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[cclib-svn] SF.net SVN: cclib:[898] branches/turbomoleparser/
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From: <ate...@us...> - 2010-04-04 21:28:17
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Revision: 898
http://cclib.svn.sourceforge.net/cclib/?rev=898&view=rev
Author: atenderholt
Date: 2010-04-04 21:28:10 +0000 (Sun, 04 Apr 2010)
Log Message:
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Merged revisions 686-897 via svnmerge from
https://cclib.svn.sf.net/svnroot/cclib/trunk
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r690 | langner | 2007-07-11 17:27:50 -0700 (Wed, 11 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 | 2007-07-11 17:31:23 -0700 (Wed, 11 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 01:10:51 -0700 (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 11:02:54 -0700 (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 12:17:29 -0700 (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 09:03:18 -0700 (Thu, 02 Aug 2007) | 1 line
Added Gaussian regression test file supplied by Christoph Steinbeck.
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r708 | langner | 2007-08-04 15:33:45 -0700 (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 | 2007-08-04 16:07:35 -0700 (Sat, 04 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 05:57:32 -0700 (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 14:41:45 -0700 (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 01:44:55 -0700 (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 | 2007-08-08 23:47:57 -0700 (Wed, 08 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 00:00:24 -0700 (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 12:16:00 -0700 (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 05:13:26 -0700 (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 09:20:16 -0700 (Mon, 13 Aug 2007) | 1 line
Minor: safety check before setting nmo=nbasis after parsing.
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r726 | langner | 2007-08-13 09:23:01 -0700 (Mon, 13 Aug 2007) | 1 line
Another minor safety check - when setting default coreelectrons after parsing.
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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).
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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).
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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.
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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.
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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.
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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.
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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).
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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
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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.
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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.
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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.
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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.
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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.
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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.
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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
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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).
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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
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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.
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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
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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.
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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.
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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.
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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...
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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
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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
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r758 | baoilleach | 2007-09-21 17:39:55 +0100 (Fri, 21 Sep 2007) | 1 line
Updates for release.
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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.
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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.
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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).
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r764 | langner | 2007-10-11 15:21:13 -0700 (Thu, 11 Oct 2007) | 1 line
Prettier printing of page names when downloading the wiki.
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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.
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r770 | baoilleach | 2007-10-22 01:25:41 -0700 (Mon, 22 Oct 2007) | 3 lines
Initialized merge tracking via "svnmerge" with revisions "1-670" from
https://cclib.svn.sourceforge.net/svnroot/cclib/branches/orca
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r771 | atenderholt | 2007-10-22 11:29:00 -0700 (Mon, 22 Oct 2007) | 2 lines
Updated CDA script, which is install along with ccget as part of cclib, to handle new ccData objects.
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r772 | baoilleach | 2007-10-22 23:59:17 -0700 (Mon, 22 Oct 2007) | 83 lines
Merged revisions 671-727,730-768,770-771 via svnmerge from
https://cclib.svn.sourceforge.net/svnroot/cclib/branches/orca
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r671 | atenderholt | 2007-07-09 23:24:16 +0100 (Mon, 09 Jul 2007) | 2 lines
Begin work on a new parser/branch for ORCA by adding single point and optimization files
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r672 | atenderholt | 2007-07-10 00:33:36 +0100 (Tue, 10 Jul 2007) | 2 lines
LogfileParser sets some attributes (nmos and coreelectrons) without first checking if other attributes (nbasis and natom) exist first
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r673 | atenderholt | 2007-07-10 01:40:33 +0100 (Tue, 10 Jul 2007) | 2 lines
Orca parser: Parse geometry information; also update ccopen and __init__.py
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r674 | atenderholt | 2007-07-10 04:01:44 +0100 (Tue, 10 Jul 2007) | 2 lines
ORCA parser: handle orbital energies, and coords if not an optimization
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r676 | atenderholt | 2007-07-10 20:24:27 +0100 (Tue, 10 Jul 2007) | 9 lines
Orca parser: support the overlap matrix, which is only printed if the following is included:
%output
Print[ P_Overlap ] 1
end
unsure of what the differences between the overlap and the one-electron integral matrices are
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r677 | atenderholt | 2007-07-10 22:30:27 +0100 (Tue, 10 Jul 2007) | 2 lines
ORCA Parser: minor bug fix when handling orbital energies of restricted calcs
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r678 | atenderholt | 2007-07-10 22:59:21 +0100 (Tue, 10 Jul 2007) | 2 lines
ORCA parser: Added support for parsing mocoeffs of restricted calcs, provided Print[ P_MOs ] 1 is added to the output section of an input file.
