21 Commits

Author SHA1 Message Date
64d3b6192b added the option to write the content of the MINUIT2.OUTPUT ascii file as yaml. This extends the previous commit from Ryan M.L. McFadden. 2024-06-18 11:16:15 +02:00
6bcb26f9d5 Merge branch 'root6' of https://bitbucket.org/muonspin/musrfit into root6 2024-06-18 08:19:01 +02:00
6b865efd3b Merged in ignore (pull request #17)
ignore all files generated from an in-repo build

Approved-by: Andreas Suter
2024-06-18 06:18:56 +00:00
caccfb175a Merged in yaml (pull request #16)
write the fit results to an easy-to-read/parse yaml file

Approved-by: Andreas Suter
2024-06-18 06:18:31 +00:00
1845b5c176 Merged in segfault (pull request #15)
fix segfault

Approved-by: Andreas Suter
2024-06-18 06:18:14 +00:00
8821112927 ignore all files generated from an in-repo build 2024-06-17 13:07:06 -03:00
833171c712 write the fit results to an easy-to-read/parse yaml file
This patch adds routines for writing a comprehensive set of fit results (i.e., parameter values, parabolic errors, asymmetric errors, covariances, correlation coefficients, etc.) for an individual `.msr` file to an easy-to-read/parse `.yaml` file.

The main motivation for the code addition is to provide users with easy access to the fit's covariance matrix without the need for "extra" manual effort (e.g., parsing the contents of `MINUIT2.OUTPUT` or `MINUIT2.root`). The other fit quantities are also included for completeness.

Reading/accessing the output is trivial using, for example, the PyYAML Python library (https://github.com/yaml/pyyaml):

```python
import yaml

with open("2125_tf_histo.yaml", "r") as fh:
	results = yaml.load(fh, Loader=yaml.SafeLoader)

cov = results["covariance"]["Field_1"]["Sigma_1"]
```

Note: the naming conventions chosen for the blocks in the `.yaml` output closely follow those used by the iminuit Python library (https://github.com/scikit-hep/iminuit).
2024-06-17 12:51:04 -03:00
61749b91c4 fix segfault
This patch provides a memory-safe alternative to the changes introduced in commit 418adfde67, which causes a segfault when the "batch mode" flag is required (i.e., for ascii/graphic export).

Note: the program name (i.e., argv[0]) has been added the list arguments passed to ROOT's TApplication. This ensures that the TApplication name matches that of the program (see 542b98b2cc/core/base/src/TApplication.cxx (L179-L180)).
2024-06-17 10:52:14 -03:00
3d92e2eefb add CPU info to the configure process. 2024-06-09 17:45:02 +02:00
b71dce9291 remove more accidently added file. 2024-06-08 16:39:57 +02:00
1aa4ce0a99 remove accidentely added file. 2024-06-08 16:36:54 +02:00
425ed02e22 update of the docu. 2024-06-08 09:23:36 +02:00
a36abfc461 updated version info, due to the macOS OpenMP support. 2024-06-08 09:17:05 +02:00
ccaba41868 modernize the way how to check/deal with OpenMP. This helps also on the macOS side. 2024-06-07 12:44:59 +02:00
418adfde67 propagate only necessary root flags to TApplication. 2024-06-06 10:06:50 +02:00
66df43c663 moved mupp examples form the mupp source destination to doc/examples. 2024-04-26 15:54:44 +02:00
4a6885f55b update of the documentation. 2024-04-23 10:50:11 +02:00
92b1aac7a6 got rid off some double brackets. 2024-04-20 18:13:09 +02:00
26e25ce10b fixed a fruther bracket bug. 2024-04-20 17:39:18 +02:00
cedaabeb98 improved bracket handling in function string generation. 2024-04-20 09:40:04 +02:00
032510fbcb update of the ChangeLog. 2024-04-19 12:44:43 +02:00
222 changed files with 546 additions and 8897 deletions

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# ignore all files generated from an in-repo build
build/

