From 335fb1e7e53d78e6cf18eab34f48cbbe7eaa513e Mon Sep 17 00:00:00 2001 From: John P Wakefield Date: Wed, 11 Dec 2024 13:58:01 -0500 Subject: [PATCH 1/9] added variable digits in output filename option; see exa MR1373 --- docs/source_docs/user_guide/inputs/output/plotfiles.rst | 3 +++ 1 file changed, 3 insertions(+) diff --git a/docs/source_docs/user_guide/inputs/output/plotfiles.rst b/docs/source_docs/user_guide/inputs/output/plotfiles.rst index 83c0d05..ed45e90 100644 --- a/docs/source_docs/user_guide/inputs/output/plotfiles.rst +++ b/docs/source_docs/user_guide/inputs/output/plotfiles.rst @@ -28,6 +28,9 @@ format (for debugging). | par_ascii_per_approx | Time period of the ascii particle output (approximate); | Real | -1 | | | if -1 then particle ascii files will not be written at this frequency | | | +----------------------+-----------------------------------------------------------------------+-------------+-----------+ +| file_digits | Number of digits to use in plotfile (plt[0-9]+) and checkpoint | Int | 5 | +| | (chk[0-9]+) filenames. | | | ++----------------------+-----------------------------------------------------------------------+-------------+-----------+ | ascent_int | Frequency of ascent pipeline; | Int | -1 | | | if -1 then ascent will not be called. | | | +----------------------+-----------------------------------------------------------------------+-------------+-----------+ -- GitLab From 37c9853c94df4bfbbfe03d663af5835c058c1004 Mon Sep 17 00:00:00 2001 From: John P Wakefield Date: Thu, 4 Sep 2025 13:46:23 -0400 Subject: [PATCH 2/9] fixed typo---related enough to leave in this PR --- docs/source_docs/user_guide/inputs/solids_model.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/source_docs/user_guide/inputs/solids_model.rst b/docs/source_docs/user_guide/inputs/solids_model.rst index 1fc5741..5ea40ae 100644 --- a/docs/source_docs/user_guide/inputs/solids_model.rst +++ b/docs/source_docs/user_guide/inputs/solids_model.rst @@ -32,7 +32,7 @@ models. The following inputs must be preceded by the "solids." root | | for specific enthalpy | | | +------------------------------------------+-------------------------------------------------------------+----------+----------+ | species | Specify which species can constitute | String | None | -| | the fluid phase [defined species must | | | +| | the solid phase [defined species must | | | | | be a subset of the species.solve | | | | | arguments]. | | | +------------------------------------------+-------------------------------------------------------------+----------+----------+ -- GitLab From d8f4d3c6ab0ec8fb4c920f9c66c0a1259f71dea6 Mon Sep 17 00:00:00 2001 From: John P Wakefield Date: Tue, 16 Sep 2025 16:22:24 -0400 Subject: [PATCH 3/9] added component density options --- docs/source_docs/user_guide/inputs/chemical_reactions.rst | 5 +++++ docs/source_docs/user_guide/inputs/initial_conditions.rst | 1 + docs/source_docs/user_guide/inputs/species_defs.rst | 7 +++++++ 3 files changed, 13 insertions(+) diff --git a/docs/source_docs/user_guide/inputs/chemical_reactions.rst b/docs/source_docs/user_guide/inputs/chemical_reactions.rst index b72dd3d..5031bb1 100644 --- a/docs/source_docs/user_guide/inputs/chemical_reactions.rst +++ b/docs/source_docs/user_guide/inputs/chemical_reactions.rst @@ -1,3 +1,6 @@ + +.. _InputsChem: + Chemical Reactions ================== @@ -27,6 +30,8 @@ The following inputs are defined using the ``chemistry`` prefix. | | | | | | | * ``ConstantVolume`` keep particles' volume constant | | | | | * ``ConstantDensity`` keep particles' density constant | | | +| | * ``Component`` compute volume and density from | | | +| | :ref:`species solid densities` | | | | | | | | +--------------------------+---------------------------------------------------------+----------+----------------+ | solids.mass_threshold | Sets a threshold value for the particles' mass. When | Real | 0 | diff --git a/docs/source_docs/user_guide/inputs/initial_conditions.rst b/docs/source_docs/user_guide/inputs/initial_conditions.rst index 12195a9..8f19ad0 100644 --- a/docs/source_docs/user_guide/inputs/initial_conditions.rst +++ b/docs/source_docs/user_guide/inputs/initial_conditions.rst @@ -124,6 +124,7 @@ please refer to :ref:`ReferenceParticleDistributions ` | | | | | * 'custom' -- user defined distribution | | | +---------------------+-----------------------------------------------------------------------+-------------+-----------+ | density.constant | Monodisperse (single valued) particle density. | Real | 0 | diff --git a/docs/source_docs/user_guide/inputs/species_defs.rst b/docs/source_docs/user_guide/inputs/species_defs.rst index ad83fcf..d1c5e49 100644 --- a/docs/source_docs/user_guide/inputs/species_defs.rst +++ b/docs/source_docs/user_guide/inputs/species_defs.rst @@ -127,6 +127,13 @@ The following inputs are for each species defined using the ``species.[species n | viscosity.molecular.Reid.C, and | Values are required for ``Reid`` species viscosity model. | | | | viscosity.molecular.Reid.D | | | | +---------------------------------------+------------------------------------------------------------------------+----------+-----------+ +| solid_density | Species density in the solid phase. | Real | -1. | +| | | | | +| | Needed for all solid species with | | | +| | :ref:`initial density` or | | | +| | :ref:`density updates` set to ``component`` or | | | +| | ``Component`` respectively. | | | ++---------------------------------------+------------------------------------------------------------------------+----------+-----------+ -- GitLab From c88a4f9dccd665864ddb9f83806879a4fa8e2f2c Mon Sep 17 00:00:00 2001 From: John P Wakefield Date: Tue, 16 Sep 2025 16:44:08 -0400 Subject: [PATCH 4/9] fixed typo --- docs/source_docs/user_guide/inputs/initial_conditions.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/source_docs/user_guide/inputs/initial_conditions.rst b/docs/source_docs/user_guide/inputs/initial_conditions.rst index 694764b..0221abd 100644 --- a/docs/source_docs/user_guide/inputs/initial_conditions.rst +++ b/docs/source_docs/user_guide/inputs/initial_conditions.rst @@ -43,7 +43,7 @@ using the compound prefix ``ic.[region].[fluid]``: +------------------------+------------------------------------------------------------------------+-------------+-----------+ -.. _InputsICSolids: +.. _InputICSolids: Solids settings ~~~~~~~~~~~~~~~ -- GitLab From ae8528a634b89a110834bb532b30df5cc4012512 Mon Sep 17 00:00:00 2001 From: John P Wakefield Date: Wed, 24 Sep 2025 13:59:02 -0400 Subject: [PATCH 5/9] updated per PR changes --- .../user_guide/inputs/chemical_reactions.rst | 5 +++-- .../user_guide/inputs/initial_conditions.rst | 11 ++++++----- docs/source_docs/user_guide/inputs/species.rst | 9 ++++----- 3 files changed, 13 insertions(+), 12 deletions(-) diff --git a/docs/source_docs/user_guide/inputs/chemical_reactions.rst b/docs/source_docs/user_guide/inputs/chemical_reactions.rst index 206b9b4..e4e317a 100644 --- a/docs/source_docs/user_guide/inputs/chemical_reactions.rst +++ b/docs/source_docs/user_guide/inputs/chemical_reactions.rst @@ -34,8 +34,9 @@ The following inputs are defined using the prefix ``chemistry``: | | | | | | | * ``ConstantVolume`` keep particle volume constant | | | | | * ``ConstantDensity`` keep particle density constant | | | -| | * ``Component`` compute volume and density from | | | -| | :ref:`species solid densities` | | | +| | * ``ConstantSpeciesDensities`` compute volume and | | | +| | density from | | | +| | :ref:`solid species densities` | | | +--------------------------+---------------------------------------------------------+----------+----------------+ | solids.mass_threshold | Sets a threshold value for the particles' mass. When | Real | 0 | | | updating the solids quantities in chemistry, check | | | diff --git a/docs/source_docs/user_guide/inputs/initial_conditions.rst b/docs/source_docs/user_guide/inputs/initial_conditions.rst index 0221abd..73e7e98 100644 --- a/docs/source_docs/user_guide/inputs/initial_conditions.rst +++ b/docs/source_docs/user_guide/inputs/initial_conditions.rst @@ -132,11 +132,12 @@ please refer to :ref:`ReferenceParticleDistributions ` | | | -| | * ``custom`` - user-defined