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From: SourceForge.net <no...@so...> - 2009-12-10 14:35:07
|
Bugs item #2908926, was opened at 2009-12-04 17:56 Message generated for change (Comment added) made by xaverxn You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=819222&aid=2908926&group_id=161285 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: Parsers Group: None Status: Open Resolution: None Priority: 5 Private: No Submitted By: xaverxn (xaverxn) Assigned to: Nobody/Anonymous (nobody) Summary: I never get the attribute 'scfvalues' Initial Comment: Hi, I'm not sure if I'm doing anything wrong here, so forgive my if this is not a bug. Using current trunk (rev. 826) or stable, I can't seem to get the attribute 'scfvalues' when parsing any of my gaussian log files ("AttributeError: 'ccData' object has no attribute 'scfvalues'"). Please try it with the file attached to my last bug report (Title "Assertion error trying ...", file g03_test_complete.log.tar.bz2). Attached find the python console output. Regards, Xaver >>> myfile=cclib.parser.ccopen('testfiles/g03_test_complete.log') >>> data = myfile.parse() [Gaussian testfiles/g03_test_complete.log INFO] Creating attribute charge: -2 [Gaussian testfiles/g03_test_complete.log INFO] Creating attribute mult: 5 [Gaussian testfiles/g03_test_complete.log INFO] Creating attribute atomnos[] [Gaussian testfiles/g03_test_complete.log INFO] Creating attribute natom: 31 [Gaussian testfiles/g03_test_complete.log INFO] Creating attribute gbasis[] [Gaussian testfiles/g03_test_complete.log INFO] Creating attribute nbasis: 286 [Gaussian testfiles/g03_test_complete.log INFO] Creating attribute nmo: 286 [Gaussian testfiles/g03_test_complete.log INFO] Creating attribute scfenergies[] [Gaussian testfiles/g03_test_complete.log INFO] Creating attribute moenergies[] [Gaussian testfiles/g03_test_complete.log INFO] Creating attribute homos[] [Gaussian testfiles/g03_test_complete.log INFO] Creating attribute grads[] [Gaussian testfiles/g03_test_complete.log INFO] Creating attribute geovalues[] [Gaussian testfiles/g03_test_complete.log INFO] Creating attribute geotargets[] [Gaussian testfiles/g03_test_complete.log INFO] Creating attribute atomcoords[] [Gaussian testfiles/g03_test_complete.log INFO] Creating attribute coreelectrons[] >>> data.scfenergies array([-55160.82711683, -55160.82713724, -55160.82713724]) >>> data.scfvalues Traceback (most recent call last): File "<stdin>", line 1, in <module> AttributeError: 'ccData' object has no attribute 'scfvalues' ---------------------------------------------------------------------- >Comment By: xaverxn (xaverxn) Date: 2009-12-10 15:35 Message: Sure. I meant using cclib fo parsing (which does not give me back single lines). ---------------------------------------------------------------------- Comment By: Noel O'Boyle (baoilleach) Date: 2009-12-10 13:03 Message: line.split()[-2] will give you '34'. ---------------------------------------------------------------------- Comment By: xaverxn (xaverxn) Date: 2009-12-10 12:58 Message: Yes, I guessed sth like this. So there is no way to extract the '34' out of the line SCF Done: E(UB+HF-LYP) = -2027.12313726 a.u. after 34 cycles ? In my understanding, that should be the same as (or a part of what) you would extract from #P log files. ---------------------------------------------------------------------- Comment By: Noel O'Boyle (baoilleach) Date: 2009-12-10 12:10 Message: Presumably your files don't contain this data (compare with dvb_gopt.out in the distribution). You need to use #P if you want scf convergence information to be included. ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=819222&aid=2908926&group_id=161285 |
|
From: SourceForge.net <no...@so...> - 2009-12-10 12:03:16
|
Bugs item #2908926, was opened at 2009-12-04 16:56 Message generated for change (Comment added) made by baoilleach You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=819222&aid=2908926&group_id=161285 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: Parsers Group: None Status: Open Resolution: None Priority: 5 Private: No Submitted By: xaverxn (xaverxn) Assigned to: Nobody/Anonymous (nobody) Summary: I never get the attribute 'scfvalues' Initial Comment: Hi, I'm not sure if I'm doing anything wrong here, so forgive my if this is not a bug. Using current trunk (rev. 826) or stable, I can't seem to get the attribute 'scfvalues' when parsing any of my gaussian log files ("AttributeError: 'ccData' object has no attribute 'scfvalues'"). Please try it with the file attached to my last bug report (Title "Assertion error trying ...", file g03_test_complete.log.tar.bz2). Attached find the python console output. Regards, Xaver >>> myfile=cclib.parser.ccopen('testfiles/g03_test_complete.log') >>> data = myfile.parse() [Gaussian testfiles/g03_test_complete.log INFO] Creating attribute charge: -2 [Gaussian testfiles/g03_test_complete.log INFO] Creating attribute mult: 5 [Gaussian testfiles/g03_test_complete.log INFO] Creating attribute atomnos[] [Gaussian testfiles/g03_test_complete.log INFO] Creating attribute natom: 31 [Gaussian testfiles/g03_test_complete.log INFO] Creating attribute gbasis[] [Gaussian testfiles/g03_test_complete.log INFO] Creating attribute nbasis: 286 [Gaussian testfiles/g03_test_complete.log INFO] Creating attribute nmo: 286 [Gaussian testfiles/g03_test_complete.log INFO] Creating attribute scfenergies[] [Gaussian testfiles/g03_test_complete.log INFO] Creating attribute moenergies[] [Gaussian testfiles/g03_test_complete.log INFO] Creating attribute homos[] [Gaussian testfiles/g03_test_complete.log INFO] Creating attribute grads[] [Gaussian testfiles/g03_test_complete.log INFO] Creating attribute geovalues[] [Gaussian testfiles/g03_test_complete.log INFO] Creating attribute geotargets[] [Gaussian testfiles/g03_test_complete.log INFO] Creating attribute atomcoords[] [Gaussian testfiles/g03_test_complete.log INFO] Creating attribute coreelectrons[] >>> data.scfenergies array([-55160.82711683, -55160.82713724, -55160.82713724]) >>> data.scfvalues Traceback (most recent call last): File "<stdin>", line 1, in <module> AttributeError: 'ccData' object has no attribute 'scfvalues' ---------------------------------------------------------------------- >Comment By: Noel O'Boyle (baoilleach) Date: 2009-12-10 12:03 Message: line.split()[-2] will give you '34'. ---------------------------------------------------------------------- Comment By: xaverxn (xaverxn) Date: 2009-12-10 11:58 Message: Yes, I guessed sth like this. So there is no way to extract the '34' out of the line SCF Done: E(UB+HF-LYP) = -2027.12313726 a.u. after 34 cycles ? In my understanding, that should be the same as (or a part of what) you would extract from #P log files. ---------------------------------------------------------------------- Comment By: Noel O'Boyle (baoilleach) Date: 2009-12-10 11:10 Message: Presumably your files don't contain this data (compare with dvb_gopt.out in the distribution). You need to use #P if you want scf convergence information to be included. ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=819222&aid=2908926&group_id=161285 |
