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Sattasathuchana T, Xu P, Bertoni C, Kim YL, Leang SS, Pham BQ, Gordon MS. The Effective Fragment Molecular Orbital Method: Achieving High Scalability and Accuracy for Large Systems. J Chem Theory Comput 2024; 20:2445-2461. [PMID: 38450638 DOI: 10.1021/acs.jctc.3c01309] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/08/2024]
Abstract
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. 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, Rcut. Rcut 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 Rcut 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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Affiliation(s)
- Tosaporn Sattasathuchana
- Department of Chemistry, Iowa State University and Ames National Laboratory, Ames, Iowa 50011, United States
| | - Peng Xu
- Department of Chemistry, Iowa State University and Ames National Laboratory, Ames, Iowa 50011, United States
| | - Colleen Bertoni
- Argonne Leadership Computing Facility, Argonne National Laboratory, Lemont, Illinois 60439, United States
| | - Yu Lim Kim
- Chemical Sciences and Engineering Division, Argonne National Laboratory, Lemont, Illinois 60439, United States
| | - Sarom S Leang
- EP Analytics, Inc., 9909 Mira Mesa Blvd Ste. 230, San Diego, California 92131, United States
| | - Buu Q Pham
- Department of Chemistry, Iowa State University and Ames National Laboratory, Ames, Iowa 50011, United States
| | - Mark S Gordon
- Department of Chemistry, Iowa State University and Ames National Laboratory, Ames, Iowa 50011, United States
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Zahariev F, Ash T, Karunaratne E, Stender E, Gordon MS, Windus TL, Pérez García M. Prediction of stability constants of metal-ligand complexes by machine learning for the design of ligands with optimal metal ion selectivity. J Chem Phys 2024; 160:042502. [PMID: 38284991 DOI: 10.1063/5.0176000] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2023] [Accepted: 12/06/2023] [Indexed: 01/30/2024] Open
Abstract
The new LOGKPREDICT program integrates HostDesigner molecular design software with the machine learning (ML) program Chemprop. By supplying HostDesigner with predicted log K values, LOGKPREDICT enhances the computer-aided molecular design process by ranking ligands directly by metal-ligand binding strength. Harnessing reliable experimental data from a historic National Institute of Standards and Technology (NIST) database and data from the International Union of Pure and Applied Chemistry (IUPAC), we train message passing neural net algorithms. The multi-metal NIST-based ML model has a root mean square error (RMSE) of 0.629 ± 0.044 (R2 of 0.960 ± 0.006), while two versions of lanthanide-only IUPAC-based ML models have, respectively, RMSE of 0.764 ± 0.073 (R2 of 0.976 ± 0.005) and 0.757 ± 0.071 (R2 of 0.959 ± 0.007). For relative log K predictions on an out-of-sample set of six ligands, demonstrating metal ion selectivity, the RMSE value reaches a commendably low 0.25. We showcase the use of LOGKPREDICT in identifying ligands with high selectivity for lanthanides in aqueous solutions, a finding supported by recent experimental evidence. We also predict new ligands yet to be verified experimentally. Therefore, our ML models implemented through LOGKPREDICT and interfaced with the ligand design software HostDesigner pave the way for designing new ligands with predetermined selectivity for competing metal ions in an aqueous solution.
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Affiliation(s)
- Federico Zahariev
- Ames National Laboratory, Ames, Iowa 50011, USA; Critical Materials Innovation Hub, Ames, Iowa 50011, USA; and Iowa State University, Ames, Iowa 50011, USA
| | - Tamalika Ash
- Ames National Laboratory, Ames, Iowa 50011, USA; Critical Materials Innovation Hub, Ames, Iowa 50011, USA; and Iowa State University, Ames, Iowa 50011, USA
| | - Erandika Karunaratne
- Ames National Laboratory, Ames, Iowa 50011, USA; Critical Materials Innovation Hub, Ames, Iowa 50011, USA; and Iowa State University, Ames, Iowa 50011, USA
| | - Erin Stender
- Ames National Laboratory, Ames, Iowa 50011, USA; Critical Materials Innovation Hub, Ames, Iowa 50011, USA; and Iowa State University, Ames, Iowa 50011, USA
| | - Mark S Gordon
- Ames National Laboratory, Ames, Iowa 50011, USA; Critical Materials Innovation Hub, Ames, Iowa 50011, USA; and Iowa State University, Ames, Iowa 50011, USA
| | - Theresa L Windus
- Ames National Laboratory, Ames, Iowa 50011, USA; Critical Materials Innovation Hub, Ames, Iowa 50011, USA; and Iowa State University, Ames, Iowa 50011, USA
| | - Marilú Pérez García
- Ames National Laboratory, Ames, Iowa 50011, USA; Critical Materials Innovation Hub, Ames, Iowa 50011, USA; and Iowa State University, Ames, Iowa 50011, USA
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Xu P, Leonard SL, O'Brien W, Gordon MS. R -8 Dispersion Interaction: Derivation and Application to the Effective Fragment Potential Method. J Phys Chem A 2024; 128:292-327. [PMID: 38150458 DOI: 10.1021/acs.jpca.3c05115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2023]
Abstract
The anisotropic and isotropic R-8 dispersion contributions (disp8) are derived and implemented within the framework of the effective fragment potential (EFP) method formulated with imaginary frequency-dependent Cartesian polarizability tensors distributed at the centroids of the localized molecular orbitals (LMOs). Two forms of damping functions, intermolecular overlap-based and Tang-Toennies, are extended for disp8. To obtain LMO polarizability tensors centered at LMO centroids, an origin-shifting transformation is derived and implemented for the dipole-octopole polarizability tensor and the quadrupole-quadrupole polarizability tensor. The analytic gradient is derived and implemented for the isotropic disp8 contribution. Relative to the previously implemented empirical EFP disp8 energy, the isotropic disp8 component of the interaction energy improves the overall agreement of the EFP dispersion energies with the symmetry-adapted perturbation theory (SAPT) benchmarks, reducing the mean absolute errors (MAEs) and mean absolute percentage errors for most of the databases examined in this work. While the anisotropic disp8 can further enhance the accuracy of the EFP dispersion energy and yield smaller MAEs, significantly overbound dispersion energies are predicted by the anisotropic disp8 when the maximum element in the intermolecular overlap matrix is greater than 0.1, possibly due to the breakdown of the approximations made in the EFP dispersion derivation at a short range. For potential energy scan databases, the newly developed EFP dispersion model with isotropic disp8 yields the overall correct curvature and good agreement with SAPT benchmarks around equilibrium and longer but overestimates the dispersion interactions at a short range. While the overlap-based dispersion-damping functions produce better MAEs than Tang-Toennies damping functions, further improvement is needed to better screen the large attractive dispersion energies at a short range (overlap >0.1).
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Affiliation(s)
- Peng Xu
- Department of Chemistry, Iowa State University and Ames National Laboratory, Ames, Iowa 50014, United States
| | - Samuel L Leonard
- Department of Chemistry, Iowa State University and Ames National Laboratory, Ames, Iowa 50014, United States
| | - William O'Brien
- Science Undergraduate Research Internship (SULI): Department of Energy, Ames National Laboratory, Iowa State University, Ames, Iowa50011-3020, United States
| | - Mark S Gordon
- Department of Chemistry, Iowa State University and Ames National Laboratory, Ames, Iowa 50014, United States
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Nakamura T, Dangi BB, Wu L, Zhang Y, Schoendorff G, Gordon MS, Yang DS. Spin-orbit coupling of electrons on separate lanthanide atoms of Pr2O2 and its singly charged cation. J Chem Phys 2023; 159:244303. [PMID: 38131482 DOI: 10.1063/5.0185579] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Accepted: 11/27/2023] [Indexed: 12/23/2023] Open
Abstract
Although it plays a critical role in the photophysics and catalysis of lanthanides, spin-orbit coupling of electrons on individual lanthanide atoms in small clusters is not well understood. The major objective of this work is to probe such coupling of the praseodymium (Pr) 4f and 6s electrons in Pr2O2 and Pr2O2+. The approach combines mass-analyzed threshold ionization spectroscopy and spin-orbit multiconfiguration second-order quasi-degenerate perturbation theory. The energies of six ionization transitions are precisely measured; the adiabatic ionization energy of the neutral cluster is 38 045 (5) cm-1. Most of the electronic states involved in these transitions are identified as spin-orbit coupled states consisting of two or more electron spins. The electron configurations of these states are 4f46s2 for the neutral cluster and 4f46s for the singly charged cation, both in planar rhombus-type structures. The spin-orbit splitting due to the coupling of the electrons on the separate Pr atoms is on the order of hundreds of wavenumbers.
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Affiliation(s)
- Taiji Nakamura
- Department of Chemistry and Ames Laboratory, Iowa State University, Ames, Iowa 50011-3111, USA
- Institute for Materials Chemistry and Engineering, Kyushu University, Nishi-ku, Fukuoka 819-0395, Japan
| | - Beni B Dangi
- Department of Chemistry, University of Kentucky, Lexington, Kentucky 40506-0055, USA
| | - Lu Wu
- Department of Chemistry, University of Kentucky, Lexington, Kentucky 40506-0055, USA
| | - Yuchen Zhang
- Department of Chemistry, University of Kentucky, Lexington, Kentucky 40506-0055, USA
| | - George Schoendorff
- Department of Chemistry and Ames Laboratory, Iowa State University, Ames, Iowa 50011-3111, USA
- Propellants Branch, Rocket Propulsion Division, Aerospace Systems Directorate, Air Force Research Laboratory, AFRL/RQRP, Edwards Air Force Base, California 93524, USA
| | - Mark S Gordon
- Department of Chemistry and Ames Laboratory, Iowa State University, Ames, Iowa 50011-3111, USA
| | - Dong-Sheng Yang
- Department of Chemistry, University of Kentucky, Lexington, Kentucky 40506-0055, USA
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Kim S, Conrad JA, Tow GM, Maginn EJ, Boatz JA, Gordon MS. Intermolecular interactions in clusters of ethylammonium nitrate and 1-amino-1,2,3-triazole. Phys Chem Chem Phys 2023; 25:30428-30457. [PMID: 37917371 DOI: 10.1039/d3cp02407e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2023]
Abstract
The intermolecular interaction energies, including hydrogen bonds (H-bonds), of clusters of the ionic liquid ethylammonium nitrate (EAN) and 1-amino-1,2,3-triazole (1-AT) based deep eutectic propellants (DeEP) are examined. 1-AT is introduced as a neutral hydrogen bond donor (HBD) to EAN in order to form a eutectic mixture. The effective fragment potential (EFP) is used to examine the bonding interactions in the DeEP clusters. The resolution of the Identity (RI) approximated second order Møller-Plesset perturbation theory (RI-MP2) and coupled cluster theory (RI-CCSD(T)) are used to validate the EFP results. The EFP method predicts that there are significant polarization and charge transfer effects in the EAN:1-AT complexes, along with Coulombic, dispersion and exchange repulsion interactions. The EFP interaction energies are in good agreement with the RI-MP2 and RI-CCSD(T) results. The quasi-atomic orbital (QUAO) bonding and kinetic bond order (KBO) analyses are additionally used to develop a conceptual and semi-quantitative understanding of the H-bonding interactions as a function of the size of the system. The QUAO and KBO analyses suggest that the H-bonds in the examined clusters follow the characteristic hydrogen bonding three-center four electron interactions. The strongest H-bonding interactions between the (EAN)1:(1-AT)n and (EAN)2:(1-AT)n (n = 1-5) complexes are observed internally within EAN; that is, between the ethylammonium cation [EA]+ and the nitrate anion ([NO3]-). The weakest H-bonding interactions occur between [NO3]- and 1-AT. Consequently, the average strengths of the H-bonds within a given (EAN)x:(1-AT)n complex decrease as more 1-AT molecules are introduced into the EAN monomer and EAN dimer. The QUAO bonding analysis suggests that 1-AT in (EAN)x:(1-AT)n can act as both a HBD and a hydrogen bond acceptor simultaneously. It is observed that two 1-AT molecules can form H-bonds to each other. Although the KBOs that correspond to H-bonding interactions in [EA]+:1-AT, [NO3]-:1-AT and between two 1-AT molecules are weaker than the H-bonds in EAN, those weak H-bond networks with 1-AT could be important to form a stable DeEP.
