From 49e355f58a212d4bcf3a4fb095580ee7f78164b2 Mon Sep 17 00:00:00 2001 From: Andreas Suter Date: Sat, 21 Feb 2026 16:04:48 +0100 Subject: [PATCH] updated the local user-docu. --- doc/html/_static/basic.css | 8 - doc/html/_static/documentation_options.js | 2 +- doc/html/_static/pygments.css | 66 +++--- doc/html/_static/searchtools.js | 13 +- doc/html/acknowledgement.html | 10 +- doc/html/any2many.html | 10 +- doc/html/bugtracking.html | 10 +- doc/html/cite.html | 10 +- doc/html/file-formats.html | 10 +- doc/html/genindex.html | 52 +++-- doc/html/index.html | 12 +- doc/html/msr2data.html | 10 +- doc/html/mupp.html | 10 +- doc/html/musr-root.html | 196 ++++++++++++++---- doc/html/musredit.html | 10 +- doc/html/objects.inv | Bin 2796 -> 2827 bytes doc/html/search.html | 10 +- doc/html/searchindex.js | 2 +- doc/html/setup-dks.html | 10 +- doc/html/setup-standard.html | 242 ++++++++++------------ doc/html/tutorial.html | 12 +- doc/html/user-libs.html | 20 +- doc/html/user-manual.html | 21 +- 23 files changed, 428 insertions(+), 318 deletions(-) diff --git a/doc/html/_static/basic.css b/doc/html/_static/basic.css index 7ebbd6d07..4738b2edc 100644 --- a/doc/html/_static/basic.css +++ b/doc/html/_static/basic.css @@ -741,14 +741,6 @@ abbr, acronym { cursor: help; } -.translated { - background-color: rgba(207, 255, 207, 0.2) -} - -.untranslated { - background-color: rgba(255, 207, 207, 0.2) -} - /* -- code displays --------------------------------------------------------- */ pre { diff --git a/doc/html/_static/documentation_options.js b/doc/html/_static/documentation_options.js index 070caee4f..19b629dfe 100644 --- a/doc/html/_static/documentation_options.js +++ b/doc/html/_static/documentation_options.js @@ -1,5 +1,5 @@ const DOCUMENTATION_OPTIONS = { - VERSION: '1.9.9', + VERSION: '1.10.0', LANGUAGE: 'en', COLLAPSE_INDEX: false, BUILDER: 'html', diff --git a/doc/html/_static/pygments.css b/doc/html/_static/pygments.css index 0d49244ed..5f2b0a250 100644 --- a/doc/html/_static/pygments.css +++ b/doc/html/_static/pygments.css @@ -6,26 +6,26 @@ span.linenos.special { color: #000000; background-color: #ffffc0; padding-left: .highlight .hll { background-color: #ffffcc } .highlight { background: #eeffcc; } .highlight .c { color: #408090; font-style: italic } /* Comment */ -.highlight .err { border: 1px solid #FF0000 } /* Error */ +.highlight .err { border: 1px solid #F00 } /* Error */ .highlight .k { color: #007020; font-weight: bold } /* Keyword */ -.highlight .o { color: #666666 } /* Operator */ +.highlight .o { color: #666 } /* Operator */ .highlight .ch { color: #408090; font-style: italic } /* Comment.Hashbang */ .highlight .cm { color: #408090; font-style: italic } /* Comment.Multiline */ .highlight .cp { color: #007020 } /* Comment.Preproc */ .highlight .cpf { color: #408090; font-style: italic } /* Comment.PreprocFile */ .highlight .c1 { color: #408090; font-style: italic } /* Comment.Single */ -.highlight .cs { color: #408090; background-color: #fff0f0 } /* Comment.Special */ +.highlight .cs { color: #408090; background-color: #FFF0F0 } /* Comment.Special */ .highlight .gd { color: #A00000 } /* Generic.Deleted */ .highlight .ge { font-style: italic } /* Generic.Emph */ .highlight .ges { font-weight: bold; font-style: italic } /* Generic.EmphStrong */ -.highlight .gr { color: #FF0000 } /* Generic.Error */ +.highlight .gr { color: #F00 } /* Generic.Error */ .highlight .gh { color: #000080; font-weight: bold } /* Generic.Heading */ .highlight .gi { color: #00A000 } /* Generic.Inserted */ -.highlight .go { color: #333333 } /* Generic.Output */ -.highlight .gp { color: #c65d09; font-weight: bold } /* Generic.Prompt */ +.highlight .go { color: #333 } /* Generic.Output */ +.highlight .gp { color: #C65D09; font-weight: bold } /* Generic.Prompt */ .highlight .gs { font-weight: bold } /* Generic.Strong */ .highlight .gu { color: #800080; font-weight: bold } /* Generic.Subheading */ -.highlight .gt { color: #0044DD } /* Generic.Traceback */ +.highlight .gt { color: #04D } /* Generic.Traceback */ .highlight .kc { color: #007020; font-weight: bold } /* Keyword.Constant */ .highlight .kd { color: #007020; font-weight: bold } /* Keyword.Declaration */ .highlight .kn { color: #007020; font-weight: bold } /* Keyword.Namespace */ @@ -33,43 +33,43 @@ span.linenos.special { color: #000000; background-color: #ffffc0; padding-left: .highlight .kr { color: #007020; font-weight: bold } /* Keyword.Reserved */ .highlight .kt { color: #902000 } /* Keyword.Type */ .highlight .m { color: #208050 } /* Literal.Number */ -.highlight .s { color: #4070a0 } /* Literal.String */ -.highlight .na { color: #4070a0 } /* Name.Attribute */ +.highlight .s { color: #4070A0 } /* Literal.String */ +.highlight .na { color: #4070A0 } /* Name.Attribute */ .highlight .nb { color: #007020 } /* Name.Builtin */ -.highlight .nc { color: #0e84b5; font-weight: bold } /* Name.Class */ -.highlight .no { color: #60add5 } /* Name.Constant */ -.highlight .nd { color: #555555; font-weight: bold } /* Name.Decorator */ -.highlight .ni { color: #d55537; font-weight: bold } /* Name.Entity */ +.highlight .nc { color: #0E84B5; font-weight: bold } /* Name.Class */ +.highlight .no { color: #60ADD5 } /* Name.Constant */ +.highlight .nd { color: #555; font-weight: bold } /* Name.Decorator */ +.highlight .ni { color: #D55537; font-weight: