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From: <la...@us...> - 2007-09-06 14:17:22
|
Revision: 751
http://cclib.svn.sourceforge.net/cclib/?rev=751&view=rev
Author: langner
Date: 2007-09-06 07:17:15 -0700 (Thu, 06 Sep 2007)
Log Message:
-----------
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.
Modified Paths:
--------------
trunk/data/Gaussian/basicGaussian03/C_bigbasis.gjf
trunk/data/Gaussian/basicGaussian03/C_bigbasis.out
trunk/src/cclib/parser/molproparser.py
trunk/test/testBasis.py
trunk/test/testdata
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From: <ate...@us...> - 2007-09-06 00:40:45
|
Revision: 750
http://cclib.svn.sourceforge.net/cclib/?rev=750&view=rev
Author: atenderholt
Date: 2007-09-05 17:40:43 -0700 (Wed, 05 Sep 2007)
Log Message:
-----------
Gaussian parser: fixed bug (#1775665) with empty mosyms when using SCF=QC; still need to add test file
Modified Paths:
--------------
trunk/src/cclib/parser/gaussianparser.py
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From: <la...@us...> - 2007-09-05 21:12:02
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Revision: 749
http://cclib.svn.sourceforge.net/cclib/?rev=749&view=rev
Author: langner
Date: 2007-09-05 14:11:59 -0700 (Wed, 05 Sep 2007)
Log Message:
-----------
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.
Modified Paths:
--------------
trunk/test/testGeoOpt.py
trunk/test/testSP.py
trunk/test/testdata
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From: <ate...@us...> - 2007-09-05 00:37:42
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Revision: 748
http://cclib.svn.sourceforge.net/cclib/?rev=748&view=rev
Author: atenderholt
Date: 2007-09-04 17:37:37 -0700 (Tue, 04 Sep 2007)
Log Message:
-----------
ADF parser: check to see if CFs are printed in mocoeffs; if so, skip them
Modified Paths:
--------------
trunk/src/cclib/parser/adfparser.py
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From: <la...@us...> - 2007-09-03 23:09:25
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Revision: 747
http://cclib.svn.sourceforge.net/cclib/?rev=747&view=rev
Author: langner
Date: 2007-09-03 16:09:21 -0700 (Mon, 03 Sep 2007)
Log Message:
-----------
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).
Modified Paths:
--------------
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/testvib.py
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From: <ate...@us...> - 2007-09-03 19:12:59
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Revision: 746
http://cclib.svn.sourceforge.net/cclib/?rev=746&view=rev
Author: atenderholt
Date: 2007-09-03 12:12:56 -0700 (Mon, 03 Sep 2007)
Log Message:
-----------
ADF parser: fixed Frags_NiCO4 parse error; now it correctly detects different create run format and skips mutiple calculations in the same log file
Modified Paths:
--------------
trunk/src/cclib/parser/adfparser.py
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From: <la...@us...> - 2007-09-03 14:56:15
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Revision: 745
http://cclib.svn.sourceforge.net/cclib/?rev=745&view=rev
Author: langner
Date: 2007-09-03 05:24:01 -0700 (Mon, 03 Sep 2007)
Log Message:
-----------
Minor: changed error message in Molpro parser upon reading bad mocoeffs to a warning.
Modified Paths:
--------------
trunk/src/cclib/parser/molproparser.py
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From: <la...@us...> - 2007-09-02 22:23:40
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Revision: 744
http://cclib.svn.sourceforge.net/cclib/?rev=744&view=rev
Author: langner
Date: 2007-09-02 15:23:33 -0700 (Sun, 02 Sep 2007)
Log Message:
-----------
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.
Modified Paths:
--------------
trunk/data/regressionfiles.txt
trunk/src/cclib/parser/molproparser.py
Removed Paths:
-------------
trunk/data/Molpro/basicMolpro2006/C_bigbasis_cart.com
trunk/data/Molpro/basicMolpro2006/C_bigbasis_cart.out
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From: <bao...@us...> - 2007-09-02 20:26:31
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Revision: 743
http://cclib.svn.sourceforge.net/cclib/?rev=743&view=rev
Author: baoilleach
Date: 2007-09-02 13:26:25 -0700 (Sun, 02 Sep 2007)
Log Message:
-----------
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.
