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Merge pull request #18 from langner/master
Bump v1.3.2 → v1.4
2 parents 59d8622 + 04fbb98 commit abb3932

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‎_sources/attributes.txt‎

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`nocoeffs`_ natural orbital coefficients array of rank 2
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`nooccnos`_ natural orbital occupation numbers array of rank 1
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`optdone`_ flags whether an optimization has converged Boolean
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`optstatus`_ optimization status for each set of atomic coordinates array of rank 1
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`scancoords`_ geometries of each scan step angstroms array of rank 3
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`scanenergies`_ energies of potential energy surface list
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`scannames`_ names of varaibles scanned list of strings
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.. _`nocoeffs`: data_notes.html#nocoeffs
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.. _`nooccnos`: data_notes.html#nooccnos
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.. _`optdone`: data_notes.html#optdone
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.. _`optstatus`: data_notes.html#optstatus
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.. _`scancoords`: data_notes.html#scancoords
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.. _`scanenergies`: data_notes.html#scanenergies
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.. _`scannames`: data_notes.html#scannames

‎_sources/changelog.txt‎

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Changelog
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=========
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Changes since cclib-1.3.2
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-------------------------
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**Feaures**
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* New parser: cclib can now parse DALTON files
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* New parser: cclib can now parse ORCA files
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* New attribute optstatus for status during geometry optimizations and scans
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* Extract atommasses for GAMESS-US (Sagar Gaur)
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* Extract atombasis, gbasis and mocoeffs for QChem
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* Extract gbasis for ORCA (Felix Plasser)
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* Handle multi-step jobs by parsing only the supersystem
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* Improve parsing vibrational symmetries and displacements for Gaussian (mwykes)
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* Improve support for compressed files (mwykes)
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* Improve and update unit test and regression suites
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* Support for Python 3.5
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**Bugfixes**
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* Fix StopIteration crashes for most parsers
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* Fix parsing basis section for Molpro job generated by Avogadro
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* Fix parsing multi-job Gaussian output with different orbitals (Geoff Hutchinson)
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* Fix parsing ORCA geometry optimization with improper internal coordinates (glideht)
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* Fix units in atom corodinates parsed from GAMESS-UK files (mwykes)
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* Fix test for vibrational frequencies in Turbomole (mwykes)
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* Fix parsing vibration symmetries for Molpro (mwykes)
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* Fix parsing egenvectors in GAMESS-US (Alexis Otero-Calvis)
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* Fix duplicate parsing of symmetry labels for Gaussian (Martin Peeks)
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Changes since cclib-1.3.1
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-------------------------
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**Features**
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* New attribute nooccnos for natural orbital occupation numbers
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* Read data from XYZ files using OpenBabel bridge
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* Start basic tests for bridge functionality
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**Bugfixes**
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* Better handling of ONIOM logfiles in Gaussian (Clyde Fare)
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* Fix IR intensity bug in Gaussian parser (Clyde Fare)
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* Fix QChem parser for OpenMP output
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* Fix parsing TDDFT/RPA transitions (Felix Plasser)
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* Fix encoding issues for UTF-8 symbols in parsers and bridges
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Changes since cclib-1.3
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-----------------------
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‎_sources/coverage.txt‎

