diff --git a/.gitignore b/.gitignore
index 8c3ede8f3125f5024c1fe01a405024d1cf5a7f19..a8be04764a48b1eb96cfac70483262e2a9a17dc7 100644
--- a/.gitignore
+++ b/.gitignore
@@ -31,6 +31,7 @@ examples/*/*.txt
examples/*/*.dot
examples/*/restart/*
examples/*/used_parameters.yml
+examples/*/unused_parameters.yml
examples/*/*/*.xmf
examples/*/*/*.png
examples/*/*/*.mp4
@@ -41,6 +42,7 @@ examples/*/*/*.hdf5
examples/*/snapshots*
examples/*/restart/*
examples/*/*/used_parameters.yml
+examples/*/*/unused_parameters.yml
examples/*/*.mpg
examples/*/gravity_checks_*.dat
@@ -80,6 +82,7 @@ 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
@@ -102,6 +105,7 @@ tests/test125cells.sh
tests/test125cellsPerturbed.sh
tests/testParser.sh
tests/testReading.sh
+tests/testSelectOutput.sh
tests/testAdiabaticIndex
tests/testRiemannExact
tests/testRiemannTRRS
diff --git a/INSTALL.swift b/INSTALL.swift
index 1782b75e34e2028110717d7873bc2c97365f8240..999a8d3655fa14a8ba1dcbd430b5146cc55ba791 100644
--- a/INSTALL.swift
+++ b/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.
diff --git a/configure.ac b/configure.ac
index 56018272debbb9e9ccb2f425eff45b97c358aec9..ff36f36aa2d0ac46aea54eb83cb8fa45601b9459 100644
--- a/configure.ac
+++ b/configure.ac
@@ -19,9 +19,6 @@
AC_INIT([SWIFT],[0.7.0],[https://gitlab.cosma.dur.ac.uk/swift/swiftsim])
swift_config_flags="$*"
-# Need to define this, instead of using fifth argument of AC_INIT, until 2.64.
-AC_DEFINE([PACKAGE_URL],["www.swiftsim.com"], [Package web pages])
-
AC_COPYRIGHT
AC_CONFIG_SRCDIR([src/space.c])
AC_CONFIG_AUX_DIR([.])
@@ -628,15 +625,51 @@ AC_SUBST([FFTW_LIBS])
AC_SUBST([FFTW_INCS])
AM_CONDITIONAL([HAVEFFTW],[test -n "$FFTW_LIBS"])
+# Check for -lprofiler usually part of the gperftools along with tcmalloc.
+have_profiler="no"
+AC_ARG_WITH([profiler],
+ [AS_HELP_STRING([--with-profiler=PATH],
+ [use cpu profiler library or specify the directory with lib @<:@yes/no@:>@]
+ )],
+ [with_profiler="$withval"],
+ [with_profiler="no"]
+)
+if test "x$with_profiler" != "xno"; then
+ if test "x$with_profiler" != "xyes" -a "x$with_profiler" != "x"; then
+ proflibs="-L$with_profiler -lprofiler"
+ else
+ proflibs="-lprofiler"
+ fi
+ AC_CHECK_LIB([profiler],[ProfilerFlush],
+ [have_profiler="yes"
+ AC_DEFINE([WITH_PROFILER],1,[Link against the gperftools profiling library.])],
+ [have_profiler="no"], $proflibs)
+
+ if test "$have_profiler" = "yes"; then
+ PROFILER_LIBS="$proflibs"
+ else
+ PROFILER_LIBS=""
+ fi
+fi
+AC_SUBST([PROFILER_LIBS])
+AM_CONDITIONAL([HAVEPROFILER],[test -n "$PROFILER_LIBS"])
+
+# Check for special allocators
+have_special_allocator="no"
+
# Check for tcmalloc a fast malloc that is part of the gperftools.
have_tcmalloc="no"
AC_ARG_WITH([tcmalloc],
- [AS_HELP_STRING([--with-tcmalloc],
+ [AS_HELP_STRING([--with-tcmalloc=PATH],
[use tcmalloc library or specify the directory with lib @<:@yes/no@:>@]
)],
[with_tcmalloc="$withval"],
[with_tcmalloc="no"]
)
+if test "x$with_tcmalloc" != "xno" -a "x$have_special_allocator" != "xno"; then
+ AC_MSG_ERROR("Cannot activate more than one alternative malloc library")
+fi
+
if test "x$with_tcmalloc" != "xno"; then
if test "x$with_tcmalloc" != "xyes" -a "x$with_tcmalloc" != "x"; then
tclibs="-L$with_tcmalloc -ltcmalloc"
@@ -660,10 +693,17 @@ if test "x$with_tcmalloc" != "xno"; then
if test "$have_tcmalloc" = "yes"; then
TCMALLOC_LIBS="$tclibs"
- # These are recommended for GCC.
- if test "$ax_cv_c_compiler_vendor" = "gnu"; then
- CFLAGS="$CFLAGS -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free"
- fi
+ AC_DEFINE([HAVE_TCMALLOC],1,[The tcmalloc library appears to be present.])
+
+ have_special_allocator="tcmalloc"
+
+ # Prevent compilers that replace the calls with built-ins (GNU 99) from doing so.
+ case "$ax_cv_c_compiler_vendor" in
+ intel | gnu | clang)
+ CFLAGS="$CFLAGS -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free"
+ ;;
+ esac
+
else
TCMALLOC_LIBS=""
fi
@@ -671,44 +711,19 @@ fi
AC_SUBST([TCMALLOC_LIBS])
AM_CONDITIONAL([HAVETCMALLOC],[test -n "$TCMALLOC_LIBS"])
-# Check for -lprofiler usually part of the gperftools along with tcmalloc.
-have_profiler="no"
-AC_ARG_WITH([profiler],
- [AS_HELP_STRING([--with-profiler],
- [use cpu profiler library or specify the directory with lib @<:@yes/no@:>@]
- )],
- [with_profiler="$withval"],
- [with_profiler="no"]
-)
-if test "x$with_profiler" != "xno"; then
- if test "x$with_profiler" != "xyes" -a "x$with_profiler" != "x"; then
- proflibs="-L$with_profiler -lprofiler"
- else
- proflibs="-lprofiler"
- fi
- AC_CHECK_LIB([profiler],[ProfilerFlush],
- [have_profiler="yes"
- AC_DEFINE([WITH_PROFILER],1,[Link against the gperftools profiling library.])],
- [have_profiler="no"], $proflibs)
-
- if test "$have_profiler" = "yes"; then
- PROFILER_LIBS="$proflibs"
- else
- PROFILER_LIBS=""
- fi
-fi
-AC_SUBST([PROFILER_LIBS])
-AM_CONDITIONAL([HAVEPROFILER],[test -n "$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],
+ [AS_HELP_STRING([--with-jemalloc=PATH],
[use jemalloc library or specify the directory with lib @<:@yes/no@:>@]
)],
[with_jemalloc="$withval"],
[with_jemalloc="no"]
)
+if test "x$with_jemalloc" != "xno" -a "x$have_special_allocator" != "xno"; then
+ AC_MSG_ERROR("Cannot activate more than one alternative malloc library")
+fi
+
if test "x$with_jemalloc" != "xno"; then
if test "x$with_jemalloc" != "xyes" -a "x$with_jemalloc" != "x"; then
jelibs="-L$with_jemalloc -ljemalloc"
@@ -720,6 +735,18 @@ if test "x$with_jemalloc" != "xno"; then
if test "$have_jemalloc" = "yes"; then
JEMALLOC_LIBS="$jelibs"
+
+ AC_DEFINE([HAVE_JEMALLOC],1,[The jemalloc library appears to be present.])
+
+ have_special_allocator="jemalloc"
+
+ # Prevent compilers that replace the regular calls with built-ins (GNU 99) from doing so.
+ case "$ax_cv_c_compiler_vendor" in
+ intel | gnu | clang)
+ CFLAGS="$CFLAGS -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free"
+ ;;
+ esac
+
else
JEMALLOC_LIBS=""
fi
@@ -727,11 +754,49 @@ 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$have_jemalloc" != "xno"; then
- AC_MSG_ERROR([Cannot use tcmalloc at same time as jemalloc])
+# Check for tbbmalloc, Intel's fast and parallel allocator
+have_tbbmalloc="no"
+AC_ARG_WITH([tbbmalloc],
+ [AS_HELP_STRING([--with-tbbmalloc=PATH],
+ [use tbbmalloc library or specify the directory with lib @<:@yes/no@:>@]
+ )],
+ [with_tbbmalloc="$withval"],
+ [with_tbbmalloc="no"]
+)
+if test "x$with_tbbmalloc" != "xno" -a "x$have_special_allocator" != "xno"; then
+ AC_MSG_ERROR("Cannot activate more than one alternative malloc library")
fi
+if test "x$with_tbbmalloc" != "xno"; then
+ if test "x$with_tbbmalloc" != "xyes" -a "x$with_tbbmalloc" != "x"; then
+ tbblibs="-L$with_tbbmalloc -ltbbmalloc_proxy -ltbbmalloc"
+ else
+ tbblibs="-ltbbmalloc_proxy -ltbbmalloc"
+ fi
+ AC_CHECK_LIB([tbbmalloc],[scalable_malloc],[have_tbbmalloc="yes"],[have_tbbmalloc="no"],
+ $tbblibs)
+
+ if test "$have_tbbmalloc" = "yes"; then
+ TBBMALLOC_LIBS="$tbblibs"
+
+ AC_DEFINE([HAVE_TBBMALLOC],1,[The TBBmalloc library appears to be present.])
+
+ have_special_allocator="TBBmalloc"
+
+ # Prevent compilers that replace the calls with built-ins (GNU 99) from doing so.
+ case "$ax_cv_c_compiler_vendor" in
+ intel | gnu | clang)
+ CFLAGS="$CFLAGS -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free"
+ ;;
+ esac
+
+ else
+ TBBMALLOC_LIBS=""
+ fi
+fi
+AC_SUBST([TBBMALLOC_LIBS])
+AM_CONDITIONAL([HAVETBBMALLOC],[test -n "$TBBMALLOC_LIBS"])
+
# Check for HDF5. This is required.
AX_LIB_HDF5
if test "$with_hdf5" != "yes"; then
@@ -753,7 +818,8 @@ if test "$with_hdf5" = "yes"; then
if test "$enable_parallel_hdf5" = "yes"; then
AC_MSG_CHECKING([for HDF5 parallel support])
-# Check if the library is capable, the header should define H5_HAVE_PARALLEL.
+
+ # Check if the library is capable, the header should define H5_HAVE_PARALLEL.
AC_COMPILE_IFELSE([AC_LANG_SOURCE([[
#include "hdf5.h"
@@ -814,6 +880,27 @@ AC_LINK_IFELSE([AC_LANG_PROGRAM(
[AC_DEFINE(HAVE__RTC,1,[Define if you have the UNICOS _rtc() intrinsic.])],[rtc_ok=no])
AC_MSG_RESULT($rtc_ok)
+# Special timers for the ARM v7 and ARM v8 platforms (taken from FFTW-3 to match their cycle.h)
+AC_ARG_ENABLE(armv8-pmccntr-el0, [AC_HELP_STRING([--enable-armv8-pmccntr-el0],[enable the cycle counter on ARMv8 via the PMCCNTR_EL0 register])], have_armv8pmccntrel0=$enableval)
+if test "$have_armv8pmccntrel0"x = "yes"x; then
+ AC_DEFINE(HAVE_ARMV8_PMCCNTR_EL0,1,[Define if you have enabled the PMCCNTR_EL0 cycle counter on ARMv8])
+fi
+
+AC_ARG_ENABLE(armv8-cntvct-el0, [AC_HELP_STRING([--enable-armv8-cntvct-el0],[enable the cycle counter on ARMv8 via the CNTVCT_EL0 register])], have_armv8cntvctel0=$enableval)
+if test "$have_armv8cntvctel0"x = "yes"x; then
+ AC_DEFINE(HAVE_ARMV8_CNTVCT_EL0,1,[Define if you have enabled the CNTVCT_EL0 cycle counter on ARMv8])
+fi
+
+AC_ARG_ENABLE(armv7a-cntvct, [AC_HELP_STRING([--enable-armv7a-cntvct],[enable the cycle counter on Armv7a via the CNTVCT register])], have_armv7acntvct=$enableval)
+if test "$have_armv7acntvct"x = "yes"x; then
+ AC_DEFINE(HAVE_ARMV7A_CNTVCT,1,[Define if you have enabled the CNTVCT cycle counter on ARMv7a])
+fi
+
+AC_ARG_ENABLE(armv7a-pmccntr, [AC_HELP_STRING([--enable-armv7a-pmccntr],[enable the cycle counter on Armv7a via the PMCCNTR register])], have_armv7apmccntr=$enableval)
+if test "$have_armv7apmccntr"x = "yes"x; then
+ AC_DEFINE(HAVE_ARMV7A_PMCCNTR,1,[Define if you have enabled the PMCCNTR cycle counter on ARMv7a])
+fi
+
# 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
# become errors, if that's an issue don't use CFLAGS for these, use an AC_SUBST().
@@ -848,6 +935,11 @@ if test "$enable_warn" != "no"; then
;;
esac
fi
+
+ # We want strict-prototypes, but this must still work even if warnings
+ # are an error.
+ AX_CHECK_COMPILE_FLAG([-Wstrict-prototypes],[CFLAGS="$CFLAGS -Wstrict-prototypes"],
+ [CFLAGS="$CFLAGS"],[$CFLAGS],[AC_LANG_SOURCE([int main(void){return 0;}])])
fi
# Various package configuration options.
@@ -1204,6 +1296,7 @@ AC_CONFIG_FILES([tests/testPeriodicBC.sh], [chmod +x tests/testPeriodicBC.sh])
AC_CONFIG_FILES([tests/testPeriodicBCPerturbed.sh], [chmod +x tests/testPeriodicBCPerturbed.sh])
AC_CONFIG_FILES([tests/testInteractions.sh], [chmod +x tests/testInteractions.sh])
AC_CONFIG_FILES([tests/testParser.sh], [chmod +x tests/testParser.sh])
+AC_CONFIG_FILES([tests/testSelectOutput.sh], [chmod +x tests/testSelectOutput.sh])
# Save the compilation options
AC_DEFINE_UNQUOTED([SWIFT_CONFIG_FLAGS],["$swift_config_flags"],[Flags passed to configure])
@@ -1211,6 +1304,11 @@ AC_DEFINE_UNQUOTED([SWIFT_CONFIG_FLAGS],["$swift_config_flags"],[Flags passed to
# Make sure the latest git revision string gets included
touch src/version.c
+# Need to define this, instead of using fifth argument of AC_INIT, until
+# 2.64. Defer until now as this redefines PACKAGE_URL, which can emit a
+# compilation error when testing with -Werror.
+AC_DEFINE([PACKAGE_URL],["www.swiftsim.com"], [Package web pages])
+
# Generate output.
AC_OUTPUT
@@ -1220,22 +1318,21 @@ AC_MSG_RESULT([
$PACKAGE_NAME v.$PACKAGE_VERSION
- Compiler : $CC
- - vendor : $ax_cv_c_compiler_vendor
- - version : $ax_cv_c_compiler_version
- - flags : $CFLAGS
- MPI enabled : $enable_mpi
- HDF5 enabled : $with_hdf5
- - parallel : $have_parallel_hdf5
- Metis enabled : $have_metis
- FFTW3 enabled : $have_fftw
- GSL enabled : $have_gsl
- libNUMA enabled : $have_numa
- GRACKLE enabled : $have_grackle
- Using tcmalloc : $have_tcmalloc
- Using jemalloc : $have_jemalloc
- CPU profiler : $have_profiler
- Pthread barriers : $have_pthread_barrier
+ Compiler : $CC
+ - vendor : $ax_cv_c_compiler_vendor
+ - version : $ax_cv_c_compiler_version
+ - flags : $CFLAGS
+ MPI enabled : $enable_mpi
+ HDF5 enabled : $with_hdf5
+ - parallel : $have_parallel_hdf5
+ Metis enabled : $have_metis
+ FFTW3 enabled : $have_fftw
+ GSL enabled : $have_gsl
+ libNUMA enabled : $have_numa
+ GRACKLE enabled : $have_grackle
+ Special allocators : $have_special_allocator
+ CPU profiler : $have_profiler
+ Pthread barriers : $have_pthread_barrier
Hydro scheme : $with_hydro
Dimensionality : $with_dimension
diff --git a/doc/RTD/DeveloperGuide/AddingTasks/addingtasks.rst b/doc/RTD-Legacy/DeveloperGuide/AddingTasks/addingtasks.rst
similarity index 100%
rename from doc/RTD/DeveloperGuide/AddingTasks/addingtasks.rst
rename to doc/RTD-Legacy/DeveloperGuide/AddingTasks/addingtasks.rst
diff --git a/doc/RTD/DeveloperGuide/Examples/Cooling/cooling.rst b/doc/RTD-Legacy/DeveloperGuide/Examples/Cooling/cooling.rst
similarity index 100%
rename from doc/RTD/DeveloperGuide/Examples/Cooling/cooling.rst
rename to doc/RTD-Legacy/DeveloperGuide/Examples/Cooling/cooling.rst
diff --git a/doc/RTD/DeveloperGuide/Examples/ExternalGravity/externalgravity.rst b/doc/RTD-Legacy/DeveloperGuide/Examples/ExternalGravity/externalgravity.rst
similarity index 100%
rename from doc/RTD/DeveloperGuide/Examples/ExternalGravity/externalgravity.rst
rename to doc/RTD-Legacy/DeveloperGuide/Examples/ExternalGravity/externalgravity.rst
diff --git a/doc/RTD/DeveloperGuide/developerguide.rst b/doc/RTD-Legacy/DeveloperGuide/developerguide.rst
similarity index 100%
rename from doc/RTD/DeveloperGuide/developerguide.rst
rename to doc/RTD-Legacy/DeveloperGuide/developerguide.rst
diff --git a/doc/RTD/FAQ/index.rst b/doc/RTD-Legacy/FAQ/index.rst
similarity index 100%
rename from doc/RTD/FAQ/index.rst
rename to doc/RTD-Legacy/FAQ/index.rst
diff --git a/doc/RTD/Innovation/AsynchronousComms/index.rst b/doc/RTD-Legacy/Innovation/AsynchronousComms/index.rst
similarity index 100%
rename from doc/RTD/Innovation/AsynchronousComms/index.rst
rename to doc/RTD-Legacy/Innovation/AsynchronousComms/index.rst
diff --git a/doc/RTD/Innovation/Caching/index.rst b/doc/RTD-Legacy/Innovation/Caching/index.rst
similarity index 100%
rename from doc/RTD/Innovation/Caching/index.rst
rename to doc/RTD-Legacy/Innovation/Caching/index.rst
diff --git a/doc/RTD/Innovation/HeirarchicalCellDecomposition/InitialDecomp.png b/doc/RTD-Legacy/Innovation/HeirarchicalCellDecomposition/InitialDecomp.png
similarity index 100%
rename from doc/RTD/Innovation/HeirarchicalCellDecomposition/InitialDecomp.png
rename to doc/RTD-Legacy/Innovation/HeirarchicalCellDecomposition/InitialDecomp.png
diff --git a/doc/RTD/Innovation/HeirarchicalCellDecomposition/SplitCell.png b/doc/RTD-Legacy/Innovation/HeirarchicalCellDecomposition/SplitCell.png
similarity index 100%
rename from doc/RTD/Innovation/HeirarchicalCellDecomposition/SplitCell.png
rename to doc/RTD-Legacy/Innovation/HeirarchicalCellDecomposition/SplitCell.png
diff --git a/doc/RTD/Innovation/HeirarchicalCellDecomposition/SplitPair.png b/doc/RTD-Legacy/Innovation/HeirarchicalCellDecomposition/SplitPair.png
similarity index 100%
rename from doc/RTD/Innovation/HeirarchicalCellDecomposition/SplitPair.png
rename to doc/RTD-Legacy/Innovation/HeirarchicalCellDecomposition/SplitPair.png
diff --git a/doc/RTD/Innovation/HeirarchicalCellDecomposition/index.rst b/doc/RTD-Legacy/Innovation/HeirarchicalCellDecomposition/index.rst
similarity index 100%
rename from doc/RTD/Innovation/HeirarchicalCellDecomposition/index.rst
rename to doc/RTD-Legacy/Innovation/HeirarchicalCellDecomposition/index.rst
diff --git a/doc/RTD/Innovation/HybridParallelism/index.rst b/doc/RTD-Legacy/Innovation/HybridParallelism/index.rst
similarity index 100%
rename from doc/RTD/Innovation/HybridParallelism/index.rst
rename to doc/RTD-Legacy/Innovation/HybridParallelism/index.rst
diff --git a/doc/RTD/Innovation/TaskBasedParallelism/OMPScaling.png b/doc/RTD-Legacy/Innovation/TaskBasedParallelism/OMPScaling.png
similarity index 100%
rename from doc/RTD/Innovation/TaskBasedParallelism/OMPScaling.png
rename to doc/RTD-Legacy/Innovation/TaskBasedParallelism/OMPScaling.png
diff --git a/doc/RTD/Innovation/TaskBasedParallelism/TasksExample.png b/doc/RTD-Legacy/Innovation/TaskBasedParallelism/TasksExample.png
similarity index 100%
rename from doc/RTD/Innovation/TaskBasedParallelism/TasksExample.png
rename to doc/RTD-Legacy/Innovation/TaskBasedParallelism/TasksExample.png
diff --git a/doc/RTD/Innovation/TaskBasedParallelism/TasksExampleConflicts.png b/doc/RTD-Legacy/Innovation/TaskBasedParallelism/TasksExampleConflicts.png
similarity index 100%
rename from doc/RTD/Innovation/TaskBasedParallelism/TasksExampleConflicts.png
rename to doc/RTD-Legacy/Innovation/TaskBasedParallelism/TasksExampleConflicts.png
diff --git a/doc/RTD/Innovation/TaskBasedParallelism/index.rst b/doc/RTD-Legacy/Innovation/TaskBasedParallelism/index.rst
similarity index 100%
rename from doc/RTD/Innovation/TaskBasedParallelism/index.rst
rename to doc/RTD-Legacy/Innovation/TaskBasedParallelism/index.rst
diff --git a/doc/RTD/Innovation/TaskGraphPartition/index.rst b/doc/RTD-Legacy/Innovation/TaskGraphPartition/index.rst
similarity index 100%
rename from doc/RTD/Innovation/TaskGraphPartition/index.rst
rename to doc/RTD-Legacy/Innovation/TaskGraphPartition/index.rst
diff --git a/doc/RTD/Innovation/Vectorisation/index.rst b/doc/RTD-Legacy/Innovation/Vectorisation/index.rst
similarity index 100%
rename from doc/RTD/Innovation/Vectorisation/index.rst
rename to doc/RTD-Legacy/Innovation/Vectorisation/index.rst
diff --git a/doc/RTD/Innovation/index.rst b/doc/RTD-Legacy/Innovation/index.rst
similarity index 96%
rename from doc/RTD/Innovation/index.rst
rename to doc/RTD-Legacy/Innovation/index.rst
index da3f2474b4c71f8030634b2f669d3d8093757171..65a9cb82230b5661f332e25ea05644ec8e2cdbf8 100644
--- a/doc/RTD/Innovation/index.rst
+++ b/doc/RTD-Legacy/Innovation/index.rst
@@ -1,5 +1,3 @@
-.. _GettingStarted:
-
What makes SWIFT different?
===========================
diff --git a/doc/RTD-Legacy/Makefile b/doc/RTD-Legacy/Makefile
new file mode 100644
index 0000000000000000000000000000000000000000..b1dfebb01c2f55530f7a8efad3c5e5bf96484c18
--- /dev/null
+++ b/doc/RTD-Legacy/Makefile
@@ -0,0 +1,177 @@
+# Makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line.
+SPHINXOPTS =
+SPHINXBUILD = sphinx-build
+PAPER =
+BUILDDIR = _build
+
+# User-friendly check for sphinx-build
+ifeq ($(shell which $(SPHINXBUILD) >/dev/null 2>&1; echo $$?), 1)
+$(error The '$(SPHINXBUILD)' command was not found. Make sure you have Sphinx installed, then set the SPHINXBUILD environment variable to point to the full path of the '$(SPHINXBUILD)' executable. Alternatively you can add the directory with the executable to your PATH. If you don't have Sphinx installed, grab it from http://sphinx-doc.org/)
+endif
+
+# Internal variables.
+PAPEROPT_a4 = -D latex_paper_size=a4
+PAPEROPT_letter = -D latex_paper_size=letter
+ALLSPHINXOPTS = -d $(BUILDDIR)/doctrees $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) .
+# the i18n builder cannot share the environment and doctrees with the others
+I18NSPHINXOPTS = $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) .
+
+.PHONY: help clean html dirhtml singlehtml pickle json htmlhelp qthelp devhelp epub latex latexpdf text man changes linkcheck doctest gettext
+
+help:
+ @echo "Please use \`make <target>' where <target> is one of"
+ @echo " html to make standalone HTML files"
+ @echo " dirhtml to make HTML files named index.html in directories"
+ @echo " singlehtml to make a single large HTML file"
+ @echo " pickle to make pickle files"
+ @echo " json to make JSON files"
+ @echo " htmlhelp to make HTML files and a HTML help project"
+ @echo " qthelp to make HTML files and a qthelp project"
+ @echo " devhelp to make HTML files and a Devhelp project"
+ @echo " epub to make an epub"
+ @echo " latex to make LaTeX files, you can set PAPER=a4 or PAPER=letter"
+ @echo " latexpdf to make LaTeX files and run them through pdflatex"
+ @echo " latexpdfja to make LaTeX files and run them through platex/dvipdfmx"
+ @echo " text to make text files"
+ @echo " man to make manual pages"
+ @echo " texinfo to make Texinfo files"
+ @echo " info to make Texinfo files and run them through makeinfo"
+ @echo " gettext to make PO message catalogs"
+ @echo " changes to make an overview of all changed/added/deprecated items"
+ @echo " xml to make Docutils-native XML files"
+ @echo " pseudoxml to make pseudoxml-XML files for display purposes"
+ @echo " linkcheck to check all external links for integrity"
+ @echo " doctest to run all doctests embedded in the documentation (if enabled)"
+
+clean:
+ rm -rf $(BUILDDIR)/*
+
+html:
+ $(SPHINXBUILD) -b html $(ALLSPHINXOPTS) $(BUILDDIR)/html
+ @echo
+ @echo "Build finished. The HTML pages are in $(BUILDDIR)/html."
+
+dirhtml:
+ $(SPHINXBUILD) -b dirhtml $(ALLSPHINXOPTS) $(BUILDDIR)/dirhtml
+ @echo
+ @echo "Build finished. The HTML pages are in $(BUILDDIR)/dirhtml."
+
+singlehtml:
+ $(SPHINXBUILD) -b singlehtml $(ALLSPHINXOPTS) $(BUILDDIR)/singlehtml
+ @echo
+ @echo "Build finished. The HTML page is in $(BUILDDIR)/singlehtml."
+
+pickle:
+ $(SPHINXBUILD) -b pickle $(ALLSPHINXOPTS) $(BUILDDIR)/pickle
+ @echo
+ @echo "Build finished; now you can process the pickle files."
+
+json:
+ $(SPHINXBUILD) -b json $(ALLSPHINXOPTS) $(BUILDDIR)/json
+ @echo
+ @echo "Build finished; now you can process the JSON files."
+
+htmlhelp:
+ $(SPHINXBUILD) -b htmlhelp $(ALLSPHINXOPTS) $(BUILDDIR)/htmlhelp
+ @echo
+ @echo "Build finished; now you can run HTML Help Workshop with the" \
+ ".hhp project file in $(BUILDDIR)/htmlhelp."
+
+qthelp:
+ $(SPHINXBUILD) -b qthelp $(ALLSPHINXOPTS) $(BUILDDIR)/qthelp
+ @echo
+ @echo "Build finished; now you can run "qcollectiongenerator" with the" \
+ ".qhcp project file in $(BUILDDIR)/qthelp, like this:"
+ @echo "# qcollectiongenerator $(BUILDDIR)/qthelp/SWIFT.qhcp"
+ @echo "To view the help file:"
+ @echo "# assistant -collectionFile $(BUILDDIR)/qthelp/SWIFT.qhc"
+
+devhelp:
+ $(SPHINXBUILD) -b devhelp $(ALLSPHINXOPTS) $(BUILDDIR)/devhelp
+ @echo
+ @echo "Build finished."
+ @echo "To view the help file:"
+ @echo "# mkdir -p $$HOME/.local/share/devhelp/SWIFT"
+ @echo "# ln -s $(BUILDDIR)/devhelp $$HOME/.local/share/devhelp/SWIFT"
+ @echo "# devhelp"
+
+epub:
+ $(SPHINXBUILD) -b epub $(ALLSPHINXOPTS) $(BUILDDIR)/epub
+ @echo
+ @echo "Build finished. The epub file is in $(BUILDDIR)/epub."
+
+latex:
+ $(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex
+ @echo
+ @echo "Build finished; the LaTeX files are in $(BUILDDIR)/latex."
+ @echo "Run \`make' in that directory to run these through (pdf)latex" \
+ "(use \`make latexpdf' here to do that automatically)."
+
+latexpdf:
+ $(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex
+ @echo "Running LaTeX files through pdflatex..."
+ $(MAKE) -C $(BUILDDIR)/latex all-pdf
+ @echo "pdflatex finished; the PDF files are in $(BUILDDIR)/latex."
+
+latexpdfja:
+ $(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex
+ @echo "Running LaTeX files through platex and dvipdfmx..."
+ $(MAKE) -C $(BUILDDIR)/latex all-pdf-ja
+ @echo "pdflatex finished; the PDF files are in $(BUILDDIR)/latex."
+
+text:
+ $(SPHINXBUILD) -b text $(ALLSPHINXOPTS) $(BUILDDIR)/text
+ @echo
+ @echo "Build finished. The text files are in $(BUILDDIR)/text."
+
+man:
+ $(SPHINXBUILD) -b man $(ALLSPHINXOPTS) $(BUILDDIR)/man
+ @echo
+ @echo "Build finished. The manual pages are in $(BUILDDIR)/man."
+
+texinfo:
+ $(SPHINXBUILD) -b texinfo $(ALLSPHINXOPTS) $(BUILDDIR)/texinfo
+ @echo
+ @echo "Build finished. The Texinfo files are in $(BUILDDIR)/texinfo."
+ @echo "Run \`make' in that directory to run these through makeinfo" \
+ "(use \`make info' here to do that automatically)."
+
+info:
+ $(SPHINXBUILD) -b texinfo $(ALLSPHINXOPTS) $(BUILDDIR)/texinfo
+ @echo "Running Texinfo files through makeinfo..."
+ make -C $(BUILDDIR)/texinfo info
+ @echo "makeinfo finished; the Info files are in $(BUILDDIR)/texinfo."
+
+gettext:
+ $(SPHINXBUILD) -b gettext $(I18NSPHINXOPTS) $(BUILDDIR)/locale
+ @echo
+ @echo "Build finished. The message catalogs are in $(BUILDDIR)/locale."
+
+changes:
+ $(SPHINXBUILD) -b changes $(ALLSPHINXOPTS) $(BUILDDIR)/changes
+ @echo
+ @echo "The overview file is in $(BUILDDIR)/changes."
+
+linkcheck:
+ $(SPHINXBUILD) -b linkcheck $(ALLSPHINXOPTS) $(BUILDDIR)/linkcheck
+ @echo
+ @echo "Link check complete; look for any errors in the above output " \
+ "or in $(BUILDDIR)/linkcheck/output.txt."
+
+doctest:
+ $(SPHINXBUILD) -b doctest $(ALLSPHINXOPTS) $(BUILDDIR)/doctest
+ @echo "Testing of doctests in the sources finished, look at the " \
+ "results in $(BUILDDIR)/doctest/output.txt."
+
+xml:
+ $(SPHINXBUILD) -b xml $(ALLSPHINXOPTS) $(BUILDDIR)/xml
+ @echo
+ @echo "Build finished. The XML files are in $(BUILDDIR)/xml."
+
+pseudoxml:
+ $(SPHINXBUILD) -b pseudoxml $(ALLSPHINXOPTS) $(BUILDDIR)/pseudoxml
+ @echo
+ @echo "Build finished. The pseudo-XML files are in $(BUILDDIR)/pseudoxml."
diff --git a/doc/RTD/Motivation/index.rst b/doc/RTD-Legacy/Motivation/index.rst
similarity index 100%
rename from doc/RTD/Motivation/index.rst
rename to doc/RTD-Legacy/Motivation/index.rst
diff --git a/doc/RTD/Physics/Gravity/gravity.rst b/doc/RTD-Legacy/Physics/Gravity/gravity.rst
similarity index 100%
rename from doc/RTD/Physics/Gravity/gravity.rst
rename to doc/RTD-Legacy/Physics/Gravity/gravity.rst
diff --git a/doc/RTD/Physics/SPH/sph.rst b/doc/RTD-Legacy/Physics/SPH/sph.rst
similarity index 100%
rename from doc/RTD/Physics/SPH/sph.rst
rename to doc/RTD-Legacy/Physics/SPH/sph.rst
diff --git a/doc/RTD/Physics/index.rst b/doc/RTD-Legacy/Physics/index.rst
similarity index 100%
rename from doc/RTD/Physics/index.rst
rename to doc/RTD-Legacy/Physics/index.rst
diff --git a/doc/RTD/conf.py b/doc/RTD-Legacy/conf.py
similarity index 98%
rename from doc/RTD/conf.py
rename to doc/RTD-Legacy/conf.py
index b4eab3d354322f8ff5e060b1795c2654eb879f90..6b65aabe54a480a29a7930f6e6f24a35b0204dcf 100644
--- a/doc/RTD/conf.py
+++ b/doc/RTD-Legacy/conf.py
@@ -25,7 +25,7 @@ import sys, os
# Add any Sphinx extension module names here, as strings. They can be extensions
# coming with Sphinx (named 'sphinx.ext.*') or your custom ones.
-extensions = ['sphinx.ext.autodoc', 'sphinx.ext.todo', 'sphinx.ext.pngmath', 'sphinx.ext.mathjax']
+extensions = ['sphinx.ext.todo', 'sphinx.ext.mathjax']
# Add any paths that contain templates here, relative to this directory.
templates_path = ['_templates']
diff --git a/doc/RTD/index.rst b/doc/RTD-Legacy/index.rst
similarity index 100%
rename from doc/RTD/index.rst
rename to doc/RTD-Legacy/index.rst
diff --git a/doc/RTD/.gitignore b/doc/RTD/.gitignore
new file mode 100644
index 0000000000000000000000000000000000000000..50239858cbc1b86a270ae88903139d91b943acd3
--- /dev/null
+++ b/doc/RTD/.gitignore
@@ -0,0 +1,2 @@
+build/*
+make.bat
diff --git a/doc/RTD/Makefile b/doc/RTD/Makefile
index b1dfebb01c2f55530f7a8efad3c5e5bf96484c18..22ff80ae32739df7d7ca97d8d2a6c6c8159b8248 100644
--- a/doc/RTD/Makefile
+++ b/doc/RTD/Makefile
@@ -1,177 +1,20 @@
-# Makefile for Sphinx documentation
+# Minimal makefile for Sphinx documentation
#
# You can set these variables from the command line.
SPHINXOPTS =
SPHINXBUILD = sphinx-build
-PAPER =
-BUILDDIR = _build
-
-# User-friendly check for sphinx-build
-ifeq ($(shell which $(SPHINXBUILD) >/dev/null 2>&1; echo $$?), 1)
-$(error The '$(SPHINXBUILD)' command was not found. Make sure you have Sphinx installed, then set the SPHINXBUILD environment variable to point to the full path of the '$(SPHINXBUILD)' executable. Alternatively you can add the directory with the executable to your PATH. If you don't have Sphinx installed, grab it from http://sphinx-doc.org/)
-endif
-
-# Internal variables.
-PAPEROPT_a4 = -D latex_paper_size=a4
-PAPEROPT_letter = -D latex_paper_size=letter
-ALLSPHINXOPTS = -d $(BUILDDIR)/doctrees $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) .
-# the i18n builder cannot share the environment and doctrees with the others
-I18NSPHINXOPTS = $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) .
-
-.PHONY: help clean html dirhtml singlehtml pickle json htmlhelp qthelp devhelp epub latex latexpdf text man changes linkcheck doctest gettext
+SPHINXPROJ = SWIFTSPHWIthFine-grainedinter-dependentTasking
+SOURCEDIR = source
+BUILDDIR = build
+# Put it first so that "make" without argument is like "make help".
help:
- @echo "Please use \`make <target>' where <target> is one of"
- @echo " html to make standalone HTML files"
- @echo " dirhtml to make HTML files named index.html in directories"
- @echo " singlehtml to make a single large HTML file"
- @echo " pickle to make pickle files"
- @echo " json to make JSON files"
- @echo " htmlhelp to make HTML files and a HTML help project"
- @echo " qthelp to make HTML files and a qthelp project"
- @echo " devhelp to make HTML files and a Devhelp project"
- @echo " epub to make an epub"
- @echo " latex to make LaTeX files, you can set PAPER=a4 or PAPER=letter"
- @echo " latexpdf to make LaTeX files and run them through pdflatex"
- @echo " latexpdfja to make LaTeX files and run them through platex/dvipdfmx"
- @echo " text to make text files"
- @echo " man to make manual pages"
- @echo " texinfo to make Texinfo files"
- @echo " info to make Texinfo files and run them through makeinfo"
- @echo " gettext to make PO message catalogs"
- @echo " changes to make an overview of all changed/added/deprecated items"
- @echo " xml to make Docutils-native XML files"
- @echo " pseudoxml to make pseudoxml-XML files for display purposes"
- @echo " linkcheck to check all external links for integrity"
- @echo " doctest to run all doctests embedded in the documentation (if enabled)"
-
-clean:
- rm -rf $(BUILDDIR)/*
-
-html:
- $(SPHINXBUILD) -b html $(ALLSPHINXOPTS) $(BUILDDIR)/html
- @echo
- @echo "Build finished. The HTML pages are in $(BUILDDIR)/html."
-
-dirhtml:
- $(SPHINXBUILD) -b dirhtml $(ALLSPHINXOPTS) $(BUILDDIR)/dirhtml
- @echo
- @echo "Build finished. The HTML pages are in $(BUILDDIR)/dirhtml."
-
-singlehtml:
- $(SPHINXBUILD) -b singlehtml $(ALLSPHINXOPTS) $(BUILDDIR)/singlehtml
- @echo
- @echo "Build finished. The HTML page is in $(BUILDDIR)/singlehtml."
-
-pickle:
- $(SPHINXBUILD) -b pickle $(ALLSPHINXOPTS) $(BUILDDIR)/pickle
- @echo
- @echo "Build finished; now you can process the pickle files."
-
-json:
- $(SPHINXBUILD) -b json $(ALLSPHINXOPTS) $(BUILDDIR)/json
- @echo
- @echo "Build finished; now you can process the JSON files."
-
-htmlhelp:
- $(SPHINXBUILD) -b htmlhelp $(ALLSPHINXOPTS) $(BUILDDIR)/htmlhelp
- @echo
- @echo "Build finished; now you can run HTML Help Workshop with the" \
- ".hhp project file in $(BUILDDIR)/htmlhelp."
-
-qthelp:
- $(SPHINXBUILD) -b qthelp $(ALLSPHINXOPTS) $(BUILDDIR)/qthelp
- @echo
- @echo "Build finished; now you can run "qcollectiongenerator" with the" \
- ".qhcp project file in $(BUILDDIR)/qthelp, like this:"
- @echo "# qcollectiongenerator $(BUILDDIR)/qthelp/SWIFT.qhcp"
- @echo "To view the help file:"
- @echo "# assistant -collectionFile $(BUILDDIR)/qthelp/SWIFT.qhc"
-
-devhelp:
- $(SPHINXBUILD) -b devhelp $(ALLSPHINXOPTS) $(BUILDDIR)/devhelp
- @echo
- @echo "Build finished."
- @echo "To view the help file:"
- @echo "# mkdir -p $$HOME/.local/share/devhelp/SWIFT"
- @echo "# ln -s $(BUILDDIR)/devhelp $$HOME/.local/share/devhelp/SWIFT"
- @echo "# devhelp"
-
-epub:
- $(SPHINXBUILD) -b epub $(ALLSPHINXOPTS) $(BUILDDIR)/epub
- @echo
- @echo "Build finished. The epub file is in $(BUILDDIR)/epub."
-
-latex:
- $(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex
- @echo
- @echo "Build finished; the LaTeX files are in $(BUILDDIR)/latex."
- @echo "Run \`make' in that directory to run these through (pdf)latex" \
- "(use \`make latexpdf' here to do that automatically)."
-
-latexpdf:
- $(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex
- @echo "Running LaTeX files through pdflatex..."
- $(MAKE) -C $(BUILDDIR)/latex all-pdf
- @echo "pdflatex finished; the PDF files are in $(BUILDDIR)/latex."
-
-latexpdfja:
- $(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex
- @echo "Running LaTeX files through platex and dvipdfmx..."
- $(MAKE) -C $(BUILDDIR)/latex all-pdf-ja
- @echo "pdflatex finished; the PDF files are in $(BUILDDIR)/latex."
-
-text:
- $(SPHINXBUILD) -b text $(ALLSPHINXOPTS) $(BUILDDIR)/text
- @echo
- @echo "Build finished. The text files are in $(BUILDDIR)/text."
-
-man:
- $(SPHINXBUILD) -b man $(ALLSPHINXOPTS) $(BUILDDIR)/man
- @echo
- @echo "Build finished. The manual pages are in $(BUILDDIR)/man."
-
-texinfo:
- $(SPHINXBUILD) -b texinfo $(ALLSPHINXOPTS) $(BUILDDIR)/texinfo
- @echo
- @echo "Build finished. The Texinfo files are in $(BUILDDIR)/texinfo."
- @echo "Run \`make' in that directory to run these through makeinfo" \
- "(use \`make info' here to do that automatically)."
-
-info:
- $(SPHINXBUILD) -b texinfo $(ALLSPHINXOPTS) $(BUILDDIR)/texinfo
- @echo "Running Texinfo files through makeinfo..."
- make -C $(BUILDDIR)/texinfo info
- @echo "makeinfo finished; the Info files are in $(BUILDDIR)/texinfo."
-
-gettext:
- $(SPHINXBUILD) -b gettext $(I18NSPHINXOPTS) $(BUILDDIR)/locale
- @echo
- @echo "Build finished. The message catalogs are in $(BUILDDIR)/locale."
-
-changes:
- $(SPHINXBUILD) -b changes $(ALLSPHINXOPTS) $(BUILDDIR)/changes
- @echo
- @echo "The overview file is in $(BUILDDIR)/changes."
-
-linkcheck:
- $(SPHINXBUILD) -b linkcheck $(ALLSPHINXOPTS) $(BUILDDIR)/linkcheck
- @echo
- @echo "Link check complete; look for any errors in the above output " \
- "or in $(BUILDDIR)/linkcheck/output.txt."
-
-doctest:
- $(SPHINXBUILD) -b doctest $(ALLSPHINXOPTS) $(BUILDDIR)/doctest
- @echo "Testing of doctests in the sources finished, look at the " \
- "results in $(BUILDDIR)/doctest/output.txt."
+ @$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
-xml:
- $(SPHINXBUILD) -b xml $(ALLSPHINXOPTS) $(BUILDDIR)/xml
- @echo
- @echo "Build finished. The XML files are in $(BUILDDIR)/xml."
+.PHONY: help Makefile
-pseudoxml:
- $(SPHINXBUILD) -b pseudoxml $(ALLSPHINXOPTS) $(BUILDDIR)/pseudoxml
- @echo
- @echo "Build finished. The pseudo-XML files are in $(BUILDDIR)/pseudoxml."
+# Catch-all target: route all unknown targets to Sphinx using the new
+# "make mode" option. $(O) is meant as a shortcut for $(SPHINXOPTS).
+%: Makefile
+ @$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
\ No newline at end of file
diff --git a/doc/RTD/README.md b/doc/RTD/README.md
new file mode 100644
index 0000000000000000000000000000000000000000..3394ce7b8b97a71a7f14fb235e49e2efb51b9f9f
--- /dev/null
+++ b/doc/RTD/README.md
@@ -0,0 +1,15 @@
+SWIFT Documentation
+===================
+
+This is the main documentation for SWIFT that can be found on ReadTheDocs.
+
+You will need the `sphinx` and `sphinx-autobuild` python packages (pip install
+them!) to build the documentation to html, as well as the `sphinx_rtd_theme`
+package which is used as the theme.
+
+To build the documentation, `make html` and then it is available in
+`build/html`.
+
+Please consider adding documentation when you add code!
