pmf-energy
Jump to navigation
Jump to search
Navigation: Documentation / Utilities / pmf-energy
pmf-energy: version 6.1090.a7cf688 (2026-06-18 21:15)
Name
pmf-energy
Synopsis
pmf-energy [OPTIONS] [--] ACCU ENE
Description
The program provides various types of energies from the PMF accumulator.
Arguments
| ACCU Name of the file containing the input PMF accumulator.
|
| ENE Name of file where the resulting energy surface will be printed. If the name is '-' then the output will be written to the standard output.
|
Options
| -r, --realm NAME Intended output. The list of supported realms can be obtained by --listrealms. (Default: dU)
|
| --listrealms List supported realms.
|
| -m, --method NAME Supported methods: raw (data taken directly from the accumulator) and gpr (Gaussian process filtered data). (Default: raw)
|
| -a, --absolute Absolute energy.
|
| -l, --limit LIMIT Only bins containing more samples than NUMBER are considered properly sampled. (Default: 0)
|
| -e, --witherror GPR: Estimate energy errors from the GPR model. RAW: Print energy errors from the PMF accumulator.
|
| --kernel NAME GPR: Kernel type. Supported types: ardse (ARD squared exponential), ardmc52 (ARD Matern class 5/2), ardmc32 (ARD Matern class 3/2), ardmc12 (ARD Matern class 1/2), default (=ardse). (Default: default)
|
| --fdkernel Use the first derivatives of the GPR kernel (only for SmootherGPR).
|
| --calclogpl GPR: Calculate logPL.
|
| -s, --sigmaf2 NUMBER GPR: Variance of the reconstructed energy surface (signal variance). (Default: 15.0)
|
| -w, --wfac SPEC GPR: Factors influencing widths of squared exponential kernels. The width is the distance between adjacent squared exponential functions multiplied by these factors in the form WFac1[xWFac2x...]. The last value pads the rest. (Default: 3.0)
|
| -n, --sigman2 SPEC Values of noise sigma squared for each CV in the form SigmaN2(1)[xSigmaN2(2)x...]. The last value pads the rest. (Default: 1e-5)
|
| --loadhyprms NAME GPR: Name of file containing the GPR hyperparameters.
|
| --slevel VALUE Sigma-level for the confidence interval. (Default: 1)
|
| --mfinfo NAME GPR: Name of file with input and predicted energy.
|
| --globalmin SPEC GPR: 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.
|
| -o, --offset NUMBER Specify the integration constant. (Default: 0)
|
| --unsampledasmax Set energy values in unsampled regions to the maximum energy from sampled regions or to the value provided by --maxenergy.
|
| --maxenergy NUMBER If set, this is the energy used for unsampled regions. (Default: 0)
|
| --includebinstat Include bin statuses (1 = sampled, 0 = unsampled, -1 = glued) in the resulting FES.
|
| --output FORMAT Output FORMAT for printing the energy surface. Supported formats: plain and gnuplot. (Default: gnuplot)
|
| --noheader Do not print a header to the output file.
|
| --printall Print results for all bins, even if not properly sampled.
|
| --fx FORMAT Output FORMAT for printing values of collective variables. (Default: %15.7e)
|
| --fe FORMAT Output FORMAT for printing results. (Default: %15.7e)
|
| --lmethod NAME GPR: Linear algebra method for LLS solution or matrix inversion. Supported algorithms: svd (SVD - singular value decomposition, divide and conquer driver), svd2 (SVD - singular value decomposition, simple driver), lu (LU factorization), ll (LL - Cholesky factorization). Possible combinations: GPR(LU, SVD, SVD2, LL, default). (Default: default)
|
| --rcond NUMBER GPR: Rank condition for SVD. The chosen value must be carefully tested. Calculation at computer precision is requested with -1 (not recommended). (Default: 1e-06)
|
| -v, --verbose Increase output verbosity.
|
| --version Output version information and exit.
|
| -h, --help Display this help and exit.
|