wip update interface

Author: jbreue16

doc/developer_guide/examples/breakthrough.py

@@ -43,7 +43,7 @@
 
 ## 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.INIT_CS = [0.0,]
 
 ## Discretization
 ### Grid cells
@@ -52,7 +52,7 @@
 model.root.input.model.unit_001.discretization.npar = 5
 
 ### Other options
-model.root.input.model.unit_001.discretization.par_disc_type = 'EQUIDISTANT_PAR'    
+model.root.input.model.unit_001.discretization.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

doc/interface/unit_operations/2d_general_rate_model.rst

@@ -93,7 +93,7 @@ For information on model equations, refer to :ref:`2d_general_rate_model_model`.
    **Type:** double  **Range:** :math:`\geq 0`
    ================  =========================
 
-``INIT_Q``
+``INIT_CS``
 
    Initial concentrations for each bound state of each component in the bead solid phase. If :math:`\texttt{ADSORPTION_MODEL_MULTIPLEX}` is 0, values for each particle type are required in type-component-major ordering (length is :math:`\texttt{NTOTALBND}`). If :math:`\texttt{ADSORPTION_MODEL_MULTIPLEX}` is 1, values for one particle type are required in component-major ordering (length is :math:`\sum_{i = 0}^{\texttt{NCOMP} - 1} \texttt{NBND}_i`).  Alternatively, values for each radial zone can be supplied. If :math:`\texttt{ADSORPTION_MODEL_MULTIPLEX}` is 0, values for each radial zone and each particle type are required in radial-type-component-major ordering (length is :math:`\texttt{NRAD} \cdot \texttt{NTOTALBND}`). If :math:`\texttt{ADSORPTION_MODEL_MULTIPLEX}` is 1, values for each radial zone and all particle types are required in radial-component-major ordering (length is :math:`\texttt{NRAD} \cdot \sum_{i = 0}^{\texttt{NCOMP} - 1} \texttt{NBND}_i`). In the radial-inhomogeneous case, the :math:`\texttt{SENS_REACTION}` field is used for indexing the radial zone when specifying parameter sensitivities.
 
@@ -105,7 +105,7 @@ For information on model equations, refer to :ref:`2d_general_rate_model_model`.
 
 ``INIT_STATE``
 
-   Full state vector for initialization (optional, :math:`\texttt{INIT_C}`, :math:`\texttt{INIT_CP}`, and :math:`\texttt{INIT_Q}` will be ignored; if length is :math:`2\texttt{NDOF}`, then the second half is used for time derivatives)
+   Full state vector for initialization (optional, :math:`\texttt{INIT_C}`, :math:`\texttt{INIT_CP}`, and :math:`\texttt{INIT_CS}` will be ignored; if length is :math:`2\texttt{NDOF}`, then the second half is used for time derivatives)
 
    **Unit:** :math:`various`
 
@@ -430,21 +430,21 @@ Group /input/model/unit_XXX/discretization - UNIT_TYPE - GENERAL_RATE_MODEL_2D
 
 ``PAR_DISC_TYPE``
 
-   Specifies the discretization scheme inside the particles for all or each particle type. Valid values are :math:`\texttt{EQUIDISTANT_PAR}`, :math:`\texttt{EQUIVOLUME_PAR}`, and :math:`\texttt{USER_DEFINED_PAR}`.
+   Specifies the discretization scheme inside the particles for all or each particle type. Valid values are :math:`\texttt{EQUIDISTANT}`, :math:`\texttt{EQUIVOLUME}`, and :math:`\texttt{USER_DEFINED}`.
 
    ================  =========================================
    **Type:** string  **Length:** :math:`1 / \texttt{NPARTYPE}`
    ================  =========================================
 
 ``PAR_DISC_VECTOR``
 
-   Node coordinates for the cell boundaries (ignored if :math:`\texttt{PAR_DISC_TYPE} \neq \texttt{USER_DEFINED_PAR}`). The coordinates are relative and have to include the endpoints 0 and 1. They are later linearly mapped to the true radial range :math:`[r_{c,j}, r_{p,j}]`. The coordinates for each particle type are appended to one long vector in type-major ordering.
+   Node coordinates for the cell boundaries (ignored if :math:`\texttt{PAR_DISC_TYPE} \neq \texttt{USER_DEFINED}`). The coordinates are relative and have to include the endpoints 0 and 1. They are later linearly mapped to the true radial range :math:`[r_{c,j}, r_{p,j}]`. The coordinates for each particle type are appended to one long vector in type-major ordering.
 
