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.gitignore
View file @ 853c5044
......@@ -13,6 +13,10 @@ config.sub
ltmain.sh
libtool
build
swift
swift_mpi
fof
fof_mpi
src/version_string.h
swift*.tar.gz
......@@ -22,11 +26,9 @@ doc/html/
doc/latex/
doc/man/
doc/Doxyfile
doc/RTD/source/SubgridModels/*/*.png
doc/RTD/source/RadiativeTransfer/full_dependency_graph_RT.png
examples/swift
examples/swift_mpi
examples/fof
examples/fof_mpi
examples/*/*/*.xmf
examples/*/*/*.dat
examples/*/*/*.png
......@@ -37,12 +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/*
......@@ -54,18 +58,34 @@ 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
examples/*/*/coolingtables
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
examples/SubgridTests/StellarEvolution/StellarEvolutionSolution*
examples/SubgridTests/CosmologicalStellarEvolution/StellarEvolutionSolution*
examples/SmallCosmoVolume/SmallCosmoVolume_DM/power_spectra
examples/SmallCosmoVolume/SmallCosmoVolume_cooling/snapshots/
examples/SmallCosmoVolume/SmallCosmoVolume_hydro/snapshots/
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
......@@ -123,11 +143,14 @@ tests/testFFT
tests/testInteractions
tests/testInteractions.sh
tests/testSymmetry
tests/testDistance
tests/testHydroMPIrules
tests/testMaths
tests/testAtomic
tests/testRandom
tests/testRandomSpacing
tests/testRandomPoisson
tests/testRandomCone
tests/testThreadpool
tests/testParser
tests/testFeedback
......@@ -142,9 +165,11 @@ tests/test125cells.sh
tests/test125cellsPerturbed.sh
tests/testParser.sh
tests/testReading.sh
tests/testNeutrinoCosmology.sh
tests/testSelectOutput.sh
tests/unused_parser_output.yml
tests/used_parser_output.yml
tests/output_list_params.yml
tests/testAdiabaticIndex
tests/testRiemannExact
tests/testRiemannTRRS
......@@ -154,7 +179,7 @@ tests/testVoronoi1D
tests/testVoronoi2D
tests/testVoronoi3D
tests/testDump
tests/testLogger
tests/testCSDS
tests/benchmarkInteractions
tests/testGravityDerivatives
tests/testGravitySpeed
......@@ -171,6 +196,10 @@ tests/testFormat.sh
tests/testCooling
tests/testComovingCooling
tests/testHashmap
tests/testNeutrinoCosmology
tests/testNeutrinoFermiDirac
tests/testLog
tests/testTimeline
tests/*.png
tests/*.txt
......@@ -182,6 +211,10 @@ theory/SPH/Flavours/sph_flavours.pdf
theory/SPH/EoS/eos.pdf
theory/SPH/*.pdf
theory/paper_pasc/pasc_paper.pdf
theory/Multipoles/alpha_derivatives.pdf
theory/Multipoles/alpha_powers.pdf
theory/Multipoles/chi_derivatives.pdf
theory/Multipoles/sigma_derivatives.pdf
theory/Multipoles/fmm.pdf
theory/Multipoles/fmm_standalone.pdf
theory/Multipoles/potential.pdf
......@@ -192,6 +225,7 @@ theory/Multipoles/mac_potential.pdf
theory/Cosmology/cosmology.pdf
theory/Cooling/eagle_cooling.pdf
theory/Gizmo/gizmo-implementation-details/gizmo-implementation-details.pdf
theory/RadiativeTransfer/GEARRT/GEARRT.pdf
m4/libtool.m4
m4/ltoptions.m4
......@@ -213,6 +247,7 @@ src/equation_of_state/planetary/*.txt
# Intel compiler optimization reports
*.optrpt
*.opt.yaml
# Object files
.deps/
......@@ -258,6 +293,9 @@ src/equation_of_state/planetary/*.txt
*.out
*.toc
## Figures
*.svg
## Intermediate documents:
*.dvi
*-converted-to.*
......@@ -365,3 +403,9 @@ sympy-plots-for-*.tex/
# vim
*.swp
# black formatting
black_formatting_env
# vscode
*.json
.gitmodules 0 → 100644
View file @ 853c5044
[submodule "csds"]
path = csds
url = https://gitlab.cosma.dur.ac.uk/lhausammann/csds-reader.git
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
......@@ -21,4 +21,14 @@ Alexei Borissov alexei.borissov@ed.ac.uk
Yannick Bahe bahe@strw.leidenuniv.nl
Roi Kugel kugel@strw.leidenuniv.nl
Evgenii Chaikin chaikin@strw.leidenuniv.nl
Sylvia Ploeckinger ploeckinger@lorentz.leidenuniv.nl
\ No newline at end of file
Sylvia Ploeckinger ploeckinger@lorentz.leidenuniv.nl
Willem Elbers willem.h.elbers@durham.ac.uk
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
CITATION.cff 0 → 100644
View file @ 853c5044
cff-version: 1.2.0
title: >-
SWIFT: SPH With Inter-dependent Fine-grained
Tasking
message: 'If you use this software, please cite it as below'
type: software
authors:
- given-names: Matthieu
family-names: Schaller
email: schaller@strw.leidenuniv.nl
affiliation: Leiden University
orcid: 'https://orcid.org/0000-0002-2395-4902'
- given-names: Gonnet
family-names: Pedro
- given-names: Peter
family-names: Draper
- given-names: Aidan
family-names: Chalk
- given-names: Bert
family-names: Vandenbroucke
- given-names: James
family-names: Willis
- given-names: Richard
family-names: Bower
- given-names: Josh
family-names: Borrow
- given-names: Loic
family-names: Hausammann
- given-names: Yves
family-names: Revaz
- given-names: Jacob
family-names: Kegerreis
- given-names: Mladen
family-names: Ivkovic
- given-names: Stuart
family-names: McAlpine
- given-names: Folkert
family-names: Nobels
- given-names: John
family-names: Helly
- given-names: Yannick
family-names: Bahé
- given-names: Willem
family-names: Elbers
- given-names: Filip
family-names: Husko
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-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 merge request.
The Python scripts in the repository use default formatting enforced by
'black'. Since 'black' formatting still strongly depends on the version,
we currently enforce use of 'black==19.3b0' using a virtual environment.
The setup of the virtual environment and formatting of all PYthon
scripts is done automatically by the Python formatting script
'format_python.sh'. Please apply this script before submitting a merge
request containing new or updated Python scripts.
The SWIFT code comes with a series of unit tests that are run automatically
when a push to the master branch occurs. The suite can be run by doing a `make
check` in the root directory. Please check that the test suite still
......
COPYING.LESSER
View file @ 853c5044
### GNU LESSER GENERAL PUBLIC LICENSE
GNU LESSER GENERAL PUBLIC LICENSE
Version 3, 29 June 2007
Version 3, 29 June 2007
Copyright (C) 2007 Free Software Foundation, Inc. <http://fsf.org/>
Everyone is permitted to copy and distribute verbatim copies
of this license document, but changing it is not allowed.
Copyright (C) 2007 Free Software Foundation, Inc.
<https://fsf.org/>
Everyone is permitted to copy and distribute verbatim copies of this
license document, but changing it is not allowed.
This version of the GNU Lesser General Public License incorporates
the terms and conditions of version 3 of the GNU General Public
License, supplemented by the additional permissions listed below.
This version of the GNU Lesser General Public License incorporates the
terms and conditions of version 3 of the GNU General Public License,
supplemented by the additional permissions listed below.
0. Additional Definitions.
#### 0. Additional Definitions.
As used herein, "this License" refers to version 3 of the GNU Lesser
General Public License, and the "GNU GPL" refers to version 3 of the GNU
General Public License.
As used herein, "this License" refers to version 3 of the GNU Lesser
General Public License, and the "GNU GPL" refers to version 3 of the
GNU General Public License.
"The Library" refers to a covered work governed by this License,
other than an Application or a Combined Work as defined below.
"The Library" refers to a covered work governed by this License, other
than an Application or a Combined Work as defined below.
An "Application" is any work that makes use of an interface provided
An "Application" is any work that makes use of an interface provided
by the Library, but which is not otherwise based on the Library.
Defining a subclass of a class defined by the Library is deemed a mode
of using an interface provided by the Library.
A "Combined Work" is a work produced by combining or linking an
Application with the Library. The particular version of the Library
A "Combined Work" is a work produced by combining or linking an
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The "Minimal Corresponding Source" for a Combined Work means the
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based on the Application, and not on the Linked Version.
The "Corresponding Application Code" for a Combined Work means the
The "Corresponding Application Code" for a Combined Work means the
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and utility programs needed for reproducing the Combined Work from the
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#### 1. Exception to Section 3 of the GNU GPL.
1. Exception to Section 3 of the GNU GPL.
You may convey a covered work under sections 3 and 4 of this License
You may convey a covered work under sections 3 and 4 of this License
without being bound by section 3 of the GNU GPL.
#### 2. Conveying Modified Versions.
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#### 3. Object Code Incorporating Material from Library Header Files.
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#### 5. Combined Libraries.
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side by side in a single library together with other library
a) Give prominent notice with each copy of the object code that the
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4. Combined Works.
You may convey a Combined Work under terms of your choice that,
taken together, effectively do not restrict modification of the
portions of the Library contained in the Combined Work and reverse
engineering for debugging such modifications, if you also do each of
the following:
a) Give prominent notice with each copy of the Combined Work that
the Library is used in it and that the Library and its use are
covered by this License.
b) Accompany the Combined Work with a copy of the GNU GPL and this license
document.
c) For a Combined Work that displays copyright notices during
execution, include the copyright notice for the Library among
these notices, as well as a reference directing the user to the
copies of the GNU GPL and this license document.
d) Do one of the following:
0) Convey the Minimal Corresponding Source under the terms of this
License, and the Corresponding Application Code in a form
suitable for, and under terms that permit, the user to
recombine or relink the Application with a modified version of
the Linked Version to produce a modified Combined Work, in the
manner specified by section 6 of the GNU GPL for conveying
Corresponding Source.
1) Use a suitable shared library mechanism for linking with the
Library. A suitable mechanism is one that (a) uses at run time
a copy of the Library already present on the user's computer
system, and (b) will operate properly with a modified version
of the Library that is interface-compatible with the Linked
Version.
e) Provide Installation Information, but only if you would otherwise
be required to provide such information under section 6 of the
GNU GPL, and only to the extent that such information is
necessary to install and execute a modified version of the
Combined Work produced by recombining or relinking the
Application with a modified version of the Linked Version. (If
you use option 4d0, the Installation Information must accompany
the Minimal Corresponding Source and Corresponding Application
Code. If you use option 4d1, you must provide the Installation
Information in the manner specified by section 6 of the GNU GPL
for conveying Corresponding Source.)
5. Combined Libraries.
You may place library facilities that are a work based on the
Library side by side in a single library together with other library
facilities that are not Applications and are not covered by this
License, and convey such a combined library under terms of your
choice, if you do both of the following:
- a) Accompany the combined library with a copy of the same work
based on the Library, uncombined with any other library
facilities, conveyed under the terms of this License.
- b) Give prominent notice with the combined library that part of it
is a work based on the Library, and explaining where to find the
accompanying uncombined form of the same work.
a) Accompany the combined library with a copy of the same work based
on the Library, uncombined with any other library facilities,
conveyed under the terms of this License.
b) Give prominent notice with the combined library that part of it
is a work based on the Library, and explaining where to find the
accompanying uncombined form of the same work.
#### 6. Revised Versions of the GNU Lesser General Public License.
6. Revised Versions of the GNU Lesser General Public License.
The Free Software Foundation may publish revised and/or new versions
The Free Software Foundation may publish revised and/or new versions
of the GNU Lesser General Public License from time to time. Such new
versions will be similar in spirit to the present version, but may
differ in detail to address new problems or concerns.
Each version is given a distinguishing version number. If the Library
as you received it specifies that a certain numbered version of the
GNU Lesser General Public License "or any later version" applies to
it, you have the option of following the terms and conditions either
of that published version or of any later version published by the
Free Software Foundation. If the Library as you received it does not
specify a version number of the GNU Lesser General Public License, you
may choose any version of the GNU Lesser General Public License ever
published by the Free Software Foundation.
If the Library as you received it specifies that a proxy can decide
Each version is given a distinguishing version number. If the
Library as you received it specifies that a certain numbered version
of the GNU Lesser General Public License "or any later version"
applies to it, you have the option of following the terms and
conditions either of that published version or of any later version
published by the Free Software Foundation. If the Library as you
received it does not specify a version number of the GNU Lesser
General Public License, you may choose any version of the GNU Lesser
General Public License ever published by the Free Software Foundation.
If the Library as you received it specifies that a proxy can decide
whether future versions of the GNU Lesser General Public License shall
apply, that proxy's public statement of acceptance of any version is
permanent authorization for you to choose that version for the
......
INSTALL.swift
View file @ 853c5044
......@@ -37,6 +37,8 @@ SWIFT has been successfully built and tested with the following compilers:
- GCC 4.8.x
- Intel ICC 15.0.x
- clang 3.4.x
- aocc 3.x
- icx (oneAPI) 2022.x
More recent versions and slightly older ones should also be able to
build the software.
......@@ -97,7 +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
......@@ -180,7 +182,7 @@ before you can build it.
documentation.
- python:
Examples and solution script use python and rely on the numpy
Examples and solution script use python 3 and rely on the numpy
library version 1.8.2 or higher.
......@@ -189,6 +191,14 @@ 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-10 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.
The Python scripts in the repository use default formatting enforced by
'black'. Since 'black' formatting still strongly depends on the version,
we currently enforce use of 'black==19.3b0' using a virtual environment.
The setup of the virtual environment and formatting of all PYthon
scripts is done automatically by the Python formatting script
'format_python.sh'. Please apply this script before submitting a merge
request containing new or updated Python scripts.
