LAMMPS Software Research Articles

Experimental and Numerical Simulation of Coal Rock Impact Energy Index Based on Peridynamics

In response to the increasing severity of the rock burst phenomenon and its relatively difficult prediction, peridynamics and indoor uniaxial compression experiments were used to calculate the changes of the internal elastic energy (t) and impact energy (c) for different rock masses during a loading process from an energy perspective. Two traditional indices for judging rock burst tendency—the rock elastic deformation energy index (WET) and the rock impact energy index (WCF)—were combined to define a new actual impact energy index (W) to more accurately determine the occurrence tendency of rock bursts. The LAMMPS software was used to simulate the internal energy changes of rock materials under pressure, and the results were compared with experimental results for verification. The results were as follows: (1) in the uniaxial compression experiments of different specimens, fine sandstone had the strongest impact resistance, followed by coarse sandstone, mudstone, bottom coal seam, and top coal seam, and the obtained material properties provide a reference for predicting the rock bursts of various rock types in practical engineering. (2) The values calculated using the actual impact energy index (W) and the simulation value were 1.75 and 1.77, respectively, which corresponded to a lower error than when the rock impact energy index (WCF) and the rock elastic deformation energy index (WET) were used individually. Thus, this index can better predict the rock burst. (3) The simulated specimen was subjected to a gradual increase in the internal stored elastic energy during compression, which gradually decreased after the ultimate compressive strength was exceeded. The degree of impact damage formed after macroscopic crushing occurred depended on its residual energy.

Nanoconfined methane flow behavior through realistic organic shale matrix under displacement pressure: a molecular simulation investigation

Academic investigations digging into the methane flow mechanisms at the nanoscale, closely related to development of shale gas reservoirs, had attracted tremendous interest in the past decade. At the same time, a good understanding of the complex essence remains challenging, while the broad theoretical scope, as well as application value, possesses great attraction. In this work, with the help of molecular dynamics methods nested in LAMMPS software, a fundamental framework is established to mimic the nanoconfined fluid flow through realistic organic shale matrix. Denoting evident discrepancy with existed contributions, shale matrix in this work is composed of specific number of kerogen molecules, rather than simple carbon-based nanotube. Recently, promotion efforts have been implemented in the academic community with the use of kerogen molecules, however, gas flow simulations are still lacking, and the pore shape in the current papers is always hypothesized as slit pores. The pore-geometry assumption seriously conflicts with the general observation phenomenon according to the advanced laboratory experiments, such as SEM image, AFM technology, that the organic pores tend to have circular pore geometry. In order to fill the knowledge gap, the circular nanopore with desirable pore size surrounded by kerogen molecules is constructed at first. The organic nanopore with various thermal maturity can be obtained by altering the kerogen molecular type, expecting to achieve more physically and theoretically similar to the realistic shale matrix. After that, methane flow simulation is performed by utilization of non-equilibrium molecular dynamics, the methane density as well as velocity distribution under different displacement pressures are depicted. Furthermore, detailed discussion with respect to the simulation results is provided. Results show that (a) displacement pressure acts as a dominant role affecting methane flow velocity and, however, fails to affect methane density distribution, a behavior mainly controlled by molecular–wall interactions; (b) the velocity distribution feature appears to be in line with the parabolic law under high atmosphere pressure, which can be attributed to small Knudsen number; (c) the simulation time will be prolonged with larger displacement pressure imposed on nanoconfined methane. Accordingly, this work can provide profound basis for accurate evaluation of nanoconfined gas flow behavior through shale matrix.

