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Re: [ESPResSo-users] H5MD file in espressomd

From: Pierre de Buyl
Subject: Re: [ESPResSo-users] H5MD file in espressomd
Date: Tue, 9 Apr 2019 14:22:39 +0200
User-agent: Mutt/1.5.23 (2014-03-12)

Dear Jiaxing,

This means that you have not built espressomd with the HDF5 library. When you
configure the code with cmake, it will list features that are found and if HDF5
is not found, H5MD will not be included. A more detailed error message was added
to espressomd recently.

To solve the problem, install HDF5 (parallel version) and re-run cmake and make.



On Tue, Apr 09, 2019 at 03:58:07PM +0800, Jiaxing Yuan wrote:
> Dear all,
> I am considering writing system configuration into the H5MD file. I use the
> following command lines as explained in the document:
> from import h5md
> ........#system setup
> h5 = h5md.H5md(filename="trajectory.h5", write_pos=True, write_vel=True)
> for i in range(100000):
>     h5.write()
> However, I encounter the following error:
> ValueError: Class 'ScriptInterface::Writer::H5mdScript' not found.
> I wonder if this is because my command lines are wrong or due to the
> missing modules in my compiled espressomd?
> Best,
> Jiaxing

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