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From: <la...@us...> - 2007-01-29 17:24:09
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Revision: 476
http://svn.sourceforge.net/cclib/?rev=476&view=rev
Author: langner
Date: 2007-01-29 09:23:47 -0800 (Mon, 29 Jan 2007)
Log Message:
-----------
Added test code for mpenergies for GAMESS and Gaussian (based on fiel from baoilleach), minor additions to the respective parsers (converting attributes to arrays).
Modified Paths:
--------------
trunk/src/cclib/parser/gamessparser.py
trunk/src/cclib/parser/gaussianparser.py
trunk/test/testall.py
Added Paths:
-----------
trunk/test/testMP.py
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From: <ate...@us...> - 2007-01-26 05:55:55
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Revision: 475
http://svn.sourceforge.net/cclib/?rev=475&view=rev
Author: atenderholt
Date: 2007-01-25 21:55:53 -0800 (Thu, 25 Jan 2007)
Log Message:
-----------
CDA method: Added progress support; the method is a bit slow with molecules larger than BH3CO and i'm guessing it can be sped up with some Numeric tricks
Modified Paths:
--------------
trunk/src/cclib/method/cda.py
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From: <la...@us...> - 2007-01-25 16:19:27
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Revision: 474
http://svn.sourceforge.net/cclib/?rev=474&view=rev
Author: langner
Date: 2007-01-25 08:19:25 -0800 (Thu, 25 Jan 2007)
Log Message:
-----------
Reversed shape of mpenergies in GAMESS and Gaussian parsers.
Modified Paths:
--------------
trunk/src/cclib/parser/gamessparser.py
trunk/src/cclib/parser/gaussianparser.py
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From: <bao...@us...> - 2007-01-25 13:29:19
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Revision: 473
http://svn.sourceforge.net/cclib/?rev=473&view=rev
Author: baoilleach
Date: 2007-01-25 05:29:16 -0800 (Thu, 25 Jan 2007)
Log Message:
-----------
Volume: Now can create a Cube file, as well as a VTK file. Just run volume.py to test (dependencies: psyco, PyQuante, pyvtk).
convertor: Added Ang-->bohr conversion
Modified Paths:
--------------
trunk/src/cclib/method/volume.py
trunk/src/cclib/parser/utils.py
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From: <ate...@us...> - 2007-01-24 22:29:50
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Revision: 472
http://svn.sourceforge.net/cclib/?rev=472&view=rev
Author: atenderholt
Date: 2007-01-24 14:29:48 -0800 (Wed, 24 Jan 2007)
Log Message:
-----------
CDA and FragmentAnalysis: check to make sure atoms actually line up (otherwise results are meaningless), and if not, log and error and return false; make sure cda script checks for True before printing results
Modified Paths:
--------------
trunk/src/cclib/method/cda.py
trunk/src/cclib/method/fragments.py
trunk/src/scripts/cda
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From: <la...@us...> - 2007-01-24 21:59:34
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Revision: 471
http://svn.sourceforge.net/cclib/?rev=471&view=rev
Author: langner
Date: 2007-01-24 13:59:30 -0800 (Wed, 24 Jan 2007)
Log Message:
-----------
Added MP2 test for GAMESS; generalized mp2energies attribute to mpenergies; support for MP2 through MP5 for Gaussian.
Modified Paths:
--------------
trunk/src/cclib/parser/gamessparser.py
trunk/src/cclib/parser/gaussianparser.py
trunk/src/cclib/parser/logfileparser.py
Added Paths:
-----------
trunk/data/GAMESS/basicGAMESS-US/water_mp2.inp
trunk/data/GAMESS/basicGAMESS-US/water_mp2.out
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From: <ate...@us...> - 2007-01-24 21:27:02
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Revision: 470
http://svn.sourceforge.net/cclib/?rev=470&view=rev
Author: atenderholt
Date: 2007-01-24 13:26:59 -0800 (Wed, 24 Jan 2007)
Log Message:
-----------
CDA script: minor bug fix
Modified Paths:
--------------
trunk/src/scripts/cda
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From: <ate...@us...> - 2007-01-24 19:21:44
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Revision: 469
http://svn.sourceforge.net/cclib/?rev=469&view=rev
Author: atenderholt
Date: 2007-01-24 11:21:21 -0800 (Wed, 24 Jan 2007)
Log Message:
-----------
CDA script: Minor bug and nicety fixes, and added it to the setup.py script
Modified Paths:
--------------
trunk/setup.py
trunk/src/scripts/cda
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From: <ate...@us...> - 2007-01-24 19:06:54
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Revision: 468
http://svn.sourceforge.net/cclib/?rev=468&view=rev
Author: atenderholt
Date: 2007-01-24 11:06:52 -0800 (Wed, 24 Jan 2007)
Log Message:
-----------
Added a script to determine CDA; input takes three files: molecule, fragment 1, fragment 2 and returns the donation, backdonation, and repulsion terms for each MO, as well as a total giving the number of "electrons" transfered. Error checking on the command line still needs to be implemented.
