cmake -DENABLE_HDF5=1 -DENABLE_HDF4=1 -DENABLE_MXML=0 ../code
-  $ make
-  $ sudo make install
-  
-
-.. index:: root-build-macports
-
-ROOT
-^^^^
-
-**The default ROOT version is based on ROOT 6.xx/yy!**
-
-ROOT installed via package installer 
-""""""""""""""""""""""""""""""""""""
-
-The lazy way to get ``ROOT`` installed is via package installer. If your macOS is directly supported 
-by the ``ROOT`` people you can download the package installer from the ``ROOT`` `download page <https://root.cern.ch/downloading-root>`_. 
-Choose the latest ``ROOT`` release and download you macOS version dmg-file, *e.g.* for macOS 10.13 (High Sierra) 
-it is at the time of writting ``root_v6.16.00.macosx64-10.13-clang91.dmg``. After the installation 
-``ROOT`` will be installed under ``/Application`` as owner root. In order to ease your life for the 
-steps to follow and assuming you are the only guy working on your Mac, you could change the owner and group of the ``ROOT`` directory: 
-
-.. code-block:: bash
-
-  $ cd /Applications
-  $ sudo chown -R <username> root_v6.16.00
-  $ sudo chgrp -R staff root_v6.16.00
-  $ sudo ln -s root_v6.16.00 root
-
-ROOT installed from source 
-""""""""""""""""""""""""""
-
-The best way to get ``ROOT`` exactly the way needed for ``musrfit`` is to install it from source. 
-Before describing it, please make sure that you have installed all required packages listed under 
-:ref:`Requested Software <supported-operating-systems>` (*e.g.* ``fftw``, ``gsl``, etc). 
-
-For the following it is assumed that ``ROOT`` shall be installed under ``$HOME/Applications``. If you want 
-to install it somewhere else, just systematically replace the related terms of the following description. 
-For the following list of commands the '$' will be given, the command prompt. Do not enter it! Also some 
-comments will be added starting with a '#' which can be omitted. They are only there to explain what is going on. 
-
-.. code-block:: bash
-
-  $ cd $HOME/Applications
-  $ git clone http://github.com/root-project/root.git
-  $ cd root
-  $ git tag -l
-  $ # git tag -l will list all available tags. In the next command choose the tag v6-10-xx
-  $ # where xx is the highest listed number, e.g. v6-16-00
-  $ git checkout -b v6-16-00 v6-16-00
-  $ # now ROOT is ready to be configured. Below you will find the minimal ROOT configuration needed.
-  $ # We will use the cmake out-of-source approach here.
-  $ mkdir root_build
-  $ cd root_build
-  $ cmake ../ -Dgminimal=ON -Dasimage=ON -Dmathmore=ON -Dminuit2=ON -Dxml=ON -DCMAKE_INSTALL_PREFIX=$HOME/Applications/root/root_exec
-  $ # next will be the make. If running on a multicore CPU you can speed up tremendously by calling
-  $ # make with the option -j <number>, where <number> is the number of threads which you want to give,
-  $ # e.g. make -j8
-  $ cmake --build ./ --clean-first -- -j8
-  $ # make will take quite a while
-  $ make install
-
-For further details see `Installing ROOT from Source <https://root.cern.ch/building-root>`_.  
-  
-Setting up Environment Variables for ROOT and musrfit
-"""""""""""""""""""""""""""""""""""""""""""""""""""""
-
-Since Apple in its wisdom decided that programs started from a shell are treated differently than Apps if it is coming to 
-system variables, we need to work harder compared to a Linux system. 
-
-**For Mac OS X < 10.8:**
-
-In order to finalize the ``ROOT`` installation and to prepare already the installation of ``musrfit`` and ``musredit`` 
-this is a good time for setting necessary environment variables for the use in Mac OS X. Here it assumed that you 
-installed ``ROOT`` from source. If you downloaded the binary package, you will need to adopt the paths accordingly. 
-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:
-
-.. code-block:: xml
-
-  <?xml version="1.0" encoding="UTF-8"?>
-  <!DOCTYPE plist PUBLIC "-//Apple//DTD PLIST 1.0//EN" "http://www.apple.com/DTDs/PropertyList-1.0.dtd">
-  <plist version="1.0">
-  <dict>
-        <key>MUSRFITPATH</key>
-        <string>$HOME/Applications/root/root_exec/bin</string> (where to find the musrfit executables)
-        <key>QTDIR</key>
-        <string>/opt/local/lib/qt3mac</string>                 (where to find Qt3 (for musrgui) or Qt4 (for musredit))
-        <key>ROOTSYS</key>
-        <string>$HOME/Applications/root/root_exec</string>     (where to find the ROOT system)
-  </dict>
-  </plist>
-
-**For Mac OS X ≥ 10.8:**  
-
-One needs to add some system variables in ``~/.profile``: 
-
-.. code-block:: bash
-
-  export ROOTSYS=$HOME/Applications/root/root_exec
-  export MUSRFITPATH=$ROOTSYS/bin
-  export PATH=$ROOTSYS/bin:$QTDIR/bin:$PATH
-  export LD_LIBRARY_PATH=$ROOTSYS/lib:$LD_LIBRARY_PATH
-
-  launchctl setenv ROOTSYS $ROOTSYS
-  launchctl setenv MUSRFITPATH $MUSRFITPATH
-  launchctl setenv PATH $PATH
-  launchctl setenv LD_LIBRARY_PATH $LD_LIBRARY_PATH
-
-After this you will need to "execute" ``.profile`` before proceeding:   
-
-.. code-block:: bash
-
-  $ source $HOME/.profile
-
-.. _note-on-catalina:
-
-Notes on macOS Catalina
-^^^^^^^^^^^^^^^^^^^^^^^
-
-Apple introduced a couple of changes on macOS Catalina compared to its previous versions of macOS which might
-be a stumble block. Here I **very** briefly try to add some notes in order to get a smooth installation for 
-``musrfit``.
-
-1. You should switch from the bash to the zsh. Please check, e.g. `Moving to zsh <https://scriptingosx.com/2019/06/moving-to-zsh/>`_. 
-2. Instead of ``.profile`` you will need to setup a ``.zprofile``.
-3. macports: currently there is a little nuisance with the ``fftw-3`` port. My bug report is already out since a while 
-   but no proper fix is available. The workaround to get it right is to install the port from source which is done by
-
-   .. code-block:: bash
-
-     $ port -s install fftw-3 
-
-   If you fail to do so, you might trigger a crash in the Fourier transform for 2^N, N=12.
-
-.. index:: fink
-
-Requirements (Fink) 
-+++++++++++++++++++
-
-Before proceeding with the usage of the `Fink`_ system first a few useful tools provided by Apple together with OS X (on the installation DVD/CDs) should be installed:
-
-**Xcode**
-   Useful developer tools including for instance the GNU compiler collection. It can be installed via the Apple App store. 
-   Starting from ``XCode`` ≥ 4.3 the command line tools need to be installed manually. The necessary command line tools 
-   can be installed via the following commands entered in the terminal
-   
-   .. code-block:: bash
-   
-     $ xcode-select --install
-     $ sudo xcodebuild -license
-     
-**X11**
-  The X-window system is automatically installed on 10.5 Leopard and 10.6 Snow Leopard. For some other versions you also 
-  will need to install `XQuartz <http://xquartz.macosforge.org/trac>`_. If ``ROOT`` runs without ``XQuartz`` *do not*
-  install it.
-
-After installing the ``Xcode`` tools go to the `Fink download page <http://www.finkproject.org/download/index.php?phpLang=en>`_, 
-download the installer for your system and follow the installation instructions on the page. By default the Fink system is 
-installed under ``/sw``. After the basic setup make sure that in ``/sw/etc/fink.conf`` the line starting with Trees reads like:   
-
-::
-
-  Trees: local/main stable/main stable/crypto unstable/main
-  
-After applying the changes above to the configuration file, the Fink core system should be upgraded to its newest version by typing in a terminal:   
-
-.. code-block:: bash
-
-  $ sudo fink selfupdate
-  
-Then the Fink system should be set up and can be used to install additional software.
-The Fink installer package also contains a graphical user interface called FinkCommander and it is 
-suggested to use that for installing the following packages (or packages with revisions close to the following) — it 
-is necessary to compile a few packages from source since no binary packages are available, however, this is done 
-automatically by the FinkCommander after you have chosen the software packages for installation:   
-
-::
-  
-  autoconf automake cmake boost1.63-nopython boost1.63.nopython-shlibs fftw3 fftw3-shlibs gsl gsl-shlibs 
-  libtool2 libtool2-shlibs libxml2 libxml2-bin libxml2-shlibs pkgconfig qt5-mac-qtbase qt5-mac-qtbase-dev-tools 
-  qt5-mac-qtsvg qt5-mac-qtsvg-shlibs 
-  
-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 ``qt5-mac`` 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): 
-
-.. code-block:: bash
-
-  $ tar xz fftw-3.x.y
-  $ cd fftw-3.x.y
-  $ ./configure --enable-single --enable-shared --enable-threads --prefix=/usr/local
-  $ make
-  $ sudo make install
-  
-Since later on the boost header files should be used and in the standard Fink installation these are found at a version 
-specific location, the later handling will be easier if a symbolic link to this files is created now in the terminal 
-(if it did not exist earlier), *e.g.*:   
-
-.. code-block:: bash
-
-  $ ln -sf /sw/include/boost-x_yy_z/boost /sw/include/boost
-  
-where ``x_yy_z`` has to be substituted by the correct version number, *e.g.* ``1_63_0``.   
-
-.. index:: nexus-build-fink
-
-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 (check for the most recent versions): 
-
-::
-
-  libjpeg hdf hdf5-cpp11 hdf5-cpp11-shlibs
-  
-Unfortunately, the ``NeXus`` libraries have to be compiled and installed directly from 
-the source code. Given the respective version number 4.4 (which are subject to change with time) 
-this can be achieved for example by:   
-
-.. code-block:: bash
-
-  $ # build NeXus
-  $ cd ..
-  $ git clone https://github.com/nexusformat/code.git nexus/code
-  $ cd nexus
-  $ # build NeXus out-of-source
-  $ mkdir build
-  $ cd build
-  $ cmake ../code -DENABLE_HDF5=1 -DENABLE_HDF4=1 -DENABLE_MXML=0
-  $ cmake --build ./ --clean-first -- -j8
-  $ sudo make install
-
-    
-.. index:: root-build-fink
-
-ROOT
-^^^^
-
-**The default ROOT version is based on ROOT 6.xx/yy!**
-
-ROOT installed via package installer 
-""""""""""""""""""""""""""""""""""""
-
-The lazy way to get ``ROOT`` installed is via package installer. If your macOS is directly supported 
-by the ``ROOT`` people you can download the package installer from the ``ROOT`` `download page <https://root.cern.ch/downloading-root>`_. 
-Choose the latest ``ROOT`` release and download you macOS version dmg-file, *e.g.* for macOS 10.13 (High Sierra) 
-it is at the time of writting ``root_v6.16.00.macosx64-10.13-clang91.dmg``. After the installation 
-``ROOT`` will be installed under ``/Application`` as owner root. In order to ease your life for the 
-steps to follow and assuming you are the only guy working on your Mac, you could change the owner and group of the ``ROOT`` directory: 
-
-.. code-block:: bash
-
-  $ cd /Applications
-  $ sudo chown -R <username> root_v6.16.00
-  $ sudo chgrp -R staff root_v6.16.00
-  $ sudo ln -s root_v6.16.00 root
-  
-ROOT installed from source
-""""""""""""""""""""""""""
-
-The best way to get ``ROOT`` exactly the way needed for ``musrfit`` is to install it from source. 
-Before describing it, please make sure that you have installed all required packages listed under 
-:ref:`Requested Software <supported-operating-systems>` (*e.g.* ``fftw``, ``gsl``, etc). 
-
-For the following it is assumed that ``ROOT`` shall be installed under ``$HOME/Applications``. If you want 
-to install it somewhere else, just systematically replace the related terms of the following description. 
-For the following list of commands the '$' will be given, the command prompt. Do not enter it! Also some 
-comments will be added starting with a '#' which can be omitted. They are only there to explain what is going on. 
-
-.. code-block:: bash
-
-  $ cd $HOME/Applications
-  $ git clone http://github.com/root-project/root.git
-  $ cd root
-  $ git tag -l
-  $ # git tag -l will list all available tags. In the next command choose the tag v6-10-xx
-  $ # where xx is the highest listed number, e.g. v6-16-00
-  $ git checkout -b v6-16-00 v6-16-00
-  $ # now ROOT is ready to be configured. Below you will find the minimal ROOT configuration needed.
-  $ # We will use the cmake out-of-source approach here.
-  $ mkdir root_build
-  $ cd root_build
-  $ cmake ../ -Dgminimal=ON -Dasimage=ON -Dmathmore=ON -Dminuit2=ON -Dxml=ON -DCMAKE_INSTALL_PREFIX=$HOME/Applications/root/root_exec
-  $ # next will be the make. If running on a multicore CPU you can speed up tremendously by calling
-  $ # make with the option -j <number>, where <number> is the number of threads which you want to give,
-  $ # e.g. make -j8
-  $ cmake --build ./ --clean-first -- -j8
-  $ # make will take quite a while
-  $ make install
-
-For further details see `Installing ROOT from Source <https://root.cern.ch/building-root>`_.  
-
-Setting up Environment Variables for ROOT and musrfit
-"""""""""""""""""""""""""""""""""""""""""""""""""""""
-
-Since Apple in its wisdom decided that programs started from a shell are treated differently than Apps if it is coming to 
-system variables, we need to work harder compared to a Linux system. 
-
-**For Mac OS X < 10.8:**
-
-In order to finalize the ``ROOT`` installation and to prepare already the installation of ``musrfit`` and ``musredit`` 
-this is a good time for setting necessary environment variables for the use in Mac OS X. Here it assumed that you 
-installed ``ROOT`` from source. If you downloaded the binary package, you will need to adopt the paths accordingly. 
-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:
-
-.. code-block:: xml
-
-  <?xml version="1.0" encoding="UTF-8"?>
-  <!DOCTYPE plist PUBLIC "-//Apple//DTD PLIST 1.0//EN" "http://www.apple.com/DTDs/PropertyList-1.0.dtd">
-  <plist version="1.0">
-  <dict>
-        <key>MUSRFITPATH</key>
-        <string>$HOME/Applications/root/root_exec/bin</string> (where to find the musrfit executables)
-        <key>QTDIR</key>
-        <string>/opt/local/lib/qt3mac</string>                 (where to find Qt3 (for musrgui) or Qt4 (for musredit))
-        <key>ROOTSYS</key>
-        <string>$HOME/Applications/root/root_exec</string>     (where to find the ROOT system)
-  </dict>
-  </plist>
-
-**For Mac OS X ≥ 10.8:**  
-
-One needs to add some system variables in ``~/.profile``: 
-
-.. code-block:: bash
-
-  export ROOTSYS=$HOME/Applications/root/root_exec
-  export MUSRFITPATH=$ROOTSYS/bin
-  export PATH=$ROOTSYS/bin:$QTDIR/bin:$PATH
-  export LD_LIBRARY_PATH=$ROOTSYS/lib:$LD_LIBRARY_PATH
-
-  launchctl setenv ROOTSYS $ROOTSYS
-  launchctl setenv MUSRFITPATH $MUSRFITPATH
-  launchctl setenv PATH $PATH
-  launchctl setenv LD_LIBRARY_PATH $LD_LIBRARY_PATH
-
-After this you will need to "execute" ``.profile`` before proceeding:   
-
-.. code-block:: bash
-
-  $ source $HOME/.profile
-
-.. index:: musrfit-build-macos
-
-musrfit
-+++++++
-
-First, the most recent source code should be downloaded. First, the most recent source code should be downloaded. 
-The preferred way of doing so is to clone the ``musrfit`` repository via git. Assuming the code should be located 
-in ``~/Applications/musrfit`` this is achieved most easily calling from the termin
-
-.. code-block:: bash
-
-  $ cd ~/Applications
-  $ git clone https://bitbucket.org/muonspin/musrfit.git 
-  $ cd musrfit
-
-or 
-
-.. code-block:: bash
-
-  $ cd ~/Applications
-  $ git clone git://gitlab.psi.ch/nemu/musrfit.git  
-  $ cd musrfit
-
-If a local repository clone is already present, one can update it using: 
-
-.. code-block:: bash
-
-  $ cd ~/Applications/musrfit
-  $ git pull
-  
-As an alternative (*if git is not available*), the source code can also be downloaded from the following 
-web-page: `musrfit at bitbucket`_.   
-   
-.. index:: musrfit-build-cmake-macos
-
-
-
-musrfit build with cmake
-^^^^^^^^^^^^^^^^^^^^^^^^
-
-Currently the following configuration switches for ``musrfit`` are available: 
-
-**-DCMAKE_INSTALL_PREFIX=<prefix-path>**
-  Specify the installation prefix, *i.e.* the place where ``musrfit`` shall be installed, *e.g.* ``$ROOTSYS`` if already defined (by default: ``/usr/local``). 
-**-Dnexus=<value>**
-  enable/disable the support of ``NeXus`` data files (requires the ``HDF4``, ``HDF5`` and ``NeXus`` libraries to be installed). 
-  <value>=1 enables ``NeXus``, <value>=0 disables ``NeXus``. The default setting, *i.e.* the switch is not provided is ``NeXus`` support is disabled. 
-**-DASlibs=<value>**
-  enable/disable the ``ASlibs``. <value>=1 enables the ``ASlibs``, <value>=0 disables the ``ASlibs``. The default setting, *i.e.* the 
-  switch is not provided is ``ASlibs`` support is disabled. For details see Documentation of :ref:`user libs <user-libs>`. 
-**-DBMWlibs=<value>**
-  enable/disable the ``BMWlibs``. <value>=1 enables the ``BMWlibs``, <value>=0 disables the ``BMWlibs``. The default setting, *i.e.* the 
-  switch is not provided is ``BMWlibs`` support is disabled. For details see Documentation of :ref:`user libs <user-libs>`.  
-**-DBNMRlibs=<value>**
-  enable/disable the ``BNMRlibs``. <value>=1 enables the ``BNMRlibs``, <value>=0 disables the ``BNMRlibs``. The default setting, 
-  *i.e.* the switch is not provided is ``BNMRlibs`` support is disabled. 
-**-Dqt_based_tools=<value>**
-  Will try to get ``musredit``, ``musrWiz``, ``musrStep``, and ``mupp`` installed, if ``Qt`` is found. 
-  By default this is enabled. Again <value>=0 means disabled, <value>=1 enabled. 
-**-Dqt_version=<value>**
-  Allows to specify which ``Qt`` version shall be tried. <value> can take the values: ``AUTO, 3, 4, 5, 6``. 
-  If the value is set to ``AUTO``, this highest installed version is chosen, otherwise the specified version is used. 
-**-Dtry_OpenMP=<value>**
-  Will check if ``OpenMP`` support is possible, and if yes use it. The default is enabled 
-
-Normally it should not be necessary to make use of any of the options except for specifying the installation path with ``-DCMAKE_INSTALL_PREFIX``. 
-``musrfit`` build with ``cmake`` takes the ``out-of-source`` approach. Therefore a typical configuration / make / install process including 
-``NeXus`` support would look like 
-
-.. code-block:: bash
-
-  $ cd $HOME/Apps/musrfit
-  $ mkdir build
-  $ cd build
-  $ cmake ../ -DCMAKE_INSTALL_PREFIX=$ROOTSYS -Dnexus=1
-  # below it is assumed that multiple cores are present, hence the -j8 option
-  $ cmake --build ./ --clean-first -- -j8
-  $ make install
-  $ /sbin/ldconfig                                  # (as superuser)
-
-  
-musrfit last step of the installation
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-
-In order to finish the installation of ``musrfit`` two more things should be done: 
-
-* Define the ``MUSRFITPATH`` environment variable containing the path to the ``musrfit`` executables and ``XML`` files. 
-  *E.g.* if the location of the example above is used append the following line to the ``~/.bashrc`` and ``~/.bash_profile`` 
-  (and then either restart the shell or call the same commands once more from the shell): 
-  
-.. code-block:: bash   
-
-  export MUSRFITPATH=$ROOTSYS/bin
-  
-* Adjust the paths where ``musrfit`` will search for data files in the installed ``musrfit_startup.xml``. For 
-  detailed information on this XML file refer to the :ref:`manual <musrfit-startup>`.   
-
-.. index:: musredit-build-macos
-
-musredit
-++++++++
-
-In the latest version of ``musrfit`` the configure script tries to determine automatically the highest 
-available Qt version. In case this is found, the editor ``musredit`` is built already together with ``musrfit``. 
-If not, try the following:
-
-.. code-block:: bash
-
-  $ cd $HOME/Apps/musrfit/src/musredit_qt5
-  $ # for some distributions you will need qmake-qt5 for the next command
-  $ qmake musredit.pro
-
-If everything went fine, ``musredit`` can be compiled and installed:
-
-.. code-block:: bash
-
-  $ make
-  $ make install
-
-In case one does not like the executable ``musredit`` to be copied to the default installation directory 
-``$ROOTSYS/bin`` the last make install can be skipped and the executable can be copied somewhere else instead.
-
-musrgui (obsolete) 
-++++++++++++++++++
-
-If Qt3 is set up the installation of the ``musrfit`` editor can be done as follows from within the shell: 
-
-.. code-block:: bash
-
-  $ cd ~/Applications/musrfit/src/musrgui
-  $ qmake musrgui.pro
-  $ make
-  $ make install
-  
-The last command copies ``musrgui.app`` to the standard program directory ``/Applications``.
-
-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! In order to 
-accomplish that, add the following lines to ``~/.profile`` and call ``musrgui`` with the specified command:
-
-.. code-block:: bash
-
-  export DYLD_LIBRARY_PATH=/opt/root-system/lib:/sw/lib:$DYLD_LIBRARY_PATH
-  alias mgui='/Applications/musrgui.app/Contents/MacOS/musrgui'
-
-Check the installation
-++++++++++++++++++++++
-
-In order to perform a quick test for finding out if the installation has been completed successfully, a few msr 
-files together with the corresponding data files can be found in the musrfit source tree at ``doc/examples/``.
-If ``musrgui`` has been installed, just open one of the ``test-*.msr`` files in the editor and test the ``musrfit`` 
-functionalities. Otherwise, if only the terminal should be used, as an initial test for instance the following could be done: 
-
-.. code-block:: bash
-
-  $ cd ~/Applications/musrfit/doc/examples
-  $ musrview test-histo-ROOT-NPP.msr
diff --git a/doc/html/_sources/tutorial.txt b/doc/html/_sources/tutorial.txt
deleted file mode 100644
index 657c0c78..00000000
--- a/doc/html/_sources/tutorial.txt
+++ /dev/null
@@ -1,417 +0,0 @@
-.. include:: <isogrk1.txt>
-.. index:: tutorial
-
-Tutorial for ``musrfit``
-========================
-
-Single-histogram-fit tutorial
------------------------------
-
-The |mgr|\SR-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 
-|mgr|\SR data. For a complete description of all options please refer to the :ref:`manual <user-manual>`. 
-
-The example deals with a diamagnetic sample that has been measured in an applied field of approximately 150 G in 
-the `GPS spectrometer <https://www.psi.ch/smus/gps>`_ at `PSI <https://www.psi.ch>`_ using the "transverse geometry". 
-In this geometry the muon spin is rotated about 50° up and the field is applied parallel to the muon momentum. 
-Hence, the relevant positron counters (to detect the spin precession) are placed above (histogram 3), below (histogram 4) and right of (histogram 5) the sample. The run numbers start from 3110. 
-
-To analyze these data (in a simple way) one starts out from the msr file ``3110_tutorial.msr`` provided together 
-with the source-code distribution in the sub-directory ``doc/examples/``. This ASCII file can be edited using any 
-text editor. For convenience the editor ``musredit`` is provided which offer some msr-file-specific functionalities 
-and additionally serve as front ends to the underlying programs. In the following it is assumed that the file is 
-open within ``musredit``.
-
-The msr file 
-++++++++++++
-
-The msr file itself is divided into different blocks; a full description of the format can be found :ref:`here <msr-file-format>`. 
-In the file ``3110_tutorial.msr`` these blocks are successively: 
-
-:ref:`The title <msr-title-block>`
-
-::
-
-  sample XYZ
-  
-A descriptive title of the file.  
-
-:ref:`The FITPARAMETER block <msr-fitparameter-block>`
-
-::
-
-  FITPARAMETER
-  #    No Name        Value     Step        Pos_Error   Boundaries
-        1 NormUp      4500      5           none        0       none    
-        2 BgUp        200       1           none        0       none    
-        3 PhaseUp     15        1           none        
-
-        4 NormDown    4500      5           none        0       none    
-        5 BgDown      200       1           none        0       none    
-        6 PhaseDown   195       1           none        
-
-        7 NormRight   600       5           none        0       none    
-        8 BgRight     40        1           none        0       none    
-        9 PhaseRight  285       1           none         
-
-       10 AsymSig1    0.17      0.01        none        0       0.33    
-       11 RateSig1    2.5       0.1         none        0       none
-       12 FieldSig1   100       1           none       
-
-       13 AsymSig2    0.02      0.01        none        0       0.33    
-       14 RateSig2    0.5       0.1         none       
-       15 FieldSig2   150       1           none
-
-The list of parameters used in the theory function to describe the set of data. 
-Each parameter has a number, a name, an initial value and an initial step (for 
-the fitting process). If a parameter should be fixed, the initial step is set 
-to 0. After a fit (see below), this block contains the determined parameter values 
-and uncertainties (in the ``Step`` column). If asymmetric errors are determined, these 
-will be listed in the ``Step`` column (negative) and the ``Pos_Error`` column (positive). 
-Optionally, lower and upper boundaries for the parameters can be specified as 
-shown above.
