Rename fields to PORE_DIFFUSION and SURFACE_DIFFUSION

Author: jbreue16

doc/developer_guide/examples/breakthrough.py

@@ -32,8 +32,8 @@
 
 ## Particle transport
 model.root.input.model.unit_001.particle_type_000.film_diffusion = [1e-5]         # m / s
-model.root.input.model.unit_001.particle_type_000.par_diffusion = [1e-10,]        # m^2 / s (mobile phase)  
-model.root.input.model.unit_001.particle_type_000.par_surfdiffusion = [0.0,]      # m^2 / s (solid phase)
+model.root.input.model.unit_001.particle_type_000.pore_diffusion = [1e-10,]        # m^2 / s (mobile phase)  
+model.root.input.model.unit_001.particle_type_000.surface_diffusion = [0.0,]      # m^2 / s (solid phase)
 
 ## Adsorption
 model.root.input.model.unit_001.particle_type_000.adsorption_model = 'MULTI_COMPONENT_LANGMUIR'

doc/interface/introduction.rst

@@ -131,7 +131,7 @@ Note that all components of component dependent datasets have to be section depe
    * - FILM_DIFFUSION
      - ✓
      - ✓
-   * - PAR_DIFFUSION
+   * - PORE_DIFFUSION
      - ✓
      - ✓
    * - PAR_SURDIFFUSION

doc/interface/parameter_dependencies.rst

@@ -78,9 +78,9 @@ Currently, the dependence of surface diffusion on the particle liquid salt compo
 Group /input/model/unit_XXX
 ---------------------------
 
-``PAR_SURFDIFFUSION_DEP``
+``SURFACE_DIFFUSION_DEP``
 
-   Parameter dependence of :math:`\texttt{PAR_SURFDIFFUSION}` on the particle liquid salt component (i.e. component with index 0). Valid dependencies are:
+   Parameter dependence of :math:`\texttt{SURFACE_DIFFUSION}` on the particle liquid salt component (i.e. component with index 0). Valid dependencies are:
 
    - :math:`\texttt{NONE}` Original parameter is used unmodified.
    - :math:`\texttt{LIQUID_SALT_EXPONENTIAL}` Original parameter is modified by exponential law of liquid phase salt concentration.
@@ -93,87 +93,87 @@ Group /input/model/unit_XXX
    **Type:** string  **Length:** :math:`1 / \texttt{NPARTYPE}`
    ================  =========================================
 
-``PAR_SURFDIFFUSION_EXPFACTOR``
+``SURFACE_DIFFUSION_EXPFACTOR``
 
    Factor :math:`\texttt{p1}` in exponential law particle surface diffusion relation
    :math:`D_{s, i, m} = \tilde{D}_{s, i, m} p_{1, i, m} exp \left(p_{2, i, m} c_{0}^{p} \right)`, where :math:`\tilde{D}_{s, i, m}` is the original surface diffusion coefficient.
-   Only required if :math:`\texttt{PAR_SURFDIFFUSION_DEP}` is :math:`\texttt{LIQUID_SALT_EXPONENTIAL}`.
+   Only required if :math:`\texttt{SURFACE_DIFFUSION_DEP}` is :math:`\texttt{LIQUID_SALT_EXPONENTIAL}`.
 
    ================  =========================  ===================================
    **Type:** double  **Range:** :math:`\geq 0`  **Length:** :math:`\texttt{NBOUND}`
    ================  =========================  ===================================
 
-   ``PAR_SURFDIFFUSION_EXPFACTOR``
+   ``SURFACE_DIFFUSION_EXPFACTOR``
    :math:`D_{s, i, m} = \tilde{D}_{s, i, m} \left[  p_{4, i, m} \left( k_{i, m} \left( c_{0}^{p} \right) \right)^{p_{5, i, m}} p_{6, i, m} exp \left( p_{7, i, m} k_{i, m} \left( c_{0}^{p} \right) \right) \right]`
    where :math:`\tilde{D}_{s, i, m}` is the original surface diffusion coefficient and 
    :math:`k_{i, m} \left( c_{0}^{p} \right) = p_{1, i, m}\left( c_{0}^{p} \right)^{p_{2, i, m}} + p_{3, i, m}`.
-   Only required if :math:`\texttt{PAR_SURFDIFFUSION_DEP}` is :math:`\texttt{LIQUID_SALT_COLLOIDAL_AFFINITY}`.
+   Only required if :math:`\texttt{SURFACE_DIFFUSION_DEP}` is :math:`\texttt{LIQUID_SALT_COLLOIDAL_AFFINITY}`.
 
