diff --git a/doc/html/_sources/setup-standard.txt b/doc/html/_sources/setup-standard.txt index 9cdc117d..671e4477 100644 --- a/doc/html/_sources/setup-standard.txt +++ b/doc/html/_sources/setup-standard.txt @@ -57,7 +57,7 @@ Additionally, *only* if ``musrfit`` should support reading of data files in the .. index:: hdf4 **HDF4** - A library and multi-object file format for storing and managing data (see `HDF4 `_). ``HDF4`` is "outdated" and its support will soon be dropped. + A library and multi-object file format for storing and managing data (see `HDF4 `_). ``HDF4`` is "outdated" and its support will soon be dropped. The single only reason why it is still required is that ISIS is not able to cope to implement HDF5 V2 of the NeXus muon instrument specification which has been agreed in 2012! .. index:: hdf5 @@ -175,18 +175,18 @@ Installation of NeXus requirements (optional) 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 At the time of this writing, the ``MXML`` support in the -NeXus project is broken, and ``HDF4`` is outdated on most platforms, hence currently only the ``HDF5`` binding is -used.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 This means, for a rpm-package based distro try something like: +NeXus project is broken, and ``HDF4`` is outdated on most platforms, yet since ISIS/RAL is still **not** up-to-date ``HDF4`` still +needs to be dragged on (comment: if you are a ISIS user, please complain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: .. code-block:: bash - $ yum install hdf5-devel + $ yum install hdf-devel hdf5-devel and on a deb-package based distro try something like: .. code-block:: bash - $ apt-get install libhdf5-dev + $ apt-get install libhdf4-dev libhdf5-dev **Only NeXus Version ≥ 4.4 is support!** @@ -206,7 +206,7 @@ A brief instruction how to get ``NeXus`` compiled from source (lines starting wi $ # next we will build NeXus out-of-source $ mkdir build $ cd build - $ cmake -DENABLE_HDF5=1 -DENABLE_HDF4=0 -DENABLE_MXML=0 ../code + $ cmake -DENABLE_HDF5=1 -DENABLE_HDF4=1 -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 @@ -566,7 +566,7 @@ and a package containing ``/usr/lib/librpc.a`` (*e.g.* ``sunrpc = 4.0-3``, but * $ # next we will build NeXus out-of-source $ mkdir build $ cd build - $ cmake -DENABLE_HDF5=1 -DENABLE_HDF4=0 -DENABLE_MXML=0 ../code + $ cmake -DENABLE_HDF5=1 -DENABLE_HDF4=1 -DENABLE_MXML=0 ../code $ make $ make install @@ -770,6 +770,11 @@ and ``C:\cygwin\bin\bash.exe`` so that they are executed with administrator priv Mac OS X / macOS ---------------- +.. warning:: + + 2019-10-10: macOS 10.15 Catalina: ``macport``/``fink``/``homebrew`` and hence ``musrfit`` are not yet ready for + this version of macOS. Likely to be ready by end of November 2019. + .. _MacPorts: https://www.macports.org/ .. _Fink: http://www.finkproject.org/ @@ -779,6 +784,12 @@ or `Fink`_ — which provides open-source software is employed to fulfill the b In the following, both possibilities (using MacPorts or Fink) are described but it is emphasized here that it should be followed only *one* of the possible routes . +.. warning:: + + If you decide to upgrade your macOS, e.g. from ``High Sierra`` to ``Mojave``, you will typically need to + unistall ``musrfit``, ``ROOT``, and `MacPorts`_ / `Fink`_ first, do the upgrade of the macOS and start the + installation of `MacPorts`_ / `Fink`_ , ``ROOT``, and ``musrfit`` from scratch! + .. index:: macports Requirements (MacPorts) @@ -871,7 +882,7 @@ To get things compiled do: $ cd nexus $ mkdir build $ cd build - $ cmake -DENABLE_HDF5=1 -DENABLE_HDF4=0 -DENABLE_MXML=0 ../code + $ cmake -DENABLE_HDF5=1 -DENABLE_HDF4=1 -DENABLE_MXML=0 ../code $ make $ sudo make install @@ -1086,7 +1097,7 @@ this can be achieved for example by: $ # build NeXus out-of-source $ mkdir build $ cd build - $ cmake ../code -DENABLE_HDF5=1 -DENABLE_HDF4=0 -DENABLE_MXML=0 + $ cmake ../code -DENABLE_HDF5=1 -DENABLE_HDF4=1 -DENABLE_MXML=0 $ cmake --build ./ --clean-first -- -j8 $ sudo make install diff --git a/doc/html/_sources/user-manual.txt b/doc/html/_sources/user-manual.txt index 667e36cc..b3dd61dd 100644 --- a/doc/html/_sources/user-manual.txt +++ b/doc/html/_sources/user-manual.txt @@ -632,7 +632,7 @@ name abbr. parameters mathematica const c const(1) const asymmetry a A(1) :math:`A` simplExpo se :math:`\lambda (\mu \mathrm{s}^{-1})` :math:`\exp(-\lambda t)` -generExpo ge :math:`\lambda (\mu \mathrm{s}^{-1}) \beta(1)` :math:`\exp\left[(-\lambda t)^\beta\right]` +generExpo ge :math:`\lambda (\mu \mathrm{s}^{-1}) \beta(1)` :math:`\exp\left[-(\lambda t)^\beta\right]` simpleGss sg :math:`\sigma (\mu \mathrm{s}^{-1})` :math:`\exp\left[-\frac{1}{2} (\sigma t)^2\right]` statGssKT stg :math:`\sigma (\mu \mathrm{s}^{-1})` :math:`\frac{1}{3} + \frac{2}{3} \left[ 1 - (\sigma t)^2\right] \exp\left[-\frac{1}{2} (\sigma t)^2\right]` statGssKTLF sgktlf :math:`\nu` (MHz), \ :math:`G_{\rm G}^{\rm LF}(t) = 1-\frac{2\sigma^2}{(2\pi\nu)^2} \left[ 1-\exp\left(- \frac{1}{2}\sigma^2t^2\right)\cos(2\pi\nu t)\right]` [#n1]_ diff --git a/doc/html/genindex.html b/doc/html/genindex.html index 33c7df2a..c063e8ba 100644 --- a/doc/html/genindex.html +++ b/doc/html/genindex.html @@ -979,7 +979,7 @@ diff --git a/doc/html/index.html b/doc/html/index.html index 8641003c..20ed2dae 100644 --- a/doc/html/index.html +++ b/doc/html/index.html @@ -185,7 +185,7 @@ diff --git a/doc/html/objects.inv b/doc/html/objects.inv index f00bacdb..dcb7a03c 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 edfaaa41..9e0464ec 100644 --- a/doc/html/search.html +++ b/doc/html/search.html @@ -94,7 +94,7 @@ diff --git 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\ No newline at end of file diff --git a/doc/html/setup-standard.html b/doc/html/setup-standard.html index 70ff116b..640b93f9 100644 --- a/doc/html/setup-standard.html +++ b/doc/html/setup-standard.html @@ -88,7 +88,7 @@ their header packages:

