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Arepo (do not merge) #925

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Commits on Mar 18, 2022

  1. add arepo directory

    @felicityguest
    felicityguest committed Mar 18, 2022
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  2. add arepo source code

    @felicityguest
    felicityguest committed Mar 18, 2022
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  3. remove '#include ./arepoconfig.h' from allvars.h

    @felicityguest
    felicityguest committed Mar 18, 2022
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  4. update Makefile to include arepo source code

    @felicityguest
    felicityguest committed Mar 18, 2022
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  5. add TODO to Makefile

    @felicityguest
    felicityguest committed Mar 18, 2022
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Commits on Mar 28, 2022

  1. rename classes

    @felicityguest
    felicityguest committed Mar 28, 2022
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  2. inherit from GravitationalDynamicsInterface

    @felicityguest
    felicityguest committed Mar 28, 2022
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  3. inherit from LiteratureReferencesMixIn

    @felicityguest
    felicityguest committed Mar 28, 2022
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  4. remove wildcard import

    @felicityguest
    felicityguest committed Mar 28, 2022
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  5. inherit from GravitationalDynamics

    @felicityguest
    felicityguest committed Mar 28, 2022
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  6. minor reformatting

    @felicityguest
    felicityguest committed Mar 28, 2022
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  7. add ArepoInterface docstring

    @felicityguest
    felicityguest committed Mar 28, 2022
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  8. add TODO re CodeWithDataDirectories

    @felicityguest
    felicityguest committed Mar 28, 2022
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  9. add set_parameters()

    @felicityguest
    felicityguest committed Mar 28, 2022
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  10. change GSL_INCL to GSL_FLAGS

    @felicityguest
    felicityguest committed Mar 28, 2022
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  11. add AMUSE_DIR conditional and include config.mk

    @felicityguest
    felicityguest committed Mar 28, 2022
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Commits on Mar 31, 2022

  1. generate interface.cc

    @felicityguest
    felicityguest committed Mar 31, 2022
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  2. update interface name in Makefile

    @felicityguest
    felicityguest committed Mar 31, 2022
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  3. update interface name in test_arepo.py

    @felicityguest
    felicityguest committed Mar 31, 2022
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  4. update arepo to Arepo

    @felicityguest
    felicityguest committed Mar 31, 2022
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Commits on Apr 1, 2022

  1. add code from arepo main.c to initialize_code() and cleanup_code()

    @felicityguest
    felicityguest committed Apr 1, 2022
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  2. comment out set_parameters() and add TODO

    @felicityguest
    felicityguest committed Apr 1, 2022
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  3. add TODO to test_arepo.py

    @felicityguest
    felicityguest committed Apr 1, 2022
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  4. add TODO to Makefile

    @felicityguest
    felicityguest committed Apr 1, 2022
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  5. remove test.cc as not needed

    @felicityguest
    felicityguest committed Apr 1, 2022
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  6. add initialize_code() and define_methods() to Arepo

    @felicityguest
    felicityguest committed Apr 1, 2022
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Commits on May 12, 2022

  1. add default parameters to arepo's interface.cc

    @mtwest2718
    mtwest2718 committed May 12, 2022
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Commits on May 13, 2022

  1. Comment out read_parameter_file in begrun, add run_sim in interface.c… 

    …c, add cleanup_code to interface.py, add set_default_parameters to initialize_code
    @mtwest2718
    mtwest2718 committed May 13, 2022
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Commits on May 18, 2022

  1. fixes

    @rieder
    rieder committed May 18, 2022
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  2. define CXX flag in Arepo makefile

    @mtwest2718
    mtwest2718 committed May 18, 2022
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  3. set_default values to match current arepo config data structures

    @mtwest2718
    mtwest2718 committed May 18, 2022
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Commits on May 19, 2022

