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A Full-Pivoting Algorithm for the Cholesky Decomposition of
Two-Electron Repulsion and Spin-Orbit Coupling Integrals
Matteo Piccardo and Alessandro Soncini
A significant reduction in the computational effort for the evalu-
ation of the electronic repulsion integrals (ERI) in ab initio quantum
chemistry calculations is obtained by using Cholesky decomposition
(CD), a numerical procedure that can remove the zero or small
eigenvalues of the ERI positive (semi)definite matrix, while avoiding
the calculation of the entire matrix. Conversely, due to its antisym-
metric character, CD cannot be directly applied to the matrix repre-
sentation of the spatial part of the two-electron spin-orbit coupling
(2e-SOC) integrals. Here, we present a computational strategy to
achieve a Cholesky representation of the spatial part of the 2e-SOC
integrals, and propose a new efficient CD algorithm for both ERI
Introduction
The electron repulsion integrals (ERI) and the two-electron spin-
orbit coupling (2e-SOC) integrals are of great importance in
quantum chemistry, the first representing the Coulomb elec-
tron–electron interactions,[1] the latter describing one of the
main spin-dependent relativistic corrections to the Born–Oppen-
heimer Hamiltonian.[2–4] However, their calculation still represents
a computationally expensive step in quantum chemistry codes
based on atomic basis sets. Moreover, the 2e-SOC integrals,
which are usually rewritten in terms of ERI derivatives,[3] need
significantly more expensive computations than ERI integrals,
due to both the higher angular momenta accessed via differenti-
ation of the basis, and the lower permutational symmetry of the
basis functions indices entering the integrals.
To reduce the computational effort for the calculation of the
2e-SOC intergals, a number of approximations have been pro-
posed in the literature. One of the most widely used is the spin-
orbit mean field (SOMF) operator derived and implemented by
Hess and coworkers,[5] which has gained popularity through the
Schimmelpfenning’s atomic mean field interaction (AMFI) imple-
mentation.[6] Within this approximation, only the one-center
two-electron integrals are computed. Less restricted approxima-
tions have been explored by Neese,[7] like the use of a semi/fully
numerical-grid based evaluation, or the use of the very popular
resolution of the identity (RI), owing to its high efficiency.[8–13] In
his conclusions, Neese affirms the need of including all the sig-
nificant multicenters two-electron SOC integrals to achieve a
good accuracy, and proposes the RI method as the best com-
promise between integral accuracy and computational time.
However, it is well known that the accuracy of the RI approxima-
tion depends on the ability of the auxiliary basis set to describe
the overlap distributions of the original set, which is not an eas-
ily controllable parameter, and that different wave function mod-
els usually need specifically optimized auxiliary basis sets.[14]
and 2e-SOC integrals. The proposed algorithm differs from previous
CD implementations by the extensive use of a full-pivoting design,
which allows a univocal definition of the Cholesky basis, once the
CD d threshold is made explicit. We show that 2d is the upper limit
for the errors affecting the reconstructed 2e-SOC integrals. The pro-
posed strategy was implemented in the ab initio program Compu-
tational Emulator of Rare Earth Systems (CERES), and tested for
computational performance on both the ERI and 2e-SOC integrals
evaluation. V
C 2017 Wiley Periodicals, Inc.
DOI: 10.1002/jcc.25062
Significant reductions in the computational effort, as well as
storage requirements, are attainable in electronic structure
theory using the Cholesky decomposition (CD).[13,15–21] CD is
the only numerical procedure that can remove the zero or
small eigenvalues of a positive (semi)definite matrix without
calculating the entire matrix. In the literature, CD has success-
fully been used to reduce the rank of the ERI matrix by elimi-
nation of the elements of no numerical significance, that is,
smaller than a specified threshold d. Differently from RI, CD is
not subjected to the problem of defining an auxiliary basis for
obtaining a fixed accuracy in a calculation, since the accuracy
simply derives from the choice of the d threshold. For this rea-
son, in the last 10 years the CD applied to the Coulomb inte-
grals has shown to give large computational savings for large
basis sets with a variety of theoretical methods, from Hartree–
Fock (HF) and density functional theory (DFT),[13] to second
order Møller–Plesset perturbation theory (MP2) and multiconfi-
gurational self-consistent field (MCSCF) methods,[22,23] and it is
currently implemented in modern packages for quantum chem-
istry, like DALTON and MOLCAS softwares.[24,25] Unfortunately,
since the Cholesky approach can only be applied to positive
(semi)definite matrices, CD is not directly applicable to the
matrix representation of the spatial part of the two-electron SOC
integrals, as this is an anti-symmetric matrix.[3]
In this article, we (i) present a strategy which allows for the
Cholesky representation of the two-electronic SOC integrals,
(ii) present a new algorithm for the CD implementation, and
(iii) test the performances of the new algorithm on the
M. Piccardo, A. Soncini
School of Chemistry, The University of Melbourne, Australia
E-mail: asoncini@unimelb.edu.au
Contract grant sponsor: Australian Research Council Discovery Project;
Contract grant number: DP150103254
C 2017 Wiley Periodicals, Inc.
V
Journal of Computational Chemistry 2017, 38, 2775–2783 2775
 FULL PAPER WWW.C-CHEM.ORG

