We wish to describe a potential energy surface by using a basis of permutationally invariant polynomials whose coefficients will be determined by numerical regression so as to smoothly fit a dataset of electronic energies as well as, perhaps, gradients. The polynomials will be powers of transformed internuclear distances, usually either Morse variables, exp(−ri,j/λ), where λ is a constant range hyperparameter, or reciprocals of the distances, 1/ri,j. The question we address is how to create the most efficient basis, including (a) which polynomials to keep or discard, (b) how many polynomials will be needed, (c) how to make sure the polynomials correctly reproduce the zero interaction at a large distance, (d) how to ensure special symmetries, and (e) how to calculate gradients efficiently. This article discusses how these questions can be answered by using a set of programs to choose and manipulate the polynomials as well as to write efficient Fortran programs for the calculation of energies and gradients. A user-friendly interface for access to monomial symmetrization approach results is also described. The software for these programs is now publicly available.

1.
J.
Behler
,
J. Chem. Phys.
145
,
170901
(
2016
).
2.
J.
Westermayr
,
M.
Gastegger
,
K. T.
Schütt
, and
R. J.
Maurer
,
J. Chem. Phys.
154
,
230903
(
2021
).
3.
D.
Koner
,
S. M.
Salehi
,
P.
Mondal
, and
M.
Meuwly
,
J. Chem. Phys.
153
,
010901
(
2020
).
4.
T.
Fröhlking
,
M.
Bernetti
,
N.
Calonaci
, and
G.
Bussi
,
J. Chem. Phys.
152
,
230902
(
2020
).
5.
T.
Mueller
,
A.
Hernandez
, and
C.
Wang
,
J. Chem. Phys.
152
,
050902
(
2020
).
6.
C.
Qu
,
Q.
Yu
,
B. L.
Van Hoozen
,
J. M.
Bowman
, and
R. A.
Vargas-Hernández
,
J. Chem. Theory Comput.
14
,
3381
(
2018
).
7.
J.
Li
,
B.
Jiang
, and
H.
Guo
,
J. Chem. Phys.
139
,
204103
(
2013
).
8.
P. L.
Houston
,
C.
Qu
,
A.
Nandi
,
R.
Conte
,
Q.
Yu
, and
J. M.
Bowman
,
J. Chem. Phys.
156
,
044120
(
2022
).
9.
A.
Nandi
,
C.
Qu
,
P. L.
Houston
,
R.
Conte
, and
J. M.
Bowman
,
J. Chem. Phys.
154
,
051102
(
2021
).
10.
J. S.
Smith
,
B. T.
Nebgen
,
R.
Zubatyuk
,
N.
Lubbers
,
C.
Devereux
,
K.
Barros
,
S.
Tretiak
,
O.
Isayev
, and
A. E.
Roitberg
,
Nat. Commun.
10
,
2903
(
2019
).
11.
B. J.
Braams
and
J. M.
Bowman
,
Int. Rev. Phys. Chem.
28
,
577
(
2009
).
12.
See https://github.com/szquchen/MSA-2.0 for MSA software with gradients; accessed 20 January 2019.
13.
B.
Jiang
,
J.
Li
, and
H.
Guo
,
J. Phys. Chem. Lett.
11
,
5120
(
2020
).
14.
B.
Jiang
,
J.
Li
, and
H.
Guo
,
Int. Rev. Phys. Chem.
35
,
479
(
2016
).
15.
R.
Dawes
and
S. A.
Ndengué
,
Int. Rev. Phys. Chem.
35
,
441
(
2016
).
16.
V.
Babin
,
C.
Leforestier
, and
F.
Paesani
,
J. Chem. Theory Comput.
9
,
5395
(
2013
).
17.
S. K.
Reddy
,
S. C.
Straight
,
P.
Bajaj
,
C.
Huy Pham
,
M.
Riera
,
D. R.
Moberg
,
M. A.
Morales
,
C.
Knight
,
A. W.
Götz
, and
F.
Paesani
,
J. Chem. Phys.
145
,
194504
(
2016
).
18.
N. M.
Kidwell
,
H.
Li
,
X.
Wang
,
J. M.
Bowman
, and
M. I.
Lester
,
Nat. Chem.
8
,
509
(
2016
).
19.
A. W.
Jasper
,
L. B.
Harding
,
C.
Knight
, and
Y.
Georgievskii
,
J. Phys. Chem. A
123
,
6210
(
2019
).
20.
C.
Qu
,
Q.
Yu
, and
J. M.
Bowman
,
Annu. Rev. Phys. Chem.
69
,
151
(
2018
).
21.
See https://www.mcs.anl.gov/research/projects/msa/ for Original MSA software; accessed 20 December 2019.
22.
Z.
Xie
and
J. M.
Bowman
,
J. Chem. Theory Comput.
6
,
26
(
2010
).
23.
V.
Babin
,
G. R.
Medders
, and
F.
