We present the latest release of PANNA 2.0 (Properties from Artificial Neural Network Architectures), a code for the generation of neural network interatomic potentials based on local atomic descriptors and multilayer perceptrons. Built on a new back end, this new release of PANNA features improved tools for customizing and monitoring network training, better graphics processing unit support including a fast descriptor calculator, new plugins for external codes, and a new architecture for the inclusion of long-range electrostatic interactions through a variational charge equilibration scheme. We present an overview of the main features of the new code, and several benchmarks comparing the accuracy of PANNA models to the state of the art, on commonly used benchmarks as well as richer datasets.

1.
J.
Behler
, “
Perspective: Machine learning potentials for atomistic simulations
,”
J. Chem. Phys.
145
,
170901
(
2016
).
2.
O. T.
Unke
,
S.
Chmiela
,
H. E.
Sauceda
,
M.
Gastegger
,
I.
Poltavsky
,
K. T.
Schütt
,
A.
Tkatchenko
, and
K.-R.
Müller
, “
Machine learning force fields
,”
Chem. Rev.
121
,
10142
10186
(
2021
).
3.
H. J.
Kulik
,
T.
Hammerschmidt
,
J.
Schmidt
,
S.
Botti
,
M. A. L.
Marques
,
M.
Boley
,
M.
Scheffler
,
M.
Todorović
,
P.
Rinke
,
C.
Oses
,
A.
Smolyanyuk
,
S.
Curtarolo
,
A.
Tkatchenko
,
A. P.
Bartók
,
S.
Manzhos
,
M.
Ihara
,
T.
Carrington
,
J.
Behler
,
O.
Isayev
,
M.
Veit
,
A.
Grisafi
,
J.
Nigam
,
M.
Ceriotti
,
K. T.
Schütt
,
J.
Westermayr
,
M.
Gastegger
,
R. J.
Maurer
,
B.
Kalita
,
K.
Burke
,
R.
Nagai
,
R.
Akashi
,
O.
Sugino
,
J.
Hermann
,
F.
Noé
,
S.
Pilati
,
C.
Draxl
,
M.
Kuban
,
S.
Rigamonti
,
M.
Scheidgen
,
M.
Esters
,
D.
Hicks
,
C.
Toher
,
P. V.
Balachandran
,
I.
Tamblyn
,
S.
Whitelam
,
C.
Bellinger
, and
L. M.
Ghiringhelli
, “
Roadmap on machine learning in electronic structure
,”
Electron. Struct.
4
,
023004
(
2022
).
4.
K. T.
Butler
,
D. W.
Davies
,
H.
Cartwright
,
O.
Isayev
, and
A.
Walsh
, “
Machine learning for molecular and materials science
,”
Nature
559
,
547
555
(
2018
).
5.
J. C.
Snyder
,
M.
Rupp
,
K.
Hansen
,
K.-R.
Müller
, and
K.
Burke
, “
Finding density functionals with machine learning
,”
Phys. Rev. Lett.
108
,
253002
(
2012
).
6.
J.
Behler
, “
Atom-centered symmetry functions for constructing high-dimensional neural network potentials
,”
J. Chem. Phys.
134
,
074106
(
2011
).
7.
J. S.
Smith
,
O.
Isayev
, and
A. E.
Roitberg
, “
ANI-1: An extensible neural network potential with DFT accuracy at force field computational cost
,”
Chem. Sci.
8
,
3192
3203
(
2017
).
8.
S.
De
,
A. P.
Bartók
,
G.
Csányi
, and
M.
Ceriotti
, “
Comparing molecules and solids across structural and alchemical space
,”
Phys. Chem. Chem. Phys.
18
,
13754
13769
(
2016
).
9.
A. P.
Bartók
,
M. C.
Payne
,
R.
Kondor
, and
G.
Csányi
, “
Gaussian approximation potentials: The accuracy of quantum mechanics, without the electrons
,”
Phys. Rev. Lett.
104
,
136403
(
2010
).
10.
G.
Csányi
,
S.
Winfield
,
J. R.
Kermode
,
A.
De Vita
,
A.
Comisso
,
N.
Bernstein
, and
M. C.
Payne
, “
Expressive programming for computational physics in Fortran 95+
,” IoP Computational Physics Newsletter Spring,
2007
.
