CHANGES.md

20.06

• 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)

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.

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)

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 in a future release. (#757)

20.02

• Fixed a bug in the nuclear burning timestep estimator when on GPUs (#745)

• rewrote the 4th order SDC hydro driver in C++ to allow code reuse with other solvers (#742), and simplified the 2nd order SDC code to do dimensional sweeps to reduce memory (#749)

• The option radiation.integrate_planck has been removed; it was only used by one test. By default we always do the full integral of the Planck function. (#740)

• Most of the radiation test problems have been moved over to a new opacity directory, rad_power_law, and all of the parameters that controlled the behavior of the power law opacity have been moved to the extern probin module. We now always expect you to pick a specific opacity implementation, so the parameter radiation.use_opacity_table_module has been removed. The "null" opacity implementation has been previously moved, and the code will fail to compile if you attempt to use it; you will need to update to rad_power_law. (See the documentation for information about how to use this new implementation.)

  Additionally, the code for the multigroup solver was effectively previously setting the Rosseland opacity, kappa_r, equal to the Planck opacity, kappa_p, if the latter was set but the former was not. There was similar unintuitive behavior for the behavior of the scattering parameter. Now you will get exactly what you ask for in the probin file, given the defaults in the _parameters file for the rad_power_law opacity. By default the constant coefficients for both are negative, which is invalid, so both must be set to a non-negative value for the code to work. Problems that were previously setting const_kappa_p but not const_kappa_r should set the latter equal to the former to maintain the same code behavior. The analogous thing should be done for the exponents (kappa_p_exp_m, kappa_p_exp_n, and kappa_p_exp_p). (#725)

• The parameter radiation.do_real_eos = 0 has been removed, and its functionality is now enabled with a new equation of state called rad_power_law. This new EOS is only compatible with the pure radiation-diffusion tests, not with castro.do_hydro = 1. (#722)

• We now default to use_retry = 1, instructing Castro to retry a step with a smaller dt if there is a CFL violation, burning failure, or negative timestep. For the burning failure, we have Castro set the Microphysics parameter abort_on_failure to .false. at a high priority (so it overrides the Microphysics default). We also check to make sure the combination of parameters makes sense at runtime. (#724)

• The parameter castro.hard_cfl_limit has been removed. (#723)

• Some unnecessary clean_state calls were removed (#721)

• Support for neutrino radiation diffusion has been removed.

• A bug was fixed in the hydro CFL timestep estimator for simplified-SDC. The timestep was more restrictive than it needed to be. (#727)

• A bug was fixed in the simplified-SDC nuclear burning timestep estimator (#733)

20.01

• A new option castro.limit_fluxes_on_large_vel has been added. It is similar to the existing option limit_fluxes_on_small_dens -- fluxes are limited to prevent the velocity in any zone from getting too high. The largest legal speed is set by castro.speed_limit. (#712) This is more general than the previous solution proposed by castro.riemann_speed_limit, so that parameter has been removed. (#714)

• The AMR parameter amr.compute_new_dt_on_regrid is now on by default. This avoids crashes that result from the CFL number being too large after regridding, because we update the timestep after seeing that larger velocity. You can still opt to set this off if you want to in your inputs file. (#720)

• We have added calls into Hypre that only exist as of version 2.15.0, so that is the new minimum requirement for Castro radiation. Note that Hypre is now hosted on GitHub at https://github.com/hypre-space/hypre.

• A new option castro.limit_fluxes_on_large_vel has been added. It is similar to the existing option limit_fluxes_on_small_dens -- fluxes are limited to prevent the velocity in any zone from getting too high. The largest legal speed is set by castro.riemann_speed_limit. (#712)

• A new option castro.apply_sources_consecutively has been added. By default we add all source terms together at once. This option, if enabled, adds the sources one at a time, so that each source sees the effect of the previously added sources. This can matter, as an example, for the sponge source term, which may be more effective if it is added after source terms such as gravity that update the velocity. (#710)

• A new option castro.ext_src_implicit has been added. The external source terms were previously only implemented as an explicit predictor-corrector scheme. The new option, if turned on, changes the handling of the external source terms to allow an implicit solve. This is done by subtracting the full old-time source and adding the full new-time source in the corrector, rather than -0.5 and +0.5 of each, respectively. It is still up to the individual problem to make sure it is consistent with this scheme if the option is turned on. (#709)

• Add option for using monopole BCs in 3D. By setting gravity.max_multipole_order to a negative number, you can use monopole gravity to fill the boundary conditions, rather than the multiple BCs. This is useful for debugging purposes. To make the behavior consistent, we now use multipole BCs by default in 2D as well. (#716)

19.12

• The use_retry mechanism has been enabled for the simplified SDC time integration method. (#695)

• A case where use_retry could result in a very small last subcycle has been avoided. (#701)

• We no longer allocate memory for sources for the species in the conserved state unless PRIM_SPECIES_HAVE_SOURCES is set (#699)

• A subroutine eos_on_host has been added to the EOS module. This is a wrapper for the EOS that must be used for CUDA builds if the EOS is being called in probinit or other places that don't run on the GPU. (#693)

• We now use VODE90 instead of VODE by default. (#677)

• A new unit test was added, model_burner, which reads in a 1-d initial model and calls the reaction network on it. This can be used to test tolerances, etc.

19.11

• The density flux limiter was simplified and fixes a race condition (#646)

• The SDC algorithm can now use Radau quadrature instead of Gauss-Lobatto quadrature. (#666)

• The option castro.ppm_reference_eigenvectors has been removed. This is now used by default with the CTU PPM solver.

