Source/header/style updates (idaholab#21885)

dschwen · Aug 18, 2022 · 0730596 · 0730596
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commit 0730596
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Showing 53 changed files with 530 additions and 363 deletions.
diff --git a/modules/optimization/examples/spherical_point_sources/adjoint.i b/modules/optimization/examples/spherical_point_sources/adjoint.i
@@ -1,8 +1,8 @@
 [Mesh]
- [fmg]
-   type = FileMeshGenerator
-   file = halfSphere.e
- []
+  [fmg]
+    type = FileMeshGenerator
+    file = halfSphere.e
+  []
 []
 
 [Variables]
@@ -36,13 +36,13 @@
     value_name = misfit/misfit_values
   []
 []
+
 [Reporters]
   [misfit]
-    type=OptimizationData
+    type = OptimizationData
   []
 []
 
-
 [BCs]
   [round]
     type = ConvectiveFluxFunction

diff --git a/modules/optimization/examples/spherical_point_sources/forward.i b/modules/optimization/examples/spherical_point_sources/forward.i
@@ -32,14 +32,14 @@
 []
 
 [DiracKernels]
-    [pt]
-      type = ReporterPointSource
-      variable = temperature
-      x_coord_name = 'point_source/x'
-      y_coord_name = 'point_source/y'
-      z_coord_name = 'point_source/z'
-      value_name = 'point_source/value'
-    []
+  [pt]
+    type = ReporterPointSource
+    variable = temperature
+    x_coord_name = 'point_source/x'
+    y_coord_name = 'point_source/y'
+    z_coord_name = 'point_source/z'
+    value_name = 'point_source/value'
+  []
 []
 
 [BCs]
@@ -66,7 +66,7 @@
   []
 []
 
-[Problem]#do we need this
+[Problem] #do we need this
   type = FEProblem
 []
 
@@ -83,7 +83,7 @@
   [point_source]
     type = ConstantVectorPostprocessor
     vector_names = 'x y z value'
-    value = '4 2.3  2.3  2.3  2.3;
+    value = '4   2.3  2.3  2.3  2.3;
              0   2.3 -2.3 -2.3  2.3;
              0   2.3  2.3 -2.3 -2.3;
              100 150  300  250  150'
@@ -99,12 +99,12 @@
 
 [Reporters]
   [measure_data]
-    type=OptimizationData
+    type = OptimizationData
   []
 []
 
 [Outputs]
-  console = true #false
+  console = true
   exodus = true
   csv = true
   file_base = 'forward'

diff --git a/modules/optimization/include/base/IsopodAppTypes.h b/modules/optimization/include/base/IsopodAppTypes.h
diff --git a/...ization/test/include/base/isopodTestApp.h → ...timization/include/base/OptimizationApp.h b/...ization/test/include/base/isopodTestApp.h → ...timization/include/base/OptimizationApp.h
@@ -11,15 +11,14 @@
 
 #include "MooseApp.h"
 
-class isopodTestApp : public MooseApp
+class OptimizationApp : public MooseApp
 {
 public:
   static InputParameters validParams();
 
-  isopodTestApp(InputParameters parameters);
-  virtual ~isopodTestApp();
+  OptimizationApp(InputParameters parameters);
+  virtual ~OptimizationApp();
 
   static void registerApps();
-  static void registerAll(Factory & f, ActionFactory & af, Syntax & s, bool use_test_objs = false);
+  static void registerAll(Factory & f, ActionFactory & af, Syntax & s);
 };
-
diff --git a/modules/optimization/include/base/OptimizationAppTypes.h b/modules/optimization/include/base/OptimizationAppTypes.h
@@ -0,0 +1,19 @@
+//* This file is part of the MOOSE framework
+//* https://www.mooseframework.org
+//*
+//* All rights reserved, see COPYRIGHT for full restrictions
+//* https://github.com/idaholab/moose/blob/master/COPYRIGHT
+//*
+//* Licensed under LGPL 2.1, please see LICENSE for details
+//* https://www.gnu.org/licenses/lgpl-2.1.html
+
+#pragma once
+
+#include "Moose.h"
+
+namespace OptimizationAppTypes
+{
+extern const ExecFlagType EXEC_FORWARD;
+extern const ExecFlagType EXEC_ADJOINT;
+extern const ExecFlagType EXEC_HOMOGENEOUS_FORWARD;
+}
diff --git a/modules/optimization/include/base/isopodApp.h b/modules/optimization/include/base/isopodApp.h
diff --git a/modules/optimization/include/controls/OptimizationMultiAppCommandLineControl.h b/modules/optimization/include/controls/OptimizationMultiAppCommandLineControl.h
@@ -1,3 +1,12 @@
+//* This file is part of the MOOSE framework
+//* https://www.mooseframework.org
+//*
+//* All rights reserved, see COPYRIGHT for full restrictions
+//* https://github.com/idaholab/moose/blob/master/COPYRIGHT
+//*
+//* Licensed under LGPL 2.1, please see LICENSE for details
+//* https://www.gnu.org/licenses/lgpl-2.1.html
+
 #pragma once
 
