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. The necessary -packages to build NeXus are MXML, (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. 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 At the time of this writing, the MXML support in the +NeXus project is broken, and HDF4 is outdated on most platforms, hence currently only the HDF5 binding is +used. Hence, the necessary package to build NeXus is HDF5. This means, for a rpm-package based distro try something like:-$ yum install mxml-devel hdf-devel hdf5-devel +$ yum install hdf5-develand on a deb-package based distro try something like:
-$ apt-get install libmxml-dev libhdf4-dev libhdf5-dev +-$ apt-get install libhdf5-dev-Note
-HDF4 support within NeXus will be dropped by musrfit in the near future. If you not urgently need -to read old ISIS NeXus files, you safely can drop it.
-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.
@@ -208,10 +206,7 @@ $ git clone https://github.com/nexusformat/code.git $ # next we will build NeXus out-of-source $ mkdir build $ cd build -$ # The next line only if HDF4 support is needed -$ cmake -DENABLE_HDF5=1 -DENABLE_HDF4=1 -DENABLE_MXML=1 ../code -$ # The next line if HDF4 support is NOT needed -$ cmake -DENABLE_HDF5=1 -DENABLE_MXML=1 ../code +$ cmake -DENABLE_HDF5=1 -DENABLE_HDF4=0 -DENABLE_MXML=0 ../code $ cmake --build ./ --clean-first $ # make install needs either to be carried out as root or sudo depending on your linux flavour. $ sudo make install @@ -500,10 +495,7 @@ the later handling will be easier if a symbolic link to these files is created n 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. -All other libraries have to be built from the sources. The following lines will track the installation of JPEG 6b, -MXML 2.9, HDF 4.2.7-patch1, and NeXus 4.3.2. The version numbers and source-code locations might of -course change with time but should be easily adjustable.
-Only NeXus version ≥ 4.4 is support!
+Only NeXus Version ≥ 4.4 is support!
@@ -770,20 +750,12 @@ please change over to musredit$ cd $ mkdir nexus $ cd nexus @@ -513,18 +505,6 @@ $ ./configure --prefix=/usr/local --enable-static $ make $ make install $ cd .. -$ curl www.msweet.org/files/project3/mxml-2.9.tar.gz -G | tar xz -$ cd mxml-2.9 -$ ./configure --prefix=/usr/local --enable-static -$ make -$ make install -$ cd .. -$ curl http://www.hdfgroup.org/ftp/HDF/HDF_Current/src/hdf-4.2.7-patch1.tar.gz -G | tar xz -$ cd hdf-4.2.7-patch1 -$ ./configure --prefix=/usr/local --enable-static --disable-fortran --with-jpeg=/usr/local -$ make -$ make install -$ cd .. $ # create a directory for the NeXus source code $ mkdir nexus $ cd nexus @@ -533,7 +513,7 @@ $ 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=1 ../code +$ cmake -DENABLE_HDF5=1 -DENABLE_HDF4=0 -DENABLE_MXML=0 ../code $ make $ make installInstallation 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 +-$ sudo port -v install hdf5Unfortunately, the minixml and NeXus libraries have to be compiled and installed directly from the source code. -Given the respective version numbers of 2.9 and 4.4.2 (which are subject to change with time. -Only NeXus Version ≥ 4.4 is support!) this can be achieved for example by:
-@@ -1230,7 +1230,7 @@ etc.$ # get and instal Mini-XML -$ cd $HOME/Applications -$ git clone https://github.com/michaelrsweet/mxml.git -$ cd mxml -$ ./configure --prefix=/usr/local -$ make -$ sudo make install -$ # get and install NeXus +Only NeXus Version ≥ 4.4 is support!
