"""Class to support tests on Aggregate class
This class provides an easy access to a prefilled, but not initiallized
object of the Aggregate class. These can be used for testing and
demonstration. There are several types of aggregates available,
distinguished by the `name` argument of the constructor.
TestAggregates Provided
-----------------------
Below we list the valid values for the `name` argument of the TestAggregate
constructor:
dimer-2 :
Dimer of two-level molecules, with positions in space
and transition dipole moments specified. No environment
is defined.
dimer-2-env :
Dimer of two-level molecules, with positions in space and
transition dipole moments specified. For each molecule
we define energy gap correlation function (energy gao
correlation functions on different sites are not correlated).
homodimer-2 :
Homo-dimer of two-level molecules (molecules with the same energy
gaps), with positions in space
and transition dipole moments specified. No environment
is defined.
homodimer-2-env :
Homo-dimer of two-level molecules, with positions in space and
transition dipole moments specified. For each molecule
we define energy gap correlation function (energy gao
correlation functions on different sites are not correlated).
Class Details
-------------
"""
from __future__ import annotations
import numpy
from ..core.managers import energy_units
from ..core.time import TimeAxis
from ..core.units import convert
from ..exceptions import QuantarheiError
from ..qm.corfunctions.correlationfunctions import CorrelationFunction
from .aggregates import Aggregate
from .modes import Mode
from .molecules import Molecule
[docs]
class TestAggregate(Aggregate):
"""Class to support tests on Aggregate class
Parameters
----------
name : str
Name characterizing the test aggregate.
Examples
--------
General dimers
>>> # Dimer of two-level systems
>>> tagg = TestAggregate(name="dimer-2")
>>> tagg.build()
>>> tagg.has_SystemBathInteraction()
False
>>> # Dimer of two-level systems with an environment
>>> tagg = TestAggregate(name="dimer-2-env")
>>> tagg.build()
>>> tagg.has_SystemBathInteraction()
True
Homo-dimers
>>> # Dimer of two-level systems
>>> tagg = TestAggregate(name="homodimer-2")
>>> tagg.build()
>>> tagg.has_SystemBathInteraction()
False
>>> # Dimer of two-level systems with an environment
>>> tagg = TestAggregate(name="homodimer-2-env")
>>> tagg.build()
>>> tagg.has_SystemBathInteraction()
True
>>> # Trimer of two-level systems without an environment
>>> tagg = TestAggregate(name="trimer-2")
>>> tagg.build()
>>> tagg.has_SystemBathInteraction()
False
"""
[docs]
def __init__(self, name: str | None = None) -> None:
"""Some more doctests
>>> TestAggregate()
Traceback (most recent call last):
...
quantarhei.exceptions.QuantarheiError: Aggregate name not specified
"""
if name is None:
raise QuantarheiError("Aggregate name not specified")
#
# Test dimer
#
if name == "dimer-2-env":
m1, m2 = self._molecules(N=2, nst=2)
# set their environment
time = TimeAxis(0, 1000, 1.0)
cpar = dict(ftype="OverdampedBrownian", reorg=20, cortime=100, T=300)
with energy_units("1/cm"):
cfce = CorrelationFunction(time, cpar)
m1.set_transition_environment((0, 1), cfce)
m2.set_transition_environment((0, 1), cfce)
super().__init__(molecules=[m1, m2])
elif name == "trimer-2-env":
m1, m2, m3 = self._molecules(N=3, nst=2)
# set their environment
time = TimeAxis(0, 1000, 1.0)
