Castro JOSS paper

JOSS_paper

JOSS paper

Release 20.10

• A new refinement scheme using the inputs file rather than the Fortran
  tagging namelist has been added. (#1243, #1246) As an example, consider:

  amr.refinement_indicators = dens temp
  
  amr.refine.dens.max_level = 1
  amr.refine.dens.value_greater = 2.0
  amr.refine.dens.field_name = density
  
  amr.refine.temp.max_level = 2
  amr.refine.temp.value_less = 1.0
  amr.refine.temp.field_name = Temp
  

  amr.refinement_indicators is a list of user-defined names for refinement
  schemes. For each defined name, amr.refine. accepts predefined fields
  describing when to tag. In the current implementation, these are max_level
  (maximum level to refine to), start_time (when to start tagging), end_time
  (when to stop tagging), value_greater (value above which we refine),
  value_less (value below which to refine), gradient (absolute value of the
  difference between adjacent cells above which we refine), and field_name
  (name of the string defining the field in the code). If a refinement indicator
  is added, either value_greater, value_less, or gradient must be provided.

• Automatic problem parameter configuration is now available to every
  problem by placing a _prob_params file in your problem directory.
  Examples can be found in most of the problems in Castro/Exec, and you
  can look at the "Setting Up Your Own Problem" section of the documentation
  for more information. This functionality is optional, however note that
  a file containing a Fortran module named "probdata_module" is now
  automatically generated, so if you have a legacy probdata.F90 file
  containing a module with that name it should be renamed. (#1210)

• The variable "center" (in the problem namespace) is now part of this
  automatically generated probdata module; at the present time, the only
  valid way to change the problem center to a value other than zero is in
  amrex_probinit(). (#1222)

• Initialization of these problem parameters is now done automatically for
  you, so a call to probdata_init() is no longer required in amrex_probinit(). (#1226)

• Problems may now be initialized in C++ instead of Fortran. Instead of implementing
  amrex_probinit() and ca_initdata(), the problem should implement the analogous
  functions initialize_problem() and initialize_problem_state_data(). If you switch to
  the new C++ initialization, be sure to delete your Prob_nd.F90 file. By default both
  implementations do nothing, so you can pick either one but do not pick both. (#1227)

• The external heat source term routines have been ported to C++
  (#1191). Any problem using an external heat source should look
  convert the code over to C++.

• The interpolate_nd.F90 file has been moved to Util/interpolate and
  is only compiled into Castro if you set USE_INTERPOLATE=TRUE

Release 20.09

• Reactions now work with MHD (#1179)

• MHD now uses the main slope routine (#1058) The order of the
  slope is now controlled by plm_iorder, just as with hydro. There
  is an additional option, mhd_limit_characteristic, that
  determines if the limiting is done on the primitive or
  characteristic variables (the default).

Release 20.08

• Rotation_Type has been removed from StateData. (#1128)

• castro.use_post_step_regrid now unconditionally regrids after
  every timestep on every level. (#898)

• An issue with gravity.max_solve_level resulting in accesses to invalid data
  (#469, #1118) has been resolved. (#1123)

• If castro.speed_limit is set to a number greater than zero, this
  will now be strictly enforced on the magnitude of the velocity. (#1115)

• When using AMR and gravity or rotation, the source terms applied after
  a reflux would have been incorrect if the previous timestep had a retry
  (#1020). This has now been fixed. (#1112)

• We now have the ability to access the problem-specific runtime
  parameters in C++ (#1093)

Release 20.07

• The master branch has been renamed the main branch. If you have an
  existing clone of Castro, then do the following to update for this
  change. First, do git checkout master if you're not already on the
  old master branch. Then do git pull. This will gather the updates
  to the repo, but will fail with the message Your configuration specifies to merge with the ref 'refs/heads/master' from the remote, but no such ref was fetched. Then you can simply do git checkout main and your local
  repo should automatically switch to that branch and track updates from
  the upstream repo on GitHub. If you like, you can then delete the old
  master branch with git branch -D master.

• The CUDA build no longer has a requirement that amr.blocking_factor
  be a multiple of 8. Though this is recommended for performance reasons,
  it was previously required due to correctness reasons because of the
  use of an AMReX Fortran function, amrex_filccn. As noted in #1048, this
  function is no longer required due to recent changes in Castro (problems
  overriding bc_fill_nd.F90 or bc_ext_fill_nd.F90 do not need to provide an
  initial fill of the ghost zone data before implementing their specific
  boundary conditions; this is now done for you). Calling this function
  may now result in race conditions and correctness issues in the CUDA
  build, so it should be removed from any problem setups. (#1049)

• The functionality that permitted the rotation rate to change as a
  function of time, castro.rotation_include_domegadt and
  castro.rotational_dPdt, has been removed. (#1045)

• A CUDA illegal memory access error in Poisson gravity and diffusion
  has been fixed (#1039).