Multi-scale simulation study on characteristics of free surface velocity curve in ductile metal spallation

The spallation characteristics of ductile tantalum metal under planar plate impact was analyzed through a multi-scale perspective. And the typical characteristics of the free-surface velocity curve on the macro-scale were interpreted from the micro-scale to reveal the physical meanings corresponding to these typical characteristics. On the macro-scale, the spallation behaviors of the ductile tantalum metal under planar-plate impact were numerically simulated through the smooth particle hydrodynamics (SPH) and Lagrange methods, and the free-surface velocity curves of the tantalum during spallation were obtained. In addition, the free-surface velocity curves obtained by the Johnson-Cook model, Steinberg-Cochran-Guinan model and Zerilli-Armstrong model were compared in the numerical simulations. Comparison with the experimental data shows that the Steinberg-Cochran-Guinan constitutive model has a better performance in the macro-level simulation. The free-surface velocity curves at different strain rates were obtained by changing the loading conditions, and the typical characteristics of the free-surface velocity curves at different strain rates were discussed. Results show that there is an exponential relationship between spall strength and strain rate, and the spall strength obtained from the simulation has a good agreement with the experimental data. On the micro-scale, the damage evolution in the spallation region was obtained by molecular dynamics simulation conducted in the LAMMPS software, and the loading strain rate was consistent with that on the macro-scale. The micro-scale simulation reveals the physical connotation of the typical characteristics of the macro-scale free-surface velocity curve. Micro-scale analysis shows that spallation is the response of damage evolution of nucleation, growth, and aggregation of voids. From the multi-scale perspective analysis, the typical characteristics on the free-surface velocity curve are closely related to the damage evolution in the spallation area: the pullback signal is a macroscopic response of the void nucleation in the spall area; the decline amplitude of the free-surface velocity curve reflects the void nucleation condition, and the spall strength reflects the nucleation strength of the voids. What’s more, the velocity rises to the first peak beyond the minima after the pullback signal reflects the rate of damage evolution. The multi-scale perspective analysis is helpful to fully understand the physical mechanism of the spallation under planar-plate impact.

Coarse-grained molecular dynamics simulations of clay compression

This paper outlines a framework for using molecular dynamics to simulate the compression of kaolinite saturated at alkaline pH (=8) in a low (1 mM) concentration solution. The particles are modelled as flat (3D) ellipsoids and their interactions are described by a modified form of the Gay-Berne potential, calibrated against DLVO theory. The LAMMPS software was used to generate monodisperse and slightly polydisperse samples, and to simulate isotropic compression to 100 kPa. The influences of sample size and strain rate on the void ratio and the arrangement of particles within the samples were investigated via parametric studies. It is useful to consider the extent to which the system temperature (a measure of the average kinetic energy) is controlled when assessing whether the applied strain rate is appropriate. It is found that the number of particles that can be considered a representative element volume is orders of magnitude larger than the number simulated in earlier studies and that larger number of particles are required in polydisperse samples than in the monodisperse case. A comparison between the results obtained and those of published experimental studies show that the methodology proposed can deliver sensible results for the material considered.

Theory for designing mechanically stable single- and double-walled SiGe nanopeapods

Herein, we utilized molecular dynamic (MD) simulations using LAMMPS software and selecting Tersoff and Lennard-Jones potentials to design and investigate mechanical properties of (8,8), (9,9), (10,10), and (11,11) single-walled and (8,8)@(11,11) double-walled silicon-germanium (SiGe) armchair nanopeapods. The number of encapsulated fullerenes and the working temperature were changed as variables to evaluate the mechanical properties. The larger nanopeapods had lower Young's modulus and failure strain, but, surprisingly enough, no significant variation was found in failure strain values by increasing the number of Si30Ge30 cages and the temperature (300-900K). Overall, higher mechanical properties were the case for double-walled SiGe nanopeapods and that the more the number of encapsulated cages, the lower the mechanical properties whatever the nanopeapod. Amazingly, fullerenes remained undamaged even after the SiGe nanopeapods ruptured. Thus, thermally/mechanically stable nanopeapods developed theoretically herein can be considered potential super-carriers for drug and gene encapsulation.