-       
-The meaning of the parameters above is explained in the following:
-
-Since a :ref:`single-histogram fit <single-histogram-fit>` should be done, some 
-histogram-specific parameters are needed. These are a normalization constant (parameter 1), 
-a parameter describing the background of uncorrelated events (parameter 2) and the initial 
-phase of the spin precession with respect to the detector (parameter 3). As stated above, 
-there are three histograms containing useful information ("Up", "Down", "Right"); hence, 
-this set of parameters has to be present for each of them (parameters 1–9).
-The remaining parameters are used to model the decay asymmetry which is assumed to be equal 
-for all histograms. In this example one has two signals (*e.g.* from the sample and the 
-sample holder), each with an amplitude (parameters 10 and 13), a depolarization rate 
-(parameters 11 and 14) and a mean field (here given in Gauss, parameters 12 and 15). 
-
-:ref:`The THEORY block <msr-theory-block>`
-
-::
-
-  THEORY
-  asymmetry     10
-  simplExpo     11          (rate)
-  TFieldCos   map1  fun1       (phase frequency)
-  +
-  asymmetry     13
-  simpleGss     14          (rate)
-  TFieldCos   map1  fun2       (phase frequency)
-  
-The THEORY block is used to define a fit-parameter-dependent theory function used to model 
-the decay asymmetry. Different :ref:`predefined <msr-theory-block>` and :ref:`user-defined <user-functions>` 
-functions can be combined here. Theory lines following each other are *multiplied* and the **+** sign 
-is used to add different (here: two) signal contributions. The numbers are the parameter numbers 
-according to the ``FITPARAMETER block``. ``map`` and ``fun`` are used to refer to 
-histogram-dependent parameters and to interrelate fit parameters, respectively (see below).  
-
-:ref:`The FUNCTIONS block <msr-functions-block>`
-
-::
-
-  FUNCTIONS
-  fun1 = gamma_mu * par12
-  fun2 = gamma_mu * par15
-  
-Here functions interrelating different fit parameters and predefined constants can be defined for 
-the use in the ``THEORY block``. In the example, the functions are used to calculate the 
-muon-spin-precession frequencies for the given fields [:math:`\nu = \gamma_\mu B / (2\pi)`]. One 
-function is used for each signal. Altogether, the theory function defined above is 
-:math:`A(t) = p_{10} e^{-p_{11} t} \cos(\varphi_i \pi/180 + \gamma_\mu p_{12} t) + p_{13} e^{-(p_{14} t)^2/2} \cos(\varphi_i \pi/180 + \gamma_\mu p_{15} t)`, where the *p* are the parameters in the ``FITPARAMETER block`` and :math:`\varphi_i = p_3, p_6, p_9` 
-depending on the histogram as shall be seen later.  
-
-:ref:`The RUN block <msr-run-block>`
-
-::
-
-  RUN data/deltat_pta_gps_3110 PIM3 PSI PSI-BIN   (name beamline institute data-file-format)
-  fittype         0         (single histogram fit)
-  norm            1
-  backgr.fit      2
-  map             3    0    0    0    0    0    0    0    0    0
-  forward         3       
-  data            1       8000    
-  t0              1     
-  fit             0       4.9    
-  packing         20  
-  
-The RUN blocks are used to collect information on the data to be analyzed. Specifically, these are: 
-
-  ::
-  
-    RUN data/deltat_pta_gps_3110 PIM3 PSI PSI-BIN   (name beamline institute data-file-format)
-    
-  The path to the data file and the file format (NEXUS, ROOT-NPP, ROOT-PPC, PSI-BIN, PSI-MDU, WKM, MUD, MDU-ASCII).
-  
-  ::
-  
-    fittype         0         (single histogram fit)
-    
-  the fit type (0 = single-histogram fit) 
-  
-  ::
-  
-    norm            1
-    
-  the number of the fit parameter representing the normalization constant 
-  
-  ::
-  
-    backgr.fit      2
-    
-  the number of the fit parameter representing the background 
-   
-  ::
-   
-    map             3    0    0    0    0    0    0    0    0    0
-     
-  the definition of the **maps** used in the ``THEORY block`` — RUN-block-specific 
-  parameters are given here; in this example, **map1** is substituted by **parameter 3** 
-  in the ``THEORY block`` for this RUN block and **map2**, **map3**, and so on are undefined.   
-   
-  ::
-   
-    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 |mgr|\s) 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.
-  
-:ref:`The COMMAND block <msr-commands-block>`
-
-::
-
-  COMMANDS
-  MINIMIZE
-  MINOS
-  SAVE
-  
-In the ``COMMANDS block``, a sequence of operations that should be performed is defined. 
-Here, the requested operations are the minimization of :math:`\chi^2` (MINIMIZE), the 
-calculation of *asymmetric errors* (MINOS) as well as saving the found parameter values 
-and uncertainties to the msr file (SAVE). A full description of the possible commands can 
-be found :ref:`here <msr-commands-block>`.   
-  
-:ref:`The FOURIER block <msr-fourier-block>`
-
-::
-  
-  FOURIER
-  units            Gauss   # units either 'Gauss', 'MHz', or 'Mc/s'
-  fourier_power    10
-  apodization      WEAK    # NONE, WEAK, MEDIUM, STRONG
-  plot             POWER   # REAL, IMAG, REAL_AND_IMAG, POWER, PHASE
-  phase            par3
-  range            0.0    600.0
-
-The ``FOURIER block`` is used to define basic settings for the Fourier transform available 
-in :ref:`musrview <musrview>`. These are: 
-  
-  ::
-  
-    units            Gauss   # units either 'Gauss', 'MHz', or 'Mc/s'
-    
-  the units of the Fourier domain 
-  
-  ::
-  
-    fourier_power    10
-    
-  the number of data points used for the discrete transform, here :math:`2^{10}=1024`.   
-  
-  ::
-  
-    apodization      WEAK    # NONE, WEAK, MEDIUM, STRONG
-    
-  the :ref:`apodization <msr-fourier-block-apodization>` to be used
-  
-  ::
-  
-    plot             POWER   # REAL, IMAG, REAL_AND_IMAG, POWER, PHASE 
-    
-  what should be plotted (real part, imaginary part, and so on) 
-  
-  ::
-  
-    phase            par3
-    
-  the initial phase of the input data is given here in degrees. Optionally, a phase parameter 
-  from the ``FITPARAMETER block`` can be given, here **par3** takes the value of **parameter 3**. 
-  
-  ::
-  
-    range            0.0    600.0
-    
-  the start and end points of the range of the Fourier transform in the units specified above 
-  
-:ref:`The PLOT block <msr-plot-block>`
-
-::
-
-  PLOT 0   (single histo plot)
-  runs     1   2   
-  range    0   4  -0.2   0.2
-  
-The ``PLOT block`` defines which data (corresponding to the given RUN blocks) is plotted when 
-:ref:`musrview <musrview>` is called. In the given example, a canvas would be drawn containing 
-the (life-time-corrected) data of the first two ``RUN blocks`` ("Up" and "Down" positron counters). 
-The abscissa would range from 0 to 4 |mgr|\s, the axis of ordinates from -0.2 to 0.2.
-It is possible to define more than one ``PLOT block``. Each ``PLOT block`` corresponds to a 
-separate canvas. Therefore, the second ``PLOT block`` in the file  
-
-::
-
-  PLOT 0   (single histo plot)
-  runs     3   
-  use_fit_ranges
-  
-produces an additional window containing the (not life-time-corrected) data of the third ``RUN block`` 
-("Right" positron counter). The abscissa ranges from 0 to 4.9 |mgr|\s (according to the fit range given 
-in the ``RUN block``).  
-
-:ref:`The STATISTIC block <msr-statistic-block>`
-
-::
-
-  STATISTIC --- 2011-07-09 10:58:44
-  chisq = 1348.1764, NDF = 1146, chisq/NDF = 1.176419
-  
-This block is the last block of a msr file. It contains some information on the fit: the 
-date and time as well as the absolute and normalized values of :math:`\chi^2` and the 
-number of degrees of freedom in the fit.
-These information only have a meaning if the fitting procedure has been executed at 
-least once and the fit has converged!   
-  
-Determine t0 and the data range using musrt0
-++++++++++++++++++++++++++++++++++++++++++++
-
-Before the given model can be fitted to the data, the data ranges and time zeros of the different 
-``RUN blocks`` have to be set correctly. This can be achieved using :ref:`musrt0 <musrt0>`. 
-Starting this program by selecting the ``musrt0`` button in ``musredit`` or calling from a terminal 
-
-.. code-block:: bash
-
-  $ musrt0 3110_tutorial.msr
-  
-opens an interactive window plotting the data of the first RUN block:  
-
-.. image:: ../images/tutorial-musrt0-1.*
-
-The green line (at bin 1) represents time zero, the blue lines the start (at bin 1) and end (at bin 8000) 
-of the data range and the optional red lines give the limits of the background range (if the background 
-shall not be determined by the fit). All lines can be either dragged to reasonable locations or set by 
-pressing the corresponding keyboard shortcuts. In the example the time zero can be set by pressing **T** 
-(which moves the green line to the bin containing the maximum number of counts), the start of the data 
-range should be set to about five bins later by zooming into the graph around bin 250 and pressing **d** 
-when the cursor is found at a suitable location:
-
-.. image:: ../images/tutorial-musrt0-2.*
-
-After all lines have been adjusted for the first histogram, one can go on to the second by pressing **q**. 
-This procedure is repeated until all ranges have been set correctly. When finished with the last histogram 
-the new t0 and data-range values will be written to the msr file. A full description of ``musrt0`` can be 
-found :ref:`here <musrt0>`.
-
-Fit the model to the data using ``musrfit``
-+++++++++++++++++++++++++++++++++++++++++++
-
-Now that the basics of the msr file have been introduced and the necessary adjustments have been done one 
-can proceed with fitting the specified model to the data. This is done by selecting the ``musrfit`` icon 
-in ``musredit`` or calling from a terminal 
-
-.. code-block:: bash
-
-  $ musrfit 3110_tutorial.msr
-  
-After the fitting procedure has finished the msr file is updated and contains the newly determined values 
-of the fit parameters.   
-
-View the data and the fit using ``musrview``
-++++++++++++++++++++++++++++++++++++++++++++
-
-The data and the corresponding fit can be visualized by choosing the ``musrview`` icon in ``musredit`` or 
-calling from a terminal 
-
-.. code-block:: bash
-
-  $ musrview 3110_tutorial.msr
-
-This creates the windows according to the given PLOT blocks in the msr file:
-
-.. image:: ../images/tutorial-musrview-1.*
-
-The basic features of ``musrview`` can be found in the ``Musrfit menu``. They include: 
-
-* export the shown data and the model to an ASCII file with comma-separated values
-* presenting the difference between the shown data and the model (keyboard shortcut: **d**)
-* calculate and show the Fourier transform of the shown data (keyboard shortcut: **f**), *e.g.* for 
-  the asymmetry of the "Up" and "Down" detectors:
-  
-.. image:: ../images/tutorial-musrview-FT.*
-
-Process multiple msr files using ``msr2data``
-+++++++++++++++++++++++++++++++++++++++++++++
-
-This short introduction is concluded by calling attention to the program :ref:`msr2data <msr2data>`. 
-As the name indicates the main purpose of this program is to extract the ``FITPARAMETER`` block 
-information from multiple msr files with the same structure and to summarize them in a single 
-ASCII file (either in ``TRIUMF DB`` format or simple columns). However, as described in detail 
-in the manual, it is not only possible to collect data from msr files but also to create new 
-msr files from a template and to process these files using ``musrfit`` on the fly.
-
-Assuming the successive runs **3111** through **3114** can be analyzed using the same model introduced 
-above for run **3110** (*e.g.* in the case one has done measurements at different temperatures) one can 
-use the file ``3110_tutorial.msr`` as template, generate the files ``3111_tutorial.msr`` through 
-``3114_tutorial.msr`` with the corresponding updates in the RUN blocks, call for each one ``musrfit`` 
-and finally summarize the FITPARAMETER block information of all processed files in an ASCII output 
-file ``tutorial-T-dependence.dat`` (simple columns). If further information on the temperature or the 
-applied field is available in the data files these will be included as well in the resulting ASCII file.
-From the terminal this would be done as follows:
-
-.. code-block:: bash
-
-  $ msr2data 3110 3114 _tutorial fit-3110 -o tutorial-T-dependence.dat data
-  
-To achieve the same in ``musredit`` (in this snapshot in the *dark theme*) one selects the ``msr2data`` icon and fills the form accordingly:  
-
-.. image:: ../images/tutorial-musredit-msr2data.*
-
-Further reading 
-+++++++++++++++
-
-This page only summarizes the very basic features and options of the programs contained in the ``musrfit`` suite. 
-For a complete description please refer to the manuals of :ref:`musrfit <musrfit>` (including :ref:`musrview <musrview>`, 
-:ref:`musrt0 <musrt0>`, and :ref:`musrFT <musrFT>`), :ref:`mupp <mupp>`, :ref:`musredit <musredit-sec>`, and :ref:`msr2data <msr2data>`. 
-
-Asymmtery-fit tutorial
-----------------------
-
-to be written yet.
diff --git a/doc/html/_sources/user-libs.txt b/doc/html/_sources/user-libs.txt
deleted file mode 100644
index 8e00db15..00000000
--- a/doc/html/_sources/user-libs.txt
+++ /dev/null
@@ -1,747 +0,0 @@
-:tocdepth: 3
-
-.. include:: <isogrk1.txt>
-.. index:: user-libs
-
-.. _user-libs:
-
-Documentation of user libs (user functions) 
-===========================================
-
-.. index:: BMW-libs
-.. _BMW-libs:
-
-Meissner-Profiles / Vortex-Lattice related functions (BMW libs)
----------------------------------------------------------------
-
-.. index:: libFitPofB
-
-libFitPofB
-++++++++++
-
-Introduction
-^^^^^^^^^^^^
-
-``libFitPofB`` is a collection of ``C++`` classes using the ``musrfit`` :ref:`user-functions <user-functions>` 
-interface in order to facilitate the usage in conjunction with ``musrfit``. The classes contained in this 
-library generally implement calculations of one-dimensional static magnetic field distributions 
-:math:`p(B)` which lead to the muon-spin depolarization functions 
-
-.. math::
-
-  {\cal P}(t) = \int p(B) \cos(\gamma_\mu B t + \varphi) dB,
-  
-where :math:`\gamma_\mu = 2 \pi \times 135.54` MHz/T is the gyromagnetic ratio of the muon and :math:`\varphi` 
-is the initial phase of the muon spins with respect to the positron detector. At the moment the only available 
-implementations deal with field distributions measured in local isotropic superconductors, either by means of 
-low-energy |mgr|\SR (see `<https://www.psi.ch/smus/lem>`_) in the Meissner state or by bulk |mgr|\SR 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.
-
-.. note:: 
-
-  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.
-  
-.. note:: 
-
-  The implementations in this library heavily rely on `FFTW3 <http://fftw.org/>`_. 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 <http://fftw.org/fftw3_doc/Wisdom.html>`_). In case this feature shall be used, a valid wisdom 
-  file has to be specified in the ``XML`` file. 
-  
-.. note::
-
-  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. 
-   
-.. note::
-
-  If these classes still prove useful and results obtained through them are part of scientific publications, 
-  an acknowledgment of the use of the library is appreciated.
-  
-LE-|mgr|\SR
-^^^^^^^^^^^
-
-.. index:: 1D-London-Meissner
-
-One-dimensional London model for the Meissner state of isotropic superconductors 
-""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
-
-The models for analyzing LE-|mgr|\SR data assume the magnetic induction :math:`B(z)` to vary only in the 
-dimension parallel to the momentum of the incident muons. In such a case the magnetic field distribution is given by 
-
-.. math::
-
-  p(B) = n(z) \left| \frac{dB(z)}{dz} \right|^{-1}
-  
-where :math:`n(z)` is the muon implantation profile simulated by ``TRIM.SP``. 
-
-Assuming an array of *N* isotropic local superconductors with a total thickness *d* in the Meissner state 
-the magnetic induction is given by solving the 1D London equation 
-
-.. math::
-
-   \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 (F. London, Superfluids: Macroscopic Theory of Superconductivity, Dover (1961), p. 34)
-
-.. math:: 
-
-   B_1(0) = B_N(d) = \mu_0H
-   
-   B_i(d_i) = B_{i+1}(d_i)
-   
-   \lambda_i^2B_i'(z)\Big\vert_{z=d_i} = \lambda_{i+1}^2B_{i+1}'(z)\Big\vert_{z=d_i}, 
-   
-where the :math:`d_i` specify the interfaces between two adjacent layers and :math:`\lambda_i` is 
-the magnetic field penetration depth in the constituent :math:`i`.
-
-The calculation of the field distribution has been set up for a superconducting half-space as well 
-as superconducting thin films with up to three superconducting layers with different penetration depths. 
-The muon-spin depolarization functions are calculated using the following lines in the ``THEORY`` block 
-of a ``musrfit`` msr file: 
-
-.. index:: TLondon1DHS
-
-**Superconducting half-space**
-
-::
-
-  userFcn  libFitPofB TLondon1DHS 1 2 3 4 5
-
-The parameters are:
-
-#. phase (deg)
-#. muon implantation energy as specified in the :ref:`XML startup <BMWlibs-XML>` file (keV)
-#. applied field (G)
-#. thickness of the dead layer (nm)
-#. magnetic field penetration depth (nm) 
-
-.. index:: TLondon1D1L
-
-**Superconducting thin film (one layer)**
-
-:: 
-
-  userFcn  libFitPofB TLondon1D1L 1 2 3 4 5 6 [a b]
-  
-The mandatory parameters are:
-
-#. phase (deg)
-#. muon implantation energy as specified in the :ref:`XML startup <BMWlibs-XML>` file (keV)
-#. applied field (G)
-#. thickness of the dead layer (nm)
-#. thickness of the actually superconducting layer (nm)
-#. magnetic field penetration depth (nm)   
-
-The optional parameters are:
-
-a. fraction f\ :sub:`1` of muons in the thin film contributing to the signal (0 ≤ f\ :sub:`1` ≤ 1)
-b. fraction f\ :sub:`s` of muons in the substrate contributing to the signal (0 ≤ f\ :sub:`s` ≤ 1)
-
-.. index:: TLondon1D2L
-
-**Superconducting thin-film bilayer heterostructure**
-
-::
-
-  userFcn  libFitPofB TLondon1D2L 1 2 3 4 5 6 7 8 [a b c]
-       
-The mandatory parameters are:
-
-#. phase (deg)
-#. muon implantation energy as specified in the :ref:`XML startup <BMWlibs-XML>` file (keV)
-#. applied field (G)
-#. thickness of the dead layer (nm)
-#. thickness of the actually superconducting first layer (nm)
-#. thickness of the actually superconducting second layer (nm)
-#. magnetic field penetration depth of the first layer (nm)
-#. magnetic field penetration depth of the second layer (nm) 
-
-The optional parameters are:
-
-a. fraction f\ :sub:`1` of muons in the dead and first layer contributing to the signal (0 ≤ f\ :sub:`1` ≤ 1)
-b. fraction f\ :sub:`2` of muons in the second layer contributing to the signal (0 ≤ f\ :sub:`2` ≤ 1)
-c. fraction f\ :sub:`s` of muons in the substrate contributing to the signal (0 ≤ f\ :sub:`s` ≤ 1) 
-
-.. index:: TLondon1D3L
-
-**Superconducting thin-film trilayer heterostructure**
-
-::
-
-  userFcn  libFitPofB TLondon1D3L 1 2 3 4 5 6 7 8 9 10 [a b c d]
-
-The mandatory parameters are:
-
-#. phase (deg)
-#. muon implantation energy as specified in the :ref:`XML startup <BMWlibs-XML>` file (keV)
-#. applied field (G)
-#. thickness of the dead layer (nm)
-#. thickness of the actually superconducting first layer (nm)
-#. thickness of the actually superconducting second layer (nm)
-#. thickness of the actually superconducting third layer (nm)
-#. magnetic field penetration depth of the first layer (nm)
-#. magnetic field penetration depth of the second layer (nm)
-#. magnetic field penetration depth of the third layer (nm) 
-
-The optional parameters are:
-
-a. fraction f\ :sub:`1` of muons in the dead and first layer contributing to the signal (0 ≤ f\ :sub:`1` ≤ 1)
-b. fraction f\ :sub:`2` of muons in the second layer contributing to the signal (0 ≤ f\ :sub:`2` ≤ 1)
-c. fraction f\ :sub:`3` of muons in the third layer contributing to the signal (0 ≤ f\ :sub:`3` ≤ 1)
-d. fraction f\ :sub:`s` of muons in the substrate contributing to the signal (0 ≤ f\ :sub:`s` ≤ 1) 
-   
-Bulk |mgr|\SR
-^^^^^^^^^^^^^
-
-.. index:: Vortex-State-Isotropic
-
-Field distributions in the mixed state of isotropic superconductors 
-"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
-
-When investigating superconductors in the mixed state by means of conventional |mgr|\SR a 
-two-dimensional flux-line lattice is probed randomly by the muons. The spatial field 
-distributions within such an ordered lattice are modeled using the Fourier series
-
-.. math::
-
-   B(\mathbf{r}) = \langle B \rangle \sum\limits_{\mathbf{K}}B_{\mathbf{K}}\exp(-\imath\mathbf{K}\mathbf{r}), 
-   
-where :math:`\mathbf{r}=(x,y)`, **K** are the reciprocal lattice vectors of a two-dimensional 
-vortex lattice and the :math:`B_{\mathbf{K}}` are the Fourier coefficients depending on the 
-magnetic penetration depth :math:`\lambda` and the superconducting coherence length :math:`\xi`. 
-The :math:`B_{\mathbf{K}}` for some specific models are as follows:    
-
-**London model with Gaussian cutoff** (E.H. Brandt, `J. Low Temp. Phys. 73, 355 (1988) <http://dx.doi.org/10.1007/BF00683568>`_.)
-
-.. math::
-
-   B_{\mathbf{K}} = \frac{\exp\left({-K^2\xi^2/2}\right)}{1 + K^2\lambda^2}
-
-**Modified London model** (T.M. Riseman *et al.*, `Phys. Rev. B 52, 10569 (1995) <http://dx.doi.org/10.1103/PhysRevB.52.10569>`_.)   
-
-.. math::
-   
-  B_{\mathbf{K}} = \frac{\exp\left({-K^2\xi^2/2(1-b)}\right)}{1 + K^2\lambda^2/(1-b)},
-    
-where :math:`b = \langle B \rangle / (\mu_0 H_{\rm c2})`. 
-
-**Analytical Ginzburg-Landau model** ( A. Yaouanc, P. Dalmas de Réotier and E.H. Brandt, `Phys. Rev. B 55, 11107 (1997) <http://dx.doi.org/10.1103/PhysRevB.55.11107>`_)
-
-.. math::
-
-  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 :math:`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
-:math:`K_1` is a modified Bessel function.
-
-Apart from the mentioned analytic models the **numerical Ginzburg-Landau model** (`E.H. Brandt, Phys. Rev. B 68, 054506 (2003). <http://dx.doi.org/10.1103/PhysRevB.68.054506>`_) is available. In this case :math:`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!**
-
-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 :ref:`XML startup <BMWlibs-XML>`.
-The muon-spin depolarization functions finally are calculated using the following lines in the THEORY block of a ``musrfit`` msr file: 
-
-.. index:: Vortex-Gaussian-CutOff
-
-**2D triangular vortex lattice, London model with Gaussian cutoff** 
-
-::
-
-  userFcn  libFitPofB TBulkTriVortexLondon 1 2 3 4
-  
-The parameters are:
-
-#. phase (deg)
-#. mean magnetic induction (G)
-#. magnetic penetration depth (nm)
-#. Ginzburg-Landau coherence length (nm)   
-
-.. index:: Vortex-London-modified
-
-**2D triangular vortex lattice, modified London model**
-
-::
-
-  userFcn  libFitPofB TBulkTriVortexML 1 2 3 4
-  
-The parameters are:
-
-#. phase (deg)
-#. mean magnetic induction (G)
-#. magnetic penetration depth (nm)
-#. Ginzburg-Landau coherence length (nm)   
-
-.. index:: Vortex-Analytic-GL
-
-**2D triangular vortex lattice, analytic Ginzburg-Landau model** 
-
-::
-
-  userFcn  libFitPofB TBulkTriVortexAGL 1 2 3 4
-  
-The parameters are:
-
-#. phase (deg)
-#. mean magnetic induction (G)
-#. magnetic penetration depth (nm)
-#. Ginzburg-Landau coherence length (nm) 
-
-.. index:: Vortex-Numeric-GL
-
-**2D triangular vortex lattice, numerical Ginzburg-Landau model**
-
-::
-
-  userFcn  libFitPofB TBulkTriVortexNGL 1 2 3 4
-  
-The parameters are:
-
-#. phase (deg)
-#. mean magnetic induction (G)
-#. magnetic penetration depth (nm)
-#. Ginzburg-Landau coherence length (nm) 
-
-.. note::
-
-  In order to improve the convergence of ``MIGRAD`` it has proven useful to use the log-likelihood 
-  maximization instead of the :math:`\chi^2` minimization routines and to choose sufficiently large 
-  initial steps for the parameters. Calling ``MINOS`` in conjunction with these functions is futile.
-
-Therefore, the :ref:`COMMANDS block <msr-commands-block>` of the msr file could look like:   
-
-::
-
-  COMMANDS
-  STRATEGY 2
-  MAX_LIKELIHOOD
-  MIGRAD
-  HESSE
-  SAVE
-  
-.. index:: BMWlibs-XML
-.. _BMWlibs-XML:
-   
-The XML startup file
-^^^^^^^^^^^^^^^^^^^^
-
-``BMW_startup.xml`` is a configuration file located in the working directory. In this file some settings 
-like the time and field resolution of the calculations as well as the present muon implantation profiles 
-for a LE-|mgr|\SR analysis have to be defined. The following XML tags are allowed to define settings: 
-
-**<debug>ONE_OR_ZERO</debug>**
-  activate the debugging output of the settings read from the XML file by setting 1, deactivate it with 0.
