From 8d857e853a1bca20bb52ca0278b073f7c09555c6 Mon Sep 17 00:00:00 2001 From: zingale Date: Thu, 7 Mar 2024 22:30:21 +0000 Subject: [PATCH] deploy: 5728a640ea7e5e7c47532402ff754e6a1a030fe6 --- docs/FlowChart.html | 8 +- docs/Hydrodynamics.html | 22 +- docs/_sources/FlowChart.rst.txt | 2 +- docs/_sources/Hydrodynamics.rst.txt | 11 +- docs/_sources/faq.rst.txt | 4 +- docs/_sources/index.rst.txt | 2 +- docs/_sources/io.rst.txt | 5 +- docs/_sources/runtime_parameters.rst.txt | 1370 +++++++++++----------- docs/faq.html | 4 +- docs/genindex.html | 24 +- docs/getting_started.html | 92 ++ docs/io.html | 25 +- docs/runtime_parameters.html | 91 +- docs/searchindex.js | 2 +- docs/visualization.html | 92 ++ 15 files changed, 1018 insertions(+), 736 deletions(-) diff --git a/docs/FlowChart.html b/docs/FlowChart.html index 1e2acbae53..1f2005496c 100644 --- a/docs/FlowChart.html +++ b/docs/FlowChart.html @@ -399,12 +399,8 @@

Single Step FlowchartIn initialize_do_advance():

  1. Create Sborder, initialized from S_old

    2. -

  2. Call clean_state() to make sure the thermodynamics are in

    3. -
-
-

sync, in particular, compute the temperature.

-
-
    +

  1. Call clean_state() to make sure the thermodynamics are in +sync, in particular, compute the temperature.

  2. [SHOCK_VAR] zero out the shock flag.

  3. Create the source corrector (if castro.source_term_predictor = 1)

diff --git a/docs/Hydrodynamics.html b/docs/Hydrodynamics.html index e49cee1da9..c1ca33726a 100644 --- a/docs/Hydrodynamics.html +++ b/docs/Hydrodynamics.html @@ -575,6 +575,14 @@

Source Terms +

Note

+

To reduce memory usage, we do not include source terms for the +advected quantities, species, and auxiliary variables in the conserved +state vector by default. If your application needs external source terms for +these variables, set USE_SPECIES_SOURCES=TRUE when compiling so that space +will be allocated for them.

+

Primitive Forms

@@ -768,7 +776,7 @@

Primitive Variable SystemEach of these steps has a variety of runtime parameters that +

Each of these steps has a variety of runtime parameters that affect their behavior. Additionally, there are some general runtime parameters for hydrodynamics:

 -

Several floors are imposed on the thermodynamic quantities to prevet unphysical +

Several floors are imposed on the thermodynamic quantities to prevet unphysical behavior:

  • castro.small_dens: (Real; default: -1.e20)

    • @@ -1025,7 +1031,7 @@

    Edge State Prediction -

    For the reconstruction of the interface states, the following apply:

    +

    For the reconstruction of the interface states, the following apply:

    • castro.ppm_type : use piecewise linear vs PPM algorithm (0 or 1; default: 1). A value of 1 is the standard piecewise parabolic @@ -1066,7 +1072,7 @@

      Riemann Problem +

      Note

      These Riemann solvers are for Newtonian hydrodynamics, however, we enforce that the interface velocity cannot exceed the speed of light in both the @@ -1211,7 +1217,7 @@

      Compute Fluxes and Update

      Temperature Fixes

      -

      There are a number of experimental options for improving the behavior +

      There are a number of experimental options for improving the behavior of the temperature in the reconstruction and interface state prediction. The options are controlled by castro.ppm_temp_fix, which takes values:

