Engineering Papers⌕ Search

SEARCH · Engineering Papers

Results for “Classical 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.

At least 37 records · Page 2
All sourcesNASA NTRSDOE OSTI
NASA NTRS2008

State of the Art Assessment of Simulation in Advanced Materials Development

Advances in both the underlying theory and in the practical implementation of molecular modeling techniques have increased their value in the advanced materials development process. The objective is to accelerate the maturation of emerging materials by tightly integrating modeling with the other critical processes: synthesis, processing, and characterization. The aims of this report are to summarize the state of the art of existing modeling tools and to highlight a number of areas in which additional development is required. In an effort to maintain focus and limit length, this survey is restricted to classical simulation techniques including molecular dynamics and Monte Carlo simulations.

Wise, Kristopher E.↗
NASA NTRSDate not supplied

REACTER: A Versatile Tool for Large-Scale Reactive Molecular Dynamics

Accurately describing reactive events over long length and time scales remains a grand challenge of computational materials science. REACTER is a general protocol for modeling chemical reactions using classical force fields, and is implemented in the popular molecular dynamics software LAMMPS. REACTER has a growing user base and has been used as a model-building tool for a variety of materials, including thermoplastics, thermosets, glassy materials and composites. The method has also been applied to accelerated modeling of reversible chemical reactions, such as the formation of electrochemical components for batteries. Recently, the REACTER protocol has received some major upgrades to enhance its ability to predict when reactions occur and to make it easier to use. Force field parameters can now be automatically assigned to newly created bonds, angles and other interactions. Advanced reaction constraints have also been added, including an Arrhenius constraint to enforce an effective activation energy, a root-mean-square-deviation option for complex geometrical constraints, and a constraint based on the total potential energy of the atoms involved in a reactive site. This potential energy constraint allows for the accurate reproduction of DFT-based tight-binding (DFTB3) predicted bond dissociation curves for mechanically induced bond breaking.

polymer simulations, molecular dynamics↗
NASA NTRS1984

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.↗
NASA NTRS2003

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↗
NASA NTRS1973

Equilibrium properties of a one-dimensional kinetic system.

One-dimensional systems of N = 500 and 250 particles in equilibrium are numerically simulated utilizing the method of molecular dynamics. Periodic boundary conditions are imposed. The classical two-body interaction potential is short range, repulsive and has a corresponding finite force. The equations of state are determined for densities both less and greater than one. Corresponding theoretical isochores are determined from models based on nearest-neighbor interactions and on a truncated virial expansion, and a comparison is made with the experimental isochores. Time independent radial distributions are constructed numerically and discussed. A change of state from a solidlike state to a fluid-gas state based on the penetrability of the particles is predicted. The transition temperatures are estimated from the radial distribution functions and the nearest-neighbor model. Self-diffusion is observed and the corresponding constants are determined from the velocity autocorrelation functions.

Williams, J. H.↗
NASA NTRS1985

The exact eigenfunctions and eigenvalues of a two-dimensional rigid rotor obtained using Gaussian wave packet dynamics

Exact eigenfunctions for a two-dimensional rigid rotor are obtained using Gaussian wave packet dynamics. The wave functions are obtained by propagating, without approximation, an infinite set of Gaussian wave packets that collectively have the correct periodicity, being coherent states appropriate to this rotational problem. This result leads to a numerical method for the semiclassical calculation of rovibrational, molecular eigenstates. Also, a simple, almost classical, approximation to full wave packet dynamics is shown to give exact results: this leads to an a posteriori justification of the De Leon-Heller spectral quantization method.

