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Re: H5md nat available

From: Jean-Noël Grad
Subject: Re: H5md nat available
Date: Fri, 6 Mar 2020 21:47:24 +0100
User-agent: Mozilla/5.0 (X11; Linux i686; rv:68.0) Gecko/20100101 Thunderbird/68.5.0

Dear Ahmad,

We've updated the user guide to make it clear how to enable feature H5MD (commit bc6a7f2 in


On 3/6/20 11:19 AM, Jean-Noël Grad wrote:
Dear Ahmad,

You'll need to recompile espresso using the CMake flag -DWITH_HDF5=ON:


On 3/6/20 10:59 AM, Ahmad Reza Motezakker wrote:
Dear All,

I have been trying to save trajectories data with h5md, but I face this error:


--------------------------------------------------------------------------- RuntimeError                               Traceback (most recent call last)
<ipython-input-11-23429f2149d1>  in<module>
1  #h5md file for trajectories
----> 2h5=  h5md.H5md(filename="trajectory.h5",  write_pos=True, write_vel=True,  write_force=True)

~/Desktop/espresso/build/src/python/espressomd/io/writer/ in__init__(self, *args, **kwargs)
27 28          def  __init__(self,  *args,  **kwargs):
---> 29raise  RuntimeError("H5md not available.")
30  else:
31      class  H5md:

RuntimeError: H5md not available.

I have installed hdf5 but it is still not working. I really appreciate that if you could help me.

Best Regards,
Ahmad Reza

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