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  • dc-oman1/swiftsim
  • swift/swiftsim
  • pdraper/swiftsim
  • tkchan/swiftsim
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.gitignore
View file @ 853c5044
......@@ -39,12 +39,14 @@ examples/*/*/*.rst
examples/*/*/*.hdf5
examples/*/*/*.csv
examples/*/*/*.dot
examples/*/*/cell_hierarchy.html
examples/**/cell_hierarchy.html
examples/*/*/energy.txt
examples/*/*/task_level.txt
examples/**/task_level.txt
examples/*/*/timesteps_*.txt
examples/*/*/SFR.txt
examples/*/*/partition_fixed_costs.h
examples/**/timesteps.txt
examples/**/SFR.txt
examples/**/statistics.txt
examples/**/partition_fixed_costs.h
examples/*/*/memuse_report-step*.dat
examples/*/*/memuse_report-step*.log
examples/*/*/restart/*
......@@ -56,7 +58,6 @@ examples/*/*/used_parameters.yml
examples/*/*/unused_parameters.yml
examples/*/*/fof_used_parameters.yml
examples/*/*/fof_unused_parameters.yml
examples/*/*/partition_fixed_costs.h
examples/*/*.mpg
examples/*/*/gravity_checks_*.dat
examples/*/*/coolingtables.tar.gz
......@@ -65,6 +66,9 @@ examples/*/*/yieldtables.tar.gz
examples/*/*/yieldtables
examples/*/*/photometry.tar.gz
examples/*/*/photometry
examples/*/*/plots
examples/*/*/snapshots
examples/*/*/restart
examples/Cooling/CoolingRates/cooling_rates
examples/Cooling/CoolingRates/cooling_element_*.dat
examples/Cooling/CoolingRates/cooling_output.dat
......@@ -73,16 +77,15 @@ examples/SubgridTests/CosmologicalStellarEvolution/StellarEvolutionSolution*
examples/SmallCosmoVolume/SmallCosmoVolume_DM/power_spectra
examples/SmallCosmoVolume/SmallCosmoVolume_cooling/snapshots/
examples/SmallCosmoVolume/SmallCosmoVolume_hydro/snapshots/
examples/SmallCosmoVolume/SmallCosmoVolume_cooling/CloudyData_UVB=HM2012.h5
examples/SmallCosmoVolume/SmallCosmoVolume_cooling/CloudyData_UVB=HM2012_shielded.h5
examples/GEAR/AgoraDisk/CloudyData_UVB=HM2012.h5
examples/GEAR/AgoraDisk/CloudyData_UVB=HM2012_shielded.h5
examples/GEAR/AgoraDisk/chemistry-AGB+OMgSFeZnSrYBaEu-16072013.h5
examples/GEAR/AgoraCosmo/CloudyData_UVB=HM2012_shielded.h5
examples/GEAR/AgoraCosmo/POPIIsw.h5
examples/GEAR/ZoomIn/CloudyData_UVB=HM2012.h5
examples/GEAR/ZoomIn/POPIIsw.h5
examples/GEAR/ZoomIn/snap/
examples/**/CloudyData_UVB=HM2012.h5
examples/**/CloudyData_UVB=HM2012_shielded.h5
examples/**/CloudyData_UVB=HM2012_high_density.h5
examples/**/chemistry-AGB+OMgSFeZnSrYBaEu-16072013.h5
examples/**/POPIIsw.h5
examples/**/GRACKLE_INFO
examples/**/snap/
examples/SinkParticles/HomogeneousBox/snapshot_0003restart.hdf5
tests/testActivePair
tests/testActivePair.sh
......
AUTHORS
View file @ 853c5044
......@@ -13,7 +13,7 @@ Josh Borrow joshua.borrow@durham.ac.uk
Loic Hausammann loic.hausammann@epfl.ch
Yves Revaz yves.revaz@epfl.ch
Jacob Kegerreis jacob.kegerreis@durham.ac.uk
Mladen Ivkovic mladen.ivkovic@epfl.ch
Mladen Ivkovic mladen.ivkovic@durham.ac.uk
Stuart McAlpine stuart.mcalpine@helsinki.fi
Folkert Nobels nobels@strw.leidenuniv.nl
John Helly j.c.helly@durham.ac.uk
......@@ -27,3 +27,8 @@ TK Chan chantsangkeung@gmail.com
Marcel van Daalen daalen@strw.leidenuniv.nl
Filip Husko filip.husko@durham.ac.uk
Orestis Karapiperis karapiperis@lorentz.leidenuniv.nl
Stan Verhoeve s06verhoeve@gmail.com
Nikyta Shchutskyi shchutskyi@lorentz.leidenuniv.nl
Will Roper w.roper@sussex.ac.uk
Darwin Roduit darwin.roduit@alumni.epfl.ch
Jonathan Davies j.j.davies@ljmu.ac.uk
CONTRIBUTING.md
View file @ 853c5044
The SWIFT source code is using a variation of the 'Google' formatting style.
The script 'format.sh' in the root directory applies the clang-format-13
The script 'format.sh' in the root directory applies the clang-format-18
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.
......
INSTALL.swift
View file @ 853c5044
......@@ -99,7 +99,7 @@ before you can build it.
- HDF5:
A HDF5 library (v. 1.8.x or higher) is required to read and
A HDF5 library (v. 1.10.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
......@@ -191,7 +191,7 @@ before you can build it.
==================
The SWIFT source code uses a variation of 'Google' style. The script
'format.sh' in the root directory applies the clang-format-13 tool with our
'format.sh' in the root directory applies the clang-format-18 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.
......
Makefile.am
View file @ 853c5044
......@@ -38,14 +38,14 @@ MYFLAGS =
# Add the source directory and the non-standard paths to the included library headers to CFLAGS
AM_CFLAGS = -I$(top_srcdir)/src -I$(top_srcdir)/argparse $(HDF5_CPPFLAGS) \
$(GSL_INCS) $(FFTW_INCS) $(NUMA_INCS) $(GRACKLE_INCS) \
$(CHEALPIX_CFLAGS)
$(CHEALPIX_CFLAGS) $(LUSTREAPI_CFLAGS)
AM_LDFLAGS = $(HDF5_LDFLAGS)
# Extra libraries.
EXTRA_LIBS = $(GSL_LIBS) $(HDF5_LIBS) $(FFTW_LIBS) $(NUMA_LIBS) $(PROFILER_LIBS) \
$(TCMALLOC_LIBS) $(JEMALLOC_LIBS) $(TBBMALLOC_LIBS) $(GRACKLE_LIBS) \
$(CHEALPIX_LIBS)
$(CHEALPIX_LIBS) $(LUSTREAPI_LIBS)
# MPI libraries.
MPI_LIBS = $(PARMETIS_LIBS) $(METIS_LIBS) $(MPI_THREAD_LIBS) $(FFTW_MPI_LIBS)
......
README
View file @ 853c5044
......@@ -6,7 +6,7 @@
/____/ |__/|__/___/_/ /_/
SPH With Inter-dependent Fine-grained Tasking
Version : 1.0.0
Version : 2025.04
Website: www.swiftsim.com
Twitter: @SwiftSimulation
......
README.md
View file @ 853c5044
......@@ -55,7 +55,7 @@ experimentation with various values is highly encouraged. Each problem will
likely require different values and the sensitivity to the details of the
physical model is something left to the users to explore.
Acknowledgment & Citation
Acknowledgement & Citation
-------------------------
The SWIFT code was last described in this paper:
......@@ -66,7 +66,7 @@ their results.
In order to keep track of usage and measure the impact of the software, we
kindly ask users publishing scientific results using SWIFT to add the following
sentence to the acknowledgment section of their papers:
sentence to the acknowledgement section of their papers:
"The research in this paper made use of the SWIFT open-source
simulation code (http://www.swiftsim.com, Schaller et al. 2018)
......@@ -81,7 +81,7 @@ Contribution Guidelines
-----------------------
The SWIFT source code uses a variation of the 'Google' formatting style.
The script 'format.sh' in the root directory applies the clang-format-10
The script 'format.sh' in the root directory applies the clang-format-18
tool with our style choices to all the SWIFT C source file. Please apply
the formatting script to the files before submitting a pull request.
......@@ -106,7 +106,7 @@ Runtime parameters
/____/ |__/|__/___/_/ /_/
SPH With Inter-dependent Fine-grained Tasking
Version : 1.0.0
Version : 2025.04
Website: www.swiftsim.com
Twitter: @SwiftSimulation
......
argparse/argparse.h
View file @ 853c5044
......@@ -105,20 +105,13 @@ int argparse_help_cb(struct argparse *self,
const struct argparse_option *option);
// built-in option macros
#define OPT_END() \
{ ARGPARSE_OPT_END, 0, NULL, NULL, 0, NULL, 0, 0 }
#define OPT_BOOLEAN(...) \
{ ARGPARSE_OPT_BOOLEAN, __VA_ARGS__ }
#define OPT_BIT(...) \
{ ARGPARSE_OPT_BIT, __VA_ARGS__ }
#define OPT_INTEGER(...) \
{ ARGPARSE_OPT_INTEGER, __VA_ARGS__ }
#define OPT_FLOAT(...) \
{ ARGPARSE_OPT_FLOAT, __VA_ARGS__ }
#define OPT_STRING(...) \
{ ARGPARSE_OPT_STRING, __VA_ARGS__ }
#define OPT_GROUP(h) \
{ ARGPARSE_OPT_GROUP, 0, NULL, NULL, h, NULL, 0, 0 }
#define OPT_END() {ARGPARSE_OPT_END, 0, NULL, NULL, 0, NULL, 0, 0}
#define OPT_BOOLEAN(...) {ARGPARSE_OPT_BOOLEAN, __VA_ARGS__}
#define OPT_BIT(...) {ARGPARSE_OPT_BIT, __VA_ARGS__}
#define OPT_INTEGER(...) {ARGPARSE_OPT_INTEGER, __VA_ARGS__}
#define OPT_FLOAT(...) {ARGPARSE_OPT_FLOAT, __VA_ARGS__}
#define OPT_STRING(...) {ARGPARSE_OPT_STRING, __VA_ARGS__}
#define OPT_GROUP(h) {ARGPARSE_OPT_GROUP, 0, NULL, NULL, h, NULL, 0, 0}
#define OPT_HELP() \
OPT_BOOLEAN('h', "help", NULL, "show this help message and exit", \
argparse_help_cb, 0, 0)
......
configure.ac
View file @ 853c5044
......@@ -16,7 +16,7 @@
# along with this program. If not, see <http://www.gnu.org/licenses/>.
# Init the project.
AC_INIT([SWIFT],[1.0.0],[https://gitlab.cosma.dur.ac.uk/swift/swiftsim])
AC_INIT([SWIFT],[2025.04],[https://gitlab.cosma.dur.ac.uk/swift/swiftsim])
swift_config_flags="$*"
AC_COPYRIGHT
......@@ -92,6 +92,7 @@ if test "$with_csds" = "yes"; then
fi
AC_CONFIG_SUBDIRS([csds])
CFLAGS="$CFLAGS $OPENMP_CFLAGS"
fi
AM_CONDITIONAL([HAVECSDS],[test $with_csds = "yes"])
......@@ -137,7 +138,6 @@ if test "$enable_ipo" = "yes"; then
CFLAGS="$CFLAGS -ipo"
LDFLAGS="$LDFLAGS -ipo"
AC_CHECK_PROGS([AR], [xiar])
AC_CHECK_PROGS([LD], [xild])
AC_CHECK_PROGS([RANLIB], [llvm-ranlib])
AC_MSG_RESULT([added oneapi interprocedural optimization support])
elif test "$ax_cv_c_compiler_vendor" = "gnu"; then
......@@ -343,7 +343,7 @@ if test "$enable_cell_graph" = "yes"; then
AC_DEFINE([SWIFT_CELL_GRAPH],1,[Enable cell graph])
fi
# Check if using our custom icbrtf is enalbled.
# Check if using our custom icbrtf is enabled.
AC_ARG_ENABLE([custom-icbrtf],
[AS_HELP_STRING([--enable-custom-icbrtf],
[Use SWIFT's custom icbrtf function instead of the system cbrtf @<:@yes/no@:>@]
......@@ -433,6 +433,20 @@ elif test "$stars_density_checks" != "no"; then
AC_DEFINE_UNQUOTED([SWIFT_STARS_DENSITY_CHECKS], [$enableval] ,[Enable stars density brute-force checks])
fi
# Check if sink density checks are on for some particles.
AC_ARG_ENABLE([sink-density-checks],
[AS_HELP_STRING([--enable-sink-density-checks],
[Activate expensive brute-force sink density checks for a fraction 1/N of all particles @<:@N@:>@]
)],
[sink_density_checks="$enableval"],
[sink_density_checks="no"]
)
if test "$sink_density_checks" = "yes"; then
AC_MSG_ERROR(Need to specify the fraction of particles to check when using --enable-sink-density-checks!)
elif test "$sink_density_checks" != "no"; then
AC_DEFINE_UNQUOTED([SWIFT_SINK_DENSITY_CHECKS], [$enableval] ,[Enable sink density brute-force checks])
fi
# Check if ghost statistics are enabled
AC_ARG_ENABLE([ghost-statistics],
[AS_HELP_STRING([--enable-ghost-statistics],
......@@ -818,6 +832,42 @@ AC_SUBST([GSL_LIBS])
AC_SUBST([GSL_INCS])
AM_CONDITIONAL([HAVEGSL],[test -n "$GSL_LIBS"])
# Check for GMP. We test for this in the standard directories by default,
# and only disable if using --with-gmp=no or --without-gmp. When a value
# is given GMP must be found.
have_gmp="no"
AC_ARG_WITH([gmp],
[AS_HELP_STRING([--with-gmp=PATH],
[root directory where GMP is installed @<:@yes/no@:>@]
)],
[with_gmp="$withval"],
[with_gmp="test"]
)
if test "x$with_gmp" != "xno"; then
if test "x$with_gmp" != "xyes" -a "x$with_gmp" != "xtest" -a "x$with_gmp" != "x"; then
GMP_LIBS="-L$with_gmp/lib -lgmp"
else
GMP_LIBS="-lgmp"
fi
# GMP is not specified, so just check if we have it.
if test "x$with_gmp" = "xtest"; then
AC_CHECK_LIB([gmp],[__gmpz_inits],[have_gmp="yes"],[have_gmp="no"],$GMP_LIBS)
if test "x$have_gmp" != "xno"; then
AC_DEFINE([HAVE_LIBGMP],1,[The GMP library appears to be present.])