-**<wisdom>PATH_TO_FILE</wisdom>**
-  specify the ``PATH_TO_FILE`` to an `FFTW3 wisdom file <http://fftw.org/fftw3_doc/Wisdom.html#Wisdom>`_ 
-  that should be used; if the ``PATH_TO_FILE`` is invalid, no ``FFTW3`` wisdom will be used.
-**<delta_t>ResT</delta_t>**
-  set the time resolution ``ResT`` for the calculated depolarization function in microseconds.
-**<delta_B>ResB</delta_B>**
-  set the field resolution ``ResB`` for the calculated field distribution in Gauss.
-**<VortexLattice></VortexLattice>**
-  set the parameters used for the calculation of the spatial field distribution of a vortex lattice.
-  
-  **<N_VortexGrid>N</N_VortexGrid>**
-    specify the number of points **N** (in each of the two dimensions) for which the fields within the 
-    vortex lattice are calculated (inside a **<VortexLattice>** environment) 
-    
-**<LEM></LEM>**     
-  set the parameters used for the calculation of LE-|mgr|\SR field distributions 
-  
-  **<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>E</energy>**
-      specify the muon energy *E* (in keV) belonging to the ``TRIM.SP`` ``RGE`` file given above (inside a **<energy_list>** environment)   
-      
-An example XML file looks as follows:      
-
-.. code-block:: xml
-
-  <?xml version="1.0" encoding="UTF-8"?>
-  <BMW>
-    <debug>0</debug>
-    <wisdom>/home/user/WordsOfWisdom.dat</wisdom>
-    <delta_t>0.01</delta_t>
-    <delta_B>0.5</delta_B>
-    <VortexLattice>
-      <N_VortexGrid>1024</N_VortexGrid>
-    </VortexLattice>
-    <LEM>
-      <data_path>/home/user/TrimSP/some-sample-</data_path>
-      <N_theory>5000</N_theory>
-      <energy_list>
-        <energy_label>02_0</energy_label>
-        <energy>2.0</energy>
-        <energy_label>03_0</energy_label>
-        <energy>3.0</energy>
-        <energy_label>03_6</energy_label>
-        <energy>3.6</energy>
-        <energy_label>05_0</energy_label>
-        <energy>5.0</energy>
-        <energy_label>05_3</energy_label>
-        <energy>5.3</energy>
-      </energy_list>
-    </LEM>
-  </BMW>
-  
-Nonlocal superconductivity related Meissner screening functions (AS libs) 
--------------------------------------------------------------------------
-
-To be written yet ...
-  
-.. index:: BNMR-libs
-.. _BNMR-libs:
-
-Functions to analyze |bgr|-NMR data (BNMR libs) 
--------------------------------------------------------------------------
-
-This is a collection of ``C++`` classes using the ``musrfit`` :ref:`user-functions <user-functions>` 
-interface in order to facilitate the usage in conjunction with ``musrfit``. It consists of two libraries: 
-
-* ``libBNMR`` contains functions to fit spin lattice relaxation (SLR) data.
-* ``libLineProfile`` contains functions to fit resonance lineshapes.
-
-
-.. note:: 
-
-  Currently it is recommended to read in the data in ASCII format as a non-|mgr|\SR fit  :ref:`(fit type 8) <non-musr-fit>`.
-
-.. index:: libBNMR
-
-libBNMR
-++++++++++
-
-In |bgr|-NMR the SLR is usually measured by implanting a pulse of :math:`^8`\ Li with a length :math:`t_0` into the sample. 
-The asymmetry is measured both during the pulse and afterwards. For a a general spin relaxation function :math:`f(t)` the time evolution of the asymmetry is then given by [`Z. Salman, et al., PRL 96, 147601 (2006) <http://dx.doi.org/10.1103/PhysRevLett.96.147601>`_]: 
-
-
-
-.. index:: SLR
-.. _SLR:
-
-.. math::  
-   P(t) = \left\{\begin{matrix}
-  \frac{\int_0^t e^{-(t-t')/\tau_{\mathrm{Li}}}f(t-t')dt'}{\int_0^t e^{-t'/\tau_{\mathrm{Li}}}dt' }       &  t\leq t_0\\[6pt]
-  \frac{\int_0^{t_0}e^{-(t_0-t')/\tau_{\mathrm{Li}}}f(t-t')dt'}{\int_0^{t_0}e^{-t'/\tau_{\mathrm{Li}}}dt'}    &  t> t_0,
-  \end{matrix}\right.
-
-where :math:`\tau_{\mathrm{Li}}=1.21`\ s is the :math:`^8`\ Li lifetime.
-
-
-Functions
-^^^^^^^^^^^^
-The ``libBNMR`` library currently contains the following functions:
-
-
-
-
-.. index:: ExpRlx
-
-**Exponential relaxation**
-
-::
-
-  userFcn libBNMR ExpRlx 1 2
-
-The parameters are:
-
-#. pulse length :math:`t_0` (s)
-#. relaxation rate :math:`\lambda` (s\ :math:`^{-1}`\ )
-
-This function implements :math:`f(t)=e^{-\lambda t}`.
-
-.. index:: SExpRlx
-
-**Stretched exponential relaxation**
-
-::
-
-  userFcn libBNMR SExpRlx 1 2 3
-
-The parameters are:
-
-#. pulse length :math:`t_0` (s)
-#. relaxation rate :math:`\lambda` (s\ :math:`^{-1}`\ )
-#. stretching exponent :math:`\beta`
-
-This function implements :math:`f(t)=e^{-(\lambda t)^{\beta}}`.
-
-
-  
-.. index:: libLineProfile
-
-libLineProfile
-+++++++++++++++++
-In addition to some simple line shapes ``libLineProfile`` contains functions to fit chemical shift anisotropies in the powder average.
-Their functional form can be found in  `M. Mehring, Principles of High Resolution NMR in Solids (Springer 1983) <http://dx.doi.org/10.1007/978-3-642-68756-3_2>`_.
-
-For an axially symmetric interaction it is given by:
-
-.. index:: Iax
-.. _Iax:
-
-.. math::
-
-      I_{\mathrm ax}(f)=\left\{\begin{matrix} \frac{1}{2\sqrt{(f_\parallel-f_\perp)(f-f_\perp)}}& f\in(f_\perp,f_\parallel)\cup(f_\parallel,f_\perp)\\[6pt] 0 & \text{otherwise}\end{matrix} \right.
-
-where :math:`f_\parallel` and :math:`f_\perp` are the frequencies that would be observed if the field is oriented paralell or perpendicular to the symmetry axis, respectively.
-
-
-| In case of a completely anisotropic interaction, the powder average can be described by the frequencies along the three principle axis :math:`f_1,f_2,f_3`.
-| Assume without loss of generality that :math:`f_1<f_2<f_3`, then
-
-.. index:: Ianiso
-.. _Ianiso:
-
-.. math::  
-      I(f)&=\left\{\begin{matrix}
-        \frac{K(m)}{\pi\sqrt{(f-f_1)(f_3-f_2)}},& f_3\geq f>f_2 \\[9pt]
-        \frac{K(m)}{\pi\sqrt{(f_3-f)(f_2-f_1)}},& f_2>f\geq f_1\\[9pt]
-        0 & \text{otherwise}
-      \end{matrix} \right.  \\
- 	\\
-      m&=\left\{\begin{matrix}
-        \frac{(f_2-f_1)(f_3-f)}{(f_3-f_2)(f-f_1)},& f_3\geq f>f_2 \\[6pt]
-        \frac{(f-f_1)(f_3-f_2)}{(f_3-f)(f_2-f_1)},& f_2>f\geq f_1\\[6pt]
-      \end{matrix} \right.  \\
- 	\\
-      K(m)&=\int_0^{\pi/2}\frac{\mathrm d\varphi}{\sqrt{1-m^2\sin^2{\varphi}}},
-
-
-:math:`K(m)` is the complete elliptic integral of the first kind.
-
-
-
-Functions
-^^^^^^^^^^^^
-The ``libLineProfile`` library currently contains the following functions:
-
-
-
-
-.. index:: LineGauss
-
-**Gaussian**
-
-::
-
-  userFcn  libLineProfile LineGauss 1 2
-
-The parameters are:
-
-#. center of the line :math:`f_0`
-#. FWHM of the line :math:`\sigma`
-
-| The height of the peak is 1.
-| The functional form is given by
-
-.. math::
-   A(f)=e^{-\frac{4\ln 2 (f-f_0)^2}{ \sigma^2}}
-
-
-.. index:: LineLorentzian
-
-**Lorentzian**
-
-::
-
-  userFcn  libLineProfile LineLorentzian 1 2
-
-The parameters are:
-
-#. center of the line :math:`f_0`
-#. FWHM of the line :math:`w`
-
-| The height of the peak is 1. 
-| The functional form is given by
-
-.. math::
-    A(f)= \frac{w^2}{4(f-f_0)^2+w^2}
-
-
-.. index:: LineLaplace
-
-**Laplacian**
-
-::
-
-  userFcn  libLineProfile LineLaplace 1 2
-
-The parameters are:
-
-#. center of the line :math:`f_0`
-#. FWHM of the line :math:`w`
-
-| The height of the peak is 1. 
-| The functional form is given by
-
-.. math::
- A(f)=e^{-2\ln 2 \left|\frac{f-f_0}{w}\right|}
-
-
-
-.. index:: LineSkewLorentzian
-
-**Skewed Lorentzian**
-
-::
-
-  userFcn  libLineProfile LineSkewLorentzian 1 2 3
-
-The parameters are:
-
-#. center of the line :math:`f_0`
-#. width of the line :math:`w`
-#. skewness parameter :math:`a`
-
-| The height of the peak is 1. 
-| The functional form is given by
-
-.. math::
-    A(f)=  \frac{w w_a}{4(f-f_0)^2+w_a^2}, \quad w_a=\frac{2w}{1+e^{a(f-f_0)}}
-
-
-
-.. index:: LineSkewLorentzian2
-
-**Skewed Lorentzian 2**
-
-::
-
-  userFcn  libLineProfile LineSkewLorentzian2 1 2 3
-
-The parameters are:
-
-#. center of the line :math:`f_0`
-#. width left of the center :math:`w_1`
-#. width right of the center :math:`w_2`
-
-| The height of the peak is 1. 
-| The functional form is given by
-
-.. math::
-    A(f)=  \left\{\begin{matrix}\frac{{w_1}^2}{4{(f-f_0)}^2+{w_1}^2},&f\leq f_0\\[9pt] \frac{{w_2}^2}{4{(f-f_0)}^2+{w_2}^2},&f>f_0\end{matrix}\right.
-
-
-
-.. index:: PowderLineAxialLor
-
-
-**Powder average of an axially symmetric interaction convoluted with a Lorentzian**
-
-::
-
-  userFcn  libLineProfile PowderLineAxialLor 1 2 3
-
-The parameters are:
-
-#.  frequency for the field oriented paralell to the symmetry axis :math:`f_\parallel`
-#.  frequency for the field oriented perpendicular to the symmetry axis :math:`f_\parallel`
-#.  FWHM of the Lorentzian :math:`w`
-
-| The height of the peak is :math:`\sim`\ 1. 
-| The functional form is given by
-
-.. math::
-    A(f)= I_{\mathrm ax}(f)\circledast\left( \frac{w^2}{4f^2+w^2} \right)
-
-with :math:`I_{\mathrm ax}(f)` defined :ref:`above <Iax>`.
-
-    
-
-.. index:: PowderLineAxialGss
-
-
-**Powder average of an axially symmetric interaction convoluted with a Gaussian**
-
-::
-
-  userFcn  libLineProfile PowderLineAxialGss 1 2 3
-
-The parameters are:
-
-#.  frequency for the field oriented paralell to the symmetry axis :math:`f_\parallel`
-#.  frequency for the field oriented perpendicular to the symmetry axis :math:`f_\parallel`
-#. FWHM of the Gaussian :math:`\sigma`
-
-| The height of the peak is :math:`\sim`\ 1. 
-| The functional form is given by
-
-.. math::
-    A(f)= I_{\mathrm ax}(f)\circledast\left( e^{-\frac{4\ln 2 (f-f_0)^2}{ \sigma^2}} \right)
-
-with :math:`I_{\mathrm ax}(f)` defined :ref:`above <Iax>`.
-
-  
-
-.. index:: PowderLineAsymLor
-
-
-**Powder average of an anisotropic interaction convoluted with a Lorentzian**
-
-::
-
-  userFcn  libLineProfile PowderLineAsymLor 1 2 3 4
-
-The parameters are:
-
-#.   :math:`f_1`
-#.   :math:`f_1`
-#.   :math:`f_3` frequencies along the principal axes
-#. FWHM of the Lorentzian :math:`w`
-
-| The height of the peak is :math:`\sim`\ 1. 
-| The functional form is given by
-
-.. math::
-    A(f)= I(f)\circledast\left( \frac{w^2}{4f^2+w^2} \right)
-
-with :math:`I(f)` defined :ref:`above <Ianiso>`. Note that :math:`f_1<f_2<f_3` is not required by the code.
-  
-    
-    
-.. index:: PowderLineAsymGss
-
-
-**Powder average of an anisotropic interaction convoluted with a Gaussian**
-
-::
-
-  userFcn  libLineProfile PowderLineAsymGss 1 2 3 4
-
-The parameters are:
-
-#.   :math:`f_1`
-#.   :math:`f_1`
-#.   :math:`f_3` frequencies along the principal axes
-#. FWHM of the Gaussian :math:`\sigma`
-
-| The height of the peak is :math:`\sim`\ 1. 
-| The functional form is given by
-
-.. math::
-    A(f)= I(f)\circledast\left( e^{-\frac{4\ln 2 (f-f_0)^2}{ \sigma^2}} \right)
-
-with :math:`I(f)` defined :ref:`above <Ianiso>`. Note that :math:`f_1<f_2<f_3` is not required by the code.
-
-
-
diff --git a/doc/html/_sources/user-manual.txt b/doc/html/_sources/user-manual.txt
deleted file mode 100644
index 75e2e0b0..00000000
--- a/doc/html/_sources/user-manual.txt
+++ /dev/null
@@ -1,2421 +0,0 @@
-:tocdepth: 3
-
-.. include:: <isogrk1.txt>
-.. index:: user-manual
-
-.. _user-manual:
-
-User manual
-===========
-
-Introduction
-------------
-
-``musrfit`` is a software tool for analyzing time-differential |mgr|\SR data. The program suite is `free software <http://www.gnu.org/philosophy/free-sw.html>`_ and licensed under the `GNU GPL version 2 <http://www.gnu.org/licenses/old-licenses/gpl-2.0.html>`_ or any later version (at your option). It is implemented in ``C++``/ROOT and uses the `MINUIT2 <http://seal.web.cern.ch/seal/MathLibs/Minuit2/html/index.html>`_ libraries developed at `CERN <http://www.cern.ch/>`_ for fitting data. Installation instructions for GNU/Linux, MS Windows, and macOS can be found under :ref:`musrfit setup <musrfit-setup>`. Recent changes of the program can be followed on the git, either `bitbucket <https://bitbucket.org/muonspin/musrfit>`_ or `gitlab <https://gitlab.psi.ch/nemu/musrfit>`_.
-
-Available Executables, Configuration Files and their Basic Usage
-----------------------------------------------------------------
-
-The philosophy is that users, based on their abilities or preferences, can work on the command line are in a more GUI based setting. Here, the command line based tools will be described. The GUI based parts are described in the :ref:`musredit <musredit-sec>`.
-
-.. index:: musrfit
-.. _musrfit:
-
-musrfit
-+++++++
-
-``musrfit`` is the actual fitting program. It defines the FCN routine passed to ``MINUIT2`` and performs :math:`\chi^2` or log-max-likelihood fitting. If called from within a shell it accepts several parameters: 
-
-**<msr-file>**
-   filename of the msr input file defining all the details needed for performing a fit to a specified set of data. This is the only mandatory parameter.
-**-k, - -keep-mn2-output**
-   selects the option for keeping the output of ``MINUIT2`` including the correlation coefficients between different parameters and renaming the files ``MINUIT2.OUTPUT`` and ``MINUIT2.root`` to ``<msr_file_without_extension>-mn2.output`` and ``<msr_file_without_extension>-mn2.root``, respectively, *e.g.* ``<msr_file>`` = ``8472.msr`` will result in ``8472-mn2.output``, ``8472-mn2.root``.
-**-c, - -chisq-only**
-   Instead of fitting the model, ``musrfit`` calculates :math:`\chi^2` or max. log-likelihood, maxLH, only once and sends the result to the standard output if called with this option. This is *e.g.* 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. 
-**-e, - -estimateN0**   
-   estimate :math:`N_0` for single histogram fits.
-**-p, - -per-run-block-chisq** 
-   will write per run block chisq/maxLH into the msr-file.
-**- -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 of 3600 sec. <timeout_tag> :math:`\leq` 0 means the timeout facility is not enabled. <timeout_tag> > 0, *e.g.* ``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`` processes 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``
-
-If called with a msr input file, *e.g.*
-
-.. code-block:: bash
-
-   $ musrfit 8472.msr
-   
-the fit described in the input file will be executed and the results will be written to a mlog output file, in the example ``8472.mlog``. When the fitting has terminated the msr file and the mlog file are swapped, so that the resultant parameter values can be found in the msr file and the mlog file contains a copy of the input file. The format of the mlog file is the same as that of the msr file. For a detailed description of the msr file format refer to the :ref:`corresponding section <msr-file-format>`.   
-
-Another example: 
-
-.. code-block:: bash
-
-   $ musrfit -c -e 8472_tf_histo.msr
-
-This will calculate the chisq/maxLH of the run 8472 after estimating the :math:`N_0`. 
-
-.. index:: musrview
-.. _musrview:
-
-musrview
-++++++++
-
-``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 is the only mandatory parameter.
-**- -help**
-  displays a small help notice in the shell explaining the basic usage of the program.
-**- -version**  
-  prints the version number of ``musrview``.
-**-f, - -fourier**  
-  will directly present the Fourier transform of the <msr_file> with Fourier options as defined in the <msr_file>. 
-**-a, - -avg**  
-  will directly present the averaged data/Fourier of the <msr_file>. 
-**-1, - -one_to_one**
-  calculate the theory points *only* at the data points.
-**- -<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 will result in 8472_0.png.
-  Supported values for ``<graphic_format_extension>`` are *eps*, *pdf*, *gif*, *jpg*, *png*, *svg*, *xpm*, and, *root*.
-**- -ascii**  
-  will generate an ascii dump of the data and theory as plotted. 
-**- -timeout <timeout>**
-  <timeout> given in seconds after which ``musrview`` terminates. If <timeout> :math:`\leq` 0, no timeout will take place. Default for <timeout> is 0. 
-  
-If called with a msr file and the ``--<graphic_format_extension>`` option, *e.g.* :: 
-
-   $ musrview 8472.msr --jpg
-
-for each PLOT block in the the msr file a file ``8472_X.jpg`` is produced where ``X`` counts the PLOT blocks starting from zero. 
-
-If called only with a msr file, *e.g.*
-
-.. code-block:: bash
-
-   $ musrview 8472.msr
-
-a ROOT canvas is drawn; it contains all experimental data and fits specified in the PLOT block of the msr file. For a description of the various plotting types refer to the :ref:`corresponding section <msr-file-format>`.
-
-Another example: 
-
-.. code-block:: bash
-
-   $ musrview 8472_tf_histo.msr -f -a
-
-will show the averaged Fourier transform of the data of run 8472.    
-
-Within the drawn canvas all standard actions applicable to ROOT canvases might be performed. In the menu bar the Musrfit menu can be found. From there some musrfit-specific actions might be taken: 
-
-**Fourier**
-  performs the Fourier transformation of the *selected data* and shows the result.
-**Difference**  
-  shows the difference between the selected data and the fit.
-**Average**
-  toggle between the current view and the averaged data view. Useful if the averaged Fourier power spectrum of lots of detectors shall be shown. 
-**Export Data**  
-  saves the selected data in a simple multi-column ASCII file.
-  
-.. index:: musrview-key-shortcuts
-
-musrview key-shortcuts
-^^^^^^^^^^^^^^^^^^^^^^
-
-Additionally, some functions can be accessed using *key-shortcuts*: 
-
-**q**
-  quits musrview.
-**d**
-  shows the difference between the selected data and the fit.
-**f**
-  performs the Fourier transformation of the selected data and shows the result.
-**a**
-  show the average of the presented data, *e.g.* the averaged Fourier power spectra of various detectors.
-**u**
-  reset the plotting range to the area given in the msr file ("un-zoom").
-**c**  
-  toggles between normal and cross-hair cursor.
-**t**
-  a plot of a **single** data set allows to toggle the color of the theory function line.
-    
-  
-.. index:: musrFT
-.. _musrFT:
-
-musrFT
-++++++
-
-``musrFT`` is an interactive graphical user interface for the presentation of Fourier transforms of *raw* |mgr|\SR histograms. It's purpose is to get a quick overview for high TF-field data, as found *e.g.* at the HAL-9500 instrument at PSI. It Fourier transforms the raw histogram data, i.e. :math:`N(t)` rather than :math:`A(t)`, and hence shows the lifetime contribution of the muon decay. This is no problem for large enough fields, but will be a *severe* problem at very low fields. ``musrFT`` is still in its early stage and should be considered a beta-version. 
-
-If called from within a shell it accepts the following parameters:
-
-**Input Files**
-  **<msr_files>**
-    msr-file name(s). These msr-files are used for the Fourier transform. It can be a list of msr-files, *e.g.* ``musrFT 3110.msr 3111.msr``
-  **-df, - -data-file <data-file>**
-    This allows to feed only |mgr|\SR data file(s) to perform the Fourier transform. Since the extended <msr-file> information are missing, they will need to be provided by to options, or ``musrFT`` tries to guess, based on :ref:`musrfit_startup.xml <musrfit-startup>` settings.
-**Options**
-  **- -help**
-    display a help and exit.
-  **- -version** 
-    output version information and exit.
-  **-g, - -graphic-format <graphic-format-extension>** 
-    will produce a graphic-output-file without starting a root session. The name is based either on the <msr-file> or the <data-file>, *e.g.* ``3310.msr -> 3310_0.png``. Supported graphic-format-extension: *eps*, *pdf*, *gif*, *jpg*, *png*, *svg*, *xpm*, and *root*. 
-  **- -dump <fln>**    
-    rather than starting a root session and showing Fourier graphs of the data, it will output the Fourier data in an ascii file <fln>. 
-  **-br, - -background-range <start> <end>**
-    background interval used to estimate the background to be subtracted before the Fourier transform. <start>, <end> to be given in bins. 
-  **-bg, - -background**
-    gives the background explicit for each histogram. 
-  **-fo, - -fourier-option <fopt>**
-    <fopt> can be '*real*', '*imag*', '*real+imag*', '*power*', or '*phase*'. If this is not defined (neither on the command line nor in the :ref:`musrfit_startup.xml <musrfit-startup>`) '*power*' will be used. 
-  **-ap, - -apodization <val>**
-    <val> can be either '*none*', '*weak*', '*medium*', '*strong*'. Default will be '*none*'.
-  **-fp, - -fourier-power <N>**
-    <N> being the Fourier power, i.e. ``2^<N>`` used for zero padding. Default is -1, i.e. *no* zero padding will be performed. 
-  **-u, - -units <units>**
-    <units> is used to define the abscissa of the Fourier transform. One may choose between the fields (*Gauss*) or (*Tesla*), the frequency (*MHz*), and the angular-frequency domain (*Mc/s*). Default will be '*MHz*'.
-  **-ph, - -phase <val>**    
-    defines the initial phase <val>. This only is of concern for '*real*', '*imag*', and '*real+imag*'. Default will be 0.0.
-  **-fr, - -fourier-range <start> <end>**    
-    Fourier range. <start>, <end> are interpreted in the units given. Default will be -1.0 for both which means, take the full Fourier range. 
-  **-tr, - -time-range <start> <end>**     
-    time domain range to be used for Fourier transform. <start>, <end> are to be given in (|mgr|\s). If nothing is provided, the full time range found in the data file(s) will be used.
-  **- -histo <list>**
-    give the <list> of histograms to be used for the Fourier transform. *E.g.* ``musrFT -df lem15_his_01234.root --histo 1 3``, will only be needed together with the option ``--data-file``. If multiple data files are given, <list> will apply to all data-files given. If ``--histo`` is not given, *all* histos of a data file will be used. <list> can be anything like: 2 3 6, or 2-17, or 1-6 9, etc. 
-  **-a, - -average**    
-    show the average of all **ALL** Fourier transformed data. 
-  **-ad, - -average-per-data-set**
-    show the average of **per-data-set** Fourier transformed data. 
-  **- -t0 <list>**    
-    A list of t0's can be provided. This in conjunction with ``--data-file`` and ``--fourier-option real`` allows to get the proper initial phase if t0's are known. If a single t0 for multiple histos is given, it is assume, that this t0 is common to *all* histos. Example: ``musrFT -df lem15_his_01234.root -fo real --t0 2750 --histo 1 3``. 
-  **-pa, - -packing <N>**
-    if <N> (an integer), the time domain data will first be packed/rebinned by <N>. 
-  **- -title <title>**
-    give a global title for the plot. 
-  **- -create-msr-file <fln>** 
-    creates a msr-file based on the command line options provided. This will help on the way to a full fitting model.
-  **-lc, - -lifetimecorrection <fudge>**
-    try to eliminate the muon life time decay. Only makes sense for low transverse fields. <fudge> is a tweaking factor (scaling factor for the estimated t0) and should be kept around 1.0. 