|
From: SourceForge.net <no...@so...> - 2009-12-10 11:58:32
|
Bugs item #2908926, was opened at 2009-12-04 17:56 Message generated for change (Comment added) made by xaverxn You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=819222&aid=2908926&group_id=161285 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: Parsers Group: None Status: Open Resolution: None Priority: 5 Private: No Submitted By: xaverxn (xaverxn) Assigned to: Nobody/Anonymous (nobody) Summary: I never get the attribute 'scfvalues' Initial Comment: Hi, I'm not sure if I'm doing anything wrong here, so forgive my if this is not a bug. Using current trunk (rev. 826) or stable, I can't seem to get the attribute 'scfvalues' when parsing any of my gaussian log files ("AttributeError: 'ccData' object has no attribute 'scfvalues'"). Please try it with the file attached to my last bug report (Title "Assertion error trying ...", file g03_test_complete.log.tar.bz2). Attached find the python console output. Regards, Xaver >>> myfile=cclib.parser.ccopen('testfiles/g03_test_complete.log') >>> data = myfile.parse() [Gaussian testfiles/g03_test_complete.log INFO] Creating attribute charge: -2 [Gaussian testfiles/g03_test_complete.log INFO] Creating attribute mult: 5 [Gaussian testfiles/g03_test_complete.log INFO] Creating attribute atomnos[] [Gaussian testfiles/g03_test_complete.log INFO] Creating attribute natom: 31 [Gaussian testfiles/g03_test_complete.log INFO] Creating attribute gbasis[] [Gaussian testfiles/g03_test_complete.log INFO] Creating attribute nbasis: 286 [Gaussian testfiles/g03_test_complete.log INFO] Creating attribute nmo: 286 [Gaussian testfiles/g03_test_complete.log INFO] Creating attribute scfenergies[] [Gaussian testfiles/g03_test_complete.log INFO] Creating attribute moenergies[] [Gaussian testfiles/g03_test_complete.log INFO] Creating attribute homos[] [Gaussian testfiles/g03_test_complete.log INFO] Creating attribute grads[] [Gaussian testfiles/g03_test_complete.log INFO] Creating attribute geovalues[] [Gaussian testfiles/g03_test_complete.log INFO] Creating attribute geotargets[] [Gaussian testfiles/g03_test_complete.log INFO] Creating attribute atomcoords[] [Gaussian testfiles/g03_test_complete.log INFO] Creating attribute coreelectrons[] >>> data.scfenergies array([-55160.82711683, -55160.82713724, -55160.82713724]) >>> data.scfvalues Traceback (most recent call last): File "<stdin>", line 1, in <module> AttributeError: 'ccData' object has no attribute 'scfvalues' ---------------------------------------------------------------------- >Comment By: xaverxn (xaverxn) Date: 2009-12-10 12:58 Message: Yes, I guessed sth like this. So there is no way to extract the '34' out of the line SCF Done: E(UB+HF-LYP) = -2027.12313726 a.u. after 34 cycles ? In my understanding, that should be the same as (or a part of what) you would extract from #P log files. ---------------------------------------------------------------------- Comment By: Noel O'Boyle (baoilleach) Date: 2009-12-10 12:10 Message: Presumably your files don't contain this data (compare with dvb_gopt.out in the distribution). You need to use #P if you want scf convergence information to be included. ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=819222&aid=2908926&group_id=161285 |
|
From: SourceForge.net <no...@so...> - 2009-12-10 11:10:55
|
Bugs item #2908926, was opened at 2009-12-04 16:56 Message generated for change (Comment added) made by baoilleach You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=819222&aid=2908926&group_id=161285 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: Parsers Group: None Status: Open Resolution: None Priority: 5 Private: No Submitted By: xaverxn (xaverxn) Assigned to: Nobody/Anonymous (nobody) Summary: I never get the attribute 'scfvalues' Initial Comment: Hi, I'm not sure if I'm doing anything wrong here, so forgive my if this is not a bug. Using current trunk (rev. 826) or stable, I can't seem to get the attribute 'scfvalues' when parsing any of my gaussian log files ("AttributeError: 'ccData' object has no attribute 'scfvalues'"). Please try it with the file attached to my last bug report (Title "Assertion error trying ...", file g03_test_complete.log.tar.bz2). Attached find the python console output. Regards, Xaver >>> myfile=cclib.parser.ccopen('testfiles/g03_test_complete.log') >>> data = myfile.parse() [Gaussian testfiles/g03_test_complete.log INFO] Creating attribute charge: -2 [Gaussian testfiles/g03_test_complete.log INFO] Creating attribute mult: 5 [Gaussian testfiles/g03_test_complete.log INFO] Creating attribute atomnos[] [Gaussian testfiles/g03_test_complete.log INFO] Creating attribute natom: 31 [Gaussian testfiles/g03_test_complete.log INFO] Creating attribute gbasis[] [Gaussian testfiles/g03_test_complete.log INFO] Creating attribute nbasis: 286 [Gaussian testfiles/g03_test_complete.log INFO] Creating attribute nmo: 286 [Gaussian testfiles/g03_test_complete.log INFO] Creating attribute scfenergies[] [Gaussian testfiles/g03_test_complete.log INFO] Creating attribute moenergies[] [Gaussian testfiles/g03_test_complete.log INFO] Creating attribute homos[] [Gaussian testfiles/g03_test_complete.log INFO] Creating attribute grads[] [Gaussian testfiles/g03_test_complete.log INFO] Creating attribute geovalues[] [Gaussian testfiles/g03_test_complete.log INFO] Creating attribute geotargets[] [Gaussian testfiles/g03_test_complete.log INFO] Creating attribute atomcoords[] [Gaussian testfiles/g03_test_complete.log INFO] Creating attribute coreelectrons[] >>> data.scfenergies array([-55160.82711683, -55160.82713724, -55160.82713724]) >>> data.scfvalues Traceback (most recent call last): File "<stdin>", line 1, in <module> AttributeError: 'ccData' object has no attribute 'scfvalues' ---------------------------------------------------------------------- >Comment By: Noel O'Boyle (baoilleach) Date: 2009-12-10 11:10 Message: Presumably your files don't contain this data (compare with dvb_gopt.out in the distribution). You need to use #P if you want scf convergence information to be included. ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=819222&aid=2908926&group_id=161285 |