  1. Merge branch 'amusecode:main' into iss9-arepo_dark_matter_interface

    @rieder
    rieder authored May 19, 2022
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  2. add #include mpi.h & run.c 

    change mpi_print to just print
    @mtwest2718
    mtwest2718 committed May 19, 2022
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  3. include GSL headers

    @rieder
    rieder committed May 19, 2022
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  4. add GSL_FLAGS to CXXFLAGS

    @rieder
    rieder committed May 19, 2022
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  5. remove include

    @rieder
    rieder committed May 19, 2022
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  6. arepo is C not C++

    @rieder
    rieder committed May 19, 2022
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  7. re-add lines

    @rieder
    rieder committed May 19, 2022
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  8. create arepo interface.h and move #include allvars.h & proto.h along … 

    …with ifdef Cpp choice there
    @mtwest2718
    mtwest2718 committed May 19, 2022
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  9. fix typo

    @rieder
    rieder committed May 19, 2022
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  10. fix paths

    @rieder
    rieder committed May 19, 2022
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Commits on May 20, 2022

  1. add #include statement for new interface.h header

    @mtwest2718
    mtwest2718 committed May 20, 2022
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  2. some fixes for c<->cpp

    @ipelupessy
    ipelupessy committed May 20, 2022
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  3. Merge branch 'iss9-arepo_dark_matter_interface' of https://github.com… 

    …/UniExeterRSE/amuse into arepo_work
    @ipelupessy
    ipelupessy committed May 20, 2022
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  4. fixes to build, note the source changes

    @ipelupessy
    ipelupessy committed May 20, 2022
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  5. fix build to detect source changes

    @ipelupessy
    ipelupessy committed May 20, 2022
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  6. move GSL_LIBS and GMP_LIBS to the end of the flags for Arepo make file

    @mtwest2718
    mtwest2718 committed May 20, 2022
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Commits on May 23, 2022

  1. remove extra mpi_init from initialize_code

    @mtwest2718
    mtwest2718 committed May 23, 2022
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Commits on May 25, 2022

  1. Default to non-periodic gravity

    @rieder
    rieder committed May 25, 2022
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Commits on Sep 19, 2022

  1. Merge branch 'amusecode:main' into iss9-arepo_dark_matter_interface

    @rieder
    rieder authored Sep 19, 2022
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Commits on Sep 28, 2022

  1. Add missing calls to memory management helpers 

    Add basic arepo test.

Co-authored-by: Steven Rieder <[email protected]>
    @stephenpcook @rieder
    stephenpcook and rieder committed Sep 28, 2022
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Commits on Sep 30, 2022

  1. small bug fix: in case HIERARCHICAL_GRAVITY is not used, and the maxi… 

    …mum used timestep sizes increases during a step, it could happen that for particles on the maximum timestep one gravity half-step is not applied (because HighestActiveTimeBin increases)
    @volkerspringel @stephenpcook
    volkerspringel authored and stephenpcook committed Sep 30, 2022
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  2. removed non-standard uint in favor of 'unsigned int'

    @volkerspringel @stephenpcook
    volkerspringel authored and stephenpcook committed Sep 30, 2022
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  3. disabled a superfluous call of get_starformtion_rate()

    @volkerspringel @stephenpcook
    volkerspringel authored and stephenpcook committed Sep 30, 2022
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  4. Merge branch 'gitlab-updates' into iss9-arepo_dark_matter_interface 

    Three of four recent commits from arepo on gitlab
(https://gitlab.mpcdf.mpg.de/vrs/arepo).

Documentation update omitted since arepo documentation has been removed
here.
    @stephenpcook
    stephenpcook committed Sep 30, 2022
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Commits on Oct 13, 2022

  1. Prepare to run Arepo example 

    Preparing to run the Arepo example `isolated_galaxy_collusionless_3d`.
Arepo flags (in `arepo/src/Makefile`) sourced from
`arepo/run/examples/myexample/Config.sh`.