Added Paths:
-----------
trunk/src/scripts/cda
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From: <la...@us...> - 2007-01-24 18:00:48
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Revision: 467
http://svn.sourceforge.net/cclib/?rev=467&view=rev
Author: langner
Date: 2007-01-24 10:00:37 -0800 (Wed, 24 Jan 2007)
Log Message:
-----------
LogFile docstring: changed units for scfenergies to eV, added units for vibirs and vibramans
Modified Paths:
--------------
trunk/src/cclib/parser/logfileparser.py
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From: <bao...@us...> - 2007-01-24 11:36:53
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Revision: 466
http://svn.sourceforge.net/cclib/?rev=466&view=rev
Author: baoilleach
Date: 2007-01-24 03:36:48 -0800 (Wed, 24 Jan 2007)
Log Message:
-----------
data: Gaussian example files for MPx calculations.
Added Paths:
-----------
trunk/data/Gaussian/basicGaussian03/water_mp2.com
trunk/data/Gaussian/basicGaussian03/water_mp2.log
trunk/data/Gaussian/basicGaussian03/water_mp3.com
trunk/data/Gaussian/basicGaussian03/water_mp3.log
trunk/data/Gaussian/basicGaussian03/water_mp4.com
trunk/data/Gaussian/basicGaussian03/water_mp4.log
trunk/data/Gaussian/basicGaussian03/water_mp5.com
trunk/data/Gaussian/basicGaussian03/water_mp5.log
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From: <ate...@us...> - 2007-01-23 19:02:24
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Revision: 465
http://svn.sourceforge.net/cclib/?rev=465&view=rev
Author: atenderholt
Date: 2007-01-23 11:02:19 -0800 (Tue, 23 Jan 2007)
Log Message:
-----------
CDA method: Add to the __init__.py function so it is exposed under cclib.method
Modified Paths:
--------------
trunk/src/cclib/method/__init__.py
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From: <ate...@us...> - 2007-01-23 02:53:23
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Revision: 464
http://svn.sourceforge.net/cclib/?rev=464&view=rev
Author: atenderholt
Date: 2007-01-22 18:53:16 -0800 (Mon, 22 Jan 2007)
Log Message:
-----------
CDA: moved debugging info out of the calculate function and into main
Modified Paths:
--------------
trunk/src/cclib/method/cda.py
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From: <ate...@us...> - 2007-01-23 02:36:12
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Revision: 463
http://svn.sourceforge.net/cclib/?rev=463&view=rev
Author: atenderholt
Date: 2007-01-22 18:36:08 -0800 (Mon, 22 Jan 2007)
Log Message:
-----------
Initial work on CDA, tested against Frenking's CDA using (BH3)(CO); works although off by a factor of two; emailing Frenking
Added Paths:
-----------
trunk/src/cclib/method/cda.py
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From: <ate...@us...> - 2007-01-22 21:59:41
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Revision: 462
http://svn.sourceforge.net/cclib/?rev=462&view=rev
Author: atenderholt
Date: 2007-01-22 13:59:29 -0800 (Mon, 22 Jan 2007)
Log Message:
-----------
Logfile baseclass: minor bug fix from adding Karol's MP2energies changes
Modified Paths:
--------------
trunk/src/cclib/parser/logfileparser.py
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From: <ate...@us...> - 2007-01-22 21:56:33
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Revision: 461
http://svn.sourceforge.net/cclib/?rev=461&view=rev
Author: atenderholt
Date: 2007-01-22 13:56:31 -0800 (Mon, 22 Jan 2007)
Log Message:
-----------
Updating the logfile baseclass to support MP2 energies (from Karol Langner)
Modified Paths:
--------------
trunk/src/cclib/parser/logfileparser.py
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From: <ate...@us...> - 2007-01-22 21:55:57
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Revision: 460
http://svn.sourceforge.net/cclib/?rev=460&view=rev
Author: atenderholt
Date: 2007-01-22 13:55:49 -0800 (Mon, 22 Jan 2007)
Log Message:
-----------
Adding support for parsing MP2 energies to the Gaussian parser (from Karol Langner)
Modified Paths:
--------------
trunk/src/cclib/parser/gaussianparser.py
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From: <ate...@us...> - 2007-01-22 21:55:02
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Revision: 459
http://svn.sourceforge.net/cclib/?rev=459&view=rev
Author: atenderholt
Date: 2007-01-22 13:54:58 -0800 (Mon, 22 Jan 2007)
Log Message:
-----------
Update the GAMESS parser to include support for parsing MP2 energies (from Karol Langner)
Modified Paths:
--------------
trunk/src/cclib/parser/gamessparser.py
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From: <bao...@us...> - 2007-01-19 14:23:25
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Revision: 458
http://svn.sourceforge.net/cclib/?rev=458&view=rev
Author: baoilleach
Date: 2007-01-19 06:23:23 -0800 (Fri, 19 Jan 2007)
Log Message:
-----------
Bugfix to volume.py: At least you can install cclib now.