|
From: SourceForge.net <no...@so...> - 2009-12-04 16:56:02
|
Bugs item #2908926, was opened at 2009-12-04 17:56 Message generated for change (Tracker Item Submitted) made by xaverxn You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=819222&aid=2908926&group_id=161285 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: Parsers Group: None Status: Open Resolution: None Priority: 5 Private: No Submitted By: xaverxn (xaverxn) Assigned to: Nobody/Anonymous (nobody) Summary: I never get the attribute 'scfvalues' Initial Comment: Hi, I'm not sure if I'm doing anything wrong here, so forgive my if this is not a bug. Using current trunk (rev. 826) or stable, I can't seem to get the attribute 'scfvalues' when parsing any of my gaussian log files ("AttributeError: 'ccData' object has no attribute 'scfvalues'"). Please try it with the file attached to my last bug report (Title "Assertion error trying ...", file g03_test_complete.log.tar.bz2). Attached find the python console output. Regards, Xaver >>> myfile=cclib.parser.ccopen('testfiles/g03_test_complete.log') >>> data = myfile.parse() [Gaussian testfiles/g03_test_complete.log INFO] Creating attribute charge: -2 [Gaussian testfiles/g03_test_complete.log INFO] Creating attribute mult: 5 [Gaussian testfiles/g03_test_complete.log INFO] Creating attribute atomnos[] [Gaussian testfiles/g03_test_complete.log INFO] Creating attribute natom: 31 [Gaussian testfiles/g03_test_complete.log INFO] Creating attribute gbasis[] [Gaussian testfiles/g03_test_complete.log INFO] Creating attribute nbasis: 286 [Gaussian testfiles/g03_test_complete.log INFO] Creating attribute nmo: 286 [Gaussian testfiles/g03_test_complete.log INFO] Creating attribute scfenergies[] [Gaussian testfiles/g03_test_complete.log INFO] Creating attribute moenergies[] [Gaussian testfiles/g03_test_complete.log INFO] Creating attribute homos[] [Gaussian testfiles/g03_test_complete.log INFO] Creating attribute grads[] [Gaussian testfiles/g03_test_complete.log INFO] Creating attribute geovalues[] [Gaussian testfiles/g03_test_complete.log INFO] Creating attribute geotargets[] [Gaussian testfiles/g03_test_complete.log INFO] Creating attribute atomcoords[] [Gaussian testfiles/g03_test_complete.log INFO] Creating attribute coreelectrons[] >>> data.scfenergies array([-55160.82711683, -55160.82713724, -55160.82713724]) >>> data.scfvalues Traceback (most recent call last): File "<stdin>", line 1, in <module> AttributeError: 'ccData' object has no attribute 'scfvalues' ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=819222&aid=2908926&group_id=161285 |
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From: SourceForge.net <no...@so...> - 2009-12-04 16:45:28
|
Bugs item #2904432, was opened at 2009-11-26 10:25 Message generated for change (Settings changed) made by baoilleach You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=819222&aid=2904432&group_id=161285 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: Parsers Group: None >Status: Closed Resolution: Works For Me Priority: 5 Private: No Submitted By: xaverxn (xaverxn) Assigned to: Nobody/Anonymous (nobody) Summary: Assertion error trying to parse this gaussian log Initial Comment: Hi, I guess this is a bug. Trying to ccopen() this gaussian log gives me: >>> import cclib >>> myfile=cclib.parser.ccopen('testfiles/g03_test_complete.log') >>> data=myfile.parse() [Gaussian testfiles/g03_test_complete.log INFO] Creating attribute charge: -2 [Gaussian testfiles/g03_test_complete.log INFO] Creating attribute mult: 5 [Gaussian testfiles/g03_test_complete.log INFO] Creating attribute atomnos[] [Gaussian testfiles/g03_test_complete.log INFO] Creating attribute natom: 31 [Gaussian testfiles/g03_test_complete.log INFO] Creating attribute gbasis[] Traceback (most recent call last): File "<stdin>", line 1, in <module> File "/usr/lib/python2.5/site-packages/cclib/parser/logfileparser.py", line 142, in parse self.extract(inputfile, line) File "/usr/lib/python2.5/site-packages/cclib/parser/gaussianparser.py", line 79, in extract assert self.natom == natom AssertionError As for the basis, this was a ub3lyp/gen job with a mixed basis set: (...) C H O 0 6-31G(d,p) **** Fe 0 tzv **** (...) ---------------------------------------------------------------------- Comment By: xaverxn (xaverxn) Date: 2009-12-04 16:44 Message: With the current trunk (rev. 826), this works for me, too, so I guess you're right. Thanks. ---------------------------------------------------------------------- Comment By: Noel O'Boyle (baoilleach) Date: 2009-12-01 10:14 Message: This works for me with the cclib development code, so it must have been fixed in the meanwhile. We will try to get out a cclib version before Christmas (!) or early in the new year. Marking as pending - Noel ---------------------------------------------------------------------- Comment By: xaverxn (xaverxn) Date: 2009-11-27 12:32 Message: I hereby place the uploaded file g03_test_complete.log.tar.bz2 in the public domain. ---------------------------------------------------------------------- Comment By: Noel O'Boyle (baoilleach) Date: 2009-11-27 11:16 Message: (Tried to respond earlier but SF was messed up) We only fix bugs for public domain log files, so can you confirm (or deny!) that you place this log file in the public domain? - Noel ---------------------------------------------------------------------- Comment By: xaverxn (xaverxn) Date: 2009-11-26 10:27 Message: Forgot to say: cclib-0.91 Python 2.5.2 (r252:60911, Jan 4 2009, 21:59:32) [GCC 4.3.2] on linux2 ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=819222&aid=2904432&group_id=161285 |
