Showing 1–30 of 30 results for author: Shang, H

A corrective agentic hybrid RAG and an operations-grounded evaluation for a scientific facility

Authors: Rajat Sainju, Dariusz Jarosz, Hairong Shang, Michael Prince, Ryan M. Aydelott, Mathew J. Cherukara, Yine Sun, Michael D. Borland

Abstract: Scientific user facilities accumulate decades of operational knowledge that no single search index covers: electronic logbooks, technical documents, internal wikis, operations chat messages, maintenance records, and live control-system data. We present APS-RAG, Advanced Photon Source Retrieval Augmented Generation, a deployed platform that makes the institutional knowledge at the Advanced Photon S… ▽ More Scientific user facilities accumulate decades of operational knowledge that no single search index covers: electronic logbooks, technical documents, internal wikis, operations chat messages, maintenance records, and live control-system data. We present APS-RAG, Advanced Photon Source Retrieval Augmented Generation, a deployed platform that makes the institutional knowledge at the Advanced Photon Source (APS) accessible to staff through natural-language queries, along with an operations-grounded evaluation. The retrieval engine fuses dense, sparse, and knowledge-graph (KG) channels with query-type-adaptive reciprocal-rank fusion, adds a corrective agentic loop, and runs a native-tool ReAct executor over a Model Context Protocol (MCP) tooling layer. We construct APS-Bench, a 50-question, question-answering (QA) dataset with auditable gold answers. Every retrieval-augmented variant numerically improves strict vital-nugget recall over a naive BM25 baseline (63.8%), with the full corrective Agentic GraphRAG scoring (70.3%). The cross-encoder reranker contributes significantly to answer quality: removing it and allowing the LLM to score relevance drastically reduces strict vital recall by 32.8%. The graph channel and corrective loop contribute positively as expected, but the performance gains are marginal. Additionally, we also compare the performance of open-source and closed-source LLMs in final answer synthesis. We release the APS-Bench construction methodology, the six-layer evaluation harness, and the underlying codebase, along with the '/aps-rag' retrieval agent skill framework, to support reproduction and adoption at other facilities. Together, the deployed platform and its operations-grounded evaluation present a promising workflow for trustworthy, statistically grounded AI assistance in facility operations, transferable to other large scientific instruments. △ Less

Submitted 27 July, 2026; originally announced July 2026.

Transformer refined quantum sampling for strongly correlated electronic structure

Authors: Xiongzhi Zeng, Ming Gong, Bowen Kan, Yi Fan, Huan Ma, Jianbin Cai, Yancheng Liu, Naibin Zhou, Tao Jiang, Shaojun Guo, Zhijie Fan, Zongkang Zhang, Yuan Li, Sirui Cao, Kai Yan, Xiaobo Zhu, Yi Luo, Honghui Shang, Zhenyu Li, Jian-Wei Pan, Jinlong Yang

Abstract: Although quantum computing offers a promising solution for strongly correlated system simulation, existing algorithms face significant bottlenecks on current noisy intermediate-scale quantum (NISQ) devices. Here, we introduce QiankunNet-QSCI, a hybrid quantum-classical framework that addresses this challenge by combining efficient quantum-sampling with a transformer neural network. An efficient un… ▽ More Although quantum computing offers a promising solution for strongly correlated system simulation, existing algorithms face significant bottlenecks on current noisy intermediate-scale quantum (NISQ) devices. Here, we introduce QiankunNet-QSCI, a hybrid quantum-classical framework that addresses this challenge by combining efficient quantum-sampling with a transformer neural network. An efficient unitary selected configuration Interaction (USCI) ansatz especially designed for quantum sampling is proposed to identify the most chemically significant electronic configurations on the Zuchongzhi 3.1 quantum processor. Subsequently, the transformer model QiankunNet learns from these sparse yet critical quantum data to infer and reconstruct the complete electronic wavefunction with high fidelity. Simulation of the challenging 40-qubit [2Fe-2S] ferredoxin active center achieves chemical accuracy. Simulation of the nitrogenase P-cluster in a 114-electron 73-orbital active space also reaches 12 milli-Hartree-level agreement with the best density matrix renormalization group (DMRG) result. QiankunNet-QSCI thus offers a practical route to accurate quantum-assisted electronic structure calculations on current devices. △ Less

Submitted 23 May, 2026; originally announced May 2026.

Implementation of the hybrid exchange-correlation functionals in the SIESTA code

Authors: Yann Pouillon, Bill Clintone Oyomo, James Sifuna, María Camarasa-Gómez, Xinming Qin, Carlos Beltrán, Fernando Gómez-Ortiz, Honghui Shang, Javier Junquera

Abstract: We present an efficient and accurate implementation of hybrid exchange-correlation (XC) functionals in the SIESTA code, enabling large-scale simulations based on Hartree-Fock-type exact exchange combined with strictly localized numerical atomic orbitals (NAOs). Our approach exploits a fitted representation of the NAOs in terms of Gaussian-type orbitals (GTOs), which allows for the analytical evalu… ▽ More We present an efficient and accurate implementation of hybrid exchange-correlation (XC) functionals in the SIESTA code, enabling large-scale simulations based on Hartree-Fock-type exact exchange combined with strictly localized numerical atomic orbitals (NAOs). Our approach exploits a fitted representation of the NAOs in terms of Gaussian-type orbitals (GTOs), which allows for the analytical evaluation of four-center electron repulsion integrals (ERIs) via the LIBINT library. This framework is seamlessly integrated with SIESTA's real-space grid and sparse-matrix infrastructure, and is combined with multiple screening techniques to control the computational complexity. We also introduce a fully analytical formulation of hybrid-functional forces and a dynamic parallel distribution scheme that ensures excellent scalability. We validate our implementation through benchmark calculations on a broad set of systems (including semiconductors, insulators, and two-dimensional materials) and demonstrate that the HSE06 functional significantly improves the prediction of band gaps compared to PBE, in close agreement with G0W0 and experimental data. We analyze in detail the trade-offs between accuracy and computational efficiency as a function of the number of Gaussians, basis set range, and integral screening thresholds. Our results confirm that hybrid functional calculations in SIESTA are now feasible for large extended systems, making accurate first-principles predictions of electronic and structural properties accessible at scale. △ Less

Submitted 28 April, 2026; originally announced April 2026.