Modified Paths:
--------------
trunk/src/cclib/method/volume.py
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From: <bao...@us...> - 2007-01-19 08:49:46
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Revision: 457
http://svn.sourceforge.net/cclib/?rev=457&view=rev
Author: baoilleach
Date: 2007-01-19 00:49:45 -0800 (Fri, 19 Jan 2007)
Log Message:
-----------
Volume.py: Adding support for unrestricted calcs, and generally getting it into better shape.
Modified Paths:
--------------
trunk/src/cclib/method/volume.py
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From: <ate...@us...> - 2007-01-02 20:12:20
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Revision: 456
http://svn.sourceforge.net/cclib/?rev=456&view=rev
Author: atenderholt
Date: 2007-01-02 12:12:14 -0800 (Tue, 02 Jan 2007)
Log Message:
-----------
Added some data files for looking at CDA
Added Paths:
-----------
trunk/data/Gaussian/CDA/
trunk/data/Gaussian/CDA/BH3.log
trunk/data/Gaussian/CDA/BH3CO-sp.log
trunk/data/Gaussian/CDA/CO.log
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From: <ate...@us...> - 2006-12-23 18:10:56
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Revision: 455
http://svn.sourceforge.net/cclib/?rev=455&view=rev
Author: atenderholt
Date: 2006-12-23 10:10:54 -0800 (Sat, 23 Dec 2006)
Log Message:
-----------
FragmentAnalysis: Work on unrestricted calcs; make assumption that if molecule is an unrestricted calc, that some of the fragments may be unrestricted. When building up the sum matrix, check to see if the fragment is unrestricted; if so, use the appropriate mocoeffs (0 or 1 depending on whether the alpha or beta sum matrix is being built). Also, if the molecule is unrestricted, create the fooverlaps2 matrix as the overlaps between alpha and beta fragment MOs should be different.
Modified Paths:
--------------
trunk/src/cclib/method/fragments.py
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From: <ate...@us...> - 2006-12-23 06:28:59
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Revision: 454
http://svn.sourceforge.net/cclib/?rev=454&view=rev
Author: atenderholt
Date: 2006-12-22 22:28:58 -0800 (Fri, 22 Dec 2006)
Log Message:
-----------
FragmentAnalysis: When creating fonames, use MO index+1 as the label to better reflect the current standard of labels starting at 1 (ie 1s as opposed to 0s) while matrix indexes start at 0.
Modified Paths:
--------------
trunk/src/cclib/method/fragments.py
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From: <ate...@us...> - 2006-12-23 05:58:33
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Revision: 453
http://svn.sourceforge.net/cclib/?rev=453&view=rev
Author: atenderholt
Date: 2006-12-22 21:58:31 -0800 (Fri, 22 Dec 2006)
Log Message:
-----------
FragmentAnalysis: convert aooverlaps into new molecular basis, resulting in the fooverlaps attribute; also has to update MPA to typecase a double into a float
Modified Paths:
--------------
trunk/src/cclib/method/fragments.py
trunk/src/cclib/method/mpa.py
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From: <ate...@us...> - 2006-12-23 05:46:18
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Revision: 452
http://svn.sourceforge.net/cclib/?rev=452&view=rev
Author: atenderholt
Date: 2006-12-22 21:46:13 -0800 (Fri, 22 Dec 2006)
Log Message:
-----------
FragmentAnalysis method: added some logging info and extended to work on unrestricted molecule with restricted fragments (although untested)
Modified Paths:
--------------
trunk/src/cclib/method/fragments.py
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