Update API

* Use Richards scope in system tests
* Added verbosity keyword for global output
* Modified API for setup of ini files
Signed-off-by: Santiago Ospina <santiago.ospina@iup.uni-heidelberg.de>

doc/default_files/common-parameters.xml

@@ -79,17 +79,11 @@ adding an empty line, make text **bold** or ``monospaced``.
   </category>
 
   <category name="adaptivity">
-    <parameter name="useAdaptivity">
-      <definition> Switches adaptive grid refinement (h-adaptivity) on (``true``) or
-        off (``false``). If enabled, an unstructured grid manager with higher computational 
-        cost is used when using rectangular / cubic grids. </definition>
-      <values> true, false </values>
-      <suggestion> false </suggestion>
-    </parameter>
-
     <parameter name="policy">
-      <definition> Defines the target policy to do adaptive grid refinement (h-adaptivity).
-        Only one policy available at the moment. </definition>
+      <definition> Switches the target policy to do adaptive grid refinement 
+        (h-adaptivity). If enabled, an unstructured grid manager with higher 
+        computational cost is used when using rectangular / cubic grids. 
+        Only one policy available at the moment.</definition>
       <values> waterFlux </values>
       <suggestion> waterFlux </suggestion>
     </parameter>
@@ -156,6 +150,14 @@ adding an empty line, make text **bold** or ``monospaced``.
     </parameter>
   </category>
 
+  <category name="output">
+    <parameter name="verbose">
+      <definition> Overall verbosity of the program </definition>
+      <suggestion> 0 </suggestion>
+      <values> 0, 1, 2, 3 </values>
+    </parameter>
+  </category>
+
   <category name="misc">
     <parameter name="debugMode">
       <definition> Switches debug mode on (``true``) or off (``false``). In debug mode,

doc/default_files/richards-parameters.xml

@@ -33,7 +33,7 @@ adding an empty line, make text **bold** or ``monospaced``.
 <dorie>
   <category name="richards.output">
     <parameter name="verbose">
-      <definition> Overall verbosity of the program </definition>
+      <definition> Verbosity of the Richards simulation </definition>
       <suggestion> 0 </suggestion>
       <values> 0, 1, 2, 3 </values>
     </parameter>

dune/dorie/dorie.cc

@@ -18,6 +18,7 @@
 
 #include "interface/richards_simulation.hh"
 #include "solver/util_grid_creator.hh"
+#include "interface/setup_inifile.hh"
 
 // #include <dune/dorie/dorie.hh> // System and DUNE Headers
 
@@ -101,10 +102,8 @@ int main(int argc, char** argv)
 			sleep(5);
 		}
 
-		Dune::Dorie::Setup::inifile(inifile);
-
 		// extract richards configuration
-		Dune::ParameterTree richards_config = inifile.sub("richards");
+		Dune::ParameterTree richards_config = Dune::Dorie::Setup::prep_ini_for_richards(inifile);
 
 		// Read necessary variables
 		const std::string gtype = inifile.get<std::string>("grid.gridType");

dune/dorie/interface/setup_inifile.hh

+#include <iostream>
+#include <memory>
+#include <vector>
+
+#include <dune/common/exceptions.hh>
+#include <dune/common/parametertree.hh>
+
+namespace Dune{
+namespace Dorie{
+
+/**
+ * @brief      Helper namespace to configurate/setup input files
+ */
+namespace Setup
+{
+	/*------------------------------------------------------------------------*//**
+	 * @brief      Set up the configuration keys for Richards simulations
+	 *
+	 * @param      ini   The inifile
+	 */
+	Dune::ParameterTree prep_ini_for_richards(const Dune::ParameterTree& ini)
+	{
+		Dune::ParameterTree richards_ini(ini.sub("richards"));
+		// move grid extensions into richards category (needed for reading parameters)
+		richards_ini["grid.extensions"] = ini["grid.extensions"];
+
+		// copy adaptivity keywords into richards category
+		if (ini.get<std::string>("adaptivity.policy") == "waterFlux")
+			richards_ini.sub("richards.adaptivity") = ini.sub("adaptivity");
+		else
+			DUNE_THROW(NotImplemented, "Not known adaptativity policy (" 
+				<< ini.get<std::string>("adaptivity.policy") << ")!");
+
+		return richards_ini;
+	}
+};
+
+}
+}
\ No newline at end of file

dune/dorie/interface/util.hh

@@ -227,35 +227,6 @@ struct BaseTraits
 
 };
 
