月別: 2015年11月

[Published online Journal of Computer Chemistry, Japan14, A25-A32, by J-STAGE]
<Title:> PCクラスタ構築のためのオープンソースLinux OS： Rocks
<Author(s):> 末原　茂
<Corresponding author E-Mill:> suehara.shigeru(at)nims.go.jp
<Abstract:> PCクラスタ環境を簡単に構築できるオープンソースのLinux OS: Rocks の特徴を紹介し，インストールする際のポイントを，PCクラスタ構築の未経験者の視点から説明する．また，本格的なジョブ管理システムの導入と，簡単な ジョブファイルを用いた具体例も示した．
<Keywords:> Rocks OS, PC cluster, Job management system, Installation, Linux
<URL:> https://www.jstage.jst.go.jp/article/jccj/14/4/14_2015-0015/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan14, 97-104, by J-STAGE]
<Title:> UO₂-ZrO₂固溶体の融点および熱伝導率の分子 動力学解析
<Author(s):> 有馬　立身
<Corresponding author E-Mill:> arima(at)nucl.kyushu-u.ac.jp

<Abstract:> 原子炉過酷事故の事象進展には溶融燃料の熱的物性が大きく影響する．溶融燃料の主な物質であるUO₂-ZrO₂固 溶体の融点を古典分子動力学法を用いて組成をパラメータとして，また熱伝導率を組成・温度を変えて固体から液体状態まで評価した．融点に関しては 固液2相共存法が単相で評価するよりも実験値に近い値を与えた．これは結晶性固体の単相に対して温度を上げても融解の核が生成しにくく，過加熱状 態に陥りやすいことを意味している．また，UO₂とZrO₂を互いに固溶させることにより融点は低 下し，それが融解エンタルピーの減少と相関することを明らかにした．熱伝導率は平衡分子動力学法によりグリーン-久保の関係式から，エネルギーと 電荷の流れの相互効果を考慮し，固体から液体状態までの格子振動の寄与を評価した．固体の熱伝導率には，ウムクラップ散乱による温度上昇に伴う低 下，低温の固溶体で見られるフォノンの不純物散乱による低下が確認できた．一方，超高温の液体状態の熱伝導率は低く，温度および組成の依存性は小 さいことが分かった．
<Keywords:> Molecular dynamics, Thermal conductivity, Melting point, UO2, ZrO2
<URL:> https://www.jstage.jst.go.jp/article/jccj/14/4/14_2015-0007/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan14, 152-154, by J-STAGE]
<Title:> Interlayer Bonding Energy of Mg-Chlorite: A Density Functional Theory Study
<Author(s):> Hiroshi SAKUMA
<Corresponding author E-Mill:> SAKUMA.Hiroshi(at)nims.go.jp

<Abstract:> 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.
<Keywords:> Separation energy, Friction, Clay mineral, Chlorite, DFT
<URL:> https://www.jstage.jst.go.jp/article/jccj/14/4/14_2015-0008/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan14, 124-130, by J-STAGE]
<Title:> The Nature of Si-O-Si Bonding via Molecular Orbital Calculations
<Author(s):> Fumiya NORITAKE, Katsuyuki KAWAMURA
<Corresponding author E-Mill:> noritake(at)eqchem.s.u-tokyo.ac.jp

<Abstract:> 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 (C_2V and 60° torsion) using M ller-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 sp^λ orbital of bridging oxygen and increase of Coulombic interaction between Si and bridging oxygen atom.
<Keywords:> Keyword Siloxanes, Silicates, Molecular Orbital Calculation, Natural Bonding Orbital Analysis
<URL:> https://www.jstage.jst.go.jp/article/jccj/14/4/14_2015-0009/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan14, 147-151, by J-STAGE]
<Title:> 分子動力学プログラムMXDORTO用可視化ソフトウェアMDVISの開発
<Author(s):> 大石　駿介, 大川　政志
<Corresponding author E-Mill:> mokawa(at)numazu-ct.ac.jp

