When there are 2 or more ligands, AARON prints the status of the first ligand twice:

================================================================================
Status for all jobs...(Fri Aug 10 12:38:01 2018)

Status for Cat1 jobs......

Pending jobs:
Cat1/R/ts2 step 1 attempt 1: No msg recorded
Cat1/S/ts1 step 1 attempt 1: No msg recorded
Cat1/S/ts2 step 1 attempt 1: No msg recorded
Cat1/S/ts3 step 1 attempt 1: No msg recorded

================================================================================
Status for all jobs...(Fri Aug 10 12:38:01 2018)

Status for Cat1 jobs......

Pending jobs:
Cat1/R/ts2 step 1 attempt 1: No msg recorded
Cat1/S/ts1 step 1 attempt 1: No msg recorded
Cat1/S/ts2 step 1 attempt 1: No msg recorded
Cat1/S/ts3 step 1 attempt 1: No msg recorded

Status for Cat2 jobs......

Pending jobs:
Cat2/R/ts2 step 1 attempt 1: No msg recorded
Cat2/S/ts1 step 1 attempt 1: No msg recorded
Cat2/S/ts2 step 1 attempt 1: No msg recorded
Cat2/S/ts3 step 1 attempt 1: No msg recorded

I noticed that in this Paper "Prospects for the Computational Design of Bipyridine N,N′‑Dioxide
Catalysts for Asymmetric Propargylation Reactions" (dx.doi.org/10.1021/cs5012553), calculations were performed in B97D/TZV(2d, 2p) level. And I found that the keyword "TZV(2d, 2p)" in Gaussian is invalid, so I'm curious about the exact command to implement this basis in Gaussian, is it "TZV" or "TZVP" ?

When initilizing, AARON sometimes prints the name of .com files to the screen. We need to clean up all of the printing of AARON. My guess is that this was added for debugging but just never removed.

[swheele2@ada4 Example2]$ Aaron example2.in
Checking for required Perl modules...
Necessary Perl modules found. Starting AARON...
Preparing to run transition state searches...
Aaron job started on Fri Aug 10 12:36:59 2018

Preparing data structures for Cat1/R/ts2...
Preparing data structures for Cat1/S/ts1...
Preparing data structures for Cat1/S/ts2...
Preparing data structures for Cat1/S/ts3...
Cat1/R/ts2/Cat1.R.ts2.1.com
Cat1/S/ts3/Cat1.S.ts3.1.com
Cat1/S/ts1/Cat1.S.ts1.1.com
Cat1/S/ts2/Cat1.S.ts2.1.com
Preparing data structures for Cat2/R/ts2...

print_SI doesn't seem to actually do anything

(try running it in /home/swheele2/Aaron_examples/new_Example1 on Ada)

I think the cat_screen command line script can be improved.

The current cat_screen script cannot take into number but not name of substituent, for example:
If you do cat_screen ts1.xyz -l Ph=Me It will rise an error for the input Ph substitute.

Second, the current cat_screen script cannot screen multiple subs meanwhile. That is in the original screen_subs perl function, if you do
$cata->screen_subs('ligand', 35,56=>Me, Ph), it will just give you two structures (35,56=Me and 35,56=Ph) not four structures. I think this should be useful and we should keep that in the cat_screen script.

In some cases, AARON will write a .com file the main catalyst/ligand directory. In these cases, AARON essentially stalls for that geometry.

For example, look in /home/swheele2/Aaron_bugs/Cat2:

[swheele2@ada4 Cat2]$ pwd
/home/swheele2/Aaron_bugs/Cat2
[swheele2@ada4 Cat2]$ ls
total 0
drwxr-s---+ 4 swheele2 wheeler 4.0K Aug 5 15:32 Cat2
-rw-r----- 1 swheele2 wheeler 3.1K Aug 6 04:06 Cat2.R.ts2.Cf2.2.com
drwxr-s---+ 4 swheele2 wheeler 4.0K Aug 6 00:15 Cat2_XYZ

[swheele2@ada4 Cf2]$ pwd
/home/swheele2/Aaron_bugs/Cat2/Cat2/R/ts2/Cf2
[swheele2@ada4 Cf2]$ ls
total 128K
-rw-r----- 1 swheele2 wheeler 547 Aug 6 04:06 Cat2.R.ts2.Cf2.2.job
-rw-r----- 1 swheele2 wheeler 1.9K Aug 6 04:38 Cat2.R.ts2.Cf2.2.job.7679661
-rw-r----- 1 swheele2 wheeler 7.3K Aug 6 06:03 Cat2.R.ts2.Cf2.2.job.7679750

We had one case where there were 3 or 4 com files located in that main directory rather than the appropriate subdirectory (unfortunately I didn't take a snapshot of that one).

The absolute energies are often not printed to the thermo.dat file

See /home/swheele2/Aaron_examples/new_Example1 on Ada

This method is called in the implementation of the Geometry::_substitute() method. However, it is not defined anywhere.

Line 1160 in Geometry.pm _RMSD() loops over reference geometry atoms ($atom1_ref). However, if this is smaller than $atom2_ref, it tries to index out of bounds.

When using input_conformers_only parameter, new substitutions on the substituent detected automatically by AARON can not be initiated.

Use G09Out to grab thermo from a .log file

Perhaps this is a case where conformations are eliminated, but the status is not being updated properly.

See /home/swheele2/chem/Tony/Example on Ada

For example, here's the end of It-indole.log
Lig1-Sub7/ts3/Cf1 finished normally
Lig1-Sub7/ts3/Cf2 finished normally

Repeated conformers:
Lig1-Sub3/ts2/Cf3
Lig1-Sub3/ts3/Cf2
Lig1-Sub6/ts2/Cf4
Lig1-Sub6/ts3/Cf4
Lig1-Sub7/ts2/Cf3
Lig1-Sub7/ts3/Cf7
Lig1-Sub7/ts3/Cf3

Jobs that have not been started and are awaiting other jobs to finish:
Lig1-Sub7/ts2/Cf4
Lig1-Sub7/ts3/Cf8
Lig1-Sub7/ts3/Cf4

Aaron finished, terminated normally
AARON stopped Fri Aug 10 06:16:13 2018

line 759 in Geometry::substitute definition:
my $sub_object = new AaronTools::Substituent( name => $sub, end => $end );
Results in error when calling bin/substitute command line tool:
Undefined subroutine &AaronTools::Substituent called at /home/deo/Aaron/AaronTools/Geometry.pm line 759.

Changing line 759 to
my $sub_object = AaronTools::Substituent->new( name => $sub, end => $end );
resolves this issue

Inspired by Victoria, using Pod::Usage along with the GetOpt is good idea to input parameters. The AaronInit.pm should be changed to make the input consistent with the command line scripts in bin.