SAMMY R-Matrix Code

SAMMY is an R-matrix Bayesian fitting program used in the analysis of nuclear cross section data.

Documentation can be found in the SAMMY Manual pdf and here

Quick Installation instructions can be found here

Detailed Installation instructions are listed here after the quick install instructions.

Features include:

• Multiple R-matrix formalisms (Reich-Moore, Single/Multiple Level Breit-Wigner, etc.)
• Neutral and charged particle projectiles (neutron, proton, alpha...)
• Experimental corrections (Doppler/resolution broadening, multiple scattering for reaction yields...)
• Bayes' method for fitting
• Resolved/Unresolved resonance region analysis
• Pre/Post processing to connect with the ENDF/B format

The structure of the code is broadly described by the image below.

Quick Installation

In a terminal execute the following commands:

$ git clone https://code.ornl.gov/RNSD/SAMMY.git
$ cd sammy/sammy
$ mkdir myscript
$ cp script/configure_sammy_gcc.sh myscript/
$ mkdir build
$ cd build
$ ../myscript/configure_sammy_gcc.sh ../
$ make -j4
$ make install

Finally run the tests with:

$ ctest -j4

Build and Test

Please note: At this writing the master branch is the only fully open-source version of SAMMY, and is therefore what would be considered ''bleeding-edge'' until a tagged version greater than 8.2.0-beta2 is released.

The SAMMY build is based on CMake from KitWare, which supports a consistent experience on LINUX, Mac, and Windows. OS specific instructions are given below for MacOS, Linux, and Windows. Guidance for common CMake errors can be found here.

SAMMY build requires:

Instead of GNU compilers it is also possible to use Intel Fortran/C++ 13.1 or higher.

There are four main steps to create an SAMMY installation:

1. CMake configuration creates a native build tree
2. Compilation compiles all executables and libraries
3. Installation deploys all executables into a configuration ready for running
4. Run test cases

CMakeLists.txt files are found throughout SAMMY. From the SAMMY root directory, these CMakeLists.txt files create a tree of included directories called the SOURCE TREE.

To configure a build, cmake is called on the root CMakeLists.txt file, namely <sammy_dir>/sammy/CMakeLists.txt. CMake takes the SOURCE TREE and creates a BUILD TREE.

The BUILD TREE contains or will contain the build configuration, Make files, and all compilation output (i.e., object files, archive libraries and binary executables).

Then make install in the build directory will install the packages, and an optional ctest command will run several tests to ensure that SAMMY built correctly.

SAMMY requires Qt, LAPACK and BLAS routines. If these libraries reside in a known location (i.e., installed by apt, yum, macports, or brew see below), the installation procedure may automatically find the libraries. Otherwise the location can be given at configuration time in configure_sammy_gcc.sh.

Recommended instructions for building is as follows. To clone the directory, if you have account credentials from ORNL (external users can start here), in a terminal type:

$ git clone git@code.ornl.gov:rnsd/sammy.git

if you want to clone without any credentials (without credentials you have limited user functionality in GitLab), type the following in the terminal:

$ git clone https://code.ornl.gov/RNSD/SAMMY.git

In the example above the main cloned directory is sammy, but it is possible to specify a different cloned directory name with the following command:

$ git clone git@code.ornl.gov:rnsd/sammy.git different_cloned_directory

In this guide, however, the main cloned directory will be referred to as sammy or the "top sammy directory" since we want to simply use the default configuration.

After cloning run the following in the terminal:

$ cd sammy/sammy
$ mkdir myscript
$ cp script/configure_sammy_gcc.sh myscript/
$ mkdir build
$ cd build

In the editor of your choice, set up your configuration options in the file configure_sammy_gcc.sh that you've copied into the myscript directory. It's best to copy the file to myscript as the myscript directory is not tracked by git and the file will not be overwritten every time you pull the latest version of sammy from the remote server. There are several paths that can be defined in the script for the build environment, such as the path/to/scale.

In the file configure_sammy_gcc.sh, it is often necessary to point SAMMY to the Qt installation, this can be done by including in the configure_sammy_gcc.sh the following line (assuming brew installed Qt binaries to "/usr/local/opt/qt@5/bin"):

export PATH="/usr/local/opt/qt@5/bin:$PATH"

From the build directory in the terminal:

$ ./configure_sammy_gcc.sh ../
$ make -j4
$ make install

Finally run the tests with:

$ ctest -j4

Note that both make and ctest take -j option (e.g. -j8) to run in parallel on several cores (e.g. 8), where the number 8 would be exchanged for however many processors you have available.