cpar = dict(ftype="OverdampedBrownian", reorg=20, cortime=100, T=300)
with energy_units("1/cm"):
cfce = CorrelationFunction(time, cpar)
m1.set_transition_environment((0, 1), cfce)
m2.set_transition_environment((0, 1), cfce)
m3.set_transition_environment((0, 1), cfce)
super().__init__(molecules=[m1, m2, m3])
elif name == "dimer-2":
m1, m2 = self._molecules(N=2, nst=2)
# set their environment
# nothing here
super().__init__(molecules=[m1, m2])
elif name == "trimer-2":
m1, m2, m3 = self._molecules(N=3, nst=2, homo=False)
super().__init__(molecules=[m1, m2, m3])
elif name == "homodimer-2-env":
m1, m2 = self._molecules(N=2, nst=2, homo=True)
# set their environment
time = TimeAxis(0, 1000, 1.0)
cpar = dict(ftype="OverdampedBrownian", reorg=20, cortime=100, T=300)
with energy_units("1/cm"):
cfce = CorrelationFunction(time, cpar)
m1.set_transition_environment((0, 1), cfce)
m2.set_transition_environment((0, 1), cfce)
super().__init__(molecules=[m1, m2])
elif name == "homodimer-2":
m1, m2 = self._molecules(N=2, nst=2, homo=True)
# set their environment
# nothing here
super().__init__(molecules=[m1, m2])
elif name == "dimer-2-vib":
m1, m2 = self._molecules(N=2, nst=2)
with energy_units("1/cm"):
mod1 = Mode(100.0)
m1.add_Mode(mod1)
mod1.set_HR(1, 0.1)
mod2 = Mode(100.0)
m2.add_Mode(mod2)
mod2.set_HR(1, 0.1)
super().__init__(molecules=[m1, m2])
def _molecules(self, N: int, nst: int, homo: bool = False) -> list | None:
"""Creates molecules to be filled into Aggregate
Testing that None is returned for wrong arguments
>>> tagg = TestAggregate("dimer-2")
>>> mols = tagg._molecules(3, 5)
>>> print(mols)
None
"""
if (N == 2) and (nst == 2):
nstates = nst
# check inputs
if nstates != 2:
raise QuantarheiError()
# set parameters
gap1 = convert(12000, "1/cm", to="int")
energies1 = numpy.zeros(nstates)
for s in range(nstates):
energies1[s] = s * gap1
if homo:
gap2 = convert(12000, "1/cm", to="int")
else:
gap2 = convert(12300, "1/cm", to="int")
energies2 = numpy.zeros(nstates)
for s in range(nstates):
energies2[s] = s * gap2
# molecules
m1 = Molecule(elenergies=energies1)
m2 = Molecule(elenergies=energies2)
# set transition dipole moments
dip1 = [0.0, 2.0, 0.0]
dip2 = [0.0, 1.3, 1.4]
m1.set_dipole(0, 1, dip1)
m2.set_dipole(0, 1, dip2)
# set molecular positions
r1 = [0.0, 0.0, 0.0]
r2 = [5.0, 0.0, 0.0]
m1.position = r1
m2.position = r2
return [m1, m2]
if (N == 3) and (nst == 2):
nstates = nst
# check inputs
if nstates != 2:
raise QuantarheiError()
# set parameters
gap1 = convert(12000, "1/cm", to="int")
energies1 = numpy.zeros(nstates)
for s in range(nstates):
energies1[s] = s * gap1
if homo:
gap2 = convert(12000, "1/cm", to="int")
gap3 = gap2
else:
gap2 = convert(12300, "1/cm", to="int")
gap3 = convert(12350, "1/cm", to="int")
energies2 = numpy.zeros(nstates)
energies3 = numpy.zeros(nstates)
for s in range(nstates):
energies2[s] = s * gap2
energies3[s] = s * gap3
# molecules
m1 = Molecule(elenergies=energies1)
m2 = Molecule(elenergies=energies2)
m3 = Molecule(elenergies=energies3)
# set transition dipole moments
dip1 = [0.0, 2.0, 0.0]
dip2 = [0.0, 1.3, 1.4]
dip3 = [1.0, 1.2, 0.0]
m1.set_dipole(0, 1, dip1)
m2.set_dipole(0, 1, dip2)
m3.set_dipole(0, 1, dip3)
# set molecular positions
r1 = [0.0, 0.0, 0.0]
r2 = [5.0, 0.0, 0.0]
r3 = [0.0, 0.0, 5.0]
m1.position = r1
m2.position = r2
m3.position = r3
return [m1, m2, m3]
return None