Energy-Based Molecular Fragmentation Methods

Collins, Michael A.; Bettens, Ryan P. A.

doi:10.1021/cr500455b

Cited by 285 publications

(314 citation statements)

References 213 publications

Supporting

Mentioning

313

Contrasting

Unclassified

Order By: Relevance

“…In Section III, we present the results. Specifically, Subsection III(B) includes a discussion on the potential energy surfaces obtained for H 9 50 in this paper, the overlapping unit is termed "derivative fragment", while the original fragments are called "primitive fragments". The word "fragment" here refers to either type.…”

Section: Introductionmentioning

confidence: 99%

Ab Initio Molecular Dynamics Using Recursive, Spatially Separated, Overlapping Model Subsystems Mixed within an ONIOM-Based Fragmentation Energy Extrapolation Technique

Iyengar

2015

J. Chem. Theory Comput.

177

View full text Add to dashboard Cite

Here, we demonstrate the application of fragment-based electronic structure calculations in (a) ab initio molecular dynamics (AIMD) and (b) reduced dimensional potential calculations, for medium- and large-sized protonated water clusters. The specific fragmentation algorithm used here is derived from ONIOM, but includes multiple, overlapping “model” systems. The interaction between the various overlapping model systems is (a) approximated by invoking the principle of inclusion-exclusion at the chosen higher level of theory and (b) within a real calculation performed at the chosen lower level of theory. The fragmentation algorithm itself is written using bit-manipulation arithmetic, which will prove to be advantageous, since the number of fragments in such methods has the propensity to grow exponentially with system size. Benchmark calculations are performed for three different protonated water clusters: H₉O₄⁺, H₁₃O₆⁺ and H(H₂O)₂₁⁺. For potential energy surface benchmarks, we sample the normal coordinates and compare our surface energies with full MP2 and CCSD(T) calculations. The mean absolute error for the fragment-based algorithm is <0.05 kcal/mol, when compared with MP2 calculations, and <0.07 kcal/mol, when compared with CCSD(T) calculations over 693 different geometries for the H₉O₄⁺ system. For the larger H(H₂O)₂₁⁺ water cluster, the mean absolute error is on the order of a 0.1 kcal/mol, when compared with full MP2 calculations for 84 different geometries, at a fraction of the computational cost. Ab initio dynamics calculations were performed for H₉O₄⁺ and H₁₃O₆⁺, and the energy conservation was found to be of the order of 0.01 kcal/mol for short trajectories (on the order of a picosecond). The trajectories were kept short because our algorithm does not currently include dynamical fragmentation, which will be considered in future publications. Nevertheless, the velocity autocorrelation functions and their Fourier transforms computed from the fragment-based AIMD approaches were found to be in excellent agreement with those computed using the respective higher level of theory from the chosen hybrid calculation.

show abstract

Section: Introductionmentioning

confidence: 99%

Ab Initio Molecular Dynamics Using Recursive, Spatially Separated, Overlapping Model Subsystems Mixed within an ONIOM-Based Fragmentation Energy Extrapolation Technique

Iyengar

2015

J. Chem. Theory Comput.

177

View full text Add to dashboard Cite

show abstract

“…30). This is reflected in a large number of different incremental fragmentation approaches 6,[31][32][33][34][35] .…”

Section: Introductionmentioning

confidence: 99%

Linear-scaling generation of potential energy surfaces using a double incremental expansion

König

Christiansen

2016

The Journal of Chemical Physics

View full text Add to dashboard Cite

We present a combination of the incremental expansion of potential energy surfaces (PESs), known as n-mode expansion, with the incremental evaluation of the electronic energy in a many-body approach. The application of semi-local coordinates in this context allows the generation of PESs in a very cost-efficient way. For this, we employ the recently introduced flexible adaptation of local coordinates of nuclei (FALCON) coordinates. By introducing an additional transformation step, concerning only a fraction of the vibrational degrees of freedom, we can achieve linear scaling of the accumulated cost of the single point calculations required in the PES generation. Numerical examples of these double incremental approaches for oligo-phenyl examplesshow fast convergence with respect to the maximum number of simultaneously treated fragments and only a modest error introduced by the additional transformation step.The approach, presented here, represents a major step towards the applicability of vibrational wave function methods to sizable, covalently bound systems. a) Electronic mail: carolink@kth.se; Present address: KTH Royal

show abstract

“…One of the challenges in QM‐MD simulations is the limited system size on account of high computational demands for solving the electronic structure problem with formal scaling of a cubic or higher with respect to system size. Several approaches have been developed to describe large systems under a full QM treatment, such as semi‐empirical methods, parallel computing of real‐space density functional theory (DFT), direct optimization of density matrix or expansion coefficients with an iterative procedure, and fragmentation‐based methods . The latter two approaches practically reduce the computational complexity to a nearly linear complexity.…”

Section: Introductionmentioning

confidence: 99%

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

View full text Add to dashboard Cite

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.

show abstract

Energy-Based Molecular Fragmentation Methods

Cited by 285 publications

References 213 publications

Ab Initio Molecular Dynamics Using Recursive, Spatially Separated, Overlapping Model Subsystems Mixed within an ONIOM-Based Fragmentation Energy Extrapolation Technique

Ab Initio Molecular Dynamics Using Recursive, Spatially Separated, Overlapping Model Subsystems Mixed within an ONIOM-Based Fragmentation Energy Extrapolation Technique

Linear-scaling generation of potential energy surfaces using a double incremental expansion

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

Contact Info

Product

Resources

About