From 4d04f45699ee601c1fdc70dd52b354880a72cf47 Mon Sep 17 00:00:00 2001 From: Andreas Suter Date: Wed, 17 Jun 2020 20:22:42 +0200 Subject: [PATCH] resolve merge conflict: update of the docu --- doc/html/.buildinfo | 2 +- doc/html/_sources/user-manual.rst.txt | 20 ++- doc/html/_static/documentation_options.js | 2 +- doc/html/acknowledgement.html | 8 +- doc/html/any2many.html | 8 +- doc/html/bugtracking.html | 8 +- doc/html/cite.html | 8 +- doc/html/genindex.html | 138 +++++++++--------- doc/html/index.html | 8 +- doc/html/msr2data.html | 8 +- doc/html/mupp.html | 8 +- doc/html/musr-root.html | 8 +- doc/html/musredit.html | 8 +- doc/html/search.html | 8 +- doc/html/searchindex.js | 2 +- doc/html/setup-dks.html | 8 +- doc/html/setup-standard.html | 8 +- doc/html/tutorial.html | 8 +- doc/html/user-libs.html | 8 +- doc/html/user-manual.html | 168 +++++++++++++--------- 20 files changed, 247 insertions(+), 197 deletions(-) diff --git a/doc/html/.buildinfo b/doc/html/.buildinfo index b66b59df..c56e72da 100644 --- a/doc/html/.buildinfo +++ b/doc/html/.buildinfo @@ -1,4 +1,4 @@ # 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: 2fd2e79340d6214c8fde0515f4f3fbe3 +config: 8f1b0a921f0f4e1d8c3f85aab9fe7bad tags: 645f666f9bcd5a90fca523b33c5a78b7 diff --git a/doc/html/_sources/user-manual.rst.txt b/doc/html/_sources/user-manual.rst.txt index b20c63dd..4f0001e5 100644 --- a/doc/html/_sources/user-manual.rst.txt +++ b/doc/html/_sources/user-manual.rst.txt @@ -774,8 +774,9 @@ A THEORY block including a user function may then look like :: The FUNCTIONS Block +++++++++++++++++++ -Here some auxiliary functions can be defined. These functions can currently *only* operate on the defined parameters. They can be used in the -:ref:`THEORY block ` and for three specific cases in the :ref:`RUN block ` (`norm`, `alpha`, and `beta`). Supported is the use of basic arithmetic: +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 ` and for three specific cases in the :ref:`RUN block ` (`norm`, `alpha`, and `beta`). +Supported is the use of basic arithmetic: :math:`+` Addition @@ -799,6 +800,21 @@ Furthermore, some constants are predefined and might also be used: The fit parameters are accessed either directly through parX, where 'X' is the number of the parameter in the :ref:`FITPARAMETER block `, *e.g.* *par5* or through a mapping with mapY, where 'Y' specifies the mapping number in the :ref:`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 `. diff --git a/doc/html/_static/documentation_options.js b/doc/html/_static/documentation_options.js index 63761070..d6330f55 100644 --- a/doc/html/_static/documentation_options.js +++ b/doc/html/_static/documentation_options.js @@ -1,6 +1,6 @@ var DOCUMENTATION_OPTIONS = { URL_ROOT: document.getElementById("documentation_options").getAttribute('data-url_root'), - VERSION: '1.6.1', + VERSION: '1.6.2', LANGUAGE: 'None', COLLAPSE_INDEX: false, FILE_SUFFIX: '.html', diff --git a/doc/html/acknowledgement.html b/doc/html/acknowledgement.html index 25468fbd..4a6644d8 100644 --- a/doc/html/acknowledgement.html +++ b/doc/html/acknowledgement.html @@ -4,7 +4,7 @@ - Acknowledgements — musrfit 1.6.1 documentation + Acknowledgements — musrfit 1.6.2 documentation @@ -30,7 +30,7 @@
  • previous |
    • -
  • musrfit 1.6.1 documentation »
    • +
  • musrfit 1.6.2 documentation »
    • @@ -100,12 +100,12 @@ extremely competent way to deal with his projects as well as to deal with the ch
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  • musrfit 1.6.1 documentation »
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  • musrfit 1.6.2 documentation »
    • diff --git a/doc/html/any2many.html b/doc/html/any2many.html index 67edf232..dc74e3df 100644 --- a/doc/html/any2many.html +++ b/doc/html/any2many.html @@ -4,7 +4,7 @@ - any2many - a Universal μSR-file-format converter — musrfit 1.6.1 documentation + any2many - a Universal μSR-file-format converter — musrfit 1.6.2 documentation @@ -30,7 +30,7 @@
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  • musrfit 1.6.1 documentation »
    • +
  • musrfit 1.6.2 documentation »
    • diff --git a/doc/html/bugtracking.html b/doc/html/bugtracking.html index bdbbd251..ff064ef5 100644 --- a/doc/html/bugtracking.html +++ b/doc/html/bugtracking.html @@ -4,7 +4,7 @@ - Bugtracking — musrfit 1.6.1 documentation + Bugtracking — musrfit 1.6.2 documentation @@ -26,7 +26,7 @@
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    • @@ -81,12 +81,12 @@ or send an e-mail to A. Suter at PSI.