-
-/**
- * @brief      Helper object to configurate input files
- */
-struct Setup
-{
-	/*------------------------------------------------------------------------*//**
-	 * @brief      Set up the configuration keys for the simulations
-	 *
-	 * @param      ini   The inifile
-	 */
-	static void inifile(Dune::ParameterTree& ini)
-	{
-		// move grid extensions into richards category (needed for reading parameters)
-		ini["richards.grid.extensions"] = ini["grid.extensions"];
-		// configure a global verbose level
-		ini["output.verbose"] = ini["richards.output.verbose"];
-
-		if (ini.get<std::string>("adaptivity.policy") == "waterFlux")
-			// copy adaptivity keywords into richards category
-			ini.sub("richards.adaptivity") = ini.sub("adaptivity");
-		else
-			DUNE_THROW(NotImplemented, "Not known adaptativity policy (" 
-				<< ini.get<std::string>("adaptivity.policy") << ")!");
-	}
-};
-
-
-
 }
 }
 

test/mass_conservation.mini.in

@@ -25,15 +25,17 @@ grid.initialLevel = 2
 grid.cells = 20 20
 grid.gridFile = {_asset_path}/meshes/square.msh
 
-richards.output.fileName = mass_conservation | unique
-richards.output.outputPath = mass_conservation | unique
+[richards]
 
-richards.boundary.file = "{_asset_path}/bcs/mass_conservation_2d.dat"
+output.fileName = mass_conservation | unique
+output.outputPath = mass_conservation | unique
 
-richards.parameters.arrayFile = "{_asset_path}/parfields/sand.h5"
+boundary.file = "{_asset_path}/bcs/mass_conservation_2d.dat"
 
-richards.time.end = 1E4
-richards.time.maxTimestep = 1E4
-richards.time.startTimestep = 1E2
+parameters.arrayFile = "{_asset_path}/parfields/sand.h5"
 
-richards.numerics.FEorder = 1
\ No newline at end of file
+time.end = 1E4
+time.maxTimestep = 1E4
+time.startTimestep = 1E2
+
+numerics.FEorder = 1
\ No newline at end of file

test/muphi.mini.in

@@ -16,15 +16,17 @@ grid.gridType = rectangular
 grid.cells = 50 200
 grid.extensions = 1 1
 
-richards.output.fileName = muphi | unique name
-richards.output.outputPath = muphi | unique name
+[richards]
 
-richards.time.end = 1.5E5
-richards.time.maxTimestep = 1E5
-richards.time.startTimestep = 1E3
+output.fileName = muphi | unique name
+output.outputPath = muphi | unique name
 
-richards.boundary.file = "{_asset_path}/bcs/muphi2d.dat"
+time.end = 1.5E5
+time.maxTimestep = 1E5
+time.startTimestep = 1E3
 
-richards.parameters.arrayFile = fft_field_muphi.h5
+boundary.file = "{_asset_path}/bcs/muphi2d.dat"
+
+parameters.arrayFile = fft_field_muphi.h5
 
 

test/ode_homogeneous_sand.mini.in

@@ -12,26 +12,27 @@ grid.cells = 1 160, 1 40, 1 20 | expand prec
 
 adaptivity.useAdaptivity = false
 
-richards.output.fileName = ode_homogeneous_sand | unique
-richards.output.outputPath = ode_homogeneous_sand | unique
+[richards]
 
-richards.boundary.file = "{_asset_path}/bcs/infiltration_2d.dat"
+output.fileName = ode_homogeneous_sand | unique
+output.outputPath = ode_homogeneous_sand | unique
 
-richards.parameters.arrayFile = "{_asset_path}/parfields/sand.h5"
+boundary.file = "{_asset_path}/bcs/infiltration_2d.dat"
 
-richards.time.end = 1E7
-richards.time.maxTimestep = 1E7
-richards.time.startTimestep = 1E4
+parameters.arrayFile = "{_asset_path}/parfields/sand.h5"
+
+time.end = 1E7
+time.maxTimestep = 1E7
+time.startTimestep = 1E4
+
+NewtonParameters.AbsoluteLimit = 1E-10
+NewtonParameters.Reduction = 1E-10
+
+numerics.penaltyFactor = 10
+numerics.FEorder = 1, 2, 3 | expand prec
 
