mindlessgen.toml

# Default configuration for the 'Mindless Molecule Generator' (MindlessGen) package
# The following file locations are searched for in ascending order:
# 1. Location specified by the `--config < str | Path >` command-line argument
# 2. Current working directory (`Path.cwd()`)
# 3. User's home directory (`Path.home()`)

[general]
# > Verbosity level defining the printout: Options: -1 = super-silent, 0 = silent, 1 = default, 2 = verbose, 3 = debug
verbosity = 1
# > Number of parallel processes to use. Corresponds to the number of physical CPU cores used. Options: <int>
parallel = 1
# > Maximum number of generation & optimization try-and-error cycles per molecule. Options: <int>
max_cycles = 200
# > Number of molecules to generate. Options: <int>
num_molecules = 1
# > Do post-processing after the optimization with another engine (e.g., `orca`). Default: false. Options: <bool>
postprocess = false
# > Switch molecule structure XYZ writing on and off. Default: true. Options: <bool>
write_xyz = true

[generate]
# > Minimum number of atoms in the generated molecule. Options: <int>
min_num_atoms = 5
# > Maximum number of atoms in the generated molecule. Options: <int>
max_num_atoms = 10
# > Initial coordinate scaling factor. Options: <float>
init_scaling = 3.0
# > Increase in the coordinate scaling factor per trial after check_distance was not met. Options: <float>
increase_scaling_factor = 1.1
# > Scaling factor for the van der Waals radii employed for the fragment detection. Options: <float>
scale_fragment_detection = 1.25
# > Scaling factor for the minimal distance between two atoms based on the sum of the van der Waals radii. Options: <float>
scale_minimal_distance = 0.8
# > Contract the coordinates after the initial generation. Leads to more cluster-like and less extended structures
# and can speed-up the generation for larger molecules significantly. Options: <bool>
contract_coords = true
# > Atom types and their minimum and maximum occurrences. Format: "<element>:<min_count>-<max_count>"
# > Elements that are not specified are only added by random selection.
# > A star sign (*) can be used as a wildcard for integer value.
element_composition = "C:2-3, H:1-2, O:1-2, N:1-*"
# > Set an exactly defined composition
# > CAUTION: Only possible if 'element_composition' is set to defined values. Example: "C:3-3, H:8-8, O:1-1"
fixed_composition = false
# > Atom types that are not chosen for random selection. Format: "<element1>, <element2>, ..."
# > CAUTION: This option is overridden by the 'element_composition' option.
# > I.e., if an element is specified in 'element_composition' with an occurrence > 0, it will be added to the molecule anyway.
forbidden_elements = "57-71, 81-*"
# > Set a charge for the molecule generation. Options: "none" (random charge assignment), "int" or <int> (fixed charge assignment)
molecular_charge = "none"

[refine]
# > Maximum number of fragment optimization cycles. Options: <int>
max_frag_cycles = 10
# > Quantum Mechanics (QM) engine to use. Options: 'xtb', 'orca'
engine = "xtb"
# > HOMO-LUMO gap threshold applied at the end of the refinement step
hlgap = 0.5
# > Debug this step. Leads to more verbose output as soon as the refinement part is reached. Options: <bool>
# > If `debug` is true, the process is terminated after the first (successful or not) refinement step.
debug = false

[postprocess]
# > Engine for the post-processing part. Options: 'xtb', 'orca'
engine = "orca"
# > Optimize geometry in the post-processing part. If `false`, only a single-point is conducted. Options: <bool>
optimize = true
# > Optimization cycles for the post-processing part. If not given, the program default is chosen. Options: <int>
opt_cycles = 5
# > Debug this step. Leads to more verbose output as soon as the post-processing part is reached. Options: <bool>
# > If `debug` is true, the process is terminated after the first (successful or not) post-processing step.
# > Note: This option is only relevant if the 'postprocess' option in the 'general' section is set to 'true'.
debug = false

[xtb]
# > Path to the xtb executable. The names `xtb` and `xtb_dev` are automatically searched for. Options: <str | Path>
xtb_path = "/path/to/xtb"
# > The GFN<n>-xTB method that should be used: Options: <int = 0> -> GFN-0-xTB, <int = 1> -> GFN-1-xTB, <int = 2> -> GFN-2-xTB
level = 2

[orca]
# > Path to the orca executable. The names `orca` and `orca_dev` are automatically searched for. Options: <str | Path>
orca_path = "/path/to/orca"
# > Functional/Method: Options: <str>
functional = "PBE"
# > Basis set: Options: <str>
basis = "def2-SVP"
# > Gridsize for the numerical integration (corresponds to `DEFGRID<gridsize>`: Options: <int => 1> = coarse, <int = 2> => medium, <int = 3> => fine
gridsize = 1
# > Maximum number of SCF cycles: Options: <int>
scf_cycles = 100