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  • index
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    B

      @@ -277,53 +277,55 @@
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    • mupp-usage
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    • musrfit-command-block-details +
    • musrfit-command-block-details
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          U

          diff --git a/doc/html/index.html b/doc/html/index.html index 238539eb..8fdd4827 100644 --- a/doc/html/index.html +++ b/doc/html/index.html @@ -4,7 +4,7 @@ - Welcome to the musrfit documentation! — musrfit 1.6.1 documentation + Welcome to the musrfit documentation! — musrfit 1.6.2 documentation @@ -26,7 +26,7 @@
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        • musrfit 1.6.1 documentation »
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        • musrfit 1.6.2 documentation »
          • diff --git a/doc/html/musredit.html b/doc/html/musredit.html index d758284d..a5e4acf3 100644 --- a/doc/html/musredit.html +++ b/doc/html/musredit.html @@ -4,7 +4,7 @@ - musredit: the GUI Based Interface to musrfit — musrfit 1.6.1 documentation + musredit: the GUI Based Interface to musrfit — musrfit 1.6.2 documentation @@ -30,7 +30,7 @@
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- a Universal \u03bcSR-file-format converter","Bugtracking","How to Cite musrfit?","Welcome to the musrfit documentation!","msr2data - A Program for Automatically Processing Multiple musrfit msr Files","mupp - \u03bcSR Parameter Plotter","MusrRoot - an Extensible Open File Format for \u03bcSR","musredit: the GUI Based Interface to musrfit","Setting up musrfit / DKS: High Speed Fitting with GPU\u2019s","Setting up musrfit on Different Platforms","Tutorial for musrfit","Documentation of user libs (user functions)","User manual"],titleterms:{"390x":9,"\u03b2":12,"\u03bcsr":[1,6,7,12,13],"function":[8,12,13],DKS:[9,13],One:12,The:[5,6,11,12,13],access:13,acknowledg:0,amd:9,analyz:12,any2mani:[1,13],app:9,asymmetri:13,asymmteri:11,automat:5,avail:[8,13],base:8,basic:[5,7,8,13],beamlineinfo:7,beta:13,block:13,bmw:12,bnmr:12,bugtrack:2,build:10,bulk:12,card:9,catalina:10,check:10,cite:3,cmake:[9,10],command:13,concept:7,concern:7,configur:[8,13],contain:7,convert:1,creat:8,cuda:9,cygwin:10,data:[11,12],defin:6,descript:13,detail:13,detectorinfo:7,determin:11,develop:9,dialog:6,differ:10,dimension:12,distribut:12,document:[4,12],driver:9,dump_head:13,enabl:[9,13],environ:10,everyth:[7,10],execut:[8,13],exhaust:7,extend:5,extens:[7,13],extract:5,featur:8,field:12,file:[1,5,7,8,11,12,13],fink:10,fit:[8,9,11,13],fitparamet:13,format:[1,7,13],fourier:13,framework:13,from:10,further:11,gener:[5,13],global:[5,13],gnu:10,gpu:[9,13],graphic:[5,6,9],gui:8,header:7,high:9,histogram:[11,13],how:3,includ:7,indic:4,info:8,inform:7,instal:[9,10],interfac:[5,6,7,8],introduct:[8,12,13],isotrop:12,k40c:9,kei:13,kit:9,known:5,last:10,lattic:12,lib:12,libbnmr:12,libfitpofb:12,liblineprofil:12,limit:5,linux:10,list:5,london:12,mac:10,maco:[9,10],macport:10,magneticfieldenvironmentinfo:7,manual:13,map:[8,13],meissner:12,minuit2:13,mix:12,mode:5,model:[11,12],msr2data:[5,11,13],msr2msr:13,msr:[5,11,13],multipl:[5,11],muon:13,mupp:6,musredit:[5,8,10],musredit_startup:8,musrfit:[3,4,5,8,9,10,11,13],musrfit_startup:13,musrft:13,musrgui:[8,10],musrroot:7,musrstep:8,musrt0:[11,13],musrview:[11,13],musrwiz:8,neg:13,nexu:10,nmr:[12,13],non:13,nonloc:12,note:10,nvidia:9,object:13,obsol:10,obsolet:10,open:7,opencl:[9,13],oper:10,option:[5,10],overview:[7,13],packag:10,paramet:[5,6,8],platform:10,plot:13,plotter:6,possibl:7,potenti:10,problem:10,process:[5,11],profil:12,program:5,provid:5,radeon:9,rang:11,read:[7,11],relat:12,represent:7,requir:[7,10],restrict:10,root