More on AARON Input Files - QChASM/Aaron GitHub Wiki

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Defaults

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
&

Custom Defaults

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
&

AARON Input Files

The following can be set in the AARON input file:

Gaussian options 

 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]

Cluster Options 

 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]

Workflow Options 

 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]
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