Comments: 27 pages, 5 figures, 5 tables

Journal ref: Computer Physics Communications, Volume 323, 2026, 110086

First observation and measurement of the ${}^{198}\text{Hg}$ bosonic transition in an optical lattice clock

Authors: Clara Zyskind, Thomas Lauprêtre, Haosen Shang, Benjamin Pointard, Rodolphe Le Targat, Jérôme Lodewyck, Sébastien Bize

Abstract: We report the first observation of the magnetic-field-induced (5d10 6s2)1S0-(5d10 6s6p)3P0 transition in a bosonic isotope of mercury, 198Hg, realized in an optical lattice clock. We characterize this new isotope, determining key features such as the quadratic Zeeman shift, the probe light shift, and the magic frequency. We also report a first comparison between the 198Hg optical lattice clock and… ▽ More We report the first observation of the magnetic-field-induced (5d10 6s2)1S0-(5d10 6s6p)3P0 transition in a bosonic isotope of mercury, 198Hg, realized in an optical lattice clock. We characterize this new isotope, determining key features such as the quadratic Zeeman shift, the probe light shift, and the magic frequency. We also report a first comparison between the 198Hg optical lattice clock and 87Sr. In this comparison, the 198Hg clock has a relative frequency stability of 6x10-16/sqrt(tau/s) and a total relative systematic uncertainty of 6.9x10-16. This comparison yields the first direct determination of the 198Hg/87Sr optical frequency ratio: 198Hg/87Sr = 2.629 315 734 684 118 1, with the same relative uncertainty. △ Less

Submitted 5 December, 2025; v1 submitted 4 December, 2025; originally announced December 2025.

Constraining Active Galactic Nucleus Jets with Spectrum and Core Shift: The Case of M87

Authors: Kouichi Hirotani, Hsien Shang, Ruben Krasnopolsky, Satoki Matsushita, Britton Jeter, Keiichi Asada

Abstract: We analytically model stationary and axisymmetric active galactic nucleus jets, assuming energy conservation along each magnetic flux tube. Using very-long-baseline interferometry (VLBI) observations and published general relativistic magnetohydrodynamic simulations, we constrain the evolution of the bulk Lorentz factor, the magnetization parameter, and the magnetic field strength along the jet. W… ▽ More We analytically model stationary and axisymmetric active galactic nucleus jets, assuming energy conservation along each magnetic flux tube. Using very-long-baseline interferometry (VLBI) observations and published general relativistic magnetohydrodynamic simulations, we constrain the evolution of the bulk Lorentz factor, the magnetization parameter, and the magnetic field strength along the jet. We then infer the electron density, emission coefficient, and absorption coefficient at each point, and integrate the radiative transfer equation to compute the spectral energy distribution (SED) and the core shift of the synchrotron emission from the relativistic jet. Applying the method to the M87 jet, we find that the hot plasmas are injected at the altitude of seven Schwarzschild radii from the black hole (BH), that the M87 jet is likely composed of a pair plasma, and that the jet flowline geometry is quasi-parabolic as reported at much greater distances. Fitting the nonthermal fraction of the leptonic jet as a function of position, we also find that most of the radio photons are emitted within 1000 Schwarzschild radii from the BH. Although hadronic jets do not reproduce all the VLBI observations consistently in our model, we also discuss that their heavy mass allows a stronger magnetic field within the observational constraints, leading to an inverted SED in sub-millimeter wavelengths by the thermal emission from the jet base. It is therefore implied that contemporaneous observations of the M87 jet with Atacama Large Millimeter/submillimeter Array (ALMA) and VLBI could discriminate the jet composition and its collimation within the central 100 Schwarzschild radii. △ Less

Submitted 8 August, 2025; originally announced August 2025.

Comments: 26 pages, 21 figures. Astrophysical Journal in press

NNQS-AFQMC: Neural network quantum states enhanced fermionic quantum Monte Carlo

Authors: Zhi-Yu Xiao, Bowen Kan, Huan Ma, Bowen Zhao, Honghui Shang

Abstract: We introduce an efficient approach to implement neural network quantum states (NNQS) as trial wavefunctions in auxiliary-field quantum Monte Carlo (AFQMC). NNQS are a recently developed class of variational ansätze capable of flexibly representing many-body wavefunctions, though they often incur a high computational cost during optimization. AFQMC, on the other hand, is a powerful stochastic proje… ▽ More We introduce an efficient approach to implement neural network quantum states (NNQS) as trial wavefunctions in auxiliary-field quantum Monte Carlo (AFQMC). NNQS are a recently developed class of variational ansätze capable of flexibly representing many-body wavefunctions, though they often incur a high computational cost during optimization. AFQMC, on the other hand, is a powerful stochastic projector approach for ground-state calculations, but it normally requires an approximate constraint via a trial wavefunction or trial density matrix, whose quality affects the accuracy. Recently it has been shown (Xiao et al, arXiv2505.18519) that a broad class of highly correlated wave-functions can be integrated into AFQMC through stochastic sampling techniques. In this work, we apply this approach and present a direct integration of NNQS with AFQMC, allowing NNQS to serve as high-quality trial wavefunctions for AFQMC with manageable computational cost. We test the NNQS-AFQMC method on the challenging nitrogen molecule (N$_2$) at stretched geometries. Our results demonstrate that AFQMC with an NNQS trial wavefunction can attain near-exact total energies, highlighting the potential of AFQMC with NNQS to overcome longstanding challenges in strongly correlated electronic structure calculations. We also outline future research directions for improving this promising methodology. △ Less

Submitted 3 October, 2025; v1 submitted 10 July, 2025; originally announced July 2025.

Polytropic Wind-Driven Bubbles and their Shock Structures in Radially Stratified Ambient Media

Authors: Dmitrii Zagorulia, Hsien Shang, Ruben Krasnopolsky

Abstract: We extend the analytic expressions for polytropic wind-driven bubbles and their shock structures, formulated initially in Koo and McKee 1992(a,b), focusing on spherically symmetric configurations in astrophysical environments with $ρ\propto r^{-2}$, which arises naturally in the star-forming environment and has applications to winds flowing into a preexisting bubble. Wind luminosity is assumed to… ▽ More We extend the analytic expressions for polytropic wind-driven bubbles and their shock structures, formulated initially in Koo and McKee 1992(a,b), focusing on spherically symmetric configurations in astrophysical environments with $ρ\propto r^{-2}$, which arises naturally in the star-forming environment and has applications to winds flowing into a preexisting bubble. Wind luminosity is assumed to be constant, and as a result the shock velocities of these bubbles are constant in time. The ratio of specific heats is assumed to be the same in the shocked ambient medium and the shocked wind. Numerical results are presented for one selected ratio of wind density to ambient density. Exact ODEs are written for the compressed wind region and approximate solutions are found by fitting the ODE solutions. By analyzing the interactions between stellar winds and ambient media in the strong compression limit, we model the formation and evolution of spherical bubbles, highlighting their shock fronts and contact discontinuities. Our analytic method provides an intuitive approach to calculating the thickness of bubble shells, which is crucial for understanding their dynamics and observational characteristics. A numerical method explores conditions without explicitly requiring the strong compression limit, and then we compare numerical to analytical results under various conditions. △ Less

Submitted 27 May, 2025; originally announced May 2025.