Makefile.am
View file @ 853c5044
# This file is part of SWIFT.
# Copyright (c) 2012 pedro.gonnet@durham.ac.uk
# 2015 matthieu.schaller@durham.ac.uk
# 2015 schaller@strw.leidenuniv.nl
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
......@@ -19,13 +19,87 @@
ACLOCAL_AMFLAGS = -I m4
# Show the way...
SUBDIRS = src argparse examples doc tests tools
if HAVECSDS
SUBDIRS = csds
else
SUBDIRS =
endif
SUBDIRS += src argparse examples doc tests tools
if HAVEEAGLECOOLING
SUBDIRS += examples/Cooling/CoolingRates
DIST_SUBDIRS = $(SUBDIRS)
else
DIST_SUBDIRS = $(SUBDIRS) examples/Cooling/CoolingRates
endif
# Common flags
MYFLAGS =
# Add the source directory and the non-standard paths to the included library headers to CFLAGS
AM_CFLAGS = -I$(top_srcdir)/src -I$(top_srcdir)/argparse $(HDF5_CPPFLAGS) \
$(GSL_INCS) $(FFTW_INCS) $(NUMA_INCS) $(GRACKLE_INCS) \
$(CHEALPIX_CFLAGS) $(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) $(LUSTREAPI_LIBS)
# MPI libraries.
MPI_LIBS = $(PARMETIS_LIBS) $(METIS_LIBS) $(MPI_THREAD_LIBS) $(FFTW_MPI_LIBS)
MPI_FLAGS = -DWITH_MPI $(PARMETIS_INCS) $(METIS_INCS) $(FFTW_MPI_INCS)
# Programs.
bin_PROGRAMS = swift
# Also build the FOF tool?
if HAVESTANDALONEFOF
bin_PROGRAMS += fof
endif
if HAVELOGGER
SUBDIRS += logger
# Do we have the CSDS?
if HAVECSDS
LD_CSDS = csds/src/.libs/libcsds_writer.a
else
LD_CSDS =
endif
# Build MPI versions as well?
if HAVEMPI
bin_PROGRAMS += swift_mpi
if HAVESTANDALONEFOF
bin_PROGRAMS += fof_mpi
endif
endif
# engine_policy_setaffinity is available?
if HAVESETAFFINITY
ENGINE_POLICY_SETAFFINITY=| engine_policy_setaffinity
else
ENGINE_POLICY_SETAFFINITY=
endif
# Sources for swift
swift_SOURCES = swift.c
swift_CFLAGS = $(MYFLAGS) $(AM_CFLAGS) -DENGINE_POLICY="engine_policy_keep $(ENGINE_POLICY_SETAFFINITY)"
swift_LDADD = src/libswiftsim.la argparse/libargparse.la $(VELOCIRAPTOR_LIBS) $(EXTRA_LIBS) $(LD_CSDS)
# Sources for swift_mpi, do we need an affinity policy for MPI?
swift_mpi_SOURCES = swift.c
swift_mpi_CFLAGS = $(MYFLAGS) $(AM_CFLAGS) $(MPI_FLAGS) -DENGINE_POLICY="engine_policy_keep $(ENGINE_POLICY_SETAFFINITY)"
swift_mpi_LDADD = src/libswiftsim_mpi.la argparse/libargparse.la $(MPI_LIBS) $(VELOCIRAPTOR_MPI_LIBS) $(EXTRA_LIBS) $(LD_CSDS)
# Sources for fof
fof_SOURCES = swift_fof.c
fof_CFLAGS = $(MYFLAGS) $(AM_CFLAGS) -DENGINE_POLICY="engine_policy_keep $(ENGINE_POLICY_SETAFFINITY)"
fof_LDADD = src/.libs/libswiftsim.a argparse/.libs/libargparse.a $(VELOCIRAPTOR_LIBS) $(EXTRA_LIBS) $(LD_CSDS)
# Sources for fof_mpi, do we need an affinity policy for MPI?
fof_mpi_SOURCES = swift_fof.c
fof_mpi_CFLAGS = $(MYFLAGS) $(AM_CFLAGS) $(MPI_FLAGS) -DENGINE_POLICY="engine_policy_keep $(ENGINE_POLICY_SETAFFINITY)"
fof_mpi_LDADD = src/.libs/libswiftsim_mpi.a argparse/.libs/libargparse.a $(MPI_LIBS) $(VELOCIRAPTOR_MPI_LIBS) $(EXTRA_LIBS) $(LD_CSDS)
# Non-standard files that should be part of the distribution.
EXTRA_DIST = INSTALL.swift .clang-format format.sh
README
View file @ 853c5044
......@@ -6,7 +6,7 @@
/____/ |__/|__/___/_/ /_/
SPH With Inter-dependent Fine-grained Tasking
Version : 0.9.0
Version : 2025.04
Website: www.swiftsim.com
Twitter: @SwiftSimulation
......@@ -40,14 +40,16 @@ Parameters:
-k, --sinks Run with sink particles.
-u, --fof Run Friends-of-Friends algorithm to
perform black hole seeding.
--lightcone Generate lightcone outputs.
-x, --velociraptor Run with structure finding.
--line-of-sight Run with line-of-sight outputs.
--limiter Run with time-step limiter.
--sync Run with time-step synchronization
of particles hit by feedback events.
--logger Run with the particle logger.
-R, --radiation Run with radiative transfer. Work in
progress, currently has no effect.
--csds Run with the Continuous Simulation Data
Stream (CSDS).
-R, --radiation Run with radiative transfer.
--power Run with power spectrum outputs.
Simulation meta-options:
......@@ -64,10 +66,16 @@ Parameters:
GEAR model. This is equivalent to --hydro
--limiter --sync --self-gravity --stars
--star-formation --cooling --feedback.
--agora Run with all the options needed for the
AGORA model. This is equivalent to --hydro
--limiter --sync --self-gravity --stars
--star-formation --cooling --feedback.
Control options:
-a, --pin Pin runners using processor affinity.
--nointerleave Do not interleave memory allocations across
NUMA regions.
-d, --dry-run Dry run. Read the parameter file, allocates
memory but does not read the particles
from ICs. Exits before the start of time
......@@ -87,8 +95,12 @@ Parameters:
read from the parameter file. Can be used
more than once {sec:par:value}.
-r, --restart Continue using restart files.
-t, --threads=<int> The number of threads to use on each MPI
rank. Defaults to 1 if not specified.
-t, --threads=<int> The number of task threads to use on each
MPI rank. Defaults to 1 if not specified.
--pool-threads=<int> The number of threads to use on each MPI
rank for the threadpool operations.
Defaults to the numbers of task threads
if not specified.
-T, --timers=<int> Print timers every time-step.
-v, --verbose=<int> Run in verbose mode, in MPI mode 2 outputs
from all ranks.
......
README-mpi-hints.md
View file @ 853c5044
......@@ -48,3 +48,13 @@ UCX_TLS=ud_x,shm,self
UCX_RC_MLX5_TM_ENABLE=n
UCX_DC_MLX5_TM_ENABLE=n
```
These environment variables (set on the Mellanox-base cosma system in Durham)
for version 4.0.5 with the UCX backend can also be useful:
```
OMPI_MCA_btl ^openib
OMPI_MCA_btl_openib_flags 1
OMPI_MCA_plm_rsh_num_concurrent 768
OMPI_MCA_mpool_rdma_rcache_size_limit 209715200
```
\ No newline at end of file
README.md
View file @ 853c5044
<a name="logo"/>
<div align="center">
<a href="https://www.swiftsim.com/" target="_blank">
<img src="https://swift.strw.leidenuniv.nl/SWIFT_banner.jpg" alt="SWIFT banner" width="1016" height="242"></img>
</a>
</div>
SWIFT: SPH WIth Fine-grained inter-dependent Tasking
====================================================
......@@ -11,7 +18,7 @@ More general information about SWIFT is available on the project
[webpages](http://www.swiftsim.com).
For information on how to _run_ SWIFT, please consult the onboarding guide
available [here](http://www.swiftsim.com/onboarding.pdf). This includes
available [here](https://swift.strw.leidenuniv.nl/onboarding.pdf). This includes
dependencies, and a few examples to get you going.
We suggest that you use the latest release branch of SWIFT, rather than the
......@@ -48,12 +55,18 @@ 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:
https://ui.adsabs.harvard.edu/abs/2023arXiv230513380S. The core solver, the
numerical methods as well as many extensions where described there. We ask users
running SWIFT for their research to please cite this paper when they present
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)
......@@ -68,7 +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.
......@@ -93,7 +106,7 @@ Runtime parameters
/____/ |__/|__/___/_/ /_/
SPH With Inter-dependent Fine-grained Tasking
Version : 0.9.0
Version : 2025.04
Website: www.swiftsim.com
Twitter: @SwiftSimulation
......@@ -127,14 +140,16 @@ Parameters:
-k, --sinks Run with sink particles.
-u, --fof Run Friends-of-Friends algorithm to
perform black hole seeding.
--lightcone Generate lightcone outputs.
-x, --velociraptor Run with structure finding.
--line-of-sight Run with line-of-sight outputs.
--limiter Run with time-step limiter.
--sync Run with time-step synchronization
of particles hit by feedback events.
--logger Run with the particle logger.
-R, --radiation Run with radiative transfer. Work in
progress, currently has no effect.
--csds Run with the Continuous Simulation Data
Stream (CSDS).
-R, --radiation Run with radiative transfer.
--power Run with power spectrum outputs.
Simulation meta-options:
......@@ -151,10 +166,16 @@ Parameters:
GEAR model. This is equivalent to --hydro
--limiter --sync --self-gravity --stars
--star-formation --cooling --feedback.
--agora Run with all the options needed for the
GEAR model. This is equivalent to --hydro
--limiter --sync --self-gravity --stars
--star-formation --cooling --feedback.
Control options:
-a, --pin Pin runners using processor affinity.
--nointerleave Do not interleave memory allocations across
NUMA regions.
-d, --dry-run Dry run. Read the parameter file, allocates
memory but does not read the particles
from ICs. Exits before the start of time
......@@ -174,8 +195,12 @@ Parameters:
read from the parameter file. Can be used
more than once {sec:par:value}.
-r, --restart Continue using restart files.
-t, --threads=<int> The number of threads to use on each MPI
rank. Defaults to 1 if not specified.
-t, --threads=<int> The number of task threads to use on each
MPI rank. Defaults to 1 if not specified.
--pool-threads=<int> The number of threads to use on each MPI
rank for the threadpool operations.
Defaults to the numbers of task threads
if not specified.
-T, --timers=<int> Print timers every time-step.
-v, --verbose=<int> Run in verbose mode, in MPI mode 2 outputs
from all ranks.
......
argparse/argparse.c
View file @ 853c5044
......@@ -7,8 +7,9 @@
*/
#include "argparse.h"
#include "config.h"
#include <config.h>
/* System includes */
#include <assert.h>
#include <errno.h>
#include <stdio.h>
......
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)
......
autogen.sh
View file @ 853c5044
......@@ -3,7 +3,7 @@
# Update generated configuration files, i.e. do work so that a
# developer checkout can be configured.
autoreconf --install --symlink
autoreconf --install --symlink
exit
configure.ac
View file @ 853c5044
......@@ -16,25 +16,9 @@
# along with this program. If not, see <http://www.gnu.org/licenses/>.
# Init the project.
AC_INIT([SWIFT],[0.9.0],[https://gitlab.cosma.dur.ac.uk/swift/swiftsim])
AC_INIT([SWIFT],[2025.04],[https://gitlab.cosma.dur.ac.uk/swift/swiftsim])
swift_config_flags="$*"
# We want to stop when given unrecognised options. No subdirs so this is safe.
enable_option_checking=${enable_option_checking:-fatal}
if test -n "$ac_unrecognized_opts"; then
case $enable_option_checking in
no)
;;
fatal)
{ $as_echo "$as_me: error: unrecognized options: $ac_unrecognized_opts" >&2
{ (exit 1); exit 1; }; }
;;
*)
$as_echo "$as_me: WARNING: unrecognized options: $ac_unrecognized_opts" >&2
;;
esac
fi
AC_COPYRIGHT
AC_CONFIG_SRCDIR([src/space.c])
AC_CONFIG_AUX_DIR([.])
......@@ -47,13 +31,18 @@ AC_CONFIG_MACRO_DIR([m4])
: ${CFLAGS=""}
# Generate header file.
AM_CONFIG_HEADER(config.h)
AC_CONFIG_HEADERS([config.h])
# Find and test the compiler.
AX_CHECK_ENABLE_DEBUG
# Enable POSIX and platform extension preprocessor macros.
AC_USE_SYSTEM_EXTENSIONS
AC_PROG_CC
AM_PROG_CC_C_O
AC_OPENMP
# We need this for compilation hints and possibly FFTW.
AX_OPENMP
# If debug is selected then we also define SWIFT_DEVELOP_MODE to control
# any developer code options.
......@@ -68,7 +57,7 @@ AC_DEFINE([_GLIBCXX_INCLUDE_NEXT_C_HEADERS],1,[Hack for min() and max() using g+
# Enable POSIX and platform extension preprocessor macros.
AC_USE_SYSTEM_EXTENSIONS
# Check for compiler version and vendor.
# Check for C compiler version and vendor.
AX_COMPILER_VENDOR
AX_COMPILER_VERSION
......@@ -82,59 +71,88 @@ fi
# Restrict support.
AC_C_RESTRICT
# logger
AC_ARG_ENABLE([logger],
[AS_HELP_STRING([--enable-logger],
[enable the particle logger]
# CSDS
AC_ARG_ENABLE([csds],
[AS_HELP_STRING([--enable-csds],
[enable the Continuous Simulation Data Stream]
)],
[with_logger="${enableval}"],
[with_logger="no"]
[with_csds="${enableval}"],
[with_csds="no"]
)
if test "$with_logger" = "yes"; then
AC_DEFINE([WITH_LOGGER], 1, [logger enabled])
# The logger requires that long long is a 64bit type, let's
if test "$with_csds" = "yes"; then
AC_DEFINE([WITH_CSDS], 1, [csds enabled])
# Ensure that the submodule is initialized
${srcdir}/tools/update-modules csds
# The csds requires that long long is a 64bit type, let's
# check that.
AC_CHECK_SIZEOF([long long int])
if test "$ac_cv_sizeof_long_long_int" != "8"; then
AC_MSG_ERROR([The particle logger requires that 'long long int' has size 8 bytes])
AC_MSG_ERROR([The CSDS requires that 'long long int' has size 8 bytes])
fi
AC_CONFIG_SUBDIRS([csds])
CFLAGS="$CFLAGS $OPENMP_CFLAGS"
fi
AM_CONDITIONAL([HAVELOGGER],[test $with_logger = "yes"])
AM_CONDITIONAL([HAVECSDS],[test $with_csds = "yes"])
# Use best known optimization for the current architecture. Actual optimization
# happens later so we can avoid any issues it introduces with the compiler,
# but we need to know if that will happen now.
AC_ARG_ENABLE([optimization],
[AS_HELP_STRING([--enable-optimization],
[Enable compile time optimization flags for host @<:@yes/no@:>@]
)],
[enable_opt="$enableval"],
[enable_opt="yes"]
)