Modified Paths:
--------------
trunk/test/testall.py
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From: <bao...@us...> - 2007-09-02 18:08:24
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Revision: 742
http://cclib.svn.sourceforge.net/cclib/?rev=742&view=rev
Author: baoilleach
Date: 2007-09-02 11:08:19 -0700 (Sun, 02 Sep 2007)
Log Message:
-----------
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.
Modified Paths:
--------------
trunk/src/cclib/method/volume.py
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From: <la...@us...> - 2007-09-02 14:36:26
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Revision: 741
http://cclib.svn.sourceforge.net/cclib/?rev=741&view=rev
Author: langner
Date: 2007-09-02 07:36:20 -0700 (Sun, 02 Sep 2007)
Log Message:
-----------
Fix for calling cclib.parser.ccopen(..., loglevel=0), which set fupdate instead of loglevel. Also, ccopen does not use logname presently.
Modified Paths:
--------------
trunk/src/cclib/parser/logfileparser.py
trunk/src/cclib/parser/utils.py
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From: <bao...@us...> - 2007-09-02 10:46:35
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Revision: 740
http://cclib.svn.sourceforge.net/cclib/?rev=740&view=rev
Author: baoilleach
Date: 2007-09-02 03:46:32 -0700 (Sun, 02 Sep 2007)
Log Message:
-----------
Molpro tests: Enabled regression.py for Molpro. One failure on C_bigbasis_cart.out.
Modified Paths:
--------------
trunk/test/regression.py
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From: <ate...@us...> - 2007-09-02 00:44:12
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Revision: 739
http://cclib.svn.sourceforge.net/cclib/?rev=739&view=rev
Author: atenderholt
Date: 2007-09-01 17:44:10 -0700 (Sat, 01 Sep 2007)
Log Message:
-----------
Removed checked to see if ccData has been parsed as this is a leftover from when parsers kept attributes
Modified Paths:
--------------
trunk/src/cclib/method/opa.py
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From: <la...@us...> - 2007-09-01 15:50:54
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Revision: 738
http://cclib.svn.sourceforge.net/cclib/?rev=738&view=rev
Author: langner
Date: 2007-09-01 08:50:50 -0700 (Sat, 01 Sep 2007)
Log Message:
-----------
Print error warnings when failing to load bz2 module (can still be usefull in newer pythons).
Modified Paths:
--------------
trunk/src/cclib/parser/utils.py
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From: <bao...@us...> - 2007-08-30 07:09:00
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Revision: 737
http://cclib.svn.sourceforge.net/cclib/?rev=737&view=rev
Author: baoilleach
Date: 2007-08-30 00:08:53 -0700 (Thu, 30 Aug 2007)
Log Message:
-----------
Updated the openbabel and pyquante bridges to handle the new charge and multiplicity attributes.
Modified Paths:
--------------
trunk/src/cclib/bridge/cclib2openbabel.py
trunk/src/cclib/bridge/cclib2pyquante.py
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From: <la...@us...> - 2007-08-27 18:03:37
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Revision: 736
http://cclib.svn.sourceforge.net/cclib/?rev=736&view=rev
Author: langner
Date: 2007-08-27 11:03:35 -0700 (Mon, 27 Aug 2007)
Log Message:
-----------
Fixed condition in parsing mocoeffs from Molpro that broke sp_un unittest.
Modified Paths:
--------------
trunk/src/cclib/parser/molproparser.py
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From: <la...@us...> - 2007-08-27 17:26:43
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Revision: 735
http://cclib.svn.sourceforge.net/cclib/?rev=735&view=rev
Author: langner
Date: 2007-08-27 10:26:41 -0700 (Mon, 27 Aug 2007)
Log Message:
-----------
Updated attribute list for ccget with ccenergies, fragnames and frags.
Modified Paths:
--------------
trunk/src/scripts/ccget
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From: <la...@us...> - 2007-08-24 13:02:26
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Revision: 734
http://cclib.svn.sourceforge.net/cclib/?rev=734&view=rev
Author: langner
Date: 2007-08-24 06:02:22 -0700 (Fri, 24 Aug 2007)
Log Message:
-----------
Added fix regression file for Molpro that broke parsing of mocoeffs.
Modified Paths:
--------------
trunk/data/regressionfiles.txt
trunk/src/cclib/parser/molproparser.py
Property Changed:
----------------
trunk/data/Molpro/
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From: <la...@us...> - 2007-08-24 08:31:16
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Revision: 733
http://cclib.svn.sourceforge.net/cclib/?rev=733&view=rev
Author: langner
Date: 2007-08-24 01:31:08 -0700 (Fri, 24 Aug 2007)
Log Message:
-----------
Fixed methods for recent separation of ccData from LogFile (at least within those methods being tested).
