Engineering Papers⌕ Search

SEARCH · Engineering Papers

Results for “LAMMPS”

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 127 records · Page 7
All sourcesNASA NTRSDOE OSTI
NASA NTRS2017

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↗
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 NTRSDate not supplied

Implementation of Charged Particle Behavior in Discrete Element Method (DEM) Simulations

Lunar landers will agitate the surface of the Moon with an exhaust plume during descent which will, due to the particulate nature of the lunar regolith, loosen and eject grains from the surface. This ejection is not only coupled with the charged plume gas, but also results in significant particle-particle interactions. Settling of these grains after plume effects have subsided takes much longer than expected in a ballistic trajectory. The prevailing hypothesis attributes this behavior to the accumulated charge on the particles. We are thus developing a discrete element method (DEM) approach to explore these charged particle interactions on the lunar surface. The Large-scale Atomic/Molecular Massively Parallel Simulator (LAMMPS) Improved for General Granular and Granular Heat Transfer Simulations (LIGGGHTS) software package provides a DEM modeling framework for granular interactions. It includes many complexities such as non-spherical particle shapes, cohesion and frictional forces, and heat transfer, but has no provision for inter-particle electrostatic forces and charge transfer that are important to examine in the lunar environment. In this work, a standard Coulomb potential and a Yukawa potential are integrated into the LIGGGHTS framework to provide a basis for particle-particle electrostatic interactions, as well as a gravitational potential to enable inter-grain gravitational interactions. A preliminary approach to charge transfer between grains incorporating properties such as work function and electrical conductivity to the library of available material characteristics will be presented. Several scenarios have been simulated that include charged particle interactions within a diffuse granular gas, settling of charged grains into a regolith bed, sliding of granular material along an incline, and vibration of settled grains to produce a behavior similar to fluidization. There are numerous challenges to incorporate realistic interactions between complex lunar particles. Currently, grains are modeled to behave as if the entirety of the charge acts at the center of mass, such as conductors with spherical symmetry and insulators with homogeneously distributed charge. We are developing improvements that will include the use of non-spherical particle geometries, as well as reasonable approximations of insulating/dielectric materials that have non-uniform charge distributions. The cases simulated thus far will be examined in a relevant environment within a vacuum chamber to validate the simulations. These simulations will be bounded by experiments utilizing high-speed camera observations of the motion for validation. The grains in the experiment will exchange charge during their motion and this can be quantified by collection within a charge measurement device such as a Faraday cup. Such a device may be modeled within the software by defining an integration region and computing the contained charge as a function of simulation time, allowing for side-by-side comparison of simulated and measured bulk charging results. Any differences will be reconciled by updating the mathematical mechanisms described within the simulation suite. Successfully combining results from experiments within a relevant environment into the LIGGGHTS framework will improve modeling of the charged grain dynamics experienced on the Moon to provide insights into dust behavior for future lunar exploration missions.

Electrostatics↗
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 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 NTRSDate not supplied

Determination of Interfacial Energy for Solid-State Precipitation

Precipitation of strengthening phases from solid state is a critical process for many materials. For example, the high-temperature creep resistance of Ni-based superalloys is governed by ’ precipitates. However, the interfacial energy which controls the precipitation is expensive to determine experimentally. For simulations, the atomic nature of precipitation events necessitates using Molecular Dynamics (MD) so relying on fitting to a-priori experimental behavior is not required. However, the solid-state precipitation takes orders of magnitude longer time than is accessible for traditional MD simulation. Taking inspiration from Kinetic Monte-Carlo (KMC) methods for simulating diffusion on a rigid lattice, we have developed a hybrid KMC-MD approach to enable simulation of solid-state precipitation (and determination of the interfacial energy). Implementing these methods in LAMMPS, we calculated the interfacial energy for the ’ precipitation out of a super-saturated  phase in Ni-based superalloys. The resulting interfacial energy value for the Ni-Al system is well within the accuracy of experimental values, demonstrating the capability of this method. Enabling the calculation of the interfacial energy without a-priori experimental knowledge of the precipitation unlocks a more efficient ICME-based approach for guiding annealing protocols in Ni-based superalloys and other solid-state precipitation systems.

