Configuration examples

For all examples, assume the user's default configuration is the one found here.

Optimize all structures in $AARONLIB/templates/my_reaction/my_structures. AaronJr will run the "Minimum" workflow unless the template structure's filename begins with "TS"; in that case, it will run the "TS" workflow. Constraints for the TS workflow are set in the comment line of the XYZ files used as template structures (see here).

project = %{ $Reaction:reaction }
name = %{ $Reaction:template }

[Reaction]
reaction = my_reaction
template = my_structures

2-aminoethanol dihedral scan

project = examples
name = 2-aminoethanol_scan

[Geometry]
constraints = (1, 2, 3, 4)
structure.0 = NCCO
&for d in range(0, 370, 10):
    structure.d = structure.0.copy()
    structure.d.change_dihedral("1", "2", "3", "4", d)

[Job]
1 type = optimize.constrained
2 type = single-point
ppn = 4

Optimizing urea and thiourea derivatives (produces 2\*10\*10 = 200 structures).

project = examples
name = urea_derivatives

[Geometry]
structure.O = urea.xyz
&call:
    structure.S = structure.O.copy()
    structure.S.change_element("O", "S", adjust_bonds=True)

[Substitution]
&combinations:
   7 = H, Me, Et, iPr, tBu, F, Cl, Br, I, CF3
   8 = H, Me, Et, iPr, tBu, F, Cl, Br, I, CF3

[Theory]
method = b3lyp
basis = !I 6-31(G)d
        I lanl2dz
ecp = I lanl2dz

[Job]
include = Minimum
ppn = 4

Building TS structure guess from SMILES string and using AaronTools method to adjust bond lengths.

project = examples
name = SN2

[Geometry]
structure = Cl[CH3]C#N
constraints = (1, 2), (2, 6)
&call: 
    structure.change_distance(1, 2, dist=2.0)
    structure.change_distance(2, 6, dist=2.0)

[Theory]
charge = -1

[Job]
include = TS
ppn = 4