aus-integrate
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aus-integrate: version 6.1090.a7cf688 (2026-06-18 21:15)
Name
aus-integrate
Synopsis
aus-integrate [OPTIONS] [--] ACCU FEN INT TDS
Description
The program numerically integrates data from the ABF calculation.
Arguments
| ACCU Name of the file containing the input ABF accumulator.
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| FEN Name of the file containing the output free energy surface [dA(x)].
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| INT Name of the file containing the output internal energy surface [dU(x)].
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| TDS Name of the file containing the output entropic energy surface [-TdS(x)].
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Options
| --constraints Impose constraints: dA(x)/dx - dU(x)/dx - (-TdS(x)/dx) = 0.
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| -r, --realm NAME Requested realm for data processing. The list of supported realms can be obtained by --listrealms. (Default: AUS)
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| --listrealms List supported realms.
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| -a, --lmethod NAME Linear algebra method for LLS solution or matrix inversion. Supported algorithms: default, svd (SVD - divide and conquer), svd2 (SVD - simple), qr (QR factorization), lu (LU factorization), ll (Cholesky factorization). Possible combinations: GPR(LU, SVD, SVD2, LL, default). (Default: default)
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| --rcond NUMBER Rank condition for SVD. The chosen value must be carefully tested. Calculation at machine precision is requested with -1 (not recommended). (Default: 1e-06)
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| -l, --limit NUMBER Only bins containing more samples than NUMBER are considered properly sampled. (Default: 1000)
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| -s, --sigmaf2 SPEC Signal variances for each realm in the form SigmaF2(1)[xSigmaF2(2)x...]. The last value pads the rest. There are three realms. (Default: 15.0)
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| -c, --covar SPEC Signal covariances for each realm in the form CoVar(1)[xCoVar(2)x...]. The last value pads the rest. There are three realms. (Default: 0.0)
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| -w, --wfac SPEC Factors influencing widths of RBFs or squared exponential kernels. The width is the distance between adjacent functions multiplied by these factors, in the form WFac1[xWFac2x...]. The last value pads the rest. (Default: 3.0)
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| -n, --sigman2 SPEC Noise variances (sigma squared) for each CV in the form SigmaN2(1)[xSigmaN2(2)x...]. The last value pads the rest. (Default: 0.0)
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| --loadhyprms NAME Name of the file containing GPR hyperparameters.
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| --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.
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| -o, --offset NUMBER Specify the integration constant. (Default: 0)
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| -e, --witherror Estimate free energy errors.
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| --noenergy Skip calculation of energy and errors (saves time when only logML is required).
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| --balres Balance residual errors between dG, dH, and -TdS.
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| --mfinfo NAME Name of the file with input and predicted mean forces.
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| --residuals NAME Name of the file with residuals values.
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| --output FORMAT Output format for printing the free energy surface. Supported formats: plain, gnuplot. (Default: gnuplot)
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| --unsampledasmax Set energy values in unsampled regions to the maximum energy from sampled regions or to the value provided by --maxenergy.
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| --maxenergy NUMBER Energy value used for unsampled regions if set. (Default: 0)
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| --noheader Do not print a header in the output file.
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| --includebinstat Include bin statuses (1=sampled, 0=unsampled, -1=glued) in the resulting FES.
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| --fx FORMAT Output format used to print values of collective variables. (Default: %15.7e)
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| --fe FORMAT Output format used to print values of free energy. (Default: %15.7e)
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| --kernel NAME GPR kernel type. Supported types: ardse (ARD squared exponential), ardmc52 (ARD Matern class 5/2), default (=ardse). (Default: default)
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| --fdkernel Use the first derivatives of the GPR kernel (only for SmootherGPR).
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| --numdiff Use numerical differentiation of the kernel function (for testing only).
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| --useinv Use matrix inversion pathway (for testing only).
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| --calclogpl Calculate logPL.
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| --nofasterror Do not use the faster algorithm for error calculation.
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| --slevel VALUE Sigma level for confidence intervals. (Default: 1)
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| -v, --verbose Increase output verbosity.
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| --version Output version information and exit.
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| -h, --help Display this help message and exit.
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