+
+
diff --git a/doc/RTD/source/Cooling/index.rst b/doc/RTD/source/Cooling/index.rst
new file mode 100644
index 0000000000000000000000000000000000000000..46a01b2a054629b7fc13f0ea190c2a5a0fdd6d9c
--- /dev/null
+++ b/doc/RTD/source/Cooling/index.rst
@@ -0,0 +1,67 @@
+.. Equation of State
+ Loic Hausammann, 7th April 2018
+
+.. _cooling:
+
+Cooling
+=======
+
+Currently, we have 5 different cooling (EAGLE, Grackle, const-lambda, const-du
+and none). Three of them are easily solved analytically (const-lambda,
+const-du and none) while the two last requires complex chemical networks.
+
+
+Equations
+---------
+
+The first table compares the different analytical cooling while the next ones
+are specific to a given cooling. The quantities are the internal energy (\\( u
+\\)), the density \\( rho \\), the element mass fraction (\\( X_i \\)), the
+cooling function (\\(\\Lambda\\), the proton mass (\\( m_H \\)) and the time
+step condition (\\( t\_\\text{step}\\)). If not specified otherwise, all
+cooling contains a temperature floor avoiding negative temperature.
+
+.. csv-table:: Analytical Cooling
+ :header: "Variable", "Const-Lambda", "Const-du", "None"
+
+ "\\( \\frac{ \\mathrm{d}u }{ \\mathrm{d}t } \\)", "\\( -\\Lambda \\frac{\\rho^2 X_H^2}{\\rho m_H^2} \\)", "const", "0"
+ "\\( \\Delta t\_\\text{max} \\)", "\\( t\_\\text{step} \\frac{u}{\\left|\\frac{ \\mathrm{d}u }{ \\mathrm{d}t }\\right|} \\)", "\\( t\_\\text{step} \\frac{u}{\\ \\left| \\frac{ \\mathrm{d}u }{ \\mathrm{d}t }\\right|} \\)", "None"
+
+
+Grackle
+~~~~~~~
+
+Grackle is a chemistry and cooling library presented in B. Smith et al. 2016
+(do not forget to cite if used). Four different modes are available:
+equilibrium, 6 species network (H, H\\( ^+ \\), e\\( ^- \\), He, He\\( ^+ \\)
+and He\\( ^{++} \\)), 9 species network (adds H\\(^-\\), H\\(_2\\) and
+H\\(_2^+\\)) and 12 species (adds D, D\\(^+\\) and HD). Following the same
+order, the swift cooling options are ``grackle``, ``grackle1``, ``grackle2``
+and ``grackle3`` (the numbers correspond to the value of
+``primordial_chemistry`` in Grackle). It also includes some self-shielding
+methods and UV background. In order to use the Grackle cooling, you will need
+to provide an HDF5 table computed by Cloudy.
+
+When starting a simulation without providing the different fractions, the code
+supposes an equilibrium and computes the fractions automatically.
+
+Eagle
+~~~~~
+
+TODO
+
+How to Implement a New Cooling
+------------------------------
+
+The developper should provide at least one function for:
+ * writing the cooling name in HDF5
+ * cooling a particle
+ * the maximal time step possible
+ * initializing a particle
+ * computing the total energy radiated by a particle
+ * initializing the cooling parameters
+ * printing the cooling type
+
+For implementation details, see ``src/cooling/none/cooling.h``
+
+See :ref:`new_option` for the full list of changes required.
diff --git a/doc/RTD/source/EquationOfState/index.rst b/doc/RTD/source/EquationOfState/index.rst
new file mode 100644
index 0000000000000000000000000000000000000000..3558041e9513b967a2530165acec5e5f4f11a364
--- /dev/null
+++ b/doc/RTD/source/EquationOfState/index.rst
@@ -0,0 +1,50 @@
+.. Equation of State
+ Loic Hausammann, 6th April 2018
+
+.. _equation_of_state:
+
+Equation of State
+=================
+
+Currently (if the documentation was well updated), we have two different
+equation of states implemented: ideal gas and isothermal. They describe the
+relations between our main thermodynamical variables: the internal energy
+(\\(u\\)), the density (\\(\\rho\\)), the entropy (\\(A\\)) and the pressure
+(\\(P\\)).
+
+Equations
+---------
+
+In the following section, the variables not yet defined are: \\(\\gamma\\) for
+the adiabatic index and \\( c_s \\) for the speed of sound.
+
+.. csv-table:: Ideal Gas
+ :header: "Variable", "A", "u", "P"
+
+ "A", "", "\\( \\left( \\gamma - 1 \\right) u \\rho^{1-\\gamma} \\)", "\\(P \\rho^{-\\gamma} \\)"
+ "u", "\\( A \\frac{ \\rho^{ \\gamma - 1 } }{\\gamma - 1 } \\)", "", "\\(\\frac{1}{\\gamma - 1} \\frac{P}{\\rho}\\)"
+ "P", "\\( A \\rho^\\gamma \\)", "\\( \\left( \\gamma - 1\\right) u \\rho \\)", ""
+ "\\(c_s\\)", "\\(\\sqrt{ \\gamma \\rho^{\\gamma - 1} A}\\)", "\\(\\sqrt{ u \\gamma \\left( \\gamma - 1 \\right) } \\)", "\\(\\sqrt{ \\frac{\\gamma P}{\\rho} }\\)"
+
+
+.. csv-table:: Isothermal Gas
+ :header: "Variable", "A", "u", "P"
+
+
+ "A", "", "\\(\\left( \\gamma - 1 \\right) u \\rho^{1-\\gamma}\\)", ""
+ "u", "", "const", ""
+ "P", "", "\\(\\left( \\gamma - 1\\right) u \\rho \\)", ""
+ "\\( c_s\\)", "", "\\(\\sqrt{ u \\gamma \\left( \\gamma - 1 \\right) } \\)", ""
+
+
+How to Implement a New Equation of State
+----------------------------------------
+
+See :ref:`new_option` for a full list of required changes.
+
+You will need to provide a ``equation_of_state.h`` file containing: the
+definition of ``eos_parameters``, IO functions and transformations between the
+different variables: \\(u(\\rho, A)\\), \\(u(\\rho, P)\\), \\(P(\\rho,A)\\),
+\\(P(\\rho, u)\\), \\(A(\\rho, P)\\), \\(A(\\rho, u)\\), \\(c_s(\\rho, A)\\),
+\\(c_s(\\rho, u)\\) and \\(c_s(\\rho, P)\\). See other equation of state files
+to have implementation details.
diff --git a/doc/RTD/source/GettingStarted/compiling_code.rst b/doc/RTD/source/GettingStarted/compiling_code.rst
new file mode 100644
index 0000000000000000000000000000000000000000..c40f06965e15146c41bf210aec3b195032cef0e7
--- /dev/null
+++ b/doc/RTD/source/GettingStarted/compiling_code.rst
@@ -0,0 +1,108 @@
+.. Compiling the Code
+ Josh Borrow, 5th April 2018
+
+
+Compiling SWIFT
+===============
+
+Dependencies
+------------
+
+To compile SWIFT, you will need the following libraries:
+
+HDF5
+~~~~
+
+Version 1.8.x or higher is required. Input and output files are stored as HDF5
+and are compatible with the existing GADGET-2 specification. Please consider
+using a build of parallel-HDF5, as SWIFT can leverage this when writing and
+reading snapshots. We recommend using HDF5 > 1.10.x as this is `vastly superior`
+in parallel.
+
+MPI
+~~~
+A recent implementation of MPI, such as Open MPI (v2.x or higher), is required,
+or any library that implements at least the MPI 3 standard.
+
+Libtool
+~~~~~~~
+The build system depends on libtool.
+
+FFTW
+~~~~
+Version 3.3.x or higher is required for periodic gravity.
+
+METIS
+~~~~~
+METIS is used for domain decomposition and load balancing.
+
+libNUMA
+~~~~~~~
+libNUMA is used to pin threads.
+
+GSL
+~~~
+The GSL is required for cosmological integration.
+
+
+Optional Dependencies
+---------------------
+
+There are also the following _optional_ dependencies.
+
+TCmalloc/Jemalloc
+~~~~~~~~~~~~~~~~~
+TCmalloc/Jemalloc are used for faster memory allocations when available.
+
+DOXYGEN
+~~~~~~~
+You can build documentation for SWIFT with DOXYGEN.
+
+Python
+~~~~~~
+To run the examples, you will need python and some of the standard scientific libraries (numpy, matplotlib). Some examples use Python 2 scripts, but the more recent ones use Python 3 (this is specified in individual READMEs).
+
+GRACKLE
+~~~~~~~
+GRACKLE cooling is implemented in SWIFT. If you wish to take advantage of it, you will need it installed.
+
+
+Initial Setup
+-------------
+
+We use autotools for setup. To get a basic running version of the code
+(the binary is created in swiftsim/examples) on most platforms, run
+
+.. code-block:: bash
+
+ ./autogen.sh
+ ./configure
+ make
+
+
+MacOS Specific Oddities
+~~~~~~~~~~~~~~~~~~~~~~~
+
+To build on MacOS you will need to disable compiler warnings due to an
+incomplete implementation of pthread barriers. DOXYGEN also has some issues on
+MacOS, so it is best to leave it out. To configure:
+
+.. code-block:: bash
+
+ ./configure --disable-compiler-warnings --disable-doxygen-doc
+
+
+Trouble Finding Libraries
+~~~~~~~~~~~~~~~~~~~~~~~~~
+
+If the configure script is having trouble finding your libraries for you, it
+may be that they are in nonstandard locations. You can link the specific
+library locations by using ``--with-<LIBRARY>=<PATH>``. For example for the
+HDF5 library,
+
+.. code-block:: bash
+
+ ./configure --with-hdf5=/path/to/h5cc
+
+More information about what needs to be provided to these flags is given in
+``./configure --help``.
diff --git a/doc/RTD/source/GettingStarted/configuration_options.rst b/doc/RTD/source/GettingStarted/configuration_options.rst
new file mode 100644
index 0000000000000000000000000000000000000000..e37384cfd1c29cb1df82cc180a763f4859650b2e
--- /dev/null
+++ b/doc/RTD/source/GettingStarted/configuration_options.rst
@@ -0,0 +1,50 @@
+.. Configuration Options
+ Josh Borrow, 5th April 2018
+
+Configuration Options
+=====================
+
+There are many configuration options that SWIFT makes available; a few key
+ones are summarised here.
+
+Note that these need to be ran with ``./configure x`` where ``x`` is the
+configuration flag.
+
+A description of the available options of the below flags can be found by using
+``./configure --help``.
+
+``--with-hydro=gadget2``
+~~~~~~~~~~~~~~~~~~~~~~~~
+There are several hydrodynamical schemes available in SWIFT. You can choose
+between them at compile-time with this option.
+
+``--with-riemann-solver=none``
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+Some hydrodynamical schemes, for example GIZMO, require a Riemann solver.
+
+``--with-kernel=cubic-spline``
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+Several kernels are made available for use with the hydrodynamical schemes.
+Choose between them with this compile-time flag.
+
+``--with-hydro-dimension=3``
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+Run problems in 1, 2, and 3 (default) dimensions.
+
+``--with-equation-of-state=ideal-gas``
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+Several equations of state are made available with this flag. Also consider
+``--with-adiabatic-index``.
+
+``--with-cooling=none``
+~~~~~~~~~~~~~~~~~~~~~~~
+Several cooling implementations (including GRACKLE) are available.
+
+``--with-ext-potential=none``
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+Many external potentials are available for use with SWIFT. You can choose
+between them at compile time. Some examples include a central potential, a
+softened central potential, and a sinusoidal potential. You will need to
+configure, for example, the mass in your parameterfile at runtime.
+
+
diff --git a/doc/RTD/source/GettingStarted/index.rst b/doc/RTD/source/GettingStarted/index.rst
new file mode 100644
index 0000000000000000000000000000000000000000..d15a8eee2f3b9089a1c8ee033f9aa3ee7ad92a5f
--- /dev/null
+++ b/doc/RTD/source/GettingStarted/index.rst
@@ -0,0 +1,25 @@
+.. Getting Started
+ Josh Borrow, 4th April 2018
+
+Getting Started
+===============
+
+So, you want to use SWIFT? Below you should find all of the information you need
+to get up and running with some examples, and then build your own initial conditions
+for running.
+
+Also, you might want to consult our onboarding guide (available at
+http://www.swiftsim.com/onboarding.pdf) if you would like something to print out
+and keep on your desk.
+
+.. toctree::
+ :maxdepth: 2
+ :caption: Contents:
+
+ compiling_code
+ running_example
+ runtime_options
+ configuration_options
+ parameter_file
+ what_about_mpi
+ running_on_large_systems
diff --git a/doc/RTD/source/GettingStarted/parameter_file.rst b/doc/RTD/source/GettingStarted/parameter_file.rst
new file mode 100644
index 0000000000000000000000000000000000000000..32a4f1220d0dc1c65074cc14b53d2c4edd666a67
--- /dev/null
+++ b/doc/RTD/source/GettingStarted/parameter_file.rst
@@ -0,0 +1,25 @@
+.. Parameter File
+ Loic Hausammann, 1 june 2018
+
+Parameter File
+==============
+
+To run SWIFT, you will need to provide a ``yaml`` parameter file. An example is
+given in ``examples/parameter_file.yml`` which should contain all possible
+parameters. Each section in this file corresponds to a different option in
+SWIFT and are not always required depending on the configuration options and
+the run time parameters.
+
+
+Output Selection
+~~~~~~~~~~~~~~~~
+
+With SWIFT, you can select the particle fields to output in snapshot using the parameter file.
+In section ``SelectOutput``, you can remove a field by adding a parameter formatted in the
+following way ``field_parttype`` where ``field`` is the name of the field that you
+want to remove (e.g. ``Masses``) and ``parttype`` is the type of particles that
+contains this field (e.g. ``Gas``, ``DM`` or ``Star``). For a parameter, the only
+values accepted are 0 (skip this field when writing) or 1 (default, do not skip
+this field when writing).
+
+You can generate a ``yaml`` file containing all the possible fields with ``./swift -o output.yml``. By default, all the fields are written.
diff --git a/doc/RTD/source/GettingStarted/running_example.rst b/doc/RTD/source/GettingStarted/running_example.rst
new file mode 100644
index 0000000000000000000000000000000000000000..854e74cf830d58e51cf866d59a93ede6dceb57b6
--- /dev/null
+++ b/doc/RTD/source/GettingStarted/running_example.rst
@@ -0,0 +1,37 @@
+.. Running an Example
+ Josh Borrow, 5th April 2018
+
+Running an Example
+==================
+
+Now that you have built the code, you will want to run an example! To do that,
+you need to follow the following instructions (requires ``python2`` or
+``python3`` with the ``h5py`` and other standard scientific packages, as well
+as ``wget`` for grabbing the glass).
+
+.. code-block:: bash
+
+ cd examples/SodShock_3D
+ ./getGlass.sh
+ python makeIC.py
+ ../swift -s -t 4 sodShock.yml
+ python plotSolution.py 1
+
+
+This will run the 'SodShock' in 3D and produce a nice plot that shows you
+how the density has varied. Try running with GIZMO (this will take
+_significantly_ longer than with SPH) to see the difference. For that, you
+will need to reconfigure with the following options:
+
+.. code-block:: bash
+
+ ./configure \
+ --with-hydro=gizmo \
+ --with-riemann-solver=hllc
+
+
+To see the results that you should get, you should check out our developer
+wiki at https://gitlab.cosma.dur.ac.uk/swift/swiftsim/wikis/Sod_3D.
+
+If you don't get these results, please contact us on our GitHub page at
+https://github.com/SWIFTSIM/swiftsim/issues.
diff --git a/doc/RTD/source/GettingStarted/running_on_large_systems.rst b/doc/RTD/source/GettingStarted/running_on_large_systems.rst
new file mode 100644
index 0000000000000000000000000000000000000000..55eb812cef21474045931490591b3978841a4085
--- /dev/null
+++ b/doc/RTD/source/GettingStarted/running_on_large_systems.rst
@@ -0,0 +1,42 @@
+.. Running on Large Systems
+ Josh Borrow, 5th April 2018
+
+Running on Large Systems
+========================
+
+There are a few extra things to keep in mind when running SWIFT on a large
+system (i.e. over MPI on several nodes). Here are some recommendations:
+
++ Compile and run with
+ `tbbmalloc <https://www.threadingbuildingblocks.org>`_. You can add this
+ to the configuration of SWIFT by running configure with the
+ ``--with-tbbmalloc`` flag. Using this allocator, over the one included in the
+ standard library, is particularly important on systems with large core counts
+ per node. Alternatives include
+ `jemalloc <https://github.com/jemalloc/jemalloc>`_ and
+ `tcmalloc <https://github.com/gperftools/gperftools>`_, and using these
+ other allocation tools also improves performance on single-node jobs.
++ Run with one MPI rank per NUMA region, usually a socket, rather than per node.
+ Typical HPC clusters now use two chips per node. Consult with your local system
+ manager if you are unsure about your system configuration. This can be done
+ by invoking ``mpirun -np <NUMBER OF CHIPS> swift_mpi -t <NUMBER OF CORES PER CHIP>``.
+ You should also be careful to include this in your batch script, for example
+ with the `SLURM <https://slurm.schedmd.com>`_ batch system you will need to
+ include ``#SBATCH --tasks-per-node=2``.
++ Run with threads pinned. You can do this by passing the ``-a`` flag to the
+ SWIFT binary. This ensures that processes stay on the same core that spawned
+ them, ensuring that cache is accessed more efficiently.
++ Ensure that you compile with METIS. More information is available in an
+ upcoming paper, but using METIS allows for work to be distributed in a
+ more efficient way between your nodes.
+
+Your batch script should look something like the following (to run on 16 nodes
+each with 2x16 core processors for a total of 512 cores):
+
+.. code-block:: bash
+
+ #SBATCH -N 16 # Number of nodes to run on
+ #SBATCH --tasks-per-node=2 # This system has 2 chips per node
+
+ mpirun -np 32 swift_mpi -t 16 -a parameter.yml
+
diff --git a/doc/RTD/source/GettingStarted/runtime_options.rst b/doc/RTD/source/GettingStarted/runtime_options.rst
new file mode 100644
index 0000000000000000000000000000000000000000..b2ca10640d8830b9b5ecb8e117bf047af738889c
--- /dev/null
+++ b/doc/RTD/source/GettingStarted/runtime_options.rst
@@ -0,0 +1,41 @@
+.. Runtime Options
+ Josh Borrow, 5th April 2018
+
+Runtime Options
+===============
+
+SWIFT requires a number of runtime options to run and get any sensible output.
+For instance, just running the ``swift`` binary will not use any SPH or gravity;
+the particles will just sit still!
+
+Below is a list of the runtime options and when they should be used. The same list
+can be found by typing ``./swift -h``.
+
++ ``-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 validity of parameter and IC files as well as memory limits.
++ ``-D``: Always drift all particles even the ones far from active particles.
+ This emulates Gadget-[23] and GIZMO's default behaviours.
++ ``-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.
++ ``-M``: Reconstruct the multipoles every time-step.
++ ``-n``: {int} Execute a fixed number of time steps. When unset use the
+ time_end parameter to stop.
++ ``-o``: {str} Generate a default output parameter file.
++ ``-P``: {sec:par:val} Set parameter value and overwrites values read from the
+ parameters file. Can be used more than once.
++ ``-s``: Run with hydrodynamics.
++ ``-S``: Run with stars.
++ ``-t``: {int} The number of threads to use on each MPI rank. Defaults to 1 if
+ not specified.
++ ``-T``: Print timers every time-step.
++ ``-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.
++ ``-Y``: {int} Time-step frequency at which threadpool tasks are dumped.
++ ``-h``: Print a help message and exit.
diff --git a/doc/RTD/source/GettingStarted/what_about_mpi.rst b/doc/RTD/source/GettingStarted/what_about_mpi.rst
new file mode 100644
index 0000000000000000000000000000000000000000..098fd35d80d71866cb86d2342d5d54710cd73a82
--- /dev/null
+++ b/doc/RTD/source/GettingStarted/what_about_mpi.rst
@@ -0,0 +1,12 @@
+.. What about MPI? Running SWIFT on more than one node
+ Josh Borrow, 5th April 2018
+
+What about MPI? Running SWIFT on more than one node
+===================================================
+
+After compilation, you will be left with two binaries. One is called ``swift``,
+and the other ``swift_mpi``. Current wisdom is to run ``swift`` if you are only
+using one node (i.e. without any interconnect), and one MPI rank per NUMA
+region using ``swift_mpi`` for anything larger. You will need some GADGET-2
+HDF5 initial conditions to run SWIFT, as well as a compatible yaml
+parameterfile.
diff --git a/doc/RTD/source/HydroSchemes/adding_your_own.rst b/doc/RTD/source/HydroSchemes/adding_your_own.rst
new file mode 100644
index 0000000000000000000000000000000000000000..2d7e640f66153a17e19f4e4c456cd37eed19a95a
--- /dev/null
+++ b/doc/RTD/source/HydroSchemes/adding_your_own.rst
@@ -0,0 +1,119 @@
+.. Adding Hydro Schemes
+ Josh Borrow, 5th April 2018
+
+
+Adding Hydro Schemes
+====================
+
+.. toctree::
+ :maxdepth: 2
+ :hidden:
+ :caption: Contents:
+
+SWIFT is engineered to enable you to add your own hydrodynamics schemes easily.
+We enable this through the use of header files to encapsulate each scheme.
+
+Note that it's unlikely you will ever have to consider paralellism or 'loops over
+neighbours' for SWIFT; all of this is handled by the tasking system. All we ask
+for is the interaction functions that tell us how to a) compute the density
+and b) compute forces.
+
+
+Getting Started
+---------------
+
+The hydro schemes are stored in ``src/hydro``. You will need to create a folder
+with a sensible name that you are going to store your scheme-specific information
+in. Then, you will need to create the following files:
+
++ ``hydro.h``, which includes functions that are applied to particles at the end
+ of the density loop and beginning of the force loop, along with helper functions
++ ``hydro_debug.h``, which includes a quick function that prints out your particle
+ properties for debugging purposes
++ ``hydro_iact.h`` that includes the interaction functions
++ ``hydro_io.h`` which includes the information on what should be read from the
+ initial conditions file, as well as written to the output files
++ ``hydro_part.h`` which includes your particle definition. SWIFT uses an array-of
+ -structures scheme.
+
+
+``hydro.h``
+-----------
+
+As previously noted, ``hydro.h`` includes the helper functions for your scheme. You
+will need to 'fill out' the following:
+
++ ``hydro_get_comoving_internal_energy(p)`` which returns the comoving internal energy
+ of your particles (typically this will just be ``p->u``).
++ ``hydro_get_physical_internal_energy(p, cosmo)`` which returns the physical internal
+ energy. You can use the ``a_factor_internal_energy`` from the ``cosmology`` struct.
++ ``hydro_get_comoving_pressure(p)`` which returns the comoving pressure.
++ ``hydro_get_comoving_entropy(p)`` which returns the comoving entropy.
++ ``hydro_get_physical_entropy(p, cosmo)`` which returns the physical entropy. In our
+ formalism, usually there is no conversion factor here so it is the same as the
+ comoving version.
++ ``hydro_get_comoving_soundspeed(p)`` which returns the comoving sound speed.
++ ``hydro_get_physical_soundspeed(p, cosmo)`` which returns the physical sound
+ speed. You can use the ``a_factor_sound_speed``.
++ ``hydro_get_comoving_density(p)`` which returns the comoving density.
++ ``hydro_get_physical_density(p, cosmo)`` which returns the physical density.
+ You can use the ``a3_inv`` member of the ``cosmology`` struct.
++ ``hydro_get_mass(p)`` returns the mass of particle ``p``.
++ ``hydro_get_drifted_velocities(p, xp, dt_kick_hydro, dt_kick_grav, v[3])`` gets
+ the drifted velocities; this is just ``a_hydro * dt_kick_hydro`` + ``a_grav *
+ dt_kick_grav`` in most implementations.
++ ``hydro_get_energy_dt(p)`` returns the time derivative of the (comoving) internal
+ energy of the particle.
++ ``hydro_set_energy_dt(p)`` sets the time derivative of the (comoving) internal
+ energy of the particle.
++ ``hydro_compute_timestep(p, xp, hydro_props, cosmo)`` returns the timestep for
+ the hydrodynamics particles.
++ ``hydro_timestep_extra(p, dt)`` does some extra hydro operations once the
+ physical timestel for the particle is known.
++ ``hydro_init_part(p, hydro_space)`` initialises the particle in preparation for
+ the density calculation. This essentially sets properties, such as the density,
+ to zero.
++ ``hydro_end_density(p, cosmo)`` performs operations directly after the density
+ loop on each particle. Note that you will have to add a particle's self-contribution
+ at this stage as particles are never 'interacted' with themselves.
++ ``hydro_part_has_no_neighbours(p, xp, cosmo)`` resets properties to a sensible
+ value if a particle is found to have no neighbours.
++ ``hydro_prepare_force(p, xp, cosmo)`` is computed for each particle before the
+ force loop. You can use this to pre-compute particle properties that are used
+ in the force loop, but only depend on the particle itself.
++ ``hydro_reset_acceleration(p)`` resets the acceleration variables of the particles
+ to zero in preparation for the force loop.
++ ``hydro_predict_extra(p, xp, dt_drift, dt_therm)`` predicts extra particle properties
+ when drifting, such as the smoothing length.
++ ``hydro_end_force(p, cosmo)`` is called after the force loop for each particle and
+ can be used to e.g. include overall factors of the smoothing length.
++ ``hydro_kick_extra(p, xp, dt_therm)`` kicks extra variables.
++ ``hydro_convert_quantities(p, xp)`` converts quantities at the start of a run (e.g.
+ internal energy to entropy).
++ ``hydro_first_init_part(p, xp)`` is called for every particle at the start of a run
+ and is used to initialise variables.
+
+
+``hydro_debug.h``
+-----------------
+
+TBD
+
+
+``hydro_iact.h``
+----------------
+
+TBD
+
+
+``hydro_io.h``
+--------------
+
+TBD
+
+
+``hydro_part.h``
+----------------
+
+TBD
+
diff --git a/doc/RTD/source/HydroSchemes/gizmo.rst b/doc/RTD/source/HydroSchemes/gizmo.rst
new file mode 100644
index 0000000000000000000000000000000000000000..365e1dc41c27f7c92bfb33859bedad2d96f35248
--- /dev/null
+++ b/doc/RTD/source/HydroSchemes/gizmo.rst
@@ -0,0 +1,27 @@
+.. GIZMO (MFV)
+ Josh Borrow, 5th April 2018
+
+GIZMO-Like Scheme
+=================
+
+.. toctree::
+ :maxdepth: 2
+ :hidden:
+ :caption: Contents:
+
+
+There is a meshless finite volume (MFV) GIZMO-like scheme implemented in SWIFT
+(see Hopkins 2015 for more information). You will need a Riemann solver to run
+this, and configure as follows:
+
+.. code-block:: bash
+
+ ./configure --with-hydro="gizmo-mfv" --with-riemann-solver="hllc"
+
+
+We also have the meshless finite mass (MFM) GIZMO-like scheme. You can select
+this at compile-time with the following configuration flags:
+
+.. code-block:: bash
+
+ ./configure --with-hydro="gizmo-mfm" --with-riemann-solver="hllc"
diff --git a/doc/RTD/source/HydroSchemes/hopkins_sph.rst b/doc/RTD/source/HydroSchemes/hopkins_sph.rst
new file mode 100644
index 0000000000000000000000000000000000000000..bcc51e0ad96b18956f1c8e54f7bf2bf3b352c138
--- /dev/null
+++ b/doc/RTD/source/HydroSchemes/hopkins_sph.rst
@@ -0,0 +1,30 @@
+.. 'Hopkins'-SPH
+ Josh Borrow 5th April 2018
+
+Pressure-Entropy SPH
+====================
+
+.. toctree::
+ :maxdepth: 2
+ :hidden:
+ :caption: Contents:
+
+A pressure-entropy SPH scheme is available in SWIFT, inspired by Hopkins 2013.
+This includes a Monaghan AV scheme and a Balsara switch.
+
+
+.. code-block:: bash
+
+ ./configure --with-hydro="pressure-entropy"
+
+
+Pressure-Energy SPH
+===================
+
+Pressure-energy SPH is now implemented in SWIFT, and like the pressure-entropy
+scheme it includes a Monaghan AV scheme and a Balsara switch.
+
+
+.. code-block:: bash
+
+ ./configure --with-hydro="pressure-energy"
diff --git a/doc/RTD/source/HydroSchemes/index.rst b/doc/RTD/source/HydroSchemes/index.rst
new file mode 100644
index 0000000000000000000000000000000000000000..cd6c169245e83440a1258d216991763488586c0c
--- /dev/null
+++ b/doc/RTD/source/HydroSchemes/index.rst
@@ -0,0 +1,21 @@
+.. Hydrodynamics Schemes
+ Josh Borrow 4th April 2018
+
+.. _hydro:
+
+Hydrodynamics Schemes
+=====================
+
+This section of the documentation includes information on the hydrodynamics
+schemes available in SWIFT, as well as how to implement your own.
+
+.. toctree::
+ :maxdepth: 2
+ :caption: Contents:
+
+ traditional_sph
+ minimal_sph
+ hopkins_sph
+ gizmo
+ adding_your_own
+
diff --git a/doc/RTD/source/HydroSchemes/minimal_sph.rst b/doc/RTD/source/HydroSchemes/minimal_sph.rst
new file mode 100644
index 0000000000000000000000000000000000000000..1a16a23360aaba8b28920150af0d4f4b05c74c2f
--- /dev/null
+++ b/doc/RTD/source/HydroSchemes/minimal_sph.rst
@@ -0,0 +1,20 @@
+.. Minimal SPH
+ Josh Borrow 4th April 2018
+
+Minimal (Density-Energy) SPH
+============================
+
+.. toctree::
+ :maxdepth: 2
+ :hidden:
+ :caption: Contents:
+
+This scheme is a textbook implementation of Density-Energy SPH, and can be used
+as a pedagogical example. It also implements a Monaghan AV scheme, like the
+GADGET-2 scheme. It uses very similar equations, but differs in implementation
+details; namely it tracks the internal energy \(u\) as the thermodynamic
+variable, rather than entropy \(A\). To use the minimal scheme, use
+
+.. code-block:: bash
+
+ ./configure --with-hydro="minimal"
diff --git a/doc/RTD/source/HydroSchemes/traditional_sph.rst b/doc/RTD/source/HydroSchemes/traditional_sph.rst
new file mode 100644
index 0000000000000000000000000000000000000000..c69ea5f60644119b8590414ffe00a75246de49a6
--- /dev/null
+++ b/doc/RTD/source/HydroSchemes/traditional_sph.rst
@@ -0,0 +1,17 @@
+.. Traditional SPH (GADGET-2)
+ Josh Borrow 4th April 2018
+
+Traditional (Density-Entropy) SPH
+=================================
+
+.. toctree::
+ :maxdepth: 2
+ :hidden:
+ :caption: Contents:
+
+Traditional, GADGET-2-like, Density-Entropy SPH is available in SWIFT with
+a Monaghan artificial viscosity scheme and Balsara switch.
+
+To use this hydro scheme, you need no extra configuration options -- it is the
+default!
+
diff --git a/doc/RTD/source/InitialConditions/index.rst b/doc/RTD/source/InitialConditions/index.rst
new file mode 100644
index 0000000000000000000000000000000000000000..e9684ac4ffde5886f7a110de2cd7fb0fbb572a5e
--- /dev/null
+++ b/doc/RTD/source/InitialConditions/index.rst
@@ -0,0 +1,176 @@
+.. Initial Conditions
+ Josh Borrow, 5th April 2018
+
+Initial Conditions
+==================
+
+To run anything more than examples from our suite, you will need to be able to
+produce your own initial conditions for SWIFT. We use the same initial conditions
+as the popular GADGET-2 code, which uses the HDF5 file format.
+
+As the original documentation for the GADGET-2 initial conditions format is
+quite sparse, we lay out here all of the necessary components. If you are generating
+your initial conditions from python, we recommend you use the h5py package. We
+provide a writing wrapper for this for our initial conditions in
+``examples/KeplerianRing/write_gadget.py``.
+
+You can find out more about the HDF5 format on their webpages, here:
+https://support.hdfgroup.org/HDF5/doc/H5.intro.html
+
+
+Structure of the File
+---------------------
+
+There are several groups that contain 'auxilliary' information, such as ``Header``.
+Particle data is placed in groups that signify particle type.
+
++---------------------+------------------------+
+| Group Name | Physical Particle Type |
++=====================+========================+
+| ``PartType0`` | Gas |
++---------------------+------------------------+
+| ``PartType1`` | Dark Matter |
++---------------------+------------------------+
+| ``PartType2`` | Ignored |
++---------------------+------------------------+
+| ``PartType3`` | Ignored |
++---------------------+------------------------+
+| ``PartType4`` | Stars |
++---------------------+------------------------+
+| ``PartType5`` | Black Holes |
++---------------------+------------------------+
+
+Currently, not all of these particle types are included in SWIFT. Note that the
+only particles that have hydrodynamical forces calculated between them are those
+in ``PartType0``.
+
+
+Necessary Components
+--------------------
+
+There are several necessary components (in particular header information) in a
+SWIFT initial conditions file. Again, we recommend that you use the ``write_gadget``
+script.
+
+Header
+~~~~~~
+
+In ``Header``, the following attributes are required:
+
++ ``BoxSize``, a floating point number or N-dimensional (usually 3) array
+ that describes the size of the box.
++ ``Flag_Entropy_ICs``, a historical value that tells the code if you have
+ included entropy or internal energy values in your intial conditions files.
+ Acceptable values are 0 or 1.
++ ``NumPart_Total``, a length 6 array of integers that tells the code how many
+ particles are of each type are in the initial conditions file.
++ ``NumPart_Total_HighWord``, a historical length-6 array that tells the code
+ the number of high word particles in the initial conditions there are. If
+ you are unsure, just set this to ``[0, 0, 0, 0, 0, 0]``. This does have to be
+ present, but unlike GADGET-2, this can be a set of 0s unless you have more than
+ 2^31 particles.
++ ``NumFilesPerSnapshot``, again a historical integer value that tells the code
+ how many files there are per snapshot. You will probably want to set this to 1
+ and simply have a single HDF5 file for your initial conditions; SWIFT can
+ leverage parallel-HDF5 to read from this single file in parallel.
++ ``NumPart_ThisFile``, a length 6 array of integers describing the number of
+ particles in this file. If you have followed the above advice, this will be
+ exactly the same as the ``NumPart_Total`` array.
+
+You may want to include the following for backwards-compatibility with many
+GADGET-2 based analysis programs:
+
++ ``MassTable``, an array of length 6 which gives the masses of each particle
+ type. SWIFT ignores this and uses the individual particle masses, but some
+ programs will crash if it is not included.
++ ``Time``, the internal code time of the start (set this to 0).
+
+RuntimePars
+~~~~~~~~~~~
+
+In ``RuntimePars``, the following attributes are required:
+
++ ``PeriodicBoundaryConditionsOn``, a flag to tell the code whether or not you
+ have periodic boundaries switched on. Again, this is historical; it should be
+ set to 1 (default) if you have the code running in periodic mode, or 0 otherwise.
+
+
+Units
+~~~~~
+
+In ``Units``, you will need to specify what units your initial conditions are
+in. If these are not present, the code assumes that you are using the same
+units for your initial conditions as are in your parameterfile, but it is best
+to include them to be on the safe side. You will need:
+
++ ``Unit current in cgs (U_I)``
++ ``Unit length in cgs (U_L)``
++ ``Unit mass in cgs (U_M)``
++ ``Unit temperature in cgs (U_T)``
++ ``Unit time in cgs (U_t)``
+
+These are all floating point numbers.
+
+
+Particle Data
+~~~~~~~~~~~~~
+
+Now for the interesting part! You can include particle data groups for each
+individual particle type (e.g. ``PartType0``) that have the following _datasets_:
+
++ ``Coordinates``, an array of shape (N, 3) where N is the number of particles
+ of that type, that are the cartesian co-ordinates of the particles. Co-ordinates
+ must be positive, but will be wrapped on reading to be within the periodic box.
++ ``Velocities``, an array of shape (N, 3) that is the cartesian velocities
+ of the particles.
++ ``ParticleIDs``, an array of length N that are unique identifying numbers for
+ each particle. Note that these have to be unique to a particle, and cannot be
+ the same even between particle types. Please ensure that your IDs are positive
+ integer numbers.
++ ``Masses``, an array of length N that gives the masses of the particles.
+
+For ``PartType0`` (i.e. particles that interact through hydrodynamics), you will
+need the following auxilliary items:
+
++ ``InternalEnergy``, an array of length N that gives the internal energies of
+ the particles. For PressureEntropy, you can specify ``Entropy`` instead.
++ ``SmoothingLength``, the smoothing lenghts of the particles. These will be
+ tidied up a bit, but it is best if you provide accurate numbers.
+
+
+Summary
+~~~~~~~
+
+You should have an HDF5 file with the following structure:
+
+.. code-block:: bash
+
+ Header/
+ BoxSize=[x, y, z]
+ Flag_Entropy_ICs=1
+ NumPart_Total=[0, 1, 2, 3, 4, 5]
+ NumPart_Total_HighWord=[0, 0, 0, 0, 0, 0]
+ NumFilesPerSnapshot=1
+ NumPart_ThisFile=[0, 1, 2, 3, 4, 5]
+ RuntimePars/
+ PeriodicBoundariesOn=1
+ Units/
+ Unit current in cgs (U_I)=1.0
+ Unit length in cgs (U_L)=1.0
+ Unit mass in cgs (U_M)=1.0
+ Unit temperature in cgs (U_T)=1.0
+ Unit time in cgs (U_t)=1.0
+ PartType0/
+ Coordinates=[[x, y, z]]
+ Velocities=[[vx, vy, vz]]
+ ParticleIDs=[...]
+ Masses=[...]
+ InternalEnergy=[...]
+ SmoothingLength=[...]
+ PartType1/
+ Coordinates=[[x, y, z]]
+ Velocities=[[vx, vy, vz]]
+ ParticleIDs=[...]
+ Masses=[...]
+
+
diff --git a/doc/RTD/source/NewOption/index.rst b/doc/RTD/source/NewOption/index.rst
new file mode 100644
index 0000000000000000000000000000000000000000..a7445524017fefd99d76c80a4a1ecc646874bd7a
--- /dev/null
+++ b/doc/RTD/source/NewOption/index.rst
@@ -0,0 +1,36 @@
+.. Equation of State
+ Loic Hausammann, 7th April 2018
+
+.. _new_option:
+
+General information for adding new schemes
+==========================================
+
+The following steps are required for any new options (such as new
+:ref:`hydro`, :ref:`chemistry`, :ref:`cooling`,
+:ref:`equation_of_state`, :ref:`stars` or :ref:`gravity`)
+
+In order to add a new scheme, you will need to:
+
+1. Create a new subdirectory inside the option directory (e.g.
+ ``src/equation_of_state`` or ``src/hydro``) with an explicit name.
+
+2. Create the required new files (depending on your option, you will need
+ different files). Copy the structure of the most simple option (e.g.
+ ``src/hydro/Gadget2``, ``src/gravity/Default``, ``src/stars/Default``,
+ ``src/cooling/none``, ``src/chemistry/none`` or
+ ``src/equation_of_state/ideal_gas``)
+
+3. Add the right includes in the option file (e.g. ``src/hydro.h``,
+ ``src/gravity.h``, ``src/stars.h``, ``src/cooling.h``, ``src/chemistry.h``
+ or ``src/equation_of_state.h``) and the corresponding io file if present.
+
+4. Add the new option in ``configure.ac``. This file generates the
+ ``configure`` script and you just need to add a new option under the right
+ ``case``.
+
+5. Add your files in ``src/Makefile.am``. In order to generate the Makefiles
+ during the configuration step, a list of files is required. In
+ ``nobase_noinst_HEADERS``, add your new header files.
+
+6. Update the documentation. Add your equations/documentation to ``doc/RTD``.
diff --git a/doc/RTD/source/conf.py b/doc/RTD/source/conf.py
new file mode 100644
index 0000000000000000000000000000000000000000..031687ea5228252e2d2e44ec0bd6f53b1b64d732
--- /dev/null
+++ b/doc/RTD/source/conf.py
@@ -0,0 +1,165 @@
+# -*- coding: utf-8 -*-
+#
+# Configuration file for the Sphinx documentation builder.
+#
+# This file does only contain a selection of the most common options. For a
+# full list see the documentation:
+# http://www.sphinx-doc.org/en/stable/config
+
+# -- Path setup --------------------------------------------------------------
+
+# If extensions (or modules to document with autodoc) are in another directory,
+# add these directories to sys.path here. If the directory is relative to the
+# documentation root, use os.path.abspath to make it absolute, like shown here.
+#
+# import os
+# import sys
+# sys.path.insert(0, os.path.abspath('.'))
+
+# -- Project information -----------------------------------------------------
+
+project = 'SWIFT: SPH WIth Fine-grained inter-dependent Tasking'
+copyright = '2018, SWIFT Collaboration'
+author = 'SWIFT Team'
+
+# The short X.Y version
+version = '0.7'
+# The full version, including alpha/beta/rc tags
+release = '0.7.0'
+
+
+# -- General configuration ---------------------------------------------------
+
+# If your documentation needs a minimal Sphinx version, state it here.
+#
+# needs_sphinx = '1.0'
+
+# Add any Sphinx extension module names here, as strings. They can be
+# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
+# ones.
+extensions = [
+ 'sphinx.ext.todo',
+ 'sphinx.ext.mathjax',
+ 'sphinx.ext.githubpages',
+]
+
+# Add any paths that contain templates here, relative to this directory.
+templates_path = ['.templates']
+
+# The suffix(es) of source filenames.
+# You can specify multiple suffix as a list of string:
+#
+# source_suffix = ['.rst', '.md']
+source_suffix = '.rst'
+
+# The master toctree document.
+master_doc = 'index'
+
+# The language for content autogenerated by Sphinx. Refer to documentation
+# for a list of supported languages.
+#
+# This is also used if you do content translation via gettext catalogs.
+# Usually you set "language" from the command line for these cases.
+language = None
+
+# List of patterns, relative to source directory, that match files and
+# directories to ignore when looking for source files.
+# This pattern also affects html_static_path and html_extra_path .
+exclude_patterns = []
+
+# The name of the Pygments (syntax highlighting) style to use.
+pygments_style = 'sphinx'
+
+
+# -- Options for HTML output -------------------------------------------------
+
+# The theme to use for HTML and HTML Help pages. See the documentation for
+# a list of builtin themes.
+#
+html_theme = 'sphinx_rtd_theme'
+
+# Theme options are theme-specific and customize the look and feel of a theme
+# further. For a list of options available for each theme, see the
+# documentation.
+#
+# html_theme_options = {}
+
+# Add any paths that contain custom static files (such as style sheets) here,
+# relative to this directory. They are copied after the builtin static files,
+# so a file named "default.css" will overwrite the builtin "default.css".
+html_static_path = ['.static']
+
+# Custom sidebar templates, must be a dictionary that maps document names
+# to template names.
+#
+# The default sidebars (for documents that don't match any pattern) are
+# defined by theme itself. Builtin themes are using these templates by
+# default: ``['localtoc.html', 'relations.html', 'sourcelink.html',
+# 'searchbox.html']``.
+#
+# html_sidebars = {}
+
+
+# -- Options for HTMLHelp output ---------------------------------------------
+
+# Output file base name for HTML help builder.
+htmlhelp_basename = 'SWIFTSPHWIthFine-grainedinter-dependentTaskingdoc'
+
+
+# -- Options for LaTeX output ------------------------------------------------
+
+latex_elements = {
+ # The paper size ('letterpaper' or 'a4paper').
+ #
+ # 'papersize': 'letterpaper',
+
+ # The font size ('10pt', '11pt' or '12pt').
+ #
+ # 'pointsize': '10pt',
+
+ # Additional stuff for the LaTeX preamble.
+ #
+ # 'preamble': '',
+
+ # Latex figure (float) alignment
+ #
+ # 'figure_align': 'htbp',
+}
+
+# Grouping the document tree into LaTeX files. List of tuples
+# (source start file, target name, title,
+# author, documentclass [howto, manual, or own class]).
+latex_documents = [
+ (master_doc, 'SWIFTSPHWIthFine-grainedinter-dependentTasking.tex', 'SWIFT: SPH WIth Fine-grained inter-dependent Tasking Documentation',
+ 'Josh Borrow', 'manual'),
+]
+
+
+# -- Options for manual page output ------------------------------------------
+
+# One entry per manual page. List of tuples
+# (source start file, name, description, authors, manual section).
+man_pages = [
+ (master_doc, 'swiftsphwithfine-grainedinter-dependenttasking', 'SWIFT: SPH WIth Fine-grained inter-dependent Tasking Documentation',
+ [author], 1)
+]
+
+
+# -- Options for Texinfo output ----------------------------------------------
+
+# Grouping the document tree into Texinfo files. List of tuples
+# (source start file, target name, title, author,
+# dir menu entry, description, category)
+texinfo_documents = [
+ (master_doc, 'SWIFTSPHWIthFine-grainedinter-dependentTasking', 'SWIFT: SPH WIth Fine-grained inter-dependent Tasking Documentation',
+ author, 'SWIFTSPHWIthFine-grainedinter-dependentTasking', 'One line description of project.',
+ 'Miscellaneous'),
+]
+
+
+# -- Extension configuration -------------------------------------------------
+
+# -- Options for todo extension ----------------------------------------------
+
+# If true, `todo` and `todoList` produce output, else they produce nothing.
