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From: <la...@us...> - 2007-05-15 20:06:41
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Revision: 626
http://svn.sourceforge.net/cclib/?rev=626&view=rev
Author: langner
Date: 2007-05-15 13:06:25 -0700 (Tue, 15 May 2007)
Log Message:
-----------
Removed some code left over after debugging. Updated and standardized printed summary string for tests.
Modified Paths:
--------------
trunk/test/bettertest.py
trunk/test/testBasis.py
trunk/test/testCC.py
trunk/test/testCore.py
trunk/test/testGeoOpt.py
trunk/test/testSP.py
trunk/test/testSPun.py
trunk/test/testvib.py
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From: <ate...@us...> - 2007-05-15 19:01:27
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Revision: 625
http://svn.sourceforge.net/cclib/?rev=625&view=rev
Author: atenderholt
Date: 2007-05-15 12:01:17 -0700 (Tue, 15 May 2007)
Log Message:
-----------
ADF parser: Bug fix. Incorrect value for homo[0] was saved when parsing restricted molecules without symmetry (dvb_sp_c). Also added a regression test for this case.
Modified Paths:
--------------
trunk/src/cclib/parser/adfparser.py
trunk/test/regression.py
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From: <la...@us...> - 2007-05-10 18:26:53
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Revision: 624
http://svn.sourceforge.net/cclib/?rev=624&view=rev
Author: langner
Date: 2007-05-10 11:26:49 -0700 (Thu, 10 May 2007)
Log Message:
-----------
Small hack to make test pass with Numeric.
Modified Paths:
--------------
trunk/test/bettertest.py
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From: <la...@us...> - 2007-05-06 22:52:09
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Revision: 623
http://svn.sourceforge.net/cclib/?rev=623&view=rev
Author: langner
Date: 2007-05-06 15:52:05 -0700 (Sun, 06 May 2007)
Log Message:
-----------
Bugfix: a new handler is added to LogFile.logger only if LogFile.logger.handlers is empty, since logging.getlogger() returns the same instance for the same name (shared by all intances of one parser class).
Modified Paths:
--------------
trunk/src/cclib/parser/logfileparser.py
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From: <la...@us...> - 2007-05-02 19:34:13
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Revision: 622
http://svn.sourceforge.net/cclib/?rev=622&view=rev
Author: langner
Date: 2007-05-02 12:34:11 -0700 (Wed, 02 May 2007)
Log Message:
-----------
Removing parser-refactoring branch.
Removed Paths:
-------------
branches/parser-refactoring/
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From: <la...@us...> - 2007-05-02 19:09:56
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Revision: 621
http://svn.sourceforge.net/cclib/?rev=621&view=rev
Author: langner
Date: 2007-05-02 12:09:54 -0700 (Wed, 02 May 2007)
Log Message:
-----------
Copying trunk to parser-fractoring branch, further(?) refactoring will start from here.
Added Paths:
-----------
branches/parser-refactoring/trunk/
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From: <la...@us...> - 2007-05-02 19:05:40
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Revision: 620
http://svn.sourceforge.net/cclib/?rev=620&view=rev
Author: langner
Date: 2007-05-02 12:05:36 -0700 (Wed, 02 May 2007)
Log Message:
-----------
Temporary attributes that had initial values before parsing should not be set in __setattr__ - moved to new method before_parsing, which is called before parsing. Also: minor style edits (mainly import cleanness).
Modified Paths:
--------------
trunk/downloadwiki.py
trunk/src/cclib/method/calculationmethod.py
trunk/src/cclib/method/density.py
trunk/src/cclib/method/volume.py
trunk/src/cclib/parser/adfparser.py
trunk/src/cclib/parser/gamessparser.py
trunk/src/cclib/parser/gamessukparser.py
trunk/src/cclib/parser/gaussianparser.py
trunk/src/cclib/parser/jaguarparser.py
trunk/src/cclib/parser/logfileparser.py
trunk/src/cclib/parser/utils.py
trunk/src/cclib/progress/__init__.py
trunk/src/cclib/progress/qt4progress.py
trunk/src/cclib/progress/qtprogress.py
trunk/src/cclib/progress/textprogress.py
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From: <la...@us...> - 2007-05-02 14:55:40
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Revision: 619
http://svn.sourceforge.net/cclib/?rev=619&view=rev
Author: langner
Date: 2007-05-02 07:55:38 -0700 (Wed, 02 May 2007)
Log Message:
-----------
LogFile: stricter test for number of arguments taken by extract (now only two); added spin and mult to docstring; minor style edits.