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r679 | atenderholt | 2007-07-10 23:07:32 +0100 (Tue, 10 Jul 2007) | 2 lines
Orca test files: Realized the restricted single point calc was actually unrestricted without mocoeffs/overlaps, so it was redone. Also adding unrestricted single point.
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r680 | atenderholt | 2007-07-11 00:25:25 +0100 (Wed, 11 Jul 2007) | 2 lines
Orca parser: minor code change to work with beta spins of mocoeffs
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r681 | atenderholt | 2007-07-11 01:35:08 +0100 (Wed, 11 Jul 2007) | 2 lines
ORCA parser: Added charge and multiplicity attributes; also parser geotargets and geovalues
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r688 | atenderholt | 2007-07-11 19:53:45 +0100 (Wed, 11 Jul 2007) | 2 lines
ORCA test files: added files for ir frequency calcs
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r689 | atenderholt | 2007-07-11 19:54:11 +0100 (Wed, 11 Jul 2007) | 2 lines
ORCA parser: Added code for handling ir frequencies and intensities; units of intensities might be incorrect for the cclib standard
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r693 | atenderholt | 2007-07-12 19:51:42 +0100 (Thu, 12 Jul 2007) | 2 lines
Orca parser: two bug fixes related to duplicated aonames and mocoeffs > 9.99999
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r694 | atenderholt | 2007-07-13 05:33:09 +0100 (Fri, 13 Jul 2007) | 2 lines
ORCA data files: added raman calculations
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r695 | atenderholt | 2007-07-13 05:33:33 +0100 (Fri, 13 Jul 2007) | 2 lines
ORCA parser: added support for raman calculations
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r707 | atenderholt | 2007-08-03 22:09:47 +0100 (Fri, 03 Aug 2007) | 2 lines
ORCA data files: added MP2 calc for water and a TDDFT calc for dvb
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r723 | baoilleach | 2007-08-13 08:00:07 +0100 (Mon, 13 Aug 2007) | 1 line
Fixed small typo bug in testall.py.
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r724 | baoilleach | 2007-08-13 08:00:34 +0100 (Mon, 13 Aug 2007) | 1 line
Enabling main ORCA tests.
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r774 | atenderholt | 2007-10-24 10:16:10 -0700 (Wed, 24 Oct 2007) | 2 lines
CDA method and script: Added residuals term (contribution of lumos from Fragments A and B), as requested by a few users of PyMOlyze
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r776 | baoilleach | 2007-10-29 02:33:09 -0700 (Mon, 29 Oct 2007) | 1 line
Bumped up version to 0.8
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r779 | langner | 2007-10-29 03:51:48 -0700 (Mon, 29 Oct 2007) | 1 line
Removed basicJaguar4.2 and basicJaguar6.0 from the trunk and added them as regressions in Jaguar/Jaguar4.2 and Jaguar/Jaguar6.0, respectively. Updated all test scripts and regressionfiles.txt. Note: these new regressions are parsed but currently not tests - this remains to be added. Also: regression tests cannot read from multiple files.
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r780 | langner | 2007-10-29 05:10:50 -0700 (Mon, 29 Oct 2007) | 1 line
Removed Jaguar4.2 from visual tests and added Molpro.
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r781 | langner | 2007-10-29 05:58:34 -0700 (Mon, 29 Oct 2007) | 1 line
Updating the ADF unittest files to ADF2006.01 - all tests finish the same (still 5 fails). An update to ASF2007.01 is also on the way.
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r782 | langner | 2007-10-30 09:28:46 -0700 (Tue, 30 Oct 2007) | 1 line
Bumped basicADF2006.01 tests up to basicADF2007.01, leaving one 2006.01 test (gopt) as a regression. Test results did not change.
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r784 | langner | 2007-11-01 02:52:52 -0700 (Thu, 01 Nov 2007) | 1 line
Added **kwawrgs to __init__ arguments list of all parsers to allow for more flexible subclassing.
