描述使用TCGMSG消息包的一维聚合物能量带计算的并行处理。作为计算机，Cray T932 (32cpu)， IBM RS 60004工作站集群，以及奔腾/奔腾- pro使用了由4台个人电脑组成的PC集群。并行化是针对双电子积分以及波向量各点的对角化进行的。特别是对波向量的并行化处理被证明对能量带计算是有效的。因为我们的问题不需要大容量的矩阵运算，不能得到很长的向量长度，所以不能充分发挥超级计算机的高速性，即使在PC集群中也能得到与超级计算机匹敌的速度。我知道了。
{"title":"Parallel Processing on ab initio Crystal Orbital Calculations of One-Dimensional Polymers","authors":"H. Teramae","doi":"10.2477/JCHEMSOFT.4.73","DOIUrl":"https://doi.org/10.2477/JCHEMSOFT.4.73","url":null,"abstract":"TCGMSGメッセージパッセンジャーを用いた、一次元ポリマーのエネルギーバンド計算の並列処理について述べる。計算機として、Cray T932 (32 CPU)、IBM RS 60004台によるワークステーションクラスターならびに Pentium/Pentium-Pro を使用したパーソナルコンピューター4台からなるPCクラスターを使用した。並列化は二電子積分ならびに波数ベクトル各点における対角化に対して行なった。特に波数ベクトルに対する並列化処理はエネルギーバンド計算に対しては有効であることが判明した。対象としている問題が大容量の行列演算を必要とせず長いベクトル長が得られないため、スーパーコンピューターの高速性が十分に発揮されず、PCクラスターにおいても、スーパーコンピューターに匹敵する速度が得られることがわかった。","PeriodicalId":205210,"journal":{"name":"Journal of Chemical Software","volume":"28 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"1998-06-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"131441985","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Neural Network Reproduction of Time Series Data with Varying Amplitudes and Frequencies","authors":"Mitsue Onodera, U. Nagashima, Hiroaki Yoshida, T. Aoyama, H. Hosoya","doi":"10.2477/JCHEMSOFT.4.57","DOIUrl":"https://doi.org/10.2477/JCHEMSOFT.4.57","url":null,"abstract":"生体の断層イメージを測定する核磁気共鳴のシグナルやBelousov-Zhabotinsky反応 (BZ) などの振動反応の酸化還元ポテンシャルは、振幅と周期が時間とともに変化していく時系列データである。しかし、従来の統計的手法では振幅変化及び周期変化を同時に追うことは困難であり、その予測は難しかった。そこで本研究では、時間とともに振幅と周期が同時に変化する時系列データの予測を行うために、ニューラルネットワークからなるモデルを構築した。このモデルは、振幅変化及び周期変化の予測を行うための2つのニューラルネットワークと、それらを統括する一つのニューラルネットワークからなる。本モデルを用いて4種類のモデル関数による数値実験を行い、最小自乗法を用いた際の結果と比較したところ、学習区間においては最小自乗法の方が高い傾向があるが、予測区間においては本モデルの方が精度が高いことがわかった。特に振幅変化の予測では本モデルの方が高い精度を得ることができることがわかった。","PeriodicalId":205210,"journal":{"name":"Journal of Chemical Software","volume":"1 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"1998-06-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"131703558","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Yuji Shinohara, H. Satozono, T. Nakajima, Satoshi Suzuki, S. Mishima
The interactions of ethanol with a Bronsted acid site (a hydroxy group) and with a Lewis acid site (a metal ion) on surfaces of seven metal oxides (SiO2-Al2O3, SiO2, TiO2, ZnO, MgO, MnO and CdO) have been investigated using the DV-Xα method. The oxides were selected from a series of catalysts, whose selectivities for the dehydration and the dehydrogenation of ethanol had been experimentally determined by P. Sabatier and A. Mailhe.By comparing the results of the DV-Xα calculations from several models of ethanol interacting with the Bronsted or Lewis acid sites with the experimental selectivities, it was concluded that a proton shift from the Bronsted site to the ethanol oxygen occurs when ethanol strongly interacts with the site and that this shift changed the electronic state of ethanol for the dehydration to be favorable. These results indicate that the dehydration of ethanol on oxide catalysts proceeds by the E1 mechanism.
