sidredatacollection.cpp

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// Copyright (c) 2010, Lawrence Livermore National Security, LLC. Produced at
// the Lawrence Livermore National Laboratory. LLNL-CODE-443211. All Rights
// reserved. See file COPYRIGHT for details.
//
// This file is part of the MFEM library. For more information and source code
// availability see http://mfem.org.
//
// MFEM is free software; you can redistribute it and/or modify it under the
// terms of the GNU Lesser General Public License (as published by the Free
// Software Foundation) version 2.1 dated February 1999.


#include "../config/config.hpp"

#ifdef MFEM_USE_SIDRE

#include "fem.hpp"

#ifdef MFEM_USE_MPI
#include <sidre/IOManager.hpp>
#endif

#include <string>
#include <iomanip>      // for setw, setfill
#include <cstdio>       // for snprintf()

namespace sidre = axom::sidre;

namespace mfem
{

// Constructor that will automatically create the sidre data store and necessary
// data groups for domain and global data.
SidreDataCollection::SidreDataCollection(const std::string& collection_name,
                                         Mesh * the_mesh, bool own_mesh_data)
   : mfem::DataCollection(collection_name, the_mesh),
     m_owns_datastore(true),
     m_owns_mesh_data(own_mesh_data),
     m_meshNodesGFName("mesh_nodes")
{
   m_datastore_ptr = new sidre::DataStore();

   sidre::Group * global_grp =
      m_datastore_ptr->getRoot()->createGroup(collection_name + "_global");
   sidre::Group * domain_grp =
      m_datastore_ptr->getRoot()->createGroup(collection_name);

   m_bp_grp = domain_grp->createGroup("blueprint");
   // Currently only rank 0 adds anything to bp_index.
   m_bp_index_grp = global_grp->createGroup("blueprint_index/" + name);

   m_named_bufs_grp = domain_grp->createGroup("named_buffers");

   if (the_mesh)
   {
      SetMesh(the_mesh);
   }
#ifdef MFEM_USE_MPI
   else
   {
      m_comm = MPI_COMM_NULL;
   }
#endif
}

// Second constructor that allows external code to specify data groups to place
// domain and global data in.

// TODO - Conduit will have the capability to generate a blueprint index group
// in the future.  When this is available, all the blueprint index code can be
// removed from the data collection class.
SidreDataCollection::SidreDataCollection(const std::string& collection_name,
                                         axom::sidre::Group* bp_index_grp,
                                         axom::sidre::Group* domain_grp,
                                         bool own_mesh_data)
   : mfem::DataCollection(collection_name),
     m_owns_datastore(false),
     m_owns_mesh_data(own_mesh_data),
     m_meshNodesGFName("mesh_nodes"),
     m_datastore_ptr(NULL),
     m_bp_index_grp(bp_index_grp)
{
   m_bp_grp = domain_grp->createGroup("blueprint");

   m_named_bufs_grp = domain_grp->createGroup("named_buffers");

#ifdef MFEM_USE_MPI
   m_comm = MPI_COMM_NULL;
#endif
}

SidreDataCollection::~SidreDataCollection()
{
   attr_map.DeleteData(true);
   if (m_owns_datastore)
   {
      delete m_datastore_ptr;
   }
}

#ifdef MFEM_USE_MPI
void SidreDataCollection::SetComm(MPI_Comm comm)
{
   m_comm = comm;
   serial = false;
   appendRankToFileName = true;
   MPI_Comm_rank(m_comm, &myid);
   MPI_Comm_size(m_comm, &num_procs);
}
#endif

// protected method
sidre::Group *SidreDataCollection::named_buffers_grp() const
{
   MFEM_ASSERT(m_named_bufs_grp != NULL,
               "No group 'named_buffers' in data collection.  Verify that"
               " SetMesh was called to set the mesh in the data collection.");
   return m_named_bufs_grp;
}

// protected method
axom::sidre::View *
SidreDataCollection::alloc_view(axom::sidre::Group *grp,
                                const std::string &view_name)
{
   MFEM_ASSERT(grp, "Group pointer is NULL");
   sidre::View *v = NULL;

   if (! grp->hasView(view_name) )
   {
      v = grp->createView(view_name);
      MFEM_ASSERT(v, "error allocating View " << view_name
                  << " in group " << grp->getPathName());
   }
   else
   {
      v = grp->getView(view_name);
   }

   return v;
}

// protected method
axom::sidre::View *
SidreDataCollection::alloc_view(axom::sidre::Group *grp,
                                const std::string &view_name,
                                const axom::sidre::DataType &dtype)
{
   MFEM_ASSERT(grp, "Group pointer is NULL");
   sidre::View *v = NULL;

   if (! grp->hasView(view_name))
   {
      v = grp->createView(view_name, dtype);
      MFEM_ASSERT(v, "error allocating View " << view_name
                  << " in group " << grp->getPathName());
   }
   else
   {
      v = grp->getView(view_name);
      MFEM_ASSERT(v->getSchema().dtype().equals(dtype), "");
   }
   return v;
}

// protected method
axom::sidre::Group *
SidreDataCollection::alloc_group(axom::sidre::Group *grp,
                                 const std::string &group_name)
{
   MFEM_ASSERT(grp, "Group pointer is NULL");
   sidre::Group *g = NULL;

   if (! grp->hasGroup(group_name) )
   {
      g = grp->createGroup(group_name);
      MFEM_ASSERT(g, "error allocating Group " << group_name
                  << " in group " << grp->getPathName());
   }
   else
   {
      g = grp->getGroup(group_name);
   }
   return g;
}

