DataIO.h

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//* This file is part of the MOOSE framework
//* https://www.mooseframework.org
//*
//* All rights reserved, see COPYRIGHT for full restrictions
//* https://github.com/idaholab/moose/blob/master/COPYRIGHT
//*
//* Licensed under LGPL 2.1, please see LICENSE for details
//* https://www.gnu.org/licenses/lgpl-2.1.html

#pragma once

// MOOSE includes
#include "DualReal.h"
#include "MooseTypes.h"
#include "HashMap.h"
#include "MooseError.h"
#include "Backup.h"
#include "RankTwoTensor.h"
#include "RankThreeTensor.h"
#include "RankFourTensor.h"
#include "MooseADWrapper.h"

#include "libmesh/parallel.h"
#ifdef LIBMESH_HAVE_CXX11_TYPE_TRAITS
#include <type_traits>
#endif

// C++ includes
#include <string>
#include <vector>
#include <list>
#include <iostream>
#include <map>
#include <unordered_map>
#include <memory>

// Forward declarations
template <typename>
class ColumnMajorMatrixTempl;
typedef ColumnMajorMatrixTempl<Real> ColumnMajorMatrix;

namespace libMesh
{
template <typename T>
class NumericVector;
template <typename T>
class DenseMatrix;
template <typename T>
class DenseVector;
template <typename T>
class VectorValue;
template <typename T>
class TensorValue;
class Elem;
class Point;
}

template <typename P>
inline void storeHelper(std::ostream & stream, P & data, void * context);

template <typename P>
inline void storeHelper(std::ostream & stream, std::vector<P> & data, void * context);

template <typename P>
inline void storeHelper(std::ostream & stream, std::shared_ptr<P> & data, void * context);

template <typename P>
inline void storeHelper(std::ostream & stream, std::unique_ptr<P> & data, void * context);

template <typename P>
inline void storeHelper(std::ostream & stream, std::set<P> & data, void * context);

template <typename P, typename Q>
inline void storeHelper(std::ostream & stream, std::map<P, Q> & data, void * context);

template <typename P, typename Q>
inline void storeHelper(std::ostream & stream, std::unordered_map<P, Q> & data, void * context);

template <typename P, typename Q>
inline void storeHelper(std::ostream & stream, HashMap<P, Q> & data, void * context);

template <typename P>
inline void loadHelper(std::istream & stream, P & data, void * context);

template <typename P>
inline void loadHelper(std::istream & stream, std::vector<P> & data, void * context);

template <typename P>
inline void loadHelper(std::istream & stream, std::shared_ptr<P> & data, void * context);

template <typename P>
inline void loadHelper(std::istream & stream, std::unique_ptr<P> & data, void * context);

template <typename P>
inline void loadHelper(std::istream & stream, std::set<P> & data, void * context);

template <typename P, typename Q>
inline void loadHelper(std::istream & stream, std::map<P, Q> & data, void * context);

template <typename P, typename Q>
inline void loadHelper(std::istream & stream, std::unordered_map<P, Q> & data, void * context);

template <typename P, typename Q>
inline void loadHelper(std::istream & stream, HashMap<P, Q> & data, void * context);

template <typename T>
inline void dataStore(std::ostream & stream, T & v, void * /*context*/);

// DO NOT MODIFY THE NEXT LINE - It is used by MOOSEDocs
// *************** Global Store Declarations *****************
template <typename T>
inline void
dataStore(std::ostream & stream, T & v, void * /*context*/)
{
#ifdef LIBMESH_HAVE_CXX11_TYPE_TRAITS
  static_assert(std::is_polymorphic<T>::value == false,
                "Cannot serialize a class that has virtual "
                "members!\nWrite a custom dataStore() "
                "template specialization!\n\n");
  static_assert(std::is_trivially_copyable<T>::value,
                "Cannot serialize a class that is not trivially copyable!\nWrite a custom "
                "dataStore() template specialization!\n\n");
#endif