Comments: 21 pages, 14 figures, accepted for PASP

Nonlinear Stability and Dynamics of Supersonic Compressible Flows

Authors: Symphony Chakraborty, Hsien Shang

Abstract: The study of shear layer instability in compressible flows is key to understanding phenomena from aerodynamics to astrophysical jets. Blumen's seminal paper [``Shear layer instability of an inviscid compressible fluid," J. Fluid Mech. {\bf 40}, 769--781 (1970)] established a linear stability framework for inviscid compressible shear flows, emphasizing velocity gradients and compressibility effects… ▽ More The study of shear layer instability in compressible flows is key to understanding phenomena from aerodynamics to astrophysical jets. Blumen's seminal paper [``Shear layer instability of an inviscid compressible fluid," J. Fluid Mech. {\bf 40}, 769--781 (1970)] established a linear stability framework for inviscid compressible shear flows, emphasizing velocity gradients and compressibility effects. However, the nonlinear regime remains insufficiently explored. This research extends Blumen's framework by conducting a weakly nonlinear stability analysis using the method of multiple scales to derive amplitude equations, such as the Landau-Stuart and complex Landau equations. Perturbation variables are expanded in a power series to capture amplitude evolution beyond linear theory. Finite boundary conditions are incorporated to enhance physical applicability. The study analyzes how compressibility and Mach number influence nonlinear saturation, revealing Mach-dependent bifurcations in Kelvin-Helmholtz instability (KHI) with alternating stable and unstable regimes. Phase portraits and trajectories illustrate transitions, saturation, and spiral decay, which are relevant to astrophysical shear flows. Bifurcation analysis reveals both supercritical and subcritical Hopf behavior in compressible shear flows, underscoring the importance of nonlinear effects in the onset and evolution of flow instabilities. Qualitative and quantitative results of instability evolution have been shown from nonlinear stability analysis. This work bridges the critical gap between linear and fully nonlinear stability analyses by offering a systematic weakly nonlinear framework and the nonlinear dynamics for compressible shear layers. It generalizes the earlier linear results and provides new predictions about bifurcation behavior and long-time state selection in compressible flows. △ Less

Submitted 27 May, 2025; originally announced May 2025.

Comments: 20 pages, 9 figures, accepted for Physics of Fluids

Analytical gradients of random-phase approximation plus corrections from renormalized single excitations

Authors: Muhammad N. Tahir, Honghui Shang, Xinguo Ren

Abstract: The random-phase approximation (RPA) formulated within the adiabatic connection fluctuation-dissipation framework is a powerful approach to compute the ground-state energies and properties of molecules and materials. Its overall underbinding behavior can be effectively mitigated by a simple correction term, called renormalized single excitation (rSE) correction. Analytical gradient calculations of… ▽ More The random-phase approximation (RPA) formulated within the adiabatic connection fluctuation-dissipation framework is a powerful approach to compute the ground-state energies and properties of molecules and materials. Its overall underbinding behavior can be effectively mitigated by a simple correction term, called renormalized single excitation (rSE) correction. Analytical gradient calculations of the RPA energy have become increasingly available, enabling structural relaxations and even molecular dynamics at the RPA level. However, such calculations at the RPA+rSE level have not been reported, due to the lack of the rSE analytical gradient. Here, we present the first formulation and implementation of the analytical gradients of the rSE energy with respect to the nuclear coordinates within an atomic-orbital basis set framework, which allows us to assess the performance of RPA+rSE in determining the molecular geometries and energetics. It is found that the slight overestimation behavior of RPA for small covalently bonded molecules is strengthened by rSE, while such behavior for molecules bonded with purely dispersion interactions is corrected. We further applied the approach to the water clusters, and found that the energy difference between the low-energy isomers of water hexamers is almost unchanged when going from RPA to RPA+rSE geometries. For the bigger WATER27 test set, using the RPA+rSE geometries instead of the RPA ones leads to a slight reduction of the mean absolute error of RPA+rSE from 0.91 kcal/mol to 0.70 kcal/mol, at the complete basis set. △ Less

Submitted 12 May, 2025; originally announced May 2025.

Comments: 48 page, 3 figures and 5 tables in the main text

Coordinated international comparisons between optical clocks connected via fiber and satellite links

Authors: Thomas Lindvall, Marco Pizzocaro, Rachel M. Godun, Michel Abgrall, Daisuke Akamatsu, Anne Amy-Klein, Erik Benkler, Nishant M. Bhatt, Davide Calonico, Etienne Cantin, Elena Cantoni, Giancarlo Cerretto, Christian Chardonnet, Miguel Angel Cifuentes Marin, Cecilia Clivati, Stefano Condio, E. Anne Curtis, Heiner Denker, Simone Donadello, Sören Dörscher, Chen-Hao Feng, Melina Filzinger, Thomas Fordell, Irene Goti, Kalle Hanhijärvi , et al. (40 additional authors not shown)

Abstract: Optical clocks provide ultra-precise frequency references that are vital for international metrology as well as for tests of fundamental physics. To investigate the level of agreement between different clocks, we simultaneously measured the frequency ratios between ten optical clocks in six different countries, using fiber and satellite links. This is the largest coordinated comparison to date, fr… ▽ More Optical clocks provide ultra-precise frequency references that are vital for international metrology as well as for tests of fundamental physics. To investigate the level of agreement between different clocks, we simultaneously measured the frequency ratios between ten optical clocks in six different countries, using fiber and satellite links. This is the largest coordinated comparison to date, from which we present a subset of 38 optical frequency ratios and an evaluation of the correlations between them. Four ratios were measured directly for the first time, while others had significantly lower uncertainties than previously achieved, supporting the advance towards a redefinition of the second and the use of optical standards for international time scales. △ Less

Submitted 10 May, 2025; originally announced May 2025.

