- - t0-asymmetry
+
- t0-asymmetry
- - t0-single-histo
+
- t0-single-histo
- - technical-musrfit
+
- technical-musrfit
@@ -898,15 +878,15 @@
- - user-functions
+
- user-functions
- - user-functions-with-global-part
+
- user-functions-with-global-part
- - user-functions-without-global-part
+
- user-functions-without-global-part
|
@@ -954,7 +934,7 @@
- - xy-data
+
- xy-data
|
@@ -972,8 +952,8 @@
diff --git a/doc/html/index.html b/doc/html/index.html
index 7a96d325..3a7380cc 100644
--- a/doc/html/index.html
+++ b/doc/html/index.html
@@ -6,7 +6,7 @@
- Welcome to the musrfit documentation! — musrfit 1.7.6 documentation
+ Welcome to the musrfit documentation! — musrfit 1.8.0 documentation
@@ -14,7 +14,7 @@
-
+
@@ -145,8 +145,8 @@
diff --git a/doc/html/msr2data.html b/doc/html/msr2data.html
index 68731adf..0c6a4566 100644
--- a/doc/html/msr2data.html
+++ b/doc/html/msr2data.html
@@ -6,7 +6,7 @@
- msr2data - A Program for Automatically Processing Multiple musrfit msr Files — musrfit 1.7.6 documentation
+ msr2data - A Program for Automatically Processing Multiple musrfit msr Files — musrfit 1.8.0 documentation
@@ -14,7 +14,7 @@
-
+
@@ -380,8 +380,8 @@ fit serves as template for the second and so on. The template field stays empty
diff --git a/doc/html/mupp.html b/doc/html/mupp.html
index 8c494031..85619877 100644
--- a/doc/html/mupp.html
+++ b/doc/html/mupp.html
@@ -6,7 +6,7 @@
- mupp - μSR Parameter Plotter — musrfit 1.7.6 documentation
+ mupp - μSR Parameter Plotter — musrfit 1.8.0 documentation
@@ -14,7 +14,7 @@
-
+
@@ -277,8 +277,8 @@ SCRIPT COMMANDS:
diff --git a/doc/html/musr-root.html b/doc/html/musr-root.html
index 4be045b1..64021976 100644
--- a/doc/html/musr-root.html
+++ b/doc/html/musr-root.html
@@ -6,7 +6,7 @@
- MusrRoot - an Extensible Open File Format for μSR — musrfit 1.7.6 documentation
+ MusrRoot - an Extensible Open File Format for μSR — musrfit 1.8.0 documentation
@@ -14,7 +14,7 @@
-
+
@@ -858,8 +858,8 @@ the entry has been added. The last token,
diff --git a/doc/html/musredit.html b/doc/html/musredit.html
index d0c5f968..2ba3fdd4 100644
--- a/doc/html/musredit.html
+++ b/doc/html/musredit.html
@@ -6,7 +6,7 @@
- musredit: the GUI Based Interface to musrfit — musrfit 1.7.6 documentation
+ musredit: the GUI Based Interface to musrfit — musrfit 1.8.0 documentation
@@ -14,7 +14,7 @@
-
+
@@ -491,8 +491,8 @@ the corresponding fit parameter value, except the phases where the step will be
diff --git a/doc/html/objects.inv b/doc/html/objects.inv
index 19c24cb2..a3225345 100644
Binary files a/doc/html/objects.inv and b/doc/html/objects.inv differ
diff --git a/doc/html/search.html b/doc/html/search.html
index 9367509b..d63b4cb7 100644
--- a/doc/html/search.html
+++ b/doc/html/search.html
@@ -6,7 +6,7 @@
- Search — musrfit 1.7.6 documentation
+ Search — musrfit 1.8.0 documentation
@@ -14,7 +14,7 @@
-
+
@@ -36,7 +36,7 @@
@@ -83,8 +83,8 @@
diff --git a/doc/html/searchindex.js b/doc/html/searchindex.js
index ea895c03..21fc0122 100644
--- a/doc/html/searchindex.js
+++ b/doc/html/searchindex.js
@@ -1 +1 @@
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lob:13,calculatefield:13,energyindex:13,calcualt:13,pol:13,dpol:13,getmuonstoppingdens:13,degree2rad:13,getmagneticfield:13,fab:13,filesystem:10,vaild:13,monterei:10,wsl:10,virtualbox:10,alik:10,usage0:13,usage1:13,options1:13,usage2:13,options2:13,inputfil:13,separt:13,correspon:13,flame:13,iii:13,deltat_tdc_gps_4324:13,deltat_tdc_gps_4325:13,deduc:13,option1:13,option2:13,run_name_templ:13,instrument_nam:13,fragment:13,"_his_":13,rrrrr:13,d2019:13,lem19_his_0123:13},objects:{},objtypes:{},objnames:{},titleterms:{acknowledg:0,any2mani:[13,1],univers:1,"\u03bcsr":[12,7,13,1,6],file:[12,7,11,13,8,5,1],format:[