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Docs: Corrections to Arkane's Multidimensional Hindered Rotors docs #1784

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Docs: Corrections to Arkane's Multidimensional Hindered Rotors docs #1784

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30 changes: 17 additions & 13 deletions documentation/source/users/arkane/input.rst
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Expand Up @@ -423,12 +423,14 @@ Note that the atom labels identified within the rotor section should correspond

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 be 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 multidimensional hindered rotors, ``geometry``, ``frequencies`` need to be specified in the same way described
in detail in the last section. However, rotor files may be 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):
======================= ====================================
For HinderedRotor2D (Quantum Mechanical 2D using Q2DTor):

======================= ====================================
Parameter Description
======================= ====================================
``scandir`` file or directory containing scan energies
Expand All @@ -439,9 +441,10 @@ Parameter Description
``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):

For HinderedRotorClassicalND (Classical and Semiclassical ND rotors):
======================= ====================================
Parameter Description
======================= ====================================
Expand All @@ -453,12 +456,13 @@ Parameter Description
======================= ====================================

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 rotor objects enable calculation of partition functions for
multidimensional torsions that are particularly important for QOOH molecules and molecules involving intramolecular hydrogen
bonding. 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.
tops and sigmas instead of individual values. These rotor objects enable calculation of partition functions for
multidimensional torsions that are particularly important for QOOH molecules and molecules involving intramolecular
hydrogen bonding. 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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