19.10

• The SDC algorithm now implements the burning conditionals depending on rho and T (react_rho_min, react_rho_max, react_T_min, react_T_max) (#598, #654)

• The SDC/MOL PLM reconstruction now implements reflecting BCs on the interface states (#652, #654)

• A well-balanced scheme has been added to the piecewise linear SDC method, enabled with castro.plm_well_balanaced=1. At the moment it only supports constant gravity. (#294, $654))

• The weighting of the time-node fluxes stored in the flux registers for SDC has been fixed (#654, #658)

• As before, we can choose the reconstruction with PLM using the castro.plm_iorder flag: 1 = piecewise constant, 2 = piecewise linear slopes. Now we added a way to specify the limiter used with the linear slopes. castro.plm_limiter = 1 will use the 2nd order MC limiter and castro.plm_limiter = 2 will use the default 4th order MC limiter (previously there was no way to select the 2nd order limiter). (#654)

• The Runge-Kutta based method-of-lines integration method has been removed in favor of the SDC integration. (#657)

• A new way of specifying the problem runtime parameters has been introduced. They can now be specified in a plain text file, _prob_params, and at compile time, the probdata_module is automatically created. This automates the creation of the probdata variables, the namelist for reading them, setting them as managed for CUDA, and adds the ability to output the values to a file (like job_info). This feature is opt-in. You need to set USE_PROB_PARAMS in your GNUmakefile and then define the problem parameters in a file _prob_params in the problem directory. (#234, #619, #673)

• The time to output is now stored in the job_info file (#365)

• The SDC time advancement method has been documented

• The job_info file now reports the number of GPUs being used.

19.09

• You can now type ./Castro.gnu.ex *describe to see the list of modules / compilers the code was built with (#660)

• The reaction quantities are now computed as proper 4th order averages for the plotfile, when using sdc_order = 4 (#647)

• The velerr tagging now takes the abs() of the velocity component to ensure we tag large positive and negative velocities.

19.08.1

• Fix CUDA compilation

• Remove special treatment of 4th order outflow BCs (see #648)

19.08

• We slightly changed how the characteristic tracing is done for the CTU PPM hydro solver * we now use the limit of the parabola as the edge state if the wave is not moving toward the interface (#632)

• The CTU PPM solver now uses a lot less memory by computing the integrals under the parabolas as needed instead of precomputing and storing them (#624)

• We created a new error wrapper, castro_error(), to replace the AMReX amrex_error(). This will allow us to deal with error when on the GPU.

• The new SDC solver has had substantial improvements:

  • Explicit thermal diffusion is now implemented for both 2nd and 4th order accurate solvers. (#610)

  • There is a new option (castro.sdc_extra) for taking extra SDC iterations.

  • The Newton solver for the SDC update can now subcycle.

  • The sdc_solver_relax_factor option was fixed

  • There is now an absolute tolerance on species used in the error check for the SDC solve.

  • Some scalings of terms in the Jacobian were fixed.

  • We now use one-sided stencils for the reconstruction at physical boundaries (#633)

• The flame problem setup now can initialize conservatively from a pre-existing flame solution. The analysis routines have seen some improvements for working with 4th order accurate simulations.

• the diffusion_test unit test now works for 4th order problems.

19.07

• There is now a separate set of boundary filling routines for source terms, source_fill.F90. Previously this was handled by generic_fill.F90 (#627)

• The tagging routines have been reformulated so that they run on the GPU. Since the tags_and_untags routine in AMReX is not GPU-accelerated, we opt to directly fill in the TagBoxArray in the tagging routines. We now pass the TagBox to Fortran as an int8_t. This means that the interface to problem_tagging_nd.F90 has been updated to use integer(1).

  Castro_prob_err_list.H and other related files have been deleted as they were not actually used anywhere.

  Castro_error.cpp is now removed and there is no further support for writing custom tagging routines. The set of variables that we check for tagging is hard-coded in Castro and can be expanded as needed. Problem-specific tagging should be done through the set_problem_tags functionality. (#611)

• The dimension-specific code for problem initialization, boundary conditions, and external heat terms has been removed, as warned in the previous release notice.

19.06

• Deprecation notice: as of the 19.06 release, dimension-specific problem setups are deprecated. Presently they are opt-in by adding DIMENSION_AGNOSTIC = TRUE to your makefile, and using a Prob_nd.F90 file instead of a Prob_{1,2,3}d.F90 file. The dimension-agnostic Prob_nd.F90 is used to fill initial data for all dimensions. There is always a 3D loop over dimensions, and in 1D or 2D the unused dimensions have indices (lo, hi) = (0, 0) which is valid in Fortran. The current interface is found in Source/problems/Prob_nd.F90. Most of the problems have been converted to dimension-agnostic form and any remaining ones will be done shortly, so you can use e.g. the Sedov or DustCollapse problems to model you own problem on. The dimension agnostic problem setup also implies dimension agnostic helper routines such as in bc_fill_nd.F90 * any user-facing file ending in a 1d/2d/3d.f90 file extension is deprecated. In the 19.07 release support for these will be removed and problem setups will only work if they are dimension agnostic. Please file an issue if you need assistance converting your problem.

• Deprecation notice: as of the 19.06 release, problem-specific overrides of Castro_error.cpp, and in general custom tagging routines (including Castro_prob_err.cpp and associated files), are deprecated. The only supported mechanism for problem-specific tagging is through the set_problem_tags function in problem_tagging_nd.F90. (There are also dimension-specific versions of this file, but these are now deprecated as above.) Please file an issue if you need assistance converting your tagging setup to use the problem tagging, or if you need more data in that interface to be able to implement your tagging scheme. Support will be removed in the 19.07 release.

• Deprecation notice: as of the 19.06 release, the problem_pre_tagging_hook and problem_post_tagging_hook are deprecated. These were not actually being used in any problem. These will be removed in the 19.07 release.

19.05

• The dimension agnostic version of the external source term in ext_src_nd.F90 has been updated to use the ISO C binding interface, and two parameters, time and dt, are now passed by value * see Source/sources/ext_src_nd.F90 for the new interface.

• problem_derive_nd.f90 has been renamed to problem_derive_nd.F90.

