diff --git a/documentation/source/users/arkane/input.rst b/documentation/source/users/arkane/input.rst index 93977a8792e..a9e51620ef2 100644 --- a/documentation/source/users/arkane/input.rst +++ b/documentation/source/users/arkane/input.rst @@ -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 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~