Minor changes made in review of peridynamics module ref idaholab#11561

modules/peridynamics/include/base/PeridynamicsApp.h

@@ -24,9 +24,4 @@ class PeridynamicsApp : public MooseApp
 
   static void registerApps();
   static void registerAll(Factory & f, ActionFactory & af, Syntax & s);
-  static void registerObjects(Factory & factory);
-  static void registerObjectDepends(Factory & factory);
-  static void associateSyntax(Syntax & syntax, ActionFactory & action_factory);
-  static void associateSyntaxDepends(Syntax & syntax, ActionFactory & action_factory);
-  static void registerExecFlags(Factory & factory);
 };

modules/peridynamics/include/bcs/IntactBondsDirichletBCPD.h

@@ -18,8 +18,9 @@ template <>
 InputParameters validParams<IntactBondsDirichletBCPD>();
 
 /**
- * Defines Dirichlet boundary condition based on number of intact bonds associated with each
- * material point
+ * Class to selectively apply a Dirichlet BC based on the number of intact
+ * bonds associated with each material point. Used to stabilize nodes without
+ * a sufficient number of connections to other material points.
  */
 class IntactBondsDirichletBCPD : public NodalBC
 {
@@ -38,4 +39,7 @@ class IntactBondsDirichletBCPD : public NodalBC
 
   /// value of the AuxVariable for number of intact bonds associated with each material point
   const VariableValue & _intact_bonds_val;
+
+  /// Maximum number of intact bonds connected a node for this BC to be active
+  const unsigned int _max_intact_bonds;
 };

modules/peridynamics/include/kernels/ForceStabilizedSmallStrainMechanicsNOSPD.h

@@ -51,6 +51,8 @@ class ForceStabilizedSmallStrainMechanicsNOSPD : public MechanicsBasePD
   const MaterialProperty<RankTwoTensor> & _ddgraddv;
   const MaterialProperty<RankTwoTensor> & _ddgraddw;
   const MaterialProperty<RankFourTensor> & _Cijkl;
+  const std::vector<MaterialPropertyName> _eigenstrain_names;
+  std::vector<const MaterialProperty<RankTwoTensor> *> _deigenstrain_dT;
   ///@}
 
   /// Bond based material property for fictitious stabilization force

modules/peridynamics/include/kernels/GeneralizedPlaneStrainOffDiagNOSPD.h

@@ -17,7 +17,7 @@ template <>
 InputParameters validParams<GeneralizedPlaneStrainOffDiagNOSPD>();
 
 /**
- * Kernel class for coupled off diagonal jacobian entries of non-ordinary state-based peridynamic
+ * Kernel class for coupled off diagonal Jacobian entries of non-ordinary state-based peridynamic
  * generalized plane strain model
  */
 class GeneralizedPlaneStrainOffDiagNOSPD : public MechanicsBaseNOSPD
@@ -30,23 +30,23 @@ class GeneralizedPlaneStrainOffDiagNOSPD : public MechanicsBaseNOSPD
   virtual void computeOffDiagJacobianScalar(unsigned int jvar_num) override;
 
   /**
-   * Function to compute the full off diagonal jacobian for coupling between displacements and
+   * Function to compute the full off diagonal Jacobian for coupling between displacements and
    * scalar variable
    * @param component   The index of displacement component
    * @param jvar_num   The coupled scalar variable number
    */
   void computeDispFullOffDiagJacobianScalar(unsigned int component, unsigned int jvar_num);
 
   /**
-   * Function to compute partial off diagonal jacobian for coupling between displacements and scalar
+   * Function to compute partial off diagonal Jacobian for coupling between displacements and scalar
    * variable
    * @param component   The index of displacement component
    * @param jvar_num   The coupled scalar variable number
    */
   void computeDispPartialOffDiagJacobianScalar(unsigned int component, unsigned int jvar_num);
 
   /**
-   * Function to compute off disgonal jacobian for coupling between temperature and scalar variable
+   * Function to compute off disgonal Jacobian for coupling between temperature and scalar variable
    * @param jvar_num   The coupled scalar variable number
    */
   void computeTempOffDiagJacobianScalar(unsigned int jvar_num);

modules/peridynamics/include/kernels/GeneralizedPlaneStrainOffDiagOSPD.h

@@ -17,7 +17,7 @@ template <>
 InputParameters validParams<GeneralizedPlaneStrainOffDiagOSPD>();
 
 /**
- * Kernel class for coupled off diagonal jacobian entries of ordinary state-based peridynamic
+ * Kernel class for coupled off diagonal Jacobian entries of ordinary state-based peridynamic
  * generalized plane strain model
  */
 class GeneralizedPlaneStrainOffDiagOSPD : public MechanicsBasePD
@@ -30,23 +30,23 @@ class GeneralizedPlaneStrainOffDiagOSPD : public MechanicsBasePD
   virtual void computeOffDiagJacobianScalar(unsigned int jvar_num) override;
 