<Abstract:> 酸化物のシミュレーションに有用である分子動力学(MD)シミュレーションプログラムMXDORTO用の結果を可視化するソフトワエア Visualizer for Molecular Dynamics Simulation (MDVIS)を開発した． MDVISは，メイン，データ，オペレーション，チャートの4つのフォームで構成されている．メインフォームには3次元コンピュータグラフィックス (3DCG)によりMDシミュレーションで記録されている原子座標を連続的に表示する． オペレーションフォームの設定により特定の場所のみを表示したり，周期境界条件を考慮した拡張ができる．さらに選択した原子の軌跡を表示させる機能や選択 した2原子間の原子間距離を計算する機能を備えた．3DCGの画面に同期している温度，圧力，格子定数，密度，内部エネルギーなどのデータを数値 で表示するデータフォームとシミュレーション時間全般での変化を表示させるチャートフォームを実装した．
<Keywords:> Molecular dynamics simulation, Visualization software
<URL:> https://www.jstage.jst.go.jp/article/jccj/14/4/14_2015-0010/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan14, 117-123, by J-STAGE]
<Title:> Frenkel Defects and Interstitial Atoms in Periclase (MgO) at High Temperature by Molecular Dynamics Simulation
<Author(s):> Yasuhiro UEDA, Akira MIYAKE
<Corresponding author E-Mill:> miya(at)kueps.kyoto-u.ac.jp

<Abstract:> 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.
<Keywords:> Keyword Periclase (MgO), Molecular dynamics simulation, Frenkel defect, Interstitial atom, Diffusion
<URL:> https://www.jstage.jst.go.jp/article/jccj/14/4/14_2015-0014/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan14, 111-116, by J-STAGE]
<Title:> Molecular Dynamics Simulation of the Behavior of Beryllium Diffusion in Corundum
<Author(s):> Jun KAWANO, Muneyuki OKUYAMA, Takeshi MIYATA
<Corresponding author E-Mill:> j-kawano(at)mail.sci.hokudai.ac.jp

<Abstract:> 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.
<Keywords:> Diffusion, Molecular dynamics simulation, Corundum, Beryllium, Gemology
<URL:> https://www.jstage.jst.go.jp/article/jccj/14/4/14_2015-0016/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan14, 139-146, by J-STAGE]
<Title:> Interatomic Potential Model for Molecular Dynamics Simulation of Lithium Borate Melts/Glasses
<Author(s):> Naoya SAWAGUCHI, Kakeru YAMAGUCHI, Makoto SASAKI, Katsuyuki KAWAMURA
<Corresponding author E-Mill:> nasawa(at)mmm.muroran-it.ac.jp

<Abstract:> 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.
<Keywords:> Molecular dynamics, Lithium borate, Glass, Three-body potential, Partial ionic charge model
<URL:> https://www.jstage.jst.go.jp/article/jccj/14/4/14_2015-0017/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan14, 105-110, by J-STAGE]
<Title:> 分子動力学法によるSiO₂組成フォージャサイトの熱膨張変化の研究
<Author(s):> 大川　政志, 堤　涼, 大石　駿介, 松本　泰誠, 山口　力
<Corresponding author E-Mill:> mokawa(at)numazu-ct.ac.jp

<Abstract:> マイクロ孔を有するゼオライトは，相転移や負の熱膨張など興味深い熱的挙動を示すことが知られている．様々な温度での三次元細孔の挙動を知ることは触媒反 応の点から重要である．そこで本研究では立方晶のフォージャサイト(FAU)の構造を有するSiO₂組成ゼオライトを分子 動力学法により100 Kから1100 Kの範囲で計算を行い，格子定数および細孔に相当するスーパーケージのリング構造の変化を検討した．この温度領域において立方晶の構造は維持され格子定数 aは温度上昇とともに減少し，負の熱膨張を示した．二体相関関数からは第一近接のSiとSiの原子間距離は2種類ありそれらの温度に対する挙動が 異なり高温での負の熱膨張はSi-Si距離が減少することにより引き起こされていることが分かった．スーパーケージの12員環のリング径の平均値 は温度に対してほとんど変化しなかったが，温度上昇に伴い振幅は大きくなり600 K以上では10％以上変化することが分かった．
<Keywords:> molecular dynamics simulation, zeolite, faujasite, negative thermal expansion, ring structure
<URL:> https://www.jstage.jst.go.jp/article/jccj/14/4/14_2015-0020/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan14, 131-138, by J-STAGE]
<Title:> Molecular Dynamics Simulation of Layerd Double Hydroxide (LDH) Mineral: Hydrotalcite and Water Systems
<Author(s):> Katsuyuki KAWAMURA
<Corresponding author E-Mill:> kats(at)okayama-u.ac.jp

<Abstract:> 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.
<Keywords:> Keyword Clay mineral, Molecular dynamics simulation, Physical property, Structure, Mineral-water, Interface
<URL:> https://www.jstage.jst.go.jp/article/jccj/14/4/14_2015-0012/_article/-char/ja/