    ================  =============================  ===================================
    **Type:** double  **Range:** :math:`\mathbb{R}`  **Length:** :math:`\texttt{NBOUND}`
    ================  =============================  ===================================
 
-``PAR_SURFDIFFUSION_EXPARGMULT``
+``SURFACE_DIFFUSION_EXPARGMULT``
 
    Factor :math:`\texttt{p2}` in exponential law particle surface diffusion relation
    :math:`D_{s, i, m} = \tilde{D}_{s, i, m} p_{1, i, m} exp \left(p_{2, i, m} c_{0}^{p} \right)`
-   where :math:`\tilde{D}_{s, i, m}` is the original surface diffusion coefficient. Only required if :math:`\texttt{PAR_SURFDIFFUSION_DEP}` is :math:`\texttt{LIQUID_SALT_EXPONENTIAL}`.
+   where :math:`\tilde{D}_{s, i, m}` is the original surface diffusion coefficient. Only required if :math:`\texttt{SURFACE_DIFFUSION_DEP}` is :math:`\texttt{LIQUID_SALT_EXPONENTIAL}`.
 
    ================  =============================  ===================================
    **Type:** double  **Range:** :math:`\mathbb{R}`  **Length:** :math:`\texttt{NBOUND}`
    ================  =============================  ===================================
 
-``PAR_SURFDIFFUSION_POWFACTOR``
+``SURFACE_DIFFUSION_POWFACTOR``
 
    Factor :math:`\texttt{p1}` in power law particle surface diffusion relation
    :math:`D_{s, i, m} = \tilde{D}_{s, i, m} p_{1, i, m} \left( c_{0}^{p} \right)^{p_{2, i, m}}`
-   where :math:`\tilde{D}_{s, i, m}` is the original surface diffusion coefficient. Only required if :math:`\texttt{PAR_SURFDIFFUSION_DEP}` is :math:`\texttt{LIQUID_SALT_POWER}`.
+   where :math:`\tilde{D}_{s, i, m}` is the original surface diffusion coefficient. Only required if :math:`\texttt{SURFACE_DIFFUSION_DEP}` is :math:`\texttt{LIQUID_SALT_POWER}`.
 
    ================  =========================  ===================================
    **Type:** double  **Range:** :math:`\geq 0`  **Length:** :math:`\texttt{NBOUND}`
    ================  =========================  ===================================
 
-``PAR_SURFDIFFUSION_POWEXP``
+``SURFACE_DIFFUSION_POWEXP``
 
    Fjactor :math:`\texttt{p2}` in power law particle surface diffusion relation
    :math:`D_{s, i, m} = \tilde{D}_{s, i, m} p_{1, i, m} \left( c_{0}^{p} \right)^{p_{2, i, m}}`
-   where :math:`\tilde{D}_{s, i, m}` is the original surface diffusion coefficient. Only required if :math:`\texttt{PAR_SURFDIFFUSION_DEP}` is :math:`\texttt{LIQUID_SALT_POWER}`.
+   where :math:`\tilde{D}_{s, i, m}` is the original surface diffusion coefficient. Only required if :math:`\texttt{SURFACE_DIFFUSION_DEP}` is :math:`\texttt{LIQUID_SALT_POWER}`.
 