// protected method
std::string
SidreDataCollection::get_file_path(const std::string &filename) const
{
   std::stringstream fNameSstr;

   // Note: If non-empty, prefix_path has a separator ('/') at the end
   fNameSstr << prefix_path << filename;

   if (GetCycle() >= 0)
   {
      fNameSstr << "_" << std::setfill('0') << std::setw(pad_digits_cycle)
                << GetCycle();
   }

   return fNameSstr.str();
}

axom::sidre::View *
SidreDataCollection::AllocNamedBuffer(const std::string& buffer_name,
                                      axom::sidre::SidreLength sz,
                                      axom::sidre::TypeID type)
{
   sz = std::max(sz, sidre::SidreLength(0));
   sidre::Group *f = named_buffers_grp();
   sidre::View  *v = NULL;

   if (! f->hasView(buffer_name) )
   {
      // create a buffer view
      v = f->createViewAndAllocate(buffer_name, type, sz);
   }
   else
   {
      v = f->getView(buffer_name);
      MFEM_ASSERT(v->getTypeID() == type, "type does not match existing type");

      // Here v is the view holding the buffer in the named_buffers group, so
      // its size is the full size of the buffer.

      // check if we need to resize.
      if (!v->isApplied() || v->getNumElements() < sz)
      {
         // resize, even if the buffer has more than 1 View.
         // v->reallocate(sz); // this will not work for more than 1 view.
         sidre::DataType dtype(v->getSchema().dtype());
         dtype.set_number_of_elements(sz);
         f->destroyViewAndData(buffer_name);
         v = f->createViewAndAllocate(buffer_name, dtype);
      }
   }
   MFEM_ASSERT(v && v->isApplied(), "allocation failed");
   return v;
}

// private method
void SidreDataCollection::createMeshBlueprintStubs(bool hasBP)
{
   if (!hasBP)
   {
      m_bp_grp->createGroup("state");
      m_bp_grp->createGroup("coordsets");
      m_bp_grp->createGroup("topologies");
      m_bp_grp->createGroup("fields");
   }

   // If rank is 0, set up blueprint index state group.
   if (myid == 0)
   {
      m_bp_index_grp->createGroup("state");
      m_bp_index_grp->createGroup("coordsets");
      m_bp_index_grp->createGroup("topologies");
      m_bp_index_grp->createGroup("fields");
   }
}

// private method
void SidreDataCollection::createMeshBlueprintState(bool hasBP)
{
   if (!hasBP)
   {
      // Set up blueprint state group.
      m_bp_grp->createViewScalar("state/cycle", 0);
      m_bp_grp->createViewScalar("state/time", 0.);
      m_bp_grp->createViewScalar("state/domain", myid);
      m_bp_grp->createViewScalar("state/time_step", 0.);
   }

   // If rank is 0, set up blueprint index state group.
   if (myid == 0)
   {
      m_bp_index_grp->createViewScalar("state/cycle", 0);
      m_bp_index_grp->createViewScalar("state/time", 0.);
      m_bp_index_grp->createViewScalar("state/number_of_domains", num_procs);
   }
}

// private method
void SidreDataCollection::createMeshBlueprintCoordset(bool hasBP)
{
   int dim = mesh->SpaceDimension();
   MFEM_ASSERT(dim >= 1 && dim <= 3, "invalid mesh dimension");

   // Assuming mfem::Vertex has the layout of a double array.
   const int NUM_COORDS = sizeof(mfem::Vertex) / sizeof(double);

   const int num_vertices = mesh->GetNV();
   const int coordset_len = NUM_COORDS * num_vertices;

   // Add blueprint if not present
   if ( !hasBP )
   {
      m_bp_grp->createViewString("coordsets/coords/type", "explicit");

      sidre::DataType dtype =
         sidre::DataType::c_double(num_vertices);
      const size_t stride = dtype.stride();
      dtype.set_stride(stride*NUM_COORDS);

      // Set up views for x, y, z values
      sidre::View *vx, *vy = NULL, *vz = NULL;
      vx = m_bp_grp->createView("coordsets/coords/values/x", dtype);

      if (dim >= 2)
      {
         dtype.set_offset(dtype.offset() + stride);
         vy = m_bp_grp->createView("coordsets/coords/values/y", dtype);
      }
      if (dim >= 3)
      {
         dtype.set_offset(dtype.offset() + stride);
         vz = m_bp_grp->createView("coordsets/coords/values/z", dtype);
      }

      if (m_owns_mesh_data)
      {
         // Allocate buffer for coord values.
         sidre::Buffer* coordbuf =
            AllocNamedBuffer("vertex_coords", coordset_len)->getBuffer();

         vx->attachBuffer(coordbuf);
         if (dim >= 2) { vy->attachBuffer(coordbuf); }
         if (dim >= 3) { vz->attachBuffer(coordbuf); }
      }
      else
      {
         double *coordbuf = mesh->GetVertex(0);

         vx->setExternalDataPtr(coordbuf);
         if (dim >= 2) { vy->setExternalDataPtr(coordbuf); }
         if (dim >= 3) { vz->setExternalDataPtr(coordbuf); }
      }