Comprehensive approach to determination of space proton-induced displacement defects in silica optical fiber

Silica-based optical fibers presents a variety of applications used in radiation environments such as space, fusion facilities, accelerators and nuclear power plants. The radiation-induced displacement damage in optical fibers resulting in point defects may lead to attenuation signals that is a major concern for these applications. The present study proposes a computational approach to the calculation of the proton-induced displacement damage in vitreous silica. Therefore, Geant4 as a Monte Carlo particle transport code has been used to obtain the knock-on atom distributions caused by the interaction of space trapped proton with vitreous silica during an ISS mission. Moreover, molecular dynamics simulations using ReaxFF potential have been performed to produce the initial vitreous silica structure to evaluate the displacement damage cascades by LAMMPS package. The results show that ReaxFF has an appropriate potential to produce and evaluate the vitreous silica structure that provides better agreement with experimental data at both short-range and medium-range order. Furthermore, ODC(Si3) and NBOHC(O1) are dominant defect species created in the vitreous silica after trapped proton irradiation, where the total number of defects have increased on average by 94 for each keV increasing in PKA energy approximately.

Effects of copper nanoparticles on elastic and thermal properties of conductive polymer nanocomposites

Metallic nanoparticles are extensively used to enhance the thermal and electrical conductivity of polymer nanocomposites. However, despite many experimental studies on such composite materials, their computational analysis has remained unexplored to a large extent. In this study, we investigate the effects of cylindrical and spherical copper nanoparticles on the mechanical and thermal properties of polyethylene matrix using molecular dynamics and finite element methods. To calculate the density of the interphase zone and consequently, its elastic and thermal properties, LAMMPS package is used considering AIREBO, EAM, and Lennard‐Jones potential functions to model the interactions between nanocomposite components. Afterward, three-dimensional finite element modeling is done to obtain Young's modulus and thermal conductivity of the studied nanocomposites for different geometries, orientations, and volume fractions of nano-fillers. The results reveal that reinforcing polymer with copper nanofillers improves its thermal conductivity and elastic modulus, remarkably. Besides, nanoparticles with cylindrical geometry and [1 1 1] axial crystallographic orientation have a greater effect on the enhancement of properties than other orientations or spherical nanoparticles. Furthermore, the orientation of the nanoparticles inside the matrix in the direction of applied force and heat flux has the greatest impact on improving the properties of polymers compared to the other directions.

Phonon dispersion relations of crystalline solids based on LAMMPS package* *Project supported by the National Key R&D Program of China (Grant No. 2017YFB0406000) and the Southeast University “Zhongying Young Scholars” Project.

The phonon dispersion relations of crystalline solids play an important role in determining the mechanical and thermal properties of materials. The phonon dispersion relation, as well as the vibrational density of states, is also often used as an indicator of variation of lattice thermal conductivity with the external stress, defects, etc. In this study, a simple and fast tool is proposed to acquire the phonon dispersion relation of crystalline solids based on the LAMMPS package. The theoretical details for the calculation of the phonon dispersion relation are derived mathematically and the computational flow chart is present. The tool is first used to calculate the phonon dispersion relation of graphene with two atoms in the unit cell. Then, the phonon dispersions corresponding to several potentials or force fields, which are commonly used in the LAMMPS package to modeling the graphene, are obtained to compare with that from the DFT calculation. They are further extended to evaluate the accuracy of the used potentials before the molecular dynamics simulation. The tool is also used to calculate the phonon dispersion relation of superlattice structures that contains more than one hundred of atoms in the unit cell, which predicts the phonon band gaps along the cross-plane direction. Since the phonon dispersion relation plays an important role in the physical properties of condensed matter, the proposed tool for the calculation of the phonon dispersion relation is of great significance for predicting and explaining the mechanical and thermal properties of crystalline solids.

