Developing community codes for materials modeling

For this article, we call scientific software a community code if it is freely available, written by a team of developers who welcome user input, and has attracted users beyond the developers. There are obviously many such materials modeling codes. The authors have been part of such efforts for many years in the field of atomistic simulation, specifically for two community codes, the LAMMPS and GULP packages for molecular dynamics and lattice dynamics respectively. Here we highlight lessons we have learned about how to create such codes and the pros and cons of being part of a community effort. Many of our experiences are similar, but we also have some differences of opinion (like modeling vs modelling). Our hope is that readers will find these lessons useful as they design, implement, and distribute their own materials modelling software for others to use

Molecular-dynamics simulations of stacking-fault-induced dislocation annihilation in pre-strained ultrathin single-crystalline copper films

We report results of large-scale molecular-dynamics (MD) simulations of dynamic deformation under biaxial tensile strain of pre-strained single-crystalline nanometer-scale-thick face-centered cubic (fcc) copper films. Our results show that stacking faults, which are abundantly present in fcc metals, may play a significant role in the dissociation, cross-slip, and eventual annihilation of dislocations in small-volume structures of fcc metals. The underlying mechanisms are mediated by interactions within and between extended dislocations that lead to annihilation of Shockley partial dislocations or formation of perfect dislocations. Our findings demonstrate dislocation starvation in small-volume structures with ultra-thin film geometry, governed by a mechanism other than dislocation escape to free surfaces, and underline the significant role of geometry in determining the mechanical response of metallic small-volume structures.Comment: 28 pages, 3 figure

Equilibration of Long Chain Polymer Melts in Computer Simulations

Several methods for preparing well equilibrated melts of long chains polymers are studied. We show that the standard method in which one starts with an ensemble of chains with the correct end-to-end distance arranged randomly in the simulation cell and introduces the excluded volume rapidly, leads to deformation on short length scales. This deformation is strongest for long chains and relaxes only after the chains have moved their own size. Two methods are shown to overcome this local deformation of the chains. One method is to first pre-pack the Gaussian chains, which reduces the density fluctuations in the system, followed by a gradual introduction of the excluded volume. The second method is a double-pivot algorithm in which new bonds are formed across a pair of chains, creating two new chains each substantially different from the original. We demonstrate the effectiveness of these methods for a linear bead spring polymer model with both zero and nonzero bending stiffness, however the methods are applicable to more complex architectures such as branched and star polymer.Comment: 12 pages, 9 figure

Second Chance Language Learning: A study of what the slow language learner\u27s problems are, why they exist, and how to give the slow language learner help on a remedial basis.

In the course of our paper , we will discuss theories of why the problem of the slow language learner exists, what the problem was for our specific situation and how we personally dealt with the problem(s). Realizing that other teachers will not be facing the same physical situation we did, (that of teaching ESL to Greek students at a private Greek high school in Thessaloniki, Greece) we will discuss alternatives concerning physical facilities needed for remedial help. Lastly, we offer an annotated listing of resources dealing with these students; and suggestions for the practical application of materials and methods to facilitate the remedial student in his learning

Effects of Cutoff Functions of Tersoff Potentials on Molecular Dynamics Simulations of Thermal Transport

Past molecular dynamics studies of thermal transport have predominantly used Stillinger-Weber potentials. As materials continuously shrink, their properties increasingly depend on defect and surface effects. Unfortunately, Stillinger-Weber potentials are best used for diamond-cubic-like bulk crystals. They cannot represent the energies of many metastable phases, nor can they accurately predict the energetics of defective and surface regions. To study nanostructured materials, where these regions can dominate thermal transport, the accuracy of Tersoff potentials in representing these structures is more desirable. Based upon an analysis of thermal transport in a GaN system, we demonstrate that the cutoff function of the existing Tersoff potentials may lead to problems in determining the thermal conductivity. To remedy this issue, improved cutoff schemes are proposed and evaluated

