Engineering Papers⌕ Search

SEARCH · Engineering Papers

Results for “neural network molecular dynamics”

Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

14 records
All sourcesNASA NTRSDOE OSTI
NASA NTRS2018

Aladyn - Adaptive Neural Network Molecular Dynamics Simulation Code: Computational Materials Mini-Application

This report provides an overview and commands description of the Computational Materials mini-application, Aladyn. Aladyn is a simple molecular dynamics code written in FORTRAN 2008, which is designed to demonstrate the use of adaptive neural networks (ANNs) in atomistic simulations. The role of ANNs is to reproduce the very complex energy landscape resulting from the atomic interactions in materials with the accuracy of quantum mechanics-based energy calculations. The ANN is trained on a large set of atomic structures calculated using the density functional theory (DFT) method. The Aladyn code is being released to serve as a training testbed for students and professors in academia to explore possible optimization algorithms for parallel computing on multicore central processing unit (CPU) computers or computers utilizing many core architectures based on graphic processing units (GPUs). The effort is related to the High Performance Computing Incubator (HPCI) project at NASA Langley Research Center.

Yamakov, Vesselin I.↗
NASA NTRS2019

High-Performance Computing Optimization for Aladyn – Adaptive Neural Network Molecular Dynamics Mini-Application

This report provides a description and performance evaluation of the optimization techniques for high performance computing (HPC) implementation of the open source Computational Materials mini-application Aladyn (https://github.com/nasa/aladyn). Aladyn is a basic molecular dynamics code written in FORTRAN 2003, which is designed to demonstrate the use of adaptive neural networks (ANNs) in atomistic simulations. The role of ANNs is to efficiently reproduce the very complex energy landscape resulting from the atomic interactions in materials with the accuracy of the more expensive quantum mechanics-based calculations. The ANN is trained on a large set of atomic structures calculated using the density functional theory (DFT) method. While achieving orders of magnitude faster computational performance than DFT, the ANN-based approach was still very computationally demanding compared to the conventional approach of using empirically fitted energy functions. After its initial development, Aladyn was evaluated and optimized by experts at the NASA Advanced Supercomputing (NAS) division to exploit modern supercomputer architectures. The code has been optimized for execution on multicore central processing units (CPUs), including Intel® Skylake microarchitecture, and on graphic accelerators, such as Nvidia® V100 graphic processing units (GPUs), using Open Multi-Processing (OpenMP) and Open Accelerators (OpenACC) programming interfaces. The optimization achieved a speedup of 4.7 times the baseline version on CPU performance and an additional 2.4 times on CPU+GPU performance. Atomistic computer simulations are a fundamental tool in materials research to model material properties form physics-based first principles. Atomic interaction, governed by Quantum Mechanics (QM) require sophisticated and highly computationally demanding mathematical models to calculate [1]. Classical methods use approximate functional forms, empirically fitted through a set of variable parameters to emulate atomic energies as direct functions of atomic coordinates [2]. While empirical potentials are computationally much simpler, allowing simulations of large-scale systems of up to a trillion (1012) atoms [3], they are substantially less accurate compared to quantum calculations and applicable only to very specific atomic configurations or predefined crystallographic phases. A recently suggested approach is to use heuristic machine learning methods [4], such as those based on Adaptive Neural Networks (ANNs) to predict atomic energies, after being trained on a sufficiently large database of QM-calculated structures [5,6]. This approach reduces significantly the computational complexity, allowing for simulations of orders of magnitude larger systems compared to QM-based methods without compromising accuracy. Still, compared to classical methods using empirical energy functions, ANN methods remain two- to three orders of magnitude more computationally demanding. Hence, the computational cost of simulations, together with the need for extensive training of ANNs, still makes the practical implementation of ANN-based methods quite challenging. The purpose of the Aladyn mini-application software [7], available as open source at https://github.com/nasa/aladyn, is to be a testbed for exploring possible optimization strategies to develop highly scalable parallel algorithms for ANN-based atomistic simulations. Aladyn is aimed at utilizing the architecture of the high-end modern highperformance computing (HPC) hardware based on multicore central processing units (CPUs) equipped with graphic processing unit (GPU) accelerators. Specifically, the goal is to optimize the performance on a single HPC compute node, before implementing scaling to multi-node parallelization using message passing interface (MPI). At the same time, the open source code of Aladyn can serve as a training model for students and professors in academia.