Modified Paths:
--------------
trunk/src/cclib/method/calculationmethod.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/lpa.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/test/testcda.py
trunk/test/testpopulation.py
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From: <la...@us...> - 2007-08-17 16:36:45
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Revision: 732
http://cclib.svn.sourceforge.net/cclib/?rev=732&view=rev
Author: langner
Date: 2007-08-17 09:36:40 -0700 (Fri, 17 Aug 2007)
Log Message:
-----------
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).
Modified Paths:
--------------
trunk/test/testGeoOpt.py
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From: <cnr...@us...> - 2007-08-13 20:30:42
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Revision: 730
http://cclib.svn.sourceforge.net/cclib/?rev=730&view=rev
Author: cnrowley
Date: 2007-08-13 13:27:58 -0700 (Mon, 13 Aug 2007)
Log Message:
-----------
Added test file for closed shell single point with symmetry
Modified Paths:
--------------
branches/turbomoleparser/src/cclib/parser/turbomoleparser.py
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From: <cnr...@us...> - 2007-08-13 20:30:30
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Revision: 731
http://cclib.svn.sourceforge.net/cclib/?rev=731&view=rev
Author: cnrowley
Date: 2007-08-13 13:28:22 -0700 (Mon, 13 Aug 2007)
Log Message:
-----------
Added test file for closed shell single point with symmetry
Added Paths:
-----------
branches/turbomoleparser/data/Turbomole/basicTurbomole/dvb_sp_symm/
branches/turbomoleparser/data/Turbomole/basicTurbomole/dvb_sp_symm/GEO_OPT_CONVERGED
branches/turbomoleparser/data/Turbomole/basicTurbomole/dvb_sp_symm/basis
branches/turbomoleparser/data/Turbomole/basicTurbomole/dvb_sp_symm/control
branches/turbomoleparser/data/Turbomole/basicTurbomole/dvb_sp_symm/converged
branches/turbomoleparser/data/Turbomole/basicTurbomole/dvb_sp_symm/coord
branches/turbomoleparser/data/Turbomole/basicTurbomole/dvb_sp_symm/energy
branches/turbomoleparser/data/Turbomole/basicTurbomole/dvb_sp_symm/forceapprox
branches/turbomoleparser/data/Turbomole/basicTurbomole/dvb_sp_symm/gradient
branches/turbomoleparser/data/Turbomole/basicTurbomole/dvb_sp_symm/job.last
branches/turbomoleparser/data/Turbomole/basicTurbomole/dvb_sp_symm/job.start
branches/turbomoleparser/data/Turbomole/basicTurbomole/dvb_sp_symm/mos
branches/turbomoleparser/data/Turbomole/basicTurbomole/dvb_sp_symm/statistics
branches/turbomoleparser/data/Turbomole/basicTurbomole/dvb_sp_symm/turbo.out
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From: <bao...@us...> - 2007-08-13 18:43:11
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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
........
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:
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branches/orca/data/Gaussian/basicGaussian03/water_mp4sdq.com
branches/orca/data/Gaussian/basicGaussian03/water_mp4sdq.log
branches/orca/src/cclib/data.py
Property Changed:
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branches/orca/
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
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From: <bao...@us...> - 2007-08-13 18:25:54
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Revision: 728
http://cclib.svn.sourceforge.net/cclib/?rev=728&view=rev
Author: baoilleach
Date: 2007-08-13 11:25:52 -0700 (Mon, 13 Aug 2007)
Log Message:
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Initialized merge tracking via "svnmerge" with revisions "1-670" from
https://cclib.svn.sourceforge.net/svnroot/cclib/trunk
Property Changed:
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branches/orca/
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
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From: <la...@us...> - 2007-08-13 16:53:20
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Revision: 727
http://cclib.svn.sourceforge.net/cclib/?rev=727&view=rev
Author: langner
Date: 2007-08-13 09:53:16 -0700 (Mon, 13 Aug 2007)
Log Message:
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Updated src/cclib/parser/utils.py and logfileparser.py for parsing multiple files.
Modified Paths:
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branches/turbomoleparser/src/cclib/parser/logfileparser.py
branches/turbomoleparser/src/cclib/parser/utils.py
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
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