fi
else
AC_CHECK_LIB([gmp],[__gmpz_inits],
AC_DEFINE([HAVE_LIBGMP],1,[The GMP library appears to be present.]),
AC_MSG_ERROR(something is wrong with the GMP library!), $GMP_LIBS)
have_gmp="yes"
fi
if test "$have_gmp" = "no"; then
GMP_LIBS=""
fi
fi
AC_SUBST([GMP_LIBS])
AM_CONDITIONAL([HAVEGMP],[test -n "$GMP_LIBS"])
# Check for pthreads.
AX_PTHREAD([LIBS="$PTHREAD_LIBS $LIBS" CFLAGS="$CFLAGS $PTHREAD_CFLAGS"
CC="$PTHREAD_CC" LDFLAGS="$LDFLAGS $PTHREAD_LIBS $LIBS"],
......@@ -1381,6 +1431,38 @@ if test "$with_hdf5" = "yes"; then
fi
AM_CONDITIONAL([HAVEPARALLELHDF5],[test "$have_parallel_hdf5" = "yes"])
# Check for lustre support. Attempted by default.
have_lustreapi="no"
AC_ARG_WITH([lustreapi],
[AS_HELP_STRING([--with-lustreapi=PATH],
[use the lustre api library for some striping control @<:@yes/no@:>@]
)],
[with_lustreapi="$withval"],
[with_lustreapi="yes"]
)
if test "x$with_lustreapi" != "xno"; then
if test "x$with_lustreapi" != "xyes" -a "x$with_lustreapi" != "x"; then
LUSTREAPI_LIBS="-L$with_lustreapi -llustreapi"
LUSTREAPI_INCS="-I$with_lustreapi/include"
else
LUSTREAPI_LIBS="-llustreapi"
LUSTREAPI_INCS=""
fi
AC_CHECK_LIB([lustreapi], [llapi_obd_statfs], [have_lustreapi="yes"],
[have_lustreapi="no"],[$LUSTREAPI_LIBS])
if test "$have_lustreapi" = "yes"; then
AC_DEFINE([HAVE_LUSTREAPI],1,[The lustre API library appears to be present.])
else
LUSTREAPI_LIBS=""
fi
fi
AC_SUBST([LUSTREAPI_LIBS])
AC_SUBST([LUSTREAPI_INCS])
AM_CONDITIONAL([HAVELUSTREAPI],[test -n "$LUSTREAPI_LIBS"])
# Check for grackle.
have_grackle="no"
AC_ARG_WITH([grackle],
......@@ -1446,7 +1528,7 @@ AC_ARG_WITH([velociraptor],
if test "x$with_velociraptor" != "xno"; then
if test "x$with_velociraptor" != "xyes" -a "x$with_velociraptor" != "x"; then
VELOCIRAPTOR_LIBS="-L$with_velociraptor -lvelociraptor -lstdc++ -lhdf5"
CFLAGS="$CFLAGS -fopenmp"
CFLAGS="$CFLAGS $OPENMP_CFLAGS"
else
VELOCIRAPTOR_LIBS=""
fi
......@@ -1587,9 +1669,25 @@ else
have_chealpix="no"
fi
# Check for floating-point execeptions
AC_CHECK_FUNC(feenableexcept, AC_DEFINE([HAVE_FE_ENABLE_EXCEPT],[1],
[Defined if the floating-point exception can be enabled using non-standard GNU functions.]))
# Check for floating-point exception trapping support.
#
# We do not allow this to be enabled when optimizing as compilers do operations
# which are unsafe for speed. This can result in FPEs on valid vector
# operations when additional padding is used. This has been seen on clang and
# GCC based compilers.
if test "$enable_opt" != "yes"; then
if test "$ax_cv_c_compiler_vendor" != "oneapi"; then
AC_CHECK_FUNC(feenableexcept, AC_DEFINE([HAVE_FE_ENABLE_EXCEPT],[1],
[Defined if floating-point exceptions can be trapped.]))
else
# Default optimization for Intel is too high , -O2, so we also need
# to have debugging enabled which uses -O0 as well.
if test "$ax_enable_debug" != "no"; then
AC_CHECK_FUNC(feenableexcept, AC_DEFINE([HAVE_FE_ENABLE_EXCEPT],[1],
[Defined if floating-point exceptions can be trapped.]))
fi
fi
fi
# Check for setaffinity.
AC_CHECK_FUNC(pthread_setaffinity_np, AC_DEFINE([HAVE_SETAFFINITY],[1],
......@@ -1772,17 +1870,15 @@ if test "$have_armv7apmccntr"x = "yes"x; then
AC_DEFINE(HAVE_ARMV7A_PMCCNTR,1,[Define if you have enabled the PMCCNTR cycle counter on ARMv7a])
fi
# Check if we have native exp10 and exp10f functions. If not failback to our
# implementations. On Apple/CLANG we have __exp10, so also check for that
# Check if we have native exp10 and exp10f functions. If not fallback to our
# implementations. On Apple/CLANG/Homebrew gcc we have __exp10, so also check for that
# if the compiler is clang.
AC_CHECK_LIB([m],[exp10], [AC_DEFINE([HAVE_EXP10],1,[The exp10 function is present.])])
AC_CHECK_LIB([m],[exp10f], [AC_DEFINE([HAVE_EXP10F],1,[The exp10f function is present.])])
if test "$ax_cv_c_compiler_vendor" = "clang"; then
AC_CHECK_LIB([m],[__exp10], [AC_DEFINE([HAVE___EXP10],1,[The __exp10 function is present.])])
AC_CHECK_LIB([m],[__exp10f], [AC_DEFINE([HAVE___EXP10F],1,[The __exp10f function is present.])])
fi
AC_CHECK_LIB([m],[__exp10], [AC_DEFINE([HAVE___EXP10],1,[The __exp10 function is present.])])
AC_CHECK_LIB([m],[__exp10f], [AC_DEFINE([HAVE___EXP10F],1,[The __exp10f function is present.])])
# Check if we have native sincos and sincosf functions. If not failback to our
# Check if we have native sincos and sincosf functions. If not fallback to our
# implementations. On Apple/CLANG we have __sincos, so also check for that
# if the compiler is clang.
AC_CHECK_LIB([m],[sincos], [AC_DEFINE([HAVE_SINCOS],1,[The sincos function is present.])])
......@@ -1791,7 +1887,15 @@ if test "$ax_cv_c_compiler_vendor" = "clang"; then
AC_CHECK_LIB([m],[__sincos], [AC_DEFINE([HAVE___SINCOS],1,[The __sincos function is present.])])
AC_CHECK_LIB([m],[__sincosf], [AC_DEFINE([HAVE___SINCOSF],1,[The __sincosf function is present.])])
fi
# On Apple (CLANG or Homebrew gcc), check for __sincos and __sincosf inline functions in the headers.
AC_CHECK_HEADERS([math.h], [
AC_CHECK_DECLS([__sincos, __sincosf], [
AC_DEFINE([HAVE___SINCOS], 1, [The __sincos function is present.])
AC_DEFINE([HAVE___SINCOSF], 1, [The __sincosf function is present.])
], [], [#include <math.h>])
])
# The aocc compiler has optimized maths libraries that we should use. Check
# any clang for this support. Note do this after the basic check for maths
# as we need to make sure -lm follows. Also note needs -Ofast or -ffast-math
......@@ -1838,8 +1942,12 @@ if test "$enable_warn" != "no"; then
# Add a "choke on warning" flag if it exists
if test "$enable_warn" = "error"; then
case "$ax_cv_c_compiler_vendor" in
intel | gnu | clang | oneapi)
intel | clang | oneapi)
CFLAGS="$CFLAGS -Werror"
;;
gnu)
# Fix for issue with IPO and GCC 14
CFLAGS="$CFLAGS -Werror -Wno-alloc-size-larger-than"
;;
esac
fi
......@@ -1907,7 +2015,8 @@ AC_SUBST([SUNDIALS_INCS])
# As an example for this, see the call to AC_ARG_WITH for cooling.
AC_ARG_WITH([subgrid],
[AS_HELP_STRING([--with-subgrid=<subgrid>],
[Master switch for subgrid methods. Inexperienced user should start here. Options are: @<:@none, GEAR, AGORA, QLA, QLA-EAGLE, EAGLE, EAGLE-XL, SPIN_JET_EAGLE default: none@:>@]
[Master switch for subgrid methods. Inexperienced user should
start here. Options are: @<:@none, GEAR, GEAR-G3, AGORA, QLA, QLA-EAGLE, EAGLE, EAGLE-XL, SPIN_JET_EAGLE default: none@:>@]
)],
[with_subgrid="$withval"],
[with_subgrid=none]
......@@ -1934,12 +2043,24 @@ case "$with_subgrid" in
GEAR)
with_subgrid_cooling=grackle_0
with_subgrid_chemistry=GEAR_10
with_subgrid_pressure_floor=GEAR
with_subgrid_stars=GEAR
with_subgrid_star_formation=GEAR
with_subgrid_feedback=GEAR
with_subgrid_black_holes=none
with_subgrid_sink=GEAR
with_subgrid_extra_io=none
enable_fof=no
;;
GEAR-G3)
with_subgrid_cooling=grackle_3
with_subgrid_chemistry=GEAR_10
with_subgrid_pressure_floor=none
with_subgrid_stars=GEAR
with_subgrid_star_formation=GEAR
with_subgrid_feedback=GEAR
with_subgrid_black_holes=none
with_subgrid_sink=none
with_subgrid_sink=GEAR
with_subgrid_extra_io=none
enable_fof=no
;;
......@@ -2019,6 +2140,19 @@ case "$with_subgrid" in
with_subgrid_extra_io=none
enable_fof=yes
;;
SPIN_JET_EAGLE-XL)
with_subgrid_cooling=PS2020
with_subgrid_chemistry=EAGLE
with_subgrid_tracers=EAGLE
with_subgrid_entropy_floor=EAGLE
with_subgrid_stars=EAGLE
with_subgrid_star_formation=EAGLE
with_subgrid_feedback=EAGLE
with_subgrid_black_holes=SPIN_JET
with_subgrid_sink=none
with_subgrid_extra_io=none
enable_fof=yes
;;
*)
AC_MSG_ERROR([Unknown subgrid choice: $with_subgrid])
;;
......@@ -2089,7 +2223,7 @@ fi
# Hydro scheme.
AC_ARG_WITH([hydro],
[AS_HELP_STRING([--with-hydro=<scheme>],
[Hydro dynamics to use @<:@gadget2, minimal, pressure-entropy, pressure-energy, pressure-energy-monaghan, phantom, gizmo-mfv, gizmo-mfm, shadowfax, planetary, sphenix, gasoline, anarchy-pu default: sphenix@:>@]
[Hydro dynamics to use @<:@gadget2, minimal, pressure-entropy, pressure-energy, pressure-energy-monaghan, phantom, gizmo-mfv, gizmo-mfm, shadowswift, planetary, remix, sphenix, gasoline, anarchy-pu default: sphenix@:>@]
)],
[with_hydro="$withval"],
[with_hydro="sphenix"]
......@@ -2126,13 +2260,19 @@ case "$with_hydro" in
AC_DEFINE([GIZMO_MFM_SPH], [1], [GIZMO MFM SPH])
need_riemann_solver=yes
;;
shadowfax)
AC_DEFINE([SHADOWFAX_SPH], [1], [Shadowfax SPH])
shadowswift)
AC_DEFINE([SHADOWSWIFT], [1], [ShadowSWIFT hydrodynamics])
AC_DEFINE([MOVING_MESH_HYDRO], [1], [Moving mesh hydrodynamics])
need_moving_mesh=yes
need_riemann_solver=yes
hydro_does_mass_flux=yes
;;
planetary)
AC_DEFINE([PLANETARY_SPH], [1], [Planetary SPH])
;;
remix)
AC_DEFINE([REMIX_SPH], [1], [REMIX SPH])
;;
sphenix)
AC_DEFINE([SPHENIX_SPH], [1], [SPHENIX SPH])
;;
......@@ -2175,8 +2315,8 @@ fi
if test "$with_hydro" = "gizmo-mfv" -a "$with_spmhd" != "none"; then
AC_MSG_ERROR([Cannot use an SPMHD scheme alongside a gizmo hydro solver!"])
fi
if test "$with_hydro" = "shadowfax" -a "$with_spmhd" != "none"; then
AC_MSG_ERROR([Cannot use an SPMHD scheme alongside a gizmo hydro solver!"])
if test "$with_hydro" = "shadowswift" -a "$with_spmhd" != "none"; then
AC_MSG_ERROR([Cannot use an SPMHD scheme alongside a moving mesh hydro solver!"])
fi
# Check if debugging interactions stars is switched on.
......@@ -2347,6 +2487,34 @@ case "$with_gamma" in
;;
esac
# Adaptive softening
AC_ARG_WITH([adaptive-softening],
[AS_HELP_STRING([--with-adaptive-softening=<yes/no>],
[Adaptive softening @<:@no, yes, default: no@:>@]
)],
[with_adaptive_softening="$withval"],
[with_adaptive_softening="no"]
)
case "$with_adaptive_softening" in
no)
AC_DEFINE([FIXED_SOFTENING], [1], [No adaptive softening])
;;
yes)
AC_DEFINE([ADAPTIVE_SOFTENING], [1], [Adaptive softening])
;;
*)
AC_MSG_ERROR([Unknown adaptive softening: $with_adaptive_softening])
;;
esac
# Verify that the configuration is allowed
if test "x$with_adaptive_softening" = "xyes" -a "$with_kernel" != "wendland-C2"; then
AC_MSG_ERROR([Adaptive softening scheme requires the usage of the Wendland-C2 kernel!])
fi
if test "x$with_adaptive_softening" = "xyes" -a "$with_gravity" != "with-multi-softening"; then
AC_MSG_ERROR([Adaptive softening scheme requires the usage of the multi-softening gravity scheme!])
fi
# Riemann solver
AC_ARG_WITH([riemann-solver],
[AS_HELP_STRING([--with-riemann-solver=<solver>],
......@@ -2377,6 +2545,27 @@ if test "x$need_riemann_solver" = "xyes" -a "$with_riemann" = "none"; then
AC_MSG_ERROR([Hydro scheme $with_hydro requires selection of a Riemann solver!])
fi
# Moving mesh
AC_ARG_ENABLE([moving-mesh],
[AS_HELP_STRING([--enable-moving-mesh],
[enable the moving mesh computation]
)],
[enable_moving_mesh="${enableval}"],
[enable_moving_mesh="no"]
)
if test "x$need_moving_mesh" = "xyes"; then
enable_moving_mesh="yes"
fi
if test "$enable_moving_mesh" = "yes"; then
if test "$have_gmp" = "no"; then
AC_MSG_ERROR([GMP is required when using moving mesh!])
fi
if test "$have_gsl" = "no"; then
AC_MSG_ERROR([GSL is required when using moving mesh!])
fi
AC_DEFINE([MOVING_MESH], [1], [Unstructured Voronoi mesh])
fi
# Hydro does mass flux?
if test "x$hydro_does_mass_flux" = "xyes"; then
AC_DEFINE([HYDRO_DOES_MASS_FLUX], [1], [Hydro scheme with mass fluxes])
......@@ -2731,6 +2920,9 @@ case "$with_sink" in
none)
AC_DEFINE([SINK_NONE], [1], [No sink particle model])
;;
Basic)
AC_DEFINE([SINK_BASIC], [1], [Simple, self-contained sink model with only Bondi-Hoyle accretion and no SF.])
