From 52cf4245dc4ed292c7aa285cc6f617d80b9c71c2 Mon Sep 17 00:00:00 2001 From: Alon Grinberg Dana Date: Thu, 24 Oct 2019 10:24:24 -0400 Subject: [PATCH] Docs: Corrections to Arkane's Multidimensional Hindered Rotors docs Without an empty line between a text block and a table block, the table won't be auto-formatted. Also deleted a leading space in the text that Sphinx complained about. Also a table's header/bottom was fixed. --- documentation/source/users/arkane/input.rst | 28 ++++++++++++--------- 1 file changed, 16 insertions(+), 12 deletions(-) diff --git a/documentation/source/users/arkane/input.rst b/documentation/source/users/arkane/input.rst index e61174f7ee2..1ca9cffd027 100644 --- a/documentation/source/users/arkane/input.rst +++ b/documentation/source/users/arkane/input.rst @@ -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 @@ -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 ======================= ==================================== @@ -454,11 +457,12 @@ 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. +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 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~