+todo_include_todos = True
diff --git a/doc/RTD/source/index.rst b/doc/RTD/source/index.rst
new file mode 100644
index 0000000000000000000000000000000000000000..888945a5c0101bb6f59b574a30f1f736ad134079
--- /dev/null
+++ b/doc/RTD/source/index.rst
@@ -0,0 +1,22 @@
+.. Welcome!
+ sphinx-quickstart on Wed Apr 4 15:03:50 2018.
+ You can adapt this file completely to your liking, but it should at least
+ contain the root `toctree` directive.
+
+Welcome to SWIFT: SPH WIth Fine-grained inter-dependent Tasking's documentation!
+================================================================================
+
+Want to get started using SWIFT? Check out the on-boarding guide available
+here. SWIFT can be used as a drop-in replacement for Gadget-2 and initial
+conditions in hdf5 format for Gadget can directly be read by SWIFT. The only
+difference is the parameter file that will need to be adapted for SWIFT.
+
+.. toctree::
+ :maxdepth: 2
+
+ GettingStarted/index
+ InitialConditions/index
+ HydroSchemes/index
+ Cooling/index
+ EquationOfState/index
+ NewOption/index
diff --git a/examples/EAGLE_100/eagle_100.yml b/examples/EAGLE_100/eagle_100.yml
index a570d81f403b303a41f286cc2407ce39e10735b9..223da63701817260b32ff6718273c2cf2f08e6bf 100644
--- a/examples/EAGLE_100/eagle_100.yml
+++ b/examples/EAGLE_100/eagle_100.yml
@@ -31,7 +31,7 @@ Snapshots:
scale_factor_first: 0.92 # Scale-factor of the first snaphot (cosmological run)
time_first: 0.01 # Time of the first output (non-cosmological run) (in internal units)
delta_time: 1.10 # Time difference between consecutive outputs (in internal units)
- compression: 4
+ compression: 1
# Parameters governing the conserved quantities statistics
Statistics:
diff --git a/examples/EAGLE_12/eagle_12.yml b/examples/EAGLE_12/eagle_12.yml
index e400610d967e6a821cc46495c827a52bc42ea1aa..14035500366e9b260e77d94bcefa9c529874f35f 100644
--- a/examples/EAGLE_12/eagle_12.yml
+++ b/examples/EAGLE_12/eagle_12.yml
@@ -31,7 +31,7 @@ Snapshots:
scale_factor_first: 0.92 # Scale-factor of the first snaphot (cosmological run)
time_first: 0.01 # Time of the first output (non-cosmological run) (in internal units)
delta_time: 1.10 # Time difference between consecutive outputs (in internal units)
- compression: 4
+ compression: 1
# Parameters governing the conserved quantities statistics
Statistics:
diff --git a/examples/EAGLE_25/eagle_25.yml b/examples/EAGLE_25/eagle_25.yml
index 2a478d822cf911ca543b61900d491c05946c70ce..462ce3791204859d7d213234cac8a87e5a2c92e0 100644
--- a/examples/EAGLE_25/eagle_25.yml
+++ b/examples/EAGLE_25/eagle_25.yml
@@ -31,7 +31,6 @@ Snapshots:
scale_factor_first: 0.92 # Scale-factor of the first snaphot (cosmological run)
time_first: 0.01 # Time of the first output (non-cosmological run) (in internal units)
delta_time: 1.10 # Time difference between consecutive outputs (in internal units)
- compression: 4
# Parameters governing the conserved quantities statistics
Statistics:
diff --git a/examples/EAGLE_50/eagle_50.yml b/examples/EAGLE_50/eagle_50.yml
index 5e4193e5c1c6295ded19e12bf50f6e156d797656..1eca096132cff59b2db41ee6a0166456fa21549e 100644
--- a/examples/EAGLE_50/eagle_50.yml
+++ b/examples/EAGLE_50/eagle_50.yml
@@ -31,7 +31,7 @@ Snapshots:
scale_factor_first: 0.92 # Scale-factor of the first snaphot (cosmological run)
time_first: 0.01 # Time of the first output (non-cosmological run) (in internal units)
delta_time: 1.10 # Time difference between consecutive outputs (in internal units)
- compression: 4
+ compression: 1
# Parameters governing the conserved quantities statistics
Statistics:
diff --git a/examples/EAGLE_6/eagle_6.yml b/examples/EAGLE_6/eagle_6.yml
index 0be082dd758a974ff9c9b1c0284e3a2a3efa6d00..bac3561b08dcd018c3a8189df3a1228350658396 100644
--- a/examples/EAGLE_6/eagle_6.yml
+++ b/examples/EAGLE_6/eagle_6.yml
@@ -32,7 +32,7 @@ Snapshots:
scale_factor_first: 0.92 # Scale-factor of the first snaphot (cosmological run)
time_first: 0.01 # Time of the first output (non-cosmological run) (in internal units)
delta_time: 1.10 # Time difference between consecutive outputs (in internal units)
- compression: 4
+ compression: 1
# Parameters governing the conserved quantities statistics
Statistics:
diff --git a/examples/EAGLE_DMO_100/eagle_100.yml b/examples/EAGLE_DMO_100/eagle_100.yml
index 0548980cc6b2a785eb55781f213da4d3980cd9d5..9295aff6e21f5321cd63e7a544cce9912e3929a8 100644
--- a/examples/EAGLE_DMO_100/eagle_100.yml
+++ b/examples/EAGLE_DMO_100/eagle_100.yml
@@ -31,7 +31,7 @@ Snapshots:
scale_factor_first: 0.92 # Scale-factor of the first snaphot (cosmological run)
time_first: 0.01 # Time of the first output (non-cosmological run) (in internal units)
delta_time: 1.10 # Time difference between consecutive outputs (in internal units)
- compression: 4
+ compression: 1
# Parameters governing the conserved quantities statistics
Statistics:
diff --git a/examples/EAGLE_DMO_12/eagle_12.yml b/examples/EAGLE_DMO_12/eagle_12.yml
index f76ca2f833cfe2722ef6b68bf4105c0344a569bd..1e5d99b0abcf4cdb67c6b41c417f1e95aad5c187 100644
--- a/examples/EAGLE_DMO_12/eagle_12.yml
+++ b/examples/EAGLE_DMO_12/eagle_12.yml
@@ -31,7 +31,7 @@ Snapshots:
scale_factor_first: 0.92 # Scale-factor of the first snaphot (cosmological run)
time_first: 0.01 # Time of the first output (non-cosmological run) (in internal units)
delta_time: 1.10 # Time difference between consecutive outputs (in internal units)
- compression: 4
+ compression: 1
# Parameters governing the conserved quantities statistics
Statistics:
diff --git a/examples/EAGLE_DMO_25/eagle_25.yml b/examples/EAGLE_DMO_25/eagle_25.yml
index 4b8dcf7bf30b62ff65bbe44f4a80b31b320d167e..f31d167cc0a011121bbac85b34b8e16ce6b61bf8 100644
--- a/examples/EAGLE_DMO_25/eagle_25.yml
+++ b/examples/EAGLE_DMO_25/eagle_25.yml
@@ -31,7 +31,7 @@ Snapshots:
scale_factor_first: 0.92 # Scale-factor of the first snaphot (cosmological run)
time_first: 0.01 # Time of the first output (non-cosmological run) (in internal units)
delta_time: 1.10 # Time difference between consecutive outputs (in internal units)
- compression: 4
+ compression: 1
# Parameters governing the conserved quantities statistics
Statistics:
diff --git a/examples/EAGLE_DMO_50/eagle_50.yml b/examples/EAGLE_DMO_50/eagle_50.yml
index 181b633c498fd4b4b4b17a7bffbd32aabc1d4726..2526fa1509ba3a21870ccfcd186bf7b70f6e0ced 100644
--- a/examples/EAGLE_DMO_50/eagle_50.yml
+++ b/examples/EAGLE_DMO_50/eagle_50.yml
@@ -31,7 +31,7 @@ Snapshots:
scale_factor_first: 0.92 # Scale-factor of the first snaphot (cosmological run)
time_first: 0.01 # Time of the first output (non-cosmological run) (in internal units)
delta_time: 1.10 # Time difference between consecutive outputs (in internal units)
- compression: 4
+ compression: 1
# Parameters governing the conserved quantities statistics
Statistics:
diff --git a/examples/EvrardCollapse_3D/evrard.yml b/examples/EvrardCollapse_3D/evrard.yml
index a2b39fb1e7fa36098abe720945ece4b611eb4fe8..f9a4e69f72e6bb19b818cb985ef92122b1a10b2a 100644
--- a/examples/EvrardCollapse_3D/evrard.yml
+++ b/examples/EvrardCollapse_3D/evrard.yml
@@ -18,7 +18,7 @@ Snapshots:
basename: evrard # Common part of the name of output files
time_first: 0. # Time of the first output (in internal units)
delta_time: 0.1 # Time difference between consecutive outputs (in internal units)
- compression: 4
+ compression: 1
# Parameters governing the conserved quantities statistics
Statistics:
diff --git a/examples/GreshoVortex_3D/gresho.yml b/examples/GreshoVortex_3D/gresho.yml
index f42fcbfd00941e7b9c5c09c0d2e3118f5cc1f57d..113c03b9bd0e411bf04f29c70937ac7fab3708f3 100644
--- a/examples/GreshoVortex_3D/gresho.yml
+++ b/examples/GreshoVortex_3D/gresho.yml
@@ -21,7 +21,7 @@ Snapshots:
basename: gresho # Common part of the name of output files
time_first: 0. # Time of the first output (in internal units)
delta_time: 1e-1 # Time difference between consecutive outputs (in internal units)
- compression: 4
+ compression: 1
# Parameters governing the conserved quantities statistics
Statistics:
diff --git a/examples/KelvinHelmholtzGrowthRate_3D/kelvinHelmholtzGrowthRate.yml b/examples/KelvinHelmholtzGrowthRate_3D/kelvinHelmholtzGrowthRate.yml
index 3133e2769e81b80c18760e8258665fc1a6eee6ca..e39c01645b766ae585558452683dc8e1bdf425a8 100644
--- a/examples/KelvinHelmholtzGrowthRate_3D/kelvinHelmholtzGrowthRate.yml
+++ b/examples/KelvinHelmholtzGrowthRate_3D/kelvinHelmholtzGrowthRate.yml
@@ -18,7 +18,7 @@ Snapshots:
basename: kelvinHelmholtzGrowthRate # Common part of the name of output files
time_first: 0. # Time of the first output (in internal units)
delta_time: 0.04 # Time difference between consecutive outputs (in internal units)
- compression: 4
+ compression: 1
# Parameters governing the conserved quantities statistics
Statistics:
diff --git a/examples/Makefile.am b/examples/Makefile.am
index 95057c9bee7d3b4cc001d6c19ca39cab5d8544c4..9de393ba6c77f9bd50e1d8aff12c0d83ba8e7ddc 100644
--- a/examples/Makefile.am
+++ b/examples/Makefile.am
@@ -24,7 +24,7 @@ AM_CFLAGS = -I$(top_srcdir)/src $(HDF5_CPPFLAGS) $(GSL_INCS) $(FFTW_INCS)
AM_LDFLAGS = $(HDF5_LDFLAGS)
# Extra libraries.
-EXTRA_LIBS = $(HDF5_LIBS) $(FFTW_LIBS) $(PROFILER_LIBS) $(TCMALLOC_LIBS) $(JEMALLOC_LIBS) $(GRACKLE_LIBS) $(GSL_LIBS)
+EXTRA_LIBS = $(HDF5_LIBS) $(FFTW_LIBS) $(PROFILER_LIBS) $(TCMALLOC_LIBS) $(JEMALLOC_LIBS) $(TBBMALLOC_LIBS) $(GRACKLE_LIBS) $(GSL_LIBS)
# MPI libraries.
MPI_LIBS = $(METIS_LIBS) $(MPI_THREAD_LIBS)
diff --git a/examples/Noh_3D/noh.yml b/examples/Noh_3D/noh.yml
index 88119827501e17cc26742e8cad92a3611e83faa7..cc15af7ec190cd2c10cdff3a3ccb3f0beaf7e177 100644
--- a/examples/Noh_3D/noh.yml
+++ b/examples/Noh_3D/noh.yml
@@ -18,7 +18,7 @@ Snapshots:
basename: noh # Common part of the name of output files
time_first: 0. # Time of the first output (in internal units)
delta_time: 5e-2 # Time difference between consecutive outputs (in internal units)
- compression: 4
+ compression: 1
# Parameters governing the conserved quantities statistics
Statistics:
diff --git a/examples/SedovBlast_3D/sedov.yml b/examples/SedovBlast_3D/sedov.yml
index 2df2c432cef8afec49c687b643a872b06f9abb60..75849e33c0c644a18cd7357f901699d0d682c160 100644
--- a/examples/SedovBlast_3D/sedov.yml
+++ b/examples/SedovBlast_3D/sedov.yml
@@ -18,8 +18,8 @@ Snapshots:
basename: sedov # Common part of the name of output files
time_first: 0. # Time of the first output (in internal units)
delta_time: 1e-2 # Time difference between consecutive outputs (in internal units)
- compression: 4
-
+ compression: 1
+
# Parameters governing the conserved quantities statistics
Statistics:
delta_time: 1e-3 # Time between statistics output
@@ -33,4 +33,4 @@ SPH:
InitialConditions:
file_name: ./sedov.hdf5
smoothing_length_scaling: 3.33
-
+
diff --git a/examples/SodShockSpherical_3D/sodShock.yml b/examples/SodShockSpherical_3D/sodShock.yml
index 52c06dd65ec0b37a0ec0707315ccd15356a7b2d6..3fc4a1fb2b8cc5f6a603abf4c87ac99c7647b9bd 100644
--- a/examples/SodShockSpherical_3D/sodShock.yml
+++ b/examples/SodShockSpherical_3D/sodShock.yml
@@ -18,7 +18,7 @@ Snapshots:
basename: sodShock # Common part of the name of output files
time_first: 0. # Time of the first output (in internal units)
delta_time: 0.1 # Time difference between consecutive outputs (in internal units)
- compression: 4
+ compression: 1
# Parameters governing the conserved quantities statistics
Statistics:
diff --git a/examples/SodShock_3D/sodShock.yml b/examples/SodShock_3D/sodShock.yml
index 26fbfe4faacf2bbbfd9b077bf9f9c075ce93ef6d..6042c8090d00fef5467a7fed3d6f5a104c626f43 100644
--- a/examples/SodShock_3D/sodShock.yml
+++ b/examples/SodShock_3D/sodShock.yml
@@ -18,7 +18,7 @@ Snapshots:
basename: sodShock # Common part of the name of output files
time_first: 0. # Time of the first output (in internal units)
delta_time: 0.2 # Time difference between consecutive outputs (in internal units)
- compression: 4
+ compression: 1
# Parameters governing the conserved quantities statistics
Statistics:
diff --git a/examples/VacuumSpherical_3D/vacuum.yml b/examples/VacuumSpherical_3D/vacuum.yml
index 92164a18a46404ad7730f3411dc14953139501bb..8792f029d97f413882ae0ea6c8603d64efaddbfa 100644
--- a/examples/VacuumSpherical_3D/vacuum.yml
+++ b/examples/VacuumSpherical_3D/vacuum.yml
@@ -18,7 +18,7 @@ Snapshots:
basename: vacuum # Common part of the name of output files
time_first: 0. # Time of the first output (in internal units)
delta_time: 0.05 # Time difference between consecutive outputs (in internal units)
- compression: 4
+ compression: 1
# Parameters governing the conserved quantities statistics
Statistics:
diff --git a/examples/Vacuum_3D/vacuum.yml b/examples/Vacuum_3D/vacuum.yml
index 45a6b73d54de69d71e194ec074ebdd00cd6a57c0..cf44d2441f5009d2fc75084a2c872e3618e40912 100644
--- a/examples/Vacuum_3D/vacuum.yml
+++ b/examples/Vacuum_3D/vacuum.yml
@@ -18,7 +18,7 @@ Snapshots:
basename: vacuum # Common part of the name of output files
time_first: 0. # Time of the first output (in internal units)
delta_time: 0.1 # Time difference between consecutive outputs (in internal units)
- compression: 4
+ compression: 1
# Parameters governing the conserved quantities statistics
Statistics:
diff --git a/examples/main.c b/examples/main.c
index 4d59e97445af2f59cfcd947a805c2ed2a1218ad2..61b32c69dcce8903fbc8e79d382a9dc2bef62e94 100644
--- a/examples/main.c
+++ b/examples/main.c
@@ -54,7 +54,7 @@ struct profiler prof;
/**
* @brief Help messages for the command line parameters.
*/
-void print_help_message() {
+void print_help_message(void) {
printf("\nUsage: swift [OPTION]... PARAMFILE\n");
printf(" swift_mpi [OPTION]... PARAMFILE\n\n");
@@ -90,6 +90,8 @@ void print_help_message() {
printf(" %2s %14s %s\n", "-n", "{int}",
"Execute a fixed number of time steps. When unset use the time_end "
"parameter to stop.");
+ printf(" %2s %14s %s\n", "-o", "{str}",
+ "Generate a default output parameter file.");
printf(" %2s %14s %s\n", "-P", "{sec:par:val}",
"Set parameter value and overwrites values read from the parameters "
"file. Can be used more than once.");
@@ -195,6 +197,7 @@ int main(int argc, char *argv[]) {
int nr_threads = 1;
int with_verbose_timers = 0;
int nparams = 0;
+ char output_parameters_filename[200] = "";
char *cmdparams[PARSER_MAX_NO_OF_PARAMS];
char paramFileName[200] = "";
char restart_file[200] = "";
@@ -202,7 +205,7 @@ int main(int argc, char *argv[]) {
/* Parse the parameters */
int c;
- while ((c = getopt(argc, argv, "acCdDef:FgGhMn:P:rsSt:Tv:y:Y:")) != -1)
+ while ((c = getopt(argc, argv, "acCdDef:FgGhMn:o:P:rsSt:Tv:y:Y:")) != -1)
switch (c) {
case 'a':
#if defined(HAVE_SETAFFINITY) && defined(HAVE_LIBNUMA)
@@ -259,6 +262,15 @@ int main(int argc, char *argv[]) {
return 1;
}
break;
+ case 'o':
+ if (sscanf(optarg, "%s", output_parameters_filename) != 1) {
+ if (myrank == 0) {
+ printf("Error parsing output fields filename");
+ print_help_message();
+ }
+ return 1;
+ }
+ break;
case 'P':
cmdparams[nparams] = optarg;
nparams++;
@@ -324,6 +336,15 @@ int main(int argc, char *argv[]) {
return 1;
break;
}
+
+ /* Write output parameter file */
+ if (myrank == 0 && strcmp(output_parameters_filename, "") != 0) {
+ io_write_output_field_parameter(output_parameters_filename);
+ printf("End of run.\n");
+ return 0;
+ }
+
+ /* check inputs */
if (optind == argc - 1) {
if (!strcpy(paramFileName, argv[optind++]))
error("Error reading parameter file name.");
@@ -447,10 +468,6 @@ int main(int argc, char *argv[]) {
"values.");
for (int k = 0; k < nparams; k++) parser_set_param(params, cmdparams[k]);
}
-
- /* And dump the parameters as used. */
- // parser_print_params(¶ms);
- parser_write_params_to_file(params, "used_parameters.yml");
}
#ifdef WITH_MPI
/* Broadcast the parameter file */
@@ -713,6 +730,9 @@ int main(int argc, char *argv[]) {
"ICs.",
N_total[0], N_total[2], N_total[1]);
+ /* Verify that the fields to dump actually exist */
+ if (myrank == 0) io_check_output_fields(params, N_total);
+
/* Initialize the space with these data. */
if (myrank == 0) clocks_gettime(&tic);
space_init(&s, params, &cosmo, dim, parts, gparts, sparts, Ngas, Ngpart,
@@ -811,6 +831,7 @@ int main(int argc, char *argv[]) {
&cooling_func, &chemistry, &sourceterms);
engine_config(0, &e, params, nr_nodes, myrank, nr_threads, with_aff,
talking, restart_file);
+
if (myrank == 0) {
clocks_gettime(&toc);
message("engine_init took %.3f %s.", clocks_diff(&tic, &toc),
@@ -889,6 +910,13 @@ int main(int argc, char *argv[]) {
0)
error("Failed to generate restart filename");
+ /* dump the parameters as used. */
+
+ /* used parameters */
+ parser_write_params_to_file(params, "used_parameters.yml", 1);
+ /* unused parameters */
+ parser_write_params_to_file(params, "unused_parameters.yml", 0);
+
/* Main simulation loop */
/* ==================== */
int force_stop = 0;
@@ -943,9 +971,10 @@ int main(int argc, char *argv[]) {
/* Open file and position at end. */
file_thread = fopen(dumpfile, "a");
- fprintf(file_thread, " %03i 0 0 0 0 %lli %lli %zi %zi %zi 0 0 %lli\n",
- myrank, e.tic_step, e.toc_step, e.updates, e.g_updates,
- e.s_updates, cpufreq);
+ fprintf(file_thread,
+ " %03d 0 0 0 0 %lld %lld %lld %lld %lld 0 0 %lld\n", myrank,
+ e.tic_step, e.toc_step, e.updates, e.g_updates, e.s_updates,
+ cpufreq);
int count = 0;
for (int l = 0; l < e.sched.nr_tasks; l++) {
if (!e.sched.tasks[l].implicit && e.sched.tasks[l].toc != 0) {
@@ -981,8 +1010,8 @@ int main(int argc, char *argv[]) {
FILE *file_thread;
file_thread = fopen(dumpfile, "w");
/* Add some information to help with the plots */
- fprintf(file_thread, " %i %i %i %i %lli %lli %zi %zi %zi %i %lli\n", -2,
- -1, -1, 1, e.tic_step, e.toc_step, e.updates, e.g_updates,
+ fprintf(file_thread, " %d %d %d %d %lld %lld %lld %lld %lld %d %lld\n",
+ -2, -1, -1, 1, e.tic_step, e.toc_step, e.updates, e.g_updates,
e.s_updates, 0, cpufreq);
for (int l = 0; l < e.sched.nr_tasks; l++) {
if (!e.sched.tasks[l].implicit && e.sched.tasks[l].toc != 0) {
@@ -1035,14 +1064,15 @@ int main(int argc, char *argv[]) {
if (myrank == 0) {
/* Print some information to the screen */
- printf(" %6d %14e %14e %10.5f %14e %4d %4d %12zu %12zu %12zu %21.3f %6d\n",
- e.step, e.time, e.cosmology->a, e.cosmology->z, e.time_step,
- e.min_active_bin, e.max_active_bin, e.updates, e.g_updates,
- e.s_updates, e.wallclock_time, e.step_props);
+ printf(
+ " %6d %14e %14e %10.5f %14e %4d %4d %12lld %12lld %12lld %21.3f %6d\n",
+ e.step, e.time, e.cosmology->a, e.cosmology->z, e.time_step,
+ e.min_active_bin, e.max_active_bin, e.updates, e.g_updates, e.s_updates,
+ e.wallclock_time, e.step_props);
fflush(stdout);
fprintf(e.file_timesteps,
- " %6d %14e %14e %14e %4d %4d %12zu %12zu %12zu %21.3f %6d\n",
+ " %6d %14e %14e %14e %4d %4d %12lld %12lld %12lld %21.3f %6d\n",
e.step, e.time, e.cosmology->a, e.time_step, e.min_active_bin,
e.max_active_bin, e.updates, e.g_updates, e.s_updates,
e.wallclock_time, e.step_props);
diff --git a/examples/parameter_example.yml b/examples/parameter_example.yml
index 791db2758290e400d4ed9ffe5b8e0d4303057874..6eb277b303f440de5f92b31caecc432c54069149 100644
--- a/examples/parameter_example.yml
+++ b/examples/parameter_example.yml
@@ -37,9 +37,10 @@ SPH:
# Parameters for the self-gravity scheme
Gravity:
eta: 0.025 # Constant dimensionless multiplier for time integration.
- theta: 0.7 # Opening angle (Multipole acceptance criterion)
+ theta: 0.7 # Opening angle (Multipole acceptance criterion).
comoving_softening: 0.0026994 # Comoving softening length (in internal units).
max_physical_softening: 0.0007 # Physical softening length (in internal units).
+ rebuild_frequency: 0.01 # (Optional) Frequency of the gravity-tree rebuild in units of the number of g-particles (this is the default value).
a_smooth: 1.25 # (Optional) Smoothing scale in top-level cell sizes to smooth the long-range forces over (this is the default value).
r_cut_max: 4.5 # (Optional) Cut-off in number of top-level cells beyond which no FMM forces are computed (this is the default value).
r_cut_min: 0.1 # (Optional) Cut-off in number of top-level cells below which no truncation of FMM forces are performed (this is the default value).
diff --git a/src/Makefile.am b/src/Makefile.am
index e6e4408e5c7fdfad7a5f1b9abd199c02aea644aa..a28f1c3beb6c6da707845dabea0a7098cf34bdde 100644
--- a/src/Makefile.am
+++ b/src/Makefile.am
@@ -25,7 +25,7 @@ AM_LDFLAGS = $(HDF5_LDFLAGS) $(FFTW_LIBS) -version-info 0:0:0
GIT_CMD = @GIT_CMD@
# Additional dependencies for shared libraries.
-EXTRA_LIBS = $(HDF5_LIBS) $(PROFILER_LIBS) $(TCMALLOC_LIBS) $(JEMALLOC_LIBS) $(GRACKLE_LIB) $(GSL_LIBS)
+EXTRA_LIBS = $(HDF5_LIBS) $(FFTW_LIBS) $(PROFILER_LIBS) $(TCMALLOC_LIBS) $(JEMALLOC_LIBS) $(TBBMALLOC_LIBS) $(GRACKLE_LIB) $(GSL_LIBS)
# MPI libraries.
MPI_LIBS = $(METIS_LIBS) $(MPI_THREAD_LIBS)
diff --git a/src/atomic.h b/src/atomic.h
index bcd79d2bd7c084abf91810149c41b189f3ef1b7b..8232f93b75c95112ca8bc061c71e6b41ac1e16bb 100644
--- a/src/atomic.h
+++ b/src/atomic.h
@@ -39,13 +39,16 @@
*
* This is a text-book implementation based on an atomic CAS.
*
+ * We create a temporary union to cope with the int-only atomic CAS
+ * and the floating-point min that we want.
+ *
* @param address The address to update.
* @param y The value to update the address with.
*/
__attribute__((always_inline)) INLINE static void atomic_min_f(
- volatile float* address, float y) {
+ volatile float *const address, const float y) {
- int* int_ptr = (int*)address;
+ int *const int_ptr = (int *)address;
typedef union {
float as_float;
@@ -90,13 +93,16 @@ __attribute__((always_inline)) INLINE static void atomic_min(
*
* This is a text-book implementation based on an atomic CAS.
*
+ * We create a temporary union to cope with the int-only atomic CAS
+ * and the floating-point max that we want.
+ *
* @param address The address to update.
* @param y The value to update the address with.
*/
__attribute__((always_inline)) INLINE static void atomic_max_f(
- volatile float* address, float y) {
+ volatile float *const address, const float y) {
- int* int_ptr = (int*)address;
+ int *const int_ptr = (int *)address;
typedef union {
float as_float;
@@ -118,13 +124,16 @@ __attribute__((always_inline)) INLINE static void atomic_max_f(
*
* This is a text-book implementation based on an atomic CAS.
*
+ * We create a temporary union to cope with the int-only atomic CAS
+ * and the floating-point add that we want.
+ *
* @param address The address to update.
* @param y The value to update the address with.
*/
__attribute__((always_inline)) INLINE static void atomic_add_f(
- volatile float* address, float y) {
+ volatile float *const address, const float y) {
- int* int_ptr = (int*)address;
+ int *const int_ptr = (int *)address;
typedef union {
float as_float;
diff --git a/src/chemistry.c b/src/chemistry.c
index 44cbea1361d96c4cf1d4d3d21c3c91e5225640a5..4afa199258f56d4fc01d67c9335e87a86ead09bc 100644
--- a/src/chemistry.c
+++ b/src/chemistry.c
@@ -33,7 +33,7 @@
* @param phys_const The physical constants in internal units.
* @param data The properties to initialise.
*/
-void chemistry_init(const struct swift_params* parameter_file,
+void chemistry_init(struct swift_params* parameter_file,
const struct unit_system* us,
const struct phys_const* phys_const,
struct chemistry_global_data* data) {
diff --git a/src/chemistry.h b/src/chemistry.h
index bacc15c483c168dbf86bd34dc2af92a3eefb9e02..f9daa41db22a69a09f06be3fb560a68edac2f078 100644
--- a/src/chemistry.h
+++ b/src/chemistry.h
@@ -43,7 +43,7 @@
#endif
/* Common functions */
-void chemistry_init(const struct swift_params* parameter_file,
+void chemistry_init(struct swift_params* parameter_file,
const struct unit_system* us,
const struct phys_const* phys_const,
struct chemistry_global_data* data);
diff --git a/src/chemistry/EAGLE/chemistry.h b/src/chemistry/EAGLE/chemistry.h
index 459de24ef3c5e9140fd136155ba55d2364795fb8..96a645806a495801f6165353cad9e1c87087f8e3 100644
--- a/src/chemistry/EAGLE/chemistry.h
+++ b/src/chemistry/EAGLE/chemistry.h
@@ -78,6 +78,22 @@ __attribute__((always_inline)) INLINE static void chemistry_end_density(
struct part* restrict p, const struct chemistry_global_data* cd,
const struct cosmology* cosmo) {}
+/**
+ * @brief Sets all particle fields to sensible values when the #part has 0 ngbs.
+ *
+ * @param p The particle to act upon
+ * @param xp The extended particle data to act upon
+ * @param cd #chemistry_global_data containing chemistry informations.
+ * @param cosmo The current cosmological model.
+ */
+__attribute__((always_inline)) INLINE static void
+chemistry_part_has_no_neighbours(struct part* restrict p,
+ struct xpart* restrict xp,
+ const struct chemistry_global_data* cd,
+ const struct cosmology* cosmo) {
+ error("Needs implementing!");
+}
+
/**
* @brief Sets the chemistry properties of the (x-)particles to a valid start
* state.
@@ -108,9 +124,10 @@ __attribute__((always_inline)) INLINE static void chemistry_first_init_part(
* @param phys_const The physical constants in internal units.
* @param data The properties to initialise.
*/
-static INLINE void chemistry_init_backend(
- const struct swift_params* parameter_file, const struct unit_system* us,
- const struct phys_const* phys_const, struct chemistry_global_data* data) {
+static INLINE void chemistry_init_backend(struct swift_params* parameter_file,
+ const struct unit_system* us,
+ const struct phys_const* phys_const,
+ struct chemistry_global_data* data) {
/* Read the total metallicity */
data->initial_metal_mass_fraction_total =
diff --git a/src/chemistry/EAGLE/chemistry_io.h b/src/chemistry/EAGLE/chemistry_io.h
index aab8ec240207a47289e35a711af8b245bf2b40fa..f87807579c46fe336f45e934d828318aed0377c7 100644
--- a/src/chemistry/EAGLE/chemistry_io.h
+++ b/src/chemistry/EAGLE/chemistry_io.h
@@ -30,7 +30,8 @@
*
* @return Returns the number of fields to read.
*/
-int chemistry_read_particles(struct part* parts, struct io_props* list) {
+INLINE static int chemistry_read_particles(struct part* parts,
+ struct io_props* list) {
/* Nothing to read */
return 0;
@@ -44,7 +45,8 @@ int chemistry_read_particles(struct part* parts, struct io_props* list) {
*
* @return Returns the number of fields to write.
*/
-int chemistry_write_particles(const struct part* parts, struct io_props* list) {
+INLINE static int chemistry_write_particles(const struct part* parts,
+ struct io_props* list) {
/* List what we want to write */
list[0] = io_make_output_field("ElementAbundance", FLOAT,
@@ -101,7 +103,7 @@ int chemistry_write_particles(const struct part* parts, struct io_props* list) {
* @brief Writes the current model of SPH to the file
* @param h_grpsph The HDF5 group in which to write
*/
-void chemistry_write_flavour(hid_t h_grp) {
+INLINE static void chemistry_write_flavour(hid_t h_grp) {
io_write_attribute_s(h_grp, "Chemistry Model", "EAGLE");
for (int elem = 0; elem < chemistry_element_count; ++elem) {
diff --git a/src/chemistry/GEAR/chemistry.h b/src/chemistry/GEAR/chemistry.h
index a51051ca3ae45476986d39c868a9fc71bf7f9ae5..6212ed1efb423717b800d431a83f0e8bec7c6c6f 100644
--- a/src/chemistry/GEAR/chemistry.h
+++ b/src/chemistry/GEAR/chemistry.h
@@ -72,9 +72,10 @@ static INLINE void chemistry_print_backend(
* @param phys_const The physical constants in internal units.
* @param data The properties to initialise.
*/
-static INLINE void chemistry_init_backend(
- const struct swift_params* parameter_file, const struct unit_system* us,
- const struct phys_const* phys_const, struct chemistry_global_data* data) {
+static INLINE void chemistry_init_backend(struct swift_params* parameter_file,
+ const struct unit_system* us,
+ const struct phys_const* phys_const,
+ struct chemistry_global_data* data) {
/* read parameters */
data->initial_metallicity = parser_get_opt_param_float(
@@ -134,6 +135,22 @@ __attribute__((always_inline)) INLINE static void chemistry_end_density(
}
}
+/**
+ * @brief Sets all particle fields to sensible values when the #part has 0 ngbs.
+ *
+ * @param p The particle to act upon
+ * @param xp The extended particle data to act upon
+ * @param cd #chemistry_global_data containing chemistry informations.
+ * @param cosmo The current cosmological model.
+ */
+__attribute__((always_inline)) INLINE static void
+chemistry_part_has_no_neighbours(struct part* restrict p,
+ struct xpart* restrict xp,
+ const struct chemistry_global_data* cd,
+ const struct cosmology* cosmo) {
+ error("Needs implementing!");
+}
+
/**
* @brief Sets the chemistry properties of the (x-)particles to a valid start
* state.
diff --git a/src/chemistry/GEAR/chemistry_io.h b/src/chemistry/GEAR/chemistry_io.h
index 0557d5c520dfc7ad5eaff2b92e6588751c072df5..2a0847bebfb8c1734f21bda2f6ad55b354a7aec9 100644
--- a/src/chemistry/GEAR/chemistry_io.h
+++ b/src/chemistry/GEAR/chemistry_io.h
@@ -48,8 +48,8 @@ chemistry_get_element_name(enum chemistry_element elem) {
*
* @return Returns the number of fields to read.
*/
-__attribute__((always_inline)) INLINE static int chemistry_read_particles(
- struct part* parts, struct io_props* list) {
+INLINE static int chemistry_read_particles(struct part* parts,
+ struct io_props* list) {
/* List what we want to read */
list[0] = io_make_input_field(
@@ -69,13 +69,14 @@ __attribute__((always_inline)) INLINE static int chemistry_read_particles(
*
* @return Returns the number of fields to write.
*/
-__attribute__((always_inline)) INLINE static int chemistry_write_particles(
- const struct part* parts, struct io_props* list) {
+INLINE static int chemistry_write_particles(const struct part* parts,
+ struct io_props* list) {
/* List what we want to write */
list[0] = io_make_output_field(
"SmoothedElementAbundance", FLOAT, chemistry_element_count,
UNIT_CONV_NO_UNITS, parts, chemistry_data.smoothed_metal_mass_fraction);
+
list[1] = io_make_output_field("Z", FLOAT, 1, UNIT_CONV_NO_UNITS, parts,
chemistry_data.Z);
@@ -92,8 +93,7 @@ __attribute__((always_inline)) INLINE static int chemistry_write_particles(
* @brief Writes the current model of SPH to the file
* @param h_grp The HDF5 group in which to write
*/
-__attribute__((always_inline)) INLINE static void chemistry_write_flavour(
- hid_t h_grp) {
+INLINE static void chemistry_write_flavour(hid_t h_grp) {
io_write_attribute_s(h_grp, "Chemistry Model", "GEAR");
for (enum chemistry_element i = chemistry_element_O;
diff --git a/src/chemistry/none/chemistry.h b/src/chemistry/none/chemistry.h
index 3ca51660ddfeead2b7ad0010979b719e59c4934e..dce06ffda339e8a6c4925c7b7c430485a208adb7 100644
--- a/src/chemistry/none/chemistry.h
+++ b/src/chemistry/none/chemistry.h
@@ -59,9 +59,10 @@ chemistry_get_element_name(enum chemistry_element elem) {
* @param phys_const The physical constants in internal units.
* @param data The global chemistry information (to be filled).
*/
-static INLINE void chemistry_init_backend(
- const struct swift_params* parameter_file, const struct unit_system* us,
- const struct phys_const* phys_const, struct chemistry_global_data* data) {}
+static INLINE void chemistry_init_backend(struct swift_params* parameter_file,
+ const struct unit_system* us,
+ const struct phys_const* phys_const,
+ struct chemistry_global_data* data) {}
/**
* @brief Prints the properties of the chemistry model to stdout.
@@ -86,6 +87,20 @@ __attribute__((always_inline)) INLINE static void chemistry_end_density(
struct part* restrict p, const struct chemistry_global_data* cd,
const struct cosmology* cosmo) {}
+/**
+ * @brief Sets all particle fields to sensible values when the #part has 0 ngbs.
+ *
+ * @param p The particle to act upon
+ * @param xp The extended particle data to act upon
+ * @param cd #chemistry_global_data containing chemistry informations.
+ * @param cosmo The current cosmological model.
+ */
+__attribute__((always_inline)) INLINE static void
+chemistry_part_has_no_neighbours(struct part* restrict p,
+ struct xpart* restrict xp,
+ const struct chemistry_global_data* cd,
+ const struct cosmology* cosmo) {}
+
/**
* @brief Sets the chemistry properties of the (x-)particles to a valid start
* state.
diff --git a/src/chemistry/none/chemistry_io.h b/src/chemistry/none/chemistry_io.h
index 142d2f75ce1487393e8689edbb9a6fdb1b1e85cd..ef7e0d8d87dfeab5978f0e86bbf6279f7901d10a 100644
--- a/src/chemistry/none/chemistry_io.h
+++ b/src/chemistry/none/chemistry_io.h
@@ -29,7 +29,8 @@
*
* @return Returns the number of fields to write.
*/
-int chemistry_read_particles(struct part* parts, struct io_props* list) {
+INLINE static int chemistry_read_particles(struct part* parts,
+ struct io_props* list) {
/* update list according to hydro_io */
@@ -45,7 +46,8 @@ int chemistry_read_particles(struct part* parts, struct io_props* list) {
*
* @return Returns the number of fields to write.
*/
-int chemistry_write_particles(const struct part* parts, struct io_props* list) {
+INLINE static int chemistry_write_particles(const struct part* parts,
+ struct io_props* list) {
/* update list according to hydro_io */
@@ -59,7 +61,7 @@ int chemistry_write_particles(const struct part* parts, struct io_props* list) {
* @brief Writes the current model of SPH to the file
* @param h_grp The HDF5 group in which to write
*/
-void chemistry_write_flavour(hid_t h_grp) {
+INLINE static void chemistry_write_flavour(hid_t h_grp) {
io_write_attribute_s(h_grp, "Chemistry Model", "None");
}
diff --git a/src/clocks.c b/src/clocks.c
index fbaa83f15fafda23751d5d6c34d40750132287b5..cac0131acade08e41ee7ed4a22fabde49e197060 100644
--- a/src/clocks.c
+++ b/src/clocks.c
@@ -50,7 +50,7 @@ static int clocks_units_index = 0;
static double clocks_units_scale = 1000.0;
/* Local prototypes. */
-static void clocks_estimate_cpufreq();
+static void clocks_estimate_cpufreq(void);
/**
* @brief Get the current time.
@@ -113,7 +113,7 @@ void clocks_set_cpufreq(unsigned long long freq) {
*
* @result the CPU frequency.
*/
-unsigned long long clocks_get_cpufreq() {
+unsigned long long clocks_get_cpufreq(void) {
if (clocks_cpufreq > 0) return clocks_cpufreq;
@@ -132,7 +132,7 @@ unsigned long long clocks_get_cpufreq() {
* file (probably a overestimate) or finally just use a value of 1 with
* time units of ticks.
*/
-static void clocks_estimate_cpufreq() {
+static void clocks_estimate_cpufreq(void) {
#ifdef HAVE_CLOCK_GETTIME
/* Try to time a nanosleep() in ticks. */
@@ -241,7 +241,7 @@ ticks clocks_to_ticks(double ms) {
*
* @result the current time units.
*/
-const char *clocks_getunit() { return clocks_units[clocks_units_index]; }
+const char *clocks_getunit(void) { return clocks_units[clocks_units_index]; }
/**
* @brief returns the time since the start of the execution in seconds
@@ -252,7 +252,7 @@ const char *clocks_getunit() { return clocks_units[clocks_units_index]; }
*
* @result the time since the start of the execution
*/
-const char *clocks_get_timesincestart() {
+const char *clocks_get_timesincestart(void) {
static char buffer[40];
@@ -274,7 +274,7 @@ const char *clocks_get_timesincestart() {
* @result cpu time used in sysconf(_SC_CLK_TCK) ticks, usually 100/s not our
* usual ticks.
*/
-double clocks_get_cputime_used() {
+double clocks_get_cputime_used(void) {
struct tms tmstic;
times(&tmstic);
diff --git a/src/clocks.h b/src/clocks.h
index bdb3a6651e52f5b165e644015b91f96aa5812d57..f3901584774c7586d6a68b4415d6b443cb53c466 100644
--- a/src/clocks.h
+++ b/src/clocks.h
@@ -34,15 +34,15 @@ struct clocks_time {
void clocks_gettime(struct clocks_time *time);
double clocks_diff(struct clocks_time *start, struct clocks_time *end);
-const char *clocks_getunit();
+const char *clocks_getunit(void);
void clocks_set_cpufreq(unsigned long long freq);
-unsigned long long clocks_get_cpufreq();
+unsigned long long clocks_get_cpufreq(void);
double clocks_from_ticks(ticks tics);
ticks clocks_to_ticks(double interval);
double clocks_diff_ticks(ticks tic, ticks toc);
-const char *clocks_get_timesincestart();
+const char *clocks_get_timesincestart(void);
-double clocks_get_cputime_used();
+double clocks_get_cputime_used(void);
#endif /* SWIFT_CLOCKS_H */
diff --git a/src/collectgroup.c b/src/collectgroup.c
index b704a0a5ea33cc1c5332fc0575061ad8e38f4d21..0a7780aba1d5d41cef756d2132c75f9357796c73 100644
--- a/src/collectgroup.c
+++ b/src/collectgroup.c
@@ -36,14 +36,14 @@
/* Local collections for MPI reduces. */
struct mpicollectgroup1 {
- size_t updates, g_updates, s_updates;
+ long long updates, g_updates, s_updates;
integertime_t ti_hydro_end_min;
integertime_t ti_gravity_end_min;
int forcerebuild;
};
/* Forward declarations. */
-static void mpicollect_create_MPI_type();
+static void mpicollect_create_MPI_type(void);
/**
* @brief MPI datatype for the #mpicollectgroup1 structure.
@@ -60,7 +60,7 @@ static MPI_Op mpicollectgroup1_reduce_op;
/**
* @brief Perform any once only initialisations. Must be called once.
*/
-void collectgroup_init() {
+void collectgroup_init(void) {
#ifdef WITH_MPI
/* Initialise the MPI types. */
@@ -88,7 +88,6 @@ void collectgroup1_apply(struct collectgroup1 *grp1, struct engine *e) {
e->updates = grp1->updates;
e->g_updates = grp1->g_updates;
e->s_updates = grp1->s_updates;
- e->forcerebuild = grp1->forcerebuild;
}
/**
@@ -211,7 +210,7 @@ static void mpicollectgroup1_reduce(void *in, void *inout, int *len,
/**
* @brief Registers any MPI collection types and reduction functions.
