AaronTools raises an error when reading this file.

gemfi_beta_uTS_22.out.zip

fr = FileReader(path, get_all=True, just_geom=False)

ValueError: could not convert string to float: 'SPECTRUM'

For what it is worth, this closely related job is read without problems.
gemfi_beta_uTS_21.out.zip

Given that the ValueError looks related to the frequencies, it is notable that gemfi_beta_uTS_22.out has two imaginary frequencies.

Hello, dear developers of AaronTools,

I am using the python version of AaronTools to map new ligands on the TS template, but I encountered a bug of the map_ligand() function here.

The substrates of the reaction will rotate after the ligand mapped (changes in position), especially for cases where two substrates are separated. This error does not occur when the reaction substrate is a whole. Below are pictures of the bug I encountered.

1. Here is the situation where substrates (reactants) are a whole, no bug：
   tsa1:
   
   tsa1 after mapping:
   
   tsa1 and tsa1_mapped overlap together:
   

2. Here is the situation where reactants are separated, a substrates movement bug will occur：
   ts1:
   
   ts1 after mapping:
   
   ts1 and ts1_mapped overlap together:
   
   bug here:
   

That's all, the bug of this problem may be in geometry.py, but I can't solve it without your help. In addition, I also found that the "minimize" parameter in the map_ligand() function seems to be invalid, and when I set it to "True" and "False", there is no difference in the mapping results.

Looking forward to your reply, thank you!

Good day! I'm trying to implement AaronTools for local web server on our computational machine and currently i'm working on status check of calculation. When i'm trying to read file via FileReader class and try to check "finished" attrbute it's always equals "False", however end of .log file declares "Normal termination of Gaussian". Maybe i'm doing something wromg. Can you, please, provide some clarity about it?

Update: I've figured it out. if numpy version >1.23.5 and flag "just_geom" == false then error is raised duing parsing. Looks like np.float in spectrum script is causing problems

The theory tools for defining grids are not fully compatible with ORCA 5.0.3

when grids are set to'ultrafine', AaronTools writes ORCA inputs with:

%method
    AngularGrid  Lebedev590
    IntAcc            4.0
end

ORCA 5 uses 6 instead of Lebedev590.

Likewise 'superfinegrid' writes ! Grid7 FinalGrid7 which is not recognized in ORCA 5.0.3. The largest default grid in ORCA 5.0.3 is ! DefGrid3

I have pip installed AaronTools and received an error that calculated_bond_lengths.json is missing. Manually adding the file fixed the issue.

Hello again,

This is more of an open comment. Is there a native way to do comparisons/sorting between Geometry objects?

I think it would be useful to make Geometry objects (as well as Atoms) hashable based on their coordinates, and define an eq method, so that you could do quick comparisons between Geometry(es) using the standard python operators, or use Geometry(es) as dictionary keys to store QM properties. Is this something that sounds reasonable? I could potentially code the snippet if you feel it's coherent design-wise.

Thanks in advance, I don't want to come across as pushy - just an enthusiastic user!

Regards,

Hello, dear developers,

I am trying to use AaronTools.py to map ligands in a purely organic system (The TS template system I have tried is "Vinyl_boronic_acid_addition" reaction R/ts1.xyz in the code folder of AARON) it cannot give me a correct result. Results only the ligand which I want to add in the TS structure. So I tried to used perl version AaronTools, below is the perl program reporting error.

So how could I specify the ligand atoms in the .xyz file? Is there any other way to map ligands by AaronTools python script in this purely organic reaction?

Basically try to grab the basis set from the BSE module if we don't think it's included in the program and the user hasn't specified a path to the .gbs file or whatever

https://github.com/MolSSI-BSE/basis_set_exchange / https://pypi.org/project/basis-set-exchange/

the hyphenated version is in ORCA. Would be nice if they were both accessible via the same keyword.

A couple of bugs in substitute.py when using IUPAC or SMILES to specify substituent name.

1. For some substituents the substituent is attached opposite the group being replaced.
   For example,
   fetchMolecule.py -i methane | substitute.py -s 2=iupac:phenyl
   works fine, but
   fetchMolecule.py -i methane | substitute.py -s 2=iupac:methyl
   does not.

2. You can't specify a list of atoms to be substituted when using substituent from string.
   fetchMolecule.py -i methane | substitute.py -s 2,3=Ph
   works fine but
   fetchMolecule.py -i methane | substitute.py -s 2,3=iupac:phenyl
   does not.

Hello,

Thanks for developing this library. I, for one, am excited to see Aaron2 come along.

I think that there is a small error in SubmitProcess for SLURM:

        elif QUEUE_TYPE == "SLURM":
            args = ["sbatch", "<", job_file]

the "<" should be removed, as far as I known, because the submission command is simply sbatch job_file. At least this is what works in my cluster at the moment.

Thanks in advance!

For ORCA inputs using "Gaussian's B3LYP", automatically include "NoCosx" keyword to more closely match Gaussian results (ORCA uses RIJCOSX by default).
Similarly, add option to do "ORCA's 6-31G*" that requests Gaussian use 6-31G(d) with 5d/7f rather than the default 6d/10f, and similar for other Pople-style basis sets.