Yamakov, Vesselin I.↗
NASA NTRS2019

AladynPi – Adaptive Neural Network Molecular Dynamics Simulation Code with Physically Informed Potential: Computational Materials Mini-Application

This report provides an overview and description of commands used in the Computational Materials mini-application, AladynPi. AladynPi is an extension of a previously released mini-application, Aladyn (https://github.com/nasa/aladyn; Yamakov, V.I., and Glaessgen, E.H., NASA/TM-2018-220104). Aladyn and AladynPi are basic molecular dynamics codes written in FORTRAN 2003, which are designed to demonstrate the use of adaptive neural networks (ANNs) in atomistic simulations. The role of ANNs is to efficiently reproduce the very complex energy landscape resulting from the atomic interactions in materials with the accuracy of the more expensive quantum mechanics-based calculations. The ANN is trained on a large set of atomic structures calculated using the density functional theory method. An input for the ANN is a set of structure coefficients, characterizing the local atomic environment of each atom, for which the atomic energy is obtained in the ANN inference process. In Aladyn, the ANN gives directly the energy of interatomic interactions. In AladynPi, the ANN gives optimized parameters for a predefined empirical function, known as bond-order-potential (BOP). The parameterized BOP function is then used to calculate the energy. AladynPi code is being released to serve as a training testbed for students and professors in academia to explore possible optimization algorithms for parallel computing on multicore central processing unit (CPU) computers or computers utilizing manycore architectures based on graphic processing units (GPUs). The effort is supported by the High Performance Computing incubator (HPCi) project at NASA Langley Research Center.

Yamakov, Vesselin I.↗
NASA NTRS1992

Neural network error correction for solving coupled ordinary differential equations

A neural network is presented to learn errors generated by a numerical algorithm for solving coupled nonlinear differential equations. The method is based on using a neural network to correctly learn the error generated by, for example, Runge-Kutta on a model molecular dynamics (MD) problem. The neural network programs used in this study were developed by NASA. Comparisons are made for training the neural network using backpropagation and a new method which was found to converge with fewer iterations. The neural net programs, the MD model and the calculations are discussed.

Shelton, R. O.↗
NASA NTRSDate not supplied

Predicting Melt Properties Using Atomistic Simulations With A Highly Accurate Physically Informed Neural Network Interatomic Potential

The use of a recently developed machine learning (ML) interatomic potential for molecular dynamics simulations of aluminum melt properties will be presented. Such properties are critical for process modeling in additive manufacturing, including the melt pool size, solidification, and formation of solidification microstructures. Direct first-principles modeling of these processes is computationally prohibitive whereas simulations employing ML potentials combine the high accuracy of quantum-mechanical methods with high computational speeds. The physically-informed neural network (PINN) method used herein, integrates a high-dimensional regression implemented by an artificial neural network with a physics-based bond-order interatomic potential. PINN potentials can accurately reproduce many properties of aluminum in both crystalline-solid and liquid phases. We examine the accuracy of a PINN Al potential in predicting the density, self-diffusivity, viscosity, and the tension of the liquid surface and liquid-solid interfaces. Comparison with experimental data and ab initio molecular dynamics calculations shows very good agreement for all properties tested.