• The velocity calculated for the interface in the Riemann solve for the CGF/CG Riemann solvers can no longer exceed the speed of light. The parameter castro.riemann_speed_limit can be set to control the speed limit applied in the Riemann solver * this is useful for preventing unphysically large velocities from being created at shock fronts or near large density gradients.

• The algorithm for recalculating source terms after an AMR reflux did not set some data needed to correctly calculate positions on the fine levels, so position-dependent source terms (rotation, hybrid momentum) were being calculated incorrectly. This caused some strange effects in AMR simulations with rotation, such as binary star orbits getting wider with time and drifting relative to the system center of mass. This has now been fixed. (#599)

• density_reset_method == 3 (which, in the event of a density reset, reset to the density at the beginning of the timestep) no longer exists. (#538)

• The behavior of use_retry = 1 with retry_neg_dens_factor changed slightly since we now choose the retry timestep based on the difference between the (incorrect) negative density and the density it was reset to, rather than the old density at the beginning of the step. It still does a similar type of timestep limiting, but quantitatively the timesteps it chooses will be different. (#538)

• A sign error was fixed in the hybrid_hydro angular momentum algorithm This addresses issue #462. During commmit 0f09693, a change in signs was introduced in add_hybrid_momentum_sources, which should be analogous to linear_to_hybrid (#594)

19.04

• The runtime parameter castro.fix_mass_flux has been removed: it is not clear what the use case is, and it had no test suite coverage. (#572)

• Fixed a bug introduced in August 2015 that resulted in incorrect real bounds being passed to ca_initdata after a restart for problems using a grown domain. This would have resulted in incorrect initialization for problems using the grown restart capability if their initialization depended on the position on the grid. (#566)

• Using point-mass gravity no longer requires USE_POINTMASS = TRUE in your makefile; USE_GRAV = TRUE is sufficient. However, to compensate for this, you must now include castro.use_point_mass = 1 in your inputs file to enable the point mass. This input parameter already existed, but was defaulted to 1 since it only mattered if the compile flag was enabled. Now the default is 0.

• Also, a couple bugs in the point-mass gravity have been fixed. The algorithm was not correct in 1D and 2D, and this has been resolved. And the point mass value was not being preserved across restarts, which is an issue if you're using point_mass_fix_solution to update the point mass value as mass accretes to the center of the domain. This has been fixed as well.

• fixed a bug in the source term to (rho e) evolution when using MOL or the new SDC integration (#543, #545) and also no longer recompute the source terms after reflux for these methods (#549)

• Dimension agnostic problem setups have had the interface to the physical boundary conditions changed (hypfill, denfill, etc.). If your problem is dimension agnostic, please consult the new interfaces in Source/problems/bc_fill_nd.F90 to understand how to convert your problem. The changes are that (1) the "ca_" prefixes have been removed from the subroutine names, (2) the "time" parameter is passed by value, and (3) the (lo, hi) indices that are the target region to update the boundaries on are explicitly passed in as the first two arguments. (#546)

• removed the code to extrapolate diffusion terms to ghost cells as it is no longer necessary (#532)

• we remove enthalpy diffusion (there were no known applications of this) and species and velocity diffusion (they were 1-d only). None of these routines were regularly tested. (#534)

• the problem diagnostics in Castro/Diagnostics have been converted to C++ to remain compatible with the AMReX build system.

19.03

• Fixed a minor long-standing bug in the simplified SDC implementation involving incorrect indexing. This changes results slightly.

• a number of tests involving reactions have been moved from hydro_tests to reacting_tests (#527)

• The old spectral deferred corrections method has been renamed "simplified" SDC. It is accessed with time_integration_method = 3. This still requires building with USE_SDC = TRUE, and when building this way, the other time integration methods are unavailable.

• The 4th order hydro was extended to support general equations of state (it is still single level only). Artificial viscosity was also added.

• A framework for a new spectral deferred corrections method was added. This will allow for higher-order time integration. (#310)

• Fix a bug where the self_heat parameter was not being initialized for the burning timestep limiter (#521).

• By default, we no longer allocation storage for source terms to species in the primitive variable state. This is set via the _variables file, parsed by set_variables.py. To allow for species sources, you need to set PRIM_SPECIES_HAVE_SOURCES. This is done currently for SDC. (#519)

• renamed QVAR to NQSRC to make it clear that this is the number of source terms for the primitive variable state. We also fixed a number of places where QVAR was used instead of NQ. (#517)

• A new runtime parameter, T_guess, was created. This is used as the initial temperature guess when calling the EOS with inputs other than rho, T, for the initial Newton iteration. (#509)

• The CTU hydrodynamics driver has been rewritten in C++ (#498)

• The input parameter castro.do_ctu has been renamed castro.time_integration_method. The current legal values are 0 (CTU, the default) and 1 (MOL).

• fixed a bug in the ppm_temp_fix = 1 reconstruction * we were not doing the initial reconstruction of temperature

19.02

• The flux limiter used with the options limit_fluxes_on_low_dens was not implemented correctly. This has been fixed. (PR #493)

• the CTU hydro solver no longer does any allocation in any of the support routines * it is all done in the top-level driver. (#455)

• The CTU solver now makes explicit the range of cells looped over in the transverse routines (#456)

• The plotfile quantities divu and magvort were fixed in axisymmetric coordinates and diff_term was fixed in all geometries. (#446, 448, 449, 472)

• abar is a new derived variable (#470)

• the job_info file now stores domain information (#451), and the job_info files is also stored in checkpoints now too (#450)

• we can now refine on enuc * the nuclear energy generation rate. This is controlled by the parameters (in the &tagging probin namespace) enucerr, and max_enucerr_lev. We also moved the dxnuc tagging parameters from inputs to probin, where they are now named dxnuc_min (formerly castro.dxnuc), dxnuc_max, and max_dxnuc_lev. (#364, #437, #473)

• The diffusion cutoff now is a linear ramp instead of a discontinous cutoff. For densities less than diffuse_cutoff_density_hi, the transport coefficient is scaled linearly until the density reaches diffuse_cutoff_density, where it is zero.

