From e613a9373d53e8ba745ecf3007ed12024813f743 Mon Sep 17 00:00:00 2001 From: Kiran Eiden Date: Mon, 5 Feb 2024 14:16:54 -0800 Subject: [PATCH 1/4] 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 2/4] 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 3/4] 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 =============== From 057207947ac47754453bbae91450491de6e71d16 Mon Sep 17 00:00:00 2001 From: Kiran Eiden Date: Tue, 13 Feb 2024 15:47:30 -0800 Subject: [PATCH 4/4] Switch to double-backticks for compilation parameter --- Docs/source/Hydrodynamics.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Docs/source/Hydrodynamics.rst b/Docs/source/Hydrodynamics.rst index 44cdf3e553..edaaf8accd 100644 --- a/Docs/source/Hydrodynamics.rst +++ b/Docs/source/Hydrodynamics.rst @@ -347,7 +347,7 @@ accounted for in **Steps 1** and **6**. The source terms are: .. 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 + these variables, set ``USE_SPECIES_SOURCES=TRUE`` when compiling so that space will be allocated for them. Primitive Forms