Re: [Jmol-developers] [**VIRUS** ? (Suspect file type in archive)] Signed Applet performance

[Robert H. <ha...@st...>]

Eric, there are a number of problems with that page. I don't know about the
signed/unsigned business, but first let's get this part fixed:

//   calculate the three dimensions of the box
     jmolScript("Vx = (V1.x - V5.x)");
     jmolScript("Vy = (V1.y - V5.y)");
     jmolScript("Vz = (V1.z - V5.z)");
     jmolScript("a = sqrt(Vx*Vx + Vy*Vy + Vz*Vz)");

     jmolScript("Vx = (V1.x - V3.x)");
     jmolScript("Vy = (V1.y - V3.y)");
     jmolScript("Vz = (V1.z - V3.z)");
     jmolScript("b = sqrt(Vx*Vx + Vy*Vy + Vz*Vz)");

     jmolScript("Vx = (V1.x - V2.x)");
     jmolScript("Vy = (V1.y - V2.y)");
     jmolScript("Vz = (V1.z - V2.z)");
     jmolScript("c = sqrt(Vx*Vx + Vy*Vy + Vz*Vz)");


//   calculate the box volume
     jmolScript("volume = a * b * c ");
     vol=jmolEvaluate("volume%1");
     aa =jmolEvaluate("a%1");
     bb =jmolEvaluate("b%1");
     cc =jmolEvaluate("c%1");


This will not work properly and is very inefficient. First, get all those
script calls into one string:

"Vx = (V1.x - V5.x);Vy = (V1.y - V5.y);Vz = (V1.z - V5.z);a = sqrt(Vx*Vx +
Vy*Vy + Vz*Vz);Vx = (V1.x - V3.x)..."

With that in mind, you should probably just use:

"V1.distance(V5)"

But the more important thing is that jmolScript is asynchronous, and
jmolEvaluate is not. Really what you want is this:

a = jmolEvaluate(V1.distance(V5))
b = jmolEvaluate(V1.distance(V3))
c = jmolEvaluate(V1.distance(V2))
vol = a * b * c

you can do the rounding in JavaScript.


But.... on the other hand, it will work fine with just this little tweak:

At the top of your script tag, add this to buffer the script into Jmol:

jmolScript0 = jmolScript;

script = ""
jmolScript = function(a) {
    // buffer these into jmol -- jmolScript() by itself clears the buffer
  if (a) {
      script += ";" + a;
  } else {
      jmolScript0(script);
      script = "";
  }
}

then add

jmolScript()

just before

vol=jmolEvaluate("volume%1");

and just at the end of the drawBox() function.

You should be all set.

Really a very cool page!

Bob





On Fri, Oct 5, 2012 at 11:20 PM, eric henon <eri...@un...>wrote:

> Dear all,
>
> once more I meet one
> problem using my jMol code (attached).
>
> When using the signed applet,
> the applet becomes very very slow.
>
> For example,
> rotating my box into the jMol windows
> (I built a box that I can translate, rotate, scale)
> takes about 3-4s for each rotation, while
> it is quasi-instantaneous using the unsigned applet.
>
> Thus, only adding the true parameter in the jmolInitialize
> method substantially influences the performance
> of the applet.
>
> Is it a "standard" behavior ?
>
> Thanks in advance.
> Best regards.
> Eric Henon
>
>
>
>
>
>
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-- 
Robert M. Hanson
Larson-Anderson Professor of Chemistry
Chair, Chemistry Department
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