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Kar R, Mandal S, Thakkur V, Meyer B, Nair NN. Speeding-up Hybrid Functional-Based Ab Initio Molecular Dynamics Using Multiple Time-stepping and Resonance-Free Thermostat. J Chem Theory Comput 2023; 19:8351-8364. [PMID: 37933121 DOI: 10.1021/acs.jctc.3c00964] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2023]
Abstract
Ab initio molecular dynamics (AIMD) based on density functional theory (DFT) has become a workhorse for studying the structure, dynamics, and reactions in condensed matter systems. Currently, AIMD simulations are primarily carried out at the level of generalized gradient approximation (GGA), which is at the second rung of DFT functionals in terms of accuracy. Hybrid DFT functionals, which form the fourth rung in the accuracy ladder, are not commonly used in AIMD simulations as the computational cost involved is 100 times or higher. To facilitate AIMD simulations with hybrid functionals, we propose here an approach using multiple time stepping with adaptively compressed exchange operator and resonance-free thermostat, that could speed up the calculations by ∼30 times or more for systems with a few hundred of atoms. We demonstrate that by achieving this significant speed up and making the compute time of hybrid functional-based AIMD simulations at par with that of GGA functionals, we are able to study several complex condensed matter systems and model chemical reactions in solution with hybrid functionals that were earlier unthinkable to be performed.
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Affiliation(s)
- Ritama Kar
- Department of Chemistry, Indian Institute of Technology Kanpur (IITK), Kanpur 208016, India
| | - Sagarmoy Mandal
- Interdisciplinary Center for Molecular Materials and Computer Chemistry Center, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Nägelsbachstr. 25, Erlangen 91052, Germany
- Erlangen National High Performance Computing Center (NHR@FAU), Friedrich-Alexander-Universität Erlangen-Nürnberg, Martensstr. 1, Erlangen 91058, Germany
| | - Vaishali Thakkur
- Department of Chemistry, Indian Institute of Technology Kanpur (IITK), Kanpur 208016, India
| | - Bernd Meyer
- Interdisciplinary Center for Molecular Materials and Computer Chemistry Center, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Nägelsbachstr. 25, Erlangen 91052, Germany
- Erlangen National High Performance Computing Center (NHR@FAU), Friedrich-Alexander-Universität Erlangen-Nürnberg, Martensstr. 1, Erlangen 91058, Germany
| | - Nisanth N Nair
- Department of Chemistry, Indian Institute of Technology Kanpur (IITK), Kanpur 208016, India
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Yu VWZ, Govoni M. GPU Acceleration of Large-Scale Full-Frequency GW Calculations. J Chem Theory Comput 2022; 18:4690-4707. [PMID: 35913080 DOI: 10.1021/acs.jctc.2c00241] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Many-body perturbation theory is a powerful method to simulate electronic excitations in molecules and materials starting from the output of density functional theory calculations. By implementing the theory efficiently so as to run at scale on the latest leadership high-performance computing systems it is possible to extend the scope of GW calculations. We present a GPU acceleration study of the full-frequency GW method as implemented in the WEST code. Excellent performance is achieved through the use of (i) optimized GPU libraries, e.g., cuFFT and cuBLAS, (ii) a hierarchical parallelization strategy that minimizes CPU-CPU, CPU-GPU, and GPU-GPU data transfer operations, (iii) nonblocking MPI communications that overlap with GPU computations, and (iv) mixed precision in selected portions of the code. A series of performance benchmarks has been carried out on leadership high-performance computing systems, showing a substantial speedup of the GPU-accelerated version of WEST with respect to its CPU version. Good strong and weak scaling is demonstrated using up to 25 920 GPUs. Finally, we showcase the capability of the GPU version of WEST for large-scale, full-frequency GW calculations of realistic systems, e.g., a nanostructure, an interface, and a defect, comprising up to 10 368 valence electrons.