+To get things compiled do:
+@@ -394,28 +394,28 @@ The asymmetry is measured both during the pulse and afterwards. For a a general@@ -956,24 +928,17 @@ packages can be installed through Fink (check for the most recent versions):$ # 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 @@ -791,7 +763,7 @@ $ # next we will build NeXus out-of-source $ cd nexus $ mkdir build $ cd build -$ cmake -DENABLE_HDF5=1 -DENABLE_HDF4=1 -DENABLE_MXML=1 ../code +$ cmake -DENABLE_HDF5=1 -DENABLE_HDF4=0 -DENABLE_MXML=0 ../code $ make $ sudo make install-libjpeg hdf hdf5-cpp11 hdf5-cpp11-shlibsUnfortunately, the minixml and NeXus libraries have to be compiled and installed directly from -the source code. Given the respective version numbers of 2.9 and 4.3.2 (which are subject to change with time) +
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:
-diff --git a/doc/html/user-libs.html b/doc/html/user-libs.html index 9f4698b2..0b6f352c 100644 --- a/doc/html/user-libs.html +++ b/doc/html/user-libs.html @@ -6,7 +6,7 @@ -@@ -443,12 +443,12 @@ For a complete description please refer to the manuals of previous | -$ # first build Mini-XML -$ cd $HOME/Applications -$ git clone https://github.com/michaelrsweet/mxml.git -$ cd mxml -$ ./configure --prefix=/usr/local -$ make -$ sudo make install -$ # second build NeXus +diff --git a/doc/html/tutorial.html b/doc/html/tutorial.html index ba1cb5f1..6a117eee 100644 --- a/doc/html/tutorial.html +++ b/doc/html/tutorial.html @@ -6,7 +6,7 @@ -@@ -1315,12 +1280,12 @@ $ musrview test-histo-ROOT-NPP.msr$ # 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_HDF4=1 -DENABLE_HDF5=1 -DENABLE_MXML=1 +$ cmake ../code -DENABLE_HDF5=1 -DENABLE_HDF4=0 -DENABLE_MXML=0 $ cmake --build ./ --clean-first -- -j8 $ sudo make install- previous |
-- musrfit 1.5.0 documentation »
+- musrfit 1.5.1 documentation »
Tutorial for musrfit — musrfit 1.5.0 documentation +Tutorial for musrfit — musrfit 1.5.1 documentation @@ -14,7 +14,7 @@ - + @@ -41,7 +41,7 @@- previous |
-- musrfit 1.5.0 documentation »
+- musrfit 1.5.1 documentation »
- musrfit 1.5.0 documentation »
+- musrfit 1.5.1 documentation »
Documentation of user libs (user functions) — musrfit 1.5.0 documentation +Documentation of user libs (user functions) — musrfit 1.5.1 documentation @@ -14,7 +14,7 @@ - + @@ -41,7 +41,7 @@- previous |
-- musrfit 1.5.0 documentation »
+- musrfit 1.5.1 documentation »
where \(\tau_{\mathrm{Li}}=1.21\)s is the \(^8\)Li lifetime.
Functions¶
-The libLineProfile library currently contains the following functions:
+The libBNMR library currently contains the following functions:
Exponential relaxation
userFcn libBNMR ExpRlx 1 2The parameters are:
-
-- pulse length \(t_0\) (ms)
-- relaxation rate \(\sigma\) (ms\(^{-1}\))
+- pulse length \(t_0\) (s)
+- relaxation rate \(\lambda\) (s\(^{-1}\))
This function implements \(f(t)=e^{-\sigma t}\).
+This function implements \(f(t)=e^{-\lambda t}\).
Stretched exponential relaxation
userFcn libBNMR SExpRlx 1 2 3The parameters are:
-
-- pulse length \(t_0\) (ms)
-- relaxation rate \(\sigma\) (ms\(^{-1}\))
+- pulse length \(t_0\) (s)
+- relaxation rate \(\lambda\) (s\(^{-1}\))
- stretching exponent \(\beta\)
This function implements \(f(t)=e^{-(\sigma t)^{\beta}}\).
+This function implements \(f(t)=e^{-(\lambda t)^{\beta}}\).
@@ -662,12 +662,12 @@ K(m)&=\int_0^{\pi/2}\frac{\mathrm d\varphi}{\sqrt{1-m^2\sin^2{\varphi}}},\endiff --git a/doc/html/user-manual.html b/doc/html/user-manual.html index 40f08293..e1ed560c 100644 --- a/doc/html/user-manual.html +++ b/doc/html/user-manual.html @@ -6,7 +6,7 @@ -- previous |
-- musrfit 1.5.0 documentation »
+- musrfit 1.5.1 documentation »
User manual — musrfit 1.5.0 documentation +User manual — musrfit 1.5.1 documentation @@ -14,7 +14,7 @@ - + @@ -41,7 +41,7 @@- previous |
-- musrfit 1.5.0 documentation »
+- musrfit 1.5.1 documentation »
- 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 ration of sum of Bp+Bm and Fp+Fm). Example for alpha with fit parameter number 1:
+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 \(\sum_i \left( N_{\mathrm{fp}}(i)+N_{\mathrm{fm}}(i) \right)\)). Example for alpha with fit parameter number 1:
@@ -1880,11 +1880,11 @@ the single histogram RRF fit apply: if you not urgently need it: do notalpha 1beta-NMR Asymmetry Fit (fit type 5)¶
-For a beta-NMR asymmetry fit (fit type 5) four histograms are needed, two for positive and two for negative helicities. These are given by the forward and backward keywords +
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 background-determined intervals or specified through backgr.fix in the RUN-block.