      @@ -1242,7 +1248,7 @@

      Compute Fluxes and Update

      Flux Limiting

      -

      Multi-dimensional hydrodynamic simulations often have numerical +

      Multi-dimensional hydrodynamic simulations often have numerical artifacts that result from the sharp density gradients. A somewhat common issue, especially at low resolution, is negative densities that occur as a result of a hydro update. Castro contains a prescription diff --git a/docs/_sources/FlowChart.rst.txt b/docs/_sources/FlowChart.rst.txt index f24c4cfa7b..a47b22ad55 100644 --- a/docs/_sources/FlowChart.rst.txt +++ b/docs/_sources/FlowChart.rst.txt @@ -309,7 +309,7 @@ In the code, the objective is to evolve the state from the old time, A. Create ``Sborder``, initialized from ``S_old`` B. Call ``clean_state()`` to make sure the thermodynamics are in - sync, in particular, compute the temperature. + sync, in particular, compute the temperature. C. [``SHOCK_VAR``] zero out the shock flag. diff --git a/docs/_sources/Hydrodynamics.rst.txt b/docs/_sources/Hydrodynamics.rst.txt index 8d76bd5fdf..edaaf8accd 100644 --- a/docs/_sources/Hydrodynamics.rst.txt +++ b/docs/_sources/Hydrodynamics.rst.txt @@ -342,6 +342,14 @@ accounted for in **Steps 1** and **6**. The source terms are: S_{{\rm ext},\rho Y_k} \end{array}\right)^n. +.. index:: USE_SPECIES_SOURCES + +.. note:: To reduce memory usage, we do not include source terms for the + advected quantities, species, and auxiliary variables in the conserved + state vector by default. If your application needs external source terms for + these variables, set ``USE_SPECIES_SOURCES=TRUE`` when compiling so that space + will be allocated for them. + Primitive Forms =============== @@ -585,9 +593,6 @@ runtime parameters for hydrodynamics: See :ref:`sponge_section` for more details on the sponge. -- ``castro.normalize_species``: enforce that :math:`\sum_i X_i = 1` - (0 or 1; default: 0) - .. index:: castro.small_dens, castro.small_temp, castro.small_pres Several floors are imposed on the thermodynamic quantities to prevet unphysical diff --git a/docs/_sources/faq.rst.txt b/docs/_sources/faq.rst.txt index 4e3d03daf3..c723b745db 100644 --- a/docs/_sources/faq.rst.txt +++ b/docs/_sources/faq.rst.txt @@ -106,10 +106,10 @@ Debugging :: - print_state(mf, IntVect(D_DECL(10, 20, 30))); + print_state(mf, IntVect(AMREX_D_DECL(10, 20, 30))); Here, the IntVect has the dimension that we were compiled with - (and this is handled through the preprocessor ``D_DECL``). In + (and this is handled through the preprocessor ``AMREX_D_DECL``). In this case, we are inspecting zone (10, 20, 30), in the global index space. Note that since a multifab exists only on a single level, the integer indices here refer to the global index space on that level. diff --git a/docs/_sources/index.rst.txt b/docs/_sources/index.rst.txt index 14b646d378..0500e0bd62 100644 --- a/docs/_sources/index.rst.txt +++ b/docs/_sources/index.rst.txt @@ -60,7 +60,7 @@ https://github.com/amrex-astro/Castro filelist classlist - .. namespacelist +.. namespacelist .. toctree:: :caption: References diff --git a/docs/_sources/io.rst.txt b/docs/_sources/io.rst.txt index 1a29b56988..2054eb4e1c 100644 --- a/docs/_sources/io.rst.txt +++ b/docs/_sources/io.rst.txt @@ -271,8 +271,6 @@ radiation quantities). | (where X is any of the species | :math:`\omegadot_k = DX_k/Dt` | | | defined in the network) | | | +-----------------------------------+---------------------------------------------------+--------------------------------------+ -| ``enuc`` | Nuclear energy generation rate / gram | :math:`{\rm erg~g^{-1}~s^{-1}}` | -+-----------------------------------+---------------------------------------------------+--------------------------------------+ | ``rho_enuc`` | Nuclear energy generation rate density | :math:`{\rm erg~cm^{-3}~s^{-1}}` | +-----------------------------------+---------------------------------------------------+--------------------------------------+ | ``phiGrav`` | Gravitational potential | :math:`{\rm erg~g^{-1}}` | @@ -393,7 +391,8 @@ Derived variables | ``y_velocity``, | :math:`\ub = (\rho \ub)/\rho` | | | | ``z_velocity`` | | | | +-----------------------------------+---------------------------------------------------+-----------------------------+-----------------------------------------+ - +| ``enuc`` | Nuclear energy generation rate / gram | ``derenuc`` | :math:`{\rm erg~g^{-1}~s^{-1}}` | ++-----------------------------------+---------------------------------------------------+-----------------------------+-----------------------------------------+ problem-specific plotfile variables ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ diff --git a/docs/_sources/runtime_parameters.rst.txt b/docs/_sources/runtime_parameters.rst.txt index 3a3b2e9ec8..23c49beb0a 100644 --- a/docs/_sources/runtime_parameters.rst.txt +++ b/docs/_sources/runtime_parameters.rst.txt @@ -6,26 +6,26 @@ namespace: ``castro`` .. index:: castro.state_interp_order, castro.lin_limit_state_interp, castro.do_reflux, castro.update_sources_after_reflux, castro.allow_non_unit_aspect_zones -+--------------------------------------------+-------------------------------------------------------------+---------------+ -| parameter | description | default value | -+============================================+=============================================================+===============+ -| ``state_interp_order`` | highest order used in interpolation | 1 | -+--------------------------------------------+-------------------------------------------------------------+---------------+ -| ``lin_limit_state_interp`` | how to do limiting of the state data when interpolating 0: | 0 | -| | only prevent new extrema 1: preserve linear combinations of | | -| | state variables 2: preserve linear combinations and prevent | | -| | new extrema | | -+--------------------------------------------+-------------------------------------------------------------+---------------+ -| ``do_reflux`` | do we do the hyperbolic reflux at coarse-fine interfaces? | 1 | -+--------------------------------------------+-------------------------------------------------------------+---------------+ -| ``update_sources_after_reflux`` | whether to re-compute new-time source terms after a reflux | 1 | -| | Note: this only works for the CTU and simple-SDC | | -| | time_integration_method drivers | | -+--------------------------------------------+-------------------------------------------------------------+---------------+ -| ``allow_non_unit_aspect_zones`` | Castro was originally written assuming dx = dy = dz. This | 0 | -| | assumption is enforced at runtime. Setting | | -| | allow_non_unit_aspect_zones = 1 opts out. | | -+--------------------------------------------+-------------------------------------------------------------+---------------+ ++--------------------------------------------+-------------------------------------------------------------+-----------------------------+ +| parameter | description | default value | ++============================================+=============================================================+=============================+ +| ``state_interp_order`` | highest order used in interpolation | 1 | ++--------------------------------------------+-------------------------------------------------------------+-----------------------------+ +| ``lin_limit_state_interp`` | how to do limiting of the state data when interpolating 0: | 0 | +| | only prevent new extrema 1: preserve linear combinations of | | +| | state variables 2: preserve linear combinations and prevent | | +| | new extrema | | ++--------------------------------------------+-------------------------------------------------------------+-----------------------------+ +| ``do_reflux`` | do we do the hyperbolic reflux at coarse-fine interfaces? | 1 | ++--------------------------------------------+-------------------------------------------------------------+-----------------------------+ +| ``update_sources_after_reflux`` | whether to re-compute new-time source terms after a reflux | 1 | +| | Note: this only works for the CTU and simple-SDC | | +| | time_integration_method drivers | | ++--------------------------------------------+-------------------------------------------------------------+-----------------------------+ +| ``allow_non_unit_aspect_zones`` | Castro was originally written assuming dx = dy = dz. This | 0 | +| | assumption is enforced at runtime. Setting | | +| | allow_non_unit_aspect_zones = 1 opts out. | | ++--------------------------------------------+-------------------------------------------------------------+-----------------------------+ @@ -34,235 +34,235 @@ namespace: ``castro`` .. index:: castro.difmag, castro.small_dens, castro.small_temp, castro.small_pres, castro.small_ener, castro.do_hydro, castro.time_integration_method, castro.limit_fourth_order, castro.initialization_is_cell_average, castro.use_reconstructed_gamma1, castro.add_ext_src, castro.hybrid_hydro, castro.ppm_type, castro.ppm_do_limiting, castro.mhd_limit_characteristic, castro.ppm_temp_fix, castro.plm_iorder, castro.plm_limiter, castro.hybrid_riemann, castro.riemann_solver, castro.cg_maxiter, castro.cg_tol, castro.cg_blend, castro.use_flattening, castro.transverse_use_eos, castro.transverse_reset_density, castro.transverse_reset_rhoe, castro.dual_energy_eta1, castro.dual_energy_eta2, castro.use_pslope, castro.pslope_cutoff_density, castro.limit_fluxes_on_small_dens, castro.speed_limit, castro.do_sponge, castro.sponge_implicit, castro.ext_src_implicit, castro.source_term_predictor, castro.first_order_hydro, castro.xl_ext_bc_type, castro.xr_ext_bc_type, castro.yl_ext_bc_type, castro.yr_ext_bc_type, castro.zl_ext_bc_type, castro.zr_ext_bc_type, castro.hse_zero_vels, castro.hse_interp_temp, castro.hse_fixed_temp, castro.hse_reflect_vels, castro.fill_ambient_bc, castro.ambient_fill_dir, castro.ambient_outflow_vel, castro.clamp_ambient_temp, castro.ambient_safety_factor, castro.ambient_density, castro.ambient_temp, castro.ambient_energy, castro.sdc_order, castro.sdc_quadrature, castro.sdc_extra, castro.sdc_solver, castro.use_axisymmetric_geom_source, castro.add_sdc_react_source_to_advection, castro.hydro_memory_footprint_ratio -+--------------------------------------------+-------------------------------------------------------------+---------------+ -| parameter | description | default value | -+============================================+=============================================================+===============+ -| ``difmag`` | the coefficient of the artificial viscosity | 0.1 | -+--------------------------------------------+-------------------------------------------------------------+---------------+ -| ``small_dens`` | the small density cutoff. Densities below this value will | -1.e200 | -| | be reset | | -+--------------------------------------------+-------------------------------------------------------------+---------------+ -| ``small_temp`` | the small temperature cutoff. Temperatures below this | -1.e200 | -| | value will be reset | | -+--------------------------------------------+-------------------------------------------------------------+---------------+ -| ``small_pres`` | the small pressure cutoff. Pressures below this value will | -1.e200 | -| | be reset | | -+--------------------------------------------+-------------------------------------------------------------+---------------+ -| ``small_ener`` | the small specific internal energy cutoff. Internal | -1.e200 | -| | energies below this value will be reset | | -+--------------------------------------------+-------------------------------------------------------------+---------------+ -| ``do_hydro`` | permits hydro to be turned on and off for running pure rad | -1 | -| | problems | | -+--------------------------------------------+-------------------------------------------------------------+---------------+ -| ``time_integration_method`` | how do we advance in time? 0 = CTU + Strang, 1 is not used, | 0 | -| | 2 = SDC, 3 = simplified-SDC | | -+--------------------------------------------+-------------------------------------------------------------+---------------+ -| ``limit_fourth_order`` | do we use a limiter with the fourth-order accurate | 1 | -| | reconstruction? | | -+--------------------------------------------+-------------------------------------------------------------+---------------+ -| ``initialization_is_cell_average`` | for fourth order, we usually assume that the initialization | 0 | -| | is done to cell centers and we convert to cell-averages. | | -| | With this option, we take the initialization as cell- | | -| | averages (except for T, which we compute to fourth-order | | -| | through the EOS after initialization). | | -+--------------------------------------------+-------------------------------------------------------------+---------------+ -| ``use_reconstructed_gamma1`` | should we use a reconstructed version of Gamma_1 in the | 0 | -| | Riemann solver? or the default zone average (requires SDC | | -| | integration, since we do not trace) | | -+--------------------------------------------+-------------------------------------------------------------+---------------+ -| ``add_ext_src`` | if true, define an additional source term | 0 | -+--------------------------------------------+-------------------------------------------------------------+---------------+ -| ``hybrid_hydro`` | whether to use the hybrid advection scheme that updates | 0 | -| | z-angular momentum, cylindrical momentum, and azimuthal | | -| | momentum (3D only) | | -+--------------------------------------------+-------------------------------------------------------------+---------------+ -| ``ppm_type`` | reconstruction type: 0: piecewise linear; 1: classic | 1 | -| | Colella \& Woodward ppm; | | -+--------------------------------------------+-------------------------------------------------------------+---------------+ -| ``ppm_do_limiting`` | do we limit the ppm parabola? | 1 | -+--------------------------------------------+-------------------------------------------------------------+---------------+ -| ``mhd_limit_characteristic`` | For MHD + PLM, do we limit on characteristic or primitive | 1 | -| | variables | | -+--------------------------------------------+-------------------------------------------------------------+---------------+ -| ``ppm_temp_fix`` | various methods of giving temperature a larger role in the | 0 | -| | reconstruction---see Zingale \& Katz 2015 | | -+--------------------------------------------+-------------------------------------------------------------+---------------+ -| ``plm_iorder`` | for piecewise linear, reconstruction order to use 1 = | 2 | -| | piecewise constant, 2 = piecewise linear | | -+--------------------------------------------+-------------------------------------------------------------+---------------+ -| ``plm_limiter`` | for piecewise linear, what limiter to use? 1 = 2nd order | 2 | -| | MC, 2 = 4th order MC | | -+--------------------------------------------+-------------------------------------------------------------+---------------+ -| ``hybrid_riemann`` | do we drop from our regular Riemann solver to HLL when we | 0 | -| | are in shocks to avoid the odd-even decoupling instability? | | -+--------------------------------------------+-------------------------------------------------------------+---------------+ -| ``riemann_solver`` | which Riemann solver do we use: 0: Colella, Glaz, \& | 0 | -| | Ferguson (a two-shock solver); 1: Colella \& Glaz (a two- | | -| | shock solver) 2: HLLC | | -+--------------------------------------------+-------------------------------------------------------------+---------------+ -| ``cg_maxiter`` | for the Colella \& Glaz Riemann solver, the maximum number | 12 | -| | of iterations to take when solving for the star state | | -+--------------------------------------------+-------------------------------------------------------------+---------------+ -| ``cg_tol`` | for the Colella \& Glaz Riemann solver, the tolerance to | 1.0e-5 | -| | demand in finding the star state | | -+--------------------------------------------+-------------------------------------------------------------+---------------+ -| ``cg_blend`` | for the Colella \& Glaz Riemann solver, what to do if we do | 2 | -| | not converge to a solution for the star state. 0 = do | | -| | nothing; print iterations and exit 1 = revert to the | | -| | original guess for p-star 2 = do a bisection search for | | -| | another 2 * cg_maxiter iterations. | | -+--------------------------------------------+-------------------------------------------------------------+---------------+ -| ``use_flattening`` | flatten the reconstructed profiles around shocks to prevent | 1 | -| | them from becoming too thin | | -+--------------------------------------------+-------------------------------------------------------------+---------------+ -| ``transverse_use_eos`` | after we add the transverse correction to the interface | 0 | -| | states, replace the predicted pressure with an EOS call | | -| | (using :math:`e` and :math:`\rho`). | | -+--------------------------------------------+-------------------------------------------------------------+---------------+ -| ``transverse_reset_density`` | if the transverse interface state correction, if the new | 1 | -| | density is negative, then replace all of the interface | | -| | quantities with their values without the transverse | | -| | correction. | | -+--------------------------------------------+-------------------------------------------------------------+---------------+ -| ``transverse_reset_rhoe`` | if the interface state for :math:`(\rho e)` is negative | 0 | -| | after we add the transverse terms, then replace the | | -| | interface value of :math:`(\rho e)` with a value | | -| | constructed from the :math:`(\rho e)` evolution equation | | -+--------------------------------------------+-------------------------------------------------------------+---------------+ -| ``dual_energy_eta1`` | Threshold value of (E - K) / E such that above eta1, the | 1.0e0 | -| | hydrodynamic pressure is derived from E - K; otherwise, we | | -| | use the internal energy variable UEINT. | | -+--------------------------------------------+-------------------------------------------------------------+---------------+ -| ``dual_energy_eta2`` | Threshold value of (E - K) / E such that above eta2, we | 1.0e-4 | -| | update the internal energy variable UEINT to match E - K. | | -| | Below this, UEINT remains unchanged. | | -+--------------------------------------------+-------------------------------------------------------------+---------------+ -| ``use_pslope`` | for the piecewise linear reconstruction, do we subtract off | 0 | -| | :math:`(\rho g)` from the pressure before limiting? This | | -| | is a well-balanced method that does well with HSE | | -+--------------------------------------------+-------------------------------------------------------------+---------------+ -| ``pslope_cutoff_density`` | if we are using pslope, below what density to we turn off | -1.e20 | -| | the well-balanced reconstruction? | | -+--------------------------------------------+-------------------------------------------------------------+---------------+ -| ``limit_fluxes_on_small_dens`` | Should we limit the density fluxes so that we do not create | 0 | -| | small densities? | | -+--------------------------------------------+-------------------------------------------------------------+---------------+ -| ``speed_limit`` | Enforce the magnitude of the velocity to be no larger than | 0.0 | -| | this number (and optionally limit the fluxes as well). Only | | -| | applies if it is greater than 0. | | -+--------------------------------------------+-------------------------------------------------------------+---------------+ -| ``do_sponge`` | permits sponge to be turned on and off | 0 | -+--------------------------------------------+-------------------------------------------------------------+---------------+ -| ``sponge_implicit`` | if we are using the sponge, whether to use the implicit | 1 | -| | solve for it | | -+--------------------------------------------+-------------------------------------------------------------+---------------+ -| ``ext_src_implicit`` | if we are using user-defined source terms, are these solved | 0 | -| | implicitly? | | -+--------------------------------------------+-------------------------------------------------------------+---------------+ -| ``source_term_predictor`` | extrapolate the source terms (gravity and rotation) to | 0 | -| | :math:`n+1/2` timelevel for use in the interface state | | -| | prediction | | -+--------------------------------------------+-------------------------------------------------------------+---------------+ -| ``first_order_hydro`` | set the flattening parameter to zero to force the | 0 | -| | reconstructed profiles to be flat, resulting in a first- | | -| | order method | | -+--------------------------------------------+-------------------------------------------------------------+---------------+ -| ``xl_ext_bc_type`` | if we are doing an external -x boundary condition, who do | -1 | -| | we interpret it? 1 = HSE | | -+--------------------------------------------+-------------------------------------------------------------+---------------+ -| ``xr_ext_bc_type`` | if we are doing an external +x boundary condition, who do | -1 | -| | we interpret it? 1 = HSE | | -+--------------------------------------------+-------------------------------------------------------------+---------------+ -| ``yl_ext_bc_type`` | if we are doing an external -y boundary condition, who do | -1 | -| | we interpret it? 1 = HSE | | -+--------------------------------------------+-------------------------------------------------------------+---------------+ -| ``yr_ext_bc_type`` | if we are doing an external +y boundary condition, who do | -1 | -| | we interpret it? 1 = HSE | | -+--------------------------------------------+-------------------------------------------------------------+---------------+ -| ``zl_ext_bc_type`` | if we are doing an external -z boundary condition, who do | -1 | -| | we interpret it? 1 = HSE | | -+--------------------------------------------+-------------------------------------------------------------+---------------+ -| ``zr_ext_bc_type`` | if we are doing an external +z boundary condition, who do | -1 | -| | we interpret it? 1 = HSE | | -+--------------------------------------------+-------------------------------------------------------------+---------------+ -| ``hse_zero_vels`` | if we are doing HSE boundary conditions, do we zero the | 0 | -| | velocity? | | -+--------------------------------------------+-------------------------------------------------------------+---------------+ -| ``hse_interp_temp`` | if we are doing HSE boundary conditions, should we get the | 0 | -| | temperature via interpolation (constant gradient) or hold | | -| | it constant? | | -+--------------------------------------------+-------------------------------------------------------------+---------------+ -| ``hse_fixed_temp`` | if we are doing HSE boundary conditions and holding the | -1.e200 | -| | temperature constant, then set it to a fixed value at the | | -| | boundaries (only if positive) | | -+--------------------------------------------+-------------------------------------------------------------+---------------+ -| ``hse_reflect_vels`` | if we are doing HSE boundary conditions, how do we treat | 0 | -| | the velocity? reflect? or outflow? | | -+--------------------------------------------+-------------------------------------------------------------+---------------+ -| ``fill_ambient_bc`` | fills physical domain boundaries with the ambient state | 0 | -+--------------------------------------------+-------------------------------------------------------------+---------------+ -| ``ambient_fill_dir`` | which direction do we do ambient BCs? -1 = all, 0 = x, 1 = | -1 | -| | y, 2 = z | | -+--------------------------------------------+-------------------------------------------------------------+---------------+ -| ``ambient_outflow_vel`` | in the ambient region, do we do a basic outflow in the | 0 | -| | normal direction of the velocity (with a min/max to ensure | | -| | it is outgoing) | | -+--------------------------------------------+-------------------------------------------------------------+---------------+ -| ``clamp_ambient_temp`` | clamps the ambient material to the ambient temperature | 0 | -+--------------------------------------------+-------------------------------------------------------------+---------------+ -| ``ambient_safety_factor`` | specifies the upper limit, as a multiple of the ambient | 1.1e0 | -| | density, for operations that are applied to ambient | | -| | material, such as clamping T. | | -+--------------------------------------------+-------------------------------------------------------------+---------------+ -| ``ambient_density`` | density of the ambient material (should default to the same | -1.e200 | -| | as small_dens) | | -+--------------------------------------------+-------------------------------------------------------------+---------------+ -| ``ambient_temp`` | temperature of the ambient material (should default to the | -1.e200 | -| | same as small_temp) | | -+--------------------------------------------+-------------------------------------------------------------+---------------+ -| ``ambient_energy`` | energy of the ambient material (should default to the same | -1.e200 | -| | as small_ener) | | -+--------------------------------------------+-------------------------------------------------------------+---------------+ -| ``sdc_order`` | integration order for SDC integration valid options are 2 | 2 | -| | and 4 | | -+--------------------------------------------+-------------------------------------------------------------+---------------+ -| ``sdc_quadrature`` | which quadrature type to use with SDC? 0 = Gauss-Lobatto, | 0 | -| | 1 = Radau | | -+--------------------------------------------+-------------------------------------------------------------+---------------+ -| ``sdc_extra`` | number of extra SDC iterations to take beyond the order. | 0 | -| | This only applies for true SDC. | | -+--------------------------------------------+-------------------------------------------------------------+---------------+ -| ``sdc_solver`` | which SDC nonlinear solver to use? 1 = Newton, 2 = VODE, 3 | 1 | -| | = VODE for first iter | | -+--------------------------------------------+-------------------------------------------------------------+---------------+ -| ``use_axisymmetric_geom_source`` | for 2-d axisymmetry, do we include the geometry source | 1 | -| | terms from Bernand-Champmartin? | | -+--------------------------------------------+-------------------------------------------------------------+---------------+ -| ``add_sdc_react_source_to_advection`` | for simplified-SDC, do we add the reactive source | 1 | -| | prediction to the interface states used in the advective | | -| | source construction? | | -+--------------------------------------------+-------------------------------------------------------------+---------------+ -| ``hydro_memory_footprint_ratio`` | In GPU builds, the hydro advance typically results in a | -1.0 | -| | large amount of extra temporary memory allocated due to the | | -| | large tile sizes that are used for computational | | -| | efficiency. If you want to constrain the code's GPU memory | | -| | footprint at the expense of throughput, set the following | | -| | parameter to some number greater than 0. This controls the | | -| | ratio of additional extra memory that can be allocated by | | -| | the hydro relative to the size of the base state | | -| | (indirectly, by controlling the hydro tile size and then | | -| | synchronizing each time the amount of currently allocated | | -| | fab memory reaches the target limit). Choosing a value only | | -| | slightly larger than 0 means that you want very little | | -| | additional memory allocated, and you will take a relatively | | -| | large performance hit, while choosing a value much greater | | -| | than 1.0 would result in maximum throughput but also | | -| | maximum memory footprint. You will likely have to | | -| | experimentally find a good ratio for your use case, but a | | -| | ratio around 2.0 - 4.0 is likely to yield a reasonable | | -| | balance between memory footprint and throughput. Note: the | | -| | first timestep will be very slow when using this option. | | -+--------------------------------------------+-------------------------------------------------------------+---------------+ ++--------------------------------------------+-------------------------------------------------------------+-----------------------------+ +| parameter | description | default value | ++============================================+=============================================================+=============================+ +| ``difmag`` | the coefficient of the artificial viscosity | 0.1 | ++--------------------------------------------+-------------------------------------------------------------+-----------------------------+ +| ``small_dens`` | the small density cutoff. Densities below this value will | -1.e200 | +| | be reset | | ++--------------------------------------------+-------------------------------------------------------------+-----------------------------+ +| ``small_temp`` | the small temperature cutoff. Temperatures below this | -1.e200 | +| | value will be reset | | ++--------------------------------------------+-------------------------------------------------------------+-----------------------------+ +| ``small_pres`` | the small pressure cutoff. Pressures below this value will | -1.e200 | +| | be reset | | ++--------------------------------------------+-------------------------------------------------------------+-----------------------------+ +| ``small_ener`` | the small specific internal energy cutoff. Internal | -1.e200 | +| | energies below this value will be reset | | ++--------------------------------------------+-------------------------------------------------------------+-----------------------------+ +| ``do_hydro`` | permits hydro to be turned on and off for running pure rad | -1 | +| | problems | | ++--------------------------------------------+-------------------------------------------------------------+-----------------------------+ +| ``time_integration_method`` | how do we advance in time? 0 = CTU + Strang, 1 is not used, | 0 | +| | 2 = SDC, 3 = simplified-SDC | | ++--------------------------------------------+-------------------------------------------------------------+-----------------------------+ +| ``limit_fourth_order`` | do we use a limiter with the fourth-order accurate | 1 | +| | reconstruction? | | ++--------------------------------------------+-------------------------------------------------------------+-----------------------------+ +| ``initialization_is_cell_average`` | for fourth order, we usually assume that the initialization | 0 | +| | is done to cell centers and we convert to cell-averages. | | +| | With this option, we take the initialization as cell- | | +| | averages (except for T, which we compute to fourth-order | | +| | through the EOS after initialization). | | ++--------------------------------------------+-------------------------------------------------------------+-----------------------------+ +| ``use_reconstructed_gamma1`` | should we use a reconstructed version of Gamma_1 in the | 0 | +| | Riemann solver? or the default zone average (requires SDC | | +| | integration, since we do not trace) | | ++--------------------------------------------+-------------------------------------------------------------+-----------------------------+ +| ``add_ext_src`` | if true, define an additional source term | 0 | ++--------------------------------------------+-------------------------------------------------------------+-----------------------------+ +| ``hybrid_hydro`` | whether to use the hybrid advection scheme that updates | 0 | +| | z-angular momentum, cylindrical momentum, and azimuthal | | +| | momentum (3D only) | | ++--------------------------------------------+-------------------------------------------------------------+-----------------------------+ +| ``ppm_type`` | reconstruction type: 0: piecewise linear; 1: classic | 1 | +| | Colella \& Woodward ppm; | | ++--------------------------------------------+-------------------------------------------------------------+-----------------------------+ +| ``ppm_do_limiting`` | do we limit the ppm parabola? | 1 | ++--------------------------------------------+-------------------------------------------------------------+-----------------------------+ +| ``mhd_limit_characteristic`` | For MHD + PLM, do we limit on characteristic or primitive | 1 | +| | variables | | ++--------------------------------------------+-------------------------------------------------------------+-----------------------------+ +| ``ppm_temp_fix`` | various methods of giving temperature a larger role in the | 0 | +| | reconstruction---see Zingale \& Katz 2015 | | ++--------------------------------------------+-------------------------------------------------------------+-----------------------------+ +| ``plm_iorder`` | for piecewise linear, reconstruction order to use 1 = | 2 | +| | piecewise constant, 2 = piecewise linear | | ++--------------------------------------------+-------------------------------------------------------------+-----------------------------+ +| ``plm_limiter`` | for piecewise linear, what limiter to use? 1 = 2nd order | 2 | +| | MC, 2 = 4th order MC | | ++--------------------------------------------+-------------------------------------------------------------+-----------------------------+ +| ``hybrid_riemann`` | do we drop from our regular Riemann solver to HLL when we | 0 | +| | are in shocks to avoid the odd-even decoupling instability? | | ++--------------------------------------------+-------------------------------------------------------------+-----------------------------+ +| ``riemann_solver`` | which Riemann solver do we use: 0: Colella, Glaz, \& | 0 | +| | Ferguson (a two-shock solver); 1: Colella \& Glaz (a two- | | +| | shock solver) 2: HLLC | | ++--------------------------------------------+-------------------------------------------------------------+-----------------------------+ +| ``cg_maxiter`` | for the Colella \& Glaz Riemann solver, the maximum number | 12 | +| | of iterations to take when solving for the star state | | ++--------------------------------------------+-------------------------------------------------------------+-----------------------------+ +| ``cg_tol`` | for the Colella \& Glaz Riemann solver, the tolerance to | 1.0e-5 | +| | demand in finding the star state | | ++--------------------------------------------+-------------------------------------------------------------+-----------------------------+ +| ``cg_blend`` | for the Colella \& Glaz Riemann solver, what to do if we do | 2 | +| | not converge to a solution for the star state. 0 = do | | +| | nothing; print iterations and exit 1 = revert to the | | +| | original guess for p-star 2 = do a bisection search for | | +| | another 2 * cg_maxiter iterations. | | ++--------------------------------------------+-------------------------------------------------------------+-----------------------------+ +| ``use_flattening`` | flatten the reconstructed profiles around shocks to prevent | 1 | +| | them from becoming too thin | | ++--------------------------------------------+-------------------------------------------------------------+-----------------------------+ +| ``transverse_use_eos`` | after we add the transverse correction to the interface | 0 | +| | states, replace the predicted pressure with an EOS call | | +| | (using :math:`e` and :math:`\rho`). | | ++--------------------------------------------+-------------------------------------------------------------+-----------------------------+ +| ``transverse_reset_density`` | if the transverse interface state correction, if the new | 1 | +| | density is negative, then replace all of the interface | | +| | quantities with their values without the transverse | | +| | correction. | | ++--------------------------------------------+-------------------------------------------------------------+-----------------------------+ +| ``transverse_reset_rhoe`` | if the interface state for :math:`(\rho e)` is negative | 0 | +| | after we add the transverse terms, then replace the | | +| | interface value of :math:`(\rho e)` with a value | | +| | constructed from the :math:`(\rho e)` evolution equation | | ++--------------------------------------------+-------------------------------------------------------------+-----------------------------+ +| ``dual_energy_eta1`` | Threshold value of (E - K) / E such that above eta1, the | 1.0e0 | +| | hydrodynamic pressure is derived from E - K; otherwise, we | | +| | use the internal energy variable UEINT. | | ++--------------------------------------------+-------------------------------------------------------------+-----------------------------+ +| ``dual_energy_eta2`` | Threshold value of (E - K) / E such that above eta2, we | 1.0e-4 | +| | update the internal energy variable UEINT to match E - K. | | +| | Below this, UEINT remains unchanged. | | ++--------------------------------------------+-------------------------------------------------------------+-----------------------------+ +| ``use_pslope`` | for the piecewise linear reconstruction, do we subtract off | 0 | +| | :math:`(\rho g)` from the pressure before limiting? This | | +| | is a well-balanced method that does well with HSE | | ++--------------------------------------------+-------------------------------------------------------------+-----------------------------+ +| ``pslope_cutoff_density`` | if we are using pslope, below what density to we turn off | -1.e20 | +| | the well-balanced reconstruction? | | ++--------------------------------------------+-------------------------------------------------------------+-----------------------------+ +| ``limit_fluxes_on_small_dens`` | Should we limit the density fluxes so that we do not create | 0 | +| | small densities? | | ++--------------------------------------------+-------------------------------------------------------------+-----------------------------+ +| ``speed_limit`` | Enforce the magnitude of the velocity to be no larger than | 0.0 | +| | this number (and optionally limit the fluxes as well). Only | | +| | applies if it is greater than 0. | | ++--------------------------------------------+-------------------------------------------------------------+-----------------------------+ +| ``do_sponge`` | permits sponge to be turned on and off | 0 | ++--------------------------------------------+-------------------------------------------------------------+-----------------------------+ +| ``sponge_implicit`` | if we are using the sponge, whether to use the implicit | 1 | +| | solve for it | | ++--------------------------------------------+-------------------------------------------------------------+-----------------------------+ +| ``ext_src_implicit`` | if we are using user-defined source terms, are these solved | 0 | +| | implicitly? | | ++--------------------------------------------+-------------------------------------------------------------+-----------------------------+ +| ``source_term_predictor`` | extrapolate the source terms (gravity and rotation) to | 0 | +| | :math:`n+1/2` timelevel for use in the interface state | | +| | prediction | | ++--------------------------------------------+-------------------------------------------------------------+-----------------------------+ +| ``first_order_hydro`` | set the flattening parameter to zero to force the | 0 | +| | reconstructed profiles to be flat, resulting in a first- | | +| | order method | | ++--------------------------------------------+-------------------------------------------------------------+-----------------------------+ +| ``xl_ext_bc_type`` | if we are doing an external -x boundary condition, who do | -1 | +| | we interpret it? 1 = HSE | | ++--------------------------------------------+-------------------------------------------------------------+-----------------------------+ +| ``xr_ext_bc_type`` | if we are doing an external +x boundary condition, who do | -1 | +| | we interpret it? 1 = HSE | | ++--------------------------------------------+-------------------------------------------------------------+-----------------------------+ +| ``yl_ext_bc_type`` | if we are doing an external -y boundary condition, who do | -1 | +| | we interpret it? 1 = HSE | | ++--------------------------------------------+-------------------------------------------------------------+-----------------------------+ +| ``yr_ext_bc_type`` | if we are doing an external +y boundary condition, who do | -1 | +| | we interpret it? 1 = HSE | | ++--------------------------------------------+-------------------------------------------------------------+-----------------------------+ +| ``zl_ext_bc_type`` | if we are doing an external -z boundary condition, who do | -1 | +| | we interpret it? 1 = HSE | | ++--------------------------------------------+-------------------------------------------------------------+-----------------------------+ +| ``zr_ext_bc_type`` | if we are doing an external +z boundary condition, who do | -1 | +| | we interpret it? 1 = HSE | | ++--------------------------------------------+-------------------------------------------------------------+-----------------------------+ +| ``hse_zero_vels`` | if we are doing HSE boundary conditions, do we zero the | 0 | +| | velocity? | | ++--------------------------------------------+-------------------------------------------------------------+-----------------------------+ +| ``hse_interp_temp`` | if we are doing HSE boundary conditions, should we get the | 0 | +| | temperature via interpolation (constant gradient) or hold | | +| | it constant? | | ++--------------------------------------------+-------------------------------------------------------------+-----------------------------+ +| ``hse_fixed_temp`` | if we are doing HSE boundary conditions and holding the | -1.e200 | +| | temperature constant, then set it to a fixed value at the | | +| | boundaries (only if positive) | | ++--------------------------------------------+-------------------------------------------------------------+-----------------------------+ +| ``hse_reflect_vels`` | if we are doing HSE boundary conditions, how do we treat | 0 | +| | the velocity? reflect? or outflow? | | ++--------------------------------------------+-------------------------------------------------------------+-----------------------------+ +| ``fill_ambient_bc`` | fills physical domain boundaries with the ambient state | 0 | ++--------------------------------------------+-------------------------------------------------------------+-----------------------------+ +| ``ambient_fill_dir`` | which direction do we do ambient BCs? -1 = all, 0 = x, 1 = | -1 | +| | y, 2 = z | | ++--------------------------------------------+-------------------------------------------------------------+-----------------------------+ +| ``ambient_outflow_vel`` | in the ambient region, do we do a basic outflow in the | 0 | +| | normal direction of the velocity (with a min/max to ensure | | +| | it is outgoing) | | ++--------------------------------------------+-------------------------------------------------------------+-----------------------------+ +| ``clamp_ambient_temp`` | clamps the ambient material to the ambient temperature | 0 | ++--------------------------------------------+-------------------------------------------------------------+-----------------------------+ +| ``ambient_safety_factor`` | specifies the upper limit, as a multiple of the ambient | 1.1e0 | +| | density, for operations that are applied to ambient | | +| | material, such as clamping T. | | ++--------------------------------------------+-------------------------------------------------------------+-----------------------------+ +| ``ambient_density`` | density of the ambient material (should default to the same | -1.e200 | +| | as small_dens) | | ++--------------------------------------------+-------------------------------------------------------------+-----------------------------+ +| ``ambient_temp`` | temperature of the ambient material (should default to the | -1.e200 | +| | same as small_temp) | | ++--------------------------------------------+-------------------------------------------------------------+-----------------------------+ +| ``ambient_energy`` | energy of the ambient material (should default to the same | -1.e200 | +| | as small_ener) | | ++--------------------------------------------+-------------------------------------------------------------+-----------------------------+ +| ``sdc_order`` | integration order for SDC integration valid options are 2 | 2 | +| | and 4 | | ++--------------------------------------------+-------------------------------------------------------------+-----------------------------+ +| ``sdc_quadrature`` | which quadrature type to use with SDC? 0 = Gauss-Lobatto, | 0 | +| | 1 = Radau | | ++--------------------------------------------+-------------------------------------------------------------+-----------------------------+ +| ``sdc_extra`` | number of extra SDC iterations to take beyond the order. | 0 | +| | This only applies for true SDC. | | ++--------------------------------------------+-------------------------------------------------------------+-----------------------------+ +| ``sdc_solver`` | which SDC nonlinear solver to use? 1 = Newton, 2 = VODE, 3 | 1 | +| | = VODE for first iter | | ++--------------------------------------------+-------------------------------------------------------------+-----------------------------+ +| ``use_axisymmetric_geom_source`` | for 2-d axisymmetry, do we include the geometry source | 1 | +| | terms from Bernand-Champmartin? | | ++--------------------------------------------+-------------------------------------------------------------+-----------------------------+ +| ``add_sdc_react_source_to_advection`` | for simplified-SDC, do we add the reactive source | 1 | +| | prediction to the interface states used in the advective | | +| | source construction? | | ++--------------------------------------------+-------------------------------------------------------------+-----------------------------+ +| ``hydro_memory_footprint_ratio`` | In GPU builds, the hydro advance typically results in a | -1.0 | +| | large amount of extra temporary memory allocated due to the | | +| | large tile sizes that are used for computational | | +| | efficiency. If you want to constrain the code's GPU memory | | +| | footprint at the expense of throughput, set the following | | +| | parameter to some number greater than 0. This controls the | | +| | ratio of additional extra memory that can be allocated by | | +| | the hydro relative to the size of the base state | | +| | (indirectly, by controlling the hydro tile size and then | | +| | synchronizing each time the amount of currently allocated | | +| | fab memory reaches the target limit). Choosing a value only | | +| | slightly larger than 0 means that you want very little | | +| | additional memory allocated, and you will take a relatively | | +| | large performance hit, while choosing a value much greater | | +| | than 1.0 would result in maximum throughput but also | | +| | maximum memory footprint. You will likely have to | | +| | experimentally find a good ratio for your use case, but a | | +| | ratio around 2.0 - 4.0 is likely to yield a reasonable | | +| | balance between memory footprint and throughput. Note: the | | +| | first timestep will be very slow when using this option. | | ++--------------------------------------------+-------------------------------------------------------------+-----------------------------+ @@ -271,74 +271,74 @@ namespace: ``castro`` .. index:: castro.fixed_dt, castro.initial_dt, castro.dt_cutoff, castro.max_dt, castro.cfl, castro.init_shrink, castro.change_max, castro.check_dt_before_advance, castro.check_dt_after_advance, castro.plot_per_is_exact, castro.small_plot_per_is_exact, castro.use_retry, castro.retry_subcycle_factor, castro.retry_small_density_cutoff, castro.abundance_failure_tolerance, castro.abundance_failure_rho_cutoff, castro.use_post_step_regrid, castro.max_subcycles, castro.sdc_iters, castro.stopping_criterion_field, castro.stopping_criterion_value -+--------------------------------------------+-------------------------------------------------------------+---------------+ -| parameter | description | default value | -+============================================+=============================================================+===============+ -| ``fixed_dt`` | a fixed timestep to use for all steps (negative turns it | -1.0 | -| | off) | | -+--------------------------------------------+-------------------------------------------------------------+---------------+ -| ``initial_dt`` | the initial timestep (negative uses the step returned from | -1.0 | -| | the timestep constraints) | | -+--------------------------------------------+-------------------------------------------------------------+---------------+ -| ``dt_cutoff`` | the smallest valid timestep, as a fraction of the current | 1.e-12 | -| | simulation time. if we go below this, we abort. | | -+--------------------------------------------+-------------------------------------------------------------+---------------+ -| ``max_dt`` | the largest valid timestep---limit all timesteps to be no | 1.e200 | -| | larger than this | | -+--------------------------------------------+-------------------------------------------------------------+---------------+ -| ``cfl`` | the effective Courant number to use---we will not allow the | 0.8 | -| | hydrodynamic waves to cross more than this fraction of a | | -| | zone over a single timestep | | -+--------------------------------------------+-------------------------------------------------------------+---------------+ -| ``init_shrink`` | a factor by which to reduce the first timestep from that | 1.0 | -| | requested by the timestep estimators | | -+--------------------------------------------+-------------------------------------------------------------+---------------+ -| ``change_max`` | the maximum factor by which the timestep can increase or | 1.1 | -| | decrease from one step to the next. Must be greater than | | -| | 1.0---use max_dt to set a cap on the timestep. | | -+--------------------------------------------+-------------------------------------------------------------+---------------+ -| ``check_dt_before_advance`` | whether to check that we will take a valid timestep before | 1 | -| | the advance | | -+--------------------------------------------+-------------------------------------------------------------+---------------+ -| ``check_dt_after_advance`` | whether to check that we took a valid timestep after the | 1 | -| | advance | | -+--------------------------------------------+-------------------------------------------------------------+---------------+ -| ``plot_per_is_exact`` | enforce that the AMR plot interval must be hit exactly | 0 | -+--------------------------------------------+-------------------------------------------------------------+---------------+ -| ``small_plot_per_is_exact`` | enforce that the AMR small plot interval must be hit | 0 | -| | exactly | | -+--------------------------------------------+-------------------------------------------------------------+---------------+ -| ``use_retry`` | Retry a timestep if it violated the timestep-limiting | 1 | -| | criteria or other checks (negative density, burn failure) | | -| | over the course of an advance. The criteria will suggest a | | -| | new timestep that satisfies the criteria, and we will do | | -| | subcycled timesteps on the same level until we reach the | | -| | original target time. | | -+--------------------------------------------+-------------------------------------------------------------+---------------+ -| ``retry_subcycle_factor`` | When performing a retry, the factor to multiply the current | 0.5 | -| | timestep by when trying again. | | -+--------------------------------------------+-------------------------------------------------------------+---------------+ -| ``retry_small_density_cutoff`` | Skip retries for small (or negative) density if the zone's | -1.e200 | -| | density prior to the update was below this threshold. | | -+--------------------------------------------+-------------------------------------------------------------+---------------+ -| ``abundance_failure_tolerance`` | Set the threshold for failing the species abundance | 1.e-2 | -| | validity check. | | -+--------------------------------------------+-------------------------------------------------------------+---------------+ -| ``abundance_failure_rho_cutoff`` | Do not abort for invalid species abundances if the zone's | -1.e200 | -| | density is below this threshold. | | -+--------------------------------------------+-------------------------------------------------------------+---------------+ -| ``use_post_step_regrid`` | Regrid after every timestep. | 0 | -+--------------------------------------------+-------------------------------------------------------------+---------------+ -| ``max_subcycles`` | Do not permit more subcycled timesteps than this parameter. | 10 | -| | Set to a negative value to disable this criterion. | | -+--------------------------------------------+-------------------------------------------------------------+---------------+ -| ``sdc_iters`` | Number of iterations for the simplified SDC advance. | 2 | -+--------------------------------------------+-------------------------------------------------------------+---------------+ -| ``stopping_criterion_field`` | Field to use for determining whether to stop the | "" | -| | simulation. | | -+--------------------------------------------+-------------------------------------------------------------+---------------+ -| ``stopping_criterion_value`` | Threshold value for determining whether to stop. | 1.e200 | -+--------------------------------------------+-------------------------------------------------------------+---------------+ ++--------------------------------------------+-------------------------------------------------------------+-----------------------------+ +| parameter | description | default value | ++============================================+=============================================================+=============================+ +| ``fixed_dt`` | a fixed timestep to use for all steps (negative turns it | -1.0 | +| | off) | | ++--------------------------------------------+-------------------------------------------------------------+-----------------------------+ +| ``initial_dt`` | the initial timestep (negative uses the step returned from | -1.0 | +| | the timestep constraints) | | ++--------------------------------------------+-------------------------------------------------------------+-----------------------------+ +| ``dt_cutoff`` | the smallest valid timestep, as a fraction of the current | 1.e-12 | +| | simulation time. if we go below this, we abort. | | ++--------------------------------------------+-------------------------------------------------------------+-----------------------------+ +| ``max_dt`` | the largest valid timestep---limit all timesteps to be no | 1.e200 | +| | larger than this | | ++--------------------------------------------+-------------------------------------------------------------+-----------------------------+ +| ``cfl`` | the effective Courant number to use---we will not allow the | 0.8 | +| | hydrodynamic waves to cross more than this fraction of a | | +| | zone over a single timestep | | ++--------------------------------------------+-------------------------------------------------------------+-----------------------------+ +| ``init_shrink`` | a factor by which to reduce the first timestep from that | 1.0 | +| | requested by the timestep estimators | | ++--------------------------------------------+-------------------------------------------------------------+-----------------------------+ +| ``change_max`` | the maximum factor by which the timestep can increase or | 1.1 | +| | decrease from one step to the next. Must be greater than | | +| | 1.0---use max_dt to set a cap on the timestep. | | ++--------------------------------------------+-------------------------------------------------------------+-----------------------------+ +| ``check_dt_before_advance`` | whether to check that we will take a valid timestep before | 1 | +| | the advance | | ++--------------------------------------------+-------------------------------------------------------------+-----------------------------+ +| ``check_dt_after_advance`` | whether to check that we took a valid timestep after the | 1 | +| | advance | | ++--------------------------------------------+-------------------------------------------------------------+-----------------------------+ +| ``plot_per_is_exact`` | enforce that the AMR plot interval must be hit exactly | 0 | ++--------------------------------------------+-------------------------------------------------------------+-----------------------------+ +| ``small_plot_per_is_exact`` | enforce that the AMR small plot interval must be hit | 0 | +| | exactly | | ++--------------------------------------------+-------------------------------------------------------------+-----------------------------+ +| ``use_retry`` | Retry a timestep if it violated the timestep-limiting | 1 | +| | criteria or other checks (negative density, burn failure) | | +| | over the course of an advance. The criteria will suggest a | | +| | new timestep that satisfies the criteria, and we will do | | +| | subcycled timesteps on the same level until we reach the | | +| | original target time. | | ++--------------------------------------------+-------------------------------------------------------------+-----------------------------+ +| ``retry_subcycle_factor`` | When performing a retry, the factor to multiply the current | 0.5 | +| | timestep by when trying again. | | ++--------------------------------------------+-------------------------------------------------------------+-----------------------------+ +| ``retry_small_density_cutoff`` | Skip retries for small (or negative) density if the zone's | -1.e200 | +| | density prior to the update was below this threshold. | | ++--------------------------------------------+-------------------------------------------------------------+-----------------------------+ +| ``abundance_failure_tolerance`` | Set the threshold for failing the species abundance | 1.e-2 | +| | validity check. | | ++--------------------------------------------+-------------------------------------------------------------+-----------------------------+ +| ``abundance_failure_rho_cutoff`` | Do not abort for invalid species abundances if the zone's | -1.e200 | +| | density is below this threshold. | | ++--------------------------------------------+-------------------------------------------------------------+-----------------------------+ +| ``use_post_step_regrid`` | Regrid after every timestep. | 0 | ++--------------------------------------------+-------------------------------------------------------------+-----------------------------+ +| ``max_subcycles`` | Do not permit more subcycled timesteps than this parameter. | 10 | +| | Set to a negative value to disable this criterion. | | ++--------------------------------------------+-------------------------------------------------------------+-----------------------------+ +| ``sdc_iters`` | Number of iterations for the simplified SDC advance. | 2 | ++--------------------------------------------+-------------------------------------------------------------+-----------------------------+ +| ``stopping_criterion_field`` | Field to use for determining whether to stop the | "" | +| | simulation. | | ++--------------------------------------------+-------------------------------------------------------------+-----------------------------+ +| ``stopping_criterion_value`` | Threshold value for determining whether to stop. | 1.e200 | ++--------------------------------------------+-------------------------------------------------------------+-----------------------------+ @@ -347,58 +347,58 @@ namespace: ``castro`` .. index:: castro.dtnuc_e, castro.dtnuc_X, castro.dtnuc_X_threshold, castro.do_react, castro.react_T_min, castro.react_T_max, castro.react_rho_min, castro.react_rho_max, castro.disable_shock_burning, castro.shock_detection_threshold, castro.shock_detection_include_sources, castro.T_guess, castro.drive_initial_convection, castro.drive_initial_convection_tmax, castro.drive_initial_convection_reinit_period -+--------------------------------------------+-------------------------------------------------------------+---------------+ -| parameter | description | default value | -+============================================+=============================================================+===============+ -| ``dtnuc_e`` | Limit the timestep based on how much the burning can change | 1.e200 | -| | the internal energy of a zone. The timestep is equal to | | -| | ``dtnuc`` :math:`\cdot\,(e / \dot{e})`. | | -+--------------------------------------------+-------------------------------------------------------------+---------------+ -| ``dtnuc_X`` | Limit the timestep based on how much the burning can change | 1.e200 | -| | the species mass fractions of a zone. The timestep is equal | | -| | to ``dtnuc`` :math:`\cdot\,(X / \dot{X})`. | | -+--------------------------------------------+-------------------------------------------------------------+---------------+ -| ``dtnuc_X_threshold`` | If we are using the timestep limiter based on changes in | 1.e-3 | -| | $X$, set a threshold on the species abundance below which | | -| | the limiter is not applied. This helps prevent the timestep | | -| | from becoming very small due to changes in trace species. | | -+--------------------------------------------+-------------------------------------------------------------+---------------+ -| ``do_react`` | permits reactions to be turned on and off -- mostly for | -1 | -| | efficiency's sake | | -+--------------------------------------------+-------------------------------------------------------------+---------------+ -| ``react_T_min`` | minimum temperature for allowing reactions to occur in a | 0.0 | -| | zone | | -+--------------------------------------------+-------------------------------------------------------------+---------------+ -| ``react_T_max`` | maximum temperature for allowing reactions to occur in a | 1.e200 | -| | zone | | -+--------------------------------------------+-------------------------------------------------------------+---------------+ -| ``react_rho_min`` | minimum density for allowing reactions to occur in a zone | 0.0 | -+--------------------------------------------+-------------------------------------------------------------+---------------+ -| ``react_rho_max`` | maximum density for allowing reactions to occur in a zone | 1.e200 | -+--------------------------------------------+-------------------------------------------------------------+---------------+ -| ``disable_shock_burning`` | disable burning inside hydrodynamic shock regions note: | 0 | -| | requires compiling with `USE_SHOCK_VAR=TRUE` | | -+--------------------------------------------+-------------------------------------------------------------+---------------+ ++--------------------------------------------+-------------------------------------------------------------+-----------------------------+ +| parameter | description | default value | ++============================================+=============================================================+=============================+ +| ``dtnuc_e`` | Limit the timestep based on how much the burning can change | 1.e200 | +| | the internal energy of a zone. The timestep is equal to | | +| | ``dtnuc`` :math:`\cdot\,(e / \dot{e})`. | | ++--------------------------------------------+-------------------------------------------------------------+-----------------------------+ +| ``dtnuc_X`` | Limit the timestep based on how much the burning can change | 1.e200 | +| | the species mass fractions of a zone. The timestep is equal | | +| | to ``dtnuc`` :math:`\cdot\,(X / \dot{X})`. | | ++--------------------------------------------+-------------------------------------------------------------+-----------------------------+ +| ``dtnuc_X_threshold`` | If we are using the timestep limiter based on changes in | 1.e-3 | +| | $X$, set a threshold on the species abundance below which | | +| | the limiter is not applied. This helps prevent the timestep | | +| | from becoming very small due to changes in trace species. | | ++--------------------------------------------+-------------------------------------------------------------+-----------------------------+ +| ``do_react`` | permits reactions to be turned on and off -- mostly for | -1 | +| | efficiency's sake | | ++--------------------------------------------+-------------------------------------------------------------+-----------------------------+ +| ``react_T_min`` | minimum temperature for allowing reactions to occur in a | 0.0 | +| | zone | | ++--------------------------------------------+-------------------------------------------------------------+-----------------------------+ +| ``react_T_max`` | maximum temperature for allowing reactions to occur in a | 1.e200 | +| | zone | | ++--------------------------------------------+-------------------------------------------------------------+-----------------------------+ +| ``react_rho_min`` | minimum density for allowing reactions to occur in a zone | 0.0 | ++--------------------------------------------+-------------------------------------------------------------+-----------------------------+ +| ``react_rho_max`` | maximum density for allowing reactions to occur in a zone | 1.e200 | ++--------------------------------------------+-------------------------------------------------------------+-----------------------------+ +| ``disable_shock_burning`` | disable burning inside hydrodynamic shock regions note: | 0 | +| | requires compiling with `USE_SHOCK_VAR=TRUE` | | ++--------------------------------------------+-------------------------------------------------------------+-----------------------------+ | ``shock_detection_threshold`` | shock detection threshold for grad{P} / P | 0.6666666666666666666666_rt | -+--------------------------------------------+-------------------------------------------------------------+---------------+ -| ``shock_detection_include_sources`` | do we subtract off the hydrostatic pressure when evaluating | 1 | -| | a shock? | | -+--------------------------------------------+-------------------------------------------------------------+---------------+ -| ``T_guess`` | initial guess for the temperature when inverting the EoS | 1.e8 | -| | (e.g. when calling eos_input_re) | | -+--------------------------------------------+-------------------------------------------------------------+---------------+ -| ``drive_initial_convection`` | if set to 1, we interpolate from the initial model to get | 0 | -| | the temperature used to call the burner. This prevents | | -| | reactions from going nonlinear and running away in place | | -| | before a convective field is established. | | -+--------------------------------------------+-------------------------------------------------------------+---------------+ -| ``drive_initial_convection_tmax`` | maximum time over which to do the drive_initial_convection | 1.e200 | -| | procedure | | -+--------------------------------------------+-------------------------------------------------------------+---------------+ -| ``drive_initial_convection_reinit_period`` | frequency with which to re-initialize the thermodynamic | 1.e200 | -| | data while preserving the velocity field during | | -| | drive_initial_convection | | -+--------------------------------------------+-------------------------------------------------------------+---------------+ ++--------------------------------------------+-------------------------------------------------------------+-----------------------------+ +| ``shock_detection_include_sources`` | do we subtract off the hydrostatic pressure when evaluating | 1 | +| | a shock? | | ++--------------------------------------------+-------------------------------------------------------------+-----------------------------+ +| ``T_guess`` | initial guess for the temperature when inverting the EoS | 1.e8 | +| | (e.g. when calling eos_input_re) | | ++--------------------------------------------+-------------------------------------------------------------+-----------------------------+ +| ``drive_initial_convection`` | if set to 1, we interpolate from the initial model to get | 0 | +| | the temperature used to call the burner. This prevents | | +| | reactions from going nonlinear and running away in place | | +| | before a convective field is established. | | ++--------------------------------------------+-------------------------------------------------------------+-----------------------------+ +| ``drive_initial_convection_tmax`` | maximum time over which to do the drive_initial_convection | 1.e200 | +| | procedure | | ++--------------------------------------------+-------------------------------------------------------------+-----------------------------+ +| ``drive_initial_convection_reinit_period`` | frequency with which to re-initialize the thermodynamic | 1.e200 | +| | data while preserving the velocity field during | | +| | drive_initial_convection | | ++--------------------------------------------+-------------------------------------------------------------+-----------------------------+ @@ -407,20 +407,20 @@ namespace: ``castro`` .. index:: castro.diffuse_temp, castro.diffuse_cutoff_density, castro.diffuse_cutoff_density_hi, castro.diffuse_cond_scale_fac -+--------------------------------------------+-------------------------------------------------------------+---------------+ -| parameter | description | default value | -+============================================+=============================================================+===============+ -| ``diffuse_temp`` | enable thermal diffusion | 0 | -+--------------------------------------------+-------------------------------------------------------------+---------------+ -| ``diffuse_cutoff_density`` | set a cutoff density for diffusion -- we zero the term out | -1.e200 | -| | below this density | | -+--------------------------------------------+-------------------------------------------------------------+---------------+ -| ``diffuse_cutoff_density_hi`` | secondary cutoff density -- there will be a linear dropoff | -1.e200 | -| | in the diffusion coefficient between this and the primary | | -| | cutoff density. This should be the larger of the two | | -+--------------------------------------------+-------------------------------------------------------------+---------------+ -| ``diffuse_cond_scale_fac`` | scaling factor for conductivity | 1.0 | -+--------------------------------------------+-------------------------------------------------------------+---------------+ ++--------------------------------------------+-------------------------------------------------------------+-----------------------------+ +| parameter | description | default value | ++============================================+=============================================================+=============================+ +| ``diffuse_temp`` | enable thermal diffusion | 0 | ++--------------------------------------------+-------------------------------------------------------------+-----------------------------+ +| ``diffuse_cutoff_density`` | set a cutoff density for diffusion -- we zero the term out | -1.e200 | +| | below this density | | ++--------------------------------------------+-------------------------------------------------------------+-----------------------------+ +| ``diffuse_cutoff_density_hi`` | secondary cutoff density -- there will be a linear dropoff | -1.e200 | +| | in the diffusion coefficient between this and the primary | | +| | cutoff density. This should be the larger of the two | | ++--------------------------------------------+-------------------------------------------------------------+-----------------------------+ +| ``diffuse_cond_scale_fac`` | scaling factor for conductivity | 1.0 | ++--------------------------------------------+-------------------------------------------------------------+-----------------------------+ @@ -429,56 +429,56 @@ namespace: ``castro`` .. index:: castro.do_grav, castro.moving_center, castro.grav_source_type, castro.do_rotation, castro.rotational_period, castro.rotation_include_centrifugal, castro.rotation_include_coriolis, castro.rot_source_type, castro.implicit_rotation_update, castro.rot_axis, castro.use_point_mass, castro.point_mass, castro.point_mass_fix_solution, castro.gw_dist, castro.point_mass_offset_is_true, castro.point_mass_location_offset -+--------------------------------------------+-------------------------------------------------------------+---------------+ -| parameter | description | default value | -+============================================+=============================================================+===============+ -| ``do_grav`` | permits gravity calculation to be turned on and off | -1 | -+--------------------------------------------+-------------------------------------------------------------+---------------+ -| ``moving_center`` | to we recompute the center used for the multipole gravity | 0 | -| | solve each step? | | -+--------------------------------------------+-------------------------------------------------------------+---------------+ -| ``grav_source_type`` | determines how the gravitational source term is added to | 4 | -| | the momentum and energy state variables. | | -+--------------------------------------------+-------------------------------------------------------------+---------------+ -| ``do_rotation`` | permits rotation calculation to be turned on and off | -1 | -+--------------------------------------------+-------------------------------------------------------------+---------------+ -| ``rotational_period`` | the rotation period for the corotating frame | -1.e200 | -+--------------------------------------------+-------------------------------------------------------------+---------------+ -| ``rotation_include_centrifugal`` | permits the centrifugal terms in the rotation to be turned | 1 | -| | on and off | | -+--------------------------------------------+-------------------------------------------------------------+---------------+ -| ``rotation_include_coriolis`` | permits the Coriolis terms in the rotation to be turned on | 1 | -| | and off | | -+--------------------------------------------+-------------------------------------------------------------+---------------+ -| ``rot_source_type`` | determines how the rotation source terms are added to the | 4 | -| | momentum and energy equations | | -+--------------------------------------------+-------------------------------------------------------------+---------------+ -| ``implicit_rotation_update`` | we can do a implicit solution of the rotation update to | 1 | -| | allow for better coupling of the Coriolis terms | | -+--------------------------------------------+-------------------------------------------------------------+---------------+ -| ``rot_axis`` | the coordinate axis (:math:`x=1`, :math:`y=2`, :math:`z=3`) | 3 | -| | for the rotation vector | | -+--------------------------------------------+-------------------------------------------------------------+---------------+ -| ``use_point_mass`` | include a central point mass | 0 | -+--------------------------------------------+-------------------------------------------------------------+---------------+ -| ``point_mass`` | mass of the point mass | 0.0 | -+--------------------------------------------+-------------------------------------------------------------+---------------+ -| ``point_mass_fix_solution`` | if we have a central point mass, we can prevent mass from | 0 | -| | building up in the zones adjacent to it by keeping their | | -| | density constant and adding their mass to the point mass | | -| | object | | -+--------------------------------------------+-------------------------------------------------------------+---------------+ -| ``gw_dist`` | Distance (in kpc) used for calculation of the gravitational | 0.0 | -| | wave amplitude (this will be calculated along all three | | -| | coordinate axes). Only relevant if castro.sum_interval > 0 | | -| | and if set to a positive number. A standard value in the | | -| | literature is 10.0 (kpc). | | -+--------------------------------------------+-------------------------------------------------------------+---------------+ -| ``point_mass_offset_is_true`` | This integer is used to activate parallel plane 1/r**2 | 0 | -| | gravity. | | -+--------------------------------------------+-------------------------------------------------------------+---------------+ -| ``point_mass_location_offset`` | | 0.0 | -+--------------------------------------------+-------------------------------------------------------------+---------------+ ++--------------------------------------------+-------------------------------------------------------------+-----------------------------+ +| parameter | description | default value | ++============================================+=============================================================+=============================+ +| ``do_grav`` | permits gravity calculation to be turned on and off | -1 | ++--------------------------------------------+-------------------------------------------------------------+-----------------------------+ +| ``moving_center`` | to we recompute the center used for the multipole gravity | 0 | +| | solve each step? | | ++--------------------------------------------+-------------------------------------------------------------+-----------------------------+ +| ``grav_source_type`` | determines how the gravitational source term is added to | 4 | +| | the momentum and energy state variables. | | ++--------------------------------------------+-------------------------------------------------------------+-----------------------------+ +| ``do_rotation`` | permits rotation calculation to be turned on and off | -1 | ++--------------------------------------------+-------------------------------------------------------------+-----------------------------+ +| ``rotational_period`` | the rotation period for the corotating frame | -1.e200 | ++--------------------------------------------+-------------------------------------------------------------+-----------------------------+ +| ``rotation_include_centrifugal`` | permits the centrifugal terms in the rotation to be turned | 1 | +| | on and off | | ++--------------------------------------------+-------------------------------------------------------------+-----------------------------+ +| ``rotation_include_coriolis`` | permits the Coriolis terms in the rotation to be turned on | 1 | +| | and off | | ++--------------------------------------------+-------------------------------------------------------------+-----------------------------+ +| ``rot_source_type`` | determines how the rotation source terms are added to the | 4 | +| | momentum and energy equations | | ++--------------------------------------------+-------------------------------------------------------------+-----------------------------+ +| ``implicit_rotation_update`` | we can do a implicit solution of the rotation update to | 1 | +| | allow for better coupling of the Coriolis terms | | ++--------------------------------------------+-------------------------------------------------------------+-----------------------------+ +| ``rot_axis`` | the coordinate axis (:math:`x=1`, :math:`y=2`, :math:`z=3`) | 3 | +| | for the rotation vector | | ++--------------------------------------------+-------------------------------------------------------------+-----------------------------+ +| ``use_point_mass`` | include a central point mass | 0 | ++--------------------------------------------+-------------------------------------------------------------+-----------------------------+ +| ``point_mass`` | mass of the point mass | 0.0 | ++--------------------------------------------+-------------------------------------------------------------+-----------------------------+ +| ``point_mass_fix_solution`` | if we have a central point mass, we can prevent mass from | 0 | +| | building up in the zones adjacent to it by keeping their | | +| | density constant and adding their mass to the point mass | | +| | object | | ++--------------------------------------------+-------------------------------------------------------------+-----------------------------+ +| ``gw_dist`` | Distance (in kpc) used for calculation of the gravitational | 0.0 | +| | wave amplitude (this will be calculated along all three | | +| | coordinate axes). Only relevant if castro.sum_interval > 0 | | +| | and if set to a positive number. A standard value in the | | +| | literature is 10.0 (kpc). | | ++--------------------------------------------+-------------------------------------------------------------+-----------------------------+ +| ``point_mass_offset_is_true`` | This integer is used to activate parallel plane 1/r**2 | 0 | +| | gravity. | | ++--------------------------------------------+-------------------------------------------------------------+-----------------------------+ +| ``point_mass_location_offset`` | | 0.0 | ++--------------------------------------------+-------------------------------------------------------------+-----------------------------+ @@ -487,35 +487,35 @@ namespace: ``castro`` .. index:: castro.sponge_lower_radius, castro.sponge_upper_radius, castro.sponge_lower_density, castro.sponge_upper_density, castro.sponge_lower_pressure, castro.sponge_upper_pressure, castro.sponge_lower_factor, castro.sponge_upper_factor, castro.sponge_target_x_velocity, castro.sponge_target_y_velocity, castro.sponge_target_z_velocity, castro.sponge_timescale -+--------------------------------------------+-------------------------------------------------------------+---------------+ -| parameter | description | default value | -+============================================+=============================================================+===============+ -| ``sponge_lower_radius`` | Minimum simulation distance from center to start applying | -1.0 | -| | the sponge | | -+--------------------------------------------+-------------------------------------------------------------+---------------+ -| ``sponge_upper_radius`` | Simulation distance from the center at which the sponge is | -1.0 | -| | fully applied | | -+--------------------------------------------+-------------------------------------------------------------+---------------+ -| ``sponge_lower_density`` | Minimum density at which to start applying the sponge | -1.0 | -+--------------------------------------------+-------------------------------------------------------------+---------------+ -| ``sponge_upper_density`` | Density at which the sponge is fully applied | -1.0 | -+--------------------------------------------+-------------------------------------------------------------+---------------+ -| ``sponge_lower_pressure`` | Minimum pressure at which to start applying the sponge | -1.0 | -+--------------------------------------------+-------------------------------------------------------------+---------------+ -| ``sponge_upper_pressure`` | Pressure at which the sponge is fully applied | -1.0 | -+--------------------------------------------+-------------------------------------------------------------+---------------+ -| ``sponge_lower_factor`` | Scaling factor for the sponge below the low end | 0.0 | -+--------------------------------------------+-------------------------------------------------------------+---------------+ -| ``sponge_upper_factor`` | Scaling factor for the sponge above the high end | 1.0 | -+--------------------------------------------+-------------------------------------------------------------+---------------+ -| ``sponge_target_x_velocity`` | Target x-velocity for the sponge to drive to | 0.0 | -+--------------------------------------------+-------------------------------------------------------------+---------------+ -| ``sponge_target_y_velocity`` | Target y-velocity for the sponge to drive to | 0.0 | -+--------------------------------------------+-------------------------------------------------------------+---------------+ -| ``sponge_target_z_velocity`` | Target z-velocity for the sponge to drive to | 0.0 | -+--------------------------------------------+-------------------------------------------------------------+---------------+ -| ``sponge_timescale`` | Timescale on which the sponge operates | -1.0 | -+--------------------------------------------+-------------------------------------------------------------+---------------+ ++--------------------------------------------+-------------------------------------------------------------+-----------------------------+ +| parameter | description | default value | ++============================================+=============================================================+=============================+ +| ``sponge_lower_radius`` | Minimum simulation distance from center to start applying | -1.0 | +| | the sponge | | ++--------------------------------------------+-------------------------------------------------------------+-----------------------------+ +| ``sponge_upper_radius`` | Simulation distance from the center at which the sponge is | -1.0 | +| | fully applied | | ++--------------------------------------------+-------------------------------------------------------------+-----------------------------+ +| ``sponge_lower_density`` | Minimum density at which to start applying the sponge | -1.0 | ++--------------------------------------------+-------------------------------------------------------------+-----------------------------+ +| ``sponge_upper_density`` | Density at which the sponge is fully applied | -1.0 | ++--------------------------------------------+-------------------------------------------------------------+-----------------------------+ +| ``sponge_lower_pressure`` | Minimum pressure at which to start applying the sponge | -1.0 | ++--------------------------------------------+-------------------------------------------------------------+-----------------------------+ +| ``sponge_upper_pressure`` | Pressure at which the sponge is fully applied | -1.0 | ++--------------------------------------------+-------------------------------------------------------------+-----------------------------+ +| ``sponge_lower_factor`` | Scaling factor for the sponge below the low end | 0.0 | ++--------------------------------------------+-------------------------------------------------------------+-----------------------------+ +| ``sponge_upper_factor`` | Scaling factor for the sponge above the high end | 1.0 | ++--------------------------------------------+-------------------------------------------------------------+-----------------------------+ +| ``sponge_target_x_velocity`` | Target x-velocity for the sponge to drive to | 0.0 | ++--------------------------------------------+-------------------------------------------------------------+-----------------------------+ +| ``sponge_target_y_velocity`` | Target y-velocity for the sponge to drive to | 0.0 | ++--------------------------------------------+-------------------------------------------------------------+-----------------------------+ +| ``sponge_target_z_velocity`` | Target z-velocity for the sponge to drive to | 0.0 | ++--------------------------------------------+-------------------------------------------------------------+-----------------------------+ +| ``sponge_timescale`` | Timescale on which the sponge operates | -1.0 | ++--------------------------------------------+-------------------------------------------------------------+-----------------------------+ @@ -524,11 +524,11 @@ namespace: ``castro`` .. index:: castro.bndry_func_thread_safe -+--------------------------------------------+-------------------------------------------------------------+---------------+ -| parameter | description | default value | -+============================================+=============================================================+===============+ -| ``bndry_func_thread_safe`` | | 1 | -+--------------------------------------------+-------------------------------------------------------------+---------------+ ++--------------------------------------------+-------------------------------------------------------------+-----------------------------+ +| parameter | description | default value | ++============================================+=============================================================+=============================+ +| ``bndry_func_thread_safe`` | | 1 | ++--------------------------------------------+-------------------------------------------------------------+-----------------------------+ @@ -537,15 +537,15 @@ namespace: ``castro`` .. index:: castro.grown_factor, castro.star_at_center -+--------------------------------------------+-------------------------------------------------------------+---------------+ -| parameter | description | default value | -+============================================+=============================================================+===============+ -| ``grown_factor`` | the factor by which to extend the domain upon restart for | 1 | -| | embiggening | | -+--------------------------------------------+-------------------------------------------------------------+---------------+ -| ``star_at_center`` | used with the embiggening routines to determine how to | -1 | -| | extend the domain | | -+--------------------------------------------+-------------------------------------------------------------+---------------+ ++--------------------------------------------+-------------------------------------------------------------+-----------------------------+ +| parameter | description | default value | ++============================================+=============================================================+=============================+ +| ``grown_factor`` | the factor by which to extend the domain upon restart for | 1 | +| | embiggening | | ++--------------------------------------------+-------------------------------------------------------------+-----------------------------+ +| ``star_at_center`` | used with the embiggening routines to determine how to | -1 | +| | extend the domain | | ++--------------------------------------------+-------------------------------------------------------------+-----------------------------+ @@ -554,21 +554,21 @@ namespace: ``castro`` .. index:: castro.do_scf_initial_model, castro.scf_maximum_density, castro.scf_equatorial_radius, castro.scf_polar_radius, castro.scf_relax_tol, castro.scf_max_iterations -+--------------------------------------------+-------------------------------------------------------------+---------------+ -| parameter | description | default value | -+============================================+=============================================================+===============+ -| ``do_scf_initial_model`` | Should we use SCF to construct the initial model? | 0 | -+--------------------------------------------+-------------------------------------------------------------+---------------+ -| ``scf_maximum_density`` | Maximum density on the domain when using SCF | -1.e6 | -+--------------------------------------------+-------------------------------------------------------------+---------------+ -| ``scf_equatorial_radius`` | Equatorial and polar radii of the star constructed by SCF | -1.e9 | -+--------------------------------------------+-------------------------------------------------------------+---------------+ -| ``scf_polar_radius`` | | -1.e9 | -+--------------------------------------------+-------------------------------------------------------------+---------------+ -| ``scf_relax_tol`` | SCF relaxation tolerance | 1.e-3 | -+--------------------------------------------+-------------------------------------------------------------+---------------+ -| ``scf_max_iterations`` | Maximum number of SCF iterations | 30 | -+--------------------------------------------+-------------------------------------------------------------+---------------+ ++--------------------------------------------+-------------------------------------------------------------+-----------------------------+ +| parameter | description | default value | ++============================================+=============================================================+=============================+ +| ``do_scf_initial_model`` | Should we use SCF to construct the initial model? | 0 | ++--------------------------------------------+-------------------------------------------------------------+-----------------------------+ +| ``scf_maximum_density`` | Maximum density on the domain when using SCF | -1.e6 | ++--------------------------------------------+-------------------------------------------------------------+-----------------------------+ +| ``scf_equatorial_radius`` | Equatorial and polar radii of the star constructed by SCF | -1.e9 | ++--------------------------------------------+-------------------------------------------------------------+-----------------------------+ +| ``scf_polar_radius`` | | -1.e9 | ++--------------------------------------------+-------------------------------------------------------------+-----------------------------+ +| ``scf_relax_tol`` | SCF relaxation tolerance | 1.e-3 | ++--------------------------------------------+-------------------------------------------------------------+-----------------------------+ +| ``scf_max_iterations`` | Maximum number of SCF iterations | 30 | ++--------------------------------------------+-------------------------------------------------------------+-----------------------------+ @@ -577,15 +577,15 @@ namespace: ``castro`` .. index:: castro.do_special_tagging, castro.max_tagging_radius -+--------------------------------------------+-------------------------------------------------------------+---------------+ -| parameter | description | default value | -+============================================+=============================================================+===============+ -| ``do_special_tagging`` | | 0 | -+--------------------------------------------+-------------------------------------------------------------+---------------+ -| ``max_tagging_radius`` | Maximum radius from the center (in units of the domain | 10.0e0 | -| | width) where tagging is allowed. The default choice implies | | -| | no restriction. | | -+--------------------------------------------+-------------------------------------------------------------+---------------+ ++--------------------------------------------+-------------------------------------------------------------+-----------------------------+ +| parameter | description | default value | ++============================================+=============================================================+=============================+ +| ``do_special_tagging`` | | 0 | ++--------------------------------------------+-------------------------------------------------------------+-----------------------------+ +| ``max_tagging_radius`` | Maximum radius from the center (in units of the domain | 10.0e0 | +| | width) where tagging is allowed. The default choice implies | | +| | no restriction. | | ++--------------------------------------------+-------------------------------------------------------------+-----------------------------+ @@ -594,57 +594,57 @@ namespace: ``castro`` .. index:: castro.v, castro.dump_old, castro.domain_is_plane_parallel, castro.print_update_diagnostics, castro.sum_interval, castro.sum_per, castro.job_name, castro.output_at_completion, castro.reset_checkpoint_time, castro.reset_checkpoint_step, castro.store_omegadot, castro.store_burn_weights, castro.abort_on_invalid_params -+--------------------------------------------+-------------------------------------------------------------+---------------+ -| parameter | description | default value | -+============================================+=============================================================+===============+ -| ``v`` | verbosity level (higher numbers mean more output) | 0 | -+--------------------------------------------+-------------------------------------------------------------+---------------+ -| ``dump_old`` | do we dump the old state into the checkpoint files too? | 0 | -+--------------------------------------------+-------------------------------------------------------------+---------------+ -| ``domain_is_plane_parallel`` | do we assume the domain is plane parallel when computing | 0 | -| | some of the derived quantities (e.g. radial velocity). | | -| | Note: this will always assume that the last spatial | | -| | dimension is vertical | | -+--------------------------------------------+-------------------------------------------------------------+---------------+ -| ``print_update_diagnostics`` | display information about updates to the state (how much | (0, 1) | -| | mass, momentum, energy added) | | -+--------------------------------------------+-------------------------------------------------------------+---------------+ -| ``sum_interval`` | how often (number of coarse timesteps) to compute integral | -1 | -| | sums (for runtime diagnostics) | | -+--------------------------------------------+-------------------------------------------------------------+---------------+ -| ``sum_per`` | how often (simulation time) to compute integral sums (for | -1.0e0 | -| | runtime diagnostics) | | -+--------------------------------------------+-------------------------------------------------------------+---------------+ -| ``job_name`` | a string describing the simulation that will be copied into | "Castro" | -| | the plotfile's ``job_info`` file | | -+--------------------------------------------+-------------------------------------------------------------+---------------+ -| ``output_at_completion`` | write a final plotfile and checkpoint upon completion | 1 | -+--------------------------------------------+-------------------------------------------------------------+---------------+ -| ``reset_checkpoint_time`` | Do we want to reset the time in the checkpoint? This ONLY | -1.e200 | -| | takes effect if amr.regrid_on_restart = 1 and | | -| | amr.checkpoint_on_restart = 1, (which require that max_step | | -| | and stop_time be less than the value in the checkpoint) and | | -| | you set it to value greater than this default value. | | -+--------------------------------------------+-------------------------------------------------------------+---------------+ -| ``reset_checkpoint_step`` | Do we want to reset the number of steps in the checkpoint? | -1 | -| | This ONLY takes effect if amr.regrid_on_restart = 1 and | | -| | amr.checkpoint_on_restart = 1, (which require that max_step | | -| | and stop_time be less than the value in the checkpoint) and | | -| | you set it to value greater than this default value. | | -+--------------------------------------------+-------------------------------------------------------------+---------------+ -| ``store_omegadot`` | Do we store the species creation rates in the plotfile? | 0 | -| | Note, if this option is enabled then more memory will be | | -| | allocated to hold the results of the burn | | -+--------------------------------------------+-------------------------------------------------------------+---------------+ -| ``store_burn_weights`` | Do we store the burn weights as a diagnostic in the | 0 | -| | plotfile? Note, if this option is enabled then more | | -| | memory will be allocated to hold the results of the burn | | -+--------------------------------------------+-------------------------------------------------------------+---------------+ -| ``abort_on_invalid_params`` | Do we abort the run if the inputs file specifies a runtime | 0 | -| | parameter that we don't know about? Note: this will only | | -| | take effect for those namespaces where 100% of the runtime | | -| | parameters are managed by the python scripts. | | -+--------------------------------------------+-------------------------------------------------------------+---------------+ ++--------------------------------------------+-------------------------------------------------------------+-----------------------------+ +| parameter | description | default value | ++============================================+=============================================================+=============================+ +| ``v`` | verbosity level (higher numbers mean more output) | 0 | ++--------------------------------------------+-------------------------------------------------------------+-----------------------------+ +| ``dump_old`` | do we dump the old state into the checkpoint files too? | 0 | ++--------------------------------------------+-------------------------------------------------------------+-----------------------------+ +| ``domain_is_plane_parallel`` | do we assume the domain is plane parallel when computing | 0 | +| | some of the derived quantities (e.g. radial velocity). | | +| | Note: this will always assume that the last spatial | | +| | dimension is vertical | | ++--------------------------------------------+-------------------------------------------------------------+-----------------------------+ +| ``print_update_diagnostics`` | display information about updates to the state (how much | (0, 1) | +| | mass, momentum, energy added) | | ++--------------------------------------------+-------------------------------------------------------------+-----------------------------+ +| ``sum_interval`` | how often (number of coarse timesteps) to compute integral | -1 | +| | sums (for runtime diagnostics) | | ++--------------------------------------------+-------------------------------------------------------------+-----------------------------+ +| ``sum_per`` | how often (simulation time) to compute integral sums (for | -1.0e0 | +| | runtime diagnostics) | | ++--------------------------------------------+-------------------------------------------------------------+-----------------------------+ +| ``job_name`` | a string describing the simulation that will be copied into | "Castro" | +| | the plotfile's ``job_info`` file | | ++--------------------------------------------+-------------------------------------------------------------+-----------------------------+ +| ``output_at_completion`` | write a final plotfile and checkpoint upon completion | 1 | ++--------------------------------------------+-------------------------------------------------------------+-----------------------------+ +| ``reset_checkpoint_time`` | Do we want to reset the time in the checkpoint? This ONLY | -1.e200 | +| | takes effect if amr.regrid_on_restart = 1 and | | +| | amr.checkpoint_on_restart = 1, (which require that max_step | | +| | and stop_time be less than the value in the checkpoint) and | | +| | you set it to value greater than this default value. | | ++--------------------------------------------+-------------------------------------------------------------+-----------------------------+ +| ``reset_checkpoint_step`` | Do we want to reset the number of steps in the checkpoint? | -1 | +| | This ONLY takes effect if amr.regrid_on_restart = 1 and | | +| | amr.checkpoint_on_restart = 1, (which require that max_step | | +| | and stop_time be less than the value in the checkpoint) and | | +| | you set it to value greater than this default value. | | ++--------------------------------------------+-------------------------------------------------------------+-----------------------------+ +| ``store_omegadot`` | Do we store the species creation rates in the plotfile? | 0 | +| | Note, if this option is enabled then more memory will be | | +| | allocated to hold the results of the burn | | ++--------------------------------------------+-------------------------------------------------------------+-----------------------------+ +| ``store_burn_weights`` | Do we store the burn weights as a diagnostic in the | 0 | +| | plotfile? Note, if this option is enabled then more | | +| | memory will be allocated to hold the results of the burn | | ++--------------------------------------------+-------------------------------------------------------------+-----------------------------+ +| ``abort_on_invalid_params`` | Do we abort the run if the inputs file specifies a runtime | 0 | +| | parameter that we don't know about? Note: this will only | | +| | take effect for those namespaces where 100% of the runtime | | +| | parameters are managed by the python scripts. | | ++--------------------------------------------+-------------------------------------------------------------+-----------------------------+ @@ -653,11 +653,11 @@ namespace: ``castro`` .. index:: castro.do_radiation -+--------------------------------------------+-------------------------------------------------------------+---------------+ -| parameter | description | default value | -+============================================+=============================================================+===============+ -| ``do_radiation`` | do we enable radiation for a radiation-hydrodynamics run? | -1 | -+--------------------------------------------+-------------------------------------------------------------+---------------+ ++--------------------------------------------+-------------------------------------------------------------+-----------------------------+ +| parameter | description | default value | ++============================================+=============================================================+=============================+ +| ``do_radiation`` | do we enable radiation for a radiation-hydrodynamics run? | -1 | ++--------------------------------------------+-------------------------------------------------------------+-----------------------------+ @@ -666,11 +666,11 @@ namespace: ``castro`` .. index:: castro.do_tracer_particles -+--------------------------------------------+-------------------------------------------------------------+---------------+ -| parameter | description | default value | -+============================================+=============================================================+===============+ -| ``do_tracer_particles`` | permits tracer particle calculation to be turned on and off | 0 | -+--------------------------------------------+-------------------------------------------------------------+---------------+ ++--------------------------------------------+-------------------------------------------------------------+-----------------------------+ +| parameter | description | default value | ++============================================+=============================================================+=============================+ +| ``do_tracer_particles`` | permits tracer particle calculation to be turned on and off | 0 | ++--------------------------------------------+-------------------------------------------------------------+-----------------------------+ @@ -680,14 +680,14 @@ namespace: ``diffusion`` .. index:: diffusion.v, diffusion.mlmg_maxorder -+--------------------------------------------+-------------------------------------------------------------+---------------+ -| parameter | description | default value | -+============================================+=============================================================+===============+ -| ``v`` | the level of verbosity for the diffusion solve (higher | 0 | -| | number means more output) | | -+--------------------------------------------+-------------------------------------------------------------+---------------+ -| ``mlmg_maxorder`` | Use MLMG as the operator | 4 | -+--------------------------------------------+-------------------------------------------------------------+---------------+ ++--------------------------------------------+-------------------------------------------------------------+-----------------------------+ +| parameter | description | default value | ++============================================+=============================================================+=============================+ +| ``v`` | the level of verbosity for the diffusion solve (higher | 0 | +| | number means more output) | | ++--------------------------------------------+-------------------------------------------------------------+-----------------------------+ +| ``mlmg_maxorder`` | Use MLMG as the operator | 4 | ++--------------------------------------------+-------------------------------------------------------------+-----------------------------+ @@ -697,50 +697,50 @@ namespace: ``gravity`` .. index:: gravity.gravity_type, gravity.const_grav, gravity.direct_sum_bcs, gravity.drdxfac, gravity.max_multipole_order, gravity.v, gravity.no_sync, gravity.do_composite_phi_correction, gravity.max_solve_level, gravity.get_g_from_phi, gravity.mlmg_max_fmg_iter, gravity.mlmg_agglomeration, gravity.mlmg_consolidation, gravity.mlmg_nsolve -+--------------------------------------------+-------------------------------------------------------------+---------------+ -| parameter | description | default value | -+============================================+=============================================================+===============+ -| ``gravity_type`` | what type | "fillme" | -+--------------------------------------------+-------------------------------------------------------------+---------------+ -| ``const_grav`` | if doing constant gravity, what is the acceleration | 0.0 | -+--------------------------------------------+-------------------------------------------------------------+---------------+ -| ``direct_sum_bcs`` | Check if the user wants to compute the boundary conditions | 0 | -| | using the brute force method. Default is false, since this | | -| | method is slow. | | -+--------------------------------------------+-------------------------------------------------------------+---------------+ -| ``drdxfac`` | ratio of dr for monopole gravity binning to grid resolution | 1 | -+--------------------------------------------+-------------------------------------------------------------+---------------+ -| ``max_multipole_order`` | the maximum mulitpole order to use for multipole BCs when | 0 | -| | doing Poisson gravity | | -+--------------------------------------------+-------------------------------------------------------------+---------------+ -| ``v`` | the level of verbosity for the gravity solve (higher number | 0 | -| | means more output on the status of the solve / multigrid | | -+--------------------------------------------+-------------------------------------------------------------+---------------+ -| ``no_sync`` | do we perform the synchronization at coarse-fine | 0 | -| | interfaces? | | -+--------------------------------------------+-------------------------------------------------------------+---------------+ -| ``do_composite_phi_correction`` | should we apply a lagged correction to the potential that | 1 | -| | gets us closer to the composite solution? This makes the | | -| | resulting fine grid calculation slightly more accurate, at | | -| | the cost of an additional Poisson solve per timestep. | | -+--------------------------------------------+-------------------------------------------------------------+---------------+ -| ``max_solve_level`` | For all gravity types, we can choose a maximum level for | MAX_LEV-1 | -| | explicitly calculating the gravity and associated | | -| | potential. Above that level, we interpolate from coarser | | -| | levels. | | -+--------------------------------------------+-------------------------------------------------------------+---------------+ -| ``get_g_from_phi`` | For non-Poisson gravity, do we want to construct the | 0 | -| | gravitational acceleration by taking the gradient of the | | -| | potential, rather than constructing it directly? | | -+--------------------------------------------+-------------------------------------------------------------+---------------+ -| ``mlmg_max_fmg_iter`` | how many FMG cycles? | 0 | -+--------------------------------------------+-------------------------------------------------------------+---------------+ -| ``mlmg_agglomeration`` | Do agglomeration? | 1 | -+--------------------------------------------+-------------------------------------------------------------+---------------+ -| ``mlmg_consolidation`` | | 1 | -+--------------------------------------------+-------------------------------------------------------------+---------------+ -| ``mlmg_nsolve`` | Do N-Solve? | 0 | -+--------------------------------------------+-------------------------------------------------------------+---------------+ ++--------------------------------------------+-------------------------------------------------------------+-----------------------------+ +| parameter | description | default value | ++============================================+=============================================================+=============================+ +| ``gravity_type`` | what type | "fillme" | ++--------------------------------------------+-------------------------------------------------------------+-----------------------------+ +| ``const_grav`` | if doing constant gravity, what is the acceleration | 0.0 | ++--------------------------------------------+-------------------------------------------------------------+-----------------------------+ +| ``direct_sum_bcs`` | Check if the user wants to compute the boundary conditions | 0 | +| | using the brute force method. Default is false, since this | | +| | method is slow. | | ++--------------------------------------------+-------------------------------------------------------------+-----------------------------+ +| ``drdxfac`` | ratio of dr for monopole gravity binning to grid resolution | 1 | ++--------------------------------------------+-------------------------------------------------------------+-----------------------------+ +| ``max_multipole_order`` | the maximum mulitpole order to use for multipole BCs when | 0 | +| | doing Poisson gravity | | ++--------------------------------------------+-------------------------------------------------------------+-----------------------------+ +| ``v`` | the level of verbosity for the gravity solve (higher number | 0 | +| | means more output on the status of the solve / multigrid | | ++--------------------------------------------+-------------------------------------------------------------+-----------------------------+ +| ``no_sync`` | do we perform the synchronization at coarse-fine | 0 | +| | interfaces? | | ++--------------------------------------------+-------------------------------------------------------------+-----------------------------+ +| ``do_composite_phi_correction`` | should we apply a lagged correction to the potential that | 1 | +| | gets us closer to the composite solution? This makes the | | +| | resulting fine grid calculation slightly more accurate, at | | +| | the cost of an additional Poisson solve per timestep. | | ++--------------------------------------------+-------------------------------------------------------------+-----------------------------+ +| ``max_solve_level`` | For all gravity types, we can choose a maximum level for | MAX_LEV-1 | +| | explicitly calculating the gravity and associated | | +| | potential. Above that level, we interpolate from coarser | | +| | levels. | | ++--------------------------------------------+-------------------------------------------------------------+-----------------------------+ +| ``get_g_from_phi`` | For non-Poisson gravity, do we want to construct the | 0 | +| | gravitational acceleration by taking the gradient of the | | +| | potential, rather than constructing it directly? | | ++--------------------------------------------+-------------------------------------------------------------+-----------------------------+ +| ``mlmg_max_fmg_iter`` | how many FMG cycles? | 0 | ++--------------------------------------------+-------------------------------------------------------------+-----------------------------+ +| ``mlmg_agglomeration`` | Do agglomeration? | 1 | ++--------------------------------------------+-------------------------------------------------------------+-----------------------------+ +| ``mlmg_consolidation`` | | 1 | ++--------------------------------------------+-------------------------------------------------------------+-----------------------------+ +| ``mlmg_nsolve`` | Do N-Solve? | 0 | ++--------------------------------------------+-------------------------------------------------------------+-----------------------------+ @@ -750,30 +750,30 @@ namespace: ``particles`` .. index:: particles.v, particles.particle_init_file, particles.particle_restart_file, particles.restart_from_nonparticle_chkfile, particles.particle_output_file, particles.timestamp_dir, particles.timestamp_density, particles.timestamp_temperature -+--------------------------------------------+-------------------------------------------------------------+---------------+ -| parameter | description | default value | -+============================================+=============================================================+===============+ -| ``v`` | the level of verbosity for the tracer particle (0 or 1) | 0 | -+--------------------------------------------+-------------------------------------------------------------+---------------+ -| ``particle_init_file`` | the name of an input file containing the total particle | "" | -| | number and the initial position of each particle. | | -+--------------------------------------------+-------------------------------------------------------------+---------------+ -| ``particle_restart_file`` | the name of a file with new particles at restart | "" | -+--------------------------------------------+-------------------------------------------------------------+---------------+ -| ``restart_from_nonparticle_chkfile`` | to restart from a checkpoint that was written with | 0 | -| | ``USE_PARTICLES`` =FALSE | | -+--------------------------------------------+-------------------------------------------------------------+---------------+ -| ``particle_output_file`` | the name of timestamp files. | "" | -+--------------------------------------------+-------------------------------------------------------------+---------------+ -| ``timestamp_dir`` | the name of a directory in which timestamp files are | "" | -| | stored. | | -+--------------------------------------------+-------------------------------------------------------------+---------------+ -| ``timestamp_density`` | whether the local densities at given positions of particles | 1 | -| | are stored in output files | | -+--------------------------------------------+-------------------------------------------------------------+---------------+ -| ``timestamp_temperature`` | whether the local temperatures at given positions of | 0 | -| | particles are stored in output files | | -+--------------------------------------------+-------------------------------------------------------------+---------------+ ++--------------------------------------------+-------------------------------------------------------------+-----------------------------+ +| parameter | description | default value | ++============================================+=============================================================+=============================+ +| ``v`` | the level of verbosity for the tracer particle (0 or 1) | 0 | ++--------------------------------------------+-------------------------------------------------------------+-----------------------------+ +| ``particle_init_file`` | the name of an input file containing the total particle | "" | +| | number and the initial position of each particle. | | ++--------------------------------------------+-------------------------------------------------------------+-----------------------------+ +| ``particle_restart_file`` | the name of a file with new particles at restart | "" | ++--------------------------------------------+-------------------------------------------------------------+-----------------------------+ +| ``restart_from_nonparticle_chkfile`` | to restart from a checkpoint that was written with | 0 | +| | ``USE_PARTICLES`` =FALSE | | ++--------------------------------------------+-------------------------------------------------------------+-----------------------------+ +| ``particle_output_file`` | the name of timestamp files. | "" | ++--------------------------------------------+-------------------------------------------------------------+-----------------------------+ +| ``timestamp_dir`` | the name of a directory in which timestamp files are | "" | +| | stored. | | ++--------------------------------------------+-------------------------------------------------------------+-----------------------------+ +| ``timestamp_density`` | whether the local densities at given positions of particles | 1 | +| | are stored in output files | | ++--------------------------------------------+-------------------------------------------------------------+-----------------------------+ +| ``timestamp_temperature`` | whether the local temperatures at given positions of | 0 | +| | particles are stored in output files | | ++--------------------------------------------+-------------------------------------------------------------+-----------------------------+ @@ -783,36 +783,36 @@ namespace: ``radiation`` .. index:: radiation.prop_temp_floor, radiation.flatten_pp_threshold, radiation.comoving, radiation.closure, radiation.limiter, radiation.fspace_advection_type, radiation.plot_lambda, radiation.plot_kappa_p, radiation.plot_kappa_r, radiation.plot_lab_Er, radiation.plot_lab_flux, radiation.plot_com_flux -+--------------------------------------------+-------------------------------------------------------------+---------------+ -| parameter | description | default value | -+============================================+=============================================================+===============+ -| ``prop_temp_floor`` | | 0.0 | -+--------------------------------------------+-------------------------------------------------------------+---------------+ -| ``flatten_pp_threshold`` | | -1.0 | -+--------------------------------------------+-------------------------------------------------------------+---------------+ -| ``comoving`` | are we in a comoving reference frame? | 1 | -+--------------------------------------------+-------------------------------------------------------------+---------------+ -| ``closure`` | which closure relation to use 0: f = lambda 1: f = 1/3 2: f | 3 | -| | = 1 - 2 * lambda 3: f = lambda + (lambda * R)^2 4: f = 1/3 | | -| | + 2/3 (lambda * R)^2 | | -+--------------------------------------------+-------------------------------------------------------------+---------------+ -| ``limiter`` | which limiter to use 0: no limiter 2: Lev-Pom limiter 12: | 2 | -| | Bruenn 22: square root 32: Minerbo | | -+--------------------------------------------+-------------------------------------------------------------+---------------+ -| ``fspace_advection_type`` | frequency space advection type | 2 | -+--------------------------------------------+-------------------------------------------------------------+---------------+ -| ``plot_lambda`` | do we plot the flux limiter lambda? | 0 | -+--------------------------------------------+-------------------------------------------------------------+---------------+ -| ``plot_kappa_p`` | do we plot the Planck mean opacity? | 0 | -+--------------------------------------------+-------------------------------------------------------------+---------------+ -| ``plot_kappa_r`` | do we plot the Rosseland mean opacity? | 0 | -+--------------------------------------------+-------------------------------------------------------------+---------------+ -| ``plot_lab_Er`` | do we plot the lab radiation energy? | 0 | -+--------------------------------------------+-------------------------------------------------------------+---------------+ -| ``plot_lab_flux`` | do we plot the lab radiation flux? | 0 | -+--------------------------------------------+-------------------------------------------------------------+---------------+ -| ``plot_com_flux`` | do we plot the comoving frame radiation flux? | 0 | -+--------------------------------------------+-------------------------------------------------------------+---------------+ ++--------------------------------------------+-------------------------------------------------------------+-----------------------------+ +| parameter | description | default value | ++============================================+=============================================================+=============================+ +| ``prop_temp_floor`` | | 0.0 | ++--------------------------------------------+-------------------------------------------------------------+-----------------------------+ +| ``flatten_pp_threshold`` | | -1.0 | ++--------------------------------------------+-------------------------------------------------------------+-----------------------------+ +| ``comoving`` | are we in a comoving reference frame? | 1 | ++--------------------------------------------+-------------------------------------------------------------+-----------------------------+ +| ``closure`` | which closure relation to use 0: f = lambda 1: f = 1/3 2: f | 3 | +| | = 1 - 2 * lambda 3: f = lambda + (lambda * R)^2 4: f = 1/3 | | +| | + 2/3 (lambda * R)^2 | | ++--------------------------------------------+-------------------------------------------------------------+-----------------------------+ +| ``limiter`` | which limiter to use 0: no limiter 2: Lev-Pom limiter 12: | 2 | +| | Bruenn 22: square root 32: Minerbo | | ++--------------------------------------------+-------------------------------------------------------------+-----------------------------+ +| ``fspace_advection_type`` | frequency space advection type | 2 | ++--------------------------------------------+-------------------------------------------------------------+-----------------------------+ +| ``plot_lambda`` | do we plot the flux limiter lambda? | 0 | ++--------------------------------------------+-------------------------------------------------------------+-----------------------------+ +| ``plot_kappa_p`` | do we plot the Planck mean opacity? | 0 | ++--------------------------------------------+-------------------------------------------------------------+-----------------------------+ +| ``plot_kappa_r`` | do we plot the Rosseland mean opacity? | 0 | ++--------------------------------------------+-------------------------------------------------------------+-----------------------------+ +| ``plot_lab_Er`` | do we plot the lab radiation energy? | 0 | ++--------------------------------------------+-------------------------------------------------------------+-----------------------------+ +| ``plot_lab_flux`` | do we plot the lab radiation flux? | 0 | ++--------------------------------------------+-------------------------------------------------------------+-----------------------------+ +| ``plot_com_flux`` | do we plot the comoving frame radiation flux? | 0 | ++--------------------------------------------+-------------------------------------------------------------+-----------------------------+ @@ -822,25 +822,25 @@ namespace: ``radsolve`` .. index:: radsolve.level_solver_flag, radsolve.use_hypre_nonsymmetric_terms, radsolve.reltol, radsolve.abstol, radsolve.maxiter, radsolve.alpha, radsolve.beta, radsolve.v -+--------------------------------------------+-------------------------------------------------------------+---------------+ -| parameter | description | default value | -+============================================+=============================================================+===============+ -| ``level_solver_flag`` | the linear solver option to use | 1 | -+--------------------------------------------+-------------------------------------------------------------+---------------+ -| ``use_hypre_nonsymmetric_terms`` | | 0 | -+--------------------------------------------+-------------------------------------------------------------+---------------+ -| ``reltol`` | | 1.e-10 | -+--------------------------------------------+-------------------------------------------------------------+---------------+ -| ``abstol`` | | 1.e-10 | -+--------------------------------------------+-------------------------------------------------------------+---------------+ -| ``maxiter`` | | 40 | -+--------------------------------------------+-------------------------------------------------------------+---------------+ -| ``alpha`` | | 1.0 | -+--------------------------------------------+-------------------------------------------------------------+---------------+ -| ``beta`` | | 1.0 | -+--------------------------------------------+-------------------------------------------------------------+---------------+ -| ``v`` | | 0 | -+--------------------------------------------+-------------------------------------------------------------+---------------+ ++--------------------------------------------+-------------------------------------------------------------+-----------------------------+ +| parameter | description | default value | ++============================================+=============================================================+=============================+ +| ``level_solver_flag`` | the linear solver option to use | 1 | ++--------------------------------------------+-------------------------------------------------------------+-----------------------------+ +| ``use_hypre_nonsymmetric_terms`` | | 0 | ++--------------------------------------------+-------------------------------------------------------------+-----------------------------+ +| ``reltol`` | | 1.e-10 | ++--------------------------------------------+-------------------------------------------------------------+-----------------------------+ +| ``abstol`` | | 1.e-10 | ++--------------------------------------------+-------------------------------------------------------------+-----------------------------+ +| ``maxiter`` | | 40 | ++--------------------------------------------+-------------------------------------------------------------+-----------------------------+ +| ``alpha`` | | 1.0 | ++--------------------------------------------+-------------------------------------------------------------+-----------------------------+ +| ``beta`` | | 1.0 | ++--------------------------------------------+-------------------------------------------------------------+-----------------------------+ +| ``v`` | | 0 | ++--------------------------------------------+-------------------------------------------------------------+-----------------------------+ diff --git a/docs/faq.html b/docs/faq.html index 77b18a9b5d..4894b800b4 100644 --- a/docs/faq.html +++ b/docs/faq.html @@ -223,11 +223,11 @@