11.
V. L.
Deringer
and
G.
Csányi
, “
Machine learning based interatomic potential for amorphous carbon
,”
Phys. Rev. B
95
,
094203
(
2017
).
12.
Y.
Shaidu
,
E.
Küçükbenli
,
R.
Lot
,
F.
Pellegrini
,
E.
Kaxiras
, and
S.
de Gironcoli
, “
A systematic approach to generating accurate neural network potentials: The case of carbon
,”
npj Comput. Mater.
7
,
52
(
2021
).
13.
N.
Artrith
and
J.
Behler
, “
High-dimensional neural network potentials for metal surfaces: A prototype study for copper
,”
Phys. Rev. B
85
,
045439
(
2012
).
14.
A. C. P.
Jain
,
D.
Marchand
,
A.
Glensk
,
M.
Ceriotti
, and
W. A.
Curtin
, “
Machine learning for metallurgy III: A neural network potential for Al-Mg-Si
,”
Phys. Rev. Mater.
5
,
053805
(
2021
).
15.
R.
Drautz
, “
Atomic cluster expansion for accurate and transferable interatomic potentials
,”
Phys. Rev. B
99
,
014104
(
2019
).
16.
D. P.
Kovács
,
C.
van der Oord
,
J.
Kucera
,
A. E. A.
Allen
,
D. J.
Cole
,
C.
Ortner
, and
G.
Csányi
, “
Linear atomic cluster expansion force fields for organic molecules: Beyond RMSE
,”
J. Chem. Theory Comput.
17
,
7696
7711
(
2021
).
17.
J.
Gilmer
,
S. S.
Schoenholz
,
P. F.
Riley
,
O.
Vinyals
, and
G. E.
Dahl
, “
Neural message passing for quantum chemistry
,” in
International Conference on Machine Learning
(
PMLR
,
2017
), pp.
1263
1272
.
18.
N.
Lubbers
,
J. S.
Smith
, and
K.
Barros
, “
Hierarchical modeling of molecular energies using a deep neural network
,”
J. Chem. Phys.
148
,
241715
(
2018
).
19.
K. T.
Schütt
,
H. E.
Sauceda
,
P.-J.
Kindermans
,
A.
Tkatchenko
, and
K.-R.
Müller
, “
SchNet—A deep learning architecture for molecules and materials
,”
J. Chem. Phys.
148
,
241722
(
2018
).
20.
J.
Gasteiger
,
J.
Groß
, and
S.
Günnemann
, “
Directional message passing for molecular graphs
,” presented at International Conference on Learning Representations (ICLR),
2020
.
21.
J.
Gasteiger
,
F.
Becker
, and
S.
Günnemann
, “
GemNet: Universal directional graph neural networks for molecules
,”
Adv. Neural Inf. Process. Syst.
34
,
6790
6802
(
2021
).
22.
M.
Haghighatlari
,
J.
Li
,
X.
Guan
,
O.
Zhang
,
A.
Das
,
C. J.
Stein
,
F.
Heidar-Zadeh
,
M.
Liu
,
M.
Head-Gordon
,
L.
Bertels
et al, “
NewtonNet: A Newtonian message passing network for deep learning of interatomic potentials and forces
,”
Digital Discovery
1
,
333
343
(
2022
).
23.
V. G.
Satorras
,
E.
Hoogeboom
, and
M.
Welling
, “
E(n) equivariant graph neural networks
,” in
International Conference on Machine Learning
(
PMLR
,
2021
), pp.
9323
9332
.
24.
S.
Batzner
,
A.
Musaelian
,
L.
Sun
,
M.
Geiger
,
J. P.
Mailoa
,
M.
Kornbluth
,
N.
Molinari
,
T. E.
Smidt
, and
B.
Kozinsky
, “
E(3)-equivariant graph neural networks for data-efficient and accurate interatomic potentials
,”
Nat. Commun.
13
,
2453
(
2022
).
25.
I.
Batatia
,
D. P.
Kovacs
,
G.
Simm
,
C.
Ortner
, and
G.
Csányi
, “
MACE: Higher order equivariant message passing neural networks for fast and accurate force fields
,”
Adv. Neural Inf. Process. Syst.
