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From: Jonathan G. <gu...@uw...> - 2009-06-09 19:11:17
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Bob et al.
I need some help figuring out what is going on with the file
readers. I don't seem to be able to find where the actual version of
readAtomSetCollection(BufferedReader reader) that reads more than MOs
is located. I must be missing it. I've looked at the
AtomSetCollection...java files and all the GAMESSReader files. Is
the generic reader in one of the other speciality reader files? I'm
sure I've just missed it, but need to figure out the logic for
associating MOs with a frame. Am I even looking in the right place?
Are the frames built later?
Jonathan
Dr. Jonathan H. Gutow
Chemistry Department gu...@uw...
UW-Oshkosh Office:920-424-1326
800 Algoma Boulevard FAX:920-424-2042
Oshkosh, WI 54901
http://www.uwosh.edu/faculty_staff/gutow/
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From: Robert H. <ha...@st...> - 2009-06-10 03:16:10
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Johathan, I'm guessing you are not using Eclipse. I recommend it -- then you just start clicking on names to find anything you want. Ah, let's see. The Gamess reader is an abstract class - GamessUK and GamessUS being the instantiated ones. They are subclasses of AtomSetCollectionReader. (org.jmol.adapters.smarter.AtomSetCollectionReader.java) In fact, the Gamess reader itself is a subclass of MOReader, another abstract class. MOs certainly could be associated with any model. They start out in a Hashtable that is stored in the AuxilliaryInfo Hashtable. There's no general way set up to move these around, but it wouldn't be difficult. It's just a Vector of MOs and associated wave function basis information. When they get loaded by ModelLoader.java, they get associated with the models as they are read. Bob On Tue, Jun 9, 2009 at 2:10 PM, Jonathan Gutow <gu...@uw...> wrote: > Bob et al. > I need some help figuring out what is going on with the file > readers. I don't seem to be able to find where the actual version of > readAtomSetCollection(BufferedReader reader) that reads more than MOs > is located. I must be missing it. I've looked at the > AtomSetCollection...java files and all the GAMESSReader files. Is > the generic reader in one of the other speciality reader files? I'm > sure I've just missed it, but need to figure out the logic for > associating MOs with a frame. Am I even looking in the right place? > Are the frames built later? > > Jonathan > > Dr. Jonathan H. Gutow > Chemistry Department gu...@uw... > UW-Oshkosh Office:920-424-1326 > 800 Algoma Boulevard FAX:920-424-2042 > Oshkosh, WI 54901 > http://www.uwosh.edu/faculty_staff/gutow/ > > > > > > > ------------------------------------------------------------------------------ > Crystal Reports - New Free Runtime and 30 Day Trial > Check out the new simplified licensing option that enables unlimited > royalty-free distribution of the report engine for externally facing > server and web deployment. > http://p.sf.net/sfu/businessobjects > _______________________________________________ > 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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From: Jonathan G. <gu...@uw...> - 2009-06-10 03:57:40
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On Jun 9, 2009, at 10:16 PM, Robert Hanson wrote: > Johathan, I'm guessing you are not using Eclipse. I recommend it -- > then you just start clicking on names to find anything you want. > Ah, let's see. The Gamess reader is an abstract class - GamessUK > and GamessUS being the instantiated ones. They are subclasses of > AtomSetCollectionReader. > (org.jmol.adapters.smarter.AtomSetCollectionReader.java) In fact, > the Gamess reader itself is a subclass of MOReader, another > abstract class. I am using eclipse and that matches with what I found. The problem I was running into was that eclipse kept linking me back to the abstract classes and not the actual code. What is unclear to me trying to follow the code is when the atoms for a frame are read in and when the MOs are read in. It looks to me as if they might be done on separate passes. If that is true that could explain why all the MOs are being associated with the first and last frame of a multi- frame GAMESS file and not with the frame to which they belong. > > MOs certainly could be associated with any model. They start out in > a Hashtable that is stored in the AuxilliaryInfo Hashtable. There's > no general way set up to move these around, but it wouldn't be > difficult. It's just a Vector of MOs and associated wave function > basis information. When they get loaded by ModelLoader.java, they > get associated with the models as they are read. I think ModelLoader is the set of routines I haven't yet looked at. Thanks. I'll take a look at that. Jonathan > > Bob > > > > On Tue, Jun 9, 2009 at 2:10 PM, Jonathan Gutow <gu...@uw...> > wrote: > Bob et al. > I need some help figuring out what is going on with the file > readers. I don't seem to be able to find where the actual version of > readAtomSetCollection(BufferedReader reader) that reads more than MOs > is located. I must be missing it. I've looked at the > AtomSetCollection...java files and all the GAMESSReader files. Is > the generic reader in one of the other speciality reader files? I'm > sure I've just missed it, but need to figure out the logic for > associating MOs with a frame. Am I even looking in the right place? > Are the frames built later? > > Jonathan > > Dr. Jonathan H. Gutow > Chemistry Department gu...