      Compilingmf, you can dump out the state as:

      -
      print_state(mf, IntVect(D_DECL(10, 20, 30)));
+
      print_state(mf, IntVect(AMREX_D_DECL(10, 20, 30)));
 
      
 
      
 
      Here, the IntVect has the dimension that we were compiled with
-(and this is handled through the preprocessor D_DECL). In
+(and this is handled through the preprocessor AMREX_D_DECL). In
 this case, we are inspecting zone (10, 20, 30), in the global index
 space. Note that since a multifab exists only on a single level, the
 integer indices here refer to the global index space on that level.
      
diff --git a/docs/genindex.html b/docs/genindex.html
index 5356dd1518..b1e89f5d22 100644
--- a/docs/genindex.html
+++ b/docs/genindex.html
@@ -450,7 +450,7 @@ 
      C

    • castro.abundance_failure_tolerance, [1], [2]
      • -
    • castro.add_ext_src, [1] +
    • castro.add_ext_src, [1]
    • castro.add_sdc_react_source_to_advection
      • @@ -504,7 +504,7 @@

      C

    • castro.do_grav
      • -
    • castro.do_hydro, [1] +
    • castro.do_hydro, [1]
    • castro.do_radiation
      • @@ -518,7 +518,7 @@

      C

    • castro.do_special_tagging
      • -
    • castro.do_sponge, [1] +
    • castro.do_sponge, [1]
    • castro.do_tracer_particles
      • @@ -582,7 +582,7 @@

      C

    • castro.job_name
      • -
    • castro.limit_fluxes_on_small_dens, [1], [2] +
    • castro.limit_fluxes_on_small_dens, [1], [2]
    • castro.limit_fourth_order
      • @@ -598,7 +598,7 @@

      C

    • castro.moving_center
      • -
    • castro.normalize_species +
    • castro.normalize_species
    • castro.output_at_completion, [1]
      • @@ -618,9 +618,9 @@

      C

    • castro.ppm_do_limiting
      • -
    • castro.ppm_temp_fix, [1] +
    • castro.ppm_temp_fix, [1]
      • -
    • castro.ppm_type, [1] +
    • castro.ppm_type, [1]
    • castro.print_update_diagnostics
      • @@ -644,7 +644,7 @@

      C

    • castro.riemann_solver
      • -
    • castro.riemann_speed_limit +
    • castro.riemann_speed_limit
    • castro.rot_axis
      • @@ -680,15 +680,15 @@

      C

    • castro.shock_detection_threshold
      • -
    • castro.small_dens, [1], [2], [3] +
    • castro.small_dens, [1], [2], [3]
    • castro.small_ener
    • castro.small_plot_per_is_exact
      • -
    • castro.small_pres, [1] +
    • castro.small_pres, [1]
      • -
    • castro.small_temp, [1] +
    • castro.small_temp, [1]
    • castro.source_term_predictor
      • @@ -2709,6 +2709,8 @@

      U

    • USE_SHOCK_VAR, [1]
    • USE_SIMPLIFIED_SDC, [1], [2] +
      • +
    • USE_SPECIES_SOURCES
    • USE_TRUE_SDC, [1], [2]
      • diff --git a/docs/getting_started.html b/docs/getting_started.html index 05adb8fd61..c1a30199a1 100644 --- a/docs/getting_started.html +++ b/docs/getting_started.html @@ -317,6 +317,98 @@

      Visualization of the ResultsDocs/source/yt_example.ipynb in the Castro repo.

