Merge pull request #263 from LLNL/rc-v2024.01.1

v2024.01.1 Patch Release

RELEASE_NOTES.md

@@ -1,3 +1,24 @@
+Version v2024.01.1 -- Release date 2024-02-17
+==============================================
+  * Important Notes:
+    * This is a patch release for v2024.01.0.
+
+Notable changes include:
+
+  * New features/ API changes:
+    * Adding an optional second-stage problem start-up hook to the Physics package interface: Physics::initializeProblemStartupDependencies.  The idea is to keep basic sizing
+      of arrays and such in the first stage (Physics::initializeProblemStartup), while this new hook is used for updating any initial Physics state (and therefore provides a
+      State and StateDerivatives object).
+
+  * Build changes / improvements:
+    * 
+
+  * Bug Fixes / improvements:
+    * Fixed bug with ConstantBoundary in the presence of porosity with the new porosity models introduced in v2024.01.00.
+    * Updating header lists for including Spheral modules in external projects.
+    * Adding effective viscous pressure back to FSISPH.
+    * Initial volumes for damage models were incorrectly not taking into account pore space when computing failure statistics for seeding flaws.  Fixed.
+
 Version v2024.01.00 -- Release date 2024-01-19
 ==============================================
   * Important Notes:

cmake/SpheralVersion.cmake

@@ -1 +1 @@
-set(SPHERAL_VERSION 2024.01.0)
+set(SPHERAL_VERSION 2024.01.1)

docs/conf.py

@@ -26,9 +26,9 @@
 author = 'J. Michael Owen'
 
 # The short X.Y version
-version = '2024.01.0'
+version = '2024.01.1'
 # The full version, including alpha/beta/rc tags
-release = '2024.01.0'
+release = '2024.01.1'
 
 
 # -- General configuration ---------------------------------------------------

docs/conf.py.in

@@ -26,9 +26,9 @@ copyright = '2012, LLNS'
 author = 'J. Michael Owen'
 
 # The short X.Y version
-version = '2024.01.0'
+version = '2024.01.1'
 # The full version, including alpha/beta/rc tags
-release = '2024.01.0'
+release = '2024.01.1'
 
 
 # -- General configuration ---------------------------------------------------

docs/developer/dev/continuous_deployment.rst

@@ -9,7 +9,7 @@ to their environment.
 
 On LC systems we maintain:
   * ``Spheral/risky``
-  * ``Spheral/2024.01.0``
+  * ``Spheral/2024.01.1``
   * ``Spheral/2023.06.0``
   * ``Spheral/2023.03.1``
   * ``Spheral/2023.03.0`` (deprecated as of TOSS4 upgrade)

src/ArtificialViscosity/CullenDehnenViscosity.cc

@@ -90,8 +90,8 @@ initializeProblemStartup(DataBase<Dimension>& dataBase) {
   mR = dataBase.newFluidFieldList(0.0, "mR");
   mVsig = dataBase.newFluidFieldList(0.0, "mVsig");
 
-  FieldList<Dimension, Scalar>& rvQ = myq.CqMultiplier();
-  FieldList<Dimension, Scalar>& rvL = myq.ClMultiplier();
+  auto& rvQ = myq.CqMultiplier();
+  auto& rvL = myq.ClMultiplier();
   rvQ = dataBase.newFluidFieldList(malphMin, HydroFieldNames::ArtificialViscousCqMultiplier);  // This will override the Q initializer intializing these to unity.
   rvL = dataBase.newFluidFieldList(malphMin, HydroFieldNames::ArtificialViscousClMultiplier);
 }
@@ -104,17 +104,17 @@ void
 CullenDehnenViscosity<Dimension>::
 registerState(DataBase<Dimension>& dataBase,
               State<Dimension>& state) {
-  dataBase.resizeFluidFieldList(mPrevDvDt, Vector::zero, "mPrevDvDt", false);
-  dataBase.resizeFluidFieldList(mPrevDivV, 0.0, "mPrevDivV", false);
-  dataBase.resizeFluidFieldList(mCullAlpha, 1.0, "mCullAlpha", false);
+  CHECK(mPrevDvDt.numFields() == dataBase.numFluidNodeLists());
+  CHECK(mPrevDivV.numFields() == dataBase.numFluidNodeLists());
+  CHECK(mCullAlpha.numFields() == dataBase.numFluidNodeLists());
   state.enroll(mPrevDvDt);
   state.enroll(mPrevDivV);
   state.enroll(mCullAlpha);
 
-  FieldList<Dimension, Scalar>& rvAlphaQ = myq.CqMultiplier();
-  FieldList<Dimension, Scalar>& rvAlphaL = myq.ClMultiplier();
-  state.enroll(rvAlphaQ, std::make_shared<IncrementCullenMultipliers<Dimension>>(malphMin, malphMax, mboolHopkins));
-  state.enroll(rvAlphaL);
+  auto& rvQ = myq.CqMultiplier();
+  auto& rvL = myq.ClMultiplier();
+  state.enroll(rvQ, make_policy<IncrementCullenMultipliers<Dimension>>(malphMin, malphMax, mboolHopkins));
+  state.enroll(rvL);
 }
 
