Bypassing the Kohn-Sham equations with machine learning

Last year, at least 30,000 scientific papers used the Kohn–Sham scheme of density functional theory to solve electronic structure problems in a wide variety of scientific fields. Machine learning holds the promise of learning the energy functional via examples, bypassing the need to solve the Kohn–Sham equations. This should yield substantial savings in computer time, allowing larger systems and/or longer time-scales to be tackled, but attempts to machine-learn this functional have been limited by the need to find its derivative. The present work overcomes this difficulty by directly learning the density-potential and energy-density maps for test systems and various molecules. We perform the first molecular dynamics simulation with a machine-learned density functional on malonaldehyde and are able to capture the intramolecular proton transfer process. Learning density models now allows the construction of accurate density functionals for realistic molecular systems.Machine learning allows electronic structure calculations to access larger system sizes and, in dynamical simulations, longer time scales. Here, the authors perform such a simulation using a machine-learned density functional that avoids direct solution of the Kohn-Sham equations.

[1]  Michele Parrinello,et al.  Quickstep: Fast and accurate density functional calculations using a mixed Gaussian and plane waves approach , 2005, Comput. Phys. Commun..

[2]  Karsten W. Jacobsen,et al.  An object-oriented scripting interface to a legacy electronic structure code , 2002, Comput. Sci. Eng..

[3]  K. Burke,et al.  Ions in solution: density corrected density functional theory (DC-DFT). , 2014, The Journal of chemical physics.

[4]  Bernhard Schölkopf,et al.  Nonlinear Component Analysis as a Kernel Eigenvalue Problem , 1998, Neural Computation.

[5]  W. Kohn,et al.  Self-Consistent Equations Including Exchange and Correlation Effects , 1965 .

[6]  Bernhard Schölkopf,et al.  A Generalized Representer Theorem , 2001, COLT/EuroCOLT.

[7]  Wade Babcock,et al.  Computational materials science , 2004 .

[8]  J. W.,et al.  The Journal of Physical Chemistry , 1900, Nature.

[9]  G. Schatz The journal of physical chemistry letters , 2009 .

[10]  John C. Snyder,et al.  Orbital-free bond breaking via machine learning. , 2013, The Journal of chemical physics.

[11]  Joost VandeVondele,et al.  cp2k: atomistic simulations of condensed matter systems , 2014 .

[12]  Kun Yao,et al.  Kinetic Energy of Hydrocarbons as a Function of Electron Density and Convolutional Neural Networks. , 2015, Journal of chemical theory and computation.

[14]  Matthias Krack,et al.  Pseudopotentials for H to Kr optimized for gradient-corrected exchange-correlation functionals , 2005 .

[15]  Michele Parrinello,et al.  Generalized neural-network representation of high-dimensional potential-energy surfaces. , 2007, Physical review letters.

[16]  R. Dreizler,et al.  Density Functional Theory: An Approach to the Quantum Many-Body Problem , 1991 .

[17]  K. Müller,et al.  Machine Learning Predictions of Molecular Properties: Accurate Many-Body Potentials and Nonlocality in Chemical Space , 2015, The journal of physical chemistry letters.

[18]  Eunji Sim,et al.  Improved DFT Potential Energy Surfaces via Improved Densities. , 2015, The journal of physical chemistry letters.

[19]  G. Kresse,et al.  From ultrasoft pseudopotentials to the projector augmented-wave method , 1999 .

[20]  Vijay S Pande,et al.  Learning Kinetic Distance Metrics for Markov State Models of Protein Conformational Dynamics. , 2013, Journal of chemical theory and computation.

[21]  Mark E. Tuckerman,et al.  Reversible multiple time scale molecular dynamics , 1992 .

[22]  M. Klein,et al.  Nosé-Hoover chains : the canonical ensemble via continuous dynamics , 1992 .

[23]  Alexandre Tkatchenko,et al.  Quantum-chemical insights from deep tensor neural networks , 2016, Nature Communications.

[24]  Blöchl,et al.  Projector augmented-wave method. , 1994, Physical review. B, Condensed matter.

[25]  C. Q. Lee,et al.  The Computer Journal , 1958, Nature.

[26]  Vladimir N. Vapnik,et al.  The Nature of Statistical Learning Theory , 2000, Statistics for Engineering and Information Science.

[27]  M. V. Rossum,et al.  In Neural Computation , 2022 .

[28]  Kieron Burke,et al.  Corrections to Thomas-Fermi densities at turning points and beyond. , 2014, Physical review letters.

[29]  Kristof T. Schütt,et al.  How to represent crystal structures for machine learning: Towards fast prediction of electronic properties , 2013, 1307.1266.

[30]  Anubhav Jain,et al.  A high-throughput infrastructure for density functional theory calculations , 2011 .

[31]  Eunji Sim,et al.  Understanding and reducing errors in density functional calculations. , 2012, Physical review letters.

[32]  Yanli Wang,et al.  Quantum ESPRESSO: a modular and open-source software project for quantum simulations of materials , 2009 .

[33]  Klaus-Robert Müller,et al.  Kernels, Pre-images and Optimization , 2013, Empirical Inference.

[34]  Srihari Keshavamurthy,et al.  Annual Review of Physical Chemistry , 2018 .

[35]  Klaus-Robert Müller,et al.  Optimizing transition states via kernel-based machine learning. , 2012, The Journal of chemical physics.

[36]  Klaus-Robert Müller,et al.  Machine learning of accurate energy-conserving molecular force fields , 2016, Science Advances.