Reimers, J. R.↗
NASA NTRSDate not supplied

Building and Breaking Carbon Composites with REACTER

Carbon composites have become indispensable for aerospace and other high-performance applications, and a detailed picture of their morphology and failure mechanisms remains difficult to obtain through experiment. REACTER is a versatile computational modeling tool for atomistic molecular dynamics designed to model chemical reactions at the speed and length scales of classical force fields.1 In this work, several recent features of REACTER were applied to the creation and subsequent mechanical testing of two classes of carbon composites, carbon-fiber reinforced polymers (CFRP) and carbon nanotube (CNT) composites. Carbon fiber core morphologies were created by the method of Desai et al.,2 but using the advanced reaction constraints framework of REACTER, their proposed multistep procedure was reduced to a single uninterrupted molecular dynamics simulation. The carbon fiber filler was embedded into a polymer matrix by simulated in situ polymerization of several thermosetting resins, including bismaleimide and polyarylacetylene, to obtain the final CFRP model. To generate the second class of carbon composite, CNT networks were grown dynamically using the new ‘create atoms’ feature of REACTER, and similarly infiltrated with resin to obtain CNT composites. The resulting models were compared directly to experiment using simulated high resolution transmission electron microscopy and x-ray diffraction. Failure mechanisms were elucidated by simulating mechanically induced bond breaking, as characterized by third-order DFT-based tight-binding (DFTB3) simulations, via a reaction constraint on the total potential energy of the involved atoms.

Molecular Dynamics↗
NASA NTRSDate not supplied

REACTER: A Heuristic Method for Reactive Molecular Dynamics

REACTER (www.reacter.org) is a heuristic protocol that enables the simulation of complex reactions using atomistic molecular dynamics (MD) with a fixed-valence force field. Incorporating reactions into classical MD with this approach allows modeling of reactive systems over greatly-increased time scales, enabling systems to be modeled with MD that would not otherwise be feasible. One or more competing multi-step reactions or series of reactions can be invoked simultaneously. Special treatment can be applied to neighboring atoms to relax high energy configurations while the simulation progresses. The original version of REACTER, which was implemented in the open-source LAMMPS simulation package as fix bond/react, was only available for serial simulations. This work describes the expansion of fix bond/react for use in parallel simulations, as well as the addition of various new options, including deletion of reaction by-products, reversible reactions, and custom reaction constraints. These new capabilities are demonstrated through large-scale simulations (200,000+ atoms) of the polymerization of polystyrene and nylon 6,6. The morphologies of both polymers are analyzed after reaching >99% extent of polymerization. Finally, the newly-added reversible reactions feature is demonstrated by rupturing these highly-entangled systems under uniaxial strain by defining a chain scission reaction.

polymer simulations, molecular dynamics↗
NASA NTRS1980

Changes in "thermal lens" measure diffusivity

In an extension of "thermal lens" effect to new applications and better resolution, two laser beams combine to rapidly measure thermal diffusivity and other molecular dynamic properties. New double-beam technique handles very small samples unlike classical techniques for measuring diffusivity. It can be used for measurements on samples undergoing stress, making it applicable to data collection for structural engineering.

Gupta, A.↗
NASA NTRS1972

Dynamics of the molecular and atomic mechanisms for the hydrogen-iodine exchange reaction.

The molecular and atomic mechanisms for the hydrogen-iodine exchange reaction are treated theoretically by means of extensive classical trajectories calculated on a reasonable potential energy surface on which the single adjustable parameter is the iodine-core effective charge. The analysis shows the molecular mechanism to be dynamically forbidden, but gives an over-all rate constant for the atomic mechanism that is in agreement with the experimental values. It is indicated that the formation of a weak H2I complex plays an important dynamical role if the atomic mechanism is limited to reactions with collision complexes involving no more than two hydrogen atoms and two iodine atoms. Excellent agreement with experiment is obtained for the rate constant for the recombination I+I+H2 yields I2+H2 and its negative temperature coefficient.

Raff, L. M.↗
NASA NTRS2022

Building and Breaking Carbon Composites with REACTER

Carbon-based composites have become indispensable materials in aerospace and other high-performance applications, yet obtaining a detailed, nanoscale understanding of their morphology and failure mechanisms using only experimental methods remains a difficult challenge. REACTER is a versatile computational modeling tool for atomistic molecular dynamics simulations designed to model chemical reactions at the speed and length scales of classical force fields. In this work, several recent features of REACTER were applied to the creation and subsequent mechanical testing of two classes of carbon composites: carbon nanotube (CNT) composites and carbon fiber reinforced polymers (CFRP). A network of CNTs was grown dynamically using the new ‘create atoms’ feature of REACTER. The CNT filler was embedded into a polyarylacetylene (PAA) matrix by simulated in situ polymerization to obtain the final composite model. To generate the second class of carbon composite, fully carbonized (graphitic) carbon fiber morphologies were created by the method of Desai et al. [1], but using the advanced reaction constraints framework of REACTER. Two fiber models were created, representing a circular carbon fiber core and a flat surface, and similarly infiltrated with resin to obtain the final CFRP structure. Failure mechanisms were elucidated by simulating mechanically induced bond breaking, as characterized by third order DFT-based tight-binding simulations, via a reaction constraint on the total potential energy of the involved atoms.

