Saved Run

from fys2160_md import Run, System, MDSimulation
saved = Run.load("runs/gas")

Loading a run reads files and does not start a simulation.

Member	Meaning
Run.load(path)	Read one saved run folder
Run.find(directory="runs")	List recognized metadata folders
run.path	Resolved directory path
run.metadata	Configuration, units, completion status and output settings
run.thermo	Pandas DataFrame read from thermo.csv
run.iter_frames()	Stream saved frame dictionaries one at a time
run.load_frames()	Stack all frames in memory; raises if none were saved
run.view(...)	Self-contained HTML trajectory player for notebook output

Replay

saved.view(max_frames=150, max_atoms=1500, projection="orthographic", zoom=1.0)

The player is drawn with OMOVI when it can be loaded (see the live view notes); renderer="basic" selects the built-in renderer. The default samples at most 150 saved frames and 3000 atoms; full recorded data remain on disk. projection is orthographic or perspective; initial zoom must be between 0.25 and 3. With OMOVI, zoom 1 shows the whole box and larger values magnify its centre. Camera controls and playback work in exported HTML. This needs WebGL 2, but no Python kernel, remote scripts or simulation server.

Recorded quantities

Group	Columns
Clock	step, time
State	temperature, pressure, volume, density, atom_density
Energy	kinetic_energy, potential_energy, total_energy
Response	compressibility_factor, enthalpy, heat_added
Pressure control	barostat_energy, extended_enthalpy

Energies are totals. Divide by N for energy per atom or molecule. density uses that same particle count; atom_density always counts atoms. For NPH/NPT, enthalpy uses target pressure; otherwise it uses instantaneous pressure. See physics conventions for precise definitions.

Files on disk

runs/gas/
  metadata.json
  thermo.csv
  checkpoint.npz
  frames/0000000.npz
  frames/0000001.npz
  ...

Frame arrays include positions, unwrapped coordinates, velocities, box, step and time. A final checkpoint is kept even when trajectory_every=None.

continued = sim.run(saved.state, steps=1000, storage_name="continued")

A Run refers to a directory, not an immutable copy. Replacing that storage name also changes what previously created Run objects read.

Plot the recorded data

import matplotlib.pyplot as plt

result = Run.load("runs/gas")
data = result.thermo
plt.figure(figsize=(8, 5))
plt.subplot(2, 1, 1)
plt.plot(data.time, data.temperature)
plt.ylabel("Temperature")
plt.subplot(2, 1, 2)
plt.plot(data.time, data.pressure)
plt.ylabel("Pressure")
plt.xlabel("Time")
plt.tight_layout()
plt.show()

thermo is a pandas DataFrame: read columns, calculate means and use ordinary NumPy, pandas and Matplotlib tools for your analysis.

For an isolated gravity run, view(particle_radius=0.035) sets a display-only marker radius; it does not change the force. The default is 0.035 for gravity, and half the atom's sigma for LJ. Open-system playback has no box edges or position wrapping. The camera can omit distant particles, but they remain in saved data and in the force/energy calculation.