bold } /* Name.Entity */ .highlight .ne { color: #007020 } /* Name.Exception */ -.highlight .nf { color: #06287e } /* Name.Function */ +.highlight .nf { color: #06287E } /* Name.Function */ .highlight .nl { color: #002070; font-weight: bold } /* Name.Label */ -.highlight .nn { color: #0e84b5; font-weight: bold } /* Name.Namespace */ +.highlight .nn { color: #0E84B5; font-weight: bold } /* Name.Namespace */ .highlight .nt { color: #062873; font-weight: bold } /* Name.Tag */ -.highlight .nv { color: #bb60d5 } /* Name.Variable */ +.highlight .nv { color: #BB60D5 } /* Name.Variable */ .highlight .ow { color: #007020; font-weight: bold } /* Operator.Word */ -.highlight .w { color: #bbbbbb } /* Text.Whitespace */ +.highlight .w { color: #BBB } /* Text.Whitespace */ .highlight .mb { color: #208050 } /* Literal.Number.Bin */ .highlight .mf { color: #208050 } /* Literal.Number.Float */ .highlight .mh { color: #208050 } /* Literal.Number.Hex */ .highlight .mi { color: #208050 } /* Literal.Number.Integer */ .highlight .mo { color: #208050 } /* Literal.Number.Oct */ -.highlight .sa { color: #4070a0 } /* Literal.String.Affix */ -.highlight .sb { color: #4070a0 } /* Literal.String.Backtick */ -.highlight .sc { color: #4070a0 } /* Literal.String.Char */ -.highlight .dl { color: #4070a0 } /* Literal.String.Delimiter */ -.highlight .sd { color: #4070a0; font-style: italic } /* Literal.String.Doc */ -.highlight .s2 { color: #4070a0 } /* Literal.String.Double */ -.highlight .se { color: #4070a0; font-weight: bold } /* Literal.String.Escape */ -.highlight .sh { color: #4070a0 } /* Literal.String.Heredoc */ -.highlight .si { color: #70a0d0; font-style: italic } /* Literal.String.Interpol */ -.highlight .sx { color: #c65d09 } /* Literal.String.Other */ +.highlight .sa { color: #4070A0 } /* Literal.String.Affix */ +.highlight .sb { color: #4070A0 } /* Literal.String.Backtick */ +.highlight .sc { color: #4070A0 } /* Literal.String.Char */ +.highlight .dl { color: #4070A0 } /* Literal.String.Delimiter */ +.highlight .sd { color: #4070A0; font-style: italic } /* Literal.String.Doc */ +.highlight .s2 { color: #4070A0 } /* Literal.String.Double */ +.highlight .se { color: #4070A0; font-weight: bold } /* Literal.String.Escape */ +.highlight .sh { color: #4070A0 } /* Literal.String.Heredoc */ +.highlight .si { color: #70A0D0; font-style: italic } /* Literal.String.Interpol */ +.highlight .sx { color: #C65D09 } /* Literal.String.Other */ .highlight .sr { color: #235388 } /* Literal.String.Regex */ -.highlight .s1 { color: #4070a0 } /* Literal.String.Single */ +.highlight .s1 { color: #4070A0 } /* Literal.String.Single */ .highlight .ss { color: #517918 } /* Literal.String.Symbol */ .highlight .bp { color: #007020 } /* Name.Builtin.Pseudo */ -.highlight .fm { color: #06287e } /* Name.Function.Magic */ -.highlight .vc { color: #bb60d5 } /* Name.Variable.Class */ -.highlight .vg { color: #bb60d5 } /* Name.Variable.Global */ -.highlight .vi { color: #bb60d5 } /* Name.Variable.Instance */ -.highlight .vm { color: #bb60d5 } /* Name.Variable.Magic */ +.highlight .fm { color: #06287E } /* Name.Function.Magic */ +.highlight .vc { color: #BB60D5 } /* Name.Variable.Class */ +.highlight .vg { color: #BB60D5 } /* Name.Variable.Global */ +.highlight .vi { color: #BB60D5 } /* Name.Variable.Instance */ +.highlight .vm { color: #BB60D5 } /* Name.Variable.Magic */ .highlight .il { color: #208050 } /* Literal.Number.Integer.Long */ \ No newline at end of file diff --git a/doc/html/_static/searchtools.js b/doc/html/_static/searchtools.js index 2c774d17a..91f4be57f 100644 --- a/doc/html/_static/searchtools.js +++ b/doc/html/_static/searchtools.js @@ -513,9 +513,11 @@ const Search = { // perform the search on the required terms searchTerms.forEach((word) => { const files = []; + // find documents, if any, containing the query word in their text/title term indices + // use Object.hasOwnProperty to avoid mismatching against prototype properties const arr = [ - { files: terms[word], score: Scorer.term }, - { files: titleTerms[word], score: Scorer.title }, + { files: terms.hasOwnProperty(word) ? terms[word] : undefined, score: Scorer.term }, + { files: titleTerms.hasOwnProperty(word) ? titleTerms[word] : undefined, score: Scorer.title }, ]; // add support for partial matches if (word.length > 2) { @@ -547,8 +549,9 @@ const Search = { // set score for the word in each file recordFiles.forEach((file) => { - if (!scoreMap.has(file)) scoreMap.set(file, {}); - scoreMap.get(file)[word] = record.score; + if (!scoreMap.has(file)) scoreMap.set(file, new Map()); + const fileScores = scoreMap.get(file); + fileScores.set(word, record.score); }); }); @@ -587,7 +590,7 @@ const Search = { break; // select one (max) score for the file. - const score = Math.max(...wordList.map((w) => scoreMap.get(file)[w])); + const score = Math.max(...wordList.map((w) => scoreMap.get(file).get(w))); // add result to the result list results.push([ docNames[file], diff --git a/doc/html/acknowledgement.html b/doc/html/acknowledgement.html index 30c1bf321..78561acce 100644 --- a/doc/html/acknowledgement.html +++ b/doc/html/acknowledgement.html @@ -6,14 +6,14 @@ - Acknowledgements — musrfit 1.9.9 documentation - + Acknowledgements — musrfit V1.10.0 + - + @@ -112,8 +112,8 @@ extremely competent way to deal with his projects as well as to deal with the ch
-

