Merge branch 'master' into swift-velociraptor-C

.gitignore

@@ -26,19 +26,29 @@ examples/swift_mpi
 examples/*/*.xmf
 examples/*/*.h5
 examples/*/*.png
+examples/*/*.mp4
 examples/*/*.txt
 examples/*/*.dot
+examples/*/restart/*
 examples/*/used_parameters.yml
+examples/*/unused_parameters.yml
 examples/*/*/*.xmf
 examples/*/*/*.png
+examples/*/*/*.mp4
 examples/*/*/*.txt
 examples/*/*/*.dot
+examples/*/*/*.rst
+examples/*/*/*.hdf5
+examples/*/snapshots*
+examples/*/restart/*
 examples/*/*/used_parameters.yml
 examples/*/err_file*
 examples/*/out_file*
 examples/*/stf_output*
 examples/*/stf_ouput*
 examples/*/log*
+examples/*/*/unused_parameters.yml
+examples/*/*.mpg
 examples/*/gravity_checks_*.dat
 
 tests/testActivePair
@@ -64,7 +74,7 @@ tests/swift_dopair_125_standard.dat
 tests/brute_force_125_perturbed.dat
 tests/swift_dopair_125_perturbed.dat
 tests/brute_force_pair_active.dat
-tests/brute_force_dopair2_active.dat 
+tests/brute_force_dopair2_active.dat
 tests/swift_dopair2_force_active.dat
 tests/brute_force_periodic_BC_perturbed.dat
 tests/swift_dopair_active.dat
@@ -75,7 +85,9 @@ tests/test_nonsym_density_1_vec.dat
 tests/test_nonsym_density_2_vec.dat
 tests/test_nonsym_force_1_vec.dat
 tests/test_nonsym_force_2_vec.dat
+tests/potential.dat
 tests/testGreetings
+tests/testSelectOutput
 tests/testReading
 tests/testSingle
 tests/testTimeIntegration
@@ -98,6 +110,9 @@ tests/test125cells.sh
 tests/test125cellsPerturbed.sh
 tests/testParser.sh
 tests/testReading.sh
+tests/testSelectOutput.sh
+tests/unused_parser_output.yml
+tests/used_parser_output.yml
 tests/testAdiabaticIndex
 tests/testRiemannExact
 tests/testRiemannTRRS
@@ -112,6 +127,11 @@ tests/benchmarkInteractions
 tests/testGravityDerivatives
 tests/testPotentialSelf
 tests/testPotentialPair
+tests/testEOS
+tests/testEOS*.txt
+tests/testEOS*.png
+tests/testUtilities
+tests/testCbrt
 
 theory/latex/swift.pdf
 theory/SPH/Kernels/kernels.pdf
@@ -292,4 +312,7 @@ sympy-plots-for-*.tex/
 *.xdy
 
 # macOS
-*.DS_Store
\ No newline at end of file
+*.DS_Store
+
+#ctags
+*tags

INSTALL.swift

@@ -96,18 +96,21 @@ SWIFT depends on a number of third party libraries that should be available
 before you can build it.
 
 
- - HDF5: a HDF5 library (v. 1.8.x or higher) is required to read and
-         write particle data. One of the commands "h5cc" or "h5pcc"
-         should be available. If "h5pcc" is located them a parallel
-         HDF5 built for the version of MPI located should be
-         provided. If the command is not available then it can be
-         located using the "--with-hfd5" configure option. The value
-         should be the full path to the "h5cc" or "h5pcc" commands.
-
-
- - MPI: to run on more than one node an MPI library that fully
-        supports MPI_THREAD_MULTIPLE.  Before running configure the
-        "mpirun" command should be available in the shell. If your
+ - HDF5:
+	A HDF5 library (v. 1.8.x or higher) is required to read and
+        write particle data. One of the commands "h5cc" or "h5pcc"
+        should be available. If "h5pcc" is located then a parallel
+        HDF5 built for the version of MPI located should be
+        provided. If the command is not available then it can be
+        located using the "--with-hdf5" configure option. The value
+        should be the full path to the "h5cc" or "h5pcc" commands.
+        SWIFT makes effective use of parallel HDF5 when running on more than
+        one node, so this option is highly recommended.
+
+ - MPI:
+	To run on more than one node an MPI library that fully
+        supports MPI_THREAD_MULTIPLE is required.  Before running configure
+        the "mpirun" command should be available in the shell. If your
         command isn't called "mpirun" then define the "MPIRUN"
         environment variable, either in the shell or when running
         configure.
@@ -116,57 +119,69 @@ before you can build it.
 	much like the CC one. Use this when your MPI compiler has a
 	none-standard name.
 
- - GSL: To use cosmological time integration, a version of the GSL
-        must be available. 
+ - GSL:
+	To use cosmological time integration, a version of the GSL
+	must be available.
 
- - libtool: The build system relies on libtool as well as the other autotools.
+ - FFTW 3.x:
+	To run with periodic gravity forces, a build of the FFTW 3
+	library must be available. Note that SWIFT does not make use
+	of the parallel capability of FFTW. Calculations are done by
+	single MPI nodes independently.
 
-
-                           Optional Dependencies
-                           =====================
+- libtool:
+	The build system relies on libtool as well as the other autotools.
 
