def test_reduced_density_matrix(
mol_num,
j_constant_value,
elocalex_value,
ph_info,
ph_phys_dim,
evolve_dt,
nsteps,
temperature,
):
ph_list = [
Phonon.simple_phonon(Quantity(omega, "cm^{-1}"),
Quantity(displacement, "a.u."), ph_phys_dim)
for omega, displacement in ph_info
]
mol_list = MolList([Mol(Quantity(elocalex_value, "a.u."), ph_list)] *
mol_num,
Quantity(j_constant_value, "eV"),
scheme=3)
ct = ChargeTransport(mol_list,
temperature=Quantity(temperature, "K"),
stop_at_edge=False,
rdm=True)
ct.evolve(evolve_dt, nsteps)
for rdm, e in zip(ct.reduced_density_matrices, ct.e_occupations_array):
# best we can do?
assert np.allclose(np.diag(rdm), e)
def test_adaptive_zero_t(method):
np.random.seed(0)
evolve_config = EvolveConfig(method=method, guess_dt=0.1, adaptive=True)
ct = ChargeTransport(band_limit_mol_list,
evolve_config=evolve_config,
stop_at_edge=True)
ct.evolve(evolve_dt=5.)
assert_band_limit(ct, 1e-2)
def test_bandlimit_zero_t(method, evolve_dt, nsteps, rtol, scheme):
np.random.seed(0)
evolve_config = EvolveConfig(method)
ct = ChargeTransport(band_limit_mol_list.switch_scheme(scheme),
evolve_config=evolve_config)
ct.stop_at_edge = True
ct.evolve(evolve_dt, nsteps)
assert_band_limit(ct, rtol)
def test_band_limit_finite_t(
mol_num,
j_constant_value,
elocalex_value,
ph_info,
ph_phys_dim,
evolve_dt,
nsteps,
scheme,
):
ph_list = [
Phonon.simple_phonon(Quantity(omega, "cm^{-1}"),
Quantity(displacement, "a.u."), ph_phys_dim)
for omega, displacement in ph_info
]
mol_list = MolList(
[Mol(Quantity(elocalex_value, "a.u."), ph_list)] * mol_num,
Quantity(j_constant_value, "eV"),
scheme=scheme,
)
ct1 = ChargeTransport(mol_list, stop_at_edge=False)
ct1.evolve(evolve_dt, nsteps)
ct2 = ChargeTransport(mol_list, temperature=low_t, stop_at_edge=False)
ct2.evolve(evolve_dt, nsteps)
assert ct1.is_similar(ct2)
def test_gaussian_bond_dim():
compress_config = CompressConfig(
criteria=CompressCriteria.fixed,
bonddim_distri=BondDimDistri.center_gauss,
max_bonddim=10,
)
evolve_config = EvolveConfig(guess_dt=0.1, adaptive=True)
ct = ChargeTransport(
band_limit_mol_list,
compress_config=compress_config,
evolve_config=evolve_config,
)
ct.stop_at_edge = True
ct.evolve(evolve_dt=2.)
assert_band_limit(ct, 1e-2)
def test_zt_init_state():
ph = Phonon.simple_phonon(Quantity(1), Quantity(1), 10)
mol_list = MolList([Mol(Quantity(0), [ph])], Quantity(0), scheme=3)
mpo = Mpo(mol_list)
mps = Mps.random(mol_list, 1, 10)
optimize_mps(mps, mpo)
ct = ChargeTransport(mol_list)
assert mps.angle(ct.latest_mps) == pytest.approx(1)
def test_similar(mol_num, j_constant_value, elocalex_value, ph_info,
ph_phys_dim, evolve_dt, nsteps):
ph_list = [
Phonon.simple_phonon(Quantity(omega, "cm^{-1}"),
Quantity(displacement, "a.u."), ph_phys_dim)
for omega, displacement in ph_info
]
mol_list = MolList([Mol(Quantity(elocalex_value, "a.u."), ph_list)] *
mol_num,
Quantity(j_constant_value, "eV"),
scheme=3)
ct1 = ChargeTransport(mol_list)
ct1.evolve(evolve_dt, nsteps)
ct2 = ChargeTransport(mol_list)
ct2.evolve(evolve_dt + 1e-5, nsteps)
assert ct1.is_similar(ct2)
def test_ft_init_state():
ph = Phonon.simple_phonon(Quantity(1), Quantity(1), 10)
mol_list = MolList([Mol(Quantity(0), [ph])], Quantity(0), scheme=3)
temperature = Quantity(0.1)
mpo = Mpo(mol_list)
init_mpdm = MpDm.max_entangled_ex(mol_list)
tp = ThermalProp(init_mpdm, mpo, space="EX", exact=True)
tp.evolve(nsteps=20, evolve_time=temperature.to_beta() / 2j)
ct = ChargeTransport(mol_list, temperature=temperature)
tp_mpdm = MpDmFull.from_mpdm(tp.latest_mps)
ct_mpdm = MpDmFull.from_mpdm(ct.latest_mps)
assert tp_mpdm.angle(ct_mpdm) == pytest.approx(1)
def test_scheme4_finite_t(mol_num, j_constant_value, elocalex_value, ph_info,
ph_phys_dim, evolve_dt, nsteps):
temperature = Quantity(1, "a.u.")
