Mode

Class representing intramolecular vibrations.

The Mode class is a user class through which the user defines an intra molecular mode.

The vibrational mode is supposed to be an intramolecular mode of some molecule. This class is therefore aware of its Molecule class. Once it knows in which Molecule object it lives, it creates instances of the class Submode (as many as there are electronic states in the Molecule). Submods hold the parameters of the mode respective to a give electronic state of the monomer

These parameters have to be set after the mode is registered in the Molecule, and therefore there is an issue of consistency of the class. Currently, the consistency is completely in the hands of the user.

Class Details

class quantarhei.builders.modes.Mode(frequency=1.0)

Vibrational mode

Parameters:omega (float) – vibrational frequency

Examples

>>> import quantarhei as qr
>>> mol = qr.Molecule([0.0, 1.0])
>>> md = Mode(frequency=0.2)
>>> mol.add_Mode(md)

>>> print(md.get_energy(1))
0.2

This class is units management aware

>>> import quantarhei as qr
>>> with qr.energy_units("1/cm"):
...     md = Mode(250.0)
>>> mol.add_Mode(md)
>>> print(md.get_energy(0))
0.047091289182721326

>>> mol.get_number_of_modes()
2

Attributes:

monomer_set

nel

Methods

copy()	Returns a shallow copy of the self
deepcopy()	Returns a deep copy of the self
get_HR(N)	Returns Huang-Rhys factor of vib.
get_SubMode(N)	Returns the SubMode class of a give electronic state of the molecule
get_energy(N[, no_conversion])	Returns frequency of the mode corresponding to Nth electronic state
get_frequency(N)	Returns vibrational frequency
get_mode_environment()	Returns interaction of this mode with a bosonic bath
get_nmax(N)	Returns maximum quantum number of the mode at electronic state N
get_shift(N)	Returns the shift of the PES of the mode at Nth electronic state
load(filename[, test])	Loads an object from a file and returns it
loaddir(dirname)	Returns a directory of objects saved into a directory
save(filename[, comment, test])	Saves the object with all its content into a file
savedir(dirname[, tag, comment, test])	Saves an object into directory containing a file with unique name
scopy()	Creates a copy of the object by saving and loading it
set_HR(N, hr)	Sets Huang-Rhys factor of the PES on the Nth electronic state
set_Molecule(monomer)	Assigns this mode to a given monomer.
set_all(N, param)	Sets all the parameters of an intramolecular mode at once
set_energy(N, omega)	Sets energy/frequency of the mode relative to a molecular state
set_frequency(N, omega)	Sets vibrational frequency
set_mode_environment(corfce)	Set linear interaction with a bosonic environment
set_nmax(N, nmax)	Sets maximum quantum number of the mode in an electronic state N
set_shift(N, shift)	Sets the potential energy surface shift with respect to ground state

convert_energy_2_current_u
convert_energy_2_internal_u
convert_length_2_current_u
convert_length_2_internal_u
unit_repr
unit_repr_latex

get_HR(N)

Returns Huang-Rhys factor of vib. mode in Nth electronic state

Parameters:N (int) – Index of the electronic state

Examples

>>> import quantarhei as qr
>>> mol = qr.TestMolecule("two-levels-1-mode")
>>> mod = mol.get_Mode(0)
>>> mod.get_HR(0)
0.0

>>> mod.set_HR(1, 1.0)
>>> print("{0:.2f}".format(mod.get_HR(1)))
1.00

>>> mod.get_HR(0)
0.0

get_SubMode(N)

Returns the SubMode class of a give electronic state of the molecule

Parameters:N (int) – Index of the electronic state

Examples

>>> import quantarhei as qr
>>> mol = qr.TestMolecule("two-levels-1-mode")
>>> mod = mol.get_Mode(0)
>>> sm = mod.get_SubMode(1)

>>> print(sm.omega, sm.shift, sm.nmax)
1.0 0.0 2

get_energy(N, no_conversion=True)

Returns frequency of the mode corresponding to Nth electronic state

Parameters:

• N (int) – Index of the electronic state
• no_conversion (bool) – If set to True, the function does not react to units management

Examples

>>> import quantarhei as qr
>>> mol = qr.TestMolecule("two-levels-1-mode")
>>> mod = mol.get_Mode(0)
>>> mod.get_energy(1)
1.0

>>> with qr.energy_units("1/cm"):
...     mod.get_energy(1)  # default is `no_conversion=True`
1.0

>>> with qr.energy_units("1/cm"):
...     mod.get_energy(1, no_conversion=False)  # default is `no_conversion=True`
5308.837458876145

get_frequency(N)

Returns vibrational frequency

Usage of this method is deprecated, use get_energy instead

Parameters:N (int) – Index of the electronic state

Examples

>>> import quantarhei as qr
>>> mol = qr.TestMolecule("two-levels-1-mode")
>>> mod = mol.get_Mode(0)
>>> mod.set_energy(1, 1.3)

This function is deprecated and it throws a warning text when it is run

>>> mod.get_frequency(1) # doctest: +ELLIPSIS
function  <function Mode.get_frequency at ...>  is deprecated
1.3

get_mode_environment()

Returns interaction of this mode with a bosonic bath

get_nmax(N)

Returns maximum quantum number of the mode at electronic state N

Parameters:N (int) – Index of the electronic state

Examples

Default value of nmax is 2

>>> import quantarhei as qr
>>> mol = qr.TestMolecule("two-levels-1-mode")
>>> mod = mol.get_Mode(0)
>>> mod.get_nmax(0)
2
>>> mod.get_nmax(1)
2

get_shift(N)