      +
      import yt
+import matplotlib.pyplot as plt
+import numpy as np
+
+# set matplotlib formatting to be the same as yt
+plt.rcParams['font.size'] = 14
+plt.rcParams['font.family'] = 'serif'
+plt.rcParams['mathtext.fontset'] = 'stix'
+
      +
      +
      # load data from file
+ds = yt.load('../../Exec/hydro_tests/Sedov/sedov_2d_cyl_in_cart_plt00150/', hint="castro")
+
      +
      +
      yt : [INFO     ] 2020-05-29 16:40:16,890 Parameters: current_time              = 0.1
+yt : [INFO     ] 2020-05-29 16:40:16,891 Parameters: domain_dimensions         = [32 32  1]
+yt : [INFO     ] 2020-05-29 16:40:16,891 Parameters: domain_left_edge          = [0. 0. 0.]
+yt : [INFO     ] 2020-05-29 16:40:16,892 Parameters: domain_right_edge         = [1. 1. 1.]
+
      +
      +
      # print out fields available for plotting
+print([f for _,f in ds.field_list])
+
      +
      +
      ['Gamma_1', 'MachNumber', 'StateErr_0', 'StateErr_1', 'StateErr_2', 'Temp', 'X(X)', 'abar', 'angular_momentum_x', 'angular_momentum_y', 'angular_momentum_z', 'circvel', 'density', 'divu', 'eint_E', 'eint_e', 'entropy', 'kineng', 'logden', 'magmom', 'magvel', 'magvort', 'pressure', 'radvel', 'rho_E', 'rho_X', 'rho_e', 'soundspeed', 'x_velocity', 'xmom', 'y_velocity', 'ymom', 'z_velocity', 'zmom']
+
      +
      +
      # plot the density
+fig = yt.SlicePlot(ds, 'z', 'density')
+
+# save plot to file
+fig.save('sedov_density.png')
+
+fig
+
      +
      +
      yt : [INFO     ] 2020-05-29 16:40:17,234 xlim = 0.000000 1.000000
+yt : [INFO     ] 2020-05-29 16:40:17,235 ylim = 0.000000 1.000000
+yt : [INFO     ] 2020-05-29 16:40:17,235 xlim = 0.000000 1.000000
+yt : [INFO     ] 2020-05-29 16:40:17,236 ylim = 0.000000 1.000000
+yt : [INFO     ] 2020-05-29 16:40:17,237 Making a fixed resolution buffer of (('gas', 'density')) 800 by 800
+yt : [INFO     ] 2020-05-29 16:40:17,392 Saving plot sedov_density.png
+
      +
      +
      # plot the temperature and annotate the grids
+fig = yt.SlicePlot(ds, 'z', 'Temp')
+fig.annotate_grids(linewidth=2, alpha=1, edgecolors='red')
+fig.annotate_cell_edges(line_width=0.0005, alpha=0.4, color='white')
+fig
+
      +
      +
      yt : [INFO     ] 2020-05-29 16:40:17,748 xlim = 0.000000 1.000000
+yt : [INFO     ] 2020-05-29 16:40:17,749 ylim = 0.000000 1.000000
+yt : [INFO     ] 2020-05-29 16:40:17,750 xlim = 0.000000 1.000000
+yt : [INFO     ] 2020-05-29 16:40:17,750 ylim = 0.000000 1.000000
+yt : [INFO     ] 2020-05-29 16:40:17,751 Making a fixed resolution buffer of (('boxlib', 'Temp')) 800 by 800
+yt : [WARNING  ] 2020-05-29 16:40:17,897 Supplied id_loc but draw_ids is False. Not drawing grid ids
+yt : [WARNING  ] 2020-05-29 16:40:17,899 Supplied id_loc but draw_ids is False. Not drawing grid ids
+yt : [WARNING  ] 2020-05-29 16:40:17,901 Supplied id_loc but draw_ids is False. Not drawing grid ids
+yt : [WARNING  ] 2020-05-29 16:40:17,903 Supplied id_loc but draw_ids is False. Not drawing grid ids
+yt : [WARNING  ] 2020-05-29 16:40:17,905 Supplied id_loc but draw_ids is False. Not drawing grid ids
+yt : [WARNING  ] 2020-05-29 16:40:17,906 Supplied id_loc but draw_ids is False. Not drawing grid ids
+yt : [WARNING  ] 2020-05-29 16:40:17,908 Supplied id_loc but draw_ids is False. Not drawing grid ids
+yt : [WARNING  ] 2020-05-29 16:40:17,910 Supplied id_loc but draw_ids is False. Not drawing grid ids
+yt : [WARNING  ] 2020-05-29 16:40:17,911 Supplied id_loc but draw_ids is False. Not drawing grid ids
+
      +
      +
      # create a line plot of the density parallel to the x-axis that cuts through the
+# point of maximum density
+
+_, c = ds.find_max("density") # find the location of the point of maximum density
+ax = 0 # take cut parallel to x-axis
+
+# use ortho_ray to cut through c
+ray = ds.ortho_ray(ax, (c[1], c[2]))
+
+# sort values by x so there are no discontinuities in the line plot
+srt = np.argsort(ray['x'])
+
+fig, ax = plt.subplots(figsize=(8,6))
+ax.plot(ray['x'][srt], ray['density'][srt])
+ax.set_xlabel(r'$x$ (cm)')
+ax.set_ylabel(r'$\rho$ (g/cm$^3$)')
+ax.set_xlim([ray['x'][srt][0], ray['x'][srt][-1]])
+
+fig.savefig('dens_plot.png')
+
      +
      +
      yt : [INFO     ] 2020-05-29 16:40:18,254 Max Value is 3.51160e+00 at 0.7558593750000000 0.7558593750000000 0.5000000000000000
+
      +
      +_images/yt_example_5_1.png

Amrvis

diff --git a/docs/io.html b/docs/io.html index e5de52ce42..f14ae568b9 100644 --- a/docs/io.html +++ b/docs/io.html @@ -415,43 +415,39 @@

Native variables\(\omegadot_k = DX_k/Dt\)

\({\rm s^{-1}}\)

-

enuc

-

Nuclear energy generation rate / gram

-

\({\rm erg~g^{-1}~s^{-1}}\)

- -

rho_enuc

+

rho_enuc

Nuclear energy generation rate density

\({\rm erg~cm^{-3}~s^{-1}}\)

-

phiGrav

+

phiGrav

Gravitational potential

\({\rm erg~g^{-1}}\)

-

grav_x, grav_y, +

grav_x, grav_y, grav_z

Gravitational acceleration

\({\rm cm~s^{-2}}\)

-

rmom

+

rmom

Radial momentum (defined for HYBRID_MOMENTUM)

\({\rm g~cm^{-2}~s^{-1}}\)

-

lmom

+

lmom

Angular momentum (\(\theta\); defined for HYBRID_MOMENTUM)

\({\rm g~cm^{-2}~s^{-1}}\)

-

pmom

+

pmom

z-momentum (defined for HYBRID_MOMENTUM)

\({\rm g~cm^{-2}~s^{-1}}\)

-

Shock

+

Shock

Shock flag (= 1 if a zone has a shock; defined for SHOCK)

–

-

rad, rad0, rad1, +

rad, rad0, rad1, …

Radiation energy density (for multigroup radiation, each group has its @@ -654,6 +650,11 @@

Derived variablesdervel

\(\cms\)

+

enuc

+

Nuclear energy generation rate / gram

+

derenuc

+

\({\rm erg~g^{-1}~s^{-1}}\)

+

diff --git a/docs/runtime_parameters.html b/docs/runtime_parameters.html index d99fa14f3c..cd6e6a3b02 100644 --- a/docs/runtime_parameters.html +++ b/docs/runtime_parameters.html @@ -666,7 +666,96 @@

namespace: cast

reactions

-

diffusion

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +

parameter

description

default value

dtnuc_e

Limit the timestep based on how much the burning can change +the internal energy of a zone. The timestep is equal to +dtnuc \(\cdot\,(e / \dot{e})\).

1.e200

dtnuc_X

Limit the timestep based on how much the burning can change +the species mass fractions of a zone. The timestep is equal +to dtnuc \(\cdot\,(X / \dot{X})\).

1.e200

dtnuc_X_threshold

If we are using the timestep limiter based on changes in +\(X\), set a threshold on the species abundance below which +the limiter is not applied. This helps prevent the timestep +from becoming very small due to changes in trace species.

1.e-3

do_react

permits reactions to be turned on and off – mostly for +efficiency’s sake

-1

react_T_min

minimum temperature for allowing reactions to occur in a +zone

0.0

react_T_max

maximum temperature for allowing reactions to occur in a +zone

1.e200

react_rho_min

minimum density for allowing reactions to occur in a zone

0.0

react_rho_max

maximum density for allowing reactions to occur in a zone

1.e200

disable_shock_burning

disable burning inside hydrodynamic shock regions note: +requires compiling with USE_SHOCK_VAR=TRUE

0

shock_detection_threshold

shock detection threshold for grad{P} / P

0.6666666666666666666666_rt

shock_detection_include_sources

do we subtract off the hydrostatic pressure when evaluating +a shock?

1

T_guess

initial guess for the temperature when inverting the EoS +(e.g. when calling eos_input_re)

1.e8

drive_initial_convection

if set to 1, we interpolate from the initial model to get +the temperature used to call the burner. This prevents +reactions from going nonlinear and running away in place +before a convective field is established.

0

drive_initial_convection_tmax

maximum time over which to do the drive_initial_convection +procedure

1.e200

drive_initial_convection_reinit_period

frequency with which to re-initialize the thermodynamic +data while preserving the velocity field during +drive_initial_convection

