wavefunction_analysis.dynamics package

Submodules

wavefunction_analysis.dynamics.dimers_in_crystal module

add_molecule(ix, iy, iz, inverse, abc, angles, elements, scales)

add_molecules_cell(n_images, abc, angles, elements, scales)

cal_dipole_interactions(dipoles, coords)

dipole_dipole_interaction(d1, d2, r1, r2)

d1, d2: dipoles (x,y,z) r1, r2: dipole center coordinates (x, y, z)

get_center_of_mass(atmsym, coords)

read_unit_cell_info(ciff)

translate_molecule(ix, iy, iz, abc, angles, elements, coords0)

write_eda_files(elements, coordinates, mol)

write_xyz_files(elements, coordinates, mol)

wavefunction_analysis.dynamics.electronic_dynamics_gs module

class CurvyElectronicDynamicsStep(key)

Bases: ElectronicDynamicsStep

refer: Herbert 2004 JCP 10.1063/1.1814934

cal_electronic_energy_force(F, P, Z)

cy_get_mass_on_basis(F)

cy_orbital_response()

cy_update_delta(G, mass_bas)

cy_update_density(P, Z)

euler_step(G, mass_bas)

get_electronic_kinetic_energy(velocities, mass)

init_electronic_density_static(coords)

leapfrog_step(G, mass_bas)

update_electronic_density_static(coords)

update_electronic_density_static2(coords)

velocity_verlet_step(G, mass_bas, half)

class ElectronicDynamicsStep(key, **kwargs)

Bases: object

cal_electronic_force()

get_ortho_basis(ovlp=None)

init_electronic_density_static(coords, *args, **kwargs)

setup_electronic_basis(coords, *args, **kwargs)

update_electronic_density_dynamics(coords)

update_electronic_density_static(coords, *args, **kwargs)

class ExtendedLagElectronicDynamicsStep(key)

Bases: ElectronicDynamicsStep

refer: Niklasson 2009 JCP 10.1063/1.3148075

Niklasson 2017 JCP 10.1063/1.4985893 Niklasson 2020 JCP 10.1063/1.5143270

init_electronic_density_static(coords)

init_xl_variables()

static_extended_lagrange()

update_electronic_density_static(coords)

xl_auxiliary_density_dotdot()

xl_build_fock(coords)

xl_build_fock_init(coords, k)

class GrassmannElectronicDynamicsStep(key)

Bases: ElectronicDynamicsStep

init_electronic_density_static(coords)

interpolation(coords)

update_electronic_density_static(coords)

update_gamma_lagrange(coords)

cal_electronic_energy1(mf, P1, Z=None, method='lowdin')

normal energy

cal_electronic_energy2(mf, P1, Z=None, method='lowdin')

extended lagrange energy

cal_electronic_force(mf, P1, P2=None, P3=None, F=None, Z=None, method='lowdin')

cal_idempotency(P, S=None)

cal_pulay_force(mf, F, P, Fao, Pao, Z, method='lowdin')

density_purification(P, S=None)

run_pyscf_gs(scf_method, mol, functional, *args, **kwargs)

wavefunction_analysis.dynamics.exciton_dynamics module

class Dynamics(key, **kwargs)

Bases: object

kernel()

plot_time_variables(fig_name=None)

class ExcitonDynamicsStep(key={}, **kwargs)

Bases: object

analyze_wf_property(coefficients=None, c2=None)

cal_energy(hamiltonian=None, coefficients=None)

cal_force(coordinate, coefficients=None)

cal_ipr_value(coefficients=None, c2=None)

cal_r_correlation(coefficients=None, c2=None)

check_sanity()

check the input parameters

convert_parameter_units(unit_dict)

get_exciton_couplings(coordinate)

get_exciton_diagonal(coordinate)

get_exciton_hamiltonian(coordinate)

get_exciton_hamiltonian0()

get_exciton_hamiltonian1(coordinate)

get_exciton_hamiltonian2(coordinate)

get_initial_coefficients(coordinate)

get_unit_cell_info(cif)

process_parameters()

update_coefficients(coordinate, coordinate1=None, dt=None)

class ExcitonDynamicsStep3D(key={}, **kwargs)

Bases: ExcitonDynamicsStep

cal_force(coordinate, coefficients=None)

get_exciton_couplings(coordinate)

process_parameters()

class OscillatorDynamicsStep(key={}, **kwargs)

Bases: harmonic_oscillator

convert_parameter_units(unit_dict)

required input:

mass in amu frequency in meV

get_phonon_hamiltonian(velocity=None, coordinate=None, mass=None, omega2=None)

get_boltzmann_beta(temperature)

wavefunction_analysis.dynamics.molecular_dynamics module

class MolecularDynamics(key, ed_key={}, ph_key={}, **kwargs)

Bases: object

plot_time_variables(fig_name=None)

run_dynamics()

set_electronic_step(key, **kwargs)

set_nuclear_step(key)

set_photon_step(key, **kwargs)

plot_time_variables(total_time, nsteps, dists, energies)

wavefunction_analysis.dynamics.oscillator_dynamics module

class NuclearDynamicsStep(key={}, **kwargs)

Bases: harmonic_oscillator

convert_parameter_units(unit_dict)

get_potential_energy(mass=None, coordinate=None, omega2=None)

init_coordinate_velocity(init_method=None)

generate the initial oscillator coordinate and velocities n_site: number of total molecular sites

init_velocity_random(etrans=None, sigma=0.0001, scale=0.1, seed=12345)

random kinetic energy for atoms at three directions

init_velocity_thermo(temp=None, seed=1385448536)

random velocity following Boltzmann distribution

project_force(force, mass=None, coords=None)

project_velocity(velocity, mass=None, coords=None)

update_coordinate_velocity(force, half=1, **kwargs)

angular_property(mass, coords, props)

get_boltzmann_beta(temperature)

class harmonic_oscillator(key={}, **kwargs)

Bases: object

euler_step(force)

get_energy(velocity, mass=None, coordinate=None, omega2=None)

get_kinetic_energy(velocity, mass=None)

get_potential_energy(mass=None, coordinate=None, omega2=None)

init_coordinate_velocity(n_site=None, init_method=None)

generate the initial oscillator coordinate and velocities n_site: number of total molecular sites

leapfrog_step(force)

recursive_exploration_step(force, force_func, **kwargs)

update_coordinate_velocity(force, half=1, **kwargs)

velocity_verlet_step(force, half)

remove_trans_rotat_force(force, mass, coords)

remove_trans_rotat_velocity(velocity, mass, coords)

wavefunction_analysis.dynamics.photon_dynamics module

class PhotonDynamicsStep(key, **kwargs)

Bases: object

get_initial_density(ntot, ns)

update_density(molecular_dipole, dt, half=1)

class PhotonDynamicsStep2(key={}, **kwargs)

Bases: harmonic_oscillator

convert_parameter_units(unit_dict)

get_minimim_displacement(molecular_dipole)

update_density(molecular_dipole, dt, half=1)

get_trans_amplitude(ntot, coupling=1.0, energy=None, vector=False)

Module contents