19.01.4

• fixed the .zenodo.json

19.01

• The User's Guide is now automatically built from the development branch using travis.

• we now store the job_info file in the checkpoints (#450)

• we now automatically generate Doxygen docs along with the User's Guide and have started adding docstrings throughout the code. (#461)

• The MG solver was optimized a bit (#464)

18.12

• fixed a bug in the CUDA version of the MOL integrator * it was setting the interface states incorrectly.

• removed ppm_type = 2. This was not used for science simulations because it was never shown to be completely stable. In the near future, the full fourth order method will be merged which will be a better replacement.

• a bug was fixed in the 1-d SDC integration * we were not applying the reactive source terms to the hydrodynamics interface prediction.

• we now apply the source terms for PLM before the transverse routines. This is more consistent with the PPM version.

• the angular momentum in the plotfile is not computed with respect to the center array initialized in the probinit

• fixed a bug in 2-d with rotation * we were adding the source terms to the out-of-plane velocity twice in the prediction of the interface states, resulting in an overall first-order approximation there.

• fixed an issue that resulted in the custom knapsack distribution map not generating a useful distribution map for the reactions. Also, fixed an edge case where this custom distribution map could cause a numerical overflow and code crash. (#382)

• rewrote the reconstruction routines to eliminate temporary arrays to make them GPU friendly

• the documentation was converted to sphinx

• changed the interface to the conductivity routines so the conductivity is not part of eos_t (#431)

18.11

• we've restructured the CTU solver to no longer use a slab approach in 3d. This is in preparation for offloading the solver to GPUs.

• a few minor bugs were fixed in the transverse routines of the CTU solver with radiation

• simplified conductivity interface to match the eos interface by moving the conductivity variable in the arguments into the eos type.

18.10

• fixed handling of external BCs (#402)

• unified some CUDA hydro solver code with the method-of-lines code

• offloaded gravity source terms, rotation, reactions, and sponge to GPUs with CUDA

• merged the different dimensional versions of the CTU consup routine into a single routine (#399)

• removed the unsafe option "allow_negative_energy"

18.09

• we now only trace under sources that are non-zero, to save computational expense. (#381)

• we now update T for consistency when we reset a small internal energy, e (#384)

• The parameter dual_energy_update_E_from_e has been removed, and the default behavior is now that the total energy (E) will not be changed when we reset the internal energy (e). This will cause changes in simulation output. (#368)

• The probin parameter eos_input_is_constant is now true by default. This means that when calling the EOS in the mode eos_input_re, the energy will not be updated after the EOS call (e.g. by the Newton iteration scheme in Helmholtz). This will cause changes in simulation output. (#368)

• the problem-specific runtime parameters (probin) are now written to the job_info file (#380)

• we now skip the initial EOS call prior to the burn * this was redundant because we already did a clean_state (#377)

• we now support recent versions of hypre (#373)

18.08

• the old use_mlmg_solver parameters were removed * this has been the only multigrid solver in Castro for some time, so the parameters had no effect.

• The parameter dual_energy_eta3 was removed. This had been introduced mostly for testing purposes and ended up being unnecessary. Also, the EOS call at the beginning of the burn was removed; this should provide a modest computational gain. Answers may change at the level of the EOS tolerance (#377).

• The functionality that checks for a regrid at the end of the timestep will now apply all tagging criteria, not just the t_sound / t_enuc criterion.

• A bug was fixed that occurred when a retry was triggered in the middle of a group of subcycles, rather than at the beginning of the advance (#358).

• A bug with the logic of refluxing when using retries was fixed (#357).

• Tagging can now be done on relative gradients, in addition to the existing capability for absolute gradients (#354). For example, tempgrad_rel is a relative gradient criterion that will tag a zone with temperature T if any adjacent zone has a temperature that is different by more than tempgrad_rel * T. The tagging is enabled up to a given level with the parameter max_tempgrad_rel_lev. The corresponding new tagging criteria for other fields are named similarly.

• Retries can now be done in a dynamic fashion (#179). An advance is itself a subcycled advance always, and we keep subcycling until we are done with the step. By default we still do only a single timestep when use_retry is not enabled, but this helps in cases where we have to reject the timestep for (say) a CFL violation, and then during the retry the CFL criterion is violated again. In the past, we would simply have to abort the run if this happened. Now we can cut the timestep again and keep going. Additionally, if you set abort_on_false to F in your probin file's extern parameters, then a burn in Microphysics will not cause an abort of the run, and Castro now knows how to deal with that by doing a retry and taking a shorter timestep (under the logic that most burn failures come from taking too large of a hydrodynamic timestep for the burner to be able to keep up).

18.07

• A new GPU (CUDA) hydrodynamics solver (based on the method-of-lines solver) has been added, based on the work initially done in StarLord. This is a work in progress, and requires the "gpu" branch of AMReX.

• We removed all dependencies on the AMReX F_BoxLib source, in preparation for this source being removed in the future.

• we now set the number of variables at compile time, by parsing the _variables file and interpreting which options are set in the preprocessor. Note that a side effect of this change is that the number of radiation groups is now set at compile time instead of at runtime. This change is needed for the GPU port.

  To set the number of radiation groups, set NGROUPS=4, e.g. for 4 groups, in your problem's GNUmakefile. Similar options exist for neutrinos.

  A related change is that it is now possible to set the number of advected quantities (that are not species or EOS auxillary fields) via NUMADV in your GNUmakefile.

18.06

• The new multilevel multigrid solvers (MLMG) in the AMReX framework are now the default for self-gravity and constructing the operator for explicit diffusion.

• A new test problem, the classic double Mach reflection, was added.