[37]  Atsuto Seko,et al.  Sparse representation for a potential energy surface , 2014, 1403.7995.

[38]  Robert Tibshirani,et al.  The Elements of Statistical Learning: Data Mining, Inference, and Prediction, 2nd Edition , 2001, Springer Series in Statistics.

[39]  Charles H. Ward Materials Genome Initiative for Global Competitiveness , 2012 .

[40]  Burke,et al.  Generalized Gradient Approximation Made Simple. , 1996, Physical review letters.

[41]  M. J. D. Powell,et al.  An efficient method for finding the minimum of a function of several variables without calculating derivatives , 1964, Comput. J..

[42]  Junmei Wang,et al.  Development and testing of a general amber force field , 2004, J. Comput. Chem..

[43]  Martins,et al.  Efficient pseudopotentials for plane-wave calculations. , 1991, Physical review. B, Condensed matter.

[44]  Michael I. Jordan,et al.  Advances in Neural Information Processing Systems 30 , 1995 .

[45]  Gunnar Rätsch,et al.  Input space versus feature space in kernel-based methods , 1999, IEEE Trans. Neural Networks.

[46]  E. Ungureanu,et al.  Molecular Physics , 2008, Nature.

[47]  Journal of Chemical Physics , 1932, Nature.

[48]  Paul L A Popelier,et al.  Prediction of Intramolecular Polarization of Aromatic Amino Acids Using Kriging Machine Learning. , 2014, Journal of chemical theory and computation.

[49]  P. Kollman,et al.  A well-behaved electrostatic potential-based method using charge restraints for deriving atomic char , 1993 .

[50]  P. Hohenberg,et al.  Inhomogeneous Electron Gas , 1964 .

[51]  Zhenwei Li,et al.  Molecular dynamics with on-the-fly machine learning of quantum-mechanical forces. , 2015, Physical review letters.

[52]  Klaus-Robert Müller,et al.  Nonlinear gradient denoising: Finding accurate extrema from inaccurate functional derivatives , 2015 .

[53]  K. Müller,et al.  Fast and accurate modeling of molecular atomization energies with machine learning. , 2011, Physical review letters.

[54]  Mark E. Tuckerman,et al.  Exploiting multiple levels of parallelism in Molecular Dynamics based calculations via modern techniques and software paradigms on distributed memory computers , 2000 .

[55]  R. Kondor,et al.  Gaussian approximation potentials: the accuracy of quantum mechanics, without the electrons. , 2009, Physical review letters.

[56]  Anubhav Jain,et al.  Finding Nature’s Missing Ternary Oxide Compounds Using Machine Learning and Density Functional Theory , 2010 .

[57]  D. Ruppert The Elements of Statistical Learning: Data Mining, Inference, and Prediction , 2004 .

[58]  Gunnar Rätsch,et al.  An introduction to kernel-based learning algorithms , 2001, IEEE Trans. Neural Networks.

[59]  A. Müller Journal of Physics Condensed Matter , 2008 .

[60]  Michele Parrinello,et al.  A hybrid Gaussian and plane wave density functional scheme , 1997 .

[61]  J. Perdew,et al.  Density-functional approximation for the correlation energy of the inhomogeneous electron gas. , 1986, Physical review. B, Condensed matter.

[62]  J. VandeVondele,et al.  An efficient orbital transformation method for electronic structure calculations , 2003 .

[63]  Paolo Ruggerone,et al.  Computational Materials Science X , 2002 .

[64]  Li Li,et al.  Understanding Machine-learned Density Functionals , 2014, ArXiv.

[65]  Hans-Joachim Werner,et al.  A simple and efficient CCSD(T)-F12 approximation. , 2007, The Journal of chemical physics.

[66]  Teter,et al.  Separable dual-space Gaussian pseudopotentials. , 1996, Physical review. B, Condensed matter.

[67]  G. G. Stokes "J." , 1890, The New Yale Book of Quotations.

[68]  Kieron Burke,et al.  Electronic structure via potential functional approximations. , 2011, Physical review letters.

[69]  A. Becke Density-functional thermochemistry. III. The role of exact exchange , 1993 .

[70]  Kieron Burke,et al.  DFT: A Theory Full of Holes? , 2014, Annual review of physical chemistry.

[71]  Klaus-Robert Müller,et al.  Assessment and Validation of Machine Learning Methods for Predicting Molecular Atomization Energies. , 2013, Journal of chemical theory and computation.

[72]  Vladimir Vovk,et al.  Empirical Inference , 2011, Springer Berlin Heidelberg.

[73]  Joost VandeVondele,et al.  Gaussian basis sets for accurate calculations on molecular systems in gas and condensed phases. , 2007, The Journal of chemical physics.

[74]  R. Williams,et al.  Journal of American Chemical Society , 1979 .

[75]  A. Zunger,et al.  Self-interaction correction to density-functional approximations for many-electron systems , 1981 .

[76]  Klaus-Robert Müller,et al.  Finding Density Functionals with Machine Learning , 2011, Physical review letters.

[77]  M. Tuckerman,et al.  Heavy-atom skeleton quantization and proton tunneling in "intermediate-barrier" hydrogen bonds. , 2001, Physical review letters.

[78]  Kieron Burke,et al.  Pure density functional for strong correlation and the thermodynamic limit from machine learning , 2016, 1609.03705.

[79]  Li Li,et al.  Understanding Kernel Ridge Regression: Common behaviors from simple functions to density functionals , 2015, ArXiv.