:[7,10],rrf:13,run:[5,7,13],runhead:7,runinfo:7,sampleenvironmentinfo:7,screen:12,script:6,sdk:9,set:[9,10],shortcut:13,singl:[11,13],softwar:[9,10],some:7,sourc:10,speed:9,startup:12,state:12,statist:13,step:10,structur:5,summari:6,superconduct:12,superconductor:12,support:[9,10,13],system:10,tabl:4,technic:13,tesla:9,theori:[8,13],titl:13,tmusrrunhead:7,tmusrrunphysicalquant:7,tree:7,tutori:11,type:[5,13],univers:1,usag:[5,6,8,13],user:[5,6,7,12,13],using:11,valid:7,variabl:[6,10],via:[9,10],view:11,vortex:12,welcom:4,window:10,without:13,write:7,xml:[8,12,13]}}) diff --git a/doc/html/setup-dks.html b/doc/html/setup-dks.html index c8edb33f..e5835bca 100644 --- a/doc/html/setup-dks.html +++ b/doc/html/setup-dks.html @@ -4,7 +4,7 @@ i - Setting up musrfit / DKS: High Speed Fitting with GPU’s — musrfit 1.6.1 documentation + Setting up musrfit / DKS: High Speed Fitting with GPU’s — musrfit 1.6.2 documentation @@ -30,7 +30,7 @@ i
        • previous |
          • -
        • musrfit 1.6.1 documentation »
          • +
        • musrfit 1.6.2 documentation »
          • @@ -309,12 +309,12 @@ The only thing you need previous | -
        • musrfit 1.6.1 documentation »
          • +
        • musrfit 1.6.2 documentation »
          • diff --git a/doc/html/setup-standard.html b/doc/html/setup-standard.html index 9528f27c..5983b78e 100644 --- a/doc/html/setup-standard.html +++ b/doc/html/setup-standard.html @@ -4,7 +4,7 @@ - Setting up musrfit on Different Platforms — musrfit 1.6.1 documentation + Setting up musrfit on Different Platforms — musrfit 1.6.2 documentation @@ -30,7 +30,7 @@
        • previous |
          • -
        • musrfit 1.6.1 documentation »
          • +
        • musrfit 1.6.2 documentation »
          • @@ -1293,12 +1293,12 @@ $ musrview test-histo-ROOT-NPP.msr
        • previous |
          • -
        • musrfit 1.6.1 documentation »
          • +
        • musrfit 1.6.2 documentation »
          • diff --git a/doc/html/tutorial.html b/doc/html/tutorial.html index e1f7e635..df48a2e9 100644 --- a/doc/html/tutorial.html +++ b/doc/html/tutorial.html @@ -4,7 +4,7 @@ - Tutorial for musrfit — musrfit 1.6.1 documentation + Tutorial for musrfit — musrfit 1.6.2 documentation @@ -30,7 +30,7 @@
        • previous |
          • -
        • musrfit 1.6.1 documentation »
          • +
        • musrfit 1.6.2 documentation »
          • @@ -431,12 +431,12 @@ For a complete description please refer to the manuals of previous | -
        • musrfit 1.6.1 documentation »
          • +
        • musrfit 1.6.2 documentation »
          • diff --git a/doc/html/user-libs.html b/doc/html/user-libs.html index 0c50a76a..b8b96603 100644 --- a/doc/html/user-libs.html +++ b/doc/html/user-libs.html @@ -4,7 +4,7 @@ - Documentation of user libs (user functions) — musrfit 1.6.1 documentation + Documentation of user libs (user functions) — musrfit 1.6.2 documentation @@ -30,7 +30,7 @@
        • previous |
          • -
        • musrfit 1.6.1 documentation »
          • +
        • musrfit 1.6.2 documentation »
          • @@ -647,12 +647,12 @@ K(m)&=\int_0^{\pi/2}\frac{\mathrm d\varphi}{\sqrt{1-m^2\sin^2{\varphi}}},\en
        • previous |
          • -
        • musrfit 1.6.1 documentation »
          • +
        • musrfit 1.6.2 documentation »
          • diff --git a/doc/html/user-manual.html b/doc/html/user-manual.html index 607b5033..0669160a 100644 --- a/doc/html/user-manual.html +++ b/doc/html/user-manual.html @@ -4,7 +4,7 @@ - User manual — musrfit 1.6.1 documentation + User manual — musrfit 1.6.2 documentation @@ -30,7 +30,7 @@
        • previous |
          • -
        • musrfit 1.6.1 documentation »
          • +
        • musrfit 1.6.2 documentation »
          • @@ -896,8 +896,9 @@ instead of specifying the parameters directly.

