PLUMED and Python

[Ondrej Marsalek]

Dear PLUMED developers,

I would like to use PLUMED from Python and would like to get your
input on the topic. Has any work been done in that direction? I see
that there is something for ASE and PLUMED 1.3, have there been any
updates for 2.x?

My tentative plan is to use Cython to wrap the C interface. I am very
much open to suggestions for alternatives. Would you be interested in
joining the work and/or in including the interface in PLUMED itself?

Thank you,
Ondrej

[Giovanni Bussi]

Hi Ondrej,

I am not aware of any attempt with PLUMED 2 + python.

You can either wrap C or C++ interface. They are basically equivalent, the only advantage of the C++ one is that it takes care of initialization and finalization in constructor/destructor, so it could be slightly more user friendly.

I have very little experience with python so I cannot suggest the best route.

Thanks!

Giovanni

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[davide branduardi]

Hi!

You might want to take inspiration from what Rosa Bulo did for plumed1, there is still her wrapper in the old package plumed1.3 that was meant to work with ASE.

Ciao

D

[Ondrej Marsalek]

On Wed, Sep 24, 2014 at 10:25 AM, Giovanni Bussi
<giovann...@gmail.com> wrote:
> Hi Ondrej,
>
> I am not aware of any attempt with PLUMED 2 + python.
>
> You can either wrap C or C++ interface. They are basically equivalent, the
> only advantage of the C++ one is that it takes care of initialization and
> finalization in constructor/destructor, so it could be slightly more user
> friendly.

Seeing that the C++ API is a wrapper over the C one anyway, I will try
to do basically the same in Python.

I will post here once I have something to share.

Ondrej

[Ondrej Marsalek]

I ended up using ctypes. Here is the pull request:

https://github.com/plumed/plumed2/pull/109

where I would like to ask for feedback on the code. It needs some
testing and polishing (including documentation), but the overall
structure is there. I hope that once it's finished, it can be included
in the code base.

Ondrej