Comments: 25 pages, 6 figures

Journal ref: Optica 12, 843 (2025)

Roadmap on Advancements of the FHI-aims Software Package

Authors: Joseph W. Abbott, Carlos Mera Acosta, Alaa Akkoush, Alberto Ambrosetti, Viktor Atalla, Alexej Bagrets, Jörg Behler, Daniel Berger, Hannah Bertschi, Björn Bieniek, Jonas Björk, Volker Blum, Saeed Bohloul, Connor L. Box, Nicholas Boyer, Danilo Simoes Brambila, Gabriel A. Bramley, Kyle R. Bryenton, María Camarasa-Gómez, Christian Carbogno, Fabio Caruso, Sucismita Chutia, Michele Ceriotti, Gábor Csányi, William Dawson , et al. (181 additional authors not shown)

Abstract: Electronic-structure theory is the foundation of the description of materials including multiscale modeling of their properties and functions. Obviously, without sufficient accuracy at the base, reliable predictions are unlikely at any level that follows. The software package FHI-aims has proven to be a game changer for accurate free-energy calculations because of its scalability, numerical precis… ▽ More Electronic-structure theory is the foundation of the description of materials including multiscale modeling of their properties and functions. Obviously, without sufficient accuracy at the base, reliable predictions are unlikely at any level that follows. The software package FHI-aims has proven to be a game changer for accurate free-energy calculations because of its scalability, numerical precision, and its efficient handling of density functional theory (DFT) with hybrid functionals and van der Waals interactions. It treats molecules, clusters, and extended systems (solids and liquids) on an equal footing. Besides DFT, FHI-aims also includes quantum-chemistry methods, descriptions for excited states and vibrations, and calculations of various types of transport. Recent advancements address the integration of FHI-aims into an increasing number of workflows and various artificial intelligence (AI) methods. This Roadmap describes the state-of-the-art of FHI-aims and advancements that are currently ongoing or planned. △ Less

Submitted 20 April, 2026; v1 submitted 30 April, 2025; originally announced May 2025.

Comments: arXiv admin note: Includes articles arXiv:2502.02460, arXiv:2501.02550, arXiv:2411.01680, arXiv:2501.16091, arXiv:2411.04951

R-JET: A postprocessing code for radiative transport in relativistic jets

Authors: Kouichi Hirotani, Hsien Shang, Ruben Krasnopolsky, Kenichi Nishikawa

Abstract: We describe a post-processing radiative transport code for computing the spectra, the coreshift, and the surface-brightness distribution of special relativistic jets with arbitrary optical thickness. The jet consists of an electron-positron pair plasma and an electron-proton normal plasma. Electrons and positrons are relativistic and composed of thermal and nonthermal components, while protons are… ▽ More We describe a post-processing radiative transport code for computing the spectra, the coreshift, and the surface-brightness distribution of special relativistic jets with arbitrary optical thickness. The jet consists of an electron-positron pair plasma and an electron-proton normal plasma. Electrons and positrons are relativistic and composed of thermal and nonthermal components, while protons are non-relativistic and non-radiating. The fraction of a pair plasma, as well as the fraction of a nonthermal component can be arbitrarily chosen. Only the synchrotron process is considered for emission and absorption when the radiative-transfer equation is integrated along our lines of sight. We describe a suite of test problems, and confirm the frequency dependence of the coreshift in the Konigl jet model, when the plasma is composed of nonthermal component alone. Finally, we illustrate the capabilities of the code with model calculations, demonstrating that the jet will exhibit a limb-brightened structure in general when it is energized by the rotational energy of the black hole. It is also demonstrated that such limb-brightened jets show a ring-like structure in the brightness map when we observe the jet launching region nearly face-on. △ Less

Submitted 12 March, 2025; originally announced March 2025.

Comments: 21 pages, 12 figures, Astrophysical Journal in press

Advancing Nonadiabatic Molecular Dynamics Simulations for Solids: Achieving Supreme Accuracy and Efficiency with Machine Learning

Authors: Changwei Zhang, Yang Zhong, Zhi-Guo Tao, Xinming Qing, Honghui Shang, Zhenggang Lan, Oleg V. Prezhdo, Xin-Gao Gong, Weibin Chu, Hongjun Xiang

Abstract: Non-adiabatic molecular dynamics (NAMD) simulations have become an indispensable tool for investigating excited-state dynamics in solids. In this work, we propose a general framework, N$^2$AMD which employs an E(3)-equivariant deep neural Hamiltonian to boost the accuracy and efficiency of NAMD simulations. The preservation of Euclidean symmetry of Hamiltonian enables N$^2$AMD to achieve state-of-… ▽ More Non-adiabatic molecular dynamics (NAMD) simulations have become an indispensable tool for investigating excited-state dynamics in solids. In this work, we propose a general framework, N$^2$AMD which employs an E(3)-equivariant deep neural Hamiltonian to boost the accuracy and efficiency of NAMD simulations. The preservation of Euclidean symmetry of Hamiltonian enables N$^2$AMD to achieve state-of-the-art performance. Distinct from conventional machine learning methods that predict key quantities in NAMD, N$^2$AMD computes these quantities directly with a deep neural Hamiltonian, ensuring supreme accuracy, efficiency, and consistency. Furthermore, N$^2$AMD demonstrates excellent generalizability and enables seamless integration with advanced NAMD techniques and infrastructures. Taking several extensively investigated semiconductors as the prototypical system, we successfully simulate carrier recombination in both pristine and defective systems at large scales where conventional NAMD often significantly underestimates or even qualitatively incorrectly predicts lifetimes. This framework not only boosts the efficiency and precision of NAMD simulations but also opens new avenues to advance materials research. △ Less

Submitted 13 August, 2024; originally announced August 2024.

Comments: 25 pages, 7 figures

TensorMD: Scalable Tensor-Diagram based Machine Learning Interatomic Potential on Heterogeneous Many-Core Processors

Authors: Xin Chen, Yucheng Ouyang, Xin Chen, Zhenchuan Chen, Rongfen Lin, Xingyu Gao, Lifang Wang, Fang Li, Yin Liu, Honghui Shang, Haifeng Song

Abstract: Molecular dynamics simulations have emerged as a potent tool for investigating the physical properties and kinetic behaviors of materials at the atomic scale, particularly in extreme conditions. Ab initio accuracy is now achievable with machine learning based interatomic potentials. With recent advancements in high-performance computing, highly accurate and large-scale simulations become feasible.… ▽ More Molecular dynamics simulations have emerged as a potent tool for investigating the physical properties and kinetic behaviors of materials at the atomic scale, particularly in extreme conditions. Ab initio accuracy is now achievable with machine learning based interatomic potentials. With recent advancements in high-performance computing, highly accurate and large-scale simulations become feasible. This study introduces TensorMD, a new machine learning interatomic potential (MLIP) model that integrates physical principles and tensor diagrams. The tensor formalism provides a more efficient computation and greater flexibility for use with other scientific codes. Additionally, we proposed several portable optimization strategies and developed a highly optimized version for the new Sunway supercomputer. Our optimized TensorMD can achieve unprecedented performance on the new Sunway, enabling simulations of up to 52 billion atoms with a time-to-solution of 31 ps/step/atom, setting new records for HPC + AI + MD. △ Less

Submitted 12 October, 2023; v1 submitted 12 October, 2023; originally announced October 2023.

