13 results on '"Yao, Yi"'
Search Results
2. Efficient all-electron hybrid density functionals for atomistic simulations beyond 10 000 atoms.
- Author
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Kokott, Sebastian, Merz, Florian, Yao, Yi, Carbogno, Christian, Rossi, Mariana, Havu, Ville, Rampp, Markus, Scheffler, Matthias, and Blum, Volker
- Subjects
DENSITY functionals ,CENTRAL processing units ,CHEMICAL systems ,ICE crystals ,ATOMS - Abstract
Hybrid density functional approximations (DFAs) offer compelling accuracy for ab initio electronic-structure simulations of molecules, nanosystems, and bulk materials, addressing some deficiencies of computationally cheaper, frequently used semilocal DFAs. However, the computational bottleneck of hybrid DFAs is the evaluation of the non-local exact exchange contribution, which is the limiting factor for the application of the method for large-scale simulations. In this work, we present a drastically optimized resolution-of-identity-based real-space implementation of the exact exchange evaluation for both non-periodic and periodic boundary conditions in the all-electron code FHI-aims, targeting high-performance central processing unit (CPU) compute clusters. The introduction of several new refined message passing interface (MPI) parallelization layers and shared memory arrays according to the MPI-3 standard were the key components of the optimization. We demonstrate significant improvements of memory and performance efficiency, scalability, and workload distribution, extending the reach of hybrid DFAs to simulation sizes beyond ten thousand atoms. In addition, we also compare the runtime performance of the PBE, HSE06, and PBE0 functionals. As a necessary byproduct of this work, other code parts in FHI-aims have been optimized as well, e.g., the computation of the Hartree potential and the evaluation of the force and stress components. We benchmark the performance and scaling of the hybrid DFA-based simulations for a broad range of chemical systems, including hybrid organic–inorganic perovskites, organic crystals, and ice crystals with up to 30 576 atoms (101 920 electrons described by 244 608 basis functions). [ABSTRACT FROM AUTHOR]
- Published
- 2024
- Full Text
- View/download PDF
3. Efficient exact exchange using Wannier functions and other related developments in planewave-pseudopotential implementation of RT-TDDFT.
- Author
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Shepard, Christopher, Zhou, Ruiyi, Bost, John, Carney, Thomas E., Yao, Yi, and Kanai, Yosuke
- Subjects
TIME-dependent density functional theory ,PSEUDOPOTENTIAL method ,ELECTROSTATIC interaction ,ELECTRIC fields ,ELECTRONIC structure - Abstract
The plane-wave pseudopotential (PW-PP) formalism is widely used for the first-principles electronic structure calculation of extended periodic systems. The PW-PP approach has also been adapted for real-time time-dependent density functional theory (RT-TDDFT) to investigate time-dependent electronic dynamical phenomena. In this work, we detail recent advances in the PW-PP formalism for RT-TDDFT, particularly how maximally localized Wannier functions (MLWFs) are used to accelerate simulations using the exact exchange. We also discuss several related developments, including an anti-Hermitian correction for the time-dependent MLWFs (TD-MLWFs) when a time-dependent electric field is applied, the refinement procedure for TD-MLWFs, comparison of the velocity and length gauge approaches for applying an electric field, and elimination of long-range electrostatic interaction, as well as usage of a complex absorbing potential for modeling isolated systems when using the PW-PP formalism. [ABSTRACT FROM AUTHOR]
