Issue with "Trajectory" when using partial dump (subset of atoms)

dynasor
1

Dear users,

I’m currently working with a LAMMPS trajectory that contains only a subset of atoms (specifically, only carbon atoms were dumped from a larger system of 28,800 atoms). The dumped trajectory includes 9,600 C atoms, whose original LAMMPS atom IDs range up to [1, 4,7, … 28,798].

When I try to load this trajectory using:

trajectory_filename = 'dynasor.posvel'
traj = Trajectory(trajectory_filename,
                  trajectory_format='lammps_internal', frame_stop=500000)

I get the following error:

IndexError: index 9600 is out of bounds for axis 0 with size 9600

So, is there a way to tell dynasor to treat the trajectory as self-contained, ignoring global atom ID expectations?

or do I have to dump all atoms and only uses specific atoms that I want to calculate?

Any advice or clarification would be really appreciated.

Thanks a lot!

2

Hi,
Could you provide the full error message to better understand where in dynasor its coming from?
You could also try to use the mdanalysis reader which should be able to parse lammps trajectories and see if that works.

3

Sorry for late response,

Below is the error message.

---------------------------------------------------------------------------
IndexError                                Traceback (most recent call last)
Cell In[45], line 2
      1 trajectory_filename = 'dynasor.posvel'
----> 2 traj = Trajectory(trajectory_filename,
      3                   trajectory_format='lammps_internal', frame_stop=500000, atomic_indices = atomic_indice)

File ~\anaconda3\Lib\site-packages\dynasor\trajectory\trajectory.py:106, in Trajectory.__init__(self, filename, trajectory_format, atomic_indices, length_unit, time_unit, frame_start, frame_stop, frame_step)
    104 # Get two frames to set cell etc.
    105 frame0 = next(self._reader_obj)
--> 106 frame1 = next(self._reader_obj)
    107 self._cell = frame0.cell
    108 self._n_atoms = frame0.n_atoms

File ~\anaconda3\Lib\site-packages\dynasor\trajectory\lammps_trajectory_reader.py:191, in LammpsTrajectoryReader.__next__(self)
    188     raise StopIteration
    190 if self._first_called:
--> 191     self._get_next()
    192 else:
    193     self._get_first()

File ~\anaconda3\Lib\site-packages\dynasor\trajectory\lammps_trajectory_reader.py:175, in LammpsTrajectoryReader._get_next(self)
    173     self._x[II] = data[:, self._x_I]
    174 else:
--> 175     self._x[II] = self._x_map(data[:, self._x_I])
    176 if self._v_I is not None:
    177     self._v[II] = data[:, self._v_I]

IndexError: index 9600 is out of bounds for axis 0 with size 9600

Also, I have attached a part of dump file.
dynasor.txt (14.1 KB)