pim schravendijk wrote: >I couldn't use Jmol to open a 185 MB multiframe xyz file. I increased >the memory available for java (via -Xms and -Xmx) to 1 GB, but this >didn't help. The file opens in vmd without problems, using 5 % memory >on a 1 GB system. That is about 50 MB, java allocates 64 MB on default >(one can see that because jmol normally stops after using up 62 MB), >so in theory, one should be able to do systems that are big enough >without having to cross the default java memory barrier. > >What is the issue here? I guess Jmol creates an object for every >single coordinate in the xyz system. Otherwise one wouldn't be able to >manipulate objects over all the frames instantaneously. The size of an >object is probably larger than just the coordinates given in the input >file, so memory size is blown up when going from xyz file to working >memory. > > > I think that's the issue. Is there any chance you could live with just one frame present at a time? Sort of a streaming video idea?
>Cutting the file up seems the way to go. But would it be possible to >have Jmol do that by itself? some sort of 'read multiframe' option >where it detects multiframe files and reads them one frame at a time? > > load "myfile" 3 loads just the third frame. Haven't considered load "myfile 3-4 But it's certainly worth looking at. Only problem here is that it would require some retooling of all the multifile readers. Not so bad, really, but a task. >Or are there too many disadvantages to that (not being able to edit >objects in frames that aren't read yet, long loading times per frame). >I guess also a problem is that one cannot always assume that the atom >types and order stay constant over the multiframe file. > > > Be more specific about your plans for that large file? Could it stream? >Just some thoughts here, would be nice if Jmol could handle files like >this without human interference or external shell scripts :) > > > I've certainly thought about this. There is the concept, undocumented, of a "trajectory" that doesn't have quite the overhead of a full file load. In a trajectory, the atoms are all the same in each frame, so there is just one reasonably sized set of atoms, and only the coordinates are changed when you go from frame to frame. That's in Jmol now, but I haven't experimented with it much. Bob -- Robert M. Hanson Professor of Chemistry St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 ------------------------------------------------------------------------- This SF.net email is sponsored by: Splunk Inc. Still grepping through log files to find problems? Stop. Now Search log events and configuration files using AJAX and a browser. Download your FREE copy of Splunk now >> http://get.splunk.com/ _______________________________________________ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