    ================  ========================  ===============================================
    **Type:** double  **Range:** :math:`[0,1]`  **Length:** :math:`sum_i (\texttt{NPAR}_i + 1)`
    ================  ========================  ===============================================
 
-``PAR_BOUNDARY_ORDER``
+``FV_BOUNDARY_ORDER``
 
    Order of accuracy of outer particle boundary condition. Optional, defaults to 2.
 

doc/interface/unit_operations/cstr.rst

@@ -93,7 +93,7 @@ For information on model equations, refer to :ref:`cstr_model`.
    **Type:** double  **Range:** :math:`\geq 0`  **Length:** 1
    ================  =========================  =============
 
-``INIT_Q``
+``INIT_CS``
 
    Initial concentrations for each bound state of each component in the bead solid phase of each particle type in type-component-major ordering. This field is optional and defaults to all 0.
 
@@ -105,7 +105,7 @@ For information on model equations, refer to :ref:`cstr_model`.
 
 ``INIT_STATE``
 
-   Full state vector for initialization (optional, :math:`\texttt{INIT_C}`, :math:`\texttt{INIT_Q}`, and :math:`\texttt{INIT_VOLUME}` will be ignored; if length is :math:`2\texttt{NDOF}`, then the second half is used for time derivatives)
+   Full state vector for initialization (optional, :math:`\texttt{INIT_C}`, :math:`\texttt{INIT_CS}`, and :math:`\texttt{INIT_VOLUME}` will be ignored; if length is :math:`2\texttt{NDOF}`, then the second half is used for time derivatives)
 
    **Unit:** :math:`various`
 

doc/interface/unit_operations/general_rate_model.rst

@@ -93,7 +93,7 @@ For information on model equations, refer to :ref:`general_rate_model_model`.
    **Type:** double  **Range:** :math:`\geq 0`  **Length:** :math:`\texttt{NCOMP} / \texttt{NPARTYPE} \cdot \texttt{NCOMP}`
    ================  =========================  ===========================================================================
 
-``INIT_Q``
+``INIT_CS``
 
    Initial concentrations for each bound state of each component in the bead solid phase. If :math:`\texttt{ADSORPTION_MODEL_MULTIPLEX}` is :math:`0`, values for each particle type are required in type-component-major ordering (length is :math:`\texttt{NTOTALBND}`). If :math:`\texttt{ADSORPTION_MODEL_MULTIPLEX}` is :math:`1`, values for one particle type are required in component-major ordering (length is :math:`\sum_{i = 0}^{\texttt{NCOMP} - 1} \texttt{NBND}_i`).
 
@@ -105,7 +105,7 @@ For information on model equations, refer to :ref:`general_rate_model_model`.
 
 ``INIT_STATE``
 
-   Full state vector for initialization (optional, :math:`\texttt{INIT_C}`, :math:`\texttt{INIT_CP}`, and :math:`\texttt{INIT_Q}` will be ignored; if length is :math:`2\texttt{NDOF}`, then the second half is used for time derivatives)
+   Full state vector for initialization (optional, :math:`\texttt{INIT_C}`, :math:`\texttt{INIT_CP}`, and :math:`\texttt{INIT_CS}` will be ignored; if length is :math:`2\texttt{NDOF}`, then the second half is used for time derivatives)
 
    **Unit:** :math:`various`
 
@@ -333,15 +333,15 @@ Group /input/model/unit_XXX/discretization - UNIT_TYPE - GENERAL_RATE_MODEL
 
 ``PAR_DISC_TYPE``
 
-   Specifies the discretization scheme inside the particles for all or each particle type. Valid values are :math:`\texttt{EQUIDISTANT_PAR}`, :math:`\texttt{EQUIVOLUME_PAR}`, and :math:`\texttt{USER_DEFINED_PAR}`.
+   Specifies the discretization scheme inside the particles for all or each particle type. Valid values are :math:`\texttt{EQUIDISTANT}`, :math:`\texttt{EQUIVOLUME}`, and :math:`\texttt{USER_DEFINED}`.
 