Static and dynamic buckling behavior of CNTS with S-W defects

The excellent performance of carbon nanotubes (CNTs) allows them to be widely employed in various micro- and nano-electromechanical devices. However, different imperfections such as Stone–Wales (S-W) defects often arise in these structures during the preparation process. In this paper, special attention is paid to the effects of the number and location of defects as well as the diameter and chiral angle of CNTs on the static and dynamic buckling of CNTs with S-W defects. First, LAMMPS software is used to simulate the molecular dynamics (MDs) of CNTs with S-W defects, and their static buckling performances are discussed. Then based on the static buckling data, the dynamic buckling vibration performance of CNTs with S-W defects is analyzed in the context of the nonlocal elastic theory. Finally, the effective range of nonlocal parameters is established via the MD modeling. The results show that the existence of S-W defects will reduce the buckling performance and vibration characteristics of CNTs, and an increase in the number of defects will aggravate the influence of diameter and chiral angle on the buckling performance as well as the natural frequency and amplitude of the nanotube’s axial vibration.

The molecular dynamics study of aluminum nanoparticles effect on the atomic behavior of argon atoms inside zigzag nanochannel

Aluminum (Al) nanoparticles effects on the atomic behavior of Argon (Ar) fluid inside the zigzag nanochannel are described in this study. For this purpose, Molecular Dynamics (MD) approach is used with a LAMMPS package. Computationally, Ar base fluid and ArAl nanofluid is modeled with Universal Force Field (UFF) and Embedded Atom Model (EAM). Total energy, density, velocity, and temperature profiles for the atomic behavior of base fluid/nanofluid are presented. Results show that the Al nanoparticles cause increasing of the density, velocity, and temperature profiles value to 0.106 atom/Å3, 0.044 Å/ps, and 551.02 K, respectively. So we conclude the Al nanoparticles adding to Ar atoms in non-ideal (zigzag) nanochannel can change atomic behavior of the base fluid effectively and optimize the Ar performance for heat/mass transfer applications.

The effects of external force and electrical field on the agglomeration of Fe3O4 nanoparticles in electroosmotic flows in microchannels using molecular dynamics simulation

Recent progress in nanoparticle construction can be seen as a breakthrough in increasing heat transfer methods. The small size of particles and low volume fraction of particles leads to solving agglomeration and pressure drop problems and reduce the cost of storing and transporting nanofluids. Molecular dynamics simulation is one of the essential branches of computational physics that can predict various structures' atomic behavior. In this study, the effects of external electrostatic force and external electrical field on the density, velocity, temperature of atomic structures, and agglomeration of Fe3O4 nanoparticles in a copper microchannel are investigated. The results of the physical properties of this structure are estimated using molecular dynamics simulation and LAMMPS software. The results show that with increasing the applied external electrostatic force the maximum velocity is converged to 0.0071 Å /ps. Also, adding an external electrical field to the simulated nanofluid, the maximum values of density, velocity, and temperature are estimated to 1.32 g/cm3, 0.0078 Å /ps, and 345 K, respectively. The external electrical field has a significant and essential role in the agglomeration process in atomic structures. Finally, it is observed that by increasing the external electrical field, the time required for the agglomeration process increases to 2.26 ns.

Atomistic Simulation Study of Mechanical Deformation of Al-Mg-Si Alloys

Aluminum alloys have been attracting significant attention. Especially Al-Mg-Si alloys can exhibit an excellent balance between strength and ductility. Deformation mechanisms and microstructural evolution are still challenging issues. Accordingly, to describe how the type of phase influence mechanical behaviour of Al/Mg/Si alloys, in this paper atomic simulations are performed to investigate the uniaxial compressive behaviour of Al-Mg-Si ternary phases. The compression is at the same strain rate (3.1010 s−1); using Modified Embedded Atom Method (MEAM) potential to model the deformation behaviour. From these simulations, we get the total radial distribution function; the stress-strain responses to describe the elastic and plastic behaviors of GP-AlMg4Si6, U2-Al4Mg4Si4 and β-Al3Mg2Si6 phases. For a Detailed description of which phase influence hardness and ductility of these alloys; the mechanical properties are determined and presented. These stress-strain curves obtained show a rapid increase in stress up to a maximum followed by a gradual drop when the specimen fails by ductile fracture. From the results, it was found that GP-AlMg4Si6 & U2-Al4Mg4Si4 phases are brittle under uniaxial compressive loading while β-Al3Mg2Si6 phase is very ductile under the same compressive loading. The engineering stress-strain relationship suggests that β-Al3Mg2Si6 phase have high elasticity limit, ability to resist deformation and have the advantage of being highly malleable. Molecular dynamics software LAMMPS was used to simulate and build the Al-Mg-Si ternary system.