A Unified Model for Bipolar Outflows from Young Stars: Apparent Magnetic Jet Acceleration

Authors: Hsien Shang, Ruben Krasnopolsky, Chun-Fan Liu

Abstract: We explore a new, efficient mechanism that can power toroidally magnetized jets up to two to three times their original terminal velocity after they enter a self-similar phase of magnetic acceleration. Underneath the elongated outflow lobe formed by a magnetized bubble, a wide-angle free wind, through the interplay with its ambient toroid, is compressed and accelerated around its axial jet. The ex… ▽ More We explore a new, efficient mechanism that can power toroidally magnetized jets up to two to three times their original terminal velocity after they enter a self-similar phase of magnetic acceleration. Underneath the elongated outflow lobe formed by a magnetized bubble, a wide-angle free wind, through the interplay with its ambient toroid, is compressed and accelerated around its axial jet. The extremely magnetic bubble can inflate over its original size, depending on the initial Alfvén Mach number $M_A$ of the launched flow. The shape-independent slope $\partial{}v_r/\partial{}r=2/3t$ is a salient feature of the self-similarity in the acceleration phase. Peculiar kinematic signatures are observable in the position--velocity (PV) diagrams and can combine with other morphological signatures as probes for the density-collimated jets arising in toroidally dominated magnetized winds. The apparent second acceleration is powered by the decrease of the toroidal magnetic field but operates far beyond the scales of the primary magnetocentrifugal launch region and the free asymptotic terminal state. Rich implications may connect the jets arising from the youngest protostellar outflows such as HH 211 and HH 212 and similar systems with parsec-scale jets across the mass and evolutionary spectra. △ Less

Submitted 20 January, 2023; originally announced January 2023.

Comments: 21 pages, 8 figures, 1 table, to appear in Astrophysical Journal Letters (2023)

Journal ref: The Astrophysical Journal Letters, 945:L1 (21pp), 2023 March 1

A Unified Model for Bipolar Outflows from Young Stars: Kinematic Signatures of Jets, Winds, and Their Magnetic Interplay with the Ambient Toroids

Authors: Hsien Shang, Chun-Fan Liu, Ruben Krasnopolsky, Liang-Yao Wang

Abstract: Kinematic signatures of the jet, winds, multicavities, and episodic shells arising in the unified model of bipolar outflows developed in Shang et al.\ (2020), in which an outflow forms by radially directed, wide-angle toroidally magnetized winds interacting with magnetized isothermal toroids, are extracted in the form of position--velocity diagrams. Elongated outflow lobes, driven by magnetized wi… ▽ More Kinematic signatures of the jet, winds, multicavities, and episodic shells arising in the unified model of bipolar outflows developed in Shang et al.\ (2020), in which an outflow forms by radially directed, wide-angle toroidally magnetized winds interacting with magnetized isothermal toroids, are extracted in the form of position--velocity diagrams. Elongated outflow lobes, driven by magnetized winds and their interplay with the environment, are dominated by extended bubble structures with mixing layers beyond the conventional thin-shell models. The axial cylindrically stratified density jet carries a broad profile near the base, across the projected velocity of the wide-angle wind, and narrows down along the axis with the collimated flow. The reverse shock encloses the magnetized free wind, forms an innermost cavity, and deflects the flow pattern. Shear, Kelvin--Helmholtz instabilities, and pseudopulses add fine and distinctive features between the jet--shell components, and the fluctuating jet velocities. The broad webbed velocity features connect the extremely high and the low velocities across the multicavities, mimicking nested outflowing slower-wind components. Rings and ovals in the perpendicular cuts trace multicavities at different heights, and the compressed ambient gap regions enrich the low-velocity features with protruding spikes. Our kinematic signatures capture the observed systematics of the high-, intermediate-, and low-velocity components from Class 0 to II jet--outflow systems in molecular and atomic lines. The nested shells observed in HH 212, HH 30, and DG Tau B are naturally explained. Outflows as bubbles are ubiquitous and form an inevitable integrative outcome of the interaction between wind and ambient media. △ Less

Submitted 18 January, 2023; originally announced January 2023.

Comments: 66 pages, 26 figures, 3 tables, to appear in the Astrophysical Journal (2023)

Journal ref: The Astrophysical Journal, 944:230 (55pp), 2023 February 20

Q$^2$Chemistry: A quantum computation platform for quantum chemistry

Authors: Yi Fan, Jie Liu, Xiongzhi Zeng, Zhiqian Xu, Honghui Shang, Zhenyu Li, Jinlong Yang

Abstract: Quantum computer provides new opportunities for quantum chemistry. In this article, we present a versatile, extensible, and efficient software package, named Q$^2$Chemistry, for developing quantum algorithms and quantum inspired classical algorithms in the field of quantum chemistry. In Q$^2$Chemistry, wave function and Hamiltonian can be conveniently mapped into the qubit space, then quantum circ… ▽ More Quantum computer provides new opportunities for quantum chemistry. In this article, we present a versatile, extensible, and efficient software package, named Q$^2$Chemistry, for developing quantum algorithms and quantum inspired classical algorithms in the field of quantum chemistry. In Q$^2$Chemistry, wave function and Hamiltonian can be conveniently mapped into the qubit space, then quantum circuits can be generated according to a specific quantum algorithm already implemented in the package or newly developed by the users. The generated circuits can be dispatched to either a physical quantum computer, if available, or to the internal virtual quantum computer realized by simulating quantum circuit on classical supercomputers. As demonstrated by our benchmark simulations with up to 72 qubit, Q$^2$Chemistry achieves excellent performance in simulating medium scale quantum circuits. Application of Q$^2$Chemistry to simulate molecules and periodic systems are given with performance analysis. △ Less

Submitted 23 August, 2022; originally announced August 2022.

Journal ref: JUSTC, 2022, 52(12): 2

Large-Scale Simulation of Quantum Computational Chemistry on a New Sunway Supercomputer

Authors: Honghui Shang, Li Shen, Yi Fan, Zhiqian Xu, Chu Guo, Jie Liu, Wenhao Zhou, Huan Ma, Rongfen Lin, Yuling Yang, Fang Li, Zhuoya Wang, Yunquan Zhang, Zhenyu Li

Abstract: Quantum computational chemistry (QCC) is the use of quantum computers to solve problems in computational quantum chemistry. We develop a high performance variational quantum eigensolver (VQE) simulator for simulating quantum computational chemistry problems on a new Sunway supercomputer. The major innovations include: (1) a Matrix Product State (MPS) based VQE simulator to reduce the amount of mem… ▽ More Quantum computational chemistry (QCC) is the use of quantum computers to solve problems in computational quantum chemistry. We develop a high performance variational quantum eigensolver (VQE) simulator for simulating quantum computational chemistry problems on a new Sunway supercomputer. The major innovations include: (1) a Matrix Product State (MPS) based VQE simulator to reduce the amount of memory needed and increase the simulation efficiency; (2) a combination of the Density Matrix Embedding Theory with the MPS-based VQE simulator to further extend the simulation range; (3) A three-level parallelization scheme to scale up to 20 million cores; (4) Usage of the Julia script language as the main programming language, which both makes the programming easier and enables cutting edge performance as native C or Fortran; (5) Study of real chemistry systems based on the VQE simulator, achieving nearly linearly strong and weak scaling. Our simulation demonstrates the power of VQE for large quantum chemistry systems, thus paves the way for large-scale VQE experiments on near-term quantum computers. △ Less

Submitted 8 July, 2022; originally announced July 2022.