-  **- -timeout <timeout>**
-    <timeout> given in seconds after which ``musrFT`` terminates. If <timeout> :math:`\leq` 0, no timeout will take place. Default <timeout> is 3600 sec. 
-    
-**Example 1**
-  
-.. code-block:: bash
-  
-  $ musrFT -df tdc_hifi_2014_00153.mdu --title "MnSi" -tr 0 10 -fr 7.0 7.6 -u Tesla --histo 2-17 -a
-    
-will take time range from t=0..10 |mgr|\s, will show the Fourier transform in units of Tesla from B=7.0..7.6 Tesla of the detectors 2-17. Rather than showing the 16 individual Fourier transforms, the average of all Fourier spectra will be shown. t0's will be guessed by the maximum of the time domain histogram (assuming a prompt peak!!).
-
-**Example 2**
-
-.. code-block:: bash
-
-  $ musrFT -df tdc_hifi_2014_00153.mdu -tr 0 10 -fr 7.0 7.6 -u Tesla --histo 2-17 --title "MnSi average, T=50K, B=7.5T" -a -g pdf
-  
-as **Example 1** but rather than showing an interactive GUI, the output will be dumped into a pdf-file. The file name will be ``tdc_hifi_2014_00153.pdf``.   
-
-**Example 3**
-
-.. code-block:: bash
-
-  $ musrFT -df tdc_hifi_2014_00153.mdu -tr 0 10 -fr 7.0 7.6 -u Tesla --histo 2-17 --title "MnSi average, T=50K, B=7.5T" -a --dump MnSi.dat
-
-as **Example 1** but rather than showing an interactive GUI, the output will be dumped into the ascii file ``MnSi.dat``. 
-
-Within the drawn canvas all standard actions applicable to ROOT canvases might be performed. In the menu bar the ``MusrFT`` menu can be found. From there some ``musrFT``-specific actions might be taken
-
-**Fourier** 
-  allows to switch between different Fourier transform representations '*Power*', '*Real*', ... 
-**Average**
-  toggle between the current view and the averaged data view. 
-**Average per Data Set**
-  toggle between the current view and the per data set average view. 
-**Export Data**
-  saves the selected data in a simple multi-column ASCII file.
-  
-.. index:: musrFT-key-shortcuts
-
-musrFT key-shortcuts
-^^^^^^^^^^^^^^^^^^^^
-
-Additionally, some functions can be accessed using key-shortcuts: 
-
-**q**
-  quits musrFT.
-**a**
-  toggle between average of the presented data and single Fourier histos, *e.g.* the averaged Fourier power spectra of various detectors. 
-**d**
-  toggle between average per data set and single Fourier histos, *e.g.* the averaged Fourier power spectra of various detectors for the different data sets given. 
-**u**
-  reset the plotting range to the area given in the msr-file or the form the command line ("unzoom").
-**c**
-  toggles between normal and crosshair cursor. 
-
-.. index:: musrt0
-.. _musrt0:
-
-musrt0
-++++++
-
-``musrt0`` is a user interface allowing to determine 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 :ref:`RUN blocks <msr-run-block>` 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> :math:`\leq` 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. 
-
-The interactive mode of ``musrt0`` is started if the program is called with a sole msr-file argument, *e.g.*   
-
-.. code-block:: bash
-
-  $ musrt0 8472.msr
-  
-Then a ROOT canvas depicting the histogram of the data set mentioned first in the :ref:`RUN blocks <msr-run-block>` block is drawn in different colors:
-
-.. image:: ../images/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: 
-
-
-**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. 
-**u**
-  unzoom to the full range.
-**t**
-  set t0 bin position. 
-**T**
-  automatically set t0, *i.e.* jump to the maximum of the histogram. 
-**b**
-  set the lower limit of the background range bin. 
-**B**
-  set the upper limit of the background range bin. 
-**d**
-  set the lower limit of the data range bin. 
-**D**
-  set the upper limit of the data range bin. 
-
-When all channels have been set correctly for the first histogram, pressing of the key **q** opens the subsequent histogram listed in a :ref:`RUN block <msr-run-block>` and the respective channels can be updated there. This procedure is repeated until all histograms given in the RUN blocks are processed.
-
-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 (close icon) is equivalent to pressing **Q**, *i.e.* ``musrt0`` is simply terminated. 
-  
-
-.. index:: msr2msr
-
-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). 
-**- -help**
-  displays a small help notice in the shell explaining the basic usage of the program. 
-
-A typical example then looks like: 
-
-.. code-block:: bash
-
-  $ msr2msr 8472-WKM.msr 8472-musrfit.msr
-  
-If the input file has already the ``musrfit`` msr file structure, the output file will be just a copy of the input file.   
-
-msr2data
-++++++++
-
-For details concerning ``msr2data`` see the section :ref:`msr2data <msr2data>`.
-
-.. index:: any2many
-.. _any2many:
-
-any2many
-++++++++
-
-``any2many`` is a |mgr|\SR data file converter. Currently different facilities (PSI, TRIUMF, ISIS, J-PARC) are saving their |mgr|\SR data files in different formats, or even worse some instruments are using other |mgr|\SR 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 |mgr|\SR data file formats:
-
-**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:   
-  
-**-f <filenameList-input>**
-  where <filenameList-input> is a space separated list of file names (not starting with a '-'), *e.g.* ``2010/lem10_his_0111.root 2010/lem10_his_0113.root``.  
-**-o <outputFileName>**
-  this option allows to given an output-file-name for the converted file. This option only makes sense if <filenameList-input> is a single input-file-name!   
-**-r <runList-input>**
-  where <runList-input> is a list of run numbers separated by spaces of the form: <run1> <run2> <run3> etc., or a sequence of runs <runStart>-<runEnd>, *e.g.* 111-123. This option cannot be combined with -f and vice versa.  
-**-t <in-template> <out-template>**
-  where <in-/out-template> are templates to generate real file names from run numbers. The following template tags can be used: ``[yy]`` for year, and ``[rrrr]`` for the run number. If the run number tag is used, the number of 'r' will give the number of digits used with leading zeros, *e.g.* ``[rrrrrr]`` and run 123 will result in 000123. Similarly ``[yyyy]`` will result in something like 1999, whereas ``[yy]`` into something like 99. For more details best check the examples below. 
-**-c <in-Format> <out-Format>**
-  this is used to tell ``any2many`` what is the input-file-format and into which output-file-format the data shall be converted. The possible input-/output-file-formats are listed above.
-**-h**
-  This option is for MusrRoot input files only! Select the the histo groups to be exported. is a space separated list of the histo group, *e.g.* ``-h 0, 20`` will try to export the histo 0 (NPP) and 20 (PPC). A histo-group is defined via the RedGreen offset in the MusrRoot file format. It is used *e.g.* in red/green mode measurements. If this option is omitted in a conversion from MusrRoot to something, the first group will be exported only!   
-**-p <output-path>**
-  where <output-path> is the output path for the converted files. If no <output-path> is given, the current directory will be used, unless the option **-s** is used. 
-**-y <year>**
-  here a <year> in the form ``yy`` or ``yyyy`` can be given. If this is the case, any automatic file name generation which needs a year will use this given one. 
-**-s**
-  with this option the output data file will be sent to the stdout. It is intended to be used together with web applications.    
-**-rebin <n>**
-  where <n> is the number of bins to be packed/rebinned.   
-**-z [g|b] <compressed>**
-  where <compressed> is the output file name (without extension) of the compressed data collection, and 'g' will result in ``.tar.gz``, and 'b' in ``.tar.bz2`` files.  
-**--help**
-  displays a help notice in the shell explaining the basic usage of the program. 
-**--version**
-  shows the current version of ``any2many``. 
-
-If the template option `-t` is absent, the output file name will be generated according to the input data file name (not possible with <runList-input>), and the output data format.
-
-Here now a couple of examples which should help to understand the switches.   
-  
-.. code-block:: bash
-
-  $ any2many -f 2010/lem10_his_0123.root -c ROOT ASCII -rebin 25
-
-Will take the *LEM ROOT* file ``2010/lem10_his_0123.root`` rebin it by 25 and convert it to *ASCII*. The output file name will be ``lem10_his_0123.ascii``, and the file will be saved in the current directory. The data in ``lem10_his_0123.ascii`` are written in columns. 
-
-.. code-block:: bash
-
-  $ any2many -f 2010/lem10_his_0123.root -c ROOT NEXUS2-HDF5 -o 2010/lem10_his_0123_v2.nxs
-  
-Will take the *LEM ROOT* file ``2010/lem10_his_0123.root`` and convert it to *NeXus* IDF V2. The output file name will be ``lem10_his_0123_v2.nxs``, and will be saved in the current directory.  
-
-.. code-block:: bash
-
-  $ any2many -r 123 137 -c PSI-BIN MUD -t d[yyyy]/deltat_tdc_gps_[rrrr].bin [rrrrrr].msr -y 2001
-
-Will take the run 123 and 137, will generate the input file names: ``d2001/deltat_tdc_gps_0123.bin`` and ``d2001/deltat_tdc_gps_0137.bin``, read these files, and convert them to the output files with names ``000123.msr` and `000137.msr``, respectively.   
-
-.. code-block:: bash
-
-  $ any2many -r 100-117 -c PSI-MDU ASCII -t d[yyyy]/deltat_tdc_alc_[rrrr].mdu [rrr].ascii -y 2011 -s
-  
-Will take the runs 100 through 117 and convert the *PSI-MDU* input files to *ASCII* output and instead of saving them into a file, they will be spit to the standard output. 
-
-.. code-block:: bash
-
-  $ any2many -r 100-117 -c NEXUS ROOT -t d[yyyy]/psi_gps_[rrrr].NXS psi_[yyyy]_gps_[rrrr].root -z b psi_gps_run_100to117
-
-Will take the runs 100 through 117 and convert the *NeXus* input files to *ROOT* output. Afterwards these new files will be collected in a compressed archive ``psi_gps_run_100to117.tar.bz2``.   
-  
-.. code-block:: bash
-
-  $ any2many -f 2010/lem10_his_0123.root 2010/lem10_his_0012.root -c ROOT ROOT -rebin 25  
-  
-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``. 
-
-.. index:: dump_header
-
-dump_header
-+++++++++++
-
-``dump_header`` is a little program which tries to read a |mgr|\SR data file and sends the relevant information (required header info, start of the histos, etc.) to the standard output. Currently the following |mgr|\SR data file formats are supported: *MusrROOT*, *ROOT* (old LEM format), *PSI-BIN*, *PSI-MDU*, *NeXus* (IDF1 and IDF2), *MUD*, and *WKM*. 
-
-
-**-rn, - -runNo <runNo>**
-  run number of the header to be dumped. 
-**-fn, - -fileName <fileName>**
-  muSR data file name. 
-**-ff, - -fileFormat <fileFormat>**
-  where <fileFormat> is one of the above listed ones. 
-**-y, - -year <year>**
-  <year> has to be a 4 digit value, *e.g.* 2005, if provided it is used to generate the file name for the given <runNo>, otherwise the current year is used. If a file name is given, this option has no effect. 
-**-s, --summary**
-  this option is used for LE-|mgr|\SR data sets only. It will, additionally to the header information, print the summary file content. 
-**--psi-bulk <opt>**
-  where <opt> consists of two items: (i) pta or tdc, (ii) the instrument name, *i.e.* gps, ltf, dolly, gpd, or hifi. This is needed in combination with the file formats *PSI-BIN* and *PSI-MDU* when providing a run number. 
-**-h, --help**
-  will show a short help. 
-**-v, --version**
-  will print the current version. 
-  
-Examples:   
-
-.. code-block:: bash
-
-  $ dump_header -fn tdc_hifi_2015_00123.mdu -y 2015
-
-will dump the header information for the run 123 of the HAL-9500 instrument of the year 2015.   
-  
-.. code-block:: bash
-
-  $ dump_header -rn 123 -ff PSI-MDU --psi-bulk tdc hifi -y 2015
-  
-the same as the previous example, except that the file name is constructed via the number and the additionally provided information.   
-
-.. code-block:: bash
-
-  $ dump_header -rn 3456 -s
-  
-Will dump the LEM header information of run 3456 including the content of the run summary file.   
-
-.. _Pearson's: http://en.wikipedia.org/wiki/Pearson's_chi-square_test
-.. index:: musrfit-startup
-.. _musrfit-startup:
-
-musrfit_startup.xml
-+++++++++++++++++++
-
-``musrfit_startup.xml`` is a configuration file located at ``$HOME\.musrfit``. 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 :math:`\chi^2` for each :ref:`RUN block <msr-run-block>` will be written to the :ref:`STATISTIC block <msr-statistic-block>` of the resulting msr file. Additionally, 
-  in case a :math:`\chi^2` single-histogram fit is done, also `Pearson's`_ :math:`\chi^2` will be added. 
-**<fourier_settings></fourier_settings>**
-  set the default parameters for the Fourier transform in ``musrview``. For further details refer to the description of the :ref:`FOURIER block <msr-fourier-block>` in the msr file.
-  
-  **<units>UNITS</units>**
-    specify the units of the frequency or field-domain. Valid units are *Gauss*, *MHz* and *Mc/s* (inside a <fourier_settings> environment). 
-  **<fourier_power>n</fourier_power>**
-    specify the number of points :math:`2^n (n < 21)` to be used for the Fourier transform (inside a <fourier_settings> environment).
-  **<apodization>APOD</apodization>**
-    set the default apodization method. Valid apodizations are *none*, *weak*, *medium*, and *strong* (inside a <fourier_settings> environment). 
-  **<plot>PLOT</plot>**
-    specify which part of the Fourier transform is plotted by default. You can choose between *real*, *imag*, *real_and_imag*, *power*, and *phase* (inside a <fourier_settings> environment).   
-  **<phase>PH</phase>**
-    set the initial phase shift PH (in degrees) of the data to be Fourier transformed (inside a <fourier_settings> environment).  
-  **<phase_increment>PHINCR</phase_increment>**
-    change the default value of the phase increment (in degrees) used for the phase optimization to PHINCR (inside a <fourier_settings> environment).
-
-**<root_settings></root_settings>**
-  change the default ROOT settings.    
-  
-  **<marker_list></marker_list>**
-    specify the order in which ``musrview`` should use markers when plotting data (inside a <root_settings> environment). 
-    
-    **<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). 
-
-An example would look like:
-
-.. code-block:: xml
-
-   <?xml version="1.0" encoding="UTF-8"?>
-   <musrfit xmlns="https://intranet.psi.ch/MUSR/MusrFit">
-       <data_path>/mnt/data/nemu/his</data_path>
-       <write_per_run_block_chisq>y</write_per_run_block_chisq>
-       <fourier_settings>
-           <units>Gauss</units>
-           <fourier_power>0</fourier_power>
-           <apodization>none</apodization>
-           <plot>real_and_imag</plot>
-           <phase>0.0</phase>
-           <phase_increment>1.0</phase_increment>
-       </fourier_settings>
-       <root_settings>
-           <marker_list>
-               <!-- Root marker numbers -->
-               <marker>24</marker>
-               <marker>25</marker>
-               <marker>26</marker>
-               <marker>27</marker>
-           </marker_list>
-           <color_list>
-               <!-- Color as RGB coded string -->
-               <color>0,0,0</color>
-               <color>255,0,0</color>
-               <color>0,255,0</color>
-               <color>0,0,255</color>
-           </color_list>
-       </root_settings>
-   </musrfit>
-      
-.. index:: msr-file-format
-.. _msr-file-format:
-
-Description of the msr File Format
-----------------------------------
-
-The programs are using an input file to control their action. This input file has the extension ``.msr`` (msr file). The msr file is built up from different blocks. Each block starts with a keyword and is, with the exception of the title, terminated by an empty line. Comments start with the character ``#``. The various input blocks are described below.
-
-.. index:: msr-title-block
-.. _msr-title-block:
-
-The Title
-+++++++++
-
-The first line of the msr file is the title line. Unlike all the other input blocks, it does not start with a block keyword. It is just a simple text line, in which any information can be placed. The title text will be used in the graphical representation of the data as a headline. 
-
-.. index:: msr-fitparameter-block
-.. _msr-fitparameter-block:
-
-The FITPARAMETER Block 
-++++++++++++++++++++++
-
-The FITPARAMETER block is used to define the fit parameters in a MINUIT typical style. There are various possible parameter definitions which are listed here: ::
-
-   1. <no> <name> <value> <step>
-   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 [#f1]_, <value> is the initial guess of the parameter, <step> the inital step width, <lower/upper_boundary> is the lower/upper boundary for the parameter [#f2]_.    
-
-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. 
-
-A typical example looks like this: ::
-
-   FITPARAMETER
-   #       No   Name      Value     Step       Pos_Error    Boundaries
-           1   alpha     1          0.02       none         0       1.8
-           2   asy       0.1042     0.004713   none         0       0.33
-           3   phase     15         1.0        none
-           4   freq      0.9        0.0379     none
-           5   rate      0.03       0.00579    none
-           
-There is also the possibility to constrain the parameters to semi-defined intervals (like par > a or par < b). The syntax is as follows: ::
-
-   FITPARAMETER
-   #       No   Name      Value     Step       Pos_Error    Boundaries
-   # Specify only a lower boundary for the parameter
-           1   Asy1      0.04501   -0.00208    0.00211      0       none
-
-   # Specify only an upper boundary for the parameter
-           2   Rate1     0.14245   -0.02501    0.02279      none    10
-
-   # Specify lower and upper boundaries for the parameter
-           3   Asy2      0.14501   -0.00208    0.00211      0       0.33
-
-   # Do not specify boundaries at all
-           4   Field2    343.212   -2.27960    2.27885      
-           5   Rate2     0.42045   -0.02501    0.02279      none    none
-
-           
-.. rubric:: Notes
-
-.. [#f1] A standard string without whitespace. 
-.. [#f2] According to the MINUIT manual this should be avoided whenever possible! 
-
-
-.. index:: msr-theory-block
-.. _msr-theory-block:
-
-The THEORY Block
-++++++++++++++++
-
-The THEORY block is used to define the fit function. There is a set of predefined functions available. It is also possible to use externally defined functions. How to use them will be explained afterwards, here only the predefined functions are described. 
-
-============ ======= =============================================== ============================================================================================================================================================================================================================================================ ======
-name         abbr.   parameters                                      mathematical expression                                                                                                                                                                                                                                      notes
-============ ======= =============================================== ============================================================================================================================================================================================================================================================ ======
-const        c       const(1)                                        const
-asymmetry    a       A(1)                                            :math:`A`
-simplExpo    se      :math:`\lambda (\mu \mathrm{s}^{-1})`           :math:`\exp(-\lambda t)`
-generExpo    ge      :math:`\lambda (\mu \mathrm{s}^{-1}) \beta(1)`  :math:`\exp\left[-(\lambda t)^\beta\right]`
-simpleGss    sg      :math:`\sigma (\mu \mathrm{s}^{-1})`            :math:`\exp\left[-\frac{1}{2} (\sigma t)^2\right]`
-statGssKT    stg     :math:`\sigma (\mu \mathrm{s}^{-1})`            :math:`\frac{1}{3} + \frac{2}{3} \left[ 1 - (\sigma t)^2\right] \exp\left[-\frac{1}{2} (\sigma t)^2\right]`
-statGssKTLF  sgktlf  :math:`\nu` (MHz), \                            :math:`G_{\rm G}^{\rm LF}(t) = 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]`                                                                                                                     [#n1]_
-                     :math:`\sigma (\mu \mathrm{s}^{-1})`               :math:`+ \frac{2\sigma^4}{(2\pi\nu)^3} \int_0^t \exp\left(- \frac{1}{2}\sigma^2\tau^2\right) \sigma(2\pi\nu\tau) d\tau`
-dynGssKTLF   dgktlf  :math:`\nu` (MHz), \               
-                     :math:`\sigma (\mu \mathrm{s}^{-1})`, \         :math:`\frac{1}{2\pi i} \int_{\gamma+i\infty}^{\gamma-i\infty} \frac{f_{\rm G}(s+\Gamma)}{1-\Gamma f_{\rm G}(s+\Gamma)} \exp(s t) ds`,                                                                                                                       [#n2]_                                              
-                     :math:`\Gamma` (MHz)                               where :math:`f_{\rm G}(s) = \int_0^\infty G_{\rm G}^{\rm LF}(t) \exp(-s t) dt`
-statExpKT    sekt    :math:`\lambda (\mu \mathrm{s}^{-1})`           :math:`\frac{1}{3} + \frac{2}{3} \left[ 1 - \lambda t\right] \exp(-\lambda t)`                                                                                                                                                                               [#n3]_
-statExpKTLF  sektlf  :math:`\nu` (MHz), \                            :math:`1 - \frac{a}{2\pi\nu} j_1(2\pi\nu t) \exp(-a t)`                                                                                                                                                                                                      [#n4]_
-                     :math:`a (\mu \mathrm{s}^{-1})`                   :math:`- \left(\frac{a}{2\pi\nu}\right)^2 \left[j_0(2\pi\nu t)\exp(-a t)-1\right]` 
-                                                                       :math:`- a \left[1+\left(\frac{a}{2\pi\nu}\right)^2\right] \int_0^t \exp(-a\tau) j_0(2\pi\nu\tau) d\tau = G_{\rm L}^{\rm LF}(t)`
-dynExpKTLF   dektlf  :math:`\nu` (MHz), \                            :math:`\frac{1}{2\pi i} \int_{\gamma+i\infty}^{\gamma-i\infty} \frac{f_{\rm L}(s+\Gamma)}{1-\Gamma f_{\rm L}(s+\Gamma)} \exp(s t) ds`,                                                                                                                       [#n5]_
-                     :math:`a (\mu \mathrm{s}^{-1})`, \                 where :math:`f_{\rm L}(s) = \int_0^\infty G_{\rm L}^{\rm LF}(t) \exp(-s t) dt`
-                     :math:`\Gamma` (MHz)
-combiLGKT    lgkt    :math:`\lambda (\mu \mathrm{s}^{-1})`, \        :math:`\frac{1}{3} + \frac{2}{3} (1 - \sigma^2 t^2 -\lambda t) \exp\left(-\frac{\sigma^2 t^2}{2}-\lambda t\right)`
-                     :math:`\sigma (\mu \mathrm{s}^{-1})`
-strKT        skt     :math:`\sigma (\mu \mathrm{s}^{-1}),~\beta(1)`  :math:`\frac{1}{3} + \frac{2}{3} \left[ 1 - (\sigma t)^\beta\right] \exp\left[-(\sigma t)^\beta / \beta \right]`                                                                                                                                             [#n6]_
-spinGlass    spg     :math:`\lambda (\mu \mathrm{s}^{-1})`, \        :math:`\frac{1}{3} \exp\left(-\sqrt{\Omega t}\right) +` 
-                     :math:`\gamma (\mu \mathrm{s}^{-1})`, \            :math:`+ \frac{2}{3} \left(1 - \frac{q\lambda^2 t^2}{\sqrt{\Omega t+ q\lambda^2 t^2}}\right) \exp(-\sqrt{\Omega t + q \lambda^2 t^2})`,
-                     :math:`q (1)`                                      :math:`\Omega t = \frac{4 \lambda^2 (1-q) t}{\gamma}`                                                                          
-rdAnisoHf    rahf    :math:`\nu` (MHz), \                            :math:`\frac{1}{6} (1-\nu t/2) \exp(-\nu t/2) +`                                                                                                                                                                                                             [#n7]_
-                     :math:`\lambda (\mu \mathrm{s}^{-1})`              :math:`+ \frac{1}{3} (1 - \nu t/4) \exp(-\frac{\nu t + 2.44949 \lambda t}{4})`
-TFieldCos    tf      :math:`\varphi (^\circ), \nu` (MHz)             :math:`\cos\left(2\pi\nu t + \frac{\pi \varphi}{180}\right)`
-internFld    if      :math:`\alpha (1), \varphi (^\circ)`, \         :math:`\alpha \cos\left(2\pi\nu t + \frac{\pi \varphi}{180}\right) \exp(-\lambda_{\rm T}t) +`
-                     :math:`\nu` (MHz), \                               :math:`+ (1-\alpha) \exp(-\lambda_{\rm L} t)`
-                     :math:`\lambda_{\rm T} (\mu \mathrm{s}^{-1})`,\
-                     :math:`\lambda_{\rm L} (\mu \mathrm{s}^{-1})`
-Bessel       b       :math:`\varphi (^\circ), \nu` (MHz)             :math:`j_0\left(2\pi\nu t + \frac{\pi \varphi}{180}\right)`
-internbsl    ib      :math:`\alpha (1), \varphi (^\circ)`, \         :math:`\alpha j_0\left(2\pi\nu t + \frac{\pi \varphi}{180}\right) \exp(-\lambda_{\rm T}t) +`
-                     :math:`\nu` (MHz), \                               :math:`+ (1-\alpha) \exp(-\lambda_{\rm L} t)`
-                     :math:`\lambda_{\rm T} (\mu \mathrm{s}^{-1})`,\
-                     :math:`\lambda_{\rm L} (\mu \mathrm{s}^{-1})`
-internFldGK  ifgk    :math:`\alpha (1), \nu` (MHz), \                :math:`\alpha\left[\cos(2\pi\nu t)-\frac{\sigma^2 t}{2\pi\nu}\sin(2\pi\nu t)\right]\exp(-\sigma^2 t^2/2)+`                     
-                     :math:`\sigma (\mu \mathrm{s}^{-1})`, \            :math:`+ (1-\alpha) \exp(-(\lambda t)^\beta)`                                                                                                                                                                                                             [#n8]_
-                     :math:`\lambda (\mu\mathrm{s}^{-1}), \beta (1)` 
-internFldLL  ifll    :math:`\alpha (1), \nu` (MHz), \                :math:`\alpha\left[\cos(2\pi\nu t)-\frac{a}{2\pi\nu}\sin(2\pi\nu t)\right]\exp(-a t)+`
-                     :math:`a (\mu \mathrm{s}^{-1})`, \                 :math:`+ (1-\alpha) \exp(-(\lambda t)^\beta)`                                                                                                                                                                                                                  [#n9]_
-                     :math:`\lambda (\mu\mathrm{s}^{-1}), \beta (1)`
-abragam      ab      :math:`\sigma (\mu \mathrm{s}^{-1})`, \         :math:`\exp\left[-\frac{\sigma^2}{\gamma^2} (e^{-\gamma t} - 1 + \gamma t)\right]`
-                     :math:`\gamma` (MHz)
-skewedGss    skg     :math:`\varphi (^\circ), \nu` (MHz) \           :math:`\frac{\sigma_{-}}{\sigma_{+}+\sigma_{-}} \exp\left[\frac{\sigma_{-}^2 t^2}{2}\right] \left\{\cos(2\pi\nu t + \frac{\pi\varphi}{180}) + \sin(2\pi\nu t + \frac{\pi\varphi}{180}) \mathrm{Erfi}\left(\frac{\sigma_{-} t}{\sqrt{2}}\right)\right\} +`    [#n10]_
-                     :math:`\sigma_{+} (\mu \mathrm{s}^{-1})`, \        :math:`+ \frac{\sigma_{+}}{\sigma_{+}+\sigma_{-}} \exp\left[\frac{\sigma_{+}^2 t^2}{2}\right] \left\{\cos(2\pi\nu t + \frac{\pi\varphi}{180}) - \sin(2\pi\nu t + \frac{\pi\varphi}{180}) \mathrm{Erfi}\left(\frac{\sigma_{+} t}{\sqrt{2}}\right)\right\}`
-                     :math:`\sigma_{-} (\mu \mathrm{s}^{-1})`
-staticNKZF   snkzf   :math:`\Delta_0 (\mu \mathrm{s}^{-1})`, \       :math:`\frac{1}{3} + \frac{2}{3}\left(\frac{1}{1+R_b^2\Delta_0^2 t^2}\right)^{3/2} \left(1 - \frac{\Delta_0^2 t^2}{1+R_b^2\Delta_0^2 t^2}\right) \exp\left[-\frac{\Delta_0^2 t^2}{2(1+R_b^2\Delta_0^2 t^2)}\right]`                                          [#n11]_
-                     :math:`R_b = \Delta_{\rm GbG}/\Delta_0 (1)`
-staticNKTF   snktf   :math:`\varphi (^\circ), \nu` (MHz), \          :math:`\sqrt{\frac{1}{1+R_b^2 \Delta_0^2 t^2}} \exp\left[-\frac{\Delta_0^2 t^2}{2(1+R_b^2 \Delta_0^2 t^2)}\right] \cos(2\pi\nu t + \varphi)`                                                                                                                 see [13]
-                     :math:`\Delta_0 (\mu \mathrm{s}^{-1})`, \
-                     :math:`R_b = \Delta_{\rm GbG}/\Delta_0 (1)`     
-dynamicNKZF  dnkzf   :math:`\Delta_0 (\mu \mathrm{s}^{-1})`, \       :math:`\sqrt{\frac{1}{1+4 R_b^2 \Delta_0^2 \Theta(t)}} \exp\left[-\frac{2\Delta_0^2 \Theta(t)}{1+4 R_b^2 \Delta_0^2 \Theta(t)}\right]`,                                                                                                                      see [13]   
-                     :math:`R_b = \Delta_{\rm GbG}/\Delta_0 (1)`, \     :math:`\Theta(t) = \frac{\exp(-\nu_c t) -1 -\nu_c t}{\nu_c^2}`
-                     :math:`\nu_c` (MHz)
-dynamicNKTF  dnktf   :math:`\varphi (^\circ), \nu` (MHz), \          :math:`\sqrt{\frac{1}{1+2 R_b^2 \Delta_0^2 \Theta(t)}} \exp\left[-\frac{\Delta_0^2 \Theta(t)}{1+2 R_b^2 \Delta_0^2 \Theta(t)}\right] \cos(2\pi\nu t + \varphi)`,                                                                                             see [13]   
-                     :math:`\Delta_0 (\mu \mathrm{s}^{-1})`, \          :math:`\Theta(t) = \frac{\exp(-\nu_c t) -1 -\nu_c t}{\nu_c^2}`
-                     :math:`R_b = \Delta_{\rm GbG}/\Delta_0 (1)`, \
-                     :math:`\nu_c` (MHz)
-muMinusExpTF mmsetf  :math:`N_0 (1), \tau (\mu \mathrm{s}^{-1})`, \  :math:`N_0 \exp(-t/\tau) \left[ 1 + A \exp(-\lambda t) \cos(2 \pi \nu t + \varphi) \right]`                                                                                                                                                                  [#n12]_
-                     :math:`A (1), \lambda (\mu \mathrm{s}^{-1})`, \
-                     :math:`\varphi (^\circ), \nu` (MHz)
-polynom      p       :math:`t_0 ([t]), a_0 (1)`, \                   :math:`\sum_{k=0}^n a_k (t-t_0)^k`
-                     :math:`a_1 (t), \ldots, a_n (1)`
-============ ======= =============================================== ============================================================================================================================================================================================================================================================ ======
-
-.. rubric:: Notes
-
-.. [#n1] `R.S. Hayano <http://link.aps.org/doi/10.1103/PhysRevB.20.850>`_ *et al.*, Phys. Rev. B **20**, 850 (1979).  -- **not** DKS ready.