;;
GEAR)
AC_DEFINE([SINK_GEAR], [1], [GEAR sink particle model])
;;
......@@ -2742,7 +2934,7 @@ esac
# Forcing terms
AC_ARG_WITH([forcing],
[AS_HELP_STRING([--with-forcing=<term>],
[Hydrodynamics forcing terms @<:@none, roberts-flow, roberts-flow-acceleration default: none@:>@]
[Hydrodynamics forcing terms @<:@none, roberts-flow, roberts-flow-acceleration , abc-flowdefault: none@:>@]
)],
[with_forcing="$withval"],
[with_forcing="none"]
......@@ -2757,6 +2949,9 @@ case "$with_forcing" in
roberts-flow-acceleration)
AC_DEFINE([FORCING_ROBERTS_FLOW_ACCELERATION], [1], [Roberts' flow external forcing terms entering the equations as an acceleration term])
;;
abc-flow)
AC_DEFINE([FORCING_ABC_FLOW], [1], [ABC flow external forcing terms])
;;
*)
AC_MSG_ERROR([Unknown external forcing term: $with_forcing])
;;
......@@ -2971,6 +3166,7 @@ case "$with_rt" in
AC_DEFINE([RT_GEAR], [1], [GEAR M1 closure scheme])
number_group=${with_rt#*_}
AC_DEFINE_UNQUOTED([RT_NGROUPS], [$number_group], [Number of photon groups to follow])
AC_DEFINE([MPI_SYMMETRIC_FORCE_INTERACTION_RT], [1], [Do symmetric MPI interactions])
if test "$number_group" = "0"; then
AC_MSG_ERROR([GEAR-RT: Cannot work with zero photon groups])
......@@ -2985,9 +3181,14 @@ case "$with_rt" in
AC_DEFINE([SWIFT_RT_DEBUG_CHECKS], [1], [additional debugging checks for RT])
fi
if test "$with_hydro" != "gizmo-mfv"; then
AC_MSG_ERROR([GEAR-RT: Cannot work without gizmo-mfv hydro. Compile using --with-hydro=gizmo-mfv])
fi
case "$with_hydro" in
"gizmo-mfv" | "sphenix")
# allowed.
;;
*)
AC_MSG_ERROR([GEAR-RT: Cannot work without gizmo-mfv or sphenix hydro. Compile using --with-hydro=gizmo-mfv or --with-hydro=sphenix])
;;
esac
if test "$with_rt_riemann_solver" = "none"; then
AC_MSG_ERROR([GEAR-RT: You need to select an RT Riemann solver (--with-rt-riemann-solver=...)])
......@@ -3059,6 +3260,9 @@ AM_CONDITIONAL([HAVEEAGLEKINETICFEEDBACK], [test "$with_feedback" = "EAGLE-kinet
# check if using grackle cooling
AM_CONDITIONAL([HAVEGRACKLECOOLING], [test "$with_cooling" = "grackle"])
# check if using EAGLE floor
AM_CONDITIONAL([HAVEEAGLEFLOOR], [test "$with_entropy_floor" = "EAGLE"])
# check if using gear feedback
AM_CONDITIONAL([HAVEGEARFEEDBACK], [test "$with_feedback" = "GEAR"])
......@@ -3101,6 +3305,9 @@ AM_CONDITIONAL([HAVESPHM1RTRT], [test "${with_rt:0:7}" = "SPHM1RT"])
# Check if using GEAR-RT radiative transfer
AM_CONDITIONAL([HAVEGEARRT], [test "${with_rt:0:4}" = "GEAR"])
# Check if using Moving mesh
AM_CONDITIONAL([HAVE_MOVING_MESH], [test "$enable_moving_mesh" = "yes"])
......@@ -3152,12 +3359,14 @@ AC_MSG_RESULT([
MPI enabled : $enable_mpi
HDF5 enabled : $with_hdf5
- parallel : $have_parallel_hdf5
LUSTRE API enabled : $have_lustreapi
METIS/ParMETIS : $have_metis / $have_parmetis
FFTW3 enabled : $have_fftw
- threaded/openmp : $have_threaded_fftw / $have_openmp_fftw
- MPI : $have_mpi_fftw
- ARM : $have_arm_fftw
GSL enabled : $have_gsl
GMP enabled : $have_gmp
HEALPix C enabled : $have_chealpix
libNUMA enabled : $have_numa
GRACKLE enabled : $have_grackle
......@@ -3168,6 +3377,7 @@ AC_MSG_RESULT([
VELOCIraptor enabled : $have_velociraptor
FoF activated: : $enable_fof
Lightcones enabled : $enable_lightcone
Moving-mesh enabled : $enable_moving_mesh
Hydro scheme : $with_hydro
Dimensionality : $with_dimension
......@@ -3176,6 +3386,7 @@ AC_MSG_RESULT([
Adiabatic index : $with_gamma
Riemann solver : $with_riemann
SPMHD scheme : $with_spmhd
Adaptive softening : $with_adaptive_softening
Gravity scheme : $with_gravity
Multipole order : $with_multipole_order
......
doc/Doxyfile.in
View file @ 853c5044
# Doxyfile 1.8.17
# Doxyfile 1.9.8
# This file describes the settings to be used by the documentation system
# doxygen (www.doxygen.org) for a project.
......@@ -12,6 +12,16 @@
# For lists, items can also be appended using:
# TAG += value [value, ...]
# Values that contain spaces should be placed between quotes (\" \").
#
# Note:
#
# Use doxygen to compare the used configuration file with the template
# configuration file:
# doxygen -x [configFile]
# Use doxygen to compare the used configuration file with the template
# configuration file without replacing the environment variables or CMake type
# replacement variables:
# doxygen -x_noenv [configFile]
#---------------------------------------------------------------------------
# Project related configuration options
......@@ -60,16 +70,28 @@ PROJECT_LOGO =
OUTPUT_DIRECTORY = .