# Interprocedural optimization support. Needs special handling for linking and
# archiving as well as compilation with Intels, needs to be done before
# libtool is configured (to use correct LD).
# Interprocedural optimization support. Can need special handling for linking
# and archiving as well as compilation. Needs to be done before libtool is
# configured so we use the correct LD. It can give good improvements for
# clang based compilers, so the default is enabled, but we make that
# disabled when not optimizing or debugging support is enabled.
enable_ipo_default="yes";
if test "x$ax_enable_debug" = "xyes" -o "x$enable_opt" != "xyes"; then
enable_ipo_default="no";
AC_MSG_WARN([Interprocedural optimization support default is changed to false])
fi
AC_ARG_ENABLE([ipo],
[AS_HELP_STRING([--enable-ipo],
[Enable interprocedural optimization @<:@no/yes@:>@]
[Enable interprocedural optimization [default=yes unless debugging]]
)],
[enable_ipo="$enableval"],
[enable_ipo="no"]
[enable_ipo="$enable_ipo_default"]
)
if test "$enable_ipo" = "yes"; then
if test "$ax_cv_c_compiler_vendor" = "intel"; then
CFLAGS="$CFLAGS -ip -ipo"
LDFLAGS="$LDFLAGS -ipo"
: ${AR="xiar"}
: ${LD="xild"}
AC_CHECK_PROGS([AR], [xiar])
AC_CHECK_PROGS([LD], [xild])
AC_MSG_RESULT([added Intel interprocedural optimization support])
elif test "$ax_cv_c_compiler_vendor" = "oneapi"; then
CFLAGS="$CFLAGS -ipo"
LDFLAGS="$LDFLAGS -ipo"
AC_CHECK_PROGS([AR], [xiar])
AC_CHECK_PROGS([RANLIB], [llvm-ranlib])
AC_MSG_RESULT([added oneapi interprocedural optimization support])
elif test "$ax_cv_c_compiler_vendor" = "gnu"; then
CFLAGS="$CFLAGS -flto"
LDFLAGS="$LDFLAGS -flto"
AX_COMPARE_VERSION($ax_cv_c_compiler_version, [ge], [5.0.0],
[
: ${AR="gcc-ar"}
: ${RANLIB="gcc-ranlib"}
], [:] )
[
AC_CHECK_PROGS([AR], [gcc-ar])
AC_CHECK_PROGS([RANLIB], [gcc-ranlib])
], [:] )
AC_MSG_RESULT([added GCC interprocedural optimization support])
elif test "$ax_cv_c_compiler_vendor" = "clang"; then
CFLAGS="$CFLAGS -flto -fuse-ld=gold"
LDFLAGS="$LDFLAGS -XCClinker -fuse-ld=gold"
: ${AR="llvm-ar"}
: ${LD="ld.gold"}
: ${RANLIB="llvm-ranlib"}
CFLAGS="$CFLAGS -flto"
LDFLAGS="$LDFLAGS -flto"
AC_CHECK_PROGS([RANLIB], [llvm-ranlib])
AC_MSG_RESULT([added LLVM interprocedural optimization support])
else
AC_MSG_WARN([Compiler does not support interprocedural optimization])
......@@ -154,9 +172,11 @@ AC_ARG_ENABLE([mpi],
[enable_mpi="$enableval"],
[enable_mpi="yes"]
)
# Use extra flags set by AC_PROG_CC as part of $CC. Currently undocumented as ac_cv_prog_cc_stdc,
# so could change.
good_mpi="yes"
if test "$enable_mpi" = "yes"; then
AX_MPI([CC="$MPICC" AC_DEFINE(HAVE_MPI, 1, [Define if you have the MPI library.]) ])
AX_MPI([CC="$MPICC $ac_cv_prog_cc_stdc" AC_DEFINE(HAVE_MPI, 1, [Define if you have the MPI library.]) ], [enable_mpi="no"])
MPI_LIBRARY="Unknown MPI"
# Various MPI implementations require additional libraries when also using
......@@ -218,15 +238,18 @@ AM_CONDITIONAL([HAVEMPI],[test $enable_mpi = "yes"])
# Indicate that MPIRUN can be modified by an environment variable
AC_ARG_VAR(MPIRUN, Path to the mpirun command if non-standard)
# Add libtool support (now that CC is defined).
LT_INIT
# Add libtool support (now that CC is defined). Disable shared libraries by default.
LT_INIT([disable-shared])
# Need C99 and inline support.
AC_PROG_CC_C99
# Need C99 and inline support. Only for autoconfs to version 2.69.
m4_version_prereq([2.71], [], [AC_PROG_CC_C99])
# Need inline support.
AC_C_INLINE
# If debugging try to show inlined functions.
if test "x$enable_debug" = "xyes"; then
if test "x$ax_enable_debug" = "xyes"; then
# Show inlined functions.
if test "$ax_cv_c_compiler_vendor" = "gnu"; then
# Would like to use -gdwarf and let the compiler pick a good version
......@@ -237,6 +260,8 @@ if test "x$enable_debug" = "xyes"; then
CFLAGS="$CFLAGS $inline_EXTRA_FLAGS"
elif test "$ax_cv_c_compiler_vendor" = "intel"; then
CFLAGS="$CFLAGS -debug inline-debug-info"
elif test "$ax_cv_c_compiler_vendor" = "oneapi"; then
CFLAGS="$CFLAGS -debug inline-debug-info"
fi
fi
......@@ -279,7 +304,7 @@ AC_ARG_ENABLE([threadpool-debugging],
)
if test "$enable_threadpool_debugging" = "yes"; then
AC_DEFINE([SWIFT_DEBUG_THREADPOOL],1,[Enable threadpool debugging])
LDFLAGS="$LDFLAGS -rdynamic"
LDFLAGS="$LDFLAGS -rdynamic -ldl"
fi
# Check if the general timers are switched on.
......@@ -318,7 +343,7 @@ if test "$enable_cell_graph" = "yes"; then
AC_DEFINE([SWIFT_CELL_GRAPH],1,[Enable cell graph])
fi
# Check if using our custom icbrtf is enalbled.
# Check if using our custom icbrtf is enabled.
AC_ARG_ENABLE([custom-icbrtf],
[AS_HELP_STRING([--enable-custom-icbrtf],
[Use SWIFT's custom icbrtf function instead of the system cbrtf @<:@yes/no@:>@]
......@@ -354,6 +379,18 @@ if test "$enable_naive_interactions_stars" = "yes"; then
AC_DEFINE([SWIFT_USE_NAIVE_INTERACTIONS_STARS],1,[Enable use of naive cell interaction functions for stars])
fi
# Check whether we want to default to naive cell interactions (stars)
AC_ARG_ENABLE([naive-interactions-rt],
[AS_HELP_STRING([--enable-naive-interactions-rt],
[Activate use of naive cell interaction functions for stars in RT tasks@<:@yes/no@:>@]
)],
[enable_naive_interactions_rt="$enableval"],
[enable_naive_interactions_rt="no"]
)
if test "$enable_naive_interactions_rt" = "yes"; then
AC_DEFINE([SWIFT_USE_NAIVE_INTERACTIONS_RT],1,[Enable use of naive cell interaction functions for stars in RT tasks])
fi
# Check if gravity force checks are on for some particles.
AC_ARG_ENABLE([gravity-force-checks],
[AS_HELP_STRING([--enable-gravity-force-checks=<N>],
......@@ -362,12 +399,68 @@ AC_ARG_ENABLE([gravity-force-checks],
[gravity_force_checks="$enableval"],
[gravity_force_checks="no"]
)
if test "$gravity_force_checks" == "yes"; then
if test "$gravity_force_checks" = "yes"; then
AC_MSG_ERROR(Need to specify the fraction of particles to check when using --enable-gravity-force-checks!)
elif test "$gravity_force_checks" != "no"; then
AC_DEFINE_UNQUOTED([SWIFT_GRAVITY_FORCE_CHECKS], [$enableval] ,[Enable gravity brute-force checks])
fi
# Check if hydro density checks are on for some particles.
AC_ARG_ENABLE([hydro-density-checks],
[AS_HELP_STRING([--enable-hydro-density-checks],
[Activate expensive brute-force hydro density checks for a fraction 1/N of all particles @<:@N@:>@]
)],
[hydro_density_checks="$enableval"],
[hydro_density_checks="no"]
)
if test "$hydro_density_checks" = "yes"; then
AC_MSG_ERROR(Need to specify the fraction of particles to check when using --enable-hydro-density-checks!)
elif test "$hydro_density_checks" != "no"; then
AC_DEFINE_UNQUOTED([SWIFT_HYDRO_DENSITY_CHECKS], [$enableval] ,[Enable hydro density brute-force checks])
fi
# Check if stars density checks are on for some particles.
AC_ARG_ENABLE([stars-density-checks],
[AS_HELP_STRING([--enable-stars-density-checks],
[Activate expensive brute-force stars density checks for a fraction 1/N of all particles @<:@N@:>@]
)],
[stars_density_checks="$enableval"],
[stars_density_checks="no"]
)
if test "$stars_density_checks" = "yes"; then
AC_MSG_ERROR(Need to specify the fraction of particles to check when using --enable-stars-density-checks!)
elif test "$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], [$enableval] ,[Enable sink density brute-force checks])
fi
# Check if ghost statistics are enabled
AC_ARG_ENABLE([ghost-statistics],
[AS_HELP_STRING([--enable-ghost-statistics],
[Gather statistics about the ghost iterations for hydro, stars and black holes in N bins @<:@N@:>@]
)],
[ghost_stats="$enableval"],
[ghost_stats="no"]
)
if test "$ghost_stats" == "yes"; then
AC_MSG_ERROR(Need to specify the number of bins when using --enable-ghost-statistics!)
elif test "$ghost_stats" != "no"; then
AC_DEFINE_UNQUOTED([SWIFT_GHOST_STATS], [$enableval] ,[Enable ghost statistics for hydro, stars and black holes])
fi
# Check whether we want to switch on glass making
AC_ARG_ENABLE([glass-making],
[AS_HELP_STRING([--enable-glass-making],
......@@ -376,7 +469,7 @@ AC_ARG_ENABLE([glass-making],
[gravity_glass_making="$enableval"],
[gravity_glass_making="no"]
)
if test "$gravity_glass_making" == "yes"; then
if test "$gravity_glass_making" = "yes"; then
AC_DEFINE([SWIFT_MAKE_GRAVITY_GLASS], 1, [Make the code run in a way to produce a glass file for gravity/cosmology])
fi
......@@ -388,7 +481,7 @@ AC_ARG_ENABLE([no-gravity-below-id],
[no_gravity_below_id="$enableval"],
[no_gravity_below_id="no"]
)
if test "$no_gravity_below_id" == "yes"; then
if test "$no_gravity_below_id" = "yes"; then
AC_MSG_ERROR(Need to specify the ID below which particles get zero forces when using --enable-no-gravity-below-id!)
elif test "$no_gravity_below_id" != "no"; then
AC_DEFINE_UNQUOTED([SWIFT_NO_GRAVITY_BELOW_ID], [$enableval] ,[Particles with smaller ID than this will have zero gravity forces])
......@@ -402,7 +495,7 @@ AC_ARG_ENABLE([boundary-particles],
[boundary_particles="$enableval"],
[boundary_particles="no"]
)
if test "$boundary_particles" == "yes"; then
if test "$boundary_particles" = "yes"; then
AC_MSG_ERROR(Need to specify the ID below which particles get zero forces when using --enable-boundary-particles!)
elif test "$boundary_particles" != "no"; then
AC_DEFINE_UNQUOTED([SWIFT_NO_GRAVITY_BELOW_ID], [$enableval] ,[Particles with smaller ID than this will have zero gravity forces])
......@@ -417,7 +510,7 @@ AC_ARG_ENABLE([fixed-boundary-particles],
[fixed_boundary_particles="$enableval"],
[fixed_boundary_particles="no"]
)
if test "$fixed_boundary_particles" == "yes"; then
if test "$fixed_boundary_particles" = "yes"; then
AC_MSG_ERROR(Need to specify the ID below which particles get zero forces when using --enable-boundary-particles!)
elif test "$fixed_boundary_particles" != "no"; then
AC_DEFINE_UNQUOTED([SWIFT_NO_GRAVITY_BELOW_ID], [$enableval] ,[Particles with smaller ID than this will have zero gravity forces])
......@@ -425,6 +518,18 @@ elif test "$fixed_boundary_particles" != "no"; then
AC_DEFINE_UNQUOTED([SWIFT_FIXED_BOUNDARY_PARTICLES], [$enableval] ,[Particles with smaller ID than this will be considered as boundaries.])
fi
# Check if fixed entropy is on for settling planetary initial conditions
AC_ARG_ENABLE([planetary-fixed-entropy],
[AS_HELP_STRING([--enable-planetary-fixed-entropy],
[Force entropies to stay fixed for settling planetary initial conditions @<:@yes/no@:>@]
)],
[planetary_fixed_entropy="$enableval"],
[planetary_fixed_entropy="no"]
)
if test "$planetary_fixed_entropy" = "yes"; then
AC_DEFINE([PLANETARY_FIXED_ENTROPY],1,[Enable planetary fixed entropy])
fi
# Check whether we have any of the ARM v8.1 tick timers
AX_ASM_ARM_PMCCNTR
AX_ASM_ARM_CNTVCT
......@@ -475,16 +580,6 @@ fi
# Define HAVE_POSIX_MEMALIGN if it works.
AX_FUNC_POSIX_MEMALIGN
# Only optimize if allowed, otherwise assume user will set CFLAGS as
# appropriate.
AC_ARG_ENABLE([optimization],
[AS_HELP_STRING([--enable-optimization],
[Enable compile time optimization flags for host @<:@yes/no@:>@]
)],
[enable_opt="$enableval"],
[enable_opt="yes"]
)
# Disable vectorisation for known compilers. This switches off optimizations
# that could be enabled above, so in general should be appended. Slightly odd
# implementation as want to describe as --disable-vec, but macro is enable
......@@ -509,6 +604,9 @@ AC_ARG_ENABLE([hand-vec],
HAVEVECTORIZATION=0
# Only optimize if allowed, otherwise assume user will set CFLAGS as
# appropriate. Note argument check is done earlier so we can configure
# other options related to optimization.
if test "$enable_opt" = "yes" ; then
# Choose the best flags for this compiler and architecture
......@@ -516,29 +614,55 @@ if test "$enable_opt" = "yes" ; then
AX_CC_MAXOPT
ac_test_CFLAGS="yes"
# Choose the best flags for the gravity sub-library on this compiler and architecture
# Choose the best flags for the gravity sub-library on this compiler and
# architecture. Note we use OpenMP as a compiler hints for loop vectorization.
GRAVITY_CFLAGS="$GRAVITY_CFLAGS $OPENMP_CFLAGS"
if test "$ax_cv_c_compiler_vendor" = "intel"; then
case "$icc_flags" in
*CORE-AVX512*)
GRAVITY_CFLAGS="$GRAVITY_CFLAGS -qopt-zmm-usage=high"
;;
*)
AC_MSG_WARN([No additional flags needed for gravity on this platform])
AC_MSG_NOTICE([No additional flags needed for gravity on this platform])
;;
esac
elif test "$ax_cv_c_compiler_vendor" = "oneapi"; then
case "$icc_flags" in
*CORE-AVX512*)
GRAVITY_CFLAGS="$GRAVITY_CFLAGS -qopt-zmm-usage=high"
;;
*)
AC_MSG_NOTICE([No additional flags needed for gravity on this platform])
;;
esac
elif test "$ax_cv_c_compiler_vendor" = "gnu"; then
if test "$gcc_handles_avx512" = "yes"; then
case "$ax_gcc_arch" in
case "$ax_cv_gcc_archflag" in
*skylake-avx512*)
GRAVITY_CFLAGS="$GRAVITY_CFLAGS -mprefer-vector-width=512"
;;
*)
AC_MSG_WARN([No additional flags needed for gravity on this platform])
AC_MSG_NOTICE([No additional flags needed for gravity on this platform])
;;
esac
else
AC_MSG_WARN([No additional flags needed for gravity on this platform])
AC_MSG_NOTICE([No additional flags needed for gravity on this platform])
fi
elif test "$ax_cv_c_compiler_vendor" = "clang"; then
# Could be a number of compilers. Check for aocc specific flags we want
# to use.
AX_CHECK_COMPILE_FLAG("-zopt", [GRAVITY_CFLAGS="$GRAVITY_CFLAGS -fvectorize -zopt"])
case "$ax_cv_gcc_archflag" in
*skylake-avx512*)
GRAVITY_CFLAGS="$GRAVITY_CFLAGS -mprefer-vector-width=512"
;;
*znver[[4-9]])
GRAVITY_CFLAGS="$GRAVITY_CFLAGS -mprefer-vector-width=512"
;;
*)
:
;;
esac
else
AC_MSG_WARN([Do not know what best gravity vectorization flags to choose for this compiler])
fi
......@@ -559,6 +683,9 @@ if test "$enable_opt" = "yes" ; then
if test "$ax_cv_c_compiler_vendor" = "intel"; then
CFLAGS="$CFLAGS -no-vec -no-simd"
AC_MSG_RESULT([disabled Intel vectorization])
elif test "$ax_cv_c_compiler_vendor" = "oneapi"; then
CFLAGS="$CFLAGS -no-vec"
AC_MSG_RESULT([disabled oneAPI vectorization])
elif test "$ax_cv_c_compiler_vendor" = "gnu"; then
CFLAGS="$CFLAGS -fno-tree-vectorize"
AC_MSG_RESULT([disabled GCC vectorization])
......@@ -575,7 +702,6 @@ if test "$enable_opt" = "yes" ; then
fi
AM_CONDITIONAL([HAVEVECTORIZATION],[test -n "$HAVEVECTORIZATION"])
# Add address sanitizer options to flags, if requested. Only useful for GCC
# version 4.8 and later and clang.
AC_ARG_ENABLE([sanitizer],
......@@ -596,7 +722,20 @@ if test "$enable_san" = "yes"; then
fi
if test "$enable_san" = "yes"; then
CFLAGS="$CFLAGS -fsanitize=address -fno-omit-frame-pointer"
AC_MSG_RESULT([added address sanitizer support])
AC_MSG_RESULT([Adding address sanitizer support... yes])
# Check if we have access to the __lsan_ignore_object() call for
# marking memory allocations as deliberately leaked.
AC_LINK_IFELSE([AC_LANG_SOURCE([[
#include <stdlib.h>
#include <sanitizer/lsan_interface.h>
int main(int argc, char *argv[]) {
void *p = malloc(1);
__lsan_ignore_object(p);
return 0;
}]])],
[AC_DEFINE(HAVE_LSAN_IGNORE_OBJECT, 1, [Have __lsan_ignore_object() call])],
[AC_MSG_WARN([Sanitizer enabled but no __lsan_ignore_object()])])
else
AC_MSG_WARN([Compiler does not support address sanitizer option])
fi
......@@ -629,10 +768,20 @@ if test "$enable_ubsan" = "yes"; then
fi
fi
# MPI mesh gravity
AC_ARG_ENABLE([mpi-mesh-gravity],
[AS_HELP_STRING([--enable-mpi-mesh-gravity],
[enable parallel mesh gravity (requires FFTW MPI library) @<:@no/yes@:>@]
)],
[with_mpi_mesh_gravity="${enableval}"],
[with_mpi_mesh_gravity="no"]
)
# Autoconf stuff.
AC_PROG_INSTALL
AC_PROG_MAKE_SET
AC_HEADER_STDC
AC_PROG_EGREP
# Check for the libraries we will need.
AC_CHECK_LIB(m,sqrt,,AC_MSG_ERROR(something is wrong with the math library!))