   }

   // If rank 0, set up blueprint index for coordinate set.
   if (myid == 0)
   {
      m_bp_index_grp->createViewString(
         "coordsets/coords/path", m_bp_grp->getPathName() + "/coordsets/coords");

      m_bp_index_grp->getGroup("coordsets/coords")->copyView(
         m_bp_grp->getView("coordsets/coords/type") );

      m_bp_index_grp->createViewString(
         "coordsets/coords/coord_system/type", "cartesian");

      // These are empty views, their existence in the group tree is used to
      // define the number of dims
      m_bp_index_grp->createView("coordsets/coords/coord_system/axes/x");

      if (dim >= 2)
      {
         m_bp_index_grp->createView("coordsets/coords/coord_system/axes/y");
      }

      if (dim == 3)
      {
         m_bp_index_grp->createView("coordsets/coords/coord_system/axes/z");
      }
   }

   if (m_owns_mesh_data)
   {
      double *coord_values = GetNamedBuffer("vertex_coords")->getData();
      // Change ownership of the mesh vertex data to sidre
      mesh->ChangeVertexDataOwnership(coord_values, coordset_len, hasBP);
   }
}

// private method
void SidreDataCollection::
createMeshBlueprintTopologies(bool hasBP, const std::string& mesh_name)
{
   const bool isBdry = (mesh_name == "boundary");

   const int num_elements = !isBdry
                            ? mesh->GetNE()
                            : mesh->GetNBE();

   const std::string mesh_topo_str = "topologies/" + mesh_name;
   const std::string mesh_attr_str = mesh_name + "_material_attribute";

   int element_size = 0;
   int num_indices = 0;
   int geom = 0;
   std::string eltTypeStr = "point";

   if (num_elements > 0)
   {
      mfem::Element *elem = !isBdry
                            ? mesh->GetElement(0)
                            : mesh->GetBdrElement(0);
      element_size = elem->GetNVertices();

      num_indices = num_elements * element_size;

      // Find the element shape
      // Note: Assumes homogeneous elements, so only check the first element
      geom = elem->GetGeometryType();
      eltTypeStr = getElementName(elem->GetType());
   }

   // Create the blueprint "topology" group, if not present
   if ( !hasBP )
   {
      sidre::Group* topology_grp = m_bp_grp->createGroup(mesh_topo_str);

      topology_grp->createViewString("type", "unstructured");
      topology_grp->createViewString("elements/shape", eltTypeStr);
      topology_grp->createViewAndAllocate(
         "elements/connectivity", sidre::INT_ID, num_indices);
      topology_grp->createViewString("coordset", "coords");

      // If the mesh has nodes, set the name of the GridFunction holding the
      // mesh nodes in the blueprint group.
      if (!isBdry && mesh->GetNodes() != NULL)
      {
         topology_grp->createViewString("grid_function",m_meshNodesGFName);
      }
   }

   // Add the mesh's attributes as an attribute field
   RegisterAttributeField(mesh_attr_str, isBdry);

   // Change ownership or copy the element arrays into Sidre
   if (num_elements > 0)
   {
      sidre::View* conn_view =
         m_bp_grp->getGroup(mesh_topo_str)->getView("elements/connectivity");

      // The SidreDataCollection always owns these arrays:
      Array<int> conn_array(conn_view->getData<int*>(), num_indices);
      Array<int>* attr_array = attr_map.Get(mesh_attr_str);
      if (!isBdry)
      {
         mesh->GetElementData(geom, conn_array, *attr_array);
      }
      else
      {
         mesh->GetBdrElementData(geom, conn_array, *attr_array);
      }
      MFEM_ASSERT(!conn_array.OwnsData(), "");
      MFEM_ASSERT(!attr_array->OwnsData(), "");
   }

   // If rank 0, set up blueprint index for topologies group
   if (myid == 0)
   {
      const std::string m_bp_grp_path = m_bp_grp->getPathName();

      if (isBdry)
      {
         // "Shallow" copy the m_bp_grp view into the m_bp_index_grp sub-group.
         // Note that the "topologies/mesh" sub-group has to exist, i.e. this
         // method should be called first with mesh_name = "mesh".
         m_bp_index_grp->getGroup("topologies/mesh")
         ->copyView( m_bp_grp->getView("topologies/mesh/boundary_topology") );
      }

      sidre::Group *bp_index_topo_grp =
         m_bp_index_grp->createGroup(mesh_topo_str);
      sidre::Group *topology_grp = m_bp_grp->getGroup(mesh_topo_str);

      bp_index_topo_grp->createViewString(
         "path", m_bp_grp_path + "/" + mesh_topo_str);
      bp_index_topo_grp->copyView( topology_grp->getView("type") );
      bp_index_topo_grp->copyView( topology_grp->getView("coordset") );

      // If the mesh has nodes, set the name of the GridFunction holding the
      // mesh nodes in the blueprint_index group.
      if (!isBdry && mesh->GetNodes() != NULL)
      {
         bp_index_topo_grp->copyView(topology_grp->getView("grid_function"));
      }
   }
}

// private method
#ifdef MFEM_USE_MPI
void SidreDataCollection::createMeshBlueprintAdjacencies(bool hasBP)
{
   ParMesh *pmesh = dynamic_cast<ParMesh*>(mesh);

   const int GRP_SZ = 25;
   char group_str[GRP_SZ];

