IsotropicSQA is an isotropic, homogeneous neutrino QKE evolution code
written by Jim Kneller and Sherwood Richers. It relies on NuLib, a
neutrino interaction rate library written by Evan O'Connor.

To build the program, the following prerequisites need to be
installed. The HDF5 location needs to be pointed to in the Makefile,
but after that compiling is done with a simple

  make

Running the program requires a primitive parameter file, which is a
text file with parameters each on a separate line in the correct
order. An example parameter file is included in
parameters_template. To run, execute

  sqa2.psma.x parameters

The output will be an HDF5 file called "f.h5" that contains the
dimensionless distribution function information:
r(cm)  - proxy for the time (r=ct)
dr_block(cm) - proxy for the block timestep (dr=cdt). Stored for
               recovery purposes
dr_int(cm)   - proxy for the interaction integration timestep
               (dr=cdt). Stored for recovery purposes.
dr_osc(cm)   - proxy for the oscillation integration timestep
               (dr=cdt). Stored for recovery purposes.
fmatrixf     - dimensionless distribution function. Accessed with
               [time][helicity][energy][flavor1][flavor2][0=real,1=imaginary]

########
# HDF5 #
########

HDF5 is used by NuLib to create and read the opacity tables and by
IsotropicSQA to read opacity tables and output results. IT MUST BE
COMPILED BY THE SAME FORTRAN COMPILER COMPILING NULIB. If you can get
away with a copy already installed by "apt-get install
libhdf5-serial-dev" (check on ubuntu using "dpkg -l | grep 'hdf5'"
without the quotes) or some other means that's fine, but chances are
that it was compiled with a different compiler and you will have to
recompile it yourself. You will also have to change the values of the
hdf5 path in make.inc to reflect the system's location for the hdf5
files. Below are instructions for installing the latest version tested
into the "external" directory.

If you need to compile your own copy of hdf5, download the tarball and
extract the table:

    wget http://www.hdfgroup.org/ftp/HDF5/current/src/hdf5-1.8.13.tar.gz
    tar -xvf hdf5-1.8.16.tar.gz -C external
    rm hdf5-1.8.16.tar.gz

Go into the directory

    cd external/hdf5-1.8.16

Configure the make process. Some versions of gcc have a bug that
causes hdf5 to fail tests if any optimization is enabled, so there are
two examples below. The only tested compilers are intel and GNU.

    FC=gfortran CC=gcc CXX=g++  ./configure --enable-fortran --enable-cxx   #for GNU compilers
    FC=ifort    CC=icc CXX=icpc ./configure --enable-fortran --enable-cxx   #for Intel compilers

Build and test the binaries. This takes quite a while.

    make
    make test
    make install

Everything actually needed for compiling, linking, and running the
code is in the external/hdf5-1.8.13/hdf5 subdirectory. The default
hdf5 path in make.inc.template points to this location. Make sure that
the mpi compiler wrapper scripts (mpif90, etc) use the same compiler
that you used to compile hdf5 (see the beginning of the prerequisites
section).



#########
# NuLib #
#########
NuLib calculates the neutrino opacities based on a tabulated equation
of state (EOS). It must be built to yeild the executable to generate
the table and the libraries used by sedona to read the table. It must
be run to generate the opacity table before running IsotropicSQA. This is
all described below.

--Building------------

NuLib is publicly available at <nulib.org>, but is also contained
within IsotropicSQA as a git submodule. This makes it easy to pair a commit
of sedona with a commit of nulib, so results are entirely
reproducible. That is, each sedona commit knows which commit of NuLib
to check out to make the both codes exactly as they were at the time
of sedona's commit. To download NuLib, execute the following in the

base directory. It will automatically download into the "external"
directory.

    git submodule init
    git submodule update

Check that your parallel compiler wrapper script uses the same
compiler that was used to build HDF5 (see the top of the prerequisites
section). Then build NuLib

  cd NuLib
  make

If you want to generate an opacity table, you need to edit the
location of an EOS table in the NuLib/parameters file. The rest of the
NuLib parameters are only relevant when including weak reaction rate
tables for individual nuclei, which we have never used, so they can be
ignored. Note that if you are using an EOS that includes light nuclei
(e.g., Hempel*, SFHo/x), you have to change the make.inc file to say
NUCLEI_HEMPEL=1 (near the end of the file) and recompile.