# If the CREATE_SUBDIRS tag is set to YES then doxygen will create 4096 sub-
# directories (in 2 levels) under the output directory of each output format and
# will distribute the generated files over these directories. Enabling this
# If the CREATE_SUBDIRS tag is set to YES then doxygen will create up to 4096
# sub-directories (in 2 levels) under the output directory of each output format
# and will distribute the generated files over these directories. Enabling this
# option can be useful when feeding doxygen a huge amount of source files, where
# putting all generated files in the same directory would otherwise causes
# performance problems for the file system.
# performance problems for the file system. Adapt CREATE_SUBDIRS_LEVEL to
# control the number of sub-directories.
# The default value is: NO.
CREATE_SUBDIRS = NO
# Controls the number of sub-directories that will be created when
# CREATE_SUBDIRS tag is set to YES. Level 0 represents 16 directories, and every
# level increment doubles the number of directories, resulting in 4096
# directories at level 8 which is the default and also the maximum value. The
# sub-directories are organized in 2 levels, the first level always has a fixed
# number of 16 directories.
# Minimum value: 0, maximum value: 8, default value: 8.
# This tag requires that the tag CREATE_SUBDIRS is set to YES.
CREATE_SUBDIRS_LEVEL = 8
# If the ALLOW_UNICODE_NAMES tag is set to YES, doxygen will allow non-ASCII
# characters to appear in the names of generated files. If set to NO, non-ASCII
# characters will be escaped, for example _xE3_x81_x84 will be used for Unicode
......@@ -81,26 +103,18 @@ ALLOW_UNICODE_NAMES = NO
# The OUTPUT_LANGUAGE tag is used to specify the language in which all
# documentation generated by doxygen is written. Doxygen will use this
# information to generate all constant output in the proper language.
# Possible values are: Afrikaans, Arabic, Armenian, Brazilian, Catalan, Chinese,
# Chinese-Traditional, Croatian, Czech, Danish, Dutch, English (United States),
# Esperanto, Farsi (Persian), Finnish, French, German, Greek, Hungarian,
# Indonesian, Italian, Japanese, Japanese-en (Japanese with English messages),
# Korean, Korean-en (Korean with English messages), Latvian, Lithuanian,
# Macedonian, Norwegian, Persian (Farsi), Polish, Portuguese, Romanian, Russian,
# Serbian, Serbian-Cyrillic, Slovak, Slovene, Spanish, Swedish, Turkish,
# Ukrainian and Vietnamese.
# Possible values are: Afrikaans, Arabic, Armenian, Brazilian, Bulgarian,
# Catalan, Chinese, Chinese-Traditional, Croatian, Czech, Danish, Dutch, English
# (United States), Esperanto, Farsi (Persian), Finnish, French, German, Greek,
# Hindi, Hungarian, Indonesian, Italian, Japanese, Japanese-en (Japanese with
# English messages), Korean, Korean-en (Korean with English messages), Latvian,
# Lithuanian, Macedonian, Norwegian, Persian (Farsi), Polish, Portuguese,
# Romanian, Russian, Serbian, Serbian-Cyrillic, Slovak, Slovene, Spanish,
# Swedish, Turkish, Ukrainian and Vietnamese.
# The default value is: English.
OUTPUT_LANGUAGE = English
# The OUTPUT_TEXT_DIRECTION tag is used to specify the direction in which all
# documentation generated by doxygen is written. Doxygen will use this
# information to generate all generated output in the proper direction.
# Possible values are: None, LTR, RTL and Context.
# The default value is: None.
OUTPUT_TEXT_DIRECTION = None
# If the BRIEF_MEMBER_DESC tag is set to YES, doxygen will include brief member
# descriptions after the members that are listed in the file and class
# documentation (similar to Javadoc). Set to NO to disable this.
......@@ -217,6 +231,14 @@ QT_AUTOBRIEF = NO
MULTILINE_CPP_IS_BRIEF = NO
# By default Python docstrings are displayed as preformatted text and doxygen's
# special commands cannot be used. By setting PYTHON_DOCSTRING to NO the
# doxygen's special commands can be used and the contents of the docstring
# documentation blocks is shown as doxygen documentation.
# The default value is: YES.
PYTHON_DOCSTRING = YES
# If the INHERIT_DOCS tag is set to YES then an undocumented member inherits the
# documentation from any documented member that it re-implements.
# The default value is: YES.
......@@ -240,25 +262,19 @@ TAB_SIZE = 8
# the documentation. An alias has the form:
# name=value
# For example adding
# "sideeffect=@par Side Effects:\n"
# "sideeffect=@par Side Effects:^^"
# will allow you to put the command \sideeffect (or @sideeffect) in the
# documentation, which will result in a user-defined paragraph with heading
# "Side Effects:". You can put \n's in the value part of an alias to insert
# newlines (in the resulting output). You can put ^^ in the value part of an
# alias to insert a newline as if a physical newline was in the original file.
# When you need a literal { or } or , in the value part of an alias you have to
# escape them by means of a backslash (\), this can lead to conflicts with the
# commands \{ and \} for these it is advised to use the version @{ and @} or use
# a double escape (\\{ and \\})
# "Side Effects:". Note that you cannot put \n's in the value part of an alias
# to insert newlines (in the resulting output). You can put ^^ in the value part
# of an alias to insert a newline as if a physical newline was in the original
# file. When you need a literal { or } or , in the value part of an alias you
# have to escape them by means of a backslash (\), this can lead to conflicts
# with the commands \{ and \} for these it is advised to use the version @{ and
# @} or use a double escape (\\{ and \\})
ALIASES =
# This tag can be used to specify a number of word-keyword mappings (TCL only).
# A mapping has the form "name=value". For example adding "class=itcl::class"
# will allow you to use the command class in the itcl::class meaning.
TCL_SUBST =
# Set the OPTIMIZE_OUTPUT_FOR_C tag to YES if your project consists of C sources
# only. Doxygen will then generate output that is more tailored for C. For
# instance, some of the names that are used will be different. The list of all
......@@ -300,18 +316,21 @@ OPTIMIZE_OUTPUT_SLICE = NO
# extension. Doxygen has a built-in mapping, but you can override or extend it
# using this tag. The format is ext=language, where ext is a file extension, and
# language is one of the parsers supported by doxygen: IDL, Java, JavaScript,
# Csharp (C#), C, C++, D, PHP, md (Markdown), Objective-C, Python, Slice,
# Fortran (fixed format Fortran: FortranFixed, free formatted Fortran:
# Csharp (C#), C, C++, Lex, D, PHP, md (Markdown), Objective-C, Python, Slice,
# VHDL, Fortran (fixed format Fortran: FortranFixed, free formatted Fortran:
# FortranFree, unknown formatted Fortran: Fortran. In the later case the parser
# tries to guess whether the code is fixed or free formatted code, this is the
# default for Fortran type files), VHDL, tcl. For instance to make doxygen treat
# .inc files as Fortran files (default is PHP), and .f files as C (default is
# Fortran), use: inc=Fortran f=C.
# default for Fortran type files). For instance to make doxygen treat .inc files
# as Fortran files (default is PHP), and .f files as C (default is Fortran),
# use: inc=Fortran f=C.
#
# Note: For files without extension you can use no_extension as a placeholder.
#
# Note that for custom extensions you also need to set FILE_PATTERNS otherwise
# the files are not read by doxygen.
# the files are not read by doxygen. When specifying no_extension you should add
# * to the FILE_PATTERNS.
#
# Note see also the list of default file extension mappings.
EXTENSION_MAPPING =
......@@ -334,6 +353,17 @@ MARKDOWN_SUPPORT = YES
TOC_INCLUDE_HEADINGS = 5
# The MARKDOWN_ID_STYLE tag can be used to specify the algorithm used to
# generate identifiers for the Markdown headings. Note: Every identifier is
# unique.
# Possible values are: DOXYGEN use a fixed 'autotoc_md' string followed by a
# sequence number starting at 0 and GITHUB use the lower case version of title
# with any whitespace replaced by '-' and punctuation characters removed.
# The default value is: DOXYGEN.
# This tag requires that the tag MARKDOWN_SUPPORT is set to YES.
MARKDOWN_ID_STYLE = DOXYGEN
# When enabled doxygen tries to link words that correspond to documented
# classes, or namespaces to their corresponding documentation. Such a link can
# be prevented in individual cases by putting a % sign in front of the word or
......@@ -445,6 +475,27 @@ TYPEDEF_HIDES_STRUCT = NO
LOOKUP_CACHE_SIZE = 0
# The NUM_PROC_THREADS specifies the number of threads doxygen is allowed to use
# during processing. When set to 0 doxygen will based this on the number of
# cores available in the system. You can set it explicitly to a value larger
# than 0 to get more control over the balance between CPU load and processing
# speed. At this moment only the input processing can be done using multiple
# threads. Since this is still an experimental feature the default is set to 1,
# which effectively disables parallel processing. Please report any issues you
# encounter. Generating dot graphs in parallel is controlled by the
# DOT_NUM_THREADS setting.
# Minimum value: 0, maximum value: 32, default value: 1.
NUM_PROC_THREADS = 1
# If the TIMESTAMP tag is set different from NO then each generated page will
# contain the date or date and time when the page was generated. Setting this to
# NO can help when comparing the output of multiple runs.
# Possible values are: YES, NO, DATETIME and DATE.
# The default value is: NO.
TIMESTAMP = YES
#---------------------------------------------------------------------------
# Build related configuration options
#---------------------------------------------------------------------------
......@@ -508,6 +559,13 @@ EXTRACT_LOCAL_METHODS = NO
EXTRACT_ANON_NSPACES = NO
# If this flag is set to YES, the name of an unnamed parameter in a declaration
# will be determined by the corresponding definition. By default unnamed
# parameters remain unnamed in the output.
# The default value is: YES.
RESOLVE_UNNAMED_PARAMS = YES
# If the HIDE_UNDOC_MEMBERS tag is set to YES, doxygen will hide all
# undocumented members inside documented classes or files. If set to NO these
# members will be included in the various overviews, but no documentation
......@@ -519,7 +577,8 @@ HIDE_UNDOC_MEMBERS = NO
# If the HIDE_UNDOC_CLASSES tag is set to YES, doxygen will hide all
# undocumented classes that are normally visible in the class hierarchy. If set
# to NO, these classes will be included in the various overviews. This option
# has no effect if EXTRACT_ALL is enabled.
# will also hide undocumented C++ concepts if enabled. This option has no effect
# if EXTRACT_ALL is enabled.
# The default value is: NO.
HIDE_UNDOC_CLASSES = NO
......@@ -545,12 +604,20 @@ HIDE_IN_BODY_DOCS = NO
INTERNAL_DOCS = NO
# If the CASE_SENSE_NAMES tag is set to NO then doxygen will only generate file
# names in lower-case letters. If set to YES, upper-case letters are also
# allowed. This is useful if you have classes or files whose names only differ
# in case and if your file system supports case sensitive file names. Windows
# (including Cygwin) ands Mac users are advised to set this option to NO.
# The default value is: system dependent.
# With the correct setting of option CASE_SENSE_NAMES doxygen will better be
# able to match the capabilities of the underlying filesystem. In case the
# filesystem is case sensitive (i.e. it supports files in the same directory
# whose names only differ in casing), the option must be set to YES to properly
# deal with such files in case they appear in the input. For filesystems that
# are not case sensitive the option should be set to NO to properly deal with
# output files written for symbols that only differ in casing, such as for two
# classes, one named CLASS and the other named Class, and to also support
# references to files without having to specify the exact matching casing. On
# Windows (including Cygwin) and MacOS, users should typically set this option
# to NO, whereas on Linux or other Unix flavors it should typically be set to
# YES.
# Possible values are: SYSTEM, NO and YES.
# The default value is: SYSTEM.
CASE_SENSE_NAMES = YES
......@@ -568,6 +635,12 @@ HIDE_SCOPE_NAMES = YES
HIDE_COMPOUND_REFERENCE= NO
# If the SHOW_HEADERFILE tag is set to YES then the documentation for a class
# will show which file needs to be included to use the class.
# The default value is: YES.
SHOW_HEADERFILE = YES
# If the SHOW_INCLUDE_FILES tag is set to YES then doxygen will put a list of
# the files that are included by a file in the documentation of that file.
# The default value is: YES.
......@@ -725,7 +798,8 @@ FILE_VERSION_FILTER =
# output files in an output format independent way. To create the layout file
# that represents doxygen's defaults, run doxygen with the -l option. You can
# optionally specify a file name after the option, if omitted DoxygenLayout.xml
# will be used as the name of the layout file.
# will be used as the name of the layout file. See also section "Changing the
# layout of pages" for information.
#
# Note that if you run doxygen from a directory containing a file called
# DoxygenLayout.xml, doxygen will parse it automatically even if the LAYOUT_FILE
......@@ -771,24 +845,50 @@ WARNINGS = YES
WARN_IF_UNDOCUMENTED = YES
# If the WARN_IF_DOC_ERROR tag is set to YES, doxygen will generate warnings for
# potential errors in the documentation, such as not documenting some parameters
# in a documented function, or documenting parameters that don't exist or using
# markup commands wrongly.
# potential errors in the documentation, such as documenting some parameters in
# a documented function twice, or documenting parameters that don't exist or
# using markup commands wrongly.
# The default value is: YES.
WARN_IF_DOC_ERROR = YES
# If WARN_IF_INCOMPLETE_DOC is set to YES, doxygen will warn about incomplete
# function parameter documentation. If set to NO, doxygen will accept that some
# parameters have no documentation without warning.
# The default value is: YES.
WARN_IF_INCOMPLETE_DOC = YES
# This WARN_NO_PARAMDOC option can be enabled to get warnings for functions that
# are documented, but have no documentation for their parameters or return
# value. If set to NO, doxygen will only warn about wrong or incomplete
# parameter documentation, but not about the absence of documentation. If
# EXTRACT_ALL is set to YES then this flag will automatically be disabled.
# value. If set to NO, doxygen will only warn about wrong parameter
# documentation, but not about the absence of documentation. If EXTRACT_ALL is
# set to YES then this flag will automatically be disabled. See also
# WARN_IF_INCOMPLETE_DOC
# The default value is: NO.
WARN_NO_PARAMDOC = NO
# If WARN_IF_UNDOC_ENUM_VAL option is set to YES, doxygen will warn about
# undocumented enumeration values. If set to NO, doxygen will accept
# undocumented enumeration values. If EXTRACT_ALL is set to YES then this flag
# will automatically be disabled.
# The default value is: NO.
WARN_IF_UNDOC_ENUM_VAL = NO
# If the WARN_AS_ERROR tag is set to YES then doxygen will immediately stop when
# a warning is encountered.
# a warning is encountered. If the WARN_AS_ERROR tag is set to FAIL_ON_WARNINGS
# then doxygen will continue running as if WARN_AS_ERROR tag is set to NO, but
# at the end of the doxygen process doxygen will return with a non-zero status.
# If the WARN_AS_ERROR tag is set to FAIL_ON_WARNINGS_PRINT then doxygen behaves
# like FAIL_ON_WARNINGS but in case no WARN_LOGFILE is defined doxygen will not
# write the warning messages in between other messages but write them at the end
# of a run, in case a WARN_LOGFILE is defined the warning messages will be
# besides being in the defined file also be shown at the end of a run, unless
# the WARN_LOGFILE is defined as - i.e. standard output (stdout) in that case
# the behavior will remain as with the setting FAIL_ON_WARNINGS.
# Possible values are: NO, YES, FAIL_ON_WARNINGS and FAIL_ON_WARNINGS_PRINT.
# The default value is: NO.
WARN_AS_ERROR = NO
......@@ -799,13 +899,27 @@ WARN_AS_ERROR = NO
# and the warning text. Optionally the format may contain $version, which will
# be replaced by the version of the file (if it could be obtained via
# FILE_VERSION_FILTER)
# See also: WARN_LINE_FORMAT
# The default value is: $file:$line: $text.
WARN_FORMAT = "$file:$line: $text"
# In the $text part of the WARN_FORMAT command it is possible that a reference
# to a more specific place is given. To make it easier to jump to this place
# (outside of doxygen) the user can define a custom "cut" / "paste" string.
# Example:
# WARN_LINE_FORMAT = "'vi $file +$line'"
# See also: WARN_FORMAT
# The default value is: at line $line of file $file.
WARN_LINE_FORMAT = "at line $line of file $file"