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Affiliation(s)
- Shinae Kim
- Department of Chemistry and Ames Laboratory, Iowa State University, Ames, IA 50011, USA.
- Combustion Research Facility, Sandia National Laboratories, Livermore, California 94550, USA
| | - Justin A Conrad
- Department of Chemistry and Ames Laboratory, Iowa State University, Ames, IA 50011, USA.
| | - Garrett M Tow
- Department of Chemical & Biomolecular Engineering, University of Notre Dame, Notre Dame, Indiana 46556, USA
| | - Edward J Maginn
- Department of Chemical & Biomolecular Engineering, University of Notre Dame, Notre Dame, Indiana 46556, USA
| | - Jerry A Boatz
- Aerospace Systems Directorate, Air Force Research Laboratory, Edwards Air Force Base, California 93524, USA
| | - Mark S Gordon
- Department of Chemistry and Ames Laboratory, Iowa State University, Ames, IA 50011, USA.
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Datta D, Gordon MS. Accelerating Coupled-Cluster Calculations with GPUs: An Implementation of the Density-Fitted CCSD(T) Approach for Heterogeneous Computing Architectures Using OpenMP Directives. J Chem Theory Comput 2023; 19:7640-7657. [PMID: 37878756 DOI: 10.1021/acs.jctc.3c00876] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2023]
Abstract
An algorithm is presented for the coupled-cluster singles, doubles, and perturbative triples correction [CCSD(T)] method based on the density fitting or the resolution-of-the-identity (RI) approximation for performing calculations on heterogeneous computing platforms composed of multicore CPUs and graphics processing units (GPUs). The directive-based approach to GPU offloading offered by the OpenMP application programming interface has been employed to adapt the most compute-intensive terms in the RI-CCSD amplitude equations with computational costs scaling as O ( N O 2 N V 4 ) , O ( N O 3 N V 3 ) , and O ( N O 4 N V 2 ) (where NO and NV denote the numbers of correlated occupied and virtual orbitals, respectively) and the perturbative triples correction to execute on GPU architectures. The pertinent tensor contractions are performed using an accelerated math library such as cuBLAS or hipBLAS. Optimal strategies are discussed for splitting large data arrays into tiles to fit them into the relatively small memory space of the GPUs, while also minimizing the low-bandwidth CPU-GPU data transfers. The performance of the hybrid CPU-GPU RI-CCSD(T) code is demonstrated on pre-exascale supercomputers composed of heterogeneous nodes equipped with NVIDIA Tesla V100 and A100 GPUs and on the world's first exascale supercomputer named "Frontier", the nodes of which consist of AMD MI250X GPUs. Speedups within the range 4-8× relative to the recently reported CPU-only algorithm are obtained for the GPU-offloaded terms in the RI-CCSD amplitude equations. Applications to polycyclic aromatic hydrocarbons containing 16-66 carbon atoms demonstrate that the acceleration of the hybrid CPU-GPU code for the perturbative triples correction relative to the CPU-only code increases with the molecule size, attaining a speedup of 5.7× for the largest circumovalene molecule (C66H20). The GPU-offloaded code enables the computation of the perturbative triples correction for the C60 molecule using the cc-pVDZ/aug-cc-pVTZ-RI basis sets in 7 min on Frontier when using 12,288 AMD GPUs with a parallel efficiency of 83.1%.
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Affiliation(s)
- Dipayan Datta
- Department of Chemistry and Ames Laboratory, Iowa State University, 2416 Pammel Drive, Ames, Iowa 50011-2416, United States
| | - Mark S Gordon
- Department of Chemistry and Ames Laboratory, Iowa State University, 2416 Pammel Drive, Ames, Iowa 50011-2416, United States
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Zahariev F, Xu P, Westheimer BM, Webb S, Galvez Vallejo J, Tiwari A, Sundriyal V, Sosonkina M, Shen J, Schoendorff G, Schlinsog M, Sattasathuchana T, Ruedenberg K, Roskop LB, Rendell AP, Poole D, Piecuch P, Pham BQ, Mironov V, Mato J, Leonard S, Leang SS, Ivanic J, Hayes J, Harville T, Gururangan K, Guidez E, Gerasimov IS, Friedl C, Ferreras KN, Elliott G, Datta D, Cruz DDA, Carrington L, Bertoni C, Barca GMJ, Alkan M, Gordon MS. The General Atomic and Molecular Electronic Structure System (GAMESS): Novel Methods on Novel Architectures. J Chem Theory Comput 2023; 19:7031-7055. [PMID: 37793073 DOI: 10.1021/acs.jctc.3c00379] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/06/2023]
Abstract
The primary focus of GAMESS over the last 5 years has been the development of new high-performance codes that are able to take effective and efficient advantage of the most advanced computer architectures, both CPU and accelerators. These efforts include employing density fitting and fragmentation methods to reduce the high scaling of well-correlated (e.g., coupled-cluster) methods as well as developing novel codes that can take optimal advantage of graphical processing units and other modern accelerators. Because accurate wave functions can be very complex, an important new functionality in GAMESS is the quasi-atomic orbital analysis, an unbiased approach to the understanding of covalent bonds embedded in the wave function. Best practices for the maintenance and distribution of GAMESS are also discussed.
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Affiliation(s)
- Federico Zahariev
- Department of Chemistry and Ames Laboratory, Iowa State University, Ames, Iowa 50014, United States
| | - Peng Xu
- Department of Chemistry and Ames Laboratory, Iowa State University, Ames, Iowa 50014, United States
| | - Bryce M Westheimer
- Department of Chemistry and Ames Laboratory, Iowa State University, Ames, Iowa 50014, United States
| | - Simon Webb
- VeraChem LLC, 12850 Middlebrook Road, Suite 205, Germantown, Maryland 20874-5244, United States
| | - Jorge Galvez Vallejo
- Department of Chemistry and Ames Laboratory, Iowa State University, Ames, Iowa 50014, United States
- Research School of Computer Science, Australian National University, Canberra, ACT 2601, Australia
| | - Ananta Tiwari
- EP Analytics, Inc., 9909 Mira Mesa Boulevard, Suite 230, San Diego, California 92131, United States
| | - Vaibhav Sundriyal
- Department of Computational Modeling and Simulation Engineering, Old Dominion University, Norfolk, Virginia 23529, United States
| | - Masha Sosonkina
- Department of Computational Modeling and Simulation Engineering, Old Dominion University, Norfolk, Virginia 23529, United States
| | - Jun Shen
- Department of Chemistry, Michigan State University, East Lansing, Michigan 48824, United States
| | - George Schoendorff
- Propellants Branch, Rocket Propulsion Division, Aerospace Systems Directorate, Air Force Research Laboratory, AFRL/RQRP, Edwards Air Force Base, California 93524, United States
| | - Megan Schlinsog
- Department of Chemistry and Ames Laboratory, Iowa State University, Ames, Iowa 50014, United States
| | - Tosaporn Sattasathuchana
- Department of Chemistry and Ames Laboratory, Iowa State University, Ames, Iowa 50014, United States
| | - Klaus Ruedenberg
- Department of Chemistry and Ames Laboratory, Iowa State University, Ames, Iowa 50014, United States
| | - Luke B Roskop
- Hewlett-Packard Enterprise, 2131 Lindau Lane #1000, Bloomington, Minnesota 55425, United States
| | | | - David Poole
- Department of Chemistry and Ames Laboratory, Iowa State University, Ames, Iowa 50014, United States
- School of Chemistry & Biochemistry, Georgia Institute of Technology, Athens, Georgia 30332, United States
| | - Piotr Piecuch
- Department of Chemistry and Department of Physics and Astronomy, Michigan State University, East Lansing, Michigan 48824, United States
| | - Buu Q Pham
- Department of Chemistry and Ames Laboratory, Iowa State University, Ames, Iowa 50014, United States
| | - Vladimir Mironov
- Department of Chemistry, Kyungpook National University, Daegu 41566, South Korea
| | - Joani Mato
- Physical Sciences Division, Pacific Northwest National Laboratory, 902 Battelle Boulevard, P.O. Box 999, MS K1-83, Richland, Washington 99352, United States
| | - Sam Leonard
- Department of Chemistry and Ames Laboratory, Iowa State University, Ames, Iowa 50014, United States
| | - Sarom S Leang
- EP Analytics, Inc., 9909 Mira Mesa Boulevard, Suite 230, San Diego, California 92131, United States
| | - Joe Ivanic
- Advanced Biomedical Computational Science, Frederick National Laboratory for Cancer Research, Frederick, Maryland 21702, United States
| | - Jackson Hayes
- Department of Chemistry and Ames Laboratory, Iowa State University, Ames, Iowa 50014, United States
| | - Taylor Harville
- Department of Chemistry and Ames Laboratory, Iowa State University, Ames, Iowa 50014, United States
| | - Karthik Gururangan
- Department of Chemistry, Michigan State University, East Lansing, Michigan 48824, United States
| | - Emilie Guidez
- Department of Chemistry, University of Colorado Denver, Denver, Colorado 80217, United States
| | - Igor S Gerasimov
- Department of Chemistry, Kyungpook National University, Daegu 41566, South Korea
| | - Christian Friedl
- Institut für Theoretische Physik, Johannes Kepler Universität Linz, Altenberger Str. 69, 4040 Linz, Austria
| | - Katherine N Ferreras
- Department of Chemistry and Ames Laboratory, Iowa State University, Ames, Iowa 50014, United States
| | - George Elliott
- Department of Chemistry and Ames Laboratory, Iowa State University, Ames, Iowa 50014, United States
| | - Dipayan Datta
- Department of Chemistry and Ames Laboratory, Iowa State University, Ames, Iowa 50014, United States
| | - Daniel Del Angel Cruz
- Department of Chemistry and Ames Laboratory, Iowa State University, Ames, Iowa 50014, United States
| | - Laura Carrington
- EP Analytics, Inc., 9909 Mira Mesa Boulevard, Suite 230, San Diego, California 92131, United States
| | - Colleen Bertoni
- Argonne Leadership Computing Facility, Argonne National Laboratory, Lemont, Illinois 60439, United States
| | - Giuseppe M J Barca
- Research School of Computer Science, Australian National University, Canberra, ACT 2601, Australia
| | - Melisa Alkan
- Department of Chemistry and Ames Laboratory, Iowa State University, Ames, Iowa 50014, United States
| | - Mark S Gordon
- Department of Chemistry and Ames Laboratory, Iowa State University, Ames, Iowa 50014, United States
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Del Angel Cruz D, Galvez Vallejo JL, Gordon MS. Analysis of the bonding in tetrahedrane and phosphorus-substituted tetrahedranes. Phys Chem Chem Phys 2023; 25:27276-27292. [PMID: 37791459 DOI: 10.1039/d3cp03619g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/05/2023]
Abstract
The bonding structures of tetrahedrane, phosphatetrahedrane, diphosphatetrahedrane and triphosphatetrahedrane are studied by employing an intrinsic quasi-atomic orbital analysis. Ethane, cyclopropane and tetrahedral P4 are employed as reference systems. The orbital analysis is paired with the computation of strain energies via isodesmic reactions. The results show that the increase in geometric strain upon transition from ethane to cyclopropane to tetrahedrane weakens the CC bonds, despite leading to shorter C-C interatomic distances. With the increase in strain, the orbitals centered on C and involved in the bonding of the cage structure are observed to have elevated p-character, and the orbital structure of C deviates from sp3 hybridization. The systematic substitution of CH groups by P atoms in the cage structure of tetrahedrane leads to stronger CC bonds, larger angles in the cage structures of the resulting phosphatetrahedranes, lower p-character in the orbitals involved in the bonding of the cages, and lower strain energies. It is found that P is more amenable to strained molecular arrangements than is C, and that the propensity of a given atom to hybridize s and p functions, or the lack thereof, has implications in the stability of molecules with strained geometries. The combination of the calculations presented here with the existing literature provides insight into the apparent propensity of tetrahedrane and P4 to 'break' their tetrahedral structures. Trends in the bonding interactions, such as bond strengths, s- and p-orbital characters and charge transfer are identified and related to the strain energy observed in each of the analyzed systems.