3
decomposition of both two-electron ERI and SOC integrals. In obtained by expressing the operator r12 =r12 as the gradient of
particular, the proposed implementation differs from previous the inverse electronic distance with respect to the coordinate
implementations by the use of a full-pivoting strategy, which of the second electron
allows a clear and univocal definition of the Cholesky basis, r12 1
showing improved performances in computational time and 3 5r2 r
r12
(4)
12
disk space consumption.
thus, obtaining, when eq. (4) is plugged in eq. (1), a linear
combination of ERI integrals in which the overlap distributions
Two-Electron SOC Integrals
of both electrons are differentiated only once:
The spatial part of the two-electron SOC integrals in a real $ 21
% & $ 21 % 21 '
hprjEabg r2b r12 r1g jqsi5Eabg hprjr1g q r2b r12 s 2r12 r2b s i
basis {p} is[2] & '
! " " # 52Eabg hpr2b rjr1g qsi1hprjr1g qr2b si
" r12 " $ % $ %
" "
pð1Þrð2Þ" 3 3r1 "qð1Þsð2Þ (1)
r12 52Eabg prg qjrb rs 2Eabg prg qjrrb s
defining the elements of an antisymmetric matrix. The usual (5)
way to evaluate integral eq. (1) is to express the operator r12 = where now hprjr1c qr2b si is not symmetric with respect to
3
r12 as a gradient of the inverse electronic distance with respect the b $ c permutation.
to the coordinate of electron 1, using Regardless of whether eq. (3) or (5) are used, it is clear that
r12 1 the spatial part of the 2e-SOC integrals on the {q} basis can be
52r1 (2)
3
r12 r12 rewritten as linear combinations of ERIs calculated on the
expanded basis fvp g5fpg1frpg. Since the space spanned by
where r1 5ðr1x ; r1y ; r1z Þ. Using this relation, the a compo-
the expanded overlap distribution basis fvp vq g is an inner
nent (a5x; y; z) of eq. (1) can be expressed as 21
$ % & $ 21 % 21 ' product space with respect to the positive definite r12 metric,
21
hprj2Eabg r1b r12 r1g jqsi52Eabg hprj r1b r12 r1g q 2r12 r1b r1g q si
the terms entering eqs. (3) and (5) fulfil the Cauchy–Schwarz
& '
5Eabg hr1b prjr1g qsi1hprjr1b r1g qsi inequalities
$ % $ % $ %
5Eabg rb prg qjrs j ra prb qjrs j2 # ra prb qjra prb q ðrsjrsÞ (6)
$ %2 $ %
(3) j pra qjrrb s j # ðpra qjpra qÞ rrb sjrrb s (7)
& '
where Eabc is the Levi–Civita symbol, the hprjr1b ð1=r12 Þr1c q si
term has been manipulated by integration by parts, and the Thus, our first result is that either eq. (6) or (7) can be used to
hprjr1b r1c qsi term cancels to zero because of the b $ c per- prescreen each ERI component of the 2e-SOC integrals appear-
mutational symmetry. h12j12i and ð11j22Þ are the ERIs in short- ing in eqs. (3) and (5) separately, and in fact we will argue in
hand physicists’ and chemists’ (Mulliken) notation, respectively. the following section that eq. (7) lead to a more efficient algo-
In the literature, the SOC integrals are usually calculated as rithm to implement such prescreening within a CD algorithm.
combinations of ERI derivatives by the use of eq. (3) (see e.g.,
Helgaker and Taylor[26]). Equation (3) shows that the 2e-SOC
integrals can be expressed as linear combinations of ERI inte-
Cholesky Representation
grals, in which the overlap distributions {pq} from the original
basis {p} need to be differentiated twice. In the light of the results presented in the previous section,
A different strategy we propose, here, to achieve an efficient we observe that the integrals entering eq. (3) lead to the defi-
Cholesky decomposition algorithm for the 2e-SOC integrals, is nition of the positive (semi)definite matrix

pp pq ... rx prx p ... rx pry q ...

pp ðppjppÞ ...
pq ðpqjppÞ ðpqjpqÞ ...
... ... ... ...
(8)
rx prx p ðrx prx pjppÞ ðrx prx pjpqÞ ... ðrx prx pjrx prx pÞ ...
... ... ... ...
$ % $ % $ % $ %
rx pry q rx pry qjpp rx pry pjpq ... rx pry qjrx prx p ... rx pry qjrx pry q ...
... ...

which has maximal rank ½nðn11Þ=213nð3n11Þ=2%55n2 12n (note of atomic basis functions. Conversely, the integrals entering eq. (5)
the permutational symmetry of the indices), where n is the number lead to the definition of a smaller positive (semi)definite matrix

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 WWW.C-CHEM.ORG FULL PAPER

prx p prx q ... qrx p ... pry p ...

