Merge pull request #6013 from gassmoeller/update_parameters

Update parameters

doc/sphinx/parameters/Discretization.md

@@ -9,7 +9,7 @@
 ### __Parameter name:__ Composition polynomial degree
 **Default value:** 2
 
-**Pattern:** [Integer range 0...2147483647 (inclusive)]
+**Pattern:** [List of <[Integer range 0...2147483647 (inclusive)]> of length 0...4294967295 (inclusive)]
 
 **Documentation:** The polynomial degree to use for the composition variable(s). As an example, a value of 2 for this parameter will yield either the element $Q_2$ or $DGQ_2$ for the compositional field(s), depending on whether we use continuous or discontinuous field(s).
 
@@ -37,7 +37,7 @@ Be careful if you choose 1 as the degree. The resulting element is not stable an
 ### __Parameter name:__ Use discontinuous composition discretization
 **Default value:** false
 
-**Pattern:** [Bool]
+**Pattern:** [List of <[Bool]> of length 0...4294967295 (inclusive)]
 
 **Documentation:** Whether to use a composition discretization that is discontinuous as opposed to continuous. This then requires the assembly of face terms between cells, and weak imposition of boundary terms for the composition field via the discontinuous Galerkin method.
 
@@ -151,17 +151,17 @@ For an in-depth discussion of these issues and a quantitative evaluation of the
 ### __Parameter name:__ Use limiter for discontinuous composition solution
 **Default value:** false
 
-**Pattern:** [Bool]
+**Pattern:** [List of <[Bool]> of length 0...4294967295 (inclusive)]
 
-**Documentation:** Whether to apply the bound preserving limiter as a correction after having the discontinuous composition solution. Currently we apply this only to the compositional solution if the &rsquo;Global composition maximum&rsquo; and &rsquo;Global composition minimum&rsquo; are already defined in the .prm file. This limiter keeps the discontinuous solution in the range given by Global composition maximum&rsquo; and &rsquo;Global composition minimum&rsquo;.
+**Documentation:** Whether to apply the bound preserving limiter as a correction after having the discontinuous composition solution. The limiter will only have an effect if the &rsquo;Global composition maximum&rsquo; and &rsquo;Global composition minimum&rsquo; parameters are defined in the .prm file. This limiter keeps the discontinuous solution in the range given by Global composition maximum&rsquo; and &rsquo;Global composition minimum&rsquo;. The number of input values in this parameter separated by &rsquo;,&rsquo; has to be one or the number of the compositional fields. When only one value is supplied, this same value is assumed for all compositional fields, otherwise each value represents if the limiter should be applied to the respective compositional field. Because this limiter modifies the solution it no longer satisfies the assembled equation. Therefore, the nonlinear residual for this field is meaningless, and in nonlinear solvers we will ignore the residual for this field to evaluate if the nonlinear solver has converged.
 
 (parameters:Discretization/Stabilization_20parameters/Use_20limiter_20for_20discontinuous_20temperature_20solution)=
 ### __Parameter name:__ Use limiter for discontinuous temperature solution
 **Default value:** false
 
 **Pattern:** [Bool]
 
-**Documentation:** Whether to apply the bound preserving limiter as a correction after computing the discontinuous temperature solution. Currently we apply this only to the temperature solution if the &rsquo;Global temperature maximum&rsquo; and &rsquo;Global temperature minimum&rsquo; are already defined in the .prm file. This limiter keeps the discontinuous solution in the range given by &rsquo;Global temperature maximum&rsquo; and &rsquo;Global temperature minimum&rsquo;.
+**Documentation:** Whether to apply the bound preserving limiter as a correction after computing the discontinuous temperature solution. The limiter will only have an effect if the &rsquo;Global temperature maximum&rsquo; and &rsquo;Global temperature minimum&rsquo; parameters are defined in the .prm file. This limiter keeps the discontinuous solution in the range given by &rsquo;Global temperature maximum&rsquo; and &rsquo;Global temperature minimum&rsquo;. Because this limiter modifies the solution it no longer satisfies the assembled equation. Therefore, the nonlinear residual for this field is meaningless, and in nonlinear solvers we will ignore the residual for this field to evaluate if the nonlinear solver has converged.
 