FilerReader has problems with ORCA outputs computed with double hybrid methods using the (default) RI approximation

I could not open files that used
! pwpb95 def2-qzvpp def2-qZVPP/C tightscf or ! dsd-pbep86 d3 def2-qzvpp def2-qZVPP/C tightscf

Notably, I could open files that used a double hybrid method without the RI approximation, eg
! dsd-pbep86 d3 def2-qzvpP def2-qZVPP/C tightscf noRI

The difference is in the line
RI-MP2 CORRELATION ENERGY: -1.414209774 Eh with RI versus
MP2 CORRELATION ENERGY : -1.414382553 Eh without RI

I think the error basically boils down to the fact that there is no space separating ENERGY and : in
RI-MP2 CORRELATION ENERGY: whereas there is a space in
MP2 CORRELATION ENERGY :

File ~/anaconda3/envs/python/lib/python3.10/site-packages/AaronTools/fileIO.py:1105, in FileReader.read_file(self, get_all, just_geom, scan_read_all, freq_name, conf_name, nbo_name, max_length)
   1103     self.read_mol2(f)
   1104 elif self.file_type == "out":
...
-> 1686     item = line.split()[-6] + " correlation energy"
   1687     self.other[item] = float(line.split()[-2])
   1689 elif re.match("E\(\S+\)\s+...\s+-?\d+\.\d+$", line):

IndexError: list index out of range

Does fr.all_geom access all geometries except the final geometry? The following ORCA job has 5 geometries and fr.all_geom accesses four of them.

! m062x 6-31+G** opt freq

* xyz 0 1
O   0.0000   0.0000   0.0000
H   1.0000   0.0000   0.0000
H   0.0000   1.0000   0.0000
*

This became confusing when parsing outputs of compound jobs, eg

* xyz 0 1
O   0.0000   0.0000   0.0000
H   1.0000   0.0000   0.0000
H   0.0000   1.0000   0.0000
*

%compound

New_Step
! m062x 6-31+G** opt freq # job1
Step_End

New_Step
! m062x 6-311+G** # job2
Step_End

New_Step
! b3lyp def2-tzvp # job3
Step_End
End

In this example:

fr = FileReader(path, get_all=True, just_geom=False)

ejob1 = fr.all_geom[-2][1]['energy']
ejob2 = fr.all_geom[-1][1]['energy']
ejob3 = fr['energy']

It would have helped me if the documentation said something like fr.all_geom returns the attributes of all geometries except the final geometry in the output.

(In the %compound job above, this is complicated by the fact that the last three single point energies in the file all correspond different calculations on the same geometry.)

We seem to be catching T = 0K as a special case, but then treating it incorrectly.
At 0K, H and G are equal to E + ZPVE, not E.

(To convince yourself of this, compare the output from grabThermo.py at T = 0 and T = 0.000001)

AaronTools is missing radii for the lanthanides and actinides, which prevents SEQCROW from opening ORCA output files for molecules containing such atoms.

Part 1:

basis = BasisSet(
                [Basis(def2-svp, ['all', '!Ru']),
                 Basis('sdd', 'tm')], 
                [ECP("sdd", 'tm')])

for Gaussian files gives,

C H N O 0
6-31g*
****
Ru 0
sdd
****

Ru 0
sdd

and for ORCA files gives,

%basis
    newGTO            Ru "sdd" end
    newECP            Ru "sdd" end
end

This works for the Gaussian job, but ORCA will error out with Error: Pure ECPs not allowed in GTO definition

The ORCA job will work with

! b3lyp 6-31G*
%basis
    newECP            Ru "sdd" end
    newGTO            Ru "def2-svp" end
end

or with

! b3lyp def2-svp
%basis
    newECP            Ru "sdd" end
end

Part 2

basis = BasisSet(
                [Basis(def2-svp, AnyNonTransitionMetal),
                 Basis('lanl2dz', 'tm')], 
                [ECP("lanl2dz", 'tm')])

gives an error

File ~/anaconda3/envs/python/lib/python3.10/site-packages/AaronTools/theory/basis.py:149, in Basis.__init__(self, name, elements, aux_type, user_defined, oniom_layer, atoms)
    146     ele = ele.lstrip("!")
    147     not_any = True
--> 149 if ele.lower() == "all":
    150     if not_any:
    151         not_anys.append(AnyTransitionMetal())

AttributeError: type object 'AnyNonTransitionMetal' has no attribute 'lower'

The same problem arrises for AnyTransitionMetal

Part 3 (not important to me, but thought it would be worth reporting)

basis = BasisSet(
                [Basis(def2-svp, ['all', '!Ru']),
                 Basis('lanl2dz', 'tm')], 
                [ECP("lanl2dz", 'tm')])

for Gaussian files gives,

C H N O 0
6-31g*
****
Ru 0
lanl2dz
****

Ru 0
lanl2dz

and the orca file gives

%basis
    newGTO            Ru "lanl2dz" end
    newECP            Ru "lanl2dz" end
end

This works for the Gaussian file, but fails for ORCA with Unknown ECP requested! Please consult the manual for available ECPs.
The ORCA job will run with,

%basis
    newGTO            Ru "lanl2dz" end
    newECP            Ru "HayWadt" end
end

I am not entirely sure if this is a bug or not but when I load a gaussian 16 scan file it loads "all" of the structures and not just the "optimized" ones along the path (so a 72 point scan ends up having over 500 structures). Is there anyway to fix this? (ChimeraX1.4 and most recent SEQCROW on mac)

Thanks a bunch!

When I use solvent = ImplicitSolvent("SMD", "water") to write an ORCA input file, the resulting file contains

! CPCM(water)
%cpcm
    smd    true
end

This input raises an error in ORCA 5.0.3

	 Error: Missing keyword in CPCM block
	 Missing keyword : SMDsolvent

A functional input looks like

! CPCM
%cpcm
    smd    true
    SMDsolvent "water"
end

It is fine to work around this by adding ORCA_BLOCKS={'cpcm':['SMDsolvent "water"']} to 'geom.write'. It would be nice if this was built in.