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Affiliation(s)
| | - Jorge L Galvez Vallejo
- Department of Chemistry, Iowa State University, Ames, Iowa 50011, USA.
- School of Computing, Australian National University, Canberra, ACT 2601, Australia
| | - Mark S Gordon
- Department of Chemistry, Iowa State University, Ames, Iowa 50011, USA.
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Galvez Vallejo JL, Snowdon C, Stocks R, Kazemian F, Yan Yu FC, Seidl C, Seeger Z, Alkan M, Poole D, Westheimer BM, Basha M, De La Pierre M, Rendell A, Izgorodina EI, Gordon MS, Barca GMJ. Toward an extreme-scale electronic structure system. J Chem Phys 2023; 159:044112. [PMID: 37497819 DOI: 10.1063/5.0156399] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2023] [Accepted: 07/03/2023] [Indexed: 07/28/2023] Open
Abstract
Electronic structure calculations have the potential to predict key matter transformations for applications of strategic technological importance, from drug discovery to material science and catalysis. However, a predictive physicochemical characterization of these processes often requires accurate quantum chemical modeling of complex molecular systems with hundreds to thousands of atoms. Due to the computationally demanding nature of electronic structure calculations and the complexity of modern high-performance computing hardware, quantum chemistry software has historically failed to operate at such large molecular scales with accuracy and speed that are useful in practice. In this paper, novel algorithms and software are presented that enable extreme-scale quantum chemistry capabilities with particular emphasis on exascale calculations. This includes the development and application of the multi-Graphics Processing Unit (GPU) library LibCChem 2.0 as part of the General Atomic and Molecular Electronic Structure System package and of the standalone Extreme-scale Electronic Structure System (EXESS), designed from the ground up for scaling on thousands of GPUs to perform high-performance accurate quantum chemistry calculations at unprecedented speed and molecular scales. Among various results, we report that the EXESS implementation enables Hartree-Fock/cc-pVDZ plus RI-MP2/cc-pVDZ/cc-pVDZ-RIFIT calculations on an ionic liquid system with 623 016 electrons and 146 592 atoms in less than 45 min using 27 600 GPUs on the Summit supercomputer with a 94.6% parallel efficiency.
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Affiliation(s)
| | - Calum Snowdon
- School of Computing, Australian National University, Canberra 2601, ACT, Australia
| | - Ryan Stocks
- School of Computing, Australian National University, Canberra 2601, ACT, Australia
| | - Fazeleh Kazemian
- School of Computing, Australian National University, Canberra 2601, ACT, Australia
| | - Fiona Chuo Yan Yu
- School of Computing, Australian National University, Canberra 2601, ACT, Australia
| | - Christopher Seidl
- School of Computing, Australian National University, Canberra 2601, ACT, Australia
| | - Zoe Seeger
- School of Chemistry, Monash University, Clayton 3800, VIC, Australia
| | - Melisa Alkan
- Department of Chemistry, Iowa State University, Ames, Iowa 50011-3111, USA
| | - David Poole
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
| | - Bryce M Westheimer
- Department of Chemistry, Iowa State University, Ames, Iowa 50011-3111, USA
| | - Mehaboob Basha
- Pawsey Supercomputing Research Centre, Kensington, WA 6151, Australia
| | | | - Alistair Rendell
- College of Science and Engineering, Flinders University, Adelaide, SA 5042, Australia
| | | | | | - Giuseppe M J Barca
- School of Computing, Australian National University, Canberra 2601, ACT, Australia
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10
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Alkan M, Pham BQ, Hammond JR, Gordon MS. Enabling Fortran Standard Parallelism in GAMESS for Accelerated Quantum Chemistry Calculations. J Chem Theory Comput 2023. [PMID: 37343236 DOI: 10.1021/acs.jctc.3c00380] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/23/2023]
Abstract
The performance of Fortran 2008 DO CONCURRENT (DC) relative to OpenACC and OpenMP target offloading (OTO) with different compilers is studied for the GAMESS quantum chemistry application. Specifically, DC and OTO are used to offload the Fock build, which is a computational bottleneck in most quantum chemistry codes, to GPUs. The DC Fock build performance is studied on NVIDIA A100 and V100 accelerators and compared with the OTO versions compiled by the NVIDIA HPC, IBM XL, and Cray Fortran compilers. The results show that DC can speed up the Fock build by 3.0× compared with that of the OTO model. With similar offloading efforts, DC is a compelling programming model for offloading Fortran applications to GPUs.
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Affiliation(s)
- Melisa Alkan
- Department of Chemistry and Ames Laboratory, Iowa State University, Ames, Iowa 50011, United States
| | - Buu Q Pham
- Department of Chemistry and Ames Laboratory, Iowa State University, Ames, Iowa 50011, United States
| | - Jeff R Hammond
- NVIDIA Corporation, Porkkalankatu 1, Helsinki 00180, Finland
| | - Mark S Gordon
- Department of Chemistry and Ames Laboratory, Iowa State University, Ames, Iowa 50011, United States
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11
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Komarov K, Mironov V, Lee S, Pham BQ, Gordon MS, Choi CH. High-performance strategies for the recent MRSF-TDDFT in GAMESS. J Chem Phys 2023; 158:2890476. [PMID: 37184015 DOI: 10.1063/5.0148005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Accepted: 05/02/2023] [Indexed: 05/16/2023] Open
Abstract
Multiple ERI (Electron Repulsion Integral) tensor contractions (METC) with several matrices are ubiquitous in quantum chemistry. In response theories, the contraction operation, rather than ERI computations, can be the major bottleneck, as its computational demands are proportional to the multiplicatively combined contributions of the number of excited states and the kernel pre-factors. This paper presents several high-performance strategies for METC. Optimal approaches involve either the data layout reformations of interim density and Fock matrices, the introduction of intermediate ERI quartet buffer, and loop-reordering optimization for a higher cache hit rate. The combined strategies remarkably improve the performance of the MRSF (mixed reference spin flip)-TDDFT (time-dependent density functional theory) by nearly 300%. The results of this study are not limited to the MRSF-TDDFT method and can be applied to other METC scenarios.
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Affiliation(s)
- Konstantin Komarov
- Center for Quantum Dynamics, Pohang University of Science and Technology, Pohang 37673, South Korea
| | - Vladimir Mironov
- Department of Chemistry, Kyungpook National University, Daegu 41566, South Korea
| | - Seunghoon Lee
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, USA
| | - Buu Q Pham
- Department of Chemistry and Ames Laboratory, Iowa State University, Ames, Iowa 50011, USA
| | - Mark S Gordon
- Department of Chemistry and Ames Laboratory, Iowa State University, Ames, Iowa 50011, USA
| | - Cheol Ho Choi
- Department of Chemistry, Kyungpook National University, Daegu 41566, South Korea
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12
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Pham BQ, Carrington L, Tiwari A, Leang SS, Alkan M, Bertoni C, Datta D, Sattasathuchana T, Xu P, Gordon MS. Porting fragmentation methods to GPUs using an OpenMP API: Offloading the resolution-of-the-identity second-order Møller-Plesset perturbation method. J Chem Phys 2023; 158:2887208. [PMID: 37114705 DOI: 10.1063/5.0143424] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Accepted: 04/10/2023] [Indexed: 04/29/2023] Open
Abstract
Using an OpenMP Application Programming Interface, the resolution-of-the-identity second-order Møller-Plesset perturbation (RI-MP2) method has been off-loaded onto graphical processing units (GPUs), both as a standalone method in the GAMESS electronic structure program and as an electron correlation energy component in the effective fragment molecular orbital (EFMO) framework. First, a new scheme has been proposed to maximize data digestion on GPUs that subsequently linearizes data transfer from central processing units (CPUs) to GPUs. Second, the GAMESS Fortran code has been interfaced with GPU numerical libraries (e.g., NVIDIA cuBLAS and cuSOLVER) for efficient matrix operations (e.g., matrix multiplication, matrix decomposition, and matrix inversion). The standalone GPU RI-MP2 code shows an increasing speedup of up to 7.5× using one NVIDIA V100 GPU with one IBM 42-core P9 CPU for calculations on fullerenes of increasing size from 40 to 260 carbon atoms using the 6-31G(d)/cc-pVDZ-RI basis sets. A single Summit node with six V100s can compute the RI-MP2 correlation energy of a cluster of 175 water molecules using the correlation consistent basis sets cc-pVDZ/cc-pVDZ-RI containing 4375 atomic orbitals and 14 700 auxiliary basis functions in ∼0.85 h. In the EFMO framework, the GPU RI-MP2 component shows near linear scaling for a large number of V100s when computing the energy of an 1800-atom mesoporous silica nanoparticle in a bath of 4000 water molecules. The parallel efficiencies of the GPU RI-MP2 component with 2304 and 4608 V100s are 98.0% and 96.1%, respectively.
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Affiliation(s)
- Buu Q Pham
- Department of Chemistry and Ames Laboratory, Iowa State University, Ames, Iowa 50011, USA
| | | | | | | | - Melisa Alkan
- Department of Chemistry and Ames Laboratory, Iowa State University, Ames, Iowa 50011, USA
| | - Colleen Bertoni
- Leadership Computing Facility, Argonne National Laboratory, Lemont, Illinois 60439, USA
| | - Dipayan Datta
- Department of Chemistry and Ames Laboratory, Iowa State University, Ames, Iowa 50011, USA
| | | | - Peng Xu
- Department of Chemistry and Ames Laboratory, Iowa State University, Ames, Iowa 50011, USA
| | - Mark S Gordon
- Department of Chemistry and Ames Laboratory, Iowa State University, Ames, Iowa 50011, USA
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13
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Dunning TH, Gordon MS, Xantheas SS. The nature of the chemical bond. J Chem Phys 2023; 158:130401. [PMID: 37031137 DOI: 10.1063/5.0148500] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/10/2023] Open
Affiliation(s)
- Thom H Dunning
- Department of Chemistry, University of Washington, Seattle, Washington 98195, USA
| | - Mark S Gordon
- Department of Chemistry and Ames Laboratory, Iowa State University, Ames, Iowa 50011, USA
| | - Sotiris S Xantheas
- Department of Chemistry, University of Washington, Seattle, Washington 98195, USA
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14
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Pham BQ, Alkan M, Gordon MS. Porting Fragmentation Methods to Graphical Processing Units Using an OpenMP Application Programming Interface: Offloading the Fock Build for Low Angular Momentum Functions. J Chem Theory Comput 2023; 19:2213-2221. [PMID: 37011288 DOI: 10.1021/acs.jctc.2c01137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/05/2023]
Abstract
A framework to offload four-index two-electron repulsion integrals to graphical processing units (GPUs) using OpenMP is discussed. The method has been applied to the Fock build for low angular momentum s and p functions in both the restricted Hartree-Fock (RHF) and in the effective fragment molecular orbital (EFMO) framework. Benchmark calculations for the GPU code for the pure RHF method show an increasing speedup relative to the existing OpenMP CPU code in GAMESS from 1.04 to 52× for clusters of 70-569 water molecules. The parallel efficiency on 24 NVIDIA V100 GPU boards also increases when increasing the system size: from 75 to 94% for water clusters that contain 303-1120 molecules. In the EFMO framework, the GPU Fock build shows a high linear scalability up to 4608 V100s with a parallel efficiency of 96% for calculations on a solvated mesoporous silica nanoparticle system with ∼67,000 basis functions.
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Affiliation(s)
- Buu Q Pham
- Department of Chemistry, Iowa State University, Ames, Iowa 50011, United States
| | - Melisa Alkan
- Department of Chemistry, Iowa State University, Ames, Iowa 50011, United States
| | - Mark S Gordon
- Department of Chemistry, Iowa State University, Ames, Iowa 50011, United States
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15
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Galvez Vallejo JL, Tow GM, Maginn EJ, Pham BQ, Datta D, Gordon MS. Quantum Chemical Modeling of Propellant Degradation. J Phys Chem A 2023; 127:1874-1882. [PMID: 36791340 DOI: 10.1021/acs.jpca.2c08722] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/17/2023]
Abstract
An ab initio quantum chemical approach for the modeling of propellant degradation is presented. Using state-of-the-art bonding analysis techniques and composite methods, a series of potential degradation reactions are devised for a sample hydroxyl-terminated-polybutadiene (HTPB) type solid fuel. By applying thermochemical procedures and isodesmic reactions, accurate thermochemical quantities are obtained using a modified G3 composite method based on the resolution of the identity. The calculated heats of formation for the different structures produced presents an ∼2 kcal/mol average error when compared against experimental values.
