Re: [Jmol-users] Jmol -- testing requested (FF issue)

2015-08-26 Thread Otis Rothenberger
Bob,

I cleaned my FF problem out so that there would not be any confusion. My issue 
was related to a known FF bug with document.execCommand. Easy solution was to 
opt FF out on the commands that were related to object resizing. This was not a 
Local Storage issue as I originally thought.

With the above problem removes, here is FF errors - not seen on Chrome of 
Safari. The first is the familiar omnipresent FF depreciation warning:

MLHttpRequest on the main thread is deprecated because of its detrimental 
effects to the end user's experience. For more help http://xhr.spec.whatwg.org/ 
jquery.min.js:4:0

not well-formed package.js:1:1

syntax error corejmol.z.js:1:1

syntax error UnknownServiceException.js:1:1

syntax error JmolBinary.js:1:1

syntax error PrecisionRenderer.js:1:1

JSmol exec jmolApplet0 start applet null -- OK JSmol.min.nojq.js:82:366 
(not an error)

syntax error corescript.z.js:1:1

not well-formed methane.txt:1:6

syntax error coretext.z.js:1:1

syntax error PropertyManager.js:1:1

syntax error coreprop.z.js:1:1


Otis

--
Otis Rothenberger
o...@chemagic.com
http://chemagic.com

 On Aug 25, 2015, at 3:30 PM, Otis Rothenberger osrot...@chemagic.com wrote:
 
 Paul and Bob,
 
 Chrome appears OK for me. Firefox is whining about a whole mess of syntax 
 errors in various Jmol .js files. I must admit that FF is becoming a real 
 pain for me. I haven’t checked for a while. I see it’s having problems with 
 my Local Storage error catching, but that’s unrelated to the various Jmol .js 
 syntax errors. I can fix that.
 
 I show the Developer menu on Safari. That’s how I access the JavaScript 
 console. It’s also where I turn off local file restrictions. This Developer 
 menu item does not show by default.
 
 Again, just to be clear. I am running double click .htm from my desktop - no 
 server. I run with an Internet connection because my locally run page 
 interacts with Internet data sources.
 
 I guess I should also mention that I’m running JSmol.min.nojq.js
 
 The Chrome that seems to be behaving for me is Version 44.0.2403.157 
 (64-bit). Since I’m running local files, I use a terminal start-up to allow 
 this.
 
 Otis
 
 
 
 
 --
 Otis Rothenberger
 o...@chemagic.com
 http://chemagic.com
 
 On Aug 25, 2015, at 2:46 PM, Paul PILLOT paulpil...@gmail.com wrote:
 
 Thanks Otis,
 I am also running pages from my local web server (localhost). I haven’t 
 spotted the setting you are referring to. 
 I have made further tests with firefox 40 and Chrome 44.
 The three browsers give the same consistent error messages (that don’t 
 prevent jsmol from working).
 
 Paul
 
 Le 25-08-2015 à 14:34, Otis Rothenberger osrot...@chemagic.com a écrit :
 
 Bob and Paul,
 
 I’m not seeing this (below) in MacOS X 10.10.4 (Yosemite) and Safari 8.0.7.
 
 I should mention that I’m running locally with internet connection - i.e. 
 all my AJAX remote calls working.
 
 This means that I run Safari with “Disable Local File Restrictions” checked.
 
 Otis
 
 --
 Otis Rothenberger
 o...@chemagic.com
 http://chemagic.com
 
 
 
 --
 ___
 Jmol-users mailing list
 Jmol-users@lists.sourceforge.net
 https://lists.sourceforge.net/lists/listinfo/jmol-users
 
 
 
 
 --
 ___
 Jmol-users mailing list
 Jmol-users@lists.sourceforge.net
 https://lists.sourceforge.net/lists/listinfo/jmol-users




--
___
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users


Re: [Jmol-users] Jmol -- testing requested (FF issue)

2015-08-26 Thread Otis Rothenberger
OK

I should have mentioned that the page works just fine.


--
Otis Rothenberger
o...@chemagic.com
http://chemagic.com

 On Aug 26, 2015, at 10:36 AM, Robert Hanson hans...@stolaf.edu wrote:
 
 OK, thanks, Otis. All of those are just standard warnings, not errors.
 ​
 --
 ___
 Jmol-users mailing list
 Jmol-users@lists.sourceforge.net
 https://lists.sourceforge.net/lists/listinfo/jmol-users




--
___
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users


Re: [Jmol-users] Jmol -- testing requested (FF issue)

2015-08-26 Thread Robert Hanson
OK, thanks, Otis. All of those are just standard warnings, not errors.
​
--
___
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users


[Jmol-users] Feature Request: HPModes for Gaussian File Reader

2015-08-26 Thread Kubasik, Matthew A.
Dear Bob,

Could you and the Jmol development community consider adding the reading of 
“High Precision” modes (g09 option freq(HPModes)) to Jmol’s Gaussian file 
reader?

Additionally, if the displacement vectors could be added to atom properties, 
that would be great!

Currently, Jmol will reads this section of a Gaussian output file:

  1  2  3
  A  A  A
 Frequencies -- 11.138112.490815.3386
 Red. masses --  4.5657 4.9034 5.4670
 Frc consts  --  0.0003 0.0005 0.0008
 IR Inten--  0.2569 0.0415 0.0019
  Atom  AN  X  Y  ZX  Y  ZX  Y  Z
 1   6 0.01   0.01   0.01 0.04   0.02   0.10 0.09  -0.05  -0.01
 2   6 0.01   0.01  -0.02 0.00  -0.01   0.15 0.10  -0.03   0.01
 3   1 0.03   0.00  -0.03-0.02   0.00   0.17 0.08  -0.02   0.02
 4   6 0.00   0.02  -0.03 0.00  -0.04   0.19 0.15  -0.02   0.01
 5   1 0.01   0.02  -0.05-0.03  -0.06   0.23 0.16   0.00   0.02
 6   6-0.02   0.03  -0.02 0.03  -0.05   0.17 0.18  -0.03  -0.01
…

This provides atomic displacement properties, such as  {model=m and 
atomno=n}.vxyz, as well as vX, vY, and VZ.

The Gaussian formatting for HPModes is like this:

   1 2 3 4 5
   A A A A A
   Frequencies ---11.1381   12.4908   15.3386   18.8667   21.7801
Reduced masses --- 4.56574.90345.46704.72614.7314
   Force constants --- 0.00030.00050.00080.00100.0013
IR Intensities --- 0.25690.04150.00190.08090.0278
 Coord Atom Element:
   1 1 6  0.00808   0.03641   0.08901  -0.04609   0.03999
   2 1 6  0.00694   0.02030  -0.05281   0.01034   0.03379
   3 1 6  0.01135   0.09711  -0.01221  -0.02791  -0.04076
   1 2 6  0.01455   0.00394   0.10466  -0.01421   0.00668
   2 2 6  0.00958  -0.00739  -0.03172   0.03848   0.01153
   3 2 6 -0.01679   0.15117   0.00826  -0.07526   0.05221
…

Perhaps these data could be put into atomic properties of vHPxyz, vHPx, vHPy, 
and vHPz?

I tried to extract HPmodes by using y.find() and y.replace and y.split() 
functions and for loops, etc, after loading the file into a variable, but I am 
confident that adding this feature to the native Gaussian file reader would be 
more elegant.

Thoughts?

Matt
--
___
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users