1.e200

+

diffusion

diff --git a/docs/searchindex.js b/docs/searchindex.js index bfcfa14897..532a70d7f8 100644 --- a/docs/searchindex.js +++ b/docs/searchindex.js @@ -1 +1 @@ -Search.setIndex({"docnames": ["AMR", "ConvertCheckpoint", "EOS", "FlowChart", "Hydrodynamics", "Introduction", "MAESTRO_restart", "Particles", "Preface", "Verification", "build_system", "class/classCastro", "class/classDiffusion", "class/classGradPhiPhysBCFunct", "class/classGravity", "class/classHypreABec", "class/classHypreExtMultiABec", "class/classMGRadBndry", "class/classMGRadBndryBld", "class/classNGBndry", "class/classNGBndryBld", "class/classRadBndry", "class/classRadBndryBld", "class/classRadSolve", "class/classRadiation", "classlist", "creating_a_problem", "debugging", "development", "diffusion", "faq", "file/Castro_8H", "file/Castro__bc__fill__nd_8H", "file/Castro__diffusion_8H", "file/Castro__generic__fill_8H", "file/Castro__gravity_8H", "file/Castro__hydro_8H", "file/Castro__io_8H", "file/Castro__mhd_8H", "file/Castro__react_8H", "file/Castro__react__util_8H", "file/Castro__rotation_8H", "file/Castro__sdc_8H", "file/Castro__sdc__util_8H", "file/Castro__sources_8H", "file/Castro__util_8H", "file/Derive_8H", "file/Diffusion_8H", "file/Gravity_8H", "file/Gravity__util_8H", "file/HABEC_8H", "file/HypreABec_8H", "file/HypreExtMultiABec_8H", "file/MGRadBndry_8H", "file/MGutils_8H", "file/NGBndry_8H", "file/Problem_8H", "file/Problem__Derive_8H", "file/Problem__Derives_8H", "file/RadBndry_8H", "file/RadDerive_8H", "file/RadHydro_8H", "file/RadSolve_8H", "file/RadTypes_8H", "file/Radiation_8H", "file/Rotation_8H", "file/advection__util_8H", "file/ambient_8H", "file/binary_8H", "file/blackbody_8H", "file/castro__limits_8H", "file/diffusion__util_8H", "file/ext__bc__types_8H", "file/filt__prim_8H", "file/filter_8H", "file/flatten_8H", "file/fluxlimiter_8H", "file/fourth__center__average_8H", "file/global_8H", "file/hybrid_8H", "file/math_8H", "file/mhd__eigen_8H", "file/mhd__sizes_8H", 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29, 30, 108, 109, 111, 113, 116, 117, 118, 119, 120, 121, 122, 125, 126, 128, 129], "exampl": [0, 1, 2, 3, 4, 7, 9, 26, 28, 30, 108, 109, 112, 113, 114, 117, 118, 119, 124, 127], "refinement_ind": 0, "den": [0, 26], "temp": [0, 4, 23, 24, 62, 64, 113, 129], "max_level": [0, 1, 6, 112], "value_great": 0, "2": [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 19, 24, 26, 29, 30, 31, 36, 42, 43, 48, 51, 52, 55, 61, 64, 69, 79, 82, 83, 84, 90, 100, 103, 105, 108, 109, 110, 112, 113, 114, 115, 116, 117, 119, 120, 122, 123, 124, 125, 126, 127, 129, 130], "field_nam": 0, "value_less": 0, "list": [0, 1, 4, 8, 11, 26, 30, 31, 111, 113, 117, 119, 121], "name": [0, 1, 3, 4, 5, 6, 7, 9, 10, 11, 26, 30, 31, 86, 94, 108, 112, 113, 119, 121, 122, 125], "For": [0, 1, 2, 3, 4, 6, 7, 9, 10, 11, 15, 24, 26, 27, 30, 31, 36, 44, 51, 64, 79, 108, 109, 110, 113, 114, 115, 117, 118, 119, 120, 121, 122, 124, 125, 128], "each": [0, 2, 3, 4, 5, 7, 9, 10, 11, 12, 14, 21, 24, 26, 28, 30, 31, 36, 47, 48, 59, 64, 108, 109, 110, 112, 113, 115, 117, 119, 122, 125, 126, 127, 128], "accept": [0, 1, 118], "predefin": 0, "field": [0, 9, 11, 14, 29, 31, 35, 36, 48, 66, 90, 109, 111, 114, 117, 122, 125, 129, 130], "when": [0, 1, 2, 3, 4, 6, 8, 10, 11, 17, 21, 26, 28, 30, 31, 36, 53, 59, 109, 110, 113, 115, 117, 118, 119, 120, 121, 122, 125, 127, 128], "These": [0, 3, 4, 5, 10, 26, 29, 108, 109, 110, 113, 116, 117, 119, 121, 124, 125, 127, 128], "maximum": [0, 3, 9, 14, 26, 48, 109, 112, 113, 118, 119, 122, 124, 127, 129], "start_tim": 0, "start": [0, 1, 3, 4, 5, 6, 7, 11, 26, 31, 109, 110, 111, 112, 113, 116, 121, 122, 125, 126, 127, 128], "end_tim": 0, "stop": [0, 24, 30, 64, 117, 122, 127], "valu": [0, 1, 2, 4, 6, 7, 11, 14, 17, 21, 24, 26, 29, 30, 31, 48, 53, 55, 59, 63, 64, 84, 98, 109, 110, 112, 113, 114, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 129], "abov": [0, 1, 3, 4, 9, 16, 28, 52, 109, 110, 112, 116, 117, 120, 122, 124, 125, 127], "below": [0, 3, 4, 6, 11, 27, 29, 30, 31, 108, 109, 117, 119, 120, 122, 125, 126, 127], "absolut": [0, 14, 24, 48, 64, 109, 117], "between": [0, 1, 4, 5, 7, 9, 10, 11, 14, 27, 29, 31, 48, 109, 110, 112, 113, 115, 120, 122, 124, 125, 126], "adjac": [0, 109, 122], "cell": [0, 1, 3, 4, 6, 7, 9, 11, 14, 16, 26, 30, 31, 36, 41, 42, 44, 48, 52, 79, 84, 109, 110, 112, 114, 119, 120, 122, 125, 130], "relative_gradi": 0, "rel": [0, 14, 24, 48, 64, 108, 109, 117, 120, 122, 130], "string": [0, 6, 11, 14, 24, 30, 31, 37, 44, 48, 64, 86, 94, 121, 122], "code": [0, 1, 3, 4, 5, 6, 8, 9, 10, 26, 29, 30, 109, 112, 113, 115, 116, 118, 121, 122, 127, 130], "If": [0, 1, 2, 3, 4, 6, 7, 8, 9, 10, 11, 14, 19, 26, 27, 30, 31, 42, 48, 55, 108, 109, 110, 112, 113, 114, 117, 118, 119, 120, 122, 125, 127, 128], "indic": [0, 4, 6, 11, 26, 30, 31, 36, 109, 120, 124, 125, 127], "ad": [0, 3, 6, 26, 27, 33, 36, 109, 115, 122, 125, 126], "either": [0, 3, 4, 7, 10, 11, 26, 28, 31, 36, 66, 108, 110, 113, 116, 117, 125, 127], "must": [0, 1, 3, 4, 6, 7, 11, 14, 19, 24, 28, 29, 31, 48, 55, 64, 108, 109, 112, 117, 119, 120, 122, 124, 127], "physic": [0, 5, 7, 13, 14, 24, 48, 64, 84, 105, 109, 112, 120, 121, 122, 130], "boundari": [0, 5, 10, 13, 14, 32, 36, 48, 84, 85, 105, 116, 120, 122, 126], "cannot": [0, 4, 30, 117], "poisson": [0, 3, 5, 14, 48, 113, 122, 124, 125, 130], "graviti": [0, 3, 4, 5, 8, 11, 25, 26, 31, 107, 110, 111, 112, 113, 116, 119, 120, 121, 130], "solver": [0, 3, 4, 8, 9, 10, 15, 24, 25, 26, 36, 51, 64, 100, 107, 109, 110, 112, 113, 114, 115, 116, 119, 122, 123, 125, 127, 130], "your": [0, 1, 2, 3, 4, 6, 7, 8, 29, 30, 108, 109, 111, 112, 113, 116, 117, 122, 125, 127, 128], "met": 0, "thei": [0, 2, 3, 4, 10, 11, 31, 108, 109, 110, 112, 113, 117, 118, 119, 125], "ignor": [0, 3, 4, 17, 21, 26, 29, 30, 53, 59, 109, 112, 117, 127], "sometim": [0, 4, 6, 27, 125], "wish": [0, 4, 6, 108, 114], "forc": [0, 30, 65, 84, 113, 122, 125, 127], "derefin": 0, "even": [0, 4, 6, 10, 11, 30, 31, 109, 116, 119, 122, 130], "other": [0, 1, 2, 3, 4, 7, 11, 24, 26, 30, 31, 33, 64, 108, 109, 110, 113, 117, 119, 120, 121, 122, 124, 127], "accomplish": 0, "anoth": [0, 3, 7, 11, 31, 42, 109, 113, 116, 120, 122, 124], "ani": [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 14, 26, 28, 30, 31, 36, 39, 44, 48, 101, 108, 109, 110, 112, 113, 115, 119, 121, 125, 127], "less": [0, 108, 113, 122], "than": [0, 1, 3, 4, 6, 11, 30, 31, 108, 109, 117, 119, 120, 122, 124, 127, 128], "e4": 0, "could": [0, 1, 4, 10, 30, 117, 119, 125, 127], "do": [0, 1, 2, 3, 4, 6, 9, 10, 11, 14, 26, 27, 28, 30, 31, 36, 44, 48, 65, 108, 109, 112, 113, 114, 115, 117, 118, 119, 120, 122, 123, 125, 127, 128], "dencutoff": 0, "lise": 0, "under": [0, 8, 10, 26, 36, 84, 108, 109], "appear": [0, 3, 4, 8, 9, 28, 29, 110, 112, 113, 114, 116, 120, 125], "after": [0, 1, 3, 4, 7, 10, 11, 24, 28, 31, 44, 64, 109, 112, 113, 114, 117, 122], "those": [0, 1, 3, 4, 5, 8, 29, 108, 109, 113, 118, 122, 125, 128], "so": [0, 1, 2, 3, 4, 10, 11, 15, 24, 26, 28, 29, 30, 31, 36, 51, 64, 66, 108, 109, 110, 113, 115, 117, 118, 119, 120, 122, 124, 125, 126, 127, 129, 130], "appli": [0, 3, 4, 5, 9, 11, 26, 28, 31, 36, 44, 109, 117, 119, 120, 122, 124, 126], "all": [0, 1, 2, 4, 6, 7, 8, 9, 10, 11, 14, 16, 24, 26, 27, 30, 31, 36, 44, 48, 52, 64, 101, 108, 109, 110, 112, 113, 114, 115, 117, 118, 119, 120, 121, 122, 123, 124, 125, 127, 128], "done": [0, 2, 3, 4, 5, 6, 8, 9, 10, 11, 26, 27, 28, 30, 31, 108, 109, 110, 113, 114, 115, 120, 122, 125], "abil": [0, 9, 116], "own": [0, 28, 108, 111, 113, 116, 117, 125], "through": [0, 3, 4, 9, 26, 28, 30, 36, 39, 100, 105, 108, 109, 112, 116, 117, 118, 120, 122, 125, 126, 127, 129], "c": [0, 2, 3, 4, 6, 8, 9, 10, 11, 15, 16, 23, 24, 25, 26, 27, 30, 31, 42, 43, 50, 51, 52, 62, 64, 69, 80, 83, 84, 103, 106, 107, 108, 109, 112, 113, 117, 120, 121, 124, 125, 129, 130], "function": [0, 3, 4, 9, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 28, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 59, 60, 61, 62, 64, 65, 66, 67, 68, 69, 71, 73, 74, 75, 76, 77, 79, 80, 81, 83, 84, 85, 86, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 108, 109, 116, 117, 120, 121, 125, 127], "problem_tag": [0, 11, 26, 31, 107], "h": [0, 2, 3, 4, 8, 10, 24, 26, 30, 107, 108, 110, 117, 118, 121, 124, 125, 130], "entir": [0, 3, 11, 31, 115, 125, 127], "state": [0, 5, 6, 9, 10, 11, 14, 17, 21, 24, 26, 29, 30, 31, 32, 33, 35, 36, 39, 40, 41, 42, 43, 44, 48, 53, 59, 64, 66, 79, 84, 85, 90, 91, 92, 95, 96, 100, 102, 104, 105, 107, 108, 111, 113, 114, 116, 117, 118, 122, 124, 125, 127, 130], "includ": [0, 1, 3, 4, 7, 8, 9, 10, 11, 15, 26, 30, 31, 34, 42, 47, 48, 51, 52, 53, 55, 59, 62, 64, 65, 99, 108, 109, 110, 113, 114, 116, 117, 119, 120, 122, 125], "temperatur": [0, 2, 3, 5, 7, 9, 11, 12, 24, 26, 29, 31, 33, 47, 64, 109, 110, 113, 117, 118, 120, 122, 124, 125, 127, 129, 130], "veloc": [0, 3, 4, 5, 7, 9, 11, 26, 31, 36, 65, 84, 105, 109, 110, 113, 120, 122, 125, 126], "etc": [0, 1, 3, 4, 6, 10, 26, 30, 44, 108, 112, 113, 115, 116, 125, 128], "arrai": [0, 9, 10, 11, 12, 14, 16, 19, 23, 24, 26, 31, 36, 44, 47, 48, 52, 55, 62, 64, 96, 109, 113, 118, 125, 126], "statu": [0, 11, 31, 122], "everi": [0, 4, 11, 30, 31, 109, 112, 113, 119, 122, 125, 127, 128], "here": [0, 1, 2, 3, 4, 6, 7, 9, 10, 11, 14, 26, 27, 30, 31, 44, 48, 108, 109, 110, 112, 113, 114, 116, 117, 118, 119, 121, 123, 125, 126, 127, 128], "present": [0, 3, 4, 109, 115, 116, 120, 124], "compress": [0, 4, 8, 116, 118, 125, 130], "equat": [0, 3, 4, 5, 7, 8, 9, 10, 11, 14, 24, 26, 29, 31, 36, 48, 64, 84, 105, 108, 109, 110, 111, 116, 117, 118, 122, 124, 125, 126, 130], "self": [0, 3, 8, 10, 11, 31, 109, 111, 116, 119, 122, 125, 130], "compon": [0, 3, 4, 7, 11, 14, 15, 16, 26, 31, 36, 44, 48, 51, 52, 66, 79, 109, 110, 112, 114, 118, 120, 125, 130], "close": [0, 9, 24, 25, 64, 107, 130], "relat": [0, 4, 6, 11, 14, 31, 48, 117, 118, 120, 122, 127], "ident": [0, 4, 110, 127], "miniati": [0, 114, 130], "colella": [0, 4, 84, 100, 122, 130], "jcp": [0, 130], "2007": [0, 117, 130], "content": [0, 30], "larg": [0, 2, 3, 4, 9, 11, 29, 31, 109, 112, 113, 117, 119, 122, 125, 127, 128], "origin": [0, 1, 3, 4, 9, 65, 109, 116, 117, 120, 122, 124, 125], "paper": [0, 4, 5, 8, 9, 116, 117, 125, 130], "18": [0, 3, 4, 109, 116, 125, 129, 130], "most": [0, 1, 2, 3, 6, 10, 108, 109, 113, 117, 118, 120, 124, 125], "signific": [0, 8], "strategi": [0, 3, 4, 6, 8, 119], "emploi": [0, 7], "regardless": [0, 4, 101, 117, 125, 127], "new": [0, 1, 3, 4, 5, 8, 9, 11, 14, 26, 28, 31, 33, 35, 36, 39, 41, 44, 48, 108, 109, 112, 117, 118, 119, 120, 121, 122, 124, 125, 128, 130], "fundament": [0, 113], "over": [0, 2, 3, 4, 5, 7, 11, 14, 27, 31, 36, 41, 44, 48, 84, 100, 109, 110, 113, 115, 117, 122, 125, 127], "collect": [0, 108, 125], "flux": [0, 3, 5, 9, 11, 15, 23, 24, 25, 29, 30, 31, 36, 41, 50, 51, 62, 64, 66, 79, 100, 107, 109, 113, 120, 122, 125, 130], "regist": [0, 3, 11, 24, 31, 64, 113, 125], "inform": [0, 3, 4, 5, 11, 24, 26, 27, 30, 31, 64, 108, 110, 113, 115, 118, 122, 125, 128], "hyperbol": [0, 3, 11, 24, 31, 64, 122, 130], "part": [0, 2, 3, 4, 26, 36, 109, 110, 113, 117, 120, 125, 127], "delta": [0, 3, 4, 14, 29, 46, 48, 109, 110, 117, 118, 120, 126, 127], "fb": [0, 3, 4], "t_c": 0, "A": [0, 2, 3, 4, 7, 8, 9, 10, 11, 13, 15, 25, 26, 28, 29, 31, 36, 51, 100, 107, 108, 109, 113, 116, 119, 120, 122, 124, 125, 127, 128, 130], "f": [0, 3, 4, 8, 9, 11, 24, 31, 36, 64, 99, 100, 103, 117, 122, 125, 126, 129, 130], "sum": [0, 3, 11, 14, 31, 48, 109, 117, 122], "t_f": 0, "analog": [0, 108, 109, 116, 120], "end": [0, 2, 3, 4, 7, 9, 10, 11, 30, 31, 109, 113, 114, 120, 122, 124, 126, 127], "store": [0, 2, 3, 7, 11, 14, 26, 28, 31, 36, 42, 44, 48, 79, 108, 109, 113, 117, 118, 122, 125], "mismatch": [0, 3, 109], "normal": [0, 3, 4, 6, 11, 30, 31, 36, 110, 122, 125], "phi": [0, 3, 4, 11, 13, 14, 31, 41, 48, 109, 124, 125], "interfac": [0, 3, 9, 11, 24, 29, 31, 36, 64, 79, 100, 109, 114, 118, 122, 125], "f_": [0, 126], "frac": [0, 2, 3, 4, 9, 11, 29, 31, 109, 110, 113, 114, 117, 120, 124, 126, 127], "partial": [0, 2, 3, 4, 9, 29, 114, 117, 120], "n": [0, 2, 3, 4, 10, 11, 24, 26, 31, 36, 49, 61, 64, 69, 77, 109, 113, 117, 120, 122, 124, 125, 127, 130], "want": [0, 1, 2, 3, 6, 7, 11, 26, 30, 31, 44, 108, 109, 113, 114, 117, 122, 124, 125, 126, 127, 128], "composit": [0, 10, 11, 14, 31, 48, 109, 117, 122, 124], "satisfi": [0, 3, 11, 14, 31, 48, 109, 119, 122], "multilevel": [0, 3, 14, 48, 109], "version": [0, 3, 4, 10, 11, 23, 24, 27, 31, 36, 39, 62, 64, 108, 110, 113, 116, 117, 121, 122], "4": [0, 1, 3, 4, 6, 7, 9, 14, 28, 48, 61, 82, 108, 109, 110, 112, 113, 114, 115, 116, 117, 119, 120, 122, 123, 125, 127, 129, 130], "just": [0, 3, 4, 10, 14, 36, 42, 44, 48, 84, 100, 105, 110, 114, 124, 125, 126], "match": [0, 2, 6, 26, 109, 113, 122], "goal": [0, 3], "across": [0, 4, 10, 14, 21, 48, 59, 109, 113, 115, 116, 117, 125], "zero": [0, 3, 4, 9, 11, 24, 26, 29, 30, 31, 36, 64, 109, 110, 122, 127], "out": [0, 3, 4, 6, 7, 9, 11, 24, 30, 31, 64, 108, 113, 115, 117, 120, 122, 125, 128, 129], "At": [0, 2, 3, 4, 5, 9, 10, 30, 109, 120, 121, 124, 125, 126], "can": [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 24, 26, 27, 28, 29, 30, 31, 36, 39, 51, 64, 66, 108, 109, 110, 112, 113, 115, 116, 117, 118, 119, 120, 121, 122, 124, 125, 127, 128], "overlin": 0, "ub": [0, 3, 4, 5, 29, 113, 118, 125], "provision": 0, "assum": [0, 1, 2, 3, 4, 7, 9, 24, 29, 42, 44, 64, 109, 113, 117, 118, 120, 122, 124, 125], "ha": [0, 1, 3, 4, 6, 10, 11, 26, 27, 30, 31, 36, 108, 109, 113, 114, 117, 118, 119, 124, 125, 127], "been": [0, 1, 16, 28, 36, 52, 101, 113, 117, 119, 124, 125], "averag": [0, 1, 3, 4, 7, 9, 11, 31, 36, 42, 109, 114, 122, 125], "down": [0, 1, 4, 11, 29, 31, 113], "underli": [0, 113, 125], "consist": [0, 3, 4, 6, 7, 11, 31, 111, 112, 118, 122, 125, 130], "two": [0, 1, 2, 3, 4, 7, 9, 11, 26, 31, 100, 108, 109, 113, 116, 117, 118, 120, 121, 122, 124, 125, 127, 130], "reflux": [0, 11, 24, 25, 31, 64, 107, 122], "In": [0, 1, 3, 4, 6, 7, 8, 9, 10, 26, 27, 28, 29, 30, 108, 109, 113, 114, 115, 117, 118, 120, 122, 123, 125, 127, 130], "updat": [0, 6, 10, 11, 23, 24, 31, 36, 38, 44, 62, 64, 108, 109, 110, 115, 117, 118, 120, 122, 124, 125, 126], "conserv": [0, 3, 5, 6, 11, 24, 31, 36, 42, 64, 66, 109, 113, 114, 118, 120, 125, 130], "variabl": [0, 1, 2, 3, 6, 7, 9, 10, 11, 14, 15, 26, 27, 28, 30, 31, 36, 37, 43, 45, 48, 51, 61, 66, 69, 72, 78, 82, 89, 99, 103, 108, 109, 110, 114, 117, 118, 120, 122, 125, 126, 128], "adjust": [0, 1, 24, 64, 109, 116], "gravit": [0, 3, 4, 5, 10, 11, 14, 31, 35, 48, 84, 109, 113, 116, 122, 124, 125, 130], "reflect": [0, 26, 36, 122, 125], "rho": [0, 2, 3, 4, 5, 6, 7, 9, 11, 24, 29, 30, 31, 49, 64, 84, 99, 105, 107, 109, 113, 114, 117, 118, 120, 122, 124, 125, 126, 127, 129], "star": [0, 3, 4, 6, 29, 109, 116, 122, 130], "v": [0, 4, 7, 8, 11, 15, 24, 31, 51, 61, 64, 65, 99, 113, 117, 118, 119, 122, 127, 130], "volum": [0, 5, 7, 9, 11, 12, 14, 25, 29, 31, 36, 41, 44, 45, 47, 48, 107, 109, 113, 125, 130], "correct": [0, 2, 3, 4, 5, 8, 10, 11, 17, 21, 25, 31, 41, 53, 59, 107, 111, 117, 122, 125, 130], "support": [0, 3, 8, 10, 14, 27, 48, 108, 113, 114, 117, 120, 123, 124, 127], "onli": [0, 1, 3, 4, 5, 6, 7, 9, 10, 11, 14, 17, 21, 24, 26, 29, 30, 31, 32, 48, 53, 59, 64, 84, 109, 110, 112, 113, 114, 117, 118, 119, 120, 121, 122, 124, 125, 127], "note": [0, 1, 2, 3, 4, 9, 10, 11, 26, 28, 30, 31, 44, 108, 109, 110, 112, 113, 114, 117, 118, 119, 120, 122, 124, 125, 127, 130], "enabl": [0, 4, 10, 26, 27, 29, 30, 108, 109, 110, 112, 113, 114, 115, 117, 118, 120, 122, 124, 125, 127], "disabl": [0, 6, 108, 110, 112, 115, 117, 118, 122, 127], "via": [0, 3, 4, 5, 7, 8, 10, 26, 27, 29, 30, 108, 109, 110, 113, 114, 115, 116, 117, 118, 120, 121, 122, 125, 127, 130], "do_reflux": [0, 122], "axisymmetr": [0, 3, 4, 5, 9, 26, 44, 100, 109], "1d": [0, 1, 4, 6, 9, 109, 113, 125, 127], "spheric": [0, 6, 9, 100, 109, 112, 116, 124, 130], "coordin": [0, 3, 4, 6, 7, 9, 14, 26, 28, 36, 48, 79, 100, 108, 109, 112, 117, 122, 130], "sinc": [0, 1, 3, 4, 6, 7, 28, 30, 109, 110, 117, 122, 125], "express": [0, 3, 26, 109, 114, 117, 123], "diverg": [0, 3, 11, 24, 31, 36, 64, 130], "geometri": [0, 1, 3, 4, 9, 11, 15, 17, 18, 19, 20, 21, 22, 23, 24, 26, 31, 32, 34, 44, 46, 51, 53, 55, 59, 60, 62, 64, 79, 85, 90, 91, 92, 96, 100, 122], "separ": [0, 2, 3, 4, 15, 24, 51, 64, 109, 112, 114, 117, 120, 125], "hydro": [0, 2, 4, 5, 10, 11, 26, 31, 44, 66, 75, 107, 109, 115, 116, 117, 122, 125], "case": [0, 1, 3, 4, 6, 9, 11, 14, 26, 29, 30, 31, 48, 108, 109, 113, 117, 119, 120, 122, 123, 125, 127], "deriv": [0, 4, 7, 11, 19, 24, 25, 26, 31, 55, 64, 107, 109, 120, 122, 125, 127], "well": [0, 1, 3, 4, 7, 26, 105, 109, 110, 113, 117, 118, 122, 124, 125, 128], "account": [0, 3, 4, 109, 120], "e": [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 26, 29, 30, 31, 36, 38, 44, 69, 72, 84, 99, 103, 105, 108, 109, 113, 114, 116, 117, 118, 119, 120, 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125, 130], "second": [0, 1, 3, 4, 7, 11, 29, 31, 36, 117, 120, 125], "respons": [0, 26, 116, 124, 125], "r": [0, 1, 3, 4, 6, 9, 15, 23, 24, 36, 49, 51, 61, 62, 64, 65, 68, 97, 99, 104, 109, 112, 113, 117, 120, 122, 124, 126, 129, 130], "equiv": [0, 4, 29, 109, 127], "pi": [0, 3, 6, 9, 14, 48, 69, 107, 109, 113, 114, 126], "g": [0, 1, 2, 3, 4, 5, 6, 9, 10, 11, 14, 26, 29, 30, 31, 36, 44, 48, 74, 84, 88, 105, 108, 109, 113, 116, 117, 119, 120, 122, 125, 129, 130], "nabla": [0, 3, 4, 9, 14, 29, 48, 109, 113, 114, 117, 118], "cdot": [0, 3, 4, 9, 29, 109, 113, 114, 118, 120, 127], "_c": 0, "Then": [0, 1, 2, 3, 4, 6, 7, 28, 108, 109, 117, 124], "label": [0, 4, 109, 120], "eq": [0, 4, 24, 64, 117, 120], "gravsync": 0, "bf": [0, 3, 4, 6, 113, 114, 120], "final": [0, 3, 4, 11, 26, 29, 31, 36, 109, 110, 112, 113, 119, 120, 121, 122, 124, 125, 127], "directli": [0, 2, 3, 4, 26, 28, 109, 110, 113, 118, 120, 122, 124, 125, 128], "interpol": [0, 1, 4, 6, 7, 11, 14, 26, 30, 31, 48, 109, 118, 122, 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96, 107, 108, 109, 111, 115, 117, 118, 119, 120, 122, 124, 125, 126, 127, 130], "regard": 0, "reli": [0, 4, 113, 124], "itself": [0, 109, 125], "global": [0, 26, 30, 44, 107, 109, 113, 125], "construct": [0, 3, 4, 9, 26, 29, 33, 35, 36, 41, 44, 105, 109, 110, 122, 124, 126, 127, 130], "depend": [0, 1, 2, 3, 4, 6, 9, 10, 11, 26, 28, 31, 108, 109, 115, 117, 118, 120, 125], "wa": [0, 1, 3, 8, 9, 11, 30, 31, 108, 110, 113, 115, 116, 118, 121, 122, 124, 125, 128], "hydrodynam": [0, 3, 5, 7, 8, 11, 26, 29, 31, 36, 41, 79, 100, 113, 115, 116, 117, 118, 122, 123, 125, 130], "associ": [0, 2, 4, 11, 31, 44, 109, 113, 122, 125], "retroact": 0, "one": [0, 1, 3, 4, 7, 9, 10, 11, 24, 26, 27, 30, 31, 42, 64, 109, 110, 113, 115, 116, 117, 119, 120, 121, 122, 124, 125, 127, 128], "imagin": [0, 6, 30], "perfect": [0, 116], "world": 0, "would": [0, 1, 3, 4, 8, 9, 14, 28, 48, 109, 112, 113, 114, 117, 118, 122, 127], "comput": [0, 1, 3, 5, 6, 7, 8, 9, 11, 14, 24, 26, 31, 36, 41, 44, 48, 64, 65, 79, 84, 105, 109, 110, 112, 113, 115, 116, 117, 118, 122, 125, 126, 130], "inde": [0, 2], "did": [0, 11, 31, 113], "subcycl": [0, 3, 5, 11, 31, 109, 122], "march": [0, 28, 130], "along": [0, 4, 7, 9, 11, 31, 109, 113, 118, 120, 122, 124, 125], "timestep": [0, 3, 4, 5, 9, 11, 24, 30, 31, 33, 35, 36, 39, 41, 44, 64, 84, 108, 109, 111, 113, 115, 118, 120, 122, 125, 126], "some": [0, 1, 3, 4, 5, 6, 10, 11, 26, 27, 30, 31, 108, 109, 112, 113, 115, 116, 117, 118, 120, 122, 125, 126, 128], "like": [0, 1, 2, 3, 4, 7, 26, 30, 108, 109, 110, 112, 114, 115, 116, 117, 119, 120, 122, 125, 126, 127, 128], "flash": [0, 4, 116, 130], "actual": [0, 3, 14, 36, 44, 48, 108, 109, 117, 119, 121, 125, 128], "fulli": [0, 3, 4, 122], "complet": [0, 2, 3, 15, 29, 51, 120, 122, 125], "But": [0, 2, 3, 30, 113, 125], "architectur": [0, 115], "up": [0, 3, 8, 9, 11, 17, 21, 29, 31, 44, 53, 59, 108, 109, 110, 111, 113, 116, 117, 119, 122, 124, 125, 127, 128], "alwai": [0, 2, 3, 4, 6, 10, 15, 24, 28, 30, 51, 64, 112, 113, 122, 125, 128], "given": [0, 2, 3, 4, 7, 8, 11, 14, 26, 27, 30, 31, 33, 36, 44, 48, 108, 109, 110, 113, 117, 118, 119, 120, 121, 122, 124, 125, 127], "immedi": [0, 3, 112, 113, 117, 121], "henc": [0, 3], "befor": [0, 1, 3, 4, 6, 11, 30, 31, 33, 44, 105, 109, 110, 118, 120, 121, 122, 127], "occur": [0, 4, 27, 28, 30, 44, 109, 118, 119], "One": [0, 7, 124], "wai": [0, 3, 26, 28, 109, 115, 117, 120, 124, 125], "fix": [0, 6, 8, 27, 28, 30, 108, 120, 122, 124, 129], "suggest": [0, 27, 122, 127], "explicitli": [0, 3, 4, 29, 109, 113, 119, 120, 122, 125], "result": [0, 1, 3, 4, 7, 8, 42, 44, 109, 119, 120, 122, 125, 128, 130], "work": [0, 3, 4, 5, 10, 11, 26, 31, 36, 108, 109, 110, 113, 114, 117, 119, 120, 122, 128], "center": [0, 3, 4, 7, 8, 9, 11, 14, 26, 29, 31, 36, 42, 44, 48, 79, 84, 90, 109, 110, 112, 113, 114, 120, 122, 125, 126, 130], "advect": [0, 3, 4, 7, 79, 116, 118, 120, 122, 125, 130], "mathbf": [0, 4, 109, 120], "rid": 0, "mass": [0, 2, 3, 5, 9, 11, 14, 26, 30, 31, 41, 44, 48, 112, 113, 116, 120, 122, 124, 127, 130], "motion": [0, 7, 120], "see": [0, 2, 3, 4, 5, 6, 9, 11, 26, 29, 30, 31, 36, 108, 109, 112, 113, 115, 117, 118, 120, 122, 124, 125, 127, 128], "explicit": [0, 3, 4, 5, 29, 125, 126], "coupl": [0, 3, 4, 5, 8, 9, 10, 109, 114, 118, 120, 122, 123, 124, 125, 130], "sever": [0, 3, 4, 26, 27, 108, 109, 113, 115, 117, 118, 120, 124, 130], "mean": [0, 1, 2, 4, 7, 9, 24, 26, 28, 29, 64, 108, 109, 113, 114, 115, 117, 119, 122, 125, 127], "corrector": [0, 3, 11, 31, 44, 109, 120], "too": [0, 3, 9, 11, 30, 31, 117, 122], "easi": [0, 128], "write": [0, 3, 4, 10, 11, 26, 31, 113, 116, 122, 125], "energi": [0, 2, 3, 5, 9, 11, 24, 29, 31, 36, 44, 64, 66, 91, 109, 113, 114, 116, 117, 118, 122, 125, 126, 127, 130], "now": [0, 1, 3, 4, 6, 11, 15, 31, 51, 101, 108, 109, 125], "standard": [0, 2, 3, 4, 6, 9, 26, 84, 108, 109, 113, 116, 120, 122], "its": [0, 4, 7, 8, 9, 26, 28, 108, 109, 113, 117, 120, 124, 125, 127], "linear": [0, 3, 4, 9, 10, 36, 79, 105, 109, 114, 116, 122, 125, 130], "acceler": [0, 3, 5, 24, 25, 41, 64, 65, 107, 109, 113, 117, 122, 125], "repres": [0, 1, 2, 4, 7, 42, 109, 114, 117, 118, 120, 124], "more": [0, 3, 4, 6, 7, 26, 27, 30, 108, 109, 110, 113, 115, 117, 119, 120, 122, 124, 125, 127, 128], "complic": [0, 3], "might": [0, 1, 2, 26, 30], "easili": [0, 4, 24, 64, 113, 125], "represent": 0, "nuclear": [0, 4, 5, 8, 113, 115, 118, 125, 127, 130], "reaction": [0, 3, 4, 5, 8, 9, 10, 11, 31, 39, 42, 108, 111, 114, 115, 116, 117, 122, 123, 125, 130], "network": [0, 4, 5, 6, 10, 26, 30, 108, 112, 113, 115, 118, 121, 127, 130], "analyt": [0, 2, 9, 113, 116, 123], "possibl": [0, 3, 6, 7, 30, 108, 109, 117, 118, 120], "becaus": [0, 1, 3, 4, 6, 9, 11, 31, 44, 109, 112, 117, 119, 120, 125], "instead": [0, 2, 3, 4, 26, 30, 108, 113, 114, 117, 118, 125, 127], "choos": [0, 3, 4, 108, 109, 112, 120, 122, 125, 127], "save": [0, 2, 3, 11, 14, 31, 33, 35, 36, 39, 41, 44, 48, 117, 129], "were": [0, 8, 9, 30, 109, 113, 119, 125], "subtract": 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36, 64, 108, 113, 122, 124, 125, 126, 127, 128], "high": [0, 1, 3, 4, 9, 109, 110, 112, 122, 125, 126, 130], "paramet": [0, 3, 4, 11, 12, 14, 15, 16, 17, 19, 21, 22, 23, 24, 27, 30, 31, 32, 33, 35, 36, 39, 41, 44, 47, 48, 51, 52, 53, 55, 59, 62, 64, 65, 66, 79, 84, 85, 86, 90, 91, 92, 94, 96, 100, 101, 105, 108, 109, 111, 113, 114, 118, 119, 120, 122, 123, 125, 126, 127, 129], "update_sources_after_reflux": [0, 122], "automat": [0, 7, 10, 27, 28, 108, 115, 125], "amend": 0, "futur": [0, 10], "releas": [0, 3, 4, 5, 108, 117, 124], "simul": [0, 1, 2, 3, 4, 6, 7, 9, 11, 14, 26, 31, 44, 48, 85, 90, 91, 92, 96, 108, 109, 113, 115, 119, 122, 125, 128, 130], "take": [0, 2, 3, 4, 6, 8, 9, 11, 27, 30, 31, 36, 42, 100, 108, 109, 110, 112, 115, 117, 119, 120, 121, 122, 123, 125, 126, 127, 129], "howev": [0, 1, 4, 7, 29, 117, 120, 124], "situat": [0, 4, 108, 109], "consid": [0, 1, 3, 4, 7, 29, 109, 119, 120, 125, 127], "discuss": [0, 3, 4, 8, 109, 112, 116, 117, 120, 125], "about": [0, 3, 8, 11, 26, 30, 31, 108, 109, 113, 117, 120, 122, 125, 126], "ratio": [0, 1, 4, 11, 17, 21, 31, 53, 59, 109, 112, 122], "taken": [0, 3, 109, 113, 117, 125, 127], "advoc": 0, "consequ": [0, 4], "thu": [0, 1, 4, 6, 109, 112], "moment": [0, 3, 10, 109, 110], "": [0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 14, 23, 26, 27, 29, 30, 31, 36, 38, 44, 48, 62, 73, 74, 84, 97, 98, 100, 108, 109, 110, 112, 114, 115, 116, 117, 120, 122, 124, 125, 127, 128, 130], "thought": [0, 6], "reveal": 0, "modifi": [0, 1, 4, 8, 10, 14, 48, 109, 113, 117, 119, 120, 128], "didn": [0, 3], "full": [0, 3, 4, 5, 9, 10, 11, 26, 31, 41, 100, 108, 109, 114, 123, 125, 127, 128], "old": [0, 3, 9, 11, 14, 31, 33, 35, 36, 39, 41, 44, 48, 109, 118, 120, 122, 125], "miss": [0, 30], "assumpt": [0, 109, 122], "make": [0, 1, 3, 4, 6, 9, 11, 14, 24, 26, 30, 31, 48, 64, 108, 109, 110, 112, 113, 115, 117, 118, 119, 120, 121, 122, 125, 127, 128, 129], "answer": 0, "ye": 0, "date": [0, 108], "cours": [0, 6, 113, 122], "last": [0, 3, 6, 7, 11, 24, 26, 28, 30, 31, 64, 110, 117, 122, 125], "equal": [0, 1, 4, 7, 109, 112, 117, 120, 123, 125, 127], "true": [0, 3, 4, 6, 7, 10, 11, 14, 26, 27, 29, 30, 31, 36, 42, 44, 45, 48, 66, 84, 105, 108, 109, 110, 112, 114, 115, 117, 118, 119, 120, 122, 124, 125], "piecewis": [0, 3, 4, 9, 30, 36, 105, 114, 122, 130], "constant": [0, 2, 3, 4, 5, 9, 10, 17, 21, 24, 29, 30, 53, 59, 64, 109, 110, 117, 120, 122, 124, 130], "order": [0, 3, 4, 5, 6, 7, 8, 10, 11, 29, 31, 36, 108, 109, 119, 122, 123, 125, 130], "accur": [0, 3, 36, 109, 110, 116, 120, 122, 123, 124], "3": [0, 1, 3, 4, 5, 6, 7, 9, 10, 11, 24, 26, 29, 31, 36, 43, 45, 49, 61, 64, 65, 68, 69, 77, 79, 80, 82, 84, 100, 103, 108, 109, 110, 112, 113, 114, 116, 117, 119, 120, 122, 123, 125, 127, 129, 130], "fair": 0, "halfwai": [0, 112], "half": [0, 3, 4, 9, 109, 127], "mathemat": 0, "split": [0, 3, 11, 31, 114, 130], "weight": [0, 3, 9, 11, 31, 36, 44, 117, 122], "noth": [0, 3, 4, 6, 11, 31, 109, 117, 122], "prevent": [0, 9, 11, 30, 31, 117, 122, 126, 127], "u": [0, 3, 4, 6, 7, 11, 14, 28, 30, 31, 36, 43, 48, 61, 66, 83, 84, 99, 108, 109, 110, 113, 114, 116, 118, 120, 122, 124, 125, 127], "point": [0, 3, 6, 9, 11, 14, 26, 30, 31, 48, 108, 116, 117, 120, 122, 124, 129, 130], "why": [0, 114], "potenti": [0, 3, 10, 14, 27, 28, 41, 48, 109, 113, 116, 118, 122, 124, 125], "condit": [0, 4, 5, 9, 13, 14, 28, 32, 36, 48, 85, 116, 118, 122, 124, 126, 127, 130], "begin": [0, 2, 3, 4, 9, 26, 28, 30, 108, 109, 114, 120, 126], "practic": [0, 2, 4, 109, 111, 115, 117, 130], "call": [0, 1, 2, 3, 4, 6, 10, 11, 14, 15, 24, 30, 31, 36, 48, 51, 64, 109, 117, 118, 120, 122, 124, 125, 127, 128], "modif": [0, 3, 4], "being": [0, 4, 30, 113, 115, 116, 125, 126, 127], "appropri": [0, 11, 14, 26, 29, 31, 48, 109, 110, 117, 120], "remain": [0, 4, 9, 109, 120, 122], "unchang": [0, 3, 4, 110, 118, 120, 122], "intent": [0, 26], "simpli": [0, 3, 4, 26, 30, 36, 110, 117, 118, 120, 121, 124, 125, 128], "instantan": [0, 7, 42], "method": [0, 4, 7, 9, 10, 11, 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119, 120, 121, 122, 124, 125, 126, 127], "limit": [0, 5, 9, 11, 24, 30, 31, 36, 64, 66, 84, 100, 105, 109, 110, 113, 114, 118, 122, 124, 125, 127, 130], "scheme": [0, 3, 4, 7, 36, 114, 115, 117, 122, 123, 130], "from": [0, 3, 4, 5, 7, 9, 10, 11, 14, 24, 26, 28, 30, 31, 36, 44, 48, 64, 65, 84, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 122, 124, 125, 126, 127, 128, 129, 130], "input": [0, 1, 2, 3, 4, 6, 7, 10, 11, 24, 26, 27, 29, 30, 31, 36, 41, 42, 44, 64, 66, 74, 79, 101, 105, 108, 109, 111, 113, 116, 117, 118, 119, 120, 121, 122, 124, 125, 126, 127], "file": [0, 3, 5, 6, 8, 10, 11, 14, 27, 28, 29, 30, 108, 109, 111, 113, 116, 117, 118, 119, 120, 121, 122, 125, 126, 128, 129], "exampl": [0, 1, 2, 3, 4, 7, 9, 26, 28, 30, 108, 109, 112, 113, 114, 117, 118, 119, 124, 127], "refinement_ind": 0, "den": [0, 26], "temp": [0, 4, 23, 24, 62, 64, 108, 113, 128, 129], "max_level": [0, 1, 6, 