ph_list = [
Phonon.simple_phonon(Quantity(omega, "cm^{-1}"),
Quantity(displacement, "a.u."), ph_phys_dim)
for omega, displacement in ph_info
]
mol_list = MolList([Mol(Quantity(elocalex_value, "a.u."), ph_list)] *
mol_num, Quantity(j_constant_value, "eV"))
ct1 = ChargeTransport(mol_list.switch_scheme(3),
temperature=temperature,
stop_at_edge=False)
ct1.evolve(evolve_dt, nsteps)
ct2 = ChargeTransport(mol_list.switch_scheme(4),
temperature=temperature,
stop_at_edge=False)
ct2.evolve(evolve_dt, nsteps)
assert ct1.is_similar(ct2, rtol=1e-2)
def test_reduced_density_matrix(
mol_num,
j_constant_value,
elocalex_value,
ph_info,
ph_phys_dim,
evolve_dt,
nsteps,
temperature,
):
ph_list = [
Phonon.simple_phonon(Quantity(omega, "cm^{-1}"),
Quantity(displacement, "a.u."), ph_phys_dim)
for omega, displacement in ph_info
]
mol_list3 = MolList(
[Mol(Quantity(elocalex_value, "a.u."), ph_list)] * mol_num,
Quantity(j_constant_value, "eV"),
scheme=3,
)
ct3 = ChargeTransport(mol_list3,
temperature=Quantity(temperature, "K"),
stop_at_edge=False,
rdm=True)
ct3.evolve(evolve_dt, nsteps)
mol_list4 = mol_list3.switch_scheme(4)
ct4 = ChargeTransport(mol_list4,
temperature=Quantity(temperature, "K"),
stop_at_edge=False,
rdm=True)
ct4.evolve(evolve_dt, nsteps)
for rdm3, rdm4, e in zip(ct3.reduced_density_matrices,
ct4.reduced_density_matrices,
ct3.e_occupations_array):
assert np.allclose(rdm3, rdm4, atol=1e-3)
assert np.allclose(np.diag(rdm3), e)
lams = hr_factors * omegas_au
phonons = [
Phonon.simplest_phonon(Quantity(o), Quantity(l), lam=True)
for o, l in zip(omegas_au, lams)
]
j_matrix_au = j_matrix_cm * cm2au
mlist = []
for j in np.diag(j_matrix_au):
m = Mol(Quantity(j), phonons)
mlist.append(m)
# starts from 1
mol_arangement = np.array([7, 5, 3, 1, 2, 4, 6]) - 1
mol_list = MolList(list(np.array(mlist)[mol_arangement]),
j_matrix_au[mol_arangement][:, mol_arangement])
evolve_dt = 40
evolve_config = EvolveConfig(evolve_dt=evolve_dt)
compress_config = CompressConfig(CompressCriteria.fixed, max_bonddim=16)
ct = ChargeTransport(mol_list,
evolve_config=evolve_config,
compress_config=compress_config)
ct.dump_dir = "./fmo"
ct.job_name = 'hybrid'
ct.stop_at_edge = False
ct.evolve(evolve_dt=evolve_dt, nsteps=10)
new_evolve_config = EvolveConfig(EvolveMethod.tdvp_mctdh_new)
ct.latest_mps.evolve_config = ct.evolve_config = new_evolve_config
ct.evolve(evolve_dt=evolve_dt, nsteps=100000)
if __name__ == "__main__":
if len(sys.argv) != 2:
print("No or more than one parameter file are provided, abort")
exit(1)
parameter_path = sys.argv[1]
with open(parameter_path) as fin:
param = yaml.safe_load(fin)
log.register_file_output(
os.path.join(param["output dir"], param["fname"] + ".log"), "w")
mol_list, temperature = load_from_dict(param, 3, False)
compress_config = CompressConfig(threshold=1e-4)
evolve_config = EvolveConfig(adaptive=True, evolve_dt=2)
ct = ChargeTransport(
mol_list,
temperature=temperature,
compress_config=compress_config,
evolve_config=evolve_config,
rdm=False,
)