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‎_sources/coverage_dev.txt‎

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attributes ADF DALTON GAMESS GAMESSUK Gaussian Jaguar Molpro NWChem ORCA Psi QChem
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================= ================= ================= ================= ================= ================= ================= ================= ================= ================= ================= =================
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`aonames`_ N/A T/D √ √ √ √ √ √ √ T/D √
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`aooverlaps`_ √ N/A √ √ √ √ √ √ √ N/P T/D
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`aooverlaps`_ √ T/D √ √ √ √ √ √ √ N/P N/P
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`atombasis`_ T/D √ √ √ √ √ √ √ √ √ √
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`atomcharges`_ √ T/D √ √ √ √ √ √ √ √ √
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`atomcoords`_ √ √ √ √ √ √ √ √ √ √ √
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`etrotats`_ T/D T/D T/D T/D √ T/D T/D T/D T/D T/D T/D
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`etsecs`_ √ √ √ T/D √ √ T/D T/D √ T/D √
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`etsyms`_ √ √ √ T/D √ √ T/D T/D √ T/D √
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`fonames`_ √ T/D N/A N/A N/A N/A N/A N/A N/A N/A N/A
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`fooverlaps`_ √ T/D N/A N/A N/A N/A N/A N/A N/A N/A N/A
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`fragnames`_ √ T/D N/A N/A N/A N/A N/A N/A N/A N/A N/A
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`frags`_ √ T/D N/A N/A N/A N/A N/A N/A N/A N/A N/A
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`fonames`_ √ N/A N/A N/A N/A N/A N/A N/A N/A N/A N/A
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`fooverlaps`_ √ N/A N/A N/A N/A N/A N/A N/A N/A N/A N/A
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`fragnames`_ √ N/A N/A N/A N/A N/A N/A N/A N/A N/A N/A
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`frags`_ √ N/A N/A N/A N/A N/A N/A N/A N/A N/A N/A
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`freeenergy`_ T/D T/D T/D T/D T/D T/D T/D T/D T/D T/D √
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`gbasis`_ T/D √ √ √ √ √ √ √ √ √ √
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`geotargets`_ √ √ √ √ √ √ √ √ √ √ √
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`vibanharms`_ T/D T/D T/D T/D T/D T/D T/D T/D T/D T/D T/D
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`vibdisps`_ √ √ √ √ √ √ √ T/D √ T/D √
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`vibfreqs`_ √ √ √ √ √ √ √ T/D √ T/D √
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`vibirs`_ √ √ √ √ √ √ √ T/D √ T/D √
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`vibirs`_ √ √ √ √ √ √ √ T/D √ N/P √
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`vibramans`_ T/D √ √ √ √ T/D T/D T/D √ T/D √
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`vibsyms`_ T/D √ T/D T/D √ √ √ T/D T/D T/D T/D
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================= ================= ================= ================= ================= ================= ================= ================= ================= ================= ================= =================

‎_sources/data.txt‎

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Description of parsed data
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--------------------------
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Click the attribute name in the table below to go the notes for a particular attribute. All arrays are Numpy arrays of type 'd' (if containing floats) or 'i' (if containing integers).
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Click the attribute name in the table below to go the notes and specifications for a particular attribute. All arrays are Numpy arrays of type 'd' (if containing floats) or 'i' (if containing integers).
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.. include:: attributes.rst
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‎_sources/data_dev.txt‎

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Description of parsed data
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--------------------------
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Click the attribute name in the table below for the specifications for a particular attribute. All arrays are Numpy arrays of type 'd' (if containing floats) or 'i' (if containing integers).
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Click the attribute name in the table below to go to the notes and specifications for a particular attribute. All arrays are Numpy arrays of type 'd' (if containing floats) or 'i' (if containing integers).
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.. include:: attributes_dev.rst
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‎_sources/development.txt‎

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.. _`Travis CI`: https://travis-ci.org/cclib/cclib
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.. |travis_prod| image:: https://travis-ci.org/cclib/cclib.svg?branch=v1.3.2
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.. |travis_prod| image:: https://travis-ci.org/cclib/cclib.svg?branch=v1.4
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.. |travis_master| image:: https://travis-ci.org/cclib/cclib.svg?branch=master
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.. _`data directory`: https://github.com/cclib/cclib/tree/master/test