Additionally, only if musrfit should support reading of data files in the NeXus format the following libraries are needed:

HDF4
-
A library and multi-object file format for storing and managing data (see HDF4). HDF4 is “outdated” and its support will soon be dropped.
+
A library and multi-object file format for storing and managing data (see HDF4). HDF4 is “outdated” and its support will soon be dropped. The single only reason why it is still required is that ISIS is not able to cope to implement HDF5 V2 of the NeXus muon instrument specification which has been agreed in 2012!
HDF5
@@ -180,16 +180,16 @@ the source code from the corresponding website, or to clone the git repo. If you 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, 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:

+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:

-
$ yum install hdf5-devel
+
$ yum install hdf-devel hdf5-devel
 

and on a deb-package based distro try something like:

-
$ apt-get install libhdf5-dev
+
$ apt-get install libhdf4-dev libhdf5-dev
 
@@ -206,7 +206,7 @@ $ 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=0 -DENABLE_MXML=0 ../code +$ cmake -DENABLE_HDF5=1 -DENABLE_HDF4=1 -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 @@ -513,7 +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=0 -DENABLE_MXML=0 ../code +$ cmake -DENABLE_HDF5=1 -DENABLE_HDF4=1 -DENABLE_MXML=0 ../code $ make $ make install @@ -684,11 +684,22 @@ and C:\cygwin\bin\bash.exe

Mac OS X / macOS

+
+

Warning

+

2019-10-10: macOS 10.15 Catalina: macport/fink/homebrew and hence musrfit are not yet ready for +this version of macOS. Likely to be ready by end of November 2019.

+

With Mac OS X / macOS the situation is up to some extent similar like on MS Windows but still different since Mac OS X is a UNIX system. The similarity is that also on OS X a helping framework — either MacPorts or Fink — which provides open-source software is employed to fulfill the basic software requirements of musrfit. In the following, both possibilities (using MacPorts or Fink) are described but it is emphasized here that it should be followed only one of the possible routes .

+
+

Warning

+

If you decide to upgrade your macOS, e.g. from High Sierra to Mojave, you will typically need to +unistall musrfit, ROOT, and MacPorts / Fink first, do the upgrade of the macOS and start the +installation of MacPorts / Fink , ROOT, and musrfit from scratch!

+

Requirements (MacPorts)

Before proceeding with the usage of the MacPorts system first a few useful tools provided by Apple together @@ -763,7 +774,7 @@ $ # next we will build NeXus out-of-source $ cd nexus $ mkdir build $ cd build -$ cmake -DENABLE_HDF5=1 -DENABLE_HDF4=0 -DENABLE_MXML=0 ../code +$ cmake -DENABLE_HDF5=1 -DENABLE_HDF4=1 -DENABLE_MXML=0 ../code $ make $ sudo make install

@@ -938,7 +949,7 @@ $ cd nexus $ # build NeXus out-of-source $ mkdir build $ cd build -$ cmake ../code -DENABLE_HDF5=1 -DENABLE_HDF4=0 -DENABLE_MXML=0 +$ cmake ../code -DENABLE_HDF5=1 -DENABLE_HDF4=1 -DENABLE_MXML=0 $ cmake --build ./ --clean-first -- -j8 $ sudo make install
@@ -1285,7 +1296,7 @@ $ musrview test-histo-ROOT-NPP.msr diff --git a/doc/html/user-manual.html b/doc/html/user-manual.html index e1ed560c..f746f0e1 100644 --- a/doc/html/user-manual.html +++ b/doc/html/user-manual.html @@ -616,7 +616,7 @@ in case a \(\chi^2\) single-histogram fit is done, als generExpo ge \(\lambda (\mu \mathrm{s}^{-1}) \beta(1)\) -\(\exp\left[(-\lambda t)^\beta\right]\) +\(\exp\left[-(\lambda t)^\beta\right]\)   simpleGss @@ -2294,7 +2294,7 @@ In case this cannot be ensured, the parallelization can be disabled by ̵