• fix an issue in the retry logic that could sometimes result in an overflow of the estimated number of subcycle steps.

• Improved the behavior of retries when they hit CFL violations (#334, #335).

18.05

• Gamma_1 is now a derived variable

• a new diffusion solver is implemented that uses the new muligrid framework in AMReX to compute the diffusive operator. This can be enabled with diffusion.use_mlmg_solver = 1.

18.04

• The job_info file now indicates which runtime parameters were changed from their default value (#314)

• Improvements made to the 4th order hydro solver for single-level

18.03

• The option ppm_trace_sources has been removed * we now always trace on source terms with ppm. Additionally, all sources are now traced, not just momentum sources.

• The method-of-lines integrator has been rewritten. It now works properly with sources. Note: it is not intended for multilevel yet. (#288, #287, #286, #164, #291, #137)

18.02

• The approximate state Riemann solvers have been split into two parts: the computation of the interface state and the evaluation of the fluxes from this interface state. This gives additional flexibililty in using these solvers in other methods.

18.01

• The parameter dtnuc_mode has been removed. This was initially used for testing various forms of the burning timestep limiter before a final form was settled on.

• Minor inconsistencies in how the external and diffusion source terms were constructed when simultaneously using reactions (#268, #269) have been fixed (#271).

• The deprecated parameter castro.use_colglaz is removed. It was deprecated in June 2016 because it was obsoleted by the parameter castro.riemann_solver, which can be set to 1 to use the Colella and Glaz Riemann solver.

• The state variable indicies in Fortran are now all defined in a single file, Source/driver/_variables. This makes it much clearer and consistent and will allow for autodocumentation and clean-ups for GPU acceleration in the future.

17.12

• The sponge can now operate based on pressure. The new parameters belong in the sponge namelist, and are named sponge_lower_pressure and sponge_upper_pressure. It works on the same principle as the density sponge.

• The sponge can now drive the system to a particular velocity (the default is still zero velocity). The new parameters belong in the sponge namelist in your probin file, and are named sponge_target_{x,y,z}_velocity.

• The SDC_Source_Type StateData was removed, as its purpose is now supplanted by the change to always keep the source terms in StateData (see below), and it was thus redundant. This does not change code output but does mean that old checkpoints generated while using SDC are no longer compatible with the current code. Normally we strive to maintain forward compatibility of checkpoints, but this change was considered justified because SDC is still considered an experimental feature under development and to our knowledge no production science runs have yet been done using SDC.

• The parameter gravity.max_solve_level was removed. This was added to work around convergence issues in the multigrid solve, but those convergence issues have since been fixed, so the parameter is no longer used.

• The Source_Type StateData now holds the actual old- and new-time sources (previously it held the source term predictor). This StateData is used to fill the sources_for_hydro MultiFab which provides the source terms used in the hydrodynamic update. Since it is StateData, this operation is done with a FillPatch. Consequently the sources_for_hydro data has meaningful data in both physical domain ghost zones and ghost zones at a coarse-fine interface (previously it only had meaningful data on fully interior ghost zones). Checkpoints will now have both old and new data. This change does result in a difference in the simulation output for simulations with source terms, as the answer will be different at the boundaries and at coarse-fine interfaces. (#116, #253) A related bug when using SDC was fixed too. (#56)

• The parameter castro.keep_sources_until_end has been removed.

• Source terms (gravity, rotation, etc.) have now been all coalesced into a single MultiFab. This reduces the memory footprint of the code. This negates the need for the code parameters update_state_between_sources and coalesce_update_diagnostics, so they have been removed. This will cause a change in results: the previous code behavior was to update the state with each successive source term as it was applied at the new time. Now every source term will be calculated using the same new-time state (the one coming out of the hydro) and the source terms are all applied to the state in one shot at the end. Note that both this and the old approach are second-order accurate in time. For problems that combine multiple source terms, this will cause changes that are larger than roundoff. In particular, if rotation is used in conjunction with other source terms, changes will be relatively large, because the Coriolis force depends on the velocity, so the source term is a bit different now that it is seeing a different velocity. (#165, #249)

• As of 17.10, there is a new option castro.plot_per_is_exact. If this is set to 1, timesteps will be shortened to exactly hit the time interval specified by amr.plot_per. An issue with this (#242) was fixed (#243) where an incorrect timestep would be taken after a restart if the previous step had been shortened.

• We can now use the new multigrid solver from AMReX (implemented in C++) instead of the older Fortran solver (#241). This is enabled with gravity.use_mlmg_solver=1. Note, this only works in 3-d currently. This has several options:

  gravity.mlmg_max_fmg_iter = 0 : This integer parameter determines how many FMG cycles will be performed before switching to V-cycle.

  gravity.mlmg_agglomeration = 0 : This boolean flag determines if AMR level 0 grids will be agglomerated as the grids are coarsen in the multi-grid hierarchy.

  gravity.mlmg_consolidation = 0 : This boolean flag determines if grids on an AMR fine level that is in a single-level solve or the lowest AMR level of a multi-level composite solve will be consolidated as the grids are coarsen in the multi-grid hierarchy. Here, consolidation means the grids will be moved to fewer MPI processes.

  Numerical experiments have show this scales better than the old solver.

• Apply the sources to the state's ghost zones (#255). This fixes #213 * it ensures the advances give a valid update for the ghost zones in the State_Type.

17.11.1

• Minor bug fixes from the 17.11 release. There is a corresponding 17.11.1 release of AMReX.

17.11

• A bug was fixed in non-Cartesian simulations with AMR (1D spherical and 2D cylindrical). The bug was introduced around version 17.02 and resulted in incorrect synchronization of the pressure term in the momentum equations. The effect would have manifested as non-conservation of momentum or strange effects at coarse-fine interfaces.

• The sponge is now always time centered. The option to do otherwise was introduced in 17.02, and has now been removed. Additionally, the form of the energy source term has been corrected for the time centered case, and brought into line with how we do the energy source term for other sources. (Issue #7, Issue #57)

• Fixed a bug in the fix for #188.

