Thanks for the info on the Gaussian .out files. The missing " Entering Gaussian System" I believe is due to the fact on Windows the jobs are submitted thru a GUI and the info for the "Link 0" command is already known so the program starts on Link 1. This is likely common to all Gaussian for Windows output files (certainly all I have available). It is pretty simple to edit output files to add the "Entering Gaussian System" line or I believe it would be safe to parse for the " Entering Link 1" comment.
Rick Spinney -----Original Message----- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of [EMAIL PROTECTED] Sent: Saturday, July 09, 2005 4:56 PM To: [email protected] Subject: Jmol-developers digest, Vol 1 #904 - 11 msgs Send Jmol-developers mailing list submissions to [email protected] To subscribe or unsubscribe via the World Wide Web, visit https://lists.sourceforge.net/lists/listinfo/jmol-developers or, via email, send a message with subject or body 'help' to [EMAIL PROTECTED] You can reach the person managing the list at [EMAIL PROTECTED] When replying, please edit your Subject line so it is more specific than "Re: Contents of Jmol-developers digest..." Today's Topics: 1. Re: Gaussian .out files ([EMAIL PROTECTED]) 2. Re: Gaussian .out files (Dr P. Murray-Rust) 3. Re: Gaussian .out files (=?ISO-8859-1?Q?Ren=E9_Kanters?=) 4. scripting pages on sourceforge (=?ISO-8859-1?Q?Ren=E9_Kanters?=) 5. Re: scripting pages on sourceforge (Miguel) 6. Re: scripting pages on sourceforge (Nicolas Vervelle) 7. Re: scripting pages on sourceforge (Nicolas Vervelle) 8. Re: scripting pages on sourceforge (=?ISO-8859-1?Q?Ren=E9_Kanters?=) 9. Re: scripting pages on sourceforge (=?ISO-8859-1?Q?Ren=E9_Kanters?=) 10. Re: scripting pages on sourceforge (Nicolas Vervelle) 11. Re: scripting pages on sourceforge (=?ISO-8859-1?Q?Ren=E9_Kanters?=) --__--__-- Message: 1 Date: Sat, 9 Jul 2005 12:26:48 +0200 From: [EMAIL PROTECTED] To: [email protected], =?iso-8859-1?b?UmVu6Q==?= Kanters <[EMAIL PROTECTED]> Cc: [email protected] Subject: Re: [Jmol-developers] Gaussian .out files Reply-To: [email protected] Citeren Ren=E9 Kanters <[EMAIL PROTECTED]>: > I took a quick look at the files you attached. In neither case is the =20 > resolver able to determine the type of file, i.e., it isn't able to =20 > figure out that it is a Gaussian file. The resolver expects to see the = =20 > string "Entering Gaussian System" early on. In neither of your files =20 > that was there, which is peculiar because I understand that Gaussian =20 > really should do that. >=20 > So to make these files work I did: > In the acetone.g03.out: > replace the first line: > Entering Link 1 =3D c:\G03W\l1.exe PID=3D 2100. > with > Entering Gaussian System Are the strings "Entering Link" common in g03 files? If so, we might add = them to the resolver... =20 Egon --__--__-- Message: 2 From: "Dr P. Murray-Rust" <[EMAIL PROTECTED]> To: [email protected] Subject: Re: [Jmol-developers] Gaussian .out files Date: 09 Jul 2005 11:43:21 +0100 Reply-To: [email protected] On Jul 9 2005, [EMAIL PROTECTED] wrote: > Citeren Ren=E9 Kanters <[EMAIL PROTECTED]>: > > I took a quick look at the files you attached. In neither case is the = =20 > > resolver able to determine the type of file, i.e., it isn't able to =20 > > figure out that it is a Gaussian file. The resolver expects to see the = =20 > > string "Entering Gaussian System" early on. In neither of your files = =20 > > that was there, which is peculiar because I understand that Gaussian = =20 > > really should do that. I spent a considerable time writing parsers for Gaussian output.