© Copyright 2025, Andreas Suter. - Last updated on Jun 07, 2025. +

© Copyright 2026, Andreas Suter. + Last updated on Feb 21, 2026.

diff --git a/doc/html/any2many.html b/doc/html/any2many.html index dd45ebea7..f2b02e438 100644 --- a/doc/html/any2many.html +++ b/doc/html/any2many.html @@ -6,14 +6,14 @@ - any2many - a Universal μSR-file-format converter — musrfit 1.9.9 documentation - + any2many - a Universal μSR-file-format converter — musrfit V1.10.0 + - + @@ -102,8 +102,8 @@ For a detailed description see -

© Copyright 2025, Andreas Suter. - Last updated on Jun 07, 2025. +

© Copyright 2026, Andreas Suter. + Last updated on Feb 21, 2026.

diff --git a/doc/html/bugtracking.html b/doc/html/bugtracking.html index 38e6619cf..261aa0e5e 100644 --- a/doc/html/bugtracking.html +++ b/doc/html/bugtracking.html @@ -6,14 +6,14 @@ - Bugtracking — musrfit 1.9.9 documentation - + Bugtracking — musrfit V1.10.0 + - + @@ -101,8 +101,8 @@ or send an e-mail to A. Suter at PSI.

-

© Copyright 2025, Andreas Suter. - Last updated on Jun 07, 2025. +

© Copyright 2026, Andreas Suter. + Last updated on Feb 21, 2026.

diff --git a/doc/html/cite.html b/doc/html/cite.html index 6e99bc137..55b8548b7 100644 --- a/doc/html/cite.html +++ b/doc/html/cite.html @@ -6,14 +6,14 @@ - How to Cite musrfit? — musrfit 1.9.9 documentation - + How to Cite musrfit? — musrfit V1.10.0 + - + @@ -114,8 +114,8 @@
-

© Copyright 2025, Andreas Suter. - Last updated on Jun 07, 2025. +

© Copyright 2026, Andreas Suter. + Last updated on Feb 21, 2026.

diff --git a/doc/html/file-formats.html b/doc/html/file-formats.html index b9dc7dc7d..9cd8adfca 100644 --- a/doc/html/file-formats.html +++ b/doc/html/file-formats.html @@ -6,14 +6,14 @@ - Short description and references to the supported file-formats — musrfit 1.9.9 documentation - + Short description and references to the supported file-formats — musrfit V1.10.0 + - + @@ -415,8 +415,8 @@ Between detectors, there will be an empty line.

-

© Copyright 2025, Andreas Suter. - Last updated on Jun 07, 2025. +

© Copyright 2026, Andreas Suter. + Last updated on Feb 21, 2026.

diff --git a/doc/html/genindex.html b/doc/html/genindex.html index 7634f44be..cfb09b292 100644 --- a/doc/html/genindex.html +++ b/doc/html/genindex.html @@ -5,14 +5,14 @@ - Index — musrfit 1.9.9 documentation - + Index — musrfit V1.10.0 + - + @@ -273,9 +273,9 @@ @@ -289,7 +289,7 @@ @@ -337,15 +337,13 @@

M

- +
    -
  • root-build-macports +
  • root-build-macports
  • root-cern
    • @@ -669,8 +667,8 @@
    -

    © Copyright 2025, Andreas Suter. - Last updated on Jun 09, 2025. +

    © Copyright 2026, Andreas Suter. + Last updated on Feb 21, 2026.

    diff --git a/doc/html/index.html b/doc/html/index.html index 47c19403d..067aea0e9 100644 --- a/doc/html/index.html +++ b/doc/html/index.html @@ -6,14 +6,14 @@ - Welcome to the musrfit documentation! — musrfit 1.9.9 documentation - + Welcome to the musrfit documentation! — musrfit V1.10.0 + - + @@ -106,7 +106,7 @@
  • Documentation of user libs (user functions)
    • Meissner-Profiles / Vortex-Lattice related functions (BMW libs)
      • -
    • Supeconducting Gap-Integrals to calculate \(1/\lambda^2\) vs \(T\)
      • +
    • Superconducting Gap-Integrals to calculate \(1/\lambda^2\) vs \(T\)
    • Nonlocal superconductivity related Meissner screening functions (AS libs)
    • Depth resolved information (AS libs)
    • Functions to analyze β-NMR data (BNMR libs)
      • @@ -198,8 +198,8 @@
      -

      © Copyright 2025, Andreas Suter. - Last updated on Jun 09, 2025. +

      © Copyright 2026, Andreas Suter. + Last updated on Feb 21, 2026.

      diff --git a/doc/html/msr2data.html b/doc/html/msr2data.html index a10d69c9e..610f4ff4a 100644 --- a/doc/html/msr2data.html +++ b/doc/html/msr2data.html @@ -6,14 +6,14 @@ - msr2data - A Program for Automatically Processing Multiple musrfit msr Files — musrfit 1.9.9 documentation - + msr2data - A Program for Automatically Processing Multiple musrfit msr Files — musrfit V1.10.0 + - + @@ -428,8 +428,8 @@ fit serves as template for the second and so on. The template field stays empty
      -

      © Copyright 2025, Andreas Suter. - Last updated on Jun 07, 2025. +

      © Copyright 2026, Andreas Suter. + Last updated on Feb 21, 2026.

      diff --git a/doc/html/mupp.html b/doc/html/mupp.html index 8464e8ef9..f0f503949 100644 --- a/doc/html/mupp.html +++ b/doc/html/mupp.html @@ -6,14 +6,14 @@ - mupp - μSR Parameter Plotter — musrfit 1.9.9 documentation - + mupp - μSR Parameter Plotter — musrfit V1.10.0 + - + @@ -308,8 +308,8 @@ SCRIPT COMMANDS:
      -

      © Copyright 2025, Andreas Suter. - Last updated on Jun 07, 2025. +

      © Copyright 2026, Andreas Suter. + Last updated on Feb 21, 2026.

      diff --git a/doc/html/musr-root.html b/doc/html/musr-root.html index 07b9a2db4..4822a835b 100644 --- a/doc/html/musr-root.html +++ b/doc/html/musr-root.html @@ -6,14 +6,14 @@ - MusrRoot - an Extensible Open File Format for μSR — musrfit 1.9.9 documentation - + MusrRoot - an Extensible Open File Format for μSR — musrfit V1.10.0 + - + @@ -134,13 +134,20 @@ which allows to inspect these files. This browser (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.

        • +

      • TFolder/TDirectory: this are the top level objects in the MusrRoot file.

      • TH1F: Hold the μ-decay-histograms.

        • -

      • TObjArray: Holding collection of header information.

        • +

      • TObjArray/TDirectory: 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 μ-decay-histograms can be directly plotted, are even fitted, out of the box.

      +
      +

      Note

      +

      Since TFolder has bee marked as deprecated from the ROOT team, we +will gradually switch over to use TDirectory instead. This will have a minimal impact on +the following, as you will see. In the description to follow, the term “folder” will be used +synonymous with “directory”. Only if necessary it will be distinguished.

      +

      MusrRoot an Extensible Open File Format for μSR

      @@ -173,7 +180,7 @@ For instance, the μ-decay-histograms can be directly plotted, are even fitted, 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 μSR-run. The list of the minimal number of required “folders” of the RunHeader is given in the following structure:

      +

      The RunHeader contains all needed meta-information to describe a μSR-run. The list of the minimal number of required “folders” of the RunHeader is given in the following structure (deprecated):

      RunHeader (TFolder) ---|
                        |- RunInfo (TObjArray)
                        |- DetectorInfo (TObjArray)
@@ -182,8 +189,24 @@ in C/C++|- BeamlineInfo (TObjArray)
      +

      In case it is already switched to TDirectory, it will look like this (default starting 2026):

      +
      RunHeader (TDirectory) ---|
+                          |- RunInfo (TDirectory)
+                          |- DetectorInfo (TDirectory)
+                          |- SampleEnvironmentInfo (TDirectory)
+                          |- MagneticFieldEnvironmentInfo (TDirectory)
+                          |- BeamlineInfo (TDirectory)
+
      +

      In brackets the object type is given. RunInfo contains most information relevant for the user and will be itemized in RunInfo Overview and RunInfo Required. DetectorInfo contains detector specific information, like detector name, time zero bin, etc. (details is found under DetectorInfo Required). SampleEnvironmentInfo (details under SampleEnvironmentInfo Required), and MagneticFieldEnvironmentInfo (details under MagneticFieldEnvironmentInfo Required) store additional, more detailed information concerning the sample environment. BeamlineInfo stores beamline relevant information (details under BeamlineInfo 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.).