{"title":"Study of the Interaction of Ethanol with the Bronsted and Lewis Acid Sites on Metal Oxide Surfaces Using the DV-X.ALPHA. Method.","authors":"Yuji Shinohara, H. Satozono, T. Nakajima, Satoshi Suzuki, S. Mishima","doi":"10.2477/JCHEMSOFT.4.41","DOIUrl":"https://doi.org/10.2477/JCHEMSOFT.4.41","url":null,"abstract":"The interactions of ethanol with a Bronsted acid site (a hydroxy group) and with a Lewis acid site (a metal ion) on surfaces of seven metal oxides (SiO2-Al2O3, SiO2, TiO2, ZnO, MgO, MnO and CdO) have been investigated using the DV-Xα method. The oxides were selected from a series of catalysts, whose selectivities for the dehydration and the dehydrogenation of ethanol had been experimentally determined by P. Sabatier and A. Mailhe.By comparing the results of the DV-Xα calculations from several models of ethanol interacting with the Bronsted or Lewis acid sites with the experimental selectivities, it was concluded that a proton shift from the Bronsted site to the ethanol oxygen occurs when ethanol strongly interacts with the site and that this shift changed the electronic state of ethanol for the dehydration to be favorable. These results indicate that the dehydration of ethanol on oxide catalysts proceeds by the E1 mechanism.","PeriodicalId":205210,"journal":{"name":"Journal of Chemical Software","volume":"18 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"1998-06-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"126761286","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
We investigated the application of an X-ray diffraction method to determine ammonium nitrate in dynamite more simply and accurately without a separation procedure. In this method, organonitro compounds were removed from the sample using diethyl ether for safety, and the residue was dried. Next, the sample was directly measured by the X-ray diffraction method. The determination of ammonium nitrate content was calculated by multivariate analysis such as cluster analysis and principal component analysis. The calculated values were in fair agreement with theoretical values.
{"title":"Determination of Ammonium Nitrate in Dynamite without Separation by Multivariate Analysis Using X-ray Diffractometer","authors":"T. Mitsui, Motoyasu Satoh","doi":"10.2477/JCHEMSOFT.4.33","DOIUrl":"https://doi.org/10.2477/JCHEMSOFT.4.33","url":null,"abstract":"We investigated the application of an X-ray diffraction method to determine ammonium nitrate in dynamite more simply and accurately without a separation procedure. In this method, organonitro compounds were removed from the sample using diethyl ether for safety, and the residue was dried. Next, the sample was directly measured by the X-ray diffraction method. The determination of ammonium nitrate content was calculated by multivariate analysis such as cluster analysis and principal component analysis. The calculated values were in fair agreement with theoretical values.","PeriodicalId":205210,"journal":{"name":"Journal of Chemical Software","volume":"14 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"1998-03-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"123863036","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Takeshi Uno, Y. Kawashima, Jin-Bei Zhang, Haruhisa Hayashi, K. Yamana, H. Nakano
We developed a molecular graphics system, named “Modrast-P”, which reads coordinates in the Protein Data Bank of Brookhaven National Laboratory format (PDB). This graphics system displays three-dimensional structures of proteins and nucleic acids with various representations and shows molecular models clipped by single plane, double plane, and a cylinder defined arbitrarily. This system runs on the OpenWindows of Sun Microsystems workstation and most functions of it can be operated easily by a mouse or buttons. We also developed an information retrieval system which can seek the target file in CD-ROM by author name, keyword, or amino acid sequence.
{"title":"Development of a Display and Retrieval System for the Protein Data Bank on Sun Microsystems Workstation","authors":"Takeshi Uno, Y. Kawashima, Jin-Bei Zhang, Haruhisa Hayashi, K. Yamana, H. Nakano","doi":"10.2477/JCHEMSOFT.4.1","DOIUrl":"https://doi.org/10.2477/JCHEMSOFT.4.1","url":null,"abstract":"We developed a molecular graphics system, named “Modrast-P”, which reads coordinates in the Protein Data Bank of Brookhaven National Laboratory format (PDB). This graphics system displays three-dimensional structures of proteins and nucleic acids with various representations and shows molecular models clipped by single plane, double plane, and a cylinder defined arbitrarily. This system runs on the OpenWindows of Sun Microsystems workstation and most functions of it can be operated easily by a mouse or buttons. We also developed an information retrieval system which can seek the target file in CD-ROM by author name, keyword, or amino acid sequence.","PeriodicalId":205210,"journal":{"name":"Journal of Chemical Software","volume":"72 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"1998-03-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"116065542","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Development of a CAI Program Utilizing Spreadsheet Data Files and a Collection of Data","authors":"Y. Honma","doi":"10.2477/JCHEMSOFT.4.11","DOIUrl":"https://doi.org/10.2477/JCHEMSOFT.4.11","url":null,"abstract":"","PeriodicalId":205210,"journal":{"name":"Journal of Chemical Software","volume":"330 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"1998-03-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"116790149","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
CyberMol, an interactive molecular graphics program system on the World Wide Web (WWW) using the Common Gateway Interface (CGI) is presented. The molecular coordinates which are inputted from the WWW browser can be transferred to the Virtual Reality Modeling Language (VRML) format file and viewed as a molecular model by using a VRML viewer on the WWW. The vibrational modes calculated by the ab initio molecular orbital program GAUSSIAN 94 can be visualized. The organic molecular structure database and the search engine for displaying molecular models by using the VRML viewer are also provided.