• The parameter castro.track_grid_losses has been removed. (#1035)

• The parameter castro.print_fortran_warnings, which no longer had any
  effect, has been removed. (#1036)

• PPM reconstruction has been added to the MHD solver (#1002)

• The Reactions_Type StateData has been reworked so that its first
  NumSpec components are rho * omegadot rather than omegadot; then,
  the NumAux auxiliary components are stored, if the network has any
  auxiliary variables; then, rho * enuc is stored (enuc itself is
  removed), and finally the burn weights are stored. The checkpoint
  version has been incremented, so this version of the code cannot
  restart from checkpoints generated with earlier versions of the
  code. (#927)

• A bug where refluxing between AMR levels resulted in incorrect results
  when a retry occurred in the previous timestep has been fixed. (#1018)

Castro 20.06

20.06

• The parameter castro.density_reset_method has been removed. A density
  reset now unconditionally sets the density to small_dens, the temperature
  to small_temp, and zeros out the velocities. (#989)

• A constrained-transport corner transport upwind MHD solver has been
  added. This can be used by compiling with USE_MPI = TRUE. Presently
  it only works for a single level (no AMR). (#307)

• A burning timestep limiter dtnuc_T has been added which restricts the
  burning from updating the temperature by more than the factor
  dtnuc_T * T / dT/dt. (#972)

• The reaction weights metric implemented in version 20.05 (#863) has been
  added to the simplified SDC reactions driver. (#930)

• When using the simplified SDC integration scheme, we now save new-time
  Reactions_Type data to plotfiles. (#929)

Castro 20.05

20.05

• The parameter use_custom_knapsack_weights and its associated
  functionality have been removed. (#877)

• We've changed how the runtime parameters are stored. Previously
  they were static members of their respective class, but this
  prevented their use in lambda-capture functions on GPUs. Now the
  runtime parameters are grouped into namespaces as extern managed
  data. (#873)

• We currently have a scheme for storing reactions weightings, which
  are a measure of the number of RHS evaluations during the burn and
  therefore a proxy for the difficulty of the burn. These weights were
  added as separate StateData depending on the runtime option
  use_custom_knapsack_weights. Now, instead we place the weights
  directly in the Reactions_Type StateData as a new component.

  The number of ghost zones in Reactions_Type is increased to 4.

  The checkpoint version has now been incremented; this version of the
  code will not be able to restart from a checkpoint generated by earlier
  versions of the code. (#863)

• The meaning of dt_cutoff has changed: it is now the fraction of the
  current simulation time which dt may be no smaller than, instead of
  being an absolute measure. We now have set a non-zero default
  (1.e-12) as well. (#865)

• Backwards compatibility in restarting from a checkpoint is no longer
  supported. Checkpoints from older versions of the code (as determined
  by the checkpoint version in the CastroHeader file in the checkpoint
  directory) cannot be restarted from. (#860)

• Added an option to do CTU reactions in C++. A compile flag
  USE_CXX_REACTIONS is added which switches to the C++ integrator
  in Microphysics. Since we will be doing a phased implementation
  of the networks in Microphysics, this is opt-in for now. (#836)

• More of the core routines have been ported to C++, including the
  hydro and diffusion timestep estimators (#853) and the sponge
  (#857)

• AMReX provides CpuBndryFuncFab and GpuBndryFuncFab which are very
  similar to what generic_fill and hypfill did. The AMReX
  implementations are now used. We still have a hypfill and denfill
  function, so that existing problems are not broken, but the main
  one in Source/ no longer calls amrex_filcc (it only has the
  ambient code now). The problems that do override bc_fill_nd.F90
  are thus no longer required to call amrex_filcc. (#837)

• We now always issue a timestep retry if the density after an
  advance is negative (or less than small_dens). The parameter
  castro.retry_neg_dens_factor is removed. The parameter
  castro.retry_tolerance is also removed as it no longer has
  any effect. (#796)

• The timestep control parameter castro.change_max now also will
  prevent the timestep by shrinking too much in one timestep
  (previously it would only prevent it from growing too much).
  If change_max is violated in a timestep we will do a retry
  to take more graceful steps. (#844)

• We now check if the problem setup initialized the density or
  temperature to a value near small_dens or small_temp and abort.
  If this happens, the recourse is to adjust small_dens and
  small_temp to a meaningful value for your problem. (#822)

• The src_q multifab was removed and instead we convert the
  conserved state sources to primitive state sources FAB by FAB.
  This saves a lot of memory at the expense of an EOS call. (#829)

• The plm_well_balanced option was removed. It was essentially the
  same as use_pslope except it was lower order and only worked with
  constant gravity. use_pslope now works with both CTU+PLM and
  SDC2+PLM. A new test problem, hse_convergence, was added to look
  at the behavior of the different reconstruction methods with HSE.