      +

      Before elaborating more on the required items within this structure, a few words on the ROOT types used here: RunHeader is a TFolder (deprecated) or a TDirectory object.

      +
        +

      1. In case of the deprecated TFolder RunHeader`, 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.).

        2. +

      2. In case the top entry RunHeader is a TDirectory object, all potential “sub-directories” are +indeed TDirectory objects as well. In this case, the data are represented by TObjString objects.

        3. +

      RunInfo Overview

      @@ -306,8 +329,47 @@ is introduced to deal with physical quantities. They always can be represented i -

      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 TMusrRunPhysicalQuantity - Possible Representations.

      -

      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.

      +

      Not all of these values are needed to be given and depending on which are given, the representation in the MusrRoot file will be different (handled by TMusrRunHeader). Examples are given in the comment column of the table above. For details see TMusrRunPhysicalQuantity - Possible Representations.

      +

      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. Here is a table with the data representation

      +
      + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +

      X

      data type

      comment

      0

      TString

      default ROOT type

      1

      Int_t

      2

      Double_t

      3

      TMusrRunPhysicalQuantity

      TMusrRunHeader type

      4

      TStringVector

      type cast to vector<TString>

      5

      TIntVector

      type cast to vector<Int_T>

      6

      TDoubleVector

      type cast to vector<Double_t>

      +

      The next section will explain this in much more detail.

      _images/MusrRoot-RunInfo.png

      TMusrRunHeader mock up. The red shaded entries are of type TMusrRunPhysicalQuantity

      @@ -338,11 +400,11 @@ is derived which is extending the base class to the needs of the instrument.

      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

      -
      TMusrRunHeader *header = new TMusrRunHeader();
+
      std::unique_ptr<TMusrRunHeader> header = std::make_unique<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
      
+
      header is the instance of TMusrRunHeader. Here the concept of a unique pointer (std::unique_ptr) has been used to ensure that no memory leaks are present.  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
      
 
      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);
@@ -364,18 +426,52 @@ is derived which is extending the base class to the needs of the instrument.
      
 
      header->Set("DetectorInfo/Detector001/Time Zero Bin", 3419.0);
 
      
 
      
-
      To write the whole run header into a file would look something like this:
      
-
      TFile *f = new TFile(fileName, "RECREATE", "write_musrRoot_runHeader");
+
      To write the whole run header into a file would look something like this (deprecated TFolder version):
      
+
      // create TMusrRunHeader object
+std::unique_ptr<TMusrRunHeader> header = std::make_unique<TMusrRunHeader>();
+
+// set some stuff
+header->Set("DetectorInfo/Detector001/Time Zero Bin", 3419.0);
+header->Set("Something/Somewhere/Strange", "Test String");
+// add more stuff in the header (not shown)
+
+// create TFile object. It is assumed the fileName is given
+std::unique_ptr<TFile> f = std::make_unique<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");
+std::unique_ptr<TFolder> runHeader = std::make_unique<TFolder>("RunHeader", "MusrRoot Run Header Info");
+
+// create the "folder" structure
+if (header->FillFolder(runHeader)) {
+  runHeader->Write(); // write run header to file
+}
+
+f->Close();
+
      
+
      
+
      In the TDirectory version it will look like this:
      
+
      // create TMusrRunHeader object
+std::unique_ptr<TMusrRunHeader> header = std::make_unique<TMusrRunHeader>();
+
+// set some stuff
+header->Set("DetectorInfo/Detector001/Time Zero Bin", 3419.0);
+header->Set("Something/Somewhere/Strange", "Test String");
+// add more stuff in the header (not shown)
+
+// create TFile object. It is assumed the fileName is given
+std::unique_ptr<TFile> f = std::make_unique<TFile>(fileName, "RECREATE", "write_musrRoot_runHeader");
+if (f->IsZombie()) {
+  return -1;
+}
+
+// create the needed TDirectory object
+TDirectory* runHeader = f->mkdir("RunHeader");
 
 // create the "directory" structure
-if (header->FillFolder(runHeader)) {
+if (header->FillDirectory(runHeader)) {
   runHeader->Write(); // write run header to file
 }
 
@@ -385,41 +481,69 @@ is derived which is extending the base class to the needs of the instrument.

      Reading a MusrRoot Run Header

      -

      The following code snippet shows how the extract the full run header from the MusrRoot file.

      -
      TFile *f = new TFile(fileName, "READ", "read_musrRoot_runHeader");
+
      The following code snippet shows how the extract the full run header from the MusrRoot file.
+First in the deprecate TFolder version:
      
+
      // create TFile. It is assumed that fileName is present
+std::unique_ptr<TFile> f = std::make_unique<TFile>(fileName, "READ", "read_musrRoot_runHeader");
 if (f->IsZombie()) {
-  delete f;
   return -1;
 }
 
-TFolder *runHeader = 0;
+// get the TFolder object from the TFile
+TFolder *runHeader = nullptr;
 f->GetObject("RunHeader", runHeader);
-if (runHeader == 0) {
-  cerr << endl << ">> **ERROR** Couldn't get top folder RunHeader";
-  closeFile(f);
+if (runHeader == nullptr) {
+  std::cerr << std::endl << ">> **ERROR** Couldn't get top folder RunHeader";
   return -1;
 }
 
-TMusrRunHeader *header = new TMusrRunHeader(fileName);
+// create the TMusrRunHeader object
+std::unique_ptr<TMusrRunHeader> header = std::make_unique<TMusrRunHeader>(fileName);
 
+// fill the internal data structure of the TMusrRunHeader object
 if (!header->ExtractAll(runHeader)) {
-  cerr << endl << ">> **ERROR** couldn't extract all RunHeader information";
-  closeFile(f);
+  std::cerr << std::endl << ">> **ERROR** couldn't extract all RunHeader information";
   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
      
+
      The same with the TDirectory version:
      
+
      // create TFile. It is assumed that fileName is present
+std::unique_ptr<TFile> f = std::make_unique<TFile>(fileName, "READ", "read_musrRoot_runHeader");
+if (f->IsZombie()) {
+  return -1;
+}
+
+// get the TDirectory object from the TFile. Note: Here on the top level a TDirectoryFile is needed
+TDirectoryFile *runHeader = nullptr;
+f->GetObject("RunHeader", runHeader);
+if (runHeader == nullptr) {
+  std::cerr << std::endl << ">> **ERROR** Couldn't get top folder RunHeader";
+  return -1;
+}
+
+// create the TMusrRunHeader object
+std::unique_ptr<TMusrRunHeader> header = std::make_unique<TMusrRunHeader>(fileName);
+
+// fill the internal data structure of the TMusrRunHeader object
+if (!header->ExtractAll(runHeader)) {
+  std::cerr << std::endl << ">> **ERROR** couldn't extract all RunHeader information";
+  return -1;
+}
+
+f->Close();
+
      
