Thread: [cclib-svn] SF.net SVN: cclib: [549] branches/cclib-0.7

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Revision: 549
          http://svn.sourceforge.net/cclib/?rev=549&view=rev
Author:   baoilleach
Date:     2007-02-27 01:43:42 -0800 (Tue, 27 Feb 2007)

Log Message:
-----------
Merged revisions 481-537,540-542,544-546 via svnmerge from 
https://cclib.svn.sourceforge.net/svnroot/cclib/trunk

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  r481 | langner | 2007-01-30 23:39:01 +0000 (Tue, 30 Jan 2007) | 1 line

  Introducing LogFile.parse(), and parse() of child classes renamed to extract(). Addition of fupdate and cupdate to GAMESS.extract().
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  r482 | langner | 2007-01-31 14:31:59 +0000 (Wed, 31 Jan 2007) | 1 line

  Moved generic conversion of attributes to arrays from .extract() to .parse() - conversion takes place only if attribute is not already an array. Also: fixed dimensions of geovalues in Jaguar parser so that it can be converted to an array (there is no first energy change, so it is set to zero); moenergies is not converted to an array, kept as a list of rank-1 arrays, as per wiki. No changes when running tests.
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  r483 | langner | 2007-02-01 10:34:03 +0000 (Thu, 01 Feb 2007) | 1 line

  Moved conversion of moenergies and scfvalues to lists of arrays to LogFile.parse() from specific parsers. No changes in tests.
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  r484 | langner | 2007-02-01 13:42:37 +0000 (Thu, 01 Feb 2007) | 1 line

  Added IOError arounf call to openlogfile in ccopen, which returns None.
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  r485 | langner | 2007-02-01 13:44:23 +0000 (Thu, 01 Feb 2007) | 1 line

  Set LogFile.parsed to False at end of LogFile.clean().
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  r486 | langner | 2007-02-01 13:54:00 +0000 (Thu, 01 Feb 2007) | 1 line

  Rewrote condition for self.extract() call in LogFile.parse() to an AttributeError exception.
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  r487 | langner | 2007-02-01 14:08:36 +0000 (Thu, 01 Feb 2007) | 1 line

  Moved to LogFile.parse(): creation of default coreelectrons; setting default value of nmo to nbasis; setting self.parsed to True after parsing.
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  r488 | baoilleach | 2007-02-02 08:11:18 +0000 (Fri, 02 Feb 2007) | 1 line

  Volume.py: Calculates electron density now. I realised that there was no shortcut (at least that I could think of). You just need to iterate over all of the occupied orbitals and add up the squares of the wavefunctions.
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  r489 | langner | 2007-02-02 16:11:25 +0000 (Fri, 02 Feb 2007) | 1 line

  Move to LogFile.parse from extract method of specific parsers: opening/closing file object, initializing and final update of self.progress.
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  r490 | baoilleach | 2007-02-02 16:20:02 +0000 (Fri, 02 Feb 2007) | 1 line

  Volume: Minor type correction (float-->integer) required for the Numeric version I'm using on Windows.
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  r491 | langner | 2007-02-02 17:23:33 +0000 (Fri, 02 Feb 2007) | 1 line

  Created LogFile.updateprogress() for updating LogFile.progress; replaced code with a call to the method in all parsers.
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  r493 | langner | 2007-02-03 10:57:17 +0000 (Sat, 03 Feb 2007) | 1 line

  Modifying LogFile.__setattr__ to update LogFile.logger for elements of LogFile.attrlist.
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  r494 | langner | 2007-02-03 11:13:55 +0000 (Sat, 03 Feb 2007) | 1 line

  Oops, moving back to revision 492. Previous commit belongs in the parser-refactoring branch.
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  r513 | baoilleach | 2007-02-09 19:45:10 +0000 (Fri, 09 Feb 2007) | 1 line

  Wrote gbasis for Jaguar. Looks fine, but after adding some more tests, there are several failures for different parsers, so need to look into these.
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  r514 | baoilleach | 2007-02-11 21:23:57 +0000 (Sun, 11 Feb 2007) | 1 line

  Corrected a basis fn test. Passes for Gaussian. All of the GAMESS ones have only half the correct number due to symmetry issues. Am unsure about the Jaguar ones, as I thought I had it all figured out.
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  r515 | baoilleach | 2007-02-13 10:17:44 +0000 (Tue, 13 Feb 2007) | 1 line

  GAMESS parser now handles gbasis correctly for symmetrical molecules.
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  r516 | langner | 2007-02-13 10:49:25 +0000 (Tue, 13 Feb 2007) | 1 line

  Fixed names and docstrings of MP tests for messages in testall.py
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  r518 | baoilleach | 2007-02-14 08:09:21 +0000 (Wed, 14 Feb 2007) | 1 line

  GAMESSUK gbasis now works fine for symmetrical molecules. Corrected small error in GAMESS gbasis.
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  r519 | baoilleach | 2007-02-14 09:30:58 +0000 (Wed, 14 Feb 2007) | 1 line