7,13,1],convert:1,bugtrack:2,how:3,cite:3,musrfit:[10,13,3,11,8,4,5,9],welcom:4,document:[12,4],indic:4,tabl:4,msr2data:[5,11,13],program:5,automat:5,process:[5,11],multipl:[5,11],msr:[5,11,13],basic:[5,7,8,13],type:[5,13],usag:[5,13,8,6],run:[5,7,13],list:5,structur:5,option:[5,10],paramet:[5,8,6],global:[5,13],mode:5,gener:[5,13],extract:5,extend:5,known:5,limit:5,graphic:[5,6,9],user:[12,7,13,5,6],interfac:[5,7,8,6],provid:5,musredit:[5,8,10],mupp:6,plotter:6,defin:6,variabl:[10,6],dialog:6,script:6,summari:6,musrroot:7,extens:[7,13],open:7,some:7,concern:7,root:[7,10],inform:7,contain:7,runhead:7,runinfo:7,overview:[7,13],tmusrrunhead:7,concept:7,header:7,write:7,read:[7,11],valid:7,requir:[7,10],detectorinfo:7,sampleenvironmentinfo:7,magneticfieldenvironmentinfo:7,beamlineinfo:7,exhaust:7,tree:7,includ:7,everyth:[7,10],tmusrrunphysicalquant:7,possibl:7,represent:7,gui:8,base:8,introduct:[13,12,8],avail:[13,8],execut:[13,8],configur:[13,8],musrgui:[8,10],musredit_startup:8,xml:[13,12,8],featur:8,musrwiz:8,theori:[13,8],"function":[13,12,8],map:[13,8],fit:[13,11,8,9],info:8,creat:8,musrstep:8,set:[10,9],high:9,speed:9,gpu:[13,9],tesla:9,k40c:9,nvidia:9,driver:9,instal:[10,9],cuda:9,via:[10,9],cmake:[10,9],amd:9,card:9,radeon:9,"390x":9,app:9,softwar:[10,9],develop:9,kit:9,sdk:9,enabl:[13,9],opencl:[13,9],support:[13,10,9],maco:[10,9],differ:10,platform:10,oper:10,system:10,restrict:10,gnu:10,linux:10,nexu:10,build:10,last:10,step:10,depreci:[],check:10,window:10,cygwin:[],potenti:[],problem:[],mac:10,macport:10,packag:10,from:10,sourc:10,environ:10,note:10,catalina:10,fink:10,obsolet:10,tutori:11,singl:[13,11],histogram:[13,11],determin:11,data:[11,12],rang:11,musrt0:[13,11],model:[11,12],view:11,musrview:[13,11],further:11,asymmteri:11,lib:12,meissner:12,profil:12,vortex:12,lattic:12,relat:12,bmw:12,libfitpofb:12,dimension:12,london:12,state:12,isotrop:12,superconductor:12,bulk:12,field:12,distribut:12,mix:12,startup:12,nonloc:12,superconduct:12,screen:12,analyz:12,"\u03b2":12,nmr:[13,12],bnmr:12,libbnmr:12,liblineprofil:12,manual:13,kei:13,shortcut:13,musrft:13,msr2msr:13,dump_head:13,musrfit_startup:13,descript:13,titl:13,fitparamet:13,block:13,command:13,minuit2:13,detail:13,fourier:13,plot:13,statist:13,rrf:13,asymmetri:13,neg:13,muon:13,beta:13,non:13,without:13,object:13,access:13,rge:13,handler:13,low:13,energi:13,technic:13,framework:13,deprec:10,addrun:13},envversion:43})
\ No newline at end of file
diff --git a/doc/html/setup-dks.html b/doc/html/setup-dks.html
index 5735baf6..716b7d05 100644
--- a/doc/html/setup-dks.html
+++ b/doc/html/setup-dks.html
@@ -6,7 +6,7 @@
- Setting up musrfit / DKS: High Speed Fitting with GPU’s — musrfit 1.7.6 documentation
+ Setting up musrfit / DKS: High Speed Fitting with GPU’s — musrfit 1.8.0 documentation
@@ -14,7 +14,7 @@
-
+
@@ -266,8 +266,8 @@ The only thing you need DKS
diff --git a/doc/html/setup-standard.html b/doc/html/setup-standard.html
index e85712a8..e245d05f 100644
--- a/doc/html/setup-standard.html
+++ b/doc/html/setup-standard.html
@@ -6,7 +6,7 @@
- Setting up musrfit on Different Platforms — musrfit 1.7.6 documentation
+ Setting up musrfit on Different Platforms — musrfit 1.8.0 documentation
@@ -14,7 +14,7 @@
-
+
@@ -120,9 +120,8 @@ and manjaro <https://de.manjaro.org/>.
- MS Windows
Native MS Windows support is currently not available. Potential ways to get musrfit running are:
-- via installation of Linux via the Microsoft App store for Windows 10.
+- via installation of Linux via the Microsoft App store for Windows 10/11 (see Install Linux on Windows with WSL).
- via installation of the virtual machine on which you install Linux (probably the easiest for most Windows users).
-- via cygwin.
