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# -*- 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
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