   // TODO(JRC): Separate this out into group hierarchy setup and data allocation
   // stages like all of the other "createMeshBlueprint*" functions.
   MFEM_VERIFY(hasBP == false, "The case hasBP == true is not supported yet!");

   sidre::Group* adjset_grp = NULL;
   if (pmesh->GetNGroups() > 1)
   {
      adjset_grp = m_bp_grp->createGroup("adjsets/mesh");
      adjset_grp->createViewString("association", "vertex");
      adjset_grp->createViewString("topology", "mesh");

      if (myid == 0) { m_bp_index_grp->createGroup("adjsets"); }
   }

   for (int gi = 1; gi < pmesh->GetNGroups(); ++gi)
   {
      int num_gneighbors = pmesh->gtopo.GetGroupSize(gi);
      int num_gvertices = pmesh->GroupNVertices(gi);

      // Skip creation of empty groups
      if (num_gneighbors > 1 && num_gvertices > 0)
      {
         std::snprintf(group_str, GRP_SZ, "groups/g%d_%d",
                       pmesh->gtopo.GetGroupMasterRank(gi),
                       pmesh->gtopo.GetGroupMasterGroup(gi));
         sidre::Group* group_grp = adjset_grp->createGroup(group_str);

         sidre::View* gneighbors_view =
            group_grp->createViewAndAllocate(
               "neighbors", sidre::INT_ID, num_gneighbors - 1);
         int* gneighbors_data = gneighbors_view->getData<int*>();

         // skip local domain when adding Blueprint neighbors
         const int* gneighbors = pmesh->gtopo.GetGroup(gi);
         for (int ni = 0, noff = 0; ni < num_gneighbors; ++ni)
         {
            if ( gneighbors[ni] == 0 )
            {
               noff++;
            }
            else
            {
               gneighbors_data[ni - noff] =
                  pmesh->gtopo.GetNeighborRank(gneighbors[ni]);
            }
         }

         sidre::View* gvertices_view =
            group_grp->createViewAndAllocate(
               "values", sidre::INT_ID, num_gvertices);
         int* gvertices_data = gvertices_view->getData<int*>();

         for (int vi = 0; vi < num_gvertices; ++vi)
         {
            gvertices_data[vi] = pmesh->GroupVertex(gi, vi);
         }
      }
   }
}
#endif

// private method
void SidreDataCollection::verifyMeshBlueprint()
{
   // Conduit will have a verify mesh blueprint capability in the future.
   // Add call to that when it's available to check actual contents in sidre.
}


bool SidreDataCollection::HasBoundaryMesh() const
{
   // check if this rank has any boundary elements
   int hasBndElts = mesh->GetNBE() > 0 ? 1 : 0;

#ifdef MFEM_USE_MPI
   // check if any rank has boundary elements
   ParMesh *pmesh = dynamic_cast<ParMesh*>(mesh);
   if (pmesh)
   {
      int hasBndElts_g;
      MPI_Allreduce(&hasBndElts, &hasBndElts_g, 1,
                    MPI_INT, MPI_MAX,pmesh->GetComm());

      hasBndElts = hasBndElts_g;
   }
#endif

   return hasBndElts > 0? true : false;
}

void SidreDataCollection::SetMesh(Mesh *new_mesh)
{
   DataCollection::SetMesh(new_mesh);

   // hasBP is used to indicate if the data currently in the blueprint should be
   // used to replace the data in the mesh.
   bool hasBP = m_bp_grp->getNumViews() > 0 || m_bp_grp->getNumGroups() > 0;
   bool has_bnd_elts = HasBoundaryMesh();

   createMeshBlueprintStubs(hasBP);
   createMeshBlueprintState(hasBP);
   createMeshBlueprintCoordset(hasBP);

   GridFunction *nodes = new_mesh->GetNodes();

   // register the "mesh" topology in the blueprint.
   createMeshBlueprintTopologies(hasBP, "mesh");

   if (has_bnd_elts)
   {
      // Set the "boundary_topology" of "mesh" to "boundary".
      m_bp_grp->createViewString("topologies/mesh/boundary_topology", "boundary");

      // register the "boundary" topology in the blueprint.
      createMeshBlueprintTopologies(hasBP, "boundary");
   }

#ifdef MFEM_USE_MPI
   ParMesh *new_pmesh = dynamic_cast<ParMesh*>(new_mesh);
   m_comm = new_pmesh ? new_pmesh->GetComm() : MPI_COMM_NULL;
   if (new_pmesh)
   {
      createMeshBlueprintAdjacencies(hasBP);
   }
#endif

   if (nodes)
   {
      // See the comment at the definition of 'hasBP' above.
      if (hasBP)
      {
         // Get the bp mesh nodes name.
         sidre::View *v_bp_nodes_name =
            m_bp_grp->getView("topologies/mesh/grid_function");
         std::string bp_nodes_name(v_bp_nodes_name->getString());

         // Check that the names match, e.g. when loading the collection.
         MFEM_VERIFY(m_meshNodesGFName == bp_nodes_name,
                     "mismatch of requested and blueprint mesh nodes names");
         // Support renaming bp_nodes_name --> m_meshNodesGFName ?
      }

      if (m_owns_mesh_data)
      {
         // Make sure Sidre owns the data of the new_mesh's Nodes.
         if (!GetNamedBuffer(m_meshNodesGFName))
         {
            int sz = new_mesh->GetNodalFESpace()->GetVSize();
            double *gfData = AllocNamedBuffer(m_meshNodesGFName, sz)->getData();