# ct.stop_at_edge = True
# ct.memory_limit = 2 ** 30 # 1 GB
# ct.memory_limit /= 10 # 100 MB
ct.dump_dir = param["output dir"]
ct.job_name = param["fname"]
ct.custom_dump_info["comment"] = param["comment"]
# ct.latest_mps.compress_add = True
logger.debug(f"ground energy of the Hamiltonian: {ct.mpo_e_lbound:g}")
ct.evolve(param.get("evolve dt"), param.get("nsteps"),
param.get("evolve time"))
# ct.evolve(evolve_dt, 100, param.get("evolve time"))
hr_factors *= TOTAL_HR / hr_factors.sum()
lams = hr_factors * omegas_au
phonons = [
Phonon.simplest_phonon(Quantity(o), Quantity(l), lam=True)
for o, l in zip(omegas_au, lams)
]
j_matrix_au = j_matrix_cm * cm2au
mlist = []
for j in np.diag(j_matrix_au):
m = Mol(Quantity(j), phonons)
mlist.append(m)
# starts from 1
mol_arangement = np.array([7, 5, 3, 1, 2, 4, 6]) - 1
mol_list = MolList(list(np.array(mlist)[mol_arangement]),
j_matrix_au[mol_arangement][:, mol_arangement])
evolve_dt = 160
evolve_config = EvolveConfig(EvolveMethod.tdvp_ps, guess_dt=evolve_dt)
compress_config = CompressConfig(CompressCriteria.fixed, max_bonddim=32)
ct = ChargeTransport(mol_list,
evolve_config=evolve_config,
compress_config=compress_config,
init_electron=InitElectron.fc)
ct.dump_dir = "./"
ct.job_name = 'fmo'
ct.stop_at_edge = False
ct.evolve(evolve_dt=evolve_dt, evolve_time=40000)
def test_evolve(mol_num, j_constant_value, elocalex_value, ph_info,
ph_phys_dim, evolve_dt, nsteps):
ph_list = [
Phonon.simple_phonon(Quantity(omega, "cm^{-1}"),
Quantity(displacement, "a.u."), ph_phys_dim)
for omega, displacement in ph_info
]
mol_list = MolList(
[Mol(Quantity(elocalex_value, "a.u."), ph_list)] * mol_num,
Quantity(j_constant_value, "eV"),
scheme=3,
)
ct1 = ChargeTransport(mol_list, stop_at_edge=False)
half_nsteps = nsteps // 2
ct1.evolve(evolve_dt, half_nsteps)
ct1.evolve(evolve_dt, nsteps - half_nsteps)
ct2 = ChargeTransport(mol_list, stop_at_edge=False)
ct2.evolve(evolve_dt, nsteps)
assert ct1.is_similar(ct2)
assert_iterable_equal(ct1.get_dump_dict(), ct2.get_dump_dict())
# test dump
ct2.dump_dir = "."
ct2.job_name = "test"
ct2.dump_dict()
os.remove("test.npz")
def test_32backend(switch_to_32backend):
evolve_config = EvolveConfig(evolve_dt=4, adaptive=True)
ct = ChargeTransport(band_limit_mol_list, evolve_config=evolve_config)
ct.stop_at_edge = True
ct.evolve()
assert_band_limit(ct, 1e-2)
def test_compress_add(mol_num, j_constant_value, elocalex_value, ph_info,
ph_phys_dim, evolve_dt, nsteps):
ph_list = [
Phonon.simple_phonon(Quantity(omega, "cm^{-1}"),
Quantity(displacement, "a.u."), ph_phys_dim)
for omega, displacement in ph_info
]
mol_list = MolList([Mol(Quantity(elocalex_value, "a.u."), ph_list)] *
mol_num,
Quantity(j_constant_value, "eV"),
scheme=3)
ct1 = ChargeTransport(mol_list, temperature=Quantity(298, "K"))
ct1.reduced_density_matrices = None
ct1.evolve(evolve_dt, nsteps)
ct2 = ChargeTransport(mol_list, temperature=Quantity(298, "K"))
ct2.reduced_density_matrices = None
ct2.latest_mps.compress_add = True
ct2.evolve(evolve_dt, nsteps)
assert ct1.is_similar(ct2, rtol=1e-2)