Gpr-opthyprms

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gpr-opthyprms: version 6.1090.a7cf688 (2026-06-18 21:15)

Name

gpr-opthyprms

Synopsis

gpr-opthyprms [OPTIONS] [--] ACCU REALM HYPRMS

Description

The program finds optimal GPR hyperparameters, which maximize logarithm of marginal likelihood. The optimization is performed by the L-BFGS optimizer employing either analytical or numerical gradients of logML w.r.t. hyperparameters.

Arguments

ACCU Name of the file containing the input PMF accumulator.

REALM Realm for GPR hyperparameter optimization. The list of supported realms can be obtained by --listrealms.

HYPRMS Name of the file containing the optimized hyperparameters.

Options

--listrealms List supported realms.

-t, --target NAME Specify the optimized target, which can be either logml (log of marginal likelihood) or logpl (log of pseudo-likelihood from leave-one-out cross-validation, LOO-CV). (Default: logml)

-l, --limit LIMIT Only bins containing more samples than NUMBER are considered properly sampled. (Default: 1000)

-a, --lmethod NAME Linear algebra method for matrix inversion. Supported algorithms: default, svd (SVD – singular value decomposition, divide-and-conquer driver), svd2 (SVD – singular value decomposition, simple driver), lu (LU factorization), and ll (LL – Cholesky factorization). (Default: default)

-r, --rcond NUMBER Rank condition for SVD. The chosen value must be carefully tested. Calculation at computer precision is requested with -1 (not recommended). (Default: 1e-06)

-s, --sigmaf2 SPEC Variance of the reconstructed free-energy surface (signal variance) in the form SigmaF2(1)[xSigmaF2(2)[x...]]. The last value pads the rest. (Default: 15.0)

--minsigmaf2 NUMBER Minimum value of SigmaF2. (Default: 0.1)

-o, --covar SPEC Covariances between GPR tasks in the form CoVar1[xCoVar2[x...]]. The last value pads the rest. (Default: 0.0)

--mincovar NUMBER Minimum value of CoVar. (Default: -1000)

-w, --wfac SPEC Characteristic scale of collective variables in the form WFac1[xWFac2[x...]]. The last value pads the rest. (Default: 3.0)

--minwfac NUMBER Minimum value of WFac. (Default: 0.1)

-n, --sigman2 SPEC Noise variances (σ²) for each CV in the form SigmaN2(1)[xSigmaN2(2)[x...]]. The last value pads the rest. (Default: 1e-5)

--minsigman2 NUMBER Minimum value of SigmaN2. (Default: 0)

--enablesigmaf2 SPEC Enable optimization of SigmaF2 hyperparameters. Flags are specified in the form SigmaF2(1)Enabled[xSigmaF2(2)Enabled[x...]] with F and T for disabled and enabled, respectively. The last value pads the rest. (Default: F)

--enablecovar SPEC Enable optimization of CoVar hyperparameters. Flags are specified in the form CoVar1Enabled[xCoVar2Enabled[x...]] with F and T for disabled and enabled, respectively. The last value pads the rest. (Default: F)

--enablewfac SPEC Enable optimization of WFac hyperparameters. Flags are specified in the form WFac1Enabled[xWFac2Enabled[x...]] with F and T for disabled and enabled, respectively. The last value pads the rest. (Default: F)

--enablesigman2 SPEC Enable optimization of SigmaN2 hyperparameters. Flags are specified in the form SigmaN2(1)Enabled[xSigmaN2(2)Enabled[x...]] with F and T for disabled and enabled, respectively. The last value pads the rest. (Default: F)

--numeric Use numerical gradients.

--noptsteps NUMBER Maximum number of optimization steps. (Default: 100)

--nresets NUMBER Maximum number of resets due to insufficient optimization progress. (Default: 3)

--termeps NUMBER Termination criterion for the L-BFGS optimizer (see L-BFGS code). (Default: 1e-05)

--termval NUMBER Termination criterion for the L-BFGS optimizer. Minimum change of the optimized property. (Default: 1e-06)

--nlbfgscorr NUMBER Number of corrections used in an L-BFGS update. (Default: 10)

--test Compare analytical and numerical gradients for input hyperparameters.

--cd5 Use the 5-point stencil for numerical differentiation.

--loadhyprms NAME Name of the file containing the GPR hyperparameters.

--stat Calculate detailed GPR statistics using the optimized hyperparameters.

--sptype Determine the type of stationary point.

--kernel NAME GPR kernel type. Supported types: ardse (ARD squared exponential), ardmc52 (ARD Matérn class 5/2), default (=ardse). (Default: default)

--fdkernel Use the first derivatives of the GPR kernel (only for SmootherGPR).

--useinv Use the matrix inversion pathway (for testing only).

--calclogpl Calculate logPL for --stat if --target is not logpl.

--globalmin SPEC Position of the global minimum provided as a single string in the form CV1xCV2x...xCVn (relevant for error determination). If not set, the position is determined automatically.

-v, --verbose Increase output verbosity.

--version Output version information and exit.

-h, --help Display this help and exit.