Merge branch 'master' into streaming_io

Conflicts:
	src/Makefile.am

.gitignore

@@ -22,8 +22,6 @@ doc/Doxyfile
 
 examples/swift
 examples/swift_mpi
-examples/swift_fixdt
-examples/swift_fixdt_mpi
 examples/*.xmf
 examples/used_parameters.yml
 examples/energy.txt
@@ -80,9 +78,12 @@ tests/testRiemannHLLC
 tests/testMatrixInversion
 
 theory/latex/swift.pdf
-theory/kernel/kernels.pdf
-theory/kernel/kernel_derivatives.pdf
-theory/kernel/kernel_definitions.pdf
+theory/SPH/Kernels/kernels.pdf
+theory/SPH/Kernels/kernel_derivatives.pdf
+theory/SPH/Kernels/kernel_definitions.pdf
+theory/SPH/Flavours/sph_flavours.pdf
+theory/SPH/EoS/eos.pdf
+theory/SPH/*.pdf
 theory/paper_pasc/pasc_paper.pdf
 
 m4/libtool.m4

AUTHORS

@@ -8,3 +8,6 @@ John A. Regan 		john.a.regan@durham.ac.uk
 Angus Lepper		angus.lepper@ed.ac.uk
 Tom Theuns 		tom.theuns@durham.ac.uk
 Richard G. Bower	r.g.bower@durham.ac.uk
+Stefan Arridge		stefan.arridge@durham.ac.uk
+Massimiliano Culpo	massimiliano.culpo@googlemail.com
+Yves Revaz   		yves.revaz@epfl.ch

INSTALL.swift

@@ -83,39 +83,65 @@ 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.
+ - 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: an optional MPI library that fully supports MPI_THREAD_MULTIPLE.
-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.
+ - 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
+        command isn't called "mpirun" then define the "MPIRUN"
+        environment variable, either in the shell or when running
+        configure.
 
-The MPI compiler can be controlled using the MPICC variable, much like
-the CC one. Use this when your MPI compiler has a none-standard name.
+	The MPI compiler can be controlled using the MPICC variable,
+	much like the CC one. Use this when your MPI compiler has a
+	none-standard name.
 
 
-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".
+ - libtool: The build system relies on libtool.
 
 
-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.
+                           Optional Dependencies
+                           =====================
 
 
-DOXYGEN: the doxygen library is required to create the SWIFT API
-documentation.
+ - 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".
+
+
+ - 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: 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.
+
+
+ - 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.
 
 
 

README

@@ -13,25 +13,25 @@ See INSTALL.swift for install instructions.
 
 Usage: swift [OPTION]... PARAMFILE
        swift_mpi [OPTION]... PARAMFILE
-       swift_fixdt [OPTION]... PARAMFILE
-       swift_fixdt_mpi [OPTION]... PARAMFILE
 
 Valid options are:
   -a          Pin runners using processor affinity
   -c          Run with cosmological time integration
+  -C          Run with cooling
   -d          Dry run. Read the parameter file, allocate memory but does not read 
               the particles from ICs and exit before the start of time integration.
               Allows user to check validy of parameter and IC files as well as memory limits.
+  -D          Always drift all particles even the ones far from active particles.
   -e          Enable floating-point exceptions (debugging mode)
   -f    {int} Overwrite the CPU frequency (Hz) to be used for time measurements
   -g          Run with an external gravitational potential
   -G          Run with self-gravity
-  -n    {int} Execute a fixed number of time steps. When unset use the time_end
-              parameter to stop. 
+  -n    {int} Execute a fixed number of time steps. When unset use the time_end parameter to stop. 
   -s          Run with SPH
   -t    {int} The number of threads to use on each MPI rank. Defaults to 1 if not specified.
-  -v     [12] Increase the level of verbosity 1: MPI-rank 0 writes 
-              2: All MPI-ranks write
+  -v     [12] Increase the level of verbosity
+  	      1: MPI-rank 0 writes
+	      2: All MPI-ranks write
   -y    {int} Time-step frequency at which task graphs are dumped
   -h          Print this help message and exit
 

configure.ac

@@ -16,7 +16,13 @@
 # along with this program.  If not, see <http://www.gnu.org/licenses/>.
 