Precipitation↗
NASA NTRSDate not supplied

Scalable Variable Charge Molecular Dynamics Simulations of Metal-Oxide Systems

Interfaces between metals and oxides are an important feature in many technologically relevant materials, e.g., oxidation of metal surfaces, oxide-dispersion strengthened (ODS) alloys, dielectric components, and thermal barrier coatings among others. Experimental studies of such interfaces are challenging since the majority are buried within the bulk, making computational modeling an attractive alternative. Molecular dynamics (MD) simulations operate at the length scales relevant to many interface-mediated mechanisms, but the requisite interatomic potentials for metal-oxide systems require computationally expensive variable charge schemes to account for the disparate bonding types, thus often limiting their effectiveness. Here we introduce several improvements to the charge transfer interatomic potential (CTIP) model which enable greater computational efficiency for large scale MD simulations. Then, using a new CTIP parametrization for the Ni-O system, we demonstrate its capabilities to capture critical atomic scale mechanisms associated with metal-oxide interfaces. Long time scale simulations (>10 ns) are used to investigate high temperature oxidation and oxide precipitation from the melt, and large length scale simulations (> 1 million atoms) are used to study the interaction of dislocations with oxide particles. We have implemented the new CTIP model in the widely used, open-source MD code LAMMPS.

Gabriel Plummer↗
NASA NTRSDate not supplied

Simulations of Yarn Micro-Mechanics of Woven Heat Shield Materials (3MDCP)

Carbon and phenolic fibers are commonly used in ablative thermal protection materials, such as 3-dimensional Mid-Density Carbon Phenolic (3MDCP), a 3D-woven composite comprised of mixed-fiber yarn bundles. Predicting the micro-mechanical response and fracture of twisted yarns composed of brittle and ductile fibers requires a modeling approach that captures per-fiber yielding, fiber fracture, and inter-fiber friction and contact. This work presents an extended bonded particle model (BPM) for discrete element method (DEM) simulation of fiber and yarn mechanics, implemented in LAMMPS. The model builds on the incremental bond formulation of Guo et al. and introduces a piecewise elasto-plastic constitutive law for axial extension, enabling representation of fibers that yield before failure. 3MDCP yarns were constructed using measured fiber radius distributions and helical twist geometry. Tensile simulations of single-ply 3MDCP yarns show good agreement with vender stress–strain results. Fiber breakage models also show details on yarn breakage propagration, centered radially in the yarn. Yarn breakage of multi-ply 3MDCP also matched experimental observations in per-ply breakage; however, predicted yarn breakage strength were found higher than experimental observations.

Woven↗
NASA NTRSDate not supplied

Simulations of Yarn Micro-Mechanics of Woven Heat Shield Materials

Carbon and phenolic fibers are commonly used in ablative thermal protection materials, such as 3-dimensional Mid-Density Carbon Phenolic (3MDCP), a 3D-woven composite comprised of mixed-fiber yarn bundles. Predicting the micro-mechanical response and fracture of twisted yarns composed of brittle and ductile fibers requires a modeling approach that captures per-fiber yielding, fiber fracture, and inter-fiber friction and contact. This work presents an extended bonded particle model (BPM) for discrete element method (DEM) simulation of fiber and yarn mechanics, implemented in LAMMPS. The model builds on the incremental bond formulation of Guo et al. and introduces a piecewise elasto-plastic constitutive law for axial extension, enabling representation of fibers that yield before failure. 3MDCP yarns were constructed using measured fiber radius distributions and helical twist geometry. Tensile simulations of single-ply 3MDCP yarns show good agreement with vender stress–strain results. Fiber breakage models also show details on yarn breakage propagration, centered radially in the yarn. Yarn breakage of multi-ply 3MDCP also matched experimental observations in per-ply breakage; however, predicted yarn breakage strength were found higher than experimental observations.

