diff --git a/.gitignore b/.gitignore index 1ec5b16db..b03d82e42 100644 --- a/.gitignore +++ b/.gitignore @@ -92,6 +92,5 @@ src/PBGWraps/SpheralModules_WildMagic.C build-* src/*/*cc.2.cc src/*/*cc.3.cc -/build/*/x64 -/build/*/*.user -*.aps +src/*/*/*cc.2.cc +src/*/*/*cc.3.cc diff --git a/RELEASE_NOTES.md b/RELEASE_NOTES.md index 0d92262b4..51fbae516 100644 --- a/RELEASE_NOTES.md +++ b/RELEASE_NOTES.md @@ -24,6 +24,7 @@ Notable changes include: * Bug Fixes / improvements: * Wrappers for MPI calls are simplified and improved. + * Time step estimate due to velocity divergence in RZ space has been fixed. 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Document - - - Document - - - - python.exe %(RelativeDir)..\helpers\InstantiationGenerator.py "%(FullPath)" %(RelativeDir)%(Filename).3.cc 3 - python.exe %(RelativeDir)..\helpers\InstantiationGenerator.py "%(FullPath)" %(RelativeDir)%(Filename).2.cc 2 - - Building 2 and 3 dim instantiation for %(Filename) - %(RelativeDir)%(Filename).2.cc;%(RelativeDir)%(Filename).3.cc;%(Outputs) - - - Document - - - Document - - - Document - - - Document - - - Document - - - Document - - - Document - - - Document - - - Document - - - Document - - - Document - - - Document - - - Document - - - Document - - - Document - - - Document - - - Document - - - Document - - - Document - - - Document - - - Document - - - Document - - - Document - - - Document - - - Document - - - Document - - - - - - - - - - - - - - - - - - - - diff --git a/build/spheral_utilities/spheral_utilities.vcxproj.filters b/build/spheral_utilities/spheral_utilities.vcxproj.filters deleted file mode 100644 index b1536a02c..000000000 --- a/build/spheral_utilities/spheral_utilities.vcxproj.filters +++ /dev/null @@ -1,361 +0,0 @@ - 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- - Header Files\Utilities - - - Header Files\Utilities - - - Header Files\Utilities - - - Header Files\Utilities - - - Header Files\Utilities - - - Header Files\Utilities - - - Header Files\Utilities - - - Header Files\Utilities - - - Header Files\Utilities - - - Header Files\Utilities - - - Header Files\Utilities - - - Header Files\Utilities - - - Header Files\Utilities - - - Header Files\Utilities - - - Header Files\Utilities - - - Header Files\Utilities - - - Header Files\Utilities - - - Header Files\Utilities - - - Header Files\Utilities - - - Header Files\Utilities - - - - - Inst Files - - - Inst Files - - - Inst Files - - - Inst Files - - - Inst Files - - - Inst Files - - - Inst Files - - - - - Header Files\Utilities - - - Header Files\Utilities - - - Header Files\Utilities - - - Header Files\Utilities - - - Header Files\Utilities - - - Header Files\Utilities - - - Header Files\Utilities - - - Header Files\Utilities - - - Header Files\Utilities - - - Header Files\Utilities - - - Header Files\Utilities - - - Header Files\Utilities - - - \ No newline at end of file diff --git a/cmake/InstallTPLs.cmake b/cmake/InstallTPLs.cmake index 7c17fcd64..ee5317486 100644 --- a/cmake/InstallTPLs.cmake +++ b/cmake/InstallTPLs.cmake @@ -10,6 +10,7 @@ set(TPL_SPHERAL_CMAKE_DIR ${SPHERAL_ROOT_DIR}/cmake/tpl) # Initialize TPL options