@@ -405,14 +404,14 @@ $ musrview test-histo-ROOT-NPP.msr
MS Windows
Note
- The description here is only for the very brave ones. It hasn’t been tested for quite a while and therefore gives you
-rather a flavour of what needs to be done rather than a real instruction how to setup musrfit. If you just need
-musrfit to work on a MS Windows platform, it is recommended to install it via a linux virtual machine!
+ For adventurous guys using Windows 10/11, there is the possibility to activate the built in Ubuntu bash-shell. It allows
+to install musrfit as described in the Linux section. For details to setup the Linux sub-system for MS Windows
+see Install Linux on Windows with WSL.
Note
- For adventurous guys using Windows 10, there is the possibility to activate the built in Ubuntu bash-shell. It allows
-to install musrfit as described in the Linux section.
+ Another possibility is to setup linux as a virtual machine with VirtualBox are other alike tools. This way you separate
+Linux / ROOT / musrfit from the default MS Windows system.
Note
@@ -420,259 +419,13 @@ to install musrfit as
in the absolute path or in case you do, do not wonder if some errors occur! msr files, however, might be saved in such
directories like ...\My Documents\...
- Under Windows a native installation is not supported but there is the possibility to run musrfit through cygwin
-which has the great advantage that one gains additionally various nice UNIX tools also for other purposes.
-Please also be aware of the fact that the X server which is going to be installed with Cygwin has to be started
-(e.g. by selecting it from the “Programs” folder) before any graphical application (musrview, musrgui, etc.) is started.
-
- Requirements
-
- Setting up Cygwin
- For the start go to the Cygwin website, download the setup file and use it to install Cygwin 1.7 or newer. During the installation
-process you will be asked where you want to install Cygwin and normally the default choice should just be fine. At some point you
-will be asked which packages should be installed. Make sure that you choose at least the following (or packages with revisions close
-to the following) in order to fulfill the musrfit requirements and be able to work with this base system:
- a2ps, alternatives, autoconf, automake, base-cygwin, base-files, base-passwd bash, bash-completion,
-bc, binutils, bison, boost, boost-devel, bzip2, cmake, colorgcc, coreutils, curl, cygutils, cygwin,
-editrights, fftw3, findutils, flex, font-adobe-dpi100, font-adobe-dpi75, font-alias,
-font-bitstream-dpi100, font-bitstream-dpi75, font-encodings, font-ibm-type1, font-sun-misc, font-util,
-font-xfree86-type1, fontconfig, freeglut, gawk, gcc-tools-autoconf, gcc-tools-automake, gcc4,
-gcc4-core, gcc4-fortran, gcc4-g++, gccmakedep, gd, gettext, ghostscript, ghostscript-fonts-std,
-giflib, gmp, grep, groff, gsl, gsl-apps, gsl-devel, gv, gzip, inputproto, jasper, jpeg, lapack,
-less, libboost, libbz2_1, libcharset1, libcurl4, libfftw3-devel, libfftw3_3, libgcc1, libgd-devel,
-libgif-devel, libGL-devel, libGL1, libGLU-devel, libGLU1, libglut-devel, libglut3, libgmp-devel,
-libgmp3, libgomp1, libICE-devel, libICE6, libjpeg-devel, libjpeg62, liblapack-devel, libmpfr-devel,
-libmpfr1, libncurses-devel, libncurses9, libOSMesa-devel, libOSMesa7, libpng, libpng14, libpng14-devel,
-libreadline6, libSM-devel, libSM6, libssh2_1, libstdc++6, libstdc++6-devel, libtiff-devel, libtiff5,
-libtool, libX11-devel, libX11_6, libXau-devel, libXau6, libXaw7, libxcb-devel, libxcb-xlib-devel,
-libXcursor-devel, libXcursor1, libXdmcp-devel, libXdmcp6, libXext-devel, libXext6, libXfixes-devel,
-libXfixes3, libXfont-devel, libXfont1, libXft-devel, libXft2, libXi-devel, libXi6, libxkbfile1,
-libxml2, libxml2-devel, libXmu-devel, libXmu6, libXpm-devel, libXpm4, libXrender-devel, libXrender1,
-libXt-devel, libXt6, login, m4, make, makedepend, man, mpfr, nano, opengl, openssh, openssl, pdftk,
-perl, ping, pkg-config, psutils, python, qt3, qt3-bin, qt3-devel, readline, rebase, rgb, rsync, run,
-screen, sed, subversion, tar, tcltk, terminfo, unzip, util-linux, vim, w32api, which,
-X-start-menu-icons, xauth, xextproto, xfontsel, xinit, xkbcomp, xkeyboard-config, xkill, xlogo,
-xlsfonts, xorg-cf-files, xorg-scripts, xorg-server, xproto, xrdb, xrefresh, xset, xterm, zip, zlib,
-zlib-devel, zlib0, libQt3Support4-devel, libQtAssistantClient4-devel, libQtCore4-devel,
-libQtDBus4-devel, libQtDesigner4-devel, libQtGui4-devel, libQtHelp4-devel, libQtNetwork4-devel,
-libQtOpenGL4-devel, libQtScript4-devel, libQtScriptTools4-devel, libQtSql4-devel, libQtSvg4-devel,
-libQtTest4-devel, libQtWebKit4-devel, libQtXml4-devel, libQtXmlPatterns4-devel
-
-
- After these installations already most of the required software is present and the Cygwin shell can be started now for the further steps!