    ================  =============================  ===================================
    **Type:** double  **Range:** :math:`\mathbb{R}`  **Length:** :math:`\texttt{NBOUND}`
    ================  =============================  ===================================
 
-``PAR_SURFDIFFUSION_LOGKEQFACTOR``
+``SURFACE_DIFFUSION_LOGKEQFACTOR``
 
    Factor :math:`\texttt{p1}` in colloidal affinity law particle surface diffusion relation
    :math:`D_{s, i, m} = \tilde{D}_{s, i, m} \left[  p_{4, i, m} \left( k_{i, m} \left( c_{0}^{p} \right) \right)^{p_{5, i, m}} p_{6, i, m} exp \left( p_{7, i, m} k_{i, m} \left( c_{0}^{p} \right) \right) \right]`
    where :math:`\tilde{D}_{s, i, m}` is the original surface diffusion coefficient and 
    :math:`k_{i, m} \left( c_{0}^{p} \right) = p_{1, i, m}\left( c_{0}^{p} \right)^{p_{2, i, m}} + p_{3, i, m}`.
-   Only required if :math:`\texttt{PAR_SURFDIFFUSION_DEP}` is :math:`\texttt{LIQUID_SALT_COLLOIDAL_AFFINITY}`.
+   Only required if :math:`\texttt{SURFACE_DIFFUSION_DEP}` is :math:`\texttt{LIQUID_SALT_COLLOIDAL_AFFINITY}`.
 
    ================  =============================  ===================================
    **Type:** double  **Range:** :math:`\mathbb{R}`  **Length:** :math:`\texttt{NBOUND}`
    ================  =============================  ===================================
 
-``PAR_SURFDIFFUSION_LOGKEQEXP``
+``SURFACE_DIFFUSION_LOGKEQEXP``
 
    Factor :math:`\texttt{p2}` in colloidal affinity law particle surface diffusion relation
    :math:`D_{s, i, m} = \tilde{D}_{s, i, m} \left[  p_{4, i, m} \left( k_{i, m} \left( c_{0}^{p} \right) \right)^{p_{5, i, m}} p_{6, i, m} exp \left( p_{7, i, m} k_{i, m} \left( c_{0}^{p} \right) \right) \right]`
    where :math:`\tilde{D}_{s, i, m}` is the original surface diffusion coefficient and 
    :math:`k_{i, m} \left( c_{0}^{p} \right) = p_{1, i, m}\left( c_{0}^{p} \right)^{p_{2, i, m}} + p_{3, i, m}`.
-   Only required if :math:`\texttt{PAR_SURFDIFFUSION_DEP}` is :math:`\texttt{LIQUID_SALT_COLLOIDAL_AFFINITY}`.
+   Only required if :math:`\texttt{SURFACE_DIFFUSION_DEP}` is :math:`\texttt{LIQUID_SALT_COLLOIDAL_AFFINITY}`.
 
    ================  =============================  ===================================
    **Type:** double  **Range:** :math:`\mathbb{R}`  **Length:** :math:`\texttt{NBOUND}`
    ================  =============================  ===================================
 
-``PAR_SURFDIFFUSION_LOGKEQCONST``
+``SURFACE_DIFFUSION_LOGKEQCONST``
 
    Factor :math:`\texttt{p3}` in colloidal affinity law particle surface diffusion relation
    :math:`D_{s, i, m} = \tilde{D}_{s, i, m} \left[  p_{4, i, m} \left( k_{i, m} \left( c_{0}^{p} \right) \right)^{p_{5, i, m}} p_{6, i, m} exp \left( p_{7, i, m} k_{i, m} \left( c_{0}^{p} \right) \right) \right]`
    where :math:`\tilde{D}_{s, i, m}` is the original surface diffusion coefficient and 
    :math:`k_{i, m} \left( c_{0}^{p} \right) = p_{1, i, m}\left( c_{0}^{p} \right)^{p_{2, i, m}} + p_{3, i, m}`.
-   Only required if :math:`\texttt{PAR_SURFDIFFUSION_DEP}` is :math:`\texttt{LIQUID_SALT_COLLOIDAL_AFFINITY}`.
+   Only required if :math:`\texttt{SURFACE_DIFFUSION_DEP}` is :math:`\texttt{LIQUID_SALT_COLLOIDAL_AFFINITY}`.
 
