[gmx-developers] Writing TNG with libtng_io

[Jonathan Barnoud]

Dear all,

With other developers of MDAnalysis, we are working on a python wrapper 
for the TNG library. While it is aimed at being used in MDAnalysis, this 
wrapper is written to be used standalone. More details can be found at 
<http://www.mdanalysis.org/pytng/>.

I am working on the writing of a basic TNG file. I want to be able to 
write particle positions  and a box shape for each frame. Each frame can 
have an arbitrary time attached to it. I did manage to do this in this 
pull request: <https://github.com/MDAnalysis/pytng/pull/18>, and in this 
minimal example jupyter notebook: 
<https://gist.github.com/jbarnoud/b8f750f116b76aba1b205babc001b569>. 
Both cases are written in cython rather than C, but they call the same 
functions from the tng_io library that a C program would.

There are a few things I am not completely sure about, though.

1. When I write the box shape with `tng_util_box_shape_write` or 
`tng_util_box_shape_with_time_write`, I do not manage to read it back 
with gromacs. Both 'gmx check' and 'gmx dump' fail to read the box with 
the following message:

     TNG library: Cannot uncompress data block. 
/home/jon/src/gromacs-2016.3/src/external/tng_io/src/lib/tng_io.c:5298

I did solve the problem by using `tng_util_generic_write` (or its 
`with_time` equivalent) and by setting the compression to 
`TNG_UNCOMPRESSED`.

Does gromacs support the TNG_GZIP_COMPRESSION that is the default for 
the high level `tng_util_box_shape_write` function? If so, what should I 
do to have it working?

2. I write an arbitrary time with each frame. The time is arbitrary in 
the sense that I do not know before hand what is the time that the user 
of the library will provide for the frame, and that the time difference 
between two consecutive frames do not have to be constant (nor even 
positive). I managed this by setting the number of frames per frame set 
to 1, and to set the time per frame to 0.

Is it possible to have the arbitrary time with more than one frame per 
frame set? I did get some results by setting the time per frame for each 
frame using the time difference with the previous frame, but I got some 
strange behaviors when the difference was 0; and 
`tng_time_per_frame_set` refuses negative values.

Also, I noticed that all the `tng_util_*_with_time_write` functions 
expect the time to be expressed in seconds, while 
`tng_time_per_frame_set` expects picoseconds. Is there a reason for this 
discrepancy?

Thank you for any insight you may provide,
Jonathan Barnoud

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