Adding animate method to Trajectory

[prince-mathews]

• Within the ´animate´ method inside the Trajectory class, it wasn't possible to include ´stride´, ´atom_indices´, ´snapshot_indices´ or ´repeat´ arguments.

[coveralls]

Pull Request Test Coverage Report for Build 3401805185

• 13 of 31 (41.94%) changed or added relevant lines in 2 files are covered.
• 1 unchanged line in 1 file lost coverage.
• Overall coverage increased (+9.0e**-05%**) to 68.647%

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Changes Missing Coverage	Covered Lines	Changed/Added Lines	%
pyiron_atomistics/atomistics/job/atomistic.py	1	4	25.0%
pyiron_atomistics/atomistics/structure/has_structure.py	12	27	44.44%

Files with Coverage Reduction	New Missed Lines	%
pyiron_atomistics/atomistics/job/atomistic.py	1	75.6%

Totals
Change from base Build 3361607611:	9.0e-05%
Covered Lines:	12086
Relevant Lines:	17606

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💛 - Coveralls

[pmrv]

Looks good to me, thanks!

[pmrv]

You had also code for the creation of a Trajectory from a list of structures, right? Can you add that as well as a method to Trajectory? Something like

class Trajectory:
  ...
  @classmethod
  def from_structure_list(cls, structures):
     # somehow get all positions, etc. from all structures
     return cls(positions, ...)

[prince-mathews]

You had also code for the creation of a Trajectory from a list of structures, right? Can you add that as well as a method to Trajectory? Something like

class Trajectory:
  ...
  @classmethod
  def from_structure_list(cls, structures):
     # somehow get all positions, etc. from all structures
     return cls(positions, ...)

Isn't this something the Trajectory class does by itself?
I don't have a code, I just provide the Trajectory class the initial structure, positions of the structures I want to see in the trajectory and the Trajectory is created by the class itself.

[pmrv]

Mh, I was thinking really turning a list of Atoms objects into a trajectory. But I remember now that the Trajectory class only works with "canonical" structures (equal number of particles everywhere). I'll add some stuff to this branch.

[pmrv]

I've added some code to move animate over to HasStructure. That means that a lot more jobs can now be animated (StructureContainer/TrainingContainer/StructureStorage/TrainingStorage/etc.).