            // See the comment at the definition of 'hasBP' above.
            if (!hasBP)
            {
               MFEM_ASSERT(nodes->Size() == sz, "");
               std::memcpy(gfData, nodes->GetData(), sizeof(double) * sz);
            }
         }
         // Since the named buffer for m_meshNodesGFName exists, the call to
         // RegisterField() below will replace the data of the nodes with the
         // data from the named buffer.
      }
      else
      {
         // Make sure Sidre does not have a named buffer for m_meshNodesGFName.
         MFEM_VERIFY(GetNamedBuffer(m_meshNodesGFName) == NULL, "");
      }

      RegisterField(m_meshNodesGFName, nodes);

      if (own_data)
      {
         // Avoid double delete calls (for the nodes gf) when (own_data == true)
         // and the new_mesh owns its Nodes --> take ownership from new_mesh.
         // When new_mesh does not own its Nodes and (own_data == true), we can
         // not take ownership --> verify that does not happen.
         MFEM_VERIFY(new_mesh->OwnsNodes(), "mesh does not own its nodes, "
                     "can not take ownership");
         new_mesh->SetNodesOwner(false);
      }
   }
}

#ifdef MFEM_USE_MPI
void SidreDataCollection::SetMesh(MPI_Comm comm, Mesh *new_mesh)
{
   // use SidreDataCollection's custom SetMesh, then set MPI info
   SetMesh(new_mesh);

   m_comm = comm;
   MPI_Comm_rank(comm, &myid);
   MPI_Comm_size(comm, &num_procs);
}
#endif

void SidreDataCollection::
SetGroupPointers(axom::sidre::Group *bp_index_grp,
                 axom::sidre::Group *domain_grp)
{
   MFEM_VERIFY(domain_grp->hasGroup("blueprint"),
               "Domain group does not contain a blueprint group.");

   m_bp_grp = domain_grp->getGroup("blueprint");
   m_bp_index_grp = bp_index_grp;
   m_named_bufs_grp = domain_grp->getGroup("named_buffers");
}

void SidreDataCollection::Load(const std::string& path,
                               const std::string& protocol)
{
   DataCollection::DeleteAll();
   // Reset DataStore?

#ifdef MFEM_USE_MPI
   if (m_comm != MPI_COMM_NULL)
   {
      axom::sidre::IOManager reader(m_comm);
      reader.read(m_bp_grp->getDataStore()->getRoot(), path);
   }
   else
#endif
   {
      m_bp_grp->load(path, protocol);
   }

   // If the data collection created the datastore, it knows the layout of where
   // the domain and global groups are, and can restore them after the Load().
   //
   // If the data collection did not create the datastore, the host code must
   // reset these pointers after the load operation and also reset the state
   // variables.
   if (m_owns_datastore)
   {
      SetGroupPointers(m_datastore_ptr->getRoot()->getGroup(name + "_global"),
                       m_datastore_ptr->getRoot()->getGroup(name));

      UpdateStateFromDS();
   }
}

void SidreDataCollection::LoadExternalData(const std::string& path)
{
#ifdef MFEM_USE_MPI
   if (m_comm != MPI_COMM_NULL)
   {
      axom::sidre::IOManager reader(m_comm);
      reader.loadExternalData(m_bp_grp->getDataStore()->getRoot(), path);
   }
   else
#endif
   {
      m_bp_grp->loadExternalData(path);
   }
}

void SidreDataCollection::UpdateStateFromDS()
{
   SetTime( m_bp_grp->getView("state/time")->getData<double>() );
   SetCycle( m_bp_grp->getView("state/cycle")->getData<int>() );
   SetTimeStep( m_bp_grp->getView("state/time_step")->getData<double>() );
}

void SidreDataCollection::UpdateStateToDS()
{
   m_bp_grp->getView("state/cycle")->setScalar(GetCycle());
   m_bp_grp->getView("state/time")->setScalar(GetTime());
   m_bp_grp->getView("state/time_step")->setScalar(GetTimeStep());

   if (myid == 0)
   {
      m_bp_index_grp->getView("state/cycle")->setScalar(GetCycle());
      m_bp_index_grp->getView("state/time")->setScalar(time);
   }
}

void SidreDataCollection::PrepareToSave()
{
   verifyMeshBlueprint();
   UpdateStateToDS();
}

void SidreDataCollection::Save()
{
   std::string filename = name;
   std::string protocol = "sidre_hdf5";

   Save(filename, protocol);
}

void SidreDataCollection::Save(const std::string& filename,
                               const std::string& protocol)
{
   PrepareToSave();

   create_directory(prefix_path, mesh, myid);

   std::string file_path = get_file_path(filename);

   sidre::Group * blueprint_indicies_grp = m_bp_index_grp->getParent();
#ifdef MFEM_USE_MPI
   if (m_comm != MPI_COMM_NULL)
   {
      axom::sidre::IOManager writer(m_comm);
      sidre::DataStore *datastore = m_bp_grp->getDataStore();
      writer.write(datastore->getRoot(), num_procs, file_path, protocol);
      if (myid == 0)
      {
         if (protocol == "sidre_hdf5")
         {
            writer.writeGroupToRootFile(blueprint_indicies_grp,
                                        file_path + ".root");
         }
         // Root file support only available in hdf5.
         else
         {
            writer.write(blueprint_indicies_grp, 1,
                         file_path + ".root", protocol);
         }
      }
   }
   else
#endif
   {
      // If serial, use sidre group writer.
      m_bp_grp->save(file_path, protocol);

      blueprint_indicies_grp
      ->save(file_path + ".root", protocol);
   }
}

// private method
void SidreDataCollection::
addScalarBasedGridFunction(const std::string &field_name, GridFunction *gf,
                           const std::string &buffer_name,
                           axom::sidre::SidreLength offset)
{
   sidre::Group* grp = m_bp_grp->getGroup("fields/" + field_name);
   MFEM_ASSERT(grp != NULL, "field " << field_name << " does not exist");

   const int numDofs = gf->FESpace()->GetVSize();

   if (gf->GetData() == NULL)
   {
      AllocNamedBuffer(buffer_name, offset + numDofs);
      // gf->data is set below.
   }