+
      
+
      The overloaded routine ExtractAll(TFolder *runHeader) and ExtractAll(TDirectory *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
      
 
      Bool_t ok;
 Int_t ival;
 header->Get("RunInfo/Run Number", ival, ok);
 if (ok)
-  cout << endl << "Run Number: " << ival;
+  std::cout << std::endl << "Run Number: " << ival;
 else
-  cout << endl << "**ERROR** Couldn't obtain the 'Run Number'.";
+  std::cout << std::endl << "**ERROR** Couldn't obtain the 'Run Number'.";
 
      
 
      
 
      Reading a TMusrRunPhysicalQuantity object, e.g. the sample temperature looks like this
      
@@ -427,11 +551,11 @@ is derived which is extending the base class to the needs of the instrument.
      
 
 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();
+  std::cout << std::endl << "Sample Temperature: " << prop.GetValue() << " +- ";
+  std::cout << prop.GetError() << " " << prop.GetUnit().Data();
+  std::cout << "; SP: " << prop.GetDemand() << "; " << prop.GetDescription().Data();
 } else {
-  cout << endl << "**ERROR** Couldn't obtain the 'Sample Temperature'.";
+  std::cout << std::endl << "**ERROR** Couldn't obtain the 'Sample Temperature'.";
 }
      @@ -887,8 +1011,8 @@ the entry has been added. The last token, -

      © Copyright 2025, Andreas Suter. - Last updated on Jun 07, 2025. +

      © Copyright 2026, Andreas Suter. + Last updated on Feb 21, 2026.

      diff --git a/doc/html/musredit.html b/doc/html/musredit.html index 6789b2dbd..4e10a0471 100644 --- a/doc/html/musredit.html +++ b/doc/html/musredit.html @@ -6,14 +6,14 @@ - musredit: the GUI Based Interface to musrfit — musrfit 1.9.9 documentation - + musredit: the GUI Based Interface to musrfit — musrfit V1.10.0 + - + @@ -569,8 +569,8 @@ the corresponding fit parameter value, except the phases where the step will be
      -

      © Copyright 2025, Andreas Suter. - Last updated on Jun 07, 2025. +

      © Copyright 2026, Andreas Suter. + Last updated on Feb 21, 2026.

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      -

      © Copyright 2025, Andreas Suter. - Last updated on Jun 09, 2025. +

      © Copyright 2026, Andreas Suter. + Last updated on Feb 21, 2026.

      diff --git a/doc/html/searchindex.js b/doc/html/searchindex.js index e23825375..af1d7bde4 100644 --- a/doc/html/searchindex.js +++ b/doc/html/searchindex.js @@ -1 +1 @@ -Search.setIndex({"alltitles": {"AMD APP Software Development Kit (SDK) to enable OpenCL support": [[10, "amd-app-software-development-kit-sdk-to-enable-opencl-support"]], "ASCII file format for non-\u03bcSR": [[4, "ascii-file-format-for-non-mgrsr"]], "Acknowledgements": [[0, null]], "Asymmetry Fit (fit type 2)": [[14, "asymmetry-fit-fit-type-2"]], "Asymmetry RRF Fit (fit type 3)": [[14, "asymmetry-rrf-fit-fit-type-3"]], "Asymmtery-fit tutorial": [[12, "asymmtery-fit-tutorial"]], "Available Executable, Configuration Files and their Basic Usage": [[9, "available-executable-configuration-files-and-their-basic-usage"]], "Available Executables, Configuration Files and their Basic Usage": [[14, "available-executables-configuration-files-and-their-basic-usage"]], "Basic Types of Usage": [[6, "basic-types-of-usage"]], "BeamlineInfo (Required)": [[8, "beamlineinfo-required"]], "Bugtracking": [[2, null]], "Bulk \u03bcSR": [[13, "bulk-mgrsr"]], "Check the installation": [[11, "check-the-installation"], [11, "id18"]], "DAT: CSV like file format for non-\u03bcSR": [[4, "dat-csv-like-file-format-for-non-mgrsr"]], "DB file format for non-\u03bcSR": [[4, "db-file-format-for-non-mgrsr"]], "DKS Command Overview": [[14, "dks-command-overview"]], "DKS extensions of the COMMANDS block enabling GPU and general OpenCL support": [[14, "dks-extensions-of-the-commands-block-enabling-gpu-and-general-opencl-support"]], "Define Variable Dialog": [[7, "define-variable-dialog"]], "Depth resolved information (AS libs)": [[13, "depth-resolved-information-as-libs"]], "Description of the msr File Format": [[14, "description-of-the-msr-file-format"]], "DetectorInfo (Required)": [[8, "detectorinfo-required"]], "Determine t0 and the data range using musrt0": [[12, "determine-t0-and-the-data-range-using-musrt0"]], "Documentation of user libs (user functions)": [[13, null]], "Driver Installation for an AMD Graphic Card, e.g. Radeon R9 390X": [[10, "driver-installation-for-an-amd-graphic-card-e-g-radeon-r9-390x"]], "Driver Installation for the Tesla K40c": [[10, "driver-installation-for-the-tesla-k40c"]], "Everything but ROOT and NeXus": [[11, "everything-but-root-and-nexus"]], "Exhaustive MusrRoot Tree Including Everything Required": [[8, "exhaustive-musrroot-tree-including-everything-required"]], "Field distributions in the mixed state of isotropic superconductors": [[13, "field-distributions-in-the-mixed-state-of-isotropic-superconductors"]], "File Generation": [[6, "file-generation"]], "Fit Types": [[14, "fit-types"]], "Fit the model to the data using musrfit": [[12, "fit-the-model-to-the-data-using-musrfit"]], "Functions": [[13, "functions"], [13, "id1"], [14, "functions"]], "Functions to analyze \u03b2-NMR data (BNMR libs)": [[13, "functions-to-analyze-bgr-nmr-data-bnmr-libs"]], "Further reading": [[12, "further-reading"]], "GNU/Linux": [[11, "gnu-linux"]], "How to Cite musrfit?": [[3, null]], "Indices and tables": [[5, "indices-and-tables"]], "Install via cmake": [[10, "install-via-cmake"]], "Installation of CUDA": [[10, "installation-of-cuda"]], "Installation of DKS": [[10, "installation-of-dks"]], "Installation of DKS and musrfit": [[10, "installation-of-dks-and-musrfit"]], "Installation of NeXus requirements (optional)": [[11, "installation-of-nexus-requirements-optional"], [11, "index-22"], [11, "index-25"]], "Installation of musrfit for DKS": [[10, "installation-of-musrfit-for-dks"]], "Introduction": [[9, "introduction"], [13, "introduction"], [14, "introduction"]], "Known Limitations": [[6, "known-limitations"]], "LE-\u03bcSR": [[13, "le-mgrsr"]], "MDU file format (psi) for \u03bcSR": [[4, "mdu-file-format-psi-for-mgrsr"]], "MS Windows": [[11, "ms-windows"]], "MUD file format (triumf) for \u03bcSR": [[4, "mud-file-format-triumf-for-mgrsr"]], "Mac OS X / macOS": [[11, "mac-os-x-macos"]], "MagneticFieldEnvironmentInfo (Required)": [[8, "magneticfieldenvironmentinfo-required"]], "Maps": [[14, "maps"]], "Meissner-Profiles / Vortex-Lattice related functions (BMW libs)": [[13, "meissner-profiles-vortex-lattice-related-functions-bmw-libs"]], "Minuit2 Command Overview": [[14, "minuit2-command-overview"]], "MusrRoot - an Extensible Open File Format for \u03bcSR": [[8, null]], "MusrRoot an Extensible Open File Format for \u03bcSR": [[8, "id1"]], "MusrRoot file format (PSI) for \u03bcSR": [[4, "musrroot-file-format-psi-for-mgrsr"]], "NeXus file format (isis) for \u03bcSR": [[4, "nexus-file-format-isis-for-mgrsr"]], "Negative Muon \u03bcSR Fit (fit type 4)": [[14, "negative-muon-mgrsr-fit-fit-type-4"]], "Non-\u03bcSR Fit (fit type 8)": [[14, "non-mgrsr-fit-fit-type-8"]], "Nonlocal superconductivity related Meissner screening functions (AS libs)": [[13, "nonlocal-superconductivity-related-meissner-screening-functions-as-libs"]], "Notes on macOS Catalina and newer": [[11, "notes-on-macos-catalina-and-newer"]], "OS Restrictions": [[11, "os-restrictions"]], "One-dimensional London model for the Meissner state of isotropic superconductors": [[13, "one-dimensional-london-model-for-the-meissner-state-of-isotropic-superconductors"]], "Optional Parameters": [[6, "optional-parameters"]], "PSI-BIN file format (psi) for \u03bcSR": [[4, "psi-bin-file-format-psi-for-mgrsr"]], "Parameter Extraction": [[6, "parameter-extraction"]], "Process multiple msr files using msr2data": [[12, "process-multiple-msr-files-using-msr2data"]], "ROOT": [[11, "index-16"], [11, "index-23"], [11, "index-26"]], "ROOT file format (psi/lem before 2012) for \u03bcSR": [[4, "root-file-format-psi-lem-before-2012-for-mgrsr"]], "ROOT installed from source": [[11, "root-installed-from-source"], [11, "id11"]], "ROOT installed via Homebrew": [[11, "root-installed-via-homebrew"]], "ROOT installed via package installer": [[11, "root-installed-via-package-installer"]], "Reading a 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\ No newline at end of file diff --git a/doc/html/setup-dks.html b/doc/html/setup-dks.html index c2b86a5e8..f3e68be0d 100644 --- a/doc/html/setup-dks.html +++ b/doc/html/setup-dks.html @@ -6,14 +6,14 @@ - Setting up musrfit / DKS: High Speed Fitting with GPU’s — musrfit 1.9.9 documentation - + Setting up musrfit / DKS: High Speed Fitting with GPU’s — musrfit V1.10.0 + - + @@ -319,8 +319,8 @@ The only thing you need -