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Affiliation(s)
- Jorge L Galvez Vallejo
- Department of Chemistry and Ames Laboratory, Iowa State University, Ames, Iowa 50014, United States
| | - Garrett M Tow
- Department of Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Edward J Maginn
- Department of Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Buu Q Pham
- Department of Chemistry and Ames Laboratory, Iowa State University, Ames, Iowa 50014, United States
| | - Dipayan Datta
- Department of Chemistry and Ames Laboratory, Iowa State University, Ames, Iowa 50014, United States
| | - Mark S Gordon
- Department of Chemistry and Ames Laboratory, Iowa State University, Ames, Iowa 50014, United States
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16
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Westheimer BM, Gordon MS. General, Rigorous Approach for the Treatment of Interfragment Covalent Bonds. J Phys Chem A 2022; 126:6995-7006. [PMID: 36166638 DOI: 10.1021/acs.jpca.2c04015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A generalized, projection-based transformation of the method-agnostic Fock operator in various ab initio fragment-based quantum chemistry methods has been developed for the treatment of interfragment covalent bonds. This transformation freezes the relevant localized molecular orbital associated with each interfragment bond, thereby restricting the variational subspace of the fragment wave functions, in order to maintain the proper physical characteristics of the involved covalent bonds. In addition, sets of orbitals that would lead to multiple occupancy of certain orbitals are explicitly removed from the variational space. The transformation is developed for the specific case of mutually orthonormal frozen and unfrozen orbitals within each fragment. The newly developed approach is then used to study model systems with two popular ab initio fragment-based methods, and the results of these calculations are compared to those obtained by existing methodologies. Analysis is focused on both quantitative and qualitative accuracy as well as computational scalability and stability. Other methods for which the developed formalisms are appropriate are outlined, and future extensions of the methods are discussed.
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Affiliation(s)
- Bryce M Westheimer
- Iowa State University, Ames, Iowa 50011, United States.,Ames Laboratory, Ames, Iowa 50011, United States
| | - Mark S Gordon
- Iowa State University, Ames, Iowa 50011, United States.,Ames Laboratory, Ames, Iowa 50011, United States
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17
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Zhang Y, Nakamura T, Wu L, Wenjin Cao W, Schoendorff G, Gordon MS, Yang DS. Electronic states and transitions of PrO and PrO+ probed by threshold ionization spectroscopy and spin-orbit multiconfiguration perturbation theory. J Chem Phys 2022; 157:114304. [DOI: 10.1063/5.0113741] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The precise ionization energy of praseodymium oxide (PrO) seeded in supersonic molecular beams is measured with mass-analyzed threshold ionization (MATI) spectroscopy. A total of 33 spin-orbit (SO) states of PrO and 23 SO states of PrO+ are predicted by second-order multiconfigurational quasi-degenerate perturbation (MCQDPT2) theory. Electronic transitions from four low-energy SO levels of the neutral molecule to the ground state of the singly charged cation are identified by combining the MATI spectroscopic measurements with the MCQDPT2 calculations. The precise ionization energy is used to reassess the ionization energies and the reaction enthalpies of the Pr + O → PrO+ + e- chemi-ionization reaction reported in the literature. An empirical formula that uses atomic electronic parameters is proposed to predict the ionization energies of lanthanide monooxides, and the empirical calculations match well with available precise experimental measurements.
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Affiliation(s)
- Yuchen Zhang
- Chemistry, University of Kentucky, United States of America
| | - Taiji Nakamura
- Gunma University Faculty of Engineering Graduate School of Engineering Department of Chemistry and Bioengineering, Japan
| | - Lu Wu
- University of Kentucky, United States of America
| | | | - George Schoendorff
- Propellants Branch, Rocket Propulsion Division, Air Force Research Laboratory Aerospace Systems Directorate Edwards AFB, United States of America
| | - Mark S. Gordon
- Department of Chemistry, Iowa State University, United States of America
| | - Dong-Sheng Yang
- Department of Chemistry, University of Kentucky, United States of America
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18
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Galvez Vallejo JL, Barca GM, Gordon MS. High-performance GPU-accelerated evaluation of electron repulsion integrals. Mol Phys 2022. [DOI: 10.1080/00268976.2022.2112987] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/15/2022]
Affiliation(s)
| | - Giuseppe M.J. Barca
- Department of Computer Science, Australian National University, Canberra, Australia
| | - Mark S. Gordon
- Department of Chemistry, Iowa State University, Ames, United States
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19
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Markutsya S, Haley A, Gordon MS. Coarse-Grained Water Model Development for Accurate Dynamics and Structure Prediction. ACS Omega 2022; 7:25898-25904. [PMID: 35910114 PMCID: PMC9330847 DOI: 10.1021/acsomega.2c03857] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Accepted: 06/30/2022] [Indexed: 06/15/2023]
Abstract
Several coarse-graining (CG) methods have been combined to develop a CG model of water capable of the accurate prediction of structure and dynamics properties. The multiscale coarse-graining (MS-CG) method based on force matching and the PDF-based coarse-graining method were used for accurate dynamics prediction. The iterative Boltzmann inversion (IBI) method was added for accurate structure representation. The approach is applied to bulk water, and the results show close reproduction of the CG structure when compared with the reference atomistic data. The combination of MS-CG and IBI methods facilitates the development of CG force fields at different temperatures based on a single MS-CG coarse-graining procedure. The dynamic properties of the CG water model closely match those obtained from the reference atomistic system. The general application of this approach to any existing coarse-graining methods is discussed.
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Affiliation(s)
- Sergiy Markutsya
- Department
of Mechanical Engineering, University of
Kentucky, Paducah, Kentucky 42001, United States
| | - Austin Haley
- Department
of Mechanical Engineering, University of
Kentucky, Paducah, Kentucky 42001, United States
| | - Mark S. Gordon
- Department
of Chemistry and Ames Laboratory, Iowa State
University, Ames, Iowa 50011, United States
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20
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Kim YL, Evans JW, Gordon MS. Molecular interactions in diffusion-controlled aldol condensation with mesoporous silica nanoparticles. Phys Chem Chem Phys 2022; 24:10475-10487. [PMID: 35441640 DOI: 10.1039/d2cp00952h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The aldol reaction of p-nitrobenzaldehyde in amino-catalyzed mesoporous silica nanoparticles (MSN) has revealed varying catalytic activity with the size of the pores of MSN. The pore size dependence related to the reactivity indicates that the diffusion process is important. A detailed molecular-level analysis for understanding diffusion requires assessment of the noncovalent interactions of the molecular species involved in the aldol reaction with each other, with the solvent, and with key functional groups on the pore surface. Such an analysis is presented here based upon the effective fragment potential (EFP). The EFP method can calculate the intermolecular interactions, decomposed into Coulomb, polarization, dispersion, exchange-repulsion, and charge-transfer interactions. In this study, the potential energy surfaces corresponding to each intermolecular interaction are analyzed for homo- and hetero-dimers with various configurations. The monomers that compose dimers are five molecules such as p-nitrobenzaldehyde, acetone, n-hexane, propylamine, and silanol. The results illustrate that the dispersion interaction is crucial in most dimers.
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Affiliation(s)
- Yu Lim Kim
- Ames Laboratory - US Department of Energy, Iowa State University, Ames, Iowa 50011, USA.,Department of Chemistry, Iowa State University, Ames, Iowa 50010, USA
| | - James W Evans
- Ames Laboratory - US Department of Energy, Iowa State University, Ames, Iowa 50011, USA.,Department of Physics, Iowa State University, Ames, Iowa 50011, USA
| | - Mark S Gordon
- Ames Laboratory - US Department of Energy, Iowa State University, Ames, Iowa 50011, USA.,Department of Chemistry, Iowa State University, Ames, Iowa 50010, USA
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21
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Harville T, Gordon MS. Intramolecular Hydrogen Bonding Analysis. J Chem Phys 2022; 156:174302. [DOI: 10.1063/5.0090648] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The quasi-atomic orbital (QUAO) bonding analysis is used to study intramolecular hydrogen bonding (IMHB) in salicylic acid and an intermediate that is crucial to the synthesis of aspirin. The bonding analysis rigorously explores IMHB through directly accessing information that is intrinsic to the molecular wave function, thereby bypassing the need for intrinsically biased methods. The variables that effect the strength of IMHB are determined using kinetic bond orders (KBO), QUAO populations, and QUAO hybridizations. Important properties include both the interatomic distance between the hydrogen and oxygen participating in the IMHB and the hybridization on the oxygen. The bonding analysis further shows that each intramolecular hydrogen bond is a 4-electron 3-center bond. The bonding analysis is used to understand how aromatic reactivity changes due to the effect of functional groups on the aromatic ring.
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Affiliation(s)
| | - Mark S. Gordon
- Department of Chemistry, Iowa State University, United States of America
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22
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Poole D, Galvez Vallejo JL, Gordon MS. A Task-Based Approach to Parallel Restricted Hartree-Fock Calculations. J Chem Theory Comput 2022; 18:2144-2161. [PMID: 35377639 DOI: 10.1021/acs.jctc.1c00820] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In recent years, parallelism via multithreading has become extremely important to the optimization of high-performance electronic structure theory codes. Such multithreading is generally achieved via OpenMP constructs, using a fork-join threading model to enable thread-level data parallelism within the code. An alternative approach to multithreading is task-based parallelism, which displays multiple benefits relative to fork-join thread parallelism. A novel Restricted Hartree-Fock (RHF) algorithm, utilizing task-based parallelism to achieve optimal performance, was developed and implemented into the JuliaChem electronic structure theory software package. The new RHF algorithm utilizes a unique method of shell quartet batch creation, enabling construction and distribution of fine-grained shell quartet batches in a load-balanced manner using the Julia task construct. These shell quartet batches are then distributed statically across message-passing interface (MPI) ranks and dynamically across threads within an MPI rank, requiring no explicit inter-rank or interthread synchronization to do so. Compared to the hybrid MPI/OpenMP RHF algorithm present in the GAMESS software package, the task-based algorithm demonstrates speedups of up to ∼40% for systems in the S22(3) test set of molecules, with system sizes up to ∼1000 basis functions. The JuliaChem algorithm demonstrates the viability of both the task-based parallelism model and the Julia programming language for construction of performant electronic structure theory codes targeting systems of a size of chemical interest.
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Affiliation(s)
- David Poole
- Department of Chemistry and Ames Laboratory, Iowa State University, Ames, Iowa 50011, United States
| | - Jorge L Galvez Vallejo
- Department of Chemistry and Ames Laboratory, Iowa State University, Ames, Iowa 50011, United States
| | - Mark S Gordon
- Department of Chemistry and Ames Laboratory, Iowa State University, Ames, Iowa 50011, United States
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23
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Kim YL, Gordon MS, Garcia A, Evans JW. Rotational and translational diffusion of liquid n-hexane: EFP-based molecular dynamics analysis. J Chem Phys 2022; 156:114503. [DOI: 10.1063/5.0079212] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Molecular Dynamics (MD) simulations based on the Effective Fragment Potential (EFP) method are utilized to provide a comprehensive assessment of diffusion in liquid n-hexane. We decompose translational diffusion into components along and orthogonal to the long axis of the molecule. Rotational diffusion is decomposed into tumbling and spinning motions about this axis. Our analysis yields four corresponding diffusion coefficients which are related to diagonal entries in the complete 6 × 6 diffusion tensor accounting for the three rotational and three translational degrees of freedom and for the potential coupling between them. However, coupling between different degrees of freedom is expected to be minimal for a natural choice of the molecular body-fixed axis, so then off-diagonal entries in the tensor are negligible. This expectation is supported by a hydrodynamic analysis of the diffusion tensor which treats the liquid surrounding the molecule being tracked as a viscous continuum. Thus, the EFP MD analysis provides a comprehensive characterization of diffusion and also reveals expected shortcomings of the hydrodynamic treatment, particularly for rotational diffusion, when applied to neat liquids.