• Conductivity_dir has been renamed CONDUCTIVITY_DIR to be consistent with EOS_DIR and NETWORK_DIR

• we no longer get the compositional derivatives as part of the EOS call. If you need this functionality, you need to set the preprocessor variable (in Fortran), EXTRA_THERMO

• you can now use a system's BLAS routines, instead of compiling the versions from Microphysics by setting USE_SYSTEM_BLAS=TRUE. This then looks at BLAS_LIBRARY for the link line.

17.10

• It is sometimes useful to be able to do some sort of initialization phase in your simulation, stop with a checkpoint, and then restart (possibly with different options) to do the main phase of the run. In this case, you may want to reset the simulation time to zero for analysis purposes. The new option castro.reset_checkpoint_time allows you to do this: by setting it to the time you want, the checkpoint you generate will have this new time. Similarly, castro.reset_checkpoint_step allows you to reset the timestep number (for example, to 0). Both options only work when you're using amr.checkpoint_on_restart=1, which itself requires amr.regrid_on_restart=1. This option is only intended to be used for the case where you're generating this checkpoint, so you also need to temporarily set max_step and stop_time to the target values you're resetting them to, to prevent further steps after the restart. After you have the new checkpoint, then you can undo those temporary variables and continue your run as usual.

• A minor error in the gravity source terms was fixed (#109). This error should not normally have been observable.

• fixed a bug in the artifical viscosity in 1-d in non-Cartesian geometries (issue #175)

• the README.md now describes the process to become a "core developer" of Castro, and what this means.

• Network_dir has been renamed NETWORK_DIR and EOS_dir has been renamed EOS_DIR. All of the problem GNUmakefiles have been updated. The old names will continue to work in the near future, but users are encouraged to change any of their problems to use the new all-caps names (PR #184)

• the density flux limiting functionality now has a small tolerance (#185). It has also been documented (#193).

• the timestep retry is now conservative * this was accomplished by saving the density fluxes to use in the conservative gravity update (#178). Also, a bug in the timestep retry for Poisson gravity was fixed (#188).

17.09

• the Source/ directory structure has been reorganized, putting the source files into directories by physics and eliminating the Src_1d, Src_2d, ... subdirectories

• the Riemann solvers have been merged into a single dimensional-agnostic version in Src_nd. In 2-d there was an issue with how the Godunov state for the CG solver was stored on interfaces, which would affect the internal enery evolution.

• the PLM and PPM reconstruction routines were merged into a single dimensional-agnostic version in hydro/

• the characteristic tracing routines were merged into dimensional-agnostic versions in hydro/ and radiation/. This change fixed and outstanding issue * the PLM reconstruction in 1-d now uses a reference state. (issue #11)

17.08

• the option castro.limit_fluxes_on_small_dens now only limits on density as the name suggests. It originally also limited fluxes if the internal energy would go negative, but this caused problems in runs with MPI, so it was removed. It was not strictly needed anyway, as the normal logic for handling negative internal energies is reliable.

• two errors were fixed in the implementation of the triggered regrid at the end of a timestep. The method now correctly conserves fluid variables at coarse-fine boundaries.

• the XGRAPH stuff that output xmgr-compatible 1-d ASCII profiles

• fixed a bug where the gravity runtime parameters were not being properly initialized in the Fortran side of the code.

• the viscosity routine is now separate from conductivity in Microphysics/. Also, Castro can now use the stellar conductivity that is part of StarKiller.

• the StarKiller-astro Microphysics repo now uses a denser table for the Helmholtz EOS (thanks to Frank Timmes). If you are using this EOS, the new table will be soft-linked to your build directory automatically. If you have an old copy laying around, it might fail to run, with an I/O error.

17.07

• start of some code cleaning for eventual GPU offload support merging from StarLord

• added a framework for method-of-lines integration of the hydrodynamics. This does not do characteristic tracing, but instead does reconstruction through multiple stages of an ODE integrator. At the moment, radiation is not supported.

17.06

• we now require the AMReX library instead of the BoxLib library

• the Microphysics repository that we rely on for the EOS and reaction networks is now part of the starkiller-astro github. You can change your clone to refer to this via:

  git remote set-url origin ssh://[email protected]/starkiller-astro/Microphysics

• a new mechanism for using a stability criterion to trigger a regrid at the end of a timestep was added (PR #122)

• some cleaning of the logic for momentum fluxes and limit_hydro_fluxes_on_small_dens (issues #130, #131)

17.05

• some protections added in the retry code

17.04

• rewrote the conservative gravity formulation to work off of the potential. This gives the best conservation with AMR. This is equivalent to the description in Appendix B from Katz et al. (2016).

17.03

• the new refluxing method introduced in 16.11 has been removed, as it was determined to not provide any benefit in accuracy.

• new derived plot variables are available when using thermal diffusion, including the conductivity, diffusion coefficient, and the entire diffusion term to the energy equation. (issue #104)

• when all derived variables were stored in the plotfile, we were storing the mass fractions twice. E.g. for he4, we were saving "he4" and "X(he4)". Now only the latter is stored.