A Random Batch Ewald Method for Charged Particles in the Isothermal-Isobaric Ensemble

We develop an accurate, highly efficient and scalable random batch Ewald (RBE) method to conduct simulations in the isothermal-isobaric ensemble (the NPT ensemble) for charged particles in a periodic box. After discretizing the Langevin equations of motion derived using suitable Lagrangians, the RBE method builds the mini-batch strategy into the Fourier space in the Ewald summation for the pressure and forces so the computational cost is reduced from $\mathcal{O}(N^2)$ to $\mathcal{O}(N)$ per time step. We implement the method in the LAMMPS package and report accurate simulation results for both dynamical quantities and statistics for equilibrium for typical systems including all-atom bulk water and a semi-isotropic membrane system. Numerical simulations on massive supercomputing cluster are also performed to show promising CPU efficiency of RBE.

Molecular dynamics simulation concerning nanofluid boiling phenomenon affected by the external electric field: Effects of number of nanoparticles through Pt, Fe, and Au microchannels

The present work was conducted to estimate the effects of the electric field on H2O/Fe3O4 nanofluid dynamical behavior in an atomic microchannel. The physical attributes of these structures were simulated using the LAMMPS package. Certain physical parameters were recorded, such as kinetic energy, potential/atom energy, radial distribution function, density, temperature, and velocity profiles of nanofluid in various microchannels structure. Enhancing the outer electric field resulted in boiling phenomena in H2O/Fe3O4 nanofluid in a shorter time. Furthermore, our findings revealed that the strength of the outer electric field is an essential factor in nanofluid atomic behavior. Numerically, by external electric field strength enhancing, the highest values of velocity, density, and temperature reach to 0.038 g/cm3, 0.083 Å/ps, and 714 K. Also, the boiling phenomena in nanofluid structure occurred after 0.5 ns, 0.25 ns, and 0.21 ns.

Structural and transport properties for the superionic conductors AgI and RbAg4I5 through molecular dynamic simulation

AgI and RbAg4I5 are the typical superionic conductors. In this work, molecular dynamics (MD) simulations were performed to obtain their structural (radial and pair distribution function) and dynamic transport properties (mean square displacements, MSD). For AgI, with bcc structure, a pairwise potential based on Coulomb–Buckingham potential, NV E (increasing T), NPT (decreasing T) ensembles, MD steps (MDS) of 0.175 × 105, and the LAMMPS package were used. The temperature was increased 100 K above the melting temperature and when decreased. The MSD as a function of time of Ag-ions and I-ions shows the same behavior. For RbAg4I5, P4132 as space group, a new interatomic potential, NV E ensemble, MDS = 105, and the Moldy package at room temperature were used. The MSD of Rb-ions and I-ions shows a liquid-like behavior, and the Ag-ions are the highest mobility. Better results for the PDF and MSD were achieved, which is in good agreement with experimental data.

Molecular Dynamics Simulation of a Superhydrophobic Cellulose Derivative Targeted for Eco‐Friendly Packaging Material

AbstractA major issue concerned with using synthetic polymers as packaging materials is the difficulty in the disposal or reuse which in turn is leading to environmental pollution. Design of eco‐friendly alternative materials or modified polymers is being done to overcome or address this issue. In this article, a design is proposed of a new cellulose derivative which consists of cellulose layered with nonacosan‐10‐ol and nonacosane‐5,10‐diol molecules targeted toward achieving superior nonwettability while assuring both physical strength and reusability. An atomistic model of this new material (called as Adulose from now) that had 24 cellulose chains and 48 molecules of each of the other wax materials is used in this study. Molecular dynamic simulations are performed on this material using LAMMPS software at 0 atm and 300 K for an isothermal‐isobaric ensemble. The stress–strain behavior is studied by conducting deformation simulations while the contact angle simulations of this material are evaluated to confirm the nonwettability (or hydrophobicity). Preliminary simulations show that Adulose has very good mechanical properties like its ultimate stress value is almost similar to that of polyethylene and an average contact angle of over 150° is achieved from the simulations.

