Theoretical Uncertainties

4) Theoretical Uncertainties

This section controls perturbation model, uncertainty magnitudes, distributions, and convergence thresholds for parameter classes.

4.1 Global perturbation and score-balance keys

Keyword	Default value	Description
max_std	4	Maximum deviation from initial model.
freq_mode	"batch"	Frequency perturbation mode. Possible values: "batch" or "individual". Individual mode has not been thoroughly tested.
weight_theory	1.0	Raw theory contribution weight; normalized at runtime with weight_experiments.
weight_experiments	1.0	Raw experiment contribution weight; normalized at runtime with weight_theory.
specific_std	{}	Per-parameter override map for standard deviations. An entry overrides the global std_<ptype> for that parameter and governs the sampling scale, the scoring weight, and the perturbation boundaries (trusted range): a larger value widens the accepted bounds, a smaller one tightens them. Parameters without an entry fall back to the global std_<ptype>.

4.2 Standard deviations (std_*)

Keyword	Default value	Description
std_we	1.0	Well and bimolecular fragments energy uncertainty (kcal/mol).
std_be	1.5	Barrier energy uncertainty (kcal/mol).
std_ifc	1.1	Individual vibrational frequency multiplicative uncertainty. Multiplicative factor.
std_bfc	1.05	Batch vibrational frequency multiplicative uncertainty. Multiplicative factor.
std_hrs	0.1	Hindered rotor uncertainty. Percentage.
std_if	1.1	Imaginary frequency multiplicative uncertainty. Multiplicative factor.
std_fact	0.25	Energy transfer factor uncertainty. Percentage.
std_pow	0.075	Energy transfer power uncertainty. Percentage.
std_epsilon	0.1	Lennard-Jones epsilon uncertainty. Percentage.
std_sig	0.1	Lennard-Jones sigma uncertainty. Percentage.
std_sfc	2.0	Symmetry-factor uncertainty for barrierless reactions. While the symmetry has no uncertainty, this parameter allows to scale the state density. Multiplicative factor.
std_mrc	1.5	Multi-dimensional rotor symmetry uncertainty. While the symmetry has no uncertainty, this parameter allows to scale the state density. Multiplicative factor.

Distribution restrictions. Each parameter belongs to a category that constrains which sampling distribution (distrib_*) it may use:

• Multiplicative parameters (if, sfc, mrc, bfc, and the individual/batch frequencies) accept only log-normal or log-uniform.
• Additive (we, be, pow) and percentage (hrs, sigma, epsilon, fact) parameters accept only uniform or normal.

Any other combination cancels the run. In the GUI, only the valid distributions for a parameter's category are selectable.

For multiplicative parameters the theory-score distance is measured in log space as ln(value / reference) / ln(uncertainty), so the penalty is symmetric under a factor and its inverse and consistent with the log-normal (log-space) perturbation of these parameters. Additive and percentage parameters keep their linear distance.

4.3 Convergence thresholds (conv_*)

Keyword	Default value	Description
max_score	4.0	Convergence threshold. Maximum score for the best-model ensemble has to be lower.
score_conv	2	Convergence threshold. Average score for best-model ensemble has to be lower.
param_conv	0.01	Parameter-space convergence threshold used for both parameter values and standard deviations. For additive and percentage parameters it is a percentage (relative change). For multiplicative parameters (if, sfc, mrc, bfc, frequencies) genetic-algorithm convergence is measured in log space as `
conv_we	0.1	Convergence threshold for well energies.(kcal/mol)
conv_be	0.1	Convergence threshold for barrier energies.(kcal/mol)
conv_pow	0.01	Convergence threshold for energy transfer power.