Three parallel algorithms for classical molecular dynamics are presented. The first assigns each processor a fixed subset of atoms; the second assigns each a fixed subset of inter-atomic forces to compute; the third assigns each a fixed spatial region. The algorithms are suitable for molecular dynamics models which can be difficult to parallelize efficiently—those with short-range forces where the neighbors of each atom change rapidly. They can be implemented on any distributed-memory parallel machine which allows for message-passing of data between independently executing processors. The algorithms are tested on a standard Lennard-Jones benchmark problem for system sizes ranging from 500 to 100,000,000 atoms on several parallel supercomputers--the nCUBE 2, Intel iPSC/860 and Paragon, and Cray T3D. Comparing the results to the fastest reported vectorized Cray Y-MP and C90 algorithm shows that the current generation of parallel machines is competitive with conventional vector supercomputers even for small problems. For large problems, the spatial algorithm achieves parallel efficiencies of 90% and a 1840-node Intel Paragon performs up to 165 faster than a single Cray C9O processor. Trade-offs between the three algorithms and guidelines for adapting them to more complex molecular dynamics simulations are also discussed.

Fast parallel algorithms for short-range molecular dynamics

다중혈관 관상동맥 환자에서 y-문합을 이용하여 양쪽 내흉동맥만을 사용한 우회술의 조기 성적

Natural gas hydrates are solid, non-stoichiometric compounds of small gas molecules and water. They form when the constituents come into contact at low temperature and high pressure. The physical properties of these compounds, most notably that they are non-flowing crystalline solids that are denser than typical fluid hydrocarbons and that the gas molecules they contain are effectively compressed, give rise to numerous applications in the broad areas of energy and climate effects. In particular, they have an important bearing on flow assurance and safety issues in oil and gas pipelines, they offer a largely unexploited means of energy recovery and transportation, and they could play a significant role in past and future climate change.

Fundamental principles and applications of natural gas hydrates

This chapter assesses long-term projections of climate change for the end of the 21st century and beyond, where the forced signal depends on the scenario and is typically larger than the internal variability of the climate system. Changes are expressed with respect to a baseline period of 1986-2005, unless otherwise stated.

Chapter 12 - Long-term climate change: Projections, commitments and irreversibility

OUTPU T 29 OUTPU T 30 OUTPU T 31 OUTPU T 32 OUTPU T 25 OUTPU T 26 OUTPU T 27 OUTPU T 28 OUTPU T 21 OUTPU T 22 OUTPU T 23 OUTPU T 24 OUTPU T 17 OUTPU T 18 OUTPU T 19 OUTPU T 20 OUTPU T 13 OUTPU T 14 OUTPU T 15 OUTPU T 16 OUTPU T 9 OUTPU T 10 OUTPU T 11 OUTPU T 12 OUTPU T 5 OUTPU T 6 OUTPU T 7 OUTPU T 8 OUTPU T 1 OUTPU T 2 OUTPU T 3 OUTPU T 4 29 30 31 32 25 26 27 28 21 22 23 24 17 18 19 20 13 14 15 16 9

A User’s Guide

https://escholarship.org/content/qt6jt0z4nz/qt6jt0z4nz.pdf?t=q1l32u

On the importance of phase saturation heterogeneity in the analysis of laboratory studies of hydrate dissociation

Geochemical environments, fates, and effects are modeled for methane released into seawater by the decomposition of climate-sensitive clathrates. A contemporary global background cycle is first constructed, within the framework of the Parallel Ocean Program. Input from organics in the upper thermocline is related to oxygen levels, and microbial consumption is parameterized from available rate measurements. Seepage into bottom layers is then superimposed, representing typical seabed fluid flow. The resulting CH{sub 4} distribution is validated against surface saturation ratios, vertical sections, and slope plume studies. Injections of clathrate-derived methane are explored by distributing a small number of point sources around the Arctic continental shelf, where stocks are extensive and susceptible to instability during the first few decades of global warming. Isolated bottom cells are assigned dissolved gas fluxes from porous-media simulation. Given the present bulk removal pattern, methane does not penetrate far from emission sites. Accumulated effects, however, spread to the regional scale following the modeled current system. Both hypoxification and acidification are documented. Sensitivity studies illustrate a potential for material restrictions to broaden the perturbations, since methanotrophic consumers require nutrients and trace metals. When such factors are considered, methane buildup within the Arctic basin is enhanced. However, freshened polar surface waters act as a barrier to atmospheric transfer, diverting products into the deep return flow. Uncertainties in the logic and calculations are enumerated including those inherent in high-latitude clathrate abundance, buoyant effluent rise through the column, representation of the general circulation, and bacterial growth kinetics.

/pdf/marine-methane-cycle-simulations-for-the-period-of-early-zo6483zqmd.pdf

Marine methane cycle simulations for the period of early global warming

The behavior of fluids in confined spaces is important in several research fields, including the oil and gas industry, because of the importance of confined hydrocarbons in unconventional shale reservoirs. A large percentage of the hydrocarbons are contained in nanoscale shale pores, and as a result, interactions between fluid molecules and the pore walls become significant to the fluid behavior and cause deviations of the fluid properties from bulk properties. In this work, classical molecular dynamics (MD) simulations and grand canonical Monte Carlo (GCMC) simulations are performed to model kerogen pores in shale reservoirs and their effect on adsorption selectivity and phase equilibria of hydrocarbon mixtures in a wide range of temperatures and pressures. A slit pore made of graphite walls is used to represent the basic unit where a fluid may be stored in shale reservoirs. The separation between graphite layers is varied to observe the effect of confinement on the adsorption selectivity and phase equil...

/pdf/phase-behavior-of-methane-ethane-mixtures-in-nanopores-3jv214pes7.pdf

George J. Moridis

Papers

On the importance of phase saturation heterogeneity in the analysis of laboratory studies of hydrate dissociation

Marine methane cycle simulations for the period of early global warming

Phase Behavior of Methane–Ethane Mixtures in Nanopores

Toward Production From Gas Hydrates: Assessment of Resources, Technology and Potential

Coupled Hydrologic, Thermal and Geomechanical Analysis of Well Bore Stability in Hydrate-Bearing Sediments