  // Moose::out<<"Generic dataStore"<<std::endl;
  stream.write((char *)&v, sizeof(v));
}

template <typename T>
inline void
dataStore(std::ostream & /*stream*/, T *& /*v*/, void * /*context*/)
{
  mooseError("Attempting to store a raw pointer type: \"",
             demangle(typeid(T).name()),
             " *\" as restartable data!\nWrite a custom dataStore() template specialization!\n\n");
}

void dataStore(std::ostream & stream, Point & p, void * context);

template <typename T, typename U>
inline void
dataStore(std::ostream & stream, std::pair<T, U> & p, void * context)
{
  storeHelper(stream, p.first, context);
  storeHelper(stream, p.second, context);
}

template <typename T>
inline void
dataStore(std::ostream & stream, std::vector<T> & v, void * context)
{
  // First store the size of the vector
  unsigned int size = v.size();
  stream.write((char *)&size, sizeof(size));

  for (unsigned int i = 0; i < size; i++)
    storeHelper(stream, v[i], context);
}

template <typename T>
inline void
dataStore(std::ostream & stream, std::shared_ptr<T> & v, void * context)
{
  T * tmp = v.get();

  storeHelper(stream, tmp, context);
}

template <typename T>
inline void
dataStore(std::ostream & stream, std::unique_ptr<T> & v, void * context)
{
  T * tmp = v.get();

  storeHelper(stream, tmp, context);
}

template <typename T>
inline void
dataStore(std::ostream & stream, std::set<T> & s, void * context)
{
  // First store the size of the set
  unsigned int size = s.size();
  stream.write((char *)&size, sizeof(size));

  typename std::set<T>::iterator it = s.begin();
  typename std::set<T>::iterator end = s.end();

  for (; it != end; ++it)
  {
    T & x = const_cast<T &>(*it);
    storeHelper(stream, x, context);
  }
}

template <typename T>
inline void
dataStore(std::ostream & stream, std::list<T> & l, void * context)
{
  // First store the size of the set
  unsigned int size = l.size();
  stream.write((char *)&size, sizeof(size));

  typename std::list<T>::iterator it = l.begin();
  typename std::list<T>::iterator end = l.end();

  for (; it != end; ++it)
  {
    T & x = const_cast<T &>(*it);
    storeHelper(stream, x, context);
  }
}

template <typename T, typename U>
inline void
dataStore(std::ostream & stream, std::map<T, U> & m, void * context)
{
  // First store the size of the map
  unsigned int size = m.size();
  stream.write((char *)&size, sizeof(size));

  typename std::map<T, U>::iterator it = m.begin();
  typename std::map<T, U>::iterator end = m.end();

  for (; it != end; ++it)
  {
    T & key = const_cast<T &>(it->first);

    storeHelper(stream, key, context);

    storeHelper(stream, it->second, context);
  }
}

template <typename T, typename U>
inline void
dataStore(std::ostream & stream, std::unordered_map<T, U> & m, void * context)
{
  // First store the size of the map
  unsigned int size = m.size();
  stream.write((char *)&size, sizeof(size));

  typename std::unordered_map<T, U>::iterator it = m.begin();
  typename std::unordered_map<T, U>::iterator end = m.end();

  for (; it != end; ++it)
  {
    T & key = const_cast<T &>(it->first);

    storeHelper(stream, key, context);

    storeHelper(stream, it->second, context);
  }
}

template <typename T, typename U>
inline void
dataStore(std::ostream & stream, HashMap<T, U> & m, void * context)
{
  // First store the size of the map
  unsigned int size = m.size();
  stream.write((char *)&size, sizeof(size));

  typename HashMap<T, U>::iterator it = m.begin();
  typename HashMap<T, U>::iterator end = m.end();

  for (; it != end; ++it)
  {
    T & key = const_cast<T &>(it->first);

    storeHelper(stream, key, context);

    storeHelper(stream, it->second, context);
  }
}

// Specializations (defined in .C)
template <>
void dataStore(std::ostream & stream, Real & v, void * /*context*/);
template <>
void dataStore(std::ostream & stream, std::string & v, void * /*context*/);
template <>
void dataStore(std::ostream & stream, ColumnMajorMatrix & v, void * /*context*/);
template <>
void dataStore(std::ostream & stream, const Elem *& e, void * context);
template <>
void dataStore(std::ostream & stream, const Node *& n, void * context);
template <>
void dataStore(std::ostream & stream, Elem *& e, void * context);
template <>
void dataStore(std::ostream & stream, Node *& n, void * context);
template <>
void dataStore(std::ostream & stream, std::stringstream & s, void * context);
template <>
void dataStore(std::ostream & stream, std::stringstream *& s, void * context);
template <>
void dataStore(std::ostream & stream, DualReal & dn, void * context);

template <std::size_t N>
inline void
dataStore(std::ostream & stream, DualReal (&dn)[N], void * context)
{
  for (std::size_t i = 0; i < N; ++i)
    dataStore(stream, dn[i], context);
}

template <typename T>
void
dataStore(std::ostream & stream, NumericVector<T> & v, void * context)
{
  v.close();