# The WARN_LOGFILE tag can be used to specify a file to which warning and error
# messages should be written. If left blank the output is written to standard
# error (stderr).
# error (stderr). In case the file specified cannot be opened for writing the
# warning and error messages are written to standard error. When as file - is
# specified the warning and error messages are written to standard output
# (stdout).
WARN_LOGFILE =
......@@ -825,40 +939,74 @@ INPUT = @top_srcdir@ \
@top_srcdir@/examples \
@top_srcdir@/src/hydro/Minimal \
@top_srcdir@/src/hydro/Gadget2 \
@top_srcdir@/src/hydro/SPHENIX \
@top_srcdir@/src/gravity/Default \
@top_srcdir@/src/gravity/MultiSoftening \
@top_srcdir@/src/riemann \
@top_srcdir@/src/potential/point_mass \
@top_srcdir@/src/equation_of_state/ideal_gas \
@top_srcdir@/src/equation_of_state/isothermal \
@top_srcdir@/src/equation_of_state/barotropic \
@top_srcdir@/src/cooling/const_du \
@top_srcdir@/src/cooling/const_lambda \
@top_srcdir@/src/cooling/Compton \
@top_srcdir@/src/cooling/EAGLE \
@top_srcdir@/src/cooling/PS2020 \
@top_srcdir@/src/cooling/grackle \
@top_srcdir@/src/chemistry/AGORA \
@top_srcdir@/src/chemistry/EAGLE \
@top_srcdir@/src/chemistry/GEAR \
@top_srcdir@/src/chemistry/QLA \
@top_srcdir@/src/chemistry/none \
@top_srcdir@/src/entropy_floor/EAGLE \
@top_srcdir@/src/pressure_floor/GEAR \
@top_srcdir@/src/star_formation/EAGLE \
@top_srcdir@/src/star_formation/GEAR \
@top_srcdir@/src/star_formation/QLA \
@top_srcdir@/src/star_formation/none \
@top_srcdir@/src/tracers/EAGLE \
@top_srcdir@/src/stars/EAGLE \
@top_srcdir@/src/stars/GEAR \
@top_srcdir@/src/stars/Basic \
@top_srcdir@/src/stars/None \
@top_srcdir@/src/feedback/none \
@top_srcdir@/src/feedback/AGORA \
@top_srcdir@/src/feedback/EAGLE \
@top_srcdir@/src/feedback/EAGLE_thermal \
@top_srcdir@/src/feedback/EAGLE_kinetic \
@top_srcdir@/src/feedback/GEAR \
@top_srcdir@/src/black_holes/Default \
@top_srcdir@/src/black_holes/EAGLE \
@top_srcdir@/src/black_holes/SPIN_JET \
@top_srcdir@/src/sink/Basic \
@top_srcdir@/src/sink/Default \
@top_srcdir@/src/sink/GEAR \
@top_srcdir@/src/forcing \
@top_srcdir@/src/fvpm_geometry \
@top_srcdir@/src/rt \
@top_srcdir@/src/extra_io \
@top_srcdir@/src/neutrino \
@top_srcdir@/csds
# This tag can be used to specify the character encoding of the source files
# that doxygen parses. Internally doxygen uses the UTF-8 encoding. Doxygen uses
# libiconv (or the iconv built into libc) for the transcoding. See the libiconv
# documentation (see: https://www.gnu.org/software/libiconv/) for the list of
# possible encodings.
# documentation (see:
# https://www.gnu.org/software/libiconv/) for the list of possible encodings.
# See also: INPUT_FILE_ENCODING
# The default value is: UTF-8.
INPUT_ENCODING = UTF-8
# This tag can be used to specify the character encoding of the source files
# that doxygen parses The INPUT_FILE_ENCODING tag can be used to specify
# character encoding on a per file pattern basis. Doxygen will compare the file
# name with each pattern and apply the encoding instead of the default
# INPUT_ENCODING) if there is a match. The character encodings are a list of the
# form: pattern=encoding (like *.php=ISO-8859-1). See cfg_input_encoding
# "INPUT_ENCODING" for further information on supported encodings.
INPUT_FILE_ENCODING =
# If the value of the INPUT tag contains directories, you can use the
# FILE_PATTERNS tag to specify one or more wildcard patterns (like *.cpp and
# *.h) to filter out the source-files in the directories.
......@@ -867,13 +1015,15 @@ INPUT_ENCODING = UTF-8
# need to set EXTENSION_MAPPING for the extension otherwise the files are not
# read by doxygen.
#
# If left blank the following patterns are tested:*.c, *.cc, *.cxx, *.cpp,
# *.c++, *.java, *.ii, *.ixx, *.ipp, *.i++, *.inl, *.idl, *.ddl, *.odl, *.h,
# *.hh, *.hxx, *.hpp, *.h++, *.cs, *.d, *.php, *.php4, *.php5, *.phtml, *.inc,
# *.m, *.markdown, *.md, *.mm, *.dox (to be provided as doxygen C comment),
# *.doc (to be provided as doxygen C comment), *.txt (to be provided as doxygen
# C comment), *.py, *.pyw, *.f90, *.f95, *.f03, *.f08, *.f, *.for, *.tcl, *.vhd,
# *.vhdl, *.ucf, *.qsf and *.ice.
# Note the list of default checked file patterns might differ from the list of
# default file extension mappings.
#
# If left blank the following patterns are tested:*.c, *.cc, *.cxx, *.cxxm,
# *.cpp, *.cppm, *.c++, *.c++m, *.java, *.ii, *.ixx, *.ipp, *.i++, *.inl, *.idl,
# *.ddl, *.odl, *.h, *.hh, *.hxx, *.hpp, *.h++, *.ixx, *.l, *.cs, *.d, *.php,
# *.php4, *.php5, *.phtml, *.inc, *.m, *.markdown, *.md, *.mm, *.dox (to be
# provided as doxygen C comment), *.py, *.pyw, *.f90, *.f95, *.f03, *.f08,
# *.f18, *.f, *.for, *.vhd, *.vhdl, *.ucf, *.qsf and *.ice.
FILE_PATTERNS =
......@@ -912,10 +1062,7 @@ EXCLUDE_PATTERNS = *.md
# (namespaces, classes, functions, etc.) that should be excluded from the
# output. The symbol name can be a fully qualified name, a word, or if the
# wildcard * is used, a substring. Examples: ANamespace, AClass,
# AClass::ANamespace, ANamespace::*Test
#
# Note that the wildcards are matched against the file with absolute path, so to
# exclude all test directories use the pattern */test/*
# ANamespace::AClass, ANamespace::*Test
EXCLUDE_SYMBOLS =
......@@ -960,6 +1107,11 @@ IMAGE_PATH =
# code is scanned, but not when the output code is generated. If lines are added
# or removed, the anchors will not be placed correctly.
#
# Note that doxygen will use the data processed and written to standard output
# for further processing, therefore nothing else, like debug statements or used
# commands (so in case of a Windows batch file always use @echo OFF), should be
# written to standard output.
#
# Note that for custom extensions or not directly supported extensions you also
# need to set EXTENSION_MAPPING for the extension otherwise the files are not
# properly processed by doxygen.
......@@ -1001,6 +1153,15 @@ FILTER_SOURCE_PATTERNS =
USE_MDFILE_AS_MAINPAGE =
# The Fortran standard specifies that for fixed formatted Fortran code all
# characters from position 72 are to be considered as comment. A common
# extension is to allow longer lines before the automatic comment starts. The
# setting FORTRAN_COMMENT_AFTER will also make it possible that longer lines can
# be processed before the automatic comment starts.
# Minimum value: 7, maximum value: 10000, default value: 72.
FORTRAN_COMMENT_AFTER = 72
#---------------------------------------------------------------------------
# Configuration options related to source browsing
#---------------------------------------------------------------------------
......@@ -1088,16 +1249,24 @@ USE_HTAGS = NO
VERBATIM_HEADERS = YES
# If the CLANG_ASSISTED_PARSING tag is set to YES then doxygen will use the
# clang parser (see: http://clang.llvm.org/) for more accurate parsing at the
# cost of reduced performance. This can be particularly helpful with template
# rich C++ code for which doxygen's built-in parser lacks the necessary type
# information.
# clang parser (see:
# http://clang.llvm.org/) for more accurate parsing at the cost of reduced
# performance. This can be particularly helpful with template rich C++ code for
# which doxygen's built-in parser lacks the necessary type information.
# Note: The availability of this option depends on whether or not doxygen was
# generated with the -Duse_libclang=ON option for CMake.
# The default value is: NO.
CLANG_ASSISTED_PARSING = NO
# If the CLANG_ASSISTED_PARSING tag is set to YES and the CLANG_ADD_INC_PATHS
# tag is set to YES then doxygen will add the directory of each input to the
# include path.
# The default value is: YES.
# This tag requires that the tag CLANG_ASSISTED_PARSING is set to YES.
CLANG_ADD_INC_PATHS = YES
# If clang assisted parsing is enabled you can provide the compiler with command
# line options that you would normally use when invoking the compiler. Note that
# the include paths will already be set by doxygen for the files and directories
......@@ -1107,10 +1276,13 @@ CLANG_ASSISTED_PARSING = NO
CLANG_OPTIONS =
# If clang assisted parsing is enabled you can provide the clang parser with the
# path to the compilation database (see:
# http://clang.llvm.org/docs/HowToSetupToolingForLLVM.html) used when the files
# were built. This is equivalent to specifying the "-p" option to a clang tool,
# such as clang-check. These options will then be passed to the parser.
# path to the directory containing a file called compile_commands.json. This
# file is the compilation database (see:
# http://clang.llvm.org/docs/HowToSetupToolingForLLVM.html) containing the
# options used when the source files were built. This is equivalent to
# specifying the -p option to a clang tool, such as clang-check. These options
# will then be passed to the parser. Any options specified with CLANG_OPTIONS
# will be added as well.
# Note: The availability of this option depends on whether or not doxygen was
# generated with the -Duse_libclang=ON option for CMake.
......@@ -1127,17 +1299,11 @@ CLANG_DATABASE_PATH =
ALPHABETICAL_INDEX = YES
# The COLS_IN_ALPHA_INDEX tag can be used to specify the number of columns in
# which the alphabetical index list will be split.
# Minimum value: 1, maximum value: 20, default value: 5.
# This tag requires that the tag ALPHABETICAL_INDEX is set to YES.
COLS_IN_ALPHA_INDEX = 5
# In case all classes in a project start with a common prefix, all classes will
# be put under the same header in the alphabetical index. The IGNORE_PREFIX tag
# can be used to specify a prefix (or a list of prefixes) that should be ignored
# while generating the index headers.
# The IGNORE_PREFIX tag can be used to specify a prefix (or a list of prefixes)
# that should be ignored while generating the index headers. The IGNORE_PREFIX
# tag works for classes, function and member names. The entity will be placed in
# the alphabetical list under the first letter of the entity name that remains
# after removing the prefix.
# This tag requires that the tag ALPHABETICAL_INDEX is set to YES.
IGNORE_PREFIX =
......@@ -1216,7 +1382,12 @@ HTML_STYLESHEET =
# Doxygen will copy the style sheet files to the output directory.
# Note: The order of the extra style sheet files is of importance (e.g. the last
# style sheet in the list overrules the setting of the previous ones in the
# list). For an example see the documentation.
# list).
# Note: Since the styling of scrollbars can currently not be overruled in
# Webkit/Chromium, the styling will be left out of the default doxygen.css if
# one or more extra stylesheets have been specified. So if scrollbar
# customization is desired it has to be added explicitly. For an example see the
# documentation.
# This tag requires that the tag GENERATE_HTML is set to YES.
HTML_EXTRA_STYLESHEET =
......@@ -1231,9 +1402,22 @@ HTML_EXTRA_STYLESHEET =
HTML_EXTRA_FILES =
# The HTML_COLORSTYLE tag can be used to specify if the generated HTML output
# should be rendered with a dark or light theme.
# Possible values are: LIGHT always generate light mode output, DARK always
# generate dark mode output, AUTO_LIGHT automatically set the mode according to
# the user preference, use light mode if no preference is set (the default),
# AUTO_DARK automatically set the mode according to the user preference, use
# dark mode if no preference is set and TOGGLE allow to user to switch between
# light and dark mode via a button.
# The default value is: AUTO_LIGHT.
# This tag requires that the tag GENERATE_HTML is set to YES.
HTML_COLORSTYLE = AUTO_LIGHT
# The HTML_COLORSTYLE_HUE tag controls the color of the HTML output. Doxygen
# will adjust the colors in the style sheet and background images according to
# this color. Hue is specified as an angle on a colorwheel, see
# this color. Hue is specified as an angle on a color-wheel, see
# https://en.wikipedia.org/wiki/Hue for more information. For instance the value
# 0 represents red, 60 is yellow, 120 is green, 180 is cyan, 240 is blue, 300
# purple, and 360 is red again.
......@@ -1243,7 +1427,7 @@ HTML_EXTRA_FILES =
HTML_COLORSTYLE_HUE = 220
# The HTML_COLORSTYLE_SAT tag controls the purity (or saturation) of the colors
# in the HTML output. For a value of 0 the output will use grayscales only. A
# in the HTML output. For a value of 0 the output will use gray-scales only. A
# value of 255 will produce the most vivid colors.
# Minimum value: 0, maximum value: 255, default value: 100.
# This tag requires that the tag GENERATE_HTML is set to YES.
......@@ -1261,15 +1445,6 @@ HTML_COLORSTYLE_SAT = 100
HTML_COLORSTYLE_GAMMA = 80
# If the HTML_TIMESTAMP tag is set to YES then the footer of each generated HTML
# page will contain the date and time when the page was generated. Setting this
# to YES can help to show when doxygen was last run and thus if the
# documentation is up to date.
# The default value is: NO.
# This tag requires that the tag GENERATE_HTML is set to YES.
HTML_TIMESTAMP = YES
# If the HTML_DYNAMIC_MENUS tag is set to YES then the generated HTML
# documentation will contain a main index with vertical navigation menus that
# are dynamically created via JavaScript. If disabled, the navigation index will
......@@ -1289,6 +1464,13 @@ HTML_DYNAMIC_MENUS = YES
HTML_DYNAMIC_SECTIONS = NO
# If the HTML_CODE_FOLDING tag is set to YES then classes and functions can be
# dynamically folded and expanded in the generated HTML source code.
# The default value is: YES.
# This tag requires that the tag GENERATE_HTML is set to YES.
HTML_CODE_FOLDING = YES
# With HTML_INDEX_NUM_ENTRIES one can control the preferred number of entries
# shown in the various tree structured indices initially; the user can expand
# and collapse entries dynamically later on. Doxygen will expand the tree to
......@@ -1304,10 +1486,11 @@ HTML_INDEX_NUM_ENTRIES = 100
# If the GENERATE_DOCSET tag is set to YES, additional index files will be
# generated that can be used as input for Apple's Xcode 3 integrated development
# environment (see: https://developer.apple.com/xcode/), introduced with OSX
# 10.5 (Leopard). To create a documentation set, doxygen will generate a
# Makefile in the HTML output directory. Running make will produce the docset in
# that directory and running make install will install the docset in
# environment (see:
# https://developer.apple.com/xcode/), introduced with OSX 10.5 (Leopard). To
# create a documentation set, doxygen will generate a Makefile in the HTML
# output directory. Running make will produce the docset in that directory and
# running make install will install the docset in
# ~/Library/Developer/Shared/Documentation/DocSets so that Xcode will find it at
# startup. See https://developer.apple.com/library/archive/featuredarticles/Doxy
# genXcode/_index.html for more information.
......@@ -1324,6 +1507,13 @@ GENERATE_DOCSET = NO
DOCSET_FEEDNAME = "Doxygen generated docs"
