ENH: Fix several compilation errors in the TimeIntegrators

module.

ContactHandling/CMakeLists.txt

@@ -13,6 +13,7 @@ target_link_libraries(ContactHandling
     Event
     Collision
     Simulators
+    Solvers
 )
 
 if(BUILD_TESTING)

ContactHandling/UnitTests/CMakeLists.txt

@@ -14,6 +14,8 @@ target_link_libraries(${Module}UnitTestRunner
     Collision
     Simulators
     Mesh
-    ContactHandling)
+    ContactHandling
+    Solvers
+    )
 
 simple_test(${Module} --reporter=spec)

Core/SceneObject.h

@@ -68,7 +68,7 @@ public:
     /// \brief Abstract object initialization
     virtual void initialize() = 0;
 
-    virtual bool configure(std::string ConfigFile) = 0;
+    virtual bool configure(const std::string &ConfigFile) = 0;
 
     /// \brief Load the initial posiitons, velocities etc.,
     virtual void loadInitialStates() = 0;

Core/StaticSceneObject.cpp

@@ -56,7 +56,7 @@ void StaticSceneObject::loadInitialStates()
 {
 }
 
-bool StaticSceneObject::configure(const std::string /*ConfigFile*/)
+bool StaticSceneObject::configure(const std::string &/*ConfigFile*/)
 {
     return false;
 }

Core/StaticSceneObject.h

@@ -65,7 +65,7 @@ public:
     void loadInitialStates() override;
 
     /// \brief configure the static scene object using external config file (optional)
-    bool configure(const std::string ConfigFile) override;
+    bool configure(const std::string &ConfigFile) override;
 
     void printInfo() const override;
 

Examples/AVMNidus/CMakeLists.txt

@@ -14,6 +14,7 @@ target_link_libraries(${APP}
   ContactHandling
   Event
   IO
+  Solvers
   )
 
 set_target_properties(${APP}

Examples/FEMSimulator/CMakeLists.txt

@@ -13,6 +13,7 @@ target_link_libraries(${APP}
   IO
   Devices
   VirtualTools
+  Solvers
 )
 
 set_target_properties(${APP}

Examples/LaparoscopicCamera/CMakeLists.txt

@@ -12,6 +12,7 @@ target_link_libraries(${APP}
   IO
   Devices
   VirtualTools
+  Solvers
 )
 
 set_target_properties(${APP}

Examples/Shaders/CMakeLists.txt

@@ -11,6 +11,7 @@ target_link_libraries(${APP}
   Mesh
   Event
   IO
+  Solvers
   )
 
 set_target_properties(${APP}

Simulators/CMakeLists.txt

@@ -5,12 +5,14 @@ simmedtk_add_library(Simulators
     VegaFemSceneObject.cpp
     VegaFemSimulator.cpp
     VegaObjectConfig.cpp
+    VegaFEMDeformableSceneObject.cpp
   PUBLIC_HEADERS
     DefaultSimulator.h
     SceneObjectDeformable.h
     VegaFemSceneObject.h
     VegaFemSimulator.h
     VegaObjectConfig.h
+    VegaFEMDeformableSceneObject.h
 )
 
 target_link_libraries(Simulators
@@ -22,6 +24,8 @@ target_link_libraries(Simulators
     IO
     Devices
     VirtualTools
+    Solvers
+    TimeIntegrators
   PUBLIC
     VegaFEM::configFile
     VegaFEM::vega-getopts
@@ -36,9 +40,14 @@ target_link_libraries(Simulators
     VegaFEM::loadList
     VegaFEM::objMesh
     VegaFEM::volumetricMesh
+    VegaFEM::forceModel
     )
 
 target_include_directories(Simulators
   PRIVATE
     ${CMAKE_SOURCE_DIR}/include
     )
+
+if(BUILD_TESTING)
+  add_subdirectory(UnitTests)
+endif()

Simulators/DeformableSceneObject.h

@@ -75,7 +75,7 @@ public:
     ///
     /// \brief Initialize the ode solver.
     ///
-    bool init()
+    void initialize() override
     {
         auto thisPointer = this->safeDownCast<DeformableSceneObject>();
         switch(integrationScheme)
@@ -92,11 +92,14 @@ public:
             {
                 std::cerr << "Invalid time integration scheme." << std::endl;
             }
-
-            return false;
         }
     }
 
+    virtual bool configure(const std::string &)
+    {
+        return false;
+    }
+
     ///
     /// \brief Update states
     ///
@@ -130,7 +133,7 @@ public:
     ///
     std::shared_ptr<OdeSystemState> getCurrentState()
     {
-        this->currentState;
+        return this->currentState;
     }
 
     ///
@@ -138,9 +141,29 @@ public:
     ///
     std::shared_ptr<OdeSystemState> getPreviousState()
     {
-        this->previousState;
+        return this->previousState;
     }
 
