From armin@nrcgeb.ac.ir Sat Jul 26 05:13:32 1997 Received: from genetic.nrcgeb.ac.ir for armin@nrcgeb.ac.ir by www.ccl.net (8.8.3/950822.1) id EAA06932; Sat, 26 Jul 1997 04:18:16 -0400 (EDT) Received: from AMS ([194.225.65.221]) by genetic.nrcgeb.ac.ir (4.1/SMI-4.1) id AA15187; Sat, 26 Jul 97 12:50:52 EDT Date: Sat, 26 Jul 97 12:50:52 EDT Message-Id: <9707261650.AA15187@genetic.nrcgeb.ac.ir> X-Sender: armin@genetic Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" To: chemistry@www.ccl.net From: armin@nrcgeb.ac.ir (Armin M. Sobhani) Subject: Re: CCL:Object-oriented means for computational chemist X-Mailer: Dear Ping, For a good example on doing Object-Oriented programming (including inheritance) in conventional C (OOPC), please refer to the article below: Linowes J.S. "It's an Attitude: There's a lot of extra coding, but you can do object-oriented programming in conventional C", Byte Magazine, Vol.13 No.8 August 1988, pp. 219-224 Ping Du wrote: >there is a point that I would like to bring up. That is, is it >possible to implement an OO design using a non-OO language? The main >design features of OOD are abstraction, encapsulation, and >inheritance. One may achieve abstraction and encapsulation in a >non-OO language by forcing discipline. For example, use struct in C >as if there were classes and access data members through "interface" >functions. However, implementing inheritance is impossible without >an OO language. Inheritance is pobably the most important feature of Regards, Armin +----------------------------------------------------------------+ | __()__ NRCGEB: | Armin M. Sobhani | | //\\//\\ National | Email: armin@nrcgeb.ac.ir | | // (()) \\ Research | madadkar@pars.ipm.ac.ir | |(( (()) )) Center for | URL : http://www.nrcgeb.ac.ir/armin| | \\ (()) // Genetic | Tel : +98 21 6418310 | | \\_/\_// Engineering & | Fax : +98 21 6419834 | | (NRCGEB) Biotechnology | P.O.Box: 14155-6343, Tehran, IRAN | +----------------------------------------------------------------+ | Once you understand the universe at the atomic level | | everything else is easy. -Richard P. Feynman | +----------------------------------------------------------------+ From gmercier@mail.med.upenn.edu Sat Jul 26 11:13:34 1997 Received: from mail.med.upenn.edu for gmercier@mail.med.upenn.edu by www.ccl.net (8.8.3/950822.1) id KAA07836; Sat, 26 Jul 1997 10:56:24 -0400 (EDT) Received: (from gmercier@localhost) by mail.med.upenn.edu (8.8.5/8.8.5) id KAA00230 for chemistry@www.ccl.net; Sat, 26 Jul 1997 10:56:27 -0400 (EDT) From: "Gustavo A. Mercier Jr" Message-Id: <199707261456.KAA00230@mail.med.upenn.edu> Subject: Finite Diff.: Mapping Grid->XYZ How? To: chemistry@www.ccl.net Date: Sat, 26 Jul 1997 10:56:27 -0400 (EDT) X-Mailer: ELM [version 2.4 PL23-upenn3.1] MIME-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Hi! I am a bit confused about the way that finite difference methods map a grid onto a coordinate system. I am particularly interested in the way that the Univ. of Houston Brownian Dyn. package does it. This package uses a finite difference method to solve the Linearized Poisson Boltzman Eq. (I believe it is the same implementation in Delphi.) For simplicity let me talk about a 1D grid. In the input you specify the grid size. You also specify the X coordinate for the center of the grid, and the grid step. This is simple enough. My question is what are the values for X? Case: grid size 6, center 0.0, and step size 0.5 One way: grid indices: 1 2 3 4 5 6 center: 0 X values: -1.25 -0.75 -0.25 0.25 0.75 1.25 Another way: grid indices: 0 1 2 3 4 5 6 center: 0 X values: -1.5 -1.0 -0.5 0 0.5 1.0 1.5 And the value at index 0 is just a dummy. The situation seems clearer (or easier) with odd grid sizes. Case: grid size 7, center 0.0, step size 0.5 grid indices: 1 2 3 4 5 6 7 center: 0 X values: -1.5 -1.5 -0.5 0.0 0.5 1.0 1.5 but it can also get muddled! grid indices:0 1 2 3 4 5 6 7 center: 0 X #: -1.75 -1.25 -0.75 -0.25 0.25 0.75 1.25 1.75 With the value at index 0 just a dummy point. The UHBD output prints the left most X coordinate, but calls it a "nonexistent point". Is that the dummy above? Could anyone shed some light on this, or even better provide "accepted" formulas to get the ranges/values of X at the grid vertices (points), if there are standard ways of doing the mapping? Thanks! -- ("`-/")_.-'"``-._ Gustavo A. Mercier,Jr.,MD,PhD (. . `) -._ )-;-,_() Division of Nuclear Medicine (v_,)' _ )`-.\ ``- Dept. of Radiology _;- _,-_/ / ((,' University of Pennsylvania ((,.-' ((,/ 3400 Spruce St. gmercier@mail.med.upenn.edu Philadelphia, PA 19104 215-662-3069/3091 fax: 215-349-5843