35
,
11423
11436
(
2022
).
26.
A.
Musaelian
,
S.
Batzner
,
A.
Johansson
,
L.
Sun
,
C. J.
Owen
,
M.
Kornbluth
, and
B.
Kozinsky
, “
Learning local equivariant representations for large-scale atomistic dynamics
,”
Nat. Commun.
14
,
579
(
2023
).
27.
I.
Batatia
,
S.
Batzner
,
D. P.
Kovács
,
A.
Musaelian
,
G. N.
Simm
,
R.
Drautz
,
C.
Ortner
,
B.
Kozinsky
, and
G.
Csányi
, “
The design space of E(3)-equivariant atom-centered interatomic potentials
,” arXiv:2205.06643 (
2022
).
28.
R.
Lot
,
F.
Pellegrini
,
Y.
Shaidu
, and
E.
Küçükbenli
, “
PANNA: Properties from artificial neural network architectures
,”
Comput. Phys. Commun.
256
,
107402
(
2020
).
29.
H.
Wang
,
L.
Zhang
,
J.
Han
, and
W.
E
, “
DeePMD-kit: A deep learning package for many-body potential energy representation and molecular dynamics
,”
Comput. Phys. Commun.
228
,
178
184
(
2018
).
30.
J.
Zeng
,
D.
Zhang
,
D.
Lu
,
P.
Mo
,
Z.
Li
,
Y.
Chen
,
M.
Rynik
,
L.
Huang
,
Z.
Li
,
S.
Shi
,
Y.
Wang
,
H.
Ye
,
P.
Tuo
,
J.
Yang
,
Y.
Ding
,
Y.
Li
,
D.
Tisi
,
Q.
Zeng
,
H.
Bao
,
Y.
Xia
,
J.
Huang
,
K.
Muraoka
,
Y.
Wang
,
J.
Chang
,
F.
Yuan
,
S. L.
Bore
,
C.
Cai
,
Y.
Lin
,
B.
Wang
,
J.
Xu
,
J.-X.
Zhu
,
C.
Luo
,
Y.
Zhang
,
R. E. A.
Goodall
,
W.
Liang
,
A. K.
Singh
,
S.
Yao
,
J.
Zhang
,
R.
Wentzcovitch
,
J.
Han
,
J.
Liu
,
W.
Jia
,
D. M.
York
,
W.
E
,
R.
Car
,
L.
Zhang
, and
H.
Wang
, “
DeePMD-kit v2: A software package for deep potential models
,”
J. Chem. Phys.
159
(
5
),
054801
(
2023
).
31.
N.
Artrith
and
A.
Urban
, “
An implementation of artificial neural-network potentials for atomistic materials simulations: Performance for TiO2
,”
Comput. Mater. Sci.
114
,
135
150
(
2016
).
32.
A.
Khorshidi
and
A. A.
Peterson
, “
Amp: A modular approach to machine learning in atomistic simulations
,”
Comput. Phys. Commun.
207
,
310
324
(
2016
).
33.
X.
Gao
,
F.
Ramezanghorbani
,
O.
Isayev
,
J. S.
Smith
, and
A. E.
Roitberg
, “
TorchANI: A free and open source PyTorch-based deep learning implementation of the ANI neural network potentials
,”
J. Chem. Inf. Model.
60
,
3408
3415
(
2020
).
34.
K.
Lee
,
D.
Yoo
,
W.
Jeong
, and
S.
Han
, “
SIMPLE-NN: An efficient package for training and executing neural-network interatomic potentials
,”
Comput. Phys. Commun.
242
,
95
103
(
2019
).
35.
N.
Artrith
,
A.
Urban
, and
G.
Ceder
, “
Efficient and accurate machine-learning interpolation of atomic energies in compositions with many species
,”
Phys. Rev. B
96
,
014112
(
2017
).
36.
M.
Abadi
,
A.
Agarwal
,
P.
Barham
,
E.
Brevdo
,
Z.
Chen
,
C.
Citro
,
G. S.
Corrado
,
A.
Davis
,
J.
Dean
,
M.
Devin
,
S.
Ghemawat
,
I.
Goodfellow
,
A.
Harp
,
G.