......@@ -683,6 +832,42 @@ AC_SUBST([GSL_LIBS])
AC_SUBST([GSL_INCS])
AM_CONDITIONAL([HAVEGSL],[test -n "$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 $LIBS"],
......@@ -696,7 +881,7 @@ have_pthread_barrier="no"
AC_CHECK_LIB(pthread, pthread_barrier_init,
have_pthread_barrier="yes",
AC_MSG_WARN(POSIX implementation does not have barriers. SWIFT will use home-made ones.))
if test "x$have_pthread_barrier" == "xyes"; then
if test "x$have_pthread_barrier" = "xyes"; then
AC_DEFINE([HAVE_PTHREAD_BARRIERS], [1], [The posix library implements barriers])
fi
......@@ -728,7 +913,22 @@ if test "x$with_metis" != "xno"; then
fi
AC_CHECK_LIB([metis],[METIS_PartGraphKway], [have_metis="yes"],
[have_metis="no"], $METIS_LIBS)
if test "$have_metis" == "yes"; then
# Recent METIS releases have an external GKlib, test for that before
# giving up. Assume sane and in the same directories.
if test "x$have_metis" = "xno"; then
if test "x$with_metis" != "xyes" -a "x$with_metis" != "x"; then
METIS_LIBS="-L$with_metis/lib -lmetis -lGKlib"
METIS_INCS="-I$with_metis/include"
else
METIS_LIBS="-lmetis -lGKlib"
METIS_INCS=""
fi
AC_CHECK_LIB([metis],[METIS_PartGraphRecursive], [have_metis="yes"],
[have_metis="no"], $METIS_LIBS)
fi
if test "$have_metis" = "yes"; then
AC_DEFINE([HAVE_METIS],1,[The METIS library is present.])
else
AC_MSG_ERROR("Failed to find a METIS library")
......@@ -761,10 +961,9 @@ if test "x$with_parmetis" != "xno"; then
fi
AC_CHECK_LIB([parmetis],[ParMETIS_V3_RefineKway], [have_parmetis="yes"],
[have_parmetis="no"], $PARMETIS_LIBS)
if test "$have_parmetis" == "no"; then
# A build may use an external METIS library, check for that.
if test "$have_parmetis" = "no"; then
if test "x$with_parmetis" != "xyes" -a "x$with_parmetis" != "x"; then
PARMETIS_LIBS="-L$with_parmetis/lib -lparmetis -lmetis"
PARMETIS_INCS="-I$with_parmetis/include"
......@@ -775,9 +974,23 @@ if test "x$with_parmetis" != "xno"; then
# Note use different function to avoid caching of first check.
AC_CHECK_LIB([parmetis],[ParMETIS_V3_PartKway], [have_parmetis="yes"],
[have_parmetis="no"], [$METIS_LIBS $PARMETIS_LIBS])
fi
# A build may use an external GKlib in later releases...
if test "$have_parmetis" = "no"; then
if test "x$with_parmetis" != "xyes" -a "x$with_parmetis" != "x"; then
PARMETIS_LIBS="-L$with_parmetis/lib -lparmetis -lGKlib"
PARMETIS_INCS="-I$with_parmetis/include"
else
PARMETIS_LIBS="-lparmetis -lGKlib"
PARMETIS_INCS=""
fi
# Note use different function to avoid caching of first check.
AC_CHECK_LIB([parmetis],[ParMETIS_V3_PartGeom], [have_parmetis="yes"],
[have_parmetis="no"], [$METIS_LIBS $PARMETIS_LIBS])
fi
if test "$have_parmetis" == "yes"; then
if test "$have_parmetis" = "yes"; then
AC_DEFINE([HAVE_PARMETIS],1,[The ParMETIS library is present.])
else
AC_MSG_ERROR("Failed to find a ParMETIS library")
......@@ -799,8 +1012,11 @@ AH_VERBATIM([__STDC_FORMAT_MACROS],
# Check for FFTW. We test for this in the standard directories by default,
# and only disable if using --with-fftw=no or --without-fftw. When a value
# is given FFTW must be found.
# If FFTW is found, we check whether this is the threaded version.
# If FFTW is found, we check whether this is the threaded or openmp version.
have_fftw="no"
have_mpi_fftw="no"
have_threaded_fftw="no"
have_openmp_fftw="no"
AC_ARG_WITH([fftw],
[AS_HELP_STRING([--with-fftw=PATH],
[root directory where fftw is installed @<:@yes/no@:>@]
......@@ -853,14 +1069,69 @@ if test "x$with_fftw" != "xno"; then
# Verify that the library is threaded
AC_CHECK_LIB([fftw3],[fftw_init_threads],[have_threaded_fftw="yes"],
[have_threaded_fftw="no"], $FFTW_THREADED_LIBS)
[have_threaded_fftw="no"], $FFTW_THREADED_LIBS)
# If found, update things
if test "x$have_threaded_fftw" = "xyes"; then
AC_DEFINE([HAVE_THREADED_FFTW],1,[The threaded FFTW library appears to be present.])
FFTW_LIBS=$FFTW_THREADED_LIBS
FFTW_INCS=$FFTW_THREADED_INCS
have_fftw="yes - threaded"
else
# Same checks for OpenMP if preferred threaded failed.
if test "x$with_fftw" != "xyes" -a "x$with_fftw" != "xtest" -a "x$with_fftw" != "x"; then
FFTW_OPENMP_LIBS="-L$with_fftw/lib -lfftw3_omp -lfftw3"
FFTW_OPENMP_INCS="-I$with_fftw/include"
else
FFTW_OPENMP_LIBS="-lfftw3_omp -lfftw3"
FFTW_OPENMP_INCS=""
fi
# Verify that the library works. Note requires AX_OPENMP called above.
old_CFLAGS=$CFLAGS
CFLAGS="$CFLAGS $OPENMP_CFLAGS"
AC_CHECK_LIB([fftw3],[fftw_init_threads],[have_openmp_fftw="yes"],
[have_openmp_fftw="no"], $FFTW_OPENMP_LIBS)
# If found, update things
if test "x$have_openmp_fftw" = "xyes"; then
# Note OpenMP and pthreads use mostly the same calls, so define both.
AC_DEFINE([HAVE_THREADED_FFTW],1,[The threaded OpenMP FFTW library appears to be present.])
AC_DEFINE([HAVE_OPENMP_FFTW],1,[The OpenMP FFTW library appears to be present.])
FFTW_LIBS=$FFTW_OPENMP_LIBS
FFTW_INCS=$FFTW_OPENMP_INCS
else
# Put CFLAGS back.
CFLAGS=$old_CFLAGS
fi
fi
fi
# If MPI mesh gravity is not disabled, check whether we have the MPI version of FFTW
if test "x$enable_mpi" = "xyes" -a "x$with_mpi_mesh_gravity" != "xno"; then
# Was FFTW's location specifically given?
if test "x$with_fftw" != "xyes" -a "x$with_fftw" != "xtest" -a "x$with_fftw" != "x"; then
FFTW_MPI_LIBS="-L$with_fftw/lib -lfftw3_mpi -lfftw3"
FFTW_MPI_INCS="-I$with_fftw/include"
else
FFTW_MPI_LIBS="-lfftw3_mpi -lfftw3"
FFTW_MPI_INCS=""
fi
# Verify that the library has MPI support
AC_CHECK_LIB([fftw3],[fftw_mpi_init],[have_mpi_fftw="yes"],
[have_mpi_fftw="no"], $FFTW_MPI_LIBS)
# If found, update things. Don't add MPI flags to FFTW_*_LIBS etc because
# we don't want to link the MPI library into the non-MPI swift executable.
if test "x$have_mpi_fftw" = "xyes"; then
AC_DEFINE([HAVE_MPI_FFTW],1,[The MPI FFTW library appears to be present.])
else
if test "x$with_mpi_mesh_gravity" = "xyes" ; then
AC_MSG_ERROR("Unable to find FFTW MPI library for MPI mesh gravity")
fi
fi
fi
fi
......@@ -872,6 +1143,7 @@ AC_ARG_WITH([arm-fftw],
[with_arm_fftw="$withval"],
[with_arm_fftw=no]
)
have_arm_fftw="no"
if test "x$with_arm_fftw" != "xno"; then
# Was FFTW's location specifically given?
......@@ -888,14 +1160,12 @@ if test "x$with_arm_fftw" != "xno"; then
AC_CHECK_LIB([armpl_lp64],[fftw_malloc],[have_fftw="yes"],[have_fftw="no"],$FFTW_LIBS)
if test "x$have_arm_fftw" != "xno"; then
AC_DEFINE([HAVE_FFTW],1,[The FFTW library appears to be present.])
have_fftw="yes - ARM"
fi
# FFTW was specified, check that it was a valid location.
else
AC_CHECK_LIB([armpl_lp64],[fftw_malloc],
AC_DEFINE([HAVE_FFTW],1,[The FFTW library appears to be present.]),
AC_MSG_ERROR(something is wrong with the FFTW library!), $FFTW_LIBS)
have_fftw="yes - ARM"
fi
# FFTW was requested not to be used.
......@@ -933,6 +1203,10 @@ AC_SUBST([FFTW_LIBS])
AC_SUBST([FFTW_INCS])
AM_CONDITIONAL([HAVEFFTW],[test -n "$FFTW_LIBS"])
AC_SUBST([FFTW_MPI_LIBS])
AC_SUBST([FFTW_MPI_INCS])
AM_CONDITIONAL([HAVEMPIFFTW],[test -n "$FFTW_MPI_LIBS"])
# Check for -lprofiler usually part of the gperftools along with tcmalloc.
have_profiler="no"
AC_ARG_WITH([profiler],
......@@ -1007,7 +1281,7 @@ if test "x$with_tcmalloc" != "xno"; then
# Prevent compilers that replace the calls with built-ins (GNU 99) from doing so.
case "$ax_cv_c_compiler_vendor" in
intel | gnu | clang)
intel | gnu | clang | oneapi)
CFLAGS="$CFLAGS -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free"
;;
esac
......@@ -1050,7 +1324,7 @@ if test "x$with_jemalloc" != "xno"; then
# Prevent compilers that replace the regular calls with built-ins (GNU 99) from doing so.
case "$ax_cv_c_compiler_vendor" in
intel | gnu | clang)
intel | gnu | clang | oneapi)
CFLAGS="$CFLAGS -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free"
;;
esac
......@@ -1093,7 +1367,7 @@ if test "x$with_tbbmalloc" != "xno"; then
# Prevent compilers that replace the calls with built-ins (GNU 99) from doing so.
case "$ax_cv_c_compiler_vendor" in
intel | gnu | clang)
intel | gnu | clang | oneapi)
CFLAGS="$CFLAGS -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free"
;;
esac
......@@ -1115,45 +1389,6 @@ AC_ARG_WITH([random-seed],
)
AC_DEFINE_UNQUOTED([SWIFT_RANDOM_SEED_XOR], [$with_random_seed],[Value of the random seed.])
# Check for python.
have_python="no"
AC_ARG_WITH([python],
[AS_HELP_STRING([--with-python=PATH],
[root directory where python is installed @<:@yes/no@:>@]
)],
[with_python="$withval"],
[with_python="no"]
)
if test "x$with_python" != "xno"; then
if test "$with_python" == ""; then
# use linux default python
with_python="/usr/"
fi
AM_PATH_PYTHON([3], [], [AC_MSG_ERROR(python not found)])
AC_ARG_VAR([PYTHON_LIBS], [Linking flags for python, bypassing python-config])
AC_ARG_VAR([PYTHON_INCS], [Include flags for python, bypassing python-config])
AC_ARG_VAR([PYTHON_CONFIG], [Path to python-config])
AS_IF([test -z "$PYTHON_INCS"], [
AS_IF([test -z "$PYTHON_CONFIG"], [
AC_PATH_PROGS([PYTHON_CONFIG],
[python$PYTHON_VERSION-config python-config],
[no],
[`dirname $PYTHON`])
AS_IF([test "$PYTHON_CONFIG" = no], [AC_MSG_ERROR([cannot find python-config for $PYTHON.])])
])
AC_MSG_CHECKING([python include flags])
PYTHON_INCS=`$PYTHON_CONFIG --includes`
PYTHON_LIBS=`$PYTHON_CONFIG --ldflags`
AC_MSG_RESULT([$PYTHON_INCS])
AC_MSG_RESULT([$PYTHON_LIBS])
])
have_python="yes"
AC_DEFINE([HAVE_PYTHON],1,[Python appears to be present.])
fi
AC_SUBST([PYTHON_INCS])
AC_SUBST([PYTHON_LIBS])
AM_CONDITIONAL([HAVEPYTHON],[test -n "$PYTHON_INCS"])
# Check for HDF5. This is required.
AX_LIB_HDF5
......@@ -1196,6 +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 "$LUSTREAPI_LIBS"])
# Check for grackle.
have_grackle="no"
AC_ARG_WITH([grackle],
......@@ -1218,7 +1485,6 @@ if test "x$with_grackle" != "xno"; then
have_grackle="yes"
echo $GRACKLE_LIBS
AS_VAR_APPEND([GRACKLE_LIBS], ["$FCLIBS"])
AC_CHECK_LIB(
......@@ -1227,14 +1493,30 @@ if test "x$with_grackle" != "xno"; then
[AC_DEFINE([HAVE_GRACKLE],1,[The GRACKLE library appears to be present.])