- Published
- 2024
- Full Text
- View/download PDF
4. Exact constraints and appropriate norms in machine-learned exchange-correlation functionals.
- Author
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Pokharel, Kanun, Furness, James W., Yao, Yi, Blum, Volker, Irons, Tom J. P., Teale, Andrew M., and Sun, Jianwei
- Subjects
FUNCTIONALS ,ELECTRON density ,KINETIC energy ,MACHINE learning ,ENERGY density - Abstract
Machine learning techniques have received growing attention as an alternative strategy for developing general-purpose density functional approximations, augmenting the historically successful approach of human-designed functionals derived to obey mathematical constraints known for the exact exchange-correlation functional. More recently, efforts have been made to reconcile the two techniques, integrating machine learning and exact-constraint satisfaction. We continue this integrated approach, designing a deep neural network that exploits the exact constraint and appropriate norm philosophy to de-orbitalize the strongly constrained and appropriately normed (SCAN) functional. The deep neural network is trained to replicate the SCAN functional from only electron density and local derivative information, avoiding the use of the orbital-dependent kinetic energy density. The performance and transferability of the machine-learned functional are demonstrated for molecular and periodic systems. [ABSTRACT FROM AUTHOR]
- Published
- 2022
- Full Text
- View/download PDF
5. All-electron real-time and imaginary-time time-dependent density functional theory within a numeric atom-centered basis function framework.
- Author
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Hekele, Joscha, Yao, Yi, Kanai, Yosuke, Blum, Volker, and Kratzer, Peter
- Subjects
- *
TIME-dependent density functional theory , *SELF-consistent field theory , *QUANTUM theory , *SMALL molecules - Abstract
Real-time time-dependent density functional theory (RT-TDDFT) is an attractive tool to model quantum dynamics by real-time propagation without the linear response approximation. Sharing the same technical framework of RT-TDDFT, imaginary-time time-dependent density functional theory (it-TDDFT) is a recently developed robust-convergence ground state method. Presented here are high-precision all-electron RT-TDDFT and it-TDDFT implementations within a numerical atom-centered orbital (NAO) basis function framework in the FHI-aims code. We discuss the theoretical background and technical choices in our implementation. First, RT-TDDFT results are validated against linear-response TDDFT results. Specifically, we analyze the NAO basis sets' convergence for Thiel's test set of small molecules and confirm the importance of the augmentation basis functions for adequate convergence. Adopting a velocity-gauge formalism, we next demonstrate applications for systems with periodic boundary conditions. Taking advantage of the all-electron full-potential implementation, we present applications for core level spectra. For it-TDDFT, we confirm that within the all-electron NAO formalism, it-TDDFT can successfully converge systems that are difficult to converge in the standard self-consistent field method. We finally benchmark our implementation for systems up to ∼500 atoms. The implementation exhibits almost linear weak and strong scaling behavior. [ABSTRACT FROM AUTHOR]
- Published
- 2021
- Full Text
- View/download PDF
6. Simulating electronic excitation and dynamics with real-time propagation approach to TDDFT within plane-wave pseudopotential formulation.
- Author
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Shepard, Christopher, Zhou, Ruiyi, Yost, Dillon C., Yao, Yi, and Kanai, Yosuke
- Subjects
ELECTRONIC excitation ,TIME-dependent density functional theory - Abstract
We give a perspective on simulating electronic excitation and dynamics using the real-time propagation approach to time-dependent density functional theory (RT-TDDFT) in the plane-wave pseudopotential formulation. RT-TDDFT is implemented in various numerical formalisms in recent years, and its practical application often dictates the most appropriate implementation of the theory. We discuss recent developments and challenges, emphasizing numerical aspects of studying real systems. Several applications of RT-TDDFT simulation are discussed to highlight how the approach is used to study interesting electronic excitation and dynamics phenomena in recent years. [ABSTRACT FROM AUTHOR]
- Published
- 2021
- Full Text
- View/download PDF
7. Temperature dependence of nuclear quantum effects on liquid water via artificial neural network model based on SCAN meta-GGA functional.