 # Init the project.
-AC_INIT([SWIFT],[0.4.0])
+AC_INIT([SWIFT],[0.4.0],[https://gitlab.cosma.dur.ac.uk/swift/swiftsim])
+swift_config_flags="$*"
+
+#  Need to define this, instead of using fifth argument of AC_INIT, until 2.64.
+AC_DEFINE([PACKAGE_URL],["www.swiftsim.com"], [Package web pages])
+
+AC_COPYRIGHT
 AC_CONFIG_SRCDIR([src/space.c])
 AC_CONFIG_AUX_DIR([.])
 AM_INIT_AUTOMAKE
@@ -155,6 +161,45 @@ LT_INIT
 AC_PROG_CC_C99
 AC_C_INLINE
 
+# If debugging try to show inlined functions.
+if test "x$enable_debug" = "xyes"; then
+   #  Show inlined functions.
+   if test "$ax_cv_c_compiler_vendor" = "gnu"; then
+      # Would like to use -gdwarf and let the compiler pick a good version
+      # but that doesn't always work.
+      AX_CHECK_COMPILE_FLAG([-gdwarf -fvar-tracking-assignments],
+        [inline_EXTRA_FLAGS="-gdwarf -fvar-tracking-assignments"],
+        [inline_EXTRA_FLAGS="-gdwarf-2 -fvar-tracking-assignments"])
+      CFLAGS="$CFLAGS $inline_EXTRA_FLAGS"
+   elif test "$ax_cv_c_compiler_vendor" = "intel"; then
+      CFLAGS="$CFLAGS -debug inline-debug-info"
+   fi
+fi
+
+# Check if task debugging is on.
+AC_ARG_ENABLE([task-debugging],
+   [AS_HELP_STRING([--enable-task-debugging],
+     [Store task timing information and generate task dump files @<:@yes/no@:>@]
+   )],
+   [enable_task_debugging="$enableval"],
+   [enable_task_debugging="no"]
+)
+if test "$enable_task_debugging" = "yes"; then
+   AC_DEFINE([SWIFT_DEBUG_TASKS],1,[Enable task debugging])
+fi
+
+# Check if expensive debugging is on.
+AC_ARG_ENABLE([debugging-checks],
+   [AS_HELP_STRING([--enable-debugging-checks],
+     [Activate expensive consistency checks @<:@yes/no@:>@]
+   )],
+   [enable_debugging_checks="$enableval"],
+   [enable_debugging_checks="no"]
+)
+if test "$enable_debugging_checks" = "yes"; then
+   AC_DEFINE([SWIFT_DEBUG_CHECKS],1,[Enable expensive debugging])
+fi
+
 # Define HAVE_POSIX_MEMALIGN if it works.
 AX_FUNC_POSIX_MEMALIGN
 
@@ -251,7 +296,6 @@ if test "$enable_san" = "yes"; then
    fi
 fi
 
-
 # Autoconf stuff.
 AC_PROG_INSTALL
 AC_PROG_MAKE_SET
@@ -307,7 +351,7 @@ AC_ARG_WITH([tcmalloc],
    [with_tcmalloc="no"]
 )
 if test "x$with_tcmalloc" != "xno"; then
-   if test "x$with_tcmalloc" != "xyes" && test "x$with_tcmalloc" != "x"; then
+   if test "x$with_tcmalloc" != "xyes" -a "x$with_tcmalloc" != "x"; then
       tclibs="-L$with_tcmalloc -ltcmalloc"
    else
       tclibs="-ltcmalloc"
@@ -317,7 +361,7 @@ if test "x$with_tcmalloc" != "xno"; then
 
    #  Could just have the minimal version.
    if test "$have_tcmalloc" = "no"; then
-      if test "x$with_tcmalloc" != "xyes" && test "x$with_tcmalloc" != "x"; then
+      if test "x$with_tcmalloc" != "xyes" -a "x$with_tcmalloc" != "x"; then
          tclibs="-L$with_tcmalloc -ltcmalloc_minimal"
       else
          tclibs="-ltcmalloc_minimal"
@@ -340,7 +384,7 @@ fi
 AC_SUBST([TCMALLOC_LIBS])
 AM_CONDITIONAL([HAVETCMALLOC],[test -n "$TCMALLOC_LIBS"])
 
