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add documentation for multidimensional hindered rotors
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mjohnson541 committed Aug 5, 2019
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Expand Up @@ -421,6 +421,44 @@ for specifying the same ``rotors`` entry are commented out)::

Note that the atom labels identified within the rotor section should correspond to the indicated geometry.

Multidimensional Hindered Rotors
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
For multidimensional hindered rotors, ``geometry``, ``frequencies``need to be specified in the same way described in detail in the last section. However,
rotor files may specified by either a 1D rotor scan file as in the last section (1D rotors only) or as a directory.
The directory must contain a list of energy files in the format ``something_name_rotorAngle1_rotorAngle2_rotorAngle3(...).log``.

For HinderedRotor2D (Quantum Mechanical 2D using Q2DTor):
======================= ====================================
Parameter Description
======================= ====================================
``scandir`` file or directory containing scan energies
``pivots1`` The indices of the atoms in the first rotor torsional bond
``top1`` The indices of all atoms on one side of the first torsional bond (including the pivot atom)
``symmetry1`` The symmetry number of the first rotor
``pivots2`` The indices of the atoms in the second rotor torsional bond
``top2`` The indices of all atoms on one side of the second torsional bond (including the pivot atom)
``symmetry2`` The symmetry number of the second rotor
``symmetry`` Q2DTor simplifying symmetry code, default is ``none``
======================= ===================================

For HinderedRotorClassicalND (Classical and Semiclassical ND rotors):
======================= ====================================
Parameter Description
======================= ====================================
``scandir`` file or directory containing scan energies
``pivots`` The list of the indices of the atoms in each rotor torsional bond
``tops`` The list of the indices of all atoms on one side of each torsional bond (including the pivot atom)
``sigmas`` The list of symmetry numbers for each torsional bond
``semiclassical`` Indicates whether to use the semiclassical rotor correction (highly recommended)
======================= ====================================

The inputs are mostly the same as the last section except that HinderedRotorClassicalND takes lists of pivots,
tops and sigmas instead of individual values. These rotors enable calculation of partition functions for
multidimensional torsions. It is worth noting that HinderedRotor2D can take on the order of hours to run. To mitigate this the
.evals file in the directories Q2DTor directories are searched for automatically and used if present to reduce runtime to seconds.
This means if you have run a system with HinderedRotor2D and wish to rerun the system and recalculate the HinderedRotor2D
you should delete the .evals file. HinderedRotorClassicalND usually runs quickly for lower dimensional torsions.

Additional parameters for pressure dependent networks
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

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