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At least 91 records · Page 5

Scalability of a Low-Cost Multi-Teraflop Linux Cluster for High-End Classical Atomistic and Quantum Mechanical Simulations

Scalability of a low-cost, Intel Xeon-based, multi-Teraflop Linux cluster is tested for two high-end scientific applications: Classical atomistic simulation based on the molecular dynamics method and quantum mechanical calculation based on the density functional theory. These scalable parallel applications use space-time multiresolution algorithms and feature computational-space decomposition, wavelet-based adaptive load balancing, and spacefilling-curve-based data compression for scalable I/O. Comparative performance tests are performed on a 1,024-processor Linux cluster and a conventional higher-end parallel supercomputer, 1,184-processor IBM SP4. The results show that the performance of the Linux cluster is comparable to that of the SP4. We also study various effects, such as the sharing of memory and L2 cache among processors, on the performance.

Kikuchi, Hideaki↗

Atomistic Design and Simulations of Nanoscale Machines and Assembly

Over the three years of this project, we made significant progress on critical theoretical and computational issues in nanoscale science and technology, particularly in:(1) Fullerenes and nanotubes, (2) Characterization of surfaces of diamond and silicon for NEMS applications, (3) Nanoscale machine and assemblies, (4) Organic nanostructures and dendrimers, (5) Nanoscale confinement and nanotribology, (6) Dynamic response of nanoscale structures nanowires (metals, tubes, fullerenes), (7) Thermal transport in nanostructures.

Goddard, William A., III↗

An Overview of the State of the Art in Atomistic and Multiscale Simulation of Fracture

The emerging field of nanomechanics is providing a new focus in the study of the mechanics of materials, particularly in simulating fundamental atomic mechanisms involved in the initiation and evolution of damage. Simulating fundamental material processes using first principles in physics strongly motivates the formulation of computational multiscale methods to link macroscopic failure to the underlying atomic processes from which all material behavior originates. This report gives an overview of the state of the art in applying concurrent and sequential multiscale methods to analyze damage and failure mechanisms across length scales.

Saether, Erik↗

Molecular Dynamics Simulations of Liquid and Polymer Electrolytes for Energy Storage Devices

Advancing beyond current lithium-ion technology is necessary in order to enable energy storage devices for electric airplanes. Electrolyte stability is a key limiting factor, yet the design of improved electrolytes remains a formidable challenge. Molecular dynamics (MD) simulations are a powerful tool for studying electrolytes, since they can be used to evaluate structural, thermodynamic, and transport properties, and can provide molecular-level detail often inaccessible to experimental techniques. Our computational materials groups at the NASA Ames Research Center has developed models and methods to accurately simulate both liquid and polymer electrolytes.We report the results from atomistic MD simulations of several electrolyte materials, with lithium salts dissolved in ionic liquids, dimethoxyethane (DME), and polyethylene oxide (PEO). For improved accuracy, we employ polarizable models, where each atom is given an environment-dependent atomic dipole. The simulations accurately predict bulk transport properties, including viscosity, diffusion, and ionic conductivity, in quantitative agreement with available experimental data. Moreover, the simulations provide important insights into the solvation structure of the lithium ions.We also report the results from coarse-grained MD simulations of polyanion electrolytes. In order to more efficiently capture the longer length- and time-scales of these systems, we employ a generic bead-spring model. These simulations provide important insight into how the polymer chain architecture and ionic interaction strengths affect the ionic aggregation behavior and cation dynamics. Despite the simplicity of the model, the simulations yield qualitative agreement with experimental data for similar systems.

Abbott, Lauren J.↗

Parallel Grand-Canonical Monte Carlo (ParaGrandMC) User’s Manual Version 2.0

This manual describes the commands and command line options for the Parallel Grand Canonical Monte Carlo version 2.0 (ParaGrandMC.2.0) simulation code. This is a highly scalable parallel FORTRAN 2003 code for simulating the thermodynamic evolution of materials at the atomic level, and predicting their thermodynamic state, phase diagram, chemical composition and mechanical properties. The code is specifically designed to simulate multi-component alloy systems, predict solid-state phase transformations such as austenite-martensite transformations, precipitate formation, recrystallization, capillary effects at interfaces, surface absorption, etc., which can aid the design of novel metallic alloys. While the software is mainly tailored for modeling metal alloys, it can also be used for other types of solid-state systems, and to some degree for liquid or gaseous systems, including multiphase systems forming solid-liquid-gas interfaces. In addition to performing Monte Carlo (MC) simulations, the code can also perform Molecular Dynamics (MD) and Langevin Dynamics (LD) simulations, which can be combined and interchanged with MC for faster and more efficient system evolution. A detailed description of the MC part of the code is provided in the NASA ParaGrandMC report: NASA/CR–2016-219202; http://www.sti.nasa.gov.

