API Reference

Analyzer(info_name[, echo_details])	Class for analyzing correlation functions.
Berry(model[, overlap, echo_details])	Berry curvature and Chern number calculator.
BerryData(prefix)	Data class of Berry connection and curvature.
CachedSample([directory])	Sample with attributes loaded from disk.
ConfigParser(file_name)	Parser for *_config.dat and *_info.dat
DiagConfig()	Class for representing Diagonalization parameters.
DiagSolver(model[, overlap, echo_details])	Base class for solvers based on exact diagonalization.
GeneralOrbitalMap()	Helper class for converting orbital indices between pc and sc representations in general cases.
HopDict(num_orb)	Class for holding hopping terms in matrix form, reserved for compatibility with old version of TBPlaS.
JobInfo(file_name)	Container of parameters produced by TBPM calculations.
Lindhard(model[, overlap, echo_details])	Lindhard function calculator.
MPIEnv([echo_details])	Wrapper over MPI4PY APIs.
PCHopNotFoundError(hop_ind)	Exception for a non-existing Hopping term.
PCInterHopping(pc_bra, pc_ket)	Class for holding hopping terms between different primitive cells in hetero-structure.
ParamFit(k_points[, weights])	Class for fitting on-site energies and hopping parameters to reference band data.
PrimitiveCell([lat_vec, origin, unit])	Class for representing the primitive cell.
ProgressBar(num_tasks[, num_scales])	Class for reporting the progress for a time-consuming task.
RegularOrbitalMap(dim, num_orb_pc)	Similar to GeneralOrbitalMap, but the orbitals are generated using a 4-fold loops over dim_a, dim_b, dim_c and num_orb_pc.
RegularOrbitalMapVac(dim, num_orb_pc, ...)	Similar to RegularOrbitalMap, but can handle cases with vacancies.
SCInterHopping(sc_bra, sc_ket)	Container class for hopping terms between different supercells within the sample.
SK()	Class for evaluating hopping integrals using Slater-Koster formula.
SOC()	Class for evaluating spin-orbital coupling terms.
SOCTable()	Hard-coded spin-orbital coupling term table, generated using the 'print_soc_table' method of 'SOC' class.
SOCTable2()	Hard-coded spin-orbital coupling term table, taking from https://journals.aps.org/prb/abstract/10.1103/PhysRevB.82.245412
Sample(*args)	Combination of SuperCell and SCInterHopping.
SpinData(prefix)	Data class of spin texture.
SpinTexture(model[, overlap, echo_details])	Spin texture calculator.
SuperCell(prim_cell, dim[, pbc, check_dim, ...])	Class for representing a supercell from which the sample is constructed.
TBPMConfig()	Class for representing TBPM parameters.
TBPMSolver(model[, echo_details])	Wrapper class over C++ TBPM subroutines.
TestHelper(tester)	Helper class that makes unittest easier.
Timer()	Class for measuring the time usage of function calls within programs.
Visualizer([echo_details])	Class for quick data visualization.
Z2(model[, overlap, echo_details])	Class for evaluating the Z2 topological invariant.
calc_bands(model, k_path, **kwargs)	Function for quick calculation of band structure.
calc_dos(model, k_points, **kwargs)	Function for quick calculation of dos.
cart2frac(lat_vec, cart_coord[, origin])	Convert Cartesian coordinates to fractional coordinates. :param lat_vec: (3, 3) float64 array Cartesian coordinates of lattice vectors, with each ROW being a vector :param cart_coord: (num_coord, 3) float64 array Cartesian coordinates to convert :param origin: (3, ) float64 array Cartesian coordinate of lattice origin :return: (num_coord, 3) float64 array fractional coordinates in basis of lattice vectors.
cart2frac_s(lat_vec, cart_coord[, origin])	Convert a single Cartesian coordinate to fractional. :param lat_vec: (3, 3) float64 array Cartesian coordinates of lattice vectors, with each ROW being a vector :param cart_coord: (3, ) float64 array Cartesian coordinate to convert :param origin: (3, ) float64 array Cartesian coordinate of lattice origin :return: (3, ) float64 array fractional coordinate in basis of lattice vectors.
extend_prim_cell(prim_cell[, dim])	Extend primitive cell along a, b and c directions.
find_neighbors(cell_bra[, cell_ket, a_max, ...])	Find neighbours between the (0, 0, 0) cell of model_bra and nearby cells of cell_ket up to given cutoff distance.