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Affiliation(s)
- Victor Wen-Zhe Yu
- Materials Science Division, Argonne National Laboratory, Lemont, Illinois 60439, United States
| | - Marco Govoni
- Materials Science Division, Argonne National Laboratory, Lemont, Illinois 60439, United States.,Pritzker School of Molecular Engineering, The University of Chicago, Chicago, Illinois 60637, United States
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Bystrom K, Kozinsky B. CIDER: An Expressive, Nonlocal Feature Set for Machine Learning Density Functionals with Exact Constraints. J Chem Theory Comput 2022; 18:2180-2192. [PMID: 35235322 DOI: 10.1021/acs.jctc.1c00904] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Machine learning (ML) has recently gained attention as a means to develop more accurate exchange-correlation (XC) functionals for density functional theory, but functionals developed thus far need to be improved on several metrics, including accuracy, numerical stability, and transferability across chemical space. In this work, we introduce a set of nonlocal features of the density called the CIDER formalism, which we use to train a Gaussian process model for the exchange energy that obeys the critical uniform scaling rule for exchange. The resulting CIDER exchange functional is significantly more accurate than any semilocal functional tested here, and it has good transferability across main-group molecules. This work therefore serves as an initial step toward more accurate exchange functionals, and it also introduces useful techniques for developing robust, physics-informed XC models via ML.
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Affiliation(s)
- Kyle Bystrom
- John A. Paulson School of Engineering and Applied Sciences, Harvard University, , Cambridge, Massachusetts 02138, United States
| | - Boris Kozinsky
- John A. Paulson School of Engineering and Applied Sciences, Harvard University, , Cambridge, Massachusetts 02138, United States
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Mandal S, Kar R, Klöffel T, Meyer B, Nair NN. Improving the scaling and performance of multiple time stepping-based molecular dynamics with hybrid density functionals. J Comput Chem 2022; 43:588-597. [PMID: 35147988 DOI: 10.1002/jcc.26816] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2021] [Revised: 01/07/2022] [Accepted: 01/18/2022] [Indexed: 12/18/2022]
Abstract
Density functionals at the level of the generalized gradient approximation (GGA) and a plane-wave basis set are widely used today to perform ab initio molecular dynamics (AIMD) simulations. Going up in the ladder of accuracy of density functionals from GGA (second rung) to hybrid density functionals (fourth rung) is much desired pertaining to the accuracy of the latter in describing structure, dynamics, and energetics of molecular and condensed matter systems. On the other hand, hybrid density functional based AIMD simulations are about two orders of magnitude slower than GGA based AIMD for systems containing ~100 atoms using ~100 compute cores. Two methods, namely MTACE and s-MTACE, based on a multiple time step integrator and adaptively compressed exchange operator formalism are able to provide a speed-up of about 7-9 in performing hybrid density functional based AIMD. In this work, we report an implementation of these methods using a task-group based parallelization within the CPMD program package, with the intention to take advantage of the large number of compute cores available on modern high-performance computing platforms. We present here the boost in performance achieved through this algorithm. This work also identifies the computational bottleneck in the s-MTACE method and proposes a way to overcome it.
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Affiliation(s)
- Sagarmoy Mandal
- Department of Chemistry, Indian Institute of Technology Kanpur (IITK), Kanpur, India.,Interdisciplinary Center for Molecular Materials and Computer Chemistry Center, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Erlangen, Germany.,Erlangen National High Performance Computing Center (NHR@FAU), Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Ritama Kar
- Department of Chemistry, Indian Institute of Technology Kanpur (IITK), Kanpur, India
| | - Tobias Klöffel
- Interdisciplinary Center for Molecular Materials and Computer Chemistry Center, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Erlangen, Germany.,Erlangen National High Performance Computing Center (NHR@FAU), Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Bernd Meyer
- Interdisciplinary Center for Molecular Materials and Computer Chemistry Center, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Erlangen, Germany.,Erlangen National High Performance Computing Center (NHR@FAU), Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Nisanth N Nair
- Department of Chemistry, Indian Institute of Technology Kanpur (IITK), Kanpur, India
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Mandal S, Thakkur V, Nair NN. Achieving an Order of Magnitude Speedup in Hybrid-Functional- and Plane-Wave-Based Ab Initio Molecular Dynamics: Applications to Proton-Transfer Reactions in Enzymes and in Solution. J Chem Theory Comput 2021; 17:2244-2255. [PMID: 33740375 DOI: 10.1021/acs.jctc.1c00009] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Ab initio molecular dynamics (MD) with hybrid density functionals and a plane wave basis is computationally expensive due to the high computational cost of exact exchange energy evaluation. Recently, we proposed a strategy to combine adaptively compressed exchange (ACE) operator formulation and a multiple time step integration scheme to reduce the computational cost significantly [J. Chem. Phys. 2019, 151, 151102 ]. However, it was found that the construction of the ACE operator, which has to be done at least once in every MD time step, is computationally expensive. In the present work, systematic improvements are introduced to further speed up by employing localized orbitals for the construction of the ACE operator. By this, we could achieve a computational speedup of an order of magnitude for a periodic system containing 32 water molecules. Benchmark calculations were carried out to show the accuracy and efficiency of the method in predicting the structural and dynamical properties of bulk water. To demonstrate the applicability, computationally intensive free-energy computations at the level of hybrid density functional theory were performed to investigate (a) methyl formate hydrolysis reaction in neutral aqueous media and (b) proton-transfer reaction within the active-site residues of the class C β-lactamase enzyme.