    ================  =============================  ===================================
    **Type:** double  **Range:** :math:`\mathbb{R}`  **Length:** :math:`\texttt{NBOUND}`

doc/interface/sensitivities.rst

@@ -55,7 +55,7 @@ Group /input/sensitivity/param_XXX
 
 ``SENS_PARTYPE``
 
-   Particle type index (:math:`-1` if parameter is independent of particle types, see the multiplexing of the corresponding parameter, e.g. `PAR_DIFFUSION_MULTIPLEX`)
+   Particle type index (:math:`-1` if parameter is independent of particle types, see the multiplexing of the corresponding parameter, e.g. `PORE_DIFFUSION_MULTIPLEX`)
 
    =============  ==========================  ===========================
    **Type:** int  **Range:** :math:`\geq -1`  **Length:** :math:`\geq 1`

doc/interface/unit_operations/2d_general_rate_model.rst

@@ -278,47 +278,47 @@ For information on model equations, refer to :ref:`2d_general_rate_model_model`.
    **Type:** int  **Range:** :math:`\{0, \dots, 3 \}`  **Length:** 1
    =============  ===================================  =============
 
-``PAR_DIFFUSION``
+``PORE_DIFFUSION``
 
    Effective particle diffusion coefficients of each component in each particle type
 
    **Unit:** :math:`\mathrm{m}_{\mathrm{MP}}^{2}\,\mathrm{s}^{-1}`
 
    ================  ======================  ========================================================
-   **Type:** double  **Range:** :math:`> 0`  **Length:** see :math:`\texttt{PAR_DIFFUSION_MULTIPLEX}`
+   **Type:** double  **Range:** :math:`> 0`  **Length:** see :math:`\texttt{PORE_DIFFUSION_MULTIPLEX}`
    ================  ======================  ========================================================
 
-``PAR_DIFFUSION_MULTIPLEX``
+``PORE_DIFFUSION_MULTIPLEX``
 
-   Multiplexing mode of :math:`\texttt{PAR_DIFFUSION}`. Determines whether :math:`\texttt{PAR_DIFFUSION}` is treated as component-, type-, and/or section-independent.  This field is optional. When left out, multiplexing behavior is inferred from the length of :math:`\texttt{PAR_DIFFUSION}`.  Valid modes are:
+   Multiplexing mode of :math:`\texttt{PORE_DIFFUSION}`. Determines whether :math:`\texttt{PORE_DIFFUSION}` is treated as component-, type-, and/or section-independent.  This field is optional. When left out, multiplexing behavior is inferred from the length of :math:`\texttt{PORE_DIFFUSION}`.  Valid modes are:
 
-  0. Component-dependent, type-independent, section-independent; length of :math:`\texttt{PAR_DIFFUSION}` is :math:`\texttt{NCOMP}`
-  1. Component-dependent, type-independent, section-dependent; length of :math:`\texttt{PAR_DIFFUSION}` is :math:`\texttt{NCOMP} \cdot \texttt{NSEC}`; ordering is section-major
-  2. Component-dependent, type-dependent, section-independent; length of :math:`\texttt{PAR_DIFFUSION}` is :math:`\texttt{NCOMP} \cdot \texttt{NPARTYPE}`; ordering is type-major
-  3. Component-dependent, type-dependent, section-dependent; length of :math:`\texttt{PAR_DIFFUSION}` is :math:`\texttt{NCOMP} \cdot \texttt{NPARTYPE} \cdot \texttt{NSEC}`; ordering is section-type-major
+  0. Component-dependent, type-independent, section-independent; length of :math:`\texttt{PORE_DIFFUSION}` is :math:`\texttt{NCOMP}`
+  1. Component-dependent, type-independent, section-dependent; length of :math:`\texttt{PORE_DIFFUSION}` is :math:`\texttt{NCOMP} \cdot \texttt{NSEC}`; ordering is section-major
+  2. Component-dependent, type-dependent, section-independent; length of :math:`\texttt{PORE_DIFFUSION}` is :math:`\texttt{NCOMP} \cdot \texttt{NPARTYPE}`; ordering is type-major
+  3. Component-dependent, type-dependent, section-dependent; length of :math:`\texttt{PORE_DIFFUSION}` is :math:`\texttt{NCOMP} \cdot \texttt{NPARTYPE} \cdot \texttt{NSEC}`; ordering is section-type-major
 
