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More on AARON Input Files
Default levels of theory, etc. can be specified in $QCHASM/Aaron/.aaronrc and $HOME/.aaronrc.
In the previous tutorials, we relied on the defaults in $QCHASM/Aaron/.aaronrc to avoid having to specify many different keywords.
We could, of course, list values for all keywords.
For instance, if the contents of $QCHASM/Aaron/.aaronrc are as follows:
gen=/home/group/wheeler/basis/
Default
solvent=Dichloromethane
solvent_model=PCM
temperature=298
low_method=PM6
method=B97D
basis=def2tzvp
denfit=1
charge=0
mult=1
wall=12
n_procs=20
short_wall=2
short_procs=2
then the following two input files are equivalent:
reaction_type=Allylation template=NN-dioxide_example charge=1 method=b97d denfit=true basis=6-31G &Ligands Cat1: 18=F 21=F &
reaction_type=Allylation template=NN-dioxide_example charge=1 solvent=Dichloromethane solvent_model=PCM temperature=298 low_method=PM6 method=b97d denfit=true basis=6-31G charge=0 mult=1 wall=12 n_procs=20 short_wall=2 short_procs=2 &Ligands Cat1: 18=F 21=F &
One can also specify custom default levels of theory for different types of reactions, thus greatly simplifying AARON input files.
The most obvious use of this approach is to define default levels of theory for transition metal catalyzed reactions.
For instance, suppose you put the following in $HOME/.aaronrc:
gen=/scratch/group/wheeler/basis
Default
solvent=gas
temperature=298
low_method=PM6
method=M062X
basis=6-31G
denfit=0
charge=0
mult=1
wall=24
n_procs=20
short_wall=2
short_procs=2
TM_Default
solvent=gas
temperature=298
low_method=PM6
method=M06
basis=tm lanl2dz
basis=6-31G
ecp=tm lanl2dz
denfit=1
charge=0
mult=1
wall=48
n_procs=20
short_wall=2
short_procs=2
You can then invoke the 'TM_Default' (Note that this is case-sensitive!) in an input file using:
custom=TM_Default
For example, the following input files are equivalent:
reaction_type=Ir-Indole template=CH3 custom=TM_Default charge=1 mult=1 &Ligands Lig1: None & &Substrates Sub3: 25=CF3 &
reaction_type=Ir-Indole template=CH3 solvent=gas low_method=PM6 method=M06 basis=tm LANL2DZ ecp=tm LANL2DZ basis=6-31G denfit=0 charge=1 mult=1 wall=48 &Ligands Lig1: None & &Substrates Sub3: 25=CF3 &
The following can be set in the AARON input file:
low_method=[either DFT functional or semi-empirical method used for Step1] method=[DFT functional used for Steps2-4] high_method=[DFT functional used for single point energy (Step5)] low_basis=[if low_method is not semi-empirical, then you must specify the basis set used for Step1] low_ecp=[ecp for Step1 if low_method is not semi-empirical] basis=[basis set used for Steps2-4] ecp=[ecp used for Steps2-4] high_basis=[basis set used for single point energy (Step5)] high_ecp=[ecp used for single point energy (Step5)] gen=[name of gen basis set] temperature=[temperature in K] denfit=[true|false. Controls whether 'denfit' option is invoked] solvent_model=[pcm, smd, etc ; defaults to pcm if solvent is specified] solvent=[dichloromethane, water, etc] high_solvent=[solvent used for single point energy (Step5)] high_solvent_model=[solvent model used for single point energy (Step5)] grid=[integration grid keyword] emp_dispersion=[empirical dispersion keywords. e.g. emp_dispersion=GD3] high_emp_dispersion=[empirical dispersion keywords for single point energy (Step5)] custom=[alias for custom defaults (case sensitive). See above]
n_procs=[number of processors for steps2-5] wall=[walltime in hours for steps2-5] short_procs=[number of cores for step1] short_wall=[walltime in hours for step1] submission_template=[path to a template job file to use instead of AaronTools/template.job]
reaction_type=[name of a TS library] template=[name of template for the specified TS library] input_conformers_only=[0|1. Controls whether or not to do a conformer search. Default: 0//do conformer search] full_conformers=[0|1. Controls whether or not to do hierarchical conformer search. Default: 0//do hierarchical search] multistep=[0|1. Whether the reaction is multistep or single-step. Default: 0//single step] rmsd_cutoff=[real number. RMSD cutoff for deciding if a conformer is a duplicate. Default: 0.15] d_cutoff=[real number. Amount a constrained bond can change before reverting to a previous step. Default: 0.35] ignore_hbonds=[1|0. Ignore connectivity changes involving H and N, O, or F. Default: 1]