From e62b9e80e8595696fcceb0bfc7b38b1216425d87 Mon Sep 17 00:00:00 2001
From: Arne Morten Kvarving <arne.morten.kvarving@sintef.no>
Date: Mon, 11 Oct 2021 13:45:11 +0200
Subject: [PATCH] header changes to satisfy iwyu

---
 AdvectionDiffusionArgs.C                      |  4 +++
 AdvectionDiffusionArgs.h                      |  3 ++
 Common/AdvectionDiffusion/ADFluidProperties.C | 17 ++++++++++-
 Common/AdvectionDiffusion/ADFluidProperties.h |  5 +++-
 .../AdvectionDiffusion/AdvectionDiffusion.C   | 14 +++++++--
 .../AdvectionDiffusion/AdvectionDiffusion.h   | 16 ++++++++--
 .../AdvectionDiffusionBDF.C                   | 22 ++++++++++----
 .../AdvectionDiffusionBDF.h                   | 17 ++++++++---
 .../AdvectionDiffusionExplicit.C              | 15 +++++++++-
 .../AdvectionDiffusionExplicit.h              | 12 ++++++++
 .../AdvectionDiffusionImplicit.C              | 16 +++++++++-
 .../AdvectionDiffusionImplicit.h              | 11 +++++++
 .../AdvectionDiffusionSource.C                | 10 +++++--
 .../AdvectionDiffusionSource.h                |  2 ++
 Common/AdvectionDiffusion/SIMAD.C             | 12 +++++++-
 Common/AdvectionDiffusion/SIMAD.h             |  6 ++++
 Test/TestSIMAD.C                              |  6 ++++
 main_AdvectionDiffusion.C                     | 29 +++++++++++++------
 18 files changed, 187 insertions(+), 30 deletions(-)

diff --git a/AdvectionDiffusionArgs.C b/AdvectionDiffusionArgs.C
index 6696112..f86a482 100644
--- a/AdvectionDiffusionArgs.C
+++ b/AdvectionDiffusionArgs.C
@@ -15,6 +15,10 @@
 #include "Utilities.h"
 #include "tinyxml.h"
 
+#include <cstring>
+#include <string>
+#include <strings.h>
+
 
 bool AdvectionDiffusionArgs::parseArg (const char* argv)
 {
diff --git a/AdvectionDiffusionArgs.h b/AdvectionDiffusionArgs.h
index 36fc01b..9bcc2e0 100644
--- a/AdvectionDiffusionArgs.h
+++ b/AdvectionDiffusionArgs.h
@@ -19,6 +19,9 @@
 #include "TimeIntUtils.h"
 
 
+class TiXmlElement;
+
+
 /*!
   \brief Class holding application parameters.
 */
diff --git a/Common/AdvectionDiffusion/ADFluidProperties.C b/Common/AdvectionDiffusion/ADFluidProperties.C
index 0cb9579..0fe886b 100644
--- a/Common/AdvectionDiffusion/ADFluidProperties.C
+++ b/Common/AdvectionDiffusion/ADFluidProperties.C
@@ -15,10 +15,20 @@
 #include "ADFluidProperties.h"
 
 #include "IFEM.h"
-#include "tinyxml.h"
+#include "Functions.h"
+#include "LogStream.h"
+#include "Function.h"
 #include "Utilities.h"
 #include "Vec3.h"
 
+#include <cassert>
+#include <map>
+#include <ostream>
+#include "tinyxml.h"
+#include <utility>
+#include <vector>
+
+
 namespace AD {
 
 FluidProperties::FluidProperties() :
@@ -27,6 +37,11 @@ FluidProperties::FluidProperties() :
 }
 
 
+FluidProperties::~FluidProperties()
+{
+}
+
+
 void FluidProperties::parse(const TiXmlElement* elem)
 {
   // Type of scaling to use
diff --git a/Common/AdvectionDiffusion/ADFluidProperties.h b/Common/AdvectionDiffusion/ADFluidProperties.h
index 55d0ed9..2f1a8e8 100644
--- a/Common/AdvectionDiffusion/ADFluidProperties.h
+++ b/Common/AdvectionDiffusion/ADFluidProperties.h
@@ -14,10 +14,10 @@
 #ifndef _AD_FLUID_PROPERTIES_H
 #define _AD_FLUID_PROPERTIES_H
 
-#include "Functions.h"
 #include <memory>
 #include <string>
 
+class RealFunc;
 class TiXmlElement;
 class Vec3;
 
@@ -39,6 +39,9 @@ class FluidProperties
   //! \brief Empty constructor.
   FluidProperties();
 