prx p ðprx pjprx pÞ ...
prx q ðprx qjprx pÞ ðprx qjprx qÞ ...
... ... ... ...
(9)
qrx p ðqrx pjprx pÞ ðqrx pjprx qÞ ... ðqrx pjqrx pÞ ...
... ... ... ...
$ % $ % $ % $ %
pry p pry pjprx p pry pjprx q ... pry pjqrx p ... pry pjpry p ...
... ...

jDKIJ j2 # DKII DKJJ (15)

which has maximal rank 3n2 . A positive (semi)definite matrix
can be decomposed by CD, which allows to determine its ele-
ments of numerical significance without calculating the entire
matrix. It is clear at this point that the matrix in eq. (9) has to
be preferred to the matrix in eq. (8), both due to its smaller
maximal rank, and, especially, due to the absence of the
ðrprqjrrrsÞ integrals, involving the computationally expen-
sive quadruple differentiations. We then propose, here, to eval-
uate the terms entering the spatial part of the two-electron
SOC integrals from the Cholesky representation of the matrix
eq. (9). Note that our proposed approach bears similarities to
the attempt made by O’Neal and Simons at treating the geo-
metrical derivatives of ERIs with the CD technique.[18]
As well-known from the CD theory,[13,15–21] the two-electron
integrals ðpq!jr!s Þ, where now q! can be either the q function or
its derivative, can be represented by
X
N
ðpq!jr!s Þ & ð I j J Þ ' LKI LKJ
K51
If carried through to completion, the decomposition of the M
matrix into N5rankðMÞ Cholesky vectors would be computa-
tionally more expensive than the evaluation of the full M
matrix by conventional means. However, within a given thresh-
old for the integral numerical precision, the effective rank of M
is smaller than its full dimension, due to the physical content
of the basis, like near redundancy and saturation.[16] This
means that the number of Cholesky vectors needed to numer-
ically represent all the M elements (the effective rank) is signif-
icantly smaller than rankðMÞ. The CD is a recursive procedure
in which the Cholesky vector at the Kth recursion is calculated
from the residual matrix of ðK21Þth recursion. The key is to
carry on the decomposition taking care that at any step in the
calculation (say the Kth step), DK21
KK is the largest remaining
element in the residual matrix. The decomposition can be
stopped when
(10) DK21
KK # d (16)

where d is a given threshold, after the computation of N5K21

where I and J are, respectively, the super indices correspond-
Cholesky vectors. In this representation, the MIJ integrals with I;
ing to the ðp; q!Þ and ðr; !s Þ overlap distributions, LK the Kth
J # N are represented exactly (within the machine precision),
Cholesky vector, and N the total number of Cholesky vectors.
while the integrals with I; J > N with absolute accuracy d. This
LK has elements,
means that the largest integrals (in absolute value) are repre-
vffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffi sented exactly, that has been shown to be the main reason
u
u X
I21 $ %
why the CD technique gives accurate results for ERI evaluations
LII 5tMII 2
2
LKI (11)
K51 even with rather large values of the decomposition
! threshold.[21,27]
1 XJ21
Moreover, the DKIK residuals can be estimated by eq. (15)
LJI 5 I MIJ 2 LKI LKJ with I > J (12)
LI K51 (i.e., by just looking for the residual diagonals) before their
explicit calculation, then discharged from the decomposition
where MIJ 5ð I j J Þ. From eqs. (11) and (12), the residual matrix of the Kth and subsequent vectors if their absolute values are
after the Kth vector calculation has elements smaller than d. As a consequence, the effective dimension of
the Cholesky vectors, that is, the number of significant ele-
XK
ments, decreases during the decomposition, and only a frac-
DKIJ 5MIJ 2 LTI LTJ with I; J > K (13)
tion of the original integrals needs to be computed to
T51
represent the integrals with d accuracy.
with the properties (Cauchy–Schwarz inequality),[16] Finally, in addition to savings in integral evaluation time and
storage, the CD can give major saving in the transformation of
jMIJ j2 # MII MJJ (14) two-electron integrals from the atomic (AO) to the molecular

