cclib-svn

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

[<bao...@us...>]

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

........
  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.
........
  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
........
  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
........
  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.
........
  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).
........
  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.
........
  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.
........
  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).
........
  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()
........
  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(). 
........
  r706 | baoilleach | 2007-08-02 17:03:18 +0100 (Thu, 02 Aug 2007) | 1 line
  
  Added Gaussian regression test file supplied by Christoph Steinbeck.
........
  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.
........
  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.
........
  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.
........
  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.
........
  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.
........
  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.
........
  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.
........
  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.
........
  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.
........
  r725 | langner | 2007-08-13 17:20:16 +0100 (Mon, 13 Aug 2007) | 1 line
  
  Minor: safety check before setting nmo=nbasis after parsing.
........
  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.
........

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/


This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.

[cclib-svn] SF.net SVN: cclib: [769] branches/orca

[<ate...@us...>]

Revision: 769
          http://cclib.svn.sourceforge.net/cclib/?rev=769&view=rev
Author:   atenderholt
Date:     2007-10-21 21:38:19 -0700 (Sun, 21 Oct 2007)

Log Message:
-----------
Merged revisions 729-768 via svnmerge from 
https://cclib.svn.sourceforge.net/svnroot/cclib/trunk

................
  r732 | langner | 2007-08-17 09:36:40 -0700 (Fri, 17 Aug 2007) | 1 line
  
  Added extracoods and extrascfs to GeoOpt unittest for comparing coords with geovalues and scfvalues with geovalues, respectively. Used for ADF and Molpro tests (fixed some more with this).
................
  r733 | langner | 2007-08-24 01:31:08 -0700 (Fri, 24 Aug 2007) | 1 line
  
  Fixed methods for recent separation of ccData from LogFile (at least within those methods being tested).
................
  r734 | langner | 2007-08-24 06:02:22 -0700 (Fri, 24 Aug 2007) | 1 line
  
  Added fix regression file for Molpro that broke parsing of mocoeffs.
................
  r735 | langner | 2007-08-27 10:26:41 -0700 (Mon, 27 Aug 2007) | 1 line
  
  Updated attribute list for ccget with ccenergies, fragnames and frags.
................
  r736 | langner | 2007-08-27 11:03:35 -0700 (Mon, 27 Aug 2007) | 1 line
  
  Fixed condition in parsing mocoeffs from Molpro that broke sp_un unittest.
................
  r737 | baoilleach | 2007-08-30 00:08:53 -0700 (Thu, 30 Aug 2007) | 1 line
  
  Updated the openbabel and pyquante bridges to handle the new charge and multiplicity attributes.
................
  r738 | langner | 2007-09-01 08:50:50 -0700 (Sat, 01 Sep 2007) | 1 line
  
  Print error warnings when failing to load bz2 module (can still be usefull in newer pythons).
................
  r739 | atenderholt | 2007-09-01 17:44:10 -0700 (Sat, 01 Sep 2007) | 2 lines
  
  Removed checked to see if ccData has been parsed as this is a leftover from when parsers kept attributes
................
  r740 | baoilleach | 2007-09-02 03:46:32 -0700 (Sun, 02 Sep 2007) | 1 line
  
  Molpro tests: Enabled regression.py for Molpro. One failure on C_bigbasis_cart.out.
................
  r741 | langner | 2007-09-02 07:36:20 -0700 (Sun, 02 Sep 2007) | 1 line
  
  Fix for calling cclib.parser.ccopen(..., loglevel=0), which set fupdate instead of loglevel. Also, ccopen does not use logname presently.
................
  r742 | baoilleach | 2007-09-02 11:08:19 -0700 (Sun, 02 Sep 2007) | 1 line
  
  volume.py: Updated for recent changes in the parser, and the numeric-->numpy transition. Needed to replace a.flat with a.ravel() as they are no longer equivalent.
................
  r743 | baoilleach | 2007-09-02 13:26:25 -0700 (Sun, 02 Sep 2007) | 1 line
  
  testall: Now can take the name of a parser, so it's possible to just run the tests for a particular parser. Note to self: need to combine testmodule() and testall() as there is duplication.
................
  r744 | langner | 2007-09-02 15:23:33 -0700 (Sun, 02 Sep 2007) | 1 line
  
  Moved C_bigbasis_cart Molpro test to regressions (as a duplicate of C_bigbasis with bogus output); issue an error to the logger upon reading stars ('***') when parsing mocoeffs, so that it doesn't break the parser.
................
  r745 | langner | 2007-09-03 05:24:01 -0700 (Mon, 03 Sep 2007) | 1 line
  
  Minor: changed error message in Molpro parser upon reading bad mocoeffs to a warning.
................
  r746 | atenderholt | 2007-09-03 12:12:56 -0700 (Mon, 03 Sep 2007) | 2 lines
  
  ADF parser: fixed Frags_NiCO4 parse error; now it correctly detects different create run format and skips mutiple calculations in the same log file
................
  r747 | langner | 2007-09-03 16:09:21 -0700 (Mon, 03 Sep 2007) | 1 line
  
  The number of tests skipped (when PASS is in the docstring) is now monitored by setting a 'skipped' attribute in bettertest.TestCase.run() and using it in the summary of testall(). Also, merged testmodule() and testall() in testall.py (as suggested by Noel).
................
  r748 | atenderholt | 2007-09-04 17:37:37 -0700 (Tue, 04 Sep 2007) | 2 lines
  