-The experimental asymmetry \(a(k)\) then is calculated from the four histograms:
+The experimental asymmetry \(a(k)\) is then calculated from the four histograms:
\[a(k)=\frac{\left[N_{\mathrm{fp}}(k)-B_{\mathrm{fp}}\right]-\left[N_{\mathrm{bp}}(k)-B_{\mathrm{bp}}\right]}{\left[N_{\mathrm{fp}}(k)-B_{\mathrm{fp}}\right]+\left[N_{\mathrm{bp}}(k)-B_{\mathrm{bp}}\right]} - \frac{\left[N_{\mathrm{fm}}(k)-B_{\mathrm{fm}}\right]-\left[N_{\mathrm{bm}}(k)-B_{\mathrm{bm}}\right]}{\left[N_{\mathrm{fm}}(k)-B_{\mathrm{fm}}\right]+\left[N_{\mathrm{bm}}(k)-B_{\mathrm{bm}}\right]},\]@@ -1893,12 +1893,12 @@ efficiencies, solid angles and initial asymmetries of the two detectors can be s
- \(N_{\mathrm{fp}}(k)\): counts in the forward histogram channel with positive helicity \(k\)
- \(N_{\mathrm{bp}}(k)\): counts in the backward histogram channel with positive helicity \(k\)
-- :math:` B_{mathrm{fp}}`: constant background in the forward histogram with positive helicity (RUN block: backgr.fix or background)
-- :math:` B_{mathrm{bp}}`: constant background in the backward histogram with positive helicity (RUN block: backgr.fix or background)
+- \(B_{\mathrm{fp}}\): constant background in the forward histogram with positive helicity (RUN block: backgr.fix or background)
+- \(B_{\mathrm{bp}}\): constant background in the backward histogram with positive helicity (RUN block: backgr.fix or background)
- \(N_{\mathrm{fm}}(k)\): counts in the forward histogram channel with negative helicity \(k\)
- \(N_{\mathrm{bm}}(k)\): counts in the backward histogram channel with negative helicity \(k\)
-- :math:` B_{mathrm{fm}}`: constant background in the forward histogram with negative helicity (RUN block: backgr.fix or background)
-- :math:` B_{mathrm{bm}}`: constant background in the backward histogram with negative helicity (RUN block: backgr.fix or background)
+- \(B_{\mathrm{fm}}\): constant background in the forward histogram with negative helicity (RUN block: backgr.fix or background)
+- \(B_{\mathrm{bm}}\): constant background in the backward histogram with negative helicity (RUN block: backgr.fix or background)
This theoretical asymmetry \(a(t)\) is used to fit the function
@@ -1914,7 +1914,8 @@ efficiencies, solid angles and initial asymmetries of the two detectors can be sFor the graphical representation in plot type 5 the equation above is rearranged to get \(A(t)\):
-\[A(t)=\frac{(\alpha -1)+(\alpha +1)a(t)}{(\alpha\beta +1)+(\alpha\beta -1)a(t)}-\frac{(\alpha +1)a(t)-(\alpha -1)}{(\alpha\beta +1)+(1-\alpha\beta)a(t)}=\frac{\alpha\left[N_{\mathrm{fp}}(t)-B_{\mathrm{fp}}\right]-\left[N_{\mathrm{bp}}(t)-B_{\mathrm{bp}}\right]}{\alpha\beta\left[N_{\mathrm{fp}}(t)-B_{\mathrm{fp}}\right]+\left[N_{\mathrm{bp}}(t)-B_{\mathrm{bp}}\right]} -\frac{\alpha\left[N_{\mathrm{fm}}(t)-B_{\mathrm{fm}}\right]-\left[N_{\mathrm{bm}}(t)-B_{\mathrm{bm}}\right]}{\alpha\beta\left[N_{\mathrm{fm}}(t)-B_{\mathrm{fm}}\right]+\left[N_{\mathrm{bm}}(t)-B_{\mathrm{bm}}\right]}\]+\[\begin{split}A(t) &= \frac{(\alpha -1)+(\alpha +1)a(t)}{(\alpha\beta+1)+(\alpha\beta -1)a(t)}-\frac{(\alpha +1)a(t)-(\alpha-1)}{(\alpha\beta +1)+(1-\alpha\beta)a(t)} \\ +&= \frac{\alpha\left[N_{\mathrm{fp}}(t)-B_{\mathrm{fp}}\right]-\left[N_{\mathrm{bp}}(t)-B_{\mathrm{bp}}\right]}{\alpha\beta\left[N_{\mathrm{fp}}(t)-B_{\mathrm{fp}}\right]+\left[N_{\mathrm{bp}}(t)-B_{\mathrm{bp}}\right]} -\frac{\alpha\left[N_{\mathrm{fm}}(t)-B_{\mathrm{fm}}\right]-\left[N_{\mathrm{bm}}(t)-B_{\mathrm{bm}}\right]}{\alpha\beta\left[N_{\mathrm{fm}}(t)-B_{\mathrm{fm}}\right]+\left[N_{\mathrm{bm}}(t)-B_{\mathrm{bm}}\right]}\end{split}\]and plotted together with the function given in the THEORY block.
@@ -2288,12 +2289,12 @@ In case this cannot be ensured, the parallelization can be disabled by ̵- previous |
-- musrfit 1.5.0 documentation »
+- musrfit 1.5.1 documentation »