The Effective Fragment Molecular Orbital Method: Achieving High Scalability and Accuracy for Large Systems

Sattasathuchana, Tosaporn; Xu, Peng; Bertoni, Colleen; Kim, Yu Lim; Leang, Sarom S.; Pham, Buu Q.; Gordon, Mark S.

doi:10.1021/acs.jctc.3c01309

Title: The Effective Fragment Molecular Orbital Method: Achieving High Scalability and Accuracy for Large Systems

Journal Article · 06 March 2024 · Journal of Chemical Theory and Computation

DOI: https://doi.org/10.1021/acs.jctc.3c01309 · OSTI ID:2337498

Sattasathuchana, Tosaporn ^[1];

^[1]; Bertoni, Colleen ^[2]; Kim, Yu Lim ^[3]; Leang, Sarom S. ^[4]; Pham, Buu Q. ^[1];

^[1]

Ames Lab., and Iowa State Univ., Ames, IA (United States)
Argonne National Laboratory (ANL), Argonne, IL (United States). Argonne Leadership Computing Facility (ALCF)
Argonne National Laboratory (ANL), Argonne, IL (United States)
EP Analytics, San Diego, CA (United States)

The effective fragment molecular orbital (EFMO) method has been developed to predict the total energy of a very large molecular system accurately (with respect to the underlying quantum mechanical method) and efficiently by taking advantage of the locality of strong chemical interactions and employing a two-level hierarchical parallelism. The accuracy of the EFMO method is partly attributed to the accurate and robust intermolecular interaction prediction between distant fragments, in particular, the many-body polarization and dispersion effects, which require the generation of static and dynamic polarizability tensors by solving the coupled perturbed Hartree–Fock (CPHF) and time-dependent HF (TDHF) equations, respectively. Solving the CPHF and TDHF equations is the main EFMO computational bottleneck due to the inefficient (serial) and I/O-intensive implementation of the CPHF and TDHF solvers. In this work, the efficiency and scalability of the EFMO method are significantly improved with a new CPU memory-based implementation for solving the CPHF and TDHF equations that are parallelized by either message passing interface (MPI) or hybrid MPI/OpenMP. Here, the accuracy of the EFMO method is demonstrated for both covalently bonded systems and noncovalently bound molecular clusters by systematically examining the effects of basis sets and a key distance-related cutoff parameter, R_cut. R_cut determines whether a fragment pair (dimer) is treated by the chosen ab initio method or calculated using the effective fragment potential (EFP) method (separated dimers). Decreasing the value of Rcut increases the number of separated (EFP) dimers, thereby decreasing the computational effort. It is demonstrated that excellent accuracy (<1 kcal/mol error per fragment) can be achieved when using a sufficiently large basis set with diffuse functions coupled with a small R_cut value. With the new parallel implementation, the total EFMO wall time is substantially reduced, especially with a high number of MPI ranks. Given a sufficient workload, nearly ideal strong scaling is achieved for the CPHF and TDHF parts of the calculation. For the first time, EFMO calculations with the inclusion of long-range polarization and dispersion interactions on a hydrated mesoporous silica nanoparticle with explicit water solvent molecules (more than 15k atoms) are achieved on a massively parallel supercomputer using nearly 1000 physical nodes. In addition, EFMO calculations on the carbinolamine formation step of an amine-catalyzed aldol reaction at the nanoscale with explicit solvent effects are presented.

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Research Organization:: Ames Laboratory (AMES), Ames, IA (United States); Argonne National Laboratory (ANL), Argonne, IL (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Advanced Scientific Computing Research (ASCR); USDOE Office of Science (SC), Basic Energy Sciences (BES). Scientific User Facilities (SUF); National Science Foundation (NSF)

Grant/Contract Number:: AC02-07CH11358; AC02-06CH11357

OSTI ID:: 2337498

Alternate ID(s):: OSTI ID: 2476201

Report Number(s):: IS-J--11,284

Journal Information:: Journal of Chemical Theory and Computation, Journal Name: Journal of Chemical Theory and Computation Journal Issue: 6 Vol. 20; ISSN 1549-9618

Publisher:: American Chemical SocietyCopyright Statement

Country of Publication:: United States

Language:: English

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37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CHEMISTRY
algorithms
chemical calculations
interaction energies
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polarizability

Title: The Effective Fragment Molecular Orbital Method: Achieving High Scalability and Accuracy for Large Systems

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