Modified Paths:
--------------
trunk/src/cclib/parser/logfileparser.py
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From: <bao...@us...> - 2007-04-29 20:42:56
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Revision: 618
http://svn.sourceforge.net/cclib/?rev=618&view=rev
Author: baoilleach
Date: 2007-04-29 13:42:53 -0700 (Sun, 29 Apr 2007)
Log Message:
-----------
Added two new attributes: mult (for spin multiplicity) and charge. Should "mult" be called "spin" instead?
Modified Paths:
--------------
trunk/src/cclib/parser/adfparser.py
trunk/src/cclib/parser/gamessparser.py
trunk/src/cclib/parser/gamessukparser.py
trunk/src/cclib/parser/gaussianparser.py
trunk/src/cclib/parser/jaguarparser.py
trunk/src/cclib/parser/logfileparser.py
trunk/src/scripts/ccget
trunk/test/testGeoOpt.py
trunk/test/testSPun.py
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From: <bao...@us...> - 2007-04-27 16:28:08
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Revision: 617
http://svn.sourceforge.net/cclib/?rev=617&view=rev
Author: baoilleach
Date: 2007-04-27 09:28:05 -0700 (Fri, 27 Apr 2007)
Log Message:
-----------
Used nose to run doctests and found some failures...not related to recent refactoring though.
Modified Paths:
--------------
trunk/src/cclib/bridge/cclib2biopython.py
trunk/src/cclib/bridge/cclib2pyquante.py
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From: <la...@us...> - 2007-04-27 13:36:02
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Revision: 616
http://svn.sourceforge.net/cclib/?rev=616&view=rev
Author: langner
Date: 2007-04-27 06:35:47 -0700 (Fri, 27 Apr 2007)
Log Message:
-----------
Numeric -> NumPy transition. All imports & method calls changed. Numeric should still work (import option), but not tested. Otherwise, all tests pass.
Modified Paths:
--------------
trunk/INSTALL
trunk/src/cclib/bridge/cclib2pyquante.py
trunk/src/cclib/method/cda.py
trunk/src/cclib/method/cspa.py
trunk/src/cclib/method/density.py
trunk/src/cclib/method/fragments.py
trunk/src/cclib/method/mbo.py
trunk/src/cclib/method/mpa.py
trunk/src/cclib/method/opa.py
trunk/src/cclib/method/population.py
trunk/src/cclib/method/volume.py
trunk/src/cclib/parser/adfparser.py
trunk/src/cclib/parser/gamessparser.py
trunk/src/cclib/parser/gamessukparser.py
trunk/src/cclib/parser/gaussianparser.py
trunk/src/cclib/parser/jaguarparser.py
trunk/src/cclib/parser/logfileparser.py
trunk/src/scripts/cda
trunk/test/bettertest.py
trunk/test/testBasis.py
trunk/test/testCC.py
trunk/test/testCI.py
trunk/test/testCore.py
trunk/test/testGeoOpt.py
trunk/test/testMP.py
trunk/test/testSP.py
trunk/test/testSPun.py
trunk/test/testTD.py
trunk/test/testall.py
trunk/test/testcda.py
trunk/test/testvib.py
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From: <la...@us...> - 2007-04-27 11:01:06
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Revision: 615
http://svn.sourceforge.net/cclib/?rev=615&view=rev
Author: langner
Date: 2007-04-27 04:00:58 -0700 (Fri, 27 Apr 2007)
Log Message:
-----------
Simple condition that can speed up parsing a bit: do not call extract() for lines that are only whitespace.
