[gmx-developers] Help needed with tng_io library

[Semen Esilevsky]

Dear Magnus,
Thank you very much for explanations!

So,  is there any boolet-proof  way of finding out how many position sets are in the trajectory? 


Another question is which function should I preferebly use to get the positions - tng_util_particle_data_next_frame_read() or tng_util_pos_read_range()? The later gives me an array of floats, which I need, but I suspect that it is much slower because of seeking for frame. Is it so?

I'm looking forward to see my stupid mistake, which leads to problems #2 and #3.

Regards,
Semen





On Friday, August 8, 2014 12:07 PM, Magnus Lundborg <magnus.lundborg at scilifelab.se> wrote:


>
>
>Hi Semen,
>
>I found some extra time, so I will try to clarify some things below.
>
>On 2014-08-07 12:16, Semen Esilevsky wrote:
>> Dear All,
>> I'm currently trying to add support for tng files to my code and I realised that I can't understand the logic of the library at all. I'm definetely doing something wrong, but can't figure out a mistake.
>> The tng code is got from the latest git. Test trajectory is generated by Gromacs 5.0.
>>
>>
>> I can open the tng file and can extract, for example, position exponential correctly, but after that...
>>
>>
>> Problem #1: getting number of frames.
>>
>> int64_t n1,n2;
>> tng_num_frames_get(trj, &n1);
>> tng_num_frame_sets_get(trj, &n2);
>>
>> This gets
>> n1 = 10761
>> n2 = 1086
>>
>> The correct number of frames is 1086.
>>
>> What on Earth is returned from tng_num_frames_get()?
>One thing that is slightly difficult with TNG is that different kinds of 
>data can be written at different intervals, e.g. it can have positions 
>written every 100th frame, forces every 200th frame, velocities every 
>250th frame etc. To make this a bit more graspable in GROMACS every md 
>step is considered a frame when writing the TNG file (it would be 
>possible to let the n steps between frames be the greatest common 
>denominator of the written data types as well). The default when writing 
>TNG from a GROMACS simulation is to keep 100 frames of the most 
>frequently written data in each frame set. When generating a TNG from 
>trjconv (like the file you provided) it is not as easy to predict what 
>data to expect and the output frequency of it. Therefore a frame set is 
>created every time data is written - this will probably be changed in 
>the future to facilitate more efficient compression from trjconv too.
>>
>> Problem #2: Reading past the end of file.
>>
>> stat = tng_util_particle_data_next_frame_read(trj, TNG_TRAJ_POSITIONS, &values,
>>                                                    &datatype, &frame, &physical_time);
>>
>> This function should return false when no more frames are available, right? It doesn't do this and reads forever returning garbage in values when called in a loop. stat is always true. How should I use it correctly to finish reading at the end of file?
>> Also concerning the strange thing with the number of frames and frame sets - what it reads actually each time?
>>
>> Problem #3: tng_util_pos_read_range() behaves insane
>>
>> int n=0;
>> bool stat = true;
>> while(stat){
>>      stat = tng_util_pos_read_range(trj,n,n, &ptr, &len);
>>      n++;
>> }
>>
>> This always stops at n=10 (why?!), while the number of frames is 1086! What I'm doing wrong here?
>I will have a look at this, and will try to give more details next week 
>when I've got more time.
>>
>> I've also tried VMD plugin from pre-release VMD 1.9.2. It is said that this plugin is contributed by Gromacs developers, so it should work in principle. It doesn't work because of the bug #2 - it reads forever beyond the end of file.
>This bug was discovered a few days after the release and is fixed in the 
>TNG library in the TNG repository. The fix is included in the 
>release-5-0 branch of GROMACS, but I don't think there has been any bug 
>fix release. I also think it will be fixed in the next VMD pre-release.
>>
>> The test tng file is here: https://drive.google.com/file/d/0Bx_ng_72VH8BQlFsTGJOVC1oMjQ/edit?usp=sharing
>>
>>
>> Any help is appreciated!
>I hope the answers help you at least a bit. Please tell me if anything 
>is unclear and I will try to explain it better.
>
>Kind Regards,
>
>Magnus
>
>>
>> Sincerely,
>> Semen
>>
>
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