Comments: 13 pages, accepted by SC conference

Localized resolution of identity approach to the analytical gradients of random-phase approximation ground-state energy: algorithm and benchmarks

Authors: Muhammad N. Tahir, Tong Zhu, Honghui Shang, Jia Li, Volker Blum, Xinguo Ren

Abstract: We develop and implement a formalism which enables calculating the analytical gradients of particle-hole random-phase approximation (RPA) ground-state energy with respect to the atomic positions within the atomic orbital basis set framework. Our approach is based on a localized resolution of identity (LRI) approximation for evaluating the two-electron Coulomb integrals and their derivatives, and t… ▽ More We develop and implement a formalism which enables calculating the analytical gradients of particle-hole random-phase approximation (RPA) ground-state energy with respect to the atomic positions within the atomic orbital basis set framework. Our approach is based on a localized resolution of identity (LRI) approximation for evaluating the two-electron Coulomb integrals and their derivatives, and the density functional perturbation theory for computing the first-order derivatives of the Kohn-Sham (KS) orbitals and orbital energies. Our implementation allows one to relax molecular structures at the RPA level using both Gaussian-type orbitals (GTOs) and numerical atomic orbitals (NAOs). Benchmark calculations show that our approach delivers high numerical precision compared to previous implementations. A careful assessment of the quality of RPA geometries for small molecules reveals that post-KS RPA systematically overestimates the bond lengths. We furthermore optimized the geometries of the four low-lying water hexamers -- cage, prism, cyclic and book isomers, and determined the energy hierarchy of these four isomers using RPA. The obtained RPA energy ordering is in good agreement with that yielded by the coupled cluster method with single, double and perturbative triple excitations, despite that the dissociation energies themselves are appreciably underestimated. The underestimation of the dissociation energies by RPA is well corrected by the renormalized single excitation correction. △ Less

Submitted 2 September, 2021; originally announced September 2021.

Comments: 15 pages, 1 figure, five tables

Predicting hyperlinks via hypernetwork loop structure

Authors: Liming Pan, Hui-Juan Shang, Peiyan Li, Haixing Dai, Wei Wang, Lixin Tian

Abstract: While links in simple networks describe pairwise interactions between nodes, it is necessary to incorporate hypernetworks for modeling complex systems with arbitrary-sized interactions. In this study, we focus on the hyperlink prediction problem in hypernetworks, for which the current state-of-art methods are latent-feature-based. A practical algorithm via topological features, which can provide u… ▽ More While links in simple networks describe pairwise interactions between nodes, it is necessary to incorporate hypernetworks for modeling complex systems with arbitrary-sized interactions. In this study, we focus on the hyperlink prediction problem in hypernetworks, for which the current state-of-art methods are latent-feature-based. A practical algorithm via topological features, which can provide understandings of the organizational principles of hypernetworks, is still lacking. For simple networks, local clustering or loop reflects the correlations among nodes; therefore, loop-based link prediction algorithms have achieved accurate performance. Extending the idea to hyperlink prediction faces several challenges. For instance, what is an effective way of defining loops for prediction is not clear yet; besides, directly comparing topological statistics of variable-sized hyperlinks could introduce biases in hyperlink cardinality. In this study, we address the issues and propose a loop-based hyperlink prediction approach. First, we discuss and define the loops in hypernetworks; then, we transfer the loop-features into a hyperlink prediction algorithm via a simple modified logistic regression. Numerical experiments on multiple real-world datasets demonstrate superior performance compared to the state-of-the-art methods. △ Less

Submitted 16 March, 2021; originally announced March 2021.

Interaction of large- and small-scale dynamos in isotropic turbulent flows from GPU-accelerated simulations

Authors: Miikka S. Väisälä, Johannes Pekkilä, Maarit J. Käpylä, Matthias Rheinhardt, Hsien Shang, Ruben Krasnopolsky

Abstract: Magnetohydrodynamical (MHD) dynamos emerge in many different astrophysical situations where turbulence is present, but the interaction between large-scale (LSD) and small-scale dynamos (SSD) is not fully understood. We performed a systematic study of turbulent dynamos driven by isotropic forcing in isothermal MHD with magnetic Prandtl number of unity, focusing on the exponential growth stage. Both… ▽ More Magnetohydrodynamical (MHD) dynamos emerge in many different astrophysical situations where turbulence is present, but the interaction between large-scale (LSD) and small-scale dynamos (SSD) is not fully understood. We performed a systematic study of turbulent dynamos driven by isotropic forcing in isothermal MHD with magnetic Prandtl number of unity, focusing on the exponential growth stage. Both helical and non-helical forcing was employed to separate the effects of LSD and SSD in a periodic domain. Reynolds numbers (Rm) up to $\approx 250$ were examined and multiple resolutions used for convergence checks. We ran our simulations with the Astaroth code, designed to accelerate 3D stencil computations on graphics processing units (GPUs) and to employ multiple GPUs with peer-to-peer communication. We observed a speedup of $\approx 35$ in single-node performance compared to the widely used multi-CPU MHD solver Pencil Code. We estimated the growth rates both from the averaged magnetic fields and their power spectra. At low Rm, LSD growth dominates, but at high Rm SSD appears to dominate in both helically and non-helically forced cases. Pure SSD growth rates follow a logarithmic scaling as a function of Rm. Probability density functions of the magnetic field from the growth stage exhibit SSD behaviour in helically forced cases even at intermediate Rm. We estimated mean-field turbulence transport coefficients using closures like the second-order correlation approximation (SOCA). They yield growth rates similar to the directly measured ones and provide evidence of $α$ quenching. Our results are consistent with the SSD inhibiting the growth of the LSD at moderate Rm, while the dynamo growth is enhanced at higher Rm. △ Less

Submitted 16 December, 2020; originally announced December 2020.

