Otis, Chlorination_of_anisoleF.TXT contains what? A gaussian log file?
I think your script has 9 different start points, but they all proceed in a
positive direction from that point?
I guess I want to re-order the frames in a Gaussian file, ie show 57 to 26,
then immediately jump to frame 1 and then show 1-25. This would involve going
backwards for the first sequence and forwards for the next.
Actually, more importantly, I am trying to figure out how to get those
chemists who are not familiar with the type of script below not to be afraid of
trying. So I want to keep it as simple and generic as possible for them.
I guess Bob may have to write code to implement eg frame 57-26,1-25; and then
run the animation in that order?
On 2 Feb 2014, at 13:01, Otis Rothenberger <osrot...@chemagic.com> wrote:
> Henry,
>
> I'm not sure if this helps your situation, but we run animations in our own
> loop (e.g. below). You can pretty much do whatever you want with respect to
> frame display:
>
> var filePath = "animations/Chlorination_of_anisoleF.TXT";
> var frameInterval = .1;
> load @filePath;hide *;background black;set echo top center;font echo 36
> serif;color echo yellow;echo VMK Molecular Movies|Presents|Aromatic
> Clorination Reaction;delay 3;
> animation off;hover off;color label pink;select formalCharge <> 0;label
> %C;set echo top left;font echo 16 sansserif;
> color echo yellow;select *;var j = getProperty("modelInfo","modelCount");
> for (var i = 1; i <= j; i++){
> frame @i;
> if (i == 2){display *;echo Start with a bit of aluminum chloride.;delay
> 3;echo;}
> if (i == 3){display *;echo Add some dichlorine.;delay 3;echo;}
> if (i == 18){display *;echo Add anisole.;delay 3;echo;}
> if (i == 79){display *;echo A cyclohexadienyl cation intermediate;delay
> 3;echo;}
> if (i == 81){display *;echo A resonance contributor;delay 3;echo;}
> if (i == 86){display *;echo Another resonance contributor;delay 3;echo;}
> if (i == 93){display *;echo A 4th resonance contributor;delay 3;echo;}
> if (i == 159){display *;echo Loss of a proton, ;delay 3;echo;}
> if (i == 167){display *;echo regenerates the aromatic ring.;delay 3;}
> delay @{frameInterval};
> }
> echo The final product is 1-chloro-4-methoxy-benzene.;delay 3;boundbox
> {*};centerat boundbox;zoom 0;
>
> Otis
> --
> Otis Rothenberger
> o...@chemagic.com
> http://chemagic.com
>
> On Feb 2, 2014, at 3:57 AM, Rzepa, Henry S <h.rz...@imperial.ac.uk> wrote:
>
>> Has anybody solved this one?
>>
>> Gaussian computes an IRC by starting at the transition state (frame 1)
>> and following the IRC down to a rest in one direction (lets say frame 25),
>> then starting again from the geometry of frame 1 (this will now be numbered
>> 26) and computing the IRC in the other direction, down to say frame 51.
>>
>> So to display a smooth IRC (one capable of palindromic reversal), one needs
>> to load the frames in the order:
>>
>> 51 > 27 > 1 > 25 (this avoids repeating 26, which is the same as 1).
>>
>> Unless I missed it, I do not think the frame command can be used to set up
>> this sequence? Can anyone enlighten me?
>>
>> I would point out that it is not unusual to compute IRCs with a total of
>> perhaps 400 frames, and loading and animating these frames is going to be a
>> tough ask of JSmol (and possibly Jmol as well). Perhaps one should not try
>> IRCs with so many frames at all?
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>
>
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