-#  Check for -lprofiler usually part of the gpreftools along with tcmalloc.
+#  Check for -lprofiler usually part of the gperftools along with tcmalloc.
 have_profiler="no"
 AC_ARG_WITH([profiler],
    [AS_HELP_STRING([--with-profiler],
@@ -350,7 +394,7 @@ AC_ARG_WITH([profiler],
    [with_profiler="yes"]
 )
 if test "x$with_profiler" != "xno"; then
-   if test "x$with_profiler" != "xyes" && test "x$with_profiler" != "x"; then
+   if test "x$with_profiler" != "xyes" -a "x$with_profiler" != "x"; then
       proflibs="-L$with_profiler -lprofiler"
    else
       proflibs="-lprofiler"
@@ -367,6 +411,38 @@ fi
 AC_SUBST([PROFILER_LIBS])
 AM_CONDITIONAL([HAVEPROFILER],[test -n "$PROFILER_LIBS"])
 
+#  Check for jemalloc another fast malloc that is good with contention.
+have_jemalloc="no"
+AC_ARG_WITH([jemalloc],
+   [AS_HELP_STRING([--with-jemalloc],
+      [use jemalloc library or specify the directory with lib @<:@yes/no@:>@]
+   )],
+   [with_jemalloc="$withval"],
+   [with_jemalloc="no"]
+)
+if test "x$with_jemalloc" != "xno"; then
+   if test "x$with_jemalloc" != "xyes" -a "x$with_jemalloc" != "x"; then
+      jelibs="-L$with_jemalloc -ljemalloc"
+   else
+      jelibs="-ljemalloc"
+   fi
+   AC_CHECK_LIB([jemalloc],[malloc_usable_size],[have_jemalloc="yes"],[have_jemalloc="no"],
+                $jelibs)
+
+   if test "$have_jemalloc" = "yes"; then
+      JEMALLOC_LIBS="$jelibs"
+   else
+      JEMALLOC_LIBS=""
+   fi
+fi
+AC_SUBST([JEMALLOC_LIBS])
+AM_CONDITIONAL([HAVEJEMALLOC],[test -n "$JEMALLOC_LIBS"])
+
+#  Don't allow both tcmalloc and jemalloc.
+if test "x$have_tcmalloc" != "xno" -a "x$have_jemalloc" != "xno"; then
+   AC_MSG_ERROR([Cannot use tcmalloc at same time as jemalloc])
+fi
+
 # Check for HDF5. This is required.
 AX_LIB_HDF5
 
@@ -428,8 +504,9 @@ if test "$ac_cv_header_fftw3_h" = "yes"; then
 fi
 AC_SUBST([FFTW_LIBS])
 
-# Check for Intel intrinsics header optionally used by vector.h.
+# Check for Intel and PowerPC intrinsics header optionally used by vector.h.
 AC_CHECK_HEADERS([immintrin.h])
+AC_CHECK_HEADERS([altivec.h])
 
 # Check for timing functions needed by cycle.h.
 AC_HEADER_TIME
@@ -451,7 +528,7 @@ AC_LINK_IFELSE([AC_LANG_PROGRAM(
 AC_MSG_RESULT($rtc_ok)
 
 # Add warning flags by default, if these can be used. Option =error adds
-# -Werror to GCC, clang and Intel.  Note do this last as compiler tests may 
+# -Werror to GCC, clang and Intel.  Note do this last as compiler tests may
 # become errors, if that's an issue don't use CFLAGS for these, use an AC_SUBST().
 AC_ARG_ENABLE([compiler-warnings],
    [AS_HELP_STRING([--enable-compiler-warnings],
@@ -461,7 +538,7 @@ AC_ARG_ENABLE([compiler-warnings],
    [enable_warn="error"]
 )
 if test "$enable_warn" != "no"; then
-   
+
     # AX_CFLAGS_WARN_ALL does not give good warning flags for the Intel compiler
     # We will do this by hand instead and only default to the macro for unknown compilers
     case "$ax_cv_c_compiler_vendor" in
@@ -475,7 +552,7 @@ if test "$enable_warn" != "no"; then
 	     AX_CFLAGS_WARN_ALL
 	  ;;
     esac
-    
+
     # Add a "choke on warning" flag if it exists
     if test "$enable_warn" = "error"; then
        case "$ax_cv_c_compiler_vendor" in
@@ -486,6 +563,222 @@ if test "$enable_warn" != "no"; then
     fi
 fi
 
