Trajectory¶

Analysis almost never cares about a single snapshot. How do you hold many frames in time order without inventing a second data model?

A Trajectory is an eager, ordered sequence of Frame objects. Each element is still one frame — blocks, metadata, optional box. Time stacks snapshots; it does not replace them.

What it is not: a lazy file cursor. Seekable readers live under molpy.io / molrs trajectory readers; construct a Trajectory when you want an in-memory sequence with len, indexing, and slicing.

Building a trajectory from a list¶

Pass a list (or any iterable that is materialised on construction):

import molpy as mp

frames = []
for i in range(5):
    f = mp.Frame()
    f["atoms"] = mp.Block({"x": [float(i)], "y": [0.0], "z": [0.0]})
    f.meta = {"time": i * 10.0}
    frames.append(f)

traj = mp.Trajectory(frames)
print(len(traj))  # 5
print(traj[0]["atoms"]["x"])  # [0.]

Iterables are materialized¶

The constructor accepts any iterable, but materializes it immediately into the native container. Use molpy.io.read_lammps_trajectory or molpy.io.read_xyz_trajectory when data must remain lazy and seekable on disk.

def make_frames(n):
    for i in range(n):
        f = mp.Frame()
        f["atoms"] = mp.Block({"x": [float(i)], "y": [0.0], "z": [0.0]})
        f.meta = {"time": i * 0.5}
        yield f


traj_from_iterable = mp.Trajectory(make_frames(1000))
print(len(traj_from_iterable))  # 1000

The generator is consumed during construction. File readers avoid that eager materialization.

Slicing and indexing¶

For list-backed trajectories, standard Python indexing and slicing work as expected. Indexing returns a Frame; slicing returns a new Trajectory.

first_two = traj[:2]
print(len(first_two))  # 2

strided = traj[::2]
print(len(strided))  # 3

last = traj[-1]
print(last.meta["time"])  # 40.0

Slicing with a stride (traj[::n]) is a convenient way to downsample for quick inspection.

Transforms with map¶

map applies a function to every frame immediately and returns a new trajectory. The original frames are unchanged.

def shift_x(frame):
    new = mp.Frame()
    x = frame["atoms"]["x"]
    new["atoms"] = mp.Block(
        {
            "x": x + 10.0,
            "y": frame["atoms"]["y"],
            "z": frame["atoms"]["z"],
        }
    )
    new.meta = frame.meta
    return new


shifted = traj.map(shift_x)

shifted_list = list(shifted)
print(shifted_list[0]["atoms"]["x"])  # [10.]
print(traj[0]["atoms"]["x"])  # [0.] — original unchanged

When to use Trajectory¶

Use Trajectory when time is part of the scientific question — following an observable over many snapshots, computing time correlations, or iterating through an I/O stream. If you only need a single state, Frame remains the right abstraction.

The trajectory does not invent a new kind of system state. It keeps frame meaning intact while adding temporal ordering. That is the entire point: one structure, many times.