[cclib-svn] SF.net SVN: cclib: [729] branches/orca

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Revision: 729
          http://cclib.svn.sourceforge.net/cclib/?rev=729&view=rev
Author:   baoilleach
Date:     2007-08-13 11:43:00 -0700 (Mon, 13 Aug 2007)

Log Message:
-----------
Merged revisions 671-728 via svnmerge from 
https://cclib.svn.sourceforge.net/svnroot/cclib/trunk

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  r675 | langner | 2007-07-10 11:32:03 +0100 (Tue, 10 Jul 2007) | 1 line

  Small fix in GAMESS parser: block with eigenvectors can also end in a blank line if something follows (density matrix). Updated GAMESS MP2 test that has this.
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  r682 | langner | 2007-07-11 09:52:45 +0100 (Wed, 11 Jul 2007) | 1 line

  Small fix in setup.py: install data files to catalog from the correct Python version
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  r683 | langner | 2007-07-11 10:09:34 +0100 (Wed, 11 Jul 2007) | 1 line

  Minor fix: checking of presence of PASS in test docstring in Python2.4
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  r684 | langner | 2007-07-11 10:21:31 +0100 (Wed, 11 Jul 2007) | 1 line

  Reverting data/GAMESS/basicGAMESS-US/water_mp2 test files to that before r675, new files will be added as regressions.
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  r685 | langner | 2007-07-11 11:13:19 +0100 (Wed, 11 Jul 2007) | 1 line

  Added extended water_mp2_nprint9 regression to GAMESS-US (has more data after eigenvectors).
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  r690 | langner | 2007-07-12 01:27:50 +0100 (Thu, 12 Jul 2007) | 1 line

  ***MAJOR CHANGE*** Parser and data objects are now separate. When called, Logfile.parse() returns an instance of cclibData, which contains any parsed attributes that are in _attrlist. All calls will now need to be of the form data = ccopen(...).parse(). Note that the parsing code itself (method Logfile.extract) is unchanged. Test statistics unchanged.
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  r691 | langner | 2007-07-12 01:31:23 +0100 (Thu, 12 Jul 2007) | 1 line

  Fixed parsing statement in regression.py, and added *.out in GAMESS-US directory.
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  r692 | langner | 2007-07-12 09:10:51 +0100 (Thu, 12 Jul 2007) | 1 line

  Made ccget usable after recent parser-data separation. Also, a small fix im GAMESS parser for older versions (regression added).
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  r696 | baoilleach | 2007-07-14 19:02:54 +0100 (Sat, 14 Jul 2007) | 8 lines

  (1) Moved cclibData from logfileparser.py to ../data.py, and renamed to ccData
  (2) Added methods to ccData: listify() and arrayify() to convert array attributes to and from lists
  (3) Commented out __setattr__ magic, in favour of a call to arrayify() in logfileparser.py
  (4) Added the writejson() method to ccData, which either returns a JSON string, or writes it to a file
  Notes:
  (1) pickle now works, both for the arrayified ccData, and the listified one. 
  (2) ccData._attrlist is duplicated by ccData._attrtypes.keys()
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  r697 | baoilleach | 2007-07-15 20:17:29 +0100 (Sun, 15 Jul 2007) | 1 line

  data.py: Added readjson() method, the evil twin of ccData.writejson(). 
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  r706 | baoilleach | 2007-08-02 17:03:18 +0100 (Thu, 02 Aug 2007) | 1 line

  Added Gaussian regression test file supplied by Christoph Steinbeck.
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  r708 | langner | 2007-08-04 23:33:45 +0100 (Sat, 04 Aug 2007) | 1 line

  Added another condition so that ccopen recognizes Molpro log files. Made better Molpro GeoOpt test. Added code to Molpro parser for scftargets and scfvalues.
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  r709 | langner | 2007-08-05 00:07:35 +0100 (Sun, 05 Aug 2007) | 1 line

  In preparation to release 0.8, dropped support of Numeric - removed all references in cclib.
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  r710 | langner | 2007-08-05 13:57:32 +0100 (Sun, 05 Aug 2007) | 1 line

  Fixed parsing Molpro moenergies/mocoeffs when they are printed several times.
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  r711 | langner | 2007-08-05 22:41:45 +0100 (Sun, 05 Aug 2007) | 1 line

  Changes needed for parsing multipole files into one object - openlogfile and ccopen also accept a list in the argument 'filename', plus related changes in test code. Works exactly the same as parsing concatenated files. Also, removed miscalaneous debris from lofileparser.py.
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  r713 | langner | 2007-08-08 09:44:55 +0100 (Wed, 08 Aug 2007) | 1 line

  Introducing nocoeffs: Natural Orbital Coefficients, an laternate for mocoeffs after some post-HF calculations (CIS, MP2). Added code to GAMESS-US and Gaussian parsers, expanded some CIS/MP2 data files, added nocoeffs to attribute lists. Also added a few appropriate methods to MP2/CIS unittests, and added Gaussian MP4(SDQ) test files and unittests.
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  r716 | baoilleach | 2007-08-09 07:47:57 +0100 (Thu, 09 Aug 2007) | 1 line