+    ///////////////////////////////////////////////////////////////////////////////
+    //////////// TODO: These are pure virtual methods from superclass. ////////////
+    ////////////    They should be removed in the future.              ////////////
+    ///////////////////////////////////////////////////////////////////////////////
+
+    ///serialize function explicity writes the object to the memory block
+    ///each scene object should know how to write itself to a memory block
+    void serialize(void *){}
+
+    ///Unserialize function can recover the object from the memory location
+    void unSerialize(void *){};
+
+    ///this function may not be used
+    ///every Scene Object should know how to clone itself. Since the data structures will be
+    ///in the beginning of the modules(such as simulator, viewer, collision etc.)
+    std::shared_ptr<SceneObject> clone(){return nullptr;};
+
+    /// \brief print information related the scene object
+    void printInfo() const{};
+
 protected:
     std::shared_ptr<TimeIntegrator> odeSolver; ///> Integration scheme
 

Simulators/UnitTests/CMakeLists.txt

+set(Module Simulators)
+
+add_executable(${Module}UnitTestRunner
+  ${BANDIT_RUNNER}
+  VegaFEMDeformableSceneObjectSpec.cpp
+)
+
+target_compile_options(${Module}UnitTestRunner PRIVATE $<$<CXX_COMPILER_ID:GNU>:-Wno-old-style-cast -Wno-multichar -Wno-type-limits>)
+target_link_libraries(${Module}UnitTestRunner Core Mesh IO Solvers TimeIntegrators Simulators)
+simple_test(${Module} --reporter=xunit)

Simulators/UnitTests/VegaFEMDeformableSceneObjectSpec.cpp

+// This file is part of the SimMedTK project.
+// Copyright (c) Center for Modeling, Simulation, and Imaging in Medicine,
+//                        Rensselaer Polytechnic Institute
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+//     http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+//
+//---------------------------------------------------------------------------
+//
+// Authors:
+//
+// Contact:
+//---------------------------------------------------------------------------
+
+#include <bandit/bandit.h>
+#include <memory>
+#include <iostream>
+
+// SimMedTK includes
+#include "Simulators/VegaFEMDeformableSceneObject.h"
+
+using namespace bandit;
+using namespace core;
+
+go_bandit([]()
+{
+    describe("Vega Deformable Scene Object", [&]()
+    {
+        VegaFEMDeformableSceneObject sceneObject("box.veg","box.config");
+//         auto sceneObject = std::make_shared<VegaFEMDeformableSceneObject>("box.veg","box.config");
+//         it("constructs ", [&]()
+//         {
+//             AssertThat(sceneObject != nullptr, IsTrue());
+//         });
+     });
+
+});

Simulators/VegaFemSceneObject.cpp

@@ -73,7 +73,7 @@ std::shared_ptr<SceneObject> VegaFemSceneObject::clone()
     return safeDownCast<SceneObject>();
 }
 
-bool VegaFemSceneObject::configure(const std::string ConfigFile)
+bool VegaFemSceneObject::configure(const std::string &ConfigFile)
 {
     femConfig = std::make_shared<VegaObjectConfig>();
 

Simulators/VegaFemSceneObject.h

@@ -87,7 +87,7 @@ public:
     void initialize() override;
 
     /// \brief configure the vega fem scene object using external config file
-    bool configure(const std::string ConfigFile) override;
+    bool configure(const std::string &ConfigFile) override;
 
     /// \brief load initial displacements and velocities of the nodes
     void loadInitialStates() override;

Solvers/InexactNewton.cpp

@@ -124,6 +124,7 @@ void InexactNewton::updateJacobian(const core::Vectord &x)
     }
 
     const core::SparseMatrixd &jacobianMatrix = this->jacobian(x);
+    const core::Vectord &f = this->nonLinearSystem->getFunctionValue();
 
     if(!(jacobianMatrix.innerSize() > 0))
     {// TODO: Print message and/or log error.
@@ -131,9 +132,8 @@ void InexactNewton::updateJacobian(const core::Vectord &x)
     }
 
     auto linearSystem = std::make_shared<LinearSolverType::LinearSystemType>(
-                            jacobianMatrix, this->f);
+                            jacobianMatrix, f);
     this->linearSolver->setSystem(linearSystem);
-
 }
 
 //---------------------------------------------------------------------------

Solvers/InexactNewton.h

@@ -226,7 +226,7 @@ private:
     double relativeTolerance;                       ///> Relative (to the rhs) tolerance (Default: 1.0e-6).
     double gamma;                                   ///> Internal parameter used to update the forcing term  (Default: 0.9).
     double etaMax;                                  ///> Maximum tolerance for the linear solver (Default: 0.9).
-    size_t maxIterations;                           ///> Maximum number of nonlinear iterations (Default: 40).
+    size_t maxIterations;                           ///> Maximum number of nonlinear iterations (Default: 50).
     bool useArmijo;                                 ///> True if Armijo liner search is desired (Default: true).
 };
 

Solvers/NonLinearSolver.h

@@ -123,7 +123,6 @@ public:
     void setUpdateIterate(const UpdateIterateType &newUpdateIterate);
 
 protected:
-    core::Vectord f;                ///< Storage for function evaluations
     std::array<double, 2> sigma;    ///< Safeguarding bounds for the line search
     double alpha;                   ///< Parameter to measure decrease
     size_t armijoMax;               ///< Maximum number of step length reductions