*/
-static void mpicollect_create_MPI_type() {
+static void mpicollect_create_MPI_type(void) {
if (MPI_Type_contiguous(sizeof(struct mpicollectgroup1), MPI_BYTE,
&mpicollectgroup1_type) != MPI_SUCCESS ||
diff --git a/src/collectgroup.h b/src/collectgroup.h
index f2014ed254fdde7ea293224751061d824782b4a7..8bf8a9d1b75f9a5ddb3f19fa9cdb4103e044ea59 100644
--- a/src/collectgroup.h
+++ b/src/collectgroup.h
@@ -35,7 +35,7 @@ struct engine;
struct collectgroup1 {
/* Number of particles updated */
- size_t updates, g_updates, s_updates;
+ long long updates, g_updates, s_updates;
/* Times for the time-step */
integertime_t ti_hydro_end_min, ti_hydro_end_max, ti_hydro_beg_max;
@@ -45,7 +45,7 @@ struct collectgroup1 {
int forcerebuild;
};
-void collectgroup_init();
+void collectgroup_init(void);
void collectgroup1_apply(struct collectgroup1 *grp1, struct engine *e);
void collectgroup1_init(struct collectgroup1 *grp1, size_t updates,
size_t g_updates, size_t s_updates,
diff --git a/src/common_io.c b/src/common_io.c
index 8b173adb7b5e5a014b0967b4fd04aef5ee6606e9..494a702125cf873946d06855b5683216cb2aceaf 100644
--- a/src/common_io.c
+++ b/src/common_io.c
@@ -25,12 +25,17 @@
#include "common_io.h"
/* Local includes. */
+#include "chemistry_io.h"
#include "engine.h"
#include "error.h"
+#include "gravity_io.h"
#include "hydro.h"
+#include "hydro_io.h"
#include "io_properties.h"
#include "kernel_hydro.h"
#include "part.h"
+#include "part_type.h"
+#include "stars_io.h"
#include "threadpool.h"
#include "units.h"
#include "version.h"
@@ -340,6 +345,7 @@ void io_write_code_description(hid_t h_file) {
io_write_attribute_s(h_grpcode, "CFLAGS", compilation_cflags());
io_write_attribute_s(h_grpcode, "HDF5 library version", hdf5_version());
io_write_attribute_s(h_grpcode, "Thread barriers", thread_barrier_version());
+ io_write_attribute_s(h_grpcode, "Allocators", allocator_version());
#ifdef HAVE_FFTW
io_write_attribute_s(h_grpcode, "FFTW library version", fftw3_version());
#endif
@@ -805,3 +811,157 @@ void io_collect_dm_gparts(const struct gpart* const gparts, size_t Ntot,
error("Collected the wrong number of dm particles (%zu vs. %zu expected)",
count, Ndm);
}
+
+/**
+ * @brief Verify the io parameter file
+ *
+ * @param params The #swift_params
+ * @param N_total The total number of each particle type.
+ */
+void io_check_output_fields(const struct swift_params* params,
+ const long long N_total[3]) {
+
+ /* Create some fake particles as arguments for the writing routines */
+ struct part p;
+ struct xpart xp;
+ struct spart sp;
+ struct gpart gp;
+
+ /* Copy N_total to array with length == 6 */
+ const long long nr_total[swift_type_count] = {N_total[0], N_total[1], 0,
+ 0, N_total[2], 0};
+
+ /* Loop over all particle types to check the fields */
+ for (int ptype = 0; ptype < swift_type_count; ptype++) {
+
+ int num_fields = 0;
+ struct io_props list[100];
+
+ /* Don't do anything if no particle of this kind */
+ if (nr_total[ptype] == 0) continue;
+
+ /* Gather particle fields from the particle structures */
+ switch (ptype) {
+
+ case swift_type_gas:
+ hydro_write_particles(&p, &xp, list, &num_fields);
+ num_fields += chemistry_write_particles(&p, list + num_fields);
+ break;
+
+ case swift_type_dark_matter:
+ darkmatter_write_particles(&gp, list, &num_fields);
+ break;
+
+ case swift_type_star:
+ star_write_particles(&sp, list, &num_fields);
+ break;
+
+ default:
+ error("Particle Type %d not yet supported. Aborting", ptype);
+ }
+
+ /* loop over each parameter */
+ for (int param_id = 0; param_id < params->paramCount; param_id++) {
+ const char* param_name = params->data[param_id].name;
+
+ char section_name[PARSER_MAX_LINE_SIZE];
+
+ /* Skip if wrong section */
+ sprintf(section_name, "SelectOutput:");
+ if (strstr(param_name, section_name) == NULL) continue;
+
+ /* Skip if wrong particle type */
+ sprintf(section_name, "_%s", part_type_names[ptype]);
+ if (strstr(param_name, section_name) == NULL) continue;
+
+ int found = 0;
+
+ /* loop over each possible output field */
+ for (int field_id = 0; field_id < num_fields; field_id++) {
+ char field_name[PARSER_MAX_LINE_SIZE];
+ sprintf(field_name, "SelectOutput:%s_%s", list[field_id].name,
+ part_type_names[ptype]);
+
+ if (strcmp(param_name, field_name) == 0) {
+ found = 1;
+ /* check if correct input */
+ int retParam = 0;
+ char str[PARSER_MAX_LINE_SIZE];
+ sscanf(params->data[param_id].value, "%d%s", &retParam, str);
+
+ /* Check that we have a 0 or 1 */
+ if (retParam != 0 && retParam != 1)
+ message(
+ "WARNING: Unexpected input for %s. Received %i but expect 0 or "
+ "1. ",
+ field_name, retParam);
+
+ /* Found it, so move to the next one. */
+ break;
+ }
+ }
+ if (!found)
+ message(
+ "WARNING: Trying to dump particle field '%s' (read from '%s') that "
+ "does not exist.",
+ param_name, params->fileName);
+ }
+ }
+}
+
+/**
+ * @brief Write the output field parameters file
+ *
+ * @param filename The file to write
+ */
+void io_write_output_field_parameter(const char* filename) {
+
+ FILE* file = fopen(filename, "w");
+ if (file == NULL) error("Error opening file '%s'", filename);
+
+ /* Loop over all particle types */
+ fprintf(file, "SelectOutput:\n");
+ for (int ptype = 0; ptype < swift_type_count; ptype++) {
+
+ int num_fields = 0;
+ struct io_props list[100];
+
+ /* Write particle fields from the particle structure */
+ switch (ptype) {
+
+ case swift_type_gas:
+ hydro_write_particles(NULL, NULL, list, &num_fields);
+ num_fields += chemistry_write_particles(NULL, list + num_fields);
+ break;
+
+ case swift_type_dark_matter:
+ darkmatter_write_particles(NULL, list, &num_fields);
+ break;
+
+ case swift_type_star:
+ star_write_particles(NULL, list, &num_fields);
+ break;
+
+ default:
+ break;
+ }
+
+ if (num_fields == 0) continue;
+
+ /* Output a header for that particle type */
+ fprintf(file, " # Particle Type %s\n", part_type_names[ptype]);
+
+ /* Write all the fields of this particle type */
+ for (int i = 0; i < num_fields; ++i)
+ fprintf(file, " %s_%s: 1\n", list[i].name, part_type_names[ptype]);
+
+ fprintf(file, "\n");
+ }
+
+ fclose(file);
+
+ printf(
+ "List of valid ouput fields for the particle in snapshots dumped in "
+ "'%s'.\n",
+ filename);
+}
diff --git a/src/common_io.h b/src/common_io.h
index d9e676db934b58ee476f18894acf55c4d38344f9..f26a635a66f40424984238e586fcdf5bc752fc99 100644
--- a/src/common_io.h
+++ b/src/common_io.h
@@ -100,4 +100,9 @@ void io_duplicate_star_gparts(struct threadpool* tp, struct spart* const sparts,
struct gpart* const gparts, size_t Nstars,
size_t Ndm);
+void io_check_output_fields(const struct swift_params* params,
+ const long long N_total[3]);
+
+void io_write_output_field_parameter(const char* filename);
+
#endif /* SWIFT_COMMON_IO_H */
diff --git a/src/cooling.c b/src/cooling.c
index 57d1928a5d59ac2ff46c6cd20a45d69dec25ec60..154b859f74402d9e9a8adf1fb6c796b5195b8cd1 100644
--- a/src/cooling.c
+++ b/src/cooling.c
@@ -34,7 +34,7 @@
* @param phys_const The physical constants in internal units.
* @param cooling The cooling properties to initialize
*/
-void cooling_init(const struct swift_params* parameter_file,
+void cooling_init(struct swift_params* parameter_file,
const struct unit_system* us,
const struct phys_const* phys_const,
struct cooling_function_data* cooling) {
diff --git a/src/cooling.h b/src/cooling.h
index 9d1001d360a1816837381e9aa52b17ba47f50fce..0fb04b9e484d989e746a254fc1934dc20033fb09 100644
--- a/src/cooling.h
+++ b/src/cooling.h
@@ -43,7 +43,7 @@
#endif
/* Common functions */
-void cooling_init(const struct swift_params* parameter_file,
+void cooling_init(struct swift_params* parameter_file,
const struct unit_system* us,
const struct phys_const* phys_const,
struct cooling_function_data* cooling);
diff --git a/src/cooling/EAGLE/cooling.h b/src/cooling/EAGLE/cooling.h
index bdf3801887256cb97ae1d5b6a3095250764aa822..f059d995c65cf791f0692ab5d8505f92c1a206ca 100644
--- a/src/cooling/EAGLE/cooling.h
+++ b/src/cooling/EAGLE/cooling.h
@@ -109,10 +109,11 @@ __attribute__((always_inline)) INLINE static float cooling_get_radiated_energy(
* @param phys_const The physical constants in internal units.
* @param cooling The cooling properties to initialize
*/
-static INLINE void cooling_init_backend(
- const struct swift_params* parameter_file, const struct unit_system* us,
- const struct phys_const* phys_const,
- struct cooling_function_data* cooling) {}
+static INLINE void cooling_init_backend(struct swift_params* parameter_file,
+ const struct unit_system* us,
+ const struct phys_const* phys_const,
+ struct cooling_function_data* cooling) {
+}
/**
* @brief Prints the properties of the cooling model to stdout.
diff --git a/src/cooling/const_du/cooling.h b/src/cooling/const_du/cooling.h
index ba8211174919419c37856dc1fcbdaa73b23e319e..b6fea7eea7b0fb208c4bffece425ec836d5df0c0 100644
--- a/src/cooling/const_du/cooling.h
+++ b/src/cooling/const_du/cooling.h
@@ -163,10 +163,10 @@ __attribute__((always_inline)) INLINE static float cooling_get_radiated_energy(
* @param phys_const The physical constants in internal units.
* @param cooling The cooling properties to initialize
*/
-static INLINE void cooling_init_backend(
- const struct swift_params* parameter_file, const struct unit_system* us,
- const struct phys_const* phys_const,
- struct cooling_function_data* cooling) {
+static INLINE void cooling_init_backend(struct swift_params* parameter_file,
+ const struct unit_system* us,
+ const struct phys_const* phys_const,
+ struct cooling_function_data* cooling) {
cooling->cooling_rate =
parser_get_param_double(parameter_file, "ConstCooling:cooling_rate");
diff --git a/src/cooling/const_lambda/cooling.h b/src/cooling/const_lambda/cooling.h
index 43ca7ab75b0bce370d7405e52cea9b54335ae73c..f1a7abdbe14a39d98bbd01eb36ba870c8af0ee1a 100644
--- a/src/cooling/const_lambda/cooling.h
+++ b/src/cooling/const_lambda/cooling.h
@@ -171,10 +171,10 @@ __attribute__((always_inline)) INLINE static float cooling_get_radiated_energy(
* @param phys_const The physical constants in internal units.
* @param cooling The cooling properties to initialize
*/
-static INLINE void cooling_init_backend(
- const struct swift_params* parameter_file, const struct unit_system* us,
- const struct phys_const* phys_const,
- struct cooling_function_data* cooling) {
+static INLINE void cooling_init_backend(struct swift_params* parameter_file,
+ const struct unit_system* us,
+ const struct phys_const* phys_const,
+ struct cooling_function_data* cooling) {
const double lambda_cgs =
parser_get_param_double(parameter_file, "LambdaCooling:lambda_cgs");
diff --git a/src/cooling/grackle/cooling.h b/src/cooling/grackle/cooling.h
index dd59e9af1431681a8c5bdc1e5cb0c22053063651..cb77b63294aacee425b917c1900eefd7ebfa5f34 100644
--- a/src/cooling/grackle/cooling.h
+++ b/src/cooling/grackle/cooling.h
@@ -771,7 +771,7 @@ __attribute__((always_inline)) INLINE static void cooling_init_grackle(
* @param cooling The cooling properties to initialize
*/
__attribute__((always_inline)) INLINE static void cooling_init_backend(
- const struct swift_params* parameter_file, const struct unit_system* us,
+ struct swift_params* parameter_file, const struct unit_system* us,
const struct phys_const* phys_const,
struct cooling_function_data* cooling) {
diff --git a/src/cooling/grackle/cooling_io.h b/src/cooling/grackle/cooling_io.h
index 5a6edb8f1c559a7b495351e256559f251b97c1cf..faf84cf97d8449d54f2727ec26b16a9d81d117c6 100644
--- a/src/cooling/grackle/cooling_io.h
+++ b/src/cooling/grackle/cooling_io.h
@@ -133,7 +133,7 @@ __attribute__((always_inline)) INLINE static int cooling_write_particles(
* @param cooling The cooling properties to initialize
*/
__attribute__((always_inline)) INLINE static void cooling_read_parameters(
- const struct swift_params* parameter_file,
+ struct swift_params* parameter_file,
struct cooling_function_data* cooling) {
parser_get_param_string(parameter_file, "GrackleCooling:CloudyTable",
diff --git a/src/cooling/none/cooling.h b/src/cooling/none/cooling.h
index 5081c7cbe6c4b5168da082ead80687226f9d0c16..0cc465adcdad8fe19afe4a9867e5d68a22ed9119 100644
--- a/src/cooling/none/cooling.h
+++ b/src/cooling/none/cooling.h
@@ -119,10 +119,11 @@ __attribute__((always_inline)) INLINE static float cooling_get_radiated_energy(
* @param phys_const The physical constants in internal units.
* @param cooling The cooling properties to initialize
*/
-static INLINE void cooling_init_backend(
- const struct swift_params* parameter_file, const struct unit_system* us,
- const struct phys_const* phys_const,
- struct cooling_function_data* cooling) {}
+static INLINE void cooling_init_backend(struct swift_params* parameter_file,
+ const struct unit_system* us,
+ const struct phys_const* phys_const,
+ struct cooling_function_data* cooling) {
+}
/**
* @brief Prints the properties of the cooling model to stdout.
diff --git a/src/cosmology.c b/src/cosmology.c
index 4da9528784b1fb7fdb04761b77a3c0056a32f41a..09472fd77cd98185ff8799e79f687b6552bcd901 100644
--- a/src/cosmology.c
+++ b/src/cosmology.c
@@ -387,8 +387,7 @@ void cosmology_init_tables(struct cosmology *c) {
* @param phys_const The physical constants in the current system of units.
* @param c The #cosmology to initialise.
*/
-void cosmology_init(const struct swift_params *params,
- const struct unit_system *us,
+void cosmology_init(struct swift_params *params, const struct unit_system *us,
const struct phys_const *phys_const, struct cosmology *c) {
/* Read in the cosmological parameters */
diff --git a/src/cosmology.h b/src/cosmology.h
index 109b80a57d8dbc4eb942dd4ecbbc0db84198100b..ea992d12deffbe60154ea56ca5fff69a1b06587c 100644
--- a/src/cosmology.h
+++ b/src/cosmology.h
@@ -181,8 +181,7 @@ double cosmology_get_therm_kick_factor(const struct cosmology *cosmo,
double cosmology_get_delta_time(const struct cosmology *c, double a1,
double a2);
-void cosmology_init(const struct swift_params *params,
- const struct unit_system *us,
+void cosmology_init(struct swift_params *params, const struct unit_system *us,
const struct phys_const *phys_const, struct cosmology *c);
void cosmology_init_no_cosmo(struct cosmology *c);
diff --git a/src/cycle.h b/src/cycle.h
index f220ecd120b14db0a8cdaf5d1105be4bd0e70831..842510e066e2f6f94e736851bf636c9a73e4f25f 100644
--- a/src/cycle.h
+++ b/src/cycle.h
@@ -519,8 +519,19 @@ INLINE_ELAPSED(inline)
#define HAVE_TICK_COUNTER
#endif
+#if defined(HAVE_ARMV7A_PMCCNTR)
+typedef uint64_t ticks;
+static inline ticks getticks(void) {
+ uint32_t r;
+ asm volatile("mrc p15, 0, %0, c9, c13, 0" : "=r"(r));
+ return r;
+}
+INLINE_ELAPSED(inline)
+#define HAVE_TICK_COUNTER
+#endif
+
#if defined(__aarch64__) && defined(HAVE_ARMV8_CNTVCT_EL0) && \
- !defined(HAVE_ARMV8CC)
+ !defined(HAVE_ARMV8_PMCCNTR_EL0)
typedef uint64_t ticks;
static inline ticks getticks(void) {
uint64_t Rt;
@@ -531,7 +542,7 @@ INLINE_ELAPSED(inline)
#define HAVE_TICK_COUNTER
#endif
-#if defined(__aarch64__) && defined(HAVE_ARMV8CC)
+#if defined(__aarch64__) && defined(HAVE_ARMV8_PMCCNTR_EL0)
typedef uint64_t ticks;
static inline ticks getticks(void) {
uint64_t cc = 0;
diff --git a/src/debug.c b/src/debug.c
index 93d14952f523be5f1d1fa90484e9e7951f8e3f6e..05c21de0a73bba3a5e867a4265de0a5c14736a14 100644
--- a/src/debug.c
+++ b/src/debug.c
@@ -642,7 +642,7 @@ void getProcMemUse(long *size, long *resident, long *share, long *trs,
/**
* @brief Print the current memory use of the process. A la "top".
*/
-void printProcMemUse() {
+void printProcMemUse(void) {
long size;
long resident;
long share;
diff --git a/src/debug.h b/src/debug.h
index 1e482c05c5af2dfebff1a254018fb1802df6cc5d..c9d65ad06cf5307a5fd8596c9c5b6c8b83cb6d9e 100644
--- a/src/debug.h
+++ b/src/debug.h
@@ -51,5 +51,5 @@ void dumpCellRanks(const char *prefix, struct cell *cells_top, int nr_cells);
void getProcMemUse(long *size, long *resident, long *share, long *trs,
long *lrs, long *drs, long *dt);
-void printProcMemUse();
+void printProcMemUse(void);
#endif /* SWIFT_DEBUG_H */
diff --git a/src/engine.c b/src/engine.c
index ffa24e306024f2886c7766352e2212a55896dc75..5f05225522e69a5d754f3d056186aa4be70bb4a8 100644
--- a/src/engine.c
+++ b/src/engine.c
@@ -3854,6 +3854,11 @@ void engine_rebuild(struct engine *e, int clean_smoothing_length_values) {
/* Print the status of the system */
if (e->verbose) engine_print_task_counts(e);
+ /* Clear the counters of updates since the last rebuild */
+ e->updates_since_rebuild = 0;
+ e->g_updates_since_rebuild = 0;
+ e->s_updates_since_rebuild = 0;
+
/* Flag that a rebuild has taken place */
e->step_props |= engine_step_prop_rebuild;
@@ -4108,13 +4113,13 @@ void engine_collect_end_of_step(struct engine *e, int apply) {
MPI_COMM_WORLD) != MPI_SUCCESS)
error("Failed to aggregate particle counts.");
if (in_ll[0] != (long long)e->collect_group1.updates)
- error("Failed to get same updates, is %lld, should be %ld", in_ll[0],
+ error("Failed to get same updates, is %lld, should be %lld", in_ll[0],
e->collect_group1.updates);
if (in_ll[1] != (long long)e->collect_group1.g_updates)
- error("Failed to get same g_updates, is %lld, should be %ld", in_ll[1],
+ error("Failed to get same g_updates, is %lld, should be %lld", in_ll[1],
e->collect_group1.g_updates);
if (in_ll[2] != (long long)e->collect_group1.s_updates)
- error("Failed to get same s_updates, is %lld, should be %ld", in_ll[2],
+ error("Failed to get same s_updates, is %lld, should be %lld", in_ll[2],
e->collect_group1.s_updates);
int buff = 0;
@@ -4550,14 +4555,15 @@ void engine_step(struct engine *e) {
if (e->nodeID == 0) {
/* Print some information to the screen */
- printf(" %6d %14e %14e %10.5f %14e %4d %4d %12zu %12zu %12zu %21.3f %6d\n",
- e->step, e->time, e->cosmology->a, e->cosmology->z, e->time_step,
- e->min_active_bin, e->max_active_bin, e->updates, e->g_updates,
- e->s_updates, e->wallclock_time, e->step_props);
+ printf(
+ " %6d %14e %14e %10.5f %14e %4d %4d %12lld %12lld %12lld %21.3f %6d\n",
+ e->step, e->time, e->cosmology->a, e->cosmology->z, e->time_step,
+ e->min_active_bin, e->max_active_bin, e->updates, e->g_updates,
+ e->s_updates, e->wallclock_time, e->step_props);
fflush(stdout);
fprintf(e->file_timesteps,
- " %6d %14e %14e %14e %4d %4d %12zu %12zu %12zu %21.3f %6d\n",
+ " %6d %14e %14e %14e %4d %4d %12lld %12lld %12lld %21.3f %6d\n",
e->step, e->time, e->cosmology->a, e->time_step, e->min_active_bin,
e->max_active_bin, e->updates, e->g_updates, e->s_updates,
e->wallclock_time, e->step_props);
@@ -4644,11 +4650,6 @@ void engine_step(struct engine *e) {
gravity_exact_force_check(e->s, e, 1e-1);
#endif
- /* Let's trigger a non-SPH rebuild every-so-often for good measure */
- if (!(e->policy & engine_policy_hydro) && // MATTHIEU improve this
- (e->policy & engine_policy_self_gravity) && e->step % 20 == 0)
- e->forcerebuild = 1;
-
/* Collect the values of rebuild from all nodes and recover the (integer)
* end of the next time-step. Do these together to reduce the collective MPI
* calls per step, but some of the gathered information is not applied just
@@ -4656,6 +4657,17 @@ void engine_step(struct engine *e) {
engine_collect_end_of_step(e, 0);
e->forcerebuild = e->collect_group1.forcerebuild;
+ /* Update the counters */
+ e->updates_since_rebuild += e->collect_group1.updates;
+ e->g_updates_since_rebuild += e->collect_group1.g_updates;
+ e->s_updates_since_rebuild += e->collect_group1.s_updates;
+
+ /* Trigger a tree-rebuild if we passed the frequency threshold */
+ if ((e->policy & engine_policy_self_gravity) &&
+ ((double)e->g_updates_since_rebuild >
+ ((double)e->total_nr_gparts) * e->gravity_properties->rebuild_frequency))
+ e->forcerebuild = 1;
+
/* Save some statistics ? */
if (e->ti_end_min >= e->ti_next_stats && e->ti_next_stats > 0)
e->save_stats = 1;
@@ -5353,7 +5365,7 @@ void engine_dump_snapshot(struct engine *e) {
/**
* @brief Returns the initial affinity the main thread is using.
*/
-static cpu_set_t *engine_entry_affinity() {
+static cpu_set_t *engine_entry_affinity(void) {
static int use_entry_affinity = 0;
static cpu_set_t entry_affinity;
@@ -5372,7 +5384,7 @@ static cpu_set_t *engine_entry_affinity() {
* @brief Ensure the NUMA node on which we initialise (first touch) everything
* doesn't change before engine_init allocates NUMA-local workers.
*/
-void engine_pin() {
+void engine_pin(void) {
#ifdef HAVE_SETAFFINITY
cpu_set_t *entry_affinity = engine_entry_affinity();
@@ -5394,7 +5406,7 @@ void engine_pin() {
/**
* @brief Unpins the main thread.
*/
-void engine_unpin() {
+void engine_unpin(void) {
#ifdef HAVE_SETAFFINITY
pthread_t main_thread = pthread_self();
cpu_set_t *entry_affinity = engine_entry_affinity();
@@ -5430,10 +5442,9 @@ void engine_unpin() {
* @param chemistry The chemistry information.
* @param sourceterms The properties of the source terms function.
*/
-void engine_init(struct engine *e, struct space *s,
- const struct swift_params *params, long long Ngas,
- long long Ngparts, long long Nstars, int policy, int verbose,
- struct repartition *reparttype,
+void engine_init(struct engine *e, struct space *s, struct swift_params *params,
+ long long Ngas, long long Ngparts, long long Nstars,
+ int policy, int verbose, struct repartition *reparttype,
const struct unit_system *internal_units,
const struct phys_const *physical_constants,
struct cosmology *cosmo, const struct hydro_props *hydro,
@@ -5561,10 +5572,9 @@ void engine_init(struct engine *e, struct space *s,
* @param verbose Is this #engine talkative ?
* @param restart_file The name of our restart file.
*/
-void engine_config(int restart, struct engine *e,
- const struct swift_params *params, int nr_nodes, int nodeID,
- int nr_threads, int with_aff, int verbose,
- const char *restart_file) {
+void engine_config(int restart, struct engine *e, struct swift_params *params,
+ int nr_nodes, int nodeID, int nr_threads, int with_aff,
+ int verbose, const char *restart_file) {
/* Store the values and initialise global fields. */
e->nodeID = nodeID;
@@ -6238,8 +6248,12 @@ void engine_recompute_displacement_constraint(struct engine *e) {
/* Get the counts of each particle types */
const long long total_nr_dm_gparts =
e->total_nr_gparts - e->total_nr_parts - e->total_nr_sparts;
- float count_parts[swift_type_count] = {
- e->total_nr_parts, total_nr_dm_gparts, 0.f, 0.f, e->total_nr_sparts, 0.f};
+ float count_parts[swift_type_count] = {(float)e->total_nr_parts,
+ (float)total_nr_dm_gparts,
+ 0.f,
+ 0.f,
+ (float)e->total_nr_sparts,
+ 0.f};
/* Count of particles for the two species */
const float N_dm = count_parts[1];
diff --git a/src/engine.h b/src/engine.h
index 18c95b3c39f87df863cc6e17f5a005346a335dae..044bf6c895b50855c005e95082ceb2bbfdcbf55b 100644
--- a/src/engine.h
+++ b/src/engine.h
@@ -187,7 +187,12 @@ struct engine {
integertime_t ti_beg_max;
/* Number of particles updated in the previous step */
- size_t updates, g_updates, s_updates;
+ long long updates, g_updates, s_updates;
+
+ /* Number of updates since the last rebuild */
+ long long updates_since_rebuild;
+ long long g_updates_since_rebuild;
+ long long s_updates_since_rebuild;
/* Properties of the previous step */
int step_props;
@@ -311,7 +316,7 @@ struct engine {
struct sourceterms *sourceterms;
/* The (parsed) parameter file */
- const struct swift_params *parameter_file;
+ struct swift_params *parameter_file;
/* Temporary struct to hold a group of deferable properties (in MPI mode
* these are reduced together, but may not be required just yet). */
@@ -350,10 +355,9 @@ void engine_drift_top_multipoles(struct engine *e);
void engine_reconstruct_multipoles(struct engine *e);
void engine_print_stats(struct engine *e);
void engine_dump_snapshot(struct engine *e);
-void engine_init(struct engine *e, struct space *s,
- const struct swift_params *params, long long Ngas,
- long long Ngparts, long long Nstars, int policy, int verbose,
- struct repartition *reparttype,
+void engine_init(struct engine *e, struct space *s, struct swift_params *params,
+ long long Ngas, long long Ngparts, long long Nstars,
+ int policy, int verbose, struct repartition *reparttype,
const struct unit_system *internal_units,
const struct phys_const *physical_constants,
struct cosmology *cosmo, const struct hydro_props *hydro,
@@ -362,10 +366,9 @@ void engine_init(struct engine *e, struct space *s,
const struct cooling_function_data *cooling_func,
const struct chemistry_global_data *chemistry,
struct sourceterms *sourceterms);
-void engine_config(int restart, struct engine *e,
- const struct swift_params *params, int nr_nodes, int nodeID,
- int nr_threads, int with_aff, int verbose,
- const char *restart_file);
+void engine_config(int restart, struct engine *e, struct swift_params *params,
+ int nr_nodes, int nodeID, int nr_threads, int with_aff,
+ int verbose, const char *restart_file);
void engine_launch(struct engine *e);
void engine_prepare(struct engine *e);
void engine_init_particles(struct engine *e, int flag_entropy_ICs,
@@ -385,8 +388,8 @@ void engine_makeproxies(struct engine *e);
void engine_redistribute(struct engine *e);
void engine_print_policy(struct engine *e);
int engine_is_done(struct engine *e);
-void engine_pin();
-void engine_unpin();
+void engine_pin(void);
+void engine_unpin(void);
void engine_clean(struct engine *e);
int engine_estimate_nr_tasks(struct engine *e);
diff --git a/src/equation_of_state/ideal_gas/equation_of_state.h b/src/equation_of_state/ideal_gas/equation_of_state.h
index 36b3511558e1c38c9135c689f45eea17220be053..0d57f6a5ce51091f82e79b009b0e85f1368d51cf 100644
--- a/src/equation_of_state/ideal_gas/equation_of_state.h
+++ b/src/equation_of_state/ideal_gas/equation_of_state.h
@@ -178,7 +178,7 @@ __attribute__((always_inline)) INLINE static float gas_soundspeed_from_pressure(
*/
__attribute__((always_inline)) INLINE static void eos_init(
struct eos_parameters *e, const struct phys_const *phys_const,
- const struct unit_system *us, const struct swift_params *params) {}
+ const struct unit_system *us, struct swift_params *params) {}
/**
* @brief Print the equation of state
*
diff --git a/src/equation_of_state/isothermal/equation_of_state.h b/src/equation_of_state/isothermal/equation_of_state.h
index c7afac6caaacf354f8067218fbe2013b9287309a..540bf073cee106b91e2a9f4ecedb1b20238856fd 100644
--- a/src/equation_of_state/isothermal/equation_of_state.h
+++ b/src/equation_of_state/isothermal/equation_of_state.h
@@ -195,7 +195,7 @@ __attribute__((always_inline)) INLINE static float gas_soundspeed_from_pressure(
*/
__attribute__((always_inline)) INLINE static void eos_init(
struct eos_parameters *e, const struct phys_const *phys_const,
- const struct unit_system *us, const struct swift_params *params) {
+ const struct unit_system *us, struct swift_params *params) {
e->isothermal_internal_energy =
parser_get_param_float(params, "EoS:isothermal_internal_energy");
diff --git a/src/equation_of_state/planetary/equation_of_state.h b/src/equation_of_state/planetary/equation_of_state.h
index d7a7f64f87bb126094163ada16dbd05e48d8cf8d..61e23dc0b4eb82e9ae5c0869f7a10dfff97fc45e 100644
--- a/src/equation_of_state/planetary/equation_of_state.h
+++ b/src/equation_of_state/planetary/equation_of_state.h
@@ -54,7 +54,7 @@ enum eos_planetary_type_id {
eos_planetary_type_HM80 = 2,
eos_planetary_type_ANEOS = 3,
eos_planetary_type_SESAME = 4,
-} __attribute__((packed));
+};
/**
* @brief Minor type for the planetary equation of state.
@@ -104,7 +104,7 @@ enum eos_planetary_material_id {
/*! SESAME iron */
eos_planetary_id_SESAME_iron =
eos_planetary_type_SESAME * eos_planetary_type_factor,
-} __attribute__((packed));
+};
/* Individual EOS function headers. */
#include "aneos.h"
@@ -132,7 +132,8 @@ __attribute__((always_inline)) INLINE static float
gas_internal_energy_from_entropy(float density, float entropy,
enum eos_planetary_material_id mat_id) {
- const enum eos_planetary_type_id type = mat_id / eos_planetary_type_factor;
+ const enum eos_planetary_type_id type =
+ (enum eos_planetary_type_id)(mat_id / eos_planetary_type_factor);
/* Select the material base type */
switch (type) {
@@ -241,7 +242,8 @@ gas_internal_energy_from_entropy(float density, float entropy,
__attribute__((always_inline)) INLINE static float gas_pressure_from_entropy(
float density, float entropy, enum eos_planetary_material_id mat_id) {
- const enum eos_planetary_type_id type = mat_id / eos_planetary_type_factor;
+ const enum eos_planetary_type_id type =
+ (enum eos_planetary_type_id)(mat_id / eos_planetary_type_factor);
/* Select the material base type */
switch (type) {
@@ -344,7 +346,8 @@ __attribute__((always_inline)) INLINE static float gas_pressure_from_entropy(
__attribute__((always_inline)) INLINE static float gas_entropy_from_pressure(
float density, float P, enum eos_planetary_material_id mat_id) {
- const enum eos_planetary_type_id type = mat_id / eos_planetary_type_factor;
+ const enum eos_planetary_type_id type =
+ (enum eos_planetary_type_id)(mat_id / eos_planetary_type_factor);
/* Select the material base type */
switch (type) {
@@ -445,7 +448,8 @@ __attribute__((always_inline)) INLINE static float gas_entropy_from_pressure(
__attribute__((always_inline)) INLINE static float gas_soundspeed_from_entropy(
float density, float entropy, enum eos_planetary_material_id mat_id) {
- const enum eos_planetary_type_id type = mat_id / eos_planetary_type_factor;
+ const enum eos_planetary_type_id type =
+ (enum eos_planetary_type_id)(mat_id / eos_planetary_type_factor);
/* Select the material base type */
switch (type) {
@@ -549,8 +553,8 @@ __attribute__((always_inline)) INLINE static float gas_soundspeed_from_entropy(
__attribute__((always_inline)) INLINE static float
gas_entropy_from_internal_energy(float density, float u,
enum eos_planetary_material_id mat_id) {
-
- const enum eos_planetary_type_id type = mat_id / eos_planetary_type_factor;
+ const enum eos_planetary_type_id type =
+ (enum eos_planetary_type_id)(mat_id / eos_planetary_type_factor);
/* Select the material base type */
switch (type) {
@@ -654,7 +658,8 @@ __attribute__((always_inline)) INLINE static float
gas_pressure_from_internal_energy(float density, float u,
enum eos_planetary_material_id mat_id) {
- const enum eos_planetary_type_id type = mat_id / eos_planetary_type_factor;
+ const enum eos_planetary_type_id type =
+ (enum eos_planetary_type_id)(mat_id / eos_planetary_type_factor);
/* Select the material base type */
switch (type) {
@@ -762,7 +767,8 @@ __attribute__((always_inline)) INLINE static float
gas_internal_energy_from_pressure(float density, float P,
enum eos_planetary_material_id mat_id) {
- const enum eos_planetary_type_id type = mat_id / eos_planetary_type_factor;
+ const enum eos_planetary_type_id type =
+ (enum eos_planetary_type_id)(mat_id / eos_planetary_type_factor);
/* Select the material base type */
switch (type) {
@@ -867,7 +873,8 @@ __attribute__((always_inline)) INLINE static float
gas_soundspeed_from_internal_energy(float density, float u,
enum eos_planetary_material_id mat_id) {
- const enum eos_planetary_type_id type = mat_id / eos_planetary_type_factor;
+ const enum eos_planetary_type_id type =
+ (enum eos_planetary_type_id)(mat_id / eos_planetary_type_factor);
/* Select the material base type */
switch (type) {
@@ -975,7 +982,8 @@ gas_soundspeed_from_internal_energy(float density, float u,
__attribute__((always_inline)) INLINE static float gas_soundspeed_from_pressure(
float density, float P, enum eos_planetary_material_id mat_id) {
- const enum eos_planetary_type_id type = mat_id / eos_planetary_type_factor;
+ const enum eos_planetary_type_id type =
+ (enum eos_planetary_type_id)(mat_id / eos_planetary_type_factor);
/* Select the material base type */
switch (type) {
@@ -1075,7 +1083,7 @@ __attribute__((always_inline)) INLINE static float gas_soundspeed_from_pressure(
*/
__attribute__((always_inline)) INLINE static void eos_init(
struct eos_parameters *e, const struct phys_const *phys_const,
- const struct unit_system *us, const struct swift_params *params) {
+ const struct unit_system *us, struct swift_params *params) {
// Table file names
char HM80_HHe_table_file[PARSER_MAX_LINE_SIZE];
diff --git a/src/gravity.h b/src/gravity.h
index 073b0b053275491c555e28a7fe91e6ce4bf64a43..6497de8294dfa3f207332ff696ddb992c875eb28 100644
--- a/src/gravity.h
+++ b/src/gravity.h
@@ -36,7 +36,7 @@ struct engine;
struct space;
void gravity_exact_force_ewald_init(double boxSize);
-void gravity_exact_force_ewald_free();
+void gravity_exact_force_ewald_free(void);
void gravity_exact_force_ewald_evaluate(double rx, double ry, double rz,
double corr_f[3], double *corr_p);
void gravity_exact_force_compute(struct space *s, const struct engine *e);
diff --git a/src/gravity/Default/gravity_io.h b/src/gravity/Default/gravity_io.h
index 7b8ec2c8fef04cc4a4fc6836d8bb895b24d3c41f..7f453179641e2ba16b30e3172ddd7853245a1d2f 100644
--- a/src/gravity/Default/gravity_io.h
+++ b/src/gravity/Default/gravity_io.h
@@ -21,8 +21,8 @@
#include "io_properties.h"
-void convert_gpart_pos(const struct engine* e, const struct gpart* gp,
- double* ret) {
+INLINE static void convert_gpart_pos(const struct engine* e,
+ const struct gpart* gp, double* ret) {
if (e->s->periodic) {
ret[0] = box_wrap(gp->x[0], 0.0, e->s->dim[0]);
@@ -35,8 +35,8 @@ void convert_gpart_pos(const struct engine* e, const struct gpart* gp,
}
}
-void convert_gpart_vel(const struct engine* e, const struct gpart* gp,
- float* ret) {
+INLINE static void convert_gpart_vel(const struct engine* e,
+ const struct gpart* gp, float* ret) {
const int with_cosmology = (e->policy & engine_policy_cosmology);
const struct cosmology* cosmo = e->cosmology;
@@ -62,9 +62,9 @@ void convert_gpart_vel(const struct engine* e, const struct gpart* gp,
ret[2] = gp->v_full[2] + gp->a_grav[2] * dt_kick_grav;
/* Conversion from internal units to peculiar velocities */
- ret[0] *= cosmo->a2_inv;
- ret[1] *= cosmo->a2_inv;
- ret[2] *= cosmo->a2_inv;
+ ret[0] *= cosmo->a_inv;
+ ret[1] *= cosmo->a_inv;
+ ret[2] *= cosmo->a_inv;
}
/**
@@ -74,8 +74,9 @@ void convert_gpart_vel(const struct engine* e, const struct gpart* gp,
* @param list The list of i/o properties to read.
* @param num_fields The number of i/o fields to read.
*/
-void darkmatter_read_particles(struct gpart* gparts, struct io_props* list,
- int* num_fields) {
+INLINE static void darkmatter_read_particles(struct gpart* gparts,
+ struct io_props* list,
+ int* num_fields) {
/* Say how much we want to read */
*num_fields = 4;
@@ -98,8 +99,9 @@ void darkmatter_read_particles(struct gpart* gparts, struct io_props* list,
* @param list The list of i/o properties to write.
* @param num_fields The number of i/o fields to write.
*/
-void darkmatter_write_particles(const struct gpart* gparts,
- struct io_props* list, int* num_fields) {
+INLINE static void darkmatter_write_particles(const struct gpart* gparts,
+ struct io_props* list,
+ int* num_fields) {
/* Say how much we want to write */
*num_fields = 5;
diff --git a/src/gravity_properties.c b/src/gravity_properties.c
index 928765cc14f856929cb30e936c6044d87b70186a..481ed2cd5e35382cd85d9bec4f94c109738ffb70 100644
--- a/src/gravity_properties.c
+++ b/src/gravity_properties.c
@@ -35,11 +35,19 @@
#define gravity_props_default_a_smooth 1.25f
#define gravity_props_default_r_cut_max 4.5f
#define gravity_props_default_r_cut_min 0.1f
+#define gravity_props_default_rebuild_frequency 0.01f
-void gravity_props_init(struct gravity_props *p,
- const struct swift_params *params,
+void gravity_props_init(struct gravity_props *p, struct swift_params *params,
const struct cosmology *cosmo) {
+ /* Tree updates */
+ p->rebuild_frequency =
+ parser_get_opt_param_float(params, "Gravity:rebuild_frequency",
+ gravity_props_default_rebuild_frequency);
+
+ if (p->rebuild_frequency < 0.f || p->rebuild_frequency > 1.f)
+ error("Invalid tree rebuild frequency. Must be in [0., 1.]");
+
/* Tree-PM parameters */
p->a_smooth = parser_get_opt_param_float(params, "Gravity:a_smooth",
gravity_props_default_a_smooth);
@@ -116,12 +124,16 @@ void gravity_props_print(const struct gravity_props *p) {
message("Self-gravity tree cut-off: r_cut_max=%f", p->r_cut_max);
message("Self-gravity truncation cut-off: r_cut_min=%f", p->r_cut_min);
+
+ message("Self-gravity tree update frequency: f=%f", p->rebuild_frequency);
}
#if defined(HAVE_HDF5)
void gravity_props_print_snapshot(hid_t h_grpgrav,
const struct gravity_props *p) {
+ io_write_attribute_f(h_grpgrav, "Tree update frequency",
+ p->rebuild_frequency);
io_write_attribute_f(h_grpgrav, "Time integration eta", p->eta);
io_write_attribute_f(
h_grpgrav, "Comoving softening length",
diff --git a/src/gravity_properties.h b/src/gravity_properties.h
index f36a39a6e187b8b397a5f597692f5a37c982aa7a..7faaa88d5e82b7882404269009b2f0542896eee1 100644
--- a/src/gravity_properties.h
+++ b/src/gravity_properties.h
@@ -36,6 +36,9 @@
*/
struct gravity_props {
+ /*! Frequency of tree-rebuild in units of #gpart updates. */
+ float rebuild_frequency;
+
/*! Mesh smoothing scale in units of top-level cell size */
float a_smooth;
@@ -79,8 +82,7 @@ struct gravity_props {
};
void gravity_props_print(const struct gravity_props *p);
-void gravity_props_init(struct gravity_props *p,
- const struct swift_params *params,
+void gravity_props_init(struct gravity_props *p, struct swift_params *params,
const struct cosmology *cosmo);
void gravity_update(struct gravity_props *p, const struct cosmology *cosmo);
diff --git a/src/hydro/Default/hydro.h b/src/hydro/Default/hydro.h
index b1a999b63143437cab8518cfdd96885533d7401e..2c3a9c46f0500fb20aa3cfa2e5feb682b3dcec63 100644
--- a/src/hydro/Default/hydro.h
+++ b/src/hydro/Default/hydro.h
@@ -339,7 +339,7 @@ __attribute__((always_inline)) INLINE static void hydro_part_has_no_neighbours(
/* Re-set problematic values */
p->rho = p->mass * kernel_root * h_inv_dim;
- p->density.wcount = kernel_root * kernel_norm * h_inv_dim;
+ p->density.wcount = kernel_root * h_inv_dim;
p->rho_dh = 0.f;
p->density.wcount_dh = 0.f;
p->density.div_v = 0.f;
@@ -423,7 +423,7 @@ __attribute__((always_inline)) INLINE static void hydro_reset_acceleration(
/* Reset the time derivatives. */
p->force.u_dt = 0.0f;
p->force.h_dt = 0.0f;
- p->force.v_sig = 0.0f;
+ p->force.v_sig = p->force.soundspeed;
}
/**
diff --git a/src/hydro/Default/hydro_io.h b/src/hydro/Default/hydro_io.h
index 542cc21d41741a203adacb4560c6bd701e3af758..d47c96fbf32e1ee00346888aaf2e8afabc22abc3 100644
--- a/src/hydro/Default/hydro_io.h
+++ b/src/hydro/Default/hydro_io.h
@@ -31,8 +31,9 @@
* @param list The list of i/o properties to read.
* @param num_fields The number of i/o fields to read.
*/
-void hydro_read_particles(struct part* parts, struct io_props* list,
- int* num_fields) {
+INLINE static void hydro_read_particles(struct part* parts,
+ struct io_props* list,
+ int* num_fields) {
*num_fields = 8;
@@ -55,8 +56,9 @@ void hydro_read_particles(struct part* parts, struct io_props* list,
UNIT_CONV_DENSITY, parts, rho);
}
-void convert_part_pos(const struct engine* e, const struct part* p,
- const struct xpart* xp, double* ret) {
+INLINE static void convert_part_pos(const struct engine* e,
+ const struct part* p,
+ const struct xpart* xp, double* ret) {
if (e->s->periodic) {
ret[0] = box_wrap(p->x[0], 0.0, e->s->dim[0]);
@@ -69,8 +71,9 @@ void convert_part_pos(const struct engine* e, const struct part* p,
}
}
-void convert_part_vel(const struct engine* e, const struct part* p,
- const struct xpart* xp, float* ret) {
+INLINE static void convert_part_vel(const struct engine* e,
+ const struct part* p,
+ const struct xpart* xp, float* ret) {
const int with_cosmology = (e->policy & engine_policy_cosmology);
const struct cosmology* cosmo = e->cosmology;
@@ -98,13 +101,14 @@ void convert_part_vel(const struct engine* e, const struct part* p,
hydro_get_drifted_velocities(p, xp, dt_kick_hydro, dt_kick_grav, ret);
/* Conversion from internal units to peculiar velocities */
- ret[0] *= cosmo->a2_inv;
- ret[1] *= cosmo->a2_inv;
- ret[2] *= cosmo->a2_inv;
+ ret[0] *= cosmo->a_inv;
+ ret[1] *= cosmo->a_inv;
+ ret[2] *= cosmo->a_inv;
}
-void convert_part_potential(const struct engine* e, const struct part* p,
- const struct xpart* xp, float* ret) {
+INLINE static void convert_part_potential(const struct engine* e,
+ const struct part* p,
+ const struct xpart* xp, float* ret) {
if (p->gpart != NULL)
ret[0] = gravity_get_comoving_potential(p->gpart);
@@ -119,8 +123,10 @@ void convert_part_potential(const struct engine* e, const struct part* p,
* @param list The list of i/o properties to write.