   /**
-   * Function to compute the full off diagonal jacobian for coupling between displacements and
+   * Function to compute the full off diagonal Jacobian for coupling between displacements and
    * scalar variable
    * @param component   The index of displacement component
    * @param jvar_num   The coupled scalar variable number
    */
   void computeDispFullOffDiagJacobianScalar(unsigned int component, unsigned int jvar_num);
 
   /**
-   * Function to compute partial off diagonal jacobian for coupling between displacements and scalar
+   * Function to compute partial off diagonal Jacobian for coupling between displacements and scalar
    * variable
    * @param component   The index of displacement component
    * @param jvar_num   The coupled scalar variable number
    */
   void computeDispPartialOffDiagJacobianScalar(unsigned int component, unsigned int jvar_num);
 
   /**
-   * Function to compute off disgonal jacobian for coupling between temperature and scalar variable
+   * Function to compute off disgonal Jacobian for coupling between temperature and scalar variable
    * @param jvar_num   The coupled scalar variable number
    */
   void computeTempOffDiagJacobianScalar(unsigned int jvar_num);

modules/peridynamics/include/kernels/HeatSourceBPD.h

@@ -27,8 +27,6 @@ class HeatSourceBPD : public KernelBasePD
 protected:
   virtual void computeLocalResidual() override;
 
-  ///@{ Power density values
-  double _power_density;
-  const Function * _power_density_function;
-  ///@}
+  /// Power density function
+  const Function & _power_density;
 };

modules/peridynamics/include/kernels/MechanicsBaseNOSPD.h

@@ -42,5 +42,9 @@ class MechanicsBaseNOSPD : public MechanicsBasePD
   const MaterialProperty<RankTwoTensor> & _ddgraddv;
   const MaterialProperty<RankTwoTensor> & _ddgraddw;
   const MaterialProperty<RankFourTensor> & _Jacobian_mult;
+  const std::vector<MaterialPropertyName> _eigenstrain_names;
+  std::vector<const MaterialProperty<RankTwoTensor> *> _deigenstrain_dT;
+  ///@}
+
   ///@}
 };

modules/peridynamics/include/kernels/MechanicsBasePD.h

@@ -57,11 +57,6 @@ class MechanicsBasePD : public DerivativeMaterialInterface<KernelBasePD>
   /// number of displacement components
   unsigned int _ndisp;
 
-  ///@{ Material point based material property for eigen strains
-  const std::vector<MaterialPropertyName> _eigenstrain_names;
-  std::vector<const MaterialProperty<RankTwoTensor> *> _deigenstrain_dT;
-  ///@}
-
   ///@{ Parameters for out-of-plane strain in weak plane stress formulation
   const bool _out_of_plane_strain_coupled;
   MooseVariableFEBase * _out_of_plane_strain_var;

modules/peridynamics/include/materials/ThermalConstantHorizonBPD.h

@@ -26,5 +26,5 @@ class ThermalConstantHorizonBPD : public ThermalMaterialBaseBPD
   ThermalConstantHorizonBPD(const InputParameters & parameters);
 
 protected:
-  virtual void computePDMicroConductivity() override;
+  void computePDMicroConductivity(const Real ave_thermal_conductivity) override;
 };

modules/peridynamics/include/materials/ThermalMaterialBaseBPD.h

@@ -40,27 +40,22 @@ class ThermalMaterialBaseBPD : public MaterialBasePD
 
   /**
    * Function to compute micro-conductivity
+   * @param ave_thermal_conductivity average thermal conductivity for the current element
    */
-  virtual void computePDMicroConductivity() = 0;
+  virtual void computePDMicroConductivity(const Real ave_thermal_conductivity) = 0;
 
   ///@{ Temperature variable and values
   MooseVariableFEBase & _temp_var;
   std::vector<Real> _temp;
   ///@}
 
-  /// Constant thermal conductivity
-  const Real _thermal_conductivity;
-
-  /// Functional thermal conductivity
-  const Function * _thermal_conductivity_function;
-
   ///@{ Material properties to be stored
   MaterialProperty<Real> & _bond_heat_flow;
   MaterialProperty<Real> & _bond_dQdT;
   ///@}
 
   /// Thermal conductivity
-  Real _kappa;
+  const MaterialProperty<Real> & _thermal_conductivity;
 