   /*
    *  Mesh blueprint for a scalar-based grid function is of the form
    *    /fields/field_name/basis
    *              -- string value is GridFunction's FEC::Name
    *    /fields/field_name/values
    *              -- array of size numDofs
    */

   // Make sure we have the View "values".
   sidre::View *vv = alloc_view(grp, "values");

   // Describe and apply the "values" View.
   // If the data store has buffer for field_name (e.g. AllocNamedBuffer was
   // called, or it was loaded from file), use that buffer.
   sidre::View *bv = named_buffers_grp()->getView(buffer_name);
   if (bv)
   {
      MFEM_ASSERT(bv->hasBuffer() && bv->isDescribed(), "");

      // named buffers always have offset 0
      MFEM_ASSERT(bv->getSchema().dtype().offset() == 0, "");
      MFEM_ASSERT(bv->getNumElements() >= offset + numDofs, "");

      if (vv->isEmpty())
      {
         vv->attachBuffer(bv->getBuffer())
         ->apply(sidre::DOUBLE_ID, numDofs, offset);
      }

      gf->NewDataAndSize(vv->getData(), numDofs);
   }
   else
   {
      // If we are not managing the grid function's data,
      // create a view with the external data
      vv->setExternalDataPtr(sidre::DOUBLE_ID, numDofs, gf->GetData());
   }
   MFEM_ASSERT((numDofs > 0 && vv->isApplied()) ||
               (numDofs == 0 && vv->isEmpty() && vv->isDescribed()),
               "invalid View state");
   MFEM_ASSERT(numDofs == 0 || vv->getData() == gf->GetData(),
               "View data is different from GridFunction data");
   MFEM_ASSERT(vv->getNumElements() == numDofs,
               "View size is different from GridFunction size");
}

// private method
void SidreDataCollection::
addVectorBasedGridFunction(const std::string& field_name, GridFunction *gf,
                           const std::string &buffer_name,
                           axom::sidre::SidreLength offset)
{
   sidre::Group* grp = m_bp_grp->getGroup("fields/" + field_name);
   MFEM_ASSERT(grp != NULL, "field " << field_name << " does not exist");

   const int FLD_SZ = 20;
   char fidxName[FLD_SZ];

   int vdim = gf->FESpace()->GetVDim();
   int ndof = gf->FESpace()->GetNDofs();
   Ordering::Type ordering = gf->FESpace()->GetOrdering();

   if (gf->GetData() == NULL)
   {
      AllocNamedBuffer(buffer_name, offset + vdim*ndof);
      // gf->data is set below.
   }

   /*
    *  Mesh blueprint for a vector-based grid function is of the form
    *    /fields/field_name/basis
    *              -- string value is GridFunction's FEC::Name
    *    /fields/field_name/values/x0
    *    /fields/field_name/values/x1
    *    ...
    *    /fields/field_name/values/xn
    *              -- each coordinate is an array of size ndof
    */

   // Get/create the Group "values".
   sidre::Group *vg = alloc_group(grp, "values");

   // Create the Views "x0", "x1", etc inside the "values" Group, vg.
   // If we have a named buffer for field_name, attach it to the Views;
   // otherwise set the Views to use gf->GetData() as external data.
   sidre::DataType dtype = sidre::DataType::c_double(ndof);
   const int entry_stride = (ordering == Ordering::byNODES ? 1 : vdim);
   const int vdim_stride  = (ordering == Ordering::byNODES ? ndof : 1);
   dtype.set_stride(dtype.stride()*entry_stride);

   sidre::View *bv = named_buffers_grp()->getView(buffer_name);
   if (bv)
   {
      MFEM_ASSERT(bv->hasBuffer() && bv->isDescribed(), "");

      // named buffers always have offset 0
      MFEM_ASSERT(bv->getSchema().dtype().offset() == 0, "");
      dtype.set_offset(dtype.element_bytes()*offset);

      for (int d = 0;  d < vdim; d++)
      {
         std::snprintf(fidxName, FLD_SZ, "x%d", d);
         sidre::View *xv = alloc_view(vg, fidxName, dtype);
         xv->attachBuffer(bv->getBuffer());
         dtype.set_offset(dtype.offset() + dtype.element_bytes()*vdim_stride);
      }

      gf->NewDataAndSize(bv->getData<double*>() + offset, vdim*ndof);
   }
   else
   {
      for (int d = 0;  d < vdim; d++)
      {
         std::snprintf(fidxName, FLD_SZ, "x%d", d);
         sidre::View *xv = alloc_view(vg, fidxName, dtype);
         xv->setExternalDataPtr(gf->GetData());
         dtype.set_offset(dtype.offset() + dtype.element_bytes()*vdim_stride);
      }
   }