          The FUNCTIONS Block

          -

          Here some auxiliary functions can be defined. These functions can currently only operate on the defined parameters. They can be used in the -THEORY block and for three specific cases in the RUN block (norm, alpha, and beta). Supported is the use of basic arithmetic:

          +

          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 THEORY block and for three specific cases in the RUN block (norm, alpha, and beta). +Supported is the use of basic arithmetic:

          \(+\)

          Addition

          @@ -919,6 +920,37 @@ acosh(), asinh(), atanh(), exp(), log(), ln(), sqrt(), pow(base, exponent)

          The fit parameters are accessed either directly through parX, where ‘X’ is the number of the parameter in the FITPARAMETER block, e.g. par5 or through a mapping with mapY, where ‘Y’ specifies the mapping number in the RUN block as explained below.

          +

          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 THEORY block.

          It follows an example to illustrate the usage of functions in the THEORY block. The total asymmetry of a signal @@ -948,7 +980,7 @@ consisting of two parts should be a fit parameter. The fraction of each of the p

          -

          The 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 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:

            @@ -1052,7 +1084,7 @@ Syntax: rrf_phase <phase>, where the value <phase> is given in degre
          -

          The 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

          @@ -1126,7 +1158,7 @@ a short digression is needed.

          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

          -
          +
          ADDRUN <run_file_name> <beamline> <facility> <file_format> (optional)

          If an ADDRUN is just following after a RUN statement, these runs will be added. More than one ADDRUN statements are possible, i.e. adding up as many runs as wished. It is also possible to add runs with different file formats. If the t0’s are given in the data files, the ADDRUN statement is all what is needed, otherwise just add the t0’s with the addt0 statement.

          For a Single Histogram Fit or a MuMinus Fit it will be

          addt0 t0AddRun1
@@ -1144,7 +1176,7 @@ a short digression is needed.
          
 
          ADDRUN is not available for the fit type Non-muSR Fit.
          -
          +
          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

          @@ -1168,7 +1200,7 @@ a short digression is needed.

