35945 2003-12-16 08:08 0000 Tinker 4.1 Ebuild 2005-12-03 12:20:55 0000 1 1 1 Unclassified Gentoo Linux Ebuilds unspecified All Linux RESOLVED FIXED EBUILD P2 enhancement --- 1 jwarren@cheesefoam.dyndns.org sci@gentoo.org jwarren@cheesefoam.dyndns.org 2003-12-16 08:08:36 0000 Tinker is a molecular modeling and computations package geared towards high-speed calculations on large systems and molecules. It comes with a java-based interface called "Force Field Explorer", which is still under development - i.e. it is sometimes quite cranky and unstable, depending on the version of JRE and Java3D you have installed. Tinker itself, however, which runs from the command line, is rock-solid. Reproducible: Always Steps to Reproduce: 1. 2. 3. This package depends upon Java3D for FFE, and FFE is totally unstable with the 1.3.1 beta of Java3D. As a result, you should use the 1.3-FCS version with this package for right now. Though FFE is problematic, the core Tinker application, as stated above, works very well, and is very stable. Tinker is VERY fast when it comes to large-scale computations. jwarren@cheesefoam.dyndns.org 2003-12-16 08:09:28 0000 Created an attachment (id=22301) Tinker 4.1 ebuild dberkholz@gentoo.org 2003-12-30 13:10:16 0000 Ah, cool. This is one of the things I've wanted to get to but haven't had the chance. I'll look at it soon. jwarren@cheesefoam.dyndns.org 2004-02-25 07:20:02 0000 Created an attachment (id=26329) Updated Tinker 4.1 ebuild This is a full ebuild for Tinker 4.1 which fixes the problem associated with the missing parameter files. Energy minimizations now work fine - all parameter files are now properly placed into the "/usr/local/tinker/params" directory where the belong. dberkholz@gentoo.org 2004-02-25 08:03:23 0000 Gentoo can't install to /usr/local, that's for personal use. We stick to /usr. jwarren@cheesefoam.dyndns.org 2004-02-25 08:08:37 0000 Created an attachment (id=26330) DIFF patch to fix the paths for the ebuild This patch fixes all of the destinations to the proper /usr/tinker directory. jwarren@cheesefoam.dyndns.org 2004-02-25 09:47:03 0000 Created an attachment (id=26333) Diff to fix Tinker ebuild to use the Java3D now in Portage Now depends upon dev-java/blackdown-java3d. jwarren@cheesefoam.dyndns.org 2004-02-27 12:40:39 0000 I think the version of Java3d in Portage works ok now. With the path fixes and the portage Java3D, the Force Field Explorer GUI runs pretty well, being much less prone to random crashes. I think all things being equal, this is about as stable as this package is going to be short of actual updates on the part of the program itself. I'll make an updated ebuild for this app to use ICC/IFC during compilation, and upload a full ebuild. Other than that, though, I think this one is about as good as it's gonna get. dberkholz@gentoo.org 2004-02-29 20:39:03 0000 For the ICC/IFC stuff, make sure it doesn't use USE flags. It should just respect the environment variables $CC and $FC. dberkholz@gentoo.org 2004-04-02 16:08:16 0000 Please turn all the spaces indenting the various parts into tabs. I'd like to take a look at this. dberkholz@gentoo.org 2004-12-14 23:41:57 0000 WebMO 5.0, just released, added support for >=tinker-4.2. Since I'm a huge fan of WebMO, I've suddenly become more interested in making something happen with this. I emailed the upstream author and requested a friendlier distribution style, with a versioned tarball. dberkholz@gentoo.org 2004-12-15 00:11:59 0000 By the way, 4.2's distribution method really sucks, the way it looks. There's crap all over the place, and most of it isn't even in the (unversioned) tarball. jwarren@cheesefoam.dyndns.org 2004-12-15 06:48:49 0000 That's an understatement. I did spend some time messing with it, but was unable to figure out how to manually dig out all of the necessary files out of the distribution - I was able to update the tinker executables themselves to the 4.2 rev, but the ffe GUI is still a nightmare. Since I have no experience with JBuilder or building java apps period, I'm not sure how to proceed on this. In theory, I would suggest we go with grabbing the tinker source executable from: ftp://dasher.wustl.edu/pub/tinker.tar.gz And the FFE source from: http://dasher.wustl.edu/ffe/ffe-source.jar And compiling ffe from the source. It's really a shame that the distribution method is so bad - as I'm forced to use the Windows version now. Sadly, the 4.2 rev, when installed, works VERY well. I still use it via CLI on a linux box to do long-term calculations, but for simple stuff I use the Windows one, since that is the only thing which plays nice for the time being. dberkholz@gentoo.org 2004-12-15 09:29:56 0000 I just got an email from Jay Ponder that basically said, (summary) "We won't make it easier to start using because it's difficult to use properly once it does work." We'd probably be better off just creating a custom tarball with whatever we need in it, in addition to the tinker.tar.gz. dberkholz@gentoo.org 2005-12-03 12:20:55 0000 I've just added tinker-4.2 to the tree, but I can't get FFE working. I'd really appreciate if you could take a look at that. 22301 2003-12-16 08:09 0000 Tinker 4.1 ebuild tinker-4.1.ebuild text/plain IyBDb3B5cmlnaHQgMTk5OS0yMDAzIEdlbnRvbyBUZWNobm9sb2dpZXMsIEluYy4KIyBEaXN0cmli dXRlZCB1bmRlciB0aGUgdGVybXMgb2YgdGhlIEdOVSBHZW5lcmFsIFB1YmxpYyBMaWNlbnNlIHYy CiMgJEhlYWRlcjogL2hvbWUvY3Zzcm9vdC9nZW50b28teDg2L2FwcC1zY2kvdGlua2VyL3Rpbmtl ci00LjEuZWJ1aWxkLHYgMS4wIDIwMDMvMTIvMTUgMjA6MDc6MTQgQ2hlZXNlZm9hbSBFeHAgJAoK REVTQ1JJUFRJT049IlRJTktFUiBpcyBhIG1vbGVjdWxhciBtb2RlbGluZyBwYWNrYWdlIHdoaWNo IGluY2x1ZGVzIGZvcmNlIGZpZWxkcyBmb3IgaGFuZGluZyBsYXJnZSBtb2xlY3VsZXMgYW5kIGxh cmdlIHN5c3RlbXMsIHN1Y2ggYXMgQU1CRVIgYW5kIENIQVJNTS4gIEEgSmF2YSBiYXNlZCB2aXN1 YWxpemF0aW9uIGZyb250IGVuZCBpcyBpbmNsdWRlZC4iCkhPTUVQQUdFPSJodHRwOi8vZGFzaGVy Lnd1c3RsLmVkdS90aW5rZXIvIgpTUkNfVVJJPSJmdHA6Ly9kYXNoZXIud3VzdGwuZWR1L3B1Yi90 aW5rZXIudGFyLmd6IgoKTElDRU5TRT0iVGlua2VyIgpTTE9UPSIwIgpLRVlXT1JEUz0ieDg2IgoK REVQRU5EPSJkZXYtamF2YS9qYXZhM2QiClM9IiR7V09SS0RJUn0vdGlua2VyL3NvdXJjZSIKCnNy 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