      © Copyright 2025, Andreas Suter. - Last updated on Jun 07, 2025. +

      © Copyright 2026, Andreas Suter. + Last updated on Feb 21, 2026.

      diff --git a/doc/html/setup-standard.html b/doc/html/setup-standard.html index 696cd9b81..8cf50031e 100644 --- a/doc/html/setup-standard.html +++ b/doc/html/setup-standard.html @@ -6,14 +6,14 @@ - Setting up musrfit on Different Platforms — musrfit 1.9.9 documentation - + Setting up musrfit on Different Platforms — musrfit V1.10.0 + - + @@ -55,8 +55,8 @@
    • GNU/Linux
      • -

      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 (also Alma, Rocky), Fedora, @@ -207,9 +202,9 @@ Currently the MXML<

      -

      GNU/Linux

      +

      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 @@ -251,14 +246,12 @@ the installation would look like:

      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”…

      -
      -

      Installation of NeXus requirements (optional)

      +
      +

      Usage 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:

      +GNU/Linux distribution or if this is not the case, the packages can be installed from the source code. The necessary packages +to build NeXus-support for musrfit are HDF4 and HDF5. This means, for a rpm-package based distro try something like:

      $ yum install hdf-devel hdf5-devel
      @@ -270,28 +263,10 @@ needs to be dragged on (comment: if you are a ISIS user, please complain about <
      -

      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.

      -

      A brief instruction how to get NeXus compiled from source (lines starting with ‘#’ are comments only):

      -
      $ 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
-$ # install needs either to be carried out as root or sudo depending on your linux flavour.
-$ sudo cmake --install ./
-
      -
      +

      How NeXus-support is enabled in musrfit is described in the musrfit setup sections below: musrfit build with cmake.

      -
      -

      ROOT

      +
      +

      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 @@ -364,7 +339,7 @@ $ cmake --build

      -

      musrfit

      +

      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

      @@ -390,20 +365,24 @@ will needed to switch branches first.

      $ git pull $ cd build $ xargs rm < install_manifest.txt +$ cmake ../ $ cmake --build ./ --clean-first $ cmake --install ./

      As an alternative (if git is not available), the source code can also be downloaded from the following web-page: musrfit at bitbucket

      -

      musrfit build with cmake

      +

      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). +

      -Dnexus=<value>

      enable/disable the support of NeXus data files (requires at least the HDF5 library 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.

      +
      -DHAVE_HDF4=<value>

      tell musrfit, whether NeXus-support should include HDF4 as well. <value>=1 notifies the presence of HDF4. This option is obviously +only relevant if NeXus is enabled as well.

      +
      -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 user libs.

      @@ -424,11 +403,11 @@ If the value is set to -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

      +NeXus support (including HDF4) would look like

      $ cd $HOME/Apps/musrfit
 $ mkdir build
 $ cd build
-$ cmake ../ -DCMAKE_INSTALL_PREFIX=$ROOTSYS -Dnexus=1
+$ cmake ../ -DCMAKE_INSTALL_PREFIX=$ROOTSYS -Dnexus=1 -DHAVE_HDF4=1
 # below it is assumed that multiple cores are present, hence the -j8 option
 $ cmake --build ./ --clean-first -- -j8
 $ cmake --install ./
@@ -437,7 +416,7 @@ $ /sbin/ldconfig
      -

      musrfit last step of the installation

      +

      musrfit last step of the installation

      In order to finish the installation of musrfit two more things should be done:

        @@ -455,7 +434,7 @@ detailed information on this XML file refer to the
      -

      musredit

      +

      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.