-Inside the shell the POSIX naming convention applies, therefore, paths will be given with separating “/” instead of “” in DOS. The file
-structure accessible through this shell can also be accessed through the Windows Explorer — just go to the directory which you specified
-as “cygwin root” during the installation: this is the equivalent to “/” in the shell. By default, the different hard drives or network shares
-like C:\ can be found at /cygdrive/c/ in the shell — the cygdrive prefix can in principle also be changed but for now we stick to the default.
- Since later on the boost header files should be used and in the standard Cygwin installation these are found at a version specific location,
-the later handling will be easier if a symbolic link to these files is created now in the terminal (in case it had not been present before):
- $ ln -sf /usr/include/boost-x_yy_z/boost /usr/include/boost
-
-
- where x_yy_z has to be substituted by the correct version number, e.g. 1_33_1.
-
-
- Everything but ROOT and NeXus
-
-
- Installation of NeXus requirements (optional)
- Only if musrfit should support reading data files in the NeXus format the further required software has
-to be set up. Under Cygwin of all the required libraries only HDF5 is available. The packages hdf5 and
-libhdf5-devel can be installed through the Cygwin setup. One should also make sure that bison, flex
-and a package containing /usr/lib/librpc.a (e.g. sunrpc = 4.0-3, but not sunrpc = 4.0-4) are installed.
- Only NeXus Version ≥ 4.4 is support!
- $ cd
-$ mkdir nexus
-$ cd nexus
-$ curl http://www.hdfgroup.org/ftp/lib-external/jpeg/src/jpegsrc.v6b.tar.gz -G | tar xz
-$ cd jpeg-6b
-$ ./configure --prefix=/usr/local --enable-static
-$ make
-$ make install
-$ cd ..
-$ # create a directory for the NeXus source code
-$ mkdir nexus
-$ cd nexus
-$ # get the source code from the master repository
-$ git clone https://github.com/nexusformat/code.git
-$ # next we will build NeXus out-of-source
-$ mkdir build
-$ cd build
-$ cmake -DENABLE_HDF5=1 -DENABLE_HDF4=1 -DENABLE_MXML=0 ../code
-$ make
-$ make install
-
-
-
-
- ROOT
- In order to install the ROOT system, there are two possibilities:
-
-Download the precompiled Cygwin GCC 4.3 (or newer) package of the most recent ROOT version
-from the web page and unpack it in a Cygwin shell
-(in order to get the line endings correctly) at the final location. Suppose the package has been
-downloaded to C:\ and the ROOT tree should be in C:\root, this is achieved by:
-$ cd /cygdrive/c
-$ tar xzf root_v5.xx.yy.win32gcc-gcc-4.3.tar.gz
-
-
-
-If due to some reason there was no precompiled Cygwin GCC 4.3 package available or ROOT should
-be built from source, one has to visit the web page,
-download the ‘complete source tree for all systems’ and save it for instance in C:\.
-Then go to the Cygwin shell and unpack this source tree, configure it (here using the minimal set of options)
-and compile it as follows right below:
-$ cd /cygdrive/c
-$ tar xzf root_v5.xx.yy.source.tar.gz
-$ cd root
-$ ./configure win32gcc --gminimal --enable-asimage --enable-mathmore --enable-minuit2 --enable-xml
-$ make
-
-
-
-In order to finalize the ROOT installation and to prepare already the installation of musrfit and
-musredit this is a good time for setting necessary environment variables for the use in Cygwin. For
-accomplishing that put the following lines at the end of the /home/Username/.bashrc (C:\cygwin\home\Username\.bashrc
-for the user Username and the cygwin root at C:\cygwin):
-export DISPLAY=:0.0
-export QTDIR=/usr/lib/qt4
-export ROOTSYS=/cygdrive/c/root
-export PATH=$ROOTSYS/bin:$QTDIR/bin:/usr/i686-pc-cygwin/bin:$PATH
-export MUSRFITPATH=$ROOTSYS/bin
-
-
-
-
- Afterwards close the Cygwin shell and reopen it again for the installation of musrfit.
-
-
-
- musrfit
- First, the most recent source code should be downloaded. The preferred way of doing so is to clone the musrfit
-repository via git. Assuming the code should be located in ~/musrfit this is achieved most easily calling from the terminal
- $ cd
-$ git clone https://bitbucket.org/muonspin/musrfit.git
-
-
- or
- $ cd
-$ git clone git://gitlab.psi.ch/nemu/musrfit.git
-
-
- If the repository had been checked out already before, one can update the local copy using:
- $ cd musrfit
-$ git pull
-
-
- As an alternative (if git is not available), the source code can also be downloaded from the following
-web-page: musrfit at bitbucket.