=20 Unfortunately it varies very considerably between versions - more than=20 other programs. So you cannot rely on messages like this occurring in every= =20 case. > >=20 > > So to make these files work I did: > > In the acetone.g03.out: > > replace the first line: > > Entering Link 1 =3D c:\G03W\l1.exe PID=3D 2100. > > with > > Entering Gaussian System >=20 > Are the strings "Entering Link" common in g03 files? If so, we might add= =20 > them to the resolver... Again this is system-dependent. Gaussian consists of components called=20 links and some, but not all, implementations emit these messages. Without= =20 these messages it is almost impossible to write a full Gausian parser - you= =20 cannot tell where one link stops and the next starts. It is possible to=20 cherry-pick some fields but nothing can be relied upon. Other systems like GAMESS are starting to use CML/XML as the markup and=20 this will revolutionise this area. P. > =20 > Egon >=20 >=20 > ------------------------------------------------------- This SF.Net=20 > email is sponsored by the 'Do More With Dual!' webinar happening July 14= =20 > at 8am PDT/11am EDT. We invite you to explore the latest in dual core and= =20 > dual graphics technology at this free one hour event hosted by HP, AMD,= =20 > and NVIDIA. To register visit http://www.hp.com/go/dualwebinar=20 > _______________________________________________ Jmol-developers mailing= =20 > list [EMAIL PROTECTED] > https://lists.sourceforge.net/lists/listinfo/jmol-developers >=20 --=20 Peter Murray-Rust Unilever Centre for Molecular Informatics Chemistry Department, Cambridge University Lensfield Road, CAMBRIDGE, CB2 1EW, UK Tel: +44-1223-763069 Fax: +44 1223 763076=20 --__--__-- Message: 3 From: =?ISO-8859-1?Q?Ren=E9_Kanters?= <[EMAIL PROTECTED]> Subject: Re: [Jmol-developers] Gaussian .out files Date: Sat, 9 Jul 2005 08:49:41 -0400 To: [email protected] Reply-To: [email protected] Hi Egon and Peter, I just did a 'head -4' on the our sample gaussian (output) files and=20 compared the results. I used -4, because from interpreting the=20 Resolver.java code, I deduce (hopefully correctly so) that the Resolver=20= only looks at the first 4 lines of the file (as long as they are=20 shorter than 16K or so?). Each of them start with the ' Entering Gaussian System'...., except for=20= 4-cyanophenylnitrene-Benzazirine-TS.g94.out, which has that on the 2nd=20= line. So they all resolve properly. These files seem to have been=20 created by Gaussian 94, 98, and 03 and on Linux/Unix type systems. If it is indeed the case that Windows (his g03 output) does not put '=20 Entering Gaussian System' but ' Entering Link 1' in the first line in=20 stead, the problem will be solved (at least for that file, and possibly=20= all G03W files?). The problem remains with the other file, which has 5 lines (the last of=20= them empty) before the real output because I don't believe the Resolver=20= ever reads far enough ahead to see what it should be seeing.... So=20 another solution needs to be found for this kind of circumstances... May I suggest as a possibility for the application (since it won't work=20= for the applet) to have an 'interpret as' popup that allows one to=20 define what the resolver should be (the default selection would be=20 'automatic' to have the current method of resolving do it). This would=20= allow somebody to determine whether or not the automatic resolving is=20 causing a problem, which could make them take a look at the contents of=20= the file to investigate the cause. So in short: 1) adding the record 'Entering Link 1' would help 2) there will still be cases where the output file may not be resolved=20= properly Cheers, Ren=E9 On Jul 9, 2005, at 6:43 AM, Dr P. Murray-Rust wrote: > On Jul 9 2005, [EMAIL PROTECTED] wrote: > >> Citeren Ren=E9 Kanters <[EMAIL PROTECTED]>: >> > I took a quick look at the files you attached. In neither case is=20= >> the > resolver able to determine the type of file, i.e., it isn't=20 >> able to > figure out that it is a Gaussian file. The resolver=20 >> expects to see the > string "Entering Gaussian System" early on. In=20= >> neither of your files > that was there, which is peculiar because I=20= >> understand that Gaussian > really should do that. > > I spent a considerable time writing parsers for Gaussian output.