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r785 | langner | 2007-11-05 06:42:58 -0800 (Mon, 05 Nov 2007) | 1 line
Updated Jaguar test files to 7.0; rewrote fragments in parser concerning vibirs/vibdisps and moenergies/mosyms in order to parse output from all Jaguar versions correctly (regressions for 4.2, 6.0 and 6.5 now all parse OK).
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r786 | langner | 2007-11-05 11:04:21 -0800 (Mon, 05 Nov 2007) | 1 line
Force ADF parser to parse scfenergies for SP calculations from Total Bonding decomposition output (I don't think ADF prints it before that... if it does, tell me where...); pass test for atombasis since th ADF parser does not parse this yet.
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r787 | langner | 2007-11-05 13:13:30 -0800 (Mon, 05 Nov 2007) | 1 line
New version of ADF test files dvb_sp_b, with output needed for scfvalues to be parsed (appropriate test now OK).
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r788 | langner | 2007-11-05 13:34:53 -0800 (Mon, 05 Nov 2007) | 1 line
Tiny fix: need to read both dvb_ir.out and dvb_ir.log in order to parse Molpro vibration output; testvib now has no errors.
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r789 | langner | 2007-11-05 14:32:50 -0800 (Mon, 05 Nov 2007) | 1 line
ORCA: quick hacks to parser for atombasis, scfenergies, scftargets and scfvalues - not necessarily reliable or pretty, but enough for testSP; modified basisdict and b3lyp_energy for OrcaSPTest since the test was done for 3-21G (should be rerun in STO-3G for consistency); updated setup.py so basicORCA data files are installed along with cclib.
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r790 | langner | 2007-11-06 01:14:32 -0800 (Tue, 06 Nov 2007) | 1 line
ORCA: pass all symmetry tests since the program knows none; modify basisdict and b3lypenerhy where appropriate since the tests were run in 3-21G instead of STO-3G.
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r791 | baoilleach | 2007-11-06 02:12:51 -0800 (Tue, 06 Nov 2007) | 9 lines
Merged revisions 783 via svnmerge from
https://cclib.svn.sourceforge.net/svnroot/cclib/branches/cclib-0.8
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r783 | baoilleach | 2007-10-31 13:12:43 +0000 (Wed, 31 Oct 2007) | 1 line
Fixed bug parsing C_bigmult.log. Added regression test.
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r792 | langner | 2007-11-06 12:08:43 -0800 (Tue, 06 Nov 2007) | 1 line
Spruced up (I hope) readjson/writejson functions and added analogous readpickle/writepickle functions.
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r793 | langner | 2007-11-06 12:09:58 -0800 (Tue, 06 Nov 2007) | 1 line
Added cclib.egg-info to svn:ignore property list.
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r794 | baoilleach | 2007-11-07 08:23:58 -0800 (Wed, 07 Nov 2007) | 1 line
GAMESS: Extraction of etoscs enabled for basicPCGAMESS/dvb_td.out (I added a regression test). I still have one test file (supplied by a user) to sort out...
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r795 | baoilleach | 2007-11-08 01:34:09 -0800 (Thu, 08 Nov 2007) | 1 line
GAMESS US: Added a TD-DFT calculation, and the code the parse it. PC-GAMESS is increasingly becoming a fork.
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r796 | baoilleach | 2007-11-14 05:57:02 -0800 (Wed, 14 Nov 2007) | 1 line
TD-DFT tightening up: tests for values for etoscs, etenergies and etsecs. Need to discuss this on list as it affects CI also...
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r797 | baoilleach | 2007-11-16 09:22:15 -0800 (Fri, 16 Nov 2007) | 1 line
More TD-DFT related commits including some datafiles for GAMESS for triplet excitations.
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r798 | baoilleach | 2007-11-16 09:24:14 -0800 (Fri, 16 Nov 2007) | 1 line
Forgot to commit these two datafiles...
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r799 | baoilleach | 2007-11-18 11:55:03 -0800 (Sun, 18 Nov 2007) | 1 line
tests: More testing of the triplet excitations...(note to self: still need to sort out that CI stuff...)
