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From: <ate...@us...> - 2006-12-21 19:49:24
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Revision: 451
http://svn.sourceforge.net/cclib/?rev=451&view=rev
Author: atenderholt
Date: 2006-12-21 11:49:19 -0800 (Thu, 21 Dec 2006)
Log Message:
-----------
OPA: Bug fix; had to alter some code because of the new mocoeffs definition
Modified Paths:
--------------
trunk/src/cclib/method/opa.py
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From: <ate...@us...> - 2006-12-20 00:07:36
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Revision: 450
http://svn.sourceforge.net/cclib/?rev=450&view=rev
Author: atenderholt
Date: 2006-12-19 16:07:32 -0800 (Tue, 19 Dec 2006)
Log Message:
-----------
Methods: Begin work on CDA method by creating class to convert from basis built on atomic orbitals to basis built from fragment molecular orbitals
Modified Paths:
--------------
trunk/src/cclib/method/__init__.py
Added Paths:
-----------
trunk/src/cclib/method/fragments.py
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From: <ate...@us...> - 2006-12-19 23:59:51
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Revision: 449
http://svn.sourceforge.net/cclib/?rev=449&view=rev
Author: atenderholt
Date: 2006-12-19 15:59:49 -0800 (Tue, 19 Dec 2006)
Log Message:
-----------
CSPA method: fixed a potential bug in cspa where assigning numeric arrays doesn't work because of incorrect type casting (float->double)
Modified Paths:
--------------
trunk/src/cclib/method/cspa.py
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From: <bao...@us...> - 2006-12-10 21:27:48
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Revision: 448
http://svn.sourceforge.net/cclib/?rev=448&view=rev
Author: baoilleach
Date: 2006-12-10 13:27:46 -0800 (Sun, 10 Dec 2006)
Log Message:
-----------
Mocoeffs API change: Updated ADF parser to use new definition of mocoeffs.
Modified Paths:
--------------
trunk/src/cclib/parser/adfparser.py
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From: <bao...@us...> - 2006-12-10 19:32:06
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Revision: 447
http://svn.sourceforge.net/cclib/?rev=447&view=rev
Author: baoilleach
Date: 2006-12-10 11:31:57 -0800 (Sun, 10 Dec 2006)
Log Message:
-----------
Added tests for vibramans, and fixed any problems arising. Specifically, GAMESSUK wasn't extracting raman data, and GAMESS had 3N instead of 3N-6.
Modified Paths:
--------------
trunk/src/cclib/parser/gamessparser.py
trunk/src/cclib/parser/gamessukparser.py
trunk/test/testvib.py
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From: <bao...@us...> - 2006-12-10 18:37:50
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Revision: 446
http://svn.sourceforge.net/cclib/?rev=446&view=rev
Author: baoilleach
Date: 2006-12-10 10:37:45 -0800 (Sun, 10 Dec 2006)
Log Message:
-----------
Bug fix ADF atomnos: atomnos was a list, not an array. Have also added a test to testGeoOpt.py for this.
Modified Paths:
--------------
trunk/src/cclib/parser/adfparser.py
trunk/test/testGeoOpt.py
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From: <bao...@us...> - 2006-12-08 21:18:07
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Revision: 445
http://svn.sourceforge.net/cclib/?rev=445&view=rev
Author: baoilleach
Date: 2006-12-08 13:18:05 -0800 (Fri, 08 Dec 2006)
Log Message:
-----------
vibdisps added for ADF. All current tests for vibrations pass, but just need to add a few more for Raman.
Modified Paths:
--------------
trunk/src/cclib/parser/adfparser.py
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From: <bao...@us...> - 2006-12-08 14:32:57
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Revision: 444
http://svn.sourceforge.net/cclib/?rev=444&view=rev
Author: baoilleach
Date: 2006-12-08 06:32:49 -0800 (Fri, 08 Dec 2006)
Log Message:
-----------
Following from a reply to my question on the GAMESS users list, I've converted the IR intensity units into km/mol.
Modified Paths:
--------------
trunk/src/cclib/parser/gamessparser.py
trunk/src/cclib/parser/utils.py
trunk/test/testvib.py
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From: <bao...@us...> - 2006-12-08 13:58:14
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Revision: 443
http://svn.sourceforge.net/cclib/?rev=443&view=rev
Author: baoilleach
Date: 2006-12-08 05:58:07 -0800 (Fri, 08 Dec 2006)
Log Message:
-----------
New vib tests: Added tests for the values of the highest energy frequency and the maximum ir intensity. All of the programs use the same units (km mol-1) except for GAMESS and PCGAMESS which use weird units which I don't know how to convert. I've asked on the GAMESS users mailing list for help.
Modified Paths:
--------------
trunk/test/testvib.py
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From: <bao...@us...> - 2006-12-08 09:40:05
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Revision: 442
http://svn.sourceforge.net/cclib/?rev=442&view=rev
Author: baoilleach
Date: 2006-12-08 01:40:00 -0800 (Fri, 08 Dec 2006)
Log Message:
-----------
Added vibdisps for Jaguar.