          -
          +
          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 \(\alpha = N_{0,b}/N_{0,f}\) and \(\beta = A_{0,b}/A_{0,f}\). If the parameters are not specified in the RUN block, for each one the value of 1 is assumed (for fittype 5, alpha is estimated from the ratio of \(\sum_i \left( N_{\mathrm{bp}}(i)+N_{\mathrm{bm}}(i) \right)\) and \(\sum_i \left( N_{\mathrm{fp}}(i)+N_{\mathrm{fm}}(i) \right)\)). Both, alpha as well as beta can be expressed through a function. Example for alpha with fit parameter number 1:

          alpha 1
          @@ -1179,7 +1211,7 @@ a short digression is needed.

          -
          +
          norm (fit type 0)

          Number of the fit parameter that represents the normalization constant \(N_0\) of the histogram; the value of this parameter is given either per nanosecond or per bin (see below). It is possible to substitute the parameter number by a function, for instance to relate \(N_0\)’s of different histograms through an \(\alpha\) parameter. Example for a norm defined by fit parameter number 12:

          @@ -1192,25 +1224,25 @@ parameter. Example for a
          -
          +
          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 below). If this keyword is present, any information on a background line are ignored.

          -
          +
          lifetime (fit type 0)

          Fit parameter representing the lifetime of the muon. If it is not specified the value \(\tau_\mu=2.197019~ \mu\mathrm{s}\) 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 PLOT block, which allows switching between histogram view and asymmetry view much quicker.

          -
          +
          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 THEORY and FUNCTIONS blocks (see also maps). The first ten maps are always present and have the value 0 if not used; however, the total number of maps is not restricted!

          -
          +
          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
@@ -1219,7 +1251,7 @@ are always present and have the value 0 if not used; however, the total number o
          -
          +
          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
@@ -1241,12 +1273,12 @@ are always present and have the value 0 if not used; however, the total number o
          -
          +
          backgr.fix (fit types 0, 1, 2, 3, 5)

          A fixed constant background in counts per nanosecond or per bin (see below) may be given at this point. The background is specified for all histograms in the order \(B_f B_b [B_r B_l]\). If this keyword is present, any information on a background line is ignored.

          -
          +
          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
@@ -1254,7 +1286,7 @@ In case histograms are being grouped, the specified channels are interpreted wit
          -
          +
          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: \(k_{f,\rm first} k_{f,\rm last} k_{b,\rm first} k_{b, \rm last} [k_{r,\rm first} k_{r,\rm last} k_{l,\rm first} k_{l,\rm last}]\). In case histograms are being grouped, the specified channels are interpreted with respect to the first histograms. Example:

          @@ -1263,7 +1295,7 @@ In case histograms are being grouped, the specified channels are interpreted wit
          -
          +
          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:

          @@ -1272,7 +1304,7 @@ Typically these channels are referred to as
          +
          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: \(k_{f,\rm first} k_{f,\rm last} k_{b,\rm first} k_{b, \rm last} [k_{r,\rm first} k_{r,\rm last} k_{l,\rm first} k_{l,\rm last}]\). @@ -1282,7 +1314,7 @@ In case histograms are being grouped, the specified channels are interpreted wit

          -
          +
          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.
@@ -1290,7 +1322,7 @@ In case histograms are being grouped, the specified channels are interpreted wit
          -
          +
          t0 (fit type 2, 3, 5)

          The numbers of time-zero channels of the histograms in the order \(t_{0,f} t_{0,b}\). 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)
@@ -1298,25 +1330,25 @@ In case histograms are being grouped, the specified channels are interpreted wit
          -
          +
          addt0 (fit type 0, 1, 4)

          The number of the time-zero channel of the histogram. If grouping of histograms is present (see forward) the same syntax as for t0 applies. If one addt0 is given, the total number of addt0’s needs to be equal to the total number of ADDRUN’s!

          -
          +
          addt0 (fit type 2, 3, 5)

          The numbers of time-zero channels of the histograms in the order \(t_{0,f} t_{0,b} [t_{0,r} t_{0,l}]\). If grouping of histograms is present (see forward) the same syntax as for t0 applies. If one addt0 is given, the total number of addt0’s needs to be equal to the total number of ADDRUN’s!