+  //! \brief Destructor.
+  ~FluidProperties();
+
   //! \brief Parses material parementers from an XML element.
   void parse(const TiXmlElement*);
 
diff --git a/Common/AdvectionDiffusion/AdvectionDiffusion.C b/Common/AdvectionDiffusion/AdvectionDiffusion.C
index 6b57e22..29402fd 100644
--- a/Common/AdvectionDiffusion/AdvectionDiffusion.C
+++ b/Common/AdvectionDiffusion/AdvectionDiffusion.C
@@ -12,13 +12,23 @@
 //==============================================================================
 
 #include "AdvectionDiffusion.h"
-#include "FiniteElement.h"
-#include "ElmNorm.h"
+
 #include "AnaSol.h"
+#include "ElmNorm.h"
+#include "FiniteElement.h"
 #include "Function.h"
 #include "Fields.h"
+#include "Integrand.h"
+#include "LocalIntegral.h"
+#include "Vec3.h"
 #include "Vec3Oper.h"
 
+#include <algorithm>
+#include <cmath>
+#include <ext/alloc_traits.h>
+#include <iostream>
+#include <vector>
+
 
 AdvectionDiffusion::AdvectionDiffusion (unsigned short int n,
                                         AdvectionDiffusion::Stabilization s)
diff --git a/Common/AdvectionDiffusion/AdvectionDiffusion.h b/Common/AdvectionDiffusion/AdvectionDiffusion.h
index cd08c47..62b40f9 100644
--- a/Common/AdvectionDiffusion/AdvectionDiffusion.h
+++ b/Common/AdvectionDiffusion/AdvectionDiffusion.h
@@ -14,15 +14,27 @@
 #ifndef _ADVECTION_DIFFUSION_H
 #define _ADVECTION_DIFFUSION_H
 
-#include "IntegrandBase.h"
+#include "ADFluidProperties.h"
+
 #include "ElmMats.h"
 #include "EqualOrderOperators.h"
-#include "ADFluidProperties.h"
+#include "IntegrandBase.h"
+#include "MatVec.h"
+#include "SIMenums.h"
 #include "TimeIntUtils.h"
 
+#include <array>
+#include <cstddef>
 #include <memory>
+#include <string>
+
 
+class AnaSol;
+class Fields;
+class FiniteElement;
+class LocalIntegral;
 class RealFunc;
+class Vec3;
 class VecFunc;
 
 
diff --git a/Common/AdvectionDiffusion/AdvectionDiffusionBDF.C b/Common/AdvectionDiffusion/AdvectionDiffusionBDF.C
index afddbd0..bda3f5e 100644
--- a/Common/AdvectionDiffusion/AdvectionDiffusionBDF.C
+++ b/Common/AdvectionDiffusion/AdvectionDiffusionBDF.C
@@ -13,14 +13,26 @@
 //==============================================================================
 
 #include "AdvectionDiffusionBDF.h"
+#include "ADFluidProperties.h"
+
 #include "FiniteElement.h"
-#include "TimeDomain.h"
-#include "ElmNorm.h"
-#include "AnaSol.h"
+#include "Fields.h"
 #include "Function.h"
-#include "Vec3Oper.h"
-#include "Utilities.h"
+#include "LocalIntegral.h"
 #include "StabilizationUtils.h"
+#include "TimeDomain.h"
+#include "Utilities.h"
+#include "Vec3Oper.h"
+
+#include <array>
+#include <cstddef>
+#include <ext/alloc_traits.h>
+#include <iostream>
+#include <memory>
+
+
+class AnaSol;
+class NormBase;
 
 
 AdvectionDiffusionBDF::AdvectionDiffusionBDF (unsigned short int n,
diff --git a/Common/AdvectionDiffusion/AdvectionDiffusionBDF.h b/Common/AdvectionDiffusion/AdvectionDiffusionBDF.h
index 0207002..0a75704 100644
--- a/Common/AdvectionDiffusion/AdvectionDiffusionBDF.h
+++ b/Common/AdvectionDiffusion/AdvectionDiffusionBDF.h
@@ -16,11 +16,20 @@
 
 #include "AdvectionDiffusion.h"
 #include "BDF.h"
+#include "Integrand.h"
+#include "MatVec.h"
+#include "SIMenums.h"
 #include "TimeIntUtils.h"
-#include "Fields.h"
-#include "TimeIntUtils.h"
-#include <array>
-#include <memory>
+
+#include <vector>
+
+
+class AnaSol;
+class FiniteElement;
+class LocalIntegral;
+class NormBase;
+class Vec3;
+struct TimeDomain;
 
 
 /*!
diff --git a/Common/AdvectionDiffusion/AdvectionDiffusionExplicit.C b/Common/AdvectionDiffusion/AdvectionDiffusionExplicit.C
index eaee1ba..bb64ff3 100644
--- a/Common/AdvectionDiffusion/AdvectionDiffusionExplicit.C
+++ b/Common/AdvectionDiffusion/AdvectionDiffusionExplicit.C
@@ -13,8 +13,21 @@
 //==============================================================================
 