flatten_matrix(data)	Convert matrix with only one ROW or COLUMN to a ROW vector. :param data: (1, num_col) or (num_row, 1) array matrix to convert :return: (num_col, ) or (num_row, ) vector.
frac2cart(lat_vec, frac_coord[, origin])	Convert fractional coordinates to Cartesian coordinates. :param lat_vec: (3, 3) float64 array Cartesian coordinates of lattice vectors, with each ROW being a vector :param frac_coord: (num_coord, 3) float64 array fractional coordinates to convert in basis of lattice vectors :param origin: (3, ) float64 array Cartesian coordinate of lattice origin :return: (num_coord, 3) float64 array Cartesian coordinates converted from fractional coordinates.
frac2cart_s(lat_vec, frac_coord[, origin])	Convert a single fractional coordinate to Cartesian. :param lat_vec: (3, 3) float64 array Cartesian coordinates of lattice vectors, with each ROW being a vector :param frac_coord: (3, ) float64 array fractional coordinate to convert in basis of lattice vectors :param origin: (3, ) float64 array Cartesian coordinate of lattice origin :return: (3, ) float64 array Cartesian coordinate converted from fractional coordinate.
gen_kdist(lat_vec, kpoints)	Convert k_path generated by gen_path into distances in reciprocal space. :param lat_vec: (3, 3) float64 array Cartesian coordinates of lattice vectors, with each ROW being a vector :param kpoints: (nk, 3) float64 array fractional coordinates of kpoints :return: (nk, ) float64 array distance in reciprocal space in unit of reciprocal lattice vectors.
gen_kmesh(grid_size)	Generate uniform mesh grid in the first Brillouin zone. :param grid_size: (na, nb, nc) dimension of mesh grid along three directions :return: (na*nb*nc, 3) float64 array fractional coordinates of kpoints in the grid.
gen_kpath(hs_kpoints, num_interp)	Generate path in the reciprocal space connecting highly symmetric k-points. :param hs_kpoints: (nk, 3) float64 array fractional coordinates of highly symmetric k-points :param num_interp: (nk-1, ) tuple of integers numbers of intermediate k-points between two highly symmetric k-points :return: (kpath, hs_index) kpath: (sum(num_interp)+1, 3) float64 array fractional coordinates of k-points along the path hs_index: (nk, ) int32 array indices of highly symmetric k-points in kpath.
gen_lattice_vectors([a, b, c, alpha, beta, ...])	Generate lattice vectors from given lattice parameters.
gen_reciprocal_vectors(lat_vec)	Generate reciprocal lattice vectors from real-space lattice vectors.
gen_seeds(num_seeds)	Generate a list of random numbers from /dev/urandom as seeds for Python random number generator.
get_datetime([fmt])	Return current date and time.
get_lattice_area(lat_vec[, direction])	Calculate the area along given direction. :param lat_vec: (3, 3) float64 array Cartesian coordinates of lattice vectors, with each ROW being a vector :param direction: direction along which the area is evaluated, should be in ("a", "b", "c") :return: area along given direction in squared unit of lattice vectors.
get_lattice_volume(lat_vec)	Calculate the volume formed by lattice vectors. :param lat_vec: (3, 3) float64 array Cartesian coordinates of lattice vectors, with each ROW being a vector :return: lattice volume in cubic unit of lattice vectors.
get_qe_indices(config, energies)	Get the indices of quasi-eigenstates in energies, for calculating and analyzing DC conductivity. :param config: 'Config' instance parameters controlling TBPM calculation :param energies: (num_eng,) float64 array energies corresponding to TBPM steps, for indexing the quasi-eigenstates :return: indices of the quasi-eigenstates.
h5_load_complex(file_name, key[, transpose, ...])	Load a double complex matrix from hdf5 file.
h5_load_double(file_name, key[, transpose, ...])	Load a double matrix from hdf5 file.
h5_repack_directory([dir_name])	Repack all h5 files under given directory.
h5_repack_file(file_name)	Repack h5 file after shrinking dataset to free disk usage.
load_ac_cond(prefix[, data_name])	Load AC Conductivity from file. :param prefix: prefix of data file :param data_name: name of data file :return: (omegas, ac_cond) omegas: (num_omega,) float64 array energies in eV ac_cond: (num_omega,) complex128 array AC conductivity in e**2/(hbar*nm) in 3d case and e**2/hbar in 2d case.
