How to Modify LAMMPS: From the Prospective of a Particle Method Researcher

LAMMPS is a powerful simulator originally developed for molecular dynamics that, today, also accounts for other particle-based algorithms such as DEM, SPH, or Peridynamics. The versatility of this software is further enhanced by the fact that it is open-source and modifiable by users. This property suits particularly well Discrete Multiphysics and hybrid models that combine multiple particle methods in the same simulation. Modifying LAMMPS can be challenging for researchers with little coding experience. The available material explaining how to modify LAMMPS is either too basic or too advanced for the average researcher. In this work, we provide several examples, with increasing level of complexity, suitable for researchers and practitioners in physics and engineering, who are familiar with coding without been experts. For each feature, step by step instructions for implementing them in LAMMPS are shown to allow researchers to easily follow the procedure and compile a new version of the code. The aim is to fill a gap in the literature with particular reference to the scientific community that uses particle methods for (discrete) multiphysics.

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Open-Source Accelerated Vortex Particle Methods for Unsteady Flow Simulation

Volume 3: Computational Fluid Dynamics; Micro and Nano Fluid Dynamics ◽

10.1115/fedsm2020-20486 ◽

2020 ◽

Author(s):

Mark J. Stock ◽

Adrin Gharakhani

Keyword(s):

Open Source ◽

Hybrid Approach ◽

Flow Simulation ◽

Hardware Acceleration ◽

Particle Method ◽

Boundary Region ◽

Particle Methods ◽

Vortex Particle Method ◽

Vorticity Transport ◽

Vortex Particle

Abstract A new open-source CFD solver is being developed based on the vorticity transport equations for simulation of unsteady incompressible flow in complex geometries. This is a hybrid approach, which uses a compact high-order finite-difference method to predict the flow in the near-boundary region and a Lagrangian Vortex Particle Method (LVPM) for the off-boundary vorticity-containing region. This paper focuses on the latter, presenting the particular LVPM implemented in the package and demonstrating selected benchmarks from simulations of flow in 2D lid-driven cavity, flow around a rotating cylinder (both at Re = 1,000), and impulsively started flow over a sphere at Re = 25, 40, 60, 80, 100. In addition, novel ideas on the development of an efficient and lightweight Graphical User Interface (GUI), as well as new approaches to cross-platform hardware acceleration for Teraflop/s computing on a desktop — achieving over two orders of magnitude speedup vs. an optimized serial code — are discussed.

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Numerical Methods for the Kinetic Theory of Fluids

10.1093/oso/9780199592357.003.0010 ◽

2018 ◽

Author(s):

Sauro Succi

Keyword(s):

Molecular Dynamics ◽

Monte Carlo ◽

Numerical Methods ◽

Kinetic Theory ◽

Computational Efficiency ◽

Lattice Boltzmann ◽

Direct Simulation Monte Carlo ◽

Particle Methods ◽

Direct Simulation ◽

Simulation Monte Carlo

This chapter provides a bird’s eye view of the main numerical particle methods used in the kinetic theory of fluids, the main purpose being of locating Lattice Boltzmann in the broader context of computational kinetic theory. The leading numerical methods for dense and rarified fluids are Molecular Dynamics (MD) and Direct Simulation Monte Carlo (DSMC), respectively. These methods date of the mid 50s and 60s, respectively, and, ever since, they have undergone a series of impressive developments and refinements which have turned them in major tools of investigation, discovery and design. However, they are both very demanding on computational grounds, which motivates a ceaseless demand for new and improved variants aimed at enhancing their computational efficiency without losing physical fidelity and vice versa, enhance their physical fidelity without compromising computational viability.

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Optimization of Moving Particle Semi-Implicit (MPS) Method and Studying of Flow Instability

Volume 8: Computational Fluid Dynamics (CFD); Nuclear Education and Public Acceptance ◽

10.1115/icone26-81948 ◽

2018 ◽

Author(s):

Kailun Guo ◽

Ronghua Chen ◽

Suizheng Qiu ◽

Wenxi Tian ◽

Guanghui Su ◽

...

