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Merge pull request #297 from MolSSI-BSE/fix_esc
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Fix docstring and other escape sequence issues
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@bennybp
bennybp authored Jan 2, 2024
2 parents df2ec0c + d065ea1 commit 1043458
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Showing 2 changed files with 34 additions and 34 deletions.
66 changes: 33 additions & 33 deletions basis_set_exchange/ints.py
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Original file line number Diff line number Diff line change
Expand Up @@ -28,11 +28,11 @@
# ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
# POSSIBILITY OF SUCH DAMAGE.

'''
"""
One-center integrals for Gaussian-type and Slater-type orbitals
Written by Susi Lehtola, 2020
'''
"""

from math import gamma, sqrt

Expand All @@ -44,15 +44,15 @@


def _transform_numpy(C0, P0):
'''Transforms the primitive integrals P into the contracted basis C using NumPy'''
"""Transforms the primitive integrals P into the contracted basis C using NumPy"""
C = numpy.asarray(C0)
P = numpy.asarray(P0)
np_result = numpy.dot(numpy.dot(C, P), C.T)
return [[np_result[i][j] for i in range(np_result.shape[0])] for j in range(np_result.shape[1])]


def _matmul(A, B):
'''Matrix multiply'''
"""Matrix multiply"""
assert (len(A[0]) == len(B))
result = [[0.0 for i in range(len(B[0]))] for j in range(len(A))]
for i in range(len(A)):
Expand All @@ -63,7 +63,7 @@ def _matmul(A, B):


def _transform_python(C, P):
'''Transforms the primitive integrals P into the contracted basis C in pure Python'''
"""Transforms the primitive integrals P into the contracted basis C in pure Python"""

# C transpose
nrows = len(C)
Expand All @@ -74,7 +74,7 @@ def _transform_python(C, P):


def _to_float(M):
'''Transforms a vector or matrix from string representation to floating point representation'''
"""Transforms a vector or matrix from string representation to floating point representation"""

nrows = len(M)
if isinstance(M[0], list):
Expand All @@ -93,7 +93,7 @@ def _to_float(M):


def _to_int(M):
'''Transforms a vector from string representation to int representation'''
"""Transforms a vector from string representation to int representation"""
nrows = len(M)
if isinstance(M[0], str):
return [int(M[i]) for i in range(nrows)]
Expand All @@ -102,7 +102,7 @@ def _to_int(M):


def _transform(C, P):
'''Transforms the primitive integrals P into the contracted basis C in numpy if it's available'''
"""Transforms the primitive integrals P into the contracted basis C in numpy if it's available"""

if _use_numpy:
return _transform_numpy(C, P)
Expand All @@ -111,12 +111,12 @@ def _transform(C, P):


def _zero_matrix(N):
'''Allocates a zero matrix of size N x N'''
"""Allocates a zero matrix of size N x N"""
return [[0.0 for _ in range(N)] for _ in range(N)]


def _normalize_contraction(contr, ovl):
'''Returns a normalized contraction matrix given the overlap matrix'''
"""Returns a normalized contraction matrix given the overlap matrix"""

# Number of contractions
nprim = len(contr[0])
Expand All @@ -140,11 +140,11 @@ def _normalize_contraction(contr, ovl):


def _gto_overlap(exps, l):
'''Computes the primitive overlap matrix for the given exponents,
"""Computes the primitive overlap matrix for the given exponents,
assuming the basis functions are of the spherical form r^l exp(-z
r^2).
'''
"""
assert (isinstance(l, int) and l >= 0)

def ovl(a, b, l):
Expand All @@ -162,11 +162,11 @@ def ovl(a, b, l):


def gto_overlap_contr(exps0, contr0, l):
'''Computes the overlap matrix in the contracted basis, assuming the
basis functions are of the spherical form r^l \sum_i c_i exp(-z_i
"""Computes the overlap matrix in the contracted basis, assuming the
basis functions are of the spherical form r^l \\sum_i c_i exp(-z_i
r^2).
'''
"""