distribution | | | +| | * ``constant`` - specified constant | | | +| | * ``uniform`` - uniform distribution | | | +| | * ``normal`` - normal distribution | | | +| | * ``constantspeciesdensities`` - from | | | +| | :ref:`species densities` | | | +| | * ``custom`` - user-defined distribution | | | +---------------------+-----------------------------------------------------------------------+-------------+-----------+ | density.constant | Monodisperse (single valued) particle density. | Real | 0 | | | Required for ``constant`` distributions. | | | diff --git a/docs/source_docs/user_guide/inputs/species.rst b/docs/source_docs/user_guide/inputs/species.rst index 0cb378c..105c90a 100644 --- a/docs/source_docs/user_guide/inputs/species.rst +++ b/docs/source_docs/user_guide/inputs/species.rst @@ -137,16 +137,15 @@ The following inputs are defined for each species using the prefix ``species.[sp | viscosity.molecular.Reid.C | Values are required for ``Reid`` species viscosity model. | | | | viscosity.molecular.Reid.D | | | | +---------------------------------------+------------------------------------------------------------------------+----------+-----------+ -| solid_density | Species density in the solid phase. | Real | -1. | +| density | Species density (only valid for solid phase species). | Real | 0. | | | | | | -| | Needed for all solid species with | | | +| | Needed for all solid species if | | | | | :ref:`initial density` or | | | -| | :ref:`density updates` set to ``component`` or | | | -| | ``Component`` respectively. | | | +| | :ref:`density updates` is set to | | | +| | ``constantspeciesdensities`` or ``ConstantSpeciesDensities`` resp. | | | +---------------------------------------+------------------------------------------------------------------------+----------+-----------+ - Example inputs -------------- -- GitLab From 40c51408693f76ce09bf649a45b1e077c4b69826 Mon Sep 17 00:00:00 2001 From: Roberto Porcu Date: Tue, 21 Oct 2025 14:25:40 -0400 Subject: [PATCH 6/9] update the docs with the latest changes in corresponding commit --- .../user_guide/inputs/chemical_reactions.rst | 90 +++++++++---------- .../user_guide/inputs/initial_conditions.rst | 4 +- .../user_guide/inputs/solids_model.rst | 15 ++++ .../source_docs/user_guide/inputs/species.rst | 6 +- 4 files changed, 64 insertions(+), 51 deletions(-) diff --git a/docs/source_docs/user_guide/inputs/chemical_reactions.rst b/docs/source_docs/user_guide/inputs/chemical_reactions.rst index e4e317a..5f122ac 100644 --- a/docs/source_docs/user_guide/inputs/chemical_reactions.rst +++ b/docs/source_docs/user_guide/inputs/chemical_reactions.rst @@ -8,51 +8,51 @@ Defining chemical reactions The following inputs are defined using the prefix ``chemistry``: -+--------------------------+---------------------------------------------------------+----------+----------------+ -| | Description | Type | Default | -+==========================+=========================================================+==========+================+ -| solve | Specify the name(s) of the chemical reactions or set | String | | -| | to None to disable the chemistry solver. The name(s) | | | -| | assigned to the chemistry solver are used to specify | | | -| | the chemical reactions equations. | | | -+--------------------------+---------------------------------------------------------+----------+----------------+ -| [reaction0].reaction | Chemical formula for the given reaction. The string | String | | -| | given as input must not contain white space and | | | -| | the reaction direction has to be specified as '\-\->' | | | -| | or '<\-\-'. Chemical species phases must be defined as | | | -| | '(g)' for the fluid phase or '(s)' for the solid phase. | | | -+--------------------------+---------------------------------------------------------+----------+----------------+ -| mass_balance_tolerance | Tolerance used to test chemical formula conserves mass. | Real | 1e-12 | -| | | | | -| | |tol_eq| | | | -| | | | | -+--------------------------+---------------------------------------------------------+----------+----------------+ -| solids.update_type | How to update solids quantities due to chemical | | ConstantVolume | -| | reactions. | | | -| | | | | -| | Options: | | | -| | | | | -| | * ``ConstantVolume`` keep particle volume constant | | | -| | * ``ConstantDensity`` keep particle density constant | | | -| | * ``ConstantSpeciesDensities`` compute volume and | | | -| | density from | | | -| | :ref:`solid species densities` | | | -+--------------------------+---------------------------------------------------------+----------+----------------+ -| solids.mass_threshold | Sets a threshold value for the particles' mass. When | Real | 0 | -| | updating the solids quantities in chemistry, check | | | -| | whether the solids mass is below the threshold, and in | | | -| | that case set the particle as invalid and remove it. | | | -+--------------------------+---------------------------------------------------------+----------+----------------+ -| solids.radius_threshold | Sets a threshold value for the particles' radius. When | Real | 0 | -| | updating the solids quantities in chemistry, check | | | -| | whether the solids radius is below the threshold, and | | | -| | in that case set the particle as invalid and remove it. | | | -+--------------------------+---------------------------------------------------------+----------+----------------+ -| solids.density_threshold | Sets a threshold value for the particles' density. When | Real | 0 | -| | updating the solids quantities in chemistry, check | | | -| | whether the solids density is below the threshold, and | | | -| | in that case set the particle as invalid and remove it. | | | -+--------------------------+---------------------------------------------------------+----------+----------------+ ++--------------------------+---------------------------------------------------------+----------+-----------------+ +| | Description | Type | Default | ++==========================+=========================================================+==========+=================+ +| solve | Specify the name(s) of the chemical reactions or set | String | | +| | to None to disable the chemistry solver. The name(s) | | | +| | assigned to the chemistry solver are used to specify | | | +| | the chemical reactions equations. | | | ++--------------------------+---------------------------------------------------------+----------+-----------------+ +| [reaction0].reaction | Chemical formula for the given reaction. The string | String | | +| | given as input must not contain white space and | | | +| | the reaction direction has to be specified as '\-\->' | | | +| | or '<\-\-'. Chemical species phases must be defined as | | | +| | '(g)' for the fluid phase or '(s)' for the solid phase. | | | ++--------------------------+---------------------------------------------------------+----------+-----------------+ +| mass_balance_tolerance | Tolerance used to test chemical formula conserves mass. | Real | 1e-12 | +| | | | | +| | |tol_eq| | | | +| | | | | ++--------------------------+---------------------------------------------------------+----------+-----------------+ +| solids.update_type | How to update solids quantities due to chemical | | Constant_Volume | +| | reactions. | | | +| | | | | +| | Options: | | | +| | | | | +| | * ``Constant_Volume`` keep particle volume constant | | | +| | * ``Constant_Density`` keep particle density constant | | | +| | * ``Constant_Species_Densities`` compute volume and | | | +| | density from | | | +| | :ref:`solid species densities` | | | ++--------------------------+---------------------------------------------------------+----------+-----------------+ +| solids.mass_threshold | Sets a threshold value for the particles' mass. When | Real | 0 | +| | updating the solids quantities in chemistry, check | | | +| | whether the solids mass is below the threshold, and in | | | +| | that case set the particle as invalid and remove it. | | | ++--------------------------+---------------------------------------------------------+----------+-----------------+ +| solids.radius_threshold | Sets a threshold value for the particles' radius. When | Real | 0 | +| | updating the solids quantities in chemistry, check | | | +| | whether the solids radius is below the threshold, and | | | +| | in that case set the particle as invalid and remove it. | | | ++--------------------------+---------------------------------------------------------+----------+-----------------+ +| solids.density_threshold | Sets a threshold value for the particles' density. When | Real | 0 | +| | updating the solids quantities in chemistry, check | | | +| | whether the solids density is below the threshold, and | | | +| | in that case set the particle as invalid and remove it. | | | ++--------------------------+---------------------------------------------------------+----------+-----------------+ Choosing the integrator type for the chemistry ODE integration operation that is performed to determine the fluid and solids phases transfer quantities due to diff --git a/docs/source_docs/user_guide/inputs/initial_conditions.rst b/docs/source_docs/user_guide/inputs/initial_conditions.rst index 73e7e98..d8fbbe7 100644 --- a/docs/source_docs/user_guide/inputs/initial_conditions.rst +++ b/docs/source_docs/user_guide/inputs/initial_conditions.rst @@ -43,7 +43,7 @@ using the compound prefix ``ic.[region].[fluid]``: +------------------------+------------------------------------------------------------------------+-------------+-----------+ -.. _InputICSolids: +.. _InputsICSolids: Solids settings ~~~~~~~~~~~~~~~ @@ -135,8 +135,6 @@ please refer to :ref:`ReferenceParticleDistributions ` | | | | | * ``custom`` - user-defined distribution | | | +---------------------+-----------------------------------------------------------------------+-------------+-----------+ | density.constant | Monodisperse (single valued) particle density. | Real | 0 | diff --git a/docs/source_docs/user_guide/inputs/solids_model.rst b/docs/source_docs/user_guide/inputs/solids_model.rst index c3ec6cb..91a2054 100644 --- a/docs/source_docs/user_guide/inputs/solids_model.rst +++ b/docs/source_docs/user_guide/inputs/solids_model.rst @@ -1,6 +1,9 @@ Solids model ============ + +.. _InputsSolids: + Solids settings --------------- @@ -16,6 +19,18 @@ models. The following inputs are defined with the prefix ``solids``: +------------------------------------------+-------------------------------------------------------------+----------+----------+ | molecular_weight | Value of constant solid molecular weight. | Real | 0 | +------------------------------------------+-------------------------------------------------------------+----------+----------+ +| density | Specify which density model to use for solids. | String | None | +| | | | | +| | Options: | | | +| | | | | +| | * ``none`` - solids density specified through initial and | | | +| | boundary conditions; | | | +| | * ``mixture`` - solids density computed as a weighted | | | +| | average of the solid phase species densities. It requires | | | +| | constant :ref:`species densities` to | | | +| | be defined by the user. | | | +| | | | | ++------------------------------------------+-------------------------------------------------------------+----------+----------+ | specific_heat | Specify which specific heat model to use for solids. | String | constant | | | | | | | | Options: | | | diff --git a/docs/source_docs/user_guide/inputs/species.rst b/docs/source_docs/user_guide/inputs/species.rst index 105c90a..31b0c45 100644 --- a/docs/source_docs/user_guide/inputs/species.rst +++ b/docs/source_docs/user_guide/inputs/species.rst @@ -137,12 +137,12 @@ The following inputs are defined for each species using the prefix ``species.