 // MOOSE includes

diff --git a/modules/optimization/include/executioners/Optimize.h b/modules/optimization/include/executioners/Optimize.h
@@ -1,3 +1,12 @@
+//* This file is part of the MOOSE framework
+//* https://www.mooseframework.org
+//*
+//* All rights reserved, see COPYRIGHT for full restrictions
+//* https://github.com/idaholab/moose/blob/master/COPYRIGHT
+//*
+//* Licensed under LGPL 2.1, please see LICENSE for details
+//* https://www.gnu.org/licenses/lgpl-2.1.html
+
 #pragma once
 
 #include "Steady.h"

diff --git a/modules/optimization/include/multiapps/OptimizeFullSolveMultiApp.h b/modules/optimization/include/multiapps/OptimizeFullSolveMultiApp.h
@@ -1,6 +1,17 @@
+//* This file is part of the MOOSE framework
+//* https://www.mooseframework.org
+//*
+//* All rights reserved, see COPYRIGHT for full restrictions
+//* https://github.com/idaholab/moose/blob/master/COPYRIGHT
+//*
+//* Licensed under LGPL 2.1, please see LICENSE for details
+//* https://www.gnu.org/licenses/lgpl-2.1.html
+
 #pragma once
+
 // fixme lynn this is included because MultiApp probably needs it
 #include "libmesh/numeric_vector.h"
+
 // MOOSE includes
 #include "FullSolveMultiApp.h"
 

diff --git a/modules/optimization/include/optimizationreporters/ObjectiveGradientMinimize.h b/modules/optimization/include/optimizationreporters/ObjectiveGradientMinimize.h
@@ -1,3 +1,12 @@
+//* This file is part of the MOOSE framework
+//* https://www.mooseframework.org
+//*
+//* All rights reserved, see COPYRIGHT for full restrictions
+//* https://github.com/idaholab/moose/blob/master/COPYRIGHT
+//*
+//* Licensed under LGPL 2.1, please see LICENSE for details
+//* https://www.gnu.org/licenses/lgpl-2.1.html
+
 #pragma once
 
 #include "OptimizationReporter.h"

diff --git a/modules/optimization/include/optimizationreporters/ObjectiveMinimize.h b/modules/optimization/include/optimizationreporters/ObjectiveMinimize.h
@@ -1,3 +1,12 @@
+//* This file is part of the MOOSE framework
+//* https://www.mooseframework.org
+//*
+//* All rights reserved, see COPYRIGHT for full restrictions
+//* https://github.com/idaholab/moose/blob/master/COPYRIGHT
+//*
+//* Licensed under LGPL 2.1, please see LICENSE for details
+//* https://www.gnu.org/licenses/lgpl-2.1.html
+
 #pragma once
 
 #include "OptimizationReporter.h"

diff --git a/modules/optimization/include/optimizationreporters/OptimizationReporter.h b/modules/optimization/include/optimizationreporters/OptimizationReporter.h
@@ -1,3 +1,12 @@
+//* This file is part of the MOOSE framework
+//* https://www.mooseframework.org
+//*
+//* All rights reserved, see COPYRIGHT for full restrictions
+//* https://github.com/idaholab/moose/blob/master/COPYRIGHT
+//*
+//* Licensed under LGPL 2.1, please see LICENSE for details
+//* https://www.gnu.org/licenses/lgpl-2.1.html
+
 #pragma once
 
 #include "OptimizationData.h"

diff --git a/modules/optimization/include/postprocessors/ConstantValuePostprocessor.h b/modules/optimization/include/postprocessors/ConstantValuePostprocessor.h
@@ -1,3 +1,12 @@
+//* This file is part of the MOOSE framework
+//* https://www.mooseframework.org
+//*
+//* All rights reserved, see COPYRIGHT for full restrictions
+//* https://github.com/idaholab/moose/blob/master/COPYRIGHT
+//*
+//* Licensed under LGPL 2.1, please see LICENSE for details
+//* https://www.gnu.org/licenses/lgpl-2.1.html
+
 #pragma once
 
 #include "GeneralPostprocessor.h"
@@ -15,8 +24,8 @@ class ConstantValuePostprocessor : public GeneralPostprocessor
 
   ConstantValuePostprocessor(const InputParameters & parameters);
 
-  virtual void initialize() override;
-  virtual void execute() override;
+  virtual void initialize() override{};
+  virtual void execute() override{};
   virtual PostprocessorValue getValue() override;
 
 protected:

diff --git a/modules/optimization/include/transfers/OptimizationParameterTransfer.h b/modules/optimization/include/transfers/OptimizationParameterTransfer.h
@@ -1,6 +1,14 @@
+//* This file is part of the MOOSE framework
+//* https://www.mooseframework.org
+//*
+//* All rights reserved, see COPYRIGHT for full restrictions
+//* https://github.com/idaholab/moose/blob/master/COPYRIGHT
+//*
+//* Licensed under LGPL 2.1, please see LICENSE for details
+//* https://www.gnu.org/licenses/lgpl-2.1.html
+
 #pragma once
 