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@ -1,7 +1,7 @@
# - musrfit
cmake_minimum_required(VERSION 3.17)
project(musrfit VERSION 1.9.3 LANGUAGES C CXX)
project(musrfit VERSION 1.9.5 LANGUAGES C CXX)
#--- musrfit specific options -------------------------------------------------
option(nexus "build optional NeXus support. Needed for ISIS" OFF)
@ -109,13 +109,13 @@ find_package(FFTW3 REQUIRED)
find_package(LibXml2 REQUIRED)
#--- check for OpenMP ---------------------------------------------------------
if (try_OpenMP AND NOT APPLE)
if (try_OpenMP)
find_package(OpenMP)
if (OpenMP_FOUND)
if (OpenMP_CXX_FOUND)
add_definitions(-DHAVE_GOMP)
set(HAVE_GOMP 1 CACHE INTERNAL "Have GOMP")
endif (OpenMP_FOUND)
endif (try_OpenMP AND NOT APPLE)
endif (OpenMP_CXX_FOUND)
endif (try_OpenMP)
#--- check for Qt -------------------------------------------------------------
if (qt_based_tools)
@ -249,6 +249,8 @@ set(CMAKE_INSTALL_RPATH "${rpath}")
add_subdirectory(src)
#--- write summary of the installation
cmake_host_system_information(RESULT PROCESSOR QUERY PROCESSOR_DESCRIPTION)
message("")
message("|-----------------------------------------------------------------------|")
message("| |")
@ -256,8 +258,9 @@ message("| Summary
message("| |")
message("|-----------------------------------------------------------------------|")
message("")
message(" System: ${CMAKE_HOST_SYSTEM_NAME} ${CMAKE_SYSTEM_PROCESSOR} - ${CMAKE_HOST_SYSTEM_VERSION}")
message(" -------")
message(" System: ${CMAKE_HOST_SYSTEM_NAME} ${CMAKE_SYSTEM_PROCESSOR} - ${CMAKE_HOST_SYSTEM_VERSION}")
message(" Processor: ${PROCESSOR} (${CMAKE_SYSTEM_PROCESSOR})")
message(" ----------")
message("")
message(" musrfit Version: ${musrfit_VERSION}")
message(" ----------------")

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@ -12,6 +12,11 @@ or
https://bitbucket.org/muonspin/musrfit/commits/all
Release of V1.9.3, 2024/04/19
=============================
fix of function string generation from AST.
Release of V1.9.2, 2023/10/25
=============================

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VERSION: '1.9.1',
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LANGUAGE: 'None',
COLLAPSE_INDEX: false,
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@ -1,376 +0,0 @@
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* Humdinger <humdingerb@gmail.com>
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@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>Acknowledgements &mdash; musrfit 1.9.1 documentation</title>
<title>Acknowledgements &mdash; musrfit 1.9.4 documentation</title>
@ -30,7 +30,9 @@
<link rel="index" title="Index" href="genindex.html" />
<link rel="search" title="Search" href="search.html" />
<link rel="next" title="Bugtracking" href="bugtracking.html" />
<link rel="prev" title="MusrRoot - an Extensible Open File Format for μSR" href="musr-root.html" />
<link rel="prev" title="MusrRoot - an Extensible Open File Format for μSR" href="musr-root.html" />
<link href="_static/style.css" rel="stylesheet" type="text/css">
<script src="_static/js/modernizr.min.js"></script>
@ -199,7 +201,7 @@ extremely competent way to deal with his projects as well as to deal with the ch
<div role="contentinfo">
<p>
&copy; Copyright 2023, Andreas Suter.
Last updated on Aug 17, 2023.
Last updated on Jun 08, 2024.
</p>
</div>
@ -221,7 +223,7 @@ extremely competent way to deal with his projects as well as to deal with the ch
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT:'./',
VERSION:'1.9.1',
VERSION:'1.9.4',
LANGUAGE:'None',
COLLAPSE_INDEX:false,
FILE_SUFFIX:'.html',

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@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>any2many - a Universal μSR-file-format converter &mdash; musrfit 1.9.1 documentation</title>
<title>any2many - a Universal μSR-file-format converter &mdash; musrfit 1.9.4 documentation</title>
@ -30,7 +30,9 @@
<link rel="index" title="Index" href="genindex.html" />
<link rel="search" title="Search" href="search.html" />
<link rel="next" title="Short description and references to the supported file-formats" href="file-formats.html" />
<link rel="prev" title="msr2data - A Program for Automatically Processing Multiple musrfit msr Files" href="msr2data.html" />
<link rel="prev" title="msr2data - A Program for Automatically Processing Multiple musrfit msr Files" href="msr2data.html" />
<link href="_static/style.css" rel="stylesheet" type="text/css">
<script src="_static/js/modernizr.min.js"></script>
@ -189,7 +191,7 @@ For a detailed description see <a class="reference internal" href="user-manual.h
<div role="contentinfo">
<p>
&copy; Copyright 2023, Andreas Suter.
Last updated on Aug 17, 2023.
Last updated on Jun 08, 2024.
</p>
</div>
@ -211,7 +213,7 @@ For a detailed description see <a class="reference internal" href="user-manual.h
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT:'./',
VERSION:'1.9.1',
VERSION:'1.9.4',
LANGUAGE:'None',
COLLAPSE_INDEX:false,
FILE_SUFFIX:'.html',