      @@ -504,9 +483,9 @@ directories like ..

      Mac OS X / macOS

      Note

      -

      macOS 15 alias Sequoia: musrfit is ready for Sequoia on Intel and Apple Silicon based macs, both running natively. -The DKS version of musrfit for macOS Sequoia is ready as well. -This is true for the Homebrew, MacPorts still has some issues (as of 23.09.24). Typically this should be fixed in a month.

      +

      macOS 26 alias Tahoe: musrfit is ready for Tahoe on Intel and Apple Silicon based macs, both running natively. +The DKS version of musrfit for macOS Tahoe is ready as well. +This is true for the Homebrew (tested on Apple Silicon and MacPorts on Intel).

      Note

      @@ -525,7 +504,7 @@ unistall musrfitMacPorts / Homebrew , ROOT, and musrfit from scratch!

      -

      Requirements (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:

      @@ -581,34 +560,16 @@ add a new line pointing to your local copy, e.g.

      With Qt6, 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!

      -
      -

      Installation of NeXus requirements (optional)

      +
      +

      Usage of NeXus requirements (optional)

      Only if musrfit should support reading data files in the NeXus format the further required packages are set up:

      $ sudo port -v install hdf4 hdf5
      -

      hdf4 is likely not available anymore.

      -

      Only NeXus Version ≥ 4.4 is support!

      -

      To get things compiled do:

      -
      $ # 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
-$ # in case hdf4 is present
-$ cmake -DENABLE_HDF5=1 -DENABLE_HDF4=1 -DENABLE_MXML=0 ../code
-$ # in case hdf4 is **not** present
-$ cmake -DENABLE_HDF5=1 -DENABLE_HDF4=0 -DENABLE_MXML=0 ../code
-$ cmake --build ./
-$ sudo cmake --install ./
-
      -
      +

      How NeXus-support is enabled in musrfit is described in the musrfit setup sections below: musrfit build with cmake.

      -
      -

      ROOT

      +
      +

      ROOT

      The default ROOT version is based on ROOT 6.xx/yy!

      ROOT installed via package installer
      @@ -625,8 +586,8 @@ $ sudo ln -
      -
      -
      ROOT installed from source
      +
      -

      Requirements (Homebrew)

      +

      Requirements (Homebrew)

      Before proceeding with the usage of Homebrew, 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. @@ -745,31 +706,23 @@ For example to install 

      $ brew install cmake
      -
      -

      Installation of NeXus requirements (optional)

      +
      +

      Usage of NeXus requirements (optional)

      Only if musrfit should support reading data files in the NeXus format the further required -packages can be installed through Homebrew (Note: hdf4 is not supported anymore):

      +packages can be installed through Homebrew (Note: hdf4 is not supported anymore, but you can install it from source):

      $ brew install hdf5
      -

      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:

      -
      $ # 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=0 -DENABLE_MXML=0
-$ cmake --build ./ --clean-first -- -j8
-$ sudo cmake --install ./
+
      HDF4 install from source code (do it only when you need it):
      
+
      $ cd ~/Applications
+$ git clone https://github.com/HDFGroup/hdf4.git
 
      
 
      
+
      Follow the build instructions which can be found under hdf4/release_docs/USING_HDF4_CMake.txt.
      
+
      How NeXus-support is enabled in musrfit is described in the musrfit setup sections below: musrfit build with cmake.
      -
      -

      ROOT

      +
      +

      ROOT

      The default ROOT version is based on ROOT 6.xx/yy!

      ROOT installed via Homebrew
      @@ -777,7 +730,7 @@ $ sudo cmake musrfit       setup below.

      -
      ROOT installed from source
      +
      ROOT installed from source (recommended)

      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 Requested Software (e.g. fftw, gsl, etc).

      @@ -839,11 +792,6 @@ into the file ~/.Ma export MUSRFITPATH=$ROOTSYS/bin export PATH=$ROOTSYS/bin:$QTDIR/bin:$PATH export DYLD_LIBRARY_PATH=$ROOTSYS/lib/root:/usr/local/lib:$DYLD_LIBRARY_PATH - -launchctl setenv ROOTSYS $ROOTSYS -launchctl setenv MUSRFITPATH $MUSRFITPATH -launchctl setenv PATH $PATH -launchctl setenv DYLD_LIBRARY_PATH $DYLD_LIBRARY_PATH

      If ROOT has been installed via source/compilation:

      @@ -851,22 +799,55 @@ launchctl setenv DYLD_LIBRARY_PATH export MUSRFITPATH=$ROOTSYS/bin export PATH=$ROOTSYS/bin:$QTDIR/bin:$PATH export LD_LIBRARY_PATH=$ROOTSYS/lib:/usr/local/lib:$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” .zprofile before proceeding:

      $ source $HOME/.zprofile
      +

      In addition: create the the file musrfit.environment.plist under ~/Library/LaunchAgents/ with the following content (example for homebrew):

      +
      <?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>Label</key>
+    <string>ch.psi.musrfit.environment</string>
+    <key>ProgramArguments</key>
+    <array>
+        <string>sh</string>
+        <string>-c</string>
+        <string>
+        ROOTSYS=$HOME/Applications/root/root_exec
+        QTDIR=$(brew --prefix)/opt/qt@6
+        OpenMP_ROOT=$(brew --prefix)/opt/libomp
+
+        launchctl setenv ROOTSYS "$ROOTSYS"
+        launchctl setenv MUSRFITPATH "$ROOTSYS/bin"
+        launchctl setenv PATH "$ROOTSYS/bin:$QTDIR/bin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin"
+        launchctl setenv DYLD_LIBRARY_PATH "$ROOTSYS/lib:/usr/local/lib"
+        launchctl setenv OpenMP_ROOT "$OpenMP_ROOT"
+        </string>
+    </array>
+    <key>RunAtLoad</key>
+    <true/>
+</dict>
+</plist>
+
      +
      +

      and launch it once via

      +
      launchctl load ~/Library/LaunchAgents/musrfit.environment.plist
+
      +
      +

      If you use macports, replace in musrfit.environment.plist the lines for QTDIR and OpenMP_ROOT by

      +
      QTDIR=/opt/local/libexec/qt6
+OpenMP_ROOT=/opt/local/include/libomp
+
      +
      -
      -

      musrfit

      +
      +

      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

      @@ -888,15 +869,18 @@ $ 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.

      -
      -

      musrfit build with cmake

      +
      +

      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). +

      -Dnexus=<value>

      enable/disable the support of NeXus data files (requires at least the HDF5 library 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.

      +
      -DHAVE_HDF4=<value>

      tell musrfit, whether NeXus-support should include HDF4 as well. <value>=1 notifies the presence of HDF4. This option is obviously +only relevant if NeXus is enabled as well.

      +
      -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 user libs.