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(MO) basis. Because each integral is expressed by eq. (10), the
transformation of the I and J indices to the MO basis set (here
s and r indices) can be realized by[24]
Xn X
n
LKs!r 5 Cps LKp!q Cqr (17)
p51 q51
where Cpq are the LCAO-MO expansion coefficients.[28] Note
that the above transformation needs to be performed sepa-
rately for each x, y, and z component, if q! is the derivative of
qth function (i.e., to transform the two-electron SOC integrals
to the MO basis).
It is straightforward to estimate the error affecting the SOC
integrals when estimated by the procedure proposed here.
Assuming the error affecting each of the four integral entering
eq. (5) is # d, the error DSOC affecting the overall two-electron
SOC integral is given by
pffiffiffiffiffiffiffiffi
DSOC # 4 d2 52d (18)
$ %
Note that, even if the largest pra qjrrb s integrals (in abso-
lute value) are represented exactly by their Cholesky represen-
tation, this is not strictly true for the SOC integrals, due to the
summations and subtractions entering eq. (5).
While we will only discuss, here, the application of our pro-
posed CD algorithm to the complete representation of the 2e-
SOC integrals, our strategy can easily be coupled with approxi-
mations involving the calculation of a reduced number of 2e-
SOC integrals, for example the SOC one-center approxima-
tion[29] or the one-center CD (1C-CD) methodology,[20] where
only one-center or two-center integrals, respectively, would be
decomposed. Finally, we remark that any computational
model, which utilizes density fitting (DF) or resolution-of-
identity (RI) of the two-electron integrals,[8,11,12] can easily be
adapted to an approach with Cholesky decomposition,[21,22,30]
and that the Cholesky representation of the two-electron inte-
grals can be of particular interest within the DF approximation
as generator of auxiliary basis sets.[30]
Full-Pivoting Algorithm
A CD algorithm for both ERIs and ERI derivatives matrices, as
presented in eq. (9), has been implemented in the Computa-
tional Emulator of Rare Earth Systems (CERES) code.[31] The
implementation is written in C1111, taking advantage of the
object-oriented programming. A particular attention has been
dedicated to the parallelization of the CD code where appro-
priate, by use of openMP application programming interface
(API) specification for parallel programming.
In the CD, the matrix of the integrals is iteratively decom-
posed column by column (i.e., Cholesky–Crout algorithm),
and a decomposition step corresponds to the transforma-
tion of one column of integrals into a new Cholesky vector.
To perform the CD in the way which exploits the rank
reduction, all the residual diagonals [see eq. (13)] are evalu-
ated and sorted in their nonincreasing order at the end of
each step, and the elements in the Cholesky matrix
2778 Journal of Computational Chemistry 2017, 38, 2775–2783
accordingly reorganized. The main problems dealing with
CD are then three: (i) the integrals calculation, (ii) the ongo-
ing reorganizations of the rows and columns of the Cho-
lesky matrix, (iii) the calculation of the residuals, with the
associated reading/saving of the elements of numerical sig-
nificance from/to the Cholesky vectors calculated in the pre-
vious/current iterations.
i. The integrals calculation is performed by the use of Libcint
library, a general and efficient integral library for Gaussian
$ %
basis functions.[32] The code for ðpqjrsÞ and pra qjrrb s inte-
grals were built by the use of the Libcint built-in symbolic
algebra tool for the integrals implementation. The calculation is
atomic shell-based for computational efficiency, which means
that the entire set of integrals ðPQjRSÞ is computed at once,
with P; Q; R; S shells indices. This does not perform well with
the Cholesky procedure, as the latter requires individual col-
umns of integrals ðpqj ( (Þ at each step, instead of the set of
columns ðPQj ( (Þ, where ðPQj is the shell pair to which (p,q)
belongs. This can lead to a massive discarding and recalculation
of the integrals, due to the need of decomposing the columns
in the set ðPQj ( (Þ in nonconsecutive steps, while following the
nonincreasing order of the residual diagonals. To avoid this
overhead, the strategy that has been adopted to date consists
of generating new Cholesky vectors from the calculated shell
pair set as long as the new residual diagonal elements (within
the shell pair) are at most a span factor smaller than the largest
residual diagonal element of the shell pair itself.[19,24] This
approach has two consequences: first, the total number of Cho-
lesky vectors depends weakly on the chosen span factor and,
second, a number of shell pair integral columns may be calcu-
lated more than once.
In our implementation, we adopted a different strategy. We
rigorously decompose at any step the column under the larg-
est remaining diagonal, thus implementing a full-pivoting
algorithm. The integral recalculation is avoided by the use of
both the main memory and the disk. After the calculation of
ðPQj ( (Þ set, the integrals belonging to the right-most nonsig-
nificant columns in the Cholesky matrix (i.e., under the diago-
nals smaller than d) are directly discarded, while the significant
integrals are temporarily ordered in memory in their columns.
Then, all the columns except the one under decomposition
are downloaded on a scratch binary file, ready to be quickly
reloaded in the subsequent steps, by means of random file
access directly to their positions. These file positions are in
fact stored as pointers on specific attributes of the C11
objects describing the diagonal elements (see below). This
strategy avoids the integral recalculation, while the overhead
due to the I/O operations is small.
ii. The use of the C11 object-oriented design allows a clear
code structure, and an easy management of the rows and col-
umns reordering. Key elements of the CD, the diagonals are
implemented as C11 objects collecting all their specifications
as attributes (e.g., integral value, functions indices, shell indi-
ces, pointer to position on the disk of the corresponding col-
umn of integrals). The latter are collected in a vector (i.e.,
C11 object composition), which is in turn an attribute of a
more complex object collecting all the information and
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 WWW.C-CHEM.ORG
