We review an open source Linux OS, "Rocks" for building a PC-cluster environment that can be utilized for a scalable computation. Some key points for easy installation and typical examples for using a job management system, etc. are also presented.
Melting points of UO2-ZrO2 solid solutions and their thermal conductivities from solid to liquid state were evaluated using the classical molecular dynamics simulation with the interatomic potential function developed by Pedone et al. The one- and two-phase simulations have been performed to investigate the melting point with varying the chemical composition. Both approaches showed that the melting point was the lowest around 50 mol% ZrO2 content and that the enthalpy of fusion also simultaneously was the smallest. However, the melting points calculated even by the two-phase simulation, which gave the better result than the one-phase simulation, were almost 300 K-600 K higher than the experimental ones. The thermal conductivities of the solid solutions were evaluated by the Green-Kubo approach in the equilibrium MD system. In the temperature region below the melting point, the thermal conductivity decreased with increasing temperature because of Umklapp scattering, and the solid solution with ZrO2 content around 50 mol% had the lowest thermal conductivity at low temperatures where the impurity scattering had a maximum effect to lower the thermal conductivity. On the other hand, the thermal conductivity of liquid UO2-ZrO2 was relatively low, and it was almost independent of temperature and the chemical composition.
We have performed molecular dynamics (MD) simulations including the vibration of the zeolite framework for some siliceous faujasite (Si-FAU) under various temperatures. MD simulation was carried out with MXDTRICL program under NPT ensemble. The calculation well reproduced the structure of Si-FAU after the structural relaxation at 300K. Negative thermal expansion was found over the temperature range of 100 to 1100K. The liner thermal expansion coefficient was estimated as −2.94×10−6 K−1, and this value was almost the same as the experimental value (−4.2×10−6 K−1). The changes of ring size of 12-membered ring in Si-FAU against time or temperature was investigated. The average ring size of the 12-membered ring in Si-FAU was almost the same in the temperature range from 100K to 1100K, but the variation of ring size against time became large with increasing temperature. The maximum ring size increased with temperature until 1100 K and it is an interesting finding that the ring size expanded ca. 15% by the thermal vibration.
Molecular dynamics (MD) simulations are highly useful for analyzing atomic behavior during diffusion, especially in systems that are difficult to investigate experimentally. The focus of the present study was the diffusion behavior of Be in corundum, which was analyzed by MD calculations. First, we derived new potential parameter sets for O, Al, and Be. This parameter set was verified to well reproduce the structures and properties of corundum, bromellite, and chrysoberyl. Based on MD simulations of corundum containing Be as interstitial atoms, where the simulations were performed using the newly derived potential parameters, the diffusion coefficient was estimated to be approximately 10−7 cm2/s at around 2100 K. This is consistent with previously published experimental results, which confirms the validity of the MD simulation. The present calculations also reveal the detailed atomic movement, where Be atoms jump between Al sites and/or interstitial sites, and that the activation energy of this process is approximately 1.1 × 102 kJ/mol.
An analysis program was newly developed to explore the vacancies and interstitial atoms and to determine atomic migration, i.e., atomic diffusion. We applied this program to the results calculated by the molecular dynamics (MD) simulation of periclase (MgO) in which Schottky defects (vacancies) were not initially introduced. Generation, migration and extinction of Frenkel defects and interstitial atoms for only magnesium ion were first observed at high temperature in this MD system and they strongly corresponded to the change of the mean square distance (MSD) of magnesium ion in MD system. On the other hand, we could not observe Frenkel defects and interstitial atoms for oxygen ion and MSD value of oxygen ion had almost constant value. Generation, migration and extinction of Frenkel defects and interstitial atoms cannot be ignored for the diffusion process at high temperature.
The nature of Si-O bonding and Si-O-Si bridging is discussed using molecular orbital calculations. We found the equilibrium geometries for two pyrosilisic acid molecules (C2V and 60° torsion) using Møller-Plesset perturbation theory and 6-311G (d,p) split valence basis set. The bent configuration of the Si-O-Si angle in equilibrium geometries can be explained by the balance of Coulombic repulsion between SiO4 tetrahedra and the energy of lone pair orbitals belonging to bridging oxygen atom without concerning the contribution of d-p π-bonding from the results of natural bonding orbital analysis. The energy surfaces of two pyrosilisic acid molecules with varying Si-O length to the bridging oxygen and Si-O-Si angle were calculated and we found the relationship between Si-O length to the bridging and Si-O-Si bridging angle. The Si-O bonding strengthens with increasing Si-O-Si angle because of stabilization in energy of Si-O bonding orbital with decreasing the hybridization index λ in spλ orbital of bridging oxygen and increase of Coulombic interaction between Si and bridging oxygen atom.
Some clay minerals are used and expected as barrier materials for engineering and in nature. Hydrotalcite, Mg6Al2[(OH)16|CO3]4H2O and a kind of LDH (layered double hydroxides), is one of the most effective candidates for the anion adsorbents and the barrier. In this study, the behavior of hydrotalcite was investigated by means of the molecular dynamics method. Cl− and I-hydrotalcite − water systems were simulated for various mineral/water ratios. The structure and dynamic properties are predicted. Water at the surface of hydrotalcite shows the electric double layer composed of Stern layer of one H2O molecular layer thickness and large self-diffusion coefficient of H2O and diffusion layer of 2.5 nm thickness at the interface.
An improved interatomic potential model was proposed for molecular dynamics simulations of lithium borate melt/glass systems. Charge of ion was reconsidered and a new composition dependent ionic charge model was suggested. A new three-body potential model controlling B-O-B angles was also proposed. The three-body term functioned to avoid square network ring consisted of B-O bonds, without preventing the change of boron coordination number between three and four. The edge-shared tetrahedra of four-coordination boron observed in the previous simulation were cleared by applying this three-body potential model.
We have developed a visualization software for molecular dynamics (MD) simulation program MXDORTO under "object oriented program." We have named it "Visualizer for Molecular Dynamics Simulation (MDVIS)." The each atom position calculated by MD program is displayed continuously in main form. Inter atomic bonds and the trajectory of each atom can be shown in main form, too. The result of simulation such as temperature, pressure, density, molar volume, cell parameters and internal energy is plotted versus simulation time in chart form.
Interlayer bonding energy (ILBE) of Mg-chlorite was calculated based on the density functional theory with dispersion force correction (DFT-D2). The calculated ILBE of Mg-chlorite was smaller than brucite, phlogopite, gibbsite, and muscovite and was comparable to talc, kaolinite, pyrophyllite, and lizardite. The attractive interaction between layers would be generated by the weak hydrogen bond between layers. The ILBE of Mg-chlorite should be the minimum ILBE in natural chlorite group, since the natural chlorite shows the isomorphic substitution which induces high layer charge resulting in stronger attractive interaction between layers like phlogopite and muscovite.