  ADF parser: check to see if CFs are printed in mocoeffs; if so, skip them
................
  r749 | langner | 2007-09-05 14:11:59 -0700 (Wed, 05 Sep 2007) | 1 line
  
  Moved some common tests from GeoOpt to SP, and vice versa. Added PASS or modified relevant failing test methods - a few for ADF remain. Added Jaguar6.0 to GeoOpt test.
................
  r750 | atenderholt | 2007-09-05 17:40:43 -0700 (Wed, 05 Sep 2007) | 2 lines
  
  Gaussian parser: fixed bug (#1775665)  with empty mosyms when using SCF=QC; still need to add test file
................
  r751 | langner | 2007-09-06 07:17:15 -0700 (Thu, 06 Sep 2007) | 1 line
  
  Added C_bigbasis test to testdata and created BigBasisTest unittests where the files exist. Created expanded such Gaussian test file with gbasis output. Small fix in Molpro parser for basis function indices larger than 99.
................
  r752 | baoilleach | 2007-09-21 03:43:10 -0700 (Fri, 21 Sep 2007) | 1 line
  
  Fixed bug and simplified code for when running tests with Python 2.4.
................
  r753 | baoilleach | 2007-09-21 03:44:05 -0700 (Fri, 21 Sep 2007) | 1 line
  
  GAMESS-UK tests: Tidying up GAMESS-UK failures due to recent addition of tests.
................
  r754 | baoilleach | 2007-09-21 08:49:30 -0700 (Fri, 21 Sep 2007) | 1 line
  
  Bumping up version to 0.8b and updating manifest.py...going to copy to release branch now...
................
  r759 | baoilleach | 2007-09-21 09:46:56 -0700 (Fri, 21 Sep 2007) | 3 lines
  
  Initialized merge tracking via "svnmerge" with revisions "1-754" from 
  https://cclib.svn.sourceforge.net/svnroot/cclib/branches/cclib-0.8
................
  r760 | baoilleach | 2007-09-21 09:50:44 -0700 (Fri, 21 Sep 2007) | 9 lines
  
  Merged revisions 758 via svnmerge from 
  https://cclib.svn.sourceforge.net/svnroot/cclib/branches/cclib-0.8
  
  ........
    r758 | baoilleach | 2007-09-21 17:39:55 +0100 (Fri, 21 Sep 2007) | 1 line
    
    Updates for release.
  ........
................
  r761 | langner | 2007-09-27 09:23:50 -0700 (Thu, 27 Sep 2007) | 1 line
  
  Added conditioned returns and other things in a few places in order to stop crashing Gaussian log files for counterpoise calcualtions. Uploaded and added an appropriate regression file.
................
  r762 | langner | 2007-09-27 11:08:09 -0700 (Thu, 27 Sep 2007) | 1 line
  
  One more conditioned return to cope with counterpoise calcualtions and parse only the entire basis set (the logical choice). Parsing output from such jobs still gives non-standard results for other attributes (scfenergies, etc.), since they are parsed for both the supermolecule and all fragments.
................
  r763 | langner | 2007-10-11 15:06:40 -0700 (Thu, 11 Oct 2007) | 1 line
  
  Update ANNOUNCE and CHANGELOG with information from the new release (0.8b).
................
  r764 | langner | 2007-10-11 15:21:13 -0700 (Thu, 11 Oct 2007) | 1 line
  
  Prettier printing of page names when downloading the wiki.
................
  r765 | baoilleach | 2007-10-13 03:34:42 -0700 (Sat, 13 Oct 2007) | 1 line
  
  Edited changelog: Removed reference to setuptools, which unfortunately hasn't had it to release. Removed reference to parser refactoring, which although an important change, isn't a feature that affects the users.
................

Modified Paths:
--------------
    branches/orca/ANNOUNCE
    branches/orca/CHANGELOG
    branches/orca/INSTALL
    branches/orca/THANKS
    branches/orca/data/Gaussian/basicGaussian03/C_bigbasis.gjf
    branches/orca/data/Gaussian/basicGaussian03/C_bigbasis.out
    branches/orca/data/regressionfiles.txt
    branches/orca/downloadwiki.py
    branches/orca/manifest.py
    branches/orca/setup.py
    branches/orca/src/cclib/__init__.py
    branches/orca/src/cclib/bridge/cclib2openbabel.py
    branches/orca/src/cclib/bridge/cclib2pyquante.py
    branches/orca/src/cclib/method/calculationmethod.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/gaussianparser.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/test/bettertest.py
    branches/orca/test/regression.py
    branches/orca/test/testBasis.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/testSPun.py
    branches/orca/test/testTD.py
    branches/orca/test/testall.py
    branches/orca/test/testcda.py
    branches/orca/test/testdata
    branches/orca/test/testpopulation.py
    branches/orca/test/testvib.py

Removed Paths:
-------------
    branches/orca/data/Molpro/basicMolpro2006/C_bigbasis_cart.com
    branches/orca/data/Molpro/basicMolpro2006/C_bigbasis_cart.out

Property Changed:
----------------
    branches/orca/
    branches/orca/data/Molpro/


This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.