High performance computing↗

Enabling Computational Nanotechnology through JavaGenes in a Cycle Scavenging Environment

A genetic algorithm procedure is developed and implemented for fitting parameters for many-body inter-atomic force field functions for simulating nanotechnology atomistic applications using portable Java on cycle-scavenged heterogeneous workstations. Given a physics based analytic functional form for the force field, correlated parameters in a multi-dimensional environment are typically chosen to fit properties given either by experiments and/or by higher accuracy quantum mechanical simulations. The implementation automates this tedious procedure using an evolutionary computing algorithm operating on hundreds of cycle-scavenged computers. As a proof of concept, we demonstrate the procedure for evaluating the Stillinger-Weber (S-W) potential by (a) reproducing the published parameters for Si using S-W energies in the fitness function, and (b) evolving a "new" set of parameters using semi-empirical tightbinding energies in the fitness function. The "new" parameters are significantly better suited for Si cluster energies and forces as compared to even the published S-W potential.

Globus, Al↗

Computationally Guided Design of Polymer-Coated Microparticles as Reusable Materials

Long-duration space exploration missions and sustained lunar or Martian surface operations present greater demands for multifunctional and reusable materials. By scaling down the amount of material to be launched from Earth, both mission cost and risk can be reduced. In this regard, leveraging in-space manufacturing capabilities with reusable feedstock materials is an attractive option, as it will allow for articles to be generated on demand, utilized, and then recycled for additional use. NASA’s Enabling Sustained Presence Using Recyclables (ESPUR) project aims to develop reusable materials using polymer-coated microparticles that are bonded via reversible Diels-Alder reactions, where only modest heat is needed to trigger the reverse reaction and enable reuse. For proof-of-concept demonstration, research is currently focused on the fabrication of epoxy microparticles that contain a copoly(carbonate urethane) coating with maleimide and furan functionalities. Here, we discuss the integration of computational materials modeling approaches to help navigate the large design space in this development effort. We perform molecular dynamics (MD) simulations with atomistic and coarse-grained models of the copolymer, which allow us to evaluate the effects of design parameters like the molecular weight and composition on the molecular interactions and chain dynamics. We show how the properties change with the reversible bonds. We also leverage discrete element method (DEM) simulations to assess how microparticle design parameters like the size ratio and volume fraction can be tuned to increase the packing density and number of microparticle contacts to improve the mechanical properties. Our results demonstrate how computational tools can be used in close collaboration with experimental efforts to accelerate material design.

reusable materials↗

Nanoscale Bio-engineering Solutions for Space Exploration: The Nanopore Sequencer

Characterization of biological systems at the molecular level and extraction of essential information for nano-engineering design to guide the nano-fabrication of solid-state sensors and molecular identification devices is a computational challenge. The alpha hemolysin protein ion channel is used as a model system for structural analysis of nucleic acids like DNA. Applied voltage draws a DNA strand and surrounding ionic solution through the biological nanopore. The subunits in the DNA strand block ion flow by differing amounts. Atomistic scale simulations are employed using NASA supercomputers to study DNA translocation, with the aim to enhance single DNA subunit identification. Compared to protein channels, solid-state nanopores offer a better temporal control of the translocation of DNA and the possibility to easily tune its chemistry to increase the signal resolution. Potential applications for NASA missions, besides real-time genome sequencing include astronaut health, life detection and decoding of various genomes.