-.. [#n2] R.S. Hayano *et al.*, Phys. Rev. B **20**, 850 (1979)., 
-         `P. Dalmas de Réotier <http://dx.doi.org/10.1088/0953-8984/4/18/020>`_ and A. Yaouanc, J. Phys.: Condens. Matter **4**, 4533 (1992).,
-         `A. Keren <http://link.aps.org/doi/10.1103/PhysRevB.50.10039>`_, Phys. Rev. B **50**, 10039 (1994). -- **not** DKS ready.
-.. [#n3] `Y.J. Uemura <http://link.aps.org/doi/10.1103/PhysRevB.31.546>`_ *et al.*, Phys. Rev. B **31**, 546 (1985). -- **not** DKS ready.
-.. [#n4] Y.J. Uemura *et al.*, Phys. Rev. B **31**, 546 (1985). -- **not** DKS ready.
-.. [#n5] R.S. Hayano *et al.*, Phys. Rev. B **20**, 850 (1979)., P. Dalmas de Réotier and A. Yaouanc, J. Phys.: Condens. Matter **4**, 4533 (1992). -- **not** DKS ready.
-.. [#n6] `M.R. Crook <http://dx.doi.org/10.1088/0953-8984/9/5/018>`_ and R. Cywinski, J. Phys.: Condens. Matter **9** 1149 (1997).
-.. [#n7] `R.E. Turner <http://link.aps.org/doi/10.1103/PhysRevB.34.4467>`_ and D.R. Harshman, Phys. Rev. B **34**, 4467 (1986). 
-.. [#n8] `E.I. Kornilov <https://doi.org/10.1016/0375-9601(91)90959-C>`_ and V.Yu. Pomjakushin, Physics Letters A **153**, 364, (1991).
-         In the original work, :math:`\alpha=2/3,\, \lambda=0,\, \beta=1`. If you find values strongly deviating from these values you should question your analysis approach.
-.. [#n9] `M.I. Larkin <https://doi.org/10.1016/S0921-4526(00)00337-9>`_ *et al.*, Physica B: Condensed Matter **289-290**, 153 (2000).
-         In the original work, :math:`\alpha=2/3,\, \lambda=0,\, \beta=1`. If you find values strongly deviating from these values you should question your analysis approach.
-.. [#n10] `see memo <http://lmu.web.psi.ch/musrfit/memos/skewedGaussian.pdf>`_ -- **not** DKS ready.
-.. [#n11] `D.R. Noakes <http://link.aps.org/doi/10.1103/PhysRevB.56.2352>`_ and G.M. Kalvius, Phys. Rev. B **56**, 2352 (1997); 
-         A. Yaouanc and P. Dalmas de Réotier "Muon Spin Rotation, Relaxation, and Resonance" Oxford Scientific Publication; 
-         simplifying the original formulae by eliminating :math:`\Delta_{\rm eff}` via the identity 
-         :math:`\Delta_{\rm eff}^2 = (1+R_b^2)\Delta_0`.
-.. [#n12] This function is explicit for :math:`\mu^-`! Do not try to use it for :math:`\mu^+`!         
-
-.. _msr-map-intro:
-
-Maps
-^^^^
-
-There are two situations where the theory function needs an additional switch/map allowing a compact and flexible handling of the fit.
-
-#. Typically your spectrometer has a couple of detectors. Hence, in a TF experiment all these detectors will have at least a different initial phase. 
-   Maps allow exactly to deal with this difficulty.
-#. In case different runs are fitted simultaneously, it is very often necessary that for a given theory function, some parameters are run-dependent. 
-   An example could be a temperature scan, where the parameters (asymmetry, depolarization rates, etc.) will depend on the temperature.   
-
-In order to handle such situations, a mapping of parameters in the THEORY block is possible. That means, instead of a parameter number, 
-the mapping of the parameter is given. The definition of the mapping block is part of the :ref:`RUN block <msr-run-block>` and will be described there. 
-For example ::
-
-   THEORY
-   asymmetry 2
-   simplExpo 3
-   TFieldCos map1 5
-
-means that the phase parameter of ``TFieldCos`` will be mapped to :ref:`RUN block <msr-run-block>`, and hence every detector will have its individual phase.
-   
-Functions
-^^^^^^^^^
-
-Yet another useful feature is the possibility to define functions in the :ref:`FUNCTIONS block <msr-functions-block>`. 
-Within the :ref:`THEORY block <msr-theory-block>` these functions can be addressed as funX, where 'X' is the function number, *e.g.* fun2.
-Whereas the theory is operating on the parameters and the time, functions currently can *only* operate on the parameters.
-
-.. _msr-theory-block-user-functions:
-
-User Functions 
-^^^^^^^^^^^^^^
-
-In the case complicated and not predefined functions are needed to fit data, ``musrfit`` offers the possibility to implement external functions 
-and introduce them to ``musrfit`` through the ROOT dictionary mechanism. The detailed rules these user-defined functions have to obey will be discussed 
-in the according :ref:`section <user-functions>`. Here only the syntax for the msr file is provided. To call a user function in the :ref:`THEORY block <msr-theory-block>` the 
-keyword ``userFcn`` is used. It is followed by the name of the shared library which holds the C++ class where the function is implemented and the name of 
-the class. Finally, all parameters are given in the order needed by the class. Of course it is also possible to use mapped parameters or functions 
-instead of specifying the parameters directly. 
-
-A THEORY block including a user function may then look like ::
-
-   THEORY
-   asymmetry 1
-   userFcn libMyLibrary.so TMyFunction 2 3 4 map1 fun1
-   +
-   ...
-
-
-.. index:: msr-functions-block
-.. _msr-functions-block:
-
-The FUNCTIONS Block
-+++++++++++++++++++
-
-Here some auxiliary functions can be defined. These functions can currently *only* operate on the defined parameters, and some meta information from the data files. 
-They can be used in the :ref:`THEORY block <msr-theory-block>` and for three specific cases in the :ref:`RUN block <msr-run-block>` (`norm`, `alpha`, and `beta`). 
-Supported is the use of basic arithmetic:
-
-:math:`+`
-  Addition
-:math:`-`
-  Subtraction
-:math:`*`
-  Multiplication
-:math:`/`
-  Division
-:math:`()`
-  The standard use of parentheses
-
-The following functions are built-in and can be used in a function definition: **cos(), sin(), tan(), acos(), asin(), atan(), cosh(), sinh(), tanh(), 
-acosh(), asinh(), atanh(), exp(), log(), ln(), sqrt(), pow(base, exponent)**. 
-  
-Furthermore, some constants are predefined and might also be used:
-
-* **gamma_mu** = :math:`\gamma_\mu/(2\pi) = 0.0135538817~\mathrm{MHz/G}`
-* **pi** = :math:`\pi = 3.14159265358979323846`
-
-The fit parameters are accessed either directly through parX, where 'X' is the number of the parameter in the :ref:`FITPARAMETER block <msr-fitparameter-block>`, 
-*e.g.* *par5* or through a mapping with mapY, where 'Y' specifies the mapping number in the :ref:`RUN block <msr-run-block>` as explained below. 
-
-
-.. index:: meta-information
-
-The available meta information form the data files are:
-
-+------------------+--------------+---------+---------------------+
-| Meta Information | Symbol       | Units   | Comments            |
-+------------------+--------------+---------+---------------------+
-| **Field**        | *B* or *b*   | `(G)`   |                     |
-+------------------+--------------+---------+---------------------+
-| **Energy**       | *En* or *en* | `(keV)` | mainly LEM          |
-+------------------+--------------+---------+---------------------+
-| **Temperature**  | *Tx*         | `(K)`   | x=0,1,.. e.g. *t0*  |
-+------------------+--------------+---------+---------------------+
-
-The defined functions are denoted as funX, where 'X' is the function number, *i.e.* fun1, fun2, etc. and have to be placed separately on one 
-line each. Afterwards they can be used in the :ref:`THEORY block <msr-theory-block>`.
-
-It follows an example to illustrate the usage of functions in the :ref:`THEORY block <msr-theory-block>`. The total asymmetry of a signal 
-consisting of two parts should be a fit parameter. The fraction of each of the parts will then be expressed as a function of the total asymmetry. 
-::
-
-   FITPARAMETER
-   #       No   Name      Value     Step       Pos_Error    Boundaries
-           1   alpha     1          0.02       none         0       1.8
-           2   phase     15         1.0        none
-           3   asy       0.2542     0.004713   none         0       0.33
-           4   rate1     15         1.0        none         0       none
-           5   frac1     0.33       0.0379     none         0       1
-           6   rate2     0.13       0.00579    none         0       10
-
-   ###############################################################
-   THEORY
-   asymmetry   fun1
-   simplExpo      4                   (rate)
-   +
-   asymmetry   fun2
-   simplExpo      6                   (rate)
-
-   ###############################################################
-   FUNCTIONS
-   fun1 = par3 * par5
-   fun2 = par3 * ( 1.0 - par5 )
-   
-   
-.. index:: msr-global-block
-.. _msr-global-block:
-
-The GLOBAL Block
-++++++++++++++++
-
-The GLOBAL block is used to collect data which otherwise need to be specified in every single run entry of the :ref:`RUN block <msr-run-block>`. 
-Therefore, this block is only present to potentially shorten the msr file and to ease the handling for the user. The logic will by like that: 
-
-#. check if the property is found in the :ref:`RUN block <msr-run-block>`.
-#. if *not* present in the :ref:`RUN block <msr-run-block>`, check whether it is present in the GLOBAL block.
-#. if still not found, try the data file.
-#. if still not found, either try to estimate it, or fire an error message. 
-
-This means that an entry present in the :ref:`RUN block <msr-run-block>` will overwrite a setting from the GLOBAL block. 
-
-Currently the supported GLOBAL block entries are: 
-
-* ``fittype``
-* ``data``
-* ``t0``
-* ``addt0``
-* ``fit``
-* ``rrf_freq`` for fittype 1, 3
-* ``rrf_packing`` for fittype 1, 3
-* ``rrf_phase`` for fittype 1, 3
-* ``packing`` for fittype 0, 2, 4, 5
-
-For a detailed discussion of these entries see the section :ref:`RUN block <msr-run-block>`.
-
-The single histo RRF fit and asymmetry RRF fit related entries (fittype 1 and 3 only) have the following syntax: 
-
-**rrf_freq**
-  Defines the RRF frequency. The exact syntax is rrf_freq <value> <unit> where <value> is the value, and <unit> can be *MHz*, *Mc*, and *T*. An example: ::
-
-    rrf_freq 7.2 T
-
-**rrf_packing**
-  for fittype 1 and fittype 3 rather than giving packing, rrf_packing <pack> has to be provided, *e.g.* ::
-
-    rrf_packing 150
-
-**rrf_phase**
-  an optional additional RRF phase can be provided (if not provided, the RRF phase will be 0.0). 
-  Syntax: rrf_phase <phase>, where the value <phase> is given in degree. Example: ::
-
-    rrf_phase 45
-
-An example snippet with, and without GLOBAL section. 
-
-With GLOBAL block:  ::
-
-  ...
-  ###############################################################
-  GLOBAL
-  fittype         0         (single histogram fit)
-  fit             0.0005  10     
-  packing         5
-
-  ###############################################################
-  RUN data/tdc_hifi_2014_00153 PIE3 PSI PSI-MDU   (name beamline institute data-file-format)
-  map             5    6    7    0    0    0    0    0    0    0    0
-  norm            8
-  backgr.fit      9
-  forward         2 
-  data            20120   409500  
-  t0              20108.0 
-  #--------------------------------------------------------------
-  RUN data/tdc_hifi_2014_00153 PIE3 PSI PSI-MDU   (name beamline institute data-file-format)
-  map            10   11   12    0    0    0    0    0    0    0    0
-  norm            13
-  backgr.fit      14
-  forward         3 
-  data            20111   409500  
-  t0              20088.0 
-  #--------------------------------------------------------------
-  RUN data/tdc_hifi_2014_00153 PIE3 PSI PSI-MDU   (name beamline institute data-file-format)
-  ...
-  
-Without GLOBAL block: ::  
-  
-  ...
-  ###############################################################
-  RUN data/tdc_hifi_2014_00153 PIE3 PSI PSI-MDU   (name beamline institute data-file-format)
-  fittype         0         (single histogram fit)
-  map             5    6    7    0    0    0    0    0    0    0    0
-  norm            8
-  backgr.fit      9
-  forward         2 
-  data            20120   409500  
-  t0              20108.0 
-  fit             0.0005  10     
-  packing         5
-  #--------------------------------------------------------------
-  RUN data/tdc_hifi_2014_00153 PIE3 PSI PSI-MDU   (name beamline institute data-file-format)
-  fittype         0         (single histogram fit)
-  map            10   11   12    0    0    0    0    0    0    0    0
-  norm            13
-  backgr.fit      14
-  forward         3 
-  data            20111   409500  
-  t0              20088.0 
-  fit             0.0005  10     
-  packing         5
-  #--------------------------------------------------------------
-  RUN data/tdc_hifi_2014_00153 PIE3 PSI PSI-MDU   (name beamline institute data-file-format)
-  fittype         0         (single histogram fit)
-  ... and many more detectors here ...
-
-    
-.. index:: msr-run-block
-.. _msr-run-block:
-
-The RUN Block 
-+++++++++++++
-
-The RUN block is used to collect the data needed for a particular run to be fitted. This includes the run name, fit type, data format, etc. 
-The RUN block is slightly differently organized than the other blocks. The information is collected via labels followed by the information. 
-Each run to be fitted has its *own* RUN block. A RUN block starts with a run-file line which has the structure ::
-
-  RUN <run_file_name> <beamline> <facility> <file_format>
- 
-where 
-
-================ ====================================================================================================
-RUN-block tag    comment 
-================ ====================================================================================================
-<run_file_name>  sub path and file name without extension  
-<beamline>       name of the beamline where the data were taken, *e.g.* MUE4. Used to generate a default path.
-<facility>       name of the facility where the data were recorded, *e.g.* PSI. Used to generate a default path. 
-<file_format>    file format: MUSR-ROOT, NEXUS, ROOT-NPP, ROOT-PPC, PSI-BIN, PSI-MDU, WKM, MUD, MDU-ASCII, ASCII, DB
-================ ====================================================================================================
-
-The tokens following the RUN statement are used to identify the run, the potential location where the run might be found, 
-and the file format in which the run data has been saved. In order to understand the meaning of all the above tokens, 
-a short digression is needed. 
-
-Where is musrfit looking for data files? There is a specific order how this is done: 
-
-1. Check if the file is found in the current directory 
-2. Check if the path (or multiple paths) was (were) given in the :ref:`XML startup file <musrfit-startup>`.
-3. Check if there is a system variable ``MUSRFULLDATAPATH``. This system variable can contain multiple search paths separated by colons, *e.g.*  
-
-  .. code-block:: bash
-
-    $ export MUSRFULLDATAPATH=/mnt/data/nemu/wkm/:/mnt/data/nemu/his/:/afs/psi.ch/user/s/smith/
-
-4. Construct the search path from the :ref:`RUN-block <msr-run-block>` information in the following way: Based on the RUN line in the RUN block, default paths will be generated, *e.g.* for 
-   ::
-
-     RUN 2007/lem07_his_2018 MUE4 PSI ROOT-NPP
-
-   the generated search path will look like 
-
-   ::
-  
-     musrFullDataPathToken/DATA/Facility/Beamline/runName.ext
-
-   where ``musrFullDataPathToken`` is extracted from the ``MUSRFULLDATAPATH`` token by token, for the above example this might lead to the path 
-
-  ::
-
-    /afs/psi.ch/user/s/smith/DATA/PSI/MUE4/2007/lem07_his_2018.root
-
-Here are some valid examples for the first line of a RUN block:
-
-::
-
-  RUN 2007/lem07_his_2018 MUE4 PSI ROOT-NPP
-  RUN 2007/lem07_2018_rb1_npp MUE4 PSI WKM
-  RUN d2007/deltat_pta_gps_2650 PIM3 PSI PSI-BIN
-  RUN d2010/tdc/deltat_tdc_gpd_8472 MUE1 PSI PSI-BIN
-  RUN beautiful-data MUE4 PSI DB
-
-After this short digression back to the RUN-block description.
-
-In order to describe the operations needed for fitting and plotting, quite some information are needed. These information are following the RUN statement and are listed below. Depending on the fit type these information vary and hence it is indicated for which fit/plot type the information is applicable
-
-.. index:: addrun
-.. _msr-addrun:
-
-**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 :ref:`Single Histogram Fit <single-histogram-fit>` or a :ref:`MuMinus Fit <negative-muon-musr-fit>` it will be 
-
-  ::
-
-    addt0 t0AddRun1
-    addt0 t0AddRun2
-    etc.
-
-  For an :ref:`Asymmetry Fit <asymmetry-fit>` this reads 
-
-  :: 
-    
-    addt0 t0AddRun1Forward t0AddRun1Backward
-    addt0 t0AddRun2Forward t0AddRun2Backward
-    etc.
-
-  How will the background and data ranges be handled in this situation? First, the ADDRUN's will be shifted in time such that all the t0's have the same channel/bin number. Subsequently, the runs will be added. The background/data range is applied to this summed up new histogram. 
-
-  ADDRUN is *not* available for the fit type :ref:`Non-muSR Fit <non-musr-fit>`. 
-
-.. index:: fittype
-.. _msr-fittype:
-
-**fittype** (required if not already defined in the GLOBAL block) 
-  This tag is used to indicate which type of fit is wished. The supported fit types are: 
-
-  **0**
-    Single Histogram Fit
-  **1**
-    Single Histogram RRF Fit (only for online analysis)
-  **2**
-    Asymmetry Fit
-  **3**
-    Asymmetry RRF Fit (only for online analysis)
-  **4**
-    MuMinus Fit. This is a single histogram fit especially for negative muon |mgr|\SR
-  **5**
-    beta-NMR Asymmetry Fit
-  **8**
-    Non-|mgr|\SR Fit   
-
-  The description of these fit types can be found in the :ref:`corresponding section <fit-types>`. Example:
-
-  ::
-   
-    fittype 0
-
-.. index:: alpha-beta
-.. _msr-alpha-beta:
-
-**alpha, beta** (fit type 2, 3, 5)
-  These parameters are used to correct the asymmetry for different detector efficiencies, solid angles and initial asymmetries. They are defined as :math:`\alpha = N_{0,b}/N_{0,f}` and :math:`\beta = A_{0,b}/A_{0,f}`. If the parameters are not specified in the :ref:`RUN block <msr-run-block>`, for each one the value of 1 is assumed (for fittype 5, alpha is estimated from the ratio of :math:`\sum_i \left( N_{\mathrm{bp}}(i)+N_{\mathrm{bm}}(i) \right)` and :math:`\sum_i \left( N_{\mathrm{fp}}(i)+N_{\mathrm{fm}}(i) \right)`). Both, `alpha` as well as `beta` can be expressed through a function. Example for alpha with fit parameter number 1:
-
-  ::
-
-    alpha 1
-
-  Example for an ``alpha`` defined via function number 1:
-  
-  ::
-  
-    alpha fun1 
-
-.. index:: norm
-.. _msr-norm:
-
-**norm** (fit type 0)
-  Number of the fit parameter that represents the normalization constant :math:`N_0` of the histogram; the value of this parameter is given either per nanosecond or per bin (see :ref:`below <msr-commands-block>`). 
-  It is possible to substitute the parameter number by a function, for instance to relate :math:`N_0`\'s of different histograms through an :math:`\alpha` 
-  parameter. Example for a ``norm`` defined by fit parameter number 12:
-  
-  ::
-  
-    norm 12
-    
-  Example for a ``norm`` defined via function number 3:
-  
-  ::
-  
-    norm fun3
-    
-.. index:: backgr.fit
-.. _msr-backgr.fit:
-
-**backgr.fit** (fit type 0)     
-  Parameter number specifying the constant background in a histogram. Its value is given either per nanosecond or per bin (see :ref:`below <msr-commands-block>`). If this keyword is present, 
-  any information on a background line are ignored. 
-  
-.. index:: lifetime
-.. _msr-lifetime:
-
-**lifetime** (fit type 0)   
-  Fit parameter representing the lifetime of the muon. If it is not specified the value :math:`\tau_\mu=2.197019~ \mu\mathrm{s}` is used in the calculations.
-
-**lifetimecorrection** (fit type 0) *obsolete*
-  Does not accept any arguments. If present, the output in ``musrview`` is corrected for the exponential decay of the muon. This item is *obsolete* in the RUN block 
-  and will be transferred to the :ref:`PLOT block <msr-plot-block>`, which allows switching between histogram view and asymmetry view much quicker.