AC_DEFINE([CONFIG_BFLOAT_8],1,[Use doubles in grackle])
],
[AC_MSG_ERROR(Cannot find grackle library! You need to have a version >= 3.1.1)],
[AC_MSG_ERROR(Cannot find grackle library! Please consult the documentation for specific version required.)],
[$GRACKLE_LIBS])
AC_CHECK_LIB(
[grackle],
[set_velocity_units],
[ : ], # : means do nothing. Leaving this argument empty triggers AC default behaviour, which breaks stuff down the line.
[AC_MSG_ERROR(Wrong grackle library version. Please consult the documentation for specifics.)],
[$GRACKLE_LIBS])
AC_CHECK_LIB(
[grackle],
[get_grackle_version],
[ : ], # : means do nothing
[AC_MSG_ERROR(Wrong grackle library version. Please consult the documentation for specifics.)],
[$GRACKLE_LIBS])
fi
AC_SUBST([GRACKLE_LIBS])
AC_SUBST([GRACKLE_INCS])
AM_CONDITIONAL([HAVEGRACKLE],[test -n "$GRACKLE_LIBS"])
# Check for VELOCIraptor.
# Check for VELOCIraptor, non-MPI.
have_velociraptor="no"
AC_ARG_WITH([velociraptor],
[AS_HELP_STRING([--with-velociraptor=PATH],
......@@ -1244,11 +1526,9 @@ AC_ARG_WITH([velociraptor],
[with_velociraptor="no"]
)
if test "x$with_velociraptor" != "xno"; then
AC_PROG_FC
AC_FC_LIBRARY_LDFLAGS
if test "x$with_velociraptor" != "xyes" -a "x$with_velociraptor" != "x"; then
VELOCIRAPTOR_LIBS="-L$with_velociraptor -lvelociraptor -lmpi -lstdc++ -lhdf5"
CFLAGS="$CFLAGS -fopenmp"
VELOCIRAPTOR_LIBS="-L$with_velociraptor -lvelociraptor -lstdc++ -lhdf5"
CFLAGS="$CFLAGS $OPENMP_CFLAGS"
else
VELOCIRAPTOR_LIBS=""
fi
......@@ -1259,8 +1539,8 @@ if test "x$with_velociraptor" != "xno"; then
AC_CHECK_LIB(
[velociraptor],
[InitVelociraptor],
[AC_DEFINE([HAVE_VELOCIRAPTOR],1,[The VELOCIraptor library appears to be present.])],
[AC_MSG_ERROR(Cannot find VELOCIraptor library at $with_velociraptor or incompatible HDF5 library loaded.)],
[AC_DEFINE([HAVE_VELOCIRAPTOR],1,[The non-MPI VELOCIraptor library appears to be present.])],
[AC_MSG_ERROR(Cannot find non-MPI VELOCIraptor library at $with_velociraptor or incompatible HDF5 library loaded.)],
[$VELOCIRAPTOR_LIBS $HDF5_LDFLAGS $HDF5_LIBS $GSL_LIBS]
)
fi
......@@ -1268,7 +1548,7 @@ AC_SUBST([VELOCIRAPTOR_LIBS])
AM_CONDITIONAL([HAVEVELOCIRAPTOR],[test -n "$VELOCIRAPTOR_LIBS"])
# Now that we found VELOCIraptor, let's check how it was compiled.
if test "$have_velociraptor" == "yes"; then
if test "$have_velociraptor" = "yes"; then
AC_CHECK_LIB(
[velociraptor],
[VR_NOMASS],
......@@ -1278,6 +1558,57 @@ if test "$have_velociraptor" == "yes"; then
)
fi
# Check for MPI VELOCIraptor, same as above.
have_mpi_velociraptor="no"
AC_ARG_WITH([velociraptor-mpi],
[AS_HELP_STRING([--with-velociraptor-mpi=PATH],
[Directory where MPI version of velociraptor library exists @<:@yes/no@:>@]
)],
[with_mpi_velociraptor="$withval"],
[with_mpi_velociraptor="no"]
)
if test "x$with_mpi_velociraptor" != "xno"; then
if test "x$with_mpi_velociraptor" != "xyes" -a "x$with_mpi_velociraptor" != "x"; then
VELOCIRAPTOR_MPI_LIBS="-L$with_mpi_velociraptor -lvelociraptor -lmpi -lstdc++ -lhdf5"
CFLAGS="$CFLAGS -fopenmp"
else
VELOCIRAPTOR_MPI_LIBS=""
fi
have_mpi_velociraptor="yes"
AS_VAR_APPEND([VELOCIRAPTOR_MPI_LIBS], ["$FCLIBS"])
AC_CHECK_LIB(
[velociraptor],
[InitVelociraptor],
[AC_DEFINE([HAVE_MPI_VELOCIRAPTOR],1,[The MPI VELOCIraptor library appears to be present.])],
[AC_MSG_ERROR(Cannot find MPI VELOCIraptor library at $with_mpi_velociraptor or incompatible HDF5 library loaded.)],
[$VELOCIRAPTOR_MPI_LIBS $HDF5_LDFLAGS $HDF5_LIBS $GSL_LIBS]
)
fi
AC_SUBST([VELOCIRAPTOR_MPI_LIBS])
AM_CONDITIONAL([HAVEVELOCIRAPTOR],[test -n "$VELOCIRAPTOR_MPI_LIBS"])
# Let's check how this one was compiled.
if test "$have_mpi_velociraptor" = "yes"; then
AC_CHECK_LIB(
[velociraptor],
[VR_NOMASS],
[AC_DEFINE([HAVE_VELOCIRAPTOR_WITH_NOMASS],1,[The MPI VELOCIraptor library has been compiled with the NOMASS option. Only useful if running a uniform box.])],
[AC_MSG_RESULT(VELOCIraptor not compiled to so as to *not* store masses per particle.)],
[$VELOCIRAPTOR_MPI_LIBS $HDF5_LDFLAGS $HDF5_LIBS $GSL_LIBS]
)
fi
# If we have one library, but not the other then use that for both.
if test "$have_mpi_velociraptor" = "yes" -a "$have_velociraptor" != "yes"; then
VELOCIRAPTOR_LIBS="$VELOCIRAPTOR_MPI_LIBS"
AC_SUBST([VELOCIRAPTOR_LIBS])
elif test "$have_velociraptor" = "yes" -a "$have_mpi_velociraptor" != "yes"; then
VELOCIRAPTOR_MPI_LIBS="$VELOCIRAPTOR_LIBS"
AC_SUBST([VELOCIRAPTOR_MPI_LIBS])
fi
# Check for dummy VELOCIraptor.
AC_ARG_ENABLE([dummy-velociraptor],
[AS_HELP_STRING([--enable-dummy-velociraptor],
......@@ -1306,9 +1637,57 @@ if test "$enable_velociraptor_orphans" = "yes"; then
AC_DEFINE([HAVE_VELOCIRAPTOR_ORPHANS], 1, [Orphan particles should be written out])
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 if lightcone output is on.
AC_ARG_ENABLE([lightcone],
[AS_HELP_STRING([--enable-lightcone],
[Activate lightcone outputs.],
)],
[enable_lightcone="$enableval"],
[enable_lightcone="no"]
)
if test "$enable_lightcone" = "yes"; then
# Check for healpix for lightcone maps. May require cfitsio
# This sets CHEALPIX_LIBS and CHEALPIX_CFLAGS and #defines HAVE_CHEALPIX.
# It also adds a --with-cfitsio flag in case cfitsio is installed in a
# different location from healpix.
GV_FIND_LIBRARY([cfitsio], [CFITSIO], [cfitsio], [cfitsio], [ffclos])
TMP_LIBS=${LIBS}
LIBS="${CFITSIO_LIBS} ${LIBS}"
GV_FIND_LIBRARY([chealpix], [CHEALPIX], [chealpix], [chealpix], [ang2vec])
LIBS=${TMP_LIBS}
have_chealpix=${USE_CHEALPIX}
CHEALPIX_LIBS="${CHEALPIX_LIBS} ${CFITSIO_LIBS}"
AC_DEFINE([WITH_LIGHTCONE], 1, [Enable lightcone outputs])
if test "$have_chealpix" != "yes"; then
AC_MSG_ERROR([Lightcone output requires the HEALPix C API. Please configure with --with-chealpix.])
fi
# Also need to make sure we have GSL if we're making lightcones
if test "$have_gsl" != "yes"; then
AC_MSG_ERROR([Lightcone output requires GSL. Please configure with --with-gsl.])
fi
else
have_chealpix="no"
fi
# Check for floating-point exception trapping support.
#
# We do not allow this to be enabled when optimizing as compilers do operations
# which are unsafe for speed. This can result in FPEs on valid vector
# operations when additional padding is used. This has been seen on clang and
# GCC based compilers.
if test "$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],
......@@ -1366,6 +1745,64 @@ if test "$ac_cv_func_pthread_setaffinity_np" = "yes" -a "x$with_numa" != "xno";
fi
AC_SUBST([NUMA_LIBS])
# Check for Sundials (required for the SPHM1RT library).
# There is a problems with the headers of this library
# as they do not pass the strict prototypes check when
# installed outside of the system directories. So we
# need to do this check in two phases.
have_sundials="no"
SUNDIALS_LIBS=""
SUNDIALS_INCS=""
AC_ARG_WITH([sundials],
[AS_HELP_STRING([--with-sundials=PATH],
[root directory where sundials is installed @<:@yes/no@:>@]
)],
[with_sundials="$withval"],
[with_sundials="no"]
)
if test "x$with_sundials" != "xno"; then
AC_PROG_FC
AC_FC_LIBRARY_LDFLAGS
if test "x$with_sundials" != "xyes" -a "x$with_sundials" != "x"; then
SUNDIALS_LIBS="-L$with_sundials/lib -lsundials_cvode -lsundials_nvecserial -lsundials_sunlinsoldense -lsundials_sunmatrixdense"
SUNDIALS_INCS="-I$with_sundials/include"
else
SUNDIALS_LIBS="-lsundials_cvode -lsundials_nvecserial -lsundials_sunlinsoldense -lsundials_sunmatrixdense"
SUNDIALS_INCS=""
fi
AC_CHECK_LIB([sundials_cvode], [CVode], [have_sundials="yes"],
[have_sundials="no"], $SUNDIALS_LIBS)
if test "$have_sundials" == "yes"; then
AC_DEFINE([HAVE_SUNDIALS],1,[The SUNDIALS library is present.])
else
if test "x$with_sundials" != "xyes" -a "x$with_sundials" != "x"; then
# It might be that the libraries are in
# /lib64 rather than /lib
SUNDIALS_LIBS="-L$with_sundials/lib64 -lsundials_cvode -lsundials_nvecserial -lsundials_sunlinsoldense -lsundials_sunmatrixdense"
# unset cached result of previous AC_CHECK_LIB
unset ac_cv_lib_sundials_cvode_CVode
AC_CHECK_LIB([sundials_cvode], [CVode], [have_sundials="yes"], [have_sundials="no"], $SUNDIALS_LIBS)
if test "$have_sundials" == "yes"; then
AC_DEFINE([HAVE_SUNDIALS],1,[The SUNDIALS library is present.])
else
AC_MSG_ERROR("Failed to find a SUNDIALS library")
fi
else
AC_MSG_ERROR("Failed to find a SUNDIALS library")
fi
fi
fi
AC_SUBST([SUNDIALS_LIBS])
# Check for Intel and PowerPC intrinsics header optionally used by vector.h.
AC_CHECK_HEADERS([immintrin.h], [], [],
[#ifdef HAVE_IMMINTRIN_H
......@@ -1379,8 +1816,33 @@ AC_CHECK_HEADERS([altivec.h], [], [],
])
# Check for timing functions needed by cycle.h.
AC_HEADER_TIME
AC_CHECK_HEADERS([sys/time.h c_asm.h intrinsics.h mach/mach_time.h])
AC_CHECK_HEADERS_ONCE([sys/time.h])
if test $ac_cv_header_sys_time_h = yes; then
AC_DEFINE([TIME_WITH_SYS_TIME],[1],[Define to 1 if you can safely include both <sys/time.h>
and <time.h>. This macro is obsolete.])
fi
AC_CHECK_HEADERS([sys/time.h], [], [],
[#ifdef HAVE_SYS_TIME_H
# include <sys/time.h>
#endif
])
AC_CHECK_HEADERS([c_asm.h], [], [],
[#ifdef HAVE_C_ASM_H
# include <c_asm.h>
#endif
])
AC_CHECK_HEADERS([intrinsics.h], [], [],
[#ifdef HAVE_INTRINSICS_H
# include <intrinsics.h>
#endif
])
AC_CHECK_HEADERS([mach/mach_time.h], [], [],
[#ifdef HAVE_MACH_MACH_TIME_H
# include <mach/mach_time.h>
#endif
])
AC_CHECK_TYPE([hrtime_t],[AC_DEFINE(HAVE_HRTIME_T, 1, [Define to 1 if hrtime_t
is defined in <sys/time.h>])],,
[#if HAVE_SYS_TIME_H
......@@ -1398,27 +1860,25 @@ AC_LINK_IFELSE([AC_LANG_PROGRAM(
AC_MSG_RESULT($rtc_ok)
# Special timers for the ARM v7 platforms (taken from FFTW-3 to match their cycle.h)
AC_ARG_ENABLE(armv7a-cntvct, [AC_HELP_STRING([--enable-armv7a-cntvct],[enable the cycle counter on Armv7a via the CNTVCT register])], have_armv7acntvct=$enableval)
AC_ARG_ENABLE(armv7a-cntvct, [AS_HELP_STRING([--enable-armv7a-cntvct],[enable the cycle counter on Armv7a via the CNTVCT register])], have_armv7acntvct=$enableval)
if test "$have_armv7acntvct"x = "yes"x; then
AC_DEFINE(HAVE_ARMV7A_CNTVCT,1,[Define if you have enabled the CNTVCT cycle counter on ARMv7a])
AC_DEFINE(HAVE_ARMV7A_CNTVCT,1,[Define if you have enabled the CNTVCT cycle counter on ARMv7a])
fi
AC_ARG_ENABLE(armv7a-pmccntr, [AC_HELP_STRING([--enable-armv7a-pmccntr],[enable the cycle counter on Armv7a via the PMCCNTR register])], have_armv7apmccntr=$enableval)
AC_ARG_ENABLE(armv7a-pmccntr, [AS_HELP_STRING([--enable-armv7a-pmccntr],[enable the cycle counter on Armv7a via the PMCCNTR register])], have_armv7apmccntr=$enableval)
if test "$have_armv7apmccntr"x = "yes"x; then
AC_DEFINE(HAVE_ARMV7A_PMCCNTR,1,[Define if you have enabled the PMCCNTR cycle counter on ARMv7a])
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 "$ax_cv_c_compiler_vendor" = "clang"; then
AC_CHECK_LIB([m],[__exp10], [AC_DEFINE([HAVE___EXP10],1,[The __exp10 function is present.])])
AC_CHECK_LIB([m],[__exp10f], [AC_DEFINE([HAVE___EXP10F],1,[The __exp10f function is present.])])
fi
AC_CHECK_LIB([m],[__exp10], [AC_DEFINE([HAVE___EXP10],1,[The __exp10 function is present.])])
AC_CHECK_LIB([m],[__exp10f], [AC_DEFINE([HAVE___EXP10F],1,[The __exp10f function is present.])])
# Check if we have native sincos and sincosf functions. If not failback to our
# Check if we have native sincos and sincosf functions. If not fallback to our
# implementations. On Apple/CLANG we have __sincos, so also check for that
# if the compiler is clang.
AC_CHECK_LIB([m],[sincos], [AC_DEFINE([HAVE_SINCOS],1,[The sincos function is present.])])