 //------------------------------------------------------------------------------
@@ -125,12 +125,12 @@ void
 CullenDehnenViscosity<Dimension>::
 registerDerivatives(DataBase<Dimension>& dataBase,
                     StateDerivatives<Dimension>& derivs) {
-  dataBase.resizeFluidFieldList(mPrevDivV2, 0.0, "mPrevDivV2", false);
-  dataBase.resizeFluidFieldList(mCullAlpha2, 1.0, "mCullAlpha2", false);
-  dataBase.resizeFluidFieldList(mDalphaDt, 0.0, "mDalphaDt", false);
-  dataBase.resizeFluidFieldList(mAlphaLocal, 0.0, "mAlphaLocal", false);
-  dataBase.resizeFluidFieldList(mR, 0.0, "mR", false);
-  dataBase.resizeFluidFieldList(mVsig, 0.0, "mVsig", false);
+  CHECK(mPrevDivV2.numFields() == dataBase.numFluidNodeLists());
+  CHECK(mCullAlpha2.numFields() == dataBase.numFluidNodeLists());
+  CHECK(mDalphaDt.numFields() == dataBase.numFluidNodeLists());
+  CHECK(mAlphaLocal.numFields() == dataBase.numFluidNodeLists());
+  CHECK(mR.numFields() == dataBase.numFluidNodeLists());
+  CHECK(mVsig.numFields() == dataBase.numFluidNodeLists());
   derivs.enroll(mPrevDivV2);
   derivs.enroll(mCullAlpha2);
   derivs.enroll(mDalphaDt);

src/ArtificialViscosity/MorrisMonaghanReducingViscosity.cc

@@ -129,8 +129,8 @@ template<typename Dimension>
 void
 MorrisMonaghanReducingViscosity<Dimension>::
 initializeProblemStartup(DataBase<Dimension>& dataBase) {
-  FieldList<Dimension, Scalar>& rvQ = myq.CqMultiplier();
-  FieldList<Dimension, Scalar>& rvL = myq.ClMultiplier();
+  auto& rvQ = myq.CqMultiplier();
+  auto& rvL = myq.ClMultiplier();
   rvQ = dataBase.newFluidFieldList(0.0, HydroFieldNames::ArtificialViscousCqMultiplier);  // This will override the Q initializer intializing these to unity.
   rvL = dataBase.newFluidFieldList(0.0, HydroFieldNames::ArtificialViscousClMultiplier);
   mDrvAlphaDtQ = dataBase.newFluidFieldList(0.0, IncrementBoundedState<Dimension, Scalar>::prefix() + HydroFieldNames::ArtificialViscousCqMultiplier);
@@ -145,10 +145,10 @@ void
 MorrisMonaghanReducingViscosity<Dimension>::
 registerState(DataBase<Dimension>& /*dataBase*/,
               State<Dimension>& state) {
-  FieldList<Dimension, Scalar>& rvQ = myq.CqMultiplier();
-  FieldList<Dimension, Scalar>& rvL = myq.ClMultiplier();
-  state.enroll(rvQ, std::make_shared<IncrementBoundedState<Dimension, Scalar>>(maMin,maMax));
-  state.enroll(rvL, std::make_shared<IncrementBoundedState<Dimension, Scalar>>(maMin,maMax));
+  auto& rvQ = myq.CqMultiplier();
+  auto& rvL = myq.ClMultiplier();
+  state.enroll(rvQ, make_policy<IncrementBoundedState<Dimension, Scalar>>(maMin,maMax));
+  state.enroll(rvL, make_policy<IncrementBoundedState<Dimension, Scalar>>(maMin,maMax));
 }
 
 //------------------------------------------------------------------------------

src/CRKSPH/CRKSPHHydroBase.cc

@@ -18,6 +18,7 @@
 #include "DataBase/IncrementBoundedState.hh"
 #include "DataBase/ReplaceState.hh"
 #include "DataBase/ReplaceBoundedState.hh"
+#include "DataBase/updateStateFields.hh"
 #include "Hydro/SpecificThermalEnergyPolicy.hh"
 #include "Hydro/SpecificFromTotalThermalEnergyPolicy.hh"
 #include "Hydro/PressurePolicy.hh"
@@ -149,12 +150,14 @@ CRKSPHHydroBase<Dimension>::
 template<typename Dimension>
 void
 CRKSPHHydroBase<Dimension>::
-initializeProblemStartup(DataBase<Dimension>& dataBase) {
+initializeProblemStartupDependencies(DataBase<Dimension>& dataBase,
+                                     State<Dimension>& state,
+                                     StateDerivatives<Dimension>& derivs) {
 