* @param num_fields The number of i/o fields to write.
*/
-void hydro_write_particles(const struct part* parts, const struct xpart* xparts,
- struct io_props* list, int* num_fields) {
+INLINE static void hydro_write_particles(const struct part* parts,
+ const struct xpart* xparts,
+ struct io_props* list,
+ int* num_fields) {
*num_fields = 8;
@@ -149,7 +155,7 @@ void hydro_write_particles(const struct part* parts, const struct xpart* xparts,
* @brief Writes the current model of SPH to the file
* @param h_grpsph The HDF5 group in which to write
*/
-void hydro_write_flavour(hid_t h_grpsph) {
+INLINE static void hydro_write_flavour(hid_t h_grpsph) {
/* Viscosity and thermal conduction */
io_write_attribute_s(h_grpsph, "Thermal Conductivity Model",
@@ -178,6 +184,6 @@ void hydro_write_flavour(hid_t h_grpsph) {
*
* @return 1 if entropy is in 'internal energy', 0 otherwise.
*/
-int writeEntropyFlag() { return 0; }
+INLINE static int writeEntropyFlag(void) { return 0; }
#endif /* SWIFT_DEFAULT_HYDRO_IO_H */
diff --git a/src/hydro/Gadget2/hydro.h b/src/hydro/Gadget2/hydro.h
index bc06a24e2a8245556a1042f2459273b8d750489e..26e3bf97dd1924abbe7380d1eaadce75213344df 100644
--- a/src/hydro/Gadget2/hydro.h
+++ b/src/hydro/Gadget2/hydro.h
@@ -349,7 +349,7 @@ __attribute__((always_inline)) INLINE static void hydro_part_has_no_neighbours(
/* Re-set problematic values */
p->rho = p->mass * kernel_root * h_inv_dim;
- p->density.wcount = kernel_root * kernel_norm * h_inv_dim;
+ p->density.wcount = kernel_root * h_inv_dim;
p->density.rho_dh = 0.f;
p->density.wcount_dh = 0.f;
p->density.div_v = 0.f;
diff --git a/src/hydro/Gadget2/hydro_io.h b/src/hydro/Gadget2/hydro_io.h
index 28c0eea4772f51fab35a08d43c0564472694eeeb..3f2af41dc7f0cc8f60992a15a0f09f3c90f764fe 100644
--- a/src/hydro/Gadget2/hydro_io.h
+++ b/src/hydro/Gadget2/hydro_io.h
@@ -31,8 +31,9 @@
* @param list The list of i/o properties to read.
* @param num_fields The number of i/o fields to read.
*/
-void hydro_read_particles(struct part* parts, struct io_props* list,
- int* num_fields) {
+INLINE static void hydro_read_particles(struct part* parts,
+ struct io_props* list,
+ int* num_fields) {
*num_fields = 8;
@@ -55,20 +56,21 @@ void hydro_read_particles(struct part* parts, struct io_props* list,
UNIT_CONV_DENSITY, parts, rho);
}
-void convert_part_u(const struct engine* e, const struct part* p,
- const struct xpart* xp, float* ret) {
+INLINE static void convert_part_u(const struct engine* e, const struct part* p,
+ const struct xpart* xp, float* ret) {
ret[0] = hydro_get_comoving_internal_energy(p);
}
-void convert_part_P(const struct engine* e, const struct part* p,
- const struct xpart* xp, float* ret) {
+INLINE static void convert_part_P(const struct engine* e, const struct part* p,
+ const struct xpart* xp, float* ret) {
ret[0] = hydro_get_comoving_pressure(p);
}
-void convert_part_pos(const struct engine* e, const struct part* p,
- const struct xpart* xp, double* ret) {
+INLINE static void convert_part_pos(const struct engine* e,
+ const struct part* p,
+ const struct xpart* xp, double* ret) {
if (e->s->periodic) {
ret[0] = box_wrap(p->x[0], 0.0, e->s->dim[0]);
@@ -81,8 +83,9 @@ void convert_part_pos(const struct engine* e, const struct part* p,
}
}
-void convert_part_vel(const struct engine* e, const struct part* p,
- const struct xpart* xp, float* ret) {
+INLINE static void convert_part_vel(const struct engine* e,
+ const struct part* p,
+ const struct xpart* xp, float* ret) {
const int with_cosmology = (e->policy & engine_policy_cosmology);
const struct cosmology* cosmo = e->cosmology;
@@ -110,13 +113,14 @@ void convert_part_vel(const struct engine* e, const struct part* p,
hydro_get_drifted_velocities(p, xp, dt_kick_hydro, dt_kick_grav, ret);
/* Conversion from internal units to peculiar velocities */
- ret[0] *= cosmo->a2_inv;
- ret[1] *= cosmo->a2_inv;
- ret[2] *= cosmo->a2_inv;
+ ret[0] *= cosmo->a_inv;
+ ret[1] *= cosmo->a_inv;
+ ret[2] *= cosmo->a_inv;
}
-void convert_part_potential(const struct engine* e, const struct part* p,
- const struct xpart* xp, float* ret) {
+INLINE static void convert_part_potential(const struct engine* e,
+ const struct part* p,
+ const struct xpart* xp, float* ret) {
if (p->gpart != NULL)
ret[0] = gravity_get_comoving_potential(p->gpart);
@@ -131,8 +135,10 @@ void convert_part_potential(const struct engine* e, const struct part* p,
* @param list The list of i/o properties to write.
* @param num_fields The number of i/o fields to write.
*/
-void hydro_write_particles(const struct part* parts, const struct xpart* xparts,
- struct io_props* list, int* num_fields) {
+INLINE static void hydro_write_particles(const struct part* parts,
+ const struct xpart* xparts,
+ struct io_props* list,
+ int* num_fields) {
*num_fields = 10;
@@ -185,7 +191,7 @@ void hydro_write_particles(const struct part* parts, const struct xpart* xparts,
* @brief Writes the current model of SPH to the file
* @param h_grpsph The HDF5 group in which to write
*/
-void hydro_write_flavour(hid_t h_grpsph) {
+INLINE static void hydro_write_flavour(hid_t h_grpsph) {
/* Viscosity and thermal conduction */
io_write_attribute_s(h_grpsph, "Thermal Conductivity Model",
@@ -202,6 +208,6 @@ void hydro_write_flavour(hid_t h_grpsph) {
*
* @return 1 if entropy is in 'internal energy', 0 otherwise.
*/
-int writeEntropyFlag() { return 0; }
+INLINE static int writeEntropyFlag(void) { return 0; }
#endif /* SWIFT_GADGET2_HYDRO_IO_H */
diff --git a/src/hydro/GizmoMFM/hydro.h b/src/hydro/GizmoMFM/hydro.h
index 9c4be6af359d7236e483b712065b357c6ed35402..1ab142740b641bdc9a0dff5a02b19479bae8257e 100644
--- a/src/hydro/GizmoMFM/hydro.h
+++ b/src/hydro/GizmoMFM/hydro.h
@@ -398,7 +398,7 @@ __attribute__((always_inline)) INLINE static void hydro_part_has_no_neighbours(
const float h_inv_dim = pow_dimension(h_inv); /* 1/h^d */
/* Re-set problematic values */
- p->density.wcount = kernel_root * kernel_norm * h_inv_dim;
+ p->density.wcount = kernel_root * h_inv_dim;
p->density.wcount_dh = 0.f;
p->geometry.volume = 1.0f;
p->geometry.matrix_E[0][0] = 1.0f;
@@ -421,8 +421,7 @@ __attribute__((always_inline)) INLINE static void hydro_part_has_no_neighbours(
/**
* @brief Prepare a particle for the gradient calculation.
*
- * The name of this method is confusing, as this method is really called after
- * the density loop and before the gradient loop.
+ * This function is called after the density loop and before the gradient loop.
*
* We use it to set the physical timestep for the particle and to copy the
* actual velocities, which we need to boost our interfaces during the flux
@@ -433,7 +432,7 @@ __attribute__((always_inline)) INLINE static void hydro_part_has_no_neighbours(
* @param xp The extended particle data to act upon.
* @param cosmo The cosmological model.
*/
-__attribute__((always_inline)) INLINE static void hydro_prepare_force(
+__attribute__((always_inline)) INLINE static void hydro_prepare_gradient(
struct part* restrict p, struct xpart* restrict xp,
const struct cosmology* cosmo) {
@@ -446,6 +445,18 @@ __attribute__((always_inline)) INLINE static void hydro_prepare_force(
hydro_velocities_prepare_force(p, xp);
}
+/**
+ * @brief Resets the variables that are required for a gradient calculation.
+ *
+ * This function is called after hydro_prepare_gradient.
+ *
+ * @param p The particle to act upon.
+ * @param xp The extended particle data to act upon.
+ * @param cosmo The cosmological model.
+ */
+__attribute__((always_inline)) INLINE static void hydro_reset_gradient(
+ struct part* restrict p) {}
+
/**
* @brief Finishes the gradient calculation.
*
@@ -461,6 +472,28 @@ __attribute__((always_inline)) INLINE static void hydro_end_gradient(
hydro_gradients_finalize(p);
+#ifdef GIZMO_LLOYD_ITERATION
+ /* reset the gradients to zero, as we don't want them */
+ hydro_gradients_init(p);
+#endif
+}
+
+/**
+ * @brief Prepare a particle for the force calculation.
+ *
+ * This function is called in the extra_ghost task to convert some quantities
+ * coming from the gradient loop over neighbours into quantities ready to be
+ * used in the force loop over neighbours.
+ *
+ * @param p The particle to act upon
+ * @param xp The extended particle data to act upon
+ * @param cosmo The current cosmological model.
+ */
+__attribute__((always_inline)) INLINE static void hydro_prepare_force(
+ struct part* restrict p, struct xpart* restrict xp,
+ const struct cosmology* cosmo) {
+
+ /* Initialise values that are used in the force loop */
p->gravity.mflux[0] = 0.0f;
p->gravity.mflux[1] = 0.0f;
p->gravity.mflux[2] = 0.0f;
@@ -470,11 +503,6 @@ __attribute__((always_inline)) INLINE static void hydro_end_gradient(
p->conserved.flux.momentum[1] = 0.0f;
p->conserved.flux.momentum[2] = 0.0f;
p->conserved.flux.energy = 0.0f;
-
-#ifdef GIZMO_LLOYD_ITERATION
- /* reset the gradients to zero, as we don't want them */
- hydro_gradients_init(p);
-#endif
}
/**
diff --git a/src/hydro/GizmoMFM/hydro_io.h b/src/hydro/GizmoMFM/hydro_io.h
index 171132eacfcd43feeec57d3c16b5a458171b1d79..59d579f70cd4aedc728dbf42038eff78d4c507d5 100644
--- a/src/hydro/GizmoMFM/hydro_io.h
+++ b/src/hydro/GizmoMFM/hydro_io.h
@@ -40,8 +40,9 @@
* @param list The list of i/o properties to read.
* @param num_fields The number of i/o fields to read.
*/
-void hydro_read_particles(struct part* parts, struct io_props* list,
- int* num_fields) {
+INLINE static void hydro_read_particles(struct part* parts,
+ struct io_props* list,
+ int* num_fields) {
*num_fields = 8;
@@ -72,8 +73,8 @@ void hydro_read_particles(struct part* parts, struct io_props* list,
* @param p Particle.
* @param ret (return) Internal energy of the particle
*/
-void convert_u(const struct engine* e, const struct part* p,
- const struct xpart* xp, float* ret) {
+INLINE static void convert_u(const struct engine* e, const struct part* p,
+ const struct xpart* xp, float* ret) {
ret[0] = hydro_get_comoving_internal_energy(p);
}
@@ -85,8 +86,8 @@ void convert_u(const struct engine* e, const struct part* p,
* @param p Particle.
* @param ret (return) Entropic function of the particle
*/
-void convert_A(const struct engine* e, const struct part* p,
- const struct xpart* xp, float* ret) {
+INLINE static void convert_A(const struct engine* e, const struct part* p,
+ const struct xpart* xp, float* ret) {
ret[0] = hydro_get_comoving_entropy(p);
}
@@ -97,8 +98,8 @@ void convert_A(const struct engine* e, const struct part* p,
* @param p Particle.
* @return Total energy of the particle
*/
-void convert_Etot(const struct engine* e, const struct part* p,
- const struct xpart* xp, float* ret) {
+INLINE static void convert_Etot(const struct engine* e, const struct part* p,
+ const struct xpart* xp, float* ret) {
#ifdef GIZMO_TOTAL_ENERGY
ret[0] = p->conserved.energy;
#else
@@ -112,8 +113,9 @@ void convert_Etot(const struct engine* e, const struct part* p,
#endif
}
-void convert_part_pos(const struct engine* e, const struct part* p,
- const struct xpart* xp, double* ret) {
+INLINE static void convert_part_pos(const struct engine* e,
+ const struct part* p,
+ const struct xpart* xp, double* ret) {
if (e->s->periodic) {
ret[0] = box_wrap(p->x[0], 0.0, e->s->dim[0]);
@@ -126,8 +128,9 @@ void convert_part_pos(const struct engine* e, const struct part* p,
}
}
-void convert_part_vel(const struct engine* e, const struct part* p,
- const struct xpart* xp, float* ret) {
+INLINE static void convert_part_vel(const struct engine* e,
+ const struct part* p,
+ const struct xpart* xp, float* ret) {
const int with_cosmology = (e->policy & engine_policy_cosmology);
const struct cosmology* cosmo = e->cosmology;
@@ -155,13 +158,14 @@ void convert_part_vel(const struct engine* e, const struct part* p,
hydro_get_drifted_velocities(p, xp, dt_kick_hydro, dt_kick_grav, ret);
/* Conversion from internal units to peculiar velocities */
- ret[0] *= cosmo->a2_inv;
- ret[1] *= cosmo->a2_inv;
- ret[2] *= cosmo->a2_inv;
+ ret[0] *= cosmo->a_inv;
+ ret[1] *= cosmo->a_inv;
+ ret[2] *= cosmo->a_inv;
}
-void convert_part_potential(const struct engine* e, const struct part* p,
- const struct xpart* xp, float* ret) {
+INLINE static void convert_part_potential(const struct engine* e,
+ const struct part* p,
+ const struct xpart* xp, float* ret) {
if (p->gpart != NULL)
ret[0] = gravity_get_comoving_potential(p->gpart);
@@ -176,8 +180,10 @@ void convert_part_potential(const struct engine* e, const struct part* p,
* @param list The list of i/o properties to write.
* @param num_fields The number of i/o fields to write.
*/
-void hydro_write_particles(const struct part* parts, const struct xpart* xparts,
- struct io_props* list, int* num_fields) {
+INLINE static void hydro_write_particles(const struct part* parts,
+ const struct xpart* xparts,
+ struct io_props* list,
+ int* num_fields) {
*num_fields = 11;
@@ -215,7 +221,7 @@ void hydro_write_particles(const struct part* parts, const struct xpart* xparts,
* @brief Writes the current model of SPH to the file
* @param h_grpsph The HDF5 group in which to write
*/
-void hydro_write_flavour(hid_t h_grpsph) {
+INLINE static void hydro_write_flavour(hid_t h_grpsph) {
/* Gradient information */
io_write_attribute_s(h_grpsph, "Gradient reconstruction model",
HYDRO_GRADIENT_IMPLEMENTATION);
@@ -239,6 +245,6 @@ void hydro_write_flavour(hid_t h_grpsph) {
*
* @return 1 if entropy is in 'internal energy', 0 otherwise.
*/
-int writeEntropyFlag() { return 0; }
+INLINE static int writeEntropyFlag(void) { return 0; }
#endif /* SWIFT_GIZMO_MFM_HYDRO_IO_H */
diff --git a/src/hydro/GizmoMFV/hydro.h b/src/hydro/GizmoMFV/hydro.h
index 1d5abeaaf63d88b02817a691f160c537d0b1915b..6916fe33272692316354385b723ce9969606b6a2 100644
--- a/src/hydro/GizmoMFV/hydro.h
+++ b/src/hydro/GizmoMFV/hydro.h
@@ -398,7 +398,7 @@ __attribute__((always_inline)) INLINE static void hydro_part_has_no_neighbours(
const float h_inv_dim = pow_dimension(h_inv); /* 1/h^d */
/* Re-set problematic values */
- p->density.wcount = kernel_root * kernel_norm * h_inv_dim;
+ p->density.wcount = kernel_root * h_inv_dim;
p->density.wcount_dh = 0.f;
p->geometry.volume = 1.0f;
p->geometry.matrix_E[0][0] = 1.0f;
@@ -421,8 +421,7 @@ __attribute__((always_inline)) INLINE static void hydro_part_has_no_neighbours(
/**
* @brief Prepare a particle for the gradient calculation.
*
- * The name of this method is confusing, as this method is really called after
- * the density loop and before the gradient loop.
+ * This function is called after the density loop and before the gradient loop.
*
* We use it to set the physical timestep for the particle and to copy the
* actual velocities, which we need to boost our interfaces during the flux
@@ -433,7 +432,7 @@ __attribute__((always_inline)) INLINE static void hydro_part_has_no_neighbours(
* @param xp The extended particle data to act upon.
* @param cosmo The cosmological model.
*/
-__attribute__((always_inline)) INLINE static void hydro_prepare_force(
+__attribute__((always_inline)) INLINE static void hydro_prepare_gradient(
struct part* restrict p, struct xpart* restrict xp,
const struct cosmology* cosmo) {
@@ -452,8 +451,6 @@ __attribute__((always_inline)) INLINE static void hydro_prepare_force(
* Just a wrapper around hydro_gradients_finalize, which can be an empty method,
* in which case no gradients are used.
*
- * This method also initializes the force loop variables.
- *
* @param p The particle to act upon.
*/
__attribute__((always_inline)) INLINE static void hydro_end_gradient(
@@ -461,6 +458,28 @@ __attribute__((always_inline)) INLINE static void hydro_end_gradient(
hydro_gradients_finalize(p);
+#ifdef GIZMO_LLOYD_ITERATION
+ /* reset the gradients to zero, as we don't want them */
+ hydro_gradients_init(p);
+#endif
+}
+
+/**
+ * @brief Prepare a particle for the force calculation.
+ *
+ * This function is called in the extra_ghost task to convert some quantities
+ * coming from the gradient loop over neighbours into quantities ready to be
+ * used in the force loop over neighbours.
+ *
+ * @param p The particle to act upon
+ * @param xp The extended particle data to act upon
+ * @param cosmo The current cosmological model.
+ */
+__attribute__((always_inline)) INLINE static void hydro_prepare_force(
+ struct part* restrict p, struct xpart* restrict xp,
+ const struct cosmology* cosmo) {
+
+ /* Initialise values that are used in the force loop */
p->gravity.mflux[0] = 0.0f;
p->gravity.mflux[1] = 0.0f;
p->gravity.mflux[2] = 0.0f;
@@ -470,11 +489,6 @@ __attribute__((always_inline)) INLINE static void hydro_end_gradient(
p->conserved.flux.momentum[1] = 0.0f;
p->conserved.flux.momentum[2] = 0.0f;
p->conserved.flux.energy = 0.0f;
-
-#ifdef GIZMO_LLOYD_ITERATION
- /* reset the gradients to zero, as we don't want them */
- hydro_gradients_init(p);
-#endif
}
/**
@@ -497,6 +511,18 @@ __attribute__((always_inline)) INLINE static void hydro_reset_acceleration(
p->force.h_dt = 0.0f;
}
+/**
+ * @brief Resets the variables that are required for a gradient calculation.
+ *
+ * This function is called after hydro_prepare_gradient.
+ *
+ * @param p The particle to act upon.
+ * @param xp The extended particle data to act upon.
+ * @param cosmo The cosmological model.
+ */
+__attribute__((always_inline)) INLINE static void hydro_reset_gradient(
+ struct part* restrict p) {}
+
/**
* @brief Sets the values to be predicted in the drifts to their values at a
* kick time
diff --git a/src/hydro/GizmoMFV/hydro_io.h b/src/hydro/GizmoMFV/hydro_io.h
index c1b151230f3198a30d6696e36a2704156804fdce..92e4378f071cb71678929716be86588a3405f40e 100644
--- a/src/hydro/GizmoMFV/hydro_io.h
+++ b/src/hydro/GizmoMFV/hydro_io.h
@@ -40,8 +40,9 @@
* @param list The list of i/o properties to read.
* @param num_fields The number of i/o fields to read.
*/
-void hydro_read_particles(struct part* parts, struct io_props* list,
- int* num_fields) {
+INLINE static void hydro_read_particles(struct part* parts,
+ struct io_props* list,
+ int* num_fields) {
*num_fields = 8;
@@ -72,8 +73,8 @@ void hydro_read_particles(struct part* parts, struct io_props* list,
* @param p Particle.
* @param ret (return) Internal energy of the particle
*/
-void convert_u(const struct engine* e, const struct part* p,
- const struct xpart* xp, float* ret) {
+INLINE static void convert_u(const struct engine* e, const struct part* p,
+ const struct xpart* xp, float* ret) {
ret[0] = hydro_get_comoving_internal_energy(p);
}
@@ -85,8 +86,8 @@ void convert_u(const struct engine* e, const struct part* p,
* @param p Particle.
* @param ret (return) Entropic function of the particle
*/
-void convert_A(const struct engine* e, const struct part* p,
- const struct xpart* xp, float* ret) {
+INLINE static void convert_A(const struct engine* e, const struct part* p,
+ const struct xpart* xp, float* ret) {
ret[0] = hydro_get_comoving_entropy(p);
}
@@ -97,8 +98,8 @@ void convert_A(const struct engine* e, const struct part* p,
* @param p Particle.
* @return Total energy of the particle
*/
-void convert_Etot(const struct engine* e, const struct part* p,
- const struct xpart* xp, float* ret) {
+INLINE static void convert_Etot(const struct engine* e, const struct part* p,
+ const struct xpart* xp, float* ret) {
#ifdef GIZMO_TOTAL_ENERGY
ret[0] = p->conserved.energy;
#else
@@ -112,8 +113,9 @@ void convert_Etot(const struct engine* e, const struct part* p,
#endif
}
-void convert_part_pos(const struct engine* e, const struct part* p,
- const struct xpart* xp, double* ret) {
+INLINE static void convert_part_pos(const struct engine* e,
+ const struct part* p,
+ const struct xpart* xp, double* ret) {
if (e->s->periodic) {
ret[0] = box_wrap(p->x[0], 0.0, e->s->dim[0]);
@@ -126,8 +128,9 @@ void convert_part_pos(const struct engine* e, const struct part* p,
}
}
-void convert_part_vel(const struct engine* e, const struct part* p,
- const struct xpart* xp, float* ret) {
+INLINE static void convert_part_vel(const struct engine* e,
+ const struct part* p,
+ const struct xpart* xp, float* ret) {
const int with_cosmology = (e->policy & engine_policy_cosmology);
const struct cosmology* cosmo = e->cosmology;
@@ -155,13 +158,14 @@ void convert_part_vel(const struct engine* e, const struct part* p,
hydro_get_drifted_velocities(p, xp, dt_kick_hydro, dt_kick_grav, ret);
/* Conversion from internal units to peculiar velocities */
- ret[0] *= cosmo->a2_inv;
- ret[1] *= cosmo->a2_inv;
- ret[2] *= cosmo->a2_inv;
+ ret[0] *= cosmo->a_inv;
+ ret[1] *= cosmo->a_inv;
+ ret[2] *= cosmo->a_inv;
}
-void convert_part_potential(const struct engine* e, const struct part* p,
- const struct xpart* xp, float* ret) {
+INLINE static void convert_part_potential(const struct engine* e,
+ const struct part* p,
+ const struct xpart* xp, float* ret) {
if (p->gpart != NULL)
ret[0] = gravity_get_comoving_potential(p->gpart);
@@ -176,8 +180,10 @@ void convert_part_potential(const struct engine* e, const struct part* p,
* @param list The list of i/o properties to write.
* @param num_fields The number of i/o fields to write.
*/
-void hydro_write_particles(const struct part* parts, const struct xpart* xparts,
- struct io_props* list, int* num_fields) {
+INLINE static void hydro_write_particles(const struct part* parts,
+ const struct xpart* xparts,
+ struct io_props* list,
+ int* num_fields) {
*num_fields = 11;
@@ -215,7 +221,7 @@ void hydro_write_particles(const struct part* parts, const struct xpart* xparts,
* @brief Writes the current model of SPH to the file
* @param h_grpsph The HDF5 group in which to write
*/
-void hydro_write_flavour(hid_t h_grpsph) {
+INLINE static void hydro_write_flavour(hid_t h_grpsph) {
/* Gradient information */
io_write_attribute_s(h_grpsph, "Gradient reconstruction model",
HYDRO_GRADIENT_IMPLEMENTATION);
@@ -239,6 +245,6 @@ void hydro_write_flavour(hid_t h_grpsph) {
*
* @return 1 if entropy is in 'internal energy', 0 otherwise.
*/
-int writeEntropyFlag() { return 0; }
+INLINE static int writeEntropyFlag(void) { return 0; }
#endif /* SWIFT_GIZMO_MFV_HYDRO_IO_H */
diff --git a/src/hydro/Minimal/hydro.h b/src/hydro/Minimal/hydro.h
index 3f9d99683bde4ed6db64d8aaa5b111e2f67f0969..812f8ad72de55ad7990ee6ef88223a401780bc4b 100644
--- a/src/hydro/Minimal/hydro.h
+++ b/src/hydro/Minimal/hydro.h
@@ -367,7 +367,7 @@ __attribute__((always_inline)) INLINE static void hydro_part_has_no_neighbours(
/* Re-set problematic values */
p->rho = p->mass * kernel_root * h_inv_dim;
- p->density.wcount = kernel_root * kernel_norm * h_inv_dim;
+ p->density.wcount = kernel_root * h_inv_dim;
p->density.rho_dh = 0.f;
p->density.wcount_dh = 0.f;
}
@@ -426,7 +426,7 @@ __attribute__((always_inline)) INLINE static void hydro_reset_acceleration(
/* Reset the time derivatives. */
p->u_dt = 0.0f;
p->force.h_dt = 0.0f;
- p->force.v_sig = 0.0f;
+ p->force.v_sig = p->force.soundspeed;
}
/**
diff --git a/src/hydro/Minimal/hydro_debug.h b/src/hydro/Minimal/hydro_debug.h
index 541029ee06dd2799443fc89b688d7baca3fae0f8..73ffc26b8acf687a5445591ddccd72ea8e8fa8ae 100644
--- a/src/hydro/Minimal/hydro_debug.h
+++ b/src/hydro/Minimal/hydro_debug.h
@@ -36,16 +36,17 @@
__attribute__((always_inline)) INLINE static void hydro_debug_particle(
const struct part* p, const struct xpart* xp) {
printf(
- "x=[%.3e,%.3e,%.3e], "
- "v=[%.3e,%.3e,%.3e],v_full=[%.3e,%.3e,%.3e] \n a=[%.3e,%.3e,%.3e], "
- "u=%.3e, du/dt=%.3e v_sig=%.3e, P=%.3e\n"
- "h=%.3e, dh/dt=%.3e wcount=%d, m=%.3e, dh_drho=%.3e, rho=%.3e, "
- "time_bin=%d\n",
+ "\n "
+ "x=[%.6g, %.6g, %.6g], v=[%.3g, %.3g, %.3g], \n "
+ "v_full=[%.3g, %.3g, %.3g], a=[%.3g, %.3g, %.3g], \n "
+ "m=%.3g, u=%.3g, du/dt=%.3g, P=%.3g, c_s=%.3g, \n "
+ "v_sig=%.3g, h=%.3g, dh/dt=%.3g, wcount=%.3g, rho=%.3g, \n "
+ "dh_drho=%.3g, time_bin=%d \n",
p->x[0], p->x[1], p->x[2], p->v[0], p->v[1], p->v[2], xp->v_full[0],
xp->v_full[1], xp->v_full[2], p->a_hydro[0], p->a_hydro[1], p->a_hydro[2],
- p->u, p->u_dt, p->force.v_sig, hydro_get_comoving_pressure(p), p->h,
- p->force.h_dt, (int)p->density.wcount, p->mass, p->density.rho_dh, p->rho,
- p->time_bin);
+ p->mass, p->u, p->u_dt, hydro_get_comoving_pressure(p),
+ p->force.soundspeed, p->force.v_sig, p->h, p->force.h_dt,
+ p->density.wcount, p->rho, p->density.rho_dh, p->time_bin);
}
#endif /* SWIFT_MINIMAL_HYDRO_DEBUG_H */
diff --git a/src/hydro/Minimal/hydro_io.h b/src/hydro/Minimal/hydro_io.h
index 380d6120e05acf2e015ece6f133df02fad3b761d..879255640fc1a1d6a06a666c80d3860c9c31ab64 100644
--- a/src/hydro/Minimal/hydro_io.h
+++ b/src/hydro/Minimal/hydro_io.h
@@ -45,8 +45,9 @@
* @param list The list of i/o properties to read.
* @param num_fields The number of i/o fields to read.
*/
-void hydro_read_particles(struct part* parts, struct io_props* list,
- int* num_fields) {
+INLINE static void hydro_read_particles(struct part* parts,
+ struct io_props* list,
+ int* num_fields) {
*num_fields = 8;
@@ -69,20 +70,21 @@ void hydro_read_particles(struct part* parts, struct io_props* list,
UNIT_CONV_DENSITY, parts, rho);
}
-void convert_S(const struct engine* e, const struct part* p,
- const struct xpart* xp, float* ret) {
+INLINE static void convert_S(const struct engine* e, const struct part* p,
+ const struct xpart* xp, float* ret) {
ret[0] = hydro_get_comoving_entropy(p);
}
-void convert_P(const struct engine* e, const struct part* p,
- const struct xpart* xp, float* ret) {
+INLINE static void convert_P(const struct engine* e, const struct part* p,
+ const struct xpart* xp, float* ret) {
ret[0] = hydro_get_comoving_pressure(p);
}
-void convert_part_pos(const struct engine* e, const struct part* p,
- const struct xpart* xp, double* ret) {
+INLINE static void convert_part_pos(const struct engine* e,
+ const struct part* p,
+ const struct xpart* xp, double* ret) {
if (e->s->periodic) {
ret[0] = box_wrap(p->x[0], 0.0, e->s->dim[0]);
@@ -95,8 +97,9 @@ void convert_part_pos(const struct engine* e, const struct part* p,
}
}
-void convert_part_vel(const struct engine* e, const struct part* p,
- const struct xpart* xp, float* ret) {
+INLINE static void convert_part_vel(const struct engine* e,
+ const struct part* p,
+ const struct xpart* xp, float* ret) {
const int with_cosmology = (e->policy & engine_policy_cosmology);
const struct cosmology* cosmo = e->cosmology;
@@ -124,13 +127,14 @@ void convert_part_vel(const struct engine* e, const struct part* p,
hydro_get_drifted_velocities(p, xp, dt_kick_hydro, dt_kick_grav, ret);
/* Conversion from internal units to peculiar velocities */
- ret[0] *= cosmo->a2_inv;
- ret[1] *= cosmo->a2_inv;
- ret[2] *= cosmo->a2_inv;
+ ret[0] *= cosmo->a_inv;
+ ret[1] *= cosmo->a_inv;
+ ret[2] *= cosmo->a_inv;
}
-void convert_part_potential(const struct engine* e, const struct part* p,
- const struct xpart* xp, float* ret) {
+INLINE static void convert_part_potential(const struct engine* e,
+ const struct part* p,
+ const struct xpart* xp, float* ret) {
if (p->gpart != NULL)
ret[0] = gravity_get_comoving_potential(p->gpart);
@@ -146,8 +150,10 @@ void convert_part_potential(const struct engine* e, const struct part* p,
* @param list The list of i/o properties to write.
* @param num_fields The number of i/o fields to write.
*/
-void hydro_write_particles(const struct part* parts, const struct xpart* xparts,
- struct io_props* list, int* num_fields) {
+INLINE static void hydro_write_particles(const struct part* parts,
+ const struct xpart* xparts,
+ struct io_props* list,
+ int* num_fields) {
*num_fields = 10;
@@ -182,7 +188,7 @@ void hydro_write_particles(const struct part* parts, const struct xpart* xparts,
* @brief Writes the current model of SPH to the file
* @param h_grpsph The HDF5 group in which to write
*/
-void hydro_write_flavour(hid_t h_grpsph) {
+INLINE static void hydro_write_flavour(hid_t h_grpsph) {
/* Viscosity and thermal conduction */
/* Nothing in this minimal model... */
@@ -200,6 +206,6 @@ void hydro_write_flavour(hid_t h_grpsph) {
*
* @return 1 if entropy is in 'internal energy', 0 otherwise.
*/
-int writeEntropyFlag() { return 0; }
+INLINE static int writeEntropyFlag(void) { return 0; }
#endif /* SWIFT_MINIMAL_HYDRO_IO_H */
diff --git a/src/hydro/MinimalMultiMat/hydro.h b/src/hydro/MinimalMultiMat/hydro.h
index 5383ffda8fe67a591691766e4150e75a9dbd4cb0..cfad6b2b2b389da9f423540cb30f1df4cebc5416 100644
--- a/src/hydro/MinimalMultiMat/hydro.h
+++ b/src/hydro/MinimalMultiMat/hydro.h
@@ -368,7 +368,7 @@ __attribute__((always_inline)) INLINE static void hydro_part_has_no_neighbours(
/* Re-set problematic values */
p->rho = p->mass * kernel_root * h_inv_dim;
- p->density.wcount = kernel_root * kernel_norm * h_inv_dim;
+ p->density.wcount = kernel_root * h_inv_dim;
p->density.rho_dh = 0.f;
p->density.wcount_dh = 0.f;
}
@@ -429,7 +429,7 @@ __attribute__((always_inline)) INLINE static void hydro_reset_acceleration(
/* Reset the time derivatives. */
p->u_dt = 0.0f;
p->force.h_dt = 0.0f;
- p->force.v_sig = 0.0f;
+ p->force.v_sig = p->force.soundspeed;
}
/**
diff --git a/src/hydro/MinimalMultiMat/hydro_debug.h b/src/hydro/MinimalMultiMat/hydro_debug.h
index d8fe73313fbb175faa9547970c6680346dad0a1b..17b624ad0f660152be4ba685905a3c855e1761f8 100644
--- a/src/hydro/MinimalMultiMat/hydro_debug.h
+++ b/src/hydro/MinimalMultiMat/hydro_debug.h
@@ -38,16 +38,17 @@
__attribute__((always_inline)) INLINE static void hydro_debug_particle(
const struct part* p, const struct xpart* xp) {
printf(
- "x=[%.3e,%.3e,%.3e], "
- "v=[%.3e,%.3e,%.3e],v_full=[%.3e,%.3e,%.3e] \n a=[%.3e,%.3e,%.3e], "
- "u=%.3e, du/dt=%.3e v_sig=%.3e, P=%.3e\n"
- "h=%.3e, dh/dt=%.3e wcount=%d, m=%.3e, dh_drho=%.3e, rho=%.3e, "
- "time_bin=%d, mat_id=%d\n",
+ "\n "
+ "x=[%.6g, %.6g, %.6g], v=[%.3g, %.3g, %.3g], \n "
+ "v_full=[%.3g, %.3g, %.3g], a=[%.3g, %.3g, %.3g], \n "
+ "m=%.3g, u=%.3g, du/dt=%.3g, P=%.3g, c_s=%.3g, \n "
+ "v_sig=%.3g, h=%.3g, dh/dt=%.3g, wcount=%.3g, rho=%.3g, \n "
+ "dh_drho=%.3g, time_bin=%d, mat_id=%d \n",
p->x[0], p->x[1], p->x[2], p->v[0], p->v[1], p->v[2], xp->v_full[0],
xp->v_full[1], xp->v_full[2], p->a_hydro[0], p->a_hydro[1], p->a_hydro[2],
- p->u, p->u_dt, p->force.v_sig, hydro_get_comoving_pressure(p), p->h,
- p->force.h_dt, (int)p->density.wcount, p->mass, p->density.rho_dh, p->rho,
- p->time_bin, p->mat_id);
+ p->mass, p->u, p->u_dt, hydro_get_comoving_pressure(p),
+ p->force.soundspeed, p->force.v_sig, p->h, p->force.h_dt,
+ p->density.wcount, p->rho, p->density.rho_dh, p->time_bin, p->mat_id);
}
#endif /* SWIFT_MINIMAL_MULTI_MAT_HYDRO_DEBUG_H */
diff --git a/src/hydro/MinimalMultiMat/hydro_io.h b/src/hydro/MinimalMultiMat/hydro_io.h
index 2a5eeb6a54d079ae72e1591116a8984b0d7a6f38..7f41f5e227b6c8a8904b5546a2568b4700109abd 100644
--- a/src/hydro/MinimalMultiMat/hydro_io.h
+++ b/src/hydro/MinimalMultiMat/hydro_io.h
@@ -46,8 +46,9 @@
* @param list The list of i/o properties to read.
* @param num_fields The number of i/o fields to read.
*/
-void hydro_read_particles(struct part* parts, struct io_props* list,
- int* num_fields) {
+INLINE static void hydro_read_particles(struct part* parts,
+ struct io_props* list,
+ int* num_fields) {
*num_fields = 9;
@@ -68,24 +69,25 @@ void hydro_read_particles(struct part* parts, struct io_props* list,
UNIT_CONV_ACCELERATION, parts, a_hydro);
list[7] = io_make_input_field("Density", FLOAT, 1, OPTIONAL,
UNIT_CONV_DENSITY, parts, rho);
- list[8] =
- io_make_input_field("MaterialID", INT, 1, OPTIONAL, 1, parts, mat_id);
+ list[8] = io_make_input_field("MaterialID", INT, 1, COMPULSORY,
+ UNIT_CONV_NO_UNITS, parts, mat_id);
}
-void convert_S(const struct engine* e, const struct part* p,
- const struct xpart* xp, float* ret) {
+INLINE static void convert_S(const struct engine* e, const struct part* p,
+ const struct xpart* xp, float* ret) {
ret[0] = hydro_get_comoving_entropy(p);
}
-void convert_P(const struct engine* e, const struct part* p,
- const struct xpart* xp, float* ret) {
+INLINE static void convert_P(const struct engine* e, const struct part* p,
+ const struct xpart* xp, float* ret) {
ret[0] = hydro_get_comoving_pressure(p);
}
-void convert_part_pos(const struct engine* e, const struct part* p,
- const struct xpart* xp, double* ret) {
+INLINE static void convert_part_pos(const struct engine* e,
+ const struct part* p,
+ const struct xpart* xp, double* ret) {
if (e->s->periodic) {
ret[0] = box_wrap(p->x[0], 0.0, e->s->dim[0]);
@@ -98,8 +100,9 @@ void convert_part_pos(const struct engine* e, const struct part* p,
}
}
-void convert_part_vel(const struct engine* e, const struct part* p,
- const struct xpart* xp, float* ret) {
+INLINE static void convert_part_vel(const struct engine* e,
+ const struct part* p,
+ const struct xpart* xp, float* ret) {
const int with_cosmology = (e->policy & engine_policy_cosmology);
const struct cosmology* cosmo = e->cosmology;
@@ -127,13 +130,14 @@ void convert_part_vel(const struct engine* e, const struct part* p,
hydro_get_drifted_velocities(p, xp, dt_kick_hydro, dt_kick_grav, ret);
/* Conversion from internal units to peculiar velocities */
- ret[0] *= cosmo->a2_inv;
- ret[1] *= cosmo->a2_inv;
- ret[2] *= cosmo->a2_inv;
+ ret[0] *= cosmo->a_inv;
+ ret[1] *= cosmo->a_inv;
+ ret[2] *= cosmo->a_inv;
}
-void convert_part_potential(const struct engine* e, const struct part* p,
- const struct xpart* xp, float* ret) {
+INLINE static void convert_part_potential(const struct engine* e,
+ const struct part* p,
+ const struct xpart* xp, float* ret) {
if (p->gpart != NULL)
ret[0] = gravity_get_comoving_potential(p->gpart);
@@ -149,8 +153,10 @@ void convert_part_potential(const struct engine* e, const struct part* p,
* @param list The list of i/o properties to write.
* @param num_fields The number of i/o fields to write.
*/
-void hydro_write_particles(const struct part* parts, const struct xpart* xparts,
- struct io_props* list, int* num_fields) {
+INLINE static void hydro_write_particles(const struct part* parts,
+ const struct xpart* xparts,
+ struct io_props* list,
+ int* num_fields) {
*num_fields = 11;
@@ -186,7 +192,7 @@ void hydro_write_particles(const struct part* parts, const struct xpart* xparts,
* @brief Writes the current model of SPH to the file
* @param h_grpsph The HDF5 group in which to write
*/
-void hydro_write_flavour(hid_t h_grpsph) {
+INLINE static void hydro_write_flavour(hid_t h_grpsph) {
/* Viscosity and thermal conduction */
/* Nothing in this minimal model... */
@@ -204,6 +210,6 @@ void hydro_write_flavour(hid_t h_grpsph) {
*
* @return 1 if entropy is in 'internal energy', 0 otherwise.
*/
-int writeEntropyFlag() { return 0; }
+INLINE static int writeEntropyFlag(void) { return 0; }
#endif /* SWIFT_MINIMAL_MULTI_MAT_HYDRO_IO_H */
diff --git a/src/hydro/PressureEnergy/hydro.h b/src/hydro/PressureEnergy/hydro.h
index 1e0d8208e82f7f48691d1df7603a6b02d1471c12..ea086daeeb1e93d7f1476302564fb4182a6fb611 100644
--- a/src/hydro/PressureEnergy/hydro.h
+++ b/src/hydro/PressureEnergy/hydro.h
@@ -403,7 +403,7 @@ __attribute__((always_inline)) INLINE static void hydro_part_has_no_neighbours(
p->rho = p->mass * kernel_root * h_inv_dim;
p->pressure_bar =
p->mass * p->u * hydro_gamma_minus_one * kernel_root * h_inv_dim;
- p->density.wcount = kernel_root * kernel_norm * h_inv_dim;
+ p->density.wcount = kernel_root * h_inv_dim;
p->density.rho_dh = 0.f;
p->density.wcount_dh = 0.f;
p->density.pressure_bar_dh = 0.f;
@@ -480,7 +480,7 @@ __attribute__((always_inline)) INLINE static void hydro_reset_acceleration(
/* Reset the time derivatives. */
p->u_dt = 0.0f;
p->force.h_dt = 0.0f;
- p->force.v_sig = 0.0f;
+ p->force.v_sig = p->force.soundspeed;
}
/**
diff --git a/src/hydro/PressureEnergy/hydro_io.h b/src/hydro/PressureEnergy/hydro_io.h
index 776e7653ac3152e1594f25a33796a470dfcf69d3..78967faec218f0efffbb624c4e8d25af214aad94 100644
--- a/src/hydro/PressureEnergy/hydro_io.h
+++ b/src/hydro/PressureEnergy/hydro_io.h
@@ -43,8 +43,9 @@
* @param list The list of i/o properties to read.
* @param num_fields The number of i/o fields to read.
*/
-void hydro_read_particles(struct part* parts, struct io_props* list,
- int* num_fields) {
+INLINE static void hydro_read_particles(struct part* parts,
+ struct io_props* list,
+ int* num_fields) {
*num_fields = 8;
@@ -67,26 +68,27 @@ void hydro_read_particles(struct part* parts, struct io_props* list,
UNIT_CONV_DENSITY, parts, rho);
}
-void convert_u(const struct engine* e, const struct part* p,
- const struct xpart* xp, float* ret) {
+INLINE static void convert_u(const struct engine* e, const struct part* p,
+ const struct xpart* xp, float* ret) {
ret[0] = hydro_get_comoving_internal_energy(p);
}
-void convert_S(const struct engine* e, const struct part* p,
- const struct xpart* xp, float* ret) {
+INLINE static void convert_S(const struct engine* e, const struct part* p,
+ const struct xpart* xp, float* ret) {
ret[0] = hydro_get_comoving_entropy(p);
}
-void convert_P(const struct engine* e, const struct part* p,
- const struct xpart* xp, float* ret) {
+INLINE static void convert_P(const struct engine* e, const struct part* p,
+ const struct xpart* xp, float* ret) {
ret[0] = hydro_get_comoving_pressure(p);
}
-void convert_part_pos(const struct engine* e, const struct part* p,
- const struct xpart* xp, double* ret) {
+INLINE static void convert_part_pos(const struct engine* e,
+ const struct part* p,
+ const struct xpart* xp, double* ret) {
if (e->s->periodic) {
ret[0] = box_wrap(p->x[0], 0.0, e->s->dim[0]);
@@ -99,8 +101,9 @@ void convert_part_pos(const struct engine* e, const struct part* p,
}
}
-void convert_part_vel(const struct engine* e, const struct part* p,
- const struct xpart* xp, float* ret) {
+INLINE static void convert_part_vel(const struct engine* e,
+ const struct part* p,
+ const struct xpart* xp, float* ret) {
const int with_cosmology = (e->policy & engine_policy_cosmology);
const struct cosmology* cosmo = e->cosmology;
@@ -128,9 +131,9 @@ void convert_part_vel(const struct engine* e, const struct part* p,
hydro_get_drifted_velocities(p, xp, dt_kick_hydro, dt_kick_grav, ret);
/* Conversion from internal units to peculiar velocities */
- ret[0] *= cosmo->a2_inv;
- ret[1] *= cosmo->a2_inv;
- ret[2] *= cosmo->a2_inv;
+ ret[0] *= cosmo->a_inv;
+ ret[1] *= cosmo->a_inv;
+ ret[2] *= cosmo->a_inv;
}
/**
@@ -140,8 +143,10 @@ void convert_part_vel(const struct engine* e, const struct part* p,
* @param list The list of i/o properties to write.
