#201 fixed problems preventing passing of tests

include/actions/RedbackMechAction.h

@@ -35,6 +35,8 @@ class RedbackMechAction : public Action
 protected:
   /// if this vector is not empty the variables, kernels and materials are restricted to these subdomains
   std::vector<SubdomainName> _subdomain_names;
+  /// indicates, if the vector of subdomain names is set (dont set block restrictions, if not)
+  const bool _subdomain_names_set;
 };
 
 #endif // REDBACKMECHACTION_H

src/actions/RedbackMechAction.C

@@ -31,7 +31,7 @@ RedbackMechAction::validParams()
   params.addParam<std::string>(
       "appended_property_name", "", "Name appended to material properties to make them unique");
   params.addParam<std::vector<SubdomainName>>(
-      "block",
+      "block",{},
       "The list of ids of the blocks (subdomain) that the mechanics kernels will be applied to");
 
   // changed this from true to false
@@ -47,7 +47,8 @@ RedbackMechAction::RedbackMechAction(const InputParameters & params)
     _disp_r(getParam<NonlinearVariableName>("disp_r")),
     _temp(getParam<NonlinearVariableName>("temp")),
     _pore_pres(getParam<NonlinearVariableName>("pore_pres")),
-    _subdomain_names(getParam<std::vector<SubdomainName>>("block"))
+    _subdomain_names(getParam<std::vector<SubdomainName>>("block")),
+    _subdomain_names_set(isParamSetByUser("block"))
 {
 }
 
@@ -132,6 +133,22 @@ RedbackMechAction::act()
       name << short_name;
       name << i;
 
+      // // get subdomain IDs
+      // std::set<SubdomainID> _subdomain_ids;
+      // for (auto & name : _subdomain_names)
+      // {
+      //   auto id = _mesh->getSubdomainID(name);
+      //   if (id == Moose::INVALID_BLOCK_ID)
+      //     paramError("block", "Subdomain \"" + name + "\" not found in mesh.");
+      //   else
+      //     _subdomain_ids.insert(id);
+      // }
+      //
+      // // Make sure that all mesh subdomains have the same coordinate system
+      // const auto & all_subdomains =
+      //     _subdomain_names.empty() ? _problem->mesh().meshSubdomains() : _subdomain_ids;
+      //     if (_subdomain_names_set)
+      //       params.set<std::vector<SubdomainName>>("block") = _subdomain_names;
       params.set<std::vector<SubdomainName>>("block") = _subdomain_names;
       params.set<unsigned int>("component") = i;
       params.set<NonlinearVariableName>("variable") = vars[i];

src/base/RedbackApp.C

@@ -29,6 +29,8 @@ InputParameters
 RedbackApp::validParams()
 {
   InputParameters params = MooseApp::validParams();
+  params.set<bool>("use_legacy_material_output") = false;
+  params.set<bool>("use_legacy_initial_residual_evaluation_behavior") = false;
   return params;
 }
 
@@ -42,11 +44,10 @@ RedbackApp::~RedbackApp() {}
 void
 RedbackApp::registerAll(Factory & f, ActionFactory & af, Syntax & s)
 {
+  ModulesApp::registerAllObjects<RedbackApp>(f, af, s);
   Registry::registerObjectsTo(f, {"RedbackApp"});
   Registry::registerActionsTo(af, {"RedbackApp"});
 
-  ModulesApp::registerAll(f, af, s);
-
   /* register custom execute flags, action syntax, etc. here */
   RedbackApp::associateSyntax(s, af);
 }

src/main.C

@@ -1,27 +1,18 @@
-#include "AppFactory.h"
-#include "Moose.h"
-#include "MooseApp.h"
-#include "MooseInit.h"
-#include "RedbackApp.h"
+//* 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
 
-// Create a performance log
-PerfLog Moose::perf_log("Redback");
+#include "RedbackApp.h"
+#include "MooseMain.h"
 
 // Begin the main program.
 int
 main(int argc, char * argv[])
 {
-  // Initialize MPI, solvers and MOOSE
-  MooseInit init(argc, argv);
-
-  // Register this application's MooseApp and any it depends on
-  RedbackApp::registerApps();
-
-  // Create an instance of the application and store it in a smart pointer for easy cleanup
-  std::shared_ptr<MooseApp> app = AppFactory::createAppShared("RedbackApp", argc, argv);
-
-  // Execute the application
-  app->run();
-
-  return 0;
+  return Moose::main<RedbackApp>(argc, argv);
 }

src/materials/RedbackFluidMaterial.C

@@ -133,9 +133,9 @@ RedbackFluidMaterial::computeRedbackTerms()
   _froude_number[_qp] = _froude_number_param;
   _viscosity_ratio[_qp] = _viscosity_ratio_param;
 
-  Real fluid_density;
-  fluid_density = (1 + _fluid_compressibility_param * _pore_pres[_qp] -
-                   _fluid_thermal_expansion_param * _T[_qp]);
+  // Real fluid_density;
+  // fluid_density = (1 + _fluid_compressibility_param * _pore_pres[_qp] -
+  //                  _fluid_thermal_expansion_param * _T[_qp]);
 