 
- - METIS: a build of the METIS library can be optionally used to
-          optimize the load between MPI nodes (requires an MPI
-          library). This should be found in the standard installation
-          directories, or pointed at using the "--with-metis"
-          configuration option.  In this case the top-level
-          installation directory of the METIS build should be
-          given. Note to use METIS you should at least supply
-          "--with-metis".
 
+                           Optional Dependencies
+                           =====================
 
- - libNUMA: a build of the NUMA library can be used to pin the threads
-            to the physical core of the machine SWIFT is running
-            on. This is not always necessary as the OS scheduler may
-            do a good job at distributing the threads among the
-            different cores on each computing node.
 
+ - METIS:
+	a build of the METIS library can be optionally used to
+        optimize the load between MPI nodes (requires an MPI
+        library). This should be found in the standard installation
+        directories, or pointed at using the "--with-metis"
+        configuration option.  In this case the top-level installation
+        directory of the METIS build should be given. Note to use
+        METIS you should supply at least "--with-metis".
 
- - TCMalloc: a build of the TCMalloc library (part of gperftools) can
-             be used to obtain faster allocations than the standard C
-             malloc function part of glibc. The option "-with-tcmalloc"
-	     should be passed to the configuration script to use it.
+- libNUMA:
+	a build of the NUMA library can be used to pin the threads to
+        the physical core of the machine SWIFT is running on. This is
+        not always necessary as the OS scheduler may do a good job at
+        distributing the threads among the different cores on each
+        computing node.
 
+ - tcmalloc / jemalloc / TBBmalloc:
+	a build of the tcmalloc library (part of gperftools), jemalloc
+	or TBBmalloc can be used be used to obtain faster and more
+	scalable allocations than the standard C malloc function part
+	of glibc. Using one of these is highly recommended on systems
+	with many cores per node. One of the options
+	"--with-tcmalloc", "--with-jemalloc" or "--with-tbbmalloc"
+	should be passed to the configuration script to use it.
 
- - gperftools: a build of gperftools can be used to obtain good
-               profiling of the code. The option "-with-profiler"
-               needs to be passed to the configuration script to use
-               it.
+ - gperftools:
+	a build of gperftools can be used to obtain good profiling of
+        the code. The option "--with-profiler" needs to be passed to
+        the configuration script to use it.
 
+ - DOXYGEN:
+	the doxygen library is required to create the SWIFT API
+        documentation.
 
- - DOXYGEN: the doxygen library is required to create the SWIFT API
-            documentation.
+ - python:
+	Examples and solution script use python and rely on the numpy
+	library version 1.8.2 or higher.
 
- - python:  Examples and solution script use python and rely on the
-   	    numpy library version 1.8.2 or higher.
 
 
                              SWIFT Coding style
                              ==================
 
-The SWIFT source code is using a variation of the 'Google' style. The
-script 'format.sh' in the root directory applies the clang-format-3.8
-tool with our style choices to all the SWIFT C source file. Please
-apply the formatting script to the files before submitting a merge
-request.
+The SWIFT source code uses a variation of 'Google' style. The script
+'format.sh' in the root directory applies the clang-format-3.8 tool with our
+style choices to all the SWIFT C source file. Please apply the formatting
+script to the files before submitting a merge request.

doc/Doxyfile.in

@@ -765,8 +765,9 @@ INPUT		       += @top_srcdir@/src/gravity/Default
 INPUT		       += @top_srcdir@/src/stars/Default
 INPUT		       += @top_srcdir@/src/riemann
 INPUT		       += @top_srcdir@/src/potential/point_mass
-INPUT		       += @top_srcdir@/src/cooling/none
-INPUT		       += @top_srcdir@/src/chemistry/none
+INPUT		       += @top_srcdir@/src/equation_of_state/ideal_gas
+INPUT		       += @top_srcdir@/src/cooling/EAGLE
+INPUT		       += @top_srcdir@/src/chemistry/EAGLE
 
 # This tag can be used to specify the character encoding of the source files
 # that doxygen parses. Internally doxygen uses the UTF-8 encoding. Doxygen uses
@@ -817,7 +818,7 @@ EXCLUDE_SYMLINKS       = NO
 # Note that the wildcards are matched against the file with absolute path, so to
 # exclude all test directories for example use the pattern */test/*
 
-EXCLUDE_PATTERNS       =
+EXCLUDE_PATTERNS       = *.md
 
 # The EXCLUDE_SYMBOLS tag can be used to specify one or more symbol names
 # (namespaces, classes, functions, etc.) that should be excluded from the
@@ -1956,7 +1957,7 @@ MACRO_EXPANSION        = YES
 # The default value is: NO.
 # This tag requires that the tag ENABLE_PREPROCESSING is set to YES.
 
-EXPAND_ONLY_PREDEF     = YES
+EXPAND_ONLY_PREDEF     = NO
 
 # If the SEARCH_INCLUDES tag is set to YES, the include files in the
 # INCLUDE_PATH will be searched if a #include is found.
@@ -1990,8 +1991,10 @@ INCLUDE_FILE_PATTERNS  =
 
 PREDEFINED             = "__attribute__(x)= "
 PREDEFINED             += HAVE_HDF5
+PREDEFINED             += HAVE_FFTW
 PREDEFINED             += WITH_MPI
 PREDEFINED             += WITH_VECTORIZATION
+PREDEFINED             += __GNUC__
 
 # If the MACRO_EXPANSION and EXPAND_ONLY_PREDEF tags are set to YES then this
 # tag can be used to specify a list of macro names that should be expanded. The