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Affiliation(s)
- Yu Lim Kim
- Ames Laboratory – U.S. Department of Energy, Iowa State University, Ames, Iowa 50011, USA
- Department of Chemistry, Iowa State University, Ames, Iowa 50010, USA
| | - Mark S. Gordon
- Ames Laboratory – U.S. Department of Energy, Iowa State University, Ames, Iowa 50011, USA
- Department of Chemistry, Iowa State University, Ames, Iowa 50010, USA
| | - Andres Garcia
- Ames Laboratory – U.S. Department of Energy, Iowa State University, Ames, Iowa 50011, USA
- Department of Physics and Astronomy, Iowa State University, Ames, Iowa 50010, USA
| | - James W. Evans
- Ames Laboratory – U.S. Department of Energy, Iowa State University, Ames, Iowa 50011, USA
- Department of Physics and Astronomy, Iowa State University, Ames, Iowa 50010, USA
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24
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Wu L, Schoendorff G, Zhang Y, Roudjane M, Gordon MS, Yang DS. Excited states of lutetium oxide and its singly charged cation. J Chem Phys 2022; 156:084303. [DOI: 10.1063/5.0084483] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Vibronic spectra of lutetium oxide (LuO) seeded in supersonic molecule beams are investigated with mass-analyzed threshold ionization (MATI) spectroscopy and second-order multiconfigurational quasi-degenerate perturbation (MCQDPT2) theory. Six states of LuO and four states of LuO+ are located by the MCQDPT2 calculations, and an a3Π(LuO+) ← C2Σ+ (LuΟ) transition is observed by the MATI measurement. The vibronic spectra show abnormal vibrational intervals for both the neural and cation excited states, and the abnormality is attributed to vibrational perturbations induced by interactions with neighboring states.
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Affiliation(s)
- Lu Wu
- Department of Chemistry, University of Kentucky, Lexington, Kentucky 40506-0055, USA
| | - George Schoendorff
- Department of Chemistry, Iowa State University, Ames, Iowa 50011-3111, USA
- Propellants Branch, Rocket Propulsion Division, Aerospace Systems Directorate, Air Force Research Laboratory, AFRL/RQRP, Edwards Air Force Base, California 93524, USA
| | - Yuchen Zhang
- Department of Chemistry, University of Kentucky, Lexington, Kentucky 40506-0055, USA
| | - Mourad Roudjane
- Department of Chemistry, University of Kentucky, Lexington, Kentucky 40506-0055, USA
| | - Mark S. Gordon
- Department of Chemistry, Iowa State University, Ames, Iowa 50011-3111, USA
| | - Dong-Sheng Yang
- Department of Chemistry, University of Kentucky, Lexington, Kentucky 40506-0055, USA
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25
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Smith DGA, Lolinco AT, Glick ZL, Lee J, Alenaizan A, Barnes TA, Borca CH, Di Remigio R, Dotson DL, Ehlert S, Heide AG, Herbst MF, Hermann J, Hicks CB, Horton JT, Hurtado AG, Kraus P, Kruse H, Lee SJR, Misiewicz JP, Naden LN, Ramezanghorbani F, Scheurer M, Schriber JB, Simmonett AC, Steinmetzer J, Wagner JR, Ward L, Welborn M, Altarawy D, Anwar J, Chodera JD, Dreuw A, Kulik HJ, Liu F, Martínez TJ, Matthews DA, Schaefer HF, Šponer J, Turney JM, Wang LP, De Silva N, King RA, Stanton JF, Gordon MS, Windus TL, Sherrill CD, Burns LA. Quantum Chemistry Common Driver and Databases (QCDB) and Quantum Chemistry Engine (QCEngine): Automation and interoperability among computational chemistry programs. J Chem Phys 2021; 155:204801. [PMID: 34852489 DOI: 10.1063/5.0059356] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Community efforts in the computational molecular sciences (CMS) are evolving toward modular, open, and interoperable interfaces that work with existing community codes to provide more functionality and composability than could be achieved with a single program. The Quantum Chemistry Common Driver and Databases (QCDB) project provides such capability through an application programming interface (API) that facilitates interoperability across multiple quantum chemistry software packages. In tandem with the Molecular Sciences Software Institute and their Quantum Chemistry Archive ecosystem, the unique functionalities of several CMS programs are integrated, including CFOUR, GAMESS, NWChem, OpenMM, Psi4, Qcore, TeraChem, and Turbomole, to provide common computational functions, i.e., energy, gradient, and Hessian computations as well as molecular properties such as atomic charges and vibrational frequency analysis. Both standard users and power users benefit from adopting these APIs as they lower the language barrier of input styles and enable a standard layout of variables and data. These designs allow end-to-end interoperable programming of complex computations and provide best practices options by default.
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Affiliation(s)
- Daniel G A Smith
- Molecular Sciences Software Institute, Blacksburg, Virginia 24060, USA
| | | | - Zachary L Glick
- Center for Computational Molecular Science and Technology, School of Chemistry and Biochemistry, and School of Computational Science and Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
| | - Jiyoung Lee
- Department of Chemistry, Iowa State University, Ames, Iowa 50011, USA
| | - Asem Alenaizan
- Center for Computational Molecular Science and Technology, School of Chemistry and Biochemistry, and School of Computational Science and Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
| | - Taylor A Barnes
- Molecular Sciences Software Institute, Blacksburg, Virginia 24060, USA
| | - Carlos H Borca
- Center for Computational Molecular Science and Technology, School of Chemistry and Biochemistry, and School of Computational Science and Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
| | - Roberto Di Remigio
- Department of Chemistry, Centre for Theoretical and Computational Chemistry, UiT, The Arctic University of Norway, N-9037 Tromsø, Norway
| | - David L Dotson
- Open Force Field Initiative, University of Colorado Boulder, Boulder, Colorado 80309, USA
| | - Sebastian Ehlert
- Mulliken Center for Theoretical Chemistry, Institut für Physikalische und Theoretische Chemie, Universität Bonn, Beringstraße 4, D-53115 Bonn, Germany
| | - Alexander G Heide
- Center for Computational Quantum Chemistry, University of Georgia, Athens, Georgia 30602, USA
| | - Michael F Herbst
- Applied and Computational Mathematics, RWTH Aachen University, Schinkelstr. 2, 52062 Aachen, Germany
| | - Jan Hermann
- FU Berlin, Department of Mathematics and Computer Science, 14195 Berlin, Germany
| | - Colton B Hicks
- Department of Chemistry, Stanford University, Stanford, California 94305, USA
| | - Joshua T Horton
- Department of Chemistry, Lancaster University, Lancaster LA1 4YW, United Kingdom
| | - Adrian G Hurtado
- Institute for Advanced Computational Science, Stony Brook University, Stony Brook, New York 11794-5250, USA
| | - Peter Kraus
- School of Molecular and Life Sciences, Curtin University, GPO Box U1987, Perth 6845, WA, Australia
| | - Holger Kruse
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65 Brno, Czech Republic
| | | | - Jonathon P Misiewicz
- Center for Computational Quantum Chemistry, University of Georgia, Athens, Georgia 30602, USA
| | - Levi N Naden
- Molecular Sciences Software Institute, Blacksburg, Virginia 24060, USA
| | | | - Maximilian Scheurer
- Interdisciplinary Center for Scientific Computing, Heidelberg University, Im Neuenheimer Feld 205, 69120 Heidelberg, Germany
| | - Jeffrey B Schriber
- Center for Computational Molecular Science and Technology, School of Chemistry and Biochemistry, and School of Computational Science and Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
| | - Andrew C Simmonett
- Laboratory of Computational Biology, National Institutes of Health-National Heart, Lung and Blood Institute, Bethesda, Maryland 20892, USA
| | - Johannes Steinmetzer
- Institute of Physical Chemistry, Friedrich Schiller University Jena, Jena, Germany
| | - Jeffrey R Wagner
- Open Force Field Initiative, University of Colorado Boulder, Boulder, Colorado 80309, USA
| | - Logan Ward
- Data Science and Learning Division, Argonne National Laboratory, Lemont, Illinois 60439, USA
| | - Matthew Welborn
- Molecular Sciences Software Institute, Blacksburg, Virginia 24060, USA
| | - Doaa Altarawy
- Molecular Sciences Software Institute, Blacksburg, Virginia 24060, USA
| | - Jamshed Anwar
- Department of Chemistry, Lancaster University, Lancaster LA1 4YW, United Kingdom
| | - John D Chodera
- Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | - Andreas Dreuw
- Interdisciplinary Center for Scientific Computing, Heidelberg University, Im Neuenheimer Feld 205, 69120 Heidelberg, Germany
| | - Heather J Kulik
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Fang Liu
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Todd J Martínez
- Department of Chemistry, Stanford University, Stanford, California 94305, USA
| | - Devin A Matthews
- The Institute for Computational Engineering and Sciences, The University of Texas at Austin, Austin, Texas 78712, USA
| | - Henry F Schaefer
- Center for Computational Quantum Chemistry, University of Georgia, Athens, Georgia 30602, USA
| | - Jiří Šponer
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65 Brno, Czech Republic
| | - Justin M Turney
- Center for Computational Quantum Chemistry, University of Georgia, Athens, Georgia 30602, USA
| | - Lee-Ping Wang
- Department of Chemistry, University of California Davis, Davis, California 95616, USA
| | - Nuwan De Silva
- Department of Chemistry, Iowa State University, Ames, Iowa 50011, USA
| | - Rollin A King
- Department of Chemistry, Bethel University, St. Paul, Minnesota 55112, USA
| | - John F Stanton
- Quantum Theory Project, The University of Florida, 2328 New Physics Building, Gainesville, Florida 32611-8435, USA
| | - Mark S Gordon
- Department of Chemistry and Ames Laboratory, Iowa State University, Ames, Iowa 50011, USA
| | - Theresa L Windus
- Department of Chemistry and Ames Laboratory, Iowa State University, Ames, Iowa 50011, USA
| | - C David Sherrill
- Center for Computational Molecular Science and Technology, School of Chemistry and Biochemistry, and School of Computational Science and Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
| | - Lori A Burns
- Center for Computational Molecular Science and Technology, School of Chemistry and Biochemistry, and School of Computational Science and Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
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Barca GMJ, Alkan M, Galvez-Vallejo JL, Poole DL, Rendell AP, Gordon MS. Faster Self-Consistent Field (SCF) Calculations on GPU Clusters. J Chem Theory Comput 2021; 17:7486-7503. [PMID: 34780186 DOI: 10.1021/acs.jctc.1c00720] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A novel implementation of the self-consistent field (SCF) procedure specifically designed for high-performance execution on multiple graphics processing units (GPUs) is presented. The algorithm offloads to GPUs the three major computational stages of the SCF, namely, the calculation of one-electron integrals, the calculation and digestion of electron repulsion integrals, and the diagonalization of the Fock matrix, including SCF acceleration via DIIS. Performance results for a variety of test molecules and basis sets show remarkable speedups with respect to the state-of-the-art parallel GAMESS CPU code and relative to other widely used GPU codes for both single and multi-GPU execution. The new code outperforms all existing multi-GPU implementations when using eight V100 GPUs, with speedups relative to Terachem ranging from 1.2× to 3.3× and speedups of up to 28× over QUICK on one GPU and 15× using eight GPUs. Strong scaling calculations show nearly ideal scalability up to 8 GPUs while retaining high parallel efficiency for up to 18 GPUs.