load_bands(prefix[, data_name])	Load band structure. :param prefix: prefix of data file :param data_name: name of data file :return: (k_len, bands) k_len: (num_kpt,) float64 array, length of k-path bands: (num_kpt, num_bands) float64 array, band structure.
load_berry(prefix[, data_name])	Load Berry curvature. :param prefix: prefix of data files :param data_name: name of data file :return: (kpt_cart, bands, omega_xy) kpt_cart: (num_kpt, 3) float64 array Cartesian coordinates of k-points bands: (num_kpt, num_states) float64 array energies in eV omega_xy: (num_kpt, num_states) float64 array Berry curvature in NM^2.
load_corr_ac_cond(prefix[, data_name])	Load AC Conductivity correlation function. :param prefix: prefix of data file :param data_name: name of data file :return: (4, num_steps) complex128 array AC correlation function along xx, yx, xy, yy directions Unit is e^2/h_bar^2 * (eV)^2 * nm^2.
load_corr_bands(prefix[, data_name])	Load band structure correlation function. :param prefix: prefix of data file :param data_name: name of data file :return: (k_len, corr_bands) k_len: (num_kpt, ) float64 array length of kpath in 1/nm corr_bands: (num_kpt, num_steps+1) complex128 array correlation for each k-point.
load_corr_dc_cond(prefix[, data_name])	Load DC conductivity correlation function. :param prefix: prefix of data file :param data_name: name of data file :return: (corr_dos, corr_dc_cond) corr_dos: (num_steps,) complex128 array dimensionless DOS correlation function corr_dc_cond: (2, num_eng, num_steps_dc) complex128 array DC conductivity correlation function in e^2/h_bar^2 * (eV)^2 * nm^2 in accordance with config.dckb_energies.
load_corr_dos(prefix[, data_name])	Load DOS correlation function. :param prefix: prefix of data file :param data_name: name of data file :return: (num_steps+1, ) complex128 array dimensionless DOS correlation function.
load_corr_dyn_pol(prefix[, data_name])	Load dynamic polarizability correlation function. :param prefix: prefix of data file :param data_name: name of data file :return: (num_qpt, num_steps) float64 array dimensionless Dynamical polarization correlation function.
load_dos(prefix[, data_name])	Load DOS. :param prefix: prefix of data file :param data_name: name of data file :return: (energies, dos) energies: (num_eng,) float64 array energies determined by e_min, e_max and e_step dos: (num_eng,) float64 array density of states in states/eV.
load_dyn_pol(prefix[, data_name])	Load dynamic polarizability from file. :param prefix: prefix of data file :param data_name: name of data file :return: (omegas, dyn_pol) omegas: (num_omega,) float64 array energies in eV dyn_pol: (num_qpt, num_omega) complex128 array dynamic polarizability in 1/(eV*nm**2) or 1/(eV*nm**3).
load_epsilon(prefix[, data_name])	Load dielectric function from file. :param prefix: prefix of data file :param data_name: name of data file :return: (omegas, epsilon) omegas: (num_omega,) float64 array energies in eV epsilon: (num_qpt, num_omega) complex128 array relative dielectric function.
load_hall_cond(prefix[, data_name])	Load LDOS data produced by Haydock method. :param prefix: prefix of data file :param data_name: name of data file :return: (energies, conductivity) energies: (num_eng, ) float64 array chemical potentials specified in config.dckb_energies conductivity: (num_eng, ) float64 array Hall conductivity according to energies.
load_ldos_haydock(prefix[, data_name])	Load LDOS data produced by Haydock method. :param prefix: prefix of data file :param data_name: name of data file :return: (energies, ldos) energies: (2*num_steps+1, ) float64 array energies in eV ldos: (2*num_steps+1, ) float64 array LDOS value to corresponding energies in 1/eV.
load_quasi_eigen(prefix[, data_name])	Load squared quasi-eigenstates. :param prefix: prefix of data file :param data_name: name of data file :return: (num_qe, num_orb) float64 array Each row is a squared quasi-eigenstate at energy of config.qe_energies.
load_spin(prefix[, data_name])	Load spin data. :param prefix: prefix of data files :param data_name: name of data file :return: (kpt_cart, bands, sigma_x, sigma_y, sigma_z) kpt_cart: (num_kpt, 3) bands: (num_kpt, num_states) sigma_* (num_kpt, num_states).