Comments: 22 pages, 23 figures, 2 tables, Accepted for publication in the Astrophysical Journal

Report number: NORDITA-2020-067

Prospects for 10^{-18} Instability Laser Referenced on Thermal Atomic Ensembles

Authors: Haosen Shang, Duo Pan, Xiaogang Zhang, Xiaobo Xue, Tiantian Shi, Jingbiao Chen

Abstract: A thermal atomic ensemble-based laser source with superior frequency stability is proposed that relies on the accumulated contributions from an abundance of nonzero-transverse-velocity atomic ensembles. Compared with the traditional case in which only atoms with near-zero transverse velocities are utilized, the amplitude of the optical Ramsey fringes for a thermal calcium beam can be dramatically… ▽ More A thermal atomic ensemble-based laser source with superior frequency stability is proposed that relies on the accumulated contributions from an abundance of nonzero-transverse-velocity atomic ensembles. Compared with the traditional case in which only atoms with near-zero transverse velocities are utilized, the amplitude of the optical Ramsey fringes for a thermal calcium beam can be dramatically enhanced by three orders of magnitude or more, thus, the signal-to-noise ratio can be improved 33-fold. Based on the recent results of atomic interferometry-based laser stabilization, a quantum projection noise-limited frequency instability less than 2E-17/tau^0.5 is feasible. Such an ultrastable laser has promising applications in diverse areas, including metrology and astronomy. △ Less

Submitted 6 December, 2020; originally announced December 2020.

The static parallel distribution algorithms for hybrid density-functional calculations in HONPAS package

Authors: Xinming Qin, Honghui Shang, Lei Xu, Wei Hu, Jinlong Yang, Shigang Li, Yunquan Zhang

Abstract: Hybrid density-functional calculation is one of the most commonly adopted electronic structure theory used in computational chemistry and materials science because of its balance between accuracy and computational cost. Recently, we have developed a novel scheme called NAO2GTO to achieve linear scaling (Order-N) calculations for hybrid density-functionals. In our scheme, the most time-consuming st… ▽ More Hybrid density-functional calculation is one of the most commonly adopted electronic structure theory used in computational chemistry and materials science because of its balance between accuracy and computational cost. Recently, we have developed a novel scheme called NAO2GTO to achieve linear scaling (Order-N) calculations for hybrid density-functionals. In our scheme, the most time-consuming step is the calculation of the electron repulsion integrals (ERIs) part. So how to create an even distribution of these ERIs in parallel implementation is an issue of particular importance. Here, we present two static scalable distributed algorithms for the ERIs computation. Firstly, the ERIs are distributed over ERIs shell pairs. Secondly, the ERIs is distributed over ERIs shell quartets. In both algorithms, the calculation of ERIs is independent of each other, so the communication time is minimized. We show our speedup results to demonstrate the performance of these static parallel distributed algorithms in the Hefei Order-N packages for \textit{ab initio} simulations (HONPAS). △ Less

Submitted 8 September, 2020; originally announced September 2020.

Journal ref: The International Journal of High Performance Computing Applications(2019)

The dynamic parallel distribution algorithm for hybrid density-functional calculations in HONPAS package

Authors: Honghui Shang, Lei Xu, Baodong Wu, Xinming Qin, Yunquan Zhang, Jinlong Yang

Abstract: This work presents a dynamic parallel distribution scheme for the Hartree-Fock exchange~(HFX) calculations based on the real-space NAO2GTO framework. The most time-consuming electron repulsion integrals~(ERIs) calculation is perfectly load-balanced with 2-level master-worker dynamic parallel scheme, the density matrix and the HFX matrix are both stored in the sparse format, the network communicati… ▽ More This work presents a dynamic parallel distribution scheme for the Hartree-Fock exchange~(HFX) calculations based on the real-space NAO2GTO framework. The most time-consuming electron repulsion integrals~(ERIs) calculation is perfectly load-balanced with 2-level master-worker dynamic parallel scheme, the density matrix and the HFX matrix are both stored in the sparse format, the network communication time is minimized via only communicating the index of the batched ERIs and the final sparse matrix form of the HFX matrix. The performance of this dynamic scalable distributed algorithm has been demonstrated by several examples of large scale hybrid density-functional calculations on Tianhe-2 supercomputers, including both molecular and solid states systems with multiple dimensions, and illustrates good scalability. △ Less

Submitted 8 September, 2020; originally announced September 2020.

Journal ref: Computer Physics Communications,2020

Efficient Parallel Linear Scaling Method to get the Response Density Matrix in All-Electron Real-Space Density-Functional Perturbation Theory

Authors: Honghui Shang, Wanzhen Liang, Yunquan Zhang, Jinlong Yang

Abstract: The real-space density-functional perturbation theory (DFPT) for the computations of the response properties with respect to the atomic displacement and homogeneous electric field perturbation has been recently developed and implemented into the all-electron, numeric atom-centered orbitals electronic structure package FHI-aims. It is found that the bottleneck for large scale applications is the co… ▽ More The real-space density-functional perturbation theory (DFPT) for the computations of the response properties with respect to the atomic displacement and homogeneous electric field perturbation has been recently developed and implemented into the all-electron, numeric atom-centered orbitals electronic structure package FHI-aims. It is found that the bottleneck for large scale applications is the computation of the response density matrix, which scales as $O(N^3)$. Here for the response properties with respect to the homogeneous electric field, we present an efficient parallel linear scaling algorithm for the response density matrix calculation. Our scheme is based on the second-order trace-correcting purification and the parallel sparse matrix-matrix multiplication algorithms. The new scheme reduces the formal scaling from $O(N^3)$ to $O(N)$, and shows good parallel scalability over tens of thousands of cores. As demonstrated by extensive validation, we achieve a rapid computation of accurate polarizabilities using DFPT. Finally, the computational efficiency of this scheme has been illustrated by making the scaling tests and scalability tests on massively parallel computer systems. △ Less

Submitted 8 September, 2020; originally announced September 2020.

Improving Proton Dose Calculation Accuracy by Using Deep Learning

Authors: Chao Wu, Dan Nguyen, Yixun Xing, Ana Barragan Montero, Jan Schuemann, Haijiao Shang, Yuehu Pu, Steve Jiang

Abstract: Accurate dose calculation is vitally important for proton therapy. Pencil beam (PB) model-based dose calculation is fast but inaccurate due to the approximation when dealing with inhomogeneities. Monte Carlo (MC) dose calculation is the most accurate method, but it is time consuming. We hypothesize that deep learning methods can boost the accuracy of PB dose calculation to the level of MC. In this… ▽ More Accurate dose calculation is vitally important for proton therapy. Pencil beam (PB) model-based dose calculation is fast but inaccurate due to the approximation when dealing with inhomogeneities. Monte Carlo (MC) dose calculation is the most accurate method, but it is time consuming. We hypothesize that deep learning methods can boost the accuracy of PB dose calculation to the level of MC. In this work, we developed a deep learning model that converts PB to MC doses for different tumor sites. The proposed model is based on our newly developed hierarchically densely connected U-Net (HD U-Net) network, and it uses the PB dose and patient CT image as inputs to generate the MC dose. We used 290 patients (90 with head and neck, 93 with liver, 75 with prostate, and 32 with lung cancer) to train, validate, and test the model. For each tumor site, we performed four numerical experiments to explore various combinations of training datasets. Training the model on data from all tumor sites together and using the dose distribution of each individual beam as input yielded the best performance for all four tumor sites. The average gamma index (1mm/1% criteria) between the converted dose and the MC dose was 92.8%, 92.7%, 89.7% and 99.6% for head and neck, liver, lung, and prostate test patients, respectively. The average time for dose conversion for a single field was less than 4 seconds. In conclusion, our deep learning-based approach can quickly boost the accuracy of proton PB dose distributions to that of MC dose distributions. The trained model can be readily adapted to new datasets for different tumor sites and from different hospitals through transfer learning. This model can be added as a plug-in to the clinical workflow of proton therapy treatment planning to improve the accuracy of proton dose calculation. △ Less

Submitted 6 April, 2020; originally announced April 2020.