Keyword(s):

Multiphase Flows ◽

Flow Instability ◽

Free Particle ◽

Particle Method ◽

Severe Accident ◽

Particle Methods ◽

Two Phase ◽

Mps Method ◽

Viscosity Term ◽

Moving Particle

Multiphase flow widely exists in the nature and engineering. The two-phase flow is the highlight of the studies about the flow in the vessel and steam explosion in nuclear severe accidents. The Moving Particle Semi-implicit (MPS) method is a fully-Lagrangian particle method without grid mesh which focuses on tracking the single particle and concerns with its movement. It has advantages in tracking complex multiphase flows compared with gird methods, and thus shows great potential in predicting multiphase flows. The objective of this thesis is to develop a general multiphase particle method based on the original MPS method and thus this work is of great significance for improving the numerical method for simulating the instability in reactor severe accident and two-phase flows in vessel. This research is intended to provide a study of the instability based on the MPS method. Latest achievements of mesh-free particle methods in instability are researched and a new multiphase MPS method, which is based on the original one, for simulating instability has been developed and validated. Based on referring to other researchers’ papers, the Pressure Poisson Equation (PPE), the viscosity term, the free surface particle determination part and the surface tension model are optimized or added. The numerical simulation on stratification behavior of two immiscible flows is carried out and results are analyzed after data processing. It is proved that the improved MPS method is more accurate than the original method in analysis of multiphase flows. In this paper, the main purposes are simulating and discussing Rayleigh-Taylor (R-T) instability and Kelvin-Helmholtz (K-H) instability. R-T and K-H instability play an important role in the mixing process of many layered flows. R-T instability occurs when a lower density fluid is supported by another density higher fluid or higher density fluid is accelerated by lower density fluid, and the resulting small perturbation increases and eventually forms turbulence. K-H instability is a small disturbance for two different densities, such as waves, at the interface of the two-phase fluid after giving a fixed acceleration in the fluid. Turbulence generated by R-T instability and K-H instability has an important effect in applications such as astrophysics, geophysics, and nuclear science.

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3D Simulation of Molten Metal Freezing Behaviour Using Finite Volume Particle Method

18th International Conference on Nuclear Engineering: Volume 2 ◽

10.1115/icone18-29198 ◽

2010 ◽

Author(s):

Rida S. N. Mahmudah ◽

Masahiro Kumabe ◽

Takahito Suzuki ◽

LianCheng Guo ◽

Koji Morita ◽

...

Keyword(s):

Molten Metal ◽

Finite Volume ◽

Particle Method ◽

Metal Structure ◽

Freezing Behavior ◽

Severe Accident ◽

Particle Methods ◽

Freezing Process ◽

Penetration Length ◽

Moving Particle

Understanding the freezing behavior of molten metal in flow channels is of importance for severe accident analysis of liquid metal reactors. In order to simulate its fundamental behavior, a 3D fluid dynamics code was developed using Finite Volume Particle (FVP) method, which is one of the moving particle methods. This method, which is fully Lagrangian particle method, assumes that each moving particle occupies certain volume. The governing equations that determine the phase change process are solved by discretizing its gradient and Laplacian terms with the moving particles. The motions of each particle and heat transfer between particles are calculated through interaction with its neighboring particles. A series of experiments for fundamental freezing behavior of molten metal during penetration on to a metal structure was also performed to provide data for the validation of the developed code. The comparison between simulation and experimental results indicates that the present 3D code using the FVP method can successfully reproduce the observed freezing process such as molten metal temperature profile, frozen molten metal shape and its penetration length on the metal structure.

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Continuum and Molecular Dynamics Studies of the Hydrodynamics of Colloids Straddling a Fluid Interface

Annual Review of Fluid Mechanics ◽

10.1146/annurev-fluid-032621-043917 ◽

2021 ◽

Vol 54 (1) ◽

Author(s):

Charles Maldarelli ◽

Nicole T. Donovan ◽

Subramaniam Chembai Ganesh ◽

Subhabrata Das ◽

Joel Koplik

Keyword(s):

Molecular Dynamics ◽

Characteristic Size ◽

Two Dimensions ◽

Annual Review ◽

Publication Date ◽

Fluid Interfaces ◽

Particle Interactions ◽

Fluid Interface ◽

Interfacial Energies ◽

Multiple Particle

Colloid-sized particles (10 nm–10 μm in characteristic size) adsorb onto fluid interfaces, where they minimize their interfacial energy by straddling the surface, immersing themselves partly in each phase bounding the interface. The energy minimum achieved by relocation to the surface can be orders of magnitude greater than the thermal energy, effectively trapping the particles into monolayers, allowing them freedom only to translate and rotate along the surface. Particles adsorbed at interfaces are models for the understanding of the dynamics and assembly of particles in two dimensions and have broad technological applications, importantly in foam and emulsion science and in the bottom-up fabrication of new materials based on their monolayer assemblies. In this review, the hydrodynamics of the colloid motion along the surface is examined from both continuum and molecular dynamics frameworks. The interfacial energies of adsorbed particles is discussed first, followed by the hydrodynamics, starting with isolated particles followed by pairwise and multiple particle interactions. The effect of particle shape is emphasized, and the role played by the immersion depth and the surface rheology is discussed; experiments illustrating the applicability of the hydrodynamic studies are also examined. Expected final online publication date for the Annual Review of Fluid Mechanics, Volume 54 is January 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

