Tutorial 1 - Reading data¶

The HISTORY, ARCHIVE and CONFIG classes expects two things, the filename of the history file and a list of atoms to read. They will return a polypy.read.Trajectory object, which stores the the atom labels (Trajectory.atom_list), datatype (Trajectory.datatype), cartesian coordinates (Trajectory.cartesian_coordinates), fractiona coordinates (Trajectory.fractional_coordinates), reciprocal lattice vectors (Trajectory.reciprocal_lv), lattice vectors (Trajectory.lv) cell lengths (Trajectory.cell_lengths), total atoms in the file (Trajectory.atoms_in_history), timesteps (Trajectory.timesteps), total atoms per timestep (Trajectory.total_atoms).

HISTORY Files¶

from polypy import read as rd

history = rd.History("../example_data/HISTORY_CaF2", ["CA", "F"])

print(history.trajectory.fractional_trajectory)

[[0.5170937  0.51658126 0.51643485]
 [0.51658126 0.61669107 0.61654466]
 [0.61669107 0.51658126 0.61691069]
 ...
 [0.46866197 0.25395423 0.58485915]
 [0.37035211 0.58795775 0.45221831]
 [0.36552817 0.48637324 0.17484859]]

print(history.trajectory.timesteps)

print(history.trajectory.atoms_in_history)

print(history.trajectory.total_atoms)

It is often necessary to remove the equilibriation timesteps from the simulation. This can be accomlished with the remove_initial_timesteps method to remove timesteps at the start of the simulation and the remove_final_timesteps, to remove timesteps at the end of the simulation.

new_history = history.trajectory.remove_initial_timesteps(10)
print(new_history.timesteps)

new_history = new_history.remove_final_timesteps(10)
print(new_history.timesteps)

It is possible to return the trajectory for a single timestep within the history file or to return the trajectory for a single atom.

config_ca = history.trajectory.get_atom("CA")

print(config_ca.fractional_trajectory)

[[0.5170937  0.51658126 0.51643485]
 [0.51658126 0.61669107 0.61654466]
 [0.61669107 0.51658126 0.61691069]
 ...
 [0.31458099 0.41869718 0.41764085]
 [0.42742958 0.32461268 0.42507042]
 [0.42485915 0.42183099 0.31564789]]

config_1 = history.trajectory.get_config(1)

print(config_1.fractional_trajectory)

[[0.53227339 0.51016082 0.50950292]
 [0.52116228 0.62894737 0.61761696]
 [0.62240497 0.50526316 0.6056652 ]
 ...
 [0.39444444 0.44974415 0.45102339]
 [0.45599415 0.37865497 0.39890351]
 [0.36343202 0.49309211 0.3690424 ]]

CONFIG Files¶

config = rd.Config("../example_data/CONFIG", ["CA", "F"])

print(config.trajectory.fractional_trajectory)

[[0.51666667 0.51666667 0.51666667]
 [0.51666667 0.61666667 0.61666667]
 [0.61666667 0.51666667 0.61666667]
 ...
 [0.36666667 0.46666667 0.46666667]
 [0.46666667 0.36666667 0.36666667]
 [0.36666667 0.46666667 0.36666667]]

DLMONTE¶

archive = rd.Archive("../example_data/ARCHIVE_Short", ["AL"])

print(archive.trajectory.timesteps)