    ================  =================================================
    **Type:** string  **Length:** :math:`1` / :math:`\texttt{NPARTYPE}`
    ================  =================================================
 
 ``PAR_DISC_VECTOR``
 
-   Node coordinates for the cell boundaries (ignored if :math:`\texttt{PAR_DISC_TYPE} \neq \texttt{USER_DEFINED_PAR}`). The coordinates are relative and have to include the endpoints :math:`0` and :math:`1`. They are later linearly mapped to the true radial range :math:`[r_{c,j}, r_{p,j}]`. The coordinates for each particle type are appended to one long vector in type-major ordering.
+   Node coordinates for the cell boundaries (ignored if :math:`\texttt{PAR_DISC_TYPE} \neq \texttt{USER_DEFINED}`). The coordinates are relative and have to include the endpoints :math:`0` and :math:`1`. They are later linearly mapped to the true radial range :math:`[r_{c,j}, r_{p,j}]`. The coordinates for each particle type are appended to one long vector in type-major ordering.
 
    ================  ========================  ================================================
    **Type:** double  **Range:** :math:`[0,1]`  **Length:** :math:`\sum_i (\texttt{NPAR}_i + 1)`
@@ -384,7 +384,7 @@ Finite Volumes (Default)
    **Type:** int  **Range:** :math:`\geq 1`  **Length:** :math:`1` / :math:`\texttt{NPARTYPE}`
    =============  =========================  =================================================
 
-``PAR_BOUNDARY_ORDER``
+``FV_BOUNDARY_ORDER``
 
    Order of accuracy of outer particle boundary condition. Optional, defaults to :math:`2`.
 

doc/interface/unit_operations/lumped_rate_model_with_pores.rst

@@ -84,7 +84,7 @@ For information on model equations, refer to :ref:`lumped_rate_model_with_pores_
    **Type:** double  **Range:** :math:`\geq 0`  **Length:** :math:`\texttt{NCOMP} / \texttt{NPARTYPE} \cdot \texttt{NCOMP}`
    ================  =========================  ===========================================================================
 
-``INIT_Q``
+``INIT_CS``
    Initial concentrations for each bound state of each component in the bead solid phase. If :math:`\texttt{ADSORPTION_MODEL_MULTIPLEX}` is :math:`0`, values for each particle type are required in type-component-major ordering (length is :math:`\texttt{NTOTALBND}`). If :math:`\texttt{ADSORPTION_MODEL_MULTIPLEX}` is :math:`1`, values for one particle type are required in component-major ordering (length is :math:`\sum_{i = 0}^{\texttt{NCOMP} - 1} \texttt{NBND}_i`).
 
    **Unit:** :math:`\mathrm{mol}\,\mathrm{m}_{\mathrm{SP}}^{-3}`
@@ -94,7 +94,7 @@ For information on model equations, refer to :ref:`lumped_rate_model_with_pores_
    ================  =========================
 
 ``INIT_STATE``
-   Full state vector for initialization (optional, :math:`\texttt{INIT_C}`, :math:`\texttt{INIT_CP}`, and :math:`\texttt{INIT_Q}` will be ignored; if length is :math:`2\texttt{NDOF}`, then the second half is used for time derivatives)
+   Full state vector for initialization (optional, :math:`\texttt{INIT_C}`, :math:`\texttt{INIT_CP}`, and :math:`\texttt{INIT_CS}` will be ignored; if length is :math:`2\texttt{NDOF}`, then the second half is used for time derivatives)
 
    **Unit:** :math:`various`
 

doc/interface/unit_operations/lumped_rate_model_without_pores.rst

@@ -59,7 +59,7 @@ For information on model equations, refer to :ref:`lumped_rate_model_without_por
    **Type:** double  **Range:** :math:`\geq 0`  **Length:** :math:`\texttt{NCOMP}`
    ================  =========================  ===================================
 
-``INIT_Q``
+``INIT_CS``
 
    Initial concentrations for each bound state of each component in the bead solid phase in component-major ordering
 
@@ -71,7 +71,7 @@ For information on model equations, refer to :ref:`lumped_rate_model_without_por
 
 ``INIT_STATE``
 
-   Full state vector for initialization (optional, :math:`\texttt{INIT_C}` and :math:`\texttt{INIT_Q}` will be ignored; if length is :math:`2\texttt{NDOF}`, then the second half is used for time derivatives)
+   Full state vector for initialization (optional, :math:`\texttt{INIT_C}` and :math:`\texttt{INIT_CS}` will be ignored; if length is :math:`2\texttt{NDOF}`, then the second half is used for time derivatives)
 
    **Unit:** :math:`various`