Tutorial¶

Butane Simulation¶

In this tutorial we will use the GeometricMD package to compute a transition path for a butane molecule. The files for the simulation, along with the scripts, are available in the example directory of the GeometricMD package.

Single Process¶

from geometricmd.curve_shorten import compute_trajectory
from geometricmd.geometry import Curve

# Import ASE read function if getting molecule data from compatible file
from ase.io import read

# This example uses the EMT calculator for simplicity
from ase.calculators.emt import EMT

# Read in the molecule data for the initial point
start_point = read('x0.xyz')

# In order to compute the potential energy a calculator must be attached to the start atoms object
start_point.set_calculator(EMT())

# Read in the molecule data for the final point
end_point = read('xN.xyz')

# Create a GeometricMD curve object to represent the trajectory.
traj = Curve(start_point, end_point, 12, 1E+03)

# Perform the molecular simulation.
compute_trajectory(traj, 10, 1E+03, 0.01, 'Butane', {'processes': 1})

Multiple Processes¶

from geometricmd.curve_shorten import compute_trajectory
from geometricmd.geometry import Curve
from multiprocessing import cpu_count

# Import ASE read function if getting molecule data from compatible file
from ase.io import read

# This example uses the EMT calculator for simplicity
from ase.calculators.emt import EMT

# Read in the molecule data for the initial point
start_point = read('x0.xyz')

# In order to compute the potential energy a calculator must be attached to the start atoms object
start_point.set_calculator(EMT())

# Read in the molecule data for the final point
end_point = read('xN.xyz')

# Create a GeometricMD curve object to represent the trajectory.
traj = Curve(start_point, end_point, 12, 1E+03)

# Perform the molecular simulation.
compute_trajectory(traj, 10, 1E+03, 0.01, 'Butane', {'processes': (cpu_count()-1)})