def setUp(self):
np.random.seed(0) # set random seed in order for the examples to reproduce the exact references
# list of decay functions by state
molecule = Molecule()
# define system as a crystal
self.system = crystal_system(molecules=[molecule], # molecule to use as reference
scaled_site_coordinates=[[0.0, 0.0]],
unitcell=[[5.0, 1.0],
[1.0, 5.0]],
dimensions=[2, 2], # supercell size
orientations=[[0.0, 0.0, np.pi / 2]]) # if element is None then random, if list then Rx Ry Rz
# set initial exciton
self.system.add_excitation_index(s1, 1)
self.system.add_excitation_index(s1, 0)
# set additional system parameters
self.system.cutoff_radius = 8 # interaction cutoff radius in Angstrom
conditions=conditions,
molecule=molecule,
lattice={
'size': [4, 4, 4],
'parameters': [3.0, 3.0, 3.0]
}, # Angstroms
orientation=[0.8492, 1.0803,
0.4389]) # (Rx, Ry, Rz) if None then random orientation
system_2 = crystal_system(
conditions=conditions,
molecules=[molecule, molecule],
scaled_site_coordinates=[[0, 0, 0], [0.5, 0.5, 0.0]],
unitcell=[[6.32367864, 0.0000000, -4.35427391],
[0.00000000, 5.7210000, 0.00000000],
[0.00000000, 0.0000000, 8.39500000]],
dimensions=[2, 2, 2],
orientations=[
[-2.4212, -1.8061,
1.9804], # if element is None then random, if list then oriented
[2.4212, -1.8061, -1.9804],
None
])
system = system_2 # choose 2
system.transfer_scheme = transfer_scheme
system.cutoff_radius = 8
system.add_excitation_index('s1', 0)
#system.add_excitation_center('s1')
# Donor: 558 / Acceptor: 447
# Donor: 558 / Acceptor: 540
] # eV
# define system as a crystal
molecule = Molecule()
#print(molecule, molecule.state, molecule.state.get_center())
molecule2 = Molecule(site_energy=2)
print(molecule2, molecule2.state, molecule2.state.get_center())
print(molecule, molecule.state, molecule.state.get_center())
system = crystal_system(
molecules=[molecule, molecule], # molecule to use as reference
scaled_site_coordinates=[[0.0, 0.0], [0.0, 0.5]],
unitcell=[[5.0, 1.0], [1.0, 5.0]],
dimensions=[2, 2], # supercell size
orientations=[[0.0, 0.0, np.pi / 2], [0.0, 0.0, 0.0]
]) # if element is None then random, if list then Rx Ry Rz
print([m.site_energy for m in system.molecules])
print(system.get_ground_states())
# set initial exciton
system.add_excitation_index(s1, 0)
system.add_excitation_index(s1, 1)
# set additional system parameters
system.process_scheme = [
GoldenRule(
initial_states=(s1, gs),
1.2e-3] # b
# Vibrations
vibrational_model = MarcusModel(reorganization_energies={(gs, s1): 0.07,
(s1, gs): 0.07,
(gs, t1): 0.07, # assuming triplet same reorganization
(t1, gs): 0.07}, # energy as singlet
temperature=300)
#################################################################################
# 2D model (plane a-b) , not diffusion in C
molecule = Molecule()
system = crystal_system(molecules=[molecule, molecule], # molecule to use as reference
scaled_site_coordinates=[[0.0, 0.0],
[0.5, 0.5]],
unitcell=[[7.3347, 0.0000],
[-0.2242, 6.0167]],
dimensions=[4, 4], # supercell size
orientations=[[0.0, 0.0, np.pi/8],
[0.0, 0.0, -np.pi/8]]) # if element is None then random, if list then Rx Ry Rz
system.cutoff_radius = 8.1 # Angstroms
# Transport
system.process_scheme = [GoldenRule(initial_states=(s1, gs), final_states=(gs, s1),
electronic_coupling_function=electronic_coupling_direction,
arguments={'couplings': singlet_couplings},
vibrations=vibrational_model,
description='singlet transport'),
GoldenRule(initial_states=(t1, gs), final_states=(gs, t1),
electronic_coupling_function=electronic_coupling_direction,
arguments={'couplings': triplet_couplings},
# store structure in file
struct_c.to(filename='naphtalene.cif')
struct_c.to(filename='POSCAR')
scale_factor = 50
molecule = Molecule(
states=[State(label='gs', energy=0.0),
State(label='s1', energy=1.0)],
transition_moment={
('s1', 'gs'): dipole * scale_factor,
('s2', 'gs'): dipole2 * scale_factor
}, # transition dipole moment of the molecule (Debye)
)
system = crystal_system(conditions={},
molecules=[molecule],
scaled_site_coordinates=[position],
unitcell=lattice.matrix,
dimensions=[1, 1, 1],
orientations=[params])
print('TM: {}'.format(
system.molecules[0].get_transition_moment(to_state='s1')))
print('TM_test: {}'.format(
get_dipole_in_basis(
np.array(dipole) * ATOMIC_TO_ANGS_EL * scale_factor, ev_dipole,
ev)))
visualize_system(system)
visualize_system(system, dipole='s1')