Returns the shift of the PES of the mode at Nth electronic state

Parameters:N (int) – Index of the electronic state

Examples

>>> import quantarhei as qr
>>> mol = qr.TestMolecule("two-levels-1-mode")
>>> mod = mol.get_Mode(0)
>>> mod.get_shift(0)
0.0

>>> mod.get_shift(1)
0.0

>>> mod.set_shift(1, 1.0)
>>> mod.get_shift(1)
1.0

set_HR(N, hr)

Sets Huang-Rhys factor of the PES on the Nth electronic state

Parameters:

• N (int) – Index of the state for which we set. Setting for N=0 gives exception
• hr (float) – Huang-Rhys factor. Dimensionless quantity (ratio of reorganization energy and vibrational quantum)

Examples

>>> import quantarhei as qr
>>> mol = qr.TestMolecule("two-levels-1-mode")
>>> mod = mol.get_Mode(0)
>>> mod.set_HR(1, 1.0)

HR is the shift square devide by 2

>>> freq = mod.get_energy(1)
>>> sft = mod.get_shift(1)
>>> hr = (sft**2)/2.0
>>> print("{0:.2f}".format(hr))
1.00

set_Molecule(monomer)

Assigns this mode to a given monomer.

When set, the mode knows on how many electronic states it is supposed to live. This method is called by the Molecule’s add_Mode method.

Parameters:monomer (quantarhei.Molecule) – Molecule object to which this Mode will be assigned

Examples

set_Molecule should not be called directly, except of some (hard to imagine) special cases. The add_Mode method of the Molecule class does some extra work to keep consistent record of the Modes in the Molecule. Here, the difference between set_Molecule and add_Mode method of the Molecule class is demonstrated.

>>> import quantarhei as qr
>>> mol1 = qr.Molecule([0.0, 2.0])
>>> mol2 = qr.Molecule([0.0, 2.0])
>>> mod1 = qr.Mode(0.2)
>>> mod2 = qr.Mode(0.2)

>>> mol1.add_Mode(mod1)
>>> mod2.set_Molecule(mol2)

The number of modes recorded is consistent

>>> print(mol1.get_number_of_modes())
1
>>> print(len(mod1.submodes))
2

The number of modes in this case is not consistent. The Mode knows that it has SubModes, but Molecule has no mode recorded.

>>> print(mol2.get_number_of_modes())
0
>>> print(len(mod2.submodes))
2

set_all(N, param)

Sets all the parameters of an intramolecular mode at once

Parameters:

• N (int) – Index of the electronic states for which we set the mode parameters
• param (list like) – List of the mode parameters in the following order corresponding to the properties of the SubMode class, i.e. omega, shift, nmax. The parameters omega is units managed.

Examples

>>> import quantarhei as qr
>>> mol = qr.TestMolecule("two-levels-1-mode")
>>> mod = mol.get_Mode(0)
>>> mod.set_all(1, [1.2, 0.8, 3])

>>> print("{0:1.2f}".format(mod.get_HR(1)))
0.32

>>> mod.get_shift(1)
0.8

>>> mod.get_energy(1)
1.2

>>> mod.get_nmax(1)
3

Energy is units management sensitive

>>> with qr.energy_units("1/cm"):
...     mod.set_all(1, [1200, 0.8, 3])
>>> mod.get_energy(1)
0.22603818807706239

set_energy(N, omega)

Sets energy/frequency of the mode relative to a molecular state

Parameters:

• N (int) – Index of the electronic state for we set frequency
• omega (float) – Energy of the vibrational quantum / frequency of the oscillator

Examples

>>> import quantarhei as qr
>>> mol = qr.TestMolecule("two-levels-1-mode")
>>> mod = mol.get_Mode(0)
>>> mod.set_energy(1, 1.3)
>>> mod.get_energy(1)
1.3

>>> with qr.energy_units("1/cm"):
...     mod.set_energy(1, 1300.0)
>>> mod.get_energy(1)
0.2448747037501509

set_frequency(N, omega)

Sets vibrational frequency

Usage of this method is deprecated, use set_energy instead

Parameters:

• N (int) – Index of the electronic state
• omega (float) – Vibrational frequency

Examples

>>> import quantarhei as qr
>>> mol = qr.TestMolecule("two-levels-1-mode")
>>> mod = mol.get_Mode(0)

This function is deprecated and it throws a warning text when it is run

>>> mod.set_frequency(1, 1.3) # doctest: +ELLIPSIS
function  <function Mode.set_frequency at ...>  is deprecated

>>> mod.get_energy(1)
1.3

set_mode_environment(corfce)

Set linear interaction with a bosonic environment

set_nmax(N, nmax)

Sets maximum quantum number of the mode in an electronic state N

Parameters:

• N (int) – Index of the electronic state
• nmax (int) – Maximum quantum number to be set

Examples

>>> import quantarhei as qr
>>> mol = qr.TestMolecule("two-levels-1-mode")
>>> mod = mol.get_Mode(0)

Hamiltonian of a two-level molecule with one vibrational mode, for which we take 5 levels in each electronic state, has 10 levels

>>> mod.set_nmax(0, 5)
>>> mod.set_nmax(1, 5)
>>> H = mol.get_Hamiltonian()
>>> print(H.dim)
10

set_shift(N, shift)

Sets the potential energy surface shift with respect to ground state

The shift is dimensionless. frequency*(shift^2)/2 is the reorganization energy.

Parameters:

• N (int) – Index of the electronic state for we set frequency
• shift (float) – Shift of the PES with respect to ground state

Examples

>>> import quantarhei as qr
>>> mol = qr.TestMolecule("two-levels-1-mode")
>>> mod = mol.get_Mode(0)
>>> mod.set_shift(1, 0.1)
>>> mod.get_shift(1)
0.1