include(${SPHERAL_ROOT_DIR}/cmake/spheral/SpheralHandleTPL.cmake) +include(${SPHERAL_ROOT_DIR}/cmake/spheral/SpheralHandleExt.cmake) #----------------------------------------------------------------------------------- # Submodules @@ -74,6 +75,9 @@ list(APPEND SPHERAL_BLT_DEPENDS axom ) # from using object libraries with newer version of axom foreach(_comp ${AXOM_COMPONENTS_ENABLED}) get_target_property(axom_deps axom::${_comp} INTERFACE_LINK_LIBRARIES) + # strip cuda out so we have control over when cuda is enabled + list(REMOVE_DUPLICATES axom_deps) + list(REMOVE_ITEM axom_deps cuda) blt_convert_to_system_includes(TARGET ${axom_deps}) list(APPEND SPHERAL_BLT_DEPENDS ${axom_deps}) endforeach() diff --git a/cmake/spheral/SpheralHandleExt.cmake b/cmake/spheral/SpheralHandleExt.cmake new file mode 100644 index 000000000..2e33773cb --- /dev/null +++ b/cmake/spheral/SpheralHandleExt.cmake @@ -0,0 +1,30 @@ + +#---------------------------------------------------------------------------------------- +# Spheral_Handle_Ext +#---------------------------------------------------------------------------------------- + +# ---------------------- +# INPUT VARIABLES +# ---------------------- +# : REQUIRED : name of target TPL +# APPLE : REQUIRED : flag for Mac OSX + +# ---------------------- +# OUTPUT VARIABLES +# ---------------------- +# _libs : list of library names with modified extension +#---------------------------------------------------------------------------------------- + +function(Spheral_Handle_Ext lib_name APPLE) + + if(APPLE) + set(SHARED_EXT "dylib") + else() + set(SHARED_EXT "so") + endif() + + if(ENABLE_STATIC_TPL) + string(REPLACE ".${SHARED_EXT}" ".a;" ${lib_name}_libs ${${lib_name}_libs}) + endif() + +endfunction() diff --git a/cmake/tpl/polytope.cmake b/cmake/tpl/polytope.cmake index d1ccd3418..faa3562ff 100644 --- a/cmake/tpl/polytope.cmake +++ b/cmake/tpl/polytope.cmake @@ -1 +1,6 @@ set(${lib_name}_libs libpolytope.a) + +if(APPLE) + set(${lib_name}_libs libpolytope.dylib) +endif() +Spheral_Handle_Ext(${lib_name} APPLE) diff --git a/cmake/tpl/silo.cmake b/cmake/tpl/silo.cmake index f259177ab..95db76b5b 100644 --- a/cmake/tpl/silo.cmake +++ b/cmake/tpl/silo.cmake @@ -1 +1,6 @@ set(${lib_name}_libs libsiloh5.a) + +if(APPLE) + set(${lib_name}_libs libsiloh5.dylib) +endif() +Spheral_Handle_Ext(${lib_name} APPLE) diff --git a/src/Boundary/ReflectingBoundary.hh b/src/Boundary/ReflectingBoundary.hh index c85ec770f..a96dcbdc9 100644 --- a/src/Boundary/ReflectingBoundary.hh +++ b/src/Boundary/ReflectingBoundary.hh @@ -11,7 +11,6 @@ #include "Boundary/Boundary.hh" #include "Boundary/PlanarBoundary.hh" #include "RK/RKCorrectionParams.hh" -#include "boost/unordered_map.hpp" #include "Eigen/Sparse" @@ -99,7 +98,7 @@ public: private: //--------------------------- Private Interface ---------------------------// Tensor mReflectOperator; - boost::unordered_map> mrkReflectOperators; + std::unordered_map> mrkReflectOperators; }; } diff --git a/src/Damage/computeFragmentField.cc b/src/Damage/computeFragmentField.cc index 1f7f15856..134296d1c 100644 --- a/src/Damage/computeFragmentField.cc +++ b/src/Damage/computeFragmentField.cc @@ -81,6 +81,7 @@ computeFragmentField(const NodeList& nodes, const double linkRadius, const Field& density, const Field& damage, + const Field& mask, const double densityThreshold, const double damageThreshold, const bool assignDustToFragments) { @@ -92,6 +93,7 @@ computeFragmentField(const NodeList& nodes, REQUIRE(nodes.numGhostNodes() == 0); REQUIRE(density.nodeListPtr() == &nodes); REQUIRE(damage.nodeListPtr() == &nodes); + const auto haveMask = mask.numInternalElements() == nodes.numInternalNodes(); #ifdef USE_MPI // Get the rank and total number of processors. @@ -137,7 +139,8 @@ computeFragmentField(const NodeList& nodes, // Simultaneously remove them from the set of globalNodesRemaining. int numDustNodes = 0; for (auto i = 0u; i != nodes.numInternalNodes(); ++i) { - if (damage(i).Trace() > damageThreshold || density(i) < densityThreshold) { + int maski = haveMask ? mask(i) : -1; + if (damage(i).Trace() > damageThreshold || density(i) < densityThreshold || maski > 0) { result(i) = maxGlobalID + 1; ++numDustNodes; vector::iterator removeItr = find(globalNodesRemaining.begin(), diff --git a/src/Damage/computeFragmentField.hh b/src/Damage/computeFragmentField.hh index b0645d626..55951cd3d 100644 --- a/src/Damage/computeFragmentField.hh +++ b/src/Damage/computeFragmentField.hh @@ -16,6 +16,7 @@ computeFragmentField(const NodeList& nodeList, const double linkRadius, const Field& density, const Field& damage, + const Field& mask, const double densityThreshold, const double damageThreshold, const bool assignDustToFragments); diff --git a/src/Damage/computeFragmentFieldInst.cc.py b/src/Damage/computeFragmentFieldInst.cc.py index 4d7f79876..b6fe2f80a 100644 --- a/src/Damage/computeFragmentFieldInst.cc.py +++ b/src/Damage/computeFragmentFieldInst.cc.py @@ -5,6 +5,6 @@ #include "Damage/computeFragmentField.cc" namespace Spheral { - template Field, int> computeFragmentField(const NodeList >&, const double, const Field, Dim< %(ndim)s >::Scalar>&, const Field, Dim< %(ndim)s >::SymTensor>&, const double, const double, const bool); + template Field, int> computeFragmentField(const NodeList >&, const double, const Field, Dim< %(ndim)s >::Scalar>&, const Field, Dim< %(ndim)s >::SymTensor>&, const Field, int>&, const double, const double, const bool); } """ diff --git a/src/Damage/identifyFragments.py b/src/Damage/identifyFragments.py index 1acb9b349..7f46127f6 100644 --- a/src/Damage/identifyFragments.py +++ b/src/Damage/identifyFragments.py @@ -57,7 +57,8 @@ def identifyFragments(nodeList, # The C++ method does the heavy lifting. # Compute the fragments on the undamaged NodeList. - result = computeFragMethod(nodeList, linkRadius, density, damageField, densityThreshold, damageThreshold, assignDustToFragments) + mask = nodeList.mask(); + result = computeFragMethod(nodeList, linkRadius, density, damageField, mask, densityThreshold, damageThreshold, assignDustToFragments) numFragments = mpi.allreduce(max(list(result.internalValues()) + [0]), mpi.MAX) numFragments += 1 diff --git a/src/KernelIntegrator/BilinearIndex.hh b/src/KernelIntegrator/BilinearIndex.hh index 8dbe8b7d9..f8118694a 100644 --- a/src/KernelIntegrator/BilinearIndex.hh +++ b/src/KernelIntegrator/BilinearIndex.hh @@ -8,7 +8,6 @@ #include #include -// #include #include "DataBase/DataBase.hh" #include "Field/FieldList.hh" @@ -30,7 +29,6 @@ public: // Typedefs for bilinear indexing typedef typename std::pair Pair; typedef typename std::unordered_map> MapPair; - // typedef typename std::unordered_map> MapPair; typedef typename std::vector VectorPair; typedef FieldList PairToFlat; typedef FieldList FlatToPair; @@ -38,7 +36,6 @@ public: // Typedefs for surface indexing typedef typename std::array ArrayDim; typedef typename std::unordered_map> MapNormal; - // typedef typename std::unordered_map> MapNormal; typedef typename std::vector NormalType; typedef FieldList NormalToFlat; typedef FieldList FlatToNormal; diff --git a/src/Mesh/LineMesh.cc b/src/Mesh/LineMesh.cc index 92f0555dc..46e2bc549 100644 --- a/src/Mesh/LineMesh.cc +++ b/src/Mesh/LineMesh.cc @@ -58,7 +58,6 @@ reconstructInternal(const vector >::Vector>& localGenerators, // Is there anything to do? if (allReduce(unsigned(localGenerators.size()), SPHERAL_OP_SUM) == 0) return; - // Pre-conditions. BEGIN_CONTRACT_SCOPE { diff --git a/src/Mesh/Mesh.cc b/src/Mesh/Mesh.cc index 17ef07fc9..f1a42ac19 100644 --- a/src/Mesh/Mesh.cc +++ b/src/Mesh/Mesh.cc @@ -3,11 +3,12 @@ // // Created by JMO, Tue Oct 12 23:07:22 PDT 2010 //----------------------------------------------------------------------------// -#include "boost/unordered_map.hpp" -#include "boost/functional/hash.hpp" +#include +#include +#include #include "boost/bimap.hpp" using namespace boost; -using ::boost::unordered_map; +using ::std::unordered_map; using std::min; using std::max; using std::abs; @@ -756,7 +757,7 @@ generateDomainInfo() { // Hash the node positions. We want these sorted by key as well // to make testing if a key is present fast. vector nodeHashes; - boost::unordered_map key2nodeID; + std::map key2nodeID; nodeHashes.reserve(numNodes()); for (unsigned i = 0; i != numNodes(); ++i) { nodeHashes.push_back(hashPosition(mNodePositions[i], xmin, xmax, boxInv)); @@ -855,7 +856,7 @@ generateDomainInfo() { // Determine which process owns each shared node. We use the convention that the process // with the lowest rank wins. - boost::unordered_map nodeOwner; + std::unordered_map nodeOwner; for (unsigned k = 0; k != mNeighborDomains.size(); ++k) { for (unsigned j = 0; j != mSharedNodes[k].size(); ++j) { CHECK(k < mSharedNodes.size() and j < mSharedNodes[k].size()); diff --git a/src/PYB11/Damage/Damage_PYB11.py b/src/PYB11/Damage/Damage_PYB11.py index 8c49e45c1..67c4d373d 100644 --- a/src/PYB11/Damage/Damage_PYB11.py +++ b/src/PYB11/Damage/Damage_PYB11.py @@ -101,6 +101,7 @@ def computeFragmentField(nodeList = "const NodeList<%(Dimension)s>&", linkRadius = "const double", density = "const Field<%(Dimension)s, double>&", damage = "const Field<%(Dimension)s, typename %(Dimension)s::SymTensor>&", + mask = "const Field<%(Dimension)s, int>&", densityThreshold = "const double", damageThreshold = "const double", assignDustToFragments = "const bool"): diff --git a/src/Physics/GenericHydro.cc b/src/Physics/GenericHydro.cc index