# This tag determines the URL of the docset feed. A documentation feed provides
# an umbrella under which multiple documentation sets from a single provider
# (such as a company or product suite) can be grouped.
# This tag requires that the tag GENERATE_DOCSET is set to YES.
DOCSET_FEEDURL =
# This tag specifies a string that should uniquely identify the documentation
# set bundle. This should be a reverse domain-name style string, e.g.
# com.mycompany.MyDocSet. Doxygen will append .docset to the name.
......@@ -1349,8 +1539,12 @@ DOCSET_PUBLISHER_NAME = Publisher
# If the GENERATE_HTMLHELP tag is set to YES then doxygen generates three
# additional HTML index files: index.hhp, index.hhc, and index.hhk. The
# index.hhp is a project file that can be read by Microsoft's HTML Help Workshop
# (see: https://www.microsoft.com/en-us/download/details.aspx?id=21138) on
# Windows.
# on Windows. In the beginning of 2021 Microsoft took the original page, with
# a.o. the download links, offline the HTML help workshop was already many years
# in maintenance mode). You can download the HTML help workshop from the web
# archives at Installation executable (see:
# http://web.archive.org/web/20160201063255/http://download.microsoft.com/downlo
# ad/0/A/9/0A939EF6-E31C-430F-A3DF-DFAE7960D564/htmlhelp.exe).
#
# The HTML Help Workshop contains a compiler that can convert all HTML output
# generated by doxygen into a single compiled HTML file (.chm). Compiled HTML
......@@ -1380,7 +1574,7 @@ CHM_FILE =
HHC_LOCATION =
# The GENERATE_CHI flag controls if a separate .chi index file is generated
# (YES) or that it should be included in the master .chm file (NO).
# (YES) or that it should be included in the main .chm file (NO).
# The default value is: NO.
# This tag requires that the tag GENERATE_HTMLHELP is set to YES.
......@@ -1407,6 +1601,16 @@ BINARY_TOC = NO
TOC_EXPAND = NO
# The SITEMAP_URL tag is used to specify the full URL of the place where the
# generated documentation will be placed on the server by the user during the
# deployment of the documentation. The generated sitemap is called sitemap.xml
# and placed on the directory specified by HTML_OUTPUT. In case no SITEMAP_URL
# is specified no sitemap is generated. For information about the sitemap
# protocol see https://www.sitemaps.org
# This tag requires that the tag GENERATE_HTML is set to YES.
SITEMAP_URL =
# If the GENERATE_QHP tag is set to YES and both QHP_NAMESPACE and
# QHP_VIRTUAL_FOLDER are set, an additional index file will be generated that
# can be used as input for Qt's qhelpgenerator to generate a Qt Compressed Help
......@@ -1425,7 +1629,8 @@ QCH_FILE =
# The QHP_NAMESPACE tag specifies the namespace to use when generating Qt Help
# Project output. For more information please see Qt Help Project / Namespace
# (see: https://doc.qt.io/archives/qt-4.8/qthelpproject.html#namespace).
# (see:
# https://doc.qt.io/archives/qt-4.8/qthelpproject.html#namespace).
# The default value is: org.doxygen.Project.
# This tag requires that the tag GENERATE_QHP is set to YES.
......@@ -1433,8 +1638,8 @@ QHP_NAMESPACE = org.doxygen.Project
# The QHP_VIRTUAL_FOLDER tag specifies the namespace to use when generating Qt
# Help Project output. For more information please see Qt Help Project / Virtual
# Folders (see: https://doc.qt.io/archives/qt-4.8/qthelpproject.html#virtual-
# folders).
# Folders (see:
# https://doc.qt.io/archives/qt-4.8/qthelpproject.html#virtual-folders).
# The default value is: doc.
# This tag requires that the tag GENERATE_QHP is set to YES.
......@@ -1442,16 +1647,16 @@ QHP_VIRTUAL_FOLDER = doc
# If the QHP_CUST_FILTER_NAME tag is set, it specifies the name of a custom
# filter to add. For more information please see Qt Help Project / Custom
# Filters (see: https://doc.qt.io/archives/qt-4.8/qthelpproject.html#custom-
# filters).
# Filters (see:
# https://doc.qt.io/archives/qt-4.8/qthelpproject.html#custom-filters).
# This tag requires that the tag GENERATE_QHP is set to YES.
QHP_CUST_FILTER_NAME =
# The QHP_CUST_FILTER_ATTRS tag specifies the list of the attributes of the
# custom filter to add. For more information please see Qt Help Project / Custom
# Filters (see: https://doc.qt.io/archives/qt-4.8/qthelpproject.html#custom-
# filters).
# Filters (see:
# https://doc.qt.io/archives/qt-4.8/qthelpproject.html#custom-filters).
# This tag requires that the tag GENERATE_QHP is set to YES.
QHP_CUST_FILTER_ATTRS =
......@@ -1463,9 +1668,9 @@ QHP_CUST_FILTER_ATTRS =
QHP_SECT_FILTER_ATTRS =
# The QHG_LOCATION tag can be used to specify the location of Qt's
# qhelpgenerator. If non-empty doxygen will try to run qhelpgenerator on the
# generated .qhp file.
# The QHG_LOCATION tag can be used to specify the location (absolute path
# including file name) of Qt's qhelpgenerator. If non-empty doxygen will try to
# run qhelpgenerator on the generated .qhp file.
# This tag requires that the tag GENERATE_QHP is set to YES.
QHG_LOCATION =
......@@ -1508,16 +1713,28 @@ DISABLE_INDEX = NO
# to work a browser that supports JavaScript, DHTML, CSS and frames is required
# (i.e. any modern browser). Windows users are probably better off using the
# HTML help feature. Via custom style sheets (see HTML_EXTRA_STYLESHEET) one can
# further fine-tune the look of the index. As an example, the default style
# sheet generated by doxygen has an example that shows how to put an image at
# the root of the tree instead of the PROJECT_NAME. Since the tree basically has
# the same information as the tab index, you could consider setting
# DISABLE_INDEX to YES when enabling this option.
# further fine tune the look of the index (see "Fine-tuning the output"). As an
# example, the default style sheet generated by doxygen has an example that
# shows how to put an image at the root of the tree instead of the PROJECT_NAME.
# Since the tree basically has the same information as the tab index, you could
# consider setting DISABLE_INDEX to YES when enabling this option.
# The default value is: NO.
# This tag requires that the tag GENERATE_HTML is set to YES.
GENERATE_TREEVIEW = NO
# When both GENERATE_TREEVIEW and DISABLE_INDEX are set to YES, then the
# FULL_SIDEBAR option determines if the side bar is limited to only the treeview
# area (value NO) or if it should extend to the full height of the window (value
# YES). Setting this to YES gives a layout similar to
# https://docs.readthedocs.io with more room for contents, but less room for the
# project logo, title, and description. If either GENERATE_TREEVIEW or
# DISABLE_INDEX is set to NO, this option has no effect.
# The default value is: NO.
# This tag requires that the tag GENERATE_HTML is set to YES.
FULL_SIDEBAR = NO
# The ENUM_VALUES_PER_LINE tag can be used to set the number of enum values that
# doxygen will group on one line in the generated HTML documentation.
#
......@@ -1542,6 +1759,24 @@ TREEVIEW_WIDTH = 250
EXT_LINKS_IN_WINDOW = NO
# If the OBFUSCATE_EMAILS tag is set to YES, doxygen will obfuscate email
# addresses.
# The default value is: YES.
# This tag requires that the tag GENERATE_HTML is set to YES.
OBFUSCATE_EMAILS = YES
# If the HTML_FORMULA_FORMAT option is set to svg, doxygen will use the pdf2svg
# tool (see https://github.com/dawbarton/pdf2svg) or inkscape (see
# https://inkscape.org) to generate formulas as SVG images instead of PNGs for
# the HTML output. These images will generally look nicer at scaled resolutions.
# Possible values are: png (the default) and svg (looks nicer but requires the
# pdf2svg or inkscape tool).
# The default value is: png.
# This tag requires that the tag GENERATE_HTML is set to YES.
HTML_FORMULA_FORMAT = png
# Use this tag to change the font size of LaTeX formulas included as images in
# the HTML documentation. When you change the font size after a successful
# doxygen run you need to manually remove any form_*.png images from the HTML
......@@ -1551,17 +1786,6 @@ EXT_LINKS_IN_WINDOW = NO
FORMULA_FONTSIZE = 10
# Use the FORMULA_TRANSPARENT tag to determine whether or not the images
# generated for formulas are transparent PNGs. Transparent PNGs are not
# supported properly for IE 6.0, but are supported on all modern browsers.
#
# Note that when changing this option you need to delete any form_*.png files in
# the HTML output directory before the changes have effect.
# The default value is: YES.
# This tag requires that the tag GENERATE_HTML is set to YES.
FORMULA_TRANSPARENT = YES
# The FORMULA_MACROFILE can contain LaTeX \newcommand and \renewcommand commands
# to create new LaTeX commands to be used in formulas as building blocks. See
# the section "Including formulas" for details.
......@@ -1579,11 +1803,29 @@ FORMULA_MACROFILE =
USE_MATHJAX = YES
# With MATHJAX_VERSION it is possible to specify the MathJax version to be used.
# Note that the different versions of MathJax have different requirements with
# regards to the different settings, so it is possible that also other MathJax
# settings have to be changed when switching between the different MathJax
# versions.
# Possible values are: MathJax_2 and MathJax_3.
# The default value is: MathJax_2.
# This tag requires that the tag USE_MATHJAX is set to YES.
MATHJAX_VERSION = MathJax_2
# When MathJax is enabled you can set the default output format to be used for
# the MathJax output. See the MathJax site (see:
# http://docs.mathjax.org/en/latest/output.html) for more details.
# the MathJax output. For more details about the output format see MathJax
# version 2 (see:
# http://docs.mathjax.org/en/v2.7-latest/output.html) and MathJax version 3
# (see:
# http://docs.mathjax.org/en/latest/web/components/output.html).
# Possible values are: HTML-CSS (which is slower, but has the best
# compatibility), NativeMML (i.e. MathML) and SVG.
# compatibility. This is the name for Mathjax version 2, for MathJax version 3
# this will be translated into chtml), NativeMML (i.e. MathML. Only supported
# for NathJax 2. For MathJax version 3 chtml will be used instead.), chtml (This
# is the name for Mathjax version 3, for MathJax version 2 this will be
# translated into HTML-CSS) and SVG.
# The default value is: HTML-CSS.
# This tag requires that the tag USE_MATHJAX is set to YES.
......@@ -1596,22 +1838,29 @@ MATHJAX_FORMAT = HTML-CSS
# MATHJAX_RELPATH should be ../mathjax. The default value points to the MathJax
# Content Delivery Network so you can quickly see the result without installing
# MathJax. However, it is strongly recommended to install a local copy of
# MathJax from https://www.mathjax.org before deployment.
# The default value is: https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/.
# MathJax from https://www.mathjax.org before deployment. The default value is:
# - in case of MathJax version 2: https://cdn.jsdelivr.net/npm/mathjax@2
# - in case of MathJax version 3: https://cdn.jsdelivr.net/npm/mathjax@3
# This tag requires that the tag USE_MATHJAX is set to YES.
MATHJAX_RELPATH = http://cdn.mathjax.org/mathjax/latest
# The MATHJAX_EXTENSIONS tag can be used to specify one or more MathJax
# extension names that should be enabled during MathJax rendering. For example
# for MathJax version 2 (see
# https://docs.mathjax.org/en/v2.7-latest/tex.html#tex-and-latex-extensions):
# MATHJAX_EXTENSIONS = TeX/AMSmath TeX/AMSsymbols
# For example for MathJax version 3 (see
# http://docs.mathjax.org/en/latest/input/tex/extensions/index.html):
# MATHJAX_EXTENSIONS = ams
# This tag requires that the tag USE_MATHJAX is set to YES.
MATHJAX_EXTENSIONS =
# The MATHJAX_CODEFILE tag can be used to specify a file with javascript pieces
# of code that will be used on startup of the MathJax code. See the MathJax site
# (see: http://docs.mathjax.org/en/latest/output.html) for more details. For an
# (see:
# http://docs.mathjax.org/en/v2.7-latest/output.html) for more details. For an
# example see the documentation.
# This tag requires that the tag USE_MATHJAX is set to YES.
......@@ -1658,7 +1907,8 @@ SERVER_BASED_SEARCH = NO
#
# Doxygen ships with an example indexer (doxyindexer) and search engine
# (doxysearch.cgi) which are based on the open source search engine library
# Xapian (see: https://xapian.org/).
# Xapian (see:
# https://xapian.org/).
#
# See the section "External Indexing and Searching" for details.
# The default value is: NO.
......@@ -1671,8 +1921,9 @@ EXTERNAL_SEARCH = NO
#
# Doxygen ships with an example indexer (doxyindexer) and search engine
# (doxysearch.cgi) which are based on the open source search engine library
# Xapian (see: https://xapian.org/). See the section "External Indexing and
# Searching" for details.
# Xapian (see:
# https://xapian.org/). See the section "External Indexing and Searching" for
# details.
# This tag requires that the tag SEARCHENGINE is set to YES.
SEARCHENGINE_URL =
......@@ -1767,7 +2018,7 @@ COMPACT_LATEX = NO
# The default value is: a4.
# This tag requires that the tag GENERATE_LATEX is set to YES.
PAPER_TYPE = a4wide
PAPER_TYPE = a4
# The EXTRA_PACKAGES tag can be used to specify one or more LaTeX package names
# that should be included in the LaTeX output. The package can be specified just
......@@ -1781,29 +2032,31 @@ PAPER_TYPE = a4wide
EXTRA_PACKAGES =
# The LATEX_HEADER tag can be used to specify a personal LaTeX header for the
# generated LaTeX document. The header should contain everything until the first
# chapter. If it is left blank doxygen will generate a standard header. See
# section "Doxygen usage" for information on how to let doxygen write the
# default header to a separate file.
# The LATEX_HEADER tag can be used to specify a user-defined LaTeX header for
# the generated LaTeX document. The header should contain everything until the
# first chapter. If it is left blank doxygen will generate a standard header. It
# is highly recommended to start with a default header using
# doxygen -w latex new_header.tex new_footer.tex new_stylesheet.sty
# and then modify the file new_header.tex. See also section "Doxygen usage" for
# information on how to generate the default header that doxygen normally uses.
#
# Note: Only use a user-defined header if you know what you are doing! The
# following commands have a special meaning inside the header: $title,
# $datetime, $date, $doxygenversion, $projectname, $projectnumber,
# $projectbrief, $projectlogo. Doxygen will replace $title with the empty
# string, for the replacement values of the other commands the user is referred
# to HTML_HEADER.
# Note: Only use a user-defined header if you know what you are doing!
# Note: The header is subject to change so you typically have to regenerate the
# default header when upgrading to a newer version of doxygen. The following
# commands have a special meaning inside the header (and footer): For a
# description of the possible markers and block names see the documentation.
# This tag requires that the tag GENERATE_LATEX is set to YES.
LATEX_HEADER =
# The LATEX_FOOTER tag can be used to specify a personal LaTeX footer for the
# generated LaTeX document. The footer should contain everything after the last
# chapter. If it is left blank doxygen will generate a standard footer. See
# The LATEX_FOOTER tag can be used to specify a user-defined LaTeX footer for
# the generated LaTeX document. The footer should contain everything after the
# last chapter. If it is left blank doxygen will generate a standard footer. See
# LATEX_HEADER for more information on how to generate a default footer and what
# special commands can be used inside the footer.
#
# Note: Only use a user-defined footer if you know what you are doing!
# special commands can be used inside the footer. See also section "Doxygen
# usage" for information on how to generate the default footer that doxygen
# normally uses. Note: Only use a user-defined footer if you know what you are
# doing!
# This tag requires that the tag GENERATE_LATEX is set to YES.
LATEX_FOOTER =
......@@ -1836,18 +2089,26 @@ LATEX_EXTRA_FILES =
PDF_HYPERLINKS = YES
# If the USE_PDFLATEX tag is set to YES, doxygen will use pdflatex to generate
# the PDF file directly from the LaTeX files. Set this option to YES, to get a
# higher quality PDF documentation.
# If the USE_PDFLATEX tag is set to YES, doxygen will use the engine as
# specified with LATEX_CMD_NAME to generate the PDF file directly from the LaTeX
# files. Set this option to YES, to get a higher quality PDF documentation.
#
# See also section LATEX_CMD_NAME for selecting the engine.
# The default value is: YES.
# This tag requires that the tag GENERATE_LATEX is set to YES.
USE_PDFLATEX = YES
# If the LATEX_BATCHMODE tag is set to YES, doxygen will add the \batchmode
# command to the generated LaTeX files. This will instruct LaTeX to keep running
# if errors occur, instead of asking the user for help. This option is also used
# when generating formulas in HTML.
# The LATEX_BATCHMODE tag signals the behavior of LaTeX in case of an error.
# Possible values are: NO same as ERROR_STOP, YES same as BATCH, BATCH In batch
# mode nothing is printed on the terminal, errors are scrolled as if <return> is
# hit at every error; missing files that TeX tries to input or request from
# keyboard input (\read on a not open input stream) cause the job to abort,
# NON_STOP In nonstop mode the diagnostic message will appear on the terminal,
# but there is no possibility of user interaction just like in batch mode,
# SCROLL In scroll mode, TeX will stop only for missing files to input or if
# keyboard input is necessary and ERROR_STOP In errorstop mode, TeX will stop at
# each error, asking for user intervention.
# The default value is: NO.
# This tag requires that the tag GENERATE_LATEX is set to YES.
......@@ -1860,16 +2121,6 @@ LATEX_BATCHMODE = NO
LATEX_HIDE_INDICES = NO
# If the LATEX_SOURCE_CODE tag is set to YES then doxygen will include source
# code with syntax highlighting in the LaTeX output.
#
# Note that which sources are shown also depends on other settings such as
# SOURCE_BROWSER.
# The default value is: NO.
# This tag requires that the tag GENERATE_LATEX is set to YES.
LATEX_SOURCE_CODE = NO
# The LATEX_BIB_STYLE tag can be used to specify the style to use for the
# bibliography, e.g. plainnat, or ieeetr. See
# https://en.wikipedia.org/wiki/BibTeX and \cite for more info.
......@@ -1878,14 +2129,6 @@ LATEX_SOURCE_CODE = NO
LATEX_BIB_STYLE = plain
# If the LATEX_TIMESTAMP tag is set to YES then the footer of each generated
# page will contain the date and time when the page was generated. Setting this
# to NO can help when comparing the output of multiple runs.
# The default value is: NO.
# This tag requires that the tag GENERATE_LATEX is set to YES.
LATEX_TIMESTAMP = NO
# The LATEX_EMOJI_DIRECTORY tag is used to specify the (relative or absolute)
# path from which the emoji images will be read. If a relative path is entered,
# it will be relative to the LATEX_OUTPUT directory. If left blank the
......@@ -1950,16 +2193,6 @@ RTF_STYLESHEET_FILE =
RTF_EXTENSIONS_FILE =
# If the RTF_SOURCE_CODE tag is set to YES then doxygen will include source code
# with syntax highlighting in the RTF output.
#
# Note that which sources are shown also depends on other settings such as
# SOURCE_BROWSER.
# The default value is: NO.
# This tag requires that the tag GENERATE_RTF is set to YES.
RTF_SOURCE_CODE = NO
#---------------------------------------------------------------------------
