CVS commit: wip/py-cclib

To: pkgsrc-wip-cvs%lists.sourceforge.net@localhost
Subject: CVS commit: wip/py-cclib
From: "Kamel Ibn Aziz Derouiche" <jihbed%users.sourceforge.net@localhost>
Date: Wed, 10 Jun 2015 22:11:26 +0000
Module name:	wip
Committed by:	jihbed
Date:		Wed Jun 10 22:11:10 UTC 2015

Modified Files:
	wip/py-cclib: Makefile PLIST distinfo
Added Files:
	wip/py-cclib/patches: patch-setup.py
Removed Files:
	wip/py-cclib/patches: patch-aa

Log Message:

	Changes since cclib-1.2:

Features:
    * New parser: cclib can now parse NWChem files
    * New parser: cclib can now parse Psi (versions 3 and 4) files
    * New parser: cclib can now parse QChem files (by Eric Berquist)
    * New method: Nuclear (currently calculates the repulsion energy)
    * Handle Gaussian basis set output with GFPRINT keyword
    * Attribute optdone reverted to single Boolean value by default
    * Add --verbose and --future options to ccget and parsers
    * Replaced PC-GAMESS test files with newer Firefly versions
    * Updated test file versions to GAMESS-UK 8.0

Bugfixes:
    * Handle GAMESS-US file with LZ value analysis (Martin Rahm)
    * Handle Gaussian jobs with stars in output (Russell Johnson, NIST)
    * Handle ORCA singlet-only TD calculations (May A.)
    * Fix parsing of Gaussian jobs with fragments and ONIOM output
    * Use UTF-8 encodings for files that need them (Matt Ernst)

Changes since cclib-1.1:

Features:
    * Move project to github
    * Transition to Python 3 (Python 2.7 will still work)
    * Add a multifile mode to ccget script
    * Extract vibrational displacements for ORCA
    * Extract natural atom charges for Gaussian (Fedor Zhuravlev)
    * New attribute optdone flags converged geometry optimization
    * Updated test file versions to ADF2013.01, GAMESS-US 2012,
    Gaussian09, Molpro 2012 and ORCA 3.0.1

Bugfixes:
    * Ignore unicode errors in logfiles
    * Handle Guassian jobs with terse output (basis set count not reported)
    * Handle Gaussian jobs using IndoGuess (Scott McKechnie)
    * Handle Gaussian file with irregular ONION gradients  (Tamilmani S)
    * Handle ORCA file with SCF convergence issue (Melchor Sanchez)
    * Handle Gaussian file with problematic IRC output (Clyde Fare)
    * Handle ORCA file with AM1 output (Julien Id?)
    * Handle GAMESS-US output with irregular frequency format (Andrew Warden)

Changes since cclib-1.0.1:

Features:
	* Add progress info for all parsers
	* Support ONIOM calculations in Gaussian (Karen Hemelsoet)
	* New attribute atomcharges extracts Mulliken and Lowdin atomic
	charges if present
	* New attribute atomspins extracts Mulliken and Lowdin atomic spin
	densities if present
	* New thermodynamic attributes: freeenergy, temperature, enthalpy
	(Edward	Holland)
	* Extract PES information: scanenergies, scancoords, scanparm, scannames
	(Edward Holland)

Bugfixes:
	* Handle coupled cluster energies in Gaussian 09 (Bj?rn Dahlgren)
	* Vibrational displacement vectors missing for Gaussian 09 (Bj?rn
	Dahlgren)
	* Fix problem parsing vibrational frequencies in some GAMESS-US files
	* Fix missing final scfenergy in ADF geometry optimisations
	* Fix missing final scfenergy for ORCA where a specific number of SCF
	cycles has been specified
	* ORCA scfenergies not parsed if COSMO solvent effects included
	* Allow spin unrestricted calculations to use the fragment MO overlaps
	correctly for the MPA and CDA calculations
	* Handle Gaussian MO energies that are printed as a row of asterisks
	(Jerome Kieffer)
	* Add more explicit license notices, and allow LGPL versions after 2.1
	* Support Firefly calculations where nmo != nbasis (Pavel Solntsev)
	* Fix problem parsing vibrational frequency information in recent
	GAMESS (US) files (Chengju Wang)
	* Apply patch from Chengju Wang to handle GAMESS calculations with more
	than 99 atoms
	* Handle Gaussian files with more than 99 atoms having pseudopotentials
	(Bj?rn Baumeier)

Changes since cclib-1.0:

Features:
	* New attribute atommasses - atomic masses in Dalton
	* Added support for Gaussian geometry optimisations that change
	the number of linearly independent basis functions over the
	course of the calculation