Stolc, Viktor↗

Nanoscale Bioengineering Solutions for Space Exploration the Nanopore Sequencer

Characterization of biological systems at the molecular level and extraction of essential information for nano-engineering design to guide the nano-fabrication of solid-state sensors and molecular identification devices is a computational challenge. The alpha hemolysin protein ion channel is used as a model system for structural analysis of nucleic acids like DNA. Applied voltage draws a DNA strand and surrounding ionic solution through the biological nanopore. The subunits in the DNA strand block ion flow by differing amounts. Atomistic scale simulations are employed using NASA supercomputers to study DNA translocation. with the aim to enhance single DNA subunit identification. Compared to protein channels, solid-state nanopores offer a better temporal control of the translocation of DNA and the possibility to easily tune its chemistry to increase the signal resolution. Potential applications for NASA missions, besides real-time genome sequencing include astronaut health, life detection and decoding of various genomes. http://phenomrph.arc.nasa.gov/index.php

Ioana, Cozmuta↗

Computer simulation of surface and film processes

All the investigations which were performed employed in one way or another a computer simulation technique based on atomistic level considerations. In general, three types of simulation methods were used for modeling systems with discrete particles that interact via well defined potential functions: molecular dynamics (a general method for solving the classical equations of motion of a model system); Monte Carlo (the use of Markov chain ensemble averaging technique to model equilibrium properties of a system); and molecular statics (provides properties of a system at T = 0 K). The effects of three-body forces on the vibrational frequencies of triatomic cluster were investigated. The multilayer relaxation phenomena for low index planes of an fcc crystal was analyzed also as a function of the three-body interactions. Various surface properties for Si and SiC system were calculated. Results obtained from static simulation calculations for slip formation were presented. The more elaborate molecular dynamics calculations on the propagation of cracks in two-dimensional systems were outlined.

Tiller, W. A.↗

Modeling Chemical Reactions in Classical Molecular Dynamics Simulations

An algorithm capable of incorporating multi-step reaction mechanisms into atomistic molecular dynamics (MD) simulations using traditional fixed valence force fields is proposed and implemented within the framework of LAMMPS (Large-scale Atomic Molecular Massively Parallel Simulator). This extension, referred to as fix bond/react, enables bonding topology modifications during a running MD simulation using pre- and post-reaction bonding templates to carry out a pre-specified reaction. Candidate reactants are first identified by interatomic separation, followed by the application of a generalized topology matching algorithm to confirm they match the pre-reaction template. This is followed by a topology conversion to match the post-reaction template and a dynamic relaxation to minimize high energy configurations. Two case studies, the condensation polymerization of nylon 6,6 and the formation of a highly-crosslinked epoxy, are simulated to demonstrate the robustness, stability, and speed of the algorithm. Improvements which could increase its utility are discussed.

Jacob R Gissinger↗

Multiscale Modeling of Intergranular Fracture in Aluminum: Constitutive Relation For Interface Debonding

Intergranular fracture is a dominant mode of failure in ultrafine grained materials. In the present study, the atomistic mechanisms of grain-boundary debonding during intergranular fracture in aluminum are modeled using a coupled molecular dynamics finite element simulation. Using a statistical mechanics approach, a cohesive-zone law in the form of a traction-displacement constitutive relationship, characterizing the load transfer across the plane of a growing edge crack, is extracted from atomistic simulations and then recast in a form suitable for inclusion within a continuum finite element model. The cohesive-zone law derived by the presented technique is free of finite size effects and is statistically representative for describing the interfacial debonding of a grain boundary (GB) interface examined at atomic length scales. By incorporating the cohesive-zone law in cohesive-zone finite elements, the debonding of a GB interface can be simulated in a coupled continuum-atomistic model, in which a crack starts in the continuum environment, smoothly penetrates the continuum-atomistic interface, and continues its propagation in the atomistic environment. This study is a step towards relating atomistically derived decohesion laws to macroscopic predictions of fracture and constructing multiscale models for nanocrystalline and ultrafine grained materials.

Yamakov, V.↗

Computational Modeling Method for Superalloys

Computer modeling based on theoretical quantum techniques has been largely inefficient due to limitations on the methods or the computer needs associated with such calculations, thus perpetuating the notion that little help can be expected from computer simulations for the atomistic design of new materials. In a major effort to overcome these limitations and to provide a tool for efficiently assisting in the development of new alloys, we developed the BFS method for alloys, which together with the experimental results from previous and current research that validate its use for large-scale simulations, provide the ideal grounds for developing a computationally economical and physically sound procedure for supplementing the experimental work at great cost and time savings.