methods concerning the Cholesky data management (e.g.,
sorting and Cauchy–Schwartz evaluation methods). In this
setup, the in-memory position of the elements in the calcu-
lated Cholesky vectors is independent from the order of the
diagonal elements (as these positions are stored as attributes
of the diagonal objects), allowing for minimal reordering of
the memory.
iii. The calculation of the residuals by eq. (13) follows the
calculation/reloading of the integrals. Whether the residuals
estimation is more or less expensive than the integral calcula-
tion depends on the basis set (i.e., number of primitive Gaus-
sians and maximum angular momentum quantum numbers),
the number of the Cholesky vectors already calculated, and
the value chosen for the decomposition threshold, which
determines the number of the significant rows in the new vec-
tor, as pointed out in the previous section. Noting that the off-
diagonal elements in the calculated Cholesky vectors enter the
CD of the new vectors always via the corresponding rows [see
eq. (12)], the first become of no use in the decomposition pro-
cedure as soon as the corresponding rows in the new Cho-
lesky vectors are classified as no longer significant. Our
algorithm keeps the significant elements of the calculated
Cholesky vectors in the main memory as long as the amount
of allocated memory allows. At each step, once a Cholesky
vector is completed, the residual diagonals are updated and
reordered, the rows and the columns in the Cholesky matrix
are revalued as significant or nonsignificant by eq. (15), and
the elements belonging to the no longer significant rows are
discarded after having been pushed at the end of their Cho-
lesky vectors, freeing the associated memory. This dynamical
reordering ensures the use of the smallest amount of memory
at any step, while the overhead due to the reordering is
negligible.
At the end of each decomposition step, the new Cholesky
vector is written on an output file saving just its nonzero ele-
ments, contiguously ordered on the disk by I super index
mapped on the order of the functions in the basis set. The
number of Cholesky vectors spanned by each row is also
saved on disk, in a dedicated vector of integers (guide vector),
which is updated at any step. This strategy allows for an easy
reconstruction of the Cholesky vectors, where the position of
the nonzero elements is determined by the guide vector, and
for a minimal amount of stored data. Moreover, it allows a fast
transformation when using eq. (17). Note that the AO to MO
basis transformation is executed vector by vector, reordering
the elements LKI of the Kth vector in their matrix form LKp!q ,
then contracting them with the LCAO coefficients matrix.
Being the position of the nonzero elements in each vector
explicit, the first contraction is executed just on the rows and
columns of the reconstructed matrix which contains at least
one nonzero element, with a significant reduction of the num-
ber of multiplications when dealing with the right-most
vectors.
An on-the-fly evaluation of the memory usage can switch
the calculation to the disk-supported mode when the available
memory is not sufficient. In this mode, the last calculated vec-
tors are recovered at each iteration from the disk, while the
FULL PAPER
algorithm continues the reordering and deallocation of the
nonsignificant elements in the vectors stored in memory. The
vectors read from disk are reloaded and kept in memory as
soon as space becomes available.
Computational Considerations
Some considerations must be taken into account when evalu-
ating the computational performances of the strategy pro-
posed in the previous sections for the 2e-SOC integrals
calculation, which involve the use of eq. (5) coupled with the
Cholesky representation of the matrix in eq. (9), with respect
to their complete evaluation performed by eq. (3).
First, we note that the integrals ðpra qjrra sÞ (i.e., with the
same cartesian component of the derivatives for electron 1
and 2), while present in the matrix eq. (9), they are not needed
to evaluate eq. (5). However, given the shell-based organisa-
tion of the integral calculation in any modern code, evaluation
of these additional integrals does not introduce computational
overhead, as the code makes all the integrals ðPrQjRrSÞ avail-
able at once (i.e., evaluates the integrals for all the functions
belonging to the four shells, and for all nine possible combina-
tions of the two derivatives).[2]
More importantly, we note that the number of ERI that needs
to be computed to evaluate the 2e-SOC integrals via eq. (5) is
larger than the number of ERI required if the same evaluation is
carried out via eq. (3), due to the lower permutational symme-
try of ðPrQjRrSÞ with respect to ðrPrQjRSÞ. This indicates
that eq. (3) is a more efficient strategy to perform the full
unscreened evaluation of the 2e-SOC integrals. Conversely, the
CD of the 2e-SOC integrals via eqs. (9) and (5) will become compu-
tationally convenient with respect to the direct unscreened evalu-
ation if the rank reduction achieved by CD is large.
It is possible to make a conservative estimate of the number
of Cholesky vectors below which the maximal number of inte-
grals that needs to be calculated during a CD becomes smaller
than the number of integrals calculated in a direct unscreened
evaluation of the 2e-SOC using eq. (3). Thus to pursue the
direct unscreened calculation of the 2e-SOC integrals via eq.
(3) we need to evaluate all the ðrPrQjRSÞ shell combinations,
amounting to:
mðm11Þ mðm11Þ 1 $ 2 %
5 m 12m11 m2 (19)
2 2 4
where m is the number of shells partitioning the basis set. If
we follow instead the proposed CD strategy using eqs. (5) and
(9), conservatively assuming that (i) the row-discharging strat-
egy described in the previous section is not pursued (ii) the
first N columns belong to N different shell sets, then at most
Nm2 shell-integrals calculations will be necessary to evaluate
the first N Cholesky vectors.
Hence, we can obtain a threshold number of significant
Cholesky vectors Nth (related to a threshold accuracy dth ), for
which the number of shells-based integral calculations
required for the direct unscreened evaluation of the 2e-SOC
integrals reported in eq. (19) will be matched by the maximal
Journal of Computational Chemistry 2017, 38, 2775–2783 2779
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Table 1. Cholesky decomposition (CD) of ERIs for different molecular systems.