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Affiliation(s)
- Giuseppe M J Barca
- School of Computing, Australian National University, Canberra, ACT 2601, Australia
| | - Melisa Alkan
- Department of Chemistry and Ames Laboratory, Iowa State University, Ames, Iowa 50011, United States
| | - Jorge L Galvez-Vallejo
- Department of Chemistry and Ames Laboratory, Iowa State University, Ames, Iowa 50011, United States
| | - David L Poole
- Department of Chemistry and Ames Laboratory, Iowa State University, Ames, Iowa 50011, United States
| | - Alistair P Rendell
- College of Science and Engineering, Flinders University, Adelaide, SA 5042, Australia
| | - Mark S Gordon
- Department of Chemistry and Ames Laboratory, Iowa State University, Ames, Iowa 50011, United States
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Harville T, Gordon MS. Electronic Structure Theory Calculations Using Modern Architectures: KNL vs Haswell. J Chem Theory Comput 2021; 17:6910-6917. [PMID: 34699218 DOI: 10.1021/acs.jctc.1c00705] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The time to solution and parallel efficiency of several commonly used electronic structure methods (Hartree-Fock, density functional theory, second order perturbation theory, resolution of the identity second order perturbation theory, coupled cluster) are evaluated on both the Intel Xeon Haswell and the Intel Xeon Phi Knights Landing (KNL) architectures. The Haswell completes the benchmark calculations with a faster time to solution than the KNL for all molecules and methods tested. While the Haswell exhibits an average speedup of at least 3.5 relative to the KNL for all nonthreaded computations, the KNL has a better parallel efficiency than the Haswell with increasing core counts. The architectures are further tested using a more computationally costly coupled cluster method on a transition state reaction. The Haswell appears to be the best choice to minimize the time to solution, though for very large systems and high levels of theory that require memory intensive processes the superior memory hierarchy and larger on node memory of the KNL can make it a better choice. These results are used to showcase aspects of novel architectures that will increase efficiency for quantum chemistry applications.
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Affiliation(s)
- Taylor Harville
- Department of Chemistry and Ames Laboratory, Iowa State University, Ames, Iowa 50011, United States
| | - Mark S Gordon
- Department of Chemistry and Ames Laboratory, Iowa State University, Ames, Iowa 50011, United States
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Pham BQ, Datta D, Gordon MS. PDG: A Composite Method Based on the Resolution of the Identity. J Phys Chem A 2021; 125:9421-9429. [PMID: 34658243 DOI: 10.1021/acs.jpca.1c06186] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The Gaussian-3 (G3) composite approach for thermochemical properties is revisited in light of the enhanced computational efficiency and reduced memory costs by applying the resolution-of-the-identity (RI) approximation for two-electron repulsion integrals (ERIs) to the computationally demanding component methods in the G3 model: the energy and gradient computations via the second-order Møller-Plesset perturbation theory (MP2) and the energy computations using the coupled-cluster singles-doubles method augmented with noniterative triples corrections [CCSD(T)]. Efficient implementation of the RI-based methods is achieved by employing a hybrid distributed/shared memory model based on MPI and OpenMP. The new variant of the G3 composite approach based on the RI approximation is termed the RI-G3 scheme, or alternatively the PDG method. The accuracy of the new RI-G3/PDG scheme is compared to the "standard" G3 composite approach that employs the memory-expensive four-center ERIs in the MP2 and CCSD(T) calculations. Taking the computation of the heats of formation of the closed-shell molecules in the G3/99 test set as a test case, it is demonstrated that the RI approximation introduces negligible changes to the mean absolute errors relative to the standard G3 model (less than 0.1 kcal/mol), while the standard deviations remain unaltered. The efficiency and memory requirements for the RI-MP2 and RI-CCSD(T) methods are compared to the standard MP2 and CCSD(T) approaches, respectively. The hybrid MPI/OpenMP-based RI-MP2 energy plus gradient computation is found to attain a 7.5× speedup over the standard MP2 calculations. For the most demanding CCSD(T) calculations, the application of the RI approximation is found to nearly halve the memory demand, confer about a 4-5× speedup for the CCSD iterations, and reduce the computational time for the compute-intensive triples correction step by several hours.
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29
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Westheimer BM, Gordon MS. Scalable ab initio fragmentation methods based on a truncated expansion of the non-orthogonal molecular orbital model. J Chem Phys 2021; 155:154101. [PMID: 34686043 DOI: 10.1063/5.0064864] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
An alternative formulation of the non-orthogonal molecular orbital model of electronic structure theory is developed based on the expansion of the inverse molecular orbital overlap matrix. From this model, a hierarchy of ab initio fragment-based quantum chemistry methods, referred to as the nth-order expanded non-orthogonal molecular orbital methods, are developed using a minimal number of approximations, each of which is frequently employed in intermolecular interaction theory. These novel methods are compared to existing fragment-based quantum chemistry methods, and the implications of those significant differences, where they exist, between the methods developed herein and those already existing methods are examined in detail. Computational complexities and theoretical scaling are also analyzed and discussed. Future extensions for the hierarchy of methods, to account for additional intrafragment and interfragment interactions, are outlined.
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Affiliation(s)
| | - Mark S Gordon
- Department of Chemistry, Iowa State University, Ames, Iowa 50011, USA
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Abstract
The quasi-atomic orbital (QUAO) bonding analysis introduced by Ruedenberg and co-workers is used to develop an understanding of the hydrogen bonds in small water clusters, from the dimer through the hexamer (bag, boat, book, cyclic, prism and cage conformers). Using kinetic bond orders as a metric, it is demonstrated that as the number of waters in simple cyclic clusters increases, the hydrogen bonds strengthen, from the dimer through the cyclic hexamer. However, for the more complex hexamer isomers, the strength of the hydrogen bonds varies, depending on whether the cluster contains double acceptors and/or double donors. The QUAO analysis also reveals the three-center bonding nature of hydrogen bonds in water clusters.
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31
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Brenner V, Véry T, Schmidt MW, Gordon MS, Hoyau S, Ben Amor N. Model protein excited states: MRCI calculations with large active spaces vs CC2 method. J Chem Phys 2021; 154:214105. [PMID: 34240962 DOI: 10.1063/5.0048146] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Benchmarking calculations on excited states of models of phenylalanine protein chains are presented to assess the ability of alternative methods to the standard and most commonly used multiconfigurational wave function-based method, the complete active space self-consistent field (CASSCF), in recovering the non-dynamical correlation for systems that become not affordable by the CASSCF. The exploration of larger active spaces beyond the CASSCF limit is benchmarked through three strategies based on the reduction in the number of determinants: the restricted active space self-consistent field, the generalized active space self-consistent field (GASSCF), and the occupation-restricted multiple active space (ORMAS) schemes. The remaining dynamic correlation effects are then added by the complete active space second-order perturbation theory and by the multireference difference dedicated configuration interaction methods. In parallel, the approximate second-order coupled cluster (CC2), already proven to be successful for small building blocks of model proteins in one of our previous works [Ben Amor et al., J. Chem. Phys. 148, 184105 (2018)], is investigated to assess its performances for larger systems. Among the different alternative strategies to CASSCF, our results highlight the greatest efficiency of the GASSCF and ORMAS schemes in the systematic reduction of the configuration interaction expansion without loss of accuracy in both nature and excitation energies of both singlet ππ* and nπ* CO excited states with respect to the equivalent CASSCF calculations. Guidelines for an optimum applicability of this scheme to systems requiring active spaces beyond the complete active space limit are then proposed. Finally, the extension of the CC2 method to such large systems without loss of accuracy is demonstrated, highlighting the great potential of this method to treat accurately excited states, mainly single reference, of very large systems.
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Affiliation(s)
- Valérie Brenner
- LIDYL, CEA, CNRS, Université Paris-Saclay, 91191 Gif-sur-Yvette, France
| | - Thibaut Véry
- LIDYL, CEA, CNRS, Université Paris-Saclay, 91191 Gif-sur-Yvette, France
| | - Michael W Schmidt
- Department of Chemistry, Iowa State University, Ames, Iowa 5001, USA
| | - Mark S Gordon
- Department of Chemistry, Iowa State University, Ames, Iowa 5001, USA
| | - Sophie Hoyau
- Université de Toulouse, UPS, LCPQ (Laboratoire de Chimie et Physique Quantiques), IRSAMC, 118, rte de Narbonne, F-31062 Toulouse Cedex, France
| | - Nadia Ben Amor
- Université de Toulouse, UPS, LCPQ (Laboratoire de Chimie et Physique Quantiques), IRSAMC, 118, rte de Narbonne, F-31062 Toulouse Cedex, France
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32
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Datta D, Gordon MS. A Massively Parallel Implementation of the CCSD(T) Method Using the Resolution-of-the-Identity Approximation and a Hybrid Distributed/Shared Memory Parallelization Model. J Chem Theory Comput 2021; 17:4799-4822. [PMID: 34279094 DOI: 10.1021/acs.jctc.1c00389] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A parallel algorithm is described for the coupled-cluster singles and doubles method augmented with a perturbative correction for triple excitations [CCSD(T)] using the resolution-of-the-identity (RI) approximation for two-electron repulsion integrals (ERIs). The algorithm bypasses the storage of four-center ERIs by adopting an integral-direct strategy. The CCSD amplitude equations are given in a compact quasi-linear form by factorizing them in terms of amplitude-dressed three-center intermediates. A hybrid MPI/OpenMP parallelization scheme is employed, which uses the OpenMP-based shared memory model for intranode parallelization and the MPI-based distributed memory model for internode parallelization. Parallel efficiency has been optimized for all terms in the CCSD amplitude equations. Two different algorithms have been implemented for the rate-limiting terms in the CCSD amplitude equations that entail O(NO2NV4) and O(NO3NV3)-scaling computational costs, where NO and NV denote the number of correlated occupied and virtual orbitals, respectively. One of the algorithms assembles the four-center ERIs requiring NV4 and NO2NV2-scaling memory costs in a distributed manner on a number of MPI ranks, while the other algorithm completely bypasses the assembling of quartic memory-scaling ERIs and thus largely reduces the memory demand. It is demonstrated that the former memory-expensive algorithm is faster on a few hundred cores, while the latter memory-economic algorithm shows a better strong scaling in the limit of a few thousand cores. The program is shown to exhibit a near-linear scaling, in particular for the compute-intensive triples correction step, on up to 8000 cores. The performance of the program is demonstrated via calculations involving molecules with 24-51 atoms and up to 1624 atomic basis functions. As the first application, the complete basis set (CBS) limit for the interaction energy of the π-stacked uracil dimer from the S66 data set has been investigated. This work reports the first calculation of the interaction energy at the CCSD(T)/aug-cc-pVQZ level without local orbital approximation. The CBS limit for the CCSD correlation contribution to the interaction energy was found to be -8.01 kcal/mol, which agrees very well with the value -7.99 kcal/mol reported by Schmitz, Hättig, and Tew [ Phys. Chem. Chem. Phys. 2014, 16, 22167-22178]. The CBS limit for the total interaction energy was estimated to be -9.64 kcal/mol.
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Affiliation(s)
- Dipayan Datta
- Department of Chemistry and Ames Laboratory, Iowa State University, 2416 Pammel Drive, Ames 50011-2416, Iowa United States of America
| | - Mark S Gordon
- Department of Chemistry and Ames Laboratory, Iowa State University, 2416 Pammel Drive, Ames 50011-2416, Iowa United States of America
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Zahariev F, Gordon MS. Combined quantum Monte Carlo - effective fragment molecular orbital method: fragmentation across covalent bonds. Phys Chem Chem Phys 2021; 23:14308-14314. [PMID: 34164632 DOI: 10.1039/d0cp06528e] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The previously developed combined Quantum Monte Carlo-Effective Fragment Molecular Orbital (QMC-EFMO) method is extended to systems in which the fragmentation process cuts across covalent molecular bonds. The extended QMC-EFMO capability is demonstrated on a few model systems: the glycine tetramer, the diglycine reaction to form a dipeptide, silica-based rings, and polyalanine chains of increasing length. The agreement between full QMC and QMC-EFMO for the correlation energy is within 2 kcal mol-1 and for the correlation energy differences is within 1 kcal mol-1.
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Affiliation(s)
- F Zahariev
- Department of Chemistry and Ames Laboratory Iowa State University, Ames, IA 50011, USA.
| | - M S Gordon
- Department of Chemistry and Ames Laboratory Iowa State University, Ames, IA 50011, USA.