 (parameters:Discretization/Stabilization_20parameters/alpha)=
 ### __Parameter name:__ alpha

doc/sphinx/parameters/Gravity_20model.md

@@ -53,6 +53,14 @@
 
 (parameters:Gravity_20model/Function)=
 ## **Subsection:** Gravity model / Function
+(parameters:Gravity_20model/Function/Coordinate_20system)=
+### __Parameter name:__ Coordinate system
+**Default value:** cartesian
+
+**Pattern:** [Selection cartesian|spherical|depth ]
+
+**Documentation:** A selection that determines the assumed coordinate system for the function variables. Allowed values are ‘cartesian’, ‘spherical’, and ‘depth’. ‘spherical’ coordinates are interpreted as r,phi or r,phi,theta in 2d/3d respectively with theta being the polar angle. ‘depth’ will create a function, in which only the first parameter is non-zero, which is interpreted to be the depth of the point.
+
 (parameters:Gravity_20model/Function/Function_20constants)=
 ### __Parameter name:__ Function constants
 **Default value:**

doc/sphinx/parameters/Heating_20model.md

@@ -91,10 +91,18 @@ The formula is interpreted as having units W/kg.
 
 **Pattern:** [Double 0...MAX_DOUBLE (inclusive)]
 
-**Documentation:** The specific rate of heating due to radioactive decay (or other bulk sources you may want to describe). This parameter corresponds to the variable $H$ in the temperature equation stated in the manual, and the heating term is $ho H$. Units: W/kg.
+**Documentation:** The specific rate of heating due to radioactive decay (or other bulk sources you may want to describe). This parameter corresponds to the variable $H$ in the temperature equation stated in the manual, and the heating term is $\rho H$. Units: W/kg.
 
 (parameters:Heating_20model/Function)=
 ## **Subsection:** Heating model / Function
+(parameters:Heating_20model/Function/Coordinate_20system)=
+### __Parameter name:__ Coordinate system
+**Default value:** cartesian
+
+**Pattern:** [Selection cartesian|spherical|depth ]
+
+**Documentation:** A selection that determines the assumed coordinate system for the function variables. Allowed values are ‘cartesian’, ‘spherical’, and ‘depth’. ‘spherical’ coordinates are interpreted as r,phi or r,phi,theta in 2d/3d respectively with theta being the polar angle. ‘depth’ will create a function, in which only the first parameter is non-zero, which is interpreted to be the depth of the point.
+
 (parameters:Heating_20model/Function/Function_20constants)=
 ### __Parameter name:__ Function constants
 **Default value:**

doc/sphinx/parameters/Initial_20temperature_20model.md

@@ -751,13 +751,13 @@ If the function you are describing represents a vector-valued function with mult
 
 **Documentation:** The file name of the spherical harmonics coefficients from Ritsema et al.
 
-(parameters:Initial_20temperature_20model/S40RTS_20perturbation/Maximum_20order)=
-### __Parameter name:__ Maximum order
+(parameters:Initial_20temperature_20model/S40RTS_20perturbation/Maximum_20degree)=
+### __Parameter name:__ Maximum degree
 **Default value:** 20
 
 **Pattern:** [Integer range 0...2147483647 (inclusive)]
 
-**Documentation:** The maximum order the users specify when reading the data file of spherical harmonic coefficients, which must be smaller than the maximum order the data file stored. This parameter will be used only if ’Specify a lower maximum order’ is set to true.
+**Documentation:** The maximum degree the users specify when reading the data file of spherical harmonic coefficients, which must be smaller than the maximum degree the data file stored. This parameter will be used only if ’Specify a lower maximum degree’ is set to true.
 