 [_ode]
+
 flux = -5.55e-6
 head_abstol = 3E-6, 2E-8, 6E-8 | expand prec
 flux_abstol = 5E-11, 1E-9, 3E-12 | expand prec
-
-[richards.NewtonParameters]
-AbsoluteLimit = 1E-10
-Reduction = 1E-10
-
-[richards.numerics]
-penaltyFactor = 10
-FEorder = 1, 2, 3 | expand prec
\ No newline at end of file

test/ode_homogeneous_silt.mini.in

@@ -12,26 +12,27 @@ grid.cells = 1 160, 1 40, 1 20 | expand prec
 
 adaptivity.useAdaptivity = false
 
-richards.output.fileName = ode_homogeneous_silt | unique
-richards.output.outputPath = ode_homogeneous_silt | unique
+[richards]
 
-richards.boundary.file = "{_asset_path}/bcs/infiltration_2d.dat"
+output.fileName = ode_homogeneous_silt | unique
+output.outputPath = ode_homogeneous_silt | unique
 
-richards.parameters.arrayFile = "{_asset_path}/parfields/silt.h5"
+boundary.file = "{_asset_path}/bcs/infiltration_2d.dat"
 
-richards.time.end = 1E7
-richards.time.maxTimestep = 1E7
-richards.time.startTimestep = 1E4
+parameters.arrayFile = "{_asset_path}/parfields/silt.h5"
+
+time.end = 1E7
+time.maxTimestep = 1E7
+time.startTimestep = 1E4
+
+NewtonParameters.AbsoluteLimit = 1E-10
+NewtonParameters.Reduction = 1E-10
+
+numerics.penaltyFactor = 10
+numerics.FEorder = 1, 2, 3 | expand prec
 
 [_ode]
+
 flux = -5.55e-6
 head_abstol = 6E-6, 4E-6, 9E-6 | expand prec
-flux_abstol = 2E-9, 2E-8, 3E-9 | expand prec
-
-[richards.NewtonParameters]
-AbsoluteLimit = 1E-10
-Reduction = 1E-10
-
-[richards.numerics]
-penaltyFactor = 10
-FEorder = 1, 2, 3 | expand prec
\ No newline at end of file
+flux_abstol = 2E-9, 2E-8, 3E-9 | expand prec
\ No newline at end of file

test/ode_layered.mini.in

@@ -12,26 +12,27 @@ grid.cells = 1 160, 1 40, 1 20 | expand prec
 
 adaptivity.useAdaptivity = false
 
-richards.output.fileName = ode_layered | unique
-richards.output.outputPath = ode_layered | unique
+[richards]
 
-richards.boundary.file = "{_asset_path}/bcs/infiltration_2d.dat"
+output.fileName = ode_layered | unique
+output.outputPath = ode_layered | unique
 
-richards.parameters.arrayFile = "{_asset_path}/parfields/layered.h5"
+boundary.file = "{_asset_path}/bcs/infiltration_2d.dat"
 
-richards.time.end = 1E7
-richards.time.maxTimestep = 1E7
-richards.time.startTimestep = 1E4
+parameters.arrayFile = "{_asset_path}/parfields/layered.h5"
+
+time.end = 1E7
+time.maxTimestep = 1E7
+time.startTimestep = 1E4
+
+NewtonParameters.AbsoluteLimit = 1E-10
+NewtonParameters.Reduction = 1E-10
+
+numerics.penaltyFactor = 10
+numerics.FEorder = 1, 2, 3 | expand prec
 
 [_ode]
+
 flux = -5.55e-6
 head_abstol = 3E-5, 4E-8, 4E-6 | expand prec
 flux_abstol = 5E-10, 4E-9, 5E-11 | expand prec
-
-[richards.NewtonParameters]
-AbsoluteLimit = 1E-10
-Reduction = 1E-10
-
-[richards.numerics]
-penaltyFactor = 10
-FEorder = 1, 2, 3 | expand prec
\ No newline at end of file

test/parallel_reference.mini.in

@@ -15,15 +15,17 @@ grid.extensions = 1 1, 1 1 1 | expand dim
 
 adaptivity.useAdaptivity = false
 
-richards.output.fileName = parallel_reference_{_dimension}
-richards.output.outputPath = parallel_reference_{_dimension}
+[richards]
 