  numeric_index_type size = v.local_size();

  for (numeric_index_type i = v.first_local_index(); i < v.first_local_index() + size; i++)
  {
    T r = v(i);
    dataStore(stream, r, context);
  }
}

template <typename T>
void
dataStore(std::ostream & stream, DenseVector<T> & v, void * context)
{
  unsigned int m = v.size();
  stream.write((char *)&m, sizeof(m));
  for (unsigned int i = 0; i < v.size(); i++)
  {
    T r = v(i);
    dataStore(stream, r, context);
  }
}

template <typename T>
void dataStore(std::ostream & stream, TensorValue<T> & v, void * context);

template <typename T>
void dataStore(std::ostream & stream, DenseMatrix<T> & v, void * context);

template <typename T>
void dataStore(std::ostream & stream, VectorValue<T> & v, void * context);

template <typename T>
void
dataStore(std::ostream & stream, RankTwoTensorTempl<T> & rtt, void * context)
{
  dataStore(stream, rtt._coords, context);
}

template <typename T>
void
dataStore(std::ostream & stream, RankThreeTensorTempl<T> & rtt, void * context)
{
  dataStore(stream, rtt._vals, context);
}

template <typename T>
void
dataStore(std::ostream & stream, RankFourTensorTempl<T> & rft, void * context)
{
  dataStore(stream, rft._vals, context);
}

template <typename T>
inline void
dataStore(std::ostream & stream, MooseADWrapper<T> & dn_wrapper, void * context)
{
  dataStore(stream, dn_wrapper.value(), context);
  if (dn_wrapper._dual_number)
  {
    unsigned int m = 1;
    stream.write((char *)&m, sizeof(m));
    dataStore(stream, *dn_wrapper._dual_number, context);
  }
  else
  {
    unsigned int m = 0;
    stream.write((char *)&m, sizeof(m));
  }
}

// DO NOT MODIFY THE NEXT LINE - It is used by MOOSEDocs
// *************** Global Load Declarations *****************
template <typename T>
inline void
dataLoad(std::istream & stream, T & v, void * /*context*/)
{
  stream.read((char *)&v, sizeof(v));
}

template <typename T>
void
dataLoad(std::istream & /*stream*/, T *& /*v*/, void * /*context*/)
{
  mooseError("Attempting to load a raw pointer type: \"",
             demangle(typeid(T).name()),
             " *\" as restartable data!\nWrite a custom dataLoad() template specialization!\n\n");
}

template <typename T, typename U>
inline void
dataLoad(std::istream & stream, std::pair<T, U> & p, void * context)
{
  loadHelper(stream, p.first, context);
  loadHelper(stream, p.second, context);
}

template <typename T>
inline void
dataLoad(std::istream & stream, std::vector<T> & v, void * context)
{
  // First read the size of the vector
  unsigned int size = 0;
  stream.read((char *)&size, sizeof(size));

  v.resize(size);

  for (unsigned int i = 0; i < size; i++)
    loadHelper(stream, v[i], context);
}

template <typename T>
inline void
dataLoad(std::istream & stream, std::shared_ptr<T> & v, void * context)
{
  T * tmp = v.get();

  loadHelper(stream, tmp, context);
}

template <typename T>
inline void
dataLoad(std::istream & stream, std::unique_ptr<T> & v, void * context)
{
  T * tmp = v.get();

  loadHelper(stream, tmp, context);
}

template <typename T>
inline void
dataLoad(std::istream & stream, std::set<T> & s, void * context)
{
  // First read the size of the set
  unsigned int size = 0;
  stream.read((char *)&size, sizeof(size));

  for (unsigned int i = 0; i < size; i++)
  {
    T data;
    loadHelper(stream, data, context);
    s.insert(std::move(data));
  }
}

template <typename T>
inline void
dataLoad(std::istream & stream, std::list<T> & l, void * context)
{
  // First read the size of the set
  unsigned int size = 0;
  stream.read((char *)&size, sizeof(size));

  for (unsigned int i = 0; i < size; i++)
  {
    T data;
    loadHelper(stream, data, context);
    l.push_back(std::move(data));
  }
}

template <typename T, typename U>
inline void
dataLoad(std::istream & stream, std::map<T, U> & m, void * context)
{
  m.clear();

  // First read the size of the map
  unsigned int size = 0;
  stream.read((char *)&size, sizeof(size));

  for (unsigned int i = 0; i < size; i++)
  {
    T key;
    loadHelper(stream, key, context);