# Convert exponents and contractions to floating point
exps = _to_float(exps0)
Expand All @@ -177,10 +177,10 @@ def gto_overlap_contr(exps0, contr0, l):


def _gto_R(exps, l):
'''Computes the <r> matrix for the given exponents, assuming the basis
"""Computes the <r> matrix for the given exponents, assuming the basis
functions are of the normalized spherical form r^l exp(-z r^2).
'''
"""
assert (isinstance(l, int) and l >= 0)

def rval(a, b, l):
Expand All @@ -199,11 +199,11 @@ def rval(a, b, l):


def gto_R_contr(exps0, contr0, l):
'''Computes the r matrix in the contracted basis, assuming the basis
functions are of the spherical form r^l \sum_i c_i exp(-z_i r^2).
"""Computes the r matrix in the contracted basis, assuming the basis
functions are of the spherical form r^l \\sum_i c_i exp(-z_i r^2).
The function also takes care of proper normalization.
'''
"""

# Convert exponents and contractions to floating point
exps = _to_float(exps0)
Expand All @@ -220,10 +220,10 @@ def gto_R_contr(exps0, contr0, l):


def _gto_Rsq(exps, l):
'''Computes the r^2 matrix for the given exponents, assuming the basis
"""Computes the r^2 matrix for the given exponents, assuming the basis
functions are of the normalized spherical form r^l exp(-z r^2).
'''
"""
assert (isinstance(l, int) and l >= 0)

def rsq(a, b, l):
Expand All @@ -242,11 +242,11 @@ def rsq(a, b, l):


def gto_Rsq_contr(exps0, contr0, l):
'''Computes the r^2 matrix in the contracted basis, assuming the basis
functions are of the spherical form r^l \sum_i c_i exp(-z_i r^2).
"""Computes the r^2 matrix in the contracted basis, assuming the basis
functions are of the spherical form r^l \\sum_i c_i exp(-z_i r^2).
The function also takes care of proper normalization.
'''
"""

# Convert exponents and contractions to floating point
exps = _to_float(exps0)
Expand All @@ -263,11 +263,11 @@ def gto_Rsq_contr(exps0, contr0, l):


def _sto_overlap(exps, ns):
'''Computes the primitive overlap matrix for the given exponents and
"""Computes the primitive overlap matrix for the given exponents and
primary quantum numbers, assuming the basis functions are of the
spherical form r^(n-1) exp(-z r).
'''
"""
assert (len(exps) == len(ns))

def ovl(za, zb, na, nb):
Expand All @@ -285,10 +285,10 @@ def ovl(za, zb, na, nb):


def sto_overlap_contr(exps0, contr0, ns0):
'''Computes the overlap matrix in the contracted basis, assuming the
"""Computes the overlap matrix in the contracted basis, assuming the
basis functions are of the spherical form r^(n-1) exp(-z r).
'''
"""
# Convert exponents and contractions to floating point
exps = _to_float(exps0)
contr = _to_float(contr0)
Expand All @@ -300,11 +300,11 @@ def sto_overlap_contr(exps0, contr0, ns0):


def _sto_Rsq(exps, ns):
'''Computes the primitive r^2 matrix for the given exponents and
"""Computes the primitive r^2 matrix for the given exponents and
primary quantum numbers, assuming the basis functions are of the
spherical form r^(n-1) exp(-z r).
'''
"""
assert (len(exps) == len(ns))

def rsq(za, zb, na, nb):
Expand All @@ -322,10 +322,10 @@ def rsq(za, zb, na, nb):


def sto_Rsq_contr(exps0, contr0, ns0):
'''Computes the r^2 matrix in the contracted basis, assuming the basis
"""Computes the r^2 matrix in the contracted basis, assuming the basis
functions are of the spherical form r^(n-1) exp(-z r).
'''
"""
# Convert exponents and contractions to floating point
exps = _to_float(exps0)
contr = _to_float(contr0)
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2 changes: 1 addition & 1 deletion basis_set_exchange/readers/ricdlib.py
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Original file line number Diff line number Diff line change
Expand Up @@ -44,7 +44,7 @@
charge_line_re = re.compile(r'^\s*({})\s+(\d+)\s+(\d+)\s*$'.format(helpers.floating_re_str))
dummy_line_re = re.compile(r'^\s*Dummy reference line.\s*$')
# nprim, ncontr, functype
shell_start_re = re.compile('^\s*(\d+)\s+(\d+)\s+(\d+)\s*$')
shell_start_re = re.compile(r'^\s*(\d+)\s+(\d+)\s+(\d+)\s*$')

# Floating point data
array_data_re = re.compile(r'^\s*(?:\s({}))+\s*$'.format(helpers.floating_re_str))
Expand Down

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