From ffe19b5c8b20bcff03c10c7e6e79c0df77bd3e41 Mon Sep 17 00:00:00 2001 From: Jonas Landsgesell Date: Tue, 30 Oct 2018 12:58:27 +0100 Subject: [PATCH 1/2] fixes #2286 --- doc/sphinx/io.rst | 10 ++++++++++ 1 file changed, 10 insertions(+) diff --git a/doc/sphinx/io.rst b/doc/sphinx/io.rst index 9616fc45788..23617cc8e1a 100644 --- a/doc/sphinx/io.rst +++ b/doc/sphinx/io.rst @@ -250,6 +250,16 @@ call the H5md objects :meth:`espressomd.io.writer.h5md.H5md.write` method withou After the last write call, you have to call the ``close()`` method to remove the backup file and to close the datasets etc. +H5MD files can be read and modified with the python module h5py. For example all positions stored in the file called "h5mdfile.h5" can be read using + +.. code:: python + + import h5py + h5file = h5py.File("h5mdfile.h5", 'r') + positions = h5file['particles/atoms/position/value'] + +Further the files can be inspected with the GUI tool hdfview. + .. _Writing MPI-IO binary files: Writing MPI-IO binary files From 7b39030d8dbb31c00186b77d6a43a12df82a67ac Mon Sep 17 00:00:00 2001 From: Kai Szuttor <2150555+KaiSzuttor@users.noreply.github.com> Date: Tue, 30 Oct 2018 13:06:56 +0100 Subject: [PATCH 2/2] Mention the h5py documentation --- doc/sphinx/io.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/doc/sphinx/io.rst b/doc/sphinx/io.rst index 23617cc8e1a..c7faa9dd8ab 100644 --- a/doc/sphinx/io.rst +++ b/doc/sphinx/io.rst @@ -250,7 +250,7 @@ call the H5md objects :meth:`espressomd.io.writer.h5md.H5md.write` method withou After the last write call, you have to call the ``close()`` method to remove the backup file and to close the datasets etc. -H5MD files can be read and modified with the python module h5py. For example all positions stored in the file called "h5mdfile.h5" can be read using +H5MD files can be read and modified with the python module h5py (for documentation see `h5py `_). For example all positions stored in the file called "h5mdfile.h5" can be read using .. code:: python