# Configuration options related to the man page output
#---------------------------------------------------------------------------
......@@ -2056,27 +2289,44 @@ GENERATE_DOCBOOK = NO
DOCBOOK_OUTPUT = docbook
# If the DOCBOOK_PROGRAMLISTING tag is set to YES, doxygen will include the
# program listings (including syntax highlighting and cross-referencing
# information) to the DOCBOOK output. Note that enabling this will significantly
# increase the size of the DOCBOOK output.
# The default value is: NO.
# This tag requires that the tag GENERATE_DOCBOOK is set to YES.
DOCBOOK_PROGRAMLISTING = NO
#---------------------------------------------------------------------------
# Configuration options for the AutoGen Definitions output
#---------------------------------------------------------------------------
# If the GENERATE_AUTOGEN_DEF tag is set to YES, doxygen will generate an
# AutoGen Definitions (see http://autogen.sourceforge.net/) file that captures
# AutoGen Definitions (see https://autogen.sourceforge.net/) file that captures
# the structure of the code including all documentation. Note that this feature
# is still experimental and incomplete at the moment.
# The default value is: NO.
GENERATE_AUTOGEN_DEF = NO
#---------------------------------------------------------------------------
# Configuration options related to Sqlite3 output
#---------------------------------------------------------------------------
# If the GENERATE_SQLITE3 tag is set to YES doxygen will generate a Sqlite3
# database with symbols found by doxygen stored in tables.
# The default value is: NO.
GENERATE_SQLITE3 = NO
# The SQLITE3_OUTPUT tag is used to specify where the Sqlite3 database will be
# put. If a relative path is entered the value of OUTPUT_DIRECTORY will be put
# in front of it.
# The default directory is: sqlite3.
# This tag requires that the tag GENERATE_SQLITE3 is set to YES.
SQLITE3_OUTPUT = sqlite3
# The SQLITE3_OVERWRITE_DB tag is set to YES, the existing doxygen_sqlite3.db
# database file will be recreated with each doxygen run. If set to NO, doxygen
# will warn if an a database file is already found and not modify it.
# The default value is: YES.
# This tag requires that the tag GENERATE_SQLITE3 is set to YES.
SQLITE3_RECREATE_DB = YES
#---------------------------------------------------------------------------
# Configuration options related to the Perl module output
#---------------------------------------------------------------------------
......@@ -2151,7 +2401,8 @@ SEARCH_INCLUDES = YES
# The INCLUDE_PATH tag can be used to specify one or more directories that
# contain include files that are not input files but should be processed by the
# preprocessor.
# preprocessor. Note that the INCLUDE_PATH is not recursive, so the setting of
# RECURSIVE has no effect here.
# This tag requires that the tag SEARCH_INCLUDES is set to YES.
INCLUDE_PATH = @top_srcdir@/src
......@@ -2172,7 +2423,7 @@ INCLUDE_FILE_PATTERNS =
# recursively expanded use the := operator instead of the = operator.
# This tag requires that the tag ENABLE_PREPROCESSING is set to YES.
PREDEFINED = "__attribute__(x)= " \
PREDEFINED = "__attribute__(x)=" \
HAVE_HDF5 \
HAVE_FFTW \
WITH_MPI \
......@@ -2223,15 +2474,15 @@ TAGFILES =
GENERATE_TAGFILE =
# If the ALLEXTERNALS tag is set to YES, all external class will be listed in
# the class index. If set to NO, only the inherited external classes will be
# listed.
# If the ALLEXTERNALS tag is set to YES, all external classes and namespaces
# will be listed in the class and namespace index. If set to NO, only the
# inherited external classes will be listed.
# The default value is: NO.
ALLEXTERNALS = NO
# If the EXTERNAL_GROUPS tag is set to YES, all external groups will be listed
# in the modules index. If set to NO, only the current project's groups will be
# in the topic index. If set to NO, only the current project's groups will be
# listed.
# The default value is: YES.
......@@ -2245,18 +2496,9 @@ EXTERNAL_GROUPS = YES
EXTERNAL_PAGES = YES
#---------------------------------------------------------------------------
# Configuration options related to the dot tool
# Configuration options related to diagram generator tools
#---------------------------------------------------------------------------
# If the CLASS_DIAGRAMS tag is set to YES, doxygen will generate a class diagram
# (in HTML and LaTeX) for classes with base or super classes. Setting the tag to
# NO turns the diagrams off. Note that this option also works with HAVE_DOT
# disabled, but it is recommended to install and use dot, since it yields more
# powerful graphs.
# The default value is: YES.
CLASS_DIAGRAMS = NO
# You can include diagrams made with dia in doxygen documentation. Doxygen will
# then run dia to produce the diagram and insert it in the documentation. The
# DIA_PATH tag allows you to specify the directory where the dia binary resides.
......@@ -2272,7 +2514,7 @@ HIDE_UNDOC_RELATIONS = YES
# If you set the HAVE_DOT tag to YES then doxygen will assume the dot tool is
# available from the path. This tool is part of Graphviz (see:
# http://www.graphviz.org/), a graph visualization toolkit from AT&T and Lucent
# https://www.graphviz.org/), a graph visualization toolkit from AT&T and Lucent
# Bell Labs. The other options in this section have no effect if this option is
# set to NO
# The default value is: YES.
......@@ -2289,49 +2531,73 @@ HAVE_DOT = NO
DOT_NUM_THREADS = 0
# When you want a differently looking font in the dot files that doxygen
# generates you can specify the font name using DOT_FONTNAME. You need to make
# sure dot is able to find the font, which can be done by putting it in a
# standard location or by setting the DOTFONTPATH environment variable or by
# setting DOT_FONTPATH to the directory containing the font.
# The default value is: Helvetica.
# DOT_COMMON_ATTR is common attributes for nodes, edges and labels of
# subgraphs. When you want a differently looking font in the dot files that
# doxygen generates you can specify fontname, fontcolor and fontsize attributes.
# For details please see <a href=https://graphviz.org/doc/info/attrs.html>Node,
# Edge and Graph Attributes specification</a> You need to make sure dot is able
# to find the font, which can be done by putting it in a standard location or by
# setting the DOTFONTPATH environment variable or by setting DOT_FONTPATH to the
# directory containing the font. Default graphviz fontsize is 14.
# The default value is: fontname=Helvetica,fontsize=10.
# This tag requires that the tag HAVE_DOT is set to YES.
DOT_COMMON_ATTR = "fontname=Helvetica,fontsize=10"
# DOT_EDGE_ATTR is concatenated with DOT_COMMON_ATTR. For elegant style you can
# add 'arrowhead=open, arrowtail=open, arrowsize=0.5'. <a
# href=https://graphviz.org/doc/info/arrows.html>Complete documentation about
# arrows shapes.</a>
# The default value is: labelfontname=Helvetica,labelfontsize=10.
# This tag requires that the tag HAVE_DOT is set to YES.
DOT_FONTNAME =
DOT_EDGE_ATTR = "labelfontname=Helvetica,labelfontsize=10"
# The DOT_FONTSIZE tag can be used to set the size (in points) of the font of
# dot graphs.
# Minimum value: 4, maximum value: 24, default value: 10.
# DOT_NODE_ATTR is concatenated with DOT_COMMON_ATTR. For view without boxes
# around nodes set 'shape=plain' or 'shape=plaintext' <a
# href=https://www.graphviz.org/doc/info/shapes.html>Shapes specification</a>
# The default value is: shape=box,height=0.2,width=0.4.
# This tag requires that the tag HAVE_DOT is set to YES.
DOT_FONTSIZE = 10
DOT_NODE_ATTR = "shape=box,height=0.2,width=0.4"
# By default doxygen will tell dot to use the default font as specified with
# DOT_FONTNAME. If you specify a different font using DOT_FONTNAME you can set
# the path where dot can find it using this tag.
# You can set the path where dot can find font specified with fontname in
# DOT_COMMON_ATTR and others dot attributes.
# This tag requires that the tag HAVE_DOT is set to YES.
DOT_FONTPATH =
# If the CLASS_GRAPH tag is set to YES then doxygen will generate a graph for
# each documented class showing the direct and indirect inheritance relations.
# Setting this tag to YES will force the CLASS_DIAGRAMS tag to NO.
# If the CLASS_GRAPH tag is set to YES or GRAPH or BUILTIN then doxygen will
# generate a graph for each documented class showing the direct and indirect
# inheritance relations. In case the CLASS_GRAPH tag is set to YES or GRAPH and
# HAVE_DOT is enabled as well, then dot will be used to draw the graph. In case
# the CLASS_GRAPH tag is set to YES and HAVE_DOT is disabled or if the
# CLASS_GRAPH tag is set to BUILTIN, then the built-in generator will be used.
# If the CLASS_GRAPH tag is set to TEXT the direct and indirect inheritance
# relations will be shown as texts / links.
# Possible values are: NO, YES, TEXT, GRAPH and BUILTIN.
# The default value is: YES.
# This tag requires that the tag HAVE_DOT is set to YES.
CLASS_GRAPH = YES
CLASS_GRAPH = TEXT
# If the COLLABORATION_GRAPH tag is set to YES then doxygen will generate a
# graph for each documented class showing the direct and indirect implementation
# dependencies (inheritance, containment, and class references variables) of the
# class with other documented classes.
# class with other documented classes. Explicit enabling a collaboration graph,
# when COLLABORATION_GRAPH is set to NO, can be accomplished by means of the
# command \collaborationgraph. Disabling a collaboration graph can be
# accomplished by means of the command \hidecollaborationgraph.
# The default value is: YES.
# This tag requires that the tag HAVE_DOT is set to YES.
COLLABORATION_GRAPH = YES
# If the GROUP_GRAPHS tag is set to YES then doxygen will generate a graph for
# groups, showing the direct groups dependencies.
# groups, showing the direct groups dependencies. Explicit enabling a group
# dependency graph, when GROUP_GRAPHS is set to NO, can be accomplished by means
# of the command \groupgraph. Disabling a directory graph can be accomplished by
# means of the command \hidegroupgraph. See also the chapter Grouping in the
# manual.
# The default value is: YES.
# This tag requires that the tag HAVE_DOT is set to YES.
......@@ -2354,10 +2620,32 @@ UML_LOOK = NO
# but if the number exceeds 15, the total amount of fields shown is limited to
# 10.
# Minimum value: 0, maximum value: 100, default value: 10.
# This tag requires that the tag HAVE_DOT is set to YES.
# This tag requires that the tag UML_LOOK is set to YES.
UML_LIMIT_NUM_FIELDS = 10
# If the DOT_UML_DETAILS tag is set to NO, doxygen will show attributes and
# methods without types and arguments in the UML graphs. If the DOT_UML_DETAILS
# tag is set to YES, doxygen will add type and arguments for attributes and
# methods in the UML graphs. If the DOT_UML_DETAILS tag is set to NONE, doxygen
# will not generate fields with class member information in the UML graphs. The
# class diagrams will look similar to the default class diagrams but using UML
# notation for the relationships.
# Possible values are: NO, YES and NONE.
# The default value is: NO.
# This tag requires that the tag UML_LOOK is set to YES.
DOT_UML_DETAILS = NO
# The DOT_WRAP_THRESHOLD tag can be used to set the maximum number of characters
# to display on a single line. If the actual line length exceeds this threshold
# significantly it will wrapped across multiple lines. Some heuristics are apply
# to avoid ugly line breaks.
# Minimum value: 0, maximum value: 1000, default value: 17.
# This tag requires that the tag HAVE_DOT is set to YES.
DOT_WRAP_THRESHOLD = 17
# If the TEMPLATE_RELATIONS tag is set to YES then the inheritance and
# collaboration graphs will show the relations between templates and their
# instances.
......@@ -2369,7 +2657,9 @@ TEMPLATE_RELATIONS = NO
# If the INCLUDE_GRAPH, ENABLE_PREPROCESSING and SEARCH_INCLUDES tags are set to
# YES then doxygen will generate a graph for each documented file showing the
# direct and indirect include dependencies of the file with other documented
# files.
# files. Explicit enabling an include graph, when INCLUDE_GRAPH is is set to NO,
# can be accomplished by means of the command \includegraph. Disabling an
# include graph can be accomplished by means of the command \hideincludegraph.
# The default value is: YES.
# This tag requires that the tag HAVE_DOT is set to YES.
......@@ -2378,7 +2668,10 @@ INCLUDE_GRAPH = YES
# If the INCLUDED_BY_GRAPH, ENABLE_PREPROCESSING and SEARCH_INCLUDES tags are
# set to YES then doxygen will generate a graph for each documented file showing
# the direct and indirect include dependencies of the file with other documented
# files.
# files. Explicit enabling an included by graph, when INCLUDED_BY_GRAPH is set
# to NO, can be accomplished by means of the command \includedbygraph. Disabling
# an included by graph can be accomplished by means of the command
# \hideincludedbygraph.
# The default value is: YES.
# This tag requires that the tag HAVE_DOT is set to YES.
......@@ -2418,23 +2711,32 @@ GRAPHICAL_HIERARCHY = YES
# If the DIRECTORY_GRAPH tag is set to YES then doxygen will show the
# dependencies a directory has on other directories in a graphical way. The
# dependency relations are determined by the #include relations between the
# files in the directories.
# files in the directories. Explicit enabling a directory graph, when
# DIRECTORY_GRAPH is set to NO, can be accomplished by means of the command
# \directorygraph. Disabling a directory graph can be accomplished by means of
# the command \hidedirectorygraph.
# The default value is: YES.
# This tag requires that the tag HAVE_DOT is set to YES.
DIRECTORY_GRAPH = YES
# The DIR_GRAPH_MAX_DEPTH tag can be used to limit the maximum number of levels
# of child directories generated in directory dependency graphs by dot.
# Minimum value: 1, maximum value: 25, default value: 1.
# This tag requires that the tag DIRECTORY_GRAPH is set to YES.
DIR_GRAPH_MAX_DEPTH = 1
# The DOT_IMAGE_FORMAT tag can be used to set the image format of the images
# generated by dot. For an explanation of the image formats see the section
# output formats in the documentation of the dot tool (Graphviz (see:
# http://www.graphviz.org/)).
# https://www.graphviz.org/)).
# Note: If you choose svg you need to set HTML_FILE_EXTENSION to xhtml in order
# to make the SVG files visible in IE 9+ (other browsers do not have this
# requirement).
# Possible values are: png, png:cairo, png:cairo:cairo, png:cairo:gd, png:gd,
# png:gd:gd, jpg, jpg:cairo, jpg:cairo:gd, jpg:gd, jpg:gd:gd, gif, gif:cairo,
# gif:cairo:gd, gif:gd, gif:gd:gd, svg, png:gd, png:gd:gd, png:cairo,
# png:cairo:gd, png:cairo:cairo, png:cairo:gdiplus, png:gdiplus and
# Possible values are: png, jpg, jpg:cairo, jpg:cairo:gd, jpg:gd, jpg:gd:gd,
# gif, gif:cairo, gif:cairo:gd, gif:gd, gif:gd:gd, svg, png:gd, png:gd:gd,
# png:cairo, png:cairo:gd, png:cairo:cairo, png:cairo:gdiplus, png:gdiplus and
# png:gdiplus:gdiplus.
# The default value is: png.
# This tag requires that the tag HAVE_DOT is set to YES.
......@@ -2466,11 +2768,12 @@ DOT_PATH =
DOTFILE_DIRS =
# The MSCFILE_DIRS tag can be used to specify one or more directories that
# contain msc files that are included in the documentation (see the \mscfile
# command).
# You can include diagrams made with dia in doxygen documentation. Doxygen will
# then run dia to produce the diagram and insert it in the documentation. The
# DIA_PATH tag allows you to specify the directory where the dia binary resides.
# If left empty dia is assumed to be found in the default search path.
MSCFILE_DIRS =
DIA_PATH =
# The DIAFILE_DIRS tag can be used to specify one or more directories that
# contain dia files that are included in the documentation (see the \diafile
......@@ -2479,10 +2782,10 @@ MSCFILE_DIRS =
DIAFILE_DIRS =
# When using plantuml, the PLANTUML_JAR_PATH tag should be used to specify the
# path where java can find the plantuml.jar file. If left blank, it is assumed
# PlantUML is not used or called during a preprocessing step. Doxygen will
# generate a warning when it encounters a \startuml command in this case and
# will not generate output for the diagram.
# path where java can find the plantuml.jar file or to the filename of jar file
# to be used. If left blank, it is assumed PlantUML is not used or called during
# a preprocessing step. Doxygen will generate a warning when it encounters a
# \startuml command in this case and will not generate output for the diagram.
PLANTUML_JAR_PATH =
......@@ -2520,18 +2823,6 @@ DOT_GRAPH_MAX_NODES = 50
MAX_DOT_GRAPH_DEPTH = 0
# Set the DOT_TRANSPARENT tag to YES to generate images with a transparent
# background. This is disabled by default, because dot on Windows does not seem
# to support this out of the box.
#
# Warning: Depending on the platform used, enabling this option may lead to
# badly anti-aliased labels on the edges of a graph (i.e. they become hard to
# read).
# The default value is: NO.
# This tag requires that the tag HAVE_DOT is set to YES.
DOT_TRANSPARENT = NO
# Set the DOT_MULTI_TARGETS tag to YES to allow dot to generate multiple output
# files in one run (i.e. multiple -o and -T options on the command line). This
# makes dot run faster, but since only newer versions of dot (>1.8.10) support
......@@ -2544,14 +2835,34 @@ DOT_MULTI_TARGETS = YES
# If the GENERATE_LEGEND tag is set to YES doxygen will generate a legend page
# explaining the meaning of the various boxes and arrows in the dot generated
# graphs.
# Note: This tag requires that UML_LOOK isn't set, i.e. the doxygen internal
# graphical representation for inheritance and collaboration diagrams is used.
# The default value is: YES.
# This tag requires that the tag HAVE_DOT is set to YES.
GENERATE_LEGEND = YES
# If the DOT_CLEANUP tag is set to YES, doxygen will remove the intermediate dot
# If the DOT_CLEANUP tag is set to YES, doxygen will remove the intermediate
# files that are used to generate the various graphs.
#
# Note: This setting is not only used for dot files but also for msc temporary
# files.
# The default value is: YES.
# This tag requires that the tag HAVE_DOT is set to YES.
DOT_CLEANUP = YES
# You can define message sequence charts within doxygen comments using the \msc
# command. If the MSCGEN_TOOL tag is left empty (the default), then doxygen will
# use a built-in version of mscgen tool to produce the charts. Alternatively,
# the MSCGEN_TOOL tag can also specify the name an external tool. For instance,
# specifying prog as the value, doxygen will call the tool as prog -T
# <outfile_format> -o <outputfile> <inputfile>. The external tool should support
# output file formats "png", "eps", "svg", and "ismap".
MSCGEN_TOOL =
# The MSCFILE_DIRS tag can be used to specify one or more directories that
# contain msc files that are included in the documentation (see the \mscfile
# command).
MSCFILE_DIRS =
doc/RTD/source/AnalysisTools/index.rst
View file @ 853c5044
......@@ -176,7 +176,7 @@ A short summary of the scripts in ``tools/task_plots/``:
whole step and per thread and the minimum and maximum times spent per task type.
- ``iplot_tasks.py``:
An interactive task plot, showing what thread was doing what task and for
how long for a step. **Needs python2 and the tkinter module**.
how long for a step. **Needs the tkinter module**.
- ``plot_tasks.py``:
Creates a task plot image, showing what thread was doing what task and for how long.
