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: float = 1.0)[source]#

Bases: UnitsManaged, Saveable, OpenSystem

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

property monomer_set: Any#

property nel: Any#

set_Molecule(monomer: Any) → None[source]#

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_frequency(N: int, omega: float) → None[source]#

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 raises a deprecation warning when it is run

>>> mod.set_frequency(1, 1.3)

>>> mod.get_energy(1)
1.3

set_energy(N: int, omega: float) → None[source]#

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_shift(N: int, shift: float) → None[source]#

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

set_nmax(N: int, nmax: int) → None[source]#

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_HR(N: int, hr: float) → None[source]#

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

get_frequency(N: int) → float | ndarray[source]#

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 raises a deprecation warning when it is run

>>> mod.get_frequency(1)
1.3

get_energy(N: int, no_conversion: bool = True) → float | ndarray[source]#

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_shift(N: int) → float[source]#

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

get_nmax(N: int) → int[source]#

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_HR(N: int) → float[source]#

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

set_all(N: int, param: list) → None[source]#

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

get_SubMode(N: int) → object[source]#

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

set_mode_environment(corfce: Any) → None[source]#: Set linear interaction with a bosonic environment

get_mode_environment() → object[source]#: Returns interaction of this mode with a bosonic bath