      @@ -926,11 +910,11 @@ If the value is set to NeXus support would look like

      +NeXus-support (including HDF4-support) would look like

      $ cd $HOME/Apps/musrfit
 $ mkdir build
 $ cd build
-$ cmake ../ -DCMAKE_INSTALL_PREFIX=$ROOTSYS -Dnexus=1
+$ cmake ../ -DCMAKE_INSTALL_PREFIX=$ROOTSYS -Dnexus=1 -DHAVE_HDF4=1
 # below it is assumed that multiple cores are present, hence the -j8 option
 $ cmake --build ./ --clean-first -- -j8
 $ cmake --install ./
@@ -947,7 +931,7 @@ The configuration, build, and install process might look like this:
      
 
      $ cd $HOME/Apps/musrfit
 $ mkdir build
 $ cd build
-$ cmake ../ -DCMAKE_INSTALL_PREFIX=$ROOTSYS -Dnexus=1 -DCMAKE_PREFIX_PATH="/opt/local/libexec/qt6/lib/cmake;/opt/local/include/libomp"
+$ cmake ../ -DCMAKE_INSTALL_PREFIX=$ROOTSYS -Dnexus=1 -DHAVE_HDF4=1 -DCMAKE_PREFIX_PATH="/opt/local/libexec/qt6/lib/cmake;/opt/local/include/libomp"
 # below it is assumed that multiple cores are present, hence the -j8 option
 $ cmake --build ./ --clean-first -- -j8
 $ cmake --install ./
@@ -972,8 +956,8 @@ detailed information on this XML file refer to the
      -
      -

      musredit

      +
      +

      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.

      @@ -1021,8 +1005,8 @@ $ musrview test-histo-ROOT-NPP.msr
      -

      © Copyright 2025, Andreas Suter. - Last updated on Jun 07, 2025. +

      © Copyright 2026, Andreas Suter. + Last updated on Feb 21, 2026.

      diff --git a/doc/html/tutorial.html b/doc/html/tutorial.html index 6e3f69995..9b09c115e 100644 --- a/doc/html/tutorial.html +++ b/doc/html/tutorial.html @@ -6,14 +6,14 @@ - Tutorial for musrfit — musrfit 1.9.9 documentation - + Tutorial for musrfit — musrfit V1.10.0 + - + @@ -180,7 +180,7 @@ sample holder), each with an amplitude (parameters 10 and 13), a depolarization

      The THEORY block is used to define a fit-parameter-dependent theory function used to model -the decay asymmetry. Different predefined and user-defined +the decay asymmetry. Different predefined and user-defined 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 @@ -439,8 +439,8 @@ For a complete description please refer to the manuals of -

      © Copyright 2025, Andreas Suter. - Last updated on Jun 07, 2025. +

      © Copyright 2026, Andreas Suter. + Last updated on Feb 21, 2026.

      diff --git a/doc/html/user-libs.html b/doc/html/user-libs.html index c2dea918c..3123235d0 100644 --- a/doc/html/user-libs.html +++ b/doc/html/user-libs.html @@ -6,14 +6,14 @@ - Documentation of user libs (user functions) — musrfit 1.9.9 documentation - + Documentation of user libs (user functions) — musrfit V1.10.0 + - + @@ -60,7 +60,7 @@
    • -
  • Supeconducting Gap-Integrals to calculate \(1/\lambda^2\) vs \(T\)
    • +
  • Superconducting Gap-Integrals to calculate \(1/\lambda^2\) vs \(T\)
  • Nonlocal superconductivity related Meissner screening functions (AS libs)
  • Depth resolved information (AS libs)
  • Functions to analyze β-NMR data (BNMR libs)
      @@ -120,7 +120,7 @@

      libFitPofB

      Introduction

      -

      libFitPofB is a collection of C++ classes using the musrfit user-functions +

      libFitPofB is a collection of C++ classes using the musrfit 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 \(p(B)\) which lead to the muon-spin depolarization functions

      @@ -425,8 +425,8 @@ The expected name of the
      -
      -

      Supeconducting Gap-Integrals to calculate \(1/\lambda^2\) vs \(T\)

      +
      +

      Superconducting Gap-Integrals to calculate \(1/\lambda^2\) vs \(T\)

      The details about the various superconducting gap-integrals are found in the pdf-file GapIntegrals.pdf which can be found in the musrfit source under <musrfit-dir>/src/external/libGapIntegrals/.

      @@ -546,7 +546,7 @@ rge-files (muon stoppping profiles). For this the library reads at start-up the

      Functions to analyze β-NMR data (BNMR libs)

      -

      This is a collection of C++ classes using the musrfit user-functions +

      This is a collection of C++ classes using the musrfit 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.

        • @@ -784,8 +784,8 @@ K(m)&=\int_0^{\pi/2}\frac{\mathrm d\varphi}{\sqrt{1-m^2\sin^2{\varphi}}},\en
        -

        © Copyright 2025, Andreas Suter. - Last updated on Jun 07, 2025. +

        © Copyright 2026, Andreas Suter. + Last updated on Feb 21, 2026.

        diff --git a/doc/html/user-manual.html b/doc/html/user-manual.html index 7f6e81f73..207bf7dc9 100644 --- a/doc/html/user-manual.html +++ b/doc/html/user-manual.html @@ -6,14 +6,14 @@ - User manual — musrfit 1.9.9 documentation - + User manual — musrfit V1.10.0 + - + @@ -917,7 +917,7 @@ in case a \(\chi^2\) single-hi

internFld

if

ifld

\(\alpha (1), \varphi (^\circ)\), \(\nu\) (MHz), \(\lambda_{\rm T} (\mu \mathrm{s}^{-1})\),\(\lambda_{\rm L} (\mu \mathrm{s}^{-1})\)
\(\alpha \cos\left(2\pi\nu t + \frac{\pi \varphi}{180}\right) \exp(-\lambda_{\rm T}t) +\)

\(+ (1-\alpha) \exp(-\lambda_{\rm L} t)\)

@@ -1245,6 +1245,7 @@ Therefore, this block is only present to potentially shorten the msr file and to

  • data

  • t0

  • addt0

    • +

  • deadtime-cor 0, 1, 2, 3

  • fit

  • rrf_freq for fittype 1, 3

  • rrf_packing for fittype 1, 3

    • @@ -1594,6 +1595,14 @@ numbers or the name of the variables as given in the DB header.

    +
    deadtime-cor

    Allows for pulsed sources (currently test with ISIS NeXus files) to perform a deadtime correction on the data.

    +
    deadtime-cor file
+
    +
    +

    Allowed parameters are no, i.e. no deadtime correction; file, i.e. apply deadtime correction according to the +parameters dead_time and good_frames read from the NeXus file; estimate will allow in the future to estimate +the deadtime parameter directley (not yet implemented)

    +
    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.

    @@ -2764,8 +2773,8 @@ The syntax here is attribute driven

    -

    © Copyright 2025, Andreas Suter. - Last updated on Jun 09, 2025. +

    © Copyright 2026, Andreas Suter. + Last updated on Feb 21, 2026.