   /// Micro-conductivity
   Real _Kij;

modules/peridynamics/include/materials/ThermalVariableHorizonBPD.h

@@ -26,5 +26,5 @@ class ThermalVariableHorizonBPD : public ThermalMaterialBaseBPD
   ThermalVariableHorizonBPD(const InputParameters & parameters);
 
 protected:
-  virtual void computePDMicroConductivity() override;
+  void computePDMicroConductivity(const Real ave_thermal_conductivity) override;
 };

modules/peridynamics/src/base/PeridynamicsApp.C

@@ -36,13 +36,6 @@ PeridynamicsApp::registerApps()
   registerApp(PeridynamicsApp);
 }
 
-void
-PeridynamicsApp::registerObjects(Factory & factory)
-{
-  mooseDeprecated("use registerAll instead of registerObjects");
-  Registry::registerObjectsTo(factory, {"PeridynamicsApp"});
-}
-
 static void
 associateSyntaxInner(Syntax & syntax, ActionFactory & /*action_factory*/)
 {
@@ -61,34 +54,6 @@ PeridynamicsApp::registerAll(Factory & f, ActionFactory & af, Syntax & s)
   TensorMechanicsApp::registerAll(f, af, s);
 }
 
-void
-PeridynamicsApp::registerObjectDepends(Factory & factory)
-{
-  mooseDeprecated("use registerAll instead of registerObjectsDepends");
-  TensorMechanicsApp::registerObjects(factory);
-}
-
-void
-PeridynamicsApp::associateSyntax(Syntax & syntax, ActionFactory & action_factory)
-{
-  mooseDeprecated("use registerAll instead of associateSyntax");
-  Registry::registerActionsTo(action_factory, {"PeridynamicsApp"});
-  associateSyntaxInner(syntax, action_factory);
-}
-
-void
-PeridynamicsApp::associateSyntaxDepends(Syntax & syntax, ActionFactory & action_factory)
-{
-  mooseDeprecated("use registerAll instead of registerObjectsDepends");
-  TensorMechanicsApp::associateSyntax(syntax, action_factory);
-}
-
-void
-PeridynamicsApp::registerExecFlags(Factory & /*factory*/)
-{
-  mooseDeprecated("use registerAll instead of registerExecFlags");
-}
-
 extern "C" void
 PeridynamicsApp__registerApps()
 {

modules/peridynamics/src/bcs/IntactBondsDirichletBCPD.C

@@ -16,11 +16,13 @@ InputParameters
 validParams<IntactBondsDirichletBCPD>()
 {
   InputParameters params = validParams<NodalBC>();
-  params.addClassDescription("Class to apply Dirichlet BC based on the number of intact bonds "
-                             "associated with each material point.");
+  params.addClassDescription(
+      "Class to selectively apply a Dirichlet BC based on the number of intact "
+      "bonds associated with each material point. Used to stabilize nodes without "
+      "a sufficient number of connections to other material points.");
   params.addRequiredCoupledVar(
       "intact_bonds_variable",
-      "Name of auxiliary variable for number of intact bonds at each material point");
+      "Name of auxiliary variable containing the number of intact bonds at each material point");
 
   return params;
 }
@@ -29,7 +31,8 @@ IntactBondsDirichletBCPD::IntactBondsDirichletBCPD(const InputParameters & param
   : NodalBC(parameters),
     _pdmesh(dynamic_cast<PeridynamicsMesh &>(_mesh)),
     _u_old(_var.dofValuesOld()),
-    _intact_bonds_val(coupledValue("intact_bonds_variable"))
+    _intact_bonds_val(coupledValue("intact_bonds_variable")),
+    _max_intact_bonds(_pdmesh.dimension() - 1)
 {
 }
 
@@ -43,7 +46,7 @@ bool
 IntactBondsDirichletBCPD::shouldApply()
 {
   bool should_apply = false;
-  if (_intact_bonds_val[0] < _pdmesh.dimension())
+  if (_intact_bonds_val[0] <= _max_intact_bonds)
     should_apply = true;
 
   return should_apply;

modules/peridynamics/src/kernels/FiniteStrainMechanicsNOSPD.C

@@ -20,8 +20,9 @@ validParams<FiniteStrainMechanicsNOSPD>()
 {
   InputParameters params = validParams<MechanicsBaseNOSPD>();
   params.addClassDescription(
-      "Class for calculating residual and Jacobian for Self-stabilized Non-Ordinary "
-      "State-based PeriDynamic (SNOSPD) formulation under finite strain assumptions");
+      "Class for calculating residual and Jacobian for the Self-stabilized "
+      "Non-Ordinary State-based PeriDynamic (SNOSPD) formulation under finite "
+      "strain assumptions");
 