Modified Paths:
--------------
trunk/src/cclib/parser/jaguarparser.py
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From: <ate...@us...> - 2006-12-08 02:05:37
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Revision: 441
http://svn.sourceforge.net/cclib/?rev=441&view=rev
Author: atenderholt
Date: 2006-12-07 18:05:30 -0800 (Thu, 07 Dec 2006)
Log Message:
-----------
ADF parser: Fixed errors that the regression.py script shows. One was related to the "symlist" not having the correct size for a nonsymmetric case because it only printed orbitals 26-45. The second relating to moenergies (references to moenergies when there was only a self.moenergies in the scope).
Modified Paths:
--------------
trunk/src/cclib/parser/adfparser.py
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From: <ate...@us...> - 2006-12-07 18:29:55
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Revision: 440
http://svn.sourceforge.net/cclib/?rev=440&view=rev
Author: atenderholt
Date: 2006-12-07 10:29:42 -0800 (Thu, 07 Dec 2006)
Log Message:
-----------
ADF: Parser fragment information since there isn't a one-to-one correspondence between atoms and fragments
Modified Paths:
--------------
trunk/src/cclib/parser/adfparser.py
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From: <bao...@us...> - 2006-12-07 12:20:30
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Revision: 439
http://svn.sourceforge.net/cclib/?rev=439&view=rev
Author: baoilleach
Date: 2006-12-07 04:20:06 -0800 (Thu, 07 Dec 2006)
Log Message:
-----------
Removed Molpro references as it's all now on a branch.
Modified Paths:
--------------
trunk/src/cclib/parser/__init__.py
trunk/src/cclib/parser/logfileparser.py
trunk/src/cclib/parser/utils.py
trunk/test/testGeoOpt.py
trunk/test/testall.py
Removed Paths:
-------------
trunk/data/Molpro/
trunk/src/cclib/parser/molproparser.py
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From: <bao...@us...> - 2006-12-07 12:09:13
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Revision: 438
http://svn.sourceforge.net/cclib/?rev=438&view=rev
Author: baoilleach
Date: 2006-12-07 04:09:02 -0800 (Thu, 07 Dec 2006)
Log Message:
-----------
Preparation of the Molpro parser branch.
Modified Paths:
--------------
branches/molpro/data/regressionfiles.txt
branches/molpro/setup.py
branches/molpro/src/cclib/parser/__init__.py
branches/molpro/src/cclib/parser/logfileparser.py
branches/molpro/src/cclib/parser/utils.py
branches/molpro/test/testGeoOpt.py
branches/molpro/test/testSP.py
branches/molpro/test/testall.py
branches/molpro/test/testvib.py
Removed Paths:
-------------
branches/molpro/data/ADF/
branches/molpro/data/GAMESS/
branches/molpro/data/GAMESS-UK/
branches/molpro/data/Gaussian/
branches/molpro/data/Jaguar/
branches/molpro/src/cclib/bridge/
branches/molpro/src/cclib/method/
branches/molpro/src/cclib/parser/adfparser.py
branches/molpro/src/cclib/parser/gamessparser.py
branches/molpro/src/cclib/parser/gamessukparser.py
branches/molpro/src/cclib/parser/gaussianparser.py
branches/molpro/src/cclib/parser/jaguarparser.py
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From: <bao...@us...> - 2006-12-05 13:45:34
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Revision: 437
http://svn.sourceforge.net/cclib/?rev=437&view=rev
Author: baoilleach
Date: 2006-12-05 05:45:05 -0800 (Tue, 05 Dec 2006)
Log Message:
-----------
Creating a branch solely for the development of the MOLPRO parser.
Added Paths:
-----------
branches/molpro/
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From: <bao...@us...> - 2006-12-05 09:27:56
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Revision: 436
http://svn.sourceforge.net/cclib/?rev=436&view=rev
Author: baoilleach
Date: 2006-12-05 01:27:51 -0800 (Tue, 05 Dec 2006)
Log Message:
-----------
mocoeffs: Updated for gamessuk and jaguar (to some extent). Needed to update the tests for gamessuk.
Modified Paths:
--------------
trunk/src/cclib/parser/gamessukparser.py
trunk/src/cclib/parser/jaguarparser.py
trunk/test/testSPun.py
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From: <bao...@us...> - 2006-12-05 08:09:36
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Revision: 435
http://svn.sourceforge.net/cclib/?rev=435&view=rev
Author: baoilleach
Date: 2006-12-05 00:09:28 -0800 (Tue, 05 Dec 2006)
Log Message:
-----------
API Change: mocoeffs is now a list of arrays. I've updated the unit tests, and two of the parsers (Gamess, Gaussian).
