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

Effect of strain on gas adsorption in tight gas carbonates: A DFT study

We employ ab initio calculations and investigate the single-crystalline elastic properties of (Ca,Mg)CO3 crystals covering the whole range of concentrations from pure calcite CaCO3 to pure magnesite MgCO3. Studying different distributions of Ca and Mg atoms within 30-atom supercells, our theoretical results show that the energetically most favorable configurations are characterized by elastic constants that nearly monotonously increase with the Mg content. Based on the first principles-derived single-crystalline elastic anisotropy, the integral elastic response of (Ca,Mg)CO3 polycrystals is determined employing a mean-field self-consistent homogenization method. As in case of single-crystalline elastic properties, the computed polycrystalline elastic parameters sensitively depend on the chemical composition and show a significant stiffening impact of Mg atoms on calcite crystals in agreement with the experimental findings. Our analysis also shows that it is not advantageous to use a higher-scale two-phase mix of stoichiometric calcite and magnesite instead of substituting Ca atoms by Mg ones on the atomic scale. Such two-phase composites are not significantly thermodynamically favorable and do not provide any strong additional stiffening effect.

Ab initio study of single-crystalline and polycrystalline elastic properties of Mg-substituted calcite crystals

Calcium carbonate is one of the most abundant minerals on Earth and a component of natural biogenic materials and man-made cements. The interactions between hydrated calcium carbonate surfaces at nanometer confinement are relevant in dissolution and crystallization processes as well as in adsorption of organic fluids in natural reservoirs. In this work we quantify using atomistic molecular dynamics simulations the water mediated interactions between calcium carbonate surfaces at nanometer separations. We investigate two calcium carbonate polymorphs, calcite and aragonite. We show that the adsorption behavior of water on the (1014) surface of calcite and the (001) surface of aragonite is very different. These differences are reflected in intersurface forces between the two mineral surfaces. The interactions between surfaces feature an oscillatory behavior whose origin is connected to the structuring of water at an intersurface separation <1 nm. We observe adhesion between the surfaces and demonstrate that...

/pdf/interactions-between-hydrated-calcium-carbonate-surfaces-at-hb0lgj90wu.pdf

Interactions Between Hydrated Calcium Carbonate Surfaces at Nanoconfinement Conditions

Biogenic twinned microplatelets of the anhydrous guanine (AG) β form have been found in copepod cuticles and scallop eyes, which function as multilayer reflectors. In this work, twinned AG β microplatelets with morphologies such as cross-shape and square-shape were synthesized for the first time in the presence of a polyvinylpyrrolidone additive in formamide and water. The twinning angle of the two c diffraction vectors (84°) for the synthetic twinned guanine crystals is very similar to that of biogenic twinned guanine microplatelets observed in scallop eyes. The angles between the two observed c diffraction vectors of the synthetic twinned AG β form microplatelets were about 84° and 20°, while a twinning angle of 84° was observed in the biogenic twinned guanine microplatelets exposing the (100) face. We proposed a formation mechanism for the twinned guanine microplatelet crystals. The formation of the twinned crystals with angles of 84° and 20° between the c diffraction vectors might be related to the attachment of G-quartet molecular assemblies on the guanine plate-like crystals with a certain angle at the early stage of crystallization.

Controlled crystallization of twinned crystalline guanine microplatelets

Deformation twinning provides a mechanism for energy dissipation in crystalline structures, with important implications on the mechanical response of carbonate biogenic materials. Carbonate crystals can incorporate magnesium, e.g. in the sea, modifying their elastic response significantly. We present a full atom computational investigation of the dependence of the twinning response of calcite with magnesium content, covering compositions compatible with three main structures, calcite, dolomite and magnesite. We find, in agreement with experiments that the incorporation of magnesium disfavors twinning as a dissipation mechanism in ordered structures (dolomite, magnesite), however the response is strongly dependent on the arrangement of the magnesium ions in the crystal structure. We show that structures with a high content of magnesium (>33%) in a disordered arrangement, lead to plastic response before twinning or fracturing. We demonstrate that the position of the magnesium ions plays a key role in the determination of the crystal deformation mode. This observation is correlated with the formation of percolation clusters of magnesium in magnesian calcites.

/pdf/plastic-deformation-and-twinning-mechanisms-in-magnesian-tyri9ko1fa.pdf

Plastic deformation and twinning mechanisms in magnesian calcites: a non-equilibrium computer simulation study

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Plastic deformation and twinning mechanisms in magnesian calcites: a non-equilibrium computer simulation study