Paesani
,
J. Chem. Theory Comput.
10
,
1599
(
2014
).
24.
M.
Riera
,
E. P.
Yeh
, and
F.
Paesani
,
J. Chem. Theory Comput.
16
,
2246
(
2020
).
25.
T.
Győri
and
G.
Czakó
,
J. Comput. Theory Chem.
16
,
51
(
2020
).
26.
D. R.
Moberg
and
A. W.
Jasper
,
J. Chem. Theory Comput.
17
,
5440
(
2021
).
27.
D. R.
Moberg
,
A. W.
Jasper
, and
M. J.
Davis
,
J. Phys. Chem. Lett.
12
,
9169
(
2021
).
28.
A. S.
Abbott
,
J. M.
Turney
,
B.
Zhang
,
D. G. A.
Smith
,
D.
Altarawy
, and
H. F.
Schaefer
,
J. Chem. Theory Comput.
15
,
4386
(
2019
).
29.
D.
Koner
and
M.
Meuwly
,
J. Chem. Theory Comput.
16
,
5474
(
2020
).
30.
S.
Carter
,
S. J.
Culik
, and
J. M.
Bowman
,
J. Chem. Phys.
107
,
10458
(
1997
).
31.
J. M.
Bowman
,
S.
Carter
, and
X.
Huang
,
Int. Rev. Phys. Chem.
22
,
533
(
2003
).
32.
Y.
Shu
,
J.
Kryven
,
A. G.
Sampaio de Oliveira-Filho
,
L.
Zhang
,
G.-L.
Song
,
S. L.
Li
,
R.
Meana-Pañeda
,
B.
Fu
,
J. M.
Bowman
, and
D. G.
Truhlar
,
J. Chem. Phys.
151
,
104311
(
2019
).
33.
J.
Li
,
Z.
Varga
,
D. G.
Truhlar
, and
H.
Guo
,
J. Chem. Theory Comput.
16
,
4822
(
2020
).
34.
Z.
Varga
and
D. G.
Truhlar
,
Phys. Chem. Chem. Phys.
23
,
26273
(
2021
).
35.
Z.
Varga
,
Y.
Liu
,
J.
Li
,
Y.
Paukku
,
H.
Guo
, and
D. G.
Truhlar
,
J. Chem. Phys.
154
,
084304
(
2021
).
36.
Y.
Paukku
,
K. R.
Yang
,
Z.
Varga
, and
D. G.
Truhlar
,
J. Chem. Phys.
139
,
044309
(
2013
).
37.
J. M.
Bowman
,
C.
Qu
,
R.
Conte
,
A.
Nandi
,
P. L.
Houston
, and
Q.
Yu
,
J. Chem. Phys.
156
,
240901
(
2022
).
38.
Wolfram Research, Inc., “Mathematica, Version 12.0,” Champaign, IL, 2019.
39.
R.
Conte
,
P. L.
Houston
, and
J. M.
Bowman
,
J. Chem. Phys.
140
,
151101
(
2014
).
40.
C.
Qu
,
R.
Conte
,
P. L.
Houston
, and
J. M.
Bowman
,
Phys. Chem. Chem. Phys.
17
,
8172
(
2015
).
41.
Z.
Homayoon
,
R.
Conte
,
C.
Qu
, and
J. M.
Bowman
,
J. Chem. Phys.
143
,
084302
(
2015
).
42.
Q.
Wang
and
J. M.
Bowman
,
J. Chem. Phys.
147
,
161714
(
2017
).
43.
A.
Nandi
,
C.
Qu
, and
J. M.
Bowman
,
J. Chem. Phys.
151
,
084306
(
2019
).
44.
R.
Conte
,
C.
Qu
,
P. L.
Houston
, and
J. M.
Bowman
,
J. Chem. Theory Comput.
16
,
3264
(
2020
).
45.
A.
Nandi
,
C.
Qu
, and
J. M.
Bowman
,
J. Chem. Theory Comp.
15
,
2826
(
2019
).
46.
R.
Conte
,
P. L.
Houston
,
C.
Qu
,
J.
Li
, and
J. M.
Bowman
,
J. Chem. Phys.
153
,
244301
(
2020
).
47.
P. L.
Houston
,
R.
Conte
,
C.
Qu
, and
J. M.
Bowman
,
J. Chem. Phys.
153
,
024107
(
2020
).
48.
C.
Qu
,
P. L.
Houston
,
R.
Conte
,
A.
Nandi
, and
J. M.
Bowman
,
J. Phys. Chem. Lett.
12
,
4902
(
2021
).
49.
C.
Qu
,
R.
Conte
,
P. L.
Houston
, and
J. M.
Bowman
,
Phys. Chem. Chem. Phys.
23
,
7758
(
2021
).
50.
A.
Nandi
,
C.
Qu
,
P. L.
Houston
,
R.
Conte
,
Q.
Yu
, and
J. M.
Bowman
,
J. Phys. Chem. Lett.
12
,
10318
(
2021
).