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@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>Bugtracking &mdash; musrfit 1.9.1 documentation</title>
<title>Bugtracking &mdash; musrfit 1.9.4 documentation</title>
@ -29,7 +29,9 @@
<link rel="stylesheet" href="_static/pygments.css" type="text/css" />
<link rel="index" title="Index" href="genindex.html" />
<link rel="search" title="Search" href="search.html" />
<link rel="prev" title="Acknowledgements" href="acknowledgement.html" />
<link rel="prev" title="Acknowledgements" href="acknowledgement.html" />
<link href="_static/style.css" rel="stylesheet" type="text/css">
<script src="_static/js/modernizr.min.js"></script>
@ -187,7 +189,7 @@ or send an e-mail to A. Suter at PSI.</p>
<div role="contentinfo">
<p>
&copy; Copyright 2023, Andreas Suter.
Last updated on Aug 17, 2023.
Last updated on Jun 08, 2024.
</p>
</div>
@ -209,7 +211,7 @@ or send an e-mail to A. Suter at PSI.</p>
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT:'./',
VERSION:'1.9.1',
VERSION:'1.9.4',
LANGUAGE:'None',
COLLAPSE_INDEX:false,
FILE_SUFFIX:'.html',

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@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>How to Cite musrfit? &mdash; musrfit 1.9.1 documentation</title>
<title>How to Cite musrfit? &mdash; musrfit 1.9.4 documentation</title>
@ -30,7 +30,9 @@
<link rel="index" title="Index" href="genindex.html" />
<link rel="search" title="Search" href="search.html" />
<link rel="next" title="Tutorial for musrfit" href="tutorial.html" />
<link rel="prev" title="Welcome to the musrfit documentation!" href="index.html" />
<link rel="prev" title="Welcome to the musrfit documentation!" href="index.html" />
<link href="_static/style.css" rel="stylesheet" type="text/css">
<script src="_static/js/modernizr.min.js"></script>
@ -201,7 +203,7 @@
<div role="contentinfo">
<p>
&copy; Copyright 2023, Andreas Suter.
Last updated on Aug 17, 2023.
Last updated on Jun 08, 2024.
</p>
</div>
@ -223,7 +225,7 @@
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT:'./',
VERSION:'1.9.1',
VERSION:'1.9.4',
LANGUAGE:'None',
COLLAPSE_INDEX:false,
FILE_SUFFIX:'.html',

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@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>Short description and references to the supported file-formats &mdash; musrfit 1.9.1 documentation</title>
<title>Short description and references to the supported file-formats &mdash; musrfit 1.9.4 documentation</title>
@ -30,7 +30,9 @@
<link rel="index" title="Index" href="genindex.html" />
<link rel="search" title="Search" href="search.html" />
<link rel="next" title="MusrRoot - an Extensible Open File Format for μSR" href="musr-root.html" />
<link rel="prev" title="any2many - a Universal μSR-file-format converter" href="any2many.html" />
<link rel="prev" title="any2many - a Universal μSR-file-format converter" href="any2many.html" />
<link href="_static/style.css" rel="stylesheet" type="text/css">
<script src="_static/js/modernizr.min.js"></script>
@ -501,7 +503,7 @@ Between detectors, there will be an empty line.</p>
<div role="contentinfo">
<p>
&copy; Copyright 2023, Andreas Suter.
Last updated on Aug 24, 2023.
Last updated on Jun 08, 2024.
</p>
</div>
@ -523,7 +525,7 @@ Between detectors, there will be an empty line.</p>
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT:'./',
VERSION:'1.9.1',
VERSION:'1.9.4',
LANGUAGE:'None',
COLLAPSE_INDEX:false,
FILE_SUFFIX:'.html',

