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Auto optical isomer ex symmetry arkane #1571

Merged
merged 6 commits into from
Apr 25, 2019
Merged

Auto optical isomer ex symmetry arkane #1571

merged 6 commits into from
Apr 25, 2019

Commits on Apr 24, 2019

  1. Inheritance for Log files Arkane 

    This commit makes the Log file readers for QChem, Gaussian and
Molepro inherit from the base Log class, which can reduce code
duplication going forward.

To do this, the method `determine_qm_software` was removed from
the Log class as this causes circular import errors, and the
`Log` class was moved to a separate file, in accordance with PEP-8.

Methods used in all child classes are added to the parent Log
class.

This commit also modified methods calling `determine_qm_software`,
and references to `isinstance(x,Log)` were altered to not include
the children log files.
    @goldmanm
    goldmanm committed Apr 24, 2019
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  2. Allow no opticalIsomers parameter in Arkane 

    Previously, not having the number of opticalIsomers would throw
and error. Now the computer can estimate the number of optical
isomers, so no input is accepted.
    @goldmanm
    goldmanm committed Apr 24, 2019
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  3. Get loadConformer to automatically estimate optical isomers 

    Prevously loadConformer required an integer input for optical isomers.
This commit allows this method to call the Symmetry package and estimate
the value automatically.
    @goldmanm
    goldmanm committed Apr 24, 2019
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  4. Get Arkane to use Symmetry package for symmetry/optical isomers 

    Created new method get_optical_isomers_and_symmetry_number in Log class
This method allows Log objects to calculate the number of optical
isomers and symmetry numbers contained within a log file.
This was taken and modified from the equivalent method in ARC (credits to Alon).

Remove symfromlog parameter. If using the RMG QM symmetry package,
the symfromlog parameter is not necessary and confusing.
This commit removes the need for such a parameter.

Get Arkane to use Symmetry package for symmetry.
This commit uses the Symmetry package to estimate symmetry if not
explicitly given by the user by modifying the gaussian, molpro,
and qchem parsers.
    @goldmanm
    goldmanm committed Apr 24, 2019
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  5. Test symmetry,optical isomers loaded

    @goldmanm
    goldmanm committed Apr 24, 2019
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  6. Require linear parameter for Arkane statmech jobs 

    Previously, no error was raised when the `linear` parameter was not
implemented properly. This could hide information about incorrect
calculations if the user is not properly implementing the parameter.

This commit raises an error if no `linear` parameter is given.
    @goldmanm
    goldmanm committed Apr 24, 2019
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