51.
S.
Li
,
W.
Li
, and
J.
Ma
,
Acc. Chem. Res.
47
,
2712
(
2014
).
52.
X.
He
,
T.
Zhu
,
X.
Wang
,
J.
Liu
, and
J. Z. H.
Zhang
,
Acc. Chem. Res.
47
,
2748
(
2014
).
53.
M. A.
Collins
,
M. W.
Cvitkovic
, and
R. P. A.
Bettens
,
Acc. Chem. Res.
47
,
2776
(
2014
).
54.
C.
Qu
and
J. M.
Bowman
,
J. Chem. Phys.
150
,
141101
(
2019
).
55.
R.
Conte
,
C.
Qu
, and
J. M.
Bowman
,
J. Chem. Theory Comput.
11
,
1631
(
2015
).
56.
A. G.
Baydin
and
B. A.
Pearlmutter
, in
JMLR: Workshop and Conference Proceedings, ICML 2014 AutoML Workshop
(
MIT Press
,
2014
), Vol. 1.
57.
A. G.
Baydin
,
B. A.
Pearlmutter
,
A. A.
Radul
, and
J. M.
Siskind
,
J. Mach. Learn. Res.
18
,
5595
5637
(
2017
).
58.
A.
Nandi
,
R.
Conte
,
C.
Qu
,
P. L.
Houston
,
Q.
Yu
, and
J. M.
Bowman
,
J. Chem. Theory Comput.
18
,
5527
(
2022
).
59.
R.
Conte
,
A.
Nandi
,
C.
Qu
,
Q.
Yu
,
P. L.
Houston
, and
J. M.
Bowman
,
J. Phys. Chem. A
126
,
7709
(
2022
).
60.
J. D.
Bender
,
S.
Doraiswamy
,
D. G.
Truhlar
, and
G. V.
Candler
,
J. Chem. Phys.
140
,
054302
(
2014
).
61.
R.
Dawes
,
D. L.
Thompson
,
Y.
Guo
,
A. F.
Wagner
, and
M.
Minkoff
,
J. Chem. Phys.
126
,
184108
(
2007
).
62.
R.
Dawes
,
D. L.
Thompson
,
A. F.
Wagner
, and
M.
Minkoff
,
J. Chem. Phys.
128
,
084107
(
2008
).
63.
R.
Dawes
,
A. F.
Wagner
, and
D. L.
Thompson
,
J. Phys. Chem. A
113
,
4709
(
2009
).
64.
Y.
Guo
,
I.
Tokmakov
,
D. L.
Thompson
,
A. F.
Wagner
, and
M.
Minkoff
,
J. Chem. Phys.
127
,
214106
(
2007
).
65.
J.
Ischtwan
and
M. A.
Collins
,
J. Chem. Phys.
100
,
8080
(
1994
).
66.
G. G.
Maisuradze
and
D. L.
Thompson
,
J. Phys. Chem. A
107
,
7118
(
2003
).
67.
G. G.
Maisuradze
,
D. L.
Thompson
,
A. F.
Wagner
, and
M.
Minkoff
,
J. Chem. Phys.
119
,
10002
(
2003
).
68.
I. V.
Tokmakov
,
A. F.
Wagner
,
M.
Minkoff
, and
D. L.
Thompson
,
Theor. Chem. Acc.
118
,
755
(
2007
).
69.
P.
Lancaster
and
K.
Šalkauskas
,
Math. Comput.
37
,
141
(
1981
).
70.
P.
Lancaster
and
K.
Šalkauskas
,
Curve and Surface Fitting: An Introduction
(
Academic Press
,
London
,
1986
).
71.
Q.
Yu
,
C.
Qu
,
P. L.
Houston
,
R.
Conte
,
A.
Nandi
, and
J. M.
Bowman
,
J. Phys. Chem. Lett.
13
,
5068
(
2022
).
72.
L.
Lodi
,
J.
Tennyson
, and
O. L.
Polyansky
,
J. Chem. Phys.
135
,
034113
(
2011
).
73.
B.
Yang
,
P.
Zhang
,
C.
Qu
,
X. H.
Wang
,
P. C.
Stancil
,
J. M.
Bowman
,
N.
Balakrishnan
,
B. M.
McLaughlin
, and
R. C.
Forrey
,
J. Phys. Chem. A
122
,
1511
(
2018
).
74.
B.
Yang
,
P.
Zhang
,
C.
Qu
,
P. C.
Stancil
,
J. M.
Bowman
,
N.
Balakrishnan
, and
R. C.
Forrey
,
Phys. Chem. Chem. Phys.
20
,
28425
(
2018
).
75.
B.
Yang
,
P.
Zhang
,
C.
Qu
,
P. C.
Stancil
,
J. M.
Bowman
,
N.
Balakrishnan
, and
R. C.
Forrey
,
Chem. Phys.
532
,
110695
(
2020
).

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