• created a post_simulation() function that is called at the end of a simulation. An example is provided by test_diffusion where we output the norm of the error against the analytic solution. (issue #107, 108)

17.02

• diagnostic information about how source terms update the state has been overhauled and made uniform. All source terms, including hydro and resets, print their changes to the state in the same format. The parameter print_energy_diagnostics has been renamed print_update_diagnostics, and a new parameter coalesce_update_diagnostics has been added so that you can combine all of the old-time and new-time updates into one print. (issue #58)

• to support both single and double precision, all of the floating point declarations use the amrex_real type defined in the amrex_fort_module * this is set to single or double precision at compile time. All constants also now use this type. For brevity, we rename it to 'rt' in the use statement. (issue #34)

• the sponge is now time-centered by default (issue #7)

• the ppm_temp_fix stuff has been documented and made consistent across dimensions (issue #25)

• the job info git information is now the output of git describe, this gives more information, including the last tag, how far we are from the tag, and an abbreviated hash. It also indicates if your working directory is dirty

17.01

• the radiation-specific version of computeTemp has been removed and instead everything goes through the main Castro computeTemp. This affects, in particular, how we treated small internal energies in radiation. (issue #64)

• the radiation-specific versions of umeth and consup have been merged with the pure hydro routines. This gives round-off level differences. This also now uses all velocity components in the kinetic energy correction for radiation. (issues #66, 70)

• a minor bug was fixed in the 3-d radiation characteristic tracing, regarding which gamma_1 (gamc) is used.

16.12a

• fix a restart bug with radiation that was introduced after 16.10 (this was cherry-picked from development) (issues #76, 78)

16.12

• BoxLib now requires a C++ 11 compiler by default. As part of this transition, PArrays are replaced by C++ Arrays. Additionally, changes to the BoxLib build system mean that we only need to supple COMP for the compiler. FCOMP is now ignored.

• The User's Guide has been updated to reflect the current flow of the algorithm.

16.11

• we now distinguish between gravity (which can include a constant gravitational acceleration) and self-gravity, with the GRAVITY and SELF_GRAVITY preprocessor directives

• some work on the sync between levels was done * this will be described in a forthcoming paper. The main change by default is that after a reflux, we recompute the value of the source terms on the affected levels so that the new-time source term knows about the updated state due to the flux. For gravity, this resembles what the original Castro paper described for a sync source, but this is now done in a consistent way for all source terms. This should be fairly cheap which is why it is enabled by default, but you can disable it (see castro.update_sources_after_reflux). An additional optional change is a new strategy for refluxing (see castro.reflux_strategy). In the existing standard method, we only reflux after all fine timesteps over a coarse timestep have completed. In the new method, we do a partial reflux at the end of each fine timestep. This means that the coarse state used in time interpolation for the fine level is slightly more accurate as we go for later fine timesteps. It should also be needed for self-consistently conserving energy for gravity. At present it is more expensive than the standard method when there are gravity sync solves because there are more of them, but the tradeoff is that the simulation is more accurate.

• the order of computing the temperature and reseting internal energy was changed in a few spots. This will change results by default.

• the radiation-specific source was moved into the Radiation/ subdirectory

16.10

• the parameter first_order_hydro has been moved from the radiation namespace to the castro namespace

• the problem setups have been moved into sub-directory categories to make it easier to read (issue #32)

• the way we we use tolerances in the multigrid solve for Poisson gravity has changed. The old behavior is that you would pass in gravity.ml_tol as the relative tolerance on each grid level, and absolute tolerances would not be used. This suffered from some defects, notably that on fine grids you often had to loosen the relative tolerance on each higher level to achieve convergence, and in certain cases the scheme would fail completely, for example if the fine grids were not covering the mass on the grid. We now use an input parameter gravity.abs_tol which controls the absolute scale of the tolerance. This can either be an array of values, one for each level, or a single scalar value. If it is the latter, then the absolute tolerance passed into the multigrid scheme is the tolerance multiplied by the maximum value of the RHS over the entire domain. On the coarse grid, then, the absolute tolerance is 4piGrho_maxabs_tol, and on fine grids this is multiplied by ref_ratio**2. If you do not specify gravity.abs_tol, then a reasonable value is selected for the coarse level, and the same scheme is used to give it reasonable values on the fine levels as well. The parameter gravity.ml_tol has been renamed gravity.rel_tol, and has the same meaning as before, but it now defaults to zero. gravity.ml_tol is now deprecated, and will be removed in a future release. Note that the tolerance used in determining convergence is always the less restrictive of the relative and absolute tolerance requirements. gravity.delta_tol has been removed. (issue #43)

• the radiation hydro solver, that used to live in CastroRadiation.git has now been completely integrated into the main Castro git repo. The history was preserved in the transition It has also been cleaned up a little (issues #24, #31, #33, #48)

  The radiation build variable Network_inputs was renamed to NETWORK_INPUTS for consistency.

  The EOSes that used to come with CastroRadiation are available in Microphysics.git

• the gravity and diffusion runtime parameters have been moved to the master _cpp_parameters file (issue #42)

• enthalpy, species, and temperature diffusion are now properly time-centered (issue #22), and a bug in the hi boundary inflow boundary conditions for diffusion was fixed (issue #41)

• a flux limiter has been added that limits the size of the hydro fluxes if they would cause rho or (rho e) to go negative. This can be used with castro.limit_hydro_fluxes_on_small_dens = 1.

• a bug for single-level problems with Poisson gravity has been fixed where the multi-grid tolerance was being set to an uninitialized value

• a flaw in the source terms for the primitive variables in the hydro update has been fixed, so that source terms like gravity should no longer affect the pressure and (rho e) interface states (issue #19)

• the prediction of source terms to the half-time used in the hydrodynamics reconstruction was not being done properly. This has been fixed (issue #18)

• the radiation hydro ppm now implements the ppm_predict_gammae option

• we no longer ship VODE or BLAS with Castro * these are provided by the separate Microphysics git repo

• the documentation of the architecture of Castro has been significantly improved (issues #20, #23, #29, #31)

16.09:

• the PPM tracing routine for radiation was synced up with the pure hydro version. In particular, it now supports ppm_trace_sources, implements the reference states and fixes an issue with the flattening.

• The 1-d PPM routine was also updated to support tracing, predicting gamma_e instead of (rho e), and an inconsistency in the flattening was fixed.

• the parameters ppm_reference and ppm_reference_edge_limit have been removed * there was no reason to use anything other than the defaults

• the parameter ppm_tau_in_tracing has been removed. The useful part of this is preserved in the ppm_predict_gammae = 1 functionality, which uses a different set of primitive variables (tau, u, p, gamma_e) in the prediction of the interface states.