Stochastic Constrained Extended System Dynamics for Solving Charge Equilibration Models.

We present a new stochastic extended Lagrangian molecular dynamics solution to charge equilibration that eliminates self-consistent field (SCF) calculations, thus eliminating the computational bottleneck in solving the charge distribution with standard SCF solvers. By formulating both charges and chemical potential as latent variables and introducing a holonomic constraint that satisfies charge conservation, the SC-XLMD method accurately reproduces thermodynamic, dynamic, and structural properties within the framework of ReaxFF for a bulk water system and highly reactive RDX molecules simulated at high temperature. The SC-XLMD method shows excellent computational performance and is available in the publicly available LAMMPS package.

Atomistic strain and structural analysis of 120 MeV Ni ions irradiated CdSe nanocrystals through molecular dynamics simulation method

Swift heavy ion (SHI) irradiation modifies the physical and chemical properties of semiconductor sample like CdSe nanocrystals by inducing vacancies and structural change in the lattice system. Here, the atomistic strain analysis has been performed using molecular dynamics (MD) simulation on the SHI irradiated CdSe nanocrystals by approximating interatomic interaction as (ZBL) potential. MD simulation based on LAMMPS package has been employed for better understanding the time response of the sample with swift heavy ion irradiation. The primary knock-on atom (PKA) method has been used for the simulation that starts the cascade of energy transfer, which triggers the displacement of atoms. Initial parameters of PKA have been obtained from the SRIM simulation of the irradiation effect of 120 MeV Ni ions. Finally, the time evolution of the system has been studied.

The molecular dynamics simulation of thermal manner of Ar/Cu nanofluid flow: The effects of spherical barriers size

In this computational work, we focus on spherical barrier effects on the thermal behaviour of Ar/Cu nanofluid with molecular dynamics simulation. LAMMPS software is implemented in our study with Universal Force Field and Embedded Atom Model force field for various atomic structures in the simulation box. The thermal behaviour study of Ar/Cu nanofluid is done with physical parameters calculations such as atomic temperature, total energy, number of nanofluid atoms at gas phase, radial distribution function, and thermal conductivity of Ar/Cu nanofluid. By atomic barrier adding to our simulated plates, the atomic phase transition occurs in fewer time steps. Numerically, phase transition in the simulated nanofluid occurs in 610,000-time steps by Pt spherical barriers simulation (with 15 Å radius). By increasing the atomic barrier size, the number of nanofluid atoms in which phase transition occur in them is increased. From these simulations results, we conclude that, heat flux in Ar/Cu nanofluid increases but thermal conductivity of the foremost constant. Numerically, the thermal conductivity of Ar/Cu nanofluid reaches to 0.016 W/m.K by atomic barrier radius increasing to 15 Å.

Structure and Energy of 〈110〉 Symmetric Tilt Boundaries in Polycrystalline Tungsten

A computer simulation of the structure and energy of 〈110〉 symmetric tilt boundaries has been performed for polycrystalline tungsten. Calculations have been made using an embedded atom potential implemented in the LAMMPS software. It has been shown that structure of the 〈110〉 symmetric tilt boundaries can consist of a limited number of structural elements. The energy and width of grain boundaries for different misorientations, as well as energies of vacancy formation have been determined via molecular statistics simulation of grain boundaries. The correlation between the energy of vacancy formation in grain boundaries and changes in the boundary structure has been analyzed.