......@@ -1428,6 +1888,29 @@ if test "$ax_cv_c_compiler_vendor" = "clang"; then
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
# so only when optimizing.
if test "$enable_opt" = "yes" -a "$ax_cv_c_compiler_vendor" = "clang"; then
have_almfast="yes"
AC_CHECK_LIB([almfast],[amd_fastexp],[LIBS="-fveclib=AMDLIBM -fsclrlib=AMDLIBM -lalmfast -lamdlibm $LIBS"],[have_almfast="no"],[-lamdlibm -lm])
if test "$have_almfast" = "no"; then
# Less optimized version.
AC_CHECK_LIB([amdlibm],[sqrt],,,[-lm])
fi
fi
# Check for glibc extension backtrace().
AC_CHECK_FUNCS([backtrace backtrace_symbols])
# Add warning flags by default, if these can be used. Option =error adds
# -Werror to GCC, clang and Intel. Note do this last as compiler tests may
......@@ -1444,12 +1927,13 @@ if test "$enable_warn" != "no"; then
# AX_CFLAGS_WARN_ALL does not give good warning flags for the Intel compiler
# We will do this by hand instead and only default to the macro for unknown compilers
case "$ax_cv_c_compiler_vendor" in
gnu | clang)
gnu | clang | oneapi)
CFLAGS="$CFLAGS -Wall -Wextra -Wno-unused-parameter -Wshadow"
;;
intel)
CFLAGS="$CFLAGS -w2 -Wunused-variable -Wshadow"
;;
*)
AX_CFLAGS_WARN_ALL
;;
......@@ -1458,8 +1942,12 @@ if test "$enable_warn" != "no"; then
# Add a "choke on warning" flag if it exists
if test "$enable_warn" = "error"; then
case "$ax_cv_c_compiler_vendor" in
intel | gnu | clang)
intel | clang | oneapi)
CFLAGS="$CFLAGS -Werror"
;;
gnu)
# Fix for issue with IPO and GCC 14
CFLAGS="$CFLAGS -Werror -Wno-alloc-size-larger-than"
;;
esac
fi
......@@ -1499,6 +1987,26 @@ if test "$have_numa" != "no"; then
fi
AC_SUBST([NUMA_INCS])
# Second part of the Sundials library checks.
# We now decide if we need to use -isystem to
# get around the strict-prototypes problem. Assumes
# isystem is available when strict-prototypes is.
if test "x$with_sundials" != "xno"; then
if test "x$with_sundials" != "xyes" -a "x$with_sundials" != "x"; then
case "$CFLAGS" in
*strict-prototypes*)
SUNDIALS_INCS="-isystem$with_sundials/include"
;;
*)
SUNDIALS_INCS="-I$with_sundials/include"
;;
esac
fi
fi
AC_SUBST([SUNDIALS_INCS])
# Various package configuration options.
# Master subgrid options
......@@ -1507,7 +2015,8 @@ AC_SUBST([NUMA_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, QLA, EAGLE, EAGLE-XL 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="$withval"],
[with_subgrid=none]
......@@ -1523,6 +2032,7 @@ with_subgrid_stars=none
with_subgrid_star_formation=none
with_subgrid_feedback=none
with_subgrid_sink=none
with_subgrid_extra_io=none
case "$with_subgrid" in
yes)
......@@ -1538,7 +2048,32 @@ case "$with_subgrid" in
with_subgrid_star_formation=GEAR
with_subgrid_feedback=GEAR
with_subgrid_black_holes=none
with_subgrid_sink=GEAR
with_subgrid_extra_io=none
enable_fof=no
;;
GEAR-G3)
with_subgrid_cooling=grackle_3
with_subgrid_chemistry=GEAR_10
with_subgrid_pressure_floor=none
with_subgrid_stars=GEAR
with_subgrid_star_formation=GEAR
with_subgrid_feedback=GEAR
with_subgrid_black_holes=none
with_subgrid_sink=GEAR
with_subgrid_extra_io=none
enable_fof=no
;;
AGORA)
with_subgrid_cooling=grackle_0
with_subgrid_chemistry=AGORA
with_subgrid_pressure_floor=GEAR
with_subgrid_stars=GEAR
with_subgrid_star_formation=GEAR
with_subgrid_feedback=AGORA
with_subgrid_black_holes=none
with_subgrid_sink=none
with_subgrid_extra_io=none
enable_fof=no
;;
QLA)
......@@ -1546,27 +2081,41 @@ case "$with_subgrid" in
with_subgrid_chemistry=QLA
with_subgrid_tracers=none
with_subgrid_entropy_floor=QLA
with_subgrid_stars=none
with_subgrid_stars=basic
with_subgrid_star_formation=QLA
with_subgrid_feedback=none
with_subgrid_black_holes=none
with_subgrid_sink=none
with_subgrid_extra_io=none
enable_fof=no
;;
EAGLE)
with_subgrid_cooling=EAGLE
with_subgrid_chemistry=EAGLE
with_subgrid_tracers=EAGLE
with_subgrid_entropy_floor=EAGLE
QLA-EAGLE)
with_subgrid_cooling=QLA-EAGLE
with_subgrid_chemistry=QLA
with_subgrid_tracers=none
with_subgrid_entropy_floor=QLA
with_subgrid_stars=basic
with_subgrid_star_formation=QLA
with_subgrid_feedback=none
with_subgrid_black_holes=none
with_subgrid_sink=none
enable_fof=no
;;
EAGLE)
with_subgrid_cooling=EAGLE
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=EAGLE
with_subgrid_sink=none
with_subgrid_extra_io=none
enable_fof=yes
;;
EAGLE-XL)
with_subgrid_cooling=COLIBRE
with_subgrid_cooling=PS2020
with_subgrid_chemistry=EAGLE
with_subgrid_tracers=EAGLE
with_subgrid_entropy_floor=EAGLE
......@@ -1575,6 +2124,33 @@ case "$with_subgrid" in
with_subgrid_feedback=EAGLE
with_subgrid_black_holes=EAGLE
with_subgrid_sink=none
with_subgrid_extra_io=none
enable_fof=yes
;;
SPIN_JET_EAGLE)
with_subgrid_cooling=EAGLE
with_subgrid_chemistry=EAGLE
with_subgrid_tracers=EAGLE
with_subgrid_entropy_floor=EAGLE
with_subgrid_stars=EAGLE
with_subgrid_star_formation=EAGLE
with_subgrid_feedback=EAGLE
with_subgrid_black_holes=SPIN_JET
with_subgrid_sink=none
with_subgrid_extra_io=none
enable_fof=yes
;;
SPIN_JET_EAGLE-XL)
with_subgrid_cooling=PS2020
with_subgrid_chemistry=EAGLE
with_subgrid_tracers=EAGLE
with_subgrid_entropy_floor=EAGLE
with_subgrid_stars=EAGLE
with_subgrid_star_formation=EAGLE
with_subgrid_feedback=EAGLE
with_subgrid_black_holes=SPIN_JET
with_subgrid_sink=none
with_subgrid_extra_io=none
enable_fof=yes
;;
*)
......@@ -1647,13 +2223,16 @@ fi
# Hydro scheme.
AC_ARG_WITH([hydro],
[AS_HELP_STRING([--with-hydro=<scheme>],
[Hydro dynamics to use @<:@gadget2, minimal, pressure-entropy, pressure-energy, pressure-energy-monaghan, phantom, gizmo-mfv, gizmo-mfm, shadowfax, planetary, sphenix, anarchy-pu default: sphenix@:>@]
[Hydro dynamics to use @<:@gadget2, minimal, pressure-entropy, pressure-energy, pressure-energy-monaghan, phantom, gizmo-mfv, gizmo-mfm, shadowswift, planetary, remix, sphenix, gasoline, anarchy-pu default: sphenix@:>@]
)],
[with_hydro="$withval"],
[with_hydro="sphenix"]
)
case "$with_hydro" in
none)
AC_DEFINE([NONE_SPH], [1], [No hydro])
;;
gadget2)
AC_DEFINE([GADGET2_SPH], [1], [Gadget-2 SPH])
;;
......@@ -1674,19 +2253,32 @@ case "$with_hydro" in
;;
gizmo-mfv)
AC_DEFINE([GIZMO_MFV_SPH], [1], [GIZMO MFV SPH])
need_riemann_solver=yes
hydro_does_mass_flux=yes
;;
gizmo-mfm)
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])
;;
gasoline)
AC_DEFINE([GASOLINE_SPH], [1], [Gasoline SPH])
;;
anarchy-du)
AC_DEFINE([SPHENIX_SPH], [1], [SPHENIX SPH])
;;
......@@ -1694,12 +2286,39 @@ case "$with_hydro" in
AC_DEFINE([ANARCHY_PU_SPH], [1], [ANARCHY (PU) SPH])
;;
*)
AC_MSG_ERROR([Unknown hydrodynamics scheme: $with_hydro])
;;
esac
# SPMHD scheme.
AC_ARG_WITH([spmhd],
[AS_HELP_STRING([--with-spmhd=<scheme>],
[Magneto Hydro Dynamics SPH scheme to use @<:@none, direct-induction, direct-induction-fede, vector-potential default:none@:>@]
)],
[with_spmhd="$withval"],
[with_spmhd="none"]
)
case "$with_spmhd" in
none)
AC_DEFINE([NONE_MHD], [1], [No mhd])
;;
*)
AC_MSG_ERROR([Unknown magneto-hydrodynamics scheme: $with_spmhd])
;;
esac
if test "$with_hydro" = "gizmo-mfm" -a "$with_spmhd" != "none"; then
AC_MSG_ERROR([Cannot use an SPMHD scheme alongside a gizmo hydro solver!"])
fi
if test "$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" = "shadowswift" -a "$with_spmhd" != "none"; then
AC_MSG_ERROR([Cannot use an SPMHD scheme alongside a moving mesh hydro solver!"])
fi
# Check if debugging interactions stars is switched on.
AC_ARG_ENABLE([debug-interactions-stars],
[AS_HELP_STRING([--enable-debug-interactions-stars],
......@@ -1710,7 +2329,7 @@ AC_ARG_ENABLE([debug-interactions-stars],
)
if test "$enable_debug_interactions_stars" != "no"; then
AC_DEFINE([DEBUG_INTERACTIONS_STARS],1,[Enable interaction debugging for stars])
if test "$enable_debug_interactions_stars" == "yes"; then
if test "$enable_debug_interactions_stars" = "yes"; then
AC_DEFINE([MAX_NUM_OF_NEIGHBOURS_STARS],256,[The maximum number of particle neighbours to be logged for stars])
[enable_debug_interactions_stars="yes (Logging up to 256 neighbours)"]
else
......@@ -1730,7 +2349,7 @@ AC_ARG_ENABLE([debug-interactions],
if test "$enable_debug_interactions" != "no"; then
if test "$with_hydro" = "gadget2"; then
AC_DEFINE([DEBUG_INTERACTIONS_SPH],1,[Enable interaction debugging])
if test "$enable_debug_interactions" == "yes"; then
if test "$enable_debug_interactions" = "yes"; then
AC_DEFINE([MAX_NUM_OF_NEIGHBOURS],256,[The maximum number of particle neighbours to be logged])
[enable_debug_interactions="yes (Logging up to 256 neighbours)"]
else
......@@ -1752,7 +2371,7 @@ AC_ARG_ENABLE([debug-interactions-sinks],
)
if test "$enable_debug_interactions_sinks" != "no"; then
AC_DEFINE([DEBUG_INTERACTIONS_SINKS],1,[Enable interaction debugging for sinks])
if test "$enable_debug_interactions_sinks" == "yes"; then
if test "$enable_debug_interactions_sinks" = "yes"; then
AC_DEFINE([MAX_NUM_OF_NEIGHBOURS_SINKS],256,[The maximum number of particle neighbours to be logged for sinks])
[enable_debug_interactions_sinks="yes (Logging up to 256 neighbours)"]
else
......@@ -1819,7 +2438,7 @@ esac
# Equation of state
AC_ARG_WITH([equation-of-state],
[AS_HELP_STRING([--with-equation-of-state=<EoS>],
[equation of state @<:@ideal-gas, isothermal-gas, planetary default: ideal-gas@:>@]
[equation of state @<:@ideal-gas, isothermal-gas, barotropic-gas, planetary default: ideal-gas@:>@]
)],
[with_eos="$withval"],
[with_eos="ideal-gas"]
......@@ -1830,6 +2449,9 @@ case "$with_eos" in
;;
isothermal-gas)
AC_DEFINE([EOS_ISOTHERMAL_GAS], [1], [Isothermal gas equation of state])
;;
barotropic-gas)
AC_DEFINE([EOS_BAROTROPIC_GAS], [1], [Barotropic gas equation of state])
;;
planetary)
AC_DEFINE([EOS_PLANETARY], [1], [All planetary equations of state])
......@@ -1865,6 +2487,34 @@ case "$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 "$with_gravity" != "with-multi-softening"; then
AC_MSG_ERROR([Adaptive softening scheme requires the usage of the multi-softening gravity scheme!])
fi
# Riemann solver
AC_ARG_WITH([riemann-solver],
[AS_HELP_STRING([--with-riemann-solver=<solver>],
......@@ -1890,10 +2540,98 @@ case "$with_riemann" in
AC_MSG_ERROR([Unknown Riemann solver: $with_riemann])
;;
esac
if test "x$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$hydro_does_mass_flux" = "xyes"; then
AC_DEFINE([HYDRO_DOES_MASS_FLUX], [1], [Hydro scheme with mass fluxes])
fi
# chemistry function
AC_ARG_WITH([chemistry],
[AS_HELP_STRING([--with-chemistry=<function>],
[chemistry function @<:@none, GEAR_*, AGORA, QLA, EAGLE default: none@:>@
For GEAR, you need to provide the number of elements (e.g. GEAR_10)]
)],
[with_chemistry="$withval"],
[with_chemistry="none"]
)
if test "$with_subgrid" != "none"; then
if test "$with_chemistry" != "none"; then
AC_MSG_ERROR([Cannot provide with-subgrid and with-chemistry together])
else
with_chemistry="$with_subgrid_chemistry"
fi
fi
with_chemistry_name="none"
case "$with_chemistry" in
none)
AC_DEFINE([CHEMISTRY_NONE], [1], [No chemistry function])
;;
GEAR_*)
AC_DEFINE([CHEMISTRY_GEAR], [1], [Chemistry taken from the GEAR model])
number_element=${with_chemistry#*_}
AC_DEFINE_UNQUOTED([GEAR_CHEMISTRY_ELEMENT_COUNT], [$number_element], [Number of element to follow])
with_chemistry_name="GEAR (with $number_element elements)"
with_chemistry="GEAR"
;;
AGORA)
AC_DEFINE([CHEMISTRY_AGORA], [1], [Chemistry taken from the AGORA model])
with_chemistry_name="AGORA"
;;
QLA)
AC_DEFINE([CHEMISTRY_QLA], [1], [Chemistry taken from the Quick-Lyman-alpha model])
with_chemistry_name="QLA"
;;
EAGLE)
AC_DEFINE([CHEMISTRY_EAGLE], [1], [Chemistry taken from the EAGLE model])
with_chemistry_name="EAGLE (9 elements + smoothing)"
;;
*)
AC_MSG_ERROR([Unknown chemistry function: $with_chemistry])
;;
esac
if test "$with_chemistry" != "none"; then
if test "$enable_hand_vec" = "yes"; then
if test "$enable_vec" = "yes"; then
if test "$with_hydro" = "gadget2"; then
AC_MSG_ERROR([Cannot run with hand vectorisation and chemistry yet. Please use --disable-hand-vec])
fi
fi
fi
fi
# Cooling function
AC_ARG_WITH([cooling],
[AS_HELP_STRING([--with-cooling=<model>],
[cooling function @<:@none, const-du, const-lambda, QLA, EAGLE, COLIBRE, Wiersma, Ploeckinger, grackle_* default: none@:>@.