-
- musrfit build with cmake
- Currently the following configuration switches for musrfit are available:
-
-- -DCMAKE_INSTALL_PREFIX=<prefix-path>
-- Specify the installation prefix, i.e. the place where musrfit shall be installed, e.g. $ROOTSYS if already defined (by default: /usr/local)
-- -Dnexus=<value>
-- enable/disable the support of NeXus data files (requires the HDF4, HDF5 and NeXus libraries to be installed).
-<value>=1 enables NeXus, <value>=0 disables NeXus. The default setting, i.e. the switch is not provided is NeXus support is disabled.
-- -DASlibs=<value>
-- enable/disable the ASlibs. <value>=1 enables the ASlibs, <value>=0 disables the ASlibs.
-The default setting, i.e. the switch is not provided is ASlibs support is disabled. For details see Documentation of user libs.
-- -DBMWlibs=<value>
-- enable/disable the BMWlibs. <value>=1 enables the BMWlibs, <value>=0 disables the BMWlibs.
-The default setting, i.e. the switch is not provided is BMWlibs support is disabled. For details see Documentation of user libs.
-- -DBNMRlibs=<value>
-- enable/disable the BNMRlibs. <value>=1 enables the BNMRlibs, <value>=0 disables the BNMRlibs.
-The default setting, i.e. the switch is not provided is BNMRlibs support is disabled.
-- -Dqt_based_tools=<value>
-- Will try to get musredit, musrWiz, musrStep, and mupp installed, if Qt is found.
-By default this is enabled. Again <value>=0 means disabled, <value>=1 enabled.
-- -Dqt_version=<value>
-- Allows to specify which Qt version shall be tried. <value> can take the values: AUTO, 3, 4, 5, 6.
-If the value is set to AUTO, this highest installed version is chosen, otherwise the specified version is used.
-- -Dtry_OpenMP=<value>
-- Will check if OpenMP support is possible, and if yes use it. The default is enabled.
-
- Normally it should not be necessary to make use of any of the options except for specifying the installation path with
--DCMAKE_INSTALL_PREFIX. musrfit build with cmake takes the out-of-source approach. Therefore a typical
-configuration / make / install process including NeXus support would look like
- $ cd $HOME/Apps/musrfit
-$ mkdir build
-$ cd build
-$ cmake ../ -DCMAKE_INSTALL_PREFIX=$ROOTSYS -Dnexus=1
-# below it is assumed that multiple cores are present, hence the -j8 option
-$ cmake --build ./ --clean-first -- -j8
-$ make install
-$ /sbin/ldconfig # (as superuser)
-
-
-
-
-
- musredit
- In the latest version of musrfit the configure script tries to determine automatically if
-Qt4.5 or higher is set up on the machine. In case this is found, the editor musredit is built
-readily with musrfit. If not, try the following:
- $ cd src/musredit
-$ qmake-qt4 musredit.pro
-
-
- If everything went fine musredit can be compiled and installed:
-
- In case one likes to get the editor started just with starting the X server from the Windows start
-menu the file ~/.startxwinrc with the following contents can be created:
- #!/bin/sh
-
-export DISPLAY=:0.0
-export QTDIR=/usr/lib/qt4
-export ROOTSYS=/cygdrive/c/root
-export PATH=$ROOTSYS/bin:$QTDIR/bin:/usr/i686-pc-cygwin/bin:$PATH
-export MUSRFITPATH=$ROOTSYS/bin
-
-musredit &
-
-
-
-
- musrgui (depreciated)
- If Qt4.5 or higher is not available but Qt3 is set up musrgui can be installed. For this
-please follow the instructions for the musredit installation where simply every musredit occurrence
-has to be replaced by musrgui, and qt4 is replaced by qt3.
-
-
- Check the installation
- In order to perform a quick test for finding out if the installation has been completed successfully,
-a few msr files together with the corresponding data files can be found in the musrfit source tree
-at doc/examples/.
-If musrgui has been installed, just open one of the test-*.msr files in the editor and test
-the musrfit functionalities. Otherwise, if only the terminal should be used, as an initial test
-for instance the following could be done:
- $ cd doc/examples
-$ musrview test-histo-ROOT-NPP.msr
-
-
-
-
- Potential Problems
- It might be that especially when running on Windows 7 musredit and musrgui produce errors like a
-“STATUS_ACCESS_VIOLATION”. In this case, try to do the following: Close all Cygwin programs (including
-the terminals and X server) and run from a Windows command prompt (cmd)
- $ C:\cygwin\bin\ash.exe /bin/rebaseall
-
-
- If this does not resolve the problem, try to change the compatibility settings of C:\cygwin\bin\sh.exe
-and C:\cygwin\bin\bash.exe so that they are executed with administrator privileges.
-
Mac OS X / macOS
Note
- macOS 11.3 alias Big Sur: musrfit is ready for Big Sur on Intel and M1 (Apple Silicon) based macs, both running natively.
-The DKS version of musrfit for macOS Big Sur is ready as well.
+ macOS 12 alias Monterey: musrfit is ready for Monterey on Intel and M1 (Apple Silicon) based macs, both running natively.
+The DKS version of musrfit for macOS Monterey is ready as well.
Note
@@ -691,7 +444,7 @@ unistall musrfit, MacPorts / Fink , 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:
@@ -748,8 +501,8 @@ add a new line pointing to your local copy, e.g.
