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dft_tools/triqs/h5/base.hpp
Olivier Parcollet f2c7d449cc First commit : triqs libs version 1.0 alpha1 
for earlier commits, see TRIQS0.x repository.
2013-07-17 19:24:07 +02:00

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/*******************************************************************************
*
* TRIQS: a Toolbox for Research in Interacting Quantum Systems
*
* Copyright (C) 2011-2013 by O. Parcollet
*
* TRIQS is free software: you can redistribute it and/or modify it under the
* terms of the GNU General Public License as published by the Free Software
* Foundation, either version 3 of the License, or (at your option) any later
* version.
*
* TRIQS is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
* FOR A PARTICULAR PURPOSE. See the GNU General Public License for more
* details.
*
* You should have received a copy of the GNU General Public License along with
* TRIQS. If not, see <http://www.gnu.org/licenses/>.
*
******************************************************************************/
#ifndef TRIQS_H5_BASE_H
#define TRIQS_H5_BASE_H
#include <triqs/utility/mini_vector.hpp>
#include <type_traits>
#include <H5Cpp.h>
#include "hdf5_hl.h"
#include <boost/type_traits/is_complex.hpp>
namespace triqs {
inline std::string get_triqs_hdf5_data_scheme(bool) { return "bool";}
inline std::string get_triqs_hdf5_data_scheme(int) { return "int";}
inline std::string get_triqs_hdf5_data_scheme(long) { return "long";}
inline std::string get_triqs_hdf5_data_scheme(long long) { return "long long";}
inline std::string get_triqs_hdf5_data_scheme(unsigned int) { return "int";}
inline std::string get_triqs_hdf5_data_scheme(unsigned long) { return "unsigned long";}
inline std::string get_triqs_hdf5_data_scheme(unsigned long long) { return "unsigned long long";}
inline std::string get_triqs_hdf5_data_scheme(float) { return "float";}
inline std::string get_triqs_hdf5_data_scheme(double) { return "double";}
inline std::string get_triqs_hdf5_data_scheme(long double) { return "long double";}
inline std::string get_triqs_hdf5_data_scheme(std::complex<double>) { return "complex";}
namespace h5 {
using utility::mini_vector;
// conversion of C type to HDF5 native
inline H5::PredType native_type_from_C(char) { return H5::PredType::NATIVE_CHAR; }
inline H5::PredType native_type_from_C(signed char) { return H5::PredType::NATIVE_SCHAR; }
inline H5::PredType native_type_from_C(unsigned char) { return H5::PredType::NATIVE_UCHAR; }
inline H5::PredType native_type_from_C(short) { return H5::PredType::NATIVE_SHORT; }
inline H5::PredType native_type_from_C(unsigned short) { return H5::PredType::NATIVE_USHORT; }
inline H5::PredType native_type_from_C(int) { return H5::PredType::NATIVE_INT; }
inline H5::PredType native_type_from_C(unsigned) { return H5::PredType::NATIVE_UINT; }
inline H5::PredType native_type_from_C(long) { return H5::PredType::NATIVE_LONG; }
inline H5::PredType native_type_from_C(unsigned long) { return H5::PredType::NATIVE_ULONG; }
inline H5::PredType native_type_from_C(long long) { return H5::PredType::NATIVE_LLONG; }
inline H5::PredType native_type_from_C(unsigned long long) { return H5::PredType::NATIVE_ULLONG; }
inline H5::PredType native_type_from_C(float) { return H5::PredType::NATIVE_FLOAT; }
inline H5::PredType native_type_from_C(double) { return H5::PredType::NATIVE_DOUBLE; }
inline H5::PredType native_type_from_C(long double) { return H5::PredType::NATIVE_LDOUBLE; }
