scholarly journals Introducing DDEC6 Atomic Population Analysis: Part 5. New Method to Compute Polarizabilities and Dispersion Coefficients

2018 ◽  
Author(s):  
Thomas Manz ◽  
Taoyi Chen ◽  
Daniel J. Cole ◽  
Nidia Gabaldon Limas ◽  
Benjamin Fiszbein

Polarizabilities and London dispersion forces are important to many chemical processes. Leading terms in these forces are often modeled using polarizabilities and C<sub>n</sub> (n=6, 8, 9, 10 …) dispersion coefficients. Force fields for classical atomistic simulations can be constructed using atom-in-material dispersion coefficients and polarizabilities. This article addresses the key question of how to efficiently assign these parameters to constituent atoms in a material so that properties of the whole material are better reproduced. We develop a new set of scaling laws and computational algorithms (called MCLF) to do this in an accurate and computationally efficient manner across diverse material types. We introduce a conduction limit upper bound and m-scaling to describe the different behaviors of surface and buried atoms. We validate MCLF by comparing results to high-level benchmarks for isolated neutral and charged atoms, diverse diatomic molecules, various polyatomic molecules (e.g., polyacenes, fullerenes, and small organic and inorganic molecules), and dense solids (including metallic, covalent, and ionic). MCLF provides the non-directionally screened polarizabilities required to construct force fields, the directionally-screened static polarizability tensor components and eigenvalues, and environmentally screened C<sub>6</sub> coefficients. Overall, MCLF has improved accuracy and lower computational cost than the TS-SCS method. For TS-SCS, we compared charge partitioning methods and show DDEC6 partitioning yields more accurate results than Hirshfeld partitioning. MCLF also gives approximations for C<sub>8</sub>, C<sub>9</sub>, and C<sub>10</sub> dispersion coefficients and Quantum Drude Oscillator parameters. For sufficiently large systems, our method’s required computational time and memory scale linearly with increasing system size. This is a huge improvement over the cubic computational time of direct matrix inversion. As demonstrations, we study an ice crystal containing >250,000 atoms in the unit cell and the HIV reverse transcriptase enzyme complexed with an inhibiter molecule. This method should find widespread applications to parameterize classical force fields and DFT+dispersion methods.

Author(s):  
Thomas Manz ◽  
Taoyi Chen ◽  
Daniel J. Cole ◽  
Nidia Gabaldon Limas ◽  
Benjamin Fiszbein

Polarizabilities and London dispersion forces are important to many chemical processes. Leading terms in these forces are often modeled using polarizabilities and C<sub>n</sub> (n=6, 8, 9, 10 …) dispersion coefficients. Force fields for classical atomistic simulations can be constructed using atom-in-material dispersion coefficients and polarizabilities. This article addresses the key question of how to efficiently assign these parameters to constituent atoms in a material so that properties of the whole material are better reproduced. We develop a new set of scaling laws and computational algorithms (called MCLF) to do this in an accurate and computationally efficient manner across diverse material types. We introduce a conduction limit upper bound and m-scaling to describe the different behaviors of surface and buried atoms. We validate MCLF by comparing results to high-level benchmarks for isolated neutral and charged atoms, diverse diatomic molecules, various polyatomic molecules (e.g., polyacenes, fullerenes, and small organic and inorganic molecules), and dense solids (including metallic, covalent, and ionic). MCLF provides the non-directionally screened polarizabilities required to construct force fields, the directionally-screened static polarizability tensor components and eigenvalues, and environmentally screened C<sub>6</sub> coefficients. Overall, MCLF has improved accuracy and lower computational cost than the TS-SCS method. For TS-SCS, we compared charge partitioning methods and show DDEC6 partitioning yields more accurate results than Hirshfeld partitioning. MCLF also gives approximations for C<sub>8</sub>, C<sub>9</sub>, and C<sub>10</sub> dispersion coefficients and Quantum Drude Oscillator parameters. For sufficiently large systems, our method’s required computational time and memory scale linearly with increasing system size. This is a huge improvement over the cubic computational time of direct matrix inversion. As demonstrations, we study an ice crystal containing >250,000 atoms in the unit cell and the HIV reverse transcriptase enzyme complexed with an inhibiter molecule. This method should find widespread applications to parameterize classical force fields and DFT+dispersion methods.