Discrete Element Method↗
DOE OSTI2024

Development of Thermal Scattering Law and Cross Sections of Hydrogen in Paraffin Wax

Paraffin wax is frequently used as a neutron moderator and shielding material. The main component of paraffin wax is straight-chain alkanes (n-alkanes). The deposition of paraffin wax is primarily attributed to the crystallization of n-alkanes. It is important to gain a deeper understanding of the mechanisms underlying the behavior of paraffin wax, which would impact the thermal scattering Law (TSL) and cross sections and affect the analysis of neutronic and critical systems. In this work, a classical molecular dynamics (CMD) simulation model was used in LAMMPS to create the TSL and cross sections at room temperature and pressure. To generate the required velocity autocorrelation functions (VACF), previously published data were used to validate the approach and models by comparing them with key model parameters. The phonon density of state (DOS) was calculated using Fourier transformation of the normalized VACF. This DOS was used as the primary input to estimate the TSL (S($a$, $β$)) and cross sections of hydrogen in paraffin wax. The TSL and cross sections of hydrogen were estimated using the Full Law Analysis Scattering System Hub (FLASSH) code. The cross section of hydrogen in paraffin wax is consistent with other hydrocarbon materials such as polyethylene with deviations due to structure in the lowest energy region.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2024

Site-Projected Thermal Conductivity: Application to Defects, Interfaces, and Homogeneously Disordered Materials

With the rapid advance of high-performance computing and electronic technologies, understanding thermal conductivity in materials has become increasingly important. This study presents a novel method: the site-projected thermal conductivity that quantitatively estimates the local (atomic) contribution to heat transport, leveraging the Green–Kubo thermal transport equations. The effectiveness of this approach on disordered and amorphous graphene, amorphous silicon, and grain boundaries in silicon–germanium alloys is demonstrated. Amorphous graphene reveals a percolation behavior for thermal transport. The results highlight the potential of the method to provide new insights into the thermal behavior of materials, offering a promising avenue for materials design and performance optimization.

36 MATERIALS SCIENCE↗
DOE OSTI2024

Disorder-induced heating in molecular atmospheric pressure plasmas

Abstract Recent work has shown that ions are strongly coupled in atmospheric pressure plasmas when the ionization fraction is sufficiently large, leading to a temperature increase from disorder-induced heating (DIH) that is not accounted for in standard modelling techniques. Here, we extend this study to molecular plasmas. A main finding is that the energy gained by ions in DIH gets spread over both translational and rotational degrees of freedom on a nanosecond timescale, causing the final ion and neutral gas temperatures to be lower in the molecular case than in the atomic case. A model is developed for the equilibrium temperature that agrees well with molecular dynamics simulations. The model and simulations are also applied to pressures up to ten atmospheres. We conclude that DIH is a significant and predictable phenomena in molecular atmospheric pressure plasmas.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2024

Protocol-dependent frictional granular jamming simulations: cyclical, compression, and expansion

Granular matter takes many paths to pack in natural and industrial processes. The path influences the packing microstructure, particularly for frictional grains. We perform discrete element modeling simulations of different paths to construct packings of frictional spheres. Specifically, we explore four stress-controlled protocols implementing packing expansions and compressions in various combinations thereof. We characterize the eventual packed states through their dependence of the packing fraction and coordination number on packing pressure, identifying non-monotonicities with pressure that correlate with the fraction of frictional contacts. These stress-controlled, bulk-like particle simulations access very low-pressure packings, namely, the marginally stable limit, and demonstrate the strong protocol dependence of frictional granular matter.

36 MATERIALS SCIENCE↗
DOE OSTI2025

Thermodynamics of Liquid Uranium from Atomistic and Ab Initio Modeling

We present thermodynamic properties for liquid uranium obtained from classical molecular dynamics (MD) simulations and the first-principles theory. The coexisting phases method incorporated within MD modeling defines the melting temperature of uranium in good agreement with the experiment. The calculated melting enthalpy is in agreement with the experimental range. Classical MD simulations show that ionic contribution to the total specific heat of uranium does not depend on temperature. The density of states at the Fermi level, which is a crucial parameter in the determination of the electronic contribution to the total specific heat of liquid uranium, is calculated by ab initio all electron density functional theory (DFT) formalism applied to the atomic configurations generated by classical MD. The calculated specific heat of liquid uranium is compared with the previously calculated specific heat of solid γ-uranium at high temperatures. The liquid uranium cannot be supercooled below T sc ≈ 800 K or approximately about 645 K below the calculated melting point, although, the self-diffusion coefficient approaches zero at T D ≈ 700 K. Uranium metal can be supercooled about 1.5 times more than it can be overheated. The features of the temperature hysteresis are discussed.