inline H5::PredType native_type_from_C(bool) { return H5::PredType::NATIVE_SCHAR; }
inline H5::PredType native_type_from_C(std::string) { return H5::PredType::C_S1; }
// conversion of C type to HDF5 native
// NEED TO CHANGE THIS ? It is not standard... We should fix a standard or have a trait
inline H5::PredType h5_type_from_C(char) { return H5::PredType::NATIVE_CHAR; }
inline H5::PredType h5_type_from_C(signed char) { return H5::PredType::NATIVE_SCHAR; }
inline H5::PredType h5_type_from_C(unsigned char) { return H5::PredType::NATIVE_UCHAR; }
inline H5::PredType h5_type_from_C(short) { return H5::PredType::NATIVE_SHORT; }
inline H5::PredType h5_type_from_C(unsigned short) { return H5::PredType::NATIVE_USHORT; }
inline H5::PredType h5_type_from_C(int) { return H5::PredType::NATIVE_INT; }
inline H5::PredType h5_type_from_C(unsigned) { return H5::PredType::NATIVE_UINT; }
inline H5::PredType h5_type_from_C(long) { return H5::PredType::NATIVE_LONG; }
inline H5::PredType h5_type_from_C(unsigned long) { return H5::PredType::NATIVE_ULONG; }
inline H5::PredType h5_type_from_C(long long) { return H5::PredType::NATIVE_LLONG; }
inline H5::PredType h5_type_from_C(unsigned long long) { return H5::PredType::NATIVE_ULLONG; }
inline H5::PredType h5_type_from_C(float) { return H5::PredType::NATIVE_FLOAT; }
inline H5::PredType h5_type_from_C(double) { return H5::PredType::NATIVE_DOUBLE; }
inline H5::PredType h5_type_from_C(long double) { return H5::PredType::NATIVE_LDOUBLE; }
inline H5::PredType h5_type_from_C(bool) { return H5::PredType::NATIVE_SCHAR; }
inline H5::PredType h5_type_from_C(std::string) { return H5::PredType::C_S1; }
// If it is complex<T> return T else T
template<typename T> struct remove_complex { typedef T type;};
template<typename T> struct remove_complex<std::complex<T> > { typedef T type;};
template<typename T> struct remove_complex<std::complex<const T> > { typedef T type;};
template<typename T> struct remove_complex<const T>: remove_complex<T>{};
//------------- compute the data type (removing complex) ----------------------------------
// in memory
template <typename S> H5::PredType data_type_memory () { return native_type_from_C(typename remove_complex<S>::type()); }
// the type of data to put in the file_or_group
template <typename V> H5::PredType data_type_file () { return h5_type_from_C(typename remove_complex<V>::type());}
//------------- compute void * pointer to the data ----------------------------------
template <typename S>
typename std::enable_if< boost::is_complex<S>::value, typename std::conditional<std::is_const<S>::value, const void *, void *>::type >::type
get_data_ptr (S * p) {
typedef typename std::conditional<std::is_const<S>::value, const typename S::value_type, typename S::value_type>::type T;
return reinterpret_cast<T*>(p);
}
template <typename S >
typename std::enable_if< !boost::is_complex<S>::value, typename std::conditional<std::is_const<S>::value, const void *, void *>::type >::type
get_data_ptr (S * p) {return p;}
// dataspace from lengths and strides. Correct for the complex. strides must be >0
template<int R, bool IsComplex>
H5::DataSpace dataspace_from_LS (
mini_vector<hsize_t, R> const & Ltot,
mini_vector<hsize_t, R> const & L,
mini_vector<hsize_t, R> const & S,
mini_vector<hsize_t, R> const & offset = mini_vector<hsize_t,R>() )
{
static const unsigned int rank = R + (IsComplex ? 1 : 0);
hsize_t totdimsf[rank], dimsf [rank], stridesf[rank], offsetf[rank]; // dataset dimensions
