I don't have a specific file giving me the problem, I am currently testing
the various functionalities we're interested in to write down a quick
reference guide for my group. I just try a simple line like:
ellipsoid test axes {1.0 0.0 0.0} {0.0 0.5 0.0} {0.0 0.0 0.5}
and I get the bug. The latest version on which I manage to visualize
ellipsoids is 13.0.8, and even there, I can't see them in any other form
than the 'solid' one (in this case I tried something like:
set ellipsoidBall OFF
set ellipsodAxes ON
ellipsoid test axes {1.0 0.0 0.0} {0.0 0.5 0.0} {0.0 0.0 0.5}
and I still get a ball).
Simone
2012/11/26 Robert Hanson <hans...@stolaf.edu>
> send me the offending file, please. I was sure I fixed that.
>
>
>
> On Mon, Nov 26, 2012 at 5:34 AM, Simone Sturniolo <
> simonesturni...@gmail.com> wrote:
>
>> Hi,
>>
>> I tried downloading the new 13.1.9 release from Sourceforge, and even
>> compiling the source code for 13.1.10_dev, but I still have bugs with
>> ellipsoids. Now, instead of a dot, I see a large square when I try them. It
>> seems odd to me that it could be system-specific, but just to stay on the
>> safe side, I'm currently running the Java SE Runtime Environment version
>> 1.7.0_09 on Mageia Linux.
>>
>> Simone
>>
>>
>> 2012/11/25 Robert Hanson <hans...@stolaf.edu>
>>
>>> Thank you, Nico, for releasing 13.0.9 and 13.1.9.
>>>
>>> The only new features in 13.1.9 involve the MO and isosurface MO
>>> commands. It's an interesting idea suggested by Leonardo Jorge that
>>> should have wider applications. Basically it allows one to see the
>>> contribution to electron density by any subset of orbitals. Especially
>>> interesting, I think, is the display for degenerate orbitals. This is
>>> interesting
>>> because it brings back the molecular symmetry inherent in a pair of
>>> degenerate orbitals without necessarily showing the total overall
>>> electron
>>> density. I added total electron density as well because that was
>>> relatively easy to implement. That calculation does take some time,
>>> however, since it has to calculate the electron density for each occupied
>>> orbital.
>>>
>>> Bob
>>>
>>>
>>> MO or (ISOSURFACE MO) DENSITY
>>> -- electron density
>>> -- same as MO [1] SQUARED
>>> -- takes some time!
>>>
>>> MO HOMO|LUMO|NEXT|PREV|[c1 n2 c2 n2...] SQUARED
>>> -- Squares wave functions as it combines them.
>>> -- That is, displays the collective electron density (if occupied)
>>> -- if [...] is not given, groups orbitals by energy
>>> -- examples:
>>> load c6h6.smol;mo homo squared // displays symmetric squared sum of
>>> two degenerate orbitals
>>> load co2.smol; mo homo squared // displays cylindrical electron
>>> density
>>> mo next squared // lumo, provided homo was just displayed
>>>
>>> bug fixes:
>>>
>>> bug fix: Molden reader tweaks
>>> bug fix: Jmol application toolbar picking tool should not select none
>>> bug fix: ellipsoid rendering fails
>>> bug fix: translucent echo oddities in Jmol 13.1.8
>>> bug fix: lost volume rendering in 13.1.8
>>> bug fix: CASTEP density reader fails to reset origin to 0 0 0 in mapping
>>> bug fix: UTF files with BOM (byte order marker) present not read
>>> correctly
>>> bug fix: UTF files within GZIP or ZIP files not read correctly
>>> bug fix: set picking draw no longer works in Jmol 13.0 or 13.1
>>> bug fix: translucent echo backgrounds lost in 13.1.8
>>> bug fix: select resno=@{n+3} fails in 12.2, 13.0, and 13.1
>>> bug fix: isosurface AtomicOrbital broken in 13.1.8
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>> --
>>> 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
>>>
>>>
>>>
>>>
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>>>
>>
>>
>> --
>> _______________
>>
>> Nuovo indirizzo e-mail:
>> simonesturni...@gmail.com
>>
>>
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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
>
>
>
>
> ------------------------------------------------------------------------------
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> web console. Get in-depth insight into apps, servers, databases, vmware,
> SAP, cloud infrastructure, etc. Download 30-day Free Trial.
> Pricing starts from $795 for 25 servers or applications!
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>
>
--
_______________
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