Castro 20.04.1

Castro 20.04.1

Castro 20.04

20.04

• A potential undefined flux from the HLL solver when using
  hybrid_riemann has been fixed (#823)

• The parameter castro.allow_small_energy has been removed. The
  code behavior is now similar to what it would have been with
  allow_small_energy == 0 (the internal energy can never be
  smaller than that allowed by small_temp). (#817)

• The BC interfaces have been merged and converted to a new FAB
  interface as part of the port to C++. (#819)

• All boundary fill interfaces other than hypfill and denfill have
  been removed. So, we no longer support overriding the boundary
  conditions for data other than State_Type. Radiation still has
  its own set of custom boundary conditions that can be accessed
  through the inputs file, as described in the docs. (#815)

• The conversion of the CTU hydrodynamics code to C++ continues.
  The Riemann solvers were converted to C++ (#801) and the
  hybrid momentum routines (#805), the PLM reconstruction (#814),
  the conversion of primitive to conserved variables (#804)

• We've changed how the backup for retries is done. Presently if
  use_retry is enabled we make a pre-emptive copy of the StateData
  right at the beginning of the timestep. Now we only backup when
  we detect that a retry is needed (#812)

Castro 20.03

20.03

• We now depend on the fundamental constants from Microphysics
  instead of keep our own copy in Castro (#787)

• We removed the ppm_predict_gammae option for the CTU hydro solver.
  This was not used frequently and did not show much difference with
  the default (rho e) reconstruction. (#780)

• The Microphysics "extern" parameters are now available in C++

• We've started converting the CTU hydro solver from Fortran to C++
  (#731). The PPM reconstruction is now done in C++ (#784).

• The option ppm_temp_fix = 3 was removed. This used a
  temperature-based eigensystem for characteristic tracing but was
  never used for production science.

• If a derived variable has multiple components, all components are now
  added to plotfiles. Previously only the first component was used. (#758)

• We have updated our workflow when it comes to Castro's dependencies.

  Previously Castro shipped with it a minimal set of microphysics that
  allowed basic problem setups like Sedov to compile, and more advanced
  setups (like ones that include nuclear burning) required downloading
  the starkiller-astro Microphysics repository as an additional step.
  Now, that Microphysics repository is a requirement for using Castro.
  If you are a current user of the Microphysics repository and prefer
  the current workflow where you maintain Microphysics as a separate
  installation from Castro, no change in your workflow is necessary:
  if MICROPHYSICS_HOME is set as an environment variable, Castro will
  use the Microphysics installation in that directory. However we have
  also added Microphysics as a git submodule to Castro, which is now
  the required path if you previously were not using the more advanced
  microphysics (but is also a possibility for those previously using a
  standalone Microphysics installation). To obtain this, you can use
  git submodule update --init --recursive from the top-level directory
  of Castro. The developer team ensures that the version of Microphysics
  that you obtain this way is consistent with the current version of Castro.
  Then, you can keep up to date with the code mostly as normal, except now
  using git pull --recurse-submodules instead of git pull.

  Similarly, AMReX is now maintained as a git submodule rather than as an
  external standalone installation. If you use the same git submodule command
  as above, you'll obtain AMReX. As with Microphysics, you may opt to
  rely on your own installation of AMReX by setting the AMREX_HOME
  environment variable. However you are then responsible for keeping it
  in sync with Castro; if you use the submodule, then you'll get the version
  of AMReX that we have tested to ensure compatibility with the current
  version of Castro. (#651, #760, #762, #765)

• The names of the conserved state variables in C++ (Density, Xmom, etc.)
  have been changed to match the names in Fortran (URHO, UMX, etc.).
  For user code, this will only affect problem-specific setup code
  like Prob.cpp that references specific state variables. For compatibility,
  we have kept a copy of the old names around that redirect to the
  new names, but the old names are now considered deprecated and will
  be removed