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Re: [Jmol-developers] A question about console commands
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From: Robert H. <ha...@st...> - 2012-05-02 15:57:46
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define "radical." That word has several meanings. Also, "every point on the
isosurface -- you mean EVERY point -- 20,000 points?
Are you saying that you want to put, say, a CH3 group at 20,000 points
around the structure, check that energy, and then go back to the original
model and color the isosurface based on that?
1) You can get the list of all points on an isosurface. It's part of the
properties you can get:
load caffeine.xyz
isosurface vdw
print getProperty("isosurfaceInfo.vertices[1]")
{-5.0150366 -0.16369441 0.70243025}
print getProperty("isosurfaceInfo.vertices").length
148354
That's a heck of a lot of radicals.
But, true, you can't go in and individually color individual points on an
isosurface. You would really color individually all 148354 points?
Bob
On Tue, May 1, 2012 at 11:26 PM, Andrew Long <and...@gm...>wrote:
> Actually I've found JMOL has most of the import functions I need. Let me
> see if I can outline what I have in mind a bit more clearly.
>
> 1)import minimized chemical structure from gaussian out file into
> JMOL(exists in JMOL already)
> 2)generate an isosurface of points ala the dots command or isosurface
> molecular.(exists in JMOL already)
> 3)for every point on the isosurface, use that location as the location of
> a radical fragment and add that to the original structure. Export the new
> Radical+starting molecule to an input file to be read by a computational
> program (ex. Gaussian)(I've already created a rough chunk of code to
> generate gaussian input files)
> 4)repeat 3) for every point on the isosurface(todo)
> 5)run Calculations on the generated input files to generate the energies +
> other stuff of all the new radical+base molecule structures
> 6)import data from the previous step(exists in JMOL)
> 7)color the isosurface with the data from step 6) (maybe exists?)
> 8)display colored isosurface(exists in JMOL)
>
> Basically what I want is an electrostatic potential map<http://web.chem.ucsb.edu/%7Ekalju/chem162/public/images/Barbital_c2v_HFD_elpot.png>but with other data such as energy of the conformations instead of
> electrostatic potential. I'm doing a simplified version of the above by
> hand using a 2D surface over a planar molecule and while I've been getting
> good results its incredibly time consuming and the results are somewhat
> difficult to visualize. Thanks again for the help.
>
> Cheers Andrew
>
>
>
>
> On Wed, May 2, 2012 at 12:40 AM, Robert Hanson <ha...@st...> wrote:
>
>>
>>
>> On Tue, May 1, 2012 at 9:07 AM, Andrew Long <and...@gm...>wrote:
>>
>>> Thanks again for the help. Well let me outline what I'm trying to do
>>> and maybe you can help guide me into a better direction. I wanted to use
>>> JMOL to generate surfaces (ala isosurface) which the points of that surface
>>> could be used to generate input files for computational programs(ala
>>> gaussian and another specialized one). Then I wanted JMOL to pull in the
>>> output files, regenerate the surfaces and create 3D heat maps for display.
>>>
>>
>> "points of which" being what? You mean special points, like cusps, or
>> you mean points like "click on a point on the surface"?
>>
>> Do you have control over the format of the data that Jmol will use for
>> the surface creation? We read a lot of standard formats of various types.
>> Happy to add more, within reason.
>>
>>
>>
>>> I noticed that JMOL seemed to have most of that already built in hence
>>> the interest. I didn't get the impression that the scripting language was
>>> flexible enough todo that although there's so much functionality I wouldn't
>>> be surprised if I missed it.
>>>
>>>
>> You wouldn't use the scripting language to actually do the math of
>> surface creation, but in terms of commands that do things, that's just
>> standard user-defined functions. No need to make new core Jmol commands.
>>
>> Give me an example of what the desired command would look like.
>>
>> Bob
>>
>>
>>> Cheers Andrew
>>>
>>>
>>> On Tue, May 1, 2012 at 9:03 AM, Robert Hanson <ha...@st...>wrote:
>>>
>>>> Andrew,
>>>>
>>>> That sounds terrifically interesting. Muon spectroscopy. Nice!
>>>>
>>>> Please don't add new commands to Jmol. At least not that way. You can
>>>> create functions in Jmol using the function command just within a script,
>>>> and do just about anything with that.
>>>>
>>>> What sort of commands are you interested in adding? Let me help you.
>>>>
>>>> Bob
>>>>
>>>>
>>>> On Mon, Apr 30, 2012 at 4:57 PM, Andrew Long <
>>>> and...@gm...> wrote:
>>>>
>>>>> Hello Everyone
>>>>>
>>>>> I'm a grad student who is interested in adding some specialized
>>>>> functions for muon spectroscopy to JMOL. I was wondering if there is any
>>>>> special tricks to adding new console commands to jmol. I've gotten to the
>>>>> point where It accepts the new function (no script error command expected)
>>>>> but the function doesn't seem to want to run. (I've included some cope
>>>>> fragments and output below). I went and added some debuging statements
>>>>> (just system.out.println) into the main functions in the script evaluator
>>>>> but once the molecule is loaded into jmol none of the functions print out
>>>>> when a command is entered. Does anything else need to be added besides a
>>>>> couple lines in tokens (in order to be recognized) and adding a case in the
>>>>> instruction dispatch loop? At this point I have a feeling I might be
>>>>> missing something. Thanks for your time
>>>>>
>>>>> Cheers Andrew
>>>>>
>>>>>
>>>>> Console output
>>>>>
>>>>> $ asdfasdf
>>>>> script ERROR: command expected
>>>>> ----
>>>>> >> asdfasdf <<
>>>>> $ examplecommand
>>>>> $ write xyz
>>>>> 4
>>>>>
>>>>> H -4.47785 -0.17300 0.00000
>>>>> H -3.87856 0.17300 0.00000
>>>>> H 0.00000 0.00000 0.34600
>>>>> H 0.00000 0.00000 -0.34600
>>>>>
>>>>> $
>>>>>
>>>>>
>>>>> excerpt from scriptevaluator
>>>>>
>>>>>
>>>>> ..........
