Research and development on computafional chemistry technologies by using "multiple molecular objective"approach adapted for large scale distdbuted processing

适合大规模分布式处理的“多分子目标”计算化学技术研究与开发

• 批准号: 17300094
• 负责人: GOTO Hitoshi
• 金额: $ 10.49万
• 依托单位: Toyohashi University of Technology
• 依托单位国家: 日本
• 项目类别: Grant-in-Aid for Scientific Research (B)
• 财政年份: 2005
• 资助国家: 日本
• 起止时间: 2005 至 2007
• 项目状态: 已结题
• 来源: https://kaken.nii.ac.jp/grant/KAKENHI-PROJECT-17300094/
• 关键词: Computational Chemistry; Molecular Crystal Simulation; Crystal Polymorphism; Charge Equilibration; Density Functional Theory; Parallel Distributed Processing Technique; Heterogeneous Computer Cluster; マルチコア; マルチスレッド; 電荷平衡法(QEq); 高速多重極展開法(FMM)

This project consists of three major parts : (1) the construction of the molecular calculation platform for the multi-molecular objective method,(2) the development of molecular calculation techniques adopted for the high-accurate hierarchized molecule simulation,(3) the development of load distribution algorithm optimized for hetero-computational task resources. Outline of the each research result is shown in the following : (1) With the aim of the improvement in the parallelization efficiency and computation accuracy by the multi-molecular objective method, crystal simulation technique of the large scale system was developed. As a result of the "molecular objective" approach, we have reached to large-scale finite crystal calculation of 0.1 μm diameter composed of four hundred million atoms within accuracy guarantee to the 14 digits of total intermolecular interaction energy. The practical application of thermodynamic analysis between crystal polymorphisms and their phase transition a … More lso can available. (2) Solution methods for TDHF/TDDFT time dependence Schrodinger equation and hyperpolarizability by using the multi-wavelet basis set have been successfully developed. At this stage, these results are not so easy to apply into the large scale system, it can greatly expected anytime soon that extended to the development to density functional theory for the heterogeneous system. (3) In the hetero distributed computing environment, we have successfully developed a new fundamental algorithm for efficient load distribution, and the performance of HPL(High Performance Linpack)and various benchmark programs are better than those of the other established model. On the other hand, it has noted that the performance for calculation task of the molecular simulation is insufficient for the practical usage. Therefore, although the development of the practical load distribution algorithm has still faced with some difficult problems, we have started to study some efficient load distribution algorithms adapted to the recent multi-core/multithread system. Less

本项目主要包括三个部分：（1）多分子目标方法的分子计算平台的构建;（2）高精度分层分子模拟的分子计算技术的开发;（3）异构计算任务资源优化的负载分配算法的开发。（1）以提高多分子目标方法的并行化效率和计算精度为目标，发展了大规模体系的晶体模拟技术。由于采用了“分子目标”方法，在保证14位总分子间相互作用能的精度下，我们实现了由4亿个原子组成的0.1 μm直径的大规模有限晶体的计算。介绍了晶体多晶型与相变热力学分析的实际应用， ...更多信息 也可以提供。(2)利用多小波基组成功地求解了TDHF/TDDFT含时薛定谔方程和超极化率。在现阶段，这些结果还不容易应用到大尺度系统中，但很快就可以推广到非均相系统的密度泛函理论的发展。(3)在异构分布式计算环境下，我们成功地开发了一种新的高效负载分配的基本算法，HPL（High Performance Linpack）和各种基准测试程序的性能都优于其它已建立的模型。另一方面，注意到分子模拟的计算任务的性能对于实际使用是不足的。因此，尽管实用负载分配算法的开发仍然面临一些难题，但我们已经开始研究一些适应当前多核/多线程系统的高效负载分配算法。少

项目成果

AMBERを用いたDPCミセルのMDシミュレーション

使用 AMBER 对 DPC 胶束进行 MD 模拟

• 发表时间: 2006
• 期刊: CICSJ Bulletin 24(5)
• 作者: K. Hattanda;S. Ichikawa;後藤仁志
• 通讯作者: 後藤仁志

Proposed Mechanism for Diterpene Synthases in the Formation of Phomactatriene and Taxadiene: Experimental Results on Biosynthetic Study, Biomimetic Reactions and Examination of the Cyclization Pathway by ab initio Calculations

双萜合成酶在形成磷三烯和紫杉二烯过程中提出的机制：生物合成研究、仿生反应的实验结果以及通过从头算计算检查环化途径的实验结果

• 发表时间: 2005
• 期刊: Organic Biomolelucar Chemistry 3(15)
• 作者: T. Tokiwano;T. Endo;T. Tsukagoshi;H. Goto;E. Fukushi;H. Oikawa
• 通讯作者: H. Oikawa

Entropy-or enthalpy-driven collapse of strongly charged polymer chains in a one-component charged fluid of counterions or coions

反离子或反离子的单组分带电流体中强带电聚合物链的熵或焓驱动的塌缩

• 发表时间: 2005
• 期刊: Journal of Chemical Physics 123
• 作者: T. Sumi;C. Suzuki;H. Sekino
• 通讯作者: H. Sekino

Entropy- or enthalpy-driven collapse of strongly charged polymer chains in a one-component charged fluid of counterions or colons

抗衡离子或冒号的单组分带电流体中强带电聚合物链的熵或焓驱动的塌缩

• 发表时间: 2005
• 期刊: Journal of Chemical Physics 123
• 作者: T. Sumi;C. Suzuki;H. Sekino
• 通讯作者: H. Sekino

Incorporation of Solvent Effect into NQEq (New Charge Equilibration), and Applying it for Molecular Force Field Calculation

将溶剂效应纳入NQEq（新电荷平衡）并应用于分子力场计算

• 发表时间: 2005
• 期刊: Kinozairyo 11
• 作者: Naommi;Nakayama;Umpei;Nagashima;Hitoshi;Goto
• 通讯作者: Goto