-richards.time.end = 1E5
-richards.time.maxTimestep = 1E5
-richards.time.startTimestep = 1E3
+output.fileName = parallel_reference_{_dimension}
+output.outputPath = parallel_reference_{_dimension}
 
-richards.boundary.file = "{_asset_path}/bcs/infiltration_2d.dat", "{_asset_path}/bcs/infiltration_3d.dat" | expand dim
+time.end = 1E5
+time.maxTimestep = 1E5
+time.startTimestep = 1E3
 
-richards.parameters.arrayFile = "{_asset_path}/parfields/fft_2d_miller.h5", "{_asset_path}/parfields/fft_3d_miller.h5" | expand dim
-richards.parameters.scale = 1 1, 1 1 1 | expand dim
-richards.parameters.offset = 0 0, 0 0 0 | expand dim
\ No newline at end of file
+boundary.file = "{_asset_path}/bcs/infiltration_2d.dat", "{_asset_path}/bcs/infiltration_3d.dat" | expand dim
+
+parameters.arrayFile = "{_asset_path}/parfields/fft_2d_miller.h5", "{_asset_path}/parfields/fft_3d_miller.h5" | expand dim
+parameters.scale = 1 1, 1 1 1 | expand dim
+parameters.offset = 0 0, 0 0 0 | expand dim
\ No newline at end of file

test/parallel_reference_compare.mini.in

@@ -21,15 +21,17 @@ grid.extensions = 1 1, 1 1 1 | expand dim
 
 adaptivity.useAdaptivity = false
 
-richards.output.fileName = parallel_reference_compare | unique
-richards.output.outputPath = parallel_reference_compare | unique
+[richards]
 
-richards.time.end = 1E5
-richards.time.maxTimestep = 1E5
-richards.time.startTimestep = 1E3
+output.fileName = parallel_reference_compare | unique
+output.outputPath = parallel_reference_compare | unique
 
-richards.boundary.file = "{_asset_path}/bcs/infiltration_2d.dat", "{_asset_path}/bcs/infiltration_3d.dat" | expand dim
+time.end = 1E5
+time.maxTimestep = 1E5
+time.startTimestep = 1E3
 
-richards.parameters.arrayFile = "{_asset_path}/parfields/fft_2d_miller.h5", "{_asset_path}/parfields/fft_3d_miller.h5" | expand dim
-richards.parameters.scale = 1 1, 1 1 1 | expand dim
-richards.parameters.offset = 0 0, 0 0 0 | expand dim
\ No newline at end of file
+boundary.file = "{_asset_path}/bcs/infiltration_2d.dat", "{_asset_path}/bcs/infiltration_3d.dat" | expand dim
+
+parameters.arrayFile = "{_asset_path}/parfields/fft_2d_miller.h5", "{_asset_path}/parfields/fft_3d_miller.h5" | expand dim
+parameters.scale = 1 1, 1 1 1 | expand dim
+parameters.offset = 0 0, 0 0 0 | expand dim
\ No newline at end of file

test/reference_2d.mini.in

@@ -19,13 +19,15 @@ adaptivity.threshold = 5E-8
 adaptivity.refinementFraction = 0.05
 adaptivity.maxLevel = 7
 
-richards.output.fileName = reference_2d | unique name
-richards.output.outputPath = reference_2d | unique name
+[richards]
 
-richards.time.end = 1E5
-richards.time.maxTimestep = 1E5
-richards.time.startTimestep = 1E3
+output.fileName = reference_2d | unique name
+output.outputPath = reference_2d | unique name
 
-richards.boundary.file = "{_asset_path}/bcs/infiltration_2d.dat"
+time.end = 1E5
+time.maxTimestep = 1E5
+time.startTimestep = 1E3
 
-richards.parameters.arrayFile = "{_asset_path}/parfields/fft_2d.h5", "{_asset_path}/parfields/fft_2d_miller.h5" | expand distribution
+boundary.file = "{_asset_path}/bcs/infiltration_2d.dat"
+
+parameters.arrayFile = "{_asset_path}/parfields/fft_2d.h5", "{_asset_path}/parfields/fft_2d_miller.h5" | expand distribution

test/reference_3d.mini.in

@@ -16,16 +16,18 @@ grid.gridFile = "{_asset_path}/meshes/3dcube.msh"
 adaptivity.useAdaptivity = false
 adaptivity.threshold = 1E-6
 