Modified Paths:
--------------
trunk/src/cclib/parser/logfileparser.py
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From: <la...@us...> - 2007-04-26 13:18:06
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Revision: 614
http://svn.sourceforge.net/cclib/?rev=614&view=rev
Author: langner
Date: 2007-04-26 06:17:26 -0700 (Thu, 26 Apr 2007)
Log Message:
-----------
Parser paradigm shift: moved loop over lines in file object to LogFile.parse(); extract() is now called repeatedly instead of once. All variables used across calls in extract() are now attributes of the parser, and are deleted after parsing. Note: comments in the parsers were aligned with code to make bulk indentation possible. No changes in tests and regression results.
Modified Paths:
--------------
trunk/src/cclib/parser/adfparser.py
trunk/src/cclib/parser/gamessparser.py
trunk/src/cclib/parser/gamessukparser.py
trunk/src/cclib/parser/gaussianparser.py
trunk/src/cclib/parser/jaguarparser.py
trunk/src/cclib/parser/logfileparser.py
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From: <la...@us...> - 2007-04-26 11:40:49
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Revision: 613
http://svn.sourceforge.net/cclib/?rev=613&view=rev
Author: langner
Date: 2007-04-26 04:40:46 -0700 (Thu, 26 Apr 2007)
Log Message:
-----------
Made fupdate and cupdate attributes of the parser class - don't have to be passed to extract() anymore.
Modified Paths:
--------------
trunk/src/cclib/parser/adfparser.py
trunk/src/cclib/parser/gamessparser.py
trunk/src/cclib/parser/gamessukparser.py
trunk/src/cclib/parser/gaussianparser.py
trunk/src/cclib/parser/jaguarparser.py
trunk/src/cclib/parser/logfileparser.py
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From: <la...@us...> - 2007-04-26 11:11:28
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Revision: 612
http://svn.sourceforge.net/cclib/?rev=612&view=rev
Author: langner
Date: 2007-04-26 04:11:25 -0700 (Thu, 26 Apr 2007)
Log Message:
-----------
Introduced _nodelete for deleting temporary attributes created during parsing; attrlist renamed to _attrlist and supplemented; _attrtypes now holds the expected types for all attributes, which is checked after parsing; moved a few things around and added comments.
Modified Paths:
--------------
trunk/src/cclib/parser/logfileparser.py
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From: <la...@us...> - 2007-04-25 17:06:51
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Revision: 611
http://svn.sourceforge.net/cclib/?rev=611&view=rev
Author: langner
Date: 2007-04-25 10:05:49 -0700 (Wed, 25 Apr 2007)
Log Message:
-----------
Method logger.info called for new attributes in LogFile.__setattr__; all calls in extract() removed for all parser.
Modified Paths:
--------------
trunk/data/GAMESS/basicGAMESS-US/water_cis_saps.out
trunk/src/cclib/parser/adfparser.py
trunk/src/cclib/parser/gamessparser.py
trunk/src/cclib/parser/gamessukparser.py
trunk/src/cclib/parser/gaussianparser.py
trunk/src/cclib/parser/jaguarparser.py
trunk/src/cclib/parser/logfileparser.py
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From: <bao...@us...> - 2007-04-24 08:55:53
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Revision: 610
http://svn.sourceforge.net/cclib/?rev=610&view=rev
Author: baoilleach
Date: 2007-04-24 01:48:47 -0700 (Tue, 24 Apr 2007)
Log Message:
-----------
G03 parser bugfix contd: To avoid printing out extra log messages, I needed to change things around a bit. Previously, a log message was shown twice saying that mocoeffs was being created (which it shouldn't be).
Modified Paths:
--------------
trunk/src/cclib/parser/gaussianparser.py
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From: <bao...@us...> - 2007-04-24 06:20:31
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Revision: 609
http://svn.sourceforge.net/cclib/?rev=609&view=rev
Author: baoilleach
Date: 2007-04-23 23:20:29 -0700 (Mon, 23 Apr 2007)
Log Message:
-----------
G03 parser bugfix: cclib was failing to parse 'pop=regular' G03 output files. This was because of problems with mocoeffs. I've uploaded the bugfix, the unit test, and the test file provided by Yafei Dai. The fix is basically not to define mocoeffs.