@uw... > UW-Oshkosh Office: > 920-424-1326 > 800 Algoma Boulevard FAX:920-424-2042 > Oshkosh, WI 54901 > http://www.uwosh.edu/faculty_staff/gutow/ > > > > > > ---------------------------------------------------------------------- > -------- > Crystal Reports - New Free Runtime and 30 Day Trial > Check out the new simplified licensing option that enables unlimited > royalty-free distribution of the report engine for externally facing > server and web deployment. > http://p.sf.net/sfu/businessobjects > _______________________________________________ > 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 > ---------------------------------------------------------------------- > -------- > Crystal Reports - New Free Runtime and 30 Day Trial > Check out the new simplified licensing option that enables unlimited > royalty-free distribution of the report engine for externally facing > server and web deployment. > http://p.sf.net/sfu/businessobjects > _______________________________________________ > Jmol-developers mailing list > Jmo...@li... > https://lists.sourceforge.net/lists/listinfo/jmol-developers Dr. Jonathan H. Gutow Chemistry Department gu...@uw... UW-Oshkosh Office:920-424-1326 800 Algoma Boulevard FAX:920-424-2042 Oshkosh, WI 54901 http://www.uwosh.edu/faculty_staff/gutow/ |
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From: Robert H. <ha...@st...> - 2009-06-10 14:41:06
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The "abstract classes" are the code... On Tue, Jun 9, 2009 at 10:57 PM, Jonathan Gutow <gu...@uw...> wrote: > > On Jun 9, 2009, at 10:16 PM, Robert Hanson wrote: > > > Johathan, I'm guessing you are not using Eclipse. I recommend it -- > > then you just start clicking on names to find anything you want. > > Ah, let's see. The Gamess reader is an abstract class - GamessUK > > and GamessUS being the instantiated ones. They are subclasses of > > AtomSetCollectionReader. > > (org.jmol.adapters.smarter.AtomSetCollectionReader.java) In fact, > > the Gamess reader itself is a subclass of MOReader, another > > abstract class. > I am using eclipse and that matches with what I found. The problem I > was running into was that eclipse kept linking me back to the > abstract classes and not the actual code. What is unclear to me > trying to follow the code is when the atoms for a frame are read in > and when the MOs are read in. It looks to me as if they might be > done on separate passes. single pass, but coordinates come first. > If that is true that could explain why all > the MOs are being associated with the first and last frame of a multi- > frame GAMESS file and not with the frame to which they belong. how do you know which ones they belong in? send file? > > > > > MOs certainly could be associated with any model. They start out in > > a Hashtable that is stored in the AuxilliaryInfo Hashtable. There's > > no general way set up to move these around, but it wouldn't be > > difficult. It's just a Vector of MOs and associated wave function > > basis information. When they get loaded by ModelLoader.java, they > > get associated with the models as they are read. > I think ModelLoader is the set of routines I haven't yet looked at. > Thanks. I'll take a look at that. > > Jonathan > > > > Bob > > > > > > > > On Tue, Jun 9, 2009 at 2:10 PM, Jonathan Gutow <gu...@uw...> > > wrote: > > Bob et al. > > I need some help figuring out what is going on with the file > > readers. I don't seem to be able to find where the actual version of > > readAtomSetCollection(BufferedReader reader) that reads more than MOs > > is located. I must be missing it. I've looked at the > > AtomSetCollection...java files and all the GAMESSReader files. Is > > the generic reader in one of the other speciality reader files? I'm > > sure I've just missed it, but need to figure out the logic for > > associating MOs with a frame. Am I even looking in the right place? > > Are the frames built later? > > > > Jonathan > > > > Dr. Jonathan H. Gutow > > Chemistry Department gu...@uw... > > UW-Oshkosh Office: > > 920-424-1326 > > 800 Algoma Boulevard FAX:920-424-2042 > > Oshkosh, WI 54901 > > http://www.uwosh.edu/faculty_staff/gutow/ > > > > > > > > > > > > ---------------------------------------------------------------------- > > -------- > > Crystal Reports - New Free Runtime and 30 Day Trial > > Check out the new simplified licensing option that enables unlimited > > royalty-free distribution of the report engine for externally facing > > server and web deployment. > > http://p.sf.net/sfu/businessobjects > > _______________________________________________ > > 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 > > ---------------------------------------------------------------------- > > -------- > > Crystal Reports - New Free Runtime and 30 Day Trial > > Check out the new simplified licensing option that enables unlimited > > royalty-free distribution of the report engine for externally facing > > server and web deployment. > > http://p.sf.net/sfu/businessobjects > > _______________________________________________ > > Jmol-developers mailing list > > Jmo...@li... > > https://lists.sourceforge.net/lists/listinfo/jmol-developers > > Dr. Jonathan H. Gutow > Chemistry Department gu...@uw... > UW-Oshkosh Office:920-424-1326 > 800 Algoma Boulevard FAX:920-424-2042 > Oshkosh, WI 54901 > http://www.uwosh.edu/faculty_staff/gutow/ > > > > > > > ------------------------------------------------------------------------------ > Crystal Reports - New Free Runtime and 30 Day Trial > Check out the new simplified licensing option that enables unlimited > royalty-free distribution of the report engine for externally facing > server and web deployment. > http://p.sf.net/sfu/businessobjects > _______________________________________________ > 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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