=20 > Unfortunately it varies very considerably between versions - more than=20= > other programs. So you cannot rely on messages like this occurring in=20= > every case. > >> > > So to make these files work I did: >> > In the acetone.g03.out: >> > replace the first line: >> > Entering Link 1 =3D c:\G03W\l1.exe PID=3D 2100. >> > with >> > Entering Gaussian System >> Are the strings "Entering Link" common in g03 files? If so, we might=20= >> add them to the resolver... > > Again this is system-dependent. Gaussian consists of components called=20= > links and some, but not all, implementations emit these messages.=20 > Without these messages it is almost impossible to write a full Gausian=20= > parser - you cannot tell where one link stops and the next starts. It=20= > is possible to cherry-pick some fields but nothing can be relied upon. > > Other systems like GAMESS are starting to use CML/XML as the markup=20 > and this will revolutionise this area. > > P. > >> Egon >> ------------------------------------------------------- This SF.Net=20= >> email is sponsored by the 'Do More With Dual!' webinar happening July=20= >> 14 at 8am PDT/11am EDT. We invite you to explore the latest in dual=20= >> core and dual graphics technology at this free one hour event hosted=20= >> by HP, AMD, and NVIDIA. To register visit=20 >> http://www.hp.com/go/dualwebinar=20 >> _______________________________________________ Jmol-developers=20 >> mailing list [EMAIL PROTECTED] >> https://lists.sourceforge.net/lists/listinfo/jmol-developers > > --=20 > Peter Murray-Rust > Unilever Centre for Molecular Informatics > Chemistry Department, Cambridge University > Lensfield Road, CAMBRIDGE, CB2 1EW, UK > Tel: +44-1223-763069 Fax: +44 1223 763076 > > > ------------------------------------------------------- > This SF.Net email is sponsored by the 'Do More With Dual!' webinar=20 > happening > July 14 at 8am PDT/11am EDT. We invite you to explore the latest in=20 > dual > core and dual graphics technology at this free one hour event hosted=20= > by HP, > AMD, and NVIDIA. To register visit http://www.hp.com/go/dualwebinar > _______________________________________________ > Jmol-developers mailing list > [email protected] > https://lists.sourceforge.net/lists/listinfo/jmol-developers > --__--__-- Message: 4 To: [email protected] From: =?ISO-8859-1?Q?Ren=E9_Kanters?= <[EMAIL PROTECTED]> Date: Sat, 9 Jul 2005 12:39:07 -0400 Subject: [Jmol-developers] scripting pages on sourceforge Reply-To: [email protected] Hi, I was looking at the http://jmol.sourceforge.net/scripting/ page and=20 noticed that all the applets show in yellow the following message: Jmol developer alert! progressbar is REQUIRED ... otherwise users will have no indicate that the applet is loading <applet code=3D'JmolApplet' ... > <param name=3D'progressbar' value=3D'true' /> ....... This suggests that the pages and the examples of how to use Jmol should=20= be updated? Ren=E9 --__--__-- Message: 5 Date: Sat, 9 Jul 2005 12:59:12 -0400 (EDT) Subject: Re: [Jmol-developers] scripting pages on sourceforge From: "Miguel" <[EMAIL PROTECTED]> To: [email protected] Reply-To: [email protected] > Hi, > > I was looking at the http://jmol.sourceforge.net/scripting/ page and > noticed that all the applets show in yellow the following message: > > Jmol developer alert=21 > > progressbar is REQUIRED ... otherwise users > will have no indicate that the applet is loading > > <applet code=3D'JmolApplet' ... > > <param name=3D'progressbar' value=3D'true' /> > ....... > > This suggests that the pages and the examples of how to use Jmol should= > be updated? Hmmm ... Perhaps the pages got accidentally changed when the language translations= were being made. The Jmol.js in the official 10.00 release includes the 'progressbar' settings. This requirement has been dropped in the development versions of Jmol.js/JmolApplet*.jar. The web site uses the Jmol.js JavaScript library. I do not understand why= it would be broken. Perhaps it