Modified Paths:
--------------
trunk/src/cclib/parser/gamessparser.py
trunk/src/cclib/parser/gaussianparser.py
trunk/test/testSP.py
trunk/test/testSPun.py
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From: <bao...@us...> - 2006-12-01 13:19:59
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Revision: 434
http://svn.sourceforge.net/cclib/?rev=434&view=rev
Author: baoilleach
Date: 2006-12-01 05:19:48 -0800 (Fri, 01 Dec 2006)
Log Message:
-----------
API updates: In relation to definition of moenergies, fixed testall.py, testSPun.py and jaguarparser.py.
Jaguar: Type of homos array "i" wasn't specified.
TestSP: Now tests a Jaguar6.0 file containing mocoeffs; none of the 4.5 or 6.5 files do.
Modified Paths:
--------------
trunk/src/cclib/parser/jaguarparser.py
trunk/test/testSP.py
trunk/test/testSPun.py
trunk/test/testall.py
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From: <bao...@us...> - 2006-12-01 10:17:31
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Revision: 433
http://svn.sourceforge.net/cclib/?rev=433&view=rev
Author: baoilleach
Date: 2006-12-01 02:17:28 -0800 (Fri, 01 Dec 2006)
Log Message:
-----------
API change moenergies: Changing moenergies from a rank 2 Numeric array to a list of rank 1 arrays. For the ADF moenergies, removed the requirement that it be of length nbasis. Did GAMESS, GAMESSUK, Gaussian, ADF. Jaguar here we come!
Modified Paths:
--------------
trunk/src/cclib/parser/adfparser.py
trunk/src/cclib/parser/gamessparser.py
trunk/src/cclib/parser/gamessukparser.py
trunk/src/cclib/parser/gaussianparser.py
trunk/test/testGeoOpt.py
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From: <bao...@us...> - 2006-11-30 14:06:20
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Revision: 432
http://svn.sourceforge.net/cclib/?rev=432&view=rev
Author: baoilleach
Date: 2006-11-30 06:06:17 -0800 (Thu, 30 Nov 2006)
Log Message:
-----------
Fixed open babel bridge: (1) No longer depends on pyopenbabel. (2) Weird Numeric effects caused SetVector to choke. Needed to convert the coords array to a list using .tolist() before SetVector would accept the parameters.
Modified Paths:
--------------
trunk/src/cclib/bridge/cclib2openbabel.py
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From: <bao...@us...> - 2006-11-29 20:24:59
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Revision: 431
http://svn.sourceforge.net/cclib/?rev=431&view=rev
Author: baoilleach
Date: 2006-11-29 12:24:56 -0800 (Wed, 29 Nov 2006)
Log Message:
-----------
Bug fix for vibfreqs and vibirs GAMESS-UK: Was extracting 59 vibfreqs and vibirs (instead of 54). Fixed.
Modified Paths:
--------------
trunk/src/cclib/parser/gamessukparser.py
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From: <bao...@us...> - 2006-11-29 20:13:38
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Revision: 430
http://svn.sourceforge.net/cclib/?rev=430&view=rev
Author: baoilleach
Date: 2006-11-29 12:13:36 -0800 (Wed, 29 Nov 2006)
Log Message:
-----------
(1) Adding new data to test the ability of GAMESS parser to handle linear molecules
(2) GAMESS parser now removes rotations and translations
(3) Added new tests to testvib.py for various vibration attributes. Note to self: add test to make sure we're all using the same units.
Modified Paths:
--------------
trunk/src/cclib/parser/gamessparser.py
trunk/test/testvib.py
Added Paths:
-----------
trunk/data/GAMESS/basicPCGAMESS/CN_ir.in
trunk/data/GAMESS/basicPCGAMESS/CN_ir.out
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From: <bao...@us...> - 2006-11-29 19:41:34
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Revision: 429
http://svn.sourceforge.net/cclib/?rev=429&view=rev
Author: baoilleach
Date: 2006-11-29 11:41:30 -0800 (Wed, 29 Nov 2006)
Log Message:
-----------
API change: Renamed vibcarts to vibdisps.
Modified Paths:
--------------
trunk/src/cclib/parser/gamessparser.py
trunk/src/cclib/parser/gamessukparser.py
trunk/src/cclib/parser/gaussianparser.py
trunk/src/scripts/ccget
trunk/test/testvib.py
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From: <bao...@us...> - 2006-11-28 15:16:32
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Revision: 428
http://svn.sourceforge.net/cclib/?rev=428&view=rev
Author: baoilleach
Date: 2006-11-28 07:16:11 -0800 (Tue, 28 Nov 2006)
Log Message:
-----------
Added vibcarts to GAMESS-UK: Note to self; need to rename all instances of vibcarts to vibdisps.
Modified Paths:
--------------
trunk/src/cclib/parser/gamessukparser.py
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From: <bao...@us...> - 2006-11-28 15:03:32
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Revision: 427
http://svn.sourceforge.net/cclib/?rev=427&view=rev
Author: baoilleach
Date: 2006-11-28 07:03:22 -0800 (Tue, 28 Nov 2006)
Log Message:
-----------
Bug fix GAMESS-UK: atomnos was not being extracted at all! An empty list was just created.
Modified Paths:
--------------
trunk/src/cclib/parser/gamessukparser.py
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