{"title":"CyberMol-A Molecular Graphics Program System on the World Wide Web Using the Common Gateway Interface","authors":"H. Yoshida, H. Matsuura","doi":"10.2477/JCHEMSOFT.3.157","DOIUrl":"https://doi.org/10.2477/JCHEMSOFT.3.157","url":null,"abstract":"CyberMol, an interactive molecular graphics program system on the World Wide Web (WWW) using the Common Gateway Interface (CGI) is presented. The molecular coordinates which are inputted from the WWW browser can be transferred to the Virtual Reality Modeling Language (VRML) format file and viewed as a molecular model by using a VRML viewer on the WWW. The vibrational modes calculated by the ab initio molecular orbital program GAUSSIAN 94 can be visualized. The organic molecular structure database and the search engine for displaying molecular models by using the VRML viewer are also provided.","PeriodicalId":205210,"journal":{"name":"Journal of Chemical Software","volume":"11 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"1997-07-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"117099853","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
MOLDA for Windows, an interactive personal-computer molecular modeling and molecular graphics program, which can be used as an interface to the ab initio molecular orbital program GAUSSIAN 94, the molecular dynamics simulation program AMBER 4.0 and the molecular mechanics program MM2, is described. The molecular model constructed by using MOLDA can be transferred to the Virtual Reality Modeling Language (VRML) format file and viewed by using a VRML viewer on the World Wide Web (WWW).
介绍了可作为从头算分子轨道程序GAUSSIAN 94、分子动力学模拟程序AMBER 4.0和分子力学程序MM2接口的交互式个人计算机分子建模和分子图形程序MOLDA for Windows。利用MOLDA构建的分子模型可以转换为虚拟现实建模语言(VRML)格式文件，并通过万维网上的VRML查看器进行查看。
{"title":"MOLDA for Windows -A Molecular Modeling and Molecular Graphics Program Using a VRML Viewer on Personal Computers","authors":"H. Yoshida, H. Matsuura","doi":"10.2477/JCHEMSOFT.3.147","DOIUrl":"https://doi.org/10.2477/JCHEMSOFT.3.147","url":null,"abstract":"MOLDA for Windows, an interactive personal-computer molecular modeling and molecular graphics program, which can be used as an interface to the ab initio molecular orbital program GAUSSIAN 94, the molecular dynamics simulation program AMBER 4.0 and the molecular mechanics program MM2, is described. The molecular model constructed by using MOLDA can be transferred to the Virtual Reality Modeling Language (VRML) format file and viewed by using a VRML viewer on the World Wide Web (WWW).","PeriodicalId":205210,"journal":{"name":"Journal of Chemical Software","volume":"77 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"1997-07-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"127595661","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
利用校内LocalArea Network (LAN)试制了新的授课系统，以World-Wide Web (WWW)系统为核心，这是一种结合了电子公告栏和电子邮件系统的客户端服务器系统。该讲课系统是为文科大学的自然科学学习补习教育而开发的，把教学内容有机地组合成文字、图像等多媒体教材。通过对所有听课者开放的答疑环节，教师和学生之间可以进行交流，还加入了课程结业认证考试。教师可以随时监测学生的使用情况，本系统的优点是学生不受时间安排的限制，可以在必要的时候学习必要的内容。特别适合为基础学习能力不足的学生进行预备、补习等课程。
{"title":"A Trial of a New Lecture System Corresponding to the Era of Network","authors":"Hisao Suzuki, Shunji Isawa, S. Ozaki, Takayuki Yano","doi":"10.2477/JCHEMSOFT.3.165","DOIUrl":"https://doi.org/10.2477/JCHEMSOFT.3.165","url":null,"abstract":"学内LocalArea Network (LAN) を利用した新しい講義システムを試作した.World-Wide Web (WWW) システムを中核とし, 電子掲示板および電子メールシステムを組み合わせたクライアント・サーバシステムである.この講義システムは文系大学の自然科学学習のための補習教育用に開発したもので, 教育内容をテキストや画像などのマルチメディア教材として有機的に組み合わせて構成してある.受講者すべてに開かれた質疑応答コーナーを通じて教師と学生間のコミュニケーションが可能となっている.コース修了認定テストも組み込んでいる.学生の利用状況は教師側からいつでもモニターできる.本システムは, 学生にとっては時間割に拘束されることなく, 必要なときに必要な個所を学習できる利点がある.特に, 基礎学力の不足した学生のための予備的・補習的授業などに適している.","PeriodicalId":205210,"journal":{"name":"Journal of Chemical Software","volume":"12 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"1997-07-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"131975235","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Elucidation of fragmentation pathway of long chain base by molecular orbital calculation","authors":"H. Kishine, A. Hayashi","doi":"10.2477/JCHEMSOFT.3.139","DOIUrl":"https://doi.org/10.2477/JCHEMSOFT.3.139","url":null,"abstract":"スフィンゴ脂質の構成成分である長鎖塩基のトリメチルシリル (TMS) 誘導体のEI/MS分析において検出され、分子量の決定に必要な [M-15(CH3)]+と[M-15-90 (TMSOH)]+のイオンについて、MOPACのAM1法を用いて分子軌道 (MO) 計算により、そのフラグメンテーションを予測した。その結果、 [M-15] +のイオンは1位の第一級アルコールに結合したTMS基からメチルラジカルが脱離して環状構造をつくり、ついでTMSOHが脱離して [M-15-90] +のイオンが生成すると推測された。またベースピークであるm/z132 ([H2NCHCH2OTMS] +) のイオンについてもMO計算を行い、イオン構造を推定した。","PeriodicalId":205210,"journal":{"name":"Journal of Chemical Software","volume":"121 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"1997-07-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"117175770","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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