+# Various package configuration options.
+
+# Hydro scheme.
+AC_ARG_WITH([hydro],
+   [AS_HELP_STRING([--with-hydro=<scheme>],
+      [Hydro dynamics to use @<:@gadget2, minimal, hopkins, default, gizmo default: gadget2@:>@]
+   )],
+   [with_hydro="$withval"],
+   [with_hydro="gadget2"]
+)
+case "$with_hydro" in
+   gadget2)
+      AC_DEFINE([GADGET2_SPH], [1], [Gadget-2 SPH])
+   ;; 
+   minimal)
+      AC_DEFINE([MINIMAL_SPH], [1], [Minimal SPH])
+   ;; 
+   hopkins)
+      AC_DEFINE([HOPKINS_PE_SPH], [1], [Pressure-Entropy SPH])
+   ;; 
+   default)
+      AC_DEFINE([DEFAULT_SPH], [1], [Default SPH])
+   ;; 
+   gizmo)
+      AC_DEFINE([GIZMO_SPH], [1], [GIZMO SPH])
+   ;; 
+
+   *)
+      AC_MSG_ERROR([Unknown hydrodynamics scheme: $with_hydro])
+   ;;
+esac
+
+# SPH Kernel function
+AC_ARG_WITH([kernel],
+   [AS_HELP_STRING([--with-kernel=<kernel>],
+      [Kernel function to use @<:@cubic-spline, quartic-spline, quintic-spline, wendland-C2, wendland-C4, wendland-C6 default: cubic-spline@:>@]
+   )],
+   [with_kernel="$withval"],
+   [with_kernel="cubic-spline"]
+)
+case "$with_kernel" in
+   cubic-spline)
+      AC_DEFINE([CUBIC_SPLINE_KERNEL], [1], [Cubic spline kernel])
+   ;;    
+   quartic-spline)
+      AC_DEFINE([QUARTIC_SPLINE_KERNEL], [1], [Quartic spline kernel])
+   ;;    
+   quintic-spline)
+      AC_DEFINE([QUINTIC_SPLINE_KERNEL], [1], [Quintic spline kernel])
+   ;;    
+   wendland-C2)
+      AC_DEFINE([WENDLAND_C2_KERNEL], [1], [Wendland-C2 kernel])
+   ;;    
+   wendland-C4)
+      AC_DEFINE([WENDLAND_C4_KERNEL], [1], [Wendland-C4 kernel])
+   ;;    
+   wendland-C6)
+      AC_DEFINE([WENDLAND_C6_KERNEL], [1], [Wendland-C6 kernel])
+   ;;    
+   *)
+      AC_MSG_ERROR([Unknown kernel function: $with_kernel])
+   ;;
+esac
+
+#  Dimensionality of the hydro scheme.
+AC_ARG_WITH([hydro-dimension],
+   [AS_HELP_STRING([--with-hydro-dimension=<dim>],
+      [dimensionality of problem @<:@3/2/1 default: 3@:>@]
+   )],
+   [with_dimension="$withval"],
+   [with_dimension="3"]
+)
+case "$with_dimension" in
+   1)
+      AC_DEFINE([HYDRO_DIMENSION_1D], [1], [1D analysis])
+   ;; 
+   2)
+      AC_DEFINE([HYDRO_DIMENSION_2D], [2], [2D analysis])
+   ;; 
+   3)
+      AC_DEFINE([HYDRO_DIMENSION_3D], [3], [3D analysis])
+   ;; 
+   *)
+      AC_MSG_ERROR([Dimensionality must be 1, 2 or 3])
+   ;;
+esac
+
+#  Equation of state
+AC_ARG_WITH([equation-of-state],
+   [AS_HELP_STRING([--with-equation-of-state=<EoS>],
+      [equation of state @<:@ideal-gas, isothermal-gas default: ideal-gas@:>@]
+   )],
+   [with_eos="$withval"],
+   [with_eos="ideal-gas"]
+)
+case "$with_eos" in
+   ideal-gas)
+      AC_DEFINE([EOS_IDEAL_GAS], [1], [Ideal gas equation of state])
+   ;; 
+   isothermal-gas)
+      AC_DEFINE([EOS_ISOTHERMAL_GAS], [1], [Isothermal gas equation of state])
+   ;; 
+   *)
+      AC_MSG_ERROR([Unknown equation of state: $with_eos])
+   ;;
+esac
+
+#  Adiabatic index
+AC_ARG_WITH([adiabatic-index],
+   [AS_HELP_STRING([--with-adiabatic-index=<gamma>],
+      [adiabatic index @<:@5/3, 7/5, 4/3, 2 default: 5/3@:>@]
+   )],
+   [with_gamma="$withval"],
+   [with_gamma="5/3"]
+)
+case "$with_gamma" in
+   5/3)