-  
-.. index:: map
-.. _msr-map:
-
-**map**  
-  On this line the mapping of run-dependent parameters is done. Parameter numbers given here may be accessed through map1, map2, etc. in the 
-  :ref:`THEORY <msr-theory-block>` and :ref:`FUNCTIONS <msr-functions-block>` blocks (see also :ref:`maps <msr-map-intro>`). The first ten maps 
-  are always present and have the value 0 if not used; however, the total number of maps is not restricted! 
-  
-.. index:: forward
-.. _msr-forward:
-
-**forward** (fit type 0, 1, 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 
-  
-.. index:: forward-backward
-.. _msr-forward-backward:
-
-**forward, backward** (fit types 2, 3)   
-  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
-    # build forward/backward asymmetry with groupings 1+2+3 and 7+8+9
-    forward   1 2 3
-    backward  7 8 9
-    # build forward/backward asymmetry with groupings 1+2+3 and 7+8+9 (alternative notation)
-    forward   1-3
-    backward  7-9
-
-**forward, backward** (fit type 5)   
-  Numbers of the histograms in the data file that should be taken to calculate the asymmetry. Two forward and backward histograms should be given indicationg positive and negative helicities. The asymmetry from opposite helicities will be subtracted. Examples: 
-  
-  ::
-  
-    # build forward/backward asymmetry with histogram 1 and 3 then subtract asymmetry built with histograms 2 and 4
-    forward  1 2
-    backward 3 4
-
-.. index:: backgr.fix
-.. _msr-backgr.fix:
-
-**backgr.fix** (fit types 0, 1, 2, 3, 5)    
-  A fixed constant background in counts per nanosecond or per bin (see :ref:`below <msr-commands-block>`) may be given at this point. 
-  The background is specified for all histograms in the order :math:`B_f B_b [B_r B_l]`. If this keyword is present, *any* information on a ``background`` line is ignored. 
-    
-.. index:: background-single-histo
-.. _msr-background-single-histo:
-
-**background** (fit type 0, 1)     
-  The numbers of the first and the last channel of an interval from which the constant background should be calculated are specified here. 
-  In case histograms are being grouped, the specified channels are interpreted with respect to the first histogram. Example:
-  
-  ::
-  
-    background  100  18000
-    
-.. index:: background-asymmetry
-.. _msr-background-asymmetry:
-
-**background** (fit types 2, 3, 5)     
-  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: :math:`k_{f,\rm first} k_{f,\rm last} k_{b,\rm first} k_{b, \rm last} [k_{r,\rm first} k_{r,\rm last} k_{l,\rm first} k_{l,\rm last}]`. 
-  In case histograms are being grouped, the specified channels are interpreted with respect to the first histograms. Example:
-  
-  ::
-  
-    background  61  184   57  145     
-
-.. index:: data-single-histo
-.. _msr-data-single-histo:
- 
-**data** (fit type 0, 1, 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. 
-  Typically these channels are referred to as ``first good bin`` / ``last good bin`` (fgb/lgb). Example:
-   
-  ::
-   
-    data  165   7965   
-     
-.. index:: data-asymmetry
-.. _msr-data-asymmetry:
-
-**data** (fit type 2, 3, 5) 
-  The numbers of the first and the last channel of an interval from which the data is taken are specified here. 
-  Typically these channels are referred to as first good bin / last good bin (fgb/lgb). For all the histograms this is 
-  done together in the following order: :math:`k_{f,\rm first} k_{f,\rm last} k_{b,\rm first} k_{b, \rm last} [k_{r,\rm first} k_{r,\rm last} k_{l,\rm first} k_{l,\rm last}]`. 
-  In case histograms are being grouped, the specified channels are interpreted with respect to the first histograms. Example:
-  
-  ::
-  
-    data  207   7994    167   8009    
-    
-.. index:: t0-single-histo
-.. _msr-t0-single-histo:
-
-**t0** (fit type 0, 1, 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. 
-
-.. index:: t0-asymmetry
-.. _msr-t0-asymmetry:
-
-**t0** (fit type 2, 3, 5)     
-  The numbers of time-zero channels of the histograms in the order :math:`t_{0,f} t_{0,b}`. For fit type 5, the time-zero is the channel of the start of beam pulse. 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)
-
-.. index:: addt0-single-histo
-.. _msr-addt0-single-histo:
-
-**addt0** (fit type 0, 1, 4) 
-  The number of the time-zero channel of the histogram. If grouping of histograms is present (see :ref:`forward <msr-forward>`) the 
-  same syntax as for :ref:`t0 <msr-t0-single-histo>` applies. If one addt0 is given, the total number of addt0's needs to be equal to 
-  the total number of :ref:`ADDRUN <msr-addrun>`\'s! 
-  
-.. index:: addt0-asymmetry
-.. _msr-addt0-asymmetry:
-
-**addt0** (fit type 2, 3, 5) 
-  The numbers of time-zero channels of the histograms in the order :math:`t_{0,f} t_{0,b} [t_{0,r} t_{0,l}]`. 
-  If grouping of histograms is present (see :ref:`forward <msr-forward-backward>`) the same syntax as for :ref:`t0 <msr-t0-asymmetry>` applies. 
-  If one addt0 is given, the total number of addt0's needs to be equal to the total number of :ref:`ADDRUN <msr-addrun>`\'s! 
-  
-  
-.. index:: xy-data
-.. _msr-xy-data:
-
-**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. 
-
-.. index:: fit
-.. _msr-fit:
-
-**fit**   
-  The range of data that should be considered when the fitting is done. For the |mgr|\SR fit types 0, 1, 2, 3, and 4 the 
-  starting and end times are given in micro-seconds. For the non-|mgr|\SR 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), the data range will be used as fit range.** 
-  
-  An example for a |mgr|\SR fit:
-  
-  ::
-  
-    fit 0.1 8.5
-  
-  Which means that the fitting window will span from 0.1 to 8.5 micro-seconds.
-  
-  Another possibility for the |mgr|\SR fits is to give the fit range in bins, rather than time. The syntax is then:
-  
-  ::
-  
-    fit fgb+<n0> lgb-<n1>,
-    
-  where ``fgb`` and ``lgb`` are label tags which refer to the 'first good bin' and the 'last good bin' defined 
-  either in the :ref:`data <msr-data-single-histo>` tag of the run block, data file, are estimated based on T0. 
-  ``<n0>`` and ``<n1>`` are offsets (given in bins) allowing to change the fit window compared to the data window. 
-  An example:
-  
-  ::
-  
-    fit fgb+150 lgb-1332
-    
-.. index:: packing
-.. _msr-packing:
-
-**packing**
-  Number of data channels to be binned together. For the non-|mgr|\SR fit type 8 the binning is supposed to be 1. 
-  For the single histogram RRF fit (fittype 1) and asymmetry RRF fit (fittype 3) this parameter is meaningless. 
-  
-.. index:: msr-commands-block
-.. _msr-commands-block:
-
-The COMMANDS Block
-++++++++++++++++++
-
-The COMMANDS block is used to specify the commands which are passed from ``musrfit`` to ``MINUIT2``. The supported commands 
-after the ``COMMANDS`` keyword are listed in the two tables below (:ref:`minuit2-command-overview` and :ref:`dks-command-overview`) 
-and further described in :ref:`musrfit-command-block-details`.
-
-.. index:: minuit2-command-overview
-.. _minuit2-command-overview:
-
-Minuit2 Command Overview
-^^^^^^^^^^^^^^^^^^^^^^^^
-
-+--------------------+-------------------------------------+------------------------------------------+
-| **Cmd**            | brief description                   | Reference                                |
-+====================+=====================================+==========================================+
-| **STRATEGY**       | 0 (low), 1 (default), and 2 (high)  | [#f3]_                                   |
-+--------------------+-------------------------------------+------------------------------------------+
-| **MIGRAD**         | This is the best minimizer for      | [#f3]_                                   |
-|                    | nearly all functions.               |                                          |
-+--------------------+-------------------------------------+------------------------------------------+
-| **SIMPLEX**        | This genuine multidimensional       | [#f3]_                                   |
-|                    | minimization routine is usually     |                                          |
-|                    | much slower than MIGRAD.            |                                          |
-+--------------------+-------------------------------------+------------------------------------------+
-| **MINIMIZE**       | This is equivalent to MIGRAD,       | [#f3]_                                   |
-|                    | except that if MIGRAD fails, it     |                                          |
-|                    | reverts to SIMPLEX and then calls   |                                          |
-|                    | MIGRAD again.                       |                                          |
-+--------------------+-------------------------------------+------------------------------------------+
-| **MINOS**          | Calculate parameter errors taking   | [#f3]_                                   |
-|                    | into account both parameter         |                                          |
-|                    | correlations and non-linearities.   |                                          |
-+--------------------+-------------------------------------+------------------------------------------+
-| **HESSE**          | Calculates an error matrix.         | [#f3]_                                   |
-+--------------------+-------------------------------------+------------------------------------------+
-| **SAVE**           | Writes the ``MINUIT2.OUTPUT`` and   |                                          |
-|                    | ``MINUIT2.root`` files which        |                                          |
-|                    | contained detailed information      |                                          |
-|                    | about the fit, like the             |                                          |
-|                    | ``COVARIANCE MATRIX``,              |                                          |
-|                    | ``CORRELATION COEFFICIENTS``, etc.  |                                          |
-+--------------------+-------------------------------------+------------------------------------------+
-| **SET BATCH**      | Obsolate. Only present for          |                                          |
-|                    | backward compatibilty.              |                                          |
-+--------------------+-------------------------------------+------------------------------------------+
-| **END RETURN**     | Obsolete. Only present for          |                                          |
-|                    | backward compatibility.             |                                          |
-+--------------------+-------------------------------------+------------------------------------------+
-| **MAX_LIKELIHOOD** | If present, use max. log likelihood | see :ref:`musrfit-command-block-details` |
-|                    | rather than the default             |                                          |
-|                    | :math:`\chi^2`.                     |                                          |
-+--------------------+-------------------------------------+------------------------------------------+
-| **PRINT_LEVEL**    | Prints more or less messages to the | [#f3]_                                   |
-|                    | stdout. Allowed values: 0-3         |                                          |
-+--------------------+-------------------------------------+------------------------------------------+
-| **SCAN**           | A command line based option, which  | [#f3]_                                   |
-|                    | allows to scan :math:`\chi^2` by    |                                          |
-|                    | vary a single parameter.            |                                          |
-|                    | ``SCAN`` needs to be followed by    |                                          |
-|                    | the command ``MNPLOT``.             |                                          |
-+--------------------+-------------------------------------+------------------------------------------+
-| **CONTOURS**       | A command line based option. It     | [#f3]_                                   |
-|                    | allows to plot the contour of       |                                          |
-|                    | parX vs parY.                       |                                          |
-|                    | ``CONTOURS`` needs to be followed   |                                          |
-|                    | by the command ``MNPLOT``.          |                                          |
-+--------------------+-------------------------------------+------------------------------------------+
-| **MNPLOT**         | Helper command for the commands     |                                          |
-|                    | ``SCAN`` and ``CONTOURS``.          |                                          |
-+--------------------+-------------------------------------+------------------------------------------+
-| **FIX**            | Allows to fix parameters on the     | see :ref:`musrfit-command-block-details` |
-|                    | command level. It can help to guide |                                          |
-|                    | a complicated fit (e.g. muonium     |                                          |
-|                    | :math:`\mu^+`.                      |                                          |
-+--------------------+-------------------------------------+------------------------------------------+
-| **RELEASE**        | Allows to release parameters on the | see :ref:`musrfit-command-block-details` |
-|                    | command level which have been fixed |                                          |
-|                    | before. It can help to guide        |                                          |
-|                    | a complicated fit (e.g. muonium     |                                          |
-|                    | :math:`\mu^+`.                      |                                          |
-+--------------------+-------------------------------------+------------------------------------------+
-| **RESTORE**        | Releases **all** fixed parameters.  | see :ref:`musrfit-command-block-details` |
-+--------------------+-------------------------------------+------------------------------------------+
-| **FIT_RANGE**      | Allows to change the fit range on   | see :ref:`musrfit-command-block-details` |
-|                    | the command level. This might be    |                                          |
-|                    | helpful in conjunction with         |                                          |
-|                    | multiple signals in the spectrum.   |                                          |
-+--------------------+-------------------------------------+------------------------------------------+
-| **SCALE_N0_BKG**   | For histogram fits only.            | see :ref:`musrfit-command-block-details` |
-|                    | If set true (default), it will      |                                          |
-|                    | scale :math:`N_0` to 1/ns,          |                                          |
-|                    | Otherwise :math:`N_0` is given in   |                                          |
-|                    | counts.                             |                                          |
-+--------------------+-------------------------------------+------------------------------------------+
-| **SECTOR**         | Allows to output :math:`\chi^2` or  | see :ref:`musrfit-command-block-details` |
-|                    | maxLH values for a sub-range of the |                                          |
-|                    | fitted time range.                  |                                          |
-|                    | Used for statistical analysis only. |                                          |
-+--------------------+-------------------------------------+------------------------------------------+
-
-.. rubric:: Minuit2 Command Notes
-
-.. [#f3] see `MINUIT2 users guide <https://root.cern.ch/root/htmldoc/guides/minuit2/Minuit2.html>`_
-
-
-.. index:: dks-command-overview
-.. _dks-command-overview:
-
-DKS Command Overview
-^^^^^^^^^^^^^^^^^^^^
-
-+--------------------+--------------------------------------+--------------+
-| **DKS Extension**  | brief description                    | Reference    |
-+====================+======================================+==============+
-| **OpenMP**         | Invoke OpenMP if allowed by the OS.  | [#f4]_       |
-|                    | Currently macOS does *not* support   |              |
-|                    | OpenMP out of the box. All Linux     |              |
-|                    | flavours do so.                      |              |
-+--------------------+--------------------------------------+--------------+
-| **CUDA**           | For properly setup Nvidia graphic    | [#f5]_       |
-|                    | cards (e.g. Tesla K40c).             |              |
-|                    | Allows to off-load the minimization  |              |
-|                    | to the GPU. Speedups of up to 50     |              |
-|                    | are possible!                        |              |
-+--------------------+--------------------------------------+--------------+
-| **OpenCL-CPU**     | Invoke OpenCL on the CPU if the      | [#f6]_       |
-|                    | OS supports it. This might be useful |              |
-|                    | for macOS.                           |              |
-+--------------------+--------------------------------------+--------------+
-| **OpenCL-GPU**     | Invoke OpenCL on the GPU if the      | [#f6]_       |
-|                    | OS supports it. This might be useful |              |
-|                    | for macOS and for systems having a   |              |
-|                    | powerful AMD graphics card in place. |              |
-+--------------------+--------------------------------------+--------------+
-
-.. rubric:: DKS Command Notes
-
-.. [#f4] Standard ``musrfit`` as well as DKS support `OpenMP <https://www.openmp.org/>`_.
-         It allows to use all your threads of your CPU(s) during the minimization.
-
-.. [#f5] This is only supported for the ``DKS`` version of ``musrfit``. For details about
-         ``CUDA`` see `NVIDIA <https://developer.nvidia.com/cuda-zone>`_.
-
-.. [#f6] This is only supported for the ``DKS`` version of ``musrfit``. For details about
-         ``OpenCL`` see `the Khronos Group <https://www.khronos.org/opencl/>`_.
-
-
-.. index:: musrfit-command-block-details
-.. _musrfit-command-block-details:
-
-``musrfit`` Command Block Details
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-
-A standard COMMANDS block then looks like this:
-
-::
-
-  COMMANDS
-  MINIMIZE
-  MINOS
-  SAVE
-
-Additional to the commands listed above also the command **MAX_LIKELIHOOD** is valid. This keyword can be placed anywhere in 
-the block and switches from the default :math:`\chi^2` minimization to the log likelihood maximization which can be advantageous 
-if one is dealing with low-statistics data.
-
-Furthermore, it is possible to call the ``MINUIT2`` methods **SCAN** and **CONTOURS** together with **MNPLOT**. 
-Exemplary invocations are as follows:
-
-::
-
-  COMMANDS
-  SCAN 7
-  MNPLOT
-
-or
-
-::
-
-  COMMANDS
-  MINIMIZE
-  CONTOURS 8 9
-  MNPLOT
-  SAVE
-
-Sometimes it is necessary to guide ``MINUIT2`` to the global optimum. For this purpose it is useful to have the commands 
-**FIX <list_of_param_to_be_fixed>**, **RELEASE <list_of_param_to_be_fixed>**, and **RESTORE** at hand. **<list_of_param_to_be_fixed>** 
-is a list of the parameters to be fixed/released. It is a space- or comma-separated list of either parameter numbers and/or parameter names. 
-**RESTORE** releases all the fixed parameters. A typical example could look like:  
-
-::
-
-  COMMANDS
-  FIX Freq1, Freq2
-  MINIMIZE
-  RESTORE
-  MINIMIZE
-  MINOS
-  SAVE
-  
-It is important to understand that before **MINOS** is called, all the fixed parameters need to be released and another minimizer 
-command (**MINIMIZE**, **MIGRAD**, or **SIMPLEX**) needs to be in place, otherwise musrfit will assume that the still fixed parameters 
-have to be handled as constant parameters, *i.e.* setting the <step> value of the parameter to zero.   
-
-For even more complex fitting the additional command **FIT_RANGE [RESET | t**\ :sub:`start` **t**\ :sub:`end` **| t**\ :sub:`s1` **t**\ :sub:`e1` 
-**t**\ :sub:`s2` **t**\ :sub:`e2` **... t**\ :sub:`sn` **t**\ :sub:`en` **]** is provided. It allows to change the fit range during different iterations. 
-The command **FIT_RANGE t**\ :sub:`start` **t**\ :sub:`end` changes the current fit range for all the runs present in the msr file. 
-**FIT_RANGE RESET** will restore to the original fit ranges as provided in the :ref:`RUN block <msr-run-block>`. If for each run of the 
-msr file an individual fit range should be used, the third option applies. Here **n** has to correspond to the number of runs in the RUN block. 
-
-As for the run block, there is a 2\ :sup:`nd` flavor how the **FIT_RANGE** can be changed, namely giving the fit range in bins, 
-*i.e.* **FIT_RANGE [ RESET | fgb+<n0> lgb-<n1> | fgb+<n00> lgb-<n01> fgb+<n10> lgb-<n11> ... fgb+<nN0> lgb-<nN1> ]** where **N** is the number of available run blocks. 
-The idea is inline with the above syntax and the syntax describe for the fit range (fit) of the :ref:`RUN block <msr-run-block>`. 
-
-A typical example could look like:
-
-::
-
-  COMMANDS
-  FIT_RANGE 0.0 0.8
-  MINIMIZE
-  FIT_RANGE RESET
-  MINIMIZE
-  MINOS
-  SAVE
-
-or
-
-::
-
-  COMMANDS
-  FIT_RANGE fgb+15 lgb-1332 fgb+17 lgb-1330
-  MINIMIZE
-  FIT_RANGE RESET
-  MINIMIZE
-  MINOS
-  SAVE
-  
-The command **SCALE_N0_BKG TRUE | FALSE** is only used in conjunction with single-histogram fits. 
-The default is **SCALE_N0_BKG TRUE** which will result in a scaling of *N(t)* such that it is given in ns\ :sup:`-1`, whereas with **SCALE_N0_BKG FALSE** 
-*no scaling* is performed and *N(t)* will be given in bin\ :sup:`-1`. If the command is not present at all, it will be interpreted as if **SCALE_N0_BKG TRUE** was present.
-
-For "debug" purposes it is possible to force MINUIT2 to print out additional information. The COMMAND block command is **PRINT_LEVEL <n>**, 
-where **<n>** can have the values 0,1,2, or 3. A typical example could look like:
-
-::
-
-  COMMANDS
-  MIGRAD
-  SAVE
-  PRINT_LEVEL 2
-  MINOS
-  SAVE
-
-Here the MINOS command will print out lot of additional information to the standard output. Notice there are 2 SAVE commands here. This will write the result of 
-MIGRAD to the MINUIT2.OUTPUT file and at the end append the MINOS results to this file.  
-  
-The command **SECTOR <list-of-sector-times>**, where ``<list-of-sector-times>`` is a list of time values (space or comma separated) which have to range between the fit-start-time and the fit-end-time, allows to report :math:`\chi^2` and maxLH values for sub-intervals of the given fit-range. Its only purpose is for a statistical analysis of complicated fits. The results will be written to the ``MINUIT2.OUTPUT`` file.
-
-An example might look like this (assuming a fit-range from 0.005 to 10 us):
-
-::
-
-  COMMANDS
-  MINIMIZE
-  MINOS
-  SECTOR 5.0, 7.5, 9.0
-  SAVE
-
-*Note:* If a fit is invoked, the sector command results will only be written to file, if the fit *has converged*!
-
-.. index:: msr-commands-block-dks
-.. _msr-commands-block-dks:
-
-DKS extensions of the COMMANDS block enabling GPU and general OpenCL support
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-
-In case you are running the musrfit / DKS version, there are a couple commands which allow you to control the way how the fit shall be performed. These commands are: 
-
-============== ===========================================================================================================
-Command        Purpose
-============== ===========================================================================================================
-**OpenMP**     tries to run multi-threading via OpenMP if available
-**CUDA**       tries to run the fit on a NVIDIA card as *e.g.* the Tesla K40c 
-**OpenCL-CPU** tries to run multi-threading via OpenCL on the CPU. This is useful for macOS 
-**OpenCL-GPU** tries to run multi-threading via OpenCL on the GPU. This is used for AMD cards, but also works for NVIDIA 
-============== ===========================================================================================================
-
-**OpenMP** is the default if none of these tags are found in the COMMANDS block. 
-
-In case the defined THEORY is *not* ready to run on the accelerator, ``musrfit`` will fall back to the default behavior. 
-In the :ref:`THEORY table <msr-theory-block>` all the functions which are currently *not* GPU ready are labeled by "not DKS ready" in the reference column or corresponding footnote. 
-
-.. index:: msr-fourier-block
-.. _msr-fourier-block:
-
-The FOURIER Block 
-+++++++++++++++++
-
-If a Fourier transform is carried out the results are plotted within ``musrview``. As input data the actual data *shown* in ``musrview`` is used, 
-*i.e.* the currently time range shown in ``musrview``! In the FOURIER block of the msr file all necessary parameters for calculating and presenting 
-the Fourier transform of the data specified in the :ref:`PLOT block <msr-plot-block>` is given. If the FOURIER block is not present in the msr file, 
-either the parameters set in the :ref:`XML startup <musrfit-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: 
-
-.. index:: fourier-block-units
-.. _msr-fourier-block-units:
-
-**units**
-  Here is specified in which domain the Fourier-transformed data is presented. One may choose between the fields (*Gauss*) or (*Tesla*), the frequency (*MHz*), and the angular-frequency domain (*Mc/s*). 
-  
-.. index:: fourier-block-fourier_power
-.. _msr-fourier-block-fourier_power:
-
-**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 2\ :sup:`n`. **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*)! 
-
-.. index:: fourier-block-dc-corrected
-.. _msr-fourier-block-dc-corrected:
-
-**dc-corrected**
-  a flag to remove a potential DC-offset of the signal. Allowed entries are ``dc-corrected true | 1 | false | 0``. 
-  
-.. index:: fourier-block-apodization
-.. _msr-fourier-block-apodization:
-
-**apodization** 
-  Here is decided if the data should be apodized before the Fourier transform is performed and if yes, which apodization should be used (for further details about apodization of 
-  |mgr|\SR data refer to the `PhD thesis of T.M. Riseman (UBC) <https://open.library.ubc.ca/cIRcle/collections/ubctheses/831/items/1.0085550>`_). 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
-
-  .. math::
-
-     \sum_{k=0}^4 c_k \left(\frac{i}{n}\right)^{2k},
-   
-  where *i* is the data-point index and *n* is the total number of data points. The coefficients *c*\ :sub:`j` for the different apodizations are given by:
-  
-  **WEAK**
-    :math:`c_0 = 1.0,\, c_1 = -1.319391,\, c_2 = 0.703484,\, c_3=c_4=0.0`
-  **MEDIUM**
-    :math:`c_0 = 1.0,\, c_1 = -1.831292,\, c_2 = 0.983734,\, c_3=c_4=0.0`
-  **STRONG**
-    :math:`c_0 = 1.0,\, c_1 = -2.708894,\, c_2 = 2.953575,\, c_3=-1.599128,\, c_4=0.399782`
-  
-.. index:: fourier-block-plot
-.. _msr-fourier-block-plot:
-
-**plot**  
-  At this point it is possible to set the part of the Fourier-transformed data which should be plotted by default if the Fourier transform is done by pressing the *f*-key in ``musrview``. 
-  The argument may be one of the following: 
-  
-  **real**
-    The real part of the (complex) Fourier transform is plotted. 
-  **imag**
-    The imaginary part of the Fourier transform is plotted. 
-  **real_and_imag**
-    Both the real and the imaginary parts of the Fourier transform are shown. 
-  **power**
-    The absolute value of the Fourier transform is depicted. 
-  **phase**
-    The phase of the Fourier transform is plotted. 
-
-.. index:: fourier-block-phase
-.. _msr-fourier-block-phase:
-
-**phase**
-  If a real Fourier shall be plotted, it is necessary to adopt the phases of the different detectors. The number of potentially provided phases can be either **one**, which means that this phase will be applied to *all* Fourier spectra, 
-  or the number of phases have to correspond to the number of runs in the plot block.
-  
-  Currently there are three options:
-  
-  #. The phases for each run/detector are given explicitly, *i.e.* 
-  
-     .. code-block:: bash
-     
-        phase val0 sep val1 sep ... sep valN
-        
-     where ``val0``, ``val1``, etc. are explicitly given phases (*i.e.* doubles), and ``sep`` is one of the following allowed separators: ``space``, ``,``, ``;``, or ``tab``.