   // Initialize the pressure, sound speed, and entropy.
-  dataBase.fluidPressure(mPressure);
-  dataBase.fluidSoundSpeed(mSoundSpeed);
-  dataBase.fluidEntropy(mEntropy);
+  updateStateFields<Dimension>(HydroFieldNames::pressure, state, derivs);
+  updateStateFields<Dimension>(HydroFieldNames::soundSpeed, state, derivs);
+  updateStateFields<Dimension>(HydroFieldNames::entropy, state, derivs);
 }
 
 //------------------------------------------------------------------------------
@@ -168,8 +171,6 @@ registerState(DataBase<Dimension>& dataBase,
 
   // Create the local storage for time step mask, pressure, sound speed, and correction fields.
   dataBase.resizeFluidFieldList(mTimeStepMask, 1, HydroFieldNames::timeStepMask);
-  // dataBase.fluidPressure(mPressure);
-  // dataBase.fluidSoundSpeed(mSoundSpeed);
   dataBase.resizeFluidFieldList(mEntropy,    0.0,                   HydroFieldNames::entropy, false);
   dataBase.resizeFluidFieldList(mPressure,   0.0,                   HydroFieldNames::pressure, false);
   dataBase.resizeFluidFieldList(mSoundSpeed, 0.0,                   HydroFieldNames::soundSpeed, false);

src/CRKSPH/CRKSPHHydroBase.hh

@@ -63,7 +63,9 @@ public:
 
   // Tasks we do once on problem startup.
   virtual
-  void initializeProblemStartup(DataBase<Dimension>& dataBase) override;
+  void initializeProblemStartupDependencies(DataBase<Dimension>& dataBase,
+                                            State<Dimension>& state,
+                                            StateDerivatives<Dimension>& derivs) override;
 
   // Register the state Hydro expects to use and evolve.
   virtual 

src/CRKSPH/CRKSPHHydroBaseRZ.cc

@@ -104,10 +104,19 @@ CRKSPHHydroBaseRZ::
 //------------------------------------------------------------------------------
 void
 CRKSPHHydroBaseRZ::
-initializeProblemStartup(DataBase<Dim<2> >& dataBase) {
-
+initializeProblemStartup(DataBase<Dim<2>>& dataBase) {
   GeometryRegistrar::coords(CoordinateType::RZ);
+}
 
+//------------------------------------------------------------------------------
+// On problem start up some dependent state needs to be calculated
+//------------------------------------------------------------------------------
+void
+CRKSPHHydroBaseRZ::
+initializeProblemStartupDependencies(DataBase<Dim<2>>& dataBase,
+                                     State<Dim<2>>& state,
+                                     StateDerivatives<Dim<2>>& derivs) {
+
   // Correct the mass to mass/r.
   auto mass = dataBase.fluidMass();
   const auto pos = dataBase.fluidPosition();
@@ -121,7 +130,7 @@ initializeProblemStartup(DataBase<Dim<2> >& dataBase) {
   }
 
   // Do general initializations.
-  CRKSPHHydroBase<Dim<2> >::initializeProblemStartup(dataBase);
+  CRKSPHHydroBase<Dim<2> >::initializeProblemStartupDependencies(dataBase, state, derivs);
 
   // Convert back to mass.
   for (unsigned nodeListi = 0; nodeListi != numNodeLists; ++nodeListi) {
@@ -138,8 +147,8 @@ initializeProblemStartup(DataBase<Dim<2> >& dataBase) {
 //------------------------------------------------------------------------------
 void
 CRKSPHHydroBaseRZ::
-registerState(DataBase<Dim<2> >& dataBase,
-              State<Dim<2> >& state) {
+registerState(DataBase<Dim<2>>& dataBase,
+              State<Dim<2>>& state) {
 
   // The base class does most of it.
   CRKSPHHydroBase<Dim<2> >::registerState(dataBase, state);

src/CRKSPH/CRKSPHHydroBaseRZ.hh

@@ -62,9 +62,19 @@ public:
   // Destructor.
   virtual ~CRKSPHHydroBaseRZ();
 
-  // Tasks we do once on problem startup.
-  virtual
-  void initializeProblemStartup(DataBase<Dimension>& dataBase) override;
+  // An optional hook to initialize once when the problem is starting up.
+  // Typically this is used to size arrays once all the materials and NodeLists have
+  // been created.  It is assumed after this method has been called it is safe to
+  // call Physics::registerState for instance to create full populated State objects.
+  virtual void initializeProblemStartup(DataBase<Dimension>& dataBase) override;
+
+  // A second optional method to be called on startup, after Physics::initializeProblemStartup has
+  // been called.
+  // One use for this hook is to fill in dependendent state using the State object, such as
+  // temperature or pressure.
+  virtual void initializeProblemStartupDependencies(DataBase<Dimension>& dataBase,
+                                                    State<Dimension>& state,
+                                                    StateDerivatives<Dimension>& derivs) override;
 
   // Register the state Hydro expects to use and evolve.
   virtual