+      AC_DEFINE([HYDRO_GAMMA_5_3], [5./3.], [Adiabatic index is 5/3])
+   ;; 
+   7/5)
+      AC_DEFINE([HYDRO_GAMMA_7_5], [7./5.], [Adiabatic index is 7/5])
+   ;; 
+   4/3)
+      AC_DEFINE([HYDRO_GAMMA_4_3], [4./3.], [Adiabatic index is 4/3])
+   ;; 
+   2)
+      AC_DEFINE([HYDRO_GAMMA_2_1], [2.], [Adiabatic index is 2])
+   ;; 
+   *)
+      AC_MSG_ERROR([Unknown adiabatic index: $with_gamma])
+   ;;
+esac
+
+#  Riemann solver
+AC_ARG_WITH([riemann-solver],
+   [AS_HELP_STRING([--with-riemann-solver=<solver>],
+      [riemann solver (gizmo-sph only) @<:@none, exact, trrs, hllc, default: none@:>@]
+   )],
+   [with_riemann="$withval"],
+   [with_riemann="none"]
+)
+case "$with_riemann" in
+   none)
+      AC_DEFINE([RIEMANN_SOLVER_NONE], [1], [No Riemann solver])
+   ;; 
+   exact)
+      AC_DEFINE([RIEMANN_SOLVER_EXACT], [1], [Exact Riemann solver])
+   ;; 
+   trrs)
+      AC_DEFINE([RIEMANN_SOLVER_TRRS], [1], [Two Rarefaction Riemann Solver])
+   ;; 
+   hllc)
+      AC_DEFINE([RIEMANN_SOLVER_HLLC], [1], [Harten-Lax-van Leer-Contact Riemann solver])
+   ;; 
+   *)
+      AC_MSG_ERROR([Unknown Riemann solver: $with_riemann])
+   ;;
+esac
+
+#  Cooling function
+AC_ARG_WITH([cooling],
+   [AS_HELP_STRING([--with-cooling=<function>],
+      [cooling function @<:@none, const-du, const-lambda, grackle default: none@:>@]
+   )],
+   [with_cooling="$withval"],
+   [with_cooling="none"]
+)
+case "$with_cooling" in
+   none)
+      AC_DEFINE([COOLING_NONE], [1], [No cooling function])
+   ;; 
+   const-du)
+      AC_DEFINE([COOLING_CONST_DU], [1], [Const du/dt cooling function])
+   ;; 
+   const-lambda)
+      AC_DEFINE([COOLING_CONST_LAMBDA], [1], [Const Lambda cooling function])
+   ;; 
+   grackle)
+      AC_DEFINE([COOLING_GRACKLE], [1], [Cooling via the grackle library])
+   ;; 
+   *)
+      AC_MSG_ERROR([Unknown cooling function: $with_cooling])
+   ;;
+esac
+
+#  External potential
+AC_ARG_WITH([ext-potential],
+   [AS_HELP_STRING([--with-ext-potential=<pot>],
+      [external potential @<:@none, point-mass, isothermal, softened-isothermal, disc-patch default: none@:>@]
+   )],
+   [with_potential="$withval"],
+   [with_potential="none"]
+)
+case "$with_potential" in
+   none)
+      AC_DEFINE([EXTERNAL_POTENTIAL_NONE], [1], [No external potential])
+   ;; 
+   point-mass)
+      AC_DEFINE([EXTERNAL_POTENTIAL_POINTMASS], [1], [Point-mass external potential])
+   ;; 
+   isothermal)
+      AC_DEFINE([EXTERNAL_POTENTIAL_ISOTHERMAL], [1], [Isothermal external potential])
+   ;; 
+   softened-isothermal)
+      AC_DEFINE([EXTERNAL_POTENTIAL_SOFTENED_ISOTHERMAL], [1], [Softened isothermal external potential])
+   ;; 
+   disc-patch)
+      AC_DEFINE([EXTERNAL_POTENTIAL_DISC_PATCH], [1], [Disc-patch external potential])
+   ;; 
+   *)
+      AC_MSG_ERROR([Unknown external potential: $with_potential])
+   ;;
+esac
+
+
+
 # Check for git, needed for revision stamps.
 AC_PATH_PROG([GIT_CMD], [git])
 AC_SUBST([GIT_CMD])
@@ -504,6 +797,9 @@ AC_CONFIG_FILES([tests/test27cellsPerturbed.sh], [chmod +x tests/test27cellsPert
 AC_CONFIG_FILES([tests/test125cells.sh], [chmod +x tests/test125cells.sh])
 AC_CONFIG_FILES([tests/testParser.sh], [chmod +x tests/testParser.sh])
 
