Update units to generalized interface (#471)

* all GRM LRMP LRM 1D and 2D units

* rename fields to `PORE_DIFFUSION` and `SURFACE_DIFFUSION`

* 2D units: rename `COL_DISPERSION` to `COL_DISPERSION_AXIAL`

* replace `PARTICLE_TYPE` by transport model bools

Author: jbreue16

doc/developer_guide/examples/breakthrough.py

@@ -26,43 +26,39 @@
 model.root.input.model.unit_001.col_porosity = 0.37             # -
 model.root.input.model.unit_001.par_porosity = 0.33             # -
 model.root.input.model.unit_001.par_radius = 1e-6               # m
-                                                                
-## Transport
+                
+## Bulk transport
 model.root.input.model.unit_001.col_dispersion = 1e-8           # m^2 / s (interstitial volume)
-model.root.input.model.unit_001.film_diffusion = [1e-5]         # m / s
-model.root.input.model.unit_001.par_diffusion = [1e-10,]        # m^2 / s (mobile phase)  
-model.root.input.model.unit_001.par_surfdiffusion = [0.0,]      # m^2 / s (solid phase)
+
+## 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.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.adsorption_model = 'MULTI_COMPONENT_LANGMUIR'
-model.root.input.model.unit_001.nbound = [1]
-model.root.input.model.unit_001.adsorption.is_kinetic = True    # Kinetic binding
-model.root.input.model.unit_001.adsorption.mcl_ka = [1.0,]      # m^3 / (mol * s)   (mobile phase)
-model.root.input.model.unit_001.adsorption.mcl_kd = [1.0,]      # 1 / s (desorption)
-model.root.input.model.unit_001.adsorption.mcl_qmax = [100.0,]  # mol / m^3   (solid phase)
+model.root.input.model.unit_001.particle_type_000.adsorption_model = 'MULTI_COMPONENT_LANGMUIR'
+model.root.input.model.unit_001.particle_type_000.nbound = [1]
+model.root.input.model.unit_001.particle_type_000.adsorption.is_kinetic = True    # Kinetic binding
+model.root.input.model.unit_001.particle_type_000.adsorption.mcl_ka = [1.0,]      # m^3 / (mol * s)   (mobile phase)
+model.root.input.model.unit_001.particle_type_000.adsorption.mcl_kd = [1.0,]      # 1 / s (desorption)
+model.root.input.model.unit_001.particle_type_000.adsorption.mcl_qmax = [100.0,]  # mol / m^3   (solid phase)
 
 ## Initial conditions
 model.root.input.model.unit_001.init_c = [0.0,]
-model.root.input.model.unit_001.init_q = [0.0,]
+model.root.input.model.unit_001.particle_type_000.init_cp = [0.0,]
+model.root.input.model.unit_001.particle_type_000.init_cs = [0.0,]
 
 ## Discretization
 ### Grid cells
-model.root.input.model.unit_001.discretization.spatial_method = "FV"
-model.root.input.model.unit_001.discretization.ncol = 20
-model.root.input.model.unit_001.discretization.npar = 5
-
+model.root.input.model.unit_001.discretization.spatial_method = "DG" # "FV" recommended for strong gradients, where DG might oscillate
+model.root.input.model.unit_001.discretization.polydeg = 3 # recommended to be increased up to 5 if higher resolution is desired for smooth solutions
+model.root.input.model.unit_001.discretization.nelem = 3 # recommended to be increased if higher resolution is desired
+model.root.input.model.unit_001.particle_type_000.discretization.spatial_method = "DG"
+model.root.input.model.unit_001.particle_type_000.discretization.par_polydeg = 3 # recommended to be increased if higher resolution is desired
+model.root.input.model.unit_001.particle_type_000.discretization.par_nelem = 1 #  recommended to stay fixed at 1 except for targeted resolution of particle (ie user defined par_disc_type)
 ### Other options
-model.root.input.model.unit_001.discretization.par_disc_type = 'EQUIDISTANT_PAR'    
+model.root.input.model.unit_001.discretization.particle_type_000.par_disc_type = 'EQUIDISTANT'    
 model.root.input.model.unit_001.discretization.use_analytic_jacobian = 1
-model.root.input.model.unit_001.discretization.reconstruction = 'WENO'
-model.root.input.model.unit_001.discretization.gs_type = 1
-model.root.input.model.unit_001.discretization.max_krylov = 0
-model.root.input.model.unit_001.discretization.max_restarts = 10
-model.root.input.model.unit_001.discretization.schur_safety = 1.0e-8
-
-model.root.input.model.unit_001.discretization.weno.boundary_model = 0
-model.root.input.model.unit_001.discretization.weno.weno_eps = 1e-10
-model.root.input.model.unit_001.discretization.weno.weno_order = 3
 
 ## Outlet
 model.root.input.model.unit_002.unit_type = 'OUTLET'

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`