.gitignore

@@ -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

+[submodule "csds"]
+	path = csds
+	url = https://gitlab.cosma.dur.ac.uk/lhausammann/csds-reader.git

AUTHORS

@@ -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

+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

 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

-### 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
+Application with the Library.  The particular version of the Library
 with which the Combined Work was made is also called the "Linked
 Version".
 
-The "Minimal Corresponding Source" for a Combined Work means the
+  The "Minimal Corresponding Source" for a Combined Work means the
 Corresponding Source for the Combined Work, excluding any source code
 for portions of the Combined Work that, considered in isolation, are
 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
 object code and/or source code for the Application, including any data
 and utility programs needed for reproducing the Combined Work from the
 Application, but excluding the System Libraries of the Combined Work.
 
-#### 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.
+  2. Conveying Modified Versions.
 
-If you modify a copy of the Library, and, in your modifications, a
+  If you modify a copy of the Library, and, in your modifications, a
 facility refers to a function or data to be supplied by an Application
 that uses the facility (other than as an argument passed when the
 facility is invoked), then you may convey a copy of the modified
 version:
 
--   a) under this License, provided that you make a good faith effort
-    to ensure that, in the event an Application does not supply the
-    function or data, the facility still operates, and performs
-    whatever part of its purpose remains meaningful, or
--   b) under the GNU GPL, with none of the additional permissions of
-    this License applicable to that copy.
+   a) under this License, provided that you make a good faith effort to
+   ensure that, in the event an Application does not supply the
+   function or data, the facility still operates, and performs
+   whatever part of its purpose remains meaningful, or
+
+   b) under the GNU GPL, with none of the additional permissions of
+   this License applicable to that copy.
 
-#### 3. Object Code Incorporating Material from Library Header Files.
+  3. Object Code Incorporating Material from Library Header Files.
 
-The object code form of an Application may incorporate material from a
-header file that is part of the Library. You may convey such object
+  The object code form of an Application may incorporate material from
+a header file that is part of the Library.  You may convey such object
 code under terms of your choice, provided that, if the incorporated
 material is not limited to numerical parameters, data structure
 layouts and accessors, or small macros, inline functions and templates
 (ten or fewer lines in length), you do both of the following:
 
--   a) Give prominent notice with each copy of the object code that
-    the Library is used in it and that the Library and its use are
-    covered by this License.
--   b) Accompany the object code with a copy of the GNU GPL and this
-    license document.
-
-#### 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
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--   e) Provide Installation Information, but only if you would
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-    4d0, the Installation Information must accompany the Minimal
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-    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
+   a) Give prominent notice with each copy of the object code that the
+   Library is used in it and that the Library and its use are
+   covered by this License.
+
+   b) Accompany the object code with a copy of the GNU GPL and this license
+   document.
+
+  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

@@ -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

 # 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

@@ -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

@@ -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

+<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

@@ -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

@@ -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

@@ -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
 

csds @ 0523433a

+Subproject commit 0523433a7880e58e22b2215afd0104ea58786962

doc/Makefile.am

 # 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

@@ -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

 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!