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Re: [ESPResSo-users] Espresso input/output with Python

From: Kai Szuttor
Subject: Re: [ESPResSo-users] Espresso input/output with Python
Date: Fri, 23 Dec 2016 09:51:24 +0100
User-agent: Mutt/1.5.24 (2015-08-30)

Hi Michael,

please use the python branch if you want the latest features of the
python interface. There is an in-core implementation of the hdf5 format
which is documented and also has a sample script.
Please keep in mind that you have to install the hdf5-plugin for VMD
available on github in order to be able to read the written h5 files of

As far as I know the imd stuff is not ported and won't be ported to
python, instead we have an openGL and mayavi visualization (also
available in the python branch).


On Thu, Dec 22, 2016 at 04:46:25PM -0600, Michael Winokur wrote:
>    Hello,
>    I am starting to make sure I can use some basic functions and it seems
>    that the best way at present to transfer data to VMD is by the hdf5
>    read/write functions.A  I've been trying to get to work but
>    this sample file generates an error message:A 
>    Traceback (most recent call last):
>    A  File "<stdin>", line 35, in <module>
>    A  File "espressomd/h5md.pyx", line 247, in
>    espressomd.h5md.write_to_h5.pos
> (/home/winokur/Espresso/espresso-master/build/src/python/espressomd/h5md.cpp:7376)
>    AttributeError: 'System' object has no attribute 'n_part'
>    My version of Espresso is from the "master" git download.A 
>    Also, will the imd communication protocol be ported to Python?
>    Thanks,
>    Michael

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