def calculate_isolate_molecular_levels(self, tp):
atoms = self.isolate_atoms
atoms.pbc = True
p = tp.gpw_kwargs.copy()
p['nbands'] = None
if 'mixer' in p:
if not tp.spinpol:
p['mixer'] = Mixer(0.1, 5, weight=100.0)
else:
p['mixer'] = MixerDif(0.1, 5, weight=100.0)
p['poissonsolver'] = PoissonSolver(nn=2)
if type(p['basis']) is dict and len(p['basis']) == len(tp.atoms):
p['basis'] = 'dzp'
raise Warning('the dict basis is not surpported in isolate atoms')
if 'txt' in p and p['txt'] != '-':
p['txt'] = 'isolate_' + p['txt']
atoms.set_calculator(GPAW(**p))
atoms.get_potential_energy()
setups = atoms.calc.wfs.setups
self.project_basis_in_molecule = get_atom_indices(
self.project_atoms_in_molecule, setups)
kpt = atoms.calc.wfs.kpt_u[0]
s_mm = atoms.calc.wfs.S_qMM[0]
c_nm = eig_states_norm(kpt.C_nM, s_mm)
self.isolate_eigen_values = kpt.eps_n
self.isolate_eigen_vectors = c_nm
self.isolate_s_mm = s_mm
def calculate_isolate_molecular_levels(self, tp):
atoms = self.isolate_atoms
atoms.pbc = True
p = tp.gpw_kwargs.copy()
p['nbands'] = None
if 'mixer' in p:
if not tp.spinpol:
p['mixer'] = Mixer(0.1, 5, weight=100.0)
else:
p['mixer'] = MixerDif(0.1, 5, weight=100.0)
p['poissonsolver'] = PoissonSolver(nn=2)
if type(p['basis']) is dict and len(p['basis']) == len(tp.atoms):
p['basis'] = 'dzp'
raise Warning('the dict basis is not surpported in isolate atoms')
if 'txt' in p and p['txt'] != '-':
p['txt'] = 'isolate_' + p['txt']
atoms.set_calculator(GPAW(**p))
atoms.get_potential_energy()
setups = atoms.calc.wfs.setups
self.project_basis_in_molecule = get_atom_indices(
self.project_atoms_in_molecule, setups)
kpt = atoms.calc.wfs.kpt_u[0]
s_mm = atoms.calc.wfs.S_qMM[0]
c_nm = eig_states_norm(kpt.C_nM, s_mm)
self.isolate_eigen_values = kpt.eps_n
self.isolate_eigen_vectors = c_nm
self.isolate_s_mm = s_mm
def initialize(self, tp):
kw = tp.analysis_parameters
if self.restart:
self.initialize_selfenergy_and_green_function(tp)
else:
self.selfenergies = tp.selfenergies
p = self.set_default_analysis_parameters()
for key in kw:
if key in [
'energies', 'lead_pairs', 'dos_project_atoms',
'project_equal_atoms', 'project_molecular_levels',
'isolate_atoms', 'dos_project_orbital',
'trans_project_orbital', 'eig_trans_channel_energies',
'eig_trans_channel_num', 'dos_realspace_energies'
]:
p[key] = kw[key]
for key in p:
vars(self)[key] = p[key]
ef = tp.lead_fermi[0]
path = tp.contour.get_plot_path()
self.energies = path.energies
self.my_energies = path.my_energies
self.weights = path.weights
self.my_weights = path.my_weights
self.nids = path.nids
self.my_nids = path.my_nids
for variable in [
self.eig_trans_channel_energies, self.dos_realspace_energies
]:
if variable is not None:
variable = np.array(variable) + ef
ecomm = tp.contour.comm
if self.eig_trans_channel_energies is not None:
self.my_eig_trans_channel_energies = np.array_split(
self.eig_trans_channel_energies, ecomm.size)[ecomm.rank]
self.my_eig_trans_channel_nids = np.array_split(
np.arange(len(self.eig_trans_channel_energies)),
ecomm.size)[ecomm.rank]
if self.dos_realspace_energies is not None:
self.my_dos_realspace_energies = np.array_split(
self.dos_realspace_energies, ecomm.size)[ecomm.rank]
self.my_dos_realspace_nids = np.array_split(
np.arange(len(self.dos_realspace_energies)),
ecomm.size)[ecomm.rank]
setups = tp.inner_setups
self.project_atoms_in_device = self.project_equal_atoms[0]
self.project_atoms_in_molecule = self.project_equal_atoms[1]
self.project_basis_in_device = get_atom_indices(
self.project_atoms_in_device, setups)
if self.isolate_atoms is not None:
self.calculate_isolate_molecular_levels(tp)
self.overhead_data_saved = False
if world.rank == 0:
if not os.access('analysis_data', os.F_OK):
os.mkdir('analysis_data')
if not os.access('analysis_data/ionic_step_0', os.F_OK):
os.mkdir('analysis_data/ionic_step_0')
world.barrier()
self.data = {}
def initialize(self, tp):
kw = tp.analysis_parameters
if self.restart:
self.initialize_selfenergy_and_green_function(tp)
else:
self.selfenergies = tp.selfenergies
p = self.set_default_analysis_parameters()
for key in kw:
if key in ['energies', 'lead_pairs', 'dos_project_atoms',
'project_equal_atoms', 'project_molecular_levels',
'isolate_atoms', 'dos_project_orbital',
'trans_project_orbital', 'eig_trans_channel_energies',
'eig_trans_channel_num', 'dos_realspace_energies']:
p[key] = kw[key]
for key in p:
vars(self)[key] = p[key]
ef = tp.lead_fermi[0]
path = tp.contour.get_plot_path()
self.energies = path.energies
self.my_energies = path.my_energies
self.weights = path.weights
self.my_weights = path.my_weights
self.nids = path.nids
self.my_nids = path.my_nids
for variable in [self.eig_trans_channel_energies,
self.dos_realspace_energies]:
if variable is not None:
variable = np.array(variable) + ef
ecomm = tp.contour.comm
if self.eig_trans_channel_energies is not None:
self.my_eig_trans_channel_energies = np.array_split(
self.eig_trans_channel_energies, ecomm.size)[ecomm.rank]
self.my_eig_trans_channel_nids = np.array_split(
np.arange(len(self.eig_trans_channel_energies)),
ecomm.size)[ecomm.rank]
if self.dos_realspace_energies is not None:
self.my_dos_realspace_energies = np.array_split(
self.dos_realspace_energies, ecomm.size)[ecomm.rank]
self.my_dos_realspace_nids = np.array_split(
np.arange(len(self.dos_realspace_energies)),
ecomm.size)[ecomm.rank]
setups = tp.inner_setups
self.project_atoms_in_device = self.project_equal_atoms[0]
self.project_atoms_in_molecule = self.project_equal_atoms[1]
self.project_basis_in_device = get_atom_indices(
self.project_atoms_in_device, setups)
if self.isolate_atoms is not None:
self.calculate_isolate_molecular_levels(tp)
self.overhead_data_saved = False
if world.rank == 0:
if not os.access('analysis_data', os.F_OK):
os.mkdir('analysis_data')
if not os.access('analysis_data/ionic_step_0', os.F_OK):
os.mkdir('analysis_data/ionic_step_0')
world.barrier()
self.data = {}