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From: SourceForge.net <no...@so...> - 2009-12-04 16:44:14
|
Bugs item #2904432, was opened at 2009-11-26 11:25 Message generated for change (Comment added) made by xaverxn You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=819222&aid=2904432&group_id=161285 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: Parsers Group: None >Status: Open Resolution: Works For Me Priority: 5 Private: No Submitted By: xaverxn (xaverxn) Assigned to: Nobody/Anonymous (nobody) Summary: Assertion error trying to parse this gaussian log Initial Comment: Hi, I guess this is a bug. Trying to ccopen() this gaussian log gives me: >>> import cclib >>> myfile=cclib.parser.ccopen('testfiles/g03_test_complete.log') >>> data=myfile.parse() [Gaussian testfiles/g03_test_complete.log INFO] Creating attribute charge: -2 [Gaussian testfiles/g03_test_complete.log INFO] Creating attribute mult: 5 [Gaussian testfiles/g03_test_complete.log INFO] Creating attribute atomnos[] [Gaussian testfiles/g03_test_complete.log INFO] Creating attribute natom: 31 [Gaussian testfiles/g03_test_complete.log INFO] Creating attribute gbasis[] Traceback (most recent call last): File "<stdin>", line 1, in <module> File "/usr/lib/python2.5/site-packages/cclib/parser/logfileparser.py", line 142, in parse self.extract(inputfile, line) File "/usr/lib/python2.5/site-packages/cclib/parser/gaussianparser.py", line 79, in extract assert self.natom == natom AssertionError As for the basis, this was a ub3lyp/gen job with a mixed basis set: (...) C H O 0 6-31G(d,p) **** Fe 0 tzv **** (...) ---------------------------------------------------------------------- >Comment By: xaverxn (xaverxn) Date: 2009-12-04 17:44 Message: With the current trunk (rev. 826), this works for me, too, so I guess you're right. Thanks. ---------------------------------------------------------------------- Comment By: Noel O'Boyle (baoilleach) Date: 2009-12-01 11:14 Message: This works for me with the cclib development code, so it must have been fixed in the meanwhile. We will try to get out a cclib version before Christmas (!) or early in the new year. Marking as pending - Noel ---------------------------------------------------------------------- Comment By: xaverxn (xaverxn) Date: 2009-11-27 13:32 Message: I hereby place the uploaded file g03_test_complete.log.tar.bz2 in the public domain. ---------------------------------------------------------------------- Comment By: Noel O'Boyle (baoilleach) Date: 2009-11-27 12:16 Message: (Tried to respond earlier but SF was messed up) We only fix bugs for public domain log files, so can you confirm (or deny!) that you place this log file in the public domain? - Noel ---------------------------------------------------------------------- Comment By: xaverxn (xaverxn) Date: 2009-11-26 11:27 Message: Forgot to say: cclib-0.91 Python 2.5.2 (r252:60911, Jan 4 2009, 21:59:32) [GCC 4.3.2] on linux2 ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=819222&aid=2904432&group_id=161285 |
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From: Xaver W. <xav...@we...> - 2009-12-04 16:38:11
|
Hi,
OK, since you seem to be talking about the latest svn code, I got the latest
revision now.
> Let met just input on this at the moment. In fact cclib.parser.ccopen can
> process an input stream, which can an open file object or instance of
> StringIO.StringIO. Generally, whatever can be read and
> implements 'read', 'next' and other methods.
I don't get errors while Gaussian(stringiofile).parse(), so it seems to
generally work. However, I don't get an scfenergies attribute from
StringIO.StringIO(" Entering Gaussian System, Link 0=/opt/g03/g03/g03\n SCF
Done: E(UB+HF-LYP) = -887.172106755 A.U. after 59 cycles")
, and ccopen() doesn't recognize it as Gaussian type. Well, I guess that's
because cclib is not really made to handle small fake logfiles. As I don't
have the time to test how to trick it, I think I'll take Karol's friendly
offer and put sth like that as a feature request on sourceforge...
(But first I'll wait if it is a bug that sometimes, I don't get an scfvalues
attribute even for real gaussian03 log files. I'll post a bug report on that)
> How did you test that the file is still open?
I can't remember, but it doesn't matter. I'd just like to know if I have
to 'do' sth to cleanly close my log files at the end of my program code. You
know, sth like
ccopen(myfile)
...
ccclose(myfile)
...or does cclib handle this?
Regards,
Xaver
Am Monday 30 November 2009 19:09:57 schrieb Karol M. Langner:
> On Monday 30 November 2009 16:29:04 Noel O'Boyle wrote:
> > > - Can I trick cclib into reading a string instead of a file? Noel
> > > pointed me to StringIO objects. However, StringIO
> > >
> > > simulates an "opened file" while cclib needs a non-open file, right?:
> > >>>> mimicfile=StringIO.StringIO(" Entering Gaussian System, Link
> > >
> > > 0=/opt/g03/g03/g03\n SCF Done: E(UB+HF-LYP) = -887.172106755
> > > A.U. after 59 cycles")
> > >
> > >>>> myfile = cclib.parser.Gaussian("mimicfile")
> >
> > You passed the string mimicfile - you should pass the variable, e.g.
> > Gaussian(mimicfile). However, cclib has been written to parse entire
> > files, not portions of files, so this example may not work.
>
> Let met just input on this at the moment. In fact cclib.parser.ccopen can
> process an input stream, which can an open file object or instance of
> StringIO.StringIO. Generally, whatever can be read and
> implements 'read', 'next' and other methods.
>
> >>> import cclib
> >>> print cclib.parser.ccopen.__doc__
>
> Guess the identity of a particular log file and return an instance of it.
>
> Inputs:
> source - a single logfile, a list of logfiles, or an input stream
>
> Returns:
> one of ADF, GAMESS, GAMESS UK, Gaussian, Jaguar, Molpro, ORCA, or
> None (if it cannot figure it out or the file does not exist).
>
> Currently passing a string would generate an error, but that functionality
> could be added quite easily. If needed, please file a feature request and
> I'm sure Noel or I could implement it pretty fast.