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Schoendorff G, Ruedenberg K, Gordon MS. Multiple Bonding in Rhodium Monoboride. Quasi-atomic Analyses of the Ground and Low-Lying Excited States. J Phys Chem A 2021; 125:4836-4846. [PMID: 34042447 DOI: 10.1021/acs.jpca.1c02860] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The bonding structures of the ground state and the lowest five excited states of rhodium monoboride are identified by determining the quasi-atomic orbitals in full valence space MCSCF wave functions and the interactions between these orbitals. A quadruple bond, namely two π-bonds and two σ-bonds, is identified and characterized for the X1Σ+ ground state, in agreement with a previous report (Cheung J. Phys. Chem. Lett. 2020, 11, 659-663). However, in all excited states, the bonding is predicted to be weaker because, in these states, one of the σ-bonding interactions has a small magnitude. In the a3Δ and A1Δ states, the bond order is between a triple and quadruple bond. In the b3Σ+ state, the Rh-B linkage is a triple bond. In the c3Π and B1Π states, the atoms are linked by a double bond due to an additional weakening of the two π-bonds. The decreases in the predicted bond strengths are reflected in the decreases of the predicted binding energies and in the increases of the predicted bond lengths from the X1Σ+ ground state to the c3Π and the B1Π excited states. Notably, the 5pσ orbital of rhodium, which is vacant in the ground state of the atom, plays a significant role in the molecule.
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Affiliation(s)
- George Schoendorff
- Department of Chemistry, Virginia Military Institute, Lexington, Virginia 24450, United States.,Department of Chemistry and Ames Laboratory, Iowa State University, Ames, Iowa 50011-3111, United States
| | - Klaus Ruedenberg
- Department of Chemistry and Ames Laboratory, Iowa State University, Ames, Iowa 50011-3111, United States
| | - Mark S Gordon
- Department of Chemistry and Ames Laboratory, Iowa State University, Ames, Iowa 50011-3111, United States
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Gerasimov IS, Zahariev F, Leang SS, Tesliuk A, Gordon MS, Medvedev MG. Introducing LibXC into GAMESS (US). Mendeleev Communications 2021. [DOI: 10.1016/j.mencom.2021.04.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Kim YL, Han Y, Evans JW, Gordon MS. Effective Fragment Potential-Based Molecular Dynamics Studies of Diffusion in Acetone and Hexane. J Phys Chem A 2021; 125:3398-3405. [PMID: 33861600 DOI: 10.1021/acs.jpca.1c01865] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
To facilitate more reliable descriptions of transport properties in liquids, molecular dynamics (MD) simulations are performed based on the effective fragment potential (EFP) method derived from first-principles quantum mechanics (in contrast to MD based upon empirically fitted potentials). The EFP method describes molecular interactions in terms of Coulomb, polarization/induction, dispersion, exchange-repulsion, and charge-transfer interactions. The EFP MD simulations described in this paper, performed on hexane and acetone, are able to track the mean-square displacement of molecules for sufficient time to reliably extract translational diffusion coefficients. The results reported here are in reasonable agreement with experiment.
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Affiliation(s)
- Yu Lim Kim
- Ames Laboratory, US Department of Energy, Iowa State University, Ames, Iowa 50011, United States.,Department of Chemistry, Iowa State University, Ames, Iowa 50010, United States
| | - Yong Han
- Ames Laboratory, US Department of Energy, Iowa State University, Ames, Iowa 50011, United States.,Department of Physics & Astronomy, Iowa State University, Ames, Iowa 50010, United States
| | - James W Evans
- Ames Laboratory, US Department of Energy, Iowa State University, Ames, Iowa 50011, United States.,Department of Physics & Astronomy, Iowa State University, Ames, Iowa 50010, United States
| | - Mark S Gordon
- Ames Laboratory, US Department of Energy, Iowa State University, Ames, Iowa 50011, United States.,Department of Chemistry, Iowa State University, Ames, Iowa 50010, United States
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Xu P, Sattasathuchana T, Guidez E, Webb SP, Montgomery K, Yasini H, Pedreira IFM, Gordon MS. Computation of host-guest binding free energies with a new quantum mechanics based mining minima algorithm. J Chem Phys 2021; 154:104122. [PMID: 33722015 DOI: 10.1063/5.0040759] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
A new method called QM-VM2 is presented that efficiently combines statistical mechanics with quantum mechanical (QM) energy potentials in order to calculate noncovalent binding free energies of host-guest systems. QM-VM2 efficiently couples the use of semi-empirical QM (SEQM) energies and geometry optimizations with an underlying molecular mechanics (MM) based conformational search, to find low SEQM energy minima, and allows for processing of these minima at higher levels of ab initio QM theory. A progressive geometry optimization scheme is introduced as a means to increase conformational sampling efficiency. The newly implemented QM-VM2 is used to compute the binding free energies of the host molecule cucurbit[7]uril and a set of 15 guest molecules. The results are presented along with comparisons to experimentally determined binding affinities. For the full set of 15 host-guest complexes, which have a range of formal charges from +1 to +3, SEQM-VM2 based binding free energies show poor correlation with experiment, whereas for the ten +1 complexes only, a significant correlation (R2 = 0.8) is achieved. SEQM-VM2 generation of conformers followed by single-point ab initio QM calculations at the dispersion corrected restricted Hartree-Fock-D3(BJ) and TPSS-D3(BJ) levels of theory, as post-processing corrections, yields a reasonable correlation with experiment for the full set of host-guest complexes (R2 = 0.6 and R2 = 0.7, respectively) and an excellent correlation for the +1 formal charge set (R2 = 1.0 and R2 = 0.9, respectively), as long as a sufficiently large basis set (triple-zeta quality) is employed. The importance of the inclusion of configurational entropy, even at the MM level, for the achievement of good correlation with experiment was demonstrated by comparing the calculated ΔE values with experiment and finding a considerably poorer correlation with experiment than for the calculated free energy ΔE - TΔS. For the complete set of host-guest systems with the range of formal charges, it was observed that the deviation of the predicted binding free energy from experiment correlates somewhat with the net charge of the systems. This observation leads to a simple empirical interpolation scheme to improve the linear regression of the full set.
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Affiliation(s)
- Peng Xu
- Department of Chemistry, Iowa State University, Ames, Iowa 50014, USA
| | | | - Emilie Guidez
- Department of Chemistry, University of Colorado Denver, Denver, Colorado 80204, USA
| | - Simon P Webb
- VeraChem LLC, 12850 Middlebrook Rd. Ste 205, Germantown, Maryland 20874-5244, USA
| | | | - Hussna Yasini
- Department of Chemistry, University of Colorado Denver, Denver, Colorado 80204, USA
| | - Iara F M Pedreira
- Department of Chemistry, University of Colorado Denver, Denver, Colorado 80204, USA
| | - Mark S Gordon
- Department of Chemistry, Iowa State University, Ames, Iowa 50014, USA
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Abstract
A broad range of approaches to many-body dispersion are discussed, including empirical approaches with multiple fitted parameters, augmented density functional-based approaches, symmetry adapted perturbation theory, and a supermolecule approach based on coupled cluster theory. Differing definitions of "body" are considered, specifically atom-based vs molecule-based approaches.
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Affiliation(s)
- Peng Xu
- Department of Chemistry, Iowa State University, Ames, Iowa 50014, United States
| | - Melisa Alkan
- Department of Chemistry, Iowa State University, Ames, Iowa 50014, United States
| | - Mark S Gordon
- Department of Chemistry, Iowa State University, Ames, Iowa 50014, United States
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Barca GMJ, Galvez-Vallejo JL, Poole DL, Rendell AP, Gordon MS. High-Performance, Graphics Processing Unit-Accelerated Fock Build Algorithm. J Chem Theory Comput 2020; 16:7232-7238. [DOI: 10.1021/acs.jctc.0c00768] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Giuseppe M. J. Barca
- Research School of Computer Science, Australian National University, Canberra, Australian Capital Territory 2601, Australia
| | - Jorge L. Galvez-Vallejo
- Department of Chemistry and Ames Laboratory, Iowa State University, Ames, Iowa 50011, United States
| | - David L. Poole
- Department of Chemistry and Ames Laboratory, Iowa State University, Ames, Iowa 50011, United States
| | - Alistair P. Rendell
- College of Science and Engineering, Flinders University, Adelaide, South Australia 5042, Australia
| | - Mark S. Gordon
- Department of Chemistry and Ames Laboratory, Iowa State University, Ames, Iowa 50011, United States
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Abstract
This work examines the electronic structure and apparent instability of ethylenedione (OCCO), including an analysis of the singlet and triplet potential energy surfaces along the bending vibrations. While the singlet state is inherently unstable due to the Renner-Teller effect, theory predicts the triplet state to have a stable minimum on the potential energy surface. The stability of the triplet state is examined in detail, taking into account spin-orbit interactions. Using multireference quantum chemical methods, the lifetime of the triplet state is estimated to be in the picosecond range, significantly lower than previously computed. A quasi-atomic molecular orbital (QUAO) analysis is also used to elucidate the nature of bonding along the potential energy surface in both the singlet and triplet states. These calculations confirm the transient nature of the OCCO molecule, although they do not fully explain the lack of experimental detection via spectroscopy, which is known have the capability to probe even shorter lifetimes.
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Affiliation(s)
- Joani Mato
- Department of Chemistry and Ames Laboratory, Iowa State University, Ames, Iowa 50011, United States
| | - David Poole
- Department of Chemistry and Ames Laboratory, Iowa State University, Ames, Iowa 50011, United States
| | - Mark S Gordon
- Department of Chemistry and Ames Laboratory, Iowa State University, Ames, Iowa 50011, United States
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Affiliation(s)
- Mark S. Gordon
- Department of Chemistry and Ames Laboratory, Iowa State University, Ames, Iowa 50011, United States
| | - Theresa L. Windus
- Department of Chemistry and Ames Laboratory, Iowa State University, Ames, Iowa 50011, United States
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42
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Abstract
The molecular energy of Si2H2 geometric structures increases in the order dibridged < trans-bent < linear, in contrast to acetylene, C2H2, for which the linear structure is the global minimum. In this study, the intra-atomic (antibonding) and bonding contributions to the total molecular energy of these valence isoelectronic molecules are computed by expressing the density matrices of the full valence space multiconfiguration self-consistent field wave function in terms of quasi-atomic orbitals. The analysis shows that the intra-atomic contributions to the molecular energy become less favorable in the order dibridged → trans-bent → linear for both C2H2 and Si2H2. By contrast, the inter-atomic bonding contributions become energetically more favorable in that order for both C2H2 and Si2H2. The two systems differ as follows. For Si2H2, the antibonding intra-atomic energy changes that occur when the dibridged molecule reconstructs into the trans-bent and linear structures prevail over the interatomic interactions that induce bond formation. In contrast, for C2H2, the interatomic interactions that create bonds prevail over the intra-atomic energy changes that occur when the dibridged molecule reconstructs into the trans-bent and linear structures. The intra-atomic energy changes that occur in these systems are related to the hybridization of the heavy atoms in an analogous manner to the hybridization of C in CH4 from (2s)2(2p)2 to sp3 hybrid orbitals.