has a mixture of development/released code= . I am not currently in a good position to fix it and would appreciate it i= f someone else could investigate. Miguel --__--__-- Message: 6 Date: Sat, 09 Jul 2005 19:39:37 +0200 From: Nicolas Vervelle <[EMAIL PROTECTED]> To: [email protected] Subject: Re: [Jmol-developers] scripting pages on sourceforge Reply-To: [email protected] Hi, Miguel wrote: >>Hi, >> >>I was looking at the http://jmol.sourceforge.net/scripting/ page and >>noticed that all the applets show in yellow the following message: >> >>Jmol developer alert! >> >>progressbar is REQUIRED ... otherwise users >>will have no indicate that the applet is loading >> >><applet code='JmolApplet' ... > >> <param name='progressbar' value='true' /> >>....... >> >>This suggests that the pages and the examples of how to use Jmol should >>be updated? >> >> > >Hmmm ... > >Perhaps the pages got accidentally changed when the language translations >were being made. > > I saw the problem before translating the website. At the time, since version 10.00 was new and the website wasn't updated from v9 to v10, I didn't report it. Note: several pages are still pre-v10. >The Jmol.js in the official 10.00 release includes the 'progressbar' >settings. > >This requirement has been dropped in the development versions of >Jmol.js/JmolApplet*.jar. > > Currently, the version of Jmol that is on the website is 10.00.11 (not the official 10.00.00). I replaced it in may to take advantage of unicode characters in scripts (to finish french translation) >The web site uses the Jmol.js JavaScript library. I do not understand why >it would be broken. Perhaps it has a mixture of development/released code.. > > The scripting page *does not* uses the Jmol.js library. The applet is used directly with an <applet> tag. I think the problem is there since switching to v10.00.00. Below is an example of what is in the xml source files. I can do the modification, just tell me what to add <applet name="flash" code="JmolApplet" archive="JmolApplet.jar" codebase="[codebase]" width="300" height="100" align="left" mayscript="true"> <param name="bgcolor" value="teal"> <param name="script" value="<snip>"> </applet> >I am not currently in a good position to fix it and would appreciate it if >someone else could investigate. > > Investigation done :) Nicolas --__--__-- Message: 7 Date: Sat, 09 Jul 2005 20:15:59 +0200 From: Nicolas Vervelle <[EMAIL PROTECTED]> To: [email protected] Subject: Re: [Jmol-developers] scripting pages on sourceforge Reply-To: [email protected] Nicolas Vervelle wrote: > Below is an example of what is in the xml source files. > I can do the modification, just tell me what to add Nevermind, I found what to do > > <applet name="flash" code="JmolApplet" archive="JmolApplet.jar" > codebase="[codebase]" > width="300" height="100" align="left" mayscript="true"> > <param name="bgcolor" value="teal"> <param name="progressbar" value="true"> > <param name="script" value="<snip>"> > </applet> I am updating the website. It should be done in 15 or 30 minutes. Could you check if it works for you ? Nicolas --__--__-- Message: 8 From: =?ISO-8859-1?Q?Ren=E9_Kanters?= <[EMAIL PROTECTED]> Subject: Re: [Jmol-developers] scripting pages on sourceforge Date: Sat, 9 Jul 2005 15:26:22 -0400 To: [email protected] Reply-To: [email protected] Hi Nicolas, I should say that I am using Safari on Mac OS X. The first section 'Eye Candy...' only shows a green display and the=20 popup suggests that 'No atoms loaded' Basic scripting: when I select WIREFRAME or SHADED TypeError - Value undefined (results of expression=20 document.jmol.setSetyle is not object. When I click on a molecule file (second line) I get TypeError - Value undefined (result of expression document.jmol.load)=20 is not object. Wireframe rotation give: TypeError - Value undefined (result of expression=20 document.jmol.setWireframeRotation) is not object. Perspective Depths: TypeError - Value undefined (result of expression=20 