    U & value = m[key];
    loadHelper(stream, value, context);
  }
}

template <typename T, typename U>
inline void
dataLoad(std::istream & stream, std::unordered_map<T, U> & m, void * context)
{
  m.clear();

  // First read the size of the map
  unsigned int size = 0;
  stream.read((char *)&size, sizeof(size));

  for (unsigned int i = 0; i < size; i++)
  {
    T key;
    loadHelper(stream, key, context);

    U & value = m[key];
    loadHelper(stream, value, context);
  }
}

template <typename T, typename U>
inline void
dataLoad(std::istream & stream, HashMap<T, U> & m, void * context)
{
  // First read the size of the map
  unsigned int size = 0;
  stream.read((char *)&size, sizeof(size));

  for (unsigned int i = 0; i < size; i++)
  {
    T key;
    loadHelper(stream, key, context);

    U & value = m[key];
    loadHelper(stream, value, context);
  }
}

// Specializations (defined in .C)
template <>
void dataLoad(std::istream & stream, Real & v, void * /*context*/);
template <>
void dataLoad(std::istream & stream, std::string & v, void * /*context*/);
template <>
void dataLoad(std::istream & stream, ColumnMajorMatrix & v, void * /*context*/);
template <>
void dataLoad(std::istream & stream, const Elem *& e, void * context);
template <>
void dataLoad(std::istream & stream, const Node *& e, void * context);
template <>
void dataLoad(std::istream & stream, Elem *& e, void * context);
template <>
void dataLoad(std::istream & stream, Node *& e, void * context);
template <>
void dataLoad(std::istream & stream, std::stringstream & s, void * context);
template <>
void dataLoad(std::istream & stream, std::stringstream *& s, void * context);
template <>
void dataLoad(std::istream & stream, DualReal & dn, void * context);

template <typename T>
void
dataLoad(std::istream & stream, NumericVector<T> & v, void * context)
{
  numeric_index_type size = v.local_size();
  for (numeric_index_type i = v.first_local_index(); i < v.first_local_index() + size; i++)
  {
    T r = 0;
    dataLoad(stream, r, context);
    v.set(i, r);
  }
  v.close();
}

template <typename T>
void
dataLoad(std::istream & stream, DenseVector<T> & v, void * context)
{
  unsigned int n = 0;
  stream.read((char *)&n, sizeof(n));
  v.resize(n);
  for (unsigned int i = 0; i < n; i++)
  {
    T r = 0;
    dataLoad(stream, r, context);
    v(i) = r;
  }
}

template <typename T>
void dataLoad(std::istream & stream, TensorValue<T> & v, void * context);

template <typename T>
void dataLoad(std::istream & stream, DenseMatrix<T> & v, void * context);

template <typename T>
void dataLoad(std::istream & stream, VectorValue<T> & v, void * context);

template <typename T>
void
dataLoad(std::istream & stream, RankTwoTensorTempl<T> & rtt, void * context)
{
  dataLoad(stream, rtt._coords, context);
}

template <typename T>
void
dataLoad(std::istream & stream, RankThreeTensorTempl<T> & rtt, void * context)
{
  dataLoad(stream, rtt._vals, context);
}

template <typename T>
void
dataLoad(std::istream & stream, RankFourTensorTempl<T> & rft, void * context)
{
  dataLoad(stream, rft._vals, context);
}

template <typename T>
inline void
dataLoad(std::istream & stream, MooseADWrapper<T> & dn_wrapper, void * context)
{
  dataLoad(stream, dn_wrapper.value(), context);
  unsigned int n = 0;
  stream.read((char *)&n, sizeof(n));
  if (n)
  {
    dn_wrapper._dual_number = libmesh_make_unique<typename MooseADWrapper<T>::DNType>();
    dataLoad(stream, *dn_wrapper._dual_number, context);
  }
}

// Scalar Helper Function
template <typename P>
inline void
storeHelper(std::ostream & stream, P & data, void * context)
{
  dataStore(stream, data, context);
}

// Vector Helper Function
template <typename P>
inline void
storeHelper(std::ostream & stream, std::vector<P> & data, void * context)
{
  dataStore(stream, data, context);
}

// std::shared_ptr Helper Function
template <typename P>
inline void
storeHelper(std::ostream & stream, std::shared_ptr<P> & data, void * context)
{
  dataStore(stream, data, context);
}

// std::unique Helper Function
template <typename P>
inline void
storeHelper(std::ostream & stream, std::unique_ptr<P> & data, void * context)
{
  dataStore(stream, data, context);
}