Modified Paths:
--------------
trunk/data/regressionfiles.txt
trunk/src/cclib/parser/gaussianparser.py
trunk/test/regression.py
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From: <bao...@us...> - 2007-03-30 10:28:11
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Revision: 608
http://svn.sourceforge.net/cclib/?rev=608&view=rev
Author: baoilleach
Date: 2007-03-30 03:28:08 -0700 (Fri, 30 Mar 2007)
Log Message:
-----------
Typos: Need to use standard names for the comp chem programs in the tests, for the test results to be summarised correctly at the end of testall.py.
Modified Paths:
--------------
trunk/test/testCI.py
trunk/test/testMP.py
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From: <bao...@us...> - 2007-03-30 10:22:16
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Revision: 607
http://svn.sourceforge.net/cclib/?rev=607&view=rev
Author: baoilleach
Date: 2007-03-30 03:22:14 -0700 (Fri, 30 Mar 2007)
Log Message:
-----------
Added Adam's Au2-fixed.adfout.gz to regressionfiles.txt. It's parsed correctly, but overall two parse errors remain.
Modified Paths:
--------------
trunk/data/regressionfiles.txt
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From: <la...@us...> - 2007-03-29 19:19:53
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Revision: 606
http://svn.sourceforge.net/cclib/?rev=606&view=rev
Author: langner
Date: 2007-03-29 12:19:29 -0700 (Thu, 29 Mar 2007)
Log Message:
-----------
Unnormalized etsecs in GAMESS for hamtyp-dets in CIS calcualtions.
Modified Paths:
--------------
trunk/src/cclib/parser/gamessparser.py
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From: <la...@us...> - 2007-03-29 19:07:23
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Revision: 605
http://svn.sourceforge.net/cclib/?rev=605&view=rev
Author: langner
Date: 2007-03-29 12:07:14 -0700 (Thu, 29 Mar 2007)
Log Message:
-----------
Branch GAMESS CIS tests into two - using SAPS and determinant-based hamiltonians. The DETS test seems to give incorrect oscillator strengths, so it is not tested at present (I will seek the reason for the inconsistency, though). Appropriate modifications to the GAMESS parser and testCI.py.
Modified Paths:
--------------
trunk/src/cclib/parser/gamessparser.py
trunk/test/testCI.py
Added Paths:
-----------
trunk/data/GAMESS/basicGAMESS-US/water_cis_dets.inp
trunk/data/GAMESS/basicGAMESS-US/water_cis_dets.out
trunk/data/GAMESS/basicGAMESS-US/water_cis_saps.inp
trunk/data/GAMESS/basicGAMESS-US/water_cis_saps.out
Removed Paths:
-------------
trunk/data/GAMESS/basicGAMESS-US/water_cis.inp
trunk/data/GAMESS/basicGAMESS-US/water_cis.out
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From: <la...@us...> - 2007-03-28 12:28:11
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Revision: 604
http://svn.sourceforge.net/cclib/?rev=604&view=rev
Author: langner
Date: 2007-03-28 05:28:07 -0700 (Wed, 28 Mar 2007)
Log Message:
-----------
Parse etoscs from GAMESS-US CIS calculations. Test also length of etoscs in testCI.
Modified Paths:
--------------
trunk/src/cclib/parser/gamessparser.py
trunk/test/testCI.py
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From: <la...@us...> - 2007-03-28 12:14:18
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Revision: 603
http://svn.sourceforge.net/cclib/?rev=603&view=rev
Author: langner
Date: 2007-03-28 05:14:12 -0700 (Wed, 28 Mar 2007)
Log Message:
-----------
Test only the absolute value of coefficients in etsecs (testCI).
Modified Paths:
--------------
trunk/test/testCI.py
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From: <ate...@us...> - 2007-03-27 23:50:25
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Revision: 602
http://svn.sourceforge.net/cclib/?rev=602&view=rev
Author: atenderholt
Date: 2007-03-27 16:50:21 -0700 (Tue, 27 Mar 2007)
Log Message:
-----------
ADF parser: Bug fix for the HgMeBr_zso_orig.out file. ADF2006.01 adds an extra note and blank after saying how many basis functions there are.
Modified Paths:
--------------
trunk/src/cclib/parser/adfparser.py
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