-richards.fileName = reference_3d | unique name
-richards.outputPath = reference_3d | unique name
+[richards]
 
-richards.time.end = 1E5
-richards.time.maxTimestep = 1E5
-richards.time.startTimestep = 1E4
+fileName = reference_3d | unique name
+outputPath = reference_3d | unique name
 
-richards.boundary.file = "{_asset_path}/bcs/infiltration_3d.dat"
+time.end = 1E5
+time.maxTimestep = 1E5
+time.startTimestep = 1E4
 
-richards.parameters.arrayFile = "{_asset_path}/parfields/fft_3d.h5", "{_asset_path}/parfields/fft_3d_miller.h5" | expand
-richards.parameters.scale = 1 1 1
-richards.parameters.offset = 0 0 0
-richards.parameters.interpolation = linear
+boundary.file = "{_asset_path}/bcs/infiltration_3d.dat"
+
+parameters.arrayFile = "{_asset_path}/parfields/fft_3d.h5", "{_asset_path}/parfields/fft_3d_miller.h5" | expand
+parameters.scale = 1 1 1
+parameters.offset = 0 0 0
+parameters.interpolation = linear

test/reference_evaporation.mini.in

@@ -18,13 +18,15 @@ grid.gridFile = "{_asset_path}/meshes/square.msh"
 adaptivity.useAdaptivity = false
 adaptivity.threshold = 1E-7
 
-richards.output.fileName = reference_evaporation | unique name
-richards.output.outputPath = reference_evaporation | unique name
+[richards]
 
-richards.time.end = 1E6
-richards.time.maxTimestep = 1E6
-richards.time.startTimestep = 1E3
+output.fileName = reference_evaporation | unique name
+output.outputPath = reference_evaporation | unique name
 
-richards.boundary.file = "{_asset_path}/bcs/infiltration_evaporation_2d.dat"
+time.end = 1E6
+time.maxTimestep = 1E6
+time.startTimestep = 1E3
 
-richards.parameters.arrayFile = "{_asset_path}/parfields/fft_2d.h5"
+boundary.file = "{_asset_path}/bcs/infiltration_evaporation_2d.dat"
+
+parameters.arrayFile = "{_asset_path}/parfields/fft_2d.h5"

test/reference_interpolators.mini.in

@@ -18,14 +18,16 @@ grid.gridFile = "{_asset_path}/meshes/square.msh"
 adaptivity.useAdaptivity = true
 adaptivity.threshold = 7E-8
 
-richards.output.fileName = reference_interpolators | unique name
-richards.output.outputPath = reference_interpolators | unique name
+[richards]
 
-richards.time.end = 1E5
-richards.time.maxTimestep = 1E5
-richards.time.startTimestep = 1E3
+output.fileName = reference_interpolators | unique name
+output.outputPath = reference_interpolators | unique name
 
-richards.boundary.file = "{_asset_path}/bcs/infiltration_2d.dat"
+time.end = 1E5
+time.maxTimestep = 1E5
+time.startTimestep = 1E3
 
-richards.parameters.arrayFile = "{_asset_path}/parfields/fft_2d_miller.h5"
-richards.parameters.interpolation = linear, cubic | expand
+boundary.file = "{_asset_path}/bcs/infiltration_2d.dat"
+
+parameters.arrayFile = "{_asset_path}/parfields/fft_2d_miller.h5"
+parameters.interpolation = linear, cubic | expand

test/run.mini.in

@@ -14,15 +14,17 @@ grid.extensions = 1 1
 
 adaptivity.useAdaptivity = false
 
-richards.output.fileName = run | unique name
-richards.output.outputPath = run | unique name
+[richards]
 
-richards.time.end = 1E4
-richards.time.maxTimestep = 1E4
-richards.time.startTimestep = 5E2
+output.fileName = run | unique name
+output.outputPath = run | unique name
 
-richards.boundary.file = "{_asset_path}/bcs/infiltration_2d.dat"
+time.end = 1E4
+time.maxTimestep = 1E4
+time.startTimestep = 5E2
 
-richards.parameters.arrayFile = ${CMAKE_CURRENT_BINARY_DIR}/csv.h5
+boundary.file = "{_asset_path}/bcs/infiltration_2d.dat"
+
+parameters.arrayFile = ${CMAKE_CURRENT_BINARY_DIR}/csv.h5