>
> - Karol
|
|
From: Noel O'B. <bao...@gm...> - 2009-12-03 18:24:35
|
We're waiting for Numpy. 2009/12/3 Adam Tenderholt <a-t...@st...>: > Are there plans to port to python 3.x? Or have we done it already and I've just been living under a rock? I bring this up because I found the following guide about porting: > > http://ptgmedia.pearsoncmg.com/imprint_downloads/informit/promotions/python/python2python3.pdf > > Adam > > > ------------------------------------------------------------------------------ > Join us December 9, 2009 for the Red Hat Virtual Experience, > a free event focused on virtualization and cloud computing. > Attend in-depth sessions from your desk. Your couch. Anywhere. > http://p.sf.net/sfu/redhat-sfdev2dev > _______________________________________________ > cclib-devel mailing list > ccl...@li... > https://lists.sourceforge.net/lists/listinfo/cclib-devel > |
|
From: Adam T. <a-t...@st...> - 2009-12-03 18:20:02
|
Are there plans to port to python 3.x? Or have we done it already and I've just been living under a rock? I bring this up because I found the following guide about porting: http://ptgmedia.pearsoncmg.com/imprint_downloads/informit/promotions/python/python2python3.pdf Adam |
|
From: SourceForge.net <no...@so...> - 2009-12-01 10:14:57
|
Bugs item #2904432, was opened at 2009-11-26 10:25 Message generated for change (Settings changed) made by baoilleach You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=819222&aid=2904432&group_id=161285 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: Parsers Group: None >Status: Pending >Resolution: Works For Me Priority: 5 Private: No Submitted By: xaverxn (xaverxn) Assigned to: Nobody/Anonymous (nobody) Summary: Assertion error trying to parse this gaussian log Initial Comment: Hi, I guess this is a bug. Trying to ccopen() this gaussian log gives me: >>> import cclib >>> myfile=cclib.parser.ccopen('testfiles/g03_test_complete.log') >>> data=myfile.parse() [Gaussian testfiles/g03_test_complete.log INFO] Creating attribute charge: -2 [Gaussian testfiles/g03_test_complete.log INFO] Creating attribute mult: 5 [Gaussian testfiles/g03_test_complete.log INFO] Creating attribute atomnos[] [Gaussian testfiles/g03_test_complete.log INFO] Creating attribute natom: 31 [Gaussian testfiles/g03_test_complete.log INFO] Creating attribute gbasis[] Traceback (most recent call last): File "<stdin>", line 1, in <module> File "/usr/lib/python2.5/site-packages/cclib/parser/logfileparser.py", line 142, in parse self.extract(inputfile, line) File "/usr/lib/python2.5/site-packages/cclib/parser/gaussianparser.py", line 79, in extract assert self.natom == natom AssertionError As for the basis, this was a ub3lyp/gen job with a mixed basis set: (...) C H O 0 6-31G(d,p) **** Fe 0 tzv **** (...) ---------------------------------------------------------------------- >Comment By: Noel O'Boyle (baoilleach) Date: 2009-12-01 10:14 Message: This works for me with the cclib development code, so it must have been fixed in the meanwhile. We will try to get out a cclib version before Christmas (!) or early in the new year. Marking as pending - Noel ---------------------------------------------------------------------- Comment By: xaverxn (xaverxn) Date: 2009-11-27 12:32 Message: I hereby place the uploaded file g03_test_complete.log.tar.bz2 in the public domain. ---------------------------------------------------------------------- Comment By: Noel O'Boyle (baoilleach) Date: 2009-11-27 11:16 Message: (Tried to respond earlier but SF was messed up) We only fix bugs for public domain log files, so can you confirm (or deny!) that you place this log file in the public domain? - Noel ---------------------------------------------------------------------- Comment By: xaverxn (xaverxn) Date: 2009-11-26 10:27 Message: Forgot to say: cclib-0.91 Python 2.5.2 (r252:60911, Jan 4 2009, 21:59:32) [GCC 4.3.2] on linux2 ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=819222&aid=2904432&group_id=161285 |
|
From: Karol M. L. <kar...@gm...> - 2009-11-30 17:59:51
|
On Monday 30 November 2009 16:29:04 Noel O'Boyle wrote:
> > - Can I trick cclib into reading a string instead of a file? Noel
> > pointed me to StringIO objects. However, StringIO
> >
> > simulates an "opened file" while cclib needs a non-open file, right?:
> >>>> mimicfile=StringIO.StringIO(" Entering Gaussian System, Link
> >
> > 0=/opt/g03/g03/g03\n SCF Done: E(UB+HF-LYP) = -887.172106755
> > A.U. after 59 cycles")
> >
> >>>> myfile = cclib.parser.Gaussian("mimicfile")
>
> You passed the string mimicfile - you should pass the variable, e.g.
> Gaussian(mimicfile). However, cclib has been written to parse entire
> files, not portions of files, so this example may not work.
Let met just input on this at the moment. In fact cclib.parser.ccopen can
process an input stream, which can an open file object or instance of
StringIO.StringIO. Generally, whatever can be read and
implements 'read', 'next' and other methods.
>>> import cclib
>>> print cclib.parser.ccopen.__doc__
Guess the identity of a particular log file and return an instance of it.
Inputs:
source - a single logfile, a list of logfiles, or an input stream
Returns:
one of ADF, GAMESS, GAMESS UK, Gaussian, Jaguar, Molpro, ORCA, or
None (if it cannot figure it out or the file does not exist).
Currently passing a string would generate an error, but that functionality
could be added quite easily. If needed, please file a feature request and
I'm sure Noel or I could implement it pretty fast.
- Karol
--
written by Karol Langner
Mon Nov 30 19:03:23 CET 2009
|
|
From: Noel O'B. <bao...@gm...> - 2009-11-30 15:29:17
|
2009/11/30 Xaver Wurzenberger <xav...@we...>:
> Hi guys,
>
> I've got a few questions about using cclib. Actually, Noel asked me to cc them
> here, but I thought it might make sense to generally discuss them here. I
> hope they're not too much "newbie-questions", because I'm not really advanced
> in programming and python.
>
> -In which case is the variable 'scfvalues' (not) created?
> I tried to get it with a couple of gaussian03 log files, but it was never
> existant.
If the values are present, they will be parsed, so this may be a bug.
> -When is cclib closing its input file?
> From my understanding of the source code, that should be done after
> parsing (?! logparser.py/line 145 in current stable), but it seems the files
> are still open when testing it in a
> python console. Just wondering if I have to do anything to cleanly have all
> files closed at the end of my code.
How did you test that the file is still open?
> - Can I trick cclib into reading a string instead of a file? Noel pointed me
> to StringIO objects. However, StringIO
> simulates an "opened file" while cclib needs a non-open file, right?:
>>>> mimicfile=StringIO.StringIO(" Entering Gaussian System, Link
> 0=/opt/g03/g03/g03\n SCF Done: E(UB+HF-LYP) = -887.172106755 A.U. after
> 59 cycles")
>>>> myfile = cclib.parser.Gaussian("mimicfile")
You passed the string mimicfile - you should pass the variable, e.g.
Gaussian(mimicfile). However, cclib has been written to parse entire
files, not portions of files, so this example may not work.
>
> Thanks in advance,
> Xaver W.
>
> ------------------------------------------------------------------------------
> Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day
> trial. Simplify your report design, integration and deployment - and focus on
> what you do best, core application coding. Discover what's new with
> Crystal Reports now. http://p.sf.net/sfu/bobj-july
> _______________________________________________
> cclib-devel mailing list
> ccl...@li...