d5bef07b3..9d4109f41 100644 --- a/src/Physics/GenericHydro.cc +++ b/src/Physics/GenericHydro.cc @@ -168,7 +168,7 @@ dt(const DataBase& dataBase, if (GeometryRegistrar::coords() == CoordinateType::Spherical) { Fdiv = +[](const Tensor& DvDxi, const Vector& posi, const Vector& veli) { return DvDxi[0] + 2.0*veli[0]*safeInv(posi[0]); }; } else if (GeometryRegistrar::coords() == CoordinateType::RZ) { - Fdiv = +[](const Tensor& DvDxi, const Vector& posi, const Vector& veli) { return DvDxi.Trace() + veli[0]*safeInv(posi[0]); }; + Fdiv = +[](const Tensor& DvDxi, const Vector& posi, const Vector& veli) { return DvDxi.Trace() + veli[1]*safeInv(posi[1]); }; } // Loop over every fluid node. diff --git a/src/RK/RKCorrections.hh b/src/RK/RKCorrections.hh index 200dca325..7342e2a3b 100644 --- a/src/RK/RKCorrections.hh +++ b/src/RK/RKCorrections.hh @@ -12,8 +12,8 @@ #include "Field/FieldList.hh" #include "Geometry/CellFaceFlag.hh" #include "Physics/Physics.hh" -#include "boost/unordered_map.hpp" +#include #include namespace Spheral { @@ -141,7 +141,7 @@ private: const RKVolumeType mVolumeType; const bool mNeedHessian; const bool mUpdateInFinalize; - boost::unordered_map> mWR; + std::unordered_map> mWR; // State FieldList mVolume; @@ -149,7 +149,7 @@ private: // Corrections FieldList mSurfaceArea; FieldList mNormal; - boost::unordered_map>> mCorrections; + std::unordered_map>> mCorrections; // Voronoi stuff FieldList mSurfacePoint; diff --git a/src/SPH/SolidSPHHydroBase.cc b/src/SPH/SolidSPHHydroBase.cc index 2295f311a..701aad84a 100644 --- a/src/SPH/SolidSPHHydroBase.cc +++ b/src/SPH/SolidSPHHydroBase.cc @@ -357,6 +357,7 @@ evaluateDerivatives(const typename Dimension::Scalar /*time*/, const auto mu = state.fields(SolidFieldNames::shearModulus, 0.0); const auto damage = state.fields(SolidFieldNames::tensorDamage, SymTensor::zero); const auto pTypes = state.fields(SolidFieldNames::particleTypes, int(0)); + const auto fragID = state.fields(SolidFieldNames::fragmentIDs, int(0)); CHECK(mass.size() == numNodeLists); CHECK(position.size() == numNodeLists); CHECK(velocity.size() == numNodeLists); @@ -370,6 +371,7 @@ evaluateDerivatives(const typename Dimension::Scalar /*time*/, CHECK(mu.size() == numNodeLists); CHECK(damage.size() == numNodeLists); CHECK(pTypes.size() == numNodeLists); + CHECK(fragID.size() == numNodeLists); // Derivative FieldLists. auto rhoSum = derivatives.fields(ReplaceState::prefix() + HydroFieldNames::massDensity, 0.0); @@ -479,6 +481,7 @@ evaluateDerivatives(const typename Dimension::Scalar /*time*/, const auto Hdeti = Hi.Determinant(); const auto safeOmegai = safeInv(omegai, tiny); const auto pTypei = pTypes(nodeListi, i); + const auto fragIDi = fragID(nodeListi, i); CHECK(mi > 0.0); CHECK(rhoi > 0.0); CHECK(Hdeti > 0.0); @@ -513,6 +516,7 @@ evaluateDerivatives(const typename Dimension::Scalar /*time*/, const auto Hdetj = Hj.Determinant(); const auto safeOmegaj = safeInv(omegaj, tiny); const auto pTypej = pTypes(nodeListj, j); + const auto fragIDj = fragID(nodeListj, j); CHECK(mj > 0.0); CHECK(rhoj > 0.0); CHECK(Hdetj > 0.0); @@ -539,6 +543,18 @@ evaluateDerivatives(const typename Dimension::Scalar /*time*/, // Flag if at least one particle is free (0). const auto freeParticle = (pTypei == 0 or pTypej == 0); + // Flag to turn off forces between different fragments, + // only if the two particles are moving away from each other. + auto fragdir = true; + if (fragIDi != fragIDj) { + const auto rdiff = ri-rj; + const auto vdiff = vi-vj; + const auto vdot = vdiff.dot(rdiff); + if (vdot > 0.0) { + fragdir = false; + } + } + // Determine how we're applying damage. const auto fDij = pairs[kk].f_couple; @@ -637,7 +653,7 @@ evaluateDerivatives(const typename Dimension::Scalar /*time*/, sigmarhoi = safeOmegai*sigmai/(rhoi*rhoi); sigmarhoj = safeOmegaj*sigmaj/(rhoj*rhoj); const auto deltaDvDt = sigmarhoi*gradWi + sigmarhoj*gradWj - Qacci - Qaccj; - if (freeParticle) { + if (freeParticle && fragdir) { DvDti += mj*deltaDvDt; DvDtj -= mi*deltaDvDt; } diff --git a/src/Strength/SolidFieldNames.cc b/src/Strength/SolidFieldNames.cc index 6920134b9..a630ae7e7 100644 --- a/src/Strength/SolidFieldNames.cc +++ b/src/Strength/SolidFieldNames.cc @@ -36,3 +36,4 @@ const std::string Spheral::SolidFieldNames::fDSjutzi = "f deviatoric stress fact const std::string Spheral::SolidFieldNames::fragmentIDs = "fragment index"; const std::string Spheral::SolidFieldNames::particleTypes = "particle type"; const std::string Spheral::SolidFieldNames::meltSpecificEnergy = "melt specific energy"; +const std::string Spheral::SolidFieldNames::mask = "mask"; diff --git a/src/Strength/SolidFieldNames.hh b/src/Strength/SolidFieldNames.hh index 47066d7d7..b40e40177 100644 --- a/src/Strength/SolidFieldNames.hh +++ b/src/Strength/SolidFieldNames.hh @@ -41,6 +41,7 @@ struct SolidFieldNames { static const std::string fragmentIDs; static const std::string particleTypes; static const std::string meltSpecificEnergy; + static const std::string mask; }; } diff --git a/src/Utilities/Tree.hh b/src/Utilities/Tree.hh index 331e81a52..5940490e8 100644 --- a/src/Utilities/Tree.hh +++ b/src/Utilities/Tree.hh @@ -15,7 +15,7 @@ #include #include -#include "boost/unordered_map.hpp" +#include #include "NullCellValue.hh" #include "UniqueNodeLeaf.hh" @@ -88,7 +88,7 @@ public: //--------------------------- Private Interface ----------------------------// // Define the types we use to build the tree. - typedef boost::unordered_map TreeLevel; + typedef std::unordered_map TreeLevel; typedef std::vector Tree; // Private data. diff --git a/src/Utilities/iterateIdealH.cc b/src/Utilities/iterateIdealH.cc index 612ca3b82..308118349 100644 --- a/src/Utilities/iterateIdealH.cc +++ b/src/Utilities/iterateIdealH.cc @@ -278,7 +278,7 @@ iterateIdealH(DataBase& dataBase, maxDeltaH = allReduce(maxDeltaH, SPHERAL_OP_MAX); // Output the statitics. - if (Process::getRank() == 0) + if (Process::getRank() == 0 && maxIterations > 1) cerr << "iterateIdealH: (iteration, deltaH) = (" << itr << ", " << maxDeltaH << ")" @@ -347,7 +347,7 @@ iterateIdealH(DataBase& dataBase, // Report the final timing. const auto t1 = clock(); - if (Process::getRank() == 0) + if (Process::getRank() == 0 && maxIterations > 1) cerr << "iterateIdealH: required a total of " << (t1 - t0)/CLOCKS_PER_SEC << " seconds."