def get_norm_cgto(ang_number,exponents,coefs_shell):
"""Gets the norms of contracted GTOs in a shell."""
from math import sqrt,pow
from BioNanoLEGO.DenseMatrix import asmatrix,empty
# Threshold of the norms
NORM_THRESHOLD = 1e-17
# Gets the number of contractions
num_contrs = len(coefs_shell)
# Gets the number of primitives
num_prims = len(exponents)
# Initializes the norms of contracted GTOs
norm_cgto = [0]*num_contrs
# Sets the power
expnt_power = float(ang_number)+1.5
# Sets up the matrix of radical overlap between two primitive GTOs
rad_overlap = asmatrix(empty((num_prims,num_prims)))
for iprim in xrange(num_prims):
for jprim in xrange(num_prims):
rad_overlap[iprim,jprim] = \
pow(2*sqrt(exponents[iprim]*exponents[jprim])/ \
(exponents[iprim]+exponents[jprim]),expnt_power)
# Gets the norms of contracted GTOs
for icontr in xrange(num_contrs):
coeff_matrix = asmatrix(coefs_shell[icontr])
norm_cgto[icontr] = sqrt((coeff_matrix*rad_overlap*coeff_matrix.transpose())[0,0])
if norm_cgto[icontr] < NORM_THRESHOLD:
raise ZeroDivisionError("Norm '%f' of CGTO '%d' is smaller than the threshold '%f'!" \
% (norm_cgto[icontr],icontr,NORM_THRESHOLD))
return norm_cgto
def getOneInt(self,other,operator,**options):
"""Calculates the integral of an one-electron operator.
other: Basis sets of ket.
molecule: Molecule class defined in Molecule.py.
operator: One-electron operator, function object, see Gen1Int.py for example.
"""
from BioNanoLEGO.DenseMatrix import empty,asmatrix
# Parallelize here, using dynamic parallelization
# MASTER sends first initial jobs to all SLAVES, SLAVES do the job,
# and send the results back, MASTER receives the result from one SLAVE,
# does some computations (like reduce the number of working nodes),
# and sends new job to it with job_tag and increases the number of
# working nodes, or sends terminator_tag.
# Sets up the integral matrix, using row-major order
one_int = asmatrix(empty((self.num_basis_functions,other.num_basis_functions)))
#from Parallel import mpi
for idx_bra in xrange(self.num_shells):
# Indices of basis functions in bra-shell
strt_row = self.idx_shell[idx_bra]+1
end_row = self.idx_shell[idx_bra+1]
for idx_ket in xrange(other.num_shells):
# Indices of basis functions in ket-shell
strt_col = other.idx_shell[idx_ket]+1
end_col = other.idx_shell[idx_ket+1]
