Chaste  Release::2018.1
CellVecData.hpp
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35 
36 #ifndef CELLVECDATA_HPP_
37 #define CELLVECDATA_HPP_
38 
39 #include <boost/shared_ptr.hpp>
40 #include <map>
41 #include <string>
42 #include <vector>
43 
44 #include <petscvec.h>
45 
46 #include "AbstractCellProperty.hpp"
47 #include "ChasteSerialization.hpp"
48 #include <boost/serialization/base_object.hpp>
49 #include <boost/serialization/map.hpp>
50 #include <boost/serialization/array.hpp>
51 #include "Exception.hpp"
52 #include "ArchiveLocationInfo.hpp"
53 
54 
63 {
64 private:
65 
69  std::map<std::string, Vec> mCellVecData;
70 
74  bool mFreeVecs;
75 
84  template<class Archive>
85  void serialize(Archive & archive, const unsigned int version)
86  {
87  archive & boost::serialization::base_object<AbstractCellProperty>(*this);
88  }
89 
90 public:
91 
95  CellVecData();
96 
101  CellVecData(const CellVecData& rAnotherCellVecData);
102 
107  CellVecData(const std::map<std::string, Vec>& rCellVecDataMap);
108 
113  virtual ~CellVecData();
114 
121  void SetItem(const std::string& rVariableName, Vec data);
122 
130  Vec GetItem(const std::string& rVariableName) const;
131 
135  unsigned GetNumItems() const;
136 
142  std::vector<std::string> GetKeys() const;
143 };
144 
146 // Declare identifier for the serializer
148 
149 
150 namespace boost
151 {
152 namespace serialization
153 {
154 template<class Archive>
155 inline void save_construct_data(
156  Archive & ar, const CellVecData * t, const unsigned int file_version)
157 {
158  unsigned map_size = t->GetNumItems();
159  ar << map_size;
160 
161  std::vector<std::string> keys = t->GetKeys();
162 
163  for (std::vector<std::string>::iterator iter = keys.begin(); iter != keys.end(); ++iter)
164  {
165  std::string key = *iter;
166  ar << key;
167  Vec vec_data = t->GetItem(key);
168 
169  // Machinery for archiving a sequential PETSc Vec as a boost make_array.
170  double *p_vec_data;
171  VecGetArray(vec_data, &p_vec_data);
172  PetscInt size, local_size;
173  VecGetSize(vec_data, &size);
174  VecGetLocalSize(vec_data, &local_size);
175  // This will fail if we run in parallel and the vector is shared MPI (size is global)
176  assert( local_size == size);
177  ar << size;
178  ar << make_array(p_vec_data, size);
179  VecRestoreArray(vec_data, &p_vec_data);
180 
181  //std::string archive_filename = ArchiveLocationInfo::GetArchiveDirectory() + key + ".vec";
182  //PetscTools::DumpPetscObject(t->GetItem(key), archive_filename);
183  }
184 
185 }
186 
187 template<class Archive>
188 inline void load_construct_data(
189  Archive & ar, CellVecData * t, const unsigned int file_version)
190 {
191  unsigned map_size;
192  ar >> map_size;
193 
194  std::map<std::string, Vec> archived_cell_vec_data;
195  for (unsigned map_entry = 0; map_entry < map_size; ++map_entry)
196  {
197  std::string key;
198  ar >> key;
199 
200  // Un-archive vector data and construct a new PETSc Vec for it
201  PetscInt size;
202  ar >> size;
203  Vec archived_vec = PetscTools::CreateVec(size);
204  double *p_archived_vec;
205  VecGetArray(archived_vec, &p_archived_vec);
206  ar >> make_array<double>(p_archived_vec, size);
207  VecRestoreArray(archived_vec, &p_archived_vec);
208 
209  //std::string archive_filename = ArchiveLocationInfo::GetArchiveDirectory() + key + ".vec";
210  //PetscTools::ReadPetscObject(archived_vec, archive_filename);
211 
212  archived_cell_vec_data[key] = archived_vec;
213  }
214 
215  ::new(t)CellVecData(archived_cell_vec_data);
216 }
217 }
218 }
219 
220 #endif /* CELLVECDATA_HPP_ */
std::map< std::string, Vec > mCellVecData
Definition: CellVecData.hpp:69
Vec GetItem(const std::string &rVariableName) const
Definition: CellVecData.cpp:84
static Vec CreateVec(int size, int localSize=PETSC_DECIDE, bool ignoreOffProcEntries=true)
Definition: PetscTools.cpp:214
void serialize(Archive &archive, const unsigned int version)
Definition: CellVecData.hpp:85
friend class boost::serialization::access
Definition: CellVecData.hpp:77
void SetItem(const std::string &rVariableName, Vec data)
Definition: CellVecData.cpp:79
std::vector< std::string > GetKeys() const
virtual ~CellVecData()
Definition: CellVecData.cpp:67
#define CHASTE_CLASS_EXPORT(T)
unsigned GetNumItems() const
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