for (size_t u=0; u<R ; ++u) { offsetf[u] = offset[u]; dimsf[u] = L[u]; totdimsf[u] = Ltot[u]; stridesf[u] = S[u]; }
if (IsComplex) { offsetf[rank-1]=0; dimsf[rank-1]=2; totdimsf[rank-1] = 2; stridesf[rank-1]=1; }
H5::DataSpace ds ( rank, totdimsf );
ds.selectHyperslab (H5S_SELECT_SET , dimsf, offsetf, stridesf);
return ds;
}
#define TRIQS_ARRAYS_H5_CATCH_EXCEPTION \
catch( triqs::runtime_error const & error) { throw triqs::runtime_error() << error.what();}\
catch( H5::AttributeIException const & error ) { error.printError(); TRIQS_RUNTIME_ERROR<<"H5 Attribute error"; }\
catch( H5::DataSetIException const & error ) { error.printError(); TRIQS_RUNTIME_ERROR<<"H5 DataSet error"; }\
catch( H5::DataSpaceIException const & error ) { error.printError(); TRIQS_RUNTIME_ERROR<<"H5 DataSpace error"; }\
catch( H5::DataTypeIException const & error ) { error.printError(); TRIQS_RUNTIME_ERROR<<"H5 DataType error"; }\
catch( H5::FileIException const & error ) { error.printError(); TRIQS_RUNTIME_ERROR<<"H5 File error"; }\
catch( H5::GroupIException const & error ) { error.printError(); TRIQS_RUNTIME_ERROR<<"H5 Group error"; }\
catch( H5::IdComponentException const & error ) { error.printError(); TRIQS_RUNTIME_ERROR<<"H5 IdComponentException error"; }\
catch( H5::LibraryIException const & error ) { error.printError(); TRIQS_RUNTIME_ERROR<<"H5 LibraryIException error"; }\
catch( H5::PropListIException const & error ) { error.printError(); TRIQS_RUNTIME_ERROR<<"H5 PropListIException error"; }\
catch( H5::ReferenceException const & error ) { error.printError(); TRIQS_RUNTIME_ERROR<<"H5 ReferenceException error"; }\
catch(...) { TRIQS_RUNTIME_ERROR<<"H5 unknown error";}
/****************** Write string attribute *********************************************/
inline void write_string_attribute ( H5::H5Object const * obj, std::string name, std::string value ) {
H5::DataSpace attr_dataspace = H5::DataSpace(H5S_SCALAR);
// Create new string datatype for attribute
H5::StrType strdatatype(H5::PredType::C_S1, value.size());
// Set up write buffer for attribute
//const H5std_string strwritebuf (value);
// Create attribute and write to it
H5::Attribute myatt_in = obj->createAttribute(name.c_str(), strdatatype, attr_dataspace);
//myatt_in.write(strdatatype, strwritebuf);
myatt_in.write(strdatatype, (void *)(value.c_str()));
}
/****************** Read string attribute *********************************************/
/// Return the attribute name of obj, and "" if the attribute does not exist.
inline std::string read_string_attribute (H5::H5Object const * obj, std::string name ) {
std::string value ="";
H5::Attribute attr;
if (H5LTfind_attribute(obj -> getId(), name.c_str() )==0) return value;// not present
// can not find how to get the size with hl. Using full interface
//herr_t err2 = H5LTget_attribute_string(gr.getId(), x.c_str(), name.c_str() , &(buf.front()) ) ;
//value.append( &(buf.front()) );
try { attr= obj->openAttribute(name.c_str());}
catch (H5::AttributeIException) { return value;}
try {
H5::DataSpace dataspace = attr.getSpace();
int rank = dataspace.getSimpleExtentNdims();
if (rank != 0) TRIQS_RUNTIME_ERROR << "Reading a string attribute and got rank !=0";
size_t size = attr.getStorageSize();
H5::StrType strdatatype(H5::PredType::C_S1, size+1);
std::vector<char> buf(size+1, 0x00);
attr.read(strdatatype, (void *)(&buf[0]));
value.append( &(buf.front()) );
}
TRIQS_ARRAYS_H5_CATCH_EXCEPTION;
return value;
}
}}
#endif
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