   // Gravity term in the momentum kernel
   _gravity_term[_qp] = _gravity_param / pow(_froude_number[_qp], 2);

src/materials/RedbackMaterial.C

@@ -22,9 +22,9 @@ RedbackMaterial::validParams()
   InputParameters params = Material::validParams();
 
   params.addParam<std::vector<std::string>>(
-      "init_from_functions__params", "The names of the parameters to be initialised as functions.");
+      "init_from_functions__params",{}, "The names of the parameters to be initialised as functions.");
   params.addParam<std::vector<FunctionName>>(
-      "init_from_functions__function_names",
+      "init_from_functions__function_names",{},
       "The corresponding names of the functions to be used for the parameters "
       "to be initialised as functions.");
   params.addRangeCheckedParam<Real>("phi0", 0.0, "phi0>=0 & phi0<1", "initial porosity value.");
@@ -614,7 +614,7 @@ _ar_F[_qp] * _delta[_qp] * (1 - _total_porosity[_qp]) * (1 - _solid_ratio[_qp])
   if (_are_convective_terms_on)
   {
     Real solid_density, fluid_density;
-    Real lambda_m_star, one_minus_phi_lambda_s, phi_lambda_f;
+    Real /*lambda_m_star,*/ one_minus_phi_lambda_s, phi_lambda_f;
     RealVectorValue mixture_velocity, normalized_gravity;
 
     // Forming the partial densities and gravity terms
@@ -649,8 +649,8 @@ _ar_F[_qp] * _delta[_qp] * (1 - _total_porosity[_qp]) * (1 - _solid_ratio[_qp])
     phi_lambda_f = _total_porosity[_qp] * _fluid_thermal_expansion[_qp]; // normalized thermal
                                                                          // expansion coefficient of
                                                                          // the fluid phase
-    lambda_m_star =
-        one_minus_phi_lambda_s + phi_lambda_f; // normalized compressibility of the mixture
+    // lambda_m_star =
+    //     one_minus_phi_lambda_s + phi_lambda_f; // normalized compressibility of the mixture
 
     // Forming the velocities through mechanics and Darcy's flow law
     if (_total_porosity[_qp] != 0)

src/materials/RedbackMechMaterial.C

@@ -54,7 +54,7 @@ RedbackMechMaterial::validParams()
   // params.addRequiredParam< std::vector<Real> >("yield_stress", "Input data as
   // pairs of equivalent plastic strain and yield stress: Should start with
   // equivalent plastic strain 0");
-  params.addParam<std::vector<Real>>("yield_stress",
+  params.addParam<std::vector<Real>>("yield_stress",{},
                                      "Input data as pairs of equivalent "
                                      "plastic strain and yield stress: Should "
                                      "start with equivalent plastic strain 0");
@@ -96,7 +96,7 @@ RedbackMechMaterial::validParams()
       "temperature_reference", 0.0, "Reference temperature used for thermal expansion");
   params.addParam<Real>("pressure_reference", 0.0, "Reference pressure used for compressibility");
   params.addParam<std::vector<FunctionName>>(
-      "initial_stress",
+      "initial_stress",{},
       "A list of functions describing the initial stress. If provided, there "
       "must be 9 of these, corresponding to the xx, yx, zx, xy, yy, zy, xz, yz, "
       "zz components respectively.  If not provided, all components of the "
@@ -316,9 +316,10 @@ RedbackMechMaterial::computeStrain()
   for (_qp = 0; _qp < _qrule->n_points(); ++_qp)
   {
     // Deformation gradient
-    RankTwoTensor A(
+    auto A = RankTwoTensor ::initializeFromRows(
         _grad_disp_x[_qp], _grad_disp_y[_qp], _grad_disp_z[_qp]); // Deformation gradient
-    RankTwoTensor Fbar(_grad_disp_x_old[_qp],
+    auto Fbar = RankTwoTensor ::initializeFromRows(
+                       _grad_disp_x_old[_qp],
                        _grad_disp_y_old[_qp],
                        _grad_disp_z_old[_qp]); // Old Deformation gradient
 

src/meshgenerators/BreakMeshBySidesetGenerator.C

@@ -1067,13 +1067,13 @@ BreakMeshBySidesetGenerator::addLowerDElements(MeshBase & mesh)
 subdomain_id_type
 BreakMeshBySidesetGenerator::findFreeBlockId(MeshBase & mesh)
 {
-  auto blocks = MooseMeshUtils::getSubdomainIDs(mesh, {"ANY_BLOCK_ID"});
-  std::set<subdomain_id_type> current_block_ids(blocks.begin(), blocks.end());
+  std::set<subdomain_id_type> currentBlockIds;
+  mesh.subdomain_ids(currentBlockIds);
   bool free_block_not_found = true;
   subdomain_id_type free_id;
   for (free_id = 0; free_id < std::numeric_limits<subdomain_id_type>::max(); free_id++)
   {
-    if (current_block_ids.count(free_id) == 0)
+    if (currentBlockIds.count(free_id) == 0)
     {
       // bid is not in the set, block ID is free
       free_block_not_found = false;

tests/image_meshing/adaptivity_loop.i

@@ -18,7 +18,7 @@
 [Functions]
   [./image_func]
     type = ImageFunction
-    threshold = 90
+    threshold = 6e4
     file_suffix = png
     #these 2 lines needs to be paste in the next step of the simulation
     #the image folder and the images selected

tests/image_meshing/image_reader.i

@@ -21,7 +21,7 @@
     type = ImageSubdomainGenerator
     input = generate
     file_suffix = png
-    threshold = 90
+    threshold = 6e4
     #the image folder and the images selected
     file_base = stack/test_0
     #file_range = '32'