Evaporation of Lennard-Jones Fluids

Evaporation and condensation at a liquid/vapor interface are ubiquitous interphase mass and energy transfer phenomena that are still not well understood. We have carried out large scale molecular dynamics simulations of Lennard-Jones (LJ) fluids composed of monomers, dimers, or trimers to investigate these processes with molecular detail. For LJ monomers in contact with a vacuum, the evaporation rate is found to be very high with significant evaporative cooling and an accompanying density gradient in the liquid domain near the liquid/vapor interface. Increasing the chain length to just dimers significantly reduces the evaporation rate. We confirm that mechanical equilibrium plays a key role in determining the evaporation rate and the density and temperature profiles across the liquid/vapor interface. The velocity distributions of evaporated molecules and the evaporation and condensation coefficients are measured and compared to the predictions of an existing model based on kinetic theory of gases. Our results indicate that for both monatomic and polyatomic molecules, the evaporation and condensation coefficients are equal when systems are not far from equilibrium and smaller than one, and decrease with increasing temperature. For the same reduced temperature $T/T_c$, where $T_c$ is the critical temperature, these two coefficients are higher for LJ dimers and trimers than for monomers, in contrast to the traditional viewpoint that they are close to unity for monatomic molecules and decrease for polyatomic molecules. Furthermore, data for the two coefficients collapse onto a master curve when plotted against a translational length ratio between the liquid and vapor phase.Comment: revised version, 15 pages, 15 figures, to appear in J. Chem. Phy

Simulation and experimental study of rheological properties of CeO2 – water nanofluid

Open Access. This article is distributed under the terms of the Creative Commons Attribution License which permits any use, distribution, and reproduction in any medium, provided the original author(s) and the source are credited.Metal oxide nanoparticles offer great merits over controlling rheological, thermal, chemical and physical properties of solutions. The effectiveness of a nanoparticle to modify the properties of a fluid depends on its diffusive properties with respect to the fluid. In this study, rheological properties of aqueous fluids (i.e. water) were enhanced with the addition of CeO2 nanoparticles. This study was characterized by the outcomes of simulation and experimental results of nanofluids. The movement of nanoparticles in the fluidic media was simulated by a large-scale molecular thermal dynamic program (i.e. LAMMPS). The COMPASS force field was employed with smoothed particle hydrodynamic potential (SPH) and discrete particle dynamics potential (DPD). However, this study develops the understanding of how the rheological properties are affected due to the addition of nanoparticles in a fluid and the way DPD and SPH can be used for accurately estimating the rheological properties with Brownian effect. The rheological results of the simulation were confirmed by the convergence of the stress autocorrelation function, whereas experimental properties were measured using a rheometer. These rheological values of simulation were obtained and agreed within 5 % of the experimental values; they were identified and treated with a number of iterations and experimental tests. The results of the experiment and simulation show that 10 % CeO2 nanoparticles dispersion in water has a viscosity of 2.0–3.3 mPasPeer reviewedFinal Published versio

Sensitivity analysis of a computational model of the IKK-NF-{\kappa}B-I{\kappa}B{\alpha}-A20 signal transduction network

The NF-{\kappa}B signaling network plays an important role in many different compartments of the immune system during immune activation. Using a computational model of the NF-{\kappa}B signaling network involving two negative regulators, I{\kappa}B{\alpha} and A20, we performed sensitivity analyses with three different sampling methods and present a ranking of the kinetic rate variables by the strength of their influence on the NF-{\kappa}B signaling response. We also present a classification of temporal response profiles of nuclear NF-{\kappa}B concentration into six clusters, which can be regrouped to three biologically relevant clusters. Lastly, based upon the ranking, we constructed a reduced network of the IKK-NF-{\kappa}B-I{\kappa}B{\alpha}-A20 signal transduction.Comment: 32 pages, 8 figure

Understanding the Scalability of Molecular Simulation Using Empirical Performance Modeling

The final authenticated publication is available online at https://doi.org/10.1007/978-3-030-17872-7_8.Molecular dynamics (MD) simulation allows for the study of static and dynamic properties of molecular ensembles at various molecular scales, from monatomics to macromolecules such as proteins and nucleic acids. It has applications in biology, materials science, biochemistry, and biophysics. Recent developments in simulation techniques spurred the emergence of the computational molecular engineering (CME) field, which focuses specifically on the needs of industrial users in engineering. Within CME, the simulation code ms2 allows users to calculate thermodynamic properties of bulk fluids. It is a parallel code that aims to scale the temporal range of the simulation while keeping the execution time minimal. In this paper, we use empirical performance modeling to study the impact of simulation parameters on the execution time. Our approach is a systematic workflow that can be used as a blue-print in other fields that aim to scale their simulation codes. We show that the generated models can help users better understand how to scale the simulation with minimal increase in execution time.BMBF, 01IH16008D, Verbundprojekt: TaLPas - Task-basierte Lastverteilung und Auto-Tuning in der PartikelsimulationDFG, 323299120, ExtraPeak - Automatische Leistungsmodellierung von HPC-Anwendungen mit multiplen Modellparameter