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Re: [Jmol-developers] Nano@home co-operation
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From: Miguel <mt...@mt...> - 2003-10-18 15:39:20
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>> It would be helpful for me to understand what type of potential >> applications you are thinking of ... >> >> Are you thinking of Jmol for viewing molecules? > Yes. We want to develop a kind of CAD tool for designing our own > molecules from the bottom up. Hmmm ... interesting ... > We call it a Computer Aided Molecular Design tool. Sounds like it is more important that you look at CDK than at Jmol. > We also want to use it to display results of molecular > modelling packages, which ones are unknown at the moment but we are > thinking about VASP? I don't know anything about this kind of thing. > We also want to develop our own scripting > language (probably in Python using Jython). Very good. You will need to build some powerful tools. >> is it in the context of an applet or of a standalone application? > Standalone application. OK >>> I would be grateful Miguel if you could give me more details about >>> this new 3D engine you are working on. It would help me defending our= >>> possible co-operation to the other critical project members. >> >>You said 'defending' ... what else are you looking at? > > Nothing at the moment=21 I have to defend my proposition of using Java > instead of some other language to develop our software. There are > others > in our group who would prefer to do it in C or C++. > We want our software to run on Windows and Linux systems at least. > Speed > is in fact the only factor that works against using Java for our > project but I think looking at the demo of your new engine that we > should go for it. Runtime speed is *not* a factor. I think I may have said this in my previous email ... I think that for th= e level of your application, Java code is only 10-20% slower. You are not writing systems code. Tell one of your developers to take a few days, write some benchmarks, an= d test it for himself/herself. Java will be slightly slower, but not enough= to really matter. What matters for your project is developer productivity. I think that you= r developers will be more productive using Java, especially your best developers. Java *will* be slower if the developers are wasteful in generating lots o= f garbage at runtime. But those same developers would have cost you more *development time* in the C++ world. I think that Java losing mindshare and going =22out of fashion=22 is a mo= re legitimate concern. See additional comments below. > There are just too many benefits in using Java. > Jmol is also, I think, one of the better examples of a =91general=92 > molecular visualisation package. Not too specific, not too big so it > should be fairly easy to strip it from the parts we will not need for > our software. > Did you test Jmol on a Linux or other unix system? Most of my development is done on RedHat Linux. When I am traveling I do development on a Win32 laptop. Egon uses a Sun. > Are you developing with the latest J2SE release (1.4.2_01)? Yes > I have noticed a considerable improvement in speed compared to 1.4. It is good to hear that you think it is faster. Sun PR said that it was faster. The specific graphics operations I want are still too slow. (I said that the graphics operations are slow, not that Java is inherently slow.) >> But it would be good to have someone else take a critical look at it, > or to use it heavily. > We will do that=21 Not to worry=21 :-) Good. Now, for my random thoughts. In fact, my blunt advice: I spent many years programming in C and C++ ... I have been programming i= n Java for 11 months. Frankly, I would not dream of doing your project in C++. You want to be cross-platform, Win + *nix. Which offers a more portable cross-platform *environment* of systems calls? You want to build a complicated CAD system. This is not a low-end system,= it is a high-end system. Your target users will have good hardware, multiple CPUs. You will want to use those CPUs to check the validity of structures in real-time. Which offers a more portable way of managing threads, Java or C++? You want to do some distributed computed ... in the form if your screen saver. Which language is better suited for managing distributed processes= ? Something *very* important for you should be availability of molecular modeling libraries. I honestly have no idea whether Java or C++ has bette= r stuff. But this is *much* more important than measly performance considerations. I believe that C++ has an advantage over Java in the area of OpenGL support, but you are not currently thinking of using OpenGL. Finally, I am going to going to say something that may surprise you. I don't think you should use Jmol ... you should use Java3D (or OpenGL if= you choose the C++ path). You are building a complex system that is targeted at users who will be running on high-end hardware. And we are talking about high-end hardware when you start to deplay 2 or 3 years from now. Your target users will *absolutely* have 3D graphics hardware. You should use it. I am not a fan of Java3D ... as a broad market product. Nevertheless it does work (I assume) and it does have its place. And I think its place is= for applications like yours. Java3D will slowly gain broader support and acceptance over the coming years. Training ... I am sure that you are hoping to have a team of developers. If you use Java3D/OpenGL then it will be much easier to train your developers and get them up to speed. Jmol is small and attractive and a more complete package for rendering molecules. But I think your project will outgrow it quickly. In summary, if it was my project - I would decide which chemical modeling libray to use. If there was a clear winner in the C++ world that may sway me to use C++ - I would use Java over C++ - I would use Java3D or OpenGL instead of jmol Let me know what you think. Don't hold back ... I didn't :-) Miguel > > Regards, > > Val=E8re > > > > > > ------------------------------------------------------- > This SF.net email sponsored by: Enterprise Linux Forum Conference & > Expo The Event For Linux Datacenter Solutions & Strategies in The > Enterprise Linux in the Boardroom; in the Front Office; & in the > Server Room http://www.enterpriselinuxforum.com > _______________________________________________ > Jmol-developers mailing list > Jmol-developers=40lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/jmol-developers -------------------------------------------------- Miguel Howard miguel=40howards.org c/Pe=F1a Primera 11-13 esc dcha 6B 37002 Salamanca Espa=F1a Spain -------------------------------------------------- telefono casa 923 27 10 82 movil 650 52 54 58 -------------------------------------------------- To call from the US dial 9:00 am Pacific US =3D home 011 34 923 27 10 82 12:00 noon Eastern US =3D cell 011 34 650 52 54 58 6:00 pm Spain -------------------------------------------------- |