Bugfixes:
	* Handle triplet PM3 calculations in Gaussian03 (Greg Magoon)
	* Some Gaussian09 calculations were missing atomnos (Marius Retegan)
	* Handle multiple pseudopotentials in Gaussian03 (Tiago Silva)
	* Handle Gaussian calculations with >999 basis functions
	* ADF versions > 2007 no longer print overlap info by default
	* Handle parsing Firefly calculations that fail
	* Fix parsing of ORCA calculation (Marius Retegan)

Change since cclib-0.9:

Features:
	* Handle PBC calculations from Gaussian
	* Updates to handle Gaussian09
	* Support TDDFT calculations from ADF
	* A number of improvements for GAMESS support
	* ccopen now supports any file-like object with a read() method, so it
	can parse across HTTP

Bugfixes:
	* Many many additional files parsed thanks to bugs reported by users

Change since cclib-0.8:

Features:
	* New parser: cclib can now parse ORCA files
	* Added option to use setuptools instead of distutils.core for installing
	* Improved handling of CI and TD-DFT data: TD-DFT data extracted from
	GAMESS and etsecs standardised across all parsers
	* Test suite changed to include output from only the newest program versions

Bugfixes:
	* A small number of parsing errors were fixed

Change since cclib-0.7:

Features:
	* New parser: cclib can now parse Molpro files
	* Separation of parser and data objects: Parsed data is now returned
	as a ccData object that can be pickled, and converted to and from JSON
	* Parsers: multiple files can be parsed with one parse command
	* NumPy support: Dropped Numeric support in favour of NumPy
	* API addition: 'charge' for molecular charge
	* API addition: 'mult' for spin multiplicity
	* API addition: 'atombasis' for indices of atom orbitals on each atom
	* API addition: 'nocoeffs' for Natural Orbital (NO) coefficients
	* GAMESS-US parser: added 'etoscs' (CIS calculations)
	* Jaguar parser: added 'mpenergies' (LMP2 calcualtions)
	* Jaguar parser: added 'etenergies' and 'etoscs' (CIS calculations)
	* New method: Lowdin Population Analysis (LPA)
	* Tests: unittests can be run from the Python interpreter, and for
	a single parser; the number of "passed" tests is also counted and shown

Bugfixes:
	* Several parsing errors were fixed
	* Fixed some methods to work with different numbers of alpha and beta
	MO coefficients in mocoeffs (MPA, CSPA, OPA)

Changes since cclib-0.6.1:

Features:
	* New parser: cclib can now parse Jaguar files
	* ccopen: Can handle log files which have been compressed into .zip,
	.bz2 or .gz files.
	* API addition: 'gbasis' holds the Gaussian basis set
	* API addition: 'coreelectrons' contains the number of core electrons
	in each atom's pseudopotential
	* API addition: 'mpenergies' holds the Moller-Plesset corrected
	molecular electronic energies
	* API addition: 'vibdisps' holds the Cartesian displacement vectors
	* API change: 'mocoeffs' is now a list of rank 2 arrays, rather than a
	rank 3 array
	* API change: 'moenergies' is now a list of rank 1 arrays, rather than
	rank 2 array
	* GAMESS-UK parser: added 'vibramans'
	* New method: Charge Decomposition Analysis (CDA) for studying
	electron donation, back donation, and repulsion between fragments
	in a molecule
	* New method: Fragment Analysis for studing bonding interactions 
	between two or more fragments in a molecule
	* New method: Ability to calculate the electron density or
	wavefunction

Bugfixes:
	* GAMESS parser:
		Failed to parse frequency calculation with imaginary frequencies
		Rotations and translations now not included in frequencies
		Failed to parse a DFT calculation
	* GAMESS-UK parser:
		'atomnos' not being extracted
		Rotations and translations now not included in frequencies
	* bridge to OpenBabel: No longer dependent on pyopenbabel

Changes since cclib-0.6.0:

Bugfixes:
	* cclib: The "import cclib.parsers" statement failed due to
	references to Molpro and Jaguar parsers which are not present
	* Gaussian parser: Failed to parse single point calculations
	where the input coords are a z-matrix, and symmetry is turned off.

