# -*- coding: utf-8 -*- # # Copyright (c) 2018, the cclib development team # # This file is part of cclib (http://cclib.github.io) and is distributed under # the terms of the BSD 3-Clause License. """Utilities often used by cclib parsers and scripts""" import sys import numpy # See https://github.com/kachayev/fn.py/commit/391824c43fb388e0eca94e568ff62cc35b543ecb if sys.version_info <= (3, 3): import operator def accumulate(iterable, func=operator.add): """Return running totals""" # accumulate([1,2,3,4,5]) --> 1 3 6 10 15 # accumulate([1,2,3,4,5], operator.mul) --> 1 2 6 24 120 it = iter(iterable) try: total = next(it) except StopIteration: return yield total for element in it: total = func(total, element) yield total else: from itertools import accumulate def find_package(package): """Check if a package exists without importing it. Derived from https://stackoverflow.com/a/14050282 """ if sys.version_info.major == 2: import pkgutil return pkgutil.find_loader(package) is not None else: import importlib module_spec = importlib.util.find_spec(package) return module_spec is not None and module_spec.loader is not None def symmetrize(m, use_triangle='lower'): """Symmetrize a square NumPy array by reflecting one triangular section across the diagonal to the other. """ if use_triangle not in ('lower', 'upper'): raise ValueError if not len(m.shape) == 2: raise ValueError if not (m.shape[0] == m.shape[1]): raise ValueError dim = m.shape[0] lower_indices = numpy.tril_indices(dim, k=-1) upper_indices = numpy.triu_indices(dim, k=1) ms = m.copy() if use_triangle == 'lower': ms[upper_indices] = ms[lower_indices] if use_triangle == 'upper': ms[lower_indices] = ms[upper_indices] return ms def convertor(value, fromunits, tounits): """Convert from one set of units to another. Sources: NIST 2010 CODATA (http://physics.nist.gov/cuu/Constants/index.html) Documentation of GAMESS-US or other programs as noted """ _convertor = { "time_au_to_fs": lambda x: x * 0.02418884, "fs_to_time_au": lambda x: x / 0.02418884, "Angstrom_to_bohr": lambda x: x * 1.8897261245, "bohr_to_Angstrom": lambda x: x * 0.5291772109, "wavenumber_to_eV": lambda x: x / 8065.54429, "wavenumber_to_hartree": lambda x: x / 219474.6313708, "wavenumber_to_kcal/mol": lambda x: x / 349.7550112, "wavenumber_to_kJ/mol": lambda x: x / 83.5934722814, "wavenumber_to_nm": lambda x: 1e7 / x, "wavenumber_to_Hz": lambda x: x * 29.9792458, "eV_to_wavenumber": lambda x: x * 8065.54429, "eV_to_hartree": lambda x: x / 27.21138505, "eV_to_kcal/mol": lambda x: x * 23.060548867, "eV_to_kJ/mol": lambda x: x * 96.4853364596, "hartree_to_wavenumber": lambda x: x * 219474.6313708, "hartree_to_eV": lambda x: x * 27.21138505, "hartree_to_kcal/mol": lambda x: x * 627.50947414, "hartree_to_kJ/mol": lambda x: x * 2625.4996398, "kcal/mol_to_wavenumber": lambda x: x * 349.7550112, "kcal/mol_to_eV": lambda x: x / 23.060548867, "kcal/mol_to_hartree": lambda x: x / 627.50947414, "kcal/mol_to_kJ/mol": lambda x: x * 4.184, "kJ/mol_to_wavenumber": lambda x: x * 83.5934722814, "kJ/mol_to_eV": lambda x: x / 96.4853364596, "kJ/mol_to_hartree": lambda x: x / 2625.49963978, "kJ/mol_to_kcal/mol": lambda x: x / 4.184, "nm_to_wavenumber": lambda x: 1e7 / x, # Taken from GAMESS docs, "Further information", # "Molecular Properties and Conversion Factors" "Debye^2/amu-Angstrom^2_to_km/mol": lambda x: x * 42.255, # Conversion for charges and multipole moments. "e_to_coulomb": lambda x: x * 1.602176565 * 1e-19, "e_to_statcoulomb": lambda x: x * 4.80320425 * 1e-10, "coulomb_to_e": lambda x: x * 0.6241509343 * 1e19, "statcoulomb_to_e": lambda x: x * 0.2081943527 * 1e10, "ebohr_to_Debye": lambda x: x * 2.5417462300, "ebohr2_to_Buckingham": lambda x: x * 1.3450341749, "ebohr2_to_Debye.ang": lambda x: x * 1.3450341749, "ebohr3_to_Debye.ang2": lambda x: x * 0.7117614302, "ebohr4_to_Debye.ang3": lambda x: x * 0.3766479268, "ebohr5_to_Debye.ang4": lambda x: x * 0.1993134985, } return _convertor["%s_to_%s" % (fromunits, tounits)](value) class PeriodicTable(object): """Allows conversion between element name and atomic no.""" def __init__(self): self.element = [ None, 'H', 'He', 'Li', 'Be', 'B', 'C', 'N', 'O', 'F', 'Ne', 'Na', 'Mg', 'Al', 'Si', 'P', 'S', 'Cl', 'Ar', 'K', 'Ca', 'Sc', 'Ti', 'V', 'Cr', 'Mn', 'Fe', 'Co', 'Ni', 'Cu', 'Zn', 'Ga', 'Ge', 'As', 'Se', 'Br', 'Kr', 'Rb', 'Sr', 'Y', 'Zr', 'Nb', 'Mo', 'Tc', 'Ru', 'Rh', 'Pd', 'Ag', 'Cd', 'In', 'Sn', 'Sb', 'Te', 'I', 'Xe', 'Cs', 'Ba', 'La', 'Ce', 'Pr', 'Nd', 'Pm', 'Sm', 'Eu', 'Gd', 'Tb', 'Dy', 'Ho', 'Er', 'Tm', 'Yb', 'Lu', 'Hf', 'Ta', 'W', 'Re', 'Os', 'Ir', 'Pt', 'Au', 'Hg', 'Tl', 'Pb', 'Bi', 'Po', 'At', 'Rn', 'Fr', 'Ra', 'Ac', 'Th', 'Pa', 'U', 'Np', 'Pu', 'Am', 'Cm', 'Bk', 'Cf', 'Es', 'Fm', 'Md', 'No', 'Lr', 'Rf', 'Db', 'Sg', 'Bh', 'Hs', 'Mt', 'Ds', 'Rg', 'Cn', 'Uut', 'Fl', 'Uup', 'Lv', 'Uus', 'Uuo'] self.number = {} for i in range(1, len(self.element)): self.number[self.element[i]] = i class WidthSplitter: """Split a line based not on a character, but a given number of field widths. """ def __init__(self, widths): self.start_indices = [0] + list(accumulate(widths))[:-1] self.end_indices = list(accumulate(widths)) def split(self, line, truncate=True): """Split the given line using the field widths passed in on class initialization. """ elements = [line[start:end].strip() for (start, end) in zip(self.start_indices, self.end_indices)] # Handle lines that contain fewer fields than specified in the # widths; they are added as empty strings, so remove them. if truncate: while len(elements) and elements[-1] == '': elements.pop() return elements