 #include "AdvectionDiffusionExplicit.h"
-#include "FiniteElement.h"
+#include "ADFluidProperties.h"
+
+#include "ElmMats.h"
 #include "Function.h"
+#include "MatVec.h"
+#include "Vec3.h"
+
+#include <ext/alloc_traits.h>
+#include <memory>
+#include <vector>
+
+
+class FiniteElement;
+class LocalIntegral;
+class NormBase;
 
 
 AdvectionDiffusionExplicit::AdvectionDiffusionExplicit (unsigned short int n,
diff --git a/Common/AdvectionDiffusion/AdvectionDiffusionExplicit.h b/Common/AdvectionDiffusion/AdvectionDiffusionExplicit.h
index 5f30b73..0b6a574 100644
--- a/Common/AdvectionDiffusion/AdvectionDiffusionExplicit.h
+++ b/Common/AdvectionDiffusion/AdvectionDiffusionExplicit.h
@@ -15,8 +15,20 @@
 #define _ADVECTION_DIFFUSION_EXPLICIT_H
 
 #include "AdvectionDiffusion.h"
+
+#include "Integrand.h"
+#include "SIMenums.h"
 #include "TimeIntUtils.h"
 
+#include <cstddef>
+
+
+class AnaSol;
+class FiniteElement;
+class LocalIntegral;
+class NormBase;
+class Vec3;
+
 
 /*!
   \brief Class representing the integrand of a time-dependent
diff --git a/Common/AdvectionDiffusion/AdvectionDiffusionImplicit.C b/Common/AdvectionDiffusion/AdvectionDiffusionImplicit.C
index 3f32a0c..6954044 100644
--- a/Common/AdvectionDiffusion/AdvectionDiffusionImplicit.C
+++ b/Common/AdvectionDiffusion/AdvectionDiffusionImplicit.C
@@ -13,11 +13,25 @@
 //==============================================================================
 
 #include "AdvectionDiffusionImplicit.h"
+#include "ADFluidProperties.h"
+
+#include "ElmMats.h"
 #include "FiniteElement.h"
 #include "Function.h"
-#include "TimeDomain.h"
+#include "MatVec.h"
+#include "matrix.h"
+#include "Vec3.h"
 #include "Vec3Oper.h"
 
+#include <cstddef>
+#include <memory>
+#include <vector>
+
+
+class AnaSol;
+class LocalIntegral;
+class NormBase;
+
 
 AdvectionDiffusionImplicit::AdvectionDiffusionImplicit (unsigned short int n,
                                                         TimeIntegration::Method method,
diff --git a/Common/AdvectionDiffusion/AdvectionDiffusionImplicit.h b/Common/AdvectionDiffusion/AdvectionDiffusionImplicit.h
index e7c3bb3..bb2ceb8 100644
--- a/Common/AdvectionDiffusion/AdvectionDiffusionImplicit.h
+++ b/Common/AdvectionDiffusion/AdvectionDiffusionImplicit.h
@@ -16,9 +16,20 @@
 #define _ADVECTION_DIFFUSION_IMPLICIT_H
 
 #include "AdvectionDiffusion.h"
+
+#include "Integrand.h"
+#include "SIMenums.h"
 #include "TimeIntUtils.h"
 
 
+class AnaSol;
+class FiniteElement;
+class LocalIntegral;
+class NormBase;
+struct TimeDomain;
+class Vec3;
+
+
 /*!
   \brief Class representing the integrand of Advection-Diffusion problem
          with implicit time stepping.
diff --git a/Common/AdvectionDiffusion/AdvectionDiffusionSource.C b/Common/AdvectionDiffusion/AdvectionDiffusionSource.C
index 9272f95..015eb87 100644
--- a/Common/AdvectionDiffusion/AdvectionDiffusionSource.C
+++ b/Common/AdvectionDiffusion/AdvectionDiffusionSource.C
@@ -12,13 +12,17 @@
 //==============================================================================
 
 #include "AdvectionDiffusionSource.h"
-#include "ExprFunctions.h"
-#include "IFEM.h"
 #include "ADFluidProperties.h"
+
 #include "Functions.h"
-#include "Vec3Oper.h"
+#include "IFEM.h"
+#include "LogStream.h"
 #include "Utilities.h"
+#include "Vec3Oper.h"
 
+#include <ostream>
+#include <string>
+#include <vector>
 #include <tinyxml.h>
 
 
diff --git a/Common/AdvectionDiffusion/AdvectionDiffusionSource.h b/Common/AdvectionDiffusion/AdvectionDiffusionSource.h
index e5c9626..2719054 100644
--- a/Common/AdvectionDiffusion/AdvectionDiffusionSource.h
+++ b/Common/AdvectionDiffusion/AdvectionDiffusionSource.h
@@ -17,6 +17,8 @@
 
