mirror of
https://github.com/triqs/dft_tools
synced 2024-12-25 05:43:40 +01:00
4af1afbdaf
- For users : only change is :
H5::H5File in apps. to be replaced by triqs::h5::file, same API.
- using only the C API because :
- it is cleaner, better documented, more examples.
- it is the native hdf5 interface.
- simplify the installation e.g. on mac. Indeed, hdf5 is
usually installed without C++ interface, which is optional.
E.g. EPD et al., brew by default.
Also the infamous mpi+ hdf5_cpp bug, for which we have no clean solution.
- clean the notion of parent of a group. Not needed, better iterate function in C LT API.
- modified doc : no need for C++ bindings any more.
- modified cmake to avoid requiring CPP bindings.
103 lines
3.7 KiB
C++
103 lines
3.7 KiB
C++
/*******************************************************************************
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*
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* TRIQS: a Toolbox for Research in Interacting Quantum Systems
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*
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* Copyright (C) 2011-2014 by O. Parcollet
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*
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* TRIQS is free software: you can redistribute it and/or modify it under the
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* terms of the GNU General Public License as published by the Free Software
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* Foundation, either version 3 of the License, or (at your option) any later
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* version.
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*
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* TRIQS is distributed in the hope that it will be useful, but WITHOUT ANY
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* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
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* FOR A PARTICULAR PURPOSE. See the GNU General Public License for more
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* details.
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*
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* You should have received a copy of the GNU General Public License along with
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* TRIQS. If not, see <http://www.gnu.org/licenses/>.
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*
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******************************************************************************/
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#include "./base.hpp"
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namespace triqs {
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namespace h5 {
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//------------------------------------------------
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// dataspace from lengths and strides. Correct for the complex. strides must be >0
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dataspace dataspace_from_LS(int R, bool is_complex, hsize_t const *Ltot, hsize_t const *L, hsize_t const *S,
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hsize_t const *offset) {
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int rank = R + (is_complex ? 1 : 0);
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hsize_t totdimsf[rank], dimsf[rank], stridesf[rank], offsetf[rank]; // dataset dimensions
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for (size_t u = 0; u < R; ++u) {
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offsetf[u] = (offset ? offset[u] : 0);
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dimsf[u] = L[u];
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totdimsf[u] = Ltot[u];
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stridesf[u] = S[u];
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}
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if (is_complex) {
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offsetf[rank - 1] = 0;
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dimsf[rank - 1] = 2;
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totdimsf[rank - 1] = 2;
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stridesf[rank - 1] = 1;
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}
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dataspace ds = H5Screate_simple(rank, totdimsf, NULL);
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if (!ds.is_valid()) TRIQS_RUNTIME_ERROR << "Can not create the dataset";
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herr_t err = H5Sselect_hyperslab(ds, H5S_SELECT_SET, offsetf, stridesf, dimsf, NULL);
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if (err < 0) TRIQS_RUNTIME_ERROR << "Can not set hyperslab";
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return ds;
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}
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/****************** Write string attribute *********************************************/
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void write_string_attribute(hid_t id, std::string name, std::string value) {
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datatype strdatatype = H5Tcopy(H5T_C_S1);
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auto status = H5Tset_size(strdatatype, value.size() + 1);
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// auto status = H5Tset_size(strdatatype, H5T_VARIABLE);
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if (status < 0) TRIQS_RUNTIME_ERROR << "Internal error in H5Tset_size";
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dataspace space = H5Screate(H5S_SCALAR);
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attribute attr = H5Acreate2(id, name.c_str(), strdatatype, space, H5P_DEFAULT, H5P_DEFAULT);
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if (!attr.is_valid()) TRIQS_RUNTIME_ERROR << "Can not create the attribute " << name;
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status = H5Awrite(attr, strdatatype, (void *)(value.c_str()));
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if (status < 0) TRIQS_RUNTIME_ERROR << "Can not write the attribute " << name;
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}
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/****************** Read string attribute *********************************************/
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/// Return the attribute name of obj, and "" if the attribute does not exist.
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std::string read_string_attribute(hid_t id, std::string name) {
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// if the attribute is not present, return 0
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if (H5LTfind_attribute(id, name.c_str()) == 0) return ""; // not present
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attribute attr = H5Aopen(id, name.c_str(), H5P_DEFAULT);
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if (!attr.is_valid()) TRIQS_RUNTIME_ERROR << "Can not open the attribute " << name;
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dataspace space = H5Aget_space(attr);
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int rank = H5Sget_simple_extent_ndims(space);
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if (rank != 0) TRIQS_RUNTIME_ERROR << "Reading a string attribute and got rank !=0";
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datatype strdatatype = H5Aget_type(attr);
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std::vector<char> buf(H5Aget_storage_size(attr) + 1, 0x00);
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auto err = H5Aread(attr, strdatatype, (void *)(&buf[0]));
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if (err < 0) TRIQS_RUNTIME_ERROR << "Can not read the attribute" << name;
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std::string ret = "";
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ret.append(&(buf.front()));
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return ret;
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}
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}
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}
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