molecular dynamics↗
NASA NTRSDate not supplied

Modeling Ring-Opening Polymerization with Machine-Learned Committors

Many important industrial and biological processes depend on ring-opening polymerization (ROP), including large-scale production polymers, such as nylon 6, and a variety of biodegradable polymers and high-performance resins. Large-scale simulations (>200K atoms) of ROP were performed using a deep neural network-based method that captured the effect of the local chemical environment of the reactive sites using training data from quantum chemical methods. The utility of this method was demonstrated by modeling the cationic ROP of bis-benzoxazine, a promising resin for use in advanced high-temperature application composites (>200°C). Density functional theory calculations were used to map out the various ring opening and polymerization reaction paths that occur during the thermal processing of bis-benzoxazine. The probabilities of these reactions, as a function of local atomic configurations, were used to construct committor functions using a neural network approach. The learned committor functions were then used to determine when a particular reaction occurred within the REACTER framework for reactive molecular dynamics simulations. The experimentally observed exotherm that occurs during bis-benzoxazine ROP was captured in an effective manner in the simulations by imposing a local heating of the system that corresponds to the enthalpy of reaction for each reaction. The dependence of the final polymer morphology on the ROP reaction temperature was analyzed at the molecular scale. The results presented in this work indicate that machine-learned committor functions are a promising approach for incorporating high-fidelity reactivity criteria that capture the effect of local chemical environments into large-scale polymerization simulations.

machine learning, polymer simulations, molecular d↗
NASA NTRS2020

Ultrafast Melting at Metal-Semiconductor Interfaces: A Molecular Dynamics Study

Quantifying the thermodynamics of interfacial melting is important for several applications such as laser machining and designing radiation hardened electronic devices. Due to the short time and length scales that are involved in the process, molecular simulations provide an ideal path for understating the interfacial melting phenomena. In this work we investigate tungsten (W) – silicon carbide (SiC) interfaces which are relevant in modern high-power electronic devices. Classical molecular dynamics simulations along with the two-temperature model (TTM) were used to study the radiation induced melting of the interface while a neural network-based machine learning framework was used to track the transient re-crystallization process. The damage endured by the semiconductor at the interface following the radiation event is discussed in detail while the re-crystallization of the metal is described in terms of the classical nucleation theory.

Ashwin Ravichandran↗
NASA NTRS2000

Rayleigh Scattering Diagnostic for Simultaneous Measurements of Dynamic Density and Velocity

A flow diagnostic technique based on the molecular Rayleigh scattering of laser light is used to obtain dynamic density and velocity data in turbulent flows. The technique is based on analyzing the Rayleigh scattered light with a Fabry-Perot interferometer and recording information about the interference pattern with a multiple anode photomultiplier tube (PMT). An artificial neural network is used to process the signals from the PMT to recover the velocity time history, which is then used to calculate the velocity power spectrum. The technique is illustrated using simulated data. The results of an experiment to measure the velocity power spectrum in a low speed (100 rn/sec) flow are also presented.

Seasholtz, Richard G.↗
NASA NTRSDate not supplied

Quantum Hardware-Enabled Molecular Dynamics via Transfer Learning

The ability to perform ab initio molecular dynamics simulations using potential energy surfaces provided by quantum computers would open the door to virtually exact dynamics for a variety of chemical and biochemical systems, with impacts on catalysis and biophysics. Nonetheless, performing molecular dynamics on surfaces produced by quantum hardware has been hampered by the noisy energies typically produced by quantum computers and challenges associated with computing gradients and scaling to large systems interest. A recent set of advances in machine learning, known as transfer learning, provides a new path forward for molecular dynamics simulations on quantum hardware. Transfer learning offers a workaround, where one first trains models on larger, less accurate classical datasets and then refines them on smaller, more accurate quantum datasets. We explore this approach by training machine learning models to predict a molecule's potential energy based on its geometric structure using Behler-Parrinello neural networks. When successfully trained, the model enables energy gradient predictions necessary for dynamic simulations. To reduce the quantum resources needed, the model is initially trained with data derived from classical density functional theory and subsequently refined with a smaller dataset obtained from a variational quantum eigensolver optimization of the unitary coupled cluster ansatz. We show that this approach significantly reduces the size of the needed quantum training dataset while capturing the high accuracies needed within quantum chemistry simulations. The success of this two-step training method opens more opportunities to apply machine learning models on quantum data, a significant stride towards efficient quantum-classical hybrid computational models.

quantum computing↗
NASA NTRS2019

Physically-Informed Artificial Neural Networks for Atomistic Modeling of Materials

A new approach is presented for the development of classical interatomic potentials using physically-informed neural networks (PINN) combined with an analytical bond-order atomic interaction model. Due to the strong physical underpinnings, the PINN potentials demonstrate much better transferability than the existing machine-learning potentials while drastically improving the accuracy in comparison with traditional potentials. PINN potentials can be constructed for both metallic and covalent materials in a unified manner. A number of applications of PINN potentials to large-scale molecular dynamics and Monte Carlo simulations and calculation of thermal and mechanical properties of diverse materials are demonstrated. Some of the specific materials systems include silicon and aluminum, as well as alloys and compounds. Computational aspects of PINN potentials are discussed and future developments in this field are outlined.

