[gmx-developers] Help needed with tng_io library
yesint4 at yahoo.com
Thu Aug 7 12:19:30 CEST 2014
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.
n1 = 10761
n2 = 1086
The correct number of frames is 1086.
What on Earth is returned from tng_num_frames_get()?
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
bool stat = true;
stat = tng_util_pos_read_range(trj,n,n, &ptr, &len);
This always stops at n=10 (why?!), while the number of frames is 1086! What I'm doing wrong here?
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.
The test tng file is here: https://drive.google.com/file/d/0Bx_ng_72VH8BQlFsTGJOVC1oMjQ/edit?usp=sharing
Any help is appreciated!
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