Block‐adaptive quantum mechanics: An adaptive divide‐and‐conquer approach to interactive quantum chemistry

Bosson, Maël; Grudinin, Sergei; Redon, Stéphane

doi:10.1002/jcc.23157

Cited by 8 publications

(10 citation statements)

References 42 publications

(58 reference statements)

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“…This method has already been shown to be feasible for the interactive study of structures containing only carbon and hydrogen. 11,12 It has the advantage of being non-iterative as the Fock operator does not depend on the molecular orbital coefficients owing to the severe approximation involved. Moreover, only a few simple integrals have to be evaluated.…”

Section: Standard Semi-empirical Methodsmentioning

confidence: 99%

“…9 Recently, we have investigated real-time reactivity exploration 10 in the framework of the SAMSON environment, for which a fast semi-empirical method for structure optimisations of hydrocarbons is already available. 11,12 In this work, we explore the physical meaning of externally controlled congurational changes in molecular assemblies. We work out the requirements for treating molecular assemblies in virtual environments and how much of the underlying physical theory can be recovered in an interactive exploration of chemical reactivity.…”

Section: Introductionmentioning

confidence: 99%

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Studying chemical reactivity in a virtual environment

Haag

Reiher

2014

Faraday Discuss.

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Chemical reactivity of a set of reactants is determined by its potential (electronic) energy (hyper)surface. The high dimensionality of this surface renders it difficult to efficiently explore reactivity in a large reactive system. Exhaustive sampling techniques and search algorithms are not straightforward to employ as it is not clear which explored path will eventually produce the minimum energy path of a reaction passing through a transition structure. Here, the chemist's intuition would be of invaluable help, but it cannot be easily exploited because (1) no intuitive and direct tool for the scientist to manipulate molecular structures is currently available and because (2) quantum chemical calculations are inherently expensive in terms of computational effort. In this work, we elaborate on how the chemist can be reintroduced into the exploratory process within a virtual environment that provides immediate feedback and intuitive tools to manipulate a reactive system. We work out in detail how this immersion should take place. We provide an analysis of modern semi-empirical methods which already today are candidates for the interactive study of chemical reactivity. Implications of manual structure manipulations for their physical meaning and chemical relevance are carefully analysed in order to provide sound theoretical foundations for the interpretation of the interactive reactivity exploration.

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Section: Standard Semi-empirical Methodsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Studying chemical reactivity in a virtual environment

Haag

Reiher

2014

Faraday Discuss.

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“…The ASED-MO method has already been advantageously used to simulate rather large systems with a divideand-conquer technique as implemented in the SAMSON code. 39,40 Additionally, it was used to obtain optimized geometries of adsorbed molecules on metallic [41][42][43][44] and semiconducting surfaces. 45,46…”

Section: The Ased-mo Theorymentioning

confidence: 99%

Toward interactive scanning tunneling microscopy simulations of large-scale molecular systems in real time

Dubois

Bouju

Rochefort

2018

Journal of Applied Physics

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We have developed a simulation tool in which structural or chemical modifications of an adsorbed molecular layer can be interactively performed, and where structural relaxation and nearly real-time evaluation of a scanning tunneling microscopy (STM) image are considered. This approach is built from an optimized integration of the atomic superposition and electron delocalization molecular orbital theory (ASED-MO) to which a van der Waals correction term is added in conjunction with a non-linear optimization algorithm based on the Broyden-Fletcher-Goldfarb-Shanno method. This integrated approach provides reliable optimized geometries for adsorbed species on metallic surfaces in a reasonable time. Although we performed a major revision of the ASED-MO parameters, the proposed computational approach can accurately reproduce the geometries of a various amount of covalent molecules and weakly bonded complexes contained in two welldefined datasets. More importantly, the relaxation of adsorbed species on a metal surface leads to molecular geometries in good agreement with experimental and Density Functional Theory results. Then, the electronic structure obtained from ASED-MO is used to compute the STM image of the system nearly in real-time using the Tersoff-Hamann formalism. We developed a parallelization strategy that use Graphics Processing Units (GPU) to reduce the computing time of STM simulation by a factor of 30. Such improvements allow one to simulate STM images of large supramolecular arrangements and to investigate the influence of realistic local chemical or structural defects on metal surfaces.

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“…ARPS modify the system's dynamic by freezing the movement of slowest particles, which reduces the time needed to update forces in a simulation. ARPS has been originally developed for pairwise force fields like Lennard‐Jones interactions but has already been applied to first‐principles simulations and more recently, to the computation of long‐range interactions . A parallel version has also been developed and implemented in LAMMPS .…”

Section: Introductionmentioning

confidence: 99%

Incremental solver for orbital‐free density functional theory

Rousse

Redon

2019

J Comput Chem

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First-principle calculations are still a challenge since they require a great amount of computational time. In this article, we introduce a new algorithm to perform orbital-free density functional theory (OF-DFT) calculations. Our new algorithm focuses computational efforts on important parts of the particle system, which, in the context of adaptively restrained particle simulations (ARPS) allows us to accelerate particle simulations. MethodologyBefore we describe our method, we first introduce the molecular dynamics in which simulations will take place, ARPS, and then recall the main ideas and equations behind the OF-DFT.Adaptively-restrained particle simulations ARPS freeze the slowest particle movements so that the number of moved particles at each time step decreases.Briefly, ARPS manage the behavior of particles by using their kinetic energy K and 2 thresholds: ε r , the fully-restrained threshold, and ε f , the full-dynamics threshold. If K ≤ ε r , the particle is 1 3 . Different implementations of OF-DFT computation have been tested, either in Fourier space [2] or in real space with finite elements [32] or with finite differences. [8] Fastest implementations, like PROFESS, use Fourier space. This is because the computational bottleneck of real-space WWW.C-CHEM.ORG

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Block‐adaptive quantum mechanics: An adaptive divide‐and‐conquer approach to interactive quantum chemistry

Cited by 8 publications

References 42 publications

Studying chemical reactivity in a virtual environment

Studying chemical reactivity in a virtual environment

Toward interactive scanning tunneling microscopy simulations of large-scale molecular systems in real time

Incremental solver for orbital‐free density functional theory

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