Other CMake flags, e.g. CMAKE_Fortran_COMPILER, CMAKE_Fortran_FLAGS, CMAKE_C_COMPILER, CMAKE_C_FLAGS, CMAKE_CXX_COMPILER, and CMAKE_CXX_FLAGS may be modified in the cmake command invocation line to update the compilers or compiler flags to the desired settings.

Windows 10 (not updated for versions > 8.2.0-beta2)

Modern versions of SAMMY have not been fully tested on Windows OS's, but have been successfully built and tested on Windows Subsytem for Linux WSL. WSL can be used to run a Linux operating system as an application inside the Windows OS directly interacting with files in the Windows OS. SAMMY has been built and tested in Ubuntu for WSL. To set up the Ubuntu application in Windows you may follow the Microsoft documentation on their website, but the basics are repeated here.

$ Enable-WindowsOptionalFeature -Online -FeatureName Microsoft-Windows-Subsystem-Linux

$ sudo apt-get update
$ sudo apt-get upgrade

$ sh -c "$(curl -fsSL https://raw.githubusercontent.com/Linuxbrew/install/master/install.sh)"

export PATH=/home/linuxbrew/.linuxbrew/bin:$PATH

$ sudo apt-get update
$ sudo apt-get install build-essential
$ brew install gcc
$ brew install cmake
$ sudo apt install qt5
$ sudo apt install liblapack-dev libblas-dev
$ sudo apt install default-jdk
$ brew install hdf5

Mac OSX

XCode is needed to compile SAMMY on a Mac OS X computer. It is available free from the App Store. In addition, the command line options from XCode must be installed. This can typically be accomplished by running the following in the command line:

xcode-select --install

and following any prompts given by the MacOS.

The latest version of macports, download-able from http://www.macports.org, can be used to download required programs as well as Homebrew (Homebrew works with both OS's), but this package manager is no longer being tested by the authors.

/usr/bin/ruby -e "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/master/install)"

$ brew install gcc
$ brew install cmake
$ brew install qt@5
$ brew install hdf5

$ brew install openblas

$ export CC=${CC:-clang}
$ export CXX=${CXX:-clang++}
$ export F90=${F90:-gfortran}

Linux-Ubuntu

When installing the required software for SAMMY for a Linux OS (tested on Ubuntu) you should start with a general update:

$ sudo apt-get update
$ sudo apt-get upgrade

to get the latest and greatest tools for Ubuntu.

$ sh -c "$(curl -fsSL https://raw.githubusercontent.com/Linuxbrew/install/master/install.sh)"

export PATH=/home/linuxbrew/.linuxbrew/bin:$PATH

$ brew install gcc
$ brew install cmake
$ brew install qt@5
$ brew install hdf5

$ apt install liblapack-dev libblas-dev

Common CMake Errors

--   Searching for lib 'ScaleUtilsEndfLib' ...
-- NOTE: Did not find a lib in the lib set "ScaleUtilsEndfLib" for the TPL 'SCALE'!
-- ERROR: Could not find the libraries for the TPL 'SCALE'!
-- TIP: If the TPL 'SCALE' is on your system then you can set:
     -DSCALE_LIBRARY_DIRS='<dir0>;<dir1>;...'
   to point to the directories where these libraries may be found.
   Or, just set:
     -DTPL_SCALE_LIBRARIES='<path-to-libs0>;<path-to-libs1>;...'
   to point to the full paths for the libraries which will
   bypass any search for libraries and these libraries will be used without
   question in the build.  (But this will result in a build-time error
   if not all of the necessary symbols are found.)
-- ERROR: Failed finding all of the parts of TPL 'SCALE' (see above), Aborting!

-D SCALE_LIBRARY_DIRS='<dir>'

-D ${SCALE_INSTALL_PATH}='/Users/<username>/sammy/scale/install'

Changing the Array Size (Legacy versions only)

-D SAMMY_ARRAY_SIZE:INT=100000000 \

-D SAMMY_ARRAY_SIZE:INT=2000000000 \

Compiler Options, etc. (Legacy versions only)

$ export F77=f90

$ setenv F77 f90

$ export FFLAGS=-Wall

$ setenv FFLAGS -Wall

Other Useful Commands

$ make clean      <- removes all generated object and source files