DEAL_II_NAMESPACE_OPEN
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-// links because the they are longer than 80 characters
+// links because they are longer than 80 characters
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/**
* Namespace containing the HDF5 interface.
*
* The [Hierarchical Data Format (HDF)](https://www.hdfgroup.org/) is a cross
- * platform and high I/O performance format designed to store large amounts of
+ * platform and a high I/O performance format designed to store large amounts of
* data. It supports serial and MPI I/O access. This set of classes provides an
* interface to the [HDF5 library](https://www.hdfgroup.org/downloads/hdf5/).
*
* # Groups, Datasets and attributes
- * The HDF5 file is organized in
+ * An HDF5 file is organized in
* [groups](https://bitbucket.hdfgroup.org/pages/HDFFV/hdf5doc/master/browse/html/UG/HDF5_Users_Guide-Responsive%20HTML5/HDF5_Users_Guide/Groups/HDF5_Groups.htm)
* and
* [datasets](https://bitbucket.hdfgroup.org/pages/HDFFV/hdf5doc/master/browse/html/UG/HDF5_Users_Guide-Responsive%20HTML5/HDF5_Users_Guide/Datasets/HDF5_Datasets.htm).
* is a small meta data. The methods HDF5Object::get_attribute() and
* HDF5Object::set_attribute() can be used to get and set attributes.
*
- * An example is below
+ * An example is shown below
* @code
* HDF5::File data_file(filename, HDF5::File::Mode::create);
* double double_attribute = 2.2;
- * data_file.set_attribute("double_attribute", double attribute);
+ * data_file.set_attribute("double_attribute", double_attribute);
* auto group = data_file.create_group("group");
* group.set_attribute("simulation_type", std::string("elastic_equation"));
* auto dataset = group.create_dataset<double>("dataset_name", dimensions);
* An HDF5 file can be opened/created with serial (one single process) or
* MPI support (several processes access the same HDF5 file).
* File::File(const std::string &, const FileAccessMode)
- * opens/creates a HDF5 file for serial operations.
+ * opens/creates an HDF5 file for serial operations.
* File::File(const std::string &, const FileAccessMode, const MPI_Comm)
* creates or opens an HDF5 file in parallel using MPI. The HDF5 calls that
* modify the structure of the file are always collective, whereas writing
* }
* @endcode
*
- * ## Query the I/O mode that HDF5 used on the last parallel I/O call
+ * ## Query the I/O mode that HDF5 used in the last parallel I/O call
* The default access mode in the deal.II's HDF5 C++ interface is collective
* which is typically faster since it allows MPI to do more optimizations. In
* some cases, such as when there is type conversion, the HDF5 library can
* In cases where maximum performance is a requirement, it is important to
* make sure that all MPI read/write operations are collective. The HDF5 library
* provides API routines that can be used after the read/write I/O operations to
- * query the I/O mode. If DataSet::query_io_mode() is set to True, then after
+ * query the I/O mode. If DataSet::query_io_mode is True, then after
* every read/write operation the deal.II's HDF5 interface calls the routines
* [H5Pget_mpio_actual_io_mode()](https://support.hdfgroup.org/HDF5/doc/RM/RM_H5P.html#Property-GetMpioActualIoMode)
* and
* [H5Pget_mpio_no_collective_cause()](https://support.hdfgroup.org/HDF5/doc/RM/RM_H5P.html#Property-GetMpioNoCollectiveCause).
- * The results are stored in DataSet::io_mode(),
- * DataSet::local_no_collective_cause() and
- * DataSet::get_global_no_collective_cause(). We suggest to query the I/O mode
+ * The results are stored in DataSet::io_mode, DataSet::local_no_collective_cause
+ * and DataSet::get_global_no_collective_cause. We suggest to query the I/O mode
* only in Debug mode because it requires calling additional HDF5 routines.
*
* The following code can be used to query the I/O method.
