request from RR main

.gitignore

@@ -82,6 +82,7 @@ temp_print_trace.*
 *.json
 *.bak
 *.processor.*
+*.directory
 .clang_complete
 .failed_tests
 compile_commands.json

doc/content/source/kernels/ADAnisotropicDiffusion.md

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+# ADAnisotropicDiffusion
+
+!syntax description /Kernels/ADAnisotropicDiffusion
+
+The weak form of this kernel is $\left( \grad w, \grad u \right)$, where $w$ is the test function and $u$ is the variable (or the coupled variable).
+
+## Example Input File Syntax
+
+!syntax parameters /Kernels/ADAnisotropicDiffusion
+
+!syntax inputs /Kernels/ADAnisotropicDiffusion
+
+!syntax children /Kernels/ADAnisotropicDiffusion

doc/content/source/kernels/ADPoroMechanicsCoupling.md

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+# ADPoroMechanicsCoupling
+
+!syntax description /Kernels/ADPoroMechanicsCoupling
+
+## Example Input File Syntax
+
+!syntax parameters /Kernels/ADPoroMechanicsCoupling
+
+!syntax inputs /Kernels/ADPoroMechanicsCoupling
+
+!syntax children /Kernels/ADPoroMechanicsCoupling

doc/content/source/kernels/ADPorousFlowTimeDerivative.md

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+# ADPorousFlowTimeDerivative
+
+!syntax description /Kernels/ADPorousFlowTimeDerivative
+
+## Example Input File Syntax
+
+!syntax parameters /Kernels/ADPorousFlowTimeDerivative
+
+!syntax inputs /Kernels/ADPorousFlowTimeDerivative
+
+!syntax children /Kernels/ADPorousFlowTimeDerivative

doc/content/source/kernels/ADSPFPressureTimeDerivative.md

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+# ADSPFPressureTimeDerivative
+
+!syntax description /Kernels/ADSPFPressureTimeDerivative
+
+## Example Input File Syntax
+
+!syntax parameters /Kernels/ADSPFPressureTimeDerivative
+
+!syntax inputs /Kernels/ADSPFPressureTimeDerivative
+
+!syntax children /Kernels/ADSPFPressureTimeDerivative

doc/content/source/kernels/ADSPFVolStrTimeDerivative.md

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+# ADSPFVolStrTimeDerivative
+
+!syntax description /Kernels/ADSPFVolStrTimeDerivative
+
+## Example Input File Syntax
+
+!syntax parameters /Kernels/ADSPFVolStrTimeDerivative
+
+!syntax inputs /Kernels/ADSPFVolStrTimeDerivative
+
+!syntax children /Kernels/ADSPFVolStrTimeDerivative

doc/content/source/materials/ADComputePorosity.md

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+# ADComputePorosity
+
+!syntax description /Materials/ADComputePorosity
+
+## Overview
+
+This equation calculates porosity evolution in porous solids in terms of variation of fluid pressure and solid volumetric strain:
+
+\begin{equation}
+  \phi = \phi_0 + \frac{p}{M} + \alpha \epsilon_v,
+\end{equation}
+where $\phi$ is the solid porosity; $\phi_0$ is the initial solid porosity; $M$ is biot's modulus; $\alpha$ is the Biot’s coefficient; and $\epsilon_v$ is the solid volumetric strain.
+
+## Example Input File Syntax
+
+!syntax parameters /Materials/ADComputePorosity
+
+!syntax inputs /Materials/ADComputePorosity
+
+!syntax children /Materials/ADComputePorosity

doc/content/source/materials/ComputeCrackOpeningDisplacement.md

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+# ComputeCrackOpeningDisplacement
+
+!syntax description /Materials/ComputeCrackOpeningDisplacement
+
+## Overview
+
+Crack opening calculation is accomplished using the gradient of damage variable, $\grad d$, which is used to define the unit vector perpendicular to the crack plane as $\normal^d = \grad d/\norm{\grad d}$. The crack opening field is then calculated as
+
+\begin{equation}
+\varw_n = h^e \left( \normal^d \cdot \strain \cdot \normal^d \right),
+\end{equation}
+where $h^e$ is the edge length of the current element.
+
+## Example Input File Syntax
+
+!syntax parameters /Materials/ComputeCrackOpeningDisplacement
+
+!syntax inputs /Materials/ComputeCrackOpeningDisplacement
+
+!syntax children /Materials/ComputeCrackOpeningDisplacement