// Set Helper Function
template <typename P>
inline void
storeHelper(std::ostream & stream, std::set<P> & data, void * context)
{
  dataStore(stream, data, context);
}

// Map Helper Function
template <typename P, typename Q>
inline void
storeHelper(std::ostream & stream, std::map<P, Q> & data, void * context)
{
  dataStore(stream, data, context);
}

// Unordered_map Helper Function
template <typename P, typename Q>
inline void
storeHelper(std::ostream & stream, std::unordered_map<P, Q> & data, void * context)
{
  dataStore(stream, data, context);
}

// HashMap Helper Function
template <typename P, typename Q>
inline void
storeHelper(std::ostream & stream, HashMap<P, Q> & data, void * context)
{
  dataStore(stream, data, context);
}

// Scalar Helper Function
template <typename P>
inline void
loadHelper(std::istream & stream, P & data, void * context)
{
  dataLoad(stream, data, context);
}

// Vector Helper Function
template <typename P>
inline void
loadHelper(std::istream & stream, std::vector<P> & data, void * context)
{
  dataLoad(stream, data, context);
}

// std::shared_ptr Helper Function
template <typename P>
inline void
loadHelper(std::istream & stream, std::shared_ptr<P> & data, void * context)
{
  dataLoad(stream, data, context);
}

// Unique Pointer Helper Function
template <typename P>
inline void
loadHelper(std::istream & stream, std::unique_ptr<P> & data, void * context)
{
  dataLoad(stream, data, context);
}

// Set Helper Function
template <typename P>
inline void
loadHelper(std::istream & stream, std::set<P> & data, void * context)
{
  dataLoad(stream, data, context);
}

// Map Helper Function
template <typename P, typename Q>
inline void
loadHelper(std::istream & stream, std::map<P, Q> & data, void * context)
{
  dataLoad(stream, data, context);
}

// Unordered_map Helper Function
template <typename P, typename Q>
inline void
loadHelper(std::istream & stream, std::unordered_map<P, Q> & data, void * context)
{
  dataLoad(stream, data, context);
}

// HashMap Helper Function
template <typename P, typename Q>
inline void
loadHelper(std::istream & stream, HashMap<P, Q> & data, void * context)
{
  dataLoad(stream, data, context);
}

// Specializations for Backup type
template <>
inline void
dataStore(std::ostream & stream, Backup *& backup, void * context)
{
  dataStore(stream, backup->_system_data, context);

  for (unsigned int i = 0; i < backup->_restartable_data.size(); i++)
    dataStore(stream, backup->_restartable_data[i], context);
}

template <>
inline void
dataLoad(std::istream & stream, Backup *& backup, void * context)
{
  dataLoad(stream, backup->_system_data, context);

  for (unsigned int i = 0; i < backup->_restartable_data.size(); i++)
    dataLoad(stream, backup->_restartable_data[i], context);
}

void dataLoad(std::istream & stream, Point & p, void * context);

namespace libMesh
{
namespace Parallel
{
template <typename T>
class Packing<std::basic_string<T>>
{
public:
  static const unsigned int size_bytes = 4;

  typedef T buffer_type;

  static unsigned int get_string_len(typename std::vector<T>::const_iterator in)
  {
    unsigned int string_len = reinterpret_cast<const unsigned char &>(in[size_bytes - 1]);
    for (signed int i = size_bytes - 2; i >= 0; --i)
    {
      string_len *= 256;
      string_len += reinterpret_cast<const unsigned char &>(in[i]);
    }
    return string_len;
  }

  static unsigned int packed_size(typename std::vector<T>::const_iterator in)
  {
    return get_string_len(in) + size_bytes;
  }

  static unsigned int packable_size(const std::basic_string<T> & s, const void *)
  {
    return s.size() + size_bytes;
  }

  template <typename Iter>
  static void pack(const std::basic_string<T> & b, Iter data_out, const void *)
  {
    unsigned int string_len = b.size();
    for (unsigned int i = 0; i != size_bytes; ++i)
    {
      *data_out++ = (string_len % 256);
      string_len /= 256;
    }

    std::copy(b.begin(), b.end(), data_out);
  }

  static std::basic_string<T> unpack(typename std::vector<T>::const_iterator in, void *)
  {
    unsigned int string_len = get_string_len(in);

    std::ostringstream oss;
    for (unsigned int i = 0; i < string_len; ++i)
      oss << reinterpret_cast<const unsigned char &>(in[i + size_bytes]);

    in += size_bytes + string_len;

    return oss.str();
  }
};

} // namespace Parallel

} // namespace libMesh