From e613a9373d53e8ba745ecf3007ed12024813f743 Mon Sep 17 00:00:00 2001 From: Kiran Eiden Date: Mon, 5 Feb 2024 14:16:54 -0800 Subject: [PATCH 1/3] Add documentation for USE_SPECIES_SOURCES flag --- Docs/source/Hydrodynamics.rst | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/Docs/source/Hydrodynamics.rst b/Docs/source/Hydrodynamics.rst index 8d76bd5fdf..3ad3a526c3 100644 --- a/Docs/source/Hydrodynamics.rst +++ b/Docs/source/Hydrodynamics.rst @@ -297,7 +297,11 @@ Source Terms We now compute explicit source terms for each variable in :math:`\Qb` and :math:`\Ub`. The primitive variable source terms will be used to construct time-centered fluxes. The conserved variable source will be used to -advance the solution. We neglect reaction source terms since they are +advance the solution. 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. We neglect reaction source terms since they are accounted for in **Steps 1** and **6**. The source terms are: .. math:: From 669e57f0f3464c9e3bc8d4d8c3302222837f81fb Mon Sep 17 00:00:00 2001 From: Kiran Eiden Date: Mon, 5 Feb 2024 14:25:27 -0800 Subject: [PATCH 2/3] Remove documentation on normalize_species parameter --- Docs/source/Hydrodynamics.rst | 3 --- 1 file changed, 3 deletions(-) diff --git a/Docs/source/Hydrodynamics.rst b/Docs/source/Hydrodynamics.rst index 3ad3a526c3..f8c497fa09 100644 --- a/Docs/source/Hydrodynamics.rst +++ b/Docs/source/Hydrodynamics.rst @@ -589,9 +589,6 @@ 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 From a944b3e8882858b22406e64348409a61b0b2b3d8 Mon Sep 17 00:00:00 2001 From: Kiran Eiden Date: Tue, 13 Feb 2024 14:31:28 -0800 Subject: [PATCH 3/3] Incorporate Mike's recommendations --- Docs/source/Hydrodynamics.rst | 14 +++++++++----- 1 file changed, 9 insertions(+), 5 deletions(-) diff --git a/Docs/source/Hydrodynamics.rst b/Docs/source/Hydrodynamics.rst index f8c497fa09..44cdf3e553 100644 --- a/Docs/source/Hydrodynamics.rst +++ b/Docs/source/Hydrodynamics.rst @@ -297,11 +297,7 @@ Source Terms We now compute explicit source terms for each variable in :math:`\Qb` and :math:`\Ub`. The primitive variable source terms will be used to construct time-centered fluxes. The conserved variable source will be used to -advance the solution. 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. We neglect reaction source terms since they are +advance the solution. We neglect reaction source terms since they are accounted for in **Steps 1** and **6**. The source terms are: .. math:: @@ -346,6 +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 ===============