* @param num_fields The number of i/o fields to write.
*/
-void hydro_write_particles(const struct part* parts, const struct xpart* xparts,
- struct io_props* list, int* num_fields) {
+INLINE static void hydro_write_particles(const struct part* parts,
+ const struct xpart* xparts,
+ struct io_props* list,
+ int* num_fields) {
*num_fields = 9;
@@ -173,7 +178,7 @@ void hydro_write_particles(const struct part* parts, const struct xpart* xparts,
* @brief Writes the current model of SPH to the file
* @param h_grpsph The HDF5 group in which to write
*/
-void hydro_write_flavour(hid_t h_grpsph) {
+INLINE static void hydro_write_flavour(hid_t h_grpsph) {
/* Viscosity and thermal conduction */
/* Nothing in this minimal model... */
@@ -191,6 +196,6 @@ void hydro_write_flavour(hid_t h_grpsph) {
*
* @return 1 if entropy is in 'internal energy', 0 otherwise.
*/
-int writeEntropyFlag() { return 0; }
+INLINE static int writeEntropyFlag(void) { return 0; }
#endif /* SWIFT_MINIMAL_HYDRO_IO_H */
diff --git a/src/hydro/PressureEntropy/hydro.h b/src/hydro/PressureEntropy/hydro.h
index 87d46c6d43f0d4f6de6d18f5400b38f0fc4d0f55..e4b7cf06e083638a94526cc1f9e7212cf19dfad4 100644
--- a/src/hydro/PressureEntropy/hydro.h
+++ b/src/hydro/PressureEntropy/hydro.h
@@ -357,7 +357,7 @@ __attribute__((always_inline)) INLINE static void hydro_part_has_no_neighbours(
/* Re-set problematic values */
p->rho = p->mass * kernel_root * h_inv_dim;
p->rho_bar = p->mass * kernel_root * h_inv_dim;
- p->density.wcount = kernel_root * kernel_norm * h_inv_dim;
+ p->density.wcount = kernel_root * h_inv_dim;
p->density.rho_dh = 0.f;
p->density.wcount_dh = 0.f;
p->density.pressure_dh = 0.f;
@@ -441,7 +441,7 @@ __attribute__((always_inline)) INLINE static void hydro_reset_acceleration(
p->force.h_dt = 0.0f;
/* Reset maximal signal velocity */
- p->force.v_sig = 0.0f;
+ p->force.v_sig = p->force.soundspeed;
}
/**
diff --git a/src/hydro/PressureEntropy/hydro_io.h b/src/hydro/PressureEntropy/hydro_io.h
index 78371c1eb21fafed56e89d46690d0cf1e0f2a0f0..8c11bf6e334e18b10217e90f6573a42e40880955 100644
--- a/src/hydro/PressureEntropy/hydro_io.h
+++ b/src/hydro/PressureEntropy/hydro_io.h
@@ -42,8 +42,9 @@
* @param list The list of i/o properties to read.
* @param num_fields The number of i/o fields to read.
*/
-void hydro_read_particles(struct part* parts, struct io_props* list,
- int* num_fields) {
+INLINE static void hydro_read_particles(struct part* parts,
+ struct io_props* list,
+ int* num_fields) {
*num_fields = 8;
@@ -67,20 +68,21 @@ void hydro_read_particles(struct part* parts, struct io_props* list,
UNIT_CONV_DENSITY, parts, rho);
}
-void convert_u(const struct engine* e, const struct part* p,
- const struct xpart* xp, float* ret) {
+INLINE static void convert_u(const struct engine* e, const struct part* p,
+ const struct xpart* xp, float* ret) {
ret[0] = hydro_get_comoving_internal_energy(p);
}
-void convert_P(const struct engine* e, const struct part* p,
- const struct xpart* xp, float* ret) {
+INLINE static void convert_P(const struct engine* e, const struct part* p,
+ const struct xpart* xp, float* ret) {
ret[0] = hydro_get_comoving_pressure(p);
}
-void convert_part_pos(const struct engine* e, const struct part* p,
- const struct xpart* xp, double* ret) {
+INLINE static void convert_part_pos(const struct engine* e,
+ const struct part* p,
+ const struct xpart* xp, double* ret) {
if (e->s->periodic) {
ret[0] = box_wrap(p->x[0], 0.0, e->s->dim[0]);
@@ -93,8 +95,9 @@ void convert_part_pos(const struct engine* e, const struct part* p,
}
}
-void convert_part_vel(const struct engine* e, const struct part* p,
- const struct xpart* xp, float* ret) {
+INLINE static void convert_part_vel(const struct engine* e,
+ const struct part* p,
+ const struct xpart* xp, float* ret) {
const int with_cosmology = (e->policy & engine_policy_cosmology);
const struct cosmology* cosmo = e->cosmology;
@@ -122,13 +125,14 @@ void convert_part_vel(const struct engine* e, const struct part* p,
hydro_get_drifted_velocities(p, xp, dt_kick_hydro, dt_kick_grav, ret);
/* Conversion from internal units to peculiar velocities */
- ret[0] *= cosmo->a2_inv;
- ret[1] *= cosmo->a2_inv;
- ret[2] *= cosmo->a2_inv;
+ ret[0] *= cosmo->a_inv;
+ ret[1] *= cosmo->a_inv;
+ ret[2] *= cosmo->a_inv;
}
-void convert_part_potential(const struct engine* e, const struct part* p,
- const struct xpart* xp, float* ret) {
+INLINE static void convert_part_potential(const struct engine* e,
+ const struct part* p,
+ const struct xpart* xp, float* ret) {
if (p->gpart != NULL)
ret[0] = gravity_get_comoving_potential(p->gpart);
@@ -143,8 +147,10 @@ void convert_part_potential(const struct engine* e, const struct part* p,
* @param list The list of i/o properties to write.
* @param num_fields The number of i/o fields to write.
*/
-void hydro_write_particles(const struct part* parts, const struct xpart* xparts,
- struct io_props* list, int* num_fields) {
+INLINE static void hydro_write_particles(const struct part* parts,
+ const struct xpart* xparts,
+ struct io_props* list,
+ int* num_fields) {
*num_fields = 11;
@@ -180,7 +186,7 @@ void hydro_write_particles(const struct part* parts, const struct xpart* xparts,
* @brief Writes the current model of SPH to the file
* @param h_grpsph The HDF5 group in which to write
*/
-void hydro_write_flavour(hid_t h_grpsph) {
+INLINE static void hydro_write_flavour(hid_t h_grpsph) {
/* Viscosity and thermal conduction */
/* Nothing in this minimal model... */
@@ -201,6 +207,6 @@ void hydro_write_flavour(hid_t h_grpsph) {
*
* @return 1 if entropy is in 'internal energy', 0 otherwise.
*/
-int writeEntropyFlag() { return 0; }
+INLINE static int writeEntropyFlag(void) { return 0; }
#endif /* SWIFT_PRESSURE_ENTROPY_HYDRO_IO_H */
diff --git a/src/hydro/Shadowswift/hydro.h b/src/hydro/Shadowswift/hydro.h
index 36078798cdd1ac68a456134fd7887408752f18c9..025779f17496e7bf30fdf12353c4381c7d6292ce 100644
--- a/src/hydro/Shadowswift/hydro.h
+++ b/src/hydro/Shadowswift/hydro.h
@@ -257,7 +257,7 @@ __attribute__((always_inline)) INLINE static void hydro_part_has_no_neighbours(
const float h_inv_dim = pow_dimension(h_inv); /* 1/h^d */
/* Re-set problematic values */
- p->density.wcount = kernel_root * kernel_norm * h_inv_dim;
+ p->density.wcount = kernel_root * h_inv_dim;
p->density.wcount_dh = 0.f;
}
diff --git a/src/hydro/Shadowswift/hydro_io.h b/src/hydro/Shadowswift/hydro_io.h
index 8525d22025c1943529ddcd86cf3a42ba0ae4f5d4..1f6bb86e62c6a3359d1242328775c6e4067ef8f2 100644
--- a/src/hydro/Shadowswift/hydro_io.h
+++ b/src/hydro/Shadowswift/hydro_io.h
@@ -32,8 +32,9 @@
* @param list The list of i/o properties to read.
* @param num_fields The number of i/o fields to read.
*/
-void hydro_read_particles(struct part* parts, struct io_props* list,
- int* num_fields) {
+INLINE static void hydro_read_particles(struct part* parts,
+ struct io_props* list,
+ int* num_fields) {
*num_fields = 8;
@@ -64,8 +65,8 @@ void hydro_read_particles(struct part* parts, struct io_props* list,
* @param p Particle.
* @return Internal energy of the particle
*/
-void convert_u(const struct engine* e, const struct part* p,
- const struct xpart* xp, float* ret) {
+INLINE static void convert_u(const struct engine* e, const struct part* p,
+ const struct xpart* xp, float* ret) {
ret[0] = hydro_get_internal_energy(p);
}
@@ -76,8 +77,8 @@ void convert_u(const struct engine* e, const struct part* p,
* @param p Particle.
* @return Entropic function of the particle
*/
-void convert_A(const struct engine* e, const struct part* p,
- const struct xpart* xp, float* ret) {
+INLINE static void convert_A(const struct engine* e, const struct part* p,
+ const struct xpart* xp, float* ret) {
ret[0] = hydro_get_entropy(p);
}
@@ -88,8 +89,8 @@ void convert_A(const struct engine* e, const struct part* p,
* @param p Particle.
* @return Total energy of the particle
*/
-void convert_Etot(const struct engine* e, const struct part* p,
- const struct xpart* xp, float* ret) {
+INLINE static void convert_Etot(const struct engine* e, const struct part* p,
+ const struct xpart* xp, float* ret) {
#ifdef SHADOWFAX_TOTAL_ENERGY
return p->conserved.energy;
#else
@@ -107,8 +108,9 @@ void convert_Etot(const struct engine* e, const struct part* p,
#endif
}
-void convert_part_pos(const struct engine* e, const struct part* p,
- const struct xpart* xp, double* ret) {
+INLINE static void convert_part_pos(const struct engine* e,
+ const struct part* p,
+ const struct xpart* xp, double* ret) {
if (e->s->periodic) {
ret[0] = box_wrap(p->x[0], 0.0, e->s->dim[0]);
@@ -128,8 +130,10 @@ void convert_part_pos(const struct engine* e, const struct part* p,
* @param list The list of i/o properties to write.
* @param num_fields The number of i/o fields to write.
*/
-void hydro_write_particles(const struct part* parts, const struct xpart* xparts,
- struct io_props* list, int* num_fields) {
+INLINE static void hydro_write_particles(const struct part* parts,
+ const struct xpart* xparts,
+ struct io_props* list,
+ int* num_fields) {
*num_fields = 13;
@@ -168,7 +172,7 @@ void hydro_write_particles(const struct part* parts, const struct xpart* xparts,
* @brief Writes the current model of SPH to the file
* @param h_grpsph The HDF5 group in which to write
*/
-void hydro_write_flavour(hid_t h_grpsph) {
+INLINE static void hydro_write_flavour(hid_t h_grpsph) {
/* Gradient information */
io_write_attribute_s(h_grpsph, "Gradient reconstruction model",
HYDRO_GRADIENT_IMPLEMENTATION);
@@ -189,4 +193,4 @@ void hydro_write_flavour(hid_t h_grpsph) {
*
* @return 1 if entropy is in 'internal energy', 0 otherwise.
*/
-int writeEntropyFlag() { return 0; }
+INLINE static int writeEntropyFlag(void) { return 0; }
diff --git a/src/hydro_properties.c b/src/hydro_properties.c
index e63679eaad3c7f61fe67e63326ca59a04c1caffb..c5448f77353e1859c1f8853394bbefbe26d0a3a9 100644
--- a/src/hydro_properties.c
+++ b/src/hydro_properties.c
@@ -52,7 +52,7 @@
void hydro_props_init(struct hydro_props *p,
const struct phys_const *phys_const,
const struct unit_system *us,
- const struct swift_params *params) {
+ struct swift_params *params) {
/* Kernel properties */
p->eta_neighbours = parser_get_param_float(params, "SPH:resolution_eta");
diff --git a/src/hydro_properties.h b/src/hydro_properties.h
index 2799f6c86eec7f0ebf140643c5ab7fa9b60e6273..64a840692db677704b8617e962d7883505983cc0 100644
--- a/src/hydro_properties.h
+++ b/src/hydro_properties.h
@@ -86,7 +86,7 @@ void hydro_props_print(const struct hydro_props *p);
void hydro_props_init(struct hydro_props *p,
const struct phys_const *phys_const,
const struct unit_system *us,
- const struct swift_params *params);
+ struct swift_params *params);
#if defined(HAVE_HDF5)
void hydro_props_print_snapshot(hid_t h_grpsph, const struct hydro_props *p);
diff --git a/src/parallel_io.c b/src/parallel_io.c
index 6cd15be2948a0e46e5a1f8d79bdba8a443a5c454..d37c8632675dc13e487e0c80e2f7390f5c14e527 100644
--- a/src/parallel_io.c
+++ b/src/parallel_io.c
@@ -49,12 +49,13 @@
#include "io_properties.h"
#include "kernel_hydro.h"
#include "part.h"
+#include "part_type.h"
#include "stars_io.h"
#include "units.h"
#include "xmf.h"
/* The current limit of ROMIO (the underlying MPI-IO layer) is 2GB */
-#define HDF5_PARALLEL_IO_MAX_BYTES 2000000000LL
+#define HDF5_PARALLEL_IO_MAX_BYTES 2147000000LL
/* Are we timing the i/o? */
//#define IO_SPEED_MEASUREMENT
@@ -84,7 +85,7 @@ void readArray_chunk(hid_t h_data, hid_t h_plist_id,
/* Can't handle writes of more than 2GB */
if (N * props.dimension * typeSize > HDF5_PARALLEL_IO_MAX_BYTES)
- error("Dataset too large to be written in one pass!");
+ error("Dataset too large to be read in one pass!");
/* Allocate temporary buffer */
void* temp = malloc(num_elements * typeSize);
@@ -205,6 +206,57 @@ void readArray(hid_t grp, struct io_props props, size_t N, long long N_total,
const hid_t h_data = H5Dopen2(grp, props.name, H5P_DEFAULT);
if (h_data < 0) error("Error while opening data space '%s'.", props.name);
+/* Parallel-HDF5 1.10.2 incorrectly reads data that was compressed */
+/* We detect this here and crash with an error message instead of */
+/* continuing with garbage data. */
+#if H5_VERSION_LE(1, 10, 2) && H5_VERSION_GE(1, 10, 2)
+ if (mpi_rank == 0) {
+
+ /* Recover the list of filters that were applied to the data */
+ const hid_t h_plist = H5Dget_create_plist(h_data);
+ if (h_plist < 0)
+ error("Error getting property list for data set '%s'", props.name);
+
+ /* Recover the number of filters in the list */
+ const int n_filters = H5Pget_nfilters(h_plist);
+
+ for (int n = 0; n < n_filters; ++n) {
+
+ unsigned int flag;
+ size_t cd_nelmts = 32;
+ unsigned int* cd_values = malloc(cd_nelmts * sizeof(unsigned int));
+ size_t namelen = 256;
+ char* name = calloc(namelen, sizeof(char));
+ unsigned int filter_config;
+
+ /* Recover the n^th filter in the list */
+ const H5Z_filter_t filter =
+ H5Pget_filter(h_plist, n, &flag, &cd_nelmts, cd_values, namelen, name,
+ &filter_config);
+ if (filter < 0)
+ error("Error retrieving %d^th (%d) filter for data set '%s'", n,
+ n_filters, props.name);
+
+ /* Now check whether the deflate filter had been applied */
+ if (filter == H5Z_FILTER_DEFLATE)
+ error(
+ "HDF5 1.10.2 cannot correctly read data that was compressed with "
+ "the 'deflate' filter.\nThe field '%s' has had this filter applied "
+ "and the code would silently read garbage into the particle arrays "
+ "so we'd rather stop here. You can:\n - Recompile the code with an "
+ "earlier or older version of HDF5.\n - Use the 'h5repack' tool to "
+ "remove the filter from the ICs (e.g. h5repack -f NONE -i in_file "
+ "-o out_file).\n",
+ props.name);
+
+ free(name);
+ free(cd_values);
+ }
+
+ H5Pclose(h_plist);
+ }
+#endif
+
/* Create property list for collective dataset read. */
const hid_t h_plist_id = H5Pcreate(H5P_DATASET_XFER);
H5Pset_dxpl_mpio(h_plist_id, H5FD_MPIO_COLLECTIVE);
@@ -838,6 +890,7 @@ void prepare_file(struct engine* e, const char* baseName, long long N_total[6],
const struct xpart* xparts = e->s->xparts;
const struct gpart* gparts = e->s->gparts;
const struct spart* sparts = e->s->sparts;
+ struct swift_params* params = e->parameter_file;
FILE* xmfFile = 0;
int periodic = e->s->periodic;
int numFiles = 1;
@@ -965,7 +1018,14 @@ void prepare_file(struct engine* e, const char* baseName, long long N_total[6],
h_grp =
H5Gcreate(h_file, "/Parameters", H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
if (h_grp < 0) error("Error while creating parameters group");
- parser_write_params_to_hdf5(e->parameter_file, h_grp);
+ parser_write_params_to_hdf5(e->parameter_file, h_grp, 1);
+ H5Gclose(h_grp);
+
+ /* Print the runtime unused parameters */
+ h_grp = H5Gcreate(h_file, "/UnusedParameters", H5P_DEFAULT, H5P_DEFAULT,
+ H5P_DEFAULT);
+ if (h_grp < 0) error("Error while creating parameters group");
+ parser_write_params_to_hdf5(e->parameter_file, h_grp, 0);
H5Gclose(h_grp);
/* Print the system of Units used in the spashot */
@@ -1017,10 +1077,19 @@ void prepare_file(struct engine* e, const char* baseName, long long N_total[6],
error("Particle Type %d not yet supported. Aborting", ptype);
}
- /* Prepare everything */
- for (int i = 0; i < num_fields; ++i)
- prepareArray(e, h_grp, fileName, xmfFile, partTypeGroupName, list[i],
- N_total[ptype], snapshot_units);
+ /* Prepare everything that is not cancelled */
+ for (int i = 0; i < num_fields; ++i) {
+
+ /* Did the user cancel this field? */
+ char field[PARSER_MAX_LINE_SIZE];
+ sprintf(field, "SelectOutput:%s_%s", list[i].name,
+ part_type_names[ptype]);
+ int should_write = parser_get_opt_param_int(params, field, 1);
+
+ if (should_write)
+ prepareArray(e, h_grp, fileName, xmfFile, partTypeGroupName, list[i],
+ N_total[ptype], snapshot_units);
+ }
/* Close particle group */
H5Gclose(h_grp);
@@ -1072,6 +1141,7 @@ void write_output_parallel(struct engine* e, const char* baseName,
struct gpart* dmparts = NULL;
const struct spart* sparts = e->s->sparts;
const struct cooling_function_data* cooling = e->cooling_func;
+ struct swift_params* params = e->parameter_file;
/* Number of unassociated gparts */
const size_t Ndm = Ntot > 0 ? Ntot - (Ngas + Nstars) : 0;
@@ -1261,11 +1331,20 @@ void write_output_parallel(struct engine* e, const char* baseName,
error("Particle Type %d not yet supported. Aborting", ptype);
}
- /* Write everything */
- for (int i = 0; i < num_fields; ++i)
- writeArray(e, h_grp, fileName, partTypeGroupName, list[i], Nparticles,
- N_total[ptype], mpi_rank, offset[ptype], internal_units,
- snapshot_units);
+ /* Write everything that is not cancelled */
+ for (int i = 0; i < num_fields; ++i) {
+
+ /* Did the user cancel this field? */
+ char field[PARSER_MAX_LINE_SIZE];
+ sprintf(field, "SelectOutput:%s_%s", list[i].name,
+ part_type_names[ptype]);
+ int should_write = parser_get_opt_param_int(params, field, 1);
+
+ if (should_write)
+ writeArray(e, h_grp, fileName, partTypeGroupName, list[i], Nparticles,
+ N_total[ptype], mpi_rank, offset[ptype], internal_units,
+ snapshot_units);
+ }
/* Free temporary array */
if (dmparts) {
diff --git a/src/parser.c b/src/parser.c
index af9ef5fd6b7228dd4ad96640b59322175586862b..78d8aef2c3194acd0a9128867e6e5867a0cbc7b0 100644
--- a/src/parser.c
+++ b/src/parser.c
@@ -57,12 +57,23 @@ static void find_duplicate_section(const struct swift_params *params,
static int lineNumber = 0;
/**
- * @brief Reads an input file and stores each parameter in a structure.
+ * @brief Initialize the parser structure.
*
* @param file_name Name of file to be read
* @param params Structure to be populated from file
*/
+void parser_init(const char *file_name, struct swift_params *params) {
+ params->paramCount = 0;
+ params->sectionCount = 0;
+ strcpy(params->fileName, file_name);
+}
+/**
+ * @brief Reads an input file and stores each parameter in a structure.
+ *
+ * @param file_name Name of file to be read
+ * @param params Structure to be populated from file
+ */
void parser_read_file(const char *file_name, struct swift_params *params) {
/* Open file for reading */
FILE *file = fopen(file_name, "r");
@@ -71,9 +82,7 @@ void parser_read_file(const char *file_name, struct swift_params *params) {
char line[PARSER_MAX_LINE_SIZE];
/* Initialise parameter count. */
- params->paramCount = 0;
- params->sectionCount = 0;
- strcpy(params->fileName, file_name);
+ parser_init(file_name, params);
/* Check if parameter file exits. */
if (file == NULL) {
@@ -143,6 +152,7 @@ void parser_set_param(struct swift_params *params, const char *namevalue) {
if (!updated) {
strcpy(params->data[params->paramCount].name, name);
strcpy(params->data[params->paramCount].value, value);
+ params->data[params->paramCount].used = 0;
params->paramCount++;
if (params->paramCount == PARSER_MAX_NO_OF_PARAMS)
error("Too many parameters, current maximum is %d.", params->paramCount);
@@ -359,6 +369,7 @@ static void parse_value(char *line, struct swift_params *params) {
* section. */
strcpy(params->data[params->paramCount].name, tmpStr);
strcpy(params->data[params->paramCount].value, token);
+ params->data[params->paramCount].used = 0;
if (params->paramCount == PARSER_MAX_NO_OF_PARAMS - 1) {
error(
"Maximal number of parameters in parameter file reached. Aborting "
@@ -418,6 +429,7 @@ static void parse_section_param(char *line, int *isFirstParam,
strcpy(params->data[params->paramCount].name, paramName);
strcpy(params->data[params->paramCount].value, token);
+ params->data[params->paramCount].used = 0;
if (params->paramCount == PARSER_MAX_NO_OF_PARAMS - 1) {
error("Maximal number of parameters in parameter file reached. Aborting !");
} else {
@@ -432,7 +444,7 @@ static void parse_section_param(char *line, int *isFirstParam,
* @param name Name of the parameter to be found
* @return Value of the parameter found
*/
-int parser_get_param_int(const struct swift_params *params, const char *name) {
+int parser_get_param_int(struct swift_params *params, const char *name) {
char str[PARSER_MAX_LINE_SIZE];
int retParam = 0;
@@ -447,6 +459,9 @@ int parser_get_param_int(const struct swift_params *params, const char *name) {
params->data[i].name, params->data[i].value, str);
}
+ /* this parameter has been used */
+ params->data[i].used = 1;
+
return retParam;
}
}
@@ -463,8 +478,7 @@ int parser_get_param_int(const struct swift_params *params, const char *name) {
* @param name Name of the parameter to be found
* @return Value of the parameter found
*/
-char parser_get_param_char(const struct swift_params *params,
- const char *name) {
+char parser_get_param_char(struct swift_params *params, const char *name) {
char str[PARSER_MAX_LINE_SIZE];
char retParam = 0;
@@ -479,6 +493,9 @@ char parser_get_param_char(const struct swift_params *params,
params->data[i].name, params->data[i].value, str);
}
+ /* this parameter has been used */
+ params->data[i].used = 1;
+
return retParam;
}
}
@@ -495,8 +512,7 @@ char parser_get_param_char(const struct swift_params *params,
* @param name Name of the parameter to be found
* @return Value of the parameter found
*/
-float parser_get_param_float(const struct swift_params *params,
- const char *name) {
+float parser_get_param_float(struct swift_params *params, const char *name) {
char str[PARSER_MAX_LINE_SIZE];
float retParam = 0.f;
@@ -511,6 +527,9 @@ float parser_get_param_float(const struct swift_params *params,
params->data[i].name, params->data[i].value, str);
}
+ /* this parameter has been used */
+ params->data[i].used = 1;
+
return retParam;
}
}
@@ -527,8 +546,7 @@ float parser_get_param_float(const struct swift_params *params,
* @param name Name of the parameter to be found
* @return Value of the parameter found
*/
-double parser_get_param_double(const struct swift_params *params,
- const char *name) {
+double parser_get_param_double(struct swift_params *params, const char *name) {
char str[PARSER_MAX_LINE_SIZE];
double retParam = 0.;
@@ -542,6 +560,10 @@ double parser_get_param_double(const struct swift_params *params,
"characters '%s'.",
params->data[i].name, params->data[i].value, str);
}
+
+ /* this parameter has been used */
+ params->data[i].used = 1;
+
return retParam;
}
}
@@ -558,11 +580,14 @@ double parser_get_param_double(const struct swift_params *params,
* @param name Name of the parameter to be found
* @param retParam (return) Value of the parameter found
*/
-void parser_get_param_string(const struct swift_params *params,
- const char *name, char *retParam) {
+void parser_get_param_string(struct swift_params *params, const char *name,
+ char *retParam) {
+
for (int i = 0; i < params->paramCount; i++) {
if (!strcmp(name, params->data[i].name)) {
strcpy(retParam, params->data[i].value);
+ /* this parameter has been used */
+ params->data[i].used = 1;
return;
}
}
@@ -578,8 +603,8 @@ void parser_get_param_string(const struct swift_params *params,
* @param def Default value of the parameter of not found.
* @return Value of the parameter found
*/
-int parser_get_opt_param_int(const struct swift_params *params,
- const char *name, int def) {
+int parser_get_opt_param_int(struct swift_params *params, const char *name,
+ int def) {
char str[PARSER_MAX_LINE_SIZE];
int retParam = 0;
@@ -594,10 +619,22 @@ int parser_get_opt_param_int(const struct swift_params *params,
params->data[i].name, params->data[i].value, str);
}
+ /* this parameter has been used */
+ params->data[i].used = 1;
+
return retParam;
}
}
+ /* Generate string for new parameter */
+ sprintf(str, "%s: %i", name, def);
+
+ /* Add it to params */
+ parser_set_param(params, str);
+
+ /* Set parameter as used */
+ params->data[params->paramCount - 1].used = 1;
+
return def;
}
@@ -609,8 +646,8 @@ int parser_get_opt_param_int(const struct swift_params *params,
* @param def Default value of the parameter of not found.
* @return Value of the parameter found
*/
-char parser_get_opt_param_char(const struct swift_params *params,
- const char *name, char def) {
+char parser_get_opt_param_char(struct swift_params *params, const char *name,
+ char def) {
char str[PARSER_MAX_LINE_SIZE];
char retParam = 0;
@@ -625,10 +662,22 @@ char parser_get_opt_param_char(const struct swift_params *params,
params->data[i].name, params->data[i].value, str);
}
+ /* this parameter has been used */
+ params->data[i].used = 1;
+
return retParam;
}
}
+ /* Generate string for new parameter */
+ sprintf(str, "%s: %c", name, def);
+
+ /* Add it to params */
+ parser_set_param(params, str);
+
+ /* Set parameter as used */
+ params->data[params->paramCount - 1].used = 1;
+
return def;
}
@@ -640,8 +689,8 @@ char parser_get_opt_param_char(const struct swift_params *params,
* @param def Default value of the parameter of not found.
* @return Value of the parameter found
*/
-float parser_get_opt_param_float(const struct swift_params *params,
- const char *name, float def) {
+float parser_get_opt_param_float(struct swift_params *params, const char *name,
+ float def) {
char str[PARSER_MAX_LINE_SIZE];
float retParam = 0.f;
@@ -656,10 +705,22 @@ float parser_get_opt_param_float(const struct swift_params *params,
params->data[i].name, params->data[i].value, str);
}
+ /* this parameter has been used */
+ params->data[i].used = 1;
+
return retParam;
}
}
+ /* Generate string for new parameter */
+ sprintf(str, "%s: %f", name, def);
+
+ /* Add it to params */
+ parser_set_param(params, str);
+
+ /* Set parameter as used */
+ params->data[params->paramCount - 1].used = 1;
+
return def;
}
@@ -671,7 +732,7 @@ float parser_get_opt_param_float(const struct swift_params *params,
* @param def Default value of the parameter of not found.
* @return Value of the parameter found
*/
-double parser_get_opt_param_double(const struct swift_params *params,
+double parser_get_opt_param_double(struct swift_params *params,
const char *name, double def) {
char str[PARSER_MAX_LINE_SIZE];
@@ -686,10 +747,23 @@ double parser_get_opt_param_double(const struct swift_params *params,
"characters '%s'.",
params->data[i].name, params->data[i].value, str);
}
+
+ /* this parameter has been used */
+ params->data[i].used = 1;
+
return retParam;
}
}
+ /* Generate string for new parameter */
+ sprintf(str, "%s: %lf", name, def);
+
+ /* Add it to params */
+ parser_set_param(params, str);
+
+ /* Set parameter as used */
+ params->data[params->paramCount - 1].used = 1;
+
return def;
}
@@ -701,16 +775,30 @@ double parser_get_opt_param_double(const struct swift_params *params,
* @param def Default value of the parameter of not found.
* @param retParam (return) Value of the parameter found
*/
-void parser_get_opt_param_string(const struct swift_params *params,
- const char *name, char *retParam,
- const char *def) {
+void parser_get_opt_param_string(struct swift_params *params, const char *name,
+ char *retParam, const char *def) {
+
for (int i = 0; i < params->paramCount; i++) {
if (!strcmp(name, params->data[i].name)) {
strcpy(retParam, params->data[i].value);
+
+ /* this parameter has been used */
+ params->data[i].used = 1;
+
return;
}
}
+ /* Generate string for new parameter */
+ char str[PARSER_MAX_LINE_SIZE];
+ sprintf(str, "%s: %s", name, def);
+
+ /* Add it to params */
+ parser_set_param(params, str);
+
+ /* Set parameter as used */
+ params->data[params->paramCount - 1].used = 1;
+
strcpy(retParam, def);
}
@@ -727,6 +815,7 @@ void parser_print_params(const struct swift_params *params) {
for (int i = 0; i < params->paramCount; i++) {
printf("Parameter name: %s\n", params->data[i].name);
printf("Parameter value: %s\n", params->data[i].value);
+ printf("Parameter used: %i\n", params->data[i].used);
}
}
@@ -736,9 +825,10 @@ void parser_print_params(const struct swift_params *params) {
*
* @param params Structure that holds the parameters
* @param file_name Name of file to be written
+ * @param write_used Write used fields or unused fields.
*/
void parser_write_params_to_file(const struct swift_params *params,
- const char *file_name) {
+ const char *file_name, int write_used) {
FILE *file = fopen(file_name, "w");
char section[PARSER_MAX_LINE_SIZE] = {0};
char param_name[PARSER_MAX_LINE_SIZE] = {0};
@@ -748,6 +838,16 @@ void parser_write_params_to_file(const struct swift_params *params,
fprintf(file, "%s\n", PARSER_START_OF_FILE);
for (int i = 0; i < params->paramCount; i++) {
+ if (write_used && !params->data[i].used) {
+#ifdef SWIFT_DEBUG_CHECKS
+ message(
+ "Parameter `%s` was not used. "
+ "Only the parameter used are written.",
+ params->data[i].name);
+#endif
+ continue;
+ } else if (!write_used && params->data[i].used)
+ continue;
/* Check that the parameter name contains a section name. */
if (strchr(params->data[i].name, PARSER_VALUE_CHAR)) {
/* Copy the parameter name into a temporary string and find the section
@@ -773,16 +873,30 @@ void parser_write_params_to_file(const struct swift_params *params,
}
/* End of file identifier in YAML. */
- fprintf(file, PARSER_END_OF_FILE);
+ fprintf(file, "%s\n", PARSER_END_OF_FILE);
fclose(file);
}
#if defined(HAVE_HDF5)
-void parser_write_params_to_hdf5(const struct swift_params *params, hid_t grp) {
- for (int i = 0; i < params->paramCount; i++)
+/**
+ * @brief Write the contents of the parameter structure to a hdf5 file
+ *
+ * @param params Structure that holds the parameters
+ * @param grp HDF5 group
+ * @param write_used Write used fields or unused fields.
+ */
+void parser_write_params_to_hdf5(const struct swift_params *params, hid_t grp,
+ int write_used) {
+
+ for (int i = 0; i < params->paramCount; i++) {
+ if (write_used && !params->data[i].used)
+ continue;
+ else if (!write_used && params->data[i].used)
+ continue;
io_write_attribute_s(grp, params->data[i].name, params->data[i].value);
+ }
}
#endif
diff --git a/src/parser.h b/src/parser.h
index 58f4a53ea2114dbed29f49e2b5ccca69239b45e3..2b06fce03cbfe2d6a73bc28960bc83bc822e4459 100644
--- a/src/parser.h
+++ b/src/parser.h
@@ -39,6 +39,7 @@
struct parameter {
char name[PARSER_MAX_LINE_SIZE];
char value[PARSER_MAX_LINE_SIZE];
+ int used;
};
struct section {
@@ -55,35 +56,34 @@ struct swift_params {
};
/* Public API. */
+void parser_init(const char *file_name, struct swift_params *params);
void parser_read_file(const char *file_name, struct swift_params *params);
void parser_print_params(const struct swift_params *params);
void parser_write_params_to_file(const struct swift_params *params,
- const char *file_name);
+ const char *file_name, int write_all);
void parser_set_param(struct swift_params *params, const char *desc);
-char parser_get_param_char(const struct swift_params *params, const char *name);
-int parser_get_param_int(const struct swift_params *params, const char *name);
-float parser_get_param_float(const struct swift_params *params,
- const char *name);
-double parser_get_param_double(const struct swift_params *params,
- const char *name);
-void parser_get_param_string(const struct swift_params *params,
- const char *name, char *retParam);
+char parser_get_param_char(struct swift_params *params, const char *name);
+int parser_get_param_int(struct swift_params *params, const char *name);
+float parser_get_param_float(struct swift_params *params, const char *name);
+double parser_get_param_double(struct swift_params *params, const char *name);
+void parser_get_param_string(struct swift_params *params, const char *name,
+ char *retParam);
-char parser_get_opt_param_char(const struct swift_params *params,
- const char *name, char def);
-int parser_get_opt_param_int(const struct swift_params *params,
- const char *name, int def);
-float parser_get_opt_param_float(const struct swift_params *params,
- const char *name, float def);
-double parser_get_opt_param_double(const struct swift_params *params,
+char parser_get_opt_param_char(struct swift_params *params, const char *name,
+ char def);
+int parser_get_opt_param_int(struct swift_params *params, const char *name,
+ int def);
+float parser_get_opt_param_float(struct swift_params *params, const char *name,
+ float def);
+double parser_get_opt_param_double(struct swift_params *params,
const char *name, double def);
-void parser_get_opt_param_string(const struct swift_params *params,
- const char *name, char *retParam,
- const char *def);
+void parser_get_opt_param_string(struct swift_params *params, const char *name,
+ char *retParam, const char *def);
#if defined(HAVE_HDF5)
-void parser_write_params_to_hdf5(const struct swift_params *params, hid_t grp);
+void parser_write_params_to_hdf5(const struct swift_params *params, hid_t grp,
+ int write_all);
#endif
/* Dump/restore. */
diff --git a/src/part.c b/src/part.c
index 1b696a8cbc135fd2c128b5ad705a0e6e24a2d5c8..050e10e9cdd0ab56adcd34ba3e6f2d35c274f14a 100644
--- a/src/part.c
+++ b/src/part.c
@@ -259,7 +259,7 @@ MPI_Datatype multipole_mpi_type;
/**
* @brief Registers MPI particle types.
*/
-void part_create_mpi_types() {
+void part_create_mpi_types(void) {
/* This is not the recommended way of doing this.
One should define the structure field by field
diff --git a/src/part.h b/src/part.h
index e6750ea864bf3785df0b4ebe011e0ad741d7b5c7..03ec331cb17b95b0133be568d6e857a44d1eaf73 100644
--- a/src/part.h
+++ b/src/part.h
@@ -104,7 +104,7 @@ extern MPI_Datatype gpart_mpi_type;
extern MPI_Datatype spart_mpi_type;
extern MPI_Datatype multipole_mpi_type;
-void part_create_mpi_types();
+void part_create_mpi_types(void);
#endif
#endif /* SWIFT_PART_H */
diff --git a/src/partition.c b/src/partition.c
index 8feae3b7a8dce7c78310a3b35762d31b439c69e3..85a51dddf2797e7d203da95abc42639c29f11aa6 100644
--- a/src/partition.c
+++ b/src/partition.c
@@ -1041,7 +1041,7 @@ void partition_initial_partition(struct partition *initial_partition,
*/
void partition_init(struct partition *partition,
struct repartition *repartition,
- const struct swift_params *params, int nr_nodes) {
+ struct swift_params *params, int nr_nodes) {
#ifdef WITH_MPI
diff --git a/src/partition.h b/src/partition.h
index 3ad479c6b1b343106ac736e2d9c77aa9bc93cf60..ec7d670a43537c4717090b857b6e6ba9186b8f1c 100644
--- a/src/partition.h
+++ b/src/partition.h
@@ -76,7 +76,7 @@ int partition_space_to_space(double *oldh, double *oldcdim, int *oldnodeID,
struct space *s);
void partition_init(struct partition *partition,
struct repartition *repartition,
- const struct swift_params *params, int nr_nodes);
+ struct swift_params *params, int nr_nodes);
/* Dump/restore. */
void partition_store_celllist(struct space *s, struct repartition *reparttype);
diff --git a/src/physical_constants.c b/src/physical_constants.c
index b1dbeaeecfbf2e056a68b7866766bb07efb5efba..2c0ea6191b20e7786b0e2c55356b6c9decf7b0a4 100644
--- a/src/physical_constants.c
+++ b/src/physical_constants.c
@@ -38,8 +38,7 @@
* @param params The parsed parameter file.
* @param internal_const The physical constants to initialize.
*/
-void phys_const_init(const struct unit_system *us,
- const struct swift_params *params,
+void phys_const_init(const struct unit_system *us, struct swift_params *params,
struct phys_const *internal_const) {
/* Units are declared as {U_M, U_L, U_t, U_I, U_T} */
diff --git a/src/physical_constants.h b/src/physical_constants.h
index b0f929632ba8a55a57376975597e444a8344e4fc..606e7eeb584fc670c5c690aa9dfa683330ea3644 100644
--- a/src/physical_constants.h
+++ b/src/physical_constants.h
@@ -89,8 +89,7 @@ struct phys_const {
double const_earth_mass;
};
-void phys_const_init(const struct unit_system* us,
- const struct swift_params* params,
+void phys_const_init(const struct unit_system* us, struct swift_params* params,
struct phys_const* internal_const);
void phys_const_print(const struct phys_const* internal_const);
diff --git a/src/potential.c b/src/potential.c
index 1fda6fc8752ff626a5262d7824ea68fd3bc16d46..a313598dae36569f8de9bf15078719886805a2a3 100644
--- a/src/potential.c
+++ b/src/potential.c
@@ -35,7 +35,7 @@
* @param s The #space we run in.
