Journal of Chemical Software
Online ISSN : 1883-8359
Print ISSN : 0918-0761
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Volume 6 , Issue 4
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  • Setsuro SUGATA, Yoshihiro ABE
    Volume 6 (2000) Issue 4 Pages 127-136
    Released: February 28, 2001
    JOURNALS FREE ACCESS
    The “double-glazed vessel model" (DGV model) is an imaginary model modified from the previously reported “test tube model", and is drawn graphically by computer. The vessel has a double wall, the inner wall of which has a pinhole near the bottom. The “mass of gathered solute molecules" is considered to be liquid, and is referred to merely as “solute". At equilibrium, the solute levels in the two compartments become equal. The inner and outer compartments form the shapes of solute in the stationary and mobile phases, respectively. For example, a vessel with cylindrical (inner) and trumpet-shaped (outer) walls is devoted to the convex (Langmuir-type) isotherm. Computer simulations of chromatography using the DGV model directly explained the asymmetric peaks caused by nonlinear isotherms. For example, the explanation of the tailing peak caused by convex isotherm, “as much solute is transferred (relatively to that remaining in the stationary phase) at the center of the band rather than at the edges, i.e. as the center moves faster than the edges, the chromatogram exhibits tailing", is directly understood from the simulated result (Figure 4A).
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  • Hirohito TSUE, Naoko TSUE
    Volume 6 (2000) Issue 4 Pages 137-144
    Released: February 28, 2001
    JOURNALS FREE ACCESS
    A new program has been developed for analyzing composition in an analytical sample that involves solvent molecules along with a target compound. It has the ability to handle three different kinds of solvents at a time though one of them is fixed as water. The calculation is carried out successively by the construction of a determinant, by transformation to the normal equation, and finally by the application of the Gauss elimination method. Logical analyses on compounds 14 were performed as an example of the use of this program. Taken in the light of experimental procedures in the laboratory, the present program will enable us to easily analyze most of the samples that show disagreement between the theoretical value and the observed one.
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  • Hidehiko NAKANO, Sumio TOKITA, Yoshiro NAKATA, Tadayosi YOSHIMURA, Hir ...
    Volume 6 (2000) Issue 4 Pages 145-156
    Released: February 28, 2001
    JOURNALS FREE ACCESS
    An electronic publishing system for “The Journal of Chemical Software" was developed. With this system, processes to prepare HTML and PDF(Portable Document Format) files to distribute through the Internet and to create printed issues were integrated. Manuscripts received from authors by electronic medium such as floppy disk or e-mail are converted to the SGML(Standard Generalized Markup Language) documents with authoring software( XSoft InContext2) for SGML. The SGML documents are then converted to HTML file for distribution through the internet and LaTeX source file to make printed issue with programs almost automatically. By applying this system, the operations for publishing with both electronic and printed media were simplified and the quality of printing was greatly improved.
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  • Yoshiro NAKATA, Toshiharu TAKIZAWA, Masami UEBAYASHI, Tatsuya NAKANO
    Volume 6 (2000) Issue 4 Pages 157-164
    Released: February 28, 2001
    JOURNALS FREE ACCESS
    A molecular graphics program was developed by using the OpenGL routine. The molecular coordinates in the three types of formats can be viewed as a molecular model. This program is written in the Visual C++ language and runs on any personal computers where MS-Windows is installed.
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  • Tohru SASAKI, Umpei NAGASHIMA, Masaru TSUKADA
    Volume 6 (2000) Issue 4 Pages 165-174
    Released: February 28, 2001
    JOURNALS FREE ACCESS
    We have developed a program for first principles DVXα calculations using an object-oriented programming language C++. Based on the program we have also developed a special purpose parallel computer for DVXα calculations, which realizes super high performance and cost-down of large scale DVXα calculation.
    The special purpose computer consists one host-board (Sparc Station10/74MHz) and 16 acceleration-boards. 4 TI320C40 processors are equipped on a board. The acceleration-board system has 64 processors connected to each other by VME-bus.
    The matrix elements generation step where more than 90% calculation time spends was parallelized on the system. In the case of Si78B6H53cluster, the special purpose computer is almost 40 times faster than that by a lone Sparc Station10 processor. Speed up of the matrix elements generation step is more than 100 times though 64 times is the theoretical maximum. Thus, super-linear speed up has been observed.
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