Author(s):  
Pei Cao ◽  
Zhaoyan Fan ◽  
Robert X. Gao ◽  
J. Tang

This research aims at unleashing the potential of additive manufacturing technology in industrial design that can produce structures/devices with irregular component geometries to reduce sizes/weights. We explore, by means of path-finding, the length minimization of freeform hydraulic piping network in compact space under given constraints. Previous studies on path-finding have mainly focused on enhancing computational efficiency due to the need to produce rapid results in such as navigation and video-game applications. In this research, we develop a new Focal Any-Angle A* approach that combines the merits of grid-based method and visibility graph-based method. Specifically, we formulate pruned visibility graphs preserving only the useful portion of the vertices and then find the optimal path based on the candidate vertices using A*. The reduced visibility graphs enable us to outperform approximations and maintain the optimality of exact algorithms in a more efficient manner. The algorithm proposed is compared to the traditional A* on Grids, Theta* and A* on visibility graphs in terms of path length, number of nodes evaluated, as well as computational time. As demonstrated and validated through case studies, the proposed method is capable of finding the shortest path with tractable computational cost, which provides a viable design tool for the additive manufacturing of piping network systems.


2020 ◽  
Author(s):  
Marcelo Damasceno ◽  
Hélio Ribeiro Neto ◽  
Tatiane Costa ◽  
Aldemir Cavalini Júnior ◽  
Ludimar Aguiar ◽  
...  

Abstract Fluid-structure interaction modeling tools based on computational fluid dynamics (CFD) produce interesting results that can be used in the design of submerged structures. However, the computational cost of simulations associated with the design of submerged offshore structures is high. There are no high-performance platforms devoted to the analysis and optimization of these structures using CFD techniques. In this context, this work aims to present a computational tool dedicated to the construction of Kriging surrogate models in order to represent the time domain force responses of submerged risers. The force responses obtained from high-cost computational simulations are used as outputs for training and validated the surrogate models. In this case, different excitations are applied in the riser aiming at evaluating the representativeness of the obtained Kriging surrogate model. A similar investigation is performed by changing the number of samples and the total time used for training purposes. The present methodology can be used to perform the dynamic analysis in different submerged structures with a low computational cost. Instead of solving the motion equation associated with the fluid-structure system, a Kriging surrogate model is used. A significant reduction in computational time is expected, which allows the realization of different analyses and optimization procedures in a fast and efficient manner for the design of this type of structure.


Author(s):  
Tu Huynh-Kha ◽  
Thuong Le-Tien ◽  
Synh Ha ◽  
Khoa Huynh-Van

This research work develops a new method to detect the forgery in image by combining the Wavelet transform and modified Zernike Moments (MZMs) in which the features are defined from more pixels than in traditional Zernike Moments. The tested image is firstly converted to grayscale and applied one level Discrete Wavelet Transform (DWT) to reduce the size of image by a half in both sides. The approximation sub-band (LL), which is used for processing, is then divided into overlapping blocks and modified Zernike moments are calculated in each block as feature vectors. More pixels are considered, more sufficient features are extracted. Lexicographical sorting and correlation coefficients computation on feature vectors are next steps to find the similar blocks. The purpose of applying DWT to reduce the dimension of the image before using Zernike moments with updated coefficients is to improve the computational time and increase exactness in detection. Copied or duplicated parts will be detected as traces of copy-move forgery manipulation based on a threshold of correlation coefficients and confirmed exactly from the constraint of Euclidean distance. Comparisons results between proposed method and related ones prove the feasibility and efficiency of the proposed algorithm.