Irving
,
M.
Isard
,
Y.
Jia
,
R.
Jozefowicz
,
L.
Kaiser
,
M.
Kudlur
,
J.
Levenberg
,
D.
Mané
,
R.
Monga
,
S.
Moore
,
D.
Murray
,
C.
Olah
,
M.
Schuster
,
J.
Shlens
,
B.
Steiner
,
I.
Sutskever
,
K.
Talwar
,
P.
Tucker
,
V.
Vanhoucke
,
V.
Vasudevan
,
F.
Viégas
,
O.
Vinyals
,
P.
Warden
,
M.
Wattenberg
,
M.
Wicke
,
Y.
Yu
, and
X.
Zheng
, “
TensorFlow: Large-scale machine learning on heterogeneous systems
,”
2015
, software available from tensorflow.org.
37.
A. P.
Thompson
,
H. M.
Aktulga
,
R.
Berger
,
D. S.
Bolintineanu
,
W. M.
Brown
,
P. S.
Crozier
,
P. J.
in’t Veld
,
A.
Kohlmeyer
,
S. G.
Moore
,
T. D.
Nguyen
,
R.
Shan
,
M. J.
Stevens
,
J.
Tranchida
,
C.
Trott
, and
S. J.
Plimpton
, “
LAMMPS—A flexible simulation tool for particle-based materials modeling at the atomic, meso, and continuum scales
,”
Comput. Phys. Commun.
271
,
108171
(
2022
).
38.
A. H.
Larsen
,
J. J.
Mortensen
,
J.
Blomqvist
,
I. E.
Castelli
,
R.
Christensen
,
M.
Dułak
,
J.
Friis
,
M. N.
Groves
,
B.
Hammer
,
C.
Hargus
et al, “
The atomic simulation environment—A Python library for working with atoms
,”
J. Phys.: Condens. Matter
29
,
273002
(
2017
).
39.
E. B.
Tadmor
,
R. S.
Elliott
,
J. P.
Sethna
,
R. E.
Miller
, and
C. A.
Becker
, “
The potential of atomistic simulations and the knowledgebase of interatomic models
,”
JOM
63
,
17
(
2011
).
40.
F.
Pellegrini
,
R.
Lot
,
Y.
Shaidu
, and
E.
Küçükbenli
, (
2023
). “
PANNA—Properties from artificial neural network architectures
,” Gitlab. https://gitlab.com/PANNAdevs/panna
41.
F.
Pellegrini
,
R.
Lot
,
Y.
Shaidu
, and
E.
Küçükbenli
, (
2023
). “
PANNA documentation
,” Gitlab. https://pannadevs.gitlab.io/pannadoc/
42.
P.
Giannozzi
,
O.
Andreussi
,
T.
Brumme
,
O.
Bunau
,
M.
Buongiorno Nardelli
,
M.
Calandra
,
R.
Car
,
C.
Cavazzoni
,
D.
Ceresoli
,
M.
Cococcioni
,
N.
Colonna
,
I.
Carnimeo
,
A.
Dal Corso
,
S.
de Gironcoli
,
P.
Delugas
,
R. A.
DiStasio
,
A.
Ferretti
,
A.
Floris
,
G.
Fratesi
,
G.
Fugallo
,
R.
Gebauer
,
U.
Gerstmann
,
F.
Giustino
,
T.
Gorni
,
J.
Jia
,
M.
Kawamura
,
H.-Y.
Ko
,
A.
Kokalj
,
E.
Küçükbenli
,
M.
Lazzeri
,
M.
Marsili
,
N.
Marzari
,
F.
Mauri
,
N. L.
Nguyen
,
H.-V.
Nguyen
,
A.
Otero-de-la-Roza
,
L.
Paulatto
,
S.
Poncé
,
D.
Rocca
,
R.
Sabatini
,
B.
Santra
,
M.
Schlipf
,
A. P.
Seitsonen
,
A.
Smogunov
,
I.
Timrov
,
T.
Thonhauser
,
P.
Umari
,
N.
Vast
,
X.
Wu
, and
S.
Baroni
, “
Advanced capabilities for materials modelling with Quantum ESPRESSO
,”
J. Phys.: Condens. Matter
29
,
465901
(
2017
).