Co-authored-by: thomasguillet <[email protected]>
    @stephenpcook @thomasguillet
    stephenpcook and thomasguillet committed Oct 13, 2022
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  2. Placeholder functions for evolution code

    @stephenpcook
    stephenpcook committed Oct 13, 2022
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Commits on Oct 26, 2022

  1. Add flags to arepo makefile

    @stephenpcook
    stephenpcook committed Oct 26, 2022
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Commits on Nov 4, 2022

  1. Add Arepo flags to parent Makefile 

    May want to remove from child makefile to avoid duplication.

Co-authored-by: Steven Rieder <[email protected]>
    @stephenpcook @rieder
    stephenpcook and rieder committed Nov 4, 2022
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Commits on Nov 10, 2022

  1. Force stop and skip dump 

    Add Arepo flag "Multiple restarts" (effect not fully tested).

Co-authored-by: Steven Rieder <[email protected]>
    @stephenpcook @rieder
    stephenpcook and rieder committed Nov 10, 2022
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  2. Add evolve_model function 

    Modify test parameters.

Co-authored-by: Steven Rieder <[email protected]>
    @stephenpcook @rieder
    stephenpcook and rieder committed Nov 10, 2022
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  3. Change snapshot format 

    Avoid HDF5 - we will use AMUSE to extract data instead of snapshotting.
    @stephenpcook
    stephenpcook committed Nov 10, 2022
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  4. Remove unnecessary Arepo flag 

    The multiple restarts flag keeps more than one restart file for unreliable
systems.
    @stephenpcook
    stephenpcook committed Nov 10, 2022
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  5. Set restart flag in initization 

    Re-add initialization code to test script.
    @stephenpcook
    stephenpcook committed Nov 10, 2022
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Commits on Nov 15, 2022

  1. Add get_position interface function 

    Include naive find_particle_with_ID to be optimized later.

Co-authored-by: Thomas Guillet <[email protected]>
    @stephenpcook @thomasguillet
    stephenpcook and thomasguillet committed Nov 15, 2022
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Commits on Nov 17, 2022

  1. Add arepo get functions 

    Currently with a naive search for particle ID.
    @stephenpcook
    stephenpcook committed Nov 17, 2022
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Commits on Nov 18, 2022

  1. Add Arepo particle ID lookup 

    Using `size_t` for the output position ID, but this is defined in Arepo
as an unsigned int.
    @stephenpcook
    stephenpcook committed Nov 18, 2022
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  2. Match Arepo interface with Gadget2

    @stephenpcook
    stephenpcook committed Nov 18, 2022
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Commits on Dec 2, 2022

  1. Add comments to Arepo interface

    @stephenpcook
    stephenpcook committed Dec 2, 2022
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  2. Add script to track and plot particles 

    Based on test_simple.py.
    @stephenpcook
    stephenpcook committed Dec 2, 2022
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Commits on Dec 22, 2022

  1. Add HDF5 flags to Makefiles, remove missing call 

    Removed call to missing `write_compile_time_options_in_hdf5` function in
`src/io/io.c`.  In Arepo this function is written to a file by a perl
script at compile time.
    @stephenpcook
    stephenpcook committed Dec 22, 2022
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  2. Add interface getters for gas pressure, density 

    Also fill in gravitational acceleration getter.
    @stephenpcook
    stephenpcook committed Dec 22, 2022
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  3. Re-add HAVE_HDF5 Arepo flag

    @stephenpcook
    stephenpcook committed Dec 22, 2022
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  4. Change Makefiles + interface to run Noh 3D example 

    This breaks the former "collisionless galaxy 3D" example, since the
Arepo compiler flags are hard-coded into the Makefiles.

Once the ICs file has been copied from the Arepo source (as outlined in
ICs.placeholder) the new python script `test_noh3d.py` runs the example
and saves figures of the output at t = 0.1, 1.0 and 1.9.
    @stephenpcook
    stephenpcook committed Dec 22, 2022
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