DIRECT Traditional CD (MOLCAS) Full-pivoting CD (CERES)

System Basis size Full rank Time Shells Vectors Time t%(ints) Shells Vectors Time t%(ints)
1. 264 34,980 78 s (4.8 Gb) 42 3248 (0.8 Gb) 115 s 18% 90 3034 (0.5 Gb) 75 (85) s 8%
2. 340 57,970 215 s (13.9 Gb) 36 3746 (1.5 Gb) 251 s 25% 96 3575 (1.0 Gb) 174 (226) s 7%
3. 356 63,546 44 m (15.9 Gb) 77 2848 (1.4 Gb) 30 m 86% 77 2721 (0.8 Gb) 20 m 91%
4. 433 93,961 660 s (35.5 Gb) 77 3434 (1.8 Gb) 10 m 40% 213 3275 (0.8 Gb) 118 (276) s 17%
The results in the column DIRECT have been obtained calculating and saving all the unique shell-quartets of indices for ERIs. The values between
parenthesis in the “Time” column are obtained using the nonoptimized general contractions form of the basis sets. The CD threshold is d51028 for 1.
and 2., d51026 for 3. and 4.

number of shell-based integral calculations necessary to per-
form a CD via the strategy proposed here, by solving:
1$ 2 %
m2 Nth 5 m 12m11 m2
4 CCse set of geometries reported in Ref. [39], while the geome-
which gives Nth 5ðm2 12m11Þ=4.
This indicates that to achieve an efficient CD of the 2e-SOC
integrals via the strategy proposed here, basis sets including a
large number of shells, each containing a small number of
functions (e.g., one- or two-contractions per shells) will be bet-
ter performing than basis sets collecting a small number of
shells, each containing a large number of functions (i.e., multi-
ple contractions per shells). We also note that this observation
holds true for an efficient CD of the ERIs, because the shell-
driven estimation of the integrals also in this case can lead to
the computation of a large number of nonsignificant columns
of integrals.
Finally, we highlight that Nth indicates savings in the integral
evaluations when compared with a higher number of calcu-
lated Cholesky vectors, but cannot give clear information
when correlated with a smaller number of calculated Cholesky
vectors, because of the assumptions made in its definition.
Examples and Performance
In this section, we present some examples of CD for both ERIs
and 2e-SOC integrals, carried out using the algorithm pro-
posed above. Our code CERES has been compiled with GCC
4.8.4 compiler at -O2 level of optimization, and all computa-
tions run on a single CPU core Intel Core(TM) i7-4790 at
3.60 GHz, DDR3 memory at 1600 MHz, SSHD at 5400 rpm rota-
tion rate, and SATA 3.1 (6.0 Gb/s) connection. At first, the full
pivoting strategy has been tested for the ERIs decomposition
for different molecular systems, comparing its computational
performances with the traditional algorithm, as implemented
in MOLCAS package.[24] MOLCAS has been compiled with GNU
Fortran, at the same optimization level of our CERES code.
The systems studied are benzene (1.) and cis-acrolein (2.),
coupled with the Dunning correlation-consistent valence cc-
pVTZ and cc-pVQZ basis sets,[33,34] respectively, and [Dy(aca-
c)3(H2O)2] complex, coupled with both the multiple-contracted
ANO-RCC basis[35] (3.), and the segmented all-electron relativis-
tically contracted (SARC) (4.) basis set. The ANO-RCC set is
contracted to [8s7p4d3f2g1h] for Dy, [3s2p] for C and O, and
[2s1p] for H. The SARC2-QZVP-DKH set[36] for Dy has been
used in conjunction with the valence double-zeta 6–31G
basis[37,38] for H, C, and O (hereafter just labeled as SARC2).
The geometries for benzene and cis-acrolein come from the
(20)
try for Dy complex from its crystallographic structure, reported
in Ref. [40].
The CD timing and number of Cholesky vectors obtained
from the decomposition of the ERIs are reported in Table 1.
The quite conservative d51028 for benzene and cis-acrolein,
and d51026 for the [Dy(acac)3(H2O)2] complex, have been
selected as CD thresholds (see Refs. [20] and [41] for more
details on the d influence on the energy accuracy). The imple-
mentation proposed, here, shows better performance than
what reported in the literature, with respect to both timing
and disk usage. The number of Cholesky vectors calculated
with the full-pivoting algorithm, which is now the true effec-
tive rank of the ERI matrix or the dimension of the Cholesky
basis for the specified threshold d, is in all cases significantly
smaller than those calculated with the traditional algorithm.
Moreover, the percentages of time dedicated to the integral
calculations reported in Table 1 indicate that MOLCAS’ algo-
rithm spends a longer time on the integral calculation, mainly
due to the shells-partitioning of the basis functions, discussed
above, and the integral recalculations (i.e., 21% of the calcu-
lated shell-pairs are repeated for CD of 1., 24% for 2., 13% for
3., and 30% for 4.). The avoided integral recalculation per-
formed by the algorithm, here, proposed, together with the
smaller number of Cholesky vectors obtained from the decom-
position, leads to a significant reduction of the decomposition
times. Moreover, our algorithm shows better computational
performances even completely neglecting the integral timings
(i.e., 94, 188, 252, and 360 s for traditional algorithm decompo-
sitions vs. 69, 161, 108, and 98 s for full-pivoting decomposi-
tions, respectively), and it is noteworthy that CD is always less
time consuming than the complete evaluations of the ERIs
(see column DIRECT).
In Table 1, the full rank of ERI matrix is reported together
with the size of the basis set, and the partitioning in shells. As
pointed out in the previous section, the partition into shells
plays an important role in the speed up of the decomposition.
The reduced form of the basis sets obtained by optimizing the
general contractions (see Ref. [42]) with the functions grouped
in a larger number of shells, have to be preferred to the