- ``plot_threadpool.py``:
......
doc/RTD/source/CitingSWIFT/index.rst
View file @ 853c5044
......@@ -52,18 +52,19 @@ following bibtex citation block:
@ARTICLE{2023arXiv230513380S,
author = {{Schaller}, Matthieu and others},
title = "{Swift: A modern highly-parallel gravity and smoothed particle hydrodynamics solver for astrophysical and cosmological applications}",
journal = {arXiv e-prints},
keywords = {Astrophysics - Instrumentation and Methods for Astrophysics, Astrophysics - Cosmology and Nongalactic Astrophysics, Astrophysics - Earth and Planetary Astrophysics, Astrophysics - Astrophysics of Galaxies, Computer Science - Distributed, Parallel, and Cluster Computing},
year = 2023,
title = "{SWIFT: A modern highly-parallel gravity and smoothed particle hydrodynamics solver for astrophysical and cosmological applications}",
journal = {\mnras},
keywords = {software: simulations, methods: numerical, software: public release, Astrophysics - Instrumentation and Methods for Astrophysics, Astrophysics - Cosmology and Nongalactic Astrophysics, Astrophysics - Earth and Planetary Astrophysics, Astrophysics - Astrophysics of Galaxies, Computer Science - Distributed, Parallel, and Cluster Computing},
year = 2024,
month = may,
eid = {arXiv:2305.13380},
pages = {arXiv:2305.13380},
doi = {10.48550/arXiv.2305.13380},
volume = {530},
number = {2},
pages = {2378-2419},
doi = {10.1093/mnras/stae922},
archivePrefix = {arXiv},
eprint = {2305.13380},
primaryClass = {astro-ph.IM},
adsurl = {https://ui.adsabs.harvard.edu/abs/2023arXiv230513380S},
adsurl = {https://ui.adsabs.harvard.edu/abs/2024MNRAS.530.2378S},
adsnote = {Provided by the SAO/NASA Astrophysics Data System}
}
......@@ -101,5 +102,4 @@ code. This corresponds to the following bibtex citation block:
When using models or parts of the code whose details were introduced in other
papers, we kindly ask that the relevant work is properly acknowledge and
cited. This includes the :ref:`subgrid`, the :ref:`planetary` extensions, the
hydrodynamics and radiative transfer implementations, or the particle-based
:ref:`neutrinos`.
:ref:`hydro` and :ref:`rt`, or the particle-based :ref:`neutrinos`.
doc/RTD/source/ExternalPotentials/index.rst
View file @ 853c5044
......@@ -374,7 +374,7 @@ The parameters of the model are:
Mdisk_Msun: 6.8e10 # Mass of the disk (in M_sun)
Rdisk_kpc: 3.0 # Effective radius of the disk (in kpc)
Zdisk_kpc: 0.280 # Scale-height of the disk (in kpc)
amplitude: 1.0 # Amplitude of the bulge
amplitude_Msun_per_kpc3: 1.0e10 # Amplitude of the bulge (in M_sun/kpc^3)
r_1_kpc: 1.0 # Reference radius for amplitude of the bulge (in kpc)
alpha: 1.8 # Exponent of the power law of the bulge
r_c_kpc: 1.9 # Cut-off radius of the bulge (in kpc)
......@@ -383,6 +383,65 @@ The parameters of the model are:
Note that the default value of the "Hubble constant" here seems odd. As it
enters multiplicatively with the :math:`f_1` term, the absolute normalisation is
actually not important.
Dynamical friction
..................
This potential can be supplemented by a dynamical friction force, following the Chandrasekhar’s dynamical friction formula,
where the velocity distribution function is assumed to be Maxwellian (Binney & Tremaine 2008, eq. 8.7):
:math:`\frac{\rm{d} \vec{v}_{\rm M}}{\rm{d} t}=-\frac{4\pi G^2M_{\rm sat}\rho \ln \Lambda}{v^3_{\rm{M}}} \left[ \rm{erf}(X) - \frac{2 X}{\sqrt\pi} e^{-X^2} \right] \vec{v}_{\rm M}`,
with:
:math:`X = \frac{v_{\rm{M}}}{\sqrt{2} \sigma}`, :math:`\sigma` being the radius-dependent velocity dispersion of the galaxy.
This latter is computed using the Jeans equations, assuming a spherical component. It is provided by a polynomial fit of order 16.
The velocity dispersion is floored to :math:`\sigma_{\rm min}`, a free parameter.
:math:`\ln \Lambda` is the Coulomb parameter.
:math:`M_{\rm sat}` is the mass of the in-falling satellite on which the dynamical friction is supposed to act.
To prevent very high values of the dynamical friction that can occurs at the center of the model, the acceleration is multiplied by:
:math:`\rm{max} \left(0, \rm{erf}\left( 2\, \frac{ r-r_{\rm{core}} }{r_{\rm{core}}} \right) \right)`
This can also mimic the decrease of the dynamical friction due to a core.
The additional parameters for the dynamical friction are:
.. code:: YAML
with_dynamical_friction: 0 # Are we running with dynamical friction ? 0 -> no, 1 -> yes
df_lnLambda: 5.0 # Coulomb logarithm
df_sigma_floor_km_p_s : 10.0 # Minimum velocity dispersion for the velocity dispersion model
df_satellite_mass_in_Msun : 1.0e10 # Satellite mass in solar mass
df_core_radius_in_kpc: 10 # Radius below which the dynamical friction vanishes.
df_polyfit_coeffs00: -2.96536595e-31 # Polynomial fit coefficient for the velocity dispersion model (order 16)
df_polyfit_coeffs01: 8.88944631e-28 # Polynomial fit coefficient for the velocity dispersion model (order 15)
df_polyfit_coeffs02: -1.18280578e-24 # Polynomial fit coefficient for the velocity dispersion model (order 14)
df_polyfit_coeffs03: 9.29479457e-22 # Polynomial fit coefficient for the velocity dispersion model (order 13)
df_polyfit_coeffs04: -4.82805265e-19 # Polynomial fit coefficient for the velocity dispersion model (order 12)
df_polyfit_coeffs05: 1.75460211e-16 # Polynomial fit coefficient for the velocity dispersion model (order 11)
df_polyfit_coeffs06: -4.59976540e-14 # Polynomial fit coefficient for the velocity dispersion model (order 10)
df_polyfit_coeffs07: 8.83166045e-12 # Polynomial fit coefficient for the velocity dispersion model (order 9)
df_polyfit_coeffs08: -1.24747700e-09 # Polynomial fit coefficient for the velocity dispersion model (order 8)
df_polyfit_coeffs09: 1.29060404e-07 # Polynomial fit coefficient for the velocity dispersion model (order 7)
df_polyfit_coeffs10: -9.65315026e-06 # Polynomial fit coefficient for the velocity dispersion model (order 6)
df_polyfit_coeffs11: 5.10187806e-04 # Polynomial fit coefficient for the velocity dispersion model (order 5)
df_polyfit_coeffs12: -1.83800281e-02 # Polynomial fit coefficient for the velocity dispersion model (order 4)
df_polyfit_coeffs13: 4.26501444e-01 # Polynomial fit coefficient for the velocity dispersion model (order 3)
df_polyfit_coeffs14: -5.78038064e+00 # Polynomial fit coefficient for the velocity dispersion model (order 2)
df_polyfit_coeffs15: 3.57956721e+01 # Polynomial fit coefficient for the velocity dispersion model (order 1)
df_polyfit_coeffs16: 1.85478908e+02 # Polynomial fit coefficient for the velocity dispersion model (order 0)
df_timestep_mult : 0.1 # Dimensionless pre-factor for the time-step condition for the dynamical friction force
How to implement your own potential
-----------------------------------
......
doc/RTD/source/FriendsOfFriends/parameter_description.rst
View file @ 853c5044
......@@ -27,7 +27,7 @@ whether or not the given particle type is in this category. Types not present
in either category are ignored entirely.
The second important parameter is the minimal size of groups to retain in
the catalogues. This is given in terms of number of particles (of all types)
the catalogues. This is given in terms of number of *linking* particles
via the parameter ``min_group_size``. When analysing simulations, to
identify haloes, the common practice is to set this to ``32`` in order to
not plague the catalogue with too many small, likely unbound, structures.
......
doc/RTD/source/FriendsOfFriends/stand_alone_fof.rst
View file @ 853c5044
......@@ -35,6 +35,9 @@ additional field for each particle. This contains the ``GroupID`` of
each particle and can be used to find all the particles in a given
halo and to link them to the information stored in the catalogue.
The particle fields written to the snapshot can be modified using the
:ref:`Output_selection_label` options.
.. warning::
Note that since not all particle properties are read in stand-alone
......
doc/RTD/source/GettingStarted/compiling_code.rst
View file @ 853c5044
......@@ -31,10 +31,10 @@ 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
Version 1.10.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*
reading snapshots. We recommend using HDF5 >= 1.12.x as this is *vastly superior*
in parallel.
HDF5 is widely available through system package managers.
......@@ -105,6 +105,16 @@ GRACKLE
GRACKLE cooling is implemented in SWIFT. If you wish to take advantage of it, you
will need it installed. It can be found `here <https://github.com/grackle-project/grackle>`_.
.. warning::
(State 2023) Grackle is experiencing current development, and the API is subject
to changes in the future. For convenience, a frozen version is hosted as a fork
on github here: https://github.com/mladenivkovic/grackle-swift .
The version available there will be tried and tested and ensured to work with
SWIFT.
Additionally, that repository hosts files necessary to install that specific
version of grackle with spack.
HEALPix C library
~~~~~~~~~~~~~~~~~~~
......
doc/RTD/source/HydroSchemes/adaptive_softening.rst 0 → 100644
View file @ 853c5044
.. Adding Hydro Schemes
Matthieu Schaller, 23/02/2024
.. _adaptive_softening:
Adaptive Softening
==================
.. toctree::
:maxdepth: 2
:hidden:
:caption: Contents:
We implement the method of Price & Monaghan (2007). This add correction terms to
the SPH equations of motions to account for the change in energy and momentum
created by the change in gravitationl potential generated by the change of
softening. The softening length is tied to the gas' smoothing length and is
thus adapting with the changes in density field. To use adaptive softening, use
.. code-block:: bash
./configure --with-adaptive-softening=yes
The adaptive softening scheme is implemented for all the SPH schemes above but
only for the Wendland-C2 kernel as it is the kernel used for the gravity
softening throughout the code.
doc/RTD/source/HydroSchemes/index.rst
View file @ 853c5044
......@@ -2,7 +2,7 @@
Josh Borrow 4th April 2018
.. _hydro:
Hydrodynamics Schemes
=====================
......@@ -39,6 +39,8 @@ In case the case of a 2 loop scheme, SWIFT removes the gradient loop and the ext
sphenix_sph
gasoline_sph
phantom_sph
remix_sph
adaptive_softening
gizmo
shadowswift
adding_your_own
doc/RTD/source/HydroSchemes/remix_sph.rst 0 → 100644
View file @ 853c5044
.. REMIX SPH
Thomas Sandnes, 13th May 2025
.. _remix_sph:
REMIX SPH
==============================================
.. toctree::
:maxdepth: 2
:hidden:
:caption: Contents:
REMIX is an SPH scheme designed to alleviate effects that typically suppress
mixing and instability growth at density discontinuities in SPH simulations
(Sandnes et al. 2025). REMIX addresses this problem by directly targeting sources
of kernel smoothing error and discretisation error, resulting in a generalised,
material-independent formulation that improves the treatment both of
discontinuities within a single material, for example in an ideal gas, and of
interfaces between dissimilar materials. The scheme combines:
+ An evolved density estimate to avoid the kernel smoothing error in the
standard SPH integral density estimate;
+ Thermodynamically consistent, conservative equations of motion, with
free functions chosen to limit zeroth-order error;
+ Linear-order reproducing kernels with grad-h terms and a vacuum interface
treatment;
+ A "kernel normalising term" to avoid potential accumulation of error in
the evolved density estimate, such that densities are ensured to remain
representative of the distribution of particle masses in the simulation volume;
+ Advanced artificial viscosity and diffusion schemes with linear reconstruction
of quantities to particle midpoints, and a set of novel improvements to
effectively switch between treatments for shock-capturing under compression and
noise-smoothing in shearing regions.
To configure with this scheme, use
.. code-block:: bash
./configure --with-hydro=remix --with-equation-of-state=planetary
This scheme allows multiple materials,
meaning that different SPH particles can be assigned different
`equations of state <equations_of_state.html>`_ (EoS).
Every SPH particle then requires and carries the additional ``MaterialID`` flag
from the initial conditions file. This flag indicates the particle's material
and which EoS it should use. Note that configuring with
``--with-equation-of-state=planetary`` is required for this scheme, although
for simulations that use a single, ideal gas EoS, setting all MaterialIDs to
``0`` and including
.. code-block:: yaml
EoS:
planetary_use_idg_def: 1
in the parameter file are the only EoS-related additions needed compared with
other non-Planetary hydro schemes. Note also that since densities are evolved in
time, initial particle densities are required in initial conditions.
We additionally recommend configuring with ``--with-kernel=wendland-C2`` and with
.. code-block:: yaml
SPH:
resolution_eta: 1.487
in the parameter file for improved hydrodynamic behaviour and since this is the
configuration used for the validation simulations of Sandnes et al. (2025).
The current implementation of the REMIX hydro scheme has been validated for
planetary applications and various hydrodynamic test cases, and does not include
all necessary functionality for e.g. cosmological simulations.
Default parameters used in the artificial viscosity and diffusion schemes and the
normalising term (see Sandnes et al. 2025) are:
.. code-block:: c
#define const_remix_visc_alpha 1.5f
#define const_remix_visc_beta 3.f
#define const_remix_visc_epsilon 0.1f
#define const_remix_visc_a 2.0f / 3.0f
#define const_remix_visc_b 1.0f / 3.0f
#define const_remix_difn_a_u 0.05f
#define const_remix_difn_b_u 0.95f
#define const_remix_difn_a_rho 0.05f
#define const_remix_difn_b_rho 0.95f
#define const_remix_norm_alpha 1.0f
#define const_remix_slope_limiter_exp_denom 0.04f
These can be changed in ``src/hydro/REMIX/hydro_parameters.h``.
doc/RTD/source/HydroSchemes/shadowswift.rst 0 → 100644
View file @ 853c5044
.. ShadowSWIFT (Moving mesh hydrodynamics)
Yolan Uyttenhove September 2023
ShadowSWIFT (moving mesh hydrodynamics)
=======================================
.. warning::
The moving mesh hydrodynamics solver is currently in the process of being merged into master and will **NOT**
work on the master branch. To use it, compile the code using the ``moving_mesh`` branch.
This is an implementation of the moving-mesh finite-volume method for hydrodynamics in SWIFT.
To use this scheme, a Riemann solver is also needed. Configure SWIFT as follows:
.. code-block:: bash
./configure --with-hydro="shadowswift" --with-riemann-solver="hllc"
Current status
~~~~~~~~~~~~~~
Due to the completely different task structure compared to SPH hydrodynamics, currently only a subset of the features of
SWIFT is supported in this scheme.
- Hydrodynamics is fully supported in 1D, 2D and 3D and over MPI.
- Both self-gravity and external potentials are supported.
- Cosmological time-integration is supported.
- Cooling and chemistry are supported, with the exception of the ``GEAR_diffusion`` chemistry scheme. Metals are
properly according to mass fluxes.
- Choice between periodic, reflective, open, inflow and vacuum boundary conditions (for non-periodic boundary
conditions, the desired variant must be selected in ``const.h``). Additionally, reflective boundary conditions
are applied to SWIFT's boundary particles. Configure with ``--with-boundary-particles=<N>`` to use this (e.g. to
simulate walls).
Caveats
~~~~~~~
These are currently the main limitations of the ShadowSWIFT hydro scheme:
- Unlike SPH the cells of the moving mesh must form a partition of the entire simulation volume. This means that there
cannot be empty SWIFT cells and vacuum must be explicitly represented by zero (or negligible) mass particles.
- Most other subgrid physics, most notably, star formation and stellar feedback are not supported yet.
- No MHD schemes are supported.
- No radiative-transfer schemes are supported.