112], "value_great": 0, "2": [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 19, 24, 26, 29, 30, 31, 36, 42, 43, 48, 51, 52, 55, 61, 64, 69, 79, 82, 83, 84, 90, 100, 103, 105, 108, 109, 110, 112, 113, 114, 115, 116, 117, 119, 120, 122, 123, 124, 125, 126, 127, 128, 129, 130], "field_nam": 0, "value_less": 0, "list": [0, 1, 4, 8, 11, 26, 30, 31, 111, 113, 117, 119, 121], "name": [0, 1, 3, 4, 5, 6, 7, 9, 10, 11, 26, 30, 31, 86, 94, 108, 112, 113, 119, 121, 122, 125], "For": [0, 1, 2, 3, 4, 6, 7, 9, 10, 11, 15, 24, 26, 27, 30, 31, 36, 44, 51, 64, 79, 108, 109, 110, 113, 114, 115, 117, 118, 119, 120, 121, 122, 124, 125, 128], "each": [0, 2, 3, 4, 5, 7, 9, 10, 11, 12, 14, 21, 24, 26, 28, 30, 31, 36, 47, 48, 59, 64, 108, 109, 110, 112, 113, 115, 117, 119, 122, 125, 126, 127, 128], "accept": [0, 1, 118], "predefin": 0, "field": [0, 9, 11, 14, 29, 31, 35, 36, 48, 66, 90, 108, 109, 111, 114, 117, 122, 125, 128, 129, 130], "when": [0, 1, 2, 3, 4, 6, 8, 10, 11, 17, 21, 26, 28, 30, 31, 36, 53, 59, 109, 110, 113, 115, 117, 118, 119, 120, 121, 122, 125, 127, 128], "These": [0, 3, 4, 5, 10, 26, 29, 108, 109, 110, 113, 116, 117, 119, 121, 124, 125, 127, 128], "maximum": [0, 3, 9, 14, 26, 48, 108, 109, 112, 113, 118, 119, 122, 124, 127, 128, 129], "start_tim": 0, "start": [0, 1, 3, 4, 5, 6, 7, 11, 26, 31, 109, 110, 111, 112, 113, 116, 121, 122, 125, 126, 127, 128], "end_tim": 0, "stop": [0, 24, 30, 64, 117, 122, 127], "valu": [0, 1, 2, 4, 6, 7, 11, 14, 17, 21, 24, 26, 29, 30, 31, 48, 53, 55, 59, 63, 64, 84, 98, 108, 109, 110, 112, 113, 114, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129], "abov": [0, 1, 3, 4, 9, 16, 28, 52, 109, 110, 112, 116, 117, 120, 122, 124, 125, 127], "below": [0, 3, 4, 6, 11, 27, 29, 30, 31, 108, 109, 117, 119, 120, 122, 125, 126, 127], "absolut": [0, 14, 24, 48, 64, 109, 117], "between": [0, 1, 4, 5, 7, 9, 10, 11, 14, 27, 29, 31, 48, 109, 110, 112, 113, 115, 120, 122, 124, 125, 126], "adjac": [0, 109, 122], "cell": [0, 1, 3, 4, 6, 7, 9, 11, 14, 16, 26, 30, 31, 36, 41, 42, 44, 48, 52, 79, 84, 109, 110, 112, 114, 119, 120, 122, 125, 130], "relative_gradi": 0, "rel": [0, 14, 24, 48, 64, 108, 109, 117, 120, 122, 130], "string": [0, 6, 11, 14, 24, 30, 31, 37, 44, 48, 64, 86, 94, 121, 122], "code": [0, 1, 3, 4, 5, 6, 8, 9, 10, 26, 29, 30, 109, 112, 113, 115, 116, 118, 121, 122, 127, 130], "If": [0, 1, 2, 3, 4, 6, 7, 8, 9, 10, 11, 14, 19, 26, 27, 30, 31, 42, 48, 55, 108, 109, 110, 112, 113, 114, 117, 118, 119, 120, 122, 125, 127, 128], "indic": [0, 4, 6, 11, 26, 30, 31, 36, 109, 120, 124, 125, 127], "ad": [0, 3, 6, 26, 27, 33, 36, 109, 115, 122, 125, 126], "either": [0, 3, 4, 7, 10, 11, 26, 28, 31, 36, 66, 108, 110, 113, 116, 117, 125, 127], "must": [0, 1, 3, 4, 6, 7, 11, 14, 19, 24, 28, 29, 31, 48, 55, 64, 108, 109, 112, 117, 119, 120, 122, 124, 127], "physic": [0, 5, 7, 13, 14, 24, 48, 64, 84, 105, 109, 112, 120, 121, 122, 130], "boundari": [0, 5, 10, 13, 14, 32, 36, 48, 84, 85, 105, 116, 120, 122, 126], "cannot": [0, 4, 30, 117], "poisson": [0, 3, 5, 14, 48, 113, 122, 124, 125, 130], "graviti": [0, 3, 4, 5, 8, 11, 25, 26, 31, 107, 110, 111, 112, 113, 116, 119, 120, 121, 130], "solver": [0, 3, 4, 8, 9, 10, 15, 24, 25, 26, 36, 51, 64, 100, 107, 109, 110, 112, 113, 114, 115, 116, 119, 122, 123, 125, 127, 130], "your": [0, 1, 2, 3, 4, 6, 7, 8, 29, 30, 108, 109, 111, 112, 113, 116, 117, 122, 125, 127, 128], "met": 0, "thei": [0, 2, 3, 4, 10, 11, 31, 108, 109, 110, 112, 113, 117, 118, 119, 125], "ignor": [0, 3, 4, 17, 21, 26, 29, 30, 53, 59, 109, 112, 117, 127], "sometim": [0, 4, 6, 27, 125], "wish": [0, 4, 6, 108, 114], "forc": [0, 30, 65, 84, 113, 122, 125, 127], "derefin": 0, "even": [0, 4, 6, 10, 11, 30, 31, 109, 116, 119, 122, 130], "other": [0, 1, 2, 3, 4, 7, 11, 24, 26, 30, 31, 33, 64, 108, 109, 110, 113, 117, 119, 120, 121, 122, 124, 127], "accomplish": 0, "anoth": [0, 3, 7, 11, 31, 42, 109, 113, 116, 120, 122, 124], "ani": [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 14, 26, 28, 30, 31, 36, 39, 44, 48, 101, 108, 109, 110, 112, 113, 115, 119, 121, 125, 127], "less": [0, 108, 113, 122], "than": [0, 1, 3, 4, 6, 11, 30, 31, 108, 109, 117, 119, 120, 122, 124, 127, 128], "e4": 0, "could": [0, 1, 4, 10, 30, 117, 119, 125, 127], "do": [0, 1, 2, 3, 4, 6, 9, 10, 11, 14, 26, 27, 28, 30, 31, 36, 44, 48, 65, 108, 109, 112, 113, 114, 115, 117, 118, 119, 120, 122, 123, 125, 127, 128], "dencutoff": 0, "lise": 0, "under": [0, 8, 10, 26, 36, 84, 108, 109], "appear": [0, 3, 4, 8, 9, 28, 29, 110, 112, 113, 114, 116, 120, 125], "after": [0, 1, 3, 4, 7, 10, 11, 24, 28, 31, 44, 64, 109, 112, 113, 114, 117, 122], "those": [0, 1, 3, 4, 5, 8, 29, 108, 109, 113, 118, 122, 125, 128], "so": [0, 1, 2, 3, 4, 10, 11, 15, 24, 26, 28, 29, 30, 31, 36, 51, 64, 66, 108, 109, 110, 113, 115, 117, 118, 119, 120, 122, 124, 125, 126, 127, 128, 129, 130], "appli": [0, 3, 4, 5, 9, 11, 26, 28, 31, 36, 44, 109, 117, 119, 120, 122, 124, 126], "all": [0, 1, 2, 4, 6, 7, 8, 9, 10, 11, 14, 16, 24, 26, 27, 30, 31, 36, 44, 48, 52, 64, 101, 108, 109, 110, 112, 113, 114, 115, 117, 118, 119, 120, 121, 122, 123, 124, 125, 127, 128], "done": [0, 2, 3, 4, 5, 6, 8, 9, 10, 11, 26, 27, 28, 30, 31, 108, 109, 110, 113, 114, 115, 120, 122, 125], "abil": [0, 9, 116], "own": [0, 28, 108, 111, 113, 116, 117, 125], "through": [0, 3, 4, 9, 26, 28, 30, 36, 39, 100, 105, 108, 109, 112, 116, 117, 118, 120, 122, 125, 126, 127, 128, 129], "c": [0, 2, 3, 4, 6, 8, 9, 10, 11, 15, 16, 23, 24, 25, 26, 27, 30, 31, 42, 43, 50, 51, 52, 62, 64, 69, 80, 83, 84, 103, 106, 107, 108, 109, 112, 113, 117, 120, 121, 124, 125, 128, 129, 130], "function": [0, 3, 4, 9, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 28, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 59, 60, 61, 62, 64, 65, 66, 67, 68, 69, 71, 73, 74, 75, 76, 77, 79, 80, 81, 83, 84, 85, 86, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 108, 109, 116, 117, 120, 121, 125, 127], "problem_tag": [0, 11, 26, 31, 107], "h": [0, 2, 3, 4, 8, 10, 24, 26, 30, 107, 108, 110, 117, 118, 121, 124, 125, 130], "entir": [0, 3, 11, 31, 115, 125, 127], "state": [0, 5, 6, 9, 10, 11, 14, 17, 21, 24, 26, 29, 30, 31, 32, 33, 35, 36, 39, 40, 41, 42, 43, 44, 48, 53, 59, 64, 66, 79, 84, 85, 90, 91, 92, 95, 96, 100, 102, 104, 105, 107, 108, 111, 113, 114, 116, 117, 118, 122, 124, 125, 127, 130], "includ": [0, 1, 3, 4, 7, 8, 9, 10, 11, 15, 26, 30, 31, 34, 42, 47, 48, 51, 52, 53, 55, 59, 62, 64, 65, 99, 108, 109, 110, 113, 114, 116, 117, 119, 120, 122, 125], "temperatur": [0, 2, 3, 5, 7, 9, 11, 12, 24, 26, 29, 31, 33, 47, 64, 108, 109, 110, 113, 117, 118, 120, 122, 124, 125, 127, 128, 129, 130], "veloc": [0, 3, 4, 5, 7, 9, 11, 26, 31, 36, 65, 84, 105, 109, 110, 113, 120, 122, 125, 126], "etc": [0, 1, 3, 4, 6, 10, 26, 30, 44, 108, 112, 113, 115, 116, 125, 128], "arrai": [0, 9, 10, 11, 12, 14, 16, 19, 23, 24, 26, 31, 36, 44, 47, 48, 52, 55, 62, 64, 96, 109, 113, 118, 125, 126], "statu": [0, 11, 31, 122], "everi": [0, 4, 11, 30, 31, 109, 112, 113, 119, 122, 125, 127, 128], "here": [0, 1, 2, 3, 4, 6, 7, 9, 10, 11, 14, 26, 27, 30, 31, 44, 48, 108, 109, 110, 112, 113, 114, 116, 117, 118, 119, 121, 123, 125, 126, 127, 128], "present": [0, 3, 4, 109, 115, 116, 120, 124], "compress": [0, 4, 8, 116, 118, 125, 130], "equat": [0, 3, 4, 5, 7, 8, 9, 10, 11, 14, 24, 26, 29, 31, 36, 48, 64, 84, 105, 108, 109, 110, 111, 116, 117, 118, 122, 124, 125, 126, 130], "self": [0, 3, 8, 10, 11, 31, 109, 111, 116, 119, 122, 125, 130], "compon": [0, 3, 4, 7, 11, 14, 15, 16, 26, 31, 36, 44, 48, 51, 52, 66, 79, 109, 110, 112, 114, 118, 120, 125, 130], "close": [0, 9, 24, 25, 64, 107, 130], "relat": [0, 4, 6, 11, 14, 31, 48, 117, 118, 120, 122, 127], "ident": [0, 4, 110, 127], "miniati": [0, 114, 130], "colella": [0, 4, 84, 100, 122, 130], "jcp": [0, 130], "2007": [0, 117, 130], "content": [0, 30], "larg": [0, 2, 3, 4, 9, 11, 29, 31, 109, 112, 113, 117, 119, 122, 125, 127, 128], "origin": [0, 1, 3, 4, 9, 65, 109, 116, 117, 120, 122, 124, 125], "paper": [0, 4, 5, 8, 9, 116, 117, 125, 130], "18": [0, 3, 4, 108, 109, 116, 125, 128, 129, 130], "most": [0, 1, 2, 3, 6, 10, 108, 109, 113, 117, 118, 120, 124, 125], "signific": [0, 8], "strategi": [0, 3, 4, 6, 8, 119], "emploi": [0, 7], "regardless": [0, 4, 101, 117, 125, 127], "new": [0, 1, 3, 4, 5, 8, 9, 11, 14, 26, 28, 31, 33, 35, 36, 39, 41, 44, 48, 108, 109, 112, 117, 118, 119, 120, 121, 122, 124, 125, 128, 130], "fundament": [0, 113], "over": [0, 2, 3, 4, 5, 7, 11, 14, 27, 31, 36, 41, 44, 48, 84, 100, 109, 110, 113, 115, 117, 122, 125, 127], "collect": [0, 108, 125], "flux": [0, 3, 5, 9, 11, 15, 23, 24, 25, 29, 30, 31, 36, 41, 50, 51, 62, 64, 66, 79, 100, 107, 109, 113, 120, 122, 125, 130], "regist": [0, 3, 11, 24, 31, 64, 113, 125], "inform": [0, 3, 4, 5, 11, 24, 26, 27, 30, 31, 64, 108, 110, 113, 115, 118, 122, 125, 128], "hyperbol": [0, 3, 11, 24, 31, 64, 122, 130], "part": [0, 2, 3, 4, 26, 36, 109, 110, 113, 117, 120, 125, 127], "delta": [0, 3, 4, 14, 29, 46, 48, 109, 110, 117, 118, 120, 126, 127], "fb": [0, 3, 4], "t_c": 0, "A": [0, 2, 3, 4, 7, 8, 9, 10, 11, 13, 15, 25, 26, 28, 29, 31, 36, 51, 100, 107, 108, 109, 113, 116, 119, 120, 122, 124, 125, 127, 128, 130], "f": [0, 3, 4, 8, 9, 11, 24, 31, 36, 64, 99, 100, 103, 108, 117, 122, 125, 126, 128, 129, 130], "sum": [0, 3, 11, 14, 31, 48, 109, 117, 122], "t_f": 0, "analog": [0, 108, 109, 116, 120], "end": [0, 2, 3, 4, 7, 9, 10, 11, 30, 31, 109, 113, 114, 120, 122, 124, 126, 127], "store": [0, 2, 3, 7, 11, 14, 26, 28, 31, 36, 42, 44, 48, 79, 108, 109, 113, 117, 118, 122, 125], "mismatch": [0, 3, 109], "normal": [0, 3, 4, 6, 11, 30, 31, 36, 110, 122, 125], "phi": [0, 3, 4, 11, 13, 14, 31, 41, 48, 109, 124, 125], "interfac": [0, 3, 9, 11, 24, 29, 31, 36, 64, 79, 100, 109, 114, 118, 122, 125], "f_": [0, 126], "frac": [0, 2, 3, 4, 9, 11, 29, 31, 109, 110, 113, 114, 117, 120, 124, 126, 127], "partial": [0, 2, 3, 4, 9, 29, 114, 117, 120], "n": [0, 2, 3, 4, 10, 11, 24, 26, 31, 36, 49, 61, 64, 69, 77, 109, 113, 117, 120, 122, 124, 125, 127, 130], "want": [0, 1, 2, 3, 6, 7, 11, 26, 30, 31, 44, 108, 109, 113, 114, 117, 122, 124, 125, 126, 127, 128], "composit": [0, 10, 11, 14, 31, 48, 109, 117, 122, 124], "satisfi": [0, 3, 11, 14, 31, 48, 109, 119, 122], "multilevel": [0, 3, 14, 48, 109], "version": [0, 3, 4, 10, 11, 23, 24, 27, 31, 36, 39, 62, 64, 108, 110, 113, 116, 117, 121, 122], "4": [0, 1, 3, 4, 6, 7, 9, 14, 28, 48, 61, 82, 108, 109, 110, 112, 113, 114, 115, 116, 117, 119, 120, 122, 123, 125, 127, 128, 129, 130], "just": [0, 3, 4, 10, 14, 36, 42, 44, 48, 84, 100, 105, 110, 114, 124, 125, 126], "match": [0, 2, 6, 26, 109, 113, 122], "goal": [0, 3], "across": [0, 4, 10, 14, 21, 48, 59, 109, 113, 115, 116, 117, 125], "zero": [0, 3, 4, 9, 11, 24, 26, 29, 30, 31, 36, 64, 109, 110, 122, 127], "out": [0, 3, 4, 6, 7, 9, 11, 24, 30, 31, 64, 108, 113, 115, 117, 120, 122, 125, 128, 129], "At": [0, 2, 3, 4, 5, 9, 10, 30, 109, 120, 121, 124, 125, 126], "can": [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 24, 26, 27, 28, 29, 30, 31, 36, 39, 51, 64, 66, 108, 109, 110, 112, 113, 115, 116, 117, 118, 119, 120, 121, 122, 124, 125, 127, 128], "overlin": 0, "ub": [0, 3, 4, 5, 29, 113, 118, 125], "provision": 0, "assum": [0, 1, 2, 3, 4, 7, 9, 24, 29, 42, 44, 64, 109, 113, 117, 118, 120, 122, 124, 125], "ha": [0, 1, 3, 4, 6, 10, 11, 26, 27, 30, 31, 36, 108, 109, 113, 114, 117, 118, 119, 124, 125, 127], "been": [0, 1, 16, 28, 36, 52, 101, 113, 117, 119, 124, 125], "averag": [0, 1, 3, 4, 7, 9, 11, 31, 36, 42, 109, 114, 122, 125], "down": [0, 1, 4, 11, 29, 31, 113], "underli": [0, 113, 125], "consist": [0, 3, 4, 6, 7, 11, 31, 111, 112, 118, 122, 125, 130], "two": [0, 1, 2, 3, 4, 7, 9, 11, 26, 31, 100, 108, 109, 113, 116, 117, 118, 120, 121, 122, 124, 125, 127, 130], "reflux": [0, 11, 24, 25, 31, 64, 107, 122], "In": [0, 1, 3, 4, 6, 7, 8, 9, 10, 26, 27, 28, 29, 30, 108, 109, 113, 114, 115, 117, 118, 120, 122, 123, 125, 127, 130], "updat": [0, 6, 10, 11, 23, 24, 31, 36, 38, 44, 62, 64, 108, 109, 110, 115, 117, 118, 120, 122, 124, 125, 126], "conserv": [0, 3, 5, 6, 11, 24, 31, 36, 42, 64, 66, 109, 113, 114, 118, 120, 125, 130], "variabl": [0, 1, 2, 3, 6, 7, 9, 10, 11, 14, 15, 26, 27, 28, 30, 31, 36, 37, 43, 45, 48, 51, 61, 66, 69, 72, 78, 82, 89, 99, 103, 108, 109, 110, 114, 117, 118, 120, 122, 125, 126, 128], "adjust": [0, 1, 24, 64, 109, 116], "gravit": [0, 3, 4, 5, 10, 11, 14, 31, 35, 48, 84, 109, 113, 116, 122, 124, 125, 130], "reflect": [0, 26, 36, 122, 125], "rho": [0, 2, 3, 4, 5, 6, 7, 9, 11, 24, 29, 30, 31, 49, 64, 84, 99, 105, 107, 108, 109, 113, 114, 117, 118, 120, 122, 124, 125, 126, 127, 128, 129], "star": [0, 3, 4, 6, 29, 109, 116, 122, 130], "v": [0, 4, 7, 8, 11, 15, 24, 31, 51, 61, 64, 65, 99, 113, 117, 118, 119, 122, 127, 130], "volum": [0, 5, 7, 9, 11, 12, 14, 25, 29, 31, 36, 41, 44, 45, 47, 48, 107, 109, 113, 125, 130], "correct": [0, 2, 3, 4, 5, 8, 10, 11, 17, 21, 25, 31, 41, 53, 59, 107, 111, 117, 122, 125, 130], "support": [0, 3, 8, 10, 14, 27, 48, 108, 113, 114, 117, 120, 123, 124, 127], "onli": [0, 1, 3, 4, 5, 6, 7, 9, 10, 11, 14, 17, 21, 24, 26, 29, 30, 31, 32, 48, 53, 59, 64, 84, 109, 110, 112, 113, 114, 117, 118, 119, 120, 121, 122, 124, 125, 127], "note": [0, 1, 2, 3, 4, 9, 10, 11, 26, 28, 30, 31, 44, 108, 109, 110, 112, 113, 114, 117, 118, 119, 120, 122, 124, 125, 127, 130], "enabl": [0, 4, 10, 26, 27, 29, 30, 108, 109, 110, 112, 113, 114, 115, 117, 118, 120, 122, 124, 125, 127], "disabl": [0, 6, 108, 110, 112, 115, 117, 118, 122, 127], "via": [0, 3, 4, 5, 7, 8, 10, 26, 27, 29, 30, 108, 109, 110, 113, 114, 115, 116, 117, 118, 120, 121, 122, 125, 127, 130], "do_reflux": [0, 122], "axisymmetr": [0, 3, 4, 5, 9, 26, 44, 100, 109], "1d": [0, 1, 4, 6, 9, 109, 113, 125, 127], "spheric": [0, 6, 9, 100, 109, 112, 116, 124, 130], "coordin": [0, 3, 4, 6, 7, 9, 14, 26, 28, 36, 48, 79, 100, 108, 109, 112, 117, 122, 130], "sinc": [0, 1, 3, 4, 6, 7, 28, 30, 109, 110, 117, 122, 125], "express": [0, 3, 26, 109, 114, 117, 123], "diverg": [0, 3, 11, 24, 31, 36, 64, 130], "geometri": [0, 1, 3, 4, 9, 11, 15, 17, 18, 19, 20, 21, 22, 23, 24, 26, 31, 32, 34, 44, 46, 51, 53, 55, 59, 60, 62, 64, 79, 85, 90, 91, 92, 96, 100, 122], "separ": [0, 2, 3, 4, 15, 24, 51, 64, 109, 112, 114, 117, 120, 125], "hydro": [0, 2, 4, 5, 10, 11, 26, 31, 44, 66, 75, 107, 109, 115, 116, 117, 122, 125], "case": [0, 1, 3, 4, 6, 9, 11, 14, 26, 29, 30, 31, 48, 108, 109, 113, 117, 119, 120, 122, 123, 125, 127], "deriv": [0, 4, 7, 11, 19, 24, 25, 26, 31, 55, 64, 107, 109, 120, 122, 125, 127], "well": [0, 1, 3, 4, 7, 26, 105, 109, 110, 113, 117, 118, 122, 124, 125, 128], "account": [0, 3, 4, 109, 120], "e": [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 26, 29, 30, 31, 36, 38, 44, 69, 72, 84, 99, 103, 105, 108, 109, 113, 114, 116, 117, 118, 119, 120, 122, 125, 127, 130], "due": [0, 3, 4, 30, 44, 108, 109, 116, 120, 122, 125], "On": [0, 3, 24, 64, 108, 109, 117, 130], "form": [0, 3, 5, 9, 11, 26, 31, 36, 108, 109, 112, 113, 114, 117, 121, 124, 125, 126], "residu": [0, 24, 64, 117], "compos": [0, 125], "contribut": [0, 3, 4, 5, 8, 11, 15, 29, 31, 44, 51, 109, 114, 117, 130], "first": [0, 1, 2, 3, 4, 6, 7, 10, 11, 17, 21, 25, 26, 28, 30, 31, 36, 53, 59, 84, 107, 108, 109, 110, 113, 114, 115, 116, 117, 120, 122, 123, 124, 125, 127, 128], "degre": 0, "current": [0, 2, 3, 5, 8, 10, 11, 14, 28, 29, 31, 33, 35, 36, 39, 41, 44, 48, 65, 108, 109, 113, 114, 115, 120, 122, 125, 127], "doe": [0, 1, 3, 4, 6, 9, 10, 11, 26, 29, 31, 36, 108, 109, 110, 113, 116, 117, 120, 122, 124, 125], "have": [0, 1, 2, 3, 4, 5, 6, 8, 10, 11, 14, 16, 27, 28, 30, 31, 48, 52, 101, 108, 109, 110, 112, 113, 114, 115, 116, 117, 119, 120, 122, 124, 125, 127, 128], "solv": [0, 3, 4, 7, 8, 11, 14, 15, 25, 31, 36, 48, 51, 100, 107, 109, 114, 117, 118, 120, 122, 123, 124, 125, 130], "second": [0, 1, 3, 4, 7, 11, 29, 31, 36, 117, 120, 125], "respons": [0, 26, 116, 124, 125], "r": [0, 1, 3, 4, 6, 9, 15, 23, 24, 36, 49, 51, 61, 62, 64, 65, 68, 97, 99, 104, 108, 109, 112, 113, 117, 120, 122, 124, 126, 128, 129, 130], "equiv": [0, 4, 29, 109, 127], "pi": [0, 3, 6, 9, 14, 48, 69, 107, 109, 113, 114, 126], "g": [0, 1, 2, 3, 4, 5, 6, 9, 10, 11, 14, 26, 29, 30, 31, 36, 44, 48, 74, 84, 88, 105, 108, 109, 113, 116, 117, 119, 120, 122, 125, 128, 129, 130], "nabla": [0, 3, 4, 9, 14, 29, 48, 109, 113, 114, 117, 118], "cdot": [0, 3, 4, 9, 29, 109, 113, 114, 118, 120, 122, 127], "_c": 0, "Then": [0, 1, 2, 3, 4, 6, 7, 28, 108, 109, 117, 124], "label": [0, 4, 109, 120], "eq": [0, 4, 24, 64, 117, 120], "gravsync": 0, "bf": [0, 3, 4, 6, 113, 114, 120], "final": [0, 3, 4, 11, 26, 29, 31, 36, 109, 110, 112, 113, 119, 120, 121, 122, 124, 125, 127], "directli": [0, 2, 3, 4, 26, 28, 109, 110, 113, 118, 120, 122, 124, 125, 128], "interpol": [0, 1, 4, 6, 7, 11, 14, 26, 30, 31, 48, 109, 118, 122, 125], "coarsest": [0, 1, 6, 109, 112], "calcul": [0, 1, 4, 9, 11, 14, 31, 33, 36, 44, 48, 109, 112, 113, 117, 122, 124, 127, 130], "transmit": 0, "effect": [0, 3, 4, 6, 9, 44, 109, 113, 114, 120, 122, 127, 130], "coarser": [0, 1, 11, 31, 109, 122, 125, 127], "cc": [0, 4, 12, 14, 47, 48, 54, 117, 126], "particular": [0, 3, 4, 9, 28, 109, 112, 113, 117, 120, 125, 127], "no_sync": [0, 14, 48, 109, 122], "care": [0, 24, 64, 110, 117, 125, 126], "okai": 0, "he": [0, 44], "happen": [0, 3, 4, 30, 113, 118], "region": [0, 1, 4, 24, 26, 36, 64, 108, 122, 125, 126, 127], "low": [0, 4, 9, 110, 112, 116, 122, 127, 130], "don": [0, 1, 3, 6, 10, 11, 30, 31, 108, 113, 118, 122, 125], "t": [0, 1, 2, 3, 4, 5, 6, 7, 9, 10, 11, 24, 29, 30, 31, 33, 44, 64, 66, 69, 88, 108, 109, 113, 114, 117, 118, 120, 122, 124, 125, 126, 127, 130], "affect": [0, 4, 10, 29, 30, 109, 117, 120, 123, 125, 127], "substanti": [0, 3, 5, 8], "pose": [0, 4], "problem": [0, 1, 2, 3, 6, 10, 11, 24, 29, 30, 31, 64, 85, 86, 89, 94, 96, 107, 108, 109, 111, 115, 117, 118, 119, 120, 122, 124, 125, 126, 127, 130], "regard": 0, "reli": [0, 4, 113, 124], "itself": [0, 109, 125], "global": [0, 26, 30, 44, 107, 109, 113, 125], "construct": [0, 3, 4, 9, 26, 29, 33, 35, 36, 41, 44, 105, 109, 110, 122, 124, 126, 127, 130], "depend": [0, 1, 2, 3, 4, 6, 9, 10, 11, 26, 28, 31, 108, 109, 115, 117, 118, 120, 125], "wa": [0, 1, 3, 8, 9, 11, 30, 31, 108, 110, 113, 115, 116, 118, 121, 122, 124, 125, 128], "hydrodynam": [0, 3, 5, 7, 8, 11, 26, 29, 31, 36, 41, 79, 100, 113, 115, 116, 117, 118, 122, 123, 125, 130], "associ": [0, 2, 4, 11, 31, 44, 109, 113, 122, 125], "retroact": 0, "one": [0, 1, 3, 4, 7, 9, 10, 11, 24, 26, 27, 30, 31, 42, 64, 109, 110, 113, 115, 116, 117, 119, 120, 121, 122, 124, 125, 127, 128], "imagin": [0, 6, 30], "perfect": [0, 116], "world": 0, "would": [0, 1, 3, 4, 8, 9, 14, 28, 48, 109, 112, 113, 114, 117, 118, 122, 127], "comput": [0, 1, 3, 5, 6, 7, 8, 9, 11, 14, 24, 26, 31, 36, 41, 44, 48, 64, 65, 79, 84, 105, 109, 110, 112, 113, 115, 116, 117, 118, 122, 125, 126, 130], "inde": [0, 2], "did": [0, 11, 31, 113], "subcycl": [0, 3, 5, 11, 31, 109, 122], "march": [0, 28, 130], "along": [0, 4, 7, 9, 11, 31, 109, 113, 118, 120, 122, 124, 125], "timestep": [0, 3, 4, 5, 9, 11, 24, 30, 31, 33, 35, 36, 39, 41, 44, 64, 84, 108, 109, 111, 113, 115, 118, 120, 122, 125, 126], "some": [0, 1, 3, 4, 5, 6, 10, 11, 26, 27, 30, 31, 108, 109, 112, 113, 115, 116, 117, 118, 120, 122, 125, 126, 128], "like": [0, 1, 2, 3, 4, 7, 26, 30, 108, 109, 110, 112, 114, 115, 116, 117, 119, 120, 122, 125, 126, 127, 128], "flash": [0, 4, 116, 130], "actual": [0, 3, 14, 36, 44, 48, 108, 109, 117, 119, 121, 125, 128], "fulli": [0, 3, 4, 122], "complet": [0, 2, 3, 15, 29, 51, 120, 122, 125], "But": [0, 2, 3, 30, 113, 125], "architectur": [0, 115], "up": [0, 3, 8, 9, 11, 17, 21, 29, 31, 44, 53, 59, 108, 109, 110, 111, 113, 116, 117, 119, 122, 124, 125, 127, 128], "alwai": [0, 2, 3, 4, 6, 10, 15, 24, 28, 30, 51, 64, 112, 113, 122, 125, 128], "given": [0, 2, 3, 4, 7, 8, 11, 14, 26, 27, 30, 31, 33, 36, 44, 48, 108, 109, 110, 113, 117, 118, 119, 120, 121, 122, 124, 125, 127], "immedi": [0, 3, 112, 113, 117, 121], "henc": [0, 3], "befor": [0, 1, 3, 4, 6, 11, 30, 31, 33, 44, 105, 109, 110, 118, 120, 121, 122, 127], "occur": [0, 4, 27, 28, 30, 44, 109, 118, 119, 122], "One": [0, 7, 124], "wai": [0, 3, 26, 28, 109, 115, 117, 120, 124, 125], "fix": [0, 6, 8, 27, 28, 30, 108, 120, 122, 124, 128, 129], "suggest": [0, 27, 122, 127], "explicitli": [0, 3, 4, 29, 109, 113, 119, 120, 122, 125], "result": [0, 1, 3, 4, 7, 8, 42, 44, 109, 119, 120, 122, 125, 128, 130], "work": [0, 3, 4, 5, 10, 11, 26, 31, 36, 108, 109, 110, 113, 114, 117, 119, 120, 122, 128], "center": [0, 3, 4, 7, 8, 9, 11, 14, 26, 29, 31, 36, 42, 44, 48, 79, 84, 90, 109, 110, 112, 113, 114, 120, 122, 125, 126, 130], "advect": [0, 3, 4, 7, 79, 116, 118, 120, 122, 125, 130], "mathbf": [0, 4, 109, 120], "rid": 0, "mass": [0, 2, 3, 5, 9, 11, 14, 26, 30, 31, 41, 44, 48, 112, 113, 116, 120, 122, 124, 127, 130], "motion": [0, 7, 120], "see": [0, 2, 3, 4, 5, 6, 9, 11, 26, 29, 30, 31, 36, 108, 109, 112, 113, 115, 117, 118, 120, 122, 124, 125, 127, 128], "explicit": [0, 3, 4, 5, 29, 125, 126], "coupl": [0, 3, 4, 5, 8, 9, 10, 109, 114, 118, 120, 122, 123, 124, 125, 130], "sever": [0, 3, 4, 26, 27, 108, 109, 113, 115, 117, 118, 120, 124, 130], "mean": [0, 1, 2, 4, 7, 9, 24, 26, 28, 29, 64, 108, 109, 113, 114, 115, 117, 119, 122, 125, 127], "corrector": [0, 3, 11, 31, 44, 109, 120], "too": [0, 3, 9, 11, 30, 31, 117, 122], "easi": [0, 128], "write": [0, 3, 4, 10, 11, 26, 31, 113, 116, 122, 125], "energi": [0, 2, 3, 5, 9, 11, 24, 29, 31, 36, 44, 64, 66, 91, 109, 113, 114, 116, 117, 118, 122, 125, 126, 127, 130], "now": [0, 1, 3, 4, 6, 11, 15, 31, 51, 101, 108, 109, 125], "standard": [0, 2, 3, 4, 6, 9, 26, 84, 108, 109, 113, 116, 120, 122], "its": [0, 4, 7, 8, 9, 26, 28, 108, 109, 113, 117, 120, 124, 125, 127], "linear": [0, 3, 4, 9, 10, 36, 79, 105, 109, 114, 116, 122, 125, 130], "acceler": [0, 3, 5, 24, 25, 41, 64, 65, 107, 109, 113, 117, 122, 125], "repres": [0, 1, 2, 4, 7, 42, 109, 114, 117, 118, 120, 124], "more": [0, 3, 4, 6, 7, 26, 27, 30, 108, 109, 110, 113, 115, 117, 119, 120, 122, 124, 125, 127, 128], "complic": [0, 3], "might": [0, 1, 2, 26, 30], "easili": [0, 4, 24, 64, 113, 125], "represent": 0, "nuclear": [0, 4, 5, 8, 113, 115, 118, 125, 127, 130], "reaction": [0, 3, 4, 5, 8, 9, 10, 11, 31, 39, 42, 108, 111, 114, 115, 116, 117, 122, 123, 125, 130], "network": [0, 4, 5, 6, 10, 26, 30, 108, 112, 113, 115, 118, 121, 127, 130], "analyt": [0, 2, 9, 113, 116, 123], "possibl": [0, 3, 6, 7, 30, 108, 109, 117, 118, 120], "becaus": [0, 1, 3, 4, 6, 9, 11, 31, 44, 109, 112, 117, 119, 120, 125], "instead": [0, 2, 3, 4, 26, 30, 108, 113, 114, 117, 118, 125, 127], "choos": [0, 3, 4, 108, 109, 112, 120, 122, 125, 127], "save": [0, 2, 3, 11, 14, 31, 33, 35, 36, 39, 41, 44, 48, 108, 117, 128, 129], "were": [0, 8, 9, 30, 109, 113, 119, 125], "subtract": [0, 4, 84, 105, 109, 110, 120, 122, 125], "previous": [0, 3, 11, 31], "sync": [0, 3, 14, 24, 48, 64, 109], "re": [0, 1, 11, 14, 31, 48, 109, 113, 117, 118, 122, 125], "get": [0, 3, 4, 9, 11, 14, 24, 26, 30, 31, 33, 36, 44, 48, 64, 109, 110, 111, 113, 120, 122, 123, 125, 128], "almost": [0, 4, 115], "ideal": [0, 2, 5, 29, 109, 114, 130], "behavior": [0, 4, 26, 30, 108, 109, 110, 112, 117, 121, 130], "aren": 0, "essenti": [0, 3, 4, 9, 26, 36, 110, 119, 124, 125], "had": [0, 3, 109], "cost": [0, 44, 109, 119, 122], "common": [0, 4, 10, 26], "seriou": 0, "onc": [0, 1, 7, 9, 11, 16, 17, 21, 30, 31, 44, 52, 53, 59, 128], "you": [0, 1, 2, 3, 4, 6, 8, 9, 10, 24, 26, 27, 29, 30, 44, 64, 108, 109, 112, 113, 114, 115, 117, 120, 122, 124, 125, 127, 128], "alreadi": [0, 3, 30, 117, 118, 119, 125], "know": [0, 1, 3, 26, 30, 108, 113, 122, 125, 127], "neglig": 0, "compar": [0, 1, 3, 9, 116, 117, 125], "sai": [0, 1, 113, 125, 127], "believ": 0, "recomput": [0, 4, 109, 122], "them": [0, 3, 4, 24, 26, 36, 64, 108, 113, 122, 124, 125, 126, 127, 128], "high": [0, 1, 3, 4, 9, 109, 110, 112, 122, 125, 126, 130], "paramet": [0, 3, 4, 11, 12, 14, 15, 16, 17, 19, 21, 22, 23, 24, 27, 30, 31, 32, 33, 35, 36, 39, 41, 44, 47, 48, 51, 52, 53, 55, 59, 62, 64, 65, 66, 79, 84, 85, 86, 90, 91, 92, 94, 96, 100, 101, 105, 108, 109, 111, 113, 114, 118, 119, 120, 122, 123, 125, 126, 127, 128, 129], "update_sources_after_reflux": [0, 122], "automat": [0, 7, 10, 27, 28, 108, 115, 125], "amend": 0, "futur": [0, 10], "releas": [0, 3, 4, 5, 108, 117, 124], "simul": [0, 1, 2, 3, 4, 6, 7, 9, 11, 14, 26, 31, 44, 48, 85, 90, 91, 92, 96, 108, 109, 113, 115, 119, 122, 125, 128, 130], "take": [0, 2, 3, 4, 6, 8, 9, 11, 27, 30, 31, 36, 42, 100, 108, 109, 110, 112, 115, 117, 119, 120, 121, 122, 123, 125, 126, 127, 128, 129], "howev": [0, 1, 4, 7, 29, 117, 120, 124], "situat": [0, 4, 108, 109], "consid": [0, 1, 3, 4, 7, 29, 109, 119, 120, 125, 127], "discuss": [0, 3, 4, 8, 109, 112, 116, 117, 120, 125], "about": [0, 3, 8, 11, 26, 30, 31, 108, 109, 113, 117, 120, 122, 125, 126], "ratio": [0, 1, 4, 11, 17, 21, 31, 53, 59, 109, 112, 122], "taken": [0, 3, 109, 113, 117, 125, 127], "advoc": 0, "consequ": [0, 4], "thu": [0, 1, 4, 6, 109, 112], "moment": [0, 3, 10, 109, 110], "": [0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 14, 23, 26, 27, 29, 30, 31, 36, 38, 44, 48, 62, 73, 74, 84, 97, 98, 100, 108, 109, 110, 112, 114, 115, 116, 117, 120, 122, 124, 125, 127, 128, 130], "thought": [0, 6], "reveal": 0, "modifi": [0, 1, 4, 8, 10, 14, 48, 109, 113, 117, 119, 120, 128], "didn": [0, 3], "full": [0, 3, 4, 5, 9, 10, 11, 26, 31, 41, 100, 108, 109, 114, 123, 125, 127, 128], "old": [0, 3, 9, 11, 14, 31, 33, 35, 36, 39, 41, 44, 48, 109, 118, 120, 122, 125], "miss": [0, 30], "assumpt": [0, 109, 122], "make": [0, 1, 3, 4, 6, 9, 11, 14, 24, 26, 30, 31, 48, 64, 108, 109, 110, 112, 113, 115, 117, 118, 119, 120, 121, 122, 125, 127, 128, 129], "answer": 0, "ye": 0, "date": [0, 108], "cours": [0, 6, 113, 122], "last": [0, 3, 6, 7, 11, 24, 26, 28, 30, 31, 64, 110, 117, 122, 125], "equal": [0, 1, 4, 7, 109, 112, 117, 120, 122, 123, 125, 127], "true": [0, 3, 4, 6, 7, 10, 11, 14, 26, 27, 29, 30, 31, 36, 42, 44, 45, 48, 66, 84, 105, 108, 109, 110, 112, 114, 115, 117, 118, 119, 120, 122, 124, 125], "piecewis": [0, 3, 4, 9, 30, 36, 105, 114, 122, 130], "constant": [0, 2, 3, 4, 5, 9, 10, 17, 21, 24, 29, 30, 53, 59, 64, 109, 110, 117, 120, 122, 124, 130], "order": [0, 3, 4, 5, 6, 7, 8, 10, 11, 29, 31, 36, 108, 109, 119, 122, 123, 125, 130], "accur": [0, 3, 36, 109, 110, 116, 120, 122, 123, 124], "3": [0, 1, 3, 4, 5, 6, 7, 9, 10, 11, 24, 26, 29, 31, 36, 43, 45, 49, 61, 64, 65, 68, 69, 77, 79, 80, 82, 84, 100, 103, 108, 109, 110, 112, 113, 114, 116, 117, 119, 120, 122, 123, 125, 127, 128, 129, 130], "fair": 0, "halfwai": [0, 112], "half": [0, 3, 4, 9, 109, 127], "mathemat": 0, "split": [0, 3, 11, 31, 114, 130], "weight": [0, 3, 9, 11, 31, 36, 44, 117, 122], "noth": [0, 3, 4, 6, 11, 31, 109, 117, 122], "prevent": [0, 9, 11, 30, 31, 117, 122, 126, 127], "u": [0, 3, 4, 6, 7, 11, 14, 28, 30, 31, 36, 43, 48, 61, 66, 83, 84, 99, 108, 109, 110, 113, 114, 116, 118, 120, 122, 124, 125, 127], "point": [0, 3, 6, 9, 11, 14, 26, 30, 31, 48, 108, 116, 117, 120, 122, 124, 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"castro.scf_equatorial_radius": [[122, "index-9"]], "castro.scf_max_iterations": [[122, "index-9"]], "castro.scf_maximum_density": [[122, "index-9"]], "castro.scf_polar_radius": [[122, "index-9"]], "castro.scf_relax_tol": [[122, "index-9"]], "castro.sdc_extra": [[122, "index-1"]], "castro.sdc_iters": [[122, "index-2"]], "castro.sdc_solver": [[122, "index-1"]], "castro.shock_detection_include_sources": [[122, "index-3"]], "castro.shock_detection_threshold": [[122, "index-3"]], "castro.small_ener": [[122, "index-1"]], "castro.small_plot_per_is_exact": [[122, "index-2"]], "castro.source_term_predictor": [[122, "index-1"]], "castro.speed_limit": [[122, "index-1"]], "castro.sponge_implicit": [[122, "index-1"]], "castro.sponge_lower_density": [[122, "index-6"]], "castro.sponge_lower_factor": [[122, "index-6"]], "castro.sponge_lower_pressure": [[122, "index-6"]], "castro.sponge_lower_radius": [[122, "index-6"]], "castro.sponge_target_x_velocity": [[122, "index-6"]], 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yt