J Hickman↗
NASA NTRS2002

Research in Computational Astrobiology

We present results from several projects in the new field of computational astrobiology, which is devoted to advancing our understanding of the origin, evolution and distribution of life in the Universe using theoretical and computational tools. We have developed a procedure for calculating long-range effects in molecular dynamics using a plane wave expansion of the electrostatic potential. This method is expected to be highly efficient for simulating biological systems on massively parallel supercomputers. We have perform genomics analysis on a family of actin binding proteins. We have performed quantum mechanical calculations on carbon nanotubes and nucleic acids, which simulations will allow us to investigate possible sources of organic material on the early earth. Finally, we have developed a model of protobiological chemistry using neural networks.

Chaban, Galina↗
NASA NTRSDate not supplied

Machine-Learned Committor Functions for Reactive Molecular Dynamics

Reactive molecular dynamics (MD) is a powerful tool for atomistic-scale modeling of a diverse range of chemical processes. However, scaling these simulations to large systems and long times scales remains a challenge because of the complexity of the potential energy function required. The authors previously developed a heuristic approach, called REACTER, that incorporates reactivity in MD simulations in a less general but much more computationally efficient manner. REACTER uses standard, fixed valence force fields as the underlying potentialenergy surface for describing all interatomic interactions but adds a procedure for enforcing user-defined reactions that occur when certain geometric constraints on relative atomic positions are satisfied. Further, these bonding changes can be accepted or rejected with a probability related tothe local thermal energy. This work seeks to generalize this approach by replacing the set of user defined geometric constraints and energetic criteria with a committor function that specifies the probability of a reaction occurring on the basis of the local atomic configuration. The committor function is a useful mathematical tool for modeling rare events but, unfortunately, is very difficult to compute for realistic systems in a general way. This work describes a method for approximating the committor function using a machine learning approach, specifically a deep neural network trained with data from reactive MD and DFT-based dynamics simulations. This network is coupled to the existing REACTER protocol, as implemented in the LAMMPS MD package, and used to make on-the-fly predictions of reaction probabilities without the more extensive user input previously required. The new method is demonstrated using the polymerization of polystyrene as a case study. Although very dependent on the quality and quantity of training data, machine-learned committor functions show promise as a method for incorporating reaction probability from higher level calculations into highly scalable MD simulations.

polymer simulations↗
NASA NTRS2024

Theoretical Prediction of Thermal Expansion Anisotropy for Y 2 Si 2 O 7 Environmental Barrier Coatings Using a Deep Neural Network Potential and Comparison to Experiment

Environmental barrier coatings (EBCs) are an enabling technology for silicon carbide (SiC)-based ceramic matrix composites (CMCs) in extreme environments such as gas turbine engines. However, development of new coating systems is hindered by the large design space and difficulty in predicting properties for these materials. Density Functional Theory (DFT) has successfully been used to model and predict some thermodynamic and thermo-mechanical properties of high-temperature ceramics for EBCs, although these calculations are challenging due to their high computational costs. In this work, we use machine learning to train a deep neural network potential (DNP) for Y 2 Si 2 O 7 , which is then applied to calculate thermodynamic and thermo-mechanical properties at near-DFT accuracy much faster and using less computational resources than DFT. We use this DNP to predict phonon-based thermodynamic properties of Y 2 Si 2 O 7 with good agreement to DFT and experiments. We also utilize the DNP to calculate the anisotropic, lattice direction-dependent coefficients of thermal expansion (CTEs) for Y 2 Si 2 O 7 . Molecular dynamics trajectories using the DNP correctly demonstrate accurate prediction of the anisotropy of the CTE in good agreement with diffraction experiments. In the future, this DNP could be applied to accelerate additional property calculations for Y 2 Si 2 O 7 compared to DFT or experiments.

rare earth silicates↗