Over the last couple of years I have created a number of web pages using Jmol, to support research publications in inorganic main-groups chemistry or for undergraduate teaching.
I have created a portfolio web page https://www.staff.ncl.ac.uk/bruce.tattershall/jmolapps/portfolio.html showing six different examples of these, to try to encourage my colleagues to do likewise, but I have to start by telling them to use a Java-enabled browser. It would be much better if I didn't need to. All of my web pages offer the user a choice of using the Java Jmol applet or the HTML5.0 JSmol applet, implemented using the concatenation of JSmol.min.js and Jmol2.js as recommended in http://wiki.jmol.org/index.php/Jmol_JavaScript_Object and patching the value of use in the Info variable for Jmol.getApplet("JmolApplet0", Info) accordingly. For all of my web pages, using IE11 and the Java plugin, and taking my offered Java Jmol applet option, works excellently, producing Jmol_S models. Firefox for Windows with the Java plugin is also fine. Moving to Chrome and necessarily taking the HTML5.0 JSmol applet option also works very well for models of molecular geometry, including reaction path animations. However, models of orbital surfaces, or contour plots of orbitals on a plane, are much too slow to load. An example is provided from https://www.staff.ncl.ac.uk/bruce.tattershall/teaching/chy135/co2mo/co2.php in which MOs for CO2 may be picked from an energy level diagram. This calling page is fine with either applet, but the called page which generates the model for the chosen MO, is not. An example, with the query string set for HTML5.0 JSmol use, is https://www.staff.ncl.ac.uk/bruce.tattershall/teaching/chy135/co2mo/showjmol.php?use=HTML5&filestem=co2&basis=MO&orbital=sigma_C(2p)O(2p)&orbno=9&winno=1 In Chrome, this takes 20 seconds, and about the same in Firefox (compared with 4 seconds for the Java Jmol applet option), while IE11 takes 35 seconds, in each case running in a dual core 2.93GHz 32-bit PC running Windows 7. (IE11 without Java is unacceptable anyway because its mouse response in rotating models is too slow and jerky, for any kind of model.) The orbital data comes from an NBO calculation, so the orbital distribution is calculated entirely within the applet. By calling the functions to calculate an mo surface or to calculate a contour plot on the yz plane, from a LoadStructCallback function, I can ensure that the data loading is done only once. Putting on breakpoints in a debugger shows that this is not the time-consuming part. It appears to be that it is calculating the mo surface which is taking the bulk of the time. I should be very happy if someone more expert in using JSmol could look at the page source of the example above, and let me know if I am doing something poorly. The .php script is only doing the obvious in interpreting the query string: everything of consequence in using JSmol is visible in the delivered HTML/Javascript page source. Thanks Bruce Tattershall School of Chemistry, Newcastle University, England ------------------------------------------------------------------------------ Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot _______________________________________________ Jmol-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-users