[sp | viscosity.molecular.Reid.C | Values are required for ``Reid`` species viscosity model. | | | | viscosity.molecular.Reid.D | | | | +---------------------------------------+------------------------------------------------------------------------+----------+-----------+ -| density | Species density (only valid for solid phase species). | Real | 0. | +| density | Constant species density (used only for solid phase species). | Real | 0. | | | | | | | | Needed for all solid species if | | | -| | :ref:`initial density` or | | | +| | :ref:`solids density` is seto to ``mixture`` or | | | | | :ref:`density updates` is set to | | | -| | ``constantspeciesdensities`` or ``ConstantSpeciesDensities`` resp. | | | +| | ``Constant_Species_Densities`` | | | +---------------------------------------+------------------------------------------------------------------------+----------+-----------+ -- GitLab From 66a481823b55f9a7a73b9ef046844124f48fbd5b Mon Sep 17 00:00:00 2001 From: Roberto Porcu Date: Tue, 21 Oct 2025 15:23:53 -0400 Subject: [PATCH 7/9] minor spelling fixes --- docs/source_docs/user_guide/inputs/species.rst | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/docs/source_docs/user_guide/inputs/species.rst b/docs/source_docs/user_guide/inputs/species.rst index 31b0c45..14a9898 100644 --- a/docs/source_docs/user_guide/inputs/species.rst +++ b/docs/source_docs/user_guide/inputs/species.rst @@ -137,10 +137,10 @@ The following inputs are defined for each species using the prefix ``species.[sp | viscosity.molecular.Reid.C | Values are required for ``Reid`` species viscosity model. | | | | viscosity.molecular.Reid.D | | | | +---------------------------------------+------------------------------------------------------------------------+----------+-----------+ -| density | Constant species density (used only for solid phase species). | Real | 0. | +| density | Constant species density (only used for solid phase species). | Real | 0. | | | | | | | | Needed for all solid species if | | | -| | :ref:`solids density` is seto to ``mixture`` or | | | +| | :ref:`solids density` is set to ``mixture`` or | | | | | :ref:`density updates` is set to | | | | | ``Constant_Species_Densities`` | | | +---------------------------------------+------------------------------------------------------------------------+----------+-----------+ -- GitLab From 6eeb9f9dc4da36d805c80b6a47833808de05508b Mon Sep 17 00:00:00 2001 From: Roberto Porcu Date: Tue, 21 Oct 2025 15:33:29 -0400 Subject: [PATCH 8/9] reduce differences wrt main --- docs/source_docs/user_guide/inputs/initial_conditions.rst | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/docs/source_docs/user_guide/inputs/initial_conditions.rst b/docs/source_docs/user_guide/inputs/initial_conditions.rst index d8fbbe7..5171d19 100644 --- a/docs/source_docs/user_guide/inputs/initial_conditions.rst +++ b/docs/source_docs/user_guide/inputs/initial_conditions.rst @@ -132,10 +132,10 @@ please refer to :ref:`ReferenceParticleDistributions Date: Tue, 21 Oct 2025 15:42:31 -0400 Subject: [PATCH 9/9] minor improvement to explain the inputs logic --- docs/source_docs/user_guide/inputs/chemical_reactions.rst | 4 +++- docs/source_docs/user_guide/inputs/solids_model.rst | 1 - 2 files changed, 3 insertions(+), 2 deletions(-) diff --git a/docs/source_docs/user_guide/inputs/chemical_reactions.rst b/docs/source_docs/user_guide/inputs/chemical_reactions.rst index 5f122ac..be1ad1e 100644 --- a/docs/source_docs/user_guide/inputs/chemical_reactions.rst +++ b/docs/source_docs/user_guide/inputs/chemical_reactions.rst @@ -36,7 +36,9 @@ The following inputs are defined using the prefix ``chemistry``: | | * ``Constant_Density`` keep particle density constant | | | | | * ``Constant_Species_Densities`` compute volume and | | | | | density from | | | -| | :ref:`solid species densities` | | | +| | :ref:`solid species densities`. | | | +| | It requires :ref:`solids density model` | | | +| | to be set to ``mixture``. | | | +--------------------------+---------------------------------------------------------+----------+-----------------+ | solids.mass_threshold | Sets a threshold value for the particles' mass. When | Real | 0 | | | updating the solids quantities in chemistry, check | | | diff --git a/docs/source_docs/user_guide/inputs/solids_model.rst b/docs/source_docs/user_guide/inputs/solids_model.rst index 91a2054..de55244 100644 --- a/docs/source_docs/user_guide/inputs/solids_model.rst +++ b/docs/source_docs/user_guide/inputs/solids_model.rst @@ -1,7 +1,6 @@ Solids model ============ - .. _InputsSolids: Solids settings -- GitLab