          -
          +
          xy-data (fit type 8)

          Specification of the data from an ASCII or DB file which should be used as x and y data (in this order). For a simple ASCII file the column numbers are used, in the case of a DB file one can either specify the variable numbers or the name of the variables as given in the DB header.

          -
          +
          fit

          The range of data that should be considered when the fitting is done. For the μSR fit types 0, 1, 2, 3, and 4 the starting and end times are given in micro-seconds. For the non-μSR fit type 8 the starting and end points of the fitting range are given in the units of the x data.

          @@ -1339,19 +1371,19 @@ An example:

          -
          +
          packing

          Number of data channels to be binned together. For the non-μSR fit type 8 the binning is supposed to be 1. For the single histogram RRF fit (fittype 1) and asymmetry RRF fit (fittype 3) this parameter is meaningless.

          -

          The 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 (Minuit2 Command Overview and DKS Command Overview) and further described in musrfit Command Block Details.

          -

          Minuit2 Command Overview

          +

          Minuit2 Command Overview

          @@ -1499,7 +1531,7 @@ Used for statistical analysis only.

          -

          DKS Command Overview

          +

          DKS Command Overview

          @@ -1560,7 +1592,7 @@ It allows to use all your threads of your CPU(s) during the minimization.

          -

          musrfit Command Block Details

          +

          musrfit Command Block Details

          A standard COMMANDS block then looks like this:

          COMMANDS
 MINIMIZE
@@ -1657,7 +1689,7 @@ MIGRAD to the MINUIT2.OUTPUT file and at the end append the MINOS results to thi
 
          Note: If a fit is invoked, the sector command results will only be written to file, if the fit has converged!
          -

          DKS extensions of the COMMANDS block enabling GPU and general OpenCL support

          +

          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:

          @@ -1690,27 +1722,27 @@ In the -

          The 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 PLOT block is given. If the FOURIER block is not present in the msr file, either the parameters set in the XML startup file or the system defaults are taken when the Fourier transform is performed. The block starts with the FOURIER keyword and may contain the following entries on the successive lines:

          -
          +
          units

          Here is specified in which domain the Fourier-transformed data is presented. One may choose between the fields (Gauss) or (Tesla), the frequency (MHz), and the angular-frequency domain (Mc/s).

          -
          +
          fourier_power

          It is possible (but not necessary) to set the number of data points used for the Fourier transform here. As argument the exponent n<21 of a power of 2 is accepted. The number of data points is then 2n. Attention: If the number of points given here is bigger than the actual number of available data points, the input data vector is filled with zeros until the number of requested points is reached (zero padding)!

          -
          +
          dc-corrected

          a flag to remove a potential DC-offset of the signal. Allowed entries are dc-corrected true | 1 | false | 0.

          -
          +
          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 μSR data refer to the PhD thesis of T.M. Riseman (UBC)). 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

          @@ -1727,7 +1759,7 @@ keyword is therefore one of the following: NONE, WEAK, MEDIUM o
          -
          +
          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:

          @@ -1744,7 +1776,7 @@ The argument may be one of the following:

          -
          +
          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:

          @@ -1796,12 +1828,12 @@ list example, the first parameter number will be the reference phase. The compac
          -
          +
          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.

          -
          +
          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.

          @@ -1817,20 +1849,20 @@ The given interval will be used for an automatic phasing of the real Fourier tra
          -

          The 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 fit types. Additionally, it is possible to provide information using the following keywords:

          -
          +
          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).

          -
          +
          runs

          The numbers of the runs to be plotted have to be put here. The runs are numbered according to their appearance in the RUN block. The numbers is either a space separated list of numbers, an interval e.g. 1-16, or a combination of both.

          -
          +
          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):

          @@ -1843,7 +1875,7 @@ micro-seconds and the N in counts (types 0-4) or in counts/nsec (type 0
          -
          +
          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:

          t1min t1max t2min t2max … tnmin tnmax [ Nmin N max ] (n = the number of runs to be plotted)

          @@ -1855,31 +1887,31 @@ micro-seconds and the N in counts (types 0-4) or in counts/nsec (type 0
          -
          +
          use_fit_ranges [ ymin ymax ]

          The fit ranges of the individual runs are used to present the data. Optionally, an ordinate range can be provided.