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Affiliation(s)
- Sagarmoy Mandal
- Department of Chemistry, Indian Institute of Technology Kanpur (IITK), Kanpur 208016, India.,Interdisciplinary Center for Molecular Materials and Computer Chemistry Center, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Nägelsbachstr. 25, Erlangen 91052, Germany
| | - Vaishali Thakkur
- Department of Chemistry, Indian Institute of Technology Kanpur (IITK), Kanpur 208016, India
| | - Nisanth N Nair
- Department of Chemistry, Indian Institute of Technology Kanpur (IITK), Kanpur 208016, India
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Schwarz K, Groenenboom MC, Moffat TP, Sundararaman R, Vinson J. Resolving the Geometry/Charge Puzzle of the c(2 × 2)-Cl Cu(100) Electrode. J Phys Chem Lett 2021; 12:440-446. [PMID: 33356303 PMCID: PMC8237333 DOI: 10.1021/acs.jpclett.0c03115] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Potential-induced changes in charge and surface structure are significant drivers of the reactivity of electrochemical interfaces but are frequently difficult to decouple from the effects of surface solvation. Here, we consider the Cu(100) surface with a c(2 × 2)-Cl adlayer, a model surface with multiple geometry measurements under both ultrahigh vacuum and electrochemical conditions. Under aqueous electrochemical conditions, the measured Cu-Cl interplanar separation (dCu-Cl) increases by at least 0.3 Å relative to that under ultrahigh vacuum conditions. This large geometry change is unexpected for a hydrophobic surface, and it requires invoking a negative charge on the Cl-covered surface which is much greater than expected from the work function and our capacitance measurements. To resolve this inconsistency we employ ab initio calculations and find that the Cu-Cl separation increases with charging at a rate of 0.7 Å/e- per Cl atom. The larger Cu-Cl bond distance increases the surface dipole and, therefore, the work function of the interface, contributing to the negative charge under fixed potential electrochemical conditions. Interactions with water are not needed to explain either the large charge or large Cu-Cl interplanar spacing of this surface under electrochemical conditions.
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Affiliation(s)
- Kathleen Schwarz
- Material Measurement Laboratory, National Institute of Standards and Technology, 100 Bureau Drive, Gaithersburg, Maryland 20899, United States
| | - Mitchell C Groenenboom
- Material Measurement Laboratory, National Institute of Standards and Technology, 100 Bureau Drive, Gaithersburg, Maryland 20899, United States
| | - Thomas P Moffat
- Material Measurement Laboratory, National Institute of Standards and Technology, 100 Bureau Drive, Gaithersburg, Maryland 20899, United States
| | - Ravishankar Sundararaman
- Department of Materials Science and Engineering, Rensselaer Polytechnic Institute, 110 Eighth Street, Troy, New York 12180, United States
| | - John Vinson
- Material Measurement Laboratory, National Institute of Standards and Technology, 100 Bureau Drive, Gaithersburg, Maryland 20899, United States
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