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Affiliation(s)
- Emilie B Guidez
- Department of Chemistry, University of Colorado Denver, Denver, Colorado 80204, United States
| | - Mark S Gordon
- Department of Chemistry and Ames Laboratory USDOE, Iowa State University, Ames, Iowa 50011, United States
| | - Klaus Ruedenberg
- Department of Chemistry and Ames Laboratory USDOE, Iowa State University, Ames, Iowa 50011, United States
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Truhlar DG, Hiberty PC, Shaik S, Gordon MS, Danovich D. Berichtigung: Orbitals and the Interpretation of Photoelectron Spectroscopy and (e,2e) Ionization Experiments. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202007475] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Truhlar DG, Hiberty PC, Shaik S, Gordon MS, Danovich D. Corrigendum: Orbitals and the Interpretation of Photoelectron Spectroscopy and (e,2e) Ionization Experiments. Angew Chem Int Ed Engl 2020; 59:12574. [DOI: 10.1002/anie.202007475] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Affiliation(s)
- David Poole
- Department of Chemistry and Ames Laboratory, Iowa State University, Ames, Iowa 50011, United States
| | - Jorge L. Galvez Vallejo
- Department of Chemistry and Ames Laboratory, Iowa State University, Ames, Iowa 50011, United States
| | - Mark S. Gordon
- Department of Chemistry and Ames Laboratory, Iowa State University, Ames, Iowa 50011, United States
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Gordon MS, Barca G, Leang SS, Poole D, Rendell AP, Galvez Vallejo JL, Westheimer B. Novel Computer Architectures and Quantum Chemistry. J Phys Chem A 2020; 124:4557-4582. [DOI: 10.1021/acs.jpca.0c02249] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Mark S. Gordon
- Department of Chemistry and Ames Laboratory, Iowa State University, Ames, Iowa 50011, United States
| | - Giuseppe Barca
- Research School of Computer Science, Australian National University, Canberra, ACT 2601, Australia
| | - Sarom S. Leang
- EP Analytics, 12121 Scripps Summit Drive, Suite 130, San Diego, California 92131, United States
| | - David Poole
- Department of Chemistry and Ames Laboratory, Iowa State University, Ames, Iowa 50011, United States
| | - Alistair P. Rendell
- College of Science and Engineering, Flinders University, Adelaide, SA 5042, Australia
| | - Jorge L. Galvez Vallejo
- Department of Chemistry and Ames Laboratory, Iowa State University, Ames, Iowa 50011, United States
| | - Bryce Westheimer
- Department of Chemistry and Ames Laboratory, Iowa State University, Ames, Iowa 50011, United States
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Barca GMJ, Bertoni C, Carrington L, Datta D, De Silva N, Deustua JE, Fedorov DG, Gour JR, Gunina AO, Guidez E, Harville T, Irle S, Ivanic J, Kowalski K, Leang SS, Li H, Li W, Lutz JJ, Magoulas I, Mato J, Mironov V, Nakata H, Pham BQ, Piecuch P, Poole D, Pruitt SR, Rendell AP, Roskop LB, Ruedenberg K, Sattasathuchana T, Schmidt MW, Shen J, Slipchenko L, Sosonkina M, Sundriyal V, Tiwari A, Galvez Vallejo JL, Westheimer B, Włoch M, Xu P, Zahariev F, Gordon MS. Recent developments in the general atomic and molecular electronic structure system. J Chem Phys 2020; 152:154102. [PMID: 32321259 DOI: 10.1063/5.0005188] [Citation(s) in RCA: 482] [Impact Index Per Article: 120.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
A discussion of many of the recently implemented features of GAMESS (General Atomic and Molecular Electronic Structure System) and LibCChem (the C++ CPU/GPU library associated with GAMESS) is presented. These features include fragmentation methods such as the fragment molecular orbital, effective fragment potential and effective fragment molecular orbital methods, hybrid MPI/OpenMP approaches to Hartree-Fock, and resolution of the identity second order perturbation theory. Many new coupled cluster theory methods have been implemented in GAMESS, as have multiple levels of density functional/tight binding theory. The role of accelerators, especially graphical processing units, is discussed in the context of the new features of LibCChem, as it is the associated problem of power consumption as the power of computers increases dramatically. The process by which a complex program suite such as GAMESS is maintained and developed is considered. Future developments are briefly summarized.
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Affiliation(s)
- Giuseppe M J Barca
- Research School of Computer Science, Australian National University, Canberra, ACT 2601, Australia
| | - Colleen Bertoni
- Argonne Leadership Computing Facility, Argonne National Laboratory, Lemont, Illinois 60439, USA
| | - Laura Carrington
- EP Analytics, 12121 Scripps Summit Dr. Ste. 130, San Diego, California 92131, USA
| | - Dipayan Datta
- Department of Chemistry and Ames Laboratory, Iowa State University, Ames, Iowa 50011, USA
| | - Nuwan De Silva
- Department of Physical and Biological Sciences, Western New England University, Springfield, Massachusetts 01119, USA
| | - J Emiliano Deustua
- Department of Chemistry, Michigan State University, East Lansing, Michigan 48824, USA
| | - Dmitri G Fedorov
- Research Center for Computational Design of Advanced Functional Materials (CD-FMat), National Institute of Advanced Industrial Science and Technology (AIST), Umezono 1-1-1, Tsukuba 305-8568, Japan
| | - Jeffrey R Gour
- Microsoft, 15590 NE 31st St., Redmond, Washington 98052, USA
| | - Anastasia O Gunina
- Department of Chemistry and Ames Laboratory, Iowa State University, Ames, Iowa 50011, USA
| | - Emilie Guidez
- Department of Chemistry, University of Colorado Denver, Denver, Colorado 80217, USA
| | - Taylor Harville
- Department of Chemistry and Ames Laboratory, Iowa State University, Ames, Iowa 50011, USA
| | - Stephan Irle
- Computational Science and Engineering Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37830, USA
| | - Joe Ivanic
- Advanced Biomedical Computational Science, Frederick National Laboratory for Cancer Research, Frederick, Maryland 21702, USA
| | - Karol Kowalski
- Physical Sciences Division, Battelle, Pacific Northwest National Laboratory, K8-91, P.O. Box 999, Richland, Washington 99352, USA
| | - Sarom S Leang
- EP Analytics, 12121 Scripps Summit Dr. Ste. 130, San Diego, California 92131, USA
| | - Hui Li
- Department of Chemistry, University of Nebraska, Lincoln, Nebraska 68588, USA
| | - Wei Li
- School of Chemistry and Chemical Engineering, Key Laboratory of Mesoscopic Chemistry of Ministry of Education, Institute of Theoretical and Computational Chemistry, Nanjing University, Nanjing 210023, People's Republic of China
| | - Jesse J Lutz
- Center for Computing Research, Sandia National Laboratories, Albuquerque, New Mexico 87185, USA
| | - Ilias Magoulas
- Department of Chemistry, Michigan State University, East Lansing, Michigan 48824, USA
| | - Joani Mato
- Department of Chemistry and Ames Laboratory, Iowa State University, Ames, Iowa 50011, USA
| | - Vladimir Mironov
- Department of Chemistry, Lomonosov Moscow State University, Leninskie Gory 1/3, Moscow 119991, Russian Federation
| | - Hiroya Nakata
- Kyocera Corporation, Research Institute for Advanced Materials and Devices, 3-5-3 Hikaridai Seika-cho, Souraku-gun, Kyoto 619-0237, Japan
| | - Buu Q Pham
- Department of Chemistry and Ames Laboratory, Iowa State University, Ames, Iowa 50011, USA
| | - Piotr Piecuch
- Department of Chemistry, Michigan State University, East Lansing, Michigan 48824, USA
| | - David Poole
- Department of Chemistry and Ames Laboratory, Iowa State University, Ames, Iowa 50011, USA
| | - Spencer R Pruitt
- Department of Chemistry and Ames Laboratory, Iowa State University, Ames, Iowa 50011, USA
| | - Alistair P Rendell
- Research School of Computer Science, Australian National University, Canberra, ACT 2601, Australia
| | - Luke B Roskop
- Cray Inc., a Hewlett Packard Enterprise Company, 2131 Lindau Ln #1000, Bloomington, Minnesota 55425, USA
| | - Klaus Ruedenberg
- Department of Chemistry and Ames Laboratory, Iowa State University, Ames, Iowa 50011, USA
| | | | - Michael W Schmidt
- Department of Chemistry and Ames Laboratory, Iowa State University, Ames, Iowa 50011, USA
| | - Jun Shen
- Department of Chemistry, Michigan State University, East Lansing, Michigan 48824, USA
| | - Lyudmila Slipchenko
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, USA
| | - Masha Sosonkina
- Department of Computational Modeling and Simulation Engineering, Old Dominion University, Norfolk, Virginia 23529, USA
| | - Vaibhav Sundriyal
- Department of Computational Modeling and Simulation Engineering, Old Dominion University, Norfolk, Virginia 23529, USA
| | - Ananta Tiwari
- EP Analytics, 12121 Scripps Summit Dr. Ste. 130, San Diego, California 92131, USA
| | - Jorge L Galvez Vallejo
- Department of Chemistry and Ames Laboratory, Iowa State University, Ames, Iowa 50011, USA
| | - Bryce Westheimer
- Department of Chemistry and Ames Laboratory, Iowa State University, Ames, Iowa 50011, USA
| | - Marta Włoch
- 530 Charlesina Dr., Rochester, Michigan 48306, USA
| | - Peng Xu
- Department of Chemistry and Ames Laboratory, Iowa State University, Ames, Iowa 50011, USA
| | - Federico Zahariev
- Department of Chemistry and Ames Laboratory, Iowa State University, Ames, Iowa 50011, USA
| | - Mark S Gordon
- Department of Chemistry and Ames Laboratory, Iowa State University, Ames, Iowa 50011, USA
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48
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Pham BQ, Gordon MS. Development of the FMO/RI-MP2 Fully Analytic Gradient Using a Hybrid-Distributed/Shared Memory Programming Model. J Chem Theory Comput 2020; 16:1039-1054. [PMID: 31899632 DOI: 10.1021/acs.jctc.9b01082] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The fully analytic gradient of the second-order Møller-Plesset perturbation theory (MP2) with the resolution-of-the-identity (RI) approximation in the fragment molecular orbital (FMO) framework is derived and implemented using a hybrid multilevel parallel programming model, a combination of the general distributed data interface (GDDI) and the OpenMP API. The FMO/MP2 analytic gradient contains three parts, i.e., the internal fragment component, the electrostatic potential (ESP) component, and the response terms. The RI approximation is applied to the internal fragment MP2 gradient term, whose MP2 densities and monomer MP2 Lagrangians are shared with the ESP and the response terms. The FMO/RI-MP2 analytic gradient implementation is validated against the numerical gradient (with errors ∼10-6-10-5 Hartree/Bohr) and the energy conservation in molecular dynamics (MD) simulations using NVE ensembles. The RI approximation introduces an error of ∼10-5 Hartree/Bohr with a speedup of 4.0-8.0× compared with the currently available GDDI FMO/MP2 gradient. The node linear scaling of the fragmentation framework due to multilevel parallelism is well-preserved and is demonstrated in single-point gradient calculations of large water clusters (e.g., 1120 and 2165 molecules) using 300-800 KNL compute nodes with a parallel efficiency of more than 90%.
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Affiliation(s)
- Buu Q Pham
- Department of Chemistry and Ames Laboratory , Iowa State University , Ames , Iowa 50011 , United States
| | - Mark S Gordon
- Department of Chemistry and Ames Laboratory , Iowa State University , Ames , Iowa 50011 , United States
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49
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Abstract
Analytic non-adiabatic coupling matrix elements (NACME) are derived and implemented for the spin-flip occupation restricted multiple active space configuration interaction (SF-ORMAS-CI) method.
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Affiliation(s)
- Joani Mato
- Department of Chemistry and Ames Laboratory
- Iowa State University
- Ames
- USA
| | - Mark S. Gordon
- Department of Chemistry and Ames Laboratory
- Iowa State University
- Ames
- USA
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50
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Abstract
Many-body dispersion has gained considerable attention over the past decade, particularly for condensed phase systems. However, quantitatively accurate studies of many-body dispersion have only recently become feasible due to challenges in reliability and accuracy. Currently available methodologies for calculating many-body dispersion have been challenged, with recent evidence suggesting, for example, that dispersion-corrected density functional theory (DFT) schemes cannot consistently predict many-body dispersion accurately. This study evaluates many-body dispersion energies using a composite approach that employs singles and doubles coupled cluster theory with perturbative/noniterative triples, CCSD(T), combined with an extrapolation to the complete basis set (CBS) limit. The combined CCSD(T)/CBS approach is applied to Arn and (H2O)n, n = 3-10, clusters, and a new data set called S22(3), which includes trimers generated based on the S22 data set. In these systems, the many-body dispersion provides a very small contribution to the total interaction energy of all of the systems studied, generally 3% or less of the total interaction energy. Two-body dispersion is the dominant dispersion contribution and many-body dispersion contributes no more than 5.7% of the total dispersion energy, generally staying below 2%.
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Affiliation(s)
- Melisa Alkan
- Department of Chemistry , Iowa State University , Ames , Iowa 50011 , United States.,Ames Laboratory , Ames , Iowa 50011 , United States
| | - Peng Xu
- Department of Chemistry , Iowa State University , Ames , Iowa 50011 , United States.,Ames Laboratory , Ames , Iowa 50011 , United States
| | - Mark S Gordon
- Department of Chemistry , Iowa State University , Ames , Iowa 50011 , United States.,Ames Laboratory , Ames , Iowa 50011 , United States
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