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 WWW.C-CHEM.ORG FULL PAPER

Table 2. Cholesky decomposition (CD) for 2e-SOC integrals.

DIRECT CD

System Basis size Shells Time Full rank Nth d Vectors Time t%(ints)
24
1. 264 90 7.7 m (28 Gb) 209,088 2070 10 1749 (1.3 Gb) 3.3 m 18%
1025 2321 (1.8 Gb) 5.3 m 16%
1026 3106 (2.6 Gb) 8.9 m 14%
1027 3831 (3.5 Gb) 14.3 m 12%
1028 4689 (4.5 Gb) 22.7 m 10%
2. 340 96 21.9 m (77 Gb) 346,800 2352 1024 2319 (2.8 Gb) 12.2 m 17%
1025 2900 (4.0 Gb) 20.0 m 14%
1026 3659 (5.3 Gb) 28.0 m 13%
1027 4317 (6.8 Gb) 41.1 m 12%
1028 4705 (8.3 Gb) 51.9 m 12%
3. 356 77 8.0 h (94 Gb) 380,208 1521 1024 2942 (3.5 Gb) 4.4 h 93%
1025 3793 (5.6 Gb) 5.6 h 90%
1026 5028 (8.1 Gb) 7.0 h 88%
1027 6242 (10.9 Gb) 14.7 h 92%
1028 6427 (13.5 Gb) 18.9 h 92%
4. 433 213 63.2 m (200 Gb) 562,467 11,449 1024 3721 (3.8 Gb) 18.3 m 27%
1025 4774 (5.9 Gb) 29.7 m 23%
1026 6196 (8.4 Gb) 48.0 m 19%
1027 7919 (11.4 Gb) 77.7 m 16%
1028 8510 (14.9 Gb) 114.2 m 13%
The results in the column DIRECT have been obtained calculating and saving all the unique shell-quartets of indices for the integrals given by eq. (3).
Nth is defined in eq. (20).

generally contracted form,[43–45] leading to a smaller number
of shells. As evident from the number of shells reported in
Table 1, the MOLCAS code uses the generally contracted
forms. The best performance of our code for the ERI decompo-
sition was achieved for [Dy(acac)3(H2O)2] using the SARC2
basis set, in which case CERES takes about 2.5 min using 433
functions partitioned in 213 shells, while MOLCAS takes about
10 min using 433 functions grouped in 77 shells. In all cases
explored here, our code performs faster decompositions with
respect to MOLCAS, also when using the generally contracted
form of the basis. The latter leads to a slightly different num-
ber of vectors for cis-acrolein (3566). Conversely, it is notewor-
thy that our proposed algorithm shows better performances
for [Dy(acac)3(H2O)2] also when using the ANO-RCC basis set,
where both MOLCAS and CERES use the same shells partition-
ing of the basis functions. Finally, our proposed algorithm dis-
plays a more optimized use of disk space when storing the
Cholesky vectors, leading to time savings for I/O operations,
due both to a smaller number of calculated vectors as a con-
sequence of full pivoting, and to the storage strategy pro-
posed here.
The number of Cholesky vectors generated by decomposi-
$ %
tion of the matrices collecting the pra qjrrb s integrals are
shown in Table 2. Different thresholds have been chosen to
study the computational performances of the proposed CD
with respect to the 2e-SOC integrals complete calculations by
eq. (3) (hereafter called direct evaluation). Here, the rank
reduction obtained by CD is huge with respect to that
achieved for the ERIs using equal threshold. The number of
Cholesky vectors for the 2e-SOC integrals representation is
never larger than twice the number of Cholesky vectors for
ERIs, while the increase in the full rank is about sixfold with
respect to rank of the ERI matrix. The CD of the 2e-SOC
integrals is about 20–30 times more time consuming than the
CD of ERIs.
Good computational performances are obtained when deal-
ing with a large number of shells, as shown by the decomposi-
tions of [Dy(acac)3(H2O)2] integrals using a SARC2 basis set.
For this system, CD is computationally less expensive than the
complete direct evaluation (64 min) when using thresholds
higher than 1027 . The number of calculated Cholesky vectors
is always much smaller that the threshold number of columns
Nth estimated via eq. (20) (11,449), which indicates that a sig-
nificantly smaller number of integrals has been calculated by
CD respect to the integrals calculated by their complete evalu-
ation using eq. (3). This is confirmed by the timings for the
integral evaluations within CDs, reported in Table 2 as percen-
tages of the whole CD timings, which are smaller than 22% of
the direct evaluation time for all the d thresholds showed in
the Table (e.g., about 14 min for d51028 vs. 64 min).
The situation is different for the heavily contracted ANO-
RCC basis set, where the number of Cholesky vectors (5028) is
more than three times the threshold number of columns given
by eq. (20) (1521). In this case, Nth cannot give a clear informa-
tion about possible savings in the integral calculations. From
the numerical evaluation, the integral calculations while per-
forming CD take about 4, 5, and 6 h for d equal to 1024 ; 1025 ,
and 1026 , respectively, which are 50%, 63%, and 86% of the
timings for the direct 2e-SOC integrals computation. This percen-
tages still indicate savings in the integral calculations, but they
are not as good as those obtained for system 4. Here, the vector
decomposition takes less than 10% of the whole decomposition
time, which means that the better performances showed by CD
with respect to the direct evaluation by eq. (3), when using
d51024 ; 1025 , and 1026 , mainly come from the savings in the
integrals computations. Conversely, CDs performed with smaller