doc/content/source/materials/ComputeFluidMobility.md

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+# ComputeFluidMobility
+
+!syntax description /Materials/ComputeFluidMobility
+
+## Overview
+
+\begin{equation}
+  \boldsymbol{\lambda} = \frac{\bold{k}}{\mu} + d^{\xi}\frac{\bold{k}^d}{\mu},
+\end{equation}
+where
+in which $\xi$ is an exponent used to localize the increased permeability along the fracture. $\bold{k}/\mu$ is the fluid mobility in intact bulk porous solid, while $\bold{k}^d/\mu$ is the additional permeability in the damaged domain.
+
+## Example Input File Syntax
+
+!syntax parameters /Materials/ComputeFluidMobility
+
+!syntax inputs /Materials/ComputeFluidMobility
+
+!syntax children /Materials/ComputeFluidMobility

include/diracKernel/DiracSource.h

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+//* This file is part of the RACCOON application
+//* being developed at Dolbow lab at Duke University
+//* http://dolbow.pratt.duke.edu
+
+#pragma once
+
+// Moose Includes
+#include "DiracKernel.h"
+
+class DiracSource : public DiracKernel
+{
+public:
+  static InputParameters validParams();
+  DiracSource(const InputParameters & parameters);
+
+  virtual void addPoints() override;
+  virtual Real computeQpResidual() override;
+
+protected:
+  /// position of the dirac source
+  Point _point;
+
+  /// numbe of dimensions
+  int _dim;
+  Real _fL;
+
+  /// list of parameters for the source equation
+  Real _t1;
+  Real _tRT;
+  Real _tL;
+  Real _tP;
+  Real _p0;
+  Real _d1;
+  Real _upcoeff;
+  Real _downcoeff;
+
+  /// fluid density
+  Real _rho;
+
+  /// number of acoustic shots
+  Real _num_shots;
+};

include/ics/PhasefieldShapes.h

@@ -0,0 +1,28 @@
+//* This file is part of the RACCOON application
+//* being developed at Dolbow lab at Duke University
+//* http://dolbow.pratt.duke.edu
+
+#pragma once
+
+// MOOSE Includes
+#include "InitialCondition.h"
+
+/**
+ * PhasefieldShapes just returns a constant value.
+ */
+class PhasefieldShapes : public InitialCondition
+{
+public:
+  static InputParameters validParams();
+  PhasefieldShapes(const InputParameters & parameters);
+
+  virtual Real value(const Point & p);
+
+private:
+  Real _epsilon;
+  std::vector<Real> _centers_tips;
+  std::vector<std::string> _shapes;
+  std::vector<std::string> _gradients;
+  std::vector<Real> _gradient_values;
+  Real _fluid_phase;
+};

include/kernels/ADAnisotropicDiffusion.h

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+//* This file is part of the RACCOON application
+//* being developed at Dolbow lab at Duke University
+//* http://dolbow.pratt.duke.edu
+
+#pragma once
+
+#include "ADKernel.h"
+#include "BaseNameInterface.h"
+
+class ADAnisotropicDiffusion : public ADKernel, public BaseNameInterface
+{
+public:
+  static InputParameters validParams();
+
+  ADAnisotropicDiffusion(const InputParameters & parameters);
+
+protected:
+  virtual ADReal computeQpResidual() override;
+
+  /// gradient of the coupled variable
+  const ADVariableGradient & _grad_v;
+
+  /// The anisotropic diffusivity
+  const ADMaterialProperty<RankTwoTensor> & _D;
+};