    =============  ===================================  =============
    **Type:** int  **Range:** :math:`\{0, \dots, 3 \}`  **Length:** 1
    =============  ===================================  =============
 
-``PAR_SURFDIFFUSION``
+``SURFACE_DIFFUSION``
 
    Particle surface diffusion coefficients of each bound state of each component in each particle type (optional, defaults to all :math:`0~m_{SP}^2 s^{-1}`)
 
    **Unit:** :math:`\mathrm{m}_{\mathrm{SP}}^{2}\,\mathrm{s}^{-1}`
 
    ================  =========================  ============================================================
-   **Type:** double  **Range:** :math:`\geq 0`  **Length:** see :math:`\texttt{PAR_SURFDIFFUSION_MULTIPLEX}`
+   **Type:** double  **Range:** :math:`\geq 0`  **Length:** see :math:`\texttt{SURFACE_DIFFUSION_MULTIPLEX}`
    ================  =========================  ============================================================
 
-``PAR_SURFDIFFUSION_MULTIPLEX``
+``SURFACE_DIFFUSION_MULTIPLEX``
 
-   Multiplexing mode of :math:`\texttt{PAR_SURFDIFFUSION}`. Determines whether :math:`\texttt{PAR_SURFDIFFUSION}` is treated as component-, type-, and/or section-independent.  This field is optional. When left out, multiplexing behavior is inferred from the length of :math:`\texttt{PAR_SURFDIFFUSION}`.  Valid modes are:
+   Multiplexing mode of :math:`\texttt{SURFACE_DIFFUSION}`. Determines whether :math:`\texttt{SURFACE_DIFFUSION}` is treated as component-, type-, and/or section-independent.  This field is optional. When left out, multiplexing behavior is inferred from the length of :math:`\texttt{SURFACE_DIFFUSION}`.  Valid modes are:
 
-  0. Component-dependent, type-independent, section-independent; length of :math:`\texttt{PAR_SURFDIFFUSION}` is :math:`\texttt{NBND}`; ordering is component-major
-  1. Component-dependent, type-independent, section-dependent; length of :math:`\texttt{PAR_SURFDIFFUSION}` is :math:`\texttt{NBND} \cdot \texttt{NSEC}`; ordering is section-component-major
-  2. Component-dependent, type-dependent, section-independent; length of :math:`\texttt{PAR_SURFDIFFUSION}` is :math:`\texttt{NTOTALBND}`; ordering is type-component-major
-  3. Component-dependent, type-dependent, section-dependent; length of :math:`\texttt{PAR_SURFDIFFUSION}` is :math:`\texttt{NTOTALBND} \cdot \texttt{NSEC}`; ordering is section-type-component-major
+  0. Component-dependent, type-independent, section-independent; length of :math:`\texttt{SURFACE_DIFFUSION}` is :math:`\texttt{NBND}`; ordering is component-major
+  1. Component-dependent, type-independent, section-dependent; length of :math:`\texttt{SURFACE_DIFFUSION}` is :math:`\texttt{NBND} \cdot \texttt{NSEC}`; ordering is section-component-major
+  2. Component-dependent, type-dependent, section-independent; length of :math:`\texttt{SURFACE_DIFFUSION}` is :math:`\texttt{NTOTALBND}`; ordering is type-component-major
+  3. Component-dependent, type-dependent, section-dependent; length of :math:`\texttt{SURFACE_DIFFUSION}` is :math:`\texttt{NTOTALBND} \cdot \texttt{NSEC}`; ordering is section-type-component-major
 
    =============  ===================================  =============
    **Type:** int  **Range:** :math:`\{0, \dots, 3 \}`  **Length:** 1