With Qt5, musredit will be installed. If it happens that you used musrgui in the past,
please change over to musredit since there will be no further development for musrgui anymore!
-
- Installation of NeXus requirements (optional)
+
+ Installation 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
@@ -770,8 +523,8 @@ $ sudo make install
-
- ROOT
+
+ ROOT
The default ROOT version is based on ROOT 6.xx/yy!
ROOT installed via package installer
@@ -848,15 +601,15 @@ into the file ~/.MacOSX/environme
export ROOTSYS=$HOME/Applications/root/root_exec
export MUSRFITPATH=$ROOTSYS/bin
export PATH=$ROOTSYS/bin:$QTDIR/bin:$PATH
-export LD_LIBRARY_PATH=$ROOTSYS/lib:$LD_LIBRARY_PATH
+export DYLD_LIBRARY_PATH=$ROOTSYS/lib:$DYLD_LIBRARY_PATH
launchctl setenv ROOTSYS $ROOTSYS
launchctl setenv MUSRFITPATH $MUSRFITPATH
launchctl setenv PATH $PATH
-launchctl setenv LD_LIBRARY_PATH $LD_LIBRARY_PATH
+launchctl setenv DYLD_LIBRARY_PATH $DYLD_LIBRARY_PATH
-After this you will need to “execute” .profile before proceeding:
+After this you will need to “execute” .profile or .zprofile before proceeding:
@@ -883,7 +636,7 @@ but no proper fix is available. The workaround to get it right is to install the
- Requirements (Fink)
+ Requirements (Fink)
Before proceeding with the usage of the Fink system first a few useful tools provided by Apple together with OS X (on the installation DVD/CDs) should be installed:
- Xcode
@@ -940,8 +693,8 @@ specific location, the later handling will be easier if a symbolic link to this
where x_yy_z has to be substituted by the correct version number, e.g. 1_63_0.
-
- Installation of NeXus requirements (optional)
+
+ Installation of NeXus requirements (optional)
Only if musrfit should support reading data files in the NeXus format the further required
packages can be installed through Fink (check for the most recent versions):
libjpeg hdf hdf5-cpp11 hdf5-cpp11-shlibs
@@ -963,11 +716,11 @@ $ sudo make install
-
- ROOT
+
+ ROOT
The default ROOT version is based on ROOT 6.xx/yy!
-
- ROOT installed via package installer
+
+ ROOT installed via package installer
The lazy way to get ROOT installed is via package installer. If your macOS is directly supported
by the ROOT people you can download the package installer from the ROOT download page.
Choose the latest ROOT release and download you macOS version dmg-file, e.g. for macOS 10.13 (High Sierra)
@@ -981,8 +734,8 @@ $ sudo ln -s root_v6.16.00 root
-
- ROOT installed from source
+
+ ROOT installed from source
The best way to get ROOT exactly the way needed for musrfit is to install it from source.
Before describing it, please make sure that you have installed all required packages listed under
Requested Software (e.g. fftw, gsl, etc).
@@ -1012,8 +765,8 @@ $ make install
For further details see Installing ROOT from Source.
-
- Setting up Environment Variables for ROOT and musrfit
+
+ Setting up Environment Variables for ROOT and musrfit
Since Apple in its wisdom decided that programs started from a shell are treated differently than Apps if it is coming to
system variables, we need to work harder compared to a Linux system.
For Mac OS X < 10.8:
@@ -1056,8 +809,8 @@ launchctl setenv LD_LIBRARY_PATH $LD_LIBRARY_PATH
-
- 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
@@ -1079,8 +832,8 @@ $ 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>
@@ -1120,8 +873,8 @@ $ /sbin/ldconfig # (as superus
-
- 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:
- Define the MUSRFITPATH environment variable containing the path to the musrfit executables and XML files.
@@ -1137,8 +890,8 @@ 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.
If not, try the following:
@@ -1174,8 +927,8 @@ accomplish that, add the following lines to
-
- Check the installation
+
+ Check the installation
In order to perform a quick test for finding out if the installation has been completed successfully, a few msr
files together with the corresponding data files can be found in the musrfit source tree at doc/examples/.
If musrgui has been installed, just open one of the test-*.msr files in the editor and test the musrfit
@@ -1203,8 +956,8 @@ $ musrview test-histo-ROOT-NPP.msr
diff --git a/doc/html/tutorial.html b/doc/html/tutorial.html
index 5a964abb..7d8c580f 100644
--- a/doc/html/tutorial.html
+++ b/doc/html/tutorial.html
@@ -6,7 +6,7 @@
- Tutorial for musrfit — musrfit 1.7.6 documentation
+ Tutorial for musrfit — musrfit 1.8.0 documentation
@@ -14,7 +14,7 @@
-
+
diff --git a/doc/html/user-libs.html b/doc/html/user-libs.html
index 553fcc18..e22c1c06 100644
--- a/doc/html/user-libs.html
+++ b/doc/html/user-libs.html
@@ -6,7 +6,7 @@
- Documentation of user libs (user functions) — musrfit 1.7.6 documentation
+ Documentation of user libs (user functions) — musrfit 1.8.0 documentation
@@ -14,7 +14,7 @@
-
+
@@ -611,8 +611,8 @@ K(m)&=\int_0^{\pi/2}\frac{\mathrm d\varphi}{\sqrt{1-m^2\sin^2{\varphi}}},\en
diff --git a/doc/html/user-manual.html b/doc/html/user-manual.html
index 3f6a6f7b..7af6869d 100644
--- a/doc/html/user-manual.html
+++ b/doc/html/user-manual.html
@@ -6,7 +6,7 @@
- User manual — musrfit 1.7.6 documentation
+ User manual — musrfit 1.8.0 documentation
@@ -14,7 +14,7 @@
-
+
@@ -443,12 +443,77 @@ Supported values for <graphic_
Will dump the LEM header information of run 3456 including the content of the run summary file.