include/kernels/ADPoroMechanicsCoupling.h

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+//* This file is part of the RACCOON application
+//* being developed at Dolbow lab at Duke University
+//* http://dolbow.pratt.duke.edu
+
+#pragma once
+
+#include "ADKernel.h"
+#include "BaseNameInterface.h"
+
+class ADPoroMechanicsCoupling : public ADKernel, public BaseNameInterface
+{
+public:
+  static InputParameters validParams();
+
+  ADPoroMechanicsCoupling(const InputParameters & parameters);
+
+protected:
+  virtual ADReal computeQpResidual();
+
+  /// biot coefficient
+  const ADMaterialProperty<Real> & _coefficient;
+
+  /// fluid pore pressure
+  const ADVariableValue & _porepressure;
+
+  /// component integer
+  unsigned int _component;
+};

include/kernels/ADPorousFlowTimeDerivative.h

@@ -0,0 +1,30 @@
+//* This file is part of the RACCOON application
+//* being developed at Dolbow lab at Duke University
+//* http://dolbow.pratt.duke.edu
+
+#pragma once
+
+#include "ADTimeKernel.h"
+#include "BaseNameInterface.h"
+
+class ADPorousFlowTimeDerivative : public ADTimeKernel, public BaseNameInterface
+{
+public:
+  static InputParameters validParams();
+
+  ADPorousFlowTimeDerivative(const InputParameters & parameters);
+
+protected:
+  virtual ADReal computeQpResidual() override;
+
+  // @{ The current and old values of porosity used to compute its time derivative.
+  const ADMaterialProperty<Real> & _porosity;
+  const MaterialProperty<Real> & _porosity_old;
+  // @}
+
+  /// The saturation
+  const ADVariableValue & _S;
+
+  /// The time derivative of the saturation
+  const ADVariableValue & _S_dot;
+};

include/kernels/ADSPFPressureTimeDerivative.h

@@ -0,0 +1,21 @@
+//* This file is part of the RACCOON application
+//* being developed at Dolbow lab at Duke University
+//* http://dolbow.pratt.duke.edu
+
+#pragma once
+
+#include "ADTimeDerivative.h"
+#include "BaseNameInterface.h"
+
+class ADSPFPressureTimeDerivative : public ADTimeDerivative, public BaseNameInterface
+{
+public:
+  static InputParameters validParams();
+
+  ADSPFPressureTimeDerivative(const InputParameters & parameters);
+
+protected:
+  virtual ADReal precomputeQpResidual() override;
+
+  const ADMaterialProperty<Real> & _B;
+};

include/kernels/ADSPFVolStrTimeDerivative.h

@@ -0,0 +1,27 @@
+//* This file is part of the RACCOON application
+//* being developed at Dolbow lab at Duke University
+//* http://dolbow.pratt.duke.edu
+
+#pragma once
+
+#include "ADTimeKernel.h"
+#include "BaseNameInterface.h"
+
+class ADSPFVolStrTimeDerivative : public ADTimeKernel, public BaseNameInterface
+{
+public:
+  static InputParameters validParams();
+
+  ADSPFVolStrTimeDerivative(const InputParameters & parameters);
+
+protected:
+  virtual ADReal computeQpResidual() override;
+
+  // @{ The current and the old strain
+  const ADMaterialProperty<RankTwoTensor> & _strain;
+  const MaterialProperty<RankTwoTensor> & _strain_old;
+  // @}
+
+  /// The Biot coefficient
+  const ADMaterialProperty<Real> & _alpha;
+};

include/materials/ADComputePorosity.h

@@ -0,0 +1,29 @@
+//* This file is part of the RACCOON application
+//* being developed at Dolbow lab at Duke University
+//* http://dolbow.pratt.duke.edu
+
+#pragma once
+
+#include "Material.h"
+
+class ADComputePorosity : public Material
+{
+public:
+  static InputParameters validParams();
+
+  ADComputePorosity(const InputParameters & parameters);
+
+protected:
+  virtual void initQpStatefulProperties() override;
+  virtual void computeQpProperties() override;
+
+  const ADVariableValue & _porepressure;
+  const ADMaterialProperty<RankTwoTensor> & _strain;
+
+  ADMaterialProperty<Real> & _porosity;
+  const MaterialProperty<Real> & _porosity_old;
+  const Real _initial_porosity;
+
+  const ADMaterialProperty<Real> & _alpha;
+  const ADMaterialProperty<Real> & _M;
+};