-// MOOSE includes
 #include "MultiAppTransfer.h"
 #include "ReporterInterface.h"
 

diff --git a/modules/optimization/src/actions/AddOptimizationReporterAction.C b/modules/optimization/src/actions/AddOptimizationReporterAction.C
@@ -1,10 +1,19 @@
+//* This file is part of the MOOSE framework
+//* https://www.mooseframework.org
+//*
+//* All rights reserved, see COPYRIGHT for full restrictions
+//* https://github.com/idaholab/moose/blob/master/COPYRIGHT
+//*
+//* Licensed under LGPL 2.1, please see LICENSE for details
+//* https://www.gnu.org/licenses/lgpl-2.1.html
+
 #include "AddOptimizationReporterAction.h"
 
 #include "Factory.h"
 #include "FEProblemBase.h"
 #include "OptimizationReporter.h"
 
-registerMooseAction("isopodApp", AddOptimizationReporterAction, "add_reporter");
+registerMooseAction("OptimizationApp", AddOptimizationReporterAction, "add_reporter");
 
 InputParameters
 AddOptimizationReporterAction::validParams()
@@ -14,7 +23,10 @@ AddOptimizationReporterAction::validParams()
   return params;
 }
 
-AddOptimizationReporterAction::AddOptimizationReporterAction(InputParameters params) : MooseObjectAction(params) {}
+AddOptimizationReporterAction::AddOptimizationReporterAction(InputParameters params)
+  : MooseObjectAction(params)
+{
+}
 
 void
 AddOptimizationReporterAction::act()

diff --git a/modules/optimization/src/auxkernels/MaterialScaledGradientVector.C b/modules/optimization/src/auxkernels/MaterialScaledGradientVector.C
@@ -1,6 +1,6 @@
 #include "MaterialScaledGradientVector.h"
 
-registerMooseObject("isopodApp", MaterialScaledGradientVector);
+registerMooseObject("OptimizationApp", MaterialScaledGradientVector);
 
 InputParameters
 MaterialScaledGradientVector::validParams()

diff --git a/modules/optimization/src/base/IsopodAppTypes.C b/modules/optimization/src/base/IsopodAppTypes.C
diff --git a/modules/optimization/src/base/OptimizationApp.C b/modules/optimization/src/base/OptimizationApp.C
@@ -0,0 +1,71 @@
+//* This file is part of the MOOSE framework
+//* https://www.mooseframework.org
+//*
+//* All rights reserved, see COPYRIGHT for full restrictions
+//* https://github.com/idaholab/moose/blob/master/COPYRIGHT
+//*
+//* Licensed under LGPL 2.1, please see LICENSE for details
+//* https://www.gnu.org/licenses/lgpl-2.1.html
+
+#include "OptimizationApp.h"
+#include "HeatConductionApp.h"
+#include "StochasticToolsApp.h"
+#include "Moose.h"
+#include "AppFactory.h"
+#include "MooseSyntax.h"
+#include "ExecFlagRegistry.h"
+
+#include "OptimizationAppTypes.h"
+
+InputParameters
+OptimizationApp::validParams()
+{
+  InputParameters params = MooseApp::validParams();
+
+  // Do not use legacy DirichletBC, that is, set DirichletBC default for preset = true
+  params.set<bool>("use_legacy_material_output") = false;
+
+  return params;
+}
+
+OptimizationApp::OptimizationApp(InputParameters parameters) : MooseApp(parameters)
+{
+  OptimizationApp::registerAll(_factory, _action_factory, _syntax);
+}
+
+OptimizationApp::~OptimizationApp() {}
+
+void
+OptimizationApp::registerAll(Factory & f, ActionFactory & af, Syntax & s)
+{
+  Registry::registerObjectsTo(f, {"OptimizationApp"});
+  Registry::registerActionsTo(af, {"OptimizationApp"});
+
+  auto & syntax = s;
+
+  // Form Function actions
+  registerSyntaxTask("AddOptimizationReporterAction", "OptimizationReporter", "add_reporter");
+
+  HeatConductionApp::registerAll(f, af, s);
+  StochasticToolsApp::registerAll(f, af, s);
+}
+
+void
+OptimizationApp::registerApps()
+{
+  registerApp(OptimizationApp);
+}
+
+/***************************************************************************************************
+ *********************** Dynamic Library Entry Points - DO NOT MODIFY ******************************
+ **************************************************************************************************/
+extern "C" void
+OptimizationApp__registerAll(Factory & f, ActionFactory & af, Syntax & s)
+{
+  OptimizationApp::registerAll(f, af, s);
+}
+extern "C" void
+OptimizationApp__registerApps()
+{
+  OptimizationApp::registerApps();
+}