[cooling function @<:@none, const-du, const-lambda, QLA, EAGLE, PS2020, Wiersma, grackle_* default: none@:>@.
For Grackle, you need to provide the primordial chemistry parameter (e.g. grackle_0)]
)],
[with_cooling="$withval"],
......@@ -1908,94 +2646,62 @@ if test "$with_subgrid" != "none"; then
fi
fi
with_cooling_name="none"
case "$with_cooling" in
none)
AC_DEFINE([COOLING_NONE], [1], [No cooling function])
;;
const-du)
AC_DEFINE([COOLING_CONST_DU], [1], [Const du/dt cooling function])
with_cooling_name=$with_cooling
;;
const-lambda)
AC_DEFINE([COOLING_CONST_LAMBDA], [1], [Const Lambda cooling function])
;;
compton)
AC_DEFINE([COOLING_COMPTON], [1], [Compton cooling off the CMB])
with_cooling_name=$with_cooling
;;
grackle_*)
if test "$have_grackle" != "yes"; then
AC_MSG_ERROR([Grackle cooling: You need the grackle library for Grackle cooling. (--with-grackle=PATH)])
fi
AC_DEFINE([COOLING_GRACKLE], [1], [Cooling via the grackle library])
primordial_chemistry=${with_cooling:8}
primordial_chemistry=${with_cooling#*_}
AC_DEFINE_UNQUOTED([COOLING_GRACKLE_MODE], [$primordial_chemistry], [Grackle chemistry network])
with_cooling_name="Grackle $primordial_chemistry"
with_cooling="grackle"
;;
QLA)
AC_DEFINE([COOLING_QLA], [1], [Cooling following the Quick-Lyman-alpha model])
with_cooling="QLA (Ploeckinger+20 tables) with constant primordial Z"
with_cooling_name="QLA (Ploeckinger+20 tables) with constant primordial Z"
;;
QLA-EAGLE)
AC_DEFINE([COOLING_QLA_EAGLE], [1], [Cooling following the Quick-Lyman-alpha model])
with_cooling_name="QLA (Wiersma+09 tables) with constant primordial Z"
;;
EAGLE)
AC_DEFINE([COOLING_EAGLE], [1], [Cooling following the EAGLE model (Wiersma+09 tables)])
with_cooling="EAGLE (Wiersma+09 tables)"
with_cooling_name="EAGLE (Wiersma+09 tables)"
;;
Wiersma)
AC_DEFINE([COOLING_EAGLE], [1], [Cooling following the EAGLE model (Wiersma+09 tables)])
with_cooling="EAGLE (Wiersma+09 tables)"
with_cooling_name="EAGLE (Wiersma+09 tables)"
;;
COLIBRE)
AC_DEFINE([COOLING_COLIBRE], [1], [Cooling following the COLIBRE model (Ploeckinger+20 tables)])
with_cooling="COLIBRE (Ploeckinger+20 tables)"
PS2020)
AC_DEFINE([COOLING_PS2020], [1], [Cooling following the PS2020 model (Ploeckinger+20 tables)])
with_cooling_name="PS2020 (Ploeckinger+20 tables)"
;;
Ploeckinger)
AC_DEFINE([COOLING_COLIBRE], [1], [Cooling following the COLIBRE model (Ploeckinger+20 tables)])
with_cooling="COLIBRE (Ploeckinger+20 tables)"
COLIBRE)
AC_MSG_ERROR([This cooling model changed name. Please use 'PS2020'.])
;;
*)
AC_MSG_ERROR([Unknown cooling function: $with_cooling])
;;
esac
# chemistry function
AC_ARG_WITH([chemistry],
[AS_HELP_STRING([--with-chemistry=<function>],
[chemistry function @<:@none, GEAR_*, QLA, EAGLE default: none@:>@
For GEAR, you need to provide the number of elements (e.g. GEAR_10)]
)],
[with_chemistry="$withval"],
[with_chemistry="none"]
)
if test "$with_subgrid" != "none"; then
if test "$with_chemistry" != "none"; then
AC_MSG_ERROR([Cannot provide with-subgrid and with-chemistry together])
else
with_chemistry="$with_subgrid_chemistry"
fi
fi
case "$with_chemistry" in
none)
AC_DEFINE([CHEMISTRY_NONE], [1], [No chemistry function])
;;
GEAR_*)
AC_DEFINE([CHEMISTRY_GEAR], [1], [Chemistry taken from the GEAR model])
number_element=${with_chemistry:5}
AC_DEFINE_UNQUOTED([GEAR_CHEMISTRY_ELEMENT_COUNT], [$number_element], [Number of element to follow])
;;
QLA)
AC_DEFINE([CHEMISTRY_QLA], [1], [Chemistry taken from the Quick-Lyman-alpha model])
;;
EAGLE)
AC_DEFINE([CHEMISTRY_EAGLE], [1], [Chemistry taken from the EAGLE model])
;;
*)
AC_MSG_ERROR([Unknown chemistry function: $with_chemistry])
;;
esac
if test "$with_chemistry" != "none"; then
if test "$enable_hand_vec" == "yes"; then
if test "$enable_vec" == "yes"; then
if test "$with_hydro" == "gadget2"; then
AC_MSG_ERROR([Cannot run with hand vectorisation and chemistry yet. Please use --disable-hand-vec])
fi
fi
if test "$with_cooling" = "EAGLE" || test "$with_cooling" = "PS2020"; then
if test "$with_chemistry" = "none"; then
AC_MSG_ERROR([Cannot run with EAGLE or PS2020 cooling without chemistry. Please pick a chemistry model])
fi
fi
......@@ -2028,17 +2734,46 @@ case "$with_tracers" in
;;
esac
# Extra fields added to snapshots at i/o time
AC_ARG_WITH([extra_io],
[AS_HELP_STRING([--with-extra-io=<function>],
[Extra i/o field: @<:@none, EAGLE default: none@:>@]
)],
[with_extra_io="$withval"],
[with_extra_io="none"]
)
if test "$with_subgrid" != "none"; then
if test "$with_extra_io" != "none"; then
AC_MSG_ERROR([Cannot provide with-subgrid and with-extra_io together])
else
with_extra_io="$with_subgrid_extra_io"
fi
fi
case "$with_extra_io" in
none)
AC_DEFINE([EXTRA_IO_NONE], [1], [No extra_io function])
;;
EAGLE)
AC_DEFINE([EXTRA_IO_EAGLE], [1], [Extra i/o fields taken from the EAGLE model])
;;
*)
AC_MSG_ERROR([Unknown extra-io choice: $with_extra_io])
;;
esac
# Stellar model.
AC_ARG_WITH([stars],
[AS_HELP_STRING([--with-stars=<model>],
[Stellar model to use @<:@none, EAGLE, GEAR, debug default: none@:>@]
[Stellar model to use @<:@none, basic, EAGLE, GEAR, default: basic@:>@]
)],
[with_stars="$withval"],
[with_stars="none"]
[with_stars="basic"]
)
if test "$with_subgrid" != "none"; then
if test "$with_stars" != "none"; then
if test "$with_stars" != "basic"; then
AC_MSG_ERROR([Cannot provide with-subgrid and with-stars together])
else
with_stars="$with_subgrid_stars"
......@@ -2052,10 +2787,12 @@ case "$with_stars" in
GEAR)
AC_DEFINE([STARS_GEAR], [1], [GEAR stellar model])
;;
basic)
AC_DEFINE([STARS_BASIC], [1], [Basic stellar model])
;;
none)
AC_DEFINE([STARS_NONE], [1], [Basic stellar model])
AC_DEFINE([STARS_NONE], [1], [No stellar model])
;;
*)
AC_MSG_ERROR([Unknown stellar model: $with_stars])
;;
......@@ -2064,7 +2801,7 @@ esac
# Feedback model
AC_ARG_WITH([feedback],
[AS_HELP_STRING([--with-feedback=<model>],
[Feedback model to use @<:@none, EAGLE, GEAR default: none@:>@]
[Feedback model to use @<:@none, EAGLE, EAGLE-thermal, EAGLE-kinetic, GEAR, AGORA default: none@:>@]
)],
[with_feedback="$withval"],
[with_feedback="none"]
......@@ -2078,12 +2815,27 @@ if test "$with_subgrid" != "none"; then
fi
fi
with_feedback_name="none"
case "$with_feedback" in
EAGLE-kinetic)
AC_DEFINE([FEEDBACK_EAGLE_KINETIC], [1], [EAGLE kinetic stellar feedback and evolution model])
with_feedback_name="EAGLE kinetic stellar feedback and evolution model"
;;
EAGLE-thermal)
AC_DEFINE([FEEDBACK_EAGLE_THERMAL], [1], [EAGLE thermal stellar feedback and evolution model])
with_feedback_name="EAGLE thermal stellar feedback and evolution model"
;;
EAGLE)
AC_DEFINE([FEEDBACK_EAGLE], [1], [EAGLE stellar feedback and evolution model])
AC_DEFINE([FEEDBACK_EAGLE_THERMAL], [1], [EAGLE thermal stellar feedback and evolution model])
with_feedback_name="EAGLE thermal stellar feedback and evolution model"
;;
GEAR)
AC_DEFINE([FEEDBACK_GEAR], [1], [GEAR stellar feedback and evolution model])
with_feedback_name="GEAR"
;;
AGORA)
AC_DEFINE([FEEDBACK_AGORA], [1], [AGORA stellar feedback and evolution model])
with_feedback_name="AGORA"
;;
none)
AC_DEFINE([FEEDBACK_NONE], [1], [No feedback])
......@@ -2094,10 +2846,30 @@ case "$with_feedback" in
;;
esac
# For models using ray-based feedback, let the users set different numbers of rays
AC_ARG_WITH([number-of-SNII-rays],
[AS_HELP_STRING([--with-number-of-SNII-rays], [Number of rays to use for the SNII feedback (default: 1)])],
[with_number_of_SNII_rays="$withval"],
[with_number_of_SNII_rays="1"])
AC_DEFINE_UNQUOTED([FEEDBACK_NR_RAYS_SNII], [$with_number_of_SNII_rays], [Number of rays to use for the SNII feedback])
AC_ARG_WITH([number-of-SNIa-rays],
[AS_HELP_STRING([--with-number-of-SNIa-rays], [Number of rays to use for the SNIa feedback (default: 1)])],
[with_number_of_SNIa_rays="$withval"],
[with_number_of_SNIa_rays="1"])
AC_DEFINE_UNQUOTED([FEEDBACK_NR_RAYS_SNIa], [$with_number_of_SNIa_rays], [Number of rays to use for the SNIa feedback])
AC_ARG_WITH([number-of-AGN-rays],
[AS_HELP_STRING([--with-number-of-AGN-rays], [Number of rays to use for the AGN feedback (default: 50)])],
[with_number_of_AGN_rays="$withval"],
[with_number_of_AGN_rays="50"])
AC_DEFINE_UNQUOTED([FEEDBACK_NR_RAYS_AGN], [$with_number_of_AGN_rays], [Number of rays to use for the AGN feedback])
# Black hole model.
AC_ARG_WITH([black-holes],
[AS_HELP_STRING([--with-black-holes=<model>],
[Black holes model to use @<:@none, EAGLE default: none@:>@]
[Black holes model to use @<:@none, EAGLE, SPIN_JET default: none@:>@]
)],
[with_black_holes="$withval"],
[with_black_holes="none"]
......@@ -2118,6 +2890,10 @@ case "$with_black_holes" in
EAGLE)
AC_DEFINE([BLACK_HOLES_EAGLE], [1], [EAGLE black hole model])
;;
SPIN_JET)
AC_DEFINE([BLACK_HOLES_SPIN_JET], [1], [Spin and jet black hole model])
with_black_holes="SPIN_JETS (Husko+22)"
;;
*)
AC_MSG_ERROR([Unknown black-hole model: $with_black_holes])
;;
......@@ -2126,7 +2902,7 @@ esac
# Sink model.
AC_ARG_WITH([sink],
[AS_HELP_STRING([--with-sink=<model>],
[Sink particle model to use @<:@none, default: none@:>@]
[Sink particle model to use @<:@none, GEAR, default: none@:>@]
)],
[with_sink="$withval"],
[with_sink="none"]
......@@ -2144,15 +2920,48 @@ 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])
;;
*)
AC_MSG_ERROR([Unknown sink particle model model: $with_sink])
;;
esac
# Forcing terms
AC_ARG_WITH([forcing],
[AS_HELP_STRING([--with-forcing=<term>],
[Hydrodynamics forcing terms @<:@none, roberts-flow, roberts-flow-acceleration , abc-flowdefault: none@:>@]
)],
[with_forcing="$withval"],
[with_forcing="none"]
)
case "$with_forcing" in
none)
AC_DEFINE([FORCING_NONE], [1], [No external forcing terms])
;;
roberts-flow)
AC_DEFINE([FORCING_ROBERTS_FLOW], [1], [Roberts' flow external forcing terms])
;;
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: $with_forcing])
;;
esac
# External potential
AC_ARG_WITH([ext-potential],
[AS_HELP_STRING([--with-ext-potential=<pot>],
[external potential @<:@none, point-mass, point-mass-ring, point-mass-softened, isothermal, nfw, nfw_mn, hernquist, disc-patch, sine-wave, constant, default: none@:>@]
[external potential @<:@none, point-mass, point-mass-softened, isothermal, nfw, nfw-mn, hernquist, hernquist-sdmh05, disc-patch, sine-wave, MWPotential2014, constant, default: none@:>@]
)],
[with_potential="$withval"],
[with_potential="none"]
......@@ -2170,10 +2979,13 @@ case "$with_potential" in
hernquist)
AC_DEFINE([EXTERNAL_POTENTIAL_HERNQUIST], [1], [Hernquist external potential])
;;
hernquist-sdmh05)
AC_DEFINE([EXTERNAL_POTENTIAL_HERNQUIST_SDMH05], [1], [Hernquist external potential following Springel, Di Matteo & Hernquist 2005])
;;
nfw)
AC_DEFINE([EXTERNAL_POTENTIAL_NFW], [1], [Navarro-Frenk-White external potential])
;;
nfw_mn)
nfw-mn)
AC_DEFINE([EXTERNAL_POTENTIAL_NFW_MN], [1], [Navarro-Frenk-White + Miyamoto-Nagai disk external potential])
;;
disc-patch)
......@@ -2182,12 +2994,12 @@ case "$with_potential" in
sine-wave)
AC_DEFINE([EXTERNAL_POTENTIAL_SINE_WAVE], [1], [Sine wave external potential in 1D])
;;
point-mass-ring)
AC_DEFINE([EXTERNAL_POTENTIAL_POINTMASS_RING], [1], [Point mass potential for Keplerian Ring (Hopkins 2015).])
;;
point-mass-softened)
AC_DEFINE([EXTERNAL_POTENTIAL_POINTMASS_SOFT], [1], [Softened point-mass potential with form 1/(r^2 + softening^2).])
