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Merge pull request #205 from pierrelb/PM6
Adding PM6 and PM7 methods to the Quantum Mechanics thermo calculations. There's an extra option in the input file to select the method. This also closes #204. We may want more options in the future, but that's a new issue.
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‎documentation/source/reference/index.rst‎

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:mod:`rmgpy.kinetics` Kinetics models of chemical reaction rates
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:mod:`rmgpy.molecule` Molecular representations using chemical graph theory
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:mod:`rmgpy.pdep` Pressure-dependent kinetics from master equation models
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:mod:`rmgpy.qm` On-the-fly quantum calculations
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:mod:`rmgpy.quantity` Physical quantities and unit conversions
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:mod:`rmgpy.reaction` Chemical reactions
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:mod:`rmgpy.rmg` Automatic reaction mechanism generation
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kinetics/index
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molecule/index
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pdep/index
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qm/index
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quantity/index
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reaction/index
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rmg/index

‎documentation/source/reference/qm/gaussian.rst‎

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***********************
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rmgpy.qm.gaussian
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***********************
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.. autoclass:: rmgpy.qm.gaussian.Gaussian
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.. autoclass:: rmgpy.qm.gaussian.GaussianMol
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.. autoclass:: rmgpy.qm.gaussian.GaussianMolPM3
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.. autoclass:: rmgpy.qm.gaussian.GaussianMolPM6

‎documentation/source/reference/qm/index.rst‎

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*************************************************
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QMTP (:mod:`rmgpy.qm`)
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*************************************************
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.. module:: rmgpy.qm
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The :mod:`rmgpy.qm` subpackage contains classes and functions for working
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with molecular geometries, and interfacing with quantum chemistry software.
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Main
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======
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.. currentmodule:: rmgpy.qm.main
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======================= ========================================================
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Class Description
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======================= ========================================================
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:class:`QMSettings` A class to store settings related to quantum mechanics calculations
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:class:`QMCalculator` An object to store settings and previous calculations
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======================= ========================================================
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Molecule
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==========
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.. currentmodule:: rmgpy.qm.molecule
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======================= ========================================================
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Class Description
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======================= ========================================================
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:class:`Geometry` A geometry, used for quantum calculations
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:class:`QMMolecule` A base class for QM Molecule calculations
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======================= ========================================================
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QM Data
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=========
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.. currentmodule:: rmgpy.qm.qmdata
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======================= ========================================================
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Class/Function Description
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======================= ========================================================
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:class:`QMData` General class for data extracted from a QM calculation
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:class:`CCLibData` QM Data extracted from a cclib data object
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======================= ========================================================
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QM Verifier
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=============
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.. currentmodule:: rmgpy.qm.qmverifier
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======================= ========================================================
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Class/Function Description
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======================= ========================================================
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:class:`QMVerifier` Verifies whether a QM job was succesfully completed
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======================= ========================================================
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Symmetry
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==========
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.. currentmodule:: rmgpy.qm.symmetry
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============================== ========================================================
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Class/Function Description
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============================== ========================================================
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:class:`PointGroup` A symmetry Point Group
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:class:`PointGroupCalculator` Wrapper type to determine molecular symmetry point groups based on 3D coordinates
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:class:`SymmetryJob` Determine the point group using the SYMMETRY program
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============================== ========================================================
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Gaussian
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===========
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.. currentmodule:: rmgpy.qm.gaussian
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======================= ========================================================
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Class/Function Description
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======================= ========================================================
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:class:`Gaussian` A base class for all QM calculations that use Gaussian
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:class:`GaussianMol` A base Class for calculations of molecules using Gaussian.
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:class:`GaussianMolPM3` A base Class for calculations of molecules using Gaussian at PM3.
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:class:`GaussianMolPM6` A base Class for calculations of molecules using Gaussian at PM6.
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======================= ========================================================
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Mopac
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=======
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.. currentmodule:: rmgpy.qm.mopac
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======================= ========================================================
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Class/Function Description
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======================= ========================================================
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:class:`Mopac` A base class for all QM calculations that use Mopac
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:class:`MopacMol` A base Class for calculations of molecules using Mopac.
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:class:`MopacMolPM3` A base Class for calculations of molecules using Mopac at PM3.
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:class:`MopacMolPM6` A base Class for calculations of molecules using Mopac at PM6.
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:class:`MopacMolPM7` A base Class for calculations of molecules using Mopac at PM7.
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======================= ========================================================
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.. toctree::
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:hidden:
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main
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molecule
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qmdata
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qmverifier
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symmetry
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gaussian
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mopac
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‎documentation/source/reference/qm/main.rst‎

