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Re: [ESPResSo-users] Writing and reading with H5MD


From: ICP
Subject: Re: [ESPResSo-users] Writing and reading with H5MD
Date: Wed, 1 Mar 2017 16:12:47 +0100

espresso is currently only able to write H5MD files. We currently dont plan to read those files in espresso but there is a python module called h5py with which you are able to read the trajectory into numpy arrays. It seems your userguide is not up to date. If you are using the development version of espresso please build the sphinx documentation via "make sphinx".

Kai Szuttor
Institute for Computational Physics
Universit├Ąt Stuttgart
Allmandring 3
Room 1.084
70569 Stuttgart, Germany
Phone:+49(0)711/685-67707

On 1 Mar 2017, at 14:46, Clemens Jochum <address@hidden> wrote:

Dear all,

according to the userguide initializing a H5MD file works as follows:

    from espressomd import h5md
    system = espressomd.system()
    h5 = h5md.h5md("File.h5",system)

However, the module "h5md" is not found by the pypresso interpreter. It is also stated that the sample script "h5md_WriteFile.py" shows the usage of H5MD files. However, that sample file does not exist.

According to a different sample script called "h5md.py", H5MD format can be used like this:

    from espressomd.io.writer import h5md
    h5_file = h5md.H5md(filename="sample.h5", write_pos=True, write_vel=True, ... )
    h5_file.write()

This works, but it is not stated anywhere how to read from the H5MD file. In particular, I want to load the particle coordinates to visualize some snapshots of my system's trajectory.

Does anyone know how to do that? Or can anyone point me towards literature, how to use the H5MD format properly in espresso?

Many thanks and best regards,

Clemens


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