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Solution-Responsive Particle Size Adaptivity in Lagrangian Vortex Particle Methods

10.1115/fedsm2021-65621 ◽

2021 ◽

Author(s):

Mark J. Stock ◽

Adrin Gharakhani

Keyword(s):

Particle Size ◽

Particle Method ◽

Adaptive Method ◽

Particle Methods ◽

Core Size ◽

Large Particle Size ◽

The Core ◽

Vortex Particle Method ◽

Computational Resources ◽

Vortex Particle

Abstract In order to minimize the computational resources necessary for a given level of accuracy in a Lagrangian Vortex Particle Method, a novel particle core size adaptivity scheme has been created. The method adapts locally to the solution while preventing large particle size gradients, and optionally adapts globally to focus effort on important regions. It is implemented in the diffusion solver, which uses the Vorticity Redistribution Method, by allowing and accounting for variations in the core radius of participating particles. We demonstrate the effectiveness of this new method on the diffusion of a δ-function and impulsively started flow over a circular cylinder at Re = 9,500. In each case, the adaptive method provides solutions with marginal loss of accuracy but with substantially fewer computational elements.

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Scientific Authorship and E-commons

Thinking Machines and the Philosophy of Computer Science ◽

10.4018/978-1-61692-014-2.ch012 ◽

2010 ◽

pp. 193-205

Author(s):

Luc Schneider

Keyword(s):

Open Access ◽

Open Source ◽

Scientific Knowledge ◽

Scientific Community ◽

Scientific Literature ◽

Source Model ◽

Public Domain ◽

Scientific Publications ◽

Scientific Authorship ◽

The Web

This contribution tries to assess how the Web is changing the ways in which scientific knowledge is produced, distributed and evaluated, in particular how it is transforming the conventional conception of scientific authorship. After having properly introduced the notions of copyright, public domain and (e-)commons, I will critically assess James Boyle's (2003, 2008) thesis that copyright and scientific (e-) commons are antagonistic, but I will mostly agree with the related claim by Stevan Harnad (2001a,b, 2008) that copyright has become an obstacle to the accessibility of scientific works. I will even go further and argue that Open Access schemes not only solve the problem of the availability of scientific literature, but may also help to tackle the uncontrolled multiplication of scientific publications, since these publishing schemes are based on free public licenses allowing for (acknowledged) re-use of texts. However, the scientific community does not seem to be prepared yet to move towards an Open Source model of authorship, probably due to concerns related to attributing credit and responsability for the expressed hypotheses and results. Some strategies and tools that may encourage a change of academic mentality in favour of a conception of scientific authorship modelled on the Open Source paradigm are discussed.

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A physically consistent particle method for incompressible fluid flow calculation

Computational Particle Mechanics ◽

10.1007/s40571-020-00313-w ◽

2020 ◽

Author(s):

Masahiro Kondo

Keyword(s):

Mechanical Energy ◽

Particle Method ◽

Free Surface Flow ◽

Surface Flow ◽

Particle Methods ◽

Analytical Mechanics ◽

Time Step ◽

Consistent System ◽

Energy Behavior ◽

Dissipation Property

AbstractIn general, mechanical energy monotonically decreases in a physically consistent system, constructed with conservative force and dissipative force. This feature is important in designing a particle method, which is a discrete system approximating continuum fluid with particles. When the discretized system can be fit into a framework of analytical mechanics, it will be a physically consistent system which prevents instability like particle scattering along with unphysical mechanical energy increase. This is the case also in incompressible particle methods. However, most incompressible particle methods do not satisfy the physical consistency, and they need empirical relaxations to suppress the system instability due to the unphysical energy behavior. In this study, a new incompressible particle method with the physical consistency, moving particle full-implicit (MPFI) method, is developed, where the discretized interaction forces are related to an analytical mechanical framework for the systems with dissipation. Moreover, a new pressure evaluation technique based on the virial theorem is proposed for the system. Using the MPFI method, static pressure, droplet extension, standing wave and dam break calculations were conducted. The capability to predict pressure and motion of incompressible free surface flow was presented, and energy dissipation property depending on the particle size and time step width was studied through the calculations.

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