* @param potential The external potential properties to initialize
*/
-void potential_init(const struct swift_params* parameter_file,
+void potential_init(struct swift_params* parameter_file,
const struct phys_const* phys_const,
const struct unit_system* us, const struct space* s,
struct external_potential* potential) {
diff --git a/src/potential.h b/src/potential.h
index 680d4e235fdf7a7666901f34a82f62feda4ae9bb..814b83c69180631db21e392704c0279808a6f03e 100644
--- a/src/potential.h
+++ b/src/potential.h
@@ -47,7 +47,7 @@
#endif
/* Now, some generic functions, defined in the source file */
-void potential_init(const struct swift_params* parameter_file,
+void potential_init(struct swift_params* parameter_file,
const struct phys_const* phys_const,
const struct unit_system* us, const struct space* s,
struct external_potential* potential);
diff --git a/src/potential/disc_patch/potential.h b/src/potential/disc_patch/potential.h
index ab229d009c692db727e8f2341c3c49813f74f2b8..40c747314994cfdc4a38679d747e3351e4fbd4d1 100644
--- a/src/potential/disc_patch/potential.h
+++ b/src/potential/disc_patch/potential.h
@@ -269,9 +269,9 @@ external_gravity_get_potential_energy(
* @param potential The external potential properties to initialize
*/
static INLINE void potential_init_backend(
- const struct swift_params* parameter_file,
- const struct phys_const* phys_const, const struct unit_system* us,
- const struct space* s, struct external_potential* potential) {
+ struct swift_params* parameter_file, const struct phys_const* phys_const,
+ const struct unit_system* us, const struct space* s,
+ struct external_potential* potential) {
potential->surface_density = parser_get_param_double(
parameter_file, "DiscPatchPotential:surface_density");
diff --git a/src/potential/isothermal/potential.h b/src/potential/isothermal/potential.h
index c974618d7b581884f871863bb83200b8cecee7a5..4267c9becc7251ffe276b69f078e374504c22aab 100644
--- a/src/potential/isothermal/potential.h
+++ b/src/potential/isothermal/potential.h
@@ -162,9 +162,9 @@ external_gravity_get_potential_energy(
* @param potential The external potential properties to initialize
*/
static INLINE void potential_init_backend(
- const struct swift_params* parameter_file,
- const struct phys_const* phys_const, const struct unit_system* us,
- const struct space* s, struct external_potential* potential) {
+ struct swift_params* parameter_file, const struct phys_const* phys_const,
+ const struct unit_system* us, const struct space* s,
+ struct external_potential* potential) {
potential->x =
s->dim[0] / 2. +
diff --git a/src/potential/none/potential.h b/src/potential/none/potential.h
index a8550cad702891ff211539c95c42eca57418c464..2303f2531d059660a063a92be999405f05e9e6aa 100644
--- a/src/potential/none/potential.h
+++ b/src/potential/none/potential.h
@@ -98,9 +98,9 @@ external_gravity_get_potential_energy(
* @param potential The external potential properties to initialize
*/
static INLINE void potential_init_backend(
- const struct swift_params* parameter_file,
- const struct phys_const* phys_const, const struct unit_system* us,
- const struct space* s, struct external_potential* potential) {}
+ struct swift_params* parameter_file, const struct phys_const* phys_const,
+ const struct unit_system* us, const struct space* s,
+ struct external_potential* potential) {}
/**
* @brief Prints the properties of the external potential to stdout.
diff --git a/src/potential/point_mass/potential.h b/src/potential/point_mass/potential.h
index adea9d912056fd07e134fb98a7603030e897ec7a..db875842d51f6c0a28dd1308fd7dd1728e746ce4 100644
--- a/src/potential/point_mass/potential.h
+++ b/src/potential/point_mass/potential.h
@@ -152,9 +152,9 @@ external_gravity_get_potential_energy(
* @param potential The external potential properties to initialize
*/
static INLINE void potential_init_backend(
- const struct swift_params* parameter_file,
- const struct phys_const* phys_const, const struct unit_system* us,
- const struct space* s, struct external_potential* potential) {
+ struct swift_params* parameter_file, const struct phys_const* phys_const,
+ const struct unit_system* us, const struct space* s,
+ struct external_potential* potential) {
potential->x =
parser_get_param_double(parameter_file, "PointMassPotential:position_x");
diff --git a/src/potential/point_mass_ring/potential.h b/src/potential/point_mass_ring/potential.h
index ebf047ea7c1f946536300f976713893e66295c59..551efe32521a5c5ee8068ba409dbb81547103e8f 100644
--- a/src/potential/point_mass_ring/potential.h
+++ b/src/potential/point_mass_ring/potential.h
@@ -192,9 +192,9 @@ external_gravity_get_potential_energy(
* @param potential The external potential properties to initialize
*/
static INLINE void potential_init_backend(
- const struct swift_params* parameter_file,
- const struct phys_const* phys_const, const struct unit_system* us,
- const struct space* s, struct external_potential* potential) {
+ struct swift_params* parameter_file, const struct phys_const* phys_const,
+ const struct unit_system* us, const struct space* s,
+ struct external_potential* potential) {
potential->x =
parser_get_param_double(parameter_file, "PointMassPotential:position_x");
diff --git a/src/potential/point_mass_softened/potential.h b/src/potential/point_mass_softened/potential.h
index 83a79ea3cddbff37fdd70d58d70afcaf46f7bc0e..80959ec923cbedcbea5fba3293c8ae4f94f65679 100644
--- a/src/potential/point_mass_softened/potential.h
+++ b/src/potential/point_mass_softened/potential.h
@@ -179,9 +179,9 @@ external_gravity_get_potential_energy(
* @param potential The external potential properties to initialize
*/
static INLINE void potential_init_backend(
- const struct swift_params* parameter_file,
- const struct phys_const* phys_const, const struct unit_system* us,
- const struct space* s, struct external_potential* potential) {
+ struct swift_params* parameter_file, const struct phys_const* phys_const,
+ const struct unit_system* us, const struct space* s,
+ struct external_potential* potential) {
potential->x =
parser_get_param_double(parameter_file, "PointMassPotential:position_x");
diff --git a/src/potential/sine_wave/potential.h b/src/potential/sine_wave/potential.h
index 1a4ee8aae8238c5db4c99eacb9e96bd967bcc7c4..8a1786baaf9ed0b0683ea16fdefee997ecb4eceb 100644
--- a/src/potential/sine_wave/potential.h
+++ b/src/potential/sine_wave/potential.h
@@ -117,9 +117,9 @@ external_gravity_get_potential_energy(
* @param potential The external potential properties to initialize
*/
static INLINE void potential_init_backend(
- const struct swift_params* parameter_file,
- const struct phys_const* phys_const, const struct unit_system* us,
- const struct space* s, struct external_potential* potential) {
+ struct swift_params* parameter_file, const struct phys_const* phys_const,
+ const struct unit_system* us, const struct space* s,
+ struct external_potential* potential) {
potential->amplitude =
parser_get_param_double(parameter_file, "SineWavePotential:amplitude");
diff --git a/src/profiler.c b/src/profiler.c
index 1dd1a41cc336942d17790e96c8f883d65e54a51f..58fd279d312d3c752d65ccaceab803ace66fddac 100644
--- a/src/profiler.c
+++ b/src/profiler.c
@@ -146,8 +146,8 @@ void profiler_write_all_timing_info_headers(const struct engine *e,
void profiler_write_timing_info(const struct engine *e, ticks time,
FILE *file) {
- fprintf(file, " %6d %14e %14e %10zu %10zu %10zu %21.3f\n", e->step, e->time,
- e->time_step, e->updates, e->g_updates, e->s_updates,
+ fprintf(file, " %6d %14e %14e %10lld %10lld %10lld %21.3f\n", e->step,
+ e->time, e->time_step, e->updates, e->g_updates, e->s_updates,
clocks_from_ticks(time));
fflush(file);
}
diff --git a/src/runner.c b/src/runner.c
index 5a382a916abda9dddd45dcb5e703578457f0548a..96d68745a5a134b9a6c516f277a768364c9339b0 100644
--- a/src/runner.c
+++ b/src/runner.c
@@ -606,8 +606,10 @@ void runner_do_extra_ghost(struct runner *r, struct cell *c, int timer) {
#ifdef EXTRA_HYDRO_LOOP
struct part *restrict parts = c->parts;
+ struct xpart *restrict xparts = c->xparts;
const int count = c->count;
const struct engine *e = r->e;
+ const struct cosmology *cosmo = e->cosmology;
TIMER_TIC;
@@ -625,11 +627,23 @@ void runner_do_extra_ghost(struct runner *r, struct cell *c, int timer) {
/* Get a direct pointer on the part. */
struct part *restrict p = &parts[i];
+ struct xpart *restrict xp = &xparts[i];
if (part_is_active(p, e)) {
- /* Get ready for a force calculation */
+ /* Finish the gradient calculation */
hydro_end_gradient(p);
+
+ /* As of here, particle force variables will be set. */
+
+ /* Compute variables required for the force loop */
+ hydro_prepare_force(p, xp, cosmo);
+
+ /* The particle force values are now set. Do _NOT_
+ try to read any particle density variables! */
+
+ /* Prepare the particle for the force loop over neighbours */
+ hydro_reset_acceleration(p);
}
}
}
@@ -710,9 +724,13 @@ void runner_do_ghost(struct runner *r, struct cell *c, int timer) {
const float h_old_dim = pow_dimension(h_old);
const float h_old_dim_minus_one = pow_dimension_minus_one(h_old);
float h_new;
+ int has_no_neighbours = 0;
if (p->density.wcount == 0.f) { /* No neighbours case */
+ /* Flag that there were no neighbours */
+ has_no_neighbours = 1;
+
/* Double h and try again */
h_new = 2.f * h_old;
} else {
@@ -729,7 +747,8 @@ void runner_do_ghost(struct runner *r, struct cell *c, int timer) {
p->density.wcount_dh * h_old_dim +
hydro_dimension * p->density.wcount * h_old_dim_minus_one;
- h_new = h_old - f / f_prime;
+ /* Avoid floating point exception from f_prime = 0 */
+ h_new = h_old - f / (f_prime + FLT_MIN);
#ifdef SWIFT_DEBUG_CHECKS
if ((f > 0.f && h_new > h_old) || (f < 0.f && h_new < h_old))
@@ -768,13 +787,30 @@ void runner_do_ghost(struct runner *r, struct cell *c, int timer) {
p->h = hydro_h_max;
/* Do some damage control if no neighbours at all were found */
- if (p->density.wcount == kernel_root * kernel_norm)
+ if (has_no_neighbours) {
hydro_part_has_no_neighbours(p, xp, cosmo);
+ chemistry_part_has_no_neighbours(p, xp, chemistry, cosmo);
+ }
}
}
- /* We now have a particle whose smoothing length has converged */
+/* We now have a particle whose smoothing length has converged */
+
+#ifdef EXTRA_HYDRO_LOOP
+
+ /* As of here, particle gradient variables will be set. */
+ /* The force variables are set in the extra ghost. */
+
+ /* Compute variables required for the gradient loop */
+ hydro_prepare_gradient(p, xp, cosmo);
+
+ /* The particle gradient values are now set. Do _NOT_
+ try to read any particle density variables! */
+
+ /* Prepare the particle for the gradient loop over neighbours */
+ hydro_reset_gradient(p);
+#else
/* As of here, particle force variables will be set. */
/* Compute variables required for the force loop */
@@ -785,6 +821,8 @@ void runner_do_ghost(struct runner *r, struct cell *c, int timer) {
/* Prepare the particle for the force loop over neighbours */
hydro_reset_acceleration(p);
+
+#endif /* EXTRA_HYDRO_LOOP */
}
/* We now need to treat the particles whose smoothing length had not
@@ -1630,13 +1668,20 @@ void runner_do_end_force(struct runner *r, struct cell *c, int timer) {
gravity_end_force(gp, const_G);
#ifdef SWIFT_NO_GRAVITY_BELOW_ID
+
+ /* Get the ID of the gpart */
+ long long id = 0;
+ if (gp->type == swift_type_gas)
+ id = e->s->parts[-gp->id_or_neg_offset].id;
+ else if (gp->type == swift_type_star)
+ id = e->s->sparts[-gp->id_or_neg_offset].id;
+ else if (gp->type == swift_type_black_hole)
+ error("Unexisting type");
+ else
+ id = gp->id_or_neg_offset;
+
/* Cancel gravity forces of these particles */
- if ((gp->type == swift_type_dark_matter &&
- gp->id_or_neg_offset < SWIFT_NO_GRAVITY_BELOW_ID) ||
- (gp->type == swift_type_gas &&
- parts[-gp->id_or_neg_offset].id < SWIFT_NO_GRAVITY_BELOW_ID) ||
- (gp->type == swift_type_star &&
- sparts[-gp->id_or_neg_offset].id < SWIFT_NO_GRAVITY_BELOW_ID)) {
+ if (id < SWIFT_NO_GRAVITY_BELOW_ID) {
/* Don't move ! */
gp->a_grav[0] = 0.f;
@@ -1653,14 +1698,27 @@ void runner_do_end_force(struct runner *r, struct cell *c, int timer) {
/* Check that this gpart has interacted with all the other
* particles (via direct or multipoles) in the box */
- if (gp->num_interacted != e->total_nr_gparts)
+ if (gp->num_interacted != e->total_nr_gparts) {
+
+ /* Get the ID of the gpart */
+ long long my_id = 0;
+ if (gp->type == swift_type_gas)
+ my_id = e->s->parts[-gp->id_or_neg_offset].id;
+ else if (gp->type == swift_type_star)
+ my_id = e->s->sparts[-gp->id_or_neg_offset].id;
+ else if (gp->type == swift_type_black_hole)
+ error("Unexisting type");
+ else
+ my_id = gp->id_or_neg_offset;
+
error(
"g-particle (id=%lld, type=%s) did not interact "
- "gravitationally "
- "with all other gparts gp->num_interacted=%lld, "
- "total_gparts=%lld (local num_gparts=%zd)",
- gp->id_or_neg_offset, part_type_names[gp->type],
- gp->num_interacted, e->total_nr_gparts, e->s->nr_gparts);
+ "gravitationally with all other gparts "
+ "gp->num_interacted=%lld, total_gparts=%lld (local "
+ "num_gparts=%zd)",
+ my_id, part_type_names[gp->type], gp->num_interacted,
+ e->total_nr_gparts, e->s->nr_gparts);
+ }
}
#endif
}
diff --git a/src/serial_io.c b/src/serial_io.c
index 9403caad7670b9af369f4b3598b8a05cf2d0d9e9..4074f9bd54754f4b50a0e62a6a54089efb4d5bfb 100644
--- a/src/serial_io.c
+++ b/src/serial_io.c
@@ -49,6 +49,7 @@
#include "io_properties.h"
#include "kernel_hydro.h"
#include "part.h"
+#include "part_type.h"
#include "stars_io.h"
#include "units.h"
#include "xmf.h"
@@ -233,6 +234,11 @@ void prepareArray(const struct engine* e, hid_t grp, char* fileName,
error("Error while setting chunk size (%llu, %llu) for field '%s'.",
chunk_shape[0], chunk_shape[1], props.name);
+ /* Impose check-sum to verify data corruption */
+ h_err = H5Pset_fletcher32(h_prop);
+ if (h_err < 0)
+ error("Error while setting checksum options for field '%s'.", props.name);
+
/* Impose data compression */
if (e->snapshot_compression > 0) {
h_err = H5Pset_shuffle(h_prop);
@@ -727,6 +733,7 @@ void write_output_serial(struct engine* e, const char* baseName,
struct gpart* dmparts = NULL;
const struct spart* sparts = e->s->sparts;
const struct cooling_function_data* cooling = e->cooling_func;
+ struct swift_params* params = e->parameter_file;
FILE* xmfFile = 0;
/* Number of unassociated gparts */
@@ -872,7 +879,14 @@ void write_output_serial(struct engine* e, const char* baseName,
h_grp =
H5Gcreate(h_file, "/Parameters", H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
if (h_grp < 0) error("Error while creating parameters group");
- parser_write_params_to_hdf5(e->parameter_file, h_grp);
+ parser_write_params_to_hdf5(e->parameter_file, h_grp, 1);
+ H5Gclose(h_grp);
+
+ /* Print the runtime unused parameters */
+ h_grp = H5Gcreate(h_file, "/UnusedParameters", H5P_DEFAULT, H5P_DEFAULT,
+ H5P_DEFAULT);
+ if (h_grp < 0) error("Error while creating parameters group");
+ parser_write_params_to_hdf5(e->parameter_file, h_grp, 0);
H5Gclose(h_grp);
/* Print the system of Units used in the spashot */
@@ -1005,11 +1019,20 @@ void write_output_serial(struct engine* e, const char* baseName,
error("Particle Type %d not yet supported. Aborting", ptype);
}
- /* Write everything */
- for (int i = 0; i < num_fields; ++i)
- writeArray(e, h_grp, fileName, xmfFile, partTypeGroupName, list[i],
- Nparticles, N_total[ptype], mpi_rank, offset[ptype],
- internal_units, snapshot_units);
+ /* Write everything that is not cancelled */
+ for (int i = 0; i < num_fields; ++i) {
+
+ /* Did the user cancel this field? */
+ char field[PARSER_MAX_LINE_SIZE];
+ sprintf(field, "SelectOutput:%s_%s", list[i].name,
+ part_type_names[ptype]);
+ int should_write = parser_get_opt_param_int(params, field, 1);
+
+ if (should_write)
+ writeArray(e, h_grp, fileName, xmfFile, partTypeGroupName, list[i],
+ Nparticles, N_total[ptype], mpi_rank, offset[ptype],
+ internal_units, snapshot_units);
+ }
/* Free temporary array */
if (dmparts) {
diff --git a/src/single_io.c b/src/single_io.c
index d7afdd4a886ccde9701e7665f978e4e2ffa907aa..975487a1d954e0144f4675f4b90b7cd3b70f3a13 100644
--- a/src/single_io.c
+++ b/src/single_io.c
@@ -48,6 +48,7 @@
#include "io_properties.h"
#include "kernel_hydro.h"
#include "part.h"
+#include "part_type.h"
#include "stars_io.h"
#include "units.h"
#include "xmf.h"
@@ -239,6 +240,11 @@ void writeArray(const struct engine* e, hid_t grp, char* fileName,
error("Error while setting chunk size (%llu, %llu) for field '%s'.",
chunk_shape[0], chunk_shape[1], props.name);
+ /* Impose check-sum to verify data corruption */
+ h_err = H5Pset_fletcher32(h_prop);
+ if (h_err < 0)
+ error("Error while setting checksum options for field '%s'.", props.name);
+
/* Impose data compression */
if (e->snapshot_compression > 0) {
h_err = H5Pset_shuffle(h_prop);
@@ -315,8 +321,9 @@ void writeArray(const struct engine* e, hid_t grp, char* fileName,
* @todo Read snapshots distributed in more than one file.
*
*/
-void read_ic_single(char* fileName, const struct unit_system* internal_units,
- double dim[3], struct part** parts, struct gpart** gparts,
+void read_ic_single(const char* fileName,
+ const struct unit_system* internal_units, double dim[3],
+ struct part** parts, struct gpart** gparts,
struct spart** sparts, size_t* Ngas, size_t* Ngparts,
size_t* Nstars, int* periodic, int* flag_entropy,
int with_hydro, int with_gravity, int with_stars,
@@ -593,6 +600,7 @@ void write_output_single(struct engine* e, const char* baseName,
struct gpart* dmparts = NULL;
const struct spart* sparts = e->s->sparts;
const struct cooling_function_data* cooling = e->cooling_func;
+ struct swift_params* params = e->parameter_file;
/* Number of unassociated gparts */
const size_t Ndm = Ntot > 0 ? Ntot - (Ngas + Nstars) : 0;
@@ -724,7 +732,14 @@ void write_output_single(struct engine* e, const char* baseName,
h_grp =
H5Gcreate(h_file, "/Parameters", H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
if (h_grp < 0) error("Error while creating parameters group");
- parser_write_params_to_hdf5(e->parameter_file, h_grp);
+ parser_write_params_to_hdf5(e->parameter_file, h_grp, 1);
+ H5Gclose(h_grp);
+
+ /* Print the runtime unused parameters */
+ h_grp = H5Gcreate(h_file, "/UnusedParameters", H5P_DEFAULT, H5P_DEFAULT,
+ H5P_DEFAULT);
+ if (h_grp < 0) error("Error while creating parameters group");
+ parser_write_params_to_hdf5(e->parameter_file, h_grp, 0);
H5Gclose(h_grp);
/* Print the system of Units used in the spashot */
@@ -823,10 +838,19 @@ void write_output_single(struct engine* e, const char* baseName,
error("Particle Type %d not yet supported. Aborting", ptype);
}
- /* Write everything */
- for (int i = 0; i < num_fields; ++i)
- writeArray(e, h_grp, fileName, xmfFile, partTypeGroupName, list[i], N,
- internal_units, snapshot_units);
+ /* Write everything that is not cancelled */
+ for (int i = 0; i < num_fields; ++i) {
+
+ /* Did the user cancel this field? */
+ char field[PARSER_MAX_LINE_SIZE];
+ sprintf(field, "SelectOutput:%s_%s", list[i].name,
+ part_type_names[ptype]);
+ int should_write = parser_get_opt_param_int(params, field, 1);
+
+ if (should_write)
+ writeArray(e, h_grp, fileName, xmfFile, partTypeGroupName, list[i], N,
+ internal_units, snapshot_units);
+ }
/* Free temporary array */
if (dmparts) {
diff --git a/src/single_io.h b/src/single_io.h
index 26b849716e3e018d9a10c5c5c513ad26c7ccb274..aa1a3b7de82e6f882b3a59064eb351e7c65c6aab 100644
--- a/src/single_io.h
+++ b/src/single_io.h
@@ -29,8 +29,9 @@
#include "part.h"
#include "units.h"
-void read_ic_single(char* fileName, const struct unit_system* internal_units,
- double dim[3], struct part** parts, struct gpart** gparts,
+void read_ic_single(const char* fileName,
+ const struct unit_system* internal_units, double dim[3],
+ struct part** parts, struct gpart** gparts,
struct spart** sparts, size_t* Ngas, size_t* Ndm,
size_t* Nstars, int* periodic, int* flag_entropy,
int with_hydro, int with_gravity, int with_stars,
diff --git a/src/sourceterms.c b/src/sourceterms.c
index 994658740a50a764edd3988ef7d6b78e00546f8f..993045e61503e4e78b855816921bc057706b76d1 100644
--- a/src/sourceterms.c
+++ b/src/sourceterms.c
@@ -36,7 +36,7 @@
* @param us The current internal system of units
* @param source the structure that has all the source term properties
*/
-void sourceterms_init(const struct swift_params *parameter_file,
+void sourceterms_init(struct swift_params *parameter_file,
struct unit_system *us, struct sourceterms *source) {
#ifdef SOURCETERMS_SN_FEEDBACK
supernova_init(parameter_file, us, source);
diff --git a/src/sourceterms.h b/src/sourceterms.h
index a5d0c3c727d70d50fb3388d5e5e3cc3d6362276f..407d2f19362531a3fd3537889593c484319919b5 100644
--- a/src/sourceterms.h
+++ b/src/sourceterms.h
@@ -41,7 +41,7 @@ struct sourceterms {
#include "sourceterms/sn_feedback/sn_feedback.h"
#endif
-void sourceterms_init(const struct swift_params* parameter_file,
+void sourceterms_init(struct swift_params* parameter_file,
struct unit_system* us, struct sourceterms* source);
void sourceterms_print(struct sourceterms* source);
diff --git a/src/sourceterms/sn_feedback/sn_feedback.h b/src/sourceterms/sn_feedback/sn_feedback.h
index f2f224ce871ebb768c318aef42a690861dd974df..411673c37e82ff89d906425d1cadaa135c46a38d 100644
--- a/src/sourceterms/sn_feedback/sn_feedback.h
+++ b/src/sourceterms/sn_feedback/sn_feedback.h
@@ -171,7 +171,7 @@ __attribute__((always_inline)) INLINE static void supernova_feedback_apply(
*/
__attribute__((always_inline)) INLINE static void supernova_init(
- const struct swift_params* parameter_file, struct unit_system* us,
+ struct swift_params* parameter_file, struct unit_system* us,
struct sourceterms* source) {
source->supernova.time = parser_get_param_double(parameter_file, "SN:time");
source->supernova.energy =
diff --git a/src/space.c b/src/space.c
index 457d04f6066ea9ea1cd75e9a5eb5db9265207505..4a9f3bacf6c2bfbc07bc66034c49bbf2e9a4b434 100644
--- a/src/space.c
+++ b/src/space.c
@@ -2361,7 +2361,7 @@ void space_first_init_parts_mapper(void *restrict map_data, int count,
const struct cosmology *cosmo = s->e->cosmology;
const struct phys_const *phys_const = s->e->physical_constants;
const struct unit_system *us = s->e->internal_units;
- const float a_factor_vel = cosmo->a * cosmo->a;
+ const float a_factor_vel = cosmo->a;
const struct hydro_props *hydro_props = s->e->hydro_properties;
const float u_init = hydro_props->initial_internal_energy;
@@ -2436,7 +2436,7 @@ void space_first_init_gparts_mapper(void *restrict map_data, int count,
const struct space *restrict s = (struct space *)extra_data;
const struct cosmology *cosmo = s->e->cosmology;
- const float a_factor_vel = cosmo->a * cosmo->a;
+ const float a_factor_vel = cosmo->a;
const struct gravity_props *grav_props = s->e->gravity_properties;
for (int k = 0; k < count; k++) {
@@ -2493,7 +2493,7 @@ void space_first_init_sparts_mapper(void *restrict map_data, int count,
#endif
const struct cosmology *cosmo = s->e->cosmology;
- const float a_factor_vel = cosmo->a * cosmo->a;
+ const float a_factor_vel = cosmo->a;
for (int k = 0; k < count; k++) {
/* Convert velocities to internal units */
@@ -2648,7 +2648,7 @@ void space_convert_quantities(struct space *s, int verbose) {
* parts with a cutoff below half the cell width are then split
* recursively.
*/
-void space_init(struct space *s, const struct swift_params *params,
+void space_init(struct space *s, struct swift_params *params,
const struct cosmology *cosmo, double dim[3],
struct part *parts, struct gpart *gparts, struct spart *sparts,
size_t Npart, size_t Ngpart, size_t Nspart, int periodic,
@@ -3122,7 +3122,7 @@ void space_check_cosmology(struct space *s, const struct cosmology *cosmo,
if (fabs(Omega_m - cosmo->Omega_m) > 1e-3)
error(
"The matter content of the simulation does not match the cosmology "
- "in the parameter file comso.Omega_m=%e Omega_m=%e",
+ "in the parameter file cosmo.Omega_m=%e Omega_m=%e",
cosmo->Omega_m, Omega_m);
}
}
diff --git a/src/space.h b/src/space.h
index 546b06a609d30e5b9f40bf8ee9f92f03faf83576..c6b695a06042e4417ea419b2b86884815b903809 100644
--- a/src/space.h
+++ b/src/space.h
@@ -209,7 +209,7 @@ void space_gparts_sort(struct gpart *gparts, struct part *parts,
void space_sparts_sort(struct spart *sparts, int *ind, int *counts,
int num_bins, ptrdiff_t sparts_offset);
void space_getcells(struct space *s, int nr_cells, struct cell **cells);
-void space_init(struct space *s, const struct swift_params *params,
+void space_init(struct space *s, struct swift_params *params,
const struct cosmology *cosmo, double dim[3],
struct part *parts, struct gpart *gparts, struct spart *sparts,
size_t Npart, size_t Ngpart, size_t Nspart, int periodic,
@@ -243,9 +243,9 @@ void space_gparts_get_cell_index(struct space *s, int *gind, int *cell_counts,
void space_sparts_get_cell_index(struct space *s, int *sind, int *cell_counts,
struct cell *cells, int verbose);
void space_synchronize_particle_positions(struct space *s);
-void space_do_parts_sort();
-void space_do_gparts_sort();
-void space_do_sparts_sort();
+void space_do_parts_sort(void);
+void space_do_gparts_sort(void);
+void space_do_sparts_sort(void);
void space_first_init_parts(struct space *s, int verbose);
void space_first_init_gparts(struct space *s, int verbose);
void space_first_init_sparts(struct space *s, int verbose);
diff --git a/src/stars/Default/star_io.h b/src/stars/Default/star_io.h
index c3dc31096383533e1e15fa65615d2c9aac0f43e3..7ad29f0a935c002b1337c2a75d6f987c05c9bb43 100644
--- a/src/stars/Default/star_io.h
+++ b/src/stars/Default/star_io.h
@@ -28,8 +28,8 @@
* @param list The list of i/o properties to read.
* @param num_fields The number of i/o fields to read.
*/
-void star_read_particles(struct spart* sparts, struct io_props* list,
- int* num_fields) {
+INLINE static void star_read_particles(struct spart* sparts,
+ struct io_props* list, int* num_fields) {
/* Say how much we want to read */
*num_fields = 4;
@@ -52,8 +52,9 @@ void star_read_particles(struct spart* sparts, struct io_props* list,
* @param list The list of i/o properties to write.
* @param num_fields The number of i/o fields to write.
*/
-void star_write_particles(const struct spart* sparts, struct io_props* list,
- int* num_fields) {
+INLINE static void star_write_particles(const struct spart* sparts,
+ struct io_props* list,
+ int* num_fields) {
/* Say how much we want to read */
*num_fields = 4;
diff --git a/src/statistics.c b/src/statistics.c
index 62a4f9a1420e88712e8fb527fc4d3db7f4b0abc0..bdca6cfb4ef84bb64aa4776bfc600b0727e0d606 100644
--- a/src/statistics.c
+++ b/src/statistics.c
@@ -396,7 +396,7 @@ void stats_add_MPI(void *in, void *inout, int *len, MPI_Datatype *datatype) {
/**
* @brief Registers MPI #statistics type and reduction function.
*/
-void stats_create_MPI_type() {
+void stats_create_MPI_type(void) {
/* This is not the recommended way of doing this.
One should define the structure field by field
diff --git a/src/statistics.h b/src/statistics.h
index e8cddda1e855d156070b8a000cb15b515f127740..adc9f5b6a24a093419b7dd644404a68ef736a685 100644
--- a/src/statistics.h
+++ b/src/statistics.h
@@ -77,7 +77,7 @@ extern MPI_Datatype statistics_mpi_type;
extern MPI_Op statistics_mpi_reduce_op;
void stats_add_MPI(void* in, void* out, int* len, MPI_Datatype* datatype);
-void stats_create_MPI_type();
+void stats_create_MPI_type(void);
#endif
#endif /* SWIFT_STATISTICS_H */
diff --git a/src/swift.h b/src/swift.h
index 7691720942f32d29d3269ccdd7adbe8db32280bf..17f7c5c7e4e56ed1650d6cdd078060244c67b643 100644
--- a/src/swift.h
+++ b/src/swift.h
@@ -29,8 +29,10 @@
#include "cell.h"
#include "chemistry.h"
#include "clocks.h"
+#include "common_io.h"
#include "const.h"
#include "cooling.h"
+#include "cooling_struct.h"
#include "cosmology.h"
#include "cycle.h"
#include "debug.h"
diff --git a/src/timers.c b/src/timers.c
index fec111dd939528bd0648609d8a1f5f83e595ec02..e3beda71310b6a177833db73e207179e5a4b5468 100644
--- a/src/timers.c
+++ b/src/timers.c
@@ -110,7 +110,7 @@ void timers_reset(unsigned long long mask) {
* @brief Re-set all the timers.
*
*/
-void timers_reset_all() { timers_reset(timers_mask_all); }
+void timers_reset_all(void) { timers_reset(timers_mask_all); }
/**
* @brief Outputs all the timers to the timers dump file.
@@ -145,4 +145,4 @@ void timers_open_file(int rank) {
/**
* @brief Close the file containing the timer info.
*/
-void timers_close_file() { fclose(timers_file); }
+void timers_close_file(void) { fclose(timers_file); }
diff --git a/src/timers.h b/src/timers.h
index 38ede8251eb5d640282e728e17d9330956a1cba8..82132865769604a2ac2e7be3541e2f2f4164f6c3 100644
--- a/src/timers.h
+++ b/src/timers.h
@@ -119,10 +119,10 @@ INLINE static ticks timers_toc(unsigned int t, ticks tic) {
#endif
/* Function prototypes. */
-void timers_reset_all();
+void timers_reset_all(void);
void timers_reset(unsigned long long mask);
void timers_open_file(int rank);
-void timers_close_file();
+void timers_close_file(void);
void timers_print(int step);
#endif /* SWIFT_TIMERS_H */
diff --git a/src/tools.h b/src/tools.h
index bb141101a3bf6fad38a83a15ea7f6bb5de86e9f8..a54510000d3c2843e8d60047752b19a46bd502d9 100644
--- a/src/tools.h
+++ b/src/tools.h
@@ -52,6 +52,6 @@ int compare_values(double a, double b, double threshold, double *absDiff,
double *absSum, double *relDiff);
int compare_particles(struct part a, struct part b, double threshold);
-long get_maxrss();
+long get_maxrss(void);
#endif /* SWIFT_TOOL_H */
diff --git a/src/units.c b/src/units.c
index ae33b0c263dc014dbaf5406a8dcdc8ed254d26dd..48f0a3aee6e348b5df24ac41b308aebf6f70224a 100644
--- a/src/units.c
+++ b/src/units.c
@@ -77,8 +77,7 @@ void units_init(struct unit_system* us, double U_M_in_cgs, double U_L_in_cgs,
* @param params The parsed parameter file.
* @param category The section of the parameter file to read from.
*/
-void units_init_from_params(struct unit_system* us,
- const struct swift_params* params,
+void units_init_from_params(struct unit_system* us, struct swift_params* params,
const char* category) {
char buffer[200];
@@ -104,9 +103,8 @@ void units_init_from_params(struct unit_system* us,
* @param category The section of the parameter file to read from.
* @param def The default unit system to copy from if required.
*/
-void units_init_default(struct unit_system* us,
- const struct swift_params* params, const char* category,
- const struct unit_system* def) {
+void units_init_default(struct unit_system* us, struct swift_params* params,
+ const char* category, const struct unit_system* def) {
if (!def) error("Default unit_system not allocated");
diff --git a/src/units.h b/src/units.h
index a6169d0a2f0e79156428f21d6096d66da7782837..829a1ce542500308cbc64a2463545fbd23921eef 100644
--- a/src/units.h
+++ b/src/units.h
@@ -98,11 +98,10 @@ enum unit_conversion_factor {
void units_init_cgs(struct unit_system*);
void units_init(struct unit_system* us, double U_M_in_cgs, double U_L_in_cgs,
double U_t_in_cgs, double U_C_in_cgs, double U_T_in_cgs);
-void units_init_from_params(struct unit_system*, const struct swift_params*,
+void units_init_from_params(struct unit_system*, struct swift_params*,
const char* category);
-void units_init_default(struct unit_system* us,
- const struct swift_params* params, const char* category,
- const struct unit_system* def);
+void units_init_default(struct unit_system* us, struct swift_params* params,
+ const char* category, const struct unit_system* def);
int units_are_equal(const struct unit_system* a, const struct unit_system* b);
diff --git a/src/vector.h b/src/vector.h
index 9048e273759ae0c0978c8ddbf26a810d4761f464..a1ecddc6ed68ef659759665f15f25aa7e32dc908 100644
--- a/src/vector.h
+++ b/src/vector.h
@@ -493,7 +493,7 @@ __attribute__((always_inline)) INLINE vector vector_set1(const float x) {
* @return temp set #vector.
* @return A #vector filled with zeros.
*/
-__attribute__((always_inline)) INLINE vector vector_setzero() {
+__attribute__((always_inline)) INLINE vector vector_setzero(void) {
vector temp;
temp.v = vec_setzero();
diff --git a/src/version.c b/src/version.c
index 54749721de96bde010f56965152c536b08672230..69f70b9aec3549c061c162f2ce183f8fafcc2e9f 100644
--- a/src/version.c
+++ b/src/version.c
@@ -146,7 +146,7 @@ const char *configuration_options(void) {
static int initialised = 0;
static const char *config = SWIFT_CONFIG_FLAGS;
if (!initialised) {
- snprintf(buf, 1024, "'%s'", config);
+ snprintf(buf, 1024, "'%.1021s'", config);
initialised = 1;
}
return buf;
@@ -162,7 +162,7 @@ const char *compilation_cflags(void) {
static int initialised = 0;
static const char *cflags = SWIFT_CFLAGS;
if (!initialised) {
- snprintf(buf, 1024, "'%s'", cflags);
+ snprintf(buf, 1024, "'%.1021s'", cflags);
initialised = 1;
}
return buf;
@@ -272,12 +272,12 @@ const char *mpi_version(void) {
#else
/* Use autoconf guessed value. */
static char lib_version[60] = {0};
- snprintf(lib_version, 60, "%s", SWIFT_MPI_LIBRARY);
+ snprintf(lib_version, 60, "%.60s", SWIFT_MPI_LIBRARY);
#endif
/* Numeric version. */
MPI_Get_version(&std_version, &std_subversion);
- snprintf(version, 80, "%s (MPI std v%i.%i)", lib_version, std_version,
+ snprintf(version, 80, "%.60s (MPI std v%i.%i)", lib_version, std_version,
std_subversion);
#else
sprintf(version, "Code was not compiled with MPI support");
@@ -345,7 +345,7 @@ const char *libgsl_version(void) {
static char version[256] = {0};
#if defined(HAVE_LIBGSL)
- sprintf(version, "%s", gsl_version);
+ sprintf(version, "%.255s", gsl_version);
#else
sprintf(version, "Unknown version");
#endif
@@ -368,6 +368,26 @@ const char *thread_barrier_version(void) {
return version;
}
+/**
+ * @brief return the allocator library used in SWIFT.
+ *
+ * @result description of the allocation library
+ */
+const char *allocator_version(void) {
+
+ static char version[256] = {0};
+#if defined(HAVE_TBBMALLOC)
+ sprintf(version, "TBB malloc");
+#elif defined(HAVE_TCMALLOC)
+ sprintf(version, "tc-malloc");
+#elif defined(HAVE_JEMALLOC)
+ sprintf(version, "je-malloc");
+#else
+ sprintf(version, "Compiler version (probably glibc)");
+#endif
+ return version;
+}
+
/**
* @brief Prints a greeting message to the standard output containing code
* version and revision number
diff --git a/src/version.h b/src/version.h
index 3163f242c50e56c64cc709b13dfe926f93672a00..44119b6a3bbdf57c3f0195bae5ff329d05c61fd5 100644
--- a/src/version.h
+++ b/src/version.h
@@ -36,6 +36,7 @@ const char* hdf5_version(void);
const char* fftw3_version(void);
const char* libgsl_version(void);
const char* thread_barrier_version(void);
+const char* allocator_version(void);
void greetings(void);
#endif /* SWIFT_VERSION_H */
diff --git a/tests/Makefile.am b/tests/Makefile.am
index 891eef3f518f83c17b66623e3dac1832512d31f3..e8f2a4f0ae39254c28e981fef5e36866e56395d8 100644
--- a/tests/Makefile.am
+++ b/tests/Makefile.am
@@ -17,7 +17,7 @@
# Add the source directory and the non-standard paths to the included library headers to CFLAGS
AM_CFLAGS = -I$(top_srcdir)/src $(HDF5_CPPFLAGS) $(GSL_INCS) $(FFTW_INCS)
-AM_LDFLAGS = ../src/.libs/libswiftsim.a $(HDF5_LDFLAGS) $(HDF5_LIBS) $(FFTW_LIBS) $(GRACKLE_LIBS) $(GSL_LIBS) $(PROFILER_LIBS)
+AM_LDFLAGS = ../src/.libs/libswiftsim.a $(HDF5_LDFLAGS) $(HDF5_LIBS) $(FFTW_LIBS) $(TCMALLOC_LIBS) $(JEMALLOC_LIBS) $(TBBMALLOC_LIBS) $(GRACKLE_LIBS) $(GSL_LIBS) $(PROFILER_LIBS)
# List of programs and scripts to run in the test suite
TESTS = testGreetings testMaths testReading.sh testSingle testKernel testSymmetry \
@@ -27,7 +27,7 @@ TESTS = testGreetings testMaths testReading.sh testSingle testKernel testSymmetr
testMatrixInversion testThreadpool testDump testLogger testInteractions.sh \
testVoronoi1D testVoronoi2D testVoronoi3D testGravityDerivatives \
testPeriodicBC.sh testPeriodicBCPerturbed.sh testPotentialSelf \
- testPotentialPair testEOS testUtilities
+ testPotentialPair testEOS testUtilities testSelectOutput.sh
# List of test programs to compile
check_PROGRAMS = testGreetings testReading testSingle testTimeIntegration \
@@ -37,7 +37,8 @@ check_PROGRAMS = testGreetings testReading testSingle testTimeIntegration \
testAdiabaticIndex testRiemannExact testRiemannTRRS \
testRiemannHLLC testMatrixInversion testDump testLogger \
testVoronoi1D testVoronoi2D testVoronoi3D testPeriodicBC \
- testGravityDerivatives testPotentialSelf testPotentialPair testEOS testUtilities
+ testGravityDerivatives testPotentialSelf testPotentialPair testEOS testUtilities \
+ testSelectOutput
# Rebuild tests when SWIFT is updated.
$(check_PROGRAMS): ../src/.libs/libswiftsim.a
@@ -49,6 +50,8 @@ testMaths_SOURCES = testMaths.c
testReading_SOURCES = testReading.c
+testSelectOutput_SOURCES = testSelectOutput.c
+
testSymmetry_SOURCES = testSymmetry.c
# Added because of issues using memcmp on clang 4.x
@@ -120,4 +123,4 @@ EXTRA_DIST = testReading.sh makeInput.py testActivePair.sh \
tolerance_27_normal.dat tolerance_27_perturbed.dat tolerance_27_perturbed_h.dat tolerance_27_perturbed_h2.dat \
tolerance_testInteractions.dat tolerance_pair_active.dat tolerance_pair_force_active.dat \
fft_params.yml tolerance_periodic_BC_normal.dat tolerance_periodic_BC_perturbed.dat \
- testEOS.sh testEOS_plot.sh
+ testEOS.sh testEOS_plot.sh testSelectOutput.sh selectOutput.yml
diff --git a/tests/selectOutput.yml b/tests/selectOutput.yml
new file mode 100644
index 0000000000000000000000000000000000000000..1778935146b19992e25efcb320d8cc523c6472a5
--- /dev/null
+++ b/tests/selectOutput.yml
@@ -0,0 +1,12 @@
+SelectOutput:
+ # Particle Type 0
+ Coordinates_Gas: 1 # check if written when specified
+ Velocities_Gas: 0 # check if not written when specified
+ Masses_Gas: -5 # check warning if not 0 or 1 and if written
+ Pot_Gas: 1 # check warning if wrong name
+ # Density_Gas: 1 # check if written when not specified
+
+# 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).
+ CFL_condition: 0.1 # Courant-Friedrich-Levy condition for time integration.
diff --git a/tests/test125cells.c b/tests/test125cells.c
index a50b847308422cbf10f58c737811934979d21899..ddce3176d463f2ef754bf82b364858085e317e4b 100644
--- a/tests/test125cells.c
+++ b/tests/test125cells.c
@@ -268,7 +268,7 @@ struct cell *make_cell(size_t n, const double offset[3], double size, double h,
const size_t count = n * n * n;
const double volume = size * size * size;
- struct cell *cell = malloc(sizeof(struct cell));
+ struct cell *cell = (struct cell *)malloc(sizeof(struct cell));
bzero(cell, sizeof(struct cell));
if (posix_memalign((void **)&cell->parts, part_align,
@@ -637,8 +637,8 @@ int main(int argc, char *argv[]) {
main_cell = cells[62];
/* Construct the real solution */
- struct solution_part *solution =
- malloc(main_cell->count * sizeof(struct solution_part));
+ struct solution_part *solution = (struct solution_part *)malloc(
+ main_cell->count * sizeof(struct solution_part));
get_solution(main_cell, solution, rho, vel, press, size);
ticks timings[27];
@@ -759,7 +759,7 @@ int main(int argc, char *argv[]) {
/* Dump if necessary */
if (n == 0) {
- sprintf(outputFileName, "swift_dopair_125_%s.dat",
+ sprintf(outputFileName, "swift_dopair_125_%.150s.dat",
outputFileNameExtension);
dump_particle_fields(outputFileName, main_cell, solution, 0);
}
@@ -876,7 +876,8 @@ int main(int argc, char *argv[]) {
/* Output timing */
message("Brute force calculation took : %15lli ticks.", toc - tic);
- sprintf(outputFileName, "brute_force_125_%s.dat", outputFileNameExtension);
+ sprintf(outputFileName, "brute_force_125_%.150s.dat",
+ outputFileNameExtension);
dump_particle_fields(outputFileName, main_cell, solution, 0);
/* Clean things to make the sanitizer happy ... */
diff --git a/tests/test27cells.c b/tests/test27cells.c
index e60262df71f6dc455e944b82a337261a57bcc9bc..ada1b782cfff3866bf26937391007947e9c9a175 100644
--- a/tests/test27cells.c
+++ b/tests/test27cells.c
@@ -98,7 +98,7 @@ struct cell *make_cell(size_t n, double *offset, double size, double h,
const size_t count = n * n * n;
const double volume = size * size * size;
float h_max = 0.f;
- struct cell *cell = malloc(sizeof(struct cell));
+ struct cell *cell = (struct cell *)malloc(sizeof(struct cell));
bzero(cell, sizeof(struct cell));
if (posix_memalign((void **)&cell->parts, part_align,
@@ -502,7 +502,7 @@ int main(int argc, char *argv[]) {
#if defined(TEST_DOSELF_SUBSET) || defined(TEST_DOPAIR_SUBSET)
int *pid = NULL;
int count = 0;
- if ((pid = malloc(sizeof(int) * main_cell->count)) == NULL)
+ if ((pid = (int *)malloc(sizeof(int) * main_cell->count)) == NULL)
error("Can't allocate memory for pid.");
for (int k = 0; k < main_cell->count; k++)
if (part_is_active(&main_cell->parts[k], &engine)) {
@@ -546,7 +546,7 @@ int main(int argc, char *argv[]) {
/* Dump if necessary */
if (i % 50 == 0) {
- sprintf(outputFileName, "swift_dopair_27_%s.dat",
+ sprintf(outputFileName, "swift_dopair_27_%.150s.dat",
outputFileNameExtension);
dump_particle_fields(outputFileName, main_cell, cells);
}
@@ -589,7 +589,7 @@ int main(int argc, char *argv[]) {
end_calculation(main_cell, &cosmo);
/* Dump */
- sprintf(outputFileName, "brute_force_27_%s.dat", outputFileNameExtension);
+ sprintf(outputFileName, "brute_force_27_%.150s.dat", outputFileNameExtension);
dump_particle_fields(outputFileName, main_cell, cells);
/* Output timing */
diff --git a/tests/testActivePair.c b/tests/testActivePair.c
index 0453f6d5896eaa53b0f44a567d353d7d8e8fb7df..6889a18887894af0a9434f786df21dbf842e87e5 100644
--- a/tests/testActivePair.c
+++ b/tests/testActivePair.c
@@ -59,7 +59,7 @@ struct cell *make_cell(size_t n, double *offset, double size, double h,
const size_t count = n * n * n;
const double volume = size * size * size;
float h_max = 0.f;
- struct cell *cell = malloc(sizeof(struct cell));
+ struct cell *cell = (struct cell *)malloc(sizeof(struct cell));
bzero(cell, sizeof(struct cell));
if (posix_memalign((void **)&cell->parts, part_align,
@@ -578,8 +578,9 @@ int main(int argc, char *argv[]) {
runner->e = &engine;
/* Create output file names. */
- sprintf(swiftOutputFileName, "swift_dopair_%s.dat", outputFileNameExtension);
- sprintf(bruteForceOutputFileName, "brute_force_pair_%s.dat",
+ sprintf(swiftOutputFileName, "swift_dopair_%.150s.dat",
+ outputFileNameExtension);
+ sprintf(bruteForceOutputFileName, "brute_force_pair_%.150s.dat",
outputFileNameExtension);
/* Delete files if they already exist. */
@@ -632,9 +633,9 @@ int main(int argc, char *argv[]) {
finalise = &end_calculation_force;
/* Create new output file names. */
- sprintf(swiftOutputFileName, "swift_dopair2_force_%s.dat",
+ sprintf(swiftOutputFileName, "swift_dopair2_force_%.150s.dat",
outputFileNameExtension);
- sprintf(bruteForceOutputFileName, "brute_force_dopair2_%s.dat",
+ sprintf(bruteForceOutputFileName, "brute_force_dopair2_%.150s.dat",
outputFileNameExtension);
/* Delete files if they already exist. */
diff --git a/tests/testAdiabaticIndex.c b/tests/testAdiabaticIndex.c
index 64a60fd2aa1f85a9a28fa312922f5fd68daa62d7..60ecefa264f48bed2d4df205766dc392a1a03d0f 100644
--- a/tests/testAdiabaticIndex.c
+++ b/tests/testAdiabaticIndex.c
@@ -16,7 +16,6 @@
* along with this program. If not, see <http://www.gnu.org/licenses/>.