          -
          +
          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.

          -
          +
          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!

          -
          +
          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!

          -
          +
          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.

          -
          +
          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.

          -
          +
          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 FITPARAMETER block.

          Notes:
            @@ -1913,7 +1945,7 @@ The theory, however, is filtered via -

            The 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 \(\chi^2\) and the number of degrees of freedom in the fit. If enabled in the XML file for \(\chi^2\)-single-histogram fits also Pearson’s @@ -1922,9 +1954,9 @@ If enabled in the

          -

          Fit Types

          +

          Fit Types

          -

          Single Histogram Fit (fit type 0)

          +

          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

          \[N(t) = N_0 e^{-t/\tau_\mu} [ 1 + A(t) ] + N_{\rm bkg}\]
          @@ -1944,7 +1976,7 @@ If the option lifetimecorrection is set in the PLOT block the asymmetry \[A(t) = \frac{N(t) - N_{\rm bkg}}{N_0} e^{+t/\tau_\mu} - 1\]
          -

          Single Histogram RRF Fit (fit type 1)

          +

          Single Histogram RRF Fit (fit type 1)

          The single-histogram RRF fit (fit type 1) is used to fit the rotating reference frame asymmetry \(A_{\rm rrf}(t)\) 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. \(A_{\rm rrf}(t)\) is estimated the following way (for more details see the @@ -1968,7 +2000,7 @@ of the \(N_0\) estimate, line 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

          -

          Asymmetry Fit (fit type 2)

          +

          Asymmetry Fit (fit type 2)

          For an asymmetry fit (fit type 2) two histograms are needed. These are given by the forward and backward keywords in the RUN block. Additionally, the parameters alpha and 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 @@ -2002,13 +2034,13 @@ efficiencies, solid angles and initial asymmetries of the two detectors can be s

          and plotted together with the function given in the THEORY block.

          -

          Asymmetry RRF Fit (fit type 3)

          +

          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!

          -

          Negative Muon μSR Fit (fit type 4)

          +

          Negative Muon μSR Fit (fit type 4)

          The negative muon μSR fit (fit type 4) is used for single histogram fits of MuMinus, i.e.

          \[N(t) = \sum_i N_i\,\mathrm{e}^{-t/\tau_i} \left[ 1 + A_i(t)\right] + N_{\rm bkg}(t)\]
          @@ -2024,7 +2056,7 @@ the single histogram RRF fit apply: if you not urgently need it: do not

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

          -

          beta-NMR Asymmetry Fit (fit type 5)

          +

          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 forward and backward keywords in the RUN block. Additionally, the parameters alpha and 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 @@ -2064,7 +2096,7 @@ efficiencies, solid angles and initial asymmetries of the two detectors can be s

          and plotted together with the function given in the THEORY block.

          -

          Non-μSR Fit (fit type 8)

          +

          Non-μSR Fit (fit type 8)

          In the case of a non-μSR fit (fit type 8) the fitting function is

          \[y = f(x),\]
          @@ -2073,7 +2105,7 @@ efficiencies, solid angles and initial asymmetries of the two detectors can be s
          -

          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:

          @@ -2091,7 +2123,7 @@ In order to do so, basically two things are needed:

          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.

          -

          User Function without global user-function-object access

          +

          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 \(f_a(x) = \sin(a x)/(a x)\), where the parameter \(a\) 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 @@ -2194,7 +2226,7 @@ refer to the remark at the end of this section.

          -

          User Function with global user-function-object access

          +

          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 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 @@ -2334,7 +2366,7 @@ In case this cannot be ensured, the parallelization can be disabled by –di

          -

          Technical Description of the musrfit framework

          +

          Technical Description of the musrfit framework

          A technical description of the musrfit framework can be found on its own docu.

          @@ -2433,12 +2465,12 @@ In case this cannot be ensured, the parallelization can be disabled by –di
        • previous |
          • -
        • musrfit 1.6.1 documentation »
          • +
        • musrfit 1.6.2 documentation »