Re: [Jmol-users] drawing cones

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

Well, it's symmetry axis is along Z, so just shorten or lengthen Z to change
the opening angle. Or change X and Y distances. Right?

On Wed, Oct 6, 2010 at 12:30 PM, Pshemak Maslak <pm...@ch...> wrote:

>  On 10/4/2010 1:14 PM, Robert Hanson wrote:
>
> yes, I think so. Just adjust the vector parameters to make it any size you
> want.
>
>
> The top of the jvxl file with the cone:
> [...]
> functionXY
> curveAsStringXY
> -2 -5.0 -5.0 -5.0 ANGSTROMS
> </jvxlFileTitle>
> <jvxlVolumeData origin="{-5.0 -5.0
> -5.0}">
> <<<< changing these changes origin
> <jvxlVolumeVector type="0" count="51" vector="{0.2 0.0
> 0.0}"></jvxlVolumeVector>                    <<<< changing these changes
> size
> <jvxlVolumeVector type="1" count="51" vector="{0.0 0.2
> 0.0}"></jvxlVolumeVector>                    <<<< changing these changes
> size
> <jvxlVolumeVector type="2" count="51" vector="{0.0 0.0
> 0.2}"></jvxlVolumeVector>                    <<<< changing these changes
> size
> [....]
>
> I can change the origin, or size or make it elliptic (if the vectors are
> not the same), but I do not know how to change the opening angle.
>
>
> Thanks for your help,
>
> PM
>
>
>  On Mon, Oct 4, 2010 at 11:08 AM, Pshemak Maslak <pm...@ch...> wrote:
>
>>
>> On 10/1/2010 11:04 PM, Robert Hanson wrote:
>> >
>> > I lied. OK, see the JVXL file at
>> >
>> > http://stolaf.edu/people/hansonr/chemapps/jmol/docs/misc/cone.jvxl
>> >
>> > for a the surface z = sqrt(x^2 + y^2). Because it is a JVXL file, you
>> > can go in and change the axes, change the scaling, change the origin,
>> > etc., and have any cone you want. Even elliptical cones.
>>
>>  Thank you very much for creating this nice cone. Can I change its
>> opening angle directly in the jvxl file?
>>
>>
>> >
>> > This was created at
>> >
>> >
>> http://chemapps.stolaf.edu/jmol/docs/examples-11/isosurface.htm?USSIGNEDAPPLET&topic=14
>> > <
>> http://chemapps.stolaf.edu/jmol/docs/examples-11/isosurface.htm?USSIGNEDAPPLET&topic=14
>> >
>> >
>> > by entering
>> >
>> > Math.sqrt(x^2 + y^2) into the input box, clicking the link discussed
>> > there to "set the function" and then issuing the following on the
>> > command line:
>> >
>> > javascript "x0=-5;y0=-5;dx=.2;dy=.2";isosurface functionXY
>> > "curveAsStringXY" {-5 -5 -5} {-51 0.2 0 0} {51 0 0.2 0} {51 0 0 0.2};
>> >
>> > followed by
>> >
>> > write isosurface "cone.jvxl"
>>
>>  I tried that (under item 14, after zapping the preloaded model). I
>> entered "Math.sqrt(x^2 + y^2)" into the box and clicked the "click here
>> to set the function" link (confirmed by the message window). After
>> entering the script (above) on the command line I am getting a very
>> complicated "egg-box" shape.
>>
>> If I do not click on the "click here to set the function" link I get a
>> half of an ellipsoid (a "cone" with parabolic cross-sections) with the
>> above script..
>>
>> I am sure I am doing something wrong.
>>
>> All below is above my head (I speak no programming language :-(). And
>> that is my problem.
>>
>> Thanks for your help,
>>
>> PM
>>
>>
>> >
>> >
>>  > That instructs Jmol to get the Z coordinate of the function from the
>> > JavaScript function curveAsStringXY, which reads:
>> >
>> > function curveAsStringXY(app, nX, nY) {
>> >   var i1 = Math.abs(parseInt(""+nX));
>> >   var i2 = Math.abs(0.0 + parseInt(""+nY));
>> >   var s = ""
>> >   for (var i = 0; i < i1; i++)
>> >     for (var j = 0; j < i2; j++) {
>> >       s+= curveXY("",i, j) + "\n";
>> >     }
>> >   return s;
>> >
>> > }
>> >
>> >
>> > x0 = 0
>> > y0 = 0
>> > dx = 1
>> > dy = 1
>> > x = 0
>> > y = 0
>> >
>> > function curveXY(app, ix, iy) {
>> >  setXY(ix, iy)
>> >  return eval(myfunction);
>> > }
>> >
>> > function setXY(ix, iy) {
>> >  x = ix * dx + x0
>> >  y = iy * dy + y0
>> > }
>> >
>> >
>> > function setFunction(f,isSilent){
>> >   myfunction =
>> > (arguments.length<1?document.getElementById("fOfXY").value:f)
>> >   var x=1
>> >   var y=1
>> >   var z=NaN
>> >   try{eval("z="+myfunction)}catch(e){alert(e)}
>> >   if(isNaN(z)){
>> >     alert("Your function is invalid")
>> >     myfunction = "(x*x+y*y)"
>> >   }
>> >   try{curveXY("",1,1)}catch(e){alert(e);return}
>> >   if (!isSilent)alert("The function Jmol will use is now z=" +
>> > myfunction)
>> > }
>> >
>> > myfunction = "(x*x + y*y)/3"
>> > setFunction(myfunction,1)
>> >
>> >
>>
>>
>>
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>
>
>
> --
> Robert M. Hanson
> Professor of Chemistry
> St. Olaf College
> 1520 St. Olaf Ave.
> Northfield, MN 55057
> http://www.stolaf.edu/people/hansonr
> phone: 507-786-3107
>
>
> 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
>
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-- 
Robert M. Hanson
Professor of Chemistry
St. Olaf College
1520 St. Olaf Ave.
Northfield, MN 55057
http://www.stolaf.edu/people/hansonr
phone: 507-786-3107


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