  Removed all reference to gbasis for Jaguar. Be gone!
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  r520 | baoilleach | 2007-02-14 19:59:44 +0000 (Wed, 14 Feb 2007) | 1 line

  Jaguar parser, atomcoords: Got two more tests to pass by avoiding including the input geometry twice
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  r521 | baoilleach | 2007-02-16 14:16:01 +0000 (Fri, 16 Feb 2007) | 1 line

  GAMESS-UK MPx test files: Uploaded test files for MP2 and MP3, which seems to be all that's available.
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  r522 | baoilleach | 2007-02-17 12:22:42 +0000 (Sat, 17 Feb 2007) | 1 line

  Tests: (1) Simplified testMP and added tests for GAMESS-UK. (2) Moved CDA test code from cda.py to testcda.py.
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  r523 | atenderholt | 2007-02-17 21:02:52 +0000 (Sat, 17 Feb 2007) | 2 lines

  CDA: Moved extra value of 2 into the result matrix, to better agree with Frenking's code.
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  r524 | langner | 2007-02-18 15:09:17 +0000 (Sun, 18 Feb 2007) | 1 line

  GAMESS-UK parser: code for parsing mpenergies; small hack to scfenergies parsing code also needed.
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  r525 | baoilleach | 2007-02-19 13:12:32 +0000 (Mon, 19 Feb 2007) | 1 line

  Changed all float arrays to explicitly use typecode 'd'. Integer arrays should explicitly use typecode 'i'. (Need to add note on devel attribute wiki table). testcda.py now works for me.
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  r526 | baoilleach | 2007-02-19 15:42:14 +0000 (Mon, 19 Feb 2007) | 1 line

  Combination of Karol's original code and some of mine to allow different docstrings for different MP levels in testMP.py
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  r527 | atenderholt | 2007-02-19 17:20:31 +0000 (Mon, 19 Feb 2007) | 2 lines

  Added some assertion statements to testcda to check if its results agree with Frenking's cda
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  r528 | baoilleach | 2007-02-21 08:05:58 +0000 (Wed, 21 Feb 2007) | 1 line

  2 more tests pass! Fixed problem with length of geotargets in Jaguar.
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  r529 | baoilleach | 2007-02-21 09:23:13 +0000 (Wed, 21 Feb 2007) | 1 line

  Small fix: pyopenbabel not longer a dependency of cclib2openbabel.py.
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  r530 | langner | 2007-02-21 11:08:55 +0000 (Wed, 21 Feb 2007) | 1 line

  Overriding test methods for aooverlaps, mocoeffs, and mosyms for Jaguar 4.2 and 6.5, since the test files do not contain them.
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  r531 | langner | 2007-02-21 11:34:06 +0000 (Wed, 21 Feb 2007) | 1 line

  One more method overriden for jaguar 6.0 parser: for mosyms in SPun test (also not in out file).
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  r532 | langner | 2007-02-21 12:11:30 +0000 (Wed, 21 Feb 2007) | 1 line

  Overriding last failed Jaguar 6.5 test: for moenergies (again, because the test files are incomplete; here, ipvirt=-1 is missing from te input file.
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  r534 | baoilleach | 2007-02-21 19:48:48 +0000 (Wed, 21 Feb 2007) | 1 line

  Revert: debug statements in jaguarparser.py included in r532 by accident
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  r535 | baoilleach | 2007-02-21 20:08:45 +0000 (Wed, 21 Feb 2007) | 1 line

  testSPun.py: Changed the test for Jag6.5 moenergies to fit the log file, which doesn't contain the full no. of moenergies.
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  r536 | baoilleach | 2007-02-21 20:42:14 +0000 (Wed, 21 Feb 2007) | 1 line

  Using unittest with testcda. Also added a framework for automatically running all 'methods' tests, called methods.py.
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  r537 | langner | 2007-02-22 10:56:43 +0000 (Thu, 22 Feb 2007) | 1 line

  Minor typos in docstrings.
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  r540 | baoilleach | 2007-02-22 14:11:34 +0000 (Thu, 22 Feb 2007) | 4 lines

  (1) Added tests for coreelectrons
  (2) Modified logfileparser to set some arrays to 'i' not 'd'
  (3) Modified assertArrayEquals to produce better error messages
  (4) Fixed minor typo in testMP
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  r541 | atenderholt | 2007-02-22 20:04:46 +0000 (Thu, 22 Feb 2007) | 2 lines

  ADF data files: Added MoOCl4 (DZP basis set, frozen core on Mo)
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  r542 | baoilleach | 2007-02-22 21:22:02 +0000 (Thu, 22 Feb 2007) | 1 line

  GAMESS-UK data files for coreelectrons
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  r544 | baoilleach | 2007-02-24 12:29:48 +0000 (Sat, 24 Feb 2007) | 4 lines