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r800 | langner | 2007-11-19 05:24:20 -0800 (Mon, 19 Nov 2007) | 1 line
Added support for python-cjson and python-json alongside simpjejson as alternatives, with any of these modules loaded dynamically upon read/write (see load_json in data.py). Added short comment about JSON to INSTALL.
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r801 | langner | 2007-11-19 10:07:12 -0800 (Mon, 19 Nov 2007) | 1 line
Removed all read/write function and methods from cclibData - refer to "[cclib-devel] Further JSON support" thread for rationale.
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r802 | langner | 2007-11-19 10:11:58 -0800 (Mon, 19 Nov 2007) | 1 line
Added optional argument 'tolists' to cclibData.getattributes for convenience.
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r803 | langner | 2007-11-19 13:29:10 -0800 (Mon, 19 Nov 2007) | 1 line
Import from setuptools ONLY if requested ('egg' in sys.argv), becuase I observe strange behavior when it is used.
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r804 | baoilleach | 2007-11-26 09:09:20 -0800 (Mon, 26 Nov 2007) | 1 line
ORCA: Added support for TD-DFT
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r805 | baoilleach | 2007-11-26 09:10:59 -0800 (Mon, 26 Nov 2007) | 1 line
Tests: Forgot to check in this test, which I've moved from TestTD.py to here as unrestricted calculations often need more work.
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r811 | langner | 2008-05-13 12:15:49 -0700 (Tue, 13 May 2008) | 1 line
Quick fix to Jaguar parser for ptnh3_2_H2O_2_2plus output sent in by Jean-Didier Mar?\195?\169chal. Added the output file to regressions, also.
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r812 | atenderholt | 2008-05-13 17:37:41 -0700 (Tue, 13 May 2008) | 2 lines
ADF parser: fixed a bug that didn't correctly determine symmetry labels for an unrestricted, d3h calculation (regression file WH6-opt.adfout)
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r813 | langner | 2008-05-23 10:21:14 -0700 (Fri, 23 May 2008) | 1 line
Removing regression ptnh3_2_H2O_2_2plus (Jaguar 7.0) per request of author.
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r814 | atenderholt | 2008-05-29 17:11:28 -0700 (Thu, 29 May 2008) | 2 lines
Bug fix, gaussian: frequency displacements were not parsed correctly when that section of the code was re-written back around revision 667 (i think).
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r815 | baoilleach | 2008-06-15 05:02:08 -0700 (Sun, 15 Jun 2008) | 1 line
etsec, CI and Jaguar: Updated Jaguar parser to extract the correct etsecs (follow on from etsec work around Nov 11 2007). Updated testCI to handle the new values.
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r816 | baoilleach | 2008-06-15 05:03:29 -0700 (Sun, 15 Jun 2008) | 1 line
Minor fix for bridge __init__.py to handle import error when importing Biopython.
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r817 | baoilleach | 2008-06-15 05:53:52 -0700 (Sun, 15 Jun 2008) | 1 line
Getting ready for release branch of cclib 0.9
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r822 | langner | 2008-06-17 01:08:15 -0700 (Tue, 17 Jun 2008) | 1 line
Updated changelog a bit.
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r823 | langner | 2008-06-17 01:26:15 -0700 (Tue, 17 Jun 2008) | 1 line
Added reference to the paper.
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r824 | baoilleach | 2008-07-07 12:18:43 -0700 (Mon, 07 Jul 2008) | 1 line
Minor edit
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r826 | baoilleach | 2008-07-07 13:36:00 -0700 (Mon, 07 Jul 2008) | 1 line
Bump version to 0.9
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r829 | atenderholt | 2008-07-21 10:50:47 -0700 (Mon, 21 Jul 2008) | 2 lines
ADF test file: adding dvb_td files for a TD-DFT calculation
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r830 | atenderholt | 2008-07-21 14:37:43 -0700 (Mon, 21 Jul 2008) | 2 lines
ADF parser: implemented etenergies, etoscs, etsyms, and etsecs. have only tested on dvb_td.adfout and a personal research file.
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r831 | atenderholt | 2008-07-22 11:01:05 -0700 (Tue, 22 Jul 2008) | 2 lines
TD test: adding support for testing the ADF dvb_td logfile.
