On 04/05/2015 05:58 AM, Robert Hanson wrote: > Rolf, I think you could have a lot of fun with the "JavaScript" functions > Jmol provides. Jmol never does loops like that. Instead it initializes a > "three-dimensional binary tree" -- we call it a "binary forest" :) -- and > you specify a point and a radius, then iterate until done. It is far far > faster. The class is java.bspt.Bspf. It could be used outside of Jmol, I > think. > Currently I would rather try to add the minimization algorithm to Java than to Javascript since it should work fast for Java and Javascript. But it will take quite some time until I can start with that.
As a first step I replaced my current grid implementation by using the "within" command. Now there is already a small gain with 100 atoms. and with ~1200 atoms 100 iterations need 400 seconds compared to 980 seconds without optimization and 1400 seconds with my grid implementation (being still slower than without grid). > I did some minor tweaks of the FOR command, and I also added what I think > is a nice syntax that loops 2-3 times faster than (i=1; i < n; i++) > > for (var i FROM [1 10000] ) { > ...increments up > } > > for (var i FROM [10 -1]) { > ...increments down > } > Very nice Bob, thank you. I observe the same speedup with IcedTea Java. > bug fix: for (var i in hashArray) {....} broken (also in 14.2; not fixed > there) I thought this didn't work because it wasn't implemented since it wasn't mentioned in the 'for' documentation. Q: Does 'i' contain the hash key (as in Perl) or the value? Regards, Rolf -- Rolf Huehne Postdoc Leibniz Institute for Age Research - Fritz Lipmann Institute (FLI) Beutenbergstrasse 11 07745 Jena, Germany Phone: +49 3641 65 6205 Fax: +49 3641 65 6210 E-Mail: rhue...@fli-leibniz.de Website: http://www.fli-leibniz.de Scientific Director: Prof. Dr. K. Lenhard Rudolph Head of Administration: Dr. Daniele Barthel Chairman of Board of Trustees: Dennys Klein VAT No: DE 153 925 464 Register of Associations: No. 230296, Amtsgericht Jena Tax Number: 162/141/08228 ------------------------------------------------------------------------------ BPM Camp - Free Virtual Workshop May 6th at 10am PDT/1PM EDT Develop your own process in accordance with the BPMN 2 standard Learn Process modeling best practices with Bonita BPM through live exercises http://www.bonitasoft.com/be-part-of-it/events/bpm-camp-virtual- event?utm_ source=Sourceforge_BPM_Camp_5_6_15&utm_medium=email&utm_campaign=VA_SF _______________________________________________ Jmol-developers mailing list Jmol-developers@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-developers