 #include <memory>
 
+
+class Vec3;
 class TiXmlElement;
 
 
diff --git a/Common/AdvectionDiffusion/SIMAD.C b/Common/AdvectionDiffusion/SIMAD.C
index d8f3f20..72569c2 100644
--- a/Common/AdvectionDiffusion/SIMAD.C
+++ b/Common/AdvectionDiffusion/SIMAD.C
@@ -18,19 +18,29 @@
 #include "AdvectionDiffusionExplicit.h"
 #include "AdvectionDiffusionImplicit.h"
 #include "AdvectionDiffusionSource.h"
+
 #include "AnaSol.h"
 #include "ASMstruct.h"
 #include "DataExporter.h"
+#include "EqualOrderOperators.h"
 #include "ExprFunctions.h"
 #include "IFEM.h"
+#include "IntegrandBase.h"
+#include "LogStream.h"
 #include "Profiler.h"
 #include "SIM1D.h"
 #include "SIM2D.h"
 #include "SIM3D.h"
 #include "TimeStep.h"
-#include "tinyxml.h"
 #include "Utilities.h"
 
+#include <cmath>
+#include <cstdlib>
+#include <ostream>
+#include "strings.h"
+#include "tinyxml.h"
+#include <utility>
+
 
 template<class Dim, class Integrand>
 SIMAD<Dim,Integrand>::SIMAD (Integrand& ad, bool alone) :
diff --git a/Common/AdvectionDiffusion/SIMAD.h b/Common/AdvectionDiffusion/SIMAD.h
index a0c90a6..4a4fca6 100644
--- a/Common/AdvectionDiffusion/SIMAD.h
+++ b/Common/AdvectionDiffusion/SIMAD.h
@@ -14,6 +14,7 @@
 #ifndef _SIM_AD_H
 #define _SIM_AD_H
 
+#include "MatVec.h"
 #include "SIMMultiPatchModelGen.h"
 #include "SIMsolution.h"
 #include "SIMconfigure.h"
@@ -22,10 +23,15 @@
 #include "PETScSupport.h"
 #endif
 
+#include <cstddef>
+#include <iosfwd>
+#include <string>
+
 
 class DataExporter;
 class SIMoutput;
 class TimeStep;
+class TiXmlElement;
 
 
 /*!
diff --git a/Test/TestSIMAD.C b/Test/TestSIMAD.C
index 3b81eb1..a6d8269 100644
--- a/Test/TestSIMAD.C
+++ b/Test/TestSIMAD.C
@@ -10,9 +10,15 @@
 //!
 //==============================================================================
 
+#include "AdvectionDiffusion.h"
 #include "AdvectionDiffusionBDF.h"
+#include "ADFluidProperties.h"
 #include "SIMAD.h"
+
 #include "SIM2D.h"
+#include "TimeIntUtils.h"
+
+#include <string>
 
 #include "gtest/gtest.h"
 
diff --git a/main_AdvectionDiffusion.C b/main_AdvectionDiffusion.C
index 18803f4..0614122 100644
--- a/main_AdvectionDiffusion.C
+++ b/main_AdvectionDiffusion.C
@@ -11,23 +11,34 @@
 //!
 //==============================================================================
 
+#include "AdvectionDiffusion.h"
+#include "AdvectionDiffusionArgs.h"
+#include "AdvectionDiffusionBDF.h"
+#include "AdvectionDiffusionExplicit.h"
+#include "AdvectionDiffusionImplicit.h"
+#include "SIMAD.h"
+
+#include "ASMenums.h"
 #include "IFEM.h"
+#include "LogStream.h"
+#include "Profiler.h"
 #include "SIM2D.h"
 #include "SIM3D.h"
+#include "SIMconfigure.h"
 #include "SIMExplicitRK.h"
 #include "SIMExplicitRKE.h"
 #include "SIMExplicitLMM.h"
 #include "SIMImplicitLMM.h"
+#include "SIMoptions.h"
+#include "SIMSolver.h"
 #include "SIMSolverAdap.h"
-#include "SIMAD.h"
-#include "AdvectionDiffusionArgs.h"
-#include "AdvectionDiffusionBDF.h"
-#include "AdvectionDiffusionExplicit.h"
-#include "AdvectionDiffusionImplicit.h"
-#include "Profiler.h"
-#include <stdlib.h>
-#include <string.h>
-#include <ctype.h>
+#include "TimeStep.h"
+#include "TimeIntUtils.h"
+
+#include <algorithm>
+#include <iostream>
+#include <string>
+#include <vector>
 
 
 /*!