document.jmol.setPerspectiveDepth) is not object. and the backgrounds work. The advanced Scripting section seems to work. Showing Animations: Clicking on any of the buttons doesn't do anything in the applet, but=20 does show in the status bar: command expected : .... where the ... is the script that is supposed to be executed, i.e, the=20 string passed to the play() method by the onClickHandler. Ren=E9 On Jul 9, 2005, at 2:15 PM, Nicolas Vervelle wrote: > > > Nicolas Vervelle wrote: > >> Below is an example of what is in the xml source files. >> I can do the modification, just tell me what to add > > Nevermind, I found what to do > >> >> <applet name=3D"flash" code=3D"JmolApplet" archive=3D"JmolApplet.jar" >> codebase=3D"[codebase]" >> width=3D"300" height=3D"100" align=3D"left" mayscript=3D"true"> >> <param name=3D"bgcolor" value=3D"teal"> > > <param name=3D"progressbar" value=3D"true"> > >> <param name=3D"script" value=3D"<snip>"> >> </applet> > > I am updating the website. It should be done in 15 or 30 minutes. > Could you check if it works for you ? > > Nicolas > > > > > ------------------------------------------------------- > This SF.Net email is sponsored by the 'Do More With Dual!' webinar=20 > happening > July 14 at 8am PDT/11am EDT. We invite you to explore the latest in=20 > dual > core and dual graphics technology at this free one hour event hosted=20= > by HP, > AMD, and NVIDIA. To register visit http://www.hp.com/go/dualwebinar > _______________________________________________ > Jmol-developers mailing list > [email protected] > https://lists.sourceforge.net/lists/listinfo/jmol-developers > --__--__-- Message: 9 From: =?ISO-8859-1?Q?Ren=E9_Kanters?= <[EMAIL PROTECTED]> Subject: Re: [Jmol-developers] scripting pages on sourceforge Date: Sat, 9 Jul 2005 15:38:47 -0400 To: [email protected] Reply-To: [email protected] Nicolas, I forgot to mention that I am not getting the yellow applet with the=20 alert text anymore. So you did fix it. Ren=E9 --__--__-- Message: 10 Date: Sat, 09 Jul 2005 21:53:58 +0200 From: Nicolas Vervelle <[EMAIL PROTECTED]> To: [email protected] Subject: Re: [Jmol-developers] scripting pages on sourceforge Reply-To: [email protected] Hi, I have some of the same problems on IE6 / w2k. This page is not in the navigation bar at the top of each page, how did=20 you find it ? I wonder if it should still be here. Miguel, Egon ? Ren=E9 Kanters wrote: > Hi Nicolas, > > I should say that I am using Safari on Mac OS X. > > The first section 'Eye Candy...' only shows a green display and the=20 > popup suggests that 'No atoms loaded' Apparently, the file is not loaded because quotes are surrounding the=20 filename: FileManager.openFile('jmol.mol') error opening http://jmol.sourceforge.net/scripting/'jmol.mol' java.io.FileNotFoundException:=20 http://jmol.sourceforge.net/scripting/'jmol.mol' I have removed the quotes, it works for me now. Can you confirm ? > Basic scripting: > when I select WIREFRAME or SHADED > TypeError - Value undefined (results of expression=20 > document.jmol.setSetyle is not object. > When I click on a molecule file (second line) I get > TypeError - Value undefined (result of expression document.jmol.load)=20 > is not object. > Wireframe rotation give: > TypeError - Value undefined (result of expression=20 > document.jmol.setWireframeRotation) is not object. > Perspective Depths: > TypeError - Value undefined (result of expression=20 > document.jmol.setPerspectiveDepth) is not object. > and the backgrounds work. I don't see the errors, but nothing happens in IE6. I will let Miguel, Egon or someone else look at it. > The advanced Scripting section seems to work. Good :) > Showing Animations: > Clicking on any of the buttons doesn't do anything in the applet, but=20 > does show in the status bar: > command expected : .... > where the ... is the script that is supposed to be executed, i.e, the=20 > string passed to the play() method by the onClickHandler. Well, if I am not mistaken, this is because the script is incorrect=20 (animate is not a Jmol command according to Bob Hanson doc). What commands should be there instead ? Nicolas --__--__-- Message: 11 From: =?ISO-8859-1?Q?Ren=E9_Kanters?