Direct Calculation of Self-Gravitational Force for Infinitesimally Thin Gaseous Disks Using Adaptive Mesh Refinement

Authors: Yao-Huan Tseng, Hsien Shang, Chien-Chang Yen

Abstract: Yen et al. (2012) advanced a direct approach for the calculation of self-gravitational force to second order accuracy based on uniform grid discretization. This method improves the accuracy of N-body calculation by using exact integration of kernel functions and employing the Fast Fourier Transform (FFT) to reduce complexity of computation to nearly linear. This direct approach is free of artifici… ▽ More Yen et al. (2012) advanced a direct approach for the calculation of self-gravitational force to second order accuracy based on uniform grid discretization. This method improves the accuracy of N-body calculation by using exact integration of kernel functions and employing the Fast Fourier Transform (FFT) to reduce complexity of computation to nearly linear. This direct approach is free of artificial boundary conditions, however, the applicability is limited by the uniform discretization of grids. We report here an advancement in the direct method with the implementation of adaptive mesh refinement (AMR) and maintaining second-order accuracy, which breaks the barrier set by uniform grid discretization. The adoption of graphic process units (GPUs) can significantly speed up the computation and make application of this method possible to astrophysical systems of gaseous disk galaxies and protoplanetary disks. △ Less

Submitted 8 January, 2020; originally announced January 2020.

Comments: 16 pages

Journal ref: The Astrophysical Journal Supplement Series, 244:26 (13pp), 2019 October

All-Electron, Real-Space Perturbation Theory for Homogeneous Electric Fields: Theory, Implementation, and Application within DFT

Authors: Honghui Shang, Nathaniel Raimbault, Patrick Rinke, Matthias Scheffler, Mariana Rossi, Christian Carbogno

Abstract: Within density-functional theory, perturbation theory~(PT) is the state-of-the-art formalism for assessing the response to homogeneous electric fields and the associated material properties, e.g., polarizabilities, dielectric constants, and Raman intensities. Here we derive a real-space formulation of PT and present an implementation within the all-electron, numeric atom-centered orbitals electron… ▽ More Within density-functional theory, perturbation theory~(PT) is the state-of-the-art formalism for assessing the response to homogeneous electric fields and the associated material properties, e.g., polarizabilities, dielectric constants, and Raman intensities. Here we derive a real-space formulation of PT and present an implementation within the all-electron, numeric atom-centered orbitals electronic structure code FHI-aims that allows for massively-parallel calculations. As demonstrated by extensive validation, this allows the rapid computation of accurate response properties of molecules and solids. As an application showcase, we present harmonic and anharmonic Raman spectra, the latter obtained by combining hundreds of thousands of PT calculations with \textit{ab initio} molecular dynamics. By using the PBE exchange-correlation functional with many-body van der Waals corrections, we obtain spectra in good agreement with experiment especially with respect to lineshapes for the isolated paracetamol molecule and two polymorphs of the paracetamol crystal. △ Less

Submitted 21 June, 2018; v1 submitted 2 March, 2018; originally announced March 2018.

Journal ref: New Journal of Physics (2018)

The Moving-Grid Effect in the Harmonic Vibrational Frequency Calculations with Numeric Atom-Centered Orbitals

Authors: Honghui Shang, Jinlong Yang

Abstract: When using atom-centered integration grids, the portion of the grid that belongs to a certain atom also moves when this atom is displaced. In the paper, we investigate the moving-grid effect in the calculation of the harmonic vibrational frequencies when using all-electron full-potential numeric atomic-centered orbitals as the basis set. We find that, unlike the first order derivative (i.e., force… ▽ More When using atom-centered integration grids, the portion of the grid that belongs to a certain atom also moves when this atom is displaced. In the paper, we investigate the moving-grid effect in the calculation of the harmonic vibrational frequencies when using all-electron full-potential numeric atomic-centered orbitals as the basis set. We find that, unlike the first order derivative (i.e., forces), the moving-grid effect plays an essential role for the second order derivatives (i.e., vibrational frequencies). Further analysis reveals that predominantly diagonal force constant terms are affected, which can be bypassed efficiently by invoking translational symmetry. Our approaches have been demonstrated in both finite (molecules) and extended (periodic) systems. △ Less

Submitted 19 March, 2020; v1 submitted 30 December, 2017; originally announced January 2018.

Journal ref: J. Phys. Chem. A, 2020

Disk Formation Enabled by Enhanced Resistivity

Authors: Ruben Krasnopolsky, Zhi-Yun Li, Hsien Shang

Abstract: Disk formation in magnetized cloud cores is hindered by magnetic braking. Previous work has shown that for realistic levels of core magnetization, the magnetic field suppresses the formation of rotationally supported disks during the protostellar mass accretion phase of low-mass star formation both in the ideal MHD limit and in the presence of ambipolar diffusion for typical rates of cosmic ray io… ▽ More Disk formation in magnetized cloud cores is hindered by magnetic braking. Previous work has shown that for realistic levels of core magnetization, the magnetic field suppresses the formation of rotationally supported disks during the protostellar mass accretion phase of low-mass star formation both in the ideal MHD limit and in the presence of ambipolar diffusion for typical rates of cosmic ray ionization. Additional effects, such as ohmic dissipation, the Hall effect, and protostellar outflow, are needed to weaken the magnetic braking and enable the formation of persistent, rotationally supported, protostellar disks. In this paper, we first demonstrate that the classic microscopic resistivity is not large enough to enable disk formation by itself. We then experiment with a set of enhanced values for the resistivity in the range $η=10^{17}$--$10^{22}$ cm^2/s. We find that a value of order $10^{19}$ cm^2/s is needed to enable the formation of a 100 AU-scale Keplerian disk; the value depends somewhat on the degree of core magnetization. The required resistivity is a few orders of magnitude larger than the classic microscopic values. Whether it can be achieved naturally during protostellar collapse remains to be determined. △ Less

Submitted 4 June, 2010; originally announced June 2010.

Comments: 10 pages, 11 figures

Journal ref: Astrophysical Journal 716 (2010) 1541-1550