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r832 | atenderholt | 2008-07-24 21:07:59 -0700 (Thu, 24 Jul 2008) | 2 lines
ADF parser: minor fix to (hopefully) handle transitions with multiple symmetries (A' and A")
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r833 | baoilleach | 2008-07-25 08:21:00 -0700 (Fri, 25 Jul 2008) | 1 line
Adding a failing testfile supplied by Bill Gunn. It's easy to fix, but before I do, I just want to add some regression tests to make sure I don't mess anything up.
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r834 | langner | 2008-08-11 14:03:29 -0700 (Mon, 11 Aug 2008) | 1 line
Fixed GAMESS parser so that it does not break when not all MO vectors are printed. This is checked by regression test 2CO.ccsd.aug-cc-pVDZ.out. Still, the outcome is not understandable.
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r835 | langner | 2008-08-11 14:10:12 -0700 (Mon, 11 Aug 2008) | 1 line
Added 2CO.ccsd.aug-cc-pVDZ.out to GAMESS regression tests - case of not all MO vectors being printed.
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r836 | langner | 2008-08-11 14:28:44 -0700 (Mon, 11 Aug 2008) | 1 line
Added a few digits to the hartree_to_eV conversion factor (27.2113845).
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r837 | atenderholt | 2008-09-03 18:53:41 -0700 (Wed, 03 Sep 2008) | 2 lines
Lowdin population analysis: moved the routine for calculating S^x and S^(1-x) out of the loop since these only need to be calculated once; results in a significant speed improvement
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r838 | baoilleach | 2009-02-04 13:53:01 -0800 (Wed, 04 Feb 2009) | 1 line
Added test file supplied by Manuel Melle-Franco and fixed bug in Gaussian vibsym parsing
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r839 | baoilleach | 2009-02-08 08:27:10 -0800 (Sun, 08 Feb 2009) | 1 line
Handle exception importing openbabel.
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r840 | baoilleach | 2009-02-08 08:28:12 -0800 (Sun, 08 Feb 2009) | 1 line
Handle PBC (periodic boundary condition) calcs in Gaussian. Test case from Nuno Bandeira.
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r843 | baoilleach | 2009-02-25 03:51:57 -0800 (Wed, 25 Feb 2009) | 1 line
Fix for filenames in unicode, e.g. that contain accented characters. Such unicode filenames are generated by GaussSum if the path to the file contains such a character.
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r844 | baoilleach | 2009-04-03 08:02:15 -0700 (Fri, 03 Apr 2009) | 1 line
Fix for Gaussian coreelectrons parser error.
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r845 | langner | 2009-04-06 04:54:43 -0700 (Mon, 06 Apr 2009) | 1 line
Fix for 'trimmed' Gaussian log file (missing MOs) cyclopropenyl.rhf.g03.cut.log.
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r846 | langner | 2009-04-06 15:08:16 -0700 (Mon, 06 Apr 2009) | 1 line
Fixed bug 1767309 concerning atomcoords in non-standard symmetry treatment (symm=follow). Added file attached to bug as a regression test (with explicit test function).
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r847 | langner | 2009-04-06 15:46:03 -0700 (Mon, 06 Apr 2009) | 1 line
Fixed bug 2738818 concerning nosymm and atomcoords in Gaussian parser, and added anb appropriate regression test function.
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r848 | langner | 2009-04-06 17:43:03 -0700 (Mon, 06 Apr 2009) | 1 line
GAMESS parser: issue warning on exception when parsing moenergies. Added regression test cyclopentadienyl.rhf.gms.out.cut.bz2.
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r849 | baoilleach | 2009-06-04 04:32:30 -0700 (Thu, 04 Jun 2009) | 1 line
Parse failure for an AM1 Gaussian calc. Fixed and added test file.
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r850 | langner | 2009-07-15 08:11:01 -0700 (Wed, 15 Jul 2009) | 1 line
Add code to parse gradients (forces) from Gaussian calcs - new attribute 'grad'.
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r851 | langner | 2009-07-15 08:42:12 -0700 (Wed, 15 Jul 2009) | 1 line
Added unit test for grad attribute in testGeoOpt for Gaussian parser.
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r852 | langner | 2009-07-15 08:47:21 -0700 (Wed, 15 Jul 2009) | 1 line
Fixed coding error in unit test for grad attribute in testGeoOpt for Gaussian parser.