36 MATERIALS SCIENCE↗
DOE OSTI2025

Synergistic Density Functional Theory and Molecular Dynamics Approach to Elucidate PNIPAM–Water Interaction Mechanisms

This study employs Density Functional Theory (DFT) and Molecular Dynamics (MD) simulations to investigate interactions between water molecules and Poly(N-isopropylacrylamide) (PNIPAM). DFT reveals preferential water binding sites, with enhanced binding energy observed in the linker zone. Quantum Theory of Atoms in Molecules (QTAIM) and electron localization function (ELF) analyses highlight the roles of hydrogen bonding and steric hindrance. MD simulations unveil temperature-dependent hydration dynamics, with structural transitions marked by changes in the radius of gyration (Rg) and the radial distribution function (RDF), aligning with DFT findings. Our work goes beyond prior studies by combining a DFT, QTAIM and MD simulations approach across different PNIPAM monomer-to-30mer structures. It introduces a systematic quantification of pseudo-saturation thresholds and explores water clustering dynamics with structural specificity, which have not been previously reported in the literature. These novel insights establish a more complete molecular-level picture of PNIPAM hydration behavior and temperature responsiveness, emphasizing the importance of amide hydrogen and carbonyl oxygen sites in hydrogen bonding, which weakens above the lower critical solution temperature (LCST), resulting in increased hydrophobicity and paving the way for understanding water sorption mechanisms, offering guidance for future applications such as dehumidification and atmospheric water harvesting.

08 HYDROGEN↗
NASA NTRSDate not supplied

Particle-Based Fiber Models of Woven Materials for Earth Entry Thermal Protection

Applications requiring materials with layer-to-layer strength, from basketry to thermal protection systems, use interlaced, three-dimensional woven materials. NASA is developing and deploying woven material heat shields for missions, including Artemis I (3D-MAT for compression pads) and potentially Mars Sample Return - Earth Entry System. These materials are complex, hierarchical and must protect from extreme environments and phenomena, such as deformation, impact and high-enthalpy heating. Woven material performance depends on microstructure, damage and weave geometry. Therefore, fiber-specific models are needed to simulate fiber contacts within the weave hierarchical geometry (fiber to tow to yarn to weave) and the inherent directionality of fibers. Explicit fiber models can simulate how weave microstructure evolution affects thermal and mechanical properties. We parameterize a discrete element bonded particle models (DEM-BPM) of fibers to capture thermal and mechanical behavior within and between fibers, with bonded and contact forces, respectively. We study the proportion of heat transfer and stress via the contact network, fiber bonds and the weave geometry, for example, with respect to yarn warp-weft identity (whether it interlaces weave layers). Our results demonstrate the importance of explicit fiber modeling for connecting microstructure with thermal and mechanical properties.

woven material↗
NASA NTRSDate not supplied

Particle-Based Fiber Models of Woven Materials for Earth Entry Thermal Protection

Applications requiring materials with layer-to-layer strength, from basketry to thermal protection systems, use interlaced, three-dimensional woven materials. NASA is developing and deploying woven material heat shields for missions, including Artemis I (3D-MAT for compression pads) and potentially Mars Sample Return - Earth Entry System. These materials are complex, hierarchical and must protect from extreme environments and phenomena, such as deformation, impact and high-enthalpy heating. Woven material performance depends on microstructure, damage and weave geometry. Therefore, fiber-specific models are needed to simulate fiber contacts within the weave hierarchical geometry (fiber to tow to yarn to weave) and the inherent directionality of fibers. Explicit fiber models can simulate how weave microstructure evolution affects thermal and mechanical properties. We parameterize a discrete element bonded particle models (DEM-BPM) of fibers to capture thermal and mechanical behavior within and between fibers, with bonded and contact forces, respectively. We study the proportion of heat transfer and stress via the contact network, fiber bonds and the weave geometry, for example, with respect to yarn warp-weft identity (whether it interlaces weave layers). Our results demonstrate the importance of explicit fiber modeling for connecting microstructure with thermal and mechanical properties.

woven material↗