Add support for HALMD files (H5MD)

[kain88-de]

HALMD is an MD code that uses HDF5 for it's file format. The C++ wrapper they have written for it is modeled on h5py. So a reader using H5py should be relatively easy to write.

[orbeckst]

Can we use the wrapper directly (code-wise and license-wise)?
You can probably take off the proposal tag and just add help wanted --- I think that we generally encourage adding new formats, especially some that might not be ubiquitous (yet). Do you have test trajectories and/or access to the HALMD?

[kain88-de]

I would write our own wrapper the C++ code relies a lot on templates. I should be able to organize a short trajectory.

[orbeckst]

We just need someone to do it ;-)

[KaiSzuttor]

In that context I would prefer to implement a H5MD reader (and writer). It's a format convention that uses hdf5 (used by LAMMPS and ESPResSo ). Therefore the h5py module could be used to implement such a reader. Is anybody working on such a reader or could anybody give me some hints how to best start to implement such a reader?

[richardjgowers]

Any new format is always a good addition, nobody is looking at h5md yet.

I should really write a wiki page on writing a Reader, but here goes...

All trajectory information is stored inside a Timestep (ts) object, (mda.coordinates.base.Timestep). Atoms etc then point to the arrays contained inside the ts.

The Reader is responsible for filling the contents of ts. It should inherit from mda.coordinates.base.Reader then define:

• __init__ to prepare things, allocate a ts and read the 0th frame
• _read_next_frame read the next frame (filling ts and returning it)
• _read_frame skip to frame i and read it (by filling ts) and then return ts

Most other stuff (iteration etc) is defined in the base class, so you just need to define those hooks. I think PDB is a fairly clear implementation of this:
https://github.com/MDAnalysis/mdanalysis/blob/develop/package/MDAnalysis/coordinates/PDB.py

Readers are added automatically into the list of known readers once you define the format attribute in their class, so format='H5MD' would make any files with a .h5md suffix get passed to that Reader. So once you've imported the class somewhere (either inside the package or outside), you could load a mda.Universe like this:

import MDAnalysis as mda
u = mda.Universe('myfile.pdb','myfile.h5md')

So the signature is (topology, trajectory), you can use xyz/gro/pdb/etc as a topology, not sure what you've got.

There is already a python interface to h5md, maybe this would be useful as a start:
https://github.com/pdebuyl/pyh5md

Let me know if you need any more info!

[KaiSzuttor]

Thanks a lot for your comments, that is a good starting point. The h5md python package is actually not necessary in my opinion since it only ensures the format convention for the trajectories. I think we should stick to the more generic h5py package since development is more active on that package and we will have the respective dependency on one of those packages (in fact one more if we use pyh5md, since it depends on h5py itself). Whats your opinion on that?

[richardjgowers]

Yep, if you don't need it don't use it.

On Thu, 19 May 2016 09:27 Kai Szuttor, notifications@github.com wrote:

Thanks a lot for your comments, that is a good starting point. The h5md
python package is actually not necessary in my opinion since it only
ensures the format convention for the trajectories. I think we should stick
to the more generic h5py package since development is more active on that
package and we will have the respective dependency on one of those packages
(in fact one more if we use pyh5md, since it depends on h5py itself). Whats
your opinion on that?

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#762 (comment)

[orbeckst]

Nice intro, @richardjgowers! Why don't you just copy it to the wiki? ;-)

Am May 19, 2016 um 1:00 schrieb Richard Gowers notifications@github.com:

I should really write a wiki page on writing a Reader, but here goes..

[KaiSzuttor]

Can somebody quickly give me a hint on where i have to add new files to the build system in order its recognized as a package?

[kain88-de]

A python file? You can place it in 'MDAnalysis/coordinatesalong with the other files. You can then include it inMDAnalysis/coordinates/init.py` to load it automatically into the namespace with the other packages.

[jdetle]

Hi, in addition to what @kain88-de said, when you ran setup.py did you do a
developer installation?

On Tue, May 24, 2016 at 8:46 AM kain88-de notifications@github.com wrote:

A python file? You can place it in 'MDAnalysis/coordinatesalong with the
other files. You can then include it inMDAnalysis/coordinates/init.py`
to load it automatically into the namespace with the other packages.

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#762 (comment)

Have a wonderful day,
John J. Detlefs