- Author
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Yao, Yi and Kanai, Yosuke
- Subjects
- *
ARTIFICIAL neural networks , *QUANTUM liquids , *RADIAL distribution function , *DENSITY functional theory , *CONDENSED matter - Abstract
We investigate the temperature dependence of nuclear quantum effects (NQEs) on structural and dynamic properties of liquid water by training a neural network force field using first-principles molecular dynamics (FPMD) based on the strongly constrained and appropriately normed meta-generalized gradient approximation exchange-correlation approximation. The FPMD simulation based on density functional theory has become a powerful computational approach for studying a wide range of condensed phase systems. However, its large computational cost makes it difficult to incorporate NQEs in the simulation and investigate temperature dependence of various properties. To circumvent this difficulty, we use an artificial neural network model and employ the thermostatted ring polymer MD approach for studying the temperature dependence of NQEs on various properties. The NQEs generally bring the radial distribution functions closer to the experimental measurements. Translational diffusivity and rotational dynamics of water molecules are both slowed down by the NQEs. The competing inter-molecular and intra-molecular quantum effects on hydrogen bonds, as discussed by Habershon, Markland, and Manolopoulos [J. Chem. Phys. 131(2), 024501 (2019)], can explain the observed temperature dependence of the NQEs on the dynamical properties in our simulation. [ABSTRACT FROM AUTHOR]
- Published
- 2020
- Full Text
- View/download PDF
8. All-electron ab initio Bethe-Salpeter equation approach to neutral excitations in molecules with numeric atom-centered orbitals.
- Author
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Liu, Chi, Kloppenburg, Jan, Yao, Yi, Ren, Xinguo, Appel, Heiko, Kanai, Yosuke, and Blum, Volker
- Subjects
BETHE-Salpeter equation ,TIME-dependent density functional theory ,QUASIPARTICLES ,SMALL molecules ,MOLECULES ,OPTICAL spectra - Abstract
The Bethe-Salpeter equation (BSE) based on GW quasiparticle levels is a successful approach for calculating the optical gaps and spectra of solids and also for predicting the neutral excitations of small molecules. We here present an all-electron implementation of the GW+BSE formalism for molecules, using numeric atom-centered orbital (NAO) basis sets. We present benchmarks for low-lying excitation energies for a set of small organic molecules, denoted in the literature as "Thiel's set." Literature reference data based on Gaussian-type orbitals are reproduced to about one millielectron-volt precision for the molecular benchmark set, when using the same GW quasiparticle energies and basis sets as the input to the BSE calculations. For valence correlation consistent NAO basis sets, as well as for standard NAO basis sets for ground state density-functional theory with extended augmentation functions, we demonstrate excellent convergence of the predicted low-lying excitations to the complete basis set limit. A simple and affordable augmented NAO basis set denoted "tier2+aug2" is recommended as a particularly efficient formulation for production calculations. We finally demonstrate that the same convergence properties also apply to linear-response time-dependent density functional theory within the NAO formalism. [ABSTRACT FROM AUTHOR]
- Published
- 2020
- Full Text
- View/download PDF
9. Propagation of maximally localized Wannier functions in real-time TDDFT.
- Author
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Yost, Dillon C., Yao, Yi, and Kanai, Yosuke
- Subjects
- *
TIME-dependent density functional theory , *ELECTRONIC excitation , *UNITARY transformations , *QUANTUM theory - Abstract
Real-time, time-dependent density functional theory (RT-TDDFT) has gained popularity as a first-principles approach to study a variety of excited-state phenomena such as optical excitations and electronic stopping. Within RT-TDDFT simulations, the gauge freedom of the time-dependent electronic orbitals can be exploited for numerical and scientific convenience while the unitary transformation does not alter physical properties calculated from the quantum dynamics of electrons. Exploiting this gauge freedom, we demonstrate the propagation of maximally localized Wannier functions within RT-TDDFT. We illustrate its great utility through a number of examples including its application to optical excitation in extended systems using the so-called length gauge, interpreting electronic stopping excitation, and simulating electric field-driven quantized charge transport. We implemented the approach within our plane-wave pseudopotential RT-TDDFT module of the QB@LL code, and the performance of the implementation is also discussed. [ABSTRACT FROM AUTHOR]
- Published
- 2019
- Full Text
- View/download PDF
10. Erratum: "Propagation of maximally localized Wannier functions in real-time TDDFT" [J. Chem. Phys. 150, 194113 (2019)].