+# Save the compilation options
+AC_DEFINE_UNQUOTED([SWIFT_CONFIG_FLAGS],["$swift_config_flags"],[Flags passed to configure])
+
 # Report general configuration.
 AC_MSG_RESULT([
    Compiler        : $CC
@@ -517,7 +813,19 @@ AC_MSG_RESULT([
    FFTW3 enabled   : $have_fftw3
    libNUMA enabled : $have_numa
    Using tcmalloc  : $have_tcmalloc
+   Using jemalloc  : $have_jemalloc
    CPU profiler    : $have_profiler
+
+   Hydro scheme       : $with_hydro
+   Dimensionality     : $with_dimension
+   Kernel function    : $with_kernel
+   Equation of state  : $with_eos
+   Adiabatic index    : $with_gamma
+   Riemann solver     : $with_riemann
+   Cooling function   : $with_cooling
+   External potential : $with_potential
+   Task debugging     : $enable_task_debugging
+   Debugging checks   : $enable_debugging_checks
 ])
 
 # Generate output.

doc/Doxyfile.in

@@ -760,8 +760,11 @@ WARN_LOGFILE           =
 # Note: If this tag is empty the current directory is searched.
 
 INPUT                  =  @top_srcdir@ @top_srcdir@/src @top_srcdir@/tests @top_srcdir@/examples
-INPUT		       += @top_srcdir@/src/hydro/Minimal @top_srcdir@/src/gravity/Default
-INPUT		       += @top_srcdir@/src/riemann 
+INPUT		       += @top_srcdir@/src/hydro/Minimal
+INPUT		       += @top_srcdir@/src/gravity/Default
+INPUT		       += @top_srcdir@/src/riemann
+INPUT		       += @top_srcdir@/src/potential/point_mass
+INPUT		       += @top_srcdir@/src/cooling/const_du
 
 # 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

examples/CoolingBox/coolingBox.yml

+# Define the system of units to use internally. 
+InternalUnitSystem:
+  UnitMass_in_cgs:     2.0e33   # Solar masses
+  UnitLength_in_cgs:   3.0857e21   # Kiloparsecs
+  UnitVelocity_in_cgs: 1.0e5   # Time unit is cooling time
+  UnitCurrent_in_cgs:  1   # Amperes
+  UnitTemp_in_cgs:     1   # Kelvin
+
+# Parameters governing the time integration
+TimeIntegration:
+  time_begin: 0.    # The starting time of the simulation (in internal units).
+  time_end:   4.    # The end time of the simulation (in internal units).
+  dt_min:     1e-4  # The minimal time-step size of the simulation (in internal units).
+  dt_max:     1e-4  # The maximal time-step size of the simulation (in internal units).
+
+# Parameters governing the snapshots
+Snapshots:
+  basename:            coolingBox # Common part of the name of output files
+  time_first:          0.         # Time of the first output (in internal units)
+  delta_time:          1.0e-1       # Time difference between consecutive outputs (in internal units)
+
+# Parameters governing the conserved quantities statistics
+Statistics:
+  delta_time:          1e-2 # Time between statistics output
+
+# Parameters for the hydrodynamics scheme
+SPH:
+  resolution_eta:        1.2348   # Target smoothing length in units of the mean inter-particle separation (1.2348 == 48Ngbs with the cubic spline kernel).
+  delta_neighbours:      0.1      # The tolerance for the targetted number of neighbours.
+  CFL_condition:         0.1      # Courant-Friedrich-Levy condition for time integration.
+  
+# Parameters related to the initial conditions
+InitialConditions:
+  file_name:  ./coolingBox.hdf5     # The file to read
+
+# Dimensionless pre-factor for the time-step condition
+LambdaCooling:
+  lambda_cgs:                 1.0e-22    # Cooling rate (in cgs units)
+  minimum_temperature:         1.0e4  # Minimal temperature (Kelvin)
+  mean_molecular_weight:       0.59   # Mean molecular weight
+  hydrogen_mass_abundance:     0.75   # Hydrogen mass abundance (dimensionless)
+  cooling_tstep_mult:          1.0    # Dimensionless pre-factor for the time-step condition

examples/CoolingBox/energy_plot.py

+import numpy as np
+import matplotlib.pyplot as plt
+import h5py as h5
+import sys
+
+stats_filename = "./energy.txt"
+snap_filename = "coolingBox_000.hdf5"