-     For example
-     
-     .. code-block:: bash
-     
-        phase   -3.2, 175.9
-        
-  #. The phases for each run/detector are given as phase parameter from the :ref:`FITPARAMETER block <msr-fitparameter-block>`, *e.g.* par3, which would 
-     take the value of parameter number 3. More explicitly
-     
-     .. code-block:: bash
-     
-        phase parX0 sep parX1 sep ... sep parXN
-        
-     where the same rules applies as for explicit phase values. An example could look like this
-     
-     .. code-block:: bash
-     
-        phase par7, par12, par17, par22, par27, par32, par37, par42, par47, par52, par57, par62, par67, par72, par77, par82
-        
-     One might prefer to express the phases in respect to a reference counter, *e.g.* the forward counter is the reference counter phase (fcp) whereas
-     the backward counter phase (bcp) is expressed as bcp = fcp + relative_bcp. If the fitting is done along these lines, the phases in the Fourier
-     block can be expressed the following way
-     
-     .. code-block:: bash
-     
-        phase parRX0 sep parX1 sep ... sep parXN
-        
-     which means that ``X0`` is the reference phase, and all the other phases are relative phases in respect to ``X0``, *i.e.* the absolut phase of
-     ``Xj`` would be the summ of the values of ``parX0`` and ``parXj`` etc. The reference phase in the list is marked by ``parR`` rather than ``par``.
-     Obviously only *one* reference phase can be defined!
-  
-  #. Often the phases in the parameter block follow a clear list structure. This allows to write the Fourier phase parameters in a more compact form
-  
-     .. code-block:: none
-     
-        phase par(X0, offset, #param)
-        
-     with ``X0`` the first phase parameter index, ``offset`` being the offset to the next phase parameter, and ``#param`` being the number of phase parameters to be used.
-     This means that the previous example can be compacted to
-     
-     .. code-block:: none
-     
-        phase par(7, 5, 16)
-        
-     As in the phase parameter list examples before, also here a reference phase with relative phases might be wished. Differently to the phase parameter
-     list example, the first parameter number will be the reference phase. The compact notation here is
-     
-     .. code-block:: none
-     
-        phase parR(X0, offest, #param)
-  
-.. index:: fourier-block-range_for_phase_correction
-.. _msr-fourier-block-range_for_phase_correction:
-
-**range_for_phase_correction**
-  An interval in Fourier space given in units as define with the 'units' tag, or the tag 'all' in which case the range given under 'range' will be used. 
-  The given interval will be used for an automatic phasing of the real Fourier transform. This will allow to add real Fourier spectra coherently.   
-
-.. index:: fourier-block-range
-.. _msr-fourier-block-range:
-
-**range**  
-  The plotting range is set here. The interval is specified through its start and end points given in the *units* set after the **units** tag. 
-  
-Altogether, a possible FOURIER block might look like that: 
-
-::
-
-  FOURIER
-  units Mc/s
-  fourier_power 12
-  apodization NONE
-  plot real_and_imag
-  phase par5, par8
-  range 0.0 17.03
-  
-.. index:: msr-plot-block
-.. _msr-plot-block:
-
-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 have to match the :ref:`fit types <fit-types>`. 
-Additionally, it is possible to provide information using the following keywords: 
-
-.. index:: msr-plot-block-lifetimecorrection
-.. _msr-plot-block-lifetimecorrection:
-
-**lifetimecorrection**
-  Does not accept any arguments. If present, the output in ``musrview`` is corrected for the exponential decay of the muon. Only relevant for (type 0). 
-
-.. index:: msr-plot-block-runs
-.. _msr-plot-block-runs:
-
-**runs**
-  The numbers of the runs to be plotted have to be put here. The runs are numbered according to their appearance in the :ref:`RUN block <msr-run-block>`.
-  The numbers is either a space separated list of numbers, an interval *e.g.* 1-16, or a combination of both.
-  
-.. index:: msr-plot-block-range
-.. _msr-plot-block-range:
-
-**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 
-  micro-seconds and the *N* in counts (types 0-4) or in counts/nsec (type 0, 1): 
-  
-  fit type 0-4 *without* lifetimecorrection:
-    *t*\ :sub:`min` *t*\ :sub:`max` [ *N*\ :sub:`min` *N*\ :sub:`max` ] 
-  fit type 0-3 *with* lifetimecorrection:
-    *t*\ :sub:`min` *t*\ :sub:`max` [ *A*\ :sub:`min` *A*\ :sub:`max` ] 
-  fit type 8:
-    *x*\ :sub:`min` *x*\ :sub:`max` [ *y*\ :sub:`min` *y*\ :sub:`max` ]
-    
-.. index:: msr-plot-block-sub_ranges
-.. _msr-plot-block-sub_ranges:
-
-**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: 
-  
-  fit type 0-4 *without* lifetimecorrection:
-    *t*\ :sup:`1`\ :sub:`min`  *t*\ :sup:`1`\ :sub:`max` *t*\ :sup:`2`\ :sub:`min` *t*\ :sup:`2`\ :sub:`max` ... *t*\ :sup:`n`\ :sub:`min` *t*\ :sup:`n`\ :sub:`max` [ *N*\ :sub:`min` *N* :sub:`max` ] (n = the number of runs to be plotted) 
-  fit type 0-3 *with* lifetimecorrection:
-    *t*\ :sup:`1`\ :sub:`min`  *t*\ :sup:`1`\ :sub:`max` *t*\ :sup:`2`\ :sub:`min` *t*\ :sup:`2`\ :sub:`max` ... *t*\ :sup:`n`\ :sub:`min` *t*\ :sup:`n`\ :sub:`max` [ *A*\ :sub:`min` *A* :sub:`max` ] (n = the number of runs to be plotted) 
-  fit type 8:
-    *not yet implemented*
-    
-.. index:: msr-plot-block-use_fit_ranges
-.. _msr-plot-block-use_fit_ranges:
-
-**use_fit_ranges** [ *y*\ :sub:`min` *y*\ :sub:`max` ]
-    The fit ranges of the individual runs are used to present the data. Optionally, an ordinate range can be provided.     
-
-.. index:: msr-plot-block-view_packing
-.. _msr-plot-block-view_packing:
-
-**view_packing**     
-  The data are presented in the packing given here rather than the binning used for the fit. **WARNING:** This is a global option and applies to all PLOT-blocks. 
-  
-.. index:: msr-plot-block-logx
-.. _msr-plot-block-logx:
-
-**logx**
-  Will present the time axis in a logarithmic scale. *So far no checking of negative and zero-valued data is performed, hence expect interesting output!* 
-  
-.. index:: msr-plot-block-logy
-.. _msr-plot-block-logy:
-
-**logy**
-  Will present the axis of ordinates in a logarithmic scale. *So far no checking of negative and zero-valued data is performed, hence expect interesting output!*
-  
-.. index:: msr-plot-block-rrf_packing
-.. _msr-plot-block-rrf_packing:
-
-**rrf_packing** value
-  In the rotating-reference-frame (RRF) representation, this will be the value for the packing. **WARNING:** For the time being, this is a global option and applies to all PLOT blocks.   
-  
-.. index:: msr-plot-block-rrf_freq
-.. _msr-plot-block-rrf_freq:
-
-**rrf_freq** value unit
-  This entry provides the RRF "frequency" given by the value and the unit which can be: *kHz*, *MHz*, *Mc/s*, *G*, or *T*. 
-
-.. index:: msr-plot-block-rrf_phase
-.. _msr-plot-block-rrf_phase:
-
-**rrf_phase** value
-  A phase of the RRF can be provided, either as a value in degrees, or as a parX, *e.g.* par4, where 'X' is supposed to be the phase parameter number in the :ref:`FITPARAMETER block <msr-fitparameter-block>`. 
-
-**Notes:**
-  * If no plot range is given at all, the fit range of the first run also serves as time window for the plot.   
-  * In the case no information on the axis of ordinates is available, the plotting range is chosen so that all data can be presented.
-  * It is possible to define multiple PLOT blocks. Each PLOT block generates its own ROOT canvas.
-
-A typical PLOT block could look like 
-
-::
-
-  ###############################################################
-  PLOT 0   (single histo plot)
-  lifetimecorrection
-  runs    1-16   
-  range   0   9.07   -0.5   0.5
-
-A few comments concerning the rotating reference frame (rrf) plot option: the idea of the rrf is to transform a high frequency 
-|mgr|\SR spectrum into a low frequency spectrum. This is essentially done by multiplying the original asymmetry 
-:math:`A(t)` by :math:`\cos(\omega_{\rm rrf} t + \phi_{\rm rrf})`. This leads to two frequency shifted copies of the original 
-:math:`A(t)`, one shifted downwards in frequency by :math:`\omega_{\rm rrf}` (the wanted one) and one upwards (the unwanted one). 
-In order to get rid of the upward shifted spectrum, the **rrf_packing** is used, we just over-bin the high frequency copy.
-The theory, however, is filtered via `Kaiser filter <https://en.wikipedia.org/wiki/Kaiser_window>`_. Here a short example: 
-
-::
-
-  ###############################################################
-  PLOT 1   (single histo RRF plot)
-  runs     1   
-  range    0   10   -0.3   0.3
-  rrf_freq 13900 G
-  rrf_packing 75
-    
-.. index:: msr-statistc-block
-.. _msr-statistic-block:
-
-The STATISTIC Block
-+++++++++++++++++++
-
-The STATISTIC block is the last block of a msr file. It contains some information on the fit: the date and time as well as 
-the absolute and normalized values of :math:`\chi^2` and the number of degrees of freedom in the fit.
-If enabled in the :ref:`XML file <musrfit-startup>` for :math:`\chi^2`-single-histogram fits also `Pearson's`_ 
-:math:`\chi^2` will be written to the STATISTIC block.
-
-*These information only have a meaning if the fitting procedure has been executed at least once and the fit has converged!* 
-
-.. index:: fit-types
-.. _fit-types:
-
-Fit Types
----------
-
-.. index:: single-histogram-fit
-.. _single-histogram-fit:
-
-Single Histogram Fit (fit type 0)
-+++++++++++++++++++++++++++++++++
-
-The single-histogram fit (fit type 0) is used to fit a function directly to the raw data using
-
-.. math::
-   N(t) = N_0 e^{-t/\tau_\mu} [ 1 + A(t) ] + N_{\rm bkg}
-   
-The parameters are given by:
-  * :math:`N(t)`: rebinned decay histograms
-  * :math:`N_0`: normalization constant of the histogram (RUN block: :ref:`norm <msr-norm>`)
-  * :math:`\tau_\mu`: lifetime of the muon (RUN block: :ref:`lifetime <msr-lifetime>`)
-  * :math:`N_{\rm bkg}`: constant background (RUN block: :ref:`backgr.fit <msr-backgr.fit>`, :ref:`backgr.fix <msr-backgr.fix>`,  or :ref:`background <msr-background-single-histo>`)  
-  * :math:`A(t)`: decay asymmetry/depolarization function as given in the :ref:`THEORY block <msr-theory-block>`)
-
-In the plot type 0 without ``lifetimecorrection`` the rebinned histogram and the function *N(t)* written above are presented. 
-If the option lifetimecorrection is *set* in the PLOT block the asymmetry is plotted: 
-
-.. math::
-   A(t) = \frac{N(t) - N_{\rm bkg}}{N_0} e^{+t/\tau_\mu} - 1 
-
-.. index:: single-histogram-rrf-fit
-.. _single-histogram-rrf-fit:
-
-Single Histogram RRF Fit (fit type 1)
-+++++++++++++++++++++++++++++++++++++
-
-The single-histogram RRF fit (fit type 1) is used to fit the rotating reference frame asymmetry :math:`A_{\rm rrf}(t)` extracted from the raw data. 
-The currently implemented version will fail at low fields/frequencies (for about < 1 Tesla). The same is true, if multiple frequencies with large 
-enough separation are present, *e.g.* when dealing with muonium. :math:`A_{\rm rrf}(t)` is estimated the following way (for more details see the 
-RRF memo (<musrfit>/doc/memos/rrf/rrf-notes.pdf)):
-
-  #. define the background :math:`N_{\rm bkg}`, and subtract it from the raw histogram. 
-  #. calculate the property :math:`M(t) = [N(t)-N_{\rm bkg}] \exp(+t/\tau)`. 
-  #. estimate :math:`N_0`. This is the most tricky part. From this calculate :math:`A(t) = M(t)/N_0 -1`. 
-  #. now the RRF transformation takes place: :math:`A_{\rm rrf}(t) = 2 \cos(\omega_{\rm rrf} t + \phi_{\rm rrf}) A(t)`. 
-     In Fourier space this is leading to :math:`[A(\omega-\omega_{\rm rrf})+A(\omega+\omega_{\rm rrf})]`.
-  #. in order to get rid if the :math:`A(\omega+\omega_{\rm rrf})` component, :math:`A_{\rm rrf}(t)` is over-binned 
-     by the :ref:`rrf_packing <msr-plot-block-rrf_packing>`. This results in a signal :math:`\langle A_{\rm rrf}(t) \rangle_{p}` 
-     which ideally is :math:`A(t)` shifted down in frequency by :math:`\omega_{\rm rrf}`. 
-
-The single histogram RRF fit was introduced for online analysis **only**. It is leading to many uncontrolled effects like ghost lines due to imperfection 
-of the :math:`N_0` estimate, line shape distortion due to dispersive filtering originating from the packing, back folding problems if 
-:math:`\omega_{\rm rrf}` is not properly chosen, the error estimates on the fitted parameters is substantially worse, *etc.* 
-**In summary: if you not urgently need it: do not use it! There are better ways to deal with the analysis of high frequency data!**
-For more details see the rrf-memo found in the source code under <musrfit>/doc/memo/rrf/rrf-notes.pdf or `Musrfit–Real Time Parameter Fitting Using GPUs <http://dx.doi.org/10.7566/JPSCP.21.011051>`_
-
-.. index:: asymmetry-fit
-.. _asymmetry-fit:
-
-Asymmetry Fit (fit type 2)
-++++++++++++++++++++++++++
-
-For an asymmetry fit (fit type 2) two histograms are needed. These are given by the :ref:`forward <msr-forward-backward>` and :ref:`backward <msr-forward-backward>` keywords 
-in the :ref:`RUN block <msr-run-block>`. Additionally, the parameters :ref:`alpha <msr-alpha-beta>` and :ref:`beta <msr-alpha-beta>` which relate the detector 
-efficiencies, solid angles and initial asymmetries of the two detectors can be supplied. The constant background for the two histograms is either given by 
-:ref:`background-determined intervals <msr-background-asymmetry>` or specified through :ref:`backgr.fix <msr-backgr.fix>` in the :ref:`RUN-block <msr-run-block>`. 
-
-The experimental asymmetry :math:`a(k)` then is inferred from the two histograms:
-
-.. math::
-
-   a(k)=\frac{\left[N_{\mathrm{f}}(k)-B_{\mathrm{f}}\right]-\left[N_{\mathrm{b}}(k)-B_{\mathrm{b}}\right]}{\left[N_{\mathrm{f}}(k)-B_{\mathrm{f}}\right]+\left[N_{\mathrm{b}}(k)-B_{\mathrm{b}}\right]},
-   
-with
-
-   * :math:`N_{\mathrm{f}}(k)`: counts in the **forward** histogram channel :math:`k`
-   * :math:`N_{\mathrm{b}}(k)`: counts in the **backward** histogram channel :math:`k`
-   * :math:` B_{\mathrm{f}}`: constant background in the **forward** histogram (RUN block: :ref:`backgr.fix <msr-backgr.fix>` or :ref:`background <msr-background-asymmetry>`) 
-   * :math:` B_{\mathrm{b}}`: constant background in the **backward** histogram (RUN block: :ref:`backgr.fix <msr-backgr.fix>` or :ref:`background <msr-background-asymmetry>`) 
-   
-This theoretical asymmetry :math:`a(t)` is used to fit the function   
-
-.. math::
-
-   a(t)=\frac{(\alpha\beta +1)A(t)-(\alpha -1)}{(\alpha +1)-(\alpha\beta -1)A(t)}, 
-    
-where
-
-   * :math:`\alpha`: accounts for the different detector efficiencies and solid angles (RUN block: :ref:`alpha <msr-alpha-beta>`).
-   * :math:`\beta`: accounts for the different detector asymmetries (RUN block: :ref:`beta <msr-alpha-beta>`).
-   * :math:`A(t)`: is the depolarization function as given in the :ref:`THEORY block <msr-theory-block>`.
-   
-For the graphical representation in plot type 2 the equation above is rearranged to get :math:`A(t)`:   
-
-.. math::
-
-    A(t)=\frac{(\alpha -1)+(\alpha +1)a(t)}{(\alpha\beta +1)+(\alpha\beta -1)a(t)}=\frac{\alpha\left[N_{\mathrm{f}}(t)-B_{\mathrm{f}}\right]-\left[N_{\mathrm{b}}(t)-B_{\mathrm{b}}\right]}{\alpha\beta\left[N_{\mathrm{f}}(t)-B_{\mathrm{f}}\right]+\left[N_{\mathrm{b}}(t)-B_{\mathrm{b}}\right]} 
-    
-and plotted together with the function given in the THEORY block.     
-
-.. index:: asymmetry-rrf-fit
-.. _asymmetry-rrf-fit:
-
-Asymmetry RRF Fit (fit type 3)
-++++++++++++++++++++++++++++++
-
-For asymmetry RRF Fit (fit type 3) two histograms are needed. In a first step, the unbinned asymmetry is formed as described for the asymmetry fit. 
-Afterwards the RRF transformation is carried out, *i.e.* point 4. and 5. as sketched in the single histogramm RRF fit. The same reservations as for 
-the single histogram RRF fit apply: **if you not urgently need it: do not use it! There are better ways to deal with the analysis of high frequency data!**
-
-.. index:: negative-muon-musr-fit
-.. _negative-muon-musr-fit:
-
-Negative Muon |mgr|\SR Fit (fit type 4)
-+++++++++++++++++++++++++++++++++++++++
-
-The negative muon |mgr|\SR fit (fit type 4) is used for single histogram fits of MuMinus, *i.e.*
-
-.. math::
-
-   N(t) = \sum_i N_i\,\mathrm{e}^{-t/\tau_i} \left[ 1 + A_i(t)\right] + N_{\rm bkg}(t) 
-
-where :math:`i` runs over the different lifetime channels of :math:`\mu^{-}`, and 
-   
-   * :math:`N_i`: counts of lifetime channel :math:`i`
-   * :math:`\tau_i`: lifetime of lifetime channel :math:`i` 
-   * :math:`A_i(t)`: depolarization function of lifetime channel :math:`i`
-   * :math:`N_{\rm bkg}(t)`: :math:`N_{\rm bkg}(t)= N_{\rm bkg,0} + \sum_k N_{\rm bkg,k} \cos(k \omega_{\rm cyclotron} t)` the background 
-   
-Since MuMinus is quite generic, the full functional depends has to be written in the :ref:`THEORY Block <msr-theory-block>`.
-   
-.. index:: bnmr-asymmetry-fit
-.. _bnmr-asymmetry-fit:
-
-beta-NMR Asymmetry Fit (fit type 5)
-+++++++++++++++++++++++++++++++++++
-
-Four histograms are needed for a beta-NMR asymmetry fit (fit type 5), two for positive helecity and two for negative. These are given by the :ref:`forward <msr-forward-backward>` and :ref:`backward <msr-forward-backward>` keywords 
-in the :ref:`RUN block <msr-run-block>`. Additionally, the parameters :ref:`alpha <msr-alpha-beta>` and :ref:`beta <msr-alpha-beta>` which relate the detector 
-efficiencies, solid angles and initial asymmetries of the two detectors can be supplied. The constant background for the two histograms is either given by 
-:ref:`background-determined intervals <msr-background-asymmetry>` or specified through :ref:`backgr.fix <msr-backgr.fix>` in the :ref:`RUN-block <msr-run-block>`. 
-
-The experimental asymmetry :math:`a(k)` is then calculated from the four histograms:
-
-.. math::
-
-   a(k)=\frac{\left[N_{\mathrm{fp}}(k)-B_{\mathrm{fp}}\right]-\left[N_{\mathrm{bp}}(k)-B_{\mathrm{bp}}\right]}{\left[N_{\mathrm{fp}}(k)-B_{\mathrm{fp}}\right]+\left[N_{\mathrm{bp}}(k)-B_{\mathrm{bp}}\right]}
-   - \frac{\left[N_{\mathrm{fm}}(k)-B_{\mathrm{fm}}\right]-\left[N_{\mathrm{bm}}(k)-B_{\mathrm{bm}}\right]}{\left[N_{\mathrm{fm}}(k)-B_{\mathrm{fm}}\right]+\left[N_{\mathrm{bm}}(k)-B_{\mathrm{bm}}\right]},
-   
-with
-
-   * :math:`N_{\mathrm{fp}}(k)`: counts in the **forward** histogram channel with positive helicity :math:`k`
-   * :math:`N_{\mathrm{bp}}(k)`: counts in the **backward** histogram channel with positive helicity :math:`k`
-   * :math:`B_{\mathrm{fp}}`: constant background in the **forward** histogram with positive helicity (RUN block: :ref:`backgr.fix <msr-backgr.fix>` or :ref:`background <msr-background-asymmetry>`) 
-   * :math:`B_{\mathrm{bp}}`: constant background in the **backward** histogram with positive helicity (RUN block: :ref:`backgr.fix <msr-backgr.fix>` or :ref:`background <msr-background-asymmetry>`) 
-   * :math:`N_{\mathrm{fm}}(k)`: counts in the **forward** histogram channel with negative helicity :math:`k`
-   * :math:`N_{\mathrm{bm}}(k)`: counts in the **backward** histogram channel with negative helicity :math:`k`
-   * :math:`B_{\mathrm{fm}}`: constant background in the **forward** histogram with negative helicity (RUN block: :ref:`backgr.fix <msr-backgr.fix>` or :ref:`background <msr-background-asymmetry>`) 
-   * :math:`B_{\mathrm{bm}}`: constant background in the **backward** histogram with negative helicity (RUN block: :ref:`backgr.fix <msr-backgr.fix>` or :ref:`background <msr-background-asymmetry>`) 
-   
-This theoretical asymmetry :math:`a(t)` is used to fit the function   
-
-.. math::
-
-   a(t)=\frac{(\alpha\beta +1)A(t)-(\alpha -1)}{(\alpha +1)-(\alpha\beta -1)A(t)} - \frac{(\alpha -1)-(\alpha\beta 1)A(t)}{(\alpha +1)+(\alpha\beta -1)Am(t)}, 
-    
-where
-
-   * :math:`\alpha`: accounts for the different detector efficiencies and solid angles (RUN block: :ref:`alpha <msr-alpha-beta>`).
-   * :math:`\beta`: accounts for the different detector asymmetries (RUN block: :ref:`beta <msr-alpha-beta>`).
-   * :math:`A(t)`: is the depolarization function as given in the :ref:`THEORY block <msr-theory-block>`.
-   
-For the graphical representation in plot type 5 the equation above is rearranged to get :math:`A(t)`:   
-
-.. math::
-
-    A(t) &= \frac{(\alpha -1)+(\alpha +1)a(t)}{(\alpha\beta+1)+(\alpha\beta -1)a(t)}-\frac{(\alpha +1)a(t)-(\alpha-1)}{(\alpha\beta +1)+(1-\alpha\beta)a(t)} \\
-    &= \frac{\alpha\left[N_{\mathrm{fp}}(t)-B_{\mathrm{fp}}\right]-\left[N_{\mathrm{bp}}(t)-B_{\mathrm{bp}}\right]}{\alpha\beta\left[N_{\mathrm{fp}}(t)-B_{\mathrm{fp}}\right]+\left[N_{\mathrm{bp}}(t)-B_{\mathrm{bp}}\right]} -\frac{\alpha\left[N_{\mathrm{fm}}(t)-B_{\mathrm{fm}}\right]-\left[N_{\mathrm{bm}}(t)-B_{\mathrm{bm}}\right]}{\alpha\beta\left[N_{\mathrm{fm}}(t)-B_{\mathrm{fm}}\right]+\left[N_{\mathrm{bm}}(t)-B_{\mathrm{bm}}\right]}
-    
-and plotted together with the function given in the THEORY block.     
-
-    
-.. index:: non-musr-fit
-.. _non-musr-fit:
-
-Non-|mgr|\SR Fit (fit type 8)
-+++++++++++++++++++++++++++++
-
-In the case of a non-|mgr|\SR fit (fit type 8) the fitting function is 
-
-.. math::
-
-   y = f(x),
-   
-where :math:`x, y` are given by :ref:`xy-data <msr-xy-data>` in the :ref:`RUN block <msr-run-block>`, and :math:`f(x)` is the function defined in the :ref:`THEORY block <msr-theory-block>`. 
-
-The same applies for the plot with plot type 8. 
-
-.. index:: user-functions
-.. _user-functions:
-
-User Functions
---------------
-
-``musrfit`` offers the possibility to plug-in user-defined functions implemented in ``C++`` classes to the fitting and plotting routines. 
-In order to do so, basically two things are needed: 
-
-  #. a shared library containing the compiled class with the defined function.
-  #. a `ROOT dictionary <https://root.cern.ch/interacting-shared-libraries-rootcling>`_ that contains information about the functions in the shared library.
-
-There are two possible ways to implement user functions and both will be explained below: 
-
-  #. a user function *without* global user-function-object access
-  #. a user function *with* global user-function-object access 
-  
-Since the first is simpler this will be explained using an explicit example, before it is discussed why the second option is needed and how it can be used. 
-
-.. index:: user-functions-without-global-part
-.. _user-functions-without-global-part:
-
-User Function without global user-function-object access
-++++++++++++++++++++++++++++++++++++++++++++++++++++++++
-
-In the following it is explained in detail how the implementation of a user function is done using the simple example of :math:`f_a(x) = \sin(a x)/(a x)`, 
-where the parameter :math:`a` should be determined by the fit. Although not necessary for this simple example, the source code is split into two parts, 
-namely a header file ``TMyFunction.h`` containing the class declaration and a second file ``TMyFunction.cpp`` including the function implementation
-(the name of these files is your choice!). 