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***********************
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rmgpy.qm.main
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***********************
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.. autoclass:: rmgpy.qm.main.QMSettings
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.. autoclass:: rmgpy.qm.main.QMCalculator

‎documentation/source/reference/qm/molecule.rst‎

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***********************
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rmgpy.qm.molecule
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***********************
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.. autoclass:: rmgpy.qm.molecule.Geometry
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.. autoclass:: rmgpy.qm.molecule.QMMolecule

‎documentation/source/reference/qm/mopac.rst‎

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***********************
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rmgpy.qm.mopac
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***********************
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.. autoclass:: rmgpy.qm.mopac.Mopac
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.. autoclass:: rmgpy.qm.mopac.MopacMol
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.. autoclass:: rmgpy.qm.mopac.MopacMolPM3
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.. autoclass:: rmgpy.qm.mopac.MopacMolPM6
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.. autoclass:: rmgpy.qm.mopac.MopacMolPM7

‎documentation/source/reference/qm/qmdata.rst‎

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***********************
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rmgpy.qm.qmdata
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***********************
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.. autoclass:: rmgpy.qm.qmdata.QMData
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.. autoclass:: rmgpy.qm.qmdata.CCLibData

‎documentation/source/reference/qm/qmverifier.rst‎

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***********************
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rmgpy.qm.qmverifier
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***********************
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.. autoclass:: rmgpy.qm.qmverifier.QMVerifier

‎documentation/source/reference/qm/symmetry.rst‎

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***********************
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rmgpy.qm.symmetry
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***********************
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.. autoclass:: rmgpy.qm.symmetry.PointGroup
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.. autoclass:: rmgpy.qm.symmetry.PointGroupCalculator
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.. autoclass:: rmgpy.qm.symmetry.SymmetryJob

‎documentation/source/users/rmg/input.rst‎

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On the fly Quantum Calculations
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===============================
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This block is used when quantum mechanical calculations are desired to determine thermodynamic parameters.
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These calculations are only run if the molecule is not included in a specified thermo library.
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The ``onlyCyclics`` option, if ``True``, only runs these calculations for cyclic species.
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In this case, group additive estimates are used for all other species.
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Molecular geometries are estimated via RDKit [RDKit]_.
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Either MOPAC (2009 and 2012) or GAUSSIAN (2003 and 2009) can be used
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with the semi-empirical pm3, pm6, and pm7 (pm7 only available in MOPAC2012),
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specified in the software and method blocks.
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A folder can be specified to store the files used in these calculations,
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however if not specified this defaults to a `QMfiles` folder in the output folder.
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The calculations are also only run on species with a maximum radical number set by the user.
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If a molecule has a higher radical number, the molecule is saturated with hydrogen atoms, then
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quantum mechanical calculations with subsequent hydrogen bond incrementation is used to determine the
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thermodynamic parameters.
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The following is an example of the quantum mechanics options ::
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quantumMechanics(
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software='mopac',
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method='pm3',
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fileStore='QMfiles',
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scratchDirectory = None,
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onlyCyclics = True,
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maxRadicalNumber = 0,
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)
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.. [RDKit] RDKit: Open-source cheminformatics; http://www.rdkit.org
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Pressure Dependence
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===================
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