Bozzolo, Guillermo↗

Fracture of Carbon Nanotube - Amorphous Carbon Composites: Molecular Modeling

Carbon nanotubes (CNTs) are promising candidates for use as reinforcements in next generation structural composite materials because of their extremely high specific stiffness and strength. They cannot, however, be viewed as simple replacements for carbon fibers because there are key differences between these materials in areas such as handling, processing, and matrix design. It is impossible to know for certain that CNT composites will represent a significant advance over carbon fiber composites before these various factors have been optimized, which is an extremely costly and time intensive process. This work attempts to place an upper bound on CNT composite mechanical properties by performing molecular dynamics simulations on idealized model systems with a reactive forcefield that permits modeling of both elastic deformations and fracture. Amorphous carbon (AC) was chosen for the matrix material in this work because of its structural simplicity and physical compatibility with the CNT fillers. It is also much stiffer and stronger than typical engineering polymer matrices. Three different arrangements of CNTs in the simulation cell have been investigated: a single-wall nanotube (SWNT) array, a multi-wall nanotube (MWNT) array, and a SWNT bundle system. The SWNT and MWNT array systems are clearly idealizations, but the SWNT bundle system is a step closer to real systems in which individual tubes aggregate into large assemblies. The effect of chemical crosslinking on composite properties is modeled by adding bonds between the CNTs and AC. The balance between weakening the CNTs and improving fiber-matrix load transfer is explored by systematically varying the extent of crosslinking. It is, of course, impossible to capture the full range of deformation and fracture processes that occur in real materials with even the largest atomistic molecular dynamics simulations. With this limitation in mind, the simulation results reported here provide a plausible upper limit on achievable CNT composite properties and yield some insight on the influence of processing conditions on the mechanical properties of CNT composites.

Jensen, Benjamin D.↗

Fracture Prediction of Epoxy Resin using Morse Bond Potential Embedded in GAFF using Molecular Dynamics Simulations

A generic method is developed to investigate the fracture behavior of an epoxy resin using atomistic molecular (MD) dynamics simulations. The epoxy system consisted of the stoichiometric mixture of tetra-/tri-functional epoxies and di-functional hardener molecules and was cured with a step-growth crosslinking algorithm. A hybrid force field (hFF) in which Morse bond function were added in second generation-general Amber Force Field (GAFF2) was used to capture bond breaking of the crosslinked epoxy system under uniaxial deformation. The Morse bond parameters for covalent bonds in the crosslinked backbone were fit to dissociation curves computed by CASPT2/6-311+G**. After the systems in various crosslink densities were obtained and equilibrated, the full length of stress-strain (𝜎-𝜀) curve was produced including initial elastic regime, yielding, plastic flow, strain hardening, and progressive failure. We found that the hFF was effective in studying the dissociation of crosslinked polymers and understanding the failure mechanism. In the results, the hFF delivered the same elastic property obtained from the unmodified force field GAFF. The stress-strain curve, however, began to be distinct in the plastic regime due to broken covalent bonds capable of altering the tensile behavior. Once the stress reached maximum, it progressively decreased until the ultimate failure (𝜎=0). Since hFF employed the existing GAFF functions with including a minimal change of its bond potential, this approach is easier to perform and computationally more efficient for unveiling the fracture behavior of polymer materials at the molecular level than other approaches with reactive force fields. We expect this approach will be utilized to accelerate the material-by-design process for thermosets by incorporate data from molecular models.

Changwoon Jang↗

Hot Structure Concepts and Materials for Space Exploration Project

Hot structures are multifunctional material systems that integrate the functions of thermal protection systems (TPS) and primary structure to increase mass efficiency in aerospace vehicles. The goal of this project was to improve our capabilities for developing lightweight, reusable, and reliable hot structures concepts to enable advanced space exploration missions. Specifically, current hot structure carbon/carbon (C/C) composite material systems have low interlaminar strength, which can lead to material failures at low load levels, and large material property variability in as-fabricated parts. Two parallel paths were followed to address these shortcomings. First, analysis models were developed to identify the conditions under which excessive interlaminar stresses occur and to evaluate the potential of stitching the C/C laminae to improve the interlaminar thermal-structural response. This effort included the development of high-fidelity, fracture-based thermal-structural finite element analysis models to evaluate critical features needed to produce efficient hot structure concepts. The second path focused on developing atomistic and mesoscale simulation tools to model the fabrication process in an effort to reduce the time and cost of production while improving the quality of the resulting parts. Aspects of the process currently being investigated include the infusion of the matrix precursor into the fiber preform, the cure of the precursor molecules into their polymeric form, and the carbonization and graphitization of the polymer to form the carbon matrix material. Results of the 6-month study are presented herein.

thermal↗