  More data files:
  (1) Bug: GAMESS fails when parsing an imaginary frequency (worth checking using planar ammonia with other codes)
  (2) PC-GAMESS can do TDDFT!
  (3) PC-GAMESS can do MP2/3/4
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  r545 | baoilleach | 2007-02-24 13:44:03 +0000 (Sat, 24 Feb 2007) | 4 lines

  A few fixes for GAMESS:
  (1) Was failing to parse a DFT calculation
  (2) frequencies: When leaving out the 5/6 rotations and translations, I found that they aren't always the first 5/6
  (3) frequencies: Can now handle imaginary frequencies (returned as a negative value)
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  r546 | baoilleach | 2007-02-25 21:05:35 +0000 (Sun, 25 Feb 2007) | 1 line

  Bumped up versions to cclib-0.7b. Added some text to CHANGELOG, but needs some more work.
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Revision Links:
--------------
    http://svn.sourceforge.net/cclib/?rev=492&view=rev

Modified Paths:
--------------
    branches/cclib-0.7/CHANGELOG
    branches/cclib-0.7/INSTALL
    branches/cclib-0.7/setup.py
    branches/cclib-0.7/src/cclib/__init__.py
    branches/cclib-0.7/src/cclib/bridge/__init__.py
    branches/cclib-0.7/src/cclib/method/cda.py
    branches/cclib-0.7/src/cclib/method/cspa.py
    branches/cclib-0.7/src/cclib/method/density.py
    branches/cclib-0.7/src/cclib/method/fragments.py
    branches/cclib-0.7/src/cclib/method/mbo.py
    branches/cclib-0.7/src/cclib/method/mpa.py
    branches/cclib-0.7/src/cclib/method/opa.py
    branches/cclib-0.7/src/cclib/method/population.py
    branches/cclib-0.7/src/cclib/method/volume.py
    branches/cclib-0.7/src/cclib/parser/adfparser.py
    branches/cclib-0.7/src/cclib/parser/gamessparser.py
    branches/cclib-0.7/src/cclib/parser/gamessukparser.py
    branches/cclib-0.7/src/cclib/parser/gaussianparser.py
    branches/cclib-0.7/src/cclib/parser/jaguarparser.py
    branches/cclib-0.7/src/cclib/parser/logfileparser.py
    branches/cclib-0.7/src/cclib/parser/utils.py
    branches/cclib-0.7/src/scripts/cda
    branches/cclib-0.7/test/bettertest.py
    branches/cclib-0.7/test/testBasis.py
    branches/cclib-0.7/test/testGeoOpt.py
    branches/cclib-0.7/test/testMP.py
    branches/cclib-0.7/test/testSPun.py
    branches/cclib-0.7/test/testall.py

Added Paths:
-----------
    branches/cclib-0.7/data/ADF/basicADF2004.01/MoOCl4-sp.adfin
    branches/cclib-0.7/data/ADF/basicADF2004.01/MoOCl4-sp.adfout
    branches/cclib-0.7/data/GAMESS/basicGAMESS-US/nh3_ts_ir.inp
    branches/cclib-0.7/data/GAMESS/basicGAMESS-US/nh3_ts_ir.out
    branches/cclib-0.7/data/GAMESS/basicPCGAMESS/dvb_td.inp
    branches/cclib-0.7/data/GAMESS/basicPCGAMESS/dvb_td.out
    branches/cclib-0.7/data/GAMESS/basicPCGAMESS/water_mp2.inp
    branches/cclib-0.7/data/GAMESS/basicPCGAMESS/water_mp2.out
    branches/cclib-0.7/data/GAMESS/basicPCGAMESS/water_mp3.inp
    branches/cclib-0.7/data/GAMESS/basicPCGAMESS/water_mp3.out
    branches/cclib-0.7/data/GAMESS/basicPCGAMESS/water_mp4.inp
    branches/cclib-0.7/data/GAMESS/basicPCGAMESS/water_mp4.out
    branches/cclib-0.7/data/GAMESS/basicPCGAMESS/water_mp4_sdtq.inp
    branches/cclib-0.7/data/GAMESS/basicPCGAMESS/water_mp4_sdtq.out
    branches/cclib-0.7/data/GAMESS-UK/basicGAMESS-UK/MoOCl4-sp.in
    branches/cclib-0.7/data/GAMESS-UK/basicGAMESS-UK/MoOCl4-sp.out
    branches/cclib-0.7/data/GAMESS-UK/basicGAMESS-UK/water_mp2.in
    branches/cclib-0.7/data/GAMESS-UK/basicGAMESS-UK/water_mp2.out
    branches/cclib-0.7/data/GAMESS-UK/basicGAMESS-UK/water_mp3.in
    branches/cclib-0.7/data/GAMESS-UK/basicGAMESS-UK/water_mp3.out
    branches/cclib-0.7/test/methods.py
    branches/cclib-0.7/test/testCore.py
    branches/cclib-0.7/test/testcda.py

Property Changed:
----------------
    branches/cclib-0.7/

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