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mindlessgen.toml
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mindlessgen.toml
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# Default configuration for the 'Mindless Molecule GENerator' (MindlessGen) package
# Following file locations are searched for in the following 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: 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 = 100
# > Number of molecules to generate. Options: <int>
num_molecules = 1
# > Do post-processing (checking for HL gap, etc.) after the optimization. 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 = 1.3
# > Scaling factor for the employed van der Waals radii. Options: <float>
scale_vdw_radii = 1.3333
# > Scaling factor for the minimal bondlength based on the sum of the van der Waals radii. Options: <float>
scale_minimal_bondlength = 0.75
# > 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-*"
# > 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.
# > Example: forbidden_elements = "18,57-*"
forbidden_elements = "57-71, 81-*"
[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