43.
G.
Kresse
and
J.
Furthmüller
, “
Efficient iterative schemes for ab initio total-energy calculations using a plane-wave basis set
,”
Phys. Rev. B
54
,
11169
11186
(
1996
).
44.
C. W.
Glass
,
A. R.
Oganov
, and
N.
Hansen
, “
USPEX—Evolutionary crystal structure prediction
,”
Comput. Phys. Commun.
175
,
713
720
(
2006
).
45.
D. P.
Kingma
and
J.
Ba
, “
Adam: A method for stochastic optimization
,” presented at International Conference on Learning Representations (ICLR),
2015
.
46.
S. S.
Schoenholz
and
E. D.
Cubuk
, “
JAX, MD: A framework for differentiable physics
,” in
Advances in Neural Information Processing Systems
(
Curran Associates, Inc.
,
2020
), Vol.
33
.
47.
S. A.
Ghasemi
,
A.
Hofstetter
,
S.
Saha
, and
S.
Goedecker
, “
Interatomic potentials for ionic systems with density functional accuracy based on charge densities obtained by a neural network
,”
Phys. Rev. B
92
,
045131
(
2015
).
48.
T. W.
Ko
,
J. A.
Finkler
,
S.
Goedecker
, and
J.
Behler
, “
A fourth-generation high-dimensional neural network potential with accurate electrostatics including non-local charge transfer
,”
Nat. Commun.
12
,
398
(
2021
).
49.
L. D.
Jacobson
,
J. M.
Stevenson
,
F.
Ramezanghorbani
,
D.
Ghoreishi
,
K.
Leswing
,
E. D.
Harder
, and
R.
Abel
, “
Transferable neural network potential energy surfaces for closed-shell organic molecules: Extension to ions
,”
J. Chem. Theory Comput.
18
,
2354
2366
(
2022
).
50.
M.
Amsler
,
S.
Rostami
,
H.
Tahmasbi
,
E. R.
Khajehpasha
,
S.
Faraji
,
R.
Rasoulkhani
, and
S. A.
Ghasemi
, “
FLAME: A library of atomistic modeling environments
,”
Comput. Phys. Commun.
256
,
107415
(
2020
).
51.
Y.
Shaidu
,
F.
Pellegrini
,
E.
Küçükbenli
,
R.
Lot
, and
S.
de Gironcoli
, “
Incorporating long-range electrostatics in neural network potentials via variational charge equilibration from shortsighted ingredients
,” npj Comp. Mater. (submitted) (
2023
).
52.
A. S.
Christensen
and
O. A.
Von Lilienfeld
, “
On the role of gradients for machine learning of molecular energies and forces
,”
Mach. Learn.: Sci. Technol.
1
,
045018
(
2020
).
53.
C.
Devereux
,
J. S.
Smith
,
K. K.
Huddleston
,
K.
Barros
,
R.
Zubatyuk
,
O.
Isayev
, and
A. E.
Roitberg
, “
Extending the applicability of the ANI deep learning molecular potential to sulfur and halogens
,”
J. Chem. Theory Comput.
16
,
4192
4202
(
2020
).
54.
P.
Izmailov
,
D.
Podoprikhin
,
T.
Garipov
,
D.
Vetrov
, and
A. G.
Wilson
, “
Averaging weights leads to wider optima and better generalization
,” in
Proceedings of the Thirty-Fourth Conference on Uncertainty in Artificial Intelligence
(AUAI Press, 2018), pp. 876-885.
55.
G.
Hinton
,
O.
Vinyals
, and
J.
Dean
, “
Distilling the knowledge in a neural network
,” presented at NIPS Deep Learning and Representation Learning Workshop,
2015
.
56.
F.
Pellegrini
,
R.
Lot
,
Y.
Shaidu
, and
E.
Küçükbenli
, (
2023
). “
Carbon dataset
,” Zenodo. https://doi.org/10.5281/zenodo.8095485
57.
F.
Pellegrini
,
R.
Lot
,
Y.
Shaidu
, and
E.
Küçükbenli
, (
2023
). “
Carbon potentials
,” Zenodo. https://doi.org/10.5281/zenodo.8095733

Supplementary Material

You do not currently have access to this content.