@@ -1688,3 +1688,148 @@ def get_orb_from_str(orbs):
16881688 orbitals = [(int (orb [0 ]), Orbital (orb_labs .index (orb [1 :]))) for orb in orbs ]
16891689 orb_label = f"{ orbitals [0 ][0 ]} { orbitals [0 ][1 ].name } { orbitals [1 ][0 ]} { orbitals [1 ][1 ].name } # type: ignore
16901690 return orb_label , orbitals
1691+
1692+
1693+ class LobsterMatrices :
1694+ """
1695+ Class to read Matrices file generated by LOBSTER (e.g. hamiltonMatrices.lobster).
1696+
1697+ Attributes:
1698+ for filename == "hamiltonMatrices.lobster"
1699+ onsite_energies (list[np.arrays]): List real part of onsite energies from the matrices each k-point.
1700+ average_onsite_energies (dict): dict with average onsite elements energies for all k-points with keys as
1701+ basis used in the LOBSTER computation (uses only real part of matrix).
1702+ hamilton_matrices (dict[np.arrays]) : dict with the complex hamilton matrix
1703+ at each k-point with k-point and spin as keys
1704+
1705+ for filename == "coefficientMatrices.lobster"
1706+
1707+ onsite_coefficients (list[np.arrays]): List real part of onsite coefficients from the matrices each k-point.
1708+ average_onsite_coefficient (dict): dict with average onsite elements coefficients for all k-points with keys as
1709+ basis used in the LOBSTER computation (uses only real part of matrix).
1710+ coefficient_matrices (dict[np.arrays]) : dict with the coefficients matrix
1711+ at each k-point with k-point and spin as keys
1712+
1713+ for filename == "transferMatrices.lobster"
1714+
1715+ onsite_transfer (list[np.arrays]): List real part of onsite transfer coefficients from the matrices at each
1716+ k-point.
1717+ average_onsite_transfer (dict): dict with average onsite elements transfer coefficients for all k-points with
1718+ keys as basis used in the LOBSTER computation (uses only real part of matrix).
1719+ transfer_matrices (dict[np.arrays]) : dict with the coefficients matrix at
1720+ each k-point with k-point and spin as keys
1721+
1722+ for filename == "overlapMatrices.lobster"
1723+
1724+ onsite_overlaps (list[np.arrays]): List real part of onsite overlaps from the matrices each k-point.
1725+ average_onsite_overlaps (dict): dict with average onsite elements overlaps for all k-points with keys as
1726+ basis used in the LOBSTER computation (uses only real part of matrix).
1727+ overlap_matrices (dict[np.arrays]) : dict with the overlap matrix at
1728+ each k-point with k-point as keys
1729+ """
1730+
1731+ def __init__ (self , e_fermi = None , filename : str = "hamiltonMatrices.lobster" ):
1732+ """
1733+ Args:
1734+ filename: filename for the hamiltonMatrices file, typically "hamiltonMatrices.lobster".
1735+ e_fermi: fermi level in eV for the structure only
1736+ relevant if input file contains hamilton matrices data
1737+ """
1738+
1739+ self ._filename = filename
1740+ # hamiltonMatrices
1741+ with zopen (self ._filename , "rt" ) as f :
1742+ file_data = f .readlines ()
1743+ if len (file_data ) == 0 :
1744+ raise OSError ("Please check provided input file, it seems to be empty" )
1745+
1746+ pattern_coeff_hamil_trans = r"(\d+)\s+kpoint\s+(\d+)" # regex pattern to extract spin and k-point number
1747+ pattern_overlap = r"kpoint\s+(\d+)" # regex pattern to extract k-point number
1748+
1749+ if "hamilton" in self ._filename :
1750+ if e_fermi is None :
1751+ raise ValueError ("Please provide the fermi energy in eV " )
1752+ self .onsite_energies , self .average_onsite_energies , self .hamilton_matrices = self ._parse_matrix (
1753+ file_data = file_data , pattern = pattern_coeff_hamil_trans , e_fermi = e_fermi
1754+ )
1755+
1756+ elif "coefficient" in self ._filename :