> https://lists.sourceforge.net/lists/listinfo/cclib-devel
>
|
|
From: Xaver W. <xav...@we...> - 2009-11-30 15:22:17
|
Hi guys,
I've got a few questions about using cclib. Actually, Noel asked me to cc them
here, but I thought it might make sense to generally discuss them here. I
hope they're not too much "newbie-questions", because I'm not really advanced
in programming and python.
-In which case is the variable 'scfvalues' (not) created?
I tried to get it with a couple of gaussian03 log files, but it was never
existant.
-When is cclib closing its input file?
From my understanding of the source code, that should be done after
parsing (?! logparser.py/line 145 in current stable), but it seems the files
are still open when testing it in a
python console. Just wondering if I have to do anything to cleanly have all
files closed at the end of my code.
- Can I trick cclib into reading a string instead of a file? Noel pointed me
to StringIO objects. However, StringIO
simulates an "opened file" while cclib needs a non-open file, right?:
>>> mimicfile=StringIO.StringIO(" Entering Gaussian System, Link
0=/opt/g03/g03/g03\n SCF Done: E(UB+HF-LYP) = -887.172106755 A.U. after
59 cycles")
>>> myfile = cclib.parser.Gaussian("mimicfile")
>>> print myfile
Gaussian log file mimicfile
>>> myfile.parse()
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "/usr/lib/python2.6/site-packages/cclib/parser/logfileparser.py", line
104, in parse
inputfile = utils.openlogfile(self.filename)
File "/usr/lib/python2.6/site-packages/cclib/parser/utils.py", line 61, in
openlogfile
fileobject = open(filename, "r")
IOError: [Errno 2] No such file or directory: 'mimicfile'
>>> cclib.parser.ccopen(mimicfile)
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "/usr/lib/python2.6/site-packages/cclib/parser/utils.py", line 96, in
ccopen
for line in inputfile:
File "/usr/lib/python2.6/fileinput.py", line 253, in next
line = self.readline()
File "/usr/lib/python2.6/fileinput.py", line 343, in readline
self._file = self._openhook(self._filename, self._mode)
File "/usr/lib/python2.6/fileinput.py", line 387, in hook_compressed
return open(filename, mode)
IOError: [Errno 2] No such file or directory: ' Entering Gaussian System, Link
0=/opt/g03/g03/g03\n'
Thanks in advance,
Xaver W.
|
|
From: SourceForge.net <no...@so...> - 2009-11-27 12:32:53
|
Bugs item #2904432, was opened at 2009-11-26 11:25 Message generated for change (Comment added) made by xaverxn You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=819222&aid=2904432&group_id=161285 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: Parsers Group: None Status: Open Resolution: None Priority: 5 Private: No Submitted By: xaverxn (xaverxn) Assigned to: Nobody/Anonymous (nobody) Summary: Assertion error trying to parse this gaussian log Initial Comment: Hi, I guess this is a bug. Trying to ccopen() this gaussian log gives me: >>> import cclib >>> myfile=cclib.parser.ccopen('testfiles/g03_test_complete.log') >>> data=myfile.parse() [Gaussian testfiles/g03_test_complete.log INFO] Creating attribute charge: -2 [Gaussian testfiles/g03_test_complete.log INFO] Creating attribute mult: 5 [Gaussian testfiles/g03_test_complete.log INFO] Creating attribute atomnos[] [Gaussian testfiles/g03_test_complete.log INFO] Creating attribute natom: 31 [Gaussian testfiles/g03_test_complete.log INFO] Creating attribute gbasis[] Traceback (most recent call last): File "<stdin>", line 1, in <module> File "/usr/lib/python2.5/site-packages/cclib/parser/logfileparser.py", line 142, in parse self.extract(inputfile, line) File "/usr/lib/python2.5/site-packages/cclib/parser/gaussianparser.py", line 79, in extract assert self.natom == natom AssertionError As for the basis, this was a ub3lyp/gen job with a mixed basis set: (...) C H O 0 6-31G(d,p) **** Fe 0 tzv **** (...) ---------------------------------------------------------------------- >Comment By: xaverxn (xaverxn) Date: 2009-11-27 13:32 Message: I hereby place the uploaded file g03_test_complete.log.tar.bz2 in the public domain. ---------------------------------------------------------------------- Comment By: Noel O'Boyle (baoilleach) Date: 2009-11-27 12:16 Message: (Tried to respond earlier but SF was messed up) We only fix bugs for public domain log files, so can you confirm (or deny!) that you place this log file in the public domain? - Noel ---------------------------------------------------------------------- Comment By: xaverxn (xaverxn) Date: 2009-11-26 11:27 Message: Forgot to say: cclib-0.91 Python 2.5.2 (r252:60911, Jan 4 2009, 21:59:32) [GCC 4.3.2] on linux2 ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=819222&aid=2904432&group_id=161285 |
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From: SourceForge.net <no...@so...> - 2009-11-27 11:16:06
|
Bugs item #2904432, was opened at 2009-11-26 10:25 Message generated for change (Comment added) made by baoilleach You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=819222&aid=2904432&group_id=161285 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: Parsers Group: None Status: Open Resolution: None Priority: 5 Private: No Submitted By: xaverxn (xaverxn) Assigned to: Nobody/Anonymous (nobody) Summary: Assertion error trying to parse this gaussian log Initial Comment: Hi, I guess this is a bug. Trying to ccopen() this gaussian log gives me: >>> import cclib >>> myfile=cclib.parser.ccopen('testfiles/g03_test_complete.log') >>> data=myfile.parse() [Gaussian testfiles/g03_test_complete.log INFO] Creating attribute charge: -2 [Gaussian testfiles/g03_test_complete.log INFO] Creating attribute mult: 5 [Gaussian testfiles/g03_test_complete.log INFO] Creating attribute atomnos[] [Gaussian testfiles/g03_test_complete.log INFO] Creating attribute natom: 31 [Gaussian testfiles/g03_test_complete.log INFO] Creating attribute gbasis[] Traceback (most recent call last): File "<stdin>", line 1, in <module> File "/usr/lib/python2.5/site-packages/cclib/parser/logfileparser.py", line 142, in parse self.extract(inputfile, line) File "/usr/lib/python2.5/site-packages/cclib/parser/gaussianparser.py", line 79, in extract assert self.natom == natom AssertionError As for the basis, this was a ub3lyp/gen job with a mixed basis set: (...) C H O 0 6-31G(d,p) **** Fe 0 tzv **** (...) ---------------------------------------------------------------------- >Comment By: Noel O'Boyle (baoilleach) Date: 2009-11-27 11:16 Message: (Tried to respond earlier but SF was messed up) We only fix bugs for public domain log files, so can you confirm (or deny!) that you place this log file in the public domain? - Noel ---------------------------------------------------------------------- Comment By: xaverxn (xaverxn) Date: 2009-11-26 10:27 Message: Forgot to say: cclib-0.91 Python 2.5.2 (r252:60911, Jan 4 2009, 21:59:32) [GCC 4.3.2] on linux2 ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=819222&aid=2904432&group_id=161285 |