Example notebook

Using the plotfiles generated in the example in the Getting Started section, here we demonstrate how to use yt to load and visualize data. This section was generated from a Jupyter notebook which can be found in Docs/source/yt_example.ipynb in the Castro repo.

+
import yt
+import matplotlib.pyplot as plt
+import numpy as np
+
+# set matplotlib formatting to be the same as yt
+plt.rcParams['font.size'] = 14
+plt.rcParams['font.family'] = 'serif'
+plt.rcParams['mathtext.fontset'] = 'stix'
+
+
+
# load data from file
+ds = yt.load('../../Exec/hydro_tests/Sedov/sedov_2d_cyl_in_cart_plt00150/', hint="castro")
+
+
+
yt : [INFO     ] 2020-05-29 16:40:16,890 Parameters: current_time              = 0.1
+yt : [INFO     ] 2020-05-29 16:40:16,891 Parameters: domain_dimensions         = [32 32  1]
+yt : [INFO     ] 2020-05-29 16:40:16,891 Parameters: domain_left_edge          = [0. 0. 0.]
+yt : [INFO     ] 2020-05-29 16:40:16,892 Parameters: domain_right_edge         = [1. 1. 1.]
+
+
+
# print out fields available for plotting
+print([f for _,f in ds.field_list])
+
+
+
['Gamma_1', 'MachNumber', 'StateErr_0', 'StateErr_1', 'StateErr_2', 'Temp', 'X(X)', 'abar', 'angular_momentum_x', 'angular_momentum_y', 'angular_momentum_z', 'circvel', 'density', 'divu', 'eint_E', 'eint_e', 'entropy', 'kineng', 'logden', 'magmom', 'magvel', 'magvort', 'pressure', 'radvel', 'rho_E', 'rho_X', 'rho_e', 'soundspeed', 'x_velocity', 'xmom', 'y_velocity', 'ymom', 'z_velocity', 'zmom']
+
+
+
# plot the density
+fig = yt.SlicePlot(ds, 'z', 'density')
+
+# save plot to file
+fig.save('sedov_density.png')
+
+fig
+
+
+
yt : [INFO     ] 2020-05-29 16:40:17,234 xlim = 0.000000 1.000000
+yt : [INFO     ] 2020-05-29 16:40:17,235 ylim = 0.000000 1.000000
+yt : [INFO     ] 2020-05-29 16:40:17,235 xlim = 0.000000 1.000000
+yt : [INFO     ] 2020-05-29 16:40:17,236 ylim = 0.000000 1.000000
+yt : [INFO     ] 2020-05-29 16:40:17,237 Making a fixed resolution buffer of (('gas', 'density')) 800 by 800
+yt : [INFO     ] 2020-05-29 16:40:17,392 Saving plot sedov_density.png
+
+
+
# plot the temperature and annotate the grids
+fig = yt.SlicePlot(ds, 'z', 'Temp')
+fig.annotate_grids(linewidth=2, alpha=1, edgecolors='red')
+fig.annotate_cell_edges(line_width=0.0005, alpha=0.4, color='white')
+fig
+
+
+
yt : [INFO     ] 2020-05-29 16:40:17,748 xlim = 0.000000 1.000000
+yt : [INFO     ] 2020-05-29 16:40:17,749 ylim = 0.000000 1.000000
+yt : [INFO     ] 2020-05-29 16:40:17,750 xlim = 0.000000 1.000000
+yt : [INFO     ] 2020-05-29 16:40:17,750 ylim = 0.000000 1.000000
+yt : [INFO     ] 2020-05-29 16:40:17,751 Making a fixed resolution buffer of (('boxlib', 'Temp')) 800 by 800
+yt : [WARNING  ] 2020-05-29 16:40:17,897 Supplied id_loc but draw_ids is False. Not drawing grid ids
+yt : [WARNING  ] 2020-05-29 16:40:17,899 Supplied id_loc but draw_ids is False. Not drawing grid ids
+yt : [WARNING  ] 2020-05-29 16:40:17,901 Supplied id_loc but draw_ids is False. Not drawing grid ids
+yt : [WARNING  ] 2020-05-29 16:40:17,903 Supplied id_loc but draw_ids is False. Not drawing grid ids
+yt : [WARNING  ] 2020-05-29 16:40:17,905 Supplied id_loc but draw_ids is False. Not drawing grid ids
+yt : [WARNING  ] 2020-05-29 16:40:17,906 Supplied id_loc but draw_ids is False. Not drawing grid ids
+yt : [WARNING  ] 2020-05-29 16:40:17,908 Supplied id_loc but draw_ids is False. Not drawing grid ids
+yt : [WARNING  ] 2020-05-29 16:40:17,910 Supplied id_loc but draw_ids is False. Not drawing grid ids
+yt : [WARNING  ] 2020-05-29 16:40:17,911 Supplied id_loc but draw_ids is False. Not drawing grid ids
+
+
+
# create a line plot of the density parallel to the x-axis that cuts through the
+# point of maximum density
+
+_, c = ds.find_max("density") # find the location of the point of maximum density
+ax = 0 # take cut parallel to x-axis
+
+# use ortho_ray to cut through c
+ray = ds.ortho_ray(ax, (c[1], c[2]))
+
+# sort values by x so there are no discontinuities in the line plot
+srt = np.argsort(ray['x'])
+
+fig, ax = plt.subplots(figsize=(8,6))
+ax.plot(ray['x'][srt], ray['density'][srt])
+ax.set_xlabel(r'$x$ (cm)')
+ax.set_ylabel(r'$\rho$ (g/cm$^3$)')
+ax.set_xlim([ray['x'][srt][0], ray['x'][srt][-1]])
+
+fig.savefig('dens_plot.png')
+
+
+
yt : [INFO     ] 2020-05-29 16:40:18,254 Max Value is 3.51160e+00 at 0.7558593750000000 0.7558593750000000 0.5000000000000000
+
+
+_images/yt_example_5_1.png

parameter