 (parameters:Initial_20temperature_20model/S40RTS_20perturbation/Reference_20temperature)=
 ### __Parameter name:__ Reference temperature
@@ -783,13 +783,13 @@ If the function you are describing represents a vector-valued function with mult
 
 **Documentation:** This will set the heterogeneity prescribed by S20RTS or S40RTS to zero down to the specified depth (in meters). Note that your resolution has to be adequate to capture this cutoff. For example if you specify a depth of 660km, but your closest spherical depth layers are only at 500km and 750km (due to a coarse resolution) it will only zero out heterogeneities down to 500km. Similar caution has to be taken when using adaptive meshing.
 
-(parameters:Initial_20temperature_20model/S40RTS_20perturbation/Specify_20a_20lower_20maximum_20order)=
-### __Parameter name:__ Specify a lower maximum order
+(parameters:Initial_20temperature_20model/S40RTS_20perturbation/Specify_20a_20lower_20maximum_20degree)=
+### __Parameter name:__ Specify a lower maximum degree
 **Default value:** false
 
 **Pattern:** [Bool]
 
-**Documentation:** Option to use a lower maximum order when reading the data file of spherical harmonic coefficients. This is probably used for the faster tests or when the users only want to see the spherical harmonic pattern up to a certain order.
+**Documentation:** Option to use a lower maximum degree when reading the data file of spherical harmonic coefficients. This is probably used for the faster tests or when the users only want to see the spherical harmonic pattern up to a certain degree.
 
 (parameters:Initial_20temperature_20model/S40RTS_20perturbation/Spline_20knots_20depth_20file_20name)=
 ### __Parameter name:__ Spline knots depth file name
@@ -875,13 +875,13 @@ If the function you are describing represents a vector-valued function with mult
 
 **Documentation:** The file name of the spherical harmonics coefficients from Auer et al.
 
-(parameters:Initial_20temperature_20model/SAVANI_20perturbation/Maximum_20order)=
-### __Parameter name:__ Maximum order
+(parameters:Initial_20temperature_20model/SAVANI_20perturbation/Maximum_20degree)=
+### __Parameter name:__ Maximum degree
 **Default value:** 20
 
 **Pattern:** [Integer range 0...2147483647 (inclusive)]
 
-**Documentation:** The maximum order the users specify when reading the data file of spherical harmonic coefficients, which must be smaller than the maximum order the data file stored. This parameter will be used only if ’Specify a lower maximum order’ is set to true.
+**Documentation:** The maximum degree the users specify when reading the data file of spherical harmonic coefficients, which must be smaller than the maximum degree the data file stored. This parameter will be used only if ’Specify a lower maximum degree’ is set to true.
 
 (parameters:Initial_20temperature_20model/SAVANI_20perturbation/Reference_20temperature)=
 ### __Parameter name:__ Reference temperature
@@ -907,13 +907,13 @@ If the function you are describing represents a vector-valued function with mult
 
 **Documentation:** This will set the heterogeneity prescribed by SAVANI to zero down to the specified depth (in meters). Note that your resolution has to be adequate to capture this cutoff. For example if you specify a depth of 660km, but your closest spherical depth layers are only at 500km and 750km (due to a coarse resolution) it will only zero out heterogeneities down to 500km. Similar caution has to be taken when using adaptive meshing.
 
-(parameters:Initial_20temperature_20model/SAVANI_20perturbation/Specify_20a_20lower_20maximum_20order)=
-### __Parameter name:__ Specify a lower maximum order
+(parameters:Initial_20temperature_20model/SAVANI_20perturbation/Specify_20a_20lower_20maximum_20degree)=
+### __Parameter name:__ Specify a lower maximum degree
 **Default value:** false
 
 **Pattern:** [Bool]
 
-**Documentation:** Option to use a lower maximum order when reading the data file of spherical harmonic coefficients. This is probably used for the faster tests or when the users only want to see the spherical harmonic pattern up to a certain order.
+**Documentation:** Option to use a lower maximum degree when reading the data file of spherical harmonic coefficients. This is probably used for the faster tests or when the users only want to see the spherical harmonic pattern up to a certain degree.
 
 (parameters:Initial_20temperature_20model/SAVANI_20perturbation/Spline_20knots_20depth_20file_20name)=
 ### __Parameter name:__ Spline knots depth file name