* @code
* auto dataset = group.create_dataset<double>("name", dimensions);
* #ifdef DEBUG
- * dataset.query_io_mode(true);
+ * dataset.set_query_io_mode(true);
* #endif
*
* if (Utilities::MPI::this_mpi_process(mpi_communicator) == 0)
* dataset.write_none<double>();
* }
*
- * if(dataset.query_io_mode()){
+ * if(dataset.get_query_io_mode()){
* pcout << "IO mode: " << dataset.io_mode() << std::endl;
* pcout << "Local no collective cause: "
* << dataset.local_no_collective_cause() << std::endl;
* Local no collective cause: H5D_MPIO_COLLECTIVE
* Global no collective cause: H5D_MPIO_COLLECTIVE
* @endcode
- * See DataSet::io_mode(), DataSet::local_no_collective_cause() and
+ * See DataSet::get_io_mode(), DataSet::get_local_no_collective_cause() and
* DataSet::get_global_no_collective_cause() for all the possible return
* codes.
*
* stored as HDF5 compound datatypes compatible with
* [h5py](https://www.h5py.org/) and [numpy](http://www.numpy.org/).
*
- * This python script writes the parameters for a deal.II simulation:
+ * The following python script writes the parameters for a deal.II simulation:
* ~~~~~~~~~~~~~{.py}
* h5_file = h5py.File('simulation.hdf5','w')
* data = h5_file.create_group('data')
public:
/**
- * Reads data of the dataset.
+ * Reads all the data of the dataset.
*
* Datatype conversion takes place at the time of the read operation and is
* automatic. See the <a
* Value | Meaning
* ------------------------------ | -------
* H5D_MPIO_NO_COLLECTIVE | No collective I/O was performed. Collective I/O was not requested or collective I/O isn't possible on this dataset.
- * H5D_MPIO_CHUNK_INDEPENDENT | HDF5 performed one the chunk collective optimization schemes and each chunk was accessed independently.
- * H5D_MPIO_CHUNK_COLLECTIVE | HDF5 performed one the chunk collective optimization schemes and each chunk was accessed collectively.
- * H5D_MPIO_CHUNK_MIXED | HDF5 performed one the chunk collective optimization schemes and some chunks were accessed independently, some collectively.
+ * H5D_MPIO_CHUNK_INDEPENDENT | HDF5 performed chunk collective optimization schemes and each chunk was accessed independently.
+ * H5D_MPIO_CHUNK_COLLECTIVE | HDF5 performed chunk collective optimization and each chunk was accessed collectively.
+ * H5D_MPIO_CHUNK_MIXED | HDF5 performed chunk collective optimization and some chunks were accessed independently, some collectively.
* H5D_MPIO_CONTIGUOUS_COLLECTIVE | Collective I/O was performed on a contiguous dataset.
*/
std::string
* Value | Meaning
* ------------------------------ | -------
* H5D_MPIO_NO_COLLECTIVE | No collective I/O was performed. Collective I/O was not requested or collective I/O isn't possible on this dataset.
- * H5D_MPIO_CHUNK_INDEPENDENT | HDF5 performed one the chunk collective optimization schemes and each chunk was accessed independently.
- * H5D_MPIO_CHUNK_COLLECTIVE | HDF5 performed one the chunk collective optimization schemes and each chunk was accessed collectively.
- * H5D_MPIO_CHUNK_MIXED | HDF5 performed one the chunk collective optimization schemes and some chunks were accessed independently, some collectively.
+ * H5D_MPIO_CHUNK_INDEPENDENT | HDF5 performed chunk collective optimization and each chunk was accessed independently.
+ * H5D_MPIO_CHUNK_COLLECTIVE | HDF5 performed chunk collective optimization and each chunk was accessed collectively.
+ * H5D_MPIO_CHUNK_MIXED | HDF5 performed chunk collective optimization and some chunks were accessed independently, some collectively.
* H5D_MPIO_CONTIGUOUS_COLLECTIVE | Collective I/O was performed on a contiguous dataset.
*/
H5D_mpio_actual_io_mode_t
};
/**
- * Creates or opens a HDF5 file for serial operations. This call does not
- * require MPI support. It creates or opens a HDF5 file depending on the
+ * Creates or opens an HDF5 file for serial operations. This call does not
+ * require MPI support. It creates or opens an HDF5 file depending on the
* value of @p mode.
*/
File(const std::string &name, const FileAccessMode mode);
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