= <[EMAIL PROTECTED]> Subject: Re: [Jmol-developers] scripting pages on sourceforge Date: Sat, 9 Jul 2005 16:55:15 -0400 To: [email protected] Reply-To: [email protected] Hi Nicolas, Trying to hunt down on how I got there I did come across this one=20 http://jmol.sourceforge.net/applet/ (referenced from the wiki) which=20 also has the yellow boxes.... That is also the page that has the link. It is in the section 'Creating=20= a web page'. The eye candy works now. Ren=E9 On Jul 9, 2005, at 3:53 PM, Nicolas Vervelle wrote: > Hi, > > I have some of the same problems on IE6 / w2k. > > This page is not in the navigation bar at the top of each page, how=20 > did you find it ? > I wonder if it should still be here. Miguel, Egon ? > > > Ren=E9 Kanters wrote: > >> Hi Nicolas, >> >> I should say that I am using Safari on Mac OS X. >> >> The first section 'Eye Candy...' only shows a green display and the=20= >> popup suggests that 'No atoms loaded' > > Apparently, the file is not loaded because quotes are surrounding the=20= > filename: > FileManager.openFile('jmol.mol') > error opening http://jmol.sourceforge.net/scripting/'jmol.mol' > java.io.FileNotFoundException:=20 > http://jmol.sourceforge.net/scripting/'jmol.mol' > > I have removed the quotes, it works for me now. Can you confirm ? > >> Basic scripting: >> when I select WIREFRAME or SHADED >> TypeError - Value undefined (results of expression=20 >> document.jmol.setSetyle is not object. >> When I click on a molecule file (second line) I get >> TypeError - Value undefined (result of expression document.jmol.load)=20= >> is not object. >> Wireframe rotation give: >> TypeError - Value undefined (result of expression=20 >> document.jmol.setWireframeRotation) is not object. >> Perspective Depths: >> TypeError - Value undefined (result of expression=20 >> document.jmol.setPerspectiveDepth) is not object. >> and the backgrounds work. > > I don't see the errors, but nothing happens in IE6. > I will let Miguel, Egon or someone else look at it. > >> The advanced Scripting section seems to work. > > Good :) > >> Showing Animations: >> Clicking on any of the buttons doesn't do anything in the applet, but=20= >> does show in the status bar: >> command expected : .... >> where the ... is the script that is supposed to be executed, i.e, the=20= >> string passed to the play() method by the onClickHandler. > > Well, if I am not mistaken, this is because the script is incorrect=20 > (animate is not a Jmol command according to Bob Hanson doc). > What commands should be there instead ? > > Nicolas > > > > > ------------------------------------------------------- > This SF.Net email is sponsored by the 'Do More With Dual!' webinar=20 > happening > July 14 at 8am PDT/11am EDT. We invite you to explore the latest in=20 > dual > core and dual graphics technology at this free one hour event hosted=20= > by HP, > AMD, and NVIDIA. To register visit http://www.hp.com/go/dualwebinar > _______________________________________________ > Jmol-developers mailing list > [email protected] > https://lists.sourceforge.net/lists/listinfo/jmol-developers > --__--__-- _______________________________________________ Jmol-developers mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-developers End of Jmol-developers Digest ------------------------------------------------------- This SF.Net email is sponsored by the 'Do More With Dual!' webinar happening July 14 at 8am PDT/11am EDT. We invite you to explore the latest in dual core and dual graphics technology at this free one hour event hosted by HP, AMD, and NVIDIA. To register visit http://www.hp.com/go/dualwebinar _______________________________________________ Jmol-developers mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-developers