   params.addRequiredParam<unsigned int>(
       "component",

modules/peridynamics/src/kernels/ForceStabilizedSmallStrainMechanicsNOSPD.C

@@ -20,11 +20,15 @@ validParams<ForceStabilizedSmallStrainMechanicsNOSPD>()
 {
   InputParameters params = validParams<MechanicsBasePD>();
   params.addClassDescription("Class for calculating residual and Jacobian for Non-Ordinary "
-                             "State-based PeriDynamic solid mechanics formulation");
+                             "State-based PeriDynamic solid mechanics formulation using a "
+                             "fictitious force method for stabilization.");
 
   params.addRequiredParam<unsigned int>(
       "component",
       "An integer corresponding to the variable this kernel acts on (0 for x, 1 for y, 2 for z)");
+  params.addParam<std::vector<MaterialPropertyName>>(
+      "eigenstrain_names",
+      "List of eigenstrains to be coupled in non-ordinary state-based mechanics kernels");
 
   return params;
 }
@@ -40,9 +44,14 @@ ForceStabilizedSmallStrainMechanicsNOSPD::ForceStabilizedSmallStrainMechanicsNOS
     _ddgraddv(getMaterialProperty<RankTwoTensor>("ddeformation_gradient_dv")),
     _ddgraddw(getMaterialProperty<RankTwoTensor>("ddeformation_gradient_dw")),
     _Cijkl(getMaterialProperty<RankFourTensor>("elasticity_tensor")),
+    _eigenstrain_names(getParam<std::vector<MaterialPropertyName>>("eigenstrain_names")),
+    _deigenstrain_dT(_eigenstrain_names.size()),
     _sf_coeff(getMaterialProperty<Real>("stabilization_force_coeff")),
     _component(getParam<unsigned int>("component"))
 {
+  for (unsigned int i = 0; i < _deigenstrain_dT.size(); ++i)
+    _deigenstrain_dT[i] =
+        &getMaterialPropertyDerivative<RankTwoTensor>(_eigenstrain_names[i], _temp_var->name());
 }
 
 void

modules/peridynamics/src/kernels/GeneralizedPlaneStrainOffDiagNOSPD.C

@@ -21,7 +21,7 @@ validParams<GeneralizedPlaneStrainOffDiagNOSPD>()
 {
   InputParameters params = validParams<MechanicsBaseNOSPD>();
   params.addClassDescription(
-      "Class for calculating off-diagonal jacobian corresponding to "
+      "Class for calculating off-diagonal Jacobian corresponding to "
       "coupling between displacements (or temperature) with scalar out-of-plane strain for "
       "generalized plane strain using SNOSPD formulation");
   params.addCoupledVar("scalar_out_of_plane_strain",
@@ -37,7 +37,7 @@ GeneralizedPlaneStrainOffDiagNOSPD::GeneralizedPlaneStrainOffDiagNOSPD(
 {
   // Consistency check
   if (_disp_var.size() != 2)
-    mooseError("GeneralizedPlaneStrain only works for two dimensional case!");
+    mooseError("GeneralizedPlaneStrain only works for two dimensional models!");
 }
 
 void

modules/peridynamics/src/kernels/HeatSourceBPD.C

@@ -20,18 +20,13 @@ validParams<HeatSourceBPD>()
   InputParameters params = validParams<KernelBasePD>();
   params.addClassDescription("Class for calculating residual from heat source for bond-based "
                              "peridynamic heat conduction formulation");
-  params.addParam<Real>("power_density", 0, "Volumetric heat source density");
-  params.addParam<FunctionName>("power_density_function",
-                                "Function describing the volumetric heat source density");
+  params.addRequiredParam<FunctionName>("power_density", "Volumetric heat source density");
 
   return params;
 }
 
 HeatSourceBPD::HeatSourceBPD(const InputParameters & parameters)
-  : KernelBasePD(parameters),
-    _power_density(getParam<Real>("power_density")),
-    _power_density_function(
-        isParamValid("power_density_function") ? &getFunction("power_density_function") : NULL)
+  : KernelBasePD(parameters), _power_density(getFunction("power_density"))
 {
 }
 
@@ -41,13 +36,8 @@ HeatSourceBPD::computeLocalResidual()
   // get the total_bonds for each node
   unsigned int nn_i = _pdmesh.getNNeighbors(_current_elem->node_id(0));
   unsigned int nn_j = _pdmesh.getNNeighbors(_current_elem->node_id(1));
+  Point p;
 
-  if (_power_density_function)
-  {
-    Point p;
-    _power_density = _power_density_function->value(_t, p);
-  }
-
-  _local_re(0) = -_power_density * _vols_ij[0] / nn_i;
-  _local_re(1) = -_power_density * _vols_ij[1] / nn_j;
+  _local_re(0) = -_power_density.value(_t, p) * _vols_ij[0] / nn_i;
+  _local_re(1) = -_power_density.value(_t, p) * _vols_ij[1] / nn_j;
 }