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Changes in cclib-1.5.3
Features:
* New attribute transprop for electronic transitions (Jonathon Vandezande)
* Support grads attribute in Psi4 (Adam Abbott)
* Support grads attribute in Molpro (Oskar Weser)
* Support optstatus for IRCs and in Psi4 (Emmanuel LaTruelle)
* Updated test file versions to Gaussian16 (Andrew S. Rosen)
* Add ability to write XYZ coordinates for arbitrary indices
Bugfixes:
* Fixed ccwrite script and added unit tests (Georgy Frolov)
* Fixed closed shell determination for Gaussian (Jaime Rodríguez-Guerra)
* Fixed parsing of natom for >9999 atoms in Gaussian (Jaime Rodríguez-Guerra)
* Fixed parsing of ADF jobs with no title
* Fixed parsing of charge and core electrons when usin ECPs in QChem
* Fixed parsing of scfvalues for malformed output in Gaussian
Changes in cclib-1.5.2:
Features:
* Support for writing Molden and WFX files (Sagar Gaur)
* Support for thermochesmitry attributes in ORCA (Jonathon Vandezande)
* Support for chelpg atomic charges in ORCA (Richard Gowers)
* Updated test file versions to GAMESS-US 2017 (Sagar Gaur)
* Added option to print full arrays with ccget (Sagar Gaur)
Bugfixes:
* Fxied polarizability parsing bug in DALTON (Maxim Stolyarchuk)
* Fixed IRC parsing in Gaussian for large trajectories (Dénes Berta, LaTruelle)
* Fixed coordinate parsing for heavy elements in ORCA (Jonathon Vandezande)
* Fixed parsing of large mocoeffs in fixed width format for QChem (srtlg)
* Fixed parsing of large polarizabilities in fixed width format for DALTON (Maxim Stolyarchuk)
* Fixed parsing molecular orbitals when there are more than basis set functions in QChem
Changes in cclib-1.5.1:
Features:
* New attribute polarizabilities for static or dynamic dipole polarizability
* New attribute pressure for thermochemistry (renpj)
* Add property to detect closed shells in parsed data
* Handle RPA excited state calculation in ORCA, in addition to TDA
* Support for Python 3.6
Bugfixes:
* Restore alias cclib.parser.ccopen for backwards compatibility
* Fixed parsing thermochemistry for single atoms in QChem
* Fixed handling of URLs (Alexey Alnatanov)
* Fixed Atom object creation in biopython bridge (Nitish Garg)
* Fixed ccopen when working with multiple files
Changes in cclib-1.5:
Features:
* Support for both reading and writing CJSON (Sanjeed Schamnad)
* New parser: cclib can now parse MOPAC files (Geoff Hutchison)
* New attribute time tracks coordinates for dynamics jobs (Ramon Crehuet)
* New attribute metadata holds miscellaneous information not in other attributes (bwang2453)
* Extract moments attribute for Gaussian (Geoff Hutchison)
* Extract atombasis for ADF in simple cases (Felix Plaser)
* License change to BSD 3-Clause License
Bugfixes:
* Correct parsing of several attributes for ROHF calculations
* Fixed precision of scfvalues in ORCA
* Fixed MO parsing from older versions of Firefly (mkrompiec)
Changes in cclib-1.4.1:
Features:
* Preliminary support for writing CJSON (Sanjeed Schamnad)
* Tentative support for BOMD trajectories in Gaussian (Ramon Crehuet)
* Support for atombasis in ADF (Felix Plasser)
* Support for nocoeffs and nooccnos in Molpro
Bugfixes:
* Fix for non-standard basis sets in DALTON
* Fix for non-standard MO coefficient printin in GAMESS
Changes in cclib-1.4:
Features:
* New parser: cclib can now parse DALTON files
* New parser: cclib can now parse ORCA files
* New attribute optstatus for status during geometry optimizations and scans
* Extract atommasses for GAMESS-US (Sagar Gaur)
* Extract atombasis, gbasis and mocoeffs for QChem
* Extract gbasis for ORCA (Felix Plasser)
* Handle multi-step jobs by parsing only the supersystem
* Improve parsing vibrational symmetries and displacements for Gaussian (mwykes)
* Improve support for compressed files (mwykes)
* Improve and update unit test and regression suites
* Support for Python 3.5
Bugfixes:
* Fix StopIteration crashes for most parsers
* Fix parsing basis section for Molpro job generated by Avogadro
* Fix parsing multi-job Gaussian output with different orbitals (Geoff Hutchinson)
* Fix parsing ORCA geometry optimization with improper internal coordinates (glideht)
* Fix units in atom corodinates parsed from GAMESS-UK files (mwykes)
* Fix test for vibrational frequencies in Turbomole (mwykes)
* Fix parsing vibration symmetries for Molpro (mwykes)
* Fix parsing egenvectors in GAMESS-US (Alexis Otero-Calvis)
* Fix duplicate parsing of symmetry labels for Gaussian (Martin Peeks)
Changes in cclib-1.3.1:
Features:
* New attribute nooccnos for natural orbital occupation numbers
* Read data from XYZ files using OpenBabel bridge
* Start basic tests for bridge functionality
Bugfixes:
* Better handling of ONIOM logfiles in Gaussian (Clyde Fare)
* Fix IR intensity bug in Gaussian parser (Clyde Fare)
* Fix QChem parser for OpenMP output
* Fix parsing TDDFT/RPA transitions (Felix Plasser)
* Fix encoding issues for UTF-8 symbols in parsers and bridges
Changes in cclib-1.3:
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 in cclib-1.2:
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 Idé)
* Handle GAMESS-US output with irregular frequency format (Andrew Warden)
Changes in cclib-1.1:
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 (Björn Dahlgren)
* Vibrational displacement vectors missing for Gaussian 09 (Björn
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
(Björn Baumeier)
Changes in cclib-1.0.1:
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)
Changes in cclib-1.0:
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
Changes in cclib-0.9:
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
Changes in cclib-0.8:
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 in cclib-0.7:
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 in cclib-0.6.1:
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 in cclib-0.6:
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 in cclib-0.6b:
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 in cclib-0.5:
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.