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From: SourceForge.net <no...@so...> - 2009-11-26 14:47:12
|
Bugs item #2904432, was opened at 2009-11-26 10:25 Message generated for change (Settings changed) made by xaverxn You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=819222&aid=2904432&group_id=161285 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: Parsers Group: None Status: Open Resolution: None Priority: 5 Private: No Submitted By: xaverxn (xaverxn) Assigned to: Nobody/Anonymous (nobody) Summary: Assertion error trying to parse this gaussian log Initial Comment: Hi, I guess this is a bug. Trying to ccopen() this gaussian log gives me: >>> import cclib >>> myfile=cclib.parser.ccopen('testfiles/g03_test_complete.log') >>> data=myfile.parse() [Gaussian testfiles/g03_test_complete.log INFO] Creating attribute charge: -2 [Gaussian testfiles/g03_test_complete.log INFO] Creating attribute mult: 5 [Gaussian testfiles/g03_test_complete.log INFO] Creating attribute atomnos[] [Gaussian testfiles/g03_test_complete.log INFO] Creating attribute natom: 31 [Gaussian testfiles/g03_test_complete.log INFO] Creating attribute gbasis[] Traceback (most recent call last): File "<stdin>", line 1, in <module> File "/usr/lib/python2.5/site-packages/cclib/parser/logfileparser.py", line 142, in parse self.extract(inputfile, line) File "/usr/lib/python2.5/site-packages/cclib/parser/gaussianparser.py", line 79, in extract assert self.natom == natom AssertionError As for the basis, this was a ub3lyp/gen job with a mixed basis set: (...) C H O 0 6-31G(d,p) **** Fe 0 tzv **** (...) ---------------------------------------------------------------------- >Comment By: xaverxn (xaverxn) Date: 2009-11-26 10:27 Message: Forgot to say: cclib-0.91 Python 2.5.2 (r252:60911, Jan 4 2009, 21:59:32) [GCC 4.3.2] on linux2 ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=819222&aid=2904432&group_id=161285 |
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From: SourceForge.net <no...@so...> - 2009-11-26 14:46:07
|
Bugs item #2904432, was opened at 2009-11-26 10:25 Message generated for change (Settings changed) made by xaverxn You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=819222&aid=2904432&group_id=161285 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: Parsers Group: None Status: Open Resolution: None Priority: 5 Private: No Submitted By: xaverxn (xaverxn) Assigned to: Nobody/Anonymous (nobody) Summary: Assertion error trying to parse this gaussian log Initial Comment: Hi, I guess this is a bug. Trying to ccopen() this gaussian log gives me: >>> import cclib >>> myfile=cclib.parser.ccopen('testfiles/g03_test_complete.log') >>> data=myfile.parse() [Gaussian testfiles/g03_test_complete.log INFO] Creating attribute charge: -2 [Gaussian testfiles/g03_test_complete.log INFO] Creating attribute mult: 5 [Gaussian testfiles/g03_test_complete.log INFO] Creating attribute atomnos[] [Gaussian testfiles/g03_test_complete.log INFO] Creating attribute natom: 31 [Gaussian testfiles/g03_test_complete.log INFO] Creating attribute gbasis[] Traceback (most recent call last): File "<stdin>", line 1, in <module> File "/usr/lib/python2.5/site-packages/cclib/parser/logfileparser.py", line 142, in parse self.extract(inputfile, line) File "/usr/lib/python2.5/site-packages/cclib/parser/gaussianparser.py", line 79, in extract assert self.natom == natom AssertionError As for the basis, this was a ub3lyp/gen job with a mixed basis set: (...) C H O 0 6-31G(d,p) **** Fe 0 tzv **** (...) ---------------------------------------------------------------------- >Comment By: xaverxn (xaverxn) Date: 2009-11-26 10:27 Message: Forgot to say: cclib-0.91 Python 2.5.2 (r252:60911, Jan 4 2009, 21:59:32) [GCC 4.3.2] on linux2 ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=819222&aid=2904432&group_id=161285 |
|
From: SourceForge.net <no...@so...> - 2009-11-26 10:27:41
|
Bugs item #2904432, was opened at 2009-11-26 11:25 Message generated for change (Settings changed) made by xaverxn You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=819222&aid=2904432&group_id=161285 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. >Category: Parsers Group: None Status: Open Resolution: None Priority: 5 Private: No Submitted By: xaverxn (xaverxn) Assigned to: Nobody/Anonymous (nobody) Summary: Assertion error trying to parse this gaussian log Initial Comment: Hi, I guess this is a bug. Trying to ccopen() this gaussian log gives me: >>> import cclib >>> myfile=cclib.parser.ccopen('testfiles/g03_test_complete.log') >>> data=myfile.parse() [Gaussian testfiles/g03_test_complete.log INFO] Creating attribute charge: -2 [Gaussian testfiles/g03_test_complete.log INFO] Creating attribute mult: 5 [Gaussian testfiles/g03_test_complete.log INFO] Creating attribute atomnos[] [Gaussian testfiles/g03_test_complete.log INFO] Creating attribute natom: 31 [Gaussian testfiles/g03_test_complete.log INFO] Creating attribute gbasis[] Traceback (most recent call last): File "<stdin>", line 1, in <module> File "/usr/lib/python2.5/site-packages/cclib/parser/logfileparser.py", line 142, in parse self.extract(inputfile, line) File "/usr/lib/python2.5/site-packages/cclib/parser/gaussianparser.py", line 79, in extract assert self.natom == natom AssertionError As for the basis, this was a ub3lyp/gen job with a mixed basis set: (...) C H O 0 6-31G(d,p) **** Fe 0 tzv **** (...) ---------------------------------------------------------------------- >Comment By: xaverxn (xaverxn) Date: 2009-11-26 11:27 Message: Forgot to say: cclib-0.91 Python 2.5.2 (r252:60911, Jan 4 2009, 21:59:32) [GCC 4.3.2] on linux2 ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=819222&aid=2904432&group_id=161285 |
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From: SourceForge.net <no...@so...> - 2009-11-26 10:25:09
|