  Added test for ensuring that the first row and colm of aooverlaps are identical. There is an annoying bug in GAMESS-UK parser which causes some of the overlap matrix to be parsed incorrectly.
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  r717 | baoilleach | 2007-08-09 08:00:24 +0100 (Thu, 09 Aug 2007) | 1 line

  Fixed bug in GAMESSUK parser: The parser assumed that there were twelve columns of data in the overlap matrix.
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  r720 | langner | 2007-08-09 20:16:00 +0100 (Thu, 09 Aug 2007) | 1 line

  Minor: added MANIFEST to svn:ignore on trunk, so it doesn't interfere after building distributions.
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  r722 | langner | 2007-08-11 13:13:26 +0100 (Sat, 11 Aug 2007) | 1 line

  Added geotargets/geovalues and vibdisps to Molpro parser, and enhanced gopt test files for non-default geotargets. Added a call after_parsing() method in LogFile.parse, in analogy to LogFile.before_parsing(). Also, removed some garbage in Gaussian parser from previous commits.
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  r725 | langner | 2007-08-13 17:20:16 +0100 (Mon, 13 Aug 2007) | 1 line

  Minor: safety check before setting nmo=nbasis after parsing.
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  r726 | langner | 2007-08-13 17:23:01 +0100 (Mon, 13 Aug 2007) | 1 line

  Another minor safety check - when setting default coreelectrons after parsing.
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Modified Paths:
--------------
    branches/orca/INSTALL
    branches/orca/data/GAMESS/basicGAMESS-US/water_cis_dets.inp
    branches/orca/data/GAMESS/basicGAMESS-US/water_cis_dets.out
    branches/orca/data/GAMESS/basicGAMESS-US/water_mp2.inp
    branches/orca/data/GAMESS/basicGAMESS-US/water_mp2.out
    branches/orca/data/Gaussian/basicGaussian03/metadata.txt
    branches/orca/data/Gaussian/basicGaussian03/water_cis.com
    branches/orca/data/Gaussian/basicGaussian03/water_cis.log
    branches/orca/data/Gaussian/basicGaussian03/water_mp2.com
    branches/orca/data/Gaussian/basicGaussian03/water_mp2.log
    branches/orca/data/Gaussian/basicGaussian03/water_mp3.com
    branches/orca/data/Gaussian/basicGaussian03/water_mp3.log
    branches/orca/data/Gaussian/basicGaussian03/water_mp4.com
    branches/orca/data/Gaussian/basicGaussian03/water_mp4.log
    branches/orca/data/Gaussian/basicGaussian03/water_mp5.com
    branches/orca/data/Gaussian/basicGaussian03/water_mp5.log
    branches/orca/data/Molpro/basicMolpro2006/dvb_gopt.com
    branches/orca/data/Molpro/basicMolpro2006/dvb_gopt.log
    branches/orca/data/Molpro/basicMolpro2006/dvb_gopt.out
    branches/orca/data/regressionfiles.txt
    branches/orca/setup.py
    branches/orca/src/cclib/bridge/cclib2biopython.py
    branches/orca/src/cclib/bridge/cclib2openbabel.py
    branches/orca/src/cclib/method/cda.py
    branches/orca/src/cclib/method/cspa.py
    branches/orca/src/cclib/method/density.py
    branches/orca/src/cclib/method/fragments.py
    branches/orca/src/cclib/method/lpa.py
    branches/orca/src/cclib/method/mbo.py
    branches/orca/src/cclib/method/mpa.py
    branches/orca/src/cclib/method/opa.py
    branches/orca/src/cclib/method/population.py
    branches/orca/src/cclib/method/volume.py
    branches/orca/src/cclib/parser/adfparser.py
    branches/orca/src/cclib/parser/gamessparser.py
    branches/orca/src/cclib/parser/gamessukparser.py
    branches/orca/src/cclib/parser/gaussianparser.py
    branches/orca/src/cclib/parser/jaguarparser.py
    branches/orca/src/cclib/parser/logfileparser.py
    branches/orca/src/cclib/parser/molproparser.py
    branches/orca/src/cclib/parser/utils.py
    branches/orca/src/scripts/ccget
    branches/orca/src/scripts/cda
    branches/orca/test/bettertest.py
    branches/orca/test/regression.py
    branches/orca/test/testCC.py
    branches/orca/test/testCI.py
    branches/orca/test/testCore.py
    branches/orca/test/testGeoOpt.py
    branches/orca/test/testMP.py
    branches/orca/test/testSP.py
    branches/orca/test/testTD.py
    branches/orca/test/testall.py
    branches/orca/test/testdata
    branches/orca/test/testpopulation.py

Added Paths:
-----------
    branches/orca/data/Gaussian/basicGaussian03/water_mp4sdq.com
    branches/orca/data/Gaussian/basicGaussian03/water_mp4sdq.log
    branches/orca/src/cclib/data.py

Property Changed:
----------------
    branches/orca/

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