Changes since cclib-0.6b:

Features
	* ADF parser: If some MO eigenvalues are not present, the parser
	does not fail, but uses values of 99999 instead and A symmetry

Bugfixes
	* ADF parser: The following bugs have been fixed
	P/D orbitals for single atoms not handled correctly
	Problem parsing homos in unrestricted calculations
	Problem skipping the Create sections in certain calculations  
	* Gaussian parser: The following bugs have been fixed
	Parser failed if standard orientation not found
	* ccget: aooverlaps not included when using --list option

Changes since cclib-0.5:

Features
	* New parser: GAMESS-UK parser
	* API addition: the .clean() method
	  The .clean() method of a parser clears all of the parsed
	  attributes. This is useful if you need to reparse during
	  the course of a calculation.
	* Function rename: guesstype() has been renamed to ccopen()
	* Speed up: Calculation of Overlap Density of States has
	  been sped up by two orders of magnitude

Bugfixes
	* ccget: Passing multiple filenames now works on Windows too
	* ADF parser: The following bugs have been fixed
	  Problem with parsing SFOs in certain log files
	  Handling of molecules with orbitals of E symmetry
	  Couldn't find the HOMO in log files from new versions of ADF
	  Parser used to miss attributes if SCF not converged
	  For a symmetrical molecule, mocoeffs were in the wrong order and
	  the homo was not identified correctly if degenerate
	* Gaussian parser: The following bugs have been fixed
	  SCF values was not extracting the dEnergy value
	  Was extracting Depolar P instead of Raman activity
	* ccopen: Minor problems fixed with identification of log files

Changes since cclib-0.5b:

Features
	* src/scripts/ccget: Added handling of multiple filenames.
	  
	  It's now possible to use ccget as follows:
	  ccget *.log
	  
	  This is a good way of checking out whether cclib is able to
	  parse all of the files in a given directory.
	  
	  Also possible is:
	  ccget homos *.log

	* Change of license: Changed license from GPL to LGPL

Bugfixes
	* src/cclib/parser/gamessparser.py: Bugfix: gamessparser was dying
	  on GAMESS VERSION = 12 DEC 2003 gopts, as it was unable to parse
	  the scftargets.
	* src/cclib/parser/gamessparser.py: Remove assertion to catch
	  instances where scftargets is unset. This occurs in the case of
	  failed calculations (e.g. wrong multiplicity).
	* src/cclib/parser/adfparser.py: Fixed one of the errors with the
	  Mo5Obdt2-c2v-opt.adfout example, which had to do with the SFOs
	  being made of more than two combinations of atoms (4, because of
	  rotation in c2v point group).
	  
	  At least one error is still present with atomcoords. It looks
	  like non-coordinate integers are being parsed as well, which
	  makes some of the atomcoords list have more than the 3 values
	  for x,y,z.
	* src/cclib/parser/adfparser.py: Hopefully fixed the last error in
	  Mo5Obdt2-c2v-opt. Problem was that it was adding
	  line.split()[5:], but sometimes there was more than 3 fields
	  left, so it was changed to [5:8]. Need to check actual parsed
	  values to make sure it is parsed correctly.
	* data/Gaussian, logfiledist, src/cclib/parser/gaussianparser.py,
	  test/regression.py: Bug fix: Mo4OSibdt2-opt.log has no
	  atomcoords despite being a geo-opt. This was due to the fact
	  that the parser was extracting "Input orientation" and not
	  "Standard orientation". It's now changed to "Standard
	  orientation" which works for all of the files in the repository.


To generate a diff of this commit:
cvs -z3 rdiff -u -r0 -r1.1 wip/py-cclib/patches/patch-setup.py
cvs -z3 rdiff -u -r1.1.1.1 -r0 wip/py-cclib/patches/patch-aa
cvs -z3 rdiff -u -r1.1.1.1 -r1.2 wip/py-cclib/distinfo
cvs -z3 rdiff -u -r1.2 -r1.3 wip/py-cclib/PLIST
cvs -z3 rdiff -u -r1.3 -r1.4 wip/py-cclib/Makefile

To view a diff of this commit:
http://pkgsrc-wip.cvs.sourceforge.net/pkgsrc-wip/wip/py-cclib/patches/patch-setup.py?r1=0&r2=1.1
http://pkgsrc-wip.cvs.sourceforge.net/pkgsrc-wip/wip/py-cclib/patches/patch-aa?r1=1.1.1.1&r2=0
http://pkgsrc-wip.cvs.sourceforge.net/pkgsrc-wip/wip/py-cclib/distinfo?r1=1.1.1.1&r2=1.2
http://pkgsrc-wip.cvs.sourceforge.net/pkgsrc-wip/wip/py-cclib/PLIST?r1=1.2&r2=1.3
http://pkgsrc-wip.cvs.sourceforge.net/pkgsrc-wip/wip/py-cclib/Makefile?r1=1.3&r2=1.4

Please note that diffs are not public domain; they are subject to the
copyright notices on the relevant files.

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