Bugs item #2904432, was opened at 2009-11-26 11:25 Message generated for change (Tracker Item Submitted) made by xaverxn You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=819222&aid=2904432&group_id=161285 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: None Group: None Status: Open Resolution: None Priority: 5 Private: No Submitted By: xaverxn (xaverxn) Assigned to: Nobody/Anonymous (nobody) Summary: Assertion error trying to parse this gaussian log Initial Comment: Hi, I guess this is a bug. Trying to ccopen() this gaussian log gives me: >>> import cclib >>> myfile=cclib.parser.ccopen('testfiles/g03_test_complete.log') >>> data=myfile.parse() [Gaussian testfiles/g03_test_complete.log INFO] Creating attribute charge: -2 [Gaussian testfiles/g03_test_complete.log INFO] Creating attribute mult: 5 [Gaussian testfiles/g03_test_complete.log INFO] Creating attribute atomnos[] [Gaussian testfiles/g03_test_complete.log INFO] Creating attribute natom: 31 [Gaussian testfiles/g03_test_complete.log INFO] Creating attribute gbasis[] Traceback (most recent call last): File "<stdin>", line 1, in <module> File "/usr/lib/python2.5/site-packages/cclib/parser/logfileparser.py", line 142, in parse self.extract(inputfile, line) File "/usr/lib/python2.5/site-packages/cclib/parser/gaussianparser.py", line 79, in extract assert self.natom == natom AssertionError As for the basis, this was a ub3lyp/gen job with a mixed basis set: (...) C H O 0 6-31G(d,p) **** Fe 0 tzv **** (...) ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=819222&aid=2904432&group_id=161285 |
|
From: Noel O'B. <bao...@gm...> - 2009-10-31 15:05:50
|
Hello Karol, A GaussSum user has sent me a Gaussian09 bug report, so I've running our basic suite through Gaussian09. I'm emailing here to avoid duplication of effort...So far, I find only one problem, and that's with dvb_sp_basis_b.log, not any of the ir/raman/td-dft calcs! I'll check these in over the next few days. - Noel |
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From: Noel O'B. <bao...@gm...> - 2009-10-27 11:47:25
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Hello all,
I've been trying to write a plugin for Avogadro to use cclib, but
there's one or two things causing import problems. One of these is
urllib - the reason why it's causing problems isn't very interesting
(just a C extension that isn't available in Avogadro's Python on
Windows), but I was thinking that there's no need for cclib to be
importing it in the first place.
Our existing code for openlogfile can already handle any file-like
object. That is, you can pass a string (as a StringIO) into ccopen,
and it will work. You can also pass a url.urlopen("http://whatever")
into openlogfile and it will work fine (AFAIK). Since urls are already
handled in this way, I don't think we need a second way to handle them
via urllib (and removing it will solve one of my import problems).
- Noel
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From: Mark M. <mo...@oc...> - 2009-10-21 13:50:09
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Hi Karol,
Your fix for exam17 works great! I went ahead and wrote a parsing
routine to parse the Force Constant Matrix of a GAMESS output file. Not
sure if your interested in adding it to your code. It is pasted at the
end of the message.
Mark
Code to put in gamessparser.py:
The below parsing routine creates a numpy matrix and fills it with the
force constant values in the GAMESS output file.
Numpy matrices don't like to be sparse, so I padded the matrix with
blank entries to make it square.
When those blanks are set to a float in arrayify in data.py an error
occurs.
The hessian _attrtypes needs to be changed to list to fix the error.
# MJM-----------
if line.find("CARTESIAN FORCE CONSTANT MATRIX") >= 0:
self.logger.info("Creating attribute hessian")
for i in range(1,7):
line = inputfile.next()
hessx = []
hessy =[]
hessz = []
while line.find("--") < 0:
index=int(line[0:3])-1
if len(hessx) <= index:
hessx.insert(index,[])
hessy.insert(index,[])
hessz.insert(index,[])
hessx[index].extend([line[20:29].strip(),
line[29:38].strip(),
line[38:47].strip(), line[47:56].strip(),
line[56:65].strip(),line[65:74].strip()])
line = inputfile.next()
hessy[index].extend([line[20:29].strip(),
line[29:38].strip(),
line[38:47].strip(), line[47:56].strip(),
line[56:65].strip(),line[65:74].strip()])
line = inputfile.next()
hessz[index].extend([line[20:29].strip(),
line[29:38].strip(),
line[38:47].strip(), line[47:56].strip(),
line[56:65].strip(),line[65:74].strip()])
line = inputfile.next()
if line.isspace():
for i in range(1,5):
line = inputfile.next()
if line.find("--") >= 0:
break
longest=0
for x in hessx[:]:
if len(x) > longest:
longest=len(x)
for i in range(0,len(hessx)):
for j in range(0,longest-len(hessx[i])):
hessx[i].append('')
hessy[i].append('')
hessz[i].append('')
self.hessian=numpy.vstack((hessx[0],hessy[0],hessz[0]))
for i in range(1,len(hessx)):
self.hessian=numpy.vstack([self.hessian,hessx[i],
hessy[i],hessz[i]])
#------------------------
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From: Karol M. L. <kar...@gm...> - 2009-10-19 16:25:05
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My bad. We arrify these things after parsing, and I forgot about that when looking at the parser. I fixed the wiki page again. Karol On Monday 19 October 2009 10:46:30 Noel O'Boyle wrote: > I was surprised to hear this because we don't use lists except where > necessary. I checked the Gaussian parser and it is an array of rank 2. > So it looks like an error in the GAMESS parser. > > - Noel > > 2009/10/17 Karol M. Langner <kar...@gm...>: > > @list: Note that I fixed the parsed data tables on the wiki, it said > > that scftargets is an array of rank 2, but in fact it is a list of > > arrays of rank 1. > > > > Cheers, > > Karol -- written by Karol Langner Mon Oct 19 18:14:02 CEST 2009 |
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From: Noel O'B. <bao...@gm...> - 2009-10-19 08:46:40
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I was surprised to hear this because we don't use lists except where necessary. I checked the Gaussian parser and it is an array of rank 2. So it looks like an error in the GAMESS parser. - Noel 2009/10/17 Karol M. Langner <kar...@gm...>: > @list: Note that I fixed the parsed data tables on the wiki, it said that > scftargets is an array of rank 2, but in fact it is a list of arrays of > rank 1. > > Cheers, > Karol |
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