*
******************************************************************************/
-
#include "../config.h"
#include <fenv.h>
@@ -42,7 +41,7 @@ void check_value(float a, float b, const char* s) {
* @brief Check that the pre-defined adiabatic index constants contain correct
* values
*/
-void check_constants() {
+void check_constants(void) {
float val;
val = 0.5 * (hydro_gamma + 1.0f) / hydro_gamma;
@@ -115,7 +114,7 @@ void check_functions(float x) {
/**
* @brief Check adiabatic index constants and power functions
*/
-int main() {
+int main(int argc, char* argv[]) {
/* Initialize CPU frequency, this also starts time. */
unsigned long long cpufreq = 0;
diff --git a/tests/testDump.c b/tests/testDump.c
index fa68ef9869f2f3ac2ee790b9815e42f73976ac9f..f47a44256536d6ac1d9676c844f7081a6daa5ca4 100644
--- a/tests/testDump.c
+++ b/tests/testDump.c
@@ -38,7 +38,7 @@
void dump_mapper(void *map_data, int num_elements, void *extra_data) {
struct dump *d = (struct dump *)extra_data;
size_t offset;
- char *out_string = dump_get(d, 7, &offset);
+ char *out_string = (char *)dump_get(d, 7, &offset);
char out_buff[8];
/* modulo due to bug in gcc, should be removed */
snprintf(out_buff, 8, "%06zi\n", (offset / 7) % 1000000);
diff --git a/tests/testEOS.c b/tests/testEOS.c
index 2e72d3d1768f3a6ea4ab1665a099efeb28f8f3f9..595dd0726a0a4a1606390cd38eb06c71399acb78 100644
--- a/tests/testEOS.c
+++ b/tests/testEOS.c
@@ -86,7 +86,7 @@ int main(int argc, char *argv[]) {
float rho, log_rho, log_u, P;
struct unit_system us;
const struct phys_const *phys_const = 0; // Unused placeholder
- const struct swift_params *params = 0; // Unused placeholder
+ struct swift_params *params = 0; // Unused placeholder
const float J_kg_to_erg_g = 1e4; // Convert J/kg to erg/g
char filename[64];
// Output table params
@@ -274,5 +274,5 @@ int main(int argc, char *argv[]) {
return 0;
}
#else
-int main() { return 0; }
+int main(int argc, char *argv[]) { return 0; }
#endif
diff --git a/tests/testFFT.c b/tests/testFFT.c
index b93ec9731687a1b08ea7c0abe075d302bd0e8786..5661ec6d98652cd8cbf229f1f345663d422ae588 100644
--- a/tests/testFFT.c
+++ b/tests/testFFT.c
@@ -22,7 +22,7 @@
#ifndef HAVE_FFTW
-int main() { return 0; }
+int main(int argc, char *argv[]) { return 0; }
#else
@@ -44,8 +44,7 @@ int is_close(double x, double y, double abs_err) {
return (abs(x - y) < abs_err);
}
-int main() {
-
+int main(int argc, char *argv[]) {
/* Initialize CPU frequency, this also starts time. */
unsigned long long cpufreq = 0;
clocks_set_cpufreq(cpufreq);
@@ -69,7 +68,8 @@ int main() {
gparts[0].mass = 1.f;
/* Read the parameter file */
- struct swift_params *params = malloc(sizeof(struct swift_params));
+ struct swift_params *params =
+ (struct swift_params *)malloc(sizeof(struct swift_params));
parser_read_file("fft_params.yml", params);
struct cosmology cosmo;
@@ -117,10 +117,10 @@ int main() {
/* Now check that we got the right answer */
int nr_cells = space.nr_cells;
- double *r = malloc(nr_cells * sizeof(double));
- double *m = malloc(nr_cells * sizeof(double));
- double *pot = malloc(nr_cells * sizeof(double));
- double *pot_exact = malloc(nr_cells * sizeof(double));
+ double *r = (double *)malloc(nr_cells * sizeof(double));
+ double *m = (double *)malloc(nr_cells * sizeof(double));
+ double *pot = (double *)malloc(nr_cells * sizeof(double));
+ double *pot_exact = (double *)malloc(nr_cells * sizeof(double));
FILE *file = fopen("potential.dat", "w");
for (int i = 0; i < nr_cells; ++i) {
diff --git a/tests/testGravityDerivatives.c b/tests/testGravityDerivatives.c
index 1e58dcc49a9fe277ddbc6982b71cfd741992e3b3..a6a709cb1a71d7b23fc1a9528aa718f378448265 100644
--- a/tests/testGravityDerivatives.c
+++ b/tests/testGravityDerivatives.c
@@ -924,7 +924,7 @@ void test(double x, double y, double tol, double min, const char* name) {
/* message("'%s' (%e -- %e) OK!", name, x, y); */
}
-int main() {
+int main(int argc, char* argv[]) {
/* Initialize CPU frequency, this also starts time. */
unsigned long long cpufreq = 0;
diff --git a/tests/testGreetings.c b/tests/testGreetings.c
index 2f17bddf5731692d515675d2a21f6c3b4a725ebf..ea2819d4616ed1f1d87c61065bf09fce4043243a 100644
--- a/tests/testGreetings.c
+++ b/tests/testGreetings.c
@@ -19,7 +19,7 @@
#include "swift.h"
-int main() {
+int main(int argc, char *argv[]) {
greetings();
diff --git a/tests/testInteractions.c b/tests/testInteractions.c
index 5473dc2588d66e0df2e3e3caddfc04ba3e6f7a2c..b8d4073c179238370684c2b0cf15944e613ce002 100644
--- a/tests/testInteractions.c
+++ b/tests/testInteractions.c
@@ -748,6 +748,6 @@ int main(int argc, char *argv[]) {
#else
-int main() { return 1; }
+int main(int argc, char *argv[]) { return 1; }
#endif
diff --git a/tests/testKernel.c b/tests/testKernel.c
index dc29d053c2049c9253290db81ea9991828bd5e1b..e3a13a4d54697f32c100b1f149a768a342da37a7 100644
--- a/tests/testKernel.c
+++ b/tests/testKernel.c
@@ -29,7 +29,7 @@
const int numPoints = (1 << 28);
-int main() {
+int main(int argc, char *argv[]) {
/* Initialize CPU frequency, this also starts time. */
unsigned long long cpufreq = 0;
diff --git a/tests/testKernelGrav.c b/tests/testKernelGrav.c
index b4a5e4d9f1ff05d8f34840dd19b2a2ccb9ec79b5..36d65ae1d0cc4a7807f60203e8f057e6a9d83cb5 100644
--- a/tests/testKernelGrav.c
+++ b/tests/testKernelGrav.c
@@ -58,7 +58,7 @@ float gadget(float r, float epsilon) {
}
}
-int main() {
+int main(int argc, char *argv[]) {
const float h = 3.f;
const float r_max = 6.f;
diff --git a/tests/testLogger.c b/tests/testLogger.c
index 9ec08607383fdb192b7ba994e4af506fde12fea9..b954b67ad6044ae5ec734706f7a1a4ff181541d8 100644
--- a/tests/testLogger.c
+++ b/tests/testLogger.c
@@ -63,7 +63,7 @@ void test_log_parts(struct dump *d) {
/* Recover the last part from the dump. */
bzero(&p, sizeof(struct part));
size_t offset_old = offset;
- int mask = logger_read_part(&p, &offset, d->data);
+ int mask = logger_read_part(&p, &offset, (const char *)d->data);
printf(
"Recovered part at offset %#016zx with mask %#04x: p.x[0]=%e, "
"p.v[0]=%e.\n",
@@ -76,7 +76,7 @@ void test_log_parts(struct dump *d) {
/* Recover the second part from the dump (only position). */
bzero(&p, sizeof(struct part));
offset_old = offset;
- mask = logger_read_part(&p, &offset, d->data);
+ mask = logger_read_part(&p, &offset, (const char *)d->data);
printf(
"Recovered part at offset %#016zx with mask %#04x: p.x[0]=%e, "
"p.v[0]=%e.\n",
@@ -89,7 +89,7 @@ void test_log_parts(struct dump *d) {
/* Recover the first part from the dump. */
bzero(&p, sizeof(struct part));
offset_old = offset;
- mask = logger_read_part(&p, &offset, d->data);
+ mask = logger_read_part(&p, &offset, (const char *)d->data);
printf(
"Recovered part at offset %#016zx with mask %#04x: p.x[0]=%e, "
"p.v[0]=%e.\n",
@@ -131,7 +131,7 @@ void test_log_gparts(struct dump *d) {
/* Recover the last part from the dump. */
bzero(&p, sizeof(struct gpart));
size_t offset_old = offset;
- int mask = logger_read_gpart(&p, &offset, d->data);
+ int mask = logger_read_gpart(&p, &offset, (const char *)d->data);
printf(
"Recovered gpart at offset %#016zx with mask %#04x: p.x[0]=%e, "
"p.v[0]=%e.\n",
@@ -144,7 +144,7 @@ void test_log_gparts(struct dump *d) {
/* Recover the second part from the dump. */
bzero(&p, sizeof(struct gpart));
offset_old = offset;
- mask = logger_read_gpart(&p, &offset, d->data);
+ mask = logger_read_gpart(&p, &offset, (const char *)d->data);
printf(
"Recovered gpart at offset %#016zx with mask %#04x: p.x[0]=%e, "
"p.v[0]=%e.\n",
@@ -157,7 +157,7 @@ void test_log_gparts(struct dump *d) {
/* Recover the first part from the dump. */
bzero(&p, sizeof(struct gpart));
offset_old = offset;
- mask = logger_read_gpart(&p, &offset, d->data);
+ mask = logger_read_gpart(&p, &offset, (const char *)d->data);
printf(
"Recovered gpart at offset %#016zx with mask %#04x: p.x[0]=%e, "
"p.v[0]=%e.\n",
@@ -189,7 +189,7 @@ void test_log_timestamps(struct dump *d) {
/* Recover the three timestamps. */
size_t offset_old = offset;
t = 0;
- int mask = logger_read_timestamp(&t, &offset, d->data);
+ int mask = logger_read_timestamp(&t, &offset, (const char *)d->data);
printf("Recovered timestamp %020llu at offset %#016zx with mask %#04x.\n", t,
offset_old, mask);
if (t != 30) {
@@ -199,7 +199,7 @@ void test_log_timestamps(struct dump *d) {
offset_old = offset;
t = 0;
- mask = logger_read_timestamp(&t, &offset, d->data);
+ mask = logger_read_timestamp(&t, &offset, (const char *)d->data);
printf("Recovered timestamp %020llu at offset %#016zx with mask %#04x.\n", t,
offset_old, mask);
if (t != 20) {
@@ -209,7 +209,7 @@ void test_log_timestamps(struct dump *d) {
offset_old = offset;
t = 0;
- mask = logger_read_timestamp(&t, &offset, d->data);
+ mask = logger_read_timestamp(&t, &offset, (const char *)d->data);
printf("Recovered timestamp %020llu at offset %#016zx with mask %#04x.\n", t,
offset_old, mask);
if (t != 10) {
diff --git a/tests/testMaths.c b/tests/testMaths.c
index 3d8f9a8f9db0cf01276eff89aa44157008cbddc6..2abb3aa99902323597b3d20fb19769a8ea1bafbe 100644
--- a/tests/testMaths.c
+++ b/tests/testMaths.c
@@ -25,7 +25,7 @@
#include <math.h>
#include <stdio.h>
-int main() {
+int main(int argc, char *argv[]) {
const int numPoints = 60000;
diff --git a/tests/testMatrixInversion.c b/tests/testMatrixInversion.c
index 9a45cd52d6f5d3ec96cc6d3f34fd683971f4cf19..a15e0dab7ec793cf4a914b6eb89c63863ab24fb0 100644
--- a/tests/testMatrixInversion.c
+++ b/tests/testMatrixInversion.c
@@ -95,7 +95,7 @@ void multiply_matrices(float A[3][3], float B[3][3], float C[3][3]) {
#endif
}
-int main() {
+int main(int argc, char* argv[]) {
float A[3][3], B[3][3], C[3][3];
setup_matrix(A);
diff --git a/tests/testParser.c b/tests/testParser.c
index f1211199924df728dfe57376781dc07fe862cec7..c50e9b1a5473c1406e97894f211cc94aa7689d12 100644
--- a/tests/testParser.c
+++ b/tests/testParser.c
@@ -35,9 +35,6 @@ int main(int argc, char *argv[]) {
/* Print the contents of the structure to stdout. */
parser_print_params(¶m_file);
- /* Print the contents of the structure to a file in YAML format. */
- parser_write_params_to_file(¶m_file, "parser_output.yml");
-
/* Retrieve parameters and store them in variables defined above.
* Have to specify the name of the parameter as it appears in the
* input file: testParserInput.yaml.*/
@@ -50,7 +47,8 @@ int main(int argc, char *argv[]) {
parser_get_param_double(¶m_file, "Simulation:start_time");
const int kernel = parser_get_param_int(¶m_file, "kernel");
- const int optional = parser_get_opt_param_int(¶m_file, "optional", 1);
+ const int optional =
+ parser_get_opt_param_int(¶m_file, "Simulation:optional", 1);
char ic_file[PARSER_MAX_LINE_SIZE];
parser_get_param_string(¶m_file, "IO:ic_file", ic_file);
@@ -62,6 +60,10 @@ int main(int argc, char *argv[]) {
no_of_threads, no_of_time_steps, max_h, start_time, ic_file, kernel,
optional);
+ /* Print the contents of the structure to a file in YAML format. */
+ parser_write_params_to_file(¶m_file, "used_parser_output.yml", 1);
+ parser_write_params_to_file(¶m_file, "unused_parser_output.yml", 0);
+
assert(no_of_threads == 16);
assert(no_of_time_steps == 10);
assert(fabs(max_h - 1.1255) < 0.00001);
diff --git a/tests/testPeriodicBC.c b/tests/testPeriodicBC.c
index 385de9752f361f4f015eb64a466473324901030f..ffaa3bda0ccb62cd44169e228086267d2399c31f 100644
--- a/tests/testPeriodicBC.c
+++ b/tests/testPeriodicBC.c
@@ -78,7 +78,7 @@ struct cell *make_cell(size_t n, double *offset, double size, double h,
enum velocity_types vel) {
const size_t count = n * n * n;
const double volume = size * size * size;
- struct cell *cell = malloc(sizeof(struct cell));
+ struct cell *cell = (struct cell *)malloc(sizeof(struct cell));
bzero(cell, sizeof(struct cell));
if (posix_memalign((void **)&cell->parts, part_align,
@@ -512,9 +512,9 @@ int main(int argc, char *argv[]) {
}
/* Create output file names. */
- sprintf(swiftOutputFileName, "swift_periodic_BC_%s.dat",
+ sprintf(swiftOutputFileName, "swift_periodic_BC_%.150s.dat",
outputFileNameExtension);
- sprintf(bruteForceOutputFileName, "brute_force_periodic_BC_%s.dat",
+ sprintf(bruteForceOutputFileName, "brute_force_periodic_BC_%.150s.dat",
outputFileNameExtension);
/* Delete files if they already exist. */
diff --git a/tests/testPotentialPair.c b/tests/testPotentialPair.c
index 53fc54ccdd63a9a9150b6701c1a76ac20af91d4c..1f7b0ab0c2577e3b2adc71ca8c121d275679b63d 100644
--- a/tests/testPotentialPair.c
+++ b/tests/testPotentialPair.c
@@ -82,7 +82,7 @@ double acceleration(double mass, double r, double H, double rlr) {
return r * acc * (4. * x * S_prime(2 * x) - 2. * S(2. * x) + 2.);
}
-int main() {
+int main(int argc, char *argv[]) {
/* Initialize CPU frequency, this also starts time. */
unsigned long long cpufreq = 0;
@@ -150,8 +150,10 @@ int main() {
cj.ti_gravity_end_max = 8;
/* Allocate multipoles */
- ci.multipole = malloc(sizeof(struct gravity_tensors));
- cj.multipole = malloc(sizeof(struct gravity_tensors));
+ ci.multipole =
+ (struct gravity_tensors *)malloc(sizeof(struct gravity_tensors));
+ cj.multipole =
+ (struct gravity_tensors *)malloc(sizeof(struct gravity_tensors));
bzero(ci.multipole, sizeof(struct gravity_tensors));
bzero(cj.multipole, sizeof(struct gravity_tensors));
diff --git a/tests/testPotentialSelf.c b/tests/testPotentialSelf.c
index 6d31f079fa79f7463637ec71dc2c75f37a10b129..25c441b399c9c3ed71479d26bd373e053817036d 100644
--- a/tests/testPotentialSelf.c
+++ b/tests/testPotentialSelf.c
@@ -85,7 +85,7 @@ double acceleration(double mass, double r, double H, double rlr) {
return r * acc * (4. * x * S_prime(2 * x) - 2. * S(2. * x) + 2.);
}
-int main() {
+int main(int argc, char *argv[]) {
/* Initialize CPU frequency, this also starts time. */
unsigned long long cpufreq = 0;
diff --git a/tests/testReading.c b/tests/testReading.c
index ca1e0ef69078c5e384a9cd4eab1098923ce9f279..6b4ca8717ec4508f7e23fde6f287877684c358b8 100644
--- a/tests/testReading.c
+++ b/tests/testReading.c
@@ -23,7 +23,7 @@
/* Includes. */
#include "swift.h"
-int main() {
+int main(int argc, char *argv[]) {
size_t Ngas = 0, Ngpart = 0, Nspart = 0;
int periodic = -1;
diff --git a/tests/testRiemannExact.c b/tests/testRiemannExact.c
index bce7c52d422f966e10d530cdcbc8f6d20431e153..aa630a76f5f82bd87dc15f00d7d90dff2405e749 100644
--- a/tests/testRiemannExact.c
+++ b/tests/testRiemannExact.c
@@ -169,7 +169,7 @@ void check_riemann_solution(struct riemann_statevector* WL,
/**
* @brief Check the exact Riemann solver on the Toro test problems
*/
-void check_riemann_exact() {
+void check_riemann_exact(void) {
struct riemann_statevector WL, WR, Whalf;
/* Test 1 */
@@ -296,7 +296,7 @@ void check_riemann_exact() {
/**
* @brief Check the symmetry of the TRRS Riemann solver
*/
-void check_riemann_symmetry() {
+void check_riemann_symmetry(void) {
float WL[5], WR[5], Whalf1[5], Whalf2[5], n_unit1[3], n_unit2[3], n_norm,
vij[3], totflux1[5], totflux2[5];
@@ -395,7 +395,7 @@ void check_riemann_symmetry() {
/**
* @brief Check the exact Riemann solver
*/
-int main() {
+int main(int argc, char* argv[]) {
/* Initialize CPU frequency, this also starts time. */
unsigned long long cpufreq = 0;
diff --git a/tests/testRiemannHLLC.c b/tests/testRiemannHLLC.c
index b988825eb0535fcdc46baa1db1203d0dbac3537a..0cce0f9d144f7be9000d368d6ac28e8e49c7d9aa 100644
--- a/tests/testRiemannHLLC.c
+++ b/tests/testRiemannHLLC.c
@@ -85,7 +85,7 @@ int are_symmetric(float a, float b) {
/**
* @brief Check the symmetry of the HLLC Riemann solver for a random setup
*/
-void check_riemann_symmetry() {
+void check_riemann_symmetry(void) {
float WL[5], WR[5], n_unit1[3], n_unit2[3], n_norm, vij[3], totflux1[5],
totflux2[5];
@@ -150,7 +150,7 @@ void check_riemann_symmetry() {
/**
* @brief Check the HLLC Riemann solver
*/
-int main() {
+int main(int argc, char *argv[]) {
/* Initialize CPU frequency, this also starts time. */
unsigned long long cpufreq = 0;
diff --git a/tests/testRiemannTRRS.c b/tests/testRiemannTRRS.c
index 4a0eac0be23581e175d2c0e599b786fd4508b14a..2c7098367a1ca8db84f097ad01aa2e1e411c433d 100644
--- a/tests/testRiemannTRRS.c
+++ b/tests/testRiemannTRRS.c
@@ -105,7 +105,7 @@ void check_riemann_solution(struct riemann_statevector* WL,
/**
* @brief Check the TRRS Riemann solver on the Toro test problems
*/
-void check_riemann_trrs() {
+void check_riemann_trrs(void) {
struct riemann_statevector WL, WR, Whalf;
/* Test 1 */
@@ -232,7 +232,7 @@ void check_riemann_trrs() {
/**
* @brief Check the symmetry of the TRRS Riemann solver
*/
-void check_riemann_symmetry() {
+void check_riemann_symmetry(void) {
float WL[5], WR[5], Whalf1[5], Whalf2[5], n_unit1[3], n_unit2[3], n_norm,
vij[3], totflux1[5], totflux2[5];
@@ -311,7 +311,7 @@ void check_riemann_symmetry() {
/**
* @brief Check the TRRS Riemann solver
*/
-int main() {
+int main(int argc, char* argv[]) {
/* check the TRRS Riemann solver */
check_riemann_trrs();
diff --git a/tests/testSPHStep.c b/tests/testSPHStep.c
index 08d6abaa7521de2a7d12fd9672db0d24a5a20a97..63834d94b7696e160dd7ca487ab7e9f1e943abfb 100644
--- a/tests/testSPHStep.c
+++ b/tests/testSPHStep.c
@@ -27,7 +27,7 @@
*/
struct cell *make_cell(size_t N, float cellSize, int offset[3], int id_offset) {
size_t count = N * N * N;
- struct cell *cell = malloc(sizeof(struct cell));
+ struct cell *cell = (struct cell *)malloc(sizeof(struct cell));
bzero(cell, sizeof(struct cell));
struct part *part;
struct xpart *xpart;
@@ -93,7 +93,7 @@ void runner_dopair1_density(struct runner *r, struct cell *ci, struct cell *cj);
void runner_dopair2_force(struct runner *r, struct cell *ci, struct cell *cj);
/* Run a full time step integration for one cell */
-int main() {
+int main(int argc, char *argv[]) {
#ifndef DEFAULT_SPH
return 0;
diff --git a/tests/testSelectOutput.c b/tests/testSelectOutput.c
new file mode 100644
index 0000000000000000000000000000000000000000..3bedddd03784bafddd4599c124929a6d88fbd9b0
--- /dev/null
+++ b/tests/testSelectOutput.c
@@ -0,0 +1,162 @@
+/*******************************************************************************
+ * This file is part of SWIFT.
+ * Copyright (C) 2015 Matthieu Schaller (matthieu.schaller@durham.ac.uk).
+ *
+ * This program is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU Lesser General Public License as published
+ * by the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with this program. If not, see <http://www.gnu.org/licenses/>.
+ *
+ ******************************************************************************/
+
+/* Some standard headers. */
+#include <stdlib.h>
+
+/* Includes. */
+#include "swift.h"
+
+void select_output_engine_init(struct engine *e, struct space *s,
+ struct cosmology *cosmo,
+ struct swift_params *params,
+ struct cooling_function_data *cooling,
+ struct hydro_props *hydro_properties) {
+ /* set structures */
+ e->s = s;
+ e->cooling_func = cooling;
+ e->parameter_file = params;
+ e->cosmology = cosmo;
+ e->policy = engine_policy_hydro;
+ e->hydro_properties = hydro_properties;
+
+ /* initialization of threadpool */
+ threadpool_init(&e->threadpool, 1);
+
+ /* set parameters */
+ e->verbose = 1;
+ e->time = 0;
+ e->snapshot_output_count = 0;
+ e->snapshot_compression = 0;
+ e->snapshot_label_delta = 1;
+};
+
+void select_output_space_init(struct space *s, double *dim, int periodic,
+ size_t Ngas, size_t Nspart, size_t Ngpart,
+ struct part *parts, struct spart *sparts,
+ struct gpart *gparts) {
+ s->periodic = periodic;
+ for (int i = 0; i < 3; i++) {
+ s->dim[i] = dim[i];
+ }
+
+ /* init space particles */
+ s->nr_parts = Ngas;
+ s->nr_sparts = Nspart;
+ s->nr_gparts = Ngpart;
+
+ s->parts = parts;
+ s->gparts = gparts;
+ s->sparts = sparts;
+
+ /* Allocate the extra parts array for the gas particles. */
+ if (posix_memalign((void **)&s->xparts, xpart_align,
+ Ngas * sizeof(struct xpart)) != 0)
+ error("Failed to allocate xparts.");
+ bzero(s->xparts, Ngas * sizeof(struct xpart));
+};
+
+void select_output_space_clean(struct space *s) { free(s->xparts); };
+
+void select_output_engine_clean(struct engine *e) {
+ threadpool_clean(&e->threadpool);
+}
+
+int main(int argc, char *argv[]) {
+
+ /* Initialize CPU frequency, this also starts time. */
+ unsigned long long cpufreq = 0;
+ clocks_set_cpufreq(cpufreq);
+
+ char *base_name = "testSelectOutput";
+ size_t Ngas = 0, Ngpart = 0, Nspart = 0;
+ int periodic = -1;
+ int flag_entropy_ICs = -1;
+ double dim[3];
+ struct part *parts = NULL;
+ struct gpart *gparts = NULL;
+ struct spart *sparts = NULL;
+
+ /* parse parameters */
+ message("Reading parameters.");
+ struct swift_params param_file;
+ char *input_file = "selectOutput.yml";
+ parser_read_file(input_file, ¶m_file);
+
+ /* Default unit system */
+ message("Initialization of the unit system.");
+ struct unit_system us;
+ units_init_cgs(&us);
+
+ /* Default physical constants */
+ message("Initialization of the physical constants.");
+ struct phys_const prog_const;
+ phys_const_init(&us, ¶m_file, &prog_const);
+
+ /* Read data */
+ message("Reading initial conditions.");
+ read_ic_single("input.hdf5", &us, dim, &parts, &gparts, &sparts, &Ngas,
+ &Ngpart, &Nspart, &periodic, &flag_entropy_ICs, 1, 0, 0, 0, 1.,
+ 1, 0);
+
+ /* pseudo initialization of the space */
+ message("Initialization of the space.");
+ struct space s;
+ select_output_space_init(&s, dim, periodic, Ngas, Nspart, Ngpart, parts,
+ sparts, gparts);
+
+ /* initialization of cosmology */
+ message("Initialization of the cosmology.");
+ struct cosmology cosmo;
+ cosmology_init_no_cosmo(&cosmo);
+
+ /* pseudo initialization of cooling */
+ message("Initialization of the cooling.");
+ struct cooling_function_data cooling;
+
+ /* pseudo initialization of hydro */
+ message("Initialization of the hydro.");
+ struct hydro_props hydro_properties;
+ hydro_props_init(&hydro_properties, &prog_const, &us, ¶m_file);
+
+ /* pseudo initialization of the engine */
+ message("Initialization of the engine.");
+ struct engine e;
+ select_output_engine_init(&e, &s, &cosmo, ¶m_file, &cooling,
+ &hydro_properties);
+
+ /* check output selection */
+ message("Checking output parameters.");
+ long long N_total[swift_type_count] = {Ngas, Ngpart, 0, 0, Nspart, 0};
+ io_check_output_fields(¶m_file, N_total);
+
+ /* write output file */
+ message("Writing output.");
+ write_output_single(&e, base_name, &us, &us);
+
+ /* Clean-up */
+ message("Cleaning memory.");
+ select_output_engine_clean(&e);
+ select_output_space_clean(&s);
+ cosmology_clean(&cosmo);
+ free(parts);
+ free(gparts);
+
+ return 0;
+}
diff --git a/tests/testSelectOutput.py b/tests/testSelectOutput.py
new file mode 100644
index 0000000000000000000000000000000000000000..aec7f4671fb2768acde768fd9929168559ebb3cb
--- /dev/null
+++ b/tests/testSelectOutput.py
@@ -0,0 +1,54 @@
+###############################################################################
+ # This file is part of SWIFT.
+ # Copyright (c) 2015 Bert Vandenbroucke (bert.vandenbroucke@ugent.be)
+ # Matthieu Schaller (matthieu.schaller@durham.ac.uk)
+ #
+ # This program is free software: you can redistribute it and/or modify
+ # it under the terms of the GNU Lesser General Public License as published
+ # by the Free Software Foundation, either version 3 of the License, or
+ # (at your option) any later version.
+ #
+ # This program is distributed in the hope that it will be useful,
+ # but WITHOUT ANY WARRANTY; without even the implied warranty of
+ # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ # GNU General Public License for more details.
+ #
+ # You should have received a copy of the GNU Lesser General Public License
+ # along with this program. If not, see <http://www.gnu.org/licenses/>.
+ #
+ ##############################################################################
+
+# Check the output done with swift
+
+import h5py
+
+filename = "testSelectOutput_0000.hdf5"
+log_filename = "select_output.log"
+
+# Read the simulation data
+sim = h5py.File(filename, "r")
+part0 = sim["/PartType0"]
+
+# check presence / absence fields
+if "Velocities" in part0:
+ raise Exception("`Velocities` present in HDF5 but should not be written")
+
+if "Coordinates" not in part0:
+ raise Exception("`Coordinates` not present in HDF5 but should be written")
+
+if "Masses" not in part0:
+ raise Exception("`Masses` not present in HDF5 but should be written")
+
+if "Density" not in part0:
+ raise Exception("`Density` not present in HDF5 but should be written")
+
+
+# check error detection
+with open(log_filename, "r") as f:
+ data = f.read()
+
+if "SelectOutput:Masses_Gas" not in data:
+ raise Exception("Input error in `SelectOuput:Masses_Gas` not detected")
+
+if "SelectOutput:Pot_Gas" not in data:
+ raise Exception("Parameter name error not detected for `SelectOutput:Pot_Gas`")
diff --git a/tests/testSelectOutput.sh.in b/tests/testSelectOutput.sh.in
new file mode 100644
index 0000000000000000000000000000000000000000..85fd999643f82fd10d96013ad360a75a441a9e1a
--- /dev/null
+++ b/tests/testSelectOutput.sh.in
@@ -0,0 +1,14 @@
+#!/bin/bash
+
+echo "Creating initial conditions"
+python @srcdir@/makeInput.py
+
+echo "Generating output"
+./testSelectOutput 2>&1 | tee select_output.log
+
+echo "Checking output"
+python @srcdir@/testSelectOutput.py
+
+rm -f testSelectOutput_0000.hdf5 testSelectOutput.xmf select_output.log
+
+echo "Test passed"
diff --git a/tests/testSingle.c b/tests/testSingle.c
index e2ec35bc4382658be7754b9c11fc3a3dbe4bbdc1..52fe51c529b8c3b43f9c5f03fe44b5b742acfc07 100644
--- a/tests/testSingle.c
+++ b/tests/testSingle.c
@@ -142,6 +142,6 @@ int main(int argc, char *argv[]) {
}
#else
-int main() { return 0; }
+int main(int argc, char *argv[]) { return 0; }
#endif
diff --git a/tests/testSymmetry.c b/tests/testSymmetry.c
index 1ab493a7c149070dc667a2377ab205df7f873856..886290ab984603d0afb3201377611598cd7163e4 100644
--- a/tests/testSymmetry.c
+++ b/tests/testSymmetry.c
@@ -16,7 +16,6 @@
* along with this program. If not, see <http://www.gnu.org/licenses/>.
*
******************************************************************************/
-
#include "../config.h"
#include <fenv.h>
@@ -32,7 +31,7 @@ void print_bytes(void *p, size_t len) {
printf(")\n");
}
-void test() {
+void test(void) {
#if defined(SHADOWFAX_SPH)
/* Initialize the Voronoi simulation box */
diff --git a/tests/testTimeIntegration.c b/tests/testTimeIntegration.c
index 972e6f2323c0401c70de2990bcb088f95b3dfd83..2034c402a2d626a7b503613f6cade821ec438151 100644
--- a/tests/testTimeIntegration.c
+++ b/tests/testTimeIntegration.c
@@ -26,7 +26,7 @@
* @brief Test the kick-drift-kick leapfrog integration
* via a Sun-Earth simulation
*/
-int main() {
+int main(int argc, char *argv[]) {
struct cell c;
int i;
@@ -63,10 +63,10 @@ int main() {
/* Create a particle */
struct part *parts = NULL;
- parts = malloc(sizeof(struct part));
+ parts = (struct part *)malloc(sizeof(struct part));
bzero(parts, sizeof(struct part));
struct xpart *xparts = NULL;
- xparts = malloc(sizeof(struct xpart));
+ xparts = (struct xpart *)malloc(sizeof(struct xpart));
bzero(xparts, sizeof(struct xpart));
/* Put the particle on the orbit */
diff --git a/tests/testUtilities.c b/tests/testUtilities.c
index b835faba9026661361c8828fce5c18beb2b80889..963e4d2233bbd56f7d61d5e2a0d2424006aa63ab 100644
--- a/tests/testUtilities.c
+++ b/tests/testUtilities.c
@@ -23,7 +23,7 @@
/**
* @brief Test generic utility functions
*/
-int main() {
+int main(int argc, char *argv[]) {
/// Test find_value_in_monot_incr_array()
int n = 100;
float array[n];
diff --git a/tests/testVoronoi1D.c b/tests/testVoronoi1D.c
index d16a36d9449d7bfdb2c74408efad61b219b1d7e3..083d9aaa279f241ae1ac4d0bfaeb2780a39574a4 100644
--- a/tests/testVoronoi1D.c
+++ b/tests/testVoronoi1D.c
@@ -16,10 +16,9 @@
* along with this program. If not, see <http://www.gnu.org/licenses/>.
*
******************************************************************************/
-
#include "hydro/Shadowswift/voronoi1d_algorithm.h"
-int main() {
+int main(int argc, char *argv[]) {
double box_anchor[1] = {-0.5};
double box_side[1] = {2.};
diff --git a/tests/testVoronoi2D.c b/tests/testVoronoi2D.c
index 509d3ab69976fa8618db389ebd87eedb9ea34409..60a71624904c11a3cdb3b90906189df60bfc6956 100644
--- a/tests/testVoronoi2D.c
+++ b/tests/testVoronoi2D.c
@@ -16,14 +16,13 @@
* along with this program. If not, see <http://www.gnu.org/licenses/>.
*
******************************************************************************/
-
#include "hydro/Shadowswift/voronoi2d_algorithm.h"
#include "tools.h"
/* Number of cells used to test the 2D interaction algorithm */
#define TESTVORONOI2D_NUMCELL 100
-int main() {
+int main(int argc, char *argv[]) {
/* initialize simulation box */
double anchor[3] = {-0.5f, -0.5f, -0.5f};
diff --git a/tests/testVoronoi3D.c b/tests/testVoronoi3D.c
index b4f219a41368bb3ce4e8111ae44c43e7fa1f7441..db5c33aa6e4ef0792373febd5d773a6d1198db29 100644
--- a/tests/testVoronoi3D.c
+++ b/tests/testVoronoi3D.c
@@ -53,7 +53,7 @@
*
* @return Volume of the simulation box as it is stored in the global variables.
*/
-float voronoi_get_box_volume() {
+float voronoi_get_box_volume(void) {
return VORONOI3D_BOX_SIDE_X * VORONOI3D_BOX_SIDE_Y * VORONOI3D_BOX_SIDE_Z;
}
@@ -129,7 +129,7 @@ float voronoi_get_box_face(unsigned long long id, float *face_midpoint) {
/**
* @brief Check if voronoi_volume_tetrahedron() works
*/
-void test_voronoi_volume_tetrahedron() {
+void test_voronoi_volume_tetrahedron(void) {
float v1[3] = {0., 0., 0.};
float v2[3] = {0., 0., 1.};
float v3[3] = {0., 1., 0.};
@@ -142,7 +142,7 @@ void test_voronoi_volume_tetrahedron() {
/**
* @brief Check if voronoi_centroid_tetrahedron() works
*/
-void test_voronoi_centroid_tetrahedron() {
+void test_voronoi_centroid_tetrahedron(void) {
float v1[3] = {0., 0., 0.};
float v2[3] = {0., 0., 1.};
float v3[3] = {0., 1., 0.};
@@ -158,7 +158,7 @@ void test_voronoi_centroid_tetrahedron() {
/**
* @brief Check if voronoi_calculate_cell() works
*/
-void test_calculate_cell() {
+void test_calculate_cell(void) {
double box_anchor[3] = {VORONOI3D_BOX_ANCHOR_X, VORONOI3D_BOX_ANCHOR_Y,
VORONOI3D_BOX_ANCHOR_Z};
@@ -234,7 +234,7 @@ void test_calculate_cell() {
assert(cell.face_midpoints[5][2] == face_midpoint[2] - cell.x[2]);
}
-void test_paths() {
+void test_paths(void) {
float u, l, q;
int up, us, uw, lp, ls, lw, qp, qs, qw;
float r2, dx[3];
@@ -1240,7 +1240,7 @@ void set_coordinates(struct part *p, double x, double y, double z,
}
#endif
-void test_degeneracies() {
+void test_degeneracies(void) {
#ifdef SHADOWFAX_SPH
int idx = 0;
/* make a small cube */
@@ -1308,7 +1308,7 @@ void test_degeneracies() {
#endif
}
-int main() {
+int main(int argc, char *argv[]) {
/* Set the all enclosing simulation box dimensions */
double box_anchor[3] = {VORONOI3D_BOX_ANCHOR_X, VORONOI3D_BOX_ANCHOR_Y,
diff --git a/theory/Cosmology/coordinates.tex b/theory/Cosmology/coordinates.tex
index e3a22eaae025e6911e8aca92d6d29bf5fa82bf21..bc593606026217f345e2f77d90cee3f6632b3cef 100644
--- a/theory/Cosmology/coordinates.tex
+++ b/theory/Cosmology/coordinates.tex
@@ -40,19 +40,29 @@ $\Psi \equiv \frac{1}{2}a\dot{a}\mathbf{r}_i^2$ and obtain
-\frac{\phi'}{a},\\
\phi' &= a\phi + \frac{1}{2}a^2\ddot{a}\mathbf{r}_i'^2.\nonumber
\end{align}
-Finally, we introduce the velocities $\mathbf{v}' \equiv
-a^2\dot{\mathbf{r}'}$ that are used internally by the code. Note that these
-velocities \emph{do not} have a physical interpretation. We caution that they
-are not the peculiar velocities, nor the Hubble flow, nor the total
-velocities\footnote{One additional inconvenience of our choice of
+Finally, we introduce the velocities
+$\mathbf{v}' \equiv a^2\dot{\mathbf{r}'}$ that are used internally by
+the code. Note that these velocities \emph{do not} have a physical
+interpretation. We caution that they are not the peculiar velocities
+($\mathbf{v}_{\rm p} \equiv a\dot{\mathbf{r}'} =
+\frac{1}{a}\mathbf{v}'$), nor the Hubble flow
+($\mathbf{v}_{\rm H} \equiv \dot{a}\mathbf{r}'$), nor the total
+velocities
+($\mathbf{v}_{\rm tot} \equiv \mathbf{v}_{\rm p} + \mathbf{v}_{\rm H}
+= \dot{a}\mathbf{r}' + \frac{1}{a}\mathbf{v}'$) and also differ from
+the convention used in \gadget snapshots
+($\sqrt{a} \dot{\mathbf{r}'}$) and other related simulation
+codes\footnote{One additional inconvenience of our choice of
generalised coordinates is that our velocities $\mathbf{v}'$ and
sound-speed $c'$ do not have the same dependencies on the
scale-factor. The signal velocity entering the time-step calculation
- will hence read $v_{\rm sig} = a\dot{\mathbf{r}'} + c = \frac{1}{a} \left(
+ will hence read
+ $v_{\rm sig} = a\dot{\mathbf{r}'} + c = \frac{1}{a} \left(
|\mathbf{v}'| + a^{(5 - 3\gamma)/2}c'\right)$.}.
-This choice implies that $\dot{v}' = a \ddot{r}$. Using the SPH
-definition of density, $\rho_i' =
-\sum_jm_jW(\mathbf{r}_{j}'-\mathbf{r}_{i}',h_i') =
+% This choice implies that $\dot{v}' = a \ddot{r}$.
+
+Using the SPH definition of density,
+$\rho_i' = \sum_jm_jW(\mathbf{r}_{j}'-\mathbf{r}_{i}',h_i') =
\sum_jm_jW_{ij}'(h_i')$, we can follow \cite{Price2012} and apply the
Euler-Lagrange equations to write
\begin{alignat}{3}
diff --git a/theory/Multipoles/bibliography.bib b/theory/Multipoles/bibliography.bib
index c3d1289584cab55cd8e0d4d0765d70e22f0fcf2e..547b82159cef01e1da65efb32fc7e3d47a66112e 100644
--- a/theory/Multipoles/bibliography.bib
+++ b/theory/Multipoles/bibliography.bib
@@ -191,4 +191,61 @@ keywords = "adaptive algorithms"
adsnote = {Provided by the SAO/NASA Astrophysics Data System}
}
+@ARTICLE{Hubber2011,
+ author = {{Hubber}, D.~A. and {Batty}, C.~P. and {McLeod}, A. and {Whitworth}, A.~P.
+ },
+ title = "{SEREN - a new SPH code for star and planet formation simulations. Algorithms and tests}",
+ journal = {\aap},
+ keywords = {hydrodynamics, methods: numerical, stars: formation},
+ year = 2011,
+ month = may,
+ volume = 529,
+ eid = {A27},
+ pages = {A27},
+ doi = {10.1051/0004-6361/201014949},
+ adsurl = {http://adsabs.harvard.edu/abs/2011A%26A...529A..27H},
+ adsnote = {Provided by the SAO/NASA Astrophysics Data System}
+}
+
+
+@ARTICLE{Klessen1997,
+ author = {{Klessen}, R.},
+ title = "{GRAPESPH with fully periodic boundary conditions - Fragmentation of molecular clouds}",
+ journal = {\mnras},
+ keywords = {Molecular Clouds, Interstellar Matter, Fragmentation, Astronomical Models, Computer Programs, Boundary Conditions},
+ year = 1997,
+ month = nov,
+ volume = 292,
+ pages = {11},
+ doi = {10.1093/mnras/292.1.11},
+ adsurl = {http://adsabs.harvard.edu/abs/1997MNRAS.292...11K},
+ adsnote = {Provided by the SAO/NASA Astrophysics Data System}
+}
+
+@ARTICLE{Hernquist1991,
+ author = {{Hernquist}, L. and {Bouchet}, F.~R. and {Suto}, Y.},
+ title = "{Application of the Ewald method to cosmological N-body simulations}",
+ journal = {\apjs},
+ keywords = {Computational Astrophysics, Galactic Structure, Hubble Constant, Many Body Problem, Astronomical Models, Boundary Conditions, Spatial Resolution},
+ year = 1991,
+ month = feb,
+ volume = 75,
+ pages = {231-240},
+ doi = {10.1086/191530},
+ adsurl = {http://adsabs.harvard.edu/abs/1991ApJS...75..231H},
+ adsnote = {Provided by the SAO/NASA Astrophysics Data System}
+}
+
+@ARTICLE{Ewald1921,
+ author = {{Ewald}, P.~P.},
+ title = "{Die Berechnung optischer und elektrostatischer Gitterpotentiale}",
+ journal = {Annalen der Physik},
+ year = 1921,
+ volume = 369,
+ pages = {253-287},
+ doi = {10.1002/andp.19213690304},
+ adsurl = {http://adsabs.harvard.edu/abs/1921AnP...369..253E},
+ adsnote = {Provided by the SAO/NASA Astrophysics Data System}
+}
+
diff --git a/theory/Multipoles/exact_forces.tex b/theory/Multipoles/exact_forces.tex
new file mode 100644
index 0000000000000000000000000000000000000000..2602c2db1c06eb496d4c450e0d33ee87d28831e8
--- /dev/null
+++ b/theory/Multipoles/exact_forces.tex
@@ -0,0 +1,20 @@
+\subsection{Exact forces for accuracy checks}
+\label{ssec:exact_forces}
+
+To assess the accuracy of the gravity solver, \swift can also compute
+the gravitational forces and potential for a subset of particles using
+a simple direct summation method. This is obviously much slower and
+should only be used for code testing purposes. The forces for a
+selection of particles are computed every time-step if they are active
+and dumped to a file alongside the forces computed by the FMM method.
+
+In the case where periodic boundary conditions are used, we apply the
+\cite{Ewald1921} summation technique to include the contribution to
+the forces of all the infinite periodic replications of the particle
+distribution. We use the approximation to the infinite series of terms
+proposed by \cite{Hernquist1991}\footnote{Note, however, that there is
+a typo in their formula for the force correction terms. The correct
+expression is given by \cite{Klessen1997} \citep[see
+also][]{Hubber2011}.}, which we tabulate in one octant using 64
+equally spaced bins along each spatial direction spanning and the
+range $[0,L]$, where $L$ is the side-length of the box.
diff --git a/theory/Multipoles/fmm_standalone.tex b/theory/Multipoles/fmm_standalone.tex
index 65d6b522f3a6a1f9ede41091a39f4f5145cf041c..1b597fa636650cd09469b9952f7a14bdf22ce35f 100644
--- a/theory/Multipoles/fmm_standalone.tex
+++ b/theory/Multipoles/fmm_standalone.tex
@@ -35,6 +35,7 @@ Making gravity great again.
\input{fmm_summary}
%\input{gravity_derivatives}
\input{mesh_summary}
+\input{exact_forces}
\bibliographystyle{mnras}
\bibliography{./bibliography.bib}