VelocityVerlet

	VelocityVerlet
FixStrain	NVTBerendsen

Name

VelocityVerlet — The MD method implementing Velocity Verlet dynamics.

Synopsis

Namespace: NanoLanguage

VelocityVerlet(
initial_velocity,
time_step
)

Description

Constructor for the MD method implementing Velocity Verlet dynamics.

VelocityVerlet Arguments

initial_velocity

A class that implements a distribution of initial velocities for the particles in the MD simulation.

Type: An instance of a class that defines the initial momenta - e.g. MaxwellBoltzmannDistribution.

Default:


          MaxwellBoltzmannDistribution()

time_step

The time-step interval used in the MD simulation.

Type: A unit of type Time.

Default:


          1.0e-15 seconds (1 femtosecond)

Usage Examples

Perform a micro-canonical molecular dynamics run of 10 steps on a water molecule, using the Verlet Velocity MD method:

# Define elements
elements = [Oxygen, Hydrogen, Hydrogen]

# Define coordinates
cartesian_coordinates = [[  0.0,  -1.70000000e-05,   1.20198000e-01],
                         [  0.0,   7.59572000e-01,  -4.86714000e-01],
                         [  0.0,  -7.59606000e-01,  -4.86721000e-01]]*Angstrom

# Set up configuration
molecule_configuration = MoleculeConfiguration(
    elements=elements,
    cartesian_coordinates=cartesian_coordinates
    )

# Define a calculator
molecule_configuration.setCalculator(LCAOCalculator())

# Perform MD
md_configuration = MolecularDynamics(molecule_configuration,
                                     log_filename='velocityverlet.nc',
                                     method=VelocityVerlet(),
                                     steps=10)

# Save the final configuration
nlsave('velocityverlet.nc', md_configuration)

velocityverlet.py

Notes

Uses the Verlet algorithm to perform a mikro-canonical classical molecular-dynamics simulation, i.e. the energy of the system is constant during the simulation.


FixStrain		NVTBerendsen