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@ -9,7 +9,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>Index &mdash; musrfit 1.9.1 documentation</title>
<title>Index &mdash; musrfit 1.9.4 documentation</title>
@ -29,7 +29,9 @@
<link rel="stylesheet" href="_static/css/theme.css" type="text/css" />
<link rel="stylesheet" href="_static/pygments.css" type="text/css" />
<link rel="index" title="Index" href="#" />
<link rel="search" title="Search" href="search.html" />
<link rel="search" title="Search" href="search.html" />
<link href="_static/style.css" rel="stylesheet" type="text/css">
<script src="_static/js/modernizr.min.js"></script>
@ -243,7 +245,7 @@
</li>
<li><a href="user-manual.html#index-74">bnmr-asymmetry-fit</a>
</li>
<li><a href="user-libs.html#index-16">BNMR-libs</a>
<li><a href="user-libs.html#index-17">BNMR-libs</a>
</li>
<li><a href="setup-standard.html#index-2">boost-c++</a>
</li>
@ -275,7 +277,7 @@
</li>
<li><a href="file-formats.html#index-2">db-file-format</a>
</li>
<li><a href="user-libs.html#index-15">DepthProf-lib</a>
<li><a href="user-libs.html#index-16">DepthProf-lib</a>
</li>
<li><a href="setup-dks.html#index-0">dks</a>
</li>
@ -299,7 +301,7 @@
<h2 id="E">E</h2>
<table style="width: 100%" class="indextable genindextable"><tr>
<td style="width: 33%; vertical-align: top;"><ul>
<li><a href="user-libs.html#index-19">ExpRlx</a>
<li><a href="user-libs.html#index-20">ExpRlx</a>
</li>
</ul></td>
</tr></table>
@ -345,6 +347,8 @@
<h2 id="G">G</h2>
<table style="width: 100%" class="indextable genindextable"><tr>
<td style="width: 33%; vertical-align: top;"><ul>
<li><a href="user-libs.html#index-14">gap-integral-libs</a>
</li>
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<li><a href="user-libs.html#index-22">Iax</a>
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<li><a href="user-libs.html#index-18">libBNMR</a>
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<li><a href="user-libs.html#index-25">LineLorentzian</a>
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<li><a href="user-libs.html#index-27">LineSkewLorentzian</a>
<li><a href="user-libs.html#index-28">LineSkewLorentzian</a>
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<li><a href="user-libs.html#index-28">LineSkewLorentzian2</a>
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<li><a href="user-manual.html#index-69">single-histogram-fit</a>
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@ -653,7 +657,7 @@
<td style="width: 33%; vertical-align: top;"><ul>
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<li><a href="user-libs.html#index-18">SLR</a>
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<li><a href="setup-standard.html#index-1">supported-operating-systems</a>
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@ -749,7 +753,7 @@
<div role="contentinfo">
<p>
&copy; Copyright 2023, Andreas Suter.
Last updated on Aug 24, 2023.
Last updated on Jun 08, 2024.
</p>
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@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>Welcome to the musrfit documentation! &mdash; musrfit 1.9.1 documentation</title>
<title>Welcome to the musrfit documentation! &mdash; musrfit 1.9.4 documentation</title>
@ -29,7 +29,9 @@
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@ -182,6 +184,7 @@
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<li class="toctree-l1"><a class="reference internal" href="user-libs.html">Documentation of user libs (user functions)</a><ul>
<li class="toctree-l2"><a class="reference internal" href="user-libs.html#meissner-profiles-vortex-lattice-related-functions-bmw-libs">Meissner-Profiles / Vortex-Lattice related functions (BMW libs)</a></li>
<li class="toctree-l2"><a class="reference internal" href="user-libs.html#supeconducting-gap-integrals-to-calculate-vs">Supeconducting Gap-Integrals to calculate <span class="math notranslate nohighlight">\(1/\lambda^2\)</span> vs <span class="math notranslate nohighlight">\(T\)</span></a></li>
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@ -282,7 +285,7 @@
<div role="contentinfo">
<p>
&copy; Copyright 2023, Andreas Suter.
Last updated on Aug 24, 2023.
Last updated on Jun 08, 2024.
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@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>msr2data - A Program for Automatically Processing Multiple musrfit msr Files &mdash; musrfit 1.9.1 documentation</title>
<title>msr2data - A Program for Automatically Processing Multiple musrfit msr Files &mdash; musrfit 1.9.4 documentation</title>
@ -30,7 +30,9 @@
<link rel="index" title="Index" href="genindex.html" />
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@ -516,7 +518,7 @@ fit serves as template for the second and so on. The template field stays empty
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<p>
&copy; Copyright 2023, Andreas Suter.
Last updated on Aug 17, 2023.
Last updated on Jun 08, 2024.
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@ -538,7 +540,7 @@ fit serves as template for the second and so on. The template field stays empty
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