1757+ self .onsite_coefficients , self .average_onsite_coefficient , self .coefficient_matrices = self ._parse_matrix (
1758+ file_data = file_data , pattern = pattern_coeff_hamil_trans , e_fermi = 0
1759+ )
1760+
1761+ elif "transfer" in self ._filename :
1762+ self .onsite_transfer , self .average_onsite_transfer , self .transfer_matrices = self ._parse_matrix (
1763+ file_data = file_data , pattern = pattern_coeff_hamil_trans , e_fermi = 0
1764+ )
1765+
1766+ elif "overlap" in self ._filename :
1767+ self .onsite_overlaps , self .average_onsite_overlaps , self .overlap_matrices = self ._parse_matrix (
1768+ file_data = file_data , pattern = pattern_overlap , e_fermi = 0
1769+ )
1770+
1771+ @staticmethod
1772+ def _parse_matrix (file_data , pattern , e_fermi ):
1773+ complex_matrices = {}
1774+ matrix_diagonal_values = []
1775+ start_inxs_real = []
1776+ end_inxs_real = []
1777+ start_inxs_imag = []
1778+ end_inxs_imag = []
1779+ # get indices of real and imaginary part of matrix for each k point
1780+ for i , line in enumerate (file_data ):
1781+ line = line .strip ()
1782+ if "Real parts" in line :
1783+ start_inxs_real .append (i + 1 )
1784+ if i == 1 : # ignore the first occurrence as files start with real matrices
1785+ pass
1786+ else :
1787+ end_inxs_imag .append (i - 1 )
1788+ matches = re .search (pattern , file_data [i - 1 ])
1789+ if matches and len (matches .groups ()) == 2 :
1790+ k_point = matches .group (2 )
1791+ complex_matrices [k_point ] = {}
1792+ if "Imag parts" in line :
1793+ end_inxs_real .append (i - 1 )
1794+ start_inxs_imag .append (i + 1 )
1795+ # explicitly add the last line as files end with imaginary matrix
1796+ if i == len (file_data ) - 1 :
1797+ end_inxs_imag .append (len (file_data ))
1798+
1799+ # extract matrix data and store diagonal elements
1800+ for start_inx_real , end_inx_real , start_inx_imag , end_inx_imag in zip (
1801+ start_inxs_real , end_inxs_real , start_inxs_imag , end_inxs_imag
1802+ ):
1803+ # matrix with text headers
1804+ matrix_real = file_data [start_inx_real :end_inx_real ]
1805+ matrix_imag = file_data [start_inx_imag :end_inx_imag ]
1806+
1807+ # extract only numerical data and convert to numpy arrays
1808+ matrix_array_real = np .array ([line .split ()[1 :] for line in matrix_real [1 :]], dtype = float )
1809+ matrix_array_imag = np .array ([line .split ()[1 :] for line in matrix_imag [1 :]], dtype = float )
1810+
1811+ # combine real and imaginary parts to create a complex matrix
1812+ comp_matrix = matrix_array_real + 1j + matrix_array_imag
1813+
1814+ matches = re .search (pattern , file_data [start_inx_real - 2 ])
1815+ if matches and len (matches .groups ()) == 2 :
1816+ spin = Spin .up if matches .group (1 ) == "1" else Spin .down
1817+ k_point = matches .group (2 )
1818+ complex_matrices [k_point ].update ({spin : comp_matrix })
1819+ elif matches and len (matches .groups ()) == 1 :
1820+ k_point = matches .group (1 )
1821+ complex_matrices .update ({k_point : comp_matrix })
1822+ matrix_diagonal_values .append (comp_matrix .real .diagonal () - e_fermi )
1823+
1824+ # extract elements basis functions as list
1825+ elements_basis_functions = [
1826+ line .split ()[:1 ][0 ] for line in matrix_real if line .split ()[:1 ][0 ] != "basisfunction"
1827+ ]
1828+
1829+ # get average row-wise
1830+ average_matrix_diagonal_values = np .array (matrix_diagonal_values , dtype = float ).mean (axis = 0 )
1831+
1832+ # get a dict with basis functions as keys and average values as values
1833+ average_average_matrix_diag_dict = dict (zip (elements_basis_functions , average_matrix_diagonal_values ))
1834+
1835+ return matrix_diagonal_values , average_average_matrix_diag_dict , complex_matrices
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