- Author
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Yost, Dillon C., Yao, Yi, and Kanai, Yosuke
- Subjects
- *
UNITARY operators - Published
- 2019
- Full Text
- View/download PDF
11. Plane-wave pseudopotential implementation and performance of SCAN meta-GGA exchange-correlation functional for extended systems.
- Author
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Yao Y and Kanai Y
- Abstract
We present the implementation and performance of the strongly constrained and appropriately normed, SCAN, meta-GGA exchange-correlation (XC) approximation in the planewave-pseudopotential (PW-PP) formalism using the Troullier-Martins pseudopotential scheme. We studied its performance by applying the PW-PP implementation to several practical applications of interest in condensed matter sciences: (a) crystalline silicon and germanium, (b) martensitic phase transition energetics of phosphorene, and (c) a single water molecule physisorption on a graphene sheet. Given the much-improved accuracy over the GGA functionals and its relatively low computational cost compared to hybrid XC functionals, the SCAN functional is highly promising for various practical applications of density functional theory calculations for condensed matter systems. At same time, the SCAN meta-GGA functional appears to require more careful attention to numerical details. The meta-GGA functional shows more significant dependence on the fast Fourier transform grid, which is used for evaluating the XC potential in real space in the PW-PP formalism, than other more conventional GGA functionals do. Additionally, using pseudopotentials that are generated at a different/lower level of XC approximation could introduce noticeable errors in calculating some properties such as phase transition energetics.
- Published
- 2017
- Full Text
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12. Diffusion quantum Monte Carlo study of martensitic phase transition energetics: The case of phosphorene.
- Author
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Reeves KG, Yao Y, and Kanai Y
- Abstract
Recent technical advances in dealing with finite-size errors make quantum Monte Carlo methods quite appealing for treating extended systems in electronic structure calculations, especially when commonly used density functional theory (DFT) methods might not be satisfactory. We present a theoretical study of martensitic phase transition energetics of a two-dimensional phosphorene by employing diffusion Monte Carlo (DMC) approach. The DMC calculation supports DFT prediction of having a rather diffusive barrier that is characterized by having two transition states, in addition to confirming that the so-called black and blue phases of phosphorene are essentially degenerate. At the same time, the DFT calculations do not provide the quantitative accuracy in describing the energy changes for the martensitic phase transition even when hybrid exchange-correlation functional is employed. We also discuss how mechanical strain influences the stabilities of the two phases of phosphorene.
- Published
- 2016
- Full Text
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13. Communication: Modeling of concentration dependent water diffusivity in ionic solutions: Role of intermolecular charge transfer.
- Author
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Yao Y, Berkowitz ML, and Kanai Y
- Subjects
- Ions chemistry, Models, Molecular, Solutions, Diffusion, Potassium Chloride chemistry, Quantum Theory, Sodium Chloride chemistry, Water chemistry
- Abstract
The translational diffusivity of water in solutions of alkali halide salts depends on the identity of ions, exhibiting dramatically different behavior even in solutions of similar salts of NaCl and KCl. The water diffusion coefficient decreases as the salt concentration increases in NaCl. Yet, in KCl solution, it slightly increases and remains above bulk value as salt concentration increases. Previous classical molecular dynamics simulations have failed to describe this important behavior even when polarizable models were used. Here, we show that inclusion of dynamical charge transfer among water molecules produces results in a quantitative agreement with experiments. Our results indicate that the concentration-dependent diffusivity reflects the importance of many-body effects among the water molecules in aqueous ionic solutions. Comparison with quantum mechanical calculations shows that a heterogeneous and extended distribution of charges on water molecules around the ions due to ion-water and also water-water charge transfer plays a very important role in controlling water diffusivity. Explicit inclusion of the charge transfer allows us to model accurately the difference in the concentration-dependent water diffusivity between Na(+) and K(+) ions in simulations, and it is likely to impact modeling of a wide range of systems for medical and technological applications.
- Published
- 2015
- Full Text
- View/download PDF
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