+
+ addRun
+ addRun allows to add the histograms of various runs and save the result in a file.
+This can be done either by a list of runs (option1), or by a run file (option2).
+ usage0: addRun [--help | -h] | [--version | -v]
+usage1: addRun <options1> -rl <runList>
+usage2: addRun <options2> -in <inputFile>
+
+ <option1>:
+ -t0 <ival>: <ival> is a comma separted list of global t0-bin`s, or
+ <ival> is a comma separted list of '-1', then it is assumed that there is a prompt peak.
+ Under this condition the t0-bin will be determined automatically by
+ the position of the max-value of the corresponing histograms.
+ If t0's are not provided, t0-bin will be taken from the file.
+ -f <format>: <format> is the output file format to be used.
+ For supported formats see below.
+ -y <year> : the year at which runs were measured. Format yyyy.
+ If not provided, the current year is used.
+ -i <instrument> : <instrument> is one of gps, ltf, flame, gpd, hifi, dolly, lem
+ -m <dev> : <dev> is pta or tdc (only needed for bulk). Default: tdc
+ -o <fln> : output file name.
+ -rl <runList> can be:
+ (i) <run0> <run1> <run2> ... <runN> : run numbers, e.g. 123 124
+ (ii) <run0>-<runN> : a range, e.g. 123-125 -> 123 124 125
+ (iii) <run0>:<runN>:<step> : a sequence, e.g. 123:127:2 -> 123 125 127
+ <step> will give the step width and has to be a positive number!
+ a <runList> can also combine (i)-(iii), e.g. 123 128-130 133, etc.
+
+ <option2>:
+ -f <format>: <format> is file format of the output-file to be used.
+ -o <fln> : output file name.
+ -in <inputFile>: the file name of the file containing the necessary run information
+ to add runs with various t0's, fgb's, lgb's, different years, etc.
+ The structure of the <inputFile> is:
+ Lines starting with a '%' and empty lines are ignored.
+ A single run needs to provide the following information:
+ file <path-name>: needs to be a full path name
+ t0 <t0-bin> : needs to be the t0 bin or
+ 0 to take the t0 bin from the file, or
+ -1 for automatic determination via prompt peak (see above).
+ Example:
+ % file 1. 6 histos present, hence 6 t0-bins
+ file /home/test/data/deltat_tdc_gps_4324.bin
+ t0 401, 400, 399, 400, 358, 400
+ % file 2, take t0-bins from the file
+ file /home/test/data/deltat_tdc_gps_4325.bin
+ % file 3, deduce to t0-bin's from the prompt peak
+ file /home/test/data/deltat_tdc_gps_4325.bin
+ t0 -1, -1, -1, -1, -1, -1
+
+ Supported uSR file formats:
+ MusrRoot, PSI-BIN, PSI-MDU, MUD, NeXus
+
+
+
- musrfit_startup.xml
+ musrfit_startup.xml
musrfit_startup.xml is a configuration file located at $HOME\.musrfit. In this file the following XML tags are allowed to define settings:
- <data_path>PATH_TO_DATA</data_path>
- add the new path PATH_TO_DATA where musrfit and musrview will search for data files.
+- <run_name_template inst=”instrument_name”>template</run_name_template>
+instrument_name is the name of the instrument, e.g. gps. template allows to generate the potential path fragment where to search for files.
+These path fragments are added to all present data_path. This is used e.g. by addRun in order to find runs. To illustrate this here an example:
+d%yyyy%/tdc/lem%yy%_his_%rrrr%.root.
+%yyyy% will be replaced by the provided year (4 digits, e.g. 2020). %yy% will be replaced by the provided year (2 digits, e.g. 18).
+%rrrr% will be replaced by the run number. Here 4 r are given, hence the run 123 will be replaced to 0123, i.e. leading zero’s will be added.
+For the given example %rrrrr% would be replaced to 00123 etc.
+If the year is 2019 and the run 123, the above template would be expanded to
+d2019/tdc/lem19_his_0123.root.
+
- <write_per_run_block_chisq>y/n</write_per_run_block_chisq>
- if enabled \(\chi^2\) for each RUN block will be written to the STATISTIC block of the resulting msr file. Additionally,
in case a \(\chi^2\) single-histogram fit is done, also Pearson’s \(\chi^2\) will be added.