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r853 | langner | 2009-07-15 09:06:25 -0700 (Wed, 15 Jul 2009) | 1 line
Use numpy.issubdtype instead of Pythonic isinstance, since numpy now defines it's own scalar types. This fixes many failures that come up when using recent versions of numpy.
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r854 | langner | 2009-07-16 02:09:13 -0700 (Thu, 16 Jul 2009) | 1 line
Parse natom only once in GAMESS - failsafe for jobs where fragments are considered (number of atoms can vary).
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r855 | langner | 2009-07-18 04:14:50 -0700 (Sat, 18 Jul 2009) | 1 line
Add ability to retrieve remote files via HTTP and parse them locally in cclib.parser.ccopen.
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r856 | langner | 2009-07-19 02:08:50 -0700 (Sun, 19 Jul 2009) | 1 line
Use modern '*args, **kargs' syntax in ccopen.
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r857 | langner | 2009-07-19 02:12:12 -0700 (Sun, 19 Jul 2009) | 1 line
Add optional argument stream (default sys.stdout) passed to logging.StreamHandler.
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r858 | langner | 2009-07-19 13:52:30 -0700 (Sun, 19 Jul 2009) | 1 line
Minimal, nondisruptice changes to handle input streams in ccopen and logfile.__init__(). This allows open files, StringIO objects, and almost anything with a read() method to be passed. A few small changes and the script ccget would now be capable of accepting piped input (which would be really convenient and cool).
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r859 | langner | 2009-07-20 08:20:58 -0700 (Mon, 20 Jul 2009) | 1 line
Small fix to bypass assertion failures for Gaussian ONIOM calcs. Note that this does not mean ONION output is parsed, it merely does not crash cclib.
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r860 | langner | 2009-07-20 09:56:48 -0700 (Mon, 20 Jul 2009) | 1 line
Use isinstance and types.StringTypes when checking the type of input in order to account for both str and unicode objects.
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r861 | langner | 2009-07-20 14:07:04 -0700 (Mon, 20 Jul 2009) | 1 line
Reorder import alphabetically.
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r862 | langner | 2009-07-20 14:08:21 -0700 (Mon, 20 Jul 2009) | 1 line
Rely on numpy only (no Numeric support) in ORCA parser.
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r863 | langner | 2009-07-20 15:00:17 -0700 (Mon, 20 Jul 2009) | 1 line
Moved ccopen to its own module in order to avoid circular imports.
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r864 | langner | 2009-07-20 15:07:48 -0700 (Mon, 20 Jul 2009) | 1 line
Fixed and clean up imports.
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r865 | langner | 2009-07-20 15:12:41 -0700 (Mon, 20 Jul 2009) | 1 line
Fixed small bug pointed out by pychecker.
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r866 | langner | 2009-07-28 03:23:39 -0700 (Tue, 28 Jul 2009) | 1 line
Small fix for MCSCF calculations; added regression file lif.r=5.6.mcscf.accd.4x4.out.bz2.
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r867 | langner | 2009-09-07 02:13:12 -0700 (Mon, 07 Sep 2009) | 1 line
Convert atomno to int in case it is a different numpy dtype.
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r868 | baoilleach | 2009-10-09 06:39:53 -0700 (Fri, 09 Oct 2009) | 1 line
First Gaussian 09 log file. ZINDO/S electronic transitions.
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r869 | langner | 2009-10-17 08:20:50 -0700 (Sat, 17 Oct 2009) | 1 line
Ignore new regression directory Gaussian/Gaussian09.
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r870 | langner | 2009-10-17 08:21:51 -0700 (Sat, 17 Oct 2009) | 1 line
Fixed scftargets/scfvalues for ROHF in GAMESS-US (tested by regression test exam17.log.bz2.
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r871 | langner | 2009-10-17 08:45:20 -0700 (Sat, 17 Oct 2009) | 1 line
Fixed GAMESS parser so that standard test exam33 does not crash it, and added the log file as a regression.