#ifdef MFEM_DEBUG
   for (int d = 0;  d < vdim; d++)
   {
      std::snprintf(fidxName, FLD_SZ, "x%d", d);
      sidre::View *xv = vg->getView(fidxName);
      MFEM_ASSERT((ndof > 0 && xv->isApplied()) ||
                  (ndof == 0 && xv->isEmpty() && xv->isDescribed()),
                  "invalid View state");
      MFEM_ASSERT(ndof == 0 || xv->getData() == gf->GetData() + d*vdim_stride,
                  "View data is different from GridFunction data");
      MFEM_ASSERT(xv->getNumElements() == ndof,
                  "View size is different from GridFunction size");
   }
#endif
}

// private method
// Should only be called on mpi rank 0 ( or if serial problem ).
void SidreDataCollection::
RegisterFieldInBPIndex(const std::string& field_name, GridFunction *gf)
{
   sidre::Group *bp_field_grp = m_bp_grp->getGroup("fields/" + field_name);
   sidre::Group *bp_index_field_grp =
      m_bp_index_grp->createGroup("fields/" + field_name);

   bp_index_field_grp->createViewString( "path", bp_field_grp->getPathName() );
   bp_index_field_grp->copyView( bp_field_grp->getView("topology") );
   bp_index_field_grp->copyView( bp_field_grp->getView("basis") );

   // Note: The bp index requires GridFunction::VectorDim()
   //       since the GF might be scalar valued and have a vector basis
   //       (e.g. hdiv and hcurl spaces)
   const int number_of_components = gf->VectorDim();
   bp_index_field_grp->createViewScalar("number_of_components",
                                        number_of_components);
}

// private method
// Should only be called on mpi rank 0 ( or if serial problem ).
void SidreDataCollection::
DeregisterFieldInBPIndex(const std::string& field_name)
{
   sidre::Group * fields_grp = m_bp_index_grp->getGroup("fields");
   MFEM_VERIFY(fields_grp->hasGroup(field_name),
               "No field exists in blueprint index with name " << name);

   // Note: This will destroy all orphaned views or buffer classes under this
   // group also.  If sidre owns this field data, the memory will be deleted
   // unless it's referenced somewhere else in sidre.
   fields_grp->destroyGroup(field_name);
}

void SidreDataCollection::RegisterField(const std::string &field_name,
                                        GridFunction *gf,
                                        const std::string &buffer_name,
                                        axom::sidre::SidreLength offset)
{
   if ( field_name.empty() || buffer_name.empty() ||
        gf == NULL || gf->FESpace() == NULL )
   {
      return;
   }

   // Register field_name in the blueprint group.
   sidre::Group* f = m_bp_grp->getGroup("fields");

   if (f->hasGroup( field_name ))
   {
      // There are two possibilities:
      // 1. If HasField(field_name) is true - we are overwriting a field that
      //    was previously registered.
      // 2. Otherwise, the field was loaded from a file, or defined outside of
      //    the data collection.
      if (HasField(field_name))
      {
#ifdef MFEM_DEBUG
         // Warn about overwriting field.
         // Skip warning when re-registering the nodal grid function
         if (field_name != m_meshNodesGFName)
         {
            MFEM_WARNING("field with the name '" << field_name<< "' is already "
                         "registered, overwriting the old field");
         }
#endif
         DeregisterField(field_name);
      }
   }

   sidre::Group* grp = f->createGroup( field_name );

   // Set the "basis" string using the gf's finite element space, overwrite if
   // necessary.
   sidre::View *v = alloc_view(grp, "basis");
   v->setString(gf->FESpace()->FEColl()->Name());

   // Set the topology of the GridFunction.
   // This is always 'mesh' except for a special case with the boundary material
   // attributes field.
   v = alloc_view(grp, "topology")->setString("mesh");

   MFEM_ASSERT(gf->Size() == gf->FESpace()->GetVSize(),
               "GridFunction size does not match FiniteElementSpace size");

   // Set the data views of the grid function
   // e.g. the number of coefficients per DoF -- either scalar-valued or
   // vector-valued
   bool const isScalarValued = (gf->FESpace()->GetVDim() == 1);
   if (isScalarValued)
   {
      // Set the View "<m_bp_grp>/fields/<field_name>/values"
      addScalarBasedGridFunction(field_name, gf, buffer_name, offset);
   }
   else // vector valued
   {
      // Set the Group "<m_bp_grp>/fields/<field_name>/values"
      addVectorBasedGridFunction(field_name, gf, buffer_name, offset);
   }

   // Register field_name in the blueprint_index group.
   if (myid == 0)
   {
      RegisterFieldInBPIndex(field_name, gf);
   }

   // Register field_name + gf in field_map.
   DataCollection::RegisterField(field_name, gf);
}

void SidreDataCollection::RegisterAttributeField(const std::string& attr_name,
                                                 bool is_bdry)
{
   MFEM_ASSERT(
      mesh != NULL,
      "Need to set mesh before registering attributes in SidreDataCollection.");

   // Register attr_name in the blueprint group.
   sidre::Group* f = m_bp_grp->getGroup("fields");
   if (f->hasGroup( attr_name ))
   {
      bool isAttr = attr_map.Has(attr_name);
      bool isFld = field_map.Has(attr_name);

      if (isAttr)
      {
         MFEM_WARNING("field with the name '" << attr_name << "' is already "
                      " registered as an attribute, overwriting old values.");
         DeregisterAttributeField(attr_name);
      }
      else if (isFld)
      {
         MFEM_WARNING("field with the name '" << attr_name << "' is already "
                      " registered as a field, skipping register attribute.");
         return;
      }
   }