2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Israel F. Araujo ◽  
Daniel K. Park ◽  
Francesco Petruccione ◽  
Adenilton J. da Silva

AbstractAdvantages in several fields of research and industry are expected with the rise of quantum computers. However, the computational cost to load classical data in quantum computers can impose restrictions on possible quantum speedups. Known algorithms to create arbitrary quantum states require quantum circuits with depth O(N) to load an N-dimensional vector. Here, we show that it is possible to load an N-dimensional vector with exponential time advantage using a quantum circuit with polylogarithmic depth and entangled information in ancillary qubits. Results show that we can efficiently load data in quantum devices using a divide-and-conquer strategy to exchange computational time for space. We demonstrate a proof of concept on a real quantum device and present two applications for quantum machine learning. We expect that this new loading strategy allows the quantum speedup of tasks that require to load a significant volume of information to quantum devices.


Symmetry ◽  
2021 ◽  
Vol 13 (4) ◽  
pp. 645
Author(s):  
Muhammad Farooq ◽  
Sehrish Sarfraz ◽  
Christophe Chesneau ◽  
Mahmood Ul Hassan ◽  
Muhammad Ali Raza ◽  
...  

Expectiles have gained considerable attention in recent years due to wide applications in many areas. In this study, the k-nearest neighbours approach, together with the asymmetric least squares loss function, called ex-kNN, is proposed for computing expectiles. Firstly, the effect of various distance measures on ex-kNN in terms of test error and computational time is evaluated. It is found that Canberra, Lorentzian, and Soergel distance measures lead to minimum test error, whereas Euclidean, Canberra, and Average of (L1,L∞) lead to a low computational cost. Secondly, the performance of ex-kNN is compared with existing packages er-boost and ex-svm for computing expectiles that are based on nine real life examples. Depending on the nature of data, the ex-kNN showed two to 10 times better performance than er-boost and comparable performance with ex-svm regarding test error. Computationally, the ex-kNN is found two to five times faster than ex-svm and much faster than er-boost, particularly, in the case of high dimensional data.


2021 ◽  
Vol 11 (2) ◽  
pp. 813
Author(s):  
Shuai Teng ◽  
Zongchao Liu ◽  
Gongfa Chen ◽  
Li Cheng

This paper compares the crack detection performance (in terms of precision and computational cost) of the YOLO_v2 using 11 feature extractors, which provides a base for realizing fast and accurate crack detection on concrete structures. Cracks on concrete structures are an important indicator for assessing their durability and safety, and real-time crack detection is an essential task in structural maintenance. The object detection algorithm, especially the YOLO series network, has significant potential in crack detection, while the feature extractor is the most important component of the YOLO_v2. Hence, this paper employs 11 well-known CNN models as the feature extractor of the YOLO_v2 for crack detection. The results confirm that a different feature extractor model of the YOLO_v2 network leads to a different detection result, among which the AP value is 0.89, 0, and 0 for ‘resnet18’, ‘alexnet’, and ‘vgg16’, respectively meanwhile, the ‘googlenet’ (AP = 0.84) and ‘mobilenetv2’ (AP = 0.87) also demonstrate comparable AP values. In terms of computing speed, the ‘alexnet’ takes the least computational time, the ‘squeezenet’ and ‘resnet18’ are ranked second and third respectively; therefore, the ‘resnet18’ is the best feature extractor model in terms of precision and computational cost. Additionally, through the parametric study (influence on detection results of the training epoch, feature extraction layer, and testing image size), the associated parameters indeed have an impact on the detection results. It is demonstrated that: excellent crack detection results can be achieved by the YOLO_v2 detector, in which an appropriate feature extractor model, training epoch, feature extraction layer, and testing image size play an important role.


2021 ◽  
Vol 18 (2) ◽  
pp. 172988142199858
Author(s):  
Gianpaolo Gulletta ◽  
Eliana Costa e Silva ◽  
Wolfram Erlhagen ◽  
Ruud Meulenbroek ◽  
Maria Fernanda Pires Costa ◽  
...  