>>>>> case Token.unbind:
>>>>> unbind();
>>>>> break;
>>>>> case Token.vibration:
>>>>> vibration();
>>>>> break;
>>>>> case Token.write:
>>>>> write(null);
>>>>> break;
>>>>> case Token.exampleCommand:
>>>>> System.out.println("case Token.exampleCommand:");
>>>>> //
>>>>> break;
>>>>> case Token.zap:
>>>>> zap(true);
>>>>> break;
>>>>> case Token.zoom:
>>>>> zoom(false);
>>>>> break;
>>>>> ...........
>>>>>
>>>>> excerpt from Token
>>>>> ................
>>>>> final static int quaternion = 17 | 0 << 9 | mathfunc |
>>>>> scriptCommand;
>>>>> final static int sort = 18 | 0 << 9 | mathfunc |
>>>>> mathproperty;
>>>>> final static int count = 19 | 0 << 9 | mathfunc |
>>>>> mathproperty;
>>>>> public final static int within = 20 | 0 << 9 | mathfunc;
>>>>> final static int write = 21 | 0 << 9 | mathfunc |
>>>>> scriptCommand;
>>>>> final static int exampleCommand = 22 | 0 << 9 | mathfunc |
>>>>> scriptCommand;
>>>>>
>>>>> // xxx(a)
>>>>>
>>>>> final static int acos = 3 | 1 << 9 | mathfunc;
>>>>> final static int sin = 4 | 1 << 9 | mathfunc;
>>>>> final static int cos = 5 | 1 << 9 | mathfunc;
>>>>> final static int sqrt = 6 | 1 << 9 | mathfunc;
>>>>> ......................
>>>>>
>>>>> More from Token
>>>>> ....................
>>>>> "vector", new Token(vector),
>>>>> "vectors", null,
>>>>> "vibration", new Token(vibration),
>>>>> "while", new Token(whilecmd),
>>>>> "wireframe", new Token(wireframe),
>>>>> "write", new Token(write),
>>>>> "exampleCommand", new Token(exampleCommand),
>>>>> //exampleCommand
>>>>> "zap", new Token(zap),
>>>>> "zoom", new Token(zoom),
>>>>> "zoomTo", new Token(zoomTo),
>>>>> .............................
>>>>>
>>>>> ------------------------------------------------------------------------------
>>>>> Live Security Virtual Conference
>>>>> Exclusive live event will cover all the ways today's security and
>>>>> threat landscape has changed and how IT managers can respond.
>>>>> Discussions
>>>>> will include endpoint security, mobile security and the latest in
>>>>> malware
>>>>> threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
>>>>> _______________________________________________
>>>>> Jmol-developers mailing list
>>>>> Jmo...@li...
>>>>> 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
>>>>
>>>>
>>>> ------------------------------------------------------------------------------
>>>> Live Security Virtual Conference
>>>> Exclusive live event will cover all the ways today's security and
>>>> threat landscape has changed and how IT managers can respond.
>>>> Discussions
>>>> will include endpoint security, mobile security and the latest in
>>>> malware
>>>> threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
>>>> _______________________________________________
>>>> Jmol-developers mailing list
>>>> Jmo...@li...
>>>> https://lists.sourceforge.net/lists/listinfo/jmol-developers
>>>>
>>>>
>>>
>>>
>>> ------------------------------------------------------------------------------
>>> Live Security Virtual Conference
>>> Exclusive live event will cover all the ways today's security and
>>> threat landscape has changed and how IT managers can respond. Discussions
>>> will include endpoint security, mobile security and the latest in malware
>>> threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
>>> _______________________________________________
>>> Jmol-developers mailing list
>>> Jmo...@li...
>>> 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
>>
>>
>> ------------------------------------------------------------------------------
>> Live Security Virtual Conference
>> Exclusive live event will cover all the ways today's security and
>> threat landscape has changed and how IT managers can respond. Discussions
>> will include endpoint security, mobile security and the latest in malware
>> threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
>> _______________________________________________
>> Jmol-developers mailing list
>> Jmo...@li...
>> https://lists.sourceforge.net/lists/listinfo/jmol-developers
>>
>>
>
>
> ------------------------------------------------------------------------------
> Live Security Virtual Conference
> Exclusive live event will cover all the ways today's security and
> threat landscape has changed and how IT managers can respond. Discussions
> will include endpoint security, mobile security and the latest in malware
> threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
> _______________________________________________
> Jmol-developers mailing list
> Jmo...@li...
> 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
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