MakeTrajectory

	MakeTrajectory
LocalDeviceDensityOfStates	OpticalSpectrum

Name

MakeTrajectory — Construct a trajectory sequence of configurations, from a given Nudged Elastic Band configuration, or a list of configurations.

Synopsis

Namespace: NanoLanguage

MakeTrajectory(
configuration_list,
analysis,
*args,
**kwargs
)

Description

Construct a trajectory sequence of configurations, from a given Nudged Elastic Band configuration, or a list of configurations.

MakeTrajectory Arguments

configuration_list

Either an explicit tuple or list of configurations, or a NudgedElasticBand configuration object.

Type: tuple/list of configurations or NudgedElasticBand.

analysis

The analysis class that will be applied across the configurations. If None, no analysis is applied.

Type: A supported Analysis class name - e.g. Forces.

Default:


          None

*args

Any unnamed arguments beyond the first two - these are not used, and the method will throw an exception on encountering any.

Type: All non-keyword arguments.

**kwargs

The dictionary of supplied keyword arguments that will be passed to the analysis class across configurations.

Type: All keyword arguments.

Usage Examples

Create a Trajectory object from a list of configurations.

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

# Define coordinates.
c0 = [[  0.00,   0.00,   0.12],
      [  0.00,   0.76,  -0.48],
      [  0.00,  -0.76,  -0.48]]*Angstrom

c1 = [[  0.00,   0.00,   0.20],
      [  0.00,   0.76,  -0.48],
      [  0.00,  -0.76,  -0.48]]*Angstrom

c2 = [[  0.00,   0.00,   0.28],
      [  0.00,   0.76,  -0.48],
      [  0.00,  -0.76,  -0.48]]*Angstrom

c3 = [[  0.00,   0.00,   0.36],
      [  0.00,   0.76,  -0.48],
      [  0.00,  -0.76,  -0.48]]*Angstrom

# Define the coordinate list.
coordinates = [c0, c1, c2, c3]

# Set up a list of configurations.
configuration_list = [ MoleculeConfiguration(elements,c) for c in coordinates ]

# Create a Trajectory only - no analysis.
t = MakeTrajectory(configuration_list)

# Define calculators on each configuration - for analysis.
for c in configuration_list:
    c.setCalculator(LCAOCalculator())

# Create a Trajectory with a TotalEnergy analysis carried out on each configuration.
t = MakeTrajectory(configuration_list, TotalEnergy)

maketrajectory1.py

Create a Trajectory object from a NudgedElasticBand object.

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

# Define coordinates.
c0 = [[  0.00,   0.00,   0.12],
      [  0.00,   0.76,  -0.48],
      [  0.00,  -0.76,  -0.48]]*Angstrom

c1 = [[  0.00,   0.00,   1.20],
      [  0.00,   0.76,  -0.48],
      [  0.00,  -0.76,  -0.48]]*Angstrom

# Set up a list of configurations.
configuration_list = [ MoleculeConfiguration(elements,c) for c in [c0,c1] ]

# Create the NudgedElasticBand object.
neb = NudgedElasticBand(configuration_list)

# Set a calculator on the configurations in the NEB - for analysis.
neb.setCalculator(LCAOCalculator())

# Create a Trajectory with a TotalEnergy analysis carried out on each configuration.
t = MakeTrajectory(neb, TotalEnergy)

maketrajectory2.py

Notes


LocalDeviceDensityOfStates		OpticalSpectrum