Re: [Jmol-users] packaging success

2012-11-01 Thread Takanori Nakane
Hi, Did you try ClosureCompiler? http://closure-compiler.appspot.com/home It will remove whitespaces and rename local variables. In case of GLmol, it reduced the size more than 40%. Best regards, Takanori Nakane -- Log

Re: [Jmol-users] packaging success

2012-11-01 Thread Evans, Michael James
Very non-scientific study done with a stopwatch, but it confirms: Javascript: 14.1 seconds Java: 11.8 seconds That's the total load time for the page, from hitting Enter until caffeine appeared. Cheers, Mike On Nov 2, 2012, at 12:34 AM, Robert Hanson mailto:hans...@stolaf.edu>> wrote: How l

Re: [Jmol-users] packaging success

2012-11-01 Thread Robert Hanson
How long does it take for the load, roughly, in seconds? On Fri, Nov 2, 2012 at 12:25 AM, Evans, Michael James wrote: > I have to give a slight edge to Java on my system! Mac OS X 10.8, Safari > (Java 7). Of course, once the files have been cached, both are > lightning…but my perception is that

Re: [Jmol-users] packaging success

2012-11-01 Thread Evans, Michael James
I have to give a slight edge to Java on my system! Mac OS X 10.8, Safari (Java 7). Of course, once the files have been cached, both are lightning…but my perception is that Java is slightly faster. Something like a spinning loader image would probably help minimize the difference. Cheers, Mike

[Jmol-users] packaging success

2012-11-01 Thread Robert Hanson
OK, JSmol is loading from one core file now, with additional file loading as necessary. See http://chemapps.stolaf.edu/jmol/jsmol/test2.htm?USE=HTML5 I'm interested in which is faster, this JavaScript loading or the standard Java applet loading: http://chemapps.stolaf.edu/jmol/jsmol/test2.htm?US

Re: [Jmol-users] Generating Periodic Boundary Structure in Jmol for Molecular Dynamics

2012-11-01 Thread Oloriegbe, Suleiman
Thanks. The overlapping problem is gone, but the resulting system have incorrect number of atoms. I got 2783 atoms when using select cell=555. The structure looks perfect but the number of atoms is not. For my system of CuAlO2. I got 726 Al atoms, 726 Cu atoms and 1331 O atoms (instead of 726 *

Re: [Jmol-users] Generating Periodic Boundary Structure in Jmol for Molecular Dynamics

2012-11-01 Thread Robert Hanson
You would first select the atoms you want. For example, select cell=555 On Thu, Nov 1, 2012 at 11:59 AM, Oloriegbe, Suleiman < olorieg...@missouri.edu> wrote: > Thanks Bob, > > > > I didn't get your e-mail despite configuring jmol to allow me receive > mails from the list. I was able to copy

Re: [Jmol-users] Generating Periodic Boundary Structure in Jmol for Molecular Dynamics

2012-11-01 Thread Oloriegbe, Suleiman
Thanks Bob, I didn't get your e-mail despite configuring jmol to allow me receive mails from the list. I was able to copy your response from the mail list website (see below). I eventually use; load "filename.cif" {555 555 0} supercell { 8 8 2 } and got a supercell with small box encompass

Re: [Jmol-users] Generating Periodic Boundary Structure in Jmol for Molecular Dynamics

2012-11-01 Thread Robert Hanson
{1 1 1} indicates you want a packed cell, which duplicates atoms on faces. try {555 555 0} instead and see if that helps. On Thu, Nov 1, 2012 at 8:51 AM, Oloriegbe, Suleiman wrote: > Could anyone on the list help me with getting rid of overlapping atoms > on edges, boundaries and corners aft

[Jmol-users] Generating Periodic Boundary Structure in Jmol for Molecular Dynamics

2012-11-01 Thread Oloriegbe, Suleiman
Could anyone on the list help me with getting rid of overlapping atoms on edges, boundaries and corners after generating a superstructure from jmol through a CIF file. The XYZ file would be use as input in Molecular dynamics program LAMMPS. I use load "filename.CIF" {1 1 1} supercell {8 8 2

Re: [Jmol-users] JSmol nearly fully functional

2012-11-01 Thread Angel Herráez
Dear Jmolers, We have started to collect some information on this exciting new addition at http://wiki.jmol.org/index.php/JSmol That page is not too obviously linked yet from others, but I will keep working on that. After all, this is still in development phase and so not directly addressed to