As robots are starting to become part of our daily lives, they must be able to cooperate in a natural and efficient manner with humans to be socially accepted. Human-like morphology and motion are often considered key features for intuitive human–robot interactions because they allow human peers to easily predict the final intention of a robotic movement. Here, we present a novel motion planning algorithm, the Human-like Upper-limb Motion Planner, for the upper limb of anthropomorphic robots, that generates collision-free trajectories with human-like characteristics. Mainly inspired from established theories of human motor control, the planning process takes into account a task-dependent hierarchy of spatial and postural constraints modelled as cost functions. For experimental validation, we generate arm-hand trajectories in a series of tasks including simple point-to-point reaching movements and sequential object-manipulation paradigms. Being a major contribution to the current literature, specific focus is on the kinematics of naturalistic arm movements during the avoidance of obstacles. To evaluate human-likeness, we observe kinematic regularities and adopt smoothness measures that are applied in human motor control studies to distinguish between well-coordinated and impaired movements. The results of this study show that the proposed algorithm is capable of planning arm-hand movements with human-like kinematic features at a computational cost that allows fluent and efficient human–robot interactions.


2019 ◽  
Vol 99 (2) ◽  
pp. 1105-1130 ◽  
Author(s):  
Kun Yang ◽  
Vladimir Paramygin ◽  
Y. Peter Sheng

Abstract The joint probability method (JPM) is the traditional way to determine the base flood elevation due to storm surge, and it usually requires simulation of storm surge response from tens of thousands of synthetic storms. The simulated storm surge is combined with probabilistic storm rates to create flood maps with various return periods. However, the map production requires enormous computational cost if state-of-the-art hydrodynamic models with high-resolution numerical grids are used; hence, optimal sampling (JPM-OS) with a small number of (~ 100–200) optimal (representative) storms is preferred. This paper presents a significantly improved JPM-OS, where a small number of optimal storms are objectively selected, and simulated storm surge responses of tens of thousands of storms are accurately interpolated from those for the optimal storms using a highly efficient kriging surrogate model. This study focuses on Southwest Florida and considers ~ 150 optimal storms that are selected based on simulations using either the low fidelity (with low resolution and simple physics) SLOSH model or the high fidelity (with high resolution and comprehensive physics) CH3D model. Surge responses to the optimal storms are simulated using both SLOSH and CH3D, and the flood elevations are calculated using JPM-OS with highly efficient kriging interpolations. For verification, the probabilistic inundation maps are compared to those obtained by the traditional JPM and variations of JPM-OS that employ different interpolation schemes, and computed probabilistic water levels are compared to those calculated by historical storm methods. The inundation maps obtained with the JPM-OS differ less than 10% from those obtained with JPM for 20,625 storms, with only 4% of the computational time.


Author(s):  
K H Groves ◽  
P Bonello ◽  
P M Hai

Essential to effective aeroengine design is the rapid simulation of the dynamic performance of a variety of engine and non-linear squeeze-film damper (SFD) bearing configurations. Using recently introduced non-linear solvers combined with non-parametric identification of high-accuracy bearing models it is possible to run full-engine rotordynamic simulations, in both the time and frequency domains, at a fraction of the previous computational cost. Using a novel reduced form of Chebyshev polynomial fits, efficient and accurate identification of the numerical solution to the two-dimensional Reynolds equation (RE) is achieved. The engine analysed is a twin-spool five-SFD engine model provided by a leading manufacturer. Whole-engine simulations obtained using Chebyshev-identified bearing models of the finite difference (FD) solution to the RE are compared with those obtained from the original FD bearing models. For both time and frequency domain analysis, the Chebyshev-identified bearing models are shown to mimic accurately and consistently the simulations obtained from the FD models in under 10 per cent of the computational time. An illustrative parameter study is performed to demonstrate the unparalleled capabilities of the combination of recently developed and novel techniques utilised in this paper.


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