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

Influence of a Conductive Material and Different Anaerobic Inocula on Biochemical Methane Potential of Substrates from Alcoholic Beverage Production

The impact of a conductive material as powdered activated carbon (PAC) on the biochemical methane potential of whisky pot ale (PA) and brewery spent yeast (SY) was investigated. The test was carried out with three different types of anaerobic inocula: manure inoculum (MI), sewage sludge (SS) and granular sludge (GR). Brewery spent yeast produced partial (in sewage and granular sludge) and total (in manure inoculum) methanogenesis inhibition due to the toxicity of some of its constituents (hops extract). The inhibition was overcome by the supplementation of PAC, that improved significantly the anaerobic digestion process for SY, allowing to reach biochemical methane potential values between 657-699 L CH4 kg-1 VS and it reduced redox potential from 369 to 398 mV. The activated carbon did not improve the methane yields from whisky PA since microorganisms did not have difficulties to process this substrate; in fact, the redox potential slightly increased from 355 to 330 mV

FDCCS16 molecular simulation of the thermophysical properties and phase behaviour of impure CO2 relevant to CCS

Impurities from the CCS chain can greatly influence the physical properties of CO2. This has important design, safety and cost implications for the compression, transport and storage of CO2. There is an urgent need to understand and predict the properties of impure CO2 to assist with CCS implementation. However, CCS presents demanding modelling requirements. A suitable model must both accurately and robustly predict CO2 phase behaviour over a wide range of temperature and pressure, and maintain that predictive power for CO2 mixtures with numerous, mutually interacting chemical species. A promising technique to address this task is molecular simulation. It offers a molecular approach, with foundations in firmly established physical principles, along with the potential to predict the wide range of physical properties required for CCS. The quality of predictions from molecular simulation depends on accurate force-fields to de- scribe the interactions between CO2 and other molecules. Unfortunately, there is currently no universally applicable method to obtain force-fields suitable for molecular simulation. In this paper we present two methods of obtaining force-fields: the first being semi-empirical and the second using ab-initio quantum-chemical calculations. In the first approach we optimise the impurity force-field against measurements of the phase and pressure-volume behaviour of CO2 binary mixtures with N2, O2, Ar and H2. A gradient-free optimiser allows us to use the simulation itself as the underlying model. This leads to accurate and robust predictions under conditions relevant to CCS. In the second approach we use quantum-chemical calculations to produce ab-initio evaluations of the interactions between CO2 and relevant impurities, taking N2 as an exemplar. We use a modest number of these calculations to train a machine-learning algorithm, known as a Gaussian process, to describe these data. The resulting model is then able to accurately predict a much broader set of ab-initio force-field calculations at comparatively low numerical cost. Although our method is not yet ready to be implemented in a molecular simulation, we outline the necessary steps here. Such simulations have the potential to deliver first-principles simulation of the thermodynamic properties of impure CO2, without fitting to experimental data

Molecular Modeling and Simulation: Force Field Development, Evaporation Processes and Thermophysical Properties of Mixtures

To gain physical insight into the behavior of fluids on a microscopic level as well as to broaden the data base for thermophysical properties especially for mixtures, molecular modeling and simulation is utilized in this work. Various methods and applications are discussed, including a procedure for the development of new force field models. The evaporation of liquid nitrogen into a supercritical hydrogen atmosphere is presented as an example for large scale molecular dynamics simulation. System-size dependence and scaling behavior are discussed in the context of Kirkwood-Buff integration. Further, results for thermophysical mixture properties are presented, i.e. the Henry’s law constant of aqueous systems and diffusion coefficients of a ternary mixture

ms2: a molecular simulation tool for thermodynamic properties

This work presents the molecular simulation program ms2 that is designed for the calculation of thermodynamic properties of bulk fluids in equilibrium consisting of small electro-neutral molecules. ms2 features the two main molecular simulation techniques, molecular dynamics (MD) and Monte-Carlo. It supports the calculation of vapor-liquid equilibria of pure fluids and multi-component mixtures described by rigid molecular models on the basis of the grand equilibrium method. Furthermore, it is capable of sampling various classical ensembles and yields numerous thermodynamic properties. To evaluate the chemical potential, Widomʼs test molecule method and gradual insertion are implemented. Transport properties are determined by equilibrium MD simulations following the Green-Kubo formalism. ms2 is designed to meet the requirements of academia and industry, particularly achieving short response times and straightforward handling. It is written in Fortran90 and optimized for a fast execution on a broad range of computer architectures, spanning from single processor PCs over PC-clusters and vector computers to high-end parallel machines. The standard Message Passing Interface (MPI) is used for parallelization and ms2 is therefore easily portable to different computing platforms. Feature tools facilitate the interaction with the code and the interpretation of input and output files. The accuracy and reliability of ms2 has been shown for a large variety of fluids in preceding work