ProjectionList

	ProjectionList
MullikenPopulation	DensityOfStates

Name

ProjectionList — Class for representing a list of orbitals. Results of several analysis objects can be projected onto this limited set of orbitals.

Synopsis

Namespace: NanoLanguage

ProjectionList(
atoms,
elements,
angular_momenta
)

Description

Constructor of the ProjectionList class that keeps track of which projection orbitals are used in analysis objects such as the MolecularEnergySpectrum.

ProjectionList Arguments

atoms

List of integers specifying the atom indices to include in the projection list

Type: Any sequence of non negative integers

Default:

All

elements

List of elements to include in the projection list

Type: Any sequence of PeriodicTable Elements

Default:

All

angular_momenta

List of angular momenta, specified as integers (0=s, 1=p, ..), to include in the projection list

Type: Any sequence of non negative integers

Default:

All

ProjectionList Methods

A ProjectionList object provides the following methods:

angularMomenta(): Query for the angular momenta which are included in the projection list
atoms(): Query for the atom indices which are included in the projection list
elements(): Query for the elements which are included in the projection list
includeAll(): Query for if we include all orbitals as targets or not

Usage Examples

Calculate the Nitrogen s level within an ammonia molecule.

# Set up configuration
molecule_configuration = MoleculeConfiguration(
    elements=[Nitrogen, Hydrogen, Hydrogen, Hydrogen],
    cartesian_coordinates= [[ 0.      ,  0.      ,  0.124001],
                         [ 0.      ,  0.941173, -0.289336],
                         [ 0.81508 , -0.470587, -0.289336],
                         [-0.81508 , -0.470587, -0.289336]]*Angstrom )

# Define the calculator
calculator = HuckelCalculator()
molecule_configuration.setCalculator(calculator)

# Calculate and save the molecular energy spectrum
molecular_energy_spectrum = MolecularEnergySpectrum(
    configuration=molecule_configuration,
    energy_zero_parameter=AbsoluteEnergy,
    projection_list=ProjectionList(elements=[Nitrogen], angular_momenta = [0])
    )
nlsave('molecular.nc', molecular_energy_spectrum)

# Extract the energy
energy = molecular_energy_spectrum.evaluate()
occ = molecular_energy_spectrum.occupation()

# ... and print it out
print "level   energy(eV)    occupation"
for i in range(len(energy[0])):
    print '  %d  %12.4f  %12.4f  ' % (i, energy[0][i].inUnitsOf(eV),occ[0][i])

nh3.py


MullikenPopulation		DensityOfStates