;;
MWPotential2014)
AC_DEFINE([EXTERNAL_POTENTIAL_MWPotential2014], [1], [Milky-Way like potential composed of a Navarro-Frenk-White + Miyamoto-Nagai disk + Power spherical cuttoff external potential.])
;;
constant)
AC_DEFINE([EXTERNAL_POTENTIAL_CONSTANT], [1], [Constant gravitational acceleration.])
;;
......@@ -2197,9 +3009,9 @@ case "$with_potential" in
esac
# Entropy floor
AC_ARG_WITH([entropy-floor],
AC_ARG_WITH([entropy-floor],
[AS_HELP_STRING([--with-entropy-floor=<floor>],
[entropy floor @<:@none, QLA, EAGLE, default: none@:>@]
[entropy floor @<:@none, QLA, EAGLE, default: none@:>@]
)],
[with_entropy_floor="$withval"],
[with_entropy_floor="none"]
......@@ -2225,10 +3037,10 @@ case "$with_entropy_floor" in
*)
AC_MSG_ERROR([Unknown entropy floor model])
;;
esac
esac
# Pressure floor
AC_ARG_WITH([pressure-floor],
AC_ARG_WITH([pressure-floor],
[AS_HELP_STRING([--with-pressure-floor=<floor>],
[pressure floor @<:@none, GEAR, default: none@:>@
The hydro model needs to be compatible.]
......@@ -2254,12 +3066,12 @@ case "$with_pressure_floor" in
*)
AC_MSG_ERROR([Unknown pressure floor model])
;;
esac
esac
# Star formation
AC_ARG_WITH([star-formation],
AC_ARG_WITH([star-formation],
[AS_HELP_STRING([--with-star-formation=<sfm>],
[star formation @<:@none, QLA, EAGLE, GEAR, default: none@:>@]
[star formation @<:@none, QLA, EAGLE, GEAR, default: none@:>@]
)],
[with_star_formation="$withval"],
[with_star_formation="none"]
......@@ -2288,7 +3100,7 @@ case "$with_star_formation" in
*)
AC_MSG_ERROR([Unknown star formation model])
;;
esac
esac
AC_ARG_WITH([gadget2-physical-constants],
[AS_HELP_STRING([--with-gadget2-physical-constants],
......@@ -2314,21 +3126,104 @@ AC_DEFINE_UNQUOTED([SELF_GRAVITY_MULTIPOLE_ORDER], [$with_multipole_order], [Mul
# Radiative transfer scheme
AC_ARG_WITH([rt],
[AS_HELP_STRING([--with-rt=<scheme>],
[Radiative transfer scheme to use @<:@none, M1closure, debug default: none@:>@. This is still work in progress, currently no scheme works.]
[Radiative transfer scheme to use @<:@none, GEAR_*, SPHM1RT_*, debug default: none@:>@.
For GEAR and SPHM1RT, the number of photon groups (e.g. GEAR_4) needs to be provided.]
)],
[with_rt="$withval"],
[with_rt="none"]
)
# For GEAR-RT scheme: Select a RT Riemann solver
AC_ARG_WITH([rt-riemann-solver],
[AS_HELP_STRING([--with-rt-riemann-solver=<scheme>],
[Riemann solver for the moments of the ratiadiative transfer equation with the M1 closure to use @<:@none, HLL, GLF, default: none@:>@.
For the GEAR RT scheme, you need to select one Riemann solver.]
)],
[with_rt_riemann_solver="$withval"],
[with_rt_riemann_solver="none"]
)
case "$with_rt_riemann_solver" in
none)
AC_DEFINE([RT_RIEMANN_SOLVER_NONE], [1], [No RT riemann solver])
;;
HLL)
AC_DEFINE([RT_RIEMANN_SOLVER_HLL], [1], [HLL RT riemann solver])
;;
GLF)
AC_DEFINE([RT_RIEMANN_SOLVER_GLF], [1], [GLF RT riemann solver])
;;
*)
AC_MSG_ERROR("Unknown RT Riemann solver: $with_rt_riemann_solver")
;;
esac
case "$with_rt" in
none)
AC_DEFINE([RT_NONE], [1], [No radiative transfer scheme])
;;
M1closure)
AC_DEFINE([RT_M1], [1], [M1 closure scheme])
GEAR_*)
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])
fi
if ! test $number_group -eq $number_group; then
# abuse -eq to check whether $number_group is an integer. -eq
# only works with those.
AC_MSG_ERROR([GEAR-RT: Cannot work with non-integer photon groups])
fi
if test "$enable_debugging_checks" = "yes"; then
AC_DEFINE([SWIFT_RT_DEBUG_CHECKS], [1], [additional debugging checks for RT])
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=...)])
fi
if test "$have_grackle" != "yes"; then
AC_MSG_ERROR([GEAR-RT: You need the grackle library for GEAR-RT. (--with-grackle=PATH)])
fi
;;
debug)
AC_DEFINE([RT_DEBUG], [1], [debugging scheme])
AC_DEFINE([SWIFT_RT_DEBUG_CHECKS], [1], [additional debugging checks for RT])
;;
SPHM1RT_*)
AC_DEFINE([RT_SPHM1RT], [1], [SPHM1RT radiative transfer scheme (Chan+21: 2102.08404)])
number_group=${with_rt#*_}
AC_DEFINE_UNQUOTED([RT_NGROUPS], [$number_group], [Number of photon groups to follow])
if test "$number_group" -eq "0"; then
AC_MSG_ERROR([SPHM1RT: Cannot work with zero photon groups])
fi
if test $number_group -lt 4; then
AC_MSG_ERROR([SPHM1RT: Cannot work with < four photon groups for now])
fi
if ! test $number_group -eq $number_group; then
# abuse -eq to check whether $number_group is an integer. -eq
# only works with those.
AC_MSG_ERROR([SPHM1RT: Cannot work with non-integer photon groups])
fi
AC_MSG_CHECKING([for Sundials libraries])
AC_MSG_RESULT($have_sundials)
if test "$have_sundials" != "yes"; then
AC_MSG_ERROR([The Sundials library is not present. Sundials is required for the SPHM1RT module.])
fi
;;
*)
AC_MSG_ERROR([Unknown radiative transfer scheme: $with_rt])
......@@ -2345,27 +3240,80 @@ DX_DOXYGEN_FEATURE(OFF)
DX_INIT_DOXYGEN(SWIFT, doc/Doxyfile, doc/)
AM_CONDITIONAL([HAVE_DOXYGEN], [test "$ac_cv_path_ac_pt_DX_DOXYGEN" != ""])
# Check if using EAGLE extra I/O
AM_CONDITIONAL([HAVEEAGLEEXTRAIO], [test "${with_extra_io}" = "EAGLE"])
# Check if using QLA cooling
AM_CONDITIONAL([HAVEQLACOOLING], [test "${with_cooling:0:3}" == "QLA"])
AM_CONDITIONAL([HAVEQLACOOLING], [test "$with_cooling" = "QLA"])
AM_CONDITIONAL([HAVEQLAEAGLECOOLING], [test "$with_cooling" = "QLA-EAGLE"])
# Check if using EAGLE cooling
AM_CONDITIONAL([HAVEEAGLECOOLING], [test "${with_cooling:0:5}" == "EAGLE"])
AM_CONDITIONAL([HAVEEAGLECOOLING], [test "$with_cooling" = "EAGLE"])
# Check if using COLIBRE cooling
AM_CONDITIONAL([HAVECOLIBRECOOLING], [test "${with_cooling:0:7}" == "COLIBRE"])
# Check if using PS2020 cooling
AM_CONDITIONAL([HAVEPS2020COOLING], [test "$with_cooling" = "PS2020"])
# Check if using EAGLE feedback
AM_CONDITIONAL([HAVEEAGLEFEEDBACK], [test "$with_feedback" == "EAGLE"])
AM_CONDITIONAL([HAVEEAGLETHERMALFEEDBACK], [test "${with_feedback%-thermal}" = "EAGLE"])
AM_CONDITIONAL([HAVEEAGLEKINETICFEEDBACK], [test "$with_feedback" = "EAGLE-kinetic"])
# check if using grackle cooling
AM_CONDITIONAL([HAVEGRACKLECOOLING], [test "${with_cooling:0:7}" == "grackle"])
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 "$with_feedback" = "GEAR"])
# check if using gear feedback
AM_CONDITIONAL([HAVEGEARFEEDBACK], [test "$with_feedback" == "GEAR"])
AM_CONDITIONAL([HAVEAGORAFEEDBACK], [test "$with_feedback" = "AGORA"])
# check if using SPHENIX
AM_CONDITIONAL([HAVE_SPHENIX], [test "$with_hydro" = "sphenix"])
# check if using GADGET2 SPH
AM_CONDITIONAL([HAVE_GADGET2], [test "$with_hydro" = "gadget2"])
# check if using none chemistry
AM_CONDITIONAL([HAVE_CHEMISTRY_NONE], [test "$with_chemistry" = "none"])
# check if using GEAR chemistry
AM_CONDITIONAL([HAVE_CHEMISTRY_GEAR], [test "$with_chemistry" = "GEAR" || test "$with_chemistry" = "GEAR_DIFFUSION"])
# check if using AGORA chemistry
AM_CONDITIONAL([HAVE_CHEMISTRY_AGORA], [test "$with_chemistry" = "AGORA" || test "$with_chemistry" = "GEAR_DIFFUSION"])
# check if using default stars
AM_CONDITIONAL([HAVE_STARS_BASIC], [test "$with_stars" = "basic"])
# check if using GEAR stars
AM_CONDITIONAL([HAVE_STARS_GEAR], [test "$with_stars" = "GEAR"])
# check if using default star formation
AM_CONDITIONAL([HAVE_STAR_FORMATION_DEFAULT], [test "$with_star_formation" = "none"])
# check if using GEAR star formation
AM_CONDITIONAL([HAVE_STAR_FORMATION_GEAR], [test "$with_star_formation" = "GEAR"])
# check if using multi softening gravity
AM_CONDITIONAL([HAVE_GRAVITY_MULTISOFTENING], [test "$with_gravity" = "with-multi-softening"])
# Check if using SPHM1RT radiative transfer
AM_CONDITIONAL([HAVESPHM1RTRT], [test "${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"])
# Handle .in files.
AC_CONFIG_FILES([Makefile src/Makefile examples/Makefile examples/Cooling/CoolingRates/Makefile doc/Makefile doc/Doxyfile tests/Makefile])
AC_CONFIG_FILES([argparse/Makefile tools/Makefile logger/Makefile logger/tests/Makefile])
AC_CONFIG_FILES([argparse/Makefile tools/Makefile])
AC_CONFIG_FILES([tests/testReading.sh], [chmod +x tests/testReading.sh])
AC_CONFIG_FILES([tests/testActivePair.sh], [chmod +x tests/testActivePair.sh])
AC_CONFIG_FILES([tests/test27cells.sh], [chmod +x tests/test27cells.sh])
......@@ -2380,6 +3328,8 @@ AC_CONFIG_FILES([tests/testInteractions.sh], [chmod +x tests/testInteractions.sh
AC_CONFIG_FILES([tests/testParser.sh], [chmod +x tests/testParser.sh])
AC_CONFIG_FILES([tests/testSelectOutput.sh], [chmod +x tests/testSelectOutput.sh])
AC_CONFIG_FILES([tests/testFormat.sh], [chmod +x tests/testFormat.sh])
AC_CONFIG_FILES([tests/testNeutrinoCosmology.sh], [chmod +x tests/testNeutrinoCosmology.sh])
AC_CONFIG_FILES([tests/output_list_params.yml])
# Save the compilation options
AC_DEFINE_UNQUOTED([SWIFT_CONFIG_FLAGS],["$swift_config_flags"],[Flags passed to configure])
......@@ -2405,20 +3355,29 @@ AC_MSG_RESULT([
Compiler : $CC
- vendor : $ax_cv_c_compiler_vendor
- version : $ax_cv_c_compiler_version
- flags : $CFLAGS $OPENMP_CFLAGS
- flags : $CFLAGS
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
Sundials enabled : $have_sundials
Special allocators : $have_special_allocator
CPU profiler : $have_profiler
Pthread barriers : $have_pthread_barrier
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
......@@ -2426,6 +3385,8 @@ AC_MSG_RESULT([
Equation of state : $with_eos
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
......@@ -2433,18 +3394,20 @@ AC_MSG_RESULT([
No gravity below ID : $no_gravity_below_id
Make gravity glass : $gravity_glass_making
External potential : $with_potential
Forcing terms : $with_forcing
Pressure floor : $with_pressure_floor
Entropy floor : $with_entropy_floor
Cooling function : $with_cooling
Chemistry : $with_chemistry
Cooling function : $with_cooling_name
Chemistry : $with_chemistry_name
Tracers : $with_tracers
Stellar model : $with_stars
Star formation model : $with_star_formation
Star feedback model : $with_feedback
Star feedback model : $with_feedback_name
Sink particle model : $with_sink
Black holes model : $with_black_holes
Radiative transfer : $with_rt
Extra i/o : $with_extra_io
Atomic operations in tasks : $enable_atomics_within_tasks
Individual timers : $enable_timers
......@@ -2459,8 +3422,17 @@ AC_MSG_RESULT([
Custom icbrtf : $enable_custom_icbrtf
Boundary particles : $boundary_particles
Fixed boundary particles : $fixed_boundary_particles
Planetary fixed entropy : $planetary_fixed_entropy
Ghost statistics : $ghost_stats
Continuous Sim. Data Stream : $with_csds
Particle Logger : $with_logger
Python enabled : $have_python
------------------------]
)
------------------------])
# Report any unrecognised options loudly.
if test "$ac_unrecognized_opts" != ""; then
AC_MSG_RESULT([
*** WARNING: unrecognized options: $ac_unrecognized_opts ***
])
fi
csds @ 0523433a
Subproject commit 0523433a7880e58e22b2215afd0104ea58786962
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/COLIBRE \
@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@/logger
@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/Makefile.am
View file @ 853c5044
# This file is part of SWIFT.
# Copyright (c) 2012 Pedro Gonnet (pedro.gonnet@durham.ac.uk),
# Matthieu Schaller (matthieu.schaller@durham.ac.uk).
# Matthieu Schaller (schaller@strw.leidenuniv.nl).
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
......
doc/RTD/Makefile
View file @ 853c5044
......@@ -4,7 +4,7 @@
# You can set these variables from the command line.
SPHINXOPTS =
SPHINXBUILD = sphinx-build
SPHINXPROJ = SWIFTSPHWIthFine-grainedinter-dependentTasking
SPHINXPROJ = SWIFT-documentation
SOURCEDIR = source
BUILDDIR = build
......@@ -17,4 +17,4 @@ help:
# Catch-all target: route all unknown targets to Sphinx using the new
# "make mode" option. $(O) is meant as a shortcut for $(SPHINXOPTS).
%: Makefile
@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
\ No newline at end of file
@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
doc/RTD/README.md
View file @ 853c5044
SWIFT Documentation
===================
This is the main documentation for SWIFT that can be found on ReadTheDocs.
This is the main documentation for SWIFT that can be found on ReadTheDocs
or at `swiftsim.com/docs`.
You will need the `sphinx` and `sphinx-autobuild` python packages (pip install
them!) to build the documentation to html, as well as the `sphinx_rtd_theme`
package which is used as the theme.
To build the documentation, `make html` and then it is available in
`build/html`.
To build the documentation (from this directory), `make html` and the output
files will be created in `build/html/`.
Please consider adding documentation when you add code!
To build the latex manual (from this directory), `make latexpdf` and the output
files will be `build/latex/SWIFT-user-manual.pdf`.
Please consider adding documentation when you add code!