[WIP] First try at TNG writing #18
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jbarnoud
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## master #18 +/- ##
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- Coverage 75.92% 60.18% -15.74%
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Files 2 2
Lines 162 211 +49
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+ Hits 123 127 +4
- Misses 39 84 +45
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pytng/pytng.pyx
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| @@ -264,6 +331,64 @@ cdef class TNGFile: | |||
| self.step += 1 | |||
| return TNGFrame(xyz, time, self.step - 1, box) | |||
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| def _init_first_frame_write(self, int64_t n_atoms, | |||
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I don't like such implicit methods. Please rather make it explicit and fail in the write method if no header information was supplied.
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It is going to disappear. See bellow.
pytng/pytng.pyx
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| ok = tng_util_pos_write_interval_set(self._traj, 1) | ||
| if_not_ok(ok, 'Could not set position write interval') | ||
| ok = tng_util_box_shape_write_interval_set(self._traj, 1) |
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It seems that the library has a mechanism in place to skip some frames. From what I understand, you can call the write methods for every frame, but only every N will actually be written. These methods tell the library to write all the frames.
I just tried without and it works (previous iterations on the code didn't). So I will remove these 4 lines and move the rest of the method in write.
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Finally, this is needed. It seems that the interval is not 1 per default. As a result, not setting it (or setting it to anything else than 1) leads to only part of the frames being written.
| ok = tng_util_pos_write(self._traj, self.step, &xyz[0, 0]) | ||
| else: | ||
| ok = tng_util_pos_with_time_write(self._traj, self.step, | ||
| time, &xyz[0, 0]) |
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why write the time twice? That seems strange. Maybe we need to ask in the gromacs devel list
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I do not know. But I am also not sure it is the way to do. I am still trying to figure things out.
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I fixed the writing of the time. The time per frame has to be set for the time to be written. I also fixed the error I had when reading the box with gromacs. By default the library compresses the box using the gzip algorithm which seems to cause the problem; not compressing the box fixes it. The reading of the box seems to be broken, though. Pytng reads the first box for all the frames, while gromacs reads it right. I'll write an issue when I'll have a bit of time to reproduce the issue. Here is the notebook I use to test my experiments on pytng: https://gist.github.com/jbarnoud/fd560a13162307f6f9e12df942ba0ca1. Here is an other notebook I use to have just the minimum logic necessary: https://gist.github.com/jbarnoud/b8f750f116b76aba1b205babc001b569. I wrote this second notebook with the idea of asking a few questions on the gromacs dev mailing list. I am curious about the gzip issue for the box; and there may be a better way to write the time. One constraint with the time is that I want to be able to write arbitrary time for each frame. This means that I have to use only one frame per frame set which results in larger files. Also, I constrain the number of atoms to be constant throughout the trajectory while there is no reason to do so regarding the format alone. There is a need to be able to set some flags before starting to write. I still need to think about the API. |
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I asked some clarifications on the gromacs mailing list. The thread is there: https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-developers/2017-July/009741.html. |
Adds a `write` method to the `TNGFile` class. At that point, this method
successfully writes the positions and the box shape. It tries to write
the time, but fails. It does not try to write velocities and forces yet,
nor does it ties to write the topology.
The written file can be read by pytng. It is also read by `gmx check`,
but yields 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
currently results in a segfault
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urgh I'm getting segfaults left and right when I currently try to write anything. |
With this change I'm reminding myself of that
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Fixed my own segfault. But we get a segfault in the garbage collection when I try to copy a trajectory with pytng. This only happens when I copy the positions. |
Adds a
writemethod to theTNGFileclass. At that point, this methodsuccessfully writes the positions and the box shape. It tries to write
the time, but fails. It does not try to write velocities and forces yet,
nor does it ties to write the topology.
The written file can be read by pytng. It is also read by
gmx check,but yields the following message:
This is my first time really writing cython, and I am not completely sure about what I am doing regarding the TNG library. Feel free to assume I am wring when reading the code.
Writing the topology will likely fall out of scope for this specific PR.