MakeTrajectory¶

MakeTrajectory(configuration_list, analysis=None, **kwargs)¶

Construct a trajectory sequence of configurations, from a given nudged elastic band configuration, or a list of configurations.

Parameters:

configuration_list (list of configurations | NudgedElasticBand.) – Either an explicit list of configurations (each of type MoleculeConfiguration | BulkConfiguration | DeviceConfiguration | SurfaceConfiguration), or a NudgedElasticBand configuration object.
analysis (class) – The analysis class that will be applied across the configurations, e.g. Forces.
Default: No analysis is performed.
**kwargs – Any additional keyword arguments will be passed to the constructor of the class given in the analysis argument.

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