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r872 | langner | 2009-10-17 09:45:11 -0700 (Sat, 17 Oct 2009) | 1 line
Added standard test exam37 to regressions, which is an FMO calculation. While cclib does parse this output logically and will not (since it is native to GAMESS), it does not crash anymore after a number of small fixes. 1) all lines starting with 'INPUT CARD>' are ignored, 2) attribute homos can also be parsed in the block where orbital symmetries are printed, plus a warning is issued to the logger when this is not consistent with the first value (which occurs for ECP and some other calcs), 3) natom can also be parsed in lower case, 4) when MO coefficients stop prematurely, the parser simply breaks the current loop and mocoeffs is incomplete, 5) minor hack for parsing gradients.
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r873 | langner | 2009-10-17 09:53:00 -0700 (Sat, 17 Oct 2009) | 1 line
Minor loop redefinition so that standard GAMESS-US test exam42 does not crash the parser.
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r874 | langner | 2009-10-21 05:43:01 -0700 (Wed, 21 Oct 2009) | 1 line
Attempt to import Set from sets as set if not available (for Pythons before 2.4).
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r875 | baoilleach | 2009-10-26 07:31:44 -0700 (Mon, 26 Oct 2009) | 1 line
Minor fix to assert statements
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r876 | baoilleach | 2009-10-26 07:59:34 -0700 (Mon, 26 Oct 2009) | 1 line
Fixed bug reported by Steve George. Added test file anth1.zip
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r877 | baoilleach | 2009-10-31 08:28:25 -0700 (Sat, 31 Oct 2009) | 1 line
Add some basicGaussian09 log files and a small bugfix.
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r878 | baoilleach | 2009-11-13 07:19:15 -0800 (Fri, 13 Nov 2009) | 1 line
Fix for parsing CD in G09. Bug report and log files from Rino Pescitelli.
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r879 | baoilleach | 2009-11-16 01:20:15 -0800 (Mon, 16 Nov 2009) | 3 lines
(1) Move data.py to parser/data.py to avoid absolute import. This causes problems with GaussSum, and was probably a bad idea in the first place.
(2) Minor changes to logging to increase Avogadro compatability. Also removal of urllib dependency for the same reason. The current code can already handle file-like objects such as those returned by url.urlopen()
(3) No need for scary warning message if bunzip2 module not present so long as ImportError is raised if filename ends with .bz2
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r880 | baoilleach | 2010-01-24 13:45:30 -0800 (Sun, 24 Jan 2010) | 1 line
Fix + test case for "Failed parse of numerical Hessian vibrational frequencies. - ID: 2935847" reported by Daniel Matusek
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r881 | baoilleach | 2010-01-26 09:12:31 -0800 (Tue, 26 Jan 2010) | 1 line
Initial fix for GAMESS open shell CCSD parsing. Bug 2939920, reported by Dan Matusek
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r882 | baoilleach | 2010-02-12 03:27:50 -0800 (Fri, 12 Feb 2010) | 1 line
Gaussian03 parsing failed for PBC file from Mahesh Kumar. Fixed and added to regression suite.
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r885 | baoilleach | 2010-02-23 03:18:03 -0800 (Tue, 23 Feb 2010) | 1 line
Initial 'test' release of 1.0a
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r887 | baoilleach | 2010-02-27 10:39:58 -0800 (Sat, 27 Feb 2010) | 1 line
GAMESS has got a new MP2 program. Added test file from Paulo Abreu and fix.
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r888 | baoilleach | 2010-03-04 13:13:22 -0800 (Thu, 04 Mar 2010) | 1 line
Getting ready for cclib-1.0b
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r890 | baoilleach | 2010-03-04 13:34:38 -0800 (Thu, 04 Mar 2010) | 1 line
Minor correct on version number.
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r891 | baoilleach | 2010-03-04 13:45:31 -0800 (Thu, 04 Mar 2010) | 1 line
Update CHANGELOG with some highlights from the last 18 months!!
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r892 | baoilleach | 2010-03-06 08:32:19 -0800 (Sat, 06 Mar 2010) | 1 line
Fix for Paulo Abreu's UMP2 and ROMP2 GAMESS test files.
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r893 | baoilleach | 2010-03-07 10:42:22 -0800 (Sun, 07 Mar 2010) | 1 line
Update for cclib 1.0 release
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Revision Links:
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http://cclib.svn.sourceforge.net/cclib/?rev=667&view=rev
Property Changed:
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branches/turbomoleparser/
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