   // Generate sidre views and groups for this mesh attribute and allocate space
   addIntegerAttributeField(attr_name, is_bdry);

   if (myid == 0)
   {
      RegisterAttributeFieldInBPIndex(attr_name);
   }

   // Register new attribute array with attr_map
   sidre::View* a =
      m_bp_grp->getGroup("fields")->getGroup(attr_name)->getView("values");
   Array<int>* attr = new Array<int>(a->getData<int*>(), a->getNumElements());

   attr_map.Register(attr_name, attr, true);
}

void SidreDataCollection::RegisterAttributeFieldInBPIndex(
   const std::string& attr_name)
{
   const std::string m_bp_grp_path = m_bp_grp->getPathName();

   MFEM_ASSERT(m_bp_grp->getGroup("fields") != NULL,
               "Mesh blueprint does not have 'fields' group");
   MFEM_ASSERT(m_bp_index_grp->getGroup("fields") != NULL,
               "Mesh blueprint index does not have 'fields' group");

   // get the BP attr group
   sidre::Group* attr_grp =
      m_bp_grp->getGroup("fields")->getGroup(attr_name);

   // create blueprint index for this attribute
   sidre::Group *bp_index_attr_grp =
      m_bp_index_grp->getGroup("fields")->createGroup(attr_name);

   bp_index_attr_grp->createViewString("path", attr_grp->getPathName() );
   bp_index_attr_grp->copyView( attr_grp->getView("association") );
   bp_index_attr_grp->copyView( attr_grp->getView("topology") );
   bp_index_attr_grp->createViewScalar("number_of_components", 1);
}

void SidreDataCollection::DeregisterAttributeField(const std::string& attr_name)
{
   attr_map.Deregister(name, true);

   sidre::Group * attr_grp = m_bp_grp->getGroup("fields");
   MFEM_VERIFY(attr_grp->hasGroup(attr_name),
               "No field exists in blueprint with name " << attr_name);

   // Delete attr_name from the blueprint group.

   // Note: This will destroy all orphaned views or buffer classes under this
   // group also.  If sidre owns this field data, the memory will be deleted
   // unless it's referenced somewhere else in sidre.
   attr_grp->destroyGroup(attr_name);

   // Delete field_name from the blueprint_index group.
   if (myid == 0)
   {
      DeregisterAttributeFieldInBPIndex(attr_name);
   }

   // Delete field_name from the named_buffers group, if allocated.
   FreeNamedBuffer(attr_name);
}

void SidreDataCollection::DeregisterAttributeFieldInBPIndex(
   const std::string& attr_name)
{
   sidre::Group * fields_grp = m_bp_index_grp->getGroup("fields");
   MFEM_VERIFY(fields_grp->hasGroup(attr_name),
               "No attribute exists in blueprint index with name " << attr_name);

   // Note: This will destroy all orphaned views or buffer classes under this
   // group also.  If sidre owns this field data, the memory will be deleted
   // unless it's referenced somewhere else in sidre.
   fields_grp->destroyGroup(attr_name);
}

void SidreDataCollection::
addIntegerAttributeField(const std::string& attr_name, bool is_bdry)
{
   sidre::Group* fld_grp = m_bp_grp->getGroup("fields");
   MFEM_ASSERT(fld_grp != NULL, "'fields' group does not exist");

   const int num_elem = is_bdry? mesh->GetNBE() : mesh->GetNE();
   std::string topo_name = is_bdry ? "boundary" : "mesh";

   sidre::Group* attr_grp = fld_grp->createGroup(attr_name);
   attr_grp->createViewString("association", "element");
   attr_grp->createViewAndAllocate("values", sidre::INT_ID, num_elem);
   attr_grp->createViewString("topology", topo_name);
}

void SidreDataCollection::DeregisterField(const std::string& field_name)
{
   // Deregister field_name from field_map.
   DataCollection::DeregisterField(field_name);

   sidre::Group * fields_grp = m_bp_grp->getGroup("fields");
   MFEM_VERIFY(fields_grp->hasGroup(field_name),
               "No field exists in blueprint with name " << field_name);

   // Delete field_name from the blueprint group.

   // Note: This will destroy all orphaned views or buffer classes under this
   // group also.  If sidre owns this field data, the memory will be deleted
   // unless it's referenced somewhere else in sidre.
   fields_grp->destroyGroup(field_name);

   // Delete field_name from the blueprint_index group.
   if (myid == 0)
   {
      DeregisterFieldInBPIndex(field_name);
   }

   // Delete field_name from the named_buffers group, if allocated.
   FreeNamedBuffer(field_name);
}

// private method
std::string SidreDataCollection::getElementName(Element::Type elementEnum)
{
   // Note -- the mapping from Element::Type to string is based on
   //   enum Element::Type { POINT, SEGMENT, TRIANGLE, QUADRILATERAL,
   //                        TETRAHEDRON, HEXAHEDRON };
   // Note: -- the string names are from conduit's blueprint

   switch (elementEnum)
   {
      case Element::POINT:          return "point";
      case Element::SEGMENT:        return "line";
      case Element::TRIANGLE:       return "tri";
      case Element::QUADRILATERAL:  return "quad";
      case Element::TETRAHEDRON:    return "tet";
      case Element::HEXAHEDRON:     return "hex";
      case Element::WEDGE:
      default: ;
   }

   return "unknown";
}

} // end namespace mfem

#endif