load_states(prefix)	Load eigenvalues and eigenstates. :param prefix: prefix of data files :return: (bands, states) bands: (num_kpt, num_bands) float64 array band structure states: (num_kpt, num_bands, num_orb) complex128 array eigenstates at each k-point, with each ROW being a state.
load_wft(prefix[, data_name])	Load wave function. :param prefix: prefix of data file :param data_name: name of data file :return: (num_time, num_orb) complex128 array Each row is time-dependent wave function at config.wft_time_save.
load_z2(prefix[, data_name])	Load Z2 data. :param prefix: prefix of data file :param data_name: name of data file :return: (kb_array, phases) kb_array: (num_kb,) float64 array FRACTIONAL coordinates of the loop along b-axis phases: (num_kpt, num_occ) float64 array phases of WF centers.
make_antimonene([with_soc, soc_lambda, c])	Make antimonene primitive cell.
make_bismuth()	Make bilayer bismuth primitive cell.
make_black_phosphorus([c])	Make black phosphorus primitive cell.
make_graphene_diamond([c, t])	Make graphene primitive cell in diamond shape.
make_graphene_rect([from_scratch, c, t])	Make graphene cell in rectangular shape.
make_graphene_soc([is_qsh])	Set up the primitive cell of graphene according to Kane-Mele model.
make_graphene_sp([c])	Make 8-band graphene primitive cell.
make_hetero_layer(prim_cell, hetero_lattice, ...)	Make one layer in the hetero-structure by reshaping primitive cell to given lattice vectors. :param prim_cell: primitive cell of the layer :param hetero_lattice: (3, 3) float64 array Cartesian coordinates of hetero-structure lattice vectors in NANOMETER :param kwargs: arguments for 'reshape_prim_cell' :return: layer in the hetero-structure.
make_mos2_soc()	Make MoS2 primitive cell with SOC.
make_tmdc([material])	Make TMDC primitive cell.
merge_prim_cell(*args)	Merge primitive cells and inter-hopping dictionaries to build a large primitive cell. :param args: primitive cells and inter-hopping terms within the large primitive cell :return: merged primitive cell.
mpienv_finalize()	Finalize MPI environment.
mpienv_init()	Initialize MPI environment.
np_load_complex(file_name[, transpose, flatten])	Load a double complex matrix from text file.
np_load_double(file_name[, transpose, flatten])	Load a double matrix from text file.
print_banner_block(text[, width, mark, end])	Print a banner like #----------------------------------# # FOO # #----------------------------------# to stdout.
print_banner_line(text[, width, mark, end])	Print a banner like '#--------------- FOO ---------------#' to stdout.
reshape_prim_cell(prim_cell, lat_frac[, delta])	Reshape primitive cell to given lattice vectors. :param prim_cell: primitive cell from which the reshaped cell is constructed :param lat_frac: (3, 3) float64 array FRACTIONAL coordinates of lattice vectors of reshaped cell in basis vectors of primitive cell :param delta: small displacement added to orbital positions such that orbitals fall on cell borders will not be clipped :return: reshaped cell.
rotate_coord(coord[, angle, axis, center])	Rotate Cartesian coordinates according to Euler angles.
spiral_prim_cell(prim_cell[, angle, center, ...])	Rotate and shift primitive cell with respect to z-axis, reserved for compatibility. :param prim_cell: primitive cell to twist :param angle: twisting angle in RADIANs, NOT degrees :param center: (3, ) float64 array Cartesian coordinates of the rotation center in NANOMETER :param shift: distance of shift in NANOMETER :return: None.
split_list(raw_list, num_group[, algorithm])	Split given list into different groups.
split_range(n_max[, num_group])	Split range(n_max) into different groups.
wan2pc([seed_name, correct_hop, hop_eng_cutoff])	Create primitive cell from output of Wannier90. :param seed_name: seed_name of Wannier90 output files :param correct_hop: whether to correct hopping terms using data in seed_name_wsvec.dat :param hop_eng_cutoff: energy cutoff for hopping terms in eV Hopping terms with energy below this threshold will be dropped. :return: primitive cell created from Wannier90 output files :raise FileNotFoundError: if seed_name_wsvec.dat is not found.
window_exp(i, tnr)	Exponential window function.
window_exp_ten(i, tnr)	Exponential window function with base 10.
window_hanning(i, tnr)	Hanning window function.
write_item(f, key, value)	Write key, value pairs to file.