had to do it....
version=11.9.10_dev
# new feature: draw intersection $isosurfaceID PLANE|HKL [plane definition]
# for example:
# isosurface s1 sasurface
# draw diameter 0.1 intersection $s1 PLANE x=13 color red
# new feature: isosurface color mesh <color name> <surface definition>
# colors mesh a specific color independent of isosurface color or color
mapping.
# bug fix: rear mesh lines not visible on isosurface when surface also drawn
On Mon, Nov 30, 2009 at 6:33 PM, Robert Hanson <[email protected]> wrote:
> I think it's great you are working with them on this. Since I have the way
> to draw arbitrary lines on an isosurface in JVXL, I wonder if it would be
> possible to do that (or some contouring) after the fact with isosurface --
> sort of a combination of draw and isosurface.
>
> Bob
>
>
>
> On Mon, Nov 30, 2009 at 12:24 PM, Jonathan Gutow <[email protected]> wrote:
>
>> Bob,
>> Thanks. I think they want both contour lines and mesh. So far
>> I've
>> only worked on the mesh part. I will keep in mind that they should
>> consider changing the format they use, but first I was trying to get
>> the basic interactive functionality they wanted working in the
>> SAGEnotebook interface using what they presently generate. Once that
>> is working I should be able to get a better idea of what they really
>> want to be able to do. Then I will prod them to change the files they
>> generate appropriately. I'm trying not to get involved in too much
>> rewriting to the SAGE code, just javaScript. One major project is
>> enough!
>>
>> Jonathan
>> On Nov 30, 2009, at 11:02 AM, Robert Hanson wrote:
>>
>> > Ah -- I see I did that just for contour lines -- latest upload has
>> > the same for mesh lines. 2 pixels forward of mesh surface, so they
>> > show up in rear as well as front.
>> >
>> > On Mon, Nov 30, 2009 at 10:47 AM, Robert Hanson <[email protected]>
>> > wrote:
>> > Jonathan, are you using Jmol 11.9? I remember fixing this there -
>> > the renderer automatically pushes the mesh line just a pixel forward
>> > of the surface when rendering, even in the back. You can now
>> > customize the contour lines on an isosurface and color them any way
>> > you want. So please look into that -- contourlines instead of mesh.
>> > Talking with Jason, I think this is more what they are interested in
>> > anyway. I basically added functionality that matches Gnuplot in that
>> > regard.
>> >
>> > In addition, the latest JVXL file format now allows for arbitrary
>> > lines drawn on a mesh. Any color, any direction, any number. So that
>> > is the real way to go -- produce JVXL files that can display the
>> > desired lines and load them. "mesh" is not up to it.
>> >
>> > Bob
>> >
>> >
>> >
>> > On Fri, Nov 27, 2009 at 10:25 AM, Jonathan Gutow <[email protected]>
>> > wrote:
>> > I've been cooperating with the SAGE development team to get Jmol
>> > working better for viewing 3-D plots in SAGE. We are still discussing
>> > what a plot primitive would look like, but I ultimately think that is
>> > the way things should go.
>> >
>> > However, a separate issue of how meshes look has come up. Their
>> > first request was easy to deal with. I'm simply loading each surface
>> > twice and displaying one copy as mesh to allow for meshes of arbitrary
>> > color compared to the solid surface. We may want to include something
>> > different in the plot primitive, but this works well for now. The
>> > second issue is harder to deal with. Using either the built-in mesh
>> > or the second surface as mesh, mesh lines disappear as the surface
>> > angles back. At first I thought this was a perspective issue, but it
>> > seems to have something to do with whether solid surface or line color
>> > takes precedence for a pixel. Setting the solid surface to slightly
>> > translucent solves the problem for the case where I use a second
>> > surface to display the mesh. So the question for people who know more
>> > about the rendering is if there is a way the meshes could be made to
>> > have precedence when coloring a pixel, without making the solid
>> > surface translucent? One problem I foresee is that as we approach the
>> > vanishing point the color of the surface should take precedence.
>> > Maybe the balance needs to be adjusted?
>> >
>> > Jonathan
>> > Dr. Jonathan H. Gutow
>> > Chemistry Department [email protected]
>> > UW-Oshkosh Office:
>> > 920-424-1326
>> > 800 Algoma Boulevard FAX:920-424-2042
>> > Oshkosh, WI 54901
>> > http://www.uwosh.edu/facstaff/gutow
>> >
>> >
>> >
>> >
>> >
>> >
>> >
>> ------------------------------------------------------------------------------
>> > Let Crystal Reports handle the reporting - Free Crystal Reports 2008
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>> > _______________________________________________
>> > Jmol-developers mailing list
>> > [email protected]
>> > https://lists.sourceforge.net/lists/listinfo/jmol-developers
>> >
>> >
>> >
>> > --
>> > 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
>> >
>> >
>> >
>> > --
>> > 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
>> >
>> ------------------------------------------------------------------------------
>> > Let Crystal Reports handle the reporting - Free Crystal Reports 2008
>> > 30-Day
>> > trial. Simplify your report design, integration and deployment - and
>> > focus on
>> > what you do best, core application coding. Discover what's new with
>> > Crystal Reports now. http://p.sf.net/sfu/bobj-july
>> > _______________________________________________
>> > Jmol-developers mailing list
>> > [email protected]
>> > https://lists.sourceforge.net/lists/listinfo/jmol-developers
>>
>> Dr. Jonathan H. Gutow
>> Chemistry Department [email protected]
>> UW-Oshkosh Office:920-424-1326
>> 800 Algoma Boulevard FAX:920-424-2042
>> Oshkosh, WI 54901
>> http://www.uwosh.edu/facstaff/gutow
>>
>>
>>
>>
>>
>>
>>
>> ------------------------------------------------------------------------------
>> Let Crystal Reports handle the reporting - Free Crystal Reports 2008
>> 30-Day
>> trial. Simplify your report design, integration and deployment - and focus
>> on
>> what you do best, core application coding. Discover what's new with
>> Crystal Reports now. http://p.sf.net/sfu/bobj-july
>> _______________________________________________
>> Jmol-developers mailing list
>> [email protected]
>> https://lists.sourceforge.net/lists/listinfo/jmol-developers
>>
>
>
>
> --
> 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
>
--
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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