@@ -524,14 +589,14 @@ in case a \(\chi^2\) single-histogram fit is done, als
- The THEORY Block
+ The THEORY Block
The THEORY block is used to define the fit function. There is a set of predefined functions available. It is also possible to use externally defined functions. How to use them will be explained afterwards, here only the predefined functions are described.
@@ -956,7 +1021,7 @@ userFcn libMyLibrary.so TMyFunction 2 3 4 map1 fun1
- The FUNCTIONS Block
+ The FUNCTIONS Block
Here some auxiliary functions can be defined. These functions can currently only operate on the defined parameters, and some meta information from the data files.
They can be used in the THEORY block and for three specific cases in the RUN block (norm, alpha, and beta).
Supported is the use of basic arithmetic:
@@ -981,7 +1046,7 @@ 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:
+ The available meta information form the data files are:
@@ -1041,7 +1106,7 @@ fun2 = par3 * ( 1.0 - par5 )
- 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:
@@ -1148,7 +1213,7 @@ fittype 0 (single histogram fit)
- 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
@@ -1222,7 +1287,7 @@ RUN beautiful-data MUE4 PSI DB
After this short digression back to the RUN-block description.
In order to describe the operations needed for fitting and plotting, quite some information are needed. These information are following the RUN statement and are listed below. Depending on the fit type these information vary and hence it is indicated for which fit/plot type the information is applicable
-
+
- 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
@@ -1241,7 +1306,7 @@ etc.
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:
@@ -1266,7 +1331,7 @@ etc.
-
+
- 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
@@ -1278,7 +1343,7 @@ etc.
-
+
- 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 \(\alpha\)
@@ -1292,25 +1357,25 @@ parameter. Example for a norm
-
+
- 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
@@ -1320,7 +1385,7 @@ forward 1-10 12 # group histograms with numbers from 1 to 10 and additionally hi
-
+
- 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
@@ -1344,12 +1409,12 @@ backward 3 4
-
+
- 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:
@@ -1358,7 +1423,7 @@ 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: \(k_{f,\rm first} k_{f,\rm last} k_{b,\rm first} k_{b, \rm last} [k_{r,\rm first} k_{r,\rm last} k_{l,\rm first} k_{l,\rm last}]\).
@@ -1368,7 +1433,7 @@ 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.
@@ -1378,7 +1443,7 @@ 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
@@ -1389,7 +1454,7 @@ 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
@@ -1398,7 +1463,7 @@ t0 3419 3434 # t0 channels for groupings: forward f1 f2. 3419 t0 for f1, 3434
-
+
- 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)
@@ -1407,25 +1472,25 @@ t0 3419 3418 3417 3416 # t0 channels (assuming forward f1 f2, backward b1 b2): f
-
+
- 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
@@ -1449,19 +1514,19 @@ 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
@@ -1610,7 +1675,7 @@ Used for statistical analysis only.
- DKS Command Overview
+ DKS Command Overview
@@ -1678,7 +1743,7 @@ 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
@@ -1775,7 +1840,7 @@ SAVE
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:
@@ -1808,27 +1873,27 @@ In the THEORY table
- 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
@@ -1846,7 +1911,7 @@ 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:
@@ -1864,7 +1929,7 @@ 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.
@@ -1917,12 +1982,12 @@ 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.
@@ -1938,20 +2003,20 @@ range 0.0 17.03
- 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):
@@ -1965,7 +2030,7 @@ 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:
@@ -1978,31 +2043,31 @@ 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:
@@ -2037,7 +2102,7 @@ rrf_packing 75
- 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
@@ -2046,9 +2111,9 @@ If enabled in the XML
- 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
\[N(t) = N_0 e^{-t/\tau_\mu} [ 1 + A(t) ] + N_{\rm bkg}\]
@@ -2069,7 +2134,7 @@ 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
@@ -2093,7 +2158,7 @@ of the \(N_0\) estimate, line shape distortion due to
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
@@ -2127,13 +2192,13 @@ 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.
\[N(t) = \sum_i N_i\,\mathrm{e}^{-t/\tau_i} \left[ 1 + A_i(t)\right] + N_{\rm bkg}(t)\]
@@ -2149,7 +2214,7 @@ 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
@@ -2189,7 +2254,7 @@ 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
\[y = f(x),\]
@@ -2198,7 +2263,7 @@ 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:
@@ -2216,7 +2281,7 @@ 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
@@ -2314,7 +2379,7 @@ 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
@@ -2453,7 +2518,7 @@ In case this cannot be ensured, the parallelization can be disabled by ̵
- rge-file handler for Low-Energy μSR
+ rge-file handler for Low-Energy μSR
In the case of LE-μSR, the muon stopping distribution might have a profound impact on the muon polarization function \(P(t)\). In case of transverse field μSR measurements it can be written as
\[P(t) = \int_0^\infty n(z) \cos(\gamma_\mu B(z) t + \varphi) \, dz\]
@@ -2597,7 +2662,7 @@ here:
- 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.
@@ -2617,8 +2682,8 @@ here:
|