Can Systematic Molecular Fragmentation Be Applied to Direct Ab Initio Molecular Dynamics?

Rana

et al. 2019

J. Phys. Chem. Lett.

The many-body expansion (MBE) and its extension to overlapping fragments, the generalized (G)MBE, constitute the theoretical basis for most fragmentbased approaches for large-scale quantum chemistry. We reformulate the GMBE for use with embedding charges determined self-consistently from the fragment wave functions, in a manner that preserves the variational nature of the underlying selfconsistent field method. As a result, the analytic gradient retains the simple "sum of fragment gradients" form that is often assumed in practice, sometimes incorrectly. This obviates (without approximation) the need to solve coupled-perturbed equations, and we demonstrate stable, fragment-based ab initio molecular dynamics simulations using this technique. Energy conservation fails when charge-response contributions to the Fock matrix are neglected, even while geometry optimizations and vibrational frequency calculations may yet be accurate. Stable simulations can be recovered by means of straightforward modifications introduced here, providing a general paradigm for fragment-based ab initio molecular dynamics.

Section: The Journal Of Physical Chemistry Letterssupporting

confidence: 76%

Variational Formulation of the Generalized Many-Body Expansion with Self-Consistent Charge Embedding: Simple and Correct Analytic Energy Gradient for Fragment-Basedab InitioMolecular Dynamics

Rana

et al. 2019

J. Phys. Chem. Lett.

Int J of Quantum Chemistry

“…The square‐bracketed term in Equation ) contains an over‐counting correction, [ 42,43 ] where

p_{α_{r}}^{r, m}

refers to the number of times the α r th rank‐ r term appears in all rank‐ m terms ( m ≥ r ), with phase (−1) m . This over‐counting correction is along similar lines as those present in molecular fragmentation [ 11–13,26,33,61–67 ] as well as many‐body and double many‐body expansions. [ 28,30–35 ] Together,

E_{MBE, normalℛ}^{level, 1}

and

E_{MBE, normalℛ}^{level, 0}

in Equation ) provide an ONIOM‐like perturbation to E level, 0 and, in ONIOM‐style, the electronic energy for the α r th rank‐ r many‐body‐term is computed at two levels of theory, referred to as “level,1” and “level,0” above.…”

Section: Embedded Local Many‐body Interactions For Ab Initio Moleculamentioning

confidence: 99%

Embedded, graph‐theoretically defined many‐body approximations for wavefunction‐in‐DFT and DFT‐in‐DFT: Applications to gas‐ and condensed‐phase ab initio molecular dynamics, and potential surfaces for quantum nuclear effects

Ricard

Kumar

Iyengar

2020

We present a graph-theoretic approach to adaptively compute many-body approximations in an efficient manner to perform (a) accurate post-Hartree-Fock (HF) ab initio molecular dynamics (AIMD) at density functional theory (DFT) cost for medium-to large-sized molecular clusters, (b) hybrid DFT electronic structure calculations for condensed-phase simulations at the cost of pure density functionals, (c) reduced-cost on-the-fly basis extrapolation for gas-phase AIMD and condensed phase studies, and (d) accurate post-HF-level potential energy surfaces at DFT cost for quantum nuclear effects. The salient features of our approach are ONIOM-like in that (a) the full system (cluster or condensed phase) calculation is performed at a lower level of theory (pure DFT for condensed phase or hybrid DFT for molecular systems), and (b) this approximation is improved through a correction term that captures all many-body interactions up to any given order within a higher level of theory (hybrid DFT for condensed phase; CCSD or MP2 for cluster), combined through graph-theoretic methods. Specifically, a region of chemical interest is coarse-grained into a set of nodes and these nodes are then connected to form edges based on a given definition of local envelope (or threshold) of interactions. The nodes and edges together define a graph, which forms the basis for developing the many-body expansion. The methods are demonstrated through (a) ab initio dynamics studies on protonated water clusters and polypeptide fragments, (b) potential energy surface calculations on one-dimensional water chains such as those found in ion channels, and (c) conformational stabilization and lattice energy studies on homogeneous and heterogeneous surfaces of water with organic adsorbates using two-dimensional periodic boundary conditions.

“…[41] The total energy and Mulliken charges were converged to 10 26 au. The number of water molecules N water was varied from 100 to 1,098,500, and the box size was adjusted to fulfill the density of 1.0 g cm 21 . The orientation of water molecules was random.…”

Section: Computational Detailsmentioning

confidence: 99%

“…The latter two approaches practically reduce the computational complexity to a nearly linear complexity. Thus, interest in such low‐scaling QM‐MD simulations has become intense …”

Section: Introductionmentioning

confidence: 99%

“…Thus, interest in such low-scaling QM-MD simulations has become intense. [14][15][16][17][18][19][20][21][22][23][24][25][26] With respect to the above considerations, we recently reported a massively parallel implementation of a divide-andconquer density-functional tight-binding (DC-DFTB) method. [27] The DFTB method [28][29][30][31] can be recognized as the simplified version of the Kohn-Sham DFT.…”

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Parallel implementation of efficient charge–charge interaction evaluation scheme in periodic divide‐and‐conquer density‐functional tight‐binding calculations

Nishimura

Nakai

2017

J Comput Chem

A low-computational-cost algorithm and its parallel implementation for periodic divide-and-conquer density-functional tight-binding (DC-DFTB) calculations are presented. The developed algorithm enables rapid computation of the interaction between atomic partial charges, which is the bottleneck for applications to large systems, by means of multipole- and interpolation-based approaches for long- and short-range contributions. The numerical errors of energy and forces with respect to the conventional Ewald-based technique can be under the control of the multipole expansion order, level of unit cell replication, and interpolation grid size. The parallel performance of four different evaluation schemes combining previous approaches and the proposed one are assessed using test calculations of a cubic water box on the K computer. The largest benchmark system consisted of 3,295,500 atoms. DC-DFTB energy and forces for this system were obtained in only a few minutes when the proposed algorithm was activated and parallelized over 16,000 nodes in the K computer. The high performance using a single node workstation was also confirmed. In addition to liquid water systems, the feasibility of the present method was examined by testing solid systems such as diamond form of carbon, face-centered cubic form of copper, and rock salt form of sodium chloride. © 2017 Wiley Periodicals, Inc.