-
-To plug in the class to ``musrfit``, it is necessary that the class derives from the base class **PUserFcnBase** defined in the header file ``PUserFcnBase.h`` (which is a part of ``musrfit``). 
-In this abstract base class a function operator is defined that takes two arguments: the point where the function should be evaluated and a reference to a vector with all parameters of the function. 
-
-Therefore, the user's header file could look like the following:
-
-.. code-block:: c++
-
-  /*************************************************************************** 
- 
-  TMyFunction.h 
- 
-  ***************************************************************************/ 
- 
-  #include "PUserFcnBase.h" 
-  #include <cassert> 
-  #include <cmath> 
-  #include <vector> 
- 
-  using namespace std; 
- 
-  class TMyFunction : public PUserFcnBase { 
- 
-  public: 
-    // default constructor and destructor 
-    TMyFunction(){} 
-    ~TMyFunction(){} 
- 
-    // global user-function-access functions, here without any functionality 
-    Bool_t NeedGlobalPart() const { return false; } 
-    void SetGlobalPart(vector<void*> &globalPart, UInt_t idx) { } 
-    Bool_t GlobalPartIsValid() const { return true; } 
- 
-    // function operator 
-    Double_t operator()(Double_t, const vector<Double_t>&) const; 
- 
-    // definition of the class for the ROOT dictionary 
-    ClassDef(TMyFunction,1) 
-  };
-  
-In the header file above the constructor (destructor) of the class is empty. This is not necessary, any code that should be executed when the 
-:ref:`RUN block <msr-run-block>` is read and the class object is created (destroyed) may be implemented in the constructor (destructor). 
-Another peculiarity is the ``ClassDef`` statement at the end of the class definition. It is needed for the ROOT dictionary generation 
-and has as arguments the class name and a revision number.   
-
-Please also be aware of the const-ness of the operator(). For an introductory discussion on that topic look for example `Const_correctness <http://en.wikipedia.org/wiki/Const_correctness>`_ and the links herein. 
-
-The actual implementation of the user function is done in the second source file. In this example it only contains the definition of the function operator() declared in the header file and might look like: 
-
-.. code-block:: c++
-
-  /*************************************************************************** 
- 
-  TMyFunction.cpp 
- 
-  ***************************************************************************/ 
- 
-  #include "TMyFunction.h" 
- 
-  ClassImp(TMyFunction)  // for the ROOT dictionary 
- 
-  Double_t TMyFunction::operator()(Double_t x, const vector<Double_t> &par) const { 
-    assert(par.size()==1); // make sure the number of parameters handed to the function is correct 
-   
-    const Double_t eps = 1.0e-5;
-    Double_t arg(par[0]*x); 
- 
-    if(arg < eps) 
-      return 1.0; 
-    return sin(arg)/arg; 
-  }
-  
-Also this file contains a special statement for the ROOT dictionary generation (``ClassImp``), which is placed before the definition of the function. 
-If functions of more than one class are defined in the file, the ``ClassImp`` statements for the other classes follow right after the first one.   
-
-What is further needed for the ``ROOT`` dictionary is a so-called LinkDef file which again contains the class names of all classes that should be accessible 
-through the dictionary and has the following structure, where the "LinkDef.h" (or "linkdef.h" or "Linkdef.h") at the end of the file name is mandatory: 
-
-.. code-block:: c++
-
-  /*************************************************************************** 
- 
-  TMyLibraryLinkDef.h 
- 
-  ***************************************************************************/ 
- 
-  #ifdef __CINT__ 
- 
-  #pragma link off all globals; 
-  #pragma link off all classes; 
-  #pragma link off all functions; 
- 
-  #pragma link C++ class TMyFunction+; 
- 
-  #endif //__CINT__ 
-
-For compiling and linking it is wise to use a Makefile as for example the attached :download:`Makefile.TMyLibrary <../add-ons/Makefile.TMyLibrary>`. It assumes standard ``ROOT`` and ``musrfit`` 
-installations and defines rules for the generation of the shared library **libTMyLibrary.so** including the class and the ROOT dictionary. In order 
-to get the library built and installed on the standard ROOT path just call: 
-
-.. code-block:: bash
-
-  $ make -f Makefile.TMyLibrary
-  $ make -f Makefile.TMyLibrary install
-
-In case of a custom installation some paths in the Makefile might have to be adopted. For further information about the ROOT dictionary mechanism please 
-refer to the `documentation <https://root.cern.ch/interacting-shared-libraries-rootcling>`_.   
-
-After installing the shared library the defined user function might be used in musrfit as described :ref:`above <msr-theory-block-user-functions>`.
-
-Finally, please be aware of the :ref:`remark <user-function-important>` at the end of this section. 
-
-.. index:: user-functions-with-global-part
-.. _user-functions-with-global-part:
-
-User Function with global user-function-object access
-+++++++++++++++++++++++++++++++++++++++++++++++++++++
-
-Before explaining how to use global objects within user functions, it will be shortly explained where is the problem and why this might be a sensible approach. 
-In ``musrfit`` each :ref:`RUN block <msr-run-block>` (histogram, asymmetry, ...) is owning its own theory-function tree. An example is shown in the figure below. 
-The bluish nodes are default musrfit functions, whereas the red nodes represent user functions (here labeled by ``uF1`` and ``uF2``). Without global user-function 
-object, these nodes are independent entities. This means if the msr file contains *n* run blocks, the user function ``uF1`` will be called *n* times for each step 
-in the calculation. If the user function is performing CPU-demanding calculations this is rather inefficient.
-
-.. image:: ../images/theory-tree-with-user-fcn.*
-
-Therefore, it is possible to associate to each user function (``uFx``) a global user-function object (``g_uFx``). The idea is the following: If ``uFx`` needs to 
-perform very time-consuming calculations (*e.g.* calculate an Abrikosov vortex lattice or the nonlocal response of a superconductor in the Meissner state) this 
-can be transferred to the global user-function object (``g_uFx``) and hence the time-consuming calculation is only performed once per cycle (compared to *n* times 
-without ``g_uFx``), thus speeding up the fit.
-
-After explaining the purpose of the global user-function-object approach, some explanations how to interface it follow here. Since the interface is very close to 
-the :ref:`user function without global objects <user-functions-without-global-part>`, only the additionally necessary overhead is explained here.
-
-The user's header file could look like the following: 
-
-.. code-block:: c++
-
-  /***************************************************************************
-
-  TMyFunction.h
-
-  ***************************************************************************/
-
-  #include "PUserFcnBase.h"
-  #include <cassert>
-  #include <cmath>
-  #include <vector>
-
-  using namespace std;
-
-  class TMyGlobalFunction {
-
-  public:
-    // default constructor and destructor
-    TMyGlobalFunction(){}
-    ~TMyGlobalFunction(){}
-
-    Bool_t IsValid() { return fValid; } 
-
-    // the following function will check if something needs to be calculated, which 
-    // is the case if param != fPrevParam
-    void CalcSomethingCPUExpensive(const vector<Double_t> &param);
-
-    // this routine will return the calculated values, e.g. B(z,E) for TMyFunction::operator()()
-    // (...) here sketches only that some parameters are likley to be fed
-    Double_t GetWhatIsNeeded(...);
-
-  private:
-    Bool_t fValid;
-    vector<Double_t> fPrevParam;
-
-    // definition of the class for the ROOT-dictionary
-    ClassDef(TMyGlobalFunction,1)
-  };
-
-  class TMyFunction : public PUserFcnBase {
-
-  public:
-    // default constructor and destructor
-    TMyFunction(){}
-    ~TMyFunction(){}
-
-    // global user-function-access functions, here with some functionality
-    Bool_t NeedGlobalPart() const { return true; }
-    void SetGlobalPart(vector<void*> &globalPart, UInt_t idx);
-    Bool_t GlobalPartIsValid() const;
-
-    // function operator
-    Double_t operator()(Double_t, const vector<Double_t>&) const;
-
-  private:
-    Bool_t fValid;
-    Bool_t fInvokedGlobal;
-    Int_t  fIdxGlobal;
-    TMyGlobalFunction * fGlobalUserFcn;
-
-    // definition of the class for the ROOT dictionary
-    ClassDef(TMyFunction,1)
-  };
-
-Compared to the :ref:`user function without global objects <user-functions-without-global-part>`, here the ``NeedGlobalPart()`` method returns true 
-meaning that a global user-function object will be needed. Furthermore, the methods ``SetGlobalPart(vector<void*> &globalPart, UInt_t idx)`` and 
-``GlobalPartIsValid()`` now need to be implemented. The method ``SetGlobalPart(vector<void*> &globalPart, UInt_t idx)`` is used to link the 
-``fGlobalUserFcn`` to the global user object. This routine will look like: 
-
-.. code-block:: c++
-
-  void TMyFunction::SetGlobalPart(vector<void *> &globalPart, UInt_t idx)
-  {
-    fIdxGlobal = static_cast<Int_t>(idx);
-
-    if ((Int_t)globalPart.size() <= fIdxGlobal) { // global user function not present, invoke it
-      fGlobalUserFcn = new TMyGlobalFunction();
-      if (fGlobalUserFcn == 0) { // global user function object couldn't be invoked -> error
-        fValid = false;
-        cerr << endl << ">> TMyFunction::SetGlobalPart(): **ERROR** Couldn't invoke global user function object, sorry ..." << endl;
-      } else {  // global user function object could be invoked -> resize to global user function vector and keep the pointer to the corresponding object
-        globalPart.resize(fIdxGlobal+1);
-        globalPart[fIdxGlobal] = dynamic_cast<TMyGlobalFunction*>(fGlobalUserFcn);
-        fValid = true;
-        fInvokedGlobal = true;
-      }
-    } else { // global user function already present hence just retrieve a pointer to it
-      fValid = true;
-      fGlobalUserFcn = (TMyGlobalFunction*)globalPart[fIdxGlobal];
-    }
-  }
-
-What it does is the following: it first checks if the object is already present in the global user-function-object vector and if not creates it. If it is already present, 
-the pointer to the global object vector is just kept (see figure above). 
-
-A sketch of the method ``operator()(Double_t, const vector&) const`` will then look like (pseudo-code snippet): 
-
-.. code-block:: c++
-
-  Double_t TMyFunction::operator()(Double_t t, const vector<Double_t> &param) const
-  {
-    Double_t result = 0.0;
-
-    // do something, checking, etc.
-    ...
-
-    // call the global user function object (which will calculate something 
-    // if param has changed). Hence it will only be done once in a iteration, 
-    // and therefore only once for all run blocks.
-    fGlobalUserFcn->CalcSomethingCPUExpensive(param);
-
-    // extract the needed values from the global object
-    value(s) = fGlobalUserFcn->GetWhatIsNeeded(...);
-
-    // use 'value(s)' to do some run block specific calculations (not/less CPU demanding)
-    ...
-
-    return result;
-  }
-
-This way the efficiency of the user function can be increased by almost a factor of *n* (where *n* is the number of :ref:`RUN blocks <msr-run-block>`).   
-
-.. _user-function-important:
-.. note::
-
-  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 :ref:`single-histogram <single-histogram-fit>` and :ref:`asymmetry <asymmetry-fit>` fits the calculation of :math:`\chi^2` or the maximum 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. 
-  
-.. index:: technical-musrfit
-.. _technical-musrfit:
-    
-Technical Description of the musrfit framework
-----------------------------------------------
-
-A technical description of the musrfit framework can be found on its own `docu <http://lmu.web.psi.ch/musrfit/technical/index.html>`_. 
diff --git a/doc/html/genindex.html b/doc/html/genindex.html
index db064c63..6c48b70d 100644
--- a/doc/html/genindex.html
+++ b/doc/html/genindex.html
@@ -995,7 +995,7 @@
     </div>
     <div class="footer">
         &copy; Copyright 2021, Andreas Suter.
-      Last updated on Jan 23, 2021.
+      Last updated on Mar 01, 2021.
       Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.2.3.
     </div>
   </body>
diff --git a/doc/html/index.html b/doc/html/index.html
index 8477a1b1..cdad8e7b 100644
--- a/doc/html/index.html
+++ b/doc/html/index.html
@@ -185,7 +185,7 @@
     </div>
     <div class="footer">
         &copy; Copyright 2021, Andreas Suter.
-      Last updated on Jan 23, 2021.
+      Last updated on Mar 01, 2021.
       Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.2.3.
     </div>
   </body>
diff --git a/doc/html/objects.inv b/doc/html/objects.inv
index 2184b0a8..8148faf5 100644
Binary files a/doc/html/objects.inv and b/doc/html/objects.inv differ
diff --git a/doc/html/search.html b/doc/html/search.html
index 5e53eb9e..67218896 100644
--- a/doc/html/search.html
+++ b/doc/html/search.html
@@ -94,7 +94,7 @@
     </div>
     <div class="footer">
         &copy; Copyright 2021, Andreas Suter.
-      Last updated on Jan 23, 2021.
+      Last updated on Mar 01, 2021.
       Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.2.3.
     </div>
   </body>
diff --git a/doc/html/searchindex.js b/doc/html/searchindex.js
index 558eb4fc..612fea32 100644
--- a/doc/html/searchindex.js
+++ b/doc/html/searchindex.js
@@ -1 +1,2 @@
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opengl:13,dbuiltin_glew:13},objects:{},objtypes:{},objnames:{},titleterms:{acknowledg:0,any2mani:[12,1],univers:1,"\u03bcsr":[6,12,11,1,7],file:[12,5,11,10,1,8,7],format:[12,7,1],convert:1,bugtrack:2,how:3,cite:3,musrfit:[12,3,5,4,10,9,8,13],welcom:4,document:[11,4],indic:4,tabl:4,msr2data:[12,5,10],program:5,automat:5,process:[5,10],multipl:[5,10],msr:[12,5,10],basic:[12,8,5,7],type:[12,5],usag:[6,8,12,5],run:[12,5,7],list:5,structur:5,option:[5,13],paramet:[6,8,5],global:[12,5],mode:5,gener:[12,5],extract:5,extend:5,known:5,limit:5,graphic:[6,9,5],user:[6,12,5,11,7],interfac:[6,8,5,7],provid:5,musredit:[8,5,13],mupp:6,plotter:6,script:6,summari:6,musrroot:7,extens:[12,7],open:7,some:7,concern:7,root:[7,13],inform:7,contain:7,runhead:7,runinfo:7,overview:[12,7],tmusrrunhead:7,concept:7,header:7,write:7,read:[7,10],valid:7,requir:[7,13],detectorinfo:7,sampleenvironmentinfo:7,magneticfieldenvironmentinfo:7,beamlineinfo:7,exhaust:7,tree:7,includ:7,everyth:[7,13],tmusrrunphysicalquant:7,possibl:7,represent:7,gui:8,base:8,introduct:[12,8,11],avail:[12,8],execut:[12,8],configur:[12,8],musrgui:[8,13],musredit_startup:8,xml:[12,8,11],featur:8,musrwiz:8,theori:[12,8],"function":[12,8,11],map:[12,8],fit:[12,9,8,10],info:8,creat:8,musrstep:8,set:[9,13],high:9,speed:9,gpu:[12,9],tesla:9,k40c:9,nvidia:9,driver:9,instal:[9,13],cuda:9,via:[9,13],automak:[],cmake:[9,13],amd:9,card:9,radeon:9,"390x":9,app:9,softwar:[9,13],develop:9,kit:9,sdk:9,enabl:[12,9],opencl:[12,9],support:[12,9,13],maco:[9,13],differ:13,platform:13,oper:13,system:13,restrict:13,gnu:13,linux:13,nexu:13,build:13,last:13,step:13,obsol:[],check:13,window:13,cygwin:13,potenti:13,problem:13,mac:13,macport:13,packag:13,from:13,sourc:13,environ:13,variabl:[6,13],fink:13,obsolet:13,tutori:10,singl:[12,10],histogram:[12,10],determin:10,data:[11,10],rang:10,musrt0:[12,10],model:[11,10],view:10,musrview:[12,10],further:10,asymmteri:10,lib:11,meissner:11,profil:11,vortex:11,lattic:11,relat:11,bmw:11,libfitpofb:11,dimension:11,london:11,state:11,isotrop:11,superconductor:11,bulk:11,field:11,distribut:11,mix:11,startup:11,nonloc:11,superconduct:11,screen:11,analyz:11,"\u03b2":11,nmr:[12,11],bnmr:11,libbnmr:11,liblineprofil:11,manual:12,kei:12,shortcut:12,musrft:12,msr2msr:12,dump_head:12,musrfit_startup:12,descript:12,titl:12,fitparamet:12,block:12,command:12,fourier:12,plot:12,statist:12,rrf:12,asymmetri:12,neg:12,muon:12,non:12,without:12,object:12,access:12,technic:12,framework:12,beta:12,note:13,catalina:13,minuit2:12,detail:12,defin:6,dialog:6,depreci:13},envversion:43})
diff --git a/doc/html/setup-standard.html b/doc/html/setup-standard.html
index b1965e10..6cd5e83a 100644
--- a/doc/html/setup-standard.html
+++ b/doc/html/setup-standard.html
@@ -241,9 +241,9 @@ $ <span class="nb">cd</span> Apps
 $ git clone http://github.com/root-project/root.git
 $ <span class="nb">cd</span> root
 $ git tag -l
-$ <span class="c1"># git tag -l will list all available tags. In the next command choose the tag v6-16-00</span>
+$ <span class="c1"># git tag -l will list all available tags. In the next command choose the tag v6-22-06</span>
 $ <span class="c1"># or the latest official release number</span>
-$ git checkout -b v6-16-00 v6-16-00
+$ git checkout -b v6-22-06 v6-22-06
 $ <span class="c1"># now ROOT is ready to be configured. Below you will find the minimal ROOT configuration needed.</span>
 $ <span class="c1"># since we are using cmake build now, first we will need to create the build directory.</span>
 $ mkdir root_build
@@ -784,9 +784,9 @@ it is at the time of writting <tt class="docutils literal"><span class="pre">roo
 <tt class="docutils literal"><span class="pre">ROOT</span></tt> will be installed under <tt class="docutils literal"><span class="pre">/Application</span></tt> as owner root. In order to ease your life for the
 steps to follow and assuming you are the only guy working on your Mac, you could change the owner and group of the <tt class="docutils literal"><span class="pre">ROOT</span></tt> directory:</p>
 <div class="highlight-bash"><div class="highlight"><pre><span></span>$ <span class="nb">cd</span> /Applications
-$ sudo chown -R &lt;username&gt; root_v6.16.00
-$ sudo chgrp -R staff root_v6.16.00
-$ sudo ln -s root_v6.16.00 root
+$ sudo chown -R &lt;username&gt; root_v6.22.00
+$ sudo chgrp -R staff root_v6.22.00
+$ sudo ln -s root_v6.22.00 root
 </pre></div>
 </div>
 </div>
@@ -803,14 +803,14 @@ comments will be added starting with a &#8216;#&#8217; which can be omitted. The
 $ git clone http://github.com/root-project/root.git
 $ <span class="nb">cd</span> root
 $ git tag -l
-$ <span class="c1"># git tag -l will list all available tags. In the next command choose the tag v6-10-xx</span>
-$ <span class="c1"># where xx is the highest listed number, e.g. v6-16-00</span>
-$ git checkout -b v6-16-00 v6-16-00
+$ <span class="c1"># git tag -l will list all available tags. In the next command choose the tag v6-xx-yy</span>
+$ <span class="c1"># where xx is the highest listed number, e.g. v6-22-06</span>
+$ git checkout -b v6-22-06 v6-22-06
 $ <span class="c1"># now ROOT is ready to be configured. Below you will find the minimal ROOT configuration needed.</span>
 $ <span class="c1"># We will use the cmake out-of-source approach here.</span>
 $ mkdir root_build
 $ <span class="nb">cd</span> root_build
-$ cmake ../ -Dgminimal<span class="o">=</span>ON -Dasimage<span class="o">=</span>ON -Dmathmore<span class="o">=</span>ON -Dminuit2<span class="o">=</span>ON -Dxml<span class="o">=</span>ON -DCMAKE_INSTALL_PREFIX<span class="o">=</span><span class="nv">$HOME</span>/Applications/root/root_exec
+$ cmake ../ -Dgminimal<span class="o">=</span><span class="m">1</span> -Dasimage<span class="o">=</span><span class="m">1</span> -Dmathmore<span class="o">=</span><span class="m">1</span> -Dminuit2<span class="o">=</span><span class="m">1</span> -Dxml<span class="o">=</span><span class="m">1</span> -Dopengl<span class="o">=</span><span class="m">1</span> -Dbuiltin_glew<span class="o">=</span><span class="m">1</span> -DCMAKE_INSTALL_PREFIX<span class="o">=</span><span class="nv">$HOME</span>/Applications/root/root_exec
 $ <span class="c1"># next will be the make. If running on a multicore CPU you can speed up tremendously by calling</span>
 $ <span class="c1"># make with the option -j &lt;number&gt;, where &lt;number&gt; is the number of threads which you want to give,</span>
 $ <span class="c1"># e.g. make -j8</span>
@@ -996,14 +996,14 @@ comments will be added starting with a &#8216;#&#8217; which can be omitted. The
 $ git clone http://github.com/root-project/root.git
 $ <span class="nb">cd</span> root
 $ git tag -l
-$ <span class="c1"># git tag -l will list all available tags. In the next command choose the tag v6-10-xx</span>
-$ <span class="c1"># where xx is the highest listed number, e.g. v6-16-00</span>
-$ git checkout -b v6-16-00 v6-16-00
+$ <span class="c1"># git tag -l will list all available tags. In the next command choose the tag v6-xx-yy</span>
+$ <span class="c1"># where xx is the highest listed number, e.g. v6-22-06</span>
+$ git checkout -b v6-22-06 v6-22-06
 $ <span class="c1"># now ROOT is ready to be configured. Below you will find the minimal ROOT configuration needed.</span>
 $ <span class="c1"># We will use the cmake out-of-source approach here.</span>
 $ mkdir root_build
 $ <span class="nb">cd</span> root_build
-$ cmake ../ -Dgminimal<span class="o">=</span>ON -Dasimage<span class="o">=</span>ON -Dmathmore<span class="o">=</span>ON -Dminuit2<span class="o">=</span>ON -Dxml<span class="o">=</span>ON -DCMAKE_INSTALL_PREFIX<span class="o">=</span><span class="nv">$HOME</span>/Applications/root/root_exec
+$ cmake ../ -Dgminimal<span class="o">=</span><span class="m">1</span> -Dasimage<span class="o">=</span><span class="m">1</span> -Dmathmore<span class="o">=</span><span class="m">1</span> -Dminuit2<span class="o">=</span><span class="m">1</span> -Dxml<span class="o">=</span><span class="m">1</span> -Dopengl<span class="o">=</span><span class="m">1</span> -Dbuiltin_glew<span class="o">=</span><span class="m">1</span> -DCMAKE_INSTALL_PREFIX<span class="o">=</span><span class="nv">$HOME</span>/Applications/root/root_exec
 $ <span class="c1"># next will be the make. If running on a multicore CPU you can speed up tremendously by calling</span>
 $ <span class="c1"># make with the option -j &lt;number&gt;, where &lt;number&gt; is the number of threads which you want to give,</span>
 $ <span class="c1"># e.g. make -j8</span>
@@ -1307,7 +1307,7 @@ $ musrview test-histo-ROOT-NPP.msr
     </div>
     <div class="footer">
         &copy; Copyright 2021, Andreas Suter.
-      Last updated on Jan 23, 2021.
+      Last updated on Mar 01, 2021.
       Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.2.3.
     </div>
   </body>
diff --git a/doc/html/user-manual.html b/doc/html/user-manual.html
index 7aaee984..497e7af8 100644
--- a/doc/html/user-manual.html
+++ b/doc/html/user-manual.html
@@ -2242,11 +2242,6 @@ In this abstract base class a function operator is defined that takes two argume
   <span class="n">TMyFunction</span><span class="p">(){}</span>
   <span class="o">~</span><span class="n">TMyFunction</span><span class="p">(){}</span>
 
-  <span class="c1">// global user-function-access functions, here without any functionality</span>
-  <span class="n">Bool_t</span> <span class="n">NeedGlobalPart</span><span class="p">()</span> <span class="k">const</span> <span class="p">{</span> <span class="k">return</span> <span class="nb">false</span><span class="p">;</span> <span class="p">}</span>
-  <span class="kt">void</span> <span class="n">SetGlobalPart</span><span class="p">(</span><span class="n">vector</span><span class="o">&lt;</span><span class="kt">void</span><span class="o">*&gt;</span> <span class="o">&amp;</span><span class="n">globalPart</span><span class="p">,</span> <span class="n">UInt_t</span> <span class="n">idx</span><span class="p">)</span> <span class="p">{</span> <span class="p">}</span>
-  <span class="n">Bool_t</span> <span class="n">GlobalPartIsValid</span><span class="p">()</span> <span class="k">const</span> <span class="p">{</span> <span class="k">return</span> <span class="nb">true</span><span class="p">;</span> <span class="p">}</span>
-
   <span class="c1">// function operator</span>
   <span class="n">Double_t</span> <span class="k">operator</span><span class="p">()(</span><span class="n">Double_t</span><span class="p">,</span> <span class="k">const</span> <span class="n">vector</span><span class="o">&lt;</span><span class="n">Double_t</span><span class="o">&gt;&amp;</span><span class="p">)</span> <span class="k">const</span><span class="p">;</span>
 
@@ -2562,7 +2557,7 @@ In case this cannot be ensured, the parallelization can be disabled by <em>&#821
     </div>
     <div class="footer">
         &copy; Copyright 2021, Andreas Suter.
-      Last updated on Jan 23, 2021.
+      Last updated on Feb 26, 2021.
       Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.2.3.
     </div>
   </body>