Polymer↗
NASA NTRS1982

Ion-induced nucleation in a binary mixture

Recent ion-induced nucleation studies in a binary mixture of H2O and H2SO4 vapors indicate that conventional classical nucleation theories cannot account for the experimentally observed ion-H2O-H2SO4 microcluster spectra. An empirical-analytical, semi-molecular theory of nucleation of a binary mixture of vapors on ions has been developed. This theory includes molecular approach to ion-induced changes in dielectric properties in the immediate neighborhood of an ion core as well as the size dependence of the surface tension of the microcluster. In addition to gaseous sulfuric acid and water molecules, the effect of ion-hydrates and sulfuric acid hydrates has also been considered. This theory is further simplified by using an empirical correction factor for the electrostatic term. This correction factor has been obtained by comparing the simplified model with the molecular dynamics calculations for selected ion hydrate formation. These two theoretical models are then compared with the classical theory for a variety of experimental conditions.

Smith, A. C.↗
NASA NTRS1979

Semiclassical theory of electronically nonadiabatic transitions in molecular collision processes

An introductory account of the semiclassical theory of the S-matrix for molecular collision processes is presented, with special emphasis on electronically nonadiabatic transitions. This theory is based on the incorporation of classical mechanics with quantum superposition, and in practice makes use of the analytic continuation of classical mechanics into the complex space of time domain. The relevant concepts of molecular scattering theory and related dynamical models are described and the formalism is developed and illustrated with simple examples - collinear collision of the A+BC type. The theory is then extended to include the effects of laser-induced nonadiabatic transitions. Two bound continuum processes collisional ionization and collision-induced emission also amenable to the same general semiclassical treatment are discussed.

Lam, K. S.↗
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 NTRS1985

Laplace-transform technique for deriving thermodynamic equations from the classical microcanonical ensemble

A direct and convenient method is presented for deriving expressions which equate any thermodynamic state function to averages of specific dynamical functions and their fluctuations over the classical microcanonical distribution. Specific expressions are obtained for a variety of thermodynamic quantities. The effect of various entropy definitions on the results are assessed, and the latter are compared to previous work in the literature. The derived formulas are applied to the analysis of molecular-dynamics computer simulations.

Pearson, E. M.↗
NASA NTRS1989

Semiclassical approach to atomic and molecular interactions

A general approach, combining quantum and classical mechanics, is used to determine the electron position and velocity distributions in atoms and atomic ions (positive and negative). The Hartree-Fock electronic wave functions and the classical central field approximation are used for evaluation of the dynamic properties of the localized electrons. The distributions, which are of fundamental importance in applications of the binary encounter approximation to description of atomic and ionic collissions, are obtained in the form of simple analytical expressions. The quantum-classical distributions of this work are compared with several other distributions in Ne, Ar, and Al atoms in the ground state.

Kunc, Joseph A.↗
NASA NTRS1972

Classical scattering calculations for diatomic molecules: A general procedure and application to the microwave spectrum O2

Many properties of gaseous systems such as electromagnetic absorption and emission, sound dispersion and absorption, may be elucidated if the nature of collisions between the particles in the system is understood. A procedure for the calculation of the classical trajectories of two interacting diatomic molecules is described. The dynamics of the collision will be assumed to be that of two rigid rotors moving in a specified potential. The actual outcome of a representative sample of many trajectories at 298K was computed, and the use of these values at any temperature for calculations of various molecular properties will be described. Calculations performed for the O2 microwave spectrum are given to demonstrate the use of the procedure described.

Mingelgrin, U.↗
NASA NTRS1995

CCS Observations of the Protostellar Envelope of B335

Knowledge of the density, velocity and chemical profiles around protostars is of fundamental importance for testing dynamical models of protostar evolution and understanding the nature of the material falling onto circumstellar disks. Presented are single dish and interferometric spectral line observations of CCS towards the core of B335, a classic example of a young, low mass stellar object.

protostar formation molecular cloud cores molecule↗