Journal of Computational Chemistry 2017, 38, 2775–2783 2781

 FULL PAPER WWW.C-CHEM.ORG
thresholds compute an excessively large number of integrals,
resulting in high time-demanding decompositions.
The number of calculated Cholesky vectors is about/larger
than the Nth value for the results on the Dunning basis sets, still
not indicating a clear saving in the integral evaluations. Differ-
ently from system 3., and similarly to system 4., here, the inte-
grals calculations take less than 20% of the total CD timings,
meaning that the latter marginally influence the computational
performances, and that the bottleneck of the decomposition is
the vectors calculation. CD shows slightly smaller timings with
respect to the 2e-SOC direct evaluation when using d51024
and 1025 , while the decompositions are significantly more time
consuming when adopting smaller thresholds.
Unfortunately, this preliminary study on the possible appli-
cation of our proposed CD of 2e-SOC integrals, as currently
implemented, does not show significant computational savings
in a consistent manner. Partly, this is due to the fact that, in
comparison to the ERIs case where the Cholesky matrix is
defined by the same integrals that are needed for the direct
evaluation of ERIs, the two Cholesky matrices for the 2e-SOC
defined, here, contain more integrals than those needed for
the direct calculation of 2e-SOC integrals, which can obviously
lead to small time savings of the Cholesky approach with
respect to direct evaluation using eq. (3). In fact, as discussed
in the Computational Considerations section, for cases in
which the rank reduction is not overwhelmingly favourable,
there even exists the possibility for the Cholesky algorithm to
compute a number of integrals that exceeds of overcoming
the total number of 2e-SOC integrals directly calculated via eq.
(3). However, we still note that only the CD representation of
SOC integrals allows (i) the storage of the smallest amount of
data needed to numerically represent all the SOC integrals
with absolute accuracy smaller than 2d, (ii) the possibility of
efficient AO to MO transformations by eq. (17).
Conclusions
In this article, we presented a new algorithm for the CD of
two-electron integrals based on a full-pivoting design, and
tested a new proposed strategy to compute two-electron ERI
and SOC integrals using the Cholesky representation.
The new algorithm shows very good performance in both
time and storage savings for the case of ERIs. Full-pivoting
achieves efficiency by avoiding the recalculation of integrals,
that are usually discarded in CD algorithms due to the shell-
driven integral evaluation, and leads to a univocal definition of
the Cholesky basis, once the CD d threshold is fixed. The
results for the CD of the ERIs achieved with the new algorithm
show a significant reduction of the number of Cholesky vec-
tors with respect to previous approaches, amounting to the
true effective rank of the ERI matrix.
We also proposed a strategy to perform CD of 2e-SOC inte-
grals, based on a previously unexplored expansion of the 2e-
SOC integrals in terms of ERI integrals involving the derivatives
of overlap distribution functions of both electrons, and
showed that this strategy is expected to be efficient if the
effective rank achieved via CD is lower than a threshold rank
2782 Journal of Computational Chemistry 2017, 38, 2775–2783
Nth for which we report a rough estimate. We showed that 2d
is the upper limit for the errors affecting the reconstructed 2e-
SOC integrals. The first tests of our algorithm show that CD of
the 2e-SOC integrals is about 20–30 times more time consum-
ing that CD of ERIs, and our analysis does not indicate that a
significant computational savings can always be achieved.
Finally, our results illustrated the fact that the shell-
partitioning of the basis functions plays an important role in
the speed up of the decomposition, and that low-contracted
shells have to be preferred. On this point, we noted significant
differences in computational times when performing CD on
integrals represented on optimized general rather than gener-
ally contracted basis sets.
Keywords: Cholesky ) spin-orbit coupling ) electron repulsion
integrals ) full-pivoting ) decomposition
How to cite this article: M. Piccardo, A. Soncini. J. Comput.
Chem. 2017, 38, 2775–2783. DOI: 10.1002/jcc.25062
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Journal of Computational Chemistry 2017, 38, 2775–2783 2783