‎_sources/index.txt‎

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Summary
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-------
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The current version is **cclib 1.3.2** (see the changelog_ for what's new) and parses output files from the following programs (version in parentheses are tested):
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The current version is **cclib 1.4** (see the changelog_ for what's new) and parses output files from the following programs (version in parentheses are tested):
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- ADF_ (versions 2007 and 2013)
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- DALTON_ (versions 2013 and 2015)
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- Firefly_, formerly known as PC GAMESS (version 8.0)
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- `GAMESS (US)`_ (version 2012)
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- `GAMESS-UK`_ (version 7.0)
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- Gaussian_ (versions 03 and 09)
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- Jaguar_ (versions 7.0 and 8.3)
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- Molpro_ (versions 2006 and 2012)
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- NWChem_ (versions 6.0 and 6.5)
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- ORCA_ (versions 2.9 and 3.0)
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- Psi_ (versions 3.4 and 4.0)
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- `Q-Chem`_ (version 4.2)
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Many types of output data are parsed by cclib, including atom coordinates, orbital information, vibrational modes and TD-DFT calculations. See the page on `Extracted Data`_ for a comlete list with coverage for the different programs. Several `calculation methods`_ are also provided for interpreting the electronic properties of molecules.
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How to use cclib
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----------------
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You can download the `source package for cclib 1.3.2`_ or the `current development version`_ (from the `github repository`_). For information on packages available in various Linux distribution, installing the source code and requirements, as well as basic usage, the tutorial_ is a good place to start.
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You can download the `source package for cclib 1.4`_ or the `current development version`_ (from the `GitHub repository`_). For information on packages available in various Linux distributions, installing the source code and requirements, as well as basic usage, the tutorial_ is a good place to start.
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If you need further help, find a bug, need new features or have any question, please send email to the `mailing list`_ or submit an issue to the `tracker`_.
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About cclib
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-----------
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The code behind cclib was started as a collaboration between Noel O'Boyle, Adam Tenderholt and Karol M. Langner (see page about Development_ for details) and is licensed under the LGPL_. Other developers are encouraged to contribute to this open source project -- send an email to the `developers mailing list`_. Applications that use cclib include GaussSum_ and QMForge_.
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The code behind cclib was started as a collaboration between Noel O'Boyle, Adam Tenderholt and Karol M. Langner (see page about Development_ for details) and is licensed under the LGPL_. Other developers are encouraged to contribute to this open source project -- send an email to the `developers mailing list`_. Applications that use cclib include GaussSum_ and QMForge_. It has also been used in the literature_.
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If you use cclib in your scientific work, please support our work by adding a reference to the following article:
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| N\. M\. O'Boyle, A\. L\. Tenderholt, K\. M\. Langner, *cclib: a library for package-independent computational chemistry algorithms*, J. Comp. Chem. 29 (5), pp. 839-845, **2008** (DOI_).
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|
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A record for the latest release is also available on Zenodo_.
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.. _`open source`: http://en.wikipedia.org/wiki/Open_source
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.. _Python: http://www.python.org
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.. _LGPL: http://www.gnu.org/copyleft/lgpl.html
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.. _tutorial: tutorial.html
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.. _development: development.html
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.. _ADF: http://www.scm.com
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.. _ADF: https://www.scm.com/product/adf/
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.. _DALTON: http://daltonprogram.org
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.. _Firefly: http://classic.chem.msu.su/gran/gamess/
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.. _`GAMESS (US)`: http://www.msg.ameslab.gov/GAMESS/GAMESS.html
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.. _`GAMESS-UK`: http://www.cfs.dl.ac.uk
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.. _`Gaussian`: http://www.gaussian.com
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.. _Jaguar: http://www.schrodinger.com/ProductDescription.php?mID=6&sID=9
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.. _Molpro: http://www.molpro.net/
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.. _NWChem: http://www.nwchem-sw.org/index.php/Main_Page
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.. _ORCA: http://www.thch.uni-bonn.de/tc/orca/
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.. _Psi: http://psicode.org/
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.. _`Q-Chem`: http://q-chem.com/
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.. _`source package for cclib 1.3.2`: https://github.com/cclib/cclib/releases/download/v1.3.2/cclib-1.3.2.zip
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.. _`source package for cclib 1.4`: https://github.com/cclib/cclib/releases/download/v1.4/cclib-1.4.zip
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.. _`current development version`: https://github.com/cclib/cclib/archive/master.zip
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.. _`github repository`: https://github.com/cclib/cclib
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.. _`GitHub repository`: https://github.com/cclib/cclib
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.. _`mailing list`: https://lists.sourceforge.net/lists/listinfo/cclib-users
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.. _`developers mailing list`: https://lists.sourceforge.net/lists/listinfo/cclib-devel
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.. _`tracker`: https://github.com/cclib/cclib/issues
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.. _GaussSum: http://gausssum.sourceforge.net/
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.. _QMForge: http://qmforge.sourceforge.net/
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.. _literature: http://pubs.acs.org/doi/abs/10.1021/jacs.5b05600
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.. _DOI: http://dx.doi.org/10.1002/jcc.20823
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.. _Zenodo: http://dx.doi.org/10.5281/zenodo.44552

‎_sources/tutorial.txt‎

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Manual download and install
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The source code of the newest release of cclib (version 1.3.2) is distributed as:
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* A .zip file: https://github.com/cclib/cclib/releases/download/v1.3.2/cclib-1.3.2.zip
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* A .tar.gz file: https://github.com/cclib/cclib/releases/download/v1.3.2/cclib-1.3.2.tar.gz
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The source code of the newest release of cclib (version 1.4) is distributed as:
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* A .zip file: https://github.com/cclib/cclib/releases/download/v1.4/cclib-1.4.zip
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* A .tar.gz file: https://github.com/cclib/cclib/releases/download/v1.4/cclib-1.4.tar.gz
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* Windows binary installers (see the `newest release page`_)
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.. _`newest release page`: https://github.com/cclib/cclib/releases/tag/v1.3.2
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.. _`newest release page`: https://github.com/cclib/cclib/releases/tag/v1.4
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What next?
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