• the flux correction for axisymmetric and 1-d spherical coords has been fixed. In particular, there is now a separate flux register for the pressure term that enters as a gradient in the momentum equation.

• The sign on the gravitational potential has been flipped to be consistent with the usual convention in the physics literature, i.e. the potential is negative and we solve del**2 phi = 4 * pi * G * rho.

• Castro_advance.cpp has been significantly cleaned up. Each source term (gravity, rotation, diffusion, etc.) has a MultiFab associated with it through which it affects the state data. This has changed results slightly (typically a relative change no larger than the 1e-4 level) due to updates in the order of operations and consistency in usage on ghost zones.

• An iterative solver for coupling between reactions and hydrodynamics has been introduced, which you can enable with USE_SDC = TRUE in the makefile. The number of iterations done for each timestep is controlled with castro.sdc_max_iters.

• We changed the defaults for the gravity and rotation sources. now we do grav_source_type and rot_source_type = 4 by default. This is a conservative formulation for the energy equation that incorporates the source as a flux in the energy equation. See Katz et al. 2016 for details.

  We also do implicit_rotation_update = 1 by default * this does a slightly better coupling of the Coriolis force in the momentum equation by doing an implicit velocity update

  We also make ppm_trace_sources = 1 the default * this does parabolic reconstruction of the momentum sources and traces under them when constructing the interface states

• we now set castro.cg_blend = 2 by default. This has no effect for the default CGF Riemann solver, but for the Colella & Glaz solver (castro.riemann_solver = 1), this will augment the secant iteration for the pstar find with bisection if we fail to converge. This makes the root find for the star state more robust.

• a new "fake" setup, riemann_test_zone can be use to send a left / right hydro state to the CG Riemann solver for testing * this acts as a unit test for that solver.

• the default for castro.allow_negative_energy is now 0 * this is the safer choice.

• the default for castro.point_mass_fix_solution was changed to 0

  • this is a more expected behavior for new users.

16.08

• A new parameter gravity.max_multipole_moment_level was added. This comes into play when using the multipole solver to compute the boundary conditions on the domain for isolated mass distributions. The default behavior in Castro when constructing boundary conditions for the gravity solve is to do a multipole expansion sum over the density on the coarse grid only. If you increase the value of that new parameter from its default of 0 to some higher number, it will use the data from those more refined levels in constructing the boundary condition values.

• The file sponge_nd.f90 in Source/Src_nd/ has been renamed to sponge_nd.F90, the file extension change indicating that it can now be run through the preprocessor. Please update your local name for this file if you're overriding it in your problem setup.

• The sponge update is usually done in an implicit fashion, but you can now instead do an explicit update with castro.sponge_implicit == 0.

• the shock variable is now output if we are running with shock detection enabled

• Microphysics/eos is now Microphysics/EOS

• a number of changes were done in the Microphysics repo * see Microphysics/CHANGES for a log of those

16.07

• For consistency across the BoxLib suite of astro codes, we've renamed the main environment variables. CASTRO_HOME now replaces CASTRO_DIR; MICROPHYSICS_HOME now replaces MICROPHYSICS_DIR.

• The EOS, network, and conductivity routines have been moved to sub-directories or Castro/Microphysics/. This reflects the way the layout in the standalone Microphysics repo as well as that in Maestro.

• Some of the routines in Source/Src_nd/ have been renamed from .f90 files to .F90 files so that we can use the preprocessor. If you were using any of them (Prob_nd.f90, problem_tagging_nd.f90, Rotation_frequency.f90, or ext_src_nd.f90) by having local copies in your problem directory that overwrote them, please be sure to update the file extension so that Castro will recognize them.

• If you were using allow_negative_energy == 0, the case where (rhoE), the total gas energy of the zone, was negative was indirectly covered and it would be reset in this case due to the way the logic worked for resetting the internal energy and then updating the total energy to be consistent with it. However at one point we added an option castro.dual_energy_update_E_from_e which disabled that second update and also meant that negative (rhoE) was again possible. This possibility has now been precluded directly, by resetting (rhoE) the same way if we detect that it is negative. This should not change results unless you were using castro.dual_energy_update_E_from_e = 1. This is also a good time to plug the newer option castro.allow_small_energy, which if set to 1 will reset when you hit a (rhoe) that is less than the smallest possible energy for the (rho, small_temp, X) in that zone. Note that it requires an extra EOS call.

• The default interpolation for coarse zones into fine zones is piecewise linear. There is now an option to use piecewise constant instead * set castro.state_interp_order to 0. Note that if you use piecewise linear you can set castro.lin_limit_state_interp to 1 if you want to preserve linear combinations and therefore guarantee that, say, sum(X) = 1.

• If you set the new option castro.limit_fluxes_on_small_dens = 1, the fluxes will be explicitly limited such that a negative density is never created.

• Along similar lines, there are also new options for how to reset a negative density if one should arise. Set castro.density_reset_method = 2 to use the average of all adjacent zones instead of the default, which is the characteristics of the adjacent zone with the highest density. Set it to 3 if you want to reset it to the original zone state before the hydro update.

• We have fixed an issue where diffusion did not work correctly if add_ext_src = 0. The diffusion source term is now independent of whether you have user-defined source terms.

• ConvertCheckpoint/ now lives under Util/

• UsersGuide/ is now Docs/ * this is consistent with the other BoxLib codes

• Burning is no longer done in ghost cells for boundaries with neighbors on the same level of refinement. Instead a ghost cell fill is done to fill the like-level neighbor cells. As a consequence of this change, if reset_internal_energy() is invoked in a cell, to reset the internal energy to E - K, this reset is now reflected in the ghost cells (this is a more consistent behavior). Previously, the energy was never reset in the ghost cells.